Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008962.1 Corchorus capsularis cultivar CVL-1 contig08983, 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: 41828
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:1421 original size:3 final size:3
Alignment explanation
Indices: 1413--1454 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
1403 GTCTCCAAGC
1413 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1455 TTGCAGCTAC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:2210 original size:20 final size:20
Alignment explanation
Indices: 2185--2227 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
2175 AATCATATGA
*
2185 AATAATAATAACTAATTTTT
1 AATAATAATAACTAATTATT
2205 AATAATAATAACTAATTATT
1 AATAATAATAACTAATTATT
2225 AAT
1 AAT
2228 TTAAAAAAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (20 bp):
AATAATAATAACTAATTATT
Found at i:2303 original size:33 final size:33
Alignment explanation
Indices: 2261--2337 Score: 93
Period size: 33 Copynumber: 2.3 Consensus size: 33
2251 GGTTGCGATG
*
2261 CGGGTCGCGACCAGGCCAA-GGCGGTGTCGCGCC
1 CGGGTCGCGACCACGCCAAGGGC-GTGTCGCGCC
* *
2294 CGGGTCGCGACCACGCCATGGGCTTGTCGCGCC
1 CGGGTCGCGACCACGCCAAGGGCGTGTCGCGCC
* *
2327 CAGATCGCGAC
1 CGGGTCGCGAC
2338 ACTGCCATGA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
33 35 0.92
34 3 0.08
ACGTcount: A:0.13, C:0.38, G:0.38, T:0.12
Consensus pattern (33 bp):
CGGGTCGCGACCACGCCAAGGGCGTGTCGCGCC
Found at i:9770 original size:74 final size:73
Alignment explanation
Indices: 9641--9791 Score: 248
Period size: 74 Copynumber: 2.1 Consensus size: 73
9631 GAAGGGGAAT
*
9641 GTGTAATTACGAAAAAGGGTAGAAGGAAAGGAATGGGGGAAACCCATAGAGGGGCTTTTTAGTCA
1 GTGTAATTACGAAAAAGGATAGAAGGAAAGGAATGGGGGAAACCCATAGAGGGGCTTTTTAGTCA
9706 TCCGAAAA
66 TCCGAAAA
* * **
9714 GTGTAATTACGAAAAATGATAGAAGGAAAAGGAATGGGGGAAGCTTATAGAGGGGCTTTTTAGTC
1 GTGTAATTACGAAAAAGGATAGAAGG-AAAGGAATGGGGGAAACCCATAGAGGGGCTTTTTAGTC
9779 ATCCGAAAA
65 ATCCGAAAA
9788 GTGT
1 GTGT
9792 GAAAAAACCA
Statistics
Matches: 72, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
73 24 0.33
74 48 0.67
ACGTcount: A:0.38, C:0.09, G:0.31, T:0.22
Consensus pattern (73 bp):
GTGTAATTACGAAAAAGGATAGAAGGAAAGGAATGGGGGAAACCCATAGAGGGGCTTTTTAGTCA
TCCGAAAA
Found at i:26574 original size:17 final size:19
Alignment explanation
Indices: 26537--26575 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 19
26527 ATATATTTTA
*
26537 CTACTTTTATCATTAAGCT
1 CTACTTTTATCATTAAACT
26556 CTAC-TTTAT-ATTAAACT
1 CTACTTTTATCATTAAACT
26573 CTA
1 CTA
26576 TAGGTTTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 10 0.53
18 5 0.26
19 4 0.21
ACGTcount: A:0.31, C:0.21, G:0.03, T:0.46
Consensus pattern (19 bp):
CTACTTTTATCATTAAACT
Found at i:36687 original size:27 final size:27
Alignment explanation
Indices: 36636--36687 Score: 63
Period size: 27 Copynumber: 1.9 Consensus size: 27
36626 TGAAAATAGT
*
36636 AAATGGTATAAATAAAATTTTAAATTA
1 AAATGGTATAAATAAAATTTAAAATTA
36663 AAATGGTA-AAA-AATAATTATAAAAT
1 AAATGGTATAAATAA-AATT-TAAAAT
36688 ATTAAATTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
25 2 0.09
26 7 0.32
27 13 0.59
ACGTcount: A:0.60, C:0.00, G:0.08, T:0.33
Consensus pattern (27 bp):
AAATGGTATAAATAAAATTTAAAATTA
Found at i:36704 original size:144 final size:149
Alignment explanation
Indices: 36504--36789 Score: 429
Period size: 144 Copynumber: 1.9 Consensus size: 149
36494 CACAATAAGG
* *
36504 TTTTAAATTAAAATAGTAAAAACAAAATAATTATAAAAATATTGAATTTAATTAAATGAAAATAG
1 TTTTAAATTAAAATAGT--AAACAAAATAATTATAAAAATATTAAATTTAATTAAATGAAAATAA
* * * *
36569 AGTTTTTAGTATAATAAAACTGTATATTAAAAAATTTTAATGTATCCAAGTTTTTAATG-AAAAT
64 AGTTTTTAGTAGAATAAAACTGTACATTAAAAAATTTTAATATATCCAAGTTTTTAATGAAAAAG
36633 AGT-AAATGGTATAAATAAAA
129 AGTAAAATGGTATAAATAAAA
*
36653 TTTTAAATTAAAATGGT-AA-AAAATAATTAT-AAAATATTAAATTTAATTAAATGAAAATAAAG
1 TTTTAAATTAAAATAGTAAACAAAATAATTATAAAAATATTAAATTTAATTAAATGAAAATAAAG
** *
36715 TTTTTAGTAGAATAAAACTGTACATTAAAATTTTTTAATATATCCTAGTTTTTAATGAAAAAGAG
66 TTTTTAGTAGAATAAAACTGTACATTAAAAAATTTTAATATATCCAAGTTTTTAATGAAAAAGAG
36780 TAAAATGGTA
131 TAAAATGGTA
36790 AAAAAAGGGT
Statistics
Matches: 125, Mismatches: 10, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
144 81 0.65
145 18 0.14
146 10 0.08
149 16 0.13
ACGTcount: A:0.51, C:0.03, G:0.09, T:0.37
Consensus pattern (149 bp):
TTTTAAATTAAAATAGTAAACAAAATAATTATAAAAATATTAAATTTAATTAAATGAAAATAAAG
TTTTTAGTAGAATAAAACTGTACATTAAAAAATTTTAATATATCCAAGTTTTTAATGAAAAAGAG
TAAAATGGTATAAATAAAA
Found at i:37572 original size:47 final size:47
Alignment explanation
Indices: 37519--37614 Score: 192
Period size: 47 Copynumber: 2.0 Consensus size: 47
37509 TTATTCCTTT
37519 TTGGCTAATTGTTCAAGTAATGATCTATCCTTTGCGAAAATGTTCTA
1 TTGGCTAATTGTTCAAGTAATGATCTATCCTTTGCGAAAATGTTCTA
37566 TTGGCTAATTGTTCAAGTAATGATCTATCCTTTGCGAAAATGTTCTA
1 TTGGCTAATTGTTCAAGTAATGATCTATCCTTTGCGAAAATGTTCTA
37613 TT
1 TT
37615 TGAGATCCTA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 49 1.00
ACGTcount: A:0.27, C:0.15, G:0.17, T:0.42
Consensus pattern (47 bp):
TTGGCTAATTGTTCAAGTAATGATCTATCCTTTGCGAAAATGTTCTA
Found at i:40449 original size:24 final size:25
Alignment explanation
Indices: 40422--40474 Score: 81
Period size: 25 Copynumber: 2.2 Consensus size: 25
40412 TTCTAAACAA
*
40422 TTATTAGAAGGCC-TACTTAATCTG
1 TTATTACAAGGCCTTACTTAATCTG
*
40446 TTATTACAATGCCTTACTTAATCTG
1 TTATTACAAGGCCTTACTTAATCTG
40471 TTAT
1 TTAT
40475 CTTCTTCATG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
24 11 0.42
25 15 0.58
ACGTcount: A:0.28, C:0.17, G:0.11, T:0.43
Consensus pattern (25 bp):
TTATTACAAGGCCTTACTTAATCTG
Done.