Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014642.1 Corchorus capsularis cultivar CVL-1 contig14663, 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: 24813
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:2418 original size:12 final size:12
Alignment explanation
Indices: 2401--2426 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2391 AATTGTGGCC
2401 TTTATTCATTAA
1 TTTATTCATTAA
2413 TTTATTCATTAA
1 TTTATTCATTAA
2425 TT
1 TT
2427 GCAAGATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.08, G:0.00, T:0.62
Consensus pattern (12 bp):
TTTATTCATTAA
Found at i:11429 original size:19 final size:17
Alignment explanation
Indices: 11405--11459 Score: 74
Period size: 17 Copynumber: 3.1 Consensus size: 17
11395 TGTCAACTAG
*
11405 ATCATAGTATATATTCTAT
1 ATCATA-TATATA-TATAT
11424 ATCATATATATATATAT
1 ATCATATATATATATAT
*
11441 ATAATATATATATATAT
1 ATCATATATATATATAT
11458 AT
1 AT
11460 ATAGTAATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
17 22 0.65
18 6 0.18
19 6 0.18
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.47
Consensus pattern (17 bp):
ATCATATATATATATAT
Found at i:11432 original size:2 final size:2
Alignment explanation
Indices: 11412--11462 Score: 70
Period size: 2 Copynumber: 26.0 Consensus size: 2
11402 TAGATCATAG
*
11412 TA TA TA T- TC TA TA TCA TA TA TA TA TA TA TA TA -A TA TA TA TA
1 TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA
11453 TA TA TA TA TA
1 TA TA TA TA TA
11463 GTAATTTTTA
Statistics
Matches: 45, Mismatches: 1, Indels: 6
0.87 0.02 0.12
Matches are distributed among these distances:
1 2 0.04
2 41 0.91
3 2 0.04
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:12657 original size:23 final size:23
Alignment explanation
Indices: 12594--12671 Score: 66
Period size: 23 Copynumber: 3.2 Consensus size: 23
12584 AGAAAAATCT
*
12594 AAAAACGTTAAAGAAAAAAAAAA
1 AAAAACGTTAAAGAAAAAGAAAA
* **
12617 GAAAAAAGAAGAACAAGAAAAAGAAAA
1 -AAAAACG--TTA-AAGAAAAAGAAAA
* *
12644 AAAAACGTTAAAGAACAAGGAAA
1 AAAAACGTTAAAGAAAAAGAAAA
12667 AAAAA
1 AAAAA
12672 GAGAAAAAAC
Statistics
Matches: 42, Mismatches: 9, Indels: 7
0.72 0.16 0.12
Matches are distributed among these distances:
23 16 0.38
24 7 0.17
26 7 0.17
27 12 0.29
ACGTcount: A:0.76, C:0.05, G:0.14, T:0.05
Consensus pattern (23 bp):
AAAAACGTTAAAGAAAAAGAAAA
Found at i:12681 original size:32 final size:27
Alignment explanation
Indices: 12608--12681 Score: 80
Period size: 26 Copynumber: 2.6 Consensus size: 27
12598 ACGTTAAAGA
12608 AAAAAAAAAGAAAAAA-GAAGAACAAG
1 AAAAAAAAAGAAAAAACGAAGAACAAG
*
12634 AAAAAGAAA-AAAAAACGTTAAAGAACAAGG
1 AAAAAAAAAGAAAAAACG---AAGAACAA-G
12664 AAAAAAAAGAGAAAAAAC
1 AAAAAAAA-AGAAAAAAC
12682 AGAGAAAGAT
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
25 6 0.15
26 9 0.23
29 8 0.21
30 8 0.21
31 1 0.03
32 7 0.18
ACGTcount: A:0.77, C:0.05, G:0.15, T:0.03
Consensus pattern (27 bp):
AAAAAAAAAGAAAAAACGAAGAACAAG
Found at i:12685 original size:11 final size:11
Alignment explanation
Indices: 12605--12688 Score: 57
Period size: 11 Copynumber: 7.5 Consensus size: 11
12595 AAAACGTTAA
*
12605 AGAAAAAAAAA
1 AGAAAAAAAAG
12616 AGAAAAAAGAAG
1 AGAAAAAA-AAG
12628 A-ACAAGAAAAAG
1 AGA-AA-AAAAAG
12640 A-AAAAAAAACG
1 AGAAAAAAAA-G
** *
12651 TTAAAGAACAAG
1 AGAAA-AAAAAG
12663 -GAAAAAAAAG
1 AGAAAAAAAAG
*
12673 AGAAAAAACAG
1 AGAAAAAAAAG
12684 AGAAA
1 AGAAA
12689 GATGAACAGT
Statistics
Matches: 60, Mismatches: 6, Indels: 14
0.75 0.08 0.17
Matches are distributed among these distances:
10 10 0.17
11 29 0.48
12 14 0.23
13 7 0.12
ACGTcount: A:0.76, C:0.05, G:0.17, T:0.02
Consensus pattern (11 bp):
AGAAAAAAAAG
Found at i:12687 original size:29 final size:26
Alignment explanation
Indices: 12608--12687 Score: 72
Period size: 29 Copynumber: 2.8 Consensus size: 26
12598 ACGTTAAAGA
*
12608 AAAAAAAAAGAAAAAAGAAGAACAAG
1 AAAAAAAAAGAAAAAACAAGAACAAG
*
12634 AAAAAGAAA-AAAAAACGTTAAAGAACAAGG
1 AAAAAAAAAGAAAAAAC----AAGAACAA-G
12664 AAAAAAAAGAGAAAAAACAGAGAA
1 AAAAAAAA-AGAAAAAACA-AGAA
12688 AGATGAACAG
Statistics
Matches: 43, Mismatches: 3, Indels: 13
0.73 0.05 0.22
Matches are distributed among these distances:
25 6 0.14
26 8 0.19
28 1 0.02
29 12 0.28
30 8 0.19
31 1 0.02
32 7 0.16
ACGTcount: A:0.76, C:0.05, G:0.16, T:0.03
Consensus pattern (26 bp):
AAAAAAAAAGAAAAAACAAGAACAAG
Found at i:12690 original size:33 final size:29
Alignment explanation
Indices: 12604--12690 Score: 81
Period size: 27 Copynumber: 2.9 Consensus size: 29
12594 AAAAACGTTA
12604 AAGAAAAAAAAAAGAAAAA--AG-AAGAAC
1 AAGAAAAAAAAAA-AAAAACGAGAAAGAAC
* **
12631 AAGAAAAAGAAAAAAAAACGTTAAAGAAC
1 AAGAAAAAAAAAAAAAAACGAGAAAGAAC
12660 AAGGAAAAAAAAGAGAAAAAACAGAGAAAGA
1 AA-GAAAAAAAA-A-AAAAAAC-GAGAAAGA
12691 TGAACAGTGA
Statistics
Matches: 47, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
26 5 0.11
27 12 0.26
29 8 0.17
30 8 0.17
31 1 0.02
32 7 0.15
33 6 0.13
ACGTcount: A:0.76, C:0.05, G:0.17, T:0.02
Consensus pattern (29 bp):
AAGAAAAAAAAAAAAAAACGAGAAAGAAC
Found at i:12774 original size:26 final size:26
Alignment explanation
Indices: 12740--12800 Score: 104
Period size: 26 Copynumber: 2.3 Consensus size: 26
12730 GCGCGCGGGT
12740 CGCGACCCACCACTGGACGGGTCACG
1 CGCGACCCACCACTGGACGGGTCACG
*
12766 CGCGACCCACCACTGGACGGGTCATG
1 CGCGACCCACCACTGGACGGGTCACG
*
12792 AGCGACCCA
1 CGCGACCCA
12801 TGCCAAGGCC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.21, C:0.41, G:0.30, T:0.08
Consensus pattern (26 bp):
CGCGACCCACCACTGGACGGGTCACG
Found at i:16072 original size:29 final size:30
Alignment explanation
Indices: 15998--16072 Score: 86
Period size: 29 Copynumber: 2.6 Consensus size: 30
15988 TAGGCTGAGG
*
15998 GGGCAAGA-CGTTCCAAAATTAAAGTTCAGT
1 GGGCAAAATCGTT-CAAAATTAAAGTTCAGT
*
16028 GGGCAAAAT-GTCCAAAATTAAAGTTCAG-
1 GGGCAAAATCGTTCAAAATTAAAGTTCAGT
16056 GGAGC-AAATCGTTCAAA
1 GG-GCAAAATCGTTCAAA
16073 CGCTACAAGA
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
28 6 0.15
29 24 0.62
30 9 0.23
ACGTcount: A:0.40, C:0.16, G:0.23, T:0.21
Consensus pattern (30 bp):
GGGCAAAATCGTTCAAAATTAAAGTTCAGT
Found at i:18829 original size:14 final size:14
Alignment explanation
Indices: 18783--18829 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
18773 TTTTATGATT
18783 ATTTTATTTTTACC
1 ATTTTATTTTTACC
* **
18797 ATTTT-TATTTAAA
1 ATTTTATTTTTACC
*
18810 AGTTTATTTTTACC
1 ATTTTATTTTTACC
18824 ATTTTA
1 ATTTTA
18830 CTATTTTTCA
Statistics
Matches: 24, Mismatches: 8, Indels: 2
0.71 0.24 0.06
Matches are distributed among these distances:
13 9 0.38
14 15 0.62
ACGTcount: A:0.28, C:0.09, G:0.02, T:0.62
Consensus pattern (14 bp):
ATTTTATTTTTACC
Found at i:18987 original size:151 final size:148
Alignment explanation
Indices: 18680--18948 Score: 348
Period size: 151 Copynumber: 1.8 Consensus size: 148
18670 TTATTTTTAC
* *
18680 CATTTTTCATTATAAACTTAGATATATTAAAATGTTTTAATATACAGTTTTATTCTACTAGAAAC
1 CATTTTTCATTAAAAACTTAGATATATTAAAATGTTTTAATATACAGTTTTATTCTACTAAAAAC
* * *
18745 TCAATTTTCATTTAGTTAAATTCAATATTTTTATGATTATTTTATTTTTACCATTTTTATTTAAA
66 TCAATTTTCATTTAATTAAATTCAATATTTTTATGA-TATTTGATTTATA-CATTTTTATTTAAA
* *
18810 AGTTTATTTTTACCATTTTA
129 AGTTTATTTTGACCATATTA
* * *
18830 CTATTTTTCATTAAAAACTT-GAATATTTTAAAATTTTTTATTATACAGTTTTATTCTACTAAAA
1 C-ATTTTTCATTAAAAACTTAG-ATATATTAAAATGTTTTAATATACAGTTTTATTCTACTAAAA
* *
18894 ACTCTATTTTCATTTAATTCAATTCAATATTTTTAATG-TATTGTGA-TTATA-ATTT
64 ACTCAATTTTCATTTAATTAAATTCAATATTTTT-ATGATATT-TGATTTATACATTT
18949 ATTTTTTCCA
Statistics
Matches: 105, Mismatches: 10, Indels: 10
0.84 0.08 0.08
Matches are distributed among these distances:
148 4 0.04
150 10 0.10
151 88 0.84
152 3 0.03
ACGTcount: A:0.34, C:0.09, G:0.04, T:0.52
Consensus pattern (148 bp):
CATTTTTCATTAAAAACTTAGATATATTAAAATGTTTTAATATACAGTTTTATTCTACTAAAAAC
TCAATTTTCATTTAATTAAATTCAATATTTTTATGATATTTGATTTATACATTTTTATTTAAAAG
TTTATTTTGACCATATTA
Found at i:19746 original size:169 final size:167
Alignment explanation
Indices: 19258--19758 Score: 672
Period size: 163 Copynumber: 3.0 Consensus size: 167
19248 AGATCGCTCA
* * * * * * * *
19258 AATGTCGGGTCATCTGGGTTCAGGTCAATTCAGGTTTGATTCTTTTTTGGTGTCGAATCATATGG
1 AATGTCAGGTCATTTGGGTTCGGGTCAATTCTGGTTCGAGTC-TTTTCGGTGTCGAGTCATATGG
* * * *
19323 TCCGGATAATTTCAGGTTTGAGCTTCGGATTTCCGGGTTCGGCTCTTTTTGGGTTCGGGTCATTT
65 TTC-GATAATTTCAGGTTTGAGCTTCGGATTTTCGGGTTCGGCTCTTTTCGGATTCGGGTCATTT
*
19388 AAATATAATTAATTTCAATTCGGGTAATTTCAGGTTAAT
129 AAATATAATTAATTTCAATTCGGGTAATTTAAGGTTAAT
* * *
19427 AATGTCAGGTCATTTGGGTTGGGGTGAATTCTGATTCGAGTCTATTTCGGTGTCGAGTCATATGG
1 AATGTCAGGTCATTTGGGTTCGGGTCAATTCTGGTTCGAGTCT-TTTCGGTGTCGAGTCATATGG
* * * *
19492 TTCG-GAA----AGGTTTGAGCTTGGGATTTTCGAGTTCGGCTCTTTTCGGATTCAGGTCATTTA
65 TTCGATAATTTCAGGTTTGAGCTTCGGATTTTCGGGTTCGGCTCTTTTCGGATTCGGGTCATTTA
* *
19552 AATAAAATTAATTCCAATTCGGGTAATTTAAGGTTAAT
130 AATATAATTAATTTCAATTCGGGTAATTTAAGGTTAAT
19590 AATGTCAGGTCATTTGGGTTCGGGTCAATTCTGGTTCGAGTCTTTTCCGGTGTCGAGTCATATGG
1 AATGTCAGGTCATTTGGGTTCGGGTCAATTCTGGTTCGAGTCTTTT-CGGTGTCGAGTCATATGG
* * **
19655 TTCTGATAATTTCAGATTTGAGCTTTGGATTTTCGGGTTCTTCTCTTTTCGGATTCGGGTCATTT
65 TTC-GATAATTTCAGGTTTGAGCTTCGGATTTTCGGGTTCGGCTCTTTTCGGATTCGGGTCATTT
19720 AAATATAATTAATTTCAATTCGGGTAATTTCAA-GTTAAT
129 AAATATAATTAATTTCAATTCGGGTAATTT-AAGGTTAAT
19759 CTCTCGGATT
Statistics
Matches: 289, Mismatches: 34, Indels: 18
0.85 0.10 0.05
Matches are distributed among these distances:
162 3 0.01
163 143 0.49
164 1 0.00
165 2 0.01
167 2 0.01
168 2 0.01
169 134 0.46
170 2 0.01
ACGTcount: A:0.21, C:0.14, G:0.25, T:0.41
Consensus pattern (167 bp):
AATGTCAGGTCATTTGGGTTCGGGTCAATTCTGGTTCGAGTCTTTTCGGTGTCGAGTCATATGGT
TCGATAATTTCAGGTTTGAGCTTCGGATTTTCGGGTTCGGCTCTTTTCGGATTCGGGTCATTTAA
ATATAATTAATTTCAATTCGGGTAATTTAAGGTTAAT
Done.