Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020818.1 Corchorus olitorius cultivar O-4 contig20851, 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: 26892
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.34
Found at i:2181 original size:28 final size:28
Alignment explanation
Indices: 2144--2197 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
2134 ATGGAGTAAG
2144 AAAATAAGATTTTCAAAACTTCTCAAAA
1 AAAATAAGATTTTCAAAACTTCTCAAAA
*
2172 AAAATAAGATTTTTAAAACTTCTCAA
1 AAAATAAGATTTTCAAAACTTCTCAA
2198 GCTGTAACTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.52, C:0.13, G:0.04, T:0.31
Consensus pattern (28 bp):
AAAATAAGATTTTCAAAACTTCTCAAAA
Found at i:4064 original size:2 final size:2
Alignment explanation
Indices: 4057--4085 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
4047 CAAACCCTAG
4057 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 T
4086 TTATTTATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5084 original size:27 final size:27
Alignment explanation
Indices: 5054--5111 Score: 66
Period size: 27 Copynumber: 2.1 Consensus size: 27
5044 TTTTTTATAT
*
5054 ATATTTCTAAATTA-TCATTATTAAAA-A
1 ATATTT-T-AATTATTCATCATTAAAATA
5081 ATATTTTAATTATTTCATCATTAAAATA
1 ATATTTTAATTA-TTCATCATTAAAATA
5109 ATA
1 ATA
5112 GAAATTTATA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
25 5 0.19
26 1 0.04
27 17 0.63
28 4 0.15
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.47
Consensus pattern (27 bp):
ATATTTTAATTATTCATCATTAAAATA
Found at i:6174 original size:24 final size:25
Alignment explanation
Indices: 6118--6175 Score: 75
Period size: 24 Copynumber: 2.4 Consensus size: 25
6108 TTTCAAGCGA
6118 TTGGGCTCTGTTTTTCTTTTTCTTT
1 TTGGGCTCTGTTTTTCTTTTTCTTT
**
6143 TTTTGCTCTG-TTTTCTTGTTT-TTT
1 TTGGGCTCTGTTTTTCTT-TTTCTTT
6167 TTGGGCTCT
1 TTGGGCTCT
6176 ATCATAAACT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
24 17 0.61
25 11 0.39
ACGTcount: A:0.00, C:0.16, G:0.17, T:0.67
Consensus pattern (25 bp):
TTGGGCTCTGTTTTTCTTTTTCTTT
Found at i:6830 original size:21 final size:21
Alignment explanation
Indices: 6806--6855 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
6796 TAAGCAGGAT
**
6806 CAGATGGACGAGCATCAGCGG
1 CAGATGGACGAGCAGAAGCGG
*
6827 CAGATGGACGAGCAGAAGTGG
1 CAGATGGACGAGCAGAAGCGG
6848 CAGATGGA
1 CAGATGGA
6856 TGATTTGAGG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.32, C:0.18, G:0.40, T:0.10
Consensus pattern (21 bp):
CAGATGGACGAGCAGAAGCGG
Found at i:12872 original size:18 final size:19
Alignment explanation
Indices: 12829--12872 Score: 88
Period size: 19 Copynumber: 2.3 Consensus size: 19
12819 AATTCTGATC
12829 AATTTTTCTGATTATTTAG
1 AATTTTTCTGATTATTTAG
12848 AATTTTTCTGATTATTTAG
1 AATTTTTCTGATTATTTAG
12867 AATTTT
1 AATTTT
12873 CCTAACTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.27, C:0.05, G:0.09, T:0.59
Consensus pattern (19 bp):
AATTTTTCTGATTATTTAG
Found at i:12883 original size:18 final size:19
Alignment explanation
Indices: 12841--12883 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
12831 TTTTTCTGAT
* * *
12841 TATTTAGAATTTTTCTGAT
1 TATTTAGAATTTTCCTAAC
12860 TATTTAGAATTTTCCTAAC
1 TATTTAGAATTTTCCTAAC
12879 T-TTTA
1 TATTTA
12884 AAGTATTTCC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 4 0.19
19 17 0.81
ACGTcount: A:0.28, C:0.09, G:0.07, T:0.56
Consensus pattern (19 bp):
TATTTAGAATTTTCCTAAC
Found at i:13332 original size:120 final size:120
Alignment explanation
Indices: 13194--13431 Score: 413
Period size: 120 Copynumber: 2.0 Consensus size: 120
13184 TTTTTTTAGG
* *
13194 CAAATTATACAATACACCGTCAATGGAGTTTAGCAGACTACACAAGCGGGTCTTGAAGGGTGACA
1 CAAATTATACAATACACCGGCAATGGAGTTTAGCAGACTACACAAGCGGGTCCTGAAGGGTGACA
*
13259 TGTGTCCTCTAGGGGCTAGATTGAAATATTTAAAACTTAATTAATTAAAAAAAGA
66 TGTGTCCTCTAGGGACTAGATTGAAATATTTAAAACTTAATTAATTAAAAAAAGA
**
13314 CAAATTATACAATACACCGGCGGTGGAGTTTAGCAGACTACACAAGCGGGTCCTGAAGGGTGACA
1 CAAATTATACAATACACCGGCAATGGAGTTTAGCAGACTACACAAGCGGGTCCTGAAGGGTGACA
* *
13379 TGTGTCCTCTAGGGACTAGATTGAAATATTTTAAACTTAATTAATTCAAAAAA
66 TGTGTCCTCTAGGGACTAGATTGAAATATTTAAAACTTAATTAATTAAAAAAA
13432 TGGACATGTG
Statistics
Matches: 111, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
120 111 1.00
ACGTcount: A:0.37, C:0.16, G:0.21, T:0.26
Consensus pattern (120 bp):
CAAATTATACAATACACCGGCAATGGAGTTTAGCAGACTACACAAGCGGGTCCTGAAGGGTGACA
TGTGTCCTCTAGGGACTAGATTGAAATATTTAAAACTTAATTAATTAAAAAAAGA
Found at i:13551 original size:82 final size:82
Alignment explanation
Indices: 13426--13585 Score: 266
Period size: 82 Copynumber: 2.0 Consensus size: 82
13416 TAATTAATTC
* *
13426 AAAAAATGGACATGTGTCAACTCCATAACCCGCTTGTGGAGTCCAAAATTTACACCGCCGGTGTA
1 AAAAAATGGACATGTGTCAACTCCACAACCCGCTTGTGGAGTCCAAAATTTACACCGCCGATGTA
13491 TCAAATAATTACCCTTA
66 TCAAATAATTACCCTTA
* ***
13508 AAAAAATGGACATGTGTCAACTTCACATTTCGCTTGTGGAGTCCAAAATTTACACCGCCGATGTA
1 AAAAAATGGACATGTGTCAACTCCACAACCCGCTTGTGGAGTCCAAAATTTACACCGCCGATGTA
13573 TCAAATAATTACC
66 TCAAATAATTACC
13586 TTTTTTTTAA
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
82 72 1.00
ACGTcount: A:0.34, C:0.23, G:0.16, T:0.27
Consensus pattern (82 bp):
AAAAAATGGACATGTGTCAACTCCACAACCCGCTTGTGGAGTCCAAAATTTACACCGCCGATGTA
TCAAATAATTACCCTTA
Found at i:14423 original size:14 final size:13
Alignment explanation
Indices: 14404--14442 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
14394 AAATTGTAAA
14404 ATTTAAAAAATTT
1 ATTTAAAAAATTT
* *
14417 CATTTAAGAAATAT
1 -ATTTAAAAAATTT
14431 ATTTAAAAAATT
1 ATTTAAAAAATT
14443 CTAATATATA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
13 10 0.48
14 11 0.52
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.41
Consensus pattern (13 bp):
ATTTAAAAAATTT
Found at i:14672 original size:123 final size:127
Alignment explanation
Indices: 14428--14682 Score: 419
Period size: 131 Copynumber: 2.0 Consensus size: 127
14418 ATTTAAGAAA
14428 TATATTTAAAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAATAAAA
1 TATATTTAAAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAAT---A
*
14493 TAGGTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTGTAAAA
63 TA-GTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAA
14558 G
127 G
14559 TATATTTAAAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAAT-TA-
1 TATATTTAAAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAATATAG
* *
14622 TA-AA-GATATTAGATTTAATTAAATAAAATTAGAGTTTTTAGTTGATTAAAACTATAAAAG
66 TATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAG
14682 T
1 T
14683 TTAAACAATG
Statistics
Matches: 121, Mismatches: 3, Indels: 8
0.92 0.02 0.06
Matches are distributed among these distances:
123 54 0.45
124 2 0.02
125 2 0.02
127 2 0.02
131 61 0.50
ACGTcount: A:0.49, C:0.02, G:0.11, T:0.38
Consensus pattern (127 bp):
TATATTTAAAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAATATAG
TATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAG
Found at i:14708 original size:123 final size:127
Alignment explanation
Indices: 14435--14690 Score: 349
Period size: 123 Copynumber: 2.0 Consensus size: 127
14425 AAATATATTT
* *
14435 AAAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAATAAAATAGGTAT
1 AAAAAATTCTAAGAAATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAAT---ATA-GTAT
* **
14500 AAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTGTAAAAGTATATT
62 AAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAGTATAAA
*
14565 T
127 C
* *
14566 AAAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAAT-TA-TA-AA-G
1 AAAAAATTCTAAGAAATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAATATAGTATAAGG
* * *
14627 ATATTAGATTTAATTAAATAAAATTAGAGTTTTTAGTTGATTAAAACTATAAAAGTTTAAAC
66 ATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAGTATAAAC
14689 AA
1 AA
14691 TGGCATTTAA
Statistics
Matches: 118, Mismatches: 7, Indels: 8
0.89 0.05 0.06
Matches are distributed among these distances:
123 58 0.49
124 2 0.02
125 2 0.02
127 2 0.02
131 54 0.46
ACGTcount: A:0.50, C:0.02, G:0.11, T:0.37
Consensus pattern (127 bp):
AAAAAATTCTAAGAAATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAATATAGTATAAGG
ATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAGTATAAAC
Found at i:17993 original size:28 final size:28
Alignment explanation
Indices: 17953--18006 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
17943 TGAATACAAG
* **
17953 TTCGATTATTCAATGTGCATAGTATAAA
1 TTCGATAATTCAATGCACATAGTATAAA
17981 TTCGATAATTCAATGCACATAGTATA
1 TTCGATAATTCAATGCACATAGTATA
18007 GCCTCATGCG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.37
Consensus pattern (28 bp):
TTCGATAATTCAATGCACATAGTATAAA
Found at i:19681 original size:25 final size:25
Alignment explanation
Indices: 19653--19704 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 25
19643 GTAGTTTTTA
19653 GACTACACAAACGGGTTAAAAGGTT
1 GACTACACAAACGGGTTAAAAGGTT
* *
19678 GACTACATAAGCGGGTTAAAAGGTT
1 GACTACACAAACGGGTTAAAAGGTT
19703 GA
1 GA
19705 TAAGTACTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.38, C:0.13, G:0.27, T:0.21
Consensus pattern (25 bp):
GACTACACAAACGGGTTAAAAGGTT
Found at i:20784 original size:91 final size:92
Alignment explanation
Indices: 20629--20818 Score: 310
Period size: 91 Copynumber: 2.0 Consensus size: 92
20619 CCTTTTATTT
*
20629 TCTTTTAAACATGTCATTCGATTTAGTTCTAATTGTGAAAAGTTGAACTTTAATCATTAGAAATG
1 TCTTTTAAACATGTCATTCGATTTAGTTCTAATTGTGAAAAGTTGAACTTTAATCATCAGAAATG
20694 T-CTACTTTTCTCTAAAATAACTAAAA
66 TACTACTTTTCTCTAAAATAACTAAAA
*
20720 TCTTTTAAACATGTCATTCGATTTAGTTCTAATTGTGAAAAGTTGAACTTTAATCGTCAGAAATG
1 TCTTTTAAACATGTCATTCGATTTAGTTCTAATTGTGAAAAGTTGAACTTTAATCATCAGAAATG
20785 TGAGAGACTACTTTTCTCTAAAATAACTAAAA
66 T-----ACTACTTTTCTCTAAAATAACTAAAA
20817 TC
1 TC
20819 GATTAATTTC
Statistics
Matches: 91, Mismatches: 2, Indels: 6
0.92 0.02 0.06
Matches are distributed among these distances:
91 64 0.70
97 27 0.30
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.39
Consensus pattern (92 bp):
TCTTTTAAACATGTCATTCGATTTAGTTCTAATTGTGAAAAGTTGAACTTTAATCATCAGAAATG
TACTACTTTTCTCTAAAATAACTAAAA
Found at i:26342 original size:340 final size:335
Alignment explanation
Indices: 25719--26892 Score: 1756
Period size: 340 Copynumber: 3.5 Consensus size: 335
25709 TTCATTGGGT
*
25719 ATATGTTTTTACGAGATTCTGAATCTTGTTTCGATTTAATCAGAAATTAATTTGGAAAAAAAATA
1 ATATGTTTTTACGAGCTTCTGAATCTTGTTTCGATTTAATCAGAAATTAATTTGG-AAAAAAATA
* * *
25784 GAAAAAACCATATGTGAAGCATGAAAAGCCGTTAAATCTTTTTGGCGTTGAATTATAAATTTTTT
65 GGAAAAACCATATGTGAAGCATGAAAAGCCCTTAAATCTTTTTGGTGTTGAATTATAAATTTTTT
* * * *
25849 ATGAGTATTATGGCAAAAAATTTAGGAAAACTTTTTCGGTTTAGTTTTTGCAAAATTTTA-ACCG
130 ATGAGTACTATGGCCAAAAATTGAGGAAAAATTTTTCGGTTTAGTTTTTGCAAAATTTTAGA-CG
* * * *
25913 AAATCGTGTACTAAACATCACGGCTTCTGCCT-AAAAACGCGTTCCGGGACCCCGACTTAGTTTT
194 AAATCGTGTACTAAACATCACGGTTTCTGACTGAAAAA-GCGTTCCGGGGCCCCGACTCAGTTTT
* * *
25977 GCATGATTTTTTGGCACCCAGACTCCTTAAAATTTCTAAATTCATCTAATCAAATCTCAGCAACA
258 GCATGATTTTTTGGCACCGAGACTCCTTAAAATTTATATATTCATCTAATCAAATCTCAGCAACA
26042 CTGGACTTAAGGATATGG
323 CTGGACTT----ATA-GG
* * *
26060 ATATGTTTTTACGACCTTCTGATTCTTGTTTCGATTTAATCATAAATTAATTTGGAAAAAAATAG
1 ATATGTTTTTACGAGCTTCTGAATCTTGTTTCGATTTAATCAGAAATTAATTTGGAAAAAAATAG
* * *
26125 GAAAAACTATATGTGAAGCATGAAAACCCCTTAAATCTTTTTGGTGTTGAATTATAAATTTTTGA
66 GAAAAACCATATGTGAAGCATGAAAAGCCCTTAAATCTTTTTGGTGTTGAATTATAAATTTTTTA
* * *
26190 TGAGTACTGTGGCCAAATATTGAGGAAAAATTTTTCGGTTCAGTTTTTGCAAAATTTTAGACGAA
131 TGAGTACTATGGCCAAAAATTGAGGAAAAATTTTTCGGTTTAGTTTTTGCAAAATTTTAGACGAA
*
26255 ATCGTGTACTAAACATCACGGTTTCTGACTGAAAAAGCGTTCCGGGGCCCAGACTCAGTTTTGCA
196 ATCGTGTACTAAACATCACGGTTTCTGACTGAAAAAGCGTTCCGGGGCCCCGACTCAGTTTTGCA
26320 TGATTTTTTGGCACCGAGACTCCTTGAAAA-TTATATATTCATCTAATCAAATCTCAGCAACACT
261 TGATTTTTTGGCACCGAGACTCCTT-AAAATTTATATATTCATCTAATCAAATCTCAGCAACACT
*
26384 GGACCTA-AGG
325 GGACTTATAGG
*
26394 ATATGTTTTTACGAGCTTCTGAATCTTGTTTCGATTTAATCAGAAATAAATTTGGAAAAAAATAG
1 ATATGTTTTTACGAGCTTCTGAATCTTGTTTCGATTTAATCAGAAATTAATTTGGAAAAAAATAG
*
26459 GAAAAACCATATGTGAAGCATGAAAAGCCCTTAAATCTTTTTGGTCTTGAATTATAAATTTTTTA
66 GAAAAACCATATGTGAAGCATGAAAAGCCCTTAAATCTTTTTGGTGTTGAATTATAAATTTTTTA
* * * * *
26524 TGAGTACTATGGCCAAAAATTGAGGAAAAA-TTTTCGATTTAGTTTTTGCAACATATTAGCCCAA
131 TGAGTACTATGGCCAAAAATTGAGGAAAAATTTTTCGGTTTAGTTTTTGCAAAATTTTAGACGAA
* * * * * *
26588 ATTGTGTACTAACCATCACGGTTTCTGGCTGAAAACGCGTTCCGGGGCCCCGACTCAGTTTCGTA
196 ATCGTGTACTAAACATCACGGTTTCTGACTGAAAAAGCGTTCCGGGGCCCCGACTCAGTTTTGCA
** * * *
26653 TGA-TTTTTGGCACCGAGACTCCTTGTAATATATATTTTCATCTAATCAAGTCTCAGCAACACTG
261 TGATTTTTTGGCACCGAGACTCCTTAAAATTTATATATTCATCTAATCAAATCTCAGCAACACTG
26717 GA-TT-TCAGG
326 GACTTAT-AGG
26726 ATATGTTTTTACGAGCTTCTGAATCTTGTTTCGATTTAATCAGAAATTAATTTGG-AAAAAATAG
1 ATATGTTTTTACGAGCTTCTGAATCTTGTTTCGATTTAATCAGAAATTAATTTGGAAAAAAATAG
*
26790 GAAAAACCATATATGAAGCATGAAAAGCCCTTAAATCTTTTTGGTGTTGAATTATAAATTTTTTA
66 GAAAAACCATATGTGAAGCATGAAAAGCCCTTAAATCTTTTTGGTGTTGAATTATAAATTTTTTA
** *
26855 TGAGTACTGGGGCCAAAAATTGA-GAAAAATCTTTCGGT
131 TGAGTACTATGGCCAAAAATTGAGGAAAAATTTTTCGGT
Statistics
Matches: 764, Mismatches: 62, Indels: 24
0.90 0.07 0.03
Matches are distributed among these distances:
330 6 0.01
331 102 0.13
332 112 0.15
333 89 0.12
334 152 0.20
335 1 0.00
336 1 0.00
340 240 0.31
341 61 0.08
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Consensus pattern (335 bp):
ATATGTTTTTACGAGCTTCTGAATCTTGTTTCGATTTAATCAGAAATTAATTTGGAAAAAAATAG
GAAAAACCATATGTGAAGCATGAAAAGCCCTTAAATCTTTTTGGTGTTGAATTATAAATTTTTTA
TGAGTACTATGGCCAAAAATTGAGGAAAAATTTTTCGGTTTAGTTTTTGCAAAATTTTAGACGAA
ATCGTGTACTAAACATCACGGTTTCTGACTGAAAAAGCGTTCCGGGGCCCCGACTCAGTTTTGCA
TGATTTTTTGGCACCGAGACTCCTTAAAATTTATATATTCATCTAATCAAATCTCAGCAACACTG
GACTTATAGG
Done.