Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019362.1 Corchorus olitorius cultivar O-4 contig19395, 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: 18103
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.30
Found at i:2806 original size:32 final size:31
Alignment explanation
Indices: 2764--2839 Score: 98
Period size: 31 Copynumber: 2.4 Consensus size: 31
2754 ATTTGGGACG
* *
2764 AAATGGCAAAATTTTAAAAGTTTTAAGGGGTA
1 AAATGACAAAATTTTAAAAG-TTTAAAGGGTA
* *
2796 AAATGACAAAAATTTGAAAGTTTAAAGGGTA
1 AAATGACAAAATTTTAAAAGTTTAAAGGGTA
*
2827 AAATGAAAAAATT
1 AAATGACAAAATT
2840 AATTTTGAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
31 21 0.55
32 17 0.45
ACGTcount: A:0.51, C:0.03, G:0.18, T:0.28
Consensus pattern (31 bp):
AAATGACAAAATTTTAAAAGTTTAAAGGGTA
Found at i:2826 original size:31 final size:32
Alignment explanation
Indices: 2764--2839 Score: 102
Period size: 32 Copynumber: 2.4 Consensus size: 32
2754 ATTTGGGACG
* * *
2764 AAATGGCAAAATTTTAAAAGTTTTAAGGGGTA
1 AAATGACAAAAATTTAAAAGTTTTAAAGGGTA
*
2796 AAATGACAAAAATTTGAAAG-TTTAAAGGGTA
1 AAATGACAAAAATTTAAAAGTTTTAAAGGGTA
2827 AAATGA-AAAAATT
1 AAATGACAAAAATT
2840 AATTTTGAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
30 7 0.17
31 16 0.40
32 17 0.43
ACGTcount: A:0.51, C:0.03, G:0.18, T:0.28
Consensus pattern (32 bp):
AAATGACAAAAATTTAAAAGTTTTAAAGGGTA
Found at i:7037 original size:63 final size:63
Alignment explanation
Indices: 6938--7065 Score: 247
Period size: 63 Copynumber: 2.0 Consensus size: 63
6928 TATGGATGGG
6938 AAGAGAAGGGGGCGGCGGCACTAGGGCTTTTGTCCTCCAATCTTCAACAATTCTACCAAATAT
1 AAGAGAAGGGGGCGGCGGCACTAGGGCTTTTGTCCTCCAATCTTCAACAATTCTACCAAATAT
*
7001 AAGAGAAGGGGGCGGCGGCACTAGGGCTTTTGTCCTCCAATCTTCAACAATTCTATCAAATAT
1 AAGAGAAGGGGGCGGCGGCACTAGGGCTTTTGTCCTCCAATCTTCAACAATTCTACCAAATAT
7064 AA
1 AA
7066 TTCTAGATCT
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
63 64 1.00
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.24
Consensus pattern (63 bp):
AAGAGAAGGGGGCGGCGGCACTAGGGCTTTTGTCCTCCAATCTTCAACAATTCTACCAAATAT
Found at i:7685 original size:19 final size:18
Alignment explanation
Indices: 7652--7687 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
7642 TTGAAATAAT
7652 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
7670 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
7688 TGAGTCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAA
Found at i:7695 original size:11 final size:10
Alignment explanation
Indices: 7652--7698 Score: 53
Period size: 11 Copynumber: 4.7 Consensus size: 10
7642 TTGAAATAAT
7652 TCTTCAATGA
1 TCTTCAATGA
7662 TCTTCAA--A
1 TCTTCAATGA
*
7670 TCTTCAAATTA
1 TCTTC-AATGA
7681 TCTTCAATGA
1 TCTTCAATGA
7691 GTCTTCAA
1 -TCTTCAA
7699 AAACGATCTT
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
8 6 0.19
9 2 0.06
10 11 0.34
11 13 0.41
ACGTcount: A:0.32, C:0.21, G:0.06, T:0.40
Consensus pattern (10 bp):
TCTTCAATGA
Found at i:10895 original size:22 final size:23
Alignment explanation
Indices: 10869--10922 Score: 67
Period size: 22 Copynumber: 2.4 Consensus size: 23
10859 GGTCCGGGCG
10869 CGGCATGGCCT-GACGTGGTGCT
1 CGGCATGGCCTGGACGTGGTGCT
* *
10891 CGGCATGG-CTGGGCTTGGTGCT
1 CGGCATGGCCTGGACGTGGTGCT
*
10913 TGGCATGGCC
1 CGGCATGGCC
10923 GGGTCATGGC
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 2 0.07
22 24 0.89
23 1 0.04
ACGTcount: A:0.07, C:0.26, G:0.43, T:0.24
Consensus pattern (23 bp):
CGGCATGGCCTGGACGTGGTGCT
Found at i:17682 original size:19 final size:18
Alignment explanation
Indices: 17649--17684 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
17639 TTGAAATAAT
17649 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
17667 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
17685 TGAGTCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAA
Found at i:17692 original size:11 final size:10
Alignment explanation
Indices: 17649--17694 Score: 51
Period size: 11 Copynumber: 4.6 Consensus size: 10
17639 TTGAAATAAT
17649 TCTTCAATGA
1 TCTTCAATGA
17659 TCTTCAA--A
1 TCTTCAATGA
*
17667 TCTTCAAATTA
1 TCTTC-AATGA
17678 TCTTCAATGA
1 TCTTCAATGA
17688 GTCTTCA
1 -TCTTCA
17695 TACACGAGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
8 6 0.19
9 2 0.06
10 11 0.35
11 12 0.39
ACGTcount: A:0.30, C:0.22, G:0.07, T:0.41
Consensus pattern (10 bp):
TCTTCAATGA
Done.