BAC Information

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BAC

Clone NameMSMg01-117C20
ChromosomeY (Build37)
Map Location 1,715,938 - 1,716,453
singlet/doubletsinglet
Overlap genenone
Upstream geneUsp9y, LOC100039278, EG667079, LOC667089, Rhoay-ps1, Zfy2, Ube1y1-ps2, LOC667137, LOC100039373, LOC100039381, LOC667143, LOC100039401
Downstream geneLOC100039430, Vmn2r-ps137, LOC100039450, LOC547210, Ube1y1-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
LinkOpen Mouse BAC browser



BAC End Information

BAC end BAC-end 1BAC-end 2
end nameMSMg01-117C20.T7 (MSMg01no117_c20.b1)MSMg01-117C20.TJ (MSMg01no117_c20.g1)
ACCAG328375AG328376
length728723
length of high quality
(start - end)		668 (46 - 713)646 (74 - 719)
definitionCHROMAT_FILE: MSMg01no117_c20.b1 PHD_FILE: MSMg01no117_c20.b1.phd.1 CHEM: term DYE: big TIME: Tue May 17 18:23:38 2005CHROMAT_FILE: MSMg01no117_c20.g1 PHD_FILE: MSMg01no117_c20.g1.phd.1 CHEM: term DYE: big TIME: Tue May 17 18:23:38 2005
singlet/doubletsinglet---
BLAST hitpluralno hit data
sequence
ATCXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXCGCGG
AATTCCACTGTACTGGCGCATCAAGTACAATGGGAACAGAGAGTAGGGGC
TGGTCCTGGGAAAGAGAAAGGGGCCAATCAGTCATTTTATCCTTCCTCTC
AGGTAGCAGTTTATTTTGGTTCAAGAAACAAATATACTTTCTTTCAATGA
ATTTTATAAGTGAACAGGAAATATTTCCATCTCTCAGAACTGCCTGTGGA
AATTTTATTGTGGTTATAGGAGTTTTTTTGGGTCTATTTTCCGAAGAACA
ATTAAAGCCAGGTATGTTTAAACATACCTGTATTAGCACCAACACGGAAT
GCTGAACCGCAACACTCTATCACTTCCTAGAGAATACATAACATACTAAG
TGCCTACCTCAACACTAAAATGAAGTGAAATAAAATCAAACAAATGTACC
TTCGATAATTGTATCTAGTGCATTGGGAAGTTTATAAGATAATGAATCAA
AAAATTCAATTATCTTTATGATAAAAATAATTAGAAATGTTATGAAGGTT
AAACAATTACTACAAGAAGGGGGAGGGAGAGACCTGGGTGAGAAACCACA
CACGGAGGGGAAGAGATGAACTTGATCAAGTACTGTGGGGGGTTGTGAAA
CAGGAGTGCATTGATGAAGATCAGCAAAAAGAATGGAAACAGGCAACTTT
GTGAGGTAGGAGGTGAGAAAACCCTCTA

TCGATGXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXTTATGTTCAACACCATTTTGTCTGGAA
GAGAATGAAGAGGAAACCATATTTTTATGAAACTTAATAAATAAGTTTTC
TCCACTTAAGAATAAGAACAAATTTGTTGTTAGAGTTATAACATCTCTCT
TTTCAAAGAGACCATCTCATTACAGACATGTGTTCATTCCAACTACGAAA
TAACTAATATAATAATGTAAACTTTTAGTTATCTTCCAATATTGGTAAAT
ATTTACAATTCAACTGATTTGGTAAATCAATTCAAAACTGACATTACCAA
TTTGAAAATTAAATAACTGTTTATTAAAATTACTAAGGTATAAAAATAAG
TATGATTGCTATCAGAAAATATTGCCTTAATAAAATTAACATAAGTGAAG
TAACAATTTTACTTAATATAGATTGTATCTCATATTCATCAATACTATTT
TAAGATATTATAGTCTTCATTTTATGCATCTGGGATTAGATGACATGCTG
AATTTCAGTGCCTGAAATAATAACTAGAGATGTTAGATGACTGGGAGGAA
ACTGGATTTGATTTTTATACTTATTGTGTTTTTATAATACTAATATTAAA
TCAATTGGTTACTACACTAAAGCTTTTTGAATCACTTTTTTTCAAATTTT
AAAATCTTATGCTACCTCTTATA
quality valuesOpen.Open.




Alignment Information

BAC End 1BAC End 2
Query= MSMg01no117_c20.b1 MSMg01no117_c20.b1 CHROMAT_FILE:
MSMg01no117_c20.b1 PHD_FILE: MSMg01no117_c20.b1.phd.1 CHEM: term DYE:
big TIME: Tue May 17 18:23:38 2005
         (668 letters)



>mm_chrY_1715909_1716980
          Length = 1072

 Score =  294 bits (152), Expect = 1e-83
 Identities = 433/544 (79%), Gaps = 60/544 (11%)
 Strand = Plus / Minus

                                                                       
Query: 8   ttccactgtactggcgcatcaagtacaatgggaacagagagtaggggctg-gtcctggga 66
           ||||| ||||||||  ||||||| ||||| ||||||||||| ||| |||| | ||||| |
Sbjct: 545 ttcca-tgtactggaacatcaagaacaataggaacagagagaaggagctgag-cctggaa 488

                                                                       
Query: 67  aagaga-aaggggccaatcag-tcattttatccttcctctcaggtagcagttta-----t 119
           || ||| | ||||| |||||| || ||||||||| |||||||| ||||||||||     |
Sbjct: 487 aacagagagggggctaatcagttc-ttttatcctgcctctcagatagcagtttagttttt 429

                                                                       
Query: 120 tttggtt-caagaaacaaatatactttctttcaatgaattttataagtgaacaggaaata 178
           |||  || |||||||||||||||||||||||||||||||||| | |||||||||||||||
Sbjct: 428 ttt--ttccaagaaacaaatatactttctttcaatgaattttgttagtgaacaggaaata 371

                                                                       
Query: 179 tttccatctctcagaac-tgcctgtgga-aattttat--tgtggttataggagttttttt 234
           ||| ||||| ||||| | |  | ||| | ||||||||  |||  |||||| || ||||||
Sbjct: 370 ttttcatctatcaga-cataacagtg-acaattttatattgt--ttatagaagatttttt 315

                                                                       
Query: 235 gggtctattttccgaagaacaattaaagccaggtatgtt-taaacatacctgtattagca 293
           ||| |||||||   ||||||||| ||||||||||||||| | || ||| | ||| ||| |
Sbjct: 314 gggactattttattaagaacaatgaaagccaggtatgttgtcaa-atatcggtaatagaa 256

                                                                       
Query: 294 ccaacacggaatgctgaaccgcaacactctatcac-ttcctagagaatacataacat--- 349
           || ||| ||||||||||||| ||||| ||||  || ||||| |||||||   |||||   
Sbjct: 255 cctacatggaatgctgaacctcaacattctag-acgttcctggagaata---aacatcac 200

                                                                       
Query: 350 actaagtgcctacc-----tcaacactaaaatgaagtgaaataaaatcaaacaaatgtac 404
           |||||||    |       |||| || ||||||||     |||||||||| | ||| |||
Sbjct: 199 actaagt----a--aaaattcaa-ac-aaaatgaa-----ataaaatcaatccaatttac 153

                                                                       
Query: 405 cttcgataattgtatctagtgca-ttgggaagtttataagataatgaatcaa-aaa---a 459
           |||||||| |||||||| || || || ||||  | |||||||||| || ||| |||   |
Sbjct: 152 cttcgatatttgtatctcgt-caatttggaaactaataagataataaaccaagaaataaa 94

                                                                       
Query: 460 tt-caattatctttatga-taaaaataattagaaatgttatgaaggtt--aaacaattac 515
           || ||||||||||||||| ||||||||||||||||||||| |||| ||  ||||||| ||
Sbjct: 93  tttcaattatctttatgaataaaaataattagaaatgttaagaagttttaaaacaatcac 34

               
Query: 516 taca 519
           ||||
Sbjct: 33  taca 30


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: 6
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: 668
Length of database: 1072
Length adjustment: 10
Effective length of query: 658
Effective length of database: 1062
Effective search space:   698796
Effective search space used:   698796
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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