Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018341.1 Corchorus olitorius cultivar O-4 contig18374, 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: 20609
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.35
Found at i:6745 original size:12 final size:12
Alignment explanation
Indices: 6728--6758 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
6718 TTTGCACTCG
6728 TCTAACTACATA
1 TCTAACTACATA
6740 TCTAACTACATA
1 TCTAACTACATA
6752 TCTAACT
1 TCTAACT
6759 CTACAAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.39, C:0.26, G:0.00, T:0.35
Consensus pattern (12 bp):
TCTAACTACATA
Found at i:7121 original size:29 final size:28
Alignment explanation
Indices: 7059--7121 Score: 65
Period size: 29 Copynumber: 2.2 Consensus size: 28
7049 CGGAGTGGTT
* *
7059 TTCAACACAAATCTTCTTCATATTTCTT
1 TTCAACACAAATCTCCTTCATATTTCTC
*
7087 TCTCAACAGAAATCTCCTT-ATATTATTCTC
1 T-TCAACACAAATCTCCTTCATA-T-TTCTC
7117 TTCAA
1 TTCAA
7122 GATTCCTTCA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
28 4 0.14
29 20 0.69
30 5 0.17
ACGTcount: A:0.30, C:0.25, G:0.02, T:0.43
Consensus pattern (28 bp):
TTCAACACAAATCTCCTTCATATTTCTC
Found at i:8271 original size:2 final size:2
Alignment explanation
Indices: 8264--8297 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
8254 TGACATACCA
8264 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
8298 CAACTTGTGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9192 original size:33 final size:32
Alignment explanation
Indices: 9154--9238 Score: 87
Period size: 24 Copynumber: 2.8 Consensus size: 32
9144 TCATGAAATC
9154 ACATGATTAGTAAATAGCTTTTGGTTGATTTGA
1 ACATGATTAGTAAATAGC-TTTGGTTGATTTGA
*
9187 ACATGA-T--T-AATA--TTT--TTGGTTTGA
1 ACATGATTAGTAAATAGCTTTGGTTGATTTGA
9211 ACATGATTAGTAAATAGCCTTTGGTTGA
1 ACATGATTAGTAAATAG-CTTTGGTTGA
9239 AATTGCACGG
Statistics
Matches: 41, Mismatches: 2, Indels: 18
0.67 0.03 0.30
Matches are distributed among these distances:
24 14 0.34
25 1 0.02
26 3 0.07
27 1 0.02
28 4 0.10
29 4 0.10
30 1 0.02
31 3 0.07
32 1 0.02
33 9 0.22
ACGTcount: A:0.31, C:0.07, G:0.20, T:0.42
Consensus pattern (32 bp):
ACATGATTAGTAAATAGCTTTGGTTGATTTGA
Found at i:19466 original size:7 final size:7
Alignment explanation
Indices: 19456--19538 Score: 139
Period size: 7 Copynumber: 11.9 Consensus size: 7
19446 GGTTTTGAAA
*
19456 TTTGATT
1 TTTGAGT
19463 TTTGAGT
1 TTTGAGT
19470 TTTGAGT
1 TTTGAGT
19477 TTTGAGT
1 TTTGAGT
19484 TTTGAGT
1 TTTGAGT
19491 TTTGAGT
1 TTTGAGT
19498 TTTGAGT
1 TTTGAGT
19505 TTTGAGT
1 TTTGAGT
19512 TTTGAGT
1 TTTGAGT
*
19519 TTTGAAT
1 TTTGAGT
*
19526 TTTGAAT
1 TTTGAGT
19533 TTTGAG
1 TTTGAG
19539 CAATGAAATG
Statistics
Matches: 73, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 73 1.00
ACGTcount: A:0.17, C:0.00, G:0.25, T:0.58
Consensus pattern (7 bp):
TTTGAGT
Found at i:19714 original size:33 final size:33
Alignment explanation
Indices: 19672--19749 Score: 120
Period size: 33 Copynumber: 2.4 Consensus size: 33
19662 AGAAACTATG
* * *
19672 GATTTTGAACTTTGAGTTTTGATATGATATGCA
1 GATTTTGAACTTTGAATTTTGAAATGAAATGCA
19705 GATTTTGAACTTTGAATTTTGAAATGAAATGCA
1 GATTTTGAACTTTGAATTTTGAAATGAAATGCA
*
19738 AATTTTGAACTT
1 GATTTTGAACTT
19750 CTTAATTAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.32, C:0.06, G:0.18, T:0.44
Consensus pattern (33 bp):
GATTTTGAACTTTGAATTTTGAAATGAAATGCA
Found at i:19821 original size:55 final size:55
Alignment explanation
Indices: 19760--19896 Score: 140
Period size: 55 Copynumber: 2.5 Consensus size: 55
19750 CTTAATTAAT
*
19760 CGCACTGGAT-TATTAAGA-ATTCAA-TCTTGATCAT-GGAAACATTTCTTGGAACGAC
1 CGCACTGGATCAATTAAGAGA-TCAACTC-TGATCATCGGAAAC--TTCTTGGAACGAC
* * *
19815 CGCACTGGATCAATTTAGAGATCAACTCTGATCATCGTAAACTTCTTGGAATGAC
1 CGCACTGGATCAATTAAGAGATCAACTCTGATCATCGGAAACTTCTTGGAACGAC
* *
19870 CACACTGGATCAACTTTAG-GATCAACT
1 CGCACTGGATCAA-TTAAGAGATCAACT
19897 TAGATTTTTG
Statistics
Matches: 72, Mismatches: 5, Indels: 10
0.83 0.06 0.11
Matches are distributed among these distances:
55 42 0.58
56 22 0.31
57 8 0.11
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.29
Consensus pattern (55 bp):
CGCACTGGATCAATTAAGAGATCAACTCTGATCATCGGAAACTTCTTGGAACGAC
Found at i:19912 original size:55 final size:54
Alignment explanation
Indices: 19787--19929 Score: 155
Period size: 55 Copynumber: 2.6 Consensus size: 54
19777 AATTCAATCT
* * *
19787 TGATCATGGAAACATTTCTTGGAACGACCGCACTGGATCAATTTAGAGATCAACTC
1 TGATCATCGAAA-ACTTCTTGGAA-GACCACACTGGATCAATTTAGAGATCAACTC
*
19843 TGATCATCGTAAACTTCTTGGAATGACCACACTGGATCAACTTTAG-GATCAACT-
1 TGATCATCGAAAACTTCTTGGAA-GACCACACTGGATCAA-TTTAGAGATCAACTC
** *
19897 TAGATTTTTGAAAACTTCTATGGAAGACCACAC
1 T-GATCATCGAAAACTTCT-TGGAAGACCACAC
19930 AAGGTCGTCT
Statistics
Matches: 75, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
54 1 0.01
55 54 0.72
56 20 0.27
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.29
Consensus pattern (54 bp):
TGATCATCGAAAACTTCTTGGAAGACCACACTGGATCAATTTAGAGATCAACTC
Found at i:20032 original size:54 final size:53
Alignment explanation
Indices: 19867--20055 Score: 200
Period size: 54 Copynumber: 3.5 Consensus size: 53
19857 TTCTTGGAAT
* * * * * * *
19867 GACCACACTGGATCAACTTTAGGATCAACTTAGATTTTTGAAAACTTCTATGGAA
1 GACCACACTGGGTCATC-TTAAGATCAACTTAGATCTCTG-AAAGTTCTATGAAA
** * * *
19922 GACCACACAAGGTCGTCTGAAGATCAACTTAGACCTCT-AAAGCTTCTATGAAA
1 GACCACACTGGGTCATCTTAAGATCAACTTAGATCTCTGAAAG-TTCTATGAAA
* * *
19975 GACCAAACTGGGTCATCTTAAAATCAACTTAGATCTCTGATAAGTTTTATGAAA
1 GACCACACTGGGTCATCTTAAGATCAACTTAGATCTCTGA-AAGTTCTATGAAA
20029 GACCACACTGGGTCATCTTAAGATCAA
1 GACCACACTGGGTCATCTTAAGATCAA
20056 TTTTCTAAAG
Statistics
Matches: 109, Mismatches: 22, Indels: 7
0.79 0.16 0.05
Matches are distributed among these distances:
52 3 0.03
53 40 0.37
54 51 0.47
55 15 0.14
ACGTcount: A:0.35, C:0.21, G:0.16, T:0.28
Consensus pattern (53 bp):
GACCACACTGGGTCATCTTAAGATCAACTTAGATCTCTGAAAGTTCTATGAAA
Found at i:20261 original size:37 final size:37
Alignment explanation
Indices: 20171--20600 Score: 339
Period size: 37 Copynumber: 11.6 Consensus size: 37
20161 GAAGAGACAG
* * * * *
20171 CTAAACAAGTACCTTAAATAAG-GTTTAATAAGAAAC
1 CTAAACAGGGACCTTAAACAAGATTTTGATAAGAAAC
* * ** * **
20207 CTAAACATGAATTTTAAACAAGATTTTGATGAGACGC
1 CTAAACAGGGACCTTAAACAAGATTTTGATAAGAAAC
* *
20244 TTAAACAGGGACCTTAAATAAGGA-TTTGATAAGAAAC
1 CTAAACAGGGACCTTAAACAA-GATTTTGATAAGAAAC
* * * * *
20281 CTAAACAGGAATCTAAAACAAAAATTTTGACAAGAAAC
1 CTAAACAGGGACCTTAAAC-AAGATTTTGATAAGAAAC
* *
20319 CTAAACAGGCACCTTAAATAAGGA-TTTGATAAGAAAC
1 CTAAACAGGGACCTTAAACAA-GATTTTGATAAGAAAC
* * *
20356 CTAAACAGGGATCTTAAACAAGATTTTGATGAGACAC
1 CTAAACAGGGACCTTAAACAAGATTTTGATAAGAAAC
* * * *
20393 CTAAATAGGGACCTTAAATAAAGA-TTTAATAAGAAAT
1 CTAAACAGGGACCTTAAA-CAAGATTTTGATAAGAAAC
* ** * * * *
20430 CTAAACAGGAATGTTGAACATGATTTTGATGAGACAC
1 CTAAACAGGGACCTTAAACAAGATTTTGATAAGAAAC
* * * *
20467 CTAAATAGTGACCTTAAATAAGAATTTGATAAGAAAC
1 CTAAACAGGGACCTTAAACAAGATTTTGATAAGAAAC
* * * * *
20504 CTAAACATGGATCTTAAACAAAAATTTGATAAGACAC
1 CTAAACAGGGACCTTAAACAAGATTTTGATAAGAAAC
* *
20541 CTAAACAGGGACCTTAAATAAGGA-TTTGATAAGAAAG
1 CTAAACAGGGACCTTAAACAA-GATTTTGATAAGAAAC
* * *
20578 CTAAACCGAGATCTTAAACAAGA
1 CTAAACAGGGACCTTAAACAAGA
20601 CTTTAATGA
Statistics
Matches: 302, Mismatches: 83, Indels: 18
0.75 0.21 0.04
Matches are distributed among these distances:
36 24 0.08
37 241 0.80
38 37 0.12
ACGTcount: A:0.47, C:0.14, G:0.16, T:0.24
Consensus pattern (37 bp):
CTAAACAGGGACCTTAAACAAGATTTTGATAAGAAAC
Found at i:20425 original size:74 final size:74
Alignment explanation
Indices: 20155--20609 Score: 531
Period size: 74 Copynumber: 6.1 Consensus size: 74
20145 CCTAAACTGG
* * * * * * *
20155 GATTTTGAAGAGACAGCTAAACAAGTACCTTAAAT-AAGGTTTAATAAGAAACCTAAACATGAAT
1 GATTTTGATGAGACACCTAAACAGGGACCTTAAATAAAGATTTGATAAGAAACCTAAACAGGAAT
*
20219 TTTAAACAA
66 CTTAAACAA
* * *
20228 GATTTTGATGAGACGCTTAAACAGGGACCTTAAATAAGGATTTGATAAGAAACCTAAACAGGAAT
1 GATTTTGATGAGACACCTAAACAGGGACCTTAAATAAAGATTTGATAAGAAACCTAAACAGGAAT
*
20293 CTAAAACAAA
66 CTTAAAC-AA
* ** * * * *
20303 AATTTTGACAAGAAACCTAAACAGGCACCTTAAATAAGGATTTGATAAGAAACCTAAACAGGGAT
1 GATTTTGATGAGACACCTAAACAGGGACCTTAAATAAAGATTTGATAAGAAACCTAAACAGGAAT
20368 CTTAAACAA
66 CTTAAACAA
* * *
20377 GATTTTGATGAGACACCTAAATAGGGACCTTAAATAAAGATTTAATAAGAAATCTAAACAGGAAT
1 GATTTTGATGAGACACCTAAACAGGGACCTTAAATAAAGATTTGATAAGAAACCTAAACAGGAAT
* * *
20442 GTTGAACAT
66 CTTAAACAA
* *
20451 GATTTTGATGAGACACCTAAATAGTGACCTTAAAT-AAGAATTTGATAAGAAACCTAAACATGG-
1 GATTTTGATGAGACACCTAAACAGGGACCTTAAATAAAG-ATTTGATAAGAAACCTAAACA-GGA
20514 ATCTTAAACAA
64 ATCTTAAACAA
* * * * * *
20525 AAATTTGATAAGACACCTAAACAGGGACCTTAAATAAGGATTTGATAAGAAAGCTAAAC-CGAGA
1 GATTTTGATGAGACACCTAAACAGGGACCTTAAATAAAGATTTGATAAGAAACCTAAACAGGA-A
20589 TCTTAAACAA
65 TCTTAAACAA
* *
20599 GACTTTAATGA
1 GATTTTGATGA
Statistics
Matches: 323, Mismatches: 52, Indels: 13
0.83 0.13 0.03
Matches are distributed among these distances:
72 1 0.00
73 32 0.10
74 221 0.68
75 69 0.21
ACGTcount: A:0.46, C:0.13, G:0.16, T:0.25
Consensus pattern (74 bp):
GATTTTGATGAGACACCTAAACAGGGACCTTAAATAAAGATTTGATAAGAAACCTAAACAGGAAT
CTTAAACAA
Done.