Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024806.1 Corchorus olitorius cultivar O-4 contig24839, 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: 22704
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.31
Found at i:1360 original size:19 final size:18
Alignment explanation
Indices: 1336--1371 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
1326 TGAAGATTTA
1336 TTGAAGACAATTTGAAGAT
1 TTGAAGACAA-TTGAAGAT
*
1355 TTGAAGACCATTGAAGA
1 TTGAAGACAATTGAAGA
1372 ATAATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.08, G:0.22, T:0.28
Consensus pattern (18 bp):
TTGAAGACAATTGAAGAT
Found at i:3727 original size:2 final size:2
Alignment explanation
Indices: 3720--3758 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
3710 CGAATTTTTG
3720 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3759 AAGGGGTTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:6137 original size:145 final size:141
Alignment explanation
Indices: 5898--6287 Score: 560
Period size: 145 Copynumber: 2.8 Consensus size: 141
5888 AGTCTTTCAA
** *
5898 CAAAGTTGTGTTTAAGTTTCAATAAACCTTGCTCAAGGTTAAGTTTGCATTTGTAAGACCTTCGG
1 CAAAGTTGCATTTAAGTTTCAATAAACCTTGCTCAAGGTTAAGTTTGCATTTGTAAGACCTCCGG
* *
5963 GCACCATTTCA-AAAACCTTCGGGTATTAATTCTGATAAATCCTCCGGGTATCATTTCATTTCAT
66 GCACCATTTCAGAAAA-CTCCGGGTATTAATTCTGATAAATCCTCCCGGTATCATTTCATTTCAT
6027 CAAGTTTTTAAT
130 CAAGTTTTTAAT
6039 CAAAGTTGCATTTAAGTTTCAAAATCAAAACCTTGCTCAAGGTTAAGTTTGCATTTGTAAGACCT
1 CAAAGTTGCATTTAAGTTTC--AAT--AAACCTTGCTCAAGGTTAAGTTTGCATTTGTAAGACCT
6104 CCGGGCACCATTTCAGAAAACTCCGGGTATTAATTCTGATAAATCCTCCCGGTATCATTTCATTT
62 CCGGGCACCATTTCAGAAAACTCCGGGTATTAATTCTGATAAATCCTCCCGGTATCATTTCATTT
6169 CATCAAGTTTTTAAT
127 CATCAAGTTTTTAAT
* *
6184 CAAAGGTT-CA---AA--ATCAATAAACCTTGCTCAAGGTTGAGTTTGCATTTGTAAGACCTCCG
1 CAAA-GTTGCATTTAAGTTTCAATAAACCTTGCTCAAGGTTAAGTTTGCATTTGTAAGACCTCCG
* * * * * *
6243 GGCACAATTACAGAAACCGCCGGGTATTAATTCTGACAAGTCCTC
65 GGCACCATTTCAGAAAACTCCGGGTATTAATTCTGATAAATCCTC
6288 TGGGCATTCT
Statistics
Matches: 230, Mismatches: 13, Indels: 17
0.88 0.05 0.07
Matches are distributed among these distances:
136 79 0.34
138 3 0.01
140 2 0.01
141 18 0.08
142 2 0.01
143 3 0.01
145 116 0.50
146 7 0.03
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.33
Consensus pattern (141 bp):
CAAAGTTGCATTTAAGTTTCAATAAACCTTGCTCAAGGTTAAGTTTGCATTTGTAAGACCTCCGG
GCACCATTTCAGAAAACTCCGGGTATTAATTCTGATAAATCCTCCCGGTATCATTTCATTTCATC
AAGTTTTTAAT
Found at i:6469 original size:39 final size:40
Alignment explanation
Indices: 6417--6828 Score: 447
Period size: 40 Copynumber: 10.3 Consensus size: 40
6407 AGTCAATCAC
* * * *
6417 AATCCTATTCAGGATCTTTTCTTCATC-AATTAATTTCAA
1 AATCCTACTCAGGATCATTGCTTTATCAAATTAATTTCAA
* * *
6456 AATCCTGCTCAGGATCTTTGCTTTATCAAATTAATTTCCA
1 AATCCTACTCAGGATCATTGCTTTATCAAATTAATTTCAA
* * * *
6496 AATCCTGCTCATGATCATTGCTTTATCAAATTATTTTCAG
1 AATCCTACTCAGGATCATTGCTTTATCAAATTAATTTCAA
*
6536 AATCCTACTCCGGATCATTGCTTTATCAAAATTAATTTCAA
1 AATCCTACTCAGGATCATTGCTTTATC-AAATTAATTTCAA
*
6577 AATCCTGCTCAGGATCATTGCTTTATCAAATTAATTTCAA
1 AATCCTACTCAGGATCATTGCTTTATCAAATTAATTTCAA
* *
6617 AATCCTACTCAGGATCACTGCTGTATCAAATTAATTTCAA
1 AATCCTACTCAGGATCATTGCTTTATCAAATTAATTTCAA
* * * *
6657 AATCCTACTCAGGATCATTGCTTTATCAAGTGAATTTTAG
1 AATCCTACTCAGGATCATTGCTTTATCAAATTAATTTCAA
** * * * *
6697 AATCCTGTTCAGGATCATTTCTTTATC-AGTCAATTTCAG
1 AATCCTACTCAGGATCATTGCTTTATCAAATTAATTTCAA
* * * * *
6736 AATCCTATTCAGGATCATCT-TTTTATC-AGTCAATTTCAG
1 AATCCTACTCAGGATCAT-TGCTTTATCAAATTAATTTCAA
* * * *
6775 AATCCTATTCAGGATCCTTGCTTTATC-AGTCAATTTCAAA
1 AATCCTACTCAGGATCATTGCTTTATCAAATTAATTTC-AA
*
6815 AATCCTATTCAGGA
1 AATCCTACTCAGGA
6829 CCAGTGGCTT
Statistics
Matches: 332, Mismatches: 36, Indels: 9
0.88 0.10 0.02
Matches are distributed among these distances:
38 1 0.00
39 101 0.30
40 194 0.58
41 36 0.11
ACGTcount: A:0.30, C:0.21, G:0.10, T:0.39
Consensus pattern (40 bp):
AATCCTACTCAGGATCATTGCTTTATCAAATTAATTTCAA
Found at i:6589 original size:121 final size:121
Alignment explanation
Indices: 6417--6802 Score: 455
Period size: 121 Copynumber: 3.2 Consensus size: 121
6407 AGTCAATCAC
* * * *
6417 AATCCTATTCAGGATCTTTTCTTCATC--AATTAATTTCAAAATCCTGCTCAGGATCTTTGCTTT
1 AATCCTACTCAGGATCATTGCTTTATCAAAATTAATTTCAAAATCCTGCTCAGGATCTTTGCTTT
* * *
6480 ATCAAATTAATTTCCAAATCCTGCTCATGATCATTGCTTTATCAAATTATTTTCAG
66 ATCAAATTAATTTCCAAATCCTACTCAGGATCATTGCTTTATCAAATTAATTTCAG
* *
6536 AATCCTACTCCGGATCATTGCTTTATCAAAATTAATTTCAAAATCCTGCTCAGGATCATTGCTTT
1 AATCCTACTCAGGATCATTGCTTTATCAAAATTAATTTCAAAATCCTGCTCAGGATCTTTGCTTT
* * * *
6601 ATCAAATTAATTTCAAAATCCTACTCAGGATCACTGCTGTATCAAATTAATTTCAA
66 ATCAAATTAATTTCCAAATCCTACTCAGGATCATTGCTTTATCAAATTAATTTCAG
* * * * *
6657 AATCCTACTCAGGATCATTGCTTTATC-AAGTGAATTTTAGAATCCTGTTCAGGATCATTT-CTT
1 AATCCTACTCAGGATCATTGCTTTATCAAAATTAATTTCAAAATCCTGCTCAGGATC-TTTGCTT
* * * * * *
6720 TATC-AGTCAATTT-CAGAATCCTATTCAGGATCATCT-TTTTATC-AGTCAATTTCAG
65 TATCAAATTAATTTCCA-AATCCTACTCAGGATCAT-TGCTTTATCAAATTAATTTCAG
* *
6775 AATCCTATTCAGGATCCTTGCTTTATCA
1 AATCCTACTCAGGATCATTGCTTTATCA
6803 GTCAATTTCA
Statistics
Matches: 229, Mismatches: 32, Indels: 12
0.84 0.12 0.04
Matches are distributed among these distances:
118 35 0.15
119 50 0.22
120 32 0.14
121 112 0.49
ACGTcount: A:0.30, C:0.21, G:0.10, T:0.39
Consensus pattern (121 bp):
AATCCTACTCAGGATCATTGCTTTATCAAAATTAATTTCAAAATCCTGCTCAGGATCTTTGCTTT
ATCAAATTAATTTCCAAATCCTACTCAGGATCATTGCTTTATCAAATTAATTTCAG
Found at i:6841 original size:40 final size:38
Alignment explanation
Indices: 6341--6858 Score: 225
Period size: 40 Copynumber: 13.1 Consensus size: 38
6331 TATGTGTTTT
* * * * * *
6341 AATCCTATTCATGATCATTGTTTTATTAGTCGATTCCAG
1 AATCCTATTCAGGACCATTG-CTTATCAGTCAATTTCAG
** * * * *
6380 AATCCTGCTCAGGATCATTTCTATACCAGTCAA--TCAC
1 AATCCTATTCAGGACCATTGCT-TATCAGTCAATTTCAG
* * * * * *
6417 AATCCTATTCAGGATCTTTTCTTCATCAATTAATTTCAA
1 AATCCTATTCAGGACCATTGCTT-ATCAGTCAATTTCAG
** * * * *
6456 AATCCTGCTCAGGATCTTTGCTTTATCAAATTAATTTCCA-
1 AATCCTATTCAGGACCATTGC-TTATC-AGTCAATTT-CAG
** * * * * *
6496 AATCCTGCTCATGATCATTGCTTTATCAAATTATTTTCAG
1 AATCCTATTCAGGACCATTGC-TTATC-AGTCAATTTCAG
* * * * * *
6536 AATCCTACTCCGGATCATTGCTTTATCAAAATTAATTTCAA
1 AATCCTATTCAGGACCATTGC-TTATC--AGTCAATTTCAG
** * * * *
6577 AATCCTGCTCAGGATCATTGCTTTATCAAATTAATTTCAA
1 AATCCTATTCAGGACCATTGC-TTATC-AGTCAATTTCAG
* * * * * *
6617 AATCCTACTCAGGATCACTGCTGTATCAAATTAATTTCAA
1 AATCCTATTCAGGACCATTGCT-TATC-AGTCAATTTCAG
* * * *
6657 AATCCTACTCAGGATCATTGCTTTATCAAGTGAATTTTAG
1 AATCCTATTCAGGACCATTGC-TTATC-AGTCAATTTCAG
* * *
6697 AATCCTGTTCAGGATCATTTCTTTATCAGTCAATTTCAG
1 AATCCTATTCAGGACCATTGC-TTATCAGTCAATTTCAG
* **
6736 AATCCTATTCAGGATCATCTTTTTATCAGTCAATTTCAG
1 AATCCTATTCAGGACCAT-TGCTTATCAGTCAATTTCAG
*
6775 AATCCTATTCAGGATCC-TTGCTTTATCAGTCAATTTCAAA
1 AATCCTATTCAGGA-CCATTGC-TTATCAGTCAATTTC-AG
* **
6815 AATCCTATTCAGGACCAGTGGCTTATCAGTTGATTTCAG
1 AATCCTATTCAGGACCA-TTGCTTATCAGTCAATTTCAG
*
6854 CATCC
1 AATCC
6859 AACTCAAGAT
Statistics
Matches: 409, Mismatches: 53, Indels: 34
0.82 0.11 0.07
Matches are distributed among these distances:
36 1 0.00
37 27 0.07
38 2 0.00
39 131 0.32
40 206 0.50
41 42 0.10
ACGTcount: A:0.29, C:0.22, G:0.11, T:0.38
Consensus pattern (38 bp):
AATCCTATTCAGGACCATTGCTTATCAGTCAATTTCAG
Found at i:6870 original size:79 final size:78
Alignment explanation
Indices: 6530--6871 Score: 206
Period size: 79 Copynumber: 4.3 Consensus size: 78
6520 ATCAAATTAT
* ** * * * ** *
6530 TTTCAGAATCCTACTCCGGATCATTGCTTTATCAAAATTAATTTCAAAATCCTGCTCAGGATCAT
1 TTTCAGAATCCAACTCAAGATCCTTGCTTTATC--AGTCAATTTCAAAATCCTATTCAGGACCAT
* * *
6595 -TGCTTTATCAAATTAA
64 CGGC-TTATC-AGTCAA
* * * * * * * *
6611 TTTCAAAATCCTACTCAGGATCAC-TGCTGTATCAAATTAATTTCAAAATCCTACTCAGGATCAT
1 TTTCAGAATCCAACTCAAGATC-CTTGCTTTATC-AGTCAATTTCAAAATCCTATTCAGGACCAT
* *
6675 -TGCTTTATCAAGTGAA
64 CGGC-TTATC-AGTCAA
* *** * * * * * *
6691 TTTTAGAATCCTGTTCAGGATCATTTCTTTATCAGTCAATTTCAGAATCCTATTCAGGATCATCT
1 TTTCAGAATCCAACTCAAGATCCTTGCTTTATCAGTCAATTTCAAAATCCTATTCAGGACCATCG
**
6756 TTTTATCAGTCAA
66 GCTTATCAGTCAA
* * *
6769 TTTCAGAATCCTATTCAGGATCCTTGCTTTATCAGTCAATTTCAAAAATCCTATTCAGGACCAGT
1 TTTCAGAATCCAACTCAAGATCCTTGCTTTATCAGTCAATTTC-AAAATCCTATTCAGGACCA-T
**
6834 -GGCTTATCAGTTGA
64 CGGCTTATCAGTCAA
*
6848 TTTCAGCATCCAACTCAAGATCCT
1 TTTCAGAATCCAACTCAAGATCCT
6872 GATTTAGGAT
Statistics
Matches: 220, Mismatches: 36, Indels: 12
0.82 0.13 0.04
Matches are distributed among these distances:
78 44 0.20
79 77 0.35
80 71 0.32
81 28 0.13
ACGTcount: A:0.30, C:0.22, G:0.12, T:0.37
Consensus pattern (78 bp):
TTTCAGAATCCAACTCAAGATCCTTGCTTTATCAGTCAATTTCAAAATCCTATTCAGGACCATCG
GCTTATCAGTCAA
Found at i:10719 original size:20 final size:20
Alignment explanation
Indices: 10694--10740 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
10684 CCTAAACCAG
10694 AACCAAGCT-AAGACAAAACA
1 AACCAAGCTCAA-ACAAAACA
10714 AACCAAGCTCAAACAAAACA
1 AACCAAGCTCAAACAAAACA
10734 AACCAAG
1 AACCAAG
10741 GGCAGTTGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
20 24 0.92
21 2 0.08
ACGTcount: A:0.60, C:0.28, G:0.09, T:0.04
Consensus pattern (20 bp):
AACCAAGCTCAAACAAAACA
Found at i:11070 original size:17 final size:15
Alignment explanation
Indices: 11042--11082 Score: 55
Period size: 15 Copynumber: 2.5 Consensus size: 15
11032 CGTCAAAACA
11042 GAAAACAAATAGCTTGTT
1 GAAAA-AAATAG-TTG-T
11060 GAAAAAAATAGTTGT
1 GAAAAAAATAGTTGT
11075 GAAAAAAA
1 GAAAAAAA
11083 GATTCGGGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 9 0.39
16 3 0.13
17 6 0.26
18 5 0.22
ACGTcount: A:0.56, C:0.05, G:0.17, T:0.22
Consensus pattern (15 bp):
GAAAAAAATAGTTGT
Found at i:11080 original size:16 final size:18
Alignment explanation
Indices: 11042--11082 Score: 52
Period size: 16 Copynumber: 2.4 Consensus size: 18
11032 CGTCAAAACA
*
11042 GAAAACAAATAGCTTGTT
1 GAAAAAAAATAGCTTGTT
11060 G-AAAAAAATAG-TTG-T
1 GAAAAAAAATAGCTTGTT
11075 GAAAAAAA
1 GAAAAAAA
11083 GATTCGGGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 2 0.10
16 9 0.43
17 9 0.43
18 1 0.05
ACGTcount: A:0.56, C:0.05, G:0.17, T:0.22
Consensus pattern (18 bp):
GAAAAAAAATAGCTTGTT
Found at i:12102 original size:27 final size:29
Alignment explanation
Indices: 12073--12144 Score: 109
Period size: 26 Copynumber: 2.7 Consensus size: 29
12063 GGTCATCTAA
12073 GGGCATTTTGAGTCATTTTTGCA-TTCAG
1 GGGCATTTTGAGTCATTTTTGCATTTCAG
12101 GGGCATTTTG-GTCA--TTTGCATTTCAG
1 GGGCATTTTGAGTCATTTTTGCATTTCAG
12127 GGGCATTTT-AGTCATTTT
1 GGGCATTTTGAGTCATTTT
12145 AATCTCACTT
Statistics
Matches: 40, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
25 6 0.15
26 18 0.45
27 4 0.10
28 12 0.30
ACGTcount: A:0.17, C:0.14, G:0.25, T:0.44
Consensus pattern (29 bp):
GGGCATTTTGAGTCATTTTTGCATTTCAG
Found at i:15656 original size:17 final size:18
Alignment explanation
Indices: 15616--15656 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
15606 AATTTAGAGA
*
15616 CAGAAAAAAGGAAAAATC
1 CAGAAAAAAGAAAAAATC
*
15634 CA-AAAAAATAAAAAAT-
1 CAGAAAAAAGAAAAAATC
15650 CAGAAAA
1 CAGAAAA
15657 TCAAAAGAGG
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
16 2 0.10
17 16 0.80
18 2 0.10
ACGTcount: A:0.73, C:0.10, G:0.10, T:0.07
Consensus pattern (18 bp):
CAGAAAAAAGAAAAAATC
Found at i:17531 original size:28 final size:28
Alignment explanation
Indices: 17491--17557 Score: 116
Period size: 28 Copynumber: 2.4 Consensus size: 28
17481 GTTTTTAAGT
*
17491 CGTTTCGACAGGATTCCCCGGACCCGAA
1 CGTTACGACAGGATTCCCCGGACCCGAA
17519 CGTTACGACAGGATTCCCCGGACCCGAA
1 CGTTACGACAGGATTCCCCGGACCCGAA
*
17547 CGTTGCGACAG
1 CGTTACGACAG
17558 TCATAAATAC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.22, C:0.34, G:0.27, T:0.16
Consensus pattern (28 bp):
CGTTACGACAGGATTCCCCGGACCCGAA
Found at i:18213 original size:19 final size:19
Alignment explanation
Indices: 18189--18232 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
18179 AAAAATTCAA
18189 AATTTTATCATCAAAAATC
1 AATTTTATCATCAAAAATC
* ** *
18208 AATTTTTTTTTCGAAAATC
1 AATTTTATCATCAAAAATC
18227 AATTTT
1 AATTTT
18233 TCAAAATTTG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.39, C:0.11, G:0.02, T:0.48
Consensus pattern (19 bp):
AATTTTATCATCAAAAATC
Done.