Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007183.1 Corchorus capsularis cultivar CVL-1 contig07204, 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: 41368
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.32
Found at i:5224 original size:35 final size:36
Alignment explanation
Indices: 5178--5313 Score: 188
Period size: 35 Copynumber: 3.8 Consensus size: 36
5168 TTCTTACTAA
**
5178 ACTTAATTACCCAAAATTAAGTTACTTATTGAACT-
1 ACTTAATTACCCTGAATTAAGTTACTTATTGAACTC
5213 ACTTAATTACCCTGAATTAAGTTACTTATT-AACTC
1 ACTTAATTACCCTGAATTAAGTTACTTATTGAACTC
* *
5248 ACTTAATTACCCTGAATTAAAGTTAATTACTG-ACTC
1 ACTTAATTACCCTGAATT-AAGTTACTTATTGAACTC
* *
5284 ACTTAATTACCCTGAATTAAATTGCTTATT
1 ACTTAATTACCCTGAATTAAGTTACTTATT
5314 ACTGATTCAC
Statistics
Matches: 90, Mismatches: 8, Indels: 6
0.87 0.08 0.06
Matches are distributed among these distances:
34 4 0.04
35 54 0.60
36 32 0.36
ACGTcount: A:0.36, C:0.18, G:0.07, T:0.39
Consensus pattern (36 bp):
ACTTAATTACCCTGAATTAAGTTACTTATTGAACTC
Found at i:5295 original size:71 final size:70
Alignment explanation
Indices: 5178--5314 Score: 195
Period size: 71 Copynumber: 1.9 Consensus size: 70
5168 TTCTTACTAA
* * *
5178 ACTTAATTACCCAAAATTAAGTTACTTATTGAACTACTTAATTACCCTGAATTAAGTTACTTATT
1 ACTTAATTACCCAAAATTAAGTTAATTACTGAACTACTTAATTACCCTGAATTAAATTACTTATT
5243 AACTC
66 AACTC
** *
5248 ACTTAATTACCCTGAATTAAAGTTAATTACTG-ACTCACTTAATTACCCTGAATTAAATTGCTTA
1 ACTTAATTACCCAAAATT-AAGTTAATTACTGAACT-ACTTAATTACCCTGAATTAAATTACTTA
5312 TTA
64 TTA
5315 CTGATTCACC
Statistics
Matches: 59, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
70 19 0.32
71 40 0.68
ACGTcount: A:0.36, C:0.18, G:0.07, T:0.39
Consensus pattern (70 bp):
ACTTAATTACCCAAAATTAAGTTAATTACTGAACTACTTAATTACCCTGAATTAAATTACTTATT
AACTC
Found at i:10408 original size:30 final size:30
Alignment explanation
Indices: 10346--10766 Score: 457
Period size: 30 Copynumber: 13.6 Consensus size: 30
10336 CATGGTGTAT
*
10346 ATGACAACTTCTGGTGTCAATTGAATAAAATC
1 ATGACAACTTCTGGTGTCAATTG--CAAAATC
* **
10378 ATGACATCTTCAAGTGTCAATTGCAAAATC
1 ATGACAACTTCTGGTGTCAATTGCAAAATC
10408 ATGACAACTTCTGGTGTCAATTGCAAAAATC
1 ATGACAACTTCTGGTGTCAATTGC-AAAATC
*
10439 ATGACAACTTTTGGTGTCAATTGCAAAATC
1 ATGACAACTTCTGGTGTCAATTGCAAAATC
10469 ATGACAACTTCTGGTGTCAATTGCCAAAATC
1 ATGACAACTTCTGGTGTCAATTG-CAAAATC
*
10500 ATGACAACTTCTAGTGTCAATTGCAAAATC
1 ATGACAACTTCTGGTGTCAATTGCAAAATC
* *
10530 ATGACAACTTCTGATGTCAATTGTAAAATC
1 ATGACAACTTCTGGTGTCAATTGCAAAATC
* * *
10560 ATGACAACTTCTGGTATCAATTACAAAATG
1 ATGACAACTTCTGGTGTCAATTGCAAAATC
* *
10590 ATGACAACTTCTTGTGTGTCATTTGGAAATTTATC
1 ATGACAACTTC-TG-GTGTCAATTGCAAA---ATC
* * * *
10625 ATGACAACTTCTGATGTCATTTGTAAGATC
1 ATGACAACTTCTGGTGTCAATTGCAAAATC
** * *
10655 ATGACAACTTCTGGTGTCGTTTGTAAGATC
1 ATGACAACTTCTGGTGTCAATTGCAAAATC
* * * * *
10685 ATGACAACTACTGGTGTCATTTGTAAGACC
1 ATGACAACTTCTGGTGTCAATTGCAAAATC
* * *
10715 ATTGACAAGTTCTGGTGTCAA-TGGAGATTTATC
1 A-TGACAACTTCTGGTGTCAATTGCA-A--AATC
10748 ATGACAACTTCTGGTGTCA
1 ATGACAACTTCTGGTGTCA
10767 TTTGGAAACT
Statistics
Matches: 340, Mismatches: 38, Indels: 22
0.85 0.09 0.05
Matches are distributed among these distances:
30 187 0.55
31 77 0.23
32 47 0.14
33 14 0.04
34 2 0.01
35 13 0.04
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Consensus pattern (30 bp):
ATGACAACTTCTGGTGTCAATTGCAAAATC
Found at i:10462 original size:61 final size:60
Alignment explanation
Indices: 10346--10766 Score: 464
Period size: 61 Copynumber: 6.8 Consensus size: 60
10336 CATGGTGTAT
* **
10346 ATGACAACTTCTGGTGTCAATTGAATAAAATCATGACATCTTCAAGTGTCAATTGCAAAATC
1 ATGACAACTTCTGGTGTCAATTG-A-AAAATCATGACAACTTCTGGTGTCAATTGCAAAATC
*
10408 ATGACAACTTCTGGTGTCAATTGCAAAAATCATGACAACTTTTGGTGTCAATTGCAAAATC
1 ATGACAACTTCTGGTGTCAATTG-AAAAATCATGACAACTTCTGGTGTCAATTGCAAAATC
* *
10469 ATGACAACTTCTGGTGTCAATTGCCAAAATCATGACAACTTCTAGTGTCAATTGCAAAATC
1 ATGACAACTTCTGGTGTCAATTG-AAAAATCATGACAACTTCTGGTGTCAATTGCAAAATC
* * * * *
10530 ATGACAACTTCTGATGTCAATTGTAAAATCATGACAACTTCTGGTATCAATTACAAAATG
1 ATGACAACTTCTGGTGTCAATTGAAAAATCATGACAACTTCTGGTGTCAATTGCAAAATC
* * * * * *
10590 ATGACAACTTCTTGTGTGTCATTTGGAAATTTATCATGACAACTTCTGATGTCATTTGTAAGATC
1 ATGACAACTTC-TG-GTGTCAATT-GAAA--AATCATGACAACTTCTGGTGTCAATTGCAAAATC
** * * * * * * *
10655 ATGACAACTTCTGGTGTCGTTTGTAAGATCATGACAACTACTGGTGTCATTTGTAAGACC
1 ATGACAACTTCTGGTGTCAATTGAAAAATCATGACAACTTCTGGTGTCAATTGCAAAATC
* * **
10715 ATTGACAAGTTCTGGTGTCAATGGAGATTTATCATGACAACTTCTGGTGTCA
1 A-TGACAACTTCTGGTGTCAATTGA-A-AAATCATGACAACTTCTGGTGTCA
10767 TTTGGAAACT
Statistics
Matches: 312, Mismatches: 39, Indels: 15
0.85 0.11 0.04
Matches are distributed among these distances:
60 74 0.24
61 132 0.42
62 35 0.11
63 32 0.10
64 2 0.01
65 37 0.12
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Consensus pattern (60 bp):
ATGACAACTTCTGGTGTCAATTGAAAAATCATGACAACTTCTGGTGTCAATTGCAAAATC
Found at i:10534 original size:91 final size:90
Alignment explanation
Indices: 10346--10766 Score: 475
Period size: 91 Copynumber: 4.5 Consensus size: 90
10336 CATGGTGTAT
* **
10346 ATGACAACTTCTGGTGTCAATTGAATAAAATCATGACATCTTCAAGTGTCAATTGCAAAATCATG
1 ATGACAACTTCTGGTGTCAATTG--TAAAATCATGACAACTTCTGGTGTCAATTGCAAAATCATG
10411 ACAACTTCTGGTGTCAATTGCAAAAATC
64 ACAACTTCTGGTGTCAATTGC-AAAATC
* *
10439 ATGACAACTTTTGGTGTCAATTGCAAAATCATGACAACTTCTGGTGTCAATTGCCAAAATCATGA
1 ATGACAACTTCTGGTGTCAATTGTAAAATCATGACAACTTCTGGTGTCAATTG-CAAAATCATGA
*
10504 CAACTTCTAGTGTCAATTGCAAAATC
65 CAACTTCTGGTGTCAATTGCAAAATC
* * * *
10530 ATGACAACTTCTGATGTCAATTGTAAAATCATGACAACTTCTGGTATCAATTACAAAATGATGAC
1 ATGACAACTTCTGGTGTCAATTGTAAAATCATGACAACTTCTGGTGTCAATTGCAAAATCATGAC
* *
10595 AACTTCTTGTGTGTCATTTGGAAATTTATC
66 AACTTC-TG-GTGTCAATTGCAAA---ATC
* * * ** * *
10625 ATGACAACTTCTGATGTCATTTGTAAGATCATGACAACTTCTGGTGTCGTTTGTAAGATCATGAC
1 ATGACAACTTCTGGTGTCAATTGTAAAATCATGACAACTTCTGGTGTCAATTGCAAAATCATGAC
* * * * *
10690 AACTACTGGTGTCATTTGTAAGACC
66 AACTTCTGGTGTCAATTGCAAAATC
* * *
10715 ATTGACAAGTTCTGGTGTCAA-TGGAGATTTATCATGACAACTTCTGGTGTCA
1 A-TGACAACTTCTGGTGTCAATTGTA-A--AATCATGACAACTTCTGGTGTCA
10767 TTTGGAAACT
Statistics
Matches: 284, Mismatches: 34, Indels: 20
0.84 0.10 0.06
Matches are distributed among these distances:
90 23 0.08
91 98 0.35
92 42 0.15
93 55 0.19
94 2 0.01
95 64 0.23
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Consensus pattern (90 bp):
ATGACAACTTCTGGTGTCAATTGTAAAATCATGACAACTTCTGGTGTCAATTGCAAAATCATGAC
AACTTCTGGTGTCAATTGCAAAATC
Found at i:12097 original size:27 final size:27
Alignment explanation
Indices: 12066--12129 Score: 110
Period size: 27 Copynumber: 2.3 Consensus size: 27
12056 ATTTCTGGAA
*
12066 AACAAGGGAAAGGGACAATTAAAAAGG
1 AACAAGGGAAAGAGACAATTAAAAAGG
12093 AACAAGGGAAAGAGACAATTAAAAAGG
1 AACAAGGGAAAGAGACAATTAAAAAGG
12120 AACAGAGGGA
1 AACA-AGGGA
12130 GTATATATAT
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
27 30 0.86
28 5 0.14
ACGTcount: A:0.56, C:0.08, G:0.30, T:0.06
Consensus pattern (27 bp):
AACAAGGGAAAGAGACAATTAAAAAGG
Found at i:13113 original size:29 final size:29
Alignment explanation
Indices: 13049--13129 Score: 99
Period size: 29 Copynumber: 2.7 Consensus size: 29
13039 GCTTAATACC
* **
13049 CAAATTAGCCCCTTAACTATCCATTTTGGGA
1 CAAATTGGCCCCTTAACT-T-TTTTTTGGGA
* *
13080 CAAATTTGCCCCTTGACTTTTTTTTGGGA
1 CAAATTGGCCCCTTAACTTTTTTTTGGGA
13109 CAAATTGGCCCCTTAACTTTT
1 CAAATTGGCCCCTTAACTTTT
13130 AAAAACGAGA
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
29 27 0.61
30 1 0.02
31 16 0.36
ACGTcount: A:0.23, C:0.25, G:0.14, T:0.38
Consensus pattern (29 bp):
CAAATTGGCCCCTTAACTTTTTTTTGGGA
Found at i:13855 original size:29 final size:29
Alignment explanation
Indices: 13819--13876 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
13809 TCTCGTTTTT
*
13819 AAAAGTTAAGGGGTCAATTTGTCCCAAAA
1 AAAAGTTAAGGGGCCAATTTGTCCCAAAA
13848 AAAAGTTAAGGGGCCAATTTGTCCCAAAA
1 AAAAGTTAAGGGGCCAATTTGTCCCAAAA
13877 TGGATAGTTG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.41, C:0.16, G:0.21, T:0.22
Consensus pattern (29 bp):
AAAAGTTAAGGGGCCAATTTGTCCCAAAA
Found at i:13986 original size:2 final size:2
Alignment explanation
Indices: 13979--14004 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
13969 ATACAAATAC
13979 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
14005 GATGTCATAA
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):
AT
Found at i:18922 original size:2 final size:2
Alignment explanation
Indices: 18917--18943 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
18907 CACACACACA
18917 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
18944 ACATATGTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:20753 original size:1 final size:1
Alignment explanation
Indices: 20712--20745 Score: 59
Period size: 1 Copynumber: 34.0 Consensus size: 1
20702 TCTTTCCCCC
*
20712 TTTTTTTTTTTTTTTTTTTTTTTTTTTTCTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
20746 CTGTTTTTAC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:0.00, C:0.03, G:0.00, T:0.97
Consensus pattern (1 bp):
T
Found at i:20981 original size:2 final size:2
Alignment explanation
Indices: 20976--21000 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
20966 TTTTTGCTTC
20976 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
21001 CCACTATTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:23924 original size:6 final size:6
Alignment explanation
Indices: 23915--23940 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
23905 CTCATTCTTT
23915 CAGCCG CAGCCG CAGCCG CAGCCG CA
1 CAGCCG CAGCCG CAGCCG CAGCCG CA
23941 TGCATGTGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.19, C:0.50, G:0.31, T:0.00
Consensus pattern (6 bp):
CAGCCG
Found at i:31146 original size:2 final size:2
Alignment explanation
Indices: 31139--31163 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
31129 GTATAATTAG
31139 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 T
31164 TATTACTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:31203 original size:12 final size:12
Alignment explanation
Indices: 31182--31221 Score: 71
Period size: 12 Copynumber: 3.2 Consensus size: 12
31172 TTGTTAATAA
31182 AAAAATAATCATC
1 AAAAA-AATCATC
31195 AAAAAAATCATC
1 AAAAAAATCATC
31207 AAAAAAATCATC
1 AAAAAAATCATC
31219 AAA
1 AAA
31222 TCAGAAAAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 22 0.81
13 5 0.19
ACGTcount: A:0.68, C:0.15, G:0.00, T:0.17
Consensus pattern (12 bp):
AAAAAAATCATC
Found at i:31249 original size:13 final size:12
Alignment explanation
Indices: 31232--31265 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
31222 TCAGAAAAGT
31232 GAAAAGAAAAAA
1 GAAAAGAAAAAA
*
31244 GAAAAAAACAAAA
1 GAAAAGAA-AAAA
31257 GAAAAGAAA
1 GAAAAGAAA
31266 TAAAAACTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
12 8 0.42
13 11 0.58
ACGTcount: A:0.82, C:0.03, G:0.15, T:0.00
Consensus pattern (12 bp):
GAAAAGAAAAAA
Found at i:31270 original size:20 final size:20
Alignment explanation
Indices: 31233--31290 Score: 57
Period size: 20 Copynumber: 3.0 Consensus size: 20
31223 CAGAAAAGTG
*
31233 AAAAGAAAA-AAGAAAAAAAC
1 AAAAGAAAAGAA-ATAAAAAC
31253 AAAAGAAAAGAAATAAAAAC
1 AAAAGAAAAGAAATAAAAAC
* **
31273 -TAATTAAAGAAATAAAAA
1 AAAAGAAAAGAAATAAAAA
31291 GGAAGAAAAG
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
19 15 0.45
20 16 0.48
21 2 0.06
ACGTcount: A:0.79, C:0.03, G:0.09, T:0.09
Consensus pattern (20 bp):
AAAAGAAAAGAAATAAAAAC
Found at i:31300 original size:19 final size:19
Alignment explanation
Indices: 31255--31300 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
31245 AAAAAAACAA
*
31255 AAGAAAAGAAATAAAAACT
1 AAGAAAAGAAATAAAAACG
** *
31274 AATTAAAGAAATAAAAAGG
1 AAGAAAAGAAATAAAAACG
31293 AAGAAAAG
1 AAGAAAAG
31301 TCAAATCAGA
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.72, C:0.02, G:0.15, T:0.11
Consensus pattern (19 bp):
AAGAAAAGAAATAAAAACG
Found at i:31621 original size:11 final size:11
Alignment explanation
Indices: 31605--31630 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
31595 GGAGGACTAA
31605 AAAAAAAAAGG
1 AAAAAAAAAGG
31616 AAAAAAAAAGG
1 AAAAAAAAAGG
31627 AAAA
1 AAAA
31631 CTGGAAGCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAGG
Found at i:40494 original size:2 final size:2
Alignment explanation
Indices: 40481--40511 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
40471 ATTATTTTTC
*
40481 TA TA TG 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 TA T
40512 CTTGTTATCT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Done.