Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019984.1 Corchorus olitorius cultivar O-4 contig20017, 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: 24782
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30
Found at i:3975 original size:11 final size:10
Alignment explanation
Indices: 3959--4011 Score: 56
Period size: 11 Copynumber: 5.2 Consensus size: 10
3949 GCTTCTTGGA
3959 AATAATTCTTC
1 AATAA-TCTTC
3970 AATAATCTTC
1 AATAATCTTC
3980 -A-AATCTTC
1 AATAATCTTC
*
3988 AAATTATCTTC
1 -AATAATCTTC
3999 AATAAGTCTTC
1 AATAA-TCTTC
4010 AA
1 AA
4012 ACACGAACTT
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
8 7 0.19
9 1 0.03
10 10 0.28
11 18 0.50
ACGTcount: A:0.40, C:0.19, G:0.02, T:0.40
Consensus pattern (10 bp):
AATAATCTTC
Found at i:4011 original size:22 final size:21
Alignment explanation
Indices: 3959--4012 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 21
3949 GCTTCTTGGA
3959 AATAATTCTTC-AATAATCTTC
1 AATAA-TCTTCAAATAATCTTC
*
3980 -A-AATCTTCAAATTATCTTC
1 AATAATCTTCAAATAATCTTC
3999 AATAAGTCTTCAAA
1 AATAA-TCTTCAAA
4013 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:0.41, C:0.19, G:0.02, T:0.39
Consensus pattern (21 bp):
AATAATCTTCAAATAATCTTC
Found at i:5731 original size:50 final size:50
Alignment explanation
Indices: 5673--5778 Score: 167
Period size: 50 Copynumber: 2.1 Consensus size: 50
5663 TCTTTTATAC
* * * *
5673 CAAAAATGCCCCTTCTCGGTCGGAAGGTCCCAATTTTCGATATTTCTTTT
1 CAAAAATGCCCCTTCCCGATCGGAAGGTCCCAATTTTCAATATCTCTTTT
*
5723 CAAAAATGCCCCTTCCCGATCGGAAGGTCCCAGTTTTCAATATCTCTTTT
1 CAAAAATGCCCCTTCCCGATCGGAAGGTCCCAATTTTCAATATCTCTTTT
5773 CAAAAA
1 CAAAAA
5779 AAAGCCACTT
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.26, C:0.27, G:0.14, T:0.32
Consensus pattern (50 bp):
CAAAAATGCCCCTTCCCGATCGGAAGGTCCCAATTTTCAATATCTCTTTT
Found at i:5802 original size:52 final size:50
Alignment explanation
Indices: 5673--5811 Score: 143
Period size: 50 Copynumber: 2.7 Consensus size: 50
5663 TCTTTTATAC
* * * * * * *
5673 CAAAAATGCCCCTTCTCGGTCGGAAGGTCCCAATTTTCGATATTTCTTTT
1 CAAAAAAGCCACTTCCCGATCGGAAGGTCCCAGTTTTCAATATCTCTTTT
* *
5723 CAAAAATGCCCCTTCCCGATCGGAAGGTCCCAGTTTTCAATATCTCTTTT
1 CAAAAAAGCCACTTCCCGATCGGAAGGTCCCAGTTTTCAATATCTCTTTT
* * * *
5773 CAAAAAAAAGCCACTTCCTGGTTGGAAGGTCCCTGTTTT
1 C--AAAAAAGCCACTTCCCGATCGGAAGGTCCCAGTTTT
5812 TCCAAAAATG
Statistics
Matches: 76, Mismatches: 11, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
50 46 0.61
52 30 0.39
ACGTcount: A:0.24, C:0.27, G:0.17, T:0.32
Consensus pattern (50 bp):
CAAAAAAGCCACTTCCCGATCGGAAGGTCCCAGTTTTCAATATCTCTTTT
Found at i:5918 original size:46 final size:46
Alignment explanation
Indices: 5811--6108 Score: 295
Period size: 46 Copynumber: 6.4 Consensus size: 46
5801 GTCCCTGTTT
*
5811 TTCCAAAAATGCCCCTTCCTGGTTGGAATGGTCCCTG-TTT-TTAT-
1 TTCCAAAAATGCCCCTTCCTGGTTGGAA-GGTCCCTGATTTCTTTTA
* *
5855 TTCCAATAATGCCCCTTCCTAGTTGGAAGGTCCCTGATTTCTTTTA
1 TTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCCCTGATTTCTTTTA
* * * *
5901 TTCTAGAAATGCCCCTTCCTGGTTGGAAGGTCCCAGCA-TTCTCTTA
1 TTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCCCTG-ATTTCTTTTA
* * * *
5947 TTCTAGAAATGCCCCTTCCTGATTGGAAGGT-CCTAGTTTTCTTTTTA
1 TTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCCCT-GATTTC-TTTTA
* *
5994 TTCCAAAAATGCCCCCTCCTGGTTGGAAGGTCCC-GGTTTGCTTCTTA
1 TTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCCCTGATTT-CTT-TTA
** * * *
6041 TTCCAAAAATGCCCCTT-CTCGGTCAGAAGGTCCCAGTTTTCCTTTAAAA
1 TTCCAAAAATGCCCCTTCCT-GGTTGGAAGGTCCCTGATTT-CTTT--TA
6090 TTCCAAAAATGCCCCTTCC
1 TTCCAAAAATGCCCCTTCC
6109 CGATCGAAAG
Statistics
Matches: 215, Mismatches: 24, Indels: 24
0.82 0.09 0.09
Matches are distributed among these distances:
43 8 0.04
44 29 0.13
45 5 0.02
46 80 0.37
47 65 0.30
48 9 0.04
49 18 0.08
50 1 0.00
ACGTcount: A:0.20, C:0.28, G:0.17, T:0.35
Consensus pattern (46 bp):
TTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCCCTGATTTCTTTTA
Found at i:6014 original size:47 final size:47
Alignment explanation
Indices: 5811--6230 Score: 320
Period size: 49 Copynumber: 9.0 Consensus size: 47
5801 GTCCCTGTTT
* *
5811 TTCCAAAAATGCCCCTTCCTGGTTGGAATGGTCCC--TGTT-TTTAT-
1 TTCCAAAAATGCCCCTTCCTGGTTGGAA-GGTCCCAGTTTTCTTTTTA
* * * *
5855 TTCCAATAATGCCCCTTCCTAGTTGGAAGGTCCCTGATTTC-TTTTA
1 TTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCCCAGTTTTCTTTTTA
* * ** *
5901 TTCTAGAAATGCCCCTTCCTGGTTGGAAGGTCCCAGCATTC-TCTTA
1 TTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCCCAGTTTTCTTTTTA
* * * *
5947 TTCTAGAAATGCCCCTTCCTGATTGGAAGGTCCTAGTTTTCTTTTTA
1 TTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCCCAGTTTTCTTTTTA
* * * *
5994 TTCCAAAAATGCCCCCTCCTGGTTGGAAGGTCCCGGTTTGCTTCTTA
1 TTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCCCAGTTTTCTTTTTA
** **
6041 TTCCAAAAATGCCCCTT-CTCGGTCAGAAGGTCCCAGTTTTCCTTTAAAA
1 TTCCAAAAATGCCCCTTCCT-GGTTGGAAGGTCCCAGTTTT-CTTT-TTA
* * * * * * ***
6090 TTCCAAAAATGCCCCTTCCCGATCGAAAGGTCCAATTTTTCCTCCAATA
1 TTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCCCAGTTTT-CT-TTTTA
* * * **
6139 TTCCAAACATGCCCCTTCC-CGTTCGAAAGGTCCCAGTTTTCCTTCAATA
1 TTCCAAAAATGCCCCTTCCTGGTT-GGAAGGTCCCAGTTTT-CTT-TTTA
* * * *
6188 TTCCAAAAATTCCCCTTCCCGGTCGGAAGGTTCCA-TTTT-TTTT
1 TTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCCCAGTTTTCTTTT
6231 ACGTTACCCA
Statistics
Matches: 305, Mismatches: 58, Indels: 25
0.79 0.15 0.06
Matches are distributed among these distances:
43 6 0.02
44 26 0.09
45 5 0.02
46 79 0.26
47 75 0.25
48 8 0.03
49 103 0.34
50 3 0.01
ACGTcount: A:0.21, C:0.28, G:0.16, T:0.35
Consensus pattern (47 bp):
TTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCCCAGTTTTCTTTTTA
Found at i:6360 original size:40 final size:40
Alignment explanation
Indices: 6242--6360 Score: 123
Period size: 40 Copynumber: 3.0 Consensus size: 40
6232 CGTTACCCAG
* * *
6242 TTTGCCCTCCCCGGTCGGGAGGTGTTGTTTACAATTCCCAG
1 TTTGCCCTCCCCAGTCGGGAGGTGTTGTTTA-AATTTCCAA
* **
6283 TTTGCCCTCCCCAGTTGGGAGGTGTTGTCTT-TTTTTCCAA
1 TTTGCCCTCCCCAGTCGGGAGGTGTTGT-TTAAATTTCCAA
* * * *
6323 TTTTCCCTTCCCAGTCGGAAGGTGTTGTTTAAGTTTCC
1 TTTGCCCTCCCCAGTCGGGAGGTGTTGTTTAAATTTCC
6361 CCGTTTGCCC
Statistics
Matches: 64, Mismatches: 12, Indels: 5
0.79 0.15 0.06
Matches are distributed among these distances:
39 2 0.03
40 34 0.53
41 26 0.41
42 2 0.03
ACGTcount: A:0.12, C:0.26, G:0.24, T:0.39
Consensus pattern (40 bp):
TTTGCCCTCCCCAGTCGGGAGGTGTTGTTTAAATTTCCAA
Found at i:12920 original size:15 final size:15
Alignment explanation
Indices: 12900--12929 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
12890 CCATTCAAGG
12900 AAAAGGAGAATGTGA
1 AAAAGGAGAATGTGA
*
12915 AAAAGGAGATTGTGA
1 AAAAGGAGAATGTGA
12930 GTCCCATAAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.33, T:0.17
Consensus pattern (15 bp):
AAAAGGAGAATGTGA
Done.