Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022831.1 Corchorus olitorius cultivar O-4 contig22864, 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: 2474
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.27
Found at i:2016 original size:11 final size:11
Alignment explanation
Indices: 1997--2030 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
1987 AGGTCTATGT
1997 TTAGAATCTCA
1 TTAGAATCTCA
*
2008 TTGGAATCTCA
1 TTAGAATCTCA
*
2019 TTAGTATCTCA
1 TTAGAATCTCA
2030 T
1 T
2031 ATTAAGTAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.29, C:0.18, G:0.12, T:0.41
Consensus pattern (11 bp):
TTAGAATCTCA
Found at i:2092 original size:50 final size:49
Alignment explanation
Indices: 2032--2167 Score: 166
Period size: 50 Copynumber: 2.7 Consensus size: 49
2022 GTATCTCATA
*
2032 TTAAGTAAACCTGCTTAGGTCTACGTTTAGAATCTCATCAGAATTT-CTGT
1 TTAAGAAAACCTGCTTAGGTCT-CGTTTAGAATCTCATCAGAATTTGC-GT
* * *
2082 TTAAGAAAACCTGCTTAGGCCCCCGTTTAAAATCTCATCAGAATTTGCGT
1 TTAAGAAAACCTGCTTAGG-TCTCGTTTAGAATCTCATCAGAATTTGCGT
* * *
2132 TTAATAAAACCTGCGTAGGTCCTTGTTTAGAATCTC
1 TTAAGAAAACCTGCTTAGGT-CTCGTTTAGAATCTC
2168 CATTTAAGCA
Statistics
Matches: 73, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
50 71 0.97
51 2 0.03
ACGTcount: A:0.29, C:0.21, G:0.16, T:0.35
Consensus pattern (49 bp):
TTAAGAAAACCTGCTTAGGTCTCGTTTAGAATCTCATCAGAATTTGCGT
Found at i:2286 original size:39 final size:39
Alignment explanation
Indices: 2243--2416 Score: 141
Period size: 38 Copynumber: 4.5 Consensus size: 39
2233 AGTTTTGGTC
2243 AAGTAAACCTGCTTAGGT-C-CCTATATA-AAGTTGCCATTT
1 AAGTAAACCTGCTTAGGTCCTCCT-T-TAGAA-TTGCCATTT
*
2282 AAGTAAACCTGCTTAGGTCCTCCTTTAGAATTTCCATTT
1 AAGTAAACCTGCTTAGGTCCTCCTTTAGAATTGCCATTT
* * *
2321 TAGTAAACCTGCTTAGG-CCT-CTGCTTAGAGCTT--CGTTT
1 AAGTAAACCTGCTTAGGTCCTCCT--TTAGA-ATTGCCATTT
** * *
2359 AAGTAAACCTGCTTAGGT-CTATGTTTAGAATT-TCATCT
1 AAGTAAACCTGCTTAGGTCCT-CCTTTAGAATTGCCATTT
*
2397 AAGAAAACCTGCTTAGGTCC
1 AAGTAAACCTGCTTAGGTCC
2417 CGGCCTAGAA
Statistics
Matches: 114, Mismatches: 10, Indels: 22
0.78 0.07 0.15
Matches are distributed among these distances:
37 4 0.04
38 50 0.44
39 50 0.44
40 7 0.06
41 3 0.03
ACGTcount: A:0.27, C:0.21, G:0.17, T:0.35
Consensus pattern (39 bp):
AAGTAAACCTGCTTAGGTCCTCCTTTAGAATTGCCATTT
Found at i:2371 original size:77 final size:78
Alignment explanation
Indices: 2279--2455 Score: 209
Period size: 77 Copynumber: 2.3 Consensus size: 78
2269 AAAGTTGCCA
* * *
2279 TTTAAGTAAACCTGCTTAGGTCCT-CCTTTAGAATTTCCATTTTAGTAAACCTGCTTAGG-CCTC
1 TTTAAGTAAACCTGCTTAGGTCCTACCTTTAGAATTT-CATCTAAGAAAACCTGCTTAGGTCC-C
* * *
2342 TGCTTAGAGCTTC-G
64 GGCCTAGAACTTCTG
**
2356 TTTAAGTAAACCTGCTTAGGT-CTATGTTTAGAATTTCATCTAAGAAAACCTGCTTAGGTCCCGG
1 TTTAAGTAAACCTGCTTAGGTCCTACCTTTAGAATTTCATCTAAGAAAACCTGCTTAGGTCCCGG
*
2420 CCTAGAATTTCTG
66 CCTAGAACTTCTG
* *
2433 CTTAAGAAAACCTGCTTAGGTCC
1 TTTAAGTAAACCTGCTTAGGTCC
2456 CCGCTAAGAA
Statistics
Matches: 85, Mismatches: 11, Indels: 7
0.83 0.11 0.07
Matches are distributed among these distances:
76 31 0.36
77 53 0.62
78 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.18, T:0.35
Consensus pattern (78 bp):
TTTAAGTAAACCTGCTTAGGTCCTACCTTTAGAATTTCATCTAAGAAAACCTGCTTAGGTCCCGG
CCTAGAACTTCTG
Found at i:2373 original size:38 final size:39
Alignment explanation
Indices: 2201--2455 Score: 195
Period size: 39 Copynumber: 6.6 Consensus size: 39
2191 CTCTGTTCCG
* **
2201 TTTAAGTAAACCTGTTTAGGAT-CTCTGCTTAGAGTTTTG
1 TTTAAGTAAACCTGCTTAGG-TCCTCTGCTTAGAGTTTCA
* * * * *
2240 GTCAAGTAAACCTGCTTAGGTCC-CT-ATATAAAGTTGCCA
1 TTTAAGTAAACCTGCTTAGGTCCTCTGCT-TAGAGTT-TCA
*
2279 TTTAAGTAAACCTGCTTAGGTCCTC--CTTTAGAATTTCCA
1 TTTAAGTAAACCTGCTTAGGTCCTCTGC-TTAGAGTTT-CA
* * *
2318 TTTTAGTAAACCTGCTTAGG-CCTCTGCTTAGAGCTTCG
1 TTTAAGTAAACCTGCTTAGGTCCTCTGCTTAGAGTTTCA
* * *
2356 TTTAAGTAAACCTGCTTAGGT-CTATGTTTAGAATTTCA
1 TTTAAGTAAACCTGCTTAGGTCCTCTGCTTAGAGTTTCA
* * * * *
2394 TCTAAGAAAACCTGCTTAGGTCC-CGGCCTAGAATTTC-
1 TTTAAGTAAACCTGCTTAGGTCCTCTGCTTAGAGTTTCA
*
2431 TGCTTAAGAAAACCTGCTTAGGTCC
1 T--TTAAGTAAACCTGCTTAGGTCC
2456 CCGCTAAGAA
Statistics
Matches: 173, Mismatches: 31, Indels: 24
0.76 0.14 0.11
Matches are distributed among these distances:
37 2 0.01
38 74 0.43
39 94 0.54
40 3 0.02
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.35
Consensus pattern (39 bp):
TTTAAGTAAACCTGCTTAGGTCCTCTGCTTAGAGTTTCA
Found at i:2466 original size:39 final size:38
Alignment explanation
Indices: 2280--2466 Score: 132
Period size: 38 Copynumber: 4.8 Consensus size: 38
2270 AAGTTGCCAT
* **
2280 TTAAGTAAACCTGCTTAGGTCCTCCTTTAGAATTTCCAT-
1 TTAAGAAAACCTGCTTAGGTCC-CCGCTAGAATTT-CATC
* * * ** *
2319 TTTAGTAAACCTGCTTAGG-CCTCTGCTTAGAGCTTCGT-
1 TTAAGAAAACCTGCTTAGGTCC-CCGC-TAGAATTTCATC
* *** *
2357 TTAAGTAAACCTGCTTAGGTCTATGTTTAGAATTTCATC
1 TTAAGAAAACCTGCTTAGGTCCCCG-CTAGAATTTCATC
*
2396 -TAAGAAAACCTGCTTAGGTCCCGGCCTAGAATTTC-TGC
1 TTAAGAAAACCTGCTTAGGTCCCCG-CTAGAATTTCAT-C
2434 TTAAGAAAACCTGCTTAGGTCCCCGCTAAGAAT
1 TTAAGAAAACCTGCTTAGGTCCCCGCT-AGAAT
2467 CTCGTTTG
Statistics
Matches: 120, Mismatches: 21, Indels: 14
0.77 0.14 0.09
Matches are distributed among these distances:
37 1 0.01
38 66 0.55
39 53 0.44
ACGTcount: A:0.26, C:0.22, G:0.18, T:0.34
Consensus pattern (38 bp):
TTAAGAAAACCTGCTTAGGTCCCCGCTAGAATTTCATC
Done.