Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021597.1 Corchorus olitorius cultivar O-4 contig21630, 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: 21551
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.30
Found at i:184 original size:73 final size:71
Alignment explanation
Indices: 43--184 Score: 205
Period size: 73 Copynumber: 2.0 Consensus size: 71
33 TCCCAAAAAA
* * *
43 ATAAAATAAATATGGGGCGTTTTCAACATCAGACGCCCCCATTTAGCGGCGTTTTCGATGGAAGC
1 ATAAAATAAATATGGGGCGTTTCCAACATCAGACGCCCCCATTTAGCGGCGTTTTCGATAGAAAC
108 GCCGTT
66 GCCGTT
* *
114 ATAAAATAAAATTTGGCGGCGTTTCCAGCATCAGACGCCCCCATTTAGCGGCGTTTT-GAGTAGA
1 ATAAAAT-AAATATGG-GGCGTTTCCAACATCAGACGCCCCCATTTAGCGGCGTTTTCGA-TAGA
178 AACGCCG
63 AACGCCG
185 CAATATTTTA
Statistics
Matches: 63, Mismatches: 5, Indels: 4
0.88 0.07 0.06
Matches are distributed among these distances:
71 7 0.11
72 9 0.14
73 47 0.75
ACGTcount: A:0.27, C:0.23, G:0.24, T:0.25
Consensus pattern (71 bp):
ATAAAATAAATATGGGGCGTTTCCAACATCAGACGCCCCCATTTAGCGGCGTTTTCGATAGAAAC
GCCGTT
Found at i:1875 original size:21 final size:22
Alignment explanation
Indices: 1850--1898 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
1840 GCATTTATGT
*
1850 CATTTTCT-AATTCACTTTTGG
1 CATTTACTAAATTCACTTTTGG
* *
1871 CATTTAGTAAATTCACTTTTTG
1 CATTTACTAAATTCACTTTTGG
1893 CATTTA
1 CATTTA
1899 GTATAACATA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 6 0.25
22 18 0.75
ACGTcount: A:0.24, C:0.16, G:0.08, T:0.51
Consensus pattern (22 bp):
CATTTACTAAATTCACTTTTGG
Found at i:1884 original size:22 final size:22
Alignment explanation
Indices: 1858--1901 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
1848 GTCATTTTCT
1858 AATTCACTTTTGGCATTTAGTA
1 AATTCACTTTTGGCATTTAGTA
*
1880 AATTCACTTTTTGCATTTAGTA
1 AATTCACTTTTGGCATTTAGTA
1902 TAACATAACA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.27, C:0.14, G:0.11, T:0.48
Consensus pattern (22 bp):
AATTCACTTTTGGCATTTAGTA
Found at i:5578 original size:15 final size:15
Alignment explanation
Indices: 5522--5606 Score: 79
Period size: 15 Copynumber: 5.9 Consensus size: 15
5512 TATAATGAAG
5522 GAGTAATCAGTAAAA
1 GAGTAATCAGTAAAA
*
5537 TG-GTAAT-GGT-AAA
1 -GAGTAATCAGTAAAA
* ** *
5550 GAGCAAAGAATAAAA
1 GAGTAATCAGTAAAA
5565 GAGTAATCAGTAAAA
1 GAGTAATCAGTAAAA
*
5580 TAGTAATCAGTAAAA
1 GAGTAATCAGTAAAA
5595 GAGTAAT-AGTAA
1 GAGTAATCAGTAA
5607 TCAGTAAAGA
Statistics
Matches: 55, Mismatches: 11, Indels: 8
0.74 0.15 0.11
Matches are distributed among these distances:
12 1 0.02
13 6 0.11
14 8 0.15
15 39 0.71
16 1 0.02
ACGTcount: A:0.53, C:0.05, G:0.21, T:0.21
Consensus pattern (15 bp):
GAGTAATCAGTAAAA
Found at i:5603 original size:21 final size:20
Alignment explanation
Indices: 5578--5620 Score: 77
Period size: 21 Copynumber: 2.1 Consensus size: 20
5568 TAATCAGTAA
5578 AATAGTAATCAGTAAAAGAGT
1 AATAGTAATCAGT-AAAGAGT
5599 AATAGTAATCAGTAAAGAGT
1 AATAGTAATCAGTAAAGAGT
5619 AA
1 AA
5621 AAATGGTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 9 0.41
21 13 0.59
ACGTcount: A:0.53, C:0.05, G:0.19, T:0.23
Consensus pattern (20 bp):
AATAGTAATCAGTAAAGAGT
Found at i:5616 original size:50 final size:46
Alignment explanation
Indices: 5522--5651 Score: 126
Period size: 50 Copynumber: 2.8 Consensus size: 46
5512 TATAATGAAG
* * *
5522 GAGTAATCAGTAAAATGGTAAT-GGT-AAAGAGCAA-AGAATAAAA
1 GAGTAATCAGTAAAATAGTAATCAGTAAAAGAGTAATAGAATAAAA
5565 GAGTAATCAGTAAAATAGTAATCAGTAAAAGAGTAATAGTAATCAGTAAA
1 GAGTAATCAGTAAAATAGTAATCAGTAAAAGAGTAATAG-AAT-A--AAA
**
5615 GAGTAAAAATGGT--AATAGTAATCAGTAAAAGAGTAAT
1 GAGTAATCA--GTAAAATAGTAATCAGTAAAAGAGTAAT
5652 CAAAGAGTAA
Statistics
Matches: 73, Mismatches: 5, Indels: 11
0.82 0.06 0.12
Matches are distributed among these distances:
43 21 0.29
44 2 0.03
45 8 0.11
46 2 0.03
47 3 0.04
48 1 0.01
50 34 0.47
52 2 0.03
ACGTcount: A:0.52, C:0.05, G:0.21, T:0.22
Consensus pattern (46 bp):
GAGTAATCAGTAAAATAGTAATCAGTAAAAGAGTAATAGAATAAAA
Found at i:5623 original size:29 final size:29
Alignment explanation
Indices: 5561--5668 Score: 105
Period size: 29 Copynumber: 3.6 Consensus size: 29
5551 AGCAAAGAAT
**
5561 AAAAGAGTAATCAGTAAAAT-AGTAATCAGT-
1 AAAAGAGTAAT-AGT--AATCAGTAAAGAGTA
5591 AAAAGAGTAATAGTAATCAGTAAAGAGTA
1 AAAAGAGTAATAGTAATCAGTAAAGAGTA
5620 AAAATG-GTAATAGTAATCAGTAAAAGAGTA
1 AAAA-GAGTAATAGTAATCAGT-AAAGAGTA
5650 ATCAAAGAGTAATTAGTAA
1 A--AAAGAGTAA-TAGTAA
5669 AAGGGTAATG
Statistics
Matches: 68, Mismatches: 2, Indels: 13
0.82 0.02 0.16
Matches are distributed among these distances:
27 3 0.04
28 8 0.12
29 22 0.32
30 21 0.31
31 1 0.01
32 7 0.10
33 6 0.09
ACGTcount: A:0.54, C:0.05, G:0.19, T:0.23
Consensus pattern (29 bp):
AAAAGAGTAATAGTAATCAGTAAAGAGTA
Found at i:5736 original size:15 final size:16
Alignment explanation
Indices: 5718--5758 Score: 61
Period size: 15 Copynumber: 2.8 Consensus size: 16
5708 AAATGTTAAT
5718 AGTAATCAGTAAAA-G
1 AGTAATCAGTAAAATG
5733 AGTAATCAGTAAAATG
1 AGTAATCAGTAAAATG
5749 -GTAA-CAGTAA
1 AGTAATCAGTAA
5759 TTCAGGGTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.24
15 18 0.72
16 1 0.04
ACGTcount: A:0.51, C:0.07, G:0.20, T:0.22
Consensus pattern (16 bp):
AGTAATCAGTAAAATG
Found at i:5797 original size:21 final size:21
Alignment explanation
Indices: 5768--5848 Score: 92
Period size: 21 Copynumber: 3.8 Consensus size: 21
5758 ATTCAGGGTA
*
5768 AATAATAATCAGTAAAAGAGT
1 AATAGTAATCAGTAAAAGAGT
5789 AATAGTAATCAGT-AAAGAGT
1 AATAGTAATCAGTAAAAGAGT
* *
5809 AAAAATGGTAATTAGTAAAAGAGT
1 ---AATAGTAATCAGTAAAAGAGT
*
5833 AATAGAAATCAGTAAA
1 AATAGTAATCAGTAAA
5849 TAGTAAAAAT
Statistics
Matches: 50, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
20 7 0.14
21 25 0.50
23 11 0.22
24 7 0.14
ACGTcount: A:0.56, C:0.04, G:0.17, T:0.23
Consensus pattern (21 bp):
AATAGTAATCAGTAAAAGAGT
Found at i:5866 original size:29 final size:28
Alignment explanation
Indices: 5816--5877 Score: 79
Period size: 29 Copynumber: 2.2 Consensus size: 28
5806 AGTAAAAATG
*
5816 GTAATTAGTAAAAGAGTAATAGAAATCA
1 GTAAATAGTAAAAGAGTAATAGAAATCA
* *
5844 GTAAATAGTAAAAATAGTAATAGTAATCA
1 GTAAATAGT-AAAAGAGTAATAGAAATCA
*
5873 ATAAA
1 GTAAA
5878 AGAGTAATCA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
28 8 0.28
29 21 0.72
ACGTcount: A:0.56, C:0.03, G:0.15, T:0.26
Consensus pattern (28 bp):
GTAAATAGTAAAAGAGTAATAGAAATCA
Found at i:5984 original size:15 final size:15
Alignment explanation
Indices: 5925--5992 Score: 50
Period size: 15 Copynumber: 4.7 Consensus size: 15
5915 AATTCAGAGT
*
5925 AAAGAGTAATCAGTA
1 AAAGAGTAATCAATA
*
5940 AAAGAGTAAT-ATTA
1 AAAGAGTAATCAATA
** **
5954 ATCG-GTAAAGAATA
1 AAAGAGTAATCAATA
*
5968 AAAGAGTAATCACTA
1 AAAGAGTAATCAATA
*
5983 AAAGGGTAAT
1 AAAGAGTAAT
5993 GGTAACCATT
Statistics
Matches: 40, Mismatches: 11, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
13 4 0.10
14 10 0.25
15 26 0.65
ACGTcount: A:0.53, C:0.06, G:0.19, T:0.22
Consensus pattern (15 bp):
AAAGAGTAATCAATA
Found at i:6043 original size:10 final size:9
Alignment explanation
Indices: 6014--6052 Score: 53
Period size: 9 Copynumber: 4.3 Consensus size: 9
6004 ATTAAAATTC
6014 AAAGAGTAA
1 AAAGAGTAA
6023 AAATG-GTAA
1 AAA-GAGTAA
*
6032 AAAGATTAA
1 AAAGAGTAA
6041 AAAGAGTAA
1 AAAGAGTAA
6050 AAA
1 AAA
6053 TGGTATTCAG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
8 1 0.04
9 24 0.92
10 1 0.04
ACGTcount: A:0.67, C:0.00, G:0.18, T:0.15
Consensus pattern (9 bp):
AAAGAGTAA
Found at i:6125 original size:34 final size:34
Alignment explanation
Indices: 6039--6146 Score: 175
Period size: 34 Copynumber: 3.2 Consensus size: 34
6029 TAAAAAGATT
6039 AAAAAGAGTAAAAATGGTATTCAGTAATTAAAGT-
1 AAAAAG-GTAAAAATGGTATTCAGTAATTAAAGTA
* *
6073 AAAAA-TTAAAAATAGTATTCAGTAATTAAAGTA
1 AAAAAGGTAAAAATGGTATTCAGTAATTAAAGTA
6106 AAAAAGGTAAAAATGGTATTCAGTAATTAAAGTA
1 AAAAAGGTAAAAATGGTATTCAGTAATTAAAGTA
6140 AAAAAGG
1 AAAAAGG
6147 GCAAAAAAAT
Statistics
Matches: 68, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
32 25 0.37
33 5 0.07
34 38 0.56
ACGTcount: A:0.56, C:0.03, G:0.16, T:0.26
Consensus pattern (34 bp):
AAAAAGGTAAAAATGGTATTCAGTAATTAAAGTA
Found at i:6167 original size:37 final size:34
Alignment explanation
Indices: 6092--6173 Score: 92
Period size: 34 Copynumber: 2.3 Consensus size: 34
6082 AAATAGTATT
* * **
6092 CAGTAATTAAAGTAAAAAAGGTAAAAATGGTATT
1 CAGTAATTAAAGTAAAAAAGGAAAAAATGGAAAC
6126 CAGTAATTAAAGTAAAAAAGGGCAAAAAAATGGAAAC
1 CAGTAATTAAAGTAAAAAA-GG--AAAAAATGGAAAC
*
6163 CAGTAAATAAA
1 CAGTAATTAAA
6174 AAAGAGTAAG
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
34 19 0.47
35 2 0.05
37 19 0.47
ACGTcount: A:0.57, C:0.06, G:0.17, T:0.20
Consensus pattern (34 bp):
CAGTAATTAAAGTAAAAAAGGAAAAAATGGAAAC
Found at i:6220 original size:26 final size:27
Alignment explanation
Indices: 6170--6236 Score: 82
Period size: 26 Copynumber: 2.5 Consensus size: 27
6160 AACCAGTAAA
*
6170 TAAAAAAGAGTAAGAAGATGATAATAAG
1 TAAAAAA-AGTAAGAAAATGATAATAAG
* *
6198 TAAAAAAAGTAA-AAAATGGTAATCAG
1 TAAAAAAAGTAAGAAAATGATAATAAG
*
6224 TAAAAAGAGTAAG
1 TAAAAAAAGTAAG
6237 GGTAATCAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
26 22 0.65
27 5 0.15
28 7 0.21
ACGTcount: A:0.61, C:0.01, G:0.19, T:0.18
Consensus pattern (27 bp):
TAAAAAAAGTAAGAAAATGATAATAAG
Found at i:12895 original size:31 final size:31
Alignment explanation
Indices: 12860--12958 Score: 121
Period size: 31 Copynumber: 3.3 Consensus size: 31
12850 CTTATTAAAT
* *
12860 GCTCAATTTGGTCATAAACTTTTGAGCGATC
1 GCTCAATTTGGTCCTAAACCTTTGAGCGATC
* * *
12891 GCTCAATTTGGTCCTAAACCTTTAAAC-CT-
1 GCTCAATTTGGTCCTAAACCTTTGAGCGATC
* *
12920 GCTCAATTTAGTCCTAAACCTTTGAGTGATC
1 GCTCAATTTGGTCCTAAACCTTTGAGCGATC
12951 GCTCAATT
1 GCTCAATT
12959 CAGTCCTATT
Statistics
Matches: 56, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
29 23 0.41
30 2 0.04
31 31 0.55
ACGTcount: A:0.26, C:0.23, G:0.15, T:0.35
Consensus pattern (31 bp):
GCTCAATTTGGTCCTAAACCTTTGAGCGATC
Found at i:21469 original size:2 final size:2
Alignment explanation
Indices: 21462--21537 Score: 143
Period size: 2 Copynumber: 37.5 Consensus size: 2
21452 GAACGTGAGC
21462 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
21504 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GTA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G-A GA G
21538 TAGTAGTAGT
Statistics
Matches: 73, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 71 0.97
3 2 0.03
ACGTcount: A:0.49, C:0.00, G:0.50, T:0.01
Consensus pattern (2 bp):
GA
Done.