Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01010779.1 Corchorus olitorius cultivar O-4 contig10811, 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: 6315
ACGTcount: A:0.39, C:0.15, G:0.13, T:0.33
Found at i:849 original size:18 final size:18
Alignment explanation
Indices: 828--869 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
818 ATGACACTTG
* *
828 AAAGAAACTCTAGGGAGT
1 AAAGAAACTCAAGAGAGT
*
846 AAAGAAACTGAAGAGAGT
1 AAAGAAACTCAAGAGAGT
864 AAAGAA
1 AAAGAA
870 GAAGACTGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.55, C:0.07, G:0.26, T:0.12
Consensus pattern (18 bp):
AAAGAAACTCAAGAGAGT
Found at i:1537 original size:29 final size:31
Alignment explanation
Indices: 1505--1571 Score: 102
Period size: 31 Copynumber: 2.2 Consensus size: 31
1495 ATGCAATTTG
*
1505 GGATATAACGTTAC-AAAA-CAAGCAATTAA
1 GGATATAACGTTACGAAAAGCAACCAATTAA
*
1534 GGATATAACGTTACGAAAAGCGACCAATTAA
1 GGATATAACGTTACGAAAAGCAACCAATTAA
1565 GGATATA
1 GGATATA
1572 GTCTGTTATG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
29 14 0.41
30 4 0.12
31 16 0.47
ACGTcount: A:0.48, C:0.13, G:0.18, T:0.21
Consensus pattern (31 bp):
GGATATAACGTTACGAAAAGCAACCAATTAA
Found at i:1653 original size:11 final size:11
Alignment explanation
Indices: 1639--1675 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
1629 CGTGTCATCT
*
1639 ACGTGGATACC
1 ACGTGGATGCC
1650 ACGTGGATGCC
1 ACGTGGATGCC
*
1661 ACGCGGATGCC
1 ACGTGGATGCC
1672 ACGT
1 ACGT
1676 CATCAATTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.22, C:0.30, G:0.32, T:0.16
Consensus pattern (11 bp):
ACGTGGATGCC
Found at i:1738 original size:31 final size:31
Alignment explanation
Indices: 1703--1781 Score: 122
Period size: 31 Copynumber: 2.5 Consensus size: 31
1693 TTAACTGATT
**
1703 ATATCCTTAATTGCTTGAAATCGAAAACGTC
1 ATATCCTTAATTGCTTGAAATAAAAAACGTC
*
1734 ATATCCTTAATTGCTTGAAATAAAAAACGTT
1 ATATCCTTAATTGCTTGAAATAAAAAACGTC
*
1765 ATATCATTAATTGCTTG
1 ATATCCTTAATTGCTTG
1782 TTTTGTAACG
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.37, C:0.15, G:0.11, T:0.37
Consensus pattern (31 bp):
ATATCCTTAATTGCTTGAAATAAAAAACGTC
Found at i:1826 original size:31 final size:29
Alignment explanation
Indices: 1701--1837 Score: 103
Period size: 31 Copynumber: 4.5 Consensus size: 29
1691 CCTTAACTGA
*
1701 TTATATCCTTAATTGCTTGAAATCGAAAACG
1 TTATATCCTTAATTGCTTG-AA-CAAAAACG
* *
1732 TCATATCCTTAATTGCTTGAAATAAAAAACG
1 TTATATCCTTAATTGCTTG-AA-CAAAAACG
* ******
1763 TTATATCATTAATTGCTTGTTTTGTAACG
1 TTATATCCTTAATTGCTTGAACAAAAACG
**
1792 TTATATCCTTAATTGCTTGTGGCAACAAACG
1 TTATATCCTTAATTGCTTG-AACAA-AAACG
*
1823 TTATATCCTAAATTG
1 TTATATCCTTAATTG
1838 ATTATTTGAC
Statistics
Matches: 85, Mismatches: 19, Indels: 4
0.79 0.18 0.04
Matches are distributed among these distances:
29 22 0.26
31 63 0.74
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.39
Consensus pattern (29 bp):
TTATATCCTTAATTGCTTGAACAAAAACG
Found at i:2913 original size:60 final size:62
Alignment explanation
Indices: 2817--2957 Score: 162
Period size: 60 Copynumber: 2.3 Consensus size: 62
2807 AGAGGATAAG
* *
2817 CAAGCAATTTAGGATATAACGTTTTCTGCCGTAAGCAATTAAGGATATAACG-TTAC-AAAA
1 CAAGCAATTAAGGATATAACGTTTTCTGACGTAAGCAATTAAGGATATAACGTTTACGAAAA
** * * * ***
2877 CAAGCAATTAAGGATATAACGTTTT-TGATTTCAAGCAATTAGGGATATGACGTTTTCGATTT
1 CAAGCAATTAAGGATATAACGTTTTCTGACGT-AAGCAATTAAGGATATAACGTTTACGAAAA
2939 CAAGCAATTAAGGATATAA
1 CAAGCAATTAAGGATATAA
2958 TCAGTTAGGA
Statistics
Matches: 68, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
59 3 0.04
60 42 0.62
61 3 0.04
62 20 0.29
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.31
Consensus pattern (62 bp):
CAAGCAATTAAGGATATAACGTTTTCTGACGTAAGCAATTAAGGATATAACGTTTACGAAAA
Found at i:2915 original size:31 final size:31
Alignment explanation
Indices: 2817--2957 Score: 144
Period size: 31 Copynumber: 4.6 Consensus size: 31
2807 AGAGGATAAG
* ***
2817 CAAGCAATTTAGGATATAACGTTTTCTGCCGT
1 CAAGCAATTAAGGATATAACGTTTT-TGATTT
** ***
2849 -AAGCAATTAAGGATATAACG--TTACAAAA
1 CAAGCAATTAAGGATATAACGTTTTTGATTT
2877 CAAGCAATTAAGGATATAACGTTTTTGATTT
1 CAAGCAATTAAGGATATAACGTTTTTGATTT
* * *
2908 CAAGCAATTAGGGATATGACGTTTTCGATTT
1 CAAGCAATTAAGGATATAACGTTTTTGATTT
2939 CAAGCAATTAAGGATATAA
1 CAAGCAATTAAGGATATAA
2958 TCAGTTAGGA
Statistics
Matches: 89, Mismatches: 17, Indels: 7
0.79 0.15 0.06
Matches are distributed among these distances:
29 22 0.25
31 67 0.75
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.31
Consensus pattern (31 bp):
CAAGCAATTAAGGATATAACGTTTTTGATTT
Found at i:3161 original size:29 final size:31
Alignment explanation
Indices: 3087--3153 Score: 111
Period size: 31 Copynumber: 2.2 Consensus size: 31
3077 CCTAACAGAC
3087 TATATCCTTAATTGCTCGCTTTTCGTAACGT
1 TATATCCTTAATTGCTCGCTTTTCGTAACGT
*
3118 TATATCCTTAATTGCTTG-TTTT-GTAACGT
1 TATATCCTTAATTGCTCGCTTTTCGTAACGT
3147 TATATCC
1 TATATCC
3154 CAAATTGCAT
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
29 14 0.40
30 4 0.11
31 17 0.49
ACGTcount: A:0.21, C:0.19, G:0.12, T:0.48
Consensus pattern (31 bp):
TATATCCTTAATTGCTCGCTTTTCGTAACGT
Found at i:3795 original size:40 final size:40
Alignment explanation
Indices: 3738--3832 Score: 129
Period size: 40 Copynumber: 2.4 Consensus size: 40
3728 ATAAAAGCAA
*
3738 TACATGGAACACCAAATTTACCCTTGGCAACTACAT-AAAAT
1 TACA-GGAAAACCAAATTTACCCTTGGCAACT-CATCAAAAT
* *
3779 TACAGGAAAACCAAATTTACCTTTGGCAACTCATCCAAAT
1 TACAGGAAAACCAAATTTACCCTTGGCAACTCATCAAAAT
*
3819 TACATGAAAACCAA
1 TACAGGAAAACCAA
3833 TGGTGGAGGG
Statistics
Matches: 49, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
39 3 0.06
40 42 0.86
41 4 0.08
ACGTcount: A:0.43, C:0.24, G:0.09, T:0.23
Consensus pattern (40 bp):
TACAGGAAAACCAAATTTACCCTTGGCAACTCATCAAAAT
Found at i:5989 original size:2 final size:2
Alignment explanation
Indices: 5984--6016 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
5974 CTATCTACTA
5984 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 A
6017 CTAGTCTTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.