Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016178.1 Corchorus olitorius cultivar O-4 contig16211, 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: 20599
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.31
Found at i:2843 original size:5 final size:6
Alignment explanation
Indices: 2828--2860 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
2818 ATAAAACATG
*
2828 AAAAAG AAAAAC -AAAAC AAAAAC AAAAAC AAAA
1 AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC AAAA
2861 GAGAATTTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
5 5 0.20
6 20 0.80
ACGTcount: A:0.85, C:0.12, G:0.03, T:0.00
Consensus pattern (6 bp):
AAAAAC
Found at i:2848 original size:11 final size:12
Alignment explanation
Indices: 2828--2860 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
2818 ATAAAACATG
*
2828 AAAAAGAAAAAC
1 AAAAACAAAAAC
2840 -AAAACAAAAAC
1 AAAAACAAAAAC
2851 AAAAACAAAA
1 AAAAACAAAA
2861 GAGAATTTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.85, C:0.12, G:0.03, T:0.00
Consensus pattern (12 bp):
AAAAACAAAAAC
Found at i:2854 original size:17 final size:17
Alignment explanation
Indices: 2828--2860 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2818 ATAAAACATG
*
2828 AAAAAGAAAAACAAAAC
1 AAAAACAAAAACAAAAC
2845 AAAAACAAAAACAAAA
1 AAAAACAAAAACAAAA
2861 GAGAATTTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.85, C:0.12, G:0.03, T:0.00
Consensus pattern (17 bp):
AAAAACAAAAACAAAAC
Found at i:11993 original size:25 final size:25
Alignment explanation
Indices: 11964--12017 Score: 99
Period size: 25 Copynumber: 2.2 Consensus size: 25
11954 AGTTTGGAAA
11964 ATTATAAGTCATTAATTAAAGGTAT
1 ATTATAAGTCATTAATTAAAGGTAT
*
11989 ATTATGAGTCATTAATTAAAGGTAT
1 ATTATAAGTCATTAATTAAAGGTAT
12014 ATTA
1 ATTA
12018 AAACAATATA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.43, C:0.04, G:0.13, T:0.41
Consensus pattern (25 bp):
ATTATAAGTCATTAATTAAAGGTAT
Found at i:12338 original size:96 final size:100
Alignment explanation
Indices: 12174--12449 Score: 425
Period size: 107 Copynumber: 2.7 Consensus size: 100
12164 TGGGTATAGT
* *
12174 TTCTAGTTCATAGGTTCAAGAGCAGATGTTATGAGATTTCAATTGTCTTTGTTGGAGAAGGGGTT
1 TTCTAGTTCATAAGTTCAAGAGCAGATGTTATGAGATTTCAATTGTCTTTGTTTGAGAAGGGGTT
*
12239 TGTTGGCTC-ATA-G-A-TTAACGTTTCGGTAATA
66 TGTTGGCTCGATATGTACTAAACGTTTCGGTAATA
12270 TTCTAGTTCATAAGTTCAAGAGCAGATGTTATGAGATTTCAATTGTCTTTGTTTGAGAAGGGGTT
1 TTCTAGTTCATAAGTTCAAGAGCAGATGTTATGAGATTTCAATTGTCTTTGTTTGAGAAGGGGTT
12335 TGTTGGCTTTCGGTAATATTGTAGCTAAACGTTTCGGTAATA
66 TGTTGGC--TC-G--ATA-TGTA-CTAAACGTTTCGGTAATA
*
12377 TTCTAGTTCATAAGTTCAAGAGCAGATGTTATGAGATTTCAATTGTCTTTATTTGAGAAGGGGTT
1 TTCTAGTTCATAAGTTCAAGAGCAGATGTTATGAGATTTCAATTGTCTTTGTTTGAGAAGGGGTT
12442 TGTTGGCT
66 TGTTGGCT
12450 TTCGGTAATA
Statistics
Matches: 165, Mismatches: 4, Indels: 13
0.91 0.02 0.07
Matches are distributed among these distances:
96 70 0.42
98 2 0.01
102 3 0.02
104 1 0.01
105 2 0.01
107 87 0.53
ACGTcount: A:0.25, C:0.10, G:0.25, T:0.40
Consensus pattern (100 bp):
TTCTAGTTCATAAGTTCAAGAGCAGATGTTATGAGATTTCAATTGTCTTTGTTTGAGAAGGGGTT
TGTTGGCTCGATATGTACTAAACGTTTCGGTAATA
Found at i:13032 original size:21 final size:21
Alignment explanation
Indices: 12994--13033 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
12984 TTATGGTGGA
* *
12994 ATTATATATCTAGCTATATAT
1 ATTATATATATAGATATATAT
*
13015 ATTATATATATATATATAT
1 ATTATATATATAGATATAT
13034 GCTTGCACTC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.42, C:0.05, G:0.03, T:0.50
Consensus pattern (21 bp):
ATTATATATATAGATATATAT
Done.