Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01007323.1 Corchorus olitorius cultivar O-4 contig07348, 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, 829
Length: 1383
ACGTcount: A:0.40, C:0.14, G:0.13, T:0.32
Found at i:242 original size:84 final size:85
Alignment explanation
Indices: 114--280 Score: 259
Period size: 84 Copynumber: 2.0 Consensus size: 85
104 TATATTTAAA
*
114 AAATTATAATATATATCTAAGTTATGTAATTAAAATAGTAAAAATGGTGAAAATAAAATAGTTAT
1 AAATTATAATATATATCTAAGTTATGTAATTAAAATAGTAAAAATGGTAAAAATAAAATAGTTAT
179 AAAGAGATTAGATTTAATTAG
66 AAAGA-ATTAGATTTAATTAG
* * *
200 AAATTCTAATATAT-T-TAAGTTCTTTTAATTAAAATAGT-AAAATGGTAAAAATAAAATAGTTA
1 AAATTATAATATATATCTAAGTT-ATGTAATTAAAATAGTAAAAATGGTAAAAATAAAATAGTTA
262 TAAAGAATTAGATTTAATT
65 TAAAGAATTAGATTTAATT
281 TGTGCCAAAA
Statistics
Matches: 76, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
83 13 0.17
84 35 0.46
85 15 0.20
86 13 0.17
ACGTcount: A:0.50, C:0.02, G:0.11, T:0.37
Consensus pattern (85 bp):
AAATTATAATATATATCTAAGTTATGTAATTAAAATAGTAAAAATGGTAAAAATAAAATAGTTAT
AAAGAATTAGATTTAATTAG
Found at i:827 original size:11 final size:11
Alignment explanation
Indices: 811--859 Score: 55
Period size: 11 Copynumber: 4.4 Consensus size: 11
801 AATCTAAAAT
811 AATTATAATAA
1 AATTATAATAA
822 AATTATAATAA
1 AATTATAATAA
* *
833 AATAATCTAA-AT
1 AAT--TATAATAA
845 AATTATAATAA
1 AATTATAATAA
856 AATT
1 AATT
860 CATGAAATAA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
10 4 0.13
11 19 0.61
12 4 0.13
13 4 0.13
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (11 bp):
AATTATAATAA
Found at i:867 original size:23 final size:22
Alignment explanation
Indices: 822--878 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 22
812 ATTATAATAA
822 AATTATAATAAAATAATCTAAAT
1 AATTATAATAAAAT-ATCTAAAT
845 AATTATAATAAAAT-TCATGAAAT
1 AATTATAATAAAATATC-T-AAAT
*
868 AATAATAATAA
1 AATTATAATAA
879 TTTGCTAGGC
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
21 2 0.06
22 1 0.03
23 28 0.90
ACGTcount: A:0.61, C:0.04, G:0.02, T:0.33
Consensus pattern (22 bp):
AATTATAATAAAATATCTAAAT
Found at i:986 original size:2 final size:2
Alignment explanation
Indices: 979--1033 Score: 53
Period size: 2 Copynumber: 27.5 Consensus size: 2
969 CCCAATAAAG
979 TA TA TA TA TA GTA TA TGA TA TA TA TA TA TA TA T- TA TGA -A TA
1 TA TA TA TA TA -TA TA T-A TA TA TA TA TA TA TA TA TA T-A TA TA
*
1020 TA TA AA T- TA TA TA T
1 TA TA TA TA TA TA TA T
1034 TTCGGGGCCG
Statistics
Matches: 45, Mismatches: 2, Indels: 12
0.76 0.03 0.20
Matches are distributed among these distances:
1 3 0.07
2 37 0.82
3 5 0.11
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (2 bp):
TA
Found at i:1004 original size:20 final size:19
Alignment explanation
Indices: 979--1023 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 19
969 CCCAATAAAG
979 TATATATATAGTA-TATGATA
1 TATATATATA-TATTATGA-A
999 TATATATATATATTATGAA
1 TATATATATATATTATGAA
1018 TATATA
1 TATATA
1024 AATTATATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 9 0.38
20 15 0.62
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.47
Consensus pattern (19 bp):
TATATATATATATTATGAA
Found at i:1030 original size:22 final size:20
Alignment explanation
Indices: 982--1034 Score: 61
Period size: 22 Copynumber: 2.5 Consensus size: 20
972 AATAAAGTAT
*
982 ATATATAGTATATGATATATAT
1 ATATATA-T-TATGATATATAA
1004 ATATATATTATGAATATATAA
1 ATATATATTATG-ATATATAA
1025 ATTATATATT
1 A-TATATATT
1035 TCGGGGCCGG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
20 4 0.14
21 9 0.32
22 15 0.54
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (20 bp):
ATATATATTATGATATATAA
Done.