Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010813.1 Corchorus capsularis cultivar CVL-1 contig10834, 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: 24177
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.31
Found at i:850 original size:10 final size:10
Alignment explanation
Indices: 835--860 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
825 GAGGACTCTA
835 GAATTTTCTG
1 GAATTTTCTG
845 GAATTTTCTG
1 GAATTTTCTG
855 GAATTT
1 GAATTT
861 GGCAGCAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.23, C:0.08, G:0.19, T:0.50
Consensus pattern (10 bp):
GAATTTTCTG
Found at i:1454 original size:20 final size:22
Alignment explanation
Indices: 1430--1479 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 22
1420 CAAAATAGGG
1430 TAAAAACACATAAAAATAGC-A
1 TAAAAACACATAAAAATAGCTA
** *
1451 -AAAAGTATATAAAAATAGCTA
1 TAAAAACACATAAAAATAGCTA
1472 TAAAAACA
1 TAAAAACA
1480 TGCATAATTT
Statistics
Matches: 22, Mismatches: 5, Indels: 3
0.73 0.17 0.10
Matches are distributed among these distances:
20 16 0.73
21 1 0.05
22 5 0.23
ACGTcount: A:0.66, C:0.10, G:0.06, T:0.18
Consensus pattern (22 bp):
TAAAAACACATAAAAATAGCTA
Found at i:1464 original size:29 final size:30
Alignment explanation
Indices: 1402--1465 Score: 71
Period size: 29 Copynumber: 2.2 Consensus size: 30
1392 CTTCAAGACC
* *
1402 TAAAAACATAAATACTAGCAAAATAGGGTA
1 TAAAAACATAAATAATAGCAAAATAGGATA
*
1432 -AAAACACATAAA-AATAGCAAAA-AGTATA
1 TAAAA-ACATAAATAATAGCAAAATAGGATA
1460 TAAAAA
1 TAAAAA
1466 TAGCTATAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
28 5 0.17
29 17 0.59
30 7 0.24
ACGTcount: A:0.64, C:0.09, G:0.09, T:0.17
Consensus pattern (30 bp):
TAAAAACATAAATAATAGCAAAATAGGATA
Found at i:6430 original size:8 final size:8
Alignment explanation
Indices: 6417--6450 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
6407 ACCTTCTTGA
6417 AAAAATTC
1 AAAAATTC
6425 AAAAATTC
1 AAAAATTC
*
6433 AGAAACTTC
1 A-AAAATTC
6442 AAAAATTC
1 AAAAATTC
6450 A
1 A
6451 TAGCCGATTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
8 16 0.70
9 7 0.30
ACGTcount: A:0.59, C:0.15, G:0.03, T:0.24
Consensus pattern (8 bp):
AAAAATTC
Found at i:15317 original size:139 final size:141
Alignment explanation
Indices: 15011--15323 Score: 515
Period size: 140 Copynumber: 2.2 Consensus size: 141
15001 TTACATAATC
*
15011 ATCAATTACAACTTTGATTGGCAAAATTAACTAACAACATGTTCAATAATTTATTTTTTTGGTAA
1 ATCAATTACAACTTTGATTGGAAAAATTAACTAACAACATGTTCAATAATTTATTTTTTTGGTAA
* *
15076 CATAATTACTAATTGATTTATTTATTTATGGTAATCTTTTTGGTGGCGATTTTATGGTAAAATTA
66 CATAATTACTAATTGATTTATTTATTTATGGTAATCTTTTTGGTAGCGATTTTATGATAAAATTA
*
15141 TATAATCATCA
131 AATAATCATCA
* *
15152 ATCAATTACAGCTTTGATT-GACAAAATTAACTAACGACATGTTCAAT-ATTTATTTTTTTGGTA
1 ATCAATTACAACTTTGATTGGA-AAAATTAACTAACAACATGTTCAATAATTTATTTTTTTGGTA
* *
15215 ACATAATTACTAATTGATTTATTTATTTATGTTAATTTTTTTGGTAGCGA-TTTATGATAAAATT
65 ACATAATTACTAATTGATTTATTTATTTATGGTAATCTTTTTGGTAGCGATTTTATGATAAAATT
*
15279 AAATAATTATCA
130 AAATAATCATCA
15291 ATCAATTACAACTTTGATTGGAAAAATTAACTA
1 ATCAATTACAACTTTGATTGGAAAAATTAACTA
15324 TCGTTCACTA
Statistics
Matches: 160, Mismatches: 10, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
139 52 0.32
140 66 0.41
141 42 0.26
ACGTcount: A:0.36, C:0.10, G:0.11, T:0.43
Consensus pattern (141 bp):
ATCAATTACAACTTTGATTGGAAAAATTAACTAACAACATGTTCAATAATTTATTTTTTTGGTAA
CATAATTACTAATTGATTTATTTATTTATGGTAATCTTTTTGGTAGCGATTTTATGATAAAATTA
AATAATCATCA
Found at i:15841 original size:28 final size:28
Alignment explanation
Indices: 15784--15841 Score: 64
Period size: 28 Copynumber: 2.1 Consensus size: 28
15774 ATTGCCAAAG
** **
15784 TTAATTAACGACTAATTTTTTTTTGCAA
1 TTAATTAACGACTAATTTTGATTCACAA
15812 TTAATTAACGACTAA-TTTGATTCACTAA
1 TTAATTAACGACTAATTTTGATTCAC-AA
15840 TT
1 TT
15842 TATTTAGTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
27 6 0.24
28 19 0.76
ACGTcount: A:0.34, C:0.12, G:0.07, T:0.47
Consensus pattern (28 bp):
TTAATTAACGACTAATTTTGATTCACAA
Found at i:16071 original size:139 final size:139
Alignment explanation
Indices: 15812--16204 Score: 538
Period size: 139 Copynumber: 2.8 Consensus size: 139
15802 TTTTTTGCAA
* * * *
15812 TTAATTAACGACTAATTTGATTCACTAATTTATTTAGTATGTTCAATCAATCTATTTTTTTTGTA
1 TTAATTAACGACTAACTTGATTCATTTATTTATTTAGCATGTTCAATCAA--T-TTTTTTTTGTA
* * *
15877 ACATAATTACTAATTGATTCATTTATTTATGGCAATATCAAATAATCATCAATCAATTATAACTT
63 ACATAATTACTAATTGATTCATTTATTTATGGAAAAATTAAATAATCATCAATCAATTATAACTT
15942 TGATT-GACAAAG
128 TGATTAG-CAAAG
* * *
15954 TTGATTAACGACTAACTTGATTCATTTATTTATTTAGCATGTTCAATCAATTTTTTTTGGTAATA
1 TTAATTAACGACTAACTTGATTCATTTATTTATTTAGCATGTTCAATCAATTTTTTTTTGTAACA
* *
16019 TAATTACTAATTGATTTATTTATTTATGGAAAAATTAAATAATCATCCATCAATTATAACTTTGA
66 TAATTACTAATTGATTCATTTATTTATGGAAAAATTAAATAATCATCAATCAATTATAACTTTGA
16084 TTAGCAAAG
131 TTAGCAAAG
* * * * *
16093 TTAACTAAGGACTAACTTGATTCATTTACTTATTTTGGATGTTCAATCAATTTATTGTTTTGTAA
1 TTAATTAACGACTAACTTGATTCATTTATTTATTTAGCATGTTCAATCAATTT-TT-TTTTGTAA
* * *
16158 CATAA-GACTAATTGATTCATTTATTTGTGGTAAAATTAAATAATCAT
64 CATAATTACTAATTGATTCATTTATTTATGGAAAAATTAAATAATCAT
16205 TAGCTTTTGG
Statistics
Matches: 224, Mismatches: 24, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
139 126 0.56
140 42 0.19
141 11 0.05
142 45 0.20
ACGTcount: A:0.36, C:0.11, G:0.09, T:0.44
Consensus pattern (139 bp):
TTAATTAACGACTAACTTGATTCATTTATTTATTTAGCATGTTCAATCAATTTTTTTTTGTAACA
TAATTACTAATTGATTCATTTATTTATGGAAAAATTAAATAATCATCAATCAATTATAACTTTGA
TTAGCAAAG
Found at i:16770 original size:211 final size:209
Alignment explanation
Indices: 16382--16775 Score: 646
Period size: 211 Copynumber: 1.9 Consensus size: 209
16372 ACCTTACAAC
16382 TTATTAAAAATCCTTAAGTAAAAACAGAAGATTCATTTTCATTAAAAAAAAAAGAAATTAAGCAA
1 TTATTAAAAATCCTTAAGTAAAAACAGAAGATTCATTTTCATTAAAAAAAAAAGAAATTAAGCAA
* *
16447 CTATTAAAGCAAATAACTAATTATTGACTATGATAATGCTTGAAATTAAATAATTCAATAAGTTA
66 CTATTAAAGCAAATAACTAACTATTGACTATGATAATGCTTGAAATTAAATAATTCAATAAGTAA
*
16512 AAATATCAAACGTAATCAATCTATTTGATTAAAAAAATTAGATGATTTGCTTTCCTTAAAGGAAA
131 AAATATCAAACGTAATCAATCTATTTGATTAAAAAAATTAAATGATTTGCTTTCCTTAAAGGAAA
16577 TAAAGTGTAATTAG
196 TAAAGTGTAATTAG
* * ** *
16591 TTATTTAAAATCTTTAAGTTTAAACAGAAGATTCATTTTCATTAAACAAAAAAGGAAAATTAAGC
1 TTATTAAAAATCCTTAAGTAAAAACAGAAGATTCATTTTCATTAAA-AAAAAAAG-AAATTAAGC
* * *
16656 AACTATTAAAGCAAATCAGTAACTATTGACTATGATCATGCTTGAAATTAAATAATTCAATAAGT
64 AACTATTAAAGCAAATAACTAACTATTGACTATGATAATGCTTGAAATTAAATAATTCAATAAGT
*
16721 AAAAAATATCAAACGTAATCAATCTATTTTATTAAAAAAA-TAAATGATTTGCTTT
129 -AAAAATATCAAACGTAATCAATCTATTTGATTAAAAAAATTAAATGATTTGCTTT
16776 GTAATTAAAT
Statistics
Matches: 170, Mismatches: 12, Indels: 4
0.91 0.06 0.02
Matches are distributed among these distances:
209 42 0.25
210 7 0.04
211 84 0.49
212 37 0.22
ACGTcount: A:0.48, C:0.10, G:0.09, T:0.33
Consensus pattern (209 bp):
TTATTAAAAATCCTTAAGTAAAAACAGAAGATTCATTTTCATTAAAAAAAAAAGAAATTAAGCAA
CTATTAAAGCAAATAACTAACTATTGACTATGATAATGCTTGAAATTAAATAATTCAATAAGTAA
AAATATCAAACGTAATCAATCTATTTGATTAAAAAAATTAAATGATTTGCTTTCCTTAAAGGAAA
TAAAGTGTAATTAG
Found at i:17566 original size:30 final size:30
Alignment explanation
Indices: 17531--17588 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
17521 TCAACTAATT
17531 AATCAATCAAAAGTAATTAATATATTTCTC
1 AATCAATCAAAAGTAATTAATATATTTCTC
** *
17561 AATCAATTTAAAGTAATTATTATATTTC
1 AATCAATCAAAAGTAATTAATATATTTC
17589 CTTTTGTCCA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.45, C:0.10, G:0.03, T:0.41
Consensus pattern (30 bp):
AATCAATCAAAAGTAATTAATATATTTCTC
Done.