Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr07 ID=Chr07-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: 60982465
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 868082 characters in sequence are not A, C, G, or T
File 50 of 204
Found at i:16510086 original size:18 final size:18
Alignment explanation
Indices: 16510053--16510105 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
16510043 ATTCAACTAA
*
16510053 ACCCAATCCAAACCCAAAT
1 ACCCAA-CCCAACCCAAAT
** *
16510072 ATTCAACCCAACCCAATT
1 ACCCAACCCAACCCAAAT
16510090 ACCCAACCCAACCCAA
1 ACCCAACCCAACCCAA
16510106 TCATAAAAAT
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
18 24 0.86
19 4 0.14
ACGTcount: A:0.43, C:0.45, G:0.00, T:0.11
Consensus pattern (18 bp):
ACCCAACCCAACCCAAAT
Found at i:16510237 original size:9 final size:9
Alignment explanation
Indices: 16510225--16510283 Score: 91
Period size: 9 Copynumber: 6.6 Consensus size: 9
16510215 TCAATTAAGT
16510225 TAATTCGGG
1 TAATTCGGG
16510234 TAATTCGGG
1 TAATTCGGG
16510243 TAATTCGGG
1 TAATTCGGG
16510252 TAATTCGGG
1 TAATTCGGG
* *
16510261 TCATTCGGT
1 TAATTCGGG
*
16510270 TAATTCGGT
1 TAATTCGGG
16510279 TAATT
1 TAATT
16510284 TTTAACCAAA
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
9 47 1.00
ACGTcount: A:0.22, C:0.12, G:0.27, T:0.39
Consensus pattern (9 bp):
TAATTCGGG
Found at i:16510357 original size:14 final size:14
Alignment explanation
Indices: 16510325--16510367 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
16510315 GTTAATTCGG
**
16510325 TTAACCGACCAAA-
1 TTAACCGAAAAAAT
16510338 TTAACCGAAAAAAT
1 TTAACCGAAAAAAT
16510352 TTAACCGAAAAAAT
1 TTAACCGAAAAAAT
16510366 TT
1 TT
16510368 TGGTTCGGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
13 11 0.41
14 16 0.59
ACGTcount: A:0.51, C:0.19, G:0.07, T:0.23
Consensus pattern (14 bp):
TTAACCGAAAAAAT
Found at i:16512300 original size:2 final size:2
Alignment explanation
Indices: 16512289--16512317 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
16512279 TTAAAACATT
16512289 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
16512318 CGCACATATA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:16515290 original size:11 final size:11
Alignment explanation
Indices: 16515276--16515340 Score: 50
Period size: 10 Copynumber: 6.2 Consensus size: 11
16515266 TTTTACATAC
16515276 TTTTTT-AATT
1 TTTTTTAAATT
16515286 TTTTTTAAA--
1 TTTTTTAAATT
*
16515295 -TTTTAAAATAT
1 TTTTTTAAAT-T
**
16515306 TTTTAAAATATT
1 TTTTTTAA-ATT
16515318 TTTTTTAAA-T
1 TTTTTTAAATT
16515328 TTTTTTAAATT
1 TTTTTTAAATT
16515339 TT
1 TT
16515341 AAAATATTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 13
0.72 0.07 0.21
Matches are distributed among these distances:
8 7 0.16
10 16 0.36
11 6 0.14
12 13 0.30
13 2 0.05
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (11 bp):
TTTTTTAAATT
Found at i:16515323 original size:42 final size:41
Alignment explanation
Indices: 16515245--16515411 Score: 209
Period size: 42 Copynumber: 4.1 Consensus size: 41
16515235 AATATATTTA
* * *
16515245 TTTTTTT-AATTTTAAAATATTTTTTACATACTTTTTTAAT
1 TTTTTTTAAATTTTAAAATATTTTTAAAATATTTTTTTAAT
*
16515285 TTTTTTTAAATTTTAAAATATTTTTAAAATATTTTTTTTAAA
1 TTTTTTTAAATTTTAAAATATTTTTAAAATA-TTTTTTTAAT
16515327 TTTTTTTAAATTTTAAAATATTTTTAAAATA--TTTTTAA-
1 TTTTTTTAAATTTTAAAATATTTTTAAAATATTTTTTTAAT
**
16515365 -TTTTAAAATATTTTTAAAATATTTTTAAAATACTTTTTTTAAT
1 TTTTTTTAA-A-TTTTAAAATATTTTTAAAATA-TTTTTTTAAT
16515408 TTTT
1 TTTT
16515412 AAAATAAAAA
Statistics
Matches: 112, Mismatches: 6, Indels: 14
0.85 0.05 0.11
Matches are distributed among these distances:
37 6 0.05
38 1 0.01
39 28 0.25
40 7 0.06
41 21 0.19
42 46 0.41
44 3 0.03
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (41 bp):
TTTTTTTAAATTTTAAAATATTTTTAAAATATTTTTTTAAT
Found at i:16515351 original size:11 final size:11
Alignment explanation
Indices: 16515295--16515402 Score: 108
Period size: 11 Copynumber: 10.4 Consensus size: 11
16515285 TTTTTTTAAA
16515295 TTTTAAAATAT
1 TTTTAAAATAT
16515306 TTTTAAAATATTT
1 TTTTAAAATA--T
*
16515319 TTTTTAAAT-T
1 TTTTAAAATAT
*
16515329 TTTT-TAA-A-
1 TTTTAAAATAT
16515337 TTTTAAAATAT
1 TTTTAAAATAT
16515348 TTTTAAAATAT
1 TTTTAAAATAT
16515359 TTTT---A-A-
1 TTTTAAAATAT
16515365 TTTTAAAATAT
1 TTTTAAAATAT
16515376 TTTTAAAATAT
1 TTTTAAAATAT
16515387 TTTTAAAATACT
1 TTTTAAAATA-T
16515399 TTTT
1 TTTT
16515403 TTAATTTTTA
Statistics
Matches: 82, Mismatches: 3, Indels: 23
0.76 0.03 0.21
Matches are distributed among these distances:
6 4 0.05
7 1 0.01
8 5 0.06
9 5 0.06
10 7 0.09
11 46 0.56
12 5 0.06
13 9 0.11
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:16515368 original size:17 final size:17
Alignment explanation
Indices: 16515348--16515381 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
16515338 TTTAAAATAT
16515348 TTTTAAAATATTTTTAA
1 TTTTAAAATATTTTTAA
16515365 TTTTAAAATATTTTTAA
1 TTTTAAAATATTTTTAA
16515382 AATATTTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TTTTAAAATATTTTTAA
Found at i:16519589 original size:33 final size:33
Alignment explanation
Indices: 16519536--16519605 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
16519526 ATTGTTTAAA
* *
16519536 TATGATTTGAACATGCTTTTGAGTATGTTTAGG
1 TATGATTTGAACATACTTTTGAGAATGTTTAGG
* * *
16519569 TATGATTTGAACATATTTTTGGGAATGTTTTGG
1 TATGATTTGAACATACTTTTGAGAATGTTTAGG
16519602 TATG
1 TATG
16519606 GTTGATAATA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.24, C:0.04, G:0.24, T:0.47
Consensus pattern (33 bp):
TATGATTTGAACATACTTTTGAGAATGTTTAGG
Found at i:16534375 original size:42 final size:42
Alignment explanation
Indices: 16534311--16534393 Score: 157
Period size: 42 Copynumber: 2.0 Consensus size: 42
16534301 CCATAGTCGT
*
16534311 TACTCAATTTATTTGAGAATATCAACTATGGCACTAGGCAGC
1 TACTAAATTTATTTGAGAATATCAACTATGGCACTAGGCAGC
16534353 TACTAAATTTATTTGAGAATATCAACTATGGCACTAGGCAG
1 TACTAAATTTATTTGAGAATATCAACTATGGCACTAGGCAG
16534394 ATGGCTGGAT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Consensus pattern (42 bp):
TACTAAATTTATTTGAGAATATCAACTATGGCACTAGGCAGC
Found at i:16549045 original size:29 final size:29
Alignment explanation
Indices: 16548983--16549081 Score: 150
Period size: 28 Copynumber: 3.5 Consensus size: 29
16548973 AAAAATAAAA
*
16548983 ATTTACCAAAACATTACAAC-TTTTTTTT
1 ATTTACCAAAATATTACAACTTTTTTTTT
16549011 ATTTACCAAAATATTACAACTTTTTTTTT
1 ATTTACCAAAATATTACAACTTTTTTTTT
*
16549040 ATTTACCAAAATATATA-AA-TATTTTTTT
1 ATTTACCAAAATAT-TACAACTTTTTTTTT
16549068 ATTTACCAAAATAT
1 ATTTACCAAAATAT
16549082 ATCAAAAAAA
Statistics
Matches: 67, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
28 41 0.61
29 24 0.36
30 2 0.03
ACGTcount: A:0.39, C:0.13, G:0.00, T:0.47
Consensus pattern (29 bp):
ATTTACCAAAATATTACAACTTTTTTTTT
Found at i:16549152 original size:27 final size:27
Alignment explanation
Indices: 16549114--16549197 Score: 134
Period size: 27 Copynumber: 3.1 Consensus size: 27
16549104 CCTGATCACC
16549114 CCAATGCCATTGGCGGCACCAAAGGTG
1 CCAATGCCATTGGCGGCACCAAAGGTG
*
16549141 CCAATGCCATTGGCGGCACCAATGGTG
1 CCAATGCCATTGGCGGCACCAAAGGTG
* *
16549168 CCAATGCCATTGGCGGTACC-AATGTG
1 CCAATGCCATTGGCGGCACCAAAGGTG
16549194 CCAA
1 CCAA
16549198 AGGACTAAAA
Statistics
Matches: 53, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
26 8 0.15
27 45 0.85
ACGTcount: A:0.25, C:0.30, G:0.27, T:0.18
Consensus pattern (27 bp):
CCAATGCCATTGGCGGCACCAAAGGTG
Found at i:16549738 original size:18 final size:19
Alignment explanation
Indices: 16549687--16549747 Score: 63
Period size: 19 Copynumber: 3.3 Consensus size: 19
16549677 CTAATATTTC
*
16549687 TATTAATTTAAAATA-TAGT
1 TATTAAATTAAAATAGTA-T
* *
16549706 TATTAAATGAGAATAGT-T
1 TATTAAATTAAAATAGTAT
*
16549724 TATTAAATTAAAATAGAAT
1 TATTAAATTAAAATAGTAT
16549743 TATTA
1 TATTA
16549748 CTTAATTAGA
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
18 15 0.44
19 18 0.53
20 1 0.03
ACGTcount: A:0.49, C:0.00, G:0.08, T:0.43
Consensus pattern (19 bp):
TATTAAATTAAAATAGTAT
Found at i:16550284 original size:27 final size:26
Alignment explanation
Indices: 16550246--16550302 Score: 87
Period size: 27 Copynumber: 2.2 Consensus size: 26
16550236 TTTTAGTCCT
16550246 TTGGCACATTGGTGCCACCAATGGCA
1 TTGGCACATTGGTGCCACCAATGGCA
* *
16550272 TTGGCACCTTTGGTGCCGCCAATGGCA
1 TTGGCA-CATTGGTGCCACCAATGGCA
16550299 TTGG
1 TTGG
16550303 GGTGATCAGG
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
26 6 0.21
27 22 0.79
ACGTcount: A:0.18, C:0.26, G:0.30, T:0.26
Consensus pattern (26 bp):
TTGGCACATTGGTGCCACCAATGGCA
Found at i:16550423 original size:29 final size:29
Alignment explanation
Indices: 16550346--16550446 Score: 161
Period size: 29 Copynumber: 3.5 Consensus size: 29
16550336 TTTTTTTTAT
16550346 ATATTTTGGTAAAT-AAAAAAAAGTT-TA
1 ATATTTTGGTAAATAAAAAAAAAGTTGTA
*
16550373 TATATTTTGATAAATAATAAAAAAAGTTGTA
1 -ATATTTTGGTAAATAA-AAAAAAAGTTGTA
16550404 ATATTTTGGTAAATAAAAAAAAAGTTGTA
1 ATATTTTGGTAAATAAAAAAAAAGTTGTA
16550433 ATATTTTGGTAAAT
1 ATATTTTGGTAAAT
16550447 TTTTATTTTT
Statistics
Matches: 68, Mismatches: 2, Indels: 5
0.91 0.03 0.07
Matches are distributed among these distances:
28 13 0.19
29 28 0.41
30 25 0.37
31 2 0.03
ACGTcount: A:0.50, C:0.00, G:0.12, T:0.39
Consensus pattern (29 bp):
ATATTTTGGTAAATAAAAAAAAAGTTGTA
Found at i:16559980 original size:16 final size:16
Alignment explanation
Indices: 16559959--16560015 Score: 87
Period size: 16 Copynumber: 3.6 Consensus size: 16
16559949 TTTGGTTCGC
*
16559959 TGTATTGGATTAGAGG
1 TGTAATGGATTAGAGG
*
16559975 TGTATTGGATTAGAGG
1 TGTAATGGATTAGAGG
*
16559991 TGTAATGGAATAGAGG
1 TGTAATGGATTAGAGG
16560007 TGTAATGGA
1 TGTAATGGA
16560016 AAAGCTGTGT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 39 1.00
ACGTcount: A:0.30, C:0.00, G:0.37, T:0.33
Consensus pattern (16 bp):
TGTAATGGATTAGAGG
Found at i:16560282 original size:18 final size:17
Alignment explanation
Indices: 16560261--16560295 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
16560251 TTATTATTAA
*
16560261 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
16560279 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
16560296 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:16560388 original size:15 final size:15
Alignment explanation
Indices: 16560360--16560400 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
16560350 ATAAAATATA
16560360 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
16560375 TATTAAATATATTAT
1 AATTAAATATATTAT
16560390 AATTAAA-ATAT
1 AATTAAATATAT
16560401 CATGAATTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
14 7 0.30
15 16 0.70
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:16560448 original size:122 final size:122
Alignment explanation
Indices: 16560244--16560539 Score: 492
Period size: 122 Copynumber: 2.4 Consensus size: 122
16560234 ATCATATTTA
16560244 AACATAATTATTATTAAATATATTTTAATTAAAATATAT-AATTTAATAAAATTCTTAATAATCA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATGAATTTAATAAAATTCTTAATAATCA
*
16560308 ATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT-
66 ATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATAAATTG
* *
16560364 AACATAATTATTATTAAATATATTATAATTAAAATATCATGAATTTAATAAAATTCTTAATAATT
1 AACATAATTATTATTAAATATATTTTAATTAAAATAT-ATGAATTTAATAAAATTCTTAATAATC
*
16560429 AATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATAATTTG
65 AATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATAAATTG
* *
16560487 AA-ATAATTAATATTAAATATATTTTAATTAAAAATATATG-ACTTAATAAAATT
1 AACATAATTATTATTAAATATATTTTAATT-AAAATATATGAATTTAATAAAATT
16560540 TAAAATAATT
Statistics
Matches: 165, Mismatches: 7, Indels: 7
0.92 0.04 0.04
Matches are distributed among these distances:
120 36 0.22
121 14 0.08
122 106 0.64
123 9 0.05
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.42
Consensus pattern (122 bp):
AACATAATTATTATTAAATATATTTTAATTAAAATATATGAATTTAATAAAATTCTTAATAATCA
ATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATAAATTG
Found at i:16560609 original size:26 final size:28
Alignment explanation
Indices: 16560580--16560640 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
16560570 TATGAATTTG
*
16560580 TATAATTTAA-AATAAT-TATTATTACA
1 TATAATTTAATAATAATATATAATTACA
*
16560606 TATAATTTAATAATAATATATAATTTCA
1 TATAATTTAATAATAATATATAATTACA
*
16560634 TAAAATT
1 TATAATT
16560641 CTTCATAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
26 10 0.33
27 6 0.20
28 14 0.47
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (28 bp):
TATAATTTAATAATAATATATAATTACA
Found at i:16560638 original size:47 final size:46
Alignment explanation
Indices: 16560587--16560730 Score: 113
Period size: 47 Copynumber: 3.1 Consensus size: 46
16560577 TTGTATAATT
16560587 TAAAATAATTATTATTACATATAATTTAATAATAATATATAATTTCA
1 TAAAATAATTATTATTA-ATATAATTTAATAATAATATATAATTTCA
* ** * *
16560634 TAAAAT--TCT-TCA-TAATA-AATTTTCTTATATGAATTTATACAATT--
1 TAAAATAAT-TATTATTAATATAA-TTTAATA-AT-AATATATA-ATTTCA
* *
16560678 TAAAATAATTAATATTAAATATAATTTAATAATGATATATAATTTCA
1 TAAAATAATTATTATT-AATATAATTTAATAATAATATATAATTTCA
16560725 TAAAAT
1 TAAAAT
16560731 TCTTAATAAT
Statistics
Matches: 72, Mismatches: 12, Indels: 26
0.65 0.11 0.24
Matches are distributed among these distances:
42 2 0.03
43 8 0.11
44 10 0.14
45 14 0.19
46 12 0.17
47 15 0.21
48 9 0.12
49 2 0.03
ACGTcount: A:0.49, C:0.05, G:0.01, T:0.44
Consensus pattern (46 bp):
TAAAATAATTATTATTAATATAATTTAATAATAATATATAATTTCA
Found at i:16560650 original size:91 final size:91
Alignment explanation
Indices: 16560555--16560760 Score: 331
Period size: 91 Copynumber: 2.3 Consensus size: 91
16560545 TAATTATAAC
* * * *
16560555 TAATAAATTATCTTATATGAATTTGTATAATTTAAAATAATTATTATTACATATAATTTAATAAT
1 TAATAAATTATCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAAT
*
16560620 AATATATAATTTCATAAAATTCTTCA
66 AATATATAATTTCATAAAATTCTTAA
*
16560646 TAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAAT
1 TAATAAATTATCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAAT
*
16560711 GATATATAATTTCATAAAATTCTTAA
66 AATATATAATTTCATAAAATTCTTAA
*
16560737 TAATAAAATATTCTTATATGAATT
1 TAATAAATTA-TCTTATATGAATT
16560761 CATATAAGAT
Statistics
Matches: 105, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
91 92 0.88
92 13 0.12
ACGTcount: A:0.47, C:0.05, G:0.02, T:0.46
Consensus pattern (91 bp):
TAATAAATTATCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAAT
AATATATAATTTCATAAAATTCTTAA
Found at i:16560722 original size:44 final size:43
Alignment explanation
Indices: 16560580--16560722 Score: 119
Period size: 44 Copynumber: 3.2 Consensus size: 43
16560570 TATGAATTTG
* *
16560580 TATAATTTAAAATAATTATTATTACATATAATTTAATAATAATA
1 TATAATTTAAAATAATTAATATTAAATATAATTTAATAAT-ATA
** * * * *
16560624 TATAATTTCATAAAATTCTTCATAATAAAT-T-TTCTTATATGAATTTA
1 TATAA-TT--TAAAATAATTAATATTAAATATAAT-TTA-AT-AATATA
*
16560671 TACAATTTAAAATAATTAATATTAAATATAATTTAATAATGATA
1 TATAATTTAAAATAATTAATATTAAATATAATTTAATAAT-ATA
16560715 TATAATTT
1 TATAATTT
16560723 CATAAAATTC
Statistics
Matches: 74, Mismatches: 16, Indels: 18
0.69 0.15 0.17
Matches are distributed among these distances:
43 3 0.04
44 32 0.43
45 7 0.09
46 7 0.09
47 22 0.30
48 3 0.04
ACGTcount: A:0.48, C:0.04, G:0.01, T:0.46
Consensus pattern (43 bp):
TATAATTTAAAATAATTAATATTAAATATAATTTAATAATATA
Found at i:16560737 original size:47 final size:47
Alignment explanation
Indices: 16560605--16560743 Score: 137
Period size: 47 Copynumber: 3.0 Consensus size: 47
16560595 TTATTATTAC
* *
16560605 ATATAATTTAATAATAATATATAATTTCATAAAATTCTTCATAATAA
1 ATATAATTTAATAATGATATATAATTTCATAAAATTCTTAATAATAA
* * * ** *
16560652 AT-T--TTCTTAT-ATGAATTTATACAATT--TAAAATAATTAATATTAA
1 ATATAATT-TAATAATG-ATATATA-ATTTCATAAAATTCTTAATAATAA
16560696 ATATAATTTAATAATGATATATAATTTCATAAAATTCTTAATAATAA
1 ATATAATTTAATAATGATATATAATTTCATAAAATTCTTAATAATAA
16560743 A
1 A
16560744 ATATTCTTAT
Statistics
Matches: 69, Mismatches: 14, Indels: 18
0.68 0.14 0.18
Matches are distributed among these distances:
44 20 0.29
45 13 0.19
46 13 0.19
47 23 0.33
ACGTcount: A:0.50, C:0.05, G:0.01, T:0.44
Consensus pattern (47 bp):
ATATAATTTAATAATGATATATAATTTCATAAAATTCTTAATAATAA
Found at i:16568867 original size:15 final size:15
Alignment explanation
Indices: 16568849--16568881 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
16568839 AACAATTATG
16568849 TTTCTTCTTCTTCCT
1 TTTCTTCTTCTTCCT
*
16568864 TTTCTTTTTCTTCCT
1 TTTCTTCTTCTTCCT
16568879 TTT
1 TTT
16568882 GTAGTTACGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (15 bp):
TTTCTTCTTCTTCCT
Found at i:16573809 original size:101 final size:101
Alignment explanation
Indices: 16573634--16573822 Score: 369
Period size: 101 Copynumber: 1.9 Consensus size: 101
16573624 AGATTGCATT
*
16573634 GTTTGAATTCCTTTAATCATGATTTCTGAAGTTGATTGGCCATGAGAATTGCTATGCCAATCTTC
1 GTTTGAATTCCTTTAATCATGATTTCTGAAGTTGATAGGCCATGAGAATTGCTATGCCAATCTTC
16573699 GGCTGTTTAAATTCCATAATGTTATTTAACATTTAA
66 GGCTGTTTAAATTCCATAATGTTATTTAACATTTAA
16573735 GTTTGAATTCCTTTAATCATGATTTCTGAAGTTGATAGGCCATGAGAATTGCTATGCCAATCTTC
1 GTTTGAATTCCTTTAATCATGATTTCTGAAGTTGATAGGCCATGAGAATTGCTATGCCAATCTTC
16573800 GGCTGTTTAAATTCCATAATGTT
66 GGCTGTTTAAATTCCATAATGTT
16573823 TAAATCACCC
Statistics
Matches: 87, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
101 87 1.00
ACGTcount: A:0.27, C:0.15, G:0.17, T:0.41
Consensus pattern (101 bp):
GTTTGAATTCCTTTAATCATGATTTCTGAAGTTGATAGGCCATGAGAATTGCTATGCCAATCTTC
GGCTGTTTAAATTCCATAATGTTATTTAACATTTAA
Found at i:16574091 original size:24 final size:23
Alignment explanation
Indices: 16574047--16574091 Score: 54
Period size: 24 Copynumber: 1.9 Consensus size: 23
16574037 GGTACTGTAG
*
16574047 TTCATTTCATGTTATTTTGGTAT
1 TTCATTTCATGTTATTATGGTAT
* *
16574070 TTCATATTCTTGTTCTTATGGT
1 TTCAT-TTCATGTTATTATGGT
16574092 CAATTTCAAG
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 5 0.28
24 13 0.72
ACGTcount: A:0.16, C:0.11, G:0.13, T:0.60
Consensus pattern (23 bp):
TTCATTTCATGTTATTATGGTAT
Found at i:16575733 original size:21 final size:21
Alignment explanation
Indices: 16575669--16575741 Score: 69
Period size: 21 Copynumber: 3.6 Consensus size: 21
16575659 ATTTTGATTT
*
16575669 TGAATGATTGAATTTAGAAAA
1 TGAAAGATTGAATTTAGAAAA
** * ***
16575690 TGGGAGAGTG-ATTT-GATTG
1 TGAAAGATTGAATTTAGAAAA
16575709 TGAAAGATTGAATTTAGAAAA
1 TGAAAGATTGAATTTAGAAAA
16575730 TGAAAGATTGAA
1 TGAAAGATTGAA
16575742 CGTGCAAGTA
Statistics
Matches: 37, Mismatches: 13, Indels: 4
0.69 0.24 0.07
Matches are distributed among these distances:
19 9 0.24
20 8 0.22
21 20 0.54
ACGTcount: A:0.42, C:0.00, G:0.26, T:0.32
Consensus pattern (21 bp):
TGAAAGATTGAATTTAGAAAA
Found at i:16585352 original size:17 final size:18
Alignment explanation
Indices: 16585330--16585371 Score: 68
Period size: 17 Copynumber: 2.4 Consensus size: 18
16585320 GACATATTAC
16585330 CCCTAATTTCTAATT-GG
1 CCCTAATTTCTAATTAGG
16585347 CCCTAATTTCTAATTAGG
1 CCCTAATTTCTAATTAGG
*
16585365 CCTTAAT
1 CCCTAAT
16585372 CAATTAGAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 15 0.65
18 8 0.35
ACGTcount: A:0.26, C:0.24, G:0.10, T:0.40
Consensus pattern (18 bp):
CCCTAATTTCTAATTAGG
Found at i:16591975 original size:21 final size:21
Alignment explanation
Indices: 16591950--16591992 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
16591940 GATCTTGATA
16591950 GTCGAATATTAAGTTGATTAT
1 GTCGAATATTAAGTTGATTAT
16591971 GTCGAATATTAAGTTGATTAT
1 GTCGAATATTAAGTTGATTAT
16591992 G
1 G
16591993 CTTATGAAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.33, C:0.05, G:0.21, T:0.42
Consensus pattern (21 bp):
GTCGAATATTAAGTTGATTAT
Found at i:16592927 original size:21 final size:21
Alignment explanation
Indices: 16592901--16592940 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
16592891 GAACAAAAAT
16592901 GACATGTTTAATAGGTTTCAG
1 GACATGTTTAATAGGTTTCAG
16592922 GACATGTTTAATAGGTTTC
1 GACATGTTTAATAGGTTTC
16592941 TAGGTAAATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.28, C:0.10, G:0.23, T:0.40
Consensus pattern (21 bp):
GACATGTTTAATAGGTTTCAG
Found at i:16593815 original size:4 final size:4
Alignment explanation
Indices: 16593808--16593953 Score: 283
Period size: 4 Copynumber: 36.5 Consensus size: 4
16593798 CAATAAATAA
16593808 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
16593856 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
*
16593904 ATAC ATAC ATAT ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
16593952 AT
1 AT
16593954 TGTAACACCC
Statistics
Matches: 140, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
4 140 1.00
ACGTcount: A:0.50, C:0.24, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:16595769 original size:43 final size:42
Alignment explanation
Indices: 16595706--16595827 Score: 104
Period size: 42 Copynumber: 2.9 Consensus size: 42
16595696 AAAAAGCTCG
* * *
16595706 TACGATGCCAAC-GTCACAGACGTGGTCTTACATGTAATGAAA
1 TACGATGCC-ACTGTCCCAGACGTGGTCTTACAAGTAATCAAA
* * *
16595748 TATCGATGCCACTGTCCCAGACAG-GATCTTTCAAGTAATCATA
1 TA-CGATGCCACTGTCCCAGAC-GTGGTCTTACAAGTAATCAAA
* * * * *
16595791 TACAATGCCAATGTCCCAAACATGGTCTTACACGTAA
1 TACGATGCCACTGTCCCAGACGTGGTCTTACAAGTAA
16595828 ATCACATATC
Statistics
Matches: 63, Mismatches: 13, Indels: 8
0.75 0.15 0.10
Matches are distributed among these distances:
42 31 0.49
43 31 0.49
44 1 0.02
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (42 bp):
TACGATGCCACTGTCCCAGACGTGGTCTTACAAGTAATCAAA
Found at i:16607418 original size:27 final size:28
Alignment explanation
Indices: 16607373--16607427 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 28
16607363 AAATAAATAC
* *
16607373 TAATAATTTTATTTGAATATA-ATTAAA
1 TAATAATTTTATTTAAATAAATATTAAA
16607400 TAATAA-TTTATTATAAATAAATATTAAA
1 TAATAATTTTATT-TAAATAAATATTAAA
16607428 ATCCTAAACC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 6 0.25
27 12 0.50
28 6 0.25
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (28 bp):
TAATAATTTTATTTAAATAAATATTAAA
Found at i:16607473 original size:21 final size:21
Alignment explanation
Indices: 16607423--16607475 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
16607413 TAAATAAATA
*
16607423 TTAAAATCCTAAACCTTGAAC
1 TTAAAATCCTAAACCCTGAAC
* * *
16607444 TCAATATCCTAAACCCTGAGC
1 TTAAAATCCTAAACCCTGAAC
16607465 TTAAAATCCTA
1 TTAAAATCCTA
16607476 GATTTGAGAG
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.40, C:0.26, G:0.06, T:0.28
Consensus pattern (21 bp):
TTAAAATCCTAAACCCTGAAC
Found at i:16607865 original size:29 final size:28
Alignment explanation
Indices: 16607832--16607886 Score: 101
Period size: 28 Copynumber: 1.9 Consensus size: 28
16607822 ACCAAAAATT
16607832 TATTTTAAAAATAAAAAAATAAAAAAAAG
1 TATTTTAAAAAT-AAAAAATAAAAAAAAG
16607861 TATTTTAAAAATAAAAAATAAAAAAA
1 TATTTTAAAAATAAAAAATAAAAAAA
16607887 TAAATATTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
28 14 0.54
29 12 0.46
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (28 bp):
TATTTTAAAAATAAAAAATAAAAAAAAG
Found at i:16607896 original size:29 final size:29
Alignment explanation
Indices: 16607832--16607895 Score: 94
Period size: 29 Copynumber: 2.2 Consensus size: 29
16607822 ACCAAAAATT
*
16607832 TATTTTAAAAATAAAAAAATAAAAAAAAG
1 TATTTTAAAAATAAAAAAATAAAAAAAAA
16607861 TATTTTAAAAAT-AAAAAATAAAAAAATAAA
1 TATTTTAAAAATAAAAAAAT-AAAAAA-AAA
16607891 TATTT
1 TATTT
16607896 ATTATATATT
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
28 7 0.22
29 18 0.56
30 7 0.22
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.30
Consensus pattern (29 bp):
TATTTTAAAAATAAAAAAATAAAAAAAAA
Found at i:16617373 original size:30 final size:30
Alignment explanation
Indices: 16617339--16617396 Score: 116
Period size: 30 Copynumber: 1.9 Consensus size: 30
16617329 AGAGCACTAA
16617339 TTATTTTATTTATATTTTTATTTAAGCTTT
1 TTATTTTATTTATATTTTTATTTAAGCTTT
16617369 TTATTTTATTTATATTTTTATTTAAGCT
1 TTATTTTATTTATATTTTTATTTAAGCT
16617397 CTTGAGTTGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.24, C:0.03, G:0.03, T:0.69
Consensus pattern (30 bp):
TTATTTTATTTATATTTTTATTTAAGCTTT
Found at i:16617392 original size:12 final size:12
Alignment explanation
Indices: 16617342--16617391 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
16617332 GCACTAATTA
16617342 TTTTATTTATAT
1 TTTTATTTATAT
16617354 TTTTATTTA-AGCT
1 TTTTATTTATA--T
16617367 TTTTATTT-TAT
1 TTTTATTTATAT
* *
16617378 TTATATTTTTAT
1 TTTTATTTATAT
16617390 TT
1 TT
16617392 AAGCTCTTGA
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
11 9 0.27
12 14 0.42
13 10 0.30
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.74
Consensus pattern (12 bp):
TTTTATTTATAT
Found at i:16626064 original size:16 final size:16
Alignment explanation
Indices: 16626045--16626078 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
16626035 TTTTTTTTGG
16626045 TTGTTTTGCTGTCATT
1 TTGTTTTGCTGTCATT
* *
16626061 TTGTTTTGTTGTTATT
1 TTGTTTTGCTGTCATT
16626077 TT
1 TT
16626079 ATTGTCATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.06, C:0.06, G:0.18, T:0.71
Consensus pattern (16 bp):
TTGTTTTGCTGTCATT
Found at i:16627463 original size:19 final size:19
Alignment explanation
Indices: 16627439--16627486 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
16627429 TTTTTCAAAT
16627439 AATTATAAAATATTAAAAA
1 AATTATAAAATATTAAAAA
* *
16627458 AATTATTAAGA-ATTATAAA
1 AATTA-TAAAATATTAAAAA
16627477 AATT-TAAAAT
1 AATTATAAAAT
16627487 TAATCTTAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
17 4 0.17
19 16 0.67
20 4 0.17
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.35
Consensus pattern (19 bp):
AATTATAAAATATTAAAAA
Found at i:16631489 original size:18 final size:18
Alignment explanation
Indices: 16631448--16631489 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
16631438 CTTCGGAAGC
* *
16631448 TTCTTCTTCTCCTTCGGA
1 TTCTTCTTCGCCTTCAGA
*
16631466 TGCTTCTTCGCCTTCAGA
1 TTCTTCTTCGCCTTCAGA
16631484 TTCTTC
1 TTCTTC
16631490 GTCTTCTTCC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.07, C:0.33, G:0.12, T:0.48
Consensus pattern (18 bp):
TTCTTCTTCGCCTTCAGA
Found at i:16635959 original size:43 final size:41
Alignment explanation
Indices: 16635886--16636050 Score: 131
Period size: 43 Copynumber: 3.9 Consensus size: 41
16635876 AGCACCGCAT
* * *
16635886 TGCATCATCAGATAAATCGAAGGAAATATACTGACACACATAG
1 TGCATCATCAGATAAA-CCAAAG-ATTATACTGACACACATAG
* *
16635929 TGCATCATCAGATAAACCAAAGTAGTTATAC---CGCGCATAG
1 TGCATCATCAGATAAACCAAAG-A-TTATACTGACACACATAG
* * *
16635969 TGCATCATCGGATAAACCGAAAGATGAATACTGACACACATAA
1 TGCATCATCAGATAAACC-AAAGAT-TATACTGACACACATAG
* *
16636012 TGCATCATC-GAATAAACCGAAGGATGAATACTGACACAC
1 TGCATCATCAG-ATAAACC-AAAGAT-TATACTGACACAC
16636051 TATACTGACA
Statistics
Matches: 103, Mismatches: 12, Indels: 14
0.80 0.09 0.11
Matches are distributed among these distances:
39 1 0.01
40 29 0.28
41 4 0.04
42 6 0.06
43 63 0.61
ACGTcount: A:0.42, C:0.21, G:0.17, T:0.20
Consensus pattern (41 bp):
TGCATCATCAGATAAACCAAAGATTATACTGACACACATAG
Found at i:16636057 original size:13 final size:13
Alignment explanation
Indices: 16636039--16636063 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
16636029 CGAAGGATGA
16636039 ATACTGACACACT
1 ATACTGACACACT
16636052 ATACTGACACAC
1 ATACTGACACAC
16636064 ATAGTGCATC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.32, G:0.08, T:0.20
Consensus pattern (13 bp):
ATACTGACACACT
Found at i:16636083 original size:56 final size:56
Alignment explanation
Indices: 16635996--16636106 Score: 161
Period size: 56 Copynumber: 2.0 Consensus size: 56
16635986 CGAAAGATGA
*
16635996 ATACTGACACACATAATGCATCATCGAATAAACCGAAGGA-TGAATACTGACACACT
1 ATACTGACACACATAATGCATCATCGAATAAACCGAAGCAGT-AATACTGACACACT
* * * *
16636052 ATACTGACACACATAGTGCATCATCGGATAAATCGAAGCAGTTATACTGACACAC
1 ATACTGACACACATAATGCATCATCGAATAAACCGAAGCAGTAATACTGACACAC
16636107 ATCATTGGAT
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
56 48 0.98
57 1 0.02
ACGTcount: A:0.41, C:0.23, G:0.15, T:0.21
Consensus pattern (56 bp):
ATACTGACACACATAATGCATCATCGAATAAACCGAAGCAGTAATACTGACACACT
Found at i:16639580 original size:107 final size:107
Alignment explanation
Indices: 16639393--16639593 Score: 307
Period size: 107 Copynumber: 1.9 Consensus size: 107
16639383 AGGATATTTA
* *
16639393 GCTATTTGGTTAAACGAGAAATCGAAACCCAACACATTAGGGCACGTTCCTCGAATTTCCAAACG
1 GCTATTTGGTCAAACGAAAAATCGAAACCCAACACATTAGGGCACGTTCCTCGAATTTCCAAACG
*
16639458 CAAAATATTATCTTACTTT-G-AAATTTTAAAAGGACACTTG
66 CAAAATATTACCTTACTTTGGAAAATTTTAAAAGGACACTTG
* * *
16639498 GCTATTTGGTCAAACGAAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTCGAATTTTCAAA
1 GCTATTTGGTCAAACG-AAAAATCGAAACCCAACACATTAGGGCACG-TTCCTCGAATTTCCAAA
*
16639563 CGCAAAATATTGCCTTACTTTGGAAAATTTT
64 CGCAAAATATTACCTTACTTTGGAAAATTTT
16639594 CCTTTTTGAA
Statistics
Matches: 85, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
105 15 0.18
106 28 0.33
107 34 0.40
108 1 0.01
109 7 0.08
ACGTcount: A:0.35, C:0.20, G:0.15, T:0.29
Consensus pattern (107 bp):
GCTATTTGGTCAAACGAAAAATCGAAACCCAACACATTAGGGCACGTTCCTCGAATTTCCAAACG
CAAAATATTACCTTACTTTGGAAAATTTTAAAAGGACACTTG
Found at i:16647077 original size:101 final size:101
Alignment explanation
Indices: 16646902--16647104 Score: 343
Period size: 101 Copynumber: 2.0 Consensus size: 101
16646892 GACTTCACTT
* ** * *
16646902 CCTCTTCGTCCACTCTGTAGCGCTTGCTTTAGTCTGTCCCATTTGTCATGGTATTCATTCCACAC
1 CCTCTTCATCCACTCCATAGCGCTTGCTTCAGTCTGTCCCACTTGTCATGGTATTCATTCCACAC
16646967 ATAATCCAATATGAGCAAAAATCGTTTCCCAACAAA
66 ATAATCCAATATGAGCAAAAATCGTTTCCCAACAAA
* *
16647003 CCTCTTCATCCACTCCATAGCGCTTGCTTCAGTCTGTCCCACTTGTCATGGTATTCATTTCGCAC
1 CCTCTTCATCCACTCCATAGCGCTTGCTTCAGTCTGTCCCACTTGTCATGGTATTCATTCCACAC
16647068 ATAATCCAATATGAGCAAAAATCGTTTCCCAACAAA
66 ATAATCCAATATGAGCAAAAATCGTTTCCCAACAAA
16647104 C
1 C
16647105 TATTCTACTA
Statistics
Matches: 95, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
101 95 1.00
ACGTcount: A:0.26, C:0.30, G:0.12, T:0.32
Consensus pattern (101 bp):
CCTCTTCATCCACTCCATAGCGCTTGCTTCAGTCTGTCCCACTTGTCATGGTATTCATTCCACAC
ATAATCCAATATGAGCAAAAATCGTTTCCCAACAAA
Found at i:16653409 original size:34 final size:35
Alignment explanation
Indices: 16653349--16653415 Score: 91
Period size: 34 Copynumber: 1.9 Consensus size: 35
16653339 CAAACATCAG
*
16653349 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
* * *
16653384 AAAACATTTTCCCG-AAATTATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
16653416 TATTTTACTG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
34 16 0.57
35 12 0.43
ACGTcount: A:0.45, C:0.13, G:0.09, T:0.33
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:16653663 original size:41 final size:41
Alignment explanation
Indices: 16653601--16653688 Score: 142
Period size: 41 Copynumber: 2.2 Consensus size: 41
16653591 AACTCGAATG
* *
16653601 TTCAGTTGTTTGGATGAAAATAGATTTTTAATTAAATAAAT
1 TTCAATTGTTGGGATGAAAATAGATTTTTAATTAAATAAAT
*
16653642 TTCAATTGTTGGGATGAAAATATATTTTTAATTAAATAAAT
1 TTCAATTGTTGGGATGAAAATAGATTTTTAATTAAATAAAT
16653683 TT-AATT
1 TTCAATT
16653689 TGGACTGCCA
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
40 4 0.09
41 40 0.91
ACGTcount: A:0.40, C:0.02, G:0.12, T:0.45
Consensus pattern (41 bp):
TTCAATTGTTGGGATGAAAATAGATTTTTAATTAAATAAAT
Found at i:16653964 original size:28 final size:28
Alignment explanation
Indices: 16653932--16653987 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
16653922 AGGAAAAAGT
16653932 AAGTAGTTTTTAAACATTTTTATATGAA
1 AAGTAGTTTTTAAACATTTTTATATGAA
16653960 AAGTAGTTTTTAAACATTTTTATATGAA
1 AAGTAGTTTTTAAACATTTTTATATGAA
16653988 TAATGTAAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.39, C:0.04, G:0.11, T:0.46
Consensus pattern (28 bp):
AAGTAGTTTTTAAACATTTTTATATGAA
Found at i:16654013 original size:2 final size:2
Alignment explanation
Indices: 16654006--16654031 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
16653996 GAAAATTTTA
16654006 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
16654032 CTTTAAATGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16654771 original size:23 final size:23
Alignment explanation
Indices: 16654744--16654789 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
16654734 CTAATACAAG
16654744 AATTTAACAAAAACACCCCCTCA
1 AATTTAACAAAAACACCCCCTCA
16654767 AATTTAACAAAAACACCCCCTCA
1 AATTTAACAAAAACACCCCCTCA
16654790 GATTAGATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.48, C:0.35, G:0.00, T:0.17
Consensus pattern (23 bp):
AATTTAACAAAAACACCCCCTCA
Found at i:16658130 original size:20 final size:19
Alignment explanation
Indices: 16658101--16658139 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
16658091 AATGACACGA
*
16658101 TCTATCTCATCACAGACAT
1 TCTATCTCATCAAAGACAT
16658120 TCTAGTCTCATCAAAGACAT
1 TCTA-TCTCATCAAAGACAT
16658140 CTGCCCCATG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.33, C:0.28, G:0.08, T:0.31
Consensus pattern (19 bp):
TCTATCTCATCAAAGACAT
Found at i:16666309 original size:111 final size:111
Alignment explanation
Indices: 16666159--16666387 Score: 440
Period size: 111 Copynumber: 2.1 Consensus size: 111
16666149 AATAAATATC
*
16666159 AAATAAGTGGAGTTTAATAAGATTTACAAAACCTTATTCTAAAATAAAATAAAAGAAGTGTAATT
1 AAATAAGTGGAGTTTAATAAGATTTAAAAAACCTTATTCTAAAATAAAATAAAAGAAGTGTAATT
16666224 CTATAGGGATTTTACTTTTATTTTATTTTACCACTGTATTTTATTT
66 CTATAGGGATTTTACTTTTATTTTATTTTACCACTGTATTTTATTT
*
16666270 AAATAAGTGGAGTTTAATAAGATTTAAAAAACTTTATTCTAAAATAAAATAAAAGAAGTGTAATT
1 AAATAAGTGGAGTTTAATAAGATTTAAAAAACCTTATTCTAAAATAAAATAAAAGAAGTGTAATT
16666335 CTATAGGGATTTTACTTTTATTTTATTTTACCACTGTATTTTATTT
66 CTATAGGGATTTTACTTTTATTTTATTTTACCACTGTATTTTATTT
16666381 AAATAAG
1 AAATAAG
16666388 GATTCGGGTC
Statistics
Matches: 116, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
111 116 1.00
ACGTcount: A:0.40, C:0.07, G:0.11, T:0.42
Consensus pattern (111 bp):
AAATAAGTGGAGTTTAATAAGATTTAAAAAACCTTATTCTAAAATAAAATAAAAGAAGTGTAATT
CTATAGGGATTTTACTTTTATTTTATTTTACCACTGTATTTTATTT
Found at i:16676842 original size:17 final size:18
Alignment explanation
Indices: 16676812--16676845 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
16676802 ATTTAAATTG
16676812 CGGTCGCGGTCGCGTTTT
1 CGGTCGCGGTCGCGTTTT
16676830 CGGTCGC-GTCGCGTTT
1 CGGTCGCGGTCGCGTTT
16676846 ATCGCGGTCG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.00, C:0.29, G:0.38, T:0.32
Consensus pattern (18 bp):
CGGTCGCGGTCGCGTTTT
Found at i:16678689 original size:14 final size:14
Alignment explanation
Indices: 16678651--16678694 Score: 56
Period size: 13 Copynumber: 3.2 Consensus size: 14
16678641 CAAAATTTAC
16678651 AATATAATTAAA-T
1 AATATAATTAAATT
16678664 AATATAAATTAAATT
1 AATAT-AATTAAATT
*
16678679 AA-ATAATTTAATT
1 AATATAATTAAATT
16678692 AAT
1 AAT
16678695 TGTTTACCCG
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
13 15 0.56
14 9 0.33
15 3 0.11
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
AATATAATTAAATT
Found at i:16681587 original size:45 final size:45
Alignment explanation
Indices: 16681495--16681587 Score: 116
Period size: 45 Copynumber: 2.1 Consensus size: 45
16681485 TTTTGGGCTC
* ***
16681495 TTTCATTTATAAATATTTGGGTCATGCAAGATTTTTTTTGGGCTT
1 TTTCATTTATAAATATTTGGGTCATGCAAGATTTTCTTTGAAATT
* *
16681540 TTTCATTTATAAATGTTTGGGTCATGCAATATTCTTCTTT-AAATT
1 TTTCATTTATAAATATTTGGGTCATGCAAGATT-TTCTTTGAAATT
16681585 TTT
1 TTT
16681588 GGGCTCTTTC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
45 36 0.88
46 5 0.12
ACGTcount: A:0.24, C:0.10, G:0.14, T:0.53
Consensus pattern (45 bp):
TTTCATTTATAAATATTTGGGTCATGCAAGATTTTCTTTGAAATT
Found at i:16681761 original size:24 final size:24
Alignment explanation
Indices: 16681726--16681801 Score: 91
Period size: 24 Copynumber: 3.2 Consensus size: 24
16681716 GGTACCATTT
*
16681726 CATTGGAAATTTAACTATAAAGTA
1 CATTGCAAATTTAACTATAAAGTA
* * *
16681750 CA-TGTCATATTTAACTATAAATTT
1 CATTG-CAAATTTAACTATAAAGTA
*
16681774 CATTGGAAATTTAACTATAAAGTA
1 CATTGCAAATTTAACTATAAAGTA
16681798 CATT
1 CATT
16681802 TGTATTTACT
Statistics
Matches: 42, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
23 2 0.05
24 38 0.90
25 2 0.05
ACGTcount: A:0.42, C:0.11, G:0.09, T:0.38
Consensus pattern (24 bp):
CATTGCAAATTTAACTATAAAGTA
Found at i:16682025 original size:25 final size:25
Alignment explanation
Indices: 16681993--16682047 Score: 103
Period size: 25 Copynumber: 2.2 Consensus size: 25
16681983 TAGTGGTTAA
16681993 AATG-GACGGTGGCTGCCCCTAATT
1 AATGAGACGGTGGCTGCCCCTAATT
16682017 AATGAGACGGTGGCTGCCCCTAATT
1 AATGAGACGGTGGCTGCCCCTAATT
16682042 AATGAG
1 AATGAG
16682048 TAAAACAAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
24 4 0.13
25 26 0.87
ACGTcount: A:0.25, C:0.22, G:0.29, T:0.24
Consensus pattern (25 bp):
AATGAGACGGTGGCTGCCCCTAATT
Found at i:16688513 original size:91 final size:91
Alignment explanation
Indices: 16687949--16688506 Score: 942
Period size: 91 Copynumber: 6.1 Consensus size: 91
16687939 ATGATTTTAG
* * *
16687949 TAAATTCATATAAGAATATTTATTATTAAGAATTTTATG-AATTATATATCATTATTAAATTATA
1 TAAATTCATATAACAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
16688013 TTTAATATTAATTATTTTAAATTATA
66 TTTAATATTAATTATTTTAAATTATA
*
16688039 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
1 TAAATTCATATAACAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
16688104 TTTAATATTAATTATTTTAAATTATA
66 TTTAATATTAATTATTTTAAATTATA
* *
16688130 TAAATTCATATAAGAAAATTTATTATCAAGAA-TTT-TGAACGAGTATATATCATTATTAAATTA
1 TAAATTCATATAACAAAATTTATTATCAAGAATTTTATGAA--ATTATATATCATTATTAAATTA
16688193 TATTTAATATTAATTATTTTAAATTATA
64 TATTTAATATTAATTATTTTAAATTATA
16688221 TAAATTCATATAACAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
1 TAAATTCATATAACAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
16688286 TTTAATATTAATTATTTTAAATTATA
66 TTTAATATTAATTATTTTAAATTATA
* *
16688312 TAAATTCACATAACAAAGTTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
1 TAAATTCATATAACAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
16688377 TTTAATATTAATTATTTTAAATTATA
66 TTTAATATTAATTATTTTAAATTATA
* * *
16688403 TAAATTCATATAACAAAATTTATTATCAAGAATTTGATGAAGTTATATATTATTATTAAATTATA
1 TAAATTCATATAACAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
* *
16688468 TTTAATAATAATTATATTAAATTATA
66 TTTAATATTAATTATTTTAAATTATA
* *
16688494 CAAATTCAAATAA
1 TAAATTCATATAA
16688507 TTAAATTATA
Statistics
Matches: 447, Mismatches: 16, Indels: 9
0.95 0.03 0.02
Matches are distributed among these distances:
89 4 0.01
90 40 0.09
91 396 0.89
92 3 0.01
93 4 0.01
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (91 bp):
TAAATTCATATAACAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
TTTAATATTAATTATTTTAAATTATA
Found at i:16688540 original size:29 final size:28
Alignment explanation
Indices: 16688504--16688602 Score: 105
Period size: 28 Copynumber: 3.6 Consensus size: 28
16688494 CAAATTCAAA
16688504 TAATTAAATTATATTTAATAATAATTAT
1 TAATTAAATTATATTTAATAATAATTAT
* * * *
16688532 TATTTTAAATTTTATTAAATCATATATT-T
1 TA-ATTAAATTATATTTAATAATA-ATTAT
*
16688561 TAATTAAAATATATTTAATAATAATTAT
1 TAATTAAATTATATTTAATAATAATTAT
*
16688589 T--TCAAATTATATTT
1 TAATTAAATTATATTT
16688603 TATACTATCA
Statistics
Matches: 57, Mismatches: 11, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
26 11 0.19
27 3 0.05
28 20 0.35
29 20 0.35
30 3 0.05
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (28 bp):
TAATTAAATTATATTTAATAATAATTAT
Found at i:16688643 original size:120 final size:120
Alignment explanation
Indices: 16688539--16688834 Score: 513
Period size: 120 Copynumber: 2.5 Consensus size: 120
16688529 TATTATTTTA
16688539 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTAT-TTCAAATTATATTT
1 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTATCTT-AAATTATATTT
*
16688603 TATACTATCATATATTATGATTTTAGGAAATTCATATAATAATATTGATTATTAAG
65 TATACTATCATATATTATGATTTGAGGAAATTCATATAATAATATTGATTATTAAG
16688659 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTATCTTAAATTATATTTT
1 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTATCTTAAATTATATTTT
* * * *
16688724 ATAGTATCATATATTATGATTTGAGTAAATTCATATAACAATATTGATTATTAAT
66 ATACTATCATATATTATGATTTGAGGAAATTCATATAATAATATTGATTATTAAG
* *
16688779 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAA
1 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTATCTTAAA
16688835 ATATGATTAA
Statistics
Matches: 168, Mismatches: 7, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
120 166 0.99
121 2 0.01
ACGTcount: A:0.44, C:0.03, G:0.04, T:0.49
Consensus pattern (120 bp):
AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTATCTTAAATTATATTTT
ATACTATCATATATTATGATTTGAGGAAATTCATATAATAATATTGATTATTAAG
Found at i:16688674 original size:61 final size:60
Alignment explanation
Indices: 16688609--16688799 Score: 180
Period size: 61 Copynumber: 3.2 Consensus size: 60
16688599 ATTTTATACT
*
16688609 ATCATATATTATGATTTTAGGAAATTCATATAATAATATTGATTATTAAGAATTTTATTAA
1 ATCATATATTATGATTTTA-GAAATTCATATAATAATATTGATTATTAATAATTTTATTAA
* * * *
16688670 ATCATATATT-TTA-ATTA-AAATAT-ATTTAATAATAATT-ATCT-TAAATTATATTTTA-TAG
1 ATCATATATTATGATTTTAGAAAT-TCATATAATAAT-ATTGAT-TATTAA-TA-ATTTTATTA-
*
16688728 T
60 A
* *
16688729 ATCATATATTATGATTTGAGTAAATTCATATAACAATATTGATTATTAATAATTTTATTAA
1 ATCATATATTATGATTTTAG-AAATTCATATAATAATATTGATTATTAATAATTTTATTAA
*
16688790 ATTATATATT
1 ATCATATATT
16688800 TTAATTAAAA
Statistics
Matches: 102, Mismatches: 14, Indels: 28
0.71 0.10 0.19
Matches are distributed among these distances:
57 18 0.18
58 8 0.08
59 19 0.19
60 4 0.04
61 27 0.26
62 9 0.09
63 17 0.17
ACGTcount: A:0.43, C:0.04, G:0.05, T:0.48
Consensus pattern (60 bp):
ATCATATATTATGATTTTAGAAATTCATATAATAATATTGATTATTAATAATTTTATTAA
Found at i:16688808 original size:18 final size:17
Alignment explanation
Indices: 16688780--16688814 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
16688770 ATTATTAATA
*
16688780 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
16688797 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
16688815 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:16689068 original size:16 final size:16
Alignment explanation
Indices: 16689047--16689079 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
16689037 TTGATTTGCT
16689047 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
16689063 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
16689079 A
1 A
16689080 ATACAGCGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.21, C:0.36, G:0.06, T:0.36
Consensus pattern (16 bp):
ATTACGCCTCTATTCC
Found at i:16690823 original size:11 final size:11
Alignment explanation
Indices: 16690802--16690862 Score: 54
Period size: 11 Copynumber: 5.5 Consensus size: 11
16690792 ACTAATCCTA
16690802 TCTCAAATTTCC
1 TCTC-AATTTCC
*
16690814 TCTCAATTTCT
1 TCTCAATTTCC
*
16690825 TCT-AATTTTTC
1 TCTCAA-TTTCC
*
16690836 TCTCAATTTGC
1 TCTCAATTTCC
*
16690847 TCTCAAATTCC
1 TCTCAATTTCC
16690858 T-TCAA
1 TCTCAA
16690863 AATTTCTCTT
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
10 6 0.15
11 29 0.71
12 6 0.15
ACGTcount: A:0.23, C:0.28, G:0.02, T:0.48
Consensus pattern (11 bp):
TCTCAATTTCC
Found at i:16690900 original size:51 final size:51
Alignment explanation
Indices: 16690838--16690935 Score: 153
Period size: 51 Copynumber: 1.9 Consensus size: 51
16690828 AATTTTTCTC
16690838 TCAATTTGCTCTCAAATTCCT-TCAAAATTTCTCTTAAATCCATATTTATTT
1 TCAATTTGCTCTCAAATTCCTCT-AAAATTTCTCTTAAATCCATATTTATTT
* * *
16690889 TCAATTTGCTCTCAAGTTCCTCTTAAATTTCTCTTAAATCCCTATTT
1 TCAATTTGCTCTCAAATTCCTCTAAAATTTCTCTTAAATCCATATTT
16690936 TTAAATAATT
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
51 42 0.98
52 1 0.02
ACGTcount: A:0.27, C:0.23, G:0.03, T:0.47
Consensus pattern (51 bp):
TCAATTTGCTCTCAAATTCCTCTAAAATTTCTCTTAAATCCATATTTATTT
Found at i:16693334 original size:28 final size:28
Alignment explanation
Indices: 16693293--16693419 Score: 160
Period size: 28 Copynumber: 4.8 Consensus size: 28
16693283 AAACCTTAAA
*
16693293 CCCTTAACCTAAAAACCCTAACCCTAA-
1 CCCTTAACCTAAAAACCCTAACACTAAT
* * * *
16693320 CCATTAACTTTAAAA--CT----CTAAA
1 CCCTTAACCTAAAAACCCTAACACTAAT
16693342 CCCTTAACCTAAAAACCCTAACACTAAT
1 CCCTTAACCTAAAAACCCTAACACTAAT
16693370 CCCTTAACCTAAAAACCCTAACACTAAT
1 CCCTTAACCTAAAAACCCTAACACTAAT
16693398 CCCTTAACCTAAAAACCCTAAC
1 CCCTTAACCTAAAAACCCTAAC
16693420 CATTAACTTT
Statistics
Matches: 86, Mismatches: 7, Indels: 13
0.81 0.07 0.12
Matches are distributed among these distances:
21 4 0.05
22 12 0.14
24 2 0.02
25 2 0.02
27 12 0.14
28 54 0.63
ACGTcount: A:0.43, C:0.35, G:0.00, T:0.22
Consensus pattern (28 bp):
CCCTTAACCTAAAAACCCTAACACTAAT
Found at i:16693359 original size:43 final size:43
Alignment explanation
Indices: 16693283--16694744 Score: 1382
Period size: 43 Copynumber: 33.5 Consensus size: 43
16693273 TTTAATTGAC
* *
16693283 AAACCTTAAACCCTTAACCTAAAAACCCTAACCCTAACCATTAACTTTA
1 AAACCCTAAACCCTTAACCTAAAAACCCTAA--C---CC-TTAACTTAA
* *
16693332 AAACTCTAAACCCTTAACCTAAAAACCCTAACACTAATCCCTTAACCTAA
1 AAACCCTAAACCCTTAACCTAAAAA--C---C-CTAA-CCCTTAACTTAA
* *
16693382 AAACCCTAACACTAATCCCTTAACCTAAAAACCCTAACCATTAACTTTA
1 AAACCCT---A--AA-CCCTTAACCTAAAAACCCTAACCCTTAACTTAA
* * *
16693431 AAACCCTAACCCCTTAACCTAAAAACCCTAACTCTTAACTTTA
1 AAACCCTAAACCCTTAACCTAAAAACCCTAACCCTTAACTTAA
** * *
16693474 AAACCCTAAACTTTTAACCTAAAAAACCTTAAACCCTTAAATTAA
1 AAACCCTAAACCCTTAACCT-AAAAACCCT-AACCCTTAACTTAA
* ** * * *
16693519 AAACACT-AACCCTTAATTTCAAAACCCTAAACCTTTAAATTAA
1 AAACCCTAAACCCTTAACCTAAAAACCCT-AACCCTTAACTTAA
* * * **
16693562 AAACCCT-AACCTTTAATCTGAAAACCCTAACCCTTAACTTTT
1 AAACCCTAAACCCTTAACCTAAAAACCCTAACCCTTAACTTAA
* *
16693604 AAACCCTAGACCCTTAA-CTTAAAACCCTTAAACCCTTAACTTAA
1 AAACCCTAAACCCTTAACCTAAAAACCC-T-AACCCTTAACTTAA
* * ** * * * *
16693648 AAACTCT-AATCCTTAAATTAATAACCGTAAACACTTAACCTAA
1 AAACCCTAAACCCTTAACCTAAAAACCCT-AACCCTTAACTTAA
* *
16693691 AAACCCT-AACCATTAACCTAAAAACCCTAGACCCTTAACATAA
1 AAACCCTAAACCCTTAACCTAAAAACCCTA-ACCCTTAACTTAA
* * * *
16693734 AAACCATAAACCCTTAACTTAAAAACCATAACCCTTAAATT-A
1 AAACCCTAAACCCTTAACCTAAAAACCCTAACCCTTAACTTAA
*
16693776 AAACCCTAAACCCTTAACCTAAAAACCCTAACCCTTAACCTAA
1 AAACCCTAAACCCTTAACCTAAAAACCCTAACCCTTAACTTAA
* *
16693819 AAACCCTAAA-CCTTAACTTAAAAACACTAGACCCTTAACTTAA
1 AAACCCTAAACCCTTAACCTAAAAACCCTA-ACCCTTAACTTAA
*
16693862 AAACCCTAAACCCTTAACCTAAAAACCCTAACCCTTAACCTAA
1 AAACCCTAAACCCTTAACCTAAAAACCCTAACCCTTAACTTAA
* * *
16693905 AAACTCTAAACCCTTAACTTAAAAACCATAAACCCTTAACTT-A
1 AAACCCTAAACCCTTAACCTAAAAACCCT-AACCCTTAACTTAA
* ** * * *
16693948 AAGCCCT-AACCCTTAAATTAAAAACCTTAAACCCTAAACCTAA
1 AAACCCTAAACCCTTAACCTAAAAACCCT-AACCCTTAACTTAA
* * * * *
16693991 AAACCTTTAAACCCTTAACTTAAAAACACTAATCCTTAAATTAA
1 AAACC-CTAAACCCTTAACCTAAAAACCCTAACCCTTAACTTAA
* * * *
16694035 TAACCCTAAACACTTAACCTAAAAACCCTAACCCTTAACCTGA
1 AAACCCTAAACCCTTAACCTAAAAACCCTAACCCTTAACTTAA
* * *
16694078 AAACCCTAAA-CCTTAACTTTAAAACACTAAACCCTTAACTTAA
1 AAACCCTAAACCCTTAACCTAAAAACCCT-AACCCTTAACTTAA
* * * *
16694121 AAACCCTAAATCCTTAACTTAAAAACCATAACCCTTAAATT-A
1 AAACCCTAAACCCTTAACCTAAAAACCCTAACCCTTAACTTAA
*
16694163 AAACCCTAAACCCTTAACCTAAAAACCCTAACCCTTAACCTAA
1 AAACCCTAAACCCTTAACCTAAAAACCCTAACCCTTAACTTAA
* *
16694206 AAACCCTAAA-CCTTAACTTAAAAACACTAACCCTTAACTTAA
1 AAACCCTAAACCCTTAACCTAAAAACCCTAACCCTTAACTTAA
* *
16694248 AAACCCTAAATCCTTAACCTAAAAACCCTAACCCTTAACCTAA
1 AAACCCTAAACCCTTAACCTAAAAACCCTAACCCTTAACTTAA
* *
16694291 AAACCCTAAACCCTTAACTTAAAAACCATAAACCCTTAACTT-A
1 AAACCCTAAACCCTTAACCTAAAAACCCT-AACCCTTAACTTAA
* ** * * *
16694334 AAGCCCT-AACCCTTAAATTAAAAACCTTAAACCCTAAACCTAA
1 AAACCCTAAACCCTTAACCTAAAAACCCT-AACCCTTAACTTAA
* * * * *
16694377 AAACCTTTAAACCCTTAACTTAAAAACACTAATCCTTAAATTAA
1 AAACC-CTAAACCCTTAACCTAAAAACCCTAACCCTTAACTTAA
* * * *
16694421 TAACCCTAAACACTTAACCTAAAAACCCTAACCCTTAACCTGA
1 AAACCCTAAACCCTTAACCTAAAAACCCTAACCCTTAACTTAA
* * *
16694464 AAACCCTAAA-CCTTAACTTTAAAACACTAAACCCTTAACTTAA
1 AAACCCTAAACCCTTAACCTAAAAACCCT-AACCCTTAACTTAA
** * *
16694507 AAACCCT-AACCCTTAAATTAAAAACACTAAAACCCTTAACCT-A
1 AAACCCTAAACCCTTAACCTAAAAACCCT--AACCCTTAACTTAA
** * *
16694550 AAACCCTAAA-CCTTAATTTAGAAACCCTAAAACCTTAACTTAA
1 AAACCCTAAACCCTTAACCTAAAAACCCT-AACCCTTAACTTAA
* ** * *
16694593 AAACCAT-AACCCTTAAATTAAAAACCATAAACCCTTAACCTAA
1 AAACCCTAAACCCTTAACCTAAAAACCCT-AACCCTTAACTTAA
* * *
16694636 AAACCCT-AACCTTTAACCTAAAAACCTTAAACCCTTAACTTTA
1 AAACCCTAAACCCTTAACCTAAAAACCCT-AACCCTTAACTTAA
* * *
16694679 AAACCCTAGACCCTTAACTTAAAAACCATAAACCCTTAACTTAA
1 AAACCCTAAACCCTTAACCTAAAAACCCT-AACCCTTAACTTAA
*
16694723 AAACCCT-AACCCTTAACTTAAA
1 AAACCCTAAACCCTTAACCTAAA
16694745 TATAATTTGA
Statistics
Matches: 1185, Mismatches: 186, Indels: 90
0.81 0.13 0.06
Matches are distributed among these distances:
42 260 0.22
43 590 0.50
44 196 0.17
45 53 0.04
46 1 0.00
49 39 0.03
50 17 0.01
51 4 0.00
53 1 0.00
54 3 0.00
55 6 0.01
56 15 0.01
ACGTcount: A:0.45, C:0.30, G:0.01, T:0.24
Consensus pattern (43 bp):
AAACCCTAAACCCTTAACCTAAAAACCCTAACCCTTAACTTAA
Found at i:16693377 original size:14 final size:13
Alignment explanation
Indices: 16693337--16693409 Score: 51
Period size: 13 Copynumber: 5.3 Consensus size: 13
16693327 CTTTAAAACT
*
16693337 CTAAACCCTTAAC
1 CTAATCCCTTAAC
*
16693350 CTAAAAACCC-TAAC
1 CT--AATCCCTTAAC
16693364 ACTAATCCCTTAAC
1 -CTAATCCCTTAAC
*
16693378 CTAAAAACCC-TAAC
1 CT--AATCCCTTAAC
16693392 ACTAATCCCTTAAC
1 -CTAATCCCTTAAC
16693406 CTAA
1 CTAA
16693410 AAACCCTAAC
Statistics
Matches: 49, Mismatches: 3, Indels: 16
0.72 0.04 0.24
Matches are distributed among these distances:
13 18 0.37
14 16 0.33
15 15 0.31
ACGTcount: A:0.42, C:0.36, G:0.00, T:0.22
Consensus pattern (13 bp):
CTAATCCCTTAAC
Found at i:16693419 original size:14 final size:15
Alignment explanation
Indices: 16693339--16693420 Score: 79
Period size: 14 Copynumber: 5.8 Consensus size: 15
16693329 TTAAAACTCT
16693339 AAACCCTTAACCTAA
1 AAACCCTTAACCTAA
16693354 AAACCC-TAACACT--
1 AAACCCTTAAC-CTAA
*
16693367 AATCCCTTAACCTAA
1 AAACCCTTAACCTAA
16693382 AAACCC-TAACACT--
1 AAACCCTTAAC-CTAA
*
16693395 AATCCCTTAACCTAA
1 AAACCCTTAACCTAA
16693410 AAACCC-TAACC
1 AAACCCTTAACC
16693421 ATTAACTTTA
Statistics
Matches: 55, Mismatches: 4, Indels: 17
0.72 0.05 0.22
Matches are distributed among these distances:
13 14 0.25
14 21 0.38
15 20 0.36
ACGTcount: A:0.44, C:0.37, G:0.00, T:0.20
Consensus pattern (15 bp):
AAACCCTTAACCTAA
Found at i:16693432 original size:22 final size:21
Alignment explanation
Indices: 16693393--16694744 Score: 1377
Period size: 21 Copynumber: 62.8 Consensus size: 21
16693383 AACCCTAACA
*
16693393 CTAATCCCTTAACCTAAAAACC
1 CTAA-CCCTTAACTTAAAAACC
* *
16693415 CTAACCATTAACTTTAAAACC
1 CTAACCCTTAACTTAAAAACC
*
16693436 CTAACCCCTTAACCTAAAAACC
1 CTAA-CCCTTAACTTAAAAACC
* *
16693458 CTAACTCTTAACTTTAAAACC
1 CTAACCCTTAACTTAAAAACC
** *
16693479 CTAAACTTTTAACCTAAAAAACC
1 CT-AACCCTTAA-CTTAAAAACC
* * *
16693502 TTAAACCCTTAAATTAAAAACA
1 CT-AACCCTTAACTTAAAAACC
* *
16693524 CTAACCCTTAATTTCAAAACC
1 CTAACCCTTAACTTAAAAACC
* *
16693545 CTAAACCTTTAAATTAAAAACC
1 CT-AACCCTTAACTTAAAAACC
* *
16693567 CTAACCTTTAA-TCTGAAAACC
1 CTAACCCTTAACT-TAAAAACC
**
16693588 CTAACCCTTAACTTTTAAACC
1 CTAACCCTTAACTTAAAAACC
16693609 CTAGACCCTTAACTT-AAAACC
1 CTA-ACCCTTAACTTAAAAACC
*
16693630 CTTAAACCCTTAACTTAAAAACT
1 C-T-AACCCTTAACTTAAAAACC
* * *
16693653 CTAATCCTTAAATTAATAACC
1 CTAACCCTTAACTTAAAAACC
* * *
16693674 GTAAACACTTAACCTAAAAACC
1 CT-AACCCTTAACTTAAAAACC
* *
16693696 CTAACCATTAACCTAAAAACC
1 CTAACCCTTAACTTAAAAACC
*
16693717 CTAGACCCTTAACATAAAAACC
1 CTA-ACCCTTAACTTAAAAACC
*
16693739 ATAAACCCTTAACTTAAAAACC
1 CT-AACCCTTAACTTAAAAACC
* *
16693761 ATAACCCTTAAATT-AAAACC
1 CTAACCCTTAACTTAAAAACC
*
16693781 CTAAACCCTTAACCTAAAAACC
1 CT-AACCCTTAACTTAAAAACC
*
16693803 CTAACCCTTAACCTAAAAACC
1 CTAACCCTTAACTTAAAAACC
* *
16693824 CTAAACCTTAACTTAAAAACA
1 CTAACCCTTAACTTAAAAACC
16693845 CTAGACCCTTAACTTAAAAACC
1 CTA-ACCCTTAACTTAAAAACC
*
16693867 CTAAACCCTTAACCTAAAAACC
1 CT-AACCCTTAACTTAAAAACC
* *
16693889 CTAACCCTTAACCTAAAAACT
1 CTAACCCTTAACTTAAAAACC
16693910 CTAAACCCTTAACTTAAAAACC
1 CT-AACCCTTAACTTAAAAACC
* *
16693932 ATAAACCCTTAACTT-AAAGCC
1 CT-AACCCTTAACTTAAAAACC
*
16693953 CTAACCCTTAAATTAAAAACC
1 CTAACCCTTAACTTAAAAACC
* * *
16693974 TTAAACCCTAAACCTAAAAACC
1 CT-AACCCTTAACTTAAAAACC
* *
16693996 TTTAAACCCTTAACTTAAAAACA
1 -CT-AACCCTTAACTTAAAAACC
* * *
16694019 CTAATCCTTAAATTAATAACC
1 CTAACCCTTAACTTAAAAACC
* *
16694040 CTAAACACTTAACCTAAAAACC
1 CT-AACCCTTAACTTAAAAACC
* *
16694062 CTAACCCTTAACCTGAAAACC
1 CTAACCCTTAACTTAAAAACC
* * *
16694083 CTAAACCTTAACTTTAAAACA
1 CTAACCCTTAACTTAAAAACC
16694104 CTAAACCCTTAACTTAAAAACC
1 CT-AACCCTTAACTTAAAAACC
*
16694126 CTAAATCCTTAACTTAAAAACC
1 CT-AACCCTTAACTTAAAAACC
* *
16694148 ATAACCCTTAAATT-AAAACC
1 CTAACCCTTAACTTAAAAACC
*
16694168 CTAAACCCTTAACCTAAAAACC
1 CT-AACCCTTAACTTAAAAACC
*
16694190 CTAACCCTTAACCTAAAAACC
1 CTAACCCTTAACTTAAAAACC
* *
16694211 CTAAACCTTAACTTAAAAACA
1 CTAACCCTTAACTTAAAAACC
16694232 CTAACCCTTAACTTAAAAACC
1 CTAACCCTTAACTTAAAAACC
* *
16694253 CTAAATCCTTAACCTAAAAACC
1 CT-AACCCTTAACTTAAAAACC
*
16694275 CTAACCCTTAACCTAAAAACC
1 CTAACCCTTAACTTAAAAACC
16694296 CTAAACCCTTAACTTAAAAACC
1 CT-AACCCTTAACTTAAAAACC
* *
16694318 ATAAACCCTTAACTT-AAAGCC
1 CT-AACCCTTAACTTAAAAACC
*
16694339 CTAACCCTTAAATTAAAAACC
1 CTAACCCTTAACTTAAAAACC
* * *
16694360 TTAAACCCTAAACCTAAAAACC
1 CT-AACCCTTAACTTAAAAACC
* *
16694382 TTTAAACCCTTAACTTAAAAACA
1 -CT-AACCCTTAACTTAAAAACC
* * *
16694405 CTAATCCTTAAATTAATAACC
1 CTAACCCTTAACTTAAAAACC
* *
16694426 CTAAACACTTAACCTAAAAACC
1 CT-AACCCTTAACTTAAAAACC
* *
16694448 CTAACCCTTAACCTGAAAACC
1 CTAACCCTTAACTTAAAAACC
* * *
16694469 CTAAACCTTAACTTTAAAACA
1 CTAACCCTTAACTTAAAAACC
16694490 CTAAACCCTTAACTTAAAAACC
1 CT-AACCCTTAACTTAAAAACC
* *
16694512 CTAACCCTTAAATTAAAAACA
1 CTAACCCTTAACTTAAAAACC
*
16694533 CTAAAACCCTTAACCT-AAAACC
1 CT--AACCCTTAACTTAAAAACC
* * *
16694555 CTAAACCTTAATTTAGAAACC
1 CTAACCCTTAACTTAAAAACC
*
16694576 CTAAAACCTTAACTTAAAAACC
1 CT-AACCCTTAACTTAAAAACC
* *
16694598 ATAACCCTTAAATTAAAAACC
1 CTAACCCTTAACTTAAAAACC
* *
16694619 ATAAACCCTTAACCTAAAAACC
1 CT-AACCCTTAACTTAAAAACC
* *
16694641 CTAACCTTTAACCTAAAAACC
1 CTAACCCTTAACTTAAAAACC
* *
16694662 TTAAACCCTTAACTTTAAAACC
1 CT-AACCCTTAACTTAAAAACC
16694684 CTAGACCCTTAACTTAAAAACC
1 CTA-ACCCTTAACTTAAAAACC
*
16694706 ATAAACCCTTAACTTAAAAACC
1 CT-AACCCTTAACTTAAAAACC
16694728 CTAACCCTTAACTTAAA
1 CTAACCCTTAACTTAAA
16694745 TATAATTTGA
Statistics
Matches: 1125, Mismatches: 165, Indels: 81
0.82 0.12 0.06
Matches are distributed among these distances:
20 46 0.04
21 518 0.46
22 486 0.43
23 75 0.07
ACGTcount: A:0.45, C:0.30, G:0.01, T:0.24
Consensus pattern (21 bp):
CTAACCCTTAACTTAAAAACC
Found at i:16694550 original size:14 final size:14
Alignment explanation
Indices: 16694528--16694562 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
16694518 CTTAAATTAA
16694528 AAACACTAAAACCCT
1 AAAC-CTAAAACCCT
*
16694543 TAACCTAAAACCCT
1 AAACCTAAAACCCT
16694557 AAACCT
1 AAACCT
16694563 TAATTTAGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
14 15 0.83
15 3 0.17
ACGTcount: A:0.49, C:0.34, G:0.00, T:0.17
Consensus pattern (14 bp):
AAACCTAAAACCCT
Found at i:16698409 original size:251 final size:250
Alignment explanation
Indices: 16697926--16698478 Score: 734
Period size: 251 Copynumber: 2.2 Consensus size: 250
16697916 GTTACTATAA
* * * *
16697926 CAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGCTAGAAGCGA
1 CAAAAGCGCGTCCACGTGGGCGCGACTTCACAAATTCTTCTCATAAATCATCATGCTAGAAGCCA
* * * *
16697991 TTTTATACTATTTGTTCAGAAACGTCAAGTCGAAATTATTTTTCCAAGACCAACTGTAGCAAAAG
66 TTTTAAACTATTTGCTCAAAAACGTCAACTCGAAATTATTTTTCCAAGACCAACTGTAGCAAAAG
* * * *
16698056 TGCGTCCACGATGGCGCGATTTCACAAATTCTTCTCAAATAGCATGCTACTTGCAGCGTTGTTTT
131 CGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTACTTGAAGCGTTGTTTT
* * * * *
16698121 ATACCATTTGCTCAGAAATGTCAACTCAAAATTATTTTTTCAGGTCCTACTGTAG
196 AAACCATTTACTCAGAAACGTCAACTCAAAATTATTTTTCCAGGACCTACTGTAG
* * * *
16698176 CAAAAGCGCGTCCACGTGGACGCGACTTCACAAATTCTTCTTATAAATCATCATGTTTG-AGCCA
1 CAAAAGCGCGTCCACGTGGGCGCGACTTCACAAATTCTTCTCATAAATCATCATGCTAGAAGCCA
* *
16698240 TTTTTTAAACTATTTGCTCAAAAACGTCAACTCGAAATTATTTCTTCCAGGACCAACTGTAGTAA
66 --TTTTAAACTATTTGCTCAAAAACGTCAACTCGAAATTATTT-TTCCAAGACCAACTGTAGCAA
*
16698305 AAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCACAA-AGCATCCTGCTTGAAGCGTT-
128 AAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCA-AATAGCATCCTACTTGAAGCGTTG
* * *
16698368 TTTTAAACTATTTACTCAGAAACGTCAAGTCGAAATTATTTTTCCAGGACCTACTGTAG
192 TTTTAAACCATTTACTCAGAAACGTCAACTCAAAATTATTTTTCCAGGACCTACTGTAG
* ** * * * * *
16698427 CAAAAGCACGTATATGTGGGCGCAACTTCAAAAATCCTTCTGATAAATCATC
1 CAAAAGCGCGTCCACGTGGGCGCGACTTCACAAATTCTTCTCATAAATCATC
16698479 CTACTTTGAT
Statistics
Matches: 263, Mismatches: 36, Indels: 7
0.86 0.12 0.02
Matches are distributed among these distances:
249 4 0.02
250 52 0.20
251 131 0.50
252 74 0.28
253 2 0.01
ACGTcount: A:0.30, C:0.23, G:0.16, T:0.30
Consensus pattern (250 bp):
CAAAAGCGCGTCCACGTGGGCGCGACTTCACAAATTCTTCTCATAAATCATCATGCTAGAAGCCA
TTTTAAACTATTTGCTCAAAAACGTCAACTCGAAATTATTTTTCCAAGACCAACTGTAGCAAAAG
CGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTACTTGAAGCGTTGTTTT
AAACCATTTACTCAGAAACGTCAACTCAAAATTATTTTTCCAGGACCTACTGTAG
Found at i:16698479 original size:125 final size:125
Alignment explanation
Indices: 16697926--16698480 Score: 668
Period size: 126 Copynumber: 4.4 Consensus size: 125
16697916 GTTACTATAA
*
16697926 CAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGCTAGAAGCG-
1 CAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGCTTGAAGCGT
* * * * *
16697990 ATTTTATACTATTTGTTCAGAAACGTCAAGTCGAAATTATTTTTCCAAGACCAACTGTAG
66 TTTTTAAACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTCCAGGACCAACTGTAG
* * * *
16698050 CAAAAGTGCGTCCACGAT-GGCGCGATTTCACAAATTCTTCTCA-AATAGCATGCTACTTGCAGC
1 CAAAAGCGCGTCCACG-TGGGCGCGATTTCACAAATTCTTCTCATAA-AGCATCCTGCTTGAAGC
* * * * * * *
16698113 GTTGTTTTATACCATTTGCTCAGAAATGTCAACTCAAAATTATTTTTTCAGGTCCTACTGTAG
64 GTT-TTTTAAACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTCCAGGACCAACTGTAG
* * * * * * *
16698176 CAAAAGCGCGTCCACGTGGACGCGACTTCACAAATTCTTCTTATAAATCATCATGTTTG-AGCCA
1 CAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGCTTGAAG-CG
*
16698240 TTTTTTAAACTATTTGCTCAAAAACGTCAACTCGAAATTATTTCTTCCAGGACCAACTGTAG
65 TTTTTTAAACTATTTGCTCAGAAACGTCAACTCGAAATTATTT-TTCCAGGACCAACTGTAG
* * *
16698302 TAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCACAAAGCATCCTGCTTGAAGCGT
1 CAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGCTTGAAGCGT
* * *
16698367 TTTTTAAACTATTTACTCAGAAACGTCAAGTCGAAATTATTTTTCCAGGACCTACTGTAG
66 TTTTTAAACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTCCAGGACCAACTGTAG
* ** * * * * * * *
16698427 CAAAAGCACGTATATGTGGGCGCAACTTCAAAAATCCTTCTGATAAATCATCCT
1 CAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCT
16698481 ACTTTGATTT
Statistics
Matches: 362, Mismatches: 60, Indels: 17
0.82 0.14 0.04
Matches are distributed among these distances:
123 2 0.01
124 54 0.15
125 98 0.27
126 204 0.56
127 4 0.01
ACGTcount: A:0.30, C:0.23, G:0.16, T:0.30
Consensus pattern (125 bp):
CAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGCTTGAAGCGT
TTTTTAAACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTCCAGGACCAACTGTAG
Found at i:16699028 original size:45 final size:45
Alignment explanation
Indices: 16698973--16699061 Score: 115
Period size: 45 Copynumber: 2.0 Consensus size: 45
16698963 ATACACAAAC
* * *
16698973 AAAGACAATAATAAGAGTACAAATAAAAATATGGGGAACAATAAT
1 AAAGACAATAATAACAATACAAATAAAAATATGGAGAACAATAAT
* * * *
16699018 AAAGAGAATAATAACAATATAAATAATAATATGGAGAATAATAA
1 AAAGACAATAATAACAATACAAATAAAAATATGGAGAACAATAA
16699062 GAGTGATATA
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
45 37 1.00
ACGTcount: A:0.62, C:0.04, G:0.13, T:0.20
Consensus pattern (45 bp):
AAAGACAATAATAACAATACAAATAAAAATATGGAGAACAATAAT
Found at i:16700662 original size:8 final size:9
Alignment explanation
Indices: 16700644--16700704 Score: 50
Period size: 9 Copynumber: 6.4 Consensus size: 9
16700634 AAAATATTTT
16700644 AAAATTAAA
1 AAAATTAAA
16700653 AAAATTAAA
1 AAAATTAAA
*
16700662 AAGTATTTTAAA
1 AA--A-ATTAAA
**
16700674 AAAATTTTA
1 AAAATTAAA
*
16700683 AAATTTAAA
1 AAAATTAAA
*
16700692 AAATTTAAA
1 AAAATTAAA
16700701 AAAA
1 AAAA
16700705 GTATTTTAAA
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
9 32 0.78
10 1 0.02
11 1 0.02
12 7 0.17
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (9 bp):
AAAATTAAA
Found at i:16700664 original size:38 final size:39
Alignment explanation
Indices: 16700595--16700716 Score: 149
Period size: 38 Copynumber: 3.0 Consensus size: 39
16700585 ACCAAAAATT
16700595 TATTTTAAAAATTAAAACAAAAATTAAAAAAGTATTTTTAAAA
1 TATTTT-AAAATT--AA-AAAAATTAAAAAAGTATTTTTAAAA
*
16700638 TATTTTAAAATTAAAAAAATT-AAAAAGTATTTTAAAAA
1 TATTTTAAAATTAAAAAAATTAAAAAAGTATTTTTAAAA
* *
16700676 AATTTTAAAATTTAAAAAATTTAAAAAAAGTA-TTTTAAAA
1 TATTTTAAAA-TTAAAAAAATT-AAAAAAGTATTTTTAAAA
16700716 T
1 T
16700717 TGAAAAAATA
Statistics
Matches: 71, Mismatches: 5, Indels: 9
0.84 0.06 0.11
Matches are distributed among these distances:
38 25 0.35
39 17 0.24
40 9 0.13
41 8 0.11
42 6 0.08
43 6 0.08
ACGTcount: A:0.60, C:0.01, G:0.02, T:0.37
Consensus pattern (39 bp):
TATTTTAAAATTAAAAAAATTAAAAAAGTATTTTTAAAA
Found at i:16700686 original size:29 final size:28
Alignment explanation
Indices: 16700653--16700725 Score: 85
Period size: 30 Copynumber: 2.5 Consensus size: 28
16700643 TAAAATTAAA
*
16700653 AAAATTAAAAAGTATTTTAAAAAA-ATTTT
1 AAAATTAAAAA--ATTTAAAAAAAGATTTT
16700682 AAAATTTAAAAAATTTAAAAAAAGTATTTT
1 AAAA-TTAAAAAATTTAAAAAAAG-ATTTT
16700712 AAAATTGAAAAAAT
1 AAAATT-AAAAAAT
16700726 AAAAAATAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
28 10 0.26
29 6 0.15
30 23 0.59
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (28 bp):
AAAATTAAAAAATTTAAAAAAAGATTTT
Found at i:16700691 original size:39 final size:39
Alignment explanation
Indices: 16700613--16700715 Score: 154
Period size: 38 Copynumber: 2.6 Consensus size: 39
16700603 AAATTAAAAC
* *
16700613 AAAAATTAAAAAAGTATTTTTAAAATATTTTAAAATTAA
1 AAAAATTAAAAAAGTATTTTAAAAAAATTTTAAAATTAA
16700652 AAAAATT-AAAAAGTATTTTAAAAAAATTTTAAAATTTAA
1 AAAAATTAAAAAAGTATTTTAAAAAAATTTTAAAA-TTAA
*
16700691 AAAATTTAAAAAAAGTATTTTAAAA
1 AAAAATT-AAAAAAGTATTTTAAAA
16700716 TTGAAAAAAT
Statistics
Matches: 58, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
38 25 0.43
39 17 0.29
41 16 0.28
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (39 bp):
AAAAATTAAAAAAGTATTTTAAAAAAATTTTAAAATTAA
Found at i:16700717 original size:38 final size:36
Alignment explanation
Indices: 16700613--16700745 Score: 128
Period size: 38 Copynumber: 3.5 Consensus size: 36
16700603 AAATTAAAAC
16700613 AAAAATTAAAAAAGTATTTTTAAAATATTTTAAAATTAA
1 AAAAATTAAAAAAGTA-TTTTAAAA-ATTTTAAAATT-A
16700652 AAAAATT-AAAAAGTATTTTAAAAAAATTTTAAAATTTA
1 AAAAATTAAAAAAGTATTTT--AAAAATTTTAAAA-TTA
** *
16700690 AAAAATTTAAAAAAAGTATTTT-AAAATTGAAAAAATA
1 AAAAA-TT-AAAAAAGTATTTTAAAAATTTTAAAATTA
*
16700727 AAAAA-TAATAAAAATATTT
1 AAAAATTAA-AAAAGTATTT
16700746 ATTATATTCG
Statistics
Matches: 83, Mismatches: 4, Indels: 18
0.79 0.04 0.17
Matches are distributed among these distances:
34 2 0.02
35 10 0.12
37 11 0.13
38 33 0.40
39 15 0.18
41 12 0.14
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (36 bp):
AAAAATTAAAAAAGTATTTTAAAAATTTTAAAATTA
Found at i:16703004 original size:20 final size:20
Alignment explanation
Indices: 16702979--16703017 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
16702969 TGAGTGCAAA
*
16702979 ATTAAAAAATTTAAAAAATT
1 ATTAAAAAAGTTAAAAAATT
*
16702999 ATTAAAAAAGTTATAAAAT
1 ATTAAAAAAGTTAAAAAAT
16703018 ATATAATTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (20 bp):
ATTAAAAAAGTTAAAAAATT
Found at i:16704981 original size:2 final size:2
Alignment explanation
Indices: 16704974--16705014 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
16704964 TTTTAAGCCT
16704974 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
16705015 TACTACTTAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:16706743 original size:30 final size:31
Alignment explanation
Indices: 16706702--16706762 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 31
16706692 GGGTTGGGAG
* *
16706702 GGGAGGGGAGTAAAAGTTTTGGGGGGAAAGT
1 GGGAGGGGAGTAAAAGTTTTGAGGGAAAAGT
*
16706733 GGGA-GGGAGTAAATGTTTTGAGGGAAAAGT
1 GGGAGGGGAGTAAAAGTTTTGAGGGAAAAGT
16706763 AAAAAGGTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 23 0.85
31 4 0.15
ACGTcount: A:0.31, C:0.00, G:0.48, T:0.21
Consensus pattern (31 bp):
GGGAGGGGAGTAAAAGTTTTGAGGGAAAAGT
Found at i:16706899 original size:9 final size:9
Alignment explanation
Indices: 16706882--16706912 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
16706872 TCGAGTTGAT
16706882 TCGAATAAC
1 TCGAATAAC
*
16706891 TCGATTAAC
1 TCGAATAAC
16706900 TCGAATAAC
1 TCGAATAAC
16706909 TCGA
1 TCGA
16706913 TTCGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:16708483 original size:20 final size:20
Alignment explanation
Indices: 16708460--16708551 Score: 84
Period size: 20 Copynumber: 4.8 Consensus size: 20
16708450 ATTAGAAATT
16708460 TTATCTTAATATTATATAAG
1 TTATCTTAATATTATATAAG
* **
16708480 TTATCTTAATATTAAACGAG
1 TTATCTTAATATTATATAAG
* * *
16708500 TTAT-GT-A-ATTAGA-AATT
1 TTATCTTAATATTATATAA-G
16708517 TTATCTTAATATTATATAAG
1 TTATCTTAATATTATATAAG
*
16708537 TTATCTTAATTTTAT
1 TTATCTTAATATTAT
16708552 GTAATTAGAA
Statistics
Matches: 56, Mismatches: 11, Indels: 10
0.73 0.14 0.13
Matches are distributed among these distances:
16 1 0.02
17 9 0.16
18 2 0.04
19 2 0.04
20 40 0.71
21 2 0.04
ACGTcount: A:0.38, C:0.05, G:0.07, T:0.50
Consensus pattern (20 bp):
TTATCTTAATATTATATAAG
Found at i:16708489 original size:57 final size:57
Alignment explanation
Indices: 16708428--16708546 Score: 238
Period size: 57 Copynumber: 2.1 Consensus size: 57
16708418 AAATTAGAAA
16708428 TTAATATTAAACGAGTTATGTAATTAGAAATTTTATCTTAATATTATATAAGTTATC
1 TTAATATTAAACGAGTTATGTAATTAGAAATTTTATCTTAATATTATATAAGTTATC
16708485 TTAATATTAAACGAGTTATGTAATTAGAAATTTTATCTTAATATTATATAAGTTATC
1 TTAATATTAAACGAGTTATGTAATTAGAAATTTTATCTTAATATTATATAAGTTATC
16708542 TTAAT
1 TTAAT
16708547 TTTATGTAAT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 62 1.00
ACGTcount: A:0.40, C:0.05, G:0.08, T:0.46
Consensus pattern (57 bp):
TTAATATTAAACGAGTTATGTAATTAGAAATTTTATCTTAATATTATATAAGTTATC
Found at i:16708539 original size:94 final size:94
Alignment explanation
Indices: 16708326--16708540 Score: 245
Period size: 94 Copynumber: 2.3 Consensus size: 94
16708316 AAATTATGTT
** *
16708326 ATTAGAAAGGAATATTATATAAGTTATGTAATTCAAAATTTTATCTTAATATTGTATAAGTTATC
1 ATTAGAAATTAATATTATATAAGTTATGTAATTCAAAATTTTATCTTAATATTATATAAGTTATC
** * *
16708391 TAAAATTAGAAATTGATGTGTACTTAGAA
66 TAAAATTAGAAAGAGATATGTAATTAGAA
* **
16708420 ATTAGAAATTAATATTAAACGAGTTATGTAATT-AGAAATTTTATCTTAATATTATATAAGTTAT
1 ATTAGAAATTAATATTATATAAGTTATGTAATTCA-AAATTTTATCTTAATATTATATAAGTTAT
* * *
16708484 CTTAATATTA-AACGAGTTATGTAATTAGAA
65 C-TAAAATTAGAAAGAGATATGTAATTAGAA
** **
16708514 ATTTTATCTTAATATTATATAAGTTAT
1 ATTAGAAATTAATATTATATAAGTTAT
16708541 CTTAATTTTA
Statistics
Matches: 99, Mismatches: 20, Indels: 4
0.80 0.16 0.03
Matches are distributed among these distances:
93 1 0.01
94 91 0.92
95 7 0.07
ACGTcount: A:0.42, C:0.04, G:0.11, T:0.43
Consensus pattern (94 bp):
ATTAGAAATTAATATTATATAAGTTATGTAATTCAAAATTTTATCTTAATATTATATAAGTTATC
TAAAATTAGAAAGAGATATGTAATTAGAA
Found at i:16710841 original size:72 final size:72
Alignment explanation
Indices: 16710762--16711006 Score: 212
Period size: 72 Copynumber: 3.4 Consensus size: 72
16710752 ATAAAACATA
** *
16710762 TTTGCGGCGCTTTA-AGGAAAGCGCCACTATAGACAATGCCAAATGACGCAGTTTCTTAACTCAT
1 TTTGCGGCG-TTTACAAAAAAGCGCCACTATAGACAATGCCAAACGACGCAGTTTCTTAACTCAT
16710826 AATACACT
65 AATACACT
** * * * * * * * * **
16710834 TTTGCGGCGTTTACAAAAAAATGCCACAACTTATATAGA-G-AAAACGGCACCGTTTATGTAAAA
1 TTTGCGGCGTTTACAAAAAAGCGCCACTA--TAGACA-ATGCCAAACGACGCAGTTTCT-TAACT
*
16710897 CATAAAACA-T
62 CATAATACACT
* ** *
16710907 ATTTGCGGTGCTTTA-AGGAAAGCGCCACTATAGACAATGCCAAACGACGCAATTTCTTAACTCA
1 -TTTGCGGCG-TTTACAAAAAAGCGCCACTATAGACAATGCCAAACGACGCAGTTTCTTAACTCA
16710971 TAATACACT
64 TAATACACT
16710980 TTTGCGGCGTTTACAAAAAAGCGCCAC
1 TTTGCGGCGTTTACAAAAAAGCGCCAC
16711007 CAAAAGCAAA
Statistics
Matches: 126, Mismatches: 36, Indels: 22
0.68 0.20 0.12
Matches are distributed among these distances:
71 9 0.07
72 54 0.43
73 24 0.19
74 34 0.27
75 5 0.04
ACGTcount: A:0.36, C:0.22, G:0.17, T:0.25
Consensus pattern (72 bp):
TTTGCGGCGTTTACAAAAAAGCGCCACTATAGACAATGCCAAACGACGCAGTTTCTTAACTCATA
ATACACT
Found at i:16710865 original size:146 final size:146
Alignment explanation
Indices: 16710705--16711006 Score: 559
Period size: 146 Copynumber: 2.1 Consensus size: 146
16710695 GCGTTTTCAG
16710705 AAAACGCCACAACTTATATAGAGAAAACGGCACCGTTTATGTAAAACATAAAACATATTTGCGGC
1 AAAACGCCACAACTTATATAGAGAAAACGGCACCGTTTATGTAAAACATAAAACATATTTGCGGC
* *
16710770 GCTTTAAGGAAAGCGCCACTATAGACAATGCCAAATGACGCAGTTTCTTAACTCATAATACACTT
66 GCTTTAAGGAAAGCGCCACTATAGACAATGCCAAACGACGCAATTTCTTAACTCATAATACACTT
16710835 TTGCGGCGTTTACAAA
131 TTGCGGCGTTTACAAA
* *
16710851 AAAATGCCACAACTTATATAGAGAAAACGGCACCGTTTATGTAAAACATAAAACATATTTGCGGT
1 AAAACGCCACAACTTATATAGAGAAAACGGCACCGTTTATGTAAAACATAAAACATATTTGCGGC
16710916 GCTTTAAGGAAAGCGCCACTATAGACAATGCCAAACGACGCAATTTCTTAACTCATAATACACTT
66 GCTTTAAGGAAAGCGCCACTATAGACAATGCCAAACGACGCAATTTCTTAACTCATAATACACTT
16710981 TTGCGGCGTTTACAAA
131 TTGCGGCGTTTACAAA
*
16710997 AAAGCGCCAC
1 AAAACGCCAC
16711007 CAAAAGCAAA
Statistics
Matches: 150, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
146 150 1.00
ACGTcount: A:0.38, C:0.22, G:0.16, T:0.24
Consensus pattern (146 bp):
AAAACGCCACAACTTATATAGAGAAAACGGCACCGTTTATGTAAAACATAAAACATATTTGCGGC
GCTTTAAGGAAAGCGCCACTATAGACAATGCCAAACGACGCAATTTCTTAACTCATAATACACTT
TTGCGGCGTTTACAAA
Found at i:16711556 original size:14 final size:14
Alignment explanation
Indices: 16711539--16711577 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
16711529 CCGTAAATCT
16711539 TAAACCCCAAACTA
1 TAAACCCCAAACTA
* *
16711553 TAAACCCTAAACTC
1 TAAACCCCAAACTA
*
16711567 CAAACCCCAAA
1 TAAACCCCAAA
16711578 TTGTAAATCT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.49, C:0.38, G:0.00, T:0.13
Consensus pattern (14 bp):
TAAACCCCAAACTA
Found at i:16711584 original size:28 final size:28
Alignment explanation
Indices: 16711539--16711601 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 28
16711529 CCGTAAATCT
16711539 TAAACCCCAAACTATAAACCCTAAACTCC
1 TAAACCCCAAACTATAAACCCTAAAC-CC
* * * *
16711568 -AAACCCCAAATTGTAAATCTTAAACCC
1 TAAACCCCAAACTATAAACCCTAAACCC
16711595 TAAACCC
1 TAAACCC
16711602 GTCAATTAAC
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
27 2 0.07
28 27 0.93
ACGTcount: A:0.44, C:0.35, G:0.02, T:0.19
Consensus pattern (28 bp):
TAAACCCCAAACTATAAACCCTAAACCC
Found at i:16711721 original size:22 final size:21
Alignment explanation
Indices: 16711680--16711721 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
16711670 ACCGTAAATC
*
16711680 TTAAACCCTAAACCATAAACA
1 TTAAACCCTAAACCACAAACA
*
16711701 TTAAACCCGTAGACCACAAAC
1 TTAAACCC-TAAACCACAAAC
16711722 CACAACCACT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.48, C:0.31, G:0.05, T:0.17
Consensus pattern (21 bp):
TTAAACCCTAAACCACAAACA
Found at i:16712340 original size:115 final size:114
Alignment explanation
Indices: 16712194--16712713 Score: 709
Period size: 114 Copynumber: 4.6 Consensus size: 114
16712184 AGTTGCTCTA
* * * * *
16712194 TAGCGGCATTTTTACATGAGCGCCACCAATTCTAATATACCTCAAGACCAAATGCTGCGTTTTGG
1 TAGCGGCGTTTTTTCATAAGCGCCACTAATTCTAATATACCTCAAGACCAAACGCTGCGTTTTGG
* * * * *
16712259 TTAAGATATTTTACGACGTTTTTTATAAGGCGCTGCTAATACTGTGCTT
66 TTAAGATATTTTGCGGCGCTTTTTATAATGCGCCGCTAATACTGTGCTT
16712308 TAGCGGCGTTTTTTGCATAAGCGCCACTAATTCTAATATACCTCAAGACCAAACGCTGCGTTTTG
1 TAGCGGCGTTTTTT-CATAAGCGCCACTAATTCTAATATACCTCAAGACCAAACGCTGCGTTTTG
* * ** **
16712373 ATTAAGCTATTTTGCGGCGCTTTTTATAATGCTTCGCTAATACTAAGCTT
65 GTTAAGATATTTTGCGGCGCTTTTTATAATGCGCCGCTAATACTGTGCTT
* * *
16712423 TAGCAGCGTTTTTTCATAAGCGCCACTAATTCTAATATACCTCAAGACAAAACGCTGTGTTTTGG
1 TAGCGGCGTTTTTTCATAAGCGCCACTAATTCTAATATACCTCAAGACCAAACGCTGCGTTTTGG
* * *
16712488 TTAAGATATTTTGCGGTGCTTTTTATAATGCACCGCTAATACAGTGCTT
66 TTAAGATATTTTGCGGCGCTTTTTATAATGCGCCGCTAATACTGTGCTT
*** * *
16712537 TAGCGGTAATTTTTCATAAGCGCCACTAGTTCTAATATACCTCAAGACCAAACGCTACGTTTTGG
1 TAGCGGCGTTTTTTCATAAGCGCCACTAATTCTAATATACCTCAAGACCAAACGCTGCGTTTTGG
* *
16712602 TTAAGATTTTTTGCGGCG-TTTTTATAATGCGCCGCTAATACTCTGCTT
66 TTAAGATATTTTGCGGCGCTTTTTATAATGCGCCGCTAATACTGTGCTT
** * * * *
16712650 TAATGGCGTTTTTTCATAGGCGCTACTAATTCTAATACACCTCAAGACCAAACGATGCGTTTTG
1 TAGCGGCGTTTTTTCATAAGCGCCACTAATTCTAATATACCTCAAGACCAAACGCTGCGTTTTG
16712714 TCAGCATTAT
Statistics
Matches: 354, Mismatches: 51, Indels: 3
0.87 0.12 0.01
Matches are distributed among these distances:
113 80 0.23
114 175 0.49
115 99 0.28
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.35
Consensus pattern (114 bp):
TAGCGGCGTTTTTTCATAAGCGCCACTAATTCTAATATACCTCAAGACCAAACGCTGCGTTTTGG
TTAAGATATTTTGCGGCGCTTTTTATAATGCGCCGCTAATACTGTGCTT
Found at i:16713946 original size:8 final size:8
Alignment explanation
Indices: 16713923--16713963 Score: 64
Period size: 8 Copynumber: 5.0 Consensus size: 8
16713913 AAGAAATAAG
16713923 TATTATAT
1 TATTATAT
16713931 TAATTATAT
1 T-ATTATAT
*
16713940 TATTATAA
1 TATTATAT
16713948 TATTATAT
1 TATTATAT
16713956 TATTATAT
1 TATTATAT
16713964 ATATAAAACA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
8 22 0.73
9 8 0.27
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (8 bp):
TATTATAT
Found at i:16714941 original size:25 final size:24
Alignment explanation
Indices: 16714913--16714975 Score: 76
Period size: 22 Copynumber: 2.6 Consensus size: 24
16714903 ACTCTAGCGC
*
16714913 GCTCTCTGATTATTAGCACGTCTGT
1 GCTCTCTG-TTATTAGCACGTCAGT
*
16714938 GCTCTCTG-TA-TAGCACTTCAGT
1 GCTCTCTGTTATTAGCACGTCAGT
16714960 GCTCTCTGTTCATTAG
1 GCTCTCTGTT-ATTAG
16714976 TGCATAACAA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
22 18 0.55
23 3 0.09
24 1 0.03
25 11 0.33
ACGTcount: A:0.16, C:0.25, G:0.19, T:0.40
Consensus pattern (24 bp):
GCTCTCTGTTATTAGCACGTCAGT
Found at i:16721803 original size:21 final size:21
Alignment explanation
Indices: 16721779--16721828 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
16721769 CAGTGTGGTT
*
16721779 AAGGGACATGGCCGTGTGACC
1 AAGGGACATGCCCGTGTGACC
*
16721800 AAGGCACATGCCCGTGTGACC
1 AAGGGACATGCCCGTGTGACC
16721821 AAGGGACA
1 AAGGGACA
16721829 CGATCATGTG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.28, C:0.26, G:0.34, T:0.12
Consensus pattern (21 bp):
AAGGGACATGCCCGTGTGACC
Found at i:16721817 original size:42 final size:42
Alignment explanation
Indices: 16721779--16721858 Score: 106
Period size: 42 Copynumber: 1.9 Consensus size: 42
16721769 CAGTGTGGTT
* * * *
16721779 AAGGGACATGGCCGTGTGACCAAGGCACATGCCCGTGTGACC
1 AAGGGACACGACCATGTGACCAAGGCACACGCCCGTGTGACC
* *
16721821 AAGGGACACGATCATGTGACCAAGGCATACGCCCGTGT
1 AAGGGACACGACCATGTGACCAAGGCACACGCCCGTGT
16721859 AAAAATAAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 32 1.00
ACGTcount: A:0.26, C:0.28, G:0.31, T:0.15
Consensus pattern (42 bp):
AAGGGACACGACCATGTGACCAAGGCACACGCCCGTGTGACC
Found at i:16732862 original size:100 final size:100
Alignment explanation
Indices: 16732745--16733133 Score: 530
Period size: 100 Copynumber: 3.9 Consensus size: 100
16732735 CCAATTACAA
* * * * * * *
16732745 TGTCGAGGAAACAAGATCCGCCGTTGT-AGCTTCAATCTGTTCAACTGCACCACTAAGGAGGTAA
1 TGTCGGGGAAACCAGATCCGCCGTTGTGA-CTTCAATCTGCTCCACTGCACCACCAGGGAAGTAA
* *
16732809 GATCTGTCGTTGTGGCTTCAATCCTTTTAATTGCGC
65 GATCTGCCGTTGTGGCTTCAATCTTTTTAATTGCGC
* *
16732845 TGTCGGGGAAACCAGATCCACCGTTGTGACTTCAATCTGCTCCACTGCACCGCCAGGGAAGTAAG
1 TGTCGGGGAAACCAGATCCGCCGTTGTGACTTCAATCTGCTCCACTGCACCACCAGGGAAGTAAG
* * *
16732910 ATCCGCCGTTGTAGCTTCAATCTTTTTAATTTCGC
66 ATCTGCCGTTGTGGCTTCAATCTTTTTAATTGCGC
* * *
16732945 TATCAGGGAAACCAGA-CCTGCCGTTGTGACTTCAATCTGCTCCACTGCACCGCCAGGGAAGTAA
1 TGTCGGGGAAACCAGATCC-GCCGTTGTGACTTCAATCTGCTCCACTGCACCACCAGGGAAGTAA
16733009 GATCTGCCGTTGTGGCTTCAATCTTTTTAATTGCGC
65 GATCTGCCGTTGTGGCTTCAATCTTTTTAATTGCGC
* * * *
16733045 TGTCGGGGAAACCAGATCTGCCGTTGTGACTTCAATCTGTTCCACTACACCACCAGGAAAGTAAG
1 TGTCGGGGAAACCAGATCCGCCGTTGTGACTTCAATCTGCTCCACTGCACCACCAGGGAAGTAAG
** *
16733110 ATCCACCGTTGCGGCTTCAATCTT
66 ATCTGCCGTTGTGGCTTCAATCTT
16733134 GTCCACTGTA
Statistics
Matches: 256, Mismatches: 30, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
99 2 0.01
100 252 0.98
101 2 0.01
ACGTcount: A:0.23, C:0.26, G:0.22, T:0.28
Consensus pattern (100 bp):
TGTCGGGGAAACCAGATCCGCCGTTGTGACTTCAATCTGCTCCACTGCACCACCAGGGAAGTAAG
ATCTGCCGTTGTGGCTTCAATCTTTTTAATTGCGC
Found at i:16733082 original size:50 final size:50
Alignment explanation
Indices: 16732808--16733082 Score: 228
Period size: 50 Copynumber: 5.5 Consensus size: 50
16732798 TAAGGAGGTA
* * * *
16732808 AGATCTGTCGTTGTGGCTTCAATCCTTTTAATTGCGCTGTCGGGGAAACC
1 AGATCTGCCGTTGTGACTTCAATCTTTTTAATTGCGCTGTCAGGGAAACC
** ** ** * * * * ***
16732858 AGATCCACCGTTGTGACTTCAATCTGCTCCACTGCACCGCCAGGGAAGTA
1 AGATCTGCCGTTGTGACTTCAATCTTTTTAATTGCGCTGTCAGGGAAACC
* * *
16732908 AGATCCGCCGTTGT-AGCTTCAATCTTTTTAATTTCGCTATCAGGGAAACC
1 AGATCTGCCGTTGTGA-CTTCAATCTTTTTAATTGCGCTGTCAGGGAAACC
* ** ** * * * * ***
16732958 AGACCTGCCGTTGTGACTTCAATCTGCTCCACTGCACCGCCAGGGAAGTA
1 AGATCTGCCGTTGTGACTTCAATCTTTTTAATTGCGCTGTCAGGGAAACC
* *
16733008 AGATCTGCCGTTGTGGCTTCAATCTTTTTAATTGCGCTGTCGGGGAAACC
1 AGATCTGCCGTTGTGACTTCAATCTTTTTAATTGCGCTGTCAGGGAAACC
16733058 AGATCTGCCGTTGTGACTTCAATCT
1 AGATCTGCCGTTGTGACTTCAATCT
16733083 GTTCCACTAC
Statistics
Matches: 162, Mismatches: 61, Indels: 4
0.71 0.27 0.02
Matches are distributed among these distances:
49 1 0.01
50 160 0.99
51 1 0.01
ACGTcount: A:0.21, C:0.26, G:0.23, T:0.30
Consensus pattern (50 bp):
AGATCTGCCGTTGTGACTTCAATCTTTTTAATTGCGCTGTCAGGGAAACC
Found at i:16733112 original size:50 final size:50
Alignment explanation
Indices: 16732865--16733141 Score: 175
Period size: 50 Copynumber: 5.5 Consensus size: 50
16732855 ACCAGATCCA
* * * *
16732865 CCGTTGTGACTTCAATCTGCTCCACTGCACCGCCAGGGAAGTAAGATCCG
1 CCGTTGTGACTTCAATCTGTTCCACTGCACCACCAGGAAAGTAAGATCTG
* ** * * * * * ** *
16732915 CCGTTGT-AGCTTCAATCTTTTTAATTTCGCTATCAGGGAAA-CCAGACCTG
1 CCGTTGTGA-CTTCAATCTGTTCCACTGCACCACCA-GGAAAGTAAGATCTG
* * *
16732965 CCGTTGTGACTTCAATCTGCTCCACTGCACCGCCAGGGAAGTAAGATCTG
1 CCGTTGTGACTTCAATCTGTTCCACTGCACCACCAGGAAAGTAAGATCTG
* * ** * * ** ** **
16733015 CCGTTGTGGCTTCAATCTTTTTAATTGCGCTGTCGGGGAAA-CCAGATCTG
1 CCGTTGTGACTTCAATCTGTTCCACTGCAC-CACCAGGAAAGTAAGATCTG
* **
16733065 CCGTTGTGACTTCAATCTGTTCCACTACACCACCAGGAAAGTAAGATCCA
1 CCGTTGTGACTTCAATCTGTTCCACTGCACCACCAGGAAAGTAAGATCTG
* *
16733115 CCGTTGCGGCTTCAATCT-TGTCCACTG
1 CCGTTGTGACTTCAATCTGT-TCCACTG
16733142 TAATGCTAAA
Statistics
Matches: 159, Mismatches: 61, Indels: 14
0.68 0.26 0.06
Matches are distributed among these distances:
49 12 0.08
50 137 0.86
51 10 0.06
ACGTcount: A:0.22, C:0.28, G:0.22, T:0.28
Consensus pattern (50 bp):
CCGTTGTGACTTCAATCTGTTCCACTGCACCACCAGGAAAGTAAGATCTG
Found at i:16733429 original size:88 final size:88
Alignment explanation
Indices: 16733335--16733560 Score: 346
Period size: 88 Copynumber: 2.6 Consensus size: 88
16733325 AGACTGGTGC
* * *
16733335 CTTCGATCTACTTCGCTGCCAGTACAGGAAGGCAAGATCTGCTATTTTCAACCTAGTCCACTACT
1 CTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGCTATTTTCAACCTACTCCACTACT
*
16733400 GCCCAGGGAGACAAGGCTGGTAT
66 GCCCAGGGAGACAAGGCTGATAT
*
16733423 CTTCGATCTGCTTCGCTGTCAGTACAGGAATGCAAGATCTG-TCATTTTCAACCTACTCCACTAC
1 CTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGCT-ATTTTCAACCTACTCCACTAC
*
16733487 TGCCCAGGGAGACAGGGCTGATAT
65 TGCCCAGGGAGACAAGGCTGATAT
* ** *
16733511 CTTCAATCTGCTTCATTGTCAGTACAGGAAGGCAAGATCTGCCATTTTCA
1 CTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGCTATTTTCA
16733561 GTTTGCTTCA
Statistics
Matches: 125, Mismatches: 11, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
87 1 0.01
88 124 0.99
ACGTcount: A:0.25, C:0.27, G:0.21, T:0.27
Consensus pattern (88 bp):
CTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGCTATTTTCAACCTACTCCACTACT
GCCCAGGGAGACAAGGCTGATAT
Found at i:16734795 original size:6 final size:6
Alignment explanation
Indices: 16734784--16734818 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
16734774 CTGCCCCTTT
*
16734784 TTTTTC TTTTTC TTTTTC TTTTTC TCTTTC TTTTT
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTT
16734819 TTGTGTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (6 bp):
TTTTTC
Found at i:16744664 original size:22 final size:23
Alignment explanation
Indices: 16744606--16744697 Score: 150
Period size: 23 Copynumber: 4.0 Consensus size: 23
16744596 ATAAGTGCCA
16744606 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
16744629 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
16744652 TACTGA-ATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
16744674 CACTGAAATGTAGTCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
16744697 C
1 C
16744698 NNNNNNNNNN
Statistics
Matches: 65, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
22 21 0.32
23 44 0.68
ACGTcount: A:0.32, C:0.25, G:0.22, T:0.22
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:16744672 original size:45 final size:46
Alignment explanation
Indices: 16744607--16744696 Score: 155
Period size: 45 Copynumber: 2.0 Consensus size: 46
16744597 TAAGTGCCAC
*
16744607 ACTGATATGTAGCCGAAGCTACCACTGATATGTAGCCGAAGCTACT
1 ACTGATATGTAGCCGAAGCTACCACTGAAATGTAGCCGAAGCTACT
*
16744653 ACTGA-ATGTAGCCGAAGCTACCACTGAAATGTAGTCGAAGCTAC
1 ACTGATATGTAGCCGAAGCTACCACTGAAATGTAGCCGAAGCTAC
16744697 CNNNNNNNNN
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
45 37 0.88
46 5 0.12
ACGTcount: A:0.32, C:0.23, G:0.22, T:0.22
Consensus pattern (46 bp):
ACTGATATGTAGCCGAAGCTACCACTGAAATGTAGCCGAAGCTACT
Found at i:16754695 original size:4 final size:4
Alignment explanation
Indices: 16754678--16754828 Score: 279
Period size: 4 Copynumber: 38.2 Consensus size: 4
16754668 TTAAATAATA
*
16754678 ATGT ATGT ACGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
16754726 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
16754774 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT A--T
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
16754820 ATGT ATGT A
1 ATGT ATGT A
16754829 AAAACTAAGA
Statistics
Matches: 143, Mismatches: 2, Indels: 4
0.96 0.01 0.03
Matches are distributed among these distances:
2 2 0.01
4 141 0.99
ACGTcount: A:0.26, C:0.01, G:0.25, T:0.49
Consensus pattern (4 bp):
ATGT
Found at i:16757604 original size:18 final size:18
Alignment explanation
Indices: 16757581--16757617 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
16757571 TCATCATTAT
16757581 TATTAGTATTAT-TATTTA
1 TATTAGT-TTATATATTTA
16757599 TATTAGTTTATATATTTA
1 TATTAGTTTATATATTTA
16757617 T
1 T
16757618 CTACATATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.62
Consensus pattern (18 bp):
TATTAGTTTATATATTTA
Found at i:16757655 original size:26 final size:26
Alignment explanation
Indices: 16757607--16757656 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
16757597 TATATTAGTT
*
16757607 TATATATTTATCTACATATTTTTATG
1 TATATATTTATCTACATAATTTTATG
*
16757633 TATATACTTTAT-TATATAATTTTA
1 TATATA-TTTATCTACATAATTTTA
16757657 GGTGTTAACA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 16 0.76
27 5 0.24
ACGTcount: A:0.34, C:0.06, G:0.02, T:0.58
Consensus pattern (26 bp):
TATATATTTATCTACATAATTTTATG
Found at i:16758514 original size:25 final size:25
Alignment explanation
Indices: 16758480--16758530 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
16758470 ATATTTGTGG
16758480 AAAGTCAAAGATATCGGTATCAAAT
1 AAAGTCAAAGATATCGGTATCAAAT
*
16758505 AAAGTCAAAGATATGGGTATCAAAT
1 AAAGTCAAAGATATCGGTATCAAAT
16758530 A
1 A
16758531 TTGGAAAGTC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.49, C:0.10, G:0.18, T:0.24
Consensus pattern (25 bp):
AAAGTCAAAGATATCGGTATCAAAT
Found at i:16758541 original size:30 final size:30
Alignment explanation
Indices: 16758477--16758565 Score: 116
Period size: 30 Copynumber: 3.1 Consensus size: 30
16758467 TCCATATTTG
*
16758477 TGGAAAGTCAAAGATATCGGTATC-AA-A-
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
16758504 T--AAAGTCAAAGATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
*
16758532 TGGAAAGTCAAAGATATGGGTATCGAGATAT
1 TGGAAAGTCAAAGATATGGGTATC-AAATAT
16758563 TGG
1 TGG
16758566 CATAAGAAAT
Statistics
Matches: 54, Mismatches: 2, Indels: 8
0.84 0.03 0.12
Matches are distributed among these distances:
25 20 0.37
26 2 0.04
27 2 0.04
28 1 0.02
30 21 0.39
31 8 0.15
ACGTcount: A:0.42, C:0.08, G:0.25, T:0.26
Consensus pattern (30 bp):
TGGAAAGTCAAAGATATGGGTATCAAATAT
Found at i:16763172 original size:25 final size:25
Alignment explanation
Indices: 16763138--16763188 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
16763128 ATATTTATGG
16763138 AAAGTCAAAGATATCGGTATCAAAT
1 AAAGTCAAAGATATCGGTATCAAAT
*
16763163 AAAGTCAAAGATATGGGTATCAAAT
1 AAAGTCAAAGATATCGGTATCAAAT
16763188 A
1 A
16763189 TTGGAAAGTC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.49, C:0.10, G:0.18, T:0.24
Consensus pattern (25 bp):
AAAGTCAAAGATATCGGTATCAAAT
Found at i:16763199 original size:30 final size:30
Alignment explanation
Indices: 16763135--16763223 Score: 116
Period size: 30 Copynumber: 3.1 Consensus size: 30
16763125 TCCATATTTA
*
16763135 TGGAAAGTCAAAGATATCGGTATC-AA-A-
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
16763162 T--AAAGTCAAAGATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
*
16763190 TGGAAAGTCAAAGATATGGGTATCGAGATAT
1 TGGAAAGTCAAAGATATGGGTATC-AAATAT
16763221 TGG
1 TGG
16763224 CATAAGAAAT
Statistics
Matches: 54, Mismatches: 2, Indels: 8
0.84 0.03 0.12
Matches are distributed among these distances:
25 20 0.37
26 2 0.04
27 2 0.04
28 1 0.02
30 21 0.39
31 8 0.15
ACGTcount: A:0.42, C:0.08, G:0.25, T:0.26
Consensus pattern (30 bp):
TGGAAAGTCAAAGATATGGGTATCAAATAT
Found at i:16766433 original size:38 final size:38
Alignment explanation
Indices: 16766382--16766457 Score: 116
Period size: 38 Copynumber: 2.0 Consensus size: 38
16766372 AAGTAAGTAG
* * **
16766382 TTGGGACTTCAGCTTGGGTGTTTGAATTGGAAAAGAAA
1 TTGGGACTTCAGCTAGGGTGTTTAAACCGGAAAAGAAA
16766420 TTGGGACTTCAGCTAGGGTGTTTAAACCGGAAAAGAAA
1 TTGGGACTTCAGCTAGGGTGTTTAAACCGGAAAAGAAA
16766458 ATGAAGCAAG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.32, C:0.11, G:0.30, T:0.28
Consensus pattern (38 bp):
TTGGGACTTCAGCTAGGGTGTTTAAACCGGAAAAGAAA
Found at i:16768683 original size:16 final size:17
Alignment explanation
Indices: 16768658--16768692 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
16768648 TTAATTCTGA
*
16768658 ATTCATTTGTGA-ATTC
1 ATTCACTTGTGACATTC
16768674 ATTCACTTGTGACATTC
1 ATTCACTTGTGACATTC
16768691 AT
1 AT
16768693 GGTGTGATTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.26, C:0.17, G:0.11, T:0.46
Consensus pattern (17 bp):
ATTCACTTGTGACATTC
Found at i:16769546 original size:25 final size:25
Alignment explanation
Indices: 16769515--16769590 Score: 84
Period size: 25 Copynumber: 3.1 Consensus size: 25
16769505 CTCTCGAGCT
*
16769515 ATATAACGGGAAGCTCATATGAGTC
1 ATATAACAGGAAGCTCATATGAGTC
* * * *
16769540 ATGTAACAGGAAGCTTATCTG-GGC
1 ATATAACAGGAAGCTCATATGAGTC
*
16769564 -TATAACAGGAAGCTCATAAGAGTC
1 ATATAACAGGAAGCTCATATGAGTC
16769588 ATA
1 ATA
16769591 CTCAGGAAGT
Statistics
Matches: 39, Mismatches: 10, Indels: 4
0.74 0.19 0.08
Matches are distributed among these distances:
23 16 0.41
24 4 0.10
25 19 0.49
ACGTcount: A:0.37, C:0.16, G:0.24, T:0.24
Consensus pattern (25 bp):
ATATAACAGGAAGCTCATATGAGTC
Found at i:16770259 original size:5 final size:5
Alignment explanation
Indices: 16770242--16770273 Score: 55
Period size: 5 Copynumber: 6.2 Consensus size: 5
16770232 AATTTAATAA
16770242 AATTC ATATTC AATTC AATTC AATTC AATTC A
1 AATTC A-ATTC AATTC AATTC AATTC AATTC A
16770274 CATACTAGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 21 0.81
6 5 0.19
ACGTcount: A:0.41, C:0.19, G:0.00, T:0.41
Consensus pattern (5 bp):
AATTC
Found at i:16778389 original size:22 final size:23
Alignment explanation
Indices: 16778364--16778409 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
16778354 TGTAAATACT
* *
16778364 AAACTCAC-ATTTTATATAAAAA
1 AAACTCACGAATTAATATAAAAA
*
16778386 AAACTTACGAATTAATATAAAAA
1 AAACTCACGAATTAATATAAAAA
16778409 A
1 A
16778410 TGAGTGAATG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 7 0.35
23 13 0.65
ACGTcount: A:0.59, C:0.11, G:0.02, T:0.28
Consensus pattern (23 bp):
AAACTCACGAATTAATATAAAAA
Found at i:16779494 original size:18 final size:19
Alignment explanation
Indices: 16779460--16779516 Score: 57
Period size: 20 Copynumber: 3.0 Consensus size: 19
16779450 TTATTTTCAC
16779460 AAATTAAATACATTA-TTA
1 AAATTAAATACATTATTTA
*
16779478 AAATTAAAATAGA-TATTTAA
1 AAATT-AAATACATTATTT-A
16779498 AAATATAAATA-ATTATTTA
1 AAAT-TAAATACATTATTTA
16779517 GATTTAATTA
Statistics
Matches: 33, Mismatches: 1, Indels: 9
0.77 0.02 0.21
Matches are distributed among these distances:
18 7 0.21
19 10 0.30
20 15 0.45
21 1 0.03
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.39
Consensus pattern (19 bp):
AAATTAAATACATTATTTA
Found at i:16779514 original size:20 final size:21
Alignment explanation
Indices: 16779460--16779516 Score: 61
Period size: 19 Copynumber: 3.0 Consensus size: 21
16779450 TTATTTTCAC
16779460 AAAT-TAAATACATTA-TTAA
1 AAATATAAATACATTATTTAA
* *
16779479 AATTA-AAATAGA-TATTTAA
1 AAATATAAATACATTATTTAA
16779498 AAATATAAATA-ATTATTTA
1 AAATATAAATACATTATTTA
16779517 GATTTAATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
18 2 0.06
19 18 0.58
20 11 0.35
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.39
Consensus pattern (21 bp):
AAATATAAATACATTATTTAA
Found at i:16780730 original size:22 final size:22
Alignment explanation
Indices: 16780697--16780749 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
16780687 AAAAAAAGAA
16780697 GCTATTTTTTTTACTATTTTCTT
1 GCTA-TTTTTTTACTATTTTCTT
* * * *
16780720 GCTGTTTTTTTATTGTTTTGTT
1 GCTATTTTTTTACTATTTTCTT
16780742 GCTATTTT
1 GCTATTTT
16780750 CTTCTTCTTC
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
22 22 0.88
23 3 0.12
ACGTcount: A:0.09, C:0.09, G:0.11, T:0.70
Consensus pattern (22 bp):
GCTATTTTTTTACTATTTTCTT
Done.