Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01009905.1 Corchorus olitorius cultivar O-4 contig09937, 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: 11122
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:63 original size:41 final size:42
Alignment explanation
Indices: 1--284 Score: 316
Period size: 41 Copynumber: 6.8 Consensus size: 42
1 TGCCCCTGTGTTATATATGTGTTTGGGGACTTTGATATAAA-
1 TGCCCCTGTGTTATATATGTGTTTGGGGACTTTGATATAAAG
* * *
42 TGCCTCTGTGTTATATATGTGTTTGAGGACTTTG-TAATAGAAT
1 TGCCCCTGTGTTATATATGTGTTTGGGGACTTTGAT-ATA-AAG
*
85 TGCCCCTGTGTTATATATGTGTTTGGGGAC-TTGA-ATATAGG
1 TGCCCCTGTGTTATATATGTGTTTGGGGACTTTGATATA-AAG
* *
126 TGCCTCTGTGTTATATATGTGTTTGAGGACTTTG-TAATAAAGG
1 TGCCCCTGTGTTATATATGTGTTTGGGGACTTTGAT-ATAAA-G
* *
169 TGCCCCTGTG-T-TATATGTGTTTGGGGACTTGGATAT-AGG
1 TGCCCCTGTGTTATATATGTGTTTGGGGACTTTGATATAAAG
* * *
208 TGCCTCTGTGTTATATATGTGTTTGAGGACTTTTGGA-ATAGAAT
1 TGCCCCTGTGTTATATATGTGTTTGGGGAC-TTT-GATATA-AAG
* *
252 TGTCCATGTGTTATATATGTGTTTGGGGACTTT
1 TGCCCCTGTGTTATATATGTGTTTGGGGACTTT
285 TTGGTTATTG
Statistics
Matches: 205, Mismatches: 23, Indels: 28
0.80 0.09 0.11
Matches are distributed among these distances:
39 10 0.05
40 3 0.01
41 104 0.51
42 15 0.07
43 46 0.22
44 27 0.13
ACGTcount: A:0.20, C:0.11, G:0.27, T:0.42
Consensus pattern (42 bp):
TGCCCCTGTGTTATATATGTGTTTGGGGACTTTGATATAAAG
Found at i:205 original size:82 final size:84
Alignment explanation
Indices: 1--283 Score: 455
Period size: 84 Copynumber: 3.4 Consensus size: 84
* **
1 TGCCCCTGTGTTATATATGTGTTTGGGGACTTTGATATAAATGCCTCTGTGTTATATATGTGTTT
1 TGCCCCTGTGTTATATATGTGTTTGGGGACTTGGATATAGGTGCCTCTGTGTTATATATGTGTTT
66 GAGGACTTTGTAATAGAAT
66 GAGGACTTTGTAATAGAAT
*
85 TGCCCCTGTGTTATATATGTGTTTGGGGACTTGAATATAGGTGCCTCTGTGTTATATATGTGTTT
1 TGCCCCTGTGTTATATATGTGTTTGGGGACTTGGATATAGGTGCCTCTGTGTTATATATGTGTTT
*
150 GAGGACTTTGTAATA-AAGG
66 GAGGACTTTGTAATAGAA-T
169 TGCCCCTGTG-T-TATATGTGTTTGGGGACTTGGATATAGGTGCCTCTGTGTTATATATGTGTTT
1 TGCCCCTGTGTTATATATGTGTTTGGGGACTTGGATATAGGTGCCTCTGTGTTATATATGTGTTT
*
232 GAGGACTTTTGGAATAGAAT
66 GAGGAC-TTTGTAATAGAAT
* *
252 TGTCCATGTGTTATATATGTGTTTGGGGACTT
1 TGCCCCTGTGTTATATATGTGTTTGGGGACTT
284 TTTGGTTATT
Statistics
Matches: 184, Mismatches: 10, Indels: 9
0.91 0.05 0.04
Matches are distributed among these distances:
82 57 0.31
83 19 0.10
84 89 0.48
85 19 0.10
ACGTcount: A:0.20, C:0.11, G:0.27, T:0.42
Consensus pattern (84 bp):
TGCCCCTGTGTTATATATGTGTTTGGGGACTTGGATATAGGTGCCTCTGTGTTATATATGTGTTT
GAGGACTTTGTAATAGAAT
Found at i:505 original size:26 final size:27
Alignment explanation
Indices: 466--516 Score: 86
Period size: 26 Copynumber: 1.9 Consensus size: 27
456 GGTTTTGGCC
*
466 CCTAACAATAATTAAGATACATTTTTA
1 CCTAACAAAAATTAAGATACATTTTTA
493 CCTAA-AAAAATTAAGATACATTTT
1 CCTAACAAAAATTAAGATACATTTT
517 CACAAATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 18 0.78
27 5 0.22
ACGTcount: A:0.47, C:0.14, G:0.04, T:0.35
Consensus pattern (27 bp):
CCTAACAAAAATTAAGATACATTTTTA
Found at i:2139 original size:29 final size:29
Alignment explanation
Indices: 2106--2161 Score: 71
Period size: 29 Copynumber: 1.9 Consensus size: 29
2096 TAAAAATCAA
2106 ATTTT-GAAAGAA-AAAAATAATTATTTTCT
1 ATTTTCGAAA-AATAAAAAT-ATTATTTTCT
*
2135 ATTTTCTAAAAATAAAAATATTATTTT
1 ATTTTCGAAAAATAAAAATATTATTTT
2162 ACACGTGACA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
29 15 0.62
30 9 0.38
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.45
Consensus pattern (29 bp):
ATTTTCGAAAAATAAAAATATTATTTTCT
Found at i:2297 original size:31 final size:30
Alignment explanation
Indices: 2257--2357 Score: 98
Period size: 31 Copynumber: 3.3 Consensus size: 30
2247 CCGTTTCATG
*
2257 GAGGGACTAAATTGATCTCTTTTCAATAATA
1 GAGGGACTAAATTGATCTATTTTC-ATAATA
* * *
2288 GAGGAACTAAATTGA-CAAATTTT-ATAATG
1 GAGGGACTAAATTGATC-TATTTTCATAATA
* *
2317 GAGGGACTAAATTGATCTTTTTTCCATAGTA
1 GAGGGACTAAATTGATCTATTTT-CATAATA
*
2348 CAGGGACTAA
1 GAGGGACTAA
2358 TTAGGTACTT
Statistics
Matches: 56, Mismatches: 10, Indels: 8
0.76 0.14 0.11
Matches are distributed among these distances:
29 23 0.41
30 2 0.04
31 31 0.55
ACGTcount: A:0.37, C:0.12, G:0.19, T:0.33
Consensus pattern (30 bp):
GAGGGACTAAATTGATCTATTTTCATAATA
Found at i:2339 original size:29 final size:29
Alignment explanation
Indices: 2254--2339 Score: 93
Period size: 29 Copynumber: 2.9 Consensus size: 29
2244 GTCCCGTTTC
*
2254 ATGGAGGGACTAAATTGATCTCTTTTCAATA
1 ATGGAGGGACTAAATTGATCT-TTTT-TATA
* * **
2285 ATAGAGGAACTAAATTGA-CAAATTTTATA
1 ATGGAGGGACTAAATTGATC-TTTTTTATA
2314 ATGGAGGGACTAAATTGATCTTTTTT
1 ATGGAGGGACTAAATTGATCTTTTTT
2340 CCATAGTACA
Statistics
Matches: 44, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
29 23 0.52
30 5 0.11
31 16 0.36
ACGTcount: A:0.36, C:0.09, G:0.19, T:0.36
Consensus pattern (29 bp):
ATGGAGGGACTAAATTGATCTTTTTTATA
Found at i:2444 original size:9 final size:8
Alignment explanation
Indices: 2425--2454 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
2415 AAAATGATGC
*
2425 AAAAACCA
1 AAAAACAA
2433 AAAAACAA
1 AAAAACAA
2441 AAAAACAA
1 AAAAACAA
2449 AAAAAC
1 AAAAAC
2455 CCAAGAATCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.83, C:0.17, G:0.00, T:0.00
Consensus pattern (8 bp):
AAAAACAA
Found at i:6454 original size:2 final size:2
Alignment explanation
Indices: 6447--6477 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
6437 ATATTGGTGG
*
6447 TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
6478 GTGACTTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:7831 original size:3 final size:3
Alignment explanation
Indices: 7825--7859 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
7815 TATTATATAT
7825 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
7860 TATTATTATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Done.