Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018435.1 Corchorus olitorius cultivar O-4 contig18468, 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: 51450
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:1438 original size:30 final size:30
Alignment explanation
Indices: 1404--1473 Score: 88
Period size: 30 Copynumber: 2.4 Consensus size: 30
1394 GTCTGTTAAA
*
1404 GCTCATGTGGCCCTCTGGTGACATGTAATT
1 GCTCATGTGGCCCTCTGATGACATGTAATT
** *
1434 GCTCATGTGGTTCTCTGATGACCTGTAATT
1 GCTCATGTGGCCCTCTGATGACATGTAATT
*
1464 -CTGATGTGGC
1 GCTCATGTGGC
1474 ACTATGAACC
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
29 8 0.24
30 26 0.76
ACGTcount: A:0.16, C:0.21, G:0.27, T:0.36
Consensus pattern (30 bp):
GCTCATGTGGCCCTCTGATGACATGTAATT
Found at i:3563 original size:23 final size:23
Alignment explanation
Indices: 3537--3583 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
3527 AGAAATTTAG
* * *
3537 CTTTATAGAGTTGAGTGTTTAAA
1 CTTTATAGAGATGACTATTTAAA
3560 CTTTATAGAGATGACTATTTAAA
1 CTTTATAGAGATGACTATTTAAA
3583 C
1 C
3584 ATAGAAATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.34, C:0.09, G:0.17, T:0.40
Consensus pattern (23 bp):
CTTTATAGAGATGACTATTTAAA
Found at i:8800 original size:25 final size:24
Alignment explanation
Indices: 8772--8833 Score: 81
Period size: 25 Copynumber: 2.6 Consensus size: 24
8762 GTGGATTGTA
*
8772 AAATAAATTGAATAATTAAGACATT
1 AAATAAATTCAATAATTAA-ACATT
* *
8797 AAATAAATTTAAGAATTAAACATT
1 AAATAAATTCAATAATTAAACATT
8821 AAA-AAATTCAATA
1 AAATAAATTCAATA
8834 CTGACCCAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
23 8 0.24
24 8 0.24
25 17 0.52
ACGTcount: A:0.60, C:0.05, G:0.05, T:0.31
Consensus pattern (24 bp):
AAATAAATTCAATAATTAAACATT
Found at i:9958 original size:22 final size:22
Alignment explanation
Indices: 9933--9974 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
9923 TATTACTAAC
9933 CTATGGTCAAGCT-ATAGTTAAT
1 CTATGGTCAAG-TAATAGTTAAT
*
9955 CTATGGTTAAGTAATAGTTA
1 CTATGGTCAAGTAATAGTTA
9975 GTTATAGGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 1 0.06
22 17 0.94
ACGTcount: A:0.33, C:0.10, G:0.19, T:0.38
Consensus pattern (22 bp):
CTATGGTCAAGTAATAGTTAAT
Found at i:14871 original size:11 final size:11
Alignment explanation
Indices: 14841--14883 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
14831 TATTACTAAC
* *
14841 CTATGGTCAAG
1 CTATGGTTAAT
*
14852 CTATAGTTAAT
1 CTATGGTTAAT
*
14863 CTATGGTTAGT
1 CTATGGTTAAT
14874 CTATGGTTAA
1 CTATGGTTAA
14884 GTAATAGTTA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.28, C:0.12, G:0.21, T:0.40
Consensus pattern (11 bp):
CTATGGTTAAT
Found at i:18429 original size:18 final size:18
Alignment explanation
Indices: 18395--18428 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
18385 GACCTCATAA
18395 TTTTTCTTTTTCATTTTC
1 TTTTTCTTTTTCATTTTC
*
18413 TTTTTGTTTTT-ATTTT
1 TTTTTCTTTTTCATTTT
18429 TTCACCCTAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.06, C:0.09, G:0.03, T:0.82
Consensus pattern (18 bp):
TTTTTCTTTTTCATTTTC
Found at i:29151 original size:2 final size:2
Alignment explanation
Indices: 29144--29178 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
29134 TACTCATGTC
29144 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
29179 ATGAATCATT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:30955 original size:25 final size:25
Alignment explanation
Indices: 30926--30975 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
30916 TATTAATTTT
30926 GGGAGAAAACGATACAACTTAATAC
1 GGGAGAAAACGATACAACTTAATAC
30951 GGGAGAAAACGATACAACTTAATAC
1 GGGAGAAAACGATACAACTTAATAC
30976 AAGATATCGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.48, C:0.16, G:0.20, T:0.16
Consensus pattern (25 bp):
GGGAGAAAACGATACAACTTAATAC
Found at i:39522 original size:2 final size:2
Alignment explanation
Indices: 39515--39544 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
39505 AAAATTTTAA
39515 AT AT 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 AT AT
39545 TGATGCTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:39582 original size:27 final size:27
Alignment explanation
Indices: 39551--39606 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
39541 ATATTGATGC
39551 TTTTTTA-ACAAAAAGATGTTTTGACTT
1 TTTTTTAGACAAAAA-ATGTTTTGACTT
***
39578 TTTTTTAGATTGAAAATGTTTTGACTT
1 TTTTTTAGACAAAAAATGTTTTGACTT
39605 TT
1 TT
39607 GATATTATCC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 21 0.84
28 4 0.16
ACGTcount: A:0.29, C:0.05, G:0.12, T:0.54
Consensus pattern (27 bp):
TTTTTTAGACAAAAAATGTTTTGACTT
Found at i:39687 original size:34 final size:34
Alignment explanation
Indices: 39644--39716 Score: 128
Period size: 34 Copynumber: 2.1 Consensus size: 34
39634 ATTTAAAAAA
* *
39644 AAGGTTTAATGGACATTTTGACCTTTTAACTTGT
1 AAGGATTAATGGACATTTTGACCCTTTAACTTGT
39678 AAGGATTAATGGACATTTTGACCCTTTAACTTGT
1 AAGGATTAATGGACATTTTGACCCTTTAACTTGT
39712 AAGGA
1 AAGGA
39717 ATGGACAAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.30, C:0.12, G:0.19, T:0.38
Consensus pattern (34 bp):
AAGGATTAATGGACATTTTGACCCTTTAACTTGT
Found at i:45288 original size:34 final size:32
Alignment explanation
Indices: 45187--45288 Score: 107
Period size: 33 Copynumber: 3.1 Consensus size: 32
45177 GTTTTTTTAT
* *
45187 ACCTAATTTGAAGCAAAACAGAGGATTTCGAA
1 ACCTAATTTCAAGAAAAACAGAGGATTTCGAA
* * *
45219 ACCTAATTTGAAGAAAGAA-AAAGGGTTTTCGAA
1 ACCTAATTTCAAGAAA-AACAGA-GGATTTCGAA
*
45252 ACCTATTTTCAAGTAAAAACAGAGGCATTTCGAA
1 ACCTAATTTCAAG-AAAAACAGAGG-ATTTCGAA
45286 ACC
1 ACC
45289 CTATGAAGCA
Statistics
Matches: 58, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
32 17 0.29
33 26 0.45
34 15 0.26
ACGTcount: A:0.43, C:0.16, G:0.18, T:0.24
Consensus pattern (32 bp):
ACCTAATTTCAAGAAAAACAGAGGATTTCGAA
Found at i:49394 original size:30 final size:30
Alignment explanation
Indices: 49358--49501 Score: 252
Period size: 30 Copynumber: 4.8 Consensus size: 30
49348 ATTTATTCTA
49358 CTTACAATTGACACCAGAAGTTGTCATGGT
1 CTTACAATTGACACCAGAAGTTGTCATGGT
49388 CTTACAATTGACACCAGAAGTTGTCATGGT
1 CTTACAATTGACACCAGAAGTTGTCATGGT
49418 CTTACAATTGACACCAGAAGTTGTCATGGT
1 CTTACAATTGACACCAGAAGTTGTCATGGT
* **
49448 CTTACAAATGACACCAGAAGTTGTCATAAT
1 CTTACAATTGACACCAGAAGTTGTCATGGT
*
49478 CTTGCAATTGACACCAGAAGTTGT
1 CTTACAATTGACACCAGAAGTTGT
49502 TATAAAAATT
Statistics
Matches: 109, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 109 1.00
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.29
Consensus pattern (30 bp):
CTTACAATTGACACCAGAAGTTGTCATGGT
Found at i:49525 original size:28 final size:28
Alignment explanation
Indices: 49485--49719 Score: 254
Period size: 28 Copynumber: 7.8 Consensus size: 28
49475 AATCTTGCAA
*
49485 TTGACACCAGAAGTTGTTATAAAAATTT
1 TTGACACCAGAAGTTGTCATAAAAATTT
* *
49513 TTGACACCAGAAGTTGTCATGAAAATTA
1 TTGACACCAGAAGTTGTCATAAAAATTT
49541 TTGACACCAGAAGTTGTCATAGCAAATTATTAT
1 TTGACACCAGAAGTTGTCATA--AAA--ATT-T
*
49574 CTTGACACCAGAAGTTGTCATGAAAATTT
1 -TTGACACCAGAAGTTGTCATAAAAATTT
49603 TTGACACCAGAAGTTGTCATATCAAATTATTAT
1 TTGACACCAGAAGTTGTCATA--AAA--ATT-T
* *
49636 CTTGACACCAGAAGTTGTCATGAAAATTA
1 -TTGACACCAGAAGTTGTCATAAAAATTT
49665 TTGACACCAGAAGTTGTCATAGCAAATTATTAT
1 TTGACACCAGAAGTTGTCATA--AAA--ATT-T
49698 CTTGACACCAGAAGTTGTCATA
1 -TTGACACCAGAAGTTGTCATA
49720 CTGAGGAAAT
Statistics
Matches: 178, Mismatches: 11, Indels: 30
0.81 0.05 0.14
Matches are distributed among these distances:
28 85 0.48
29 1 0.01
30 15 0.08
32 15 0.08
33 1 0.01
34 61 0.34
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.32
Consensus pattern (28 bp):
TTGACACCAGAAGTTGTCATAAAAATTT
Found at i:49610 original size:62 final size:62
Alignment explanation
Indices: 49456--49750 Score: 415
Period size: 62 Copynumber: 4.7 Consensus size: 62
49446 GTCTTACAAA
** *
49456 TGACACCAGAAGTTGTCAT-AATCTTGCAATTGACACCAGAAGTTGTTATA--AAA--ATT-T-T
1 TGACACCAGAAGTTGTCATGAAAATT---ATTGACACCAGAAGTTGTCATAGCAAATTATTATCT
49514 TGACACCAGAAGTTGTCATGAAAATTATTGACACCAGAAGTTGTCATAGCAAATTATTATCT
1 TGACACCAGAAGTTGTCATGAAAATTATTGACACCAGAAGTTGTCATAGCAAATTATTATCT
* *
49576 TGACACCAGAAGTTGTCATGAAAATTTTTGACACCAGAAGTTGTCATATCAAATTATTATCT
1 TGACACCAGAAGTTGTCATGAAAATTATTGACACCAGAAGTTGTCATAGCAAATTATTATCT
49638 TGACACCAGAAGTTGTCATGAAAATTATTGACACCAGAAGTTGTCATAGCAAATTATTATCT
1 TGACACCAGAAGTTGTCATGAAAATTATTGACACCAGAAGTTGTCATAGCAAATTATTATCT
*
49700 TGACACCAGAAGTTGTCATACTGAGGAAATTATTGACACTAGAAGTTGTCA
1 TGACACCAGAAGTTGTC--A-TGA--AAATTATTGACACCAGAAGTTGTCA
49751 CCCTAAGATT
Statistics
Matches: 217, Mismatches: 8, Indels: 15
0.90 0.03 0.06
Matches are distributed among these distances:
56 21 0.10
58 22 0.10
59 4 0.02
60 3 0.01
61 1 0.00
62 138 0.64
64 1 0.00
65 3 0.01
67 24 0.11
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.31
Consensus pattern (62 bp):
TGACACCAGAAGTTGTCATGAAAATTATTGACACCAGAAGTTGTCATAGCAAATTATTATCT
Done.