Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013236.1 Corchorus olitorius cultivar O-4 contig13269, 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: 10471
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.33
Found at i:108 original size:54 final size:54
Alignment explanation
Indices: 1--353 Score: 311
Period size: 54 Copynumber: 6.6 Consensus size: 54
* * * *
1 ACTCTGATCATCGGAAACTTCTT-GAACGACCACACTGGATCATCT-AGAGATCA
1 ACTCTGATCTTCGAAAACTTCTTGGAATGACCACACCGGATCATCTGA-AGATCA
* *
54 ACTCTGATCTTCGAAAACTTCTTGAAATGACCATACCGGATCATCTGAAGATCA
1 ACTCTGATCTTCGAAAACTTCTTGGAATGACCACACCGGATCATCTGAAGATCA
* * * * * *
108 ACTCTGATCTTCGAAAATTTCTTGAAACGACAACACCGGATCATCGGGAGATCA
1 ACTCTGATCTTCGAAAACTTCTTGGAATGACCACACCGGATCATCTGAAGATCA
* * * * * * * * *
162 ACTTTGATCTTTGAAAACTTCTAGGAA-GAACCGCACTGGACCTTTTGGAGATCA
1 ACTCTGATCTTCGAAAACTTCTTGGAATG-ACCACACCGGATCATCTGAAGATCA
* * * * * *
216 ACTCTGATCATCAAAAACCTCTTGGAATGACCGCACGGGATCATCTGAGGATCA
1 ACTCTGATCTTCGAAAACTTCTTGGAATGACCACACCGGATCATCTGAAGATCA
* * * * * * **
270 ACTCTGACCATT-GAAAACTTCTTGGAATGACCGCACTGGACCTTTTGGGGATCA
1 ACTCTGATC-TTCGAAAACTTCTTGGAATGACCACACCGGATCATCTGAAGATCA
*
324 ACTCTGACCATT-GAAAACTTCTTGGAATGA
1 ACTCTGATC-TTCGAAAACTTCTTGGAATGA
354 GATCAACTCT
Statistics
Matches: 250, Mismatches: 45, Indels: 9
0.82 0.15 0.03
Matches are distributed among these distances:
53 22 0.09
54 225 0.90
55 3 0.01
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (54 bp):
ACTCTGATCTTCGAAAACTTCTTGGAATGACCACACCGGATCATCTGAAGATCA
Found at i:325 original size:162 final size:162
Alignment explanation
Indices: 47--350 Score: 378
Period size: 162 Copynumber: 1.9 Consensus size: 162
37 GGATCATCTA
* * * *
47 GAGATCAACTCTGATCTTCGAAAACTTCTTGAAATGACCATACCGGATCATCTGAAGATCAACTC
1 GAGATCAACTCTGATCATCAAAAACCTCTTGAAATGACCACACCGGATCATCTGAAGATCAACTC
* * * * * *
112 TGATCTTCGAAAATTTCTTGAAACGACAACACCGGATCATCGGGAGATCAACTTTGATCTTTGAA
66 TGACCTTCGAAAACTTCTTGAAACGACAACACCGGACCATCGGGAGATCAACTCTGACCATTGAA
177 AACTTCTAGGAAGAACCGCACTGGACCTTTTG
131 AACTTCTAGGAAGAACCGCACTGGACCTTTTG
* * * *
209 GAGATCAACTCTGATCATCAAAAACCTCTTGGAATGACCGCACGGGATCATCTGAGGATCAACTC
1 GAGATCAACTCTGATCATCAAAAACCTCTTGAAATGACCACACCGGATCATCTGAAGATCAACTC
* * ** * * *
274 TGACCATT-GAAAACTTCTTGGAATGACCGCACTGGACCTTTTGGG-GATCAACTCTGACCATTG
66 TGACC-TTCGAAAACTTCTTGAAACGACAACACCGGACC-ATCGGGAGATCAACTCTGACCATTG
*
337 AAAACTTCTTGGAA
129 AAAACTTCTAGGAA
351 TGAGATCAAC
Statistics
Matches: 118, Mismatches: 22, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
162 112 0.95
163 6 0.05
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.26
Consensus pattern (162 bp):
GAGATCAACTCTGATCATCAAAAACCTCTTGAAATGACCACACCGGATCATCTGAAGATCAACTC
TGACCTTCGAAAACTTCTTGAAACGACAACACCGGACCATCGGGAGATCAACTCTGACCATTGAA
AACTTCTAGGAAGAACCGCACTGGACCTTTTG
Found at i:353 original size:108 final size:108
Alignment explanation
Indices: 1--350 Score: 395
Period size: 108 Copynumber: 3.2 Consensus size: 108
* *
1 ACTCTGATCATCGGAAACTTCTT-GAACGACCACACTGGATCATCT-AGAGATCAACTCTGATCT
1 ACTCTGATCATCGAAAACTTCTTGGAACGACCACACCGGATCATCTGAGAGATCAACTCTGATCT
* ** * * * * *
64 TCGAAAACTTCTTGAAATGACCATACCGGATCATCTGAAGATCA
66 T-GAAAACTTCTTGGAATGACCGCACTGGACCTTTTGGAGATCA
* * * * * *
108 ACTCTGATCTTCGAAAATTTCTTGAAACGACAACACCGGATCATC-GGGAGATCAACTTTGATCT
1 ACTCTGATCATCGAAAACTTCTTGGAACGACCACACCGGATCATCTGAGAGATCAACTCTGATC-
*
172 TTGAAAACTTCTAGGAA-GAACCGCACTGGACCTTTTGGAGATCA
65 TTGAAAACTTCTTGGAATG-ACCGCACTGGACCTTTTGGAGATCA
* * * * * *
216 ACTCTGATCATCAAAAACCTCTTGGAATGACCGCACGGGATCATCTGAG-GATCAACTCTGACCA
1 ACTCTGATCATCGAAAACTTCTTGGAACGACCACACCGGATCATCTGAGAGATCAACTCTGATC-
*
280 TTGAAAACTTCTTGGAATGACCGCACTGGACCTTTTGGGGATCA
65 TTGAAAACTTCTTGGAATGACCGCACTGGACCTTTTGGAGATCA
* *
324 ACTCTGACCATTGAAAACTTCTTGGAA
1 ACTCTGATCATCGAAAACTTCTTGGAA
351 TGAGATCAAC
Statistics
Matches: 201, Mismatches: 36, Indels: 11
0.81 0.15 0.04
Matches are distributed among these distances:
107 21 0.10
108 175 0.87
109 5 0.02
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (108 bp):
ACTCTGATCATCGAAAACTTCTTGGAACGACCACACCGGATCATCTGAGAGATCAACTCTGATCT
TGAAAACTTCTTGGAATGACCGCACTGGACCTTTTGGAGATCA
Found at i:358 original size:35 final size:35
Alignment explanation
Indices: 319--599 Score: 368
Period size: 35 Copynumber: 7.9 Consensus size: 35
309 ACCTTTTGGG
* ** *
319 GATCAACTCTGACCATTGAAAACTTCTTGGAATGA
1 GATCAACTCTGATCATCAAAAACTTCTTGAAATGA
*
354 GATCAACTCTGATCATAAAAAAAACTTCTTGAAATGA
1 GATCAACTCTGATCAT--CAAAAACTTCTTGAAATGA
391 GATCAACTCTGATCATCAAAAACTTCTTGAAATGA
1 GATCAACTCTGATCATCAAAAACTTCTTGAAATGA
426 GATCAACTCTGATCATCAAAAACTTCTTGAAATGA
1 GATCAACTCTGATCATCAAAAACTTCTTGAAATGA
* *
461 GATCAACTCTGATAAT-AAAAACCTTCTTGAAACGA
1 GATCAACTCTGATCATCAAAAA-CTTCTTGAAATGA
*
496 GATCAACTCTGATCATCAAAAACTTCTTGAAAGGA
1 GATCAACTCTGATCATCAAAAACTTCTTGAAATGA
* * * *
531 GATCAACTCTGATAATAAAAAAACTTCTTGAGAGGA
1 GATCAACTCTGATCAT-CAAAAACTTCTTGAAATGA
* *
567 GATCAACTCAGATC-TCAGAAAGCTTCTATGAAA
1 GATCAACTCTGATCATCA-AAAACTTCT-TGAAA
600 GACCGCACAG
Statistics
Matches: 222, Mismatches: 17, Indels: 13
0.88 0.07 0.05
Matches are distributed among these distances:
34 6 0.03
35 146 0.66
36 38 0.17
37 32 0.14
ACGTcount: A:0.41, C:0.19, G:0.14, T:0.27
Consensus pattern (35 bp):
GATCAACTCTGATCATCAAAAACTTCTTGAAATGA
Found at i:1785 original size:39 final size:39
Alignment explanation
Indices: 1707--1787 Score: 101
Period size: 39 Copynumber: 2.1 Consensus size: 39
1697 ATCTTTTTGA
** * *
1707 AAAACATTTTTTCTCTTTTAAAAAGATTGCACTTTGAGG
1 AAAACATTTTTTCTCTTTTAAAAAGATCACACCTAGAGG
*
1746 AAAACATTTTTT-TCTTTTGAAAAAGATCACGCCTAGAGG
1 AAAACATTTTTTCTCTTTT-AAAAAGATCACACCTAGAGG
1785 AAA
1 AAA
1788 GTTTCATTCC
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
38 6 0.17
39 30 0.83
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.36
Consensus pattern (39 bp):
AAAACATTTTTTCTCTTTTAAAAAGATCACACCTAGAGG
Found at i:1998 original size:20 final size:22
Alignment explanation
Indices: 1966--2011 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 22
1956 CTTTCTTCCA
1966 TCTTTTGCTTTTTCAACT-TTT
1 TCTTTTGCTTTTTCAACTATTT
*
1987 TCTTTT-CTTTTTCAATTATTT
1 TCTTTTGCTTTTTCAACTATTT
2008 TCTT
1 TCTT
2012 CATTTTTCTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 10 0.43
21 13 0.57
ACGTcount: A:0.11, C:0.17, G:0.02, T:0.70
Consensus pattern (22 bp):
TCTTTTGCTTTTTCAACTATTT
Found at i:2403 original size:14 final size:13
Alignment explanation
Indices: 2368--2415 Score: 53
Period size: 14 Copynumber: 3.5 Consensus size: 13
2358 GAAAACCGAT
*
2368 TTTTTGAAAACCC
1 TTTTTGAAAACAC
2381 TTTTCTGAAAACAC
1 TTTT-TGAAAACAC
2395 TTTCTTGAAAAGCA-
1 TTT-TTGAAAA-CAC
2409 TTTTTGA
1 TTTTTGA
2416 CTTTTGAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
13 8 0.26
14 20 0.65
15 3 0.10
ACGTcount: A:0.31, C:0.17, G:0.10, T:0.42
Consensus pattern (13 bp):
TTTTTGAAAACAC
Found at i:4948 original size:8 final size:8
Alignment explanation
Indices: 4935--5160 Score: 91
Period size: 8 Copynumber: 29.2 Consensus size: 8
4925 AAAATTATTA
4935 AAATAAAT
1 AAATAAAT
4943 AAATAAAT
1 AAATAAAT
*
4951 AAGT-AAT
1 AAATAAAT
*
4958 AGATAAAT
1 AAATAAAT
*
4966 ATATAAAT
1 AAATAAAT
4974 AGAA-AAAT
1 A-AATAAAT
* *
4982 AAGTAAAA
1 AAATAAAT
4990 AAAT-AAT
1 AAATAAAT
* *
4997 AGATGAAT
1 AAATAAAT
5005 AAA-AGAAT
1 AAATA-AAT
*
5013 AAATATAT
1 AAATAAAT
*
5021 -AATAGAT
1 AAATAAAT
*
5028 AAATAGAT
1 AAATAAAT
** *
5036 AGGTAAAA
1 AAATAAAT
5044 ATAAT-AAT
1 A-AATAAAT
5052 -AATAAAT
1 AAATAAAT
*
5059 AAATAGAT
1 AAATAAAT
**
5067 -AATAGCT
1 AAATAAAT
*
5074 AAATTAAT
1 AAATAAAT
5082 AAATAAA-
1 AAATAAAT
5089 AAGATAAA-
1 AA-ATAAAT
*
5097 AAGTAAAT
1 AAATAAAT
*
5105 AAATAGAT
1 AAATAAAT
**
5113 -AATAGTT
1 AAATAAAT
* *
5120 CAATTAAT
1 AAATAAAT
5128 AAATAAA-
1 AAATAAAT
5135 AAGATAAAT
1 AA-ATAAAT
**
5144 -TGTAAAT
1 AAATAAAT
5151 AAATAAAT
1 AAATAAAT
5159 AA
1 AA
5161 TAGTTCAATT
Statistics
Matches: 161, Mismatches: 40, Indels: 34
0.69 0.17 0.14
Matches are distributed among these distances:
6 3 0.02
7 45 0.28
8 110 0.68
9 3 0.02
ACGTcount: A:0.65, C:0.01, G:0.08, T:0.26
Consensus pattern (8 bp):
AAATAAAT
Found at i:4965 original size:27 final size:26
Alignment explanation
Indices: 4935--5162 Score: 65
Period size: 27 Copynumber: 8.8 Consensus size: 26
4925 AAAATTATTA
4935 AAATAAATAAATAAATAAGTAATAGAT
1 AAATAAATAAATAAATAA-TAATAGAT
* *
4962 AAATATATAAATAGA-AA-AATA-AGT
1 AAATAAATAAATAAATAATAATAGA-T
* * *
4986 AAAAAAAT-AATAGATGAATAAAAGAAT
1 AAATAAATAAATAAAT-AATAATAG-AT
* *
5013 AAATATAT-AATAGAT-A-AATAGAT
1 AAATAAATAAATAAATAATAATAGAT
** *
5036 AGGT-AA-AAAT-AATAATAATAAAT
1 AAATAAATAAATAAATAATAATAGAT
* *
5059 AAATAGATAATAGCTAAAT--TAATAAAT
1 AAATAAATAA-A--TAAATAATAATAGAT
*
5086 AAA-AAGATAAA-AAGTAAATAAATAGAT
1 AAATAA-ATAAATAAAT-AAT-AATAGAT
* *
5113 AATAGTTCAATTAATAAATAA-AA-AGAT
1 AA-A--TAAATAAATAAATAATAATAGAT
5140 AAATTGTAAATAAATAAATAATA
1 AAA---TAAATAAATAAATAATA
5163 GTTCAATTTT
Statistics
Matches: 148, Mismatches: 26, Indels: 53
0.65 0.11 0.23
Matches are distributed among these distances:
21 2 0.01
22 5 0.03
23 22 0.15
24 16 0.11
25 5 0.03
26 10 0.07
27 69 0.47
28 6 0.04
29 3 0.02
30 6 0.04
31 4 0.03
ACGTcount: A:0.65, C:0.01, G:0.08, T:0.26
Consensus pattern (26 bp):
AAATAAATAAATAAATAATAATAGAT
Found at i:5077 original size:46 final size:46
Alignment explanation
Indices: 5010--5163 Score: 168
Period size: 46 Copynumber: 3.3 Consensus size: 46
5000 TGAATAAAAG
* ** *
5010 AATAAATATATAATAGATAAA-TAGATAGGTAAAAATAATAATAA-TA
1 AATAAATAGATAATAGATAAATTA-ATAAATAAAAA-AATAAAAAGTA
* *
5056 AATAAATAGATAATAGCTAAATTAATAAATAAAAAGATAAAAAGTA
1 AATAAATAGATAATAGATAAATTAATAAATAAAAAAATAAAAAGTA
* * * **
5102 AATAAATAGATAATAGTTCAATTAATAAATAAAAAGATAAATTGTA
1 AATAAATAGATAATAGATAAATTAATAAATAAAAAAATAAAAAGTA
*
5148 AATAAATAAATAATAG
1 AATAAATAGATAATAG
5164 TTCAATTTTA
Statistics
Matches: 95, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
45 6 0.06
46 87 0.92
47 2 0.02
ACGTcount: A:0.63, C:0.01, G:0.08, T:0.27
Consensus pattern (46 bp):
AATAAATAGATAATAGATAAATTAATAAATAAAAAAATAAAAAGTA
Found at i:5164 original size:46 final size:46
Alignment explanation
Indices: 5054--5170 Score: 189
Period size: 46 Copynumber: 2.5 Consensus size: 46
5044 ATAATAATAA
* *
5054 TAAATAAATAGATAATAGCTAAATTAATAAATAAAAAGATAAAAAG
1 TAAATAAATAGATAATAGTTCAATTAATAAATAAAAAGATAAAAAG
**
5100 TAAATAAATAGATAATAGTTCAATTAATAAATAAAAAGATAAATTG
1 TAAATAAATAGATAATAGTTCAATTAATAAATAAAAAGATAAAAAG
*
5146 TAAATAAATAAATAATAGTTCAATT
1 TAAATAAATAGATAATAGTTCAATT
5171 TTAAAAAAAT
Statistics
Matches: 66, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 66 1.00
ACGTcount: A:0.61, C:0.03, G:0.08, T:0.29
Consensus pattern (46 bp):
TAAATAAATAGATAATAGTTCAATTAATAAATAAAAAGATAAAAAG
Found at i:7939 original size:18 final size:18
Alignment explanation
Indices: 7918--7973 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 18
7908 TATATCATGC
*
7918 ATAAAATATCCTTCAAAA
1 ATAAAATATCCTTTAAAA
7936 AT--AA-ATCCTTTAAAA
1 ATAAAATATCCTTTAAAA
*
7951 A-ATACATATCCTTTAAAA
1 ATA-AAATATCCTTTAAAA
7969 ATAAA
1 ATAAA
7974 TCCTAGGTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 10
0.70 0.07 0.23
Matches are distributed among these distances:
15 11 0.37
16 2 0.07
17 1 0.03
18 15 0.50
19 1 0.03
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.30
Consensus pattern (18 bp):
ATAAAATATCCTTTAAAA
Found at i:7945 original size:15 final size:15
Alignment explanation
Indices: 7925--7977 Score: 61
Period size: 16 Copynumber: 3.3 Consensus size: 15
7915 TGCATAAAAT
*
7925 ATCCTTCAAAAATAA
1 ATCCTTAAAAAATAA
7940 ATCCTTTAAAAAATACA
1 ATCC-TTAAAAAATA-A
*
7957 TATCCTTTAAAAATAA
1 -ATCCTTAAAAAATAA
7973 ATCCT
1 ATCCT
7978 AGGTATGCAA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
15 9 0.27
16 10 0.30
17 10 0.30
18 4 0.12
ACGTcount: A:0.49, C:0.19, G:0.00, T:0.32
Consensus pattern (15 bp):
ATCCTTAAAAAATAA
Found at i:8339 original size:13 final size:13
Alignment explanation
Indices: 8321--8347 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
8311 AAATATAATA
8321 AATATGATTTATG
1 AATATGATTTATG
8334 AATATGATTTATG
1 AATATGATTTATG
8347 A
1 A
8348 GGTTATTGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.00, G:0.15, T:0.44
Consensus pattern (13 bp):
AATATGATTTATG
Done.