Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: XM_021431680.1
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: 3321
ACGTcount: A:0.03, C:0.44, G:0.44, T:0.10
Found at i:975 original size:10 final size:11
Alignment explanation
Indices: 953--982 Score: 53
Period size: 10 Copynumber: 2.8 Consensus size: 11
943 CGCGCGGCGC
953 GCCGCGCCTGG
1 GCCGCGCCTGG
964 GCCGCGCC-GG
1 GCCGCGCCTGG
974 GCCGCGCCT
1 GCCGCGCCT
983 CGCCGGCACG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.00, C:0.50, G:0.43, T:0.07
Consensus pattern (11 bp):
GCCGCGCCTGG
Found at i:1353 original size:19 final size:20
Alignment explanation
Indices: 1326--1379 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 20
1316 TCCTGGCGGC
1326 CGCGC-GGGCCGCGGGCGCT
1 CGCGCGGGGCCGCGGGCGCT
* *
1345 -GCGCGGGGCGGGGGGCGCT
1 CGCGCGGGGCCGCGGGCGCT
*
1364 CTCGCGGGGCC-CGGGC
1 CGCGCGGGGCCGCGGGC
1380 CGCCGGGCCC
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
18 4 0.14
19 16 0.57
20 8 0.29
ACGTcount: A:0.00, C:0.37, G:0.57, T:0.06
Consensus pattern (20 bp):
CGCGCGGGGCCGCGGGCGCT
Found at i:1508 original size:23 final size:23
Alignment explanation
Indices: 1481--1535 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
1471 GGCCCCGTCC
1481 GCGCCG-GCCCGCGGTTGGGCCCG
1 GCGCCGCGCCCGCGG-TGGGCCCG
*
1504 GCGCCGCGCCGGCGGTGGGCCCG
1 GCGCCGCGCCCGCGGTGGGCCCG
* *
1527 CCGCGGCGC
1 GCGCCGCGC
1536 GCTGGCTTGC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 21 0.75
24 7 0.25
ACGTcount: A:0.00, C:0.45, G:0.49, T:0.05
Consensus pattern (23 bp):
GCGCCGCGCCCGCGGTGGGCCCG
Found at i:2335 original size:19 final size:19
Alignment explanation
Indices: 2311--2360 Score: 57
Period size: 21 Copynumber: 2.6 Consensus size: 19
2301 GTGGCGCCCC
* *
2311 CGCGGCGCGCCCTCGGGGG
1 CGCGGCGCCCCCTCCGGGG
2330 CGCGGCCGGCCCCCTCCGGGG
1 CGCGG-C-GCCCCCTCCGGGG
2351 C-CGGCGCCCC
1 CGCGGCGCCCC
2361 GGGCGCTCCG
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
18 5 0.19
19 6 0.22
20 4 0.15
21 12 0.44
ACGTcount: A:0.00, C:0.52, G:0.44, T:0.04
Consensus pattern (19 bp):
CGCGGCGCCCCCTCCGGGG
Found at i:2547 original size:18 final size:18
Alignment explanation
Indices: 2524--2657 Score: 82
Period size: 18 Copynumber: 7.4 Consensus size: 18
2514 TTGGAAGCGC
2524 GGGCGGCGGGCGGGGGCG
1 GGGCGGCGGGCGGGGGCG
* *
2542 GGGCGGGGGGCGGGGGGG
1 GGGCGGCGGGCGGGGGCG
*
2560 GGGCCGG-GGGGGCGGGGCG
1 GGG-CGGCGGGCG-GGGGCG
* *
2579 GCGCGG-GGGTGGGGGC-
1 GGGCGGCGGGCGGGGGCG
*
2595 GGG-GGCGCGCGGCGGG-G
1 GGGCGGCGGGCGG-GGGCG
*
2612 GGGCGCCGGGCGGTGGGCTG
1 GGGCGGCGGGCGG-GGGC-G
* *
2632 CGGCCGGCGGGTGGGGG-G
1 -GGGCGGCGGGCGGGGGCG
*
2650 GCGCGGCG
1 GGGCGGCG
2658 CGGGGGAAAC
Statistics
Matches: 90, Mismatches: 17, Indels: 19
0.71 0.13 0.15
Matches are distributed among these distances:
15 2 0.02
16 6 0.07
17 17 0.19
18 41 0.46
19 10 0.11
20 4 0.04
21 10 0.11
ACGTcount: A:0.00, C:0.22, G:0.75, T:0.03
Consensus pattern (18 bp):
GGGCGGCGGGCGGGGGCG
Found at i:2547 original size:22 final size:21
Alignment explanation
Indices: 2524--2629 Score: 81
Period size: 22 Copynumber: 4.8 Consensus size: 21
2514 TTGGAAGCGC
2524 GGGCGGCGGGCGGGGGCGGGG
1 GGGCGGCGGGCGGGGGCGGGG
* *
2545 CGGGGGGCGGGGGGGGGGCCGGGG
1 -GGGCGGC-GGGCGGGGG-CGGGG
* *
2569 GGGCGGGGCGGCGCGGGG-GTGG
1 GGGCGGCG-GGCG-GGGGCGGGG
*
2591 GGGCGG-GGGCGCGCGGCGGGG
1 GGGCGGCGGGCG-GGGGCGGGG
*
2612 GGGCGCCGGGCGGTGGGC
1 GGGCGGCGGGCGG-GGGC
2630 TGCGGCCGGC
Statistics
Matches: 67, Mismatches: 10, Indels: 14
0.74 0.11 0.15
Matches are distributed among these distances:
20 8 0.12
21 10 0.15
22 24 0.36
23 16 0.24
24 9 0.13
ACGTcount: A:0.00, C:0.21, G:0.77, T:0.02
Consensus pattern (21 bp):
GGGCGGCGGGCGGGGGCGGGG
Found at i:2569 original size:25 final size:24
Alignment explanation
Indices: 2524--2616 Score: 82
Period size: 25 Copynumber: 3.7 Consensus size: 24
2514 TTGGAAGCGC
2524 GGGCGGCGGGCGGGGGC-GGGGCGGG
1 GGGCGG-GGG-GGGGGCGGGGGCGGG
2549 GGGCGGGGGGGGGGCCGGGGG-GGCG
1 GGGCGGGGGGGGGG-CGGGGGCGG-G
* * *
2574 GGGCGGCGCGGGGGTGGGGGCGGG
1 GGGCGGGGGGGGGGCGGGGGCGGG
2598 GGCGCGCGGCGGGGGGGCG
1 GG-GCG-GG-GGGGGGGCG
2617 CCGGGCGGTG
Statistics
Matches: 55, Mismatches: 6, Indels: 12
0.75 0.08 0.16
Matches are distributed among these distances:
23 5 0.09
24 14 0.25
25 28 0.51
26 1 0.02
27 7 0.13
ACGTcount: A:0.00, C:0.19, G:0.80, T:0.01
Consensus pattern (24 bp):
GGGCGGGGGGGGGGCGGGGGCGGG
Found at i:2585 original size:30 final size:30
Alignment explanation
Indices: 2541--2609 Score: 90
Period size: 30 Copynumber: 2.4 Consensus size: 30
2531 GGGCGGGGGC
*
2541 GGGGCGGGG-GGCG-GGGGG-GGGGCCGGG
1 GGGGCGGGGCGGCGCGGGGGTGGGGGCGGG
2568 GGGGCGGGGCGGCGCGGGGGTGGGGGCGGG
1 GGGGCGGGGCGGCGCGGGGGTGGGGGCGGG
* *
2598 GGCGCGCGGCGG
1 GGGGCGGGGCGG
2610 GGGGGCGCCG
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
27 9 0.25
28 4 0.11
29 5 0.14
30 18 0.50
ACGTcount: A:0.00, C:0.19, G:0.80, T:0.01
Consensus pattern (30 bp):
GGGGCGGGGCGGCGCGGGGGTGGGGGCGGG
Found at i:2623 original size:15 final size:14
Alignment explanation
Indices: 2524--2629 Score: 51
Period size: 12 Copynumber: 8.3 Consensus size: 14
2514 TTGGAAGCGC
2524 GGGCG-GCGGGC-G
1 GGGCGCGCGGGCGG
2536 GGG-GCG-GGGCGG
1 GGGCGCGCGGGCGG
2548 GGG-GCG-GGG-GG
1 GGGCGCGCGGGCGG
2559 GGG-GC-C-GG-GG
1 GGGCGCGCGGGCGG
*
2569 GGGCGGGGCGGCGCGG
1 GGGC-GCGCGG-GCGG
*
2585 GGGTG-G-GGGCGG
1 GGGCGCGCGGGCGG
2597 GGGCGCGC-GGCGG
1 GGGCGCGCGGGCGG
*
2610 GGGGGCGCCGGGCGG
1 GGGCGCG-CGGGCGG
2625 TGGGC
1 -GGGC
2630 TGCGGCCGGC
Statistics
Matches: 75, Mismatches: 5, Indels: 24
0.72 0.05 0.23
Matches are distributed among these distances:
10 7 0.09
11 12 0.16
12 23 0.31
13 15 0.20
14 3 0.04
15 7 0.09
16 8 0.11
ACGTcount: A:0.00, C:0.21, G:0.77, T:0.02
Consensus pattern (14 bp):
GGGCGCGCGGGCGG
Found at i:2629 original size:14 final size:12
Alignment explanation
Indices: 2524--2612 Score: 67
Period size: 13 Copynumber: 7.2 Consensus size: 12
2514 TTGGAAGCGC
2524 GGGCGGCGGGCGG
1 GGGC-GCGGGCGG
2537 GGGCG-GGGCGG
1 GGGCGCGGGCGG
2548 GGG-GCGGG-GG
1 GGGCGCGGGCGG
* *
2558 GGGGGCCGGGGGG
1 GGGCG-CGGGCGG
*
2571 GCGGGGCGGCGCGG
1 G-GGCGCGG-GCGG
* *
2585 GGGTGGGGGCGG
1 GGGCGCGGGCGG
2597 GGGCGCGCGGCGG
1 GGGCGCG-GGCGG
2610 GGG
1 GGG
2613 GGCGCCGGGC
Statistics
Matches: 64, Mismatches: 5, Indels: 14
0.77 0.06 0.17
Matches are distributed among these distances:
10 6 0.09
11 13 0.20
12 14 0.22
13 23 0.36
14 8 0.12
ACGTcount: A:0.00, C:0.19, G:0.80, T:0.01
Consensus pattern (12 bp):
GGGCGCGGGCGG
Found at i:2635 original size:55 final size:49
Alignment explanation
Indices: 2528--2648 Score: 122
Period size: 55 Copynumber: 2.4 Consensus size: 49
2518 AAGCGCGGGC
* * *
2528 GGCGG-GCGGGGG-CGGGGCGGGGGGCGGGGGGGGGGCCGGGGGGGCGG
1 GGCGGCGCGGGGGTGGGGGCGGGGGGCGGGGGGGGGGCCCGGGCGGCGG
*
2575 GGCGGCGCGGGGGTGGGGGCGGGGGCGCGCGGCGGGGGGGCGCCGGGCGGTGG
1 GGCGGCGCGGGGGTGGGGGCGGGGG-GCG-GG-GGGGGGGC-CCGGGCGGCGG
2628 GCTGCGGC-CGGCGGGTGGGGG
1 G--GCGGCGCGG-GGGTGGGGG
2649 GGCGCGGCGC
Statistics
Matches: 61, Mismatches: 4, Indels: 10
0.81 0.05 0.13
Matches are distributed among these distances:
47 5 0.08
48 7 0.11
49 10 0.16
50 3 0.05
51 2 0.03
52 8 0.13
53 9 0.15
54 3 0.05
55 14 0.23
ACGTcount: A:0.00, C:0.21, G:0.76, T:0.03
Consensus pattern (49 bp):
GGCGGCGCGGGGGTGGGGGCGGGGGGCGGGGGGGGGGCCCGGGCGGCGG
Done.