Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga13g01121.P1
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: 7052
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Found at i:2264 original size:20 final size:18
Alignment explanation
Indices: 2241--2279 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
2231 AAATAAATTT
2241 AATTCATAAAAATATATATA
1 AATTCA-AAAAATAT-TATA
*
2261 AATTCAAAACATATTATA
1 AATTCAAAAAATATTATA
2279 A
1 A
2280 CCAAAACATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 5 0.28
19 7 0.39
20 6 0.33
ACGTcount: A:0.59, C:0.08, G:0.00, T:0.33
Consensus pattern (18 bp):
AATTCAAAAAATATTATA
Found at i:2415 original size:49 final size:49
Alignment explanation
Indices: 2354--2458 Score: 174
Period size: 49 Copynumber: 2.1 Consensus size: 49
2344 ATTTAATCCA
* *
2354 ATAATTTCCTTAAAAGTATTTAGTTTAAAGTTTAAATTTCATAACTTGC
1 ATAATTTCCTTAAAAGTATATAGTTTAAAGTTTAAATTTCATAACTTAC
* *
2403 ATAATTTCCTTAAAATTGTATAGTTTAAAGTTTAAATTTCATAACTTAC
1 ATAATTTCCTTAAAAGTATATAGTTTAAAGTTTAAATTTCATAACTTAC
2452 ATAATTT
1 ATAATTT
2459 ACATAACTTA
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
49 52 1.00
ACGTcount: A:0.38, C:0.10, G:0.07, T:0.46
Consensus pattern (49 bp):
ATAATTTCCTTAAAAGTATATAGTTTAAAGTTTAAATTTCATAACTTAC
Found at i:2460 original size:9 final size:9
Alignment explanation
Indices: 2442--2662 Score: 225
Period size: 9 Copynumber: 24.6 Consensus size: 9
2432 GTTTAAATTT
2442 CATAACTTA
1 CATAACTTA
*
2451 CATAATTTA
1 CATAACTTA
2460 CATAACTTA
1 CATAACTTA
2469 CATAA--TA
1 CATAACTTA
*
2476 CATAA-ATA
1 CATAACTTA
* * *
2484 TATATCATA
1 CATAACTTA
2493 TCATAACTTA
1 -CATAACTTA
*
2503 CATAACTCA
1 CATAACTTA
*
2512 CACAACTTA
1 CATAACTTA
2521 CATAACTTA
1 CATAACTTA
2530 -ATAACTTA
1 CATAACTTA
* *
2538 TATATATCATA
1 CATA-A-CTTA
2549 TCATAACTTA
1 -CATAACTTA
*
2559 CATAACTCA
1 CATAACTTA
2568 CATAACTTA
1 CATAACTTA
2577 CATAACTTA
1 CATAACTTA
* *
2586 CATACCTCA
1 CATAACTTA
*
2595 CATAATTTA
1 CATAACTTA
2604 CATAACTTA
1 CATAACTTA
* *
2613 CATACCTCA
1 CATAACTTA
2622 CATAACTTA
1 CATAACTTA
*
2631 CATAACTCA
1 CATAACTTA
*
2640 AATAACTTA
1 CATAACTTA
2649 CATAACTTA
1 CATAACTTA
2658 CATAA
1 CATAA
2663 TACATAAATA
Statistics
Matches: 175, Mismatches: 30, Indels: 14
0.80 0.14 0.06
Matches are distributed among these distances:
7 7 0.04
8 13 0.07
9 138 0.79
10 10 0.06
11 4 0.02
12 3 0.02
ACGTcount: A:0.45, C:0.22, G:0.00, T:0.33
Consensus pattern (9 bp):
CATAACTTA
Done.