Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018115.1 Corchorus olitorius cultivar O-4 contig18148, 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: 30177
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:9125 original size:18 final size:19
Alignment explanation
Indices: 9104--9139 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
9094 TTACTAAATA
9104 AATAATTATTATT-TTTAT
1 AATAATTATTATTATTTAT
9122 AATAATTATTATTATTTA
1 AATAATTATTATTATTTA
9140 ATATGTGCCG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
AATAATTATTATTATTTAT
Found at i:11562 original size:22 final size:22
Alignment explanation
Indices: 11501--11564 Score: 69
Period size: 22 Copynumber: 2.9 Consensus size: 22
11491 ATTATTAGAT
* *
11501 ACTATATATTAACTAATAAATA
1 ACTATATATTAATTAGTAAATA
*
11523 ACTA-ATAATTAATAAGTAAATA
1 ACTATAT-ATTAATTAGTAAATA
11545 A-TATATATTCAATTAGTAAA
1 ACTATATATT-AATTAGTAAA
11565 ATAGATGAAG
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
21 7 0.20
22 28 0.80
ACGTcount: A:0.55, C:0.06, G:0.03, T:0.36
Consensus pattern (22 bp):
ACTATATATTAATTAGTAAATA
Found at i:11948 original size:12 final size:12
Alignment explanation
Indices: 11931--11956 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
11921 TATTGAACAA
11931 GTGAAATTTAAG
1 GTGAAATTTAAG
11943 GTGAAATTTAAG
1 GTGAAATTTAAG
11955 GT
1 GT
11957 AACTATGTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.00, G:0.27, T:0.35
Consensus pattern (12 bp):
GTGAAATTTAAG
Found at i:23373 original size:35 final size:35
Alignment explanation
Indices: 23326--23428 Score: 120
Period size: 35 Copynumber: 2.9 Consensus size: 35
23316 GGGAACTTTG
*
23326 AAAACTGAATGGGAACTTTCCCAGTTTGAAAA-CTT
1 AAAACTG-ATGGGAACTTTCCCAATTTGAAAACCTT
*
23361 AAAAGCTGATGGGAACTTTCCCAATTTAAAAAACCTT
1 AAAA-CTGATGGGAACTTTCCCAATTT-GAAAACCTT
* *
23398 AAAACTGGTGGGAA-TATTCCCAATTAGAAAA
1 AAAACTGATGGGAACT-TTCCCAATTTGAAAA
23429 AAACTTGAAG
Statistics
Matches: 59, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
35 27 0.46
36 25 0.42
37 7 0.12
ACGTcount: A:0.41, C:0.17, G:0.17, T:0.26
Consensus pattern (35 bp):
AAAACTGATGGGAACTTTCCCAATTTGAAAACCTT
Found at i:23410 original size:36 final size:34
Alignment explanation
Indices: 23326--23422 Score: 115
Period size: 36 Copynumber: 2.7 Consensus size: 34
23316 GGGAACTTTG
* *
23326 AAAACTGAATGGGAACTTTCCCAGTTTGAAAACTT
1 AAAACTG-ATGGGAACTTTCCCAATTTAAAAACTT
23361 AAAAGCTGATGGGAACTTTCCCAATTTAAAAAACCTT
1 AAAA-CTGATGGGAACTTTCCCAATTT-AAAAA-CTT
*
23398 AAAACTGGTGGGAA-TATTCCCAATT
1 AAAACTGATGGGAACT-TTCCCAATT
23423 AGAAAAAAAC
Statistics
Matches: 55, Mismatches: 3, Indels: 7
0.85 0.05 0.11
Matches are distributed among these distances:
35 23 0.42
36 25 0.45
37 7 0.13
ACGTcount: A:0.38, C:0.18, G:0.16, T:0.28
Consensus pattern (34 bp):
AAAACTGATGGGAACTTTCCCAATTTAAAAACTT
Found at i:24055 original size:23 final size:22
Alignment explanation
Indices: 24029--24078 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 22
24019 GAACTCTTTA
* *
24029 CCCAAATAACTCACAATACAAGG
1 CCCAAACAACTAACAAT-CAAGG
* *
24052 CCCAACCAAGTAACAATCAAGG
1 CCCAAACAACTAACAATCAAGG
24074 CCCAA
1 CCCAA
24079 CAAGAATAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
22 10 0.43
23 13 0.57
ACGTcount: A:0.46, C:0.34, G:0.10, T:0.10
Consensus pattern (22 bp):
CCCAAACAACTAACAATCAAGG
Found at i:25720 original size:41 final size:41
Alignment explanation
Indices: 25590--25718 Score: 195
Period size: 41 Copynumber: 3.1 Consensus size: 41
25580 ACAAAAATAA
* * ** *
25590 GGACCAAATTGAATCAAATAGTAACCAGAATCCTAAATCAG
1 GGACCAAATTGTACCAAATAGTAAATAGAATCCTAAATTAG
*
25631 GGACTAAATTGTACCAAATAGTAAATAGAATCCTAAATTAG
1 GGACCAAATTGTACCAAATAGTAAATAGAATCCTAAATTAG
*
25672 GGACCATATTGTACCAAATAGTAAATAGAATCCTAAATTAG
1 GGACCAAATTGTACCAAATAGTAAATAGAATCCTAAATTAG
25713 GGACCA
1 GGACCA
25719 TACTAAACAC
Statistics
Matches: 80, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 80 1.00
ACGTcount: A:0.45, C:0.16, G:0.16, T:0.23
Consensus pattern (41 bp):
GGACCAAATTGTACCAAATAGTAAATAGAATCCTAAATTAG
Found at i:27926 original size:22 final size:22
Alignment explanation
Indices: 27898--27947 Score: 82
Period size: 22 Copynumber: 2.3 Consensus size: 22
27888 AAAAGGATGG
27898 ATGCAAAAGATACCATGCAAAA
1 ATGCAAAAGATACCATGCAAAA
* *
27920 ATGCAAAAGGTGCCATGCAAAA
1 ATGCAAAAGATACCATGCAAAA
27942 ATGCAA
1 ATGCAA
27948 CTATTAAACT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.50, C:0.18, G:0.18, T:0.14
Consensus pattern (22 bp):
ATGCAAAAGATACCATGCAAAA
Found at i:28333 original size:28 final size:28
Alignment explanation
Indices: 28301--28375 Score: 141
Period size: 28 Copynumber: 2.7 Consensus size: 28
28291 ACGTGCACTT
*
28301 AAAATGACCAAAATGCCCTTGGATATGC
1 AAAATGACCAAAATGCCCCTGGATATGC
28329 AAAATGACCAAAATGCCCCTGGATATGC
1 AAAATGACCAAAATGCCCCTGGATATGC
28357 AAAATGACCAAAATGCCCC
1 AAAATGACCAAAATGCCCC
28376 CTTAAGTGAC
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
28 46 1.00
ACGTcount: A:0.41, C:0.25, G:0.16, T:0.17
Consensus pattern (28 bp):
AAAATGACCAAAATGCCCCTGGATATGC
Found at i:29519 original size:163 final size:163
Alignment explanation
Indices: 29239--29534 Score: 425
Period size: 163 Copynumber: 1.8 Consensus size: 163
29229 GTATTGATAC
*
29239 ATGGAGGGAGAGATTTTTTTCTCCTTTTTTTGGAGGGAAAAATTCCCTCCCCACTAAAACAAAGA
1 ATGGAGGGAGAGATTTTTTTCTCCTTTGTTTGGAGGGAAAAATTCCCTCCCCACTAAAACAAAGA
* * *
29304 AAGCTTCCAACTCTAAACCTGTAATATATAGCGGCGTTTTAAAACAAGACGCCGTTAATTTGTGG
66 AAGCTTCCAACTCTAAACCTATAATATATAGCGGCGTTTTAAAACAAGACGCCGCTAATTAGTGG
29369 CGTCTAGAACAATAAACGCCGCTATTTTAATAT
131 CGTCTAGAACAATAAACGCCGCTATTTTAATAT
* * * *
29402 ATGGAGGGAGAGATTTTTTTTTTCTTTGTTTGGAGGGAAAAATTCCCTCTCC-CTAAAACAAAGT
1 ATGGAGGGAGAGATTTTTTTCTCCTTTGTTTGGAGGGAAAAATTCCCTCCCCACTAAAACAAAGA
** ** * **
29466 AATTTTCCAACTCTACGCCTATAATATATAGCGGTGTTTTTCTCAAC-AGACGCCGCTAATTAGT
66 AAGCTTCCAACTCTAAACCTATAATATATAGCGGCG-TTTT-AAAACAAGACGCCGCTAATTAGT
29530 GGCGT
129 GGCGT
29535 TTTTCTCACA
Statistics
Matches: 116, Mismatches: 15, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
162 41 0.35
163 72 0.62
164 3 0.03
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Consensus pattern (163 bp):
ATGGAGGGAGAGATTTTTTTCTCCTTTGTTTGGAGGGAAAAATTCCCTCCCCACTAAAACAAAGA
AAGCTTCCAACTCTAAACCTATAATATATAGCGGCGTTTTAAAACAAGACGCCGCTAATTAGTGG
CGTCTAGAACAATAAACGCCGCTATTTTAATAT
Done.