Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032248.1 Gossypioides kirkii chromosome KI_06
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: 60359545
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 900 characters in sequence are not A, C, G, or T
File 182 of 193
Found at i:56726184 original size:30 final size:30
Alignment explanation
Indices: 56726127--56726184 Score: 75
Period size: 30 Copynumber: 1.9 Consensus size: 30
56726117 AATAAACTTA
*
56726127 TGTTCATGTTCGTTTGTTTATTTTTAAGCT
1 TGTTCATGTTCGTTTGTTTATTGTTAAGCT
56726157 TGTTCATGTTCAGTTT-TTGT-TTGTTAAG
1 TGTTCATGTTC-GTTTGTT-TATTGTTAAG
56726185 AATTTCAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
30 20 0.80
31 5 0.20
ACGTcount: A:0.14, C:0.09, G:0.19, T:0.59
Consensus pattern (30 bp):
TGTTCATGTTCGTTTGTTTATTGTTAAGCT
Found at i:56726289 original size:23 final size:22
Alignment explanation
Indices: 56726255--56726337 Score: 69
Period size: 23 Copynumber: 3.6 Consensus size: 22
56726245 TTAATGTTGA
*
56726255 CGAACATTTTCATTCAACTTAAT
1 CGAACATGTTCA-TCAACTTAAT
* *
56726278 CGAACATGTTCA-CGAATATTAAA
1 CGAACATGTTCATC-AA-CTTAAT
*
56726301 CGAACATGTTCATGAACATATAAT
1 CGAACATGTTCATCAAC-T-TAAT
*
56726325 TGAACATGTTCAT
1 CGAACATGTTCAT
56726338 AACATGTTCA
Statistics
Matches: 48, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
21 1 0.02
22 2 0.04
23 30 0.62
24 15 0.31
ACGTcount: A:0.39, C:0.18, G:0.11, T:0.33
Consensus pattern (22 bp):
CGAACATGTTCATCAACTTAAT
Found at i:56726363 original size:13 final size:12
Alignment explanation
Indices: 56726302--56726364 Score: 67
Period size: 12 Copynumber: 5.2 Consensus size: 12
56726292 AATATTAAAC
56726302 GAACATGTTCAT
1 GAACATGTTCAT
* *
56726314 GAACAT-ATAATT
1 GAACATGTTCA-T
56726326 GAACATGTTCAT
1 GAACATGTTCAT
56726338 -AACATGTTCAT
1 GAACATGTTCAT
*
56726349 GAACAATGTTAAT
1 GAAC-ATGTTCAT
56726362 GAA
1 GAA
56726365 TAATAAACAA
Statistics
Matches: 42, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
11 13 0.31
12 17 0.40
13 12 0.29
ACGTcount: A:0.41, C:0.13, G:0.14, T:0.32
Consensus pattern (12 bp):
GAACATGTTCAT
Found at i:56728606 original size:30 final size:30
Alignment explanation
Indices: 56728565--56728798 Score: 328
Period size: 30 Copynumber: 7.8 Consensus size: 30
56728555 GGATTTAAGG
*
56728565 AAGTTTGGGGGT-AAAATGGTAATTTTGGAA
1 AAGTTTTGGGGTCAAAAT-GTAATTTTGGAA
56728595 AAGTTTTGGGGTCAAAATGTAATTTTGGAA
1 AAGTTTTGGGGTCAAAATGTAATTTTGGAA
* * *
56728625 AAGGTTTGGGGTCAAAATATAATTTTAGAA
1 AAGTTTTGGGGTCAAAATGTAATTTTGGAA
* ***
56728655 AAGTTTAGGGGTCAAAATGTAATTTCCAAA
1 AAGTTTTGGGGTCAAAATGTAATTTTGGAA
*
56728685 AAGTTTTGGGGTCAAAATATAATTTTGGAA
1 AAGTTTTGGGGTCAAAATGTAATTTTGGAA
* *
56728715 AAATTTTAGGGTCAAAATGTAATTTTGGAA
1 AAGTTTTGGGGTCAAAATGTAATTTTGGAA
* *
56728745 AAATTTTAGGGTC-AAATGTAATTTTGGAA
1 AAGTTTTGGGGTCAAAATGTAATTTTGGAA
56728774 AAGTTTTGGGGTCAAAATGTAATTT
1 AAGTTTTGGGGTCAAAATGTAATTT
56728799 CTAGACAATT
Statistics
Matches: 182, Mismatches: 20, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
29 27 0.15
30 150 0.82
31 5 0.03
ACGTcount: A:0.37, C:0.04, G:0.24, T:0.35
Consensus pattern (30 bp):
AAGTTTTGGGGTCAAAATGTAATTTTGGAA
Found at i:56730676 original size:17 final size:17
Alignment explanation
Indices: 56730654--56730697 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
56730644 TTAAATTTAA
56730654 TTAAATTTAAGAT-AAAT
1 TTAAATTTAA-ATAAAAT
*
56730671 TTAAATCTAAATAAAAT
1 TTAAATTTAAATAAAAT
*
56730688 TTAAAATTAA
1 TTAAATTTAA
56730698 CTTAAACTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
16 2 0.09
17 21 0.91
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (17 bp):
TTAAATTTAAATAAAAT
Found at i:56737014 original size:10 final size:10
Alignment explanation
Indices: 56736999--56737037 Score: 55
Period size: 10 Copynumber: 4.1 Consensus size: 10
56736989 TATTTAACCC
56736999 TTTAAAATTT
1 TTTAAAATTT
56737009 TTTAAAA--T
1 TTTAAAATTT
56737017 TTTAAAATTT
1 TTTAAAATTT
*
56737027 CTTAAAATTT
1 TTTAAAATTT
56737037 T
1 T
56737038 AAATTAATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
8 8 0.32
10 17 0.68
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (10 bp):
TTTAAAATTT
Found at i:56737020 original size:18 final size:18
Alignment explanation
Indices: 56736999--56737040 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
56736989 TATTTAACCC
*
56736999 TTTAAAATTTTTTAAAAT
1 TTTAAAATTTCTTAAAAT
56737017 TTTAAAATTTCTTAAAAT
1 TTTAAAATTTCTTAAAAT
56737035 TTTAAA
1 TTTAAA
56737041 TTAATAAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (18 bp):
TTTAAAATTTCTTAAAAT
Found at i:56737700 original size:3 final size:3
Alignment explanation
Indices: 56737694--56737756 Score: 119
Period size: 3 Copynumber: 21.3 Consensus size: 3
56737684 TTGAGGAGGG
56737694 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-A TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
56737741 TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA T
56737757 TATTATTATT
Statistics
Matches: 59, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.03
3 57 0.97
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:56737761 original size:3 final size:3
Alignment explanation
Indices: 56737755--56737801 Score: 87
Period size: 3 Copynumber: 16.0 Consensus size: 3
56737745 AATAATAATA
56737755 ATT ATT ATT ATT ATT ATT A-T ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
56737802 TAGAAGCACG
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.05
3 41 0.95
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:56738180 original size:27 final size:27
Alignment explanation
Indices: 56738143--56738210 Score: 77
Period size: 27 Copynumber: 2.5 Consensus size: 27
56738133 ATATTTGGAG
*
56738143 ATATT-TTTTATTAAT-TAATTAGTTAA
1 ATATTATTTTATTAATAT-ATTACTTAA
*
56738169 ATATTATTTTATTAATATTTTACTTAA
1 ATATTATTTTATTAATATATTACTTAA
56738196 ATATTTATTATTATT
1 ATA-TTATT-TTATT
56738211 TTATTTAGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
26 5 0.14
27 20 0.56
28 6 0.17
29 5 0.14
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.60
Consensus pattern (27 bp):
ATATTATTTTATTAATATATTACTTAA
Found at i:56738200 original size:13 final size:11
Alignment explanation
Indices: 56738173--56738215 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
56738163 AGTTAAATAT
56738173 TATTTTATTAA
1 TATTTTATTAA
56738184 TATTTTACTTAA
1 TATTTTA-TTAA
*
56738196 -ATATTTATTAT
1 TAT-TTTATTAA
56738207 TATTTTATT
1 TATTTTATT
56738216 TAGAAAATGG
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
11 18 0.64
12 10 0.36
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (11 bp):
TATTTTATTAA
Found at i:56747729 original size:52 final size:51
Alignment explanation
Indices: 56747637--56747741 Score: 131
Period size: 52 Copynumber: 2.0 Consensus size: 51
56747627 TTGTAAATGG
** * *
56747637 TAAGAAAATATTATTTAATTATTTATTTTTAATCCATTAATTATTATGATGT
1 TAAGAAAATATTATCAAATTATTTATGTTAAAT-CATTAATTATTATGATGT
*
56747689 TAAGAAAATATTATCAAATTATTTAATGTTAAAT-AGTTAATTATTATGCTGT
1 TAAGAAAATATTATCAAATTATTT-ATGTTAAATCA-TTAATTATTATGATGT
56747741 T
1 T
56747742 TAGATTAACA
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
51 1 0.02
52 38 0.83
53 7 0.15
ACGTcount: A:0.40, C:0.04, G:0.08, T:0.49
Consensus pattern (51 bp):
TAAGAAAATATTATCAAATTATTTATGTTAAATCATTAATTATTATGATGT
Found at i:56749096 original size:20 final size:20
Alignment explanation
Indices: 56749071--56749111 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
56749061 ATATATATAT
*
56749071 AAGAAATAAAAGAATAAAGA
1 AAGAAACAAAAGAATAAAGA
56749091 AAGAAACAAAAGAATAAAGA
1 AAGAAACAAAAGAATAAAGA
56749111 A
1 A
56749112 CAGAGGCTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.76, C:0.02, G:0.15, T:0.07
Consensus pattern (20 bp):
AAGAAACAAAAGAATAAAGA
Found at i:56749988 original size:182 final size:182
Alignment explanation
Indices: 56749664--56750020 Score: 624
Period size: 182 Copynumber: 2.0 Consensus size: 182
56749654 CATCGGCACA
* *
56749664 AAAAAGAAAGGAGAAAGTTATCGAGGAGTAATCGCGAAATCCGGATTTGTATTACTATAATTTAA
1 AAAAAGAAAGGAGAAAGTTATCAAGGAGTAATCACGAAATCCGGATTTGTATTACTATAATTTAA
*
56749729 ATTATTCATTATTTAATGTTTATTTCGATATTTATATTTAATAAGTGAAATTGAAATTGAAAGTG
66 ATTATTCATTATTTAATATTTATTTCGATATTTATATTTAATAAGTGAAATTGAAATTGAAAGTG
56749794 ATATGAATTGTAAATTGAAAGTCCCTATTAACTAGTCGGGCTGAGCCGGTAC
131 ATATGAATTGTAAATTGAAAGTCCCTATTAACTAGTCGGGCTGAGCCGGTAC
* * *
56749846 AAAAGGAAAGGGGAAAGTTATCAAGGAGTAATCACGAAATCCGGGTTTGTATTACTATAATTTAA
1 AAAAAGAAAGGAGAAAGTTATCAAGGAGTAATCACGAAATCCGGATTTGTATTACTATAATTTAA
* *
56749911 ATTATTCATTATTTAATATTTATTTCTATGTTTATATTTAATAAGTGAAATTGAAATTGAAAGTG
66 ATTATTCATTATTTAATATTTATTTCGATATTTATATTTAATAAGTGAAATTGAAATTGAAAGTG
* *
56749976 ATATGGATTGTAAATTGAAAGTCCCTATTAACTAGTTGGGCTGAG
131 ATATGAATTGTAAATTGAAAGTCCCTATTAACTAGTCGGGCTGAG
56750021 TTGGATATAG
Statistics
Matches: 165, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
182 165 1.00
ACGTcount: A:0.37, C:0.08, G:0.19, T:0.36
Consensus pattern (182 bp):
AAAAAGAAAGGAGAAAGTTATCAAGGAGTAATCACGAAATCCGGATTTGTATTACTATAATTTAA
ATTATTCATTATTTAATATTTATTTCGATATTTATATTTAATAAGTGAAATTGAAATTGAAAGTG
ATATGAATTGTAAATTGAAAGTCCCTATTAACTAGTCGGGCTGAGCCGGTAC
Found at i:56750704 original size:2 final size:2
Alignment explanation
Indices: 56750697--56750729 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
56750687 GGTTGTAGAA
56750697 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
56750730 CACTATATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:56755886 original size:17 final size:16
Alignment explanation
Indices: 56755866--56755945 Score: 65
Period size: 17 Copynumber: 4.9 Consensus size: 16
56755856 AAAGTTTAAA
*
56755866 TTAATTTTAAATTTATT
1 TTAA-TTTAAATTTATC
*
56755883 TTAAACTTAAATTTATC
1 TT-AATTTAAATTTATC
* *
56755900 TTAAATTTAAGTTCA-C
1 TT-AATTTAAATTTATC
*
56755916 TT-ATTTAAATTTATT
1 TTAATTTAAATTTATC
56755931 TTAGATTTAAATTTA
1 TTA-ATTTAAATTTA
56755946 ATCAAATTTA
Statistics
Matches: 51, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
14 9 0.18
15 2 0.04
16 3 0.06
17 35 0.69
18 2 0.04
ACGTcount: A:0.38, C:0.05, G:0.03, T:0.55
Consensus pattern (16 bp):
TTAATTTAAATTTATC
Found at i:56757927 original size:30 final size:30
Alignment explanation
Indices: 56757893--56757989 Score: 133
Period size: 30 Copynumber: 3.2 Consensus size: 30
56757883 GCTTATAGGT
56757893 CCCCAAAACAGTCTAGAAATTACATTTTAA
1 CCCCAAAACAGTCTAGAAATTACATTTTAA
* *
56757923 CCCCAAAATAGTCTAGAAATTACATTTTGA
1 CCCCAAAACAGTCTAGAAATTACATTTTAA
* * *
56757953 CCCCAAAACA-TCCAAAAATTACCATTTTAC
1 CCCCAAAACAGTCTAGAAATTA-CATTTTAA
56757983 CCCCAAA
1 CCCCAAA
56757990 CTTTCTAAAA
Statistics
Matches: 59, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
29 9 0.15
30 50 0.85
ACGTcount: A:0.42, C:0.28, G:0.05, T:0.25
Consensus pattern (30 bp):
CCCCAAAACAGTCTAGAAATTACATTTTAA
Found at i:56757984 original size:29 final size:30
Alignment explanation
Indices: 56757893--56758074 Score: 108
Period size: 30 Copynumber: 6.2 Consensus size: 30
56757883 GCTTATAGGT
* *
56757893 CCCCAAAACAGTCTAGAAATTA-CATTTTAA
1 CCCCAAAACA-TCCAAAAATTACCATTTTAA
* * * *
56757923 CCCCAAAATAGTCTAGAAATTA-CATTTTGA
1 CCCCAAAACA-TCCAAAAATTACCATTTTAA
56757953 CCCCAAAACATCCAAAAATTACCATTTT-A
1 CCCCAAAACATCCAAAAATTACCATTTTAA
* * * *
56757982 CCCCCAAACTTTCTAAAATT-CCATTTTTAA
1 CCCCAAAACATCCAAAAATTACCA-TTTTAA
* *** *
56758012 CCTCGATTTCA-CCAAAAATTACCGTTTT-A
1 CC-CCAAAACATCCAAAAATTACCATTTTAA
* * * *
56758041 CCCCCAAACTTTCTAAAATT-CCATTTTAA
1 CCCCAAAACATCCAAAAATTACCATTTTAA
56758070 CCCCA
1 CCCCA
56758075 GTTTTACCCA
Statistics
Matches: 117, Mismatches: 28, Indels: 15
0.73 0.17 0.09
Matches are distributed among these distances:
28 11 0.09
29 45 0.38
30 57 0.49
31 4 0.03
ACGTcount: A:0.37, C:0.29, G:0.04, T:0.30
Consensus pattern (30 bp):
CCCCAAAACATCCAAAAATTACCATTTTAA
Found at i:56758073 original size:117 final size:117
Alignment explanation
Indices: 56757909--56758273 Score: 459
Period size: 117 Copynumber: 3.1 Consensus size: 117
56757899 AACAGTCTAG
* * * * * *
56757909 AAATTA-CATTTTAACCCCAAAATAGTCTAGAAATTACATTTTGACCCCAAAACATCCAAAAATT
1 AAATTACCATTTTACCCCCAAACT-TTCTA-AAATTCCATTTTAACCCCAAATCATCCAAAAATT
56757973 ACCATTTTACCCCCAAACTTTCTAAAATTCCATTTTTAACCTCGATTTCACCAA
64 ACCATTTTACCCCCAAACTTTCTAAAATTCCATTTTTAACCTCGATTTCACCAA
* * ** *
56758027 AAATTACCGTTTTACCCCCAAACTTTCTAAAATTCCATTTTAACCCC-AGTTTTACCCAAAATTA
1 AAATTACCATTTTACCCCCAAACTTTCTAAAATTCCATTTTAACCCCAAATCAT-CCAAAAATTA
* **
56758091 TCATTTTACCCTTAAACTTTCTAAAATTCCATTTTTAACCTCGATTTCACCAA
65 CCATTTTACCCCCAAACTTTCTAAAATTCCATTTTTAACCTCGATTTCACCAA
* * * *
56758144 AAATTACCATTTTACCCTCAAACTTTCCAAAATTCCATTTTTACCCCTAATTTCA-CCAAAAA-T
1 AAATTACCATTTTACCCCCAAACTTTCTAAAATTCCATTTTAACCCC-AA-ATCATCCAAAAATT
* * *
56758207 ACTATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCAA
64 ACCATTTTACCCCCAAACTTTCTAAAATTCCATTTTTAACCTCGATTTCACCAA
*
56758261 AATTTACCATTTT
1 AAATTACCATTTT
56758274 GCCCTCGCGA
Statistics
Matches: 213, Mismatches: 29, Indels: 11
0.84 0.11 0.04
Matches are distributed among these distances:
116 2 0.01
117 179 0.84
118 16 0.08
119 15 0.07
120 1 0.00
ACGTcount: A:0.35, C:0.28, G:0.02, T:0.35
Consensus pattern (117 bp):
AAATTACCATTTTACCCCCAAACTTTCTAAAATTCCATTTTAACCCCAAATCATCCAAAAATTAC
CATTTTACCCCCAAACTTTCTAAAATTCCATTTTTAACCTCGATTTCACCAA
Found at i:56758098 original size:58 final size:59
Alignment explanation
Indices: 56757964--56758273 Score: 448
Period size: 59 Copynumber: 5.3 Consensus size: 59
56757954 CCCAAAACAT
*
56757964 CCAAAAATTACCATTTTACCCCCAAACTTTCTAAAATTCCATTTTTAACCTCGATTTCA
1 CCAAAAATTACCATTTTACCCCCAAACTTTCTAAAATTCCATTTTTAACCCCGATTTCA
* *
56758023 CCAAAAATTACCGTTTTACCCCCAAACTTTCTAAAATTCCA-TTTTAACCCC-AGTTTTA
1 CCAAAAATTACCATTTTACCCCCAAACTTTCTAAAATTCCATTTTTAACCCCGA-TTTCA
* * ** *
56758081 CCCAAAATTATCATTTTACCCTTAAACTTTCTAAAATTCCATTTTTAACCTCGATTTCA
1 CCAAAAATTACCATTTTACCCCCAAACTTTCTAAAATTCCATTTTTAACCCCGATTTCA
* * *
56758140 CCAAAAATTACCATTTTACCCTCAAACTTTCCAAAATTCCATTTTT-ACCCCTAATTTCA
1 CCAAAAATTACCATTTTACCCCCAAACTTTCTAAAATTCCATTTTTAACCCC-GATTTCA
* *
56758199 CCAAAAA-TACTATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
1 CCAAAAATTACCATTTTACCCCCAAACTTTCTAAAATTCCATTTTTAACCCCGATTTCA
*
56758257 CCAAAATTTACCATTTT
1 CCAAAAATTACCATTTT
56758274 GCCCTCGCGA
Statistics
Matches: 224, Mismatches: 21, Indels: 12
0.87 0.08 0.05
Matches are distributed among these distances:
57 1 0.00
58 101 0.45
59 121 0.54
60 1 0.00
ACGTcount: A:0.34, C:0.29, G:0.02, T:0.36
Consensus pattern (59 bp):
CCAAAAATTACCATTTTACCCCCAAACTTTCTAAAATTCCATTTTTAACCCCGATTTCA
Found at i:56758260 original size:29 final size:30
Alignment explanation
Indices: 56757967--56758273 Score: 129
Period size: 29 Copynumber: 10.4 Consensus size: 30
56757957 AAAACATCCA
* *
56757967 AAAATTACCA-TTTTACCCCCAAACTTT--CT
1 AAAATT-CCATTTTTAACCCCAAA-TTTCACC
* *
56757996 AAAATTCCATTTTTAACCTC-GATTTCACC
1 AAAATTCCATTTTTAACCCCAAATTTCACC
* * *
56758025 AAAAATTACC-GTTTTACCCCCAAACTTT--CT
1 -AAAATT-CCATTTTTAACCCCAAA-TTTCACC
* *
56758055 AAAATTCCA-TTTTAACCCC-AGTTTTACCC
1 AAAATTCCATTTTTAACCCCAAATTTCA-CC
* * *
56758084 AAAATTATCA-TTTT-ACCCTTAAACTTT--CT
1 AAAATT-CCATTTTTAACCC-CAAA-TTTCACC
* *
56758113 AAAATTCCATTTTTAACCTC-GATTTCACC
1 AAAATTCCATTTTTAACCCCAAATTTCACC
56758142 AAAAATTACCA-TTTT-ACCCTCAAACTTT--CC
1 -AAAATT-CCATTTTTAACCC-CAAA-TTTCACC
*
56758172 AAAATTCCATTTTT-ACCCCTAATTTCACC
1 AAAATTCCATTTTTAACCCCAAATTTCACC
* * *
56758201 AAAAATAC-TATTTTACCCCCAAACTTT--CC
1 AAAATTCCAT-TTTTAACCCCAAA-TTTCACC
*
56758230 AAAATTCCATTTTTAACCCC-GATTTCACC
1 AAAATTCCATTTTTAACCCCAAATTTCACC
56758259 AAAATTTACCATTTT
1 AAAA-TT-CCATTTT
56758274 GCCCTCGCGA
Statistics
Matches: 211, Mismatches: 32, Indels: 68
0.68 0.10 0.22
Matches are distributed among these distances:
26 3 0.01
27 13 0.06
28 26 0.12
29 96 0.45
30 46 0.22
31 18 0.09
32 9 0.04
ACGTcount: A:0.34, C:0.28, G:0.02, T:0.36
Consensus pattern (30 bp):
AAAATTCCATTTTTAACCCCAAATTTCACC
Found at i:56758279 original size:117 final size:117
Alignment explanation
Indices: 56757964--56758279 Score: 465
Period size: 117 Copynumber: 2.7 Consensus size: 117
56757954 CCCAAAACAT
*
56757964 CCAAAAATTACCATTTTACCCCCAAACTTTCTAAAATTCCATTTTTAACCTCGATTTCACCAAAA
1 CCAAAAA-TACTATTTTACCCCCAAACTTTCTAAAATTCCATTTTTAACCTCGATTTCACCAAAA
* * * * *
56758029 ATTACCGTTTTACCCCCAAACTTTCTAAAATTCCATTTTAACCCCAGTTTTAC
65 ATTACCATTTTACCCTCAAACTTTCCAAAATTCCATTTTAACCCCAATTTCAC
* **
56758082 CCAAAATTA-TCATTTTACCCTTAAACTTTCTAAAATTCCATTTTTAACCTCGATTTCACCAAAA
1 CCAAAAATACT-ATTTTACCCCCAAACTTTCTAAAATTCCATTTTTAACCTCGATTTCACCAAAA
*
56758146 ATTACCATTTTACCCTCAAACTTTCCAAAATTCCATTTTTACCCCTAATTTCA-
65 ATTACCATTTTACCCTCAAACTTTCCAAAATTCCATTTTAACCCC-AATTTCAC
* * *
56758199 CCAAAAATACTATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAAT
1 CCAAAAATACTATTTTACCCCCAAACTTTCTAAAATTCCATTTTTAACCTCGATTTCACCAAAAA
*
56758264 TTACCATTTTGCCCTC
66 TTACCATTTTACCCTC
56758280 GCGAGTCCAA
Statistics
Matches: 178, Mismatches: 17, Indels: 7
0.88 0.08 0.03
Matches are distributed among these distances:
117 166 0.93
118 12 0.07
ACGTcount: A:0.33, C:0.29, G:0.02, T:0.36
Consensus pattern (117 bp):
CCAAAAATACTATTTTACCCCCAAACTTTCTAAAATTCCATTTTTAACCTCGATTTCACCAAAAA
TTACCATTTTACCCTCAAACTTTCCAAAATTCCATTTTAACCCCAATTTCAC
Found at i:56759815 original size:29 final size:30
Alignment explanation
Indices: 56759757--56759815 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 30
56759747 TTCTAAAATT
56759757 AATATTAAAATTTATTGAAAACTTTATTTCC
1 AATATTAAAATTTATT-AAAACTTTATTTCC
56759788 AATATTAAAATTCT-TT-AAACTTTATTTC
1 AATATTAAAATT-TATTAAAACTTTATTTC
56759816 TAAACTTATC
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
29 12 0.44
31 14 0.52
32 1 0.04
ACGTcount: A:0.41, C:0.10, G:0.02, T:0.47
Consensus pattern (30 bp):
AATATTAAAATTTATTAAAACTTTATTTCC
Found at i:56766753 original size:18 final size:18
Alignment explanation
Indices: 56766708--56766753 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
56766698 TATATGTTAT
56766708 AAATTAC-ATAATATATA
1 AAATTACAATAATATATA
* *
56766725 AAAATAAAATAATATA-A
1 AAATTACAATAATATATA
56766742 AACATTACAATA
1 AA-ATTACAATA
56766754 TATTTTTAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
17 8 0.35
18 15 0.65
ACGTcount: A:0.65, C:0.07, G:0.00, T:0.28
Consensus pattern (18 bp):
AAATTACAATAATATATA
Found at i:56769331 original size:11 final size:11
Alignment explanation
Indices: 56769315--56769340 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
56769305 CTAATGGTGA
56769315 TTCGAATTTTG
1 TTCGAATTTTG
56769326 TTCGAATTTTG
1 TTCGAATTTTG
56769337 TTCG
1 TTCG
56769341 TTTCGAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.15, C:0.12, G:0.19, T:0.54
Consensus pattern (11 bp):
TTCGAATTTTG
Found at i:56774322 original size:22 final size:22
Alignment explanation
Indices: 56774296--56774337 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
56774286 TTTTATTGAC
*
56774296 TATTG-ATTGTTTTTTACATAAA
1 TATTGAATT-TTTTATACATAAA
56774318 TATTGAATTTTTTATACATA
1 TATTGAATTTTTTATACATA
56774338 CCATTTTCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 15 0.83
23 3 0.17
ACGTcount: A:0.33, C:0.05, G:0.07, T:0.55
Consensus pattern (22 bp):
TATTGAATTTTTTATACATAAA
Found at i:56775720 original size:22 final size:23
Alignment explanation
Indices: 56775663--56775725 Score: 83
Period size: 23 Copynumber: 2.8 Consensus size: 23
56775653 TGTAATATCC
* * *
56775663 AAATAATATTAAAAATGATAGTG
1 AAATAACATTAAAAATGCTAGCG
56775686 AAATAACATTAAAAATGCTAGCG
1 AAATAACATTAAAAATGCTAGCG
*
56775709 AAATAA-AATAAAAATGC
1 AAATAACATTAAAAATGC
56775726 ACAAAAAATA
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
22 10 0.28
23 26 0.72
ACGTcount: A:0.59, C:0.06, G:0.11, T:0.24
Consensus pattern (23 bp):
AAATAACATTAAAAATGCTAGCG
Found at i:56775963 original size:17 final size:18
Alignment explanation
Indices: 56775938--56775973 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
56775928 AAAATGGACA
*
56775938 TTAT-TTTTTGTTCAAAC
1 TTATATTTTTATTCAAAC
56775955 TTATATTTTTATTCAAAC
1 TTATATTTTTATTCAAAC
56775973 T
1 T
56775974 CTCTCATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.28, C:0.11, G:0.03, T:0.58
Consensus pattern (18 bp):
TTATATTTTTATTCAAAC
Found at i:56780321 original size:18 final size:18
Alignment explanation
Indices: 56780278--56780363 Score: 82
Period size: 18 Copynumber: 4.6 Consensus size: 18
56780268 TTTTTTGAAA
*
56780278 TTTTTAATAATTTATTAT
1 TTTTTAATAATTTATAAT
56780296 TATTTTAATAATTTATAAT
1 T-TTTTAATAATTTATAAT
* * *
56780315 TTTTTAAAAAATTATGAT
1 TTTTTAATAATTTATAAT
* *
56780333 TTTTAAATAATATTTTAGGAT
1 TTTTTAATAAT-TTATA--AT
56780354 TTTTTAATAA
1 TTTTTAATAA
56780364 CTAGTTCAGA
Statistics
Matches: 54, Mismatches: 10, Indels: 5
0.78 0.14 0.07
Matches are distributed among these distances:
18 23 0.43
19 20 0.37
21 11 0.20
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (18 bp):
TTTTTAATAATTTATAAT
Found at i:56790088 original size:22 final size:21
Alignment explanation
Indices: 56790060--56790104 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
56790050 GAGACAAGTT
56790060 TTGCTTTAATTATTTATTTATG
1 TTGCTTTAATTATTT-TTTATG
* *
56790082 TTGCTTTATTTATTTTTTCTG
1 TTGCTTTAATTATTTTTTATG
56790103 TT
1 TT
56790105 TTTTTTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 7 0.33
22 14 0.67
ACGTcount: A:0.16, C:0.07, G:0.09, T:0.69
Consensus pattern (21 bp):
TTGCTTTAATTATTTTTTATG
Found at i:56818163 original size:27 final size:28
Alignment explanation
Indices: 56818100--56818195 Score: 85
Period size: 27 Copynumber: 3.5 Consensus size: 28
56818090 AGGAATATAT
56818100 TTAAATATTTAAAATATAGTATATTCAA
1 TTAAATATTTAAAATATAGTATATTCAA
* *
56818128 -AAAATATTTAAAATATAGTTTA-TCTAA
1 TTAAATATTTAAAATATAGTATATTC-AA
* *
56818155 TTAAA-ATTTTAAATA-ATTAATATT-AA
1 TTAAATATTTAAAATATAGT-ATATTCAA
**
56818181 TTACTTATTTAAAAT
1 TTAAATATTTAAAAT
56818196 TAATATTTTA
Statistics
Matches: 54, Mismatches: 9, Indels: 11
0.73 0.12 0.15
Matches are distributed among these distances:
26 9 0.17
27 41 0.76
28 4 0.07
ACGTcount: A:0.50, C:0.03, G:0.02, T:0.45
Consensus pattern (28 bp):
TTAAATATTTAAAATATAGTATATTCAA
Found at i:56825041 original size:23 final size:22
Alignment explanation
Indices: 56824951--56825052 Score: 114
Period size: 22 Copynumber: 4.5 Consensus size: 22
56824941 TTCGCACTTC
*
56824951 GTGTGCCTACTGATTTGCGCTAT
1 GTGTGCCTACTGA-TTGCACTAT
* *
56824974 GTGCGCCTACTGATTCCACTAT
1 GTGTGCCTACTGATTGCACTAT
* * *
56824996 GTGCGCCTACTGATTGCATTGT
1 GTGTGCCTACTGATTGCACTAT
*
56825018 GTGTGCCTACTGGATTGCACTGT
1 GTGTGCCTACT-GATTGCACTAT
*
56825041 GTGTGCTTACTG
1 GTGTGCCTACTG
56825053 TTTCCCCAGC
Statistics
Matches: 69, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
22 37 0.54
23 32 0.46
ACGTcount: A:0.14, C:0.24, G:0.26, T:0.36
Consensus pattern (22 bp):
GTGTGCCTACTGATTGCACTAT
Found at i:56834928 original size:3 final size:3
Alignment explanation
Indices: 56834906--56835027 Score: 73
Period size: 3 Copynumber: 42.3 Consensus size: 3
56834896 ATATTTTTAA
* * * *
56834906 AAT AA- AAT AAAT ATT AAT AAT AA- AAT AAT AAT TAT -AC AAT ATCT
1 AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT
* * *
56834950 AAAT AAT AAT AAT AAT AAT AAT AAT ACT AA- CAT AAT AAT GA- AAT
1 -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
56834994 AAT AA- AAC AAT GAA- AA- AAT AAT AAT AA- AAT AAT A
1 AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT A
56835028 TTTTTTTGTA
Statistics
Matches: 93, Mismatches: 14, Indels: 24
0.71 0.11 0.18
Matches are distributed among these distances:
2 15 0.16
3 70 0.75
4 7 0.08
5 1 0.01
ACGTcount: A:0.66, C:0.04, G:0.02, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:56834936 original size:11 final size:11
Alignment explanation
Indices: 56834903--56835027 Score: 80
Period size: 11 Copynumber: 10.9 Consensus size: 11
56834893 TAAATATTTT
56834903 TAAAATAA-AA
1 TAAAATAATAA
56834913 TAAATATTAATAA
1 TAAA-A-TAATAA
56834926 TAAAATAATAA
1 TAAAATAATAA
*
56834937 TTATACAATATCTAAA
1 -TA-A-AATA-AT-AA
56834953 TAATAATAATAA
1 TAA-AATAATAA
*
56834965 TAATAATAATAC
1 TAA-AATAATAA
*
56834977 TAACATAATAA
1 TAAAATAATAA
*
56834988 TGAAATAATAA
1 TAAAATAATAA
*
56834999 -AACAAT--GAA
1 TAA-AATAATAA
56835008 -AAAATAATAA
1 TAAAATAATAA
56835018 TAAAATAATA
1 TAAAATAATA
56835028 TTTTTTTGTA
Statistics
Matches: 92, Mismatches: 11, Indels: 23
0.73 0.09 0.18
Matches are distributed among these distances:
8 3 0.03
9 4 0.04
10 7 0.08
11 34 0.37
12 22 0.24
13 8 0.09
14 9 0.10
15 3 0.03
16 2 0.02
ACGTcount: A:0.66, C:0.04, G:0.02, T:0.29
Consensus pattern (11 bp):
TAAAATAATAA
Found at i:56836198 original size:56 final size:55
Alignment explanation
Indices: 56836121--56836301 Score: 204
Period size: 56 Copynumber: 3.2 Consensus size: 55
56836111 AAATACGAAT
* *
56836121 AAAAAATAATTTTTTTGGGTGTTTGCCAAGTCATGACCGATACTCCTTTTATCAGATA
1 AAAAAATAA--TTTTTGGGTGTTTGTCAAGCCATGACCGATAC-CCTTTTATCAGATA
* * ** *
56836179 AAAAAAT-ATCTTTTGGGTGTCTGTCAAGCCATGACCGACACCCCCTTATTAGATA
1 AAAAAATAAT-TTTTGGGTGTTTGTCAAGCCATGACCGATACCCTTTTATCAGATA
** *
56836234 AAAAAATAATTTTGTAAGTGTTTGTCAAGCCATGATCGATACCCTCTTTATCAGATA
1 AAAAAATAATTTT-TGGGTGTTTGTCAAGCCATGACCGATACCCT-TTTATCAGATA
56836291 AAAAAA-AATTT
1 AAAAAATAATTT
56836302 GGGTGTCGGC
Statistics
Matches: 104, Mismatches: 15, Indels: 10
0.81 0.12 0.08
Matches are distributed among these distances:
55 22 0.21
56 59 0.57
57 16 0.15
58 7 0.07
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.34
Consensus pattern (55 bp):
AAAAAATAATTTTTGGGTGTTTGTCAAGCCATGACCGATACCCTTTTATCAGATA
Found at i:56839350 original size:15 final size:16
Alignment explanation
Indices: 56839325--56839363 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
56839315 AAACCCCAAA
*
56839325 TAATATTTAAAT-AATT
1 TAAT-TTTAAATAAACT
56839341 TAATTTTAAATAAACT
1 TAATTTTAAATAAACT
56839357 TAATTTT
1 TAATTTT
56839364 TTTAATTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 7 0.33
16 14 0.67
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (16 bp):
TAATTTTAAATAAACT
Found at i:56849471 original size:15 final size:15
Alignment explanation
Indices: 56849453--56849482 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
56849443 TTTAAATACT
56849453 TTTTAGAATTATATA
1 TTTTAGAATTATATA
*
56849468 TTTTAGAATTTTATA
1 TTTTAGAATTATATA
56849483 GAAAATTATT
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:0.37, C:0.00, G:0.07, T:0.57
Consensus pattern (15 bp):
TTTTAGAATTATATA
Found at i:56851959 original size:87 final size:87
Alignment explanation
Indices: 56851759--56851951 Score: 327
Period size: 87 Copynumber: 2.2 Consensus size: 87
56851749 TTATGCATAC
56851759 TCCT-GACAGCACGTGTGAGCAACATCGTTAGGGAATAGTACAAACAGACACTGTATCGATAGCT
1 TCCTCGACAGCACGTGTGAGCAACATCGTTAGGGAATAGTACAAACAGACACTGTATCGATAGCT
**
56851823 GGGGTACTGCATATGTTGCGAG
66 GGGGTACCACATATGTTGCGAG
*
56851845 TCCTCGACAGCACGTGTGAGCAACATCGTTAGGGAATAGTACAAACAGACA-TCGTATCGATAGT
1 TCCTCGACAGCACGTGTGAGCAACATCGTTAGGGAATAGTACAAACAGACACT-GTATCGATAGC
56851909 TGGGGTACCACATATGTTGCGAG
65 TGGGGTACCACATATGTTGCGAG
*
56851932 TCCTCGACAGCTCGTGTGAG
1 TCCTCGACAGCACGTGTGAG
56851952 TAGCATCGGG
Statistics
Matches: 101, Mismatches: 4, Indels: 3
0.94 0.04 0.03
Matches are distributed among these distances:
86 5 0.05
87 96 0.95
ACGTcount: A:0.28, C:0.21, G:0.27, T:0.23
Consensus pattern (87 bp):
TCCTCGACAGCACGTGTGAGCAACATCGTTAGGGAATAGTACAAACAGACACTGTATCGATAGCT
GGGGTACCACATATGTTGCGAG
Found at i:56853881 original size:18 final size:20
Alignment explanation
Indices: 56853840--56853881 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
56853830 ATTGAGAGGG
*
56853840 TTGAAAAAAAAAGATGTGAA
1 TTGAAAAAAAAAGATGTAAA
56853860 -TGAAAAAAAAA-ATG-AAA
1 TTGAAAAAAAAAGATGTAAA
56853877 TTGAA
1 TTGAA
56853882 GGGTATTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
17 2 0.10
18 7 0.35
19 11 0.55
ACGTcount: A:0.64, C:0.00, G:0.17, T:0.19
Consensus pattern (20 bp):
TTGAAAAAAAAAGATGTAAA
Found at i:56861097 original size:18 final size:16
Alignment explanation
Indices: 56861065--56861108 Score: 56
Period size: 14 Copynumber: 2.8 Consensus size: 16
56861055 ATGGGATGAT
56861065 AATAAATTTTTAATTA
1 AATAAATTTTTAATTA
56861081 AATAAA--TTTAATTA
1 AATAAATTTTTAATTA
*
56861095 ATTAAAATTTTTAA
1 AAT-AAATTTTTAA
56861109 ATCTTAAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
14 10 0.42
15 3 0.12
16 6 0.25
17 5 0.21
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
AATAAATTTTTAATTA
Found at i:56861287 original size:68 final size:68
Alignment explanation
Indices: 56861200--56861330 Score: 210
Period size: 68 Copynumber: 1.9 Consensus size: 68
56861190 CAAATTTATC
*
56861200 TCAAAGCTTGAATAATTAAAA-CTCATTAACTCAAAGATTCAATATCTTTAATTCCAATATCTTC
1 TCAAAGCTTGAATAATTAAAATC-CATTAACCCAAAGATTCAATATCTTTAATTCCAATATCTTC
56861264 TGTT
65 TGTT
** *
56861268 TCAAAGCTTGAATCTTTAAAATCCATTAACCCAAAGATTCAATATCTTTGATTCCAATATCTT
1 TCAAAGCTTGAATAATTAAAATCCATTAACCCAAAGATTCAATATCTTTAATTCCAATATCTT
56861331 TTTCCTGTTA
Statistics
Matches: 58, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
68 57 0.98
69 1 0.02
ACGTcount: A:0.37, C:0.19, G:0.06, T:0.37
Consensus pattern (68 bp):
TCAAAGCTTGAATAATTAAAATCCATTAACCCAAAGATTCAATATCTTTAATTCCAATATCTTCT
GTT
Found at i:56861598 original size:20 final size:20
Alignment explanation
Indices: 56861573--56861615 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 20
56861563 TAGTTTCACT
56861573 TAAGATTACTGTTAAGG-AGA
1 TAAGATTACTGTT-AGGAAGA
56861593 TAAGATTACTGTTAGGAAGA
1 TAAGATTACTGTTAGGAAGA
56861613 TAA
1 TAA
56861616 CGGAACTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 3 0.14
20 19 0.86
ACGTcount: A:0.42, C:0.05, G:0.23, T:0.30
Consensus pattern (20 bp):
TAAGATTACTGTTAGGAAGA
Found at i:56864860 original size:5 final size:5
Alignment explanation
Indices: 56864850--56864888 Score: 50
Period size: 5 Copynumber: 8.6 Consensus size: 5
56864840 ATTGAAATTT
56864850 TTTAA TTTAA -TT-A TTTAA --TAA TTTAA TTTAA TTTAA TTT
1 TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TTT
56864889 TAATCTAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
3 4 0.13
4 4 0.13
5 22 0.73
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (5 bp):
TTTAA
Found at i:56879800 original size:4 final size:4
Alignment explanation
Indices: 56879793--56879827 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
56879783 ATATATATAT
56879793 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATA
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATA
56879828 TTAAGTTTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.51, C:0.00, G:0.23, T:0.26
Consensus pattern (4 bp):
ATAG
Found at i:56880563 original size:3 final size:3
Alignment explanation
Indices: 56880555--56880587 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
56880545 ATGACATTTC
56880555 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
56880588 GAAATTAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:56884598 original size:22 final size:21
Alignment explanation
Indices: 56884571--56884611 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
56884561 TTTTAAAAAA
56884571 TTATTTATTAAAATATTTATAT
1 TTATTTATTAAAAT-TTTATAT
* *
56884593 TTATTTTTTTAAATTTTAT
1 TTATTTATTAAAATTTTAT
56884612 TATCTCATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (21 bp):
TTATTTATTAAAATTTTATAT
Found at i:56886264 original size:118 final size:125
Alignment explanation
Indices: 56886116--56886353 Score: 303
Period size: 129 Copynumber: 1.9 Consensus size: 125
56886106 TTTACTCGTG
* * *
56886116 CGATGCATCGATTGATTGTATGTATTAATT-AA-A-TT-AT-TTTTT-AATTTTTTAATAAA-TT
1 CGATGCACCGATTGATTGTATGTATAAATTAAATATTTAATATTTTTAAAATTTTT-ATAAAGTT
*
56886174 TTGTAACTTTTAACTAATAATATGGTTACAAAATTAAAACATAAT-ATTTTCTTTATCTTA
65 TTGTAACATTTAACTAATAATATGGTTACAAAATTAAAACATAATAATTTTCTTTATCTTA
*
56886234 CGATGCACCGGTTGATTGTATGTATAAATTAAATTGCATTTAATAAATTTTTAAAATTTTTATAA
1 CGATGCACCGATTGATTGTATGTATAAATTAAA-T--ATTTAAT--ATTTTTAAAATTTTTATAA
* *
56886299 AGTTTTGTAACATTTAATTAATAGTATGGTTACAAAATTAAAACATAATAATTTT
61 AGTTTTGTAACATTTAACTAATAATATGGTTACAAAATTAAAACATAATAATTTT
56886354 AATTTTAAAA
Statistics
Matches: 100, Mismatches: 7, Indels: 14
0.83 0.06 0.12
Matches are distributed among these distances:
118 27 0.27
119 2 0.02
123 1 0.01
124 2 0.02
125 2 0.02
128 10 0.10
129 51 0.51
130 5 0.05
ACGTcount: A:0.38, C:0.07, G:0.09, T:0.45
Consensus pattern (125 bp):
CGATGCACCGATTGATTGTATGTATAAATTAAATATTTAATATTTTTAAAATTTTTATAAAGTTT
TGTAACATTTAACTAATAATATGGTTACAAAATTAAAACATAATAATTTTCTTTATCTTA
Found at i:56888581 original size:15 final size:17
Alignment explanation
Indices: 56888545--56888585 Score: 59
Period size: 15 Copynumber: 2.5 Consensus size: 17
56888535 GTGTCTCGTT
56888545 AAAATCTTATTGAGATA
1 AAAATCTTATTGAGATA
*
56888562 AAAATCTTA-TGGGA-A
1 AAAATCTTATTGAGATA
56888577 AAAATCTTA
1 AAAATCTTA
56888586 GTAAAAGAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 10 0.43
16 4 0.17
17 9 0.39
ACGTcount: A:0.49, C:0.07, G:0.12, T:0.32
Consensus pattern (17 bp):
AAAATCTTATTGAGATA
Found at i:56890716 original size:20 final size:19
Alignment explanation
Indices: 56890688--56890744 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 19
56890678 TCAACAAAAA
56890688 TTATAAAAAAATCAAAATAAT
1 TTAT-AAAAAATCAAAAT-AT
* *
56890709 TT-TTAAAATTCAAAATAT
1 TTATAAAAAATCAAAATAT
56890727 TTATAAAAAATTCAAAAT
1 TTATAAAAAA-TCAAAAT
56890745 TTATATTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
18 4 0.13
19 16 0.53
20 8 0.27
21 2 0.07
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (19 bp):
TTATAAAAAATCAAAATAT
Found at i:56890721 original size:19 final size:20
Alignment explanation
Indices: 56890688--56890744 Score: 73
Period size: 20 Copynumber: 2.9 Consensus size: 20
56890678 TCAACAAAAA
*
56890688 TTATAAAAAAATCAAAATAAT
1 TTATAAAAAATTCAAAAT-AT
*
56890709 TT-T-TAAAATTCAAAATAT
1 TTATAAAAAATTCAAAATAT
56890727 TTATAAAAAATTCAAAAT
1 TTATAAAAAATTCAAAAT
56890745 TTATATTTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
18 4 0.13
19 12 0.39
20 13 0.42
21 2 0.06
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (20 bp):
TTATAAAAAATTCAAAATAT
Found at i:56890746 original size:18 final size:18
Alignment explanation
Indices: 56890682--56890749 Score: 57
Period size: 20 Copynumber: 3.6 Consensus size: 18
56890672 TCTCTCTCAA
* *
56890682 CAAAAATTATAAAAAAAT
1 CAAAATTTATAAAAAATT
**
56890700 CAAAATAATT-TTTAAAATT
1 CAAAAT--TTATAAAAAATT
56890719 CAAAATATTTATAAAAAATT
1 C-AAA-ATTTATAAAAAATT
56890739 CAAAATTTATA
1 CAAAATTTATA
56890750 TTTTTTAAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
18 12 0.31
19 12 0.31
20 13 0.33
21 2 0.05
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34
Consensus pattern (18 bp):
CAAAATTTATAAAAAATT
Found at i:56896938 original size:26 final size:26
Alignment explanation
Indices: 56896887--56896938 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
56896877 AATTCATTAT
* **
56896887 AAATTTAAAAAAATATGAAATTTATA
1 AAATTTAAAAAAATATAAAAAATATA
*
56896913 AAATTTTAAAAAATATAAAAAATATA
1 AAATTTAAAAAAATATAAAAAATATA
56896939 TATAAAAAAG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (26 bp):
AAATTTAAAAAAATATAAAAAATATA
Found at i:56901265 original size:20 final size:20
Alignment explanation
Indices: 56901253--56901314 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 20
56901243 GAATTAGTAG
56901253 TAGAAATAGAGAAATAGAAA
1 TAGAAATAGAGAAATAGAAA
*
56901273 TAGAAAT--AGAAACAGAATGAA
1 TAGAAATAGAGAAATAG-A--AA
56901294 TAGAAATAGAGAAATGAGAAA
1 TAGAAATAGAGAAAT-AGAAA
56901315 CATTCAGAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 11
0.72 0.04 0.23
Matches are distributed among these distances:
18 7 0.21
19 1 0.03
20 7 0.21
21 11 0.32
23 6 0.18
24 2 0.06
ACGTcount: A:0.63, C:0.02, G:0.21, T:0.15
Consensus pattern (20 bp):
TAGAAATAGAGAAATAGAAA
Found at i:56901271 original size:6 final size:6
Alignment explanation
Indices: 56901262--56901303 Score: 54
Period size: 6 Copynumber: 7.5 Consensus size: 6
56901252 GTAGAAATAG
*
56901262 AGAAAT AGAAAT AGAAAT AGAAAC AG-AAT -G-AAT AGAAAT AGA
1 AGAAAT AGAAAT AGAAAT AGAAAT AGAAAT AGAAAT AGAAAT AGA
56901304 GAAATGAGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
4 4 0.12
5 3 0.09
6 25 0.78
ACGTcount: A:0.64, C:0.02, G:0.19, T:0.14
Consensus pattern (6 bp):
AGAAAT
Found at i:56903130 original size:19 final size:20
Alignment explanation
Indices: 56903097--56903135 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
56903087 TGACAATTTT
56903097 TAAAATTATAAAAA-TAAAA
1 TAAAATTATAAAAATTAAAA
56903116 TAAAATTA-AAGAAATTAAAA
1 TAAAATTATAA-AAATTAAAA
56903136 AATATAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 2 0.11
19 11 0.61
20 5 0.28
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.26
Consensus pattern (20 bp):
TAAAATTATAAAAATTAAAA
Found at i:56903145 original size:15 final size:15
Alignment explanation
Indices: 56903097--56903150 Score: 51
Period size: 15 Copynumber: 3.7 Consensus size: 15
56903087 TGACAATTTT
*
56903097 TAAAATTATAAAA-A
1 TAAAATTAAAAAATA
*
56903111 TAAAA-T-AAAATTA
1 TAAAATTAAAAAATA
*
56903124 AAGAAATTAAAAAATA
1 TA-AAATTAAAAAATA
56903140 TAAAATTAAAA
1 TAAAATTAAAA
56903151 CAACAAGATT
Statistics
Matches: 31, Mismatches: 5, Indels: 7
0.72 0.12 0.16
Matches are distributed among these distances:
12 3 0.10
13 3 0.10
14 8 0.26
15 10 0.32
16 7 0.23
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (15 bp):
TAAAATTAAAAAATA
Found at i:56912315 original size:2 final size:2
Alignment explanation
Indices: 56912308--56912347 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
56912298 TAAATAACTA
56912308 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
56912348 GACCTTGTTG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:56920643 original size:20 final size:21
Alignment explanation
Indices: 56920618--56920657 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
56920608 CTTTAGAAAA
*
56920618 TTAAATTATTAATTC-TTTTG
1 TTAAATTATAAATTCATTTTG
56920638 TTAAATTATAAATTCATTTT
1 TTAAATTATAAATTCATTTT
56920658 AAATTAATGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.35, C:0.05, G:0.03, T:0.57
Consensus pattern (21 bp):
TTAAATTATAAATTCATTTTG
Found at i:56920935 original size:18 final size:18
Alignment explanation
Indices: 56920902--56920937 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
56920892 GCTACACTAA
*
56920902 TTAATTTTATTATCATCG
1 TTAATTTTAATATCATCG
*
56920920 TTAATTTTAATCTCATCG
1 TTAATTTTAATATCATCG
56920938 CCCATCTAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.28, C:0.14, G:0.06, T:0.53
Consensus pattern (18 bp):
TTAATTTTAATATCATCG
Found at i:56923593 original size:80 final size:79
Alignment explanation
Indices: 56923452--56923681 Score: 219
Period size: 80 Copynumber: 2.9 Consensus size: 79
56923442 TTTGATGAAT
* * * * * * * *
56923452 ATATGTTGTCAGTTTAACTGACTAGAGTTGGGCTCACAATTGCGGTTTATCCGCTAGGCACTAGG
1 ATAT-TTGTCGGTTTAACCGATTAGAGCTGGGCTCATATTTGCGGTTT-TCCGCTAAGCACTGGG
* *
56923517 TGCCAAGATTTGACGG
64 TGCCAAGACTTGACGA
* *
56923533 ATATTTGTCGGTTTAACCGATTAGAGCTAGGCTCATATTTGTGGTTTCTCCGCTAAGCACTGGGT
1 ATATTTGTCGGTTTAACCGATTAGAGCTGGGCTCATATTTGCGGTTT-TCCGCTAAGCACTGGGT
* * *
56923598 GCTAGGACTTGATGA
65 GCCAAGACTTGACGA
* * * * * *
56923613 ATATTTGTTGGTTGATCCAATTAGAGCTGGGCTCACT-TTCGCGGTTATTCTGCTAAGCACTGGG
1 ATATTTGTCGGTTTAACCGATTAGAGCTGGGCTCA-TATTTGCGGTT-TTCCGCTAAGCACTGGG
56923677 TGCCA
64 TGCCA
56923682 TAATTGTCGG
Statistics
Matches: 122, Mismatches: 25, Indels: 5
0.80 0.16 0.03
Matches are distributed among these distances:
80 116 0.95
81 6 0.05
ACGTcount: A:0.21, C:0.19, G:0.27, T:0.33
Consensus pattern (79 bp):
ATATTTGTCGGTTTAACCGATTAGAGCTGGGCTCATATTTGCGGTTTTCCGCTAAGCACTGGGTG
CCAAGACTTGACGA
Found at i:56924274 original size:23 final size:23
Alignment explanation
Indices: 56924242--56924285 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
56924232 TATGTTTATT
* *
56924242 GAATGATTTATATGTATTTGAGA
1 GAATGATTTAAATGAATTTGAGA
*
56924265 GAATGTTTTAAATGAATTTGA
1 GAATGATTTAAATGAATTTGA
56924286 ATGTTTGTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.36, C:0.00, G:0.20, T:0.43
Consensus pattern (23 bp):
GAATGATTTAAATGAATTTGAGA
Found at i:56938230 original size:9 final size:9
Alignment explanation
Indices: 56938219--56938259 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
56938209 AAATTTAATC
*
56938219 ATTTTTATC
1 ATTTTTATA
56938228 ATTTTTATTA
1 ATTTTTA-TA
56938238 ATTTTTAT-
1 ATTTTTATA
56938246 -TTTTTATA
1 ATTTTTATA
56938254 ATTTTT
1 ATTTTT
56938260 TGTCACGTGA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
7 7 0.25
9 13 0.46
10 8 0.29
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.73
Consensus pattern (9 bp):
ATTTTTATA
Found at i:56938249 original size:16 final size:16
Alignment explanation
Indices: 56938219--56938259 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 16
56938209 AAATTTAATC
56938219 ATTTTTATCATTTTTATTA
1 ATTTTTAT--TTTTTA-TA
56938238 ATTTTTATTTTTTATA
1 ATTTTTATTTTTTATA
56938254 ATTTTT
1 ATTTTT
56938260 TGTCACGTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 8 0.36
17 6 0.27
19 8 0.36
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.73
Consensus pattern (16 bp):
ATTTTTATTTTTTATA
Found at i:56943224 original size:17 final size:16
Alignment explanation
Indices: 56943198--56943249 Score: 68
Period size: 17 Copynumber: 3.1 Consensus size: 16
56943188 CCCATATTTG
56943198 ATTTTTTTTAAAATTA
1 ATTTTTTTTAAAATTA
* *
56943214 GTTTTTATTTAAAAATA
1 ATTTTT-TTTAAAATTA
56943231 ATTTTTTTTAAAATATA
1 ATTTTTTTTAAAAT-TA
56943248 AT
1 AT
56943250 ACACTAAATG
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
16 12 0.40
17 18 0.60
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (16 bp):
ATTTTTTTTAAAATTA
Found at i:56944044 original size:25 final size:24
Alignment explanation
Indices: 56944016--56944071 Score: 64
Period size: 25 Copynumber: 2.4 Consensus size: 24
56944006 ATTAAAAATA
56944016 CTAAAAACATT-AAAATAAATATTT
1 CTAAAAACATTGAAAATAAAT-TTT
*
56944040 CCTAACAA-ATTGAAAATAAATTTT
1 -CTAAAAACATTGAAAATAAATTTT
56944064 -TAAAAACA
1 CTAAAAACA
56944072 CATACTTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
22 5 0.19
23 1 0.04
24 6 0.22
25 15 0.56
ACGTcount: A:0.57, C:0.11, G:0.02, T:0.30
Consensus pattern (24 bp):
CTAAAAACATTGAAAATAAATTTT
Found at i:56944152 original size:30 final size:31
Alignment explanation
Indices: 56944112--56944174 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 31
56944102 CTTAACAAAA
* * *
56944112 AAATGTCTCTAAAATAGT-AACAAAATTAAC
1 AAATGCCTCTAAAATAATAAAAAAAATTAAC
56944142 AAATGCCTCTAAAATAATAAAAAAAATTAAC
1 AAATGCCTCTAAAATAATAAAAAAAATTAAC
56944173 AA
1 AA
56944175 TAAAATAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 16 0.55
31 13 0.45
ACGTcount: A:0.59, C:0.13, G:0.05, T:0.24
Consensus pattern (31 bp):
AAATGCCTCTAAAATAATAAAAAAAATTAAC
Found at i:56949881 original size:2 final size:2
Alignment explanation
Indices: 56949876--56949918 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
56949866 AAAATTTTTA
56949876 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
56949918 A
1 A
56949919 GTAAATTAGA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:56950837 original size:19 final size:18
Alignment explanation
Indices: 56950801--56950844 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
56950791 ATAAATTTCA
56950801 AAATTTTTATAAAAATTT
1 AAATTTTTATAAAAATTT
*
56950819 AGATTTTTA-AAAATTATTT
1 AAATTTTTATAAAA--ATTT
56950838 AAATTTT
1 AAATTTT
56950845 ATGTTGAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 4 0.18
18 8 0.36
19 10 0.45
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (18 bp):
AAATTTTTATAAAAATTT
Found at i:56956718 original size:21 final size:21
Alignment explanation
Indices: 56956680--56956719 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
56956670 TTTTTTCTTT
*
56956680 TTATTTAAAAAAGGAAAAATA
1 TTATTTAAAAAAGAAAAAATA
56956701 TTATTTAAACAAA-AAAAAA
1 TTATTTAAA-AAAGAAAAAA
56956720 GGAAAATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 14 0.82
22 3 0.18
ACGTcount: A:0.65, C:0.03, G:0.05, T:0.28
Consensus pattern (21 bp):
TTATTTAAAAAAGAAAAAATA
Found at i:56958934 original size:21 final size:21
Alignment explanation
Indices: 56958898--56958968 Score: 76
Period size: 20 Copynumber: 3.5 Consensus size: 21
56958888 ATTATTTACT
56958898 ATTTT-AATAA-GTTTTACAA
1 ATTTTAAATAATGTTTTACAA
*
56958917 ATTTTAAATAATGTTTTA-TA
1 ATTTTAAATAATGTTTTACAA
* *
56958937 ATTTTTAATAACTTTTTTACAA
1 ATTTTAAATAA-TGTTTTACAA
*
56958959 TTTTTAAATA
1 ATTTTAAATA
56958969 CGTTTTTACC
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
19 5 0.12
20 16 0.38
21 12 0.29
22 9 0.21
ACGTcount: A:0.39, C:0.04, G:0.03, T:0.54
Consensus pattern (21 bp):
ATTTTAAATAATGTTTTACAA
Found at i:56958947 original size:10 final size:10
Alignment explanation
Indices: 56958899--56959052 Score: 61
Period size: 10 Copynumber: 15.5 Consensus size: 10
56958889 TTATTTACTA
*
56958899 TTTTAATAAG
1 TTTTAATAAT
56958909 TTTTACA-AAT
1 TTTTA-ATAAT
*
56958919 TTTAAATAAT
1 TTTTAATAAT
56958929 GTTTT-ATAAT
1 -TTTTAATAAT
56958939 TTTTAATAACT
1 TTTTAATAA-T
* *
56958950 TTTTTACAAT
1 TTTTAATAAT
*
56958960 TTTTAAATACGT
1 TTTT-AATA-AT
**
56958972 TTTT-ACCAT
1 TTTTAATAAT
56958981 TTTTAATATAT
1 TTTTAATA-AT
* * *
56958992 TTTTTACAGT
1 TTTTAATAAT
*
56959002 TTTTATTAAT
1 TTTTAATAAT
*
56959012 TTTCAAT--T
1 TTTTAATAAT
*
56959020 ATTT-A-AAT
1 TTTTAATAAT
*
56959028 TTTTTATAAT
1 TTTTAATAAT
* *
56959038 TTTAAATATT
1 TTTTAATAAT
56959048 TTTTA
1 TTTTA
56959053 CAGTTCTATA
Statistics
Matches: 102, Mismatches: 29, Indels: 26
0.65 0.18 0.17
Matches are distributed among these distances:
7 1 0.01
8 7 0.07
9 11 0.11
10 56 0.55
11 22 0.22
12 5 0.05
ACGTcount: A:0.34, C:0.05, G:0.03, T:0.58
Consensus pattern (10 bp):
TTTTAATAAT
Found at i:56958974 original size:21 final size:20
Alignment explanation
Indices: 56958909--56959054 Score: 108
Period size: 21 Copynumber: 7.3 Consensus size: 20
56958899 TTTTAATAAG
* *
56958909 TTTTACAAATTTTAAATAATG
1 TTTTACAATTTTTAAAT-ATT
*
56958930 TTTTATAATTTTT-AATAACTT
1 TTTTACAATTTTTAAAT-A-TT
*
56958951 TTTTACAATTTTTAAATACGT
1 TTTTACAATTTTTAAATA-TT
*
56958972 TTTTACCATTTTTAATATATT
1 TTTTACAATTTTTAA-ATATT
* * *
56958993 TTTTACAGTTTTT-ATTA-A
1 TTTTACAATTTTTAAATATT
56959011 TTTT-CAATTATTT-AA-ATT
1 TTTTACAATT-TTTAAATATT
*
56959029 TTTTATAA-TTTTAAATATT
1 TTTTACAATTTTTAAATATT
56959048 TTTTACA
1 TTTTACA
56959055 GTTCTATATA
Statistics
Matches: 101, Mismatches: 16, Indels: 18
0.75 0.12 0.13
Matches are distributed among these distances:
17 8 0.08
18 15 0.15
19 13 0.13
20 6 0.06
21 53 0.52
22 6 0.06
ACGTcount: A:0.34, C:0.06, G:0.02, T:0.58
Consensus pattern (20 bp):
TTTTACAATTTTTAAATATT
Found at i:56959013 original size:20 final size:19
Alignment explanation
Indices: 56958886--56959014 Score: 84
Period size: 21 Copynumber: 6.4 Consensus size: 19
56958876 TTTGATTTGT
*
56958886 TAATTATTTAC-TATTTTAA
1 TAATTTTTTACAT-TTTTAA
* *
56958905 TAA-GTTTTACAAATTTTAAA
1 TAATTTTTTAC--ATTTTTAA
56958925 TAATGTTTTATA-ATTTTTAA
1 TAAT-TTTT-TACATTTTTAA
56958945 TAACTTTTTTACAATTTTTAAA
1 TAA-TTTTTTAC-ATTTTT-AA
**
56958967 TACGTTTTTACCATTTTTAA
1 TAATTTTTTA-CATTTTTAA
*
56958987 TATATTTTTTACAGTTTTTAT
1 TA-ATTTTTTACA-TTTTTAA
56959008 TAATTTT
1 TAATTTT
56959015 CAATTATTTA
Statistics
Matches: 87, Mismatches: 10, Indels: 25
0.71 0.08 0.20
Matches are distributed among these distances:
18 5 0.06
19 5 0.06
20 33 0.38
21 34 0.39
22 8 0.09
23 2 0.02
ACGTcount: A:0.33, C:0.06, G:0.03, T:0.57
Consensus pattern (19 bp):
TAATTTTTTACATTTTTAA
Found at i:56959640 original size:21 final size:21
Alignment explanation
Indices: 56959616--56959659 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
56959606 TTAGTTAACA
*
56959616 ATAATAAA-AGTTTAATTAGTT
1 ATAAAAAATAGTTTAATTA-TT
*
56959637 ATAAAAAATATTTTAATTATT
1 ATAAAAAATAGTTTAATTATT
56959658 AT
1 AT
56959660 TAAATTATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (21 bp):
ATAAAAAATAGTTTAATTATT
Found at i:56959726 original size:16 final size:16
Alignment explanation
Indices: 56959673--56959728 Score: 53
Period size: 15 Copynumber: 3.6 Consensus size: 16
56959663 ATTATAAATT
56959673 ACATAATTATATGTTAA
1 ACATAA-TATATGTTAA
* *
56959690 ACATAATAT-TTTTTA
1 ACATAATATATGTTAA
*
56959705 A-TTAATATATGTTAA
1 ACATAATATATGTTAA
*
56959720 ACCTAATAT
1 ACATAATAT
56959729 TTTTATTTTT
Statistics
Matches: 31, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
14 6 0.19
15 10 0.32
16 9 0.29
17 6 0.19
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.45
Consensus pattern (16 bp):
ACATAATATATGTTAA
Found at i:56960468 original size:31 final size:30
Alignment explanation
Indices: 56960431--56960523 Score: 98
Period size: 31 Copynumber: 3.0 Consensus size: 30
56960421 TTACACAATG
**
56960431 ATCATTGAGCTATTCAAAAGTTTTAATTTAA
1 ATCATTGAATTATTCAAAAGTTTT-ATTTAA
56960462 ATCATTGAATTATTCTAAAA-TTTTCATTTAA
1 ATCATTGAATTATTC-AAAAGTTTT-ATTTAA
* * *
56960493 GTCACTGAATTATTGAAAAGTTATTATTTAA
1 ATCATTGAATTATTCAAAAGTT-TTATTTAA
56960524 GTCACTAAGA
Statistics
Matches: 53, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
30 4 0.08
31 43 0.81
32 6 0.11
ACGTcount: A:0.39, C:0.09, G:0.09, T:0.44
Consensus pattern (30 bp):
ATCATTGAATTATTCAAAAGTTTTATTTAA
Found at i:56960524 original size:31 final size:31
Alignment explanation
Indices: 56960441--56960529 Score: 110
Period size: 31 Copynumber: 2.9 Consensus size: 31
56960431 ATCATTGAGC
* *
56960441 TATTCAAAAGTTTTAATTTAAATCATTGAAT
1 TATTCAAAAGTTTTAATTTAAGTCACTGAAT
*
56960472 TATTCTAAAA-TTTTCATTTAAGTCACTGAAT
1 TATTC-AAAAGTTTTAATTTAAGTCACTGAAT
*
56960503 TATTGAAAAGTTATT-ATTTAAGTCACT
1 TATTCAAAAGTT-TTAATTTAAGTCACT
56960530 AAGATGTTAA
Statistics
Matches: 51, Mismatches: 4, Indels: 6
0.84 0.07 0.10
Matches are distributed among these distances:
30 4 0.08
31 41 0.80
32 6 0.12
ACGTcount: A:0.38, C:0.09, G:0.08, T:0.45
Consensus pattern (31 bp):
TATTCAAAAGTTTTAATTTAAGTCACTGAAT
Found at i:56962733 original size:21 final size:22
Alignment explanation
Indices: 56962702--56962743 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
56962692 ATTAATTTCA
* *
56962702 AATATAATTTTTCATTAATAAT
1 AATATAATTTTACAATAATAAT
56962724 AATA-AATTTTACAATAATAA
1 AATATAATTTTACAATAATAA
56962744 ACAACTTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (22 bp):
AATATAATTTTACAATAATAAT
Found at i:56963460 original size:23 final size:24
Alignment explanation
Indices: 56963433--56963492 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 24
56963423 CGTTTATTTA
56963433 ATGTTCACGAACAT-TAAACGAAC
1 ATGTTCACGAACATATAAACGAAC
* **
56963456 ATGTTCATGAACATATAATTGAAC
1 ATGTTCACGAACATATAAACGAAC
* *
56963480 ACGTTCACTAACA
1 ATGTTCACGAACA
56963493 ATGTTAATGA
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
23 13 0.43
24 17 0.57
ACGTcount: A:0.42, C:0.20, G:0.12, T:0.27
Consensus pattern (24 bp):
ATGTTCACGAACATATAAACGAAC
Found at i:56963517 original size:4 final size:4
Alignment explanation
Indices: 56963508--56963533 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
56963498 AATGAATAAT
56963508 AAAC AAAC AAAC AAAC AAAC AAAC AA
1 AAAC AAAC AAAC AAAC AAAC AAAC AA
56963534 TAAAAACATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.23, G:0.00, T:0.00
Consensus pattern (4 bp):
AAAC
Found at i:56968831 original size:48 final size:46
Alignment explanation
Indices: 56968800--56968900 Score: 132
Period size: 48 Copynumber: 2.2 Consensus size: 46
56968790 TGCTGGGCAA
56968800 CAGAGAGCACACAAAGTGCTAATCAGAGAGCACACGAAGTGCTAAT
1 CAGAGAGCACACAAAGTGCTAATCAGAGAGCACACGAAGTGCTAAT
* * * *
56968846 CGGAGAGCACACACAGTGCTAATAACAGAGAGCACGA-GACGTGCTAAA
1 CAGAGAGCACACAAAGTGCTAAT--CAGAGAGCAC-ACGAAGTGCTAAT
56968894 CAGAGAG
1 CAGAGAG
56968901 TGCGCTAGTG
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
46 21 0.45
48 25 0.53
49 1 0.02
ACGTcount: A:0.41, C:0.22, G:0.27, T:0.11
Consensus pattern (46 bp):
CAGAGAGCACACAAAGTGCTAATCAGAGAGCACACGAAGTGCTAAT
Found at i:56968895 original size:23 final size:23
Alignment explanation
Indices: 56968750--56968900 Score: 121
Period size: 23 Copynumber: 6.4 Consensus size: 23
56968740 TAAACGGAAC
* * *
56968750 AAACGGAGAGTAC-CGAAGTACT
1 AAACAGAGAGCACACGAAGTGCT
*
56968772 AAACAGAGAGCACA-TAAGTGCT
1 AAACAGAGAGCACACGAAGTGCT
* *
56968794 GGGCAACAGAGAGCACACAAAGTGCT
1 ---AAACAGAGAGCACACGAAGTGCT
*
56968820 AATCAGAGAGCACACGAAGTGCT
1 AAACAGAGAGCACACGAAGTGCT
* *
56968843 AATCGGAGAGCACAC-ACAGTGCT
1 AAACAGAGAGCACACGA-AGTGCT
*
56968866 AATAACAGAGAGCACGA-GACGTGCT
1 -A-AACAGAGAGCAC-ACGAAGTGCT
56968891 AAACAGAGAG
1 AAACAGAGAG
56968901 TGCGCTAGTG
Statistics
Matches: 106, Mismatches: 13, Indels: 19
0.77 0.09 0.14
Matches are distributed among these distances:
22 18 0.17
23 49 0.46
24 2 0.02
25 28 0.26
26 9 0.08
ACGTcount: A:0.41, C:0.21, G:0.27, T:0.11
Consensus pattern (23 bp):
AAACAGAGAGCACACGAAGTGCT
Found at i:56969571 original size:14 final size:14
Alignment explanation
Indices: 56969552--56969579 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
56969542 TATCTGCTCT
56969552 GACCTTGTTACACA
1 GACCTTGTTACACA
56969566 GACCTTGTTACACA
1 GACCTTGTTACACA
56969580 AAATCAATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.29, G:0.14, T:0.29
Consensus pattern (14 bp):
GACCTTGTTACACA
Found at i:56971309 original size:26 final size:27
Alignment explanation
Indices: 56971253--56971309 Score: 73
Period size: 26 Copynumber: 2.1 Consensus size: 27
56971243 CCTCATATTT
**
56971253 TTTTTATTTTTATGAACTATTTATATT
1 TTTTTATTTTTATGAACTATTTATAAC
56971280 TTTTTATTTTT-TGAA-TATTTTATAAC
1 TTTTTATTTTTATGAACTA-TTTATAAC
56971306 TTTT
1 TTTT
56971310 AAATTATTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
25 2 0.07
26 14 0.52
27 11 0.41
ACGTcount: A:0.25, C:0.04, G:0.04, T:0.68
Consensus pattern (27 bp):
TTTTTATTTTTATGAACTATTTATAAC
Found at i:56971309 original size:27 final size:27
Alignment explanation
Indices: 56971252--56971309 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 27
56971242 ACCTCATATT
*
56971252 TTTTTTATTTTTATGAACTATTTATAT
1 TTTTTTATTTTTATGAACTATTTATAC
56971279 TTTTTTATTTTT-TGAA-TATTTTATAAC
1 TTTTTTATTTTTATGAACTA-TTTAT-AC
56971306 TTTT
1 TTTT
56971310 AAATTATTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
25 2 0.07
26 9 0.32
27 17 0.61
ACGTcount: A:0.24, C:0.03, G:0.03, T:0.69
Consensus pattern (27 bp):
TTTTTTATTTTTATGAACTATTTATAC
Found at i:56971796 original size:15 final size:16
Alignment explanation
Indices: 56971766--56971807 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
56971756 AATTAATTCT
56971766 AAATAT-TAT-ATAAA
1 AAATATATATAATAAA
56971780 AAATATATATAAT-AA
1 AAATATATATAATAAA
*
56971795 AAATTTATATAAT
1 AAATATATATAAT
56971808 GAAATTAATG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
14 6 0.24
15 17 0.68
16 2 0.08
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
AAATATATATAATAAA
Found at i:56972139 original size:15 final size:15
Alignment explanation
Indices: 56972119--56972154 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
56972109 ATTCATTCAA
56972119 ATTTAAAGATTTTTT
1 ATTTAAAGATTTTTT
56972134 ATTTAAAGATTTTTT
1 ATTTAAAGATTTTTT
56972149 ATTTAA
1 ATTTAA
56972155 TAACGAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.58
Consensus pattern (15 bp):
ATTTAAAGATTTTTT
Found at i:56980741 original size:16 final size:16
Alignment explanation
Indices: 56980722--56980752 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
56980712 ACCGATTTAC
56980722 TATTTATATTTTATTT
1 TATTTATATTTTATTT
*
56980738 TATTTATTTTTTATT
1 TATTTATATTTTATT
56980753 ATACGTACTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (16 bp):
TATTTATATTTTATTT
Found at i:56981544 original size:14 final size:14
Alignment explanation
Indices: 56981525--56981554 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
56981515 TTTGTAATGG
56981525 TATTTATAGCTTGT
1 TATTTATAGCTTGT
56981539 TATTTATAGCTTGT
1 TATTTATAGCTTGT
56981553 TA
1 TA
56981555 AAAAAAATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.23, C:0.07, G:0.13, T:0.57
Consensus pattern (14 bp):
TATTTATAGCTTGT
Found at i:56982596 original size:148 final size:148
Alignment explanation
Indices: 56982328--56982625 Score: 533
Period size: 148 Copynumber: 2.0 Consensus size: 148
56982318 AATTGCCAAA
*
56982328 ATCTTAAAAATAAAACCCCATTCACAGTACCATCACCTTGGACCCCTAATTCTCATTATCATCAT
1 ATCTTAAAAATAAAACCCCATTCACAGTACCATCACCTTGGACCCCTAATACTCATTATCATCAT
* * *
56982393 CTAACCCCATTACCCCCAAGCCCCAACATTGCTTCAGCATCGTCGTCAAGCTAGACCCAAGACGG
66 CTAACCCCATTACCCCCAAACCCCAACATTGCTTCACCATCATCGTCAAGCTAGACCCAAGACGG
56982458 AGCACGTACTTCCATTTG
131 AGCACGTACTTCCATTTG
*
56982476 ATCTTAAAAATAAAACCCTATTCACAGTACCATCACCTTGGACCCCTAATACTCATTATCATCAT
1 ATCTTAAAAATAAAACCCCATTCACAGTACCATCACCTTGGACCCCTAATACTCATTATCATCAT
* *
56982541 CTAACCCCATTACCCCCAAACCCCAGCATTGCTTCACCATCATTGTCAAGCTAGACCCAAGACGG
66 CTAACCCCATTACCCCCAAACCCCAACATTGCTTCACCATCATCGTCAAGCTAGACCCAAGACGG
56982606 AGCACGTACTTCCATTTG
131 AGCACGTACTTCCATTTG
56982624 AT
1 AT
56982626 TCAAAAGGAA
Statistics
Matches: 143, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
148 143 1.00
ACGTcount: A:0.31, C:0.34, G:0.10, T:0.25
Consensus pattern (148 bp):
ATCTTAAAAATAAAACCCCATTCACAGTACCATCACCTTGGACCCCTAATACTCATTATCATCAT
CTAACCCCATTACCCCCAAACCCCAACATTGCTTCACCATCATCGTCAAGCTAGACCCAAGACGG
AGCACGTACTTCCATTTG
Found at i:56991194 original size:16 final size:17
Alignment explanation
Indices: 56991173--56991212 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 17
56991163 TCAATTAGAC
56991173 CAAAAAAT-TTCTTTAT
1 CAAAAAATATTCTTTAT
*
56991189 CAAAAAATATTTTTTAT
1 CAAAAAATATTCTTTAT
56991206 -AAAAAAT
1 CAAAAAAT
56991213 CGATTTTAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 15 0.68
17 7 0.32
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (17 bp):
CAAAAAATATTCTTTAT
Found at i:56997981 original size:15 final size:16
Alignment explanation
Indices: 56997958--56997987 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
56997948 GTATTTGATT
56997958 TTTATATTTTAATTTA
1 TTTATATTTTAATTTA
56997974 TTTA-ATTTTAATTT
1 TTTATATTTTAATTT
56997988 TGATATTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (16 bp):
TTTATATTTTAATTTA
Found at i:56999147 original size:2 final size:2
Alignment explanation
Indices: 56999140--56999177 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
56999130 GCCAAAGGTT
56999140 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
56999178 AATAATTAGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:57012464 original size:24 final size:26
Alignment explanation
Indices: 57012437--57012486 Score: 77
Period size: 24 Copynumber: 2.0 Consensus size: 26
57012427 TAATTTATAT
*
57012437 TTTATATATCA-TTAT-ATTAAATTA
1 TTTAAATATCATTTATCATTAAATTA
57012461 TTTAAATATCATTTATCATTAAATTA
1 TTTAAATATCATTTATCATTAAATTA
57012487 AATTGTTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 10 0.43
25 4 0.17
26 9 0.39
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (26 bp):
TTTAAATATCATTTATCATTAAATTA
Found at i:57012478 original size:31 final size:31
Alignment explanation
Indices: 57012443--57012514 Score: 94
Period size: 31 Copynumber: 2.4 Consensus size: 31
57012433 ATATTTTATA
57012443 TATCATTATATTAAATTATTTAAATATCATT
1 TATCATTATATTAAATTATTTAAATATCATT
* * * *
57012474 TATCATTAAATTAAATTGTTTAAATTTTATT
1 TATCATTATATTAAATTATTTAAATATCATT
57012505 T-T-ATTATATT
1 TATCATTATATT
57012515 TAAAATTTTA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
29 7 0.19
30 1 0.03
31 28 0.78
ACGTcount: A:0.39, C:0.04, G:0.01, T:0.56
Consensus pattern (31 bp):
TATCATTATATTAAATTATTTAAATATCATT
Found at i:57015008 original size:17 final size:17
Alignment explanation
Indices: 57014986--57015023 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
57014976 AACTAACAAA
57014986 AGACAACTTGTATTAAT
1 AGACAACTTGTATTAAT
57015003 AGACAACTTGTATTAAT
1 AGACAACTTGTATTAAT
57015020 AGAC
1 AGAC
57015024 GAACCTAAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.32
Consensus pattern (17 bp):
AGACAACTTGTATTAAT
Found at i:57019829 original size:15 final size:16
Alignment explanation
Indices: 57019799--57019848 Score: 56
Period size: 15 Copynumber: 3.4 Consensus size: 16
57019789 TTTTTTAAAA
57019799 TATTT-ATA-TTATAT
1 TATTTAATATTTATAT
57019813 TATTTAATATTTA-AT
1 TATTTAATATTTATAT
57019828 TATTTAATCATTT-T-T
1 TATTTAAT-ATTTATAT
57019843 TATTTA
1 TATTTA
57019849 TTGAAATTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
14 5 0.16
15 20 0.62
16 7 0.22
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (16 bp):
TATTTAATATTTATAT
Found at i:57021401 original size:19 final size:20
Alignment explanation
Indices: 57021377--57021422 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
57021367 TGCAAAACTA
57021377 TAAAAAAATTA-AAAATTAC
1 TAAAAAAATTATAAAATTAC
* *
57021396 TAAAAATATTATAAAATTTC
1 TAAAAAAATTATAAAATTAC
57021416 -AAAAAAA
1 TAAAAAAA
57021423 AGTATTAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.28
Consensus pattern (20 bp):
TAAAAAAATTATAAAATTAC
Found at i:57021428 original size:23 final size:20
Alignment explanation
Indices: 57021378--57021441 Score: 60
Period size: 22 Copynumber: 3.1 Consensus size: 20
57021368 GCAAAACTAT
*
57021378 AAAAAA-ATTAAAAA-TTAC
1 AAAAAATATTAAAAATTTAA
*
57021396 TAAAAATATTATAAAATTTCAA
1 AAAAAATATTA-AAAATTT-AA
*
57021418 AAAAAAGTATTAATAATTTAA
1 AAAAAA-TATTAAAAATTTAA
57021439 AAA
1 AAA
57021442 GTCTAAAGCA
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
18 5 0.14
19 4 0.11
20 4 0.11
21 7 0.19
22 12 0.32
23 5 0.14
ACGTcount: A:0.66, C:0.03, G:0.02, T:0.30
Consensus pattern (20 bp):
AAAAAATATTAAAAATTTAA
Found at i:57024279 original size:20 final size:21
Alignment explanation
Indices: 57024241--57024280 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
57024231 ATTTTTCCCT
*
57024241 TTTTTAATTTTTGTAATTTCC
1 TTTTTAATTTTTATAATTTCC
*
57024262 TTTTT-ATTTTTATTATTTC
1 TTTTTAATTTTTATAATTTC
57024281 TTTCCTACGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.17, C:0.07, G:0.03, T:0.72
Consensus pattern (21 bp):
TTTTTAATTTTTATAATTTCC
Found at i:57025577 original size:37 final size:37
Alignment explanation
Indices: 57025527--57025601 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
57025517 TGGTACAAAA
57025527 TGATTCGGAAGGTATCAATGTGCTAGCAGAAGCCCCT
1 TGATTCGGAAGGTATCAATGTGCTAGCAGAAGCCCCT
57025564 TGATTCGGAAGGTATCAATGTGCTAGCAGAAGCCCCT
1 TGATTCGGAAGGTATCAATGTGCTAGCAGAAGCCCCT
57025601 T
1 T
57025602 CCAACTTAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (37 bp):
TGATTCGGAAGGTATCAATGTGCTAGCAGAAGCCCCT
Found at i:57026464 original size:10 final size:10
Alignment explanation
Indices: 57026425--57026466 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 10
57026415 AAACATAATA
57026425 ATAT-TATAT
1 ATATGTATAT
*
57026434 ATACGTATAT
1 ATATGTATAT
*
57026444 GTATGTATAT
1 ATATGTATAT
*
57026454 ATATATATAT
1 ATATGTATAT
57026464 ATA
1 ATA
57026467 AGGATATGGG
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
9 3 0.11
10 24 0.89
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.48
Consensus pattern (10 bp):
ATATGTATAT
Found at i:57035625 original size:6 final size:6
Alignment explanation
Indices: 57035611--57035644 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
57035601 GTAATCCAGA
* *
57035611 ATTTAG ATTTGG ATTTGG ATTTGG ATTTGA ATTT
1 ATTTGG ATTTGG ATTTGG ATTTGG ATTTGG ATTT
57035645 AGATGTAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.53
Consensus pattern (6 bp):
ATTTGG
Found at i:57042918 original size:39 final size:39
Alignment explanation
Indices: 57042891--57043060 Score: 259
Period size: 39 Copynumber: 4.4 Consensus size: 39
57042881 AGGATAAACT
* * * *
57042891 GGTGGCTTGGGTGGAGGAGCGTAAGTTGGTGGCTTGGTC
1 GGTGACTTGGGTGGAGGAGAGTAAGTTGGCGGCTTGCTC
* * *
57042930 GGTGACTTGGGTGGAGGAGCGTGAGTTGGCGGCTTGGTC
1 GGTGACTTGGGTGGAGGAGAGTAAGTTGGCGGCTTGCTC
*
57042969 GGTGACTTGGGTGGAGGAGAGTAAGTTGGCGGCTTGCTG
1 GGTGACTTGGGTGGAGGAGAGTAAGTTGGCGGCTTGCTC
*
57043008 GGTGACTTGGGTGGAGGAGAGTAAGTTGGCGGCTTGCTT
1 GGTGACTTGGGTGGAGGAGAGTAAGTTGGCGGCTTGCTC
57043047 GGTGACTTGGGTGG
1 GGTGACTTGGGTGG
57043061 TGGATAACCT
Statistics
Matches: 123, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 123 1.00
ACGTcount: A:0.12, C:0.11, G:0.50, T:0.27
Consensus pattern (39 bp):
GGTGACTTGGGTGGAGGAGAGTAAGTTGGCGGCTTGCTC
Found at i:57044884 original size:5 final size:5
Alignment explanation
Indices: 57044874--57044899 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
57044864 TTTTAATATT
57044874 TTTTA TTTTA TTTTA TTTTA TTTTA T
1 TTTTA TTTTA TTTTA TTTTA TTTTA T
57044900 GAATTTCTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTA
Found at i:57048363 original size:24 final size:23
Alignment explanation
Indices: 57048327--57048391 Score: 66
Period size: 22 Copynumber: 2.9 Consensus size: 23
57048317 ATTTCAAAAA
* *
57048327 ACAAAAATA-AATAAATAATTTTT
1 ACAAATATATAATAAATAA-ATTT
57048350 A-AAATTATATAAT-AATAAATTT
1 ACAAA-TATATAATAAATAAATTT
57048372 ACAAATATATAA-AAATAAAT
1 ACAAATATATAATAAATAAAT
57048392 AAATATTTTC
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
22 21 0.58
23 12 0.33
24 3 0.08
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (23 bp):
ACAAATATATAATAAATAAATTT
Found at i:57050923 original size:21 final size:21
Alignment explanation
Indices: 57050899--57050938 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
57050889 ATTTATTTTT
57050899 TAATT-TTAAAAATTCAAAAAA
1 TAATTCTTAAAAATT-AAAAAA
57050920 TAATTCTTAAAAATTAAAA
1 TAATTCTTAAAAATTAAAA
57050939 TTTATTAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (21 bp):
TAATTCTTAAAAATTAAAAAA
Found at i:57054455 original size:16 final size:17
Alignment explanation
Indices: 57054434--57054467 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
57054424 ATATAAAATT
57054434 TTACAAT-ATATATTTA
1 TTACAATAATATATTTA
*
57054450 TTACAATAATTTATTTA
1 TTACAATAATATATTTA
57054467 T
1 T
57054468 ATTTTTAATA
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:0.41, C:0.06, G:0.00, T:0.53
Consensus pattern (17 bp):
TTACAATAATATATTTA
Found at i:57054469 original size:25 final size:25
Alignment explanation
Indices: 57054440--57054492 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
57054430 AATTTTACAA
* **
57054440 TATATATTTATTACAATAATTTATT
1 TATATATTTAATACAATAAAATATT
* *
57054465 TATATTTTTAATATAATAAAATATT
1 TATATATTTAATACAATAAAATATT
57054490 TAT
1 TAT
57054493 GATAGTTTTT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (25 bp):
TATATATTTAATACAATAAAATATT
Found at i:57054847 original size:115 final size:115
Alignment explanation
Indices: 57054677--57054989 Score: 518
Period size: 115 Copynumber: 2.7 Consensus size: 115
57054667 TTCAATCTAA
* * * * * *
57054677 ATCAAGCTCAAACTTAAAAAATTGATCTAAATACTTTACATAAAACCAACGTGAATCCAAACTCA
1 ATCAAGCTCAAACTTAAAAAATTTATCTAAATACCTTACATAGAGCCAGCATGAATCCAAACTCA
*
57054742 CCCAACCCATGACATGAGCAAAATTTCAAATCCATTTTTCAAGTTTAGTC
66 CCCAACCCATGACATGAGCAAAATTTCAAATCCATTTTTCAAGTTAAGTC
* * *
57054792 ATCAAGCTCAAACTTGAAAATTTTATCTAAATACCTTACATAGAGCCAGCATGAATCCGAACTCA
1 ATCAAGCTCAAACTTAAAAAATTTATCTAAATACCTTACATAGAGCCAGCATGAATCCAAACTCA
*
57054857 CCCAACCCATGACATGAGCAAAATTTCAAGTCCATTTTTCAAGTTAAGTC
66 CCCAACCCATGACATGAGCAAAATTTCAAATCCATTTTTCAAGTTAAGTC
*
57054907 ATCAAGCTCAAACTTAAAAAATTTATCTAAATACCTTAGATAGAGCCAGCATGAATCCAAACTCA
1 ATCAAGCTCAAACTTAAAAAATTTATCTAAATACCTTACATAGAGCCAGCATGAATCCAAACTCA
57054972 CCCAACCCATGACATGAG
66 CCCAACCCATGACATGAG
57054990 ATATAATCGG
Statistics
Matches: 183, Mismatches: 15, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
115 183 1.00
ACGTcount: A:0.40, C:0.24, G:0.10, T:0.26
Consensus pattern (115 bp):
ATCAAGCTCAAACTTAAAAAATTTATCTAAATACCTTACATAGAGCCAGCATGAATCCAAACTCA
CCCAACCCATGACATGAGCAAAATTTCAAATCCATTTTTCAAGTTAAGTC
Found at i:57058017 original size:15 final size:15
Alignment explanation
Indices: 57057997--57058026 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
57057987 ACTTGCACCA
57057997 ATGTAAAACTTAAGT
1 ATGTAAAACTTAAGT
57058012 ATGTAAAACTTAAGT
1 ATGTAAAACTTAAGT
57058027 GGTTTTATAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.07, G:0.13, T:0.33
Consensus pattern (15 bp):
ATGTAAAACTTAAGT
Found at i:57069016 original size:31 final size:31
Alignment explanation
Indices: 57068981--57069041 Score: 113
Period size: 31 Copynumber: 2.0 Consensus size: 31
57068971 TAGAATTTAT
*
57068981 ATATTTTTCACAAACATACATATAATGTATA
1 ATATTTTTCACAAACATAAATATAATGTATA
57069012 ATATTTTTCACAAACATAAATATAATGTAT
1 ATATTTTTCACAAACATAAATATAATGTAT
57069042 TATAATATTA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.46, C:0.11, G:0.03, T:0.39
Consensus pattern (31 bp):
ATATTTTTCACAAACATAAATATAATGTATA
Found at i:57079143 original size:15 final size:16
Alignment explanation
Indices: 57079123--57079153 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
57079113 TAACTTCAAG
57079123 ATATACAA-AAAAAAT
1 ATATACAACAAAAAAT
57079138 ATATACAACAAAAAAT
1 ATATACAACAAAAAAT
57079154 CAATAGAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.71, C:0.10, G:0.00, T:0.19
Consensus pattern (16 bp):
ATATACAACAAAAAAT
Found at i:57104491 original size:24 final size:24
Alignment explanation
Indices: 57104464--57104512 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
57104454 AGAGAAACCG
57104464 AGATTTTAGTAGATTACAATGAAT
1 AGATTTTAGTAGATTACAATGAAT
57104488 AGATTTTAGTAGATTACAATGAAT
1 AGATTTTAGTAGATTACAATGAAT
57104512 A
1 A
57104513 TTATCCTCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.43, C:0.04, G:0.16, T:0.37
Consensus pattern (24 bp):
AGATTTTAGTAGATTACAATGAAT
Found at i:57106656 original size:18 final size:16
Alignment explanation
Indices: 57106624--57106667 Score: 56
Period size: 14 Copynumber: 2.8 Consensus size: 16
57106614 ATGAGATGAG
57106624 AATAAATTTTTAATTA
1 AATAAATTTTTAATTA
57106640 AATAAA--TTTAATTA
1 AATAAATTTTTAATTA
*
57106654 ATTAAAATTTTTAA
1 AAT-AAATTTTTAA
57106668 ACCTAAATCT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
14 10 0.42
15 3 0.12
16 6 0.25
17 5 0.21
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
AATAAATTTTTAATTA
Found at i:57110146 original size:19 final size:18
Alignment explanation
Indices: 57110107--57110146 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
57110097 CTGTATTCAC
*
57110107 TATATTTATTAATTATAT
1 TATATTTATTAAATATAT
*
57110125 TATATTCTATTAAATATTT
1 TATATT-TATTAAATATAT
57110144 TAT
1 TAT
57110147 CGCATTCATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (18 bp):
TATATTTATTAAATATAT
Found at i:57114120 original size:2 final size:2
Alignment explanation
Indices: 57114108--57114146 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
57114098 TCATTTTCCC
* *
57114108 CT CT C- CT CT CT CT CT CT CT CT CT CT TT CT CC CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
57114147 TTTGTTTTCC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:57117369 original size:14 final size:15
Alignment explanation
Indices: 57117350--57117382 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
57117340 TAAGCAAGCC
*
57117350 TATTAATTATAAT-T
1 TATTAATTAAAATAT
57117364 TATTAATTAAAATAT
1 TATTAATTAAAATAT
57117379 TATT
1 TATT
57117383 TCAATCAAAT
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:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TATTAATTAAAATAT
Found at i:57117574 original size:32 final size:32
Alignment explanation
Indices: 57117538--57117599 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
57117528 TCATAAACTT
* * *
57117538 ATAAATTGATTACTTAAATTTAATAGCTCATG
1 ATAAATTAATTAATTAAATTTAATAACTCATG
*
57117570 ATAAATTAATTAATTTAATTTAATAACTCA
1 ATAAATTAATTAATTAAATTTAATAACTCA
57117600 AATTGATTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.45, C:0.08, G:0.05, T:0.42
Consensus pattern (32 bp):
ATAAATTAATTAATTAAATTTAATAACTCATG
Found at i:57118842 original size:107 final size:107
Alignment explanation
Indices: 57118682--57118902 Score: 415
Period size: 107 Copynumber: 2.1 Consensus size: 107
57118672 GGATGCAACA
*
57118682 AACAGAAAAAAATTAACAATCAGCTGAAAGCAGAACCTAGAAGACTACATGTGATGCTCACAGCT
1 AACAAAAAAAAATTAACAATCAGCTGAAAGCAGAACCTAGAAGACTACATGTGATGCTCACAGCT
* *
57118747 CACTATTTTGTTTAAGAGAAATGTTTAAAAATTATTAAAAGC
66 CACTATTTTGCTTAAGAGAAATGTTCAAAAATTATTAAAAGC
57118789 AACAAAAAAAAATTAACAATCAGCTGAAAGCAGAACCTAGAAGACTACATGTGATGCTCACAGCT
1 AACAAAAAAAAATTAACAATCAGCTGAAAGCAGAACCTAGAAGACTACATGTGATGCTCACAGCT
57118854 CACTATTTTGCTTAAGAGAAATGTTCAAAAATTATTAAAAGC
66 CACTATTTTGCTTAAGAGAAATGTTCAAAAATTATTAAAAGC
57118896 AACAAAA
1 AACAAAA
57118903 GTTAACTCGA
Statistics
Matches: 111, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
107 111 1.00
ACGTcount: A:0.47, C:0.16, G:0.14, T:0.24
Consensus pattern (107 bp):
AACAAAAAAAAATTAACAATCAGCTGAAAGCAGAACCTAGAAGACTACATGTGATGCTCACAGCT
CACTATTTTGCTTAAGAGAAATGTTCAAAAATTATTAAAAGC
Done.