Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005211.1 Corchorus capsularis cultivar CVL-1 contig05229, 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: 5304
ACGTcount: A:0.38, C:0.11, G:0.12, T:0.38
Found at i:439 original size:25 final size:26
Alignment explanation
Indices: 394--446 Score: 90
Period size: 25 Copynumber: 2.1 Consensus size: 26
384 AGCCCTTAAT
*
394 AACAACTGCATTTTTTAGTAACCTTG
1 AACAACTGCATTTTTTAGTAACATTG
420 AACAACTGCA-TTTTTAGTAACATTG
1 AACAACTGCATTTTTTAGTAACATTG
445 AA
1 AA
447 TAAGAATATT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
25 16 0.62
26 10 0.38
ACGTcount: A:0.36, C:0.17, G:0.11, T:0.36
Consensus pattern (26 bp):
AACAACTGCATTTTTTAGTAACATTG
Found at i:2508 original size:30 final size:31
Alignment explanation
Indices: 2454--2518 Score: 105
Period size: 30 Copynumber: 2.1 Consensus size: 31
2444 AACTTTATGT
*
2454 TTTCCGATTGTACCCTTATTTTTAAAACATA
1 TTTCCAATTGTACCCTTATTTTTAAAACATA
*
2485 TTTCCAATTGTA-CCTTTTTTTTAAAACATA
1 TTTCCAATTGTACCCTTATTTTTAAAACATA
2515 TTTC
1 TTTC
2519 TAAATTATCA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 21 0.66
31 11 0.34
ACGTcount: A:0.28, C:0.18, G:0.05, T:0.49
Consensus pattern (31 bp):
TTTCCAATTGTACCCTTATTTTTAAAACATA
Found at i:3947 original size:19 final size:20
Alignment explanation
Indices: 3920--3957 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
3910 TACTATTATT
3920 TTTTGAATTT-AATATTTTAC
1 TTTTGAATTTCAAT-TTTTAC
3940 TTTT-AATTTCAATTTTTA
1 TTTTGAATTTCAATTTTTA
3958 AATGTTAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.29, C:0.05, G:0.03, T:0.63
Consensus pattern (20 bp):
TTTTGAATTTCAATTTTTAC
Found at i:4104 original size:22 final size:22
Alignment explanation
Indices: 4076--4124 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
4066 ACTATTGTTA
* *
4076 GGTTATTAAAATTTCTTAGGTT
1 GGTTATTAAAATTTCATAGGGT
*
4098 GGTTATTGAAATTTCATAGGGT
1 GGTTATTAAAATTTCATAGGGT
4120 GGTTA
1 GGTTA
4125 ATTATCACAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.27, C:0.04, G:0.24, T:0.45
Consensus pattern (22 bp):
GGTTATTAAAATTTCATAGGGT
Found at i:4521 original size:22 final size:22
Alignment explanation
Indices: 4155--4533 Score: 177
Period size: 22 Copynumber: 16.9 Consensus size: 22
4145 AGGTTATCAA
* *
4155 AGAGATTATCAAAATGTCATAG
1 AGAGGTTATCAAAATTTCATAG
*
4177 TGAGGTTAT-AAGAATTTCATAG
1 AGAGGTTATCAA-AATTTCATAG
* * *
4199 TGTGGTTAACAAAATTTCATTAG
1 AGAGGTTATCAAAATTTCA-TAG
* *
4222 -GAGGTTA-CTGATATTTCAT-G
1 AGAGGTTATC-AAAATTTCATAG
*
4242 AGGAGGTTATCAAAATTTTATAG
1 A-GAGGTTATCAAAATTTCATAG
* *
4265 TGTGGTTATCAAAATTTCATATG
1 AGAGGTTATCAAAATTTCATA-G
* *
4288 A-AGGTTATAAAAGTCTCAATTTCATAA
1 AGAGGTTAT-CAA-----AATTTCATAG
* *
4315 AGA-G-TACCAAAATTTGATAG
1 AGAGGTTATCAAAATTTCATAG
*
4335 A-AGGTTATC-AAATCTCATAG
1 AGAGGTTATCAAAATTTCATAG
* * *
4355 AGTGATTATCGAAATTTCATAG
1 AGAGGTTATCAAAATTTCATAG
4377 AGATCGGATTATCATCAAAATTTCATAG
1 AGA--GG--T-T-ATCAAAATTTCATAG
* ** * *
4405 TGTTGTTATCAAAATTTCAAATC
1 AGAGGTTATCAAAATTTCATA-G
*
4428 A-AGGTTATCAAAATTACATA-
1 AGAGGTTATCAAAATTTCATAG
* * * *
4448 ATGTGATTATCAGAATTTTATAG
1 A-GAGGTTATCAAAATTTCATAG
* * * * *
4471 AGGGGTCAACAAAATTTTATAC
1 AGAGGTTATCAAAATTTCATAG
*
4493 AGAGGTTATCAAAATTTCATAA
1 AGAGGTTATCAAAATTTCATAG
* *
4515 AGAGGTTCTCAAATTTTCA
1 AGAGGTTATCAAAATTTCA
4534 AAATGTGATT
Statistics
Matches: 268, Mismatches: 59, Indels: 60
0.69 0.15 0.16
Matches are distributed among these distances:
19 1 0.00
20 22 0.08
21 13 0.05
22 184 0.69
23 12 0.04
24 2 0.01
25 2 0.01
26 4 0.01
27 3 0.01
28 25 0.09
ACGTcount: A:0.39, C:0.10, G:0.17, T:0.35
Consensus pattern (22 bp):
AGAGGTTATCAAAATTTCATAG
Found at i:4675 original size:19 final size:19
Alignment explanation
Indices: 4642--4686 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
4632 TGGAGTAATT
*
4642 AAAATTTCAGAGAGGGTATC
1 AAAA-TTCAGAGAGGATATC
*
4662 AAAATTCAGGGAGGATATC
1 AAAATTCAGAGAGGATATC
4681 AAAATT
1 AAAATT
4687 TTATATGAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 19 0.83
20 4 0.17
ACGTcount: A:0.44, C:0.09, G:0.22, T:0.24
Consensus pattern (19 bp):
AAAATTCAGAGAGGATATC
Found at i:4705 original size:22 final size:22
Alignment explanation
Indices: 4677--5214 Score: 178
Period size: 22 Copynumber: 24.7 Consensus size: 22
4667 TCAGGGAGGA
* *
4677 TATCAAAATTTTATATGAAGGT
1 TATCAAAATTTCATAGGAAGGT
* *
4699 TATCAAAATTTCATAAGAGGGT
1 TATCAAAATTTCATAGGAAGGT
* *
4721 TATCAAAATTTCATA-GTATGT
1 TATCAAAATTTCATAGGAAGGT
* **
4742 AGATCAAAATTTCATAGGAAAAT
1 -TATCAAAATTTCATAGGAAGGT
* * *
4765 CAACAAAATTTCATAATG-AGGT
1 TATCAAAATTTCAT-AGGAAGGT
** * *
4787 TATCAAAAAATCATAGGGAGCT
1 TATCAAAATTTCATAGGAAGGT
*
4809 TATCAAAATTT--T---TA-GT
1 TATCAAAATTTCATAGGAAGGT
* * **
4825 TATCAAGATTTCATAAGAAACT
1 TATCAAAATTTCATAGGAAGGT
* * **
4847 TATCAAAATTTTATGGGGGGGTT
1 TATCAAAATTTCATAGGAAGG-T
* *
4870 TATCAAAATTTTATAGGAAGATT
1 TATCAAAATTTCATAGGAAG-GT
*
4893 TATCAAAATTTCATAGCG-AGAT
1 TATCAAAATTTCATAG-GAAGGT
* * *
4915 TATCACAATTTCATAGTG-TGAT
1 TATCAAAATTTCATAG-GAAGGT
* * *
4937 TATCAAAATTTCAGAGTG-TGAT
1 TATCAAAATTTCATAG-GAAGGT
4959 TA-CTAACAA-TTCATATGG-AGGT
1 TATC-AA-AATTTCATA-GGAAGGT
* * * * *
4981 TTTTAAATTTTCATAACG-TGGT
1 TATCAAAATTTCAT-AGGAAGGT
* * * *
5003 TATCAATATATCATATGTAGGT
1 TATCAAAATTTCATAGGAAGGT
* * ** *
5025 TATCAACATCTCATAGTGTTGTT
1 TATCAAAATTTCATAG-GAAGGT
*
5048 TATCAAAATTTCATCGGGAA-GT
1 TATCAAAATTTCAT-AGGAAGGT
*
5070 TATCAAAATTTCATATTG-AGGT
1 TATCAAAATTTCATA-GGAAGGT
* * * * *
5092 TTTTAAAATTCCTTAGGGAGGT
1 TATCAAAATTTCATAGGAAGGT
* *
5114 TAACAAAATTTCATAAGAAGGT
1 TATCAAAATTTCATAGGAAGGT
* * ** *
5136 TA-AAAAAATT-ATAAAAAGAT
1 TATCAAAATTTCATAGGAAGGT
* ** * * **
5156 TCTTGAAATTCCATAGTATCGT
1 TATCAAAATTTCATAGGAAGGT
* *
5178 TATTAAAATTTCATAGGAAGAT
1 TATCAAAATTTCATAGGAAGGT
5200 TATCAAAATTTCATA
1 TATCAAAATTTCATA
5215 ATGAGATCAT
Statistics
Matches: 380, Mismatches: 109, Indels: 54
0.70 0.20 0.10
Matches are distributed among these distances:
16 11 0.03
17 1 0.00
18 1 0.00
20 10 0.03
21 22 0.06
22 271 0.71
23 62 0.16
24 2 0.01
ACGTcount: A:0.39, C:0.10, G:0.14, T:0.36
Consensus pattern (22 bp):
TATCAAAATTTCATAGGAAGGT
Done.