Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013401.1 Corchorus olitorius cultivar O-4 contig13434, 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: 36364
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:11 original size:2 final size:2
Alignment explanation
Indices: 5--39 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1 ATAC
5 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
40 TGAATAGAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2726 original size:22 final size:21
Alignment explanation
Indices: 2674--2727 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 21
2664 TGCTTCTTGA
2674 AATAATTCTTC-AATGATCTTC
1 AATAA-TCTTCAAATGATCTTC
*
2695 -A-AATCTTCAAATTATCTTC
1 AATAATCTTCAAATGATCTTC
2714 AATAAGTCTTCAAA
1 AATAA-TCTTCAAA
2728 CACGAACTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
18 5 0.18
19 11 0.39
20 2 0.07
21 2 0.07
22 8 0.29
ACGTcount: A:0.39, C:0.19, G:0.04, T:0.39
Consensus pattern (21 bp):
AATAATCTTCAAATGATCTTC
Found at i:8347 original size:97 final size:97
Alignment explanation
Indices: 8174--8364 Score: 301
Period size: 97 Copynumber: 2.0 Consensus size: 97
8164 TAACAATTTC
* * *
8174 CCCCGATTCACTTGTGAGTCCCCATCTCTCCACGTGCGGCCCAACCCGTCAAGTCTCAAGTCAAT
1 CCCCGATTCACTTGTGAGTCCCCATCTCTCCACGTACGGCCCAACCCGTCAAGTCTAAAGCCAAT
*
8239 TACTGACCATCCAAGACTTAACCCGTGGAGTG
66 TACCGACCATCCAAGACTTAACCCGTGGAGTG
* * *
8271 CCCCGATTCACTTGTGAGTCCTCATCTCTCCCCGTACGGCCCAACTCGTCAAGTCTAAAGCCAAT
1 CCCCGATTCACTTGTGAGTCCCCATCTCTCCACGTACGGCCCAACCCGTCAAGTCTAAAGCCAAT
* *
8336 TACCGATCATCCAAGACTTAACTCGTGGA
66 TACCGACCATCCAAGACTTAACCCGTGGA
8365 TTGCGAGGGC
Statistics
Matches: 85, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
97 85 1.00
ACGTcount: A:0.24, C:0.36, G:0.17, T:0.24
Consensus pattern (97 bp):
CCCCGATTCACTTGTGAGTCCCCATCTCTCCACGTACGGCCCAACCCGTCAAGTCTAAAGCCAAT
TACCGACCATCCAAGACTTAACCCGTGGAGTG
Found at i:26574 original size:19 final size:18
Alignment explanation
Indices: 26536--26574 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
26526 GGTTCTTGTT
*
26536 TTTGTGCAATTGATCTAA
1 TTTGTGCAATTGACCTAA
*
26554 TTTGTGCAATTAGCCCTAA
1 TTTGTGCAATT-GACCTAA
26573 TT
1 TT
26575 GGATTGAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.44
Consensus pattern (18 bp):
TTTGTGCAATTGACCTAA
Found at i:26689 original size:21 final size:20
Alignment explanation
Indices: 26665--26713 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
26655 TGGAACCCTT
26665 TTGGGTTCAAGTGGTACAAAA
1 TTGGGTTCAAGTGGTAC-AAA
* * *
26686 TTGGATTTAAGTGGTTCAAA
1 TTGGGTTCAAGTGGTACAAA
26706 TTAGGGTT
1 TT-GGGTT
26714 TTTAAGGTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 5 0.22
21 18 0.78
ACGTcount: A:0.29, C:0.06, G:0.29, T:0.37
Consensus pattern (20 bp):
TTGGGTTCAAGTGGTACAAA
Found at i:29032 original size:12 final size:12
Alignment explanation
Indices: 29015--29041 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
29005 ATCCGACAAC
29015 GGCGTCGGCTCT
1 GGCGTCGGCTCT
29027 GGCGTCGGCTCT
1 GGCGTCGGCTCT
29039 GGC
1 GGC
29042 AAGGGATAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.00, C:0.33, G:0.44, T:0.22
Consensus pattern (12 bp):
GGCGTCGGCTCT
Found at i:32602 original size:28 final size:28
Alignment explanation
Indices: 32442--32600 Score: 153
Period size: 28 Copynumber: 5.5 Consensus size: 28
32432 CTTTGCTTCT
32442 CATTTTGGTCATTTTACATGTTCA-GGGG
1 CATTTTGGTCATTTT-CATGTTCAGGGGG
* * *
32470 CATTCTGGTCATTCTTCTAGGTCCAGAGGGG
1 CATTTTGGTCATT-TTC-ATGTTCAG-GGGG
* * *
32501 AATTGTGATCATTATTCATGTTC-GGGGG
1 CATTTTGGTCATT-TTCATGTTCAGGGGG
*
32529 CATTTTGGTCATTTTTCATGTCCA-GGGG
1 CATTTTGGTCA-TTTTCATGTTCAGGGGG
32557 CATTTTGGTCATTTTTCATGTTCAGGGGGG
1 CATTTTGGTCA-TTTTCATGTTCA-GGGGG
*
32587 CATTTTAGTCATTT
1 CATTTTGGTCATTT
32601 CAAGTTTATT
Statistics
Matches: 108, Mismatches: 15, Indels: 15
0.78 0.11 0.11
Matches are distributed among these distances:
28 60 0.56
29 13 0.12
30 18 0.17
31 17 0.16
ACGTcount: A:0.17, C:0.16, G:0.26, T:0.42
Consensus pattern (28 bp):
CATTTTGGTCATTTTCATGTTCAGGGGG
Done.