Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013546.1 Corchorus olitorius cultivar O-4 contig13579, 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: 24182
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.35
Found at i:6832 original size:19 final size:19
Alignment explanation
Indices: 6808--6846 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
6798 TATTGTCTTG
6808 TGTAAGGTACTCCCTCCTA
1 TGTAAGGTACTCCCTCCTA
*
6827 TGTAAGGTACTCCTTCCTA
1 TGTAAGGTACTCCCTCCTA
6846 T
1 T
6847 TCAAAATAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.28, G:0.15, T:0.36
Consensus pattern (19 bp):
TGTAAGGTACTCCCTCCTA
Found at i:9012 original size:15 final size:16
Alignment explanation
Indices: 8992--9025 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
8982 GTTTTCTAAG
*
8992 ATTATATGTATTAT-A
1 ATTATATGAATTATCA
9007 ATTATATGAATTATCA
1 ATTATATGAATTATCA
9023 ATT
1 ATT
9026 GTTTTATAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.41, C:0.03, G:0.06, T:0.50
Consensus pattern (16 bp):
ATTATATGAATTATCA
Found at i:9295 original size:46 final size:46
Alignment explanation
Indices: 9219--9310 Score: 148
Period size: 46 Copynumber: 2.0 Consensus size: 46
9209 ACCCGTATCA
*
9219 CAGGAGGTTAAACTATTGGTAAGAGTGGACCCATGCCTCAGGGGGT
1 CAGGAGGTTAAACTATTGGTAAGAGCGGACCCATGCCTCAGGGGGT
* * *
9265 CAGGGGGTTAAACTGTTGGTAAGAGCGGACCCGTGCCTCAGGGGGT
1 CAGGAGGTTAAACTATTGGTAAGAGCGGACCCATGCCTCAGGGGGT
9311 TAAACTGATT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 42 1.00
ACGTcount: A:0.23, C:0.18, G:0.38, T:0.21
Consensus pattern (46 bp):
CAGGAGGTTAAACTATTGGTAAGAGCGGACCCATGCCTCAGGGGGT
Found at i:9344 original size:39 final size:38
Alignment explanation
Indices: 9264--9398 Score: 198
Period size: 38 Copynumber: 3.5 Consensus size: 38
9254 CCTCAGGGGG
9264 TCAGGGGGTTAAACTGTTGGTAAGAGCGGACCCGTGCC
1 TCAGGGGGTTAAACTGTTGGTAAGAGCGGACCCGTGCC
** * **
9302 TCAGGGGGTTAAACTGATTTATAAGAGTGGACCCGTATC
1 TCAGGGGGTTAAACTG-TTGGTAAGAGCGGACCCGTGCC
*
9341 TCAGGAGGTTAAACTGTTGGTAAGAGCGGACCCGTGCC
1 TCAGGGGGTTAAACTGTTGGTAAGAGCGGACCCGTGCC
*
9379 TCATGGGGTTAAACTGTTGG
1 TCAGGGGGTTAAACTGTTGG
9399 CTAGACTCGA
Statistics
Matches: 83, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
38 51 0.61
39 32 0.39
ACGTcount: A:0.24, C:0.18, G:0.33, T:0.25
Consensus pattern (38 bp):
TCAGGGGGTTAAACTGTTGGTAAGAGCGGACCCGTGCC
Found at i:10547 original size:33 final size:28
Alignment explanation
Indices: 10487--10542 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
10477 TAAGATTTTT
10487 GGGTTCATGATTTTATATAGTAGTAAGA
1 GGGTTCATGATTTTATATAGTAGTAAGA
10515 GGGTTCATGATTTTATATAGTAGTAAGA
1 GGGTTCATGATTTTATATAGTAGTAAGA
10543 TAAGATAGTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.32, C:0.04, G:0.25, T:0.39
Consensus pattern (28 bp):
GGGTTCATGATTTTATATAGTAGTAAGA
Found at i:12534 original size:16 final size:16
Alignment explanation
Indices: 12484--12541 Score: 64
Period size: 16 Copynumber: 3.6 Consensus size: 16
12474 GGCAATTGGG
12484 CGGGTTCGGGTATTTT
1 CGGGTTCGGGTATTTT
** *
12500 CGGCCTCGGGT-TATGT
1 CGGGTTCGGGTAT-TTT
*
12516 CGGGTTCGGATATTTT
1 CGGGTTCGGGTATTTT
12532 CGGGTTCGGG
1 CGGGTTCGGG
12542 CTCGGGTCGG
Statistics
Matches: 32, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
15 1 0.03
16 30 0.94
17 1 0.03
ACGTcount: A:0.07, C:0.17, G:0.40, T:0.36
Consensus pattern (16 bp):
CGGGTTCGGGTATTTT
Found at i:12553 original size:17 final size:17
Alignment explanation
Indices: 12531--12565 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
12521 TCGGATATTT
*
12531 TCGGGTTCGGGCTCGGG
1 TCGGGTTCAGGCTCGGG
*
12548 TCGGGTTCATGCTCGGG
1 TCGGGTTCAGGCTCGGG
12565 T
1 T
12566 TTGATTTCGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.03, C:0.23, G:0.46, T:0.29
Consensus pattern (17 bp):
TCGGGTTCAGGCTCGGG
Found at i:14790 original size:2 final size:2
Alignment explanation
Indices: 14733--14770 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
14723 TTGATGCTCA
14733 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
14771 ACATCATTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:15642 original size:31 final size:31
Alignment explanation
Indices: 15607--15678 Score: 85
Period size: 31 Copynumber: 2.3 Consensus size: 31
15597 TAAATTATTG
*
15607 CAAATTAAAACAAAT-TAAGCATTAAATTAAA
1 CAAATTAAAA-AAATGAAAGCATTAAATTAAA
* *
15638 CAAA-TAATTAAAATGAAAGCCTTAAATTAAA
1 CAAATTAA-AAAAATGAAAGCATTAAATTAAA
15669 CAAATTAAAA
1 CAAATTAAAA
15679 GATGATAGAC
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
30 7 0.21
31 24 0.71
32 3 0.09
ACGTcount: A:0.61, C:0.10, G:0.04, T:0.25
Consensus pattern (31 bp):
CAAATTAAAAAAATGAAAGCATTAAATTAAA
Found at i:16225 original size:33 final size:32
Alignment explanation
Indices: 16186--16305 Score: 150
Period size: 33 Copynumber: 3.9 Consensus size: 32
16176 TTTCTAGTCA
16186 ATTCGGGCTCGGACGGGTTTCGGGTTCGGGCGG
1 ATTCGGGC-CGGACGGGTTTCGGGTTCGGGCGG
16219 ATTCGGGCACGGACGGGTTTCGGGTTC--G-GG
1 ATTCGGGC-CGGACGGGTTTCGGGTTCGGGCGG
16249 ---C--G-CGGACGGGTTTCGGGTTCGGGCGG
1 ATTCGGGCCGGACGGGTTTCGGGTTCGGGCGG
16275 ATTCGGGCGCGGACGGGTTTCGGGTTCGGGC
1 ATTCGGGC-CGGACGGGTTTCGGGTTCGGGC
16306 TCGGACAGCT
Statistics
Matches: 76, Mismatches: 1, Indels: 20
0.78 0.01 0.21
Matches are distributed among these distances:
23 18 0.24
25 2 0.03
26 2 0.03
27 1 0.01
29 1 0.01
30 2 0.03
31 2 0.03
33 48 0.63
ACGTcount: A:0.07, C:0.22, G:0.49, T:0.23
Consensus pattern (32 bp):
ATTCGGGCCGGACGGGTTTCGGGTTCGGGCGG
Found at i:16264 original size:56 final size:56
Alignment explanation
Indices: 16187--16311 Score: 232
Period size: 56 Copynumber: 2.2 Consensus size: 56
16177 TTCTAGTCAA
16187 TTCGGGCTCGGACGGGTTTCGGGTTCGGGCGGATTCGGGCACGGACGGGTTTCGGG
1 TTCGGGCTCGGACGGGTTTCGGGTTCGGGCGGATTCGGGCACGGACGGGTTTCGGG
* *
16243 TTCGGGCGCGGACGGGTTTCGGGTTCGGGCGGATTCGGGCGCGGACGGGTTTCGGG
1 TTCGGGCTCGGACGGGTTTCGGGTTCGGGCGGATTCGGGCACGGACGGGTTTCGGG
16299 TTCGGGCTCGGAC
1 TTCGGGCTCGGAC
16312 AGCTCTAACC
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
56 66 1.00
ACGTcount: A:0.06, C:0.22, G:0.49, T:0.22
Consensus pattern (56 bp):
TTCGGGCTCGGACGGGTTTCGGGTTCGGGCGGATTCGGGCACGGACGGGTTTCGGG
Found at i:16281 original size:23 final size:23
Alignment explanation
Indices: 16220--16273 Score: 99
Period size: 23 Copynumber: 2.3 Consensus size: 23
16210 TTCGGGCGGA
*
16220 TTCGGGCACGGACGGGTTTCGGG
1 TTCGGGCGCGGACGGGTTTCGGG
16243 TTCGGGCGCGGACGGGTTTCGGG
1 TTCGGGCGCGGACGGGTTTCGGG
16266 TTCGGGCG
1 TTCGGGCG
16274 GATTCGGGCG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.06, C:0.22, G:0.50, T:0.22
Consensus pattern (23 bp):
TTCGGGCGCGGACGGGTTTCGGG
Found at i:16771 original size:150 final size:150
Alignment explanation
Indices: 16500--16777 Score: 520
Period size: 150 Copynumber: 1.9 Consensus size: 150
16490 GTTTCATTTG
16500 TTTTCTCTTCTATGCTTCTCCAATGTTTTCAGGAAAAAATCTCCTCAGTGTGGAAGGAATGTCTC
1 TTTTCTCTTCTATGCTTCTCCAATGTTTTCAGGAAAAAATCTCCTCAGTGTGGAAGGAATGTCTC
* **
16565 TCCAGCCCTTTCAGAGGGTATATGCCGTGAATTTTCACTAGCCGAGATCAAAGCTTCTACAAACT
66 TCCAGCCCTTCCAGAGAATATATGCCGTGAATTTTCACTAGCCGAGATCAAAGCTTCTACAAACT
16630 CTTCCTTGTGGCCAAAAAAA
131 CTTCCTTGTGGCCAAAAAAA
16650 TTTTCTCTTCTATGCTTCTCCAATGTTTTCAGGAAAAAATCTCCTCAGTGTGGAAGGAATGTCTC
1 TTTTCTCTTCTATGCTTCTCCAATGTTTTCAGGAAAAAATCTCCTCAGTGTGGAAGGAATGTCTC
*
16715 TCCAGCCCTTCCAGAGAATATATGCCGTGAATTTTCTCTAGCCGAGATCAAAGCTTCTACAAA
66 TCCAGCCCTTCCAGAGAATATATGCCGTGAATTTTCACTAGCCGAGATCAAAGCTTCTACAAA
16778 AAATTTCCAT
Statistics
Matches: 124, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
150 124 1.00
ACGTcount: A:0.27, C:0.24, G:0.17, T:0.32
Consensus pattern (150 bp):
TTTTCTCTTCTATGCTTCTCCAATGTTTTCAGGAAAAAATCTCCTCAGTGTGGAAGGAATGTCTC
TCCAGCCCTTCCAGAGAATATATGCCGTGAATTTTCACTAGCCGAGATCAAAGCTTCTACAAACT
CTTCCTTGTGGCCAAAAAAA
Found at i:19488 original size:22 final size:21
Alignment explanation
Indices: 19452--19648 Score: 103
Period size: 22 Copynumber: 9.1 Consensus size: 21
19442 CTCCAATGTA
*
19452 GAAATTTGATAACCTCATTAT
1 GAAATTTGATAACCTCACTAT
*
19473 GAAATTTCAATAACCTC-CTAT
1 GAAATTT-GATAACCTCACTAT
*
19494 GAAAATTTGATAACCACACTAT
1 G-AAATTTGATAACCTCACTAT
* * *
19516 GAAATTTCGATAACCTTAGTGT
1 GAAATTT-GATAACCTCACTAT
* * *
19538 GAAGTTTTGATAATCTCCCTAT
1 GAA-ATTTGATAACCTCACTAT
* * * * *
19560 AAAATTTTGTTAATCACTCTAT
1 GAAA-TTTGATAACCTCACTAT
* *
19582 -ATAA-TTGGTAACCGCACTAT
1 GA-AATTTGATAACCTCACTAT
* * *
19602 GAAAATTTTAATAACCACACCAT
1 G-AAA-TTTGATAACCTCACTAT
* *
19625 AAAAATTTGATAACCTCCCTAT
1 -GAAATTTGATAACCTCACTAT
19647 GA
1 GA
19649 GAATGAAACT
Statistics
Matches: 131, Mismatches: 33, Indels: 24
0.70 0.18 0.13
Matches are distributed among these distances:
20 12 0.09
21 28 0.21
22 73 0.56
23 18 0.14
ACGTcount: A:0.38, C:0.18, G:0.10, T:0.34
Consensus pattern (21 bp):
GAAATTTGATAACCTCACTAT
Found at i:19897 original size:22 final size:22
Alignment explanation
Indices: 19781--19929 Score: 88
Period size: 22 Copynumber: 6.8 Consensus size: 22
19771 ATTCCCTCTC
*
19781 TATGAAATTTT-ATTAAGCTTCT-
1 TATGAAATTTTGA-TAACCTT-TG
****
19803 TATGAAATTTTGATAACCAAAC
1 TATGAAATTTTGATAACCTTTG
* *
19825 TATAAAATTTCGATAA-CTTTCG
1 TATGAAATTTTGATAACCTTT-G
* * ***
19847 TATAAAATTTTGTTAACCTCCC
1 TATGAAATTTTGATAACCTTTG
* * * *
19869 TAGGAAATTTTAATAATCTTTT
1 TATGAAATTTTGATAACCTTTG
* *
19891 TATGAAAATTTGGTAACCTTTG
1 TATGAAATTTTGATAACCTTTG
19913 TATGAAATTTTGATAAC
1 TATGAAATTTTGATAAC
19930 TACACAATGA
Statistics
Matches: 92, Mismatches: 31, Indels: 8
0.70 0.24 0.06
Matches are distributed among these distances:
21 1 0.01
22 88 0.96
23 3 0.03
ACGTcount: A:0.36, C:0.11, G:0.10, T:0.42
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTTTG
Found at i:19939 original size:22 final size:22
Alignment explanation
Indices: 19913--19995 Score: 96
Period size: 22 Copynumber: 3.8 Consensus size: 22
19903 GTAACCTTTG
19913 TATGAAATTTTGATAACTACAC
1 TATGAAATTTTGATAACTACAC
* * * *
19935 AATGAAGTTTTGATAATTTTCA-
1 TATGAAATTTTGATAA-CTACAC
* *
19957 TATGAAATTTTGGTAACCACAC
1 TATGAAATTTTGATAACTACAC
19979 TATGAAATTTTGATAAC
1 TATGAAATTTTGATAAC
19996 CTTCCCATGT
Statistics
Matches: 48, Mismatches: 11, Indels: 4
0.76 0.17 0.06
Matches are distributed among these distances:
21 2 0.04
22 43 0.90
23 3 0.06
ACGTcount: A:0.39, C:0.11, G:0.12, T:0.39
Consensus pattern (22 bp):
TATGAAATTTTGATAACTACAC
Found at i:20010 original size:44 final size:44
Alignment explanation
Indices: 19891--20014 Score: 131
Period size: 44 Copynumber: 2.8 Consensus size: 44
19881 ATAATCTTTT
* * ** * *
19891 TATGAAAATTTGGTAACCTTTGTATGAAATTTTGATAACTACAC
1 TATGAAATTTTGATAACCTTCATATGAAATTTTGGTAACCACAC
* * **
19935 AATGAAGTTTTGATAATTTTCATATGAAATTTTGGTAACCACAC
1 TATGAAATTTTGATAACCTTCATATGAAATTTTGGTAACCACAC
** *
19979 TATGAAATTTTGATAACCTTCCCATGTAATTTTGGT
1 TATGAAATTTTGATAACCTTCATATGAAATTTTGGT
20015 TTGATTGTCA
Statistics
Matches: 63, Mismatches: 17, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
44 63 1.00
ACGTcount: A:0.34, C:0.12, G:0.14, T:0.40
Consensus pattern (44 bp):
TATGAAATTTTGATAACCTTCATATGAAATTTTGGTAACCACAC
Found at i:20012 original size:66 final size:65
Alignment explanation
Indices: 19851--20012 Score: 150
Period size: 66 Copynumber: 2.4 Consensus size: 65
19841 CTTTCGTATA
* * * * ****
19851 AAATTTTGTTAACC-TCCCTAGGAAATTTTAATAATCTTTTTATGAAAATTTGGTAACCTTTGTA
1 AAATTTTGATAACCTTCCC-ATG-AATTTTGATAATCTTTATATGAAAATTTGGTAACCACACTA
19915 TG
64 TG
* * *
19917 AAATTTTGATAA-CTACACAATGAAGTTTTGATAAT-TTTCATATGAAATTTTGGTAACCACACT
1 AAATTTTGATAACCTTC-CCATGAA-TTTTGATAATCTTT-ATATGAAAATTTGGTAACCACACT
19980 ATG
63 ATG
19983 AAATTTTGATAACCTTCCCATGTAATTTTG
1 AAATTTTGATAACCTTCCCATG-AATTTTG
20013 GTTTGATTGT
Statistics
Matches: 77, Mismatches: 13, Indels: 12
0.75 0.13 0.12
Matches are distributed among these distances:
65 6 0.08
66 65 0.84
67 6 0.08
ACGTcount: A:0.34, C:0.13, G:0.12, T:0.41
Consensus pattern (65 bp):
AAATTTTGATAACCTTCCCATGAATTTTGATAATCTTTATATGAAAATTTGGTAACCACACTATG
Found at i:21696 original size:5 final size:5
Alignment explanation
Indices: 21686--21729 Score: 65
Period size: 5 Copynumber: 9.2 Consensus size: 5
21676 GTATATATAG
*
21686 TAAGA TAAGA TAAGA T-AG- TAAGA TAAGA TAAAA TAAGA TAAGA T
1 TAAGA TAAGA TAAGA TAAGA TAAGA TAAGA TAAGA TAAGA TAAGA T
21730 GTTGGTGGTG
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
3 1 0.03
4 4 0.11
5 30 0.86
ACGTcount: A:0.59, C:0.00, G:0.18, T:0.23
Consensus pattern (5 bp):
TAAGA
Found at i:21705 original size:18 final size:17
Alignment explanation
Indices: 21682--21729 Score: 73
Period size: 18 Copynumber: 2.9 Consensus size: 17
21672 TTTTGTATAT
21682 ATAGTAAGATAAGATAA
1 ATAGTAAGATAAGATAA
21699 GATAGTAAGATAAGATAA
1 -ATAGTAAGATAAGATAA
21717 A-A-TAAGATAAGAT
1 ATAGTAAGATAAGAT
21730 GTTGGTGGTG
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
15 11 0.37
16 1 0.03
17 1 0.03
18 17 0.57
ACGTcount: A:0.58, C:0.00, G:0.19, T:0.23
Consensus pattern (17 bp):
ATAGTAAGATAAGATAA
Done.