Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014603.1 Kokia drynarioides strain JFW-HI SEQ_129642, 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: 192055
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 165 characters in sequence are not A, C, G, or T
Found at i:5104 original size:16 final size:15
Alignment explanation
Indices: 5083--5134 Score: 59
Period size: 16 Copynumber: 3.3 Consensus size: 15
5073 TGAGCCTCTG
*
5083 TTCTTTCTTCTTTTGT
1 TTCTTT-TTCTTTTAT
* *
5099 TTCTTTTTTTTTTCT
1 TTCTTTTTCTTTTAT
5114 TTCTTTATTCTTTTAT
1 TTCTTT-TTCTTTTAT
5130 TTCTT
1 TTCTT
5135 ATATATATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
15 13 0.42
16 18 0.58
ACGTcount: A:0.04, C:0.15, G:0.02, T:0.79
Consensus pattern (15 bp):
TTCTTTTTCTTTTAT
Found at i:13394 original size:20 final size:21
Alignment explanation
Indices: 13356--13395 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
13346 TCTTCAGTAT
* *
13356 CCATGATGGTAAAGCATAGGC
1 CCATGAAGGTAAAGAATAGGC
13377 CCATGAAGG-AAAGAATAGG
1 CCATGAAGGTAAAGAATAGG
13396 AGGTCTCTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.40, C:0.15, G:0.30, T:0.15
Consensus pattern (21 bp):
CCATGAAGGTAAAGAATAGGC
Found at i:19230 original size:20 final size:20
Alignment explanation
Indices: 19179--19237 Score: 57
Period size: 20 Copynumber: 2.9 Consensus size: 20
19169 TGAGTTTAAT
* *
19179 AATTTATATATTTTCA-TATA
1 AATTT-TATATTTTAATTTTA
* *
19199 AATTTTGGTATTTTTATTTTA
1 AATTTT-ATATTTTAATTTTA
19220 AATTTTATATTTTAATTT
1 AATTTTATATTTTAATTT
19238 AGTTAATTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
19 1 0.03
20 22 0.69
21 9 0.28
ACGTcount: A:0.32, C:0.02, G:0.03, T:0.63
Consensus pattern (20 bp):
AATTTTATATTTTAATTTTA
Found at i:22284 original size:107 final size:102
Alignment explanation
Indices: 22082--22285 Score: 273
Period size: 107 Copynumber: 2.0 Consensus size: 102
22072 AATGCAAGAT
* * *
22082 GATACAATTGCAAGCACAACACAAGAGTACAAATTGTAAAATACATGTCCGACTAATTACAATGG
1 GATACAATTGCAAGCACAACACAAGAGTACAAATTATAAAATACATGTCCGACTAACTACAATGA
* * **
22147 CATGTAAAATCAACTTAATACGAAGTACAACAGAGAC
66 CACGTAAAATCAACTTAATACAAAACACAACAGAGAC
22184 GATACAATTGCAAGCACAACACAAGAGTACAAATTACAAATACAAATACATGTCCGACTAACTAC
1 GATACAATTGCAAGCACAACACAAGAGTACAAATT----ATA-AAATACATGTCCGACTAACTAC
* * *
22249 AATGACACGTGAAATTAACTTAATATAAAACACAACA
61 AATGACACGTAAAATCAACTTAATACAAAACACAACA
22286 ACTGAAAAAT
Statistics
Matches: 87, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
102 35 0.40
106 2 0.02
107 50 0.57
ACGTcount: A:0.48, C:0.20, G:0.12, T:0.20
Consensus pattern (102 bp):
GATACAATTGCAAGCACAACACAAGAGTACAAATTATAAAATACATGTCCGACTAACTACAATGA
CACGTAAAATCAACTTAATACAAAACACAACAGAGAC
Found at i:28846 original size:13 final size:13
Alignment explanation
Indices: 28828--28880 Score: 56
Period size: 14 Copynumber: 4.0 Consensus size: 13
28818 TTCATGCTAA
28828 TTTTATGATTTTT
1 TTTTATGATTTTT
28841 TTTTAT-ATTTTT
1 TTTTATGATTTTT
*
28853 TAATTT-TAATTTTT
1 T--TTTATGATTTTT
28867 ATTTTATGATTTTT
1 -TTTTATGATTTTT
28881 GAATTATTTG
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
12 7 0.21
13 10 0.29
14 16 0.47
15 1 0.03
ACGTcount: A:0.21, C:0.00, G:0.04, T:0.75
Consensus pattern (13 bp):
TTTTATGATTTTT
Found at i:28878 original size:20 final size:20
Alignment explanation
Indices: 28827--28879 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
28817 TTTCATGCTA
*
28827 ATTTTATGATTTTTTTTTAT
1 ATTTTATGATTTTATTTTAT
* *
28847 ATTTTTTAATTTTAATTTT-T
1 ATTTTATGATTTT-ATTTTAT
28867 ATTTTATGATTTT
1 ATTTTATGATTTT
28880 TGAATTATTT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
20 23 0.85
21 4 0.15
ACGTcount: A:0.23, C:0.00, G:0.04, T:0.74
Consensus pattern (20 bp):
ATTTTATGATTTTATTTTAT
Found at i:42950 original size:27 final size:26
Alignment explanation
Indices: 42885--42951 Score: 68
Period size: 25 Copynumber: 2.6 Consensus size: 26
42875 ATAAATTAAG
*
42885 TTTAATTCTTAATTTTCACAAGATTT
1 TTTAATTCTTAATATTCACAAGATTT
* *
42911 TTTTATT-TT-ATATTCAGAA-ATAGTT
1 TTTAATTCTTAATATTCACAAGAT--TT
42936 TTTAATTCTTAATATT
1 TTTAATTCTTAATATT
42952 TATATTATCG
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
23 2 0.06
24 8 0.24
25 10 0.30
26 8 0.24
27 5 0.15
ACGTcount: A:0.31, C:0.07, G:0.04, T:0.57
Consensus pattern (26 bp):
TTTAATTCTTAATATTCACAAGATTT
Found at i:43328 original size:16 final size:17
Alignment explanation
Indices: 43297--43330 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
43287 AGATAAAAAT
43297 ATTATTATAATAATATA
1 ATTATTATAATAATATA
*
43314 ATTATT-TAATTATATA
1 ATTATTATAATAATATA
43330 A
1 A
43331 GAGTAATTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
ATTATTATAATAATATA
Found at i:47839 original size:31 final size:31
Alignment explanation
Indices: 47804--47863 Score: 120
Period size: 31 Copynumber: 1.9 Consensus size: 31
47794 TTCTCATTGG
47804 AATTCCAAATTATATGCTTAACATTTTGTGA
1 AATTCCAAATTATATGCTTAACATTTTGTGA
47835 AATTCCAAATTATATGCTTAACATTTTGT
1 AATTCCAAATTATATGCTTAACATTTTGT
47864 AGGAATGGCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.35, C:0.13, G:0.08, T:0.43
Consensus pattern (31 bp):
AATTCCAAATTATATGCTTAACATTTTGTGA
Found at i:53130 original size:21 final size:23
Alignment explanation
Indices: 53097--53141 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
53087 TTTACTTGTT
53097 TATTTTTTAATTCAT-TAAATAA
1 TATTTTTTAATTCATGTAAATAA
*
53119 TATTTTTT-ATTCATGTAATTAA
1 TATTTTTTAATTCATGTAAATAA
53141 T
1 T
53142 GTAAATATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 6 0.29
22 15 0.71
ACGTcount: A:0.36, C:0.04, G:0.02, T:0.58
Consensus pattern (23 bp):
TATTTTTTAATTCATGTAAATAA
Found at i:53294 original size:7 final size:7
Alignment explanation
Indices: 53282--53306 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
53272 ATGAAAATAC
53282 TTAAATG
1 TTAAATG
53289 TTAAATG
1 TTAAATG
53296 TTAAATG
1 TTAAATG
53303 TTAA
1 TTAA
53307 TGCATTTGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.12, T:0.44
Consensus pattern (7 bp):
TTAAATG
Found at i:64290 original size:29 final size:31
Alignment explanation
Indices: 64258--64323 Score: 86
Period size: 30 Copynumber: 2.2 Consensus size: 31
64248 TAACCATATT
*
64258 ATAAAATA-TTAATA-TAATAA-TTTGTTTTA
1 ATAAAATATTTAATATTAA-AATTTTATTTTA
64287 ATAAAATATTTAATATTAAAATTTTATTTTA
1 ATAAAATATTTAATATTAAAATTTTATTTTA
64318 A-AAAAT
1 ATAAAAT
64324 TAACATCAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
29 8 0.24
30 13 0.39
31 12 0.36
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (31 bp):
ATAAAATATTTAATATTAAAATTTTATTTTA
Found at i:65455 original size:5 final size:5
Alignment explanation
Indices: 65445--65471 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
65435 ATTGATTTCC
65445 TTTTA TTTTA TTTTA TTTTA TTTTA TT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TT
65472 GGATTGGTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTA
Found at i:67405 original size:2 final size:2
Alignment explanation
Indices: 67398--67425 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
67388 ATAAATAGCT
67398 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
67426 CATGGATATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:79261 original size:43 final size:43
Alignment explanation
Indices: 79197--79369 Score: 182
Period size: 43 Copynumber: 4.2 Consensus size: 43
79187 ATTTGTTAAT
* * * * * *
79197 TTTAGTGGTGTTTGTGGGAAAAGTGTCGTTAAAGACCATGTTC
1 TTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGACCATGTTC
79240 TTTAGCGGCGTTTGTGAGAAAAGCGCCGCT--A-A--A---TC
1 TTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGACCATGTTC
* * *
79275 TTTAGCGGCGTTTGTGAAAAAAGGCGCTGCTACAGACCATGTTC
1 TTTAGCGGCGTTTGTGAGAAAA-GCGCCGCTAAAGACCATGTTC
* *
79319 TTTAGCGACGTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTC
1 TTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGACCATGTTC
79362 TTTAGCGG
1 TTTAGCGG
79370 GTCTTTAGCG
Statistics
Matches: 107, Mismatches: 14, Indels: 18
0.77 0.10 0.13
Matches are distributed among these distances:
35 23 0.21
36 7 0.07
38 2 0.02
39 1 0.01
40 1 0.01
41 2 0.02
43 50 0.47
44 21 0.20
ACGTcount: A:0.24, C:0.17, G:0.29, T:0.29
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGACCATGTTC
Found at i:79284 original size:35 final size:36
Alignment explanation
Indices: 79237--79351 Score: 115
Period size: 35 Copynumber: 3.0 Consensus size: 36
79227 AAAGACCATG
79237 TTCTTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAA
1 TTCTTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAA
* *
79273 -TCTTTAGCGGCGTTTGTGAAAAAAGGCGCTGCTACAGACCA
1 TTCTTTAGCGGCGTTTGTGAGAAAA-GCGCCGCT--A-A--A
* *
79314 TGTTCTTTAGCGACGTTTGTGGGAAAAGCGCCGCTAAA
1 --TTCTTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAA
79352 GACCATGTTC
Statistics
Matches: 64, Mismatches: 6, Indels: 16
0.74 0.07 0.19
Matches are distributed among these distances:
35 23 0.36
36 7 0.11
38 2 0.03
39 1 0.02
40 1 0.02
41 2 0.03
43 7 0.11
44 21 0.33
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.27
Consensus pattern (36 bp):
TTCTTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAA
Found at i:81283 original size:21 final size:21
Alignment explanation
Indices: 81259--81301 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 21
81249 TTTAACGGAA
81259 TAACTGA-AGTGACCAATTAAC
1 TAACTGATA-TGACCAATTAAC
81280 TAACTGATATGACCAATTAAC
1 TAACTGATATGACCAATTAAC
81301 T
1 T
81302 TGCCACGTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 20 0.95
22 1 0.05
ACGTcount: A:0.42, C:0.19, G:0.12, T:0.28
Consensus pattern (21 bp):
TAACTGATATGACCAATTAAC
Found at i:105118 original size:13 final size:13
Alignment explanation
Indices: 105102--105143 Score: 57
Period size: 13 Copynumber: 3.1 Consensus size: 13
105092 ACGAAAATTG
105102 AAGAAAAAAAAGA
1 AAGAAAAAAAAGA
*
105115 AAGAAAAAAGAGA
1 AAGAAAAAAAAGA
105128 AAGAAAGAAAGAAGA
1 AAGAAA-AAA-AAGA
105143 A
1 A
105144 GGAAGAAGAG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
13 18 0.72
14 3 0.12
15 4 0.16
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (13 bp):
AAGAAAAAAAAGA
Found at i:105132 original size:17 final size:18
Alignment explanation
Indices: 105110--105159 Score: 66
Period size: 17 Copynumber: 2.8 Consensus size: 18
105100 TGAAGAAAAA
105110 AAAGAAAGAAAAAAG-AG
1 AAAGAAAGAAAAAAGAAG
*
105127 AAAGAAAGAAAGAAGAAG
1 AAAGAAAGAAAAAAGAAG
*
105145 GAAGAAGAGAAAAAA
1 AAAGAA-AGAAAAAA
105160 TAAGGAAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
17 14 0.50
18 7 0.25
19 7 0.25
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (18 bp):
AAAGAAAGAAAAAAGAAG
Found at i:105152 original size:21 final size:21
Alignment explanation
Indices: 105102--105140 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
105092 ACGAAAATTG
*
105102 AAGA-AAAAAAAGAAAGAAAA
1 AAGAGAAAGAAAGAAAGAAAA
105122 AAGAGAAAGAAAGAAAGAA
1 AAGAGAAAGAAAGAAAGAA
105141 GAAGGAAGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (21 bp):
AAGAGAAAGAAAGAAAGAAAA
Found at i:105859 original size:16 final size:16
Alignment explanation
Indices: 105813--105861 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
105803 TAAACTTAGC
*
105813 TAATTAATTACCAAAA
1 TAATTAATTATCAAAA
*
105829 T-A-TAA-TATAAAAA
1 TAATTAATTATCAAAA
105842 TAATTAATTATCAAAA
1 TAATTAATTATCAAAA
105858 TAAT
1 TAAT
105862 ATCTCCATCA
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
13 7 0.26
14 4 0.15
15 4 0.15
16 12 0.44
ACGTcount: A:0.59, C:0.06, G:0.00, T:0.35
Consensus pattern (16 bp):
TAATTAATTATCAAAA
Found at i:107246 original size:43 final size:43
Alignment explanation
Indices: 107164--107248 Score: 118
Period size: 43 Copynumber: 2.0 Consensus size: 43
107154 ATTAACATGT
* *
107164 TAAATTATATTACTTGACTCGTGTTAATATGGTTGCATGTTAC
1 TAAATTATATTACTTGACTCGTATTAATATGCTTGCATGTTAC
* *
107207 TAAATTATATTACTTTACTCTTATTAATAT-CTTGACATGTTA
1 TAAATTATATTACTTGACTCGTATTAATATGCTTG-CATGTTA
107249 TTAATTGTGC
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
42 3 0.08
43 34 0.92
ACGTcount: A:0.31, C:0.12, G:0.11, T:0.47
Consensus pattern (43 bp):
TAAATTATATTACTTGACTCGTATTAATATGCTTGCATGTTAC
Found at i:107880 original size:45 final size:45
Alignment explanation
Indices: 107816--107910 Score: 136
Period size: 45 Copynumber: 2.1 Consensus size: 45
107806 GCATAGCTCA
* ** * *
107816 TCAAGCTAAGGATATCAGCCTCAGTTTGACGAGCCACCTCAATAC
1 TCAAGCTAAGAATATCAGCCTCAACTTGACGAACCACCGCAATAC
*
107861 TCAAGCTAAGAATGTCAGCCTCAACTTGACGAACCACCGCAATAC
1 TCAAGCTAAGAATATCAGCCTCAACTTGACGAACCACCGCAATAC
107906 TCAAG
1 TCAAG
107911 GGAAGGATAT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.34, C:0.29, G:0.17, T:0.20
Consensus pattern (45 bp):
TCAAGCTAAGAATATCAGCCTCAACTTGACGAACCACCGCAATAC
Found at i:108340 original size:24 final size:24
Alignment explanation
Indices: 108312--108367 Score: 96
Period size: 24 Copynumber: 2.4 Consensus size: 24
108302 TTTATTAAGT
*
108312 GAGATATTTTTGAAGAAAAGTGTA
1 GAGATATTTTTGAAGAAAAGTGGA
108336 GAGATATTTTTGAAGAAAAGTGGA
1 GAGATATTTTTGAAGAAAAGTGGA
108360 GAGA-ATTT
1 GAGATATTT
108368 GAGAGATGAA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
23 4 0.13
24 27 0.87
ACGTcount: A:0.41, C:0.00, G:0.27, T:0.32
Consensus pattern (24 bp):
GAGATATTTTTGAAGAAAAGTGGA
Found at i:111456 original size:21 final size:22
Alignment explanation
Indices: 111430--111480 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
111420 ACACATTACA
111430 TTTCTTTCCTCTC-CTTCTTCC
1 TTTCTTTCCTCTCTCTTCTTCC
* * *
111451 TTTCTTT-CTTTCTTTTCTTTC
1 TTTCTTTCCTCTCTCTTCTTCC
111472 TTTCTTTCC
1 TTTCTTTCC
111481 CGTTTATGTG
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
20 4 0.16
21 20 0.80
22 1 0.04
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (22 bp):
TTTCTTTCCTCTCTCTTCTTCC
Found at i:111459 original size:4 final size:4
Alignment explanation
Indices: 111430--111479 Score: 55
Period size: 4 Copynumber: 12.0 Consensus size: 4
111420 ACACATTACA
* * *
111430 TTTC TTTCC TCTC CTTC TTCC TTTC TTTC TTTC TTTTC TTTC TTTC TTTC
1 TTTC TTT-C TTTC TTTC TTTC TTTC TTTC TTTC -TTTC TTTC TTTC TTTC
111480 CCGTTTATGT
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
4 31 0.82
5 7 0.18
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (4 bp):
TTTC
Found at i:111467 original size:13 final size:13
Alignment explanation
Indices: 111451--111478 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
111441 TCCTTCTTCC
111451 TTTCTTTCTTTCT
1 TTTCTTTCTTTCT
111464 TTTCTTTCTTTCT
1 TTTCTTTCTTTCT
111477 TT
1 TT
111479 CCCGTTTATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (13 bp):
TTTCTTTCTTTCT
Found at i:115944 original size:30 final size:30
Alignment explanation
Indices: 115888--115947 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
115878 AAAGTAAAAT
*
115888 AATTCATAAATTAAAAAATAGGTAAATGTA
1 AATTCATAAATTAAAAAATAGATAAATGTA
115918 AATTCATAAATTAAAAAATCA-ATAAATGTA
1 AATTCATAAATTAAAAAAT-AGATAAATGTA
115948 CTATGCATAC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
30 27 0.96
31 1 0.04
ACGTcount: A:0.58, C:0.05, G:0.07, T:0.30
Consensus pattern (30 bp):
AATTCATAAATTAAAAAATAGATAAATGTA
Found at i:124801 original size:3 final size:3
Alignment explanation
Indices: 124793--124820 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
124783 ACAAACAAAA
124793 AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG A
124821 GATTTCTTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:126136 original size:10 final size:10
Alignment explanation
Indices: 126066--126130 Score: 58
Period size: 10 Copynumber: 6.4 Consensus size: 10
126056 ATTATGGAAT
*
126066 AATTATACAA
1 AATTATAAAA
* * *
126076 ACTTATACAC
1 AATTATAAAA
126086 AATTATAAAA
1 AATTATAAAA
**
126096 AATTATTTAA
1 AATTATAAAA
*
126106 CATATATAAAA
1 AAT-TATAAAA
126117 AATTATAAAA
1 AATTATAAAA
126127 AATT
1 AATT
126131 GAAAAAGTAG
Statistics
Matches: 43, Mismatches: 11, Indels: 2
0.77 0.20 0.04
Matches are distributed among these distances:
10 36 0.84
11 7 0.16
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.34
Consensus pattern (10 bp):
AATTATAAAA
Found at i:126329 original size:11 final size:10
Alignment explanation
Indices: 126270--126335 Score: 53
Period size: 11 Copynumber: 6.4 Consensus size: 10
126260 TTAATAAATA
126270 TTTATAATTTT
1 TTTATAA-TTT
*
126281 TTTATAATTC
1 TTTATAATTT
*
126291 TTAATTAATTT
1 TTTA-TAATTT
**
126302 TAAATAA-TT
1 TTTATAATTT
126311 TTTATAATTT
1 TTTATAATTT
*
126321 TTTACTAATTA
1 TTTA-TAATTT
126332 TTTA
1 TTTA
126336 AGAAACCACT
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
9 7 0.16
10 14 0.31
11 24 0.53
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (10 bp):
TTTATAATTT
Found at i:134688 original size:14 final size:15
Alignment explanation
Indices: 134662--134699 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
134652 AAAAAAAATG
134662 TAATTACTATTTT-AA
1 TAATTA-TATTTTCAA
134677 TAATTATATTTTCAA
1 TAATTATATTTTCAA
134692 TCAATTAT
1 T-AATTAT
134700 TATGTATCGT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 6 0.29
15 9 0.43
16 6 0.29
ACGTcount: A:0.39, C:0.08, G:0.00, T:0.53
Consensus pattern (15 bp):
TAATTATATTTTCAA
Found at i:137910 original size:23 final size:23
Alignment explanation
Indices: 137880--137933 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 23
137870 ACGCTAGCGC
137880 GCTTACTG-TTCAGCACTGT-GTGT
1 GCTTACTGTTTC-GCACT-TCGTGT
137903 GCTTACTGTTTCGCACTTCGTGT
1 GCTTACTGTTTCGCACTTCGTGT
*
137926 GCCTACTG
1 GCTTACTG
137934 ATTTGCGTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
22 1 0.04
23 24 0.86
24 3 0.11
ACGTcount: A:0.11, C:0.26, G:0.24, T:0.39
Consensus pattern (23 bp):
GCTTACTGTTTCGCACTTCGTGT
Found at i:139810 original size:20 final size:21
Alignment explanation
Indices: 139785--139827 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
139775 TTTTATATCT
*
139785 AAATAAAATA-AATAAATAAA
1 AAATAAAAGAGAATAAATAAA
*
139805 AAATAAAAGAGAATAATTAAA
1 AAATAAAAGAGAATAAATAAA
139826 AA
1 AA
139828 TTTAAAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.77, C:0.00, G:0.05, T:0.19
Consensus pattern (21 bp):
AAATAAAAGAGAATAAATAAA
Found at i:141406 original size:11 final size:10
Alignment explanation
Indices: 141386--141415 Score: 51
Period size: 10 Copynumber: 2.9 Consensus size: 10
141376 ATTCCGATTA
141386 TTTTAGTTTTT
1 TTTTA-TTTTT
141397 TTTTATTTTT
1 TTTTATTTTT
141407 TTTTATTTT
1 TTTTATTTT
141416 ATGTTATTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 14 0.74
11 5 0.26
ACGTcount: A:0.10, C:0.00, G:0.03, T:0.87
Consensus pattern (10 bp):
TTTTATTTTT
Found at i:142176 original size:13 final size:13
Alignment explanation
Indices: 142158--142185 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
142148 TCTGTGTAAG
142158 CTCTGCTTTTTTT
1 CTCTGCTTTTTTT
142171 CTCTGCTTTTTTT
1 CTCTGCTTTTTTT
142184 CT
1 CT
142186 TTTAATCCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.00, C:0.25, G:0.07, T:0.68
Consensus pattern (13 bp):
CTCTGCTTTTTTT
Found at i:153559 original size:3 final size:3
Alignment explanation
Indices: 153551--153597 Score: 85
Period size: 3 Copynumber: 15.7 Consensus size: 3
153541 TTGGGATACC
*
153551 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAG GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
153598 GCATAGCGGG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:154966 original size:58 final size:58
Alignment explanation
Indices: 154894--155064 Score: 215
Period size: 58 Copynumber: 3.0 Consensus size: 58
154884 TTGTTATTAA
* * **
154894 ATTTTAATAAAATTATTATTAAATATAATTTAATAAAAATAATAAATAATTTAATTGT
1 ATTTTAATATAATTATTATTAAATATAATTTAATAAAAATAATAAATAATATAATAAT
* * *
154952 ATTTTAACATAATTATTATTAAATACAATTTAAT-AAAATAATATATAATATAATAAT
1 ATTTTAATATAATTATTATTAAATATAATTTAATAAAAATAATAAATAATATAATAAT
*
155009 ATTTTTAATATAATTATTATTAAAATATGAA-TTAATAAAAATCAT-AAT-ATATAATA
1 A-TTTTAATATAATTATTATT-AAATAT-AATTTAATAAAAATAATAAATAATATAATA
155065 TTAGAAAATT
Statistics
Matches: 98, Mismatches: 11, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
57 20 0.20
58 57 0.58
59 12 0.12
60 9 0.09
ACGTcount: A:0.54, C:0.02, G:0.01, T:0.43
Consensus pattern (58 bp):
ATTTTAATATAATTATTATTAAATATAATTTAATAAAAATAATAAATAATATAATAAT
Found at i:155017 original size:17 final size:15
Alignment explanation
Indices: 154979--155022 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 15
154969 ATTAAATACA
*
154979 ATTTAATAAAATAAT
1 ATTTAATATAATAAT
*
154994 ATATAATATAATAAT
1 ATTTAATATAATAAT
155009 ATTTTTAATATAAT
1 A--TTTAATATAAT
155023 TATTATTAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
15 14 0.58
17 10 0.42
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
ATTTAATATAATAAT
Found at i:158738 original size:20 final size:20
Alignment explanation
Indices: 158706--158747 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
158696 AAAAATAACT
158706 TAAAATTTCTATATCAAAAA
1 TAAAATTTCTATATCAAAAA
*
158726 TAAATATTT-TATATCTAAAA
1 TAAA-ATTTCTATATCAAAAA
158746 TA
1 TA
158748 GTGAAAATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 16 0.80
21 4 0.20
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.40
Consensus pattern (20 bp):
TAAAATTTCTATATCAAAAA
Found at i:158748 original size:54 final size:53
Alignment explanation
Indices: 158679--158781 Score: 145
Period size: 54 Copynumber: 1.9 Consensus size: 53
158669 TCTCTTCTAG
*
158679 TTTTTATATAAAATAGTAAAAATAACTTAAAATT-TCTATATCAAAAATAAATA
1 TTTTTATATAAAATAGTAAAAATAACTTAAAATTCT-TATATAAAAAATAAATA
* * *
158732 TTTTATATCTAAAATAGTGAAAATAATTTAAAATTCTTATATAAAAAATA
1 TTTT-TATATAAAATAGTAAAAATAACTTAAAATTCTTATATAAAAAATA
158782 TCATATAAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
53 4 0.09
54 39 0.89
55 1 0.02
ACGTcount: A:0.53, C:0.05, G:0.03, T:0.39
Consensus pattern (53 bp):
TTTTTATATAAAATAGTAAAAATAACTTAAAATTCTTATATAAAAAATAAATA
Found at i:159151 original size:24 final size:26
Alignment explanation
Indices: 159095--159149 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 26
159085 ATAAAATAGT
*
159095 AAAAATAACTTAAAATTTCTATATGA
1 AAAAATAACATAAAATTTCTATATGA
*
159121 AAAAATAA-ATAAATATTT-TATATGT
1 AAAAATAACATAAA-ATTTCTATATGA
159146 AAAA
1 AAAA
159150 TAGTGAAAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
25 14 0.54
26 12 0.46
ACGTcount: A:0.58, C:0.04, G:0.04, T:0.35
Consensus pattern (26 bp):
AAAAATAACATAAAATTTCTATATGA
Found at i:165544 original size:22 final size:23
Alignment explanation
Indices: 165500--165549 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
165490 TTATAAACGT
**
165500 ATATATTTTTGAATTTGTAT-AA
1 ATATATTTTTGAATTAATATAAA
165522 ATATATTATTTGAATTAAT-TAAA
1 ATATATT-TTTGAATTAATATAAA
165545 ATATA
1 ATATA
165550 AACATATAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 8 0.33
23 16 0.67
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (23 bp):
ATATATTTTTGAATTAATATAAA
Found at i:175458 original size:3 final size:3
Alignment explanation
Indices: 175450--175476 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
175440 TATTAGACGA
175450 TGG TGG TGG TGG TGG TGG TGG TGG TGG
1 TGG TGG TGG TGG TGG TGG TGG TGG TGG
175477 CGGCGGATTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.67, T:0.33
Consensus pattern (3 bp):
TGG
Found at i:176803 original size:6 final size:6
Alignment explanation
Indices: 176792--176816 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
176782 GGATGAGGAA
176792 GTTGGT GTTGGT GTTGGT GTTGGT G
1 GTTGGT GTTGGT GTTGGT GTTGGT G
176817 AGTGAAGACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.00, G:0.52, T:0.48
Consensus pattern (6 bp):
GTTGGT
Found at i:177656 original size:20 final size:20
Alignment explanation
Indices: 177633--177672 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
177623 TTTTATAGAC
177633 TTATTATCCTTAACATATAT
1 TTATTATCCTTAACATATAT
177653 TTATTATCCTTAACATATAT
1 TTATTATCCTTAACATATAT
177673 AGAGAGCGAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.15, G:0.00, T:0.50
Consensus pattern (20 bp):
TTATTATCCTTAACATATAT
Found at i:190356 original size:75 final size:74
Alignment explanation
Indices: 190218--190356 Score: 197
Period size: 75 Copynumber: 1.9 Consensus size: 74
190208 AGTTTTGTAT
** * **
190218 CAAATTAATATTTAGATGCTGCTTTGTATTAGTTTATCAAATTAAACTAAAAATATTGTCAAATA
1 CAAATTAATATTTAGAAACTGCTTTGTATTAATTTATCAAATTAAACTAAAAATATTACCAAATA
190283 TTTTTTTAC
66 TTTTTTTAC
** *
190292 CAAATTAATATTTAGAAACTATTTTTGTATTAATTTATCAAATTAAACTAAAAATGTTACCAAAT
1 CAAATTAATATTTAGAAACT-GCTTTGTATTAATTTATCAAATTAAACTAAAAATATTACCAAAT
190357 TTAATATAAA
Statistics
Matches: 56, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
74 18 0.32
75 38 0.68
ACGTcount: A:0.42, C:0.09, G:0.06, T:0.42
Consensus pattern (74 bp):
CAAATTAATATTTAGAAACTGCTTTGTATTAATTTATCAAATTAAACTAAAAATATTACCAAATA
TTTTTTTAC
Done.