Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022098.1 Corchorus olitorius cultivar O-4 contig22131, 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: 11313
ACGTcount: A:0.32, C:0.20, G:0.15, T:0.33
Found at i:2815 original size:15 final size:15
Alignment explanation
Indices: 2797--2865 Score: 58
Period size: 15 Copynumber: 4.8 Consensus size: 15
2787 TATTATTATT
2797 ATAATAATAAGTTTA
1 ATAATAATAAGTTTA
* **
2812 ATAATTATAA-TACCA
1 ATAATAATAAGT-TTA
2827 ATAATAATAAGTTTA
1 ATAATAATAAGTTTA
2842 ATAAT--T-A-TTATA
1 ATAATAATAAGTT-TA
2854 ATAATAATAAGT
1 ATAATAATAAGT
2866 CTAAATTAAC
Statistics
Matches: 41, Mismatches: 6, Indels: 13
0.68 0.10 0.22
Matches are distributed among these distances:
11 2 0.05
12 8 0.20
13 1 0.02
14 2 0.05
15 26 0.63
16 2 0.05
ACGTcount: A:0.54, C:0.03, G:0.04, T:0.39
Consensus pattern (15 bp):
ATAATAATAAGTTTA
Found at i:2816 original size:30 final size:27
Alignment explanation
Indices: 2783--2865 Score: 112
Period size: 30 Copynumber: 3.0 Consensus size: 27
2773 ATACCACTAA
* *
2783 TAATTATTATTATTATAATAATAAGTT
1 TAATAATTATTATAATAATAATAAGTT
*
2810 TAATAATTATAATACCAATAATAATAAGTT
1 TAATAATTAT--TA-TAATAATAATAAGTT
2840 TAATAATTATTATAATAATAATAAGT
1 TAATAATTATTATAATAATAATAAGT
2866 CTAAATTAAC
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
27 22 0.45
28 2 0.04
29 2 0.04
30 23 0.47
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.43
Consensus pattern (27 bp):
TAATAATTATTATAATAATAATAAGTT
Found at i:3174 original size:2 final size:2
Alignment explanation
Indices: 3145--3218 Score: 85
Period size: 2 Copynumber: 36.5 Consensus size: 2
3135 TTTAGATTTG
* * * * *
3145 TA TA GTA TA TA AA TA TA GA TA TA AA TA TA TA GA TA TA TA GA TA
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
3188 TA TA TA TA TA TA TA GA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3219 GCTTGTTTCT
Statistics
Matches: 59, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
2 57 0.97
3 2 0.03
ACGTcount: A:0.51, C:0.00, G:0.07, T:0.42
Consensus pattern (2 bp):
TA
Found at i:3190 original size:18 final size:18
Alignment explanation
Indices: 3145--3218 Score: 98
Period size: 18 Copynumber: 4.2 Consensus size: 18
3135 TTTAGATTTG
* *
3145 TATAGTATATAAATATAGA
1 TATAG-ATATATATATATA
*
3164 TATA-A-ATATATAGATA
1 TATAGATATATATATATA
3180 TATAGATATATATATATA
1 TATAGATATATATATATA
3198 TATAGATATATATATATA
1 TATAGATATATATATATA
3216 TAT
1 TAT
3219 GCTTGTTTCT
Statistics
Matches: 49, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
16 12 0.24
17 2 0.04
18 31 0.63
19 4 0.08
ACGTcount: A:0.51, C:0.00, G:0.07, T:0.42
Consensus pattern (18 bp):
TATAGATATATATATATA
Found at i:9361 original size:17 final size:17
Alignment explanation
Indices: 9306--9354 Score: 73
Period size: 17 Copynumber: 2.9 Consensus size: 17
9296 CTAATGATTT
9306 AAGATCA-TCAGTGATGC
1 AAGATCACTC-GTGATGC
9323 AAGATCACTCGTGATGC
1 AAGATCACTCGTGATGC
*
9340 AAGATCACTGGTGAT
1 AAGATCACTCGTGAT
9355 CAAAGATTAC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
17 28 0.93
18 2 0.07
ACGTcount: A:0.33, C:0.18, G:0.24, T:0.24
Consensus pattern (17 bp):
AAGATCACTCGTGATGC
Found at i:10365 original size:17 final size:17
Alignment explanation
Indices: 10316--10371 Score: 53
Period size: 17 Copynumber: 3.3 Consensus size: 17
10306 TAAATATTTT
10316 ATATTTAATATTAAAAA
1 ATATTTAATATTAAAAA
* *
10333 ACT-TTT-TTTTTGAAAAA
1 A-TATTTAATATT-AAAAA
10350 ATATTTAATATTAAAAA
1 ATATTTAATATTAAAAA
*
10367 CTATT
1 ATATT
10372 AGTAAAAAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 8
0.70 0.12 0.19
Matches are distributed among these distances:
16 4 0.13
17 22 0.73
18 4 0.13
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (17 bp):
ATATTTAATATTAAAAA
Done.