Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018391.1 Corchorus olitorius cultivar O-4 contig18424, 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: 17995
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--40 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
41 CTAGCATTAG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2227 original size:11 final size:11
Alignment explanation
Indices: 2213--2250 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
2203 ATTCATAACA
2213 AATTTATAATT
1 AATTTATAATT
2224 AATTTATAATT
1 AATTTATAATT
2235 -ATTTGATAATT
1 AATTT-ATAATT
*
2246 TATTT
1 AATTT
2251 TATATAGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 4 0.16
11 17 0.68
12 4 0.16
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (11 bp):
AATTTATAATT
Found at i:6237 original size:2 final size:2
Alignment explanation
Indices: 6232--6257 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
6222 ACACACACAG
6232 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
6258 GTATCTTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:7644 original size:13 final size:13
Alignment explanation
Indices: 7626--7651 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
7616 TATTGATACT
7626 ATATAATATAATA
1 ATATAATATAATA
7639 ATATAATATAATA
1 ATATAATATAATA
7652 TTATTATCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
ATATAATATAATA
Found at i:8152 original size:15 final size:15
Alignment explanation
Indices: 8134--8162 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
8124 TTTTTATGTA
8134 TTTAATTAATTATAC
1 TTTAATTAATTATAC
8149 TTTAATTAATTATA
1 TTTAATTAATTATA
8163 AGGTACTTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.55
Consensus pattern (15 bp):
TTTAATTAATTATAC
Found at i:8728 original size:2 final size:2
Alignment explanation
Indices: 8721--8756 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
8711 CGTCCATTAT
8721 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
8757 AAGCTATACA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:13607 original size:19 final size:18
Alignment explanation
Indices: 13579--13614 Score: 63
Period size: 19 Copynumber: 1.9 Consensus size: 18
13569 CAGACTAATT
13579 TTTCATGGTTTATATGAA
1 TTTCATGGTTTATATGAA
13597 TTTCTATGGTTTATATGA
1 TTTC-ATGGTTTATATGA
13615 TTCTTTATTG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.25, C:0.06, G:0.17, T:0.53
Consensus pattern (18 bp):
TTTCATGGTTTATATGAA
Found at i:17913 original size:161 final size:162
Alignment explanation
Indices: 17682--17988 Score: 465
Period size: 161 Copynumber: 1.9 Consensus size: 162
17672 GATGGAGAGG
* *
17682 CTTTTTTTGGAGGGAAAAATTCTCTCCCCCCCAAAACAAAGAAAGTTTCCAACTCTACGCCTACA
1 CTTTTTTTGGAGAGAAAAATTCCCTCCCCCCCAAAACAAAGAAAGTTTCCAACTCTACGCCTACA
* *
17747 ATATATAGCAGCGTTTTGGCATA-AGACGCCGCTAAGTAGTGGCGTCTAGAAAAGGAAATGCCGC
66 ATATATAGCAGCGTTTTCGCA-ACAGACGCCGCTAAGTAGTGGCGTCTAGAAAAGGAAACGCCGC
* *
17811 TATTTTAATATATGGAGGGAAGGATTTCTTTTC
130 AATTGTAATATATGGAGGGAAGGATTTCTTTTC
* ** *
17844 CTTTTTTTGGAGAGAAAAATTCCCT-CCCCCTAAAACAAAGAATTTTTCCAACTCTACGCCTATA
1 CTTTTTTTGGAGAGAAAAATTCCCTCCCCCCCAAAACAAAGAAAGTTTCCAACTCTACGCCTACA
* * * *
17908 ATATATAGCGGCGTTTTCTCAACAGACGCCGCTAATTAGTGGCGTCTAGGAAAGGAAACGCCGCA
66 ATATATAGCAGCGTTTTCGCAACAGACGCCGCTAAGTAGTGGCGTCTAGAAAAGGAAACGCCGCA
17973 ATTGTAATATATGGAG
131 ATTGTAATATATGGAG
17989 TGAGCGA
Statistics
Matches: 130, Mismatches: 14, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
160 1 0.01
161 106 0.82
162 23 0.18
ACGTcount: A:0.31, C:0.21, G:0.20, T:0.28
Consensus pattern (162 bp):
CTTTTTTTGGAGAGAAAAATTCCCTCCCCCCCAAAACAAAGAAAGTTTCCAACTCTACGCCTACA
ATATATAGCAGCGTTTTCGCAACAGACGCCGCTAAGTAGTGGCGTCTAGAAAAGGAAACGCCGCA
ATTGTAATATATGGAGGGAAGGATTTCTTTTC
Done.