Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014421.1 Corchorus olitorius cultivar O-4 contig14454, 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: 54535
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:8759 original size:43 final size:44
Alignment explanation
Indices: 8692--8778 Score: 131
Period size: 43 Copynumber: 2.0 Consensus size: 44
8682 AGGACATTGG
** *
8692 TTAGAGTTTTAGAAATTTTGGAAAAAA-TCTGACTTGTCAAAAT
1 TTAGAGTTTTAGAAATGATAGAAAAAATTCTGACTTGTCAAAAT
*
8735 TTAGAGTTTTAGAAATGATAGAAAAAATTCTGATTTGTCAAAAT
1 TTAGAGTTTTAGAAATGATAGAAAAAATTCTGACTTGTCAAAAT
8779 CTTATTAATC
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
43 24 0.62
44 15 0.38
ACGTcount: A:0.41, C:0.06, G:0.16, T:0.37
Consensus pattern (44 bp):
TTAGAGTTTTAGAAATGATAGAAAAAATTCTGACTTGTCAAAAT
Found at i:19914 original size:15 final size:14
Alignment explanation
Indices: 19887--19926 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
19877 TCGTTTGGTA
*
19887 TTGTTTTCG-TTTT
1 TTGTTTTTGTTTTT
19900 TTGTTTTTTGTTTTT
1 TTG-TTTTTGTTTTT
19915 TTGTTTTTGTTT
1 TTGTTTTTGTTT
19927 CGTTTTTGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
13 3 0.12
14 14 0.58
15 7 0.29
ACGTcount: A:0.00, C:0.03, G:0.15, T:0.82
Consensus pattern (14 bp):
TTGTTTTTGTTTTT
Found at i:20438 original size:2 final size:2
Alignment explanation
Indices: 20393--20428 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
20383 CTTTATCCGA
*
20393 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
20429 TAACATATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:23533 original size:21 final size:22
Alignment explanation
Indices: 23482--23637 Score: 101
Period size: 22 Copynumber: 7.1 Consensus size: 22
23472 ATAAAAAATT
* * *
23482 ATAGGAAGATTAAC-AAATCTC
1 ATAGGAAGGTTATCAAAATTTC
23503 ATAGGGAAGGTTA-CAAAATTTC
1 ATA-GGAAGGTTATCAAAATTTC
23525 ATAGGAAGGTT-TACTAAAATTTC
1 ATAGGAAGGTTAT-C-AAAATTTC
* *** *
23548 AAAATTAGGTTATCAAACTTTC
1 ATAGGAAGGTTATCAAAATTTC
* *
23570 ATATGGAA-ATTATCACAATTTC
1 ATA-GGAAGGTTATCAAAATTTC
*
23592 ATAGGTAA--TTATCAAAATTTA
1 ATAGG-AAGGTTATCAAAATTTC
*
23613 ATAGGGTA-GTTATCAAAATTTC
1 ATA-GGAAGGTTATCAAAATTTC
23635 ATA
1 ATA
23638 AAGATATTCA
Statistics
Matches: 107, Mismatches: 18, Indels: 19
0.74 0.12 0.13
Matches are distributed among these distances:
21 29 0.27
22 60 0.56
23 17 0.16
24 1 0.01
ACGTcount: A:0.42, C:0.10, G:0.14, T:0.33
Consensus pattern (22 bp):
ATAGGAAGGTTATCAAAATTTC
Found at i:24662 original size:21 final size:21
Alignment explanation
Indices: 24636--24732 Score: 106
Period size: 21 Copynumber: 4.4 Consensus size: 21
24626 TGCTAGGAGT
24636 TCATTGGAGCAA-GTTCCAAGC
1 TCATTGGAG-AAGGTTCCAAGC
*
24657 TCATTGGAGAAGGTTCCAAAC
1 TCATTGGAGAAGGTTCCAAGC
*
24678 TCATTGGAGAATGTTCCAATCCAAGC
1 TCATTGGAGAA-GGT----TCCAAGC
*
24704 TCATTGGAGAAGGTTTCAAGC
1 TCATTGGAGAAGGTTCCAAGC
24725 TCATTGGA
1 TCATTGGA
24733 ATTGCCTAAG
Statistics
Matches: 65, Mismatches: 5, Indels: 12
0.79 0.06 0.15
Matches are distributed among these distances:
20 2 0.03
21 42 0.65
22 2 0.03
25 2 0.03
26 17 0.26
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.27
Consensus pattern (21 bp):
TCATTGGAGAAGGTTCCAAGC
Found at i:27270 original size:33 final size:33
Alignment explanation
Indices: 27169--27273 Score: 122
Period size: 33 Copynumber: 3.2 Consensus size: 33
27159 TTTCAAAGAG
* * * *
27169 TGTTTTAGATGTTGTTAGTGATGATACTAAACC
1 TGTTTTAGGTGTTGTTTGTGATGAAACTAAATC
** * *
27202 TAATTTAAGTGTTGTTTGTGATGACACTAAATC
1 TGTTTTAGGTGTTGTTTGTGATGAAACTAAATC
27235 TGTTTTAGGTGTTGTTTGTGATGAAAC-AAATTC
1 TGTTTTAGGTGTTGTTTGTGATGAAACTAAA-TC
27268 TGTTTT
1 TGTTTT
27274 GGATGCTAAT
Statistics
Matches: 60, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
32 3 0.05
33 57 0.95
ACGTcount: A:0.26, C:0.08, G:0.21, T:0.46
Consensus pattern (33 bp):
TGTTTTAGGTGTTGTTTGTGATGAAACTAAATC
Found at i:28787 original size:9 final size:9
Alignment explanation
Indices: 28769--28799 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
28759 TATTGATTCC
28769 TTTCCATTT
1 TTTCCATTT
*
28778 TTTTCATTT
1 TTTCCATTT
28787 TTTCCATTT
1 TTTCCATTT
28796 TTTC
1 TTTC
28800 TTTCTTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.10, C:0.19, G:0.00, T:0.71
Consensus pattern (9 bp):
TTTCCATTT
Found at i:28816 original size:20 final size:20
Alignment explanation
Indices: 28775--28819 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
28765 TTCCTTTCCA
28775 TTTTTTTCATTTTTTCCATT
1 TTTTTTTCATTTTTTCCATT
*
28795 TTTTCTTTC-TTTTTT-CGTT
1 TTTT-TTTCATTTTTTCCATT
28814 TTTTTT
1 TTTTTT
28820 CTTCAACTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
18 2 0.09
19 7 0.30
20 10 0.43
21 4 0.17
ACGTcount: A:0.04, C:0.13, G:0.02, T:0.80
Consensus pattern (20 bp):
TTTTTTTCATTTTTTCCATT
Found at i:29897 original size:21 final size:21
Alignment explanation
Indices: 29873--29912 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
29863 CATAATTTCT
* *
29873 TAAATCAGGGATTAAATTGAA
1 TAAAGCAGGGATCAAATTGAA
29894 TAAAGCAGGGATCAAATTG
1 TAAAGCAGGGATCAAATTG
29913 CATTTAATCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.45, C:0.07, G:0.23, T:0.25
Consensus pattern (21 bp):
TAAAGCAGGGATCAAATTGAA
Found at i:30069 original size:41 final size:40
Alignment explanation
Indices: 29975--30071 Score: 106
Period size: 41 Copynumber: 2.4 Consensus size: 40
29965 AATAAAATCT
* * *
29975 TAAATCAAGGGCGAAATTGAATCAATTAACGAATAAACAT
1 TAAATCAAGGACTAAATTGAATCAATTAACGAATAAACAC
* * *
30015 TCCAATTAGGGACTAAATTGAATCAATTAACGAACATAAAC-C
1 T-AAATCAAGGACTAAATTGAATCAATTAACG-A-ATAAACAC
30057 TAAATCAAGGACTAA
1 TAAATCAAGGACTAA
30072 GGTGAAAACG
Statistics
Matches: 45, Mismatches: 9, Indels: 5
0.76 0.15 0.08
Matches are distributed among these distances:
40 1 0.02
41 36 0.80
42 2 0.04
43 6 0.13
ACGTcount: A:0.48, C:0.15, G:0.13, T:0.23
Consensus pattern (40 bp):
TAAATCAAGGACTAAATTGAATCAATTAACGAATAAACAC
Found at i:32655 original size:26 final size:26
Alignment explanation
Indices: 32617--32701 Score: 134
Period size: 26 Copynumber: 3.2 Consensus size: 26
32607 TCTAAATGCG
32617 CAAATGACCAAAATGCCCCTGAAGTA
1 CAAATGACCAAAATGCCCCTGAAGTA
* * *
32643 CAAATGACTAAAATGCCCCTGAACATG
1 CAAATGACCAAAATGCCCCTGAA-GTA
32670 CAAATGACCAAAATGCCCCTGAAGTA
1 CAAATGACCAAAATGCCCCTGAAGTA
32696 CAAATG
1 CAAATG
32702 CTAATCAAGG
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
26 29 0.56
27 23 0.44
ACGTcount: A:0.42, C:0.26, G:0.15, T:0.16
Consensus pattern (26 bp):
CAAATGACCAAAATGCCCCTGAAGTA
Found at i:32682 original size:27 final size:26
Alignment explanation
Indices: 32590--32701 Score: 125
Period size: 26 Copynumber: 4.2 Consensus size: 26
32580 TAACAAACCC
* *
32590 AATGATCAAAATGCCCCTCTAAATGCGCA
1 AATGACCAAAATGCCCCT-GAAAT--GCA
* *
32619 AATGACCAAAATGCCCCTGAAGTACA
1 AATGACCAAAATGCCCCTGAAATGCA
*
32645 AATGACTAAAATGCCCCTGAACATGCA
1 AATGACCAAAATGCCCCTGAA-ATGCA
* *
32672 AATGACCAAAATGCCCCTGAAGTACA
1 AATGACCAAAATGCCCCTGAAATGCA
32698 AATG
1 AATG
32702 CTAATCAAGG
Statistics
Matches: 72, Mismatches: 10, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
26 29 0.40
27 23 0.32
28 3 0.04
29 17 0.24
ACGTcount: A:0.41, C:0.26, G:0.15, T:0.18
Consensus pattern (26 bp):
AATGACCAAAATGCCCCTGAAATGCA
Found at i:44121 original size:18 final size:18
Alignment explanation
Indices: 44098--44137 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
44088 AGTACTTGAC
44098 TTTATAATTAGTATAGAT
1 TTTATAATTAGTATAGAT
44116 TTTATAATTAGTATAGAT
1 TTTATAATTAGTATAGAT
44134 TTTA
1 TTTA
44138 ATAAAGGGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.38, C:0.00, G:0.10, T:0.53
Consensus pattern (18 bp):
TTTATAATTAGTATAGAT
Found at i:45207 original size:34 final size:34
Alignment explanation
Indices: 45165--45235 Score: 142
Period size: 34 Copynumber: 2.1 Consensus size: 34
45155 CCTCTTCTCC
45165 CTAAACACATGTTGCAAACCATCCCTAATAAGAG
1 CTAAACACATGTTGCAAACCATCCCTAATAAGAG
45199 CTAAACACATGTTGCAAACCATCCCTAATAAGAG
1 CTAAACACATGTTGCAAACCATCCCTAATAAGAG
45233 CTA
1 CTA
45236 TTTCAGCTAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.41, C:0.27, G:0.11, T:0.21
Consensus pattern (34 bp):
CTAAACACATGTTGCAAACCATCCCTAATAAGAG
Found at i:45418 original size:48 final size:49
Alignment explanation
Indices: 45346--45442 Score: 160
Period size: 48 Copynumber: 2.0 Consensus size: 49
45336 TCCCAATTTT
*
45346 AATTTTGATAGAACTTTGTCGGATA-CCCATCCCAATTTTTAATTGAGC
1 AATTTTGATAGAACTTTGTCGGATACCCCATCCCAATTATTAATTGAGC
* *
45394 AATTTTGATAGAGCTTTGTTGGATACCCCATCCCAATTATTAATTGAGC
1 AATTTTGATAGAACTTTGTCGGATACCCCATCCCAATTATTAATTGAGC
45443 TTTAGAGGTC
Statistics
Matches: 45, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
48 23 0.51
49 22 0.49
ACGTcount: A:0.29, C:0.19, G:0.15, T:0.37
Consensus pattern (49 bp):
AATTTTGATAGAACTTTGTCGGATACCCCATCCCAATTATTAATTGAGC
Found at i:47324 original size:110 final size:113
Alignment explanation
Indices: 47124--47348 Score: 348
Period size: 110 Copynumber: 2.0 Consensus size: 113
47114 ACACCAACCG
*
47124 TAGCAGTGGTAGCTGCTCGATTACATGGAGATCCATGTTAAAATTAGTTAGAGAGTTGGTTGATA
1 TAGCAGTGGTAGCTGCTCGATTACATGGAGATCCATGTTAAAA-TAGTTACAGAGTTGGTTGATA
*
47189 AAGGTTATGGCTCTGCCATTGGCAAT-AAAGAAATACGTGGTTTTGGTT
65 AAGGTTATGGCTCTACCATTGGCAATCAAAGAAATACGTGGTTTTGGTT
*
47237 TAGCAGTGGTAGCTGCTCGATTAGATGGAGATCCATGTT-AAA-AGTTACAGAGTTGGTTGATAA
1 TAGCAGTGGTAGCTGCTCGATTACATGGAGATCCATGTTAAAATAGTTACAGAGTTGGTTGATAA
* * ** *
47300 AGGTTTTGGCTCTATCATTGGCAATCGTATAAATACGTGGTTTTGGTT
66 AGGTTATGGCTCTACCATTGGCAATCAAAGAAATACGTGGTTTTGGTT
47348 T
1 T
47349 GAAAATTGGA
Statistics
Matches: 103, Mismatches: 8, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
110 42 0.41
111 20 0.19
112 3 0.03
113 38 0.37
ACGTcount: A:0.27, C:0.12, G:0.27, T:0.34
Consensus pattern (113 bp):
TAGCAGTGGTAGCTGCTCGATTACATGGAGATCCATGTTAAAATAGTTACAGAGTTGGTTGATAA
AGGTTATGGCTCTACCATTGGCAATCAAAGAAATACGTGGTTTTGGTT
Found at i:48711 original size:21 final size:21
Alignment explanation
Indices: 48685--48726 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
48675 TTCGTGTGTT
*
48685 CATGATGAACATGATTTGCAG
1 CATGATGAACAGGATTTGCAG
48706 CATGATGAACAGGATTTGCAG
1 CATGATGAACAGGATTTGCAG
48727 TAATACTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.14, G:0.26, T:0.26
Consensus pattern (21 bp):
CATGATGAACAGGATTTGCAG
Found at i:52202 original size:29 final size:29
Alignment explanation
Indices: 52147--52202 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
52137 TTGGAGATTA
*
52147 ATTGAAGATAATTTCAAGTCAGGAAGAGC
1 ATTGAAGATAATTTCAAGTCAGAAAGAGC
* *
52176 ATTGAAGAATTATTTCAAG-GAGAAAGA
1 ATTGAAG-ATAATTTCAAGTCAGAAAGA
52203 ATTAAGGATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 13 0.57
30 10 0.43
ACGTcount: A:0.45, C:0.07, G:0.23, T:0.25
Consensus pattern (29 bp):
ATTGAAGATAATTTCAAGTCAGAAAGAGC
Found at i:52863 original size:2 final size:2
Alignment explanation
Indices: 52856--52882 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
52846 CTTGTACTTT
52856 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
52883 TATTCTCATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.