Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012949.1 Corchorus olitorius cultivar O-4 contig12982, 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: 40980
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.33
Found at i:436 original size:25 final size:25
Alignment explanation
Indices: 408--468 Score: 122
Period size: 25 Copynumber: 2.4 Consensus size: 25
398 TTCCTAAAAC
408 TAGATTCAATTATTTTCTTTTAGCA
1 TAGATTCAATTATTTTCTTTTAGCA
433 TAGATTCAATTATTTTCTTTTAGCA
1 TAGATTCAATTATTTTCTTTTAGCA
458 TAGATTCAATT
1 TAGATTCAATT
469 TTTGTTCTCG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 36 1.00
ACGTcount: A:0.30, C:0.11, G:0.08, T:0.51
Consensus pattern (25 bp):
TAGATTCAATTATTTTCTTTTAGCA
Found at i:2545 original size:7 final size:7
Alignment explanation
Indices: 2533--2557 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
2523 CTGTTCCTTT
2533 TTCAGCA
1 TTCAGCA
2540 TTCAGCA
1 TTCAGCA
2547 TTCAGCA
1 TTCAGCA
2554 TTCA
1 TTCA
2558 TGTGCATTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.28, G:0.12, T:0.32
Consensus pattern (7 bp):
TTCAGCA
Found at i:5186 original size:18 final size:18
Alignment explanation
Indices: 5149--5187 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
5139 AAAGTTTTCA
* *
5149 AAATGGGATTTTGGTTTG
1 AAATGGGATTTTAGTGTG
*
5167 AAATTGGATTTTAGTGTG
1 AAATGGGATTTTAGTGTG
5185 AAA
1 AAA
5188 ACTTTGATTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.28, T:0.41
Consensus pattern (18 bp):
AAATGGGATTTTAGTGTG
Found at i:5619 original size:10 final size:9
Alignment explanation
Indices: 5599--5643 Score: 74
Period size: 9 Copynumber: 5.0 Consensus size: 9
5589 AATTCCCATG
5599 AAATGAAAA
1 AAATGAAAA
5608 AAATGAAAA
1 AAATGAAAA
5617 AAATGAAAAA
1 AAATG-AAAA
5627 AAATG-AAA
1 AAATGAAAA
5635 AAATGAAAA
1 AAATGAAAA
5644 TAAAGGCACT
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
8 8 0.24
9 17 0.50
10 9 0.26
ACGTcount: A:0.78, C:0.00, G:0.11, T:0.11
Consensus pattern (9 bp):
AAATGAAAA
Found at i:6036 original size:6 final size:6
Alignment explanation
Indices: 6020--6066 Score: 51
Period size: 6 Copynumber: 8.0 Consensus size: 6
6010 CAAGAAATTC
* * * *
6020 CAAAAA AAAAAA CAAAAA CAAATA -AAAAA TAAAAA TAAAAA CAAAAA
1 CAAAAA CAAAAA CAAAAA CAAAAA CAAAAA CAAAAA CAAAAA CAAAAA
6067 AATAAAAAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
5 4 0.11
6 31 0.89
ACGTcount: A:0.85, C:0.09, G:0.00, T:0.06
Consensus pattern (6 bp):
CAAAAA
Found at i:6053 original size:23 final size:21
Alignment explanation
Indices: 6021--6076 Score: 76
Period size: 23 Copynumber: 2.5 Consensus size: 21
6011 AAGAAATTCC
6021 AAAAAAAAAAACAAAAACAAA
1 AAAAAAAAAAACAAAAACAAA
*
6042 TAAAAAATAAAAATAAAAACAAA
1 -AAAAAA-AAAAACAAAAACAAA
6065 AAAATAAAAAAA
1 AAAA-AAAAAAA
6077 TACAATTCAA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
22 15 0.48
23 16 0.52
ACGTcount: A:0.88, C:0.05, G:0.00, T:0.07
Consensus pattern (21 bp):
AAAAAAAAAAACAAAAACAAA
Found at i:6073 original size:7 final size:7
Alignment explanation
Indices: 6021--6075 Score: 53
Period size: 7 Copynumber: 7.9 Consensus size: 7
6011 AAGAAATTCC
6021 AAAAAA-
1 AAAAAAT
*
6027 AAAAACAA
1 AAAAA-AT
6035 AAACAAAT
1 AAA-AAAT
6043 AAAAAAT
1 AAAAAAT
6050 -AAAAAT
1 AAAAAAT
6056 AAAAACA-
1 AAAAA-AT
6063 AAAAAAT
1 AAAAAAT
6070 AAAAAA
1 AAAAAA
6076 ATACAATTCA
Statistics
Matches: 42, Mismatches: 1, Indels: 11
0.78 0.02 0.20
Matches are distributed among these distances:
6 12 0.29
7 20 0.48
8 8 0.19
9 2 0.05
ACGTcount: A:0.87, C:0.05, G:0.00, T:0.07
Consensus pattern (7 bp):
AAAAAAT
Found at i:7501 original size:69 final size:69
Alignment explanation
Indices: 7408--7723 Score: 479
Period size: 69 Copynumber: 4.6 Consensus size: 69
7398 TCCGAATGAT
* *
7408 TAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCGGTTTAAGTCTTGGTTCCATCCAAGC
1 TAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTTAAGCCTTGGTTCCATCCAAGC
**
7473 CATG
66 CACA
* * * *
7477 TAGACTTTTCCATAAGTCAAACTCGTTTCCAGACGAGTCAGTTTAAGCCTTGGTTCCATCCAAGC
1 TAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTTAAGCCTTGGTTCCATCCAAGC
7542 CACA
66 CACA
* *
7546 TAGGCTTTTCTACAAGCCAAACTCGTTTCCATACGAGTCAGTTTAAGCCTTCGTTCCATCCAAGC
1 TAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTTAAGCCTTGGTTCCATCCAAGC
7611 CACA
66 CACA
* * *
7615 TAGGCTTTTCTACAAGTCAAACTCGTTTCCATATGAGTCAGTTTAAGCCTTGGTTCCATCCAAGC
1 TAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTTAAGCCTTGGTTCCATCCAAGC
*
7680 CATA
66 CACA
* * *
7684 TAGGTTTTTCCACAGGCCGAACTCGTTTCCATACGAGTCA
1 TAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCA
7724 AGCCTTACTT
Statistics
Matches: 223, Mismatches: 24, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
69 223 1.00
ACGTcount: A:0.25, C:0.28, G:0.17, T:0.30
Consensus pattern (69 bp):
TAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTTAAGCCTTGGTTCCATCCAAGC
CACA
Found at i:8209 original size:99 final size:101
Alignment explanation
Indices: 7986--8244 Score: 315
Period size: 99 Copynumber: 2.6 Consensus size: 101
7976 AAATATTCAT
* * * *
7986 GTTTAAGATCCTTGTTTAAGGTCTCAATTTAAAGTTTGCATTGATAAAACCTCCGGGTACCATTT
1 GTTTAAAATCCTTGTTCAAGGTCTCAATTCAAAGATT-CATTGATAAAACCTCCGGGTACCATTT
* *
8051 CATTTTATCAAGTTTTTTTACCAAAAATTCATGTTTAA
65 CATTTTATCAAG-TTTCTCACCAAAAATTCATGTTTAA
* * * *
8089 GTTTAAAATCCTTGTTCAAGGTCTCTATTCAGAGATT-ATTGATAAAATCTCCTGGTACCATTTC
1 GTTTAAAATCCTTGTTCAAGGTCTCAATTCAAAGATTCATTGATAAAACCTCCGGGTACCATTTC
* *
8153 ATTTTATCAAG-TTCTCATCAAAGATTCATGTTTAA
66 ATTTTATCAAGTTTCTCACCAAAAATTCATGTTTAA
* * * * **
8188 GTTTAAAATCCTTGTTCAAGGTTTCAATTCGAAGTTTGCATTGGTAAGTCCTCCGGG
1 GTTTAAAATCCTTGTTCAAGGTCTCAATTCAAAGATT-CATTGATAAAACCTCCGGG
8245 CACAAATTCA
Statistics
Matches: 132, Mismatches: 22, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
99 52 0.39
101 49 0.37
103 31 0.23
ACGTcount: A:0.29, C:0.17, G:0.15, T:0.40
Consensus pattern (101 bp):
GTTTAAAATCCTTGTTCAAGGTCTCAATTCAAAGATTCATTGATAAAACCTCCGGGTACCATTTC
ATTTTATCAAGTTTCTCACCAAAAATTCATGTTTAA
Found at i:8547 original size:30 final size:30
Alignment explanation
Indices: 8483--8799 Score: 475
Period size: 30 Copynumber: 10.8 Consensus size: 30
8473 ATTGTGTTAG
8483 TTTATTTTAATCCTGGTTGAGGATC---G-
1 TTTATTTTAATCCTGGTTGAGGATCATTGC
** *
8509 -TTATTTTAATCCTGGTTGAGGATTGTTAC
1 TTTATTTTAATCCTGGTTGAGGATCATTGC
** * *
8538 TCCATTTTAATCCTGTTTAAGGATCATTGC
1 TTTATTTTAATCCTGGTTGAGGATCATTGC
8568 TTTATTTTAATCCTGGTTGAGGATCATTGC
1 TTTATTTTAATCCTGGTTGAGGATCATTGC
*
8598 TTTATTTTAATCCTGGTTGAGGATCATTAC
1 TTTATTTTAATCCTGGTTGAGGATCATTGC
*
8628 TTTATTTTAATCCTGTTTGAGGATCATTGC
1 TTTATTTTAATCCTGGTTGAGGATCATTGC
8658 TTTATTTTAATCCTGGTTGAGGATCATTGC
1 TTTATTTTAATCCTGGTTGAGGATCATTGC
*
8688 TTTATTTTAATCCTGGTTGAGGATCATTGT
1 TTTATTTTAATCCTGGTTGAGGATCATTGC
*
8718 TTTGTTTTAATCCTGGTTGAGGATCATTGC
1 TTTATTTTAATCCTGGTTGAGGATCATTGC
*
8748 TTTATTTTAATCCTGGTTGAGGATCGTTGC
1 TTTATTTTAATCCTGGTTGAGGATCATTGC
*
8778 TTTATTTTAATCC-GGTTTAGGA
1 TTTATTTTAATCCTGGTTGAGGA
8800 CCTTTATTTG
Statistics
Matches: 263, Mismatches: 23, Indels: 7
0.90 0.08 0.02
Matches are distributed among these distances:
25 23 0.09
29 8 0.03
30 232 0.88
ACGTcount: A:0.20, C:0.13, G:0.20, T:0.47
Consensus pattern (30 bp):
TTTATTTTAATCCTGGTTGAGGATCATTGC
Found at i:8943 original size:30 final size:30
Alignment explanation
Indices: 8883--8943 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
8873 TGATTGTTTC
* * *
8883 ATTTTATTCCTGATTTAGGATCACTGCTTT
1 ATTTTAATCCTGACTTAGGATCACTACTTT
* *
8913 ATTTTAATCCTGCCTTAGGATCATTACTTT
1 ATTTTAATCCTGACTTAGGATCACTACTTT
8943 A
1 A
8944 AGTTTATTTG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.23, C:0.18, G:0.11, T:0.48
Consensus pattern (30 bp):
ATTTTAATCCTGACTTAGGATCACTACTTT
Found at i:14114 original size:2 final size:2
Alignment explanation
Indices: 14107--14142 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
14097 ATCCAACAAA
*
14107 AT AT AT AT AT AT AT AT TT 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 AT
14143 GTGTTAATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:19547 original size:32 final size:32
Alignment explanation
Indices: 19509--19584 Score: 91
Period size: 32 Copynumber: 2.4 Consensus size: 32
19499 CGCCATTAAA
**
19509 TAGCGGCGTTTCGCAATTCA-AGCGCCGCTATT
1 TAGCGGCGTTTCAAAATTCAGA-CGCCGCTATT
* * *
19541 TAGCGGCGTTTTAAAATTCAGATGCCGTTATT
1 TAGCGGCGTTTCAAAATTCAGACGCCGCTATT
19573 TAGCGGCGTTTC
1 TAGCGGCGTTTC
19585 TGTCTATAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
32 36 0.97
33 1 0.03
ACGTcount: A:0.20, C:0.22, G:0.25, T:0.33
Consensus pattern (32 bp):
TAGCGGCGTTTCAAAATTCAGACGCCGCTATT
Found at i:23460 original size:113 final size:112
Alignment explanation
Indices: 23335--23670 Score: 503
Period size: 113 Copynumber: 3.0 Consensus size: 112
23325 CGTTTTTTAC
* * *
23335 TAGAAACGCCGCTATGTTTTAGCCTCATTTTTACCAAATTTATATTTCCCAAAAAAAAATTAAAT
1 TAGAAACGCCGCTATATTTTTGCCTCATTTTTACC-AATTTATATTTCCAAAAAAAAAATTAAAT
* * * *
23400 ATAGCGGCGTTTCAAACATCAGACGCCCCCATTTAGCGGTGTTTTAGG
65 ATGGCGGCGTTTCCAACATCAGACGCCCCCATTTAGCGGCGTTTTAGA
* *
23448 TAGAAGCGCCGCTAAATTTTTGCCTCATTTTTACCCAATTTATATTT-CAAAAAAAAAATTTAAA
1 TAGAAACGCCGCTATATTTTTGCCTCATTTTTA-CCAATTTATATTTCCAAAAAAAAAA-TTAAA
* *
23512 TATGGCGGCGTTTCCAATATCAGACGCCCCCATTTAGCGGCGTTTGAGA
64 TATGGCGGCGTTTCCAACATCAGACGCCCCCATTTAGCGGCGTTTTAGA
** *
23561 TAGAAACGCCGCTATATTTTTGCCTCATTTTTATCCAATTTATATTTCCTTAAAAAAATTTAAAT
1 TAGAAACGCCGCTATATTTTTGCCTCATTTTTA-CCAATTTATATTTCCAAAAAAAAAATTAAAT
23626 ATGGCGGCGTTTCCAACATCAGACGCCCCCATTTAGCGGCGTTTT
65 ATGGCGGCGTTTCCAACATCAGACGCCCCCATTTAGCGGCGTTTT
23671 GTTTAAATTT
Statistics
Matches: 201, Mismatches: 19, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
112 10 0.05
113 181 0.90
114 10 0.05
ACGTcount: A:0.30, C:0.22, G:0.15, T:0.33
Consensus pattern (112 bp):
TAGAAACGCCGCTATATTTTTGCCTCATTTTTACCAATTTATATTTCCAAAAAAAAAATTAAATA
TGGCGGCGTTTCCAACATCAGACGCCCCCATTTAGCGGCGTTTTAGA
Found at i:23814 original size:19 final size:19
Alignment explanation
Indices: 23790--23833 Score: 88
Period size: 19 Copynumber: 2.3 Consensus size: 19
23780 CAAATGAGCA
23790 AAGACAATTTCAAGGCAAG
1 AAGACAATTTCAAGGCAAG
23809 AAGACAATTTCAAGGCAAG
1 AAGACAATTTCAAGGCAAG
23828 AAGACA
1 AAGACA
23834 GACAAACCAT
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:0.50, C:0.16, G:0.20, T:0.14
Consensus pattern (19 bp):
AAGACAATTTCAAGGCAAG
Found at i:25004 original size:2 final size:2
Alignment explanation
Indices: 24999--25025 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
24989 AATAGCTTCT
24999 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 T
25026 GTAAAGTGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:25283 original size:32 final size:32
Alignment explanation
Indices: 25232--25297 Score: 96
Period size: 32 Copynumber: 2.1 Consensus size: 32
25222 CTAGATTTCA
25232 ATTGTCTGACATTAGTTAATAAATAAAAATAT
1 ATTGTCTGACATTAGTTAATAAATAAAAATAT
* * * *
25264 ATTGTCTGATATTATTTAATACATAAATATAT
1 ATTGTCTGACATTAGTTAATAAATAAAAATAT
25296 AT
1 AT
25298 ACAGTCTAGA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.44, C:0.06, G:0.08, T:0.42
Consensus pattern (32 bp):
ATTGTCTGACATTAGTTAATAAATAAAAATAT
Found at i:27271 original size:32 final size:32
Alignment explanation
Indices: 27227--27292 Score: 105
Period size: 32 Copynumber: 2.1 Consensus size: 32
27217 CTAGATTTCA
*
27227 ATTGTCTTACATTAGTTAATAAATAAATATAT
1 ATTGTCTGACATTAGTTAATAAATAAATATAT
* *
27259 ATTGTCTGACATTATTTAATACATAAATATAT
1 ATTGTCTGACATTAGTTAATAAATAAATATAT
27291 AT
1 AT
27293 ACAGTCTAGA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.42, C:0.08, G:0.06, T:0.44
Consensus pattern (32 bp):
ATTGTCTGACATTAGTTAATAAATAAATATAT
Found at i:27898 original size:16 final size:16
Alignment explanation
Indices: 27874--27904 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
27864 ATACCTATAT
27874 TTAAATCAAGTAAATA
1 TTAAATCAAGTAAATA
*
27890 TTAACTCAAGTAAAT
1 TTAAATCAAGTAAAT
27905 TAATTAAAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.52, C:0.10, G:0.06, T:0.32
Consensus pattern (16 bp):
TTAAATCAAGTAAATA
Found at i:37950 original size:32 final size:32
Alignment explanation
Indices: 37909--37974 Score: 114
Period size: 32 Copynumber: 2.1 Consensus size: 32
37899 CTAGATTTCA
37909 ATTGTCTGACATTAGTTAATAAATAAATATAT
1 ATTGTCTGACATTAGTTAATAAATAAATATAT
* *
37941 ATTGTCTGACATTATTTAATACATAAATATAT
1 ATTGTCTGACATTAGTTAATAAATAAATATAT
37973 AT
1 AT
37975 ACAGTCTAGA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.42, C:0.08, G:0.08, T:0.42
Consensus pattern (32 bp):
ATTGTCTGACATTAGTTAATAAATAAATATAT
Done.