Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A09
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: 81831061
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 3560000 characters in sequence are not A, C, G, or T
File 131 of 259
Found at i:42536857 original size:34 final size:33
Alignment explanation
Indices: 42536773--42536878 Score: 92
Period size: 34 Copynumber: 3.0 Consensus size: 33
42536763 AATCTAATAA
*
42536773 ATTATAAAAAAATTTAAAAAT-TCATAAAAATTGTAAGT
1 ATTAT-AATAAATTTAAAAATAT-ATAAAAA-T-T-A-T
*
42536811 ATTATAATAAATTATAAAAGT-TATAATAAATTAT
1 ATTATAATAAATT-TAAAAATATATAA-AAATTAT
42536845 ATTATGAA-AAATTTAAAAATATATAAAAATTAT
1 ATTAT-AATAAATTTAAAAATATATAAAAATTAT
42536878 A
1 A
42536879 AAAAAGTCAT
Statistics
Matches: 61, Mismatches: 3, Indels: 13
0.79 0.04 0.17
Matches are distributed among these distances:
33 14 0.23
34 16 0.26
35 3 0.05
36 1 0.02
37 12 0.20
38 15 0.25
ACGTcount: A:0.58, C:0.01, G:0.04, T:0.37
Consensus pattern (33 bp):
ATTATAATAAATTTAAAAATATATAAAAATTAT
Found at i:42536882 original size:9 final size:9
Alignment explanation
Indices: 42536608--42536882 Score: 134
Period size: 9 Copynumber: 29.0 Consensus size: 9
42536598 TTCATTTTTC
*
42536608 TTATAAAAG
1 TTATAAAAA
*
42536617 TCATAAAAA
1 TTATAAAAA
*
42536626 ATATAAAAA
1 TTATAAAAA
*
42536635 TCATAAAATA
1 TTATAAAA-A
42536645 TTAGTAAAATA
1 TTA-TAAAA-A
*
42536656 TTTAAAAAAA
1 -TTATAAAAA
*
42536666 TTTTAAAAA
1 TTATAAAAA
*
42536675 GCTAT-AAAA
1 -TTATAAAAA
*
42536684 TATATTAAAGAT
1 T-TA-TAAA-AA
*
42536696 TTAGATAAAA
1 TTATA-AAAA
42536706 TTATAAAAAA
1 TTAT-AAAAA
*
42536716 TTCATAGAAAC
1 TT-ATA-AAAA
* **
42536727 TTATTAATT
1 TTATAAAAA
42536736 TTATAAAAA
1 TTATAAAAA
42536745 CTTATAAAAA
1 -TTATAAAAA
42536755 TTATAAACAA
1 TTATAAA-AA
*
42536765 TCTA-ATAAA
1 T-TATAAAAA
42536774 TTATAAAAAAA
1 TTAT--AAAAA
42536785 TT-TAAAAA
1 TTATAAAAA
42536793 TTCATAAAAA
1 TT-ATAAAAA
* **
42536803 TTGTAAGTA
1 TTATAAAAA
42536812 TTATAATAAA
1 TTATAA-AAA
*
42536822 TTATAAAAG
1 TTATAAAAA
42536831 TTATAATAAA
1 TTATAA-AAA
42536841 TTAT----A
1 TTATAAAAA
42536846 TTATGAAAAA
1 TTAT-AAAAA
42536856 TT-TAAAAA
1 TTATAAAAA
42536864 TATATAAAAA
1 T-TATAAAAA
42536874 TTATAAAAA
1 TTATAAAAA
42536883 AGTCATTTAT
Statistics
Matches: 203, Mismatches: 34, Indels: 58
0.69 0.12 0.20
Matches are distributed among these distances:
5 5 0.02
8 15 0.07
9 78 0.38
10 67 0.33
11 33 0.16
12 5 0.02
ACGTcount: A:0.59, C:0.03, G:0.04, T:0.34
Consensus pattern (9 bp):
TTATAAAAA
Found at i:42546099 original size:42 final size:42
Alignment explanation
Indices: 42545982--42546137 Score: 215
Period size: 42 Copynumber: 3.7 Consensus size: 42
42545972 TACCAAACCA
* * *
42545982 ATGCCATATCCCAGATATGGTCTTACATGTAAATCTCGTATCA
1 ATGCCATATCCCAGATATGGTCTTACACG-AAATCTCATATCG
* *
42546025 ATGCCAATAGCCCAGCTATGGTCTTACACGAAATCTCATATCG
1 ATGCC-ATATCCCAGATATGGTCTTACACGAAATCTCATATCG
* *
42546068 ATGCCATATCTCAGATATTGTCTTACACGAAATCTCATAAT-G
1 ATGCCATATCCCAGATATGGTCTTACACGAAATCTCAT-ATCG
42546110 ATGCCATATCCCAGATATGGTCTTACAC
1 ATGCCATATCCCAGATATGGTCTTACAC
42546138 ATAGTCTCGA
Statistics
Matches: 100, Mismatches: 11, Indels: 5
0.86 0.09 0.04
Matches are distributed among these distances:
42 56 0.56
43 23 0.23
44 21 0.21
ACGTcount: A:0.31, C:0.25, G:0.14, T:0.30
Consensus pattern (42 bp):
ATGCCATATCCCAGATATGGTCTTACACGAAATCTCATATCG
Found at i:42548351 original size:40 final size:40
Alignment explanation
Indices: 42548169--42548391 Score: 236
Period size: 40 Copynumber: 5.6 Consensus size: 40
42548159 TCCTCGTTCA
* * * * *
42548169 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
42548208 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
42548248 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
42548288 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* ** * * * *
42548328 AAGGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
* *
42548368 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
42548392 CAGCATTCAA
Statistics
Matches: 160, Mismatches: 20, Indels: 7
0.86 0.11 0.04
Matches are distributed among these distances:
39 37 0.23
40 115 0.72
41 8 0.05
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:42548400 original size:41 final size:41
Alignment explanation
Indices: 42548323--42548400 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
42548313 TTAGTATCTC
* * *
42548323 GCACAAAGGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
42548364 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAAGGCCTTC-GGATCTTAGCCCGGACA-CATTCA
42548401 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (41 bp):
GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:42556242 original size:40 final size:40
Alignment explanation
Indices: 42556060--42556282 Score: 236
Period size: 40 Copynumber: 5.6 Consensus size: 40
42556050 TCCTCGTTCA
* * * * *
42556060 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
42556099 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
42556139 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
42556179 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* ** * * * *
42556219 AAGGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
* *
42556259 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
42556283 CAGCATTCAA
Statistics
Matches: 160, Mismatches: 20, Indels: 7
0.86 0.11 0.04
Matches are distributed among these distances:
39 37 0.23
40 115 0.72
41 8 0.05
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:42556291 original size:41 final size:41
Alignment explanation
Indices: 42556214--42556291 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
42556204 TTAGTATCTC
* * *
42556214 GCACAAAGGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
42556255 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAAGGCCTTC-GGATCTTAGCCCGGACA-CATTCA
42556292 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (41 bp):
GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:42563995 original size:39 final size:40
Alignment explanation
Indices: 42563952--42564120 Score: 234
Period size: 40 Copynumber: 4.3 Consensus size: 40
42563942 TCCTCGTTCA
* * *
42563952 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCACG
*
42563991 AATGCCTTCGGGACATAACCCGGATTTA-CAACTCGCACG
1 AATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCACG
* *
42564030 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCACG
* * *
42564070 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCACG
*
42564110 AAGGCCTTCGG
1 AATGCCTTCGG
42564121 ATCTTAGTCC
Statistics
Matches: 118, Mismatches: 10, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
38 8 0.07
39 53 0.45
40 57 0.48
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCACG
Found at i:42564075 original size:40 final size:39
Alignment explanation
Indices: 42563952--42564173 Score: 223
Period size: 40 Copynumber: 5.6 Consensus size: 39
42563942 TCCTCGTTCA
* * * * *
42563952 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCAC
* *
42563991 AATGCCTTCGGGACATAACCCGGATTT-ACAACTCGCAC
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCAC
42564029 GAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCAC
1 -AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCAC
* *
42564069 GAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCAC
1 -AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCAC
* ** * * * *
42564109 AAAGGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC
1 -AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCAC
* *
42564150 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
42564174 CAGCATTCAA
Statistics
Matches: 158, Mismatches: 20, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
38 8 0.05
39 54 0.34
40 88 0.56
41 8 0.05
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (39 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCAC
Found at i:42564182 original size:41 final size:41
Alignment explanation
Indices: 42564105--42564182 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
42564095 TTAGTATCTC
* * *
42564105 GCACAAAGGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
42564146 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAAGGCCTTC-GGATCTTAGCCCGGACA-CATTCA
42564183 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (41 bp):
GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:42576511 original size:40 final size:40
Alignment explanation
Indices: 42576456--42576536 Score: 144
Period size: 40 Copynumber: 2.0 Consensus size: 40
42576446 CCTTAGCTGC
* *
42576456 TGATAGGGGGTTGCGTGTGGACCAAGATCGAGTTGTCAAG
1 TGATACGGGGTTGCGTGCGGACCAAGATCGAGTTGTCAAG
42576496 TGATACGGGGTTGCGTGCGGACCAAGATCGAGTTGTCAAG
1 TGATACGGGGTTGCGTGCGGACCAAGATCGAGTTGTCAAG
42576536 T
1 T
42576537 CACGAGAAAC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.22, C:0.15, G:0.38, T:0.25
Consensus pattern (40 bp):
TGATACGGGGTTGCGTGCGGACCAAGATCGAGTTGTCAAG
Found at i:42582741 original size:39 final size:40
Alignment explanation
Indices: 42582698--42582865 Score: 234
Period size: 40 Copynumber: 4.3 Consensus size: 40
42582688 TCCTCGTTCA
* * * * *
42582698 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
*
42582737 AATGCCTTCGGGAC-TAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
42582776 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
42582816 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
*
42582855 AAAGCCTTCGG
1 AATGCCTTCGG
42582866 ATCTTAGTCC
Statistics
Matches: 118, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
38 19 0.16
39 38 0.32
40 61 0.52
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:42582810 original size:40 final size:39
Alignment explanation
Indices: 42582698--42582917 Score: 230
Period size: 39 Copynumber: 5.6 Consensus size: 39
42582688 TCCTCGTTCA
* * * * *
42582698 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCAC
*
42582737 AATGCCTTCGGGAC-TAACCCGGATTTAACAACTCGCAC
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCAC
42582775 GAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCAC
1 -AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCAC
* *
42582815 GAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCAC
1 -AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCAC
* ** * ** *
42582855 AAAGCCTTC-GGATCTTAGTCCGGATAT-ATTCCTTAGCAC
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCAC
* *
42582894 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
42582918 CAGCATTCAA
Statistics
Matches: 159, Mismatches: 17, Indels: 10
0.85 0.09 0.05
Matches are distributed among these distances:
38 24 0.15
39 71 0.45
40 64 0.40
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (39 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCAC
Found at i:42590765 original size:40 final size:40
Alignment explanation
Indices: 42590583--42590805 Score: 236
Period size: 40 Copynumber: 5.6 Consensus size: 40
42590573 TCCTCGTTCA
* * * * *
42590583 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
42590622 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
42590662 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
42590702 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* ** * * * * *
42590742 AAGGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCACA
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
*
42590783 AAT-CCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
42590806 CAGCATTCAA
Statistics
Matches: 160, Mismatches: 20, Indels: 7
0.86 0.11 0.04
Matches are distributed among these distances:
39 37 0.23
40 112 0.70
41 11 0.07
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:42602464 original size:25 final size:24
Alignment explanation
Indices: 42602436--42602487 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 24
42602426 ATTCTAACAT
42602436 TATATTAAATT-GATAATAATTAATA
1 TATATTAAATTGGAT-ATAATT-ATA
*
42602461 TATATTATATTGGATATAATTATA
1 TATATTAAATTGGATATAATTATA
42602485 TAT
1 TAT
42602488 TAATAATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
24 6 0.24
25 16 0.64
26 3 0.12
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.48
Consensus pattern (24 bp):
TATATTAAATTGGATATAATTATA
Found at i:42602605 original size:31 final size:30
Alignment explanation
Indices: 42602543--42602603 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
42602533 AATGCCTGAA
* * *
42602543 AATATTTACAAAAAGAGGCATCTAATTTTT
1 AATATTTACAAAAAAAGGCAACCAATTTTT
42602573 AATATTTACAAAAAAAGAGCAACCAGATTTT
1 AATATTTACAAAAAAAG-GCAACCA-ATTTT
42602604 AAAAATTGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 16 0.62
31 5 0.19
32 5 0.19
ACGTcount: A:0.48, C:0.11, G:0.10, T:0.31
Consensus pattern (30 bp):
AATATTTACAAAAAAAGGCAACCAATTTTT
Found at i:42605455 original size:46 final size:46
Alignment explanation
Indices: 42605405--42605578 Score: 212
Period size: 46 Copynumber: 3.8 Consensus size: 46
42605395 GTTGAGCATT
42605405 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAATGTC
1 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAATGTC
* * *
42605451 CGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--AATGT-AACTAGGCATC
1 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAA-T--G--TC
* * *
42605498 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCC
1 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAATGTC
*
42605544 CGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
42605579 GTGGGTTACA
Statistics
Matches: 109, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 62 0.57
47 29 0.27
48 3 0.03
50 3 0.03
51 2 0.02
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.29
Consensus pattern (46 bp):
CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAATGTC
Found at i:42605564 original size:93 final size:93
Alignment explanation
Indices: 42605400--42605570 Score: 297
Period size: 93 Copynumber: 1.8 Consensus size: 93
42605390 GGATGGTTGA
* * * *
42605400 GCATTCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
42605465 TGAGTCCGAGTTCGTGAAATGTAACTAG
66 TGAGTCCGAGTTCGTGAAATGTAACTAG
*
42605493 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
42605558 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
42605571 ACTTATGGGT
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAAATGTAACTAG
Found at i:42614434 original size:25 final size:28
Alignment explanation
Indices: 42614397--42614454 Score: 68
Period size: 27 Copynumber: 2.1 Consensus size: 28
42614387 GTAAATCACA
*
42614397 AAAAAAATCTAAA-ACTTAAT-AAAAGAG
1 AAAAAAA-CTAAAGACTAAATCAAAAGAG
*
42614424 AAAAAAA-TAAAGACTAAATCCAAAGAG
1 AAAAAAACTAAAGACTAAATCAAAAGAG
42614451 AAAA
1 AAAA
42614455 TTATACAATC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
25 4 0.15
26 6 0.22
27 17 0.63
ACGTcount: A:0.69, C:0.09, G:0.09, T:0.14
Consensus pattern (28 bp):
AAAAAAACTAAAGACTAAATCAAAAGAG
Found at i:42625061 original size:29 final size:29
Alignment explanation
Indices: 42625026--42625157 Score: 142
Period size: 29 Copynumber: 4.6 Consensus size: 29
42625016 TAGCATAAAG
*
42625026 ACTTGGTGGACTCATACATGTC-GATTCAT
1 ACTTGGTGAACTCATACATG-CGGATTCAT
* * *
42625055 GCTTGGTGAAATCACACATGCGGATT-AT
1 ACTTGGTGAACTCATACATGCGGATTCAT
* *
42625083 ACTTGGTGAACTCATACATGAGGATCCAT
1 ACTTGGTGAACTCATACATGCGGATTCAT
** *
42625112 ACTTGGTGGGCTCATACTTGCGGATTCAT
1 ACTTGGTGAACTCATACATGCGGATTCAT
* *
42625141 ACTTGGTTAACTTATAC
1 ACTTGGTGAACTCATAC
42625158 TTAGTGAACC
Statistics
Matches: 83, Mismatches: 18, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
28 24 0.29
29 59 0.71
ACGTcount: A:0.26, C:0.20, G:0.22, T:0.33
Consensus pattern (29 bp):
ACTTGGTGAACTCATACATGCGGATTCAT
Found at i:42625117 original size:57 final size:58
Alignment explanation
Indices: 42625026--42625157 Score: 149
Period size: 57 Copynumber: 2.3 Consensus size: 58
42625016 TAGCATAAAG
* * * *
42625026 ACTTGGTGGACTCATACATGTCGATTCATGCTTGGTGAAATCACACATGCGGATT-AT
1 ACTTGGTGAACTCATACATGACGATCCATACTTGGTGAAATCACACATGCGGATTCAT
* *** * *
42625083 ACTTGGTGAACTCATACATGAGGATCCATACTTGGTGGGCTCATACTTGCGGATTCAT
1 ACTTGGTGAACTCATACATGACGATCCATACTTGGTGAAATCACACATGCGGATTCAT
* *
42625141 ACTTGGTTAACTTATAC
1 ACTTGGTGAACTCATAC
42625158 TTAGTGAACC
Statistics
Matches: 62, Mismatches: 12, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
57 45 0.73
58 17 0.27
ACGTcount: A:0.26, C:0.20, G:0.22, T:0.33
Consensus pattern (58 bp):
ACTTGGTGAACTCATACATGACGATCCATACTTGGTGAAATCACACATGCGGATTCAT
Found at i:42625158 original size:44 final size:43
Alignment explanation
Indices: 42625110--42625218 Score: 119
Period size: 44 Copynumber: 2.5 Consensus size: 43
42625100 ATGAGGATCC
* * *
42625110 ATACTTGGTGGGCTCATACTTGCGGATTCATACTTGGTTAACTT
1 ATACTT-GTGGACTCATACTTGAGGATTCATACTTGGTGAACTT
* * * *
42625154 ATACTTAGTGAACCCATACATGAGGATTCATACTTGGTGGACTT
1 ATACTT-GTGGACTCATACTTGAGGATTCATACTTGGTGAACTT
* *
42625198 GTACTTGTGGATTCATACTTG
1 ATACTTGTGGACTCATACTTG
42625219 GTGAACTATA
Statistics
Matches: 52, Mismatches: 13, Indels: 1
0.79 0.20 0.02
Matches are distributed among these distances:
43 11 0.21
44 41 0.79
ACGTcount: A:0.24, C:0.17, G:0.22, T:0.37
Consensus pattern (43 bp):
ATACTTGTGGACTCATACTTGAGGATTCATACTTGGTGAACTT
Found at i:42625186 original size:29 final size:29
Alignment explanation
Indices: 42625154--42625224 Score: 79
Period size: 29 Copynumber: 2.4 Consensus size: 29
42625144 TGGTTAACTT
*
42625154 ATACTTAGTGAACCCATACATGAGGATTC
1 ATACTTGGTGAACCCATACATGAGGATTC
* *** * *
42625183 ATACTTGGTGGACTTGTACTTGTGGATTC
1 ATACTTGGTGAACCCATACATGAGGATTC
42625212 ATACTTGGTGAAC
1 ATACTTGGTGAAC
42625225 TATACAGTAG
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.34
Consensus pattern (29 bp):
ATACTTGGTGAACCCATACATGAGGATTC
Found at i:42625203 original size:73 final size:73
Alignment explanation
Indices: 42625079--42625229 Score: 223
Period size: 73 Copynumber: 2.1 Consensus size: 73
42625069 CACATGCGGA
* * *
42625079 TTATACTTGGTGAACTCATACATGAGGATCCATACTTGGTGGGCTCATACTTGCGGATTCATACT
1 TTATACTTAGTGAACCCATACATGAGGATCCATACTTGGTGGACTCATACTTGCGGATTCATACT
*
42625144 TGGTTAAC
66 TGGTGAAC
* ** *
42625152 TTATACTTAGTGAACCCATACATGAGGATTCATACTTGGTGGACTTGTACTTGTGGATTCATACT
1 TTATACTTAGTGAACCCATACATGAGGATCCATACTTGGTGGACTCATACTTGCGGATTCATACT
42625217 TGGTGAAC
66 TGGTGAAC
42625225 -TATAC
1 TTATAC
42625230 AGTAGGATTT
Statistics
Matches: 70, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
72 5 0.07
73 65 0.93
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.35
Consensus pattern (73 bp):
TTATACTTAGTGAACCCATACATGAGGATCCATACTTGGTGGACTCATACTTGCGGATTCATACT
TGGTGAAC
Found at i:42625204 original size:15 final size:15
Alignment explanation
Indices: 42625177--42625221 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
42625167 CCATACATGA
42625177 GGATTCATACTTGGT
1 GGATTCATACTTGGT
*
42625192 GGACTT-GTACTT-GT
1 GGA-TTCATACTTGGT
42625206 GGATTCATACTTGGT
1 GGATTCATACTTGGT
42625221 G
1 G
42625222 AACTATACAG
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
13 2 0.08
14 10 0.40
15 11 0.44
16 2 0.08
ACGTcount: A:0.18, C:0.13, G:0.29, T:0.40
Consensus pattern (15 bp):
GGATTCATACTTGGT
Found at i:42625417 original size:37 final size:37
Alignment explanation
Indices: 42625375--42625464 Score: 108
Period size: 37 Copynumber: 2.4 Consensus size: 37
42625365 TTTGAAAATT
* *
42625375 TGAGGACACGTCCAACAGAATGGCATAACTTGAAACA
1 TGAGGACAAGTCCAACAGAATGGCATAACCTGAAACA
* * * **
42625412 TGAGGACAAGTCCAGCGGACTTTCATAACCTGAAACA
1 TGAGGACAAGTCCAACAGAATGGCATAACCTGAAACA
*
42625449 TGAGGCCAAGTCCAAC
1 TGAGGACAAGTCCAAC
42625465 GAACTATCGT
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
37 44 1.00
ACGTcount: A:0.37, C:0.24, G:0.22, T:0.17
Consensus pattern (37 bp):
TGAGGACAAGTCCAACAGAATGGCATAACCTGAAACA
Found at i:42632339 original size:51 final size:51
Alignment explanation
Indices: 42632262--42632460 Score: 328
Period size: 51 Copynumber: 3.9 Consensus size: 51
42632252 AGGATACATG
*
42632262 GTGGCCTTCACATAGTACCACCCTTGTAGT-CAAAGCTATTTTATTCACAAA
1 GTGGCCTTCACATAGTACCACACTTGT-GTCCAAAGCTATTTTATTCACAAA
*
42632313 GTGGCCTTCACATAGTACCACACTTGTGTCCAAAACTATTTTATTCACAAA
1 GTGGCCTTCACATAGTACCACACTTGTGTCCAAAGCTATTTTATTCACAAA
* * *
42632364 GTGACCTTCACATAGTACCACACTTTTGTCCAAAGCTATTATATTCACAAA
1 GTGGCCTTCACATAGTACCACACTTGTGTCCAAAGCTATTTTATTCACAAA
*
42632415 GTAGCCTTCACATAGTACCACACTTGTGTCCAAAGCTATTTTATTC
1 GTGGCCTTCACATAGTACCACACTTGTGTCCAAAGCTATTTTATTC
42632461 GTAAGGTTTA
Statistics
Matches: 137, Mismatches: 10, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
50 2 0.01
51 135 0.99
ACGTcount: A:0.30, C:0.26, G:0.12, T:0.32
Consensus pattern (51 bp):
GTGGCCTTCACATAGTACCACACTTGTGTCCAAAGCTATTTTATTCACAAA
Found at i:42638759 original size:51 final size:51
Alignment explanation
Indices: 42638683--42638926 Score: 375
Period size: 51 Copynumber: 4.8 Consensus size: 51
42638673 GGATACACGA
* *
42638683 TGGCCTTCACATAGTACCACCCTTGTAG-CCAAGGCTATTTTATTCACAAAG
1 TGGCCTTCACATAGTACCACACTTGT-GTCCAAAGCTATTTTATTCACAAAG
**
42638734 TGGCCTTCACATAGTACCACACTTGTGTCTGAAGCTATTTTATTCACAAAG
1 TGGCCTTCACATAGTACCACACTTGTGTCCAAAGCTATTTTATTCACAAAG
* *
42638785 TGGCCTTCACATAGTACCACACTTGTGTCCAAAGCTATTATATTCACAAAA
1 TGGCCTTCACATAGTACCACACTTGTGTCCAAAGCTATTTTATTCACAAAG
* * * *
42638836 TGTCC-TCACATAGTGCCACACTTGTGTTCAAAGCTATTATATTCACAAAG
1 TGGCCTTCACATAGTACCACACTTGTGTCCAAAGCTATTTTATTCACAAAG
42638886 TGGCCTTCACATAGTACCACACTTGTGTCCAAAGCTATTTT
1 TGGCCTTCACATAGTACCACACTTGTGTCCAAAGCTATTTT
42638927 TTTCCTAACG
Statistics
Matches: 175, Mismatches: 16, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
50 47 0.27
51 128 0.73
ACGTcount: A:0.29, C:0.25, G:0.14, T:0.32
Consensus pattern (51 bp):
TGGCCTTCACATAGTACCACACTTGTGTCCAAAGCTATTTTATTCACAAAG
Found at i:42638886 original size:101 final size:102
Alignment explanation
Indices: 42638683--42638924 Score: 373
Period size: 101 Copynumber: 2.4 Consensus size: 102
42638673 GGATACACGA
* * * *
42638683 TGGCCTTCACATAGTACCACCCTTGTAG-CCAAGGCTATTTTATTCACAAAGTGGCCTTCACATA
1 TGGCCTTCACATAGTACCACACTTGT-GTCCAAAGCTATTATATTCACAAAATGGCCTTCACATA
* *
42638747 GTACCACACTTGTGTCTGAAGCTATTTTATTCACAAAG
65 GTACCACACTTGTGTCTAAAGCTATTATATTCACAAAG
*
42638785 TGGCCTTCACATAGTACCACACTTGTGTCCAAAGCTATTATATTCACAAAATGTCC-TCACATAG
1 TGGCCTTCACATAGTACCACACTTGTGTCCAAAGCTATTATATTCACAAAATGGCCTTCACATAG
*
42638849 TGCCACACTTGTGT-TCAAAGCTATTATATTCACAAAG
66 TACCACACTTGTGTCT-AAAGCTATTATATTCACAAAG
42638886 TGGCCTTCACATAGTACCACACTTGTGTCCAAAGCTATT
1 TGGCCTTCACATAGTACCACACTTGTGTCCAAAGCTATT
42638925 TTTTTCCTAA
Statistics
Matches: 130, Mismatches: 8, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
100 1 0.01
101 80 0.62
102 49 0.38
ACGTcount: A:0.29, C:0.26, G:0.14, T:0.31
Consensus pattern (102 bp):
TGGCCTTCACATAGTACCACACTTGTGTCCAAAGCTATTATATTCACAAAATGGCCTTCACATAG
TACCACACTTGTGTCTAAAGCTATTATATTCACAAAG
Found at i:42638993 original size:24 final size:24
Alignment explanation
Indices: 42638966--42639011 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
42638956 ACTTAACACA
42638966 ATGCCATGGACTTATTTCACTTGG
1 ATGCCATGGACTTATTTCACTTGG
*
42638990 ATGCCGTGGACTTATTTCACTT
1 ATGCCATGGACTTATTTCACTT
42639012 AGCACATTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.20, C:0.22, G:0.20, T:0.39
Consensus pattern (24 bp):
ATGCCATGGACTTATTTCACTTGG
Found at i:42641035 original size:20 final size:20
Alignment explanation
Indices: 42641010--42641061 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
42641000 GAGACAATGC
42641010 ACACGCCCGTGTGCTTTGGG
1 ACACGCCCGTGTGCTTTGGG
42641030 ACACGCCCGTGTGCTTTGGG
1 ACACGCCCGTGTGCTTTGGG
*
42641050 ACACGCCTGTGT
1 ACACGCCCGTGT
42641062 CCCCTACCTG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.12, C:0.31, G:0.33, T:0.25
Consensus pattern (20 bp):
ACACGCCCGTGTGCTTTGGG
Found at i:42641155 original size:13 final size:13
Alignment explanation
Indices: 42641137--42641161 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
42641127 CCAAACACAT
42641137 GCCCGTGTTCCTA
1 GCCCGTGTTCCTA
42641150 GCCCGTGTTCCT
1 GCCCGTGTTCCT
42641162 TACACGGCCT
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:0.04, C:0.40, G:0.24, T:0.32
Consensus pattern (13 bp):
GCCCGTGTTCCTA
Found at i:42648440 original size:20 final size:21
Alignment explanation
Indices: 42648406--42648460 Score: 64
Period size: 20 Copynumber: 2.8 Consensus size: 21
42648396 GATACGTGGG
42648406 ATATGATAT--ACATGAATA-
1 ATATGATATGCACATGAATAT
42648424 ATATGATATGCACATG-ATAT
1 ATATGATATGCACATGAATAT
* *
42648444 GTATGAAATGCACATGA
1 ATATGATATGCACATGA
42648461 TGTAATCATA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
18 9 0.29
19 3 0.10
20 19 0.61
ACGTcount: A:0.44, C:0.09, G:0.16, T:0.31
Consensus pattern (21 bp):
ATATGATATGCACATGAATAT
Found at i:42648553 original size:26 final size:26
Alignment explanation
Indices: 42648511--42648672 Score: 251
Period size: 26 Copynumber: 6.3 Consensus size: 26
42648501 GAGGAAGTGC
42648511 AAAAGGGC-TATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTATTG
**
42648536 AAAAGGGCTTATGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTATTG
42648562 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTATTG
*
42648588 AAAAGGGCTTATGCCCTAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTATTG
*
42648614 AAAAGGGCTTATGCCCCAGTTTACTG
1 AAAAGGGCTTATGCCCCAGTTTATTG
42648640 AAAAGGGCTT-TGCCCCAG-TTATT-
1 AAAAGGGCTTATGCCCCAGTTTATTG
42648663 AAAAGAGGCT
1 AAAAG-GGCT
42648673 AGGCCTCCAG
Statistics
Matches: 127, Mismatches: 8, Indels: 5
0.91 0.06 0.04
Matches are distributed among these distances:
23 5 0.04
24 8 0.06
25 16 0.13
26 98 0.77
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.28
Consensus pattern (26 bp):
AAAAGGGCTTATGCCCCAGTTTATTG
Found at i:42651855 original size:24 final size:24
Alignment explanation
Indices: 42651828--42651891 Score: 83
Period size: 24 Copynumber: 2.6 Consensus size: 24
42651818 ATTGTTCAGA
*
42651828 TCAATAGAGCTTACCATTTTCATC
1 TCAATAGAGCTTACCATTATCATC
**
42651852 TCAATAGAGCTTACTGTTATCATC
1 TCAATAGAGCTTACCATTATCATC
*
42651876 TCATAAAGAGCTTACC
1 TCA-ATAGAGCTTACC
42651892 GACCATGTCT
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
24 24 0.71
25 10 0.29
ACGTcount: A:0.31, C:0.23, G:0.11, T:0.34
Consensus pattern (24 bp):
TCAATAGAGCTTACCATTATCATC
Found at i:42658990 original size:24 final size:24
Alignment explanation
Indices: 42658963--42659026 Score: 92
Period size: 24 Copynumber: 2.6 Consensus size: 24
42658953 ATTGTTCAGA
*
42658963 TCAATAGAGCTTACCATTTTCATC
1 TCAATAGAGCTTACCATTATCATC
*
42658987 TCAATAGAGCTTACTATTATCATC
1 TCAATAGAGCTTACCATTATCATC
*
42659011 TCATAAAGAGCTTACC
1 TCA-ATAGAGCTTACC
42659027 GACCATGTCT
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
24 25 0.71
25 10 0.29
ACGTcount: A:0.33, C:0.23, G:0.09, T:0.34
Consensus pattern (24 bp):
TCAATAGAGCTTACCATTATCATC
Found at i:42660272 original size:19 final size:19
Alignment explanation
Indices: 42660248--42660284 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
42660238 ACTTGAAAAG
*
42660248 TTAAAAATTTTCTATGTTT
1 TTAAAAATTTTATATGTTT
*
42660267 TTAAAATTTTTATATGTT
1 TTAAAAATTTTATATGTT
42660285 ATCAATTTAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.32, C:0.03, G:0.05, T:0.59
Consensus pattern (19 bp):
TTAAAAATTTTATATGTTT
Found at i:42663448 original size:67 final size:67
Alignment explanation
Indices: 42663362--42663488 Score: 200
Period size: 67 Copynumber: 1.9 Consensus size: 67
42663352 GTTTCTAGGT
* * *
42663362 CGTGGCAAAATAGGGCATACATACTAATTTGTCCACACAGCCACAAGACATGCCCGTGTGTCTAA
1 CGTGGCAAAACAGGGCATACATACTAACTTGTCCACACAGCCACAAGACACGCCCGTGTGTCTAA
42663427 GC
66 GC
* * *
42663429 CGTGGCAAAACAGGGCATACATACTGACTTGTCCACATAGCCACAAGACACGCCTGTGTG
1 CGTGGCAAAACAGGGCATACATACTAACTTGTCCACACAGCCACAAGACACGCCCGTGTG
42663489 CCAGGTCGTG
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
67 54 1.00
ACGTcount: A:0.31, C:0.28, G:0.22, T:0.20
Consensus pattern (67 bp):
CGTGGCAAAACAGGGCATACATACTAACTTGTCCACACAGCCACAAGACACGCCCGTGTGTCTAA
GC
Found at i:42664598 original size:9 final size:9
Alignment explanation
Indices: 42664554--42664629 Score: 54
Period size: 9 Copynumber: 8.9 Consensus size: 9
42664544 ATTACTCACA
*
42664554 TAATTTATG
1 TAATTCATG
*
42664563 TAATTCATA
1 TAATTCATG
*
42664572 T-A-TCATA
1 TAATTCATG
* *
42664579 AAATCCATG
1 TAATTCATG
42664588 TAATTCATG
1 TAATTCATG
42664597 TAATTCATG
1 TAATTCATG
42664606 TAACTT-A--
1 TAA-TTCATG
42664613 TAATTCATG
1 TAATTCATG
*
42664622 TAAATCAT
1 TAATTCAT
42664630 ATAGCTCTTA
Statistics
Matches: 53, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
6 2 0.04
7 9 0.17
8 2 0.04
9 38 0.72
10 2 0.04
ACGTcount: A:0.39, C:0.12, G:0.07, T:0.42
Consensus pattern (9 bp):
TAATTCATG
Found at i:42664622 original size:34 final size:34
Alignment explanation
Indices: 42664554--42664629 Score: 89
Period size: 34 Copynumber: 2.2 Consensus size: 34
42664544 ATTACTCACA
* *
42664554 TAATTTATGTAATTCATATATCATAAAATCCATG
1 TAATTCATGTAATTCATATAACATAAAATCCATG
* * * *
42664588 TAATTCATGTAATTCATGTAACTTATAATTCATG
1 TAATTCATGTAATTCATATAACATAAAATCCATG
*
42664622 TAAATCAT
1 TAATTCAT
42664630 ATAGCTCTTA
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.39, C:0.12, G:0.07, T:0.42
Consensus pattern (34 bp):
TAATTCATGTAATTCATATAACATAAAATCCATG
Found at i:42666744 original size:46 final size:46
Alignment explanation
Indices: 42666602--42666864 Score: 243
Period size: 47 Copynumber: 5.6 Consensus size: 46
42666592 CTGAGCTAGC
* *
42666602 GTAAGACATGTCTGGGACATGCATCGGCCAC-ATTATGAGAGCCAGT
1 GTAAGACATGTCTGGGACATGCATCGGCCTCGA-GATGAGAGCCAGT
* * * *
42666648 GTAAGACCATGTCTGAGACATGTCATCGGCATTGAGATGAG-GTCTAGT
1 GTAAGA-CATGTCTGGGACATG-CATCGGCCTCGAGATGAGAG-CCAGT
*
42666696 GTAAGACATGTCTGGGACATGCATCGGCCTCGAGACGTA-AGCCAGT
1 GTAAGACATGTCTGGGACATGCATCGGCCTCGAGATG-AGAGCCAGT
*
42666742 GTAAGACATGTCTGGGACATGCATCGG-CTACGAGATGATA-CTCAGT
1 GTAAGACATGTCTGGGACATGCATCGGCCT-CGAGATGAGAGC-CAGT
* * *
42666788 GTAAGACCATGTCTGGGACATGGCAT-TGACTTGAGAT-ATGAGCCAGT
1 GTAAGA-CATGTCTGGGACAT-GCATCGGCCTCGAGATGA-GAGCCAGT
* * *
42666835 ATAAGACCGTGTCTAGGACATGGCATCGGC
1 GTAAGA-CATGTCTGGGACAT-GCATCGGC
42666865 ACCTTACCCT
Statistics
Matches: 182, Mismatches: 20, Indels: 28
0.79 0.09 0.12
Matches are distributed among these distances:
45 4 0.02
46 68 0.37
47 79 0.43
48 30 0.16
49 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.23
Consensus pattern (46 bp):
GTAAGACATGTCTGGGACATGCATCGGCCTCGAGATGAGAGCCAGT
Found at i:42666854 original size:140 final size:141
Alignment explanation
Indices: 42666602--42666864 Score: 340
Period size: 140 Copynumber: 1.9 Consensus size: 141
42666592 CTGAGCTAGC
*
42666602 GTAAGACATGTCTGGGACATGCATCGGCCACATTATGAGAGCCAGTGTAAGACCATGTCTGAGAC
1 GTAAGACATGTCTGGGACATGCATCGGCCACATGATGAGAGCCAGTGTAAGACCATGTCTGAGAC
* * * * *
42666667 ATGTCATCGGCATTGAGATGAGGTCTAGTGTAAGACATGTCTGGGACAT-GCATCGGCCTCGAGA
66 ATGGCATCGACATTGAGATGAGGTCCAGTATAAGACATGTCTAGGACATGGCATCGGCCTCGAGA
42666731 CGTAAGCCAGT
131 CGTAAGCCAGT
* * *
42666742 GTAAGACATGTCTGGGACATGCATCGGCTACGA-GATGATA-CTCAGTGTAAGACCATGTCTGGG
1 GTAAGACATGTCTGGGACATGCATCGGCCAC-ATGATGAGAGC-CAGTGTAAGACCATGTCTGAG
* *
42666805 ACATGGCATTGAC-TTGAGAT-ATGAG-CCAGTATAAGACCGTGTCTAGGACATGGCATCGGC
64 ACATGGCATCGACATTGAGATGA-G-GTCCAGTATAAGA-CATGTCTAGGACATGGCATCGGC
42666865 ACCTTACCCT
Statistics
Matches: 106, Mismatches: 11, Indels: 11
0.83 0.09 0.09
Matches are distributed among these distances:
138 1 0.01
139 18 0.17
140 78 0.74
141 9 0.08
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.23
Consensus pattern (141 bp):
GTAAGACATGTCTGGGACATGCATCGGCCACATGATGAGAGCCAGTGTAAGACCATGTCTGAGAC
ATGGCATCGACATTGAGATGAGGTCCAGTATAAGACATGTCTAGGACATGGCATCGGCCTCGAGA
CGTAAGCCAGT
Found at i:42674312 original size:48 final size:44
Alignment explanation
Indices: 42674209--42674480 Score: 183
Period size: 46 Copynumber: 5.8 Consensus size: 44
42674199 ATTCGAGTGT
* *
42674209 GAGCTAGTGTAAGACATGTTTGGGACATGCATCGGCCACATT-ATGA-
1 GAGCCAGTGTAAGACATGTCTGGGACATGCATCGG---CATTGA-GAC
42674255 GAGCCAGTGTAAGACAATGTCTGGGACATGGCATCGGCATTGAGAC
1 GAGCCAGTGTAAGAC-ATGTCTGGGACAT-GCATCGGCATTGAGAC
* * * *
42674301 GAGGGCTAGTGTAAGACATGTCTGGGACATGCATCGACCTCGAGAC
1 GA--GCCAGTGTAAGACATGTCTGGGACATGCATCGGCATTGAGAC
* * * *
42674347 GTAAGCCAGTGTAAGACACGTCTGGGACATGCATAGGC-TACGAGAT
1 G--AGCCAGTGTAAGACATGTCTGGGACATGCATCGGCAT-TGAGAC
* * ** *
42674393 GATAGTCAGTGTAAAACCATGTCTGGGACATAGCATCAAC-TTGAGATAT
1 G--AGCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCATTGAG--AC
* * *
42674442 GAGCCAGTATAAGACCGTGTCTAGGACATGGCATCGGCA
1 GAGCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCA
42674481 CCTTAACCTA
Statistics
Matches: 184, Mismatches: 28, Indels: 26
0.77 0.12 0.11
Matches are distributed among these distances:
45 7 0.04
46 78 0.42
47 70 0.38
48 26 0.14
49 3 0.02
ACGTcount: A:0.29, C:0.19, G:0.29, T:0.22
Consensus pattern (44 bp):
GAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCATTGAGAC
Found at i:42674358 original size:46 final size:46
Alignment explanation
Indices: 42674209--42674429 Score: 214
Period size: 46 Copynumber: 4.7 Consensus size: 46
42674199 ATTCGAGTGT
* * * * *
42674209 GAGCTAGTGTAAGACATGTTTGGGACATGCATCGGCCAC-ATTATGA
1 GAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGA-GACGA
* *
42674255 GAGCCAGTGTAAGACAATGTCTGGGACATGGCATCGGCATTGAGACGA
1 GAGCCAGTGTAAGAC-ATGTCTGGGACAT-GCATCGGCCTCGAGACGA
* * *
42674303 GGGCTAGTGTAAGACATGTCTGGGACATGCATCGACCTCGAGACGTA
1 GAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGACG-A
* * *
42674350 -AGCCAGTGTAAGACACGTCTGGGACATGCATAGG-CTACGAGATGA
1 GAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCCT-CGAGACGA
* * *
42674395 TAGTCAGTGTAAAACCATGTCTGGGACATAGCATC
1 GAGCCAGTGTAAGA-CATGTCTGGGACAT-GCATC
42674430 AACTTGAGAT
Statistics
Matches: 145, Mismatches: 22, Indels: 14
0.80 0.12 0.08
Matches are distributed among these distances:
45 3 0.02
46 74 0.51
47 39 0.27
48 28 0.19
49 1 0.01
ACGTcount: A:0.29, C:0.19, G:0.30, T:0.22
Consensus pattern (46 bp):
GAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGACGA
Found at i:42674439 original size:47 final size:47
Alignment explanation
Indices: 42674214--42674476 Score: 168
Period size: 47 Copynumber: 5.6 Consensus size: 47
42674204 AGTGTGAGCT
* * * **
42674214 AGTGTAAGA-CATGTTTGGGACATGCATCGGC-C-ACATTATGAGAGCC
1 AGTGTAAGACCATGTCTGGGACATGCATCAGCTCGAGACGAT-A-AGCC
* * * ** *
42674260 AGTGTAAGACAATGTCTGGGACATGGCATCGGCATTGAGACGA-GGGCT
1 AGTGTAAGACCATGTCTGGGACAT-GCATCAGC-TCGAGACGATAAGCC
*
42674308 AGTGTAAGA-CATGTCTGGGACATGCATCGACCTCGAGACG-TAAGCC
1 AGTGTAAGACCATGTCTGGGACATGCATC-AGCTCGAGACGATAAGCC
* * *
42674354 AGTGTAAGA-CACGTCTGGGACATGCAT-AGGCTACGAGATGAT-AGTC
1 AGTGTAAGACCATGTCTGGGACATGCATCA-GCT-CGAGACGATAAGCC
* * * * *
42674400 AGTGTAAAACCATGTCTGGGACATAGCATCAACTTGAGA-TATGAGCC
1 AGTGTAAGACCATGTCTGGGACAT-GCATCAGCTCGAGACGATAAGCC
* * *
42674447 AGTATAAGACCGTGTCTAGGACATGGCATC
1 AGTGTAAGACCATGTCTGGGACAT-GCATC
42674477 GGCACCTTAA
Statistics
Matches: 172, Mismatches: 31, Indels: 27
0.75 0.13 0.12
Matches are distributed among these distances:
44 1 0.01
45 2 0.01
46 68 0.40
47 72 0.42
48 25 0.15
49 1 0.01
51 3 0.02
ACGTcount: A:0.30, C:0.19, G:0.29, T:0.22
Consensus pattern (47 bp):
AGTGTAAGACCATGTCTGGGACATGCATCAGCTCGAGACGATAAGCC
Found at i:42674447 original size:93 final size:94
Alignment explanation
Indices: 42674255--42674480 Score: 219
Period size: 93 Copynumber: 2.4 Consensus size: 94
42674245 CACATTATGA
* * * * *
42674255 GAGCCAGTGTAAGACAATGTCTGGGACATGGCATCGGCATTGAGACGAGGGCTAGTGTAAGACAT
1 GAGCCAGTGTAAGACAACGTCTGGGACATGGCATAGGCATCGAGACGAAGGCTAGTGTAAAACAT
* *
42674320 GTCTGGGACATGCATCGACCTCGAGACGT
66 GTCTGGGACATGCATCGAACTCGAGACAT
* * *
42674349 AAGCCAGTGTAAGAC-ACGTCTGGGACAT-GCATAGGC-TACGAGATGATAGTC-AGTGTAAAAC
1 GAGCCAGTGTAAGACAACGTCTGGGACATGGCATAGGCAT-CGAGACGA-AGGCTAGTGTAAAA-
* *
42674410 CATGTCTGGGACATAGCATC-AACTTGAGATAT
63 CATGTCTGGGACAT-GCATCGAACTCGAGACAT
* *** * *
42674442 GAGCCAGTATAAGACCGTGTCTAGGACATGGCATCGGCA
1 GAGCCAGTGTAAGACAACGTCTGGGACATGGCATAGGCA
42674481 CCTTAACCTA
Statistics
Matches: 107, Mismatches: 18, Indels: 12
0.78 0.13 0.09
Matches are distributed among these distances:
91 1 0.01
92 21 0.20
93 49 0.46
94 29 0.27
95 7 0.07
ACGTcount: A:0.30, C:0.20, G:0.30, T:0.21
Consensus pattern (94 bp):
GAGCCAGTGTAAGACAACGTCTGGGACATGGCATAGGCATCGAGACGAAGGCTAGTGTAAAACAT
GTCTGGGACATGCATCGAACTCGAGACAT
Found at i:42674469 original size:140 final size:141
Alignment explanation
Indices: 42674214--42674477 Score: 311
Period size: 140 Copynumber: 1.9 Consensus size: 141
42674204 AGTGTGAGCT
* * * * *
42674214 AGTGTAAGACATGTTTGGGACATGCATCGGCCACATTATGAGAGCCAGTGTAAGACAATGTCTGG
1 AGTGTAAGACACGTCTGGGACATGCATAGGCCACATGATGAGAGCCAGTGTAAAACAATGTCTGG
* ** * * * *
42674279 GACATGGCATCGGCATTGAGACGAGGGCTAGTGTAAGACATGTCTGGGACAT-GCATCGACCTCG
66 GACATAGCATCAACATTGAGACGAGAGCCAGTATAAGACATGTCTAGGACATGGCATCGACCTCG
42674343 AGACGTAAGCC
131 AGACGTAAGCC
* * * *
42674354 AGTGTAAGACACGTCTGGGACATGCATAGGCTACGA-GATGATAGTCAGTGTAAAACCATGTCTG
1 AGTGTAAGACACGTCTGGGACATGCATAGGCCAC-ATGATGAGAGCCAGTGTAAAACAATGTCTG
* *
42674418 GGACATAGCATCAAC-TTGAGA-TATGAGCCAGTATAAGACCGTGTCTAGGACATGGCATCG
65 GGACATAGCATCAACATTGAGACGA-GAGCCAGTATAAGA-CATGTCTAGGACATGGCATCG
42674478 GCACCTTAAC
Statistics
Matches: 102, Mismatches: 18, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
138 1 0.01
139 17 0.17
140 77 0.75
141 7 0.07
ACGTcount: A:0.30, C:0.19, G:0.29, T:0.22
Consensus pattern (141 bp):
AGTGTAAGACACGTCTGGGACATGCATAGGCCACATGATGAGAGCCAGTGTAAAACAATGTCTGG
GACATAGCATCAACATTGAGACGAGAGCCAGTATAAGACATGTCTAGGACATGGCATCGACCTCG
AGACGTAAGCC
Found at i:42675355 original size:42 final size:42
Alignment explanation
Indices: 42675309--42675410 Score: 186
Period size: 42 Copynumber: 2.4 Consensus size: 42
42675299 GACACAGCCA
*
42675309 TGTGTCTCAGCCGTGTGAAGGGCACGGCCTAGCACACGGGTG
1 TGTGTCTTAGCCGTGTGAAGGGCACGGCCTAGCACACGGGTG
42675351 TGTGTCTTAGCCGTGTGAAGGGCACGGCCTAGCACACGGGTG
1 TGTGTCTTAGCCGTGTGAAGGGCACGGCCTAGCACACGGGTG
*
42675393 TGTGTCTTGGCCGTGTGA
1 TGTGTCTTAGCCGTGTGA
42675411 CATTTTGGGG
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 58 1.00
ACGTcount: A:0.15, C:0.24, G:0.38, T:0.24
Consensus pattern (42 bp):
TGTGTCTTAGCCGTGTGAAGGGCACGGCCTAGCACACGGGTG
Found at i:42678374 original size:20 final size:20
Alignment explanation
Indices: 42678341--42678381 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
42678331 AGCACATGTA
42678341 TTCATAAAAATTCAAAATTT
1 TTCATAAAAATTCAAAATTT
* * *
42678361 TTCATCAAATTTCACAATTT
1 TTCATAAAAATTCAAAATTT
42678381 T
1 T
42678382 ACATTTTAGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.41, C:0.15, G:0.00, T:0.44
Consensus pattern (20 bp):
TTCATAAAAATTCAAAATTT
Found at i:42680079 original size:32 final size:32
Alignment explanation
Indices: 42680038--42680101 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
42680028 ATCCGAGTCA
42680038 GAAAAATTATTTTAAAATTAATGCATGATTTG
1 GAAAAATTATTTTAAAATTAATGCATGATTTG
*
42680070 GAAAAATTATTTTAAAATTAATGCATGGTTTG
1 GAAAAATTATTTTAAAATTAATGCATGATTTG
42680102 CATTATTATA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.42, C:0.03, G:0.14, T:0.41
Consensus pattern (32 bp):
GAAAAATTATTTTAAAATTAATGCATGATTTG
Found at i:42686497 original size:25 final size:25
Alignment explanation
Indices: 42686468--42686517 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
42686458 TTGTAACACA
42686468 TCTTATTATATAATTATCTATATTG
1 TCTTATTATATAATTATCTATATTG
42686493 TCTTATTATATAATTATCTATATTG
1 TCTTATTATATAATTATCTATATTG
42686518 AGGAATTATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.32, C:0.08, G:0.04, T:0.56
Consensus pattern (25 bp):
TCTTATTATATAATTATCTATATTG
Found at i:42686525 original size:25 final size:25
Alignment explanation
Indices: 42686472--42686528 Score: 78
Period size: 25 Copynumber: 2.3 Consensus size: 25
42686462 AACACATCTT
* **
42686472 ATTATATAATTATCTATATTGTCTT
1 ATTATATAATTATCTATATTGACGA
*
42686497 ATTATATAATTATCTATATTGAGGA
1 ATTATATAATTATCTATATTGACGA
42686522 ATTATAT
1 ATTATAT
42686529 TTAATTCTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.37, C:0.05, G:0.07, T:0.51
Consensus pattern (25 bp):
ATTATATAATTATCTATATTGACGA
Found at i:42692149 original size:12 final size:12
Alignment explanation
Indices: 42692132--42692161 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
42692122 ACTAAAAAAA
42692132 TTTTATTTTAAT
1 TTTTATTTTAAT
42692144 TTTTATTTTAAT
1 TTTTATTTTAAT
42692156 TTTTAT
1 TTTTAT
42692162 CTTTTAAGTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (12 bp):
TTTTATTTTAAT
Found at i:42692185 original size:19 final size:19
Alignment explanation
Indices: 42692163--42692206 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 19
42692153 AATTTTTATC
42692163 TTTTAAGTCCTTAAATTCGTT
1 TTTTAA-TCCTTAAATTCG-T
*
42692184 TTTTTATCCTTAAATTCGT
1 TTTTAATCCTTAAATTCGT
42692203 TTTT
1 TTTT
42692207 TTATCACATG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 5 0.23
20 12 0.55
21 5 0.23
ACGTcount: A:0.20, C:0.14, G:0.07, T:0.59
Consensus pattern (19 bp):
TTTTAATCCTTAAATTCGT
Found at i:42692208 original size:21 final size:20
Alignment explanation
Indices: 42692170--42692211 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
42692160 ATCTTTTAAG
42692170 TCCTTAAATTCGTTTTTTTA
1 TCCTTAAATTCGTTTTTTTA
42692190 TCCTTAAATTCGTTTTTTTA
1 TCCTTAAATTCGTTTTTTTA
42692210 TC
1 TC
42692212 ACATGATTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.19, C:0.17, G:0.05, T:0.60
Consensus pattern (20 bp):
TCCTTAAATTCGTTTTTTTA
Found at i:42696621 original size:15 final size:15
Alignment explanation
Indices: 42696601--42696661 Score: 77
Period size: 15 Copynumber: 4.1 Consensus size: 15
42696591 TTAAATTAAG
*
42696601 TACTTAAATTTTCAA
1 TACTTAATTTTTCAA
42696616 TACTTAATTTTTCAA
1 TACTTAATTTTTCAA
* * *
42696631 CACTTATTTTTTTAA
1 TACTTAATTTTTCAA
*
42696646 TACTTACTTTTTCAA
1 TACTTAATTTTTCAA
42696661 T
1 T
42696662 TTATCAAACA
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 39 1.00
ACGTcount: A:0.31, C:0.15, G:0.00, T:0.54
Consensus pattern (15 bp):
TACTTAATTTTTCAA
Found at i:42710509 original size:4 final size:4
Alignment explanation
Indices: 42710500--42710544 Score: 54
Period size: 4 Copynumber: 10.5 Consensus size: 4
42710490 ATATTAGGGT
*
42710500 AATA AATA AATA GATA TAATA AGATAA AATA AATA AATA AATA AA
1 AATA AATA AATA AATA -AATA A-AT-A AATA AATA AATA AATA AA
42710545 ATATGTTAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
4 27 0.75
5 7 0.19
6 2 0.06
ACGTcount: A:0.71, C:0.00, G:0.04, T:0.24
Consensus pattern (4 bp):
AATA
Found at i:42710966 original size:37 final size:37
Alignment explanation
Indices: 42710916--42710989 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
42710906 AATCATAAAG
42710916 GACTAAATTAAAATGCAATGCAAAAGCTTAAGGACTC
1 GACTAAATTAAAATGCAATGCAAAAGCTTAAGGACTC
42710953 GACTAAATTAAAATGCAATGCAAAAGCTTAAGGACTC
1 GACTAAATTAAAATGCAATGCAAAAGCTTAAGGACTC
42710990 CGAGGACAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.46, C:0.16, G:0.16, T:0.22
Consensus pattern (37 bp):
GACTAAATTAAAATGCAATGCAAAAGCTTAAGGACTC
Found at i:42711396 original size:10 final size:10
Alignment explanation
Indices: 42711378--42711410 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
42711368 GGCTATAGGG
*
42711378 CCACTGTGGT
1 CCACCGTGGT
42711388 CCACCGTGGT
1 CCACCGTGGT
42711398 CCACCGTGG-
1 CCACCGTGGT
42711407 CCAC
1 CCAC
42711411 TATTCATTGG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 4 0.18
10 18 0.82
ACGTcount: A:0.12, C:0.42, G:0.27, T:0.18
Consensus pattern (10 bp):
CCACCGTGGT
Found at i:42712675 original size:44 final size:44
Alignment explanation
Indices: 42712474--42712814 Score: 260
Period size: 44 Copynumber: 7.6 Consensus size: 44
42712464 TCATTCTACA
* * * * *
42712474 CCACTACAACTTTAGGG-GCATAGGATTAGTAGC-TTCATCTTGTT
1 CCACTGCAACTTTAGGGAG-ATAAGATTTGTAGCTTTAATC-TGCT
* * *
42712518 CCACTGCAACTTTAGGGAGATAAGACTTATAGCTTCAATCTGCT
1 CCACTGCAACTTTAGGGAGATAAGATTTGTAGCTTTAATCTGCT
* * *
42712562 CCACTGCAACTTCACGGAGATAAGATTTATAGCTTTAATCTGCT
1 CCACTGCAACTTTAGGGAGATAAGATTTGTAGCTTTAATCTGCT
* * * *
42712606 CCACTACAA-TTTCAGGAAGATAAGATTTGTAGCTTTAATTTGTT
1 CCACTGCAACTTT-AGGGAGATAAGATTTGTAGCTTTAATCTGCT
*
42712650 CCACTGCAACTTTAGGGAGATAAGATTTGCTATGGTAGATTCAATCTGC-
1 CCACTGCAACTTTAGGGAGATAAGATTTG-TA-GCT---TT-AATCTGCT
* * * * * ** * * *
42712699 CTTACTACGACTTCAAGGGTG-TTGGATCTGTAGCTTAAATCTTCT
1 C-CACTGCAACTT-TAGGGAGATAAGATTTGTAGCTTTAATCTGCT
* * * *
42712744 CCACTGAAACTTCAAGGAGATAAAATTTGTAGCTTTAATCTGCT
1 CCACTGCAACTTTAGGGAGATAAGATTTGTAGCTTTAATCTGCT
* *
42712788 CCACTACAACTTCAGGGAGATAAGATT
1 CCACTGCAACTTTAGGGAGATAAGATT
42712815 CGCTATGGTA
Statistics
Matches: 231, Mismatches: 52, Indels: 28
0.74 0.17 0.09
Matches are distributed among these distances:
43 6 0.03
44 180 0.78
45 12 0.05
46 2 0.01
48 2 0.01
49 5 0.02
50 19 0.08
51 5 0.02
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Consensus pattern (44 bp):
CCACTGCAACTTTAGGGAGATAAGATTTGTAGCTTTAATCTGCT
Found at i:42720291 original size:10 final size:9
Alignment explanation
Indices: 42720266--42720314 Score: 50
Period size: 8 Copynumber: 5.6 Consensus size: 9
42720256 ATATTAGGGT
42720266 AATAA-ATA
1 AATAAGATA
42720274 AA-AAGATA
1 AATAAGATA
42720282 GAATAAGATAA
1 -AATAAGAT-A
*
42720293 AATAAAATA
1 AATAAGATA
42720302 AATAA-ATA
1 AATAAGATA
42720310 AATAA
1 AATAA
42720315 ACAAAAAAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
7 2 0.06
8 13 0.36
9 8 0.22
10 12 0.33
11 1 0.03
ACGTcount: A:0.73, C:0.00, G:0.06, T:0.20
Consensus pattern (9 bp):
AATAAGATA
Found at i:42720295 original size:23 final size:22
Alignment explanation
Indices: 42720269--42720315 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
42720259 TTAGGGTAAT
*
42720269 AAATAAAA-AGATAGAATAAGATA
1 AAATAAAATAAATA-AATAA-ATA
42720292 AAATAAAATAAATAAATAAATA
1 AAATAAAATAAATAAATAAATA
42720314 AA
1 AA
42720316 CAAAAAAAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 5 0.23
23 13 0.59
24 4 0.18
ACGTcount: A:0.74, C:0.00, G:0.06, T:0.19
Consensus pattern (22 bp):
AAATAAAATAAATAAATAAATA
Found at i:42724028 original size:20 final size:19
Alignment explanation
Indices: 42724000--42724109 Score: 68
Period size: 19 Copynumber: 5.7 Consensus size: 19
42723990 TATTATATTT
*
42724000 TTTTTATAATTCTTTATAAA
1 TTTTAATAATT-TTTATAAA
*
42724020 TTTTAATAATTTGTATGGAAA
1 TTTTAATAATTTTTAT--AAA
*
42724041 TGTTTTAATAA-TTTT-TAGA
1 --TTTTAATAATTTTTATAAA
* * *
42724060 TTCTT-TTAA-TATTATATA
1 TT-TTAATAATTTTTATAAA
42724078 TTTT-ATAATTCTTTATAAA
1 TTTTAATAATT-TTTATAAA
42724097 TTTTAATAATTTT
1 TTTTAATAATTTT
42724110 ATGGAAACGT
Statistics
Matches: 71, Mismatches: 10, Indels: 19
0.71 0.10 0.19
Matches are distributed among these distances:
17 13 0.18
18 8 0.11
19 18 0.25
20 16 0.23
21 4 0.06
22 3 0.04
23 9 0.13
ACGTcount: A:0.35, C:0.03, G:0.05, T:0.58
Consensus pattern (19 bp):
TTTTAATAATTTTTATAAA
Found at i:42724096 original size:77 final size:77
Alignment explanation
Indices: 42723972--42724121 Score: 257
Period size: 77 Copynumber: 1.9 Consensus size: 77
42723962 GAAACTTTAG
*
42723972 ATTTTTAGATTCTTTTAATATTATATTTTTTTTATAATTCTTTATAAATTTTAATAATTTGTATG
1 ATTTTTAGATTCTTTTAATATTATA-TTATTTTATAATTCTTTATAAATTTTAATAATTT-TATG
*
42724037 GAAATGTTTTAATA
64 GAAACGTTTTAATA
42724051 ATTTTTAGATTCTTTTAATATTATA-TATTTTATAATTCTTTATAAATTTTAATAATTTTATGGA
1 ATTTTTAGATTCTTTTAATATTATATTATTTTATAATTCTTTATAAATTTTAATAATTTTATGGA
42724115 AACGTTT
66 AACGTTT
42724122 GTTAATATTG
Statistics
Matches: 69, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
76 12 0.17
77 32 0.46
79 25 0.36
ACGTcount: A:0.33, C:0.03, G:0.06, T:0.57
Consensus pattern (77 bp):
ATTTTTAGATTCTTTTAATATTATATTATTTTATAATTCTTTATAAATTTTAATAATTTTATGGA
AACGTTTTAATA
Found at i:42726390 original size:108 final size:108
Alignment explanation
Indices: 42726170--42726378 Score: 278
Period size: 110 Copynumber: 1.9 Consensus size: 108
42726160 TTAAAAACTC
* * * *
42726170 TTTTATTTATATAAATAAAATAATAAATATGTAATTATATAATGAAAATATATTTTATATATTTC
1 TTTTACTTATATAAACAAAATAATAAATATGTAATTATATAATGAAAATATATATTATATATATC
** *
42726235 ATTATGTTAAAAATATATTTTCTAATTCATTCAAAAAAATGTT
66 ATTATGTTAAAAATATATTTTCTAAGACAATCAAAAAAATGTT
*
42726278 TTTTACTTATATAAACAAAATAATAAATATGTAGTTATATATAT-ATATAATATATATTATATAT
1 TTTTACTTATATAAACAAAATAATAAATATGTAATTATATA-ATGA-A-AATATATATTATATAT
* *
42726342 ATCATTATGTTAAAAATAT-TTTTTTGAAGAGAATCAA
63 ATCATTATGTTAAAAATATATTTTCT-AAGACAATCAA
42726379 CTAATTTTTT
Statistics
Matches: 87, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
108 39 0.45
109 8 0.09
110 40 0.46
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.45
Consensus pattern (108 bp):
TTTTACTTATATAAACAAAATAATAAATATGTAATTATATAATGAAAATATATATTATATATATC
ATTATGTTAAAAATATATTTTCTAAGACAATCAAAAAAATGTT
Found at i:42726838 original size:106 final size:104
Alignment explanation
Indices: 42726583--42726838 Score: 221
Period size: 106 Copynumber: 2.4 Consensus size: 104
42726573 ATATGGATTG
**
42726583 AAAATAAATATTACACATGTAAAAATTATATTTACTAAAAATAATGATATTTGAAATAATTATTT
1 AAAATAAATATTTGACATGTAAAAATTATA-TTA-T--AAATAATGATATTTGAAATAATTATTT
* * * *** * *
42726648 TATTTTATACTATTAGAATTTATTGTACCCACAATTCAAGTGA
62 TATTTTATAATATTAGAAATCACAATACCAAAAATTCAAGTGA
* * * ** * * *
42726691 AAAACAATGATGTTTGAAATGTTTTACA-TATA-AAAATAATAATGATATTTGAAATAATTATTT
1 AAAATAA--ATATTTGACATG-TAAAAATTATATTATA-AATAATGATATTTGAAATAATTATTT
*
42726754 TATTTTATAATATTAGAAATCACAATACCAAAAATGT-AGGTGGA
62 TATTTTATAATATTAGAAATCACAATACCAAAAAT-TCAAGT-GA
42726798 TAAAATAAATATTTGACATGTAAAAATTATATTATAAATAA
1 -AAAATAAATATTTGACATGTAAAAATTATATTATAAATAA
42726839 AAATATATAA
Statistics
Matches: 112, Mismatches: 27, Indels: 20
0.70 0.17 0.13
Matches are distributed among these distances:
105 4 0.04
106 75 0.67
107 5 0.04
108 13 0.12
110 12 0.11
111 3 0.03
ACGTcount: A:0.48, C:0.06, G:0.08, T:0.38
Consensus pattern (104 bp):
AAAATAAATATTTGACATGTAAAAATTATATTATAAATAATGATATTTGAAATAATTATTTTATT
TTATAATATTAGAAATCACAATACCAAAAATTCAAGTGA
Found at i:42730633 original size:17 final size:17
Alignment explanation
Indices: 42730608--42730648 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
42730598 TTACAATTTT
*
42730608 TTTTCTTTTTTGCTTGC
1 TTTTGTTTTTTGCTTGC
*
42730625 TTTTGTTTTTTGTTTGC
1 TTTTGTTTTTTGCTTGC
*
42730642 TATTGTT
1 TTTTGTT
42730649 CTTGCTGCCT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.02, C:0.10, G:0.15, T:0.73
Consensus pattern (17 bp):
TTTTGTTTTTTGCTTGC
Found at i:42731310 original size:45 final size:45
Alignment explanation
Indices: 42731242--42731390 Score: 167
Period size: 45 Copynumber: 3.3 Consensus size: 45
42731232 TTAATATGCC
* * * *
42731242 CCACTGTAACTTCAGAGAAATAAGATTTGCTATCTTCAATCTACT
1 CCACTGCAACTTCAGAGAGATAAGATTTGATATCTTCAATCTGCT
* * *
42731287 CCACTGCACCTTCAGAGAGATAAGGTTT-ATAGT-TTTAATCTGCT
1 CCACTGCAACTTCAGAGAGATAAGATTTGATA-TCTTCAATCTGCT
* * * *
42731331 CTACTGCAACTTCAGAGAGATAAGATTTGGTTTCTTCAGTCTGCT
1 CCACTGCAACTTCAGAGAGATAAGATTTGATATCTTCAATCTGCT
*
42731376 CTACTGCAACTTCAG
1 CCACTGCAACTTCAG
42731391 GGAGGTAAAA
Statistics
Matches: 87, Mismatches: 14, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
44 37 0.43
45 50 0.57
ACGTcount: A:0.28, C:0.22, G:0.16, T:0.34
Consensus pattern (45 bp):
CCACTGCAACTTCAGAGAGATAAGATTTGATATCTTCAATCTGCT
Found at i:42731344 original size:44 final size:44
Alignment explanation
Indices: 42731224--42731354 Score: 138
Period size: 44 Copynumber: 3.0 Consensus size: 44
42731214 GATTTGTGAC
* * * * * *
42731224 TTATAGCTTTAATATGCCCCACTGTAACTTCAGAGAAATAAGAT
1 TTATAGTTTTAATCTGCTCCACTGCAACTTCAGAGAGATAAGGT
* * * *
42731268 TTGCTA-TCTTCAATCTACTCCACTGCACCTTCAGAGAGATAAGGT
1 TT-ATAGT-TTTAATCTGCTCCACTGCAACTTCAGAGAGATAAGGT
*
42731313 TTATAGTTTTAATCTGCTCTACTGCAACTTCAGAGAGATAAG
1 TTATAGTTTTAATCTGCTCCACTGCAACTTCAGAGAGATAAG
42731355 ATTTGGTTTC
Statistics
Matches: 69, Mismatches: 15, Indels: 6
0.77 0.17 0.07
Matches are distributed among these distances:
44 35 0.51
45 34 0.49
ACGTcount: A:0.31, C:0.21, G:0.15, T:0.33
Consensus pattern (44 bp):
TTATAGTTTTAATCTGCTCCACTGCAACTTCAGAGAGATAAGGT
Found at i:42731354 original size:89 final size:89
Alignment explanation
Indices: 42731224--42731390 Score: 226
Period size: 89 Copynumber: 1.9 Consensus size: 89
42731214 GATTTGTGAC
*
42731224 TTATAGCTTTAATATGCCCCACTGTAACTTCAGAGAAATAAGATTTGCTATCTTCAATCTACTCC
1 TTATAGCTTTAATATGCCCCACTGCAACTTCAGAGAAATAAGATTTGCTATCTTCAATCTACTCC
*
42731289 ACTGCACCTTCAGAGAGATAAGGT
66 ACTGCAACTTCAGAGAGATAAGGT
* * * * * * * * * *
42731313 TTATAGTTTTAATCTGCTCTACTGCAACTTCAGAGAGATAAGATTTGGTTTCTTCAGTCTGCTCT
1 TTATAGCTTTAATATGCCCCACTGCAACTTCAGAGAAATAAGATTTGCTATCTTCAATCTACTCC
42731378 ACTGCAACTTCAG
66 ACTGCAACTTCAG
42731391 GGAGGTAAAA
Statistics
Matches: 66, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
89 66 1.00
ACGTcount: A:0.28, C:0.22, G:0.16, T:0.35
Consensus pattern (89 bp):
TTATAGCTTTAATATGCCCCACTGCAACTTCAGAGAAATAAGATTTGCTATCTTCAATCTACTCC
ACTGCAACTTCAGAGAGATAAGGT
Found at i:42731413 original size:89 final size:89
Alignment explanation
Indices: 42731222--42731416 Score: 219
Period size: 89 Copynumber: 2.2 Consensus size: 89
42731212 AGGATTTGTG
* *
42731222 ACTTATAGCTTTAATATGCCCCACTGTAACTTCAGAGAAATAAGATTTGCTATCTTCAATCTACT
1 ACTTATAGCTTTAATCTGCCCCACTGCAACTTCAGAGAAATAAGATTTGCTATCTTCAATCTACT
* *
42731287 CCACTGCACCTTCAGAGAGATAAG
66 CCACTGCAACTTCAGAGAGATAAA
** * * * * * * * *
42731311 GTTTATAGTTTTAATCTGCTCTACTGCAACTTCAGAGAGATAAGATTTGGTTTCTTCAGTCTGCT
1 ACTTATAGCTTTAATCTGCCCCACTGCAACTTCAGAGAAATAAGATTTGCTATCTTCAATCTACT
* * *
42731376 CTACTGCAACTTCAGGGAGGTAAA
66 CCACTGCAACTTCAGAGAGATAAA
* *
42731400 ACTTGTGGCTTTAATCT
1 ACTTATAGCTTTAATCT
42731417 ACTCCACTAA
Statistics
Matches: 84, Mismatches: 22, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
89 84 1.00
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.34
Consensus pattern (89 bp):
ACTTATAGCTTTAATCTGCCCCACTGCAACTTCAGAGAAATAAGATTTGCTATCTTCAATCTACT
CCACTGCAACTTCAGAGAGATAAA
Found at i:42742442 original size:20 final size:20
Alignment explanation
Indices: 42742419--42742480 Score: 65
Period size: 20 Copynumber: 3.1 Consensus size: 20
42742409 TCCAAATCAA
42742419 ATAACCATTTTCCATTTCAT
1 ATAACCATTTTCCATTTCAT
* *
42742439 ATAACAACTTGT-CATTTCAT
1 ATAACCA-TTTTCCATTTCAT
* *
42742459 ACATCCA-TTTCCATTTCAT
1 ATAACCATTTTCCATTTCAT
42742478 ATA
1 ATA
42742481 TTCGGTTTCT
Statistics
Matches: 33, Mismatches: 7, Indels: 5
0.73 0.16 0.11
Matches are distributed among these distances:
18 2 0.06
19 10 0.30
20 18 0.55
21 3 0.09
ACGTcount: A:0.32, C:0.24, G:0.02, T:0.42
Consensus pattern (20 bp):
ATAACCATTTTCCATTTCAT
Found at i:42751702 original size:15 final size:15
Alignment explanation
Indices: 42751682--42751716 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
42751672 GTGGTCTCAA
*
42751682 ACCACCGTTTTCGAC
1 ACCACCATTTTCGAC
*
42751697 ACCACCATTTTTGAC
1 ACCACCATTTTCGAC
42751712 ACCAC
1 ACCAC
42751717 TAAAAAATAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.26, C:0.40, G:0.09, T:0.26
Consensus pattern (15 bp):
ACCACCATTTTCGAC
Found at i:42753193 original size:20 final size:20
Alignment explanation
Indices: 42753170--42753217 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
42753160 AAATCCAAAT
42753170 TAAAATACTAAAATTCAGGA
1 TAAAATACTAAAATTCAGGA
*
42753190 TAAAATCCTAAAATTCAGGA
1 TAAAATACTAAAATTCAGGA
42753210 TAAGAATA
1 TAA-AATA
42753218 TTGATGTGGT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 22 0.88
21 3 0.12
ACGTcount: A:0.54, C:0.10, G:0.10, T:0.25
Consensus pattern (20 bp):
TAAAATACTAAAATTCAGGA
Found at i:42754029 original size:20 final size:18
Alignment explanation
Indices: 42754000--42754050 Score: 57
Period size: 19 Copynumber: 2.7 Consensus size: 18
42753990 TATTTTGTAT
42754000 TTAATTTTAATTAATGTGA
1 TTAATTTTAATTAAT-TGA
* *
42754019 TTAATTTTTAAATACTTGA
1 TTAA-TTTTAATTAATTGA
42754038 TATAATTTTAATT
1 T-TAATTTTAATT
42754051 TATGACACAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 15 0.56
20 12 0.44
ACGTcount: A:0.37, C:0.02, G:0.06, T:0.55
Consensus pattern (18 bp):
TTAATTTTAATTAATTGA
Found at i:42755746 original size:59 final size:60
Alignment explanation
Indices: 42755661--42755787 Score: 143
Period size: 59 Copynumber: 2.1 Consensus size: 60
42755651 CCTAAATATA
* * * * *
42755661 AAAAAATTCAATAAATTTAGCACTCAATATTTTA-AAAAAAT-TCATTTAGTTATAATTCT
1 AAAAATTTCAATAAATTTAGCACTCAACA-TTTACAAAAAATGTCAATTAGTCATAACTCT
* * *
42755720 AAAAATTTCAATAAATTT-GACCCTCAACATTTACAAAATATGTCAATTAGTCCTAACTCT
1 AAAAATTTCAATAAATTTAG-CACTCAACATTTACAAAAAATGTCAATTAGTCATAACTCT
42755780 AAAAATTT
1 AAAAATTT
42755788 AAAAGAGAAT
Statistics
Matches: 57, Mismatches: 8, Indels: 5
0.81 0.11 0.07
Matches are distributed among these distances:
58 5 0.09
59 30 0.53
60 22 0.39
ACGTcount: A:0.46, C:0.14, G:0.04, T:0.36
Consensus pattern (60 bp):
AAAAATTTCAATAAATTTAGCACTCAACATTTACAAAAAATGTCAATTAGTCATAACTCT
Found at i:42756220 original size:61 final size:61
Alignment explanation
Indices: 42756107--42756221 Score: 149
Period size: 61 Copynumber: 1.9 Consensus size: 61
42756097 TTTTAAAAAA
* * * ** * *
42756107 TTTTTAGAGTTAGGACTAAATTGACAAATTTTGTAAATGTTGATGGCCAAATTTATTAAAC
1 TTTTTAGAATTAGAACTAAAATGACAAATTTTGTAAACATTAAGGGCCAAATTTATTAAAC
* *
42756168 TTTTTAGAATTAGAACTAAAATGACAATTTTTGTAAACATTAAGGGCTAAATTT
1 TTTTTAGAATTAGAACTAAAATGACAAATTTTGTAAACATTAAGGGCCAAATTT
42756222 GTTGAATTTT
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
61 45 1.00
ACGTcount: A:0.38, C:0.08, G:0.15, T:0.39
Consensus pattern (61 bp):
TTTTTAGAATTAGAACTAAAATGACAAATTTTGTAAACATTAAGGGCCAAATTTATTAAAC
Found at i:42757869 original size:22 final size:22
Alignment explanation
Indices: 42757844--42757888 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
42757834 TGTTTAATTA
42757844 TTTTTATTT-AATTAATTATATG
1 TTTTTATTTCAATTAATTA-ATG
*
42757866 TTTTTATTTCATTTAATTAATG
1 TTTTTATTTCAATTAATTAATG
42757888 T
1 T
42757889 GAATATTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 13 0.62
23 8 0.38
ACGTcount: A:0.29, C:0.02, G:0.04, T:0.64
Consensus pattern (22 bp):
TTTTTATTTCAATTAATTAATG
Found at i:42757881 original size:27 final size:28
Alignment explanation
Indices: 42757849--42757903 Score: 78
Period size: 27 Copynumber: 2.0 Consensus size: 28
42757839 AATTATTTTT
42757849 ATTTAATTAAT-T-ATATGTTTTTATTTC
1 ATTTAATTAATGTAATAT-TTTTTATTTC
42757876 ATTTAATTAATGTGAATATTTTTTATTT
1 ATTTAATTAATGT-AATATTTTTTATTT
42757904 AAATATACAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
27 11 0.44
28 1 0.04
29 9 0.36
30 4 0.16
ACGTcount: A:0.31, C:0.02, G:0.05, T:0.62
Consensus pattern (28 bp):
ATTTAATTAATGTAATATTTTTTATTTC
Found at i:42759790 original size:27 final size:26
Alignment explanation
Indices: 42759760--42759885 Score: 135
Period size: 27 Copynumber: 4.7 Consensus size: 26
42759750 AAATTGTACA
42759760 GCACTAAGTGTGCGATTCGACTATGTT
1 GCACTAAGTGTGCGATT-GACTATGTT
* * *
42759787 GCACTAAGTGTGCGAAATGAATATGAT
1 GCACTAAGTGTGCG-ATTGACTATGTT
* **
42759814 GCACTAAGTGTGCGAATTGACCATGCG
1 GCACTAAGTGTGCG-ATTGACTATGTT
* *
42759841 GCACTAAGTGTGCGAGTCTAACTATGTA
1 GCACTAAGTGTGCGA-T-TGACTATGTT
42759869 GCACTAAGTGTGCGATT
1 GCACTAAGTGTGCGATT
42759886 TGATTGTATA
Statistics
Matches: 84, Mismatches: 12, Indels: 7
0.82 0.12 0.07
Matches are distributed among these distances:
26 2 0.02
27 59 0.70
28 23 0.27
ACGTcount: A:0.28, C:0.17, G:0.27, T:0.28
Consensus pattern (26 bp):
GCACTAAGTGTGCGATTGACTATGTT
Found at i:42759824 original size:54 final size:54
Alignment explanation
Indices: 42759759--42759885 Score: 152
Period size: 54 Copynumber: 2.3 Consensus size: 54
42759749 TAAATTGTAC
* **
42759759 AGCACTAAGTGTGCGATTCGACTATGTTGCACTAAGTGTGCGAAAT-GAA-TATG-
1 AGCACTAAGTGTGCGATT-GACCATGCGGCACTAAGTGTGCG-AATCGAACTATGT
* *
42759812 ATGCACTAAGTGTGCGAATTGACCATGCGGCACTAAGTGTGCGAGTCTAACTATGT
1 A-GCACTAAGTGTGCG-ATTGACCATGCGGCACTAAGTGTGCGAATCGAACTATGT
42759868 AGCACTAAGTGTGCGATT
1 AGCACTAAGTGTGCGATT
42759886 TGATTGTATA
Statistics
Matches: 64, Mismatches: 5, Indels: 9
0.82 0.06 0.12
Matches are distributed among these distances:
53 3 0.05
54 39 0.61
55 21 0.33
56 1 0.02
ACGTcount: A:0.28, C:0.17, G:0.27, T:0.28
Consensus pattern (54 bp):
AGCACTAAGTGTGCGATTGACCATGCGGCACTAAGTGTGCGAATCGAACTATGT
Found at i:42767388 original size:27 final size:26
Alignment explanation
Indices: 42767358--42767483 Score: 135
Period size: 27 Copynumber: 4.7 Consensus size: 26
42767348 AAATTGTACA
42767358 GCACTAAGTGTGCGATTCGACTATGTT
1 GCACTAAGTGTGCGATT-GACTATGTT
* * *
42767385 GCACTAAGTGTGCGAAATGAATATGAT
1 GCACTAAGTGTGCG-ATTGACTATGTT
* **
42767412 GCACTAAGTGTGCGAATTGACCATGCG
1 GCACTAAGTGTGCG-ATTGACTATGTT
* *
42767439 GCACTAAGTGTGCGAGTCTAACTATGTA
1 GCACTAAGTGTGCGA-T-TGACTATGTT
42767467 GCACTAAGTGTGCGATT
1 GCACTAAGTGTGCGATT
42767484 TGATTGTATA
Statistics
Matches: 84, Mismatches: 12, Indels: 7
0.82 0.12 0.07
Matches are distributed among these distances:
26 2 0.02
27 59 0.70
28 23 0.27
ACGTcount: A:0.28, C:0.17, G:0.27, T:0.28
Consensus pattern (26 bp):
GCACTAAGTGTGCGATTGACTATGTT
Found at i:42767422 original size:54 final size:54
Alignment explanation
Indices: 42767357--42767483 Score: 152
Period size: 54 Copynumber: 2.3 Consensus size: 54
42767347 TAAATTGTAC
* **
42767357 AGCACTAAGTGTGCGATTCGACTATGTTGCACTAAGTGTGCGAAAT-GAA-TATG-
1 AGCACTAAGTGTGCGATT-GACCATGCGGCACTAAGTGTGCG-AATCGAACTATGT
* *
42767410 ATGCACTAAGTGTGCGAATTGACCATGCGGCACTAAGTGTGCGAGTCTAACTATGT
1 A-GCACTAAGTGTGCG-ATTGACCATGCGGCACTAAGTGTGCGAATCGAACTATGT
42767466 AGCACTAAGTGTGCGATT
1 AGCACTAAGTGTGCGATT
42767484 TGATTGTATA
Statistics
Matches: 64, Mismatches: 5, Indels: 9
0.82 0.06 0.12
Matches are distributed among these distances:
53 3 0.05
54 39 0.61
55 21 0.33
56 1 0.02
ACGTcount: A:0.28, C:0.17, G:0.27, T:0.28
Consensus pattern (54 bp):
AGCACTAAGTGTGCGATTGACCATGCGGCACTAAGTGTGCGAATCGAACTATGT
Found at i:42776468 original size:16 final size:17
Alignment explanation
Indices: 42776436--42776469 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
42776426 TATATACTTA
42776436 TAATAAATATATAAAAT
1 TAATAAATATATAAAAT
*
42776453 TAATAATTAT-TAAAAT
1 TAATAAATATATAAAAT
42776469 T
1 T
42776470 TGAACCTATG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
TAATAAATATATAAAAT
Found at i:42778018 original size:24 final size:26
Alignment explanation
Indices: 42777963--42778020 Score: 68
Period size: 24 Copynumber: 2.3 Consensus size: 26
42777953 GTTGTCTTTG
* *
42777963 TATAAAAGTAAAATGATTTATTACAT
1 TATAAAATTAAAATGATTTATTAAAT
*
42777989 T-CAAAATTAAAAT-ATTTA-TAAAT
1 TATAAAATTAAAATGATTTATTAAAT
42778012 TATAAAATT
1 TATAAAATT
42778021 CAAACTTCTT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
23 5 0.19
24 11 0.41
25 10 0.37
26 1 0.04
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.40
Consensus pattern (26 bp):
TATAAAATTAAAATGATTTATTAAAT
Found at i:42790062 original size:221 final size:221
Alignment explanation
Indices: 42789679--42790344 Score: 1206
Period size: 221 Copynumber: 3.0 Consensus size: 221
42789669 CAACTAGCAG
* * *
42789679 TCTAGTATACAGATGGCACCTCACGAGGCACTGTATGGTTATAAGTGTCGCACTCCCTTATGCTA
1 TCTAGTATACAGATGGCACCTTACGAGGCACTGTATGGTTGTAAGTGTCGCACTCCCTTATGCTG
*
42789744 GACTGAGTTGGGTGAACGACGTATTCTGGGTATGGAGTTGGTTTTTGAGACTGAGGACAAGGTCC
66 GACTGAGTTGGGTGAACGACGTATTCTGGGTCTGGAGTTGGTTTTTGAGACTGAGGACAAGGTCC
*
42789809 TTTTGATTCGAGATCGGTTGAAAGCGGCTTCTGATAAGGAGAAGTCATATGCAGATTTGAAGCGT
131 TTTTGATTCGAGATCGGCTGAAAGCGGCTTCTGATAAGGAGAAGTCATATGCAGATTTGAAGCGT
42789874 CGAGAGATAGAATATTCCGTGAGAGA
196 CGAGAGATAGAATATTCCGTGAGAGA
42789900 TCTAGTATACAGATGGCACCTTACGAGGCACTGTATGGTTGTAAGTGTCGCACTCCCTTATGCTG
1 TCTAGTATACAGATGGCACCTTACGAGGCACTGTATGGTTGTAAGTGTCGCACTCCCTTATGCTG
42789965 GACTGAGTTGGGTGAACGACGTATTCTGGGTCTGGAGTTGGTTTTTGAGACTGAGGACAAGGTCC
66 GACTGAGTTGGGTGAACGACGTATTCTGGGTCTGGAGTTGGTTTTTGAGACTGAGGACAAGGTCC
* *
42790030 TTTTGATTCGAGATCGGCTGAAAGCAGCTTCTGATAAGGAGAAGTCATATACAGATTTGAAGCGT
131 TTTTGATTCGAGATCGGCTGAAAGCGGCTTCTGATAAGGAGAAGTCATATGCAGATTTGAAGCGT
*
42790095 CGAGAAATAGAATATTCCGTGAGAGA
196 CGAGAGATAGAATATTCCGTGAGAGA
42790121 TCTAGTATACAGATGGCACCTTACGAGGCACTGTATGGTTGTAAGTGTCGCACTCCCTTATGCTG
1 TCTAGTATACAGATGGCACCTTACGAGGCACTGTATGGTTGTAAGTGTCGCACTCCCTTATGCTG
* * *
42790186 GACTGAGTTGGGTGAACGACGTATTCTGGGTCTAGAGTTGGTTTCTGAGACTGAGGACAAGGTAC
66 GACTGAGTTGGGTGAACGACGTATTCTGGGTCTGGAGTTGGTTTTTGAGACTGAGGACAAGGTCC
*
42790251 TTTTGATTCGAGATCGGCTGAAAGCGGCTTCTGATAAGGAGAAGTCATATGCAGATCTGAAGCGT
131 TTTTGATTCGAGATCGGCTGAAAGCGGCTTCTGATAAGGAGAAGTCATATGCAGATTTGAAGCGT
* *
42790316 CGAGAGATAGAATATTCTGTGGGAGA
196 CGAGAGATAGAATATTCCGTGAGAGA
42790342 TCT
1 TCT
42790345 TGTTTTCCTT
Statistics
Matches: 428, Mismatches: 17, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
221 428 1.00
ACGTcount: A:0.26, C:0.16, G:0.29, T:0.29
Consensus pattern (221 bp):
TCTAGTATACAGATGGCACCTTACGAGGCACTGTATGGTTGTAAGTGTCGCACTCCCTTATGCTG
GACTGAGTTGGGTGAACGACGTATTCTGGGTCTGGAGTTGGTTTTTGAGACTGAGGACAAGGTCC
TTTTGATTCGAGATCGGCTGAAAGCGGCTTCTGATAAGGAGAAGTCATATGCAGATTTGAAGCGT
CGAGAGATAGAATATTCCGTGAGAGA
Found at i:42793589 original size:16 final size:17
Alignment explanation
Indices: 42793558--42793590 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
42793548 TTCATAACTG
42793558 TATATCAATCATTTCAT
1 TATATCAATCATTTCAT
42793575 TATATCAAT-ATTTCAT
1 TATATCAATCATTTCAT
42793591 GCTCCATCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.36, C:0.15, G:0.00, T:0.48
Consensus pattern (17 bp):
TATATCAATCATTTCAT
Found at i:42794011 original size:46 final size:46
Alignment explanation
Indices: 42793876--42794011 Score: 184
Period size: 46 Copynumber: 3.0 Consensus size: 46
42793866 TTTGACATGA
* * * * * * *
42793876 TGCCATAGTGTCTTTCAACTATGGTTTTACTCATTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCAGGT
42793922 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
*
42793968 TGCCATGGTATCTTTCAACCATAGTCTTACACATTTCATATCAG
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
42794012 AGAGCACACT
Statistics
Matches: 81, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
45 4 0.05
46 77 0.95
ACGTcount: A:0.23, C:0.23, G:0.14, T:0.40
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
Found at i:42797592 original size:22 final size:23
Alignment explanation
Indices: 42797557--42797611 Score: 67
Period size: 22 Copynumber: 2.4 Consensus size: 23
42797547 TAAAATATAT
* *
42797557 ATAAATATATAATAAAAAATTCA
1 ATAAAAATAAAATAAAAAATTCA
* *
42797580 A-AAAAATAAAATATATAATTCA
1 ATAAAAATAAAATAAAAAATTCA
42797602 ATAAAAATAA
1 ATAAAAATAA
42797612 TAATTTTCAG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
22 18 0.67
23 9 0.33
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.27
Consensus pattern (23 bp):
ATAAAAATAAAATAAAAAATTCA
Found at i:42797850 original size:28 final size:27
Alignment explanation
Indices: 42797819--42797887 Score: 68
Period size: 28 Copynumber: 2.5 Consensus size: 27
42797809 ATTTTTGAAT
* *
42797819 TTTTTAAAATTTTTTAACTTTTTTTTTA
1 TTTTTAAAATTTTGTAAC-TATTTTTTA
*
42797847 TTTTTGTAAA-TTTGTAACTATTTTTTA
1 TTTTT-AAAATTTTGTAACTATTTTTTA
*
42797874 TTGGTTAAAATTTT
1 TT-TTTAAAATTTT
42797888 AAAATATTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
27 13 0.39
28 17 0.52
29 3 0.09
ACGTcount: A:0.26, C:0.03, G:0.06, T:0.65
Consensus pattern (27 bp):
TTTTTAAAATTTTGTAACTATTTTTTA
Found at i:42797925 original size:18 final size:19
Alignment explanation
Indices: 42797882--42797929 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 19
42797872 TATTGGTTAA
42797882 AATTTTAAAATATTTTTTG
1 AATTTTAAAATATTTTTTG
* *
42797901 AAATTTAAACTATTTTTT-
1 AATTTTAAAATATTTTTTG
*
42797919 ATTTTTAAAAT
1 AATTTTAAAAT
42797930 TTGATTTATC
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
18 8 0.33
19 16 0.67
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (19 bp):
AATTTTAAAATATTTTTTG
Found at i:42812796 original size:6 final size:6
Alignment explanation
Indices: 42812786--42812823 Score: 67
Period size: 6 Copynumber: 6.3 Consensus size: 6
42812776 TAGAAAGGGT
*
42812786 GGAGAT GGAGAG GGAGAG GGAGAG GGAGAG GGAGAG GG
1 GGAGAG GGAGAG GGAGAG GGAGAG GGAGAG GGAGAG GG
42812824 GGAGTATATA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.66, T:0.03
Consensus pattern (6 bp):
GGAGAG
Found at i:42813219 original size:23 final size:23
Alignment explanation
Indices: 42813175--42813219 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
42813165 TTATATTTTA
*
42813175 ATAATTAATTAAATAAATTATTT
1 ATAATTAATTAAATAAAATATTT
*
42813198 ATAATTGATT-AATACAAATATT
1 ATAATTAATTAAATA-AAATATT
42813220 AGACTGACTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.44
Consensus pattern (23 bp):
ATAATTAATTAAATAAAATATTT
Found at i:42816628 original size:43 final size:42
Alignment explanation
Indices: 42816570--42816720 Score: 137
Period size: 43 Copynumber: 3.5 Consensus size: 42
42816560 CAATGCCAAC
**
42816570 GTCCCAGACTTGGTCTTACATGTAATCAAATATCGATGCCACT
1 GTCCCAGACAGGGTCTTACATGTAATCAAATATCGATGCCA-T
* * *
42816613 GTCCTAGACAGGGTCTTACATGAAATTAAATA-CGATGCCGAT
1 GTCCCAGACAGGGTCTTACATGTAATCAAATATCGATGCC-AT
* * * *
42816655 GTCCCAGACATGGTCTTACACGTAAATCATAA-GTCGATGCCAAC
1 GTCCCAGACAGGGTCTTACATGT-AATCA-AATATCGATGCC-AT
*
42816699 GTCCCAGA-TGCGGTCTTACATG
1 GTCCCAGACAG-GGTCTTACATG
42816721 AAAACACATA
Statistics
Matches: 87, Mismatches: 16, Indels: 9
0.78 0.14 0.08
Matches are distributed among these distances:
42 27 0.31
43 32 0.37
44 28 0.32
ACGTcount: A:0.29, C:0.25, G:0.20, T:0.26
Consensus pattern (42 bp):
GTCCCAGACAGGGTCTTACATGTAATCAAATATCGATGCCAT
Found at i:42820494 original size:49 final size:49
Alignment explanation
Indices: 42820416--42820631 Score: 187
Period size: 49 Copynumber: 4.5 Consensus size: 49
42820406 GATGCTGACA
*
42820416 CCATGTCCCAGACATAGTCTTACACTGGCTTTCATATAGCGAGGCCGATG
1 CCATGTCCCAGACA-GGTCTTACACTGGCTTTCATATAGCGAGGCCGATG
* * * *
42820466 CCATGTCCCAGACAGGTCTTACACTGGCTCTCATCTATCG-GTGTCGATG
1 CCATGTCCCAGACAGGTCTTACACTGGCTTTCATATAGCGAG-GCCGATG
* * * * **
42820515 CCATGTCCCAGACAGGTCTTACACT-G-ATACAGA-A-C-AAGCTAATG
1 CCATGTCCCAGACAGGTCTTACACTGGCTTTCATATAGCGAGGCCGATG
* * * *
42820559 CCATATCCCAGACAGGTTTTACACTAGCTTGT-ATATCGCGAGGCCGATG
1 CCATGTCCCAGACAGGTCTTACACTGGCTT-TCATATAGCGAGGCCGATG
* * *
42820608 -TATGTCCCAGACATGCCTTACACT
1 CCATGTCCCAGACAGGTCTTACACT
42820632 AGCTCTCGTC
Statistics
Matches: 130, Mismatches: 28, Indels: 18
0.74 0.16 0.10
Matches are distributed among these distances:
44 27 0.21
45 2 0.02
46 4 0.03
47 2 0.02
48 22 0.17
49 59 0.45
50 14 0.11
ACGTcount: A:0.25, C:0.29, G:0.20, T:0.26
Consensus pattern (49 bp):
CCATGTCCCAGACAGGTCTTACACTGGCTTTCATATAGCGAGGCCGATG
Found at i:42822677 original size:75 final size:75
Alignment explanation
Indices: 42822597--42822799 Score: 228
Period size: 75 Copynumber: 2.7 Consensus size: 75
42822587 TTTGCCCTTG
* * * *
42822597 CTAGTCAAATAAACCAACATATATAATGATATGCCCAGCATTAGTCAGATACACTGGCAAAAGTT
1 CTAGTCAAATAAACCAACAAATATAATGATGTGCCCAGCATTAGTCAGATAAACTGACAAAAGTT
42822662 GTG-CTCAGCA
66 GTGCCT-AGCA
* * * * * * *
42822672 CTAGTCAGATAAACCGATAAACATAATGATGTGCCCAACATTATTCAGATAAACTGACGAAAGTT
1 CTAGTCAAATAAACCAACAAATATAATGATGTGCCCAGCATTAGTCAGATAAACTGACAAAAGTT
*
42822737 GTGCCTAGCG
66 GTGCCTAGCA
** * * * *
42822747 CTAGTCGTATAAACCAACAGATATAATGATGTGCCTAGCACTAGTTAGATAAA
1 CTAGTCAAATAAACCAACAAATATAATGATGTGCCCAGCATTAGTCAGATAAA
42822800 TTAACGATAT
Statistics
Matches: 104, Mismatches: 23, Indels: 2
0.81 0.18 0.02
Matches are distributed among these distances:
75 102 0.98
76 2 0.02
ACGTcount: A:0.38, C:0.20, G:0.17, T:0.25
Consensus pattern (75 bp):
CTAGTCAAATAAACCAACAAATATAATGATGTGCCCAGCATTAGTCAGATAAACTGACAAAAGTT
GTGCCTAGCA
Found at i:42824411 original size:48 final size:48
Alignment explanation
Indices: 42824325--42824510 Score: 246
Period size: 48 Copynumber: 3.9 Consensus size: 48
42824315 CATTAGGGTT
42824325 ATATGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCG
1 ATATGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCG
* * * * *
42824373 ATATAAGATTCCATCTAAGACCATGTCTTGGACATGGCATTGGCATTG
1 ATATGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCG
* *
42824421 ATATGAGATCCCATGTAAGACCATATCTGGGATATGGCATTGGCATCG
1 ATATGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCG
* ** * * * *
42824469 ATATGTGATTTCGTGTAACACCATGTCTGGGACCTGACATTG
1 ATATGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTG
42824511 ATATGAGACA
Statistics
Matches: 117, Mismatches: 21, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
48 117 1.00
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.29
Consensus pattern (48 bp):
ATATGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCG
Found at i:42824492 original size:96 final size:96
Alignment explanation
Indices: 42824325--42824510 Score: 273
Period size: 96 Copynumber: 1.9 Consensus size: 96
42824315 CATTAGGGTT
*
42824325 ATATGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGATATAAGATTCCATCTA
1 ATATGAGATCCCATGTAAGACCATATCTGGGACATGGCATTGGCATCGATATAAGATTCCATCTA
* * *
42824390 AGACCATGTCTTGGACATGGCATTGGCATTG
66 ACACCATGTCTGGGACATGACATTGGCATTG
* ** * * *
42824421 ATATGAGATCCCATGTAAGACCATATCTGGGATATGGCATTGGCATCGATATGTGATTTCGTGTA
1 ATATGAGATCCCATGTAAGACCATATCTGGGACATGGCATTGGCATCGATATAAGATTCCATCTA
*
42824486 ACACCATGTCTGGGACCTGACATTG
66 ACACCATGTCTGGGACATGACATTG
42824511 ATATGAGACA
Statistics
Matches: 79, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
96 79 1.00
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.29
Consensus pattern (96 bp):
ATATGAGATCCCATGTAAGACCATATCTGGGACATGGCATTGGCATCGATATAAGATTCCATCTA
ACACCATGTCTGGGACATGACATTGGCATTG
Found at i:42827107 original size:32 final size:32
Alignment explanation
Indices: 42827046--42827134 Score: 83
Period size: 32 Copynumber: 2.8 Consensus size: 32
42827036 ACTAAGTGTG
**
42827046 TATATATGTGTAGTTGGATAAAGTTGAATGTC
1 TATATATGTGTAGTTGGATAAAGCCGAATGTC
*
42827078 TATATATGTGT-GATTGGATATAA-CCGAATGTG
1 TATATATGTGTAG-TTGGATA-AAGCCGAATGTC
* * * *
42827110 TATCTAGGTGTAGTTTGATATAGCC
1 TATATATGTGTAGTTGGATAAAGCC
42827135 TATTAAGATG
Statistics
Matches: 46, Mismatches: 7, Indels: 8
0.75 0.11 0.13
Matches are distributed among these distances:
31 2 0.04
32 41 0.89
33 3 0.07
ACGTcount: A:0.29, C:0.07, G:0.25, T:0.39
Consensus pattern (32 bp):
TATATATGTGTAGTTGGATAAAGCCGAATGTC
Found at i:42827306 original size:26 final size:27
Alignment explanation
Indices: 42827277--42827345 Score: 79
Period size: 26 Copynumber: 2.6 Consensus size: 27
42827267 TTTGAGGGAT
*
42827277 GCACTAAGTGTGCGAGTTAGA-TT-TAA
1 GCACTAAGTGTGCGAATTA-ATTTCTAA
* *
42827303 GCACTATGTGTGTGAATTAATTTCTAA
1 GCACTAAGTGTGCGAATTAATTTCTAA
*
42827330 GCATTAAGTGTGCGAA
1 GCACTAAGTGTGCGAA
42827346 ATCAGTTATT
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
25 1 0.03
26 18 0.51
27 16 0.46
ACGTcount: A:0.30, C:0.12, G:0.25, T:0.33
Consensus pattern (27 bp):
GCACTAAGTGTGCGAATTAATTTCTAA
Found at i:42835732 original size:12 final size:12
Alignment explanation
Indices: 42835715--42835739 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
42835705 AACATGACCA
42835715 AAACACATATTT
1 AAACACATATTT
42835727 AAACACATATTT
1 AAACACATATTT
42835739 A
1 A
42835740 GCAATATGGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.16, G:0.00, T:0.32
Consensus pattern (12 bp):
AAACACATATTT
Found at i:42836433 original size:7 final size:7
Alignment explanation
Indices: 42836423--42836454 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
42836413 GCACAATACA
42836423 CAATGAG
1 CAATGAG
42836430 CAATGAG
1 CAATGAG
42836437 CAATGAG
1 CAATGAG
*
42836444 CAATAAG
1 CAATGAG
42836451 CAAT
1 CAAT
42836455 TTTATTGGAC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.47, C:0.16, G:0.22, T:0.16
Consensus pattern (7 bp):
CAATGAG
Found at i:42837055 original size:88 final size:88
Alignment explanation
Indices: 42836901--42837078 Score: 279
Period size: 88 Copynumber: 2.0 Consensus size: 88
42836891 ATCGGAAGTA
42836901 ATCATTTCCACTTTCTCTACTAATTTTCAGTTTTTTGGAATATAAAAGATATTATTTGGGAGGTT
1 ATCATTTCCACTTTCTCTACTAATTTTCAGTTTTTTGGAATATAAAAGATATTATTTGGGAGGTT
* *
42836966 TTGTTTTCTATAGTTCAAAATCG
66 TTGTTGTCGATAGTTCAAAATCG
* * *
42836989 ATCATTTCCACTTTCTCTACTAATTTT-TGTTCTTTTGGAATATGAAAGATATT-TTTTGGAGAG
1 ATCATTTCCACTTTCTCTACTAATTTTCAGTT-TTTTGGAATATAAAAGATATTATTTGGGAG-G
42837052 TTTTGTTGTCGATAGTTCAAAATCG
64 TTTTGTTGTCGATAGTTCAAAATCG
42837077 AT
1 AT
42837079 TTTTATGAAG
Statistics
Matches: 83, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
87 10 0.12
88 73 0.88
ACGTcount: A:0.26, C:0.12, G:0.15, T:0.47
Consensus pattern (88 bp):
ATCATTTCCACTTTCTCTACTAATTTTCAGTTTTTTGGAATATAAAAGATATTATTTGGGAGGTT
TTGTTGTCGATAGTTCAAAATCG
Found at i:42839303 original size:5 final size:5
Alignment explanation
Indices: 42839293--42839317 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
42839283 AGGGAAAAAT
42839293 TTAAA TTAAA TTAAA TTAAA TTAAA
1 TTAAA TTAAA TTAAA TTAAA TTAAA
42839318 ACTACACATA
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:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
TTAAA
Found at i:42846748 original size:21 final size:21
Alignment explanation
Indices: 42846718--42846762 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
42846708 ACTTGTTTAA
42846718 AAAAAATGTTTTAATCAATTT
1 AAAAAATGTTTTAATCAATTT
* * *
42846739 AAAAATTGTTTTACTCGATTT
1 AAAAAATGTTTTAATCAATTT
42846760 AAA
1 AAA
42846763 CATTTTCACT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.44, C:0.07, G:0.07, T:0.42
Consensus pattern (21 bp):
AAAAAATGTTTTAATCAATTT
Found at i:42846781 original size:21 final size:22
Alignment explanation
Indices: 42846757--42846797 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
42846747 TTTTACTCGA
42846757 TTTAAACAT-TTTCACTTGATT
1 TTTAAACATGTTTCACTTGATT
*
42846778 TTTAAACTTGTTTCACTTGA
1 TTTAAACATGTTTCACTTGA
42846798 GTTAAAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.27, C:0.15, G:0.07, T:0.51
Consensus pattern (22 bp):
TTTAAACATGTTTCACTTGATT
Found at i:42846949 original size:16 final size:17
Alignment explanation
Indices: 42846909--42846941 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
42846899 CTTCATCGAT
*
42846909 TCTTTGTTCAAAAATAA
1 TCTTTATTCAAAAATAA
42846926 TCTTTATTCAAAAATA
1 TCTTTATTCAAAAATA
42846942 TTTTTATTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.42, C:0.12, G:0.03, T:0.42
Consensus pattern (17 bp):
TCTTTATTCAAAAATAA
Found at i:42864568 original size:40 final size:40
Alignment explanation
Indices: 42864386--42864608 Score: 227
Period size: 40 Copynumber: 5.6 Consensus size: 40
42864376 TCCTCGTTCA
* * * * *
42864386 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
42864425 AATGCCTTCGGGACATAACCTGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
42864465 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
42864505 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* ** * * * *
42864545 AAGGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
* *
42864585 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
42864609 CAGCATTCAA
Statistics
Matches: 158, Mismatches: 22, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
39 36 0.23
40 114 0.72
41 8 0.05
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:42864617 original size:41 final size:41
Alignment explanation
Indices: 42864540--42864617 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
42864530 TTAGTATCTC
* * *
42864540 GCACAAAGGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
42864581 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAAGGCCTTC-GGATCTTAGCCCGGACA-CATTCA
42864618 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (41 bp):
GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:42870631 original size:138 final size:138
Alignment explanation
Indices: 42870459--42870713 Score: 386
Period size: 138 Copynumber: 1.8 Consensus size: 138
42870449 GTGTAATAGT
* * *
42870459 TTCATCTTGCTCCATTGCAACTTCAAGGAGATAAGATTCACTATTGTAATTTCATT-TCGACCCA
1 TTCATCTTGCTCCACTGCAACTTCAAGGAGATAAGATTCACCATTGTAATTTCATTCT-GAACCA
** *
42870523 CTGTTACTTCAGGGGTATAGGAATTGTATCTTCAATCCGATCCACTGCAACTTTAAGGATATAGG
65 CTGCAACTTCAGGGGTATAGGAATCGTATCTTCAATCCGATCCACTGCAACTTTAAGGATATAGG
42870588 ATTTGCAGC
130 ATTTGCAGC
* * * *
42870597 TTCATCTTGCTCCACTGCAACTTTAGGGGGATAAGATTCGCCATTGTAATTTCATTCTGAACCAC
1 TTCATCTTGCTCCACTGCAACTTCAAGGAGATAAGATTCACCATTGTAATTTCATTCTGAACCAC
* *
42870662 TGCAACTTCAGGGGTATAGGAATCGTATCTTCAATTCGGTCCACTGCAACTT
66 TGCAACTTCAGGGGTATAGGAATCGTATCTTCAATCCGATCCACTGCAACTT
42870714 CAGGGAGATA
Statistics
Matches: 104, Mismatches: 12, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
138 103 0.99
139 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.18, T:0.33
Consensus pattern (138 bp):
TTCATCTTGCTCCACTGCAACTTCAAGGAGATAAGATTCACCATTGTAATTTCATTCTGAACCAC
TGCAACTTCAGGGGTATAGGAATCGTATCTTCAATCCGATCCACTGCAACTTTAAGGATATAGGA
TTTGCAGC
Found at i:42870662 original size:94 final size:93
Alignment explanation
Indices: 42870564--42871287 Score: 652
Period size: 94 Copynumber: 7.8 Consensus size: 93
42870554 TCAATCCGAT
* * * * *
42870564 CCACTGCAACTTTAAGGATATAGGATTTGCAGCTTCATCTTGCTCCACTGCAACTTTAGGGGGAT
1 CCACTGCAACTTCAAGGGTATAGGATTTGTAGCTTCATCTTGCTCCACTGCAACTTCAGGGAGAT
* * * *
42870629 AAGATTCGCCATTGTAATTTCATTCTGAA-
66 AAGATTCGCTATGGTAACTTCA-TC-CAAC
* * * * * *
42870658 CCACTGCAACTTCAGGGGTATAGGAATCGTATCTTCAAT-TCGGTCCACTGCAACTTCAGGGAGA
1 CCACTGCAACTTCAAGGGTATAGGATTTGTAGCTTC-ATCTTGCTCCACTGCAACTTCAGGGAGA
* * *
42870722 TAAGATTCGTCGT-T-ATAATTTCATTCCGAC
65 TAAGATTCG-C-TATGGTAACTTCA-TCCAAC
* * * * *
42870752 CCATTACAACTACAAGGGTATAGGAATTGTAGCTTCATCTTGCTCCACTACAACTTCAGGGAGAT
1 CCACTGCAACTTCAAGGGTATAGGATTTGTAGCTTCATCTTGCTCCACTGCAACTTCAGGGAGAT
* *
42870817 AAGATTCGCTATGGTAACCTTGATCCGAC
66 AAGATTCGCTATGGTAA-CTTCATCCAAC
* * * *
42870846 CTATTGCAACTTCAAGGGTATAGGATTTGTATCTTCATCTTGC-CCTACTGCAACTTCAAGGAGA
1 CCACTGCAACTTCAAGGGTATAGGATTTGTAGCTTCATCTTGCTCC-ACTGCAACTTCAGGGAGA
*
42870910 TAAGATTCTCTATGGTAACTTCAATCCAAC
65 TAAGATTCGCTATGGTAACTTC-ATCCAAC
* * *
42870940 CCACTGCAACTTCAGGGGTATAGGATTTGTAGCTTCATCTTGCTCCACTGCAACTTTAGGTAGAT
1 CCACTGCAACTTCAAGGGTATAGGATTTGTAGCTTCATCTTGCTCCACTGCAACTTCAGGGAGAT
* * * *
42871005 AAGATTTGCTATTGTAACTTTGATCCAAT
66 AAGATTCGCTATGGTAAC-TTCATCCAAC
* ** * * ** * *
42871034 CTACTGCCTCTT-TAGGAATATAATATTTGTAGCTTCATCTTGCTCCATTGCAACTTCAGGAAGA
1 CCACTGCAACTTCAAGG-GTATAGGATTTGTAGCTTCATCTTGCTCCACTGCAACTTCAGGGAGA
42871098 TAAGATTCGCTATGGTAACTTCAATCCAAC
65 TAAGATTCGCTATGGTAACTTC-ATCCAAC
* * * * * * *
42871128 CCATTGTAACTTCAGGGGTATAGGATTTGTGGCTTCATCTTGCTCCACTGTAACTTTAAGGAGAT
1 CCACTGCAACTTCAAGGGTATAGGATTTGTAGCTTCATCTTGCTCCACTGCAACTTCAGGGAGAT
*** *
42871193 AAGATTTATTATGGTAGA-TTCAATCTAA-
66 AAGATTCGCTATGGTA-ACTTC-ATCCAAC
* * **
42871221 --A---C--CTTCAAGGGTATAAGATTTGTAGCTTCATCTTACTTTACAT-CAACTTCAGGGAGA
1 CCACTGCAACTTCAAGGGTATAGGATTTGTAGCTTCATCTTGCTCCAC-TGCAACTTCAGGGAGA
42871278 TAAGATTCGC
65 TAAGATTCGC
42871288 CATTGTGGTT
Statistics
Matches: 516, Mismatches: 97, Indels: 42
0.79 0.15 0.06
Matches are distributed among these distances:
86 51 0.10
87 1 0.00
91 1 0.00
92 1 0.00
93 14 0.03
94 434 0.84
95 14 0.03
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (93 bp):
CCACTGCAACTTCAAGGGTATAGGATTTGTAGCTTCATCTTGCTCCACTGCAACTTCAGGGAGAT
AAGATTCGCTATGGTAACTTCATCCAAC
Found at i:42870991 original size:44 final size:44
Alignment explanation
Indices: 42870528--42870995 Score: 155
Period size: 44 Copynumber: 10.1 Consensus size: 44
42870518 ACCCACTGTT
* * * *
42870528 ACTTCAGGGGTATAGGAATTGTATCTTCAATC-CGATCCACTGCA
1 ACTTCAGGGGTATAGGATTTGTAGCTTC-ATCTTGCTCCACTGCA
* * * *
42870572 ACTTTAAGGATATAGGATTTGCAGCTTCATCTTGCTCCACTGCA
1 ACTTCAGGGGTATAGGATTTGTAGCTTCATCTTGCTCCACTGCA
* * * ** **
42870616 ACTTTAGGGGGATAAGATTCGCCATTGTAATTTCAT-TCTGAACCACTGCA
1 ACTTCAGGGGTATAGGA-T-----TTGTAGCTTCATCT-TGCTCCACTGCA
* * * * *
42870666 ACTTCAGGGGTATAGGAATCGTATCTTCAAT-TCGGTCCACTGCA
1 ACTTCAGGGGTATAGGATTTGTAGCTTC-ATCTTGCTCCACTGCA
* * * * * * *
42870710 ACTTCAGGGAG-ATAAGATTCGTCGTTATAATTTCATTCCGAC-CCATTACA
1 ACTTCAGGG-GTATAGGATTTGTAGCT-TCA--TC-TT--G-CTCCACTGCA
* * * *
42870760 ACTACAAGGGTATAGGAATTGTAGCTTCATCTTGCTCCACTACA
1 ACTTCAGGGGTATAGGATTTGTAGCTTCATCTTGCTCCACTGCA
* * * * * *
42870804 ACTTCAGGGAG-ATAAGATTCGCTATG-GTAACCTTGATCCGACCTATTGCA
1 ACTTCAGGG-GTATAGGATTTG-TA-GCTTCATCTTGCTCC-A-C---TGCA
* *
42870854 ACTTCAAGGGTATAGGATTTGTATCTTCATCTTGC-CCTACTGCA
1 ACTTCAGGGGTATAGGATTTGTAGCTTCATCTTGCTCC-ACTGCA
* * * ***
42870898 ACTTCAAGGAG-ATAAGATTCTCTATGGTAACTTCAATCCAAC-CCACTGCA
1 ACTTC-AGGGGTATAGGA---T-T-T-GTAGCTTC-ATCTTGCTCCACTGCA
42870948 ACTTCAGGGGTATAGGATTTGTAGCTTCATCTTGCTCCACTGCA
1 ACTTCAGGGGTATAGGATTTGTAGCTTCATCTTGCTCCACTGCA
42870992 ACTT
1 ACTT
42870996 TAGGTAGATA
Statistics
Matches: 306, Mismatches: 78, Indels: 80
0.66 0.17 0.17
Matches are distributed among these distances:
43 8 0.03
44 136 0.44
45 22 0.07
46 6 0.02
47 6 0.02
48 5 0.02
49 18 0.06
50 99 0.32
51 6 0.02
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.31
Consensus pattern (44 bp):
ACTTCAGGGGTATAGGATTTGTAGCTTCATCTTGCTCCACTGCA
Found at i:42871376 original size:44 final size:44
Alignment explanation
Indices: 42871302--42871409 Score: 112
Period size: 44 Copynumber: 2.5 Consensus size: 44
42871292 GTGGTTTGAT
* * *
42871302 TCTGACCCACTGTAACTT-AAGGAGTCTAAGAATTATAACTTTAA
1 TCTGATCCACTGCAACTTCAAGGAGTATAAGAATTATAAC-TTAA
* * * *
42871346 TCTGATCCACTGCAACTTCAAGGA-TATAAGATTTGTAGCTTCA
1 TCTGATCCACTGCAACTTCAAGGAGTATAAGAATTATAACTTAA
*
42871389 TCTTGCTCCACTGCAACTTCA
1 TC-TGATCCACTGCAACTTCA
42871410 GGAAGATAAG
Statistics
Matches: 54, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
43 5 0.09
44 44 0.81
45 5 0.09
ACGTcount: A:0.31, C:0.23, G:0.14, T:0.32
Consensus pattern (44 bp):
TCTGATCCACTGCAACTTCAAGGAGTATAAGAATTATAACTTAA
Found at i:42871384 original size:138 final size:136
Alignment explanation
Indices: 42871223--42871703 Score: 518
Period size: 138 Copynumber: 3.5 Consensus size: 136
42871213 CAATCTAAAC
* * **
42871223 CTTCAAGGGTATAAGATTTGTAGCTTCATCTTACTTTACAT-CAACTTCAGGGAGATAAGATTCG
1 CTTCAAGGATATAAGATTTGTAGCTTCATCTTGCTCCAC-TGCAACTTCAGGGAGATAAGATTCG
* * * * * *
42871287 CCATTGTGGTTTGATTCTGACCCACTGTAACTTAAGGAGTCTAAGAATTATAACTTTAATCTGAT
65 CCATTGTAGTTT-ATTCTGACCTACTGTAACTTAAGGGGTATAAGAATTGTATCTTTAATC-GAT
42871352 CCACTGCAA
128 CCACTGCAA
*
42871361 CTTCAAGGATATAAGATTTGTAGCTTCATCTTGCTCCACTGCAACTTCAGGAAGATAAGATTC-C
1 CTTCAAGGATATAAGATTTGTAGCTTCATCTTGCTCCACTGCAACTTCAGGGAGATAAGATTCGC
* * * * * * *
42871425 TTATTATAGTTTCATT-TCGACCTATTGCAACTTCAGGGGTATATGATTTGTATCTTTAATCGAT
66 -CATTGTAGTTT-ATTCT-GACCTACTGTAACTTAAGGGGTATAAGAATTGTATCTTTAATCGAT
* **
42871489 CCAATAAAA
128 CCACTGCAA
* * * *
42871498 CTTCAAGGATATAAGATTAGTAGCTTCATCTTGCTCCATTGCAACTTTAGGGAGATAAGATTTGC
1 CTTCAAGGATATAAGATTTGTAGCTTCATCTTGCTCCACTGCAACTTCAGGGAGATAAGATTCGC
* * * * * *
42871563 CATGGTAACTTTAATCTGACCTACTGTAACTTTAGGGGTATAAAAATTGTATCTTCAATACGATC
66 CATTGT-AGTTTATTCTGACCTACTGTAACTTAAGGGGTATAAGAATTGTATCTTTAAT-CGATC
*
42871628 CACTGCAT
129 CACTGCAA
* * * * * * *
42871636 CTTCAGGGATATAGGATTTGTAGATTCATCTTGCTCCACTACAACTTTAGAGAGATAAGATTTGC
1 CTTCAAGGATATAAGATTTGTAGCTTCATCTTGCTCCACTGCAACTTCAGGGAGATAAGATTCGC
42871701 CAT
66 CAT
42871704 GGTAATATCT
Statistics
Matches: 286, Mismatches: 50, Indels: 14
0.82 0.14 0.04
Matches are distributed among these distances:
137 110 0.38
138 176 0.62
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.35
Consensus pattern (136 bp):
CTTCAAGGATATAAGATTTGTAGCTTCATCTTGCTCCACTGCAACTTCAGGGAGATAAGATTCGC
CATTGTAGTTTATTCTGACCTACTGTAACTTAAGGGGTATAAGAATTGTATCTTTAATCGATCCA
CTGCAA
Found at i:42871781 original size:90 final size:94
Alignment explanation
Indices: 42871627--42871832 Score: 226
Period size: 90 Copynumber: 2.2 Consensus size: 94
42871617 TCAATACGAT
* * *
42871627 CCACTGCATC-TTCAGGG-ATATAGGATTTGTAGATTCATCTTGCTCCACTACAACTTTAGAGAG
1 CCACTGCAACTTTAAGGGTATATAGGATTTGTAGATTCATCTTGCTCCACTACAACTTCAGAGAG
* * *
42871690 ATAAGATTTGCCATGGTAA-T-ATCTGAC
66 ATAAGACTCGCCATAGTAACTAATCTGAC
* * * * * *
42871717 CCACTGCAGCTTTAAGGGTATA-AGG-TTTGTAGCTTCATTTTGCTGCACTGCAACTTCAGGGAG
1 CCACTGCAACTTTAAGGGTATATAGGATTTGTAGATTCATCTTGCTCCACTACAACTTCAGAGAG
*
42871780 ATAAGACTCGCTATAGTAACTTCAATCTGAC
66 ATAAGACTCGCCATAGTAAC-T-AATCTGAC
*
42871811 CCACTGCAACTTTAAAGGTATA
1 CCACTGCAACTTTAAGGGTATA
42871833 GGATTTACTA
Statistics
Matches: 96, Mismatches: 14, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
90 56 0.58
91 9 0.09
92 4 0.04
94 27 0.28
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (94 bp):
CCACTGCAACTTTAAGGGTATATAGGATTTGTAGATTCATCTTGCTCCACTACAACTTCAGAGAG
ATAAGACTCGCCATAGTAACTAATCTGAC
Found at i:42885526 original size:26 final size:26
Alignment explanation
Indices: 42885478--42885536 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 26
42885468 AAAGAAATAC
42885478 TATT-TTTTTATAATAACTATT-AAA
1 TATTATTTTTATAATAACTATTAAAA
* *
42885502 TATTATTTTTAATAATAATTGTTAAAA
1 TATTATTTTT-ATAATAACTATTAAAA
*
42885529 TACTATTT
1 TATTATTT
42885537 AATATTTTAC
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
24 4 0.14
25 5 0.17
26 10 0.34
27 10 0.34
ACGTcount: A:0.41, C:0.03, G:0.02, T:0.54
Consensus pattern (26 bp):
TATTATTTTTATAATAACTATTAAAA
Found at i:42885535 original size:27 final size:26
Alignment explanation
Indices: 42885472--42885536 Score: 76
Period size: 27 Copynumber: 2.4 Consensus size: 26
42885462 GATTCAAAAG
*
42885472 AAATACTATTTTTTTATAATAACTATT
1 AAATACTA-TTTTTAATAATAACTATT
* * *
42885499 AAATATTATTTTTAATAATAATTGTT
1 AAATACTATTTTTAATAATAACTATT
42885525 AAAATACTATTT
1 -AAATACTATTT
42885537 AATATTTTAC
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
26 15 0.47
27 17 0.53
ACGTcount: A:0.43, C:0.05, G:0.02, T:0.51
Consensus pattern (26 bp):
AAATACTATTTTTAATAATAACTATT
Found at i:42889466 original size:44 final size:44
Alignment explanation
Indices: 42889410--42889496 Score: 138
Period size: 44 Copynumber: 2.0 Consensus size: 44
42889400 AATATATGTG
* * *
42889410 AGGCATCTGAGCTCATTGAGTTGGTTCGAGTTCATTATGGATGC
1 AGGCATCCGAGCTCATTGAGTTGGTCCGAGTTCACTATGGATGC
*
42889454 AGGCATCCGAGCTCGTTGAGTTGGTCCGAGTTCACTATGGATG
1 AGGCATCCGAGCTCATTGAGTTGGTCCGAGTTCACTATGGATG
42889497 TCTACATGTT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
44 39 1.00
ACGTcount: A:0.20, C:0.18, G:0.31, T:0.31
Consensus pattern (44 bp):
AGGCATCCGAGCTCATTGAGTTGGTCCGAGTTCACTATGGATGC
Found at i:42893373 original size:26 final size:26
Alignment explanation
Indices: 42893344--42893398 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
42893334 TCACCATTTT
* *
42893344 TTTGAAAGTCATAAGTGTGGAAGACA
1 TTTGAAAGTCATAAGAGAGGAAGACA
*
42893370 TTTGAAAGTCATGAGAGAGGAAGACA
1 TTTGAAAGTCATAAGAGAGGAAGACA
42893396 TTT
1 TTT
42893399 AAGGAAAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.38, C:0.07, G:0.27, T:0.27
Consensus pattern (26 bp):
TTTGAAAGTCATAAGAGAGGAAGACA
Found at i:42895714 original size:21 final size:21
Alignment explanation
Indices: 42895688--42895728 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
42895678 AAGAAGTGAA
42895688 TGAATGAATAATGATCATGAC
1 TGAATGAATAATGATCATGAC
*
42895709 TGAATGAATCATGATCATGA
1 TGAATGAATAATGATCATGA
42895729 GTTTTATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.41, C:0.10, G:0.20, T:0.29
Consensus pattern (21 bp):
TGAATGAATAATGATCATGAC
Done.