Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 ID=Chr05-JGI_221_v2.0
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: 64140413
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 820884 characters in sequence are not A, C, G, or T
File 169 of 208
Found at i:51606643 original size:30 final size:30
Alignment explanation
Indices: 51606616--51606760 Score: 155
Period size: 30 Copynumber: 4.8 Consensus size: 30
51606606 ATATATATAT
* * *
51606616 ATATATATTGCCGAATTAATTTATATATAGAT
1 ATATACATTGCCGAATTAATTTGTATAT-G-G
* ** *
51606648 ATATAAATAACCGAATTGATTTGTATATGG
1 ATATACATTGCCGAATTAATTTGTATATGG
**
51606678 ATATACATTGCTAAATTAATTTGTATATGG
1 ATATACATTGCCGAATTAATTTGTATATGG
* *
51606708 ATATACATTGCTGAATTGATTTGTATATGG
1 ATATACATTGCCGAATTAATTTGTATATGG
* *
51606738 ATATATATTGCCGAATTTATTTG
1 ATATACATTGCCGAATTAATTTG
51606761 AGCATTGGAT
Statistics
Matches: 96, Mismatches: 17, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
30 72 0.75
31 1 0.01
32 23 0.24
ACGTcount: A:0.36, C:0.07, G:0.14, T:0.43
Consensus pattern (30 bp):
ATATACATTGCCGAATTAATTTGTATATGG
Found at i:51606760 original size:60 final size:62
Alignment explanation
Indices: 51606616--51606760 Score: 186
Period size: 60 Copynumber: 2.4 Consensus size: 62
51606606 ATATATATAT
* *
51606616 ATATATATTGCCGAATTAATTTATATATAGATATATAAATAACCGAATTGATTTGTATATGG
1 ATATATATTGCCGAATTAATTTGTATATAGAGATATAAATAACCGAATTGATTTGTATATGG
* ** * ** *
51606678 ATATACATTGCTAAATTAATTTGTATAT-G-GATATACATTGCTGAATTGATTTGTATATGG
1 ATATATATTGCCGAATTAATTTGTATATAGAGATATAAATAACCGAATTGATTTGTATATGG
*
51606738 ATATATATTGCCGAATTTATTTG
1 ATATATATTGCCGAATTAATTTG
51606761 AGCATTGGAT
Statistics
Matches: 70, Mismatches: 13, Indels: 2
0.82 0.15 0.02
Matches are distributed among these distances:
60 45 0.64
61 1 0.01
62 24 0.34
ACGTcount: A:0.36, C:0.07, G:0.14, T:0.43
Consensus pattern (62 bp):
ATATATATTGCCGAATTAATTTGTATATAGAGATATAAATAACCGAATTGATTTGTATATGG
Found at i:51613774 original size:34 final size:34
Alignment explanation
Indices: 51613725--51613793 Score: 93
Period size: 34 Copynumber: 2.0 Consensus size: 34
51613715 TTGTATATGG
* *
51613725 ATATATATTGTCGAATTAATTTATATATAGATAT
1 ATATATATAGCCGAATTAATTTATATATAGATAT
* * *
51613759 ATATATATAGCCGAATTGATTTGTATATGGATAT
1 ATATATATAGCCGAATTAATTTATATATAGATAT
51613793 A
1 A
51613794 CATTGCTAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.39, C:0.04, G:0.13, T:0.43
Consensus pattern (34 bp):
ATATATATAGCCGAATTAATTTATATATAGATAT
Found at i:51613852 original size:60 final size:63
Alignment explanation
Indices: 51613705--51613871 Score: 200
Period size: 64 Copynumber: 2.7 Consensus size: 63
51613695 TTATATATTT
* * *
51613705 CCGAATTGATTTGTATATGGATATATATTG-TCGAATTAATTTATATATAGATATATATATATAG
1 CCGAATTGATTTGTATATGGATATATATTGCTCAAATT-ATTTGTATATAGA-ATATACATATAG
* *
51613769 CCGAATTGATTTGTATATGGATATACATTGCT-AAATTGATTTGTATATCG-ATATACAT-T-G
1 CCGAATTGATTTGTATATGGATATATATTGCTCAAATT-ATTTGTATATAGAATATACATATAG
* * *
51613829 CTGACTTGATTTGTATATGGATATATATTGCTGAAATTATTTG
1 CCGAATTGATTTGTATATGGATATATATTGCTCAAATTATTTG
51613872 AGCATTGGAT
Statistics
Matches: 92, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
60 35 0.38
61 6 0.07
62 7 0.08
64 43 0.47
65 1 0.01
ACGTcount: A:0.33, C:0.07, G:0.16, T:0.44
Consensus pattern (63 bp):
CCGAATTGATTTGTATATGGATATATATTGCTCAAATTATTTGTATATAGAATATACATATAG
Found at i:51613859 original size:30 final size:30
Alignment explanation
Indices: 51613696--51613871 Score: 185
Period size: 30 Copynumber: 5.7 Consensus size: 30
51613686 GTATATGTTT
* *
51613696 TATATATTTCCGAATTGATTTGTATATGGA
1 TATATATTGCTGAATTGATTTGTATATGGA
* * *
51613726 TATATATTG-TCGAATTAATTTATATATAGATA
1 TATATATTGCT-GAATTGATTTGTATAT-G-GA
*
51613758 TATATATATAGCCGAATTGATTTGTATATGGA
1 TATATAT-T-GCTGAATTGATTTGTATATGGA
* * *
51613790 TATACATTGCTAAATTGATTTGTATATCGA
1 TATATATTGCTGAATTGATTTGTATATGGA
* *
51613820 TATACATTGCTGACTTGATTTGTATATGGA
1 TATATATTGCTGAATTGATTTGTATATGGA
51613850 TATATATTGCTGAAATT-ATTTG
1 TATATATTGCTG-AATTGATTTG
51613872 AGCATTGGAT
Statistics
Matches: 121, Mismatches: 18, Indels: 14
0.79 0.12 0.09
Matches are distributed among these distances:
30 84 0.69
31 5 0.04
32 15 0.12
33 2 0.02
34 15 0.12
ACGTcount: A:0.33, C:0.07, G:0.15, T:0.45
Consensus pattern (30 bp):
TATATATTGCTGAATTGATTTGTATATGGA
Found at i:51614925 original size:15 final size:15
Alignment explanation
Indices: 51614907--51614936 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
51614897 TAGACTGTGT
51614907 TGTGCTAGGTAATGC
1 TGTGCTAGGTAATGC
51614922 TGTGCTAGGTAATGC
1 TGTGCTAGGTAATGC
51614937 CTTGTAACCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.13, G:0.33, T:0.33
Consensus pattern (15 bp):
TGTGCTAGGTAATGC
Found at i:51616526 original size:11 final size:11
Alignment explanation
Indices: 51616510--51616552 Score: 68
Period size: 11 Copynumber: 3.7 Consensus size: 11
51616500 CTGGACCAGT
51616510 AATATTTATTA
1 AATATTTATTA
51616521 AATATTTACATTA
1 AATATTT--ATTA
51616534 AATATTTATTA
1 AATATTTATTA
51616545 AATATTTA
1 AATATTTA
51616553 CGAAGTTATT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
11 19 0.63
13 11 0.37
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (11 bp):
AATATTTATTA
Found at i:51622149 original size:27 final size:27
Alignment explanation
Indices: 51622084--51622155 Score: 99
Period size: 27 Copynumber: 2.7 Consensus size: 27
51622074 TAGTCGAGGG
*
51622084 ACTGCCACAAGCGGCACCAAAGGTGCC
1 ACTGCCACAGGCGGCACCAAAGGTGCC
* * * *
51622111 AGTGGCAGAGGCTGCACCAAAGGTGCC
1 ACTGCCACAGGCGGCACCAAAGGTGCC
51622138 ACTGCCACAGGCGGCACC
1 ACTGCCACAGGCGGCACC
51622156 CCCCTTATAT
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.26, C:0.35, G:0.31, T:0.08
Consensus pattern (27 bp):
ACTGCCACAGGCGGCACCAAAGGTGCC
Found at i:51622271 original size:19 final size:19
Alignment explanation
Indices: 51622248--51622300 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
51622238 CGGTGCCGAA
51622248 AAAAGA-AAAGAAAAAGAG
1 AAAAGAGAAAGAAAAAGAG
*
51622266 AGAAAGAGAAAGAGAATAGAG
1 A-AAAGAGAAAGA-AAAAGAG
*
51622287 AAAGGAGAAAGAAA
1 AAAAGAGAAAGAAA
51622301 GAGAAAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
18 1 0.03
19 7 0.23
20 15 0.50
21 7 0.23
ACGTcount: A:0.70, C:0.00, G:0.28, T:0.02
Consensus pattern (19 bp):
AAAAGAGAAAGAAAAAGAG
Found at i:51622277 original size:14 final size:14
Alignment explanation
Indices: 51622254--51622298 Score: 58
Period size: 13 Copynumber: 3.4 Consensus size: 14
51622244 CGAAAAAAGA
*
51622254 AAAGAAAAAGAGAG
1 AAAGAGAAAGAGAG
51622268 AAAGAGAAAGAGA-
1 AAAGAGAAAGAGAG
*
51622281 ATAGAGAAAG-GAG
1 AAAGAGAAAGAGAG
51622294 AAAGA
1 AAAGA
51622299 AAGAGAAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
12 2 0.07
13 13 0.48
14 12 0.44
ACGTcount: A:0.67, C:0.00, G:0.31, T:0.02
Consensus pattern (14 bp):
AAAGAGAAAGAGAG
Found at i:51622294 original size:7 final size:6
Alignment explanation
Indices: 51622264--51622306 Score: 54
Period size: 6 Copynumber: 7.2 Consensus size: 6
51622254 AAAGAAAAAG
51622264 AGAGAA AGAGAA AGAGAA TAGAGAA AG-GAGA A-AGAA AGAGAA A
1 AGAGAA AGAGAA AGAGAA -AGAGAA AGAGA-A AGAGAA AGAGAA A
51622307 AAAATAGAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
5 4 0.12
6 23 0.70
7 6 0.18
ACGTcount: A:0.65, C:0.00, G:0.33, T:0.02
Consensus pattern (6 bp):
AGAGAA
Found at i:51627743 original size:41 final size:41
Alignment explanation
Indices: 51627685--51627907 Score: 304
Period size: 41 Copynumber: 5.4 Consensus size: 41
51627675 CTTTTCGGGA
* *
51627685 GCTTTAGCGGCGATTTTATGGAAGCGCCGCTAATGTTCTGG
1 GCTTTAGCGGCGTTTTTATGTAAGCGCCGCTAATGTTCTGG
* *
51627726 GCTTTAGCGGCGTTTTTATGTAAGCGCCGCTAATGTTATGT
1 GCTTTAGCGGCGTTTTTATGTAAGCGCCGCTAATGTTCTGG
*
51627767 GCTTTAGCGGCGTTTTTATGTAAGCGCCTCTAATGTTCTGG
1 GCTTTAGCGGCGTTTTTATGTAAGCGCCGCTAATGTTCTGG
* * *
51627808 GCTTTAGCGGCGTTTTTATTTATGCGCCGCTAATATTCTGG
1 GCTTTAGCGGCGTTTTTATGTAAGCGCCGCTAATGTTCTGG
* * * *
51627849 GATTTAGCGGCGTTTTTATGGATGCGCCGCTAAT-TCTCAGG
1 GCTTTAGCGGCGTTTTTATGTAAGCGCCGCTAATGT-TCTGG
*
51627890 CCTTTAGCGGCGCTTTTT
1 GCTTTAGCGGCG-TTTTT
51627908 TAAAAAACGC
Statistics
Matches: 163, Mismatches: 17, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
40 1 0.01
41 157 0.96
42 5 0.03
ACGTcount: A:0.15, C:0.20, G:0.27, T:0.38
Consensus pattern (41 bp):
GCTTTAGCGGCGTTTTTATGTAAGCGCCGCTAATGTTCTGG
Found at i:51627936 original size:82 final size:82
Alignment explanation
Indices: 51627687--51627947 Score: 289
Period size: 82 Copynumber: 3.2 Consensus size: 82
51627677 TTTCGGGAGC
* *
51627687 TTTAGCGGCGATTTTATGGAAGCGCCGCTAATGTTCTGGGCTTTAGCGGCGTTTTTATGTAAGCG
1 TTTAGCGGCGTTTTTATGGAAGCGCCGCTAATGTTCTGGGCTTTAGCGGCGTTTTTATATAAGCG
* *
51627752 CCGCTAATGTTATGTGC-
66 CCGCTAATATTCTGT-CA
* * * *
51627769 TTTAGCGGCGTTTTTATGTAAGCGCCTCTAATGTTCTGGGCTTTAGCGGCGTTTTTATTTATGCG
1 TTTAGCGGCGTTTTTATGGAAGCGCCGCTAATGTTCTGGGCTTTAGCGGCGTTTTTATATAAGCG
**
51627834 CCGCTAATATTCTGGGA
66 CCGCTAATATTCTGTCA
* * * *
51627851 TTTAGCGGCGTTTTTATGGATGCGCCGCTAAT-TCTCAGGCCTTTAGCGGCGCTTTTT-TAAAAA
1 TTTAGCGGCGTTTTTATGGAAGCGCCGCTAATGT-TCTGGGCTTTAGCGGCG-TTTTTAT-ATAA
*
51627914 ACGCCGCTAAT-TCTCT-TCA
63 GCGCCGCTAATAT-TCTGTCA
* *
51627933 TTTAGTGGCATTTTT
1 TTTAGCGGCGTTTTT
51627948 TAAAAAGCGC
Statistics
Matches: 152, Mismatches: 22, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
81 1 0.01
82 132 0.87
83 19 0.12
ACGTcount: A:0.17, C:0.20, G:0.25, T:0.38
Consensus pattern (82 bp):
TTTAGCGGCGTTTTTATGGAAGCGCCGCTAATGTTCTGGGCTTTAGCGGCGTTTTTATATAAGCG
CCGCTAATATTCTGTCA
Found at i:51631244 original size:6 final size:6
Alignment explanation
Indices: 51631233--51631291 Score: 75
Period size: 6 Copynumber: 9.3 Consensus size: 6
51631223 AACTGTTTAT
51631233 TTGTTA TTGTTA TT-TCTCA TTGTTA TTGTTA TTGTTA TTTGTTA TTTGTTA
1 TTGTTA TTGTTA TTGT-T-A TTGTTA TTGTTA TTGTTA -TTGTTA -TTGTTA
51631284 TTGTTA TT
1 TTGTTA TT
51631292 TAACATGTGT
Statistics
Matches: 49, Mismatches: 0, Indels: 8
0.86 0.00 0.14
Matches are distributed among these distances:
5 1 0.02
6 30 0.61
7 17 0.35
8 1 0.02
ACGTcount: A:0.15, C:0.03, G:0.14, T:0.68
Consensus pattern (6 bp):
TTGTTA
Found at i:51631292 original size:13 final size:13
Alignment explanation
Indices: 51631229--51631291 Score: 85
Period size: 13 Copynumber: 4.9 Consensus size: 13
51631219 GTAGAACTGT
51631229 TTATTTGTTATTG
1 TTATTTGTTATTG
* *
51631242 TTATTTCTCATTG
1 TTATTTGTTATTG
51631255 TTA-TTGTTATTG
1 TTATTTGTTATTG
51631267 TTATTTGTTATTTG
1 TTATTTGTTA-TTG
51631281 TTA-TTGTTATT
1 TTATTTGTTATT
51631292 TAACATGTGT
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
12 12 0.27
13 26 0.59
14 6 0.14
ACGTcount: A:0.16, C:0.03, G:0.13, T:0.68
Consensus pattern (13 bp):
TTATTTGTTATTG
Found at i:51633174 original size:12 final size:12
Alignment explanation
Indices: 51633142--51633308 Score: 94
Period size: 12 Copynumber: 14.0 Consensus size: 12
51633132 CATAATATCC
51633142 TAACTTACATAA
1 TAACTTACATAA
* *
51633154 TATCCTACATAA
1 TAACTTACATAA
51633166 TAACTTACA-AA
1 TAACTTACATAA
*
51633177 -AACTTAC---C
1 TAACTTACATAA
51633185 TAACTTACATAA
1 TAACTTACATAA
* *
51633197 TATCCTACATAA
1 TAACTTACATAA
* *
51633209 TAACTTACGTGA
1 TAACTTACATAA
51633221 TAACTTACATACA
1 TAACTTACATA-A
* *
51633234 TAAATATTCATCAA
1 TAACT-TACAT-AA
* * *
51633248 TCCAC-AACTTACA
1 T-AACTTACATA-A
**
51633261 TAACCAACATAA
1 TAACTTACATAA
*
51633273 TGACTTACATAA
1 TAACTTACATAA
*
51633285 TAACCTACATAA
1 TAACTTACATAA
*
51633297 TAACTTATATAA
1 TAACTTACATAA
51633309 CAGTACACAA
Statistics
Matches: 115, Mismatches: 30, Indels: 20
0.70 0.18 0.12
Matches are distributed among these distances:
9 7 0.06
10 7 0.06
11 2 0.02
12 77 0.67
13 14 0.12
14 6 0.05
15 2 0.02
ACGTcount: A:0.46, C:0.22, G:0.02, T:0.31
Consensus pattern (12 bp):
TAACTTACATAA
Found at i:51633374 original size:9 final size:9
Alignment explanation
Indices: 51633360--51633449 Score: 93
Period size: 9 Copynumber: 10.7 Consensus size: 9
51633350 CAAAAACAAG
51633360 ACATAACTT
1 ACATAACTT
*
51633369 ACATAACCT
1 ACATAACTT
*
51633378 ACTTAA--T
1 ACATAACTT
51633385 ACATAACTT
1 ACATAACTT
*
51633394 ACATAATTT
1 ACATAACTT
51633403 ACATAA--T
1 ACATAACTT
51633410 ACATAACTT
1 ACATAACTT
*
51633419 ACATAATTT
1 ACATAACTT
*
51633428 ACTTAA--T
1 ACATAACTT
51633435 ACATAACTT
1 ACATAACTT
51633444 ACATAA
1 ACATAA
51633450 TATCCCTTAT
Statistics
Matches: 68, Mismatches: 7, Indels: 12
0.78 0.08 0.14
Matches are distributed among these distances:
7 19 0.28
9 49 0.72
ACGTcount: A:0.47, C:0.19, G:0.00, T:0.34
Consensus pattern (9 bp):
ACATAACTT
Found at i:51633388 original size:25 final size:25
Alignment explanation
Indices: 51633360--51633450 Score: 155
Period size: 25 Copynumber: 3.6 Consensus size: 25
51633350 CAAAAACAAG
**
51633360 ACATAACTTACATAACCTACTTAAT
1 ACATAACTTACATAATTTACTTAAT
*
51633385 ACATAACTTACATAATTTACATAAT
1 ACATAACTTACATAATTTACTTAAT
51633410 ACATAACTTACATAATTTACTTAAT
1 ACATAACTTACATAATTTACTTAAT
51633435 ACATAACTTACATAAT
1 ACATAACTTACATAAT
51633451 ATCCCTTATG
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 62 1.00
ACGTcount: A:0.46, C:0.19, G:0.00, T:0.35
Consensus pattern (25 bp):
ACATAACTTACATAATTTACTTAAT
Found at i:51633389 original size:16 final size:16
Alignment explanation
Indices: 51633368--51633451 Score: 82
Period size: 16 Copynumber: 5.1 Consensus size: 16
51633358 AGACATAACT
* *
51633368 TACATAACCTACTTAA
1 TACATAACTTACATAA
51633384 TACATAACTTACATAA
1 TACATAACTTACATAA
51633400 TTTACATAA--TACATAA
1 --TACATAACTTACATAA
* *
51633416 CTTACATAATTTACTTAA
1 --TACATAACTTACATAA
51633434 TACATAACTTACATAA
1 TACATAACTTACATAA
51633450 TA
1 TA
51633452 TCCCTTATGT
Statistics
Matches: 58, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
16 45 0.78
18 13 0.22
ACGTcount: A:0.46, C:0.18, G:0.00, T:0.36
Consensus pattern (16 bp):
TACATAACTTACATAA
Found at i:51639015 original size:66 final size:66
Alignment explanation
Indices: 51638945--51639082 Score: 233
Period size: 66 Copynumber: 2.1 Consensus size: 66
51638935 GACCACAGTT
* *
51638945 GAGGTTCAAAAGAAATATGAAGAACTCCAGCTACAACTTAAAGC-AGATGCGGCAGCGAGAGAAG
1 GAGGTTCAAAAGAAATATGAAGAACTCCAGCGACAACTTAAAGCTA-ATGCGGCAGCCAGAGAAG
51639009 CA
65 CA
*
51639011 GAGGTTCAAAAGAAATATGAAGAACTCCAGCGACAACTTAAAGCTAATGCGGCATCCAGAGAAGC
1 GAGGTTCAAAAGAAATATGAAGAACTCCAGCGACAACTTAAAGCTAATGCGGCAGCCAGAGAAGC
51639076 A
66 A
51639077 GAGGTT
1 GAGGTT
51639083 GCAGCGAGAG
Statistics
Matches: 68, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
66 67 0.99
67 1 0.01
ACGTcount: A:0.41, C:0.18, G:0.25, T:0.15
Consensus pattern (66 bp):
GAGGTTCAAAAGAAATATGAAGAACTCCAGCGACAACTTAAAGCTAATGCGGCAGCCAGAGAAGC
A
Found at i:51639503 original size:43 final size:42
Alignment explanation
Indices: 51639448--51639565 Score: 166
Period size: 43 Copynumber: 2.8 Consensus size: 42
51639438 GTGAAAAATT
51639448 GCCGCTAAAGAACATGATCTTTAGCGGCGTTTGTGGGAGT-AGC
1 GCCGCTAAAGAACATGATCTTTAGCGGCGTTTGT-GGA-TAAGC
*
51639491 GCCGCTAAAGAACATGATCTTTAGCGGCGTTTGTGTATAAAGC
1 GCCGCTAAAGAACATGATCTTTAGCGGCGTTTGTGGAT-AAGC
* * *
51639534 ACCGCTAAAGAACATGACCTTTAGCGGTGTTT
1 GCCGCTAAAGAACATGATCTTTAGCGGCGTTT
51639566 TTAAAGATAA
Statistics
Matches: 69, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
41 1 0.01
42 2 0.03
43 66 0.96
ACGTcount: A:0.26, C:0.19, G:0.27, T:0.27
Consensus pattern (42 bp):
GCCGCTAAAGAACATGATCTTTAGCGGCGTTTGTGGATAAGC
Found at i:51640919 original size:15 final size:15
Alignment explanation
Indices: 51640899--51640938 Score: 80
Period size: 15 Copynumber: 2.7 Consensus size: 15
51640889 TTCTTTTTCG
51640899 GTCGATTTGCTCTCT
1 GTCGATTTGCTCTCT
51640914 GTCGATTTGCTCTCT
1 GTCGATTTGCTCTCT
51640929 GTCGATTTGC
1 GTCGATTTGC
51640939 GTCATCGGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.07, C:0.25, G:0.23, T:0.45
Consensus pattern (15 bp):
GTCGATTTGCTCTCT
Found at i:51648947 original size:22 final size:22
Alignment explanation
Indices: 51648922--51648964 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
51648912 ACACCAAAAC
*
51648922 AGGCCTTTAGCGGCGCTTTTTT
1 AGGCCTTTAGAGGCGCTTTTTT
51648944 AGGCCTTTAGAGGCGCTTTTT
1 AGGCCTTTAGAGGCGCTTTTT
51648965 AGCACTACTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.12, C:0.21, G:0.28, T:0.40
Consensus pattern (22 bp):
AGGCCTTTAGAGGCGCTTTTTT
Found at i:51649103 original size:43 final size:43
Alignment explanation
Indices: 51649049--51649304 Score: 340
Period size: 42 Copynumber: 6.0 Consensus size: 43
51649039 TTGCGGCGTT
* *
51649049 TTTACCGACAAACGCCGCTAAAGACTAGGACCTTTAGCGGCGC
1 TTTACCCACAAACGCCGCTAAAGACCAGGACCTTTAGCGGCGC
51649092 TTTACCCACAAACGCCGCTAAAGACCAGGACCTTTAGCGGCGC
1 TTTACCCACAAACGCCGCTAAAGACCAGGACCTTTAGCGGCGC
* * * *
51649135 TTT-CCTACAAACGCCGCGAAAGAACAGGACCTTTAACGGCGC
1 TTTACCCACAAACGCCGCTAAAGACCAGGACCTTTAGCGGCGC
* *
51649177 -TTCCCCACAAACGCCACTAAAGACCAGGACCTTTAGCGGCGC
1 TTTACCCACAAACGCCGCTAAAGACCAGGACCTTTAGCGGCGC
* * *
51649219 -TTCCCCACAAACGCCGCTATAGACCACGACCTTTAGCGGCGC
1 TTTACCCACAAACGCCGCTAAAGACCAGGACCTTTAGCGGCGC
* * * * *
51649261 TTTACCAACAAACGCCGCTATAGAGCA-AACCTTTAGCGACGC
1 TTTACCCACAAACGCCGCTAAAGACCAGGACCTTTAGCGGCGC
51649303 TT
1 TT
51649305 CTAGCAAAAA
Statistics
Matches: 192, Mismatches: 19, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
41 2 0.01
42 123 0.64
43 67 0.35
ACGTcount: A:0.29, C:0.34, G:0.20, T:0.18
Consensus pattern (43 bp):
TTTACCCACAAACGCCGCTAAAGACCAGGACCTTTAGCGGCGC
Found at i:51649380 original size:22 final size:24
Alignment explanation
Indices: 51649354--51649397 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
51649344 TTGTTTTAAT
51649354 TAAATAATAT-TTAT-TTTTATGA
1 TAAATAATATATTATGTTTTATGA
*
51649376 TAAATATTATATTATGTTTTAT
1 TAAATAATATATTATGTTTTAT
51649398 TTTTTTAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 9 0.47
23 4 0.21
24 6 0.32
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.57
Consensus pattern (24 bp):
TAAATAATATATTATGTTTTATGA
Found at i:51653725 original size:14 final size:14
Alignment explanation
Indices: 51653694--51653749 Score: 51
Period size: 14 Copynumber: 4.0 Consensus size: 14
51653684 AATTAATCTA
*
51653694 AACC-CTAAACCCT
1 AACCGCTAACCCCT
* *
51653707 AAACCCCTAACTCCT
1 -AACCGCTAACCCCT
* *
51653722 AACCTCTAACCGCT
1 AACCGCTAACCCCT
51653736 AACCGCTAACCCCT
1 AACCGCTAACCCCT
51653750 CTTTTACAAT
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
14 27 0.79
15 7 0.21
ACGTcount: A:0.32, C:0.46, G:0.04, T:0.18
Consensus pattern (14 bp):
AACCGCTAACCCCT
Found at i:51654140 original size:14 final size:15
Alignment explanation
Indices: 51654118--51654151 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
51654108 CTTAAACCAA
*
51654118 AATCCCTAA-TCCAT
1 AATCTCTAATTCCAT
51654132 AATCTCTAATTCCAT
1 AATCTCTAATTCCAT
51654147 AATCT
1 AATCT
51654152 ATAAACCTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.35, C:0.29, G:0.00, T:0.35
Consensus pattern (15 bp):
AATCTCTAATTCCAT
Found at i:51654586 original size:41 final size:41
Alignment explanation
Indices: 51654523--51655019 Score: 768
Period size: 41 Copynumber: 12.1 Consensus size: 41
51654513 AAAATATTTG
*
51654523 AAGCCCTGAGCATTAGCGGCGCTTCTTCAAAAACACCGCTA
1 AAGCCCTGAGCATTAGCGGCGCTTCTTCAAAAACGCCGCTA
* * * *
51654564 AAACCTTGAGCATTAGCGGCGCTTCTTCAAAAGCGCCGTTA
1 AAGCCCTGAGCATTAGCGGCGCTTCTTCAAAAACGCCGCTA
* *
51654605 AATCCCTGAGCATTCGCGGCGCTTCTTCAAAAACGCCGCTA
1 AAGCCCTGAGCATTAGCGGCGCTTCTTCAAAAACGCCGCTA
*
51654646 AAACCCTGAGCATTAGCGGCGCTT-TATCAAAAACGCCGCTA
1 AAGCCCTGAGCATTAGCGGCGCTTCT-TCAAAAACGCCGCTA
51654687 AAGCCCTGAGCATTAGCGGCGCTT-TATCAAAAACGCCGCTA
1 AAGCCCTGAGCATTAGCGGCGCTTCT-TCAAAAACGCCGCTA
*
51654728 AAGCCCTGAGCATTAGCGGCGCTTCTTCAAAAACACCGCTA
1 AAGCCCTGAGCATTAGCGGCGCTTCTTCAAAAACGCCGCTA
*
51654769 AAGCCCTG-GCATTAGCGGCGCTTCTTCAAAAACGCCGGTA
1 AAGCCCTGAGCATTAGCGGCGCTTCTTCAAAAACGCCGCTA
*
51654809 AAGCCCTGAGCATTAGCGGCGCTTATTCAAAAACGCCGCTA
1 AAGCCCTGAGCATTAGCGGCGCTTCTTCAAAAACGCCGCTA
* *
51654850 AAGCCTTGAGCATTAGCGGCGCTTATTCAAAAACGCCGCTA
1 AAGCCCTGAGCATTAGCGGCGCTTCTTCAAAAACGCCGCTA
51654891 AAGCCCTGAGCATTAGCGGCGCTTCATT-AAAAACGCCGCTA
1 AAGCCCTGAGCATTAGCGGCGCTTC-TTCAAAAACGCCGCTA
* ** *
51654932 AAGCCCTAAGCATTAGCGGCGCTTCTTCAAAAAAACCGTTA
1 AAGCCCTGAGCATTAGCGGCGCTTCTTCAAAAACGCCGCTA
* *
51654973 AAGCCCTAAGCATTAGCGGCGCTTCTTCAAAAACGCTGCTA
1 AAGCCCTGAGCATTAGCGGCGCTTCTTCAAAAACGCCGCTA
51655014 AAGCCC
1 AAGCCC
51655020 CAAAAGGTCA
Statistics
Matches: 422, Mismatches: 29, Indels: 10
0.92 0.06 0.02
Matches are distributed among these distances:
40 41 0.10
41 378 0.90
42 3 0.01
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.21
Consensus pattern (41 bp):
AAGCCCTGAGCATTAGCGGCGCTTCTTCAAAAACGCCGCTA
Found at i:51655156 original size:40 final size:39
Alignment explanation
Indices: 51655079--51655189 Score: 170
Period size: 40 Copynumber: 2.8 Consensus size: 39
51655069 TTACAAAAAA
*
51655079 CGCCGCTAATGCTC-ATTTTTAGCGGCGCTATTAGTAAAG
1 CGCCGCTAATGCTCGATTTTTAGCGGCG-TTTTAGTAAAG
*
51655118 CGCCGCTAATGCTCGATCTTTAGCGGCGTTTTATGTAAAG
1 CGCCGCTAATGCTCGATTTTTAGCGGCGTTTTA-GTAAAG
*
51655158 CGCCGCTAATGCTGGATTTTTAGCGGCGTTTT
1 CGCCGCTAATGCTCGATTTTTAGCGGCGTTTT
51655190 TTTGTCCAAA
Statistics
Matches: 66, Mismatches: 4, Indels: 3
0.90 0.05 0.04
Matches are distributed among these distances:
39 18 0.27
40 48 0.73
ACGTcount: A:0.19, C:0.23, G:0.25, T:0.33
Consensus pattern (39 bp):
CGCCGCTAATGCTCGATTTTTAGCGGCGTTTTAGTAAAG
Found at i:51659826 original size:8 final size:8
Alignment explanation
Indices: 51659808--51659841 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
51659798 GTATTCAAAA
51659808 TTAACTCAT
1 TTAA-TCAT
51659817 TTAATCAT
1 TTAATCAT
51659825 TTAATCAT
1 TTAATCAT
*
51659833 ATAATCAT
1 TTAATCAT
51659841 T
1 T
51659842 CAATTCAGTC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
8 19 0.83
9 4 0.17
ACGTcount: A:0.38, C:0.15, G:0.00, T:0.47
Consensus pattern (8 bp):
TTAATCAT
Found at i:51665399 original size:27 final size:26
Alignment explanation
Indices: 51665351--51665401 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 26
51665341 TAGAATTAAT
*
51665351 TTGTTATTCATCATTTGCTTTGTATA
1 TTGTTAATCATCATTTGCTTTGTATA
51665377 TTGTTAATCAATCATATTG-TTTGTA
1 TTGTTAATC-ATCAT-TTGCTTTGTA
51665402 AGAATTTCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 8 0.36
27 11 0.50
28 3 0.14
ACGTcount: A:0.24, C:0.10, G:0.12, T:0.55
Consensus pattern (26 bp):
TTGTTAATCATCATTTGCTTTGTATA
Found at i:51667439 original size:20 final size:20
Alignment explanation
Indices: 51667393--51667431 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
51667383 AAATAAGATT
51667393 TTGAAAAGAGAAATTTAGAGC
1 TTGAAAAGAGAAA-TTAGAGC
51667414 TTGAAAAGA-AAA-TAGAGC
1 TTGAAAAGAGAAATTAGAGC
51667432 GGTTGAAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.33
20 3 0.17
21 9 0.50
ACGTcount: A:0.51, C:0.05, G:0.23, T:0.21
Consensus pattern (20 bp):
TTGAAAAGAGAAATTAGAGC
Found at i:51676860 original size:44 final size:44
Alignment explanation
Indices: 51676802--51677432 Score: 311
Period size: 44 Copynumber: 13.7 Consensus size: 44
51676792 AAACAATAGT
* * *
51676802 GGAGCAGATCGAAGCCAGAAATCTTATCTCCTTGAGATTACAGC
1 GGAGCAGATTGAAGCTAGAAATCTTATCTCCCTGAGATTACAGC
* * *
51676846 GGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGT
1 GGAGCAGATTGAAGCTAGAAATCTTATCTCCCTGAGATTACAGC
* ** * *
51676890 GGAGCGGATT-AAAATA-AAGGATCTTATCTCTCTGA-AGTTACAGTA
1 GGAGCAGATTGAAGCTAGAA--ATCTTATCTCCCTGAGA-TTACAG-C
*
51676935 GAGTAAATCGCATCAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGC
1 G-G---A--G---CAGATTGAAGCTAGAAATCTTATCTCCCTGAGATTACAGC
* * * * *
51676988 GGAGCAGATTGAAGTTAGTAATCCTATCGCCCTGAGATTACAGT
1 GGAGCAGATTGAAGCTAGAAATCTTATCTCCCTGAGATTACAGC
* ** * * *
51677032 GGAGCGGATT-AAAATA-AAGGATCTTATCTCTCT-AAAGTTACAGTAGA
1 GGAGCAGATTGAAGCTAGAA--ATCTTATCTCCCTGAGA-TTAC---AGC
*
51677079 GTAGATTGCATCAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGC
1 G--GA--G---CAGATTGAAGCTAGAAATCTTATCTCCCTGAGATTACAGC
* * * *
51677130 GGAGTAGATTGAAGCTAGTAATCTTATCTCCCTAAGATTACAGT
1 GGAGCAGATTGAAGCTAGAAATCTTATCTCCCTGAGATTACAGC
** * *
51677174 GGAGCAGATT-AAAATA-AAGGATCTTATCTCTCTGA-AGTTACAGTAGA
1 GGAGCAGATTGAAGCTAGAA--ATCTTATCTCCCTGAGA-TTAC---AGC
*
51677221 GTAGATTGCATCAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGC
1 G--GA--G---CAGATTGAAGCTAGAAATCTTATCTCCCTGAGATTACAGC
* * *
51677272 GGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGT
1 GGAGCAGATTGAAGCTAGAAATCTTATCTCCCTGAGATTACAGC
* ** * *
51677316 GGAGCGGATT-AAAATA-AAGGATCTTATCTCTCTGA-AGTTACAGT
1 GGAGCAGATTGAAGCTAGAA--ATCTTATCTCCCTGAGA-TTACAGC
* * * * * * * *
51677360 AGAGTAAATCGCA-TTAG--GTCTTATCTCCCTGAGATTACAAC
1 GGAGCAGATTGAAGCTAGAAATCTTATCTCCCTGAGATTACAGC
** *
51677401 GGAGCAGATTGAAGCTACCAATCCTATCTCCC
1 GGAGCAGATTGAAGCTAGAAATCTTATCTCCC
51677433 CGACGTTACG
Statistics
Matches: 442, Mismatches: 88, Indels: 114
0.69 0.14 0.18
Matches are distributed among these distances:
41 26 0.06
42 7 0.02
43 21 0.05
44 266 0.60
45 2 0.00
46 1 0.00
47 9 0.02
49 10 0.02
51 9 0.02
52 1 0.00
53 1 0.00
54 70 0.16
55 13 0.03
56 6 0.01
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.27
Consensus pattern (44 bp):
GGAGCAGATTGAAGCTAGAAATCTTATCTCCCTGAGATTACAGC
Found at i:51677029 original size:98 final size:93
Alignment explanation
Indices: 51676802--51677315 Score: 271
Period size: 98 Copynumber: 5.5 Consensus size: 93
51676792 AAACAATAGT
* ** * *
51676802 GGAGCAGATCGAAGCCAGAAATCTTATCTCCTTGAGATTACAG-CGGA--G---CAGATTGAAGC
1 GGAGCAGATTGAAGTAAG-AATCTTATCTCCCTGAGATTACAGTAGGATCGCATCAGATTGAAGC
* * * *
51676861 TAGTAATCCTATCTCCCTGAGATTACAGT
65 CAGAAATCTTATCTCCCTGAGATTACAGC
* * * * *
51676890 GGAGCGGATTAAAATAAAGGATCTTATCTCTCTGA-AGTTACAGTAGAGTAAATCGCATCAGATT
1 GGAGCAGATTGAAGT-AAGAATCTTATCTCCCTGAGA-TTACAGTAG-G---ATCGCATCAGATT
51676954 GAAGCCAGAAATCTTATCTCCCTGAGATTACAGC
60 GAAGCCAGAAATCTTATCTCCCTGAGATTACAGC
* * * * * * * *
51676988 GGAGCAGATTGAAGTTAGTAATCCTATCGCCCTGAGATTACAGT-GGAGCGGATTAAAAT-AA--
1 GGAGCAGATTGAAGTAAG-AATCTTATCTCCCTGAGATTACAGTAGGATCGCATCAGATTGAAGC
* * * *
51677049 -AG-GATCTTATCTCTCT-AAAGTTACAGTAGA
65 CAGAAATCTTATCTCCCTGAGA-TTAC---AGC
** *
51677079 GTAGATTGCATCAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAG-CGGA--G--T-AGA
1 G--GA--G---CAGATTGAAGTAAG-AATCTTATCTCCCTGAGATTACAGTAGGATCGCATCAGA
* * * *
51677138 TTGAAGCTAGTAATCTTATCTCCCTAAGATTACAGT
58 TTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGC
* * * * *
51677174 GGAGCAGATTAAAATAAAGGATCTTATCTCTCTGA-AGTTACAGTAGAGTAGATTGCATCAGATT
1 GGAGCAGATTGAAGT-AAGAATCTTATCTCCCTGAGA-TTACAGT--AG--GATCGCATCAGATT
51677238 GAAGCCAGAAATCTTATCTCCCTGAGATTACAGC
60 GAAGCCAGAAATCTTATCTCCCTGAGATTACAGC
*
51677272 GGAGCAGATTGAAGCT-AGTAATCCTATCTCCCTGAGATTACAGT
1 GGAGCAGATTGAAG-TAAG-AATCTTATCTCCCTGAGATTACAGT
51677316 GGAGCGGATT
Statistics
Matches: 321, Mismatches: 58, Indels: 84
0.69 0.13 0.18
Matches are distributed among these distances:
87 4 0.01
88 73 0.23
89 7 0.02
90 1 0.00
91 5 0.02
92 2 0.01
93 18 0.06
94 3 0.01
95 6 0.02
96 2 0.01
97 8 0.02
98 187 0.58
99 5 0.02
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.27
Consensus pattern (93 bp):
GGAGCAGATTGAAGTAAGAATCTTATCTCCCTGAGATTACAGTAGGATCGCATCAGATTGAAGCC
AGAAATCTTATCTCCCTGAGATTACAGC
Found at i:51677062 original size:142 final size:142
Alignment explanation
Indices: 51676806--51677432 Score: 1019
Period size: 142 Copynumber: 4.5 Consensus size: 142
51676796 AATAGTGGAG
* *
51676806 CAGATCGAAGCCAGAAATCTTATCTCCTTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCT
1 CAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCT
51676871 ATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAG
66 ATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAG
51676936 AGTAAATCGCAT
131 AGTAAATCGCAT
*
51676948 CAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGTTAGTAATCCT
1 CAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCT
* *
51677013 ATCGCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTAAAGTTACAGTAG
66 ATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAG
* *
51677078 AGTAGATTGCAT
131 AGTAAATCGCAT
* *
51677090 CAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAGTAGATTGAAGCTAGTAATCTT
1 CAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCT
* *
51677155 ATCTCCCTAAGATTACAGTGGAGCAGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAG
66 ATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAG
* *
51677220 AGTAGATTGCAT
131 AGTAAATCGCAT
51677232 CAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCT
1 CAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCT
51677297 ATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAG
66 ATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAG
51677362 AGTAAATCG---
131 AGTAAATCGCAT
* **
51677371 C--ATT--AG---G---TCTTATCTCCCTGAGATTACAACGGAGCAGATTGAAGCTACCAATCCT
1 CAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCT
51677426 ATCTCCC
66 ATCTCCC
51677433 CGACGTTACG
Statistics
Matches: 462, Mismatches: 23, Indels: 13
0.93 0.05 0.03
Matches are distributed among these distances:
129 52 0.11
132 1 0.00
135 2 0.00
137 3 0.01
139 1 0.00
142 403 0.87
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.27
Consensus pattern (142 bp):
CAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCT
ATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAG
AGTAAATCGCAT
Found at i:51682620 original size:12 final size:10
Alignment explanation
Indices: 51682595--51682634 Score: 53
Period size: 10 Copynumber: 3.8 Consensus size: 10
51682585 GAACATGATG
51682595 AATTTTAATT
1 AATTTTAATT
51682605 AATTTTATAGTT
1 AATTTTA-A-TT
*
51682617 AATTTTGATT
1 AATTTTAATT
51682627 AATTTTAA
1 AATTTTAA
51682635 CTATTTTCGA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
10 16 0.62
11 2 0.08
12 8 0.31
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (10 bp):
AATTTTAATT
Found at i:51684944 original size:8 final size:8
Alignment explanation
Indices: 51684931--51685003 Score: 71
Period size: 8 Copynumber: 9.2 Consensus size: 8
51684921 TGGTAAGAAA
51684931 ATATTATT
1 ATATTATT
51684939 ATATTATT
1 ATATTATT
51684947 -TATT-TT
1 ATATTATT
*
51684953 A-ATTAAT
1 ATATTATT
51684960 ATAATTATT
1 AT-ATTATT
* *
51684969 ATGTTGTT
1 ATATTATT
51684977 AATATTATT
1 -ATATTATT
51684986 ATATTATT
1 ATATTATT
*
51684994 ATATTTTT
1 ATATTATT
51685002 AT
1 AT
51685004 GTTTATATGA
Statistics
Matches: 53, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
6 5 0.09
7 6 0.11
8 29 0.55
9 13 0.25
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.62
Consensus pattern (8 bp):
ATATTATT
Found at i:51686208 original size:23 final size:24
Alignment explanation
Indices: 51686178--51686224 Score: 78
Period size: 25 Copynumber: 2.0 Consensus size: 24
51686168 AACTCTTCTA
51686178 TTCAA-TTTTTTTTACTTTCCCTT
1 TTCAATTTTTTTTTACTTTCCCTT
51686201 TTCAATTTTTTTTTTACTTTCCCT
1 TTCAA-TTTTTTTTTACTTTCCCT
51686225 CCCTTTTTAC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 5 0.23
25 17 0.77
ACGTcount: A:0.13, C:0.21, G:0.00, T:0.66
Consensus pattern (24 bp):
TTCAATTTTTTTTTACTTTCCCTT
Found at i:51686479 original size:24 final size:25
Alignment explanation
Indices: 51686432--51686479 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
51686422 TTTGTACAAT
* **
51686432 TATTTTTAAAAATTTTATAGAAAAA
1 TATTTTAAAAAATTACATAGAAAAA
51686457 TATTTTAAAAAATTACATA-AAAA
1 TATTTTAAAAAATTACATAGAAAA
51686480 TAAAAAAACA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 4 0.20
25 16 0.80
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (25 bp):
TATTTTAAAAAATTACATAGAAAAA
Found at i:51694791 original size:18 final size:18
Alignment explanation
Indices: 51694768--51694803 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
51694758 GAAACTCTAT
51694768 ATCCTT-TAGGGATTTTAA
1 ATCCTTCTA-GGATTTTAA
51694786 ATCCTTCTAGGATTTTAA
1 ATCCTTCTAGGATTTTAA
51694804 TATAAATTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 15 0.88
19 2 0.12
ACGTcount: A:0.28, C:0.14, G:0.14, T:0.44
Consensus pattern (18 bp):
ATCCTTCTAGGATTTTAA
Found at i:51697584 original size:6 final size:6
Alignment explanation
Indices: 51697569--51697602 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
51697559 GTTAAGGGTT
51697569 TTTTTC -TTTTC TTTTTC TTTTTC TTTTTC TTTTT
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTT
51697603 TTGTGAAACT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 5 0.19
6 22 0.81
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTTC
Found at i:51697681 original size:7 final size:7
Alignment explanation
Indices: 51697669--51697693 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
51697659 ACTATTTGCC
51697669 AAGCTTT
1 AAGCTTT
51697676 AAGCTTT
1 AAGCTTT
51697683 AAGCTTT
1 AAGCTTT
51697690 AAGC
1 AAGC
51697694 ATGGGTGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (7 bp):
AAGCTTT
Found at i:51702385 original size:12 final size:11
Alignment explanation
Indices: 51702361--51702395 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
51702351 GACAAAAATA
*
51702361 TCTTCTTTTTT
1 TCTTTTTTTTT
51702372 TCTTTTTCTTTT
1 TCTTTTT-TTTT
51702384 TCTTTTTTTTT
1 TCTTTTTTTTT
51702395 T
1 T
51702396 TTGCGGAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 11 0.50
12 11 0.50
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (11 bp):
TCTTTTTTTTT
Found at i:51702396 original size:12 final size:12
Alignment explanation
Indices: 51702366--51702396 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
51702356 AAATATCTTC
51702366 TTTTTTTCTTTT
1 TTTTTTTCTTTT
*
51702378 TCTTTTTCTTTT
1 TTTTTTTCTTTT
51702390 TTTTTTT
1 TTTTTTT
51702397 TGCGGAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (12 bp):
TTTTTTTCTTTT
Found at i:51702964 original size:85 final size:85
Alignment explanation
Indices: 51702844--51703012 Score: 250
Period size: 85 Copynumber: 2.0 Consensus size: 85
51702834 ACGTCGCTAA
* *
51702844 CTTTTGCGGCGCTTACAGAAAAAAACGCCGTTAAAGAACATGTTCTTTAGCGGCGCTAAGAAAAT
1 CTTTAGCGGCGCTTA-AGAAAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTAAGAAAA-
51702909 AAACGCCGCTAAAGAACATGTT
64 AAACGCCGCTAAAGAACATGTT
* * * * *
51702931 CTTTAGCGGCGCTT-AGGAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGGGCTTAGGAAAAA
1 CTTTAGCGGCGCTTAAGAAAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTAAGAAAAAA
51702995 ACGCCGCTAAAGAACATG
66 ACGCCGCTAAAGAACATG
51703013 GGAAGAAAAT
Statistics
Matches: 75, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
84 20 0.27
85 42 0.56
87 13 0.17
ACGTcount: A:0.34, C:0.21, G:0.23, T:0.22
Consensus pattern (85 bp):
CTTTAGCGGCGCTTAAGAAAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTAAGAAAAAA
ACGCCGCTAAAGAACATGTT
Found at i:51702971 original size:42 final size:42
Alignment explanation
Indices: 51702844--51703012 Score: 248
Period size: 42 Copynumber: 4.0 Consensus size: 42
51702834 ACGTCGCTAA
* *
51702844 CTTTTGCGGCGCTTACAGAAAAAAACGCCGTTAAAGAACATGTT
1 CTTTAGCGGCGCTT--AGAAAAAAACGCCGCTAAAGAACATGTT
*
51702888 CTTTAGCGGCGCTAAGAAAATAAACGCCGCTAAAGAACATGTT
1 CTTTAGCGGCGCTTAGAAAA-AAACGCCGCTAAAGAACATGTT
* *
51702931 CTTTAGCGGCGCTTAGGAAAAAACGCCGCTAAAGATCATGTT
1 CTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGAACATGTT
* *
51702973 CTTTAGCGGGGCTTAGGAAAAAACGCCGCTAAAGAACATG
1 CTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGAACATG
51703013 GGAAGAAAAT
Statistics
Matches: 116, Mismatches: 8, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
42 65 0.56
43 39 0.34
44 12 0.10
ACGTcount: A:0.34, C:0.21, G:0.23, T:0.22
Consensus pattern (42 bp):
CTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGAACATGTT
Found at i:51703081 original size:42 final size:42
Alignment explanation
Indices: 51703034--51703176 Score: 200
Period size: 42 Copynumber: 3.4 Consensus size: 42
51703024 TTGCGAACGA
*
51703034 TCATGTTCTTTAGCTGCGCTTGGGAAAAAACGCCGCT-AAAG
1 TCATGTTCTTTAGCGGCGCTTGGGAAAAAACGCCGCTAAAAG
*
51703075 TTCATGTTCTTTAGCGGCGCTTGGGAAAAAACGCCACTAAAAG
1 -TCATGTTCTTTAGCGGCGCTTGGGAAAAAACGCCGCTAAAAG
* * **
51703118 TAATGTTCTATAGCGGCGCTTGGTCAAAAACGCCGCTAAAAG
1 TCATGTTCTTTAGCGGCGCTTGGGAAAAAACGCCGCTAAAAG
51703160 T-AGTGTTCTTTAGCGGC
1 TCA-TGTTCTTTAGCGGC
51703177 TCTTATTTCA
Statistics
Matches: 91, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
41 1 0.01
42 86 0.95
43 4 0.04
ACGTcount: A:0.27, C:0.21, G:0.24, T:0.27
Consensus pattern (42 bp):
TCATGTTCTTTAGCGGCGCTTGGGAAAAAACGCCGCTAAAAG
Found at i:51703657 original size:21 final size:21
Alignment explanation
Indices: 51703633--51703694 Score: 70
Period size: 21 Copynumber: 3.0 Consensus size: 21
51703623 CTATCGCTGG
*
51703633 TTCTCTCGCTGCGGCCTCTGC
1 TTCTCTCGCTGCAGCCTCTGC
* *
51703654 TTCTCTCGCTGTAGCCTCTTC
1 TTCTCTCGCTGCAGCCTCTGC
* * *
51703675 TTCCCTCACTGCTGCCTCTG
1 TTCTCTCGCTGCAGCCTCTG
51703695 TTTTAAGTTG
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.03, C:0.42, G:0.18, T:0.37
Consensus pattern (21 bp):
TTCTCTCGCTGCAGCCTCTGC
Found at i:51704832 original size:15 final size:15
Alignment explanation
Indices: 51704812--51704842 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
51704802 TTGGTTTTTG
*
51704812 TTGCTATCGTGCATT
1 TTGCTATCGGGCATT
51704827 TTGCTATCGGGCATT
1 TTGCTATCGGGCATT
51704842 T
1 T
51704843 GACGCCATGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.19, G:0.23, T:0.45
Consensus pattern (15 bp):
TTGCTATCGGGCATT
Found at i:51706102 original size:9 final size:9
Alignment explanation
Indices: 51706076--51706283 Score: 267
Period size: 9 Copynumber: 23.3 Consensus size: 9
51706066 AGTAAGGAAG
51706076 GTTATGT-A
1 GTTATGTAA
*
51706084 -TTATGCAA
1 GTTATGTAA
51706092 GTTATGTAA
1 GTTATGTAA
51706101 GTTATGTAA
1 GTTATGTAA
51706110 GTTATGTAA
1 GTTATGTAA
*
51706119 TTTATGTAA
1 GTTATGTAA
*
51706128 GTTATATAA
1 GTTATGTAA
51706137 GTTATGTAA
1 GTTATGTAA
*
51706146 GTTATTTAA
1 GTTATGTAA
*
51706155 TTTATGTAA
1 GTTATGTAA
51706164 GTTATGTAA
1 GTTATGTAA
*
51706173 GATATGTAA
1 GTTATGTAA
51706182 GTTATGTAA
1 GTTATGTAA
*
51706191 GTTATTTAA
1 GTTATGTAA
51706200 GTTATGTAA
1 GTTATGTAA
*
51706209 GTTAAGTAA
1 GTTATGTAA
*
51706218 GTTATTTAA
1 GTTATGTAA
*
51706227 TTTATGTAA
1 GTTATGTAA
*
51706236 GTTATATAA
1 GTTATGTAA
*
51706245 TTTATGTAA
1 GTTATGTAA
51706254 GTTATGTAA
1 GTTATGTAA
* *
51706263 TTTATATAA
1 GTTATGTAA
*
51706272 GTTATGCAA
1 GTTATGTAA
51706281 GTT
1 GTT
51706284 TATATATAAG
Statistics
Matches: 169, Mismatches: 29, Indels: 3
0.84 0.14 0.01
Matches are distributed among these distances:
7 5 0.03
8 1 0.01
9 163 0.96
ACGTcount: A:0.35, C:0.01, G:0.17, T:0.47
Consensus pattern (9 bp):
GTTATGTAA
Found at i:51706333 original size:16 final size:17
Alignment explanation
Indices: 51706255--51706342 Score: 63
Period size: 18 Copynumber: 5.1 Consensus size: 17
51706245 TTTATGTAAG
51706255 TTATGTAA-TTTATATAA
1 TTATGTAAGTTTATAT-A
*
51706272 GTTATGCAAGTTTATATA
1 -TTATGTAAGTTTATATA
* * * * *
51706290 TAAGTTTATGTATTGTATG
1 TTA-TGTAAGT-TTATATA
*
51706309 TTATTTAAG-TTATATA
1 TTATGTAAGTTTATATA
51706325 TTATGTAAGTTTATATA
1 TTATGTAAGTTTATATA
51706342 T
1 T
51706343 AAGTTATGAT
Statistics
Matches: 54, Mismatches: 12, Indels: 9
0.72 0.16 0.12
Matches are distributed among these distances:
16 13 0.24
17 10 0.19
18 17 0.31
19 14 0.26
ACGTcount: A:0.34, C:0.01, G:0.12, T:0.52
Consensus pattern (17 bp):
TTATGTAAGTTTATATA
Found at i:51706355 original size:26 final size:26
Alignment explanation
Indices: 51706274--51706355 Score: 73
Period size: 26 Copynumber: 3.2 Consensus size: 26
51706264 TTATATAAGT
*
51706274 TATGCAAGTTTATATATAAGTTTATG-
1 TATGTAAGTTTATATATAAG-TTATGA
* *
51706300 TATTGTATG-TTAT-T-TAAGTTATATA
1 TA-TGTAAGTTTATATATAAGTTAT-GA
51706325 TTATGTAAGTTTATATATAAGTTATGA
1 -TATGTAAGTTTATATATAAGTTATGA
51706352 TATG
1 TATG
51706356 ATTGATAAAT
Statistics
Matches: 44, Mismatches: 5, Indels: 14
0.70 0.08 0.22
Matches are distributed among these distances:
23 4 0.09
24 4 0.09
25 6 0.14
26 16 0.36
27 6 0.14
28 8 0.18
ACGTcount: A:0.34, C:0.01, G:0.15, T:0.50
Consensus pattern (26 bp):
TATGTAAGTTTATATATAAGTTATGA
Found at i:51706469 original size:9 final size:9
Alignment explanation
Indices: 51706455--51706514 Score: 75
Period size: 9 Copynumber: 6.7 Consensus size: 9
51706445 TAAATAATTA
51706455 TAAGTTATG
1 TAAGTTATG
*
51706464 TAAGTTATA
1 TAAGTTATG
*
51706473 TAATTTATG
1 TAAGTTATG
51706482 TAAGTTATG
1 TAAGTTATG
* *
51706491 TAATTTATA
1 TAAGTTATG
51706500 TAAGTTATG
1 TAAGTTATG
*
51706509 CAAGTT
1 TAAGTT
51706515 TATATATAAG
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
9 42 1.00
ACGTcount: A:0.37, C:0.02, G:0.15, T:0.47
Consensus pattern (9 bp):
TAAGTTATG
Found at i:51706480 original size:18 final size:18
Alignment explanation
Indices: 51706453--51706507 Score: 83
Period size: 18 Copynumber: 3.1 Consensus size: 18
51706443 TATAAATAAT
*
51706453 TATAAGTTATGTAAGTTA
1 TATAATTTATGTAAGTTA
51706471 TATAATTTATGTAAGTTA
1 TATAATTTATGTAAGTTA
* *
51706489 TGTAATTTATATAAGTTA
1 TATAATTTATGTAAGTTA
51706507 T
1 T
51706508 GCAAGTTTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.38, C:0.00, G:0.13, T:0.49
Consensus pattern (18 bp):
TATAATTTATGTAAGTTA
Found at i:51706483 original size:231 final size:230
Alignment explanation
Indices: 51706228--51706727 Score: 937
Period size: 231 Copynumber: 2.2 Consensus size: 230
51706218 GTTATTTAAT
51706228 TTATGTAAGTTATATAATTTATGTAAGTTATGTAATTTATATAAGTTATGCAAGTTTATATATAA
1 TTATGTAAGTTATATAATTTATGTAAGTTATGTAATTTATATAAGTTATGCAAGTTTATATATAA
51706293 GTTTATGTATTGTATGTTATTTAAGTTATATATTATGTAAGTTTATATATAAGTTATGATATGAT
66 GTTTATGTATTGTATGTTATTTAAGTTATATATTATGTAAGTTTATATATAAGTTATGATATGAT
* *
51706358 TGATAAATTTGAGTTATGTAAGTTATGCTATGATTGATAAGTTTTGAAAAATATATAGATTTTAA
131 TGATAAATTTGAGTTATGTAAGTTATGCTATGATTGATAAATTTTGAAAAAAATATAGATTTTAA
51706423 AAATATATATTAAAAATGTATATAAATAATTATAAG
196 AAA-ATATATTAAAAATGTATATAAATAATTATAAG
51706459 TTATGTAAGTTATATAATTTATGTAAGTTATGTAATTTATATAAGTTATGCAAGTTTATATATAA
1 TTATGTAAGTTATATAATTTATGTAAGTTATGTAATTTATATAAGTTATGCAAGTTTATATATAA
*
51706524 GTTTATGTATTGTATGTTATTTAAGTTATGTATTATGTAAGTTTATATATAAGTTATGATATGAT
66 GTTTATGTATTGTATGTTATTTAAGTTATATATTATGTAAGTTTATATATAAGTTATGATATGAT
51706589 TGATAAATTTGAGTTATGTAAGTTATGCTATGATTGATAAATTTTGAAAAAAATATAGATTTTAA
131 TGATAAATTTGAGTTATGTAAGTTATGCTATGATTGATAAATTTTGAAAAAAATATAGATTTTAA
*
51706654 AAAATATATTAAAAATGTATATAAATATTTATAAG
196 AAAATATATTAAAAATGTATATAAATAATTATAAG
* *
51706689 TTAGGTAAGTTATATAATTTATGTAAGTTATATAATTTA
1 TTATGTAAGTTATATAATTTATGTAAGTTATGTAATTTA
51706728 AAAATTGTTT
Statistics
Matches: 263, Mismatches: 6, Indels: 1
0.97 0.02 0.00
Matches are distributed among these distances:
230 68 0.26
231 195 0.74
ACGTcount: A:0.40, C:0.01, G:0.13, T:0.46
Consensus pattern (230 bp):
TTATGTAAGTTATATAATTTATGTAAGTTATGTAATTTATATAAGTTATGCAAGTTTATATATAA
GTTTATGTATTGTATGTTATTTAAGTTATATATTATGTAAGTTTATATATAAGTTATGATATGAT
TGATAAATTTGAGTTATGTAAGTTATGCTATGATTGATAAATTTTGAAAAAAATATAGATTTTAA
AAAATATATTAAAAATGTATATAAATAATTATAAG
Found at i:51706488 original size:27 final size:27
Alignment explanation
Indices: 51706455--51706514 Score: 93
Period size: 27 Copynumber: 2.2 Consensus size: 27
51706445 TAAATAATTA
*
51706455 TAAGTTATGTAAGTTATATAATTTATG
1 TAAGTTATGTAAGTTATATAAGTTATG
*
51706482 TAAGTTATGTAATTTATATAAGTTATG
1 TAAGTTATGTAAGTTATATAAGTTATG
*
51706509 CAAGTT
1 TAAGTT
51706515 TATATATAAG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.37, C:0.02, G:0.15, T:0.47
Consensus pattern (27 bp):
TAAGTTATGTAAGTTATATAAGTTATG
Found at i:51706714 original size:18 final size:18
Alignment explanation
Indices: 51706683--51706727 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
51706673 TATAAATATT
*
51706683 TATAAGTTAGGTAAGTTA
1 TATAATTTAGGTAAGTTA
*
51706701 TATAATTTATGTAAGTTA
1 TATAATTTAGGTAAGTTA
51706719 TATAATTTA
1 TATAATTTA
51706728 AAAATTGTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.40, C:0.00, G:0.13, T:0.47
Consensus pattern (18 bp):
TATAATTTAGGTAAGTTA
Found at i:51708851 original size:252 final size:250
Alignment explanation
Indices: 51708285--51708799 Score: 651
Period size: 251 Copynumber: 2.0 Consensus size: 250
51708275 ACTGTTCCTC
* * * * * *
51708285 AACCGAAACGGCGACGTTCTAAACATTTTGTAATACACATTTGTGGCGTTTTCAT-ACTAAACGC
1 AACC-AAACGACGACGTTCTGAACAATTTGTAATACACATTTGCGGCATTTCCATAAC-AAACGC
* * * *
51708349 CGCTAAAGCTTACAGTTGCGGCGTTTTAAATACAAACGCCACTAACGAGTTCAAATCATTTAAGA
64 CGCTAAAGATCACAGTTGCGGCGTTTTAAATAAAAACGCCAATAACGAGTTCAAATCATTTAAGA
** * * *
51708414 AAACGACGCTGTTTTTGTTCACAAAAACATATATAGATTTGCAGCGTTTCTATAAAAACGCCACT
129 AAACGACGCCATTTTCGTACACAAAAACATATATAGATTTGCAGCGTTTCAATAAAAACGCCACT
* *
51708479 ACTGTATACCTTCTGTGGCGTTTTTCATACAAACGCCACTAAAATTCAAATTCATGT
194 ACTGCATACCTTCAGTGGCGTTTTTCATACAAACGCCACTAAAATTCAAATTCATGT
* ** * * *
51708536 AACGAAACGGTGACGTTCTGAACATTTTGTAATGCACATTTGTGGCATTTCCATAACAAACGCCG
1 AACCAAACGACGACGTTCTGAACAATTTGTAATACACATTTGCGGCATTTCCATAACAAACGCCG
*
51708601 CTAAAGATCACAGTTTGCGGCGTTTTAAATAAAAACGCCAATAAGGAGTTCAAATCATTTAAGAA
66 CTAAAGATCACAG-TTGCGGCGTTTTAAATAAAAACGCCAATAACGAGTTCAAATCATTTAAGAA
* * * * *
51708666 AACGACGCCATTTTCGTACAGACAAACATTTATGGATTTGCGGCGTTTCAATACAAAACGCCACT
130 AACGACGCCATTTTCGTACACAAAAACATATATAGATTTGCAGCGTTTCAATA-AAAACGCCACT
* *
51708731 A-TAGCATACCTTCAGTGGCGTTTTTACGA-A-AAACGCCACTAAAATTCAAATTCCTTT
194 ACT-GCATACCTTCAGTGGCGTTTTT-C-ATACAAACGCCACTAAAATTCAAATTCATGT
*
51708788 AGCCAAACGACG
1 AACCAAACGACG
51708800 CTGTTTTACG
Statistics
Matches: 229, Mismatches: 29, Indels: 11
0.85 0.11 0.04
Matches are distributed among these distances:
250 64 0.28
251 97 0.42
252 65 0.28
253 2 0.01
254 1 0.00
ACGTcount: A:0.34, C:0.22, G:0.16, T:0.28
Consensus pattern (250 bp):
AACCAAACGACGACGTTCTGAACAATTTGTAATACACATTTGCGGCATTTCCATAACAAACGCCG
CTAAAGATCACAGTTGCGGCGTTTTAAATAAAAACGCCAATAACGAGTTCAAATCATTTAAGAAA
ACGACGCCATTTTCGTACACAAAAACATATATAGATTTGCAGCGTTTCAATAAAAACGCCACTAC
TGCATACCTTCAGTGGCGTTTTTCATACAAACGCCACTAAAATTCAAATTCATGT
Found at i:51725041 original size:3 final size:3
Alignment explanation
Indices: 51725033--51725065 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
51725023 TAGCCAAACT
51725033 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
51725066 CCTTAACAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:51727124 original size:12 final size:12
Alignment explanation
Indices: 51727107--51727131 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
51727097 TGGCCTTGAC
51727107 GAGGTTGAGATT
1 GAGGTTGAGATT
51727119 GAGGTTGAGATT
1 GAGGTTGAGATT
51727131 G
1 G
51727132 GTCCTCATGA
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:0.24, C:0.00, G:0.44, T:0.32
Consensus pattern (12 bp):
GAGGTTGAGATT
Found at i:51731920 original size:24 final size:24
Alignment explanation
Indices: 51731888--51731950 Score: 117
Period size: 24 Copynumber: 2.6 Consensus size: 24
51731878 ACTGCGAAGT
51731888 ACGCCAATAAAGCGGTTATAGTCG
1 ACGCCAATAAAGCGGTTATAGTCG
51731912 ACGCCAATAAAGCGGTTATAGTCG
1 ACGCCAATAAAGCGGTTATAGTCG
*
51731936 ACGCCAAAAAAGCGG
1 ACGCCAATAAAGCGG
51731951 CAGTCTGATT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.37, C:0.22, G:0.25, T:0.16
Consensus pattern (24 bp):
ACGCCAATAAAGCGGTTATAGTCG
Found at i:51735115 original size:20 final size:20
Alignment explanation
Indices: 51735073--51735115 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
51735063 ACCATTCATC
* *
51735073 AAGGTTATTTTCTTGATTTA
1 AAGGTTATTTTCTTGAATAA
* *
51735093 AAGGTTTTTTTTTTGAATAA
1 AAGGTTATTTTCTTGAATAA
51735113 AAG
1 AAG
51735116 CATTATTTGA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.30, C:0.02, G:0.16, T:0.51
Consensus pattern (20 bp):
AAGGTTATTTTCTTGAATAA
Found at i:51740796 original size:2 final size:2
Alignment explanation
Indices: 51740789--51740832 Score: 79
Period size: 2 Copynumber: 21.5 Consensus size: 2
51740779 CTCATATCTC
51740789 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AGT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT
51740832 A
1 A
51740833 ATTAAAGTTA
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 39 0.95
3 2 0.05
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:51740952 original size:2 final size:2
Alignment explanation
Indices: 51740945--51740984 Score: 71
Period size: 2 Copynumber: 19.5 Consensus size: 2
51740935 NNNNNNNNNN
51740945 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT ACT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT A
51740985 GCAATTTAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 35 0.95
3 2 0.05
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:51744051 original size:40 final size:40
Alignment explanation
Indices: 51744007--51744133 Score: 143
Period size: 40 Copynumber: 3.2 Consensus size: 40
51743997 AACACACCAG
*
51744007 TTTGACACCTAGTGCCTCATCGGATAATTCGAAGTAATAA
1 TTTGACACCTAGTGCCTCATCGGATAATCCGAAGTAATAA
* * *
51744047 TTTGACACCCAGTGCCTCATCGGCTAAACCGAAGT-A-AA
1 TTTGACACCTAGTGCCTCATCGGATAATCCGAAGTAATAA
* ** *
51744085 -TTGGCACCTAGTGCCTCATCAAATTAATCCGAAGTAGTAA
1 TTTGACACCTAGTGCCTCATCGGA-TAATCCGAAGTAATAA
*
51744125 ATTGACACC
1 TTTGACACC
51744134 CAATGTCTCA
Statistics
Matches: 71, Mismatches: 12, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
37 18 0.25
38 12 0.17
39 1 0.01
40 33 0.46
41 7 0.10
ACGTcount: A:0.32, C:0.24, G:0.17, T:0.26
Consensus pattern (40 bp):
TTTGACACCTAGTGCCTCATCGGATAATCCGAAGTAATAA
Found at i:51745038 original size:15 final size:18
Alignment explanation
Indices: 51745001--51745039 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
51744991 TAGCCTTGCG
51745001 TTTTTCTTTCTCTTTCTCT
1 TTTTTCTTT-TCTTTCTCT
51745020 TTTTTCTTTT-TTTC-CT
1 TTTTTCTTTTCTTTCTCT
51745036 TTTT
1 TTTT
51745040 GTTTTCGTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 6 0.30
17 4 0.20
18 1 0.05
19 9 0.45
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (18 bp):
TTTTTCTTTTCTTTCTCT
Found at i:51747771 original size:19 final size:19
Alignment explanation
Indices: 51747736--51747790 Score: 51
Period size: 19 Copynumber: 3.0 Consensus size: 19
51747726 CTTTACTTTA
* *
51747736 TATT-ATAATAATATAATT
1 TATTAATAATCATTTAATT
51747754 TATTAATAATCATTTAATT
1 TATTAATAATCATTTAATT
* * *
51747773 AATAAAT-ATCTTTTAATT
1 TATTAATAATCATTTAATT
51747791 ATAACACAAG
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
18 14 0.45
19 17 0.55
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (19 bp):
TATTAATAATCATTTAATT
Found at i:51747881 original size:20 final size:21
Alignment explanation
Indices: 51747856--51747897 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
51747846 ATTTGGCACC
* *
51747856 ATTTAATTTATTTAT-TTTAT
1 ATTTAATTAATTAATATTTAT
51747876 ATTTAATTAATTAATATTTAT
1 ATTTAATTAATTAATATTTAT
51747897 A
1 A
51747898 AATATCTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (21 bp):
ATTTAATTAATTAATATTTAT
Found at i:51756440 original size:22 final size:22
Alignment explanation
Indices: 51756412--51756460 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
51756402 ATAATAATGT
51756412 TGTCCGAAAGATGGTTAAATAC
1 TGTCCGAAAGATGGTTAAATAC
* * * *
51756434 TGTCCGAATGTTGTTTAAATGC
1 TGTCCGAAAGATGGTTAAATAC
51756456 TGTCC
1 TGTCC
51756461 ATTTTTTGAG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.27, C:0.16, G:0.22, T:0.35
Consensus pattern (22 bp):
TGTCCGAAAGATGGTTAAATAC
Found at i:51756507 original size:70 final size:69
Alignment explanation
Indices: 51756361--51756508 Score: 163
Period size: 69 Copynumber: 2.1 Consensus size: 69
51756351 TGATGACAAG
* * * * *
51756361 ATGCTATCCTAATGTTGGTTAAATGCTGTCCATTTTTAAGCATAATAATGTTGTCCGAAAGATGG
1 ATGCTGTCCGAATGTTGGTTAAATGCTGTCCATTTTTAAGCATAATAATGCTATCCGAAAGATGC
51756426 TTAA
66 TTAA
* * * * * **
51756430 ATACTGTCCGAATGTTGTTTAAATGCTGTCCATTTTTTGAGCATACTAATGCTAT-CTAAATTTT
1 ATGCTGTCCGAATGTTGGTTAAATGCTGTCCA-TTTTTAAGCATAATAATGCTATCCGAAA-GAT
51756494 GCTTAA
64 GCTTAA
51756500 ATGCTGTCC
1 ATGCTGTCC
51756509 ATTTTTTAGC
Statistics
Matches: 64, Mismatches: 13, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
69 32 0.50
70 32 0.50
ACGTcount: A:0.28, C:0.16, G:0.17, T:0.40
Consensus pattern (69 bp):
ATGCTGTCCGAATGTTGGTTAAATGCTGTCCATTTTTAAGCATAATAATGCTATCCGAAAGATGC
TTAA
Found at i:51756568 original size:68 final size:68
Alignment explanation
Indices: 51756496--51756694 Score: 310
Period size: 69 Copynumber: 2.9 Consensus size: 68
51756486 TAAATTTTGC
* *
51756496 TTAAATGCTGTCCATTTTTTAGCATACTAATGATATCCGAATGTTGGTTAATGCTGTCCGAATGT
1 TTAAATGCTGTCCATTTTTTAGCATACTAATGCTGTCCGAATGTTGGTTAATGCTGTCCGAATGT
51756561 TGT
66 TGT
* * * *
51756564 TTAAATGCTGTCCATTTTTTAGCATACTAATGCTGCCCAAATGTTGGTTAAATGCTATTCGAATG
1 TTAAATGCTGTCCATTTTTTAGCATACTAATGCTGTCCGAATGTTGGTT-AATGCTGTCCGAATG
51756629 TTGT
65 TTGT
* *
51756633 TTAAATGCTGTCCATTTTTTAGCATACTAATGCTGTCCGAATGTT-GTTACTGTTGTCCGAAT
1 TTAAATGCTGTCCATTTTTTAGCATACTAATGCTGTCCGAATGTTGGTTAATGCTGTCCGAAT
51756695 TATTGTGAAT
Statistics
Matches: 118, Mismatches: 12, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
67 10 0.08
68 48 0.41
69 60 0.51
ACGTcount: A:0.25, C:0.16, G:0.18, T:0.41
Consensus pattern (68 bp):
TTAAATGCTGTCCATTTTTTAGCATACTAATGCTGTCCGAATGTTGGTTAATGCTGTCCGAATGT
TGT
Found at i:51756573 original size:22 final size:22
Alignment explanation
Indices: 51756531--51756645 Score: 90
Period size: 22 Copynumber: 5.1 Consensus size: 22
51756521 ACTAATGATA
51756531 TCCGAATGTTGGTT-AATGCTG
1 TCCGAATGTTGGTTAAATGCTG
*
51756552 TCCGAATGTTGTTTAAATGCTG
1 TCCGAATGTTGGTTAAATGCTG
* * **
51756574 TCC-ATTTTTTAGCATACTAATGCTG
1 TCCGA-ATGTT-GGTTA--AATGCTG
* * *
51756599 CCCAAATGTTGGTTAAATGCTA
1 TCCGAATGTTGGTTAAATGCTG
* *
51756621 TTCGAATGTTGTTTAAATGCTG
1 TCCGAATGTTGGTTAAATGCTG
51756643 TCC
1 TCC
51756646 ATTTTTTAGC
Statistics
Matches: 71, Mismatches: 17, Indels: 11
0.72 0.17 0.11
Matches are distributed among these distances:
21 14 0.20
22 38 0.54
23 3 0.04
24 3 0.04
25 12 0.17
26 1 0.01
ACGTcount: A:0.23, C:0.17, G:0.20, T:0.40
Consensus pattern (22 bp):
TCCGAATGTTGGTTAAATGCTG
Found at i:51756583 original size:117 final size:116
Alignment explanation
Indices: 51756361--51756619 Score: 369
Period size: 117 Copynumber: 2.2 Consensus size: 116
51756351 TGATGACAAG
* * *
51756361 ATGCTATCCTAATGTTGGTTAAATGCTGTCCATTTTTAAGCATAATAATGTTGTCCGAAAGATGG
1 ATGCTATCCTAATGTTGCTTAAATGCTGTCCATTTTTAAGCATAATAATGATATCCGAAAGATGG
51756426 TTAAATACTGTCCGAATGTTGTTTAAATGCTGTCCATTTTTTGAGCATACTA
66 TTAAATACTGTCCGAATGTTGTTTAAATGCTGTCCATTTTTT-AGCATACTA
* * * * *
51756478 ATGCTAT-CTAAATTTTGCTTAAATGCTGTCCATTTTTTAGCATACTAATGATATCCGAATGTTG
1 ATGCTATCCT-AATGTTGCTTAAATGCTGTCCATTTTTAAGCATAATAATGATATCCGAAAGATG
*
51756542 GTT-AATGCTGTCCGAATGTTGTTTAAATGCTGTCCATTTTTTAGCATACTA
65 GTTAAATACTGTCCGAATGTTGTTTAAATGCTGTCCATTTTTTAGCATACTA
** * *
51756593 ATGCTGCCCAAATGTTGGTTAAATGCT
1 ATGCTATCCTAATGTTGCTTAAATGCT
51756620 ATTCGAATGT
Statistics
Matches: 126, Mismatches: 14, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
115 29 0.23
116 41 0.33
117 56 0.44
ACGTcount: A:0.27, C:0.15, G:0.17, T:0.40
Consensus pattern (116 bp):
ATGCTATCCTAATGTTGCTTAAATGCTGTCCATTTTTAAGCATAATAATGATATCCGAAAGATGG
TTAAATACTGTCCGAATGTTGTTTAAATGCTGTCCATTTTTTAGCATACTA
Found at i:51759971 original size:19 final size:19
Alignment explanation
Indices: 51759947--51760020 Score: 71
Period size: 19 Copynumber: 3.8 Consensus size: 19
51759937 CATTCTAGAA
*
51759947 TTATAAAAAACATAAAATT
1 TTATAAAAATCATAAAATT
*
51759966 TTATAAAAATTATTAGAAATT
1 TTATAAAAATCA-TA-AAATT
*
51759987 AATTA-AAAAATCATAAAACT
1 --TTATAAAAATCATAAAATT
51760007 TTATAAAAAT-ATAA
1 TTATAAAAATCATAA
51760021 TTTTGTTATG
Statistics
Matches: 46, Mismatches: 4, Indels: 11
0.75 0.07 0.18
Matches are distributed among these distances:
18 7 0.15
19 16 0.35
20 6 0.13
21 7 0.15
22 7 0.15
23 3 0.07
ACGTcount: A:0.61, C:0.04, G:0.01, T:0.34
Consensus pattern (19 bp):
TTATAAAAATCATAAAATT
Found at i:51760237 original size:14 final size:14
Alignment explanation
Indices: 51760212--51760246 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
51760202 ATTGCTTTCA
51760212 TATTTCTTTATTCTT
1 TATTT-TTTATTCTT
51760227 TATTTTTTATTCTT
1 TATTTTTTATTCTT
*
51760241 TGTTTT
1 TATTTT
51760247 ACCCATTCTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 14 0.74
15 5 0.26
ACGTcount: A:0.11, C:0.09, G:0.03, T:0.77
Consensus pattern (14 bp):
TATTTTTTATTCTT
Found at i:51764642 original size:12 final size:14
Alignment explanation
Indices: 51764612--51764643 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
51764602 CAAACAAACA
51764612 AAAAATTAGAATGT
1 AAAAATTAGAATGT
51764626 AAAAATTA-AAT-T
1 AAAAATTAGAATGT
51764638 AAAAAT
1 AAAAAT
51764644 AAAAATATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 7 0.39
13 3 0.17
14 8 0.44
ACGTcount: A:0.66, C:0.00, G:0.06, T:0.28
Consensus pattern (14 bp):
AAAAATTAGAATGT
Found at i:51765999 original size:20 final size:20
Alignment explanation
Indices: 51765974--51766013 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
51765964 AACATGTTAC
51765974 TTTTGACACTTATCAACAAT
1 TTTTGACACTTATCAACAAT
51765994 TTTTGACACTTATCAACAAT
1 TTTTGACACTTATCAACAAT
51766014 ACTTTTTCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.20, G:0.05, T:0.40
Consensus pattern (20 bp):
TTTTGACACTTATCAACAAT
Found at i:51770501 original size:30 final size:30
Alignment explanation
Indices: 51770467--51770529 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
51770457 ACTTATTTTA
51770467 TTGTTAATTTTGTTATTATTTTAAAGACAT
1 TTGTTAATTTTGTTATTATTTTAAAGACAT
* *
51770497 TTGTTAATTTTGTTATTATTTTATAGGCAT
1 TTGTTAATTTTGTTATTATTTTAAAGACAT
51770527 TTG
1 TTG
51770530 CTTGTTAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.25, C:0.03, G:0.13, T:0.59
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTATTTTAAAGACAT
Found at i:51770683 original size:12 final size:12
Alignment explanation
Indices: 51770651--51770685 Score: 54
Period size: 13 Copynumber: 2.9 Consensus size: 12
51770641 TATATATTTT
51770651 AAAATT-ATATA
1 AAAATTAATATA
51770662 AAAATATAATATA
1 AAAAT-TAATATA
51770675 AAAATTAATAT
1 AAAATTAATAT
51770686 GGGCGGGCCG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 5 0.23
12 7 0.32
13 10 0.45
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (12 bp):
AAAATTAATATA
Found at i:51770912 original size:3 final size:3
Alignment explanation
Indices: 51770904--51770947 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
51770894 ATAACGTGTT
51770904 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
51770948 GCAAAGAACA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:51771845 original size:9 final size:9
Alignment explanation
Indices: 51771823--51771893 Score: 54
Period size: 9 Copynumber: 7.6 Consensus size: 9
51771813 AATAAATTAT
51771823 TTTTTATAA
1 TTTTTATAA
* *
51771832 ATTTTATGA
1 TTTTTATAA
51771841 TTTTTAATTAA
1 TTTTT-A-TAA
51771852 TTTTTAATAA
1 TTTTT-ATAA
*
51771862 TTATTATAGA
1 TTTTTATA-A
* *
51771872 TTTTAATTA
1 TTTTTATAA
51771881 TTTTTA-AA
1 TTTTTATAA
51771889 TTTTT
1 TTTTT
51771894 TTTATACTTA
Statistics
Matches: 49, Mismatches: 10, Indels: 7
0.74 0.15 0.11
Matches are distributed among these distances:
8 6 0.12
9 20 0.41
10 14 0.29
11 9 0.18
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (9 bp):
TTTTTATAA
Found at i:51771863 original size:29 final size:30
Alignment explanation
Indices: 51771817--51771887 Score: 94
Period size: 30 Copynumber: 2.4 Consensus size: 30
51771807 GGTTTTAATA
*
51771817 AATTATTTTTTATAAATT-TTAT-GATTTTT
1 AATTATTTTTAATAAATTATTATAGA-TTTT
51771846 AATTAATTTTTAAT-AATTATTATAGATTTT
1 AATT-ATTTTTAATAAATTATTATAGATTTT
51771876 AATTATTTTTAA
1 AATTATTTTTAA
51771888 ATTTTTTTTA
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
29 16 0.42
30 20 0.53
31 2 0.05
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.61
Consensus pattern (30 bp):
AATTATTTTTAATAAATTATTATAGATTTT
Found at i:51772889 original size:21 final size:23
Alignment explanation
Indices: 51772855--51772898 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 23
51772845 ATTTCCAAAA
51772855 TTTCAAAATATTTAT-AAATTAT
1 TTTCAAAATATTTATAAAATTAT
51772877 TTTCAAAAT-TTTATAAAATTAT
1 TTTCAAAATATTTATAAAATTAT
51772899 AAAAATATCA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 5 0.24
22 16 0.76
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (23 bp):
TTTCAAAATATTTATAAAATTAT
Found at i:51773098 original size:47 final size:47
Alignment explanation
Indices: 51773029--51773120 Score: 166
Period size: 47 Copynumber: 2.0 Consensus size: 47
51773019 AGTTTATGAT
*
51773029 ACTAAAATATCTTTTCCTTTGAAATAGTTTTAAAATATATACGGTAA
1 ACTAAAATATCTTTTCCTTTGAAATAATTTTAAAATATATACGGTAA
*
51773076 ACTAAAATATCTTTTCCTTTGAAATAATTTTACAATATATACGGT
1 ACTAAAATATCTTTTCCTTTGAAATAATTTTAAAATATATACGGT
51773121 GTCAAATTTA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 43 1.00
ACGTcount: A:0.39, C:0.12, G:0.08, T:0.41
Consensus pattern (47 bp):
ACTAAAATATCTTTTCCTTTGAAATAATTTTAAAATATATACGGTAA
Found at i:51791024 original size:20 final size:20
Alignment explanation
Indices: 51790999--51791038 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
51790989 TTAATACTAC
51790999 AAAGCCTGAGTTTGGTTCAA
1 AAAGCCTGAGTTTGGTTCAA
51791019 AAAGCCTGAGTTTGGTTCAA
1 AAAGCCTGAGTTTGGTTCAA
51791039 TTTTTTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.30
Consensus pattern (20 bp):
AAAGCCTGAGTTTGGTTCAA
Found at i:51791833 original size:6 final size:6
Alignment explanation
Indices: 51791822--51791847 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
51791812 TAGTTGAGGC
51791822 ATGGCT ATGGCT ATGGCT ATGGCT AT
1 ATGGCT ATGGCT ATGGCT ATGGCT AT
51791848 ATATATATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.19, C:0.15, G:0.31, T:0.35
Consensus pattern (6 bp):
ATGGCT
Found at i:51797208 original size:10 final size:10
Alignment explanation
Indices: 51797195--51797231 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
51797185 ATGGATTAAA
*
51797195 ATTTATACAC
1 ATTTATATAC
51797205 ATTTATATAC
1 ATTTATATAC
*
51797215 ATTTACATAC
1 ATTTATATAC
51797225 ATTTATA
1 ATTTATA
51797232 AAGAATTGTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.41, C:0.14, G:0.00, T:0.46
Consensus pattern (10 bp):
ATTTATATAC
Found at i:51797474 original size:29 final size:29
Alignment explanation
Indices: 51797418--51797475 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
51797408 ACATCTACTA
* *
51797418 ACCAAAATTAAAAATTACAGTATTTTTTT
1 ACCAAAATTAAAAACTACAATATTTTTTT
* *
51797447 ACCAAATTTAAAAACTA-AATATTATTTT
1 ACCAAAATTAAAAACTACAATATTTTTTT
51797475 A
1 A
51797476 TCCTAATATT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
28 10 0.40
29 15 0.60
ACGTcount: A:0.48, C:0.10, G:0.02, T:0.40
Consensus pattern (29 bp):
ACCAAAATTAAAAACTACAATATTTTTTT
Found at i:51805634 original size:23 final size:23
Alignment explanation
Indices: 51805607--51805705 Score: 162
Period size: 23 Copynumber: 4.3 Consensus size: 23
51805597 AGTGTTATTG
*
51805607 ATCAGTGGTAGCTTCGGCTACGT
1 ATCAGTGGTAGCTTCGGCTACAT
*
51805630 TTCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
51805653 TTCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
51805676 AACAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
51805699 ATCAGTG
1 ATCAGTG
51805706 TTGCACTTAT
Statistics
Matches: 71, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 71 1.00
ACGTcount: A:0.20, C:0.21, G:0.27, T:0.31
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:51812044 original size:23 final size:23
Alignment explanation
Indices: 51812017--51812115 Score: 162
Period size: 23 Copynumber: 4.3 Consensus size: 23
51812007 AGTGTTATTG
*
51812017 ATCAGTGGTAGCTTCGGCTACGT
1 ATCAGTGGTAGCTTCGGCTACAT
*
51812040 TTCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
51812063 TTCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
51812086 AACAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
51812109 ATCAGTG
1 ATCAGTG
51812116 TTGCACTTAT
Statistics
Matches: 71, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 71 1.00
ACGTcount: A:0.20, C:0.21, G:0.27, T:0.31
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:51814069 original size:17 final size:16
Alignment explanation
Indices: 51814047--51814080 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
51814037 GAGGATGGCG
51814047 TTTGTTTGATGTTTATT
1 TTTGTTTG-TGTTTATT
*
51814064 TTTGTTTGTTTTTATT
1 TTTGTTTGTGTTTATT
51814080 T
1 T
51814081 CATAATATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.09, C:0.00, G:0.15, T:0.76
Consensus pattern (16 bp):
TTTGTTTGTGTTTATT
Found at i:51817436 original size:23 final size:23
Alignment explanation
Indices: 51817376--51817425 Score: 100
Period size: 23 Copynumber: 2.2 Consensus size: 23
51817366 TGTCTTGCTT
51817376 AACTCGATCGTACTTCCATTCTC
1 AACTCGATCGTACTTCCATTCTC
51817399 AACTCGATCGTACTTCCATTCTC
1 AACTCGATCGTACTTCCATTCTC
51817422 AACT
1 AACT
51817426 TTCACTTACT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.24, C:0.34, G:0.08, T:0.34
Consensus pattern (23 bp):
AACTCGATCGTACTTCCATTCTC
Found at i:51817717 original size:42 final size:43
Alignment explanation
Indices: 51817568--51817728 Score: 159
Period size: 43 Copynumber: 3.8 Consensus size: 43
51817558 TACCATAACA
* * * * * *
51817568 ATGCC-ATATCCCAGATATGGTATTACATG-TATCCCGTATCG
1 ATGCCAATATCCCAGACATGGTCTTACACGAAATCACATATCG
* *
51817609 ATGCTAATAGCCCA-ACCATGGTCTTACACGAAATCACATATCG
1 ATGCCAATATCCCAGA-CATGGTCTTACACGAAATCACATATCG
* *
51817652 ATGCCAATATCCCAGACATGGTCTTACACGAATTCTCATATCG
1 ATGCCAATATCCCAGACATGGTCTTACACGAAATCACATATCG
* * * *
51817695 ATTCC-ATATCCTAGATATGGTCTTACACGTAATC
1 ATGCCAATATCCCAGACATGGTCTTACACGAAATC
51817729 TCGGTAATCC
Statistics
Matches: 99, Mismatches: 17, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
41 5 0.05
42 43 0.43
43 50 0.51
44 1 0.01
ACGTcount: A:0.30, C:0.26, G:0.14, T:0.29
Consensus pattern (43 bp):
ATGCCAATATCCCAGACATGGTCTTACACGAAATCACATATCG
Found at i:51824632 original size:26 final size:26
Alignment explanation
Indices: 51824603--51824652 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
51824593 TAGTAGTGAT
*
51824603 GCAGCAACGATGCCAATAACAGTAAC
1 GCAGCAAAGATGCCAATAACAGTAAC
* *
51824629 GCAGCAAAGCTGCCAGTAACAGTA
1 GCAGCAAAGATGCCAATAACAGTA
51824653 TATGTGGCAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.40, C:0.26, G:0.22, T:0.12
Consensus pattern (26 bp):
GCAGCAAAGATGCCAATAACAGTAAC
Found at i:51825221 original size:27 final size:27
Alignment explanation
Indices: 51824840--51825215 Score: 445
Period size: 27 Copynumber: 14.0 Consensus size: 27
51824830 GGGTATAACA
* *
51824840 GTCATTTTACCTTTCGAGGGTATTTCA
1 GTCATTTTACCCTTCGAGGGTATTTCG
*
51824867 GTTATTTTACCCTTCGAGGGTATTTCG
1 GTCATTTTACCCTTCGAGGGTATTTCG
* *
51824894 ATCATTTTACCCTTCGGGGGTACTTT-G
1 GTCATTTTACCCTTCGAGGGTA-TTTCG
* *
51824921 GTCATTTTACCCTTTGAGGGTATTTCA
1 GTCATTTTACCCTTCGAGGGTATTTCG
*
51824948 GTCATTTTACCCTTCGAGGGTATTTCA
1 GTCATTTTACCCTTCGAGGGTATTTCG
*
51824975 GTTATTTTACCC-TCTGAGGGTATTTCG
1 GTCATTTTACCCTTC-GAGGGTATTTCG
* * *
51825002 GTTATTTTACCCTTCAAGGGTATTTCA
1 GTCATTTTACCCTTCGAGGGTATTTCG
* * *
51825029 GTCATTTTACCTTTCGGGGGTATTTTG
1 GTCATTTTACCCTTCGAGGGTATTTCG
* *
51825056 GTCATTTTACCCTT-AAGGGTATTTCT
1 GTCATTTTACCCTTCGAGGGTATTTCG
* *
51825082 GTCATTTTACTCTTTGAGGGTATTTCG
1 GTCATTTTACCCTTCGAGGGTATTTCG
*
51825109 GTCATTTTACCTTTCGAGGGTATTTCG
1 GTCATTTTACCCTTCGAGGGTATTTCG
* * * * *
51825136 GCCATTTAACCTTTCAAGGGCATTTCG
1 GTCATTTTACCCTTCGAGGGTATTTCG
*
51825163 GTCATTTTACCCTTTGAGGGTATTTCG
1 GTCATTTTACCCTTCGAGGGTATTTCG
* *
51825190 ATTATTTTACCCTTCG-GAGGTATTTC
1 GTCATTTTACCCTTCGAG-GGTATTTC
51825216 TTTTATATTT
Statistics
Matches: 298, Mismatches: 45, Indels: 12
0.84 0.13 0.03
Matches are distributed among these distances:
26 27 0.09
27 266 0.89
28 5 0.02
ACGTcount: A:0.17, C:0.19, G:0.20, T:0.44
Consensus pattern (27 bp):
GTCATTTTACCCTTCGAGGGTATTTCG
Found at i:51827108 original size:21 final size:21
Alignment explanation
Indices: 51827082--51827130 Score: 98
Period size: 21 Copynumber: 2.3 Consensus size: 21
51827072 AAGCATCGTT
51827082 GCGACATCAAATGGCCACGTC
1 GCGACATCAAATGGCCACGTC
51827103 GCGACATCAAATGGCCACGTC
1 GCGACATCAAATGGCCACGTC
51827124 GCGACAT
1 GCGACAT
51827131 GCAATTTATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.29, C:0.33, G:0.24, T:0.14
Consensus pattern (21 bp):
GCGACATCAAATGGCCACGTC
Found at i:51830860 original size:62 final size:62
Alignment explanation
Indices: 51830730--51830874 Score: 152
Period size: 62 Copynumber: 2.4 Consensus size: 62
51830720 TGTGGTACTG
* * * * *
51830730 ATAC-TTCA-AAATTGTCCAATGTGGTACCTGAACTACCAATTGCTGCATTATTTGGCACTT
1 ATACTTTCATAAAATGTCCAATGTGGTACATGAACTACCAATTGATGCATTATTTAGCACAT
* * * * * * *
51830790 GTACTTTCATAGAATGTCCAATGTGGTACATGAGCTATCAATTTATGTATTATTTAGTACAT
1 ATACTTTCATAAAATGTCCAATGTGGTACATGAACTACCAATTGATGCATTATTTAGCACAT
*
51830852 ATATTTTCATAAAATGT-CAATGT
1 ATACTTTCATAAAATGTCCAATGT
51830875 AATATGTATA
Statistics
Matches: 68, Mismatches: 15, Indels: 3
0.79 0.17 0.03
Matches are distributed among these distances:
60 3 0.04
61 10 0.15
62 55 0.81
ACGTcount: A:0.31, C:0.16, G:0.14, T:0.39
Consensus pattern (62 bp):
ATACTTTCATAAAATGTCCAATGTGGTACATGAACTACCAATTGATGCATTATTTAGCACAT
Found at i:51836526 original size:92 final size:91
Alignment explanation
Indices: 51836364--51836606 Score: 297
Period size: 92 Copynumber: 2.6 Consensus size: 91
51836354 TGTTCCATAT
* * * * * **
51836364 TAATACAAAGATTGATAGTTCAAGTATCACATTGAACATTTTCAAAGTATAAGTATTACATTGGA
1 TAATACAAAAATTGATAGTTCAAGTACCACATTGGATATTTTCAAAGTATAGGTACCACATTGGA
* *
51836429 TATTTTATGAAAAGTATAAGTACCAAA
66 CATTTTATG-AAAGTACAAGTACCAAA
* * * *
51836456 TAATACAAAAATTAATAGTTCAAGTACCACACTGGATATTTTCAAAGTATAGGTGCCAGATTGGA
1 TAATACAAAAATTGATAGTTCAAGTACCACATTGGATATTTTCAAAGTATAGGTACCACATTGGA
*
51836521 CATTTTATGAAAGTACAATTACCAAA
66 CATTTTATGAAAGTACAAGTACCAAA
* * * *
51836547 TAATACACAAATTGATAGTTCAAATACCATATTGGATATTTTATGAAAGTATAGGTACCA
1 TAATACAAAAATTGATAGTTCAAGTACCACATTGGATA-TTT-TCAAAGTATAGGTACCA
51836607 AATGTGACAT
Statistics
Matches: 128, Mismatches: 21, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
91 48 0.38
92 65 0.51
93 15 0.12
ACGTcount: A:0.42, C:0.12, G:0.14, T:0.32
Consensus pattern (91 bp):
TAATACAAAAATTGATAGTTCAAGTACCACATTGGATATTTTCAAAGTATAGGTACCACATTGGA
CATTTTATGAAAGTACAAGTACCAAA
Found at i:51849714 original size:34 final size:34
Alignment explanation
Indices: 51849666--51849739 Score: 103
Period size: 34 Copynumber: 2.2 Consensus size: 34
51849656 TAACAAACTT
* * *
51849666 TAACAAACTCAGCTTTCTACTCCTATTAATAAGC
1 TAACAAACTCAGCTTCCTACTACTACTAATAAGC
* *
51849700 TAACAAACTTAGCTTCCTTCTACTACTAATAAGC
1 TAACAAACTCAGCTTCCTACTACTACTAATAAGC
51849734 TAACAA
1 TAACAA
51849740 TCTCCCTAGA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.38, C:0.26, G:0.05, T:0.31
Consensus pattern (34 bp):
TAACAAACTCAGCTTCCTACTACTACTAATAAGC
Found at i:51851969 original size:76 final size:76
Alignment explanation
Indices: 51851881--51852021 Score: 210
Period size: 76 Copynumber: 1.9 Consensus size: 76
51851871 ATTCCTGAGC
* *
51851881 CCTCAAGATATAATTCGTTTTGGACTGTACAATAAACTCCTCAATTTCATTATGACCAATCACTT
1 CCTCAAAATATAATTCGTTTTGGACTATACAATAAACTCCTCAATTTCATTATGACCAATCACTT
51851946 CTTGAGTGTGT
66 CTTGAGTGTGT
* ** ** *
51851957 CCTCAAAATATAATTCTTTTTGGACTATGTAATAAACTTTTCAATTTCATTATGGCCAATCACTT
1 CCTCAAAATATAATTCGTTTTGGACTATACAATAAACTCCTCAATTTCATTATGACCAATCACTT
51852022 AATTAAAAAA
Statistics
Matches: 57, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
76 57 1.00
ACGTcount: A:0.30, C:0.20, G:0.11, T:0.39
Consensus pattern (76 bp):
CCTCAAAATATAATTCGTTTTGGACTATACAATAAACTCCTCAATTTCATTATGACCAATCACTT
CTTGAGTGTGT
Found at i:51853680 original size:3 final size:3
Alignment explanation
Indices: 51853665--51853716 Score: 54
Period size: 3 Copynumber: 18.0 Consensus size: 3
51853655 ATAGTGCATC
* * * *
51853665 ATT ATT A-T CTT ATT ATT ATT ATT ATT ATC GTT ATT ATT ATT ATC A-T
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
51853711 ATT ATT
1 ATT ATT
51853717 GTTTATACTT
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
2 2 0.05
3 37 0.95
ACGTcount: A:0.31, C:0.06, G:0.02, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:51853685 original size:6 final size:6
Alignment explanation
Indices: 51853617--51853716 Score: 55
Period size: 6 Copynumber: 16.8 Consensus size: 6
51853607 TAGGTTTTCT
* * * * * *
51853617 TTATTT TTATTAA TTATT- TTAATA TTATTA ATACTA TTA-TA GTGCATCA
1 TTATTA TTATT-A TTATTA TTATTA TTATTA TTATTA TTATTA -T-TATTA
* ** *
51853666 TTATTA -TCTTA TTATTA TTATTA TTATCG TTATTA TTATTA TCA-TA
1 TTATTA TTATTA TTATTA TTATTA TTATTA TTATTA TTATTA TTATTA
51853712 TTATT
1 TTATT
51853717 GTTTATACTT
Statistics
Matches: 69, Mismatches: 18, Indels: 14
0.68 0.18 0.14
Matches are distributed among these distances:
5 14 0.20
6 47 0.68
7 7 0.10
8 1 0.01
ACGTcount: A:0.32, C:0.06, G:0.03, T:0.59
Consensus pattern (6 bp):
TTATTA
Found at i:51853688 original size:9 final size:9
Alignment explanation
Indices: 51853617--51853716 Score: 55
Period size: 9 Copynumber: 11.2 Consensus size: 9
51853607 TAGGTTTTCT
*
51853617 TTATTTTTA
1 TTATTATTA
51853626 TTAATTATT-
1 TT-ATTATTA
*
51853635 TTAATATTA
1 TTATTATTA
* *
51853644 TTAATACTA
1 TTATTATTA
*
51853653 TTA-TAGTGCA
1 TTATTA-T-TA
*
51853663 TCATTATTA
1 TTATTATTA
*
51853672 -TCTTATTA
1 TTATTATTA
51853680 TTATTATTA
1 TTATTATTA
**
51853689 TTATCGTTA
1 TTATTATTA
51853698 TTATTATTA
1 TTATTATTA
*
51853707 TCA-TATTA
1 TTATTATTA
51853715 TT
1 TT
51853717 GTTTATACTT
Statistics
Matches: 69, Mismatches: 16, Indels: 13
0.70 0.16 0.13
Matches are distributed among these distances:
8 19 0.28
9 39 0.57
10 9 0.13
11 2 0.03
ACGTcount: A:0.32, C:0.06, G:0.03, T:0.59
Consensus pattern (9 bp):
TTATTATTA
Found at i:51853859 original size:25 final size:23
Alignment explanation
Indices: 51853812--51853857 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
51853802 ATACGTTTGA
*
51853812 TTTTATAATATATATATGCATAT
1 TTTTATAATATATATATACATAT
* *
51853835 TTTTATAATCTATATATATATAT
1 TTTTATAATATATATATACATAT
51853858 ATATACGCAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.39, C:0.04, G:0.02, T:0.54
Consensus pattern (23 bp):
TTTTATAATATATATATACATAT
Found at i:51854431 original size:95 final size:96
Alignment explanation
Indices: 51854310--51854503 Score: 295
Period size: 95 Copynumber: 2.0 Consensus size: 96
51854300 CCCTAAGGTA
*
51854310 GTGGGTTTCAATTTCTCGTTCCACCAAAT-GACTTAATATCCTTTTCAAAAA-TTTTC-AAAATA
1 GTGGGTTTCAATTTCTCGTTCCACCAAATAG-CTAAATATCCTTTT-AAAAACTTTTCAAAAATA
* *
51854372 AGGCAATATTTTGCGTTTGGAAATTCGAGGAAC
64 AGGCAATATTTTGCATTTGGAAATTCGAGAAAC
* *
51854405 GTGGGTTTCGATTTCTCGTTCGACCAAATAGCTAAATATCCTTTTAAAAACTTTTCAAAAATAAG
1 GTGGGTTTCAATTTCTCGTTCCACCAAATAGCTAAATATCCTTTTAAAAACTTTTCAAAAATAAG
*
51854470 GCAATGTTTTGCATTTGGAAATTCGAGAAAC
66 GCAATATTTTGCATTTGGAAATTCGAGAAAC
51854501 GTG
1 GTG
51854504 CCCTAAGGTG
Statistics
Matches: 90, Mismatches: 6, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
94 5 0.06
95 45 0.50
96 40 0.44
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Consensus pattern (96 bp):
GTGGGTTTCAATTTCTCGTTCCACCAAATAGCTAAATATCCTTTTAAAAACTTTTCAAAAATAAG
GCAATATTTTGCATTTGGAAATTCGAGAAAC
Found at i:51858114 original size:15 final size:15
Alignment explanation
Indices: 51858077--51858115 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 15
51858067 ATGACAAAAA
51858077 TATAATTTATCATTT
1 TATAATTTATCATTT
51858092 TAATAATTTAT-ATCTT
1 T-ATAATTTATCAT-TT
51858108 TATAATTT
1 TATAATTT
51858116 TTAAGGGATT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 10 0.45
16 12 0.55
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.59
Consensus pattern (15 bp):
TATAATTTATCATTT
Found at i:51863727 original size:20 final size:20
Alignment explanation
Indices: 51863681--51863727 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
51863671 TATATGTACG
*
51863681 TATATATTTTATACTTTCCA
1 TATATATTTTATAATTTCCA
* *
51863701 TACATATTTTATAATTTCTA
1 TATATATTTTATAATTTCCA
51863721 TATATAT
1 TATATAT
51863728 ATTTTTCTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.34, C:0.11, G:0.00, T:0.55
Consensus pattern (20 bp):
TATATATTTTATAATTTCCA
Found at i:51865388 original size:3 final size:3
Alignment explanation
Indices: 51865382--51865424 Score: 52
Period size: 3 Copynumber: 14.3 Consensus size: 3
51865372 TGGCATTGTG
* *
51865382 TTA TTA TTA TTA -TA TTA TTTA CTA TCA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA T
51865425 ATTTCCTATT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
2 2 0.06
3 29 0.85
4 3 0.09
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:51865465 original size:26 final size:24
Alignment explanation
Indices: 51865434--51865482 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
51865424 TATTTCCTAT
*
51865434 TCATATACATTCGCATATTTTATATG
1 TCATATACA-T-GCATATTTAATATG
*
51865460 TCATATATATGCATATTTAATAT
1 TCATATACATGCATATTTAATAT
51865483 ATATATATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 12 0.57
25 1 0.05
26 8 0.38
ACGTcount: A:0.35, C:0.12, G:0.06, T:0.47
Consensus pattern (24 bp):
TCATATACATGCATATTTAATATG
Found at i:51865476 original size:24 final size:23
Alignment explanation
Indices: 51865446--51865512 Score: 77
Period size: 20 Copynumber: 3.0 Consensus size: 23
51865436 ATATACATTC
* *
51865446 GCATATTTTATATGTCATATATAT
1 GCATATTTAATATAT-ATATATAT
51865470 GCATATTTAATATATATATATAT
1 GCATATTTAATATATATATATAT
*
51865493 --ATATAT-ATATATATATATAT
1 GCATATTTAATATATATATATAT
51865513 TAAGCTTTAT
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
20 14 0.35
21 5 0.12
23 8 0.20
24 13 0.32
ACGTcount: A:0.42, C:0.04, G:0.04, T:0.49
Consensus pattern (23 bp):
GCATATTTAATATATATATATAT
Found at i:51865484 original size:2 final size:2
Alignment explanation
Indices: 51865479--51865512 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
51865469 TGCATATTTA
51865479 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
51865513 TAAGCTTTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:51876070 original size:22 final size:22
Alignment explanation
Indices: 51876045--51876095 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
51876035 CTCATATTTC
*
51876045 CTCTCAATTTCCTTCCAAAATT
1 CTCTCAATTTCCTTCAAAAATT
51876067 CTCTCAATTTCCTTCAAAAATT
1 CTCTCAATTTCCTTCAAAAATT
51876089 CTCTCAA
1 CTCTCAA
51876096 ATCCATATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.29, C:0.31, G:0.00, T:0.39
Consensus pattern (22 bp):
CTCTCAATTTCCTTCAAAAATT
Found at i:51877281 original size:7 final size:7
Alignment explanation
Indices: 51877271--51877295 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
51877261 ATTCGATTGA
51877271 TATTTAG
1 TATTTAG
51877278 TATTTAG
1 TATTTAG
51877285 TATTTAG
1 TATTTAG
51877292 TATT
1 TATT
51877296 ATGTATGTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (7 bp):
TATTTAG
Found at i:51878150 original size:21 final size:20
Alignment explanation
Indices: 51878125--51878433 Score: 116
Period size: 21 Copynumber: 13.2 Consensus size: 20
51878115 CGTTCCTAAT
51878125 TTAATTAAAAACCCTAAACCC
1 TTAATTAAAAACCCT-AACCC
51878146 TTAATTAAAAACCCTAACCCTAACC
1 TTAATTAAAAACCCTAA--C---CC
* *
51878171 TAATTCAATTAAAAACCGTAAACCT
1 ---TT-AATTAAAAACCCT-AACCC
*
51878196 TTAACTTAAAAACCCTAACCTAAT
1 TTAA-TTAAAAACCCTAACC---C
* *
51878220 TTAATTAAAAACCCTAGCCTAAT
1 TTAATTAAAAACCCTAACC---C
51878243 TTAATTAAAAACCCTAAACCC
1 TTAATTAAAAACCCT-AACCC
51878264 TTAATTAAAAACCCTAACCCTAACC
1 TTAATTAAAAACCCTAA--C---CC
* *
51878289 TAATTTAATTAAAAACCCTAGCCTAAT
1 ----TTAATTAAAAACCCTAACC---C
51878316 TTAATTAAAAACCCTAAACCC
1 TTAATTAAAAACCCT-AACCC
51878337 TTAATTAAAAACCCTAACCCTAACC
1 TTAATTAAAAACCCTAA--C---CC
51878362 TAATTTAATTAAAAACCCTAAACCC
1 ----TTAATTAAAAACCCT-AACCC
*
51878387 TTAACTTAAAAACTCTAAACCC
1 TTAA-TTAAAAACCCT-AACCC
*
51878409 TTAACTTTAAAAACTCTAA-CC
1 TTAA--TTAAAAACCCTAACCC
51878430 TTAA
1 TTAA
51878434 CGTAATGTTA
Statistics
Matches: 236, Mismatches: 12, Indels: 80
0.72 0.04 0.24
Matches are distributed among these distances:
20 6 0.03
21 61 0.26
22 37 0.16
23 59 0.25
24 12 0.05
25 9 0.04
27 1 0.00
28 4 0.02
29 43 0.18
30 4 0.02
ACGTcount: A:0.46, C:0.26, G:0.01, T:0.28
Consensus pattern (20 bp):
TTAATTAAAAACCCTAACCC
Found at i:51878193 original size:50 final size:51
Alignment explanation
Indices: 51878119--51878409 Score: 253
Period size: 50 Copynumber: 6.0 Consensus size: 51
51878109 CGTCGTCGTT
51878119 CCTAATTTAATTAAAAACCCTAAACCCTTAA-TTAAAAACCCTAACCCTAA
1 CCTAATTTAATTAAAAACCCTAAACCCTTAACTTAAAAACCCTAACCCTAA
* * *
51878169 CCTAATTCAATTAAAAACCGTAAACCTTTAACTT--AAA----AACCCTAA
1 CCTAATTTAATTAAAAACCCTAAACCCTTAACTTAAAAACCCTAACCCTAA
* *
51878214 CCTAATTTAATTAAAAACCCT--AGCC-TAATTTAATTAAA----AACCCTAAA
1 CCTAATTTAATTAAAAACCCTAAACCCTTAACTTAA--AAACCCTAACCCT-AA
* * ***** *
51878261 CC---CTTAATTAAAAACCCT-AACCC-TAACCTAATTTAATTAAAAACCCTAG
1 CCTAATTTAATTAAAAACCCTAAACCCTTAACTTAA---AAACCCTAACCCTAA
51878310 CCTAATTTAATTAAAAACCCTAAACCCTTAA-TTAAAAACCCTAACCCTAA
1 CCTAATTTAATTAAAAACCCTAAACCCTTAACTTAAAAACCCTAACCCTAA
*
51878360 CCTAATTTAATTAAAAACCCTAAACCCTTAACTTAAAAACTCTAAACCCT
1 CCTAATTTAATTAAAAACCCTAAACCCTTAACTTAAAAACCCT-AACCCT
51878410 TAACTTTAAA
Statistics
Matches: 199, Mismatches: 23, Indels: 36
0.77 0.09 0.14
Matches are distributed among these distances:
42 5 0.03
43 2 0.01
44 15 0.08
45 36 0.18
46 13 0.07
47 4 0.02
49 6 0.03
50 74 0.37
51 12 0.06
52 21 0.11
53 8 0.04
54 3 0.02
ACGTcount: A:0.45, C:0.26, G:0.01, T:0.27
Consensus pattern (51 bp):
CCTAATTTAATTAAAAACCCTAAACCCTTAACTTAAAAACCCTAACCCTAA
Found at i:51878205 original size:22 final size:21
Alignment explanation
Indices: 51878161--51878355 Score: 117
Period size: 23 Copynumber: 8.5 Consensus size: 21
51878151 TAAAAACCCT
*
51878161 AACCCTAACCTAATTCAATTAAA
1 AACCCTAACC--ATTTAATTAAA
*
51878184 AACCGTAAACC-TTTAACTTAAA
1 AACCCT-AACCATTTAA-TTAAA
51878206 AACCCTAACCTAATTTAATTAAA
1 AACCCTAACC--ATTTAATTAAA
*
51878229 AACCCTAGCCTAATTTAATTAAA
1 AACCCTAACC--ATTTAATTAAA
*
51878252 AACCCTAAACC-CTTAATTAAA
1 AACCCT-AACCATTTAATTAAA
**
51878273 AACCCTAACCCTAACCTAATTTAATTAA
1 AACCCTAA-CC--ATTTAA-TT-A--AA
*
51878301 AAACCCTAGCCTAATTTAATTAAA
1 A-ACCCTAACC--ATTTAATTAAA
*
51878325 AACCCTAAACC-CTTAATTAAA
1 AACCCT-AACCATTTAATTAAA
51878346 AACCCTAACC
1 AACCCTAACC
51878356 CTAACCTAAT
Statistics
Matches: 144, Mismatches: 12, Indels: 35
0.75 0.06 0.18
Matches are distributed among these distances:
20 6 0.04
21 40 0.28
22 10 0.07
23 43 0.30
24 22 0.15
25 2 0.01
26 2 0.01
27 2 0.01
28 11 0.08
29 6 0.04
ACGTcount: A:0.46, C:0.26, G:0.02, T:0.27
Consensus pattern (21 bp):
AACCCTAACCATTTAATTAAA
Found at i:51878293 original size:73 final size:74
Alignment explanation
Indices: 51878161--51878439 Score: 364
Period size: 73 Copynumber: 3.9 Consensus size: 74
51878151 TAAAAACCCT
* * *
51878161 AACCCTAACCTAATTCAATTAAAAACCGTAAACCTTTAACTT--AAA----AACCCTAACCTAAT
1 AACCCTAACCTAATTTAATTAAAAACCCTAAACCCTTAACTTAAAAACCCTAACCCTAACCTAAT
51878220 TTAATTAAA
66 TTAATTAAA
*
51878229 AACCCTAGCCTAATTTAATTAAAAACCCTAAACCCTTAA-TTAAAAACCCTAACCCTAACCTAAT
1 AACCCTAACCTAATTTAATTAAAAACCCTAAACCCTTAACTTAAAAACCCTAACCCTAACCTAAT
51878293 TTAATTAAA
66 TTAATTAAA
*
51878302 AACCCTAGCCTAATTTAATTAAAAACCCTAAACCCTTAA-TTAAAAACCCTAACCCTAACCTAAT
1 AACCCTAACCTAATTTAATTAAAAACCCTAAACCCTTAACTTAAAAACCCTAACCCTAACCTAAT
51878366 TTAATTAAA
66 TTAATTAAA
* * * * *
51878375 AACCCTAAACC---CTTAACTTAAAAACTCTAAACCCTTAACTTTAAAAACTCTAACCTTAACGT
1 AACCCT-AACCTAATTTAA-TTAAAAACCCTAAACCCTTAAC-TTAAAAACCCTAACCCTAACCT
51878437 AAT
63 AAT
51878440 GTTAGATTTG
Statistics
Matches: 191, Mismatches: 10, Indels: 14
0.89 0.05 0.07
Matches are distributed among these distances:
67 2 0.01
68 35 0.18
69 3 0.02
71 4 0.02
72 20 0.10
73 102 0.53
74 25 0.13
ACGTcount: A:0.45, C:0.26, G:0.01, T:0.28
Consensus pattern (74 bp):
AACCCTAACCTAATTTAATTAAAAACCCTAAACCCTTAACTTAAAAACCCTAACCCTAACCTAAT
TTAATTAAA
Found at i:51878398 original size:23 final size:22
Alignment explanation
Indices: 51878366--51878434 Score: 99
Period size: 22 Copynumber: 3.2 Consensus size: 22
51878356 CTAACCTAAT
*
51878366 TTAA-TTAAAAACCCTAAACCC
1 TTAACTTAAAAACTCTAAACCC
51878387 TTAACTTAAAAACTCTAAACCC
1 TTAACTTAAAAACTCTAAACCC
51878409 TTAACTTTAAAAACTCT-AA-CC
1 TTAAC-TTAAAAACTCTAAACCC
51878430 TTAAC
1 TTAAC
51878435 GTAATGTTAG
Statistics
Matches: 45, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
21 11 0.24
22 23 0.51
23 11 0.24
ACGTcount: A:0.45, C:0.26, G:0.00, T:0.29
Consensus pattern (22 bp):
TTAACTTAAAAACTCTAAACCC
Found at i:51878578 original size:116 final size:116
Alignment explanation
Indices: 51878436--51878653 Score: 391
Period size: 116 Copynumber: 1.9 Consensus size: 116
51878426 AACCTTAACG
* * *
51878436 TAATGTTAGATTTGGAAAAATGTTTTGACTGGTACTAACAAATAATAATTTTACATAATTTGATA
1 TAATGTTAGATTTGGAAAAATATTTTGACTGGCACTAACAAATAATAATTGTACATAATTTGATA
51878501 ATTTTACTAACCATTAATACAATTTTTTGACTTAATAATTTTACATTCACA
66 ATTTTACTAACCATTAATACAATTTTTTGACTTAATAATTTTACATTCACA
* *
51878552 TAATGTTAGATTTGGAAAAATATTTTGACTGGCACTAACAATTAATAATTGTATATAATTTGATA
1 TAATGTTAGATTTGGAAAAATATTTTGACTGGCACTAACAAATAATAATTGTACATAATTTGATA
51878617 ATTTTACTAACCATTAATACAATTTTTTGACTTAATA
66 ATTTTACTAACCATTAATACAATTTTTTGACTTAATA
51878654 CAATTTATCA
Statistics
Matches: 97, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
116 97 1.00
ACGTcount: A:0.39, C:0.10, G:0.09, T:0.42
Consensus pattern (116 bp):
TAATGTTAGATTTGGAAAAATATTTTGACTGGCACTAACAAATAATAATTGTACATAATTTGATA
ATTTTACTAACCATTAATACAATTTTTTGACTTAATAATTTTACATTCACA
Found at i:51878670 original size:17 final size:18
Alignment explanation
Indices: 51878629--51878670 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
51878619 TTTACTAACC
* *
51878629 ATTAATACAATTTTTTGA
1 ATTAATACAATTTTATCA
*
51878647 CTTAATACAA-TTTATCA
1 ATTAATACAATTTTATCA
51878664 ATTAATA
1 ATTAATA
51878671 ATTTCACAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.43, C:0.10, G:0.02, T:0.45
Consensus pattern (18 bp):
ATTAATACAATTTTATCA
Done.