Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020045.1 Corchorus olitorius cultivar O-4 contig20078, 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: 20088
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.33
Found at i:3547 original size:27 final size:27
Alignment explanation
Indices: 3509--3597 Score: 169
Period size: 27 Copynumber: 3.3 Consensus size: 27
3499 GCTCTCCCTA
3509 CCACTTCGACCCCAGCAGTGGATCCTC
1 CCACTTCGACCCCAGCAGTGGATCCTC
3536 CCACTTCGACCCCAGCAGTGGATCCTC
1 CCACTTCGACCCCAGCAGTGGATCCTC
*
3563 ACACTTCGACCCCAGCAGTGGATCCTC
1 CCACTTCGACCCCAGCAGTGGATCCTC
3590 CCACTTCG
1 CCACTTCG
3598 CCTCGGGTCG
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 60 1.00
ACGTcount: A:0.19, C:0.44, G:0.18, T:0.19
Consensus pattern (27 bp):
CCACTTCGACCCCAGCAGTGGATCCTC
Found at i:4454 original size:17 final size:17
Alignment explanation
Indices: 4432--4466 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
4422 GAAAAAGTGC
4432 ATTCTTGTTGGTACATT
1 ATTCTTGTTGGTACATT
4449 ATTCTTGTTGGTACATT
1 ATTCTTGTTGGTACATT
4466 A
1 A
4467 ACATTATGCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.20, C:0.11, G:0.17, T:0.51
Consensus pattern (17 bp):
ATTCTTGTTGGTACATT
Found at i:6017 original size:32 final size:31
Alignment explanation
Indices: 5981--6191 Score: 305
Period size: 32 Copynumber: 6.5 Consensus size: 31
5971 GTGTGAATAG
5981 AAAACGCCCTTATTTAGCGGCGTCTATAGAAC
1 AAAACGCCCTTATTTAGCGGCGTCT-TAGAAC
6013 AAAACGCCCTTATTTAGCGGCGTCTATAGAAC
1 AAAACGCCCTTATTTAGCGGCGTCT-TAGAAC
6045 AAAACGCCCTTATTTAGCGGCGTCTATAGAAC
1 AAAACGCCCTTATTTAGCGGCGTCT-TAGAAC
* *
6077 AAAAACACCCTTATTTAGCGGCGTCTTAAAAAC
1 -AAAACGCCCTTATTTAGCGGCGTCTT-AGAAC
6110 AAAACGCCCTTATTTAGCGGCGTCTTGAGAAC
1 AAAACGCCCTTATTTAGCGGCGTCTT-AGAAC
* *
6142 AAAACGCCCTTATTTAACGGCGTCTTAAAATC
1 AAAACGCCCTTATTTAGCGGCGTCTTAGAA-C
6174 AAAACGCCGCTATATTTA
1 AAAACGCC-CT-TATTTA
6192 ACTGTTTTTT
Statistics
Matches: 167, Mismatches: 7, Indels: 8
0.92 0.04 0.04
Matches are distributed among these distances:
31 3 0.02
32 128 0.77
33 30 0.18
34 6 0.04
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.26
Consensus pattern (31 bp):
AAAACGCCCTTATTTAGCGGCGTCTTAGAAC
Found at i:6090 original size:97 final size:97
Alignment explanation
Indices: 5981--6166 Score: 313
Period size: 97 Copynumber: 1.9 Consensus size: 97
5971 GTGTGAATAG
* *
5981 AAAACGCCCTTATTTAGCGGCGTC-TATAGAACAAAACGCCCTTATTTAGCGGCGTCTAT-AGAA
1 AAAACACCCTTATTTAGCGGCGTCTTA-AAAACAAAACGCCCTTATTTAGCGGCGTCT-TGAGAA
*
6044 CAAAACGCCCTTATTTAGCGGCGTCTATAGAACA
64 CAAAACGCCCTTATTTAACGGCGTCTATAGAACA
6078 AAAACACCCTTATTTAGCGGCGTCTTAAAAACAAAACGCCCTTATTTAGCGGCGTCTTGAGAACA
1 AAAACACCCTTATTTAGCGGCGTCTTAAAAACAAAACGCCCTTATTTAGCGGCGTCTTGAGAACA
6143 AAACGCCCTTATTTAACGGCGTCT
66 AAACGCCCTTATTTAACGGCGTCT
6167 TAAAATCAAA
Statistics
Matches: 84, Mismatches: 3, Indels: 4
0.92 0.03 0.04
Matches are distributed among these distances:
96 1 0.01
97 81 0.96
98 2 0.02
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (97 bp):
AAAACACCCTTATTTAGCGGCGTCTTAAAAACAAAACGCCCTTATTTAGCGGCGTCTTGAGAACA
AAACGCCCTTATTTAACGGCGTCTATAGAACA
Found at i:7695 original size:58 final size:58
Alignment explanation
Indices: 7627--7756 Score: 188
Period size: 58 Copynumber: 2.2 Consensus size: 58
7617 TTATATTCTC
* * **
7627 CACTCTGCAAAATTATATTTTCCAATGACCCATTATAACATTTTTGTACATTATTGTT
1 CACTTTGCAAAATTACATTGGCCAATGACCCATTATAACATTTTTGTACATTATTGTT
* * *
7685 CACTTTGCAAAATTGCATTGGCCAATGCCCCATTATAACTTTTTTGTACATTATTGTT
1 CACTTTGCAAAATTACATTGGCCAATGACCCATTATAACATTTTTGTACATTATTGTT
*
7743 CACTTTACAAAATT
1 CACTTTGCAAAATT
7757 GAACAACTTT
Statistics
Matches: 64, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
58 64 1.00
ACGTcount: A:0.30, C:0.20, G:0.08, T:0.42
Consensus pattern (58 bp):
CACTTTGCAAAATTACATTGGCCAATGACCCATTATAACATTTTTGTACATTATTGTT
Found at i:7757 original size:58 final size:58
Alignment explanation
Indices: 7648--7757 Score: 193
Period size: 58 Copynumber: 1.9 Consensus size: 58
7638 ATTATATTTT
*
7648 CCAATGACCCATTATAACATTTTTGTACATTATTGTTCACTTTGCAAAATTGCATTGG
1 CCAATGACCCATTATAACATTTTTGTACATTATTGTTCACTTTACAAAATTGCATTGG
* *
7706 CCAATGCCCCATTATAACTTTTTTGTACATTATTGTTCACTTTACAAAATTG
1 CCAATGACCCATTATAACATTTTTGTACATTATTGTTCACTTTACAAAATTG
7758 AACAACTTTC
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
58 49 1.00
ACGTcount: A:0.29, C:0.20, G:0.10, T:0.41
Consensus pattern (58 bp):
CCAATGACCCATTATAACATTTTTGTACATTATTGTTCACTTTACAAAATTGCATTGG
Done.