BLASTN 2.2.26+


Reference: Zheng Zhang, Scott Schwartz, Lukas Wagner, and Webb
Miller (2000), "A greedy algorithm for aligning DNA sequences", J
Comput Biol 2000; 7(1-2):203-14.



Database: minirefseq_mrna
           23 sequences; 67,750 total letters



Query= random_s00

Length=128


***** No hits found *****



Lambda     K      H
    1.33    0.621     1.12 

Gapped
Lambda     K      H
    1.28    0.460    0.850 

Effective search space used: 7616765


Query= gi|356995852:1-490 Mus musculus POU domain, class 5, transcription
factor 1 (Pou5f1), transcript variant 1, mRNA

Length=490
                                                                      Score     E
Sequences producing significant alignments:                          (Bits)  Value

  gi|356995852|ref|NM_013633.3| Mus musculus POU domain, class 5,...   905    0.0   
  gi|377833530|ref|XR_141831.1| PREDICTED: Mus musculus predicted...   900    0.0   
  gi|260269517|ref|NM_001009178.2| Rattus norvegicus POU class 5 ...   734    0.0   
  gi|295390144|ref|NR_033594.1| Mus musculus predicted gene 5712 ...   446    2e-127
  gi|354487499|ref|XM_003505863.1| PREDICTED: Cricetulus griseus ...   433    1e-123


> gi|356995852|ref|NM_013633.3| Mus musculus POU domain, class 
5, transcription factor 1 (Pou5f1), transcript variant 1, mRNA
Length=1353

 Score =  905 bits (490),  Expect = 0.0
 Identities = 490/490 (100%), Gaps = 0/490 (0%)
 Strand=Plus/Plus

Query  1    GAGGTGAAACCGTCCCTAGGTGAGCCGTCTTTCCACCAGGCCCCCGGCTCGGGGTGCCCA  60
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  1    GAGGTGAAACCGTCCCTAGGTGAGCCGTCTTTCCACCAGGCCCCCGGCTCGGGGTGCCCA  60

Query  61   CCTTCCCCATGGCTGGACACCTGGCTTCAGACTTCGCCTTCTCACCCCCACCAGGTGGGG  120
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  61   CCTTCCCCATGGCTGGACACCTGGCTTCAGACTTCGCCTTCTCACCCCCACCAGGTGGGG  120

Query  121  GTGATGGGTCAGCAGGGCTGGAGCCGGGCTGGGTGGATCCTCGAACCTGGCTAAGCTTCC  180
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  121  GTGATGGGTCAGCAGGGCTGGAGCCGGGCTGGGTGGATCCTCGAACCTGGCTAAGCTTCC  180

Query  181  AAGGGCCTCCAGGTGGGCCTGGAATCGGACCAGGCTCAGAGGTATTGGGGATCTCCCCAT  240
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  181  AAGGGCCTCCAGGTGGGCCTGGAATCGGACCAGGCTCAGAGGTATTGGGGATCTCCCCAT  240

Query  241  GTCCGCCCGCATACGAGTTCTGCGGAGGGATGGCATACTGTGGACCTCAGGTTGGACTGG  300
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  241  GTCCGCCCGCATACGAGTTCTGCGGAGGGATGGCATACTGTGGACCTCAGGTTGGACTGG  300

Query  301  GCCTAGTCCCCCAAGTTGGCGTGGAGACTTTGCAGCCTGAGGGCCAGGCAGGAGCACGAG  360
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  301  GCCTAGTCCCCCAAGTTGGCGTGGAGACTTTGCAGCCTGAGGGCCAGGCAGGAGCACGAG  360

Query  361  TGGAAAGCAACTCAGAGGGAACCTCCTCTGAGCCCTGTGCCGACCGCCCCAATGCCGTGA  420
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  361  TGGAAAGCAACTCAGAGGGAACCTCCTCTGAGCCCTGTGCCGACCGCCCCAATGCCGTGA  420

Query  421  AGTTGGAGAAGGTGGAACCAACTCCCGAGGAGTCCCAGGACATGAAAGCCCTGCAGAAGG  480
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  421  AGTTGGAGAAGGTGGAACCAACTCCCGAGGAGTCCCAGGACATGAAAGCCCTGCAGAAGG  480

Query  481  AGCTAGAACA  490
            ||||||||||
Sbjct  481  AGCTAGAACA  490


> gi|377833530|ref|XR_141831.1| PREDICTED: Mus musculus predicted 
gene, 19553 (Gm19553), miscRNA
Length=570

 Score =  900 bits (487),  Expect = 0.0
 Identities = 489/490 (99%), Gaps = 0/490 (0%)
 Strand=Plus/Minus

Query  1    GAGGTGAAACCGTCCCTAGGTGAGCCGTCTTTCCACCAGGCCCCCGGCTCGGGGTGCCCA  60
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  570  GAGGTGAAACCGTCCCTAGGTGAGCCGTCTTTCCACCAGGCCCCCGGCTCGGGGTGCCCA  511

Query  61   CCTTCCCCATGGCTGGACACCTGGCTTCAGACTTCGCCTTCTCACCCCCACCAGGTGGGG  120
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  510  CCTTCCCCATGGCTGGACACCTGGCTTCAGACTTCGCCTTCTCACCCCCACCAGGTGGGG  451

Query  121  GTGATGGGTCAGCAGGGCTGGAGCCGGGCTGGGTGGATCCTCGAACCTGGCTAAGCTTCC  180
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  450  GTGATGGGTCAGCAGGGCTGGAGCCGGGCTGGGTGGATCCTCGAACCTGGCTAAGCTTCC  391

Query  181  AAGGGCCTCCAGGTGGGCCTGGAATCGGACCAGGCTCAGAGGTATTGGGGATCTCCCCAT  240
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  390  AAGGGCCTCCAGGTGGGCCTGGAATCGGACCAGGCTCAGAGGTATTGGGGATCTCCCCAT  331

Query  241  GTCCGCCCGCATACGAGTTCTGCGGAGGGATGGCATACTGTGGACCTCAGGTTGGACTGG  300
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  330  GTCCGCCCGCATACGAGTTCTGCGGAGGGATGGCATACTGTGGACCTCAGGTTGGACTGG  271

Query  301  GCCTAGTCCCCCAAGTTGGCGTGGAGACTTTGCAGCCTGAGGGCCAGGCAGGAGCACGAG  360
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  270  GCCTAGTCCCCCAAGTTGGCGTGGAGACTTTGCAGCCTGAGGGCCAGGCAGGAGCACGAG  211

Query  361  TGGAAAGCAACTCAGAGGGAACCTCCTCTGAGCCCTGTGCCGACCGCCCCAATGCCGTGA  420
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  210  TGGAAAGCAACTCAGAGGGAACCTCCTCTGAGCCCTGTGCCGACCGCCCCAATGCCGTGA  151

Query  421  AGTTGGAGAAGGTGGAACCAACTCCCGAGGAGTCCCAGGACATGAAAGCCCTGCAGAAGG  480
            ||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||
Sbjct  150  AGTTGGAGAAGGTGGAACCAACTCCAGAGGAGTCCCAGGACATGAAAGCCCTGCAGAAGG  91

Query  481  AGCTAGAACA  490
            ||||||||||
Sbjct  90   AGCTAGAACA  81


> gi|260269517|ref|NM_001009178.2| Rattus norvegicus POU class 
5 homeobox 1 (Pou5f1), mRNA
Length=1388

 Score =  734 bits (397),  Expect = 0.0
 Identities = 459/489 (94%), Gaps = 3/489 (1%)
 Strand=Plus/Plus

Query  1    GAGGTG-AAACCGTCCCTAGGTGAGCCGTCTTTCCACCAGGCCCCCGGCTCGGGGTGCCC  59
            |||||| |||| ||||||||||||| |||| |||||||||||||||||||||||| ||||
Sbjct  12   GAGGTGCAAACAGTCCCTAGGTGAGTCGTCCTTCCACCAGGCCCCCGGCTCGGGGAGCCC  71

Query  60   ACCTTCCCCATGGCTGGACACCTGGCTTCAGACTTCGCCTTCTCACCCCCACCAGGTGGG  119
            ||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||
Sbjct  72   ACCTTCCCCATGGCTGGACACCTGGCTTCAGACTTCGCCTTCTCACCCCCACCTGGTGGG  131

Query  120  GGTGATGGGTCAGCAGGGCTGGAGCCGGGCTGGGTGGATCCTCGAACCTGGCTAAGCTTC  179
            |||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||
Sbjct  132  GGTGATGGGTCAGCAGGGCTGGAGCCGGGCTGGGTGGACCCTCGAACCTGGCTAAGCTTC  191

Query  180  CAAGGGCCTCCAGGTGGGCCTGGAATCGGACCAGGCTCAGAGGTATTGGGGATCTCCCCA  239
            || ||||||||| |||||||||||||||||||||| ||||||||  ||||||||||||| 
Sbjct  192  CAGGGGCCTCCAAGTGGGCCTGGAATCGGACCAGGTTCAGAGGTGCTGGGGATCTCCCCG  251

Query  240  TGTCCGCCC-GCATACGAGTTCTGCGGAGGGATGGCATACTGTGGACCTCAGGTTGGACT  298
            ||||| ||| |||||||||||||| |||||||||||||||||||||||||||||||||||
Sbjct  252  TGTCC-CCCAGCATACGAGTTCTGTGGAGGGATGGCATACTGTGGACCTCAGGTTGGACT  310

Query  299  GGGCCTAGTCCCCCAAGTTGGCGTGGAGACTTTGCAGCCTGAGGGCCAGGCAGGAGCACG  358
            ||||||||||||||||||||||||||||||| ||||||| ||||||||||||||||||||
Sbjct  311  GGGCCTAGTCCCCCAAGTTGGCGTGGAGACTCTGCAGCCCGAGGGCCAGGCAGGAGCACG  370

Query  359  AGTGGAAAGCAACTCAGAGGGAACCTCCTCTGAGCCCTGTGCCGACCGCCCCAATGCCGT  418
            |||||| |||||||| |||||| ||||||||| ||||||| | | ||||||||  |||||
Sbjct  371  AGTGGAGAGCAACTCGGAGGGAGCCTCCTCTGGGCCCTGTACTGCCCGCCCCAGCGCCGT  430

Query  419  GAAGTTGGAGAAGGTGGAACCAACTCCCGAGGAGTCCCAGGACATGAAAGCCCTGCAGAA  478
            ||||||||||||||||||||| | |||||||||||||||||| |||||||||||||||||
Sbjct  431  GAAGTTGGAGAAGGTGGAACCTAGTCCCGAGGAGTCCCAGGATATGAAAGCCCTGCAGAA  490

Query  479  GGAGCTAGA  487
            |||||||||
Sbjct  491  GGAGCTAGA  499


> gi|295390144|ref|NR_033594.1| Mus musculus predicted gene 5712 
(Gm5712), non-coding RNA
Length=1040

 Score =  446 bits (241),  Expect = 2e-127
 Identities = 367/422 (87%), Gaps = 32/422 (8%)
 Strand=Plus/Plus

Query  69   ATGGCTGGACACCTGGCTTCAGACTTCGCCTTCTCACCCCCACCAGGTGGGGGTGATGGG  128
            |||||||||||||||||||||||||||||||||||||||| |||||||||||| ||||||
Sbjct  1    ATGGCTGGACACCTGGCTTCAGACTTCGCCTTCTCACCCC-ACCAGGTGGGGGCGATGGG  59

Query  129  TCAGCAGGGCTGGAGCCGGGCTGGGTGGATCCTCGAACCTGGCTAAGCTTCCAAGGGCCT  188
            ||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||
Sbjct  60   TCAGCAGGGCTGGAGCCGGGCTGGGTGGACCCTCGAACCTGGCTAAGCTTCCAAGGGCCT  119

Query  189  CCAGGTGGGCCTGGAATCGGACCAGGCTCAGAGGTATTGGGGATCTCCCCATGTCCGCCC  248
            |  |||||||||||||| |||||||||| |||||||||||| |||||||||||||| || 
Sbjct  120  CTGGGTGGGCCTGGAATAGGACCAGGCTTAGAGGTATTGGG-ATCTCCCCATGTCCACCG  178

Query  249  GCATACGAGTTCTGCGGAGGGATGGCATACTGTGGACCTCAGGTTGGACTGGGCCTAGTC  308
            | ||| |||||||||||||||||||||||||||||||||||||     |||| |   || 
Sbjct  179  GTATATGAGTTCTGCGGAGGGATGGCATACTGTGGACCTCAGG-----CTGG-C---GT-  228

Query  309  CCCCAAGTTGGCGTGGAGACTTTGCAGCCTGAGGGCCAGGCAGGAGCACGAGTGGAAAGC  368
                  |  |      ||||||||||||||||| |||||||| ||||| | ||||| |||
Sbjct  229  ------G--G------AGACTTTGCAGCCTGAGAGCCAGGCAAGAGCAGGTGTGGAGAGC  274

Query  369  AACTCAGAGGGAA-CCTCCTCTGAGCCCTGTGCCGACCGCCCCAATGCCGTGAAGTTGGA  427
            |||||||||| || ||| ||||| ||| |||||||||| ||||| |||||||||||||||
Sbjct  275  AACTCAGAGG-AAGCCTTCTCTGGGCCTTGTGCCGACCACCCCAGTGCCGTGAAGTTGGA  333

Query  428  GAAG-GTGGAACCAAC-TCCCGAGGAGTCCCAGGACATGAAAGCCCTGCAGAAGGAGCTA  485
            || | | ||||||| | |||||||| ||||||||||||||||| ||||||||||||||||
Sbjct  334  GATGAG-GGAACCA-CGTCCCGAGGGGTCCCAGGACATGAAAGTCCTGCAGAAGGAGCTA  391

Query  486  GA  487
            ||
Sbjct  392  GA  393


> gi|354487499|ref|XM_003505863.1| PREDICTED: Cricetulus griseus 
POU domain, class 5, transcription factor 1-like (LOC100754998), 
mRNA
Length=1077

 Score =  433 bits (234),  Expect = 1e-123
 Identities = 377/442 (85%), Gaps = 25/442 (6%)
 Strand=Plus/Plus

Query  69   ATGGCTGGACACCTGGCTTCAGACTTCGCCTTCTCACCCCCACCAGGTGGGGGTGATGGG  128
            |||||||||||||||||||||||||| ||||||||||| ||||| |||||||||||||||
Sbjct  1    ATGGCTGGACACCTGGCTTCAGACTTTGCCTTCTCACCTCCACCTGGTGGGGGTGATGGG  60

Query  129  TCAGCAGGGCTGGAGCCGGGCTGGGTGGATCCTCGAACCTGGCTAAGCTTCCAAGGGCCT  188
            |||| |||||||||||| ||||||||||| ||||| ||||||||||||||||||||||| 
Sbjct  61   TCAGGAGGGCTGGAGCCTGGCTGGGTGGACCCTCGGACCTGGCTAAGCTTCCAAGGGCCA  120

Query  189  CCAGGTGGGCCTGGAAT-----C-------GGACCAGGCTCAGAGGTATTGGGGATCTCC  236
            |||||||||||||||||     |       |||||||||||||| ||  ||||||| |||
Sbjct  121  CCAGGTGGGCCTGGAATCGGGCCAGGGGTTGGACCAGGCTCAGAAGTGCTGGGGATTTCC  180

Query  237  CCATGTCCGCCC-GCATACGAGTTCTGCGGAGGGATGGCATACTGTGGACCTCAGGTTGG  295
            || ||||| |||  ||||||||||||| |||||| |||||||||||||||||||||||||
Sbjct  181  CCTTGTCC-CCCACCATACGAGTTCTGTGGAGGGGTGGCATACTGTGGACCTCAGGTTGG  239

Query  296  ACTGGGCCTAGTCCC-CCAAGTTGGCGTGGAGACTTTGCAGCCTGAGGGCCAGGCAGGAG  354
            |||||| ||||| || ||| |||||| |||||||||  ||||||||||||||| ||||||
Sbjct  240  ACTGGGTCTAGTGCCGCCA-GTTGGCCTGGAGACTTCACAGCCTGAGGGCCAGTCAGGAG  298

Query  355  CACGAGTGGA-AAGCAACTCAGAGG-GAACCTCCTCTGAGCCCTGTGCCGACC-GCCCCA  411
            || ||||||| || | |||| |||| |  ||||| ||| ||||||| | | || | ||||
Sbjct  299  CAGGAGTGGAGAA-CGACTCGGAGGAGT-CCTCCCCTGGGCCCTGTACTG-CCAGGCCCA  355

Query  412  ATG-CC--GTGAAGTTGGAGAAGGTGGAACCAACTCCCGAGGAGTCCCAGGACATGAAAG  468
             || ||  ||||||||||||||||||||||| | ||||||||||||||||||  |||| |
Sbjct  356  TTGTCCCCGTGAAGTTGGAGAAGGTGGAACCGAGTCCCGAGGAGTCCCAGGATGTGAAGG  415

Query  469  CCCTGCAGAAGGAGCTAGAACA  490
            || |||||||||| || |||||
Sbjct  416  CCTTGCAGAAGGAACTGGAACA  437



Lambda     K      H
    1.33    0.621     1.12 

Gapped
Lambda     K      H
    1.28    0.460    0.850 

Effective search space used: 31860807


Query= hg19_dna range=chr1:1207307-1207372 5'pad=0 3'pad=0 strand=+
repeatMasking=none

Length=66
                                                                      Score     E
Sequences producing significant alignments:                          (Bits)  Value

  gi|94721341|ref|NM_001040441.1| Homo sapiens zinc finger and BT...   115    6e-29
  gi|332237160|ref|XM_003267724.1| PREDICTED: Nomascus leucogenys...   115    6e-29
  gi|332254616|ref|XM_003276378.1| PREDICTED: Nomascus leucogenys...   111    7e-28
  gi|332865370|ref|XM_527768.3| PREDICTED: Pan troglodytes zinc f...   111    7e-28
  gi|332865372|ref|XM_003318468.1| PREDICTED: Pan troglodytes zin...   111    7e-28


> gi|94721341|ref|NM_001040441.1| Homo sapiens zinc finger and 
BTB domain containing 8A (ZBTB8A), mRNA
Length=7333

 Score =  115 bits (62),  Expect = 6e-29
 Identities = 62/62 (100%), Gaps = 0/62 (0%)
 Strand=Plus/Plus

Query  5     GCCATTGCACTCCAGCCTGGGCAACAAGAGCGAAACTCCGTCTCaaaaaaaaaaaaaaaa  64
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  3677  GCCATTGCACTCCAGCCTGGGCAACAAGAGCGAAACTCCGTCTCAAAAAAAAAAAAAAAA  3736

Query  65    aa  66
             ||
Sbjct  3737  AA  3738


 Score = 99.0 bits (53),  Expect = 6e-24
 Identities = 53/53 (100%), Gaps = 0/53 (0%)
 Strand=Plus/Plus

Query  6     CCATTGCACTCCAGCCTGGGCAACAAGAGCGAAACTCCGTCTCaaaaaaaaaa  58
             |||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  2824  CCATTGCACTCCAGCCTGGGCAACAAGAGCGAAACTCCGTCTCAAAAAAAAAA  2876


> gi|332237160|ref|XM_003267724.1| PREDICTED: Nomascus leucogenys 
ATG14 autophagy related 14 homolog (S. cerevisiae) (ATG14), 
mRNA
Length=4771

 Score =  115 bits (62),  Expect = 6e-29
 Identities = 62/62 (100%), Gaps = 0/62 (0%)
 Strand=Plus/Plus

Query  5     GCCATTGCACTCCAGCCTGGGCAACAAGAGCGAAACTCCGTCTCaaaaaaaaaaaaaaaa  64
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  2865  GCCATTGCACTCCAGCCTGGGCAACAAGAGCGAAACTCCGTCTCAAAAAAAAAAAAAAAA  2924

Query  65    aa  66
             ||
Sbjct  2925  AA  2926


> gi|332254616|ref|XM_003276378.1| PREDICTED: Nomascus leucogenys 
S100P binding protein, transcript variant 2 (S100PBP), mRNA
Length=4345

 Score =  111 bits (60),  Expect = 7e-28
 Identities = 64/66 (97%), Gaps = 0/66 (0%)
 Strand=Plus/Minus

Query  1     TCAAGCCATTGCACTCCAGCCTGGGCAACAAGAGCGAAACTCCGTCTCaaaaaaaaaaaa  60
             ||| |||| |||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  2857  TCATGCCACTGCACTCCAGCCTGGGCAACAAGAGCGAAACTCCGTCTCAAAAAAAAAAAA  2798

Query  61    aaaaaa  66
             ||||||
Sbjct  2797  AAAAAA  2792


> gi|332865370|ref|XM_527768.3| PREDICTED: Pan troglodytes zinc 
finger protein 273, transcript variant 2 (ZNF273), mRNA
Length=4335

 Score =  111 bits (60),  Expect = 7e-28
 Identities = 64/66 (97%), Gaps = 0/66 (0%)
 Strand=Plus/Minus

Query  1     TCAAGCCATTGCACTCCAGCCTGGGCAACAAGAGCGAAACTCCGTCTCaaaaaaaaaaaa  60
             ||| |||||||||||||||||||||||||||||| |||||||||||||||||||||||||
Sbjct  2705  TCACGCCATTGCACTCCAGCCTGGGCAACAAGAGTGAAACTCCGTCTCAAAAAAAAAAAA  2646

Query  61    aaaaaa  66
             ||||||
Sbjct  2645  AAAAAA  2640


> gi|332865372|ref|XM_003318468.1| PREDICTED: Pan troglodytes zinc 
finger protein 273, transcript variant 1 (ZNF273), mRNA
Length=4430

 Score =  111 bits (60),  Expect = 7e-28
 Identities = 64/66 (97%), Gaps = 0/66 (0%)
 Strand=Plus/Minus

Query  1     TCAAGCCATTGCACTCCAGCCTGGGCAACAAGAGCGAAACTCCGTCTCaaaaaaaaaaaa  60
             ||| |||||||||||||||||||||||||||||| |||||||||||||||||||||||||
Sbjct  2800  TCACGCCATTGCACTCCAGCCTGGGCAACAAGAGTGAAACTCCGTCTCAAAAAAAAAAAA  2741

Query  61    aaaaaa  66
             ||||||
Sbjct  2740  AAAAAA  2735



Lambda     K      H
    1.33    0.621     1.12 

Gapped
Lambda     K      H
    1.28    0.460    0.850 

Effective search space used: 3506256


  Database: minirefseq_mrna
    Posted date:  Jun 9, 2012  2:05 PM
  Number of letters in database: 67,750
  Number of sequences in database:  23



Matrix: blastn matrix 1 -2
Gap Penalties: Existence: 0, Extension: 2.5
