Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016428.1 Corchorus capsularis cultivar CVL-1 contig16449, 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: 84727
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Found at i:326 original size:18 final size:18
Alignment explanation
Indices: 303--339 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
293 TCTTGTTGTT
303 CTGACATTTTCTGATGTA
1 CTGACATTTTCTGATGTA
*
321 CTGACATTTTGTGATGTA
1 CTGACATTTTCTGATGTA
339 C
1 C
340 CATGGATAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.22, C:0.16, G:0.19, T:0.43
Consensus pattern (18 bp):
CTGACATTTTCTGATGTA
Found at i:2534 original size:15 final size:15
Alignment explanation
Indices: 2516--2545 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2506 TTGAAAGGAA
*
2516 TGGTGATGTTGATGG
1 TGGTGATGATGATGG
2531 TGGTGATGATGATGG
1 TGGTGATGATGATGG
2546 ATGATGATAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.17, C:0.00, G:0.47, T:0.37
Consensus pattern (15 bp):
TGGTGATGATGATGG
Found at i:5589 original size:12 final size:11
Alignment explanation
Indices: 5569--5598 Score: 51
Period size: 12 Copynumber: 2.6 Consensus size: 11
5559 TCGAGCTCTG
5569 TTTTTTTTTTC
1 TTTTTTTTTTC
5580 TTTTTCTTTTTC
1 TTTTT-TTTTTC
5592 TTTTTTT
1 TTTTTTT
5599 AAGATTTTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (11 bp):
TTTTTTTTTTC
Found at i:7950 original size:50 final size:50
Alignment explanation
Indices: 7896--7995 Score: 164
Period size: 50 Copynumber: 2.0 Consensus size: 50
7886 ATTCTCTTTT
* *
7896 GTTATCTGTGATGATTGCTATAATGCAATTTATTAAATATTCTACCATCA
1 GTTATCTGTGATGATTGCTATAATGCAAGTAATTAAATATTCTACCATCA
* *
7946 GTTATCTGTGATGATTGCTATAATGGAAGTAATTGAATATTCTACCATCA
1 GTTATCTGTGATGATTGCTATAATGCAAGTAATTAAATATTCTACCATCA
7996 TTTTGAGAAG
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
50 46 1.00
ACGTcount: A:0.32, C:0.13, G:0.15, T:0.40
Consensus pattern (50 bp):
GTTATCTGTGATGATTGCTATAATGCAAGTAATTAAATATTCTACCATCA
Found at i:8775 original size:67 final size:68
Alignment explanation
Indices: 8648--8782 Score: 245
Period size: 67 Copynumber: 2.0 Consensus size: 68
8638 TAACTAACAA
8648 ATTATTATTCTATAATGATAAATCTTAAAGAGTAAATCGTGAGTCTTTCAAATGATTGATCTCAT
1 ATTATTATTCTATAATGATAAATCTTAAAGAGTAAATCGTGAGTCTTTCAAATGATTGATCTCAT
8713 GGT
66 GGT
* *
8716 ATTATTATTCTATAATGATAAATCTTAAA-AGTAAGTCGTGAGTCTTTTAAATGATTGATCTCAT
1 ATTATTATTCTATAATGATAAATCTTAAAGAGTAAATCGTGAGTCTTTCAAATGATTGATCTCAT
8780 GGT
66 GGT
8783 CAGATGAAGC
Statistics
Matches: 65, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
67 36 0.55
68 29 0.45
ACGTcount: A:0.35, C:0.10, G:0.15, T:0.41
Consensus pattern (68 bp):
ATTATTATTCTATAATGATAAATCTTAAAGAGTAAATCGTGAGTCTTTCAAATGATTGATCTCAT
GGT
Found at i:9942 original size:33 final size:34
Alignment explanation
Indices: 9900--9975 Score: 120
Period size: 33 Copynumber: 2.3 Consensus size: 34
9890 CAAACTGGTG
*
9900 GTGGCTTTGGGAG-CTTTGGTTCAGGTCGTTCTA
1 GTGGATTTGGGAGACTTTGGTTCAGGTCGTTCTA
9933 GTGGATTT-GGAGACTTTGGTTCAGGTCGTTCTA
1 GTGGATTTGGGAGACTTTGGTTCAGGTCGTTCTA
*
9966 CTGGATTTGG
1 GTGGATTTGG
9976 TGATCGTTCA
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
32 4 0.10
33 34 0.87
34 1 0.03
ACGTcount: A:0.12, C:0.13, G:0.36, T:0.39
Consensus pattern (34 bp):
GTGGATTTGGGAGACTTTGGTTCAGGTCGTTCTA
Found at i:12777 original size:17 final size:19
Alignment explanation
Indices: 12755--12791 Score: 60
Period size: 17 Copynumber: 2.1 Consensus size: 19
12745 TTTTAATTAC
12755 ATTATGATC-TT-TTATAA
1 ATTATGATCATTATTATAA
12772 ATTATGATCATTATTATAA
1 ATTATGATCATTATTATAA
12791 A
1 A
12792 AGGAGACTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 9 0.50
18 2 0.11
19 7 0.39
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.49
Consensus pattern (19 bp):
ATTATGATCATTATTATAA
Found at i:23132 original size:19 final size:19
Alignment explanation
Indices: 23108--23145 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
23098 GGCATGAATT
23108 AAAAAAGAAAAAATAAACG
1 AAAAAAGAAAAAATAAACG
* *
23127 AAAAAAGAAGAACTAAACG
1 AAAAAAGAAAAAATAAACG
23146 GGAAGAATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.74, C:0.08, G:0.13, T:0.05
Consensus pattern (19 bp):
AAAAAAGAAAAAATAAACG
Found at i:24566 original size:19 final size:19
Alignment explanation
Indices: 24542--24579 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
24532 GGCAGGAATT
24542 AAAAAAGAAAAAATAAACG
1 AAAAAAGAAAAAATAAACG
* *
24561 AAAAAAGAAGAACTAAACG
1 AAAAAAGAAAAAATAAACG
24580 GGAAGAATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.74, C:0.08, G:0.13, T:0.05
Consensus pattern (19 bp):
AAAAAAGAAAAAATAAACG
Found at i:25114 original size:20 final size:20
Alignment explanation
Indices: 25091--25129 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
25081 ACAAAGGTCC
25091 ACCCCTCCAAAACCCTCCAT
1 ACCCCTCCAAAACCCTCCAT
*
25111 ACCCCTCCAAAACCTTCCA
1 ACCCCTCCAAAACCCTCCA
25130 ACCAAACGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.31, C:0.54, G:0.00, T:0.15
Consensus pattern (20 bp):
ACCCCTCCAAAACCCTCCAT
Found at i:28206 original size:2 final size:2
Alignment explanation
Indices: 28199--28232 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
28189 CTTGAACTGC
28199 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
28233 TCCCATTCAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:30125 original size:11 final size:11
Alignment explanation
Indices: 30109--30138 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
30099 TATACTATAT
30109 CTAATTAATAC
1 CTAATTAATAC
*
30120 CTAATTAATAT
1 CTAATTAATAC
30131 CTAATTAA
1 CTAATTAA
30139 CAGTTAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.47, C:0.13, G:0.00, T:0.40
Consensus pattern (11 bp):
CTAATTAATAC
Found at i:30146 original size:22 final size:22
Alignment explanation
Indices: 30105--30151 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
30095 CCATTATACT
*
30105 ATATCTAATTAATACCTAATTA
1 ATATCTAATTAACACCTAATTA
**
30127 ATATCTAATTAACAGTTAATTA
1 ATATCTAATTAACACCTAATTA
30149 ATA
1 ATA
30152 ATGAATAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.47, C:0.11, G:0.02, T:0.40
Consensus pattern (22 bp):
ATATCTAATTAACACCTAATTA
Found at i:37323 original size:12 final size:13
Alignment explanation
Indices: 37302--37330 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
37292 TATTTGACTA
37302 TTTTCATTTTTCT
1 TTTTCATTTTTCT
37315 TTTTC-TTTTTCT
1 TTTTCATTTTTCT
37327 TTTT
1 TTTT
37331 TTAGAAAGTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.03, C:0.14, G:0.00, T:0.83
Consensus pattern (13 bp):
TTTTCATTTTTCT
Found at i:39143 original size:11 final size:11
Alignment explanation
Indices: 39127--39169 Score: 59
Period size: 11 Copynumber: 3.9 Consensus size: 11
39117 TATATTATAT
39127 CTAATTAATAG
1 CTAATTAATAG
*
39138 CTAATTAATAT
1 CTAATTAATAG
*
39149 CCAATTAATAG
1 CTAATTAATAG
*
39160 TTAATTAATA
1 CTAATTAATA
39170 ATGAATAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
11 27 1.00
ACGTcount: A:0.47, C:0.09, G:0.05, T:0.40
Consensus pattern (11 bp):
CTAATTAATAG
Found at i:39148 original size:22 final size:22
Alignment explanation
Indices: 39123--39169 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
39113 CCATTATATT
*
39123 ATATCTAATTAATAGCTAATTA
1 ATATCCAATTAATAGCTAATTA
*
39145 ATATCCAATTAATAGTTAATTA
1 ATATCCAATTAATAGCTAATTA
39167 ATA
1 ATA
39170 ATGAATAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.47, C:0.09, G:0.04, T:0.40
Consensus pattern (22 bp):
ATATCCAATTAATAGCTAATTA
Found at i:61068 original size:27 final size:28
Alignment explanation
Indices: 61032--61085 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 28
61022 ATCAAACAAG
* *
61032 AAATTAAACATGCCATAATTTCATAAGA
1 AAATTAAACATACCATAATTCCATAAGA
*
61060 AAATT-AACATACCATGATTCCATAAG
1 AAATTAAACATACCATAATTCCATAAG
61086 CAAGACCCTG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 18 0.78
28 5 0.22
ACGTcount: A:0.48, C:0.17, G:0.07, T:0.28
Consensus pattern (28 bp):
AAATTAAACATACCATAATTCCATAAGA
Found at i:72961 original size:3 final size:3
Alignment explanation
Indices: 72953--72994 Score: 75
Period size: 3 Copynumber: 14.0 Consensus size: 3
72943 ATTAACACCC
*
72953 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTG CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
72995 TTCCCTTACA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.00, C:0.33, G:0.02, T:0.64
Consensus pattern (3 bp):
CTT
Found at i:76695 original size:22 final size:22
Alignment explanation
Indices: 76653--76696 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
76643 TCAAGTGTTT
* *
76653 GTGGTTGGTGATGCGTGACATA
1 GTGGTTGGTGATGCATCACATA
*
76675 GTGGTTGGTGATGTATCACATA
1 GTGGTTGGTGATGCATCACATA
76697 ATGAGGTAGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.20, C:0.09, G:0.36, T:0.34
Consensus pattern (22 bp):
GTGGTTGGTGATGCATCACATA
Found at i:80363 original size:8 final size:7
Alignment explanation
Indices: 80331--80366 Score: 63
Period size: 7 Copynumber: 5.0 Consensus size: 7
80321 TTTGCTAATG
80331 CAAAACC
1 CAAAACC
80338 CAAAACC
1 CAAAACC
80345 CAAAACC
1 CAAAACC
80352 CAAAACCC
1 CAAAA-CC
80360 CAAAACC
1 CAAAACC
80367 AAATCCAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
7 21 0.75
8 7 0.25
ACGTcount: A:0.56, C:0.44, G:0.00, T:0.00
Consensus pattern (7 bp):
CAAAACC
Done.