Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01004890.1 Corchorus capsularis cultivar CVL-1 contig04908, 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: 24539
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.31
Found at i:42 original size:22 final size:22
Alignment explanation
Indices: 14--70 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
4 AACCCTCTTC
14 TGAAATTTTGA-AAACTAAATTA
1 TGAAATTTTGATAAACTAAA-TA
* **
36 TGAAATTTTGATAACCTTCATA
1 TGAAATTTTGATAAACTAAATA
58 TGAAATTTTGATA
1 TGAAATTTTGATA
71 TCCTCCCTGA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
22 26 0.84
23 5 0.16
ACGTcount: A:0.42, C:0.07, G:0.11, T:0.40
Consensus pattern (22 bp):
TGAAATTTTGATAAACTAAATA
Found at i:198 original size:22 final size:22
Alignment explanation
Indices: 168--297 Score: 77
Period size: 22 Copynumber: 5.9 Consensus size: 22
158 CCAAAAATAC
* * *
168 CATTATGAAATTTTGGTAATCA
1 CATTTTGAAATTTTGATAACCA
* *
190 CATTTTGAAAATTTGATAACCT
1 CATTTTGAAATTTTGATAACCA
*
212 C-TTTATGAAATTTTGATAACCT
1 CATTT-TGAAATTTTGATAACCA
* * * *
234 C-TCTATCAAATTTTGTTGACC-
1 CAT-TTTGAAATTTTGATAACCA
* * *
255 CCTCTATGAAATTTTGATAATCA
1 CAT-TTTGAAATTTTGATAACCA
* *
278 CATTATGTAATTTTGATAAC
1 CATTTTGAAATTTTGATAAC
298 ATCGCTTTAA
Statistics
Matches: 87, Mismatches: 17, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
21 4 0.05
22 80 0.92
23 3 0.03
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.42
Consensus pattern (22 bp):
CATTTTGAAATTTTGATAACCA
Found at i:220 original size:44 final size:44
Alignment explanation
Indices: 170--297 Score: 141
Period size: 44 Copynumber: 2.9 Consensus size: 44
160 AAAAATACCA
* * * *
170 TTATGAAATTTTGGTAATCACATTTTGAAAATTTGATAACCTCT
1 TTATGAAATTTTGATAATCACATTATGAAATTTTGATAACCCCT
* * * * *
214 TTATGAAATTTTGATAACCTC-TCTATCAAATTTTGTTGACCCCT
1 TTATGAAATTTTGATAATCACAT-TATGAAATTTTGATAACCCCT
* *
258 CTATGAAATTTTGATAATCACATTATGTAATTTTGATAAC
1 TTATGAAATTTTGATAATCACATTATGAAATTTTGATAAC
298 ATCGCTTTAA
Statistics
Matches: 66, Mismatches: 16, Indels: 4
0.77 0.19 0.05
Matches are distributed among these distances:
43 1 0.02
44 64 0.97
45 1 0.02
ACGTcount: A:0.33, C:0.14, G:0.10, T:0.43
Consensus pattern (44 bp):
TTATGAAATTTTGATAATCACATTATGAAATTTTGATAACCCCT
Found at i:465 original size:37 final size:37
Alignment explanation
Indices: 373--468 Score: 95
Period size: 38 Copynumber: 2.6 Consensus size: 37
363 ATCTAAGCCC
* * *
373 AAATAGGATGTTGGAGACGAAGACAAAAAGCAAAATT
1 AAATAGGACGTTGGAAACAAAGACAAAAAGCAAAATT
** * * *
410 AAATACAACAATTAGAAACAAAGAC-AAAAGATAAAATT
1 AAATAGGAC-GTTGGAAACAAAGACAAAAAG-CAAAATT
448 AAATAGGACGTTGGAAACAAA
1 AAATAGGACGTTGGAAACAAA
469 AAGTCAAATT
Statistics
Matches: 45, Mismatches: 12, Indels: 4
0.74 0.20 0.07
Matches are distributed among these distances:
37 21 0.47
38 24 0.53
ACGTcount: A:0.57, C:0.09, G:0.18, T:0.16
Consensus pattern (37 bp):
AAATAGGACGTTGGAAACAAAGACAAAAAGCAAAATT
Found at i:6039 original size:104 final size:103
Alignment explanation
Indices: 5860--6067 Score: 299
Period size: 104 Copynumber: 2.0 Consensus size: 103
5850 AAGATTCTCA
* * * *
5860 GCCATTACATTTTTTAAATCACTCCTACACACCACTATTATTTTCTCGCTATTCCTTTGCCATCC
1 GCCATTACACTTTCTAAATCACTCCTACACACCACTATTATTTTCTCGCCATTCCTTTCCCATCC
*
5925 TTCCTTCTATAACAAATAGCATAATGAAGTTAAAGGCT
66 TTCCTTCTATAACAAATAGCATAACGAAGTTAAAGGCT
* * * *
5963 GCCATTGCACTTTCTAAATCACTCCTACCGCACCACTATTATTTTCTCTCCATTCCTTTCCCTTC
1 GCCATTACACTTTCTAAATCACTCCTA-CACACCACTATTATTTTCTCGCCATTCCTTTCCCATC
** *
6028 CTTTTTTCTATAACAAATAGCCTAACGAAGTTAAAGGCT
65 CTTCCTTCTATAACAAATAGCATAACGAAGTTAAAGGCT
6067 G
1 G
6068 TCCACTAAAT
Statistics
Matches: 92, Mismatches: 12, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
103 24 0.26
104 68 0.74
ACGTcount: A:0.27, C:0.28, G:0.08, T:0.37
Consensus pattern (103 bp):
GCCATTACACTTTCTAAATCACTCCTACACACCACTATTATTTTCTCGCCATTCCTTTCCCATCC
TTCCTTCTATAACAAATAGCATAACGAAGTTAAAGGCT
Found at i:9729 original size:1 final size:1
Alignment explanation
Indices: 9725--9749 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
9715 AAACATTATT
9725 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
9750 CTGGGTTAGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:15133 original size:113 final size:112
Alignment explanation
Indices: 14933--15144 Score: 293
Period size: 113 Copynumber: 1.9 Consensus size: 112
14923 CTGACACGGC
* ** * *
14933 TCAATTCTAGATTAATCAGAGTTCAATGTGACTATTGAATATTTTCTGATACGGCTCAATTCTGG
1 TCAATTCTAGATTAATCAGAATTCAATGTGACTACCGAATA-TTTCTGAGACGACTCAATTCTGG
* *
14998 ATTAATCAGAATTCAATGTGACTA-TCGAATATTCTGACATGTCTCGAT
65 ATTAATCAAAATTCAATATGACTACT-GAATATTCTGACATGTCTCGAT
* *
15046 TCAATTCTGGATTAATCAGAATTCAATGTGACTACCGAATA-TTCTGAGACTCGATTCAATTCTG
1 TCAATTCTAGATTAATCAGAATTCAATGTGACTACCGAATATTTCTGAGA--CGACTCAATTCTG
15110 GATTAATCAAAATTCAATATGACTACTGAATATTC
64 GATTAATCAAAATTCAATATGACTACTGAATATTC
15145 CAACGCAATT
Statistics
Matches: 87, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
111 7 0.08
113 79 0.91
114 1 0.01
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.36
Consensus pattern (112 bp):
TCAATTCTAGATTAATCAGAATTCAATGTGACTACCGAATATTTCTGAGACGACTCAATTCTGGA
TTAATCAAAATTCAATATGACTACTGAATATTCTGACATGTCTCGAT
Found at i:15144 original size:55 final size:55
Alignment explanation
Indices: 14933--15144 Score: 259
Period size: 55 Copynumber: 3.8 Consensus size: 55
14923 CTGACACGGC
* * * * **
14933 TCAATTCTAGATTAATCAGAGTTCAATGTGACTATTGAATATTTTCTGATA--CGGC
1 TCAATTCTGGATTAATCAGAATTCAATGTGACTACTGAATA--TTCTGAGACTCGAT
*
14988 TCAATTCTGGATTAATCAGAATTCAATGTGACTA-TCGAATATTCTGACATGTCTCGAT
1 TCAATTCTGGATTAATCAGAATTCAATGTGACTACT-GAATATTCTG--A-GACTCGAT
*
15046 TCAATTCTGGATTAATCAGAATTCAATGTGACTACCGAATATTCTGAGACTCGAT
1 TCAATTCTGGATTAATCAGAATTCAATGTGACTACTGAATATTCTGAGACTCGAT
* *
15101 TCAATTCTGGATTAATCAAAATTCAATATGACTACTGAATATTC
1 TCAATTCTGGATTAATCAGAATTCAATGTGACTACTGAATATTC
15145 CAACGCAATT
Statistics
Matches: 139, Mismatches: 11, Indels: 14
0.85 0.07 0.09
Matches are distributed among these distances:
53 5 0.04
54 1 0.01
55 86 0.62
56 1 0.01
58 46 0.33
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.36
Consensus pattern (55 bp):
TCAATTCTGGATTAATCAGAATTCAATGTGACTACTGAATATTCTGAGACTCGAT
Done.