Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013571.1 Corchorus olitorius cultivar O-4 contig13604, 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: 25372
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Found at i:812 original size:4 final size:4
Alignment explanation
Indices: 801--1022 Score: 103
Period size: 4 Copynumber: 57.0 Consensus size: 4
791 AAAGATTTTT
* * * **
801 TTTA -TTA TTTA TTCA CT-A TTTA TTTA TTT- TTTA TTTT TTTAA ACTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT-A TTTA
* * *
847 -TTA TCTA TTTA TTTA -CTA TTTA TTTA TTTA TTTA TTT- TTAA CTATTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA -T-TTA
* * * **
894 TCTA TTTA TTTA -CTA TTTA TCTT- TTTA TTTA TTT- TTAA CTATTA TCAA
1 TTTA TTTA TTTA TTTA TTTA T-TTA TTTA TTTA TTTA TTTA -T-TTA TTTA
* * * *
942 TTTA TTTA -CTA TTTA TCTT- TTTA TTTA TTAA TTTA ATTA -TTA TCTA
1 TTTA TTTA TTTA TTTA T-TTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
* *
988 TTTA TTTA -CTA TTTA TCTT- TTTA TTTA TTAA TTTA
1 TTTA TTTA TTTA TTTA T-TTA TTTA TTTA TTTA TTTA
1023 GCCATTATCT
Statistics
Matches: 161, Mismatches: 35, Indels: 44
0.67 0.15 0.18
Matches are distributed among these distances:
3 31 0.19
4 115 0.71
5 11 0.07
6 4 0.02
ACGTcount: A:0.27, C:0.07, G:0.00, T:0.66
Consensus pattern (4 bp):
TTTA
Found at i:866 original size:46 final size:46
Alignment explanation
Indices: 802--1040 Score: 314
Period size: 46 Copynumber: 5.3 Consensus size: 46
792 AAGATTTTTT
*
802 TTAT-TATTTATTCACTATTTAT-TTATTT-TTTATTTTTTTAAACTA
1 TTATCTATTTATTTACTATTTATCTT-TTTATTTATTTTTTT-AACTA
847 TTATCTATTTATTTACTATTTAT-TTATTTATTTA--TTTTTAACTA
1 TTATCTATTTATTTACTATTTATCTT-TTTATTTATTTTTTTAACTA
891 TTATCTATTTATTTACTATTTATCTTTTTATTTA--TTTTTAACTA
1 TTATCTATTTATTTACTATTTATCTTTTTATTTATTTTTTTAACTA
* ** *
935 TTATCAATTTATTTACTATTTATCTTTTTATTTATTAATTTAATTA
1 TTATCTATTTATTTACTATTTATCTTTTTATTTATTTTTTTAACTA
** * *
981 TTATCTATTTATTTACTATTTATCTTTTTATTTATTAATTTAGCCA
1 TTATCTATTTATTTACTATTTATCTTTTTATTTATTTTTTTAACTA
1027 TTATCTATTTATTT
1 TTATCTATTTATTT
1041 GTTATTATTA
Statistics
Matches: 180, Mismatches: 9, Indels: 9
0.91 0.05 0.05
Matches are distributed among these distances:
44 79 0.44
45 11 0.06
46 86 0.48
47 4 0.02
ACGTcount: A:0.27, C:0.08, G:0.00, T:0.65
Consensus pattern (46 bp):
TTATCTATTTATTTACTATTTATCTTTTTATTTATTTTTTTAACTA
Found at i:905 original size:44 final size:44
Alignment explanation
Indices: 821--1040 Score: 329
Period size: 44 Copynumber: 5.0 Consensus size: 44
811 ATTCACTATT
*
821 TATTTAT-TTTTTATTT-TTTTAAACTATTATCTATTTATTTAC
1 TATTTATCTTTTTATTTATTTTTAACTATTATCTATTTATTTAC
863 TATTTAT-TTATTTATTTATTTTTAACTATTATCTATTTATTTAC
1 TATTTATCTT-TTTATTTATTTTTAACTATTATCTATTTATTTAC
*
907 TATTTATCTTTTTATTTATTTTTAACTATTATCAATTTATTTAC
1 TATTTATCTTTTTATTTATTTTTAACTATTATCTATTTATTTAC
*
951 TATTTATCTTTTTATTTATTAATTTAATTATTATCTATTTATTTAC
1 TATTTATCTTTTTATTTATT--TTTAACTATTATCTATTTATTTAC
* *
997 TATTTATCTTTTTATTTATTAATTTAGCCATTATCTATTTATTT
1 TATTTATCTTTTTATTTATT--TTTAACTATTATCTATTTATTT
1041 GTTATTATTA
Statistics
Matches: 166, Mismatches: 7, Indels: 6
0.93 0.04 0.03
Matches are distributed among these distances:
42 9 0.05
43 7 0.04
44 85 0.51
45 2 0.01
46 63 0.38
ACGTcount: A:0.27, C:0.08, G:0.00, T:0.65
Consensus pattern (44 bp):
TATTTATCTTTTTATTTATTTTTAACTATTATCTATTTATTTAC
Found at i:923 original size:19 final size:19
Alignment explanation
Indices: 843--1014 Score: 101
Period size: 19 Copynumber: 9.1 Consensus size: 19
833 ATTTTTTTAA
843 ACTA-TTATCTATTTATTT
1 ACTATTTATCTATTTATTT
*
861 ACTATTTATTTATTTATTT
1 ACTATTTATCTATTTATTT
*
880 ATTTTTAACTATTATCTATTTATTT
1 A---CT-A-T-TTATCTATTTATTT
*
905 ACTATTTATCTTTTTATTT
1 ACTATTTATCTATTTATTT
* * *
924 A-TTTTTAACTATTATCAATT
1 ACTATTTATCTATT-T-ATTT
944 --TATTTA-CTATTTA--T
1 ACTATTTATCTATTTATTT
* * *
958 -CTTTTTATTTATTAATTT
1 ACTATTTATCTATTTATTT
*
976 AAT-TATTATCTATTTATTT
1 ACTAT-TTATCTATTTATTT
*
995 ACTATTTATCTTTTTATTT
1 ACTATTTATCTATTTATTT
1014 A
1 A
1015 TTAATTTAGC
Statistics
Matches: 120, Mismatches: 18, Indels: 31
0.71 0.11 0.18
Matches are distributed among these distances:
14 1 0.01
15 5 0.04
16 6 0.05
17 1 0.01
18 20 0.17
19 63 0.52
20 5 0.04
21 1 0.01
22 2 0.02
23 1 0.01
24 1 0.01
25 14 0.12
ACGTcount: A:0.27, C:0.08, G:0.00, T:0.65
Consensus pattern (19 bp):
ACTATTTATCTATTTATTT
Found at i:1092 original size:24 final size:24
Alignment explanation
Indices: 1062--1122 Score: 79
Period size: 24 Copynumber: 2.5 Consensus size: 24
1052 TATTTTTCGC
* *
1062 TACCTATTTATTTA-TTATTCTCTG
1 TACCTATTTATCTATTTA-TCTCTA
*
1086 TATCTATTTATCTATTTATCTCTA
1 TACCTATTTATCTATTTATCTCTA
1110 TACCTATTTATCT
1 TACCTATTTATCT
1123 TTTTTTATTA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
24 29 0.91
25 3 0.09
ACGTcount: A:0.23, C:0.18, G:0.02, T:0.57
Consensus pattern (24 bp):
TACCTATTTATCTATTTATCTCTA
Found at i:2331 original size:22 final size:22
Alignment explanation
Indices: 2306--2364 Score: 109
Period size: 22 Copynumber: 2.7 Consensus size: 22
2296 CTCATAGCGT
*
2306 GGTTATCGAAATTTCTTAGTAA
1 GGTTATCAAAATTTCTTAGTAA
2328 GGTTATCAAAATTTCTTAGTAA
1 GGTTATCAAAATTTCTTAGTAA
2350 GGTTATCAAAATTTC
1 GGTTATCAAAATTTC
2365 ATGAGGTTTA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.34, C:0.10, G:0.15, T:0.41
Consensus pattern (22 bp):
GGTTATCAAAATTTCTTAGTAA
Found at i:2469 original size:22 final size:22
Alignment explanation
Indices: 2439--2483 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
2429 ATAATAATGT
*
2439 GGTTATCAAAATTTCACAGTAA
1 GGTTATCAAAATTACACAGTAA
* * *
2461 GGTTTTCAAGATTACATAGTAA
1 GGTTATCAAAATTACACAGTAA
2483 G
1 G
2484 TGGGTGTTTA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.38, C:0.11, G:0.18, T:0.33
Consensus pattern (22 bp):
GGTTATCAAAATTACACAGTAA
Found at i:3242 original size:3 final size:3
Alignment explanation
Indices: 3234--3276 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
3224 CCTGTTTTTT
3234 CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC C
1 CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC C
3277 ATTGCTGGCT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.00, C:0.67, G:0.00, T:0.33
Consensus pattern (3 bp):
CTC
Found at i:4848 original size:3 final size:3
Alignment explanation
Indices: 4840--4868 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
4830 TTCACTGATT
4840 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
4869 TGTGTTATGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:10183 original size:6 final size:6
Alignment explanation
Indices: 10172--10204 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
10162 GGTGTGAGCC
10172 TGGGAT TGGGAT TGGGAT TGGGAT TGGGAT TGG
1 TGGGAT TGGGAT TGGGAT TGGGAT TGGGAT TGG
10205 CAATGGCAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.15, C:0.00, G:0.52, T:0.33
Consensus pattern (6 bp):
TGGGAT
Found at i:14007 original size:2 final size:2
Alignment explanation
Indices: 13966--13995 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
13956 CTTTTGTGTA
*
13966 AT AT AT AT AT AT AT AC AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
13996 GGTTAATATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:14172 original size:31 final size:31
Alignment explanation
Indices: 14134--14193 Score: 120
Period size: 31 Copynumber: 1.9 Consensus size: 31
14124 GAGTTTTGTA
14134 AAACTTTTGAATCACCTATTATACCCTTAAT
1 AAACTTTTGAATCACCTATTATACCCTTAAT
14165 AAACTTTTGAATCACCTATTATACCCTTA
1 AAACTTTTGAATCACCTATTATACCCTTA
14194 TTTTTCGAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.35, C:0.23, G:0.03, T:0.38
Consensus pattern (31 bp):
AAACTTTTGAATCACCTATTATACCCTTAAT
Found at i:14392 original size:94 final size:93
Alignment explanation
Indices: 14231--14494 Score: 411
Period size: 94 Copynumber: 2.8 Consensus size: 93
14221 TTGTTTAAAT
* * *
14231 TTTTATAGTTTTAGTCAACTAAAATCTCAATTTTTATTTAATTAAATCTAATATCCTTATAACTA
1 TTTTATAGTTTTAATCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAACTA
*
14296 TTTTTATTTTTACCATTTTACTATTTTAC
66 -TTTTATTTTTACCATTTAACTATTTTAC
* * *
14325 TTTTATAGTTTTACTCAACTAAAACCTCTATTTTTATTTAATTAAATCTAATATCCTTAAAACTA
1 TTTTATAGTTTTAATCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAACTA
*
14390 TTTTATTTTTTACCATTTAACTATTTTAT
66 TTTTA-TTTTTACCATTTAACTATTTTAC
* * *
14419 TTTTATGGTTTTAATCAACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCCTTATATCTA
1 TTTTATAGTTTTAATCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAACTA
14484 TTTTATTTTTA
66 TTTTATTTTTA
14495 TGATATTACT
Statistics
Matches: 157, Mismatches: 12, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
93 11 0.07
94 146 0.93
ACGTcount: A:0.33, C:0.13, G:0.02, T:0.53
Consensus pattern (93 bp):
TTTTATAGTTTTAATCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAACTA
TTTTATTTTTACCATTTAACTATTTTAC
Found at i:14516 original size:52 final size:52
Alignment explanation
Indices: 14454--14561 Score: 216
Period size: 52 Copynumber: 2.1 Consensus size: 52
14444 CTCTATTTTC
14454 ATTTAATTAAATCTAATATCCTTATATCTATTTTATTTTTATGATATTACTA
1 ATTTAATTAAATCTAATATCCTTATATCTATTTTATTTTTATGATATTACTA
14506 ATTTAATTAAATCTAATATCCTTATATCTATTTTATTTTTATGATATTACTA
1 ATTTAATTAAATCTAATATCCTTATATCTATTTTATTTTTATGATATTACTA
14558 ATTT
1 ATTT
14562 GTAGCCAGAT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 56 1.00
ACGTcount: A:0.34, C:0.09, G:0.02, T:0.55
Consensus pattern (52 bp):
ATTTAATTAAATCTAATATCCTTATATCTATTTTATTTTTATGATATTACTA
Found at i:21977 original size:21 final size:21
Alignment explanation
Indices: 21950--22198 Score: 288
Period size: 21 Copynumber: 11.9 Consensus size: 21
21940 TATATGAAAC
21950 TTTGGGGTTTGACTATCAAAA
1 TTTGGGGTTTGACTATCAAAA
* * *
21971 TTCGGGG-TTGACCATCAAAC
1 TTTGGGGTTTGACTATCAAAA
* *
21991 TTTAGGGTTTGACTATAAAAA
1 TTTGGGGTTTGACTATCAAAA
* * *
22012 TTTGGGGGTTGACCATCAAAC
1 TTTGGGGTTTGACTATCAAAA
*
22033 TTTGGGGTTTGACTATAAAAA
1 TTTGGGGTTTGACTATCAAAA
* * *
22054 TTTGGGGGTTGACAATCAAAC
1 TTTGGGGTTTGACTATCAAAA
22075 TTTGGGGTTTGACTATCAAAA
1 TTTGGGGTTTGACTATCAAAA
*
22096 TTTGGGGTTTGA-TAATCAAAT
1 TTTGGGGTTTGACT-ATCAAAA
22117 TTTCGGGG-TTGACTATCAAAA
1 TTT-GGGGTTTGACTATCAAAA
* * *
22138 TTTGGGGGTTGACCATCAAAC
1 TTTGGGGTTTGACTATCAAAA
22159 TTTGGGGTTTGACTATCAAAA
1 TTTGGGGTTTGACTATCAAAA
** *
22180 TTTAAGGTTTGACCATCAA
1 TTTGGGGTTTGACTATCAA
22199 TGCGATTTGA
Statistics
Matches: 189, Mismatches: 34, Indels: 10
0.81 0.15 0.04
Matches are distributed among these distances:
20 21 0.11
21 163 0.86
22 5 0.03
ACGTcount: A:0.29, C:0.12, G:0.24, T:0.35
Consensus pattern (21 bp):
TTTGGGGTTTGACTATCAAAA
Found at i:22033 original size:42 final size:42
Alignment explanation
Indices: 21946--22198 Score: 375
Period size: 42 Copynumber: 6.0 Consensus size: 42
21936 GAAATATATG
*
21946 AAACTTTGGGGTTTGACTATCAAAA-TTCGGGGTTGACCATC
1 AAACTTTGGGGTTTGACTATCAAAATTTGGGGGTTGACCATC
* *
21987 AAACTTTAGGGTTTGACTATAAAAATTTGGGGGTTGACCATC
1 AAACTTTGGGGTTTGACTATCAAAATTTGGGGGTTGACCATC
* *
22029 AAACTTTGGGGTTTGACTATAAAAATTTGGGGGTTGACAATC
1 AAACTTTGGGGTTTGACTATCAAAATTTGGGGGTTGACCATC
* **
22071 AAACTTTGGGGTTTGACTATCAAAATTTGGGGTTTGATAATC
1 AAACTTTGGGGTTTGACTATCAAAATTTGGGGGTTGACCATC
*
22113 AAATTTTCGGGG-TTGACTATCAAAATTTGGGGGTTGACCATC
1 AAACTTT-GGGGTTTGACTATCAAAATTTGGGGGTTGACCATC
** *
22155 AAACTTTGGGGTTTGACTATCAAAATTTAAGGTTTGACCATC
1 AAACTTTGGGGTTTGACTATCAAAATTTGGGGGTTGACCATC
22197 AA
1 AA
22199 TGCGATTTGA
Statistics
Matches: 193, Mismatches: 16, Indels: 5
0.90 0.07 0.02
Matches are distributed among these distances:
41 27 0.14
42 162 0.84
43 4 0.02
ACGTcount: A:0.30, C:0.13, G:0.24, T:0.34
Consensus pattern (42 bp):
AAACTTTGGGGTTTGACTATCAAAATTTGGGGGTTGACCATC
Found at i:22326 original size:21 final size:21
Alignment explanation
Indices: 22294--22354 Score: 86
Period size: 21 Copynumber: 2.9 Consensus size: 21
22284 AATTCAATCA
22294 CCAAATTTTTGATAGTCAAACC
1 CCAAA-TTTTGATAGTCAAACC
*
22316 CCAAATTTTGATAGTTAAACC
1 CCAAATTTTGATAGTCAAACC
* *
22337 ACAAAATTTGATAGTCAA
1 CCAAATTTTGATAGTCAA
22355 CATGTTAAAC
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
21 30 0.86
22 5 0.14
ACGTcount: A:0.41, C:0.18, G:0.10, T:0.31
Consensus pattern (21 bp):
CCAAATTTTGATAGTCAAACC
Found at i:22711 original size:21 final size:21
Alignment explanation
Indices: 22660--22711 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 21
22650 TTTGATGGTT
*
22660 AAACCCCAAAGTTTGATGATC
1 AAACCCCAAAGTTTAATGATC
* * *
22681 ACATCTCAAAGTTTAAT-ATTC
1 AAACCCCAAAGTTTAATGA-TC
22702 AAACCCCAAA
1 AAACCCCAAA
22712 TTTCGATAGT
Statistics
Matches: 23, Mismatches: 7, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
20 1 0.04
21 22 0.96
ACGTcount: A:0.42, C:0.25, G:0.08, T:0.25
Consensus pattern (21 bp):
AAACCCCAAAGTTTAATGATC
Found at i:23114 original size:20 final size:20
Alignment explanation
Indices: 23091--23131 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
23081 ATATTACTAT
23091 AATA-GTATTAATTTATAATC
1 AATATGTATT-ATTTATAATC
*
23111 AATATGTATTATTTATTATC
1 AATATGTATTATTTATAATC
23131 A
1 A
23132 TATTTTTGGC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.49
Consensus pattern (20 bp):
AATATGTATTATTTATAATC
Found at i:23722 original size:16 final size:16
Alignment explanation
Indices: 23701--23732 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
23691 ATGTATGTAC
23701 ATGTATTAATTTAATT
1 ATGTATTAATTTAATT
23717 ATGTATTAATTTAATT
1 ATGTATTAATTTAATT
23733 TTAATAGGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (16 bp):
ATGTATTAATTTAATT
Done.