Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020075.1 Corchorus olitorius cultivar O-4 contig20108, 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: 20994
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:471 original size:36 final size:36
Alignment explanation
Indices: 424--493 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
414 TTCAATAACC
* *
424 TTACATCTTTTGTGATTTTGGTTATCATATTTCTTA
1 TTACATCTTTTGTAATTTTGATTATCATATTTCTTA
*
460 TTACATTTTTTGTAATTTTGATTATCATATTTCT
1 TTACATCTTTTGTAATTTTGATTATCATATTTCT
494 CCAAAATCTC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.21, C:0.10, G:0.09, T:0.60
Consensus pattern (36 bp):
TTACATCTTTTGTAATTTTGATTATCATATTTCTTA
Found at i:3958 original size:21 final size:21
Alignment explanation
Indices: 3932--3973 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
3922 GTTGTGTTTT
3932 CTTCTCAAT-AATTGCTCTAAC
1 CTTCTC-ATGAATTGCTCTAAC
*
3953 CTTCTCATGAATTTCTCTAAC
1 CTTCTCATGAATTGCTCTAAC
3974 AAATTCAGCC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 2 0.11
21 17 0.89
ACGTcount: A:0.26, C:0.29, G:0.05, T:0.40
Consensus pattern (21 bp):
CTTCTCATGAATTGCTCTAAC
Found at i:5926 original size:54 final size:54
Alignment explanation
Indices: 5844--5959 Score: 232
Period size: 54 Copynumber: 2.1 Consensus size: 54
5834 AGGTTTCCCA
5844 TTCACATAACATCTAGTGTGAAACAAATTCTCCCTTTGATTTTGAACATCCCCT
1 TTCACATAACATCTAGTGTGAAACAAATTCTCCCTTTGATTTTGAACATCCCCT
5898 TTCACATAACATCTAGTGTGAAACAAATTCTCCCTTTGATTTTGAACATCCCCT
1 TTCACATAACATCTAGTGTGAAACAAATTCTCCCTTTGATTTTGAACATCCCCT
5952 TTCACATA
1 TTCACATA
5960 TGCACTCAAA
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 62 1.00
ACGTcount: A:0.30, C:0.26, G:0.09, T:0.35
Consensus pattern (54 bp):
TTCACATAACATCTAGTGTGAAACAAATTCTCCCTTTGATTTTGAACATCCCCT
Found at i:6904 original size:26 final size:26
Alignment explanation
Indices: 6874--6923 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
6864 CTAATCAAGA
*
6874 AATCCCCAAATAACCTCCAAAACCAT
1 AATCCCCAAAAAACCTCCAAAACCAT
6900 AATCCCCAAAAAACCTCCAAAACC
1 AATCCCCAAAAAACCTCCAAAACC
6924 GCAAACTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.48, C:0.40, G:0.00, T:0.12
Consensus pattern (26 bp):
AATCCCCAAAAAACCTCCAAAACCAT
Found at i:8235 original size:34 final size:34
Alignment explanation
Indices: 8197--8302 Score: 146
Period size: 34 Copynumber: 3.2 Consensus size: 34
8187 GGGCGCATCA
* *
8197 GCAGGGTCGTCCAGTTATTATCACAACCCACTAG
1 GCAGGGTCTTCCAGTTATTATCACAACCCACTGG
* *
8231 GCAGGGTCTTCCAGTTATTAGCACAACCCTCTGGG
1 GCAGGGTCTTCCAGTTATTATCACAACCCACT-GG
8266 GCAGGGTCTTCCAGTTATTAT---AACCCACTGG
1 GCAGGGTCTTCCAGTTATTATCACAACCCACTGG
8297 GCAGGG
1 GCAGGG
8303 GCAATAAAAC
Statistics
Matches: 65, Mismatches: 6, Indels: 5
0.86 0.08 0.07
Matches are distributed among these distances:
31 8 0.12
32 7 0.11
34 29 0.45
35 21 0.32
ACGTcount: A:0.23, C:0.27, G:0.25, T:0.25
Consensus pattern (34 bp):
GCAGGGTCTTCCAGTTATTATCACAACCCACTGG
Found at i:11329 original size:15 final size:16
Alignment explanation
Indices: 11309--11342 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
11299 GTTTTCTAAG
*
11309 ATTATATGTATTAT-A
1 ATTATATGAATTATGA
11324 ATTATATGAATTATGA
1 ATTATATGAATTATGA
11340 ATT
1 ATT
11343 GTTTTATGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (16 bp):
ATTATATGAATTATGA
Found at i:11574 original size:38 final size:38
Alignment explanation
Indices: 11532--11629 Score: 162
Period size: 39 Copynumber: 2.6 Consensus size: 38
11522 TGGACTCGTA
11532 CCTCAGGGGGTTAAACTGTTGGTAAGAGTGGACACATG
1 CCTCAGGGGGTTAAACTGTTGGTAAGAGTGGACACATG
* *
11570 CCTCAGGGGGTTAAACTGATTGGTAAGAGTGGACCCGTG
1 CCTCAGGGGGTTAAACTG-TTGGTAAGAGTGGACACATG
11609 CCTCAGGGGGTT-AACTGTTGG
1 CCTCAGGGGGTTAAACTGTTGG
11630 CTAGACTCGA
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
37 4 0.07
38 23 0.40
39 30 0.53
ACGTcount: A:0.22, C:0.17, G:0.36, T:0.24
Consensus pattern (38 bp):
CCTCAGGGGGTTAAACTGTTGGTAAGAGTGGACACATG
Found at i:11611 original size:39 final size:38
Alignment explanation
Indices: 11520--11629 Score: 168
Period size: 38 Copynumber: 2.9 Consensus size: 38
11510 GGCTGTGCAT
* *
11520 AGTGGACTCGTACCTCAGGGGGTTAAACTGTTGGTAAG
1 AGTGGACACGTGCCTCAGGGGGTTAAACTGTTGGTAAG
*
11558 AGTGGACACATGCCTCAGGGGGTTAAACTGATTGGTAAG
1 AGTGGACACGTGCCTCAGGGGGTTAAACTG-TTGGTAAG
*
11597 AGTGGACCCGTGCCTCAGGGGGTT-AACTGTTGG
1 AGTGGACACGTGCCTCAGGGGGTTAAACTGTTGG
11630 CTAGACTCGA
Statistics
Matches: 66, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
37 4 0.06
38 32 0.48
39 30 0.45
ACGTcount: A:0.23, C:0.17, G:0.35, T:0.25
Consensus pattern (38 bp):
AGTGGACACGTGCCTCAGGGGGTTAAACTGTTGGTAAG
Done.