Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014324.1 Corchorus capsularis cultivar CVL-1 contig14345, 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: 68305
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:11417 original size:45 final size:45
Alignment explanation
Indices: 11362--11499 Score: 231
Period size: 45 Copynumber: 3.1 Consensus size: 45
11352 CAGTAGAGGG
* * * *
11362 AGGGGTCAGAGTTTTGATCGGATTAGGAGTTTTGGCCGGAATAGA
1 AGGGGGCAGAGTTATGATCGAAATAGGAGTTTTGGCCGGAATAGA
11407 AGGGGGCAGAGTTATGATCGAAATAGGAGTTTTGGCCGGAATAGA
1 AGGGGGCAGAGTTATGATCGAAATAGGAGTTTTGGCCGGAATAGA
*
11452 AGGGGGCAGAGTTATGATCGAAATATGAGTTTTGGCCGGAATAGA
1 AGGGGGCAGAGTTATGATCGAAATAGGAGTTTTGGCCGGAATAGA
11497 AGG
1 AGG
11500 AGTTATTTTG
Statistics
Matches: 88, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 88 1.00
ACGTcount: A:0.29, C:0.09, G:0.38, T:0.25
Consensus pattern (45 bp):
AGGGGGCAGAGTTATGATCGAAATAGGAGTTTTGGCCGGAATAGA
Found at i:23802 original size:33 final size:33
Alignment explanation
Indices: 23765--23861 Score: 169
Period size: 33 Copynumber: 3.0 Consensus size: 33
23755 CTCAACTTGT
23765 AAAGGCGTGATGAAGGCCCGTGAACTTCATTGA
1 AAAGGCGTGATGAAGGCCCGTGAACTTCATTGA
23798 AAAGGCGTGATGAAGGCCCGTGAACTTCATTGA
1 AAAGGCGTGATGAAGGCCCGTGAACTTCATTGA
* *
23831 AATGGCGTGATGAAGGCCCG-CAACTTCATTG
1 AAAGGCGTGATGAAGGCCCGTGAACTTCATTG
23862 GTTGTAAGAG
Statistics
Matches: 62, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
32 10 0.16
33 52 0.84
ACGTcount: A:0.29, C:0.20, G:0.30, T:0.22
Consensus pattern (33 bp):
AAAGGCGTGATGAAGGCCCGTGAACTTCATTGA
Found at i:32565 original size:19 final size:18
Alignment explanation
Indices: 32541--32576 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
32531 TGAAGATTTC
32541 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
32560 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
32577 ATTATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Found at i:33877 original size:15 final size:16
Alignment explanation
Indices: 33857--33890 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
33847 GATTGATTTC
*
33857 TTAGTTA-ATTTACTT
1 TTAGTTAGATTTAATT
33872 TTAGTTAGATTTAATT
1 TTAGTTAGATTTAATT
33888 TTA
1 TTA
33891 ATTCTTCTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.29, C:0.03, G:0.09, T:0.59
Consensus pattern (16 bp):
TTAGTTAGATTTAATT
Found at i:39808 original size:16 final size:16
Alignment explanation
Indices: 39763--39811 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
39753 AAGCAATTTT
*
39763 TAAGAGCAAAGCCGA-
1 TAAGAGCAAAGTCGAC
* *
39778 TTAGAGGAGAAGTCGAC
1 TAAGAGCA-AAGTCGAC
39795 TAAGAGCAAAGTCGAC
1 TAAGAGCAAAGTCGAC
39811 T
1 T
39812 TTACAAGAAG
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
15 6 0.22
16 15 0.56
17 6 0.22
ACGTcount: A:0.41, C:0.16, G:0.29, T:0.14
Consensus pattern (16 bp):
TAAGAGCAAAGTCGAC
Found at i:42434 original size:19 final size:18
Alignment explanation
Indices: 42410--42445 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
42400 TGAAGATTTC
42410 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
42429 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
42446 ATTATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Found at i:43743 original size:15 final size:16
Alignment explanation
Indices: 43723--43756 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
43713 GATTGATTTC
*
43723 TTAGTTA-ATTTACTT
1 TTAGTTAGATTTAATT
43738 TTAGTTAGATTTAATT
1 TTAGTTAGATTTAATT
43754 TTA
1 TTA
43757 ATTCTTCTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.29, C:0.03, G:0.09, T:0.59
Consensus pattern (16 bp):
TTAGTTAGATTTAATT
Found at i:55188 original size:2 final size:2
Alignment explanation
Indices: 55181--55205 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
55171 GGTTAATTGA
55181 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
55206 GTTGATGTCT
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:56768 original size:5 final size:5
Alignment explanation
Indices: 56758--56783 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
56748 TGAAGAGAAC
56758 AAATT AAATT AAATT AAATT AAATT A
1 AAATT AAATT AAATT AAATT AAATT A
56784 CTGAATTTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (5 bp):
AAATT
Found at i:64553 original size:31 final size:29
Alignment explanation
Indices: 64518--64617 Score: 87
Period size: 31 Copynumber: 3.3 Consensus size: 29
64508 AATAGGCCTG
64518 AATTGAGCAGCTTTTGAAACGTTTGGTACCA
1 AATTGAGCAG-TTTTGAAA-GTTTGGTACCA
* *
64549 AATTGAGCAGATTT-AAAGCTTTGGTACGA
1 AATTGAGCAGTTTTGAAAG-TTTGGTACCA
* * *
64578 ATTTGAGCA-TTTTCGCAAAGGTTTAGAACCA
1 AATTGAGCAGTTTT-G-AAA-GTTTGGTACCA
64609 AATTGAGCA
1 AATTGAGCA
64618 TTTAGCAAGC
Statistics
Matches: 56, Mismatches: 8, Indels: 10
0.76 0.11 0.14
Matches are distributed among these distances:
28 4 0.07
29 20 0.36
30 3 0.05
31 28 0.50
32 1 0.02
ACGTcount: A:0.33, C:0.14, G:0.22, T:0.31
Consensus pattern (29 bp):
AATTGAGCAGTTTTGAAAGTTTGGTACCA
Found at i:65652 original size:22 final size:23
Alignment explanation
Indices: 65617--65663 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
65607 GTAGTTAATC
*
65617 ATAAATTAACTAATTAAA-ACTA
1 ATAAACTAACTAATTAAATACTA
*
65639 ATAAACTAAGTAATTAAATACTA
1 ATAAACTAACTAATTAAATACTA
65662 AT
1 AT
65664 TAATTAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 16 0.73
23 6 0.27
ACGTcount: A:0.57, C:0.09, G:0.02, T:0.32
Consensus pattern (23 bp):
ATAAACTAACTAATTAAATACTA
Found at i:65675 original size:22 final size:22
Alignment explanation
Indices: 65628--65677 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
65618 TAAATTAACT
*
65628 AATTAAAACTAATAAACTAAGT
1 AATTAAAACTAATAAACTAAGA
* *
65650 AATTAAATACTAATTAATTAA-A
1 AATTAAA-ACTAATAAACTAAGA
65672 AATTAA
1 AATTAA
65678 TTTTTTTAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 13 0.54
23 11 0.46
ACGTcount: A:0.60, C:0.06, G:0.02, T:0.32
Consensus pattern (22 bp):
AATTAAAACTAATAAACTAAGA
Found at i:65678 original size:15 final size:15
Alignment explanation
Indices: 65641--65679 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
65631 TAAAACTAAT
*
65641 AAACTAAGTAATTAA
1 AAACTAATTAATTAA
*
65656 ATACTAATTAATTAA
1 AAACTAATTAATTAA
*
65671 AAATTAATT
1 AAACTAATT
65680 TTTTTAAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.56, C:0.05, G:0.03, T:0.36
Consensus pattern (15 bp):
AAACTAATTAATTAA
Done.