Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012593.1 Corchorus olitorius cultivar O-4 contig12626, 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: 31342
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:1741 original size:34 final size:34
Alignment explanation
Indices: 1698--1767 Score: 140
Period size: 34 Copynumber: 2.1 Consensus size: 34
1688 TATTAATGTA
1698 CTTGCTTCTTACAGTTGATTATATTTGGTTTAAT
1 CTTGCTTCTTACAGTTGATTATATTTGGTTTAAT
1732 CTTGCTTCTTACAGTTGATTATATTTGGTTTAAT
1 CTTGCTTCTTACAGTTGATTATATTTGGTTTAAT
1766 CT
1 CT
1768 GGAGTTATTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.20, C:0.13, G:0.14, T:0.53
Consensus pattern (34 bp):
CTTGCTTCTTACAGTTGATTATATTTGGTTTAAT
Found at i:3637 original size:49 final size:47
Alignment explanation
Indices: 3508--3649 Score: 146
Period size: 49 Copynumber: 3.0 Consensus size: 47
3498 CAAGCAATCC
* * *
3508 TTTACTTTTCA-CTGCACTTTTTCA-CAATTTTTACCACAAAATTGAACT
1 TTTAATTTTCATC-GCACTTTTT-ATCAATTTTTA-GACAAAATTGATCT
* * *
3556 TTT-ATTTTTACTTGCAACTTTTTCTCAATTTTTAAGACAAAATTGATCT
1 TTTAATTTTCA-TCGC-ACTTTTTATCAATTTTT-AGACAAAATTGATCT
*
3605 TTTAATTTTCATCGCACTTTTTATCAATTTTTTGACAAAATTGAT
1 TTTAATTTTCATCGCACTTTTTATCAATTTTTAGACAAAATTGAT
3650 TGACACGCTC
Statistics
Matches: 78, Mismatches: 10, Indels: 13
0.77 0.10 0.13
Matches are distributed among these distances:
47 17 0.22
48 21 0.27
49 33 0.42
50 7 0.09
ACGTcount: A:0.29, C:0.17, G:0.06, T:0.49
Consensus pattern (47 bp):
TTTAATTTTCATCGCACTTTTTATCAATTTTTAGACAAAATTGATCT
Found at i:4899 original size:127 final size:127
Alignment explanation
Indices: 4673--4916 Score: 427
Period size: 127 Copynumber: 1.9 Consensus size: 127
4663 GTGGGATTGA
4673 AGTTTGATAAAAACTTATTTTAAATTACATCATGTGTAATATAATTTTTTTGTTAATCTATACCT
1 AGTTTGATAAAAACTTATTTTAAATTACATCATGTGTAATATAATTTTTTTGTTAATCTATACCT
*
4738 TACTATTATAGTTATCCTCAAACTGTTGTATGCTCAACATTTGGCATTTCTCTTGTATGCTC
66 TACTATTAAAGTTATCCTCAAACTGTTGTATGCTCAACATTTGGCATTTCTCTTGTATGCTC
* * *
4800 AGTTTGATGAAAA-TTGGTTTTAAATTACATCTTGTGTAATATAATTTTTTTGTTAATCTATACC
1 AGTTTGATAAAAACTT-ATTTTAAATTACATCATGTGTAATATAATTTTTTTGTTAATCTATACC
*
4864 TTACTATTAAAGTTATCCTCAAACTGTTGTATGCTCAACATTTGGCTTTTCTC
65 TTACTATTAAAGTTATCCTCAAACTGTTGTATGCTCAACATTTGGCATTTCTC
4917 CTGTTGAGAT
Statistics
Matches: 111, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
126 2 0.02
127 109 0.98
ACGTcount: A:0.29, C:0.14, G:0.11, T:0.46
Consensus pattern (127 bp):
AGTTTGATAAAAACTTATTTTAAATTACATCATGTGTAATATAATTTTTTTGTTAATCTATACCT
TACTATTAAAGTTATCCTCAAACTGTTGTATGCTCAACATTTGGCATTTCTCTTGTATGCTC
Found at i:5123 original size:19 final size:19
Alignment explanation
Indices: 5099--5136 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
5089 AGGGATCCAA
5099 TAGATAATTATTTGAATAG
1 TAGATAATTATTTGAATAG
5118 TAGATAATTATTTGAATAG
1 TAGATAATTATTTGAATAG
5137 ACATTAGAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.16, T:0.42
Consensus pattern (19 bp):
TAGATAATTATTTGAATAG
Found at i:6621 original size:22 final size:22
Alignment explanation
Indices: 6596--6844 Score: 148
Period size: 22 Copynumber: 11.2 Consensus size: 22
6586 TAGAAATATC
6596 GATAACCACACTATGAAAATTT
1 GATAACCACACTATGAAAATTT
* * *
6618 GATAACCTCATTGTG-AAATTT
1 GATAACCACACTATGAAAATTT
* * *
6639 CGATAACCTCCCTATAAAAATTT
1 -GATAACCACACTATGAAAATTT
* * *
6662 GATAACCACAATGTGAAATTTT
1 GATAACCACACTATGAAAATTT
* *
6684 GATAAGCACACTGTG-AAATTCT
1 GATAACCACACTATGAAAATT-T
* **
6706 GATAACCACACAATGAAGTTTT
1 GATAACCACACTATGAAAATTT
* *
6728 GATAACCTCATTGTCTATGAAATTTT
1 GATAACCACA----CTATGAAAATTT
* *
6754 GATAATCACATTAT-AAAA-TT
1 GATAACCACACTATGAAAATTT
* * *
6774 GGTAATCGCACTATGAAAATTT
1 GATAACCACACTATGAAAATTT
* * * *
6796 TATAACCTCCCTATGAAATTTT
1 GATAACCACACTATGAAAATTT
* * *
6818 GTTAACCATC-CTAGGAAATTTT
1 GATAACCA-CACTATGAAAATTT
6840 GATAA
1 GATAA
6845 GAACAAATTT
Statistics
Matches: 174, Mismatches: 42, Indels: 22
0.73 0.18 0.09
Matches are distributed among these distances:
20 13 0.07
21 17 0.10
22 116 0.67
23 10 0.06
26 18 0.10
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.33
Consensus pattern (22 bp):
GATAACCACACTATGAAAATTT
Found at i:6951 original size:22 final size:22
Alignment explanation
Indices: 6869--7106 Score: 91
Period size: 22 Copynumber: 10.6 Consensus size: 22
6859 AGCCTCCCTC
* *
6869 CCTATGAAATTTTGTTAACGTT
1 CCTATGAAATTTTGATAACCTT
* * *
6891 -CTAAT-TAATTTTGATAATC-A
1 CCT-ATGAAATTTTGATAACCTT
*
6911 CACTATAAAATTTCT-ATAACCTT
1 C-CTATGAAATTT-TGATAACCTT
* *
6934 CGTATGAAATTTTGATAATC-T
1 CCTATGAAATTTTGATAACCTT
* *
6955 CCATAAGAGATTTTGATAACCTTTTTTT
1 CC-TATGAAATTTTGATAACC-----TT
** *
6983 TTTATGAAATTTTGGTAACC-T
1 CCTATGAAATTTTGATAACCTT
*
7004 CTGTATGAAATTTTGATAA--TT
1 C-CTATGAAATTTTGATAACCTT
* * *
7025 ACACTACGAAGTCTTGATAACC-T
1 -C-CTATGAAATTTTGATAACCTT
* *
7048 CCATATGAAATTTTGGTAACC-A
1 CC-TATGAAATTTTGATAACCTT
*
7070 CACTATGAAATTTTAATAACCTT
1 C-CTATGAAATTTTGATAACCTT
*
7093 CCTATGTAATTTTG
1 CCTATGAAATTTTG
7107 GTTTGATTGC
Statistics
Matches: 156, Mismatches: 38, Indels: 44
0.66 0.16 0.18
Matches are distributed among these distances:
21 20 0.13
22 115 0.74
23 5 0.03
27 15 0.10
28 1 0.01
ACGTcount: A:0.33, C:0.15, G:0.11, T:0.42
Consensus pattern (22 bp):
CCTATGAAATTTTGATAACCTT
Found at i:7061 original size:44 final size:43
Alignment explanation
Indices: 6998--7106 Score: 110
Period size: 44 Copynumber: 2.5 Consensus size: 43
6988 GAAATTTTGG
* ** * *
6998 TAACCTCTGTATGAAATTTTGATAATTACACTACGAAGTCTTGA
1 TAACCTC-CTATGAAATTTTGATAACCACACTACGAAATCTTAA
* * *
7042 TAACCTCCATATGAAATTTTGGTAACCACACTATGAAATTTTAA
1 TAACCTCC-TATGAAATTTTGATAACCACACTACGAAATCTTAA
*
7086 TAACCTTCCTATGTAATTTTG
1 TAACC-TCCTATGAAATTTTG
7107 GTTTGATTGC
Statistics
Matches: 54, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
44 51 0.94
45 3 0.06
ACGTcount: A:0.34, C:0.17, G:0.11, T:0.38
Consensus pattern (43 bp):
TAACCTCCTATGAAATTTTGATAACCACACTACGAAATCTTAA
Found at i:7903 original size:21 final size:21
Alignment explanation
Indices: 7879--7918 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
7869 ACAATACTTT
*
7879 AGTTACTGAAAAAGCTATAAC
1 AGTTACTAAAAAAGCTATAAC
* *
7900 AGTTATTAAAAAAGTTATA
1 AGTTACTAAAAAAGCTATA
7919 GATGTACCAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.50, C:0.07, G:0.12, T:0.30
Consensus pattern (21 bp):
AGTTACTAAAAAAGCTATAAC
Found at i:8707 original size:168 final size:170
Alignment explanation
Indices: 8401--8713 Score: 370
Period size: 168 Copynumber: 1.9 Consensus size: 170
8391 GTTTGGCAAG
* * * *
8401 CCACTTTCCAATGAGCTCTATTGACTTTGAAACATGACATATGAGCGATGGTTACACAAATAATG
1 CCACTTTCCAATGAGCTCTACTCACTCTGAAACATAACATATGAGCGATGGTTACACAAATAATG
* * * *
8466 CATTCGGAATTAACATTTTCTCAAGAACAACGTTCTGCGCACAAACACGTAAAATCGTGAAGTTT
66 CATTCGGAATGAACATTTCCTCAAGAACAACGTTCTGCGCACAAACACGTAAAATCGGGAAGTTG
8531 AAGTTTTAGG-TTTTGAAGTAAAGTTTTTTTTTTTCAAAC
131 AAGTTTTAGGCTTTTGAAGTAAAGTTTTTTTTTTTCAAAC
* * * *
8570 CCACTTTCCAATTAGCT-TACTCACTCTGAAACATAACATTTGGGC-ATTGGTTTCACAAATAAT
1 CCACTTTCCAATGAGCTCTACTCACTCTGAAACATAACATATGAGCGA-TGGTTACACAAATAAT
* * * **
8633 GTACTT-GGAATGAGCATTTCC-CTAAGAACAACGTT-TGGCGCTCAAACGTGCT-AAATCGGGA
65 GCA-TTCGGAATGAACATTTCCTC-AAGAACAACGTTCT-GCGCACAAACACG-TAAAATCGGGA
*
8694 AGTTGAGGTTTTAGGCTTTT
126 AGTTGAAGTTTTAGGCTTTT
8714 TAGAAAGTTT
Statistics
Matches: 120, Mismatches: 18, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
167 3 0.03
168 94 0.78
169 23 0.19
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.33
Consensus pattern (170 bp):
CCACTTTCCAATGAGCTCTACTCACTCTGAAACATAACATATGAGCGATGGTTACACAAATAATG
CATTCGGAATGAACATTTCCTCAAGAACAACGTTCTGCGCACAAACACGTAAAATCGGGAAGTTG
AAGTTTTAGGCTTTTGAAGTAAAGTTTTTTTTTTTCAAAC
Found at i:8901 original size:21 final size:22
Alignment explanation
Indices: 8872--8924 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
8862 ATTTTGCAAG
8872 TTTGATAACCT-CATATG-AAA
1 TTTGATAACCTCCATATGAAAA
*
8892 TTTCGATAACCTCCCTATGAAAA
1 TTT-GATAACCTCCATATGAAAA
8915 TTTGATAACC
1 TTTGATAACC
8925 ACACTGTAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
20 3 0.10
21 8 0.28
22 12 0.41
23 6 0.21
ACGTcount: A:0.36, C:0.21, G:0.09, T:0.34
Consensus pattern (22 bp):
TTTGATAACCTCCATATGAAAA
Found at i:9043 original size:22 final size:23
Alignment explanation
Indices: 8997--9046 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 23
8987 ATAAAATTGG
* * *
8997 TAACCGCACTATGAAAATTTTGA
1 TAACCACACCATGAAAATTTCGA
9020 TAACCACACCATG-AAATTTCGA
1 TAACCACACCATGAAAATTTCGA
9042 TAACC
1 TAACC
9047 TCCCTATGAG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
22 13 0.54
23 11 0.46
ACGTcount: A:0.40, C:0.24, G:0.10, T:0.26
Consensus pattern (23 bp):
TAACCACACCATGAAAATTTCGA
Found at i:9055 original size:22 final size:23
Alignment explanation
Indices: 8997--9055 Score: 61
Period size: 22 Copynumber: 2.7 Consensus size: 23
8987 ATAAAATTGG
* *
8997 TAACCGCA-CTATGAAAATTTTGA
1 TAACCACACCTATG-AAATTTCGA
9020 TAACCACACC-ATGAAATTTCGA
1 TAACCACACCTATGAAATTTCGA
*
9042 TAACCTC-CCTATGA
1 TAACCACACCTATGA
9056 GAATGAAACT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
21 2 0.06
22 18 0.58
23 10 0.32
24 1 0.03
ACGTcount: A:0.37, C:0.25, G:0.10, T:0.27
Consensus pattern (23 bp):
TAACCACACCTATGAAATTTCGA
Found at i:9116 original size:22 final size:23
Alignment explanation
Indices: 9084--9144 Score: 63
Period size: 22 Copynumber: 2.7 Consensus size: 23
9074 CTCTCTATGT
*
9084 ATTTTCGATAACCTCTTCT-TAAA
1 ATTTTC-ATAACCTCTCCTATAAA
*
9107 ATTTTCATAATCTC-CCTATAAA
1 ATTTTCATAACCTCTCCTATAAA
**
9129 ATTTTGTTAACCTCTC
1 ATTTTCATAACCTCTC
9145 TAGGAAATTT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
21 2 0.06
22 22 0.71
23 7 0.23
ACGTcount: A:0.30, C:0.23, G:0.03, T:0.44
Consensus pattern (23 bp):
ATTTTCATAACCTCTCCTATAAA
Found at i:9212 original size:22 final size:22
Alignment explanation
Indices: 9187--9308 Score: 90
Period size: 22 Copynumber: 5.5 Consensus size: 22
9177 CCTCCCTCCC
* *
9187 TATGAAATTTTGGTAACCTCTG
1 TATGAAATTTTGATAACCTCTA
9209 TATGAAATTTTGATAA-CTAC-A
1 TATGAAATTTTGATAACCT-CTA
*
9230 CTATGAAGTTTTGATAACCTCTA
1 -TATGAAATTTTGATAACCTCTA
* *
9253 TGTGAAATTTTGGTAA-CTAC-A
1 TATGAAATTTTGATAACCT-CTA
* * * *
9274 CTACGAAATTTTGATAATCTTTC
1 -TATGAAATTTTGATAACCTCTA
*
9297 TATGTAATTTTG
1 TATGAAATTTTG
9309 GTTTGATTGT
Statistics
Matches: 79, Mismatches: 13, Indels: 16
0.73 0.12 0.15
Matches are distributed among these distances:
21 5 0.06
22 69 0.87
23 5 0.06
ACGTcount: A:0.32, C:0.12, G:0.14, T:0.42
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTCTA
Found at i:9242 original size:44 final size:44
Alignment explanation
Indices: 9186--9308 Score: 156
Period size: 44 Copynumber: 2.8 Consensus size: 44
9176 ACCTCCCTCC
* *
9186 CTATGAAATTTTGGTAACCTCTGTATGAAATTTTGATAACTACA
1 CTATGAAATTTTGATAACCTCTATATGAAATTTTGATAACTACA
* * *
9230 CTATGAAGTTTTGATAACCTCTATGTGAAATTTTGGTAACTACA
1 CTATGAAATTTTGATAACCTCTATATGAAATTTTGATAACTACA
* * * * *
9274 CTACGAAATTTTGATAATCTTTCTATGTAATTTTG
1 CTATGAAATTTTGATAACCTCTATATGAAATTTTG
9309 GTTTGATTGT
Statistics
Matches: 67, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
44 67 1.00
ACGTcount: A:0.32, C:0.13, G:0.14, T:0.41
Consensus pattern (44 bp):
CTATGAAATTTTGATAACCTCTATATGAAATTTTGATAACTACA
Found at i:9715 original size:23 final size:18
Alignment explanation
Indices: 9669--9704 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
9659 TTATGTTTGC
9669 AGTATTGTATACTTCTTA
1 AGTATTGTATACTTCTTA
9687 AGTATTGTATACTTCTTA
1 AGTATTGTATACTTCTTA
9705 TTAATAGTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.11, G:0.11, T:0.50
Consensus pattern (18 bp):
AGTATTGTATACTTCTTA
Found at i:10104 original size:7 final size:7
Alignment explanation
Indices: 10084--10146 Score: 96
Period size: 7 Copynumber: 9.4 Consensus size: 7
10074 AATTATGTAC
10084 TTTTG-T
1 TTTTGTT
10090 TTTTG-T
1 TTTTGTT
*
10096 TTTTGGT
1 TTTTGTT
10103 TTTTGTT
1 TTTTGTT
10110 TTTTGTT
1 TTTTGTT
10117 TTTTGTT
1 TTTTGTT
10124 TTTTGTT
1 TTTTGTT
10131 TTTTGTT
1 TTTTGTT
10138 TTTT-TT
1 TTTTGTT
10144 TTT
1 TTT
10147 ACGAAAGCTA
Statistics
Matches: 55, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
6 16 0.29
7 39 0.71
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (7 bp):
TTTTGTT
Found at i:30154 original size:16 final size:16
Alignment explanation
Indices: 30118--30174 Score: 73
Period size: 17 Copynumber: 3.6 Consensus size: 16
30108 CGTTCAAATG
30118 TCGGGTCA-TTTGGGT
1 TCGGGTCATTTTGGGT
30133 TCGGGTCAATTTTGGGT
1 TCGGGTC-ATTTTGGGT
*
30150 T-GGGTCATTTTCGGTT
1 TCGGGTCATTTT-GGGT
30166 TCGGGTCAT
1 TCGGGTCAT
30175 ACGGTTCGGA
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
15 12 0.32
16 10 0.27
17 15 0.41
ACGTcount: A:0.09, C:0.14, G:0.35, T:0.42
Consensus pattern (16 bp):
TCGGGTCATTTTGGGT
Done.