Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022469.1 Corchorus olitorius cultivar O-4 contig22502, 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: 68997
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:37 original size:12 final size:12
Alignment explanation
Indices: 22--50 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
12 TTGCCATATA
22 ATTATTTGATAC
1 ATTATTTGATAC
34 ATTATTTGATAC
1 ATTATTTGATAC
46 ATTAT
1 ATTAT
51 CATTGGAGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.34, C:0.07, G:0.07, T:0.52
Consensus pattern (12 bp):
ATTATTTGATAC
Found at i:1652 original size:25 final size:25
Alignment explanation
Indices: 1624--1713 Score: 112
Period size: 25 Copynumber: 3.6 Consensus size: 25
1614 ATATAGATAT
1624 CTATTAATATACTTGGCCTAGTGGA
1 CTATTAATATACTTGGCCTAGTGGA
* * *
1649 CTATTAATATACTTTG-ATA-TAGATA
1 CTATTAATATACTTGGCCTAGT-G-GA
1674 TCTATTAATATACTTGGCCTAGTGGA
1 -CTATTAATATACTTGGCCTAGTGGA
1700 CTATTAATATACTT
1 CTATTAATATACTT
1714 TGATATAGAT
Statistics
Matches: 54, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
23 1 0.02
24 3 0.06
25 30 0.56
26 16 0.30
27 3 0.06
28 1 0.02
ACGTcount: A:0.32, C:0.13, G:0.13, T:0.41
Consensus pattern (25 bp):
CTATTAATATACTTGGCCTAGTGGA
Found at i:1667 original size:51 final size:51
Alignment explanation
Indices: 1607--1731 Score: 250
Period size: 51 Copynumber: 2.5 Consensus size: 51
1597 GAAAATTAGG
1607 TACTTTGATATAGATATCTATTAATATACTTGGCCTAGTGGACTATTAATA
1 TACTTTGATATAGATATCTATTAATATACTTGGCCTAGTGGACTATTAATA
1658 TACTTTGATATAGATATCTATTAATATACTTGGCCTAGTGGACTATTAATA
1 TACTTTGATATAGATATCTATTAATATACTTGGCCTAGTGGACTATTAATA
1709 TACTTTGATATAGATATCTATTA
1 TACTTTGATATAGATATCTATTA
1732 TTAATGTGCT
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 74 1.00
ACGTcount: A:0.34, C:0.11, G:0.13, T:0.42
Consensus pattern (51 bp):
TACTTTGATATAGATATCTATTAATATACTTGGCCTAGTGGACTATTAATA
Found at i:5395 original size:2 final size:2
Alignment explanation
Indices: 5384--5413 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
5374 TTATTGTTTT
5384 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5414 TGAAGTCTAC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:8500 original size:2 final size:2
Alignment explanation
Indices: 8493--8523 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
8483 ATAGTTATTT
8493 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
8524 TTGAGGGGAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:11133 original size:66 final size:66
Alignment explanation
Indices: 11061--11284 Score: 244
Period size: 66 Copynumber: 3.4 Consensus size: 66
11051 TTTCCCATTC
* * *
11061 AATTTTGGTAACCT-CTCCATGAAATTCTT-GTAACCTCACTATGAAATTCCAATAACCT-ATCT
1 AATTTTGGTAACCTCCT-TATGAAATT-TTGGTAACCTCACTATGAAATTCCAACAACCTCA-CA
11123 AT-A
63 ATGA
* *
11126 AAGTTTTGGTAACCTCCTTATGAAATTTTGGTAACCTCCCTATGAAATTCTAACAACCTCACAAT
1 AA-TTTTGGTAACCTCCTTATGAAATTTTGGTAACCTCACTATGAAATTCCAACAACCTCACAAT
11191 GA
65 GA
* **** *
11193 AATTTTGGTAACCTCCTTATGAAATTTTGGTAA-CTAAACTATGAAATTCTGGTAACCTC-CGTA
1 AATTTTGGTAACCTCCTTATGAAATTTTGGTAACCT-CACTATGAAATTCCAACAACCTCAC-AA
11256 TGA
64 TGA
*
11259 AAGTTTGGTAACCTCCTTATGAAATT
1 AATTTTGGTAACCTCCTTATGAAATT
11285 CTGTGATTTG
Statistics
Matches: 140, Mismatches: 12, Indels: 13
0.85 0.07 0.08
Matches are distributed among these distances:
65 7 0.05
66 127 0.91
67 6 0.04
ACGTcount: A:0.33, C:0.20, G:0.12, T:0.35
Consensus pattern (66 bp):
AATTTTGGTAACCTCCTTATGAAATTTTGGTAACCTCACTATGAAATTCCAACAACCTCACAATG
A
Found at i:11214 original size:22 final size:22
Alignment explanation
Indices: 11061--11284 Score: 176
Period size: 22 Copynumber: 10.2 Consensus size: 22
11051 TTTCCCATTC
*
11061 AATTTTGGTAACCT-CTCCATGA
1 AATTTTGGTAACCTCCT-TATGA
11083 AATTCTT-GTAACCTCAC-TATGA
1 AATT-TTGGTAACCTC-CTTATGA
**** *
11105 AATTCCAATAACCT-ATCTAT-A
1 AATTTTGGTAACCTCCT-TATGA
11126 AAGTTTTGGTAACCTCCTTATGA
1 AA-TTTTGGTAACCTCCTTATGA
*
11149 AATTTTGGTAACCTCCCTATGA
1 AATTTTGGTAACCTCCTTATGA
* *** *
11171 AATTCTAACAACCTCAC-AATGA
1 AATTTTGGTAACCTC-CTTATGA
11193 AATTTTGGTAACCTCCTTATGA
1 AATTTTGGTAACCTCCTTATGA
*
11215 AATTTTGGTAA-CTAAAC-TATGA
1 AATTTTGGTAACCT--CCTTATGA
* *
11237 AATTCTGGTAACCTCCGTATGA
1 AATTTTGGTAACCTCCTTATGA
*
11259 AAGTTTGGTAACCTCCTTATGA
1 AATTTTGGTAACCTCCTTATGA
11281 AATT
1 AATT
11285 CTGTGATTTG
Statistics
Matches: 159, Mismatches: 28, Indels: 30
0.73 0.13 0.14
Matches are distributed among these distances:
21 7 0.04
22 141 0.89
23 10 0.06
24 1 0.01
ACGTcount: A:0.33, C:0.20, G:0.12, T:0.35
Consensus pattern (22 bp):
AATTTTGGTAACCTCCTTATGA
Found at i:16925 original size:29 final size:31
Alignment explanation
Indices: 16883--16959 Score: 79
Period size: 35 Copynumber: 2.4 Consensus size: 31
16873 TTTTGTGCCA
16883 AAAAAAAGT-AAAAT-A-AATGGTTAAAGAAG
1 AAAAAAA-TAAAAATAAGAATGGTTAAAGAAG
*
16912 AAAAAAATAAAAATCAACGGTAATGGTTAACGAAG
1 AAAAAAATAAAAAT-AA--G-AATGGTTAAAGAAG
16947 AAAAAAATAAAAA
1 AAAAAAATAAAAA
16960 AAAACGGTAA
Statistics
Matches: 40, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
28 1 0.03
29 12 0.30
31 1 0.03
35 26 0.65
ACGTcount: A:0.66, C:0.04, G:0.14, T:0.16
Consensus pattern (31 bp):
AAAAAAATAAAAATAAGAATGGTTAAAGAAG
Found at i:16937 original size:35 final size:35
Alignment explanation
Indices: 16898--16970 Score: 119
Period size: 35 Copynumber: 2.1 Consensus size: 35
16888 AAGTAAAATA
**
16898 AATGGTTAAAGAAGAAAAAAATAAAAATCAACGGT
1 AATGGTTAAAGAAGAAAAAAATAAAAAAAAACGGT
*
16933 AATGGTTAACGAAGAAAAAAATAAAAAAAAACGGT
1 AATGGTTAAAGAAGAAAAAAATAAAAAAAAACGGT
16968 AAT
1 AAT
16971 ATCAACGGTT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.62, C:0.05, G:0.16, T:0.16
Consensus pattern (35 bp):
AATGGTTAAAGAAGAAAAAAATAAAAAAAAACGGT
Found at i:19618 original size:15 final size:15
Alignment explanation
Indices: 19598--19632 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
19588 ACTAACTCGA
*
19598 CAAACTCAACTGACT
1 CAAACTAAACTGACT
19613 CAAACTAAACTGACT
1 CAAACTAAACTGACT
*
19628 TAAAC
1 CAAAC
19633 ATCCAAGATC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.46, C:0.29, G:0.06, T:0.20
Consensus pattern (15 bp):
CAAACTAAACTGACT
Found at i:20207 original size:42 final size:42
Alignment explanation
Indices: 20140--20262 Score: 210
Period size: 42 Copynumber: 2.9 Consensus size: 42
20130 AATTGACCAT
* * *
20140 CCTAATAATTAAGGAAATAAATTAAATTCAGGTTTAGCCCCC
1 CCTAATAATTAAGGTAAGAATTTAAATTCAGGTTTAGCCCCC
20182 CCTAATAATTAAGGTAAGAATTTAAATTCAGGTTTAGCCCCC
1 CCTAATAATTAAGGTAAGAATTTAAATTCAGGTTTAGCCCCC
*
20224 CCTAATAATTAAGGTACGAATTTAAATTCAGGTTTAGCC
1 CCTAATAATTAAGGTAAGAATTTAAATTCAGGTTTAGCC
20263 TCTAGTTATA
Statistics
Matches: 77, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 77 1.00
ACGTcount: A:0.37, C:0.18, G:0.14, T:0.31
Consensus pattern (42 bp):
CCTAATAATTAAGGTAAGAATTTAAATTCAGGTTTAGCCCCC
Found at i:34808 original size:12 final size:12
Alignment explanation
Indices: 34791--34817 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
34781 TTAAAAGAAA
34791 AAAAAACAAAAC
1 AAAAAACAAAAC
34803 AAAAAACAAAAC
1 AAAAAACAAAAC
34815 AAA
1 AAA
34818 GCTTAAATGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.85, C:0.15, G:0.00, T:0.00
Consensus pattern (12 bp):
AAAAAACAAAAC
Found at i:44132 original size:6 final size:6
Alignment explanation
Indices: 44123--44222 Score: 85
Period size: 6 Copynumber: 16.7 Consensus size: 6
44113 CGCTGCTGCG
* * * *
44123 GCTGTT GCTG-T GGTGGTT GCTGTT GTTGTT GTTGCT GCTGTT GCTGTT
1 GCTGTT GCTGTT GCT-GTT GCTGTT GCTGTT GCTGTT GCTGTT GCTGTT
* * * * * * *
44171 GCTGCT GCTGCT GCTGTT GCTGTT GTTGTT GTTGCT GCTGCT GCTGCT
1 GCTGTT GCTGTT GCTGTT GCTGTT GCTGTT GCTGTT GCTGTT GCTGTT
44219 GCTG
1 GCTG
44223 AGCATGCCTC
Statistics
Matches: 81, Mismatches: 11, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
5 3 0.04
6 75 0.93
7 3 0.04
ACGTcount: A:0.00, C:0.18, G:0.36, T:0.46
Consensus pattern (6 bp):
GCTGTT
Found at i:44155 original size:9 final size:9
Alignment explanation
Indices: 44138--44210 Score: 56
Period size: 9 Copynumber: 7.8 Consensus size: 9
44128 TGCTGTGGTG
44138 GTTGCTGTT
1 GTTGCTGTT
*
44147 GTTGTTGTT
1 GTTGCTGTT
*
44156 GCTGCTGTTGCT
1 GTTGCTG-T--T
*
44168 GTTGCTGCT
1 GTTGCTGTT
* *
44177 GCTGCTGCT
1 GTTGCTGTT
44186 GTTGCTGTT
1 GTTGCTGTT
*
44195 GTTGTTGTT
1 GTTGCTGTT
*
44204 GCTGCTG
1 GTTGCTG
44211 CTGCTGCTGC
Statistics
Matches: 50, Mismatches: 11, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
9 42 0.84
10 1 0.02
12 7 0.14
ACGTcount: A:0.00, C:0.16, G:0.34, T:0.49
Consensus pattern (9 bp):
GTTGCTGTT
Found at i:44209 original size:3 final size:3
Alignment explanation
Indices: 44155--44222 Score: 73
Period size: 3 Copynumber: 22.7 Consensus size: 3
44145 TTGTTGTTGT
* * * * * * *
44155 TGC TGC TGT TGC TGT TGC TGC TGC TGC TGC TGT TGC TGT TGT TGT TGT
1 TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC
44203 TGC TGC TGC TGC TGC TGC TG
1 TGC TGC TGC TGC TGC TGC TG
44223 AGCATGCCTC
Statistics
Matches: 57, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.00, C:0.22, G:0.34, T:0.44
Consensus pattern (3 bp):
TGC
Found at i:59716 original size:26 final size:26
Alignment explanation
Indices: 59680--59733 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
59670 TAGTTCAAAA
*
59680 ACAACTAAAAACCACTTCTGGAGAGT
1 ACAACTAAAAAACACTTCTGGAGAGT
59706 ACAACTAAAAAACACTTCTGGAGAGT
1 ACAACTAAAAAACACTTCTGGAGAGT
59732 AC
1 AC
59734 TTCTGGATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.44, C:0.22, G:0.15, T:0.19
Consensus pattern (26 bp):
ACAACTAAAAAACACTTCTGGAGAGT
Found at i:62455 original size:21 final size:22
Alignment explanation
Indices: 62430--62484 Score: 103
Period size: 22 Copynumber: 2.5 Consensus size: 22
62420 CCAATCATGG
62430 AAAAAGCATATGTTTC-AAAAA
1 AAAAAGCATATGTTTCAAAAAA
62451 AAAAAGCATATGTTTCAAAAAA
1 AAAAAGCATATGTTTCAAAAAA
62473 AAAAAGCATATG
1 AAAAAGCATATG
62485 CACCATTCCC
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
21 16 0.48
22 17 0.52
ACGTcount: A:0.58, C:0.09, G:0.11, T:0.22
Consensus pattern (22 bp):
AAAAAGCATATGTTTCAAAAAA
Found at i:64337 original size:29 final size:29
Alignment explanation
Indices: 64305--64377 Score: 78
Period size: 29 Copynumber: 2.5 Consensus size: 29
64295 ATTTGTAGCG
*
64305 TTTGGACGTTTTGCCTTC-TGAATTTCAAT
1 TTTGGACGTTTTGCC-TCATGAACTTCAAT
* *
64334 TTTGAACATTTTG-CTCATGAACTTCAAT
1 TTTGGACGTTTTGCCTCATGAACTTCAAT
*
64362 TTTGGGATGTTTTGCC
1 TTT-GGACGTTTTGCC
64378 CCCTTAACCT
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
27 2 0.06
28 14 0.40
29 18 0.51
30 1 0.03
ACGTcount: A:0.19, C:0.16, G:0.18, T:0.47
Consensus pattern (29 bp):
TTTGGACGTTTTGCCTCATGAACTTCAAT
Found at i:64478 original size:33 final size:33
Alignment explanation
Indices: 64440--64525 Score: 127
Period size: 33 Copynumber: 2.6 Consensus size: 33
64430 GATTTTGTCC
64440 GACATGACAATGCCACGTGGGCCGGGTTGGTCT
1 GACATGACAATGCCACGTGGGCCGGGTTGGTCT
* * *
64473 GACATGACAACGCCACGTGGGTCGGGTTGGTTT
1 GACATGACAATGCCACGTGGGCCGGGTTGGTCT
* *
64506 GACATGGCAATGTCACGTGG
1 GACATGACAATGCCACGTGG
64526 TAATGCCACG
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 47 1.00
ACGTcount: A:0.20, C:0.22, G:0.36, T:0.22
Consensus pattern (33 bp):
GACATGACAATGCCACGTGGGCCGGGTTGGTCT
Found at i:64535 original size:13 final size:13
Alignment explanation
Indices: 64510--64549 Score: 62
Period size: 13 Copynumber: 3.1 Consensus size: 13
64500 TGGTTTGACA
*
64510 TGGCAATGTCACG
1 TGGCAATGCCACG
*
64523 TGGTAATGCCACG
1 TGGCAATGCCACG
64536 TGGCAATGCCACG
1 TGGCAATGCCACG
64549 T
1 T
64550 CAACGGTTCG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.23, C:0.25, G:0.30, T:0.23
Consensus pattern (13 bp):
TGGCAATGCCACG
Done.