Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011283.1 Corchorus capsularis cultivar CVL-1 contig11304, 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: 31847
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:3159 original size:3 final size:3
Alignment explanation
Indices: 3151--3185 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
3141 CATTTAGTAT
*
3151 ATA ATA ATA ATA ATA ATG ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
3186 GAATTTAGAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:3305 original size:49 final size:49
Alignment explanation
Indices: 3246--3348 Score: 129
Period size: 49 Copynumber: 2.1 Consensus size: 49
3236 AATCTGTCAA
* * *
3246 GTAGGTAAAGACGAAAAAGATTAGTTCTC-CAACTCATCATTAATCCTG-G
1 GTAGGAAAAGACGAAAAAAATTAATTCTCTC-ACTCATCATTAATCC-GAG
* *
3295 GTAGGAAAAGACGAAAAAAATTAATTCTCTCGCTCCTCATTAATCCGAG
1 GTAGGAAAAGACGAAAAAAATTAATTCTCTCACTCATCATTAATCCGAG
3344 GTAGG
1 GTAGG
3349 GATCTTTTAA
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
48 1 0.02
49 45 0.96
50 1 0.02
ACGTcount: A:0.37, C:0.18, G:0.19, T:0.25
Consensus pattern (49 bp):
GTAGGAAAAGACGAAAAAAATTAATTCTCTCACTCATCATTAATCCGAG
Found at i:3671 original size:16 final size:16
Alignment explanation
Indices: 3650--3681 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
3640 AATTAATCAA
3650 TACAAGTGGATATCGG
1 TACAAGTGGATATCGG
3666 TACAAGTGGATATCGG
1 TACAAGTGGATATCGG
3682 CTCGCGTTGA
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:0.31, C:0.12, G:0.31, T:0.25
Consensus pattern (16 bp):
TACAAGTGGATATCGG
Found at i:5609 original size:22 final size:22
Alignment explanation
Indices: 5583--5624 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
5573 GACCACTATG
5583 TGGCCGAATCTCACGGCCACCA
1 TGGCCGAATCTCACGGCCACCA
5605 TGGCCGAATCTCACGGCCAC
1 TGGCCGAATCTCACGGCCAC
5625 GTACTAACCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.21, C:0.40, G:0.24, T:0.14
Consensus pattern (22 bp):
TGGCCGAATCTCACGGCCACCA
Found at i:9348 original size:27 final size:27
Alignment explanation
Indices: 9298--9350 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
9288 TAGTGACAAT
* * *
9298 AATTATGTCTAACTTTCTTCAAAAAAA
1 AATTATGTCTAACTTACCTAAAAAAAA
9325 AATTATGTCTAACTTACCTAAAAAAA
1 AATTATGTCTAACTTACCTAAAAAAA
9351 CTAATTAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.47, C:0.15, G:0.04, T:0.34
Consensus pattern (27 bp):
AATTATGTCTAACTTACCTAAAAAAAA
Found at i:10774 original size:31 final size:31
Alignment explanation
Indices: 10725--10879 Score: 132
Period size: 31 Copynumber: 4.9 Consensus size: 31
10715 ATGTGGCTTG
* * *
10725 CCACCTGGATAAAAAAAGTAACACATGGCACA
1 CCACGTGGAT-AAAAAAGTGACACGTGGCACA
* *
10757 CCACGTGGATAAAAAAGTGACACGTTGCACG
1 CCACGTGGATAAAAAAGTGACACGTGGCACA
*
10788 CCACGTGTG-TTAAAAAGTGACACGTGGCACA
1 CCACGTG-GATAAAAAAGTGACACGTGGCACA
* * * * * *
10819 TCACATGTACCAAAAAAGTGATACGTGGCACG
1 CCACGTGGA-TAAAAAAGTGACACGTGGCACA
* * **
10851 CCTCGTGTACCAAAAAGTGACACGTGGCA
1 CCACGTGGATAAAAAAGTGACACGTGGCA
10880 TGCCACATGT
Statistics
Matches: 100, Mismatches: 20, Indels: 7
0.79 0.16 0.06
Matches are distributed among these distances:
31 66 0.66
32 34 0.34
ACGTcount: A:0.37, C:0.24, G:0.23, T:0.17
Consensus pattern (31 bp):
CCACGTGGATAAAAAAGTGACACGTGGCACA
Found at i:10887 original size:63 final size:63
Alignment explanation
Indices: 10737--10891 Score: 177
Period size: 63 Copynumber: 2.5 Consensus size: 63
10727 ACCTGGATAA
* * * * * * ***
10737 AAAAAGTAACACATGGCACACCACGTGGA-TAAAAAAGTGACACGTTGCACGCCACGTGTGTT
1 AAAAAGTGACACGTGGCACACCACATGTACCAAAAAAGTGACACGTGGCACGCCACGTGTACC
* * *
10799 AAAAAGTGACACGTGGCACATCACATGTACCAAAAAAGTGATACGTGGCACGCCTCGTGTACC
1 AAAAAGTGACACGTGGCACACCACATGTACCAAAAAAGTGACACGTGGCACGCCACGTGTACC
**
10862 AAAAAGTGACACGTGGCATGCCACATGTAC
1 AAAAAGTGACACGTGGCACACCACATGTAC
10892 TAAAGGATAT
Statistics
Matches: 77, Mismatches: 15, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
62 24 0.31
63 53 0.69
ACGTcount: A:0.36, C:0.24, G:0.23, T:0.17
Consensus pattern (63 bp):
AAAAAGTGACACGTGGCACACCACATGTACCAAAAAAGTGACACGTGGCACGCCACGTGTACC
Found at i:10891 original size:31 final size:31
Alignment explanation
Indices: 10768--10891 Score: 140
Period size: 31 Copynumber: 4.0 Consensus size: 31
10758 CACGTGGATA
* * ***
10768 AAAAAGTGACACGTTGCACGCCACGTGTGTT
1 AAAAAGTGACACGTGGCACGCCACATGTACC
**
10799 AAAAAGTGACACGTGGCACATCACATGTACC
1 AAAAAGTGACACGTGGCACGCCACATGTACC
* * *
10830 AAAAAAGTGATACGTGGCACGCCTCGTGTACC
1 -AAAAAGTGACACGTGGCACGCCACATGTACC
*
10862 AAAAAGTGACACGTGGCATGCCACATGTAC
1 AAAAAGTGACACGTGGCACGCCACATGTAC
10892 TAAAGGATAT
Statistics
Matches: 76, Mismatches: 16, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
31 50 0.66
32 26 0.34
ACGTcount: A:0.34, C:0.24, G:0.23, T:0.19
Consensus pattern (31 bp):
AAAAAGTGACACGTGGCACGCCACATGTACC
Found at i:11281 original size:13 final size:13
Alignment explanation
Indices: 11263--11287 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
11253 GCTTTTAACA
11263 AAAAAAGAAAAAG
1 AAAAAAGAAAAAG
11276 AAAAAAGAAAAA
1 AAAAAAGAAAAA
11288 ACCTGATCAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (13 bp):
AAAAAAGAAAAAG
Found at i:11318 original size:20 final size:22
Alignment explanation
Indices: 11277--11318 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
11267 AAGAAAAAGA
*
11277 AAAAAGAAAAAACCTGATCATT
1 AAAAAGAAAAAACCTGAGCATT
11299 AAAAA-AAAAAACCTG-GCATT
1 AAAAAGAAAAAACCTGAGCATT
11319 TGGATTTGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 4 0.21
21 10 0.53
22 5 0.26
ACGTcount: A:0.60, C:0.14, G:0.10, T:0.17
Consensus pattern (22 bp):
AAAAAGAAAAAACCTGAGCATT
Found at i:18183 original size:35 final size:35
Alignment explanation
Indices: 18140--18651 Score: 804
Period size: 35 Copynumber: 14.7 Consensus size: 35
18130 AGTAATAAGT
*
18140 AACTTAATTCAGGGTAATTAAGTAAGCCAGTGAAT-
1 AACTTAATTCAGGGTAATTAAGTAAGTCAGT-AATC
*
18175 AATTTAATTCAGGGTAATTAAGTAAGTC---AA-C
1 AACTTAATTCAGGGTAATTAAGTAAGTCAGTAATC
* *
18206 CACTTAATTCAGGGTAA-TAAGTAAGTTAGTAATC
1 AACTTAATTCAGGGTAATTAAGTAAGTCAGTAATC
18240 AACTTAATTCAGGGTAATTAAGTAAGTCAGTAATC
1 AACTTAATTCAGGGTAATTAAGTAAGTCAGTAATC
18275 AACTTAATTCAGGGTAATTAAGTAAGTCAGTAATC
1 AACTTAATTCAGGGTAATTAAGTAAGTCAGTAATC
* *
18310 AACTTAATTCAGGGTAATTAAGTAATTTAGTAATC
1 AACTTAATTCAGGGTAATTAAGTAAGTCAGTAATC
* *
18345 AACTTAAGTCAGGGTAATTAAGTAATTCAGTAATC
1 AACTTAATTCAGGGTAATTAAGTAAGTCAGTAATC
* *
18380 AACTTAATTCAGGGTAATTAAGTAAAGTCAATTAGT-
1 AACTTAATTCAGGGTAATTAAGT-AAGTC-AGTAATC
*
18416 AACTTAATTCAGGGTAATTAAGTAATTCAGTAATC
1 AACTTAATTCAGGGTAATTAAGTAAGTCAGTAATC
18451 AACTTAATTCAGGGTAATTAAGTAAGTCAGTAATC
1 AACTTAATTCAGGGTAATTAAGTAAGTCAGTAATC
* * *
18486 AACTTAATTCAGGGTAATTAAGTAATTCAATAATA
1 AACTTAATTCAGGGTAATTAAGTAAGTCAGTAATC
18521 AACTTAATTCAGGGTAATTAAGTAAGTCAGTAATC
1 AACTTAATTCAGGGTAATTAAGTAAGTCAGTAATC
18556 AACTTAATTCAGGGTAATTAAGTAAGTCAGTAATC
1 AACTTAATTCAGGGTAATTAAGTAAGTCAGTAATC
* *
18591 AACTTAATTCAGGTTAATTAAGTGAGTCAGTAATC
1 AACTTAATTCAGGGTAATTAAGTAAGTCAGTAATC
18626 AACTTAATTCAGGGTAATTAAGTAAG
1 AACTTAATTCAGGGTAATTAAGTAAG
18652 GGTAATTAAG
Statistics
Matches: 439, Mismatches: 29, Indels: 18
0.90 0.06 0.04
Matches are distributed among these distances:
30 9 0.02
31 17 0.04
33 2 0.00
34 21 0.05
35 359 0.82
36 27 0.06
37 4 0.01
ACGTcount: A:0.40, C:0.11, G:0.17, T:0.32
Consensus pattern (35 bp):
AACTTAATTCAGGGTAATTAAGTAAGTCAGTAATC
Found at i:18653 original size:14 final size:14
Alignment explanation
Indices: 18636--18662 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
18626 AACTTAATTC
18636 AGGGTAATTAAGTA
1 AGGGTAATTAAGTA
18650 AGGGTAATTAAGT
1 AGGGTAATTAAGT
18663 TTAGTAAGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.41, C:0.00, G:0.30, T:0.30
Consensus pattern (14 bp):
AGGGTAATTAAGTA
Found at i:22440 original size:18 final size:16
Alignment explanation
Indices: 22417--22464 Score: 53
Period size: 18 Copynumber: 2.9 Consensus size: 16
22407 GCTGGCGTCT
22417 GAGGAGGAGGTGATTGG
1 GAGGAGGAGGTG-TTGG
*
22434 CGAGGAGGGGGTGTTGG
1 -GAGGAGGAGGTGTTGG
*
22451 GA-GAGGAGGCGTTG
1 GAGGAGGAGGTGTTG
22465 CAAGCTGGGT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
15 10 0.37
16 2 0.07
17 4 0.15
18 11 0.41
ACGTcount: A:0.19, C:0.04, G:0.60, T:0.17
Consensus pattern (16 bp):
GAGGAGGAGGTGTTGG
Found at i:24789 original size:20 final size:21
Alignment explanation
Indices: 24764--24804 Score: 75
Period size: 20 Copynumber: 2.0 Consensus size: 21
24754 GCTCTAATTG
24764 ATAGTAAGAATTGAT-ATAAT
1 ATAGTAAGAATTGATAATAAT
24784 ATAGTAAGAATTGATAATAAT
1 ATAGTAAGAATTGATAATAAT
24805 TTGAATTGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.51, C:0.00, G:0.15, T:0.34
Consensus pattern (21 bp):
ATAGTAAGAATTGATAATAAT
Found at i:24812 original size:16 final size:17
Alignment explanation
Indices: 24791--24823 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
24781 AATATAGTAA
24791 GAATTGATA-ATAATTT
1 GAATTGATATATAATTT
24807 GAATTGATATATAATTT
1 GAATTGATATATAATTT
24824 AGATTGTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.42, C:0.00, G:0.12, T:0.45
Consensus pattern (17 bp):
GAATTGATATATAATTT
Found at i:26846 original size:30 final size:30
Alignment explanation
Indices: 26810--26870 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
26800 CAAGGCCCAT
26810 CGAGCAGCCCATATACATGTCGGACACCAA
1 CGAGCAGCCCATATACATGTCGGACACCAA
26840 CGAGCAGCCCATATACATGTCGGACACCAA
1 CGAGCAGCCCATATACATGTCGGACACCAA
26870 C
1 C
26871 CTGAACCCAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.33, C:0.34, G:0.20, T:0.13
Consensus pattern (30 bp):
CGAGCAGCCCATATACATGTCGGACACCAA
Found at i:28737 original size:15 final size:15
Alignment explanation
Indices: 28717--28746 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
28707 GGCATGTCAC
28717 ATGAAGTCACTAACT
1 ATGAAGTCACTAACT
*
28732 ATGAAGTCATTAACT
1 ATGAAGTCACTAACT
28747 GAGCTAGGTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.40, C:0.17, G:0.13, T:0.30
Consensus pattern (15 bp):
ATGAAGTCACTAACT
Found at i:30764 original size:16 final size:16
Alignment explanation
Indices: 30745--30795 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
30735 GAAATGTGAG
30745 TTTAATTAAATTGTAA
1 TTTAATTAAATTGTAA
* * **
30761 TTTACTT-ATTTGTGT
1 TTTAATTAAATTGTAA
30776 TTTAATTAAATTGTAA
1 TTTAATTAAATTGTAA
30792 TTTA
1 TTTA
30796 TTTATTTGTG
Statistics
Matches: 26, Mismatches: 8, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
15 11 0.42
16 15 0.58
ACGTcount: A:0.33, C:0.02, G:0.08, T:0.57
Consensus pattern (16 bp):
TTTAATTAAATTGTAA
Found at i:30783 original size:31 final size:31
Alignment explanation
Indices: 30745--30806 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
30735 GAAATGTGAG
30745 TTTAATTAAATTGTAATTTACTTATTTGTGT
1 TTTAATTAAATTGTAATTTACTTATTTGTGT
*
30776 TTTAATTAAATTGTAATTTATTTATTTGTGT
1 TTTAATTAAATTGTAATTTACTTATTTGTGT
30807 ATTTGGTTTG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.29, C:0.02, G:0.10, T:0.60
Consensus pattern (31 bp):
TTTAATTAAATTGTAATTTACTTATTTGTGT
Done.