Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010411.1 Corchorus capsularis cultivar CVL-1 contig10432, 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: 36368
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Found at i:244 original size:16 final size:16
Alignment explanation
Indices: 241--365 Score: 85
Period size: 16 Copynumber: 7.9 Consensus size: 16
231 GGTGGGTTCG
241 GGTTCGGGTTCGGGTA
1 GGTTCGGGTTCGGGTA
*
257 -CTTCGGGTTCGGGTA
1 GGTTCGGGTTCGGGTA
**
272 TTTTCGGGTTCGGGTA
1 GGTTCGGGTTCGGGTA
** * *
288 TTTTCAGGTTCTGGT-
1 GGTTCGGGTTCGGGTA
**
303 TCTGTCGGGTTCGGGTA
1 GGT-TCGGGTTCGGGTA
*
320 -TTTCGGGTTCGGGTA
1 GGTTCGGGTTCGGGTA
** *
335 TTTTCGGGTTCGGAGTC
1 GGTTCGGGTTCGG-GTA
*
352 GGATCGGGTTCGGG
1 GGTTCGGGTTCGGG
366 CCCGGGTCGG
Statistics
Matches: 92, Mismatches: 12, Indels: 10
0.81 0.11 0.09
Matches are distributed among these distances:
15 29 0.32
16 51 0.55
17 12 0.13
ACGTcount: A:0.06, C:0.15, G:0.41, T:0.38
Consensus pattern (16 bp):
GGTTCGGGTTCGGGTA
Found at i:263 original size:21 final size:22
Alignment explanation
Indices: 223--270 Score: 71
Period size: 21 Copynumber: 2.2 Consensus size: 22
213 GGCAATTGGG
**
223 CGGGTTCGGGTGGGTTCGGGTT
1 CGGGTTCGGGTGACTTCGGGTT
245 CGGGTTCGGGT-ACTTCGGGTT
1 CGGGTTCGGGTGACTTCGGGTT
266 CGGGT
1 CGGGT
271 ATTTTCGGGT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 13 0.54
22 11 0.46
ACGTcount: A:0.02, C:0.17, G:0.50, T:0.31
Consensus pattern (22 bp):
CGGGTTCGGGTGACTTCGGGTT
Found at i:286 original size:6 final size:6
Alignment explanation
Indices: 223--270 Score: 55
Period size: 6 Copynumber: 7.8 Consensus size: 6
213 GGCAATTGGG
223 CGGGTT CGGG-T -GGGTT CGGGTT CGGGTT CGGGTACTT CGGGTT CGGGT
1 CGGGTT CGGGTT CGGGTT CGGGTT CGGGTT CGGG---TT CGGGTT CGGGT
271 ATTTTCGGGT
Statistics
Matches: 37, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
4 3 0.08
5 2 0.05
6 26 0.70
9 6 0.16
ACGTcount: A:0.02, C:0.17, G:0.50, T:0.31
Consensus pattern (6 bp):
CGGGTT
Found at i:359 original size:48 final size:48
Alignment explanation
Indices: 259--365 Score: 155
Period size: 47 Copynumber: 2.2 Consensus size: 48
249 TTCGGGTACT
* *
259 TCGGGTTCGGGTATTTTCGGGTTCGGGTATTTTCAGGTTCTGGTTCTG
1 TCGGGTTCGGGTATTTTCGGGTTCGGGTATTTTCAGGTTCTGGGTCGG
*
307 TCGGGTTCGGGTA-TTTCGGGTTCGGGTATTTTCGGGTTC-GGAGTCGG
1 TCGGGTTCGGGTATTTTCGGGTTCGGGTATTTTCAGGTTCTGG-GTCGG
354 ATCGGGTTCGGG
1 -TCGGGTTCGGG
366 CCCGGGTCGG
Statistics
Matches: 54, Mismatches: 3, Indels: 4
0.89 0.05 0.07
Matches are distributed among these distances:
46 2 0.04
47 28 0.52
48 24 0.44
ACGTcount: A:0.07, C:0.15, G:0.40, T:0.38
Consensus pattern (48 bp):
TCGGGTTCGGGTATTTTCGGGTTCGGGTATTTTCAGGTTCTGGGTCGG
Found at i:1168 original size:16 final size:16
Alignment explanation
Indices: 1147--1189 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 16
1137 TCGGGTTGTC
*
1147 TCGGGTTCAGGTATTT
1 TCGGGTTCAGGTAATT
*
1163 TCGGGTTCGGGTAATT
1 TCGGGTTCAGGTAATT
1179 TCGGGTTCAGG
1 TCGGGTTCAGG
1190 CGGGTTCAGG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.12, C:0.14, G:0.37, T:0.37
Consensus pattern (16 bp):
TCGGGTTCAGGTAATT
Found at i:1258 original size:10 final size:10
Alignment explanation
Indices: 1243--1279 Score: 56
Period size: 10 Copynumber: 3.6 Consensus size: 10
1233 CGAGTTCGGA
*
1243 TTCGGGCAGG
1 TTCGGGCGGG
1253 TTCGGGCGGG
1 TTCGGGCGGG
1263 TTCGGGCGGG
1 TTCGGGCGGG
1273 TTTCGGG
1 -TTCGGG
1280 TTTCGGGTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
10 19 0.76
11 6 0.24
ACGTcount: A:0.03, C:0.19, G:0.54, T:0.24
Consensus pattern (10 bp):
TTCGGGCGGG
Found at i:3106 original size:20 final size:21
Alignment explanation
Indices: 3078--3119 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
3068 ATAGATATTC
*
3078 TACTTTCAC-AAAATGTGAGT
1 TACTCTCACGAAAATGTGAGT
*
3098 TACTCTCACGAAATTGTGAGT
1 TACTCTCACGAAAATGTGAGT
3119 T
1 T
3120 TTCTTTGTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.36
Consensus pattern (21 bp):
TACTCTCACGAAAATGTGAGT
Found at i:3143 original size:96 final size:96
Alignment explanation
Indices: 2979--3170 Score: 332
Period size: 96 Copynumber: 2.0 Consensus size: 96
2969 AGGTCTTGGG
*
2979 TTCTACTCTCACGAAATGTGAGTTACTCTCACAGAATTGTAAGTTTTCTTTGTAATTTATTTGTT
1 TTCTACTCTCACAAAATGTGAGTTACTCTCACAGAATTGTAAGTTTTCTTTGTAATTTATTTGTT
*
3044 TGTGTATTTAGTATGTTGGTAGTTATAGATA
66 TGTGTATTTAGTATGTTAGTAGTTATAGATA
* *
3075 TTCTACTTTCACAAAATGTGAGTTACTCTCAC-GAAATTGTGAGTTTTCTTTGTAATTTATTTGT
1 TTCTACTCTCACAAAATGTGAGTTACTCTCACAG-AATTGTAAGTTTTCTTTGTAATTTATTTGT
3139 TTGTGTATTTAGTATGTTAGTAGTTATAGATA
65 TTGTGTATTTAGTATGTTAGTAGTTATAGATA
3171 GTGAAATTAG
Statistics
Matches: 91, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
95 1 0.01
96 90 0.99
ACGTcount: A:0.26, C:0.10, G:0.17, T:0.47
Consensus pattern (96 bp):
TTCTACTCTCACAAAATGTGAGTTACTCTCACAGAATTGTAAGTTTTCTTTGTAATTTATTTGTT
TGTGTATTTAGTATGTTAGTAGTTATAGATA
Found at i:3470 original size:5 final size:5
Alignment explanation
Indices: 3460--3484 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
3450 CAATGTACGC
3460 ATATA ATATA ATATA ATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA
3485 TATTAATAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATATA
Found at i:9696 original size:11 final size:11
Alignment explanation
Indices: 9680--9704 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
9670 AGAAGCTTGG
9680 TTGGTTGTAGA
1 TTGGTTGTAGA
9691 TTGGTTGTAGA
1 TTGGTTGTAGA
9702 TTG
1 TTG
9705 TCTTAGCAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.00, G:0.36, T:0.48
Consensus pattern (11 bp):
TTGGTTGTAGA
Found at i:10268 original size:30 final size:31
Alignment explanation
Indices: 10208--10281 Score: 96
Period size: 30 Copynumber: 2.4 Consensus size: 31
10198 ACACTGACCC
*
10208 ATATCCTTAATTGACACAAAACGATAACGGT
1 ATATCCTGAATTGACACAAAACGATAACGGT
* * *
10239 ATATTCTGAATTGACAC-AAATGGTAACGGT
1 ATATCCTGAATTGACACAAAACGATAACGGT
*
10269 GTATCCTGAATTG
1 ATATCCTGAATTG
10282 CATTTTCGTC
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
30 22 0.59
31 15 0.41
ACGTcount: A:0.36, C:0.16, G:0.18, T:0.30
Consensus pattern (31 bp):
ATATCCTGAATTGACACAAAACGATAACGGT
Found at i:12077 original size:25 final size:25
Alignment explanation
Indices: 12049--12096 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
12039 ATTTTTTAGC
12049 ACATATT-TTTTTAAAATTAAATTTT
1 ACATATTCTTTTTAAAA-TAAATTTT
*
12074 ACATATTCTTTTTATAATAAATT
1 ACATATTCTTTTTAAAATAAATT
12097 GTCATAGTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 13 0.62
26 8 0.38
ACGTcount: A:0.40, C:0.06, G:0.00, T:0.54
Consensus pattern (25 bp):
ACATATTCTTTTTAAAATAAATTTT
Found at i:13989 original size:40 final size:41
Alignment explanation
Indices: 13867--13994 Score: 204
Period size: 41 Copynumber: 3.1 Consensus size: 41
13857 CAATTTTAAG
13867 ATATAAATTAACAAGGTGGCAACTCCAATTTGACAACAAGGT
1 ATAT-AATTAACAAGGTGGCAACTCCAATTTGACAACAAGGT
* * *
13909 ATATAATTAATAAGGTTGCAACTCCAATTTTACAACAAGGT
1 ATATAATTAACAAGGTGGCAACTCCAATTTGACAACAAGGT
*
13950 ATATAATTAACAA-GTGGCAACTCCAATTTGACAAGAAGGT
1 ATATAATTAACAAGGTGGCAACTCCAATTTGACAACAAGGT
13990 ATATA
1 ATATA
13995 CTCCCTACGT
Statistics
Matches: 79, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
40 29 0.37
41 46 0.58
42 4 0.05
ACGTcount: A:0.43, C:0.15, G:0.15, T:0.27
Consensus pattern (41 bp):
ATATAATTAACAAGGTGGCAACTCCAATTTGACAACAAGGT
Found at i:14348 original size:40 final size:40
Alignment explanation
Indices: 14237--14383 Score: 251
Period size: 39 Copynumber: 3.6 Consensus size: 40
14227 ACTGAGGGAG
*
14237 TAATTAACGAGATGGCAACTCCAATTTGACAACAAGGTATA
1 TAATTAACAAG-TGGCAACTCCAATTTGACAACAAGGTATA
*
14278 TAATTAACAAGTGG-GACTCCAATTTGACAACAAGGTATA
1 TAATTAACAAGTGGCAACTCCAATTTGACAACAAGGTATA
14317 TAATTAACAAGTGGCAACTCCAATTTGACAACAAGGTATA
1 TAATTAACAAGTGGCAACTCCAATTTGACAACAAGGTATA
14357 TAATTAACAAGGTGGCAACTCCAATTT
1 TAATTAACAA-GTGGCAACTCCAATTT
14384 CATTACGAAA
Statistics
Matches: 101, Mismatches: 3, Indels: 4
0.94 0.03 0.04
Matches are distributed among these distances:
39 38 0.38
40 37 0.37
41 26 0.26
ACGTcount: A:0.41, C:0.17, G:0.16, T:0.26
Consensus pattern (40 bp):
TAATTAACAAGTGGCAACTCCAATTTGACAACAAGGTATA
Found at i:17151 original size:14 final size:15
Alignment explanation
Indices: 17132--17168 Score: 67
Period size: 14 Copynumber: 2.5 Consensus size: 15
17122 CGTTAAGTCA
17132 TTTTTTTTCTTTT-T
1 TTTTTTTTCTTTTGT
17146 TTTTTTTTCTTTTGT
1 TTTTTTTTCTTTTGT
17161 TTTTTTTT
1 TTTTTTTT
17169 TCAAATTGGT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 13 0.59
15 9 0.41
ACGTcount: A:0.00, C:0.05, G:0.03, T:0.92
Consensus pattern (15 bp):
TTTTTTTTCTTTTGT
Found at i:17163 original size:19 final size:18
Alignment explanation
Indices: 17132--17169 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
17122 CGTTAAGTCA
17132 TTTTTTTTCTTTTTTTTT
1 TTTTTTTTCTTTTTTTTT
*
17150 TTTTCTTTTGTTTTTTTTT
1 TTTT-TTTTCTTTTTTTTT
17169 T
1 T
17170 CAAATTGGTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.00, C:0.05, G:0.03, T:0.92
Consensus pattern (18 bp):
TTTTTTTTCTTTTTTTTT
Found at i:18439 original size:11 final size:11
Alignment explanation
Indices: 18415--18466 Score: 54
Period size: 11 Copynumber: 4.8 Consensus size: 11
18405 TTGACAGCGC
18415 AACAAAAACAA
1 AACAAAAACAA
* *
18426 AACGAAAACGA
1 AACAAAAACAA
18437 AACAAAAACAA
1 AACAAAAACAA
18448 AA-AACAAA-AA
1 AACAA-AAACAA
*
18458 AACGAAAAC
1 AACAAAAAC
18467 GATGCCAAAC
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
10 9 0.27
11 24 0.73
ACGTcount: A:0.77, C:0.17, G:0.06, T:0.00
Consensus pattern (11 bp):
AACAAAAACAA
Found at i:18441 original size:16 final size:16
Alignment explanation
Indices: 18420--18468 Score: 57
Period size: 17 Copynumber: 3.1 Consensus size: 16
18410 AGCGCAACAA
18420 AAACAAAACGAAAACG
1 AAACAAAACGAAAACG
*
18436 AAACAAAAACAAAAAAC-
1 AAAC-AAAAC-GAAAACG
18453 AAA-AAAACGAAAACG
1 AAACAAAACGAAAACG
18468 A
1 A
18469 TGCCAAACGA
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
14 5 0.18
15 6 0.21
16 4 0.14
17 8 0.29
18 5 0.18
ACGTcount: A:0.76, C:0.16, G:0.08, T:0.00
Consensus pattern (16 bp):
AAACAAAACGAAAACG
Found at i:27274 original size:27 final size:26
Alignment explanation
Indices: 27231--27289 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 26
27221 TTGAGGGACT
* * *
27231 TGTTTTTATTACTATTTTTAGTAAAG
1 TGTTTTTATAAATATTTTTAGTAAAA
*
27257 TGTTTTTATAAATGATTTTTATTAAAA
1 TGTTTTTATAAAT-ATTTTTAGTAAAA
27284 TGTTTT
1 TGTTTT
27290 GGGTGCATTA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 11 0.39
27 17 0.61
ACGTcount: A:0.29, C:0.02, G:0.10, T:0.59
Consensus pattern (26 bp):
TGTTTTTATAAATATTTTTAGTAAAA
Found at i:27728 original size:15 final size:15
Alignment explanation
Indices: 27708--27741 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
27698 ATTGGATTTA
27708 TTATTACTAA-TTGTT
1 TTATTA-TAACTTGTT
27723 TTATTATAACTTGTT
1 TTATTATAACTTGTT
27738 TTAT
1 TTAT
27742 AAGTTGTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 3 0.17
15 15 0.83
ACGTcount: A:0.26, C:0.06, G:0.06, T:0.62
Consensus pattern (15 bp):
TTATTATAACTTGTT
Found at i:28576 original size:73 final size:70
Alignment explanation
Indices: 28499--28651 Score: 173
Period size: 73 Copynumber: 2.1 Consensus size: 70
28489 TAATATATCA
* * * *
28499 AGTTTTTTAATTAAAATAGTAAAATGGTAAAATA-TAAGTAATAAGGATATTAGATTTAATTATA
1 AGTTTTTTAAGTAAAATAGTAAAA---TAAAATAGTAACT-ATAAAGATATTAGATTTAATTAAA
28563 TAAAAATAG
62 TAAAAATAG
* * *
28572 AGTTTTTAGTTGAGTAAAATAGTAAAATAAAATAGTTACTATAAAGATATTATATTTAATTAAAT
1 AG-TTTT--TTAAGTAAAATAGTAAAATAAAATAGTAACTATAAAGATATTAGATTTAATTAAAT
28637 AAAAATAG
63 AAAAATAG
28645 AGTTTTT
1 AGTTTTT
28652 AGTTAAATAA
Statistics
Matches: 69, Mismatches: 7, Indels: 11
0.79 0.08 0.13
Matches are distributed among these distances:
70 1 0.01
72 4 0.06
73 41 0.59
74 7 0.10
76 16 0.23
ACGTcount: A:0.49, C:0.01, G:0.12, T:0.39
Consensus pattern (70 bp):
AGTTTTTTAAGTAAAATAGTAAAATAAAATAGTAACTATAAAGATATTAGATTTAATTAAATAAA
AATAG
Found at i:28597 original size:68 final size:70
Alignment explanation
Indices: 28516--28677 Score: 195
Period size: 73 Copynumber: 2.3 Consensus size: 70
28506 TAATTAAAAT
* * *
28516 AGTAAAATGGTAAAATATAAG-TA-ATAAGGATATTAGATTTAATTATATAAAAATAGAGTTTTT
1 AGTAAAATAGTAAAATATAAGTTACATAAAGATATTAGATTTAATTAAATAAAAATAGAGTTTTT
*
28579 AGTTG
66 AGTTA
* *
28584 AGTAAAATAGTAAAATAAAATAGTTACTATAAAGATATTATATTTAATTAAATAAAAATAGAGTT
1 AGTAAAATAGTAAAAT-ATA-AGTTAC-ATAAAGATATTAGATTTAATTAAATAAAAATAGAGTT
28649 TTTAGTTA
63 TTTAGTTA
*
28657 AATAAAACTA-TAAAAATATAA
1 AGTAAAA-TAGT-AAAATATAA
28678 AAATAGAGTT
Statistics
Matches: 79, Mismatches: 8, Indels: 10
0.81 0.08 0.10
Matches are distributed among these distances:
68 15 0.19
69 2 0.03
70 2 0.03
71 2 0.03
72 1 0.01
73 50 0.63
74 7 0.09
ACGTcount: A:0.52, C:0.01, G:0.11, T:0.35
Consensus pattern (70 bp):
AGTAAAATAGTAAAATATAAGTTACATAAAGATATTAGATTTAATTAAATAAAAATAGAGTTTTT
AGTTA
Found at i:28702 original size:39 final size:39
Alignment explanation
Indices: 28635--28710 Score: 118
Period size: 39 Copynumber: 1.9 Consensus size: 39
28625 ATTTAATTAA
28635 ATAAAAATAGAGTTTTTAGTTAAATAAAACTA-TAAAAAT
1 ATAAAAATAGAGTTTTTAGTTAAATAAAA-TAGTAAAAAT
* *
28674 ATAAAAATAGAGTTTTTAGTTGAGTAAAATAGTAAAA
1 ATAAAAATAGAGTTTTTAGTTAAATAAAATAGTAAAA
28711 TAAAATAGTT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
38 2 0.06
39 32 0.94
ACGTcount: A:0.54, C:0.01, G:0.12, T:0.33
Consensus pattern (39 bp):
ATAAAAATAGAGTTTTTAGTTAAATAAAATAGTAAAAAT
Found at i:28770 original size:109 final size:111
Alignment explanation
Indices: 28560--28781 Score: 412
Period size: 109 Copynumber: 2.0 Consensus size: 111
28550 AGATTTAATT
28560 ATATAAAAATAGAGTTTTTAGTTGAGTAAAATAGTAAAATAAAATAGTTACTATAAAGATATTAT
1 ATATAAAAATAGAGTTTTTAGTTGAGTAAAATAGTAAAATAAAATAGTTA-TATAAAGATATTAT
28625 ATTTAATTAAATAAAAATAGAGTTTTTAGTTAAATAAAACTATAAAA
65 ATTTAATTAAATAAAAATAGAGTTTTTAGTTAAATAAAACTATAAAA
*
28672 ATATAAAAATAGAGTTTTTAGTTGAGTAAAATAGTAAAATAAAATAG-T-TATAAATATATTATA
1 ATATAAAAATAGAGTTTTTAGTTGAGTAAAATAGTAAAATAAAATAGTTATATAAAGATATTATA
28735 TTTAATTAAATAAAAATAGAGTTTTTAGTTAAATAAAACTATAAAA
66 TTTAATTAAATAAAAATAGAGTTTTTAGTTAAATAAAACTATAAAA
28781 A
1 A
28782 CTTAAACAAT
Statistics
Matches: 109, Mismatches: 1, Indels: 3
0.96 0.01 0.03
Matches are distributed among these distances:
109 61 0.56
111 1 0.01
112 47 0.43
ACGTcount: A:0.53, C:0.01, G:0.09, T:0.36
Consensus pattern (111 bp):
ATATAAAAATAGAGTTTTTAGTTGAGTAAAATAGTAAAATAAAATAGTTATATAAAGATATTATA
TTTAATTAAATAAAAATAGAGTTTTTAGTTAAATAAAACTATAAAA
Found at i:32717 original size:29 final size:29
Alignment explanation
Indices: 32684--32745 Score: 97
Period size: 29 Copynumber: 2.1 Consensus size: 29
32674 GAAACTAAAT
*
32684 AATTATGTAACACGTTTATTGGTAGAAGG
1 AATTATGTAACACGTATATTGGTAGAAGG
* *
32713 AATTATGTAGCACGTATATTGGTAGACGG
1 AATTATGTAACACGTATATTGGTAGAAGG
32742 AATT
1 AATT
32746 TTAATGATTA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.34, C:0.08, G:0.24, T:0.34
Consensus pattern (29 bp):
AATTATGTAACACGTATATTGGTAGAAGG
Found at i:32797 original size:2 final size:2
Alignment explanation
Indices: 32790--32827 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
32780 CCTAATACTG
* *
32790 AT AT AT AT AT AT AT AT GT AT GT 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
32828 GATCATAATG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (2 bp):
AT
Found at i:33127 original size:20 final size:20
Alignment explanation
Indices: 33104--33141 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
33094 TATATATAAT
33104 TTGTTATAATAT-CTTTTTAA
1 TTGTT-TAATATACTTTTTAA
*
33124 TTGTTTACTATACTTTTT
1 TTGTTTAATATACTTTTT
33142 TAATAACCGT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 5 0.31
20 11 0.69
ACGTcount: A:0.24, C:0.08, G:0.05, T:0.63
Consensus pattern (20 bp):
TTGTTTAATATACTTTTTAA
Found at i:34424 original size:38 final size:38
Alignment explanation
Indices: 34373--34450 Score: 140
Period size: 38 Copynumber: 2.1 Consensus size: 38
34363 TAAAATTACC
34373 AAAAATTCAAAGTATTAAGTAAGAATGTAAGATTGTTG
1 AAAAATTCAAAGTATTAAGTAAGAATGTAAGATTGTTG
34411 AAAAATGT-AAAGTATTAAGTAAGAATGTAAGATTGTTG
1 AAAAAT-TCAAAGTATTAAGTAAGAATGTAAGATTGTTG
34449 AA
1 AA
34451 TTTGTTGAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
38 38 0.97
39 1 0.03
ACGTcount: A:0.49, C:0.01, G:0.19, T:0.31
Consensus pattern (38 bp):
AAAAATTCAAAGTATTAAGTAAGAATGTAAGATTGTTG
Found at i:36042 original size:26 final size:25
Alignment explanation
Indices: 35985--36042 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 25
35975 GACAAAAAGC
35985 TACTAAAATTACAACATATTAAGGT
1 TACTAAAATTACAACATATTAAGGT
* * *
36010 AAATAAAATTACTA-ATGATGTAAGGT
1 TACTAAAATTACAACAT-AT-TAAGGT
36036 TACTAAA
1 TACTAAA
36043 TTTATGGAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
24 2 0.08
25 13 0.50
26 11 0.42
ACGTcount: A:0.50, C:0.09, G:0.10, T:0.31
Consensus pattern (25 bp):
TACTAAAATTACAACATATTAAGGT
Done.