Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014240.1 Corchorus olitorius cultivar O-4 contig14273, 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: 17288
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:1825 original size:31 final size:31
Alignment explanation
Indices: 1759--1833 Score: 98
Period size: 31 Copynumber: 2.4 Consensus size: 31
1749 TTCTAAACTT
* * *
1759 TGGGTTTGTGTTCATCGGAAAAACTAAAAGGA
1 TGGGTTTGGGTTCATC-GAAAAACAAAAAGAA
1791 TGGGTTTGGGTTCATC-AACAAACAAAAAGAA
1 TGGGTTTGGGTTCATCGAA-AAACAAAAAGAA
1822 TGGGTTTGGGTT
1 TGGGTTTGGGTT
1834 TTTGGATTCA
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
30 2 0.05
31 22 0.56
32 15 0.38
ACGTcount: A:0.32, C:0.09, G:0.29, T:0.29
Consensus pattern (31 bp):
TGGGTTTGGGTTCATCGAAAAACAAAAAGAA
Found at i:1948 original size:25 final size:25
Alignment explanation
Indices: 1920--1971 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
1910 CTTTCCTAAT
1920 TACTCT-CTTCTCTTCTTCAGCTTTC
1 TACTCTGCTT-TCTTCTTCAGCTTTC
* *
1945 TACTCTGCTTTTTTCTTTAGCTTTC
1 TACTCTGCTTTCTTCTTCAGCTTTC
1970 TA
1 TA
1972 ATTGGCTTAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 21 0.88
26 3 0.12
ACGTcount: A:0.10, C:0.29, G:0.06, T:0.56
Consensus pattern (25 bp):
TACTCTGCTTTCTTCTTCAGCTTTC
Found at i:2169 original size:27 final size:28
Alignment explanation
Indices: 2134--2193 Score: 104
Period size: 27 Copynumber: 2.2 Consensus size: 28
2124 ATAAGCATTC
*
2134 AAAATGGGTTTGGGTTCATTAAAAAA-A
1 AAAATGGGTTTGGGTTCATAAAAAAACA
2161 AAAATGGGTTTGGGTTCATAAAAAAACA
1 AAAATGGGTTTGGGTTCATAAAAAAACA
2189 AAAAT
1 AAAAT
2194 TATGGGTTTG
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
27 25 0.81
28 6 0.19
ACGTcount: A:0.48, C:0.05, G:0.20, T:0.27
Consensus pattern (28 bp):
AAAATGGGTTTGGGTTCATAAAAAAACA
Found at i:3150 original size:40 final size:40
Alignment explanation
Indices: 3095--3170 Score: 143
Period size: 40 Copynumber: 1.9 Consensus size: 40
3085 AAGAGACCAT
3095 TTTTAAACTCTGTTTTTATTTTGCAGAGCCACAACTCATG
1 TTTTAAACTCTGTTTTTATTTTGCAGAGCCACAACTCATG
*
3135 TTTTAAACTCTGTTTTTGTTTTGCAGAGCCACAACT
1 TTTTAAACTCTGTTTTTATTTTGCAGAGCCACAACT
3171 TGTGAGTGTG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.24, C:0.20, G:0.13, T:0.43
Consensus pattern (40 bp):
TTTTAAACTCTGTTTTTATTTTGCAGAGCCACAACTCATG
Found at i:3670 original size:4 final size:4
Alignment explanation
Indices: 3658--3687 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
3648 CTTGGGATTG
*
3658 ATTT CTTT ATTT ATTT ATTT ATTT ATTT AT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT AT
3688 AGAATCCAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.73
Consensus pattern (4 bp):
ATTT
Found at i:5786 original size:29 final size:29
Alignment explanation
Indices: 5744--5812 Score: 138
Period size: 29 Copynumber: 2.4 Consensus size: 29
5734 AAAATGTCTT
5744 ACCGACCGACGGTGGACATGCCACCGATC
1 ACCGACCGACGGTGGACATGCCACCGATC
5773 ACCGACCGACGGTGGACATGCCACCGATC
1 ACCGACCGACGGTGGACATGCCACCGATC
5802 ACCGACCGACG
1 ACCGACCGACG
5813 ATAGCTGGAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.25, C:0.39, G:0.28, T:0.09
Consensus pattern (29 bp):
ACCGACCGACGGTGGACATGCCACCGATC
Found at i:6116 original size:29 final size:29
Alignment explanation
Indices: 6074--6133 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 29
6064 AAAACTTCTA
6074 CTTAATTTAACAGAGCACTTACCTTGGCT
1 CTTAATTTAACAGAGCACTTACCTTGGCT
*
6103 CTTAATTTAACAGAGCGCTTACCTTGGCT
1 CTTAATTTAACAGAGCACTTACCTTGGCT
6132 CT
1 CT
6134 GGCTCTCATG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.25, C:0.25, G:0.15, T:0.35
Consensus pattern (29 bp):
CTTAATTTAACAGAGCACTTACCTTGGCT
Found at i:6431 original size:18 final size:17
Alignment explanation
Indices: 6408--6482 Score: 59
Period size: 16 Copynumber: 4.4 Consensus size: 17
6398 TAGGGTTTTA
6408 ATATAAAATATATAT-T
1 ATATAAAATATATATAT
*
6424 ATATATAATACTAATATTAAT
1 ATATAAAATA-T-ATA-T-AT
*
6445 ATATATAATGATATATAT
1 ATATAAAAT-ATATATAT
6463 A-A-AAAATATA-ATAT
1 ATATAAAATATATATAT
6477 ATATAA
1 ATATAA
6483 TTTGTCGGTC
Statistics
Matches: 49, Mismatches: 2, Indels: 16
0.73 0.03 0.24
Matches are distributed among these distances:
14 5 0.10
15 4 0.08
16 15 0.31
17 2 0.04
18 6 0.12
19 2 0.04
20 3 0.06
21 11 0.22
22 1 0.02
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.40
Consensus pattern (17 bp):
ATATAAAATATATATAT
Found at i:6480 original size:9 final size:9
Alignment explanation
Indices: 6408--6483 Score: 62
Period size: 9 Copynumber: 7.8 Consensus size: 9
6398 TAGGGTTTTA
*
6408 ATATAAAAT
1 ATATAATAT
*
6417 ATATATTAT
1 ATATAATAT
6426 ATATAATACT
1 ATATAATA-T
6436 AATATTAATAT
1 -ATA-TAATAT
6447 ATATAATGATAT
1 ATAT-A--ATAT
* *
6459 ATATAAAAA
1 ATATAATAT
6468 ATATAATAT
1 ATATAATAT
6477 ATATAAT
1 ATATAAT
6484 TTGTCGGTCG
Statistics
Matches: 54, Mismatches: 7, Indels: 12
0.74 0.10 0.16
Matches are distributed among these distances:
9 31 0.57
10 5 0.09
11 5 0.09
12 13 0.24
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (9 bp):
ATATAATAT
Found at i:12617 original size:55 final size:55
Alignment explanation
Indices: 12535--12641 Score: 151
Period size: 55 Copynumber: 1.9 Consensus size: 55
12525 CCCATCATAA
* * * *
12535 TTTGCTAAGTATTCAGTCGCTCAATTGGCTTTTATGAACTTGAGTCAATAATGTT
1 TTTGCTAAGCATTCAGCCACTCAATTGGCTTCTATGAACTTGAGTCAATAATGTT
* * *
12590 TTTGCTAAGCATTTAGCCACTCGATTGGCTTCTATGTACTTGAGTCAATAAT
1 TTTGCTAAGCATTCAGCCACTCAATTGGCTTCTATGAACTTGAGTCAATAAT
12642 ATCTTTCCGA
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
55 45 1.00
ACGTcount: A:0.25, C:0.17, G:0.18, T:0.40
Consensus pattern (55 bp):
TTTGCTAAGCATTCAGCCACTCAATTGGCTTCTATGAACTTGAGTCAATAATGTT
Found at i:13866 original size:14 final size:14
Alignment explanation
Indices: 13847--13874 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
13837 AAATTTGAGG
13847 AATTAAGTCATCTT
1 AATTAAGTCATCTT
13861 AATTAAGTCATCTT
1 AATTAAGTCATCTT
13875 TGGGTTTCTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.14, G:0.07, T:0.43
Consensus pattern (14 bp):
AATTAAGTCATCTT
Found at i:16808 original size:2 final size:2
Alignment explanation
Indices: 16801--16841 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
16791 ATATTAAGAG
16801 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
16842 ATAAAAGAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.