Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017592.1 Corchorus olitorius cultivar O-4 contig17625, 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: 21231
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:1514 original size:17 final size:17
Alignment explanation
Indices: 1485--1518 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
1475 TATTATAATA
1485 TTTTTTTGTATAAAAAT
1 TTTTTTTGTATAAAAAT
1502 TTTTTATTG-ATAAAAAT
1 TTTTT-TTGTATAAAAAT
1519 AAAAATAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 13 0.81
18 3 0.19
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (17 bp):
TTTTTTTGTATAAAAAT
Found at i:3353 original size:18 final size:18
Alignment explanation
Indices: 3330--3369 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
3320 TTGCGTAATT
3330 CTTTAAATTTAGTGTTTC
1 CTTTAAATTTAGTGTTTC
3348 CTTTAAATTTAGTGTTTC
1 CTTTAAATTTAGTGTTTC
3366 CTTT
1 CTTT
3370 GATATTTGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.20, C:0.12, G:0.10, T:0.57
Consensus pattern (18 bp):
CTTTAAATTTAGTGTTTC
Found at i:4729 original size:22 final size:22
Alignment explanation
Indices: 4659--4805 Score: 117
Period size: 21 Copynumber: 6.9 Consensus size: 22
4649 TCTCACAGAG
* *
4659 AGATTATCAAAA-ATCATAGGA
1 AGATTATCAAAATTTCATAGGT
* *
4680 AGGTTA-CAAAATTT-ATAGGA
1 AGATTATCAAAATTTCATAGGT
* * *
4700 AAATTTATTAAAATTTCATAGTT
1 AGA-TTATCAAAATTTCATAGGT
* *
4723 AGATTATCAAAGTTTCTTATGG-
1 AGATTATCAAAATTTCATA-GGT
* * *
4745 AGTTTATCACAATTTTATAGGT
1 AGATTATCAAAATTTCATAGGT
*
4767 A-ATTATCAAAATTTAATAGGT
1 AGATTATCAAAATTTCATAGGT
4788 AG-TTATCAAAATTTCATA
1 AGATTATCAAAATTTCATA
4806 AAAATATTCA
Statistics
Matches: 98, Mismatches: 21, Indels: 14
0.74 0.16 0.11
Matches are distributed among these distances:
20 12 0.12
21 44 0.45
22 35 0.36
23 7 0.07
ACGTcount: A:0.42, C:0.07, G:0.12, T:0.38
Consensus pattern (22 bp):
AGATTATCAAAATTTCATAGGT
Found at i:7871 original size:79 final size:79
Alignment explanation
Indices: 7711--7857 Score: 208
Period size: 77 Copynumber: 1.9 Consensus size: 79
7701 TTTTGGTTGT
7711 ATAAGGAATTAAAGCTGGAATATGACATTTATAAAGGAAATTTGCTATATTTTGGAATATAGTTT
1 ATAAGGAATTAAAGCTGGAATATGACATTTATAAAGGAAATTTGCTATATTTTGGAATATAGTTT
** *
7776 GGGTTGTATAAGGA
66 GGAATGTAGAAGGA
* * * *
7790 ATAAGGAATTAAAGTTGGGATATGACA-TT-TAAGGGAATTTTGCTATATTTTGGAATATAGTTT
1 ATAAGGAATTAAAGCTGGAATATGACATTTATAAAGGAAATTTGCTATATTTTGGAATATAG-TT
7853 TGGAA
65 TGGAA
7858 ATGAGCCGTG
Statistics
Matches: 61, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
77 29 0.48
78 7 0.11
79 25 0.41
ACGTcount: A:0.37, C:0.03, G:0.23, T:0.37
Consensus pattern (79 bp):
ATAAGGAATTAAAGCTGGAATATGACATTTATAAAGGAAATTTGCTATATTTTGGAATATAGTTT
GGAATGTAGAAGGA
Found at i:9512 original size:22 final size:22
Alignment explanation
Indices: 9280--9522 Score: 159
Period size: 22 Copynumber: 11.1 Consensus size: 22
9270 CTCCAACATA
* * *
9280 GAAATATTGATAACAACACTGT
1 GAAATTTTGATAACCACACTAT
* * * * *
9302 GAAAATTTAATAATCTCATTAT
1 GAAATTTTGATAACCACACTAT
* * *
9324 GATATTTTAATAACCGGC-CTAT
1 GAAATTTTGATAACC-ACACTAT
* * *
9346 GAAAATTTGATAACCATACTGT
1 GAAATTTTGATAACCACACTAT
*
9368 GAAATTTTGATAAACACACTAT
1 GAAATTTTGATAACCACACTAT
* * *
9390 GAAATTTTGATAATCTCAGTAT
1 GAAATTTTGATAACCACACTAT
* * * *
9412 GAAATTTCGATAATCTCCCTAT
1 GAAATTTTGATAACCACACTAT
*
9434 GAAATTTTGATAATCACACTAT
1 GAAATTTTGATAACCACACTAT
* * ** *
9456 -AAA-ATTGGTAACTGCACTGT
1 GAAATTTTGATAACCACACTAT
* *
9476 GAAAATTTTGATAACCCCACCAT
1 G-AAATTTTGATAACCACACTAT
* *
9499 GAAATTTTGATAACCTCCCTAT
1 GAAATTTTGATAACCACACTAT
9521 GA
1 GA
9523 GAATGAAACT
Statistics
Matches: 169, Mismatches: 47, Indels: 10
0.75 0.21 0.04
Matches are distributed among these distances:
20 11 0.07
21 3 0.02
22 142 0.84
23 13 0.08
ACGTcount: A:0.39, C:0.16, G:0.12, T:0.34
Consensus pattern (22 bp):
GAAATTTTGATAACCACACTAT
Found at i:9606 original size:22 final size:22
Alignment explanation
Indices: 9558--9627 Score: 68
Period size: 22 Copynumber: 3.2 Consensus size: 22
9548 TGTAATCCTG
* *
9558 ATAACCTCTCAATAAAATTTTC
1 ATAACCTCCCAATGAAATTTTC
*
9580 ATAACCTCCCAATGAAATTTTG
1 ATAACCTCCCAATGAAATTTTC
* * * * *
9602 TTAACGTCCCTAGGAAATTTTA
1 ATAACCTCCCAATGAAATTTTC
9624 ATAA
1 ATAA
9628 GCACAAATTT
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.39, C:0.20, G:0.07, T:0.34
Consensus pattern (22 bp):
ATAACCTCCCAATGAAATTTTC
Found at i:9682 original size:22 final size:22
Alignment explanation
Indices: 9654--9883 Score: 166
Period size: 22 Copynumber: 10.5 Consensus size: 22
9644 ATTCCCTCCC
*
9654 TATGAAATTTTGTTAACCTTCT
1 TATGAAATTTTGATAACCTTCT
* *
9676 TATGAAATTTTGAGAACC-ACAT
1 TATGAAATTTTGATAACCTTC-T
* * * *
9698 TATAAAATTTCGATAACTTTCG
1 TATGAAATTTTGATAACCTTCT
* *
9720 TATAAAATTTT--TAACCTCCT
1 TATGAAATTTTGATAACCTTCT
* *
9740 TAAGAAATTTTGATAACCTTTT
1 TATGAAATTTTGATAACCTTCT
* *
9762 TAAGAAATTTTGGTAACCTTCT
1 TATGAAATTTTGATAACCTTCT
* *
9784 TATGAAATTTTGATAA-CTACAC
1 TATGAAATTTTGATAACCTTC-T
* * * *
9806 TATGAAGTTTTCATAATCTTCA
1 TATGAAATTTTGATAACCTTCT
* * *
9828 TATGAAATTTCGATAACC-ACAC
1 TATGAAATTTTGATAACCTTC-T
*
9850 TATTAAATTTTGATAACCTTGC-
1 TATGAAATTTTGATAACCTT-CT
*
9872 TATGTAATTTTG
1 TATGAAATTTTG
9884 GTTGATTGTC
Statistics
Matches: 161, Mismatches: 38, Indels: 18
0.74 0.18 0.08
Matches are distributed among these distances:
20 15 0.09
21 5 0.03
22 136 0.84
23 4 0.02
24 1 0.01
ACGTcount: A:0.35, C:0.14, G:0.10, T:0.42
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTTCT
Found at i:9792 original size:64 final size:64
Alignment explanation
Indices: 9654--9794 Score: 149
Period size: 64 Copynumber: 2.2 Consensus size: 64
9644 ATTCCCTCCC
* * *
9654 TATGAAATTTTGTTAACCTTCTTATGAAATTTTGAGAACCACATTATAAAATTTCGATAACTTTC
1 TATGAAA-TTT-TTAACCTCCTTAAGAAATTTTGAGAACCACATTATAAAATTTCGATAACCTTC
9719 G
64 G
* * *** * * *
9720 TATAAAATTTTTAACCTCCTTAAGAAATTTTGATAACCTTTTTA-AGAAATTTTGGTAACCTTCT
1 TATGAAATTTTTAACCTCCTTAAGAAATTTTGAGAACCACATTATA-AAATTTCGATAACCTTCG
9784 TATGAAATTTT
1 TATGAAATTTT
9795 GATAACTACA
Statistics
Matches: 62, Mismatches: 12, Indels: 4
0.79 0.15 0.05
Matches are distributed among these distances:
63 1 0.02
64 52 0.84
65 3 0.05
66 6 0.10
ACGTcount: A:0.35, C:0.13, G:0.09, T:0.43
Consensus pattern (64 bp):
TATGAAATTTTTAACCTCCTTAAGAAATTTTGAGAACCACATTATAAAATTTCGATAACCTTCG
Found at i:10022 original size:8 final size:8
Alignment explanation
Indices: 10009--10044 Score: 72
Period size: 8 Copynumber: 4.5 Consensus size: 8
9999 TTTCCTTCCA
10009 CTTCATAC
1 CTTCATAC
10017 CTTCATAC
1 CTTCATAC
10025 CTTCATAC
1 CTTCATAC
10033 CTTCATAC
1 CTTCATAC
10041 CTTC
1 CTTC
10045 CACTTCCTCC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 28 1.00
ACGTcount: A:0.22, C:0.39, G:0.00, T:0.39
Consensus pattern (8 bp):
CTTCATAC
Found at i:10914 original size:29 final size:30
Alignment explanation
Indices: 10855--10918 Score: 94
Period size: 29 Copynumber: 2.2 Consensus size: 30
10845 AAAAGGGTTG
* *
10855 ATTTGGCCAAAATTGGTAGTTCAGGGGCTT
1 ATTTGGCCAAAATTAGAAGTTCAGGGGCTT
*
10885 ATTTGGCCAAAA-TAGAAGTTTAGGGGCTT
1 ATTTGGCCAAAATTAGAAGTTCAGGGGCTT
10914 ATTTG
1 ATTTG
10919 ACTGTTGATG
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
29 19 0.61
30 12 0.39
ACGTcount: A:0.27, C:0.11, G:0.28, T:0.34
Consensus pattern (30 bp):
ATTTGGCCAAAATTAGAAGTTCAGGGGCTT
Found at i:10980 original size:21 final size:20
Alignment explanation
Indices: 10956--10998 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
10946 ATGCCACGAC
10956 AAAAAAT-GAAAATTCTCATA
1 AAAAAATCGAAAATTCTCA-A
*
10976 AAAAAATCGAAAATTTTCAA
1 AAAAAATCGAAAATTCTCAA
10996 AAA
1 AAA
10999 TATGGTTTAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.63, C:0.09, G:0.05, T:0.23
Consensus pattern (20 bp):
AAAAAATCGAAAATTCTCAA
Found at i:11231 original size:29 final size:30
Alignment explanation
Indices: 11164--11233 Score: 88
Period size: 29 Copynumber: 2.3 Consensus size: 30
11154 TCTGAAGATG
* * * *
11164 GCTTGATTTGGTCAAAATTGGTAGTTCATGG
1 GCTT-ATTTGGCCAAAATTGGAAGCTCATGA
11195 GCTTATTTGGCCAAAATT-GAAGCTCATGA
1 GCTTATTTGGCCAAAATTGGAAGCTCATGA
11224 GCTTATTTGG
1 GCTTATTTGG
11234 GCATTGGTGG
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 18 0.51
30 13 0.37
31 4 0.11
ACGTcount: A:0.24, C:0.13, G:0.26, T:0.37
Consensus pattern (30 bp):
GCTTATTTGGCCAAAATTGGAAGCTCATGA
Found at i:12726 original size:8 final size:8
Alignment explanation
Indices: 12713--12742 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
12703 CAGTATCTAG
12713 AATATTAC
1 AATATTAC
12721 AATATTAC
1 AATATTAC
12729 AATATTAC
1 AATATTAC
12737 -ATATTA
1 AATATTA
12743 GTAGAAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 6 0.27
8 16 0.73
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (8 bp):
AATATTAC
Found at i:13655 original size:13 final size:13
Alignment explanation
Indices: 13637--13662 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
13627 ATTTAATTAA
13637 ATAAATAAAAATT
1 ATAAATAAAAATT
13650 ATAAATAAAAATT
1 ATAAATAAAAATT
13663 TTTCAAATAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
ATAAATAAAAATT
Found at i:14997 original size:31 final size:31
Alignment explanation
Indices: 14940--14998 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
14930 TTCGGCTCAT
* *
14940 CTGGATTCAGGTCATTCGGGTCTCGGGTCTG
1 CTGGATTCAGGTCATGCAGGTCTCGGGTCTG
*
14971 CTGGATTTAGGGTCATGCAGGT-TCGGGT
1 CTGGATTCA-GGTCATGCAGGTCTCGGGT
14999 TTTGTCCTCA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 14 0.58
32 10 0.42
ACGTcount: A:0.12, C:0.19, G:0.37, T:0.32
Consensus pattern (31 bp):
CTGGATTCAGGTCATGCAGGTCTCGGGTCTG
Found at i:15204 original size:21 final size:22
Alignment explanation
Indices: 15180--15220 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
15170 ATTTATAATA
*
15180 TTCTTGGGTCA-TCGGGTTATT
1 TTCTCGGGTCATTCGGGTTATT
*
15201 TTCTCGGGTTATTCGGGTTA
1 TTCTCGGGTCATTCGGGTTA
15221 CGAGTTTGTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.10, C:0.15, G:0.29, T:0.46
Consensus pattern (22 bp):
TTCTCGGGTCATTCGGGTTATT
Done.