Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023428.1 Corchorus olitorius cultivar O-4 contig23461, 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: 10145
ACGTcount: A:0.30, C:0.23, G:0.21, T:0.26
Found at i:71 original size:9 final size:9
Alignment explanation
Indices: 57--82 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
47 GATGTATGGT
57 TTTTTTTTA
1 TTTTTTTTA
66 TTTTTTTTA
1 TTTTTTTTA
75 TTTTTTTT
1 TTTTTTTT
83 CCTGGGTTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.08, C:0.00, G:0.00, T:0.92
Consensus pattern (9 bp):
TTTTTTTTA
Found at i:1052 original size:21 final size:20
Alignment explanation
Indices: 1028--1098 Score: 97
Period size: 21 Copynumber: 3.4 Consensus size: 20
1018 AAAGTGCTAA
* *
1028 GACCAATTTATTAAAACAAGT
1 GACCAAGTT-TTAAGACAAGT
1049 GACCCAAGTTTTAAGACAAGT
1 GA-CCAAGTTTTAAGACAAGT
1070 GACCAAAGTTTTAAGACAAGT
1 GACC-AAGTTTTAAGACAAGT
1091 GACCAAGT
1 GACCAAGT
1099 GTAAATATCC
Statistics
Matches: 46, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
20 6 0.13
21 34 0.74
22 6 0.13
ACGTcount: A:0.42, C:0.17, G:0.17, T:0.24
Consensus pattern (20 bp):
GACCAAGTTTTAAGACAAGT
Found at i:1981 original size:41 final size:41
Alignment explanation
Indices: 1879--2206 Score: 351
Period size: 41 Copynumber: 7.8 Consensus size: 41
1869 CAATAACCAA
* *
1879 AAAGTCCCCAAACACATATATAACACAGGGGCAATTCTAT-TCC
1 AAAGTCCCCAAACACATATATAACACAGAGGC-A-CCTATAT-C
*
1922 AAAAGTCCTCAAACACATATATAACACAGAGGCACCTATATC
1 -AAAGTCCCCAAACACATATATAACACAGAGGCACCTATATC
* * * *
1964 CAAGTCCCCAAACAC--ATATAACACAGGGGCGCCTTTATTAC
1 AAAGTCCCCAAACACATATATAACACAGAGGCACCTATA-T-C
* * *
2005 AAAGTCCTCAAACACATATATAACACAGAGCCATCTATATC
1 AAAGTCCCCAAACACATATATAACACAGAGGCACCTATATC
*
2046 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTAT-TAC
1 AAAGTCCCCAAACACATATATAACACAGAGGC-AC-CTATAT-C
* **
2089 AAAGTCCTCAAACACATATATAACACAGAGGCATTTATATC
1 AAAGTCCCCAAACACATATATAACACAGAGGCACCTATATC
* *
2130 AAAGTCCCCAAACACATATATAACATAGGGGCATCTCTAT-TAC
1 AAAGTCCCCAAACACATATATAACACAGAGGCA-C-CTATAT-C
*
2173 AAAAGTCCTCAAACACATATATAACACAGAGGCA
1 -AAAGTCCCCAAACACATATATAACACAGAGGCA
2207 TTTCTCCTTA
Statistics
Matches: 240, Mismatches: 31, Indels: 26
0.81 0.10 0.09
Matches are distributed among these distances:
39 19 0.08
40 1 0.00
41 91 0.38
42 11 0.05
43 58 0.24
44 60 0.25
ACGTcount: A:0.42, C:0.27, G:0.11, T:0.20
Consensus pattern (41 bp):
AAAGTCCCCAAACACATATATAACACAGAGGCACCTATATC
Found at i:2093 original size:84 final size:85
Alignment explanation
Indices: 1879--2207 Score: 531
Period size: 84 Copynumber: 3.9 Consensus size: 85
1869 CAATAACCAA
* *
1879 AAAGTCCCCAAACACATATATAACACAGGGGCAATTCTATTCCAAAAGTCCTCAAACACATATAT
1 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACAAAAGTCCTCAAACACATATAT
*
1944 AACACAGAGGCACCTATATC
66 AACACAGAGGCATCTATATC
* ** *
1964 CAAGTCCCCAAACAC--ATATAACACAGGGGCGCCTTTATTAC-AAAGTCCTCAAACACATATAT
1 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACAAAAGTCCTCAAACACATATAT
*
2026 AACACAGAGCCATCTATATC
66 AACACAGAGGCATCTATATC
2046 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTAC-AAAGTCCTCAAACACATATAT
1 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACAAAAGTCCTCAAACACATATAT
*
2110 AACACAGAGGCATTTATATC
66 AACACAGAGGCATCTATATC
* *
2130 AAAGTCCCCAAACACATATATAACATAGGGGCATCTCTATTACAAAAGTCCTCAAACACATATAT
1 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACAAAAGTCCTCAAACACATATAT
2195 AACACAGAGGCAT
66 AACACAGAGGCAT
2208 TTCTCCTTAT
Statistics
Matches: 225, Mismatches: 16, Indels: 6
0.91 0.06 0.02
Matches are distributed among these distances:
82 53 0.24
83 21 0.09
84 103 0.46
85 48 0.21
ACGTcount: A:0.42, C:0.26, G:0.11, T:0.21
Consensus pattern (85 bp):
AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACAAAAGTCCTCAAACACATATAT
AACACAGAGGCATCTATATC
Found at i:2328 original size:2 final size:2
Alignment explanation
Indices: 2316--2344 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
2306 ACAAAATTCC
2316 TA TA T- 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
2345 CACACACATA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2355 original size:14 final size:14
Alignment explanation
Indices: 2338--2369 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
2328 ATATATATAT
2338 ATATATACACACAC
1 ATATATACACACAC
2352 ATATATACACACAC
1 ATATATACACACAC
2366 ATAT
1 ATAT
2370 GTGACAAAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (14 bp):
ATATATACACACAC
Found at i:3793 original size:24 final size:24
Alignment explanation
Indices: 3764--3818 Score: 110
Period size: 24 Copynumber: 2.3 Consensus size: 24
3754 ATGCATTAGG
3764 AGCAGGAAGAATCCTCCAACCAGC
1 AGCAGGAAGAATCCTCCAACCAGC
3788 AGCAGGAAGAATCCTCCAACCAGC
1 AGCAGGAAGAATCCTCCAACCAGC
3812 AGCAGGA
1 AGCAGGA
3819 GAACTCAGCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.38, C:0.31, G:0.24, T:0.07
Consensus pattern (24 bp):
AGCAGGAAGAATCCTCCAACCAGC
Done.