Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022249.1 Corchorus olitorius cultivar O-4 contig22282, 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: 11235
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.32
Found at i:2782 original size:3 final size:3
Alignment explanation
Indices: 2767--2855 Score: 63
Period size: 3 Copynumber: 29.7 Consensus size: 3
2757 AGTTGATGGC
* * * * *
2767 GAT GAT GAG GAT GAT GAC GAG GAT GAT GAC GAG GAT GAT GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
* * * * * *
2815 GACG GA- GAT GAC AAT GAG GAC GAT GAT GAT GAT GGT GAT GA
1 GA-T GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GA
2856 CCATGAGGAG
Statistics
Matches: 66, Mismatches: 18, Indels: 4
0.75 0.20 0.05
Matches are distributed among these distances:
2 2 0.03
3 62 0.94
4 2 0.03
ACGTcount: A:0.34, C:0.06, G:0.39, T:0.21
Consensus pattern (3 bp):
GAT
Found at i:2815 original size:12 final size:12
Alignment explanation
Indices: 2767--2855 Score: 76
Period size: 12 Copynumber: 7.7 Consensus size: 12
2757 AGTTGATGGC
2767 GATGATGAGGAT
1 GATGATGAGGAT
*
2779 GATGACGAGGAT
1 GATGATGAGGAT
*
2791 GATGACGAGGAT
1 GATGATGAGGAT
*
2803 GATGATGATGAT
1 GATGATGAGGAT
*
2815 GACG--GA-GAT
1 GATGATGAGGAT
** *
2824 GACAATGAGGAC
1 GATGATGAGGAT
*
2836 GATGATGATGAT
1 GATGATGAGGAT
*
2848 GGTGATGA
1 GATGATGA
2856 CCATGAGGAG
Statistics
Matches: 63, Mismatches: 11, Indels: 6
0.79 0.14 0.08
Matches are distributed among these distances:
9 6 0.10
10 2 0.03
11 2 0.03
12 53 0.84
ACGTcount: A:0.34, C:0.06, G:0.39, T:0.21
Consensus pattern (12 bp):
GATGATGAGGAT
Found at i:2831 original size:21 final size:22
Alignment explanation
Indices: 2767--2831 Score: 73
Period size: 21 Copynumber: 3.1 Consensus size: 22
2757 AGTTGATGGC
* *
2767 GATGATGA-GGATGATGACGAG
1 GATGATGACGGAGGATGACGAT
*
2788 GATGATGAC-GAGGATGATGAT
1 GATGATGACGGAGGATGACGAT
*
2809 GATGATGACGGA-GATGACAAT
1 GATGATGACGGAGGATGACGAT
2830 GA
1 GA
2832 GGACGATGAT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
21 35 0.95
22 2 0.05
ACGTcount: A:0.35, C:0.06, G:0.38, T:0.20
Consensus pattern (22 bp):
GATGATGACGGAGGATGACGAT
Found at i:2855 original size:30 final size:30
Alignment explanation
Indices: 2806--2864 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
2796 CGAGGATGAT
2806 GATGATGATGACGGAGATGACAATGAGGAC
1 GATGATGATGACGGAGATGACAATGAGGAC
* * *
2836 GATGATGATGATGGTGATGACCATGAGGA
1 GATGATGATGACGGAGATGACAATGAGGA
2865 GATTTAGCTC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.34, C:0.08, G:0.37, T:0.20
Consensus pattern (30 bp):
GATGATGATGACGGAGATGACAATGAGGAC
Found at i:4104 original size:45 final size:45
Alignment explanation
Indices: 4050--4153 Score: 129
Period size: 45 Copynumber: 2.3 Consensus size: 45
4040 AGGCAGCCTC
* * * **
4050 TTATTTTGTATAGGTC-CTTAATTTGCCATTATCTAGACGAGGCAT
1 TTATTTTGTATAGGTCAC-TAACTTGCAATGATCTAGAAAAGGCAT
* *
4095 TTATTTTGTATAGATCACTAACTTGCAATGATCTAGAAAAGGCCT
1 TTATTTTGTATAGGTCACTAACTTGCAATGATCTAGAAAAGGCAT
4140 TTATTTTGTATAGG
1 TTATTTTGTATAGG
4154 GTTTAGTTTT
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
45 49 0.98
46 1 0.02
ACGTcount: A:0.28, C:0.13, G:0.17, T:0.41
Consensus pattern (45 bp):
TTATTTTGTATAGGTCACTAACTTGCAATGATCTAGAAAAGGCAT
Found at i:4458 original size:24 final size:24
Alignment explanation
Indices: 4426--4475 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
4416 TCATAGATAG
* *
4426 AATTCCGTTTTTTATTCTATTGCA
1 AATTCCGTTTTTGATTCCATTGCA
*
4450 AATTCCGTTTTTGATTCCGTTGCA
1 AATTCCGTTTTTGATTCCATTGCA
4474 AA
1 AA
4476 GTACTCAGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.22, C:0.18, G:0.12, T:0.48
Consensus pattern (24 bp):
AATTCCGTTTTTGATTCCATTGCA
Found at i:4757 original size:18 final size:18
Alignment explanation
Indices: 4734--4775 Score: 84
Period size: 18 Copynumber: 2.3 Consensus size: 18
4724 TTATGATCCT
4734 CACACTTGCAAAATAGCC
1 CACACTTGCAAAATAGCC
4752 CACACTTGCAAAATAGCC
1 CACACTTGCAAAATAGCC
4770 CACACT
1 CACACT
4776 CTACAAGTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.38, C:0.36, G:0.10, T:0.17
Consensus pattern (18 bp):
CACACTTGCAAAATAGCC
Found at i:10700 original size:16 final size:16
Alignment explanation
Indices: 10661--10703 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 16
10651 AATTTTGGGT
*
10661 ACCCGAATCC-AAACG
1 ACCCGAACCCAAAACG
* *
10676 ACCCAAACCCAAAATG
1 ACCCGAACCCAAAACG
10692 ACCCGAACCCAA
1 ACCCGAACCCAA
10704 TCAACCCGAC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
15 8 0.35
16 15 0.65
ACGTcount: A:0.44, C:0.42, G:0.09, T:0.05
Consensus pattern (16 bp):
ACCCGAACCCAAAACG
Done.