Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016347.1 Corchorus capsularis cultivar CVL-1 contig16368, 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: 22599
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.35
Found at i:420 original size:22 final size:23
Alignment explanation
Indices: 383--427 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
373 ATTCTCTATT
* *
383 CTCTTGTCCTTTTCATAGTTCAA
1 CTCTTGTCATTTTCATACTTCAA
406 CTCTTGT-ATTTTCATACTTCAA
1 CTCTTGTCATTTTCATACTTCAA
428 TCCTTTACTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.20, C:0.24, G:0.07, T:0.49
Consensus pattern (23 bp):
CTCTTGTCATTTTCATACTTCAA
Found at i:1768 original size:22 final size:23
Alignment explanation
Indices: 1731--1775 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
1721 ATTCTCTATT
* *
1731 CTCTTGTCCTTTTCATAGTTCAA
1 CTCTTGTCATTTTCATACTTCAA
1754 CTCTTGT-ATTTTCATACTTCAA
1 CTCTTGTCATTTTCATACTTCAA
1776 TCCTTTACTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.20, C:0.24, G:0.07, T:0.49
Consensus pattern (23 bp):
CTCTTGTCATTTTCATACTTCAA
Found at i:5019 original size:2 final size:2
Alignment explanation
Indices: 5012--5053 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
5002 TATTAAGGTG
* *
5012 AT AT AT AT AT AT AT AT AT AC AC AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5054 CATTATCATT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:9879 original size:17 final size:17
Alignment explanation
Indices: 9829--9896 Score: 77
Period size: 17 Copynumber: 4.1 Consensus size: 17
9819 TTTTCTACCA
* *
9829 TTCTCCATATTCTCTTC
1 TTCTCTATATTCTCTTG
*
9846 TTCT-TCATATTATCTTG
1 TTCTCT-ATATTCTCTTG
9863 TTCTCTATATTCTCTTG
1 TTCTCTATATTCTCTTG
*
9880 -TCTCTCTATTCTCTTG
1 TTCTCTATATTCTCTTG
9896 T
1 T
9897 CTTGTCCATA
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
16 15 0.35
17 27 0.63
18 1 0.02
ACGTcount: A:0.12, C:0.26, G:0.04, T:0.57
Consensus pattern (17 bp):
TTCTCTATATTCTCTTG
Found at i:9889 original size:16 final size:16
Alignment explanation
Indices: 9830--9898 Score: 68
Period size: 16 Copynumber: 4.2 Consensus size: 16
9820 TTTCTACCAT
* *
9830 TCTCCATATTCTCTTC
1 TCTCTATATTCTCTTG
*
9846 T-TCTTCATATTATCTTG
1 TCTC-T-ATATTCTCTTG
9863 TTCTCTATATTCTCTTG
1 -TCTCTATATTCTCTTG
*
9880 TCTCTCTATTCTCTTG
1 TCTCTATATTCTCTTG
9896 TCT
1 TCT
9899 TGTCCATACT
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
15 2 0.05
16 19 0.43
17 19 0.43
18 2 0.05
19 2 0.05
ACGTcount: A:0.12, C:0.28, G:0.04, T:0.57
Consensus pattern (16 bp):
TCTCTATATTCTCTTG
Found at i:10208 original size:33 final size:33
Alignment explanation
Indices: 10166--10328 Score: 290
Period size: 33 Copynumber: 4.9 Consensus size: 33
10156 CTATCCTTGA
10166 ATATTAGTGGCACCTGAAGTTGTCACATCAAGC
1 ATATTAGTGGCACCTGAAGTTGTCACATCAAGC
*
10199 ATATTAGTGGCACCTGAAGTTGTAACATCAAGC
1 ATATTAGTGGCACCTGAAGTTGTCACATCAAGC
* *
10232 TTATTAGTGGCATCTGAAGTTGTCACATCAAGC
1 ATATTAGTGGCACCTGAAGTTGTCACATCAAGC
*
10265 ATATTAGTGGCACCTGAAGTTGTCACATCAAGT
1 ATATTAGTGGCACCTGAAGTTGTCACATCAAGC
10298 ATATTAGTGGCACCTGAAGTTGTCACATCAA
1 ATATTAGTGGCACCTGAAGTTGTCACATCAA
10329 AAATATAGTA
Statistics
Matches: 123, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 123 1.00
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (33 bp):
ATATTAGTGGCACCTGAAGTTGTCACATCAAGC
Found at i:10375 original size:29 final size:29
Alignment explanation
Indices: 10333--10393 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 29
10323 CATCAAAAAT
*
10333 ATAGTATTACTTTGACA-CTCGAAGTTGTC
1 ATAGTATCACTTTGACACCT-GAAGTTGTC
*
10362 ATAGTATCATTTTGACACCTGAAGTTGTC
1 ATAGTATCACTTTGACACCTGAAGTTGTC
10391 ATA
1 ATA
10394 TTAAGGATGG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 27 0.93
30 2 0.07
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.38
Consensus pattern (29 bp):
ATAGTATCACTTTGACACCTGAAGTTGTC
Found at i:10488 original size:54 final size:54
Alignment explanation
Indices: 10413--10515 Score: 161
Period size: 54 Copynumber: 1.9 Consensus size: 54
10403 GAAATATTTG
*
10413 TTTAATCGTTGCCAAAATTTGACAACCGAAGTTGTCAAACTATCCACTTAAAAC
1 TTTAATCGTTGCCAAAATTTGACAACCGAAATTGTCAAACTATCCACTTAAAAC
* * * *
10467 TTTAATTGTTGCCAAAGTTTGACACCCGAAATTGTCATACTATCCACTT
1 TTTAATCGTTGCCAAAATTTGACAACCGAAATTGTCAAACTATCCACTT
10516 TAAATTATAT
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
54 44 1.00
ACGTcount: A:0.33, C:0.22, G:0.12, T:0.33
Consensus pattern (54 bp):
TTTAATCGTTGCCAAAATTTGACAACCGAAATTGTCAAACTATCCACTTAAAAC
Found at i:11833 original size:35 final size:35
Alignment explanation
Indices: 11785--11882 Score: 160
Period size: 35 Copynumber: 2.8 Consensus size: 35
11775 TCAAATTGTG
*
11785 CAAATTTGATTGAAGGCTCCAGAAGAGCCAGTATT
1 CAAAATTGATTGAAGGCTCCAGAAGAGCCAGTATT
*
11820 TAAAATTGATTGAAGGCTCCAGAAGAGCCAGTATT
1 CAAAATTGATTGAAGGCTCCAGAAGAGCCAGTATT
* *
11855 CAAATTTGATTGAAGGCTCCGGAAGAGC
1 CAAAATTGATTGAAGGCTCCAGAAGAGC
11883 TACTATTATT
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 58 1.00
ACGTcount: A:0.35, C:0.16, G:0.24, T:0.24
Consensus pattern (35 bp):
CAAAATTGATTGAAGGCTCCAGAAGAGCCAGTATT
Found at i:12281 original size:83 final size:82
Alignment explanation
Indices: 12125--12282 Score: 244
Period size: 83 Copynumber: 1.9 Consensus size: 82
12115 GGTAAGATTG
* * *
12125 AAACATATGCTTTTGTAAACAGAAGTTTATTGATTGCATTATATTTATTGTTTGGCATGACCGCT
1 AAACAAATGCTTTTCTAAACAAAAGTTTATTGATTGCATTATATTTATTGTTTGGCATGACCGCT
*
12190 TAGGCCATCCTGATAAT
66 TAGACCATCCTGATAAT
* *
12207 AAACAAATGCTTTTCTAAACCAAAAGTTTATTGATTGCATTATGTTTATTGTTTGGCATGACCGG
1 AAACAAATGCTTTTCTAAA-CAAAAGTTTATTGATTGCATTATATTTATTGTTTGGCATGACCGC
*
12272 TTTGACCATCC
65 TTAGACCATCC
12283 CGGTTCAATT
Statistics
Matches: 68, Mismatches: 7, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
82 17 0.25
83 51 0.75
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.39
Consensus pattern (82 bp):
AAACAAATGCTTTTCTAAACAAAAGTTTATTGATTGCATTATATTTATTGTTTGGCATGACCGCT
TAGACCATCCTGATAAT
Found at i:15676 original size:17 final size:17
Alignment explanation
Indices: 15626--15693 Score: 77
Period size: 17 Copynumber: 4.1 Consensus size: 17
15616 TTTTCTACCA
* *
15626 TTCTCCATATTCTCTTC
1 TTCTCTATATTCTCTTG
*
15643 TTCT-TCATATTATCTTG
1 TTCTCT-ATATTCTCTTG
15660 TTCTCTATATTCTCTTG
1 TTCTCTATATTCTCTTG
*
15677 -TCTCTCTATTCTCTTG
1 TTCTCTATATTCTCTTG
15693 T
1 T
15694 CTTGTCCATA
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
16 15 0.35
17 27 0.63
18 1 0.02
ACGTcount: A:0.12, C:0.26, G:0.04, T:0.57
Consensus pattern (17 bp):
TTCTCTATATTCTCTTG
Found at i:15686 original size:16 final size:16
Alignment explanation
Indices: 15627--15695 Score: 68
Period size: 16 Copynumber: 4.2 Consensus size: 16
15617 TTTCTACCAT
* *
15627 TCTCCATATTCTCTTC
1 TCTCTATATTCTCTTG
*
15643 T-TCTTCATATTATCTTG
1 TCTC-T-ATATTCTCTTG
15660 TTCTCTATATTCTCTTG
1 -TCTCTATATTCTCTTG
*
15677 TCTCTCTATTCTCTTG
1 TCTCTATATTCTCTTG
15693 TCT
1 TCT
15696 TGTCCATACT
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
15 2 0.05
16 19 0.43
17 19 0.43
18 2 0.05
19 2 0.05
ACGTcount: A:0.12, C:0.28, G:0.04, T:0.57
Consensus pattern (16 bp):
TCTCTATATTCTCTTG
Found at i:17529 original size:21 final size:20
Alignment explanation
Indices: 17496--17539 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
17486 GTGGGAAGCA
*
17496 TTATAGCTATTTTAATAACTT
1 TTATAACTATTTTAATAA-TT
*
17517 TTATAACTTTTTTAATAATT
1 TTATAACTATTTTAATAATT
17537 TTA
1 TTA
17540 GATTACAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.34, C:0.07, G:0.02, T:0.57
Consensus pattern (20 bp):
TTATAACTATTTTAATAATT
Found at i:18825 original size:2 final size:2
Alignment explanation
Indices: 18818--18844 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
18808 TTAACTAGAT
18818 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
18845 GGAGTATGGA
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:18964 original size:2 final size:2
Alignment explanation
Indices: 18922--18951 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
18912 TATTAAGGTG
18922 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
18952 CAATTGTATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20681 original size:2 final size:2
Alignment explanation
Indices: 20676--20702 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
20666 TTTTTTTTAT
20676 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
20703 TTTGTTCTTT
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:21846 original size:12 final size:12
Alignment explanation
Indices: 21829--21883 Score: 92
Period size: 12 Copynumber: 4.5 Consensus size: 12
21819 TTAATACAGG
21829 TATCGACGGATA
1 TATCGACGGATA
21841 TATCGAACGGATA
1 TATCG-ACGGATA
21854 TATCGACGGATA
1 TATCGACGGATA
*
21866 TATCGATGGATA
1 TATCGACGGATA
21878 TATCGA
1 TATCGA
21884 GGTATCGATG
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
12 29 0.71
13 12 0.29
ACGTcount: A:0.35, C:0.15, G:0.24, T:0.27
Consensus pattern (12 bp):
TATCGACGGATA
Found at i:21863 original size:25 final size:24
Alignment explanation
Indices: 21829--21883 Score: 92
Period size: 25 Copynumber: 2.2 Consensus size: 24
21819 TTAATACAGG
21829 TATCGACGGATATATCGAACGGATA
1 TATCGACGGATATATCG-ACGGATA
*
21854 TATCGACGGATATATCGATGGATA
1 TATCGACGGATATATCGACGGATA
21878 TATCGA
1 TATCGA
21884 GGTATCGATG
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
24 12 0.41
25 17 0.59
ACGTcount: A:0.35, C:0.15, G:0.24, T:0.27
Consensus pattern (24 bp):
TATCGACGGATATATCGACGGATA
Done.