Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013352.1 Corchorus olitorius cultivar O-4 contig13385, 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: 31930
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Found at i:2370 original size:15 final size:15
Alignment explanation
Indices: 2337--2378 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
2327 TTACTTTGCT
*
2337 TTGTTTTCTAGTTTCA
1 TTGTTTTCT-GTTTAA
2353 TTGTTTTCTGTTTAA
1 TTGTTTTCTGTTTAA
*
2368 TTGCTTTCTGT
1 TTGTTTTCTGT
2379 CAATCTCTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 15 0.62
16 9 0.38
ACGTcount: A:0.10, C:0.12, G:0.14, T:0.64
Consensus pattern (15 bp):
TTGTTTTCTGTTTAA
Found at i:9618 original size:17 final size:18
Alignment explanation
Indices: 9596--9629 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
9586 TTATGAGCTT
*
9596 ATTGAAT-ATCTTATGTG
1 ATTGAATGATATTATGTG
9613 ATTGAATGATATTATGT
1 ATTGAATGATATTATGT
9630 TGTGCTTACA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.32, C:0.03, G:0.18, T:0.47
Consensus pattern (18 bp):
ATTGAATGATATTATGTG
Found at i:11183 original size:27 final size:27
Alignment explanation
Indices: 11117--11188 Score: 83
Period size: 27 Copynumber: 2.7 Consensus size: 27
11107 TTATGTAAAC
* *
11117 TTTAGTGGGACTAACTGAAGCACAAAA
1 TTTAGTGCGACTAATTGAAGCACAAAA
* * *
11144 ATTAGTGAC-ACTAATTTAAGCGCAAAA
1 TTTAGTG-CGACTAATTGAAGCACAAAA
11171 TTTAGTGCGACTAATTGA
1 TTTAGTGCGACTAATTGA
11189 CTGTACAGAC
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
26 1 0.03
27 35 0.97
ACGTcount: A:0.39, C:0.14, G:0.19, T:0.28
Consensus pattern (27 bp):
TTTAGTGCGACTAATTGAAGCACAAAA
Found at i:11641 original size:33 final size:33
Alignment explanation
Indices: 11604--11705 Score: 161
Period size: 33 Copynumber: 3.1 Consensus size: 33
11594 TTTGCTCAAC
11604 TTGTAAAGGCGTGATGAAGGCCCGTGAACTTCA
1 TTGTAAAGGCGTGATGAAGGCCCGTGAACTTCA
*
11637 TTGTAAAGGCGTGATGAAGGCCTGTGAACTTCA
1 TTGTAAAGGCGTGATGAAGGCCCGTGAACTTCA
* * *
11670 TTGGAACGGCGTGATGAAGGCCCGT-CACTTCA
1 TTGTAAAGGCGTGATGAAGGCCCGTGAACTTCA
11702 TTGT
1 TTGT
11706 TTGTAAGAGC
Statistics
Matches: 63, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
32 9 0.14
33 54 0.86
ACGTcount: A:0.25, C:0.19, G:0.30, T:0.26
Consensus pattern (33 bp):
TTGTAAAGGCGTGATGAAGGCCCGTGAACTTCA
Found at i:14858 original size:31 final size:31
Alignment explanation
Indices: 14821--14987 Score: 208
Period size: 31 Copynumber: 5.4 Consensus size: 31
14811 TTTTGTGCAT
* **
14821 GTGGCATGCCACGTGTCACTTTTTGAAACAC
1 GTGGCATGCCACATGTCACTTTTTGGTACAC
* * *
14852 ATGGCATGCCACGTGTCACTTTTGGGTACAC
1 GTGGCATGCCACATGTCACTTTTTGGTACAC
* * **
14883 ATGGCGTGATACATGTCACTTTTTGGTACAC
1 GTGGCATGCCACATGTCACTTTTTGGTACAC
* *
14914 GTGGCGTGCCACATGTCGCTTTTTGGTACAC
1 GTGGCATGCCACATGTCACTTTTTGGTACAC
* *
14945 GTGGCATGCCACATGTCGCTATTTGGTACAC
1 GTGGCATGCCACATGTCACTTTTTGGTACAC
14976 GTGGCATGCCAC
1 GTGGCATGCCAC
14988 GTCGGGCACC
Statistics
Matches: 121, Mismatches: 15, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 121 1.00
ACGTcount: A:0.19, C:0.25, G:0.26, T:0.30
Consensus pattern (31 bp):
GTGGCATGCCACATGTCACTTTTTGGTACAC
Found at i:16517 original size:12 final size:13
Alignment explanation
Indices: 16492--16521 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
16482 TTTGTGAGGA
16492 AAAAAGAAATAAG
1 AAAAAGAAATAAG
16505 AAAAAGAAA-AAG
1 AAAAAGAAATAAG
16517 AAAAA
1 AAAAA
16522 TGAGATGTAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 8 0.47
13 9 0.53
ACGTcount: A:0.83, C:0.00, G:0.13, T:0.03
Consensus pattern (13 bp):
AAAAAGAAATAAG
Found at i:16520 original size:5 final size:6
Alignment explanation
Indices: 16492--16521 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
16482 TTTGTGAGGA
16492 AAAAAG AAATAAG AAAAAG AAAAAG AAAAA
1 AAAAAG AAA-AAG AAAAAG AAAAAG AAAAA
16522 TGAGATGTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 17 0.74
7 6 0.26
ACGTcount: A:0.83, C:0.00, G:0.13, T:0.03
Consensus pattern (6 bp):
AAAAAG
Found at i:17096 original size:13 final size:13
Alignment explanation
Indices: 17078--17107 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
17068 ATATTAATTG
*
17078 ATTTCCCAACCTT
1 ATTTCCCAACCAT
17091 ATTTCCCAACCAT
1 ATTTCCCAACCAT
17104 ATTT
1 ATTT
17108 AATTTCCCCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.27, C:0.33, G:0.00, T:0.40
Consensus pattern (13 bp):
ATTTCCCAACCAT
Found at i:24060 original size:45 final size:46
Alignment explanation
Indices: 23993--24116 Score: 187
Period size: 45 Copynumber: 2.7 Consensus size: 46
23983 GATTATTAGT
*
23993 TGGCTATGGAGTTATAGATTCCTATCAAGGTTATTTTATAATGGA-
1 TGGCTATGGAGTTATAGTTTCCTATCAAGGTTATTTTATAATGGAG
*
24038 TGGCTATGGAGTTATAGTTTCCTATCAATGTTATTTTATAATGGAG
1 TGGCTATGGAGTTATAGTTTCCTATCAAGGTTATTTTATAATGGAG
* * *
24084 TTGTCTATGGAGTAATAGTTTCCTACCAAGGTT
1 -TGGCTATGGAGTTATAGTTTCCTATCAAGGTT
24117 TGGCACAATA
Statistics
Matches: 71, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
45 43 0.61
47 28 0.39
ACGTcount: A:0.27, C:0.10, G:0.22, T:0.41
Consensus pattern (46 bp):
TGGCTATGGAGTTATAGTTTCCTATCAAGGTTATTTTATAATGGAG
Found at i:26692 original size:23 final size:23
Alignment explanation
Indices: 26661--26713 Score: 88
Period size: 23 Copynumber: 2.3 Consensus size: 23
26651 ATATTATTAA
*
26661 ATATGATTAATGATGTATATTCAT
1 ATAT-ATTAATGATATATATTCAT
26685 ATATATTAATGATATATATTCAT
1 ATATATTAATGATATATATTCAT
26708 ATATAT
1 ATATAT
26714 ATATATTGTT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
23 24 0.86
24 4 0.14
ACGTcount: A:0.42, C:0.04, G:0.08, T:0.47
Consensus pattern (23 bp):
ATATATTAATGATATATATTCAT
Done.