Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019127.1 Corchorus olitorius cultivar O-4 contig19160, 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: 29363
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:2384 original size:17 final size:17
Alignment explanation
Indices: 2362--2395 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
2352 TCTCTCTCTC
2362 TCTCTCTCTCAAAAGTA
1 TCTCTCTCTCAAAAGTA
2379 TCTCTCTCTCAAAAGTA
1 TCTCTCTCTCAAAAGTA
2396 AAATTACCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.29, G:0.06, T:0.35
Consensus pattern (17 bp):
TCTCTCTCTCAAAAGTA
Found at i:4849 original size:19 final size:19
Alignment explanation
Indices: 4825--4863 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
4815 ATATAGGATT
4825 TTTTTTTGGCCAAAATATA
1 TTTTTTTGGCCAAAATATA
*
4844 TTTTTTTGGCCAAATTATA
1 TTTTTTTGGCCAAAATATA
4863 T
1 T
4864 ATACAGGATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.28, C:0.10, G:0.10, T:0.51
Consensus pattern (19 bp):
TTTTTTTGGCCAAAATATA
Found at i:5085 original size:6 final size:6
Alignment explanation
Indices: 5074--5121 Score: 62
Period size: 6 Copynumber: 7.7 Consensus size: 6
5064 TTGGGTTCAA
5074 TTTTCT TTTTCT TTTTCT TTTTCT TTTT-T GTTTTCAAT TTTTCT TTTT
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT -TTTTC--T TTTTCT TTTT
5122 GGTTTTTCTC
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
5 1 0.03
6 31 0.82
8 5 0.13
9 1 0.03
ACGTcount: A:0.04, C:0.12, G:0.02, T:0.81
Consensus pattern (6 bp):
TTTTCT
Found at i:5097 original size:18 final size:19
Alignment explanation
Indices: 5069--5127 Score: 68
Period size: 20 Copynumber: 3.1 Consensus size: 19
5059 CCACTTTGGG
*
5069 TTCAATTTTCTTTTTCT-TT
1 TTCATTTTTCTTTTT-TGTT
5088 TTC-TTTTTCTTTTTTGTT
1 TTCATTTTTCTTTTTTGTT
*
5106 TTCAATTTTTCTTTTTGGTT
1 TTC-ATTTTTCTTTTTTGTT
5126 TT
1 TT
5128 TCTCAGGTTG
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
17 1 0.03
18 15 0.43
19 3 0.09
20 16 0.46
ACGTcount: A:0.07, C:0.12, G:0.05, T:0.76
Consensus pattern (19 bp):
TTCATTTTTCTTTTTTGTT
Found at i:17967 original size:24 final size:21
Alignment explanation
Indices: 17939--17980 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
17929 CTTGTCACAT
17939 CATTATTAGTCAAACAGACAA
1 CATTATTAGTCAAACAGACAA
17960 CATTATTAGTCAAACAGACAA
1 CATTATTAGTCAAACAGACAA
17981 TATCATATAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.48, C:0.19, G:0.10, T:0.24
Consensus pattern (21 bp):
CATTATTAGTCAAACAGACAA
Found at i:19208 original size:2 final size:2
Alignment explanation
Indices: 19201--19231 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
19191 TAATTAAGTT
19201 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
19232 TTATCTGATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:29329 original size:2 final size:2
Alignment explanation
Indices: 29322--29358 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
29312 GGTTTGAAGT
29322 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
29359 ATTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Done.