BAC Information

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BAC

Clone NameMSMg01-301D04
ChromosomeY (Build37)
Map Location 2,869,839 - 2,870,343
singlet/doubletsinglet
Overlap genenone
Upstream geneUbe1y1-ps1, Sry, LOC100042840, LOC100042849, LOC620228, LOC667181, Rbmy1a1, LOC667189, LOC100042874, LOC667194, LOC100042881, LOC667201, LOC100039546, Rhoay-ps2, LOC100039568, LOC100041505, LOC100039581, LOC676356, LOC667217, LOC100039613, LOC100041537, LOC667227, LOC667236, EG631479, LOC667244, LOC100039652
Downstream genenone
LinkOpen Mouse BAC browser



BAC End Information

BAC end BAC-end 1BAC-end 2
end nameMSMg01-301D04.T7 (MSMg01no301_d04.b1)MSMg01-301D04.TJ (MSMg01no301_d04.g1)
ACCAG427466AG427467
length749746
length of high quality
(start - end)		617 (42 - 658)645 (71 - 715)
definitionCHROMAT_FILE: MSMg01no301_d04.b1 PHD_FILE: MSMg01no301_d04.b1.phd.1 CHEM: term DYE: big TIME: Tue May 17 21:38:32 2005CHROMAT_FILE: MSMg01no301_d04.g1 PHD_FILE: MSMg01no301_d04.g1.phd.1 CHEM: term DYE: big TIME: Tue May 17 21:38:32 2005
singlet/doubletsinglet---
BLAST hitpluralno hit data
sequence
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXCGCGGAATT
CATCACAGAATACCAGACAGAAGAAGTAAGAATTAAAGACATATTTGGGC
AAGATGAATAGTGAAGTAGAGATTAGAGCAAGCAGAAAGGACTGAGGAGA
TAGCTCACTGCTTAGGCCCACTGATTGCTTTTGCACAGGACCAGGGTTCA
ATTTCTAACACCCACATGGTTGTTCACAACCACCTGCAATTCTAGTTCTA
GACGATCTGATGACCTCTTTGGACAACACACACACACACAGACACACACA
CACGCACACACACACACACACACACACACACACACACACACACACACACA
CACACACACACACACATATACTCACCCACAGAGAAAAAAAATCTTTTAGA
AAACAATTATACAAACAAAAAGAGTCAAGTATAGTTTTATTCCCCTTTAA
TACCAGCACTCAGAAGCAGGCTAAAATATGTAAGTTGAATGACTGCCTAG
CTGATAGGTGTGTTTTCAGAATTTTCTTTTTCTTTTTCTTTTCTTTTTCT
TTTCTTTTCTTTTCTTTTCTTTTTTTTTTTTTTTTTTTTTTGATTTTAGG
ACTATTTCAGTATTTGTTTAAAGATTCTAGATTTTTTTTTTTTTTCCATT
TACTTCTTCTAATGTTTTAGGCTTTTTTTTCGCGCTTTTTAGAATTTTAC
AGGTTTCGGGTTTTTTTTTTTGGGCGGGAAGTGAAAGATGGTAACCCCC

CTXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXCTAATTTAGACAAAGTGTACCTGATGACTC
CTTGAGCCACTGAGAGTGATCTAAGCTCCACTTCAAGAATGGGGGGACAG
TGTGAGTCTTTTTGGTGCTGAAGGGATAATTCTGAGGTTTGTGTGTCAGA
AACAGGACTTGGAGGACCCAGTGACAGAGTGATAATGTTGATGTATCCAC
AAACAATCTATAAAGGATGCCATCCTTTAGAGGCAGAAAGGTTCACACCA
TGTTGGGGAAAGTAGAAATGCCAAAGACTATTGTATCTGTACAAGATCAA
GGGTCGATATGGAGAGGAGAGAAGGCCTGAATATTTCATGATTGAGACGT
CCTGGGAACCTAGAACACGCAAATCATGCAGGCCATGCAACAGCTTAATC
AATCTCCAGTGTGCTAGGAGACATTTCCCAGCTAGTTCTCCTGATAATTC
TGCTGCCTACTTCTAAAAATGGCAAGGCTTTCTCATTTTTGCTGGTCAGC
TTAATGTCTATGTCTTGGGTTCATTAACGTGCTGGCTACTCTTAAGCTCT
GAGACTTCAGGAACCCGGGTCCTGATCCTTGGACAGGGGTAATTAGGTCA
GAGGATCAGAATAAGAAGCACTTGGTGCACCTTAGATCAAGGGAGTGGAA
TTTTCATGGACTAGATCAGATCTAGTAGGTAGGTCTAGGTCCTCAN
quality valuesOpen.Open.




Alignment Information

BAC End 1BAC End 2
Query= MSMg01no301_d04.b1 MSMg01no301_d04.b1 CHROMAT_FILE:
MSMg01no301_d04.b1 PHD_FILE: MSMg01no301_d04.b1.phd.1 CHEM: term DYE:
big TIME: Tue May 17 21:38:32 2005
         (617 letters)



>mm_chrY_2869410_2870427
          Length = 1018

 Score =  650 bits (336), Expect = 0.0
 Identities = 488/602 (81%), Gaps = 108/602 (17%)
 Strand = Plus / Minus

                                                                       
Query: 24  agacagaagaagtaagaattaaagacatatttgggcaagatgaatagtgaagtagagatt 83
           |||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 934 agacagaagaagtaggaattaaagacatatttgggcaagatgaatagtgaagtagagatt 875

                                                                       
Query: 84  agagcaagcagaaaggactgaggagatagctcactgcttaggcccactgattgcttttgc 143
           ||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 874 agaacaagcagaaaggactgaggagatagctcactgcttaggcccactgattgcttttgc 815

                                                                       
Query: 144 acaggaccagggttcaatttctaacacccacatggttgttcacaaccacctgcaattcta 203
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 814 acaggaccagggttcaatttctaacacccacatggttgttcacaaccacctgcaattcta 755

                                                                       
Query: 204 gttctagacgatctgatgacctctttggacaacacacacacacacagacacacacacacg 263
           |||||||||||||||||||||||||||     ||||                        
Sbjct: 754 gttctagacgatctgatgacctctttg-----caca------------------------ 724

                                                                       
Query: 264 cacacacacacacacacacacacacacacacacacacacacacacacacacaca-cacac 322
                                              ||||||||||||||||||| |||||
Sbjct: 723 -----------------------------------acacacacacacacacacatcacac 699

                                                                       
Query: 323 acatatactcacccacagagaaaaaaaatcttttagaaaacaattatacaaacaaaaag- 381
           |||||||||||||||||||||||||||||| |||||||||||||||||||||||||||| 
Sbjct: 698 acatatactcacccacagagaaaaaaaatcctttagaaaacaattatacaaacaaaaagg 639

                                                                       
Query: 382 agtcaagtatagttttattcccctttaataccagcactcagaagcaggctaaaata-tgt 440
           |||||||||||||||||||||||||||||||||||||||||||||||||||||  | |||
Sbjct: 638 agtcaagtatagttttattcccctttaataccagcactcagaagcaggctaaac-actgt 580

                                                                       
Query: 441 aagttgaatgactgcctagctgataggtgtgttttcagaattttctttttctttttcttt 500
           |||||||||||||||||||||||||||||||||||||||||||| ||||||||||     
Sbjct: 579 aagttgaatgactgcctagctgataggtgtgttttcagaattttatttttctttt----- 525

                                                                       
Query: 501 tctttttcttttcttttcttttcttttcttttttttttttttttttttttgat------- 553
            ||||||||||||         ||||||||||||||||            |         
Sbjct: 524 -ctttttcttttc---------cttttctttttttttt------------g--ggggggg 489

                                                                       
Query: 554 -tttaggactatttcagtatttgtttaaagattctagattttttttttttttccatttac 612
            |||||||||||||||||||||||||||||||||||| |||||||||||||   ||||||
Sbjct: 488 gtttaggactatttcagtatttgtttaaagattctag-tttttttttttttg--atttac 432

             
Query: 613 tt 614
           ||
Sbjct: 431 tt 430


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: 91
Number of extensions: 5
Number of successful extensions: 5
Number of sequences better than 10.0: 1
Number of HSP's gapped: 4
Number of HSP's successfully gapped: 1
Length of query: 617
Length of database: 1018
Length adjustment: 10
Effective length of query: 607
Effective length of database: 1008
Effective search space:   611856
Effective search space used:   611856
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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