Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012797.1 Corchorus olitorius cultivar O-4 contig12830, 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: 34452
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:6026 original size:37 final size:38
Alignment explanation
Indices: 5976--6054 Score: 115
Period size: 37 Copynumber: 2.1 Consensus size: 38
5966 ATATAATTAT
* *
5976 TCATAAAGTTATGTCTATTTGGAAAGACATG-TGTTGA
1 TCATAAAGTTATGTCTATATGAAAAGACATGATGTTGA
*
6013 TCATAAGGTTATGTCTATATGAAAAGACATGTATGTTGA
1 TCATAAAGTTATGTCTATATGAAAAGACATG-ATGTTGA
6052 TCA
1 TCA
6055 AATATATAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
37 28 0.76
39 9 0.24
ACGTcount: A:0.34, C:0.09, G:0.20, T:0.37
Consensus pattern (38 bp):
TCATAAAGTTATGTCTATATGAAAAGACATGATGTTGA
Found at i:8314 original size:18 final size:18
Alignment explanation
Indices: 8291--8327 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
8281 CATGGTTCAA
8291 TCCTAGGACACCATGTAC
1 TCCTAGGACACCATGTAC
8309 TCCTAGGACACCATGTAC
1 TCCTAGGACACCATGTAC
8327 T
1 T
8328 TCGTTAGCGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.27, C:0.32, G:0.16, T:0.24
Consensus pattern (18 bp):
TCCTAGGACACCATGTAC
Found at i:8666 original size:37 final size:38
Alignment explanation
Indices: 8616--8694 Score: 97
Period size: 37 Copynumber: 2.1 Consensus size: 38
8606 ATATAATTAT
* ** *
8616 TCATAAAGTTATGTTTATTTGAAAAGACATG-TGTTGA
1 TCATAAAGTTATGTCTATACGAAAAAACATGATGTTGA
*
8653 TCATAAGGTTATGTCTATACGAAAAAACATGTATGTTGA
1 TCATAAAGTTATGTCTATACGAAAAAACATG-ATGTTGA
8692 TCA
1 TCA
8695 AATATATAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
37 26 0.74
39 9 0.26
ACGTcount: A:0.37, C:0.09, G:0.18, T:0.37
Consensus pattern (38 bp):
TCATAAAGTTATGTCTATACGAAAAAACATGATGTTGA
Found at i:11275 original size:22 final size:22
Alignment explanation
Indices: 11250--11328 Score: 61
Period size: 22 Copynumber: 3.2 Consensus size: 22
11240 ACCGAACCGG
11250 ATCGGATGGTTGGACCGGTTTA
1 ATCGGATGGTTGGACCGGTTTA
*
11272 ATCGGGAACT-GCTGGCATGTCCGGTTCTTA
1 ATC-GG-A-TGGTTGG-A---CCGG-T-TTA
11302 ATCGGATGGTTGGACCGGTTTA
1 ATCGGATGGTTGGACCGGTTTA
11324 ATCGG
1 ATCGG
11329 GAACCGCTGG
Statistics
Matches: 45, Mismatches: 2, Indels: 20
0.67 0.03 0.30
Matches are distributed among these distances:
22 11 0.24
23 3 0.07
24 9 0.20
25 2 0.04
27 2 0.04
28 9 0.20
29 3 0.07
30 6 0.13
ACGTcount: A:0.18, C:0.18, G:0.34, T:0.30
Consensus pattern (22 bp):
ATCGGATGGTTGGACCGGTTTA
Found at i:11328 original size:52 final size:52
Alignment explanation
Indices: 11250--11354 Score: 192
Period size: 52 Copynumber: 2.0 Consensus size: 52
11240 ACCGAACCGG
* *
11250 ATCGGATGGTTGGACCGGTTTAATCGGGAACTGCTGGCATGTCCGGTTCTTA
1 ATCGGATGGTTGGACCGGTTTAATCGGGAACCGCTGGCATGTCCGGTCCTTA
11302 ATCGGATGGTTGGACCGGTTTAATCGGGAACCGCTGGCATGTCCGGTCCTTA
1 ATCGGATGGTTGGACCGGTTTAATCGGGAACCGCTGGCATGTCCGGTCCTTA
11354 A
1 A
11355 AGATGTGGGA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.18, C:0.21, G:0.32, T:0.29
Consensus pattern (52 bp):
ATCGGATGGTTGGACCGGTTTAATCGGGAACCGCTGGCATGTCCGGTCCTTA
Found at i:13315 original size:19 final size:20
Alignment explanation
Indices: 13288--13325 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
13278 ATTCAAAACA
*
13288 AAATAAAAACTATCCATTTT
1 AAATAAAAACTACCCATTTT
13308 AAAT-AAAACTACCCATTT
1 AAATAAAAACTACCCATTT
13326 CAAGATAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.50, C:0.18, G:0.00, T:0.32
Consensus pattern (20 bp):
AAATAAAAACTACCCATTTT
Found at i:13333 original size:20 final size:19
Alignment explanation
Indices: 13288--13334 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
13278 ATTCAAAACA
* *
13288 AAATAAAAACTATCCATTTT
1 AAAT-AAAACTACCCATTTC
13308 AAATAAAACTACCCATTTC
1 AAATAAAACTACCCATTTC
13327 AAGATAAA
1 AA-ATAAA
13335 TATAAAGTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 15 0.62
20 9 0.38
ACGTcount: A:0.53, C:0.17, G:0.02, T:0.28
Consensus pattern (19 bp):
AAATAAAACTACCCATTTC
Found at i:13443 original size:69 final size:70
Alignment explanation
Indices: 13367--13505 Score: 174
Period size: 73 Copynumber: 2.0 Consensus size: 70
13357 TATATCATTC
* * **
13367 TAAAAAAACTGCCCATTT-AAA-AAGAACTGTCAAAAACTACTCACGTAGTGAGTGCCCTGTGTC
1 TAAAAAAACTACCCATTTAAAATAAAAACTACCAAAAACTACTCACGTAGTGAGTG-CCTGTGTC
13430 TTGTTT
65 TTGTTT
* * *
13436 TAAAAAAACTATCCATTTAAAAAATAAAAACTACCAAAAACTATTCACGTAGTGAGTGCTTGTGT
1 TAAAAAAACTACCCATTT--AAAATAAAAACTACCAAAAACTACTCACGTAGTGAGTGCCTGTGT
13501 CTTGT
64 CTTGT
13506 AAATTTAAAG
Statistics
Matches: 59, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
69 16 0.27
72 14 0.24
73 29 0.49
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (70 bp):
TAAAAAAACTACCCATTTAAAATAAAAACTACCAAAAACTACTCACGTAGTGAGTGCCTGTGTCT
TGTTT
Found at i:15721 original size:22 final size:22
Alignment explanation
Indices: 15672--15722 Score: 77
Period size: 22 Copynumber: 2.3 Consensus size: 22
15662 ACTACAAGTT
*
15672 TAAAACACATTTATCTACCCAC
1 TAAAATACATTTATCTACCCAC
15694 TAAAATACATTCTATCTACCCAC
1 TAAAATACATT-TATCTACCCAC
15717 -AAAATA
1 TAAAATA
15723 AAGACCCATA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 16 0.59
23 11 0.41
ACGTcount: A:0.45, C:0.27, G:0.00, T:0.27
Consensus pattern (22 bp):
TAAAATACATTTATCTACCCAC
Found at i:15978 original size:19 final size:20
Alignment explanation
Indices: 15948--15986 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
15938 ATCAACTCCT
*
15948 AACAACATTAAAAGAAAAGG
1 AACAACATTAAAAAAAAAGG
15968 AACAA-ATTAAAAAAAAAGG
1 AACAACATTAAAAAAAAAGG
15987 TAGTATAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.69, C:0.08, G:0.13, T:0.10
Consensus pattern (20 bp):
AACAACATTAAAAAAAAAGG
Found at i:17914 original size:178 final size:177
Alignment explanation
Indices: 17603--17939 Score: 473
Period size: 178 Copynumber: 1.9 Consensus size: 177
17593 TTCCACGATA
* ** * *
17603 AGCAGAAATTATGTAATATTAAGTAGACCGTCTATTTTGTTAACCGAAACAACTAATTATTTGGA
1 AGCAGAAATTATATAATATTAAGTAGACCGTCTATTCCGTTAACCGAAACAACAAATTATTCGGA
* * *
17668 ATCATTTTTTATACCTTGAACATTAAATTTAGTTTTCGAATCCTTCATAAAAGTTGTAGATCATG
66 AGCATTTTTGATACCTTGAACATTAAATTTAGTTTTCGAATCCTTCATAAAAGTTGTAGATAATG
* *
17733 GAACAATCTTTCAAGAGACACTTGAATCATCTAAATCAGGCATCTAG
131 GAACAATATTTCAAGAGACACTTAAATCATCTAAATCAGGCATCTAG
* *
17780 AGCA-AAAGTTATATAATATTAAGTGGATCGTCTATTCCCGTTAACCGAAACAACAAATCT-TTC
1 AGCAGAAA-TTATATAATATTAAGTAGACCGTCTATT-CCGTTAACCGAAACAACAAAT-TATTC
* *
17843 GGAAGCATTTTTGATA-CTTGAAACATTAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTAGAT
63 GGAAGCATTTTTGATACCTTG-AACATTAAATTTAGTTTTCGAATCCTTCATAAAAGTTGTAGAT
* *
17907 AATGGAACAATATTTTAATAGACACTTAAATCA
127 AATGGAACAATATTTCAAGAGACACTTAAATCA
17940 CCCTAATCGG
Statistics
Matches: 140, Mismatches: 16, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
176 3 0.02
177 33 0.24
178 103 0.74
179 1 0.01
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.34
Consensus pattern (177 bp):
AGCAGAAATTATATAATATTAAGTAGACCGTCTATTCCGTTAACCGAAACAACAAATTATTCGGA
AGCATTTTTGATACCTTGAACATTAAATTTAGTTTTCGAATCCTTCATAAAAGTTGTAGATAATG
GAACAATATTTCAAGAGACACTTAAATCATCTAAATCAGGCATCTAG
Found at i:17972 original size:178 final size:176
Alignment explanation
Indices: 17603--17988 Score: 460
Period size: 178 Copynumber: 2.2 Consensus size: 176
17593 TTCCACGATA
* ** * *
17603 AGCAGAAATTATGTAATATTAAGTAGACCGTCTATTTTGTTAACCGAAACAACTAATTATTTGGA
1 AGCA-AAATTATATAATATTAAGTAGACCGTCTATTCCGTTAACCGAAACAACAAATTATTCGGA
* * *
17668 ATCATTTTTTATACCTTGAACATTAAATTTAGTTTTCGAATCCTTCATAAAAGTTGTAGATCATG
65 AGCATTTTTGATACCTTGAACATTAAATTTAGTTTTCGAATCCTTCATAAAAGTTGTAGATAATG
* * * *
17733 GAACAATCTTTCAAGAGACACTTGAATCATCTAAATCAGGCATCTAG
130 GAACAATATTTCAAGAGACACTTAAATCACCTAAATCAGGCATCGAG
* *
17780 AGCAAAAGTTATATAATATTAAGTGGATCGTCTATTCCCGTTAACCGAAACAACAAATCT-TTCG
1 AGCAAAA-TTATATAATATTAAGTAGACCGTCTATT-CCGTTAACCGAAACAACAAAT-TATTCG
* *
17844 GAAGCATTTTTGATA-CTTGAAACATTAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTAGATA
63 GAAGCATTTTTGATACCTTG-AACATTAAATTTAGTTTTCGAATCCTTCATAAAAGTTGTAGATA
* *
17908 ATGGAACAATATTTTAATAGACACTTAAATCACCCT-AATC-GG-ATAGCCGGAG
127 ATGGAACAATATTTCAAGAGACACTTAAATCA-CCTAAATCAGGCAT---C-GAG
* *
17960 AG-AAAATTATATAATGTTAAATAGACCGT
1 AGCAAAATTATATAATATTAAGTAGACCGT
17989 TTAACCAAAC
Statistics
Matches: 178, Mismatches: 22, Indels: 17
0.82 0.10 0.08
Matches are distributed among these distances:
176 5 0.03
177 35 0.20
178 126 0.71
179 8 0.04
180 4 0.02
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (176 bp):
AGCAAAATTATATAATATTAAGTAGACCGTCTATTCCGTTAACCGAAACAACAAATTATTCGGAA
GCATTTTTGATACCTTGAACATTAAATTTAGTTTTCGAATCCTTCATAAAAGTTGTAGATAATGG
AACAATATTTCAAGAGACACTTAAATCACCTAAATCAGGCATCGAG
Found at i:18436 original size:51 final size:51
Alignment explanation
Indices: 18371--18503 Score: 205
Period size: 51 Copynumber: 2.6 Consensus size: 51
18361 ACACGTGTAC
* *
18371 AGTGTTTG-TATGTCCGGAGACAAGATTAAAACAAGAGAAAAACATTAAAAG
1 AGTGTTTGAT-TGTCCAGAGACAAGATTAAAACAAGAGAAAAACACTAAAAG
*
18422 AGTGTTTGATTGTCCAGAGACAAGATTGAAACAAGAGAAAAACACTAAAAG
1 AGTGTTTGATTGTCCAGAGACAAGATTAAAACAAGAGAAAAACACTAAAAG
*
18473 AGTGTTTGATTGTCCTGAGACAAGATCTAAA
1 AGTGTTTGATTGTCCAGAGACAAGAT-TAAA
18504 TAAGGAAAAG
Statistics
Matches: 75, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
51 71 0.95
52 4 0.05
ACGTcount: A:0.44, C:0.11, G:0.22, T:0.23
Consensus pattern (51 bp):
AGTGTTTGATTGTCCAGAGACAAGATTAAAACAAGAGAAAAACACTAAAAG
Found at i:20637 original size:15 final size:17
Alignment explanation
Indices: 20611--20642 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
20601 ACTTAGCCAC
20611 GAGTTCAATTTG-TCTG
1 GAGTTCAATTTGATCTG
20627 GAGTT-AATTTGATCTG
1 GAGTTCAATTTGATCTG
20643 ACCTTCAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.22, C:0.09, G:0.25, T:0.44
Consensus pattern (17 bp):
GAGTTCAATTTGATCTG
Found at i:21125 original size:14 final size:14
Alignment explanation
Indices: 21106--21132 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
21096 TCTACTATCT
21106 AGCCAATGAGACAA
1 AGCCAATGAGACAA
21120 AGCCAATGAGACA
1 AGCCAATGAGACA
21133 GTAATTTGGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.48, C:0.22, G:0.22, T:0.07
Consensus pattern (14 bp):
AGCCAATGAGACAA
Found at i:22010 original size:42 final size:43
Alignment explanation
Indices: 21939--22023 Score: 154
Period size: 42 Copynumber: 2.0 Consensus size: 43
21929 CATCTTCTTA
*
21939 TTAGGAATATATTTTTTTGTAATTGTTTAAGTCGGTTAGTAAG
1 TTAGGAATATATTTTTTTATAATTGTTTAAGTCGGTTAGTAAG
21982 TTAGGAATATA-TTTTTTATAATTGTTTAAGTCGGTTAGTAAG
1 TTAGGAATATATTTTTTTATAATTGTTTAAGTCGGTTAGTAAG
22024 AAGATTTTGC
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
42 30 0.73
43 11 0.27
ACGTcount: A:0.29, C:0.02, G:0.20, T:0.48
Consensus pattern (43 bp):
TTAGGAATATATTTTTTTATAATTGTTTAAGTCGGTTAGTAAG
Found at i:25420 original size:44 final size:44
Alignment explanation
Indices: 25370--25459 Score: 180
Period size: 44 Copynumber: 2.0 Consensus size: 44
25360 TCACTATTAG
25370 TAGTTTCTTATTTACATACTCTTATAATGTCATTTTCTTTGTAT
1 TAGTTTCTTATTTACATACTCTTATAATGTCATTTTCTTTGTAT
25414 TAGTTTCTTATTTACATACTCTTATAATGTCATTTTCTTTGTAT
1 TAGTTTCTTATTTACATACTCTTATAATGTCATTTTCTTTGTAT
25458 TA
1 TA
25460 AATTCGAACT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.23, C:0.13, G:0.07, T:0.57
Consensus pattern (44 bp):
TAGTTTCTTATTTACATACTCTTATAATGTCATTTTCTTTGTAT
Found at i:27856 original size:17 final size:17
Alignment explanation
Indices: 27823--27868 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 17
27813 CTGAAATTAG
*
27823 TAATAATTATTGGATAA
1 TAATAATTATTTGATAA
*
27840 TAATAATTATTTTATAA
1 TAATAATTATTTGATAA
* *
27857 TTATTATTATTT
1 TAATAATTATTT
27869 CAGTAAATAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.54
Consensus pattern (17 bp):
TAATAATTATTTGATAA
Found at i:31602 original size:9 final size:9
Alignment explanation
Indices: 31590--31631 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
31580 AACATCTTAA
31590 TATTATAAT
1 TATTATAAT
31599 TATTA-AACT
1 TATTATAA-T
*
31608 TATTATTAT
1 TATTATAAT
*
31617 TATAATAAT
1 TATTATAAT
31626 TATTAT
1 TATTAT
31632 TAGTGGTATG
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
8 2 0.07
9 24 0.89
10 1 0.04
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (9 bp):
TATTATAAT
Done.