Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015439.1 Corchorus olitorius cultivar O-4 contig15472, 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: 56108
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--39 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1 TA TA TA TA 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 TA TA TA TA T
40 TTATGTATCA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:168 original size:16 final size:15
Alignment explanation
Indices: 147--177 Score: 53
Period size: 15 Copynumber: 2.0 Consensus size: 15
137 TATAATTAAC
147 TATTATAGCATTTATT
1 TATTATA-CATTTATT
163 TATTATACATTTATT
1 TATTATACATTTATT
178 CCTAATTCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.32, C:0.06, G:0.03, T:0.58
Consensus pattern (15 bp):
TATTATACATTTATT
Found at i:11446 original size:20 final size:20
Alignment explanation
Indices: 11421--11461 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
11411 TCACCTTCTC
11421 GCTGACATGTTAGGCCATTA
1 GCTGACATGTTAGGCCATTA
11441 GCTGACATGTTAGGCCATTA
1 GCTGACATGTTAGGCCATTA
11461 G
1 G
11462 TCACGTGAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.24, C:0.20, G:0.27, T:0.29
Consensus pattern (20 bp):
GCTGACATGTTAGGCCATTA
Found at i:16546 original size:34 final size:34
Alignment explanation
Indices: 16453--16618 Score: 152
Period size: 34 Copynumber: 5.0 Consensus size: 34
16443 CCGGTAGTCC
* *
16453 TCATATTAAGTTTTGATTAATCTGGAATCGATTCATG
1 TCATATTAAGTTTCGATTAATCTGGAATCGA--GA-G
*
16490 TCATCATATTAGATTTCGATTAATCTGGAATCGAGAG
1 TCAT-AT-TAAG-TTTCGATTAATCTGGAATCGAGAG
*
16527 TCATATTAAGTTTCAATTAATCTGGAATCGAGAG
1 TCATATTAAGTTTCGATTAATCTGGAATCGAGAG
16561 TC--A-T--G---CGA-TAATCTGGAATCGAGAG
1 TCATATTAAGTTTCGATTAATCTGGAATCGAGAG
* * *
16586 TCATACTAAGTTTCGACTAATTTGGAATCGAGA
1 TCATATTAAGTTTCGATTAATCTGGAATCGAGA
16619 CTAATCTGGA
Statistics
Matches: 110, Mismatches: 7, Indels: 27
0.76 0.05 0.19
Matches are distributed among these distances:
25 19 0.17
26 2 0.02
27 1 0.01
28 1 0.01
29 1 0.01
30 1 0.01
31 1 0.01
32 1 0.01
33 3 0.03
34 40 0.36
35 3 0.03
36 2 0.02
37 9 0.08
38 3 0.03
39 3 0.03
40 20 0.18
ACGTcount: A:0.33, C:0.13, G:0.19, T:0.35
Consensus pattern (34 bp):
TCATATTAAGTTTCGATTAATCTGGAATCGAGAG
Found at i:16622 original size:17 final size:17
Alignment explanation
Indices: 16600--16634 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
16590 ACTAAGTTTC
*
16600 GACTAATTTGGAATCGA
1 GACTAATCTGGAATCGA
16617 GACTAATCTGGAATCGA
1 GACTAATCTGGAATCGA
16634 G
1 G
16635 TCATGCGTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.34, C:0.14, G:0.26, T:0.26
Consensus pattern (17 bp):
GACTAATCTGGAATCGA
Found at i:16677 original size:41 final size:41
Alignment explanation
Indices: 16620--16703 Score: 168
Period size: 41 Copynumber: 2.0 Consensus size: 41
16610 GAATCGAGAC
16620 TAATCTGGAATCGAGTCATGCGTTCATAATCGGGTTGGGAA
1 TAATCTGGAATCGAGTCATGCGTTCATAATCGGGTTGGGAA
16661 TAATCTGGAATCGAGTCATGCGTTCATAATCGGGTTGGGAA
1 TAATCTGGAATCGAGTCATGCGTTCATAATCGGGTTGGGAA
16702 TA
1 TA
16704 CTATAGTTTC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.27, C:0.14, G:0.29, T:0.30
Consensus pattern (41 bp):
TAATCTGGAATCGAGTCATGCGTTCATAATCGGGTTGGGAA
Found at i:38270 original size:15 final size:15
Alignment explanation
Indices: 38229--38272 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
38219 TCCTATGTAG
38229 CAAAAG-GAAAAACAT
1 CAAAAGAGAAAAA-AT
* *
38244 CAAAACACAAAAAAT
1 CAAAAGAGAAAAAAT
38259 CAAAAGAGAAAAAA
1 CAAAAGAGAAAAAA
38273 GAGAAAAAGC
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
15 19 0.79
16 5 0.21
ACGTcount: A:0.73, C:0.14, G:0.09, T:0.05
Consensus pattern (15 bp):
CAAAAGAGAAAAAAT
Found at i:41007 original size:19 final size:20
Alignment explanation
Indices: 40983--41039 Score: 80
Period size: 19 Copynumber: 2.9 Consensus size: 20
40973 CTGTTTAGTA
40983 ACTGTACAGATGAGATTA-C
1 ACTGTACAGATGAGATTAGC
* *
41002 ACTGTACAGATTAGATTAGGT
1 ACTGTACAGATGAGATTA-GC
41023 ACTGTACAGATGAGATT
1 ACTGTACAGATGAGATT
41040 CTTAGAGCAG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
19 17 0.52
21 16 0.48
ACGTcount: A:0.35, C:0.12, G:0.23, T:0.30
Consensus pattern (20 bp):
ACTGTACAGATGAGATTAGC
Found at i:42181 original size:49 final size:49
Alignment explanation
Indices: 42109--42293 Score: 310
Period size: 49 Copynumber: 3.9 Consensus size: 49
42099 ACTTCAAAAG
42109 GGGTATGTATGTAAGTACATGGCTTGGGCTACTTGAACTAAGCCCAAGT
1 GGGTATGTATGTAAGTACATGGCTTGGGCTACTTGAACTAAGCCCAAGT
42158 GGGTATGTATGTAAGTACATGGCTTGGGCTACTTGAACTAAGCCCAAGT
1 GGGTATGTATGTAAGTACATGGCTTGGGCTACTTGAACTAAGCCCAAGT
42207 GGGTATGTATGTAAGTACATGGCTTGGGCTACTTGAACTAAGCCCAAGT
1 GGGTATGTATGTAAGTACATGGCTTGGGCTACTTGAACTAAGCCCAAGT
* *
42256 GGGTATGT-T-T--GTTC-T-GTTTGGGCTACTTGAACTAAGCC
1 GGGTATGTATGTAAGTACATGGCTTGGGCTACTTGAACTAAGCC
42294 TAGCTAGGTA
Statistics
Matches: 134, Mismatches: 2, Indels: 6
0.94 0.01 0.04
Matches are distributed among these distances:
43 22 0.16
44 1 0.01
45 3 0.02
47 1 0.01
48 1 0.01
49 106 0.79
ACGTcount: A:0.24, C:0.16, G:0.29, T:0.31
Consensus pattern (49 bp):
GGGTATGTATGTAAGTACATGGCTTGGGCTACTTGAACTAAGCCCAAGT
Found at i:46634 original size:3 final size:3
Alignment explanation
Indices: 46620--46652 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
46610 CTGTTAGGCT
*
46620 TCA TCT TCA TCA TCA TCA TCA TCA TCA TC- TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA T
46653 TAATTAATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.27, C:0.33, G:0.00, T:0.39
Consensus pattern (3 bp):
TCA
Found at i:53000 original size:20 final size:20
Alignment explanation
Indices: 52975--53013 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
52965 TTATACGAGA
52975 CTTGT-ATGATAGAACTAGAT
1 CTTGTAATGA-AGAACTAGAT
52995 CTTGTAAATGAAGAACTAG
1 CTTGT-AATGAAGAACTAG
53014 CCAAAAGGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 5 0.29
21 8 0.47
22 4 0.24
ACGTcount: A:0.38, C:0.10, G:0.21, T:0.31
Consensus pattern (20 bp):
CTTGTAATGAAGAACTAGAT
Done.