Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013450.1 Corchorus olitorius cultivar O-4 contig13483, 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: 53255
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Found at i:2981 original size:58 final size:58
Alignment explanation
Indices: 2883--2992 Score: 152
Period size: 58 Copynumber: 1.9 Consensus size: 58
2873 ACCATGCCTC
* *
2883 GGTCCTAAAACGTCTTTTTTAGACATTTAATAAAAAAACATGTCACTCGATAAGTCTT
1 GGTCCGAAAACGTCTTTTTTAGACATCTAATAAAAAAACATGTCACTCGATAAGTCTT
* *
2941 GGTCCGAAAACGTCTTTCTTTATG-CATCTAAT-AAAGAACATGTCACTTGATA
1 GGTCCGAAAACGTCTTT-TTTA-GACATCTAATAAAAAAACATGTCACTCGATA
2993 TTTGATTAAT
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
58 34 0.74
59 11 0.24
60 1 0.02
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.34
Consensus pattern (58 bp):
GGTCCGAAAACGTCTTTTTTAGACATCTAATAAAAAAACATGTCACTCGATAAGTCTT
Found at i:4493 original size:2 final size:2
Alignment explanation
Indices: 4486--4520 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
4476 GTATTTTAAC
4486 TA TA TA TA 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 TA TA TA TA T
4521 TCTGTTAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:6139 original size:1 final size:1
Alignment explanation
Indices: 6133--6157 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
6123 TGACGCATGG
6133 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
6158 GAAAGGAGTC
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:10737 original size:3 final size:3
Alignment explanation
Indices: 10729--10773 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
10719 TAGACCCGTA
10729 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
10774 ATATATATAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:11378 original size:14 final size:14
Alignment explanation
Indices: 11355--11385 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
11345 ATATACTCCT
*
11355 TCATAGTTCATACA
1 TCATAATTCATACA
11369 TCATAATTCATACA
1 TCATAATTCATACA
11383 TCA
1 TCA
11386 ACCTGATCTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.39, C:0.23, G:0.03, T:0.35
Consensus pattern (14 bp):
TCATAATTCATACA
Found at i:13692 original size:33 final size:33
Alignment explanation
Indices: 13650--13722 Score: 128
Period size: 33 Copynumber: 2.2 Consensus size: 33
13640 GTGTTTGTCG
*
13650 TATTTATCAATGGGAGATGATTAAGCTGTTGTA
1 TATTTATCAATGGAAGATGATTAAGCTGTTGTA
*
13683 TATTTATCAATGGAAGATGATTAAGCTGTTTTA
1 TATTTATCAATGGAAGATGATTAAGCTGTTGTA
13716 TATTTAT
1 TATTTAT
13723 GTAATTTTGT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.32, C:0.05, G:0.19, T:0.44
Consensus pattern (33 bp):
TATTTATCAATGGAAGATGATTAAGCTGTTGTA
Found at i:17216 original size:2 final size:2
Alignment explanation
Indices: 17211--17246 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
17201 AATTATATAT
17211 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
17247 TATTTAGACT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:22328 original size:17 final size:17
Alignment explanation
Indices: 22306--22341 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
22296 GAAAAAAAAT
22306 TAGGACTTATATTATAA
1 TAGGACTTATATTATAA
22323 TAGGACTTATATTATAA
1 TAGGACTTATATTATAA
22340 TA
1 TA
22342 AATTTAGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.42, C:0.06, G:0.11, T:0.42
Consensus pattern (17 bp):
TAGGACTTATATTATAA
Found at i:30975 original size:3 final size:3
Alignment explanation
Indices: 30967--30994 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
30957 TTATTCTCCC
30967 TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT T
30995 TTAATTATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:38357 original size:34 final size:34
Alignment explanation
Indices: 38314--38382 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
38304 TACTACACAT
38314 AGGTAGTGTTTGGGAACTAAAATTTCGATTTGGA
1 AGGTAGTGTTTGGGAACTAAAATTTCGATTTGGA
38348 AGGTAGTGTTTGGGAACTAAAATTTCGATTTGGA
1 AGGTAGTGTTTGGGAACTAAAATTTCGATTTGGA
38382 A
1 A
38383 TTGGATTTCA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.30, C:0.06, G:0.29, T:0.35
Consensus pattern (34 bp):
AGGTAGTGTTTGGGAACTAAAATTTCGATTTGGA
Found at i:38500 original size:6 final size:6
Alignment explanation
Indices: 38489--38523 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
38479 CATAACTAAT
38489 ATTTGG ATTTGG ATTTGG ATTTGG ATTTGG ATTTG
1 ATTTGG ATTTGG ATTTGG ATTTGG ATTTGG ATTTG
38524 AGGATTTGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.17, C:0.00, G:0.31, T:0.51
Consensus pattern (6 bp):
ATTTGG
Found at i:49129 original size:2 final size:2
Alignment explanation
Indices: 49124--49154 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
49114 ATATATATAG
49124 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
49155 TGTGTGTGTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Done.