Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021787.1 Corchorus olitorius cultivar O-4 contig21820, 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: 26032
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.30
Found at i:1502 original size:36 final size:36
Alignment explanation
Indices: 1448--1517 Score: 122
Period size: 36 Copynumber: 1.9 Consensus size: 36
1438 GAGATTTTGG
* *
1448 AGAACTATGATAATCAAAATTACAAAAAATGTAATA
1 AGAAATATGATAACCAAAATTACAAAAAATGTAATA
1484 AGAAATATGATAACCAAAATTACAAAAAATGTAA
1 AGAAATATGATAACCAAAATTACAAAAAATGTAA
1518 GGTTATTGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.60, C:0.09, G:0.09, T:0.23
Consensus pattern (36 bp):
AGAAATATGATAACCAAAATTACAAAAAATGTAATA
Found at i:3854 original size:3 final size:3
Alignment explanation
Indices: 3848--3879 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
3838 AGTAAATGCT
*
3848 TTC TTC TTC TTC TTC TTT TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
3880 GCATCAGATA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (3 bp):
TTC
Found at i:21120 original size:24 final size:22
Alignment explanation
Indices: 21078--21127 Score: 57
Period size: 24 Copynumber: 2.2 Consensus size: 22
21068 ATTAAATAAA
*
21078 AATTAAAATAATAATTGAAATT
1 AATTAAAATAATAATTGAAAAT
21100 AATTATAAATAAATCAA-TGAAAAT
1 AATTA-AAAT-AAT-AATTGAAAAT
21124 AATT
1 AATT
21128 TCATGTTAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
22 5 0.21
23 4 0.17
24 13 0.54
25 2 0.08
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.34
Consensus pattern (22 bp):
AATTAAAATAATAATTGAAAAT
Found at i:22034 original size:84 final size:83
Alignment explanation
Indices: 21938--22095 Score: 264
Period size: 84 Copynumber: 1.9 Consensus size: 83
21928 AAATTATAAT
*
21938 ATATATCTAAG-TTATGTAATTAAAATAGTAAAAATGGTTAAAATAAAATAGTTATAAAGAGATT
1 ATATATCTAAGTTTATGTAATTAAAATAGT-AAAATGGTAAAAATAAAATAGTTATAAAGA-ATT
22002 AGATTTAATTATAAATTCTA
64 AGATTTAATTATAAATTCTA
* *
22022 ATATATCTAAGTTTTTTTAATTAAAATAGTAAAATGGTAAAAATAAAATAGTTATAAAGAATTAG
1 ATATATCTAAGTTTATGTAATTAAAATAGTAAAATGGTAAAAATAAAATAGTTATAAAGAATTAG
22087 ATTTAATTA
66 ATTTAATTA
22096 AATAAAAATA
Statistics
Matches: 70, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
83 14 0.20
84 40 0.57
85 16 0.23
ACGTcount: A:0.50, C:0.02, G:0.10, T:0.38
Consensus pattern (83 bp):
ATATATCTAAGTTTATGTAATTAAAATAGTAAAATGGTAAAAATAAAATAGTTATAAAGAATTAG
ATTTAATTATAAATTCTA
Found at i:22249 original size:84 final size:83
Alignment explanation
Indices: 22131--22288 Score: 255
Period size: 84 Copynumber: 1.9 Consensus size: 83
22121 ATTTTATAAT
*
22131 ATATATCTAAGTTGTGTAATTAAAATAGTAAAAATGGTAAAAATAAAATAGTTATAAAGAGATTA
1 ATATATCTAAGTTGTGTAATTAAAATAGTAAAAATAGTAAAAATAAAATAGTTATAAAGA-ATTA
*
22196 GATTTAATTATAAATTCTA
65 AATTTAATTATAAATTCTA
* *
22215 ATATATCTAAGTTTTTTTAATTAAAATAGT-AAAATAGTAAAAATAAAATAGTTATAAAGAATTA
1 ATATATCTAAG-TTGTGTAATTAAAATAGTAAAAATAGTAAAAATAAAATAGTTATAAAGAATTA
22279 AATTTAATTA
65 AATTTAATTA
22289 AATAAAAATA
Statistics
Matches: 69, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
83 13 0.19
84 40 0.58
85 16 0.23
ACGTcount: A:0.51, C:0.02, G:0.09, T:0.37
Consensus pattern (83 bp):
ATATATCTAAGTTGTGTAATTAAAATAGTAAAAATAGTAAAAATAAAATAGTTATAAAGAATTAA
ATTTAATTATAAATTCTA
Found at i:22260 original size:193 final size:193
Alignment explanation
Indices: 21931--22310 Score: 715
Period size: 193 Copynumber: 2.0 Consensus size: 193
21921 ATTTTAAAAA
*
21931 TTATAATATATATCTAAGTTATGTAATTAAAATAGTAAAAATGGTTAAAATAAAATAGTTATAAA
1 TTATAATATATATCTAAGTTATGTAATTAAAATAGTAAAAATGGTAAAAATAAAATAGTTATAAA
*
21996 GAGATTAGATTTAATTATAAATTCTAATATATCTAAGTTTTTTTAATTAAAATAGTAAAATGGTA
66 GAGATTAGATTTAATTATAAATTCTAATATATCTAAGTTTTTTTAATTAAAATAGTAAAATAGTA
*
22061 AAAATAAAATAGTTATAAAGAATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTTTAATT
131 AAAATAAAATAGTTATAAAGAATTAAATTTAATTAAATAAAAATAGAGTTTTTAGTTTTAATT
*
22124 TTATAATATATATCTAAGTTGTGTAATTAAAATAGTAAAAATGGTAAAAATAAAATAGTTATAAA
1 TTATAATATATATCTAAGTTATGTAATTAAAATAGTAAAAATGGTAAAAATAAAATAGTTATAAA
22189 GAGATTAGATTTAATTATAAATTCTAATATATCTAAGTTTTTTTAATTAAAATAGTAAAATAGTA
66 GAGATTAGATTTAATTATAAATTCTAATATATCTAAGTTTTTTTAATTAAAATAGTAAAATAGTA
*
22254 AAAATAAAATAGTTATAAAGAATTAAATTTAATTAAATAAAAATAGATTTTTTAGTT
131 AAAATAAAATAGTTATAAAGAATTAAATTTAATTAAATAAAAATAGAGTTTTTAGTT
22311 GAGTACAATT
Statistics
Matches: 182, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
193 182 1.00
ACGTcount: A:0.49, C:0.02, G:0.09, T:0.39
Consensus pattern (193 bp):
TTATAATATATATCTAAGTTATGTAATTAAAATAGTAAAAATGGTAAAAATAAAATAGTTATAAA
GAGATTAGATTTAATTATAAATTCTAATATATCTAAGTTTTTTTAATTAAAATAGTAAAATAGTA
AAAATAAAATAGTTATAAAGAATTAAATTTAATTAAATAAAAATAGAGTTTTTAGTTTTAATT
Done.