Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021436.1 Corchorus olitorius cultivar O-4 contig21469, 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: 41220
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:10399 original size:7 final size:7
Alignment explanation
Indices: 10389--10413 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
10379 AAAGGGAAAA
10389 GGGGAAT
1 GGGGAAT
10396 GGGGAAT
1 GGGGAAT
10403 GGGGAAT
1 GGGGAAT
10410 GGGG
1 GGGG
10414 GGGGGGACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.24, C:0.00, G:0.64, T:0.12
Consensus pattern (7 bp):
GGGGAAT
Found at i:23094 original size:18 final size:20
Alignment explanation
Indices: 23058--23094 Score: 60
Period size: 18 Copynumber: 1.9 Consensus size: 20
23048 TGTACAGACT
23058 AATTAGTAGGGATTTGACAG
1 AATTAGTAGGGATTTGACAG
23078 AATTAG-AGGGA-TTGACA
1 AATTAGTAGGGATTTGACA
23095 ACCTAATTGC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
19 5 0.29
20 6 0.35
ACGTcount: A:0.38, C:0.05, G:0.30, T:0.27
Consensus pattern (20 bp):
AATTAGTAGGGATTTGACAG
Found at i:36310 original size:2 final size:2
Alignment explanation
Indices: 36303--36334 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
36293 TGAGCGTTGG
36303 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
36335 CCCTGTTATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:38636 original size:167 final size:167
Alignment explanation
Indices: 38351--38696 Score: 638
Period size: 167 Copynumber: 2.1 Consensus size: 167
38341 ATAATAACAA
* *
38351 ATTTACGAGTATCTATACCCTATTATTAAAGTTATCCCCAAACGCCTGTATGCTTAGCATTTGGC
1 ATTTA-GAATATCTATACCCTATTATTAAAGTTATCCCCAAACGCCTGTATGCTCAGCATTTGGC
38416 TCTTCCCATGCTGACATTTGTCCAACGTTAATTGGTTGGGAGAAAACCAATATATATTATTATAT
65 TCTTCCCATGCTGACATTTGTCCAACGTTAATTGGTTGGGAGAAAACCAATATATATTATTATAT
38481 ATATATTTAGAATTCCAAATACAATATTTATAAATAAT
130 ATATATTTAGAATTCCAAATACAATATTTATAAATAAT
38519 ATTTAGAATATCTATACCCTATTATTAAAGTTATCCCCAAACGCCTGTATGCTCAGCATTTGGCT
1 ATTTAGAATATCTATACCCTATTATTAAAGTTATCCCCAAACGCCTGTATGCTCAGCATTTGGCT
* *
38584 CTTCCCATGCTGACATTTGTCCAACGTTAATTGGTTGTGAGAAAATCAATATATATTATTATATA
66 CTTCCCATGCTGACATTTGTCCAACGTTAATTGGTTGGGAGAAAACCAATATATATTATTATATA
38649 TATATTTAGAATTCCAAATACAATATTTATAAATAAT
131 TATATTTAGAATTCCAAATACAATATTTATAAATAAT
*
38686 ATTTAAAATAT
1 ATTTAGAATAT
38697 TGAATTATAA
Statistics
Matches: 173, Mismatches: 5, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
167 168 0.97
168 5 0.03
ACGTcount: A:0.35, C:0.16, G:0.11, T:0.38
Consensus pattern (167 bp):
ATTTAGAATATCTATACCCTATTATTAAAGTTATCCCCAAACGCCTGTATGCTCAGCATTTGGCT
CTTCCCATGCTGACATTTGTCCAACGTTAATTGGTTGGGAGAAAACCAATATATATTATTATATA
TATATTTAGAATTCCAAATACAATATTTATAAATAAT
Found at i:39769 original size:18 final size:19
Alignment explanation
Indices: 39730--39769 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
39720 GTGCTCCTGT
39730 TGTGATGCTCCCACTTTTCAA
1 TGTGATGCTCCCA--TTTCAA
39751 TGTGATGCTCCCA-TTCAA
1 TGTGATGCTCCCATTTCAA
39769 T
1 T
39770 TCTGACCATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.32
21 13 0.68
ACGTcount: A:0.20, C:0.28, G:0.15, T:0.38
Consensus pattern (19 bp):
TGTGATGCTCCCATTTCAA
Found at i:40190 original size:28 final size:30
Alignment explanation
Indices: 40115--40190 Score: 81
Period size: 28 Copynumber: 2.6 Consensus size: 30
40105 AGAAGTAGTT
40115 AATAAAAAT-AAAATAAAAGCCAGAAAACG
1 AATAAAAATAAAAATAAAAGCCAGAAAACG
**
40144 AATAAAAA-AGAATAA-AAAAG-GTGAAAA-G
1 AATAAAAATA-AA-AATAAAAGCCAGAAAACG
40172 AATAAAAATAAAAATAAAA
1 AATAAAAATAAAAATAAAA
40191 AGTTAAGAGA
Statistics
Matches: 40, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
27 2 0.05
28 15 0.38
29 14 0.35
30 7 0.17
31 2 0.05
ACGTcount: A:0.74, C:0.04, G:0.11, T:0.12
Consensus pattern (30 bp):
AATAAAAATAAAAATAAAAGCCAGAAAACG
Found at i:40191 original size:29 final size:31
Alignment explanation
Indices: 40115--40192 Score: 78
Period size: 29 Copynumber: 2.7 Consensus size: 31
40105 AGAAGTAGTT
40115 AATAAAAAT-AAAAT-AAAAGCCAGAAAACG
1 AATAAAAATAAAAATAAAAAGCCAGAAAACG
* **
40144 AAT-AAAA-AAGAATAAAAAAG-GTGAAAA-G
1 AATAAAAATAAAAAT-AAAAAGCCAGAAAACG
40172 AATAAAAATAAAAATAAAAAG
1 AATAAAAATAAAAATAAAAAG
40193 TTAAGAGAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
28 12 0.30
29 18 0.45
30 10 0.25
ACGTcount: A:0.73, C:0.04, G:0.12, T:0.12
Consensus pattern (31 bp):
AATAAAAATAAAAATAAAAAGCCAGAAAACG
Done.