Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015037.1 Kokia drynarioides strain JFW-HI SEQ_130081, whole genome shotgun sequence
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: 155156
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Warning! 427 characters in sequence are not A, C, G, or T
Found at i:2167 original size:18 final size:18
Alignment explanation
Indices: 2097--2155 Score: 73
Period size: 18 Copynumber: 3.1 Consensus size: 18
2087 AGGTGATAAC
* *
2097 GAAGACGAAGAGGAAGTG
1 GAAGACGAAGAAGAAGAG
2115 GAAGAGCAGAACGAAGAAGAG
1 GAAGA-C-GAA-GAAGAAGAG
2136 GAAGACGAAGAAGAAGAG
1 GAAGACGAAGAAGAAGAG
2154 GA
1 GA
2156 GGAGGAGGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
18 16 0.44
19 4 0.11
20 4 0.11
21 12 0.33
ACGTcount: A:0.51, C:0.07, G:0.41, T:0.02
Consensus pattern (18 bp):
GAAGACGAAGAAGAAGAG
Found at i:3345 original size:10 final size:9
Alignment explanation
Indices: 3292--3406 Score: 70
Period size: 10 Copynumber: 11.9 Consensus size: 9
3282 TATATTTTTC
3292 TTATAAAAA
1 TTATAAAAA
3301 TTATAAAAAA
1 TTAT-AAAAA
*
3311 ATATTAAAAA
1 TTA-TAAAAA
* *
3321 -AATATAAAC
1 TTATA-AAAA
3330 TTATAAAAA
1 TTATAAAAA
3339 TTGATAAAAA
1 TT-ATAAAAA
**
3349 TTTATAACTA
1 -TTATAAAAA
3359 TTATAAAAA
1 TTATAAAAA
*
3368 TTATAAACA
1 TTATAAAAA
* *
3377 TTCTCATAAA
1 TTAT-AAAAA
3387 TTATAATAAAA
1 TTAT-A-AAAA
3398 TTTATAAAA
1 -TTATAAAA
3407 TTAAATAAAA
Statistics
Matches: 81, Mismatches: 16, Indels: 17
0.71 0.14 0.15
Matches are distributed among these distances:
8 2 0.02
9 31 0.38
10 37 0.46
11 7 0.09
12 4 0.05
ACGTcount: A:0.60, C:0.04, G:0.01, T:0.35
Consensus pattern (9 bp):
TTATAAAAA
Found at i:3389 original size:28 final size:27
Alignment explanation
Indices: 3323--3406 Score: 80
Period size: 28 Copynumber: 2.9 Consensus size: 27
3313 ATTAAAAAAA
3323 TATAAACTTATAAAAATTGATAAAAATT
1 TATAAA-TTATAAAAATTGATAAAAATT
*
3351 TATAACTATTATAAAAATT-ATAAACATT
1 TATAA--ATTATAAAAATTGATAAAAATT
*
3379 CTCATAAATTATAATAAAATTTATAAAA
1 -T-ATAAATTAT-A-AAAATTGATAAAA
3407 TTAAATAAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 11
0.78 0.03 0.18
Matches are distributed among these distances:
28 18 0.38
29 13 0.28
30 11 0.23
31 5 0.11
ACGTcount: A:0.56, C:0.06, G:0.01, T:0.37
Consensus pattern (27 bp):
TATAAATTATAAAAATTGATAAAAATT
Found at i:3931 original size:18 final size:18
Alignment explanation
Indices: 3910--3961 Score: 54
Period size: 19 Copynumber: 2.9 Consensus size: 18
3900 ATTCTATATA
3910 TTTTAATATTTTATTAGT
1 TTTTAATATTTTATTAGT
* *
3928 TTTTAAAAATTATATT--T
1 TTTT-AATATTTTATTAGT
*
3945 TTTTAATAATTTATTAG
1 TTTTAATATTTTATTAG
3962 AACTTGTGTA
Statistics
Matches: 26, Mismatches: 5, Indels: 6
0.70 0.14 0.16
Matches are distributed among these distances:
16 8 0.31
17 5 0.19
18 4 0.15
19 9 0.35
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.62
Consensus pattern (18 bp):
TTTTAATATTTTATTAGT
Found at i:37021 original size:17 final size:17
Alignment explanation
Indices: 37001--37062 Score: 67
Period size: 17 Copynumber: 3.6 Consensus size: 17
36991 GGAATATAGA
37001 AGGTTAAAGGTCAAGGG
1 AGGTTAAAGGTCAAGGG
37018 AGGTT-AAGG--AAGATGG
1 AGGTTAAAGGTCAAG--GG
*
37034 AAGGTTAAAAGTCAAGGG
1 -AGGTTAAAGGTCAAGGG
37052 AGGTTAAAGGT
1 AGGTTAAAGGT
37063 TGAACATCCA
Statistics
Matches: 37, Mismatches: 2, Indels: 12
0.73 0.04 0.24
Matches are distributed among these distances:
14 3 0.08
16 6 0.16
17 20 0.54
18 5 0.14
20 3 0.08
ACGTcount: A:0.39, C:0.03, G:0.39, T:0.19
Consensus pattern (17 bp):
AGGTTAAAGGTCAAGGG
Found at i:37037 original size:34 final size:34
Alignment explanation
Indices: 36986--37058 Score: 119
Period size: 34 Copynumber: 2.1 Consensus size: 34
36976 AATATGAAAA
* *
36986 GTTAAGGAATATAGAAGGTTAAAGGTCAAGGGAG
1 GTTAAGGAAGATAGAAGGTTAAAAGTCAAGGGAG
*
37020 GTTAAGGAAGATGGAAGGTTAAAAGTCAAGGGAG
1 GTTAAGGAAGATAGAAGGTTAAAAGTCAAGGGAG
37054 GTTAA
1 GTTAA
37059 AGGTTGAACA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.41, C:0.03, G:0.36, T:0.21
Consensus pattern (34 bp):
GTTAAGGAAGATAGAAGGTTAAAAGTCAAGGGAG
Found at i:46352 original size:33 final size:33
Alignment explanation
Indices: 46307--46369 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 33
46297 TGTGGCAATC
* *
46307 CACGTGTATGTCATTTTAACAAAGTGAAAATGG
1 CACGTGTATGTCACTTCAACAAAGTGAAAATGG
*
46340 CACGTGTGTGTCACTTCAACAAAGTGAAAA
1 CACGTGTATGTCACTTCAACAAAGTGAAAA
46370 ATGATAACTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.37, C:0.16, G:0.21, T:0.27
Consensus pattern (33 bp):
CACGTGTATGTCACTTCAACAAAGTGAAAATGG
Found at i:47933 original size:19 final size:20
Alignment explanation
Indices: 47895--47949 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 20
47885 TCACCTGTAT
*
47895 TATAATATTTTTTTTAAATA
1 TATAATATTTTATTTAAATA
*
47915 TATACTATTTTATTT-AATA
1 TATAATATTTTATTTAAATA
* *
47934 TTTAGTAATTTTATTT
1 TATAAT-ATTTTATTT
47950 TTTTTCTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 8 0.27
20 22 0.73
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.62
Consensus pattern (20 bp):
TATAATATTTTATTTAAATA
Found at i:50659 original size:5 final size:5
Alignment explanation
Indices: 50649--50678 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
50639 CCATGAATGG
50649 TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA
50679 GTATTACAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
TAAAA
Found at i:67217 original size:78 final size:78
Alignment explanation
Indices: 66998--67219 Score: 320
Period size: 78 Copynumber: 2.8 Consensus size: 78
66988 AAATGAAGCG
* *
66998 GATTTTTTCTTTGAAAAATGGATGTGGGGC-AGGGTGGATTTTTTCTTTTGGATAGTGGGTATGA
1 GATTTTTTCTTTGAAAAATGGATGCGGGGCGA-GGTGGATTTTTTCTTTTGGATAGTGGGTATGG
**
67062 AATAGTTATGAGTG
65 AATAGTTATGAGCA
* * *
67076 GATTTTTTCTTTGAAAAATGGATGCGGGGCGGGGTGAATTTTTTCTTTTGGATTGTGGGTATGGA
1 GATTTTTTCTTTGAAAAATGGATGCGGGGCGAGGTGGATTTTTTCTTTTGGATAGTGGGTATGGA
*
67141 ATGGTTATGAGCA
66 ATAGTTATGAGCA
* * * *
67154 GTTTTTTTCTTTGAAAAATGGATGCGGGGCGATGTGGATTTTTTCTTCTGGATGGTGGGTATGGA
1 GATTTTTTCTTTGAAAAATGGATGCGGGGCGAGGTGGATTTTTTCTTTTGGATAGTGGGTATGGA
67219 A
66 A
67220 CGATTATGGT
Statistics
Matches: 129, Mismatches: 14, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
78 129 1.00
ACGTcount: A:0.21, C:0.06, G:0.33, T:0.41
Consensus pattern (78 bp):
GATTTTTTCTTTGAAAAATGGATGCGGGGCGAGGTGGATTTTTTCTTTTGGATAGTGGGTATGGA
ATAGTTATGAGCA
Found at i:67556 original size:2 final size:2
Alignment explanation
Indices: 67545--67573 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
67535 AATGAGATTA
67545 AT AT -T 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
67574 TTAAAAAGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:90966 original size:26 final size:26
Alignment explanation
Indices: 90936--90996 Score: 65
Period size: 26 Copynumber: 2.4 Consensus size: 26
90926 AAATTTTAAA
90936 TAATAATAA-ATCATATTTAAATAATT
1 TAATAATAATAT-ATATTTAAATAATT
* *
90962 TAAT-ATAATTATATTTTTAAATACTT
1 TAATAATAA-TATATATTTAAATAATT
90988 TAAT-ATAAT
1 TAATAATAAT
90997 GATCCATAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
25 5 0.16
26 24 0.77
27 2 0.06
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.48
Consensus pattern (26 bp):
TAATAATAATATATATTTAAATAATT
Found at i:95719 original size:24 final size:24
Alignment explanation
Indices: 95691--95813 Score: 174
Period size: 24 Copynumber: 5.1 Consensus size: 24
95681 GTAGACTGGT
95691 TAACCATTTTGGGCTCGTAAGAGC
1 TAACCATTTTGGGCTCGTAAGAGC
* ** *
95715 TAACCGTTCCGGGCTCATAAGAGC
1 TAACCATTTTGGGCTCGTAAGAGC
*
95739 TAACCATTTTGGGTTCGTAAGAGC
1 TAACCATTTTGGGCTCGTAAGAGC
* *
95763 TAACTATTTTGGGCTCGTAAGAGA
1 TAACCATTTTGGGCTCGTAAGAGC
*
95787 TAACCATTCTGGGCTCGTAAGAGC
1 TAACCATTTTGGGCTCGTAAGAGC
95811 TAA
1 TAA
95814 ATTTCTGAAA
Statistics
Matches: 84, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 84 1.00
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.28
Consensus pattern (24 bp):
TAACCATTTTGGGCTCGTAAGAGC
Found at i:98889 original size:17 final size:17
Alignment explanation
Indices: 98867--98902 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
98857 GATGTAAGTG
*
98867 AAAAATATCTATGTTAA
1 AAAAATATCTATATTAA
*
98884 AAAAATATTTATATTAA
1 AAAAATATCTATATTAA
98901 AA
1 AA
98903 TTTTGTTGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.36
Consensus pattern (17 bp):
AAAAATATCTATATTAA
Found at i:103879 original size:21 final size:22
Alignment explanation
Indices: 103843--103901 Score: 66
Period size: 21 Copynumber: 2.7 Consensus size: 22
103833 GAACTAATAT
*
103843 TAAATTATATATTTTACTATCG
1 TAAAATATATATTTTACTATCG
**
103865 TAAAATATA-ATTTTACTATTT
1 TAAAATATATATTTTACTATCG
*
103886 TAATAGTATATATTTT
1 TAA-AATATATATTTT
103902 TATAAAATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 13 0.42
22 13 0.42
23 5 0.16
ACGTcount: A:0.39, C:0.05, G:0.03, T:0.53
Consensus pattern (22 bp):
TAAAATATATATTTTACTATCG
Found at i:104304 original size:28 final size:27
Alignment explanation
Indices: 104252--104306 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 27
104242 TTTATTCAAA
*
104252 TTTGATTATATAATATTGAGCAATTTT
1 TTTGATTATATAATATTGAGAAATTTT
* *
104279 TTTGATTATTTAAATATTGATAAATTTT
1 TTTGATTATAT-AATATTGAGAAATTTT
104307 AAAATATTGG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
27 10 0.42
28 14 0.58
ACGTcount: A:0.35, C:0.02, G:0.09, T:0.55
Consensus pattern (27 bp):
TTTGATTATATAATATTGAGAAATTTT
Found at i:104306 original size:27 final size:27
Alignment explanation
Indices: 104252--104306 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
104242 TTTATTCAAA
*
104252 TTTGATTATATAATATTGAGCAATTTT
1 TTTGATTATATAATATTGAGCAAATTT
* *
104279 TTTGATTATTTAAATATTGA-TAAATTT
1 TTTGATTATAT-AATATTGAGCAAATTT
104306 T
1 T
104307 AAAATATTGG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 16 0.67
28 8 0.33
ACGTcount: A:0.35, C:0.02, G:0.09, T:0.55
Consensus pattern (27 bp):
TTTGATTATATAATATTGAGCAAATTT
Found at i:109573 original size:21 final size:21
Alignment explanation
Indices: 109534--109576 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
109524 TCTAGGTTTT
* *
109534 TAAACCCTAAACCCTAAATCA
1 TAAACCCTAAAACCAAAATCA
*
109555 TAAACCCTAAAATCAAAATCA
1 TAAACCCTAAAACCAAAATCA
109576 T
1 T
109577 CAATGAAGTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.51, C:0.28, G:0.00, T:0.21
Consensus pattern (21 bp):
TAAACCCTAAAACCAAAATCA
Found at i:109763 original size:266 final size:266
Alignment explanation
Indices: 109289--109796 Score: 946
Period size: 266 Copynumber: 1.9 Consensus size: 266
109279 GTGGAATCCC
109289 TAAACCCTAAAATCAAAATCATCAATGAAGTATTTCATTAAAAAAAGGTAAATTGTCCAGTTGGT
1 TAAACCCTAAAATCAAAATCATCAATGAAGTATTTCATTAAAAAAAGGTAAATTGTCCAGTTGGT
*
109354 CACTCAACTTTTAGGCCGTTTTCATTTTGACCACTCAAAATGAAATATTTGCAATTTTATTAGTA
66 CACTCAACTTTTAGGCCGTTTTCATTTTGACCACTCAAAATGAAATATTTGCAAATTTATTAGTA
* * * * *
109419 AACTTTTAAAGTGTTTTCATTTTAGTCACCCAAGTGTTAAATCTTTAAAGGAGGTTGATTGTACA
131 AACTTTTAAAGCGCTTTCATTTTAGTCACCCAAGTGTTAAATATTTAAACGAGGTTAATTGTACA
109484 TGCCATATCATGTTTACATTTTCATTTTGGCCACCCAACTTCTAGGTTTTTAAACCCTAAACCCT
196 TGCCATATCATGTTTACATTTTCATTTTGGCCACCCAACTTCTAGGTTTTTAAACCCTAAACCCT
109549 AAATCA
261 AAATCA
109555 TAAACCCTAAAATCAAAATCATCAATGAAGTATTTCATTAAAAAAAGGTAAATTGTCCAGTTGGT
1 TAAACCCTAAAATCAAAATCATCAATGAAGTATTTCATTAAAAAAAGGTAAATTGTCCAGTTGGT
109620 CACTCAACTTTTAGGCCGTTTTCATTTTGACCACTCAAAATGAAATATTTGCAAATTTATTAGTA
66 CACTCAACTTTTAGGCCGTTTTCATTTTGACCACTCAAAATGAAATATTTGCAAATTTATTAGTA
109685 AACTTTTAAAGCGCTTTCATTTTAGTCACCCAAGTGTTAAATATTT-AACGATGGTTAATTGTAC
131 AACTTTTAAAGCGCTTTCATTTTAGTCACCCAAGTGTTAAATATTTAAACGA-GGTTAATTGTAC
109749 ATGCCATATCATGTTTACATTTTCATTTTGGCCACCCAACTTCTAGGT
195 ATGCCATATCATGTTTACATTTTCATTTTGGCCACCCAACTTCTAGGT
109797 CACTTTCATT
Statistics
Matches: 235, Mismatches: 6, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
265 4 0.02
266 231 0.98
ACGTcount: A:0.33, C:0.18, G:0.12, T:0.36
Consensus pattern (266 bp):
TAAACCCTAAAATCAAAATCATCAATGAAGTATTTCATTAAAAAAAGGTAAATTGTCCAGTTGGT
CACTCAACTTTTAGGCCGTTTTCATTTTGACCACTCAAAATGAAATATTTGCAAATTTATTAGTA
AACTTTTAAAGCGCTTTCATTTTAGTCACCCAAGTGTTAAATATTTAAACGAGGTTAATTGTACA
TGCCATATCATGTTTACATTTTCATTTTGGCCACCCAACTTCTAGGTTTTTAAACCCTAAACCCT
AAATCA
Found at i:110692 original size:25 final size:26
Alignment explanation
Indices: 110634--110693 Score: 70
Period size: 25 Copynumber: 2.3 Consensus size: 26
110624 AGTTGATTAC
110634 AAATAATTTAGAAATAAAATAAAATT
1 AAATAATTTAGAAATAAAATAAAATT
* * *
110660 ATAA-AATTTAGAAA-GAGATTAAATT
1 A-AATAATTTAGAAATAAAATAAAATT
110685 AAATAATTT
1 AAATAATTT
110694 CAATATTATG
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
24 2 0.07
25 14 0.48
26 11 0.38
27 2 0.07
ACGTcount: A:0.60, C:0.00, G:0.07, T:0.33
Consensus pattern (26 bp):
AAATAATTTAGAAATAAAATAAAATT
Found at i:112691 original size:31 final size:31
Alignment explanation
Indices: 112632--112691 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
112622 AAATGGACCA
*
112632 TTAAAATTTTAAAGAATTAATATCTGTTTTG
1 TTAAAATTTTAAAGAATTAATATATGTTTTG
*
112663 TTAAAATTTTAAAG-CTTAATATAATGTTT
1 TTAAAATTTTAAAGAATTAATAT-ATGTTT
112692 GGTATTTGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 7 0.27
31 19 0.73
ACGTcount: A:0.40, C:0.03, G:0.08, T:0.48
Consensus pattern (31 bp):
TTAAAATTTTAAAGAATTAATATATGTTTTG
Found at i:112798 original size:31 final size:31
Alignment explanation
Indices: 112745--112816 Score: 85
Period size: 31 Copynumber: 2.3 Consensus size: 31
112735 TGTTTTTGGT
112745 CTAATTTGATACTCAAACTTGAC-ACTTTTTC
1 CTAATTTGATACTCAAACTTGACTA-TTTTTC
*
112776 CTAATTTGATAC-CTAAATTTGACTATTTTTC
1 CTAATTTGATACTC-AAACTTGACTATTTTTC
* *
112807 TTAAGTTGAT
1 CTAATTTGAT
112817 GCTTAAACGT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
30 1 0.03
31 34 0.94
32 1 0.03
ACGTcount: A:0.29, C:0.17, G:0.08, T:0.46
Consensus pattern (31 bp):
CTAATTTGATACTCAAACTTGACTATTTTTC
Found at i:118425 original size:19 final size:19
Alignment explanation
Indices: 118403--118479 Score: 56
Period size: 19 Copynumber: 4.3 Consensus size: 19
118393 GCATAGCATT
118403 AAATTAAAGTATATCTATA
1 AAATTAAAGTATATCTATA
* *
118422 AAATTATA-TA-AT-T-CA
1 AAATTAAAGTATATCTATA
* * * * *
118437 AATTTTATGTATAGC-ATT
1 AAATTAAAGTATATCTATA
118455 AAATTAAAGTATATCTATA
1 AAATTAAAGTATATCTATA
118474 AAATTA
1 AAATTA
118480 TACTTGCATT
Statistics
Matches: 39, Mismatches: 14, Indels: 10
0.62 0.22 0.16
Matches are distributed among these distances:
15 5 0.13
16 3 0.08
17 3 0.08
18 13 0.33
19 15 0.38
ACGTcount: A:0.49, C:0.05, G:0.05, T:0.40
Consensus pattern (19 bp):
AAATTAAAGTATATCTATA
Found at i:118455 original size:28 final size:28
Alignment explanation
Indices: 118377--118455 Score: 76
Period size: 28 Copynumber: 3.0 Consensus size: 28
118367 CATATGAATC
*
118377 ATAATTCAAATTTTATGCATAGCA-T-T
1 ATAATTCAAATTTTATGTATAGCATTAT
* * * **
118403 A-AATT-AAAGTATATCTATAAAATTAT
1 ATAATTCAAATTTTATGTATAGCATTAT
118429 ATAATTCAAATTTTATGTATAGCATTA
1 ATAATTCAAATTTTATGTATAGCATTA
118456 AATTAAAGTA
Statistics
Matches: 38, Mismatches: 11, Indels: 6
0.69 0.20 0.11
Matches are distributed among these distances:
24 11 0.29
25 5 0.13
26 3 0.08
27 4 0.11
28 15 0.39
ACGTcount: A:0.44, C:0.08, G:0.06, T:0.42
Consensus pattern (28 bp):
ATAATTCAAATTTTATGTATAGCATTAT
Found at i:118455 original size:52 final size:52
Alignment explanation
Indices: 118377--118481 Score: 201
Period size: 52 Copynumber: 2.0 Consensus size: 52
118367 CATATGAATC
118377 ATAATTCAAATTTTATGCATAGCATTAAATTAAAGTATATCTATAAAATTAT
1 ATAATTCAAATTTTATGCATAGCATTAAATTAAAGTATATCTATAAAATTAT
*
118429 ATAATTCAAATTTTATGTATAGCATTAAATTAAAGTATATCTATAAAATTAT
1 ATAATTCAAATTTTATGCATAGCATTAAATTAAAGTATATCTATAAAATTAT
118481 A
1 A
118482 CTTGCATTAT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.47, C:0.07, G:0.06, T:0.41
Consensus pattern (52 bp):
ATAATTCAAATTTTATGCATAGCATTAAATTAAAGTATATCTATAAAATTAT
Found at i:130980 original size:2 final size:2
Alignment explanation
Indices: 130973--130998 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
130963 ATGACTATGA
130973 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
130999 GTAGGTATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:133064 original size:31 final size:28
Alignment explanation
Indices: 133029--133085 Score: 78
Period size: 31 Copynumber: 1.9 Consensus size: 28
133019 AAAAAAACTC
*
133029 AAATACTAAATTAAATATTAAAATCAAATTT
1 AAATACCAAATTAAA-A--AAAATCAAATTT
133060 AAATACCAAATTAAAAAAAATCAAAT
1 AAATACCAAATTAAAAAAAATCAAAT
133086 ATCAAATTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 10 0.40
30 1 0.04
31 14 0.56
ACGTcount: A:0.63, C:0.09, G:0.00, T:0.28
Consensus pattern (28 bp):
AAATACCAAATTAAAAAAAATCAAATTT
Found at i:133122 original size:53 final size:54
Alignment explanation
Indices: 133018--133123 Score: 137
Period size: 53 Copynumber: 2.0 Consensus size: 54
133008 TGAAAAAAAA
* *
133018 AAAAAAAACTCAAATACTAAATTAAATATTAAAATCAAATTTAAATACCAAATT
1 AAAAAAAACTCAAATACTAAATTAAACATTAAAATCAAACTTAAATACCAAATT
* *
133072 AAAAAAAA-TCAAATA-TCAAATTAAACATTAAAA-CTAAACTTAGATCCCAAAT
1 AAAAAAAACTCAAATACT-AAATTAAACATTAAAATC-AAACTTAAATACCAAAT
133124 CATATATTAG
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
52 2 0.04
53 36 0.78
54 8 0.17
ACGTcount: A:0.60, C:0.13, G:0.01, T:0.25
Consensus pattern (54 bp):
AAAAAAAACTCAAATACTAAATTAAACATTAAAATCAAACTTAAATACCAAATT
Found at i:149089 original size:8 final size:8
Alignment explanation
Indices: 149058--149117 Score: 57
Period size: 9 Copynumber: 7.0 Consensus size: 8
149048 AATCAAATTA
149058 TTTTTATT
1 TTTTTATT
*
149066 TTTATTTTT
1 TTT-TTATT
149075 ATTTTTATT
1 -TTTTTATT
149084 TTTTTATT
1 TTTTTATT
*
149092 TTCTCTATT
1 TT-TTTATT
149101 TTATTTATT
1 TT-TTTATT
*
149110 TATTTATT
1 TTTTTATT
149118 ATTTGTCTAG
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
8 19 0.44
9 21 0.49
10 3 0.07
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.80
Consensus pattern (8 bp):
TTTTTATT
Found at i:149093 original size:6 final size:6
Alignment explanation
Indices: 149055--149086 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
149045 GGCAATCAAA
149055 TTATTT TTATTT TTATTT TTATTT TTATTT TT
1 TTATTT TTATTT TTATTT TTATTT TTATTT TT
149087 TTATTTTCTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTATTT
Found at i:150639 original size:19 final size:19
Alignment explanation
Indices: 150617--150661 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
150607 TTATATTAGG
150617 ATTTAATATTTAAGATAT-T
1 ATTTAATATTTAA-ATATGT
* *
150636 ATTTATTATTTAAATTTGT
1 ATTTAATATTTAAATATGT
150655 ATTTAAT
1 ATTTAAT
150662 TTATGTTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 3 0.14
19 19 0.86
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (19 bp):
ATTTAATATTTAAATATGT
Found at i:153000 original size:19 final size:19
Alignment explanation
Indices: 152955--153004 Score: 61
Period size: 17 Copynumber: 2.8 Consensus size: 19
152945 AAAAAAAATA
* *
152955 ATAATAAAA-AGAAAATTT
1 ATAATAAAATAAAAAAGTT
152973 AT-A-AAAATAAAAAAGTT
1 ATAATAAAATAAAAAAGTT
152990 ATAATAAAATAAAAA
1 ATAATAAAATAAAAA
153005 TATTAAATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
16 4 0.15
17 10 0.37
18 3 0.11
19 10 0.37
ACGTcount: A:0.72, C:0.00, G:0.04, T:0.24
Consensus pattern (19 bp):
ATAATAAAATAAAAAAGTT
Found at i:153013 original size:18 final size:18
Alignment explanation
Indices: 152948--153013 Score: 52
Period size: 19 Copynumber: 3.8 Consensus size: 18
152938 AAATCATAAA
*
152948 AAAAATAAT-AATAAAA-
1 AAAAATATTAAATAAAAT
*
152964 AGAAAAT-TTATA-AAAAT
1 A-AAAATATTAAATAAAAT
152981 AAAAA-AGTTATAATAAAAT
1 AAAAATA-TTA-AATAAAAT
153000 AAAAATATTAAATA
1 AAAAATATTAAATA
153014 TTAAATTTGA
Statistics
Matches: 39, Mismatches: 3, Indels: 14
0.70 0.05 0.25
Matches are distributed among these distances:
16 10 0.26
17 10 0.26
18 5 0.13
19 13 0.33
20 1 0.03
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (18 bp):
AAAAATATTAAATAAAAT
Found at i:153078 original size:17 final size:19
Alignment explanation
Indices: 153050--153088 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
153040 TTATAAAAAA
*
153050 AAAACTTATAAATATT-AT
1 AAAACTTATAAAAATTAAT
153068 AAAAC-TATAAAAATTAAT
1 AAAACTTATAAAAATTAAT
153086 AAA
1 AAA
153089 TTAATAAAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (19 bp):
AAAACTTATAAAAATTAAT
Found at i:153595 original size:19 final size:19
Alignment explanation
Indices: 153571--153629 Score: 75
Period size: 19 Copynumber: 3.1 Consensus size: 19
153561 AGTCTCATTC
153571 AAGTTTTTATAATTTTTAT
1 AAGTTTTTATAATTTTTAT
* *
153590 AAGTTTATATCAATTTTAAT
1 AAGTTTTTAT-AATTTTTAT
*
153610 -ATTTTTTATAATTTTTAT
1 AAGTTTTTATAATTTTTAT
153628 AA
1 AA
153630 AATTTTAATA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
18 8 0.24
19 17 0.52
20 8 0.24
ACGTcount: A:0.36, C:0.02, G:0.03, T:0.59
Consensus pattern (19 bp):
AAGTTTTTATAATTTTTAT
Found at i:153616 original size:29 final size:28
Alignment explanation
Indices: 153569--153639 Score: 79
Period size: 29 Copynumber: 2.4 Consensus size: 28
153559 CCAGTCTCAT
*
153569 TCAAGTTTTTATAATTTTTATAAGTTTATA
1 TCAA-TTTTAATAATTTTTATAA-TTTATA
* *
153599 TCAATTTTAATATTTTTTATAATTTTTA
1 TCAATTTTAATAATTTTTATAATTTATA
*
153627 TAAAATTTTAATA
1 T-CAATTTTAATA
153640 CGTTTTTTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
28 6 0.17
29 26 0.72
30 4 0.11
ACGTcount: A:0.37, C:0.03, G:0.03, T:0.58
Consensus pattern (28 bp):
TCAATTTTAATAATTTTTATAATTTATA
Found at i:153715 original size:10 final size:9
Alignment explanation
Indices: 153574--153702 Score: 78
Period size: 9 Copynumber: 13.0 Consensus size: 9
153564 CTCATTCAAG
153574 TTTTTATAA
1 TTTTTATAA
153583 TTTTTATAA
1 TTTTTATAA
*
153592 GTTTATATCAA
1 -TTTTTAT-AA
* *
153603 TTTTAATAT
1 TTTTTATAA
153612 TTTTTATAA
1 TTTTTATAA
153621 TTTTTATAAAA
1 TTTTTAT--AA
* *
153632 TTTTAATACGT
1 TTTTTATA--A
*
153643 TTTTTTTAA
1 TTTTTATAA
*
153652 TGTTTTAAATA
1 T-TTTTATA-A
153663 TATTTTATTAA
1 T-TTTTA-TAA
*
153674 TTTTATTAGAA
1 -TTT-TTATAA
153685 TTTTTATAA
1 TTTTTATAA
153694 TTTTTATAA
1 TTTTTATAA
153703 ATTTATATCA
Statistics
Matches: 92, Mismatches: 17, Indels: 22
0.70 0.13 0.17
Matches are distributed among these distances:
9 40 0.43
10 19 0.21
11 28 0.30
12 5 0.05
ACGTcount: A:0.34, C:0.02, G:0.03, T:0.61
Consensus pattern (9 bp):
TTTTTATAA
Done.