Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020885.1 Corchorus olitorius cultivar O-4 contig20918, 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: 53509
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--31 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1 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 T
32 GATCTGAATG
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:85 original size:20 final size:20
Alignment explanation
Indices: 60--112 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 20
50 GTTATAATAA
60 TAATGATGATG-AT-AAAAAGG
1 TAATGAT-ATGAATCAAAAA-G
80 TAATGAATATGAATCAAAAAG
1 TAATG-ATATGAATCAAAAAG
101 TAATGA-ATGAAT
1 TAATGATATGAAT
113 GTTGTTGCAT
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
19 6 0.20
20 9 0.30
21 10 0.33
22 5 0.17
ACGTcount: A:0.53, C:0.02, G:0.19, T:0.26
Consensus pattern (20 bp):
TAATGATATGAATCAAAAAG
Found at i:1367 original size:6 final size:6
Alignment explanation
Indices: 1358--1393 Score: 63
Period size: 6 Copynumber: 6.0 Consensus size: 6
1348 GCGCTCACCC
*
1358 AAATGA AAATGA AAATGA AAATGC AAATGA AAATGA
1 AAATGA AAATGA AAATGA AAATGA AAATGA AAATGA
1394 GCACCATCTG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.64, C:0.03, G:0.17, T:0.17
Consensus pattern (6 bp):
AAATGA
Found at i:6109 original size:6 final size:6
Alignment explanation
Indices: 6100--6133 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
6090 ATTTGATTGA
*
6100 TTGTAT TTGTAT TTGTAT TTGTAT TTGTAA TTGT
1 TTGTAT TTGTAT TTGTAT TTGTAT TTGTAT TTGT
6134 TGTTGGCGCA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.18, C:0.00, G:0.18, T:0.65
Consensus pattern (6 bp):
TTGTAT
Found at i:7702 original size:6 final size:6
Alignment explanation
Indices: 7691--7727 Score: 65
Period size: 6 Copynumber: 6.2 Consensus size: 6
7681 TATGATAAAG
*
7691 GGCAAC GGCAAC GGCGAC GGCAAC GGCAAC GGCAAC G
1 GGCAAC GGCAAC GGCAAC GGCAAC GGCAAC GGCAAC G
7728 CAGAGGAAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.30, C:0.32, G:0.38, T:0.00
Consensus pattern (6 bp):
GGCAAC
Found at i:12903 original size:8 final size:8
Alignment explanation
Indices: 12892--12923 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
12882 AGAGAGAGAG
12892 AGTTTCCA
1 AGTTTCCA
12900 AGTTT-CA
1 AGTTTCCA
12907 AG-TTCCA
1 AGTTTCCA
12914 AGTTTCCA
1 AGTTTCCA
12922 AG
1 AG
12924 CAAGCGGACC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
6 2 0.09
7 8 0.36
8 12 0.55
ACGTcount: A:0.28, C:0.22, G:0.16, T:0.34
Consensus pattern (8 bp):
AGTTTCCA
Found at i:33173 original size:27 final size:25
Alignment explanation
Indices: 33143--33194 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 25
33133 AGCAGTAAAG
33143 ACCAAGGACAAGGAGGTTAGGGAGTTC
1 ACCAAGGACAAGGA-GTTAGGG-GTTC
* *
33170 ACCAGGGGCAAGGAGTTAGGGGTTC
1 ACCAAGGACAAGGAGTTAGGGGTTC
33195 GAACCCCACT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 4 0.17
26 7 0.30
27 12 0.52
ACGTcount: A:0.29, C:0.15, G:0.40, T:0.15
Consensus pattern (25 bp):
ACCAAGGACAAGGAGTTAGGGGTTC
Found at i:37651 original size:43 final size:43
Alignment explanation
Indices: 37590--37675 Score: 172
Period size: 43 Copynumber: 2.0 Consensus size: 43
37580 TTATTTTACA
37590 GAAATGTCACCAATTCTAATACAAAGTTGGTAACTGGCAATGC
1 GAAATGTCACCAATTCTAATACAAAGTTGGTAACTGGCAATGC
37633 GAAATGTCACCAATTCTAATACAAAGTTGGTAACTGGCAATGC
1 GAAATGTCACCAATTCTAATACAAAGTTGGTAACTGGCAATGC
37676 AGGACGGTGA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.26
Consensus pattern (43 bp):
GAAATGTCACCAATTCTAATACAAAGTTGGTAACTGGCAATGC
Found at i:38020 original size:2 final size:2
Alignment explanation
Indices: 38013--38044 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
38003 GGCATGTAGG
38013 AT AT AT 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 AT AT AT
38045 GCCCTCCTTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:45903 original size:21 final size:21
Alignment explanation
Indices: 45863--45903 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
45853 TTTTTCCCCT
* * *
45863 TTCATTCTGTATGCATTATTC
1 TTCATGCTGTATCCACTATTC
45884 TTCATGCTGTATCCACTATT
1 TTCATGCTGTATCCACTATT
45904 TCTATGTACG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.20, C:0.22, G:0.10, T:0.49
Consensus pattern (21 bp):
TTCATGCTGTATCCACTATTC
Done.