BAC Information

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BAC

Clone NameMSMg01-409D04
ChromosomeY (Build37)
Map Location 1,657,054 - 1,657,389
singlet/doubletsinglet
Overlap genenone
Upstream geneUsp9y, LOC100039278, EG667079, LOC667089, Rhoay-ps1, Zfy2, Ube1y1-ps2, LOC667137, LOC100039373, LOC100039381, LOC667143
Downstream geneLOC100039401, LOC100039430, 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 nameMSMg01-409D04.T7 (MSMg01no409_d04.b1)MSMg01-409D04.TJ (MSMg01no409_d04.g1)
ACCAG506740AG506741
length807806
length of high quality
(start - end)
397 (43 - 439)339 (78 - 416)
definitionCHROMAT_FILE: MSMg01no409_d04.b1 PHD_FILE: MSMg01no409_d04.b1.phd.1 CHEM: term DYE: big TIME: Wed May 18 18:25:28 2005CHROMAT_FILE: MSMg01no409_d04.g1 PHD_FILE: MSMg01no409_d04.g1.phd.1 CHEM: term DYE: big TIME: Wed May 18 18:25:28 2005
singlet/doubletsinglet---
BLAST hituniqueno hit data
sequence
TXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXCGCGGAAT
TCTAACCAAGAGTACGCTAATACACAATATAAAGCTGTACTGAGAAGCCT
TAAGAAGGCAGGTATCTCACTCTGACCAGGGCTAAGGTTGTTTCGACTGT
ATTGGCTTTATTCTTCTGGAGATTCTTGTCAGGAATGGCGTCCTTTTACC
AGACCACAACAGGAAACCTTCCATATGTCTCCTTTGGTGTCTGGGCATAG
GATATGTGAGATGCATCAAGACTGATTAAAGGTCATGTTCCCTAGATGTG
AAACTGTTTCCAGGAATACGATGGTATACACAAGGTCAACTCCAGAATAC
ATAGCATCAGGTCTTTCTTGGCCAATTCAAAATTGGAGCCAAAATCTCAA
GAGACAATGTATGTGTTGACAGACTTGCTGCTATCACACAGGTCGTGGCT
TCAATTTCCAGCAATTACATTGTGACTGTTTCTCTGTCTCTCTATCTGTC
TCTCTATCTGACTCTCTGTCTTTTTGTCTCTCTGTCTCTCTGCCTCTCTC
TCTTCCCTTCAAACTCCCCACTCTCCGTATTGCTATCTCTCTGTAACTCC
TTCTTTACATGTGTTCCGTTTTTTTTCCTCTCACTCATCGGTCCCCCTTT
TTCTCTCACTCCGCCCTGGTTTCCCTTCCCCCATTTTTCATGTGTTTTTT
TTCTTCTATCCCTTCGGAGTTATTTTACTTATCTAATTTTTCTTCGCTTT
TTTCTTTTTTTATCTTATCTCTACCTTCTTTTCGTCTTTCTCTTTACTTT
GTATAAN
CCATGAXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXTTGTGAGATGATGTCATCACAGA
GGGAACCAATGGGCTAGAAAGAGAAAAGAGAGAGCCAAACTCCCTTTCAT
AATTAAACCTTTTCTATAACAGCATTATTAAATTATTTTTATATGTAAGT
CATATCCCTCCTGACCCATTCAATTTCTTCCAAATATATTCACACCTGGG
GATTAATCTTCAGAAAATTATTCTTGGGAAACACATGTGATTATTTCAAC
ATCTATAGGAGTGTGGGGGCATTATTCTCCCTACGTCATGTACACTTAAG
ATCTTTAGATACCTCCTTCCCTGTGATAGCCTTGCAGCTCACTGAGTGAC
ATGTGCATTTGATGATAAATGACACACAAACATTGAAGCACCTTACCATA
TCCTGTCACCCATATCATGTACAACATAGCAAGAACCACATCCTGAGTTG
AAAAATACAAATATATTTTTAAGTGTCTTGAAGTTATAATCCCCCTCTTA
TTCATACTATTATTTGGTACCTTGTGACTTTATATGCGTGTTCTTTACGT
GGTATTAACTCACGTCCTTTCCTGTACCTCCTTTTCATTGTTTTTCTTGT
ACTTTTATTTTACTTTTTTTATTCATTTCTTCTCCTTTTATATTTCACCC
CCCTCCTGCTATTGGCTTCTTCCCTCATTTAAACCCCCACTATCTTTATA
CCCGCCTCCCCTACAGAACACTCTCCTATTCTATCCTCTCGTTTCCTTTC
CCTACN
quality valuesOpen.Open.




Alignment Information

BAC End 1BAC End 2
Query= MSMg01no409_d04.b1 MSMg01no409_d04.b1 CHROMAT_FILE:
MSMg01no409_d04.b1 PHD_FILE: MSMg01no409_d04.b1.phd.1 CHEM: term DYE:
big TIME: Wed May 18 18:25:28 2005
         (397 letters)



>mm_chrY_1656850_1657646
          Length = 797

 Score =  265 bits (137), Expect = 3e-75
 Identities = 291/343 (84%), Gaps = 14/343 (4%)
 Strand = Plus / Minus

                                                                       
Query: 5   gaattctaaccaagagtacgctaatacacaatataaagc-tgtactgagaagccttaaga 63
           ||||||| |||| || || ||||| |||| | ||||||| | ||||||||||| ||||||
Sbjct: 540 gaattctgaccaggactaagctaacacactacataaagcat-tactgagaagcattaaga 482

                                                                       
Query: 64  aggcaggtatctcactctgaccagggctaaggttgtttc-gactgtattggctttattct 122
            |||||||| | |||||||||||| |||||||||||||| | ||||||||||||||| ||
Sbjct: 481 tggcaggtaccacactctgaccagcgctaaggttgtttcag-ctgtattggctttatcct 423

                                                                       
Query: 123 tctggagattcttgtcaggaatggcgt-ccttttaccaga-ccacaacaggaaaccttcc 180
           || || ||||| |||||| |||||  | |||  || |||| |||||||||||||||||||
Sbjct: 422 tcaggggattc-tgtcagaaatgg-atacctgatatcagatccacaacaggaaaccttcc 365

                                                                       
Query: 181 atatgtctc-ctttggtgtctgggcataggatatgtgagatgcatcaagactgattaaag 239
           ||||||||| |||| | ||||||||||||||||| |||||||||||| || |||||||| 
Sbjct: 364 atatgtctctcttt-gagtctgggcataggatatatgagatgcatcaggaatgattaaac 306

                                                                       
Query: 240 gtcatgttccctagatgtgaaac--tgtttccaggaatacgatggtatacacaaggtcaa 297
            ||||||||||||||| ||||||  | ||| |||| || | ||| ||| |||||||||| 
Sbjct: 305 ttcatgttccctagatatgaaaccat-ttt-cagggatcctatgatatccacaaggtcag 248

                                                      
Query: 298 ctccagaatacatagcatcaggtctttcttggccaattcaaaa 340
           ||||| | ||| ||| |||| ||||||||||||||||||||||
Sbjct: 247 ctccatactacgtagaatcatgtctttcttggccaattcaaaa 205


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: 5
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: 397
Length of database: 797
Length adjustment: 9
Effective length of query: 388
Effective length of database: 788
Effective search space:   305744
Effective search space used:   305744
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)