Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008561.1 Corchorus capsularis cultivar CVL-1 contig08582, 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: 70351
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:874 original size:21 final size:21
Alignment explanation
Indices: 848--912 Score: 76
Period size: 26 Copynumber: 2.9 Consensus size: 21
838 TTGGTTTCAC
848 TTGTTTGATGGAATATTACAA
1 TTGTTTGATGGAATATTACAA
*
869 TTGTTTGATGAAATTGTGTATTACAA
1 TTGTTTGATGGAA-----TATTACAA
895 TTGTTTGATGGAATATTA
1 TTGTTTGATGGAATATTA
913 TATCATCTCA
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
21 17 0.46
26 20 0.54
ACGTcount: A:0.31, C:0.03, G:0.20, T:0.46
Consensus pattern (21 bp):
TTGTTTGATGGAATATTACAA
Found at i:3930 original size:2 final size:2
Alignment explanation
Indices: 3923--3960 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
3913 ATTTTATGTC
3923 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3961 CACTATATCT
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5861 original size:156 final size:156
Alignment explanation
Indices: 5668--5952 Score: 369
Period size: 156 Copynumber: 1.8 Consensus size: 156
5658 TGCCAAGGGA
* * * * *
5668 CTTAGATTCTCTCCACAAGACTATGGAAAAAATTCTAAGTAAAACCGAGCTCTCCT-TCATGGTG
1 CTTAGATTATCTCCACAAGACTATGGAAAAAATTCTAAGTAAAACCGAACTCT-CTAACATAGAG
* * ** * *
5732 AACTAGGTTTCTCTCCCTGAATTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTC
65 AACTAGATTTCTCACCCCAAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATCCTAAGTC
5797 CAATGAAGCTAATTTTCCTTCAGTAGG
130 CAATGAAGCTAATTTTCCTTCAGTAGG
*
5824 CTTAGATTATCTCCATAA-ATCTATGGGAAAAAA-TCTAAGTAAAACCGAACTCTCTAACATAGA
1 CTTAGATTATCTCCACAAGA-CTAT-GGAAAAAATTCTAAGTAAAACCGAACTCTCTAACATAGA
* * * * *
5887 GAAGTTGATTTGTCACCCCAAACTGTCCTTAACTGAAAAACTTGCATAAGTTTTTCATCCTAAGT
64 GAACTAGATTTCTCACCCCAAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATCCTAAGT
5952 C
129 C
5953 TGTTTGAGAT
Statistics
Matches: 109, Mismatches: 17, Indels: 6
0.83 0.13 0.05
Matches are distributed among these distances:
155 3 0.03
156 98 0.90
157 8 0.07
ACGTcount: A:0.34, C:0.21, G:0.14, T:0.32
Consensus pattern (156 bp):
CTTAGATTATCTCCACAAGACTATGGAAAAAATTCTAAGTAAAACCGAACTCTCTAACATAGAGA
ACTAGATTTCTCACCCCAAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATCCTAAGTCC
AATGAAGCTAATTTTCCTTCAGTAGG
Found at i:8161 original size:11 final size:11
Alignment explanation
Indices: 8145--8169 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
8135 ATCGAAAGAT
8145 ATTAAAAAAAA
1 ATTAAAAAAAA
8156 ATTAAAAAAAA
1 ATTAAAAAAAA
8167 ATT
1 ATT
8170 CGACCAAAAA
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:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (11 bp):
ATTAAAAAAAA
Found at i:11725 original size:9 final size:9
Alignment explanation
Indices: 11711--11735 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
11701 ATGGTTTTAA
11711 TCCTTTGAC
1 TCCTTTGAC
11720 TCCTTTGAC
1 TCCTTTGAC
11729 TCCTTTG
1 TCCTTTG
11736 GATTTGATGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.08, C:0.32, G:0.12, T:0.48
Consensus pattern (9 bp):
TCCTTTGAC
Found at i:13234 original size:18 final size:18
Alignment explanation
Indices: 13207--13241 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
13197 TCAAGGTTAT
*
13207 ATAAAAAAATATTAAATA
1 ATAAAAAAATAATAAATA
*
13225 ATAAATAAATAATAAAT
1 ATAAAAAAATAATAAAT
13242 TTTTCAACCA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (18 bp):
ATAAAAAAATAATAAATA
Found at i:15372 original size:71 final size:71
Alignment explanation
Indices: 15261--15458 Score: 238
Period size: 71 Copynumber: 2.8 Consensus size: 71
15251 AAATCAACAG
* * * * *
15261 CAAATCAGCAA-TAAAATCCAATCATTTACATATAATGAACAAAACCCAATGAAACA-ACCCAAA
1 CAAATCAGCAAGTAAAATCCCATCATTTGCATGTAATGAACAAAACACAATCAAA-ATACCCAAA
*
15324 TCTAAAC
65 TATAAAC
* * * *
15331 CAAATCAACAAGTAAAATCCCATCATGTGCATGTAATGAACAAAACGCAATCAAAATACCCAAGT
1 CAAATCAGCAAGTAAAATCCCATCATTTGCATGTAATGAACAAAACACAATCAAAATACCCAAAT
15396 ATAAAC
66 ATAAAC
* * * * *
15402 CAAATCAGCAAGTAAAAACCCATAATTTGCAAGTATTAAACAAAACACAATCAAAAT
1 CAAATCAGCAAGTAAAATCCCATCATTTGCATGTAATGAACAAAACACAATCAAAAT
15459 GGTAATCGAA
Statistics
Matches: 109, Mismatches: 17, Indels: 3
0.84 0.13 0.02
Matches are distributed among these distances:
70 11 0.10
71 98 0.90
ACGTcount: A:0.52, C:0.22, G:0.07, T:0.19
Consensus pattern (71 bp):
CAAATCAGCAAGTAAAATCCCATCATTTGCATGTAATGAACAAAACACAATCAAAATACCCAAAT
ATAAAC
Found at i:25706 original size:92 final size:91
Alignment explanation
Indices: 25569--25738 Score: 243
Period size: 92 Copynumber: 1.9 Consensus size: 91
25559 TGGAAGCAAA
* ** * * * *
25569 TTTAGACACAGATATGTAGTTTCCGTGTTAAGTTCTGTTTTCAAATGAAATAAAAATTTATTTAT
1 TTTACACACAGATATGTAAATTCCGTGTTAAATTCCGTTTCCAAATGAAAT-AAAATTTATGTAT
*
25634 ATAAT-TATTATTATATTTGGAGTCGGG
65 AGAATATATT-TTATATTTGGAGTCGGG
25661 TTTACACACAGATATGTAAATTCCGTGTTAAATTCCGTTTCCAAATGAAATAAAATTTATGTATA
1 TTTACACACAGATATGTAAATTCCGTGTTAAATTCCGTTTCCAAATGAAATAAAATTTATGTATA
25726 GAATATATTTTAT
66 GAATATATTTTAT
25739 TAATATATTC
Statistics
Matches: 69, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
91 20 0.29
92 49 0.71
ACGTcount: A:0.35, C:0.09, G:0.14, T:0.42
Consensus pattern (91 bp):
TTTACACACAGATATGTAAATTCCGTGTTAAATTCCGTTTCCAAATGAAATAAAATTTATGTATA
GAATATATTTTATATTTGGAGTCGGG
Found at i:37883 original size:30 final size:30
Alignment explanation
Indices: 37842--37985 Score: 164
Period size: 30 Copynumber: 4.8 Consensus size: 30
37832 GGATGACGGT
* *
37842 ATTGTATGATTTTTAGATGTAGGTGTCGAC
1 ATTGTCTGATTTTCAGATGTAGGTGTCGAC
* *
37872 ATTGTCGGATTTTCAGATGTAGTTGTCGAC
1 ATTGTCTGATTTTCAGATGTAGGTGTCGAC
* * * *
37902 ATTTTTTTATTTTCAGATGTAGTTGAT-GAC
1 ATTGTCTGATTTTCAGATGTAGGTG-TCGAC
* * *
37932 ATTGTCTTATTTTCAGATGTAGGTGCCGAT
1 ATTGTCTGATTTTCAGATGTAGGTGTCGAC
*
37962 ATTTTCTGATTTTCAGATGTAGGT
1 ATTGTCTGATTTTCAGATGTAGGT
37986 ATTGCCAGAT
Statistics
Matches: 97, Mismatches: 15, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
30 96 0.99
31 1 0.01
ACGTcount: A:0.22, C:0.10, G:0.23, T:0.46
Consensus pattern (30 bp):
ATTGTCTGATTTTCAGATGTAGGTGTCGAC
Found at i:38027 original size:30 final size:30
Alignment explanation
Indices: 37991--38091 Score: 121
Period size: 30 Copynumber: 3.4 Consensus size: 30
37981 TAGGTATTGC
* *
37991 CAGATGTAGGTGCCATCATTGTCTTATTTT
1 CAGATGTAGTTGCCAACATTGTCTTATTTT
* * * *
38021 CAGATGTAATTGCTAACATTTTCTAATTTT
1 CAGATGTAGTTGCCAACATTGTCTTATTTT
* * *
38051 TAGATGTAGTTGCCAACATTGTTTTATTCT
1 CAGATGTAGTTGCCAACATTGTCTTATTTT
38081 CAGATGTAGTT
1 CAGATGTAGTT
38092 TCCGATGTTA
Statistics
Matches: 57, Mismatches: 14, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
30 57 1.00
ACGTcount: A:0.25, C:0.14, G:0.17, T:0.45
Consensus pattern (30 bp):
CAGATGTAGTTGCCAACATTGTCTTATTTT
Found at i:40466 original size:7 final size:7
Alignment explanation
Indices: 40454--40504 Score: 68
Period size: 7 Copynumber: 7.3 Consensus size: 7
40444 ATGTCCCTTA
40454 TAGGGTT
1 TAGGGTT
40461 TAGGG-T
1 TAGGGTT
40467 TAGGGTT
1 TAGGGTT
*
40474 TAAGGTT
1 TAGGGTT
*
40481 TAGGATT
1 TAGGGTT
40488 TAAGGGTT
1 T-AGGGTT
40496 TAGGGTT
1 TAGGGTT
40503 TA
1 TA
40505 AGCATCTTTC
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
6 6 0.16
7 26 0.68
8 6 0.16
ACGTcount: A:0.22, C:0.00, G:0.37, T:0.41
Consensus pattern (7 bp):
TAGGGTT
Found at i:40714 original size:25 final size:26
Alignment explanation
Indices: 40672--40725 Score: 83
Period size: 25 Copynumber: 2.1 Consensus size: 26
40662 TGGCAAATTT
40672 AAACTATATGGGCCGCTTAAATGTTAC
1 AAACTATA-GGGCCGCTTAAATGTTAC
*
40699 AAACTATA-GGCCGCTTAATTGTTAC
1 AAACTATAGGGCCGCTTAAATGTTAC
40724 AA
1 AA
40726 TTATTTGTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 18 0.69
27 8 0.31
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.30
Consensus pattern (26 bp):
AAACTATAGGGCCGCTTAAATGTTAC
Found at i:42337 original size:30 final size:29
Alignment explanation
Indices: 42294--42351 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
42284 GCACCTTTGC
42294 TTTGAGTTATTTTTTTATTCGACAAAATA
1 TTTGAGTTATTTTTTTATTCGACAAAATA
*
42323 TTTGAGTTATTTTTTTATTCGACGAAATA
1 TTTGAGTTATTTTTTTATTCGACAAAATA
42352 AGTATTACAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.29, C:0.07, G:0.12, T:0.52
Consensus pattern (29 bp):
TTTGAGTTATTTTTTTATTCGACAAAATA
Found at i:43061 original size:21 final size:21
Alignment explanation
Indices: 43035--43085 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
43025 AACGGATCCT
43035 TTTGGGCCTATTATCTAAAGA
1 TTTGGGCCTATTATCTAAAGA
* *
43056 TTTGGGCCTGTTATCTGAAGA
1 TTTGGGCCTATTATCTAAAGA
*
43077 ATTGGGCCT
1 TTTGGGCCT
43086 TAATTTTAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.22, C:0.16, G:0.25, T:0.37
Consensus pattern (21 bp):
TTTGGGCCTATTATCTAAAGA
Found at i:43115 original size:2 final size:2
Alignment explanation
Indices: 43108--43135 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
43098 TGAGTGCTTT
43108 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
43136 CTACATATTA
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:45314 original size:22 final size:22
Alignment explanation
Indices: 45251--45316 Score: 60
Period size: 22 Copynumber: 3.0 Consensus size: 22
45241 TATTTTGATC
*
45251 TCGGGCTCGGGTCGGGTTCGGGT
1 TCGGGTTCGGG-CGGGTTCGGGT
******
45274 TCGGGTTCGTATAATTTCGGGT
1 TCGGGTTCGGGCGGGTTCGGGT
45296 TCGGGTTCGGGCGGGTTCGGG
1 TCGGGTTCGGGCGGGTTCGGG
45317 ACGTTGACTT
Statistics
Matches: 30, Mismatches: 13, Indels: 1
0.68 0.30 0.02
Matches are distributed among these distances:
22 22 0.73
23 8 0.27
ACGTcount: A:0.05, C:0.18, G:0.47, T:0.30
Consensus pattern (22 bp):
TCGGGTTCGGGCGGGTTCGGGT
Found at i:46246 original size:12 final size:12
Alignment explanation
Indices: 46214--46252 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
46204 ATGGAATTAA
46214 ATATCCGTCG--
1 ATATCCGTCGAT
46224 ATA-CC-TCGAT
1 ATATCCGTCGAT
46234 ATATCCGTCGAT
1 ATATCCGTCGAT
46246 ATATCCG
1 ATATCCG
46253 ATATTTGTAC
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
8 3 0.12
9 2 0.08
10 6 0.24
11 2 0.08
12 12 0.48
ACGTcount: A:0.26, C:0.28, G:0.15, T:0.31
Consensus pattern (12 bp):
ATATCCGTCGAT
Found at i:46346 original size:20 final size:18
Alignment explanation
Indices: 46318--46362 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
46308 CGTCGATATT
*
46318 TATCGATATCTC-GATAAA
1 TATCGATATATCTG-TAAA
*
46336 TCTCGATATATCTGTAAA
1 TATCGATATATCTGTAAA
46354 TATCGATAT
1 TATCGATAT
46363 TAAATTAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 22 0.96
19 1 0.04
ACGTcount: A:0.36, C:0.16, G:0.11, T:0.38
Consensus pattern (18 bp):
TATCGATATATCTGTAAA
Found at i:47667 original size:13 final size:12
Alignment explanation
Indices: 47637--47679 Score: 77
Period size: 12 Copynumber: 3.5 Consensus size: 12
47627 CATCGATACC
47637 TCGATATATCCG
1 TCGATATATCCG
47649 TCGATATATCCG
1 TCGATATATCCG
47661 TTCGATATATCCG
1 -TCGATATATCCG
47674 TCGATA
1 TCGATA
47680 CCTGTATTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
12 18 0.60
13 12 0.40
ACGTcount: A:0.26, C:0.23, G:0.16, T:0.35
Consensus pattern (12 bp):
TCGATATATCCG
Found at i:58828 original size:2 final size:2
Alignment explanation
Indices: 58823--58863 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
58813 TCTGTGTGTC
58823 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
58864 GCAAACTGCA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:58828 original size:18 final size:18
Alignment explanation
Indices: 58790--58829 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
58780 TCAATCTTTC
* * *
58790 ATATGTGTGTGTGTGTGT
1 ATATGTCTGTGTGTCTAT
58808 ATATGTCTGTGTGTCTAT
1 ATATGTCTGTGTGTCTAT
58826 ATAT
1 ATAT
58830 ATATATATAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.17, C:0.05, G:0.28, T:0.50
Consensus pattern (18 bp):
ATATGTCTGTGTGTCTAT
Found at i:58903 original size:1 final size:1
Alignment explanation
Indices: 58899--58934 Score: 54
Period size: 1 Copynumber: 36.0 Consensus size: 1
58889 AAAAAAACCG
* *
58899 AAAAAGAAAAAAAAAAAAAAAAAAAAAAAACAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
58935 CAAACAAACA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:0.94, C:0.03, G:0.03, T:0.00
Consensus pattern (1 bp):
A
Found at i:58939 original size:4 final size:4
Alignment explanation
Indices: 58932--58962 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
58922 AAAAAAACAA
58932 AAAC AAAC AAAC AAAC AAAC AAAC AAAC AAA
1 AAAC AAAC AAAC AAAC AAAC AAAC AAAC AAA
58963 AAGATAGTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.77, C:0.23, G:0.00, T:0.00
Consensus pattern (4 bp):
AAAC
Found at i:61197 original size:31 final size:31
Alignment explanation
Indices: 61162--61329 Score: 159
Period size: 31 Copynumber: 5.5 Consensus size: 31
61152 GTCGACTAAT
61162 TGCTCAAATAAGGGCCTAATGTTTGCCAAAA
1 TGCTCAAATAAGGGCCTAATGTTTGCCAAAA
* * * * **
61193 TGCTCAAATAAGGGTCTGATCTTT--TAATTT
1 TGCTCAAATAAGGGCCTAATGTTTGCCAA-AA
61223 TG-TCAAATAAGGGCCTAATGTTTGCCAAAA
1 TGCTCAAATAAGGGCCTAATGTTTGCCAAAA
* * **
61253 TGCTCAAATAAGGGCCTCATCTTTG--AATT
1 TGCTCAAATAAGGGCCTAATGTTTGCCAAAA
* *
61282 TGGC-CAAATAAGGACCTAACGTTTGCCAAAA
1 T-GCTCAAATAAGGGCCTAATGTTTGCCAAAA
*
61313 TGCTCAATTAAGGGCCT
1 TGCTCAAATAAGGGCCT
61330 GTCTCATGCG
Statistics
Matches: 105, Mismatches: 24, Indels: 16
0.72 0.17 0.11
Matches are distributed among these distances:
29 40 0.38
30 8 0.08
31 57 0.54
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Consensus pattern (31 bp):
TGCTCAAATAAGGGCCTAATGTTTGCCAAAA
Found at i:61230 original size:60 final size:60
Alignment explanation
Indices: 61165--61329 Score: 258
Period size: 60 Copynumber: 2.8 Consensus size: 60
61155 GACTAATTGC
* * * *
61165 TCAAATAAGGGCCTAATGTTTGCCAAAATGCTCAAATAAGGGTCTGATCTTTTAATTTTG
1 TCAAATAAGGGCCTAATGTTTGCCAAAATGCTCAAATAAGGGCCTCATCTTTGAATTTGG
61225 TCAAATAAGGGCCTAATGTTTGCCAAAATGCTCAAATAAGGGCCTCATCTTTGAATTTGG
1 TCAAATAAGGGCCTAATGTTTGCCAAAATGCTCAAATAAGGGCCTCATCTTTGAATTTGG
* * * *
61285 CCAAATAAGGACCTAACGTTTGCCAAAATGCTCAATTAAGGGCCT
1 TCAAATAAGGGCCTAATGTTTGCCAAAATGCTCAAATAAGGGCCT
61330 GTCTCATGCG
Statistics
Matches: 97, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
60 97 1.00
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.30
Consensus pattern (60 bp):
TCAAATAAGGGCCTAATGTTTGCCAAAATGCTCAAATAAGGGCCTCATCTTTGAATTTGG
Found at i:61398 original size:31 final size:31
Alignment explanation
Indices: 61360--61491 Score: 157
Period size: 31 Copynumber: 4.3 Consensus size: 31
61350 TGACACCAAA
61360 CCCTTATTTGAGCATTTTCGATAACGTTAGG
1 CCCTTATTTGAGCATTTTCGATAACGTTAGG
61391 CCCTTATTTGAGCATTTTCGATAACGTTAGG
1 CCCTTATTTGAGCATTTTCGATAACGTTAGG
** * *
61422 CCCTTATTTG-GCCAAATT-AAAAGACCG---GG
1 CCCTTATTTGAG-CATTTTCGATA-A-CGTTAGG
*
61451 CCTTTATTTGAGCATTTTCGATAACGTTAGG
1 CCCTTATTTGAGCATTTTCGATAACGTTAGG
61482 CCCTTATTTG
1 CCCTTATTTG
61492 GCCAGATTAA
Statistics
Matches: 83, Mismatches: 10, Indels: 16
0.76 0.09 0.15
Matches are distributed among these distances:
28 2 0.02
29 16 0.19
30 6 0.07
31 57 0.69
32 2 0.02
ACGTcount: A:0.23, C:0.20, G:0.19, T:0.37
Consensus pattern (31 bp):
CCCTTATTTGAGCATTTTCGATAACGTTAGG
Found at i:61463 original size:60 final size:59
Alignment explanation
Indices: 61392--61551 Score: 232
Period size: 60 Copynumber: 2.7 Consensus size: 59
61382 AACGTTAGGC
61392 CCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGACCGGG
1 CCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGACCGGG
* * *
61451 CCTTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCCAGATTAAAAGATCGGA
1 CC-TTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGACCGGG
* **
61511 CACTTATTTGAGCATTTTTGCA-AACACTAGGCCCTTATTTG
1 C-CTTATTTGAGCATTTTCG-ATAACGTTAGGCCCTTATTTG
61552 AGCAATTAGC
Statistics
Matches: 92, Mismatches: 6, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
59 2 0.02
60 88 0.96
61 2 0.02
ACGTcount: A:0.26, C:0.20, G:0.19, T:0.35
Consensus pattern (59 bp):
CCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGACCGGG
Found at i:61931 original size:22 final size:22
Alignment explanation
Indices: 61903--61951 Score: 98
Period size: 22 Copynumber: 2.2 Consensus size: 22
61893 ATCTTTCAAT
61903 AGACACTTGAATCATATTGATC
1 AGACACTTGAATCATATTGATC
61925 AGACACTTGAATCATATTGATC
1 AGACACTTGAATCATATTGATC
61947 AGACA
1 AGACA
61952 AATATAACAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (22 bp):
AGACACTTGAATCATATTGATC
Found at i:63352 original size:21 final size:21
Alignment explanation
Indices: 63328--63368 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
63318 GAATGCGGAA
*
63328 CAACATCGGCCCAGAAGTTGT
1 CAACATAGGCCCAGAAGTTGT
* *
63349 CAACTTATGCCCAGAAGTTG
1 CAACATAGGCCCAGAAGTTG
63369 GCCTATTGAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.29, C:0.27, G:0.22, T:0.22
Consensus pattern (21 bp):
CAACATAGGCCCAGAAGTTGT
Done.