Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015235.1 Corchorus olitorius cultivar O-4 contig15268, 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: 9802
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Found at i:2116 original size:44 final size:43
Alignment explanation
Indices: 2040--2125 Score: 102
Period size: 44 Copynumber: 2.0 Consensus size: 43
2030 ATCTCCGTTG
* * *
2040 ATATGTGTTATACATCCTTCATGCATGGTCCATGT-CTTTGTAT
1 ATATATGTTATACATCCATCATGCATGATCCAT-TCCTTTGTAT
* *
2083 ATATATGTTCATACATTCATCATGCATTATCCATTCCTTTGTA
1 ATATATGTT-ATACATCCATCATGCATGATCCATTCCTTTGTA
2126 CATAGGTTCA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
43 9 0.25
44 27 0.75
ACGTcount: A:0.24, C:0.20, G:0.12, T:0.44
Consensus pattern (43 bp):
ATATATGTTATACATCCATCATGCATGATCCATTCCTTTGTAT
Found at i:2761 original size:19 final size:20
Alignment explanation
Indices: 2737--2782 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 20
2727 GAGAAAAACA
2737 AAACAAGAT-TCTTTTGAAC
1 AAACAAGATGTCTTTTGAAC
* *
2756 AAACAA-TTGTGTTTTGAAC
1 AAACAAGATGTCTTTTGAAC
2775 AAA-AAGAT
1 AAACAAGAT
2783 AAGATGAGAT
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
18 3 0.14
19 19 0.86
ACGTcount: A:0.46, C:0.11, G:0.13, T:0.30
Consensus pattern (20 bp):
AAACAAGATGTCTTTTGAAC
Found at i:3627 original size:12 final size:12
Alignment explanation
Indices: 3610--3648 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
3600 TTCACTCATC
3610 AAATTCAAATCA
1 AAATTCAAATCA
*
3622 AAATTCAAATTA
1 AAATTCAAATCA
* *
3634 AAGTTTAAATCA
1 AAATTCAAATCA
3646 AAA
1 AAA
3649 GTGAATCAAA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.59, C:0.10, G:0.03, T:0.28
Consensus pattern (12 bp):
AAATTCAAATCA
Found at i:4035 original size:13 final size:13
Alignment explanation
Indices: 3983--4035 Score: 54
Period size: 13 Copynumber: 3.9 Consensus size: 13
3973 ACTAACCAAA
*
3983 AAAAAAAGAAAAG
1 AAAAAAAGAAATG
*
3996 AAAAAAAGAGA-G
1 AAAAAAAGAAATG
4008 AAATGAAAATGAAATG
1 AAA--AAAA-GAAATG
4024 AAAAAAAGAAAT
1 AAAAAAAGAAAT
4036 AAGAAACAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
12 4 0.12
13 15 0.44
14 8 0.24
15 3 0.09
16 4 0.12
ACGTcount: A:0.75, C:0.00, G:0.17, T:0.08
Consensus pattern (13 bp):
AAAAAAAGAAATG
Found at i:5196 original size:105 final size:105
Alignment explanation
Indices: 5014--5308 Score: 455
Period size: 105 Copynumber: 2.8 Consensus size: 105
5004 TCCATAAGCC
* * *
5014 AAACTCGTTTCCAGACGAGTCAGTTGAAGCCTTGGTTCCACCCAAGCAACAGGGGCTTTTCCATA
1 AAACTCGTTTCCATACGAGTCAGTTCAAACCTTGGTTCCACCCAAGCAACAGGGGCTTTTCCATA
*
5079 AGCCAAGCTCATTTCCATATGAATTCAGTCTTCCAAGACT
66 AGCCAAGTTCATTTCCATATGAATTCAGTCTTCCAAGACT
*
5119 AAACTCGTTTCCATACGAGTCAGTTCAAACCTTGGTTCCACCCAAGCAACAGGGGCTTTCCCATA
1 AAACTCGTTTCCATACGAGTCAGTTCAAACCTTGGTTCCACCCAAGCAACAGGGGCTTTTCCATA
5184 AGCCAAGTTCATTTCCATATGAATTCAGTCTTCCAAGACT
66 AGCCAAGTTCATTTCCATATGAATTCAGTCTTCCAAGACT
* * ** * ** *
5224 AAACTCGTTTCCATGCGAGTCAGTTTAAACCTTGGTTCCGTCCAAGCCACATAGGCTTTTCCACA
1 AAACTCGTTTCCATACGAGTCAGTTCAAACCTTGGTTCCACCCAAGCAACAGGGGCTTTTCCATA
*
5289 AGCCACAGTTCGTTTCCATA
66 AGCCA-AGTTCATTTCCATA
5309 CGGTGCATTA
Statistics
Matches: 174, Mismatches: 15, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
105 161 0.93
106 13 0.07
ACGTcount: A:0.27, C:0.28, G:0.17, T:0.28
Consensus pattern (105 bp):
AAACTCGTTTCCATACGAGTCAGTTCAAACCTTGGTTCCACCCAAGCAACAGGGGCTTTTCCATA
AGCCAAGTTCATTTCCATATGAATTCAGTCTTCCAAGACT
Found at i:5370 original size:35 final size:35
Alignment explanation
Indices: 5324--5630 Score: 481
Period size: 35 Copynumber: 8.8 Consensus size: 35
5314 CATTACCATC
5324 TTCAGATGACTCGGTGTAGCATCTTCAAAGTTGAA
1 TTCAGATGACTCGGTGTAGCATCTTCAAAGTTGAA
5359 TTCAGATGACTCGGTGTAGCATCTTCAAAGTTGAA
1 TTCAGATGACTCGGTGTAGCATCTTCAAAGTTGAA
*
5394 TCCAGATGACTCGGTGTAGCATCTTCAAAGTTGAA
1 TTCAGATGACTCGGTGTAGCATCTTCAAAGTTGAA
*
5429 TCCAGATGACTCGGTGTAGCATCTTCAAAGTTGAA
1 TTCAGATGACTCGGTGTAGCATCTTCAAAGTTGAA
* *
5464 CTCAGATGACTCGGTGCAGCATCTTCTAAA-TTGAA
1 TTCAGATGACTCGGTGTAGCATCTTC-AAAGTTGAA
* *
5499 CTCAGATGACTCGGTGTAGCATCTTCGAAGTTGAA
1 TTCAGATGACTCGGTGTAGCATCTTCAAAGTTGAA
* *
5534 TCCAGATGACTCGGTGTAGCATCTTCAAAGATGAA
1 TTCAGATGACTCGGTGTAGCATCTTCAAAGTTGAA
* * * **
5569 CTCGGATGACTCGGTGTAGCTTCTTCAAAAATGAA
1 TTCAGATGACTCGGTGTAGCATCTTCAAAGTTGAA
5604 TTCAGATGACTCGGTGTAGCATCTTCA
1 TTCAGATGACTCGGTGTAGCATCTTCA
5631 TAATGGACTC
Statistics
Matches: 252, Mismatches: 18, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
34 2 0.01
35 247 0.98
36 3 0.01
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.29
Consensus pattern (35 bp):
TTCAGATGACTCGGTGTAGCATCTTCAAAGTTGAA
Found at i:5963 original size:27 final size:26
Alignment explanation
Indices: 5933--6063 Score: 129
Period size: 27 Copynumber: 4.8 Consensus size: 26
5923 TTTAAGGTCA
*
5933 TTCAGGGGCATTTTAGTCATTTGCAC
1 TTCAGGGGCATTTTGGTCATTTGCAC
5959 GTTCAGGGGCATTTTGGTCATTTGCAC
1 -TTCAGGGGCATTTTGGTCATTTGCAC
* * *
5986 GTCCATGGGCATTTTGGTCATTTTTACAC
1 -TTCAGGGGCATTTTGGTCA--TTTGCAC
* * *
6015 CT-AGGGGGTATTTTAGTCATTTGCAC
1 TTCA-GGGGCATTTTGGTCATTTGCAC
*
6041 TTCAGGGGGCATTGTGGTCATTT
1 TTCA-GGGGCATTTTGGTCATTT
6064 CTACTCCATT
Statistics
Matches: 86, Mismatches: 14, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
26 7 0.08
27 61 0.71
28 12 0.14
29 6 0.07
ACGTcount: A:0.17, C:0.18, G:0.27, T:0.39
Consensus pattern (26 bp):
TTCAGGGGCATTTTGGTCATTTGCAC
Found at i:6920 original size:16 final size:16
Alignment explanation
Indices: 6894--6932 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
6884 TCAGTTGGAG
* *
6894 GAAAAAGGGAGGAAAA
1 GAAAAAAGGAGAAAAA
*
6910 TAAAAAAGGAGAAAAA
1 GAAAAAAGGAGAAAAA
6926 GAAAAAA
1 GAAAAAA
6933 TACAGTAGAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.72, C:0.00, G:0.26, T:0.03
Consensus pattern (16 bp):
GAAAAAAGGAGAAAAA
Done.