Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019626.1 Corchorus olitorius cultivar O-4 contig19659, 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: 38225
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Found at i:1896 original size:25 final size:23
Alignment explanation
Indices: 1868--2003 Score: 67
Period size: 23 Copynumber: 5.3 Consensus size: 23
1858 TATAATAAAA
1868 ACGCAAGAACAATTTTTTTTTTATG
1 ACGCAA-AA-AATTTTTTTTTTATG
*
1893 ACGCAAAAATTTTTTTTTTTA-G
1 ACGCAAAAAATTTTTTTTTTATG
**
1915 AAAAACGCAAAAACCCTTTTTTTTTATG
1 ----ACGCAAAAA-ATTTTTTTTTTATG
1943 ACGCAGAAACAAAAAAATTTTTTTTTTATG
1 A--C-G---C-AAAAAATTTTTTTTTTATG
* ** **
1973 ACGCAGAATTTTTTTTTTTTCCG
1 ACGCAAAAAATTTTTTTTTTATG
1996 ACGCAAAA
1 ACGCAAAA
2004 CACAAAACAA
Statistics
Matches: 87, Mismatches: 11, Indels: 28
0.69 0.09 0.22
Matches are distributed among these distances:
22 1 0.01
23 33 0.38
24 4 0.05
25 6 0.07
26 10 0.11
27 12 0.14
28 2 0.02
30 14 0.16
31 5 0.06
ACGTcount: A:0.35, C:0.14, G:0.10, T:0.40
Consensus pattern (23 bp):
ACGCAAAAAATTTTTTTTTTATG
Found at i:1938 original size:50 final size:51
Alignment explanation
Indices: 1849--1947 Score: 137
Period size: 51 Copynumber: 2.0 Consensus size: 51
1839 AAAAGAAAAT
* * *
1849 AATTTTTTTTATAATAAAAACGCAAGAACAATTTTTTTTTTATGACGCAAA
1 AATTTTTTTTATAAGAAAAACGCAAAAACAACTTTTTTTTTATGACGCAAA
* * *
1900 AATTTTTTTTTTTAGAAAAACGCAAAAAC-CCTTTTTTTTTATGACGCA
1 AATTTTTTTTATAAGAAAAACGCAAAAACAACTTTTTTTTTATGACGCA
1948 GAAACAAAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
50 17 0.40
51 25 0.60
ACGTcount: A:0.37, C:0.12, G:0.08, T:0.42
Consensus pattern (51 bp):
AATTTTTTTTATAAGAAAAACGCAAAAACAACTTTTTTTTTATGACGCAAA
Found at i:2454 original size:16 final size:15
Alignment explanation
Indices: 2416--2457 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
2406 ACAGAGGTTG
*
2416 ACAGAAAGCAATTAA
1 ACAGAAAACAATTAA
2431 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
2446 ACTAGAAAACAA
1 AC-AGAAAACAA
2458 AACAAAGTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 16 0.64
16 9 0.36
ACGTcount: A:0.64, C:0.14, G:0.10, T:0.12
Consensus pattern (15 bp):
ACAGAAAACAATTAA
Found at i:10972 original size:22 final size:22
Alignment explanation
Indices: 10942--10983 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
10932 GCTTATAAAA
*
10942 TTCTTGGGTCATTCAGGTTAAC
1 TTCTCGGGTCATTCAGGTTAAC
*
10964 TTCTCGGGTCATTTAGGTTA
1 TTCTCGGGTCATTCAGGTTA
10984 CGGATTTGTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.17, C:0.17, G:0.24, T:0.43
Consensus pattern (22 bp):
TTCTCGGGTCATTCAGGTTAAC
Found at i:18306 original size:7 final size:7
Alignment explanation
Indices: 18265--18309 Score: 72
Period size: 7 Copynumber: 6.4 Consensus size: 7
18255 CATGCATGCA
*
18265 TTACTCA
1 TTACTCT
*
18272 TTACTCA
1 TTACTCT
18279 TTACTCT
1 TTACTCT
18286 TTACTCT
1 TTACTCT
18293 TTACTCT
1 TTACTCT
18300 TTACTCT
1 TTACTCT
18307 TTA
1 TTA
18310 TATATGTGGG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 37 1.00
ACGTcount: A:0.20, C:0.27, G:0.00, T:0.53
Consensus pattern (7 bp):
TTACTCT
Found at i:18407 original size:3 final size:3
Alignment explanation
Indices: 18399--18440 Score: 66
Period size: 3 Copynumber: 14.0 Consensus size: 3
18389 TTTACCAGTA
* *
18399 ACC ACC ACC ACC ATC ACC ATC ACC ACC ACC ACC ACC ACC ACC
1 ACC ACC ACC ACC ACC ACC ACC ACC ACC ACC ACC ACC ACC ACC
18441 CACAGCCACC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.33, C:0.62, G:0.00, T:0.05
Consensus pattern (3 bp):
ACC
Found at i:21933 original size:12 final size:13
Alignment explanation
Indices: 21916--21944 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
21906 TTGGCATTAA
21916 AGTTAGA-TTATT
1 AGTTAGATTTATT
21928 AGTTAGATTTATT
1 AGTTAGATTTATT
21941 AGTT
1 AGTT
21945 TTATGTTCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.44
13 9 0.56
ACGTcount: A:0.31, C:0.00, G:0.17, T:0.52
Consensus pattern (13 bp):
AGTTAGATTTATT
Found at i:29683 original size:33 final size:33
Alignment explanation
Indices: 29646--29723 Score: 113
Period size: 33 Copynumber: 2.4 Consensus size: 33
29636 CCCCGATCGT
29646 GCCCCACCATATGGGGAGGCGTCCCCAAGG-GGC
1 GCCCCACCATATGGGGAGGCGTCCCC-AGGAGGC
*
29679 GCCCCACCATATGGTGAGGCGTCCCCAGGAGGC
1 GCCCCACCATATGGGGAGGCGTCCCCAGGAGGC
* *
29712 GCCTCGCCATAT
1 GCCCCACCATAT
29724 TTTTTAAAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
32 3 0.07
33 38 0.93
ACGTcount: A:0.18, C:0.37, G:0.32, T:0.13
Consensus pattern (33 bp):
GCCCCACCATATGGGGAGGCGTCCCCAGGAGGC
Found at i:31241 original size:18 final size:19
Alignment explanation
Indices: 31218--31257 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
31208 GTCATAGCAT
31218 TTATTATTAATGTTA-TTA
1 TTATTATTAATGTTATTTA
*
31236 TTATTATTAGTGTTATTTA
1 TTATTATTAATGTTATTTA
31255 TTA
1 TTA
31258 GTCTATGCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 14 0.70
19 6 0.30
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.62
Consensus pattern (19 bp):
TTATTATTAATGTTATTTA
Found at i:33464 original size:4 final size:4
Alignment explanation
Indices: 33455--33481 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
33445 TTAAATACAC
33455 TAAT TAAT TAAT TAAT TAAT TAAT TAA
1 TAAT TAAT TAAT TAAT TAAT TAAT TAA
33482 GGCTAATCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (4 bp):
TAAT
Found at i:33570 original size:10 final size:10
Alignment explanation
Indices: 33555--33609 Score: 53
Period size: 10 Copynumber: 5.7 Consensus size: 10
33545 ACAAATTAGT
* *
33555 TAATTAATAG
1 TAATTAACAC
33565 TAATTAACAC
1 TAATTAACAC
33575 TAATT-A-AC
1 TAATTAACAC
*
33583 TACTTAACAC
1 TAATTAACAC
33593 TAATTAAC-C
1 TAATTAACAC
33602 TTAATTAA
1 -TAATTAA
33610 ATTAAACAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
8 6 0.16
9 3 0.08
10 29 0.76
ACGTcount: A:0.47, C:0.15, G:0.02, T:0.36
Consensus pattern (10 bp):
TAATTAACAC
Found at i:33707 original size:33 final size:33
Alignment explanation
Indices: 33663--33772 Score: 134
Period size: 33 Copynumber: 3.4 Consensus size: 33
33653 AAAAAAAACC
33663 GAGGCGCCTTCCAGTGGCGCCTCTGCCATGGCG
1 GAGGCGCCTTCCAGTGGCGCCTCTGCCATGGCG
* * *
33696 GGGGCGCCTTCCAGTGGCACCTCTGCCATAGCG
1 GAGGCGCCTTCCAGTGGCGCCTCTGCCATGGCG
* * * *
33729 GAGGTGCCTTCCCG-GCTCGCCTCCGCCATGGC-
1 GAGGCGCCTTCCAGTG-GCGCCTCTGCCATGGCG
33761 GAGGCGCCTTCC
1 GAGGCGCCTTCC
33773 CGGCTCGCCT
Statistics
Matches: 65, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
32 12 0.18
33 53 0.82
ACGTcount: A:0.09, C:0.39, G:0.34, T:0.18
Consensus pattern (33 bp):
GAGGCGCCTTCCAGTGGCGCCTCTGCCATGGCG
Found at i:33773 original size:32 final size:32
Alignment explanation
Indices: 33662--33796 Score: 130
Period size: 33 Copynumber: 4.2 Consensus size: 32
33652 AAAAAAAAAC
*
33662 CGAGGCGCCTTCCAGTGGCGCCTCTGCCATGG
1 CGAGGCGCCTTCCAGTGGCGCCTCCGCCATGG
* * * *
33694 CGGGGGCGCCTTCCAGTGGCACCTCTGCCATAG
1 C-GAGGCGCCTTCCAGTGGCGCCTCCGCCATGG
* * *
33727 CGGAGGTGCCTTCCCG-GCTCGCCTCCGCCATGG
1 C-GAGGCGCCTTCCAGTG-GCGCCTCCGCCATGG
* *
33760 CGAGGCGCCTTCCCG-GCTCGCCTCCGCCATGG
1 CGAGGCGCCTTCCAGTG-GCGCCTCCGCCATGG
33792 CGAGG
1 CGAGG
33797 TGAGGCACCC
Statistics
Matches: 90, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
32 37 0.41
33 53 0.59
ACGTcount: A:0.09, C:0.40, G:0.34, T:0.17
Consensus pattern (32 bp):
CGAGGCGCCTTCCAGTGGCGCCTCCGCCATGG
Found at i:36265 original size:2 final size:2
Alignment explanation
Indices: 36258--36292 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
36248 AGACAAGAAC
36258 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
36293 CTAGTAATTT
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.