BAC Information

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BAC

Clone NameMSMg01-409H17
ChromosomeY (Build37)
Map Location 1,271,944 - 1,272,380
singlet/doubletsinglet
Overlap genenone
Upstream geneJarid1d, Eif2s3y, Tspy-ps, Uty, Ddx3y, LOC100042763, LOC385246, Usp9y, LOC100039278, EG667079
Downstream geneLOC667089, Rhoay-ps1, Zfy2, Ube1y1-ps2, LOC667137, LOC100039373, LOC100039381, LOC667143, LOC100039401, LOC100039430, Vmn2r-ps137, LOC100039450, LOC547210, Ube1y1-ps1, Sry, LOC100042840, LOC100042849, LOC620228, LOC667181, Rbmy1a1, LOC667189, LOC100042874, LOC667194, LOC100042881, LOC667201, LOC100039546
LinkOpen Mouse BAC browser



BAC End Information

BAC end BAC-end 1BAC-end 2
end nameMSMg01-409H17.T7 (MSMg01no409_h17.b1)MSMg01-409H17.TJ (MSMg01no409_h17.g1)
ACCAG506956AG506957
length789777
length of high quality
(start - end)		473 (51 - 523)495 (73 - 567)
definitionCHROMAT_FILE: MSMg01no409_h17.b1 PHD_FILE: MSMg01no409_h17.b1.phd.1 CHEM: term DYE: big TIME: Wed May 18 18:25:51 2005CHROMAT_FILE: MSMg01no409_h17.g1 PHD_FILE: MSMg01no409_h17.g1.phd.1 CHEM: term DYE: big TIME: Wed May 18 18:25:51 2005
singlet/doubletsinglet---
BLAST hitpluralno hit data
sequence
NNNTTCTATXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
CGCGGAATTCAGAAAACTGCACAGGTTGCTTACTGCAAGAAGGTATTCTG
CAAAAGCAATAGATGATAAAAGTACTGAAATATCTATCAGTGCTCTACAA
TATTATATTCTAGGTGATGAAATTTCTCTTTCTCTCTGTCTCTGTGTCTC
TGTGTCTCTGTCTCTATCTCTATGTCTGTCTGTCTGTTTGTCTCTCTCTC
TCTCTCAATTTCTACTTCTCTAATACTTATTATGAATTATGATTCTTTTA
TCTTATTCCCTCCAATGGGAATGATATTGGAATGGCATCTGTAACATTCA
TTCACATTCCTACACAATTTGTGCTTTCTATTAACAATCAACTAATATCA
AAGTCACACATTCACTCAGATTACAAAATAAGATATCTGAGCTCATGTAA
AGTGATATTCTGAATCAGAGTAGGGGAAGGGCACTTCCAATGTGTAGTTT
CACTCAAGAGCATGGCTTTTAAGAACTGGTCAATTGGAAGAAGATGAGAC
AATGTATAGAAGAAGGTGTTTCTTTTGGTTTAATTTGGTTTAACTTTGTG
CCTTTAGGGTAACCCCCGTCTTTTTTATAAAATTTGATAAAAACTGGGTA
TTAACGAAAATTTGAACTGGGTGGGAAAAAGGCCCTTAAAAACAAAGGAA
TATTCTTCCGTTCCAATATGCCAACTATTTTTGATATATTTTTGATTACT
TTTTTTTCGCTAAATCCTCCCCCCACTTAACAATTTGCA

ATGCXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXCAAGAAGAAAAAACTTATGGCATAGCAT
TGAGGCAATGACACAAGGAAATAATTAGATATTAGAAAGTGCCCCTGTGT
TTCTGAATGATGCAAGACTTTATTGCTGTGTAGCCAAAGGGAAACCGAAA
TCCTTCAGAAAAATCAAAGAGAGGAGCCAAATAAACACCTTTCATCCAGC
AAGATCAAAAACTGCTCTTAGAAAACTGGCAAGGTATGCAACAGGCAAAC
AAAGTTTCTATGTCAGTAAAGAAGGATCTTCACTTATAGCCTCAATTTTA
CACTTTCTTAGTGTATCAATTTGTATAAAACATGACGTCTCAAAGAATCA
GTTTAACTAAGGGTTTAATAAATCATTCTGTGCAACTATATACCGGCTGC
ATCATTGGACTCAAACTGAATGGTCCATGTGTTGCCACTGATGTGAGCCA
TTTGCCTGTTGTCCTTCAGGAGAATTATATGACCTTCAACAAGCAATCCA
AATATGAAAAAGTAATAGGAACCTAACTCACTAACTGTGACAGACAAAGC
AATTGTTTAAGGCCACAAGTGGTTTTTTTCAGGATTCCCACCTTTGCCTG
TGGTCTGGACCTAATCCACACCCCGATATAAGGAATTTGTATATAAACTT
TCTTTTTGTTTTATAATAAAAATTATTTATAGTCTTGCCCCCTATTCTTT
GGACCATAACCTAATTTATTGTTCCTA
quality valuesOpen.Open.




Alignment Information

BAC End 1BAC End 2
Query= MSMg01no409_h17.b1 MSMg01no409_h17.b1 CHROMAT_FILE:
MSMg01no409_h17.b1 PHD_FILE: MSMg01no409_h17.b1.phd.1 CHEM: term DYE:
big TIME: Wed May 18 18:25:51 2005
         (473 letters)



>mm_chrY_1271710_1272581
          Length = 872

 Score =  308 bits (159), Expect = 7e-88
 Identities = 384/477 (80%), Gaps = 49/477 (10%)
 Strand = Plus / Plus

                                                                       
Query: 5   gaattcagaaaactgcacaggttgcttactgcaagaaggtattctgcaaaagcaata--- 61
           ||||||||||| ||||| ||| ||| ||||||||  |||| ||||||||||||||||   
Sbjct: 235 gaattcagaaacctgcagaggctgcctactgcaatcaggtcttctgcaaaagcaatacac 294

                                                                       
Query: 62  gatgataaa-agtactgaaatatctatcagtgctctacaatattatattctaggtgatga 120
           ||| ||||| |  |||||| | ||| |||||||||||||     |||||||| |||||||
Sbjct: 295 gat-ataaata--actgaattttctgtcagtgctctaca-----atattctatgtgatga 346

                                                                       
Query: 121 aatttctctttctctctgtctctgtgtctctgtgtctctgtctctatctctatgtctgtc 180
           ||  ||||  ||||||  ||||    ||||    ||||  ||||  ||||    ||| ||
Sbjct: 347 aa--tctc--tctctcaatctc----tctc----tctc--tctc--tctc----tctctc 386

                                                                       
Query: 181 tgtctgtttgtctctctctctctctcaatttctacttc-tctaatacttattatgaatta 239
           | ||      ||||||||||||||||||| ||||| || ||||| ||||| ||||||| |
Sbjct: 387 tctc------tctctctctctctctcaatatctac-tcttctaacacttagtatgaataa 439

                                                                       
Query: 240 tgattcttttatcttattccct-cca-at-gggaatgatattggaatggcatctgtaaca 296
           ||||||| |||||   ||| || | | || ||| |||||||||||||| |||||| ||||
Sbjct: 440 tgattctcttatc---ttctctgctacatagggcatgatattggaatgtcatctgcaaca 496

                                                                       
Query: 297 ttcattcacattcctacacaatttgtgctttctattaacaatcaactaatatcaaagtca 356
           ||||||||| ||||||| || |||||||||||| |||  |||||||||||||||||||||
Sbjct: 497 ttcattcactttcctactcagtttgtgctttctcttaggaatcaactaatatcaaagtca 556

                                                                       
Query: 357 cacattcactcagattacaaaataagatatctgagctcatgtaaagtgatattctgaatc 416
           |||||||||||||||||||||||||| ||||| ||||||| |||  || |||||||| | 
Sbjct: 557 cacattcactcagattacaaaataaggtatcttagctcatataac-tgttattctgagtg 615

                                                                    
Query: 417 agagtaggggaaggg-cacttccaatgtgtagtttcactcaagagcatggcttttaa 472
           ||||| || ||| || |||||||||||||||||| ||| |||||| ||||| |||||
Sbjct: 616 agagt-ggagaaaggacacttccaatgtgtagttacacccaagagtatggcctttaa 671


Lambda     K      H
    1.37    0.711     1.31 

Gapped
Lambda     K      H
    1.34    0.600     1.10 


Matrix: blastn matrix:1 -3
Gap Penalties: Existence: 2, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 9
Number of extensions: 1
Number of successful extensions: 1
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 473
Length of database: 872
Length adjustment: 10
Effective length of query: 463
Effective length of database: 862
Effective search space:   399106
Effective search space used:   399106
X1: 8 (15.9 bits)
X2: 517 (999.5 bits)
X3: 517 (999.5 bits)
S1: 8 (16.4 bits)
S2: 8 (16.2 bits)


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