Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023529.1 Corchorus olitorius cultivar O-4 contig23562, 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: 12359
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:675 original size:36 final size:36
Alignment explanation
Indices: 633--722 Score: 171
Period size: 36 Copynumber: 2.5 Consensus size: 36
623 TGTGAATGCA
633 ATGCCTAATTACTAATAATTACTAATGTGAACGATG
1 ATGCCTAATTACTAATAATTACTAATGTGAACGATG
*
669 ATGCCTAATTACTAATAATTACTAATGTGAATGATG
1 ATGCCTAATTACTAATAATTACTAATGTGAACGATG
705 ATGCCTAATTACTAATAA
1 ATGCCTAATTACTAATAA
723 AAAATGCATA
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 53 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (36 bp):
ATGCCTAATTACTAATAATTACTAATGTGAACGATG
Found at i:1011 original size:27 final size:26
Alignment explanation
Indices: 981--1068 Score: 104
Period size: 27 Copynumber: 3.3 Consensus size: 26
971 GTGAATCTAG
*
981 AATGACCAAAATGCCTCCGAACATACA
1 AATGACCAAAATGCC-CCGAACATGCA
* * *
1008 AATGACCGAAATGCCCTTGGACATGCA
1 AATGACCAAAATGCCC-CGAACATGCA
*
1035 AATGACTAAAATGCCCCTGAACATGCA
1 AATGACCAAAATGCCCC-GAACATGCA
1062 AATGACC
1 AATGACC
1069 CCAAAATCCC
Statistics
Matches: 50, Mismatches: 9, Indels: 4
0.79 0.14 0.06
Matches are distributed among these distances:
26 1 0.02
27 49 0.98
ACGTcount: A:0.40, C:0.27, G:0.16, T:0.17
Consensus pattern (26 bp):
AATGACCAAAATGCCCCGAACATGCA
Found at i:4048 original size:108 final size:108
Alignment explanation
Indices: 3915--4145 Score: 385
Period size: 108 Copynumber: 2.2 Consensus size: 108
3905 TATAACAATA
* * * *
3915 AATTTACCCTT-AAAATAAAATTAAAATTTTAATTTGGGGCTAAACCTAGTGAAATTAGTTATAT
1 AATTTACCCTTAAAAATAAAATTAAAATTCTAATTTGAGACTAAACCTAATGAAATTAGTTATAT
*
3979 ATTTTATTTTTAAAACCCTATAACAATAAATTATCAATTTTGG
66 ATTTTATTTCTAAAACCCTATAACAATAAATTATCAATTTTGG
4022 AATTTACCCTTAAAAATAAAATTAAAATTCTAATTTGAGACTAAACCTAATGAAATTAGTTATAT
1 AATTTACCCTTAAAAATAAAATTAAAATTCTAATTTGAGACTAAACCTAATGAAATTAGTTATAT
* *
4087 ATTTTATTTCTAAAACTCTATAACCATAAATTATCAATTTTGG
66 ATTTTATTTCTAAAACCCTATAACAATAAATTATCAATTTTGG
4130 AATTTA-CCTTAAAAAT
1 AATTTACCCTTAAAAAT
4146 TAATTTTTTA
Statistics
Matches: 116, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
107 21 0.18
108 95 0.82
ACGTcount: A:0.43, C:0.11, G:0.06, T:0.39
Consensus pattern (108 bp):
AATTTACCCTTAAAAATAAAATTAAAATTCTAATTTGAGACTAAACCTAATGAAATTAGTTATAT
ATTTTATTTCTAAAACCCTATAACAATAAATTATCAATTTTGG
Found at i:4659 original size:1 final size:1
Alignment explanation
Indices: 4653--4679 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
4643 CTCTTCGTTT
4653 AAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAA
4680 CTCTTTCTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:6520 original size:2 final size:2
Alignment explanation
Indices: 6513--6589 Score: 57
Period size: 2 Copynumber: 43.5 Consensus size: 2
6503 GTTTAACAAT
* *
6513 TA TA TA TA T- TA T- TA TA TA CA TA -A T- TA TA TA TA TC TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
6550 TA T- TA T- TA TA TA TA TA TA TA TA -A TA TA TT TA -A T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6587 TA T
1 TA T
6590 GTAACTAAAC
Statistics
Matches: 59, Mismatches: 6, Indels: 20
0.69 0.07 0.24
Matches are distributed among these distances:
1 10 0.17
2 49 0.83
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:6528 original size:12 final size:12
Alignment explanation
Indices: 6511--6589 Score: 69
Period size: 12 Copynumber: 6.8 Consensus size: 12
6501 CCGTTTAACA
6511 ATTATATATATT
1 ATTATATATATT
* *
6523 ATTATATACATA
1 ATTATATATATT
6535 ATTATATATATCT
1 ATTATATATAT-T
6548 A--ATAT-TATT
1 ATTATATATATT
6557 A-TATATATATAT
1 ATTATATATAT-T
*
6569 ATAATATAT-TT
1 ATTATATATATT
6580 AATTATATAT
1 -ATTATATAT
6590 GTAACTAAAC
Statistics
Matches: 55, Mismatches: 6, Indels: 12
0.75 0.08 0.16
Matches are distributed among these distances:
9 2 0.04
10 7 0.13
11 8 0.15
12 31 0.56
13 7 0.13
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.52
Consensus pattern (12 bp):
ATTATATATATT
Found at i:6586 original size:23 final size:23
Alignment explanation
Indices: 6510--6589 Score: 83
Period size: 23 Copynumber: 3.4 Consensus size: 23
6500 ACCGTTTAAC
* **
6510 AATTATATATATTATTATATACAT
1 AATTATATATA-TATAATATATTT
*
6534 AATTATATATATCTAATAT-TATT
1 AATTATATATATATAATATAT-TT
6557 -ATATATATATATATAATATATTT
1 AAT-TATATATATATAATATATTT
6580 AATTATATAT
1 AATTATATAT
6590 GTAACTAAAC
Statistics
Matches: 47, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
22 2 0.04
23 31 0.66
24 14 0.30
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (23 bp):
AATTATATATATATAATATATTT
Found at i:8591 original size:56 final size:55
Alignment explanation
Indices: 8523--8634 Score: 206
Period size: 56 Copynumber: 2.0 Consensus size: 55
8513 TGTGTTTCCT
8523 TTTCACAAAATAAATGTTATAATAAATCCTATCCCCCTATCTCTACTTAATTATTC
1 TTTCACAAAATAAATGTTATAATAAATCCTAT-CCCCTATCTCTACTTAATTATTC
*
8579 TTTCACACAATAAATGTTATAATAAATCCTATCCCCTATCTCTACTTAATTATTC
1 TTTCACAAAATAAATGTTATAATAAATCCTATCCCCTATCTCTACTTAATTATTC
8634 T
1 T
8635 ACGAAATAAA
Statistics
Matches: 55, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
55 24 0.44
56 31 0.56
ACGTcount: A:0.35, C:0.23, G:0.02, T:0.40
Consensus pattern (55 bp):
TTTCACAAAATAAATGTTATAATAAATCCTATCCCCTATCTCTACTTAATTATTC
Found at i:8647 original size:56 final size:56
Alignment explanation
Indices: 8529--8647 Score: 179
Period size: 56 Copynumber: 2.1 Consensus size: 56
8519 TCCTTTTCAC
* *
8529 AAAATAAATGTTATAATAAATCCTATCCCCCTATCTCTACTTAATTATTCTTTCAC
1 AAAATAAATGTTATAATAAATCCTATCCCCCTATCTCTACTTAATTATTCTTACAA
*
8585 ACAATAAATGTTATAATAAATCCTAT-CCCCTATCTCTACTTAATTATTC-TACGAA
1 AAAATAAATGTTATAATAAATCCTATCCCCCTATCTCTACTTAATTATTCTTAC-AA
8640 ATAAATAA
1 A-AAATAA
8648 TATTTTCTTT
Statistics
Matches: 57, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
54 2 0.04
55 25 0.44
56 30 0.53
ACGTcount: A:0.39, C:0.21, G:0.03, T:0.37
Consensus pattern (56 bp):
AAAATAAATGTTATAATAAATCCTATCCCCCTATCTCTACTTAATTATTCTTACAA
Found at i:8776 original size:41 final size:42
Alignment explanation
Indices: 8698--8779 Score: 139
Period size: 42 Copynumber: 2.0 Consensus size: 42
8688 GCTAAGGATC
8698 ATGATTTGAGTTGAGTATTTCTTAATTAACAAAGAATTTTCT
1 ATGATTTGAGTTGAGTATTTCTTAATTAACAAAGAATTTTCT
* *
8740 ATGATTTGAGTTGAGTATTT-TTAATTTACAGAGAATTTTC
1 ATGATTTGAGTTGAGTATTTCTTAATTAACAAAGAATTTTC
8780 AAGACTTAGG
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
41 18 0.47
42 20 0.53
ACGTcount: A:0.32, C:0.06, G:0.16, T:0.46
Consensus pattern (42 bp):
ATGATTTGAGTTGAGTATTTCTTAATTAACAAAGAATTTTCT
Found at i:10672 original size:28 final size:29
Alignment explanation
Indices: 10636--10713 Score: 88
Period size: 28 Copynumber: 2.8 Consensus size: 29
10626 TTCAAAGTAC
* * *
10636 AAGGTTAAAACTGTAAATTTA-ACCTTCT
1 AAGGGTAAAACGGTAAATTTATACATTCT
*
10664 AAGGGTAAAACGGT-AATTTATTCATTCT
1 AAGGGTAAAACGGTAAATTTATACATTCT
* *
10692 TAGGGTAAAACGGTAATTTTAT
1 AAGGGTAAAACGGTAAATTTAT
10714 GCCCATACAG
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
27 6 0.14
28 30 0.71
29 6 0.14
ACGTcount: A:0.37, C:0.10, G:0.17, T:0.36
Consensus pattern (29 bp):
AAGGGTAAAACGGTAAATTTATACATTCT
Found at i:11522 original size:18 final size:18
Alignment explanation
Indices: 11472--11535 Score: 58
Period size: 18 Copynumber: 3.5 Consensus size: 18
11462 ATTCCTATTT
* *
11472 TCTTCTCTTTTTCTTTTCC
1 TCTTC-CTTTCTCTTTTTC
11491 TCTTCCTTTCTCTTTTTC
1 TCTTCCTTTCTCTTTTTC
* *
11509 T-TTCCTTATGTCTTTTTT
1 TCTTCCTT-TCTCTTTTTC
*
11527 TTTTCCTTT
1 TCTTCCTTT
11536 TTCGGGCCAG
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
17 6 0.15
18 22 0.56
19 11 0.28
ACGTcount: A:0.02, C:0.27, G:0.02, T:0.70
Consensus pattern (18 bp):
TCTTCCTTTCTCTTTTTC
Found at i:11665 original size:15 final size:16
Alignment explanation
Indices: 11631--11728 Score: 67
Period size: 16 Copynumber: 6.2 Consensus size: 16
11621 CTGGACCAAG
*
11631 GCGCGCCAGGCCCAGC
1 GCGCACCAGGCCCAGC
*
11647 GCGCACCAGG-CCTGC
1 GCGCACCAGGCCCAGC
* *
11662 GCGCCAGCTGGCCCAGC
1 GCG-CACCAGGCCCAGC
* * * *
11679 GCACAGCTGGTCCAGC
1 GCGCACCAGGCCCAGC
*
11695 GCGCACCAGG-CCTGC
1 GCGCACCAGGCCCAGC
* *
11710 GCGCGCCAGACCCA-C
1 GCGCACCAGGCCCAGC
11725 GCGC
1 GCGC
11729 CAGGCCTGCT
Statistics
Matches: 65, Mismatches: 14, Indels: 7
0.76 0.16 0.08
Matches are distributed among these distances:
15 24 0.37
16 35 0.54
17 6 0.09
ACGTcount: A:0.14, C:0.47, G:0.34, T:0.05
Consensus pattern (16 bp):
GCGCACCAGGCCCAGC
Found at i:11666 original size:48 final size:47
Alignment explanation
Indices: 11613--11713 Score: 123
Period size: 48 Copynumber: 2.1 Consensus size: 47
11603 TGCTCAGGCC
* *
11613 CGCGCCTGCTGGACCAAGGCGCGC-CAGGCCCAGCGCGCACCAGGCCTG
1 CGCGCCAGCTGG-CCAA-GCGCACACAGGCCCAGCGCGCACCAGGCCTG
* * *
11661 CGCGCCAGCTGGCCCAGCGCACAGCTGGTCCAGCGCGCACCAGGCCTG
1 CGCGCCAGCTGGCCAAGCGCACA-CAGGCCCAGCGCGCACCAGGCCTG
11709 CGCGC
1 CGCGC
11714 GCCAGACCCA
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
46 5 0.11
47 3 0.07
48 38 0.83
ACGTcount: A:0.14, C:0.45, G:0.35, T:0.07
Consensus pattern (47 bp):
CGCGCCAGCTGGCCAAGCGCACACAGGCCCAGCGCGCACCAGGCCTG
Done.