Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017643.1 Corchorus olitorius cultivar O-4 contig17676, 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: 17277
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.34
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:1211 original size:82 final size:81
Alignment explanation
Indices: 1119--1281 Score: 247
Period size: 82 Copynumber: 2.0 Consensus size: 81
1109 ATAGTTTTAC
* * * * *
1119 TCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATAT-CTTATAACTATTTTATTTTAACAA
1 TCAACTAAAAAATCCATTTTTATATAATCAAATATAATATCCTTATAACTATTTTATTTT-ACAA
1183 TTTACTATTTTAAATTAA
65 TTTACTATTTT-AATTAA
*
1201 TCAACTAAAAAATCCATTTTTATATAATCAAATATAATATCCTTATAACTATTTTATTTTACCAT
1 TCAACTAAAAAATCCATTTTTATATAATCAAATATAATATCCTTATAACTATTTTATTTTACAAT
1266 TTACTATTTTAATTAA
66 TTACTATTTTAATTAA
1282 AAAAACTTTA
Statistics
Matches: 74, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
81 6 0.08
82 49 0.66
83 19 0.26
ACGTcount: A:0.40, C:0.12, G:0.00, T:0.47
Consensus pattern (81 bp):
TCAACTAAAAAATCCATTTTTATATAATCAAATATAATATCCTTATAACTATTTTATTTTACAAT
TTACTATTTTAATTAA
Found at i:1898 original size:7 final size:7
Alignment explanation
Indices: 1886--1916 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
1876 TTCTTGGTCA
1886 TTTGGGT
1 TTTGGGT
1893 TTTGGGT
1 TTTGGGT
1900 TTTGGGT
1 TTTGGGT
1907 TTTGGGT
1 TTTGGGT
1914 TTT
1 TTT
1917 TCGGGTCTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.39, T:0.61
Consensus pattern (7 bp):
TTTGGGT
Found at i:6628 original size:20 final size:19
Alignment explanation
Indices: 6591--6627 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
6581 GACTTATCTT
6591 GTCAAATCTTTAAAAAAAC
1 GTCAAATCTTTAAAAAAAC
6610 GTCAAATCTTTAAAAAAA
1 GTCAAATCTTTAAAAAAA
6628 AAGTCTAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.54, C:0.14, G:0.05, T:0.27
Consensus pattern (19 bp):
GTCAAATCTTTAAAAAAAC
Found at i:9048 original size:2 final size:2
Alignment explanation
Indices: 9041--9067 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
9031 CTAATCAAAT
9041 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 T
9068 TAGATGTAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:11212 original size:22 final size:21
Alignment explanation
Indices: 11175--11235 Score: 72
Period size: 21 Copynumber: 2.9 Consensus size: 21
11165 GGGACGTGGA
11175 CCTTGAAATTTGTCATTTTGCC
1 CCTT-AAATTTGTCATTTTGCC
*
11197 CCTTAAATTTGCTCATTTT-TC
1 CCTTAAATTTG-TCATTTTGCC
*
11218 CCTTGAATTTGT-ATTTTG
1 CCTTAAATTTGTCATTTTG
11236 GTTATATTTC
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
19 5 0.14
20 1 0.03
21 18 0.51
22 11 0.31
ACGTcount: A:0.18, C:0.20, G:0.11, T:0.51
Consensus pattern (21 bp):
CCTTAAATTTGTCATTTTGCC
Found at i:12542 original size:16 final size:17
Alignment explanation
Indices: 12521--12554 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
12511 TAAGTCATGC
12521 ACGTAGAA-TTAAAAAA
1 ACGTAGAATTTAAAAAA
12537 ACGTAGAATTTAAAAAA
1 ACGTAGAATTTAAAAAA
12554 A
1 A
12555 AACGTTAACT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.62, C:0.06, G:0.12, T:0.21
Consensus pattern (17 bp):
ACGTAGAATTTAAAAAA
Found at i:15528 original size:70 final size:69
Alignment explanation
Indices: 15406--15566 Score: 268
Period size: 70 Copynumber: 2.3 Consensus size: 69
15396 ATTTCCCGCA
* *
15406 ACAACTCCTGGACAGGACTTGGGTAACTCCTGCCCAGGTCTTGTCCTGTATTTCTGTGCTCCTCA
1 ACAAGTCCTGGACAGGACTTGGGTAACTCCTGCCCAGGTCTTGTCCTGTATTTCTGCGCTCCT-A
15471 ACAGC
65 ACAGC
* *
15476 ACAAGTCCGGGACAGGACTTGGGTAACTCCTGCCCAGGTCTTGTCCTGTATTTCTGCGTTCCTAA
1 ACAAGTCCTGGACAGGACTTGGGTAACTCCTGCCCAGGTCTTGTCCTGTATTTCTGCGCTCCTAA
15541 CAGC
66 CAGC
*
15545 CCAAGTCCTGGACAGGACTTGG
1 ACAAGTCCTGGACAGGACTTGG
15567 CCAAGATCTG
Statistics
Matches: 85, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
69 26 0.31
70 59 0.69
ACGTcount: A:0.19, C:0.30, G:0.24, T:0.27
Consensus pattern (69 bp):
ACAAGTCCTGGACAGGACTTGGGTAACTCCTGCCCAGGTCTTGTCCTGTATTTCTGCGCTCCTAA
CAGC
Found at i:16577 original size:22 final size:22
Alignment explanation
Indices: 16554--16597 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
16544 TTGGAGTGTT
16554 CCATTCTTGTTTCTTTTTTTTTC
1 CCATTCTT-TTTCTTTTTTTTTC
*
16577 CCCTTCTTTTTCTTTTTTTTT
1 CCATTCTTTTTCTTTTTTTTT
16598 AGAACAAGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.02, C:0.23, G:0.02, T:0.73
Consensus pattern (22 bp):
CCATTCTTTTTCTTTTTTTTTC
Done.