Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032249.1 Gossypioides kirkii chromosome KI_07
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: 37252039
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 2100 characters in sequence are not A, C, G, or T
File 96 of 120
Found at i:27621091 original size:14 final size:15
Alignment explanation
Indices: 27621072--27621100 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
27621062 CTCCCCCCTA
27621072 CAACT-CCAAAAACC
1 CAACTCCCAAAAACC
27621086 CAACTCCCAAAAACC
1 CAACTCCCAAAAACC
27621101 TGATCCTCCT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 5 0.36
15 9 0.64
ACGTcount: A:0.48, C:0.45, G:0.00, T:0.07
Consensus pattern (15 bp):
CAACTCCCAAAAACC
Found at i:27623158 original size:15 final size:15
Alignment explanation
Indices: 27623138--27623167 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
27623128 AGGAAGCGAA
*
27623138 AGGAAGAAGTAGAAG
1 AGGAAGAAGAAGAAG
27623153 AGGAAGAAGAAGAAG
1 AGGAAGAAGAAGAAG
27623168 CAAAGGTGTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.40, T:0.03
Consensus pattern (15 bp):
AGGAAGAAGAAGAAG
Found at i:27629732 original size:16 final size:17
Alignment explanation
Indices: 27629697--27629737 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
27629687 TATTTTATAA
27629697 ATTTTA-AAATATTTGT
1 ATTTTATAAATATTTGT
27629713 -TTTTATAAATATTT-T
1 ATTTTATAAATATTTGT
*
27629728 ATTTTTTAAA
1 ATTTTATAAA
27629738 AGCATCAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 6 0.27
16 16 0.73
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (17 bp):
ATTTTATAAATATTTGT
Found at i:27632906 original size:15 final size:15
Alignment explanation
Indices: 27632882--27632914 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
27632872 TTTTATTAAA
27632882 TTTAAAATA-TTTAT
1 TTTAAAATATTTTAT
27632896 TTTATAAATATTTTAT
1 TTTA-AAATATTTTAT
27632912 TTT
1 TTT
27632915 TTTAAGACTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 4 0.24
15 5 0.29
16 8 0.47
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (15 bp):
TTTAAAATATTTTAT
Found at i:27634035 original size:28 final size:28
Alignment explanation
Indices: 27634002--27634066 Score: 121
Period size: 28 Copynumber: 2.3 Consensus size: 28
27633992 CTAGTCCTCA
*
27634002 ATTTTCAGATATTTGGGATTCCTAGGAT
1 ATTTTCAGATATCTGGGATTCCTAGGAT
27634030 ATTTTCAGATATCTGGGATTCCTAGGAT
1 ATTTTCAGATATCTGGGATTCCTAGGAT
27634058 ATTTTCAGA
1 ATTTTCAGA
27634067 CATCCCGGAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.26, C:0.12, G:0.20, T:0.42
Consensus pattern (28 bp):
ATTTTCAGATATCTGGGATTCCTAGGAT
Found at i:27638517 original size:2 final size:2
Alignment explanation
Indices: 27638510--27638541 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
27638500 GCTAGAGGGA
*
27638510 AT AT AT AT AT TT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
27638542 CTGCTTATCT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:27641335 original size:60 final size:60
Alignment explanation
Indices: 27641257--27641374 Score: 159
Period size: 60 Copynumber: 2.0 Consensus size: 60
27641247 ACATTGATAG
* * *
27641257 TTTAGAGAAATAAGTAAAATATTTTGAAGTTTAA-AGACTAATTTAAAATGATGATCATAA
1 TTTAGAGAAATAAGTAAAATATTTTAAAATTTAAGA-ACTAATTTAAAATGATAATCATAA
* *
27641317 TTTAG-GAATATAATTAAAATATTTTAAAATTTATGAACTAATTTAAAATGATAATCAT
1 TTTAGAGAA-ATAAGTAAAATATTTTAAAATTTAAGAACTAATTTAAAATGATAATCAT
27641375 GATATGAAAA
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
59 3 0.06
60 47 0.92
61 1 0.02
ACGTcount: A:0.48, C:0.03, G:0.10, T:0.38
Consensus pattern (60 bp):
TTTAGAGAAATAAGTAAAATATTTTAAAATTTAAGAACTAATTTAAAATGATAATCATAA
Found at i:27644883 original size:18 final size:18
Alignment explanation
Indices: 27644862--27644906 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
27644852 AAAAAATTAG
27644862 GAAAATATATATAATATA
1 GAAAATATATATAATATA
* *
27644880 GAAAACATATATATTATA
1 GAAAATATATATAATATA
27644898 -AAAAT-TATA
1 GAAAATATATA
27644907 AAAATAAACT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 4 0.17
17 4 0.17
18 16 0.67
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.33
Consensus pattern (18 bp):
GAAAATATATATAATATA
Found at i:27645035 original size:21 final size:22
Alignment explanation
Indices: 27645011--27645051 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
27645001 AAATTTGTAA
27645011 TTTA-AAAAATTAAAAATATTT
1 TTTATAAAAATTAAAAATATTT
* *
27645032 TTTATAAAATTTTAAAATAT
1 TTTATAAAAATTAAAAATAT
27645052 ATAATTCTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
TTTATAAAAATTAAAAATATTT
Found at i:27645046 original size:23 final size:24
Alignment explanation
Indices: 27645020--27645072 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 24
27645010 ATTTAAAAAA
**
27645020 TTAAAAATAT-TTTTTATAAAATT
1 TTAAAAATATATAATTATAAAATT
*
27645043 TT-AAAATATATAATTCTAAAATT
1 TTAAAAATATATAATTATAAAATT
27645066 TTAAAAA
1 TTAAAAA
27645073 GGTATTTCAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
22 7 0.28
23 14 0.56
24 4 0.16
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (24 bp):
TTAAAAATATATAATTATAAAATT
Found at i:27645231 original size:2 final size:2
Alignment explanation
Indices: 27645226--27645259 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
27645216 TTTAATTTTT
27645226 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
27645260 CATTTTTAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:27645596 original size:31 final size:31
Alignment explanation
Indices: 27645544--27645605 Score: 72
Period size: 31 Copynumber: 2.0 Consensus size: 31
27645534 TTTTAATATT
* * *
27645544 TCATATATTATATTGATTAAAAATATAAAAA
1 TCATATATAATATTGAATAAAAATAGAAAAA
*
27645575 TCATATATAATATAT-AATAAAATTAGAAAAA
1 TCATATATAATAT-TGAATAAAAATAGAAAAA
27645606 AATGTTTAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
31 25 0.96
32 1 0.04
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.35
Consensus pattern (31 bp):
TCATATATAATATTGAATAAAAATAGAAAAA
Found at i:27645660 original size:22 final size:21
Alignment explanation
Indices: 27645610--27645660 Score: 50
Period size: 22 Copynumber: 2.4 Consensus size: 21
27645600 GAAAAAAATG
* * *
27645610 TTTAAAAATATTTTTATAACA
1 TTTAAAAACATTATTATAAAA
27645631 TTCT-AAAACATATATTATAAAA
1 TT-TAAAAACAT-TATTATAAAA
27645653 TTTAAAAA
1 TTTAAAAA
27645661 GTAAAAATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
21 9 0.38
22 15 0.62
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (21 bp):
TTTAAAAACATTATTATAAAA
Found at i:27652533 original size:23 final size:23
Alignment explanation
Indices: 27652506--27652649 Score: 105
Period size: 23 Copynumber: 6.3 Consensus size: 23
27652496 ACGCTAGCGC
27652506 GCTTAC-CATTCAGCACTGTGTGT
1 GCTTACTCATTC-GCACTGTGTGT
** *
27652529 GCTTACTGTTTCGCACTTTGTGT
1 GCTTACTCATTCGCACTGTGTGT
** *
27652552 GCTTACTGTTTCGCACTTTGTGT
1 GCTTACTCATTCGCACTGTGTGT
* ** *
27652575 GCCTACTGTTTCGCACTTTGTGT
1 GCTTACTCATTCGCACTGTGTGT
* ** *
27652598 GCCTACTGTTTCGCGCT-TCGTGT
1 GCTTACTCATTCGCACTGT-GTGT
* *
27652621 GCCTACTGATT-GCACTGTGTGT
1 GCTTACTCATTCGCACTGTGTGT
27652643 GCTTACT
1 GCTTACT
27652650 GTTTCCCCAG
Statistics
Matches: 110, Mismatches: 8, Indels: 7
0.88 0.06 0.06
Matches are distributed among these distances:
22 15 0.14
23 92 0.84
24 3 0.03
ACGTcount: A:0.10, C:0.25, G:0.23, T:0.42
Consensus pattern (23 bp):
GCTTACTCATTCGCACTGTGTGT
Found at i:27652574 original size:46 final size:46
Alignment explanation
Indices: 27652518--27652654 Score: 204
Period size: 46 Copynumber: 3.0 Consensus size: 46
27652508 TTACCATTCA
* *
27652518 GCACTGTGTGTGCTTACTGTTTCGCACTTTGTGTGCTTACTGTTTC
1 GCACTTTGTGTGCCTACTGTTTCGCACTTTGTGTGCTTACTGTTTC
*
27652564 GCACTTTGTGTGCCTACTGTTTCGCACTTTGTGTGCCTACTGTTTC
1 GCACTTTGTGTGCCTACTGTTTCGCACTTTGTGTGCTTACTGTTTC
* * * *
27652610 GCGCTTCGTGTGCCTACTGATT-GCACTGTGTGTGCTTACTGTTTC
1 GCACTTTGTGTGCCTACTGTTTCGCACTTTGTGTGCTTACTGTTTC
27652655 CCCAGCACTT
Statistics
Matches: 83, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
45 21 0.25
46 62 0.75
ACGTcount: A:0.09, C:0.24, G:0.24, T:0.43
Consensus pattern (46 bp):
GCACTTTGTGTGCCTACTGTTTCGCACTTTGTGTGCTTACTGTTTC
Found at i:27655182 original size:58 final size:59
Alignment explanation
Indices: 27655097--27655251 Score: 203
Period size: 58 Copynumber: 2.6 Consensus size: 59
27655087 ATATATTATA
* * *
27655097 ATTTTTACT-AATTCATATTTTAATAATAATTATATTAAAAATATTATTAAATT-ATATATT
1 ATTTTTATTAAATT-ATA-TTTAATAATAATTATATTAAAAATATAATTAAATTAAT-TAAT
*
27655157 A-TTTTATTAAATTTTATTTAATAATAATTATATT-AAAATATAATTAAATTAATTAAT
1 ATTTTTATTAAATTATATTTAATAATAATTATATTAAAAATATAATTAAATTAATTAAT
27655214 ATTTTTATTAAATTATATTTAATAATAATCT-TATTAAA
1 ATTTTTATTAAATTATATTTAATAATAAT-TATATTAAA
27655252 TTTAATAAGA
Statistics
Matches: 85, Mismatches: 5, Indels: 11
0.84 0.05 0.11
Matches are distributed among these distances:
57 19 0.22
58 50 0.59
59 11 0.13
60 5 0.06
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (59 bp):
ATTTTTATTAAATTATATTTAATAATAATTATATTAAAAATATAATTAAATTAATTAAT
Found at i:27655193 original size:26 final size:26
Alignment explanation
Indices: 27655115--27655254 Score: 93
Period size: 26 Copynumber: 4.9 Consensus size: 26
27655105 TAATTCATAT
*
27655115 TTTAATAATAATTATATTAAAAATATTA
1 TTTAATAATAATTATATT--AAATTTTA
* *
27655143 TTAAATTATATATTATTTTATTAAATTTTA
1 TTTAA-TA-ATA--ATTATATTAAATTTTA
27655173 TTTAATAATAATTATATTAAAATATAATTAA
1 TTTAATAATAATTATATT-AAAT-T--TT-A
* * * *
27655204 ATTAATTAATATTTTTATTAAATTATA
1 TTTAA-TAATAATTATATTAAATTTTA
27655231 TTTAATAATAATCT-TATTAAATTT
1 TTTAATAATAAT-TATATTAAATTT
27655255 AATAAGAATA
Statistics
Matches: 89, Mismatches: 12, Indels: 24
0.71 0.10 0.19
Matches are distributed among these distances:
26 22 0.25
27 10 0.11
28 9 0.10
29 4 0.04
30 17 0.19
31 9 0.10
32 18 0.20
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (26 bp):
TTTAATAATAATTATATTAAATTTTA
Found at i:27655223 original size:32 final size:31
Alignment explanation
Indices: 27655116--27655242 Score: 99
Period size: 32 Copynumber: 4.3 Consensus size: 31
27655106 AATTCATATT
*
27655116 TTAATAATAATTATATTAAAAATATTATTAAA
1 TTAATAATAATTATATT-AAAATATAATTAAA
* * *
27655148 TT-ATATATTATTTTATT-AAAT-T--TT-AT
1 TTAATA-ATAATTATATTAAAATATAATTAAA
27655174 TTAATAATAATTATATTAAAATATAATTAAA
1 TTAATAATAATTATATTAAAATATAATTAAA
* * * *
27655205 TTAATTAATATTTTTATTAAATTAT-ATTTAA
1 TTAA-TAATAATTATATTAAAATATAATTAAA
27655236 -TAATAAT
1 TTAATAAT
27655243 CTTATTAAAT
Statistics
Matches: 77, Mismatches: 10, Indels: 19
0.73 0.09 0.18
Matches are distributed among these distances:
26 12 0.16
27 9 0.12
28 1 0.01
29 5 0.06
30 9 0.12
31 13 0.17
32 28 0.36
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (31 bp):
TTAATAATAATTATATTAAAATATAATTAAA
Found at i:27655382 original size:39 final size:45
Alignment explanation
Indices: 27655327--27655431 Score: 116
Period size: 46 Copynumber: 2.4 Consensus size: 45
27655317 TTTCTTATTC
*
27655327 TATTACAGCATC-ATTCCATT-CAACCAA-ACACAA-T-AA-TA-T
1 TATTACAGC-TCTATTCCATTCCAACCAACAAACAATTGAATTACT
*
27655366 TATTACAGCTCTATTCCATTCCAATCAACCAAACAATTGAATTACT
1 TATTACAGCTCTATTCCATTCCAACCAA-CAAACAATTGAATTACT
*
27655412 GATTACAGCTCTATTCCATT
1 TATTACAGCTCTATTCCATT
27655432 ACAGCTCTAT
Statistics
Matches: 55, Mismatches: 3, Indels: 9
0.82 0.04 0.13
Matches are distributed among these distances:
38 2 0.04
39 17 0.31
40 6 0.11
42 5 0.09
43 1 0.02
44 2 0.04
45 2 0.04
46 20 0.36
ACGTcount: A:0.37, C:0.26, G:0.05, T:0.32
Consensus pattern (45 bp):
TATTACAGCTCTATTCCATTCCAACCAACAAACAATTGAATTACT
Found at i:27655388 original size:44 final size:46
Alignment explanation
Indices: 27655338--27655431 Score: 131
Period size: 44 Copynumber: 2.1 Consensus size: 46
27655328 ATTACAGCAT
* *
27655338 CATTCCATTCAACCAAACACAAT-AA-TA-TTATTACAGCTCTATTC
1 CATTCCAATCAACCAAACA-AATGAATTACTGATTACAGCTCTATTC
*
27655382 CATTCCAATCAACCAAACAATTGAATTACTGATTACAGCTCTATTC
1 CATTCCAATCAACCAAACAAATGAATTACTGATTACAGCTCTATTC
27655428 CATT
1 CATT
27655432 ACAGCTCTAT
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
43 2 0.05
44 20 0.45
45 2 0.05
46 20 0.45
ACGTcount: A:0.37, C:0.27, G:0.04, T:0.32
Consensus pattern (46 bp):
CATTCCAATCAACCAAACAAATGAATTACTGATTACAGCTCTATTC
Found at i:27655434 original size:16 final size:16
Alignment explanation
Indices: 27655413--27655484 Score: 126
Period size: 16 Copynumber: 4.5 Consensus size: 16
27655403 TGAATTACTG
27655413 ATTACAGCTCTATTCC
1 ATTACAGCTCTATTCC
27655429 ATTACAGCTCTATTCC
1 ATTACAGCTCTATTCC
*
27655445 ATTACAGCTCTATTCT
1 ATTACAGCTCTATTCC
*
27655461 ATTACACCTCTATTCC
1 ATTACAGCTCTATTCC
27655477 ATTACAGC
1 ATTACAGC
27655485 GAACCAAACG
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 52 1.00
ACGTcount: A:0.26, C:0.31, G:0.06, T:0.38
Consensus pattern (16 bp):
ATTACAGCTCTATTCC
Found at i:27656844 original size:76 final size:76
Alignment explanation
Indices: 27656730--27656977 Score: 239
Period size: 76 Copynumber: 3.3 Consensus size: 76
27656720 ATTTCCCGGA
* * * * * * *
27656730 AACGATGACCTACCATCCTGGATTTCTTGGA-AACGATGGTTTATCGGATCAAATTTGTTATCTC
1 AACGATGACCTACCACCCCGGACTGCCT-GACAACGATGGTTTATCGAATCAAATTTGTCATCTC
* *
27656794 GGGTTGCCCAAT
65 GGATTGCCCAAC
* ** * * *
27656806 AAGGATGACCTACCACCCCGGACTGTTTGACAACGATGGTTTATCGAATCAAATCTATCATCTTG
1 AACGATGACCTACCACCCCGGACTGCCTGACAACGATGGTTTATCGAATCAAATTTGTCATCTCG
*
27656871 GATTGCCCGAC
66 GATTGCCCAAC
* * * * * *
27656882 AACGATGACCTACCACCTCGGATTGCCTGGCAACAATGGTTTATCGAATCAAATTTGTCA-CCCC
1 AACGATGACCTACCACCCCGGACTGCCTGACAACGATGGTTTATCGAATCAAATTTGTCATCTCG
* * *
27656946 GAGTTGTCTAGC
66 GA-TTGCCCAAC
27656958 AACGATGACCTACCACCCCG
1 AACGATGACCTACCACCCCG
27656978 AATTACTCGG
Statistics
Matches: 139, Mismatches: 31, Indels: 4
0.80 0.18 0.02
Matches are distributed among these distances:
75 5 0.04
76 134 0.96
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.27
Consensus pattern (76 bp):
AACGATGACCTACCACCCCGGACTGCCTGACAACGATGGTTTATCGAATCAAATTTGTCATCTCG
GATTGCCCAAC
Found at i:27656992 original size:152 final size:152
Alignment explanation
Indices: 27656711--27656998 Score: 346
Period size: 152 Copynumber: 1.9 Consensus size: 152
27656701 TTTCAATTTG
* * * *
27656711 TCATATTGGATTTCCCGGAAACGATGACCTACCATCCTGGATTTCTTGGAAACGATGGTTTATCG
1 TCATATTGGATTGCCCGGAAACGATGACCTACCATCCTGGATTGCCTGGAAACAATGGTTTATCG
* * * * * * * * ** *
27656776 GATCAAATTTGTTATCTCGGGTTGCCCAATAAGGATGACCTACCACCCCGGACTGTTTGACAACG
66 AATCAAATTTGTCACCCCGAGTTGCCCAACAACGATGACCTACCACCCCGAACTACTCGACAACG
27656841 ATGGTTTATCGAATCAAATCTA
131 ATGGTTTATCGAATCAAATCTA
* *
27656863 TCATCTTGGATTGCCC-GACAACGATGACCTACCA-CCTCGGATTGCCTGGCAACAATGGTTTAT
1 TCATATTGGATTGCCCGGA-AACGATGACCTACCATCCT-GGATTGCCTGGAAACAATGGTTTAT
* * * * *
27656926 CGAATCAAATTTGTCACCCCGAGTTGTCTAGCAACGATGACCTACCACCCCGAATTACTCGGCAA
64 CGAATCAAATTTGTCACCCCGAGTTGCCCAACAACGATGACCTACCACCCCGAACTACTCGACAA
27656991 CGATGGTT
129 CGATGGTT
27656999 CGCAAACAAT
Statistics
Matches: 112, Mismatches: 22, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
151 5 0.04
152 107 0.96
ACGTcount: A:0.26, C:0.26, G:0.20, T:0.28
Consensus pattern (152 bp):
TCATATTGGATTGCCCGGAAACGATGACCTACCATCCTGGATTGCCTGGAAACAATGGTTTATCG
AATCAAATTTGTCACCCCGAGTTGCCCAACAACGATGACCTACCACCCCGAACTACTCGACAACG
ATGGTTTATCGAATCAAATCTA
Found at i:27658499 original size:14 final size:14
Alignment explanation
Indices: 27658480--27658509 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
27658470 GAATAGATTT
27658480 TTAATTAAATAAAA
1 TTAATTAAATAAAA
*
27658494 TTAATTAATTAAAA
1 TTAATTAAATAAAA
27658508 TT
1 TT
27658510 TTTAAACCAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
TTAATTAAATAAAA
Found at i:27661950 original size:20 final size:20
Alignment explanation
Indices: 27661902--27661950 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
27661892 ACCATTTTTA
* * *
27661902 CTTTATATACTTTAATTAGT
1 CTTTATTTAATTTAATTAAT
27661922 -TTTAGTTTAATTTAATTAAT
1 CTTTA-TTTAATTTAATTAAT
27661942 CTTTATTTA
1 CTTTATTTA
27661951 TTAGTTAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
19 4 0.17
20 16 0.67
21 4 0.17
ACGTcount: A:0.31, C:0.06, G:0.04, T:0.59
Consensus pattern (20 bp):
CTTTATTTAATTTAATTAAT
Found at i:27664563 original size:3 final size:3
Alignment explanation
Indices: 27664557--27664606 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
27664547 AAAGTTGTTG
27664557 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
27664605 TA
1 TA
27664607 CCGATTAAGT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:27665207 original size:16 final size:17
Alignment explanation
Indices: 27665170--27665204 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
27665160 ATTTCTAAAG
*
27665170 TTATGATAAAAAAAATT
1 TTATAATAAAAAAAATT
*
27665187 TTATAATAAAAATAATT
1 TTATAATAAAAAAAATT
27665204 T
1 T
27665205 ATATGTTATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (17 bp):
TTATAATAAAAAAAATT
Found at i:27665603 original size:18 final size:18
Alignment explanation
Indices: 27665564--27665602 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 18
27665554 GGTTGAATCG
27665564 TTTTAATATGTTTTTTTA
1 TTTTAATATGTTTTTTTA
27665582 TTTTAAT-T-TTTTTTATA
1 TTTTAATATGTTTTTT-TA
27665599 TTTT
1 TTTT
27665603 TTAAGTTCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 6 0.30
17 7 0.35
18 7 0.35
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.77
Consensus pattern (18 bp):
TTTTAATATGTTTTTTTA
Found at i:27667402 original size:17 final size:18
Alignment explanation
Indices: 27667373--27667416 Score: 65
Period size: 17 Copynumber: 2.6 Consensus size: 18
27667363 GGCCCAAACC
*
27667373 ATTTTGAA-ATTAAATTT
1 ATTTTGAATTTTAAATTT
27667390 ATTTT-AATTTTAAATTT
1 ATTTTGAATTTTAAATTT
27667407 ATTTTGAATT
1 ATTTTGAATT
27667417 CAATTTAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 2 0.08
17 18 0.75
18 4 0.17
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (18 bp):
ATTTTGAATTTTAAATTT
Found at i:27667410 original size:11 final size:11
Alignment explanation
Indices: 27667379--27667464 Score: 54
Period size: 11 Copynumber: 7.7 Consensus size: 11
27667369 AACCATTTTG
*
27667379 AAATTAAATTT
1 AAATTTAATTT
*
27667390 -ATTTTAATTTT
1 AAATTTAA-TTT
*
27667401 AAATTTATTTT
1 AAATTTAATTT
* *
27667412 GAATTCAATTT
1 AAATTTAATTT
27667423 AAATTTGAATTT
1 AAATTT-AATTT
27667435 -AATTTAAATTT
1 AAATTT-AATTT
27667446 AACA-TT-ATTAT
1 AA-ATTTAATT-T
27667457 AAATTTAA
1 AAATTTAA
27667465 AAATAAAAGC
Statistics
Matches: 57, Mismatches: 10, Indels: 15
0.70 0.12 0.18
Matches are distributed among these distances:
10 9 0.16
11 33 0.58
12 14 0.25
13 1 0.02
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (11 bp):
AAATTTAATTT
Found at i:27667429 original size:17 final size:17
Alignment explanation
Indices: 27667409--27667445 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
27667399 TTAAATTTAT
27667409 TTTGAATTCAATTTAAA
1 TTTGAATTCAATTTAAA
*
27667426 TTTGAATTTAATTTAAA
1 TTTGAATTCAATTTAAA
27667443 TTT
1 TTT
27667446 AACATTATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.38, C:0.03, G:0.05, T:0.54
Consensus pattern (17 bp):
TTTGAATTCAATTTAAA
Found at i:27667465 original size:6 final size:6
Alignment explanation
Indices: 27667382--27667447 Score: 50
Period size: 6 Copynumber: 11.7 Consensus size: 6
27667372 CATTTTGAAA
* * * * *
27667382 TTAAAT TT-ATT TTAATT TTAAAT TT-ATT TTGAA- TTCAAT TTAAAT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
*
27667427 TTGAAT TT-AAT TTAAAT TTAA
1 TTAAAT TTAAAT TTAAAT TTAA
27667448 CATTATTATA
Statistics
Matches: 49, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
5 17 0.35
6 32 0.65
ACGTcount: A:0.39, C:0.02, G:0.03, T:0.56
Consensus pattern (6 bp):
TTAAAT
Found at i:27668203 original size:34 final size:31
Alignment explanation
Indices: 27668159--27668225 Score: 82
Period size: 32 Copynumber: 2.1 Consensus size: 31
27668149 CATTATAAGT
*
27668159 TAAATGCATTAAATAAATATTAAGTAA-TATTTAA
1 TAAAGGCATT-AAT-AATATTAA-TAATTA-TTAA
27668193 TAAAGGCATTAATAATATTAATAATTATTAA
1 TAAAGGCATTAATAATATTAATAATTATTAA
27668224 TA
1 TA
27668226 TTATAATAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
31 9 0.29
32 10 0.32
33 3 0.10
34 9 0.29
ACGTcount: A:0.52, C:0.03, G:0.06, T:0.39
Consensus pattern (31 bp):
TAAAGGCATTAATAATATTAATAATTATTAA
Found at i:27668224 original size:16 final size:15
Alignment explanation
Indices: 27668200--27668237 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
27668190 TAATAAAGGC
27668200 ATTAATAATATTAATA
1 ATTAATAATATT-ATA
*
27668216 ATTATTAATATTATA
1 ATTAATAATATTATA
27668231 A-TAATAA
1 ATTAATAA
27668238 AGAAATTAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 5 0.25
15 4 0.20
16 11 0.55
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
ATTAATAATATTATA
Found at i:27669430 original size:29 final size:29
Alignment explanation
Indices: 27669392--27669458 Score: 89
Period size: 29 Copynumber: 2.3 Consensus size: 29
27669382 TAAACAGTTC
*
27669392 AAAAATTACATTTTGACCCCAAAACTTCA
1 AAAAATTACATTTTAACCCCAAAACTTCA
* * *
27669421 AAAAATTACATTTTAACCCCGAACCTTCC
1 AAAAATTACATTTTAACCCCAAAACTTCA
*
27669450 TAAAATTAC
1 AAAAATTAC
27669459 CGTTTCACCC
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.43, C:0.25, G:0.03, T:0.28
Consensus pattern (29 bp):
AAAAATTACATTTTAACCCCAAAACTTCA
Found at i:27669484 original size:58 final size:56
Alignment explanation
Indices: 27669391--27669793 Score: 305
Period size: 59 Copynumber: 6.9 Consensus size: 56
27669381 CTAAACAGTT
** * *
27669391 CAAAAATTA-CATTTTGACCCCAAAAC-TTCAAAAAATTACATTTTAACCCCGAACCTT-C
1 CAAAAATTACCATTTT-ACCCTTAAACTTTC-CAAAATT-CATTTTAACCCCG-A-TTTAC
* * * *
27669449 CTAAAATTACCGTTTCACCCTTAAACTTTCCAAAATCTCATTTTAACCTCGATTTCAC
1 CAAAAATTACCATTTTACCCTTAAACTTTCCAAAAT-TCATTTTAACCCCGATTT-AC
*
27669507 CAAAAAATTACCATTTTACCC-CAAACTTTCCAAAATTCTATTTTAACCCCGATTTCAC
1 C-AAAAATTACCATTTTACCCTTAAACTTTCCAAAATTC-ATTTTAACCCCGATTT-AC
* * *
27669565 CAAAAATTACCGTTTTACCCTTGAACTTTCCAAAATTCCATTTTTAACCTCGATTTCAC
1 CAAAAATTACCATTTTACCCTTAAACTTTCCAAAATT-CA-TTTTAACCCCGATTT-AC
* *
27669624 CAAAAATTACCATTTTACCCCCT-AACTTTCCAAAATTCCATTTTTAACCCCGGTTTCAC
1 CAAAAATTACCATTTTA-CCCTTAAACTTTCCAAAATT-CA-TTTTAACCCCGATTT-AC
* * * ** * * *
27669683 TAAAAATCACTATTTTACCCTCGAGCTTTCC-AAATCCCATTTTTAACCTCGATTTCAC
1 CAAAAATTACCATTTTACCCTTAAACTTTCCAAAAT-TCA-TTTTAACCCCGATTT-AC
* * *** * *
27669741 CAAAAATTATCGTTTTACCCCCGAACCTTCAAAAATCTCATTTTTAACCCCGA
1 CAAAAATTACCATTTTACCCTTAAACTTTCCAAAAT-TCA-TTTTAACCCCGA
27669794 ATTTTCCCCA
Statistics
Matches: 290, Mismatches: 41, Indels: 27
0.81 0.11 0.08
Matches are distributed among these distances:
56 2 0.01
57 21 0.07
58 131 0.45
59 132 0.46
60 4 0.01
ACGTcount: A:0.33, C:0.29, G:0.04, T:0.33
Consensus pattern (56 bp):
CAAAAATTACCATTTTACCCTTAAACTTTCCAAAATTCATTTTAACCCCGATTTAC
Found at i:27669628 original size:59 final size:59
Alignment explanation
Indices: 27669451--27669789 Score: 402
Period size: 59 Copynumber: 5.8 Consensus size: 59
27669441 GAACCTTCCT
* * **
27669451 AAAATTACCGTTTCACCCTTAAACTTTCCAAAA-TCTCA-TTTTAACCTCGATTTCACCAA
1 AAAATTACCATTTTACCCTCGAACTTTCCAAAATTC-CATTTTTAACCTCGATTTCACC-A
* * *
27669510 AAAATTACCATTTTACCC-CAAACTTTCCAAAATTCTA-TTTTAACCCCGATTTCACCA
1 AAAATTACCATTTTACCCTCGAACTTTCCAAAATTCCATTTTTAACCTCGATTTCACCA
* *
27669567 AAAATTACCGTTTTACCCTTGAACTTTCCAAAATTCCATTTTTAACCTCGATTTCACCA
1 AAAATTACCATTTTACCCTCGAACTTTCCAAAATTCCATTTTTAACCTCGATTTCACCA
* * * * *
27669626 AAAATTACCATTTTACCCCCTAACTTTCCAAAATTCCATTTTTAACCCCGGTTTCACTA
1 AAAATTACCATTTTACCCTCGAACTTTCCAAAATTCCATTTTTAACCTCGATTTCACCA
* * * *
27669685 AAAATCACTATTTTACCCTCGAGCTTTCC-AAATCCCATTTTTAACCTCGATTTCACCA
1 AAAATTACCATTTTACCCTCGAACTTTCCAAAATTCCATTTTTAACCTCGATTTCACCA
* * * * *
27669743 AAAATTATCGTTTTACCCCCGAACCTT-CAAAAATCTCATTTTTAACC
1 AAAATTACCATTTTACCCTCGAACTTTCCAAAATTC-CATTTTTAACC
27669790 CCGAATTTTC
Statistics
Matches: 240, Mismatches: 35, Indels: 10
0.84 0.12 0.04
Matches are distributed among these distances:
57 19 0.08
58 97 0.40
59 124 0.52
ACGTcount: A:0.32, C:0.29, G:0.04, T:0.35
Consensus pattern (59 bp):
AAAATTACCATTTTACCCTCGAACTTTCCAAAATTCCATTTTTAACCTCGATTTCACCA
Found at i:27669674 original size:30 final size:29
Alignment explanation
Indices: 27669588--27669674 Score: 83
Period size: 30 Copynumber: 3.0 Consensus size: 29
27669578 TTTACCCTTG
*
27669588 AACTTTCCAAAATTCCATTTTTAA-CCTC
1 AACTTTCCAAAATTCCATTTTTAACCCCC
*
27669616 GA-TTTCACCAAAAATTACCA-TTTT-ACCCCC
1 AACTTT--CC-AAAATT-CCATTTTTAACCCCC
27669646 TAACTTTCCAAAATTCCATTTTTAACCCC
1 -AACTTTCCAAAATTCCATTTTTAACCCC
27669675 GGTTTCACTA
Statistics
Matches: 47, Mismatches: 3, Indels: 16
0.71 0.05 0.24
Matches are distributed among these distances:
27 3 0.06
28 4 0.09
29 13 0.28
30 20 0.43
31 4 0.09
32 3 0.06
ACGTcount: A:0.32, C:0.31, G:0.01, T:0.36
Consensus pattern (29 bp):
AACTTTCCAAAATTCCATTTTTAACCCCC
Found at i:27669689 original size:30 final size:29
Alignment explanation
Indices: 27669489--27669748 Score: 106
Period size: 29 Copynumber: 8.9 Consensus size: 29
27669479 CAAAATCTCA
*
27669489 TTTTAACCTCGATTTCACCAAAAAATTACCA-
1 TTTTAACCCCGATTTCA-C-AAAAATT-CCAT
* *
27669520 TTTT-ACCCCAAACTTTC-C-AAAATTCTA-
1 TTTTAACCCC-GA-TTTCACAAAAATTCCAT
*
27669547 TTTTAACCCCGATTTCACCAAAAATTACC-G
1 TTTTAACCCCGATTTCA-CAAAAATT-CCAT
*
27669577 TTTT-ACCCTTGAACTTTC-C-AAAATTCCAT
1 TTTTAACCC-CG-A-TTTCACAAAAATTCCAT
*
27669606 TTTTAACCTCGATTTCACCAAAAATTACCA-
1 TTTTAACCCCGATTTCA-CAAAAATT-CCAT
* *
27669636 TTTTACCCCCTAACTTTC-C-AAAATTCCAT
1 TTTTAACCCC-GA-TTTCACAAAAATTCCAT
*
27669665 TTTTAACCCCGGTTTCACTAAAAA-T-CACT
1 TTTTAACCCCGATTTCAC-AAAAATTCCA-T
*
27669694 ATTTT-ACCCTCGAGCTTTC-C--AAATCCCAT
1 -TTTTAACCC-CGA--TTTCACAAAAATTCCAT
*
27669723 TTTTAACCTCGATTTCACCAAAAATT
1 TTTTAACCCCGATTTCA-CAAAAATT
27669749 ATCGTTTTAC
Statistics
Matches: 175, Mismatches: 19, Indels: 71
0.66 0.07 0.27
Matches are distributed among these distances:
26 8 0.05
27 15 0.09
28 32 0.18
29 47 0.27
30 46 0.26
31 11 0.06
32 16 0.09
ACGTcount: A:0.32, C:0.29, G:0.04, T:0.35
Consensus pattern (29 bp):
TTTTAACCCCGATTTCACAAAAATTCCAT
Found at i:27669723 original size:117 final size:118
Alignment explanation
Indices: 27669391--27669793 Score: 448
Period size: 117 Copynumber: 3.4 Consensus size: 118
27669381 CTAAACAGTT
* * * * *
27669391 CAAAAATTA-CATTTTGACCCCAAAAC-TTCAAAAAATTACA-TTTTAACCCCGAACCTT--CCT
1 CAAAAATTACCATTTT-ACCCCCAAACTTTC-CAAAATTCCATTTTTAACCCCG-A-TTTCACCA
* * * ** *
27669451 AAAATTACCGTTTCACCCTTAAACTTTCCAAAATCTCA-TTTTAACCTCGATTTCAC
62 AAAATCACCATTTTACCCTCGAACTTTCCAAAATCCCATTTTTAACCTCGATTTCAC
*
27669507 CAAAAAATTACCATTTTA-CCCCAAACTTTCCAAAATTCTA-TTTTAACCCCGATTTCACCAAAA
1 C-AAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAA
* * * *
27669570 ATTACCGTTTTACCCTTGAACTTTCCAAAATTCCATTTTTAACCTCGATTTCAC
65 ATCACCATTTTACCCTCGAACTTTCCAAAATCCCATTTTTAACCTCGATTTCAC
* * *
27669624 CAAAAATTACCATTTTACCCCCTAACTTTCCAAAATTCCATTTTTAACCCCGGTTTCACTAAAAA
1 CAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAAA
* *
27669689 TCACTATTTTACCCTCGAGCTTTCC-AAATCCCATTTTTAACCTCGATTTCAC
66 TCACCATTTTACCCTCGAACTTTCCAAAATCCCATTTTTAACCTCGATTTCAC
* * * * *
27669741 CAAAAATTATCGTTTTACCCCCGAACCTT-CAAAAATCTCATTTTTAACCCCGA
1 CAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTC-CATTTTTAACCCCGA
27669794 ATTTTCCCCA
Statistics
Matches: 252, Mismatches: 26, Indels: 17
0.85 0.09 0.06
Matches are distributed among these distances:
114 2 0.01
115 1 0.00
116 85 0.34
117 116 0.46
118 48 0.19
ACGTcount: A:0.33, C:0.29, G:0.04, T:0.33
Consensus pattern (118 bp):
CAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAAA
TCACCATTTTACCCTCGAACTTTCCAAAATCCCATTTTTAACCTCGATTTCAC
Found at i:27675226 original size:6 final size:6
Alignment explanation
Indices: 27675215--27675240 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
27675205 CGTACGGGCC
27675215 AAGGGA AAGGGA AAGGGA AAGGGA AA
1 AAGGGA AAGGGA AAGGGA AAGGGA AA
27675241 ATCAGCCTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.54, C:0.00, G:0.46, T:0.00
Consensus pattern (6 bp):
AAGGGA
Found at i:27675695 original size:3 final size:3
Alignment explanation
Indices: 27675687--27675714 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
27675677 CTTTAGACGT
27675687 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
27675715 ATACTTAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:27685644 original size:81 final size:81
Alignment explanation
Indices: 27685552--27685724 Score: 328
Period size: 81 Copynumber: 2.1 Consensus size: 81
27685542 TATTTCATGT
*
27685552 AATATAAAATAATTAAAATATTTTATAATAAGATATTACTTATCTATAAATTTTAATAGTTTAAA
1 AATATAAAATAATTAAAATATTTTAAAATAAGATATTACTTATCTATAAATTTTAATAGTTTAAA
27685617 TAATATAAGCATTTCA
66 TAATATAAGCATTTCA
*
27685633 AATATAAAATAATTAAAATATTTTAAAATAAGATATTACTTATTTATAAATTTTAATAGTTTAAA
1 AATATAAAATAATTAAAATATTTTAAAATAAGATATTACTTATCTATAAATTTTAATAGTTTAAA
27685698 TAATATAAGCATTTCA
66 TAATATAAGCATTTCA
27685714 AATATAAAATA
1 AATATAAAATA
27685725 TTTATCAACT
Statistics
Matches: 90, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
81 90 1.00
ACGTcount: A:0.51, C:0.04, G:0.03, T:0.41
Consensus pattern (81 bp):
AATATAAAATAATTAAAATATTTTAAAATAAGATATTACTTATCTATAAATTTTAATAGTTTAAA
TAATATAAGCATTTCA
Found at i:27687279 original size:17 final size:18
Alignment explanation
Indices: 27687242--27687279 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
27687232 GATTTTTCTT
* *
27687242 TTCCCTTTTCTTTCAATC
1 TTCCCTTTTCGTTCAACC
27687260 TTCCCTTTT-GTTCAACC
1 TTCCCTTTTCGTTCAACC
27687277 TTC
1 TTC
27687280 AAGCTTCAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.11, C:0.34, G:0.03, T:0.53
Consensus pattern (18 bp):
TTCCCTTTTCGTTCAACC
Found at i:27687770 original size:14 final size:15
Alignment explanation
Indices: 27687741--27687773 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
27687731 ACCTAATAAC
*
27687741 CCAAACCCATTTGAA
1 CCAAACCCAATTGAA
27687756 CCAAA-CCAATTGAA
1 CCAAACCCAATTGAA
27687770 CCAA
1 CCAA
27687774 GTCCAACCCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 12 0.71
15 5 0.29
ACGTcount: A:0.45, C:0.33, G:0.06, T:0.15
Consensus pattern (15 bp):
CCAAACCCAATTGAA
Found at i:27687869 original size:14 final size:14
Alignment explanation
Indices: 27687850--27687940 Score: 87
Period size: 14 Copynumber: 6.6 Consensus size: 14
27687840 TTGACTGTTA
*
27687850 ACCGTTAACCTTTG
1 ACCGTTGACCTTTG
27687864 ACCGTTGACCTTTG
1 ACCGTTGACCTTTG
* **
27687878 ACCATTGACAATTG
1 ACCGTTGACCTTTG
27687892 ACCGTTGA-CTGTTG
1 ACCGTTGACCT-TTG
* * *
27687906 GCCATTGACCATTG
1 ACCGTTGACCTTTG
*
27687920 ACCGTT-AACTTTG
1 ACCGTTGACCTTTG
27687933 ACCGTTGA
1 ACCGTTGA
27687941 TTATTTTTTC
Statistics
Matches: 60, Mismatches: 14, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
13 11 0.18
14 48 0.80
15 1 0.02
ACGTcount: A:0.22, C:0.25, G:0.20, T:0.33
Consensus pattern (14 bp):
ACCGTTGACCTTTG
Found at i:27687871 original size:7 final size:7
Alignment explanation
Indices: 27687827--27687940 Score: 70
Period size: 7 Copynumber: 16.6 Consensus size: 7
27687817 GCCATTGACT
*
27687827 TTGACCA
1 TTGACCG
*
27687834 TTGA-CT
1 TTGACCG
*
27687840 TTGACTG
1 TTGACCG
*
27687847 TTAACCG
1 TTGACCG
* *
27687854 TTAACCT
1 TTGACCG
27687861 TTGACCG
1 TTGACCG
*
27687868 TTGACCT
1 TTGACCG
*
27687875 TTGACCA
1 TTGACCG
**
27687882 TTGACAA
1 TTGACCG
27687889 TTGACCG
1 TTGACCG
*
27687896 TTGACTG
1 TTGACCG
* *
27687903 TTGGCCA
1 TTGACCG
*
27687910 TTGACCA
1 TTGACCG
27687917 TTGACCG
1 TTGACCG
* *
27687924 TT-AACT
1 TTGACCG
27687930 TTGACCG
1 TTGACCG
27687937 TTGA
1 TTGA
27687941 TTATTTTTTC
Statistics
Matches: 82, Mismatches: 23, Indels: 4
0.75 0.21 0.04
Matches are distributed among these distances:
6 9 0.11
7 73 0.89
ACGTcount: A:0.22, C:0.24, G:0.19, T:0.35
Consensus pattern (7 bp):
TTGACCG
Found at i:27687892 original size:28 final size:27
Alignment explanation
Indices: 27687861--27687940 Score: 106
Period size: 28 Copynumber: 2.9 Consensus size: 27
27687851 CCGTTAACCT
27687861 TTGACCGTTGACCTTTGACCATTGACAA
1 TTGACCGTTGA-CTTTGACCATTGACAA
* *
27687889 TTGACCGTTGACTGTTGGCCATTGACCA
1 TTGACCGTTGACT-TTGACCATTGACAA
* *
27687917 TTGACCGTTAACTTTGACCGTTGA
1 TTGACCGTTGACTTTGACCATTGA
27687941 TTATTTTTTC
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
27 11 0.24
28 35 0.76
ACGTcount: A:0.21, C:0.24, G:0.21, T:0.34
Consensus pattern (27 bp):
TTGACCGTTGACTTTGACCATTGACAA
Found at i:27689019 original size:3 final size:3
Alignment explanation
Indices: 27689007--27689039 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
27688997 TAGAATATTC
27689007 TAT T-T TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
27689040 TTGGAATTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 27 0.93
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TAT
Found at i:27701292 original size:14 final size:16
Alignment explanation
Indices: 27701263--27701299 Score: 51
Period size: 14 Copynumber: 2.4 Consensus size: 16
27701253 TTATGATAAA
27701263 AAATAAATTGTTAATT
1 AAATAAATTGTTAATT
27701279 AAATAAA-T-TTAATT
1 AAATAAATTGTTAATT
*
27701293 AATTAAA
1 AAATAAA
27701300 AAACTTAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 12 0.60
15 1 0.05
16 7 0.35
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.41
Consensus pattern (16 bp):
AAATAAATTGTTAATT
Found at i:27701296 original size:18 final size:18
Alignment explanation
Indices: 27701273--27701320 Score: 64
Period size: 18 Copynumber: 2.7 Consensus size: 18
27701263 AAATAAATTG
*
27701273 TTAATTAAATAAA-TTTAA
1 TTAATTAAA-AAACTTAAA
27701291 TTAATTAAAAAACTTAAA
1 TTAATTAAAAAACTTAAA
27701309 TTAA-TAAAAAAC
1 TTAATTAAAAAAC
27701321 AATAATCGTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
17 11 0.39
18 17 0.61
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.35
Consensus pattern (18 bp):
TTAATTAAAAAACTTAAA
Found at i:27704741 original size:23 final size:23
Alignment explanation
Indices: 27704698--27704744 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
27704688 ATTTGAATTT
*
27704698 TTTTTAAAATTTATTAAAAAATA
1 TTTTTAAAATTTACTAAAAAATA
*
27704721 TTTTTATAATTT-CTAAGAAAATA
1 TTTTTAAAATTTACTAA-AAAATA
27704744 T
1 T
27704745 ATATTTACTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 3 0.14
23 18 0.86
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (23 bp):
TTTTTAAAATTTACTAAAAAATA
Found at i:27705430 original size:21 final size:21
Alignment explanation
Indices: 27705403--27705446 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
27705393 GGAAGAAGAT
*
27705403 GAAAAAACAAGGAAGAAAGAAAA
1 GAAAAAA-AA-GAAAAAAGAAAA
27705426 GAAAAAAAAGAAAAAAGAAAA
1 GAAAAAAAAGAAAAAAGAAAA
27705447 TGAGGGCAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 11 0.55
22 2 0.10
23 7 0.35
ACGTcount: A:0.80, C:0.02, G:0.18, T:0.00
Consensus pattern (21 bp):
GAAAAAAAAGAAAAAAGAAAA
Found at i:27705557 original size:20 final size:21
Alignment explanation
Indices: 27705508--27705558 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 21
27705498 TTGACGATGG
*
27705508 TGACCAAATTAACAAAAAAAA
1 TGACCTAATTAACAAAAAAAA
** *
27705529 TGAAGTAATTAA-AATAAAAA
1 TGACCTAATTAACAAAAAAAA
27705549 TGACCTAATT
1 TGACCTAATT
27705559 TTATAGTGGC
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
20 15 0.62
21 9 0.38
ACGTcount: A:0.59, C:0.10, G:0.08, T:0.24
Consensus pattern (21 bp):
TGACCTAATTAACAAAAAAAA
Found at i:27705599 original size:18 final size:18
Alignment explanation
Indices: 27705576--27705614 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
27705566 GGCTAAACAG
27705576 ATAATTTATCTATTTTTA
1 ATAATTTATCTATTTTTA
27705594 ATAATTTATCTATTTTTA
1 ATAATTTATCTATTTTTA
27705612 ATA
1 ATA
27705615 TATAAATATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.59
Consensus pattern (18 bp):
ATAATTTATCTATTTTTA
Found at i:27718430 original size:14 final size:13
Alignment explanation
Indices: 27718393--27718435 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 13
27718383 TTATTTCATG
27718393 AAAAAAGAAAACAGT
1 AAAAAAGAAAAC--T
*
27718408 AAAAGAGAAAACT
1 AAAAAAGAAAACT
27718421 AACAAAAGAAAACT
1 AA-AAAAGAAAACT
27718435 A
1 A
27718436 TATAACATCG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 3 0.12
14 11 0.44
15 11 0.44
ACGTcount: A:0.72, C:0.09, G:0.12, T:0.07
Consensus pattern (13 bp):
AAAAAAGAAAACT
Found at i:27719354 original size:15 final size:16
Alignment explanation
Indices: 27719334--27719368 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
27719324 ATTTTTTTTA
27719334 ATTATTTAAAT-AAAT
1 ATTATTTAAATAAAAT
*
27719349 ATTATTTAACTAAAAT
1 ATTATTTAAATAAAAT
27719365 ATTA
1 ATTA
27719369 AATGCAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (16 bp):
ATTATTTAAATAAAAT
Found at i:27721043 original size:3 final size:3
Alignment explanation
Indices: 27721035--27721075 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
27721025 AGAGTGTTCA
27721035 TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TC
1 TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TC
27721076 TTCATCTGTG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.00, C:0.66, G:0.00, T:0.34
Consensus pattern (3 bp):
TCC
Found at i:27725125 original size:59 final size:59
Alignment explanation
Indices: 27725045--27725192 Score: 176
Period size: 59 Copynumber: 2.5 Consensus size: 59
27725035 AATGAATCTT
* * * *
27725045 AAAAAAATTTTAGGTATCAAATTAGTAAAAAATGTCAAGTTCAGATGT-C-AAATTG-GATC
1 AAAAAAAGTTTAGGTACCAAATTAGGAAAAAATGTCAAATTCA-A-GTACTAAATTGAG-TC
*
27725104 CAAAAAAGTTTAGGTACCAAATTAGGAAAAAATGTCAAATTCAAGTACTAAATTGAGTC
1 AAAAAAAGTTTAGGTACCAAATTAGGAAAAAATGTCAAATTCAAGTACTAAATTGAGTC
* * *
27725163 AAAAAAAGCTTAAGTACCAAATTAAGAAAA
1 AAAAAAAGTTTAGGTACCAAATTAGGAAAA
27725193 GGATCAAGTT
Statistics
Matches: 77, Mismatches: 9, Indels: 6
0.84 0.10 0.07
Matches are distributed among these distances:
57 2 0.03
58 2 0.03
59 72 0.94
60 1 0.01
ACGTcount: A:0.50, C:0.10, G:0.14, T:0.26
Consensus pattern (59 bp):
AAAAAAAGTTTAGGTACCAAATTAGGAAAAAATGTCAAATTCAAGTACTAAATTGAGTC
Found at i:27727171 original size:1 final size:1
Alignment explanation
Indices: 27727165--27727193 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
27727155 CATCGAAATT
27727165 CCCCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCC
27727194 AAAAAAAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:27727977 original size:30 final size:28
Alignment explanation
Indices: 27727929--27727993 Score: 71
Period size: 29 Copynumber: 2.2 Consensus size: 28
27727919 CCAATCCGAA
*
27727929 TATATGATGTTATAAAAATATTATATTA-AT
1 TATAT-ATGTTAAAAAAAT-TTAT-TTATAT
27727959 TATATATGTTAAATAAAATTTATTTATAT
1 TATATATGTTAAA-AAAATTTATTTATAT
27727988 T-TATAT
1 TATATAT
27727994 TTCTTTTTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
28 8 0.25
29 14 0.44
30 10 0.31
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.51
Consensus pattern (28 bp):
TATATATGTTAAAAAAATTTATTTATAT
Found at i:27728186 original size:41 final size:36
Alignment explanation
Indices: 27728104--27728182 Score: 95
Period size: 36 Copynumber: 2.1 Consensus size: 36
27728094 AAAAATTATA
* *
27728104 TTTAATACAATAAAATTTTATTTTTTTATTTTTATT
1 TTTAATACAATAAAATTTTATTTATTTATTTGTATT
*
27728140 TTTAATATAATAAAATATTTATTATATTTATGTTAGTATT
1 TTTAATACAATAAAAT-TTTATT-TATTTAT-TT-GTATT
27728180 TTT
1 TTT
27728183 TAATGTATTT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
36 15 0.42
37 6 0.17
38 6 0.17
39 2 0.06
40 7 0.19
ACGTcount: A:0.35, C:0.01, G:0.03, T:0.61
Consensus pattern (36 bp):
TTTAATACAATAAAATTTTATTTATTTATTTGTATT
Found at i:27734492 original size:52 final size:52
Alignment explanation
Indices: 27734413--27734548 Score: 263
Period size: 52 Copynumber: 2.6 Consensus size: 52
27734403 AAGAGAGAAC
27734413 AACTAGAGCATAACCAACCCCTAACACCTTATTCCATATAAGTGGATTGCCTA
1 AACTAG-GCATAACCAACCCCTAACACCTTATTCCATATAAGTGGATTGCCTA
27734466 AACTAGGCATAACCAACCCCTAACACCTTATTCCATATAAGTGGATTGCCTA
1 AACTAGGCATAACCAACCCCTAACACCTTATTCCATATAAGTGGATTGCCTA
27734518 AACTAGGCATAACCAACCCCTAACACCTTAT
1 AACTAGGCATAACCAACCCCTAACACCTTAT
27734549 CTTTAACAGA
Statistics
Matches: 83, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
52 77 0.93
53 6 0.07
ACGTcount: A:0.36, C:0.30, G:0.10, T:0.24
Consensus pattern (52 bp):
AACTAGGCATAACCAACCCCTAACACCTTATTCCATATAAGTGGATTGCCTA
Found at i:27735242 original size:23 final size:23
Alignment explanation
Indices: 27735209--27735253 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
27735199 TTTTTATTAA
* *
27735209 TTTTATGATTTTTAATAAATTTT
1 TTTTATAATTTTTAACAAATTTT
27735232 TTTTATAATTTTTAACAAATTT
1 TTTTATAATTTTTAACAAATTT
27735254 AAAATAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.62
Consensus pattern (23 bp):
TTTTATAATTTTTAACAAATTTT
Found at i:27742932 original size:15 final size:16
Alignment explanation
Indices: 27742912--27742947 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
27742902 AAATTTTTAA
27742912 AAATTATAAAAATA-T
1 AAATTATAAAAATATT
*
27742927 AAATTATTAAAATATT
1 AAATTATAAAAATATT
27742943 AAATT
1 AAATT
27742948 TTATTTTTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 13 0.68
16 6 0.32
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
AAATTATAAAAATATT
Found at i:27745341 original size:29 final size:30
Alignment explanation
Indices: 27745298--27745374 Score: 86
Period size: 31 Copynumber: 2.5 Consensus size: 30
27745288 TTTGAGTTAT
* *
27745298 AATTAAATATTTATGTGT-ATAATTGTAC-TA
1 AATTAAA-ATTTATGTATCA-AATTATACATA
27745328 AATTAAAATTTATGTATCAAATTATACATTA
1 AATTAAAATTTATGTATCAAATTATACA-TA
*
27745359 AACTAAAATTTATGTA
1 AATTAAAATTTATGTA
27745375 CAATTTTAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
29 16 0.39
30 8 0.20
31 17 0.41
ACGTcount: A:0.45, C:0.05, G:0.06, T:0.43
Consensus pattern (30 bp):
AATTAAAATTTATGTATCAAATTATACATA
Found at i:27745988 original size:20 final size:20
Alignment explanation
Indices: 27745965--27746036 Score: 78
Period size: 19 Copynumber: 3.7 Consensus size: 20
27745955 TGGTATACTG
27745965 ATAATATATTTTTAAATATT
1 ATAATATATTTTTAAATATT
*
27745985 ATAA-ATAATTTTAAA-ATT
1 ATAATATATTTTTAAATATT
*
27746003 -TAATATGTATTTTAAATATT
1 ATAATATAT-TTTTAAATATT
* *
27746023 TTATTATATTTTTA
1 ATAATATATTTTTA
27746037 TAAAATATTT
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
17 3 0.07
18 5 0.12
19 17 0.40
20 12 0.28
21 6 0.14
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (20 bp):
ATAATATATTTTTAAATATT
Found at i:27746514 original size:23 final size:23
Alignment explanation
Indices: 27746471--27746514 Score: 54
Period size: 24 Copynumber: 1.9 Consensus size: 23
27746461 TTTTTTAAGG
* *
27746471 ATGAAATTAAATTGTATATTTTT
1 ATGAAATAAAATTATATATTTTT
27746494 ATGATAATAAAATTATA-ATTT
1 ATGA-AATAAAATTATATATTT
27746515 CATCATTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 8 0.44
24 10 0.56
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.48
Consensus pattern (23 bp):
ATGAAATAAAATTATATATTTTT
Found at i:27750596 original size:5 final size:5
Alignment explanation
Indices: 27750583--27750622 Score: 62
Period size: 5 Copynumber: 7.8 Consensus size: 5
27750573 AGTATTCATG
*
27750583 ATCTA ATCTT ATCTAA ATCTA ATCTA ATCTA ATCTA ATCT
1 ATCTA ATCTA ATCT-A ATCTA ATCTA ATCTA ATCTA ATCT
27750623 TCCCTCCTTG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
5 28 0.88
6 4 0.12
ACGTcount: A:0.38, C:0.20, G:0.00, T:0.42
Consensus pattern (5 bp):
ATCTA
Found at i:27750895 original size:29 final size:29
Alignment explanation
Indices: 27750845--27750900 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
27750835 ATTTAATTTT
*
27750845 TAAAACTTTTTTATTTTAATCACTTAAAA
1 TAAAACTTTTTTAATTTAATCACTTAAAA
* *
27750874 TAAAA-TTTTTGTAATTTGATCATTTAA
1 TAAAACTTTTT-TAATTTAATCACTTAA
27750901 TTTTTAGAGT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 5 0.22
29 18 0.78
ACGTcount: A:0.39, C:0.07, G:0.04, T:0.50
Consensus pattern (29 bp):
TAAAACTTTTTTAATTTAATCACTTAAAA
Found at i:27752291 original size:2 final size:2
Alignment explanation
Indices: 27752284--27752341 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
27752274 TTTAAAATTA
27752284 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
27752326 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
27752342 TTTGCCAAAT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:27758314 original size:68 final size:67
Alignment explanation
Indices: 27758231--27758369 Score: 224
Period size: 68 Copynumber: 2.1 Consensus size: 67
27758221 ACTATTTGAA
*
27758231 TTAATCAATAAAATTAATACAAATATATAAACGATTAAAAATTACAATATAAGAAATAAATCTAA
1 TTAATCAATAAAATTAATACAAATATATAAACGATTAAAAATTAAAATATAAGAAATAAATCTAA
27758296 AT
66 AT
* * * *
27758298 TTAATTCAATAAAATTAATACAAATATATAGATGATTAAAAATTAAAATATAAGAATTAAATTTA
1 TTAA-TCAATAAAATTAATACAAATATATAAACGATTAAAAATTAAAATATAAGAAATAAATCTA
27758363 AAT
65 AAT
27758366 TTAA
1 TTAA
27758370 ACACATTAAA
Statistics
Matches: 66, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
67 4 0.06
68 62 0.94
ACGTcount: A:0.58, C:0.05, G:0.04, T:0.33
Consensus pattern (67 bp):
TTAATCAATAAAATTAATACAAATATATAAACGATTAAAAATTAAAATATAAGAAATAAATCTAA
AT
Found at i:27767091 original size:22 final size:22
Alignment explanation
Indices: 27767066--27767121 Score: 103
Period size: 22 Copynumber: 2.5 Consensus size: 22
27767056 TGGGCACTTA
27767066 TTGCTACAAGTCCCAAATTATG
1 TTGCTACAAGTCCCAAATTATG
27767088 TTGCTACAAGTCCCAAATTATG
1 TTGCTACAAGTCCCAAATTATG
*
27767110 TTGATACAAGTC
1 TTGCTACAAGTC
27767122 ATTGACACTA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.32, C:0.21, G:0.14, T:0.32
Consensus pattern (22 bp):
TTGCTACAAGTCCCAAATTATG
Found at i:27775490 original size:38 final size:38
Alignment explanation
Indices: 27775445--27775521 Score: 145
Period size: 38 Copynumber: 2.0 Consensus size: 38
27775435 AAATAAATTC
27775445 ATTTTAACATTTTACCAATAAAAATATTCAATATAAAT
1 ATTTTAACATTTTACCAATAAAAATATTCAATATAAAT
*
27775483 ATTTTAACATTTTACCATTAAAAATATTCAATATAAAT
1 ATTTTAACATTTTACCAATAAAAATATTCAATATAAAT
27775521 A
1 A
27775522 GAAGAAGCCC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.40
Consensus pattern (38 bp):
ATTTTAACATTTTACCAATAAAAATATTCAATATAAAT
Found at i:27779120 original size:25 final size:26
Alignment explanation
Indices: 27779050--27779114 Score: 105
Period size: 26 Copynumber: 2.5 Consensus size: 26
27779040 AATTTAGTAG
27779050 TTAGTAGGTGAAAGATCAAGAGTTTT
1 TTAGTAGGTGAAAGATCAAGAGTTTT
*
27779076 TTAGTAGATGAAAGATCAAGAG-TTT
1 TTAGTAGGTGAAAGATCAAGAGTTTT
*
27779101 TTAGTAGGTTAAAG
1 TTAGTAGGTGAAAG
27779115 GCCAAGGGTC
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
25 15 0.42
26 21 0.58
ACGTcount: A:0.37, C:0.03, G:0.26, T:0.34
Consensus pattern (26 bp):
TTAGTAGGTGAAAGATCAAGAGTTTT
Found at i:27782788 original size:25 final size:26
Alignment explanation
Indices: 27782726--27782796 Score: 99
Period size: 25 Copynumber: 2.8 Consensus size: 26
27782716 AATTTAGTAG
*
27782726 TTAGTAGGTGAAAGATCCAGAGTTTT
1 TTAGTAGGTGAAAGATCAAGAGTTTT
**
27782752 TTAGTAAATGAAAGATCAAGAG-TTT
1 TTAGTAGGTGAAAGATCAAGAGTTTT
*
27782777 TTAGTAGGTGAAAGGTCAAG
1 TTAGTAGGTGAAAGATCAAG
27782797 GGTCAAATCT
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
25 20 0.51
26 19 0.49
ACGTcount: A:0.37, C:0.06, G:0.27, T:0.31
Consensus pattern (26 bp):
TTAGTAGGTGAAAGATCAAGAGTTTT
Found at i:27786261 original size:19 final size:19
Alignment explanation
Indices: 27786239--27786281 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
27786229 AAATATTAAG
*
27786239 TTTTTCAAAAA-ATAAATTA
1 TTTTT-AAAAACAAAAATTA
27786258 TTTTTAAAAATCAAAAATTA
1 TTTTTAAAAA-CAAAAATTA
27786278 TTTT
1 TTTT
27786282 CATTTAAACA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 5 0.24
19 5 0.24
20 11 0.52
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.47
Consensus pattern (19 bp):
TTTTTAAAAACAAAAATTA
Found at i:27787912 original size:41 final size:41
Alignment explanation
Indices: 27787855--27787942 Score: 140
Period size: 41 Copynumber: 2.1 Consensus size: 41
27787845 ATTTTGGGTT
*
27787855 ACATCATATCTGGTTATATGGTTGAGTGATGACTTAGGCAA
1 ACATCATATCTGGTTATATGGTTGAGTGATGAATTAGGCAA
* * *
27787896 ACATCATCTCTGGTTATATGGTTGAGTGATGAATTTGGTAA
1 ACATCATATCTGGTTATATGGTTGAGTGATGAATTAGGCAA
27787937 ACATCA
1 ACATCA
27787943 AGTACAAACA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.30, C:0.12, G:0.23, T:0.35
Consensus pattern (41 bp):
ACATCATATCTGGTTATATGGTTGAGTGATGAATTAGGCAA
Found at i:27792786 original size:21 final size:19
Alignment explanation
Indices: 27792762--27792800 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 19
27792752 TTTATATTTA
27792762 TATATTGCATACATATATAAT
1 TATATT-CATACA-ATATAAT
*
27792783 TATATTTATACAATATAA
1 TATATTCATACAATATAA
27792801 AGATAAATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
20 5 0.29
21 6 0.35
ACGTcount: A:0.46, C:0.08, G:0.03, T:0.44
Consensus pattern (19 bp):
TATATTCATACAATATAAT
Found at i:27796003 original size:12 final size:13
Alignment explanation
Indices: 27795978--27796009 Score: 57
Period size: 12 Copynumber: 2.5 Consensus size: 13
27795968 TTTTATATTT
27795978 ATATAAAGGTTAA
1 ATATAAAGGTTAA
27795991 ATATAAA-GTTAA
1 ATATAAAGGTTAA
27796003 ATATAAA
1 ATATAAA
27796010 ATAGGTATCT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 12 0.63
13 7 0.37
ACGTcount: A:0.59, C:0.00, G:0.09, T:0.31
Consensus pattern (13 bp):
ATATAAAGGTTAA
Found at i:27796848 original size:47 final size:46
Alignment explanation
Indices: 27796781--27796872 Score: 157
Period size: 47 Copynumber: 2.0 Consensus size: 46
27796771 ATCTTCATCT
27796781 TCTTTGTCTGAACCATCTTACTCCACTTCCATAACCAACAATTCAA
1 TCTTTGTCTGAACCATCTTACTCCACTTCCATAACCAACAATTCAA
* *
27796827 TCTTTGTGTGAAACCATCTTACTCCACTTTCATAACCAACAATTCA
1 TCTTTGTCTG-AACCATCTTACTCCACTTCCATAACCAACAATTCA
27796873 GTTCTTTCTT
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
46 9 0.21
47 34 0.79
ACGTcount: A:0.30, C:0.30, G:0.05, T:0.34
Consensus pattern (46 bp):
TCTTTGTCTGAACCATCTTACTCCACTTCCATAACCAACAATTCAA
Found at i:27797807 original size:55 final size:53
Alignment explanation
Indices: 27797729--27797832 Score: 145
Period size: 55 Copynumber: 1.9 Consensus size: 53
27797719 CTTCTGTTAA
* *
27797729 GAAATAAATATCTAATGTTAATGAACCCTATAAGATATGATACATTTGAGCTT
1 GAAATAAATATCTAATATCAATGAACCCTATAAGATATGATACATTTGAGCTT
* * *
27797782 GAAATATAGATATCTAATATCAATGAACCTTGTAAGATATGATATATTTGA
1 GAAATA-A-ATATCTAATATCAATGAACCCTATAAGATATGATACATTTGA
27797833 ACTTAAAGAC
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
53 6 0.14
54 1 0.02
55 37 0.84
ACGTcount: A:0.42, C:0.10, G:0.13, T:0.35
Consensus pattern (53 bp):
GAAATAAATATCTAATATCAATGAACCCTATAAGATATGATACATTTGAGCTT
Found at i:27801284 original size:85 final size:85
Alignment explanation
Indices: 27801157--27801330 Score: 330
Period size: 85 Copynumber: 2.0 Consensus size: 85
27801147 ACATGTCAAC
27801157 AAAAACTCGTTCAGTTAGAGATGCTTTCTTGCCAACTGTGTGGAAAGTTTGTTTAATTGGACGAG
1 AAAAACTCGTTCAGTTAGAGATGCTTTCTTGCCAACTGTGTGGAAAGTTTGTTTAATTGGACGAG
*
27801222 CTTTCCTAACAACCGTGCAG
66 CTTTCCTAACAACAGTGCAG
*
27801242 AAAAACTCGTTCAGTTAGAGATGCTTTCTTGCCAACTTTGTGGAAAGTTTGTTTAATTGGACGAG
1 AAAAACTCGTTCAGTTAGAGATGCTTTCTTGCCAACTGTGTGGAAAGTTTGTTTAATTGGACGAG
27801307 CTTTCCTAACAACAGTGCAG
66 CTTTCCTAACAACAGTGCAG
27801327 AAAA
1 AAAA
27801331 CACGCTCTGT
Statistics
Matches: 87, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
85 87 1.00
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.32
Consensus pattern (85 bp):
AAAAACTCGTTCAGTTAGAGATGCTTTCTTGCCAACTGTGTGGAAAGTTTGTTTAATTGGACGAG
CTTTCCTAACAACAGTGCAG
Found at i:27801311 original size:42 final size:42
Alignment explanation
Indices: 27801179--27801311 Score: 124
Period size: 42 Copynumber: 3.1 Consensus size: 42
27801169 AGTTAGAGAT
27801179 GCTTTCTTGCCAACTGTGTGGAAAGTTTGTTTAATTGGACGA
1 GCTTTCTTGCCAACTGTGTGGAAAGTTTGTTTAATTGGACGA
* ** * * * ** * * * *
27801221 GCTTTCCTAACAACCGTGCAGAAAAACTCGTTCAGTTAGA-GA
1 GCTTTCTTGCCAACTGTG-TGGAAAGTTTGTTTAATTGGACGA
*
27801263 TGCTTTCTTGCCAACTTTGTGGAAAGTTTGTTTAATTGGACGA
1 -GCTTTCTTGCCAACTGTGTGGAAAGTTTGTTTAATTGGACGA
27801306 GCTTTC
1 GCTTTC
27801312 CTAACAACAG
Statistics
Matches: 63, Mismatches: 25, Indels: 6
0.67 0.27 0.06
Matches are distributed among these distances:
42 35 0.56
43 28 0.44
ACGTcount: A:0.24, C:0.18, G:0.23, T:0.35
Consensus pattern (42 bp):
GCTTTCTTGCCAACTGTGTGGAAAGTTTGTTTAATTGGACGA
Found at i:27804859 original size:129 final size:129
Alignment explanation
Indices: 27804629--27804886 Score: 464
Period size: 129 Copynumber: 2.0 Consensus size: 129
27804619 GTTAGAAATG
* *
27804629 ATCATGGTGGAGGCAGAACTTCTTGAAGGAAAGAGGAAATCATGGTAAGAGAATGAGCTAGTTGG
1 ATCATGGTGGAGGCAGAACTCCTTGAAGGAAAGAGGAAATCATGGTAAGAGAACGAGCTAGTTGG
27804694 TACATTGGAACTAAATGGCCTGCATCTCTCACTGTCACCAATGTCAGCCCCTCATATTCCTCCA
66 TACATTGGAACTAAATGGCCTGCATCTCTCACTGTCACCAATGTCAGCCCCTCATATTCCTCCA
*
27804758 ATCATGGTGGAGGCAGAACTCCTTGAAGGAAAGAGGAAATCATGGTAAGAGAACGAGCTGGTTGG
1 ATCATGGTGGAGGCAGAACTCCTTGAAGGAAAGAGGAAATCATGGTAAGAGAACGAGCTAGTTGG
*
27804823 TAGC-TTGGAACTAAATGGTCTGCATCTCTCACTGTCACCAATGTCAGCCCCTCATATTCCTCCA
66 TA-CATTGGAACTAAATGGCCTGCATCTCTCACTGTCACCAATGTCAGCCCCTCATATTCCTCCA
27804887 CATACCTCCA
Statistics
Matches: 124, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
129 123 0.99
130 1 0.01
ACGTcount: A:0.29, C:0.22, G:0.24, T:0.24
Consensus pattern (129 bp):
ATCATGGTGGAGGCAGAACTCCTTGAAGGAAAGAGGAAATCATGGTAAGAGAACGAGCTAGTTGG
TACATTGGAACTAAATGGCCTGCATCTCTCACTGTCACCAATGTCAGCCCCTCATATTCCTCCA
Found at i:27805324 original size:38 final size:39
Alignment explanation
Indices: 27805268--27805346 Score: 117
Period size: 38 Copynumber: 2.1 Consensus size: 39
27805258 AAAAACTTAT
* *
27805268 AATAGTTTTATAATTTTTTATTTTAA-TTTTAATTTTTAA
1 AATAGTTTTATAATTTTTT-TTTGAATTTTTAAATTTTAA
27805307 AATAGTTTTATAA-TTTTTTTTGAATTTTTAAATTTTAA
1 AATAGTTTTATAATTTTTTTTTGAATTTTTAAATTTTAA
27805345 AA
1 AA
27805347 AATTAATTAA
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
37 5 0.14
38 19 0.51
39 13 0.35
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.61
Consensus pattern (39 bp):
AATAGTTTTATAATTTTTTTTTGAATTTTTAAATTTTAA
Found at i:27805978 original size:17 final size:16
Alignment explanation
Indices: 27805951--27805993 Score: 59
Period size: 17 Copynumber: 2.6 Consensus size: 16
27805941 ATCAAAATCA
*
27805951 TATTTGTTATTTCTGT
1 TATTTGTTATTACTGT
27805967 TATTTAGTTATTACTGT
1 TATTT-GTTATTACTGT
27805984 TAGTTTGTTA
1 TA-TTTGTTA
27805994 ATTAGAGTAG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 5 0.21
17 16 0.67
18 3 0.12
ACGTcount: A:0.19, C:0.05, G:0.14, T:0.63
Consensus pattern (16 bp):
TATTTGTTATTACTGT
Found at i:27810461 original size:17 final size:16
Alignment explanation
Indices: 27810434--27810476 Score: 59
Period size: 17 Copynumber: 2.6 Consensus size: 16
27810424 TTATTTTCCA
*
27810434 TATTTGTTATTTCTGT
1 TATTTGTTATTACTGT
27810450 TATTTAGTTATTACTGT
1 TATTT-GTTATTACTGT
27810467 TAGTTTGTTA
1 TA-TTTGTTA
27810477 ATTAGAGTAG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 5 0.21
17 16 0.67
18 3 0.12
ACGTcount: A:0.19, C:0.05, G:0.14, T:0.63
Consensus pattern (16 bp):
TATTTGTTATTACTGT
Found at i:27815790 original size:16 final size:16
Alignment explanation
Indices: 27815765--27815798 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
27815755 TAAATAATTT
* *
27815765 TATTAGTAATAATTAA
1 TATTAATAATAATAAA
27815781 TATTAATAATAATAAA
1 TATTAATAATAATAAA
27815797 TA
1 TA
27815799 ATTTTGGTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (16 bp):
TATTAATAATAATAAA
Found at i:27815809 original size:19 final size:19
Alignment explanation
Indices: 27815755--27815803 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 19
27815745 AAATGTACAT
* *
27815755 TAAATAATTTTATTAGTAA
1 TAAATAATTTTAATAATAA
* *
27815774 TAATTAATATTAATAATAA
1 TAAATAATTTTAATAATAA
27815793 TAAATAATTTT
1 TAAATAATTTT
27815804 GGTAATTTTA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (19 bp):
TAAATAATTTTAATAATAA
Found at i:27816923 original size:30 final size:29
Alignment explanation
Indices: 27816889--27817168 Score: 171
Period size: 30 Copynumber: 9.6 Consensus size: 29
27816879 CTCGAATTTC
*
27816889 CTAAAAATTACATTTTAACCCCTAAACTT
1 CTAAAAATTACATTTTTACCCCTAAACTT
27816918 ACTAAAAATTACATTTTTACCCCTAAACTT
1 -CTAAAAATTACATTTTTACCCCTAAACTT
*
27816948 TTAAAAATTACATTTTTACCCCTAAACTT
1 CTAAAAATTACATTTTTACCCCTAAACTT
* * * * ***
27816977 -TCCAAAATTCCATTTTTTAACCTTGATTTTT
1 CT-AAAAATTACA-TTTTTACCCCT-AAACTT
* * *
27817008 CCAAAAAGTACCA-TTTTATCCC-AAACTT
1 CTAAAAATTA-CATTTTTACCCCTAAACTT
* * * * *
27817036 CCAAAAATTCCATTTTTAACCC-ATATTT
1 CTAAAAATTACATTTTTACCCCTAAACTT
* *
27817064 TTCCAAAATTACCATTTTTACCCCTAAACTT
1 CT-AAAAATTA-CATTTTTACCCCTAAACTT
* * * **
27817095 CAAAAAATTCCATTTTTA-ACCTCAATTTT
1 CTAAAAATTACATTTTTACCCCT-AAACTT
*
27817124 CCT-AAAATTACCA-TTTTACCCC-AAACTC
1 -CTAAAAATTA-CATTTTTACCCCTAAACTT
* *
27817152 CCAAAAATTCCATTTTT
1 CTAAAAATTACATTTTT
27817169 GATCTCGATT
Statistics
Matches: 190, Mismatches: 45, Indels: 32
0.71 0.17 0.12
Matches are distributed among these distances:
27 5 0.03
28 40 0.21
29 65 0.34
30 66 0.35
31 12 0.06
32 2 0.01
ACGTcount: A:0.36, C:0.25, G:0.01, T:0.38
Consensus pattern (29 bp):
CTAAAAATTACATTTTTACCCCTAAACTT
Found at i:27816977 original size:29 final size:29
Alignment explanation
Indices: 27816890--27817112 Score: 166
Period size: 29 Copynumber: 7.6 Consensus size: 29
27816880 TCGAATTTCC
* *
27816890 TAAAAATTACATTTTAACCCCTAAACTTAC
1 TAAAAATTACATTTTTACCCCTAAACTT-T
27816920 TAAAAATTACATTTTTACCCCTAAACTTT
1 TAAAAATTACATTTTTACCCCTAAACTTT
27816949 TAAAAATTACATTTTTACCCCTAAACTTT
1 TAAAAATTACATTTTTACCCCTAAACTTT
** * * ** *
27816978 CCAAAATTCCATTTTTTA-ACCTTGATTTT
1 TAAAAATTACA-TTTTTACCCCTAAACTTT
* * *
27817007 TCCAAAAAGTACCA-TTTTATCCC-AAACTTC
1 T--AAAAATTA-CATTTTTACCCCTAAACTTT
* * * * *
27817037 CAAAAATTCCATTTTTAACCC-ATATTTT
1 TAAAAATTACATTTTTACCCCTAAACTTT
* *
27817065 TCCAAAATTACCATTTTTACCCCTAAACTTC
1 T-AAAAATTA-CATTTTTACCCCTAAACTTT
* *
27817096 AAAAAATTCCATTTTTA
1 TAAAAATTACATTTTTA
27817113 ACCTCAATTT
Statistics
Matches: 149, Mismatches: 35, Indels: 19
0.73 0.17 0.09
Matches are distributed among these distances:
27 2 0.01
28 18 0.12
29 58 0.39
30 58 0.39
31 11 0.07
32 2 0.01
ACGTcount: A:0.37, C:0.23, G:0.01, T:0.39
Consensus pattern (29 bp):
TAAAAATTACATTTTTACCCCTAAACTTT
Found at i:27817038 original size:58 final size:59
Alignment explanation
Indices: 27816850--27817202 Score: 345
Period size: 59 Copynumber: 6.0 Consensus size: 59
27816840 TCTTAGAGGT
* *
27816850 CCCTAAACTGTCCAAAAATT--ATTTTTAACCTCGA-ATTTCCTAAAAATTA-CATTTTAAC
1 CCCTAAACT-TCCAAAAATTCCATTTTTAACCTTGATTTTTCC-AAAAATTACCATTTT-AC
* * * ** *
27816908 CCCTAAACTTACTAAAAATTACATTTTTACCCCTAAACTTTT--AAAAATTA-CATTTTTAC
1 CCCTAAACTT-CCAAAAATTCCATTTTTA-ACCTTGATTTTTCCAAAAATTACCA-TTTTAC
* *
27816967 CCCTAAACTTTCC-AAAATTCCATTTTTTAACCTTGATTTTTCCAAAAAGTACCATTTTAT
1 CCCTAAAC-TTCCAAAAATTCCA-TTTTTAACCTTGATTTTTCCAAAAATTACCATTTTAC
*
27817027 CCC-AAACTTCCAAAAATTCCATTTTTAACCCAT-ATTTTTCC-AAAATTACCATTTTTAC
1 CCCTAAACTTCCAAAAATTCCATTTTTAA-CCTTGATTTTTCCAAAAATTACCA-TTTTAC
* * * *
27817085 CCCTAAACTTCAAAAAATTCCATTTTTAACC-TCAATTTTCCTAAAATTACCATTTTAC
1 CCCTAAACTTCCAAAAATTCCATTTTTAACCTTGATTTTTCCAAAAATTACCATTTTAC
* * * *
27817143 CCC-AAACTCCCAAAAATTCCATTTTTGATCTCGATTTTTCTCAAAAATTACCATTTTAC
1 CCCTAAACTTCCAAAAATTCCATTTTTAACCTTGATTTTTC-CAAAAATTACCATTTTAC
27817202 C
1 C
27817203 ATCGGATGTC
Statistics
Matches: 250, Mismatches: 26, Indels: 37
0.80 0.08 0.12
Matches are distributed among these distances:
57 34 0.14
58 84 0.34
59 95 0.38
60 28 0.11
61 6 0.02
62 3 0.01
ACGTcount: A:0.35, C:0.25, G:0.02, T:0.38
Consensus pattern (59 bp):
CCCTAAACTTCCAAAAATTCCATTTTTAACCTTGATTTTTCCAAAAATTACCATTTTAC
Found at i:27817130 original size:29 final size:29
Alignment explanation
Indices: 27816860--27817199 Score: 150
Period size: 29 Copynumber: 11.6 Consensus size: 29
27816850 CCCTAAACTG
27816860 TCCAAAAATT--ATTTTTAACCTCGAA-TT
1 TCCAAAAATTCCATTTTTAACCTC-AATTT
* * *
27816887 TCCTAAAAATTACA-TTTTAACCCCTAAACTT
1 TCC-AAAAATTCCATTTTTAA--CCTCAATTT
* * * * *
27816918 ACTAAAAATTACATTTTTACCCCTAAACTTT
1 TCCAAAAATTCCATTTTTA-ACCTCAA-TTT
* * * *
27816949 T--AAAAATTACATTTTTACCCCTAAACTT
1 TCCAAAAATTCCATTTTTA-ACCTCAATTT
* *
27816977 TCC-AAAATTCCATTTTTTAACCTTGATTTT
1 TCCAAAAATTCCA-TTTTTAACC-TCAATTT
* * **
27817007 TCCAAAAAGTACCA-TTTTATCC-CAAACT
1 TCCAAAAA-TTCCATTTTTAACCTCAATTT
27817035 TCCAAAAATTCCATTTTTAACC-CATATTTT
1 TCCAAAAATTCCATTTTTAACCTCA-A-TTT
* **
27817065 TCC-AAAATTACCATTTTT-ACCCCTAAACT
1 TCCAAAAATT-CCATTTTTAACCTC-AATTT
*
27817094 TCAAAAAATTCCATTTTTAACCTCAATTT
1 TCCAAAAATTCCATTTTTAACCTCAATTT
* * **
27817123 TCCTAAAATTACCA-TTTT-ACCCCAAACT
1 TCCAAAAATT-CCATTTTTAACCTCAATTT
* * * *
27817151 CCCAAAAATTCCATTTTTGATCTCGATTTT
1 TCCAAAAATTCCATTTTTAACCTC-AATTT
27817181 TCTCAAAAATTACCATTTT
1 TC-CAAAAATT-CCATTTT
27817200 ACCATCGGAT
Statistics
Matches: 243, Mismatches: 41, Indels: 53
0.72 0.12 0.16
Matches are distributed among these distances:
27 10 0.04
28 48 0.20
29 79 0.33
30 69 0.28
31 26 0.11
32 11 0.05
ACGTcount: A:0.35, C:0.24, G:0.01, T:0.39
Consensus pattern (29 bp):
TCCAAAAATTCCATTTTTAACCTCAATTT
Found at i:27817228 original size:116 final size:116
Alignment explanation
Indices: 27816850--27817199 Score: 374
Period size: 116 Copynumber: 3.0 Consensus size: 116
27816840 TCTTAGAGGT
*
27816850 CCCTAAACTGTCCAAAAATT--ATTTTTAACCTCGAA-TTTCCTAAAAATTA-CATTTTAACCCC
1 CCCTAAACT-TCAAAAAATTCCATTTTTAACCTC-AATTTTCC-AAAAATTACCATTTT-ACCCC
* * * * * *
27816911 TAAACTTACTAAAAATTACATTTTTACCCCTAAACTTTT-AAAAATTA-CATTTTTAC
62 -AAAC-TCCCAAAAATTCCATTTTTAACCC-ATATTTTTCAAAAATTACCATTTTTAC
* * * * *
27816967 CCCTAAACTTTC-CAAAATTCCATTTTTTAACCTTGATTTTTCCAAAAAGTACCATTTTATCCCA
1 CCCTAAAC-TTCAAAAAATTCCA-TTTTTAACC-TCAATTTTCCAAAAATTACCATTTTACCCCA
* *
27817031 AACTTCCAAAAATTCCATTTTTAACCCATATTTTTCCAAAATTACCATTTTTAC
63 AACTCCCAAAAATTCCATTTTTAACCCATATTTTTCAAAAATTACCATTTTTAC
*
27817085 CCCTAAACTTCAAAAAATTCCATTTTTAACCTCAATTTTCCTAAAATTACCATTTTACCCCAAAC
1 CCCTAAACTTCAAAAAATTCCATTTTTAACCTCAATTTTCCAAAAATTACCATTTTACCCCAAAC
* *
27817150 TCCCAAAAATTCCATTTTTGATCTCGAT-TTTTCTCAAAAATTACCATTTT
66 TCCCAAAAATTCCATTTTT-AAC-CCATATTTT-TCAAAAATTACCATTTT
27817200 ACCATCGGAT
Statistics
Matches: 198, Mismatches: 22, Indels: 25
0.81 0.09 0.10
Matches are distributed among these distances:
116 59 0.30
117 55 0.28
118 51 0.26
119 21 0.11
120 12 0.06
ACGTcount: A:0.35, C:0.25, G:0.02, T:0.39
Consensus pattern (116 bp):
CCCTAAACTTCAAAAAATTCCATTTTTAACCTCAATTTTCCAAAAATTACCATTTTACCCCAAAC
TCCCAAAAATTCCATTTTTAACCCATATTTTTCAAAAATTACCATTTTTAC
Found at i:27823095 original size:21 final size:21
Alignment explanation
Indices: 27823064--27823129 Score: 80
Period size: 21 Copynumber: 3.1 Consensus size: 21
27823054 GGATTCAATG
*
27823064 GAAAAAGCAAAAAAGAAGAAGA
1 GAAAAA-CAAAAAAGAAAAAGA
27823086 GAAAAACAAAAAAGAAAAAGA
1 GAAAAACAAAAAAGAAAAAGA
* *
27823107 -AAAAGAGAAAAAAGAAAAGGA
1 GAAAA-ACAAAAAAGAAAAAGA
27823128 GA
1 GA
27823130 GGTCGAGGTG
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
20 4 0.10
21 28 0.72
22 7 0.18
ACGTcount: A:0.76, C:0.03, G:0.21, T:0.00
Consensus pattern (21 bp):
GAAAAACAAAAAAGAAAAAGA
Found at i:27823101 original size:13 final size:14
Alignment explanation
Indices: 27823082--27823118 Score: 58
Period size: 13 Copynumber: 2.7 Consensus size: 14
27823072 AAAAAAGAAG
27823082 AAGAGAAAAACAAA
1 AAGAGAAAAACAAA
*
27823096 AA-AGAAAAAGAAA
1 AAGAGAAAAACAAA
27823109 AAGAGAAAAA
1 AAGAGAAAAA
27823119 AGAAAAGGAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 12 0.57
14 9 0.43
ACGTcount: A:0.81, C:0.03, G:0.16, T:0.00
Consensus pattern (14 bp):
AAGAGAAAAACAAA
Found at i:27823119 original size:15 final size:15
Alignment explanation
Indices: 27823072--27823129 Score: 68
Period size: 15 Copynumber: 4.1 Consensus size: 15
27823062 TGGAAAAAGC
*
27823072 AAAAAAGAAGAAGAG
1 AAAAAAGAAAAAGAG
*
27823087 -AAAAACAAAAA-AG
1 AAAAAAGAAAAAGAG
27823100 -AAAAAGAAAAAGAG
1 AAAAAAGAAAAAGAG
*
27823114 AAAAAAGAAAAGGAG
1 AAAAAAGAAAAAGAG
27823129 A
1 A
27823130 GGTCGAGGTG
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
13 12 0.32
14 11 0.30
15 14 0.38
ACGTcount: A:0.78, C:0.02, G:0.21, T:0.00
Consensus pattern (15 bp):
AAAAAAGAAAAAGAG
Found at i:27823124 original size:27 final size:29
Alignment explanation
Indices: 27823066--27823124 Score: 79
Period size: 27 Copynumber: 2.1 Consensus size: 29
27823056 ATTCAATGGA
*
27823066 AAAAGCAAAAAAGAAGAAGAGAAAAACA-A
1 AAAAG-AAAAAAGAAAAAGAGAAAAACAGA
27823095 AAAAG-AAAAAGAAAAAGAGAAAAA-AGA
1 AAAAGAAAAAAGAAAAAGAGAAAAACAGA
27823122 AAA
1 AAA
27823125 GGAGAGGTCG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
26 1 0.04
27 22 0.79
29 5 0.18
ACGTcount: A:0.80, C:0.03, G:0.17, T:0.00
Consensus pattern (29 bp):
AAAAGAAAAAAGAAAAAGAGAAAAACAGA
Found at i:27824653 original size:92 final size:92
Alignment explanation
Indices: 27824494--27824917 Score: 607
Period size: 92 Copynumber: 4.5 Consensus size: 92
27824484 AAAACAATAT
* * * *
27824494 CAAGTATTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATAAAGTTTTAAACATCAATTCCTATCC
1 CAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTCAAACATCAATTCCTATCC
*
27824559 TCTTGAAGTTGCAGTGAAGTTGGATAG
66 TCTTGAAGTTGCAGTAAAGTTGGATAG
* ** *
27824586 CAAGTCTTTATCTCTTTGAAGTTGTAGTAAGAAAAAGATGAAGCTGT-AAACATCAATTCCTAAC
1 CAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCT-TCAAACATCAATTCCTATC
27824650 CTCTTGAAGTTGCAGTAAAGTTGGATAG
65 CTCTTGAAGTTGCAGTAAAGTTGGATAG
*
27824678 CAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTCAAACATAAATTCCTATCC
1 CAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTCAAACATCAATTCCTATCC
*
27824743 TCTTGAAGTTGCAGTAAAGTGGGATTAAAAACAATAG
66 TCTTGAAGTTGCAGTAAAGTTGG----------ATAG
*
27824780 CAAGTCTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAAGCTTCAAACATCAATTCCTATCC
1 CAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTCAAACATCAATTCCTATCC
27824845 TCTTGAAGTTGCAGTAAAGTTGGATAG
66 TCTTGAAGTTGCAGTAAAGTTGGATAG
* * *
27824872 TAAGTCTTTATCTCTCTGAAGTTGCAATAAGAGCAAGATGAAGCTT
1 CAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTT
27824918 TGACACCAAA
Statistics
Matches: 299, Mismatches: 21, Indels: 24
0.87 0.06 0.07
Matches are distributed among these distances:
91 1 0.00
92 208 0.70
93 1 0.00
102 89 0.30
ACGTcount: A:0.34, C:0.15, G:0.19, T:0.32
Consensus pattern (92 bp):
CAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTCAAACATCAATTCCTATCC
TCTTGAAGTTGCAGTAAAGTTGGATAG
Found at i:27824850 original size:102 final size:102
Alignment explanation
Indices: 27824674--27824869 Score: 365
Period size: 102 Copynumber: 1.9 Consensus size: 102
27824664 GTAAAGTTGG
*
27824674 ATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTCAAACATAAATTCCT
1 ATAGCAAGTCTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAAGCTTCAAACATAAATTCCT
27824739 ATCCTCTTGAAGTTGCAGTAAAGTGGGATTAAAAACA
66 ATCCTCTTGAAGTTGCAGTAAAGTGGGATTAAAAACA
*
27824776 ATAGCAAGTCTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAAGCTTCAAACATCAATTCCT
1 ATAGCAAGTCTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAAGCTTCAAACATAAATTCCT
*
27824841 ATCCTCTTGAAGTTGCAGTAAAGTTGGAT
66 ATCCTCTTGAAGTTGCAGTAAAGTGGGAT
27824870 AGTAAGTCTT
Statistics
Matches: 91, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
102 91 1.00
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.31
Consensus pattern (102 bp):
ATAGCAAGTCTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAAGCTTCAAACATAAATTCCT
ATCCTCTTGAAGTTGCAGTAAAGTGGGATTAAAAACA
Found at i:27824861 original size:52 final size:53
Alignment explanation
Indices: 27824689--27824861 Score: 160
Period size: 52 Copynumber: 3.4 Consensus size: 53
27824679 AAGTCTTTAT
* *
27824689 CTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTCAAACATAAATTCCTATC
1 CTCTCTGAAGTTGCAGTAAGAGCAAGATGAAGCTTCAAACATCAATTCCTATC
*** * *** * * * *
27824742 CTCT-TGAAGTTGCAGTAA-AGTGGGATTAA-AAAC-AATAGCAAGTCTTTAT-
1 CTCTCTGAAGTTGCAGTAAGAGCAAGATGAAGCTTCAAACATCAATTC-CTATC
**
27824791 CTCTCTGAAGTTATAGTAAGAGCAAGATGAAGCTTCAAACATCAATTCCTATC
1 CTCTCTGAAGTTGCAGTAAGAGCAAGATGAAGCTTCAAACATCAATTCCTATC
27824844 CTCT-TGAAGTTGCAGTAA
1 CTCTCTGAAGTTGCAGTAA
27824862 AGTTGGATAG
Statistics
Matches: 86, Mismatches: 28, Indels: 13
0.68 0.22 0.10
Matches are distributed among these distances:
49 11 0.13
50 16 0.19
51 14 0.16
52 29 0.34
53 16 0.19
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.29
Consensus pattern (53 bp):
CTCTCTGAAGTTGCAGTAAGAGCAAGATGAAGCTTCAAACATCAATTCCTATC
Found at i:27825063 original size:39 final size:39
Alignment explanation
Indices: 27825020--27825133 Score: 113
Period size: 39 Copynumber: 2.9 Consensus size: 39
27825010 CCTTGAGCCT
*
27825020 GGGCAGATTACCGTCAACCAATCTCTTACCCCGAGCTAG
1 GGGCAGATTACCATCAACCAATCTCTTACCCCGAGCTAG
** * * * * *
27825059 GGGCAGATTA-CATCCATTCGATCTTTTGCTCCGAGCTTG
1 GGGCAGATTACCAT-CAACCAATCTCTTACCCCGAGCTAG
* * *
27825098 GGGCAGATCACCATCAACTAATCTCCTACCCCGAGC
1 GGGCAGATTACCATCAACCAATCTCTTACCCCGAGC
27825134 CTGGAGCAGA
Statistics
Matches: 56, Mismatches: 17, Indels: 4
0.73 0.22 0.05
Matches are distributed among these distances:
38 2 0.04
39 51 0.91
40 3 0.05
ACGTcount: A:0.24, C:0.32, G:0.20, T:0.24
Consensus pattern (39 bp):
GGGCAGATTACCATCAACCAATCTCTTACCCCGAGCTAG
Found at i:27825702 original size:206 final size:206
Alignment explanation
Indices: 27825157--27826012 Score: 1183
Period size: 206 Copynumber: 4.2 Consensus size: 206
27825147 TAATTATCCA
* * * * * * * *
27825157 AAACAAGTTAGGCGGTCATCTTCTTGATGAGATACAGAGAAGTATACCAACTC--A---AGGCTC
1 AAACAAGTGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTC
* * *
27825217 AAAGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCGGGTCGAAGCAATAA
66 GATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAA
* * * *
27825282 AATGGTCAGCTTTCTGATGAGATACTGAGAGGTGGACCAAATTCGCCTTCCTGATGAGATACAGA
131 AATGGTCAGCTTCCTGATGAGATACTAAGAAGTGGACCAAATTCGCCTTCCTGATGAGATACAAA
*
27825347 GAAGCGAATTG
196 GAAGCGGATTG
* * * * * * * * * *
27825358 AAACAATTGAGGTGGTCATCTTCTTGATAAGATACAGAGAAGTATACCAACTC--A---AGGCTC
1 AAACAAGTGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTC
* * * * * * *
27825418 AAAGTAAGCAAATCTTCGAACCACAGCTTCCTAATGAGATACTGAGAAGCGGGTCAAAGCAATAA
66 GATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAA
*
27825483 AATGGTCAGCTTCCTGATGAGATACTAAGAAGTGGACCAAATTCGCCTTCCTAATGAGATACAAA
131 AATGGTCAGCTTCCTGATGAGATACTAAGAAGTGGACCAAATTCGCCTTCCTGATGAGATACAAA
**
27825548 GAAGCTTATTG
196 GAAGCGGATTG
*
27825559 AAACAAGTGATACGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTC
1 AAACAAGTGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTC
*
27825624 GATGTGAGCAAATCTTCGAACCCCAGCTTCCTTATGAGATACTGAGAAGCAGGTCGAAGCAATAA
66 GATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAA
*
27825689 AATGGTTAGCTTCCTGATGAGATACTAAGAAGTGGACCAAATTCGCCTTCCTGATGAGATACAAA
131 AATGGTCAGCTTCCTGATGAGATACTAAGAAGTGGACCAAATTCGCCTTCCTGATGAGATACAAA
*
27825754 GAAGCGGATTA
196 GAAGCGGATTG
* * * *
27825765 AAATAAGTGATGCGGTCATCTTTCTGATGAGACACTGGGAAGAAGACCAAATCAAACCCACGCTC
1 AAACAAGTGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTC
*
27825830 GATGTGAGCAAATTTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAA
66 GATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAA
* * ** *
27825895 AATGGTTAGCTTCCTGATAAGATACGGAGAAGTGGACCCAATTCGCCTTCCTGATGAGATACAAA
131 AATGGTCAGCTTCCTGATGAGATACTAAGAAGTGGACCAAATTCGCCTTCCTGATGAGATACAAA
*
27825960 GAAGCAGATTG
196 GAAGCGGATTG
27825971 AAACAAGTGATGCGGTCATCTTCCTGATGAGATACTGAGAAG
1 AAACAAGTGATGCGGTCATCTTCCTGATGAGATACTGAGAAG
27826013 CAGGTCGAAG
Statistics
Matches: 595, Mismatches: 55, Indels: 5
0.91 0.08 0.01
Matches are distributed among these distances:
201 229 0.38
203 1 0.00
206 365 0.61
ACGTcount: A:0.35, C:0.20, G:0.23, T:0.22
Consensus pattern (206 bp):
AAACAAGTGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTC
GATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAA
AATGGTCAGCTTCCTGATGAGATACTAAGAAGTGGACCAAATTCGCCTTCCTGATGAGATACAAA
GAAGCGGATTG
Found at i:27825910 original size:48 final size:48
Alignment explanation
Indices: 27825854--27826060 Score: 148
Period size: 48 Copynumber: 4.5 Consensus size: 48
27825844 TTCGAACCCC
27825854 AGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTT
1 AGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTT
* * * ** *
27825902 AGCTTCCTGATAAGATAC-G-G-AG-AAGTGGACCCAAT----TCG--
1 AGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTT
* ** * * * * *** *
27825940 -CCTTCCTGATGAGATACAAAGAAGCAGATTGAAACAAGTGATGCGGTC
1 AGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAA-TAAAATGGTT
*
27825988 ATCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTT
1 AGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTT
* *
27826036 AGCTTCCTAATGAGATACGGAGAAG
1 AGCTTCCTGATGAGATACTGAGAAG
27826061 TGAGCCAAAT
Statistics
Matches: 117, Mismatches: 30, Indels: 24
0.68 0.18 0.14
Matches are distributed among these distances:
37 15 0.13
39 1 0.01
40 4 0.03
41 7 0.06
42 1 0.01
44 9 0.08
45 2 0.02
46 2 0.02
47 1 0.01
48 44 0.38
49 31 0.26
ACGTcount: A:0.35, C:0.17, G:0.26, T:0.22
Consensus pattern (48 bp):
AGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTT
Found at i:27825989 original size:412 final size:402
Alignment explanation
Indices: 27825157--27826012 Score: 1174
Period size: 407 Copynumber: 2.1 Consensus size: 402
27825147 TAATTATCCA
* * * * * * * *
27825157 AAACAAGTTAGGCGGTCATCTTCTTGATGAGATACAGAGAAGTATACCAACTCAAGGCTCAAAGT
1 AAACAAGTGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAACGCTCAAAGT
*
27825222 GAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCGGGTCGAAGCAATAAAATGG
66 GAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGG
* * * *
27825287 TCAGCTTTCTGATGAGATACTGAGAGGTGGACCAAATTCGCCTTCCTGATGAGATACAGAGAAGC
131 TCAGCTTCCTGATGAGATACTAAGAAGTGGACCAAATTCGCCTTCCTGATGAGATACAAAGAAGC
* * * * * * * *
27825352 GAATTGAAACAATTGAGGTGGTCATCTTCTTGATAAGATACAGAGAAGTATACCAACTCAAGGCT
196 GAATTAAAACAAGTGAGGCGGTCATCTTCTTGATAAGACACAGAGAAGAAGACCAAATCAACGCT
*
27825417 CAAAGTAAGCAAATCTTCGAACCACAGCTTCCTAATGAGATACTGAGAAGCGGGTCAAAGCAATA
261 CAAAGTAAGCAAATCTTCGAACCACAGCTTCCTAATGAGATACTGAGAAGCAGGTCAAAGCAATA
* *
27825482 AAATGGTCAGCTTCCTGATGAGATACTAAGAAGTGGACCAAATTCGCCTTCCTAATGAGATACAA
326 AAATGGTCAGCTTCCTGATAAGATACGAAGAAGTGGACCAAATTCGCCTTCCTAATGAGATACAA
**
27825547 AGAAGCTTATTG
391 AGAAGCAGATTG
*
27825559 AAACAAGTGATACGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTC
1 AAACAAGTGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATC--A---ACGCTC
* * *
27825624 GATGTGAGCAAATCTTCGAACCCCAGCTTCCTTATGAGATACTGAGAAGCAGGTCGAAGCAATAA
61 AAAGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAA
*
27825689 AATGGTTAGCTTCCTGATGAGATACTAAGAAGTGGACCAAATTCGCCTTCCTGATGAGATACAAA
126 AATGGTCAGCTTCCTGATGAGATACTAAGAAGTGGACCAAATTCGCCTTCCTGATGAGATACAAA
* * * * * *
27825754 GAAGCGGATTAAAATAAGTGATGCGGTCATCTT-TCTGATGAGACACTGGGAAGAAGACCAAATC
191 GAAGCGAATTAAAACAAGTGAGGCGGTCATCTTCT-TGATAAGACACAGAGAAGAAGACCAAATC
* * * * * *
27825818 AAACCCACGCTCGATGTGAGCAAATTTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGG
255 --A---ACGCTCAAAGTAAGCAAATCTTCGAACCACAGCTTCCTAATGAGATACTGAGAAGCAGG
* * * * *
27825883 TCGAAGCAATAAAATGGTTAGCTTCCTGATAAGATACGGAGAAGTGGACCCAATTCGCCTTCCTG
315 TCAAAGCAATAAAATGGTCAGCTTCCTGATAAGATACGAAGAAGTGGACCAAATTCGCCTTCCTA
27825948 ATGAGATACAAAGAAGCAGATTG
380 ATGAGATACAAAGAAGCAGATTG
27825971 AAACAAGTGATGCGGTCATCTTCCTGATGAGATACTGAGAAG
1 AAACAAGTGATGCGGTCATCTTCCTGATGAGATACTGAGAAG
27826013 CAGGTCGAAG
Statistics
Matches: 394, Mismatches: 49, Indels: 12
0.87 0.11 0.03
Matches are distributed among these distances:
402 45 0.11
404 1 0.00
406 1 0.00
407 175 0.44
409 1 0.00
412 171 0.43
ACGTcount: A:0.35, C:0.20, G:0.23, T:0.22
Consensus pattern (402 bp):
AAACAAGTGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAACGCTCAAAGT
GAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGG
TCAGCTTCCTGATGAGATACTAAGAAGTGGACCAAATTCGCCTTCCTGATGAGATACAAAGAAGC
GAATTAAAACAAGTGAGGCGGTCATCTTCTTGATAAGACACAGAGAAGAAGACCAAATCAACGCT
CAAAGTAAGCAAATCTTCGAACCACAGCTTCCTAATGAGATACTGAGAAGCAGGTCAAAGCAATA
AAATGGTCAGCTTCCTGATAAGATACGAAGAAGTGGACCAAATTCGCCTTCCTAATGAGATACAA
AGAAGCAGATTG
Found at i:27826096 original size:134 final size:134
Alignment explanation
Indices: 27825856--27826146 Score: 449
Period size: 134 Copynumber: 2.2 Consensus size: 134
27825846 CGAACCCCAG
*
27825856 CTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTGATAAGATACG
1 CTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTAATAAGATACG
* * * * ** *
27825921 GAGAAGTGGACCCAATTCGCCTTCCTGATGAGATACAAAGAAGCAGATTGAAACAAGTGATGCGG
66 GAGAAGTGGACCAAATCCGCCTTCCTGATGAAACACAAAGAAGCAGATCAAAACAAGTGATGCAG
27825986 TCAT
131 TCAT
*
27825990 CTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTAATGAGATACG
1 CTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTAATAAGATACG
* **
27826055 GAGAAGT-GAGCCAAATCCGTCTTCCTGATGAAACACAAAGAAGTGGATCAAAACAAGTGATGCA
66 GAGAAGTGGA-CCAAATCCGCCTTCCTGATGAAACACAAAGAAGCAGATCAAAACAAGTGATGCA
27826119 GTCAT
130 GTCAT
*
27826124 CTTCCTGATGAGATACCGAGAAG
1 CTTCCTGATGAGATACTGAGAAG
27826147 AAGGCCAAGT
Statistics
Matches: 143, Mismatches: 13, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
133 2 0.01
134 141 0.99
ACGTcount: A:0.35, C:0.18, G:0.25, T:0.22
Consensus pattern (134 bp):
CTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTAATAAGATACG
GAGAAGTGGACCAAATCCGCCTTCCTGATGAAACACAAAGAAGCAGATCAAAACAAGTGATGCAG
TCAT
Found at i:27826871 original size:25 final size:25
Alignment explanation
Indices: 27826821--27826877 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 25
27826811 TCATCAACAG
* * *
27826821 TGCCATCACCAGCTTCAACTTGCTC
1 TGCCACCACCAGCTTCAACCTACTC
*
27826846 TGCCACCACCTGCTTCAACCTACTC
1 TGCCACCACCAGCTTCAACCTACTC
*
27826871 TACCACC
1 TGCCACC
27826878 GCCACTGCCA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.21, C:0.46, G:0.09, T:0.25
Consensus pattern (25 bp):
TGCCACCACCAGCTTCAACCTACTC
Found at i:27828327 original size:29 final size:30
Alignment explanation
Indices: 27828210--27828415 Score: 208
Period size: 30 Copynumber: 6.9 Consensus size: 30
27828200 CCTTGAAGGT
* *
27828210 CCCTAAACTATCC-AAAAATTATATTTTGAC
1 CCCTAAACT-TCCTAAAAATTACATTTTTAC
* * *
27828240 CCTCCAAATTTCCTAAAAATTACATTTTAAC
1 CC-CTAAACTTCCTAAAAATTACATTTTTAC
*
27828271 CCCTAAACTTCTTAAAAATTACATTTTTAC
1 CCCTAAACTTCCTAAAAATTACATTTTTAC
* * *
27828301 CCTTGAACTTCCTAAAAATTACATTTTGAC
1 CCCTAAACTTCCTAAAAATTACATTTTTAC
**
27828331 CTTTAAAC-TCCTTAAAAA-TACATTTTTAC
1 CCCTAAACTTCC-TAAAAATTACATTTTTAC
* *
27828360 CCCAAAACTT-TTAAAAATTACATTTTTAC
1 CCCTAAACTTCCTAAAAATTACATTTTTAC
*
27828389 CCCTAAACTTTCC--AAAATTCCATTTTT
1 CCCTAAAC-TTCCTAAAAATTACATTTTT
27828416 TGACCTTGAT
Statistics
Matches: 147, Mismatches: 22, Indels: 15
0.80 0.12 0.08
Matches are distributed among these distances:
28 6 0.04
29 49 0.33
30 70 0.48
31 22 0.15
ACGTcount: A:0.37, C:0.24, G:0.01, T:0.38
Consensus pattern (30 bp):
CCCTAAACTTCCTAAAAATTACATTTTTAC
Found at i:27828508 original size:59 final size:61
Alignment explanation
Indices: 27828372--27828590 Score: 156
Period size: 58 Copynumber: 3.7 Consensus size: 61
27828362 CAAAACTTTT
* **
27828372 AAAAATTA-CATTTTTACCC-CTAAACTTTCCAAAATTCCATTTTTTGACCTTGATTTTTCC
1 AAAAATTACCA-TTTTACCCTCTAAACTTTCCAAAATTCCATTTATTGACCTCAATTTTTCC
* **
27828432 AAAAAGTACCA-GATACCCTC-AAAC-TTCCAAAAATTCCA-TTATTGACCTCAATTTTTCC
1 AAAAATTACCATTTTACCCTCTAAACTTTCC-AAAATTCCATTTATTGACCTCAATTTTTCC
* * * * * *
27828490 TAAAATTACCATTTTACCCT-TGAA-TGTCTAAAATTCCATTT-TT-ATCCCCGAA-CTTTCC
1 AAAAATTACCATTTTACCCTCTAAACTTTCCAAAATTCCATTTATTGA-CCTC-AATTTTTCC
* * * * *
27828548 CAAAATTACCATTTTGCCCT-TTAAGTGTCCAAAATTACCATTT
1 AAAAATTACCATTTTACCCTCTAAACTTTCCAAAATT-CCATTT
27828591 TGCCCCACGA
Statistics
Matches: 129, Mismatches: 19, Indels: 22
0.76 0.11 0.13
Matches are distributed among these distances:
57 1 0.01
58 70 0.54
59 42 0.33
60 14 0.11
61 2 0.02
ACGTcount: A:0.32, C:0.25, G:0.05, T:0.37
Consensus pattern (61 bp):
AAAAATTACCATTTTACCCTCTAAACTTTCCAAAATTCCATTTATTGACCTCAATTTTTCC
Found at i:27828522 original size:28 final size:29
Alignment explanation
Indices: 27828491--27828591 Score: 100
Period size: 29 Copynumber: 3.5 Consensus size: 29
27828481 AATTTTTCCT
*
27828491 AAAATTACCATTTTACCCTTGAA-TGTCT
1 AAAATTACCATTTTACCCTTGAACTGTCC
* *
27828519 AAAATT-CCATTTTTATCCC-CGAACTTTCCC
1 AAAATTACCA-TTTTA-CCCTTGAACTGT-CC
* * *
27828549 AAAATTACCATTTTGCCCTTTAAGTGTCC
1 AAAATTACCATTTTACCCTTGAACTGTCC
27828578 AAAATTACCATTTT
1 AAAATTACCATTTT
27828592 GCCCCACGAG
Statistics
Matches: 59, Mismatches: 8, Indels: 11
0.76 0.10 0.14
Matches are distributed among these distances:
27 3 0.05
28 14 0.24
29 24 0.41
30 15 0.25
31 3 0.05
ACGTcount: A:0.31, C:0.25, G:0.06, T:0.39
Consensus pattern (29 bp):
AAAATTACCATTTTACCCTTGAACTGTCC
Found at i:27835679 original size:18 final size:18
Alignment explanation
Indices: 27835630--27835665 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
27835620 TAAATAATTA
*
27835630 TTAAAAATA-AAAAATAT
1 TTAAAATTATAAAAATAT
27835647 TTAAAATTATAAAAATAT
1 TTAAAATTATAAAAATAT
27835665 T
1 T
27835666 AGAATTATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (18 bp):
TTAAAATTATAAAAATAT
Found at i:27836071 original size:10 final size:10
Alignment explanation
Indices: 27836056--27836128 Score: 69
Period size: 10 Copynumber: 7.2 Consensus size: 10
27836046 TTAGATGTTG
*
27836056 TTTTTAATCA
1 TTTTTAATAA
27836066 TTTTT-ATAA
1 TTTTTAATAA
27836075 TTTATT-ATAA
1 TTT-TTAATAA
*
27836085 TTCTTAATAA
1 TTTTTAATAA
*
27836095 TTTTAAATACA
1 TTTTTAATA-A
27836106 TTTTTAATAA
1 TTTTTAATAA
*
27836116 TTATTTAAAAA
1 TT-TTTAATAA
27836127 TT
1 TT
27836129 CATGTCCACA
Statistics
Matches: 53, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
9 8 0.15
10 27 0.51
11 18 0.34
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (10 bp):
TTTTTAATAA
Found at i:27836112 original size:21 final size:21
Alignment explanation
Indices: 27836056--27836117 Score: 60
Period size: 21 Copynumber: 3.1 Consensus size: 21
27836046 TTAGATGTTG
*
27836056 TTTTTAAT-CATTTTT-ATAA
1 TTTTAAATACATTTTTAATAA
* *
27836075 -TTTATTATA-ATTCTTAATAA
1 TTTTA-AATACATTTTTAATAA
27836095 TTTTAAATACATTTTTAATAA
1 TTTTAAATACATTTTTAATAA
27836116 TT
1 TT
27836118 ATTTAAAAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
18 3 0.09
19 7 0.21
20 7 0.21
21 16 0.48
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.58
Consensus pattern (21 bp):
TTTTAAATACATTTTTAATAA
Found at i:27842426 original size:30 final size:31
Alignment explanation
Indices: 27842362--27842435 Score: 123
Period size: 31 Copynumber: 2.4 Consensus size: 31
27842352 ATGTAGATCG
* *
27842362 AATAAACCAAATTAATCTAGAAGCTATAAAA
1 AATAAATCAAATTAATCTAGAAGCAATAAAA
27842393 AATAAATCAAATTAATCTAGAAGCAAT-AAA
1 AATAAATCAAATTAATCTAGAAGCAATAAAA
27842423 AATAAATCAAATT
1 AATAAATCAAATT
27842436 GAAAATTTTC
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
30 16 0.39
31 25 0.61
ACGTcount: A:0.59, C:0.11, G:0.05, T:0.24
Consensus pattern (31 bp):
AATAAATCAAATTAATCTAGAAGCAATAAAA
Found at i:27843835 original size:45 final size:45
Alignment explanation
Indices: 27843779--27843869 Score: 173
Period size: 45 Copynumber: 2.0 Consensus size: 45
27843769 TTTAATCGAG
27843779 TGATCCAGTTGAGGGTTACACCAACTTAGTAAAACACTTAATAAA
1 TGATCCAGTTGAGGGTTACACCAACTTAGTAAAACACTTAATAAA
*
27843824 TGATCCGGTTGAGGGTTACACCAACTTAGTAAAACACTTAATAAA
1 TGATCCAGTTGAGGGTTACACCAACTTAGTAAAACACTTAATAAA
27843869 T
1 T
27843870 AGTATAATAT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.38, C:0.18, G:0.16, T:0.27
Consensus pattern (45 bp):
TGATCCAGTTGAGGGTTACACCAACTTAGTAAAACACTTAATAAA
Found at i:27849100 original size:17 final size:17
Alignment explanation
Indices: 27849065--27849107 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
27849055 CCCCCTTGAC
* *
27849065 CTTTAACCTTCCATCTT
1 CTTTAACTTTCCATATT
*
27849082 CTTTAACTTTTCATATT
1 CTTTAACTTTCCATATT
27849099 CTTGTAACT
1 CTT-TAACT
27849108 ATTTTTTCCT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
17 17 0.77
18 5 0.23
ACGTcount: A:0.21, C:0.26, G:0.02, T:0.51
Consensus pattern (17 bp):
CTTTAACTTTCCATATT
Found at i:27849559 original size:17 final size:17
Alignment explanation
Indices: 27849537--27849570 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
27849527 TTAAGTCCCA
27849537 CCACATGTAAATTTTTT
1 CCACATGTAAATTTTTT
27849554 CCACATGTAAATTTTTT
1 CCACATGTAAATTTTTT
27849571 ATTAGTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.18, G:0.06, T:0.47
Consensus pattern (17 bp):
CCACATGTAAATTTTTT
Found at i:27850208 original size:22 final size:22
Alignment explanation
Indices: 27850163--27850209 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
27850153 GTTGTAGTTG
* * *
27850163 TTTCGCTATTGTTTTTCTACTA
1 TTTCGCTATTATATTGCTACTA
*
27850185 TTTCGCTATTATATTGCTATTA
1 TTTCGCTATTATATTGCTACTA
27850207 TTT
1 TTT
27850210 TGTTGTTATT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.17, C:0.15, G:0.09, T:0.60
Consensus pattern (22 bp):
TTTCGCTATTATATTGCTACTA
Found at i:27855113 original size:17 final size:17
Alignment explanation
Indices: 27855093--27855127 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
27855083 CTGCACAATC
*
27855093 ACCAAATATCCACTGAA
1 ACCAAAAATCCACTGAA
*
27855110 ACCAAAAATCTACTGAA
1 ACCAAAAATCCACTGAA
27855127 A
1 A
27855128 ACTAAATTTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.51, C:0.26, G:0.06, T:0.17
Consensus pattern (17 bp):
ACCAAAAATCCACTGAA
Done.