Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016388.1 Corchorus olitorius cultivar O-4 contig16421, 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: 27690
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:2692 original size:5 final size:5
Alignment explanation
Indices: 2682--2706 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
2672 GGCACTTCAA
2682 ATTTT ATTTT ATTTT ATTTT ATTTT
1 ATTTT ATTTT ATTTT ATTTT ATTTT
2707 TCCTTTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
ATTTT
Found at i:3912 original size:14 final size:13
Alignment explanation
Indices: 3883--3912 Score: 51
Period size: 13 Copynumber: 2.2 Consensus size: 13
3873 TCAATTTTTT
3883 AAAGCACTTTTCA
1 AAAGCACTTTTCA
3896 AAAGCACTTTCTCA
1 AAAGCACTTT-TCA
3910 AAA
1 AAA
3913 CCCAGCCTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.62
14 6 0.38
ACGTcount: A:0.43, C:0.23, G:0.07, T:0.27
Consensus pattern (13 bp):
AAAGCACTTTTCA
Found at i:6121 original size:15 final size:15
Alignment explanation
Indices: 6073--6123 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 15
6063 TCGAAGACTC
6073 AATTAACTTAATTAG
1 AATTAACTTAATTAG
* ** *
6088 AATT-TCTTCAAAAAA
1 AATTAACTT-AATTAG
6103 AATTAACTTAATTAG
1 AATTAACTTAATTAG
6118 AATTAA
1 AATTAA
6124 TAAATTACTT
Statistics
Matches: 26, Mismatches: 8, Indels: 4
0.68 0.21 0.11
Matches are distributed among these distances:
14 3 0.12
15 20 0.77
16 3 0.12
ACGTcount: A:0.51, C:0.08, G:0.04, T:0.37
Consensus pattern (15 bp):
AATTAACTTAATTAG
Found at i:12040 original size:25 final size:25
Alignment explanation
Indices: 11993--12040 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
11983 AAAAAAAAGC
**
11993 AAAAGAAAAGTCCTTTTTTTCACTA
1 AAAAGAAAAGTCCTTTTGATCACTA
12018 AAAAGAAAAGT-CTTTATGATCAC
1 AAAAGAAAAGTCCTTT-TGATCAC
12041 CTTCCTTACG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 4 0.20
25 16 0.80
ACGTcount: A:0.44, C:0.15, G:0.10, T:0.31
Consensus pattern (25 bp):
AAAAGAAAAGTCCTTTTGATCACTA
Found at i:12479 original size:60 final size:59
Alignment explanation
Indices: 12335--12479 Score: 175
Period size: 60 Copynumber: 2.4 Consensus size: 59
12325 CTTGCTGACG
* * *
12335 TCAGACCTTTATTTGAGC-ATTTTCGATAATGTTAGGTTCTTATTTGGCCAAATTAAAAGA
1 TCAGA-CTTTATTTGAGCAATTTT-GATAACGTTAGGTACTTATTTGACCAAATTAAAAGA
* * * *
12395 TCAGACTCTTATTTAAACATTTTTGATAACGTTAGGTACTTATTTGATCAAATTAAAAGA
1 TCAGACT-TTATTTGAGCAATTTTGATAACGTTAGGTACTTATTTGACCAAATTAAAAGA
*
12455 TCGGACATTTATTTGAGCAATTTTG
1 TCAGAC-TTTATTTGAGCAATTTTG
12480 GCAAACGTTA
Statistics
Matches: 71, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
59 2 0.03
60 64 0.90
61 5 0.07
ACGTcount: A:0.32, C:0.12, G:0.15, T:0.41
Consensus pattern (59 bp):
TCAGACTTTATTTGAGCAATTTTGATAACGTTAGGTACTTATTTGACCAAATTAAAAGA
Found at i:12683 original size:20 final size:19
Alignment explanation
Indices: 12638--12704 Score: 56
Period size: 18 Copynumber: 3.8 Consensus size: 19
12628 CCTATAGAAC
*
12638 ATATATACATA-TAA-TAT
1 ATATATATATATTAAGTAT
*
12655 AT-TAT-TATATTAACTTAT
1 ATATATATATATTAA-GTAT
*
12673 ATATATATATAGT-AGTAT
1 ATATATATATATTAAGTAT
12691 ATATATA-ATATTAA
1 ATATATATATATTAA
12705 ATACTCCGAT
Statistics
Matches: 40, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
15 3 0.08
16 6 0.15
17 6 0.15
18 16 0.40
19 4 0.10
20 5 0.12
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.46
Consensus pattern (19 bp):
ATATATATATATTAAGTAT
Found at i:12758 original size:35 final size:34
Alignment explanation
Indices: 12688--12758 Score: 92
Period size: 35 Copynumber: 2.1 Consensus size: 34
12678 TATATAGTAG
*
12688 TATATATATAATATTAAATACTCCGATTTCTAAA
1 TATATATATAATATTAAATACTCCGATTTCGAAA
12722 TATATATAT-ATATATATAATACTCCGAATTT-GAAA
1 TATATATATAATAT-TA-AATACTCCG-ATTTCGAAA
12757 TA
1 TA
12759 GATTAAATTT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
33 4 0.12
34 11 0.33
35 14 0.42
36 4 0.12
ACGTcount: A:0.45, C:0.10, G:0.04, T:0.41
Consensus pattern (34 bp):
TATATATATAATATTAAATACTCCGATTTCGAAA
Found at i:15898 original size:60 final size:60
Alignment explanation
Indices: 15811--15973 Score: 247
Period size: 60 Copynumber: 2.7 Consensus size: 60
15801 GCTAATTGCT
* * * *
15811 CAAATAAGGGCCTAATGTT-TGCCAAAATGCTCAAATAAGGGTCAGATCTTTTAATTTGGC
1 CAAATAAGGGCCTAACGTTAT-CAAAAATGCTCAAATAAGGGCCAGATCTGTTAATTTGGC
*
15871 CAAATAAGGGCCTAACGTTATCAAAAATGCTCAAATAAGGGCCCGATCTGTTAATTTGGC
1 CAAATAAGGGCCTAACGTTATCAAAAATGCTCAAATAAGGGCCAGATCTGTTAATTTGGC
* *
15931 CAAATAAGGGCCTAACGTTATCGAAAATACTCAAATAAGGGCC
1 CAAATAAGGGCCTAACGTTATCAAAAATGCTCAAATAAGGGCC
15974 TGACGTCAGT
Statistics
Matches: 95, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
60 94 0.99
61 1 0.01
ACGTcount: A:0.36, C:0.19, G:0.20, T:0.25
Consensus pattern (60 bp):
CAAATAAGGGCCTAACGTTATCAAAAATGCTCAAATAAGGGCCAGATCTGTTAATTTGGC
Found at i:15909 original size:31 final size:31
Alignment explanation
Indices: 15871--15979 Score: 93
Period size: 31 Copynumber: 3.6 Consensus size: 31
15861 TTAATTTGGC
15871 CAAATAAGGGCCTAACGTTATCAAAAATGCT
1 CAAATAAGGGCCTAACGTTATCAAAAATGCT
* * **
15902 CAAATAAGGGCC---CGATCTGT-TAATTTGGC-
1 CAAATAAGGGCCTAACG-T-TATCAAAAAT-GCT
* *
15931 CAAATAAGGGCCTAACGTTATCGAAAATACT
1 CAAATAAGGGCCTAACGTTATCAAAAATGCT
*
15962 CAAATAAGGGCCTGACGT
1 CAAATAAGGGCCTAACGT
15980 CAGTTTGGAT
Statistics
Matches: 60, Mismatches: 10, Indels: 16
0.70 0.12 0.19
Matches are distributed among these distances:
28 2 0.03
29 16 0.27
30 7 0.12
31 33 0.55
32 2 0.03
ACGTcount: A:0.37, C:0.20, G:0.20, T:0.23
Consensus pattern (31 bp):
CAAATAAGGGCCTAACGTTATCAAAAATGCT
Found at i:16062 original size:31 final size:31
Alignment explanation
Indices: 16024--16127 Score: 90
Period size: 31 Copynumber: 3.4 Consensus size: 31
16014 GATATCGGGT
16024 CCTTATTTGAGCATTTTAGCAAACGTTAGGC
1 CCTTATTTGAGCATTTTAGCAAACGTTAGGC
** ** *
16055 CCTTATTTG-GTCAAATTA--AAA-GAACAGAC
1 CCTTATTTGAG-CATTTTAGCAAACG-TTAGGC
* * *
16084 CCTTATTTGAGCATTTTGGCAAACGTTAAGT
1 CCTTATTTGAGCATTTTAGCAAACGTTAGGC
16115 CCTTATTTGAGCA
1 CCTTATTTGAGCA
16128 ATTAGCCAGC
Statistics
Matches: 54, Mismatches: 13, Indels: 12
0.68 0.16 0.15
Matches are distributed among these distances:
28 1 0.02
29 19 0.35
30 2 0.04
31 31 0.57
32 1 0.02
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.35
Consensus pattern (31 bp):
CCTTATTTGAGCATTTTAGCAAACGTTAGGC
Found at i:24850 original size:6 final size:6
Alignment explanation
Indices: 24839--24865 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
24829 TTTTAACATG
24839 CTTCCT CTTCCT CTTCCT CTTCCT CTT
1 CTTCCT CTTCCT CTTCCT CTTCCT CTT
24866 GCAGGAGGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (6 bp):
CTTCCT
Found at i:25372 original size:47 final size:45
Alignment explanation
Indices: 25289--25424 Score: 188
Period size: 47 Copynumber: 2.9 Consensus size: 45
25279 AGAAACATGG
25289 TTATGTATATCTATA-TATTATATTCAT-ATATGAAGTATGAAATGC
1 TTATGTATAT-TATATTATTATATT-ATGATATGAAGTATGAAATGC
25334 TTATGTATATTATATTATTCATATGTATGATATGAAGTATGAAATGC
1 TTATGTATATTATATTATT-ATAT-TATGATATGAAGTATGAAATGC
25381 TTATGTATATTTATATTATTAT-TCATATGATATGAAGTATGAAA
1 TTATGTATA-TTATATTATTATAT--TATGATATGAAGTATGAAA
25425 CGTGATGATG
Statistics
Matches: 84, Mismatches: 1, Indels: 10
0.88 0.01 0.11
Matches are distributed among these distances:
44 4 0.05
45 14 0.17
46 7 0.08
47 49 0.58
48 10 0.12
ACGTcount: A:0.38, C:0.04, G:0.12, T:0.46
Consensus pattern (45 bp):
TTATGTATATTATATTATTATATTATGATATGAAGTATGAAATGC
Found at i:26639 original size:25 final size:24
Alignment explanation
Indices: 26611--26672 Score: 81
Period size: 25 Copynumber: 2.6 Consensus size: 24
26601 GTGGATTGTA
*
26611 AAATAAATTGAATAATTAAGACATT
1 AAATAAATTGAAGAATTAA-ACATT
*
26636 AAATAAATTTAAGAATTAAACATT
1 AAATAAATTGAAGAATTAAACATT
*
26660 AAA-AAATTCAAGA
1 AAATAAATTGAAGA
26673 CTGACCCAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
23 9 0.26
24 8 0.24
25 17 0.50
ACGTcount: A:0.60, C:0.05, G:0.06, T:0.29
Consensus pattern (24 bp):
AAATAAATTGAAGAATTAAACATT
Done.