Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016934.1 Corchorus olitorius cultivar O-4 contig16967, 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: 62963
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:7997 original size:11 final size:10
Alignment explanation
Indices: 7930--7994 Score: 57
Period size: 10 Copynumber: 6.8 Consensus size: 10
7920 TTTTAATCAT
*
7930 TAATTATTAA
1 TAATAATTAA
*
7940 TTATAATTAA
1 TAATAATTAA
*
7950 TAATAA-CAA
1 TAATAATTAA
*
7959 T-TTAAATTAA
1 TAAT-AATTAA
7969 TAATAATT-A
1 TAATAATTAA
7978 -AATAATTAA
1 TAATAATTAA
7987 TAATAATT
1 TAATAATT
7995 TAAAAAAAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 10
0.72 0.12 0.17
Matches are distributed among these distances:
8 8 0.19
9 7 0.16
10 27 0.63
11 1 0.02
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (10 bp):
TAATAATTAA
Found at i:8573 original size:2 final size:2
Alignment explanation
Indices: 8566--8598 Score: 57
Period size: 2 Copynumber: 16.0 Consensus size: 2
8556 CTGGTGAATG
8566 AT AT AT AT AT AT AT AT AT AT AT AT AT AT GAT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT
8599 TCTACAATCT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 28 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:9494 original size:33 final size:33
Alignment explanation
Indices: 9447--9511 Score: 112
Period size: 33 Copynumber: 2.0 Consensus size: 33
9437 GATGAGGCGG
* *
9447 CATATCACATATTATATGTAGAAGTTACATCAT
1 CATACCACATATTATATGTACAAGTTACATCAT
9480 CATACCACATATTATATGTACAAGTTACATCA
1 CATACCACATATTATATGTACAAGTTACATCA
9512 ACTAATTAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.18, G:0.08, T:0.34
Consensus pattern (33 bp):
CATACCACATATTATATGTACAAGTTACATCAT
Found at i:10006 original size:22 final size:22
Alignment explanation
Indices: 9978--10087 Score: 103
Period size: 22 Copynumber: 4.7 Consensus size: 22
9968 ATTATGCTAT
9978 TATATATAAAATATATTTATGA
1 TATATATAAAATATATTTATGA
*
10000 TATATATAAAATATATTTAATTA
1 TATATATAAAATATATTT-ATGA
* * * *
10023 TTTATGATGTATAAAAAATATATGTAA
1 --TAT-A--TATAAAATATATTTATGA
* *
10050 AATATATAAATTATATTTATGA
1 TATATATAAAATATATTTATGA
10072 TATATATAAAATATAT
1 TATATATAAAATATAT
10088 ATAACAAAAT
Statistics
Matches: 69, Mismatches: 13, Indels: 12
0.73 0.14 0.13
Matches are distributed among these distances:
22 45 0.65
23 3 0.04
24 1 0.01
25 5 0.07
26 1 0.01
27 2 0.03
28 12 0.17
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.45
Consensus pattern (22 bp):
TATATATAAAATATATTTATGA
Found at i:10088 original size:11 final size:11
Alignment explanation
Indices: 9978--10091 Score: 67
Period size: 11 Copynumber: 10.8 Consensus size: 11
9968 ATTATGCTAT
9978 TATATATAAAA
1 TATATATAAAA
* **
9989 TATATTTATGA
1 TATATATAAAA
10000 TATATATAAAA
1 TATATATAAAA
*
10011 TATAT-T-TAA
1 TATATATAAAA
* **
10020 T-TATTTATGA
1 TATATATAAAA
* *
10030 TGTATAAAAAA
1 TATATATAAAA
*
10041 TATATGT-AAA
1 TATATATAAAA
*
10051 -ATATATAAAT
1 TATATATAAAA
* **
10061 TATATTTATGA
1 TATATATAAAA
10072 TATATATAAAA
1 TATATATAAAA
10083 TATATATAA
1 TATATATAA
10092 CAAAATTTTT
Statistics
Matches: 74, Mismatches: 24, Indels: 10
0.69 0.22 0.09
Matches are distributed among these distances:
8 3 0.04
9 9 0.12
10 9 0.12
11 53 0.72
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (11 bp):
TATATATAAAA
Found at i:10162 original size:20 final size:20
Alignment explanation
Indices: 10128--10176 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
10118 AATATTATTT
10128 AAAACCG-CC-AAACCGCCA
1 AAAACCGACCGAAACCGCCA
*
10146 AAAATCGACCGAAACCGCCA
1 AAAACCGACCGAAACCGCCA
10166 AAAACCGACCG
1 AAAACCGACCG
10177 CCTCGGTTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
18 6 0.22
19 2 0.07
20 19 0.70
ACGTcount: A:0.45, C:0.39, G:0.14, T:0.02
Consensus pattern (20 bp):
AAAACCGACCGAAACCGCCA
Found at i:11057 original size:16 final size:16
Alignment explanation
Indices: 11036--11070 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
11026 TCAAGAAAGG
11036 AATTTAATCATGTAAA
1 AATTTAATCATGTAAA
11052 AATTTAATCATGTAAA
1 AATTTAATCATGTAAA
11068 AAT
1 AAT
11071 ATAGAGTAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.51, C:0.06, G:0.06, T:0.37
Consensus pattern (16 bp):
AATTTAATCATGTAAA
Found at i:13795 original size:17 final size:17
Alignment explanation
Indices: 13756--13799 Score: 61
Period size: 17 Copynumber: 2.6 Consensus size: 17
13746 ATAATAACGT
*
13756 TATAAGATATATAAATA
1 TATAAGAAATATAAATA
* *
13773 TGTAAGAAATATAAATG
1 TATAAGAAATATAAATA
13790 TATAAGAAAT
1 TATAAGAAAT
13800 CAAAAGATTA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.57, C:0.00, G:0.11, T:0.32
Consensus pattern (17 bp):
TATAAGAAATATAAATA
Found at i:13986 original size:2 final size:2
Alignment explanation
Indices: 13979--14011 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
13969 TGACAAAGTA
13979 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
14012 CGTGAATCAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:18600 original size:16 final size:16
Alignment explanation
Indices: 18579--18613 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
18569 TCAAGAAAGG
*
18579 AATTTAATCATGTAAA
1 AATTTAACCATGTAAA
18595 AATTTAACCATGTAAA
1 AATTTAACCATGTAAA
18611 AAT
1 AAT
18614 ATAGAGTAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.51, C:0.09, G:0.06, T:0.34
Consensus pattern (16 bp):
AATTTAACCATGTAAA
Found at i:18814 original size:17 final size:17
Alignment explanation
Indices: 18775--18818 Score: 61
Period size: 17 Copynumber: 2.6 Consensus size: 17
18765 ATAATAACGT
*
18775 TATAAGATATATAAATC
1 TATAAGAAATATAAATC
* *
18792 TGTAAGAAATATAAATG
1 TATAAGAAATATAAATC
18809 TATAAGAAAT
1 TATAAGAAAT
18819 CAAAAGATTA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.55, C:0.02, G:0.11, T:0.32
Consensus pattern (17 bp):
TATAAGAAATATAAATC
Found at i:18909 original size:17 final size:18
Alignment explanation
Indices: 18887--18922 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
18877 TTCCTTGTTT
*
18887 CAAGTAGACTA-TTTGTA
1 CAAGTAGAATATTTTGTA
18904 CAAGTAGAATATTTTGTA
1 CAAGTAGAATATTTTGTA
18922 C
1 C
18923 TTTGAAACAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.36, C:0.11, G:0.17, T:0.36
Consensus pattern (18 bp):
CAAGTAGAATATTTTGTA
Found at i:24909 original size:14 final size:16
Alignment explanation
Indices: 24874--24915 Score: 52
Period size: 14 Copynumber: 2.8 Consensus size: 16
24864 TAAAGTTTGG
*
24874 ATTCAGTACTTACAAT
1 ATTCAGTACTTACAAA
24890 ATTCAGTA-TTA-AAA
1 ATTCAGTACTTACAAA
*
24904 ATTCAGTGCTTA
1 ATTCAGTACTTA
24916 ATCTTTCAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
14 9 0.39
15 6 0.26
16 8 0.35
ACGTcount: A:0.38, C:0.14, G:0.10, T:0.38
Consensus pattern (16 bp):
ATTCAGTACTTACAAA
Found at i:28127 original size:26 final size:26
Alignment explanation
Indices: 28098--28147 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
28088 ACTATATAGC
*
28098 TTTTTAAGT-AATTTTAAATAAGAAT
1 TTTTTAAATCAATTTTAAATAAGAAT
*
28123 TTTTTAAATCAATTTTAAATTAGAA
1 TTTTTAAATCAATTTTAAATAAGAA
28148 AATTGACTAC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 8 0.36
26 14 0.64
ACGTcount: A:0.44, C:0.02, G:0.06, T:0.48
Consensus pattern (26 bp):
TTTTTAAATCAATTTTAAATAAGAAT
Found at i:29715 original size:30 final size:29
Alignment explanation
Indices: 29653--29722 Score: 86
Period size: 29 Copynumber: 2.4 Consensus size: 29
29643 ACCGAACCGT
* ****
29653 CAAATAAGCCCCTGAACTTTTATTTCGGC
1 CAAATAAGCCCCTGAACTTTAAAAAAGGC
29682 CAAATAAGCCCCTGAACTCTTAAAAAAGGC
1 CAAATAAGCCCCTGAACT-TTAAAAAAGGC
29712 CAAATAAGCCC
1 CAAATAAGCCC
29723 TGTTGCCAAG
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
29 18 0.51
30 17 0.49
ACGTcount: A:0.37, C:0.29, G:0.13, T:0.21
Consensus pattern (29 bp):
CAAATAAGCCCCTGAACTTTAAAAAAGGC
Found at i:35101 original size:21 final size:21
Alignment explanation
Indices: 35076--35125 Score: 100
Period size: 21 Copynumber: 2.4 Consensus size: 21
35066 ATTTCGTGGC
35076 CCTGATGTTAAGAATCCAAGT
1 CCTGATGTTAAGAATCCAAGT
35097 CCTGATGTTAAGAATCCAAGT
1 CCTGATGTTAAGAATCCAAGT
35118 CCTGATGT
1 CCTGATGT
35126 CAGAAGGCCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30
Consensus pattern (21 bp):
CCTGATGTTAAGAATCCAAGT
Found at i:36671 original size:33 final size:33
Alignment explanation
Indices: 36629--36697 Score: 111
Period size: 33 Copynumber: 2.1 Consensus size: 33
36619 TTGGGTCTTA
* *
36629 TTTGATAATAATCCTCCACATACGTGGATATTC
1 TTTGATAATAATACTCCACATACATGGATATTC
*
36662 TTTGATAATAATACTCCACATACATGGATCTTC
1 TTTGATAATAATACTCCACATACATGGATATTC
36695 TTT
1 TTT
36698 CAATGTTCTT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.30, C:0.20, G:0.10, T:0.39
Consensus pattern (33 bp):
TTTGATAATAATACTCCACATACATGGATATTC
Found at i:39535 original size:33 final size:33
Alignment explanation
Indices: 39493--39602 Score: 157
Period size: 33 Copynumber: 3.3 Consensus size: 33
39483 TAATCCTCTT
* * *
39493 TGGATCTTCTTTGATAATAATCATTCACATATG
1 TGGATCTTCTTTGATAATAATCCTCCACATACG
* *
39526 TGGATCTTCTTTGATGATAATCCTCCAGAATACG
1 TGGATCTTCTTTGATAATAATCCTCCA-CATACG
*
39560 TGGATCTTCTTTAATAATAATCCTCCACATACG
1 TGGATCTTCTTTGATAATAATCCTCCACATACG
39593 TGGATCTTCT
1 TGGATCTTCT
39603 GGAGACTTTA
Statistics
Matches: 68, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
33 39 0.57
34 29 0.43
ACGTcount: A:0.27, C:0.20, G:0.14, T:0.39
Consensus pattern (33 bp):
TGGATCTTCTTTGATAATAATCCTCCACATACG
Found at i:44633 original size:179 final size:177
Alignment explanation
Indices: 44321--44658 Score: 473
Period size: 179 Copynumber: 1.9 Consensus size: 177
44311 TTCTACCATA
* * ** * *
44321 AGCACAAATTATGTAATATTAAGTAGACCGTCTATTTTCGTTAACCGAAACAACTAATTTTTAGA
1 AGCAAAAATTATATAATATTAAGTAGACCGTCTATTCCCGTTAACCGAAACAACAAATTTTCAGA
*
44386 AGCAATTTTTATACCTCGAACGTTAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTAGATCATG
66 AGCAATTTTTATACCTCGAACATTAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTAGATCATG
* *
44451 GAACAACCTTTCAAGAGATACTTGAATCATCTCAATTAGACATCTGG
131 GAACAACCTTTCAAGAGACACTTAAATCATCTCAATTAGACATCTGG
* *
44498 AGCAAAAAGTTATATAATATTAAGTGGACCGTCTATTCCCGTTAACCGAAACAACAAATGTTTCG
1 AGCAAAAA-TTATATAATATTAAGTAGACCGTCTATTCCCGTTAACCGAAACAACAAAT-TTTCA
* *
44563 GAAGC-ATTTTTGAT-TCTTGAAACATTAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTAGAT
64 GAAGCAATTTTT-ATACCTCG-AACATTAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTAGAT
* * * *
44626 GATGGAACAATCTTTTAATAGACACTTAAATCA
127 CATGGAACAACCTTTCAAGAGACACTTAAATCA
44659 CTTTAATCGG
Statistics
Matches: 140, Mismatches: 17, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
177 7 0.05
178 54 0.39
179 79 0.56
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Consensus pattern (177 bp):
AGCAAAAATTATATAATATTAAGTAGACCGTCTATTCCCGTTAACCGAAACAACAAATTTTCAGA
AGCAATTTTTATACCTCGAACATTAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTAGATCATG
GAACAACCTTTCAAGAGACACTTAAATCATCTCAATTAGACATCTGG
Found at i:45177 original size:131 final size:131
Alignment explanation
Indices: 45035--45303 Score: 405
Period size: 131 Copynumber: 2.1 Consensus size: 131
45025 TGCCATTGTT
45035 TATATTTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATATAATATCCTTAT
1 TATATTTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATATAATATCCTTAT
*** * * * *
45100 AACTA-TTTAGTTTTTACCATTTTACTATTTTAATTAAAAAAATTATATATATTAGAATTTTTTA
66 AACTATTTTA-TTTTTACCAAAGTACTAATTTAATTAAAAAAATTAGATATATTAGAATTTCTAA
45164 AA
130 AA
* *
45166 TATATTTTTATAGTTTTACTCAACTAAAACCTCTATTTTTATTTAATTAAATCTAATATCCTTAT
1 TATATTTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATATAATATCCTTAT
* * * *
45231 ACCTATTTTATTTTTATCAAAGTACTAATTTAATTAAAAAACTTAGATATATTATAATTTCTAAA
66 AACTATTTTATTTTTACCAAAGTACTAATTTAATTAAAAAAATTAGATATATTAGAATTTCTAAA
45296 A
131 A
45297 TATATTT
1 TATATTT
45304 CTTAAATGAC
Statistics
Matches: 124, Mismatches: 13, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
131 120 0.97
132 4 0.03
ACGTcount: A:0.39, C:0.10, G:0.02, T:0.49
Consensus pattern (131 bp):
TATATTTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATATAATATCCTTAT
AACTATTTTATTTTTACCAAAGTACTAATTTAATTAAAAAAATTAGATATATTAGAATTTCTAAA
A
Found at i:46283 original size:31 final size:31
Alignment explanation
Indices: 46245--46304 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
46235 TTCTCAGATC
* *
46245 ATTCGGGTTTCGGCTCAT-CTGGATTTAGGTT
1 ATTCGGGTCTCGGATC-TGCTGGATTTAGGTT
46276 ATTCGGGTCTCGGATCTGCTGGATTTAGG
1 ATTCGGGTCTCGGATCTGCTGGATTTAGG
46305 GTCATGCAGG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 1 0.04
31 25 0.96
ACGTcount: A:0.13, C:0.17, G:0.32, T:0.38
Consensus pattern (31 bp):
ATTCGGGTCTCGGATCTGCTGGATTTAGGTT
Found at i:46526 original size:21 final size:22
Alignment explanation
Indices: 46502--46542 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
46492 GTTTATAATA
*
46502 TTCTTGGGTCA-TCGGGTTATC
1 TTCTCGGGTCATTCGGGTTATC
*
46523 TTCTCGGGTTATTCGGGTTA
1 TTCTCGGGTCATTCGGGTTA
46543 CGAGTTTGTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.10, C:0.17, G:0.29, T:0.44
Consensus pattern (22 bp):
TTCTCGGGTCATTCGGGTTATC
Found at i:47153 original size:10 final size:10
Alignment explanation
Indices: 47135--47189 Score: 92
Period size: 10 Copynumber: 5.5 Consensus size: 10
47125 ATACCTCGAT
47135 ATATCTGTAA
1 ATATCTGTAA
*
47145 ATATTTGTAA
1 ATATCTGTAA
47155 ATATCTGTAA
1 ATATCTGTAA
*
47165 ATATCTGCAA
1 ATATCTGTAA
47175 ATATCTGTAA
1 ATATCTGTAA
47185 ATATC
1 ATATC
47190 CATATCAAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 41 1.00
ACGTcount: A:0.40, C:0.11, G:0.09, T:0.40
Consensus pattern (10 bp):
ATATCTGTAA
Found at i:55163 original size:12 final size:12
Alignment explanation
Indices: 55146--55170 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
55136 TCGACCCTGG
55146 CGAAGCTTAATT
1 CGAAGCTTAATT
55158 CGAAGCTTAATT
1 CGAAGCTTAATT
55170 C
1 C
55171 ATGATCCAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (12 bp):
CGAAGCTTAATT
Found at i:59267 original size:12 final size:13
Alignment explanation
Indices: 59245--59274 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
59235 ACTAGCAATT
59245 AAAATCAATCAAG
1 AAAATCAATCAAG
59258 AAAA-CAATCAAG
1 AAAATCAATCAAG
59270 AAAAT
1 AAAAT
59275 TAAAGAAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.67, C:0.13, G:0.07, T:0.13
Consensus pattern (13 bp):
AAAATCAATCAAG
Done.