Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CotAD_51961
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: 2949
ACGTcount: A:0.33, C:0.17, G:0.29, T:0.20
Found at i:2341 original size:24 final size:24
Alignment explanation
Indices: 2305--2399 Score: 73
Period size: 24 Copynumber: 3.7 Consensus size: 24
2295 TGAAAGGGAA
* *
2305 AGGAAGGAAGAGGAAGAAGCCAGG
1 AGGAAAGAGGAGGAAGAAGCCAGG
*
2329 AGGAAAGAGGAGGAAGAGGAGGCCAGAA
1 AGGAAAGAGGAGGAAGA--A-GCCAG-G
* *
2357 AGAGAAGAGAGGAGGAAGAAGCTAAG
1 AG-GAA-AGAGGAGGAAGAAGCCAGG
* *
2383 AGGAAAGCGGAAGAAGA
1 AGGAAAGAGGAGGAAGA
2400 GGCCCAAAAG
Statistics
Matches: 57, Mismatches: 8, Indels: 12
0.74 0.10 0.16
Matches are distributed among these distances:
24 25 0.44
25 3 0.05
26 3 0.05
27 8 0.14
28 3 0.05
29 3 0.05
30 12 0.21
ACGTcount: A:0.48, C:0.06, G:0.44, T:0.01
Consensus pattern (24 bp):
AGGAAAGAGGAGGAAGAAGCCAGG
Found at i:2426 original size:51 final size:54
Alignment explanation
Indices: 2302--2426 Score: 143
Period size: 54 Copynumber: 2.4 Consensus size: 54
2292 AATTGAAAGG
* * *
2302 GAAAG-GAA-GGAAGAGGAAGAAGCCAGGAGGAAAGAGGAGGAAGAGGAGGCCA
1 GAAAGAGAAGGGAAGAGGAAGAAGCCAAGAGGAAAGAGGAAGAAGAGGAGCCCA
* * * *
2354 GAAAGAGAAGAGAGGAGGAAGAAGCTAAGAGGAAAGCGGAAGAAGA-G-GCCCA
1 GAAAGAGAAGGGAAGAGGAAGAAGCCAAGAGGAAAGAGGAAGAAGAGGAGCCCA
*
2406 -AAAGAGAAGGGAAGAAGAAGA
1 GAAAGAGAAGGGAAGAGGAAGA
2427 GGAAGCCAGA
Statistics
Matches: 61, Mismatches: 10, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
51 18 0.30
52 9 0.15
53 4 0.07
54 30 0.49
ACGTcount: A:0.50, C:0.07, G:0.42, T:0.01
Consensus pattern (54 bp):
GAAAGAGAAGGGAAGAGGAAGAAGCCAAGAGGAAAGAGGAAGAAGAGGAGCCCA
Found at i:2437 original size:24 final size:24
Alignment explanation
Indices: 2410--2614 Score: 92
Period size: 27 Copynumber: 7.9 Consensus size: 24
2400 GGCCCAAAAG
2410 AGAAGG-GAAGAAGAAGAGGAAGCC
1 AGAAGGAG-AGAAGAAGAGGAAGCC
* *
2434 AGAAGGAGAGAGGAAGAGGAAG-A
1 AGAAGGAGAGAAGAAGAGGAAGCC
* * *
2457 AGCTAAGAGAAGAGAAAAAAAGGAGGCC
1 AG--AAG-G-AGAGAAGAAGAGGAAGCC
* *
2485 AGAAGGAGAGAGGAAGAGGAAGAAGCTAAG
1 AGAAGGAGAGAAGAAGA-G--GAAGC---C
* *
2515 AGAAGGAGAGAGGAAGAGGAAGCTA
1 AGAAGGAGAGAAGAAGAGGAAGC-C
* *
2540 AGAGGAGGAGAGAGGAAGAGGAAG-A
1 AGA--AGGAGAGAAGAAGAGGAAGCC
* *
2565 AGCTAAGAGAAGAGAAGAAAAGGAGGCC
1 AG--AAG-G-AGAGAAGAAGAGGAAGCC
* *
2593 AGAAGGAGAGAGGAGGAGGAAG
1 AGAAGGAGAGAAGAAGAGGAAG
2615 AAGAGGCCAG
Statistics
Matches: 140, Mismatches: 22, Indels: 38
0.70 0.11 0.19
Matches are distributed among these distances:
23 2 0.01
24 39 0.28
25 15 0.11
26 8 0.06
27 54 0.39
28 4 0.03
29 1 0.01
30 17 0.12
ACGTcount: A:0.50, C:0.05, G:0.43, T:0.02
Consensus pattern (24 bp):
AGAAGGAGAGAAGAAGAGGAAGCC
Found at i:2483 original size:81 final size:81
Alignment explanation
Indices: 2341--2536 Score: 199
Period size: 81 Copynumber: 2.4 Consensus size: 81
2331 GAAAGAGGAG
* * * ** *
2341 GAAGAGGAGGCCAGAAAGAGA-AGAGAGGAGGAAGAAGCTAAGAGGAAAGCGGAAGAAGAGGCCC
1 GAAGAGGAAGCCAGAAGGAGAGAG-GAAGAGGAAGAAGCTAAGAGGAAAGCAAAAAAAGAGG-CC
2405 AAAA-GAGA-AGGGAAGAA
64 AAAAGGAGAGA-GGAAGAA
2422 GAAGAGGAAGCCAGAAGGAGAGAGGAAGAGGAAGAAGCTAAGA-GAAGAG-AAAAAAAGGAGGCC
1 GAAGAGGAAGCCAGAAGGAGAGAGGAAGAGGAAGAAGCTAAGAGGAA-AGCAAAAAAA-GAGGCC
* *
2485 AGAAGGAGAGAGGAAGAG
64 AAAAGGAGAGAGGAAGAA
*
2503 GAAGAAGCTAAG--AGAAGGAGAGAGGAAGAGGAAG
1 GAAG-AG-GAAGCCAGAAGGAGAGAGGAAGAGGAAG
2537 CTAAGAGGAG
Statistics
Matches: 99, Mismatches: 9, Indels: 14
0.81 0.07 0.11
Matches are distributed among these distances:
80 12 0.12
81 79 0.80
82 5 0.05
83 3 0.03
ACGTcount: A:0.50, C:0.07, G:0.42, T:0.02
Consensus pattern (81 bp):
GAAGAGGAAGCCAGAAGGAGAGAGGAAGAGGAAGAAGCTAAGAGGAAAGCAAAAAAAGAGGCCAA
AAGGAGAGAGGAAGAA
Found at i:2576 original size:108 final size:105
Alignment explanation
Indices: 2407--2617 Score: 343
Period size: 108 Copynumber: 2.0 Consensus size: 105
2397 AGAGGCCCAA
*
2407 AAGAGAAGGGAAGAAGAAGAGGAAGCCAGAAGGAGAGAGGAAGAGGAAGAAGCTAAGAGAAGAGA
1 AAGAGAAGGGAAGAAGAAGAGGAAGCAAGAAGGAGAGAGGAAGAGGAAGAAGCTAAGAGAAGAGA
2472 AAAAAAGGAGGCCAGAAGGAGAGAGGAAGAGGAAGAAGCT
66 AAAAAAGGAGGCCAGAAGGAGAGAGGAAGAGGAAGAAGCT
*
2512 AAGAGAA-GGAGAGAGGAAGAGGAAGCTAAGAGGAGGAGAGAGGAAGAGGAAGAAGCTAAGAGAA
1 AAGAGAAGGGA-AGAAGAAGAGGAAGC-AAGA--AGGAGAGAGGAAGAGGAAGAAGCTAAGAGAA
* *
2576 GAGAAGAAAAGGAGGCCAGAAGGAGAGAGGAGGAGGAAGAAG
62 GAGAAAAAAAGGAGGCCAGAAGGAGAGAGGAAGAGGAAGAAG
2618 AGGCCAGGAG
Statistics
Matches: 98, Mismatches: 4, Indels: 5
0.92 0.04 0.05
Matches are distributed among these distances:
104 3 0.03
105 21 0.21
106 3 0.03
108 71 0.72
ACGTcount: A:0.50, C:0.05, G:0.43, T:0.02
Consensus pattern (105 bp):
AAGAGAAGGGAAGAAGAAGAGGAAGCAAGAAGGAGAGAGGAAGAGGAAGAAGCTAAGAGAAGAGA
AAAAAAGGAGGCCAGAAGGAGAGAGGAAGAGGAAGAAGCT
Found at i:2614 original size:51 final size:51
Alignment explanation
Indices: 2418--2617 Score: 283
Period size: 51 Copynumber: 3.8 Consensus size: 51
2408 AGAGAAGGGA
*
2418 AGAAGAAGAGGAAGCCAGAAGGAGAGAGGAAGAGGAAGAAGCTAAGAGAAG
1 AGAAGAAAAGGAAGCCAGAAGGAGAGAGGAAGAGGAAGAAGCTAAGAGAAG
* *
2469 AGAAAAAAAGGAGGCCAGAAGGAGAGAGGAAGAGGAAGAAGCTAAGAGAAGG
1 AGAAGAAAAGGAAGCCAGAAGGAGAGAGGAAGAGGAAGAAGCTAAGAGAA-G
* *
2521 AGAGAGGAAGAGGAAGCTAAGAGGAGGAGAGAGGAAGAGGAAGAAGCTAAGAGAAG
1 AGA-A-GAAAAGGAAGC-CAGA--AGGAGAGAGGAAGAGGAAGAAGCTAAGAGAAG
* *
2577 AGAAGAAAAGGAGGCCAGAAGGAGAGAGGAGGAGGAAGAAG
1 AGAAGAAAAGGAAGCCAGAAGGAGAGAGGAAGAGGAAGAAG
2618 AGGCCAGGAG
Statistics
Matches: 132, Mismatches: 11, Indels: 12
0.85 0.07 0.08
Matches are distributed among these distances:
51 68 0.52
52 4 0.03
53 4 0.03
54 17 0.13
55 4 0.03
56 4 0.03
57 31 0.23
ACGTcount: A:0.50, C:0.05, G:0.43, T:0.02
Consensus pattern (51 bp):
AGAAGAAAAGGAAGCCAGAAGGAGAGAGGAAGAGGAAGAAGCTAAGAGAAG
Found at i:2626 original size:17 final size:16
Alignment explanation
Indices: 2587--2635 Score: 52
Period size: 15 Copynumber: 3.2 Consensus size: 16
2577 AGAAGAAAAG
*
2587 GAGGCCAGAAGG-AGA
1 GAGGCCAGGAGGAAGA
2602 GAGG--AGGAGGAAGAA
1 GAGGCCAGGAGGAAG-A
2617 GAGGCCAGGAGG-AGA
1 GAGGCCAGGAGGAAGA
2632 GAGG
1 GAGG
2636 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:2646 original size:30 final size:30
Alignment explanation
Indices: 2570--2647 Score: 106
Period size: 30 Copynumber: 2.6 Consensus size: 30
2560 GAAGAAGCTA
*
2570 AGAGAAGA-GAAGAA-AAGGAGGCCAGAAGG
1 AGAGAGGAGGAAGAAGAA-GAGGCCAGAAGG
* *
2599 AGAGAGGAGGAGGAAGAAGAGGCCAGGAGG
1 AGAGAGGAGGAAGAAGAAGAGGCCAGAAGG
2629 AGAGAGGAGGAAGAAGAAG
1 AGAGAGGAGGAAGAAGAAG
2648 CTAGTACGGA
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
29 7 0.16
30 34 0.79
31 2 0.05
ACGTcount: A:0.47, C:0.05, G:0.47, T:0.00
Consensus pattern (30 bp):
AGAGAGGAGGAAGAAGAAGAGGCCAGAAGG
Found at i:2669 original size:30 final size:28
Alignment explanation
Indices: 2596--2648 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 28
2586 GGAGGCCAGA
*
2596 AGGA-GAGAGGAGGAGGAAGAAGAGGCC
1 AGGAGGAGAGGAGGAGGAAGAAGAAGCC
2623 AGGAGGAGA-GAGGAGGAAGAAGAAGC
1 AGGAGGAGAGGAGGAGGAAGAAGAAGC
2649 TAGTACGGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 20 0.83
28 4 0.17
ACGTcount: A:0.43, C:0.06, G:0.51, T:0.00
Consensus pattern (28 bp):
AGGAGGAGAGGAGGAGGAAGAAGAAGCC
Found at i:2669 original size:108 final size:107
Alignment explanation
Indices: 2407--2650 Score: 325
Period size: 108 Copynumber: 2.3 Consensus size: 107
2397 AGAGGCCCAA
* * *
2407 AAGAGAAGG-GAAGAAGAAGAGGAAGC-CAGA-AGGAGAGAGGAAGAGGAAGAAGCTAAGAGAAG
1 AAGAGAAGGAG-AGAGGAAGAAGAAGCTAAGAGAGGAGAGAGGAAGAGGAAGAAGCTAAGAGAAG
*
2469 AGAAAAAAAGGAGGCCAGAAGGAGAGAGGAAGAGGAAGAAGCT
65 AGAAAAAAAGGAGGCCAGAAGGAGAGAGGAAGAGGAAGAAGCC
*
2512 AAGAGAAGGAGAGAGGAAGAGGAAGCTAAGAGGAGGAGAGAGGAAGAGGAAGAAGCTAAGAGAAG
1 AAGAGAAGGAGAGAGGAAGAAGAAGCTAAGA-GAGGAGAGAGGAAGAGGAAGAAGCTAAGAGAAG
* *
2577 AGAAGAAAAGGAGGCCAGAAGGAGAGAGGAGGAGGAAGAAGAGGCC
65 AGAAAAAAAGGAGGCCAGAAGGAGAGAGGAAGAGGAAG-A-A-GCC
* *
2623 AGGAGGA-GAGAGGAGGAAGAAGAAGCTA
1 AAGAGAAGGAGA-GAGGAAGAAGAAGCTA
2651 GTACGGAAGA
Statistics
Matches: 123, Mismatches: 8, Indels: 10
0.87 0.06 0.07
Matches are distributed among these distances:
105 23 0.19
106 4 0.03
108 68 0.55
109 1 0.01
110 5 0.04
111 22 0.18
ACGTcount: A:0.49, C:0.05, G:0.43, T:0.02
Consensus pattern (107 bp):
AAGAGAAGGAGAGAGGAAGAAGAAGCTAAGAGAGGAGAGAGGAAGAGGAAGAAGCTAAGAGAAGA
GAAAAAAAGGAGGCCAGAAGGAGAGAGGAAGAGGAAGAAGCC
Found at i:2691 original size:24 final size:24
Alignment explanation
Indices: 2603--2719 Score: 87
Period size: 24 Copynumber: 4.8 Consensus size: 24
2593 AGAAGGAGAG
2603 AGGAG-GAGGAAGAAGAGGCCAGGA
1 AGGAGAGAGGAAGAAGAGGCCA-GA
* * *
2627 GGAGAGAGGAGGAAGAAGAAGCTAGTA
1 AG-GAGA-GAGGAAGAAGAGGCCAG-A
* *
2654 CGGA-AGAGGAAGAGGAGGCCAGA
1 AGGAGAGAGGAAGAAGAGGCCAGA
* *
2677 AGGAGAGAGGAAGAGGATGCTC-GA
1 AGGAGAGAGGAAGAAGAGGC-CAGA
* *
2701 AGGAGAGAAGAGGAAGAGG
1 AGGAGAGAGGAAGAAGAGG
2720 GAGCTACAAG
Statistics
Matches: 74, Mismatches: 13, Indels: 12
0.75 0.13 0.12
Matches are distributed among these distances:
23 4 0.05
24 46 0.62
25 5 0.07
26 3 0.04
27 16 0.22
ACGTcount: A:0.42, C:0.07, G:0.48, T:0.03
Consensus pattern (24 bp):
AGGAGAGAGGAAGAAGAGGCCAGA
Found at i:2693 original size:81 final size:77
Alignment explanation
Indices: 2515--2693 Score: 220
Period size: 81 Copynumber: 2.3 Consensus size: 77
2505 AGAAGCTAAG
* *
2515 AGAAGGAGAGAGGAAGAGGAAGCTAAGAGGAGGAGAGAGGAAGAGGAAGAAGCTAAGAGAAGAGA
1 AGAAGGAGAGAGGAAGAGGAAGCAAAGAGGAGGAGAGAGGAAGAAGAAGAAGCTAAGAGAAGAG-
2580 AGAAAAGGAGGCC
65 AGAAAAGGAGGCC
* *
2593 AGAAGGAGAGAGGAGGAGGAAG-AAGAGGCCAGGAGGAGAGAGGAGGAAGAAGAAGCT-AGTACG
1 AGAAGGAGAGAGGAAGAGGAAGCAA-A-G--AGGAGGAGAGAGGAAGAAGAAGAAGCTAAG-A--
*
2656 GAAGAG-GAAGAGGAGGCC
59 GAAGAGAGAAAAGGAGGCC
2674 AGAAGGAGAGAGGAAGAGGA
1 AGAAGGAGAGAGGAAGAGGA
2694 TGCTCGAAGG
Statistics
Matches: 88, Mismatches: 6, Indels: 11
0.84 0.06 0.10
Matches are distributed among these distances:
77 1 0.01
78 22 0.25
79 1 0.01
80 2 0.02
81 56 0.64
83 6 0.07
ACGTcount: A:0.46, C:0.06, G:0.46, T:0.02
Consensus pattern (77 bp):
AGAAGGAGAGAGGAAGAGGAAGCAAAGAGGAGGAGAGAGGAAGAAGAAGAAGCTAAGAGAAGAGA
GAAAAGGAGGCC
Done.