Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019309.1 Corchorus olitorius cultivar O-4 contig19342, 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: 30876
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:7575 original size:21 final size:21
Alignment explanation
Indices: 7516--7576 Score: 86
Period size: 21 Copynumber: 2.9 Consensus size: 21
7506 CTTAGGCAAC
*
7516 TCCAATGAGCTTGAAACCTTA
1 TCCAATGAGCTTGAAACTTTA
*
7537 TCCAATGAGCTTGAAACTTTC
1 TCCAATGAGCTTGAAACTTTA
**
7558 TTGAATGAGCTTGAAACTT
1 TCCAATGAGCTTGAAACTT
7577 CTTTGTGAGT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.33
Consensus pattern (21 bp):
TCCAATGAGCTTGAAACTTTA
Found at i:14178 original size:20 final size:20
Alignment explanation
Indices: 14148--14217 Score: 61
Period size: 20 Copynumber: 3.5 Consensus size: 20
14138 CTCTCCAAAT
14148 TCAAGGCAAAGTTCTTCTCCA
1 TCAA-GCAAAGTTCTTCTCCA
**** **
14169 TCAAGCAAAGAAAATCTGAA
1 TCAAGCAAAGTTCTTCTCCA
*
14189 TCAAGCATAGTTCTTCTCCA
1 TCAAGCAAAGTTCTTCTCCA
14209 TCAA-CAAAG
1 TCAAGCAAAG
14218 CCACAACAAA
Statistics
Matches: 35, Mismatches: 14, Indels: 2
0.69 0.27 0.04
Matches are distributed among these distances:
19 4 0.11
20 27 0.77
21 4 0.11
ACGTcount: A:0.39, C:0.24, G:0.13, T:0.24
Consensus pattern (20 bp):
TCAAGCAAAGTTCTTCTCCA
Found at i:17242 original size:21 final size:21
Alignment explanation
Indices: 17202--17243 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
17192 TCCTTTGGTG
* **
17202 ATGATCTCTAATGGGTTTCAA
1 ATGATCTCCAATGGCCTTCAA
17223 ATGATCTCCAATGGCCTTCAA
1 ATGATCTCCAATGGCCTTCAA
17244 CTCTTCAAGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.33
Consensus pattern (21 bp):
ATGATCTCCAATGGCCTTCAA
Found at i:17383 original size:21 final size:21
Alignment explanation
Indices: 17359--17492 Score: 209
Period size: 21 Copynumber: 6.4 Consensus size: 21
17349 CTTAGGCAAT
*
17359 TCCAATGAGCTTGAAACCTT-C
1 TCCAATGAGCTTGGAA-CTTGC
17380 TCCAATGAGCTTGGAACCTT-C
1 TCCAATGAGCTTGGAA-CTTGC
17401 TCCAATGAGCTTGGAACTTGC
1 TCCAATGAGCTTGGAACTTGC
*
17422 TCCAATGAGTTTGGAACTTGC
1 TCCAATGAGCTTGGAACTTGC
*
17443 TCCAATGAGTTTGGAACTTGC
1 TCCAATGAGCTTGGAACTTGC
17464 TCCAATGAGCTTGGAACTTGC
1 TCCAATGAGCTTGGAACTTGC
17485 TCCAATGA
1 TCCAATGA
17493 ACTCCTAGCT
Statistics
Matches: 109, Mismatches: 3, Indels: 2
0.96 0.03 0.02
Matches are distributed among these distances:
20 3 0.03
21 106 0.97
ACGTcount: A:0.25, C:0.24, G:0.21, T:0.30
Consensus pattern (21 bp):
TCCAATGAGCTTGGAACTTGC
Found at i:20693 original size:39 final size:39
Alignment explanation
Indices: 20586--20695 Score: 130
Period size: 39 Copynumber: 2.8 Consensus size: 39
20576 ATTAACTGGT
* * *
20586 AAGCAATGATCCTAAATCAGAATCGAAATAAAACTGACA
1 AAGCAATGATCCTAAATCAGGATTGAAATAAAACTAACA
* * * *
20625 AAGCAATAATCCTAAATCATGATTGAAATATAACTAATA
1 AAGCAATGATCCTAAATCAGGATTGAAATAAAACTAACA
* * *
20664 AAGCAATGATTCTAAACCAGGATTAAAATAAA
1 AAGCAATGATCCTAAATCAGGATTGAAATAAA
20696 GCAATTATCG
Statistics
Matches: 58, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
39 58 1.00
ACGTcount: A:0.52, C:0.15, G:0.11, T:0.23
Consensus pattern (39 bp):
AAGCAATGATCCTAAATCAGGATTGAAATAAAACTAACA
Found at i:20694 original size:30 final size:30
Alignment explanation
Indices: 20660--21294 Score: 730
Period size: 30 Copynumber: 21.1 Consensus size: 30
20650 AAATATAACT
*
20660 AATAAAGCAATGATTCTAAACCAGGATTAA
1 AATAAAGCAATGATCCTAAACCAGGATTAA
* *
20690 AATAAAGCAATTATCGTAAACCAGGATT--
1 AATAAAGCAATGATCCTAAACCAGGATTAA
* *
20718 AA-AAAGCAATGATCCTAAATCAAGATTAA
1 AATAAAGCAATGATCCTAAACCAGGATTAA
* * *
20747 AATGAAA-CAATGATCCTCAACTAGGATTTA
1 AAT-AAAGCAATGATCCTAAACCAGGATTAA
*
20777 AATAAAGCAATGATCCTAAATCAGGATTAA
1 AATAAAGCAATGATCCTAAACCAGGATTAA
* * * *
20807 AA-GAAGCAATTATCCTCAACCAGGATTTA
1 AATAAAGCAATGATCCTAAACCAGGATTAA
20836 AATAAAGCAATGATCCTAAACCAGGATTAA
1 AATAAAGCAATGATCCTAAACCAGGATTAA
* * *
20866 AATGAAGCAATGATCCTCAACCAGGATTAG
1 AATAAAGCAATGATCCTAAACCAGGATTAA
*
20896 AATAAAGCAATGATCCTAAATCAGGATTAA
1 AATAAAGCAATGATCCTAAACCAGGATTAA
* * * *
20926 AATGAAGTAATGATCCTCAATCAGGATTAA
1 AATAAAGCAATGATCCTAAACCAGGATTAA
20956 AATAAAGCAATGATCCTAAACCAGGATT-A
1 AATAAAGCAATGATCCTAAACCAGGATTAA
*
20985 AA-AAAGCAATGATCCTAAATCAGGATTAA
1 AATAAAGCAATGATCCTAAACCAGGATTAA
** * *
21014 AATGGAGCAATGATCCTCAACCAGGATTTA
1 AATAAAGCAATGATCCTAAACCAGGATTAA
*
21044 AATAAAGCAATGATCCTAAATCAGGATTAA
1 AATAAAGCAATGATCCTAAACCAGGATTAA
* *
21074 AATGAAGCAATGATCCTCAACCAGGAATT-A
1 AATAAAGCAATGATCCTAAACCAGG-ATTAA
21104 AATAAAGCAATGATCCTAAACCAGGATTAA
1 AATAAAGCAATGATCCTAAACCAGGATTAA
* * * *
21134 AATGAAGCAATGATCCTCAACCAAGATTAG
1 AATAAAGCAATGATCCTAAACCAGGATTAA
*
21164 AATAAAGCAATGATCCTAAATCAGGATTAA
1 AATAAAGCAATGATCCTAAACCAGGATTAA
* * *
21194 AATGAAGTAAAGATCCTAAACCAGGATTGAAATTA
1 AATAAAGCAATGATCCTAAACCAGGATT---A--A
**
21229 ACTTATAAAGCAATGATCCTAAACCAGGATCGA
1 A---ATAAAGCAATGATCCTAAACCAGGATTAA
* * *
21262 AATGAAGCAAAT-ATCCCAAACCAGGATTGA
1 AATAAAGC-AATGATCCTAAACCAGGATTAA
21292 AAT
1 AAT
21295 GAACCGATAA
Statistics
Matches: 510, Mismatches: 76, Indels: 38
0.82 0.12 0.06
Matches are distributed among these distances:
27 21 0.04
28 26 0.05
29 38 0.07
30 388 0.76
31 9 0.02
33 3 0.01
35 2 0.00
38 23 0.05
ACGTcount: A:0.47, C:0.16, G:0.15, T:0.22
Consensus pattern (30 bp):
AATAAAGCAATGATCCTAAACCAGGATTAA
Found at i:21247 original size:38 final size:36
Alignment explanation
Indices: 21205--21369 Score: 128
Period size: 38 Copynumber: 4.6 Consensus size: 36
21195 ATGAAGTAAA
* *
21205 GATCCTAAACCAGGATTGAAATTAACTTATAAAGCAAT
1 GATCCTAAACCAGGATCGAAA-TAAC-CATAAAGCAAT
*
21243 GATCCTAAACCAGGATCG----AA--ATGAAGCAAAT
1 GATCCTAAACCAGGATCGAAATAACCATAAAGC-AAT
* * *
21274 -ATCCCAAACCAGGATTGAAATGAACCGATAAAGCAAG
1 GATCCTAAACCAGGATCGAAAT-AACC-ATAAAGCAAT
* * * *
21311 GATCCTAAATCAAGATCGCAGTAAACCAATAAAGCAAT
1 GATCCTAAACCAGGATCGAAAT-AACC-ATAAAGCAAT
21349 GATCCTAAACCAGGATCGAAA
1 GATCCTAAACCAGGATCGAAA
21370 ATAAACTGAT
Statistics
Matches: 98, Mismatches: 19, Indels: 20
0.72 0.14 0.15
Matches are distributed among these distances:
30 21 0.21
31 3 0.03
33 2 0.02
35 2 0.02
37 2 0.02
38 68 0.69
ACGTcount: A:0.45, C:0.20, G:0.16, T:0.18
Consensus pattern (36 bp):
GATCCTAAACCAGGATCGAAATAACCATAAAGCAAT
Found at i:21283 original size:68 final size:68
Alignment explanation
Indices: 21165--21328 Score: 229
Period size: 68 Copynumber: 2.4 Consensus size: 68
21155 CAAGATTAGA
** * * *
21165 ATAAAGCAATGATCCTAAATCAGGATTAAAATGAAGTAAAGATCCTAAACCAGGATTGAAATTAA
1 ATAAAGCAATGATCCTAAATCAGGATCGAAATGAAGCAAAGATCCCAAACCAGGATTGAAATGAA
**
21230 CTT
66 CCG
* *
21233 ATAAAGCAATGATCCTAAACCAGGATCGAAATGAAGCAAATATCCCAAACCAGGATTGAAATGAA
1 ATAAAGCAATGATCCTAAATCAGGATCGAAATGAAGCAAAGATCCCAAACCAGGATTGAAATGAA
21298 CCG
66 CCG
* *
21301 ATAAAGCAAGGATCCTAAATCAAGATCG
1 ATAAAGCAATGATCCTAAATCAGGATCG
21329 CAGTAAACCA
Statistics
Matches: 84, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
68 84 1.00
ACGTcount: A:0.46, C:0.17, G:0.16, T:0.20
Consensus pattern (68 bp):
ATAAAGCAATGATCCTAAATCAGGATCGAAATGAAGCAAAGATCCCAAACCAGGATTGAAATGAA
CCG
Found at i:26229 original size:22 final size:22
Alignment explanation
Indices: 26187--26229 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
26177 TTTCTGATTA
**
26187 ATTGTTTTCTTTAATTTTCTTG
1 ATTGTTTTCTTTAATAGTCTTG
26209 ATTGTTTTC-TTAGATAGTCTT
1 ATTGTTTTCTTTA-ATAGTCTT
26230 AATTACTAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 3 0.17
22 15 0.83
ACGTcount: A:0.16, C:0.09, G:0.12, T:0.63
Consensus pattern (22 bp):
ATTGTTTTCTTTAATAGTCTTG
Found at i:28599 original size:26 final size:26
Alignment explanation
Indices: 28570--28621 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
28560 TTTTCTCAAA
*
28570 CTATTTTCTTAATCTCTAGTTTAATT
1 CTATTTTATTAATCTCTAGTTTAATT
** *
28596 CTATTTTATTGTTTTCTAGTTTAATT
1 CTATTTTATTAATCTCTAGTTTAATT
28622 TGCCTATTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.21, C:0.12, G:0.06, T:0.62
Consensus pattern (26 bp):
CTATTTTATTAATCTCTAGTTTAATT
Done.