Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012452.1 Corchorus olitorius cultivar O-4 contig12485, 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: 31501
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.32
Found at i:3419 original size:18 final size:18
Alignment explanation
Indices: 3396--3431 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
3386 TTGTTTATAC
3396 CACAATTTACATATTGGG
1 CACAATTTACATATTGGG
*
3414 CACAATTTACATTTTGGG
1 CACAATTTACATATTGGG
3432 TAAAATTCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.36
Consensus pattern (18 bp):
CACAATTTACATATTGGG
Found at i:3438 original size:18 final size:18
Alignment explanation
Indices: 3399--3438 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
3389 TTTATACCAC
*
3399 AATTTACATATTGGGCAC
1 AATTTACATATTGGGCAA
* *
3417 AATTTACATTTTGGGTAA
1 AATTTACATATTGGGCAA
3435 AATT
1 AATT
3439 CTAAATGCAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.35, C:0.10, G:0.15, T:0.40
Consensus pattern (18 bp):
AATTTACATATTGGGCAA
Found at i:4974 original size:48 final size:48
Alignment explanation
Indices: 4835--4974 Score: 156
Period size: 49 Copynumber: 2.9 Consensus size: 48
4825 AGAGCAATCT
* * * *
4835 TTTACATTTCA-TGCACATTCTTCTCAATTTTTACAACAAAATTGAATC
1 TTTACTTTTCATTGCACATTTTTCTCAATTTTTA-TACAAAATTGAATA
* * * *
4883 TTTAATTTTCCTTGCACCTTTTTCTCAATTTTTATGACAAAATTGATTA
1 TTTACTTTTCATTGCACATTTTTCTCAATTTTTAT-ACAAAATTGAATA
* * *
4932 TTTACTTTTCATTGCACTTTTTTATCAATTTTTGTACAAAATT
1 TTTACTTTTCATTGCACATTTTTCTCAATTTTTATACAAAATT
4975 TATTGGCACG
Statistics
Matches: 77, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
48 16 0.21
49 61 0.79
ACGTcount: A:0.29, C:0.17, G:0.05, T:0.49
Consensus pattern (48 bp):
TTTACTTTTCATTGCACATTTTTCTCAATTTTTATACAAAATTGAATA
Found at i:10320 original size:65 final size:65
Alignment explanation
Indices: 10216--10340 Score: 187
Period size: 65 Copynumber: 1.9 Consensus size: 65
10206 GCCTTGTATT
* * **
10216 GATTCCAATTTTCTGCACTAGCCCTTGCATAGGTAGGCCAAGGATACCCCATGCATGGGTTGGAC
1 GATTCAAACTTTCTGCACTAGCCCAGGCATAGGTAGGCCAAGGATACCCCATGCATGGGTTGGAC
* * *
10281 GATTCAAACTTTCTGCACTAGCCCAGGCGTGGGTAGGCCAAGGGTACCCCATGCATGGGT
1 GATTCAAACTTTCTGCACTAGCCCAGGCATAGGTAGGCCAAGGATACCCCATGCATGGGT
10341 AGGAAAAGTT
Statistics
Matches: 53, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
65 53 1.00
ACGTcount: A:0.22, C:0.26, G:0.27, T:0.24
Consensus pattern (65 bp):
GATTCAAACTTTCTGCACTAGCCCAGGCATAGGTAGGCCAAGGATACCCCATGCATGGGTTGGAC
Found at i:11535 original size:21 final size:21
Alignment explanation
Indices: 11509--11549 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
11499 TTTAAACCCT
11509 ATTGGAGATAAGTGGTACTAA
1 ATTGGAGATAAGTGGTACTAA
** *
11530 ATTGGATCTAAGTGTTACTA
1 ATTGGAGATAAGTGGTACTA
11550 CGGTTTTTAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.07, G:0.24, T:0.34
Consensus pattern (21 bp):
ATTGGAGATAAGTGGTACTAA
Found at i:16453 original size:65 final size:65
Alignment explanation
Indices: 16367--16496 Score: 188
Period size: 65 Copynumber: 2.0 Consensus size: 65
16357 GCTTGCTATT
* * ** *
16367 GATTCCAATTTTCTACACTAGCCCTTGCATGGGTAGGCCAAGGGTACCCCATGCATGGGTTGGAC
1 GATTCAAACTTTCTACACTAGCCCAGGCATGGGTAGGCCAAGGGTACCCCATGCATGGGTAGGAC
* * *
16432 GATTCAAACTTTCTGCACTAGCCCAGGCGTGGGTAGTCCAAGGGTACCCCATGCATGGGTAGGAC
1 GATTCAAACTTTCTACACTAGCCCAGGCATGGGTAGGCCAAGGGTACCCCATGCATGGGTAGGAC
16497 CAGTTTTATC
Statistics
Matches: 57, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
65 57 1.00
ACGTcount: A:0.22, C:0.26, G:0.28, T:0.24
Consensus pattern (65 bp):
GATTCAAACTTTCTACACTAGCCCAGGCATGGGTAGGCCAAGGGTACCCCATGCATGGGTAGGAC
Found at i:20780 original size:47 final size:49
Alignment explanation
Indices: 20642--20787 Score: 210
Period size: 49 Copynumber: 3.0 Consensus size: 49
20632 CACTCAAAGC
* * *
20642 AATCTTTACTTTTCCTTGCACCTTTTTCTCAATTTTTACAACAAAATTT
1 AATCTTTACATTTCCTTGCACCTTTTTATCAATTTTTACAACAAAATTG
20691 AATCTTTA-ATTTTCCTTGCACCTTTTTATCAATTTTTACAACAAAATTG
1 AATCTTTACA-TTTCCTTGCACCTTTTTATCAATTTTTACAACAAAATTG
*
20740 AA-CATTTACATTT-CTTGCA-CTTTTTATCAATTTTTGCAACAAAATTG
1 AATC-TTTACATTTCCTTGCACCTTTTTATCAATTTTTACAACAAAATTG
20787 A
1 A
20788 TTGGCACGCT
Statistics
Matches: 90, Mismatches: 4, Indels: 8
0.88 0.04 0.08
Matches are distributed among these distances:
47 28 0.31
48 7 0.08
49 54 0.60
50 1 0.01
ACGTcount: A:0.30, C:0.19, G:0.04, T:0.47
Consensus pattern (49 bp):
AATCTTTACATTTCCTTGCACCTTTTTATCAATTTTTACAACAAAATTG
Found at i:21441 original size:87 final size:88
Alignment explanation
Indices: 21304--21477 Score: 233
Period size: 87 Copynumber: 2.0 Consensus size: 88
21294 TAACCATTTA
* * * * * * *
21304 AAAAACCACAGCCTGAAATTGCTCTGCATAATGACATATCTAATGTTCTGCTATCCCATTATATT
1 AAAAACCACAGCATGAAATTGCCCAGCATAATGACATATATAATGCTCTGCTATACCATTAGATT
* *
21369 GGTTATTAAACATTAGATTTGAC
66 GATTATTAAACATTAAATTTGAC
* *
21392 AAAAA-CACAGCATGAAATTGCCCAGCATAATGGCATATATGATGCTCTGCTATACCATTAGATT
1 AAAAACCACAGCATGAAATTGCCCAGCATAATGACATATATAATGCTCTGCTATACCATTAGATT
*
21456 GATTATTAGACATTAAATTTGA
66 GATTATTAAACATTAAATTTGA
21478 ATCTATGACA
Statistics
Matches: 74, Mismatches: 12, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
87 69 0.93
88 5 0.07
ACGTcount: A:0.36, C:0.18, G:0.14, T:0.32
Consensus pattern (88 bp):
AAAAACCACAGCATGAAATTGCCCAGCATAATGACATATATAATGCTCTGCTATACCATTAGATT
GATTATTAAACATTAAATTTGAC
Found at i:23132 original size:16 final size:17
Alignment explanation
Indices: 23100--23136 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
23090 AATTTTGGGT
*
23100 ACCCGAACCCGAAAATG
1 ACCCAAACCCGAAAATG
23117 ACCCAAACCC-AAAATG
1 ACCCAAACCCGAAAATG
23133 ACCC
1 ACCC
23137 GAACTCGATC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 10 0.53
17 9 0.47
ACGTcount: A:0.43, C:0.41, G:0.11, T:0.05
Consensus pattern (17 bp):
ACCCAAACCCGAAAATG
Found at i:24764 original size:15 final size:17
Alignment explanation
Indices: 24729--24766 Score: 55
Period size: 15 Copynumber: 2.4 Consensus size: 17
24719 AACCGAAAAC
24729 GACCC-AACCCAGAATT
1 GACCCGAACCCAGAATT
24745 GACCCGAACCCA-AA-T
1 GACCCGAACCCAGAATT
24760 GACCCGA
1 GACCCGA
24767 CATTTGAGCG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 8 0.38
16 7 0.33
17 6 0.29
ACGTcount: A:0.37, C:0.39, G:0.16, T:0.08
Consensus pattern (17 bp):
GACCCGAACCCAGAATT
Found at i:25159 original size:58 final size:58
Alignment explanation
Indices: 25089--25207 Score: 238
Period size: 58 Copynumber: 2.1 Consensus size: 58
25079 GAGTTTGTAT
25089 ACGATTCTCCAATAACTATTAACAATATTCTACATTTTCAAGCTACAAATTCCATAAG
1 ACGATTCTCCAATAACTATTAACAATATTCTACATTTTCAAGCTACAAATTCCATAAG
25147 ACGATTCTCCAATAACTATTAACAATATTCTACATTTTCAAGCTACAAATTCCATAAG
1 ACGATTCTCCAATAACTATTAACAATATTCTACATTTTCAAGCTACAAATTCCATAAG
25205 ACG
1 ACG
25208 TTAGATGAAA
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 61 1.00
ACGTcount: A:0.39, C:0.23, G:0.06, T:0.32
Consensus pattern (58 bp):
ACGATTCTCCAATAACTATTAACAATATTCTACATTTTCAAGCTACAAATTCCATAAG
Found at i:25451 original size:19 final size:20
Alignment explanation
Indices: 25423--25461 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
25413 ATAATTTTAA
*
25423 AAAATAAAAAATCAGAAAAT
1 AAAATAAAAAATAAGAAAAT
25443 AAAAT-AAAAATAAGAAAAT
1 AAAATAAAAAATAAGAAAAT
25462 CATGAAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.77, C:0.03, G:0.05, T:0.15
Consensus pattern (20 bp):
AAAATAAAAAATAAGAAAAT
Found at i:25452 original size:28 final size:28
Alignment explanation
Indices: 25422--25484 Score: 94
Period size: 28 Copynumber: 2.3 Consensus size: 28
25412 AATAATTTTA
25422 AAAAATAA-AAAATCA-GAAAATAAAAT
1 AAAAATAAGAAAATCATGAAAATAAAAT
*
25448 AAAAATAAGAAAATCATGAAAATAAAAG
1 AAAAATAAGAAAATCATGAAAATAAAAT
25476 AAATAATAA
1 AAA-AATAA
25485 ATAAATAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
26 8 0.24
27 7 0.21
28 13 0.39
29 5 0.15
ACGTcount: A:0.75, C:0.03, G:0.06, T:0.16
Consensus pattern (28 bp):
AAAAATAAGAAAATCATGAAAATAAAAT
Found at i:25612 original size:11 final size:11
Alignment explanation
Indices: 25596--25620 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
25586 AAACACTAGC
25596 AAAAATTGAAA
1 AAAAATTGAAA
25607 AAAAATTGAAA
1 AAAAATTGAAA
25618 AAA
1 AAA
25621 GGGACGAACT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.76, C:0.00, G:0.08, T:0.16
Consensus pattern (11 bp):
AAAAATTGAAA
Found at i:26066 original size:7 final size:7
Alignment explanation
Indices: 26054--26096 Score: 50
Period size: 7 Copynumber: 5.9 Consensus size: 7
26044 ACGGAGGTTA
26054 AAAAAAT
1 AAAAAAT
26061 AAAAAATTT
1 AAAAAA--T
26070 AAAAAAT
1 AAAAAAT
**
26077 AAAATGT
1 AAAAAAT
26084 AAAAAAT
1 AAAAAAT
26091 AAAAAA
1 AAAAAA
26097 GCAACTGACT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
7 23 0.77
9 7 0.23
ACGTcount: A:0.79, C:0.00, G:0.02, T:0.19
Consensus pattern (7 bp):
AAAAAAT
Found at i:26882 original size:35 final size:35
Alignment explanation
Indices: 26843--26921 Score: 149
Period size: 35 Copynumber: 2.3 Consensus size: 35
26833 TTTTGTTAGA
*
26843 TTTGAGCATGTTTCTGATTTTTCTTTGTGACTATG
1 TTTGAGCATGTTTCTGATTTTGCTTTGTGACTATG
26878 TTTGAGCATGTTTCTGATTTTGCTTTGTGACTATG
1 TTTGAGCATGTTTCTGATTTTGCTTTGTGACTATG
26913 TTTGAGCAT
1 TTTGAGCAT
26922 ATCTAATGTA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
35 43 1.00
ACGTcount: A:0.15, C:0.11, G:0.22, T:0.52
Consensus pattern (35 bp):
TTTGAGCATGTTTCTGATTTTGCTTTGTGACTATG
Found at i:27630 original size:15 final size:15
Alignment explanation
Indices: 27612--27656 Score: 63
Period size: 15 Copynumber: 3.0 Consensus size: 15
27602 TCTGCTACGG
27612 GGCCATCTCATGCAT
1 GGCCATCTCATGCAT
*
27627 GGCCATCTCATGCAG
1 GGCCATCTCATGCAT
* *
27642 GGCCTTCTAATGCAT
1 GGCCATCTCATGCAT
27657 CTCAGCCTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.20, C:0.31, G:0.22, T:0.27
Consensus pattern (15 bp):
GGCCATCTCATGCAT
Found at i:28429 original size:24 final size:25
Alignment explanation
Indices: 28397--28484 Score: 117
Period size: 25 Copynumber: 3.6 Consensus size: 25
28387 AAGGTGCTCA
* *
28397 AACTTTCTG-TTTTTACT-AGTTTAT
1 AACTTTCTGTTTTTTA-TAAGTATCT
*
28421 AACTTTCTGTTTTTTATAAGCATCT
1 AACTTTCTGTTTTTTATAAGTATCT
*
28446 AACTTTCTGTTTTTTATCAGTATCT
1 AACTTTCTGTTTTTTATAAGTATCT
28471 AACTTTCTGTTTTT
1 AACTTTCTGTTTTT
28485 GGTAATTGGG
Statistics
Matches: 57, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
24 10 0.18
25 47 0.82
ACGTcount: A:0.20, C:0.15, G:0.08, T:0.57
Consensus pattern (25 bp):
AACTTTCTGTTTTTTATAAGTATCT
Found at i:29639 original size:15 final size:15
Alignment explanation
Indices: 29619--29657 Score: 69
Period size: 15 Copynumber: 2.6 Consensus size: 15
29609 AAGAAACTCC
29619 CACTGCCCAGCACCA
1 CACTGCCCAGCACCA
*
29634 CACTGCCCAGCACCC
1 CACTGCCCAGCACCA
29649 CACTGCCCA
1 CACTGCCCA
29658 ATCCCCACTG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.23, C:0.56, G:0.13, T:0.08
Consensus pattern (15 bp):
CACTGCCCAGCACCA
Found at i:29665 original size:14 final size:14
Alignment explanation
Indices: 29646--29672 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
29636 CTGCCCAGCA
29646 CCCCACTGCCCAAT
1 CCCCACTGCCCAAT
29660 CCCCACTGCCCAA
1 CCCCACTGCCCAA
29673 CAGTCATCAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.59, G:0.07, T:0.11
Consensus pattern (14 bp):
CCCCACTGCCCAAT
Done.