Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016555.1 Corchorus olitorius cultivar O-4 contig16588, 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: 92689
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:4166 original size:27 final size:27
Alignment explanation
Indices: 4090--4158 Score: 120
Period size: 27 Copynumber: 2.6 Consensus size: 27
4080 AATTAATTTG
*
4090 AAACAAGTTTATTTTTTTTGTATCAAA
1 AAACAAGTTTAATTTTTTTGTATCAAA
*
4117 AAACAAGTTTAATTTTTTTGTATGAAA
1 AAACAAGTTTAATTTTTTTGTATCAAA
4144 AAACAAGTTTAATTT
1 AAACAAGTTTAATTT
4159 GCTCGTATCA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.41, C:0.06, G:0.09, T:0.45
Consensus pattern (27 bp):
AAACAAGTTTAATTTTTTTGTATCAAA
Found at i:4238 original size:32 final size:32
Alignment explanation
Indices: 4197--4257 Score: 122
Period size: 32 Copynumber: 1.9 Consensus size: 32
4187 GTATATAATG
4197 GCATTAAAAATGAGAGTAGTTTTTTTTTTTTT
1 GCATTAAAAATGAGAGTAGTTTTTTTTTTTTT
4229 GCATTAAAAATGAGAGTAGTTTTTTTTTT
1 GCATTAAAAATGAGAGTAGTTTTTTTTTT
4258 GATATATATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.30, C:0.03, G:0.16, T:0.51
Consensus pattern (32 bp):
GCATTAAAAATGAGAGTAGTTTTTTTTTTTTT
Found at i:11509 original size:2 final size:2
Alignment explanation
Indices: 11502--11526 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
11492 TAAGGAAATA
11502 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
11527 CAAGATACAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:12134 original size:40 final size:40
Alignment explanation
Indices: 12074--12153 Score: 133
Period size: 40 Copynumber: 2.0 Consensus size: 40
12064 GAGAGATTAC
* * *
12074 AATTCTAGATAATTAAGGGGGATATGATTTATTATAACAT
1 AATTATAGATAATTAAGGGGGATAGGATTTATCATAACAT
12114 AATTATAGATAATTAAGGGGGATAGGATTTATCATAACAT
1 AATTATAGATAATTAAGGGGGATAGGATTTATCATAACAT
12154 TTATGTGAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.41, C:0.05, G:0.19, T:0.35
Consensus pattern (40 bp):
AATTATAGATAATTAAGGGGGATAGGATTTATCATAACAT
Found at i:20634 original size:6 final size:6
Alignment explanation
Indices: 20620--20648 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
20610 ATAATAATAA
20620 TAAAA- TAAAAT TAAAAT TAAAAT TAAAAT
1 TAAAAT TAAAAT TAAAAT TAAAAT TAAAAT
20649 AACCCCAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.22
6 18 0.78
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (6 bp):
TAAAAT
Found at i:23802 original size:19 final size:19
Alignment explanation
Indices: 23752--23802 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
23742 TGTGGGATTT
23752 TTAATAA-TAATTATTCAA
1 TTAATAATTAATTATTCAA
* *
23770 TAAAATAATT-ATTATTTAA
1 T-TAATAATTAATTATTCAA
23789 TTAATAATTAATTA
1 TTAATAATTAATTA
23803 ATTTCAGTCC
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
18 8 0.30
19 18 0.67
20 1 0.04
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (19 bp):
TTAATAATTAATTATTCAA
Found at i:24174 original size:13 final size:13
Alignment explanation
Indices: 24156--24180 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
24146 AAGGTAACAA
24156 CAAAAATCATCAC
1 CAAAAATCATCAC
24169 CAAAAATCATCA
1 CAAAAATCATCA
24181 TTCATGCCAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.28, G:0.00, T:0.16
Consensus pattern (13 bp):
CAAAAATCATCAC
Found at i:39043 original size:19 final size:20
Alignment explanation
Indices: 38995--39043 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 20
38985 TGGGATTTTT
38995 AATAA-TAATTATTCAATAA
1 AATAATTAATTATTCAATAA
*
39014 AATAATT-ATTATTTAAT-A
1 AATAATTAATTATTCAATAA
*
39032 ATTAATTAATTA
1 AATAATTAATTA
39044 ATTTCAGTCC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
18 7 0.27
19 18 0.69
20 1 0.04
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (20 bp):
AATAATTAATTATTCAATAA
Found at i:52850 original size:1 final size:1
Alignment explanation
Indices: 52844--52870 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
52834 AATAAAATTT
52844 AAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAA
52871 CTAGAAATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:53993 original size:14 final size:14
Alignment explanation
Indices: 53974--54004 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
53964 GTATCCTTAA
53974 GTGTAAGTGAATTT
1 GTGTAAGTGAATTT
53988 GTGTAAGTGAATTT
1 GTGTAAGTGAATTT
54002 GTG
1 GTG
54005 CGATTATTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.26, C:0.00, G:0.32, T:0.42
Consensus pattern (14 bp):
GTGTAAGTGAATTT
Found at i:55985 original size:23 final size:23
Alignment explanation
Indices: 55955--56007 Score: 97
Period size: 23 Copynumber: 2.3 Consensus size: 23
55945 TTAATTTCAA
*
55955 TTGTATAGGCTTTGTTGCTTCTT
1 TTGTATAGGCTTTGCTGCTTCTT
55978 TTGTATAGGCTTTGCTGCTTCTT
1 TTGTATAGGCTTTGCTGCTTCTT
56001 TTGTATA
1 TTGTATA
56008 TCACTTAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.11, C:0.13, G:0.21, T:0.55
Consensus pattern (23 bp):
TTGTATAGGCTTTGCTGCTTCTT
Found at i:64179 original size:6 final size:6
Alignment explanation
Indices: 64168--64192 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
64158 AGATCCACTT
64168 GTTTTG GTTTTG GTTTTG GTTTTG G
1 GTTTTG GTTTTG GTTTTG GTTTTG G
64193 ATCAACCAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.00, G:0.36, T:0.64
Consensus pattern (6 bp):
GTTTTG
Found at i:65369 original size:19 final size:19
Alignment explanation
Indices: 65345--65386 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
65335 TCAATTTAGT
65345 CCCTAAAGGACACATGTCA
1 CCCTAAAGGACACATGTCA
65364 CCCTAAAGGACACATGTCA
1 CCCTAAAGGACACATGTCA
65383 CCCT
1 CCCT
65387 TTCAGGACCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.33, C:0.36, G:0.14, T:0.17
Consensus pattern (19 bp):
CCCTAAAGGACACATGTCA
Found at i:67523 original size:23 final size:21
Alignment explanation
Indices: 67474--67523 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
67464 TTATCAAAAA
*
67474 TCATAGGAAGGTTACAAGATT
1 TCATAGGAAGGTTACAAAATT
* *
67495 TGATAGGAAGGTTTATTAAAATT
1 TCATAGGAAGG-TTA-CAAAATT
67518 TCATAG
1 TCATAG
67524 TTAGGTTATC
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 10 0.43
22 3 0.13
23 10 0.43
ACGTcount: A:0.38, C:0.06, G:0.22, T:0.34
Consensus pattern (21 bp):
TCATAGGAAGGTTACAAAATT
Found at i:67573 original size:29 final size:29
Alignment explanation
Indices: 67515--67569 Score: 67
Period size: 29 Copynumber: 1.9 Consensus size: 29
67505 GTTTATTAAA
* ** *
67515 ATTTCATAGTTAGGTTATCAAAGCTTCAT
1 ATTTCATAGGTAAATTATCAAAGATTCAT
67544 ATTTCATAGGTAAATTATCAAA-ATTC
1 ATTTCATAGGTAAATTATCAAAGATTC
67570 CATAACGTGG
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
28 3 0.14
29 19 0.86
ACGTcount: A:0.36, C:0.13, G:0.11, T:0.40
Consensus pattern (29 bp):
ATTTCATAGGTAAATTATCAAAGATTCAT
Found at i:67583 original size:22 final size:21
Alignment explanation
Indices: 67558--67617 Score: 68
Period size: 22 Copynumber: 2.8 Consensus size: 21
67548 CATAGGTAAA
*
67558 TTATCAAAATTCCATAACG-TGG
1 TTATCAAAATT-CATAA-GATAG
*
67580 TTATCAAAATTAATAAGATAG
1 TTATCAAAATTCATAAGATAG
67601 TTATCAAAATTTCATAA
1 TTATCAAAA-TTCATAA
67618 AAATATTCAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
20 1 0.03
21 15 0.45
22 17 0.52
ACGTcount: A:0.45, C:0.12, G:0.08, T:0.35
Consensus pattern (21 bp):
TTATCAAAATTCATAAGATAG
Found at i:67675 original size:2 final size:2
Alignment explanation
Indices: 67668--67697 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
67658 GTGAAAGCTA
67668 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
67698 TTTCTTAGCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:72757 original size:14 final size:15
Alignment explanation
Indices: 72738--72767 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
72728 TGTGGGCATC
72738 TTTTTTTTCT-TTTT
1 TTTTTTTTCTATTTT
72752 TTTTTTTTCTATTTT
1 TTTTTTTTCTATTTT
72767 T
1 T
72768 CTTTATGGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.03, C:0.07, G:0.00, T:0.90
Consensus pattern (15 bp):
TTTTTTTTCTATTTT
Found at i:73645 original size:70 final size:69
Alignment explanation
Indices: 73532--73671 Score: 212
Period size: 70 Copynumber: 2.0 Consensus size: 69
73522 ACAGTGTTGA
* *
73532 ACTCTTAATTTCAGTGATTAAATTCAACCCAATTTAAGAAACGAGGATATGTAAGGAAACGGATG
1 ACTCTTAATTCCAGTGATTAAATTCAACCCAATTTAAGAAACGAGGAAATGTAA-GAAACGGATG
73597 ACTTG
65 ACTTG
*
73602 ACTCTTAATTCCAGTGATTAAA-TCGGACCCAATCTTAA-AAACGAGGAAATGTAAGAAACGGAT
1 ACTCTTAATTCCAGTGATTAAATTC-AACCCAAT-TTAAGAAACGAGGAAATGTAAGAAACGGAT
73665 GACTTG
64 GACTTG
73671 A
1 A
73672 TTTACTCACT
Statistics
Matches: 65, Mismatches: 3, Indels: 5
0.89 0.04 0.07
Matches are distributed among these distances:
69 18 0.28
70 43 0.66
71 4 0.06
ACGTcount: A:0.39, C:0.16, G:0.19, T:0.26
Consensus pattern (69 bp):
ACTCTTAATTCCAGTGATTAAATTCAACCCAATTTAAGAAACGAGGAAATGTAAGAAACGGATGA
CTTG
Found at i:79633 original size:16 final size:16
Alignment explanation
Indices: 79580--79639 Score: 52
Period size: 16 Copynumber: 3.8 Consensus size: 16
79570 GTTTGGTAGA
79580 GAGGAAA-GAAAT-GG
1 GAGGAAAGGAAATAGG
**
79594 GAAGGAAAGGAAATAAC
1 G-AGGAAAGGAAATAGG
*
79611 AAGGGAAAGGAAATAGG
1 GA-GGAAAGGAAATAGG
*
79628 GAGGAAGGGAAA
1 GAGGAAAGGAAA
79640 GGAAGTCATA
Statistics
Matches: 35, Mismatches: 7, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
14 1 0.03
15 6 0.17
16 15 0.43
17 13 0.37
ACGTcount: A:0.53, C:0.02, G:0.40, T:0.05
Consensus pattern (16 bp):
GAGGAAAGGAAATAGG
Found at i:82451 original size:60 final size:59
Alignment explanation
Indices: 82367--82519 Score: 157
Period size: 61 Copynumber: 2.5 Consensus size: 59
82357 TAATTGCTCC
* *
82367 AATAGGTCCTAAACATAT-ACGAAAATGCTCAATTTATGGC-CCATGCTTTTAATTTGGCTA
1 AATAAGTCCT-AACATATGA-GAAAATGCTCAATTTA-GGCTCCATACTTTTAATTTGGCTA
* * *
82427 AATAAAGTCCTAACATATGAGAAAATGGCTTAGTTTAGGCTCCATACTTTTAATTTGGTTA
1 AAT-AAGTCCTAACATATGAGAAAAT-GCTCAATTTAGGCTCCATACTTTTAATTTGGCTA
* ** *
82488 AATAGGATCCTAATGTATGCGAAAATGCTCAA
1 AATAAG-TCCTAACATATGAGAAAATGCTCAA
82520 ATAAGGGTTT
Statistics
Matches: 77, Mismatches: 11, Indels: 10
0.79 0.11 0.10
Matches are distributed among these distances:
60 25 0.32
61 52 0.68
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Consensus pattern (59 bp):
AATAAGTCCTAACATATGAGAAAATGCTCAATTTAGGCTCCATACTTTTAATTTGGCTA
Found at i:84244 original size:119 final size:124
Alignment explanation
Indices: 84102--84383 Score: 434
Period size: 131 Copynumber: 2.3 Consensus size: 124
84092 GGAGTGAGCC
84102 ATAGAGGTGAATCCATATATATAGTCATATATAAAGTATAACGGAA-AT-TACA-ATTGTC-AGT
1 ATAGAGGTGAATCCATATATATAGTCATATATAAAGTATAACGGAATATATA-ATATTGTCTAGT
84163 ATCATTGA-T-ATTTGA-TATTAAGATAAAAAAAACAAACCAATAATTATAGGAATTAATT
65 ATCATTGAGTCATTT-ATTATTAAGATAAAAAAAACAAACCAATAATTATAGGAATTAATT
84221 ATAGAGGTGAATCCATATATATAGTCATATATAAAGTATAACGGAATTATAATAATTATTGTCAT
1 ATAGAGGTGAATCCATATATATAGTCATATATAAAGTATAACGGAA-TAT-ATAA-TATTGTC--
84286 TGAGTATCATTGATGTCATTTATTATTAAGATAAAAAAAACAAACCAATAATTATAGGAATTAAT
61 T-AGTATCATTGA-GTCATTTATTATTAAGATAAAAAAAACAAACCAATAATTATAGGAATTAAT
84351 T
124 T
84352 ATAGAGGTGAATCCATATATATAGTCATATAT
1 ATAGAGGTGAATCCATATATATAGTCATATAT
84384 TTTCTTCAGA
Statistics
Matches: 149, Mismatches: 0, Indels: 16
0.90 0.00 0.10
Matches are distributed among these distances:
119 46 0.31
121 2 0.01
122 1 0.01
123 2 0.01
124 6 0.04
128 11 0.07
130 2 0.01
131 79 0.53
ACGTcount: A:0.45, C:0.08, G:0.13, T:0.34
Consensus pattern (124 bp):
ATAGAGGTGAATCCATATATATAGTCATATATAAAGTATAACGGAATATATAATATTGTCTAGTA
TCATTGAGTCATTTATTATTAAGATAAAAAAAACAAACCAATAATTATAGGAATTAATT
Found at i:84831 original size:21 final size:21
Alignment explanation
Indices: 84763--84906 Score: 87
Period size: 22 Copynumber: 6.6 Consensus size: 21
84753 TATTTTTATG
* *
84763 AAATTTAGATAACTATCCTATT
1 AAATTTTGATAACTA-CCTATA
* *
84785 AAATTTTGATAACCACACTATG
1 AAATTTTGATAACTAC-CTATA
*
84807 AAATTTTGATAATTACCTATA
1 AAATTTTGATAACTACCTATA
*
84828 AAATTGTGATAAACT-CC-ATAA
1 AAATTTTGAT-AACTACCTAT-A
* * *
84849 GAAACTTTGATAACATAACTATG
1 -AAATTTTGATAAC-TACCTATA
* * *
84872 AAATTTTAATAAACTTTCCTATG
1 AAATTTTGAT-AAC-TACCTATA
84895 AAATTTTG-TAAC
1 AAATTTTGATAAC
84907 CTTCTATGAT
Statistics
Matches: 96, Mismatches: 18, Indels: 17
0.73 0.14 0.13
Matches are distributed among these distances:
20 2 0.02
21 23 0.24
22 52 0.54
23 17 0.18
24 2 0.02
ACGTcount: A:0.42, C:0.13, G:0.08, T:0.37
Consensus pattern (21 bp):
AAATTTTGATAACTACCTATA
Found at i:90265 original size:54 final size:54
Alignment explanation
Indices: 90183--90292 Score: 220
Period size: 54 Copynumber: 2.0 Consensus size: 54
90173 TCAAATATCA
90183 ATGATACTAAATGACAATAATTATTGTAATTTCTGTTATACTTTATATATGACT
1 ATGATACTAAATGACAATAATTATTGTAATTTCTGTTATACTTTATATATGACT
90237 ATGATACTAAATGACAATAATTATTGTAATTTCTGTTATACTTTATATATGACT
1 ATGATACTAAATGACAATAATTATTGTAATTTCTGTTATACTTTATATATGACT
90291 AT
1 AT
90293 ATATATGGAT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 56 1.00
ACGTcount: A:0.37, C:0.09, G:0.09, T:0.45
Consensus pattern (54 bp):
ATGATACTAAATGACAATAATTATTGTAATTTCTGTTATACTTTATATATGACT
Found at i:92566 original size:10 final size:10
Alignment explanation
Indices: 92551--92577 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
92541 AACCTCACTC
92551 TCCTTTCATT
1 TCCTTTCATT
92561 TCCTTTCATT
1 TCCTTTCATT
92571 TCCTTTC
1 TCCTTTC
92578 CCTTACTTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.07, C:0.33, G:0.00, T:0.59
Consensus pattern (10 bp):
TCCTTTCATT
Done.