Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D01
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 62811768
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 736185 characters in sequence are not A, C, G, or T
File 187 of 211
Found at i:55514542 original size:46 final size:44
Alignment explanation
Indices: 55514461--55514788 Score: 227
Period size: 44 Copynumber: 7.6 Consensus size: 44
55514451 TAATACAGGA
** *
55514461 CTTATCTCCCTGAGATTACAGTGGAATAGACCAAAGAATTTCAGAT
1 CTTATCTCCCTGAGATTACAGTGGAGCAGATCAAAGAA--TCAGAT
*
55514507 CTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAG-AT-AGTAAT
1 CTTATCTCCCTGAGATTACAGTGGAGCAGATCAAAGAATCAG--AT
* * * * *
55514551 CCTATCTCCTTGAGATTACAATGGAGCGGATTAAAG-----GAT
1 CTTATCTCCCTGAGATTACAGTGGAGCAGATCAAAGAATCAGAT
* * * * * *
55514590 CTTATCTCTCT-AAAGTTACAGTAGAGAAGATC--A-CATCAGGT
1 CTTATCTCCCTGAGA-TTACAGTGGAGCAGATCAAAGAATCAGAT
* *
55514631 CTTATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATTTCAGAT
1 CTTATCTCCCTGAGATTACAGTGGAGCAGATCAAAGAA--TCAGAT
* ** * *
55514677 CTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCA-GAGAT
1 CTTATCTCCCTGAGATTACAGTGGAGCAGATCAAAG-AATCAGAT
* * *
55514721 CTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAG-A-CACTAT
1 CTTATCTCCCTGAGATTACAGTGGAGCAGATCAAAGAATCA-GAT
*
55514764 CCTATCTCCCTGA-AGTTACAGTGGA
1 CTTATCTCCCTGAGA-TTACAGTGGA
55514789 ATGGATTAAA
Statistics
Matches: 223, Mismatches: 42, Indels: 37
0.74 0.14 0.12
Matches are distributed among these distances:
37 1 0.00
38 2 0.01
39 22 0.10
41 26 0.12
42 7 0.03
43 25 0.11
44 70 0.31
45 1 0.00
46 68 0.30
47 1 0.00
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.27
Consensus pattern (44 bp):
CTTATCTCCCTGAGATTACAGTGGAGCAGATCAAAGAATCAGAT
Found at i:55516654 original size:3 final size:3
Alignment explanation
Indices: 55516646--55516671 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
55516636 GATTTAGTCC
55516646 TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
55516672 CCTATTTGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:55518980 original size:12 final size:13
Alignment explanation
Indices: 55518957--55518986 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
55518947 AATTAGAACT
55518957 AAAAAGACAAAAA
1 AAAAAGACAAAAA
55518970 AAAAAGA-AAAAA
1 AAAAAGACAAAAA
55518982 AAAAA
1 AAAAA
55518987 CTAGTGTAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.59
13 7 0.41
ACGTcount: A:0.90, C:0.03, G:0.07, T:0.00
Consensus pattern (13 bp):
AAAAAGACAAAAA
Found at i:55524875 original size:46 final size:45
Alignment explanation
Indices: 55524769--55525076 Score: 270
Period size: 37 Copynumber: 7.6 Consensus size: 45
55524759 CATATGACCT
*
55524769 CTTATCAC-TTGTC-CTTGATCAGATAAGTGTAGCTAGGCTACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
*
55524812 CTTATCACTTTGCCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCT-AAGCTACCA
*
55524858 CTTATCACTTTATCACTTGATCAGATAA--GT-G-T-AG---CCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
*
55524895 CTTATCACTTTGTCTCTTGATCAGATAA--GT-G-T-A---ACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
**
55524932 CTTATCACTTTGTTTCTTGATCAGATAA--GT-G-T-A---ACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
**
55524969 CTTATCACTTTGTTTCTTGATCAGATAA--GT-G-T-AG---CCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
* *
55525006 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGTTACAACTACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTA-AGCTACCA
55525052 CTTATCACTTTGTCACTTGATCAGA
1 CTTATCACTTTGTCACTTGATCAGA
55525077 AGTACTCAAA
Statistics
Matches: 241, Mismatches: 10, Indels: 25
0.87 0.04 0.09
Matches are distributed among these distances:
37 135 0.56
39 2 0.01
40 3 0.01
41 1 0.00
42 1 0.00
43 10 0.04
44 6 0.02
45 21 0.09
46 62 0.26
ACGTcount: A:0.27, C:0.22, G:0.15, T:0.36
Consensus pattern (45 bp):
CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
Found at i:55524896 original size:37 final size:37
Alignment explanation
Indices: 55524855--55525039 Score: 307
Period size: 37 Copynumber: 5.0 Consensus size: 37
55524845 GCTGAAGCTA
* *
55524855 CCACTTATCACTTTATCACTTGATCAGATAAGTGTAG
1 CCACTTATCACTTTGTCTCTTGATCAGATAAGTGTAG
*
55524892 CCACTTATCACTTTGTCTCTTGATCAGATAAGTGTAA
1 CCACTTATCACTTTGTCTCTTGATCAGATAAGTGTAG
* *
55524929 CCACTTATCACTTTGTTTCTTGATCAGATAAGTGTAA
1 CCACTTATCACTTTGTCTCTTGATCAGATAAGTGTAG
*
55524966 CCACTTATCACTTTGTTTCTTGATCAGATAAGTGTAG
1 CCACTTATCACTTTGTCTCTTGATCAGATAAGTGTAG
*
55525003 CCACTTATCACTTTGTCACTTGATCAGATAAGTGTAG
1 CCACTTATCACTTTGTCTCTTGATCAGATAAGTGTAG
55525040 TTACAACTAC
Statistics
Matches: 141, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 141 1.00
ACGTcount: A:0.27, C:0.21, G:0.15, T:0.38
Consensus pattern (37 bp):
CCACTTATCACTTTGTCTCTTGATCAGATAAGTGTAG
Found at i:55527180 original size:15 final size:15
Alignment explanation
Indices: 55527160--55527190 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
55527150 GTTCATATTG
*
55527160 TCCAACCTCTTTAGA
1 TCCAACATCTTTAGA
55527175 TCCAACATCTTTAGA
1 TCCAACATCTTTAGA
55527190 T
1 T
55527191 TTTCCAATCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.29, C:0.29, G:0.06, T:0.35
Consensus pattern (15 bp):
TCCAACATCTTTAGA
Found at i:55527907 original size:68 final size:67
Alignment explanation
Indices: 55527818--55527952 Score: 218
Period size: 70 Copynumber: 2.0 Consensus size: 67
55527808 TATATATATT
*
55527818 TATATATATATACCATTCCTCCTTTTAGATTGTG-TGTCTTAAAACAATTTCTGAAAAAATAGAT
1 TATATATATATACCATCCCTCCTTTTAGATTGTGTTGTCTTAAAACAATTTCTGAAAAAATAGAT
55527882 TA
66 TA
*
55527884 TATATATATATACATCATCCCTCCTTTTAGATTGTGTTTGTCTTAAAACAATTTTTGAAAAAATA
1 TATATATATATAC--CATCCCTCCTTTTAGATTGTG-TTGTCTTAAAACAATTTCTGAAAAAATA
55527949 GATT
63 GATT
55527953 GGTTTTTTTG
Statistics
Matches: 63, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
66 13 0.21
68 20 0.32
70 30 0.48
ACGTcount: A:0.36, C:0.13, G:0.09, T:0.42
Consensus pattern (67 bp):
TATATATATATACCATCCCTCCTTTTAGATTGTGTTGTCTTAAAACAATTTCTGAAAAAATAGAT
TA
Found at i:55532991 original size:18 final size:18
Alignment explanation
Indices: 55532954--55532996 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
55532944 TTTGAAAATT
* **
55532954 AAAATATATAAACATTTA
1 AAAATATATAAAAACATA
55532972 AAAATATATAAAAACATA
1 AAAATATATAAAAACATA
55532990 AAAATAT
1 AAAATAT
55532997 TTTTTTAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.28
Consensus pattern (18 bp):
AAAATATATAAAAACATA
Found at i:55533037 original size:20 final size:21
Alignment explanation
Indices: 55533000--55533051 Score: 52
Period size: 20 Copynumber: 2.5 Consensus size: 21
55532990 AAAATATTTT
*
55533000 TTTAAAAAAAACTATAAA-AG
1 TTTAAGAAAAACTATAAAGAG
* *
55533020 TTTAAGAAAAATTCTAAAGAG
1 TTTAAGAAAAACTATAAAGAG
* *
55533041 TATGAGAAAAA
1 TTTAAGAAAAA
55533052 AAACACAAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 15 0.58
21 11 0.42
ACGTcount: A:0.60, C:0.04, G:0.12, T:0.25
Consensus pattern (21 bp):
TTTAAGAAAAACTATAAAGAG
Found at i:55536811 original size:29 final size:29
Alignment explanation
Indices: 55536779--55536839 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 29
55536769 TAAAAAACAT
*
55536779 ATAAAATTA-TTAAATGTTAA-AATAGAATA
1 ATAAAATTATTTAAA-ATTAATAATA-AATA
55536808 ATAAAATTATTTAAAATTAATAATAAATA
1 ATAAAATTATTTAAAATTAATAATAAATA
55536837 ATA
1 ATA
55536840 TGACAGGCAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
29 20 0.69
30 9 0.31
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (29 bp):
ATAAAATTATTTAAAATTAATAATAAATA
Found at i:55558343 original size:20 final size:21
Alignment explanation
Indices: 55558297--55558343 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
55558287 CAAGATAAAT
55558297 ATTAATTTAATTTAATATTAAG
1 ATTAA-TTAATTTAATATTAAG
*
55558319 A-TAATTACTTTAATATTAA-
1 ATTAATTAATTTAATATTAAG
55558338 ATTAAT
1 ATTAAT
55558344 AAAATACTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
19 1 0.04
20 18 0.78
21 3 0.13
22 1 0.04
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (21 bp):
ATTAATTAATTTAATATTAAG
Found at i:55569045 original size:50 final size:50
Alignment explanation
Indices: 55568985--55569088 Score: 172
Period size: 50 Copynumber: 2.1 Consensus size: 50
55568975 ATTCTGCACC
*
55568985 CAAGCAACATGCTTCGGAATTAGGCCTTATTTCTGTTGAAACTAAAAAGG
1 CAAGCAACATGCTTCCGAATTAGGCCTTATTTCTGTTGAAACTAAAAAGG
* * *
55569035 CAAGCTACATGCTTCCGAATTAGGCCTTATTTCTGTTGGAACTAAGAAGG
1 CAAGCAACATGCTTCCGAATTAGGCCTTATTTCTGTTGAAACTAAAAAGG
55569085 CAAG
1 CAAG
55569089 TTAAGGACTA
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.28
Consensus pattern (50 bp):
CAAGCAACATGCTTCCGAATTAGGCCTTATTTCTGTTGAAACTAAAAAGG
Found at i:55575235 original size:18 final size:18
Alignment explanation
Indices: 55575212--55575246 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
55575202 ATGTATATAA
* *
55575212 AAAGAAAGCAAATAATAC
1 AAAGAAAACAAAAAATAC
55575230 AAAGAAAACAAAAAATA
1 AAAGAAAACAAAAAATA
55575247 GGCAATAATA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.74, C:0.09, G:0.09, T:0.09
Consensus pattern (18 bp):
AAAGAAAACAAAAAATAC
Found at i:55578219 original size:22 final size:22
Alignment explanation
Indices: 55578188--55578248 Score: 70
Period size: 22 Copynumber: 2.7 Consensus size: 22
55578178 TTAATATTAA
*
55578188 TATAAAAATTTTATTTAATTTT
1 TATAAAAATTTTATATAATTTT
*
55578210 TATAACAATTATT-TATAATTTT
1 TATAAAAATT-TTATATAATTTT
*
55578232 TATAATACATTTTATAT
1 TATAA-AAATTTTATAT
55578249 TTTTAATTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
22 24 0.75
23 8 0.25
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (22 bp):
TATAAAAATTTTATATAATTTT
Found at i:55581647 original size:28 final size:30
Alignment explanation
Indices: 55581607--55581662 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
55581597 ATTTTTAATA
*
55581607 TTTTTTAATATG-TTTATAAAGGAAATATT
1 TTTTTTAATATGTTTTATAAAGAAAATATT
*
55581636 TTTTTTGA-ATGTTTTATAAAGAAAATA
1 TTTTTTAATATGTTTTATAAAGAAAATA
55581663 ATTACTTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 3 0.12
29 21 0.88
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.50
Consensus pattern (30 bp):
TTTTTTAATATGTTTTATAAAGAAAATATT
Found at i:55581678 original size:29 final size:29
Alignment explanation
Indices: 55581619--55581679 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 29
55581609 TTTTAATATG
* *
55581619 TTTATAAAGGAAATATTTTTTTTGAATGT
1 TTTATAAAGAAAATATTCTTTTTGAATGT
55581648 TTTATAAAGAAAATAATTACTTTTT-AA-GT
1 TTTATAAAGAAAAT-ATT-CTTTTTGAATGT
55581677 TTT
1 TTT
55581680 TTTCCTTCCG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
29 18 0.64
30 5 0.18
31 5 0.18
ACGTcount: A:0.38, C:0.02, G:0.10, T:0.51
Consensus pattern (29 bp):
TTTATAAAGAAAATATTCTTTTTGAATGT
Found at i:55584490 original size:22 final size:21
Alignment explanation
Indices: 55584455--55584550 Score: 74
Period size: 19 Copynumber: 4.7 Consensus size: 21
55584445 AAAGGGTATC
* *
55584455 TACAAATTAAATCTCTAAGAT
1 TACAAATCATATCTCTAAGAT
55584476 TACACAATCATATCTTCTAAGAT
1 TACA-AATCATATC-TCTAAGAT
* *
55584499 TGCATATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
* *
55584518 TATATATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
* *
55584537 TGCATATCATATCT
1 TACAAATCATATCT
55584551 AAGATTGCAT
Statistics
Matches: 63, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
19 34 0.54
21 5 0.08
22 13 0.21
23 11 0.17
ACGTcount: A:0.40, C:0.17, G:0.06, T:0.38
Consensus pattern (21 bp):
TACAAATCATATCTCTAAGAT
Found at i:55584494 original size:23 final size:22
Alignment explanation
Indices: 55584455--55584512 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
55584445 AAAGGGTATC
* *
55584455 TACAAATTAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
55584476 TACACAATCATATCTTCTAAGAT
1 TACA-AATCATATCTTCTAAGAT
* *
55584499 TGCATATCATATCT
1 TACAAATCATATCT
55584513 AAGATTATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 4 0.13
22 16 0.52
23 11 0.35
ACGTcount: A:0.40, C:0.19, G:0.05, T:0.36
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:55584515 original size:19 final size:19
Alignment explanation
Indices: 55584491--55584563 Score: 128
Period size: 19 Copynumber: 3.8 Consensus size: 19
55584481 AATCATATCT
55584491 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
**
55584510 TCTAAGATTATATATCATA
1 TCTAAGATTGCATATCATA
55584529 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
55584548 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
55584564 CCTGAAGATT
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 50 1.00
ACGTcount: A:0.37, C:0.15, G:0.10, T:0.38
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:55588810 original size:46 final size:46
Alignment explanation
Indices: 55588743--55588901 Score: 270
Period size: 46 Copynumber: 3.5 Consensus size: 46
55588733 TGATCAGTGA
*
55588743 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATTTGAT
1 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGAT
*
55588789 CAAGTGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTATCTGAT
1 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGAT
55588835 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGAT
1 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGAT
55588881 C-AG-GA-ACAAGTGATAAGTGGT
1 CAAGTGACA-AAGTGATAAGTGGT
55588902 GACAAAGTGA
Statistics
Matches: 109, Mismatches: 3, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
43 1 0.01
44 16 0.15
45 2 0.02
46 90 0.83
ACGTcount: A:0.33, C:0.14, G:0.23, T:0.29
Consensus pattern (46 bp):
CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGAT
Found at i:55588909 original size:62 final size:64
Alignment explanation
Indices: 55588838--55588965 Score: 226
Period size: 62 Copynumber: 2.0 Consensus size: 64
55588828 ATCTGATCAA
55588838 GTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATC-AG-GA-ACAAGTGATAAGTG
1 GTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACA-AAGTGATAAGTG
55588900 GTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAAGTGATAAGTG
1 GTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAAGTGATAAGTG
55588964 GT
1 GT
55588966 AGCCTAACTA
Statistics
Matches: 63, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
62 44 0.70
63 2 0.03
64 16 0.25
65 1 0.02
ACGTcount: A:0.34, C:0.12, G:0.26, T:0.28
Consensus pattern (64 bp):
GTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAAGTGATAAGTG
Found at i:55588928 original size:108 final size:107
Alignment explanation
Indices: 55588792--55589006 Score: 385
Period size: 108 Copynumber: 2.0 Consensus size: 107
55588782 ATTTGATCAA
55588792 GTGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGG
1 GTGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGG
* *
55588857 TAGCTTTAGCTACACTTATCTGATCAGGAACAAGTGATAAGTG
66 TAGC-CTAACTACACTTATCTGATCAGGAACAAGTGATAAGTG
*
55588900 GTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGG
1 GTGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGG
*
55588965 TAGCCTAACTACACTTATCTGATCAGGGACAAGTGATAAGTG
66 TAGCCTAACTACACTTATCTGATCAGGAACAAGTGATAAGTG
55589007 ATCATACGTA
Statistics
Matches: 103, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
107 35 0.34
108 68 0.66
ACGTcount: A:0.33, C:0.15, G:0.24, T:0.27
Consensus pattern (107 bp):
GTGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGG
TAGCCTAACTACACTTATCTGATCAGGAACAAGTGATAAGTG
Found at i:55588965 original size:46 final size:44
Alignment explanation
Indices: 55588900--55589006 Score: 162
Period size: 46 Copynumber: 2.4 Consensus size: 44
55588890 GTGATAAGTG
* *
55588900 GTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAA
1 GTGACAAAGTGATAAGTGGTAGC-CTAACTACACTTATCTGATC-A
55588946 GTGACAAAGTGATAAGTGGTAGCCTAACTACACTTATCTGATCA
1 GTGACAAAGTGATAAGTGGTAGCCTAACTACACTTATCTGATCA
*
55588990 GGGAC-AAGTGATAAGTG
1 GTGACAAAGTGATAAGTG
55589007 ATCATACGTA
Statistics
Matches: 58, Mismatches: 3, Indels: 3
0.91 0.05 0.05
Matches are distributed among these distances:
43 12 0.21
44 5 0.09
45 18 0.31
46 23 0.40
ACGTcount: A:0.34, C:0.15, G:0.24, T:0.27
Consensus pattern (44 bp):
GTGACAAAGTGATAAGTGGTAGCCTAACTACACTTATCTGATCA
Found at i:55593364 original size:57 final size:57
Alignment explanation
Indices: 55593289--55593404 Score: 223
Period size: 57 Copynumber: 2.0 Consensus size: 57
55593279 GTTATTTTAC
*
55593289 TTAGAAAATTACTGAAGTTAGTTGAGTAAGTAGTGTATGGATTGGTTATACTTACAA
1 TTAGAAAATTACTAAAGTTAGTTGAGTAAGTAGTGTATGGATTGGTTATACTTACAA
55593346 TTAGAAAATTACTAAAGTTAGTTGAGTAAGTAGTGTATGGATTGGTTATACTTACAA
1 TTAGAAAATTACTAAAGTTAGTTGAGTAAGTAGTGTATGGATTGGTTATACTTACAA
55593403 TT
1 TT
55593405 GAGATTCGAT
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 58 1.00
ACGTcount: A:0.35, C:0.05, G:0.22, T:0.38
Consensus pattern (57 bp):
TTAGAAAATTACTAAAGTTAGTTGAGTAAGTAGTGTATGGATTGGTTATACTTACAA
Found at i:55601136 original size:29 final size:30
Alignment explanation
Indices: 55601095--55601152 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 30
55601085 TGATGGTTTT
* * *
55601095 AACCGTCCATTTTTA-TATTCGATGGTCGA
1 AACCATCCATTTTCATTAATCGATGGTCGA
*
55601124 AACCATCCCTTTTCATTAATCGATGGTCG
1 AACCATCCATTTTCATTAATCGATGGTCG
55601153 TTTGTCACCA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 12 0.50
30 12 0.50
ACGTcount: A:0.24, C:0.24, G:0.16, T:0.36
Consensus pattern (30 bp):
AACCATCCATTTTCATTAATCGATGGTCGA
Found at i:55601208 original size:29 final size:29
Alignment explanation
Indices: 55601162--55601325 Score: 156
Period size: 29 Copynumber: 5.7 Consensus size: 29
55601152 GTTTGTCACC
*
55601162 ATCCCTTTTCATAATCGATAGTCGAAGCT
1 ATCCCTTTTCATATTCGATAGTCGAAGCT
* * * * *
55601191 AACCTTTTTCATATTCGATAGCCAAAGTT
1 ATCCCTTTTCATATTCGATAGTCGAAGCT
* *
55601220 ATCCCTTTTCATATTAGATA-ACTGAAGCT
1 ATCCCTTTTCATATTCGATAGTC-GAAGCT
* * *
55601249 ATCCCTTTTCATATTCGATGGTCGTCA-CC
1 ATCCCTTTTCATATTCGATAGTCG-AAGCT
*
55601278 ATCCTTTTTCATAATT-GATAG-CTGAAGCT
1 ATCCCTTTTCAT-ATTCGATAGTC-GAAGCT
55601307 ATCCCTTTTCATATTCGAT
1 ATCCCTTTTCATATTCGAT
55601326 GATCGCAGAT
Statistics
Matches: 106, Mismatches: 22, Indels: 14
0.75 0.15 0.10
Matches are distributed among these distances:
28 6 0.06
29 95 0.90
30 5 0.05
ACGTcount: A:0.26, C:0.23, G:0.12, T:0.39
Consensus pattern (29 bp):
ATCCCTTTTCATATTCGATAGTCGAAGCT
Found at i:55601284 original size:87 final size:87
Alignment explanation
Indices: 55601162--55601321 Score: 216
Period size: 87 Copynumber: 1.8 Consensus size: 87
55601152 GTTTGTCACC
* *
55601162 ATCCCTTTTCATAATCGATAGTCGAAGCTAACCTTTTTCAT-ATTCGATAGCCAAAGTTATCCCT
1 ATCCCTTTTCATAATCGATAGTCGAAGCCAACCTTTTTCATAATT-GATAGCCAAAGCTATCCCT
55601226 TTTCATATTAGATAACTGAAGCT
65 TTTCATATTAGATAACTGAAGCT
* * * * **
55601249 ATCCCTTTTCATATTCGATGGTCGTCA-CCATCCTTTTTCATAATTGATAGCTGAAGCTATCCCT
1 ATCCCTTTTCATAATCGATAGTCG-AAGCCAACCTTTTTCATAATTGATAGCCAAAGCTATCCCT
55601313 TTTCATATT
65 TTTCATATT
55601322 CGATGATCGC
Statistics
Matches: 63, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
87 59 0.94
88 4 0.06
ACGTcount: A:0.26, C:0.23, G:0.11, T:0.39
Consensus pattern (87 bp):
ATCCCTTTTCATAATCGATAGTCGAAGCCAACCTTTTTCATAATTGATAGCCAAAGCTATCCCTT
TTCATATTAGATAACTGAAGCT
Found at i:55614276 original size:27 final size:27
Alignment explanation
Indices: 55614242--55614419 Score: 187
Period size: 27 Copynumber: 6.6 Consensus size: 27
55614232 TAAATTGTAC
55614242 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
55614269 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
55614295 ATGCACTAAGTGTGCGAGTTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
* * *
55614323 GGCACTAAGTGTGCGAGTCTAACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
55614351 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
55614378 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
55614405 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
55614420 GGCTCAATAT
Statistics
Matches: 124, Mismatches: 24, Indels: 6
0.81 0.16 0.04
Matches are distributed among these distances:
27 103 0.83
28 21 0.17
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.29
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:55614359 original size:82 final size:81
Alignment explanation
Indices: 55614243--55614398 Score: 224
Period size: 82 Copynumber: 1.9 Consensus size: 81
55614233 AAATTGTACA
* * * *
55614243 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATCTAACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
55614307 TGCGAGTTGACCATGCG
65 TGCGAGTTGACCATGCG
** *
55614324 GCACTAAGTGTGCGAGTCTAACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TCTAACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
55614389 TGCGAGTTGA
65 TGCGAGTTGA
55614399 TTATATAGCA
Statistics
Matches: 66, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
81 15 0.23
82 50 0.76
83 1 0.02
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATCTAACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAGTTGACCATGCG
Found at i:55614410 original size:82 final size:81
Alignment explanation
Indices: 55614239--55614419 Score: 220
Period size: 82 Copynumber: 2.2 Consensus size: 81
55614229 GAGTAAATTG
* * * *
55614239 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATCTAACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
55614304 GTGTGCGAGTTGACCA
66 GTGTGCGAGTTGACCA
* * ** *
55614320 TGCGGCACTAAGTGTGCGAGTCTAACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TCTAACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
**
55614384 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAGTTGACCA
* *
55614402 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
55614420 GGCTCAATAT
Statistics
Matches: 83, Mismatches: 15, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
81 18 0.22
82 65 0.78
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.29
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATCTAACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAGTTGACCA
Found at i:55622361 original size:27 final size:27
Alignment explanation
Indices: 55622327--55622504 Score: 187
Period size: 27 Copynumber: 6.6 Consensus size: 27
55622317 TAAATTGTAC
55622327 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
55622354 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
55622380 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
* * *
55622408 GGCACTAAGTGTGCGAGTCTAACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
55622436 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
55622463 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
55622490 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
55622505 GGCTCAATAT
Statistics
Matches: 125, Mismatches: 23, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
27 104 0.83
28 21 0.17
ACGTcount: A:0.28, C:0.16, G:0.28, T:0.29
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:55622444 original size:82 final size:81
Alignment explanation
Indices: 55622328--55622483 Score: 215
Period size: 82 Copynumber: 1.9 Consensus size: 81
55622318 AAATTGTACA
* * * *
55622328 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATCTAACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
55622392 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
55622409 GCACTAAGTGTGCGAGTCTAACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TCTAACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
55622474 TGCGAGTTGA
65 TGCGAATTGA
55622484 TTATATAGCA
Statistics
Matches: 65, Mismatches: 8, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
81 15 0.23
82 49 0.75
83 1 0.02
ACGTcount: A:0.28, C:0.16, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATCTAACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:55622495 original size:82 final size:81
Alignment explanation
Indices: 55622324--55622504 Score: 211
Period size: 82 Copynumber: 2.2 Consensus size: 81
55622314 GAGTAAATTG
* * * *
55622324 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATCTAACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
55622389 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
55622405 TGCGGCACTAAGTGTGCGAGTCTAACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TCTAACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
55622469 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
55622487 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
55622505 GGCTCAATAT
Statistics
Matches: 82, Mismatches: 16, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
81 18 0.22
82 64 0.78
ACGTcount: A:0.28, C:0.16, G:0.27, T:0.29
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATCTAACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:55622515 original size:27 final size:27
Alignment explanation
Indices: 55622409--55622515 Score: 81
Period size: 27 Copynumber: 3.9 Consensus size: 27
55622399 TGACCATGCG
*
55622409 GCACTAAGTGTGCGAG-TCTAACTATGTA
1 GCACTAAGTGTGCGAGCTC-AA-TATATA
** * * **
55622437 GCACTAAGTGTGCGATTTGATTACGTA
1 GCACTAAGTGTGCGAGCTCAATATATA
* * *
55622464 GCACTAAGTGTGCGAGTTGATTATATA
1 GCACTAAGTGTGCGAGCTCAATATATA
* *
55622491 GCACTGAGTGTGCGGGCTCAATATA
1 GCACTAAGTGTGCGAGCTCAATATA
55622516 CATTCGTGAA
Statistics
Matches: 66, Mismatches: 12, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
27 49 0.74
28 16 0.24
29 1 0.02
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.30
Consensus pattern (27 bp):
GCACTAAGTGTGCGAGCTCAATATATA
Found at i:55627341 original size:4 final size:4
Alignment explanation
Indices: 55627332--55627356 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
55627322 TTAATTAGTA
55627332 ACAT ACAT ACAT ACAT ACAT ACAT A
1 ACAT ACAT ACAT ACAT ACAT ACAT A
55627357 TGTAAGTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.52, C:0.24, G:0.00, T:0.24
Consensus pattern (4 bp):
ACAT
Found at i:55642315 original size:31 final size:31
Alignment explanation
Indices: 55642277--55642336 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
55642267 AATATAAAGA
* *
55642277 ATTCTTTCATTACTTAATACATTTTCATTGT
1 ATTCTTTCAATACTTAATACAGTTTCATTGT
*
55642308 ATTCTTTCAATACTTAGTACAGTTTCATT
1 ATTCTTTCAATACTTAATACAGTTTCATT
55642337 CATTCAATAC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.27, C:0.17, G:0.05, T:0.52
Consensus pattern (31 bp):
ATTCTTTCAATACTTAATACAGTTTCATTGT
Found at i:55645853 original size:3 final size:3
Alignment explanation
Indices: 55645845--55645889 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
55645835 TTTCCCTTTA
55645845 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
55645890 ATTTCTTTTC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:55649302 original size:21 final size:22
Alignment explanation
Indices: 55649265--55649308 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
55649255 ATATTTCACC
55649265 ATTTTTAAATTTAGGTATCGAT
1 ATTTTTAAATTTAGGTATCGAT
*
55649287 ATTTTTACATTT-GGTATCGAT
1 ATTTTTAAATTTAGGTATCGAT
55649308 A
1 A
55649309 CCTAACCATA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 10 0.48
22 11 0.52
ACGTcount: A:0.30, C:0.07, G:0.14, T:0.50
Consensus pattern (22 bp):
ATTTTTAAATTTAGGTATCGAT
Found at i:55651542 original size:17 final size:19
Alignment explanation
Indices: 55651515--55651557 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 19
55651505 TAATTTAATA
55651515 ATAATTTAATTA-ATTTTT
1 ATAATTTAATTATATTTTT
55651533 ATAA-TTAATTATATTTTT
1 ATAATTTAATTATATTTTT
*
55651551 ATTATTT
1 ATAATTT
55651558 TCAATTAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 7 0.32
18 13 0.59
19 2 0.09
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (19 bp):
ATAATTTAATTATATTTTT
Found at i:55652867 original size:34 final size:34
Alignment explanation
Indices: 55652796--55652867 Score: 83
Period size: 34 Copynumber: 2.1 Consensus size: 34
55652786 AGCATATATT
* * * *
55652796 TATACTTATCAACTACATGTGCCGAATGCGCATA
1 TATACTTATCAACCACATATGCCGAATGCACACA
*
55652830 TATACTTAT-AATCCACATATGCCGAATGCATACA
1 TATACTTATCAA-CCACATATGCCGAATGCACACA
55652864 TATA
1 TATA
55652868 TATATCCAAC
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
33 2 0.06
34 30 0.94
ACGTcount: A:0.36, C:0.22, G:0.11, T:0.31
Consensus pattern (34 bp):
TATACTTATCAACCACATATGCCGAATGCACACA
Found at i:55653247 original size:41 final size:41
Alignment explanation
Indices: 55653044--55653232 Score: 288
Period size: 41 Copynumber: 4.6 Consensus size: 41
55653034 TTAATTTAAA
* *
55653044 CAGATTCATCGGCACTTAGCCTGCTAGGCTTATAACCTGATT
1 CAGA-TCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATT
55653086 CAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATT
1 CAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATT
* * * *
55653127 CAAATCACCGGCATTTAGCCTGCTAGGCTTATAACCTAATT
1 CAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATT
*
55653168 CAGTTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATT
1 CAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATT
* *
55653209 CAGATCATCGGCACTTAACCTGCT
1 CAGATCACCGGCACTTAGCCTGCT
55653233 GGGCGCTATG
Statistics
Matches: 133, Mismatches: 14, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
41 129 0.97
42 4 0.03
ACGTcount: A:0.24, C:0.29, G:0.19, T:0.29
Consensus pattern (41 bp):
CAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATT
Found at i:55654233 original size:4 final size:4
Alignment explanation
Indices: 55654226--55654264 Score: 78
Period size: 4 Copynumber: 9.8 Consensus size: 4
55654216 TAAAATAGAT
55654226 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
55654265 TATATATATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 35 1.00
ACGTcount: A:0.51, C:0.23, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:55657911 original size:43 final size:43
Alignment explanation
Indices: 55657850--55657973 Score: 146
Period size: 43 Copynumber: 2.9 Consensus size: 43
55657840 ATTTTCGATA
* *
55657850 TGTGTTTTCGTGTAAGACCACGTCTGGGACGTTGGCATCGACT
1 TGTGTTTACGAGTAAGACCACGTCTGGGACGTTGGCATCGACT
*
55657893 TGTGTTTACGAGTAAGACC-CTGTCTGGGACAG-TGGCATCGATT
1 TGTGTTTACGAGTAAGACCAC-GTCTGGGAC-GTTGGCATCGACT
** *
55657936 TGTGAATAC-ATGTAAGACCACGTCTGGGATGTTGGCAT
1 TGTGTTTACGA-GTAAGACCACGTCTGGGACGTTGGCAT
55657974 TGTACGAGCT
Statistics
Matches: 70, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
42 3 0.04
43 65 0.93
44 2 0.03
ACGTcount: A:0.21, C:0.19, G:0.30, T:0.31
Consensus pattern (43 bp):
TGTGTTTACGAGTAAGACCACGTCTGGGACGTTGGCATCGACT
Found at i:55659354 original size:19 final size:20
Alignment explanation
Indices: 55659322--55659369 Score: 80
Period size: 19 Copynumber: 2.5 Consensus size: 20
55659312 AATAAATATA
55659322 TATTTTTTATTTTTTAAAAT
1 TATTTTTTATTTTTTAAAAT
55659342 TATTTTTTA-TTTTTAAAAT
1 TATTTTTTATTTTTTAAAAT
*
55659361 AATTTTTTA
1 TATTTTTTA
55659370 ATGTTTATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
19 18 0.67
20 9 0.33
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (20 bp):
TATTTTTTATTTTTTAAAAT
Found at i:55659376 original size:20 final size:20
Alignment explanation
Indices: 55659323--55659376 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 20
55659313 ATAAATATAT
* *
55659323 ATTTTTTATTTTTTAAAATT
1 ATTTTTTAATTTTTAAAATA
55659343 ATTTTTT-ATTTTTAAAATA
1 ATTTTTTAATTTTTAAAATA
*
55659362 ATTTTTTAATGTTTA
1 ATTTTTTAATTTTTA
55659377 TTTTAAAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
19 17 0.57
20 13 0.43
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (20 bp):
ATTTTTTAATTTTTAAAATA
Found at i:55662004 original size:33 final size:33
Alignment explanation
Indices: 55661967--55662037 Score: 81
Period size: 33 Copynumber: 2.2 Consensus size: 33
55661957 TGAACCAATT
*
55661967 AAAAAA-TCAATAAAATTGGCGGTTGAATCGACC
1 AAAAAACT-AATAAAACTGGCGGTTGAATCGACC
** * *
55662000 AAAAAACTAATTGAACTGGTGGTTGAATCGACT
1 AAAAAACTAATAAAACTGGCGGTTGAATCGACC
55662033 AAAAA
1 AAAAA
55662038 TAATTGAATC
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
33 31 0.97
34 1 0.03
ACGTcount: A:0.46, C:0.13, G:0.18, T:0.23
Consensus pattern (33 bp):
AAAAAACTAATAAAACTGGCGGTTGAATCGACC
Found at i:55664649 original size:11 final size:11
Alignment explanation
Indices: 55664633--55664670 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
55664623 TAAATTTTAG
55664633 TAATTTTTAAA
1 TAATTTTTAAA
55664644 TAATTTTTAAA
1 TAATTTTTAAA
*
55664655 T-ATATCTTAAA
1 TAAT-TTTTAAA
55664666 TAATT
1 TAATT
55664671 ATTTTTTAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
10 2 0.08
11 20 0.83
12 2 0.08
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (11 bp):
TAATTTTTAAA
Found at i:55675267 original size:13 final size:13
Alignment explanation
Indices: 55675249--55675274 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
55675239 CAGAGGTAAA
55675249 ACTTGTAACTTCT
1 ACTTGTAACTTCT
55675262 ACTTGTAACTTCT
1 ACTTGTAACTTCT
55675275 GCAAGAAGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.23, G:0.08, T:0.46
Consensus pattern (13 bp):
ACTTGTAACTTCT
Found at i:55679152 original size:42 final size:42
Alignment explanation
Indices: 55679092--55679288 Score: 243
Period size: 42 Copynumber: 4.7 Consensus size: 42
55679082 TCATGTTTAC
* *
55679092 TTTCCGTTCAGCTTTTTTGAGCTTCTGTTTAACCCTTATGGG
1 TTTCCGTTCAGCTCTTTTGAGCTTCTGTTTAACCCTTATGAG
*
55679134 TTTCCGTTCAGCTCTTTTGAGCTTCTGTTTAA-CTTATATGAG
1 TTTCCGTTCAGCTCTTTTGAGCTTCTGTTTAACCCT-TATGAG
* * *
55679176 TTTCTGTTCAGCTCTTTTGAGCTTTTGTTTAACCCTTATAAG
1 TTTCCGTTCAGCTCTTTTGAGCTTCTGTTTAACCCTTATGAG
* * * *
55679218 TTTTCGTTAAGCTCTTATGAGCTTCTGTTCAACCCTTATGAG
1 TTTCCGTTCAGCTCTTTTGAGCTTCTGTTTAACCCTTATGAG
* * ** *
55679260 TTTCTGTTTAGCTCTCATGAACTTCTGTT
1 TTTCCGTTCAGCTCTTTTGAGCTTCTGTT
55679289 CAGCTTTCGA
Statistics
Matches: 134, Mismatches: 19, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
41 2 0.01
42 130 0.97
43 2 0.01
ACGTcount: A:0.16, C:0.20, G:0.16, T:0.48
Consensus pattern (42 bp):
TTTCCGTTCAGCTCTTTTGAGCTTCTGTTTAACCCTTATGAG
Found at i:55679196 original size:21 final size:21
Alignment explanation
Indices: 55679092--55679293 Score: 122
Period size: 21 Copynumber: 9.6 Consensus size: 21
55679082 TCATGTTTAC
* * *
55679092 TTTCCGTTCAGCTTTTTTGAG
1 TTTCTGTTCAGCTCTTATGAG
* * * * *
55679113 CTTCTGTTTAACCCTTATGGG
1 TTTCTGTTCAGCTCTTATGAG
* *
55679134 TTTCCGTTCAGCTCTTTTGAG
1 TTTCTGTTCAGCTCTTATGAG
* * *
55679155 CTTCTGTTTAACT-TATATGAG
1 TTTCTGTTCAGCTCT-TATGAG
*
55679176 TTTCTGTTCAGCTCTTTTGAG
1 TTTCTGTTCAGCTCTTATGAG
* * * *
55679197 CTTT-TGTTTAACCCTTATAAG
1 -TTTCTGTTCAGCTCTTATGAG
*
55679218 TTT-TCGTTAAGCTCTTATGAG
1 TTTCT-GTTCAGCTCTTATGAG
* * *
55679239 CTTCTGTTCAACCCTTATGAG
1 TTTCTGTTCAGCTCTTATGAG
* * *
55679260 TTTCTGTTTAGCTCTCATGAA
1 TTTCTGTTCAGCTCTTATGAG
*
55679281 CTTCTGTTCAGCT
1 TTTCTGTTCAGCT
55679294 TTCGAACTTC
Statistics
Matches: 131, Mismatches: 45, Indels: 10
0.70 0.24 0.05
Matches are distributed among these distances:
20 5 0.04
21 121 0.92
22 5 0.04
ACGTcount: A:0.16, C:0.21, G:0.16, T:0.47
Consensus pattern (21 bp):
TTTCTGTTCAGCTCTTATGAG
Found at i:55682759 original size:23 final size:23
Alignment explanation
Indices: 55682733--55682802 Score: 69
Period size: 23 Copynumber: 3.3 Consensus size: 23
55682723 TCTGATTTAG
55682733 AATAATTCTAAGCTTTGGATACA
1 AATAATTCTAAGCTTTGGATACA
* * * *
55682756 AATAATGCTTAG-ATT---TA-G
1 AATAATTCTAAGCTTTGGATACA
55682774 AATAATTCTAAGCTTTGGATACA
1 AATAATTCTAAGCTTTGGATACA
55682797 AATAAT
1 AATAAT
55682803 GCAAACCTCA
Statistics
Matches: 34, Mismatches: 8, Indels: 10
0.65 0.15 0.19
Matches are distributed among these distances:
18 10 0.29
19 4 0.12
22 4 0.12
23 16 0.47
ACGTcount: A:0.41, C:0.10, G:0.13, T:0.36
Consensus pattern (23 bp):
AATAATTCTAAGCTTTGGATACA
Found at i:55682771 original size:41 final size:41
Alignment explanation
Indices: 55682726--55682804 Score: 158
Period size: 41 Copynumber: 1.9 Consensus size: 41
55682716 AAATCTATCT
55682726 GATTTAGAATAATTCTAAGCTTTGGATACAAATAATGCTTA
1 GATTTAGAATAATTCTAAGCTTTGGATACAAATAATGCTTA
55682767 GATTTAGAATAATTCTAAGCTTTGGATACAAATAATGC
1 GATTTAGAATAATTCTAAGCTTTGGATACAAATAATGC
55682805 AAACCTCACA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.35
Consensus pattern (41 bp):
GATTTAGAATAATTCTAAGCTTTGGATACAAATAATGCTTA
Found at i:55687827 original size:18 final size:19
Alignment explanation
Indices: 55687806--55687843 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
55687796 ATTTTGGCAT
*
55687806 TTTTATAAA-TAGTTTGAA
1 TTTTAAAAATTAGTTTGAA
*
55687824 TTTTAAAAATTATTTTGAA
1 TTTTAAAAATTAGTTTGAA
55687843 T
1 T
55687844 CTTTTTATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.39, C:0.00, G:0.08, T:0.53
Consensus pattern (19 bp):
TTTTAAAAATTAGTTTGAA
Found at i:55700989 original size:63 final size:63
Alignment explanation
Indices: 55700885--55701054 Score: 223
Period size: 63 Copynumber: 2.7 Consensus size: 63
55700875 ATCACAACAC
* ** * * * *
55700885 GCACTAGTTTATTTTACACTTGCACCACAACACGCGCAATCATTCATTGCACCAACATAGTCA
1 GCACCAGTTTATTTTACACAAGCACCACAACATGCACAATCATTCACTGCACCAACACAGTCA
* *
55700948 GCACCAGTTTATTTTACACAAGCATCACAACATGCACAATCATTCCCTGCACCAACACAGTCA
1 GCACCAGTTTATTTTACACAAGCACCACAACATGCACAATCATTCACTGCACCAACACAGTCA
* * * *
55701011 TCACCAATTTATTTTACACAAGCACCACAGCATGCTCAATCATT
1 GCACCAGTTTATTTTACACAAGCACCACAACATGCACAATCATT
55701055 TCCTACACCG
Statistics
Matches: 93, Mismatches: 14, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
63 93 1.00
ACGTcount: A:0.34, C:0.31, G:0.09, T:0.26
Consensus pattern (63 bp):
GCACCAGTTTATTTTACACAAGCACCACAACATGCACAATCATTCACTGCACCAACACAGTCA
Found at i:55702348 original size:31 final size:29
Alignment explanation
Indices: 55702280--55702367 Score: 86
Period size: 31 Copynumber: 2.9 Consensus size: 29
55702270 ATAAAATTGG
* * * *
55702280 AATAATTTAGTGATTAAATTGTAATTTTT
1 AATAATTGAGTGATCAAAGTGTAATTTCT
*
55702309 TATAATTGAGTGATCAAAGTGTAAATTTACT
1 AATAATTGAGTGATCAAAGTGT-AATTT-CT
* *
55702340 AATAATTGAGTGACCATAGGTGTAATTT
1 AATAATTGAGTGATCA-AAGTGTAATTT
55702368 AACAAAAAAA
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
29 18 0.38
30 5 0.10
31 20 0.42
32 5 0.10
ACGTcount: A:0.38, C:0.05, G:0.16, T:0.42
Consensus pattern (29 bp):
AATAATTGAGTGATCAAAGTGTAATTTCT
Found at i:55702553 original size:18 final size:19
Alignment explanation
Indices: 55702520--55702557 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
55702510 TGTTTCATGG
55702520 AAAATAACTTAGTTAATGA
1 AAAATAACTTAGTTAATGA
*
55702539 AAAATAATTTA-TTAATGA
1 AAAATAACTTAGTTAATGA
55702557 A
1 A
55702558 TAAAATAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.55, C:0.03, G:0.08, T:0.34
Consensus pattern (19 bp):
AAAATAACTTAGTTAATGA
Found at i:55704326 original size:20 final size:20
Alignment explanation
Indices: 55704296--55704341 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 20
55704286 TTAACATTAA
55704296 TAATAATTTTAAT-AGTATCTT
1 TAAT-ATTTTAATAAGTAT-TT
*
55704317 TAATATTTTATTAAGTATTT
1 TAATATTTTAATAAGTATTT
55704337 TAATA
1 TAATA
55704342 ATTATGACAC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 14 0.61
21 9 0.39
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.54
Consensus pattern (20 bp):
TAATATTTTAATAAGTATTT
Found at i:55705860 original size:31 final size:31
Alignment explanation
Indices: 55705824--55705892 Score: 111
Period size: 31 Copynumber: 2.2 Consensus size: 31
55705814 TTACAATTTT
**
55705824 GTCACTAAACTATTTGAAAGTTTTCATTTAA
1 GTCACTAAACTATTCAAAAGTTTTCATTTAA
*
55705855 GTCACTAAACTATTCAAAAGTTTTTATTTAA
1 GTCACTAAACTATTCAAAAGTTTTCATTTAA
55705886 GTCACTA
1 GTCACTA
55705893 GATTGTCAAG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.36, C:0.14, G:0.09, T:0.41
Consensus pattern (31 bp):
GTCACTAAACTATTCAAAAGTTTTCATTTAA
Found at i:55706636 original size:5 final size:5
Alignment explanation
Indices: 55706626--55706650 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
55706616 CAAAACTTTA
55706626 CTCCC CTCCC CTCCC CTCCC CTCCC
1 CTCCC CTCCC CTCCC CTCCC CTCCC
55706651 AACCCCCCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.80, G:0.00, T:0.20
Consensus pattern (5 bp):
CTCCC
Found at i:55706786 original size:30 final size:31
Alignment explanation
Indices: 55706752--55706811 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
55706742 AAACATTTTA
*
55706752 TTTTCCCCCAAAATTTTTACTCCC-TCCCAC
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
** *
55706782 TTTTCCCTTAAAACTTTTATTCCCTTCCCA
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCA
55706812 TCCCACCTCC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 20 0.80
31 5 0.20
ACGTcount: A:0.20, C:0.38, G:0.00, T:0.42
Consensus pattern (31 bp):
TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
Found at i:55720072 original size:22 final size:22
Alignment explanation
Indices: 55720040--55720108 Score: 68
Period size: 22 Copynumber: 3.1 Consensus size: 22
55720030 TATGCACTAT
*
55720040 TAAACAAAGAGCACCAAAGTGC
1 TAAACAGAGAGCACCAAAGTGC
*
55720062 TATACAGAGAGCA-CAAATGTGC
1 TAAACAGAGAGCACCAAA-GTGC
* * * *
55720084 GAAACGGAGAGCACTAATGTGC
1 TAAACAGAGAGCACCAAAGTGC
55720106 TAA
1 TAA
55720109 TAATAGGAGA
Statistics
Matches: 37, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
21 4 0.11
22 31 0.84
23 2 0.05
ACGTcount: A:0.43, C:0.19, G:0.23, T:0.14
Consensus pattern (22 bp):
TAAACAGAGAGCACCAAAGTGC
Found at i:55722065 original size:22 final size:23
Alignment explanation
Indices: 55722040--55722083 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 23
55722030 ACAATAATAA
55722040 CAAAATGACAACAAA-ACAACAT
1 CAAAATGACAACAAACACAACAT
* * *
55722062 CAAAGTGGCAGCAAACACAACA
1 CAAAATGACAACAAACACAACA
55722084 GTAAACAGTA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.57, C:0.25, G:0.11, T:0.07
Consensus pattern (23 bp):
CAAAATGACAACAAACACAACAT
Found at i:55724660 original size:45 final size:45
Alignment explanation
Indices: 55724610--55724698 Score: 160
Period size: 45 Copynumber: 2.0 Consensus size: 45
55724600 GAGCACAATC
55724610 AAATTCATATTTTCCTATATTAACAATAATATTCATACCAAGCTG
1 AAATTCATATTTTCCTATATTAACAATAATATTCATACCAAGCTG
* *
55724655 AAATTCATATTTTCTTATATTGACAATAATATTCATACCAAGCT
1 AAATTCATATTTTCCTATATTAACAATAATATTCATACCAAGCT
55724699 AAAACTTAAG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.39, C:0.17, G:0.04, T:0.39
Consensus pattern (45 bp):
AAATTCATATTTTCCTATATTAACAATAATATTCATACCAAGCTG
Found at i:55735276 original size:14 final size:14
Alignment explanation
Indices: 55735257--55735284 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
55735247 TTGCAACACT
55735257 AAAAAAGTAAAAAC
1 AAAAAAGTAAAAAC
55735271 AAAAAAGTAAAAAC
1 AAAAAAGTAAAAAC
55735285 GAGGTAAAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.79, C:0.07, G:0.07, T:0.07
Consensus pattern (14 bp):
AAAAAAGTAAAAAC
Found at i:55736432 original size:26 final size:26
Alignment explanation
Indices: 55736393--55736444 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
55736383 CATACTCAGC
55736393 CAAAAAATGACTGAACCAAGGGTAAA
1 CAAAAAATGACTGAACCAAGGGTAAA
*
55736419 CAAAAAATGGCTGAACCAAGGGTAAA
1 CAAAAAATGACTGAACCAAGGGTAAA
55736445 TAGATACCCT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.52, C:0.15, G:0.21, T:0.12
Consensus pattern (26 bp):
CAAAAAATGACTGAACCAAGGGTAAA
Found at i:55739734 original size:28 final size:27
Alignment explanation
Indices: 55739701--55739799 Score: 119
Period size: 28 Copynumber: 3.6 Consensus size: 27
55739691 TAATGAGATT
*
55739701 AGCACTAAGTGTGCGAGTTTAATTGAA
1 AGCACTAAGTGTGCGAGTATAATTGAA
*
55739728 ATGCACTAAGTGTGCGAGTATAATGGTAA
1 A-GCACTAAGTGTGCGAGTATAATTG-AA
* *
55739757 AGCACTAAGTGTGCGAGTGTGATT-ATTA
1 AGCACTAAGTGTGCGAGTATAATTGA--A
55739785 AGCACTAAGTGTGCG
1 AGCACTAAGTGTGCG
55739800 TACTTATTAA
Statistics
Matches: 63, Mismatches: 5, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
26 1 0.02
27 1 0.02
28 58 0.92
29 3 0.05
ACGTcount: A:0.31, C:0.12, G:0.28, T:0.28
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAGTATAATTGAA
Found at i:55743832 original size:41 final size:40
Alignment explanation
Indices: 55743787--55743902 Score: 128
Period size: 41 Copynumber: 2.9 Consensus size: 40
55743777 TTGTATAAAA
*
55743787 CACCGGCATAAAGCCTGCTAGGCACAAAGCCTGA-TACATTT
1 CACCGGCATAAAGCCTGCTAGGCATAAAGCCTGAGTA-A-TT
* * *
55743828 CACCGGCACAAAGCTTGCT-GGACATAAAGTCTGAAGTAATT
1 CACCGGCATAAAGCCTGCTAGG-CATAAAGCCTG-AGTAATT
* *
55743869 CACCGGCATCAAGCCTGCTAGGCATTAAGCCTGA
1 CACCGGCATAAAGCCTGCTAGGCATAAAGCCTGA
55743903 AAATCTCAGA
Statistics
Matches: 62, Mismatches: 9, Indels: 9
0.77 0.11 0.11
Matches are distributed among these distances:
40 3 0.05
41 53 0.85
42 4 0.06
43 2 0.03
ACGTcount: A:0.31, C:0.28, G:0.22, T:0.20
Consensus pattern (40 bp):
CACCGGCATAAAGCCTGCTAGGCATAAAGCCTGAGTAATT
Found at i:55744053 original size:68 final size:64
Alignment explanation
Indices: 55743942--55744118 Score: 203
Period size: 64 Copynumber: 2.7 Consensus size: 64
55743932 ATAATTTACA
* * *
55743942 ACATTAAAATTCAGTTCAAAGAA-TTTGTAACCTATATTCGAACCACACACATATGTATGTAAAA
1 ACATT-AAATTCAGCTC-AAGAACTTTATAACCTATATTCG-A--AC-CACATATGTATATAAAA
55744006 TTCAT
60 TTCAT
* *
55744011 ACATTAAATTCAGCTCAAGAACTTTATAACCTATATTTGAACCACATATGTATATAAAATTCGT
1 ACATTAAATTCAGCTCAAGAACTTTATAACCTATATTCGAACCACATATGTATATAAAATTCAT
* * **
55744075 ACATTAATTTCAGCTCAAGAACTTTAAATATATATATTCGAACC
1 ACATTAAATTCAGCTCAAGAACTTTATA-ACCTATATTCGAACC
55744119 GTATGTGCAT
Statistics
Matches: 96, Mismatches: 10, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
64 46 0.48
65 14 0.15
67 6 0.06
68 25 0.26
69 5 0.05
ACGTcount: A:0.41, C:0.18, G:0.08, T:0.33
Consensus pattern (64 bp):
ACATTAAATTCAGCTCAAGAACTTTATAACCTATATTCGAACCACATATGTATATAAAATTCAT
Found at i:55744081 original size:64 final size:67
Alignment explanation
Indices: 55743942--55744100 Score: 209
Period size: 64 Copynumber: 2.4 Consensus size: 67
55743932 ATAATTTACA
* * *
55743942 ACATTAAAATTCAGTTCAAAGAA-TTTGTAACCTATATTCGAACCACACACATATGTATGTAAAA
1 ACATT-AAATTCAGCTC-AAGAACTTTATAACCTATATTCGAA-CACACACATATGTATATAAAA
55744006 TTCAT
63 TTCAT
*
55744011 ACATTAAATTCAGCTCAAGAACTTTATAACCTATATTTG-A-AC-CACATATGTATATAAAATTC
1 ACATTAAATTCAGCTCAAGAACTTTATAACCTATATTCGAACACACACATATGTATATAAAATTC
*
55744073 GT
66 AT
*
55744075 ACATTAATTTCAGCTCAAGAACTTTA
1 ACATTAAATTCAGCTCAAGAACTTTA
55744101 AATATATATA
Statistics
Matches: 83, Mismatches: 6, Indels: 7
0.86 0.06 0.07
Matches are distributed among these distances:
64 45 0.54
65 2 0.02
67 6 0.07
68 25 0.30
69 5 0.06
ACGTcount: A:0.41, C:0.18, G:0.08, T:0.33
Consensus pattern (67 bp):
ACATTAAATTCAGCTCAAGAACTTTATAACCTATATTCGAACACACACATATGTATATAAAATTC
AT
Found at i:55748607 original size:21 final size:22
Alignment explanation
Indices: 55748583--55748626 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
55748573 AAAAAGTCAA
*
55748583 TAAATAAAAATTAT-TAAATAT
1 TAAATAAAAATCATATAAATAT
*
55748604 TAAATTAAAATCATATAAATAT
1 TAAATAAAAATCATATAAATAT
55748626 T
1 T
55748627 TTTTAAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (22 bp):
TAAATAAAAATCATATAAATAT
Found at i:55750669 original size:48 final size:48
Alignment explanation
Indices: 55750616--55750711 Score: 156
Period size: 48 Copynumber: 2.0 Consensus size: 48
55750606 AAAAAAACCA
* * *
55750616 AAAAAATAAAGGGGGACTCATGACTGATGCTTGCTTCATAAGTGGTTC
1 AAAAAATAAAAGGGGACCCATGACCGATGCTTGCTTCATAAGTGGTTC
*
55750664 AAAAAATAAAAGGGGACCCATGACCGATGTTTGCTTCATAAGTGGTTC
1 AAAAAATAAAAGGGGACCCATGACCGATGCTTGCTTCATAAGTGGTTC
55750712 TTGTATTCTT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
48 44 1.00
ACGTcount: A:0.34, C:0.16, G:0.24, T:0.26
Consensus pattern (48 bp):
AAAAAATAAAAGGGGACCCATGACCGATGCTTGCTTCATAAGTGGTTC
Found at i:55752634 original size:73 final size:73
Alignment explanation
Indices: 55752557--55752710 Score: 166
Period size: 73 Copynumber: 2.1 Consensus size: 73
55752547 TGTATAACGA
* * *
55752557 GAAGCTCATAAGAGCCATA-GTCAGAAAGCTCATGCGAGCCAATAACAGGTAGCTCCGAACAGCC
1 GAAGCTCAGAAGAGCCATATATCAGAAAGCTCAAGCGAGCC-ATAACAGGTAGCTCCGAACAGCC
*
55752621 ATTAATTGG
65 ATTAATCGG
* * * * * * * * *
55752630 GAAGCTCCGGATAGCCATATATCGGGAAGTTCAAGTGAGCCATATCAGGTAGCTCCGAAGAGCCA
1 GAAGCTCAGAAGAGCCATATATCAGAAAGCTCAAGCGAGCCATAACAGGTAGCTCCGAACAGCCA
55752695 TTAATCGG
66 TTAATCGG
*
55752703 GAAACTCA
1 GAAGCTCA
55752711 CAAAGAGCTT
Statistics
Matches: 65, Mismatches: 15, Indels: 2
0.79 0.18 0.02
Matches are distributed among these distances:
73 50 0.77
74 15 0.23
ACGTcount: A:0.34, C:0.23, G:0.25, T:0.19
Consensus pattern (73 bp):
GAAGCTCAGAAGAGCCATATATCAGAAAGCTCAAGCGAGCCATAACAGGTAGCTCCGAACAGCCA
TTAATCGG
Found at i:55752742 original size:26 final size:26
Alignment explanation
Indices: 55752685--55752747 Score: 81
Period size: 26 Copynumber: 2.4 Consensus size: 26
55752675 CAGGTAGCTC
55752685 CGAAGAGCCATTAATCGGGAAACTCA
1 CGAAGAGCCATTAATCGGGAAACTCA
* ** *
55752711 CAAAGAGCTTTTAATCGGGAAGCTCA
1 CGAAGAGCCATTAATCGGGAAACTCA
*
55752737 TGAAGAGCCAT
1 CGAAGAGCCAT
55752748 ATAACAGGAC
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.37, C:0.21, G:0.24, T:0.19
Consensus pattern (26 bp):
CGAAGAGCCATTAATCGGGAAACTCA
Found at i:55757712 original size:19 final size:20
Alignment explanation
Indices: 55757670--55757712 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
55757660 TCATGCTTTC
* *
55757670 TATTCGCATTTTCATATTCA
1 TATTCACATTTTCAAATTCA
55757690 -ATTCACATTTTCAAATT-A
1 TATTCACATTTTCAAATTCA
55757708 TATTC
1 TATTC
55757713 CACAATCACG
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
18 1 0.05
19 19 0.95
ACGTcount: A:0.30, C:0.19, G:0.02, T:0.49
Consensus pattern (20 bp):
TATTCACATTTTCAAATTCA
Found at i:55759363 original size:13 final size:13
Alignment explanation
Indices: 55759342--55759373 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
55759332 GCTTGGATCA
*
55759342 TCATCAAATAAAT
1 TCATAAAATAAAT
55759355 TCATAAAATAAAT
1 TCATAAAATAAAT
55759368 TCATAA
1 TCATAA
55759374 TTGCTGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:55760569 original size:42 final size:42
Alignment explanation
Indices: 55760517--55760622 Score: 194
Period size: 42 Copynumber: 2.5 Consensus size: 42
55760507 CATAAGCAGT
*
55760517 ATACAACACATAAAGTGCCTGAAATGACACACGTGGTGCCTA
1 ATACGACACATAAAGTGCCTGAAATGACACACGTGGTGCCTA
55760559 ATACGACACATAAAGTGCCTGAAATGACACACGTGGTGCCTA
1 ATACGACACATAAAGTGCCTGAAATGACACACGTGGTGCCTA
*
55760601 ATACGACACATATAGTGCCTGA
1 ATACGACACATAAAGTGCCTGA
55760623 TCGGCAAGGT
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 62 1.00
ACGTcount: A:0.37, C:0.24, G:0.20, T:0.20
Consensus pattern (42 bp):
ATACGACACATAAAGTGCCTGAAATGACACACGTGGTGCCTA
Found at i:55760618 original size:21 final size:22
Alignment explanation
Indices: 55760517--55760622 Score: 85
Period size: 21 Copynumber: 5.0 Consensus size: 22
55760507 CATAAGCAGT
* *
55760517 ATACAACACATAAAGTGCCTGA
1 ATACGACACATATAGTGCCTGA
* ** *
55760539 A-ATGACACACGTGGTGCCT-A
1 ATACGACACATATAGTGCCTGA
*
55760559 ATACGACACATAAAGTGCCTGA
1 ATACGACACATATAGTGCCTGA
* ** *
55760581 A-ATGACACACGTGGTGCCT-A
1 ATACGACACATATAGTGCCTGA
55760601 ATACGACACATATAGTGCCTGA
1 ATACGACACATATAGTGCCTGA
55760623 TCGGCAAGGT
Statistics
Matches: 60, Mismatches: 20, Indels: 8
0.68 0.23 0.09
Matches are distributed among these distances:
20 4 0.07
21 52 0.87
22 4 0.07
ACGTcount: A:0.37, C:0.24, G:0.20, T:0.20
Consensus pattern (22 bp):
ATACGACACATATAGTGCCTGA
Found at i:55768217 original size:16 final size:15
Alignment explanation
Indices: 55768196--55768250 Score: 56
Period size: 16 Copynumber: 3.5 Consensus size: 15
55768186 GTTTGGTTCA
*
55768196 CTGTAATGAAATATAG
1 CTGTAATG-AATAAAG
*
55768212 CTGTAATTGAATAGAG
1 CTGTAA-TGAATAAAG
*
55768228 TTGTAATGGAATAAAG
1 CTGTAAT-GAATAAAG
55768244 CTGTAAT
1 CTGTAAT
55768251 CAGTAATTCA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
15 1 0.03
16 30 0.91
17 2 0.06
ACGTcount: A:0.40, C:0.05, G:0.22, T:0.33
Consensus pattern (15 bp):
CTGTAATGAATAAAG
Found at i:55770539 original size:16 final size:16
Alignment explanation
Indices: 55770518--55770553 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
55770508 TGAATTACTG
* *
55770518 ATTACAGCTTTATTCC
1 ATTACAGCTCTATTCA
55770534 ATTACAGCTCTATTCA
1 ATTACAGCTCTATTCA
55770550 ATTA
1 ATTA
55770554 TAGTTAACCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.31, C:0.22, G:0.06, T:0.42
Consensus pattern (16 bp):
ATTACAGCTCTATTCA
Found at i:55771560 original size:22 final size:23
Alignment explanation
Indices: 55771533--55771577 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
55771523 AGGTATCTAC
55771533 AAATCAAAT-ATCTAAGATTACA
1 AAATCAAATCATCTAAGATTACA
* *
55771555 AAATCATATCTTCTAAGATTACA
1 AAATCAAATCATCTAAGATTACA
55771578 TATTATATCT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.49, C:0.16, G:0.04, T:0.31
Consensus pattern (23 bp):
AAATCAAATCATCTAAGATTACA
Found at i:55781214 original size:18 final size:19
Alignment explanation
Indices: 55781178--55781215 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
55781168 ACGGTTTGCT
* *
55781178 AAGAAAAATAGATGGAGAA
1 AAGAAAAATAAATGAAGAA
55781197 AAGAAAAA-AAATGAAGAA
1 AAGAAAAATAAATGAAGAA
55781215 A
1 A
55781216 TGTAGAAAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.71, C:0.00, G:0.21, T:0.08
Consensus pattern (19 bp):
AAGAAAAATAAATGAAGAA
Found at i:55781819 original size:5 final size:5
Alignment explanation
Indices: 55781809--55781836 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
55781799 AAAACTCATA
55781809 AAAAT AAAAT AAAAT AAAAT AAAAT AAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAA
55781837 TATATCTAGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:55785447 original size:5 final size:5
Alignment explanation
Indices: 55785437--55785488 Score: 51
Period size: 5 Copynumber: 11.0 Consensus size: 5
55785427 TTTGACCTCC
55785437 TTAAA TTAAA TT--A TTAAA TTAAAA TT--A TTAAA -TAAA TTAAA TTAAAA
1 TTAAA TTAAA TTAAA TTAAA TT-AAA TTAAA TTAAA TTAAA TTAAA TT-AAA
55785484 TTAAA
1 TTAAA
55785489 GAATTAAAGG
Statistics
Matches: 40, Mismatches: 0, Indels: 14
0.74 0.00 0.26
Matches are distributed among these distances:
3 6 0.15
4 4 0.10
5 20 0.50
6 10 0.25
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
TTAAA
Found at i:55785463 original size:14 final size:13
Alignment explanation
Indices: 55785437--55785475 Score: 62
Period size: 14 Copynumber: 3.0 Consensus size: 13
55785427 TTTGACCTCC
55785437 TTAAATTAAATTA
1 TTAAATTAAATTA
55785450 TTAAATTAAAATTA
1 TTAAATT-AAATTA
55785464 TTAAA-TAAATTA
1 TTAAATTAAATTA
55785476 AATTAAAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
12 6 0.24
13 8 0.32
14 11 0.44
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
TTAAATTAAATTA
Found at i:55785478 original size:23 final size:22
Alignment explanation
Indices: 55785441--55785486 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 22
55785431 ACCTCCTTAA
*
55785441 ATTAAATTATTAAATTAAAATT
1 ATTAAATAATTAAATTAAAATT
55785463 ATTAAATAAATTAAATTAAAATT
1 ATTAAAT-AATTAAATTAAAATT
55785486 A
1 A
55785487 AAGAATTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 7 0.32
23 15 0.68
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (22 bp):
ATTAAATAATTAAATTAAAATT
Found at i:55787229 original size:26 final size:26
Alignment explanation
Indices: 55787148--55787229 Score: 69
Period size: 26 Copynumber: 3.2 Consensus size: 26
55787138 GCACACTGCA
* *
55787148 GCTCTT-ATAAGCGTCCTG-TTATATG
1 GCTCTTCATGAGCTTCCTGATTA-ATG
** *
55787173 GCTCTTCATGAGCTTCCCAATTAAAG
1 GCTCTTCATGAGCTTCCTGATTAATG
* **
55787199 CCTCTTTGTGAGCTTCCTGATTAATG
1 GCTCTTCATGAGCTTCCTGATTAATG
55787225 GCTCT
1 GCTCT
55787230 CCGGAGCTAC
Statistics
Matches: 43, Mismatches: 12, Indels: 3
0.74 0.21 0.05
Matches are distributed among these distances:
25 6 0.14
26 34 0.79
27 3 0.07
ACGTcount: A:0.20, C:0.24, G:0.18, T:0.38
Consensus pattern (26 bp):
GCTCTTCATGAGCTTCCTGATTAATG
Found at i:55787307 original size:25 final size:25
Alignment explanation
Indices: 55787170--55787310 Score: 69
Period size: 25 Copynumber: 5.6 Consensus size: 25
55787160 GTCCTGTTAT
* *
55787170 ATGGCTCTTCATGAGCTTCCCAATTA
1 ATGGCTCTTC-GGAGCTTCCCGATTA
* * * *
55787196 AAGCCTCTTTGTGAGCTTCCTGATTA
1 ATGGCTCTTCG-GAGCTTCCCGATTA
* * *
55787222 ATGGCTCTCCGGAGCTACCTGA-T-
1 ATGGCTCTTCGGAGCTTCCCGATTA
* * *
55787245 ATGGCTTCCTT--GAACTTCTCGA-AA
1 ATGGC-T-CTTCGGAGCTTCCCGATTA
*
55787269 TATGGCTAC-CCGGAGCTTCCCGATTA
1 -ATGGCT-CTTCGGAGCTTCCCGATTA
55787295 ATGGCTCTTCGGAGCT
1 ATGGCTCTTCGGAGCT
55787311 ACTCGTTATT
Statistics
Matches: 83, Mismatches: 23, Indels: 19
0.66 0.18 0.15
Matches are distributed among these distances:
23 12 0.14
24 5 0.06
25 39 0.47
26 27 0.33
ACGTcount: A:0.20, C:0.27, G:0.21, T:0.32
Consensus pattern (25 bp):
ATGGCTCTTCGGAGCTTCCCGATTA
Found at i:55788235 original size:22 final size:22
Alignment explanation
Indices: 55788210--55788254 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
55788200 ATGTAAGTGA
55788210 TCAAATTGTTAAGTATGGATAC
1 TCAAATTGTTAAGTATGGATAC
55788232 TCAAATTGTTAAGTATGGATAC
1 TCAAATTGTTAAGTATGGATAC
55788254 T
1 T
55788255 TGATTATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.36, C:0.09, G:0.18, T:0.38
Consensus pattern (22 bp):
TCAAATTGTTAAGTATGGATAC
Found at i:55790897 original size:47 final size:47
Alignment explanation
Indices: 55790823--55790916 Score: 170
Period size: 47 Copynumber: 2.0 Consensus size: 47
55790813 CCATTCTTTC
* *
55790823 CTCTTGATTACGTAGCGTTAAGTGGCACTTGTGCAAATTCAGTAAGT
1 CTCTTGATTACGTAGCGGTAAGCGGCACTTGTGCAAATTCAGTAAGT
55790870 CTCTTGATTACGTAGCGGTAAGCGGCACTTGTGCAAATTCAGTAAGT
1 CTCTTGATTACGTAGCGGTAAGCGGCACTTGTGCAAATTCAGTAAGT
55790917 TGTTGGGTAT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 45 1.00
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.32
Consensus pattern (47 bp):
CTCTTGATTACGTAGCGGTAAGCGGCACTTGTGCAAATTCAGTAAGT
Found at i:55793121 original size:25 final size:25
Alignment explanation
Indices: 55793093--55793157 Score: 71
Period size: 25 Copynumber: 2.6 Consensus size: 25
55793083 CTGTCTTTGA
* *
55793093 TAGTATATCCTGAAACTGCTATACG
1 TAGTATATACTGAAACTACTATACG
*
55793118 TAGTATATACTGAGACTACTATA-G
1 TAGTATATACTGAAACTACTATACG
55793142 ATAG-ACTATACTGAAA
1 -TAGTA-TATACTGAAA
55793158 ACACTTAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
24 2 0.06
25 32 0.94
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (25 bp):
TAGTATATACTGAAACTACTATACG
Found at i:55799145 original size:18 final size:17
Alignment explanation
Indices: 55799119--55799166 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 17
55799109 ACAATAAGAA
55799119 AACGTTTTGAAATTGAAT
1 AACGTTTTGAAA-TGAAT
*
55799137 AACGATTTGTAAATGAAT
1 AACGTTTTG-AAATGAAT
*
55799155 AATGTTTTGAAA
1 AACGTTTTGAAA
55799167 ACAAATGACA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
17 3 0.12
18 20 0.77
19 3 0.12
ACGTcount: A:0.42, C:0.04, G:0.17, T:0.38
Consensus pattern (17 bp):
AACGTTTTGAAATGAAT
Found at i:55800311 original size:25 final size:25
Alignment explanation
Indices: 55800221--55800311 Score: 60
Period size: 25 Copynumber: 3.6 Consensus size: 25
55800211 TTCATATTCA
55800221 GGAATGCTCATACGAGCATGTA-AAC-
1 GGAA-GCTCATACGAGC-TGTATAACG
* * * **
55800246 GAAAGCTCTTTCGAGCCATATAACG
1 GGAAGCTCATACGAGCTGTATAACG
* * **
55800271 GGAAACCCATGTGAGCTGTATAACG
1 GGAAGCTCATACGAGCTGTATAACG
*
55800296 GGAAGCTCTTACGAGC
1 GGAAGCTCATACGAGC
55800312 CATTTATTGG
Statistics
Matches: 46, Mismatches: 18, Indels: 4
0.68 0.26 0.06
Matches are distributed among these distances:
23 2 0.04
24 13 0.28
25 31 0.67
ACGTcount: A:0.32, C:0.22, G:0.25, T:0.21
Consensus pattern (25 bp):
GGAAGCTCATACGAGCTGTATAACG
Found at i:55802291 original size:10 final size:11
Alignment explanation
Indices: 55802270--55802298 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
55802260 TTTCTTATTT
55802270 CTATTCTTTAG
1 CTATTCTTTAG
55802281 CTATT-TTTAG
1 CTATTCTTTAG
55802291 CTATTCTT
1 CTATTCTT
55802299 CTCACCTCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.59
11 7 0.41
ACGTcount: A:0.17, C:0.17, G:0.07, T:0.59
Consensus pattern (11 bp):
CTATTCTTTAG
Found at i:55803796 original size:6 final size:6
Alignment explanation
Indices: 55803785--55803813 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
55803775 GGCTCATCAG
55803785 GATAGA GATAGA GATAGA GATAGA GATAG
1 GATAGA GATAGA GATAGA GATAGA GATAG
55803814 GAAAGAAAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.34, T:0.17
Consensus pattern (6 bp):
GATAGA
Found at i:55804736 original size:13 final size:13
Alignment explanation
Indices: 55804718--55804742 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
55804708 ATTATTTATC
55804718 ATTTAAATATATA
1 ATTTAAATATATA
55804731 ATTTAAATATAT
1 ATTTAAATATAT
55804743 TAATAATATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
ATTTAAATATATA
Found at i:55804772 original size:12 final size:12
Alignment explanation
Indices: 55804757--55804786 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
55804747 AATATAGAAT
55804757 AATATATAAAGA
1 AATATATAAAGA
55804769 AATATATAAAGA
1 AATATATAAAGA
55804781 AA-ATAT
1 AATATAT
55804787 GTGTTATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 4 0.22
12 14 0.78
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.27
Consensus pattern (12 bp):
AATATATAAAGA
Found at i:55808073 original size:6 final size:5
Alignment explanation
Indices: 55808039--55808072 Score: 52
Period size: 5 Copynumber: 6.8 Consensus size: 5
55808029 AAAATCTACG
55808039 TTTTC -TTTC TTTTTC TTTTC TTTTC TTTTC TTTT
1 TTTTC TTTTC -TTTTC TTTTC TTTTC TTTTC TTTT
55808073 TTCTGCTTGG
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
4 4 0.15
5 19 0.70
6 4 0.15
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTTC
Found at i:55825581 original size:62 final size:62
Alignment explanation
Indices: 55825499--55825624 Score: 207
Period size: 62 Copynumber: 2.0 Consensus size: 62
55825489 GGGTGTTACA
* *
55825499 TCTATTCTACTATTTTAACATTGATTGACCTTTATGTAGGTTGCCTCTTTCAGTTACTTCTT
1 TCTATTCTACTATTTTAACATTGATTGACCTTTATGTAGATTGCCTCTTTCAGTTACCTCTT
* * *
55825561 TCTATTTTACTCTTTTAACATTGATTGACCTTTATGTAGATTGCCTCTTTTAGTTACCTCTT
1 TCTATTCTACTATTTTAACATTGATTGACCTTTATGTAGATTGCCTCTTTCAGTTACCTCTT
55825623 TC
1 TC
55825625 CTTACCATCT
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
62 59 1.00
ACGTcount: A:0.19, C:0.20, G:0.10, T:0.51
Consensus pattern (62 bp):
TCTATTCTACTATTTTAACATTGATTGACCTTTATGTAGATTGCCTCTTTCAGTTACCTCTT
Found at i:55826873 original size:22 final size:22
Alignment explanation
Indices: 55826848--55826897 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 22
55826838 CTGCTTCTTT
55826848 TGCTTTACTGCTTGTGCCTTAC
1 TGCTTTACTGCTTGTGCCTTAC
* * *
55826870 TGCTTTACTTCTTTTGCTTTAC
1 TGCTTTACTGCTTGTGCCTTAC
55826892 TGCTTT
1 TGCTTT
55826898 CGATTAGAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.08, C:0.24, G:0.14, T:0.54
Consensus pattern (22 bp):
TGCTTTACTGCTTGTGCCTTAC
Found at i:55826928 original size:36 final size:37
Alignment explanation
Indices: 55826888--55826972 Score: 136
Period size: 39 Copynumber: 2.3 Consensus size: 37
55826878 TTCTTTTGCT
*
55826888 TTACTGCTTTCGATTAGAA-TCAGGGAAAATTCTGGC
1 TTACTGCTTTCGATTAGAATTCAGGGAAAATTCTGGA
55826924 TTACTGCTTTCGATTAGAATTTTCAGGGAAAATTCTGGA
1 TTACTGCTTTCGATTAGAA--TTCAGGGAAAATTCTGGA
55826963 TTACTGCTTT
1 TTACTGCTTT
55826973 GCTTTACTGC
Statistics
Matches: 45, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
36 19 0.42
39 26 0.58
ACGTcount: A:0.26, C:0.15, G:0.20, T:0.39
Consensus pattern (37 bp):
TTACTGCTTTCGATTAGAATTCAGGGAAAATTCTGGA
Found at i:55829719 original size:13 final size:13
Alignment explanation
Indices: 55829698--55829752 Score: 65
Period size: 13 Copynumber: 4.2 Consensus size: 13
55829688 ATATTCAAAT
55829698 TTTTCAAAAACAC
1 TTTTCAAAAACAC
* *
55829711 TTCTCAAAAGCAC
1 TTTTCAAAAACAC
* * *
55829724 TTTTCCACAGCAC
1 TTTTCAAAAACAC
55829737 TTTTCAAAAACAC
1 TTTTCAAAAACAC
55829750 TTT
1 TTT
55829753 ATTGGCCCTT
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 34 1.00
ACGTcount: A:0.36, C:0.27, G:0.04, T:0.33
Consensus pattern (13 bp):
TTTTCAAAAACAC
Found at i:55830168 original size:9 final size:9
Alignment explanation
Indices: 55830154--55830206 Score: 79
Period size: 9 Copynumber: 5.9 Consensus size: 9
55830144 GATTCAACTT
55830154 GGTTAATTC
1 GGTTAATTC
55830163 GGTTAATTC
1 GGTTAATTC
* *
55830172 GGGTAATCC
1 GGTTAATTC
55830181 GGTTAATTC
1 GGTTAATTC
*
55830190 GGGTAATTC
1 GGTTAATTC
55830199 GGTTAATT
1 GGTTAATT
55830207 TTTAACTAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 38 1.00
ACGTcount: A:0.23, C:0.11, G:0.26, T:0.40
Consensus pattern (9 bp):
GGTTAATTC
Found at i:55830183 original size:18 final size:18
Alignment explanation
Indices: 55830157--55830206 Score: 91
Period size: 18 Copynumber: 2.8 Consensus size: 18
55830147 TCAACTTGGT
55830157 TAATTCGGTTAATTCGGG
1 TAATTCGGTTAATTCGGG
*
55830175 TAATCCGGTTAATTCGGG
1 TAATTCGGTTAATTCGGG
55830193 TAATTCGGTTAATT
1 TAATTCGGTTAATT
55830207 TTTAACTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.24, C:0.12, G:0.24, T:0.40
Consensus pattern (18 bp):
TAATTCGGTTAATTCGGG
Found at i:55834170 original size:16 final size:16
Alignment explanation
Indices: 55834151--55834189 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
55834141 AACACTGTAT
55834151 GATTCAAAGCTTTCGC
1 GATTCAAAGCTTTCGC
55834167 GATTCAAAGCTTTCGC
1 GATTCAAAGCTTTCGC
*
55834183 AATTCAA
1 GATTCAA
55834190 TGTTTGAGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.31
Consensus pattern (16 bp):
GATTCAAAGCTTTCGC
Found at i:55839715 original size:18 final size:20
Alignment explanation
Indices: 55839694--55839740 Score: 62
Period size: 18 Copynumber: 2.4 Consensus size: 20
55839684 ACTTTGGATT
*
55839694 TTTTATAAAT-ATTTTG-AA
1 TTTTAAAAATCATTTTGAAA
55839712 TTTTAAAAATCATTTTGAAA
1 TTTTAAAAATCATTTTGAAA
55839732 TTTTGAAAA
1 TTTT-AAAA
55839741 GAAAATTGTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
18 9 0.36
19 6 0.24
20 6 0.24
21 4 0.16
ACGTcount: A:0.43, C:0.02, G:0.06, T:0.49
Consensus pattern (20 bp):
TTTTAAAAATCATTTTGAAA
Found at i:55846639 original size:14 final size:15
Alignment explanation
Indices: 55846616--55846645 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
55846606 AATAAATTTT
55846616 AAAAGCAAAAAAAAA
1 AAAAGCAAAAAAAAA
55846631 AAAAG-AAAAAAAAA
1 AAAAGCAAAAAAAAA
55846645 A
1 A
55846646 GCGAAACAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.90, C:0.03, G:0.07, T:0.00
Consensus pattern (15 bp):
AAAAGCAAAAAAAAA
Found at i:55846640 original size:15 final size:15
Alignment explanation
Indices: 55846616--55846645 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
55846606 AATAAATTTT
*
55846616 AAAAGCAAAAAAAAA
1 AAAAGAAAAAAAAAA
55846631 AAAAGAAAAAAAAAA
1 AAAAGAAAAAAAAAA
55846646 GCGAAACAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.90, C:0.03, G:0.07, T:0.00
Consensus pattern (15 bp):
AAAAGAAAAAAAAAA
Found at i:55849874 original size:36 final size:36
Alignment explanation
Indices: 55849785--55849874 Score: 87
Period size: 36 Copynumber: 2.5 Consensus size: 36
55849775 AAATATTTGC
* * *
55849785 ATTTATATTAAAAACATTTATTATTAAATATTTATA
1 ATTTATAATCAAAATATTTATTATTAAATATTTATA
* *
55849821 ATTTATAATCTATATATTTATTATTAAAATATTT-TA
1 ATTTATAATCAAAATATTTATTATT-AAATATTTATA
55849857 ATATT-TCAAT-AAAATATT
1 AT-TTAT-AATCAAAATATT
55849875 AAGAACGGTT
Statistics
Matches: 44, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
36 31 0.70
37 13 0.30
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (36 bp):
ATTTATAATCAAAATATTTATTATTAAATATTTATA
Found at i:55852807 original size:19 final size:19
Alignment explanation
Indices: 55852783--55852874 Score: 112
Period size: 19 Copynumber: 4.8 Consensus size: 19
55852773 AGGGAAACTT
55852783 GCACACGAAGTGCATACTG
1 GCACACGAAGTGCATACTG
55852802 GCACACGAAGTGCATACTG
1 GCACACGAAGTGCATACTG
*
55852821 GCACACGAAGTGCATCCTG
1 GCACACGAAGTGCATACTG
* ** ** *
55852840 ACACATAAAGCACATTCTG
1 GCACACGAAGTGCATACTG
*
55852859 GCACACAAAGTGCATA
1 GCACACGAAGTGCATA
55852875 AAGCCGTACA
Statistics
Matches: 61, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 61 1.00
ACGTcount: A:0.35, C:0.27, G:0.22, T:0.16
Consensus pattern (19 bp):
GCACACGAAGTGCATACTG
Found at i:55859752 original size:68 final size:71
Alignment explanation
Indices: 55859611--55859755 Score: 163
Period size: 68 Copynumber: 2.1 Consensus size: 71
55859601 ATATTAAATC
* *
55859611 TATTAAATTAATAAAATATTTATCTACAAGTTAAATATTAAATTAAATTTAATATTAAGATAACC
1 TATTAAATTAATAAAATATCTATCTACAAG-TAAATATTAAATTAAATTTAATATTAAAATAACC
***
55859676 ACTTTAA
65 AAAATAA
* * **
55859683 TATTAAATTAATAAAATA-CTAT-TA-ATA-TAAGTATTAAATTAAATTTAATATTAAAATTATT
1 TATTAAATTAATAAAATATCTATCTACA-AGTAAATATTAAATTAAATTTAATATTAAAATAACC
55859744 AAAATAA
65 AAAATAA
55859751 TATTA
1 TATTA
55859756 TTTTTGGAAT
Statistics
Matches: 63, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
68 38 0.60
69 1 0.02
70 3 0.05
71 3 0.05
72 18 0.29
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.41
Consensus pattern (71 bp):
TATTAAATTAATAAAATATCTATCTACAAGTAAATATTAAATTAAATTTAATATTAAAATAACCA
AAATAA
Found at i:55859835 original size:11 final size:11
Alignment explanation
Indices: 55859819--55859843 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
55859809 CGTAATTTTT
55859819 CCACTACTCAA
1 CCACTACTCAA
55859830 CCACTACTCAA
1 CCACTACTCAA
55859841 CCA
1 CCA
55859844 TTAGTCGGCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.36, C:0.48, G:0.00, T:0.16
Consensus pattern (11 bp):
CCACTACTCAA
Found at i:55860085 original size:12 final size:13
Alignment explanation
Indices: 55860061--55860096 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
55860051 TTTCGATTTC
55860061 AAGTCCAATTTTT
1 AAGTCCAATTTTT
55860074 AAGTCCAATTTTT
1 AAGTCCAATTTTT
*
55860087 AAGTTCAATT
1 AAGTCCAATT
55860097 ACCCATTGGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.33, C:0.14, G:0.08, T:0.44
Consensus pattern (13 bp):
AAGTCCAATTTTT
Found at i:55863937 original size:30 final size:30
Alignment explanation
Indices: 55863851--55863939 Score: 76
Period size: 30 Copynumber: 3.0 Consensus size: 30
55863841 AGCAATTAAT
* * *
55863851 TAATTTTTTTA-AA-ATAAAAATATTGAAAA
1 TAATTTTTTTATAATTTATAAA-ATTAAAAA
**
55863880 TAATTTTTTTATAATTTATAATTTTAAAAA
1 TAATTTTTTTATAATTTATAAAATTAAAAA
* *
55863910 T-ATTTTTTTCTGAATTTTTAAAATTAAAAA
1 TAATTTTTTTAT-AATTTATAAAATTAAAAA
55863940 ATTAATTAAT
Statistics
Matches: 48, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
29 20 0.42
30 24 0.50
31 4 0.08
ACGTcount: A:0.46, C:0.01, G:0.02, T:0.51
Consensus pattern (30 bp):
TAATTTTTTTATAATTTATAAAATTAAAAA
Found at i:55865241 original size:54 final size:54
Alignment explanation
Indices: 55865163--55865273 Score: 177
Period size: 54 Copynumber: 2.1 Consensus size: 54
55865153 CATAATAGCT
****
55865163 TAACAACTTTTGAGTTCCAAAGTTTCGAAGTTATACATTTTCATGCATCAATAA
1 TAACAACTTTTGAGTTCCAAAGTTTCGAAGTTATACATGAAAATGCATCAATAA
*
55865217 TAACAACTTTTGAGTTCTAAAGTTTCGAAGTTATACATGAAAATGCATCAATAA
1 TAACAACTTTTGAGTTCCAAAGTTTCGAAGTTATACATGAAAATGCATCAATAA
55865271 TAA
1 TAA
55865274 TATTCATGTT
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 52 1.00
ACGTcount: A:0.39, C:0.14, G:0.12, T:0.35
Consensus pattern (54 bp):
TAACAACTTTTGAGTTCCAAAGTTTCGAAGTTATACATGAAAATGCATCAATAA
Found at i:55877232 original size:21 final size:22
Alignment explanation
Indices: 55877208--55877252 Score: 74
Period size: 21 Copynumber: 2.1 Consensus size: 22
55877198 GCCCTATGGG
55877208 AAAAGCACAGCAAAG-GAAAAA
1 AAAAGCACAGCAAAGTGAAAAA
*
55877229 AAAAGTACAGCAAAGTGAAAAA
1 AAAAGCACAGCAAAGTGAAAAA
55877251 AA
1 AA
55877253 GGAAAGCAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 14 0.64
22 8 0.36
ACGTcount: A:0.67, C:0.11, G:0.18, T:0.04
Consensus pattern (22 bp):
AAAAGCACAGCAAAGTGAAAAA
Found at i:55877249 original size:20 final size:20
Alignment explanation
Indices: 55877208--55877276 Score: 68
Period size: 20 Copynumber: 3.4 Consensus size: 20
55877198 GCCCTATGGG
55877208 AAAAGCACAGCAAAG-GAAAAA
1 AAAAGCACAGCAAAGTG--AAA
*
55877229 AAAAGTACAGCAAAGTGAAA
1 AAAAGCACAGCAAAGTGAAA
* * * *
55877249 AAAAGGAAAGCAAAATTAAA
1 AAAAGCACAGCAAAGTGAAA
55877269 AAAAGCAC
1 AAAAGCAC
55877277 TGCCAATAAA
Statistics
Matches: 40, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
20 25 0.62
21 14 0.35
22 1 0.03
ACGTcount: A:0.65, C:0.12, G:0.17, T:0.06
Consensus pattern (20 bp):
AAAAGCACAGCAAAGTGAAA
Found at i:55877405 original size:26 final size:25
Alignment explanation
Indices: 55877361--55877443 Score: 105
Period size: 26 Copynumber: 3.2 Consensus size: 25
55877351 TTAAAATTTA
55877361 AAATTAAAAA-AGTGAAAAAGCGGGG
1 AAATTAAAAATAGTGAAAAAG-GGGG
* *
55877386 AAATTAAAAATAATGGAAAAAGGGGA
1 AAATTAAAAATAGT-GAAAAAGGGGG
55877412 AAATTAAAAATAGTGAAAGAAGGGGGG
1 AAATTAAAAATAGTGAAA-AA-GGGGG
55877439 AAATT
1 AAATT
55877444 TTAAAATGGT
Statistics
Matches: 50, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
25 14 0.28
26 20 0.40
27 16 0.32
ACGTcount: A:0.57, C:0.01, G:0.27, T:0.16
Consensus pattern (25 bp):
AAATTAAAAATAGTGAAAAAGGGGG
Found at i:55877590 original size:23 final size:23
Alignment explanation
Indices: 55877550--55877604 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 23
55877540 AACCGTTAAA
55877550 AAAATAAAAAGAGAGAAAAAAAAG
1 AAAA-AAAAAGAGAGAAAAAAAAG
* *
55877574 TAAAAAAAAA-AGTGAAAAAGAAG
1 -AAAAAAAAAGAGAGAAAAAAAAG
55877597 AAAAAAAA
1 AAAAAAAA
55877605 TTGAAACTAG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
22 8 0.29
23 11 0.39
24 5 0.18
25 4 0.14
ACGTcount: A:0.80, C:0.00, G:0.15, T:0.05
Consensus pattern (23 bp):
AAAAAAAAAGAGAGAAAAAAAAG
Found at i:55877591 original size:20 final size:20
Alignment explanation
Indices: 55877568--55877610 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
55877558 AAGAGAGAAA
55877568 AAAAAGTAA-AAAAAAAAGTG
1 AAAAAG-AAGAAAAAAAAGTG
*
55877588 AAAAAGAAGAAAAAAAATTG
1 AAAAAGAAGAAAAAAAAGTG
55877608 AAA
1 AAA
55877611 CTAGTGATGG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 2 0.10
20 19 0.90
ACGTcount: A:0.77, C:0.00, G:0.14, T:0.09
Consensus pattern (20 bp):
AAAAAGAAGAAAAAAAAGTG
Found at i:55879323 original size:34 final size:34
Alignment explanation
Indices: 55879280--55879346 Score: 134
Period size: 34 Copynumber: 2.0 Consensus size: 34
55879270 TTTATTCACT
55879280 TGTGTCTTGATCCGTAGAAATCTCTAAATTATGA
1 TGTGTCTTGATCCGTAGAAATCTCTAAATTATGA
55879314 TGTGTCTTGATCCGTAGAAATCTCTAAATTATG
1 TGTGTCTTGATCCGTAGAAATCTCTAAATTATG
55879347 TTAATATCTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.28, C:0.15, G:0.18, T:0.39
Consensus pattern (34 bp):
TGTGTCTTGATCCGTAGAAATCTCTAAATTATGA
Done.