Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold496
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: 277391
ACGTcount: A:0.25, C:0.13, G:0.13, T:0.26
Warning! 63887 characters in sequence are not A, C, G, or T
Found at i:2498 original size:17 final size:17
Alignment explanation
Indices: 2476--2524 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 17
2466 TATTATTATT
*
2476 ATTTTGAAACACGAGAA
1 ATTTTGAAACACGAAAA
*
2493 ATTTTG-AAGACGTAAAA
1 ATTTTGAAACACG-AAAA
2510 ATTTGTGAAACACGA
1 ATTT-TGAAACACGA
2525 TTTTTTTTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
16 5 0.19
17 13 0.50
18 3 0.12
19 5 0.19
ACGTcount: A:0.45, C:0.10, G:0.18, T:0.27
Consensus pattern (17 bp):
ATTTTGAAACACGAAAA
Found at i:2993 original size:20 final size:21
Alignment explanation
Indices: 2968--3008 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
2958 GTGGGCCCTT
2968 TTCC-TTTTTTCTTTTTTTTC
1 TTCCTTTTTTTCTTTTTTTTC
2988 TTCCTTTTTTTTCTTTTTTTT
1 TTCC-TTTTTTTCTTTTTTTT
3009 TTGGGCCTGC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 4 0.21
22 15 0.79
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (21 bp):
TTCCTTTTTTTCTTTTTTTTC
Found at i:2994 original size:13 final size:12
Alignment explanation
Indices: 2972--3010 Score: 55
Period size: 11 Copynumber: 3.3 Consensus size: 12
2962 GCCCTTTTCC
2972 TTTT-TTCTTTT
1 TTTTCTTCTTTT
2983 TTTTCTTCCTTTT
1 TTTTCTT-CTTTT
2996 TTTTCTT-TTTT
1 TTTTCTTCTTTT
3007 TTTT
1 TTTT
3011 GGGCCTGCTG
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
11 12 0.46
12 2 0.08
13 12 0.46
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (12 bp):
TTTTCTTCTTTT
Found at i:3138 original size:22 final size:23
Alignment explanation
Indices: 3113--3156 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
3103 GGCGGTACTG
3113 GGCCTGCT-GCTGCTGCTGGGCT
1 GGCCTGCTAGCTGCTGCTGGGCT
* *
3135 GGCCTGCTAGGTGCTGTTGGGC
1 GGCCTGCTAGCTGCTGCTGGGC
3157 CTGGACTGGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.02, C:0.27, G:0.43, T:0.27
Consensus pattern (23 bp):
GGCCTGCTAGCTGCTGCTGGGCT
Found at i:3409 original size:6 final size:6
Alignment explanation
Indices: 3400--3490 Score: 101
Period size: 6 Copynumber: 14.3 Consensus size: 6
3390 CTTTTAATTT
*
3400 TTTTTC TTTTTTC TTTTTC TTTTTC TTTCTC TTTTTC TTTTTC TTTTTC
1 TTTTTC -TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC
** *
3449 TTCTCCC TTTTTC TTCTTC TTTTTTC TTTCTTC TTTCTTC TT
1 TT-TTTC TTTTTC TTTTTC -TTTTTC TTT-TTC TTT-TTC TT
3491 CTTCGGGCAG
Statistics
Matches: 73, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
6 46 0.63
7 27 0.37
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (6 bp):
TTTTTC
Found at i:3409 original size:7 final size:7
Alignment explanation
Indices: 3399--3490 Score: 66
Period size: 7 Copynumber: 13.3 Consensus size: 7
3389 ACTTTTAATT
3399 TTTTTTC
1 TTTTTTC
3406 TTTTTTC
1 TTTTTTC
*
3413 TTTTTCTT
1 TTTTT-TC
3421 TTTCTTTC
1 TTT-TTTC
3429 TCTTTTTC
1 T-TTTTTC
3437 -TTTTTC
1 TTTTTTC
3443 -TTTTTC
1 TTTTTTC
* *
3449 -TTCTCC
1 TTTTTTC
*
3455 CTTTTTC
1 TTTTTTC
*
3462 -TTCTTC
1 TTTTTTC
3468 TTTTTTC
1 TTTTTTC
*
3475 TTTCTTC
1 TTTTTTC
*
3482 TTTCTTC
1 TTTTTTC
3489 TT
1 TT
3491 CTTCGGGCAG
Statistics
Matches: 71, Mismatches: 9, Indels: 10
0.79 0.10 0.11
Matches are distributed among these distances:
6 21 0.30
7 36 0.51
8 10 0.14
9 4 0.06
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (7 bp):
TTTTTTC
Found at i:3439 original size:24 final size:24
Alignment explanation
Indices: 3397--3490 Score: 120
Period size: 24 Copynumber: 3.8 Consensus size: 24
3387 TGACTTTTAA
3397 TTTTT-TTTCT-TTTTTCTTTTTC
1 TTTTTCTTTCTCTTTTTCTTTTTC
3419 TTTTTCTTTCTCTTTTTCTTTTTC
1 TTTTTCTTTCTCTTTTTCTTTTTC
* *
3443 TTTTTCTTCTCCCTTTTTCTTCTTC
1 TTTTTCTT-TCTCTTTTTCTTTTTC
3468 TTTTTTCTTTCTTCTTTCTTCTT
1 -TTTTTCTTTC-TCTTT-TTCTT
3491 CTTCGGGCAG
Statistics
Matches: 63, Mismatches: 3, Indels: 7
0.86 0.04 0.10
Matches are distributed among these distances:
22 5 0.08
23 5 0.08
24 20 0.32
25 16 0.25
26 12 0.19
27 5 0.08
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (24 bp):
TTTTTCTTTCTCTTTTTCTTTTTC
Found at i:3446 original size:37 final size:39
Alignment explanation
Indices: 3418--3492 Score: 102
Period size: 38 Copynumber: 1.9 Consensus size: 39
3408 TTTTCTTTTT
3418 CTTTTTC-T-TTCTCTTTTTCTTTTTC-TTTTTCTTCTCC
1 CTTTTTCTTCTTCT-TTTTTCTTTTTCTTTTTTCTTCTCC
*
3455 CTTTTTCTTCTTCTTTTTTCTTTCTTCTTTCTTCTTCT
1 CTTTTTCTTCTTCTTTTTTCTTT-TTCTTTTTTCTTCT
3493 TCGGGCAGCA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
37 7 0.21
38 10 0.30
39 7 0.21
40 9 0.27
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (39 bp):
CTTTTTCTTCTTCTTTTTTCTTTTTCTTTTTTCTTCTCC
Found at i:3459 original size:43 final size:43
Alignment explanation
Indices: 3412--3494 Score: 116
Period size: 43 Copynumber: 1.9 Consensus size: 43
3402 TTTCTTTTTT
* *
3412 CTTTTTCTTTTTCTTTCTCTT-TTTCTT-TTTCTTTTTCTTCTCC
1 CTTTTTCTTCTTCTTT-T-TTCTTTCTTCTTTCTTCTTCTTCTCC
3455 CTTTTTCTTCTTCTTTTTTCTTTCTTCTTTCTTCTTCTTC
1 CTTTTTCTTCTTCTTTTTTCTTTCTTCTTTCTTCTTCTTC
3495 GGGCAGCACC
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
41 2 0.06
42 7 0.19
43 27 0.75
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (43 bp):
CTTTTTCTTCTTCTTTTTTCTTTCTTCTTTCTTCTTCTTCTCC
Found at i:3638 original size:19 final size:17
Alignment explanation
Indices: 3616--3654 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
3606 TTTTCTTGTT
3616 TTTTGCTGCTGCGTTTTTG
1 TTTTGCTGCT-C-TTTTTG
*
3635 TTTTGCTTCTCTTTTTG
1 TTTTGCTGCTCTTTTTG
3652 TTT
1 TTT
3655 CACTTTCTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 9 0.47
18 1 0.05
19 9 0.47
ACGTcount: A:0.00, C:0.15, G:0.18, T:0.67
Consensus pattern (17 bp):
TTTTGCTGCTCTTTTTG
Found at i:3850 original size:24 final size:24
Alignment explanation
Indices: 3805--3850 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
3795 TCCCCTTTCT
*
3805 TCTCTTCCATTTTCTTCTTTTTAA
1 TCTCTTCCATTTTCTTCCTTTTAA
*
3829 TCTCTT-CATTTTTTGTCCTTTT
1 TCTCTTCCATTTTCT-TCCTTTT
3851 TCTTCTTGTC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 7 0.37
24 12 0.63
ACGTcount: A:0.09, C:0.24, G:0.02, T:0.65
Consensus pattern (24 bp):
TCTCTTCCATTTTCTTCCTTTTAA
Found at i:4071 original size:59 final size:58
Alignment explanation
Indices: 3995--4134 Score: 185
Period size: 59 Copynumber: 2.4 Consensus size: 58
3985 ACGCAAAATA
*
3995 TTTGGGGTAAAAATGTAATTTT-AGGAAAATATGGGGCCAAAATGTAATTTTCA-AAAAG
1 TTTGGGGTCAAAATGTAATTTTGA-GAAAATATGGGGCCAAAATGTAATTTT-AGAAAAG
* * * *
4053 TTTAGGGGTCAAAGTGTAATTTTGAGAAAGTTTGGGGCCAAAATGTAATTTTAGCAAAG
1 TTT-GGGGTCAAAATGTAATTTTGAGAAAATATGGGGCCAAAATGTAATTTTAGAAAAG
4112 TTTGGGGTCAAAATGTAAATTTT
1 TTTGGGGTCAAAATGT-AATTTT
4135 TATTTTTTGT
Statistics
Matches: 72, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
58 16 0.22
59 55 0.76
60 1 0.01
ACGTcount: A:0.36, C:0.06, G:0.24, T:0.34
Consensus pattern (58 bp):
TTTGGGGTCAAAATGTAATTTTGAGAAAATATGGGGCCAAAATGTAATTTTAGAAAAG
Found at i:4073 original size:30 final size:28
Alignment explanation
Indices: 3995--4134 Score: 138
Period size: 29 Copynumber: 4.8 Consensus size: 28
3985 ACGCAAAATA
**
3995 TTTGGGGTAAAAATGTAATTTTAGGAAAA-
1 TTTGGGGCCAAAATGTAATTTTA--AAAAG
*
4024 TATGGGGCCAAAATGTAATTTTCAAAAAG
1 TTTGGGGCCAAAATGTAATTTT-AAAAAG
* * *
4053 TTTAGGGGTCAAAGTGTAATTTTGAGAAAG
1 TTT-GGGGCCAAAATGTAATTTT-AAAAAG
*
4083 TTTGGGGCCAAAATGTAATTTTAGCAAAG
1 TTTGGGGCCAAAATGTAATTTTA-AAAAG
*
4112 TTTGGGGTCAAAATGTAAATTTT
1 TTTGGGGCCAAAATGT-AATTTT
4135 TATTTTTTGT
Statistics
Matches: 94, Mismatches: 12, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
28 5 0.05
29 57 0.61
30 32 0.34
ACGTcount: A:0.36, C:0.06, G:0.24, T:0.34
Consensus pattern (28 bp):
TTTGGGGCCAAAATGTAATTTTAAAAAG
Found at i:4491 original size:28 final size:28
Alignment explanation
Indices: 4425--4484 Score: 120
Period size: 28 Copynumber: 2.1 Consensus size: 28
4415 ATATAAGGTC
4425 ATATACGAATAGTAGGAAGATTTAAAAT
1 ATATACGAATAGTAGGAAGATTTAAAAT
4453 ATATACGAATAGTAGGAAGATTTAAAAT
1 ATATACGAATAGTAGGAAGATTTAAAAT
4481 ATAT
1 ATAT
4485 TTTAATAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.50, C:0.03, G:0.17, T:0.30
Consensus pattern (28 bp):
ATATACGAATAGTAGGAAGATTTAAAAT
Found at i:10872 original size:12 final size:13
Alignment explanation
Indices: 10855--10883 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
10845 TTCTTATTCG
10855 ATTTATTTA-TTT
1 ATTTATTTATTTT
10867 ATTTATTTATTTT
1 ATTTATTTATTTT
10880 ATTT
1 ATTT
10884 TCATTTTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.56
13 7 0.44
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (13 bp):
ATTTATTTATTTT
Found at i:11843 original size:3 final size:3
Alignment explanation
Indices: 11779--11829 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
11769 GTTTCATATC
11779 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
11827 TTA
1 TTA
11830 GACTGTTTTA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:14001 original size:23 final size:24
Alignment explanation
Indices: 13947--14001 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 24
13937 ATTTATTTAA
* *
13947 AATAAGTAAATGAAATTAATAATT
1 AATAATTAAATGAAAATAATAATT
* *
13971 ATTTATTAAAT-AAAATAATAATT
1 AATAATTAAATGAAAATAATAATT
13994 AATAATTA
1 AATAATTA
14002 TTTAAGACAA
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
23 17 0.68
24 8 0.32
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (24 bp):
AATAATTAAATGAAAATAATAATT
Found at i:16822 original size:14 final size:14
Alignment explanation
Indices: 16789--16825 Score: 60
Period size: 13 Copynumber: 2.8 Consensus size: 14
16779 CAATAAAGAA
16789 AAAGAAA-AAATCG
1 AAAGAAAGAAATCG
16802 AAA-AAAGAAATCG
1 AAAGAAAGAAATCG
16815 AAAGAAAGAAA
1 AAAGAAAGAAA
16826 AAAAATAAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 3 0.14
13 12 0.55
14 7 0.32
ACGTcount: A:0.73, C:0.05, G:0.16, T:0.05
Consensus pattern (14 bp):
AAAGAAAGAAATCG
Found at i:19909 original size:17 final size:18
Alignment explanation
Indices: 19871--19909 Score: 64
Period size: 17 Copynumber: 2.3 Consensus size: 18
19861 TGAATGAAGT
19871 AATAATAATTATAATAAC
1 AATAATAATTATAATAAC
19889 -ATAATAATTA-AATAAC
1 AATAATAATTATAATAAC
19905 AATAA
1 AATAA
19910 AAAGTATAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 6 0.30
17 14 0.70
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (18 bp):
AATAATAATTATAATAAC
Found at i:22715 original size:14 final size:14
Alignment explanation
Indices: 22696--22736 Score: 64
Period size: 15 Copynumber: 2.8 Consensus size: 14
22686 TATATATAGA
22696 TTTTATTTTTTATT
1 TTTTATTTTTTATT
22710 TTTTATATTTTTATT
1 TTTTAT-TTTTTATT
22725 TATTTATTTTTT
1 T-TTTATTTTTT
22737 GCCTAAATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.24
15 14 0.56
16 5 0.20
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (14 bp):
TTTTATTTTTTATT
Found at i:22716 original size:23 final size:22
Alignment explanation
Indices: 22672--22736 Score: 76
Period size: 23 Copynumber: 2.8 Consensus size: 22
22662 ATTATCGTTC
* *
22672 TTTTATTTTTCATTTATATATAGA
1 TTTTATTTTTTATTT-TTTATA-A
*
22696 TTTTATTTTTTATTTTTTATAT
1 TTTTATTTTTTATTTTTTATAA
22718 TTTTATTTATTTATTTTTT
1 TTTTATTT-TTTATTTTTT
22737 GCCTAAATAA
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
22 8 0.22
23 15 0.41
24 14 0.38
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.75
Consensus pattern (22 bp):
TTTTATTTTTTATTTTTTATAA
Found at i:22718 original size:9 final size:8
Alignment explanation
Indices: 22696--22736 Score: 50
Period size: 8 Copynumber: 5.4 Consensus size: 8
22686 TATATATAGA
22696 TTTTA-TT
1 TTTTATTT
22703 TTTTA-TT
1 TTTTATTT
*
22710 TTTTATAT
1 TTTTATTT
22718 TTTTATTT
1 TTTTATTT
*
22726 ATTTATTT
1 TTTTATTT
22734 TTT
1 TTT
22737 GCCTAAATAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
7 12 0.41
8 17 0.59
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (8 bp):
TTTTATTT
Found at i:22720 original size:8 final size:7
Alignment explanation
Indices: 22696--22736 Score: 64
Period size: 7 Copynumber: 5.6 Consensus size: 7
22686 TATATATAGA
22696 TTTTATT
1 TTTTATT
22703 TTTTATT
1 TTTTATT
22710 TTTTATAT
1 TTTTAT-T
22718 TTTTATT
1 TTTTATT
22725 TATTTATT
1 T-TTTATT
22733 TTTT
1 TTTT
22737 GCCTAAATAA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
7 18 0.56
8 14 0.44
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (7 bp):
TTTTATT
Found at i:29637 original size:24 final size:24
Alignment explanation
Indices: 29610--29655 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
29600 AGAACAATCC
* *
29610 CAAAAGGAAATGCAGGAGCAACTT
1 CAAAAGCAAATGAAGGAGCAACTT
*
29634 CAAAAGCAAATGAATGAGCAAC
1 CAAAAGCAAATGAAGGAGCAAC
29656 AAAAAATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.50, C:0.17, G:0.22, T:0.11
Consensus pattern (24 bp):
CAAAAGCAAATGAAGGAGCAACTT
Found at i:32456 original size:8 final size:8
Alignment explanation
Indices: 32428--32479 Score: 54
Period size: 8 Copynumber: 6.6 Consensus size: 8
32418 TTTGAGTCGA
32428 AAAAAATG
1 AAAAAATG
**
32436 ATGAAATG
1 AAAAAATG
32444 AAAAAAATG
1 -AAAAAATG
*
32453 AAAAAGTG
1 AAAAAATG
32461 -AAAAAT-
1 AAAAAATG
32467 AAAAAATG
1 AAAAAATG
32475 AAAAA
1 AAAAA
32480 GTAAAATGGA
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
7 11 0.31
8 18 0.51
9 6 0.17
ACGTcount: A:0.73, C:0.00, G:0.13, T:0.13
Consensus pattern (8 bp):
AAAAAATG
Found at i:32462 original size:17 final size:17
Alignment explanation
Indices: 32426--32465 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
32416 ACTTTGAGTC
*
32426 GAAAAAAATGATGAAAT
1 GAAAAAAATGATAAAAT
32443 GAAAAAAATGA-AAAAGT
1 GAAAAAAATGATAAAA-T
32460 GAAAAA
1 GAAAAA
32466 TAAAAAATGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 3 0.14
17 18 0.86
ACGTcount: A:0.70, C:0.00, G:0.17, T:0.12
Consensus pattern (17 bp):
GAAAAAAATGATAAAAT
Found at i:32463 original size:22 final size:23
Alignment explanation
Indices: 32437--32487 Score: 70
Period size: 22 Copynumber: 2.3 Consensus size: 23
32427 AAAAAAATGA
32437 TGAAATGA-AAAAAATGAAAAAG
1 TGAAATGATAAAAAATGAAAAAG
*
32459 TGAAA-AATAAAAAATGAAAAAG
1 TGAAATGATAAAAAATGAAAAAG
*
32481 TAAAATG
1 TGAAATG
32488 GAGAGCCTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
21 1 0.04
22 23 0.96
ACGTcount: A:0.69, C:0.00, G:0.16, T:0.16
Consensus pattern (23 bp):
TGAAATGATAAAAAATGAAAAAG
Found at i:32464 original size:7 final size:7
Alignment explanation
Indices: 32446--32479 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
32436 ATGAAATGAA
32446 AAAAATG
1 AAAAATG
32453 AAAAAGTG
1 AAAAA-TG
*
32461 AAAAATA
1 AAAAATG
32468 AAAAATG
1 AAAAATG
32475 AAAAA
1 AAAAA
32480 GTAAAATGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.76, C:0.00, G:0.12, T:0.12
Consensus pattern (7 bp):
AAAAATG
Found at i:32464 original size:14 final size:14
Alignment explanation
Indices: 32446--32485 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 14
32436 ATGAAATGAA
*
32446 AAAAATGAAAAAGTG
1 AAAAAT-AAAAAATG
32461 AAAAATAAAAAATG
1 AAAAATAAAAAATG
32475 AAAAAGTAAAA
1 AAAAA-TAAAA
32486 TGGAGAGCCT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.75, C:0.00, G:0.12, T:0.12
Consensus pattern (14 bp):
AAAAATAAAAAATG
Found at i:34142 original size:44 final size:43
Alignment explanation
Indices: 33968--34142 Score: 102
Period size: 44 Copynumber: 4.0 Consensus size: 43
33958 TATCTCTCTA
33968 AGCAGTAGTGGAGCAGATTGAAGATGGCGGATTTTACCTCCCT
1 AGCAGTAGTGGAGCAGATTGAAGATGGCGGATTTTACCTCCCT
* * * *** ** * *
34011 -GTAGTTACAGTGGAGTACATTGAAGCCAG-TAATTCTACTTCCCT
1 AGCAG-T--AGTGGAGCAGATTGAAGATGGCGGATTTTACCTCCCT
* ** ** ** * * **
34055 GGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATTTCCCT
1 AG-CAGTAGTGGAGCAGATTGAAGATGGCGGATTTTACCTCCCT
34099 AAGCAGTAGTGGAGCAGATTGAAGATGGCGGATTTTACCTCCCT
1 -AGCAGTAGTGGAGCAGATTGAAGATGGCGGATTTTACCTCCCT
34143 GTAGTTACAG
Statistics
Matches: 90, Mismatches: 35, Indels: 13
0.65 0.25 0.09
Matches are distributed among these distances:
42 3 0.03
43 16 0.18
44 52 0.58
45 18 0.20
46 1 0.01
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.29
Consensus pattern (43 bp):
AGCAGTAGTGGAGCAGATTGAAGATGGCGGATTTTACCTCCCT
Found at i:34462 original size:132 final size:132
Alignment explanation
Indices: 33847--34434 Score: 936
Period size: 132 Copynumber: 4.5 Consensus size: 132
33837 ATTGATAAGA
* *
33847 AGCAGATTGAAGATGGCAGATTTTACCTCCCTGTGGTAACAGTGGAGTACATTGAAGCCAGTAAT
1 AGCAGATTGAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAAT
* * *
33912 TCTACTTCCCTGGACAACAGTAGAATAGATTGAAAATTTCAGATCTTATCTCTCTAAGCAGTAGT
66 TCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGT
33977 GG
131 GG
*
33979 AGCAGATTGAAGATGGCGGATTTTACCTCCCTGTAGTTACAGTGGAGTACATTGAAGCCAGTAAT
1 AGCAGATTGAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAAT
*
34044 TCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATTTCCCTAAGCAGTAGT
66 TCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGT
34109 GG
131 GG
* *
34111 AGCAGATTGAAGATGGCGGATTTTACCTCCCTGTAGTTACAGTGGAGTACATTGATGCCAGTAAT
1 AGCAGATTGAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAAT
*
34176 TCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGGTCTTATCTCCCT-A--AG--GT
66 TCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGT
34236 GG
131 GG
* *
34238 AGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTACAATGGAGTACATTGAAGCCAGTAAT
1 AGCAGATTGAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAAT
** * *
34303 TCTACTTCCCTGGGTAACAGTGGAATAGATTGAAGATTTCAGACCTTATATCCCTAAGCAGTAAG
66 TCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGT-AG
34368 -GG
130 TGG
* * * * *
34370 AGTAGATCGAAGATGGTGGATTATACCTCCTTGTGGTTACAGTGGAGTACATTGAAGCCAGTAAT
1 AGCAGATTGAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAAT
34435 CCTATCTCCC
Statistics
Matches: 426, Mismatches: 24, Indels: 12
0.92 0.05 0.03
Matches are distributed among these distances:
127 115 0.27
128 1 0.00
129 2 0.00
130 2 0.00
131 1 0.00
132 304 0.71
133 1 0.00
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.29
Consensus pattern (132 bp):
AGCAGATTGAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAAT
TCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGT
GG
Found at i:34462 original size:259 final size:262
Alignment explanation
Indices: 33847--34434 Score: 941
Period size: 259 Copynumber: 2.2 Consensus size: 262
33837 ATTGATAAGA
* *
33847 AGCAGATTGAAGATGGCAGATTTTACCTCCCTGTGGTAACAGTGGAGTACATTGAAGCCAGTAAT
1 AGCAGATTGAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAAT
* *
33912 TCTACTTCCCTGGACAACAGTAGAATAGATTGAAAATTTCAGATCTTATCTCTCTAAGCAGTAGT
66 TCTACTTCCCTGGACAACAGTGGAATAGATTGAAAATTTCAGATCTTATCTCCCTAA-CAG-AGT
* *
33977 GGAGCAGATTGAAGATGGCGGATTTTACCTCCCTGTAGTTACAGTGGAGTACATTGAAGCCAGTA
129 GGAGCAGATCGAAGATGGCGGATTTTACCTCCCTGTAGTTACAATGGAGTACATTGAAGCCAGTA
* *
34042 ATTCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATTTCCCTAAGCAGTA
194 ATTCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGACCTTATATCCCTAAGCAGTA
34107 GTGG
259 GTGG
* *
34111 AGCAGATTGAAGATGGCGGATTTTACCTCCCTGTAGTTACAGTGGAGTACATTGATGCCAGTAAT
1 AGCAGATTGAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAAT
* *
34176 TCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGGTCTTATCTCCCT-A-AG-GTGG
66 TCTACTTCCCTGGACAACAGTGGAATAGATTGAAAATTTCAGATCTTATCTCCCTAACAGAGTGG
*
34238 AGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTACAATGGAGTACATTGAAGCCAGTAAT
131 AGCAGATCGAAGATGGCGGATTTTACCTCCCTGTAGTTACAATGGAGTACATTGAAGCCAGTAAT
**
34303 TCTACTTCCCTGGGTAACAGTGGAATAGATTGAAGATTTCAGACCTTATATCCCTAAGCAGTAAG
196 TCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGACCTTATATCCCTAAGCAGT-AG
34368 -GG
260 TGG
* * * * *
34370 AGTAGATCGAAGATGGTGGATTATACCTCCTTGTGGTTACAGTGGAGTACATTGAAGCCAGTAAT
1 AGCAGATTGAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAAT
34435 CCTATCTCCC
Statistics
Matches: 301, Mismatches: 22, Indels: 7
0.91 0.07 0.02
Matches are distributed among these distances:
259 184 0.61
260 2 0.01
261 2 0.01
263 1 0.00
264 112 0.37
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.29
Consensus pattern (262 bp):
AGCAGATTGAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAAT
TCTACTTCCCTGGACAACAGTGGAATAGATTGAAAATTTCAGATCTTATCTCCCTAACAGAGTGG
AGCAGATCGAAGATGGCGGATTTTACCTCCCTGTAGTTACAATGGAGTACATTGAAGCCAGTAAT
TCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGACCTTATATCCCTAAGCAGTAGT
GG
Found at i:34630 original size:93 final size:94
Alignment explanation
Indices: 34464--34634 Score: 222
Period size: 93 Copynumber: 1.8 Consensus size: 94
34454 GTGGAATAGG
* *
34464 TTTTCTATCTTGATTAACTTATTCACTTCGAGCTTTGCTCTCAATAAATTTCATCTTATCCATTG
1 TTTTCTATCTTGATTAAC-TATTCACTTCGAGCTTAGCTCTCAACAAATTTCATCTTATCCATTG
34529 AGATAATCTTTTTCATCTTATCTCAGCAAA
65 AGATAATCTTTTTCATCTTATCTCAGCAAA
* * * * *
34559 TTTTGCTATCTTGATTAA-T-TT-ATTTCGAGCTTAGTTCTCAAGCAAATTTTATCTTGTCTATT
1 TTTT-CTATCTTGATTAACTATTCACTTCGAGCTTAGCTCTCAA-CAAATTTCATCTTATCCATT
*
34621 GTGATAATCTTTTT
64 GAGATAATCTTTTT
34635 TAAGAATTTT
Statistics
Matches: 66, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
92 17 0.26
93 31 0.47
94 1 0.02
95 4 0.06
96 13 0.20
ACGTcount: A:0.25, C:0.18, G:0.09, T:0.49
Consensus pattern (94 bp):
TTTTCTATCTTGATTAACTATTCACTTCGAGCTTAGCTCTCAACAAATTTCATCTTATCCATTGA
GATAATCTTTTTCATCTTATCTCAGCAAA
Found at i:35284 original size:131 final size:131
Alignment explanation
Indices: 35119--35400 Score: 395
Period size: 131 Copynumber: 2.2 Consensus size: 131
35109 AGATCAGAAG
** * *
35119 CACCAGCCTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAGGATTGCAGATCTTATCTCCCTTAG
1 CACCAGCCTTATCTCCCTGAGCAGCAGTGGAGTAGGCGGAAGATTGCAGATCTTATCTCCCTAAG
* * *
35184 CAGTAGTGGAGCAGATCGAAAACGGCAAATCTTATCTTTCCAAGATAGTGGGGAGTC-GATTTAA
66 CAGTAGTGGAGCAGATCGAAAACGGCAAATCTTATCTTCCCAAGATAGTAGGAAG-CAGATTTAA
35248 GC
130 GC
* * * *
35250 CACCAGCCTTGTCTCCTTGAGCAGCAGTGGAGTAGGCGGAAGATTGTAGATTTTATCTCCCTAAG
1 CACCAGCCTTATCTCCCTGAGCAGCAGTGGAGTAGGCGGAAGATTGCAGATCTTATCTCCCTAAG
* * * *
35315 CAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTCCCGAGGTAGTAGGAAGCAGATTTAAG
66 CAGTAGTGGAGCAGATCGAAAACGGCAAATCTTATCTTCCCAAGATAGTAGGAAGCAGATTTAAG
35380 C
131 C
**
35381 CACCAATCTTATCTCCCTGA
1 CACCAGCCTTATCTCCCTGA
35401 AGTTGCAGTG
Statistics
Matches: 131, Mismatches: 19, Indels: 2
0.86 0.12 0.01
Matches are distributed among these distances:
130 1 0.01
131 130 0.99
ACGTcount: A:0.27, C:0.22, G:0.26, T:0.26
Consensus pattern (131 bp):
CACCAGCCTTATCTCCCTGAGCAGCAGTGGAGTAGGCGGAAGATTGCAGATCTTATCTCCCTAAG
CAGTAGTGGAGCAGATCGAAAACGGCAAATCTTATCTTCCCAAGATAGTAGGAAGCAGATTTAAG
C
Found at i:35416 original size:44 final size:44
Alignment explanation
Indices: 35368--35640 Score: 138
Period size: 44 Copynumber: 6.4 Consensus size: 44
35358 GGTAGTAGGA
* * *
35368 AGCAGATTTAAGCCACCA-ATCTTATCTCCCTGAAGTTGCAGTGG
1 AGCAGATTAAAACCA-CAGATCTTATCTCCCTGAAGTTGCAGTAG
* *
35412 AGCAGATTAAAACCACAGATCTTATCTCTCTGAAGTTGTAGTAG
1 AGCAGATTAAAACCACAGATCTTATCTCCCTGAAGTTGCAGTAG
** * * **** *
35456 AGCAGATCGCATA--A-A-ATCTTATCT-CCTTAAGCAATAGTGG
1 AGCAGAT-TAAAACCACAGATCTTATCTCCCTGAAGTTGCAGTAG
** * * *
35496 AGCAGACAGAAGAAAC-CA-ATCCTATCTCCCTGAAGTTACAGTCA-
1 AGCAGA-TTAA-AACCACAGATCTTATCTCCCTGAAGTTGCAGT-AG
* * * * *
35540 AGCGGATTAAAACCACATATCTTATCTCTCTGAATTTGTAGTAG
1 AGCAGATTAAAACCACAGATCTTATCTCCCTGAAGTTGCAGTAG
*** * *
35584 AGCAGA-TCGCATC-CAG-TCTTATCTCCCTGAAGTTGCAGTGG
1 AGCAGATTAAAACCACAGATCTTATCTCCCTGAAGTTGCAGTAG
* *
35625 AACAGACTAAAACCAC
1 AGCAGATTAAAACCAC
35641 GAATCTCGTC
Statistics
Matches: 168, Mismatches: 47, Indels: 29
0.69 0.19 0.12
Matches are distributed among these distances:
40 18 0.11
41 36 0.21
42 9 0.05
43 21 0.12
44 82 0.49
45 2 0.01
ACGTcount: A:0.33, C:0.23, G:0.18, T:0.26
Consensus pattern (44 bp):
AGCAGATTAAAACCACAGATCTTATCTCCCTGAAGTTGCAGTAG
Found at i:35437 original size:131 final size:131
Alignment explanation
Indices: 35119--35464 Score: 318
Period size: 131 Copynumber: 2.6 Consensus size: 131
35109 AGATCAGAAG
* * ** ** *** *
35119 CACCAGCCTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAGGATTGCAGATCTTATCTCCCTTAG
1 CACCAACCTTATCTCCCTGAGCAGCAGTGGAGCAGGAGGAAAACCACAGATCTTATCTCCCTAAG
* * *
35184 CAGTAGTGGAGCAGATCGAAAACGGCAAATCTTATCTTTCCAAGATAGTGGGGAGTCGATTTAAG
66 CAGTAGTGGAGCAGATCGAAAACGGCAAATCTTATCTTCCCAAGATAGTAGGAAGTCGATTTAAG
35249 C
131 C
* * * * * * **** *
35250 CACCAGCCTTGTCTCCTTGAGCAGCAGTGGAGTAGGCGGAAGATTGTAGATTTTATCTCCCTAAG
1 CACCAACCTTATCTCCCTGAGCAGCAGTGGAGCAGGAGGAAAACCACAGATCTTATCTCCCTAAG
* * * *
35315 CAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTCCCGAGGTAGTAGGAAG-CAGATTTAA
66 CAGTAGTGGAGCAGATCGAAAACGGCAAATCTTATCTTCCCAAGATAGTAGGAAGTC-GATTTAA
35379 GC
130 GC
* ** ** *
35381 CACCAATCTTATCTCCCTGAAGTTGCAGTGGAGCA-GATTAAAACCACAGATCTTATCTCTCTGA
1 CACCAACCTTATCTCCCTG-AGCAGCAGTGGAGCAGGAGGAAAACCACAGATCTTATCTCCCT-A
** *
35445 AGTTGTAGTAGAGCAGATCG
64 AGCAGTAGTGGAGCAGATCG
35465 CATAAAATCT
Statistics
Matches: 177, Mismatches: 35, Indels: 5
0.82 0.16 0.02
Matches are distributed among these distances:
130 1 0.01
131 146 0.82
132 30 0.17
ACGTcount: A:0.27, C:0.21, G:0.25, T:0.26
Consensus pattern (131 bp):
CACCAACCTTATCTCCCTGAGCAGCAGTGGAGCAGGAGGAAAACCACAGATCTTATCTCCCTAAG
CAGTAGTGGAGCAGATCGAAAACGGCAAATCTTATCTTCCCAAGATAGTAGGAAGTCGATTTAAG
C
Found at i:35962 original size:19 final size:19
Alignment explanation
Indices: 35938--35983 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
35928 TACTAAACCG
*
35938 GCCCAAACATTAACCCTCA
1 GCCCAAACATTAACCCTAA
**
35957 GCCCAAATTTTAACCCTAA
1 GCCCAAACATTAACCCTAA
35976 GCCCAAAC
1 GCCCAAAC
35984 CTAATAGCCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.37, C:0.39, G:0.07, T:0.17
Consensus pattern (19 bp):
GCCCAAACATTAACCCTAA
Found at i:37921 original size:107 final size:106
Alignment explanation
Indices: 37653--38176 Score: 703
Period size: 107 Copynumber: 5.0 Consensus size: 106
37643 TATCCACATA
* *
37653 AAAATTTCAAAATAAGTCAATATTTTGCGTTTGGAAGTTCGAGAAAACGTGCCCTAACGTGCTGG
1 AAAATTTCAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAACGTGCTGG
* * *
37718 GTTTCGATTTCTCGTTTGATCAAATAGCCGAATATCCTTTC
66 GTTTCGATTTCTCGTTCGACCAAATAGCCAAATATCCTTTC
* * * * * *
37759 AAAATTTTAAAGTGAGGAAATA-TTTGCGTTTGGAAATTCGAGAGAACGTGCCCTAACGCGCTGG
1 AAAATTTCAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAACGTGCTGG
* * * * * *
37823 GTTTCAATTTTTCATTCGACCAAATAGCTAAAATATTCTTTA
66 GTTTCGATTTCTCGTTCGACCAAATAGC-CAAATATCCTTTC
** *
37865 AAAATTTCAAAATAAGGCAATATTTTGCGTTTAAAAAATCGAGAAAACGTGCCCTAACGTGCTGG
1 AAAATTTCAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAACGTGCTGG
37930 GTTTCGATTTCTCGTTCGACCAAATAGCCAAATATCCTTTTC
66 GTTTCGATTTCTCGTTCGACCAAATAGCCAAATATCC-TTTC
* * * *
37972 AAACTTTCAAAATAAGGCAATATTTCGCGTTTGGAAGTTCGAGAAAACGTGCCCTAACATGCTGG
1 AAAATTTCAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAACGTGCTGG
* * *
38037 GTTTCGATTTCTCGTTTGATCAAATAGCCGAATATCCTTTC
66 GTTTCGATTTCTCGTTCGACCAAATAGCCAAATATCCTTTC
* * * * * *
38078 GAAATTTCAAAGTGAGG-AA-ATATTGCGTTTGGAAATTCGAGAGAACGTGCCCTAATGTGCTGG
1 AAAATTTCAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAACGTGCTGG
*
38141 GTTTCGATTTCTCGTTCGACCAAATAGCCTAATATC
66 GTTTCGATTTCTCGTTCGACCAAATAGCCAAATATC
38177 TTCTTAACTT
Statistics
Matches: 360, Mismatches: 55, Indels: 8
0.85 0.13 0.02
Matches are distributed among these distances:
104 71 0.20
105 64 0.18
106 68 0.19
107 157 0.44
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Consensus pattern (106 bp):
AAAATTTCAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAACGTGCTGG
GTTTCGATTTCTCGTTCGACCAAATAGCCAAATATCCTTTC
Found at i:40582 original size:13 final size:13
Alignment explanation
Indices: 40564--40606 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
40554 TTTTAGTTTG
*
40564 ATTTAAAATTAGA
1 ATTTAAAATTAAA
*
40577 ATTTAAAAATAAA
1 ATTTAAAATTAAA
* *
40590 ATTCAAAATTACA
1 ATTTAAAATTAAA
40603 ATTT
1 ATTT
40607 TGCATTGAGC
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.56, C:0.05, G:0.02, T:0.37
Consensus pattern (13 bp):
ATTTAAAATTAAA
Found at i:45443 original size:70 final size:73
Alignment explanation
Indices: 45369--45534 Score: 234
Period size: 72 Copynumber: 2.3 Consensus size: 73
45359 AAAATCATAT
**
45369 ATAAACAACTATTGAATAAAACTA-ATTA-GTATAAATAAGTAGAACATAAATTCAA-ATCCAAA
1 ATAAACAACTATTGAATAAAACTAGATTACACATAAATAAGTAGAACATAAATTCAATATCCAAA
* *
45431 GACCAAAC
66 AACCAAAA
* *
45439 ATAAACAACTATT-AATAAAACTAGATTACACATAAATAAGTAGAACATAATTTTAATATCCAAA
1 ATAAACAACTATTGAATAAAACTAGATTACACATAAATAAGTAGAACATAAATTCAATATCCAAA
45503 AACCAAAA
66 AACCAAAA
*
45511 ATAAATAACTATTG-ATAAAACTAG
1 ATAAACAACTATTGAATAAAACTAG
45535 TTTAGCATTG
Statistics
Matches: 85, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
69 10 0.12
70 17 0.20
71 23 0.27
72 35 0.41
ACGTcount: A:0.56, C:0.13, G:0.06, T:0.25
Consensus pattern (73 bp):
ATAAACAACTATTGAATAAAACTAGATTACACATAAATAAGTAGAACATAAATTCAATATCCAAA
AACCAAAA
Found at i:45521 original size:72 final size:71
Alignment explanation
Indices: 45347--45534 Score: 231
Period size: 72 Copynumber: 2.7 Consensus size: 71
45337 CTTGTGAATA
* * * **
45347 AATTTT-ATATCC-AAAATCATATATAAACAACTATTGAATAAAACTA-ATTAGTATAAATAAGT
1 AATTTTAATATCCAAAAACCAAAAATAAACAACTATT-AATAAAACTAGATTAACATAAATAAGT
45409 AGAACAT
65 AGAACAT
* * * *
45416 AAATTCAA-ATCCAAAGACCAAACATAAACAACTATTAATAAAACTAGATTACACATAAATAAGT
1 AATTTTAATATCCAAAAACCAAAAATAAACAACTATTAATAAAACTAGATTA-ACATAAATAAGT
45480 AGAACAT
65 AGAACAT
* *
45487 AATTTTAATATCCAAAAACCAAAAATAAATAACTATTGATAAAACTAG
1 AATTTTAATATCCAAAAACCAAAAATAAACAACTATTAATAAAACTAG
45535 TTTAGCATTG
Statistics
Matches: 100, Mismatches: 14, Indels: 7
0.83 0.12 0.06
Matches are distributed among these distances:
69 18 0.18
70 24 0.24
71 23 0.23
72 35 0.35
ACGTcount: A:0.55, C:0.13, G:0.05, T:0.27
Consensus pattern (71 bp):
AATTTTAATATCCAAAAACCAAAAATAAACAACTATTAATAAAACTAGATTAACATAAATAAGTA
GAACAT
Found at i:48255 original size:50 final size:50
Alignment explanation
Indices: 48180--48907 Score: 449
Period size: 50 Copynumber: 14.6 Consensus size: 50
48170 GCAATGTCGA
* * * * *
48180 GGAAGTAAGATTCGCCGTCGTAGCTTCAATCTTTTCCATTACATCGCCAG
1 GGAAGTAAGATTCGCCGTTGTAGCTTCAATCTGTTCCATTGCACCGCCTG
* * * ** * ** * *
48230 GGAAGTAAGATTTGCTGTTGTAGCTTCAATCTATTTAAATGCAGTGTCGG
1 GGAAGTAAGATTCGCCGTTGTAGCTTCAATCTGTTCCATTGCACCGCCTG
** * *
48280 GGAAGCGAGATTCGCCATCGTAGCTTCAATCTGTTCCATTGCACCGCCTG
1 GGAAGTAAGATTCGCCGTTGTAGCTTCAATCTGTTCCATTGCACCGCCTG
* * * ** ****
48330 AGAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTAAATTGCAATATC-G
1 GGAAGTAAGATTCGCCGTTGTAGCTTCAATCTGTTCCATTGCACCGCCTG
* * ***
48379 ATGAAGTAAGATTCACCGTTGTAGCTTCAATCTGTTCTGCTGCACCGCCTG
1 -GGAAGTAAGATTCGCCGTTGTAGCTTCAATCTGTTCCATTGCACCGCCTG
* * ** *
48430 AGAAGTAAGATTCACCGTTGTAGCTTCAATCTGTTCCGCTGCACCGCTTG
1 GGAAGTAAGATTCGCCGTTGTAGCTTCAATCTGTTCCATTGCACCGCCTG
* * ** **** *
48480 GGAAGTAAGATTTGCCGTTGTGGCTTCAATCCT-TTAAATTGCAATATCGG
1 GGAAGTAAGATTCGCCGTTGTAGCTTCAAT-CTGTTCCATTGCACCGCCTG
* * * * *
48530 GGAAGCAAGATTCACCGTTGTAGCTTCAACCTGTTCCACTGCACCGCTTG
1 GGAAGTAAGATTCGCCGTTGTAGCTTCAATCTGTTCCATTGCACCGCCTG
* * * ** ** * *
48580 AGAAGTAAGATTCTCCGTTGTGGCTTCAATCAT-TTAAATTGCAATGTCGG
1 GGAAGTAAGATTCGCCGTTGTAGCTTCAATC-TGTTCCATTGCACCGCCTG
* * **
48630 GGAAGCAAGATTCACCGTTGTAGCTTCAATCTGTTCCGCTGCACCGCCTG
1 GGAAGTAAGATTCGCCGTTGTAGCTTCAATCTGTTCCATTGCACCGCCTG
* * * * ** * ** * *
48680 AGAAGTAATATTCACCGTTGTGGCTTCAATCCT-TTAAATTGTAATGTCAG
1 GGAAGTAAGATTCGCCGTTGTAGCTTCAAT-CTGTTCCATTGCACCGCCTG
* * *** * *
48730 GGAAGCAAGATTCGCCATTGTAGCTTCAATCTGTTCTGCTGTATCGCCTG
1 GGAAGTAAGATTCGCCGTTGTAGCTTCAATCTGTTCCATTGCACCGCCTG
* * * ** * ** * **
48780 AGAAGTAAGATTCGCAGTTGTGGCTTCAATCCT-TTAAATTGGAATGTCAA
1 GGAAGTAAGATTCGCCGTTGTAGCTTCAAT-CTGTTCCATTGCACCGCCTG
* * * * ** *
48830 GGAAGCAAGATTCACCATTGTAGCTTCAATCTATTCCGCTGCACCGCTTG
1 GGAAGTAAGATTCGCCGTTGTAGCTTCAATCTGTTCCATTGCACCGCCTG
* *
48880 AGAAGTAAGATTCGCCGTTGTGGCTTCA
1 GGAAGTAAGATTCGCCGTTGTAGCTTCA
48908 GTCCTTTAAA
Statistics
Matches: 497, Mismatches: 171, Indels: 20
0.72 0.25 0.03
Matches are distributed among these distances:
49 8 0.02
50 481 0.97
51 8 0.02
ACGTcount: A:0.25, C:0.22, G:0.22, T:0.31
Consensus pattern (50 bp):
GGAAGTAAGATTCGCCGTTGTAGCTTCAATCTGTTCCATTGCACCGCCTG
Found at i:48485 original size:100 final size:100
Alignment explanation
Indices: 48429--48919 Score: 716
Period size: 100 Copynumber: 4.9 Consensus size: 100
48419 TGCACCGCCT
* * *
48429 GAGAAGTAAGATTCACCGTTGTAGCTTCAATCTGTTCCGCTGCACCGCTTGGGAAGTAAGATTTG
1 GAGAAGCAAGATTCACCGTTGTAGCTTCAATCTGTTCCGCTGCACCGCTTGAGAAGTAAGATTCG
*
48494 CCGTTGTGGCTTCAATCCTTTAAATTGCAATATCG
66 CCGTTGTGGCTTCAATCCTTTAAATTGCAATGTCG
* * * *
48529 GGGAAGCAAGATTCACCGTTGTAGCTTCAACCTGTTCCACTGCACCGCTTGAGAAGTAAGATTCT
1 GAGAAGCAAGATTCACCGTTGTAGCTTCAATCTGTTCCGCTGCACCGCTTGAGAAGTAAGATTCG
*
48594 CCGTTGTGGCTTCAATCATTTAAATTGCAATGTCG
66 CCGTTGTGGCTTCAATCCTTTAAATTGCAATGTCG
* * * *
48629 GGGAAGCAAGATTCACCGTTGTAGCTTCAATCTGTTCCGCTGCACCGCCTGAGAAGTAATATTCA
1 GAGAAGCAAGATTCACCGTTGTAGCTTCAATCTGTTCCGCTGCACCGCTTGAGAAGTAAGATTCG
*
48694 CCGTTGTGGCTTCAATCCTTTAAATTGTAATGTCAG
66 CCGTTGTGGCTTCAATCCTTTAAATTGCAATGTC-G
* * * * * *
48730 G-GAAGCAAGATTCGCCATTGTAGCTTCAATCTGTTCTGCTGTATCGCCTGAGAAGTAAGATTCG
1 GAGAAGCAAGATTCACCGTTGTAGCTTCAATCTGTTCCGCTGCACCGCTTGAGAAGTAAGATTCG
* *
48794 CAGTTGTGGCTTCAATCCTTTAAATTGGAATGTC-
66 CCGTTGTGGCTTCAATCCTTTAAATTGCAATGTCG
* * *
48828 AAGGAAGCAAGATTCACCATTGTAGCTTCAATCTATTCCGCTGCACCGCTTGAGAAGTAAGATTC
1 GA-GAAGCAAGATTCACCGTTGTAGCTTCAATCTGTTCCGCTGCACCGCTTGAGAAGTAAGATTC
*
48893 GCCGTTGTGGCTTCAGTCCTTTAAATT
65 GCCGTTGTGGCTTCAATCCTTTAAATT
48920 ACAAACTATG
Statistics
Matches: 354, Mismatches: 34, Indels: 6
0.90 0.09 0.02
Matches are distributed among these distances:
100 352 0.99
101 2 0.01
ACGTcount: A:0.25, C:0.22, G:0.22, T:0.31
Consensus pattern (100 bp):
GAGAAGCAAGATTCACCGTTGTAGCTTCAATCTGTTCCGCTGCACCGCTTGAGAAGTAAGATTCG
CCGTTGTGGCTTCAATCCTTTAAATTGCAATGTCG
Found at i:48542 original size:200 final size:196
Alignment explanation
Indices: 48331--48919 Score: 678
Period size: 200 Copynumber: 2.9 Consensus size: 196
48321 CACCGCCTGA
* * * *
48331 GAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTAAATTGCAATATCGATGAAGTAAGATTCACC
1 GAAGCAAGATTCGCCGTTGTAGCTTCAATCTGTT--ACTGCAATATCGATGAAGTAAGATTCACC
* **** ** * *
48396 GTTGTAGCTTCAATCTGTTCTGCTGCACCGCCTGAGAAGTAAGATTCACCGTTGTAGCTTCAATC
64 GTTGTGGCTTCAATCT-TTAAATTGCAATGTC-GAGAAGCAAGATTCACCGTTGTAGCTTCAATC
* *
48461 TGTTCCGCTGCACCGCTTGGGAAGTAAGATTTGCCGTTGTGGCTTCAATCCTTTAAATTGCAATA
127 TGTTCCGCTGCACCGCTTGAGAAGTAAGATTCGCCGTTGTGGCTTCAATCCTTTAAATTGCAATA
*
48526 TCGGG
192 TCAGG
* * *** * *
48531 GAAGCAAGATTCACCGTTGTAGCTTCAACCTGTTCCACTGCACCGCTTGA-GAAGTAAGATTCTC
1 GAAGCAAGATTCGCCGTTGTAGCTTCAATCTGTT--ACTGCA-ATATCGATGAAGTAAGATTCAC
*
48595 CGTTGTGGCTTCAATCATTTAAATTGCAATGTCGGGGAAGCAAGATTCACCGTTGTAGCTTCAAT
63 CGTTGTGGCTTCAATC-TTTAAATTGCAATGTC-GAGAAGCAAGATTCACCGTTGTAGCTTCAAT
* * * *
48660 CTGTTCCGCTGCACCGCCTGAGAAGTAATATTCACCGTTGTGGCTTCAATCCTTTAAATTGTAAT
126 CTGTTCCGCTGCACCGCTTGAGAAGTAAGATTCGCCGTTGTGGCTTCAATCCTTTAAATTGCAAT
*
48725 GTCAGG
191 ATCAGG
* ** * *
48731 GAAGCAAGATTCGCCATTGTAGCTTCAATCTGTT-CTGCTGTATCGCCTGAGAAGTAAGATTCGC
1 GAAGCAAGATTCGCCGTTGTAGCTTCAATCTGTTACTGCAATATCG-AT--GAAGTAAGATTCAC
* * * *
48795 AGTTGTGGCTTCAATCCTTTAAATTGGAATGTCAAGGAAGCAAGATTCACCATTGTAGCTTCAAT
63 CGTTGTGGCTTCAAT-CTTTAAATTGCAATGTCGA-GAAGCAAGATTCACCGTTGTAGCTTCAAT
* *
48860 CTATTCCGCTGCACCGCTTGAGAAGTAAGATTCGCCGTTGTGGCTTCAGTCCTTTAAATT
126 CTGTTCCGCTGCACCGCTTGAGAAGTAAGATTCGCCGTTGTGGCTTCAATCCTTTAAATT
48920 ACAAACTATG
Statistics
Matches: 329, Mismatches: 52, Indels: 16
0.83 0.13 0.04
Matches are distributed among these distances:
196 2 0.01
197 4 0.01
200 318 0.97
201 5 0.02
ACGTcount: A:0.25, C:0.22, G:0.22, T:0.32
Consensus pattern (196 bp):
GAAGCAAGATTCGCCGTTGTAGCTTCAATCTGTTACTGCAATATCGATGAAGTAAGATTCACCGT
TGTGGCTTCAATCTTTAAATTGCAATGTCGAGAAGCAAGATTCACCGTTGTAGCTTCAATCTGTT
CCGCTGCACCGCTTGAGAAGTAAGATTCGCCGTTGTGGCTTCAATCCTTTAAATTGCAATATCAG
G
Found at i:66661 original size:26 final size:27
Alignment explanation
Indices: 66609--66671 Score: 119
Period size: 26 Copynumber: 2.4 Consensus size: 27
66599 ATAAAAAATA
66609 ACCAAAATATTATAATTTTTTTTATTT
1 ACCAAAATATTATAATTTTTTTTATTT
66636 ACCAAAATATTATAA-TTTTTTTATTT
1 ACCAAAATATTATAATTTTTTTTATTT
66662 ACCAAAATAT
1 ACCAAAATAT
66672 ACAAAAAAAC
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
26 21 0.58
27 15 0.42
ACGTcount: A:0.41, C:0.10, G:0.00, T:0.49
Consensus pattern (27 bp):
ACCAAAATATTATAATTTTTTTTATTT
Found at i:66839 original size:8 final size:8
Alignment explanation
Indices: 66822--67133 Score: 114
Period size: 10 Copynumber: 36.4 Consensus size: 8
66812 GAATGAGAGG
66822 GAAAGAAA
1 GAAAGAAA
*
66830 GAAAGGAA
1 GAAAGAAA
66838 GAAAGAAA
1 GAAAGAAA
*
66846 GGAAGGGAAA
1 -GAA-AGAAA
66856 GAAAGAAAA
1 GAAAG-AAA
*
66865 GGAAAGGAGAG
1 -GAAA-GA-AA
66876 GAAAGAAA
1 GAAAGAAA
66884 G-AA-AAA
1 GAAAGAAA
*
66890 GAAGGAAA
1 GAAAGAAA
66898 GAAAAGGAAA
1 G-AAA-GAAA
66908 TGAGAAGAAA
1 -GA-AAGAAA
*
66918 -AAATAAA
1 GAAAGAAA
66925 G-AA-AAA
1 GAAAGAAA
*
66931 GAAGGAAA
1 GAAAGAAA
66939 GAAAAGGAAA
1 G-AAA-GAAA
66949 GGAGAAGAAA
1 -GA-AAGAAA
66959 -AAAGAAA
1 GAAAGAAA
66966 GAAA-AAGA
1 GAAAGAA-A
66974 GGAAAGAAAA
1 -GAAAG-AAA
66984 GGAAAGGAGAA
1 -GAAA-GA-AA
66995 GAAA-AAA
1 GAAAGAAA
67002 GAAAGAAA
1 GAAAGAAA
67010 -AAGAGGAAA
1 GAA-A-GAAA
67019 GAAAAGGAAA
1 G-AAA-GAAA
67029 GGAGAAGAAA
1 -GA-AAGAAA
67039 -AAAGAAA
1 GAAAGAAA
67046 G-AA-AAA
1 GAAAGAAA
**
67052 GAGGGAAA
1 GAAAGAAA
67060 GAAAGGAAA
1 GAAA-GAAA
67069 GGAGAAGAAA
1 -GA-AAGAAA
67079 -AAAGAAA
1 GAAAGAAA
*
67086 GAAAATGAAT
1 G-AAA-GAAA
67096 GAAAGAAAA
1 GAAAG-AAA
67105 TGAAAGGAGAA
1 -GAAA-GA-AA
67116 GAGAA-AAA
1 GA-AAGAAA
67124 -AAAGAAA
1 GAAAGAAA
67131 GAA
1 GAA
67134 GAAGAAGAGG
Statistics
Matches: 238, Mismatches: 17, Indels: 98
0.67 0.05 0.28
Matches are distributed among these distances:
6 14 0.06
7 45 0.19
8 48 0.20
9 36 0.15
10 70 0.29
11 25 0.11
ACGTcount: A:0.69, C:0.00, G:0.30, T:0.02
Consensus pattern (8 bp):
GAAAGAAA
Found at i:66857 original size:14 final size:14
Alignment explanation
Indices: 66819--66906 Score: 63
Period size: 14 Copynumber: 6.1 Consensus size: 14
66809 GGAGAATGAG
*
66819 AGGGAAAGAAAGAA
1 AGGGAAAGAAAGGA
66833 AGGAAGAAAGAAAGGA
1 AGG--GAAAGAAAGGA
*
66849 AGGGAAAGAAAGAA
1 AGGGAAAGAAAGGA
* *
66863 AAGGAAAGGAGAGGA
1 AGGGAAA-GAAAGGA
* *
66878 A-AGAAAGAAAAAGA
1 AGGGAAAG-AAAGGA
66892 A-GGAAAGAAAAGGA
1 AGGGAAAG-AAAGGA
66906 A
1 A
66907 ATGAGAAGAA
Statistics
Matches: 60, Mismatches: 10, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
13 1 0.02
14 40 0.67
15 6 0.10
16 13 0.22
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (14 bp):
AGGGAAAGAAAGGA
Found at i:66977 original size:40 final size:40
Alignment explanation
Indices: 66856--67135 Score: 417
Period size: 40 Copynumber: 7.0 Consensus size: 40
66846 GGAAGGGAAA
*
66856 GAAAGAAAAGGAAAGGAG-AG--GAAAGAAAGAAAAAGAAG
1 GAAAGAAAAGGAAAGGAGAAGAAAAAAGAAAGAAAAAG-AG
* *
66894 GAAAGAAAAGGAAATGAGAAGAAAAAATAAAGAAAAAGAAG
1 GAAAGAAAAGGAAAGGAGAAGAAAAAAGAAAGAAAAAG-AG
66935 GAAAGAAAAGGAAAGGAGAAGAAAAAAGAAAGAAAAAGAG
1 GAAAGAAAAGGAAAGGAGAAGAAAAAAGAAAGAAAAAGAG
66975 GAAAGAAAAGGAAAGGAGAAGAAAAAAGAAAGAAAAAGAG
1 GAAAGAAAAGGAAAGGAGAAGAAAAAAGAAAGAAAAAGAG
67015 GAAAGAAAAGGAAAGGAGAAGAAAAAAGAAAGAAAAAGAGG
1 GAAAGAAAAGGAAAGGAGAAGAAAAAAGAAAGAAAAAGA-G
* *
67056 GAAAG-AAAGGAAAGGAGAAGAAAAAAGAAAGAAAATGAAT
1 GAAAGAAAAGGAAAGGAGAAGAAAAAAGAAAGAAAAAG-AG
*
67096 GAAAGAAAATGAAAGGAGAAGAGAAAAA-AAAGAAAGAAGA
1 GAAAGAAAAGGAAAGGAGAAGA-AAAAAGAAAGAAA-AAGA
67136 AGAAGAGGGA
Statistics
Matches: 225, Mismatches: 9, Indels: 13
0.91 0.04 0.05
Matches are distributed among these distances:
38 17 0.08
39 2 0.01
40 117 0.52
41 82 0.36
42 7 0.03
ACGTcount: A:0.69, C:0.00, G:0.29, T:0.02
Consensus pattern (40 bp):
GAAAGAAAAGGAAAGGAGAAGAAAAAAGAAAGAAAAAGAG
Found at i:67913 original size:27 final size:27
Alignment explanation
Indices: 67883--67937 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
67873 AAATAGGCTG
67883 ATGGAGGGGAATAAAAAGGCAGCACCA
1 ATGGAGGGGAATAAAAAGGCAGCACCA
*
67910 ATGGAGGGGAATAAAAAGGCGGCACCA
1 ATGGAGGGGAATAAAAAGGCAGCACCA
67937 A
1 A
67938 AATGTGGCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.44, C:0.15, G:0.35, T:0.07
Consensus pattern (27 bp):
ATGGAGGGGAATAAAAAGGCAGCACCA
Found at i:69204 original size:15 final size:16
Alignment explanation
Indices: 69172--69206 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
69162 ATTATTTCAA
69172 ATAAATTATACTTTTT
1 ATAAATTATACTTTTT
69188 ATAAATTATAC-TTTT
1 ATAAATTATACTTTTT
69203 ATAA
1 ATAA
69207 CACTATACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 8 0.42
16 11 0.58
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (16 bp):
ATAAATTATACTTTTT
Found at i:69213 original size:16 final size:16
Alignment explanation
Indices: 69172--69214 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
69162 ATTATTTCAA
*
69172 ATAAATTATACTTTTT
1 ATAAACTATACTTTTT
*
69188 ATAAATTATAC-TTTT
1 ATAAACTATACTTTTT
69203 ATAACACTATAC
1 ATAA-ACTATAC
69215 ATAAAAATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 8 0.32
16 17 0.68
ACGTcount: A:0.42, C:0.12, G:0.00, T:0.47
Consensus pattern (16 bp):
ATAAACTATACTTTTT
Found at i:69871 original size:366 final size:365
Alignment explanation
Indices: 69188--69905 Score: 1427
Period size: 366 Copynumber: 2.0 Consensus size: 365
69178 TATACTTTTT
69188 ATAAATTATACTTTTATAACACTATACATAAAAATTTTACATCATTAGGTCAATTCTGACCCGAT
1 ATAAATTATACTTTTATAACACTATACATAAAAATTTTACATCATTAGGTCAATTCTGACCCGAT
69253 CCGGATGACTGTCCAACATGAAAGTTCCGACGAGGACATCTATTCCGATTATGACCACTTAACCT
66 CCGGATGACTGTCCAACATGAAAGTTCCGACGAGGACATCTATTCCGATTATGACCACTTAACCT
69318 ACATAATCCACAACGCTTACCGTCGGATTTCTCCCTAATGTCTATTTCATTACGGATTCTGCTTG
131 ACATAATCCACAACGCTTACCGTCGGATTTCTCCCTAATGTCTATTTCATTACGGATTCTGCTTG
69383 ATTGCGGACAACCTCTTGGTTTCCTCCGTAGCCCTCTGTCTGGGAGAAGCCCGAAAGTCATCGGA
196 ATTGCGGACAACCTCTTGGTTTCCTCCGTAGCCCTCTGTCTGGGAGAAGCCCGAAAGTCATCGGA
69448 GACACCTCCCACGTAGATAGGTCAGGCAGGACGAGGAACTCATTTTCCTAGATACGCAATGTGCG
261 GACACCTCCCACGTAGATAGGTCAGGCAGGACGAGGAACTCATTTTCCTAGATACGCAATGTGCG
69513 CTCGAGCGTGTACACATCATCGACATAAAGATTATTTCAA
326 CTCGAGCGTGTACACATCATCGACATAAAGATTATTTCAA
69553 ATAAATTATACTTTTTATAACACTATACATAAAAATTTTACATCATTAGGTCAATTCTGACCCGA
1 ATAAATTATAC-TTTTATAACACTATACATAAAAATTTTACATCATTAGGTCAATTCTGACCCGA
69618 TCCGGATGACTGTCCAACATGAAAGTTCCGACGAGGACATCTATTCCGATTATGACCACTTAACC
65 TCCGGATGACTGTCCAACATGAAAGTTCCGACGAGGACATCTATTCCGATTATGACCACTTAACC
69683 TACATAATCCACAACGCTTACCGTCGGATTTCTCCCTAATGTCTATTTCATTACGGATTCTGCTT
130 TACATAATCCACAACGCTTACCGTCGGATTTCTCCCTAATGTCTATTTCATTACGGATTCTGCTT
69748 GATTGCGGACAACCTCTTGGTTTCCTCCGTAGCCCTCTGTCTGGGAGAAGCCCGAAAGTCATCGG
195 GATTGCGGACAACCTCTTGGTTTCCTCCGTAGCCCTCTGTCTGGGAGAAGCCCGAAAGTCATCGG
69813 AGACACCTCCCACGTAGATAGGTCAGGCAGGACGAGGAACTCATTTTCCTAGATACGCAATGTGC
260 AGACACCTCCCACGTAGATAGGTCAGGCAGGACGAGGAACTCATTTTCCTAGATACGCAATGTGC
69878 GCTCGAGCGTGTACACATCATCGACATA
325 GCTCGAGCGTGTACACATCATCGACATA
69906 TTGTTCAACA
Statistics
Matches: 352, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
365 11 0.03
366 341 0.97
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.28
Consensus pattern (365 bp):
ATAAATTATACTTTTATAACACTATACATAAAAATTTTACATCATTAGGTCAATTCTGACCCGAT
CCGGATGACTGTCCAACATGAAAGTTCCGACGAGGACATCTATTCCGATTATGACCACTTAACCT
ACATAATCCACAACGCTTACCGTCGGATTTCTCCCTAATGTCTATTTCATTACGGATTCTGCTTG
ATTGCGGACAACCTCTTGGTTTCCTCCGTAGCCCTCTGTCTGGGAGAAGCCCGAAAGTCATCGGA
GACACCTCCCACGTAGATAGGTCAGGCAGGACGAGGAACTCATTTTCCTAGATACGCAATGTGCG
CTCGAGCGTGTACACATCATCGACATAAAGATTATTTCAA
Found at i:72755 original size:12 final size:12
Alignment explanation
Indices: 72740--72775 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
72730 CTCTTCTTCC
*
72740 TCTTCTTTTTCT
1 TCTTATTTTTCT
72752 TCTTATTTTTCT
1 TCTTATTTTTCT
72764 TCTTATTTTTCT
1 TCTTATTTTTCT
72776 CCCTTCAGCT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.06, C:0.19, G:0.00, T:0.75
Consensus pattern (12 bp):
TCTTATTTTTCT
Found at i:72964 original size:26 final size:27
Alignment explanation
Indices: 72910--72972 Score: 83
Period size: 26 Copynumber: 2.4 Consensus size: 27
72900 TATTTTTTGG
** *
72910 AATATTTTGATAAATAAAAAAAATTAT
1 AATATTTTGGCAAATAAAAAAAATAAT
*
72937 AATATTTTGGCAAAT-AAAAAAGTAAT
1 AATATTTTGGCAAATAAAAAAAATAAT
72963 AATATTTTGG
1 AATATTTTGG
72973 TTATTTTTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
26 19 0.59
27 13 0.41
ACGTcount: A:0.52, C:0.02, G:0.10, T:0.37
Consensus pattern (27 bp):
AATATTTTGGCAAATAAAAAAAATAAT
Found at i:91192 original size:42 final size:41
Alignment explanation
Indices: 91142--91291 Score: 169
Period size: 42 Copynumber: 3.6 Consensus size: 41
91132 TAGTTTTCGT
* * *
91142 TTAGCTCTTATGAGCTTCTGTTCAACTCATATGAGTTTTTAA
1 TTAGCTCTTATGAGCTTCTGTTCAACCCTTATGGGTTTTT-A
* *
91184 TTAGCTCTT-TCGAGCTTCTGTTTAACCCTTCTGGGTTTTTA
1 TTAGCTCTTAT-GAGCTTCTGTTCAACCCTTATGGGTTTTTA
*
91225 TTCAACTCTTATGAGCTTCTGTTCAACCCTTATGGGTTTCTGT-
1 TT-AGCTCTTATGAGCTTCTGTTCAACCCTTATGGGTTT-T-TA
* *
91268 TTAGCACTTATGTGCTTCTGTTCA
1 TTAGCTCTTATGAGCTTCTGTTCA
91292 GCCTTCGAGC
Statistics
Matches: 92, Mismatches: 11, Indels: 10
0.81 0.10 0.09
Matches are distributed among these distances:
41 4 0.04
42 83 0.90
43 4 0.04
44 1 0.01
ACGTcount: A:0.17, C:0.21, G:0.16, T:0.46
Consensus pattern (41 bp):
TTAGCTCTTATGAGCTTCTGTTCAACCCTTATGGGTTTTTA
Found at i:91251 original size:21 final size:21
Alignment explanation
Indices: 91146--91291 Score: 89
Period size: 21 Copynumber: 7.0 Consensus size: 21
91136 TTTCGTTTAG
91146 CTCTTATGAGCTTCTGTTCAA
1 CTCTTATGAGCTTCTGTTCAA
* * * * *
91167 CTCATATGAGTTTTTAATT-AG
1 CTCTTATGAGCTTCT-GTTCAA
*
91188 CTCTT-TCGAGCTTCTGTTTAA
1 CTCTTAT-GAGCTTCTGTTCAA
* * * * * *
91209 CCCTTCTGGGTTTTTATTCAA
1 CTCTTATGAGCTTCTGTTCAA
91230 CTCTTATGAGCTTCTGTTCAA
1 CTCTTATGAGCTTCTGTTCAA
* * * * *
91251 CCCTTATGGGTTTCTGTTTAG
1 CTCTTATGAGCTTCTGTTCAA
* *
91272 CACTTATGTGCTTCTGTTCA
1 CTCTTATGAGCTTCTGTTCA
91292 GCCTTCGAGC
Statistics
Matches: 90, Mismatches: 31, Indels: 8
0.70 0.24 0.06
Matches are distributed among these distances:
20 3 0.03
21 84 0.93
22 3 0.03
ACGTcount: A:0.17, C:0.21, G:0.16, T:0.46
Consensus pattern (21 bp):
CTCTTATGAGCTTCTGTTCAA
Found at i:101963 original size:593 final size:593
Alignment explanation
Indices: 100836--102021 Score: 2372
Period size: 593 Copynumber: 2.0 Consensus size: 593
100826 ACCCTCTTAA
100836 TAGAAACAGATACCTCGAGATCTCATACCACAATCCCAAGAACAATACAATGGCATGAAATCAAC
1 TAGAAACAGATACCTCGAGATCTCATACCACAATCCCAAGAACAATACAATGGCATGAAATCAAC
100901 CTTCTTGACAGGGAGAAACTTTAGGGTGCTATAGACCTTGTGACACCAACTTCAATAAGAAACAC
66 CTTCTTGACAGGGAGAAACTTTAGGGTGCTATAGACCTTGTGACACCAACTTCAATAAGAAACAC
100966 TTCACCAAGTGGAATTTCACAACACCAAGATGGCATAGTTGAATTAATATTCAACAGGCCATGAA
131 TTCACCAAGTGGAATTTCACAACACCAAGATGGCATAGTTGAATTAATATTCAACAGGCCATGAA
101031 GAATGCCTCCAAGACATTCTTTTGAAATAGGAAATACCGACACAACTTTTAGAAGATTAAATTTA
196 GAATGCCTCCAAGACATTCTTTTGAAATAGGAAATACCGACACAACTTTTAGAAGATTAAATTTA
101096 AAAGAAGAACCAAATCCAAAAACACAAACGACAGATTTTAGGACAGCTAGAGCCTCTGTCTTTTT
261 AAAGAAGAACCAAATCCAAAAACACAAACGACAGATTTTAGGACAGCTAGAGCCTCTGTCTTTTT
101161 TATCCCAACGATATTTAGAACCAATTTACAGGGAACAGATAATTCCTCAAATATAGCTCAACCTA
326 TATCCCAACGATATTTAGAACCAATTTACAGGGAACAGATAATTCCTCAAATATAGCTCAACCTA
101226 TCTTTGCCATACAGGAAGAGAGTCCCCAAAATTCACCTAATATGTCACCAACATAGTCATCAATG
391 TCTTTGCCATACAGGAAGAGAGTCCCCAAAATTCACCTAATATGTCACCAACATAGTCATCAATG
101291 ACTAATAATGCAAGACAATGAGAAAATTCAGAAATATTTGTTCTAGAAAAATATTTTGAGATAAA
456 ACTAATAATGCAAGACAATGAGAAAATTCAGAAATATTTGTTCTAGAAAAATATTTTGAGATAAA
101356 TAAGGAATGGTGTAGAAAACACTTCCATTCCAACAAAAATAAGCAAAAAAAGAAGAAGATTATTT
521 TAAGGAATGGTGTAGAAAACACTTCCATTCCAACAAAAATAAGCAAAAAAAGAAGAAGATTATTT
101421 TAAAAATT
586 TAAAAATT
101429 TAGAAACAGATACCTCGAGATCTCATACCACAATCCCAAGAACAATACAATGGCATGAAATCAAC
1 TAGAAACAGATACCTCGAGATCTCATACCACAATCCCAAGAACAATACAATGGCATGAAATCAAC
101494 CTTCTTGACAGGGAGAAACTTTAGGGTGCTATAGACCTTGTGACACCAACTTCAATAAGAAACAC
66 CTTCTTGACAGGGAGAAACTTTAGGGTGCTATAGACCTTGTGACACCAACTTCAATAAGAAACAC
101559 TTCACCAAGTGGAATTTCACAACACCAAGATGGCATAGTTGAATTAATATTCAACAGGCCATGAA
131 TTCACCAAGTGGAATTTCACAACACCAAGATGGCATAGTTGAATTAATATTCAACAGGCCATGAA
101624 GAATGCCTCCAAGACATTCTTTTGAAATAGGAAATACCGACACAACTTTTAGAAGATTAAATTTA
196 GAATGCCTCCAAGACATTCTTTTGAAATAGGAAATACCGACACAACTTTTAGAAGATTAAATTTA
101689 AAAGAAGAACCAAATCCAAAAACACAAACGACAGATTTTAGGACAGCTAGAGCCTCTGTCTTTTT
261 AAAGAAGAACCAAATCCAAAAACACAAACGACAGATTTTAGGACAGCTAGAGCCTCTGTCTTTTT
101754 TATCCCAACGATATTTAGAACCAATTTACAGGGAACAGATAATTCCTCAAATATAGCTCAACCTA
326 TATCCCAACGATATTTAGAACCAATTTACAGGGAACAGATAATTCCTCAAATATAGCTCAACCTA
101819 TCTTTGCCATACAGGAAGAGAGTCCCCAAAATTCACCTAATATGTCACCAACATAGTCATCAATG
391 TCTTTGCCATACAGGAAGAGAGTCCCCAAAATTCACCTAATATGTCACCAACATAGTCATCAATG
101884 ACTAATAATGCAAGACAATGAGAAAATTCAGAAATATTTGTTCTAGAAAAATATTTTGAGATAAA
456 ACTAATAATGCAAGACAATGAGAAAATTCAGAAATATTTGTTCTAGAAAAATATTTTGAGATAAA
101949 TAAGGAATGGTGTAGAAAACACTTCCATTCCAACAAAAATAAGCAAAAAAAGAAGAAGATTATTT
521 TAAGGAATGGTGTAGAAAACACTTCCATTCCAACAAAAATAAGCAAAAAAAGAAGAAGATTATTT
102014 TAAAAATT
586 TAAAAATT
102022 ATAATGATAA
Statistics
Matches: 593, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
593 593 1.00
ACGTcount: A:0.42, C:0.19, G:0.15, T:0.24
Consensus pattern (593 bp):
TAGAAACAGATACCTCGAGATCTCATACCACAATCCCAAGAACAATACAATGGCATGAAATCAAC
CTTCTTGACAGGGAGAAACTTTAGGGTGCTATAGACCTTGTGACACCAACTTCAATAAGAAACAC
TTCACCAAGTGGAATTTCACAACACCAAGATGGCATAGTTGAATTAATATTCAACAGGCCATGAA
GAATGCCTCCAAGACATTCTTTTGAAATAGGAAATACCGACACAACTTTTAGAAGATTAAATTTA
AAAGAAGAACCAAATCCAAAAACACAAACGACAGATTTTAGGACAGCTAGAGCCTCTGTCTTTTT
TATCCCAACGATATTTAGAACCAATTTACAGGGAACAGATAATTCCTCAAATATAGCTCAACCTA
TCTTTGCCATACAGGAAGAGAGTCCCCAAAATTCACCTAATATGTCACCAACATAGTCATCAATG
ACTAATAATGCAAGACAATGAGAAAATTCAGAAATATTTGTTCTAGAAAAATATTTTGAGATAAA
TAAGGAATGGTGTAGAAAACACTTCCATTCCAACAAAAATAAGCAAAAAAAGAAGAAGATTATTT
TAAAAATT
Found at i:107240 original size:23 final size:23
Alignment explanation
Indices: 107174--107258 Score: 111
Period size: 23 Copynumber: 3.7 Consensus size: 23
107164 AAAAAACGAG
* *
107174 TGAACAGGAAATATTCTCTAGCA
1 TGAACAGTAAATATTCTCTGGCA
107197 TGAACAGTAGAA-A-TCTCTGGCA
1 TGAACAGTA-AATATTCTCTGGCA
107219 TGAACAGTAAATATTCTCTGGCA
1 TGAACAGTAAATATTCTCTGGCA
* *
107242 TGAATAGTGAATATTCT
1 TGAACAGTAAATATTCT
107259 TTGTAGTTTG
Statistics
Matches: 55, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
21 2 0.04
22 18 0.33
23 33 0.60
24 2 0.04
ACGTcount: A:0.36, C:0.15, G:0.19, T:0.29
Consensus pattern (23 bp):
TGAACAGTAAATATTCTCTGGCA
Found at i:107523 original size:13 final size:13
Alignment explanation
Indices: 107505--107535 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
107495 AAAAATTTAA
107505 CAAATTTTAATCT
1 CAAATTTTAATCT
*
107518 CAAATTTTAATTT
1 CAAATTTTAATCT
107531 CAAAT
1 CAAAT
107536 ATCAAATTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.42, C:0.13, G:0.00, T:0.45
Consensus pattern (13 bp):
CAAATTTTAATCT
Found at i:113832 original size:22 final size:23
Alignment explanation
Indices: 113801--113859 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 23
113791 CATTGTAGAG
*
113801 AATCTCCATTGTTC-TTGCAAAA
1 AATCTTCATTGTTCATTGCAAAA
*
113823 AATCTTCATTGTTCATTGCAAAG
1 AATCTTCATTGTTCATTGCAAAA
*
113846 AATATTCATTGTTC
1 AATCTTCATTGTTC
113860 GTCTTTTTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
22 13 0.39
23 20 0.61
ACGTcount: A:0.31, C:0.19, G:0.10, T:0.41
Consensus pattern (23 bp):
AATCTTCATTGTTCATTGCAAAA
Found at i:115187 original size:20 final size:20
Alignment explanation
Indices: 115155--115217 Score: 90
Period size: 20 Copynumber: 3.1 Consensus size: 20
115145 AAAGCACTAT
*
115155 AGTGCAAACAGGGACACCAA
1 AGTGCAAACAGGGGCACCAA
* * *
115175 AGTGTAAATAGGGGCACCGA
1 AGTGCAAACAGGGGCACCAA
115195 AGTGCAAACAGGGGCACCAA
1 AGTGCAAACAGGGGCACCAA
115215 AGT
1 AGT
115218 ACAATCCCGT
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.40, C:0.21, G:0.30, T:0.10
Consensus pattern (20 bp):
AGTGCAAACAGGGGCACCAA
Found at i:117755 original size:78 final size:78
Alignment explanation
Indices: 117626--117864 Score: 451
Period size: 78 Copynumber: 3.1 Consensus size: 78
117616 AATTTTTGTT
117626 TTGGTATGTGATGAGGTTATCTTATGAATACGTTAAATCTATCTTGAAAATATGTTGAAATGGAT
1 TTGGTATGTGATGAGGTTATCTTATGAATACGTTAAATCTATCTTGAAAATATGTTGAAATGGAT
117691 TGGTTGTGTTGGA
66 TGGTTGTGTTGGA
117704 TTGGTATGTGATGAGGTTATCTTATGAATACGTTAAATCTATCTTGAAAATATGTTGAAATGGAT
1 TTGGTATGTGATGAGGTTATCTTATGAATACGTTAAATCTATCTTGAAAATATGTTGAAATGGAT
**
117769 TGGTTGTGTTGTT
66 TGGTTGTGTTGGA
*
117782 TTGGTATGTGATGAGGTTATCTTATGAATACGTTAAATCTATCTTGAAAATATGTTGAAATAGAT
1 TTGGTATGTGATGAGGTTATCTTATGAATACGTTAAATCTATCTTGAAAATATGTTGAAATGGAT
117847 TGGTTGTGTTGGA
66 TGGTTGTGTTGGA
117860 TTGGT
1 TTGGT
117865 CTCGGTTTAA
Statistics
Matches: 156, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
78 156 1.00
ACGTcount: A:0.28, C:0.05, G:0.25, T:0.42
Consensus pattern (78 bp):
TTGGTATGTGATGAGGTTATCTTATGAATACGTTAAATCTATCTTGAAAATATGTTGAAATGGAT
TGGTTGTGTTGGA
Found at i:121861 original size:399 final size:398
Alignment explanation
Indices: 120551--121984 Score: 1734
Period size: 405 Copynumber: 3.6 Consensus size: 398
120541 CTACTCCTGA
* * * * *
120551 GGAATGTGGCACCTCAGCTAGATTAGATTCGGGGCCTTGTTGAAAAGCACTCTGTATATCCTCCA
1 GGAATGTGGCAGCTCAGCTAGATTAGGTTCTGGGCCTTGTTG-AAAGCATTATGTATATCCTCCA
* * * * *
120616 GAGATCTCGCCTCAACAACTGGTAAATCCGAATTGGTATCTGCATCACCCTGCTGATTCTCAATC
65 GAGATCTCGCCTCAACAACAGGTAAATCCGAAGTGGTATCTGCATGATCCGGCTGATTCTCAATC
* * * * *
120681 ATGCTTGGAAGAATTATTTCCTCAACATCAACTCCTTCATGAAATTGCTTAAAAGCCAAATCGAT
130 ATACTTGGAAGAATTACTTCCTCAACATCCACTCCTTCATGAAGTTGCTTAAAAGCCAAATCAAT
* * * * *
120746 GTCTTCCAA-TGATCTTGCTTCAAGAACAGGCAGCTCTGCATTGGTCTCCATCTTCATTTCCTCT
195 ATCTT-CAACCGATCTTGCTTCAAGAACAGGCAGCTCCGCATTGGTCTCCATCTTCAATTCTTCT
* * * * * * * *
120810 GTTTCTTCATGGTCATTTTTTGGTTCACCGGCAGAATTCTGACTATTTTCTTGAATGCCAGAGAC
259 ATTTCTTCAT--TCATTTTTTGGTTCACCAGCAGCATTCTCACAATCTTCTTCAATACCAGAGAC
* ** ** * * *
120875 GGCACAACCAACTTCAATCTCTTTATTAGAAACCACATCATGCTGCTCCATTTCTGATGATCCAT
322 AGCATTACCAACTTCAATCTC-TTAGAAGAAACCACATCATGCTGCTCTACTTCTGATGATCCAA
*
120940 TTCTCAAGTCTGT
386 TCCTCAAGTCTGT
* * * * *
120953 GGAAAGTGGCAGCTCGGCCAGATTAGGTTCTGGACCTTTTTGGAAAGCATTATGTATATCCTCCA
1 GGAATGTGGCAGCTCAGCTAGATTAGGTTCTGGGCCTTGTT-GAAAGCATTATGTATATCCTCCA
* * * ** * * * *
121018 GAGATCTTGCCTCGACAACAGGTAACTTTGAAGTGGAATCTTCATGATCCAGCTGATCCTCAATC
65 GAGATCTCGCCTCAACAACAGGTAAATCCGAAGTGGTATCTGCATGATCCGGCTGATTCTCAATC
* * * * *
121083 ATGCTTGCAAGAACTACTTCCTCAACATCTACACCTTCATGAAGTTGCTTAAAAGCCAAATCAAT
130 ATACTTGGAAGAATTACTTCCTCAACATCCACTCCTTCATGAAGTTGCTTAAAAGCCAAATCAAT
* *
121148 ATCTTCAACCGATCTTGCATCCAGAACAGGCAGCTCCGCATTGGTCTCCATCTTCAATTCTTCTA
195 ATCTTCAACCGATCTTGCTTCAAGAACAGGCAGCTCCGCATTGGTCTCCATCTTCAATTCTTCTA
* *
121213 TTTCTTCATATTCTTTTTTTGGTTCACCAGCAGCAACATTCTCA-AGATGTTCTTCAA-AGCCAG
260 TTTCTTC--ATTCATTTTTTGGTTCACCAGCAG---CATTCTCACA-ATCTTCTTCAATA-CCAG
* * *
121276 AGACTGC-TTGGCCAACTTCAATCTCATTAGAAGAAACCACATCATGCAGCTCTACTTCTGATGA
318 AGACAGCATT-ACCAACTTCAATCTC-TTAGAAGAAACCACATCATGCTGCTCTACTTCTGATGA
121340 TCC-ATGCCTCAAGTCTGCT
381 TCCAAT-CCTCAAGTCTG-T
* * * * * *
121359 -GAATGCGGCAGCTCAGCTGGATTAGGTTCCGGTCCTTTTATGAAAGCATTATGTATATCATCCA
1 GGAATGTGGCAGCTCAGCTAGATTAGGTTCTGGGCCTTGT-TGAAAGCATTATGTATATCCTCCA
* * * * * *
121423 GAGATCTTGCCTCGACAACAGG-AAATTCTGAAGTGGTATCTGTATGATCTGGCAGATTCTCAAT
65 GAGATCTCGCCTCAACAACAGGTAAA-TCCGAAGTGGTATCTGCATGATCCGGCTGATTCTCAAT
121487 CATACTTGGAAGAATTACTTCCTCAACATCCACTCCTTCATGAAGTTGCTTAAAAGCCAAATCAA
129 CATACTTGGAAGAATTACTTCCTCAACATCCACTCCTTCATGAAGTTGCTTAAAAGCCAAATCAA
* * * ** * *
121552 TATCTTCAACCGATCTTGCTTCAAGAACAGGTAGCTCCACATTGGTTTCTGTCTTTAGTTCTTCT
194 TATCTTCAACCGATCTTGCTTCAAGAACAGGCAGCTCCGCATTGGTCTCCATCTTCAATTCTTCT
* * *
121617 ATTTCTTC-TTCATTTTTGGGTTCACCAGCAGCATTATCACAACCTTCTTCAATACCAGAGACAG
259 ATTTCTTCATTCATTTTTTGGTTCACCAGCAGCATTCTCACAATCTTCTTCAATACCAGAGACAG
* * * *
121681 CATTACTAACTTCGATCTCTTCAGAAGAAACAACAACATGCTGCTCTACTTCTGATGATCCAATC
324 CATTACCAACTTCAATCTCTT-AGAAGAAACCACATCATGCTGCTCTACTTCTGATGATCCAATC
121746 CTCAAGTCTGT
388 CTCAAGTCTGT
* *
121757 GGAATGTGGCAGCTGAGCTAGATTAGGTTCTGGGTCTTGTTGCAAAGCATTATGTATATCCTCCA
1 GGAATGTGGCAGCTCAGCTAGATTAGGTTCTGGGCCTTGTTG-AAAGCATTATGTATATCCTCCA
*
121822 GAGATCTCGCCTCAACAACAGGTAAATCCG-AGTTGGTATCTGCATGATCCGGCTGATTCTTAAT
65 GAGATCTCGCCTCAACAACAGGTAAATCCGAAG-TGGTATCTGCATGATCCGGCTGATTCTCAAT
* *
121886 CATACTTGGAAGAATTACTTCCTCAAAATCCACTCCTTCATGAAGTTGCTTAAATGCCAAATCAA
129 CATACTTGGAAGAATTACTTCCTCAACATCCACTCCTTCATGAAGTTGCTTAAAAGCCAAATCAA
* * *
121951 TATCTTCTACTGATCTTGTTTCAAGAACAGGCAG
194 TATCTTCAACCGATCTTGCTTCAAGAACAGGCAG
121985 TCCCACACTG
Statistics
Matches: 887, Mismatches: 122, Indels: 49
0.84 0.12 0.05
Matches are distributed among these distances:
398 7 0.01
399 281 0.32
400 9 0.01
401 3 0.00
402 264 0.30
403 1 0.00
404 5 0.01
405 315 0.36
406 2 0.00
ACGTcount: A:0.27, C:0.25, G:0.17, T:0.32
Consensus pattern (398 bp):
GGAATGTGGCAGCTCAGCTAGATTAGGTTCTGGGCCTTGTTGAAAGCATTATGTATATCCTCCAG
AGATCTCGCCTCAACAACAGGTAAATCCGAAGTGGTATCTGCATGATCCGGCTGATTCTCAATCA
TACTTGGAAGAATTACTTCCTCAACATCCACTCCTTCATGAAGTTGCTTAAAAGCCAAATCAATA
TCTTCAACCGATCTTGCTTCAAGAACAGGCAGCTCCGCATTGGTCTCCATCTTCAATTCTTCTAT
TTCTTCATTCATTTTTTGGTTCACCAGCAGCATTCTCACAATCTTCTTCAATACCAGAGACAGCA
TTACCAACTTCAATCTCTTAGAAGAAACCACATCATGCTGCTCTACTTCTGATGATCCAATCCTC
AAGTCTGT
Found at i:127329 original size:30 final size:30
Alignment explanation
Indices: 127293--127374 Score: 119
Period size: 30 Copynumber: 2.7 Consensus size: 30
127283 GATCAATAAA
* *
127293 TCTTTTCCTAAAATATGTGTTGTGAATCAT
1 TCTTTTCTTAAAATATGTGTTATGAATCAT
**
127323 TCTTTTCTTAACCTATGTGTTATGAATCAT
1 TCTTTTCTTAAAATATGTGTTATGAATCAT
127353 TCTTTTCTTAAGAATATGTGTT
1 TCTTTTCTTAA-AATATGTGTT
127375 TACTCAATTT
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
30 37 0.82
31 8 0.18
ACGTcount: A:0.24, C:0.13, G:0.12, T:0.50
Consensus pattern (30 bp):
TCTTTTCTTAAAATATGTGTTATGAATCAT
Found at i:131599 original size:26 final size:27
Alignment explanation
Indices: 131562--131612 Score: 79
Period size: 26 Copynumber: 1.9 Consensus size: 27
131552 AAATATAATA
131562 TGAGTGCTAGAAT-TATA-ATTTTTTT
1 TGAGTGCTAGAATATATATATTTTTTT
131587 TGAGTGTCTAGAATATATATATTTTT
1 TGAGTG-CTAGAATATATATATTTTT
131613 ATAATTAGGT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 6 0.26
26 7 0.30
27 4 0.17
28 6 0.26
ACGTcount: A:0.29, C:0.04, G:0.16, T:0.51
Consensus pattern (27 bp):
TGAGTGCTAGAATATATATATTTTTTT
Found at i:132139 original size:40 final size:40
Alignment explanation
Indices: 132094--132228 Score: 116
Period size: 40 Copynumber: 3.4 Consensus size: 40
132084 GTTTGGAACA
*
132094 AAAGCGCCACAAAAAATCGAGCATTAGCGGCGATTTATCC
1 AAAGCGCCACAAAAAATAGAGCATTAGCGGCGATTTATCC
* * **
132134 AAAGCGCCGCTAAAGGTAGAGC-TTCAGCGGCGA-TTATCC
1 AAAGCGCCACAAAAAATAGAGCATT-AGCGGCGATTTATCC
* * * * * *
132173 GGAAGCGCCGCTAAAAATAG-GAATTAGCGGCGTTTTA-CAT
1 -AAAGCGCCACAAAAAATAGAGCATTAGCGGCGATTTATC-C
132213 AAAGCGCCACAAAAAA
1 AAAGCGCCACAAAAAA
132229 CCTAAGACCA
Statistics
Matches: 76, Mismatches: 14, Indels: 11
0.75 0.14 0.11
Matches are distributed among these distances:
39 30 0.39
40 46 0.61
ACGTcount: A:0.36, C:0.23, G:0.24, T:0.17
Consensus pattern (40 bp):
AAAGCGCCACAAAAAATAGAGCATTAGCGGCGATTTATCC
Found at i:137032 original size:17 final size:17
Alignment explanation
Indices: 137010--137042 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
137000 AAGAACAAGT
137010 TTTAAAGGTTATTTTTA
1 TTTAAAGGTTATTTTTA
137027 TTTAAAGGTTATTTTT
1 TTTAAAGGTTATTTTT
137043 GATTGGAGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.27, C:0.00, G:0.12, T:0.61
Consensus pattern (17 bp):
TTTAAAGGTTATTTTTA
Found at i:165232 original size:3 final size:3
Alignment explanation
Indices: 165218--165294 Score: 127
Period size: 3 Copynumber: 25.7 Consensus size: 3
165208 GATTTAGTCC
* *
165218 TAT TAG TAT TAT TAT TGT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
165266 TAT TAT TAT TAT TAT CAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
165295 CCTACTTATT
Statistics
Matches: 68, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 68 1.00
ACGTcount: A:0.32, C:0.01, G:0.03, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:169907 original size:19 final size:19
Alignment explanation
Indices: 169874--169921 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
169864 AATCAAAGTT
* *
169874 AAAATGAAAATGAAAAA-G
1 AAAAAGAAAAAGAAAAAGG
169892 AGAAAAGAAAAAGAAAAAGG
1 A-AAAAGAAAAAGAAAAAGG
169912 AAAAAGAAAA
1 AAAAAGAAAA
169922 GGAGAGGCCA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
18 1 0.04
19 23 0.88
20 2 0.08
ACGTcount: A:0.77, C:0.00, G:0.19, T:0.04
Consensus pattern (19 bp):
AAAAAGAAAAAGAAAAAGG
Found at i:169922 original size:5 final size:6
Alignment explanation
Indices: 169874--169921 Score: 60
Period size: 6 Copynumber: 7.7 Consensus size: 6
169864 AATCAAAGTT
* *
169874 AAAATG AAAATG AAAAAG AGAAAAG AAAAAG AAAAAGG AAAAAG AAAA
1 AAAAAG AAAAAG AAAAAG A-AAAAG AAAAAG AAAAA-G AAAAAG AAAA
169922 GGAGAGGCCA
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
6 27 0.69
7 12 0.31
ACGTcount: A:0.77, C:0.00, G:0.19, T:0.04
Consensus pattern (6 bp):
AAAAAG
Found at i:170376 original size:84 final size:84
Alignment explanation
Indices: 170281--170450 Score: 322
Period size: 84 Copynumber: 2.0 Consensus size: 84
170271 AATAAAAAAA
*
170281 CAAAAAAAAAGATGAAAAACGAAAATGAAAAATAAAAAATGAAATAGTAAAAATGGAGAGGCTAA
1 CAAAAAAAAAGATGAAAAACAAAAATGAAAAATAAAAAATGAAATAGTAAAAATGGAGAGGCTAA
170346 GGGGAAAACCCGCAAAGGG
66 GGGGAAAACCCGCAAAGGG
*
170365 CAAAAAAAAAGATGAAAAACAAAAATGAAAAATGAAAAATGAAATAGTAAAAATGGAGAGGCTAA
1 CAAAAAAAAAGATGAAAAACAAAAATGAAAAATAAAAAATGAAATAGTAAAAATGGAGAGGCTAA
170430 GGGGAAAACCCGCAAAGGG
66 GGGGAAAACCCGCAAAGGG
170449 CA
1 CA
170451 CCTTAGGCAA
Statistics
Matches: 84, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
84 84 1.00
ACGTcount: A:0.59, C:0.09, G:0.22, T:0.09
Consensus pattern (84 bp):
CAAAAAAAAAGATGAAAAACAAAAATGAAAAATAAAAAATGAAATAGTAAAAATGGAGAGGCTAA
GGGGAAAACCCGCAAAGGG
Found at i:170382 original size:13 final size:13
Alignment explanation
Indices: 170366--170408 Score: 52
Period size: 14 Copynumber: 3.2 Consensus size: 13
170356 CGCAAAGGGC
170366 AAAAA-AAAAGATG
1 AAAAACAAAA-ATG
170379 AAAAACAAAAATG
1 AAAAACAAAAATG
*
170392 AAAAATGAAAAATG
1 AAAAA-CAAAAATG
170406 AAA
1 AAA
170409 TAGTAAAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
13 13 0.48
14 14 0.52
ACGTcount: A:0.77, C:0.02, G:0.12, T:0.09
Consensus pattern (13 bp):
AAAAACAAAAATG
Found at i:170395 original size:7 final size:7
Alignment explanation
Indices: 170371--170408 Score: 51
Period size: 7 Copynumber: 5.4 Consensus size: 7
170361 AGGGCAAAAA
170371 AAAAGATG
1 AAAA-ATG
*
170379 AAAAA-C
1 AAAAATG
170385 AAAAATG
1 AAAAATG
170392 AAAAATG
1 AAAAATG
170399 AAAAATG
1 AAAAATG
170406 AAA
1 AAA
170409 TAGTAAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
6 5 0.19
7 18 0.67
8 4 0.15
ACGTcount: A:0.74, C:0.03, G:0.13, T:0.11
Consensus pattern (7 bp):
AAAAATG
Found at i:171751 original size:45 final size:45
Alignment explanation
Indices: 171649--171771 Score: 128
Period size: 44 Copynumber: 2.8 Consensus size: 45
171639 ATGAAGTTGT
* * * * *
171649 AGATCTTGCCTTCCTGTATTGACGGCGAAGCAGATTGAAGAAGCC
1 AGATCTTGCCTTCCTATACTGACAGCGAAGCAGACTAAAGAAGCC
*
171694 AG-TCTTGCCTTCCTATACTGACAGCGGAGCAGACTAAAGATAG-C
1 AGATCTTGCCTTCCTATACTGACAGCGAAGCAGACTAAAGA-AGCC
*
171738 AGATTTTGCCTTCC--TACGTCGACAGCGAAGCAGA
1 AGATCTTGCCTTCCTATAC-T-GACAGCGAAGCAGA
171772 TCGAAGACAC
Statistics
Matches: 66, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
43 3 0.05
44 36 0.55
45 27 0.41
ACGTcount: A:0.28, C:0.24, G:0.24, T:0.24
Consensus pattern (45 bp):
AGATCTTGCCTTCCTATACTGACAGCGAAGCAGACTAAAGAAGCC
Found at i:171834 original size:43 final size:42
Alignment explanation
Indices: 171786--171922 Score: 100
Period size: 43 Copynumber: 3.2 Consensus size: 42
171776 AGACACAAGC
171786 CTTGCCTCCATCGGTTGTAGTGGAGCTGGTTAAAATAGCAGAT
1 CTTGCCTCCAT-GGTTGTAGTGGAGCTGGTTAAAATAGCAGAT
** * * * * * * * *
171829 CTTGCCTTCC-TGCGTTAACAGCGAAGCAGATCGAAGACA-CA-AGC
1 CTTGCC-TCCATG-GTT-GTAGTGGAGCTGGT-TAAAATAGCAGA-T
171873 CTTGCCTCCATTGGTTGTAGTGGAGCTGGTTAAAATAGCAGAT
1 CTTGCCTCCA-TGGTTGTAGTGGAGCTGGTTAAAATAGCAGAT
171916 CTTGCCT
1 CTTGCCT
171923 TCCTGCGTTA
Statistics
Matches: 65, Mismatches: 20, Indels: 18
0.63 0.19 0.17
Matches are distributed among these distances:
42 5 0.08
43 31 0.48
44 23 0.35
45 6 0.09
ACGTcount: A:0.24, C:0.23, G:0.26, T:0.28
Consensus pattern (42 bp):
CTTGCCTCCATGGTTGTAGTGGAGCTGGTTAAAATAGCAGAT
Found at i:171850 original size:87 final size:86
Alignment explanation
Indices: 171728--172436 Score: 1057
Period size: 87 Copynumber: 8.2 Consensus size: 86
171718 CGGAGCAGAC
* **
171728 TAAAGATAGCAGATTTTGCCTTCCTACGTCGACAGCGAAGCAGATCGAAGACACAAGCCTTGCCT
1 TAAAGATAGCAGATCTTGCCTTCCTACGTTAACAGCGAAGCAGATCGAA-ACA-AAGCCTTGCCT
*
171793 CCATCGGTTGTAGTGGAGCTGGT
64 CCATCGGTTGCAGTGGAGCTGGT
*
171816 TAAA-ATAGCAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAGACACAAGCCTTGCCT
1 TAAAGATAGCAGATCTTGCCTTCCTACGTTAACAGCGAAGCAGATCGAA-ACA-AAGCCTTGCCT
* *
171880 CCATTGGTTGTAGTGGAGCTGGT
64 CCATCGGTTGCAGTGGAGCTGGT
* * * *
171903 TAAA-ATAGCAGATCTTGCCTTCCTGCGTTAACAGCGAAGTAGATCGAAAATAAATCCTTGCCTC
1 TAAAGATAGCAGATCTTGCCTTCCTACGTTAACAGCGAAGCAGATCG-AAACAAAGCCTTGCCTC
171967 CATCGGTTGCAGTGGAGCTGGT
65 CATCGGTTGCAGTGGAGCTGGT
* * * *
171989 TAAAGATAACAGATCTTGCCTTCATGCGTTAACATCGAAGCAGATCGAAAACAAAGCCTTGCCTC
1 TAAAGATAGCAGATCTTGCCTTCCTACGTTAACAGCGAAGCAGATCG-AAACAAAGCCTTGCCTC
* * *
172054 CGTCGATTGCGGTGGAGCTGGT
65 CATCGGTTGCAGTGGAGCTGGT
*
172076 TAAAGATAGCAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTC
1 TAAAGATAGCAGATCTTGCCTTCCTACGTTAACAGCGAAGCAGATCG-AAACAAAGCCTTGCCTC
*
172141 CATCGGTTGTAGTGGAGCTGGT
65 CATCGGTTGCAGTGGAGCTGGT
172163 TAAA-ATAGCAGATCTTGCCTTCCTACGTTAACAGCGAAGCAGATCGGAAACAAAGCCTTGCCTC
1 TAAAGATAGCAGATCTTGCCTTCCTACGTTAACAGCGAAGCAGATC-GAAACAAAGCCTTGCCTC
* * *
172227 CGTCGATTGCGGTGGAGCTGGT
65 CATCGGTTGCAGTGGAGCTGGT
*
172249 TAAA-ATAGCAGATCTTGCCGTCCTACGTTAACAGCGAAGCAGATCGGAAACAAAGCCTTGCCTC
1 TAAAGATAGCAGATCTTGCCTTCCTACGTTAACAGCGAAGCAGATC-GAAACAAAGCCTTGCCTC
172313 CATCGGTTGCAGTGGAGCTGGT
65 CATCGGTTGCAGTGGAGCTGGT
* *
172335 TAAAGATAGCAGATCTTACCGTCCTACGTTAACAGCGAAGCAGATCGGAAACAAAGCCTTGCCTC
1 TAAAGATAGCAGATCTTGCCTTCCTACGTTAACAGCGAAGCAGATC-GAAACAAAGCCTTGCCTC
*
172400 CATCGATTGCAGTGGAGCTGGT
65 CATCGGTTGCAGTGGAGCTGGT
172422 TAAAGATAGCAGATC
1 TAAAGATAGCAGATC
172437 GAAAATAAAT
Statistics
Matches: 580, Mismatches: 37, Indels: 9
0.93 0.06 0.01
Matches are distributed among these distances:
86 196 0.34
87 378 0.65
88 6 0.01
ACGTcount: A:0.28, C:0.23, G:0.25, T:0.24
Consensus pattern (86 bp):
TAAAGATAGCAGATCTTGCCTTCCTACGTTAACAGCGAAGCAGATCGAAACAAAGCCTTGCCTCC
ATCGGTTGCAGTGGAGCTGGT
Found at i:172074 original size:173 final size:173
Alignment explanation
Indices: 171728--172436 Score: 1098
Period size: 173 Copynumber: 4.1 Consensus size: 173
171718 CGGAGCAGAC
* ** *
171728 TAAAGATAGCAGATTTTGCCTTCCTACGTCGACAGCGAAGCAGATCGAAGACACAAGCCTTGCCT
1 TAAAGATAGCAGATCTTGCCTTCCTACGTTAACAGCGAAGCAGATCGAAAACA-AAGCCTTGCCT
* *
171793 CCATCGGTTGTAGTGGAGCTGGTTAAAATAGCAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAG
65 CCATCGGTTGCAGTGGAGCTGGTTAAAATAGCAGATCTTGCCTTCCTACGTTAACAGCGAAGCAG
* * * *
171858 ATCGAAGACACAAGCCTTGCCTCCATTGGTTGTAGTGGAGCTGGT
130 ATCGAAAACA-AAGCCTTGCCTCCATCGATTGCAGTGGAGCTGGT
* * * *
171903 TAAA-ATAGCAGATCTTGCCTTCCTGCGTTAACAGCGAAGTAGATCGAAAATAAATCCTTGCCTC
1 TAAAGATAGCAGATCTTGCCTTCCTACGTTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTC
* * * *
171967 CATCGGTTGCAGTGGAGCTGGTTAAAGATAACAGATCTTGCCTTCATGCGTTAACATCGAAGCAG
66 CATCGGTTGCAGTGGAGCTGGTTAAA-ATAGCAGATCTTGCCTTCCTACGTTAACAGCGAAGCAG
* *
172032 ATCGAAAACAAAGCCTTGCCTCCGTCGATTGCGGTGGAGCTGGT
130 ATCGAAAACAAAGCCTTGCCTCCATCGATTGCAGTGGAGCTGGT
*
172076 TAAAGATAGCAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTC
1 TAAAGATAGCAGATCTTGCCTTCCTACGTTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTC
*
172141 CATCGGTTGTAGTGGAGCTGGTTAAAATAGCAGATCTTGCCTTCCTACGTTAACAGCGAAGCAGA
66 CATCGGTTGCAGTGGAGCTGGTTAAAATAGCAGATCTTGCCTTCCTACGTTAACAGCGAAGCAGA
* * *
172206 TCGGAAACAAAGCCTTGCCTCCGTCGATTGCGGTGGAGCTGGT
131 TCGAAAACAAAGCCTTGCCTCCATCGATTGCAGTGGAGCTGGT
* *
172249 TAAA-ATAGCAGATCTTGCCGTCCTACGTTAACAGCGAAGCAGATCGGAAACAAAGCCTTGCCTC
1 TAAAGATAGCAGATCTTGCCTTCCTACGTTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTC
* *
172313 CATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTACCGTCCTACGTTAACAGCGAAGCAG
66 CATCGGTTGCAGTGGAGCTGGTTAAA-ATAGCAGATCTTGCCTTCCTACGTTAACAGCGAAGCAG
*
172378 ATCGGAAACAAAGCCTTGCCTCCATCGATTGCAGTGGAGCTGGT
130 ATCGAAAACAAAGCCTTGCCTCCATCGATTGCAGTGGAGCTGGT
172422 TAAAGATAGCAGATC
1 TAAAGATAGCAGATC
172437 GAAAATAAAT
Statistics
Matches: 495, Mismatches: 35, Indels: 9
0.92 0.06 0.02
Matches are distributed among these distances:
172 82 0.17
173 232 0.47
174 177 0.36
175 4 0.01
ACGTcount: A:0.28, C:0.23, G:0.25, T:0.24
Consensus pattern (173 bp):
TAAAGATAGCAGATCTTGCCTTCCTACGTTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTC
CATCGGTTGCAGTGGAGCTGGTTAAAATAGCAGATCTTGCCTTCCTACGTTAACAGCGAAGCAGA
TCGAAAACAAAGCCTTGCCTCCATCGATTGCAGTGGAGCTGGT
Found at i:172139 original size:43 final size:42
Alignment explanation
Indices: 172090--172225 Score: 98
Period size: 43 Copynumber: 3.2 Consensus size: 42
172080 GATAGCAGAT
172090 CTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGC
1 CTTGCCTTCCT-CGTTAACAGCGAAGCAGATCGAAAACAAAGC
** * * * * * * * *
172133 CTTGCC-TCCATCGGTT-GTAGTGGAGCTGGT-TAAAATAGCAGAT
1 CTTGCCTTCC-TC-GTTAACAGCGAAGCAGATCGAAAACA-AAG-C
*
172176 CTTGCCTTCCTACGTTAACAGCGAAGCAGATCGGAAACAAAGC
1 CTTGCCTTCCT-CGTTAACAGCGAAGCAGATCGAAAACAAAGC
172219 CTTGCCT
1 CTTGCCT
172226 CCGTCGATTG
Statistics
Matches: 64, Mismatches: 21, Indels: 16
0.63 0.21 0.16
Matches are distributed among these distances:
41 5 0.08
42 14 0.22
43 27 0.42
44 14 0.22
45 4 0.06
ACGTcount: A:0.28, C:0.26, G:0.23, T:0.24
Consensus pattern (42 bp):
CTTGCCTTCCTCGTTAACAGCGAAGCAGATCGAAAACAAAGC
Found at i:172451 original size:56 final size:56
Alignment explanation
Indices: 172373--172492 Score: 195
Period size: 56 Copynumber: 2.1 Consensus size: 56
172363 TTAACAGCGA
*
172373 AGCAGATCGGAAACAAAGCCTTGCCTCCATCGATTGCAGTGGAGCTGGTTAAAGAT
1 AGCAGATCGAAAACAAAGCCTTGCCTCCATCGATTGCAGTGGAGCTGGTTAAAGAT
* * *
172429 AGCAGATCGAAAATAAATCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGAT
1 AGCAGATCGAAAACAAAGCCTTGCCTCCATCGATTGCAGTGGAGCTGGTTAAAGAT
*
172485 AACAGATC
1 AGCAGATC
172493 TTGCCTTCAT
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
56 59 1.00
ACGTcount: A:0.32, C:0.21, G:0.25, T:0.23
Consensus pattern (56 bp):
AGCAGATCGAAAACAAAGCCTTGCCTCCATCGATTGCAGTGGAGCTGGTTAAAGAT
Found at i:172520 original size:87 final size:87
Alignment explanation
Indices: 172429--172599 Score: 270
Period size: 87 Copynumber: 2.0 Consensus size: 87
172419 GGTTAAAGAT
* * * *
172429 AGCAGATCGAAAATAAATCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAACAGATCT
1 AGCAGATCGAAAACAAAGCCTTGCCTCCAGCGATTGCAGTGGAGCTGGTTAAAGATAACAGATCT
172494 TGCCTTCATGCGTTAACAGCGA
66 TGCCTTCATGCGTTAACAGCGA
* * *
172516 AGCAGATCGAAAACAAAGCTTTGCCTCCAGCGATTGCGGTGGAGCTGGTTAAAGATAGCAGATCT
1 AGCAGATCGAAAACAAAGCCTTGCCTCCAGCGATTGCAGTGGAGCTGGTTAAAGATAACAGATCT
*
172581 TGCCTTCCTGCGTTAACAG
66 TGCCTTCATGCGTTAACAG
172600 NNNNNNNNNN
Statistics
Matches: 76, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
87 76 1.00
ACGTcount: A:0.29, C:0.22, G:0.25, T:0.25
Consensus pattern (87 bp):
AGCAGATCGAAAACAAAGCCTTGCCTCCAGCGATTGCAGTGGAGCTGGTTAAAGATAACAGATCT
TGCCTTCATGCGTTAACAGCGA
Found at i:172544 original size:143 final size:143
Alignment explanation
Indices: 172286--172579 Score: 480
Period size: 143 Copynumber: 2.1 Consensus size: 143
172276 TTAACAGCGA
* *
172286 AGCAGATCGGAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCT
1 AGCAGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAACAGATCT
* * *
172351 TACCGTCCTACGTTAACAGCGAAGCAGATCGGAAACAAAGCCTTGCCTCCATCGATTGCAGTGGA
66 TACCGTCATACGTTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCAGCGATTGCAGTGGA
172416 GCTGGTTAAAGAT
131 GCTGGTTAAAGAT
* *
172429 AGCAGATCGAAAATAAATCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAACAGATCT
1 AGCAGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAACAGATCT
* * * * *
172494 TGCCTTCATGCGTTAACAGCGAAGCAGATCGAAAACAAAGCTTTGCCTCCAGCGATTGCGGTGGA
66 TACCGTCATACGTTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCAGCGATTGCAGTGGA
172559 GCTGGTTAAAGAT
131 GCTGGTTAAAGAT
172572 AGCAGATC
1 AGCAGATC
172580 TTGCCTTCCT
Statistics
Matches: 139, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
143 139 1.00
ACGTcount: A:0.30, C:0.22, G:0.26, T:0.22
Consensus pattern (143 bp):
AGCAGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAACAGATCT
TACCGTCATACGTTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCAGCGATTGCAGTGGA
GCTGGTTAAAGAT
Found at i:172808 original size:87 final size:87
Alignment explanation
Indices: 172662--173009 Score: 588
Period size: 87 Copynumber: 4.0 Consensus size: 87
172652 NNNNNNNNNN
172662 CCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGT
1 CCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGT
172727 TAAAGATAGCAGATCTTGCCTT
66 TAAAGATAGCAGATCTTGCCTT
*
172749 CCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGCCCTGCCTCCATCGGTTGCAGTGGAGCTGGT
1 CCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGT
*
172814 TAAAGATAGCAGATCTTACCTT
66 TAAAGATAGCAGATCTTGCCTT
* * * *
172836 CCTGCGTTAACAGTGAAGCAGATCAAAAATAAATCCTTGCCTCCATCGGTTGCAGTGGAGCTGGT
1 CCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGT
* *
172901 TAAAGATAACAGATCTTGCATT
66 TAAAGATAGCAGATCTTGCCTT
* * * *
172923 CATGCATTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTAGAGCTAGT
1 CCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGT
172988 TAAAGATAGCAGATCTTGCCTT
66 TAAAGATAGCAGATCTTGCCTT
173010 TCTAAGTACT
Statistics
Matches: 241, Mismatches: 20, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
87 241 1.00
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.24
Consensus pattern (87 bp):
CCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGT
TAAAGATAGCAGATCTTGCCTT
Found at i:182465 original size:41 final size:40
Alignment explanation
Indices: 182420--182509 Score: 119
Period size: 40 Copynumber: 2.2 Consensus size: 40
182410 AGCGGCACTT
182420 TTAGCGGCGTTTGGACAAAAAACGCCAC-AAATAATCGAGCA
1 TTAGCGGCGTTT-GACAAAAAACGCCACAAAAT-ATCGAGCA
* * * *
182461 TTAGCGGCATTTTACGAAAAACGCCGCAAAATATCGAGCA
1 TTAGCGGCGTTTGACAAAAAACGCCACAAAATATCGAGCA
182501 TTAGCGGCG
1 TTAGCGGCG
182510 CTACATAAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
40 28 0.65
41 15 0.35
ACGTcount: A:0.36, C:0.22, G:0.23, T:0.19
Consensus pattern (40 bp):
TTAGCGGCGTTTGACAAAAAACGCCACAAAATATCGAGCA
Found at i:182560 original size:40 final size:41
Alignment explanation
Indices: 182420--182569 Score: 112
Period size: 40 Copynumber: 3.7 Consensus size: 41
182410 AGCGGCACTT
* * * *
182420 TTAGCGGCGTTTGGAC-AAAAAACGCCAC-AAATAATCGAGCA
1 TTAGCGGCGTTT-TACAAAAAAACGCCGCAAAAT-ACCAAGCA
* * * *
182461 TTAGCGGCATTTTAC-GAAAAACGCCGCAAAATATCGAGCA
1 TTAGCGGCGTTTTACAAAAAAACGCCGCAAAATACCAAGCA
* ** * *
182501 TTAGCGGCGCTACATAAAAAAACGCCGCTAAA-ACCAAGCA
1 TTAGCGGCGTTTTACAAAAAAACGCCGCAAAATACCAAGCA
* *
182541 TTAGCAGCGTTTTAC-AAAAAGCGCCGCAA
1 TTAGCGGCGTTTTACAAAAAAACGCCGCAA
182570 TAGAGTCACA
Statistics
Matches: 87, Mismatches: 20, Indels: 6
0.77 0.18 0.05
Matches are distributed among these distances:
39 12 0.14
40 46 0.53
41 29 0.33
ACGTcount: A:0.39, C:0.24, G:0.20, T:0.17
Consensus pattern (41 bp):
TTAGCGGCGTTTTACAAAAAAACGCCGCAAAATACCAAGCA
Found at i:182852 original size:114 final size:113
Alignment explanation
Indices: 182549--182893 Score: 546
Period size: 113 Copynumber: 3.0 Consensus size: 113
182539 CATTAGCAGC
*
182549 GTTTTACAAAAAGCGCCGCAATAGAGTCACACAGAACGACGCCGTTTTCATATATTTGGGAACAT
1 GTTTTACAAAAAGCGCCGCAATAGAGTAACACAGAACGACGCCGTTTTCATATATTTGGGAACAT
* *
182614 TAGTGGCGGTTTTTCCCAAGCGCCGCTAAAACTCCGTTCTTCAGCGGT
66 TAGTGGCGGTTTTGCCCAAGCGCCGCTAATACTCCGTTCTTCAGCGGT
* * *
182662 GTTTTATAAAAAGCGCCGCAATGGAGTAACACAGAACGACGCCGTTTTCATATGTTTGGGAACAT
1 GTTTTACAAAAAGCGCCGCAATAGAGTAACACAGAACGACGCCGTTTTCATATATTTGGGAACAT
* * *
182727 TAGTGGCGGTTTTGCCCAAGCGCCACTAATACTTCATTCTTCAGCGGT
66 TAGTGGCGGTTTTGCCCAAGCGCCGCTAATACTCCGTTCTTCAGCGGT
*
182775 GTTTTACAAAAAGCGTCGCAAATAGAGTAACACAGAACGACGCCGTTTTCATATATTTGGGAACA
1 GTTTTACAAAAAGCGCCGC-AATAGAGTAACACAGAACGACGCCGTTTTCATATATTTGGGAACA
* * * *
182840 CTAGTGGCGGTTTTTGCCCAAACGCCGCTAATAATCCGTTCTTCAGCGGC
65 TTAGTGGCGG-TTTTGCCCAAGCGCCGCTAATACTCCGTTCTTCAGCGGT
182890 GTTT
1 GTTT
182894 GGCGTTAAGC
Statistics
Matches: 210, Mismatches: 20, Indels: 2
0.91 0.09 0.01
Matches are distributed among these distances:
113 121 0.58
114 52 0.25
115 37 0.18
ACGTcount: A:0.27, C:0.23, G:0.22, T:0.28
Consensus pattern (113 bp):
GTTTTACAAAAAGCGCCGCAATAGAGTAACACAGAACGACGCCGTTTTCATATATTTGGGAACAT
TAGTGGCGGTTTTGCCCAAGCGCCGCTAATACTCCGTTCTTCAGCGGT
Found at i:183031 original size:41 final size:41
Alignment explanation
Indices: 182986--183072 Score: 111
Period size: 41 Copynumber: 2.1 Consensus size: 41
182976 TTTCATAAAC
* * *
182986 CGCCGCTGATGCTCCGCTCTAAAGCGGCGTTTATGGAGAAT
1 CGCCGCTAATGCTCCGCTCTAAAGCGGCGTTCATGGAGAAG
* * * *
183027 CGCCGCTAATGTTCCGTTCTATAGCGGCGTTCCTGGAGAAG
1 CGCCGCTAATGCTCCGCTCTAAAGCGGCGTTCATGGAGAAG
183068 CGCCG
1 CGCCG
183073 GTAANNNNNN
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.17, C:0.29, G:0.30, T:0.24
Consensus pattern (41 bp):
CGCCGCTAATGCTCCGCTCTAAAGCGGCGTTCATGGAGAAG
Found at i:199781 original size:44 final size:44
Alignment explanation
Indices: 199728--199841 Score: 149
Period size: 44 Copynumber: 2.6 Consensus size: 44
199718 TCATCGTTTT
* *
199728 AATCCGCTCCACTGCAACTTCAAGGAGATAGGA-TTAGTAGCTTC
1 AATCTGCTCCACTGCAACTTCAAGGAGATAAGACTT-GTAGCTTC
* * * *
199772 AGTCTGCTCCACTGCAATTTCAGGGAGATAAGACTTGTATCTTC
1 AATCTGCTCCACTGCAACTTCAAGGAGATAAGACTTGTAGCTTC
*
199816 AATCTGCCCCACTGCAACTTCAAGGA
1 AATCTGCTCCACTGCAACTTCAAGGA
199842 AATGAGATTT
Statistics
Matches: 59, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
44 57 0.97
45 2 0.03
ACGTcount: A:0.28, C:0.26, G:0.19, T:0.26
Consensus pattern (44 bp):
AATCTGCTCCACTGCAACTTCAAGGAGATAAGACTTGTAGCTTC
Found at i:200176 original size:218 final size:218
Alignment explanation
Indices: 199852--200289 Score: 671
Period size: 218 Copynumber: 2.0 Consensus size: 218
199842 AATGAGATTT
* **
199852 GTTTTCGATCTGTTTCACTGCCAGTACAGGAAGACAAGATCTACGGTCTTCAACCTACTCCACTG
1 GTTTTCGATCTGCTTCACTGCCAGTACAGGAAGACAAGATCTACAATCTTCAACCTACTCCACTG
* * * *
199917 TTGCTCATGGAGATAGGACTAGTGGCTTATATCTACTTCCCTATTGCCTTACGAAGATAAGATTC
66 CTGCTCAAGGAGATAGGACTAGTGGCTTAAATCTACTTCCCTATTACCTTACGAAGATAAGATTC
* * *
199982 ACCGTCTTCGATTTGCTCCACTACTG-TTCAGGGAGATAGGATCTGCAATCTTCAACCTACTCCA
131 ACCATCTTCGATTTGCTCCACTACTGCTT-AGGGAGACAAGATCTGCAATCTTCAACCTACTCCA
*
200046 CTACTGCTCAGGGAGATAGGACCA
195 CTACCGCTCAGGGAGATAGGACCA
* *
200070 GTTTTCGATCTGCTTCACTGCTAGTACAGGAAGACAAGATCTACAATCTTCAATCTACTCCACTG
1 GTTTTCGATCTGCTTCACTGCCAGTACAGGAAGACAAGATCTACAATCTTCAACCTACTCCACTG
* **
200135 CTGCTCAAGGAGATAGGACTAGTGGCTTAAATCTGCTTCCCTATTACCTTGGGAAGATAAGATTC
66 CTGCTCAAGGAGATAGGACTAGTGGCTTAAATCTACTTCCCTATTACCTTACGAAGATAAGATTC
* * *
200200 GCCATCTTCGATTTGCTCCATTACTGCTTAGGGAGACAAGATCTGCAATCTTCAACCTACTCCAT
131 ACCATCTTCGATTTGCTCCACTACTGCTTAGGGAGACAAGATCTGCAATCTTCAACCTACTCCAC
* *
200265 TGCCGCTCGGGGAGATAGGACCA
196 TACCGCTCAGGGAGATAGGACCA
200288 GT
1 GT
200290 GGCTTAAATC
Statistics
Matches: 198, Mismatches: 21, Indels: 2
0.90 0.10 0.01
Matches are distributed among these distances:
218 196 0.99
219 2 0.01
ACGTcount: A:0.26, C:0.25, G:0.20, T:0.29
Consensus pattern (218 bp):
GTTTTCGATCTGCTTCACTGCCAGTACAGGAAGACAAGATCTACAATCTTCAACCTACTCCACTG
CTGCTCAAGGAGATAGGACTAGTGGCTTAAATCTACTTCCCTATTACCTTACGAAGATAAGATTC
ACCATCTTCGATTTGCTCCACTACTGCTTAGGGAGACAAGATCTGCAATCTTCAACCTACTCCAC
TACCGCTCAGGGAGATAGGACCA
Found at i:200260 original size:132 final size:132
Alignment explanation
Indices: 200101--200421 Score: 453
Period size: 132 Copynumber: 2.4 Consensus size: 132
200091 TAGTACAGGA
* * * *
200101 AGACAAGATCTACAATCTTCAATCTACTCCACTGCTGCTCAAGGAGATAGGACTAGTGGCTTAAA
1 AGACAAGATCTGCAATCTTCAACCTACTCCACTGCTGCTCAGGGAGATAGGACCAGTGGCTTAAA
* * * * * * *
200166 TCTGCTTCCCTATTACCTTGGGAAGATAAGATTCGCCATCTTCGATTTGCTCCATTACTGCTTAG
66 TCTACTTCCATACTACCTTAGGAAGATAAGATTCGCCATCTTCGATATGCTCCACTACTACTTAG
200231 GG
131 GG
* * *
200233 AGACAAGATCTGCAATCTTCAACCTACTCCATTGCCGCTCGGGGAGATAGGACCAGTGGCTTAAA
1 AGACAAGATCTGCAATCTTCAACCTACTCCACTGCTGCTCAGGGAGATAGGACCAGTGGCTTAAA
* * *
200298 TCTACTTCTATACTGCCTTAGGAAGATAAGATTCGCCATCTTCGGTATGCTCCACTACTACTTAG
66 TCTACTTCCATACTACCTTAGGAAGATAAGATTCGCCATCTTCGATATGCTCCACTACTACTTAG
200363 GG
131 GG
* * * *
200365 AGACAGGATCTGCAATCTTCAACTTACTCCACTACTGCTTAGGGAGATAGGACCAGT
1 AGACAAGATCTGCAATCTTCAACCTACTCCACTGCTGCTCAGGGAGATAGGACCAGT
200422 TTTTGATCTA
Statistics
Matches: 165, Mismatches: 24, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
132 165 1.00
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.28
Consensus pattern (132 bp):
AGACAAGATCTGCAATCTTCAACCTACTCCACTGCTGCTCAGGGAGATAGGACCAGTGGCTTAAA
TCTACTTCCATACTACCTTAGGAAGATAAGATTCGCCATCTTCGATATGCTCCACTACTACTTAG
GG
Found at i:200263 original size:44 final size:44
Alignment explanation
Indices: 200215--200497 Score: 125
Period size: 44 Copynumber: 6.5 Consensus size: 44
200205 CTTCGATTTG
*
200215 CTCCATTACTGCTTAGGGAGACAAGATCTGCAATCTTCAACCTA
1 CTCCACTACTGCTTAGGGAGACAAGATCTGCAATCTTCAACCTA
* * * ** * * * * *
200259 CTCCATTGCCGCTCGGGGAGATAGGA-C--CAGTGGCTTAAATCTA
1 CTCCACTACTGCTTAGGGAGACAAGATCTGCAAT--CTTCAACCTA
* * * * **** *
200302 CTTCTA-TACTGCCTTAGGAAGATAAGAT-TCGCCATCTTCGGTATG
1 C-TCCACTACTG-CTTAGGGAGACAAGATCT-GCAATCTTCAACCTA
* * *
200347 CTCCACTACTACTTAGGGAGACAGGATCTGCAATCTTCAACTTA
1 CTCCACTACTGCTTAGGGAGACAAGATCTGCAATCTTCAACCTA
* * * * ** *
200391 CTCCACTACTGCTTAGGGAGATAGGA-C--CAGTTTTTGATCTA
1 CTCCACTACTGCTTAGGGAGACAAGATCTGCAATCTTCAACCTA
* * * *
200432 CTTCACTACCAG-TACAGGAAGACAAGATCTGCAATCTTCAACCTA
1 CTCCACTA-CTGCT-TAGGGAGACAAGATCTGCAATCTTCAACCTA
*
200477 CTCCACTACTGCTCAGGGAGA
1 CTCCACTACTGCTTAGGGAGA
200498 TAGGACTTAA
Statistics
Matches: 167, Mismatches: 56, Indels: 32
0.65 0.22 0.13
Matches are distributed among these distances:
41 19 0.11
42 11 0.07
43 15 0.09
44 92 0.55
45 28 0.17
47 2 0.01
ACGTcount: A:0.28, C:0.26, G:0.19, T:0.27
Consensus pattern (44 bp):
CTCCACTACTGCTTAGGGAGACAAGATCTGCAATCTTCAACCTA
Found at i:201429 original size:15 final size:16
Alignment explanation
Indices: 201401--201436 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
201391 CCTCTCCTTT
201401 TTTTTCCTTCTTTTTC
1 TTTTTCCTTCTTTTTC
*
201417 TTTTT-CTTTTTTTTC
1 TTTTTCCTTCTTTTTC
201432 TTTTT
1 TTTTT
201437 TATGAAATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 14 0.74
16 5 0.26
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (16 bp):
TTTTTCCTTCTTTTTC
Found at i:202931 original size:18 final size:18
Alignment explanation
Indices: 202908--202943 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
202898 TTCTTTTCTC
*
202908 CATTCTTAATTATCGCGT
1 CATTCTCAATTATCGCGT
202926 CATTCTCAATTATCGCGT
1 CATTCTCAATTATCGCGT
202944 TTACCCCTGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.22, C:0.25, G:0.11, T:0.42
Consensus pattern (18 bp):
CATTCTCAATTATCGCGT
Found at i:210564 original size:39 final size:39
Alignment explanation
Indices: 210510--210589 Score: 160
Period size: 39 Copynumber: 2.1 Consensus size: 39
210500 GGTGTAAGTG
210510 TTGAACAAGTATGCATCCGACACAAGTATGTTCAAGTTT
1 TTGAACAAGTATGCATCCGACACAAGTATGTTCAAGTTT
210549 TTGAACAAGTATGCATCCGACACAAGTATGTTCAAGTTT
1 TTGAACAAGTATGCATCCGACACAAGTATGTTCAAGTTT
210588 TT
1 TT
210590 CTATATTTTC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (39 bp):
TTGAACAAGTATGCATCCGACACAAGTATGTTCAAGTTT
Found at i:216197 original size:20 final size:20
Alignment explanation
Indices: 216172--216212 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
216162 ACTCAAAGAT
216172 TAATTTAATAGGTTTTTCAA
1 TAATTTAATAGGTTTTTCAA
216192 TAATTTAATAGGTTTTTCAA
1 TAATTTAATAGGTTTTTCAA
216212 T
1 T
216213 TTATCAGTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.34, C:0.05, G:0.10, T:0.51
Consensus pattern (20 bp):
TAATTTAATAGGTTTTTCAA
Found at i:216525 original size:16 final size:16
Alignment explanation
Indices: 216495--216536 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
216485 GTTATGCCCT
*
216495 TTTAGAAATTTGTAAAA
1 TTTA-AAATTAGTAAAA
216512 TTTAAAATTAGTAAAA
1 TTTAAAATTAGTAAAA
*
216528 -GTAAAATTA
1 TTTAAAATTA
216537 CACTTTAACC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
15 8 0.35
16 11 0.48
17 4 0.17
ACGTcount: A:0.52, C:0.00, G:0.10, T:0.38
Consensus pattern (16 bp):
TTTAAAATTAGTAAAA
Found at i:226700 original size:19 final size:18
Alignment explanation
Indices: 226663--226697 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
226653 TCGAAACCGG
*
226663 TCGGTTAATCGAAAAAAT
1 TCGGTTAACCGAAAAAAT
226681 TCGGTTAACCGAAAAAA
1 TCGGTTAACCGAAAAAA
226698 ATTAATAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.46, C:0.14, G:0.17, T:0.23
Consensus pattern (18 bp):
TCGGTTAACCGAAAAAAT
Found at i:226779 original size:18 final size:18
Alignment explanation
Indices: 226756--226798 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
226746 ACCCAATCTA
**
226756 AACCCAAGTATTCAACCC
1 AACCCAAGTACCCAACCC
*
226774 AACCCAATTACCCAACCC
1 AACCCAAGTACCCAACCC
226792 AACCCAA
1 AACCCAA
226799 TCATAAAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.42, C:0.44, G:0.02, T:0.12
Consensus pattern (18 bp):
AACCCAAGTACCCAACCC
Found at i:226920 original size:9 final size:9
Alignment explanation
Indices: 226906--226999 Score: 106
Period size: 9 Copynumber: 10.4 Consensus size: 9
226896 GTAGTGATTC
*
226906 AATTTGGTT
1 AATTCGGTT
*
226915 AATTTGGTT
1 AATTCGGTT
226924 AATTCGGTT
1 AATTCGGTT
226933 AATTCCGG-T
1 AATT-CGGTT
226942 AATTCCGG-T
1 AATT-CGGTT
226951 AATTCCGG-T
1 AATT-CGGTT
226960 AATTCGGTT
1 AATTCGGTT
226969 AATTCTGG-T
1 AATTC-GGTT
226978 AATTCGGTT
1 AATTCGGTT
226987 AATTCGGTT
1 AATTCGGTT
226996 AATT
1 AATT
227000 TTTAACCAAA
Statistics
Matches: 80, Mismatches: 1, Indels: 8
0.90 0.01 0.09
Matches are distributed among these distances:
8 5 0.06
9 70 0.88
10 5 0.06
ACGTcount: A:0.23, C:0.12, G:0.21, T:0.44
Consensus pattern (9 bp):
AATTCGGTT
Found at i:226944 original size:27 final size:27
Alignment explanation
Indices: 226906--226999 Score: 122
Period size: 27 Copynumber: 3.5 Consensus size: 27
226896 GTAGTGATTC
*
226906 AATTTGGTTAATT-TGGTTAATTCGGTT
1 AATTCGGTTAATTCTGG-TAATTCGGTT
*
226933 AATTCCGG-TAATTCCGGTAATTCCGG-T
1 AATT-CGGTTAATTCTGGTAATT-CGGTT
226960 AATTCGGTTAATTCTGGTAATTCGGTT
1 AATTCGGTTAATTCTGGTAATTCGGTT
226987 AATTCGGTTAATT
1 AATTCGGTTAATT
227000 TTTAACCAAA
Statistics
Matches: 59, Mismatches: 3, Indels: 10
0.82 0.04 0.14
Matches are distributed among these distances:
26 6 0.10
27 46 0.78
28 7 0.12
ACGTcount: A:0.23, C:0.12, G:0.21, T:0.44
Consensus pattern (27 bp):
AATTCGGTTAATTCTGGTAATTCGGTT
Found at i:227177 original size:12 final size:12
Alignment explanation
Indices: 227160--227184 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
227150 TGTTATTTCA
227160 GGTCGGTTAACC
1 GGTCGGTTAACC
227172 GGTCGGTTAACC
1 GGTCGGTTAACC
227184 G
1 G
227185 AATGAACACC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.24, G:0.36, T:0.24
Consensus pattern (12 bp):
GGTCGGTTAACC
Found at i:236760 original size:62 final size:57
Alignment explanation
Indices: 236673--236800 Score: 150
Period size: 57 Copynumber: 2.2 Consensus size: 57
236663 AATTGACGGT
*
236673 AAAAAGGATCTAGCCCGGACAGGTGATGCTATCCTGATATAGCCCTCCCAAAGAATATGTGTG
1 AAAAAGGATCTAGCCCAGACAGGTGAT-C--T--TGATATAGCCCTCCCAAAGAATATGTG-G
** *
236736 AAAAA-GATCTAGCCCAGATGGGTGATCTTGATATAGCCCTCCCGAAGAATATGTGG
1 AAAAAGGATCTAGCCCAGACAGGTGATCTTGATATAGCCCTCCCAAAGAATATGTGG
*
236792 AAAATGGAT
1 AAAAAGGAT
236801 TTAACCCGGA
Statistics
Matches: 59, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
56 5 0.08
57 29 0.49
59 1 0.02
61 1 0.02
62 18 0.31
63 5 0.08
ACGTcount: A:0.34, C:0.20, G:0.24, T:0.23
Consensus pattern (57 bp):
AAAAAGGATCTAGCCCAGACAGGTGATCTTGATATAGCCCTCCCAAAGAATATGTGG
Found at i:246805 original size:23 final size:23
Alignment explanation
Indices: 246770--246820 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
246760 ACCTACTTTC
* * *
246770 TTACTGTATTAATTTTCGGGGTA
1 TTACAGTAGTAATTTTCGGGATA
246793 TTACAGTAGTAATTTTCGGGATA
1 TTACAGTAGTAATTTTCGGGATA
246816 TTACA
1 TTACA
246821 CCTTAAAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.27, C:0.10, G:0.20, T:0.43
Consensus pattern (23 bp):
TTACAGTAGTAATTTTCGGGATA
Found at i:247981 original size:128 final size:128
Alignment explanation
Indices: 247753--248008 Score: 361
Period size: 128 Copynumber: 2.0 Consensus size: 128
247743 TAAACAGATT
* * * *
247753 CATGATCAATTCTTTTTGGGTCTAGTCCGATGTACTGTTAGTCCAGTCAGTCACATCTATGTCTT
1 CATGATCAATTCTTCTTGAGTCTAGTCCGATGTACTATCAGTCCAGTCAGTCACATCTATGTCTT
* * * * * ** *
247818 TATCTTTTGGGAGTCATTCGCTCTAATGTGCAAGACAAAGCATCTCC-CAAATTGGACTTGATA
66 TATCTTCTAGGAGTCATCCACTCCAATGCCCAAGACAAAACATCTCCTC-AATTGGACTTGATA
* * *
247881 CATGATCTATTCTTCTTGAGTCTAGTCCGATGTACTATCAGTCTAGTTAGTCACATCTATGTCTT
1 CATGATCAATTCTTCTTGAGTCTAGTCCGATGTACTATCAGTCCAGTCAGTCACATCTATGTCTT
247946 TATCTTCTAGGAGTCATCCACTCCAATGCCCAAGACAAAACATCTCCTCAATTGGACTTGATA
66 TATCTTCTAGGAGTCATCCACTCCAATGCCCAAGACAAAACATCTCCTCAATTGGACTTGATA
248009 GACGACATAT
Statistics
Matches: 112, Mismatches: 15, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
128 111 0.99
129 1 0.01
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.35
Consensus pattern (128 bp):
CATGATCAATTCTTCTTGAGTCTAGTCCGATGTACTATCAGTCCAGTCAGTCACATCTATGTCTT
TATCTTCTAGGAGTCATCCACTCCAATGCCCAAGACAAAACATCTCCTCAATTGGACTTGATA
Done.