Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017424.1 Corchorus olitorius cultivar O-4 contig17457, 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: 27856
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.31
Found at i:1051 original size:24 final size:24
Alignment explanation
Indices: 1019--1076 Score: 80
Period size: 24 Copynumber: 2.4 Consensus size: 24
1009 AATGGGAATT
* *
1019 GGTGGAGGAATATTCCGATTCTGA
1 GGTGGAGGAACATTCCGATTCTAA
* *
1043 GGTGGAGGAGCGTTCCGATTCTAA
1 GGTGGAGGAACATTCCGATTCTAA
1067 GGTGGAGGAA
1 GGTGGAGGAA
1077 GTGCAGGTGG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.24, C:0.12, G:0.40, T:0.24
Consensus pattern (24 bp):
GGTGGAGGAACATTCCGATTCTAA
Found at i:8404 original size:7 final size:7
Alignment explanation
Indices: 8392--8434 Score: 79
Period size: 7 Copynumber: 6.3 Consensus size: 7
8382 TTAAAAGACC
8392 TTTTCTT
1 TTTTCTT
8399 TTTTCTT
1 TTTTCTT
8406 TTTTCTT
1 TTTTCTT
8413 TTTTC-T
1 TTTTCTT
8419 TTTTCTT
1 TTTTCTT
8426 TTTTCTT
1 TTTTCTT
8433 TT
1 TT
8435 GGGTTGGGGA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
6 6 0.17
7 29 0.83
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (7 bp):
TTTTCTT
Found at i:8414 original size:13 final size:13
Alignment explanation
Indices: 8392--8434 Score: 77
Period size: 13 Copynumber: 3.2 Consensus size: 13
8382 TTAAAAGACC
8392 TTTTCTTTTTTCTT
1 TTTTCTTTTTTC-T
8406 TTTTCTTTTTTCT
1 TTTTCTTTTTTCT
8419 TTTTCTTTTTTCT
1 TTTTCTTTTTTCT
8432 TTT
1 TTT
8435 GGGTTGGGGA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
13 17 0.59
14 12 0.41
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (13 bp):
TTTTCTTTTTTCT
Found at i:8421 original size:20 final size:21
Alignment explanation
Indices: 8392--8434 Score: 79
Period size: 20 Copynumber: 2.1 Consensus size: 21
8382 TTAAAAGACC
8392 TTTTCTTTTTTCTTTTTTCTT
1 TTTTCTTTTTTCTTTTTTCTT
8413 TTTTC-TTTTTCTTTTTTCTT
1 TTTTCTTTTTTCTTTTTTCTT
8433 TT
1 TT
8435 GGGTTGGGGA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 17 0.77
21 5 0.23
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (21 bp):
TTTTCTTTTTTCTTTTTTCTT
Found at i:11862 original size:124 final size:121
Alignment explanation
Indices: 11641--11896 Score: 408
Period size: 124 Copynumber: 2.1 Consensus size: 121
11631 CAAGAAATTA
* * *
11641 TTATTTTGA-CCTTCATCAA-AGTTCAAGAAATTATCATTTCGATCTTCACCAATTATTTGAAGA
1 TTATTTTGATCC-TCACCAACA-TTCAAGAAATCATCATGTCGATCTTCACCAATTATTTGAAGA
11704 AGATTATTTTTGTTCGTTCAAGATCAAGTCTATCAAGGACCCTTGAAAGCGGATTTATT
64 AGATTATTTTTGTTCGTTCAAGATCAAGTCTATCAAGGACCCTTG-AAGCGGATTTATT
* *
11763 TTAATTTTGATCCTCACCAACATTCAAGAAATCATTATGTCGATCTTCACCAGTTTATTTGAAGA
1 TT-ATTTTGATCCTCACCAACATTCAAGAAATCATCATGTCGATCTTCACCA-ATTATTTGAAGA
11828 AGATTATTTTTGTTCGTTCAAGATCAAGTCTATCAAGGACCCTTGAAGCGGATTTATT
64 AGATTATTTTTGTTCGTTCAAGATCAAGTCTATCAAGGACCCTTGAAGCGGATTTATT
11886 TTATTTTGATC
1 TTATTTTGATC
11897 TTCATTAACA
Statistics
Matches: 125, Mismatches: 5, Indels: 8
0.91 0.04 0.06
Matches are distributed among these distances:
122 11 0.09
123 55 0.44
124 59 0.47
ACGTcount: A:0.30, C:0.17, G:0.14, T:0.39
Consensus pattern (121 bp):
TTATTTTGATCCTCACCAACATTCAAGAAATCATCATGTCGATCTTCACCAATTATTTGAAGAAG
ATTATTTTTGTTCGTTCAAGATCAAGTCTATCAAGGACCCTTGAAGCGGATTTATT
Found at i:11983 original size:44 final size:44
Alignment explanation
Indices: 11933--12056 Score: 180
Period size: 44 Copynumber: 2.8 Consensus size: 44
11923 TTTTTGTTCG
* *
11933 TTCAAGATTAAGTCGTCAAGACCCTTGAATCAAATCATCATCAA
1 TTCAAGATCAAGTCATCAAGACCCTTGAATCAAATCATCATCAA
**
11977 TTCAAGATCAAGTCATCAAGACCCTTGAATCAAATTTTCATCAA
1 TTCAAGATCAAGTCATCAAGACCCTTGAATCAAATCATCATCAA
*
12021 TTCAAGATCAAGTCATAAAGACCCCTT--ATCAAATCA
1 TTCAAGATCAAGTCATCAAGA-CCCTTGAATCAAATCA
12057 AACTCTCAAA
Statistics
Matches: 72, Mismatches: 7, Indels: 3
0.88 0.09 0.04
Matches are distributed among these distances:
43 7 0.10
44 60 0.83
45 5 0.07
ACGTcount: A:0.40, C:0.23, G:0.10, T:0.27
Consensus pattern (44 bp):
TTCAAGATCAAGTCATCAAGACCCTTGAATCAAATCATCATCAA
Found at i:16689 original size:2 final size:2
Alignment explanation
Indices: 16682--16715 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
16672 TTAATCCTCT
16682 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
16716 ATAGCATTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:18189 original size:14 final size:16
Alignment explanation
Indices: 18148--18180 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
18138 ATTGATAGAT
*
18148 AAGCACAGCAAGGTGC
1 AAGCACAACAAGGTGC
18164 AAGCACAACAAGGTGC
1 AAGCACAACAAGGTGC
18180 A
1 A
18181 GGAAACAAGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.42, C:0.24, G:0.27, T:0.06
Consensus pattern (16 bp):
AAGCACAACAAGGTGC
Found at i:18242 original size:20 final size:21
Alignment explanation
Indices: 18206--18244 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
18196 TCCAAAAAAA
*
18206 AACAACAACATCAAACCAGCC
1 AACAAAAACATCAAACCAGCC
18227 AACAAAAACA-CAAACCAG
1 AACAAAAACATCAAACCAG
18245 ACAGCAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.59, C:0.33, G:0.05, T:0.03
Consensus pattern (21 bp):
AACAAAAACATCAAACCAGCC
Found at i:20474 original size:15 final size:16
Alignment explanation
Indices: 20441--20480 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
20431 TTACTTTGCT
20441 TTGTTTTCTAGTATAA
1 TTGTTTTCTAGTATAA
*
20457 TTGTTTTC-AGTTTAA
1 TTGTTTTCTAGTATAA
*
20472 TTGCTTTCT
1 TTGTTTTCT
20481 TTCAACCTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 13 0.62
16 8 0.38
ACGTcount: A:0.17, C:0.10, G:0.12, T:0.60
Consensus pattern (16 bp):
TTGTTTTCTAGTATAA
Found at i:20854 original size:27 final size:27
Alignment explanation
Indices: 20814--20879 Score: 71
Period size: 28 Copynumber: 2.4 Consensus size: 27
20804 TTTTTTCTAA
**
20814 AAAAAAAAAATTTTGTTT-TGCGTCAAG
1 AAAAAAAATTTTTTGTTTCTGCGT-AAG
* *
20841 AAAAAAAATTTTTTTGTTTCTGCGTTAT
1 AAAAAAAA-TTTTTTGTTTCTGCGTAAG
20869 AAAAAAAATTT
1 AAAAAAAATTT
20880 CTTTTATTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
27 11 0.33
28 17 0.52
29 5 0.15
ACGTcount: A:0.44, C:0.06, G:0.11, T:0.39
Consensus pattern (27 bp):
AAAAAAAATTTTTTGTTTCTGCGTAAG
Found at i:20864 original size:29 final size:28
Alignment explanation
Indices: 20824--20889 Score: 80
Period size: 28 Copynumber: 2.3 Consensus size: 28
20814 AAAAAAAAAA
20824 TTTTGTTTTGCGTCAAGAAAAAAAATTT-
1 TTTTGTTTTGCGT-AAGAAAAAAAATTTC
* *
20852 TTTTGTTTCTGCGTTATAAAAAAAATTTC
1 TTTTGTTT-TGCGTAAGAAAAAAAATTTC
*
20881 TTTTATTTT
1 TTTTGTTTT
20890 CTGTCTTTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
28 21 0.64
29 12 0.36
ACGTcount: A:0.30, C:0.08, G:0.11, T:0.52
Consensus pattern (28 bp):
TTTTGTTTTGCGTAAGAAAAAAAATTTC
Found at i:26791 original size:50 final size:47
Alignment explanation
Indices: 26689--26825 Score: 168
Period size: 50 Copynumber: 2.8 Consensus size: 47
26679 GAGCGTGCCA
* * * *
26689 ATCAATTTTGTCAAAAAATTGATAAAAAGTAC-GATGAAAATTAAAAG
1 ATCAATTTTGTCTAAAAATTGAGAAAAAGTGCAG-TAAAAATTAAAAG
26736 ATCAATTTTGTCTTAAAAATTGAGAAAAAGATGCAAGTAAAAATTAAAAG
1 ATCAATTTTGTC-TAAAAATTGAGAAAAAG-TGC-AGTAAAAATTAAAAG
* *
26786 TTCAATTTTGTAGTAAAAATTGAGAAAAAGTGCAGTAAAA
1 ATCAATTTTGT-CTAAAAATTGAGAAAAAGTGCAGTAAAA
26826 GTAAAGGATT
Statistics
Matches: 79, Mismatches: 6, Indels: 9
0.84 0.06 0.10
Matches are distributed among these distances:
47 12 0.15
48 22 0.28
49 5 0.06
50 39 0.49
51 1 0.01
ACGTcount: A:0.51, C:0.06, G:0.15, T:0.28
Consensus pattern (47 bp):
ATCAATTTTGTCTAAAAATTGAGAAAAAGTGCAGTAAAAATTAAAAG
Done.