Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009155.1 Corchorus capsularis cultivar CVL-1 contig09176, 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: 5618
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Found at i:3439 original size:30 final size:31
Alignment explanation
Indices: 3385--3449 Score: 96
Period size: 30 Copynumber: 2.1 Consensus size: 31
3375 AACTTTATGT
* *
3385 TTTCCGATTCTACCCTTATTTTTAAAATATA
1 TTTCCAATTCTACCCTTATTTTTAAAACATA
*
3416 TTTCCAATTGTACCCTT-TTTTTAAAACATA
1 TTTCCAATTCTACCCTTATTTTTAAAACATA
3446 TTTC
1 TTTC
3450 TAAATTGCCA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
30 16 0.52
31 15 0.48
ACGTcount: A:0.28, C:0.20, G:0.03, T:0.49
Consensus pattern (31 bp):
TTTCCAATTCTACCCTTATTTTTAAAACATA
Found at i:3456 original size:31 final size:31
Alignment explanation
Indices: 3395--3456 Score: 90
Period size: 30 Copynumber: 2.0 Consensus size: 31
3385 TTTCCGATTC
* *
3395 TACCCTTATTTTTAAAATATATTTCCAATTG
1 TACCCTTATTTTTAAAACATATTTCAAATTG
3426 TACCCTT-TTTTTAAAACATATTTCTAAATTG
1 TACCCTTATTTTTAAAACATATTTC-AAATTG
3457 CCATTACTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 16 0.57
31 12 0.43
ACGTcount: A:0.32, C:0.16, G:0.03, T:0.48
Consensus pattern (31 bp):
TACCCTTATTTTTAAAACATATTTCAAATTG
Found at i:3796 original size:44 final size:42
Alignment explanation
Indices: 3725--3929 Score: 187
Period size: 44 Copynumber: 4.7 Consensus size: 42
3715 TTGTCTCTAT
* * *
3725 GTGGTTATCAAAATTTCATAAGATGGTTATTATAATTCCATGAG
1 GTGGTTATCAAAATTTCAT-AGGTGGTTATTAAAATTTCAT-AG
* ** *
3769 GAGGTTATCAAAATTTCATAGTGTGGTTACCAAAATTTCAT-T
1 GTGGTTATCAAAATTTCATAG-GTGGTTATTAAAATTTCATAG
* * **
3811 GTGGTTACCAAAATTTCATAGTGTAGTTACCAAAATTTCATAG
1 GTGGTTATCAAAATTTCATAG-GTGGTTATTAAAATTTCATAG
* *
3854 AGTGGTTACCAAAATTTCATAGGATCAGGTTATTAAAATTTCTTAG
1 -GTGGTTATCAAAATTTCATAGG-T--GGTTATTAAAATTTCATAG
*
3900 GTTGGTTATTAAAATTTCATAGGGTGGTTA
1 G-TGGTTATCAAAATTTCATA-GGTGGTTA
3930 ATTATCACAA
Statistics
Matches: 136, Mismatches: 17, Indels: 16
0.80 0.10 0.09
Matches are distributed among these distances:
42 38 0.28
43 3 0.02
44 59 0.43
45 1 0.01
46 33 0.24
47 2 0.01
ACGTcount: A:0.33, C:0.10, G:0.19, T:0.38
Consensus pattern (42 bp):
GTGGTTATCAAAATTTCATAGGTGGTTATTAAAATTTCATAG
Found at i:3830 original size:42 final size:43
Alignment explanation
Indices: 3771--3875 Score: 167
Period size: 42 Copynumber: 2.4 Consensus size: 43
3761 TCCATGAGGA
* * *
3771 GGTTATCAAAATTTCATAGTGTGGTTACCAAAATTTCAT-TGT
1 GGTTACCAAAATTTCATAGTGTAGTTACCAAAATTTCATAAGT
3813 GGTTACCAAAATTTCATAGTGTAGTTACCAAAATTTCATAGAGT
1 GGTTACCAAAATTTCATAGTGTAGTTACCAAAATTTCATA-AGT
3857 GGTTACCAAAATTTCATAG
1 GGTTACCAAAATTTCATAG
3876 GATCAGGTTA
Statistics
Matches: 58, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
42 37 0.64
44 21 0.36
ACGTcount: A:0.34, C:0.13, G:0.16, T:0.36
Consensus pattern (43 bp):
GGTTACCAAAATTTCATAGTGTAGTTACCAAAATTTCATAAGT
Found at i:3891 original size:24 final size:22
Alignment explanation
Indices: 3727--3922 Score: 136
Period size: 22 Copynumber: 8.9 Consensus size: 22
3717 GTCTCTATGT
* *
3727 GGTTATCAAAATTTCATAAG-A
1 GGTTATTAAAATTTCATAGGTA
* *
3748 TGGTTATTATAATTCCATGAGG-A
1 -GGTTATTAAAATTTCAT-AGGTA
*
3771 GGTTATCAAAATTTCATAGTGT-
1 GGTTATTAAAATTTCATAG-GTA
** *
3793 GGTTACCAAAATTTCAT-TGT-
1 GGTTATTAAAATTTCATAGGTA
**
3813 GGTTACCAAAATTTCATAGTGTA
1 GGTTATTAAAATTTCATAG-GTA
**
3836 -GTTACCAAAATTTCATAGAGT-
1 GGTTATTAAAATTTCATAG-GTA
**
3857 GGTTACCAAAATTTCATAGGATCA
1 GGTTATTAAAATTTCATAGG-T-A
* *
3881 GGTTATTAAAATTTCTTAGGTT
1 GGTTATTAAAATTTCATAGGTA
3903 GGTTATTAAAATTTCATAGG
1 GGTTATTAAAATTTCATAGG
3923 GTGGTTAATT
Statistics
Matches: 148, Mismatches: 16, Indels: 20
0.80 0.09 0.11
Matches are distributed among these distances:
20 19 0.13
21 3 0.02
22 105 0.71
23 4 0.03
24 17 0.11
ACGTcount: A:0.34, C:0.11, G:0.17, T:0.38
Consensus pattern (22 bp):
GGTTATTAAAATTTCATAGGTA
Found at i:4065 original size:22 final size:22
Alignment explanation
Indices: 4040--4088 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 22
4030 TTACTAATAC
4040 TTCATCGG-GAGGTTAT-ATAAAT
1 TTCAT-GGTGAGGTTATCA-AAAT
*
4062 TTCATGGTGTGGTTATCAAAAT
1 TTCATGGTGAGGTTATCAAAAT
4084 TTCAT
1 TTCAT
4089 ATGAATGTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
21 2 0.08
22 21 0.88
23 1 0.04
ACGTcount: A:0.29, C:0.10, G:0.20, T:0.41
Consensus pattern (22 bp):
TTCATGGTGAGGTTATCAAAAT
Found at i:4280 original size:44 final size:44
Alignment explanation
Indices: 4188--4382 Score: 186
Period size: 44 Copynumber: 4.5 Consensus size: 44
4178 TAAAGATAGA
*
4188 ATTATCAAAATTT-ATA-TGAAGATTATCAAAATTTCATAGTAT-TG
1 ATTATCAAAATTTCATAGTG-AGGTTATCAAAATTTCATA--ATGTG
* *
4232 -TTATCAAAATTTCAAAGTGAGGTTATCAAAATTACATAATGTG
1 ATTATCAAAATTTCATAGTGAGGTTATCAAAATTTCATAATGTG
* * * * * *
4275 ATTATCAAAATTTCATAGAGGGGTCAACAAAATTTTATAAAGATG
1 ATTATCAAAATTTCATAGTGAGGTTATCAAAATTTCATAATG-TG
** * *
4320 -TTATCAAAATTTCATAAAGAGGTTATCAAATTTTCAAAATGTG
1 ATTATCAAAATTTCATAGTGAGGTTATCAAAATTTCATAATGTG
4363 ATTA-CAAAAATTTCATAGTG
1 ATTATC-AAAATTTCATAGTG
4383 GTATTTCTGG
Statistics
Matches: 123, Mismatches: 21, Indels: 14
0.78 0.13 0.09
Matches are distributed among these distances:
42 2 0.02
43 17 0.14
44 100 0.81
45 4 0.03
ACGTcount: A:0.43, C:0.09, G:0.12, T:0.36
Consensus pattern (44 bp):
ATTATCAAAATTTCATAGTGAGGTTATCAAAATTTCATAATGTG
Found at i:4306 original size:66 final size:66
Alignment explanation
Indices: 4207--4355 Score: 158
Period size: 66 Copynumber: 2.3 Consensus size: 66
4197 ATTTATATGA
** * * *
4207 AGATTATCAAAATTTCATAGTATTGTTATCAAAATTTCA-AAGTGAGGTTATCAAAATTACATAA
1 AGATTATCAAAATTTCATAGTAGGGTCAACAAAATTTCATAA-AGAGGTTATCAAAATTACATAA
*
4271 TG
65 AG
* * * *
4273 TGATTATCAAAATTTCATAG-AGGGGTCAACAAAATTTTATAAAGATGTTATCAAAATTTCATAA
1 AGATTATCAAAATTTCATAGTA-GGGTCAACAAAATTTCATAAAGAGGTTATCAAAATTACATAA
4337 AG
65 AG
* *
4339 AGGTTATCAAATTTTCA
1 AGATTATCAAAATTTCA
4356 AAATGTGATT
Statistics
Matches: 68, Mismatches: 13, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
65 1 0.01
66 65 0.96
67 2 0.03
ACGTcount: A:0.42, C:0.09, G:0.13, T:0.36
Consensus pattern (66 bp):
AGATTATCAAAATTTCATAGTAGGGTCAACAAAATTTCATAAAGAGGTTATCAAAATTACATAAA
G
Found at i:4306 original size:88 final size:87
Alignment explanation
Indices: 4214--4380 Score: 223
Period size: 88 Copynumber: 1.9 Consensus size: 87
4204 TGAAGATTAT
* *
4214 CAAAATTTCAT-AGTATTGTTATCAAAATTTCA-AAGTGAGGTTATCAAAATTACATAATGTGAT
1 CAAAATTTCATAAG-A-TGTTATCAAAATTTCATAA-AGAGGTTATCAAAATTACAAAATGTGAT
4277 TATC-AAAATTTCATAGAGGGGTCAA
63 TA-CAAAAATTTCATAGAGGGGTCAA
* * *
4302 CAAAATTTTATAAAGATGTTATCAAAATTTCATAAAGAGGTTATCAAATTTTCAAAATGTGATTA
1 CAAAATTTCAT-AAGATGTTATCAAAATTTCATAAAGAGGTTATCAAAATTACAAAATGTGATTA
4367 CAAAAATTTCATAG
65 CAAAAATTTCATAG
4381 TGGTATTTCT
Statistics
Matches: 70, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
87 1 0.01
88 64 0.91
89 3 0.04
90 2 0.03
ACGTcount: A:0.43, C:0.10, G:0.13, T:0.35
Consensus pattern (87 bp):
CAAAATTTCATAAGATGTTATCAAAATTTCATAAAGAGGTTATCAAAATTACAAAATGTGATTAC
AAAAATTTCATAGAGGGGTCAA
Found at i:4327 original size:22 final size:22
Alignment explanation
Indices: 4171--4379 Score: 132
Period size: 22 Copynumber: 9.4 Consensus size: 22
4161 TGATTACCGG
4171 AATTTCATAAAGATAGAATTATCAA
1 AATTTCATAAAGAT-G--TTATCAA
4196 AATTT-ATATGAAGA--TTATCAA
1 AATTTCATA--AAGATGTTATCAA
4217 AATTTCAT--AGTATTGTTATCAA
1 AATTTCATAAAG-A-TGTTATCAA
* *
4239 AATTTCA-AAGTGAGGTTATCAA
1 AATTTCATAA-AGATGTTATCAA
* *
4261 AATTACATAATG-TGATTATCAA
1 AATTTCATAAAGATG-TTATCAA
* ** * *
4283 AATTTCATAGAGGGGTCAACAA
1 AATTTCATAAAGATGTTATCAA
*
4305 AATTTTATAAAGATGTTATCAA
1 AATTTCATAAAGATGTTATCAA
*
4327 AATTTCATAAAGAGGTTATCAA
1 AATTTCATAAAGATGTTATCAA
*
4349 ATTTTCA-AAATG-TGATTA-CAAA
1 AATTTCATAAA-GATG-TTATC-AA
4371 AATTTCATA
1 AATTTCATA
4380 GTGGTATTTC
Statistics
Matches: 146, Mismatches: 21, Indels: 36
0.72 0.10 0.18
Matches are distributed among these distances:
18 2 0.01
19 1 0.01
21 18 0.12
22 107 0.73
23 5 0.03
24 4 0.03
25 5 0.03
26 4 0.03
ACGTcount: A:0.44, C:0.09, G:0.11, T:0.35
Consensus pattern (22 bp):
AATTTCATAAAGATGTTATCAA
Found at i:4491 original size:19 final size:19
Alignment explanation
Indices: 4463--4530 Score: 55
Period size: 19 Copynumber: 3.5 Consensus size: 19
4453 ATGGAGTAAT
*
4463 CAAAATTTCAGGGAGGATAC
1 CAAAA-TTCAGAGAGGATAC
* *
4483 CAAAATTCAGAAAGGATAT
1 CAAAATTCAGAGAGGATAC
** *
4502 CGTAATTCAGTGAGGATATC
1 CAAAATTCAGAGAGGATA-C
*
4522 AAAAATTCA
1 CAAAATTCA
4531 TATGAAGGTT
Statistics
Matches: 36, Mismatches: 11, Indels: 2
0.73 0.22 0.04
Matches are distributed among these distances:
19 25 0.69
20 11 0.31
ACGTcount: A:0.44, C:0.13, G:0.19, T:0.24
Consensus pattern (19 bp):
CAAAATTCAGAGAGGATAC
Found at i:4545 original size:22 final size:22
Alignment explanation
Indices: 4518--4810 Score: 95
Period size: 22 Copynumber: 13.5 Consensus size: 22
4508 TCAGTGAGGA
*
4518 TATCAAAAATTCATATGAAGGT
1 TATCAAAATTTCATATGAAGGT
** **
4540 TATCAATTTTTCATAGTTTA-GT
1 TATCAAAATTTCATA-TGAAGGT
* * *
4562 TTTCAAAATTTCATAAGAGGGT
1 TATCAAAATTTCATATGAAGGT
* *
4584 TATCAAAATTTCATA-GTATGT
1 TATCAAAATTTCATATGAAGGT
* * * *
4605 AGATCAAAATTTCATAGGGAGAT
1 -TATCAAAATTTCATATGAAGGT
* *
4628 TAACAAAAGTTCATAATG-AGGT
1 TATCAAAATTTCAT-ATGAAGGT
* ** * * *
4650 AATCAAAAAATCATAGGGAGCT
1 TATCAAAATTTCATATGAAGGT
*
4672 TATCAAAA--T--T-TGTA-GT
1 TATCAAAATTTCATATGAAGGT
* * *
4688 TATCAAGATTTCATAAGAAAGT
1 TATCAAAATTTCATATGAAGGT
* * *
4710 TATCAAAATTTTATAGGGAGGTT
1 TATCAAAATTTCATATGAAGG-T
* * * *
4733 TATTAAAATTTTATAAGAAGATT
1 TATCAAAATTTCATATGAAG-GT
* * *
4756 TATCATAATTTCATA-GCGAGAT
1 TATCAAAATTTCATATG-AAGGT
* * *
4778 TATCACAATTTCATAGTG-TGAT
1 TATCAAAATTTCATA-TGAAGGT
4800 TATCAAAATTT
1 TATCAAAATTT
4811 TAATGTGTGA
Statistics
Matches: 199, Mismatches: 55, Indels: 34
0.69 0.19 0.12
Matches are distributed among these distances:
16 8 0.04
17 2 0.01
18 2 0.01
20 2 0.01
21 7 0.04
22 137 0.69
23 40 0.20
24 1 0.01
ACGTcount: A:0.40, C:0.09, G:0.14, T:0.37
Consensus pattern (22 bp):
TATCAAAATTTCATATGAAGGT
Found at i:4612 original size:44 final size:43
Alignment explanation
Indices: 4518--4725 Score: 124
Period size: 44 Copynumber: 4.9 Consensus size: 43
4508 TCAGTGAGGA
* * **
4518 TATCAAAAATTCATATGAAGGTTATCAATTTTTCATAGTTTAG
1 TATCAAAATTTCATAAGAAGGTTATCAAAATTTCATAGTTTAG
* *
4561 TTTTCAAAATTTCATAAGAGGGTTATCAAAATTTCATAGTATGTAG
1 -TATCAAAATTTCATAAGAAGGTTATCAAAATTTCATAGT-T-TAG
* * * * * * *
4607 -ATCAAAATTTCATAGGGAGATTAACAAAAGTTCATA-ATGAGG
1 TATCAAAATTTCATAAGAAGGTTATCAAAATTTCATAGTTTA-G
** * * * *
4649 TAATCAAAAAATCATAGGGAGCTTATCAAAATTT-GTAG--T--
1 T-ATCAAAATTTCATAAGAAGGTTATCAAAATTTCATAGTTTAG
* * *
4688 TATCAAGATTTCATAAGAAAGTTATCAAAATTTTATAG
1 TATCAAAATTTCATAAGAAGGTTATCAAAATTTCATAG
4726 GGAGGTTTAT
Statistics
Matches: 127, Mismatches: 30, Indels: 19
0.72 0.17 0.11
Matches are distributed among these distances:
38 25 0.20
39 4 0.03
41 1 0.01
42 2 0.02
43 2 0.02
44 89 0.70
45 1 0.01
46 3 0.02
ACGTcount: A:0.41, C:0.09, G:0.14, T:0.35
Consensus pattern (43 bp):
TATCAAAATTTCATAAGAAGGTTATCAAAATTTCATAGTTTAG
Found at i:4757 original size:23 final size:23
Alignment explanation
Indices: 4687--4766 Score: 81
Period size: 23 Copynumber: 3.5 Consensus size: 23
4677 AAATTTGTAG
* * *
4687 TTATCAAGATTTCATAAGAA-AG
1 TTATCAAAATTTTATAAGAAGAT
* * *
4709 TTATCAAAATTTTATAGGGAGGT
1 TTATCAAAATTTTATAAGAAGAT
*
4732 TTATTAAAATTTTATAAGAAGAT
1 TTATCAAAATTTTATAAGAAGAT
*
4755 TTATCATAATTT
1 TTATCAAAATTT
4767 CATAGCGAGA
Statistics
Matches: 45, Mismatches: 12, Indels: 1
0.78 0.21 0.02
Matches are distributed among these distances:
22 16 0.36
23 29 0.64
ACGTcount: A:0.41, C:0.05, G:0.12, T:0.41
Consensus pattern (23 bp):
TTATCAAAATTTTATAAGAAGAT
Found at i:4818 original size:22 final size:22
Alignment explanation
Indices: 4755--4821 Score: 64
Period size: 22 Copynumber: 3.0 Consensus size: 22
4745 ATAAGAAGAT
* * * *
4755 TTATCATAATTTCATAGCGAGA
1 TTATCAAAATTTAATAGTGTGA
* *
4777 TTATCACAATTTCATAGTGTGA
1 TTATCAAAATTTAATAGTGTGA
4799 TTATCAAAATTTTAAT-GTGTGA
1 TTATCAAAA-TTTAATAGTGTGA
4821 T
1 T
4822 AACTAACAAT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
22 34 0.87
23 5 0.13
ACGTcount: A:0.34, C:0.10, G:0.13, T:0.42
Consensus pattern (22 bp):
TTATCAAAATTTAATAGTGTGA
Done.