Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015476.1 Corchorus olitorius cultivar O-4 contig15509, 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: 39387
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.34
Found at i:46 original size:25 final size:25
Alignment explanation
Indices: 18--68 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
8 CATGCAGCCC
**
18 TCCTAGGGTGGCATGCCATGGAGAG
1 TCCTAGGGCAGCATGCCATGGAGAG
* *
43 TCCTAGGGCAGCATGTCATGGCGAG
1 TCCTAGGGCAGCATGCCATGGAGAG
68 T
1 T
69 GCCGCCCTCG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.20, C:0.22, G:0.37, T:0.22
Consensus pattern (25 bp):
TCCTAGGGCAGCATGCCATGGAGAG
Found at i:2600 original size:17 final size:18
Alignment explanation
Indices: 2575--2608 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
2565 GGGAGGAGGG
2575 GTTTGTTTTTT-GTTTTT
1 GTTTGTTTTTTAGTTTTT
*
2592 GTTTTTTTTTTAGTTTT
1 GTTTGTTTTTTAGTTTT
2609 AGAATAAAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.03, C:0.00, G:0.15, T:0.82
Consensus pattern (18 bp):
GTTTGTTTTTTAGTTTTT
Found at i:4235 original size:16 final size:16
Alignment explanation
Indices: 4214--4245 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
4204 AGTTTACTCT
4214 CTTCTTCATATGGACA
1 CTTCTTCATATGGACA
4230 CTTCTTCATATGGACA
1 CTTCTTCATATGGACA
4246 TGAAAAGCCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.25, G:0.12, T:0.38
Consensus pattern (16 bp):
CTTCTTCATATGGACA
Found at i:5615 original size:293 final size:293
Alignment explanation
Indices: 5030--5616 Score: 933
Period size: 294 Copynumber: 2.0 Consensus size: 293
5020 TTTTTAGTGA
* * *
5030 CTATGGAAATTACTTAAAGGCCAAATTGATGATTAATGTGGTGACTCCTTTTGGCTTTTTTTGGG
1 CTATGGAAATTACTTAAAGGCCAAATTGAGGATTAATGTGGTGACCCCTTTTGACTTTTTTTGGG
* * *
5095 CTTTTCTCACTTTTCGGGTGACTAAAAAGGCCCTTGATGAATTTTCTCCCTTACTTTTCCTGCTG
66 CTTTTCTCACTTTTCGGGTGACTAAAAACGCCCTCGATGAATTTCCTCCCTTACTTTTCCTGCTG
* *
5160 CCCTTTTTTGTAATTTACTATTTTTGTATTTATGATTAAGAGTGTTTTAATTATATATTAATTGT
131 CCCTTTTTTGTAATTTACTATTTTTATATTTATGATTAAGAGTGTTTTAATTACATATTAATTGT
* * **
5225 GTGTGGATATTAGGATTTAACAATTCAACTCTTCTGCCTGAATTCCAAAGGATTGGTGCTATAAA
196 GTGTGGATATTAGGATTTAACAATTCAACTCCTCTGCCGGAATTCCAAAGGATTAATGCTATAAA
*
5290 TGTATCTACCCGAGTGCATTAATTTGACAATTG
261 TGTATCTACCCGAGTGCATTAATTTAACAATTG
* *
5323 CTATGGAAATTACTTAAAGGCCAAATTGAGGATTAATGTGGTGCCCCCTTTTGACTTTTGTTTTG
1 CTATGGAAATTACTTAAAGGCCAAATTGAGGATTAATGTGGTGACCCCTTTTGACTTTT-TTTGG
* *
5388 TCTTTTCTCACTTTTTGGGTGACTAAAAACGCCCTCGATGAATTTCCTCCCTTACTTTTCCTGCT
65 GCTTTTCTCACTTTTCGGGTGACTAAAAACGCCCTCGATGAATTTCCTCCCTTACTTTTCCTGCT
*
5453 GCCCTTTTTTGTAATTTACTATTTTTATATTTATGATTAAGTGTGTTTTAATTACATATTAATTG
130 GCCCTTTTTTGTAATTTACTATTTTTATATTTATGATTAAGAGTGTTTTAATTACATATTAATTG
* * ** *
5518 TGTGTGGATATTAGGGTTTACCGGTTTAACTCCTCTGCCGGAA-TCCAAAGGATTAATGCTATAA
195 TGTGTGGATATTAGGATTTAACAATTCAACTCCTCTGCCGGAATTCCAAAGGATTAATGCTATAA
* *
5582 ATGTGTCTACCCGAGTTCATTAATTTAACAATTG
260 ATGTATCTACCCGAGTGCATTAATTTAACAATTG
5616 C
1 C
5617 AATCAAGATT
Statistics
Matches: 268, Mismatches: 25, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
293 106 0.40
294 162 0.60
ACGTcount: A:0.25, C:0.17, G:0.17, T:0.42
Consensus pattern (293 bp):
CTATGGAAATTACTTAAAGGCCAAATTGAGGATTAATGTGGTGACCCCTTTTGACTTTTTTTGGG
CTTTTCTCACTTTTCGGGTGACTAAAAACGCCCTCGATGAATTTCCTCCCTTACTTTTCCTGCTG
CCCTTTTTTGTAATTTACTATTTTTATATTTATGATTAAGAGTGTTTTAATTACATATTAATTGT
GTGTGGATATTAGGATTTAACAATTCAACTCCTCTGCCGGAATTCCAAAGGATTAATGCTATAAA
TGTATCTACCCGAGTGCATTAATTTAACAATTG
Found at i:7580 original size:9 final size:10
Alignment explanation
Indices: 7564--7588 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
7554 TCCATTTGAA
7564 CTTTTTTTGT
1 CTTTTTTTGT
7574 CTTTTTTTGT
1 CTTTTTTTGT
7584 CTTTT
1 CTTTT
7589 CTCCCTTGCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.00, C:0.12, G:0.08, T:0.80
Consensus pattern (10 bp):
CTTTTTTTGT
Found at i:8190 original size:42 final size:43
Alignment explanation
Indices: 8139--8232 Score: 138
Period size: 45 Copynumber: 2.2 Consensus size: 43
8129 AGTGCATTAC
* *
8139 CTAA-ATTCTA-CTCCGTCTCTAGGTAATTCATCAAAATAAAG
1 CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAG
8180 CTAATATTCTACTCCTCCATCTCTAGATAATTCATCAAAATAAAG
1 CTAATATTCTA--CCTCCATCTCTAGATAATTCATCAAAATAAAG
8225 CTAATATT
1 CTAATATT
8233 AATTGTTGCT
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
41 4 0.09
42 6 0.13
45 37 0.79
ACGTcount: A:0.37, C:0.22, G:0.06, T:0.34
Consensus pattern (43 bp):
CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAG
Found at i:9263 original size:24 final size:22
Alignment explanation
Indices: 9218--9279 Score: 70
Period size: 28 Copynumber: 2.5 Consensus size: 22
9208 TTTGTTATAT
9218 ATTTTATATATATCATAAATAATTAA
1 ATTTTATATATATCAT--A-AA-TAA
9244 ATATATTATATATATCATAAATAA
1 AT-T-TTATATATATCATAAATAA
9268 ATTTTATATATA
1 ATTTTATATATA
9280 ATAGTATAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
22 9 0.26
23 1 0.03
24 5 0.15
25 2 0.06
26 3 0.09
27 1 0.03
28 13 0.38
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (22 bp):
ATTTTATATATATCATAAATAA
Found at i:9266 original size:20 final size:20
Alignment explanation
Indices: 9241--9278 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
9231 CATAAATAAT
*
9241 TAAATATATTATATATATCA
1 TAAATAAATTATATATATCA
*
9261 TAAATAAATTTTATATAT
1 TAAATAAATTATATATAT
9279 AATAGTATAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (20 bp):
TAAATAAATTATATATATCA
Found at i:14230 original size:14 final size:14
Alignment explanation
Indices: 14211--14244 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
14201 TTTTATAACT
14211 ATTTTATTTTTACC
1 ATTTTATTTTTACC
*
14225 ATTTTATTTTTACT
1 ATTTTATTTTTACC
14239 ATTTTA
1 ATTTTA
14245 ATTTAAAAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.24, C:0.09, G:0.00, T:0.68
Consensus pattern (14 bp):
ATTTTATTTTTACC
Found at i:14292 original size:15 final size:15
Alignment explanation
Indices: 14272--14302 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
14262 GATTAACCTG
14272 TTTCTATTTGATAGT
1 TTTCTATTTGATAGT
14287 TTTCTATTTGATAGT
1 TTTCTATTTGATAGT
14302 T
1 T
14303 AATGTATTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.06, G:0.13, T:0.61
Consensus pattern (15 bp):
TTTCTATTTGATAGT
Found at i:16218 original size:21 final size:22
Alignment explanation
Indices: 16194--16234 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
16184 GTGTATAATA
*
16194 TTCTTGGGTCA-TCGGGTTATC
1 TTCTCGGGTCATTCGGGTTATC
*
16215 TTCTCGGGTTATTCGGGTTA
1 TTCTCGGGTCATTCGGGTTA
16235 CAAGTTTGTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.10, C:0.17, G:0.29, T:0.44
Consensus pattern (22 bp):
TTCTCGGGTCATTCGGGTTATC
Found at i:17162 original size:46 final size:46
Alignment explanation
Indices: 17095--17230 Score: 272
Period size: 46 Copynumber: 3.0 Consensus size: 46
17085 ACCAATTCAC
17095 AGAAATGTTAGTAAAGAAGAAACCCACCAAAATAGAAATGAAGAAG
1 AGAAATGTTAGTAAAGAAGAAACCCACCAAAATAGAAATGAAGAAG
17141 AGAAATGTTAGTAAAGAAGAAACCCACCAAAATAGAAATGAAGAAG
1 AGAAATGTTAGTAAAGAAGAAACCCACCAAAATAGAAATGAAGAAG
17187 AGAAATGTTAGTAAAGAAGAAACCCACCAAAATAGAAATGAAGA
1 AGAAATGTTAGTAAAGAAGAAACCCACCAAAATAGAAATGAAGA
17231 CGAAAGGAAA
Statistics
Matches: 90, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 90 1.00
ACGTcount: A:0.57, C:0.11, G:0.19, T:0.13
Consensus pattern (46 bp):
AGAAATGTTAGTAAAGAAGAAACCCACCAAAATAGAAATGAAGAAG
Found at i:17173 original size:27 final size:27
Alignment explanation
Indices: 17143--17219 Score: 64
Period size: 23 Copynumber: 3.1 Consensus size: 27
17133 TGAAGAAGAG
17143 AAATGTTAGTAAAGAAGAAACCCACCA
1 AAATGTTAGTAAAGAAGAAACCCACCA
* *
17170 AAA---TAG-AAATGAAG-AA--GA--G
1 AAATGTTAGTAAA-GAAGAAACCCACCA
17189 AAATGTTAGTAAAGAAGAAACCCACCA
1 AAATGTTAGTAAAGAAGAAACCCACCA
17216 AAAT
1 AAAT
17220 AGAAATGAAG
Statistics
Matches: 36, Mismatches: 4, Indels: 20
0.60 0.07 0.33
Matches are distributed among these distances:
19 3 0.08
21 1 0.03
22 7 0.19
23 10 0.28
24 7 0.19
25 1 0.03
27 7 0.19
ACGTcount: A:0.56, C:0.13, G:0.17, T:0.14
Consensus pattern (27 bp):
AAATGTTAGTAAAGAAGAAACCCACCA
Found at i:21611 original size:13 final size:13
Alignment explanation
Indices: 21593--21622 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
21583 AACCGTTAAT
21593 ATCAAAATCATAA
1 ATCAAAATCATAA
*
21606 ATCAAAGTCATAA
1 ATCAAAATCATAA
21619 ATCA
1 ATCA
21623 GAGTAAAACC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.57, C:0.17, G:0.03, T:0.23
Consensus pattern (13 bp):
ATCAAAATCATAA
Found at i:22672 original size:16 final size:15
Alignment explanation
Indices: 22635--22685 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 15
22625 TATTCCCAAA
22635 TTTT-TTCCTTATTTC
1 TTTTCTTCCTT-TTTC
*
22650 CTTTCTTCTTCTTTTT-
1 TTTTCTTC--CTTTTTC
22666 TTTTCTTCCTTTTTC
1 TTTTCTTCCTTTTTC
22681 TTTTC
1 TTTTC
22686 CATTCATTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
14 6 0.20
15 8 0.27
16 10 0.33
17 3 0.10
18 3 0.10
ACGTcount: A:0.02, C:0.24, G:0.00, T:0.75
Consensus pattern (15 bp):
TTTTCTTCCTTTTTC
Found at i:31997 original size:2 final size:2
Alignment explanation
Indices: 31990--32016 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
31980 ATGGTTGAGG
31990 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 T
32017 GCAAGTTGAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:36708 original size:20 final size:21
Alignment explanation
Indices: 36669--36710 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
36659 CCTCTCATGG
**
36669 AGCTTGGGATTTTCTTCATCA
1 AGCTTGGGATTTTCACCATCA
36690 AGCTT-GGATTTTCACCATCA
1 AGCTTGGGATTTTCACCATCA
36710 A
1 A
36711 ATATCTCTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.24, C:0.21, G:0.17, T:0.38
Consensus pattern (21 bp):
AGCTTGGGATTTTCACCATCA
Done.