BAC Information

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BAC

Clone NameMSMg01-306H12
Chromosome18 (Build37)
Map Location 38,035,810 - 38,203,961
singlet/doubletdoublet
Overlap geneDiap1, Hdac3, 4631403P03Rik, Fchsd1, Centd3
Upstream geneEG627427, Pcdha1, Pcdha@, Pcdha2, Pcdha3, Pcdha4, Pcdha5, Pcdha6, Pcdha7, Pcdha8, Pcdha9, Pcdha10, Pcdha11, Pcdha12, Pcdhac1, Pcdhac2, Pcdhb1, Pcdhb2, Pcdhb3, Pcdhb4, Pcdhb5, Pcdhb6, Pcdhb7, Pcdhb8, Pcdhb9, Pcdhb10, Pcdhb11, Pcdhb12, Pcdhb13, Pcdhb14, Pcdhb15, Pcdhb16, Pcdhb17, Pcdhb18, Pcdhb19, Pcdhb20, Pcdhb21, Pcdhb22, Slc25a2, Taf7, EG666693, Pcdhg@, Pcdhga1, Pcdhga2, Pcdhga3, Pcdhgb1, Pcdhga4, Pcdhgb2, Pcdhga5, Pcdhga6, Pcdhga7, Pcdhgb4, Pcdhga8, Pcdhgb5, Pcdhga9, Pcdhgb6, Pcdhga10, Pcdhgb7, Pcdhga11, Pcdhgb8, Pcdhga12, Pcdhgc3, Pcdhgc4, Pcdhgc5
Downstream genePcdh1, LOC100042583, 1700086O06Rik, 0610009O20Rik, Pcdh12, Rnf14, Gnpda1, LOC240219, LOC100041839, Ndfip1, Spry4, 9630014M24Rik, LOC100041865, LOC100041875, LOC100042671, LOC666809, LOC100041894, Fgf1, EG545253, Arhgap26
LinkOpen Mouse BAC browser



BAC End Information

BAC end BAC-end 1BAC-end 2
end nameMSMg01-306H12.T7 (MSMg01no306_h12.b1)MSMg01-306H12.TJ (MSMg01no306_h12.g1)
ACCAG431122AG431123
length745731
length of high quality
(start - end)		701 (45 - 745)275 (363 - 637)
definitionCHROMAT_FILE: MSMg01no306_h12.b1 PHD_FILE: MSMg01no306_h12.b1.phd.1 CHEM: term DYE: big TIME: Tue May 17 21:47:16 2005CHROMAT_FILE: MSMg01no306_h12.g1 PHD_FILE: MSMg01no306_h12.g1.phd.1 CHEM: term DYE: big TIME: Tue May 17 21:47:16 2005
singlet/doubletdoubletdoublet
BLAST hituniqueunique
Map location.(38,035,810 - 38,036,506)(38,203,687 - 38,203,961)
sequence
AATXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXCGCGGA
ATTCATAAGAAACATGTGGTTCATATCACCGTGGCTATGGTCTGTGTTGA
AAGAAGTCTGTATTAAGGCTTTGGTGGTAAGAGGTTCAGATGAGACTTAC
TCTGCTGTATCCTGAATCCTCTCTAATAGATCCTTGGAATACTCTTCAGT
TCAAAGGCTACGCTCGATGAAAGGGAAGTCTAGCTGTGTACATTCTCAAT
CCCAACCTAAGACAGCCTCTGTCTTTCCTTTAAAAGACTGTAAATAAATT
ATAAGATAAAAATTAAAAGGCAGTACAAGACATTCTTGCATGAAAATATT
CTTATGAAATCTAGTGCCATATATATTGAATATTGAGTATTTTAAAAGGC
ACCAAAAGCTGAAAAGAAACCTACATCTACTAACCAACTACAGTTTGTAG
GCTTTGTTTTTGTTTGTCTCTGATTCAAATAAATAGATAAACTACTATAA
TTGAAAATATTAAATGCCACAATTGATAATAATTTACATATTATATTTGA
GGTGCATATTTCTCTGACACACATTTTGACCTACTACAGCTTAAATAACA
AGCTCAGCTCATGTTTACTAGTAATGAGTGTCCCAGAGGAGGTTGATCCA
GGTATATAAAATAAGGTTGATTTAAACCGGGTGATAAATACACAGGTATG
TGTGTGCTTGTTTGGTTTTTTCTTTTTTAAGATTTTAGTTACTTT

CGATGAAGTGGGAGGCCTGGCGGCGCCGTTTCGCACCGGGAGGNGAACNA
NAGAATATCAGCAGGAGCCTTGGAAGCTGAGGACTTCACAAAGAGCCTGC
CCCGGGTGAGACACCAGCCAGAATGAATCATTAATATACTTCACAAAGAA
GGGGACTCTCCCCAAACGCTAATTCCATCAACCCGCGAGGCAAACTTCAG
GCTTCTTGTCCAGTGATCACACAGACTATTGTAGGGCTAGGTTTCTGCTC
TGGGGAAGCCAGAGGCCCTGTTCCTCAAACCAGGGAGGAGCCAGACCCCC
CCCCTTTAGTGGATTTAGCTGCTGAGAGAGGGCTTGTTGGGCCCATATTT
ACTGCCTGCCACACCAGCCAGGGCAGTGTAGACTGACTGGGTGCTCTAAG
GAGCCTTCACATCTTGGAGAGACATCAGTAAGAAAGCGTGTGAATGACAA
ATGAACTGTTTGAAGAAATAAGAGATTGCCTAAACCCAGAATTTGCTCGA
GTACCTGAGGGTCCTCAGCCATCCTTTAATCTCTGCACTCCTATTGGAAT
TCTTATTAACCGATGAGACATGCTAAAAAATAAGTATGAAATATCAAGGA
CCCCCACCGGATCTCCAGCCACATCCTCTGCTCACGGGTCTTTTCCTTGC
ATGGACCTCTTTCTCTTCTCTCCCCAGAAAGGTCTTGCTTGTCCTTCAGG
TCATGGGTCACCATGATAGTTCTGGTGACAT
quality valuesOpen.Open.




Alignment Information

BAC End 1BAC End 2
Query= MSMg01no306_h12.b1 MSMg01no306_h12.b1 CHROMAT_FILE:
MSMg01no306_h12.b1 PHD_FILE: MSMg01no306_h12.b1.phd.1 CHEM: term DYE:
big TIME: Tue May 17 21:47:16 2005
         (701 letters)



>mm_chr18_38035606_38036706
          Length = 1101

 Score = 1324 bits (685), Expect = 0.0
 Identities = 694/697 (99%)
 Strand = Plus / Plus

                                                                       
Query: 5   gaattcataagaaacatgtggttcatatcaccgtggctatggtctgtgttgaaagaagtc 64
           |||||||||||||| |||||||||||||||| ||||||||||||||||||||||||||||
Sbjct: 205 gaattcataagaaagatgtggttcatatcactgtggctatggtctgtgttgaaagaagtc 264

                                                                       
Query: 65  tgtattaaggctttggtggtaagaggttcagatgagacttactctgctgtatcctgaatc 124
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 265 tgtattaaggctttggtggtaagaggttcagatgagacttactctgctgtatcctgaatc 324

                                                                       
Query: 125 ctctctaatagatccttggaatactcttcagttcaaaggctacgctcgatgaaagggaag 184
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 325 ctctctaatagatccttggaatactcttcagttcaaaggctacgctcgatgaaagggaag 384

                                                                       
Query: 185 tctagctgtgtacattctcaatcccaacctaagacagcctctgtctttcctttaaaagac 244
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 385 tctagctgtgtacattctcaatcccaacctaagacagcctctgtctttcctttaaaagac 444

                                                                       
Query: 245 tgtaaataaattataagataaaaattaaaaggcagtacaagacattcttgcatgaaaata 304
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 445 tgtaaataaattataagataaaaattaaaaggcagtacaagacattcttgcatgaaaata 504

                                                                       
Query: 305 ttcttatgaaatctagtgccatatatattgaatattgagtattttaaaaggcaccaaaag 364
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 505 ttcttatgaaatctagtgccatatatattgaatattgagtattttaaaaggcaccaaaag 564

                                                                       
Query: 365 ctgaaaagaaacctacatctactaaccaactacagtttgtaggctttgtttttgtttgtc 424
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 565 ctgaaaagaaacctacatctactaaccaactacagtttgtaggctttgtttttgtttgtc 624

                                                                       
Query: 425 tctgattcaaataaatagataaactactataattgaaaatattaaatgccacaattgata 484
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 625 tctgattcaaataaatagataaactactataattgaaaatattaaatgccacaattgata 684

                                                                       
Query: 485 ataatttacatattatatttgaggtgcatatttctctgacacacattttgacctactaca 544
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 685 ataatttacatattatatttgaggtgcatatttctctgacacacattttgacctactaca 744

                                                                       
Query: 545 gcttaaataacaagctcagctcatgtttactagtaatgagtgtcccagaggaggttgatc 604
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 745 gcttaaataacaagctcagctcatgtttactagtaatgagtgtcccagaggaggttgatc 804

                                                                       
Query: 605 caggtatataaaataaggttgatttaaaccgggtgataaatacacaggtatgtgtgtgct 664
           |||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||
Sbjct: 805 caggtatataaaataaggttgacttaaaccgggtgataaatacacaggtatgtgtgtgct 864

                                                
Query: 665 tgtttggttttttcttttttaagattttagttacttt 701
           |||||||||||||||||||||||||||||||||||||
Sbjct: 865 tgtttggttttttcttttttaagattttagttacttt 901


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: 37
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: 701
Length of database: 1101
Length adjustment: 10
Effective length of query: 691
Effective length of database: 1091
Effective search space:   753881
Effective search space used:   753881
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)

Query= MSMg01no306_h12.g1 MSMg01no306_h12.g1 CHROMAT_FILE:
MSMg01no306_h12.g1 PHD_FILE: MSMg01no306_h12.g1.phd.1 CHEM: term DYE:
big TIME: Tue May 17 21:47:16 2005
         (275 letters)



>mm_chr18_38203487_38204161
          Length = 675

 Score =  524 bits (271), Expect = e-153
 Identities = 274/275 (99%)
 Strand = Plus / Minus

                                                                       
Query: 1   accagccagggcagtgtagactgactgggtgctctaaggagccttcacatcttggagaga 60
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 475 accagccagggcagtgtagactgactgggtgctctaaggagccttcacatcttggagaga 416

                                                                       
Query: 61  catcagtaagaaagcgtgtgaatgacaaatgaactgtttgaagaaataagagattgccta 120
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 415 catcagtaagaaagcgtgtgaatgacaaatgaactgtttgaagaaataagagattgccta 356

                                                                       
Query: 121 aacccagaatttgctcgagtacctgagggtcctcagccatcctttaatctctgcactcct 180
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 355 aacccagaatttgctcgagtacctgagggtcctcagccatcctttaatctctgcactcct 296

                                                                       
Query: 181 attggaattcttattaaccgatgagacatgctaaaaaataagtatgaaatatcaaggacc 240
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 295 attggaattcttattaaccgatgagacatgctaaaaaataagtatgaaatatcaaggacc 236

                                              
Query: 241 cccaccggatctccagccacatcctctgctcacgg 275
           |||||| ||||||||||||||||||||||||||||
Sbjct: 235 cccaccagatctccagccacatcctctgctcacgg 201


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: 13
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: 275
Length of database: 675
Length adjustment: 9
Effective length of query: 266
Effective length of database: 666
Effective search space:   177156
Effective search space used:   177156
X1: 7 (13.9 bits)
X2: 517 (999.5 bits)
X3: 517 (999.5 bits)
S1: 7 (14.4 bits)
S2: 7 (14.3 bits)


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