Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010962.1 Corchorus capsularis cultivar CVL-1 contig10983, 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: 34455
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Found at i:6002 original size:2 final size:2
Alignment explanation
Indices: 5995--6025 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
5985 TGTTCTACTA
5995 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
6026 CACACACGTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:7414 original size:26 final size:26
Alignment explanation
Indices: 7378--7430 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
7368 GAAATAAACC
7378 TGAGGTATAATATAATGCAATTTCAT
1 TGAGGTATAATATAATGCAATTTCAT
7404 TGAGGTATAATATAATGCAATTTCAT
1 TGAGGTATAATATAATGCAATTTCAT
7430 T
1 T
7431 CGAAGACTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.38, C:0.08, G:0.15, T:0.40
Consensus pattern (26 bp):
TGAGGTATAATATAATGCAATTTCAT
Found at i:10055 original size:146 final size:146
Alignment explanation
Indices: 9791--10061 Score: 418
Period size: 146 Copynumber: 1.9 Consensus size: 146
9781 ATTATAGTAA
* **
9791 AATAAAATTTAAATTTAAGTTAAAATATAATTCGTTCAGTTAACCGAAATATTTCGGTTCGGCTA
1 AATAAAATTTAAATTTAAGTCAAAATATAATTCAATCAGTTAACCGAAATATTTCGGTTCGGCTA
* * * *
9856 ATGTTCGGAATAGTAAACTTTGATTCGGTTAATGTTTTACAAAAATAGTATTCGGTTCATTCGGT
66 ATATTCAGAATAGGAAACTTAGATTCGGTTAATGTTTTACAAAAATAGTATTCGGTTCATTCGGT
9921 TAATACTAATTCGGTT
131 TAATACTAATTCGGTT
* * * * *
9937 AATAAATTTTAAATTTAAGTCAAAATATTATTCAATCGGTTAACCGAAATATTTCGTTTCGGTTA
1 AATAAAATTTAAATTTAAGTCAAAATATAATTCAATCAGTTAACCGAAATATTTCGGTTCGGCTA
10002 ATATTCAGAATAGGAAACTTCAG-TTCGGTTAATGTTTTACAAAAATAGTATTCGGTTCAT
66 ATATTCAGAATAGGAAACTT-AGATTCGGTTAATGTTTTACAAAAATAGTATTCGGTTCAT
10062 AAATTTTAAA
Statistics
Matches: 112, Mismatches: 12, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
146 111 0.99
147 1 0.01
ACGTcount: A:0.35, C:0.11, G:0.15, T:0.39
Consensus pattern (146 bp):
AATAAAATTTAAATTTAAGTCAAAATATAATTCAATCAGTTAACCGAAATATTTCGGTTCGGCTA
ATATTCAGAATAGGAAACTTAGATTCGGTTAATGTTTTACAAAAATAGTATTCGGTTCATTCGGT
TAATACTAATTCGGTT
Found at i:10110 original size:121 final size:123
Alignment explanation
Indices: 9929--10164 Score: 325
Period size: 122 Copynumber: 1.9 Consensus size: 123
9919 GTTAATACTA
* * *
9929 ATTCGGTTAATAAATTTTAAATTTAAGTCAAAATATTATTCAATCGGTTAACCGAAATA-TTTC-
1 ATTCGGTTAATAAATTTTAAATTTAAGTCAAAATATAATCCAATCGATTAACCGAAATATTTTCG
*
9992 GTTTCGGTTAATATTCAGAATAGGAAACTTCAGTTCGGTTAATGTTTTACAAAAATAGT
66 GTTT-GATTAATATTCAGAATAGGAAACTTCAGTTCGGTTAATGTTTTACAAAAATAGT
* * ** *
10051 ATTCGGTTCATAAATTTTAAA-TTAAGTTAAAATATAATCCGGTCGATTAATCGAAATATTTTCG
1 ATTCGGTTAATAAATTTTAAATTTAAGTCAAAATATAATCCAATCGATTAACCGAAATATTTTCG
* * * *
10115 GTTTGATTAATGTTCGGAATAGGATACTTCGGTTCGGTTAATGTTTTACA
66 GTTTGATTAATATTCAGAATAGGAAACTTCAGTTCGGTTAATGTTTTACA
10165 GTTTGGGTAA
Statistics
Matches: 99, Mismatches: 13, Indels: 4
0.85 0.11 0.03
Matches are distributed among these distances:
121 30 0.30
122 65 0.66
123 4 0.04
ACGTcount: A:0.34, C:0.11, G:0.16, T:0.39
Consensus pattern (123 bp):
ATTCGGTTAATAAATTTTAAATTTAAGTCAAAATATAATCCAATCGATTAACCGAAATATTTTCG
GTTTGATTAATATTCAGAATAGGAAACTTCAGTTCGGTTAATGTTTTACAAAAATAGT
Found at i:10285 original size:2 final size:2
Alignment explanation
Indices: 10278--10319 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
10268 ATTTGCTTCA
*
10278 AT AT AT AT AC 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 AT AT AT AT
10320 GAGTAATTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:14457 original size:27 final size:27
Alignment explanation
Indices: 14411--14469 Score: 91
Period size: 27 Copynumber: 2.2 Consensus size: 27
14401 TGCTAGTTGC
**
14411 TAATGATGTGAATCTTTTTAGATTGAT
1 TAATGATGTGAATCCATTTAGATTGAT
*
14438 TAATGATGTGGATCCATTTAGATTGAT
1 TAATGATGTGAATCCATTTAGATTGAT
14465 TAATG
1 TAATG
14470 TTTGTTCTAG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.31, C:0.05, G:0.20, T:0.44
Consensus pattern (27 bp):
TAATGATGTGAATCCATTTAGATTGAT
Found at i:17989 original size:1 final size:1
Alignment explanation
Indices: 17983--18018 Score: 72
Period size: 1 Copynumber: 36.0 Consensus size: 1
17973 CAAGGAGGAA
17983 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
18019 GAGATACAAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 35 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:18157 original size:30 final size:32
Alignment explanation
Indices: 18123--18192 Score: 108
Period size: 33 Copynumber: 2.2 Consensus size: 32
18113 AATTTGCAAA
*
18123 TAATTGTT-TTTTTTT-ATCGAAAAACAATTG
1 TAATTGTTATTTTTTTAACCGAAAAACAATTG
18153 TAATTGTTATTTTTTTAGACCGAAAAACAATTG
1 TAATTGTTATTTTTTTA-ACCGAAAAACAATTG
18186 TAATTGT
1 TAATTGT
18193 AATCGTTCAA
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
30 8 0.22
31 7 0.19
33 21 0.58
ACGTcount: A:0.34, C:0.07, G:0.11, T:0.47
Consensus pattern (32 bp):
TAATTGTTATTTTTTTAACCGAAAAACAATTG
Found at i:22609 original size:43 final size:42
Alignment explanation
Indices: 22561--22724 Score: 145
Period size: 43 Copynumber: 3.9 Consensus size: 42
22551 ACCCAATAAC
*
22561 CAAAGTCCCTAAACACAATTCTAACACAGGGGCAACTCTCTTT
1 CAAAGT-CCTAAACACAATTCTAACACAGAGGCAACTCTCTTT
* *
22604 CAAAGTCCTCAAACAC-ATTCTTAACACAGAGGC-ACTC-ATAT
1 CAAAGTCCT-AAACACAATTC-TAACACAGAGGCAACTCTCTTT
* ** * * * *
22645 CAAAGTCCCCAAGTACAATTTTAACATAGGGGCAATTCTCTTT
1 CAAAGT-CCTAAACACAATTCTAACACAGAGGCAACTCTCTTT
* * *
22688 AAAAGTCCTAAAGCACATTTTTAACACAGAGGCAACT
1 CAAAGTCCTAAA-CACAATTCTAACACAGAGGCAACT
22725 ATATCGAAGT
Statistics
Matches: 94, Mismatches: 20, Indels: 14
0.73 0.16 0.11
Matches are distributed among these distances:
41 22 0.23
42 23 0.24
43 49 0.52
ACGTcount: A:0.37, C:0.26, G:0.12, T:0.24
Consensus pattern (42 bp):
CAAAGTCCTAAACACAATTCTAACACAGAGGCAACTCTCTTT
Found at i:22664 original size:84 final size:84
Alignment explanation
Indices: 22561--22737 Score: 241
Period size: 84 Copynumber: 2.1 Consensus size: 84
22551 ACCCAATAAC
* *
22561 CAAAGTCCCTAAACACAATTCTAACACAGGGGCAACTCTCTTTCAAAGTCCTCAAA-CACATTCT
1 CAAAGTCCCCAAACACAATTCTAACACAGGGGCAACTCTCTTTAAAAGTCCT-AAAGCACATTCT
22625 TAACACAGAGGC-ACTCATAT
65 TAACACAGAGGCAACT-ATAT
** * * * *
22645 CAAAGTCCCCAAGTACAATTTTAACATAGGGGCAATTCTCTTTAAAAGTCCTAAAGCACATTTTT
1 CAAAGTCCCCAAACACAATTCTAACACAGGGGCAACTCTCTTTAAAAGTCCTAAAGCACATTCTT
22710 AACACAGAGGCAACTATAT
66 AACACAGAGGCAACTATAT
*
22729 CGAAGTCCC
1 CAAAGTCCC
22738 TAACCACATG
Statistics
Matches: 82, Mismatches: 9, Indels: 4
0.86 0.09 0.04
Matches are distributed among these distances:
83 3 0.04
84 76 0.93
85 3 0.04
ACGTcount: A:0.37, C:0.27, G:0.12, T:0.24
Consensus pattern (84 bp):
CAAAGTCCCCAAACACAATTCTAACACAGGGGCAACTCTCTTTAAAAGTCCTAAAGCACATTCTT
AACACAGAGGCAACTATAT
Found at i:25918 original size:21 final size:21
Alignment explanation
Indices: 25877--25918 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
25867 GGTAATCAAG
* *
25877 AGTTTTTAAGATTTAAACAGA
1 AGTTTTCAAGATTCAAACAGA
25898 AGTTTTCAA-ATTCAAATCAGA
1 AGTTTTCAAGATTCAAA-CAGA
25919 CTTAGTTTCA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.43, C:0.10, G:0.12, T:0.36
Consensus pattern (21 bp):
AGTTTTCAAGATTCAAACAGA
Found at i:32684 original size:89 final size:87
Alignment explanation
Indices: 32530--32694 Score: 206
Period size: 89 Copynumber: 1.9 Consensus size: 87
32520 GATGATTTGA
* * ***
32530 TTCAAGGGTCTTGACGACCTGATCTTGAATGAACAAAAATAATCTTATTCAAATATGTTGATGAA
1 TTCAAGGGTCTTGAAGACCTGATCTTGAACGAACAAAAATAATCTTATTCAAATAAACTGATGAA
*
32595 GATCAAAATAAAACAAATCCGG
66 GACCAAAATAAAACAAATCCGG
* * * *
32617 TTCAAGGGTCCTTGATAGACTTGAT-TTGGAACGAACAAAAATAATCTTCTTCAAGTAAACTGGT
1 TTCAAGGGT-CTTGA-AGACCTGATCTT-GAACGAACAAAAATAATCTTATTCAAATAAACTGAT
32681 GAAGACCAAAATAA
63 GAAGACCAAAATAA
32695 TGATTTCTTG
Statistics
Matches: 65, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
87 9 0.14
88 7 0.11
89 49 0.75
ACGTcount: A:0.41, C:0.15, G:0.17, T:0.27
Consensus pattern (87 bp):
TTCAAGGGTCTTGAAGACCTGATCTTGAACGAACAAAAATAATCTTATTCAAATAAACTGATGAA
GACCAAAATAAAACAAATCCGG
Found at i:32717 original size:122 final size:122
Alignment explanation
Indices: 32584--32848 Score: 440
Period size: 122 Copynumber: 2.2 Consensus size: 122
32574 TTATTCAAAT
* * * *
32584 ATGTTGATGAAGATCAAAATAAAACAAATCCGGTTCAAGGGTCCTTGATAGACTTGATTTGGAAC
1 ATGTTGGTGAAGATCAAAATAAAACAAATCCGCTTCAAGGGTCCTTGATAGACTTGATCTCGAAC
* *
32649 GAACAAAAATAATCTTCTTCAAGTAAACTGGTGAAGACCAAAATAATGATTTCTTGA
66 GAACAAAAATAATCTTCTTCAAATAAACCGGTGAAGACCAAAATAATGATTTCTTGA
*
32706 ATGTTGGTGAAGATCAAAATAAAATAAATCCGCTTCAAGGGTCCTTGATAGACTTGATCTCGAAC
1 ATGTTGGTGAAGATCAAAATAAAACAAATCCGCTTCAAGGGTCCTTGATAGACTTGATCTCGAAC
* *
32771 GAACAAAAATAATCTTCTTCAAATAAACCGGTGAAGATCGAAATAATGATTTCTTGA
66 GAACAAAAATAATCTTCTTCAAATAAACCGGTGAAGACCAAAATAATGATTTCTTGA
*
32828 ATGTTGGTGAAAATCAAAATA
1 ATGTTGGTGAAGATCAAAATA
32849 TTAATTTCTT
Statistics
Matches: 133, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
122 133 1.00
ACGTcount: A:0.40, C:0.14, G:0.18, T:0.28
Consensus pattern (122 bp):
ATGTTGGTGAAGATCAAAATAAAACAAATCCGCTTCAAGGGTCCTTGATAGACTTGATCTCGAAC
GAACAAAAATAATCTTCTTCAAATAAACCGGTGAAGACCAAAATAATGATTTCTTGA
Found at i:33880 original size:48 final size:48
Alignment explanation
Indices: 33804--33948 Score: 254
Period size: 48 Copynumber: 3.0 Consensus size: 48
33794 ACCCGAGTTG
* * *
33804 TTAGTTCAACTGGTAGGTGCACCGTGCCTGAACCATGAGGTCCTGGGT
1 TTAGCTCAACTGGTAGGTGCACCGTGCCTGGACCGTGAGGTCCTGGGT
33852 TTAGCTCAACTGGTAGGTGCACCGTGCCTGGACCGTGAGGTCCTGGGT
1 TTAGCTCAACTGGTAGGTGCACCGTGCCTGGACCGTGAGGTCCTGGGT
*
33900 TTAGCTCAACTGGTAGGTACACCGTGCCTGGACCGTGAGGTCCTGGGT
1 TTAGCTCAACTGGTAGGTGCACCGTGCCTGGACCGTGAGGTCCTGGGT
33948 T
1 T
33949 CAAGTCTCAC
Statistics
Matches: 93, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 93 1.00
ACGTcount: A:0.17, C:0.24, G:0.33, T:0.26
Consensus pattern (48 bp):
TTAGCTCAACTGGTAGGTGCACCGTGCCTGGACCGTGAGGTCCTGGGT
Done.