Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021724.1 Corchorus olitorius cultivar O-4 contig21757, 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: 21947
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.30
Found at i:98 original size:2 final size:2
Alignment explanation
Indices: 91--121 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
81 GAAGGAAATA
*
91 AT AT AT AT AT AT AT AT AT AT TT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
122 ATCTTAGGCT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:371 original size:22 final size:22
Alignment explanation
Indices: 346--394 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
336 TAATTAGTAC
*
346 TTAGAAAGCAAATCATTTGAAT
1 TTAGAAAACAAATCATTTGAAT
368 TTAGAAAACAAATCATTTGAAT
1 TTAGAAAACAAATCATTTGAAT
390 TTAGA
1 TTAGA
395 GTGGTAGTAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.47, C:0.08, G:0.12, T:0.33
Consensus pattern (22 bp):
TTAGAAAACAAATCATTTGAAT
Found at i:608 original size:17 final size:17
Alignment explanation
Indices: 586--626 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
576 AAAATTAGGA
586 ATAATTATTGAATAATT
1 ATAATTATTGAATAATT
**
603 ATAATTATTTCATAATT
1 ATAATTATTGAATAATT
*
620 ATTATTA
1 ATAATTA
627 GCTCAATAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (17 bp):
ATAATTATTGAATAATT
Found at i:5750 original size:11 final size:10
Alignment explanation
Indices: 5719--5743 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
5709 GGCAAATGAG
5719 AAAAGACAAA
1 AAAAGACAAA
5729 AAAAGACAAA
1 AAAAGACAAA
5739 AAAAG
1 AAAAG
5744 TTCAAAAGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.80, C:0.08, G:0.12, T:0.00
Consensus pattern (10 bp):
AAAAGACAAA
Found at i:6082 original size:111 final size:111
Alignment explanation
Indices: 5959--6164 Score: 306
Period size: 111 Copynumber: 1.9 Consensus size: 111
5949 AATATTTTAG
* * *
5959 AATTGGGCCTAAA-CTTTATTTATAAGTGATTAAACTTATTTTTCTAAAACCTTATGATAATGAG
1 AATTGGGCCTAAATC-TTATTAATAAGTGATTAAACTTATTTGTCTAAAACCTTATAATAATGAG
* *
6023 TCTCAAAATTTGAGATTTACCCTTTAAAAAAATTGAAATATAATTAT
65 TCTCAAAATTTAAGATTCACCCTTTAAAAAAATTGAAATATAATTAT
* * * *
6070 AATTGGGGCTAAATCTTATTAATAAGTGTTTAAACTTATTTGTCTAAAATCTTATAATAATGGGT
1 AATTGGGCCTAAATCTTATTAATAAGTGATTAAACTTATTTGTCTAAAACCTTATAATAATGAGT
*
6135 CTTAAAATTTAAGATTCACCCTTTAAAAAA
66 CTCAAAATTTAAGATTCACCCTTTAAAAAA
6165 TGGAATTATT
Statistics
Matches: 84, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
111 83 0.99
112 1 0.01
ACGTcount: A:0.39, C:0.11, G:0.11, T:0.39
Consensus pattern (111 bp):
AATTGGGCCTAAATCTTATTAATAAGTGATTAAACTTATTTGTCTAAAACCTTATAATAATGAGT
CTCAAAATTTAAGATTCACCCTTTAAAAAAATTGAAATATAATTAT
Found at i:7339 original size:13 final size:12
Alignment explanation
Indices: 7320--7358 Score: 51
Period size: 13 Copynumber: 3.1 Consensus size: 12
7310 GTAATACCCG
7320 AAAAACAGAGAC
1 AAAAACAGAGAC
*
7332 TTAAAACAGAGAC
1 -AAAAACAGAGAC
7345 AAGAAACAGAGAC
1 AA-AAACAGAGAC
7358 A
1 A
7359 GGAAGAGGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
12 1 0.04
13 22 0.96
ACGTcount: A:0.62, C:0.15, G:0.18, T:0.05
Consensus pattern (12 bp):
AAAAACAGAGAC
Found at i:7899 original size:23 final size:24
Alignment explanation
Indices: 7855--7901 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
7845 TAAAAAAAAA
7855 CCTGAAATCTATTCTTTTTTTTTC
1 CCTGAAATCTATTCTTTTTTTTTC
*
7879 CCTGAAAT-TGATTTTTTTTTTTT
1 CCTGAAATCT-ATTCTTTTTTTTT
7902 ACAAATTCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.17, C:0.15, G:0.06, T:0.62
Consensus pattern (24 bp):
CCTGAAATCTATTCTTTTTTTTTC
Found at i:8104 original size:29 final size:31
Alignment explanation
Indices: 8043--8104 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
8033 TAACGACAGA
* *
8043 GATTAAATTGTTCATAATTCTTTACTTCAGG
1 GATTAAATTGCTCATAATTCTTGACTTCAGG
8074 GATTAAATTGCTCA-AATT-TTGACTTCAGG
1 GATTAAATTGCTCATAATTCTTGACTTCAGG
8103 GA
1 GA
8105 CCAAAATGCA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 12 0.41
30 4 0.14
31 13 0.45
ACGTcount: A:0.31, C:0.13, G:0.16, T:0.40
Consensus pattern (31 bp):
GATTAAATTGCTCATAATTCTTGACTTCAGG
Found at i:14514 original size:76 final size:76
Alignment explanation
Indices: 14280--14965 Score: 812
Period size: 76 Copynumber: 9.1 Consensus size: 76
14270 TTTTGAGTGA
* * * *
14280 GTGGACGCTCTGCCTCACTGGTGGATGAACGGGGGCGCCCGTCTAGGCGCTCAGCCGTTGAGTGA
1 GTGGACGCTCTGCCTCACTGATGGACGAACGGGGGCGCCAGTTTAGGCGCTCAGCCGTTGAGTGA
14345 GTGGCGTCTGC
66 GTGGCGTCTGC
* * * * *
14356 ATGGACGCTCTACCTCACTGGTGGACGAACGGGGGCACCAGTCTT--G-GCACAGCCGTTGAGTG
1 GTGGACGCTCTGCCTCACTGATGGACGAACGGGGGCGCCAGT-TTAGGCGCTCAGCCGTTGAGTG
*
14418 AGTGGCGCCTGC
65 AGTGGCGTCTGC
* * * * * *
14430 GTGGACGCTCTGCCTTACTGATGGACG-ACTGGGGGCACCAGTTTAGGTGCTAAGCTGTTGAGTT
1 GTGGACGCTCTGCCTCACTGATGGACGAAC-GGGGGCGCCAGTTTAGGCGCTCAGCCGTTGAGTG
14494 AGTGGCGTCTGC
65 AGTGGCGTCTGC
* * * * * * *
14506 ATGGACGCTCGGCCTCACTGA-GAGGCGAACGGGGGCGCCAGTCTAAGCACTCAGTCGTTGAGTG
1 GTGGACGCTCTGCCTCACTGATG-GACGAACGGGGGCGCCAGTTTAGGCGCTCAGCCGTTGAGTG
*
14570 AGAGGCGTCTGC
65 AGTGGCGTCTGC
* ** * * * *
14582 GTGGACGCTCTGCCTTACTGATGGACGAACGGAAGCGCCTGTCTAGGCGCTCAGCCATTGTGTGA
1 GTGGACGCTCTGCCTCACTGATGGACGAACGGGGGCGCCAGTTTAGGCGCTCAGCCGTTGAGTGA
* *
14647 ATGGCGTCTGT
66 GTGGCGTCTGC
* * * * *
14658 GTGGACGCTCTGCCTCACTGGTGGACGAACGGAGGTGCCAGTCTT--G-GCACAACCGTTGAGTG
1 GTGGACGCTCTGCCTCACTGATGGACGAACGGGGGCGCCAGT-TTAGGCGCTCAGCCGTTGAGTG
*
14720 AGTGGCGCCTGC
65 AGTGGCGTCTGC
* * *
14732 GTGGACGCTCTGCCTCACTGATGGACGAACGGGGGCGCCAGTTTAGGTGTTAAGCCGTTGAGTGA
1 GTGGACGCTCTGCCTCACTGATGGACGAACGGGGGCGCCAGTTTAGGCGCTCAGCCGTTGAGTGA
14797 GTGGCGTCTGC
66 GTGGCGTCTGC
* * * * *
14808 GTGGACGCTCGGCCTCACTGATGGGCGAACGGGGGCGCCAGTCTAGGCACTCAGTCGTTGAGTGA
1 GTGGACGCTCTGCCTCACTGATGGACGAACGGGGGCGCCAGTTTAGGCGCTCAGCCGTTGAGTGA
*
14873 GTGGTGTCTGC
66 GTGGCGTCTGC
* *
14884 GTGGACGCTCTGCCTCACTGATAGACGAACGGGGGCGCCAGTTTAGGCGCTCAGCCGTTGTGTGA
1 GTGGACGCTCTGCCTCACTGATGGACGAACGGGGGCGCCAGTTTAGGCGCTCAGCCGTTGAGTGA
*
14949 ATGGCGTCTGC
66 GTGGCGTCTGC
*
14960 TTGGAC
1 GTGGAC
14966 ACTCGTCGTC
Statistics
Matches: 512, Mismatches: 86, Indels: 24
0.82 0.14 0.04
Matches are distributed among these distances:
73 6 0.01
74 121 0.24
75 5 0.01
76 375 0.73
77 5 0.01
ACGTcount: A:0.16, C:0.25, G:0.37, T:0.22
Consensus pattern (76 bp):
GTGGACGCTCTGCCTCACTGATGGACGAACGGGGGCGCCAGTTTAGGCGCTCAGCCGTTGAGTGA
GTGGCGTCTGC
Found at i:14718 original size:226 final size:227
Alignment explanation
Indices: 14281--14965 Score: 817
Period size: 226 Copynumber: 3.0 Consensus size: 227
14271 TTTGAGTGAG
* *
14281 TGGACGCTCTGCCTCACTG-GTGGATGAACGGGGGCGCCCGTCTAGGCGCTCAGCCGTTGAGTGA
1 TGGACGCTCTGCCTCACTGAG-GG-CGAACGGGGGCGCCAGTCTAGGCGCTCAGCCGTTGAGTGA
* * * * * *
14345 GTGGCGTCTGCATGGACGCTCTACCTCACTGGTGGACGAACGGGGGCACCAGTCT-TG-GCACAG
64 GTGGCGTCTGCGTGGACGCTCTGCCTCACTGATGGACGAACGGGGGCGCCAGTCTAGGCGCTCAG
* * *
14408 CCGTTGAGTGAGTGGCGCCTGCGTGGACGCTCTGCCTTACTGATGGACG-ACTGGGGGCACCAGT
129 CCGTTGAGTGAGTGGCGTCTGCGTGGACGCTCTGCCTCACTGATGGACGAAC-GGGGGCGCCAGT
** * * *
14472 TTAGGTGCTAAGCTGTTGAGTTAGTGGCGTCTGCA
193 TTAGGCACTAAGCCGTTGAGTGAGTGGCGCCTGCA
* * * *
14507 TGGACGCTCGGCCTCACTGAGAGGCGAACGGGGGCGCCAGTCTAAGCACTCAGTCGTTGAGTGAG
1 TGGACGCTCTGCCTCACTGAG-GGCGAACGGGGGCGCCAGTCTAGGCGCTCAGCCGTTGAGTGAG
* * ** *
14572 AGGCGTCTGCGTGGACGCTCTGCCTTACTGATGGACGAACGGAAGCGCCTGTCTAGGCGCTCAGC
65 TGGCGTCTGCGTGGACGCTCTGCCTCACTGATGGACGAACGGGGGCGCCAGTCTAGGCGCTCAGC
* * * * * * *
14637 CATTGTGTGAATGGCGTCTGTGTGGACGCTCTGCCTCACTGGTGGACGAACGGAGGTGCCAGTCT
130 CGTTGAGTGAGTGGCGTCTGCGTGGACGCTCTGCCTCACTGATGGACGAACGGGGGCGCCAGT-T
*
14702 T-GGCAC-AA-CCGTTGAGTGAGTGGCGCCTGCG
194 TAGGCACTAAGCCGTTGAGTGAGTGGCGCCTGCA
* * * * *
14733 TGGACGCTCTGCCTCACTGATGGACGAACGGGGGCGCCAGTTTAGGTGTTAAGCCGTTGAGTGAG
1 TGGACGCTCTGCCTCACTGA-GGGCGAACGGGGGCGCCAGTCTAGGCGCTCAGCCGTTGAGTGAG
* * * *
14798 TGGCGTCTGCGTGGACGCTCGGCCTCACTGATGGGCGAACGGGGGCGCCAGTCTAGGCACTCAGT
65 TGGCGTCTGCGTGGACGCTCTGCCTCACTGATGGACGAACGGGGGCGCCAGTCTAGGCGCTCAGC
* *
14863 CGTTGAGTGAGTGGTGTCTGCGTGGACGCTCTGCCTCACTGATAGACGAACGGGGGCGCCAGTTT
130 CGTTGAGTGAGTGGCGTCTGCGTGGACGCTCTGCCTCACTGATGGACGAACGGGGGCGCCAGTTT
* * * * * *
14928 AGGCGCTCAGCCGTTGTGTGAATGGCGTCTGCT
195 AGGCACTAAGCCGTTGAGTGAGTGGCGCCTGCA
14961 TGGAC
1 TGGAC
14966 ACTCGTCGTC
Statistics
Matches: 383, Mismatches: 67, Indels: 16
0.82 0.14 0.03
Matches are distributed among these distances:
225 2 0.01
226 286 0.75
227 8 0.02
228 83 0.22
229 4 0.01
ACGTcount: A:0.16, C:0.25, G:0.36, T:0.22
Consensus pattern (227 bp):
TGGACGCTCTGCCTCACTGAGGGCGAACGGGGGCGCCAGTCTAGGCGCTCAGCCGTTGAGTGAGT
GGCGTCTGCGTGGACGCTCTGCCTCACTGATGGACGAACGGGGGCGCCAGTCTAGGCGCTCAGCC
GTTGAGTGAGTGGCGTCTGCGTGGACGCTCTGCCTCACTGATGGACGAACGGGGGCGCCAGTTTA
GGCACTAAGCCGTTGAGTGAGTGGCGCCTGCA
Found at i:14826 original size:302 final size:302
Alignment explanation
Indices: 14280--14965 Score: 1079
Period size: 302 Copynumber: 2.3 Consensus size: 302
14270 TTTTGAGTGA
* * * *
14280 GTGGACGCTCTGCCTCACTGGTGGATGAACGGGGGCGCCCGTCTAGGCGCTCAGCCGTTGAGTGA
1 GTGGACGCTCTGCCTCACTGATGGACGAACGGGGGCGCCAGTCTAGGCGCTCAGCCGTTGTGTGA
* * *
14345 GTGGCGTCTGCATGGACGCTCTACCTCACTGGTGGACGAACGGGGGCACCAGTCTTGGCACAGCC
66 ATGGCGTCTGCATGGACGCTCTACCTCACTGGTGGACGAACGGAGGCACCAGTCTTGGCACAACC
*
14410 GTTGAGTGAGTGGCGCCTGCGTGGACGCTCTGCCTTACTGATGGACGACTGGGGGCACCAGTTTA
131 GTTGAGTGAGTGGCGCCTGCGTGGACGCTCTGCCTCACTGATGGACGACTGGGGGCACCAGTTTA
* *
14475 GGTGCTAAGCTGTTGAGTTAGTGGCGTCTGCATGGACGCTCGGCCTCACTGA-GAGGCGAACGGG
196 GGTGCTAAGCCGTTGAGTGAGTGGCGTCTGCATGGACGCTCGGCCTCACTGATG-GGCGAACGGG
14539 GGCGCCAGTCTAAGCACTCAGTCGTTGAGTGAGAGGCGTCTGC
260 GGCGCCAGTCTAAGCACTCAGTCGTTGAGTGAGAGGCGTCTGC
* ** * *
14582 GTGGACGCTCTGCCTTACTGATGGACGAACGGAAGCGCCTGTCTAGGCGCTCAGCCATTGTGTGA
1 GTGGACGCTCTGCCTCACTGATGGACGAACGGGGGCGCCAGTCTAGGCGCTCAGCCGTTGTGTGA
** * **
14647 ATGGCGTCTGTGTGGACGCTCTGCCTCACTGGTGGACGAACGGAGGTGCCAGTCTTGGCACAACC
66 ATGGCGTCTGCATGGACGCTCTACCTCACTGGTGGACGAACGGAGGCACCAGTCTTGGCACAACC
*
14712 GTTGAGTGAGTGGCGCCTGCGTGGACGCTCTGCCTCACTGATGGACGAAC-GGGGGCGCCAGTTT
131 GTTGAGTGAGTGGCGCCTGCGTGGACGCTCTGCCTCACTGATGGACG-ACTGGGGGCACCAGTTT
* *
14776 AGGTGTTAAGCCGTTGAGTGAGTGGCGTCTGCGTGGACGCTCGGCCTCACTGATGGGCGAACGGG
195 AGGTGCTAAGCCGTTGAGTGAGTGGCGTCTGCATGGACGCTCGGCCTCACTGATGGGCGAACGGG
* * *
14841 GGCGCCAGTCTAGGCACTCAGTCGTTGAGTGAGTGGTGTCTGC
260 GGCGCCAGTCTAAGCACTCAGTCGTTGAGTGAGAGGCGTCTGC
* *
14884 GTGGACGCTCTGCCTCACTGATAGACGAACGGGGGCGCCAGTTTAGGCGCTCAGCCGTTGTGTGA
1 GTGGACGCTCTGCCTCACTGATGGACGAACGGGGGCGCCAGTCTAGGCGCTCAGCCGTTGTGTGA
*
14949 ATGGCGTCTGCTTGGAC
66 ATGGCGTCTGCATGGAC
14966 ACTCGTCGTC
Statistics
Matches: 348, Mismatches: 34, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
302 345 0.99
303 3 0.01
ACGTcount: A:0.16, C:0.25, G:0.37, T:0.22
Consensus pattern (302 bp):
GTGGACGCTCTGCCTCACTGATGGACGAACGGGGGCGCCAGTCTAGGCGCTCAGCCGTTGTGTGA
ATGGCGTCTGCATGGACGCTCTACCTCACTGGTGGACGAACGGAGGCACCAGTCTTGGCACAACC
GTTGAGTGAGTGGCGCCTGCGTGGACGCTCTGCCTCACTGATGGACGACTGGGGGCACCAGTTTA
GGTGCTAAGCCGTTGAGTGAGTGGCGTCTGCATGGACGCTCGGCCTCACTGATGGGCGAACGGGG
GCGCCAGTCTAAGCACTCAGTCGTTGAGTGAGAGGCGTCTGC
Found at i:21163 original size:16 final size:15
Alignment explanation
Indices: 21125--21166 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
21115 GCAGAGATTG
*
21125 ACAGAAAGCAATTAA
1 ACAGAAAACAATTAA
21140 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
21155 ACTAGAAAACAA
1 AC-AGAAAACAA
21167 AGCAAAGTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 16 0.64
16 9 0.36
ACGTcount: A:0.64, C:0.14, G:0.10, T:0.12
Consensus pattern (15 bp):
ACAGAAAACAATTAA
Done.