Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012080.1 Corchorus olitorius cultivar O-4 contig12113, 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: 35632
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.31
Found at i:845 original size:24 final size:24
Alignment explanation
Indices: 806--857 Score: 70
Period size: 25 Copynumber: 2.2 Consensus size: 24
796 CTGCTGGGCC
806 GGCCTGGCGCGGCCCA-GCGCACG
1 GGCCTGGCGCGGCCCAGGCGCACG
* *
829 GGCCTGTGCGTGGCCCAGGCGCGCG
1 GGCCTG-GCGCGGCCCAGGCGCACG
854 GGCC
1 GGCC
858 AGGCCAGGCT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 6 0.24
24 9 0.36
25 10 0.40
ACGTcount: A:0.06, C:0.40, G:0.46, T:0.08
Consensus pattern (24 bp):
GGCCTGGCGCGGCCCAGGCGCACG
Found at i:912 original size:6 final size:6
Alignment explanation
Indices: 890--948 Score: 59
Period size: 6 Copynumber: 10.2 Consensus size: 6
880 GGCCCAAGCC
* * *
890 AGGAAA A-GAAA A-AAAA AGGAAA AGGAAA AGGAAG AGGAAA AAGAAA
1 AGGAAA AGGAAA AGGAAA AGGAAA AGGAAA AGGAAA AGGAAA AGGAAA
* *
936 AAGAAA AAGAAA A
1 AGGAAA AGGAAA A
949 TAAAATAAGT
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
5 9 0.19
6 38 0.81
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (6 bp):
AGGAAA
Found at i:947 original size:18 final size:18
Alignment explanation
Indices: 893--948 Score: 69
Period size: 18 Copynumber: 3.2 Consensus size: 18
883 CCAAGCCAGG
893 AAAAGAAAAA-AAAAGGA
1 AAAAGAAAAAGAAAAGGA
* * *
910 AAAGGAAAAGGAAGAGGA
1 AAAAGAAAAAGAAAAGGA
*
928 AAAAGAAAAAGAAAAAGA
1 AAAAGAAAAAGAAAAGGA
946 AAA
1 AAA
949 TAAAATAAGT
Statistics
Matches: 31, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
17 8 0.26
18 23 0.74
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (18 bp):
AAAAGAAAAAGAAAAGGA
Found at i:4480 original size:27 final size:26
Alignment explanation
Indices: 4429--4490 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 26
4419 CTGGAGAATC
*
4429 AATTACCGCAGGAAAAATTGCAGATG
1 AATTACCGCAAGAAAAATTGCAGATG
*
4455 AATTCACCGCAAGAAAAGCTTG-AGATG
1 AATT-ACCGCAAGAAAA-ATTGCAGATG
4482 AACTTACCG
1 AA-TTACCG
4491 GTGGCTGTAC
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
26 4 0.13
27 22 0.71
28 5 0.16
ACGTcount: A:0.40, C:0.19, G:0.21, T:0.19
Consensus pattern (26 bp):
AATTACCGCAAGAAAAATTGCAGATG
Found at i:7758 original size:17 final size:17
Alignment explanation
Indices: 7736--7774 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
7726 GAATTATACG
7736 ATAAATATAAATAATAA
1 ATAAATATAAATAATAA
7753 ATAAATATAAATAATAA
1 ATAAATATAAATAATAA
7770 ATAAA
1 ATAAA
7775 AGGCCACTCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (17 bp):
ATAAATATAAATAATAA
Found at i:16131 original size:20 final size:22
Alignment explanation
Indices: 16096--16146 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 22
16086 TTAAATAAAG
*
16096 TAAAATAAAAATA-TTTAAAAA
1 TAAAATTAAAATATTTTAAAAA
*
16117 TAAAATTAAAA-ATTTTAATAA
1 TAAAATTAAAATATTTTAAAAA
16138 -AAAATTAAA
1 TAAAATTAAA
16147 TCTAAATGAG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
20 10 0.37
21 17 0.63
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATTAAAATATTTTAAAAA
Found at i:20631 original size:14 final size:14
Alignment explanation
Indices: 20612--20640 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
20602 CGTGCTTTGG
20612 AAATTGTTCATTCA
1 AAATTGTTCATTCA
20626 AAATTGTTCATTCA
1 AAATTGTTCATTCA
20640 A
1 A
20641 TTAATTATCA
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:0.38, C:0.14, G:0.07, T:0.41
Consensus pattern (14 bp):
AAATTGTTCATTCA
Found at i:22560 original size:42 final size:43
Alignment explanation
Indices: 22513--22598 Score: 138
Period size: 45 Copynumber: 2.0 Consensus size: 43
22503 TTATCTAAAT
*
22513 TCTA-CTCCATCTCTAGGTAATTCATCAAAATAAAGCTAATAC
1 TCTACCTCCATCTCTAGATAATTCATCAAAATAAAGCTAATAC
22555 TCTACTCCTCCATCTCTAGATAATTCATCAAAATAAAGCTAATA
1 TCTA--CCTCCATCTCTAGATAATTCATCAAAATAAAGCTAATA
22599 GTAATTGTTG
Statistics
Matches: 40, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
42 4 0.10
45 36 0.90
ACGTcount: A:0.38, C:0.24, G:0.06, T:0.31
Consensus pattern (43 bp):
TCTACCTCCATCTCTAGATAATTCATCAAAATAAAGCTAATAC
Found at i:27010 original size:28 final size:29
Alignment explanation
Indices: 26978--27033 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
26968 GAGGAGAAGT
26978 CAACA-TTTCGAAGTCATCATCCATCTCG
1 CAACATTTTCGAAGTCATCATCCATCTCG
*
27006 CAACATTTTCGAAGTCATCATCCTTCTC
1 CAACATTTTCGAAGTCATCATCCATCTC
27034 ATTGGATATT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 5 0.19
29 21 0.81
ACGTcount: A:0.27, C:0.32, G:0.09, T:0.32
Consensus pattern (29 bp):
CAACATTTTCGAAGTCATCATCCATCTCG
Found at i:27691 original size:49 final size:51
Alignment explanation
Indices: 27577--27693 Score: 132
Period size: 51 Copynumber: 2.3 Consensus size: 51
27567 TGAATAGCTT
* ** *
27577 TTAGTCTACGGAGTTGATCATATCCCTATCTTGAAAATCGAATGATGGCAA
1 TTAGTCTAAGGAGTTGATCATATCCCTATCTTGAAAAAAGAATGATCGCAA
* * * *
27628 TTAGTCTAAAGAGTTGATCTTATGCCC-GTCTT-AAAAAAGAATGATCGTAA
1 TTAGTCTAAGGAGTTGATCATAT-CCCTATCTTGAAAAAAGAATGATCGCAA
27678 -TAGTCTAAGGAGTTGA
1 TTAGTCTAAGGAGTTGA
27694 AAACGAATGA
Statistics
Matches: 56, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
49 15 0.27
50 14 0.25
51 24 0.43
52 3 0.05
ACGTcount: A:0.33, C:0.15, G:0.21, T:0.32
Consensus pattern (51 bp):
TTAGTCTAAGGAGTTGATCATATCCCTATCTTGAAAAAAGAATGATCGCAA
Done.