Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022209.1 Corchorus olitorius cultivar O-4 contig22242, 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: 41306
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:832 original size:29 final size:30
Alignment explanation
Indices: 780--839 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 30
770 GAAGTTCGTG
*
780 TTTGAAGACTCATTGAAGACTTATTTGAAGA
1 TTTGAAGACT-ATTGAAGACTTATTTCAAGA
*
811 TTTGAAGACT-TTGAAGATTTATTTCAAGA
1 TTTGAAGACTATTGAAGACTTATTTCAAGA
840 GGAAGAATTG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 17 0.63
31 10 0.37
ACGTcount: A:0.35, C:0.08, G:0.18, T:0.38
Consensus pattern (30 bp):
TTTGAAGACTATTGAAGACTTATTTCAAGA
Found at i:2237 original size:15 final size:16
Alignment explanation
Indices: 2204--2243 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
2194 TTACTTTGCT
2204 TTGTTTTCTAGTATAA
1 TTGTTTTCTAGTATAA
*
2220 TTGTTTTCT-GTTTAA
1 TTGTTTTCTAGTATAA
*
2235 TTGCTTTCT
1 TTGTTTTCT
2244 TTCAACCTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.15, C:0.10, G:0.12, T:0.62
Consensus pattern (16 bp):
TTGTTTTCTAGTATAA
Found at i:7322 original size:109 final size:109
Alignment explanation
Indices: 7131--7346 Score: 324
Period size: 109 Copynumber: 2.0 Consensus size: 109
7121 GCATTTAATG
* * * * *
7131 TGCTTTGCATACTCATAATTTTGGTTCGTGACTGACACGAAGGTTGATATTTGTGATAGCGAACC
1 TGCTTTGCATAATCATAATTTTGGTTCGTGAATGACACGAAGGTAGATATTTGTGATACCAAACC
* *
7196 CCGTGTGCTCCACTTCCCAAAAGCAGCATAGTAATTTATTAAGA
66 CCGTGTGCTCCACTTCCCAAAAACAGCACAGTAATTTATTAAGA
* * *
7240 TGCTTTGCATAATCATAATTTTGGTTTGTGAATGACGCGGAGGTAGATATTTGTGATACCAAACC
1 TGCTTTGCATAATCATAATTTTGGTTCGTGAATGACACGAAGGTAGATATTTGTGATACCAAACC
**
7305 CCGTGTGCTCCACTTCCCAAAAACAGTGCAGTAATTTATTAA
66 CCGTGTGCTCCACTTCCCAAAAACAGCACAGTAATTTATTAA
7347 ATTCCCTCTA
Statistics
Matches: 95, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
109 95 1.00
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.32
Consensus pattern (109 bp):
TGCTTTGCATAATCATAATTTTGGTTCGTGAATGACACGAAGGTAGATATTTGTGATACCAAACC
CCGTGTGCTCCACTTCCCAAAAACAGCACAGTAATTTATTAAGA
Found at i:9924 original size:5 final size:5
Alignment explanation
Indices: 9916--9940 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
9906 AAACTAAAAA
9916 CAAAG CAAAG CAAAG CAAAG CAAAG
1 CAAAG CAAAG CAAAG CAAAG CAAAG
9941 TAAATTAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.60, C:0.20, G:0.20, T:0.00
Consensus pattern (5 bp):
CAAAG
Found at i:21692 original size:24 final size:24
Alignment explanation
Indices: 21660--21721 Score: 124
Period size: 24 Copynumber: 2.6 Consensus size: 24
21650 GGGGAAAGGA
21660 ATTGGAGGCACATACGGTTTGATG
1 ATTGGAGGCACATACGGTTTGATG
21684 ATTGGAGGCACATACGGTTTGATG
1 ATTGGAGGCACATACGGTTTGATG
21708 ATTGGAGGCACATA
1 ATTGGAGGCACATA
21722 AGGATCATCT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.27, C:0.13, G:0.32, T:0.27
Consensus pattern (24 bp):
ATTGGAGGCACATACGGTTTGATG
Found at i:21968 original size:21 final size:21
Alignment explanation
Indices: 21944--21991 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
21934 TCACATTTTG
21944 TTGTTGAACCAATTGCCCCAC
1 TTGTTGAACCAATTGCCCCAC
** *
21965 TTGTTGAGTCAATTGCCCCAT
1 TTGTTGAACCAATTGCCCCAC
21986 TTGTTG
1 TTGTTG
21992 CTCAAGATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.19, C:0.25, G:0.19, T:0.38
Consensus pattern (21 bp):
TTGTTGAACCAATTGCCCCAC
Found at i:22051 original size:21 final size:22
Alignment explanation
Indices: 22020--22068 Score: 73
Period size: 21 Copynumber: 2.3 Consensus size: 22
22010 GGCTTGGGGG
*
22020 GATTGATTGCATTAAGAAAGTT
1 GATTGAGTGCATTAAGAAAGTT
*
22042 G-TTGAGTGCATTGAGAAAGTT
1 GATTGAGTGCATTAAGAAAGTT
22063 GATTGA
1 GATTGA
22069 ACTTTTCTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 19 0.79
22 5 0.21
ACGTcount: A:0.33, C:0.04, G:0.29, T:0.35
Consensus pattern (22 bp):
GATTGAGTGCATTAAGAAAGTT
Found at i:25472 original size:42 final size:42
Alignment explanation
Indices: 25425--25537 Score: 181
Period size: 42 Copynumber: 2.7 Consensus size: 42
25415 AAGGAGGATT
*
25425 ATTGAAAGAAGATCCACATATGTGGAGGAATCATCAAAGAAG
1 ATTGAAAGAAGATCCACGTATGTGGAGGAATCATCAAAGAAG
* * *
25467 ATTGAAAGAAGATCCACGTATATGGAGGAATTATTAAAGAAG
1 ATTGAAAGAAGATCCACGTATGTGGAGGAATCATCAAAGAAG
*
25509 ATTGAAAGAAAATCCACGTATGTGGAGGA
1 ATTGAAAGAAGATCCACGTATGTGGAGGA
25538 TTATTTTCAA
Statistics
Matches: 65, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 65 1.00
ACGTcount: A:0.44, C:0.10, G:0.25, T:0.21
Consensus pattern (42 bp):
ATTGAAAGAAGATCCACGTATGTGGAGGAATCATCAAAGAAG
Found at i:25694 original size:41 final size:41
Alignment explanation
Indices: 25649--25745 Score: 167
Period size: 41 Copynumber: 2.4 Consensus size: 41
25639 ATTTTTGTTC
* *
25649 ATTCAAGATCAAGTCGTCAAGACCCTTGAGTTAAATTATCA
1 ATTCAAGATCAAGTCGCCAAGACCCTTGAATTAAATTATCA
*
25690 ATTCAAGATCAAGTTGCCAAGACCCTTGAATTAAATTATCA
1 ATTCAAGATCAAGTCGCCAAGACCCTTGAATTAAATTATCA
25731 ATTCAAGATCAAGTC
1 ATTCAAGATCAAGTC
25746 ATTCGACCAT
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.38, C:0.20, G:0.13, T:0.29
Consensus pattern (41 bp):
ATTCAAGATCAAGTCGCCAAGACCCTTGAATTAAATTATCA
Found at i:39863 original size:24 final size:25
Alignment explanation
Indices: 39831--39877 Score: 78
Period size: 24 Copynumber: 1.9 Consensus size: 25
39821 CTTATTATGA
*
39831 TTATTTTTTTGT-GTTGTTTAAGGG
1 TTATTTTTTTGTAATTGTTTAAGGG
39855 TTATTTTTTTGTAATTGTTTAAG
1 TTATTTTTTTGTAATTGTTTAAG
39878 TCAGTTAGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 12 0.57
25 9 0.43
ACGTcount: A:0.17, C:0.00, G:0.19, T:0.64
Consensus pattern (25 bp):
TTATTTTTTTGTAATTGTTTAAGGG
Found at i:40087 original size:45 final size:45
Alignment explanation
Indices: 40023--40145 Score: 228
Period size: 45 Copynumber: 2.7 Consensus size: 45
40013 CTACTTCATT
*
40023 TCTAGGTAATTCATCAAAATAAAGCTAATATTATACTCCTCCATC
1 TCTAGGTAATTCATCAAAATAAACCTAATATTATACTCCTCCATC
*
40068 TCTAGGTAATTCATCAAAATAAACCTAATATTCTACTCCTCCATC
1 TCTAGGTAATTCATCAAAATAAACCTAATATTATACTCCTCCATC
40113 TCTAGGTAATTCATCAAAATAAACCTAATATTA
1 TCTAGGTAATTCATCAAAATAAACCTAATATTA
40146 ATTGTTGCTT
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 75 1.00
ACGTcount: A:0.39, C:0.22, G:0.06, T:0.33
Consensus pattern (45 bp):
TCTAGGTAATTCATCAAAATAAACCTAATATTATACTCCTCCATC
Found at i:41152 original size:17 final size:18
Alignment explanation
Indices: 41126--41160 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
41116 GATAGTTTAT
41126 GGTAGTTTTTTTTAAATG
1 GGTAGTTTTTTTTAAATG
41144 GGTAG-TTTTTTTAAATG
1 GGTAGTTTTTTTTAAATG
41161 ATATAAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.23, C:0.00, G:0.23, T:0.54
Consensus pattern (18 bp):
GGTAGTTTTTTTTAAATG
Done.