Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007154.1 Corchorus capsularis cultivar CVL-1 contig07175, 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: 17859
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:4291 original size:39 final size:38
Alignment explanation
Indices: 4246--4349 Score: 129
Period size: 39 Copynumber: 2.7 Consensus size: 38
4236 AAATTGCCCT
* *
4246 TGTGTTATATGTGTTTAGGGACTTT-AGTATAGATACCTC
1 TGTGTTATATGTGTTT-GGGACTTTGAG-AGAGATACCCC
* *
4285 TGTGTTATATGTGTTTGAGGACTTTGAGAGAGTTGCCCC
1 TGTGTTATATGTGTTTG-GGACTTTGAGAGAGATACCCC
4324 TGTGTTATATGTGTTTGGGGACTTTG
1 TGTGTTATATGTGTTT-GGGACTTTG
4350 GGGAGAGAGA
Statistics
Matches: 58, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
38 1 0.02
39 54 0.93
40 3 0.05
ACGTcount: A:0.18, C:0.10, G:0.29, T:0.43
Consensus pattern (38 bp):
TGTGTTATATGTGTTTGGGACTTTGAGAGAGATACCCC
Found at i:6787 original size:17 final size:17
Alignment explanation
Indices: 6765--6819 Score: 67
Period size: 17 Copynumber: 3.2 Consensus size: 17
6755 AATCACCCCT
*
6765 AGATCACTAGTGATCAA
1 AGATCACCAGTGATCAA
6782 AGATCACCAGTGATGC-A
1 AGATCACCAGTGAT-CAA
* *
6799 AGATCACCGGTAATCAA
1 AGATCACCAGTGATCAA
6816 AGAT
1 AGAT
6820 TACATGGGTT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
16 1 0.03
17 31 0.94
18 1 0.03
ACGTcount: A:0.40, C:0.20, G:0.20, T:0.20
Consensus pattern (17 bp):
AGATCACCAGTGATCAA
Found at i:15164 original size:59 final size:59
Alignment explanation
Indices: 15081--15248 Score: 196
Period size: 59 Copynumber: 2.9 Consensus size: 59
15071 ACCGAGCATC
* *
15081 CATCCTTCGGTCGCACGACTTAGTGGGCATCCCCCACTCGTGCCATAAGAACGACTGAG
1 CATCCTTCGGTCGCACGACCTAGTGGGCATCCCCCACTCATGCCATAAGAACGACTGAG
* * * * * *
15140 CATCCTTCGGTCGCACGACCTAGTGGACATCTCCCATTCTTGCCATAAGAATGATTGAG
1 CATCCTTCGGTCGCACGACCTAGTGGGCATCCCCCACTCATGCCATAAGAACGACTGAG
* ** * *
15199 CATCCCTT-GGTCACATAACCCAGTGGGCAT-CCCCACTCATGCAATAAGAA
1 CAT-CCTTCGGTCGCACGACCTAGTGGGCATCCCCCACTCATGCCATAAGAA
15249 AAACGAGTAT
Statistics
Matches: 92, Mismatches: 16, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
58 16 0.17
59 72 0.78
60 4 0.04
ACGTcount: A:0.25, C:0.32, G:0.20, T:0.23
Consensus pattern (59 bp):
CATCCTTCGGTCGCACGACCTAGTGGGCATCCCCCACTCATGCCATAAGAACGACTGAG
Found at i:15383 original size:29 final size:29
Alignment explanation
Indices: 15291--15478 Score: 208
Period size: 29 Copynumber: 6.6 Consensus size: 29
15281 TGGGCACCCC
* * *
15291 CCAAAGGCATACAGCC--TAGATAAAATCC
1 CCAAAGGCATACAGCCTATACAAAAAAT-T
*
15319 CCAAAGGCATACAACCTATACAAAAAATTT
1 CCAAAGGCATACAGCCTATACAAAAAA-TT
15349 CCAAAGGCATACAGCCTATACAAAAAATT
1 CCAAAGGCATACAGCCTATACAAAAAATT
15378 CCAAAGGCATACAGCCTATAC-AAAAATCT
1 CCAAAGGCATACAGCCTATACAAAAAAT-T
* * * *
15407 CTAAAGGCATGCAGCC--TA-GATAAATT
1 CCAAAGGCATACAGCCTATACAAAAAATT
* *
15433 CCCAAAGGCATACAGCCTATGCAAAAATTT
1 -CCAAAGGCATACAGCCTATACAAAAAATT
15463 CCAAAGGCATACAGCC
1 CCAAAGGCATACAGCC
15479 AAGATAGAGT
Statistics
Matches: 137, Mismatches: 14, Indels: 17
0.82 0.08 0.10
Matches are distributed among these distances:
26 1 0.01
27 21 0.15
28 21 0.15
29 55 0.40
30 38 0.28
31 1 0.01
ACGTcount: A:0.44, C:0.26, G:0.13, T:0.18
Consensus pattern (29 bp):
CCAAAGGCATACAGCCTATACAAAAAATT
Found at i:15458 original size:56 final size:56
Alignment explanation
Indices: 15291--15484 Score: 255
Period size: 56 Copynumber: 3.4 Consensus size: 56
15281 TGGGCACCCC
* *
15291 CCAAAGGCATACAGCCTAGATAAAATCCCCAAAGGCATACAACCTATACAAAAAATTT
1 CCAAAGGCATACAGCCTAGAT-AAATTCCCAAAGGCATACAGCCTATAC-AAAAATTT
* * *
15349 CCAAAGGCATACAGCCTATACAAAAAATT-CCAAAGGCATACAGCCTATACAAAAATCT
1 CCAAAGGCATACAGCC--TA-GATAAATTCCCAAAGGCATACAGCCTATACAAAAATTT
* * *
15407 CTAAAGGCATGCAGCCTAGATAAATTCCCAAAGGCATACAGCCTATGCAAAAATTT
1 CCAAAGGCATACAGCCTAGATAAATTCCCAAAGGCATACAGCCTATACAAAAATTT
*
15463 CCAAAGGCATACAGCCAAGATA
1 CCAAAGGCATACAGCCTAGATA
15485 GAGTCCAAAT
Statistics
Matches: 118, Mismatches: 14, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
55 6 0.05
56 48 0.41
58 37 0.31
59 20 0.17
60 6 0.05
61 1 0.01
ACGTcount: A:0.44, C:0.25, G:0.13, T:0.18
Consensus pattern (56 bp):
CCAAAGGCATACAGCCTAGATAAATTCCCAAAGGCATACAGCCTATACAAAAATTT
Found at i:16143 original size:28 final size:28
Alignment explanation
Indices: 16111--16317 Score: 213
Period size: 28 Copynumber: 7.3 Consensus size: 28
16101 AAAAAAAAAG
* * * *
16111 GTGGTAGTA-TGCGCTCTAAGCTCCCAAA
1 GTGGTAGTACT-CCCTCCAAGCTCACGAA
*
16139 GTGGTAGTACTCCCTCCAAGCTTACGAA
1 GTGGTAGTACTCCCTCCAAGCTCACGAA
* * *
16167 GTGGTAGTACTCCCTCTAAAGTTCCCGAA
1 GTGGTAGTACTCCCTC-CAAGCTCACGAA
* *
16196 GTGGTAGTACTCCCTCCAAAGTTCCCGAA
1 GTGGTAGTACTCCCTCC-AAGCTCACGAA
*
16225 GTGGTAGTACTCCCTCTAAAGCTCACGAA
1 GTGGTAGTACTCCCTC-CAAGCTCACGAA
* **
16254 GTGGTAGTA-TGCCTTCCAAGCTCGTGAA
1 GTGGTAGTACT-CCCTCCAAGCTCACGAA
16282 GTGGTAGTA-TGCCCTCCAAGCTCACGAA
1 GTGGTAGTACT-CCCTCCAAGCTCACGAA
16310 GTGGTAGT
1 GTGGTAGT
16318 GCACCCCCCA
Statistics
Matches: 154, Mismatches: 20, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
28 80 0.52
29 74 0.48
ACGTcount: A:0.24, C:0.26, G:0.24, T:0.26
Consensus pattern (28 bp):
GTGGTAGTACTCCCTCCAAGCTCACGAA
Found at i:16205 original size:29 final size:29
Alignment explanation
Indices: 16111--16262 Score: 186
Period size: 29 Copynumber: 5.3 Consensus size: 29
16101 AAAAAAAAAG
* * *
16111 GTGGTAGTA-TGCGCTCT-AAGCTCCCAAA
1 GTGGTAGTACT-CCCTCTAAAGTTCCCGAA
* *
16139 GTGGTAGTACTCCCTC-CAAGCTT-ACGAA
1 GTGGTAGTACTCCCTCTAAAG-TTCCCGAA
16167 GTGGTAGTACTCCCTCTAAAGTTCCCGAA
1 GTGGTAGTACTCCCTCTAAAGTTCCCGAA
*
16196 GTGGTAGTACTCCCTCCAAAGTTCCCGAA
1 GTGGTAGTACTCCCTCTAAAGTTCCCGAA
* *
16225 GTGGTAGTACTCCCTCTAAAGCTCACGAA
1 GTGGTAGTACTCCCTCTAAAGTTCCCGAA
16254 GTGGTAGTA
1 GTGGTAGTA
16263 TGCCTTCCAA
Statistics
Matches: 109, Mismatches: 10, Indels: 9
0.85 0.08 0.07
Matches are distributed among these distances:
28 37 0.34
29 72 0.66
ACGTcount: A:0.25, C:0.26, G:0.23, T:0.26
Consensus pattern (29 bp):
GTGGTAGTACTCCCTCTAAAGTTCCCGAA
Found at i:16505 original size:29 final size:29
Alignment explanation
Indices: 16459--16661 Score: 284
Period size: 29 Copynumber: 7.1 Consensus size: 29
16449 GGAGCACGCT
* *
16459 CACCATCTTGGA--AGAGCGCCGTACACC
1 CACCATTTTGGACGAGAGCGCCGTACATC
* *
16486 CACCATTTTTGATGAGAGCGCCGTACATC
1 CACCATTTTGGACGAGAGCGCCGTACATC
16515 CACCATTTTGGACGAGAGCGCCGTACATC
1 CACCATTTTGGACGAGAGCGCCGTACATC
*
16544 CACCATTTTGGACGAGATCGCCGTACATC
1 CACCATTTTGGACGAGAGCGCCGTACATC
*
16573 CACCATTTTGGACGAGAGCGCCGTATATC
1 CACCATTTTGGACGAGAGCGCCGTACATC
* * *
16602 CACAATCTTGGACGAGAACGCCGTACATC
1 CACCATTTTGGACGAGAGCGCCGTACATC
* * *
16631 CACCATCTTGGAAGAGAGAGCCGTACATC
1 CACCATTTTGGACGAGAGCGCCGTACATC
16660 CA
1 CA
16662 TCTTGGAACA
Statistics
Matches: 158, Mismatches: 16, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
27 10 0.06
29 148 0.94
ACGTcount: A:0.27, C:0.31, G:0.22, T:0.21
Consensus pattern (29 bp):
CACCATTTTGGACGAGAGCGCCGTACATC
Found at i:16679 original size:26 final size:26
Alignment explanation
Indices: 16633--16682 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
16623 CGTACATCCA
*
16633 CCATCTTGGAAGAGAGAGCCGTACAT
1 CCATCTTGGAACAGAGAGCCGTACAT
* *
16659 CCATCTTGGAACAGGGCGCCGTAC
1 CCATCTTGGAACAGAGAGCCGTAC
16683 GCCAAGCATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.26, C:0.28, G:0.28, T:0.18
Consensus pattern (26 bp):
CCATCTTGGAACAGAGAGCCGTACAT
Done.