Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012394.1 Corchorus olitorius cultivar O-4 contig12427, 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: 19584
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Found at i:1229 original size:32 final size:32
Alignment explanation
Indices: 1162--1284 Score: 126
Period size: 32 Copynumber: 3.8 Consensus size: 32
1152 GCCAATTGTA
* *
1162 CCCAACTATTCCGAAATCG-GCTCCCGTACCAGAC
1 CCCAACTAATCCGAAATCGAG---CCATACCAGAC
* *
1196 CCCAACTAATCCGAAATCGAGCCGTAATC-GA-
1 CCCAACTAATCCGAAATCGAGCCAT-ACCAGAC
* *
1227 CCCAACTAATTCGAAATCGAGCCATACCAAAC
1 CCCAACTAATCCGAAATCGAGCCATACCAGAC
*
1259 CCCAATTAATCCGAAATCGAGCCATA
1 CCCAACTAATCCGAAATCGAGCCATA
1285 TCGAACACCA
Statistics
Matches: 77, Mismatches: 8, Indels: 10
0.81 0.08 0.11
Matches are distributed among these distances:
30 2 0.03
31 24 0.31
32 30 0.39
33 2 0.03
34 18 0.23
35 1 0.01
ACGTcount: A:0.35, C:0.35, G:0.13, T:0.17
Consensus pattern (32 bp):
CCCAACTAATCCGAAATCGAGCCATACCAGAC
Found at i:1297 original size:32 final size:31
Alignment explanation
Indices: 1196--1295 Score: 121
Period size: 32 Copynumber: 3.2 Consensus size: 31
1186 CGTACCAGAC
*
1196 CCCAACTAATCCGAAATCGAGCCGTAATCG-A
1 CCCAACTAATCCGAAATCGAGCCAT-ATCGAA
* * *
1227 CCCAACTAATTCGAAATCGAGCCATACCAAA
1 CCCAACTAATCCGAAATCGAGCCATATCGAA
*
1258 CCCCAATTAATCCGAAATCGAGCCATATCGAA
1 -CCCAACTAATCCGAAATCGAGCCATATCGAA
1290 CACCAA
1 C-CCAA
1296 TTTCGGTATT
Statistics
Matches: 58, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
30 2 0.03
31 25 0.43
32 31 0.53
ACGTcount: A:0.39, C:0.33, G:0.12, T:0.16
Consensus pattern (31 bp):
CCCAACTAATCCGAAATCGAGCCATATCGAA
Found at i:5239 original size:42 final size:45
Alignment explanation
Indices: 5188--5281 Score: 135
Period size: 45 Copynumber: 2.2 Consensus size: 45
5178 AGTGTATTAC
*
5188 CTAA-ATTCTACT-C-C-ATCTCTA-AGTAATTTATCAAAATAAAG
1 CTAATATTCTACTCCTCTATCTCTAGA-TAATTCATCAAAATAAAG
5229 CTAATATTCTACTCCTCTATCTCTAGATAATTCATCAAAATAAAG
1 CTAATATTCTACTCCTCTATCTCTAGATAATTCATCAAAATAAAG
5274 CTAATATT
1 CTAATATT
5282 AATTGTTACT
Statistics
Matches: 47, Mismatches: 1, Indels: 6
0.87 0.02 0.11
Matches are distributed among these distances:
41 4 0.09
42 8 0.17
43 1 0.02
44 1 0.02
45 32 0.68
46 1 0.02
ACGTcount: A:0.39, C:0.20, G:0.04, T:0.36
Consensus pattern (45 bp):
CTAATATTCTACTCCTCTATCTCTAGATAATTCATCAAAATAAAG
Found at i:5966 original size:95 final size:97
Alignment explanation
Indices: 5803--5999 Score: 337
Period size: 95 Copynumber: 2.1 Consensus size: 97
5793 TCATAAAGAT
* *
5803 AAAAATAGTAAATTACAAAAAATGGCAGTAGGAAAAGTAAGGGAGGAAATTTATCGAGGGCATTT
1 AAAAATAGTAAATTACAAAAAATGGCAGTAGGAAAAGTAAGGGAGGAAATTCATCGAGGACATTT
*
5868 TTAGTCATC-AGAAAAGTGAGAAAAGA-CAAAA
66 TTAGTCATCAAGAAAA-TGAGAAAAAACCAAAA
5899 AAAAATAGTAAATTACAAAAAA-GGCAGTAGGAAAAGTAAGGGAGGAAATTCATCGAGGACATTT
1 AAAAATAGTAAATTACAAAAAATGGCAGTAGGAAAAGTAAGGGAGGAAATTCATCGAGGACATTT
5963 TTAGTCATCAAGAAAATGAGAAAAAACCAAAA
66 TTAGTCATCAAGAAAATGAGAAAAAACCAAAA
5995 AAAAA
1 AAAAA
6000 AAAACAAAAG
Statistics
Matches: 96, Mismatches: 3, Indels: 4
0.93 0.03 0.04
Matches are distributed among these distances:
95 58 0.60
96 38 0.40
ACGTcount: A:0.53, C:0.08, G:0.21, T:0.18
Consensus pattern (97 bp):
AAAAATAGTAAATTACAAAAAATGGCAGTAGGAAAAGTAAGGGAGGAAATTCATCGAGGACATTT
TTAGTCATCAAGAAAATGAGAAAAAACCAAAA
Found at i:12210 original size:23 final size:23
Alignment explanation
Indices: 12184--12231 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
12174 CAAATATCTT
12184 CCATATTTCCAAAATCACAATCA
1 CCATATTTCCAAAATCACAATCA
*
12207 CCATATTTCCAGAATCACAATCA
1 CCATATTTCCAAAATCACAATCA
12230 CC
1 CC
12232 CAAATTAAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.40, C:0.33, G:0.02, T:0.25
Consensus pattern (23 bp):
CCATATTTCCAAAATCACAATCA
Found at i:17330 original size:27 final size:24
Alignment explanation
Indices: 17281--17331 Score: 66
Period size: 27 Copynumber: 2.0 Consensus size: 24
17271 GTGATTATCT
*
17281 TCACATGGATAAAAGGCAGGAATC
1 TCACATGGATAAAAGGCAAGAATC
17305 TCACATGGATGATGAAAGGCAAGAATC
1 TCACATGGAT-A--AAAGGCAAGAATC
17332 AAATGTAAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 10 0.43
25 1 0.04
27 12 0.52
ACGTcount: A:0.41, C:0.16, G:0.25, T:0.18
Consensus pattern (24 bp):
TCACATGGATAAAAGGCAAGAATC
Found at i:19554 original size:2 final size:2
Alignment explanation
Indices: 19547--19584 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
19537 AAAATAAGCG
19547 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
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):
AT
Done.