Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012122.1 Corchorus capsularis cultivar CVL-1 contig12143, 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: 16370
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31
Found at i:217 original size:26 final size:27
Alignment explanation
Indices: 171--226 Score: 78
Period size: 26 Copynumber: 2.1 Consensus size: 27
161 TTACCACTAA
171 TAATAATTAATATAATAATAAAAAGTT
1 TAATAATTAATATAATAATAAAAAGTT
* * *
198 TAATAA-TATTATAATAATAAGAGGTT
1 TAATAATTAATATAATAATAAAAAGTT
224 TAA
1 TAA
227 CGTGAAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
26 20 0.77
27 6 0.23
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.38
Consensus pattern (27 bp):
TAATAATTAATATAATAATAAAAAGTT
Found at i:315 original size:12 final size:12
Alignment explanation
Indices: 298--331 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
288 TATGGAGTAA
*
298 TTAATAATAATT
1 TTAATAATAATC
310 TTAATAATAATC
1 TTAATAATAATC
*
322 ATAATAATAA
1 TTAATAATAA
332 GTTGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (12 bp):
TTAATAATAATC
Found at i:364 original size:114 final size:113
Alignment explanation
Indices: 186--392 Score: 283
Period size: 114 Copynumber: 1.8 Consensus size: 113
176 ATTAATATAA
* * *
186 TAATAAAAAGTTTAATAATATTATAATAATAAGAGGTTTAACGTGAAAAAAGTTGTTACCATTAT
1 TAATAAAAAGTTTAATAATATCATAATAATAAGAGGTTTAACATGAAAAAAATTGTTACCATTA-
251 TTTTAGA-TTTTGTAATATGGAAAGAAAAACATAATGATATGGAGTAAT
65 TTTTAGACTTTTGTAATATGGAAAGAAAAACATAATGATATGGAGTAAT
* * ** *
299 TAATAATAATTTTAATAATAATCATAATAATAAGTTGTTTAACAT-AAAAATAATTGTTACTATT
1 TAATAAAAAGTTTAATAAT-ATCATAATAATAAGAGGTTTAACATGAAAAA-AATTGTTACCATT
* *
363 ATTTTAGACTTTTTTAATATGGAAATAAAA
64 ATTTTAGACTTTTGTAATATGGAAAGAAAA
393 TCTGGTTGGA
Statistics
Matches: 81, Mismatches: 10, Indels: 5
0.84 0.10 0.05
Matches are distributed among these distances:
113 29 0.36
114 52 0.64
ACGTcount: A:0.46, C:0.04, G:0.11, T:0.39
Consensus pattern (113 bp):
TAATAAAAAGTTTAATAATATCATAATAATAAGAGGTTTAACATGAAAAAAATTGTTACCATTAT
TTTAGACTTTTGTAATATGGAAAGAAAAACATAATGATATGGAGTAAT
Found at i:3728 original size:7 final size:7
Alignment explanation
Indices: 3710--3742 Score: 57
Period size: 7 Copynumber: 4.6 Consensus size: 7
3700 TAGGCAGATT
3710 AAATTAGA
1 AAATT-GA
3718 AAATTGA
1 AAATTGA
3725 AAATTGA
1 AAATTGA
3732 AAATTGA
1 AAATTGA
3739 AAAT
1 AAAT
3743 CTATTTCATT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 20 0.80
8 5 0.20
ACGTcount: A:0.61, C:0.00, G:0.12, T:0.27
Consensus pattern (7 bp):
AAATTGA
Found at i:6352 original size:13 final size:13
Alignment explanation
Indices: 6334--6359 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
6324 TCCAAGATAG
6334 AATGTAAAACACT
1 AATGTAAAACACT
6347 AATGTAAAACACT
1 AATGTAAAACACT
6360 TCAGAAACTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.15, G:0.08, T:0.23
Consensus pattern (13 bp):
AATGTAAAACACT
Found at i:7790 original size:20 final size:20
Alignment explanation
Indices: 7752--7811 Score: 63
Period size: 17 Copynumber: 3.0 Consensus size: 20
7742 TTTATATAAT
7752 ATAATAATTACTAATTTATATTA
1 ATAAT-ATTA-TAA-TTATATTA
7775 ATAATATTATAATTATATT-
1 ATAATATTATAATTATATTA
*
7794 CTAATA-TA-AATTATATTA
1 ATAATATTATAATTATATTA
7812 TACAACAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
17 9 0.26
18 2 0.06
19 5 0.14
20 7 0.20
21 3 0.09
22 4 0.11
23 5 0.14
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (20 bp):
ATAATATTATAATTATATTA
Found at i:7800 original size:28 final size:28
Alignment explanation
Indices: 7747--7813 Score: 75
Period size: 28 Copynumber: 2.4 Consensus size: 28
7737 TATATTTTAT
* *
7747 ATAATATAATAATTACTAATTTATATTA
1 ATAATATTATAATTACTAATTTATATAA
7775 ATAATATTATAATTA-T-ATTCTAATATAA
1 ATAATATTATAATTACTAATT-T-ATATAA
*
7803 ATTATATTATA
1 ATAATATTATA
7814 CAACAAAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
26 3 0.09
27 2 0.06
28 29 0.85
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.48
Consensus pattern (28 bp):
ATAATATTATAATTACTAATTTATATAA
Found at i:7854 original size:4 final size:4
Alignment explanation
Indices: 7845--7895 Score: 93
Period size: 4 Copynumber: 12.8 Consensus size: 4
7835 AATAATAATA
*
7845 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAT ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
7893 ATA
1 ATA
7896 AATATAATAT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
4 45 1.00
ACGTcount: A:0.51, C:0.22, G:0.00, T:0.27
Consensus pattern (4 bp):
ATAC
Found at i:7942 original size:20 final size:20
Alignment explanation
Indices: 7904--7963 Score: 63
Period size: 17 Copynumber: 3.0 Consensus size: 20
7894 TAAATATAAT
7904 ATAATAATTACTAATTTATATTA
1 ATAAT-ATTA-TAA-TTATATTA
7927 ATAATATTATAATTATATT-
1 ATAATATTATAATTATATTA
*
7946 CTAATA-TA-AATTATATTA
1 ATAATATTATAATTATATTA
7964 TACAACAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
17 9 0.26
18 2 0.06
19 5 0.14
20 7 0.20
21 3 0.09
22 4 0.11
23 5 0.14
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (20 bp):
ATAATATTATAATTATATTA
Found at i:7952 original size:28 final size:28
Alignment explanation
Indices: 7899--7965 Score: 75
Period size: 28 Copynumber: 2.4 Consensus size: 28
7889 ATACATAAAT
* *
7899 ATAATATAATAATTACTAATTTATATTA
1 ATAATATTATAATTACTAATTTATATAA
7927 ATAATATTATAATTA-T-ATTCTAATATAA
1 ATAATATTATAATTACTAATT-T-ATATAA
*
7955 ATTATATTATA
1 ATAATATTATA
7966 CAACAAAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
26 3 0.09
27 2 0.06
28 29 0.85
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.48
Consensus pattern (28 bp):
ATAATATTATAATTACTAATTTATATAA
Found at i:7985 original size:3 final size:3
Alignment explanation
Indices: 7979--8011 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
7969 CAAAAAAAGT
7979 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
8012 CATACATACA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:8045 original size:152 final size:152
Alignment explanation
Indices: 7745--8047 Score: 556
Period size: 152 Copynumber: 2.0 Consensus size: 152
7735 TATATATTTT
7745 ATATAATATAATAATTACTAATTTATATTAATAATATTATAATTATATTCTAATATAAATTATAT
1 ATATAATATAATAATTACTAATTTATATTAATAATATTATAATTATATTCTAATATAAATTATAT
*
7810 TATACAACAAAAAAAGTATAATAATAATAATAATAATACATACATACATACATACATACATACAT
66 TATACAACAAAAAAAGTATAATAATAATAATAATAATACATACATAAATACATACATACATACAT
*
7875 ACATACATACATATATACATAA
131 ACATACATACATACATACATAA
7897 ATATAATATAATAATTACTAATTTATATTAATAATATTATAATTATATTCTAATATAAATTATAT
1 ATATAATATAATAATTACTAATTTATATTAATAATATTATAATTATATTCTAATATAAATTATAT
7962 TATACAACAAAAAAAGTATAATAATAATAATAATAATA-ATA-ATAATAATACATACATACATAC
66 TATACAACAAAAAAAGTATAATAATAATAATAATAATACATACAT-A-AATACATACATACATAC
8025 ATACATACATACATACATACATA
129 ATACATACATACATACATACATA
8048 CATACATACA
Statistics
Matches: 147, Mismatches: 2, Indels: 4
0.96 0.01 0.03
Matches are distributed among these distances:
150 2 0.01
151 4 0.03
152 141 0.96
ACGTcount: A:0.54, C:0.09, G:0.01, T:0.36
Consensus pattern (152 bp):
ATATAATATAATAATTACTAATTTATATTAATAATATTATAATTATATTCTAATATAAATTATAT
TATACAACAAAAAAAGTATAATAATAATAATAATAATACATACATAAATACATACATACATACAT
ACATACATACATACATACATAA
Found at i:8080 original size:4 final size:4
Alignment explanation
Indices: 8009--8061 Score: 106
Period size: 4 Copynumber: 13.2 Consensus size: 4
7999 AATAATAATA
8009 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
8057 ATAC A
1 ATAC A
8062 AAATATTTAG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 49 1.00
ACGTcount: A:0.51, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
ATAC
Found at i:8917 original size:16 final size:14
Alignment explanation
Indices: 8885--8912 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
8875 ACTTTTAAAT
8885 TAAAATGGTAAAAA
1 TAAAATGGTAAAAA
8899 TAAAATGGTAAAAA
1 TAAAATGGTAAAAA
8913 AATAATTATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.64, C:0.00, G:0.14, T:0.21
Consensus pattern (14 bp):
TAAAATGGTAAAAA
Found at i:11668 original size:6 final size:6
Alignment explanation
Indices: 11657--11684 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
11647 GGTTTTGGAG
11657 AACCCA AACCCA AACCCA AACCCA AACC
1 AACCCA AACCCA AACCCA AACCCA AACC
11685 GTAGTTCTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (6 bp):
AACCCA
Found at i:16209 original size:11 final size:11
Alignment explanation
Indices: 16193--16217 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
16183 TCTCTGGTAA
16193 TATTATATTAT
1 TATTATATTAT
16204 TATTATATTAT
1 TATTATATTAT
16215 TAT
1 TAT
16218 AATAATAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (11 bp):
TATTATATTAT
Done.