Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017518.1 Corchorus olitorius cultivar O-4 contig17551, 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: 17056
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:633 original size:60 final size:60
Alignment explanation
Indices: 521--701 Score: 301
Period size: 60 Copynumber: 3.0 Consensus size: 60
511 CATACTTATA
* * *
521 TTCTAAATGCAACTAATAAAAACAATTTTTGCAAACGAC-AACTAATGTTAAATTGATGGAG
1 TTCTAAATGCAACAAATGAAAAC-A-TTTTGCAAATGACAAACTAATGTTAAATTGATGGAG
582 TTCTAAATGCAACAAATGAAAACATTTTGCAAATGACAAACTAATGTTAAATTGATGGAG
1 TTCTAAATGCAACAAATGAAAACATTTTGCAAATGACAAACTAATGTTAAATTGATGGAG
*
642 TTCTAAATGCAACAAATGAAAACATTTTGCAAATGACAAATTAATGTTAAATTGATGGAG
1 TTCTAAATGCAACAAATGAAAACATTTTGCAAATGACAAACTAATGTTAAATTGATGGAG
702 GATTGCTAAA
Statistics
Matches: 115, Mismatches: 4, Indels: 3
0.94 0.03 0.02
Matches are distributed among these distances:
59 12 0.10
60 82 0.71
61 21 0.18
ACGTcount: A:0.45, C:0.12, G:0.14, T:0.29
Consensus pattern (60 bp):
TTCTAAATGCAACAAATGAAAACATTTTGCAAATGACAAACTAATGTTAAATTGATGGAG
Found at i:969 original size:28 final size:28
Alignment explanation
Indices: 898--1003 Score: 122
Period size: 29 Copynumber: 3.7 Consensus size: 28
888 AAATGAACTT
*
898 AAAATGATCAAAATGCCCCTGAATATGCA
1 AAAATGACCAAAATGCCCCTGAATATG-A
* * *
927 TAAATGACCATAATGCCCCTGAATGTGA
1 AAAATGACCAAAATGCCCCTGAATATGA
** * *
955 AAAATGACCAAAATGCCCCTGGGTTTTTA
1 AAAATGACCAAAATGCCCCT-GAATATGA
984 AAAATGACCAAAATGCCCCT
1 AAAATGACCAAAATGCCCCT
1004 AGGTGATCCT
Statistics
Matches: 66, Mismatches: 10, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
28 19 0.29
29 47 0.71
ACGTcount: A:0.40, C:0.23, G:0.15, T:0.23
Consensus pattern (28 bp):
AAAATGACCAAAATGCCCCTGAATATGA
Found at i:2672 original size:20 final size:20
Alignment explanation
Indices: 2647--2686 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
2637 TCAAGACAGA
*
2647 GAAAACTATATACAATACTT
1 GAAAACCATATACAATACTT
2667 GAAAACCATATACAATACTT
1 GAAAACCATATACAATACTT
2687 TTCCTCATGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.50, C:0.17, G:0.05, T:0.28
Consensus pattern (20 bp):
GAAAACCATATACAATACTT
Found at i:6603 original size:35 final size:35
Alignment explanation
Indices: 6563--6636 Score: 130
Period size: 35 Copynumber: 2.1 Consensus size: 35
6553 AGTTCGTTTA
**
6563 TGTTCACGAACAGGCTCGTTTATTGTTCATTTAAG
1 TGTTCACGAACAACCTCGTTTATTGTTCATTTAAG
6598 TGTTCACGAACAACCTCGTTTATTGTTCATTTAAG
1 TGTTCACGAACAACCTCGTTTATTGTTCATTTAAG
6633 TGTT
1 TGTT
6637 TGTTTATATA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.23, C:0.18, G:0.18, T:0.42
Consensus pattern (35 bp):
TGTTCACGAACAACCTCGTTTATTGTTCATTTAAG
Found at i:6700 original size:16 final size:16
Alignment explanation
Indices: 6679--6710 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
6669 TATAATCATT
6679 TATATATTAATAATAA
1 TATATATTAATAATAA
*
6695 TATATATTATTAATAA
1 TATATATTAATAATAA
6711 AAATTATAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TATATATTAATAATAA
Found at i:6700 original size:18 final size:18
Alignment explanation
Indices: 6664--6805 Score: 70
Period size: 18 Copynumber: 8.1 Consensus size: 18
6654 AGCGTTCATT
* *
6664 TATTATATAATCATTTATA
1 TATTA-ATAATAATATATA
6683 TATTAATAATAATATATA
1 TATTAATAATAATATATA
6701 TTATTAATAA-AA-AT-TA
1 -TATTAATAATAATATATA
** *
6717 TAAAAATAATAATAT-TC
1 TATTAATAATAATATATA
* *
6734 TATTACCTAAT-ATATTTA
1 TATTA-ATAATAATATATA
* * *
6752 AATTAA-GAT-TTA-AT-
1 TATTAATAATAATATATA
6766 TATTATATAATATATATATA
1 TATTA-ATAATA-ATATATA
6786 TATATAATAATAAT-TATA
1 TAT-TAATAATAATATATA
6804 TA
1 TA
6806 ATATTTTGTT
Statistics
Matches: 94, Mismatches: 17, Indels: 25
0.69 0.12 0.18
Matches are distributed among these distances:
14 4 0.04
15 9 0.10
16 10 0.11
17 12 0.13
18 30 0.32
19 18 0.19
20 9 0.10
21 2 0.02
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.46
Consensus pattern (18 bp):
TATTAATAATAATATATA
Found at i:6705 original size:19 final size:19
Alignment explanation
Indices: 6663--6710 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
6653 GAGCGTTCAT
* *
6663 TTATTATATAATCATTTATA
1 TTATTA-ATAATAATATATA
6683 -TATTAATAATAATATATA
1 TTATTAATAATAATATATA
6701 TTATTAATAA
1 TTATTAATAA
6711 AAATTATAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 11 0.44
19 14 0.56
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (19 bp):
TTATTAATAATAATATATA
Found at i:6800 original size:34 final size:34
Alignment explanation
Indices: 6663--6802 Score: 87
Period size: 32 Copynumber: 4.1 Consensus size: 34
6653 GAGCGTTCAT
*
6663 TTATTATATAATCATTTATATATTAATAATAAT-ATATA
1 TTATTATATAAT-A--TATATATAAAT-ATAATAATA-A
* * *
6701 TTATTA-ATAA-AAAT-TATAAAAATAATAATAT
1 TTATTATATAATATATATATAAATATAATAATAA
** * *
6732 TCTATTACCTAATATAT-T-TAAAT-TAAGATTTAA
1 T-TATTATATAATATATATATAAATATAATA-ATAA
*
6765 TTATTATATAATATATATATATATATAATAATAA
1 TTATTATATAATATATATATAAATATAATAATAA
6799 TTAT
1 TTAT
6803 ATAATATTTT
Statistics
Matches: 79, Mismatches: 15, Indels: 20
0.69 0.13 0.18
Matches are distributed among these distances:
31 6 0.08
32 30 0.38
33 13 0.16
34 15 0.19
35 5 0.06
37 4 0.05
38 6 0.08
ACGTcount: A:0.50, C:0.03, G:0.01, T:0.46
Consensus pattern (34 bp):
TTATTATATAATATATATATAAATATAATAATAA
Found at i:6875 original size:18 final size:18
Alignment explanation
Indices: 6848--6882 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
6838 AATTATTACA
6848 TTGTTCATGAACAATTTT
1 TTGTTCATGAACAATTTT
*
6866 TTGTTTATGAACAATTT
1 TTGTTCATGAACAATTT
6883 CAATTTTTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.29, C:0.09, G:0.11, T:0.51
Consensus pattern (18 bp):
TTGTTCATGAACAATTTT
Found at i:10007 original size:19 final size:19
Alignment explanation
Indices: 9967--10008 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
9957 CATTTAGATT
* *
9967 TTTATATTGTTTATTTATA
1 TTTATATTGTTTATTCACA
9986 TTTATATT-TATTATTCACA
1 TTTATATTGT-TTATTCACA
10005 TTTA
1 TTTA
10009 CCGTATACAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 1 0.05
19 19 0.95
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.64
Consensus pattern (19 bp):
TTTATATTGTTTATTCACA
Found at i:10283 original size:17 final size:17
Alignment explanation
Indices: 10257--10291 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
10247 ATTACCATAC
*
10257 AATATGGATGAAATTTT
1 AATATAGATGAAATTTT
10274 AATATAGATGAAATTTT
1 AATATAGATGAAATTTT
10291 A
1 A
10292 TATTCACTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.46, C:0.00, G:0.14, T:0.40
Consensus pattern (17 bp):
AATATAGATGAAATTTT
Found at i:13045 original size:21 final size:21
Alignment explanation
Indices: 13019--13060 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
13009 CTCCTATACT
*
13019 AATAGCATAAATGACCAACAA
1 AATAGCATAAATAACCAACAA
*
13040 AATAGCATGAATAACCAACAA
1 AATAGCATAAATAACCAACAA
13061 CGTCACCAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.57, C:0.19, G:0.10, T:0.14
Consensus pattern (21 bp):
AATAGCATAAATAACCAACAA
Found at i:15267 original size:18 final size:19
Alignment explanation
Indices: 15228--15267 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
15218 GTGCTCTCGT
15228 TGTGATGCTCCCACTTTTCAA
1 TGTGATGCTCCCA--TTTCAA
15249 TGTGATGCTCCCA-TTCAA
1 TGTGATGCTCCCATTTCAA
15267 T
1 T
15268 TCTGACCATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.32
21 13 0.68
ACGTcount: A:0.20, C:0.28, G:0.15, T:0.38
Consensus pattern (19 bp):
TGTGATGCTCCCATTTCAA
Found at i:16123 original size:32 final size:34
Alignment explanation
Indices: 16072--16135 Score: 87
Period size: 32 Copynumber: 1.9 Consensus size: 34
16062 GATATCAACT
*
16072 ACTTTTTTTACTTGATTTATTATTTTTTTCTCTA
1 ACTTTTTTTACTTGATTTATTATTTTCTTCTCTA
* *
16106 ACTTTTTTTA-TT-TTTTATTCTTTTCTTCTC
1 ACTTTTTTTACTTGATTTATTATTTTCTTCTC
16136 CGTTTTCTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
32 15 0.56
33 2 0.07
34 10 0.37
ACGTcount: A:0.14, C:0.14, G:0.02, T:0.70
Consensus pattern (34 bp):
ACTTTTTTTACTTGATTTATTATTTTCTTCTCTA
Found at i:16477 original size:647 final size:647
Alignment explanation
Indices: 15238--16535 Score: 2508
Period size: 647 Copynumber: 2.0 Consensus size: 647
15228 TGTGATGCTC
*
15238 CCACTTTTCAATGTGATGCTCCCATTCAATTCTGACCATTGGATGCAATATCTATTTTCCTGACC
1 CCACATTTCAATGTGATGCTCCCATTCAATTCTGACCATTGGATGCAATATCTATTTTCCTGACC
15303 GTCGAATACTAAAAGATTTAACCTACTAAACCGGTTTTAAAAACCTTTTGGAATGAATTCGTATG
66 GTCGAATACTAAAAGATTTAACCTACTAAACCGGTTTTAAAAACCTTTTGGAATGAATTCGTATG
15368 TGGTAGTCCTAGTGATAGATTTTTACACCTTTTTTATTCAAACCGTTGATATCAACTACTTTTTT
131 TGGTAGTCCTAGTGATAGATTTTTACACCTTTTTTATTCAAACCGTTGATATCAACTACTTTTTT
15433 TTACTTGATTTATTATTTTTTTCTCTAACTTTTTTTATTTTTTATTCTTTTCTTCTCCGTTTTCT
196 TTACTTGATTTATTATTTTTTTCTCTAACTTTTTTTATTTTTTATTCTTTTCTTCTCCGTTTTCT
* * *
15498 TTCTGCGTTGAGCCCTCCTTCCTTTCTCATCCTTGCAAATTTCTTGTCATTATTAGTACTGATTA
261 TTCTGCATTGAGCCCTCCTTCCCTTCTCATCCTTGCAAATTTCTTGTCATTATTACTACTGATTA
15563 AGCCACCCAAAAGAAAACTTTATTTTTGTAGTTAATTGGAAAAAAATGAAAACGTGAATTCAGTA
326 AGCCACCCAAAAGAAAACTTTATTTTTGTAGTTAATTGGAAAAAAATGAAAACGTGAATTCAGTA
15628 TGTTGCTATGCAAAAGTGATAAATTTAGCCCCATTTATTTATATTTATGAAAAGTTTGCATCTTT
391 TGTTGCTATGCAAAAGTGATAAATTTAGCCCCATTTATTTATATTTATGAAAAGTTTGCATCTTT
15693 GAGCTATAATAATTAGGTGCTAGTATGTGATTGTGTATATAATATTTATGTGAATAAACAGATAA
456 GAGCTATAATAATTAGGTGCTAGTATGTGATTGTGTATATAATATTTATGTGAATAAACAGATAA
*
15758 GATGCTAATCTATTATGCTAACCTAAGAATTAAAAGGCAGGAAAATCATGGGTTATGGTCAGGAT
521 GATGCTAATCTATTATGCTAACCTAAGAATTAAAAGGCAGGAAAATCATGGGTTATGATCAGGAT
15823 GACATTGAAAGTTGGTTGAAACTAAATTCTCTTCTTGCATTGACGGTAGGATTTATTCTCCG
586 GACATTGAAAGTTGGTTGAAACTAAATTCTCTTCTTGCATTGACGGTAGGATTTATTCTCCG
15885 CCACATTTCAATGTGATGCTCCCATTCAATTCTGACCATTGGATGCAATATCTATTTTCCTGACC
1 CCACATTTCAATGTGATGCTCCCATTCAATTCTGACCATTGGATGCAATATCTATTTTCCTGACC
*
15950 GTCGGATACTAAAAGATTTAACCTACTAAACCGGTTTTAAAAACCTTTTGGAATGAATTCGTATG
66 GTCGAATACTAAAAGATTTAACCTACTAAACCGGTTTTAAAAACCTTTTGGAATGAATTCGTATG
*
16015 TGGTAGTCCTCGTGATAGATTTTTACACCTTTTTTATTCAAACCGTTGATATCAACTAC-TTTTT
131 TGGTAGTCCTAGTGATAGATTTTTACACCTTTTTTATTCAAACCGTTGATATCAACTACTTTTTT
16079 TTACTTGATTTATTATTTTTTTCTCTAACTTTTTTTATTTTTTATTCTTTTCTTCTCCGTTTTCT
196 TTACTTGATTTATTATTTTTTTCTCTAACTTTTTTTATTTTTTATTCTTTTCTTCTCCGTTTTCT
*
16144 TTCTGCATTGAGCCCTCCTTCCCTTCTCATCCTTGCAAATTTCTTGTCATTATTACTACTGGTTA
261 TTCTGCATTGAGCCCTCCTTCCCTTCTCATCCTTGCAAATTTCTTGTCATTATTACTACTGATTA
16209 AGCCACCCAAAAGAAAACTTTATTTTTGTAGTTAATTGGAAAAAAAATGAAAACGTGAATTCAGT
326 AGCCACCCAAAAGAAAACTTTATTTTTGTAGTTAATTGG-AAAAAAATGAAAACGTGAATTCAGT
16274 ATGTTGCTATGCAAAAGTGATAAATTTAGCCCCATTTATTTATATTTATGAAAAGTTTGCATCTT
390 ATGTTGCTATGCAAAAGTGATAAATTTAGCCCCATTTATTTATATTTATGAAAAGTTTGCATCTT
16339 TGAGCTATAATAATTAGGTGCTAGTATGTGATTGTGTATATAATATTTATGTGAATAAACAGATA
455 TGAGCTATAATAATTAGGTGCTAGTATGTGATTGTGTATATAATATTTATGTGAATAAACAGATA
16404 AGATGCTAATCTATTATGCTAACCTAAGAATTAAAAGGCAGGAAAATCATGGGTTATGATCAGGA
520 AGATGCTAATCTATTATGCTAACCTAAGAATTAAAAGGCAGGAAAATCATGGGTTATGATCAGGA
16469 TGACATTGAAAGTTGGTTGAAACTAAATTCTCTTCTTGCATTGACGGTAGGATTTATTCTCCG
585 TGACATTGAAAGTTGGTTGAAACTAAATTCTCTTCTTGCATTGACGGTAGGATTTATTCTCCG
16532 CCAC
1 CCAC
16536 CACCAAGGTC
Statistics
Matches: 642, Mismatches: 8, Indels: 2
0.98 0.01 0.00
Matches are distributed among these distances:
646 170 0.26
647 472 0.74
ACGTcount: A:0.29, C:0.16, G:0.15, T:0.40
Consensus pattern (647 bp):
CCACATTTCAATGTGATGCTCCCATTCAATTCTGACCATTGGATGCAATATCTATTTTCCTGACC
GTCGAATACTAAAAGATTTAACCTACTAAACCGGTTTTAAAAACCTTTTGGAATGAATTCGTATG
TGGTAGTCCTAGTGATAGATTTTTACACCTTTTTTATTCAAACCGTTGATATCAACTACTTTTTT
TTACTTGATTTATTATTTTTTTCTCTAACTTTTTTTATTTTTTATTCTTTTCTTCTCCGTTTTCT
TTCTGCATTGAGCCCTCCTTCCCTTCTCATCCTTGCAAATTTCTTGTCATTATTACTACTGATTA
AGCCACCCAAAAGAAAACTTTATTTTTGTAGTTAATTGGAAAAAAATGAAAACGTGAATTCAGTA
TGTTGCTATGCAAAAGTGATAAATTTAGCCCCATTTATTTATATTTATGAAAAGTTTGCATCTTT
GAGCTATAATAATTAGGTGCTAGTATGTGATTGTGTATATAATATTTATGTGAATAAACAGATAA
GATGCTAATCTATTATGCTAACCTAAGAATTAAAAGGCAGGAAAATCATGGGTTATGATCAGGAT
GACATTGAAAGTTGGTTGAAACTAAATTCTCTTCTTGCATTGACGGTAGGATTTATTCTCCG
Done.