Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020989.1 Corchorus olitorius cultivar O-4 contig21022, 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: 14738
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.27
Found at i:2419 original size:43 final size:43
Alignment explanation
Indices: 2371--2609 Score: 328
Period size: 43 Copynumber: 5.7 Consensus size: 43
2361 CAATAGCCAA
* *
2371 AAAGTCCCCAAACACATATATAACACAGGGGCACCTTTATTAC
1 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTAC
* * * *
2414 AAAGTCCTCAAACACATATATAACACAGAGACATCTATA-T-C
1 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTAC
*
2455 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTAC
1 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTAC
* *
2498 AAAGTCCTCAAACACATATATAACACAGAGGCAT-T-TA-TATC
1 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTA-C
2539 AAAGTCCCCAAACACATATATAACACA-GGGCATCTCTATTAC
1 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTAC
*
2581 AAAAGTCCTCAAACACATATATAACACAG
1 -AAAGTCCCCAAACACATATATAACACAG
2610 AGCCATTTCT
Statistics
Matches: 172, Mismatches: 16, Indels: 15
0.85 0.08 0.07
Matches are distributed among these distances:
40 7 0.04
41 65 0.38
42 6 0.03
43 94 0.55
ACGTcount: A:0.44, C:0.26, G:0.10, T:0.21
Consensus pattern (43 bp):
AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTAC
Found at i:2617 original size:84 final size:84
Alignment explanation
Indices: 2371--2617 Score: 424
Period size: 84 Copynumber: 2.9 Consensus size: 84
2361 CAATAGCCAA
* *
2371 AAAGTCCCCAAACACATATATAACACAGGGGCACCTTTATTACAAAGTCCTCAAACACATATATA
1 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACAAAGTCCTCAAACACATATATA
*
2436 ACACAGAGACATCTATATC
66 ACACAGAGACATTTATATC
2455 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACAAAGTCCTCAAACACATATATA
1 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACAAAGTCCTCAAACACATATATA
*
2520 ACACAGAGGCATTTATATC
66 ACACAGAGACATTTATATC
*
2539 AAAGTCCCCAAACACATATATAACACA-GGGCATCTCTATTACAAAAGTCCTCAAACACATATAT
1 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTAC-AAAGTCCTCAAACACATATAT
*
2603 AACACAGAGCCATTT
65 AACACAGAGACATTT
2618 CTCCTTATGG
Statistics
Matches: 156, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
83 14 0.09
84 142 0.91
ACGTcount: A:0.43, C:0.26, G:0.10, T:0.21
Consensus pattern (84 bp):
AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACAAAGTCCTCAAACACATATATA
ACACAGAGACATTTATATC
Found at i:2765 original size:2 final size:2
Alignment explanation
Indices: 2731--2756 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2721 TCCTATATTT
2731 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
2757 CACATATATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4120 original size:35 final size:35
Alignment explanation
Indices: 4076--4250 Score: 122
Period size: 35 Copynumber: 4.8 Consensus size: 35
4066 AGTAAATGGT
*
4076 AAGAGTAAAGAGTAAAAGAGTAATAGTAGTAAGTA
1 AAGAGTAAAGAGTAAAAGAGTAATAGTAGTCAGTA
* *
4111 AAGAATAAAGAGTAATCAAGAAAGAGTAATAATAGTCAGTA
1 AAGAGTAAAGAG---T--A-AAAGAGTAATAGTAGTCAGTA
** ** *
4152 AAGAGTAATCAACAAAAGAGTAATAGTAATCAGTAA
1 AAGAGTAAAGAGTAAAAGAGTAATAGTAGTCAGT-A
* * *
4188 AAGAGTAAAGAGTAAATG-GTAAAATGGTAAT-AGTA
1 AAGAGTAAAGAGTAAAAGAGT--AATAGTAGTCAGTA
**
4223 ATCAGTAAAGAGTAAAA-AGTAATCAGTA
1 AAGAGTAAAGAGTAAAAGAGTAAT-AGTA
4251 AAATGGTAAT
Statistics
Matches: 109, Mismatches: 20, Indels: 23
0.72 0.13 0.15
Matches are distributed among these distances:
33 3 0.03
34 3 0.03
35 48 0.44
36 18 0.17
37 8 0.07
38 1 0.01
40 1 0.01
41 27 0.25
ACGTcount: A:0.54, C:0.04, G:0.21, T:0.21
Consensus pattern (35 bp):
AAGAGTAAAGAGTAAAAGAGTAATAGTAGTCAGTA
Found at i:4135 original size:41 final size:39
Alignment explanation
Indices: 4089--4202 Score: 112
Period size: 34 Copynumber: 2.9 Consensus size: 39
4079 AGTAAAGAGT
4089 AAAAGAGTAATAGTAGTAAGTAAAGAATAAAGAGTAATCAA-
1 AAAAGAGTAATAGTA-T-AGTAAAG-ATAAAGAGTAATCAAC
* *
4130 GAAAGAGTAATA--ATAGT-CAG-TAAAGAGTAATCAAC
1 AAAAGAGTAATAGTATAGTAAAGATAAAGAGTAATCAAC
4165 AAAAGAGTAATAGTAATCAGTAAAAGAGTAAAGAGTAA
1 AAAAGAGTAATAGT-AT-AGT-AAAGA-TAAAGAGTAA
4203 ATGGTAAAAT
Statistics
Matches: 60, Mismatches: 4, Indels: 16
0.75 0.05 0.20
Matches are distributed among these distances:
34 14 0.23
35 11 0.18
36 2 0.03
37 3 0.05
38 3 0.05
39 4 0.07
41 13 0.22
43 10 0.17
ACGTcount: A:0.56, C:0.04, G:0.20, T:0.19
Consensus pattern (39 bp):
AAAAGAGTAATAGTATAGTAAAGATAAAGAGTAATCAAC
Found at i:4156 original size:20 final size:20
Alignment explanation
Indices: 4090--4160 Score: 65
Period size: 20 Copynumber: 3.5 Consensus size: 20
4080 GTAAAGAGTA
* *
4090 AAAGAGTAATAGTAGTAAGT
1 AAAGAGTAATAATAGTCAGT
* *
4110 AAAGAATAA-AGAGTAATCAAG-
1 AAAGAGTAATA-A-TAGTC-AGT
4131 AAAGAGTAATAATAGTCAGT
1 AAAGAGTAATAATAGTCAGT
4151 AAAGAGTAAT
1 AAAGAGTAAT
4161 CAACAAAAGA
Statistics
Matches: 40, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
19 3 0.08
20 22 0.55
21 12 0.30
22 3 0.08
ACGTcount: A:0.55, C:0.03, G:0.21, T:0.21
Consensus pattern (20 bp):
AAAGAGTAATAATAGTCAGT
Found at i:4230 original size:21 final size:21
Alignment explanation
Indices: 4155--4272 Score: 109
Period size: 21 Copynumber: 5.6 Consensus size: 21
4145 GTCAGTAAAG
**
4155 AGTAATCAACAAAAGAGTAAT
1 AGTAATCAGTAAAAGAGTAAT
*
4176 AGTAATCAGTAAAAGAGTAAAG
1 AGTAATCAGTAAAAGAGT-AAT
*
4198 AGTAAAT-GGTAAAATG-GTAAT
1 AGT-AATCAGTAAAA-GAGTAAT
*
4219 AGTAATCAGT-AAAGAGTAAAA
1 AGTAATCAGTAAAAGAGT-AAT
4240 AGTAATCAGTAAAATG-GTAAT
1 AGTAATCAGTAAAA-GAGTAAT
*
4261 GGTAATCAGTAA
1 AGTAATCAGTAA
4273 TTAAAATTCA
Statistics
Matches: 80, Mismatches: 9, Indels: 16
0.76 0.09 0.15
Matches are distributed among these distances:
19 1 0.01
20 8 0.10
21 48 0.60
22 18 0.22
23 5 0.06
ACGTcount: A:0.52, C:0.05, G:0.20, T:0.23
Consensus pattern (21 bp):
AGTAATCAGTAAAAGAGTAAT
Found at i:4362 original size:31 final size:32
Alignment explanation
Indices: 4306--4377 Score: 110
Period size: 31 Copynumber: 2.2 Consensus size: 32
4296 GTAAAAGGAT
*
4306 TAAAAAGAGTAAAAATGGTATTCAGTAATTAAAG
1 TAAAAAAAGTAAAAA--GTATTCAGTAATTAAAG
4340 TAAAAAAAGTAAAAA-TATTCAGTAATTAAAG
1 TAAAAAAAGTAAAAAGTATTCAGTAATTAAAG
4371 TAAAAAA
1 TAAAAAA
4378 GGCAAAAAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
31 23 0.62
34 14 0.38
ACGTcount: A:0.60, C:0.03, G:0.12, T:0.25
Consensus pattern (32 bp):
TAAAAAAAGTAAAAAGTATTCAGTAATTAAAG
Found at i:4385 original size:31 final size:31
Alignment explanation
Indices: 4324--4385 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
4314 GTAAAAATGG
*
4324 TATTCAGTAATTAAAGTAAAAAAAGTAAAAA
1 TATTCAGTAATTAAAGTAAAAAAAGCAAAAA
*
4355 TATTCAGTAATTAAAGTAAAAAAGGCAAAAA
1 TATTCAGTAATTAAAGTAAAAAAAGCAAAAA
4386 ATGGAAACTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.60, C:0.05, G:0.11, T:0.24
Consensus pattern (31 bp):
TATTCAGTAATTAAAGTAAAAAAAGCAAAAA
Found at i:4414 original size:28 final size:26
Alignment explanation
Indices: 4369--4454 Score: 95
Period size: 26 Copynumber: 3.2 Consensus size: 26
4359 CAGTAATTAA
* *
4369 AGTAAAAAAGGCAAAAAATGG-AAACT
1 AGTAAAAAAAGTAAAAAATGGTAAA-T
4395 AGTAAAAAAATGTAAGAAAATGGTAAAT
1 AGTAAAAAAA-GTAA-AAAATGGTAAAT
*
4423 AGTAAAAAGAGTAAAAAATGGT-AAT
1 AGTAAAAAAAGTAAAAAATGGTAAAT
4448 CAGTAAA
1 -AGTAAA
4455 GAGAATAAGG
Statistics
Matches: 53, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
25 3 0.06
26 23 0.43
27 7 0.13
28 17 0.32
29 3 0.06
ACGTcount: A:0.60, C:0.03, G:0.19, T:0.17
Consensus pattern (26 bp):
AGTAAAAAAAGTAAAAAATGGTAAAT
Found at i:4609 original size:28 final size:27
Alignment explanation
Indices: 4577--4635 Score: 84
Period size: 26 Copynumber: 2.2 Consensus size: 27
4567 AATGGGATCA
*
4577 GTAATTTAATTAGAAAGAGTAAAAAATG
1 GTAATTT-AGTAGAAAGAGTAAAAAATG
*
4605 GTAA-TTAGTAGAAAGAGTAGAAAATG
1 GTAATTTAGTAGAAAGAGTAAAAAATG
4631 GTAAT
1 GTAAT
4636 CAGTAATCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
26 22 0.79
27 2 0.07
28 4 0.14
ACGTcount: A:0.51, C:0.00, G:0.22, T:0.27
Consensus pattern (27 bp):
GTAATTTAGTAGAAAGAGTAAAAAATG
Found at i:4616 original size:26 final size:26
Alignment explanation
Indices: 4587--4640 Score: 90
Period size: 26 Copynumber: 2.1 Consensus size: 26
4577 GTAATTTAAT
*
4587 TAGAAAGAGTAAAAAATGGTAATTAG
1 TAGAAAGAGTAAAAAATGGTAATCAG
*
4613 TAGAAAGAGTAGAAAATGGTAATCAG
1 TAGAAAGAGTAAAAAATGGTAATCAG
4639 TA
1 TA
4641 ATCAAGAAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.52, C:0.02, G:0.24, T:0.22
Consensus pattern (26 bp):
TAGAAAGAGTAAAAAATGGTAATCAG
Found at i:8552 original size:8 final size:8
Alignment explanation
Indices: 8541--8575 Score: 54
Period size: 8 Copynumber: 4.4 Consensus size: 8
8531 GATTTCTCTC
8541 TTTCTTTT
1 TTTCTTTT
8549 TTTC-TTT
1 TTTCTTTT
8556 TTTCTTTTT
1 TTTC-TTTT
8565 TTTCTTTT
1 TTTCTTTT
8573 TTT
1 TTT
8576 TGATCAAGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
7 7 0.28
8 11 0.44
9 7 0.28
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (8 bp):
TTTCTTTT
Found at i:8565 original size:9 final size:9
Alignment explanation
Indices: 8539--8576 Score: 51
Period size: 9 Copynumber: 4.1 Consensus size: 9
8529 TTGATTTCTC
8539 TCTTTCTTTT
1 TCTTT-TTTT
8549 T-TTCTTTTT
1 TCTT-TTTTT
8558 TCTTTTTTT
1 TCTTTTTTT
8567 TCTTTTTTT
1 TCTTTTTTT
8576 T
1 T
8577 GATCAAGTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
9 22 0.85
10 4 0.15
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (9 bp):
TCTTTTTTT
Found at i:12116 original size:18 final size:17
Alignment explanation
Indices: 12093--12133 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 17
12083 AAGTTGGTAA
12093 AAAAAAAAATAGGTTAGG
1 AAAAAAAAATAGG-TAGG
* *
12111 AAAAAAAATTATGTAGG
1 AAAAAAAAATAGGTAGG
12128 AAAAAA
1 AAAAAA
12134 GAAAAAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 10 0.48
18 11 0.52
ACGTcount: A:0.66, C:0.00, G:0.17, T:0.17
Consensus pattern (17 bp):
AAAAAAAAATAGGTAGG
Done.