Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021462.1 Corchorus olitorius cultivar O-4 contig21495, 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: 23275
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.34
Found at i:3404 original size:178 final size:178
Alignment explanation
Indices: 3100--3432 Score: 490
Period size: 178 Copynumber: 1.9 Consensus size: 178
3090 TAAGCGCAAA
* ** * * * *
3100 TTATGTAATATTAAGTAGATTGTCTATTTCCGTTAACCGAAACATCTAATTCTTTGGAAGCATTT
1 TTATATAATATTAAGTAGACCGTCTATTCCCGTTAACAGAAACAACAAATTCTTTGGAAGCATTT
*
3165 TTTATACCTTGAACAATAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTAAATCATGGAACAAC
66 TTGATACCTTGAACAATAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTAAATCATGGAACAAC
*
3230 CTTTCAAGAGACACTTGAATCATCTCAATTAGACAACTGAAGCAAAAG
131 CTTTCAAGAGACACTTAAATCATCTCAATTAGACAACTGAAGCAAAAG
* *
3278 TTATATAATATTAAGTGGACCGTTTATTCCCGTTAACAGAAACAACAAATT-TTTCGGAAGCATT
1 TTATATAATATTAAGTAGACCGTCTATTCCCGTTAACAGAAACAACAAATTCTTT-GGAAGCATT
* *
3342 TTTGATA-CTTGAAACATTAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTAGATCATGGAACA
65 TTTGATACCTTG-AACAATAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTAAATCATGGAACA
* * *
3406 ATCTTTTAATAGACACTTAAATCATCT
129 ACCTTTCAAGAGACACTTAAATCATCT
3433 TAATCGGATA
Statistics
Matches: 137, Mismatches: 16, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
177 7 0.05
178 130 0.95
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Consensus pattern (178 bp):
TTATATAATATTAAGTAGACCGTCTATTCCCGTTAACAGAAACAACAAATTCTTTGGAAGCATTT
TTGATACCTTGAACAATAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTAAATCATGGAACAAC
CTTTCAAGAGACACTTAAATCATCTCAATTAGACAACTGAAGCAAAAG
Found at i:4862 original size:83 final size:83
Alignment explanation
Indices: 4768--4934 Score: 262
Period size: 83 Copynumber: 2.0 Consensus size: 83
4758 AACTAATTAA
* * *
4768 AAAACTCGAATCAAGCTTGATTTTATAGCTCGAATCAAATCAATTTTCATAAATTCATAATTATA
1 AAAACTCGAATCAAGCTTGATTCTATAGCTCAAATCAAATCAATTTTCATAAATTCATAATTAAA
*
4833 GTATAATATACTATAACT
66 ATATAATATACTATAACT
* * * *
4851 AAAACTTGAATCAAGCTTGATTCTCTAGTTCAAATCAAATCAATTTTTATAAATTCATAATTAAA
1 AAAACTCGAATCAAGCTTGATTCTATAGCTCAAATCAAATCAATTTTCATAAATTCATAATTAAA
4916 ATATAATATACTATAACT
66 ATATAATATACTATAACT
4934 A
1 A
4935 TTCAAAATAG
Statistics
Matches: 76, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
83 76 1.00
ACGTcount: A:0.44, C:0.14, G:0.06, T:0.37
Consensus pattern (83 bp):
AAAACTCGAATCAAGCTTGATTCTATAGCTCAAATCAAATCAATTTTCATAAATTCATAATTAAA
ATATAATATACTATAACT
Found at i:5149 original size:7 final size:7
Alignment explanation
Indices: 5129--5184 Score: 55
Period size: 7 Copynumber: 8.4 Consensus size: 7
5119 TTTTCTTAGG
*
5129 AAAAAGG
1 AAAAAGA
5136 AAAAAGA
1 AAAAAGA
5143 AAAAAGA
1 AAAAAGA
**
5150 ACGAAG-
1 AAAAAGA
*
5156 AAATAGA
1 AAAAAGA
5163 AAAAA-A
1 AAAAAGA
5169 AAAAA-A
1 AAAAAGA
5175 AAAAAGA
1 AAAAAGA
5182 AAA
1 AAA
5185 GAGAGAGAGA
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
6 15 0.38
7 25 0.62
ACGTcount: A:0.82, C:0.02, G:0.14, T:0.02
Consensus pattern (7 bp):
AAAAAGA
Found at i:11254 original size:139 final size:135
Alignment explanation
Indices: 11070--11527 Score: 488
Period size: 139 Copynumber: 3.4 Consensus size: 135
11060 ATTCAATAAG
** * * * *
11070 AGAATCTAGTATTATCTCAA-CCTAACCGTTGGATTAAAAGTGAGATTCACATCTGACGGTTGAT
1 AGAATCTAACATTATCTCAATCC-AACCATTGGATTAAAAGTGAGATTCAAATGTGACAGTTGAT
* *
11134 TAAAAGCTTATCTCTTCCACATAATATCCAA-AGTATGTCAAAAAAATCTAACATAACATCAAAT
65 TAAAAACTTATCTCTTCCACATAATATCCAAGA-TATGTC-AGAAAATCTAACATAACATC-AAT
* *
11198 AAATTTTAG
127 AAATTTCAA
*
11207 AGAATCTAACATTATATCTCAATCCAACCATTGGATTAAAAGCGAGATTCAAATGTGACAGTTGA
1 AGAATCTAACA-T-TATCTCAATCCAACCATTGGATTAAAAGTGAGATTCAAATGTGACAGTTGA
* * *
11272 TTAAAAACTCATCTTTTCCACATAATATCCAAGATATGTCAGAATATCT-A-AT---A-CAAT-A
64 TTAAAAACTTATCTCTTCCACATAATATCCAAGATATGTCAGAAAATCTAACATAACATCAATAA
11330 ATTTCATA
129 ATTTCA-A
* * * * *
11338 A-AATCTAACCTTATCTCAAACCAACCATTGG-TTTAAATTGAGATTCAAATGTGACTGTTGATT
1 AGAATCTAACATTATCTCAATCCAACCATTGGATTAAAAGTGAGATTCAAATGTGACAGTTGATT
** * * * *
11401 TGAATCGTTATCTCTTCCGACACAATATCCAAGACATGTCAGAAAATCTAACACAACATTCAATA
66 AAAAAC-TTATCTCTTCC-ACATAATATCCAAGATATGTCAGAAAATCTAACATAACA-TCAATA
*
11466 AATTCCAA
128 AATTTCAA
** *
11474 AGAATCTAACATTATCTCAATCCATTCGTTGGATTAAAAGTGAGATTCAAATGT
1 AGAATCTAACATTATCTCAATCCAACCATTGGATTAAAAGTGAGATTCAAATGT
11528 AACCGTTGTT
Statistics
Matches: 267, Mismatches: 37, Indels: 33
0.79 0.11 0.10
Matches are distributed among these distances:
127 31 0.12
128 28 0.10
129 28 0.10
130 15 0.06
131 5 0.02
132 1 0.00
133 1 0.00
134 1 0.00
136 8 0.03
137 41 0.15
138 27 0.10
139 78 0.29
140 3 0.01
ACGTcount: A:0.40, C:0.18, G:0.11, T:0.31
Consensus pattern (135 bp):
AGAATCTAACATTATCTCAATCCAACCATTGGATTAAAAGTGAGATTCAAATGTGACAGTTGATT
AAAAACTTATCTCTTCCACATAATATCCAAGATATGTCAGAAAATCTAACATAACATCAATAAAT
TTCAA
Found at i:11540 original size:137 final size:133
Alignment explanation
Indices: 11024--11550 Score: 445
Period size: 139 Copynumber: 3.9 Consensus size: 133
11014 TTACATACAT
* * * * * **
11024 ACAATACCCAAGAAATGTAATAAAATCTAACACAACATTCAATA---AGAGAATCTAGTATTATC
1 ACAATATCCAAGATATGTCAGAAAATCTAACACAACA-TCAATATTCAAAGAATCTAACATTATC
* * * * *
11086 TCAA-CCTAACCGTTGGATTAAAAGTGAGATTCACATCTGACGGTTGA-TT-AAAAGCTTATCTC
65 TCAATCC-AACCATTGGATTAAAAGTGAGATTCAAATGTGACAGTTGATTTGAAACG-TTATCTC
11148 TTCCAC
128 TTCCAC
* * * * *
11154 ATAATATCCAA-AGTATGTCAAAAAAATCTAACATAACATCAAATAAATTTTAGAGAATCTAACA
1 ACAATATCCAAGA-TATGTC-AGAAAATCTAACACAACATC-AAT--A-TTCAAAGAATCTAACA
* ** *
11218 TTATATCTCAATCCAACCATTGGATTAAAAGCGAGATTCAAATGTGACAGTTGATTAAAAAC-TC
60 -T-TATCTCAATCCAACCATTGGATTAAAAGTGAGATTCAAATGTGACAGTTGATTTGAAACGTT
*
11282 ATCTTTTCCAC
123 ATCTCTTCCAC
* * * *
11293 ATAATATCCAAGATATGTCAGAATATCTAATAC-A-AT-AAT-TTCATAA-AATCTAACCTTATC
1 ACAATATCCAAGATATGTCAGAAAATCTAACACAACATCAATATTCA-AAGAATCTAACATTATC
* * * * *
11353 TCAAACCAACCATTGG-TTTAAATTGAGATTCAAATGTGACTGTTGATTTGAATCGTTATCTCTT
65 TCAATCCAACCATTGGATTAAAAGTGAGATTCAAATGTGACAGTTGATTTGAAACGTTATCTCTT
11417 CCGAC
130 CC-AC
*
11422 ACAATATCCAAGACATGTCAGAAAATCTAACACAACATTCAATAAATTCCAAAGAATCTAACATT
1 ACAATATCCAAGATATGTCAGAAAATCTAACACAACA-TCAAT--ATT-CAAAGAATCTAACATT
** * * * * *
11487 ATCTCAATCCATTCGTTGGATTAAAAGTGAGATTCAAATGTAACCGTTG-TTTGAATCCTTATCT
62 ATCTCAATCCAACCATTGGATTAAAAGTGAGATTCAAATGTGACAGTTGATTTGAAACGTTATCT
11551 GTTTCACAAA
Statistics
Matches: 321, Mismatches: 48, Indels: 49
0.77 0.11 0.12
Matches are distributed among these distances:
127 31 0.10
128 28 0.09
129 33 0.10
130 27 0.08
131 21 0.07
132 1 0.00
133 4 0.01
134 3 0.01
136 6 0.02
137 53 0.17
138 36 0.11
139 71 0.22
140 4 0.01
141 3 0.01
ACGTcount: A:0.40, C:0.19, G:0.11, T:0.31
Consensus pattern (133 bp):
ACAATATCCAAGATATGTCAGAAAATCTAACACAACATCAATATTCAAAGAATCTAACATTATCT
CAATCCAACCATTGGATTAAAAGTGAGATTCAAATGTGACAGTTGATTTGAAACGTTATCTCTTC
CAC
Found at i:16046 original size:17 final size:17
Alignment explanation
Indices: 16024--16060 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
16014 GTAGAAAAAA
*
16024 ATATATCTATACTATAT
1 ATATATATATACTATAT
16041 ATATATATATACTATAT
1 ATATATATATACTATAT
16058 ATA
1 ATA
16061 AAAGTACGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATATATATACTATAT
Found at i:16116 original size:31 final size:31
Alignment explanation
Indices: 16078--16139 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
16068 GAGTTTTGTA
*
16078 AAACTTTTGAATCGCCTATTATATCCTTATT
1 AAACTTTTGAATCGCCTATTATACCCTTATT
*
16109 AAACTTTTGAATCGCCTATTATGCCCTTATT
1 AAACTTTTGAATCGCCTATTATACCCTTATT
16140 TTTTGAATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.27, C:0.21, G:0.08, T:0.44
Consensus pattern (31 bp):
AAACTTTTGAATCGCCTATTATACCCTTATT
Found at i:17407 original size:35 final size:35
Alignment explanation
Indices: 17358--17447 Score: 130
Period size: 35 Copynumber: 2.6 Consensus size: 35
17348 ATAATTTACT
*
17358 AATCCTAATCCAAATCCAATCAATCAAA-T-TAGGAA
1 AATCCTAATCCAAATCCAATCAA--AAACTCTAGAAA
*
17393 AATCCTAATTCAAATCCAATCAAAAACTCTAGAAA
1 AATCCTAATCCAAATCCAATCAAAAACTCTAGAAA
17428 AATCCTAATCCAAATCCAAT
1 AATCCTAATCCAAATCCAAT
17448 TAGGAATTGG
Statistics
Matches: 50, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
33 3 0.06
34 1 0.02
35 46 0.92
ACGTcount: A:0.49, C:0.24, G:0.03, T:0.23
Consensus pattern (35 bp):
AATCCTAATCCAAATCCAATCAAAAACTCTAGAAA
Found at i:17688 original size:29 final size:28
Alignment explanation
Indices: 17653--17719 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 28
17643 TCCACCAACA
17653 GTCAAATAAGTCCATGAACTTA-AATTTTG
1 GTCAAATAAGT-CATGAAC-TACAATTTTG
*
17682 GTCAAATAAGTCTTGAACTACCAATTTTG
1 GTCAAATAAGTCATGAACTA-CAATTTTG
*
17711 GCCAAATAA
1 GTCAAATAA
17720 ACCCTTATGT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
27 2 0.06
28 6 0.18
29 26 0.76
ACGTcount: A:0.39, C:0.16, G:0.13, T:0.31
Consensus pattern (28 bp):
GTCAAATAAGTCATGAACTACAATTTTG
Found at i:18042 original size:29 final size:30
Alignment explanation
Indices: 17978--18044 Score: 91
Period size: 30 Copynumber: 2.3 Consensus size: 30
17968 ATTGCAGAAG
* * * *
17978 GGCTTATCTGGCCAAAATTGGTAGTTTAGG
1 GGCTTATTTGGCCAAAATTGGAAGTTCAGA
18008 GGCTTATTTGGCCAAAATT-GAAGTTCAGA
1 GGCTTATTTGGCCAAAATTGGAAGTTCAGA
18037 GGCTTATT
1 GGCTTATT
18045 GACCGTTGTC
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
29 15 0.45
30 18 0.55
ACGTcount: A:0.25, C:0.13, G:0.27, T:0.34
Consensus pattern (30 bp):
GGCTTATTTGGCCAAAATTGGAAGTTCAGA
Found at i:22215 original size:16 final size:15
Alignment explanation
Indices: 22177--22218 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
22167 ACAGAGATTG
*
22177 ACAGAAAGCAATTAA
1 ACAGAAAACAATTAA
22192 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
22207 ACTAGAAAACAA
1 AC-AGAAAACAA
22219 AGCAAAGTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 16 0.64
16 9 0.36
ACGTcount: A:0.64, C:0.14, G:0.10, T:0.12
Consensus pattern (15 bp):
ACAGAAAACAATTAA
Done.