Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022110.1 Corchorus olitorius cultivar O-4 contig22143, 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: 11546
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Found at i:1067 original size:36 final size:36
Alignment explanation
Indices: 1020--1089 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
1010 TTCAATAACC
* *
1020 TTACATCTTTTGTGATTTTGGTTATCATATTTCTTA
1 TTACATCTTTTGTAATTTTGATTATCATATTTCTTA
*
1056 TTACATTTTTTGTAATTTTGATTATCATATTTCT
1 TTACATCTTTTGTAATTTTGATTATCATATTTCT
1090 CCAAAATCTC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.21, C:0.10, G:0.09, T:0.60
Consensus pattern (36 bp):
TTACATCTTTTGTAATTTTGATTATCATATTTCTTA
Found at i:2094 original size:39 final size:40
Alignment explanation
Indices: 2039--2119 Score: 128
Period size: 39 Copynumber: 2.0 Consensus size: 40
2029 ATACCTAAGA
* *
2039 ATTTAATTAATTTAAGTATTTCAGTTATTATA-GTATTAC
1 ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC
*
2078 ATTTAATTAATGTAAGTATTTTAGTTATTATATATATTAC
1 ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC
2118 AT
1 AT
2120 AGGAATTAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
39 30 0.79
40 8 0.21
ACGTcount: A:0.37, C:0.04, G:0.07, T:0.52
Consensus pattern (40 bp):
ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC
Found at i:7630 original size:9 final size:9
Alignment explanation
Indices: 7616--7691 Score: 62
Period size: 9 Copynumber: 7.8 Consensus size: 9
7606 CGACTGACAA
7616 ATTATATAT
1 ATTATATAT
*
7625 ATTATATTTT
1 ATTATA-TAT
*
7635 TTATATATAT
1 AT-TATATAT
7645 CATTATATAT
1 -ATTATATAT
7655 ATTAATATTAGT
1 ATT-ATA-TA-T
7667 ATTATATAT
1 ATTATATAT
*
7676 AATATATAT
1 ATTATATAT
*
7685 TTTATAT
1 ATTATAT
7692 TAAAACCTTA
Statistics
Matches: 54, Mismatches: 7, Indels: 12
0.74 0.10 0.16
Matches are distributed among these distances:
9 23 0.43
10 17 0.31
11 10 0.19
12 4 0.07
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.57
Consensus pattern (9 bp):
ATTATATAT
Found at i:8034 original size:29 final size:29
Alignment explanation
Indices: 7992--8051 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
7982 CATGAGAGCC
7992 AGAGCCAAGGTAAGCGCTCTGTTAAATTA
1 AGAGCCAAGGTAAGCGCTCTGTTAAATTA
8021 AGAGCCAAGGTAAGCGCTCTGTTAAATTA
1 AGAGCCAAGGTAAGCGCTCTGTTAAATTA
8050 AG
1 AG
8052 TAGAAGCTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.35, C:0.17, G:0.25, T:0.23
Consensus pattern (29 bp):
AGAGCCAAGGTAAGCGCTCTGTTAAATTA
Found at i:8151 original size:24 final size:24
Alignment explanation
Indices: 8124--8202 Score: 113
Period size: 24 Copynumber: 3.1 Consensus size: 24
8114 CCATAAATGA
8124 TTGGGATTTTGCTGTATCTCTGTT
1 TTGGGATTTTGCTGTATCTCTGTT
*
8148 TTGGGATTTTGCTGTATGTATCTCTATT
1 TTGGGATTTTGC----TGTATCTCTGTT
8176 TTGGGATTTTGCTGTATCTCTGTT
1 TTGGGATTTTGCTGTATCTCTGTT
8200 TTG
1 TTG
8203 CATTGAAGAG
Statistics
Matches: 49, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
24 26 0.53
28 23 0.47
ACGTcount: A:0.10, C:0.11, G:0.24, T:0.54
Consensus pattern (24 bp):
TTGGGATTTTGCTGTATCTCTGTT
Found at i:8177 original size:28 final size:28
Alignment explanation
Indices: 8136--8192 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
8126 GGGATTTTGC
*
8136 TGTATCTCTGTTTTGGGATTTTGCTGTA
1 TGTATCTCTATTTTGGGATTTTGCTGTA
8164 TGTATCTCTATTTTGGGATTTTGCTGTA
1 TGTATCTCTATTTTGGGATTTTGCTGTA
8192 T
1 T
8193 CTCTGTTTTG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.12, C:0.11, G:0.23, T:0.54
Consensus pattern (28 bp):
TGTATCTCTATTTTGGGATTTTGCTGTA
Found at i:8781 original size:32 final size:32
Alignment explanation
Indices: 8745--8815 Score: 106
Period size: 32 Copynumber: 2.2 Consensus size: 32
8735 ACATGGGTGA
* *
8745 TTCTCTCACAACAACCTAAAACTATCTTAGCT
1 TTCTCTCACAACAACATAAAACTATCTCAGCT
*
8777 TTCTCTCACAACAACATAAAGCTATCTCAGCT
1 TTCTCTCACAACAACATAAAACTATCTCAGCT
*
8809 TTTTCTC
1 TTCTCTC
8816 TCTCATACAC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.31, C:0.31, G:0.04, T:0.34
Consensus pattern (32 bp):
TTCTCTCACAACAACATAAAACTATCTCAGCT
Found at i:11264 original size:16 final size:15
Alignment explanation
Indices: 11226--11267 Score: 75
Period size: 15 Copynumber: 2.7 Consensus size: 15
11216 ACAGAGGTTG
11226 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
11241 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
11256 ACTAGAAAACAA
1 AC-AGAAAACAA
11268 AGCAAAGTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 17 0.65
16 9 0.35
ACGTcount: A:0.67, C:0.14, G:0.07, T:0.12
Consensus pattern (15 bp):
ACAGAAAACAATTAA
Done.