Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020576.1 Corchorus olitorius cultivar O-4 contig20609, 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: 47395
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:1229 original size:14 final size:14
Alignment explanation
Indices: 1210--1256 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
1200 TGAAATATAG
1210 TAAAATGGTAAAAA
1 TAAAATGGTAAAAA
* * *
1224 TAAAAT-TTTAAAT
1 TAAAATGGTAAAAA
1237 TAAAATGGTAAAAA
1 TAAAATGGTAAAAA
1251 TAAAAT
1 TAAAAT
1257 AATTATAAAA
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
13 10 0.38
14 16 0.62
ACGTcount: A:0.62, C:0.00, G:0.09, T:0.30
Consensus pattern (14 bp):
TAAAATGGTAAAAA
Found at i:1574 original size:148 final size:149
Alignment explanation
Indices: 1306--1660 Score: 552
Period size: 148 Copynumber: 2.4 Consensus size: 149
1296 AAATATTAAT
* **
1306 TAAAAATATTGAATTTAATTGAATGAAAATAGAGTTTTTAGTAGAATCGAACTATATATTAAAAC
1 TAAAAATATTGAATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAACTATATATTAAAAC
* *
1371 ATTTTAATATATCCAAGTTTTTAATGAAAAATAGTAATGGTAAAAATAAACTTTTAAATTAAAAT
66 ATTTTAATATATCCAACTTTTTAATGAAAAATAGTAATGGCAAAAATAAACTTTTAAATTAAAAT
1436 GATAAAAATAAAATAATTA
131 GATAAAAATAAAATAATTA
*
1455 TAAAAATATTGAATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATTAAACTATATATTAAAA-
1 TAAAAATATTGAATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAACTATATATTAAAAC
1519 ATTTTAATATATCCAACTTTTTAATGAAAAATAGTAATGGCAAAAATAAACTTTTAAATTAAAAT
66 ATTTTAATATATCCAACTTTTTAATGAAAAATAGTAATGGCAAAAATAAACTTTTAAATTAAAAT
* *
1584 GGTAAAAATAAAGTAATTA
131 GATAAAAATAAAATAATTA
* * * * *
1603 TAAATATATT-AGATTTAACTAGATAAAAATATAGAGTTTTAAGTAGAATAAAACTATA
1 TAAAAATATTGA-ATTTAATTAAAT-GAAA-ATAGAGTTTTTAGTAGAATAAAACTATA
1661 ATAGTTTAAG
Statistics
Matches: 190, Mismatches: 13, Indels: 5
0.91 0.06 0.02
Matches are distributed among these distances:
147 1 0.01
148 99 0.52
149 64 0.34
150 26 0.14
ACGTcount: A:0.51, C:0.04, G:0.09, T:0.35
Consensus pattern (149 bp):
TAAAAATATTGAATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAACTATATATTAAAAC
ATTTTAATATATCCAACTTTTTAATGAAAAATAGTAATGGCAAAAATAAACTTTTAAATTAAAAT
GATAAAAATAAAATAATTA
Found at i:1970 original size:28 final size:29
Alignment explanation
Indices: 1936--2010 Score: 89
Period size: 28 Copynumber: 2.6 Consensus size: 29
1926 ACTTGGAGTG
* * *
1936 TTTGGACGTTTTGTCTC-TGAACTTTAAT
1 TTTGGACGTTTTGCCCCTTGAACTTCAAT
* *
1964 TTTGGACATTTTACCCCTTGAACTTCAAT
1 TTTGGACGTTTTGCCCCTTGAACTTCAAT
1993 TTTGGGACGTTTTGCCCC
1 TTT-GGACGTTTTGCCCC
2011 CTCAGTTTAA
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
28 13 0.34
29 13 0.34
30 12 0.32
ACGTcount: A:0.17, C:0.21, G:0.17, T:0.44
Consensus pattern (29 bp):
TTTGGACGTTTTGCCCCTTGAACTTCAAT
Found at i:2276 original size:28 final size:29
Alignment explanation
Indices: 2213--2288 Score: 91
Period size: 29 Copynumber: 2.7 Consensus size: 29
2203 CGTTAGTCTG
* *
2213 AGGGGGCAAAACGTCCCAAATTGAAGCTC
1 AGGGGGTAAAACGTCCAAAATTGAAGCTC
* * * *
2242 AGTGGGTAGAATGTCCAAAATTGAAG-TT
1 AGGGGGTAAAACGTCCAAAATTGAAGCTC
2270 AGGGGGTAAAACGTCCAAA
1 AGGGGGTAAAACGTCCAAA
2289 CACTATAAGT
Statistics
Matches: 38, Mismatches: 9, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
28 17 0.45
29 21 0.55
ACGTcount: A:0.37, C:0.16, G:0.29, T:0.18
Consensus pattern (29 bp):
AGGGGGTAAAACGTCCAAAATTGAAGCTC
Found at i:4804 original size:22 final size:22
Alignment explanation
Indices: 4779--4829 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
4769 ATCATTGTCA
4779 ATTCTGTG-CACTATCATTCATT
1 ATTCT-TGCCACTATCATTCATT
* *
4801 ATTCTTGCCATTATCATTTATT
1 ATTCTTGCCACTATCATTCATT
*
4823 ATACTTG
1 ATTCTTG
4830 TTGTATTTCT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 2 0.08
22 23 0.92
ACGTcount: A:0.24, C:0.20, G:0.08, T:0.49
Consensus pattern (22 bp):
ATTCTTGCCACTATCATTCATT
Found at i:10833 original size:16 final size:16
Alignment explanation
Indices: 10812--10847 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
10802 AGTCCTAAAC
10812 CCGAAAAACCCAAAAT
1 CCGAAAAACCCAAAAT
* *
10828 CCGAAAGACCTAAAAT
1 CCGAAAAACCCAAAAT
10844 CCGA
1 CCGA
10848 GTAACTTGAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.50, C:0.31, G:0.11, T:0.08
Consensus pattern (16 bp):
CCGAAAAACCCAAAAT
Found at i:11630 original size:132 final size:131
Alignment explanation
Indices: 11468--11707 Score: 335
Period size: 132 Copynumber: 1.8 Consensus size: 131
11458 AACAATGTTA
* * *
11468 ATATTTTAAAAAATCTAATATATCTGAGTTTTCTAA-TT-AAATAAGTAAAATGAT-AAAATTAA
1 ATATTTAAAAAAATCTAATATATATAAGTTTTCTAATTTAAAAT-AGTAAAATGATAAAAATTAA
*
11530 A-ATTGTATAAGGATATTAGATTTAATTAAATAAAAAATAGAGTTTTTAGTTGAGTAAAACTATA
65 ATAGT-TATAAGGATATTAGATTTAATT-AA-AAAAAATAGAGTTTTTAGTTGAGTAAAACTATA
11594 AAATT
127 AAATT
* *
11599 ATATTTAAAAAAATACTAATATATATAAGTTTTTTAATTTAAAATAGTAAAATGGTAAAAATTAA
1 ATATTTAAAAAAAT-CTAATATATATAAGTTTTCTAATTTAAAATAGTAAAATGATAAAAATTAA
* *
11664 ATAGTTATAAGGATATTATATTTACTTAAAAAAAATAGAGTTTT
65 ATAGTTATAAGGATATTAGATTTAATTAAAAAAAATAGAGTTTT
11708 AAAGAAATAT
Statistics
Matches: 96, Mismatches: 8, Indels: 9
0.85 0.07 0.08
Matches are distributed among these distances:
131 13 0.14
132 34 0.35
133 14 0.15
134 33 0.34
135 2 0.02
ACGTcount: A:0.50, C:0.03, G:0.09, T:0.39
Consensus pattern (131 bp):
ATATTTAAAAAAATCTAATATATATAAGTTTTCTAATTTAAAATAGTAAAATGATAAAAATTAAA
TAGTTATAAGGATATTAGATTTAATTAAAAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAT
T
Found at i:12048 original size:93 final size:92
Alignment explanation
Indices: 11899--12084 Score: 336
Period size: 93 Copynumber: 2.0 Consensus size: 92
11889 AATACATTGG
* * *
11899 CTTCACTATTTACAAATTGAAGCGTACATAAATCAACTAGGATTGCCAAATCTCTAATTTCATCT
1 CTTCACTATTTACAAATCGAAACGTACATAAATCAACTAGAATTGCCAAATCTCTAATTTCATCT
11964 ATAACTACCAACATACTAAATACACAAA
66 ATAACTACCAACATACTAAATAC-CAAA
11992 CTTCACTATTTACAAATCGAAACGTACATAAATCAACTAGAATTGCCAAATCTCTAATTTCATCT
1 CTTCACTATTTACAAATCGAAACGTACATAAATCAACTAGAATTGCCAAATCTCTAATTTCATCT
12057 ATAACTACCAACATACTAAATACCAAA
66 ATAACTACCAACATACTAAATACCAAA
12084 C
1 C
12085 AAATAAATTA
Statistics
Matches: 90, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
92 5 0.06
93 85 0.94
ACGTcount: A:0.42, C:0.24, G:0.05, T:0.28
Consensus pattern (92 bp):
CTTCACTATTTACAAATCGAAACGTACATAAATCAACTAGAATTGCCAAATCTCTAATTTCATCT
ATAACTACCAACATACTAAATACCAAA
Found at i:12730 original size:14 final size:15
Alignment explanation
Indices: 12713--12745 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
12703 ATTTTTAAGA
12713 ATTAATTT-ATGAAT
1 ATTAATTTAATGAAT
*
12727 ATTAATTTAATTAAT
1 ATTAATTTAATGAAT
12742 ATTA
1 ATTA
12746 TTTTTTGTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (15 bp):
ATTAATTTAATGAAT
Found at i:14059 original size:2 final size:2
Alignment explanation
Indices: 14046--14092 Score: 85
Period size: 2 Copynumber: 23.0 Consensus size: 2
14036 ACTAAAAATA
14046 AT AT AT AGT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
14089 AT AT
1 AT AT
14093 GAATTCATGA
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 42 0.95
3 2 0.05
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:17365 original size:23 final size:23
Alignment explanation
Indices: 17338--17382 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
17328 GCTACTAGGG
*
17338 GGAAGCCATGACCTACTGGTATT
1 GGAAGCCATGACATACTGGTATT
*
17361 GGAAGCCATGACATGCTGGTAT
1 GGAAGCCATGACATACTGGTAT
17383 GAAATGCTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (23 bp):
GGAAGCCATGACATACTGGTATT
Found at i:26931 original size:31 final size:31
Alignment explanation
Indices: 26896--26965 Score: 140
Period size: 31 Copynumber: 2.3 Consensus size: 31
26886 AAAATAGAAA
26896 TAACCATACAAAAACAATTAACTAAAGTGAT
1 TAACCATACAAAAACAATTAACTAAAGTGAT
26927 TAACCATACAAAAACAATTAACTAAAGTGAT
1 TAACCATACAAAAACAATTAACTAAAGTGAT
26958 TAACCATA
1 TAACCATA
26966 GCAGAACTCA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.54, C:0.17, G:0.06, T:0.23
Consensus pattern (31 bp):
TAACCATACAAAAACAATTAACTAAAGTGAT
Found at i:42163 original size:1 final size:1
Alignment explanation
Indices: 42159--42186 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
42149 CAAAAAAAGC
42159 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
42187 CCCACATGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:45359 original size:13 final size:13
Alignment explanation
Indices: 45341--45365 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
45331 TTGGGGCTGA
45341 TGTGATGAGTTTT
1 TGTGATGAGTTTT
45354 TGTGATGAGTTT
1 TGTGATGAGTTT
45366 CAGGGAGCAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.00, G:0.32, T:0.52
Consensus pattern (13 bp):
TGTGATGAGTTTT
Found at i:47279 original size:2 final size:2
Alignment explanation
Indices: 47268--47302 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
47258 TATGTGATTT
*
47268 TA TA TA -A TA TA TA TA TA TA TG 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
47303 CTTATATGAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:47372 original size:2 final size:2
Alignment explanation
Indices: 47365--47395 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
47355 TTTATTTAAC
47365 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.