Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018976.1 Corchorus olitorius cultivar O-4 contig19009, 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: 42830
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:7829 original size:19 final size:19
Alignment explanation
Indices: 7805--7844 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
7795 ACTGTAGCAA
7805 TGCTGAATACTTTCAACTT
1 TGCTGAATACTTTCAACTT
7824 TGCTGAATACTTTCAACTT
1 TGCTGAATACTTTCAACTT
7843 TG
1 TG
7845 ACATCTTTGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.25, C:0.20, G:0.12, T:0.42
Consensus pattern (19 bp):
TGCTGAATACTTTCAACTT
Found at i:14182 original size:31 final size:31
Alignment explanation
Indices: 14126--14289 Score: 166
Period size: 31 Copynumber: 5.2 Consensus size: 31
14116 GGTGTCCGAC
*
14126 GTGGCACGCCACGTGTACCAAAAAAGCGACAT
1 GTGGCACGCCACGTGTA-CAAAAAAGTGACAT
*
14158 GTGGCACGCCACGTGTACAAAAAAGCGACAT
1 GTGGCACGCCACGTGTACAAAAAAGTGACAT
* * * * *
14189 GTGGTACACCACATGTACCAAAAAGTGACAC
1 GTGGCACGCCACGTGTACAAAAAAGTGACAT
* * *
14220 GTGACACGCCACATGTACCAAAAAGTGACACAT
1 GTGGCACGCCACGTGTACAAAAAAGTG--ACAT
* * * * *
14253 ATGTCACGCCATGTGTACTAAAAAGTGACAC
1 GTGGCACGCCACGTGTACAAAAAAGTGACAT
14284 GTGGCA
1 GTGGCA
14290 TACCTCGTGC
Statistics
Matches: 112, Mismatches: 18, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
31 70 0.62
32 17 0.15
33 25 0.22
ACGTcount: A:0.36, C:0.26, G:0.23, T:0.16
Consensus pattern (31 bp):
GTGGCACGCCACGTGTACAAAAAAGTGACAT
Found at i:18784 original size:22 final size:22
Alignment explanation
Indices: 18759--18824 Score: 105
Period size: 22 Copynumber: 3.0 Consensus size: 22
18749 AAAATACAGT
*
18759 ACAAGTCCTGCCTAGGACTTGG
1 ACAACTCCTGCCTAGGACTTGG
18781 ACAACTCCTGCCTAGGACTTGG
1 ACAACTCCTGCCTAGGACTTGG
* *
18803 ACAACTCCTGCCCAGAACTTGG
1 ACAACTCCTGCCTAGGACTTGG
18825 CCTGTTGAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 41 1.00
ACGTcount: A:0.24, C:0.32, G:0.23, T:0.21
Consensus pattern (22 bp):
ACAACTCCTGCCTAGGACTTGG
Found at i:23765 original size:18 final size:19
Alignment explanation
Indices: 23742--23779 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
23732 GTGCATGGGC
*
23742 TGCATGGAG-GCATGGAGA
1 TGCATGGAGACCATGGAGA
23760 TGCATGGAGACCATGGAGA
1 TGCATGGAGACCATGGAGA
23779 T
1 T
23780 AACGATGGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.29, C:0.13, G:0.39, T:0.18
Consensus pattern (19 bp):
TGCATGGAGACCATGGAGA
Found at i:25586 original size:18 final size:19
Alignment explanation
Indices: 25553--25591 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
25543 AAATATCTCC
25553 AATTAGGGCTAATTGCACA
1 AATTAGGGCTAATTGCACA
*
25572 AATTAGGTC-AATTGCACA
1 AATTAGGGCTAATTGCACA
25590 AA
1 AA
25592 AACAAGAACC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.41, C:0.15, G:0.18, T:0.26
Consensus pattern (19 bp):
AATTAGGGCTAATTGCACA
Found at i:26332 original size:16 final size:15
Alignment explanation
Indices: 26294--26335 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
26284 ACAGATGTTG
*
26294 ACAGAAAGCAATTAA
1 ACAGAAAACAATTAA
26309 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
26324 ACTAGAAAACAA
1 AC-AGAAAACAA
26336 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
Found at i:27717 original size:17 final size:18
Alignment explanation
Indices: 27695--27729 Score: 54
Period size: 17 Copynumber: 1.9 Consensus size: 18
27685 TTGAAATAAA
27695 TCTTCAAA-ATCTTCAAG
1 TCTTCAAATATCTTCAAG
27712 TCTTCAAATTATCTTCAA
1 TCTTCAAA-TATCTTCAA
27730 ATGGTCTTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
19 8 0.50
ACGTcount: A:0.34, C:0.23, G:0.03, T:0.40
Consensus pattern (18 bp):
TCTTCAAATATCTTCAAG
Found at i:28287 original size:14 final size:15
Alignment explanation
Indices: 28268--28297 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
28258 TACTAGGAAA
28268 AATAAAT-AACAAGG
1 AATAAATAAACAAGG
28282 AATAAATAAACAAGG
1 AATAAATAAACAAGG
28297 A
1 A
28298 TTGGACTTAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.67, C:0.07, G:0.13, T:0.13
Consensus pattern (15 bp):
AATAAATAAACAAGG
Found at i:33339 original size:22 final size:22
Alignment explanation
Indices: 33309--33352 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
33299 AAAATGCAGT
*
33309 ACAAGTCCTGCCCAAGACTTGG
1 ACAACTCCTGCCCAAGACTTGG
*
33331 ACAACTCCTGCCCAGGACTTGG
1 ACAACTCCTGCCCAAGACTTGG
33353 TCTATTGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.25, C:0.34, G:0.23, T:0.18
Consensus pattern (22 bp):
ACAACTCCTGCCCAAGACTTGG
Found at i:38475 original size:22 final size:22
Alignment explanation
Indices: 38447--38574 Score: 105
Period size: 22 Copynumber: 5.8 Consensus size: 22
38437 TCTCTCCACA
*
38447 CTATGAAATTTTGATAATTTCT
1 CTATGAAATTTTGATAATATCT
* *
38469 CTATGAAATTGTGATAATCAAC-
1 CTATGAAATTTTGATAAT-ATCT
* * *
38491 CTATGATATTTTGATAATCTCC
1 CTATGAAATTTTGATAATATCT
*** * ** * *
38513 CTATGGTTTTTTTTATACCAACA
1 CTAT-GAAATTTTGATAATATCT
38536 CTATGAAATTTTGATAATATCT
1 CTATGAAATTTTGATAATATCT
38558 CTATGAAATTTTGATAA
1 CTATGAAATTTTGATAA
38575 CAATACTATG
Statistics
Matches: 80, Mismatches: 23, Indels: 6
0.73 0.21 0.06
Matches are distributed among these distances:
21 1 0.01
22 64 0.80
23 15 0.19
ACGTcount: A:0.34, C:0.12, G:0.10, T:0.44
Consensus pattern (22 bp):
CTATGAAATTTTGATAATATCT
Found at i:38629 original size:22 final size:22
Alignment explanation
Indices: 38445--38631 Score: 102
Period size: 22 Copynumber: 8.6 Consensus size: 22
38435 CCTCTCTCCA
*
38445 CACTATGAAATTTTGATAATTT
1 CACTATGAAATTTTGATAATCT
* *
38467 CTCTATGAAATTGTGATAATC-
1 CACTATGAAATTTTGATAATCT
* *
38488 AACCTATGATATTTTGATAATCT
1 CA-CTATGAAATTTTGATAATCT
* ** ** * *
38511 CCCTATG-GTTTTTTTTATACCAA
1 CACTATGAAATTTTGATA-ATC-T
*
38534 CACTATGAAATTTTGATAATAT
1 CACTATGAAATTTTGATAATCT
*
38556 CTCTATGAAATTTTGATAA-CAAT
1 CACTATGAAATTTTGATAATC--T
* *
38579 -ACTATGAAA--TT-ATGACCT
1 CACTATGAAATTTTGATAATCT
* *
38597 CA-TAATAAAATTTTTATAATCT
1 CACT-ATGAAATTTTGATAATCT
38619 CACTATGAAATTT
1 CACTATGAAATTT
38632 CAATAACGAC
Statistics
Matches: 120, Mismatches: 31, Indels: 28
0.67 0.17 0.16
Matches are distributed among these distances:
18 2 0.02
19 9 0.08
20 3 0.03
21 8 0.07
22 83 0.69
23 9 0.08
24 6 0.05
ACGTcount: A:0.36, C:0.13, G:0.09, T:0.42
Consensus pattern (22 bp):
CACTATGAAATTTTGATAATCT
Found at i:39377 original size:31 final size:31
Alignment explanation
Indices: 39334--39410 Score: 118
Period size: 31 Copynumber: 2.5 Consensus size: 31
39324 GAAAAAAATA
* *
39334 AGCATTTGAGTCCCTGAAGTGGAGTTAAAAG
1 AGCAATTGAGTCCCTGAAGTAGAGTTAAAAG
**
39365 AGCAATTGAGTCCCTGAAGTAGAGTTAACGG
1 AGCAATTGAGTCCCTGAAGTAGAGTTAAAAG
39396 AGCAATTGAGTCCCT
1 AGCAATTGAGTCCCT
39411 ATCGTTACAA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.31, C:0.17, G:0.27, T:0.25
Consensus pattern (31 bp):
AGCAATTGAGTCCCTGAAGTAGAGTTAAAAG
Found at i:41619 original size:21 final size:21
Alignment explanation
Indices: 41595--41639 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
41585 TATAAGATGG
*
41595 GTTCAGGTCATTATCGGTGAA
1 GTTCAGGTCATTATCAGTGAA
*
41616 GTTCGGGTCATTATCAGTGAA
1 GTTCAGGTCATTATCAGTGAA
41637 GTT
1 GTT
41640 TAGCAAACTG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.22, C:0.13, G:0.29, T:0.36
Consensus pattern (21 bp):
GTTCAGGTCATTATCAGTGAA
Found at i:42171 original size:207 final size:207
Alignment explanation
Indices: 41809--42223 Score: 769
Period size: 207 Copynumber: 2.0 Consensus size: 207
41799 TTGACTAATA
*
41809 ATTATTAAAAAATTATGTAAAATTAAATTTTTAAAAAAATATGTTTTGGTTAAATTAAGTTTTAA
1 ATTATTAAAAAATTATGTAAAATTAAATTTTTAAAAAAATATGTTTTGGCTAAATTAAGTTTTAA
41874 ACTTTTCAAAACATATTTTTCAAAATTTTAATTATATATAATTTTCTTGTAATTATTGGTCAAAG
66 ACTTTTCAAAACATATTTTTCAAAATTTTAATTATATATAATTTTCTTGTAATTATTGGTCAAAG
* *
41939 TTTGAGATGAATTGACTAAAAAATAACAGTTAATTAAGGACAGTGAGATCTACTAGAGATAAGAC
131 TTTGAGATGAAATGACTAAAAAATAACAGTTAATTAAGGACAGAGAGATCTACTAGAGATAAGAC
42004 TAAAAAAAAAGAC
196 -AAAAAAAAAGAC
42017 ATTATTAAAAAATTATGTAAAATTAAATTTTTAAAAAAATATGTTTTGGCTAAATTAAGTTTTAA
1 ATTATTAAAAAATTATGTAAAATTAAATTTTTAAAAAAATATGTTTTGGCTAAATTAAGTTTTAA
*
42082 ACTTTTC-AAACATATTTTTTAAAATTTTAATTATATATAATTTTCTTGTAATTATTGGTCAAAG
66 ACTTTTCAAAACATATTTTTCAAAATTTTAATTATATATAATTTTCTTGTAATTATTGGTCAAAG
*
42146 TTTGAGATGAAATGACTAAAAAATAACTGTTAATTAAGGACAGAGAGATCTACTAGAGATAAGAC
131 TTTGAGATGAAATGACTAAAAAATAACAGTTAATTAAGGACAGAGAGATCTACTAGAGATAAGAC
42211 AAAAAAAAAGAC
196 AAAAAAAAAGAC
42223 A
1 A
42224 ATTTTTAATG
Statistics
Matches: 202, Mismatches: 5, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
206 13 0.06
207 118 0.58
208 71 0.35
ACGTcount: A:0.46, C:0.06, G:0.11, T:0.37
Consensus pattern (207 bp):
ATTATTAAAAAATTATGTAAAATTAAATTTTTAAAAAAATATGTTTTGGCTAAATTAAGTTTTAA
ACTTTTCAAAACATATTTTTCAAAATTTTAATTATATATAATTTTCTTGTAATTATTGGTCAAAG
TTTGAGATGAAATGACTAAAAAATAACAGTTAATTAAGGACAGAGAGATCTACTAGAGATAAGAC
AAAAAAAAAGAC
Done.