Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007752.1 Corchorus capsularis cultivar CVL-1 contig07773, 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: 30604
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:2996 original size:4 final size:5
Alignment explanation
Indices: 2970--3000 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
2960 TCTGGTCGAA
2970 ATTTT ATTTT ATTTT ATTTT A-TTT ATTTT AT
1 ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT AT
3001 ATTTTTCGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.16
5 21 0.84
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (5 bp):
ATTTT
Found at i:3107 original size:8 final size:8
Alignment explanation
Indices: 3079--3112 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
3069 GAATCGGCTA
3079 TGAATTTT
1 TGAATTTT
*
3087 TGAAGTTTC
1 TGAA-TTTT
3096 TGAATTTT
1 TGAATTTT
3104 TGAATTTT
1 TGAATTTT
3112 T
1 T
3113 CAAGAAGGTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
8 16 0.70
9 7 0.30
ACGTcount: A:0.24, C:0.03, G:0.15, T:0.59
Consensus pattern (8 bp):
TGAATTTT
Found at i:4091 original size:33 final size:34
Alignment explanation
Indices: 4054--4127 Score: 98
Period size: 33 Copynumber: 2.2 Consensus size: 34
4044 CCGAGTCGTT
* *
4054 TGGCCGGTTG-TAGCCGGCCATGTCCATGTCACG
1 TGGCCGGTTGATAGCCAGACATGTCCATGTCACG
* *
4087 TGGCCGG-TGATGGCCAGACATGTCCATGTCGCG
1 TGGCCGGTTGATAGCCAGACATGTCCATGTCACG
4120 TGGCCGGT
1 TGGCCGGT
4128 CTTGTCTCCG
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
32 2 0.06
33 33 0.94
ACGTcount: A:0.12, C:0.28, G:0.36, T:0.23
Consensus pattern (34 bp):
TGGCCGGTTGATAGCCAGACATGTCCATGTCACG
Found at i:13434 original size:13 final size:13
Alignment explanation
Indices: 13416--13443 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
13406 TATCCATTTA
13416 AAATTCGAATCCG
1 AAATTCGAATCCG
13429 AAATTCGAATCCG
1 AAATTCGAATCCG
13442 AA
1 AA
13444 TCCGAAACCG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.43, C:0.21, G:0.14, T:0.21
Consensus pattern (13 bp):
AAATTCGAATCCG
Found at i:14510 original size:30 final size:30
Alignment explanation
Indices: 14470--14532 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
14460 TGTCTTCAAG
14470 TCCATAATAAGTACTTG-GCGCATCATTCCC
1 TCCATAATAAG-ACTTGAGCGCATCATTCCC
* * *
14500 TCCATGATAAGCCTTGAGCGCATCATTCTC
1 TCCATAATAAGACTTGAGCGCATCATTCCC
14530 TCC
1 TCC
14533 CCCTTGAAGA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 4 0.14
30 25 0.86
ACGTcount: A:0.24, C:0.32, G:0.14, T:0.30
Consensus pattern (30 bp):
TCCATAATAAGACTTGAGCGCATCATTCCC
Found at i:18456 original size:40 final size:41
Alignment explanation
Indices: 18412--18490 Score: 142
Period size: 40 Copynumber: 2.0 Consensus size: 41
18402 GAAGAATGAA
*
18412 ATTAAGAATTTTTGTATATTTAT-ATAGGAAAATGTAATTT
1 ATTAAGAATTTTTGTATATTTATAAAAGGAAAATGTAATTT
18452 ATTAAGAATTTTTGTATATTTATAAAAGGAAAATGTAAT
1 ATTAAGAATTTTTGTATATTTATAAAAGGAAAATGTAAT
18491 AGGTAATAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
40 23 0.62
41 14 0.38
ACGTcount: A:0.43, C:0.00, G:0.13, T:0.44
Consensus pattern (41 bp):
ATTAAGAATTTTTGTATATTTATAAAAGGAAAATGTAATTT
Found at i:20946 original size:15 final size:15
Alignment explanation
Indices: 20926--20964 Score: 69
Period size: 15 Copynumber: 2.6 Consensus size: 15
20916 GTAGTAGCAG
*
20926 TAGTAGCAGCGGCAA
1 TAGTAGCAGCGACAA
20941 TAGTAGCAGCGACAA
1 TAGTAGCAGCGACAA
20956 TAGTAGCAG
1 TAGTAGCAG
20965 TAGGAGCAGC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.36, C:0.18, G:0.31, T:0.15
Consensus pattern (15 bp):
TAGTAGCAGCGACAA
Found at i:23385 original size:50 final size:51
Alignment explanation
Indices: 23287--23389 Score: 174
Period size: 52 Copynumber: 2.0 Consensus size: 51
23277 ACACAAACTT
23287 ATGGCAATGTAATTCATATATAATTAAATTAGATAAGAGTATATGTGTCAAG
1 ATGGCAATGTAATTCATATATAATTAAATTAGATAAGAG-ATATGTGTCAAG
23339 ATGGCAATGTAATTCATATAATAATTAAATTAGATAA-AG-TATGTGTCAAG
1 ATGGCAATGTAATTCATAT-ATAATTAAATTAGATAAGAGATATGTGTCAAG
23389 A
1 A
23390 GGTAGCTTAC
Statistics
Matches: 50, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
50 12 0.24
52 21 0.42
53 17 0.34
ACGTcount: A:0.44, C:0.06, G:0.17, T:0.34
Consensus pattern (51 bp):
ATGGCAATGTAATTCATATATAATTAAATTAGATAAGAGATATGTGTCAAG
Found at i:27293 original size:20 final size:20
Alignment explanation
Indices: 27268--27306 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
27258 GCCATGCTTC
*
27268 TGTCTCTGCCGCAACTATGT
1 TGTCTCTACCGCAACTATGT
*
27288 TGTCTCTACCGCAGCTATG
1 TGTCTCTACCGCAACTATG
27307 ACACTTTGTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.15, C:0.31, G:0.21, T:0.33
Consensus pattern (20 bp):
TGTCTCTACCGCAACTATGT
Found at i:27753 original size:16 final size:17
Alignment explanation
Indices: 27714--27761 Score: 55
Period size: 16 Copynumber: 2.9 Consensus size: 17
27704 GTATATTCCG
*
27714 CTGCGGTGACATTCT-A
1 CTGCGGTAACATTCTGA
*
27730 CTGTGGTAACATTCTGA
1 CTGCGGTAACATTCTGA
*
27747 -TGCGGTAACCTTCTG
1 CTGCGGTAACATTCTG
27762 CTGTAGCAAG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
16 26 0.96
17 1 0.04
ACGTcount: A:0.19, C:0.23, G:0.25, T:0.33
Consensus pattern (17 bp):
CTGCGGTAACATTCTGA
Done.