Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007926.1 Corchorus capsularis cultivar CVL-1 contig07947, 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: 32598
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.32
Found at i:4616 original size:2 final size:2
Alignment explanation
Indices: 4609--4634 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
4599 CCCTCCAATA
4609 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
4635 GCCAGAAAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9268 original size:107 final size:105
Alignment explanation
Indices: 9039--9301 Score: 368
Period size: 107 Copynumber: 2.5 Consensus size: 105
9029 AATTTTTCTA
* ** * *
9039 ACCCTTAAAATAAAATTTTAATTTTAATTT-GAGCTAAAATTAGTG-AATTAATTATATATTTTA
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAATTATATATTTTA
**
9102 TTTCTAAAACCCTATAACAATATTATTAATTATGGAATTT
66 TTTCTAAAACCCTATAACAATATTATTAATTATAAAATTT
* * * * *
9142 ACCCTTAAAATGAAAATAAAATTTTAATTTGGGGCTAAACTTATTGAAATTAGTTTTGTATTTTA
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAATTATATATTTTA
*
9207 TTTCTAAAACCCTATAACAATAAATTATTAATTTTAAAATTT
66 TTTCTAAAACCCTATAACAAT--ATTATTAATTATAAAATTT
*
9249 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGTTAAACTTAGTGAAATTAA
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAA
9302 GACTAAACTT
Statistics
Matches: 139, Mismatches: 17, Indels: 4
0.87 0.11 0.03
Matches are distributed among these distances:
103 26 0.19
104 12 0.09
105 36 0.26
107 65 0.47
ACGTcount: A:0.43, C:0.09, G:0.08, T:0.41
Consensus pattern (105 bp):
ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAATTATATATTTTA
TTTCTAAAACCCTATAACAATATTATTAATTATAAAATTT
Found at i:10083 original size:32 final size:32
Alignment explanation
Indices: 10044--10120 Score: 109
Period size: 32 Copynumber: 2.4 Consensus size: 32
10034 GTTAGGTTGA
* *
10044 GTTGAATTTGGATAAGGTTAATTTGAGTTTGG
1 GTTGAATTTGGATAAGGTTAATTCGAATTTGG
*
10076 GTTGAATTTGGATTAGGTTAATTCGAATTTGG
1 GTTGAATTTGGATAAGGTTAATTCGAATTTGG
* *
10108 ATTCAATTTGGAT
1 GTTGAATTTGGAT
10121 TTTAGCCCGA
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 40 1.00
ACGTcount: A:0.26, C:0.03, G:0.27, T:0.44
Consensus pattern (32 bp):
GTTGAATTTGGATAAGGTTAATTCGAATTTGG
Found at i:10553 original size:16 final size:16
Alignment explanation
Indices: 10532--10586 Score: 58
Period size: 16 Copynumber: 3.4 Consensus size: 16
10522 TCAAGTTCGG
10532 TTTTTTTGGATTCTGA
1 TTTTTTTGGATTCTGA
*
10548 TTTTTTTGGGTT-TGA
1 TTTTTTTGGATTCTGA
* * *
10563 GCTTTTTCGGATTCGGA
1 -TTTTTTTGGATTCTGA
10580 TTTTTTT
1 TTTTTTT
10587 TAGTTCAGGT
Statistics
Matches: 30, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
15 3 0.10
16 25 0.83
17 2 0.07
ACGTcount: A:0.09, C:0.07, G:0.22, T:0.62
Consensus pattern (16 bp):
TTTTTTTGGATTCTGA
Found at i:13577 original size:14 final size:14
Alignment explanation
Indices: 13558--13596 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
13548 AAGCCAGACT
*
13558 CTGACTCAAACTAA
1 CTGACTCAAACAAA
*
13572 CTGACTCAAAAAAA
1 CTGACTCAAACAAA
*
13586 CTGACTAAAAC
1 CTGACTCAAAC
13597 CCTACAGATC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.49, C:0.26, G:0.08, T:0.18
Consensus pattern (14 bp):
CTGACTCAAACAAA
Found at i:14736 original size:27 final size:27
Alignment explanation
Indices: 14693--14744 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
14683 ATAGCATTAT
* *
14693 CTAAGAAAACAATTATAATTAAGAATA
1 CTAAGAAAACAAATATAATAAAGAATA
*
14720 CTAAGAAAGCAAATATAATAAAGAA
1 CTAAGAAAACAAATATAATAAAGAA
14745 CCCTCCAACA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.62, C:0.08, G:0.10, T:0.21
Consensus pattern (27 bp):
CTAAGAAAACAAATATAATAAAGAATA
Found at i:17944 original size:2 final size:2
Alignment explanation
Indices: 17932--17978 Score: 76
Period size: 2 Copynumber: 23.0 Consensus size: 2
17922 CCGTGCGTTA
*
17932 AT AT CAT AT AT AT AT AT AT AT GT 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
17975 AT AT
1 AT AT
17979 CAAAAATCAT
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
2 40 0.95
3 2 0.05
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:19653 original size:3 final size:3
Alignment explanation
Indices: 19645--19679 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
19635 ATATATTTAT
19645 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
19680 AAAAACCATC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.31, G:0.00, T:0.34
Consensus pattern (3 bp):
ATC
Found at i:21057 original size:45 final size:45
Alignment explanation
Indices: 21008--21094 Score: 174
Period size: 45 Copynumber: 1.9 Consensus size: 45
20998 AATTCTCACT
21008 TTATCAACAATTTCTAATATTCAATTTACTCATACAATGCCTCTC
1 TTATCAACAATTTCTAATATTCAATTTACTCATACAATGCCTCTC
21053 TTATCAACAATTTCTAATATTCAATTTACTCATACAATGCCT
1 TTATCAACAATTTCTAATATTCAATTTACTCATACAATGCCT
21095 TTCCTAAAGC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.34, C:0.23, G:0.02, T:0.40
Consensus pattern (45 bp):
TTATCAACAATTTCTAATATTCAATTTACTCATACAATGCCTCTC
Found at i:28245 original size:9 final size:9
Alignment explanation
Indices: 28228--28261 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
28218 GAATTTGAAA
28228 AAAAATAAC
1 AAAAATAAC
*
28237 AATAATAAC
1 AAAAATAAC
28246 AAAAATAAC
1 AAAAATAAC
*
28255 AACAATA
1 AAAAATA
28262 TATTTAAAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.74, C:0.12, G:0.00, T:0.15
Consensus pattern (9 bp):
AAAAATAAC
Found at i:28463 original size:16 final size:15
Alignment explanation
Indices: 28442--28471 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
28432 TGCACAGAGA
28442 ATAATTAATTTCTATT
1 ATAATTAA-TTCTATT
28458 ATAATTAATTCTAT
1 ATAATTAATTCTAT
28472 CACAAGAAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.53
Consensus pattern (15 bp):
ATAATTAATTCTATT
Found at i:30601 original size:19 final size:19
Alignment explanation
Indices: 30574--30610 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
30564 ACTCAAGGGA
*
30574 TAAATAATAATAATTATTC
1 TAAAAAATAATAATTATTC
30593 TAAAAAATAATAATTATT
1 TAAAAAATAATAATTATT
30611 TATTATTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.41
Consensus pattern (19 bp):
TAAAAAATAATAATTATTC
Done.