Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013755.1 Corchorus olitorius cultivar O-4 contig13788, 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: 28064
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Found at i:3118 original size:21 final size:21
Alignment explanation
Indices: 3094--3206 Score: 192
Period size: 21 Copynumber: 5.4 Consensus size: 21
3084 CTTAGGCAAT
* *
3094 TCCAATGAGCTTGAAACATTC
1 TCCAATGAGCTTGGAACCTTC
3115 TCCAATGAGCTTGGAACCTTC
1 TCCAATGAGCTTGGAACCTTC
3136 TCCAATGAGCTTGGAACCTTC
1 TCCAATGAGCTTGGAACCTTC
3157 TCCAATGAGCTTGGAACCTTC
1 TCCAATGAGCTTGGAACCTTC
3178 TCCAATGAGCTTGGAA-CTTGC
1 TCCAATGAGCTTGGAACCTT-C
3199 TCCAATGA
1 TCCAATGA
3207 TCTCCTAGCA
Statistics
Matches: 89, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
20 3 0.03
21 86 0.97
ACGTcount: A:0.27, C:0.27, G:0.19, T:0.28
Consensus pattern (21 bp):
TCCAATGAGCTTGGAACCTTC
Found at i:13306 original size:18 final size:18
Alignment explanation
Indices: 13261--13298 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
13251 GTATCAATTG
13261 TGCTTTTTTTGTATGAAC
1 TGCTTTTTTTGTATGAAC
* *
13279 TGCTTCTTTTGTGTGAAC
1 TGCTTTTTTTGTATGAAC
13297 TG
1 TG
13299 TGTTTTTTCG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.13, C:0.13, G:0.21, T:0.53
Consensus pattern (18 bp):
TGCTTTTTTTGTATGAAC
Found at i:13999 original size:2 final size:2
Alignment explanation
Indices: 13994--14057 Score: 74
Period size: 2 Copynumber: 32.0 Consensus size: 2
13984 CATATATGTG
* * * *
13994 TA TA TA TA TA TA TA TA TA TA TG TA CA TA TA TG TA CA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
14036 TA TA TA TA TG TA CA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA
14058 CGTGTGTGTG
Statistics
Matches: 50, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (2 bp):
TA
Found at i:14205 original size:75 final size:75
Alignment explanation
Indices: 14082--14237 Score: 294
Period size: 75 Copynumber: 2.1 Consensus size: 75
14072 AAAAGTGAAA
14082 CTGCTTAGGGAATTTGAAAAAGTGATAGTCCTTATGATGATTGCCATTGAACTGATAATGATATG
1 CTGCTTAGGGAATTTGAAAAAGTGATAGTCCTTATGATGATTGCCATTGAACTGATAATGATATG
14147 AATGTTGCAT
66 AATGTTGCAT
*
14157 CTGCTTAGGGAATTTGAAAAAGTGATAGTCCTTATGATGATTGTCATTGAACTGATAATGATATG
1 CTGCTTAGGGAATTTGAAAAAGTGATAGTCCTTATGATGATTGCCATTGAACTGATAATGATATG
14222 AATGTTGCAT
66 AATGTTGCAT
*
14232 TTGCTT
1 CTGCTT
14238 CTCTGGCGAC
Statistics
Matches: 79, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
75 79 1.00
ACGTcount: A:0.31, C:0.10, G:0.22, T:0.37
Consensus pattern (75 bp):
CTGCTTAGGGAATTTGAAAAAGTGATAGTCCTTATGATGATTGCCATTGAACTGATAATGATATG
AATGTTGCAT
Found at i:24207 original size:45 final size:44
Alignment explanation
Indices: 24157--24271 Score: 142
Period size: 45 Copynumber: 2.6 Consensus size: 44
24147 AATTTTTTTT
* *
24157 AACCTCCCTATGAAATTTTTGATAACTTACCTAA-GGAATTTTGAA
1 AACCTCACTATGAAA-TTTTGATAACTT-CCGAATGGAATTTTGAA
*
24202 AACCTCACTATGAAATTTTGATAACTTCCGAATGGAATTTTGAT
1 AACCTCACTATGAAATTTTGATAACTTCCGAATGGAATTTTGAA
* * *
24246 AACCAACACTATGAGATATTGATAAC
1 AACC-TCACTATGAAATTTTGATAAC
24272 CTCCATATGA
Statistics
Matches: 62, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
43 4 0.06
44 26 0.42
45 32 0.52
ACGTcount: A:0.37, C:0.17, G:0.12, T:0.33
Consensus pattern (44 bp):
AACCTCACTATGAAATTTTGATAACTTCCGAATGGAATTTTGAA
Found at i:24218 original size:22 final size:22
Alignment explanation
Indices: 24157--24222 Score: 62
Period size: 22 Copynumber: 3.0 Consensus size: 22
24147 AATTTTTTTT
* *
24157 AACCTCCCTATGAAATTTTTGAT
1 AACCTCACTATGAAA-TTTTGAA
* * *
24180 AA-CTTACCTAAGGAATTTTGAA
1 AACCTCA-CTATGAAATTTTGAA
24202 AACCTCACTATGAAATTTTGA
1 AACCTCACTATGAAATTTTGA
24223 TAACTTCCGA
Statistics
Matches: 33, Mismatches: 8, Indels: 5
0.72 0.17 0.11
Matches are distributed among these distances:
22 22 0.67
23 11 0.33
ACGTcount: A:0.36, C:0.18, G:0.11, T:0.35
Consensus pattern (22 bp):
AACCTCACTATGAAATTTTGAA
Found at i:24240 original size:22 final size:21
Alignment explanation
Indices: 24173--24248 Score: 73
Period size: 22 Copynumber: 3.5 Consensus size: 21
24163 CCTATGAAAT
24173 TTTTGATAACTTACCTAA-GGAA
1 TTTTGATAACTT-CC-AATGGAA
* * * *
24195 TTTTGAAAACCTCACTATGAAA
1 TTTTGATAACTTC-CAATGGAA
24217 TTTTGATAACTTCCGAATGGAA
1 TTTTGATAACTTCC-AATGGAA
24239 TTTTGATAAC
1 TTTTGATAAC
24249 CAACACTATG
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
21 3 0.07
22 40 0.93
ACGTcount: A:0.36, C:0.14, G:0.13, T:0.37
Consensus pattern (21 bp):
TTTTGATAACTTCCAATGGAA
Found at i:24286 original size:22 final size:23
Alignment explanation
Indices: 24241--24295 Score: 76
Period size: 22 Copynumber: 2.4 Consensus size: 23
24231 GAATGGAATT
24241 TTGATAACCAACACTATGAGATA
1 TTGATAACCAACACTATGAGATA
** *
24264 TTGATAACCTCCA-TATGATATA
1 TTGATAACCAACACTATGAGATA
24286 TTGATAACCA
1 TTGATAACCA
24296 CGTTATCAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
22 17 0.61
23 11 0.39
ACGTcount: A:0.40, C:0.18, G:0.11, T:0.31
Consensus pattern (23 bp):
TTGATAACCAACACTATGAGATA
Found at i:24290 original size:45 final size:45
Alignment explanation
Indices: 24164--24295 Score: 110
Period size: 45 Copynumber: 2.9 Consensus size: 45
24154 TTTAACCTCC
* * * * * *
24164 CTATGAAATTTTTGATAACTTACCTAA-GGAATTTTGAAAACC-TCA
1 CTATGAAA-TATTGATAACCT-CCGAATGGAATATTGATAACCAACA
* * *
24209 CTATGAAATTTTGATAACTTCCGAATGGAATTTTGATAACCAACA
1 CTATGAAATATTGATAACCTCCGAATGGAATATTGATAACCAACA
*
24254 CTATGAGATATTGATAACCTCC-ATAT-GATATATTGATAACCA
1 CTATGAAATATTGATAACCTCCGA-ATGGA-ATATTGATAACCA
24296 CGTTATCAAA
Statistics
Matches: 76, Mismatches: 7, Indels: 8
0.84 0.08 0.09
Matches are distributed among these distances:
43 4 0.05
44 29 0.38
45 43 0.57
ACGTcount: A:0.38, C:0.16, G:0.12, T:0.34
Consensus pattern (45 bp):
CTATGAAATATTGATAACCTCCGAATGGAATATTGATAACCAACA
Found at i:24359 original size:22 final size:23
Alignment explanation
Indices: 24325--24375 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 23
24315 CCTCCATTTG
* *
24325 AATTGTTAGTAATCACACTCTGA
1 AATTGTTAATAATCACACTATGA
*
24348 AATT-TTAATAATCACATTATGA
1 AATTGTTAATAATCACACTATGA
24370 AATTGT
1 AATTGT
24376 GATAACCTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (23 bp):
AATTGTTAATAATCACACTATGA
Found at i:24416 original size:22 final size:22
Alignment explanation
Indices: 24345--24593 Score: 101
Period size: 22 Copynumber: 11.6 Consensus size: 22
24335 AATCACACTC
* * *
24345 TGAAATTTTAATAATCACATTA
1 TGAAATTTTGATAATCTCCTTA
* * *
24367 TGAAATTGTGATAACCTTGC-TA
1 TGAAATTTTGATAATC-TCCTTA
*
24389 TAAAATTTTGATAATCTCCTTA
1 TGAAATTTTGATAATCTCCTTA
*
24411 TGAAATCTTGATAA----C-TA
1 TGAAATTTTGATAATCTCCTTA
* *
24428 -CAAATTTTGATAATCTCCCTA
1 TGAAATTTTGATAATCTCCTTA
** * * *
24449 TGATTTTTTTATAACCTCATTA
1 TGAAATTTTGATAATCTCCTTA
* *
24471 TGAAATTTTGTTAATCTCCCTA
1 TGAAATTTTGATAATCTCCTTA
* *
24493 TAAAATTTTG---ATCTACATAGTA
1 TGAAATTTTGATAATCT-CCT--TA
*
24515 TGAAATTTTGATAA-CCCTCTTA
1 TGAAATTTTGATAATCTC-CTTA
* * *
24537 TAAAATTTTGA-AAACTAAAC-TA
1 TGAAATTTTGATAATCT--CCTTA
* * * *
24559 TGAAATTTTAATAACCTTCATA
1 TGAAATTTTGATAATCTCCTTA
24581 TGAAATTTTGATA
1 TGAAATTTTGATA
24594 TCCTCCCTGA
Statistics
Matches: 165, Mismatches: 42, Indels: 40
0.67 0.17 0.16
Matches are distributed among these distances:
16 11 0.07
17 2 0.01
18 1 0.01
19 4 0.02
20 2 0.01
21 7 0.04
22 129 0.78
23 6 0.04
24 2 0.01
25 1 0.01
ACGTcount: A:0.37, C:0.13, G:0.08, T:0.41
Consensus pattern (22 bp):
TGAAATTTTGATAATCTCCTTA
Found at i:24747 original size:22 final size:22
Alignment explanation
Indices: 24693--25128 Score: 143
Period size: 22 Copynumber: 20.0 Consensus size: 22
24683 ATAAATACCA
* *
24693 CTATGAAATTTTGGTAATCAC-
1 CTATGAAATTTTGATAATCTCT
* *
24714 AT-TGAAAATTTGATAATCTCT
1 CTATGAAATTTTGATAATCTCT
* *
24735 TTATGAAATTTTGATAACCTCT
1 CTATGAAATTTTGATAATCTCT
* * * * *
24757 CTATAAAATTTTGTTGACCCCT
1 CTATGAAATTTTGATAATCTCT
* *
24779 CTATGAAATTTTGATATTTTCAT
1 CTATGAAATTTTGATAATCTC-T
* * *
24802 -TATGTAATTTTGATAACCTCG
1 CTATGAAATTTTGATAATCTCT
* *
24823 CTTTGAAATTTTGATAA---CA
1 CTATGAAATTTTGATAATCTCT
*
24842 CTATGAAATTTTGCTAATCT-T
1 CTATGAAATTTTGATAATCTCT
*
24863 CCTAT-AAATTTCGATAATCCGATCT
1 -CTATGAAATTTTGATAAT-C--TCT
** *
24888 CTATGAAATTTCAATAATCACT
1 CTATGAAATTTTGATAATCTCT
* * *
24910 ATATGAGA-TTTGATAACCT-T
1 CTATGAAATTTTGATAATCTCT
* *
24930 CTATCAAATTTTGGT-A-CTCAT
1 CTATGAAATTTTGATAATCTC-T
** * *
24951 GAAATTAAGACTTTT-ATAACCT-T
1 -CTATGAA-A-TTTTGATAATCTCT
* * * *
24974 CATATGAAAGTTTGATAAGCACA
1 C-TATGAAATTTTGATAATCTCT
** * * *
24997 CTAAAAAATTTTAATAACCACAT
1 CTATGAAATTTTGATAATCTC-T
* *
25020 -TATGAAATTTTGATAACCTCC
1 CTATGAAATTTTGATAATCTCT
** *
25041 CTATGAAAGATT-AGTAACCTC-
1 CTATGAAATTTTGA-TAATCTCT
* * * *
25062 CTTATGAAATTTTGTTAACCACA
1 C-TATGAAATTTTGATAATCTCT
* *
25085 CTATGAAATTCTT-ATAACCTCG
1 CTATGAAATT-TTGATAATCTCT
*
25107 CTATGACATTTTGATAATCTCT
1 CTATGAAATTTTGATAATCTCT
25129 TTGATAACCT
Statistics
Matches: 305, Mismatches: 78, Indels: 63
0.68 0.17 0.14
Matches are distributed among these distances:
19 18 0.06
20 22 0.07
21 33 0.11
22 194 0.64
23 12 0.04
24 11 0.04
25 15 0.05
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.39
Consensus pattern (22 bp):
CTATGAAATTTTGATAATCTCT
Found at i:25103 original size:44 final size:43
Alignment explanation
Indices: 24962--25344 Score: 164
Period size: 44 Copynumber: 8.8 Consensus size: 43
24952 AAATTAAGAC
* * * * **
24962 TTTTATAACCTTCATATGAAAGTTTGATAAGCACACTAAAAAA
1 TTTTATAACCTCCTTATGAAATTTTGATAACCACACTATGAAA
* * * *
25005 TTTTAATAACCACATTATGAAATTTTGATAACCTCCCTATGAAA
1 TTTT-ATAACCTCCTTATGAAATTTTGATAACCACACTATGAAA
** *
25049 GATTAGTAACCTCCTTATGAAATTTTGTTAACCACACTATGAAA
1 TTTTA-TAACCTCCTTATGAAATTTTGATAACCACACTATGAAA
* * * *
25093 TTCTTATAACCTCGC-TATGACATTTTGATAA--TCTCTTTGATAA
1 TT-TTATAACCTC-CTTATGAAATTTTGATAACCACACTATGA-AA
** * * * * * *
25136 ---CCTAA-TTTC-TATAAAATTGTGAAAACCATACTATGAAA
1 TTTTATAACCTCCTTATGAAATTTTGATAACCACACTATGAAA
* * ** * *
25174 TTTCAATAACCT-TTCTAAAAAAATTTAATAACCTGATC-CTATGAAA
1 TTT-TATAACCTCCT-TATGAAATTTTGATAACC--A-CACTATGAAA
* * * *
25220 TTTTGGTAACCACAC-TATGAAATTTTGATAACCTTC-CCATGAAA
1 TTTT-ATAACCTC-CTTATGAAATTTTGATAACC-ACACTATGAAA
* * *
25264 TTTTGATAACTTCCGTATGAAATTTTGGTAACCAC-CTCATGAAA
1 TTTT-ATAACCTCCTTATGAAATTTTGATAACCACACT-ATGAAA
*
25308 TTATAATAACCAT-CTTATGAAATTTTGATAACCACAC
1 TT-TTATAACC-TCCTTATGAAATTTTGATAACCACAC
25345 AGAGACAAGA
Statistics
Matches: 248, Mismatches: 67, Indels: 48
0.68 0.18 0.13
Matches are distributed among these distances:
37 13 0.05
38 3 0.01
39 8 0.03
42 9 0.04
43 11 0.04
44 166 0.67
45 7 0.03
46 31 0.12
ACGTcount: A:0.38, C:0.18, G:0.09, T:0.36
Consensus pattern (43 bp):
TTTTATAACCTCCTTATGAAATTTTGATAACCACACTATGAAA
Found at i:25184 original size:22 final size:21
Alignment explanation
Indices: 25159--25341 Score: 57
Period size: 22 Copynumber: 8.2 Consensus size: 21
25149 AAATTGTGAA
25159 AACCATACTATGAAATTTCAAT
1 AACCATACTATGAAATTT-AAT
* * **
25181 AACCTTTCTAAAAAAATTTAAT
1 AACCATACT-ATGAAATTTAAT
* **
25203 AACCTGATCCTATGAAATTTTGGT
1 AACC--ATACTATGAAA-TTTAAT
* *
25227 AACCACACTATGAAATTTTGAT
1 AACCATACTATGAAA-TTTAAT
* * * *
25249 AACCTTCCCATGAAATTTTGAT
1 AACCATACTATGAAA-TTTAAT
* * **
25271 AA-CTTCCGTATGAAATTTTGGT
1 AACCATAC-TATGAAA-TTTAAT
*
25293 AACCA-CCTCATGAAATTATAAT
1 AACCATACT-ATGAAATT-TAAT
*
25315 AACCAT-CTTATGAAATTTTGAT
1 AACCATAC-TATGAAA-TTTAAT
25337 AACCA
1 AACCA
25342 CACAGAGACA
Statistics
Matches: 127, Mismatches: 23, Indels: 22
0.74 0.13 0.13
Matches are distributed among these distances:
21 8 0.06
22 93 0.73
23 15 0.12
24 11 0.09
ACGTcount: A:0.39, C:0.18, G:0.09, T:0.34
Consensus pattern (21 bp):
AACCATACTATGAAATTTAAT
Found at i:25306 original size:66 final size:66
Alignment explanation
Indices: 25213--25339 Score: 193
Period size: 66 Copynumber: 1.9 Consensus size: 66
25203 AACCTGATCC
* * *
25213 TATGAAATTTTGGTAACCACACTATGAAATTTTGATAACCTTCCCATGAAATTTTGATAACTTCC
1 TATGAAATTTTGGTAACCACACTATGAAATTATAATAACCATCCCATGAAATTTTGATAACTTCC
25278 G
66 G
**
25279 TATGAAATTTTGGTAACCAC-CTCATGAAATTATAATAACCATCTTATGAAATTTTGATAAC
1 TATGAAATTTTGGTAACCACACT-ATGAAATTATAATAACCATCCCATGAAATTTTGATAAC
25340 CACACAGAGA
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
65 2 0.04
66 53 0.96
ACGTcount: A:0.36, C:0.17, G:0.11, T:0.36
Consensus pattern (66 bp):
TATGAAATTTTGGTAACCACACTATGAAATTATAATAACCATCCCATGAAATTTTGATAACTTCC
G
Found at i:25544 original size:20 final size:20
Alignment explanation
Indices: 25506--25544 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
25496 TATTGACATT
25506 TAAAAAATTGAAATTAAAAG
1 TAAAAAATTGAAATTAAAAG
*
25526 TAAAATATT-AAATTCAAAA
1 TAAAAAATTGAAATT-AAAA
25545 AATAATAGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.64, C:0.03, G:0.05, T:0.28
Consensus pattern (20 bp):
TAAAAAATTGAAATTAAAAG
Found at i:25771 original size:164 final size:164
Alignment explanation
Indices: 25557--25881 Score: 433
Period size: 165 Copynumber: 2.0 Consensus size: 164
25547 TAATAGTAAG
* * * *
25557 GAAATTTGCATGTTCATTAACGAAATTCAATTGACAAACTTATAATTCGGTCTAAATTGAAATTT
1 GAAATTTGCATGTTCATCAACGAAAATCAATTGACAAACTTAAAATTCGGTATAAATTGAAATTT
25622 T-TAAATAATAAAATT-ATAATAAATTTTAATAATGGAAATTTAGAAATATAATTGAAAAAAGGG
66 TATAAATAAT--AATTAATAATAAATTTTAATAATGGAAATTTAGAAATATAATTGAAAAAAGGG
*
25685 TACAATC-AAAAATATAAA-TTTTCCCATTATTAATA
129 TACAATCGAAAAACATAAAGTTTT-CCATTATTAATA
* *
25720 GAAATTTGCATGTTCATCAATGAAAATCAATTTTACAAACTTAAAATTCGGTATAAATTGAAATT
1 GAAATTTGCATGTTCATCAACGAAAATCAA-TTGACAAACTTAAAATTCGGTATAAATTGAAATT
* * ** ** * *
25785 TTATGATTAATTTTTAAATAATAAATTTTAATAATGTCAGTTTAGAAATATATTTGAAAAAAGGG
65 TTATAAATAATAATT-AATAATAAATTTTAATAATGGAAATTTAGAAATATAATTGAAAAAAGGG
*
25850 TACAATCGGAAAACATAAAGTTTTCCATTATT
129 TACAATCGAAAAACATAAAGTTTTCCATTATT
25882 CGTACTTTTA
Statistics
Matches: 140, Mismatches: 16, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
163 29 0.21
164 33 0.24
165 57 0.41
166 17 0.12
167 4 0.03
ACGTcount: A:0.45, C:0.08, G:0.10, T:0.37
Consensus pattern (164 bp):
GAAATTTGCATGTTCATCAACGAAAATCAATTGACAAACTTAAAATTCGGTATAAATTGAAATTT
TATAAATAATAATTAATAATAAATTTTAATAATGGAAATTTAGAAATATAATTGAAAAAAGGGTA
CAATCGAAAAACATAAAGTTTTCCATTATTAATA
Done.