Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021643.1 Corchorus olitorius cultivar O-4 contig21676, 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: 15363
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.30
Found at i:9387 original size:28 final size:28
Alignment explanation
Indices: 9356--9412 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
9346 CAAAACCCAA
9356 AAGAAATTAGCATTTTGCATTAGTAATT
1 AAGAAATTAGCATTTTGCATTAGTAATT
9384 AAGAAATTAGCATTTTGCATTAGTAATT
1 AAGAAATTAGCATTTTGCATTAGTAATT
9412 A
1 A
9413 GGCATTAGCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.40, C:0.07, G:0.14, T:0.39
Consensus pattern (28 bp):
AAGAAATTAGCATTTTGCATTAGTAATT
Found at i:12667 original size:10 final size:11
Alignment explanation
Indices: 12641--12674 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
12631 ATATGGAATC
12641 AATAAAGGAAA
1 AATAAAGGAAA
*
12652 ATTAAA-GAAA
1 AATAAAGGAAA
12662 AATAAAGGAAA
1 AATAAAGGAAA
12673 AA
1 AA
12675 GAAAAGAAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.74, C:0.00, G:0.15, T:0.12
Consensus pattern (11 bp):
AATAAAGGAAA
Found at i:12877 original size:21 final size:21
Alignment explanation
Indices: 12822--12903 Score: 64
Period size: 21 Copynumber: 3.9 Consensus size: 21
12812 CAAAGAAATA
12822 AAGAGTAATCAGTAAA-ATGGT
1 AAGAGTAATCAGTAAAGA-GGT
* **
12843 AATG-TTAAAGAGTAAAGAGCG-
1 AA-GAGTAATCAGTAAAGAG-GT
12864 AAGAGTAATCAGTAAA-ATGGT
1 AAGAGTAATCAGTAAAGA-GGT
*
12885 AATAGTAATCAGTAAAGAG
1 AAGAGTAATCAGTAAAGAG
12904 TAATCAGTAA
Statistics
Matches: 47, Mismatches: 7, Indels: 14
0.69 0.10 0.21
Matches are distributed among these distances:
20 3 0.06
21 40 0.85
22 4 0.09
ACGTcount: A:0.49, C:0.05, G:0.24, T:0.22
Consensus pattern (21 bp):
AAGAGTAATCAGTAAAGAGGT
Found at i:12912 original size:21 final size:20
Alignment explanation
Indices: 12853--12927 Score: 62
Period size: 21 Copynumber: 3.5 Consensus size: 20
12843 AATGTTAAAG
* *
12853 AGTAAAGAGCGAAGAGTAATC
1 AGTAAAGAG-TAATAGTAATC
12874 AGTAAA-ATGGTAATAGTAATC
1 AGTAAAGA--GTAATAGTAATC
**
12895 AGTAAAGAGTAATCAGTAAAAG
1 AGTAAAGAGTAAT-AGT-AATC
12917 AGTAAAGAGTA
1 AGTAAAGAGTA
12928 GAAGAGTAAT
Statistics
Matches: 45, Mismatches: 4, Indels: 9
0.78 0.07 0.16
Matches are distributed among these distances:
20 6 0.13
21 24 0.53
22 15 0.33
ACGTcount: A:0.51, C:0.05, G:0.24, T:0.20
Consensus pattern (20 bp):
AGTAAAGAGTAATAGTAATC
Found at i:12913 original size:42 final size:42
Alignment explanation
Indices: 12820--13065 Score: 168
Period size: 42 Copynumber: 5.8 Consensus size: 42
12810 TTCAAAGAAA
**
12820 TAAAGAGTAATCAGTAAAATGGTAAT-GTTAAAGAGTAAAGAG
1 TAAAGAGTAATCAGTAAAATGGTAATAG-TAATCAGTAAAGAG
**
12862 CGAAGAGTAATCAGTAAAATGGTAATAGTAATCAGTAAAGAG
1 TAAAGAGTAATCAGTAAAATGGTAATAGTAATCAGTAAAGAG
** ** * * *
12904 TAATCAGTAAAAGAGTAAAGAGTAGAAGAGTAATAATAGTCAATAAAGAG
1 TAAAGAGT-AATCAGTAAA-A-T----G-GTAATAGTAATCAGTAAAGAG
* *
12954 TAAAGAGTAATC-----AA-GG-AAGAATAAT-AGTAAAAGAG
1 TAAAGAGTAATCAGTAAAATGGTAATAGTAATCAGT-AAAGAG
* * *
12989 TAAACAGTAAGCAGTAAAATGATAATAGTAATCAGTAAAGAG
1 TAAAGAGTAATCAGTAAAATGGTAATAGTAATCAGTAAAGAG
13031 TAAAGAGTAATCAGTAAAAAATGGTAATCAGTAAT
1 TAAAGAGTAATCAGT--AAAATGGTAAT-AGTAAT
13066 TAAAATTTAA
Statistics
Matches: 155, Mismatches: 28, Indels: 39
0.70 0.13 0.18
Matches are distributed among these distances:
34 2 0.01
35 23 0.15
36 1 0.01
37 1 0.01
40 2 0.01
41 1 0.01
42 66 0.43
43 13 0.08
44 12 0.08
45 7 0.05
49 3 0.02
50 24 0.15
ACGTcount: A:0.52, C:0.05, G:0.22, T:0.22
Consensus pattern (42 bp):
TAAAGAGTAATCAGTAAAATGGTAATAGTAATCAGTAAAGAG
Found at i:12918 original size:15 final size:15
Alignment explanation
Indices: 12888--12937 Score: 66
Period size: 15 Copynumber: 3.4 Consensus size: 15
12878 AAATGGTAAT
12888 AGTAATCAGT-AAAG
1 AGTAATCAGTAAAAG
12902 AGTAATCAGTAAAAG
1 AGTAATCAGTAAAAG
** *
12917 AGTAAAGAGTAGAAG
1 AGTAATCAGTAAAAG
12932 AGTAAT
1 AGTAAT
12938 AATAGTCAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
14 10 0.32
15 21 0.68
ACGTcount: A:0.52, C:0.04, G:0.24, T:0.20
Consensus pattern (15 bp):
AGTAATCAGTAAAAG
Found at i:12963 original size:50 final size:50
Alignment explanation
Indices: 12848--12963 Score: 119
Period size: 50 Copynumber: 2.3 Consensus size: 50
12838 ATGGTAATGT
** * * *
12848 TAAAGAGTAAAGAG-CGAAGAGTAATCAGTAAAATGGTAATAGTAATCAG
1 TAAAGAGTAAAGAGTAAAAGAGTAAACAGTAAAATGGTAATAATAATCAA
** * * *
12897 TAAAGAGTAATCAGTAAAAGAGTAAAGAGTAGAA-GAGTAATAATAGTCAA
1 TAAAGAGTAAAGAGTAAAAGAGTAAACAGTAAAATG-GTAATAATAATCAA
12947 TAAAGAGTAAAGAGTAA
1 TAAAGAGTAAAGAGTAA
12964 TCAAGGAAGA
Statistics
Matches: 53, Mismatches: 12, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
49 13 0.25
50 40 0.75
ACGTcount: A:0.53, C:0.04, G:0.23, T:0.20
Consensus pattern (50 bp):
TAAAGAGTAAAGAGTAAAAGAGTAAACAGTAAAATGGTAATAATAATCAA
Found at i:12976 original size:28 final size:27
Alignment explanation
Indices: 12895--12991 Score: 74
Period size: 28 Copynumber: 3.4 Consensus size: 27
12885 AATAGTAATC
* *
12895 AGTAAAGAGTAATCAGTAAAAGAGTAAAG
1 AGTAAAGAGTAATCA--AGAAGAATAAAG
*
12924 AGTAGAAGAGTAAT-AA-TAGTCAATAAAG
1 AGTA-AAGAGTAATCAAGAAG--AATAAAG
*
12952 AGTAAAGAGTAATCAAGGAAGAAT-AAT
1 AGTAAAGAGTAATCAA-GAAGAATAAAG
12979 AGTAAAAGAGTAA
1 AGT-AAAGAGTAA
12992 ACAGTAAGCA
Statistics
Matches: 57, Mismatches: 4, Indels: 15
0.75 0.05 0.20
Matches are distributed among these distances:
26 2 0.04
27 15 0.26
28 24 0.42
29 5 0.09
30 11 0.19
ACGTcount: A:0.56, C:0.03, G:0.23, T:0.19
Consensus pattern (27 bp):
AGTAAAGAGTAATCAAGAAGAATAAAG
Found at i:12983 original size:77 final size:74
Alignment explanation
Indices: 12902--13064 Score: 170
Period size: 77 Copynumber: 2.2 Consensus size: 74
12892 ATCAGTAAAG
* * *
12902 AGTAATCAGTAAAAGAGTAAAG-AGTAGAA-GAGTAATAATAGTCAATAAAGAGTAAAGAGTAAT
1 AGTAATCAGTAAAACAGT-AAGCAGTAAAATGA-TAATAATAATCAATAAAGAGTAAAGAGTAAT
12965 CAAGGAAGAATAAT
64 C-AGGAA-AA-AAT
** * *
12979 AGTAAAAGAGT-AAACAGTAAGCAGTAAAATGATAATAGTAATCAGTAAAGAGTAAAGAGTAATC
1 AGT-AATCAGTAAAACAGTAAGCAGTAAAATGATAATAATAATCAATAAAGAGTAAAGAGTAATC
*
13043 AGTAAAAAAT
65 AGGAAAAAAT
*
13053 GGTAATCAGTAA
1 AGTAATCAGTAA
13065 TTAAAATTTA
Statistics
Matches: 71, Mismatches: 11, Indels: 11
0.76 0.12 0.12
Matches are distributed among these distances:
73 5 0.07
74 6 0.08
75 2 0.03
76 7 0.10
77 44 0.62
78 7 0.10
ACGTcount: A:0.54, C:0.05, G:0.21, T:0.20
Consensus pattern (74 bp):
AGTAATCAGTAAAACAGTAAGCAGTAAAATGATAATAATAATCAATAAAGAGTAAAGAGTAATCA
GGAAAAAAT
Found at i:12987 original size:35 final size:33
Alignment explanation
Indices: 12899--12998 Score: 96
Period size: 35 Copynumber: 2.9 Consensus size: 33
12889 GTAATCAGTA
* *
12899 AAGAGTAATCAGTAAAAGAGTAAAGAGT-AGAAG
1 AAGAATAAT-AGTAAAAGAGTAAAGAGTAACAAG
12932 -AGTAATAATAGTCAATAAAGAGTAAAGAGTAATCAAGG
1 AAG-AATAATAGT--A-AAAGAGTAAAGAGTAA-CAA-G
*
12970 AAGAATAATAGTAAAAGAGTAAACAGTAA
1 AAGAATAATAGTAAAAGAGTAAAGAGTAA
12999 GCAGTAAAAT
Statistics
Matches: 56, Mismatches: 3, Indels: 14
0.77 0.04 0.19
Matches are distributed among these distances:
32 5 0.09
33 5 0.09
34 1 0.02
35 29 0.52
36 2 0.04
37 2 0.04
38 10 0.18
39 2 0.04
ACGTcount: A:0.56, C:0.04, G:0.22, T:0.18
Consensus pattern (33 bp):
AAGAATAATAGTAAAAGAGTAAAGAGTAACAAG
Found at i:13024 original size:21 final size:22
Alignment explanation
Indices: 12970--13049 Score: 87
Period size: 21 Copynumber: 3.8 Consensus size: 22
12960 GTAATCAAGG
*
12970 AAGAATAAT-AGTAAAAGAGTA
1 AAGAGTAATCAGTAAAAGAGTA
* *
12991 AACAGTAAGCAGTAAAATGA-T-
1 AAGAGTAATCAGTAAAA-GAGTA
*
13012 AATAGTAATCAGT-AAAGAGTA
1 AAGAGTAATCAGTAAAAGAGTA
13033 AAGAGTAATCAGTAAAA
1 AAGAGTAATCAGTAAAA
13050 AATGGTAATC
Statistics
Matches: 48, Mismatches: 6, Indels: 9
0.76 0.10 0.14
Matches are distributed among these distances:
19 2 0.04
20 4 0.08
21 29 0.60
22 11 0.23
23 2 0.04
ACGTcount: A:0.56, C:0.05, G:0.19, T:0.20
Consensus pattern (22 bp):
AAGAGTAATCAGTAAAAGAGTA
Found at i:13145 original size:33 final size:34
Alignment explanation
Indices: 13108--13178 Score: 99
Period size: 33 Copynumber: 2.1 Consensus size: 34
13098 TAAAAAATTT
* *
13108 AAAATGATATTTAGTAATTAAAGTA-AAAAGGTA
1 AAAATGATATTCAGTAATTAAAGTAGAAAAGGCA
* *
13141 AAAATGGTATTCAGTAATTAAATTAGAAAAGGCA
1 AAAATGATATTCAGTAATTAAAGTAGAAAAGGCA
13175 AAAA
1 AAAA
13179 AATGGAAACC
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
33 22 0.67
34 11 0.33
ACGTcount: A:0.55, C:0.03, G:0.15, T:0.27
Consensus pattern (34 bp):
AAAATGATATTCAGTAATTAAAGTAGAAAAGGCA
Found at i:13205 original size:27 final size:27
Alignment explanation
Indices: 13175--13249 Score: 89
Period size: 26 Copynumber: 2.8 Consensus size: 27
13165 AGAAAAGGCA
* *
13175 AAAAAATGGAAACCAGTAAAAAAAAGT
1 AAAAAATGGTAATCAGTAAAAAAAAGT
* * *
13202 AAAAGATGGTAATGAGT-AAAAAGAGT
1 AAAAAATGGTAATCAGTAAAAAAAAGT
*
13228 AAAAATTGGTAATCAGTAAAAA
1 AAAAAATGGTAATCAGTAAAAA
13250 GAGCAAGGGT
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
26 22 0.56
27 17 0.44
ACGTcount: A:0.60, C:0.04, G:0.19, T:0.17
Consensus pattern (27 bp):
AAAAAATGGTAATCAGTAAAAAAAAGT
Found at i:14517 original size:25 final size:24
Alignment explanation
Indices: 14489--14535 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 24
14479 GGCTAGGGTT
*
14489 TTGATCGGTTTGAGAGAAGGAAGTG
1 TTGAACGGTTTGAGAG-AGGAAGTG
* *
14514 TTGAAGGGTTTGAGCGAGGAAG
1 TTGAACGGTTTGAGAGAGGAAG
14536 AAGAAGAAGT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 6 0.32
25 13 0.68
ACGTcount: A:0.28, C:0.04, G:0.43, T:0.26
Consensus pattern (24 bp):
TTGAACGGTTTGAGAGAGGAAGTG
Done.