Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020378.1 Corchorus olitorius cultivar O-4 contig20411, 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: 17699
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:731 original size:10 final size:9
Alignment explanation
Indices: 706--742 Score: 56
Period size: 9 Copynumber: 4.0 Consensus size: 9
696 CTCACCGTTA
706 CTTCATTTT
1 CTTCATTTT
715 CTTCATTTGT
1 CTTCATTT-T
*
725 GTTCATTTT
1 CTTCATTTT
734 CTTCATTTT
1 CTTCATTTT
743 TGTTTTCTCC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
9 17 0.68
10 8 0.32
ACGTcount: A:0.11, C:0.19, G:0.05, T:0.65
Consensus pattern (9 bp):
CTTCATTTT
Found at i:731 original size:19 final size:19
Alignment explanation
Indices: 707--746 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
697 TCACCGTTAC
707 TTCATTTTCTTCATTTGTG
1 TTCATTTTCTTCATTTGTG
*
726 TTCATTTTCTTCATTTTTG
1 TTCATTTTCTTCATTTGTG
745 TT
1 TT
747 TTCTCCACCG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.10, C:0.15, G:0.07, T:0.68
Consensus pattern (19 bp):
TTCATTTTCTTCATTTGTG
Found at i:5971 original size:10 final size:10
Alignment explanation
Indices: 5936--5970 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
5926 ATGGCAAAAA
5936 AAAAAAAACT
1 AAAAAAAACT
5946 AAAAAAAATCT
1 AAAAAAAA-CT
*
5957 AAAAGAAACT
1 AAAAAAAACT
5967 AAAA
1 AAAA
5971 GGAAGAGAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 14 0.61
11 9 0.39
ACGTcount: A:0.77, C:0.09, G:0.03, T:0.11
Consensus pattern (10 bp):
AAAAAAAACT
Found at i:9024 original size:33 final size:33
Alignment explanation
Indices: 8983--9063 Score: 89
Period size: 30 Copynumber: 2.5 Consensus size: 33
8973 GATTACATAT
**
8983 TATTTCTAATAATATTTATTGTATATTAAATAAA
1 TATTTCTAATAATATTTATTACATATT-AATAAA
9017 TA-TTC---TAATATTTATTACATATTAATAAA
1 TATTTCTAATAATATTTATTACATATTAATAAA
* *
9046 TATTTGTAATAAAATTTA
1 TATTTCTAATAATATTTA
9064 AATGTTATTT
Statistics
Matches: 39, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
29 8 0.21
30 18 0.46
33 11 0.28
34 2 0.05
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.49
Consensus pattern (33 bp):
TATTTCTAATAATATTTATTACATATTAATAAA
Found at i:9056 original size:30 final size:30
Alignment explanation
Indices: 8992--9049 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
8982 TTATTTCTAA
**
8992 TAATATTTATTGTATATTAAATAAATATTC
1 TAATATTTATTACATATTAAATAAATATTC
9022 TAATATTTATTACATATT-AATAAATATT
1 TAATATTTATTACATATTAAATAAATATT
9050 TGTAATAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 10 0.38
30 16 0.62
ACGTcount: A:0.45, C:0.03, G:0.02, T:0.50
Consensus pattern (30 bp):
TAATATTTATTACATATTAAATAAATATTC
Found at i:9159 original size:12 final size:11
Alignment explanation
Indices: 9130--9160 Score: 53
Period size: 11 Copynumber: 2.7 Consensus size: 11
9120 ATTAATGAAC
9130 ATAAACGAGTT
1 ATAAACGAGTT
9141 ATAAACGAGTT
1 ATAAACGAGTT
9152 ATTAAACGA
1 A-TAAACGA
9161 ACAATAAACG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 12 0.63
12 7 0.37
ACGTcount: A:0.48, C:0.10, G:0.16, T:0.26
Consensus pattern (11 bp):
ATAAACGAGTT
Found at i:9812 original size:42 final size:43
Alignment explanation
Indices: 9761--9854 Score: 147
Period size: 45 Copynumber: 2.2 Consensus size: 43
9751 AGTGCATTAA
*
9761 CTAA-ATTCTA-CTCCATCTCTAGGTAATTCATCAAAATAAAG
1 CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAG
9802 CTAATATTCTACTCCTCCATCTCTAGATAATTCATCAAAATAAAG
1 CTAATATTCTA--CCTCCATCTCTAGATAATTCATCAAAATAAAG
9847 CTAATATT
1 CTAATATT
9855 AATTGTTGTT
Statistics
Matches: 48, Mismatches: 1, Indels: 4
0.91 0.02 0.08
Matches are distributed among these distances:
41 4 0.08
42 6 0.12
45 38 0.79
ACGTcount: A:0.38, C:0.22, G:0.05, T:0.34
Consensus pattern (43 bp):
CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAG
Found at i:11641 original size:31 final size:29
Alignment explanation
Indices: 11598--11683 Score: 111
Period size: 31 Copynumber: 2.9 Consensus size: 29
11588 ATTAAGGCTA
*
11598 AATGTTCAATTTGGTCCTAAACCTTTTATGG
1 AATGCTCAATTTGGTCCTAAACCTTTTA--G
11629 AATGCTCAATTTGGTCCTAAACC-TTTAG
1 AATGCTCAATTTGGTCCTAAACCTTTTAG
* *
11657 ATTTGCTCAAATTGGTCCTAAACCTTT
1 A-ATGCTCAATTTGGTCCTAAACCTTT
11684 CAAAATCTAC
Statistics
Matches: 50, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
28 2 0.04
29 20 0.40
30 6 0.12
31 22 0.44
ACGTcount: A:0.27, C:0.20, G:0.14, T:0.40
Consensus pattern (29 bp):
AATGCTCAATTTGGTCCTAAACCTTTTAG
Found at i:11673 original size:29 final size:29
Alignment explanation
Indices: 11598--11683 Score: 111
Period size: 29 Copynumber: 2.9 Consensus size: 29
11588 ATTAAGGCTA
*
11598 AATGTTCAATTTGGTCCTAAACCTTTTATGG
1 AATGCTCAATTTGGTCCTAAACC-TTTA-GG
11629 AATGCTCAATTTGGTCCTAAACCTTTA-G
1 AATGCTCAATTTGGTCCTAAACCTTTAGG
* *
11657 ATTTGCTCAAATTGGTCCTAAACCTTT
1 A-ATGCTCAATTTGGTCCTAAACCTTT
11684 CAAAATCTAC
Statistics
Matches: 51, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
28 2 0.04
29 23 0.45
30 4 0.08
31 22 0.43
ACGTcount: A:0.27, C:0.20, G:0.14, T:0.40
Consensus pattern (29 bp):
AATGCTCAATTTGGTCCTAAACCTTTAGG
Found at i:11975 original size:25 final size:27
Alignment explanation
Indices: 11947--12018 Score: 85
Period size: 26 Copynumber: 2.7 Consensus size: 27
11937 AATTTTCATC
*
11947 TCTCTATTTTTCATAACAAATA-TT-T
1 TCTCTATTTTTCATAAAAAATATTTAT
*
11972 TCTCTATTTTTTCTTAAAAAATATTTAT
1 TCTCTA-TTTTTCATAAAAAATATTTAT
*
12000 TCACTATTTCTTCATAAAA
1 TCTCTATTT-TTCATAAAA
12019 TTGGTGAGGT
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
25 6 0.15
26 14 0.36
27 5 0.13
28 14 0.36
ACGTcount: A:0.33, C:0.15, G:0.00, T:0.51
Consensus pattern (27 bp):
TCTCTATTTTTCATAAAAAATATTTAT
Found at i:12924 original size:18 final size:18
Alignment explanation
Indices: 12901--12936 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
12891 GTAGACAACT
12901 AAAATTCATGAGAAAAAA
1 AAAATTCATGAGAAAAAA
12919 AAAATTCATGAGAAAAAA
1 AAAATTCATGAGAAAAAA
12937 TATGTTTAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.67, C:0.06, G:0.11, T:0.17
Consensus pattern (18 bp):
AAAATTCATGAGAAAAAA
Found at i:17289 original size:22 final size:21
Alignment explanation
Indices: 17256--17298 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 21
17246 ATGCCCTCTC
*
17256 TTTTTCTTTTCTTTTTTTTCT
1 TTTTTCTTTTCTCTTTTTTCT
17277 TTTTTCTTATTCTCTTTTTTCT
1 TTTTTCTT-TTCTCTTTTTTCT
17299 GTGTCTTTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.02, C:0.16, G:0.00, T:0.81
Consensus pattern (21 bp):
TTTTTCTTTTCTCTTTTTTCT
Done.