Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023309.1 Corchorus olitorius cultivar O-4 contig23342, 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: 37958
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.32
Found at i:13017 original size:39 final size:39
Alignment explanation
Indices: 12939--13019 Score: 108
Period size: 39 Copynumber: 2.1 Consensus size: 39
12929 ACACGATTAT
* *
12939 TCATAAAGCTATGTCTATATGGAAAGACATATGTATTGA
1 TCATAAAGCTATGTCTATATGAAAAGACATATATATTGA
* * * *
12978 TCATAAAGTTATGTCTATATGAAAATACATGTATGTTGA
1 TCATAAAGCTATGTCTATATGAAAAGACATATATATTGA
13017 TCA
1 TCA
13020 AGTATATAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.36
Consensus pattern (39 bp):
TCATAAAGCTATGTCTATATGAAAAGACATATATATTGA
Found at i:20270 original size:84 final size:84
Alignment explanation
Indices: 20095--20340 Score: 311
Period size: 84 Copynumber: 2.9 Consensus size: 84
20085 TTCTTCCTCC
20095 CCAAAGTCCCAAAACACATTTATAACACAGGGGCAATAT-TCTCTTCAAAAGTCCTCAAGCACAT
1 CCAAAGTCCCAAAACACATTTATAACACAGGGGCAAT-TCTCTC-T-AAAAGTCCTCAAGCACAT
* *
20159 TTATAACATAAAGGCATTCATA
63 TTATAACACATAGGCATTCATA
* * *
20181 CCAAAGTCCCTAAACACATTTATAACACATGGGTAATTCTCTCTAAAAGTCCTCAAGCACATTTA
1 CCAAAGTCCCAAAACACATTTATAACACAGGGGCAATTCTCTCTAAAAGTCCTCAAGCACATTTA
*
20246 TAATACATAGGCA-TCTATA
66 TAACACATAGGCATTC-ATA
* * * * * *
20265 TCAAAGTCCCCAAGCACATTTATAACACAGGGGCAGTTCTCTC--AAAGTCTTCAAGCACATATA
1 CCAAAGTCCCAAAACACATTTATAACACAGGGGCAATTCTCTCTAAAAGTCCTCAAGCACATTTA
*
20328 TAACACATGGGCA
66 TAACACATAGGCA
20341 ATTATCTATT
Statistics
Matches: 142, Mismatches: 16, Indels: 8
0.86 0.10 0.05
Matches are distributed among these distances:
82 29 0.20
83 2 0.01
84 71 0.50
85 2 0.01
86 38 0.27
ACGTcount: A:0.38, C:0.25, G:0.12, T:0.25
Consensus pattern (84 bp):
CCAAAGTCCCAAAACACATTTATAACACAGGGGCAATTCTCTCTAAAAGTCCTCAAGCACATTTA
TAACACATAGGCATTCATA
Found at i:20279 original size:41 final size:41
Alignment explanation
Indices: 20142--20340 Score: 159
Period size: 41 Copynumber: 4.8 Consensus size: 41
20132 ATTCTCTTCA
* * * *
20142 AAAGTCCTCAAGCACATTTATAACATAAAGGCAT-TCATACC
1 AAAGTCCCCAAGCACATTTATAACACATAGGCATCT-ATATC
* * * * * * *
20183 AAAGTCCCTAAACACATTTATAACACATGGGTAATTCTCTCTA
1 AAAGTCCCCAAGCACATTTATAACACATAGG-CA-TCTATATC
* *
20226 AAAGTCCTCAAGCACATTTATAATACATAGGCATCTATATC
1 AAAGTCCCCAAGCACATTTATAACACATAGGCATCTATATC
** * *
20267 AAAGTCCCCAAGCACATTTATAACACAGGGGCAGT-TCTCTC
1 AAAGTCCCCAAGCACATTTATAACACATAGGCA-TCTATATC
** * *
20308 AAAGTCTTCAAGCACATATATAACACATGGGCA
1 AAAGTCCCCAAGCACATTTATAACACATAGGCA
20341 ATTATCTATT
Statistics
Matches: 124, Mismatches: 30, Indels: 8
0.77 0.19 0.05
Matches are distributed among these distances:
41 92 0.74
42 3 0.02
43 28 0.23
44 1 0.01
ACGTcount: A:0.38, C:0.24, G:0.12, T:0.26
Consensus pattern (41 bp):
AAAGTCCCCAAGCACATTTATAACACATAGGCATCTATATC
Found at i:25384 original size:2 final size:2
Alignment explanation
Indices: 25367--25415 Score: 80
Period size: 2 Copynumber: 24.5 Consensus size: 2
25357 TTTGAGCAAC
* *
25367 AG AG AA AG AC AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
25409 AG AG AG A
1 AG AG AG A
25416 ATTCTTACAG
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.53, C:0.02, G:0.45, T:0.00
Consensus pattern (2 bp):
AG
Found at i:26767 original size:17 final size:17
Alignment explanation
Indices: 26747--26779 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
26737 TTATATGGAT
26747 ATTTAT-ATTATTAATTA
1 ATTTATAATT-TTAATTA
26764 ATTTATAATTTTAATT
1 ATTTATAATTTTAATT
26780 GATGTAATGA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.80
18 3 0.20
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
ATTTATAATTTTAATTA
Found at i:27924 original size:93 final size:97
Alignment explanation
Indices: 27740--27931 Score: 302
Period size: 93 Copynumber: 2.0 Consensus size: 97
27730 TAAACTTTTT
*
27740 AATTAAACTAGTAATAATATGGTAAAAATAAAATAGGTATAAGGATATTAGATTTAATTAAATAA
1 AATTAAAATAGTAATAATATGGTAAAAATAAAATAGGTATAAGGATATTAGATTTAATTAAATAA
* *
27805 AAATAGAGTTTTTAGTTAAGTGAAACTA-TAA
66 AAATAGAGTTTTTAGTTAACTAAAACTATTAA
* *
27836 AATTAAAATAGT-A-AA-ATGGTAAATATAAAATAGTTATAAGGATATTAGATTTAATTAAATAA
1 AATTAAAATAGTAATAATATGGTAAAAATAAAATAGGTATAAGGATATTAGATTTAATTAAATAA
*
27898 AAATAGAGTTTTTAGTTGACTAAAACTATTAA
66 AAATAGAGTTTTTAGTTAACTAAAACTATTAA
27930 AA
1 AA
27932 AATGGCATTT
Statistics
Matches: 89, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
93 70 0.79
94 7 0.08
95 1 0.01
96 11 0.12
ACGTcount: A:0.52, C:0.02, G:0.12, T:0.34
Consensus pattern (97 bp):
AATTAAAATAGTAATAATATGGTAAAAATAAAATAGGTATAAGGATATTAGATTTAATTAAATAA
AAATAGAGTTTTTAGTTAACTAAAACTATTAA
Found at i:28838 original size:10 final size:10
Alignment explanation
Indices: 28799--28856 Score: 59
Period size: 10 Copynumber: 6.1 Consensus size: 10
28789 TAATTAATTC
*
28799 AAATAATCAA
1 AAATAATTAA
*
28809 AAATAATAAA
1 AAATAATTAA
28819 AAATAATTAA
1 AAATAATTAA
*
28829 AAATAGTT--
1 AAATAATTAA
28837 AAATAA-TAA
1 AAATAATTAA
*
28846 AAATTATTAA
1 AAATAATTAA
28856 A
1 A
28857 GGGACCCATG
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
7 1 0.03
8 5 0.12
9 5 0.12
10 29 0.73
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.28
Consensus pattern (10 bp):
AAATAATTAA
Done.