Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: evm.model.Ga11G2026
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: 2913
ACGTcount: A:0.33, C:0.17, G:0.29, T:0.20
Found at i:2332 original size:24 final size:24
Alignment explanation
Indices: 2296--2390 Score: 64
Period size: 24 Copynumber: 3.7 Consensus size: 24
2286 TGAAAGGGAA
* *
2296 AGGAAGGAAGAGGAAGAAGCCAGG
1 AGGAAAGAGGAGGAAGAAGCCAGG
*
2320 AGGAAAGAGGAGGAAGAGGAGGCCAGAA
1 AGGAAAGAGGAGGAAGA--A-GCCAG-G
* * *
2348 AGAAAAGAGAGGAGGAAGAAGCTAAG
1 AG-GAA-AGAGGAGGAAGAAGCCAGG
* *
2374 AGGAAAGCGGAAGAAGA
1 AGGAAAGAGGAGGAAGA
2391 GGCCCAAAAG
Statistics
Matches: 55, Mismatches: 10, Indels: 12
0.71 0.13 0.16
Matches are distributed among these distances:
24 25 0.45
25 2 0.04
26 3 0.05
27 8 0.15
28 3 0.05
29 2 0.04
30 12 0.22
ACGTcount: A:0.49, C:0.06, G:0.43, T:0.01
Consensus pattern (24 bp):
AGGAAAGAGGAGGAAGAAGCCAGG
Found at i:2336 original size:30 final size:30
Alignment explanation
Indices: 2292--2611 Score: 83
Period size: 27 Copynumber: 11.7 Consensus size: 30
2282 AAATTGAAAG
*
2292 GGAAAG-GAAGGAAGAGGAAGAAGCCAGGA
1 GGAAAGAGGAGGAAGAGGAAGAAGCCAGGA
*
2321 GGAAAGAGGAGGAAGAGG-AG--GCCAGAA
1 GGAAAGAGGAGGAAGAGGAAGAAGCCAGGA
* * * *
2348 AGAAA-A-GA-GAGGAGGAAGAAGCTAAGA
1 GGAAAGAGGAGGAAGAGGAAGAAGCCAGGA
* * *** *
2375 GGAAAGCGGAAGAAGAGGCCCAA---AAGA
1 GGAAAGAGGAGGAAGAGGAAGAAGCCAGGA
* * * *
2402 -G-AAG-GGAAGAAGAAGAGGAAGCCAGAA
1 GGAAAGAGGAGGAAGAGGAAGAAGCCAGGA
* *
2429 GG--AGA-GAGGAAGAGGAAGAAGCTAAGA
1 GGAAAGAGGAGGAAGAGGAAGAAGCCAGGA
** * *
2456 -G-AAGA-GAAAAAAAGG-AG--GCCAGAA
1 GGAAAGAGGAGGAAGAGGAAGAAGCCAGGA
* *
2480 GG--AGA-GAGGAAGAGGAAGAAGCTAAGA
1 GGAAAGAGGAGGAAGAGGAAGAAGCCAGGA
* * *
2507 -GAAGGAGAGAGGAAGAGGAAGAAGCTAAGA
1 GGAAAGAG-GAGGAAGAGGAAGAAGCCAGGA
* * *
2537 -G-AAGA-GAAGAAAAGG-AG--GCCAGAA
1 GGAAAGAGGAGGAAGAGGAAGAAGCCAGGA
* * * *
2561 GGAGAGAGGAGGAGGAAGAAGAGGCCAGGA
1 GGAAAGAGGAGGAAGAGGAAGAAGCCAGGA
* *
2591 GGAGAGAGGAGGAAGAAGAAG
1 GGAAAGAGGAGGAAGAGGAAG
2612 CTAGGACGGA
Statistics
Matches: 213, Mismatches: 51, Indels: 53
0.67 0.16 0.17
Matches are distributed among these distances:
24 36 0.17
25 11 0.05
26 11 0.05
27 70 0.33
28 5 0.02
29 13 0.06
30 67 0.31
ACGTcount: A:0.49, C:0.06, G:0.43, T:0.01
Consensus pattern (30 bp):
GGAAAGAGGAGGAAGAGGAAGAAGCCAGGA
Found at i:2417 original size:51 final size:54
Alignment explanation
Indices: 2293--2417 Score: 134
Period size: 54 Copynumber: 2.4 Consensus size: 54
2283 AATTGAAAGG
* * *
2293 GAAAG-GAA-GGAAGAGGAAGAAGCCAGGAGGAAAGAGGAGGAAGAGGAGGCCA
1 GAAAGAGAAGGGAAGAGGAAGAAGCCAAGAGGAAAGAGGAAGAAGAGGAGCCCA
* * * * *
2345 GAAAGAAAAGAGAGGAGGAAGAAGCTAAGAGGAAAGCGGAAGAAGA-G-GCCCA
1 GAAAGAGAAGGGAAGAGGAAGAAGCCAAGAGGAAAGAGGAAGAAGAGGAGCCCA
*
2397 -AAAGAGAAGGGAAGAAGAAGA
1 GAAAGAGAAGGGAAGAGGAAGA
2418 GGAAGCCAGA
Statistics
Matches: 59, Mismatches: 12, Indels: 5
0.78 0.16 0.07
Matches are distributed among these distances:
51 17 0.29
52 9 0.15
53 3 0.05
54 30 0.51
ACGTcount: A:0.50, C:0.07, G:0.42, T:0.01
Consensus pattern (54 bp):
GAAAGAGAAGGGAAGAGGAAGAAGCCAAGAGGAAAGAGGAAGAAGAGGAGCCCA
Found at i:2428 original size:24 final size:24
Alignment explanation
Indices: 2401--2578 Score: 83
Period size: 24 Copynumber: 6.9 Consensus size: 24
2391 GGCCCAAAAG
2401 AGAAGG-GAAGAAGAAGAGGAAGCC
1 AGAAGGAG-AGAAGAAGAGGAAGCC
* *
2425 AGAAGGAGAGAGGAAGAGGAAG-A
1 AGAAGGAGAGAAGAAGAGGAAGCC
* * *
2448 AGCTAAGAGAAGAGAAAAAAAGGAGGCC
1 AG--AAG-G-AGAGAAGAAGAGGAAGCC
* *
2476 AGAAGGAGAGAGGAAGAGGAAGAAGCTAAG
1 AGAAGGAGAGAAGAAGA-G--GAAGC---C
* *
2506 AGAAGGAGAGAGGAAGAGGAAG-A
1 AGAAGGAGAGAAGAAGAGGAAGCC
* *
2529 AGCTAAGAGAAGAGAAGAAAAGGAGGCC
1 AG--AAG-G-AGAGAAGAAGAGGAAGCC
* *
2557 AGAAGGAGAGAGGAGGAGGAAG
1 AGAAGGAGAGAAGAAGAGGAAG
2579 AAGAGGCCAG
Statistics
Matches: 116, Mismatches: 21, Indels: 34
0.68 0.12 0.20
Matches are distributed among these distances:
23 4 0.03
24 39 0.34
25 10 0.09
26 8 0.07
27 33 0.28
28 4 0.03
29 1 0.01
30 17 0.15
ACGTcount: A:0.51, C:0.05, G:0.43, T:0.02
Consensus pattern (24 bp):
AGAAGGAGAGAAGAAGAGGAAGCC
Found at i:2441 original size:51 final size:49
Alignment explanation
Indices: 2398--2510 Score: 127
Period size: 51 Copynumber: 2.2 Consensus size: 49
2388 AGAGGCCCAA
* *
2398 AAGAGAAGGGAAGAAGAAGAGGAAGCCAGAAGGAGAGAGGAAGAGGAAGAAGC
1 AAGAGAAGAGAA-AA-AA-AGGAAGCCAGAAGGAGAGAGGAAGAGGAACAA-C
* *
2451 TAAGAGAAGAGAAAAAAAGGAGGCCAGAAGGAGAGAGGAAGAGGAAGAAGC
1 -AAGAGAAGAGAAAAAAAGGAAGCCAGAAGGAGAGAGGAAGAGGAACAA-C
2502 TAAGAGAAG
1 -AAGAGAAG
2511 GAGAGAGGAA
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
51 42 0.74
52 2 0.04
53 2 0.04
54 11 0.19
ACGTcount: A:0.52, C:0.05, G:0.41, T:0.02
Consensus pattern (49 bp):
AAGAGAAGAGAAAAAAAGGAAGCCAGAAGGAGAGAGGAAGAGGAACAAC
Found at i:2474 original size:81 final size:81
Alignment explanation
Indices: 2329--2657 Score: 334
Period size: 81 Copynumber: 4.1 Consensus size: 81
2319 GAGGAAAGAG
* * * * ** *
2329 GAGGAAGAGGAGGCCAGAAAGA-AAAGAGAGGAGGAAGAAGCTAAGAGGAA-AGCGGAAGAA-GA
1 GAGGAAGAGGAAGCCAGAAGGAGAGAG-GAAGAGGAAGAAGCTAAGA-GAAGAG-AAAAAAAGGA
*
2391 GGCCCA-AAAGAGA-AGGGAA
63 GG-CCAGAAGGAGAGA-GGAA
*
2410 GAAGAAGAGGAAGCCAGAAGGAGAGAGGAAGAGGAAGAAGCTAAGAGAAGAGAAAAAAAGGAGGC
1 GAGGAAGAGGAAGCCAGAAGGAGAGAGGAAGAGGAAGAAGCTAAGAGAAGAGAAAAAAAGGAGGC
2475 CAGAAGGAGAGAGGAA
66 CAGAAGGAGAGAGGAA
* *
2491 GAGGAAGAAGCTAAG--AGAAGGAGAGAGGAAGAGGAAGAAGCTAAGAGAAGAGAAGAAAAGGAG
1 GAGGAAG-AG-GAAGCCAGAAGGAGAGAGGAAGAGGAAGAAGCTAAGAGAAGAGAAAAAAAGGAG
*
2554 GCCAGAAGGAGAGAGGAG
64 GCCAGAAGGAGAGAGGAA
* * * * * * * *
2572 GAGGAAGAAGAGGCCAGGAGGAGAGAGGAGGAAGAAGAAGCTAGGACGGAAGAG--GAAGAGGAG
1 GAGGAAGAGGAAGCCAGAAGGAGAGAGGAAGAGGAAGAAGCTAAGA--GAAGAGAAAAAAAGGAG
2635 GCCAGAAGGAGAGAGGAA
64 GCCAGAAGGAGAGAGGAA
2653 GAGGA
1 GAGGA
2658 TGCTCGAAGG
Statistics
Matches: 215, Mismatches: 22, Indels: 22
0.83 0.08 0.08
Matches are distributed among these distances:
79 2 0.01
80 11 0.05
81 187 0.87
82 6 0.03
83 9 0.04
ACGTcount: A:0.48, C:0.07, G:0.43, T:0.02
Consensus pattern (81 bp):
GAGGAAGAGGAAGCCAGAAGGAGAGAGGAAGAGGAAGAAGCTAAGAGAAGAGAAAAAAAGGAGGC
CAGAAGGAGAGAGGAA
Found at i:2590 original size:17 final size:16
Alignment explanation
Indices: 2551--2599 Score: 52
Period size: 15 Copynumber: 3.2 Consensus size: 16
2541 AGAAGAAAAG
*
2551 GAGGCCAGAAGG-AGA
1 GAGGCCAGGAGGAAGA
2566 GAGG--AGGAGGAAGAA
1 GAGGCCAGGAGGAAG-A
2581 GAGGCCAGGAGG-AGA
1 GAGGCCAGGAGGAAGA
2596 GAGG
1 GAGG
2600 AGGAAGAAGA
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
13 5 0.17
14 2 0.07
15 14 0.48
16 2 0.07
17 6 0.21
ACGTcount: A:0.39, C:0.08, G:0.53, T:0.00
Consensus pattern (16 bp):
GAGGCCAGGAGGAAGA
Found at i:2633 original size:30 final size:28
Alignment explanation
Indices: 2560--2633 Score: 89
Period size: 27 Copynumber: 2.6 Consensus size: 28
2550 GGAGGCCAGA
*
2560 AGGA-GAGAGGAGGAGGAAGAAGAGGCC
1 AGGAGGAGAGGAGGAGGAAGAAGAAGCC
*
2587 AGGAGGAGA-GAGGAGGAAGAAGAAGCT
1 AGGAGGAGAGGAGGAGGAAGAAGAAGCC
*
2614 AGGACGGAAGAGGAAGAGGA
1 AGGA-GG-AGAGGAGGAGGA
2634 GGCCAGAAGG
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
27 24 0.60
28 6 0.15
29 3 0.08
30 7 0.17
ACGTcount: A:0.43, C:0.05, G:0.50, T:0.01
Consensus pattern (28 bp):
AGGAGGAGAGGAGGAGGAAGAAGAAGCC
Found at i:2657 original size:24 final size:25
Alignment explanation
Indices: 2567--2654 Score: 92
Period size: 24 Copynumber: 3.6 Consensus size: 25
2557 AGAAGGAGAG
2567 AGGAG-GAGGAAGAAGAGGCCAGGA
1 AGGAGAGAGGAAGAAGAGGCCAGGA
* * *
2591 GGAGAGAGGAGGAAGAAGAAGCTAGGA
1 AG-GAGA-GAGGAAGAAGAGGCCAGGA
* *
2618 CGGA-AGAGGAAGAGGAGGCCA-GA
1 AGGAGAGAGGAAGAAGAGGCCAGGA
2641 AGGAGAGAGGAAGA
1 AGGAGAGAGGAAGA
2655 GGATGCTCGA
Statistics
Matches: 52, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
23 5 0.10
24 23 0.44
25 4 0.08
26 2 0.04
27 18 0.35
ACGTcount: A:0.43, C:0.07, G:0.49, T:0.01
Consensus pattern (25 bp):
AGGAGAGAGGAAGAAGAGGCCAGGA
Found at i:2666 original size:24 final size:24
Alignment explanation
Indices: 2567--2672 Score: 83
Period size: 24 Copynumber: 4.3 Consensus size: 24
2557 AGAAGGAGAG
*
2567 AGGAG-GAGGAAGAAGAGGCCAGGA
1 AGGAGAGAGGAAGAGGAGGCCA-GA
* * * *
2591 GGAGAGAGGAGGAAGAAGAAGCTAGGA
1 AG-GAGA-GAGGAAGAGGAGGCCA-GA
*
2618 CGGA-AGAGGAAGAGGAGGCCAGA
1 AGGAGAGAGGAAGAGGAGGCCAGA
*
2641 AGGAGAGAGGAAGAGGATGCTC-GA
1 AGGAGAGAGGAAGAGGAGGC-CAGA
2665 AGGAGAGA
1 AGGAGAGA
2673 AGAGGAAGAG
Statistics
Matches: 68, Mismatches: 9, Indels: 10
0.78 0.10 0.11
Matches are distributed among these distances:
23 5 0.07
24 38 0.56
25 5 0.07
26 2 0.03
27 18 0.26
ACGTcount: A:0.42, C:0.08, G:0.48, T:0.03
Consensus pattern (24 bp):
AGGAGAGAGGAAGAGGAGGCCAGA
Done.