Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013190.1 Corchorus olitorius cultivar O-4 contig13223, 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: 23319
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34
Found at i:707 original size:101 final size:101
Alignment explanation
Indices: 547--749 Score: 406
Period size: 101 Copynumber: 2.0 Consensus size: 101
537 TACAACAAGA
547 GTTTTGGTGTAGGTATGATACATCAGATAAGGCAATTCTATCTATACAATTTGAAATACTAAATA
1 GTTTTGGTGTAGGTATGATACATCAGATAAGGCAATTCTATCTATACAATTTGAAATACTAAATA
612 TCAACCTAACAGATTGTAAATTTAAATGATTCGAAT
66 TCAACCTAACAGATTGTAAATTTAAATGATTCGAAT
648 GTTTTGGTGTAGGTATGATACATCAGATAAGGCAATTCTATCTATACAATTTGAAATACTAAATA
1 GTTTTGGTGTAGGTATGATACATCAGATAAGGCAATTCTATCTATACAATTTGAAATACTAAATA
713 TCAACCTAACAGATTGTAAATTTAAATGATTCGAAT
66 TCAACCTAACAGATTGTAAATTTAAATGATTCGAAT
749 G
1 G
750 GGAGATAAGT
Statistics
Matches: 102, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
101 102 1.00
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.34
Consensus pattern (101 bp):
GTTTTGGTGTAGGTATGATACATCAGATAAGGCAATTCTATCTATACAATTTGAAATACTAAATA
TCAACCTAACAGATTGTAAATTTAAATGATTCGAAT
Found at i:5678 original size:27 final size:26
Alignment explanation
Indices: 5628--5707 Score: 79
Period size: 27 Copynumber: 3.0 Consensus size: 26
5618 TTTTGGCTTG
* *
5628 TTGCGGCAATTTTTTCAATCTTGGGTAC
1 TTGCGGC-ATTTTTGCAATTTTGGGT-C
*
5656 TTGCGGCATTTTTGCAATTTTGGGCTG
1 TTGCGGCATTTTTGCAATTTTGGG-TC
* **
5683 TTGCGTCAACTTTGCAATTTTGGGT
1 TTGCGGCATTTTTGCAATTTTGGGT
5708 TGCTGTGGGA
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
26 1 0.02
27 36 0.80
28 8 0.18
ACGTcount: A:0.15, C:0.16, G:0.25, T:0.44
Consensus pattern (26 bp):
TTGCGGCATTTTTGCAATTTTGGGTC
Found at i:5720 original size:27 final size:27
Alignment explanation
Indices: 5657--5723 Score: 71
Period size: 27 Copynumber: 2.5 Consensus size: 27
5647 CTTGGGTACT
** *
5657 TGCGGCATTTTTGCAATTTTGGGCTGT
1 TGCGGCAACTTTGCAATTTTGGGCTGC
* *
5684 TGCGTCAACTTTGCAATTTTGGGTTGC
1 TGCGGCAACTTTGCAATTTTGGGCTGC
* *
5711 TGTGGGAACTTTG
1 TGCGGCAACTTTG
5724 TCAAAAATTT
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.13, C:0.15, G:0.30, T:0.42
Consensus pattern (27 bp):
TGCGGCAACTTTGCAATTTTGGGCTGC
Found at i:5907 original size:20 final size:20
Alignment explanation
Indices: 5882--5919 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
5872 TTGTCGTAGC
5882 TTGTCTATAGGTTGCTGCCA
1 TTGTCTATAGGTTGCTGCCA
* *
5902 TTGTCTATCGTTTGCTGC
1 TTGTCTATAGGTTGCTGC
5920 GGCAGTTAGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.11, C:0.21, G:0.24, T:0.45
Consensus pattern (20 bp):
TTGTCTATAGGTTGCTGCCA
Found at i:7033 original size:26 final size:27
Alignment explanation
Indices: 6963--7035 Score: 87
Period size: 27 Copynumber: 2.7 Consensus size: 27
6953 GCATTAAAGT
* *
6963 CATCCAGGGGCATTTTAGTCATTTTCA
1 CATCCAAGGGCATTTTGGTCATTTTCA
*
6990 CATCCAGGGGCATTTTGGTCATTTGT-A
1 CATCCAAGGGCATTTTGGTCATTT-TCA
*
7017 C-TTCAAGGGCATTTTGGTC
1 CATCCAAGGGCATTTTGGTC
7036 TTTCTTTAAT
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
26 16 0.38
27 25 0.60
28 1 0.02
ACGTcount: A:0.19, C:0.21, G:0.23, T:0.37
Consensus pattern (27 bp):
CATCCAAGGGCATTTTGGTCATTTTCA
Found at i:8225 original size:28 final size:28
Alignment explanation
Indices: 8169--8243 Score: 134
Period size: 28 Copynumber: 2.7 Consensus size: 28
8159 TAGGTAGTTT
8169 AGGGGCATTTTGGTCA-TTTTTACATTC
1 AGGGGCATTTTGGTCATTTTTTACATTC
*
8196 AGGGACATTTTGGTCATTTTTTACATTC
1 AGGGGCATTTTGGTCATTTTTTACATTC
8224 AGGGGCATTTTGGTCATTTT
1 AGGGGCATTTTGGTCATTTT
8244 AAGTTCACAT
Statistics
Matches: 45, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
27 15 0.33
28 30 0.67
ACGTcount: A:0.19, C:0.13, G:0.23, T:0.45
Consensus pattern (28 bp):
AGGGGCATTTTGGTCATTTTTTACATTC
Found at i:8407 original size:37 final size:38
Alignment explanation
Indices: 8339--8421 Score: 123
Period size: 37 Copynumber: 2.2 Consensus size: 38
8329 CTTTGGGCAT
*
8339 TTTTTGCATATTTTTTTAGTAATTTAACATTGTTGACA
1 TTTTTGCATATTTTCTTAGTAATTTAACATTGTTGACA
* *
8377 TTTTTGCATA-TTTCTTAGTAATTTAGCATTGTTGGCA
1 TTTTTGCATATTTTCTTAGTAATTTAACATTGTTGACA
*
8414 TTGTTGCA
1 TTTTTGCA
8422 CTCTAATCAT
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
37 31 0.76
38 10 0.24
ACGTcount: A:0.23, C:0.10, G:0.14, T:0.53
Consensus pattern (38 bp):
TTTTTGCATATTTTCTTAGTAATTTAACATTGTTGACA
Found at i:10859 original size:41 final size:40
Alignment explanation
Indices: 10773--10903 Score: 133
Period size: 41 Copynumber: 3.2 Consensus size: 40
10763 TGGTTTTTTT
* * * **
10773 GTTCAATTCGCTCCCTGATTGAGATTTTATTTGC-TGTTTG
1 GTTCAATTTGCTCCCTGATTGAGGTTATATTT-CATAATTG
*
10813 ATTCAATTTGCTCCCTGATTGAGGTTAATATTTCATAATTG
1 GTTCAATTTGCTCCCTGATTGAGGTT-ATATTTCATAATTG
*
10854 GTTCAATTT-CGTCCCTGATTGAGGTTGATATTT-ATTTATTG
1 GTTCAATTTGC-TCCCTGATTGAGGTT-ATATTTCA-TAATTG
10895 GTTCAATTT
1 GTTCAATTT
10904 TGCCACTGAT
Statistics
Matches: 78, Mismatches: 9, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
40 26 0.33
41 52 0.67
ACGTcount: A:0.21, C:0.15, G:0.18, T:0.47
Consensus pattern (40 bp):
GTTCAATTTGCTCCCTGATTGAGGTTATATTTCATAATTG
Found at i:10913 original size:41 final size:40
Alignment explanation
Indices: 10825--10914 Score: 119
Period size: 41 Copynumber: 2.2 Consensus size: 40
10815 TCAATTTGCT
*
10825 CCCTGATTGAGGTTAATATTTCATAATTGGTTCAATTTCG
1 CCCTGATTGAGGTTAATATTTCATAATTGGTTCAATTTTG
* *
10865 TCCCTGATTGAGGTTGATATTT-ATTTATTGGTTCAATTTTG
1 -CCCTGATTGAGGTTAATATTTCA-TAATTGGTTCAATTTTG
10906 CCACTGATT
1 CC-CTGATT
10915 TAAGATTTTA
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
40 3 0.07
41 41 0.93
ACGTcount: A:0.22, C:0.14, G:0.18, T:0.46
Consensus pattern (40 bp):
CCCTGATTGAGGTTAATATTTCATAATTGGTTCAATTTTG
Found at i:15021 original size:16 final size:17
Alignment explanation
Indices: 15002--15039 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
14992 AAATAAAATA
*
15002 AAAAAAAGAAGAAA-GG
1 AAAAAAAGAAAAAATGG
*
15018 AAAAAATGAAAAAATGG
1 AAAAAAAGAAAAAATGG
15035 AAAAA
1 AAAAA
15040 GTCAGAAACT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 12 0.63
17 7 0.37
ACGTcount: A:0.76, C:0.00, G:0.18, T:0.05
Consensus pattern (17 bp):
AAAAAAAGAAAAAATGG
Done.