Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024344.1 Corchorus olitorius cultivar O-4 contig24377, 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: 18087
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Found at i:68 original size:22 final size:24
Alignment explanation
Indices: 29--75 Score: 71
Period size: 22 Copynumber: 2.0 Consensus size: 24
19 CATACTTGAC
29 ACAAGCAAGAAGAAAAAAACTTTG
1 ACAAGCAAGAAGAAAAAAACTTTG
*
53 ACAAGC-A-AAGAGAAAAACTTTG
1 ACAAGCAAGAAGAAAAAAACTTTG
75 A
1 A
76 AACTCTACAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 15 0.68
23 1 0.05
24 6 0.27
ACGTcount: A:0.57, C:0.13, G:0.17, T:0.13
Consensus pattern (24 bp):
ACAAGCAAGAAGAAAAAAACTTTG
Found at i:1898 original size:22 final size:21
Alignment explanation
Indices: 1873--1940 Score: 61
Period size: 22 Copynumber: 3.1 Consensus size: 21
1863 CCATTTAGTA
1873 ATTAAATATATATTATTTATTT
1 ATTAAA-ATATATTATTTATTT
*
1895 ATTAAGAACT-CATTATTTA-TT
1 ATTAA-AA-TATATTATTTATTT
1916 ATTTAAAATATATT-TATTATTT
1 A-TTAAAATATATTAT-TTATTT
1938 ATT
1 ATT
1941 TGATAGTATA
Statistics
Matches: 38, Mismatches: 2, Indels: 13
0.72 0.04 0.25
Matches are distributed among these distances:
20 2 0.05
21 13 0.34
22 21 0.55
23 2 0.05
ACGTcount: A:0.40, C:0.03, G:0.01, T:0.56
Consensus pattern (21 bp):
ATTAAAATATATTATTTATTT
Found at i:2346 original size:27 final size:27
Alignment explanation
Indices: 2316--2370 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
2306 CGTGCCTCTC
*
2316 ACACACAAAAAATT-CATTTTTTTTATA
1 ACACACAAAAAATTAC-TTTTTCTTATA
*
2343 ACACACACAAAATTACTTTTTCTTATA
1 ACACACAAAAAATTACTTTTTCTTATA
2370 A
1 A
2371 ATTCATATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 24 0.96
28 1 0.04
ACGTcount: A:0.44, C:0.18, G:0.00, T:0.38
Consensus pattern (27 bp):
ACACACAAAAAATTACTTTTTCTTATA
Found at i:2658 original size:30 final size:30
Alignment explanation
Indices: 2624--2684 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
2614 ATTTTTATCT
2624 TGACTTTTCTCTTATACCCTCAAATTTTAA
1 TGACTTTTCTCTTATACCCTCAAATTTTAA
2654 TGACTTTTCTCTTATACCCTCAAATTTTAA
1 TGACTTTTCTCTTATACCCTCAAATTTTAA
2684 T
1 T
2685 ATCTTACTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.26, C:0.23, G:0.03, T:0.48
Consensus pattern (30 bp):
TGACTTTTCTCTTATACCCTCAAATTTTAA
Found at i:3909 original size:30 final size:30
Alignment explanation
Indices: 3871--4309 Score: 589
Period size: 30 Copynumber: 14.7 Consensus size: 30
3861 GCTAATATAT
*
3871 ATTGACACCAGAAGTTGTCATGGTCTTACA
1 ATTGACACCAGAAGTTGTCATGCTCTTACA
* * *
3901 AATGACACCAAAAGTT-T-ATTCTACTTACA
1 ATTGACACCAGAAGTTGTCATGCT-CTTACA
*
3930 ATTGACACCAGAAGTTGTCATGGTCTTACA
1 ATTGACACCAGAAGTTGTCATGCTCTTACA
* *
3960 AATGACACCAGAAGTTGTCATGGTCTTACA
1 ATTGACACCAGAAGTTGTCATGCTCTTACA
* *
3990 AATGACACCAGAAGTTGTCATGGTCTTACA
1 ATTGACACCAGAAGTTGTCATGCTCTTACA
*
4020 ATTGACACCAGAAGTTGTCATGGTCTTACA
1 ATTGACACCAGAAGTTGTCATGCTCTTACA
* *
4050 ATTGACACCAGAAGTTGTCATGGTCGTACA
1 ATTGACACCAGAAGTTGTCATGCTCTTACA
* * *
4080 AATGACACCAGAAGTTGTCATGCTCCTGCA
1 ATTGACACCAGAAGTTGTCATGCTCTTACA
* *
4110 ATTGACACCAGAAGTTGTCATGCTCCTGCA
1 ATTGACACCAGAAGTTGTCATGCTCTTACA
* *
4140 ATTGACACCAGAAGTTGTCATGCTGTTGCA
1 ATTGACACCAGAAGTTGTCATGCTCTTACA
* * * *
4170 AGTGACACCAGAAGTTGTCATACTGTTGCA
1 ATTGACACCAGAAGTTGTCATGCTCTTACA
* *
4200 ATTGACACCATAAGTTGTCATGCTCTTGCA
1 ATTGACACCAGAAGTTGTCATGCTCTTACA
*
4230 ATTGACACCAGAAGTTGTCATGCTCTTGCA
1 ATTGACACCAGAAGTTGTCATGCTCTTACA
*
4260 ATTGACACCAGAAGTTGTCATGAT-TT-CA
1 ATTGACACCAGAAGTTGTCATGCTCTTACA
*
4288 ATTGACACCGGAAGTTGTCATG
1 ATTGACACCAGAAGTTGTCATG
4310 ATTTTACCTT
Statistics
Matches: 379, Mismatches: 27, Indels: 8
0.92 0.07 0.02
Matches are distributed among these distances:
28 26 0.07
29 23 0.06
30 327 0.86
31 3 0.01
ACGTcount: A:0.30, C:0.21, G:0.20, T:0.29
Consensus pattern (30 bp):
ATTGACACCAGAAGTTGTCATGCTCTTACA
Found at i:17059 original size:12 final size:12
Alignment explanation
Indices: 17042--17066 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
17032 TAAAGGAAAA
17042 AGCTAGGAAGGG
1 AGCTAGGAAGGG
17054 AGCTAGGAAGGG
1 AGCTAGGAAGGG
17066 A
1 A
17067 CCCTACTCCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.08, G:0.48, T:0.08
Consensus pattern (12 bp):
AGCTAGGAAGGG
Done.