Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014970.1 Corchorus olitorius cultivar O-4 contig15003, 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: 44389
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.34
Found at i:4538 original size:15 final size:16
Alignment explanation
Indices: 4508--4547 Score: 64
Period size: 15 Copynumber: 2.6 Consensus size: 16
4498 TTACTTTGCT
4508 TTGTTTTCTAGTTTAA
1 TTGTTTTCTAGTTTAA
4524 TTGTTTTCT-GTTTAA
1 TTGTTTTCTAGTTTAA
*
4539 TTGCTTTCT
1 TTGTTTTCT
4548 TTCAATCTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 14 0.61
16 9 0.39
ACGTcount: A:0.12, C:0.10, G:0.12, T:0.65
Consensus pattern (16 bp):
TTGTTTTCTAGTTTAA
Found at i:5048 original size:28 final size:28
Alignment explanation
Indices: 5008--5063 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
4998 TTTGTTTTCT
*
5008 GTTTTTGCGTTTTTCTAAAAAAAAAAAA
1 GTTTTTGCGTTTTTATAAAAAAAAAAAA
**
5036 GTTTTTGCGTTTTTATTTAAAAAAAAAA
1 GTTTTTGCGTTTTTATAAAAAAAAAAAA
5064 TTTCTTTTCT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.41, C:0.05, G:0.11, T:0.43
Consensus pattern (28 bp):
GTTTTTGCGTTTTTATAAAAAAAAAAAA
Found at i:8794 original size:21 final size:21
Alignment explanation
Indices: 8760--8799 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
8750 AATTATAAAG
**
8760 AAAAGCAATTTAAACTAAACA
1 AAAAGCAAAGTAAACTAAACA
*
8781 AAAAGCAAAGTAAATTAAA
1 AAAAGCAAAGTAAACTAAA
8800 TCTAAACTAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.65, C:0.10, G:0.07, T:0.17
Consensus pattern (21 bp):
AAAAGCAAAGTAAACTAAACA
Found at i:10071 original size:31 final size:29
Alignment explanation
Indices: 10032--10089 Score: 71
Period size: 31 Copynumber: 1.9 Consensus size: 29
10022 GTGTTCTTGA
* *
10032 TTTGGGTTAGTAACTCCCTTTTCTTTTTAC
1 TTTGGGTTACTAACACCCTTTT-TTTTTAC
*
10062 TTTGAGGTTACTAACACTCTTTTTTTTT
1 TTTG-GGTTACTAACACCCTTTTTTTTT
10090 CAGAGGGACA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 9 0.38
31 15 0.62
ACGTcount: A:0.16, C:0.17, G:0.12, T:0.55
Consensus pattern (29 bp):
TTTGGGTTACTAACACCCTTTTTTTTTAC
Found at i:11327 original size:44 final size:44
Alignment explanation
Indices: 11246--11329 Score: 107
Period size: 44 Copynumber: 1.9 Consensus size: 44
11236 TGATGTGAGG
* * * *
11246 ATGGCCGGGCCATAGCCGGCCTAGCATGCTGGCTTGGCTCGGGC
1 ATGGCCGGGCAACAGCCGACCAAGCATGCTGGCTTGGCTCGGGC
*
11290 ATGGCCGGGCAACAGCCGACCAAGCTTGCTAGG-TTGGCTC
1 ATGGCCGGGCAACAGCCGACCAAGCATGCT-GGCTTGGCTC
11330 AGAGGTGACC
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
44 32 0.94
45 2 0.06
ACGTcount: A:0.15, C:0.31, G:0.36, T:0.18
Consensus pattern (44 bp):
ATGGCCGGGCAACAGCCGACCAAGCATGCTGGCTTGGCTCGGGC
Found at i:16726 original size:29 final size:29
Alignment explanation
Indices: 16668--16908 Score: 306
Period size: 29 Copynumber: 8.4 Consensus size: 29
16658 TATTTCTTAA
*
16668 TTGGTCATTTTTGCACACTCAGGGGCATT
1 TTGGTCATTTTTGCACATTCAGGGGCATT
* * * *
16697 TTGGTCATTTTGGCATATTCAAGGGTATT
1 TTGGTCATTTTTGCACATTCAGGGGCATT
* * *
16726 TTGGTCA--TTTACACATTCAAGGACATT
1 TTGGTCATTTTTGCACATTCAGGGGCATT
* *
16753 TTGATTATTTTTGCACATTCAGGGGCATT
1 TTGGTCATTTTTGCACATTCAGGGGCATT
* * *
16782 TTGGTTATTTTTCCATATTCAGGGGCATT
1 TTGGTCATTTTTGCACATTCAGGGGCATT
* *
16811 TTGGTTATTTTTGCATATTCAGGGGCATT
1 TTGGTCATTTTTGCACATTCAGGGGCATT
*
16840 TTGGTCATTTTTGTACATTCAGGGGCATT
1 TTGGTCATTTTTGCACATTCAGGGGCATT
*
16869 TTGGTCATTTTTGCACATCCAGGGGCATT
1 TTGGTCATTTTTGCACATTCAGGGGCATT
*
16898 TTGATCATTTT
1 TTGGTCATTTT
16909 GCATACTCGG
Statistics
Matches: 185, Mismatches: 25, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
27 20 0.11
29 165 0.89
ACGTcount: A:0.20, C:0.15, G:0.22, T:0.44
Consensus pattern (29 bp):
TTGGTCATTTTTGCACATTCAGGGGCATT
Found at i:19635 original size:16 final size:16
Alignment explanation
Indices: 19604--19634 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
19594 ACAAAGCCTA
19604 GTAAAAAAAGGGTTTT
1 GTAAAAAAAGGGTTTT
19620 GTAAAAAAA-GGTTTT
1 GTAAAAAAAGGGTTTT
19635 TTTTCTCTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.45, C:0.00, G:0.23, T:0.32
Consensus pattern (16 bp):
GTAAAAAAAGGGTTTT
Found at i:33825 original size:37 final size:34
Alignment explanation
Indices: 33781--33852 Score: 144
Period size: 34 Copynumber: 2.1 Consensus size: 34
33771 CAAGCTTATG
33781 GTAAGTAGTAGTTGTAAGATGTCAAGAATGATGA
1 GTAAGTAGTAGTTGTAAGATGTCAAGAATGATGA
33815 GTAAGTAGTAGTTGTAAGATGTCAAGAATGATGA
1 GTAAGTAGTAGTTGTAAGATGTCAAGAATGATGA
33849 GTAA
1 GTAA
33853 TTAAAACTAC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 38 1.00
ACGTcount: A:0.39, C:0.03, G:0.29, T:0.29
Consensus pattern (34 bp):
GTAAGTAGTAGTTGTAAGATGTCAAGAATGATGA
Found at i:34184 original size:30 final size:30
Alignment explanation
Indices: 34148--34204 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
34138 AGTTCGTGAT
34148 TGAAGATTAATTGAAG-ATAATTTCAAGATA
1 TGAAGA-TAATTGAAGAATAATTTCAAGATA
* *
34178 TGAAGATCATTGAAGAATTATTTCAAG
1 TGAAGATAATTGAAGAATAATTTCAAG
34205 GAGCAAGAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 8 0.33
30 16 0.67
ACGTcount: A:0.44, C:0.05, G:0.18, T:0.33
Consensus pattern (30 bp):
TGAAGATAATTGAAGAATAATTTCAAGATA
Found at i:35560 original size:21 final size:21
Alignment explanation
Indices: 35534--35604 Score: 117
Period size: 21 Copynumber: 3.4 Consensus size: 21
35524 TGCTAGGAGT
35534 TCATTGGAGCAA-GTTCCAAGC
1 TCATTGGAG-AAGGTTCCAAGC
35555 TCATTGGAGAAGGTTCCAAGC
1 TCATTGGAGAAGGTTCCAAGC
*
35576 TCATTGGAGAAGGTTTCAAGC
1 TCATTGGAGAAGGTTCCAAGC
35597 TCATTGGA
1 TCATTGGA
35605 ATTGTCTAAG
Statistics
Matches: 48, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
20 2 0.04
21 46 0.96
ACGTcount: A:0.28, C:0.18, G:0.27, T:0.27
Consensus pattern (21 bp):
TCATTGGAGAAGGTTCCAAGC
Found at i:36510 original size:25 final size:24
Alignment explanation
Indices: 36474--36520 Score: 69
Period size: 26 Copynumber: 1.9 Consensus size: 24
36464 TCCTTCTATT
36474 CATCTATCATC-AAGTTTTTCATC
1 CATCTATCATCAAAGTTTTTCATC
36497 CATCTCATCCATCAAAGTTTTTCA
1 CATCT-AT-CATCAAAGTTTTTCA
36521 AATTTTTAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 5 0.24
24 2 0.10
25 4 0.19
26 10 0.48
ACGTcount: A:0.28, C:0.28, G:0.04, T:0.40
Consensus pattern (24 bp):
CATCTATCATCAAAGTTTTTCATC
Found at i:40023 original size:21 final size:21
Alignment explanation
Indices: 39997--40067 Score: 117
Period size: 21 Copynumber: 3.4 Consensus size: 21
39987 TGCTAGGAGT
39997 TCATTGGAGCAA-GTTCCAAGC
1 TCATTGGAG-AAGGTTCCAAGC
40018 TCATTGGAGAAGGTTCCAAGC
1 TCATTGGAGAAGGTTCCAAGC
*
40039 TCATTGGAGAAGGTTTCAAGC
1 TCATTGGAGAAGGTTCCAAGC
40060 TCATTGGA
1 TCATTGGA
40068 ATTGCCTAAG
Statistics
Matches: 48, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
20 2 0.04
21 46 0.96
ACGTcount: A:0.28, C:0.18, G:0.27, T:0.27
Consensus pattern (21 bp):
TCATTGGAGAAGGTTCCAAGC
Done.