Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017059.1 Corchorus olitorius cultivar O-4 contig17092, 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: 14871
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:3412 original size:38 final size:38
Alignment explanation
Indices: 3370--3445 Score: 107
Period size: 38 Copynumber: 2.0 Consensus size: 38
3360 AACATGTCTA
* *
3370 AAACTAGTCAAAATCGGTTCGATTACCCGATCCAACCG
1 AAACTAATCAAAACCGGTTCGATTACCCGATCCAACCG
* * *
3408 AAACTAATCAAAACCGGTTTGATTACCTGATTCAACCG
1 AAACTAATCAAAACCGGTTCGATTACCCGATCCAACCG
3446 TCGATTGAAC
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
38 33 1.00
ACGTcount: A:0.36, C:0.26, G:0.14, T:0.24
Consensus pattern (38 bp):
AAACTAATCAAAACCGGTTCGATTACCCGATCCAACCG
Found at i:3945 original size:11 final size:11
Alignment explanation
Indices: 3929--3953 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
3919 TTTATATAGA
3929 CATAAATATTC
1 CATAAATATTC
3940 CATAAATATTC
1 CATAAATATTC
3951 CAT
1 CAT
3954 TGTATTGGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.20, G:0.00, T:0.36
Consensus pattern (11 bp):
CATAAATATTC
Found at i:4594 original size:26 final size:26
Alignment explanation
Indices: 4556--4607 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
4546 CCGATAGTCC
*
4556 GATACCGTTATTTTTTTCTAAGAAAAA
1 GATACCGTTATTTTTTT-TAAAAAAAA
4583 GATACC-TTATTTTTTTTAAAAAAAA
1 GATACCGTTATTTTTTTTAAAAAAAA
4608 TCTAAAACAC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 8 0.33
26 10 0.42
27 6 0.25
ACGTcount: A:0.40, C:0.10, G:0.08, T:0.42
Consensus pattern (26 bp):
GATACCGTTATTTTTTTTAAAAAAAA
Found at i:5667 original size:86 final size:90
Alignment explanation
Indices: 5570--5738 Score: 211
Period size: 92 Copynumber: 1.9 Consensus size: 90
5560 TTCTTCGATG
* * * * *
5570 AATTTGATTCAAGGGTCTT-G-AT-G-GACTTGATCTTGAATAAACAGAAATAATTTTCTCCGAG
1 AATTTGATTCAAGGGTCTTCGTATGGAGACTTGATCTTGAACAAACAGAAATAATCTCCTCCAAA
5631 TGTGTTGGTGAAGATCGAACGAAAT
66 TGTGTTGGTGAAGATCGAACGAAAT
* * * *
5656 AATTTGCTTCAAGGGTCTTCGGTTTGGTAGACTTGATCTTGAGCAAACAGAAATAATCTCCTTCA
1 AATTTGATTCAAGGGTCTTC-GTATGG-AGACTTGATCTTGAACAAACAGAAATAATCTCCTCCA
5721 AATGTGTTGGTGAAGATC
64 AATGTGTTGGTGAAGATC
5739 AAAATAATGA
Statistics
Matches: 68, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
86 18 0.26
88 1 0.01
89 1 0.01
90 1 0.01
92 47 0.69
ACGTcount: A:0.30, C:0.14, G:0.23, T:0.33
Consensus pattern (90 bp):
AATTTGATTCAAGGGTCTTCGTATGGAGACTTGATCTTGAACAAACAGAAATAATCTCCTCCAAA
TGTGTTGGTGAAGATCGAACGAAAT
Found at i:5828 original size:16 final size:16
Alignment explanation
Indices: 5807--5837 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5797 GATCTTGATT
*
5807 CTTCAGGGCTTTTCTA
1 CTTCAGAGCTTTTCTA
5823 CTTCAGAGCTTTTCT
1 CTTCAGAGCTTTTCT
5838 GCCTTTGTAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.13, C:0.26, G:0.16, T:0.45
Consensus pattern (16 bp):
CTTCAGAGCTTTTCTA
Found at i:6664 original size:10 final size:11
Alignment explanation
Indices: 6639--6663 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
6629 TTAGCGAGCC
6639 TTTTCTTTTTT
1 TTTTCTTTTTT
6650 TTTTCTTTTTT
1 TTTTCTTTTTT
6661 TTT
1 TTT
6664 CGCTCTAACT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (11 bp):
TTTTCTTTTTT
Found at i:6668 original size:78 final size:77
Alignment explanation
Indices: 6576--6725 Score: 239
Period size: 78 Copynumber: 1.9 Consensus size: 77
6566 TTAGCGAGAT
6576 TTTTTTTTTCCGCTCTAACTTTTGCCTAAGCCATCCTATATAGAATTTTCAACTTAGCGAGCCTT
1 TTTTTTTTTCCGCTCTAACTTTTGCCTAAGCCATCCTATATAGAATTTTCAACTTAGCGAG-CTT
6641 TTCTTTTTTTTTTC
65 TT-TTTTTTTTTTC
* * * *
6655 TTTTTTTTT-CGCTCTAACTTTTTCCTAAGCCGTCCTTTATAGGATTTTCAACTTAGCGAGCTTT
1 TTTTTTTTTCCGCTCTAACTTTTGCCTAAGCCATCCTATATAGAATTTTCAACTTAGCGAGCTTT
6719 TTTTTTT
66 TTTTTTT
6726 GTTGGGCAGT
Statistics
Matches: 67, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
76 6 0.09
77 5 0.07
78 47 0.70
79 9 0.13
ACGTcount: A:0.17, C:0.21, G:0.10, T:0.52
Consensus pattern (77 bp):
TTTTTTTTTCCGCTCTAACTTTTGCCTAAGCCATCCTATATAGAATTTTCAACTTAGCGAGCTTT
TTTTTTTTTTTC
Found at i:9683 original size:86 final size:86
Alignment explanation
Indices: 9538--9713 Score: 325
Period size: 86 Copynumber: 2.0 Consensus size: 86
9528 GAAATTTGAG
*
9538 CTAATTCCGACTTCGTTTGCAACTTTTGCATCTTTTTAAATTAAGGACAATTGGCTTTGTCACCC
1 CTAATTCCGACTTCGTTTGCAACTTTTGCATCTTTTTAAATTAAGGACAAGTGGCTTTGTCACCC
9603 CGGTTTAAGCCATTTACTTAA
66 CGGTTTAAGCCATTTACTTAA
* *
9624 CTAATTCCGACTTCGTTTGCAACTTTTGCATCTTTTTCAGTTAAGGACAAGTGGCTTTGTCACCC
1 CTAATTCCGACTTCGTTTGCAACTTTTGCATCTTTTTAAATTAAGGACAAGTGGCTTTGTCACCC
9689 CGGTTTAAGCCATTTACTTAA
66 CGGTTTAAGCCATTTACTTAA
9710 CTAA
1 CTAA
9714 GTATTATTTT
Statistics
Matches: 87, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
86 87 1.00
ACGTcount: A:0.24, C:0.23, G:0.15, T:0.39
Consensus pattern (86 bp):
CTAATTCCGACTTCGTTTGCAACTTTTGCATCTTTTTAAATTAAGGACAAGTGGCTTTGTCACCC
CGGTTTAAGCCATTTACTTAA
Found at i:10175 original size:32 final size:32
Alignment explanation
Indices: 10133--10194 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
10123 AGCTTCAGAC
* *
10133 AGATACCACTCATTTCACAAACCATCTCCTAG
1 AGATACCACTCATCTCACAAACCAGCTCCTAG
*
10165 AGATATCACTCATCTCACAAACCAGCTCCT
1 AGATACCACTCATCTCACAAACCAGCTCCT
10195 GAAGCTACAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.34, C:0.35, G:0.06, T:0.24
Consensus pattern (32 bp):
AGATACCACTCATCTCACAAACCAGCTCCTAG
Found at i:10728 original size:22 final size:22
Alignment explanation
Indices: 10702--10770 Score: 77
Period size: 22 Copynumber: 3.1 Consensus size: 22
10692 CAGTGCGATT
* *
10702 AAAATTTTATAATGAGATTATC
1 AAAATTTAATAATGAGGTTATC
*
10724 AAAATTTCAATAAT-AGGTTATT
1 AAAATTT-AATAATGAGGTTATC
* *
10746 ATAATTTCATAATGAGGTTATC
1 AAAATTTAATAATGAGGTTATC
10768 AAA
1 AAA
10771 GTTTCATATT
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
21 5 0.13
22 28 0.74
23 5 0.13
ACGTcount: A:0.45, C:0.06, G:0.10, T:0.39
Consensus pattern (22 bp):
AAAATTTAATAATGAGGTTATC
Found at i:10775 original size:22 final size:22
Alignment explanation
Indices: 10710--10800 Score: 89
Period size: 22 Copynumber: 4.1 Consensus size: 22
10700 TTAAAATTTT
* *
10710 ATAATGAGATTATCAAAATTTC
1 ATAATGAGGTTATCAAAGTTTC
*
10732 AATAAT-AGGTTATTATAA-TTTC
1 -ATAATGAGGTTATCA-AAGTTTC
10754 ATAATGAGGTTATCAAAGTTTC
1 ATAATGAGGTTATCAAAGTTTC
* *
10776 ATATTGTGGTT-TCCAAAGTTTC
1 ATAATGAGGTTAT-CAAAGTTTC
10798 ATA
1 ATA
10801 TGGAGGTCAC
Statistics
Matches: 59, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
21 8 0.14
22 44 0.75
23 7 0.12
ACGTcount: A:0.37, C:0.09, G:0.13, T:0.41
Consensus pattern (22 bp):
ATAATGAGGTTATCAAAGTTTC
Found at i:11030 original size:20 final size:22
Alignment explanation
Indices: 10967--11154 Score: 134
Period size: 22 Copynumber: 8.6 Consensus size: 22
10957 CAAAGAGGTA
* *
10967 ATCAAAATTTCATAACGAGGTT
1 ATCAAAATTTCATAGCGTGGTT
*
10989 ATCAGAATTTCATAGCGTGGTT
1 ATCAAAATTTCATAGCGTGGTT
11011 ATCAAAATTTCAT-G-GTGGTT
1 ATCAAAATTTCATAGCGTGGTT
* * *
11031 ATCAAAATTTCAAAAGATCAT-ATT
1 ATCAAAATTTC-ATAG--CGTGGTT
**
11055 ATCAAAATTTCATATGAAT-GTT
1 ATCAAAATTTCATA-GCGTGGTT
* ***
11077 ATTAAAATTTCATA-TAAGGTT
1 ATCAAAATTTCATAGCGTGGTT
* * *
11098 ATCAAAATTTCAAAGCGAGGTA
1 ATCAAAATTTCATAGCGTGGTT
* * **
11120 ATCAAAATTTCACAGTGCAGTT
1 ATCAAAATTTCATAGCGTGGTT
11142 ATCAAAATTTCAT
1 ATCAAAATTTCAT
11155 TTAAAATTAT
Statistics
Matches: 134, Mismatches: 24, Indels: 16
0.77 0.14 0.09
Matches are distributed among these distances:
20 18 0.13
21 17 0.13
22 82 0.61
23 2 0.01
24 14 0.10
25 1 0.01
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Consensus pattern (22 bp):
ATCAAAATTTCATAGCGTGGTT
Found at i:11178 original size:18 final size:17
Alignment explanation
Indices: 11150--11194 Score: 56
Period size: 19 Copynumber: 2.6 Consensus size: 17
11140 TTATCAAAAT
11150 TTCAT-TTAAAATTATA
1 TTCATGTTAAAATTATA
11166 TCTCATGTTAAAAATTATA
1 T-TCATGTT-AAAATTATA
*
11185 TTAATGTTAA
1 TTCATGTTAA
11195 TATATAATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
16 1 0.04
17 6 0.24
18 8 0.32
19 10 0.40
ACGTcount: A:0.42, C:0.07, G:0.04, T:0.47
Consensus pattern (17 bp):
TTCATGTTAAAATTATA
Found at i:11181 original size:19 final size:18
Alignment explanation
Indices: 11157--11194 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
11147 AATTTCATTT
*
11157 AAAATTATATCTCATGTTA
1 AAAATTATAT-TAATGTTA
11176 AAAATTATATTAATGTTA
1 AAAATTATATTAATGTTA
11194 A
1 A
11195 TATATAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.42
Consensus pattern (18 bp):
AAAATTATATTAATGTTA
Found at i:13960 original size:32 final size:31
Alignment explanation
Indices: 13924--14025 Score: 96
Period size: 32 Copynumber: 3.2 Consensus size: 31
13914 TTTTGATTGA
13924 AATATATTTTAACTTTAAGTTACATATTATGT
1 AATATATTTTAACTTTAAGTTACATATT-TGT
* * * * ** * * *
13956 AATATAATATCAATTTTAATTTTGAAAATTGA
1 AATAT-ATTTTAACTTTAAGTTACATATTTGT
13988 AATATATTTTAACTTTAAGTTACATATTGTGT
1 AATATATTTTAACTTTAAGTTACATATT-TGT
14020 AATATA
1 AATATA
14026 ATATCAATTT
Statistics
Matches: 50, Mismatches: 18, Indels: 4
0.69 0.25 0.06
Matches are distributed among these distances:
31 15 0.30
32 20 0.40
33 15 0.30
ACGTcount: A:0.41, C:0.05, G:0.07, T:0.47
Consensus pattern (31 bp):
AATATATTTTAACTTTAAGTTACATATTTGT
Found at i:14021 original size:64 final size:64
Alignment explanation
Indices: 13919--14048 Score: 251
Period size: 64 Copynumber: 2.0 Consensus size: 64
13909 TGAAGTTTTG
13919 ATTGAAATATATTTTAACTTTAAGTTACATATTATGTAATATAATATCAATTTTAATTTTGAAA
1 ATTGAAATATATTTTAACTTTAAGTTACATATTATGTAATATAATATCAATTTTAATTTTGAAA
*
13983 ATTGAAATATATTTTAACTTTAAGTTACATATTGTGTAATATAATATCAATTTTAATTTTGAAA
1 ATTGAAATATATTTTAACTTTAAGTTACATATTATGTAATATAATATCAATTTTAATTTTGAAA
14047 AT
1 AT
14049 ATGCCAAAAA
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
64 65 1.00
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.47
Consensus pattern (64 bp):
ATTGAAATATATTTTAACTTTAAGTTACATATTATGTAATATAATATCAATTTTAATTTTGAAA
Found at i:14870 original size:332 final size:334
Alignment explanation
Indices: 14083--14871 Score: 959
Period size: 332 Copynumber: 2.4 Consensus size: 334
14073 TTCACAATTG
* * *
14083 TAATATCGTTTTT-TTATATTTTTTCTGAATTAATTTCTAATTAAATCGAAACAAAATTCAGATG
1 TAATATCGTTTTTCCTAT-TTTTTTCAGAATTAATTTCTAATTAAATCGAAAAAAAATTCAGATG
* * *
14147 CACATAAAAACAAATCCTTAGATCCAATATTGTGGCTGAGATTTGGTTAGATGAATA-AAGATAT
65 CTCGTAAAAACAAATCCTTAAATCC-A-A-TGTGGCTGAGATTTGGTTAGATGAATATAAGATAT
** * *
14211 TTCAAGGAGTCTCGGTGCAAAAAATCATGCAAAACAAAGCCGTGACCCTATAAGACGTTTTTAGC
127 TTCAAGGAGTCTCGGCACAAAAAATCATGCAAAACAAAGCCG-GACCCCATAACACGTTTTTAGC
* *
14276 CAAAAACCTTGATGATTAGTTCACGATTTCGGCTAAAATTTTACAAAAATTGACACGAAAGATAT
191 CAAAAACCGTGATGATTAGTACACGATTTCGGCTAAAATTTTACAAAAATTGACACGAAAGATAT
* * * * *
14341 TTCCTCAATTTTTGGCTAAAATACTCATTAAAAAATATATAATTCAATATCAAAAAAATTGAAGG
256 TTCCTCAATTTTTAGCTAAAATACTCATTAAAAAATAAATAATTCAACACCAAAAAAATTGAAAG
*
14406 GCTTTTAACGCTTC
321 CCTTTTAACGCTTC
* *
14420 TAATATTGTTTTTCCTATTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAAAATTCAGATG
1 TAATATCGTTTTTCCTATTTTTTTCAGAATTAATTTCTAATTAAATCGAAA-AAAAATTCAGATG
* * * *
14485 CTCGTAAAAATAAATCCTTAAATCTAATGTGGCTGAGATTTTGATAGATGAATATAA-ATATTTC
65 CTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAAGATATTTC
* * ** * **
14549 AAGGAGTCTTGGCACCAAAAATCATGCAAAACTGAGCC-GACCCCCTGAACACGTTTTTAGCTGA
130 AAGGAGTCTCGGCACAAAAAATCATGCAAAACAAAGCCGGACCCCAT-AACACGTTTTTAGCCAA
* * *
14613 AAACCGTGATGGTTAGTACACGATTTCGGCT-AAATTTTGCAAAAATTGATC-CGAAAGATTTTT
194 AAACCGTGATGATTAGTACACGATTTCGGCTAAAATTTTACAAAAATTGA-CACGAAAGATATTT
** *
14676 CCT-TGTTTTCTAG-TGAAAATACTCA-TAAAAAA-AAATAATTCAACGCCAAAAAAATTGAAAG
258 CCTCAATTTT-TAGCT-AAAATACTCATTAAAAAATAAATAATTCAACACCAAAAAAATTGAAAG
*
14737 CCTTTTTCACGCTTC
321 CC-TTTTAACGCTTC
* * * * * **
14752 TAATATCGTTTTTCCTATTTTATTTCAAAATTAATTTCTGATTAAATCGAAATAAGATTTAGAAA
1 TAATATCGTTTTTCCTATTTT-TTTCAGAATTAATTTCTAATTAAATCGAAAAAAAATTCAGATG
* * * *
14817 CTCGTACAAACAAATTCTTAAATCCAATGTGGCTAAGATTTGGTTTGATGAATAT
65 CTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATAT
Statistics
Matches: 389, Mismatches: 54, Indels: 23
0.83 0.12 0.05
Matches are distributed among these distances:
331 25 0.06
332 98 0.25
333 76 0.20
334 43 0.11
335 64 0.16
336 3 0.01
337 45 0.12
338 35 0.09
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.34
Consensus pattern (334 bp):
TAATATCGTTTTTCCTATTTTTTTCAGAATTAATTTCTAATTAAATCGAAAAAAAATTCAGATGC
TCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAAGATATTTCA
AGGAGTCTCGGCACAAAAAATCATGCAAAACAAAGCCGGACCCCATAACACGTTTTTAGCCAAAA
ACCGTGATGATTAGTACACGATTTCGGCTAAAATTTTACAAAAATTGACACGAAAGATATTTCCT
CAATTTTTAGCTAAAATACTCATTAAAAAATAAATAATTCAACACCAAAAAAATTGAAAGCCTTT
TAACGCTTC
Done.