Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022920.1 Corchorus olitorius cultivar O-4 contig22953, 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: 25165
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:833 original size:18 final size:18
Alignment explanation
Indices: 810--859 Score: 100
Period size: 18 Copynumber: 2.8 Consensus size: 18
800 TTGGTGAAAA
810 GTGAAAACACATATATTG
1 GTGAAAACACATATATTG
828 GTGAAAACACATATATTG
1 GTGAAAACACATATATTG
846 GTGAAAACACATAT
1 GTGAAAACACATAT
860 GATTAGTTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.46, C:0.12, G:0.16, T:0.26
Consensus pattern (18 bp):
GTGAAAACACATATATTG
Found at i:2743 original size:2 final size:2
Alignment explanation
Indices: 2736--2764 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2726 CATTCTATGC
2736 TA 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 TA T
2765 GTGTAAAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3575 original size:18 final size:18
Alignment explanation
Indices: 3551--3591 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
3541 ATGACGTGGC
3551 ATTTTATATATTTTTTAAT
1 ATTTTATAT-TTTTTTAAT
3570 -TTTTATATTTTTTTAAT
1 ATTTTATATTTTTTTAAT
3587 ATTTT
1 ATTTT
3592 CATTCCATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.43
18 12 0.57
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (18 bp):
ATTTTATATTTTTTTAAT
Found at i:3578 original size:16 final size:17
Alignment explanation
Indices: 3551--3582 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
3541 ATGACGTGGC
3551 ATTTTATATATTTTTTA
1 ATTTTATATATTTTTTA
3568 ATTTT-TATATTTTTT
1 ATTTTATATATTTTTT
3583 TAATATTTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (17 bp):
ATTTTATATATTTTTTA
Found at i:4010 original size:25 final size:24
Alignment explanation
Indices: 3962--4030 Score: 120
Period size: 25 Copynumber: 2.8 Consensus size: 24
3952 TTTGGTGGGT
*
3962 GTGTTTATGGTATACCTTTGATGG
1 GTGTTTACGGTATACCTTTGATGG
3986 GTGTTTACGGTATACCCTTTGATGG
1 GTGTTTACGGTATA-CCTTTGATGG
4011 GTGTTTACGGTATACCTTTG
1 GTGTTTACGGTATACCTTTG
4031 GTTGGTATCA
Statistics
Matches: 43, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
24 19 0.44
25 24 0.56
ACGTcount: A:0.16, C:0.13, G:0.28, T:0.43
Consensus pattern (24 bp):
GTGTTTACGGTATACCTTTGATGG
Found at i:4573 original size:16 final size:17
Alignment explanation
Indices: 4547--4580 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
4537 GTATAACTTA
4547 TTGTTTAATTTATTTAT
1 TTGTTTAATTTATTTAT
4564 TTGTTT-ATTTATTTAT
1 TTGTTTAATTTATTTAT
4580 T
1 T
4581 ACTATTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.21, C:0.00, G:0.06, T:0.74
Consensus pattern (17 bp):
TTGTTTAATTTATTTAT
Found at i:4858 original size:39 final size:38
Alignment explanation
Indices: 4801--4945 Score: 195
Period size: 39 Copynumber: 3.8 Consensus size: 38
4791 GAAGGACTCA
*
4801 AAAAAATTTGGAAGGGGGGGCGTAACGCCTCTTACACATT
1 AAAAAATTTGGAA-GGGGGGCGTAACGCCTCATAC-CATT
* *
4841 AAAAAATTTGGAAGGGGGGCGTAAGGCCTCCTACCCATT
1 AAAAAATTTGGAAGGGGGGCGTAACGCCTCATA-CCATT
*
4880 AAAAAATTTGGAAGGGGGGCGTAACGCCTCATACCA-A
1 AAAAAATTTGGAAGGGGGGCGTAACGCCTCATACCATT
* *
4917 AAAAAATTTTG-AGGGGGGCGTAAGGCCTC
1 AAAAAATTTGGAAGGGGGGCGTAACGCCTC
4946 CCCCCATATT
Statistics
Matches: 97, Mismatches: 7, Indels: 6
0.88 0.06 0.05
Matches are distributed among these distances:
36 17 0.18
37 10 0.10
38 3 0.03
39 53 0.55
40 14 0.14
ACGTcount: A:0.33, C:0.18, G:0.29, T:0.20
Consensus pattern (38 bp):
AAAAAATTTGGAAGGGGGGCGTAACGCCTCATACCATT
Found at i:4968 original size:36 final size:37
Alignment explanation
Indices: 4801--4973 Score: 172
Period size: 39 Copynumber: 4.6 Consensus size: 37
4791 GAAGGACTCA
* * *
4801 AAAAAATTTGGAAGGGGGGGCGTAACGCCTCTTACACATT
1 AAAAAATTTGGAA-GGGGGGCGTAAGGCCTC-CACCCA-T
4841 AAAAAATTTGGAAGGGGGGCGTAAGGCCTCCTACCCATT
1 AAAAAATTTGGAAGGGGGGCGTAAGGCCTCC-ACCCA-T
* * *
4880 AAAAAATTTGGAAGGGGGGCGTAACGCCT-CATACCAA
1 AAAAAATTTGGAAGGGGGGCGTAAGGCCTCCA-CCCAT
* *
4917 AAAAAATTTTG-AGGGGGGCGTAAGGCCTCCCCCCAT
1 AAAAAATTTGGAAGGGGGGCGTAAGGCCTCCACCCAT
** *
4953 ATTAGA-TTGGAAGGGGGGCGT
1 AAAAAATTTGGAAGGGGGGCGT
4974 GTCCCCTTTT
Statistics
Matches: 114, Mismatches: 15, Indels: 12
0.81 0.11 0.09
Matches are distributed among these distances:
35 3 0.03
36 32 0.28
37 12 0.11
38 4 0.04
39 50 0.44
40 13 0.11
ACGTcount: A:0.31, C:0.18, G:0.30, T:0.20
Consensus pattern (37 bp):
AAAAAATTTGGAAGGGGGGCGTAAGGCCTCCACCCAT
Found at i:6727 original size:36 final size:36
Alignment explanation
Indices: 6675--6773 Score: 144
Period size: 36 Copynumber: 2.8 Consensus size: 36
6665 CCAATTATAT
* *
6675 ATTAGGCGACTTAGGCCAGCGGCGTTATAGCCAAAC
1 ATTAGGCGACTAAGGCCAGCGGCATTATAGCCAAAC
* *
6711 ATTGGGCGACTAAGGCCAGCGGCATTATAGCCAAGC
1 ATTAGGCGACTAAGGCCAGCGGCATTATAGCCAAAC
* *
6747 ATTAGGCGACCAAGGCCAGCGACATTA
1 ATTAGGCGACTAAGGCCAGCGGCATTA
6774 CAACCAAAGA
Statistics
Matches: 56, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 56 1.00
ACGTcount: A:0.29, C:0.25, G:0.28, T:0.17
Consensus pattern (36 bp):
ATTAGGCGACTAAGGCCAGCGGCATTATAGCCAAAC
Found at i:8845 original size:25 final size:24
Alignment explanation
Indices: 8795--8863 Score: 111
Period size: 25 Copynumber: 2.8 Consensus size: 24
8785 TTTGGTGGGT
* *
8795 GTGTTTATGGTATACATTTGATGG
1 GTGTTTACGGTATACCTTTGATGG
8819 GTGTTTACGGTATACCCTTTGATGG
1 GTGTTTACGGTATA-CCTTTGATGG
8844 GTGTTTACGGTATACCTTTG
1 GTGTTTACGGTATACCTTTG
8864 TTTGGTACTC
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
24 19 0.45
25 23 0.55
ACGTcount: A:0.17, C:0.12, G:0.28, T:0.43
Consensus pattern (24 bp):
GTGTTTACGGTATACCTTTGATGG
Found at i:11936 original size:4 final size:4
Alignment explanation
Indices: 11927--11952 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
11917 ATACAATATG
11927 TTAT TTAT TTAT TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TT
11953 TGGTTTCACG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTAT
Found at i:13138 original size:11 final size:11
Alignment explanation
Indices: 13095--13132 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
13085 TTCCTATATA
*
13095 AAATAAATTAT
1 AAATTAATTAT
13106 CAAA-TAATTAT
1 -AAATTAATTAT
13117 AAATTAATTAT
1 AAATTAATTAT
13128 AAATT
1 AAATT
13133 TGTTATGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 3 0.12
11 18 0.75
12 3 0.12
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (11 bp):
AAATTAATTAT
Found at i:14582 original size:52 final size:52
Alignment explanation
Indices: 14518--14622 Score: 201
Period size: 52 Copynumber: 2.0 Consensus size: 52
14508 CTCTTCAACT
*
14518 GAGCACTCTGATTCTGAATCATACTCATAATCATTGTTAGGAAAAGCTTAGG
1 GAGCACTATGATTCTGAATCATACTCATAATCATTGTTAGGAAAAGCTTAGG
14570 GAGCACTATGATTCTGAATCATACTCATAATCATTGTTAGGAAAAGCTTAGG
1 GAGCACTATGATTCTGAATCATACTCATAATCATTGTTAGGAAAAGCTTAGG
14622 G
1 G
14623 TGGACATCGT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.30
Consensus pattern (52 bp):
GAGCACTATGATTCTGAATCATACTCATAATCATTGTTAGGAAAAGCTTAGG
Found at i:21216 original size:72 final size:72
Alignment explanation
Indices: 21099--21236 Score: 224
Period size: 72 Copynumber: 1.9 Consensus size: 72
21089 CCAGGGTCGT
*
21099 CAAGTGGTAATAAGGCTGTTGAAGATCACCCAAGAGTTAATATATCAACACCATCAAAGCATGAA
1 CAAGTGGTAATAAGGCTATTGAAGATCACCCAAGAGTTAATATATCAACACCATCAAAGCATGAA
21164 GGAGGAA
66 GGAGGAA
* * *
21171 CAAGTGGTAATAAGGCTATTGAGGATCACCCAA-ATGTTAATATATCAACATCATCAAATCATGA
1 CAAGTGGTAATAAGGCTATTGAAGATCACCCAAGA-GTTAATATATCAACACCATCAAAGCATGA
21235 AG
65 AG
21237 TAGCAATGGT
Statistics
Matches: 61, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
71 1 0.02
72 60 0.98
ACGTcount: A:0.41, C:0.17, G:0.20, T:0.22
Consensus pattern (72 bp):
CAAGTGGTAATAAGGCTATTGAAGATCACCCAAGAGTTAATATATCAACACCATCAAAGCATGAA
GGAGGAA
Found at i:21395 original size:51 final size:51
Alignment explanation
Indices: 21350--21789 Score: 275
Period size: 51 Copynumber: 8.6 Consensus size: 51
21340 ATTAGCTAAT
* ** *
21350 GGAGCAATGCTTGGAAATCATTTTGGGTTTGGGCAAAATCAATTAGCTGGA
1 GGAGCAATGCTTGAAAATCATAATGGGTTTGGGCAAAACCAATTAGCTGGA
* **
21401 GAAGCAATGCTTGAAAATCATAATGGGTTTGGGCTGAACCAATTAGCTGGA
1 GGAGCAATGCTTGAAAATCATAATGGGTTTGGGCAAAACCAATTAGCTGGA
* * *** * * *
21452 GGAGCAATGGTTGAAAATCACAATGGGTTTAATCATAATCC-TTTAGTTGGA
1 GGAGCAATGCTTGAAAATCATAATGGGTTTGGGCA-AAACCAATTAGCTGGA
* * *** * * *
21503 GGAGCAATGGTTGAAAATCACAATGGGTTTAATCATAATCC-TTTAGTTGGA
1 GGAGCAATGCTTGAAAATCATAATGGGTTTGGGCA-AAACCAATTAGCTGGA
* * *** * * *
21554 GGAGCAATGGTTGAAAATCACAATGGGTTTAATCTTAATCC-ATTAGTTGG-
1 GGAGCAATGCTTGAAAATCATAATGGGTTTGGGC-AAAACCAATTAGCTGGA
* * * * *** * *
21604 GAAAGCATTGCTTGAAATTCACAATGGGTTTAATCATAATTCC--TTAGTTGGA
1 G-GAGCAATGCTTGAAAATCATAATGGGTTTGGGCA-AA-ACCAATTAGCTGGA
* *** * *
21656 GGAGCAATGCTTGAAAATCACAATGGGTTTAATCATAATCC-ATTAGTTGGA
1 GGAGCAATGCTTGAAAATCATAATGGGTTTGGGCA-AAACCAATTAGCTGGA
* * *** * *
21707 GAAGCAATGCTTGAAAATCACAATGGGTTTAATCATAATCC-ATTAGTTGGA
1 GGAGCAATGCTTGAAAATCATAATGGGTTTGGGCA-AAACCAATTAGCTGGA
21758 GGAGCAATGCTTGAAAATCATAATGGGTTTGG
1 GGAGCAATGCTTGAAAATCATAATGGGTTTGG
21790 AGATAGGCAG
Statistics
Matches: 349, Mismatches: 33, Indels: 14
0.88 0.08 0.04
Matches are distributed among these distances:
50 4 0.01
51 338 0.97
52 7 0.02
ACGTcount: A:0.33, C:0.12, G:0.24, T:0.30
Consensus pattern (51 bp):
GGAGCAATGCTTGAAAATCATAATGGGTTTGGGCAAAACCAATTAGCTGGA
Found at i:21446 original size:102 final size:103
Alignment explanation
Indices: 21287--21787 Score: 371
Period size: 102 Copynumber: 4.9 Consensus size: 103
21277 GAACCAATTG
* * * * * *
21287 CAATTAGCTGGAGGAGCAATGCTTGGAAACCATATTAGG-TTGAATCTTAACTCATTAGCT-AAT
1 CAATTAGCTGGAGGAGCAATGCTTGAAAATCATAATGGGTTTGAAGCTGAACTCATTAGCTGAA-
* *** **
21350 GGAGCAATGCTTGGAAATCATTTTGGGTTTGGGCAAAAT
65 GGAGCAATGCTTGAAAATCACAATGGGTTTAAGCAAAAT
* * *
21389 CAATTAGCTGGAGAAGCAATGCTTGAAAATCATAATGGGTTTG-GGCTGAAC-CAATTAGCTGGA
1 CAATTAGCTGGAGGAGCAATGCTTGAAAATCATAATGGGTTTGAAGCTGAACTC-ATTAGCTGAA
* * *
21452 GGAGCAATGGTTGAAAATCACAATGGGTTTAATCATAAT
65 GGAGCAATGCTTGAAAATCACAATGGGTTTAAGCAAAAT
** * * * * * * *
21491 CCTTTAGTTGGAGGAGCAATGGTTGAAAATCACAATGGGTTT-AATCAT-AA-TCCTTTAGTTGG
1 CAATTAGCTGGAGGAGCAATGCTTGAAAATCATAATGGGTTTGAAGC-TGAACT-CATTAGCTGA
* * **
21553 AGGAGCAATGGTTGAAAATCACAATGGGTTTAATCTTAAT
64 AGGAGCAATGCTTGAAAATCACAATGGGTTTAAGCAAAAT
* * * * * * * * * * *
21593 CCATTAGTTGG-GAAAGCATTGCTTGAAATTCACAATGGGTTT-AATCAT-AATTCCTTAGTTGG
1 CAATTAGCTGGAG-GAGCAATGCTTGAAAATCATAATGGGTTTGAAGC-TGAACTCATTAGCTGA
* *
21655 AGGAGCAATGCTTGAAAATCACAATGGGTTTAATCATAAT
64 AGGAGCAATGCTTGAAAATCACAATGGGTTTAAGCAAAAT
* * * * * * *
21695 CCATTAGTTGGAGAAGCAATGCTTGAAAATCACAATGGGTTT-AATCAT-AA-TCCATTAGTTGG
1 CAATTAGCTGGAGGAGCAATGCTTGAAAATCATAATGGGTTTGAAGC-TGAACT-CATTAGCTGA
*
21757 AGGAGCAATGCTTGAAAATCATAATGGGTTT
64 AGGAGCAATGCTTGAAAATCACAATGGGTTT
21788 GGAGATAGGC
Statistics
Matches: 347, Mismatches: 41, Indels: 22
0.85 0.10 0.05
Matches are distributed among these distances:
101 3 0.01
102 336 0.97
103 8 0.02
ACGTcount: A:0.33, C:0.13, G:0.23, T:0.30
Consensus pattern (103 bp):
CAATTAGCTGGAGGAGCAATGCTTGAAAATCATAATGGGTTTGAAGCTGAACTCATTAGCTGAAG
GAGCAATGCTTGAAAATCACAATGGGTTTAAGCAAAAT
Found at i:21530 original size:153 final size:152
Alignment explanation
Indices: 21350--21787 Score: 585
Period size: 153 Copynumber: 2.9 Consensus size: 152
21340 ATTAGCTAAT
* *** *** * * *
21350 GGAGCAATGCTTGGAAATCATTTTGGGTTTGGGCAAAATCAATTAGCTGGAGAAGCAATGCTTGA
1 GGAGCAATGCTTGAAAATCACAATGGGTTTAATCATAATCCATTAGTTGGAGAAGCAATGCTTGA
* *** * *
21415 AAATCATAATGGGTTTGGGCTGAA-CCAATTAGCTGGAGGAGCAATGGTTGAAAATCACAATGGG
66 AAATCACAATGGGTTTAATCT-AATCC-ATTAGTTGGAGGAGCAATGCTTGAAAATCACAATGGG
21479 TTTAATCATAA-TCCTTTAGTTGGA
129 TTTAATCATAATTCC-TTAGTTGGA
* * * *
21503 GGAGCAATGGTTGAAAATCACAATGGGTTTAATCATAATCCTTTAGTTGGAGGAGCAATGGTTGA
1 GGAGCAATGCTTGAAAATCACAATGGGTTTAATCATAATCCATTAGTTGGAGAAGCAATGCTTGA
* * *
21568 AAATCACAATGGGTTTAATCTTAATCCATTAGTTGG-GAAAGCATTGCTTGAAATTCACAATGGG
66 AAATCACAATGGGTTTAATC-TAATCCATTAGTTGGAG-GAGCAATGCTTGAAAATCACAATGGG
21632 TTTAATCATAATTCCTTAGTTGGA
129 TTTAATCATAATTCCTTAGTTGGA
21656 GGAGCAATGCTTGAAAATCACAATGGGTTTAATCATAATCCATTAGTTGGAGAAGCAATGCTTGA
1 GGAGCAATGCTTGAAAATCACAATGGGTTTAATCATAATCCATTAGTTGGAGAAGCAATGCTTGA
*
21721 AAATCACAATGGGTTTAATCATAATCCATTAGTTGGAGGAGCAATGCTTGAAAATCATAATGGGT
66 AAATCACAATGGGTTTAATC-TAATCCATTAGTTGGAGGAGCAATGCTTGAAAATCACAATGGGT
21786 TT
130 TT
21788 GGAGATAGGC
Statistics
Matches: 248, Mismatches: 32, Indels: 10
0.86 0.11 0.03
Matches are distributed among these distances:
152 1 0.00
153 240 0.97
154 7 0.03
ACGTcount: A:0.33, C:0.13, G:0.24, T:0.30
Consensus pattern (152 bp):
GGAGCAATGCTTGAAAATCACAATGGGTTTAATCATAATCCATTAGTTGGAGAAGCAATGCTTGA
AAATCACAATGGGTTTAATCTAATCCATTAGTTGGAGGAGCAATGCTTGAAAATCACAATGGGTT
TAATCATAATTCCTTAGTTGGA
Done.