Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020703.1 Corchorus olitorius cultivar O-4 contig20736, 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: 74584
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:7779 original size:30 final size:30
Alignment explanation
Indices: 7745--7806 Score: 115
Period size: 30 Copynumber: 2.1 Consensus size: 30
7735 AACTGATATT
7745 TTCTCAATTTTAAGTACATGTCACAAGTGG
1 TTCTCAATTTTAAGTACATGTCACAAGTGG
*
7775 TTCTCAGTTTTAAGTACATGTCACAAGTGG
1 TTCTCAATTTTAAGTACATGTCACAAGTGG
7805 TT
1 TT
7807 TTGCATGCAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.27, C:0.16, G:0.18, T:0.39
Consensus pattern (30 bp):
TTCTCAATTTTAAGTACATGTCACAAGTGG
Found at i:10433 original size:21 final size:20
Alignment explanation
Indices: 10380--10433 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 20
10370 GGGATTGGAG
* *
10380 TATTTATTTATCTTGTTGTT
1 TATTTATTTATTTTCTTGTT
10400 TAATTT-TATTATTTTCTTGTT
1 T-ATTTAT-TTATTTTCTTGTT
10421 TATTTATTGTATT
1 TATTTATT-TATT
10434 GTTCACATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
20 7 0.25
21 21 0.75
ACGTcount: A:0.19, C:0.04, G:0.07, T:0.70
Consensus pattern (20 bp):
TATTTATTTATTTTCTTGTT
Found at i:10433 original size:24 final size:25
Alignment explanation
Indices: 10383--10433 Score: 61
Period size: 24 Copynumber: 2.1 Consensus size: 25
10373 ATTGGAGTAT
*
10383 TTATTTATCTTGTTGTTTAATTTTA
1 TTATTTATCTTGTTGTTTAATTGTA
*
10408 TTATTT-TCTTGTT-TATTTATTGTA
1 TTATTTATCTTGTTGT-TTAATTGTA
10432 TT
1 TT
10434 GTTCACATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
23 1 0.04
24 16 0.70
25 6 0.26
ACGTcount: A:0.18, C:0.04, G:0.08, T:0.71
Consensus pattern (25 bp):
TTATTTATCTTGTTGTTTAATTGTA
Found at i:10600 original size:11 final size:11
Alignment explanation
Indices: 10584--10615 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
10574 TTTTTCTGTT
10584 TTTTGTTTTTG
1 TTTTGTTTTTG
*
10595 TTTTGTTTTCG
1 TTTTGTTTTTG
10606 TTTTGTTTTT
1 TTTTGTTTTT
10616 ATTGCGCTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.00, C:0.03, G:0.16, T:0.81
Consensus pattern (11 bp):
TTTTGTTTTTG
Found at i:15894 original size:131 final size:132
Alignment explanation
Indices: 15660--15921 Score: 499
Period size: 131 Copynumber: 2.0 Consensus size: 132
15650 GGTAATTTTA
15660 TAGATGGCAATTAACTTTAAGAAACAAATTCCATTATTAAAAGAAAAGCATGTAGCCAGAAAATC
1 TAGATGGCAATTAACTTTAAGAAACAAATTCCATTATTAAAAGAAAAGCATGTAGCCAGAAAATC
*
15725 AATGATTAGTATAAATTCTTACGATGTTAACTGTTATTGTCAAATGCACTGAGATATTA-AAAAT
66 AATGATTAGTATAAATTCTTACGATGTTAACTGTTATTGTCAAATGCACTAAGATATTACAAAAT
15789 GT
131 GT
15791 TAGATGGCAATTAACTTTAAGAAACAAATTCCATTATTAAAAGAAAAGCATGTAGCCAGAAAATC
1 TAGATGGCAATTAACTTTAAGAAACAAATTCCATTATTAAAAGAAAAGCATGTAGCCAGAAAATC
*
15856 AATGATTAGTATAAATTCTTACGATGTTAGCTGTTATTGTCAAATGCACTAAGATATTACAAAAT
66 AATGATTAGTATAAATTCTTACGATGTTAACTGTTATTGTCAAATGCACTAAGATATTACAAAAT
15921 G
131 G
15922 GTAAGGAGAA
Statistics
Matches: 128, Mismatches: 2, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
131 122 0.95
132 6 0.05
ACGTcount: A:0.43, C:0.12, G:0.15, T:0.31
Consensus pattern (132 bp):
TAGATGGCAATTAACTTTAAGAAACAAATTCCATTATTAAAAGAAAAGCATGTAGCCAGAAAATC
AATGATTAGTATAAATTCTTACGATGTTAACTGTTATTGTCAAATGCACTAAGATATTACAAAAT
GT
Found at i:24218 original size:6 final size:6
Alignment explanation
Indices: 24179--24210 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
24169 ACAGTCATCA
*
24179 AAAACC AGAACC AAAACC AAAACC AAAACC AA
1 AAAACC AAAACC AAAACC AAAACC AAAACC AA
24211 CCTAAACCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.66, C:0.31, G:0.03, T:0.00
Consensus pattern (6 bp):
AAAACC
Found at i:26501 original size:15 final size:15
Alignment explanation
Indices: 26477--26511 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
26467 TTCTGCTGGC
*
26477 TTCTTTGGCTCCTCT
1 TTCTTGGGCTCCTCT
*
26492 TTCTTGGGCTCTTCT
1 TTCTTGGGCTCCTCT
26507 TTCTT
1 TTCTT
26512 CTTCTCTGGC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.00, C:0.29, G:0.14, T:0.57
Consensus pattern (15 bp):
TTCTTGGGCTCCTCT
Found at i:33168 original size:2 final size:2
Alignment explanation
Indices: 33157--33189 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
33147 ACCTAACTAT
33157 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
33190 CATACAAACT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:33521 original size:40 final size:40
Alignment explanation
Indices: 33462--33541 Score: 151
Period size: 40 Copynumber: 2.0 Consensus size: 40
33452 ACTTGACCAT
33462 CCTAATAATTAAGGAAATAAATTAAATTCAGGTTTAGCCC
1 CCTAATAATTAAGGAAATAAATTAAATTCAGGTTTAGCCC
*
33502 CCTAATAATTAAGGTAATAAATTAAATTCAGGTTTAGCCC
1 CCTAATAATTAAGGAAATAAATTAAATTCAGGTTTAGCCC
33542 ATCTATACTA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.41, C:0.15, G:0.12, T:0.31
Consensus pattern (40 bp):
CCTAATAATTAAGGAAATAAATTAAATTCAGGTTTAGCCC
Found at i:34743 original size:13 final size:13
Alignment explanation
Indices: 34722--34757 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
34712 GATAATTCTT
34722 TTTGACCCTCCAA
1 TTTGACCCTCCAA
*
34735 TTTGTCCCTCCAA
1 TTTGACCCTCCAA
*
34748 CTTGACCCTC
1 TTTGACCCTC
34758 ATAATAATTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.17, C:0.42, G:0.08, T:0.33
Consensus pattern (13 bp):
TTTGACCCTCCAA
Found at i:34838 original size:12 final size:12
Alignment explanation
Indices: 34821--34882 Score: 70
Period size: 12 Copynumber: 5.0 Consensus size: 12
34811 TGACACGTCA
34821 GGAGGGTCAAGT
1 GGAGGGTCAAGT
* *
34833 GGAGGGACAAATT
1 GGAGGGTC-AAGT
34846 GGAGGGTCAAGT
1 GGAGGGTCAAGT
* *
34858 GGAGGGACAAATT
1 GGAGGGTC-AAGT
34871 GGAGGGTCAAGT
1 GGAGGGTCAAGT
34883 AGCAATGCTC
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
12 20 0.50
13 20 0.50
ACGTcount: A:0.31, C:0.08, G:0.45, T:0.16
Consensus pattern (12 bp):
GGAGGGTCAAGT
Found at i:34849 original size:25 final size:25
Alignment explanation
Indices: 34821--34882 Score: 124
Period size: 25 Copynumber: 2.5 Consensus size: 25
34811 TGACACGTCA
34821 GGAGGGTCAAGTGGAGGGACAAATT
1 GGAGGGTCAAGTGGAGGGACAAATT
34846 GGAGGGTCAAGTGGAGGGACAAATT
1 GGAGGGTCAAGTGGAGGGACAAATT
34871 GGAGGGTCAAGT
1 GGAGGGTCAAGT
34883 AGCAATGCTC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 37 1.00
ACGTcount: A:0.31, C:0.08, G:0.45, T:0.16
Consensus pattern (25 bp):
GGAGGGTCAAGTGGAGGGACAAATT
Found at i:34850 original size:13 final size:13
Alignment explanation
Indices: 34832--34876 Score: 65
Period size: 13 Copynumber: 3.5 Consensus size: 13
34822 GAGGGTCAAG
34832 TGGAGGGACAAAT
1 TGGAGGGACAAAT
* *
34845 TGGAGGGTC-AAG
1 TGGAGGGACAAAT
34857 TGGAGGGACAAAT
1 TGGAGGGACAAAT
34870 TGGAGGG
1 TGGAGGG
34877 TCAAGTAGCA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
12 10 0.37
13 17 0.63
ACGTcount: A:0.31, C:0.07, G:0.47, T:0.16
Consensus pattern (13 bp):
TGGAGGGACAAAT
Found at i:43695 original size:15 final size:15
Alignment explanation
Indices: 43675--43704 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
43665 AGGCACCACT
43675 TCCCAGAAGTCCTTG
1 TCCCAGAAGTCCTTG
*
43690 TCCCAGGAGTCCTTG
1 TCCCAGAAGTCCTTG
43705 CTGAGGATTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.17, C:0.33, G:0.23, T:0.27
Consensus pattern (15 bp):
TCCCAGAAGTCCTTG
Found at i:53616 original size:1 final size:1
Alignment explanation
Indices: 53610--53660 Score: 102
Period size: 1 Copynumber: 51.0 Consensus size: 1
53600 TAAATGGGTC
53610 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
53661 ACAGTCCTGT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 50 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:55962 original size:14 final size:13
Alignment explanation
Indices: 55943--55981 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
55933 AAATTGTAAA
55943 ATTTAAAAAATTT
1 ATTTAAAAAATTT
* *
55956 CATTTAAGAAATAT
1 -ATTTAAAAAATTT
55970 ATTTAAAAAATT
1 ATTTAAAAAATT
55982 CTAATATATA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
13 10 0.48
14 11 0.52
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.41
Consensus pattern (13 bp):
ATTTAAAAAATTT
Found at i:56186 original size:124 final size:128
Alignment explanation
Indices: 55967--56224 Score: 380
Period size: 124 Copynumber: 2.0 Consensus size: 128
55957 ATTTAAGAAA
*
55967 TATATTTAAAAAATTCTAATATATATAAGTTTTTTTTAATTAAAATGGTAAAATGGTAAATATAA
1 TATATTTAAAAAATTCTAATATATATAAGTTTTTTTTAATTAAAATAGTAAAATGG---ATATAA
* * *
56032 AATAGGTTTAAGGATATTAGATTTAATTAAATAAAAATAAAGTTTTTAGTTGAGTAAAACTGTAA
63 AAT--GTATAAAGATATTAGATTTAATTAAATAAAAATAAAGTTTTTAGTTGAGTAAAACTATAA
56097 AAG
126 AAG
56100 TATATTTAAAAAATTCTAATATATATAAG-TTTTTTTAATTAAAATAGTAAAATGG-TA-AAAAT
1 TATATTTAAAAAATTCTAATATATATAAGTTTTTTTTAATTAAAATAGTAAAATGGATATAAAAT
* * *
56162 -TATAAAGATATTATATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAATTATAAAAG
66 GTATAAAGATATTAGATTTAATTAAATAAAAATAAAGTTTTTAGTTGAGTAAAACTATAAAAG
56224 T
1 T
56225 TTAAACAATG
Statistics
Matches: 118, Mismatches: 7, Indels: 9
0.88 0.05 0.07
Matches are distributed among these distances:
124 57 0.48
127 5 0.04
128 2 0.02
132 25 0.21
133 29 0.25
ACGTcount: A:0.48, C:0.01, G:0.10, T:0.40
Consensus pattern (128 bp):
TATATTTAAAAAATTCTAATATATATAAGTTTTTTTTAATTAAAATAGTAAAATGGATATAAAAT
GTATAAAGATATTAGATTTAATTAAATAAAAATAAAGTTTTTAGTTGAGTAAAACTATAAAAG
Found at i:56457 original size:19 final size:19
Alignment explanation
Indices: 56430--56466 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
56420 TAAAAAACAG
*
56430 TCACTATTTAGTGTAATGA
1 TCACAATTTAGTGTAATGA
*
56449 TCACAATTTGGTGTAATG
1 TCACAATTTAGTGTAATG
56467 GTATCATTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.30, C:0.11, G:0.19, T:0.41
Consensus pattern (19 bp):
TCACAATTTAGTGTAATGA
Found at i:59769 original size:12 final size:11
Alignment explanation
Indices: 59749--59773 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
59739 TTTTGATCCA
59749 AAATTTTTTTG
1 AAATTTTTTTG
59760 AAATTTTTTTG
1 AAATTTTTTTG
59771 AAA
1 AAA
59774 AAATAGGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.36, C:0.00, G:0.08, T:0.56
Consensus pattern (11 bp):
AAATTTTTTTG
Found at i:61225 original size:19 final size:20
Alignment explanation
Indices: 61186--61240 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 20
61176 AAGTAAAAAC
61186 AAGA-AAGA-TGAAAAAGTA
1 AAGACAAGATTGAAAAAGTA
*
61204 AAGACAAGATTGAAATAG-A
1 AAGACAAGATTGAAAAAGTA
*
61223 AAGACAAGGTTGATAAAA
1 AAGACAAGATTGA-AAAA
61241 AAATAATTTG
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
18 4 0.13
19 17 0.55
20 10 0.32
ACGTcount: A:0.60, C:0.04, G:0.22, T:0.15
Consensus pattern (20 bp):
AAGACAAGATTGAAAAAGTA
Found at i:64122 original size:21 final size:21
Alignment explanation
Indices: 64096--64229 Score: 200
Period size: 21 Copynumber: 6.4 Consensus size: 21
64086 TGCTAGAAGT
64096 TCATTGGAGCAA-GTTCCAAGC
1 TCATTGGAG-AAGGTTCCAAGC
64117 TCATTGGAGCAA-GTTCCAAGC
1 TCATTGGAG-AAGGTTCCAAGC
*
64138 TCATTGGAGAAGGTTCCAAGT
1 TCATTGGAGAAGGTTCCAAGC
*
64159 TCATTGGAGAAGGTTCCAAGT
1 TCATTGGAGAAGGTTCCAAGC
*
64180 TCATTGGAGAAGGTTCCAAGA
1 TCATTGGAGAAGGTTCCAAGC
*
64201 TCATTGGAGAAGGTTTCAAGC
1 TCATTGGAGAAGGTTCCAAGC
64222 TCATTGGA
1 TCATTGGA
64230 ATTGCCTAAG
Statistics
Matches: 108, Mismatches: 4, Indels: 2
0.95 0.04 0.02
Matches are distributed among these distances:
20 2 0.02
21 106 0.98
ACGTcount: A:0.29, C:0.17, G:0.27, T:0.27
Consensus pattern (21 bp):
TCATTGGAGAAGGTTCCAAGC
Found at i:67889 original size:68 final size:68
Alignment explanation
Indices: 67804--67939 Score: 227
Period size: 68 Copynumber: 2.0 Consensus size: 68
67794 CAGCTAATAT
* * * * *
67804 TTAATCAAAAAGATTGAGGCTCTAATCTTCAATGATAAACATCAATTAAGCAAGTATTCAACTTA
1 TTAACCAAAAAGATTGAGGCCCTAATCTCCAATGATAAACAACAATTAAACAAGTATTCAACTTA
67869 AGA
66 AGA
67872 TTAACCAAAAAGATTGAGGCCCTAATCTCCAATGATAAACAACAATTAAACAAGTATTCAACTTA
1 TTAACCAAAAAGATTGAGGCCCTAATCTCCAATGATAAACAACAATTAAACAAGTATTCAACTTA
67937 AGA
66 AGA
67940 ATAGAGCACT
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
68 63 1.00
ACGTcount: A:0.46, C:0.17, G:0.11, T:0.26
Consensus pattern (68 bp):
TTAACCAAAAAGATTGAGGCCCTAATCTCCAATGATAAACAACAATTAAACAAGTATTCAACTTA
AGA
Found at i:68337 original size:13 final size:13
Alignment explanation
Indices: 68319--68353 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
68309 AGAGGAGGGG
*
68319 GGGGGGGGGGGTA
1 GGGGGGGGGGGCA
68332 GGGGGGGGGGGCA
1 GGGGGGGGGGGCA
68345 GGGGGGGGG
1 GGGGGGGGG
68354 CAAGGCGCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.06, C:0.03, G:0.89, T:0.03
Consensus pattern (13 bp):
GGGGGGGGGGGCA
Found at i:69030 original size:24 final size:24
Alignment explanation
Indices: 69003--69049 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
68993 TAACATCATG
69003 CTTGATTGGTCAACTTCTCAACGC
1 CTTGATTGGTCAACTTCTCAACGC
*
69027 CTTGATTGGTTAACTTCTCAACG
1 CTTGATTGGTCAACTTCTCAACG
69050 TAGCCTTCCT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.21, C:0.26, G:0.17, T:0.36
Consensus pattern (24 bp):
CTTGATTGGTCAACTTCTCAACGC
Found at i:73831 original size:19 final size:18
Alignment explanation
Indices: 73798--73833 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
73788 TTGAAATTAT
73798 TCTTCAATGGTCTTCAAA
1 TCTTCAATGGTCTTCAAA
*
73816 TCTTCAAATTGTCTTCAA
1 TCTTC-AATGGTCTTCAA
73834 TAAGTCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.28, C:0.22, G:0.08, T:0.42
Consensus pattern (18 bp):
TCTTCAATGGTCTTCAAA
Done.