Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022489.1 Corchorus olitorius cultivar O-4 contig22522, 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: 79695
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:713 original size:13 final size:13
Alignment explanation
Indices: 676--706 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
666 TTCTACTACA
676 ATTTTT-AAAAAC
1 ATTTTTCAAAAAC
688 ATTTTTCAAAAAC
1 ATTTTTCAAAAAC
701 ATTTTT
1 ATTTTT
707 TCTAAACCGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 6 0.33
13 12 0.67
ACGTcount: A:0.42, C:0.10, G:0.00, T:0.48
Consensus pattern (13 bp):
ATTTTTCAAAAAC
Found at i:2160 original size:26 final size:26
Alignment explanation
Indices: 2124--2173 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
2114 TAAACTAAGA
* *
2124 ACTTTTCTTAAATAAATTACTTATAT
1 ACTTGTCTTAAATAAACTACTTATAT
2150 ACTTGTCTTAAATAAACTACTTAT
1 ACTTGTCTTAAATAAACTACTTAT
2174 CAACCAAACA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.38, C:0.14, G:0.02, T:0.46
Consensus pattern (26 bp):
ACTTGTCTTAAATAAACTACTTATAT
Found at i:3283 original size:4 final size:4
Alignment explanation
Indices: 3274--3308 Score: 61
Period size: 4 Copynumber: 8.5 Consensus size: 4
3264 ATCTGATCTC
3274 TTCT TTCT TTCT TTCT TTCT TTCTT TTCT TTCT TT
1 TTCT TTCT TTCT TTCT TTCT TTC-T TTCT TTCT TT
3309 TGTTTTTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
4 26 0.87
5 4 0.13
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (4 bp):
TTCT
Found at i:3317 original size:17 final size:17
Alignment explanation
Indices: 3274--3308 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
3264 ATCTGATCTC
3274 TTCTTTC-TTTCTTTCT
1 TTCTTTCTTTTCTTTCT
3290 TTCTTTCTTTTCTTTCT
1 TTCTTTCTTTTCTTTCT
3307 TT
1 TT
3309 TGTTTTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 7 0.39
17 11 0.61
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (17 bp):
TTCTTTCTTTTCTTTCT
Found at i:7317 original size:14 final size:14
Alignment explanation
Indices: 7298--7326 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
7288 ATTATAGTAT
7298 TGTTTTTGTATTAA
1 TGTTTTTGTATTAA
7312 TGTTTTTGTATTAA
1 TGTTTTTGTATTAA
7326 T
1 T
7327 CATGCATATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.21, C:0.00, G:0.14, T:0.66
Consensus pattern (14 bp):
TGTTTTTGTATTAA
Found at i:9269 original size:16 final size:16
Alignment explanation
Indices: 9248--9280 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
9238 ACCCTTTTGC
9248 CTATATA-TATATATTG
1 CTATATATTAT-TATTG
9264 CTATATATTATTATTG
1 CTATATATTATTATTG
9280 C
1 C
9281 ATTCAAACTG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 13 0.81
17 3 0.19
ACGTcount: A:0.33, C:0.09, G:0.06, T:0.52
Consensus pattern (16 bp):
CTATATATTATTATTG
Found at i:10786 original size:1 final size:1
Alignment explanation
Indices: 10780--10810 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
10770 CCCACAGTTT
10780 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
10811 CCCTTTCTCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:32211 original size:29 final size:31
Alignment explanation
Indices: 32165--32222 Score: 77
Period size: 29 Copynumber: 1.9 Consensus size: 31
32155 TTGTCTATAT
*
32165 AAATACGTTAATATAAAT-TA-TATAATTAA
1 AAATACGTTAATAAAAATATATTATAATTAA
32194 AAATAC-TTAACTAAAAATATATTATAATT
1 AAATACGTTAA-TAAAAATATATTATAATT
32223 TATAAATAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
28 4 0.16
29 12 0.48
30 2 0.08
31 7 0.28
ACGTcount: A:0.55, C:0.05, G:0.02, T:0.38
Consensus pattern (31 bp):
AAATACGTTAATAAAAATATATTATAATTAA
Found at i:42779 original size:28 final size:28
Alignment explanation
Indices: 42740--42793 Score: 108
Period size: 28 Copynumber: 1.9 Consensus size: 28
42730 AGTATCTGGA
42740 TTTTTAGATTTGTGAATGGAGAAAATGT
1 TTTTTAGATTTGTGAATGGAGAAAATGT
42768 TTTTTAGATTTGTGAATGGAGAAAAT
1 TTTTTAGATTTGTGAATGGAGAAAAT
42794 AGACATTTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.33, C:0.00, G:0.24, T:0.43
Consensus pattern (28 bp):
TTTTTAGATTTGTGAATGGAGAAAATGT
Found at i:43725 original size:21 final size:19
Alignment explanation
Indices: 43700--43757 Score: 71
Period size: 19 Copynumber: 2.9 Consensus size: 19
43690 GCCGCTCTAA
*
43700 TAATCTCATCTGTGCAGTACC
1 TAATCTCATCTGTACAGT--C
* *
43721 TAATCTAATCTGTACAGTG
1 TAATCTCATCTGTACAGTC
43740 TAATCTCATCTGTACAGT
1 TAATCTCATCTGTACAGT
43758 TGCTAAACAG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
19 17 0.52
21 16 0.48
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.36
Consensus pattern (19 bp):
TAATCTCATCTGTACAGTC
Found at i:46136 original size:16 final size:15
Alignment explanation
Indices: 46115--46144 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
46105 TTCCTAGGCT
46115 TGAACAAGAAAAAAAA
1 TGAACAA-AAAAAAAA
46131 TGAACAAAAAAAAA
1 TGAACAAAAAAAAA
46145 CATGTTACTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.77, C:0.07, G:0.10, T:0.07
Consensus pattern (15 bp):
TGAACAAAAAAAAAA
Found at i:78587 original size:59 final size:59
Alignment explanation
Indices: 78518--78701 Score: 273
Period size: 59 Copynumber: 3.0 Consensus size: 59
78508 TCCATTAACT
78518 CCTCTACATATATGTGCTATCAAGTAGCAACACCCATTTTAGTGTACATTAATTTCTTA
1 CCTCTACATATATGTGCTATCAAGTAGCAACACCCATTTTAGTGTACATTAATTTCTTA
*
78577 CCTCTACATATATGTGCTATCAAGTAGCAACACCCATTTTAGT-TA-ATTATTCATTCATTAA
1 CCTCTACATATATGTGCTATCAAGTAGCAACACCCATTTTAGTGTACATTAAT--TTC-TT-A
*
78638 CTCCTCTACATATATGTGCTATCAAGTAGCAACACCCATTTTTAGTGTACACTAATTTCTTA
1 --CCTCTACATATATGTGCTATCAAGTAGCAACACCCA-TTTTAGTGTACATTAATTTCTTA
78700 CC
1 CC
78702 CATTAATCAA
Statistics
Matches: 113, Mismatches: 3, Indels: 17
0.85 0.02 0.13
Matches are distributed among these distances:
57 5 0.04
58 2 0.02
59 46 0.41
60 4 0.04
61 1 0.01
62 1 0.01
63 38 0.34
64 10 0.09
65 2 0.02
66 4 0.04
ACGTcount: A:0.30, C:0.23, G:0.09, T:0.37
Consensus pattern (59 bp):
CCTCTACATATATGTGCTATCAAGTAGCAACACCCATTTTAGTGTACATTAATTTCTTA
Found at i:78676 original size:63 final size:63
Alignment explanation
Indices: 78497--78679 Score: 288
Period size: 59 Copynumber: 3.0 Consensus size: 63
78487 AATTTTTTTT
*
78497 TTAATTATTCATCCATTAACTCCTCTACATATATGTGCTATCAAGTAGCAACACCCATTTTAG
1 TTAATTATTCATTCATTAACTCCTCTACATATATGTGCTATCAAGTAGCAACACCCATTTTAG
*
78560 TGTACATTAAT--TTC-TT-A--CCTCTACATATATGTGCTATCAAGTAGCAACACCCATTTTAG
1 T-TA-ATTATTCATTCATTAACTCCTCTACATATATGTGCTATCAAGTAGCAACACCCATTTTAG
78619 TTAATTATTCATTCATTAACTCCTCTACATATATGTGCTATCAAGTAGCAACACCCATTTT
1 TTAATTATTCATTCATTAACTCCTCTACATATATGTGCTATCAAGTAGCAACACCCATTTT
78680 TAGTGTACAC
Statistics
Matches: 109, Mismatches: 3, Indels: 16
0.85 0.02 0.12
Matches are distributed among these distances:
57 5 0.05
58 2 0.02
59 46 0.42
60 2 0.02
61 2 0.02
62 2 0.02
63 43 0.39
64 2 0.02
65 5 0.05
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (63 bp):
TTAATTATTCATTCATTAACTCCTCTACATATATGTGCTATCAAGTAGCAACACCCATTTTAG
Done.