BAC Information

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BAC

Clone NameMSMg01-541L20
ChromosomeY (Build37)
Map Location 2,870,367 - 2,870,918
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 nameMSMg01-541L20.T7 (MSMg01no541_l20.b1)MSMg01-541L20.TJ (MSMg01no541_l20.g1)
ACCAG607684AG607685
length778761
length of high quality
(start - end)		703 (46 - 748)555 (73 - 627)
definitionCHROMAT_FILE: MSMg01no541_l20.b1 PHD_FILE: MSMg01no541_l20.b1.phd.1 CHEM: term DYE: big TIME: Wed May 18 21:21:31 2005CHROMAT_FILE: MSMg01no541_l20.g1 PHD_FILE: MSMg01no541_l20.g1.phd.1 CHEM: term DYE: big TIME: Wed May 18 21:21:31 2005
singlet/doublet---singlet
BLAST hitno hit dataplural
sequence
CTATXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXCGCGG
AATTCAGGATAGCAGGGTGTACAAACTGCACTCTCTCAGTCAGTAAGAGG
TTCTGTTAATGGGTCATGTGAGATTTAGGCATCCAGCGATCAGGCGGTGG
TCTAATGATGATTTCTAAGGCATGGGTCTACCACTATCATTCATTGACCT
AGAATCAGTTTATCAGCATCTTTGAGAAGTGGGGCCAAAGCATCGATAGC
TTTTAAGCACAATGGCCATCCACTGGACACTGGGTCTAGTTTTTTTGTTT
GTTTGTTTGTTTGTTTTTTGTTTTTTGTTTTTTGTTTCTTTTGTTTGTTT
CTTTGTTTGTTTTGTTTTTTGTTTTTTTTTTTTACCAGTATTCCACAGGT
TATTTTTATGGCCCCAGAGCTTAGATCAGAACCCCACTTTCTTTTCCTGC
TCATTCCTCTATATAGAGTGACAGGCTTAGTCATGTCTTGCAGGGCTAGG
GCTGGTGCACTAAGCAAGGGCTTTTTAATCTCTTTAAAGGCCTACTGGTG
TATGGGGGTCCATAAGAAAGTTCCAGTCTCTTTAGTAAAGTGTTAGAGTG
TGGCTGCCAGAGTCGCAAAGCTTGGAATCTAGAGTCTACAAAAACCAGGA
ATTCCAACAAATTCTCTCACCTGCTTTAAGGATGTTGGGATGGGGATTTG
AGTTACAGTCTTTTTCCAAGCTTCTGTCAGCCACCATTTCCTTTCCCTGA
GACTATAACCCAAATAGGTTACTTCTGN

CGATGCTXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXTCCTTTGCTTTTCTCTTGTTTCTCCAAT
TATTTCAGCAAGATTCTGCATTGCCTTTTGTTTTGGAAGATTCTCGAGGA
ATCCTAAATCCAGACTTTAGGGCAGTTATTTAAAATTCTTACTGGTGGTT
CTGACAATGGTTTCCTCTTTTTTTTTTAATTAGGTATTTTTTCATTTACA
TTTCCAATACTATCCCAAAAGTCCCCCCATACCCACCTCAACCCCAACAC
CACCACCACCCCCATATCTTGTCCCTGGCATACCCCTGAACTAAGGCATA
TAAAGTTTGCAAGACTGATGGGCCTCTCTTTCCAATGATGTTCAACTAGT
CCGTCTTCTGATACAAATGCAGCCAGAAATATGAGCACTGATAAGTTGCT
AGAAAAATGAGCTCTGCGGGGATTCTTTAGTTCATATTGTTGTTCCACTT
ATGGGATTGCAGACCCCTTAAGTTCCTTGGGTACCTTCTCTACCTCCTCC
ATTTCTGTCCCTGTGATTCATCCAATAGCTGACTGTGAGCATCCACTTCT
GTGTTTGCTAGGCCATGGCATAGCCTCACAAGAGACAGCTACATCTGGGT
CCTTCCAGCAAAATCTTGCCAGTGTATGCAATGGTGTCAGTGTTTGGAGG
CTGATTATGGGATGGATCCCTAGGAATGGCAGTCTCTACATGGTCCATCC
TTTTGTCTCAC
quality valuesOpen.Open.




Alignment Information

BAC End 1BAC End 2
Query= MSMg01no541_l20.g1 MSMg01no541_l20.g1 CHROMAT_FILE:
MSMg01no541_l20.g1 PHD_FILE: MSMg01no541_l20.g1.phd.1 CHEM: term DYE:
big TIME: Wed May 18 21:21:31 2005
         (555 letters)



>mm_chrY_2870164_2871119
          Length = 956

 Score =  818 bits (423), Expect = 0.0
 Identities = 521/559 (93%), Gaps = 14/559 (2%)
 Strand = Plus / Plus

                                                                       
Query: 4   tttgcttttctcttgtttctccaattatttcag---caagattctgcattgccttttgtt 60
           |||||||||||||||||||||||||||   |||   |||||||||||||| |||||||||
Sbjct: 204 tttgcttttctcttgtttctccaatta---cagcaccaagattctgcatttccttttgtt 260

                                                                       
Query: 61  ttggaagattctcgaggaatcctaaatccagactttagggcagttatttaaaattcttac 120
           ||||||||||||||| |||||||||||||||||||||||||||||||||||||||||| |
Sbjct: 261 ttggaagattctcgatgaatcctaaatccagactttagggcagttatttaaaattcttgc 320

                                                                       
Query: 121 tggtggttctgacaatggtttcctcttttttttttaattaggtattttttcatttacatt 180
           ||||||||||||||||||||||||| |||||||| |||||||||||||||||||||||||
Sbjct: 321 tggtggttctgacaatggtttcctcattttttttaaattaggtattttttcatttacatt 380

                                                                       
Query: 181 tccaatactatcccaaaagtccccccatacccacctcaaccccaacacc---accaccac 237
           |||||||||||||||||||||||||||||||||||||||||   |||||   ||||||||
Sbjct: 381 tccaatactatcccaaaagtccccccatacccacctcaacc---acacccctaccaccac 437

                                                                       
Query: 238 ccccatatcttgtccctggcatacccctgaactaaggcatataaagtttgcaagactgat 297
           | ||| ||||||||||||||||||||||||| ||||||||||||||||||||||||||||
Sbjct: 438 caccacatcttgtccctggcatacccctgaaataaggcatataaagtttgcaagactgat 497

                                                                       
Query: 298 gggcctctctttccaatgatgttcaactagtccgtcttctgatacaaatgcagccagaaa 357
           ||| |||||||||||||||||  |||||||||| ||||||||||||| |||||| |||||
Sbjct: 498 ggggctctctttccaatgatgaccaactagtccatcttctgatacaactgcagctagaaa 557

                                                                       
Query: 358 tatgagcactgataagttgctagaaaaatgagctctgcg-gggattctttagttcatatt 416
            |||||| |||||| |  |||||||||||||| |||| | ||| ||||||||||||||||
Sbjct: 558 catgagctctgatatgcagctagaaaaatgagttctg-gagggtttctttagttcatatt 616

                                                                       
Query: 417 gttgttccacttatgggattgcagaccccttaagttccttgggtaccttctctacctcct 476
           ||||||||||||||||||||||||||||||| || |||||||||||||||||||||||||
Sbjct: 617 gttgttccacttatgggattgcagacccctttagctccttgggtaccttctctacctcct 676

                                                                       
Query: 477 ccatttctgtccctgtgattcatccaatagctgactgtgagcatccacttctgtgtttgc 536
           ||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 677 ccatttcggtccctgtgattcatccaatagctgactgtgagcatccacttctgtgtttgc 736

                              
Query: 537 taggccatggcatagcctc 555
           |||||||||||||||||||
Sbjct: 737 taggccatggcatagcctc 755


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: 18
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: 555
Length of database: 956
Length adjustment: 10
Effective length of query: 545
Effective length of database: 946
Effective search space:   515570
Effective search space used:   515570
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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