Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021645.1 Corchorus olitorius cultivar O-4 contig21678, 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: 27004
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:1092 original size:27 final size:27
Alignment explanation
Indices: 1051--1123 Score: 110
Period size: 27 Copynumber: 2.7 Consensus size: 27
1041 GATCCAAATT
*
1051 GCTCATGACCGTCGGGATCTAATTTCG
1 GCTCATGACCATCGGGATCTAATTTCG
* *
1078 GCTTATGACCATCGGGATCTTATTTCG
1 GCTCATGACCATCGGGATCTAATTTCG
*
1105 GCTCATGACCATCAGGATC
1 GCTCATGACCATCGGGATC
1124 CACCTTGGCA
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.21, C:0.26, G:0.23, T:0.30
Consensus pattern (27 bp):
GCTCATGACCATCGGGATCTAATTTCG
Found at i:1141 original size:27 final size:27
Alignment explanation
Indices: 1111--1179 Score: 120
Period size: 27 Copynumber: 2.6 Consensus size: 27
1101 TTCGGCTCAT
1111 GACCATCAGGATCCACCTTGGCATCCC
1 GACCATCAGGATCCACCTTGGCATCCC
*
1138 GACCATCAGGATCAACCTTGGCATCCC
1 GACCATCAGGATCCACCTTGGCATCCC
*
1165 GACCATTAGGATCCA
1 GACCATCAGGATCCA
1180 ATTTATCTCA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.26, C:0.36, G:0.19, T:0.19
Consensus pattern (27 bp):
GACCATCAGGATCCACCTTGGCATCCC
Found at i:2683 original size:2 final size:2
Alignment explanation
Indices: 2676--2719 Score: 63
Period size: 2 Copynumber: 22.5 Consensus size: 2
2666 CACCATTCAA
* *
2676 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT CT TT AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2717 AT A
1 AT A
2720 AGTCTAAACG
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:3006 original size:21 final size:21
Alignment explanation
Indices: 2945--3007 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 21
2935 GCTTAACATC
*
2945 TTATTA-TTATAATTATAATAA
1 TTATTAGTTAT-ATTATAATTA
* *
2966 TTATTAG-TAGTACTAAAATTA
1 TTATTAGTTA-TATTATAATTA
2987 TTATTAGTTATATTATAATTA
1 TTATTAGTTATATTATAATTA
3008 CGTTTTTCTT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
21 31 0.91
22 3 0.09
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.51
Consensus pattern (21 bp):
TTATTAGTTATATTATAATTA
Found at i:5724 original size:12 final size:12
Alignment explanation
Indices: 5693--5731 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
5683 TTCATGATCC
*
5693 CTTTTTCCCTTT
1 CTTTTTCTCTTT
5705 CTTTTTCTCTTT
1 CTTTTTCTCTTT
*
5717 TTTTTTCT-TTT
1 CTTTTTCTCTTT
5728 CTTT
1 CTTT
5732 ATTTCAAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
11 6 0.25
12 18 0.75
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (12 bp):
CTTTTTCTCTTT
Found at i:9518 original size:23 final size:23
Alignment explanation
Indices: 9461--9519 Score: 91
Period size: 23 Copynumber: 2.6 Consensus size: 23
9451 CTCGTCGACG
* *
9461 ATTTACTTCCTCTTGAGTCAAAA
1 ATTTGCTTCCTTTTGAGTCAAAA
*
9484 ATTTGCTTCCTTTTGAGTCGAAA
1 ATTTGCTTCCTTTTGAGTCAAAA
9507 ATTTGCTTCCTTT
1 ATTTGCTTCCTTT
9520 GGTCGACAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.22, C:0.20, G:0.12, T:0.46
Consensus pattern (23 bp):
ATTTGCTTCCTTTTGAGTCAAAA
Found at i:9530 original size:21 final size:22
Alignment explanation
Indices: 9461--9530 Score: 88
Period size: 23 Copynumber: 3.1 Consensus size: 22
9451 CTCGTCGACG
* *
9461 ATTTACTTCCTCTTGAGTCAAAA
1 ATTTGCTTCCT-TTGAGTCGAAA
9484 ATTTGCTTCCTTTTGAGTCGAAA
1 ATTTGCTTCC-TTTGAGTCGAAA
*
9507 ATTTGCTTCCTTTG-GTCGACA
1 ATTTGCTTCCTTTGAGTCGAAA
9528 ATT
1 ATT
9531 CCCTAGTCGA
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
21 9 0.21
22 4 0.09
23 29 0.67
24 1 0.02
ACGTcount: A:0.23, C:0.20, G:0.14, T:0.43
Consensus pattern (22 bp):
ATTTGCTTCCTTTGAGTCGAAA
Found at i:9560 original size:15 final size:15
Alignment explanation
Indices: 9542--9579 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
9532 CCTAGTCGAC
*
9542 ACTTGCTCCTTATCG
1 ACTTGATCCTTATCG
*
9557 ACTTGATTCTTATCG
1 ACTTGATCCTTATCG
9572 ACTTGATC
1 ACTTGATC
9580 TTTTAAGTCG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.18, C:0.26, G:0.13, T:0.42
Consensus pattern (15 bp):
ACTTGATCCTTATCG
Found at i:15670 original size:22 final size:20
Alignment explanation
Indices: 15645--15695 Score: 57
Period size: 22 Copynumber: 2.4 Consensus size: 20
15635 ACCAATCTAG
15645 CAATTAAAATTATATAAGAAAA
1 CAATTAAAATT-TA-AAGAAAA
*
15667 CAATCAAGAAATTTAAAGAAAA
1 CAAT-TA-AAATTTAAAGAAAA
15689 CAATTAA
1 CAATTAA
15696 TCAAAAAGCA
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
20 1 0.04
21 1 0.04
22 15 0.60
23 3 0.12
24 5 0.20
ACGTcount: A:0.63, C:0.08, G:0.06, T:0.24
Consensus pattern (20 bp):
CAATTAAAATTTAAAGAAAA
Found at i:17004 original size:19 final size:18
Alignment explanation
Indices: 16971--17006 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
16961 TTGAAATTAT
16971 TCTTCAATGGTCTTCAAA
1 TCTTCAATGGTCTTCAAA
*
16989 TCTTCAAATTGTCTTCAA
1 TCTTC-AATGGTCTTCAA
17007 TAAATCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.28, C:0.22, G:0.08, T:0.42
Consensus pattern (18 bp):
TCTTCAATGGTCTTCAAA
Found at i:18545 original size:18 final size:18
Alignment explanation
Indices: 18522--18568 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
18512 TTTAAACTTC
18522 TTATTATTA-TAATAATAA
1 TTATTATTAGTAATAA-AA
* *
18540 TTATTAGTAGTAGTAAAA
1 TTATTATTAGTAATAAAA
18558 TTATTATTAGT
1 TTATTATTAGT
18569 TGTATTATCA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 20 0.80
19 5 0.20
ACGTcount: A:0.43, C:0.00, G:0.09, T:0.49
Consensus pattern (18 bp):
TTATTATTAGTAATAAAA
Found at i:21066 original size:17 final size:17
Alignment explanation
Indices: 21038--21094 Score: 69
Period size: 17 Copynumber: 3.4 Consensus size: 17
21028 CCACTAAAAT
*
21038 TTCCTAGGTGATCACGC
1 TTCCAAGGTGATCACGC
* * *
21055 CTCCAGGGTGATCACAC
1 TTCCAAGGTGATCACGC
*
21072 TTCCAAGGTGATAACGC
1 TTCCAAGGTGATCACGC
21089 TTCCAA
1 TTCCAA
21095 TGCTAATGCT
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
17 32 1.00
ACGTcount: A:0.25, C:0.30, G:0.21, T:0.25
Consensus pattern (17 bp):
TTCCAAGGTGATCACGC
Found at i:22841 original size:32 final size:32
Alignment explanation
Indices: 22805--22901 Score: 85
Period size: 32 Copynumber: 3.0 Consensus size: 32
22795 TAACCAAAAC
22805 TACTAAGAATAAGGTTATTGAATTGGTTGATA
1 TACTAAGAATAAGGTTATTGAATTGGTTGATA
* ** *
22837 TACTAAAAAAATACCG-TATTGAA-TGCATT--TA
1 TACT--AAGAATAAGGTTATTGAATTG-GTTGATA
22868 TACTAAGAATGTAAGGTTATTGAATTGGTTGATA
1 TACTAAGAA--TAAGGTTATTGAATTGGTTGATA
22902 GTATTATATT
Statistics
Matches: 48, Mismatches: 8, Indels: 16
0.67 0.11 0.22
Matches are distributed among these distances:
29 4 0.08
31 9 0.19
32 15 0.31
33 11 0.23
34 9 0.19
ACGTcount: A:0.39, C:0.06, G:0.19, T:0.36
Consensus pattern (32 bp):
TACTAAGAATAAGGTTATTGAATTGGTTGATA
Found at i:25227 original size:22 final size:21
Alignment explanation
Indices: 25200--25299 Score: 67
Period size: 22 Copynumber: 4.6 Consensus size: 21
25190 GCTATAATAT
*
25200 TTTGATAACCTCTCTAAGAAA
1 TTTGATAACCTCACTAAGAAA
* * **
25221 TTATGATAGCCTCCCTGTGAAA
1 TT-TGATAACCTCACTAAGAAA
* *
25243 CTTTGATAACCACACTATGAAA
1 -TTTGATAACCTCACTAAGAAA
**
25265 TTTTGATAACAACACTATA-AAA
1 -TTTGATAACCTCACTA-AGAAA
25287 TTGTGATAACCTC
1 TT-TGATAACCTC
25300 TATATGAAAA
Statistics
Matches: 62, Mismatches: 13, Indels: 7
0.76 0.16 0.09
Matches are distributed among these distances:
21 4 0.06
22 56 0.90
23 2 0.03
ACGTcount: A:0.37, C:0.20, G:0.11, T:0.32
Consensus pattern (21 bp):
TTTGATAACCTCACTAAGAAA
Found at i:25323 original size:25 final size:24
Alignment explanation
Indices: 25290--25336 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 24
25280 TATAAAATTG
25290 TGATAACCTCT-ATATGAAAATTTTT
1 TGATAACCT-TAATAT-AAAATTTTT
*
25315 TGATGACCTTAATATAAAATTT
1 TGATAACCTTAATATAAAATTT
25337 AGAATCCCAC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 8 0.40
25 12 0.60
ACGTcount: A:0.38, C:0.11, G:0.09, T:0.43
Consensus pattern (24 bp):
TGATAACCTTAATATAAAATTTTT
Found at i:25437 original size:22 final size:22
Alignment explanation
Indices: 25409--25451 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
25399 ATATGAAATT
*
25409 TTGATAACCTCCCTATAGAATG
1 TTGATAACCTCCATATAGAATG
*
25431 TTGATAACTTCCATATAGAAT
1 TTGATAACCTCCATATAGAAT
25452 TTCGTTAATC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.35, C:0.19, G:0.12, T:0.35
Consensus pattern (22 bp):
TTGATAACCTCCATATAGAATG
Found at i:25491 original size:22 final size:22
Alignment explanation
Indices: 25466--25590 Score: 123
Period size: 22 Copynumber: 5.7 Consensus size: 22
25456 TTAATCTCAC
*
25466 TATGAAATTTTGATAAGCACAA
1 TATGAAATTTTGATAAGCACAT
* *
25488 TATGAAATTTTGATTA-C-CTTT
1 TATGAAATTTTGATAAGCAC-AT
*
25509 TATGAAATTTTTG-TAACCACAT
1 TATGAAA-TTTTGATAAGCACAT
*
25531 TATGAAATTTTGATAATCACAT
1 TATGAAATTTTGATAAGCACAT
*
25553 TATGAAATTTTGAT-AGCTACAC
1 TATGAAATTTTGATAAGC-ACAT
* *
25575 TATAAAATTTCGATAA
1 TATGAAATTTTGATAA
25591 TCTGCAAAGT
Statistics
Matches: 86, Mismatches: 10, Indels: 13
0.79 0.09 0.12
Matches are distributed among these distances:
20 1 0.01
21 17 0.20
22 66 0.77
23 2 0.02
ACGTcount: A:0.39, C:0.10, G:0.10, T:0.40
Consensus pattern (22 bp):
TATGAAATTTTGATAAGCACAT
Found at i:25497 original size:44 final size:44
Alignment explanation
Indices: 25449--25593 Score: 143
Period size: 44 Copynumber: 3.3 Consensus size: 44
25439 TTCCATATAG
* *
25449 AATTTCGTTAATCTCACTATGAAATTTTGATAAGCACAATATGA
1 AATTTCGATAATCTCATTATGAAATTTTGATAAGCACAATATGA
* * * * * *
25493 AATTTTGATTACCT-TTTATGAAATTTTTG-TAACCACATTATGA
1 AATTTCGATAATCTCATTATGAAA-TTTTGATAAGCACAATATGA
* * * *
25536 AATTTTGATAATCACATTATGAAATTTTGAT-AGCTACACTATAA
1 AATTTCGATAATCTCATTATGAAATTTTGATAAGC-ACAATATGA
25580 AATTTCGATAATCT
1 AATTTCGATAATCT
25594 GCAAAGTTCA
Statistics
Matches: 80, Mismatches: 17, Indels: 8
0.76 0.16 0.08
Matches are distributed among these distances:
43 37 0.46
44 43 0.54
ACGTcount: A:0.37, C:0.12, G:0.10, T:0.41
Consensus pattern (44 bp):
AATTTCGATAATCTCATTATGAAATTTTGATAAGCACAATATGA
Done.