Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023524.1 Corchorus olitorius cultivar O-4 contig23557, 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: 6118
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.31
Found at i:429 original size:18 final size:18
Alignment explanation
Indices: 386--429 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
376 ATATTTAATT
386 CTAATTTTAATTTTATTA
1 CTAATTTTAATTTTATTA
* *
404 TTATTTTTAA-TTTATATA
1 CTAATTTTAATTTTAT-TA
422 CTAATTTT
1 CTAATTTT
430 TCTTTGATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.64
Consensus pattern (18 bp):
CTAATTTTAATTTTATTA
Found at i:2307 original size:74 final size:72
Alignment explanation
Indices: 2227--2400 Score: 196
Period size: 73 Copynumber: 2.4 Consensus size: 72
2217 AAAAACGCTT
* *
2227 TTGATGGGAACTTTCCCACTTTGAAAAC-T-AAAACTGAAAATGACGGGAACTTTCCCTAAATTG
1 TTGATGGGAACTTTCCCAATTTAAAAACTTAAAAACTG--AAT---GGGAACTTTCCC-AAATTG
2290 -AAAAC-TAAAAC
60 AAAAACTTAAAAC
*
2301 TTGATGGGAACTTTCCCAATTTAAAAACTTTGAAAAACTGAATGGGAACTTTCCCAATTTGAAAA
1 TTGATGGGAACTTTCCCAATTTAAAAAC-TT-AAAAACTGAATGGGAACTTTCCCAAATTGAAAA
2366 ACTTAAAAC
64 ACTTAAAAC
* *
2375 -TGGTGGGAACTTTCCCAATTAAAAAA
1 TTGATGGGAACTTTCCCAATTTAAAAA
2401 ACTTTGAACA
Statistics
Matches: 89, Mismatches: 5, Indels: 13
0.83 0.05 0.12
Matches are distributed among these distances:
72 5 0.06
73 41 0.46
74 32 0.36
76 4 0.04
78 7 0.08
ACGTcount: A:0.40, C:0.17, G:0.15, T:0.28
Consensus pattern (72 bp):
TTGATGGGAACTTTCCCAATTTAAAAACTTAAAAACTGAATGGGAACTTTCCCAAATTGAAAAAC
TTAAAAC
Found at i:2347 original size:38 final size:37
Alignment explanation
Indices: 2296--2408 Score: 151
Period size: 38 Copynumber: 3.0 Consensus size: 37
2286 ATTGAAAACT
2296 AAAACTTGATGGGAACTTTCCCAATTTAAAAACTTTGA
1 AAAAC-TGATGGGAACTTTCCCAATTTAAAAACTTTGA
2334 AAAACTGAATGGGAACTTTCCCAATTTGAAAAAC-TT--
1 AAAACTG-ATGGGAACTTTCCCAATTT-AAAAACTTTGA
* *
2370 AAAACTGGTGGGAACTTTCCCAATTAAAAAAACTTTGA
1 AAAACTGATGGGAACTTTCCCAATT-TAAAAACTTTGA
2408 A
1 A
2409 CATGATGAAA
Statistics
Matches: 67, Mismatches: 2, Indels: 12
0.83 0.02 0.15
Matches are distributed among these distances:
35 23 0.34
36 9 0.13
37 2 0.03
38 27 0.40
39 6 0.09
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.28
Consensus pattern (37 bp):
AAAACTGATGGGAACTTTCCCAATTTAAAAACTTTGA
Found at i:2390 original size:73 final size:74
Alignment explanation
Indices: 2271--2408 Score: 210
Period size: 73 Copynumber: 1.9 Consensus size: 74
2261 TGAAAATGAC
*
2271 GGGAACTTTCCCTAAATTGAAAACTAAAACTTGATGGGAACTTTCCCAATT-TAAAAACTTTGAA
1 GGGAACTTTCCCTAAATTGAAAACTAAAACTTGATGGGAACTTTCCCAATTAAAAAAACTTTGAA
2335 AAACTGAAT
66 AAACTGAAT
* *
2344 GGGAACTTTCCC-AATTTGAAAAACTTAAAAC-TGGTGGGAACTTTCCCAATTAAAAAAACTTTG
1 GGGAACTTTCCCTAAATTG-AAAAC-TAAAACTTGATGGGAACTTTCCCAATTAAAAAAACTTTG
2407 AA
64 AA
2409 CATGATGAAA
Statistics
Matches: 59, Mismatches: 3, Indels: 5
0.88 0.04 0.07
Matches are distributed among these distances:
72 5 0.08
73 36 0.61
74 18 0.31
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (74 bp):
GGGAACTTTCCCTAAATTGAAAACTAAAACTTGATGGGAACTTTCCCAATTAAAAAAACTTTGAA
AAACTGAAT
Found at i:2391 original size:35 final size:35
Alignment explanation
Indices: 2228--2404 Score: 166
Period size: 35 Copynumber: 4.9 Consensus size: 35
2218 AAAACGCTTT
*
2228 TGATGGGAACTTTCCCACTTTG-AAAAC-TAAAAC
1 TGATGGGAACTTTCCCAATTTGAAAAACTTAAAAC
*
2261 TGAAAATGACGGGAACTTTCCCTAAATTG-AAAAC-TAAAAC
1 TG---AT---GGGAACTTTCCC-AATTTGAAAAACTTAAAAC
2301 TTGATGGGAACTTTCCCAATTT-AAAAACTTTGAAAAAC
1 -TGATGGGAACTTTCCCAATTTGAAAAAC-TT--AAAAC
2339 TGAATGGGAACTTTCCCAATTTGAAAAACTTAAAAC
1 TG-ATGGGAACTTTCCCAATTTGAAAAACTTAAAAC
* **
2375 TGGTGGGAACTTTCCCAATTAAAAAAACTT
1 TGATGGGAACTTTCCCAATTTGAAAAACTT
2405 TGAACATGAT
Statistics
Matches: 123, Mismatches: 6, Indels: 28
0.78 0.04 0.18
Matches are distributed among these distances:
33 2 0.02
34 9 0.07
35 37 0.30
36 10 0.08
37 2 0.02
38 28 0.23
39 18 0.15
40 15 0.12
41 2 0.02
ACGTcount: A:0.40, C:0.18, G:0.15, T:0.28
Consensus pattern (35 bp):
TGATGGGAACTTTCCCAATTTGAAAAACTTAAAAC
Found at i:3384 original size:12 final size:12
Alignment explanation
Indices: 3367--3392 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
3357 ATATAGCCCC
3367 AAGCCCAAACAT
1 AAGCCCAAACAT
3379 AAGCCCAAACAT
1 AAGCCCAAACAT
3391 AA
1 AA
3393 ACATTAAGGC
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:0.54, C:0.31, G:0.08, T:0.08
Consensus pattern (12 bp):
AAGCCCAAACAT
Found at i:5864 original size:25 final size:25
Alignment explanation
Indices: 5830--5881 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
5820 GGACTCAATA
5830 CTGAGCCCAAAAGCAAATGTAACTT
1 CTGAGCCCAAAAGCAAATGTAACTT
5855 CTGAGCCCAAAAGCAAATGTAACTT
1 CTGAGCCCAAAAGCAAATGTAACTT
5880 CT
1 CT
5882 AATAATGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.38, C:0.25, G:0.15, T:0.21
Consensus pattern (25 bp):
CTGAGCCCAAAAGCAAATGTAACTT
Done.