Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr02 ID=Chr02-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: 62769430
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1067035 characters in sequence are not A, C, G, or T
File 59 of 206
Found at i:16709282 original size:2 final size:2
Alignment explanation
Indices: 16709277--16709309 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
16709267 TAATCATTTG
16709277 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
16709310 ATGGTAATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:16711163 original size:22 final size:22
Alignment explanation
Indices: 16711142--16711200 Score: 61
Period size: 21 Copynumber: 2.8 Consensus size: 22
16711132 TTTCCCTTTC
* *
16711142 CTTTTTGTT-TTATTATTTTTT
1 CTTTTTATTATTATTACTTTTT
16711163 CTTTTTATTATTATTAC-TTTT
1 CTTTTTATTATTATTACTTTTT
* *
16711184 CGTTTT-TTATTAGTACT
1 CTTTTTATTATTATTACT
16711201 GTGAGTAGAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
20 9 0.28
21 17 0.53
22 6 0.19
ACGTcount: A:0.15, C:0.08, G:0.05, T:0.71
Consensus pattern (22 bp):
CTTTTTATTATTATTACTTTTT
Found at i:16711182 original size:16 final size:16
Alignment explanation
Indices: 16711149--16711183 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
16711139 TTCCTTTTTG
* *
16711149 TTTTATTATTTTTTCT
1 TTTTATTATTATTACT
16711165 TTTTATTATTATTACT
1 TTTTATTATTATTACT
16711181 TTT
1 TTT
16711184 CGTTTTTTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.17, C:0.06, G:0.00, T:0.77
Consensus pattern (16 bp):
TTTTATTATTATTACT
Found at i:16711793 original size:22 final size:22
Alignment explanation
Indices: 16711753--16711795 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
16711743 AAAGATTTTC
**
16711753 TCTCTCAAAATTCTCTTTAAAA
1 TCTCTCAAAATAATCTTTAAAA
*
16711775 TCTCTCAAAATAATTTTTAAA
1 TCTCTCAAAATAATCTTTAAA
16711796 GTTGGGCAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.40, C:0.19, G:0.00, T:0.42
Consensus pattern (22 bp):
TCTCTCAAAATAATCTTTAAAA
Found at i:16712049 original size:25 final size:25
Alignment explanation
Indices: 16712021--16712105 Score: 73
Period size: 25 Copynumber: 3.2 Consensus size: 25
16712011 GTTGAAATCC
16712021 AAATATTAATGGATGTCTAAGATCA
1 AAATATTAATGGATGTCTAAGATCA
* * * *
16712046 AAATAGGTCTAATATGAGGTTTTGAA-ATCC
1 AAATA--T-TAAT-GGATG-TCT-AAGATCA
16712076 AAATATTAATGGATGTCTAAGATCA
1 AAATATTAATGGATGTCTAAGATCA
16712101 AAATA
1 AAATA
16712106 GGTCTAATAT
Statistics
Matches: 45, Mismatches: 8, Indels: 14
0.67 0.12 0.21
Matches are distributed among these distances:
24 2 0.04
25 15 0.33
26 3 0.07
27 5 0.11
28 5 0.11
29 3 0.07
30 10 0.22
31 2 0.04
ACGTcount: A:0.44, C:0.08, G:0.16, T:0.32
Consensus pattern (25 bp):
AAATATTAATGGATGTCTAAGATCA
Found at i:16712077 original size:55 final size:55
Alignment explanation
Indices: 16712012--16712123 Score: 224
Period size: 55 Copynumber: 2.0 Consensus size: 55
16712002 TAATTTTAAG
16712012 TTGAAATCCAAATATTAATGGATGTCTAAGATCAAAATAGGTCTAATATGAGGTT
1 TTGAAATCCAAATATTAATGGATGTCTAAGATCAAAATAGGTCTAATATGAGGTT
16712067 TTGAAATCCAAATATTAATGGATGTCTAAGATCAAAATAGGTCTAATATGAGGTT
1 TTGAAATCCAAATATTAATGGATGTCTAAGATCAAAATAGGTCTAATATGAGGTT
16712122 TT
1 TT
16712124 TAATCTTAAA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 57 1.00
ACGTcount: A:0.39, C:0.09, G:0.18, T:0.34
Consensus pattern (55 bp):
TTGAAATCCAAATATTAATGGATGTCTAAGATCAAAATAGGTCTAATATGAGGTT
Found at i:16715900 original size:41 final size:41
Alignment explanation
Indices: 16715842--16716032 Score: 328
Period size: 41 Copynumber: 4.6 Consensus size: 41
16715832 CTTAATTTAA
* *
16715842 CAGATTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATT
1 CAGA-TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATT
16715884 CAGATCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATT
1 CAGATCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATT
*
16715925 CAGATCACTGGCACTTAGCCTGCTAGGTTTATAACCTGATT
1 CAGATCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATT
* *
16715966 TAGATCACCGGCACTTAGCCTGCTAGGTTTATAACCTAATT
1 CAGATCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATT
16716007 CAGATCACCGGCACTTAGCCTGCTAG
1 CAGATCACCGGCACTTAGCCTGCTAG
16716033 ACGTATAGTC
Statistics
Matches: 142, Mismatches: 7, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
41 138 0.97
42 4 0.03
ACGTcount: A:0.24, C:0.27, G:0.20, T:0.29
Consensus pattern (41 bp):
CAGATCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATT
Found at i:16723683 original size:41 final size:41
Alignment explanation
Indices: 16723625--16723815 Score: 328
Period size: 41 Copynumber: 4.6 Consensus size: 41
16723615 CTTAATTTAA
* *
16723625 CAGATTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATT
1 CAGA-TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATT
16723667 CAGATCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATT
1 CAGATCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATT
*
16723708 CAGATCACTGGCACTTAGCCTGCTAGGTTTATAACCTGATT
1 CAGATCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATT
* *
16723749 TAGATCACCGGCACTTAGCCTGCTAGGTTTATAACCTAATT
1 CAGATCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATT
16723790 CAGATCACCGGCACTTAGCCTGCTAG
1 CAGATCACCGGCACTTAGCCTGCTAG
16723816 ACGTATAGTC
Statistics
Matches: 142, Mismatches: 7, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
41 138 0.97
42 4 0.03
ACGTcount: A:0.24, C:0.27, G:0.20, T:0.29
Consensus pattern (41 bp):
CAGATCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATT
Found at i:16724348 original size:2 final size:2
Alignment explanation
Indices: 16724341--16724368 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
16724331 TTATTTATTC
16724341 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
16724369 GCTTATTCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16727521 original size:5 final size:5
Alignment explanation
Indices: 16727511--16727580 Score: 140
Period size: 5 Copynumber: 14.0 Consensus size: 5
16727501 TTTAGTTAGT
16727511 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA
16727561 TTTTA TTTTA TTTTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA
16727581 GATATTTTTT
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 65 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTA
Found at i:16730219 original size:16 final size:17
Alignment explanation
Indices: 16730198--16730270 Score: 78
Period size: 17 Copynumber: 4.2 Consensus size: 17
16730188 ATAATAAATT
16730198 TAAAAAATATATAAAAA
1 TAAAAAATATATAAAAA
*
16730215 TAAAAAATATTATTAATAA
1 TAAAAAATA-TA-TAAAAA
* *
16730234 TAAATAAT-T-TAAAATT
1 TAAAAAATATATAAAA-A
16730250 TAAAAAATATATAAAAA
1 TAAAAAATATATAAAAA
16730267 TAAA
1 TAAA
16730271 TATTTTTAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
15 4 0.09
16 7 0.16
17 15 0.33
18 7 0.16
19 12 0.27
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
TAAAAAATATATAAAAA
Found at i:16730247 original size:34 final size:33
Alignment explanation
Indices: 16730204--16730282 Score: 88
Period size: 34 Copynumber: 2.3 Consensus size: 33
16730194 AATTTAAAAA
* *
16730204 ATATATAAAAATAAAAAATATTATTAATAATAAAT
1 ATATTTAAAAATAAAAAATA-TA-TAAAAATAAAT
*
16730239 A-ATTTAAAATTTAAAAAATATATAAAAATAAAT
1 ATATTTAAAA-ATAAAAAATATATAAAAATAAAT
*
16730272 ATTTTTAAAAA
1 ATATTTAAAAA
16730283 ATATATAATA
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
33 11 0.30
34 16 0.43
35 10 0.27
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (33 bp):
ATATTTAAAAATAAAAAATATATAAAAATAAAT
Found at i:16730248 original size:33 final size:30
Alignment explanation
Indices: 16730202--16730305 Score: 92
Period size: 33 Copynumber: 3.4 Consensus size: 30
16730192 TAAATTTAAA
*
16730202 AAATATATAAAAATAAAAAATATTATTAATAAT
1 AAATAT-TTAAAATAAAAAATA-TA-TAATAAT
*
16730235 AAATAATTTAAAATTTAAAAAATATATAAAAAT
1 AAAT-ATTTAAAA--TAAAAAATATATAATAAT
*
16730268 AAATATTT---TTAAAAAATATATAATAAT
1 AAATATTTAAAATAAAAAATATATAATAAT
16730295 -AA-ATTTAAAAT
1 AAATATTTAAAAT
16730306 TTATATTAAT
Statistics
Matches: 60, Mismatches: 5, Indels: 17
0.73 0.06 0.21
Matches are distributed among these distances:
25 4 0.07
26 2 0.03
27 17 0.28
28 1 0.02
32 4 0.07
33 19 0.32
34 4 0.07
35 9 0.15
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (30 bp):
AAATATTTAAAATAAAAAATATATAATAAT
Found at i:16730310 original size:23 final size:24
Alignment explanation
Indices: 16730248--16730321 Score: 62
Period size: 27 Copynumber: 3.0 Consensus size: 24
16730238 TAATTTAAAA
*
16730248 TTTAAAAAATATA-TAAAAATAAATA
1 TTTAAAAAATATATTAATAAT-AA-A
16730273 TTTTTAAAAAATATA-TAATAATAAA
1 --TTTAAAAAATATATTAATAATAAA
** *
16730298 TTTAAAATTTATATTAATATTAAA
1 TTTAAAAAATATATTAATAATAAA
16730322 AAATAAATAT
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
23 11 0.26
24 9 0.21
25 1 0.02
26 2 0.05
27 19 0.45
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (24 bp):
TTTAAAAAATATATTAATAATAAA
Found at i:16730322 original size:57 final size:62
Alignment explanation
Indices: 16730215--16730331 Score: 156
Period size: 58 Copynumber: 2.0 Consensus size: 62
16730205 TATATAAAAA
16730215 TAAAAAATATTATTAATAATAAATAATTTAAAATTTAAAAAATATAT-AAAAATAAATATTTT
1 TAAAAAATATTATTAATAAT-AATAATTTAAAATTTAAAAAATATATAAAAAATAAATATTTT
**
16730277 TAAAAAATA-TA-TAATAAT-A-AATTTAAAATTTATATTAATAT-TAAAAAATAAATAT
1 TAAAAAATATTATTAATAATAATAATTTAAAATTTA-AAAAATATATAAAAAATAAATAT
16730332 CCCTCACTCC
Statistics
Matches: 51, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
57 14 0.27
58 19 0.37
60 7 0.14
61 2 0.04
62 9 0.18
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (62 bp):
TAAAAAATATTATTAATAATAATAATTTAAAATTTAAAAAATATATAAAAAATAAATATTTT
Found at i:16734963 original size:22 final size:23
Alignment explanation
Indices: 16734917--16734970 Score: 101
Period size: 23 Copynumber: 2.4 Consensus size: 23
16734907 AAAATATTAA
16734917 AGTCCTTATTTTAATTATTGATT
1 AGTCCTTATTTTAATTATTGATT
16734940 AGTCCTTATTTTAATTA-TGATT
1 AGTCCTTATTTTAATTATTGATT
16734962 AGTCCTTAT
1 AGTCCTTAT
16734971 AGCATAAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 14 0.45
23 17 0.55
ACGTcount: A:0.26, C:0.11, G:0.09, T:0.54
Consensus pattern (23 bp):
AGTCCTTATTTTAATTATTGATT
Found at i:16737969 original size:19 final size:19
Alignment explanation
Indices: 16737946--16738002 Score: 64
Period size: 19 Copynumber: 3.1 Consensus size: 19
16737936 AAAATTATAA
16737946 AAAAATTCAAAATAATTT-T
1 AAAAATTCAAAAT-ATTTAT
* *
16737965 TAAAATTTAAAATATTTAT
1 AAAAATTCAAAATATTTAT
*
16737984 AAAAATTCTAAA-ATTTAT
1 AAAAATTCAAAATATTTAT
16738002 A
1 A
16738003 TTTTAAAAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
18 11 0.34
19 21 0.66
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (19 bp):
AAAAATTCAAAATATTTAT
Found at i:16738708 original size:15 final size:15
Alignment explanation
Indices: 16738688--16738726 Score: 69
Period size: 15 Copynumber: 2.6 Consensus size: 15
16738678 CACAAAAAAT
16738688 GCCGCTAACGACAAC
1 GCCGCTAACGACAAC
16738703 GCCGCTAACGACAAC
1 GCCGCTAACGACAAC
*
16738718 GTCGCTAAC
1 GCCGCTAAC
16738727 TTTTGCGGTG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.31, C:0.38, G:0.21, T:0.10
Consensus pattern (15 bp):
GCCGCTAACGACAAC
Found at i:16738835 original size:84 final size:84
Alignment explanation
Indices: 16738745--16739036 Score: 390
Period size: 84 Copynumber: 3.5 Consensus size: 84
16738735 TGCTTACAGA
*
16738745 AAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTAAGAAAATAAACGCCGCTAAAGATCAT
1 AAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTAGGAAAA-AAACGCCGCTAAAGATCAT
*
16738810 GTTCTTTAGCGGCGCTTAGG
65 GTTCTTTAGCGGCGCTTGGG
* * * *
16738830 -AAAAACGCCGCTAAAGATCATATTCTTTAGCGGCGCTTAGGAAGAAAACGCTGCTAAAGATCAT
1 AAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGC-TAGGAAAAAAACGCCGCTAAAGATCAT
*
16738894 GTTCTTTAACGGCGCTTGGG
65 GTTCTTTAGCGGCGCTTGGG
* * * * *
16738914 AAAAAACGCCGCTAAAGATCATGTTCTTTAGCGTCGCTTGGGAAAAAACGCCACTAAAGATCATG
1 AAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTAGGAAAAAAACGCCGCTAAAGATCATG
*
16738979 TTCTTTAGTGGCGCTTGGG
66 TTCTTTAGCGGCGCTTGGG
* * *
16738998 AAGAAAACGCCGCTAAAAGTA-GTGTTCTTTAGTGGCGCT
1 AA-AAAACGCCGCT-AAAGAACATGTTCTTTAGCGGCGCT
16739037 TATTTCACAA
Statistics
Matches: 182, Mismatches: 21, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
84 112 0.62
85 66 0.36
86 4 0.02
ACGTcount: A:0.32, C:0.20, G:0.24, T:0.25
Consensus pattern (84 bp):
AAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTAGGAAAAAAACGCCGCTAAAGATCATG
TTCTTTAGCGGCGCTTGGG
Found at i:16738920 original size:42 final size:42
Alignment explanation
Indices: 16738745--16739038 Score: 405
Period size: 43 Copynumber: 7.0 Consensus size: 42
16738735 TGCTTACAGA
* * *
16738745 AAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTAAGA
1 AAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGG
16738787 AAATAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGG
1 AAA-AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGG
*
16738830 -AAAAACGCCGCTAAAGATCATATTCTTTAGCGGCGCTTAGG
1 AAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGG
* * *
16738871 AAGAAAACGCTGCTAAAGATCATGTTCTTTAACGGCGCTTGGG
1 AA-AAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGG
* *
16738914 AAAAAACGCCGCTAAAGATCATGTTCTTTAGCGTCGCTTGGG
1 AAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGG
* * *
16738956 AAAAAACGCCACTAAAGATCATGTTCTTTAGTGGCGCTTGGG
1 AAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGG
*
16738998 AAGAAAACGCCGCTAAA-AGT-AGTGTTCTTTAGTGGCGCTTA
1 AA-AAAACGCCGCTAAAGA-TCA-TGTTCTTTAGCGGCGCTTA
16739039 TTTCACAAAC
Statistics
Matches: 230, Mismatches: 16, Indels: 11
0.89 0.06 0.04
Matches are distributed among these distances:
41 38 0.17
42 86 0.37
43 106 0.46
ACGTcount: A:0.32, C:0.20, G:0.23, T:0.25
Consensus pattern (42 bp):
AAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGG
Found at i:16738973 original size:127 final size:127
Alignment explanation
Indices: 16738747--16739014 Score: 412
Period size: 127 Copynumber: 2.1 Consensus size: 127
16738737 CTTACAGAAA
*
16738747 AAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTAAGAAAATAAACGCCGCTAAAGATCATGT
1 AAAACGCCGCTAAAGAACATGTTCTTTAACGGCGCTAAGAAAATAAACGCCGCTAAAGATCATGT
*
16738812 TCTTTAGCGGCGCTTAGGAAAAACGCCGCTAAAGATCATATTCTTTAGCGGCGCTTAGGAAG
66 TCTTTAGCGGCGCTTAGGAAAAACGCCACTAAAGATCATATTCTTTAGCGGCGCTTAGGAAG
* * ** *
16738874 AAAACGCTGCTAAAGATCATGTTCTTTAACGGCGCTTGGGAAA-AAACGCCGCTAAAGATCATGT
1 AAAACGCCGCTAAAGAACATGTTCTTTAACGGCGCTAAGAAAATAAACGCCGCTAAAGATCATGT
* * * * *
16738938 TCTTTAGCGTCGCTTGGGAAAAAACGCCACTAAAGATCATGTTCTTTAGTGGCGCTTGGGAAG
66 TCTTTAGCGGCGCTTAGG-AAAAACGCCACTAAAGATCATATTCTTTAGCGGCGCTTAGGAAG
16739001 AAAACGCCGCTAAA
1 AAAACGCCGCTAAA
16739015 AGTAGTGTTC
Statistics
Matches: 127, Mismatches: 13, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
126 37 0.29
127 90 0.71
ACGTcount: A:0.32, C:0.21, G:0.23, T:0.24
Consensus pattern (127 bp):
AAAACGCCGCTAAAGAACATGTTCTTTAACGGCGCTAAGAAAATAAACGCCGCTAAAGATCATGT
TCTTTAGCGGCGCTTAGGAAAAACGCCACTAAAGATCATATTCTTTAGCGGCGCTTAGGAAG
Found at i:16739523 original size:23 final size:21
Alignment explanation
Indices: 16739471--16739539 Score: 111
Period size: 21 Copynumber: 3.3 Consensus size: 21
16739461 GCTTCTATCG
16739471 CTGCTTCTCTCGCTGCAGCCT
1 CTGCTTCTCTCGCTGCAGCCT
* *
16739492 CTGCTTCTCTCGTTGTAGCCT
1 CTGCTTCTCTCGCTGCAGCCT
*
16739513 CTGCTTCTCTCGCTGCCGCCT
1 CTGCTTCTCTCGCTGCAGCCT
16739534 CTGCTT
1 CTGCTT
16739540 TAAGTTGTTG
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 43 1.00
ACGTcount: A:0.03, C:0.41, G:0.19, T:0.38
Consensus pattern (21 bp):
CTGCTTCTCTCGCTGCAGCCT
Found at i:16741645 original size:9 final size:9
Alignment explanation
Indices: 16741631--16741805 Score: 206
Period size: 9 Copynumber: 19.1 Consensus size: 9
16741621 CAATCGGTCA
16741631 AAGTTATGT
1 AAGTTATGT
*
16741640 AAGTTATTT
1 AAGTTATGT
*
16741649 AATTTATGT
1 AAGTTATGT
16741658 AAGTTATGT
1 AAGTTATGT
*
16741667 AAGTTATTT
1 AAGTTATGT
*
16741676 AATTTATGT
1 AAGTTATGT
16741685 AAGTTATGT
1 AAGTTATGT
*
16741694 AAGTTATTT
1 AAGTTATGT
*
16741703 AATTTATGT
1 AAGTTATGT
16741712 AAGTTATGT
1 AAGTTATGT
*
16741721 AAGTTATTT
1 AAGTTATGT
*
16741730 AATTTATGT
1 AAGTTATGT
*
16741739 AGGTTATGT
1 AAGTTATGT
16741748 AAGTTATGT
1 AAGTTATGT
*
16741757 AAGTTATCT
1 AAGTTATGT
*
16741766 AATTTATGT
1 AAGTTATGT
*
16741775 AAGTTATGC
1 AAGTTATGT
*
16741784 AAGCTTATAT
1 AAG-TTATGT
16741794 ACAAGTTATGT
1 --AAGTTATGT
16741805 A
1 A
16741806 TTATAACATA
Statistics
Matches: 137, Mismatches: 26, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
9 125 0.91
10 4 0.03
11 5 0.04
12 3 0.02
ACGTcount: A:0.34, C:0.02, G:0.16, T:0.48
Consensus pattern (9 bp):
AAGTTATGT
Found at i:16741669 original size:27 final size:27
Alignment explanation
Indices: 16741631--16741781 Score: 257
Period size: 27 Copynumber: 5.6 Consensus size: 27
16741621 CAATCGGTCA
16741631 AAGTTATGTAAGTTATTTAATTTATGT
1 AAGTTATGTAAGTTATTTAATTTATGT
16741658 AAGTTATGTAAGTTATTTAATTTATGT
1 AAGTTATGTAAGTTATTTAATTTATGT
16741685 AAGTTATGTAAGTTATTTAATTTATGT
1 AAGTTATGTAAGTTATTTAATTTATGT
16741712 AAGTTATGTAAGTTATTTAATTTATGT
1 AAGTTATGTAAGTTATTTAATTTATGT
* * * *
16741739 AGGTTATGTAAGTTATGTAAGTTATCT
1 AAGTTATGTAAGTTATTTAATTTATGT
*
16741766 AATTTATGTAAGTTAT
1 AAGTTATGTAAGTTAT
16741782 GCAAGCTTAT
Statistics
Matches: 118, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 118 1.00
ACGTcount: A:0.33, C:0.01, G:0.16, T:0.50
Consensus pattern (27 bp):
AAGTTATGTAAGTTATTTAATTTATGT
Found at i:16741893 original size:21 final size:21
Alignment explanation
Indices: 16741869--16741919 Score: 77
Period size: 21 Copynumber: 2.4 Consensus size: 21
16741859 AATTATTATG
16741869 TAAGTTATGCAAGCTTAAATA
1 TAAGTTATGCAAGCTTAAATA
*
16741890 TAAGTTATGCAAGCTTATATA
1 TAAGTTATGCAAGCTTAAATA
16741911 -ATAGTTATG
1 TA-AGTTATG
16741920 TATTATAACA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
20 1 0.04
21 27 0.96
ACGTcount: A:0.39, C:0.08, G:0.16, T:0.37
Consensus pattern (21 bp):
TAAGTTATGCAAGCTTAAATA
Found at i:16741903 original size:116 final size:116
Alignment explanation
Indices: 16741774--16742014 Score: 432
Period size: 116 Copynumber: 2.1 Consensus size: 116
16741764 CTAATTTATG
16741774 TAAGTTATGCAAGCTTATATACA-AGTTATGTATTATAACATAAAGTATTATGTAATTTAT-TAT
1 TAAGTTATGCAAGCTTATATA-ATAGTTATGTATTATAACATAAAGTATTATGTAATTTATGT-T
16741837 GCTATTATATATAAGTTATGTAAATTATTATGTAAGTTATGCAAGCTTAAATA
64 GCTATTATATATAAGTTATGTAAATTATTATGTAAGTTATGCAAGCTTAAATA
*
16741890 TAAGTTATGCAAGCTTATATAATAGTTATGTATTATAACATAAAGTATTATGTAATTTATGTTGT
1 TAAGTTATGCAAGCTTATATAATAGTTATGTATTATAACATAAAGTATTATGTAATTTATGTTGC
*
16741955 TATTATATATAAGTTCTGTAAATTATTATGTAAGTTATGCAAGCTTAAATA
66 TATTATATATAAGTTATGTAAATTATTATGTAAGTTATGCAAGCTTAAATA
16742006 TAAGTTATG
1 TAAGTTATG
16742015 TATTATATAA
Statistics
Matches: 121, Mismatches: 2, Indels: 4
0.95 0.02 0.03
Matches are distributed among these distances:
115 1 0.01
116 119 0.98
117 1 0.01
ACGTcount: A:0.39, C:0.05, G:0.13, T:0.43
Consensus pattern (116 bp):
TAAGTTATGCAAGCTTATATAATAGTTATGTATTATAACATAAAGTATTATGTAATTTATGTTGC
TATTATATATAAGTTATGTAAATTATTATGTAAGTTATGCAAGCTTAAATA
Found at i:16741911 original size:19 final size:19
Alignment explanation
Indices: 16741864--16741911 Score: 69
Period size: 21 Copynumber: 2.4 Consensus size: 19
16741854 ATGTAAATTA
*
16741864 TTATGTAAGTTATGCAAGC
1 TTATATAAGTTATGCAAGC
16741883 TTAAATATAAGTTATGCAAGC
1 TT--ATATAAGTTATGCAAGC
16741904 TTATATAA
1 TTATATAA
16741912 TAGTTATGTA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
19 8 0.31
21 18 0.69
ACGTcount: A:0.40, C:0.08, G:0.15, T:0.38
Consensus pattern (19 bp):
TTATATAAGTTATGCAAGC
Found at i:16742024 original size:16 final size:16
Alignment explanation
Indices: 16742003--16742066 Score: 56
Period size: 16 Copynumber: 3.9 Consensus size: 16
16741993 GCAAGCTTAA
16742003 ATATAAGTTATGTATT
1 ATATAAGTTATGTATT
* *
16742019 ATATAAGTTTTGTAAGAT
1 ATATAAGTTATGT-A-TT
* **
16742037 ATGTAAGTGGTGTATT
1 ATATAAGTTATGTATT
*
16742053 ATGTAAGTTATGTA
1 ATATAAGTTATGTA
16742067 GAAAACTTAT
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
16 25 0.66
17 2 0.05
18 11 0.29
ACGTcount: A:0.34, C:0.00, G:0.20, T:0.45
Consensus pattern (16 bp):
ATATAAGTTATGTATT
Found at i:16742063 original size:9 final size:9
Alignment explanation
Indices: 16741980--16742066 Score: 56
Period size: 9 Copynumber: 9.8 Consensus size: 9
16741970 CTGTAAATTA
16741980 TTATGTAAG
1 TTATGTAAG
*
16741989 TTATGCAAG
1 TTATGTAAG
*
16741998 CTTAAATATAAG
1 -TT--ATGTAAG
16742010 TTATGT-A-
1 TTATGTAAG
*
16742017 TTATATAAG
1 TTATGTAAG
*
16742026 TTTTGTAAG
1 TTATGTAAG
*
16742035 ATATGTAAG
1 TTATGTAAG
**
16742044 TGGTGT-A-
1 TTATGTAAG
16742051 TTATGTAAG
1 TTATGTAAG
16742060 TTATGTA
1 TTATGTA
16742067 GAAAACTTAT
Statistics
Matches: 57, Mismatches: 14, Indels: 14
0.67 0.16 0.16
Matches are distributed among these distances:
7 9 0.16
8 4 0.07
9 35 0.61
10 2 0.04
11 2 0.04
12 5 0.09
ACGTcount: A:0.34, C:0.02, G:0.20, T:0.44
Consensus pattern (9 bp):
TTATGTAAG
Found at i:16742163 original size:16 final size:16
Alignment explanation
Indices: 16742138--16742175 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
16742128 GAAAACGAAG
*
16742138 TAAA-TTTAATACTAA
1 TAAATTTTAATACAAA
16742153 TAAATTTTAATACAAA
1 TAAATTTTAATACAAA
16742169 TAAATTT
1 TAAATTT
16742176 AGAAAACTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 4 0.19
16 17 0.81
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (16 bp):
TAAATTTTAATACAAA
Found at i:16742190 original size:17 final size:17
Alignment explanation
Indices: 16742168--16742204 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
16742158 TTTAATACAA
16742168 ATAAATTTAGAAAACTT
1 ATAAATTTAGAAAACTT
16742185 ATAAATTTAGAAAACTT
1 ATAAATTTAGAAAACTT
16742202 ATA
1 ATA
16742205 TAGATATTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.54, C:0.05, G:0.05, T:0.35
Consensus pattern (17 bp):
ATAAATTTAGAAAACTT
Found at i:16747012 original size:29 final size:30
Alignment explanation
Indices: 16746969--16747027 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
16746959 AAATTGAATT
*
16746969 AAATTAAAATTTCATATATAAAATTATACA
1 AAATTAAAAGTTCATATATAAAATTATACA
* * *
16746999 AAATT-AAAGTTCATGTATGATATTATACA
1 AAATTAAAAGTTCATATATAAAATTATACA
16747028 TTAAATCAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 20 0.80
30 5 0.20
ACGTcount: A:0.51, C:0.07, G:0.05, T:0.37
Consensus pattern (30 bp):
AAATTAAAAGTTCATATATAAAATTATACA
Found at i:16750224 original size:26 final size:26
Alignment explanation
Indices: 16750195--16750248 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 26
16750185 AAATAAGTAT
* * *
16750195 TAATAATTTTATTTAATATTTATTTA
1 TAATAATTATAATTAATATTTAATTA
* *
16750221 TAATAGTTATAATTATTATTTAATTA
1 TAATAATTATAATTAATATTTAATTA
16750247 TA
1 TA
16750249 TTTAAATAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (26 bp):
TAATAATTATAATTAATATTTAATTA
Found at i:16763401 original size:22 final size:22
Alignment explanation
Indices: 16763376--16763444 Score: 102
Period size: 22 Copynumber: 3.1 Consensus size: 22
16763366 ACAAATCCTA
*
16763376 TCTCAATTTCATTCAAAAATTC
1 TCTCAATTTCCTTCAAAAATTC
**
16763398 TCTCAAAGTCCTTCAAAAATTC
1 TCTCAATTTCCTTCAAAAATTC
*
16763420 TCTCAATTTCCTTCCAAAATTC
1 TCTCAATTTCCTTCAAAAATTC
16763442 TCT
1 TCT
16763445 TAAACTCTCG
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 41 1.00
ACGTcount: A:0.32, C:0.28, G:0.01, T:0.39
Consensus pattern (22 bp):
TCTCAATTTCCTTCAAAAATTC
Found at i:16763479 original size:52 final size:51
Alignment explanation
Indices: 16763397--16763502 Score: 140
Period size: 52 Copynumber: 2.1 Consensus size: 51
16763387 TTCAAAAATT
* * *
16763397 CTCTCAAAGTCCTTCAAAAATTCTCTCAATTTCCTTCCAAAATTCTCTTAAA
1 CTCTCAAAGTCCTTCAAAAATCCTCACAATTTCCTTCCAAAAATCTC-TAAA
* * * *
16763449 CTCTCGAATTCCTTCCAAAATCCTCACAATTTCCTTCGAAAAATCTCTAAA
1 CTCTCAAAGTCCTTCAAAAATCCTCACAATTTCCTTCCAAAAATCTCTAAA
16763500 CTC
1 CTC
16763503 CATATTAAAT
Statistics
Matches: 47, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
51 7 0.15
52 40 0.85
ACGTcount: A:0.32, C:0.31, G:0.03, T:0.34
Consensus pattern (51 bp):
CTCTCAAAGTCCTTCAAAAATCCTCACAATTTCCTTCCAAAAATCTCTAAA
Found at i:16763580 original size:29 final size:29
Alignment explanation
Indices: 16763535--16763592 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
16763525 TCAATTTCAT
16763535 TTTTTTTAAAGAAAATTTTAAATATTTTTA
1 TTTTTTTAAAGAAAATTTTAAA-ATTTTTA
*
16763565 TTTTTTTAAA-ATAATTTTAAAATTTTTA
1 TTTTTTTAAAGAAAATTTTAAAATTTTTA
16763593 ATATTTTCTG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 7 0.26
29 10 0.37
30 10 0.37
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.59
Consensus pattern (29 bp):
TTTTTTTAAAGAAAATTTTAAAATTTTTA
Found at i:16763599 original size:29 final size:30
Alignment explanation
Indices: 16763537--16763599 Score: 85
Period size: 29 Copynumber: 2.1 Consensus size: 30
16763527 AATTTCATTT
*
16763537 TTTTTAAAGAAAATTTTAAATATTTTTATT
1 TTTTTAAAGAAAATTTTAAATATTTTTATA
*
16763567 TTTTTAAA-ATAATTTTAAA-ATTTTTAATA
1 TTTTTAAAGAAAATTTTAAATATTTTT-ATA
16763596 TTTT
1 TTTT
16763600 CTGCTATGGC
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
28 6 0.20
29 16 0.53
30 8 0.27
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.59
Consensus pattern (30 bp):
TTTTTAAAGAAAATTTTAAATATTTTTATA
Found at i:16769724 original size:125 final size:125
Alignment explanation
Indices: 16769502--16769904 Score: 588
Period size: 125 Copynumber: 3.2 Consensus size: 125
16769492 CACGAGGGCA
* * *
16769502 CGATTTTACACTATTTGCTCAGAAACGTCAAAAAAAAATCATTTCCTATATGACCAACTGTAGCA
1 CGATTTTACACTATTTGCTCAGAAACGTCAAAAAAAAATTATTTCCTACATGACCAACTGTAGCG
* *
16769567 AAATCGCGTCCACGAGGGCGCAATTTCACAATTTCTTCTCATATAGCATCCTAGTATCAG
66 AAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCATATAGCATCCTGGTATCAG
16769627 CGATTTTACACTATTTGCTCAGAAACGTCAAAAAAAAATTATTTCCTACATGACCAACTGTAGCG
1 CGATTTTACACTATTTGCTCAGAAACGTCAAAAAAAAATTATTTCCTACATGACCAACTGTAGCG
*
16769692 AAATCGCATCCACGAGGGCGCGATTTCACAATTTCTTCTCATATAGCATCCTGGTATCAG
66 AAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCATATAGCATCCTGGTATCAG
* *
16769752 CGATTTTATACTATTTGCTCAGAAAACGTC--AAAAAAATTATTTCTTACATGACCAACTGT-GC
1 CGATTTTACACTATTTGCTCAG-AAACGTCAAAAAAAAATTATTTCCTACATGACCAACTGTAGC
* * **
16769814 TGAAAT-GACGTCTACGAGGGCACGATTT--CAATTTCTTCTC-TGATAGCATCCTGGTAGAAG
65 -GAAATCG-CGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAT-ATAGCATCCTGGTATCAG
*
16769874 CGATTTTATACTATTTGAC-CAGAAACGTCAA
1 CGATTTTACACTATTTG-CTCAGAAACGTCAA
16769905 CTCGAAATAA
Statistics
Matches: 258, Mismatches: 13, Indels: 16
0.90 0.05 0.06
Matches are distributed among these distances:
121 8 0.03
122 48 0.19
123 4 0.02
124 51 0.20
125 140 0.54
126 7 0.03
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.30
Consensus pattern (125 bp):
CGATTTTACACTATTTGCTCAGAAACGTCAAAAAAAAATTATTTCCTACATGACCAACTGTAGCG
AAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCATATAGCATCCTGGTATCAG
Found at i:16770003 original size:51 final size:51
Alignment explanation
Indices: 16769907--16770061 Score: 215
Period size: 51 Copynumber: 3.0 Consensus size: 51
16769897 AACGTCAACT
* *
16769907 CGAAATAATTTTTTCCGGGACCCCTAAACCTTAAAAAAGCTTGCACCCTAAA
1 CGAAATAATTTTTTTC-GGACCCCTAAACCCTAAAAAAGCTTGCACCCTAAA
*
16769959 CGAAATAATTTTTTTCGGCACCCCTAAACCCT-AAAAAGCCTGCACCCTAAA
1 CGAAATAATTTTTTTCGG-ACCCCTAAACCCTAAAAAAGCTTGCACCCTAAA
** *
16770010 TAAAATAA-TTTTTTCGAGACCCCTAAACCCTAAAAAAGCTTACACCCTAAA
1 CGAAATAATTTTTTTCG-GACCCCTAAACCCTAAAAAAGCTTGCACCCTAAA
16770061 C
1 C
16770062 CCTAAAACCC
Statistics
Matches: 92, Mismatches: 8, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
50 21 0.23
51 44 0.48
52 27 0.29
ACGTcount: A:0.38, C:0.28, G:0.09, T:0.25
Consensus pattern (51 bp):
CGAAATAATTTTTTTCGGACCCCTAAACCCTAAAAAAGCTTGCACCCTAAA
Found at i:16772826 original size:28 final size:28
Alignment explanation
Indices: 16772790--16772844 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
16772780 GAAAAAATTA
16772790 AATTGTTTTAAAAAAT-AAAAATATAGG
1 AATTGTTTTAAAAAATAAAAAATATAGG
*
16772817 AATTAGTTTTAACAAATAAAAAATATAG
1 AATT-GTTTTAAAAAATAAAAAATATAG
16772845 AAAAAATACG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 4 0.16
28 11 0.44
29 10 0.40
ACGTcount: A:0.56, C:0.02, G:0.09, T:0.33
Consensus pattern (28 bp):
AATTGTTTTAAAAAATAAAAAATATAGG
Found at i:16773704 original size:12 final size:12
Alignment explanation
Indices: 16773687--16773740 Score: 71
Period size: 11 Copynumber: 4.8 Consensus size: 12
16773677 AACTAATCCT
16773687 CTCTCAAATTTC
1 CTCTCAAATTTC
16773699 CTCTC-AATTTC
1 CTCTCAAATTTC
16773710 CTCTC-AATTTC
1 CTCTCAAATTTC
16773721 CT-TCAAAATTT-
1 CTCTC-AAATTTC
16773732 CTCTCAAAT
1 CTCTCAAAT
16773741 CCATATTTAA
Statistics
Matches: 39, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
10 2 0.05
11 25 0.64
12 12 0.31
ACGTcount: A:0.26, C:0.31, G:0.00, T:0.43
Consensus pattern (12 bp):
CTCTCAAATTTC
Found at i:16773827 original size:16 final size:16
Alignment explanation
Indices: 16773802--16773832 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
16773792 CTCTATTTTT
16773802 AAATAATTTTTAAAAA
1 AAATAATTTTTAAAAA
*
16773818 AAATATTTTTTAAAA
1 AAATAATTTTTAAAA
16773833 TTTTTTTTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
AAATAATTTTTAAAAA
Found at i:16774953 original size:7 final size:7
Alignment explanation
Indices: 16774941--16774966 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
16774931 TAGTCGATTG
16774941 GTATTTA
1 GTATTTA
16774948 GTATTTA
1 GTATTTA
16774955 GTATTTA
1 GTATTTA
16774962 GTATT
1 GTATT
16774967 ATGTGTATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.15, T:0.58
Consensus pattern (7 bp):
GTATTTA
Found at i:16776181 original size:64 final size:64
Alignment explanation
Indices: 16776113--16776236 Score: 239
Period size: 64 Copynumber: 1.9 Consensus size: 64
16776103 TAAAAAATTA
*
16776113 TTTGAGTTATTTTGATATTATTTGATGTAATAACATGAGCTTAATTAATTTGTACAAATATTTT
1 TTTGAGTTATTTTGATATTATTTGATGTAATAACACGAGCTTAATTAATTTGTACAAATATTTT
16776177 TTTGAGTTATTTTGATATTATTTGATGTAATAACACGAGCTTAATTAATTTGTACAAATA
1 TTTGAGTTATTTTGATATTATTTGATGTAATAACACGAGCTTAATTAATTTGTACAAATA
16776237 ATTGAAAAAA
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
64 59 1.00
ACGTcount: A:0.34, C:0.06, G:0.13, T:0.48
Consensus pattern (64 bp):
TTTGAGTTATTTTGATATTATTTGATGTAATAACACGAGCTTAATTAATTTGTACAAATATTTT
Found at i:16779407 original size:124 final size:124
Alignment explanation
Indices: 16779241--16779590 Score: 610
Period size: 124 Copynumber: 2.8 Consensus size: 124
16779231 CCTAAACATG
* *
16779241 CTACTGTAGCAAAATCGCGTCCATGAGGGCGCGATTTTACAAATTCTTCTCAAATAGCATCCTGC
1 CTACTGTAGCAAAATCGCGTCCATGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCAGC
*
16779306 TAGAAGCGATTTTATACTATTTGCTCAAAAACGTCAAAAAAAATTATTTCTTCCATGAC
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAATTATTTCTTCCATGAC
* * *
16779365 CTACTGTAGCAAAATCACGTCCACGAGGGCGTGATTTCACAAATTCTTCTCAAATAGCATCCAGC
1 CTACTGTAGCAAAATCGCGTCCATGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCAGC
*
16779430 TAGAAGCGATTTTATACTATTTCCTCAGAAACGTCAAAAAAAATTATTTCTTCCATGAC
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAATTATTTCTTCCATGAC
* *
16779489 CTACTGTAGCAAAAGCGCGTCCATGAGGGCGCGATTTCACAAATTCTTCTCAAATAACATCCAGC
1 CTACTGTAGCAAAATCGCGTCCATGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCAGC
*
16779554 TAGAAGCGATTTTATACTATTTGATCAGAAACGTCAA
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAA
16779591 CTCGAAATTA
Statistics
Matches: 212, Mismatches: 14, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
124 212 1.00
ACGTcount: A:0.33, C:0.23, G:0.15, T:0.29
Consensus pattern (124 bp):
CTACTGTAGCAAAATCGCGTCCATGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCAGC
TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAATTATTTCTTCCATGAC
Found at i:16803383 original size:19 final size:20
Alignment explanation
Indices: 16803336--16803384 Score: 59
Period size: 18 Copynumber: 2.5 Consensus size: 20
16803326 TTAGGCCATT
16803336 ATGGGCCTCGT-TGGGCTAAA
1 ATGGG-CTCGTGTGGGCTAAA
*
16803356 ATGGG-TCGTGTGGG-TCAA
1 ATGGGCTCGTGTGGGCTAAA
16803374 ATGGGCTCGTG
1 ATGGGCTCGTG
16803385 GGCCCCACAC
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 12 0.46
19 9 0.35
20 5 0.19
ACGTcount: A:0.16, C:0.16, G:0.41, T:0.27
Consensus pattern (20 bp):
ATGGGCTCGTGTGGGCTAAA
Found at i:16806902 original size:28 final size:27
Alignment explanation
Indices: 16806851--16806904 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 27
16806841 CTGATACTAA
*
16806851 TTCTGTAATGGGCTTAGGTCCACCTGG
1 TTCTGTAATGGGCTAAGGTCCACCTGG
16806878 TTCTGTTAATGGGCTAAGG-CTCACCTG
1 TTCTG-TAATGGGCTAAGGTC-CACCTG
16806905 ATACTATGCC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 6 0.25
28 18 0.75
ACGTcount: A:0.17, C:0.22, G:0.28, T:0.33
Consensus pattern (27 bp):
TTCTGTAATGGGCTAAGGTCCACCTGG
Found at i:16817394 original size:10 final size:10
Alignment explanation
Indices: 16817379--16817406 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
16817369 CTTAGCTTAG
16817379 AATTAGGATT
1 AATTAGGATT
16817389 AATTAGGATT
1 AATTAGGATT
16817399 AATTAGGA
1 AATTAGGA
16817407 ATTTTTTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.43, C:0.00, G:0.21, T:0.36
Consensus pattern (10 bp):
AATTAGGATT
Found at i:16821904 original size:12 final size:11
Alignment explanation
Indices: 16821812--16821905 Score: 57
Period size: 12 Copynumber: 8.2 Consensus size: 11
16821802 AAATAATAAT
*
16821812 AAAACAAAA-A
1 AAAAGAAAAGA
* *
16821822 AAATGAAATGA
1 AAAAGAAAAGA
16821833 AAAAGAAATAGA
1 AAAAGAAA-AGA
*
16821845 AAAAGAAAA-T
1 AAAAGAAAAGA
** *
16821855 AATTGAAACGA
1 AAAAGAAAAGA
16821866 AAACAGAAAAGGAA
1 AAA-AGAAAA-G-A
16821880 CAAAAGAAAAGA
1 -AAAAGAAAAGA
16821892 AAAAGAGAAAGA
1 AAAAGA-AAAGA
16821904 AA
1 AA
16821906 GGAGAAAAAG
Statistics
Matches: 63, Mismatches: 13, Indels: 14
0.70 0.14 0.16
Matches are distributed among these distances:
10 12 0.19
11 17 0.27
12 22 0.35
13 2 0.03
14 7 0.11
15 3 0.05
ACGTcount: A:0.73, C:0.04, G:0.16, T:0.06
Consensus pattern (11 bp):
AAAAGAAAAGA
Found at i:16825495 original size:11 final size:12
Alignment explanation
Indices: 16825475--16825507 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
16825465 AATAAAACAA
16825475 AAAAATGAAAT-G
1 AAAAA-GAAATAG
16825487 AAAAAGAAATAG
1 AAAAAGAAATAG
16825499 AAAAAGAAA
1 AAAAAGAAA
16825508 CAAATTGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 5 0.25
12 15 0.75
ACGTcount: A:0.76, C:0.00, G:0.15, T:0.09
Consensus pattern (12 bp):
AAAAAGAAATAG
Found at i:16825556 original size:17 final size:18
Alignment explanation
Indices: 16825536--16825570 Score: 54
Period size: 17 Copynumber: 1.9 Consensus size: 18
16825526 AAAAAGGAAC
16825536 GAAAGAAA-AGAAAAAGA
1 GAAAGAAAGAGAAAAAGA
16825553 GAAAGAAAGGAGAAAAAG
1 GAAAGAAA-GAGAAAAAG
16825571 CTAGGGTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
19 8 0.50
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (18 bp):
GAAAGAAAGAGAAAAAGA
Found at i:16826551 original size:40 final size:39
Alignment explanation
Indices: 16826426--16826544 Score: 113
Period size: 37 Copynumber: 3.1 Consensus size: 39
16826416 CGACTTTGAT
* *
16826426 TTGATGAGACACTGGGTGTCAATTTACTACTTC-AGATTAA
1 TTGATGAGACACTGGGTGTCAAATTATTACTTCGA-ATT-A
* **
16826466 TTTGATGACG-CACTGGGTG-CCAA-T-TTACTTCGGTTTA
1 -TTGATGA-GACACTGGGTGTCAAATTATTACTTCGAATTA
16826503 GTTGATGAGACACTGGGTGTCAAATTATTACTTCGAATTA
1 -TTGATGAGACACTGGGTGTCAAATTATTACTTCGAATTA
16826543 TT
1 TT
16826545 CAATGAGGCA
Statistics
Matches: 63, Mismatches: 9, Indels: 14
0.73 0.10 0.16
Matches are distributed among these distances:
36 1 0.02
37 17 0.27
38 11 0.17
39 4 0.06
40 13 0.21
41 16 0.25
42 1 0.02
ACGTcount: A:0.26, C:0.15, G:0.22, T:0.37
Consensus pattern (39 bp):
TTGATGAGACACTGGGTGTCAAATTATTACTTCGAATTA
Found at i:16840429 original size:3 final size:3
Alignment explanation
Indices: 16840421--16840447 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
16840411 TAGTTAACAA
16840421 AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG
16840448 GGGAAATGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:16840626 original size:3 final size:3
Alignment explanation
Indices: 16840618--16840648 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
16840608 AGAATTTTTC
*
16840618 TCT TCT TCT TCT TCT TCT TAT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
16840649 ACACAGTGGG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.03, C:0.29, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:16841201 original size:2 final size:2
Alignment explanation
Indices: 16841194--16841228 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
16841184 ATAACATTGT
16841194 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 T
16841229 TGTTAAATGG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:16844364 original size:22 final size:22
Alignment explanation
Indices: 16844336--16844404 Score: 86
Period size: 22 Copynumber: 3.1 Consensus size: 22
16844326 TATGCACTAT
16844336 TAAACAGAGAGCACTAAAGTGC
1 TAAACAGAGAGCACTAAAGTGC
* *
16844358 TATACAGAGAACAC-AAATGTGC
1 TAAACAGAGAGCACTAAA-GTGC
* *
16844380 TAAACGGAGAGCACTAATGTGC
1 TAAACAGAGAGCACTAAAGTGC
16844402 TAA
1 TAA
16844405 TAATCGGAGA
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
21 3 0.08
22 34 0.87
23 2 0.05
ACGTcount: A:0.43, C:0.17, G:0.22, T:0.17
Consensus pattern (22 bp):
TAAACAGAGAGCACTAAAGTGC
Found at i:16846880 original size:12 final size:13
Alignment explanation
Indices: 16846863--16846895 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
16846853 TATCATTATT
16846863 TAAAATAAA-TTA
1 TAAAATAAAGTTA
16846875 TAAAATAAAGTTA
1 TAAAATAAAGTTA
*
16846888 AAAAATAA
1 TAAAATAA
16846896 TGAAGTCAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 9 0.47
13 10 0.53
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (13 bp):
TAAAATAAAGTTA
Found at i:16846958 original size:22 final size:22
Alignment explanation
Indices: 16846927--16846968 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
16846917 CTTTATTCCT
* *
16846927 AATTTCTATATATTAATAAAGG
1 AATTTATATAGATTAATAAAGG
16846949 AATTTATATAGATTAATAAA
1 AATTTATATAGATTAATAAA
16846969 TTAGCATGAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.50, C:0.02, G:0.07, T:0.40
Consensus pattern (22 bp):
AATTTATATAGATTAATAAAGG
Found at i:16848662 original size:10 final size:10
Alignment explanation
Indices: 16848647--16848671 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
16848637 ATGTATAAAA
16848647 ATAAAATATT
1 ATAAAATATT
16848657 ATAAAATATT
1 ATAAAATATT
16848667 ATAAA
1 ATAAA
16848672 CTTAAAATCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (10 bp):
ATAAAATATT
Found at i:16848686 original size:12 final size:12
Alignment explanation
Indices: 16848669--16848693 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
16848659 AAAATATTAT
16848669 AAACTTAAAATC
1 AAACTTAAAATC
16848681 AAACTTAAAATC
1 AAACTTAAAATC
16848693 A
1 A
16848694 GGGTGAGCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.16, G:0.00, T:0.24
Consensus pattern (12 bp):
AAACTTAAAATC
Found at i:16852404 original size:98 final size:98
Alignment explanation
Indices: 16852276--16852468 Score: 296
Period size: 98 Copynumber: 2.0 Consensus size: 98
16852266 AAAAATCATA
* * *
16852276 AAGGAAATTTTCCGAGTTTGGGATTATAAAGGAATTGTACCCTAACGTATTGAGTGTGATTTCTT
1 AAGGAAATATTCCGAGTTTGAGATTATAAAGGAATCGTACCCTAACGTATTGAGTGTGATTTCTT
*
16852341 AAATCTTGGATAAGCGGATGTTCTTTTAAAATG
66 AAATCTTGGATAAGCGGATGTTCCTTTAAAATG
* * * *
16852374 AAGGAAATATTCCGAGTTTGAGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGTTTTCTT
1 AAGGAAATATTCCGAGTTTGAGATTATAAAGGAATCGTACCCTAACGTATTGAGTGTGATTTCTT
* *
16852439 AGATCTTGGATAAGTGGATGTTCCTTTAAA
66 AAATCTTGGATAAGCGGATGTTCCTTTAAA
16852469 GTTTTTCATT
Statistics
Matches: 85, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
98 85 1.00
ACGTcount: A:0.29, C:0.11, G:0.23, T:0.36
Consensus pattern (98 bp):
AAGGAAATATTCCGAGTTTGAGATTATAAAGGAATCGTACCCTAACGTATTGAGTGTGATTTCTT
AAATCTTGGATAAGCGGATGTTCCTTTAAAATG
Found at i:16864001 original size:45 final size:46
Alignment explanation
Indices: 16863896--16864328 Score: 216
Period size: 45 Copynumber: 9.7 Consensus size: 46
16863886 TCGCATCTAG
* * * *
16863896 TCTTATCTCCCTGAAGTTACGGTG-GAGCAGACT-AAG-TAAGCAAG
1 TCTTATCTCCCTGAAGTTGCAGTGAGAGCAGACTGAAGAT-GGCAAA
* *
16863940 TCTTTTC-CTCCTGAAGTTGCAATGAG-GCAGACTGAAGATGGCAAA
1 TCTTATCTC-CCTGAAGTTGCAGTGAGAGCAGACTGAAGATGGCAAA
* *
16863985 TCTTATCTCCCTGAAGTTGCAGTG-GAGCAGA-TTAA-A-GCCGATAA
1 TCTTATCTCCCTGAAGTTGCAGTGAGAGCAGACTGAAGATGGC-A-AA
* * * * * * *** *
16864029 TCCTATCTCCCTGAAGTTACA-TTAGAGCGGA-TTAAAACCTCAGA
1 TCTTATCTCCCTGAAGTTGCAGTGAGAGCAGACTGAAGATGGCAAA
* * * * *
16864073 TCTTATCTCTCTGAAGTTGCA--AAGAGCAGA-TCG--TAT--CTAG
1 TCTTATCTCCCTGAAGTTGCAGTGAGAGCAGACT-GAAGATGGCAAA
* ** *
16864113 TCTTATCTCCCTAAAGTTGCAGTG-GAGCAGACT-AAGCAAAGCAAG
1 TCTTATCTCCCTGAAGTTGCAGTGAGAGCAGACTGAAG-ATGGCAAA
* ** * * *
16864158 TCTTATC-CTCCTGAAGTTGCAGTGAGTTGCAGAGAGTAGATCGCATCTAG
1 TCTTATCTC-CCTGAAGTTGCAGTGAG-AGCAGACTGAAGATGGCA---AA
* * **
16864208 TCTTATCTCTCTGAAATTGCAGTG-GAGCAGACT-AAGCAAAGCAAA
1 TCTTATCTCCCTGAAGTTGCAGTGAGAGCAGACTGAAG-ATGGCAAA
*
16864253 TCTTATC-CTCCTGAAGTTGCAGTGAGA-CAGACCGAAGATGGCAAA
1 TCTTATCTC-CCTGAAGTTGCAGTGAGAGCAGACTGAAGATGGCAAA
*
16864298 TCTTATCTCCCTGAAGTTGCGGTG-GAGCAGA
1 TCTTATCTCCCTGAAGTTGCAGTGAGAGCAGA
16864329 TTAAAGCCAA
Statistics
Matches: 299, Mismatches: 56, Indels: 67
0.71 0.13 0.16
Matches are distributed among these distances:
40 20 0.07
41 7 0.02
42 4 0.01
43 13 0.04
44 83 0.28
45 116 0.39
46 10 0.03
47 11 0.04
48 11 0.04
49 1 0.00
50 22 0.07
51 1 0.00
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Consensus pattern (46 bp):
TCTTATCTCCCTGAAGTTGCAGTGAGAGCAGACTGAAGATGGCAAA
Found at i:16864080 original size:44 final size:43
Alignment explanation
Indices: 16863983--16864103 Score: 120
Period size: 44 Copynumber: 2.8 Consensus size: 43
16863973 GAAGATGGCA
* * *
16863983 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGAT
1 AATCTTATCTCCCTGAAGTTACAGTAGAGCAGATTAAAACC-AT
* * *
16864027 AATCCTATCTCCCTGAAGTTACATTAGAGCGGATTAAAACC-T
1 AATCTTATCTCCCTGAAGTTACAGTAGAGCAGATTAAAACCAT
* * *
16864069 CAGATCTTATCTCTCTGAAGTTGCA-AAGAGCAGAT
1 -A-ATCTTATCTCCCTGAAGTTACAGTAGAGCAGAT
16864104 CGTATCTAGT
Statistics
Matches: 64, Mismatches: 11, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
42 1 0.02
43 9 0.14
44 54 0.84
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.28
Consensus pattern (43 bp):
AATCTTATCTCCCTGAAGTTACAGTAGAGCAGATTAAAACCAT
Found at i:16864250 original size:95 final size:95
Alignment explanation
Indices: 16864087--16864278 Score: 323
Period size: 95 Copynumber: 2.0 Consensus size: 95
16864077 ATCTCTCTGA
*
16864087 AGTTGCAAAGAGCAGATCGTATCTAGTCTTATCTCCCTAAAGTTGCAGTGGAGCAGACTAAGCAA
1 AGTTGCAAAGAGCAGATCGCATCTAGTCTTATCTCCCTAAAGTTGCAGTGGAGCAGACTAAGCAA
*
16864152 AGCAAGTCTTATCCTCCTGAAGTTGCAGTG
66 AGCAAATCTTATCCTCCTGAAGTTGCAGTG
* * *
16864182 AGTTGCAGAGAGTAGATCGCATCTAGTCTTATCTCTCTGAAA-TTGCAGTGGAGCAGACTAAGCA
1 AGTTGCAAAGAGCAGATCGCATCTAGTCTTATCTCCCT-AAAGTTGCAGTGGAGCAGACTAAGCA
16864246 AAGCAAATCTTATCCTCCTGAAGTTGCAGTG
65 AAGCAAATCTTATCCTCCTGAAGTTGCAGTG
16864277 AG
1 AG
16864279 ACAGACCGAA
Statistics
Matches: 91, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
95 88 0.97
96 3 0.03
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (95 bp):
AGTTGCAAAGAGCAGATCGCATCTAGTCTTATCTCCCTAAAGTTGCAGTGGAGCAGACTAAGCAA
AGCAAATCTTATCCTCCTGAAGTTGCAGTG
Found at i:16864400 original size:66 final size:66
Alignment explanation
Indices: 16864294--16864462 Score: 311
Period size: 66 Copynumber: 2.6 Consensus size: 66
16864284 CCGAAGATGG
16864294 CAAATCTTATCTCCCTGAAGTTGCGGTGGAGCAGATTAAAGCCAACAGTGGAGCGGGTTAAAACC
1 CAAATCTTATCTCCCTGAAGTTGCGGTGGAGCAGATTAAAGCCAACAGTGGAGCGGGTTAAAACC
16864359 T
66 T
*
16864360 CAAATCTTATCTCCCTGAAGTTACGGTGGAGCAGATTAAAGCCAACAGTGGAGCGGGTTAAAACC
1 CAAATCTTATCTCCCTGAAGTTGCGGTGGAGCAGATTAAAGCCAACAGTGGAGCGGGTTAAAACC
16864425 T
66 T
* *
16864426 CAGATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATT
1 CAAATCTTATCTCCCTGAAGTTGCGGTGGAGCAGATT
16864463 GGTAGATCAA
Statistics
Matches: 99, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
66 99 1.00
ACGTcount: A:0.30, C:0.21, G:0.25, T:0.24
Consensus pattern (66 bp):
CAAATCTTATCTCCCTGAAGTTGCGGTGGAGCAGATTAAAGCCAACAGTGGAGCGGGTTAAAACC
T
Found at i:16866480 original size:98 final size:98
Alignment explanation
Indices: 16866366--16866559 Score: 316
Period size: 98 Copynumber: 2.0 Consensus size: 98
16866356 AAAATCATAA
*
16866366 AGGAAATTTTTCGAGTTTGGGATTATAAAGGAATTGTGCCATAACATATTGGGTGTGATTTCTTA
1 AGGAAATATTTCGAGTTTGGGATTATAAAGGAATTGTGCCATAACATATTGGGTGTGATTTCTTA
*
16866431 AATCTTGGATAAGCGGATGTTCTTTTAAAGTGT
66 AATCTTGGATAAGCGGATGTTCCTTTAAAGTGT
* * ** *
16866464 AGGAAATATTTCGAGTTTGGGATTCTAAAGGAATTGTGCCCTAATGTATTGGGTGTGTTTTCTTA
1 AGGAAATATTTCGAGTTTGGGATTATAAAGGAATTGTGCCATAACATATTGGGTGTGATTTCTTA
*
16866529 AATCTTGGATAAGTGGATGTTCCTTTAAAGT
66 AATCTTGGATAAGCGGATGTTCCTTTAAAGT
16866560 TTTTCATTAT
Statistics
Matches: 88, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
98 88 1.00
ACGTcount: A:0.27, C:0.09, G:0.25, T:0.39
Consensus pattern (98 bp):
AGGAAATATTTCGAGTTTGGGATTATAAAGGAATTGTGCCATAACATATTGGGTGTGATTTCTTA
AATCTTGGATAAGCGGATGTTCCTTTAAAGTGT
Found at i:16874080 original size:12 final size:12
Alignment explanation
Indices: 16874063--16874130 Score: 57
Period size: 12 Copynumber: 5.6 Consensus size: 12
16874053 GATAAGAAGA
16874063 AATAATGAA-AAT
1 AATAAT-AACAAT
16874075 AATAATAACAAT
1 AATAATAACAAT
* *
16874087 AATAGTACCAAT
1 AATAATAACAAT
** *
16874099 AATAATAGGATT
1 AATAATAACAAT
*
16874111 AATAAATAATAAT
1 AAT-AATAACAAT
16874124 AATAATA
1 AATAATA
16874131 TTATTATTAG
Statistics
Matches: 45, Mismatches: 9, Indels: 4
0.78 0.16 0.07
Matches are distributed among these distances:
11 2 0.04
12 34 0.76
13 9 0.20
ACGTcount: A:0.62, C:0.04, G:0.06, T:0.28
Consensus pattern (12 bp):
AATAATAACAAT
Found at i:16874719 original size:23 final size:24
Alignment explanation
Indices: 16874689--16874746 Score: 70
Period size: 21 Copynumber: 2.6 Consensus size: 24
16874679 AAATTAAATC
16874689 TCTAAGATTACA-AAATCATATCT
1 TCTAAGATTACATAAATCATATCT
* *
16874712 TCTAAGATTGCATATATCATA---
1 TCTAAGATTACATAAATCATATCT
16874733 TCTAAGATTACATA
1 TCTAAGATTACATA
16874747 TCCTCGAAGA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
21 13 0.42
23 11 0.35
24 7 0.23
ACGTcount: A:0.41, C:0.16, G:0.07, T:0.36
Consensus pattern (24 bp):
TCTAAGATTACATAAATCATATCT
Found at i:16874735 original size:24 final size:23
Alignment explanation
Indices: 16874689--16874735 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
16874679 AAATTAAATC
16874689 TCTAAGATTACAAAATCATATCT
1 TCTAAGATTACAAAATCATATCT
* *
16874712 TCTAAGATTGCATATATCATATCT
1 TCTAAGATTACA-AAATCATATCT
16874736 AAGATTACAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 11 0.52
24 10 0.48
ACGTcount: A:0.38, C:0.17, G:0.06, T:0.38
Consensus pattern (23 bp):
TCTAAGATTACAAAATCATATCT
Found at i:16879171 original size:11 final size:11
Alignment explanation
Indices: 16879149--16879200 Score: 68
Period size: 11 Copynumber: 4.6 Consensus size: 11
16879139 AACTAATCCT
16879149 CTCTCAAATTTC
1 CTCTC-AATTTC
16879161 CTCTCAATTTC
1 CTCTCAATTTC
* *
16879172 TTCTAAATTTC
1 CTCTCAATTTC
*
16879183 CTCTCAATTTG
1 CTCTCAATTTC
16879194 CTCTCAA
1 CTCTCAA
16879201 ACTCCTTCAA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
11 30 0.86
12 5 0.14
ACGTcount: A:0.23, C:0.31, G:0.02, T:0.44
Consensus pattern (11 bp):
CTCTCAATTTC
Found at i:16879198 original size:33 final size:33
Alignment explanation
Indices: 16879148--16879222 Score: 89
Period size: 33 Copynumber: 2.2 Consensus size: 33
16879138 AAACTAATCC
* * *
16879148 TCTCTCAAATTTCCTCTC-AATTTCTTCTAAATT
1 TCTCTC-AATTTCCTCTCAAACTCCTTCAAAATT
*
16879181 TCCTCTCAATTTGCTCTCAAACTCCTTCAAAATT
1 T-CTCTCAATTTCCTCTCAAACTCCTTCAAAATT
16879215 TCTCTCAA
1 TCTCTCAA
16879223 ATCCATATTT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
33 18 0.50
34 18 0.50
ACGTcount: A:0.25, C:0.31, G:0.01, T:0.43
Consensus pattern (33 bp):
TCTCTCAATTTCCTCTCAAACTCCTTCAAAATT
Found at i:16879206 original size:22 final size:22
Alignment explanation
Indices: 16879148--16879224 Score: 88
Period size: 22 Copynumber: 3.5 Consensus size: 22
16879138 AAACTAATCC
16879148 TCTCTCAAATTTCCTCTCAATT
1 TCTCTCAAATTTCCTCTCAATT
16879170 TCT-TCTAAATTTCCTCTCAATT
1 TCTCTC-AAATTTCCTCTCAATT
*
16879192 TGCTCTCAAA-CTCCT-TCAAAATT
1 T-CTCTCAAATTTCCTCTC--AATT
16879215 TCTCTCAAAT
1 TCTCTCAAAT
16879225 CCATATTTAT
Statistics
Matches: 48, Mismatches: 1, Indels: 11
0.80 0.02 0.18
Matches are distributed among these distances:
21 4 0.08
22 32 0.67
23 10 0.21
24 2 0.04
ACGTcount: A:0.26, C:0.30, G:0.01, T:0.43
Consensus pattern (22 bp):
TCTCTCAAATTTCCTCTCAATT
Found at i:16879248 original size:51 final size:51
Alignment explanation
Indices: 16879186--16879283 Score: 135
Period size: 51 Copynumber: 1.9 Consensus size: 51
16879176 AAATTTCCTC
16879186 TCAATTTGCTCTCAAACTCCT-TCAAAATTTCTCTCAAATCCATATTTATTT
1 TCAATTTGCTCTCAAACTCCTCT-AAAATTTCTCTCAAATCCATATTTATTT
** * * *
16879237 TCAATTTGCTCTCAAGTTCCTCTTAAATTTCTCTTAAATCCCTATTT
1 TCAATTTGCTCTCAAACTCCTCTAAAATTTCTCTCAAATCCATATTT
16879284 TTAAATAATT
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
51 40 0.98
52 1 0.02
ACGTcount: A:0.27, C:0.26, G:0.03, T:0.45
Consensus pattern (51 bp):
TCAATTTGCTCTCAAACTCCTCTAAAATTTCTCTCAAATCCATATTTATTT
Found at i:16888501 original size:18 final size:16
Alignment explanation
Indices: 16888480--16888517 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 16
16888470 TCTAAATTAC
16888480 ATAATATATAAAAATATT
1 ATAA-ATAT-AAAATATT
16888498 AT-AATATAAAATATT
1 ATAAATATAAAATATT
16888513 ATAAA
1 ATAAA
16888518 CTTAAAACGG
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
15 10 0.53
16 6 0.32
17 1 0.05
18 2 0.11
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
ATAAATATAAAATATT
Found at i:16888510 original size:15 final size:16
Alignment explanation
Indices: 16888485--16888516 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
16888475 ATTACATAAT
16888485 ATATAAAAATATTATA
1 ATATAAAAATATTATA
16888501 ATAT-AAAATATTATA
1 ATATAAAAATATTATA
16888516 A
1 A
16888517 ACTTAAAACG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
ATATAAAAATATTATA
Found at i:16888982 original size:25 final size:28
Alignment explanation
Indices: 16888934--16888985 Score: 83
Period size: 25 Copynumber: 2.0 Consensus size: 28
16888924 ATAAAAATTA
16888934 ACCAAAATATTATAACTTTTTTTTATTT
1 ACCAAAATATTATAACTTTTTTTTATTT
16888962 ACCAAAATA-T-T-ACTTTTTTTTATT
1 ACCAAAATATTATAACTTTTTTTTATT
16888986 ATTTACGAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
25 13 0.54
26 1 0.04
27 1 0.04
28 9 0.38
ACGTcount: A:0.35, C:0.12, G:0.00, T:0.54
Consensus pattern (28 bp):
ACCAAAATATTATAACTTTTTTTTATTT
Found at i:16889187 original size:19 final size:19
Alignment explanation
Indices: 16889157--16889227 Score: 101
Period size: 19 Copynumber: 3.8 Consensus size: 19
16889147 TTCAACTCAT
16889157 TATTTT-ATTTAATAACTC
1 TATTTTAATTTAATAACTC
*
16889175 TATTTTAATTTAATAA-AC
1 TATTTTAATTTAATAACTC
* *
16889193 TATTCTCATTTAATAACTC
1 TATTTTAATTTAATAACTC
16889212 TATTTTAATTTAATAA
1 TATTTTAATTTAATAA
16889228 ACTATTAAGT
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
18 21 0.47
19 24 0.53
ACGTcount: A:0.38, C:0.10, G:0.00, T:0.52
Consensus pattern (19 bp):
TATTTTAATTTAATAACTC
Found at i:16889208 original size:37 final size:37
Alignment explanation
Indices: 16889163--16889233 Score: 142
Period size: 37 Copynumber: 1.9 Consensus size: 37
16889153 TCATTATTTT
16889163 ATTTAATAACTCTATTTTAATTTAATAAACTATTCTC
1 ATTTAATAACTCTATTTTAATTTAATAAACTATTCTC
16889200 ATTTAATAACTCTATTTTAATTTAATAAACTATT
1 ATTTAATAACTCTATTTTAATTTAATAAACTATT
16889234 AAGTAATACT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.39, C:0.11, G:0.00, T:0.49
Consensus pattern (37 bp):
ATTTAATAACTCTATTTTAATTTAATAAACTATTCTC
Found at i:16889476 original size:19 final size:19
Alignment explanation
Indices: 16889449--16889518 Score: 88
Period size: 19 Copynumber: 3.7 Consensus size: 19
16889439 TCAACTCATT
*
16889449 TTTTTATTTAATAACTCTA
1 TTTTAATTTAATAACTCTA
**
16889468 TTTTAATTTAATAA-AATA
1 TTTTAATTTAATAACTCTA
* *
16889486 TTCTCATTTAATAACTCTA
1 TTTTAATTTAATAACTCTA
16889505 TTTTAATTTAATAA
1 TTTTAATTTAATAA
16889519 ACTATTAAGT
Statistics
Matches: 41, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
18 14 0.34
19 27 0.66
ACGTcount: A:0.39, C:0.09, G:0.00, T:0.53
Consensus pattern (19 bp):
TTTTAATTTAATAACTCTA
Found at i:16889499 original size:37 final size:37
Alignment explanation
Indices: 16889454--16889524 Score: 133
Period size: 37 Copynumber: 1.9 Consensus size: 37
16889444 TCATTTTTTT
16889454 ATTTAATAACTCTATTTTAATTTAATAAAATATTCTC
1 ATTTAATAACTCTATTTTAATTTAATAAAATATTCTC
*
16889491 ATTTAATAACTCTATTTTAATTTAATAAACTATT
1 ATTTAATAACTCTATTTTAATTTAATAAAATATT
16889525 AAGTAATACT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.41, C:0.10, G:0.00, T:0.49
Consensus pattern (37 bp):
ATTTAATAACTCTATTTTAATTTAATAAAATATTCTC
Found at i:16889616 original size:291 final size:291
Alignment explanation
Indices: 16889088--16889787 Score: 1285
Period size: 291 Copynumber: 2.4 Consensus size: 291
16889078 GCCAAAGGAC
*
16889088 TAAAATTGGGCTAATTGCCTTCTAAGCCCTCCTTATTTATTATTTTCTTTTTATTCCCTTTCAAC
1 TAAAATTGGGCTAATTGCCTTCTAAGCCCTCCTTATTTATTATTTTCTTTTTATTCCCCTTCAAC
*
16889153 TCATTATTTTATTTAATAACTCTATTTTAATTTAATAAACTATTCTCATTTAATAACTCTATTTT
66 TCATTTTTTTATTTAATAACTCTATTTTAATTTAATAAACTATTCTCATTTAATAACTCTATTTT
16889218 AATTTAATAAACTATTAAGTAATACTTAATTTTTTAAAATTAAAATAGAGTTATTAAATGAGAGA
131 AATTTAATAAACTATTAAGTAATACTTAATTTTTTAAAATTAAAATAGAGTTATTAAATGAGAGA
16889283 ATTCTAATAAAGTGACCATTTGCAGTTTTAAGGACCTGACATGCAAATTTACCATTTTGAATTTT
196 ATTCTAATAAAGTGACCATTTGCAGTTTTAAGGACCTGACATGCAAATTTACCATTTTGAATTTT
*
16889348 GAAAGTGAATTGTTGATGTGCGCACTAAAAT
261 GAAAGTGAATTGCTGATGTGCGCACTAAAAT
*
16889379 TAAAATTGGGATAATTGCCTTCTAAGCCCTCCTTATTTATTATTTTCTTTTTATTCCCCTTCAAC
1 TAAAATTGGGCTAATTGCCTTCTAAGCCCTCCTTATTTATTATTTTCTTTTTATTCCCCTTCAAC
*
16889444 TCATTTTTTTATTTAATAACTCTATTTTAATTTAATAAAATATTCTCATTTAATAACTCTATTTT
66 TCATTTTTTTATTTAATAACTCTATTTTAATTTAATAAACTATTCTCATTTAATAACTCTATTTT
*
16889509 AATTTAATAAACTATTAAGTAATACTTAATTTTTTTAAATTAAAATAGAGTTATTAAATGAGAGA
131 AATTTAATAAACTATTAAGTAATACTTAATTTTTTAAAATTAAAATAGAGTTATTAAATGAGAGA
* *
16889574 ATTCTAATTAAGTGACCATTTGCAGTTTTAAGGACTTGACATGCAAATTTACCATTTTGAATTTT
196 ATTCTAATAAAGTGACCATTTGCAGTTTTAAGGACCTGACATGCAAATTTACCATTTTGAATTTT
*
16889639 GAAAGTGAATTGCTGCTGTGCGCACTAAAAT
261 GAAAGTGAATTGCTGATGTGCGCACTAAAAT
* *
16889670 TGAAA-TGTGGCTAATTGCCTTCTAAGCCCTCCTTATTTATTATTTTCTTTTTATTCCCCTTCGA
1 TAAAATTG-GGCTAATTGCCTTCTAAGCCCTCCTTATTTATTATTTTCTTTTTATTCCCCTTCAA
16889734 CTCATTTTTTTATTTAATAACTCTATTTTAATTTAATAAACTATTCTCATTTAA
65 CTCATTTTTTTATTTAATAACTCTATTTTAATTTAATAAACTATTCTCATTTAA
16889788 ATAAAAATAG
Statistics
Matches: 395, Mismatches: 13, Indels: 2
0.96 0.03 0.00
Matches are distributed among these distances:
290 2 0.01
291 393 0.99
ACGTcount: A:0.33, C:0.14, G:0.09, T:0.44
Consensus pattern (291 bp):
TAAAATTGGGCTAATTGCCTTCTAAGCCCTCCTTATTTATTATTTTCTTTTTATTCCCCTTCAAC
TCATTTTTTTATTTAATAACTCTATTTTAATTTAATAAACTATTCTCATTTAATAACTCTATTTT
AATTTAATAAACTATTAAGTAATACTTAATTTTTTAAAATTAAAATAGAGTTATTAAATGAGAGA
ATTCTAATAAAGTGACCATTTGCAGTTTTAAGGACCTGACATGCAAATTTACCATTTTGAATTTT
GAAAGTGAATTGCTGATGTGCGCACTAAAAT
Found at i:16889777 original size:18 final size:18
Alignment explanation
Indices: 16889740--16889792 Score: 52
Period size: 19 Copynumber: 2.8 Consensus size: 18
16889730 TCGACTCATT
* *
16889740 TTTTTATTTAATAACTCTA
1 TTTTAATTTAATAA-ACTA
16889759 TTTTAATTTAATAAACTA
1 TTTTAATTTAATAAACTA
* *
16889777 TTCTCATTTAAATAAA
1 TTTTAATTT-AATAAA
16889793 AATAGTTTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
18 10 0.34
19 19 0.66
ACGTcount: A:0.40, C:0.09, G:0.00, T:0.51
Consensus pattern (18 bp):
TTTTAATTTAATAAACTA
Found at i:16889823 original size:19 final size:19
Alignment explanation
Indices: 16889784--16889880 Score: 99
Period size: 18 Copynumber: 5.2 Consensus size: 19
16889774 CTATTCTCAT
* *
16889784 TTAAATAAAAATAGTTTTA
1 TTAAATGAAAATAGATTTA
*
16889803 TTTAAATGAGAATAG-TTTA
1 -TTAAATGAAAATAGATTTA
* *
16889822 TTAAATTAAAATAGAGTTA
1 TTAAATGAAAATAGATTTA
*
16889841 TTAAATGAGAATA-ATTTA
1 TTAAATGAAAATAGATTTA
* *
16889859 TTAAATTAAAATAGAGTTA
1 TTAAATGAAAATAGATTTA
16889878 TTA
1 TTA
16889881 CTTAATTAGA
Statistics
Matches: 64, Mismatches: 11, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
18 27 0.42
19 25 0.39
20 12 0.19
ACGTcount: A:0.49, C:0.00, G:0.10, T:0.40
Consensus pattern (19 bp):
TTAAATGAAAATAGATTTA
Found at i:16889859 original size:37 final size:37
Alignment explanation
Indices: 16889784--16889880 Score: 149
Period size: 37 Copynumber: 2.6 Consensus size: 37
16889774 CTATTCTCAT
* ** *
16889784 TTAAATAAAAATAGTTTTATTTAAATGAGAATAGTTTA
1 TTAAATTAAAATAGAGTTA-TTAAATGAGAATAATTTA
16889822 TTAAATTAAAATAGAGTTATTAAATGAGAATAATTTA
1 TTAAATTAAAATAGAGTTATTAAATGAGAATAATTTA
16889859 TTAAATTAAAATAGAGTTATTA
1 TTAAATTAAAATAGAGTTATTA
16889881 CTTAATTAGA
Statistics
Matches: 55, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
37 39 0.71
38 16 0.29
ACGTcount: A:0.49, C:0.00, G:0.10, T:0.40
Consensus pattern (37 bp):
TTAAATTAAAATAGAGTTATTAAATGAGAATAATTTA
Found at i:16889885 original size:18 final size:19
Alignment explanation
Indices: 16889819--16889880 Score: 90
Period size: 19 Copynumber: 3.3 Consensus size: 19
16889809 TGAGAATAGT
16889819 TTATTAAATTAAAATAGAG
1 TTATTAAATTAAAATAGAG
* * *
16889838 TTATTAAATGAGAATA-AT
1 TTATTAAATTAAAATAGAG
16889856 TTATTAAATTAAAATAGAG
1 TTATTAAATTAAAATAGAG
16889875 TTATTA
1 TTATTA
16889881 CTTAATTAGA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
18 15 0.42
19 21 0.58
ACGTcount: A:0.50, C:0.00, G:0.10, T:0.40
Consensus pattern (19 bp):
TTATTAAATTAAAATAGAG
Found at i:16890120 original size:20 final size:19
Alignment explanation
Indices: 16890081--16890121 Score: 64
Period size: 19 Copynumber: 2.1 Consensus size: 19
16890071 ACTTAATATT
*
16890081 TTATTAAATTAAAATAGAG
1 TTATTAAATTAAAAAAGAG
16890100 TTATTAAATTAAAAAATGAG
1 TTATTAAATTAAAAAA-GAG
16890120 TT
1 TT
16890122 GAAGGGGATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 15 0.75
20 5 0.25
ACGTcount: A:0.51, C:0.00, G:0.10, T:0.39
Consensus pattern (19 bp):
TTATTAAATTAAAAAAGAG
Found at i:16890273 original size:27 final size:27
Alignment explanation
Indices: 16890187--16890264 Score: 129
Period size: 27 Copynumber: 2.9 Consensus size: 27
16890177 ATTTTAGTCA
*
16890187 TTTGGCACCATTGGTGCCGCCAATCAC
1 TTTGGCACCATTGGTGCCGCCAATCTC
*
16890214 TTTGGCACCATTGGTGCCACCAATCTC
1 TTTGGCACCATTGGTGCCGCCAATCTC
*
16890241 TTTGGCACCTTTGGTGCCGCCAAT
1 TTTGGCACCATTGGTGCCGCCAAT
16890265 GTGATTGGCC
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 47 1.00
ACGTcount: A:0.17, C:0.32, G:0.22, T:0.29
Consensus pattern (27 bp):
TTTGGCACCATTGGTGCCGCCAATCTC
Found at i:16899104 original size:18 final size:18
Alignment explanation
Indices: 16899083--16899139 Score: 64
Period size: 18 Copynumber: 3.2 Consensus size: 18
16899073 GCCAAATTTA
16899083 TAAATTACCATTATTAAC
1 TAAATTACCATTATTAAC
* *
16899101 TAAATTATGCCA-AATTTA-
1 TAAATTA--CCATTATTAAC
16899119 TAAATTACCATTATTAAC
1 TAAATTACCATTATTAAC
16899137 TAA
1 TAA
16899140 CTCGTGAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
16 3 0.10
17 4 0.13
18 17 0.55
19 4 0.13
20 3 0.10
ACGTcount: A:0.46, C:0.14, G:0.02, T:0.39
Consensus pattern (18 bp):
TAAATTACCATTATTAAC
Found at i:16899113 original size:36 final size:36
Alignment explanation
Indices: 16899068--16899139 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
16899058 TGAAGTTACT
16899068 ATTATGCCAAATTTATAAATTACCATTATTAACTAA
1 ATTATGCCAAATTTATAAATTACCATTATTAACTAA
16899104 ATTATGCCAAATTTATAAATTACCATTATTAACTAA
1 ATTATGCCAAATTTATAAATTACCATTATTAACTAA
16899140 CTCGTGAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.44, C:0.14, G:0.03, T:0.39
Consensus pattern (36 bp):
ATTATGCCAAATTTATAAATTACCATTATTAACTAA
Found at i:16903078 original size:22 final size:21
Alignment explanation
Indices: 16903043--16903108 Score: 89
Period size: 22 Copynumber: 3.0 Consensus size: 21
16903033 CCTCTCTAAT
*
16903043 ATTTCC-TCTCAATTCCTCTCA
1 ATTTCCTTCTAAATT-CTCTCA
16903064 ATTTCCTTCTAAATTTCTCTCA
1 ATTTCCTTCTAAA-TTCTCTCA
16903086 ATTTCCTTCTAAAATTCTCTCA
1 ATTTCCTTCT-AAATTCTCTCA
16903108 A
1 A
16903109 ACTCATATTT
Statistics
Matches: 41, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
21 6 0.15
22 30 0.73
23 5 0.12
ACGTcount: A:0.24, C:0.30, G:0.00, T:0.45
Consensus pattern (21 bp):
ATTTCCTTCTAAATTCTCTCA
Found at i:16903080 original size:12 final size:11
Alignment explanation
Indices: 16903036--16903098 Score: 58
Period size: 10 Copynumber: 5.6 Consensus size: 11
16903026 AACAAATCCT
16903036 CTCTAATATTTC
1 CTCTAA-ATTTC
*
16903048 CTCTCAA-TTC
1 CTCTAAATTTC
*
16903058 CTCTCAATTTC
1 CTCTAAATTTC
16903069 CTTCTAAATTT-
1 C-TCTAAATTTC
*
16903080 CTCTCAATTTC
1 CTCTAAATTTC
16903091 CTTCTAAA
1 C-TCTAAA
16903099 ATTCTCTCAA
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
10 18 0.42
11 7 0.16
12 18 0.42
ACGTcount: A:0.24, C:0.30, G:0.00, T:0.46
Consensus pattern (11 bp):
CTCTAAATTTC
Found at i:16905154 original size:13 final size:13
Alignment explanation
Indices: 16905127--16905167 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
16905117 TAACCTAAAT
16905127 TAATTCAAAAA-CC
1 TAATT-AAAAACCC
*
16905140 TAATTAAATACCC
1 TAATTAAAAACCC
16905153 TAATTAAAAACCC
1 TAATTAAAAACCC
16905166 TA
1 TA
16905168 GCCCTAACCT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
12 4 0.16
13 21 0.84
ACGTcount: A:0.51, C:0.22, G:0.00, T:0.27
Consensus pattern (13 bp):
TAATTAAAAACCC
Found at i:16905188 original size:29 final size:29
Alignment explanation
Indices: 16905106--16905348 Score: 216
Period size: 29 Copynumber: 8.3 Consensus size: 29
16905096 TAAAAACCCT
*
16905106 AACCCTAACCCTAACCTAAATTAATTCAAA
1 AACCCTAACCCTAACCTAATTTAATT-AAA
* * ***
16905136 AA-CCTAA--TTAA-ATACCCTAATTAAA
1 AACCCTAACCCTAACCTAATTTAATTAAA
*
16905161 AACCCTAGCCCTAACCTAATTTAATTAAA
1 AACCCTAACCCTAACCTAATTTAATTAAA
* *
16905190 AACCCTAAAAACACTAATTCTAATTTAATTAAA
1 AACCCT---AACCCTAA-CCTAATTTAATTAAA
*
16905223 AACCCTAA-CCTAAACC----CTAATTAAA
1 AACCCTAACCCT-AACCTAATTTAATTAAA
16905248 AACCCTAACCCTAACCTAATTTAATTAAA
1 AACCCTAACCCTAACCTAATTTAATTAAA
16905277 AACCCTAAAAACCCTAATCCTAATTTAATTAAA
1 AACCCT---AACCCTAA-CCTAATTTAATTAAA
* *
16905310 GACCCTAACCCTAACCTAATTTAATTCAA
1 AACCCTAACCCTAACCTAATTTAATTAAA
*
16905339 AACCTTAACC
1 AACCCTAACC
16905349 TAAATTATTT
Statistics
Matches: 173, Mismatches: 22, Indels: 37
0.75 0.09 0.16
Matches are distributed among these distances:
25 25 0.14
26 14 0.08
27 3 0.02
28 3 0.02
29 60 0.35
30 14 0.08
32 14 0.08
33 40 0.23
ACGTcount: A:0.46, C:0.27, G:0.01, T:0.26
Consensus pattern (29 bp):
AACCCTAACCCTAACCTAATTTAATTAAA
Found at i:16905245 original size:87 final size:87
Alignment explanation
Indices: 16905092--16905370 Score: 309
Period size: 87 Copynumber: 3.2 Consensus size: 87
16905082 TTTTAAACCC
* * * *
16905092 TAATTAAAAACCCTAACCCTAACCCTAA-CCTAAATTAATTCAAAAA-CCTAA-TTAAATACCCT
1 TAATTAAAAACCCTAA---AAACACTAATCCTAATTTAATT-AAAAACCCTAACCT-AA-ACCCT
*
16905154 AATTAAAAACCCTAGCCCTAACCTAATT
60 AATTAAAAACCCTAACCCTAACCTAATT
*
16905182 TAATTAAAAACCCTAAAAACACTAATTCTAATTTAATTAAAAACCCTAACCTAAACCCTAATTAA
1 TAATTAAAAACCCTAAAAACACTAATCCTAATTTAATTAAAAACCCTAACCTAAACCCTAATTAA
16905247 AAACCCTAACCCTAACCTAATT
66 AAACCCTAACCCTAACCTAATT
* *
16905269 TAATTAAAAACCCTAAAAACCCTAATCCTAATTTAATTAAAGACCCTAACCCT-AA-CCTAATT-
1 TAATTAAAAACCCTAAAAACACTAATCCTAATTTAATTAAAAACCCTAA-CCTAAACCCTAATTA
* ** ** * *
16905331 TAATTCAAAACCTTAACCTAAAT
65 AAAACCCTAACCCTAACCTAATT
*
16905354 TATTTAAAAACCCTAAA
1 TAATTAAAAACCCTAAA
16905371 CTAAGTTAAC
Statistics
Matches: 168, Mismatches: 17, Indels: 13
0.85 0.09 0.07
Matches are distributed among these distances:
85 32 0.19
86 7 0.04
87 92 0.55
88 20 0.12
89 1 0.01
90 16 0.10
ACGTcount: A:0.47, C:0.25, G:0.01, T:0.27
Consensus pattern (87 bp):
TAATTAAAAACCCTAAAAACACTAATCCTAATTTAATTAAAAACCCTAACCTAAACCCTAATTAA
AAACCCTAACCCTAACCTAATT
Found at i:16905252 original size:13 final size:13
Alignment explanation
Indices: 16905215--16905255 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
16905205 AATTCTAATT
16905215 TAATTAAAAACCC
1 TAATTAAAAACCC
*
16905228 TAACCT--AAACCC
1 TAA-TTAAAAACCC
16905240 TAATTAAAAACCC
1 TAATTAAAAACCC
16905253 TAA
1 TAA
16905256 CCCTAACCTA
Statistics
Matches: 23, Mismatches: 2, Indels: 6
0.74 0.06 0.19
Matches are distributed among these distances:
11 1 0.04
12 9 0.39
13 12 0.52
14 1 0.04
ACGTcount: A:0.51, C:0.27, G:0.00, T:0.22
Consensus pattern (13 bp):
TAATTAAAAACCC
Found at i:16905263 original size:25 final size:24
Alignment explanation
Indices: 16905215--16905268 Score: 83
Period size: 25 Copynumber: 2.2 Consensus size: 24
16905205 AATTCTAATT
16905215 TAATTAAAAACCCTAACCTAAACCC
1 TAATTAAAAACCCTAACCTAAA-CC
16905240 TAATTAAAAACCCTAACCCT-AACC
1 TAATTAAAAACCCTAA-CCTAAACC
16905264 TAATT
1 TAATT
16905269 TAATTAAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
24 7 0.25
25 18 0.64
26 3 0.11
ACGTcount: A:0.46, C:0.30, G:0.00, T:0.24
Consensus pattern (24 bp):
TAATTAAAAACCCTAACCTAAACC
Found at i:16905329 original size:24 final size:24
Alignment explanation
Indices: 16905282--16905330 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
16905272 TTAAAAACCC
* **
16905282 TAAAAACCCTAATCCTAATTTAAT
1 TAAAAACCCTAACCCTAACCTAAT
*
16905306 TAAAGACCCTAACCCTAACCTAAT
1 TAAAAACCCTAACCCTAACCTAAT
16905330 T
1 T
16905331 TAATTCAAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.43, C:0.27, G:0.02, T:0.29
Consensus pattern (24 bp):
TAAAAACCCTAACCCTAACCTAAT
Found at i:16905347 original size:23 final size:23
Alignment explanation
Indices: 16905316--16905379 Score: 74
Period size: 23 Copynumber: 2.8 Consensus size: 23
16905306 TAAAGACCCT
* *
16905316 AACCCTAACCTAATTTAATTCAA
1 AACCCTAACCTAAATTAATTAAA
* *
16905339 AACCTTAACCTAAATTATTTAAA
1 AACCCTAACCTAAATTAATTAAA
* *
16905362 AACCCTAAACTAAGTTAA
1 AACCCTAACCTAAATTAA
16905380 CAATGTTACA
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.47, C:0.22, G:0.02, T:0.30
Consensus pattern (23 bp):
AACCCTAACCTAAATTAATTAAA
Found at i:16905594 original size:117 final size:117
Alignment explanation
Indices: 16905376--16905594 Score: 332
Period size: 117 Copynumber: 1.9 Consensus size: 117
16905366 CTAAACTAAG
*
16905376 TTAACAATGTTACATTCACGTAATGTTAGATTTGAAAAAATGTTTTGACTGGTACTAAAAATTAA
1 TTAACAATGTTACATTCACATAATGTTAGATTTGAAAAAATGTTTTGACTGGTACTAAAAATTAA
* *
16905441 TAAATTTACATAATTTGATAGTTTTACTAACCATTAACATAATTTTTTTGAC
66 TAAATTTACATAATTTGATAATTTTACTAACAATTAACATAATTTTTTTGAC
* * ** *
16905493 TTAATAATTTTACATTCACATAATGTTAGATTTGGTAAAATGTTTTGACTGGTACTAACAATTAA
1 TTAACAATGTTACATTCACATAATGTTAGATTTGAAAAAATGTTTTGACTGGTACTAAAAATTAA
* *
16905558 TAAATTTATACT-ATTTGATAATTTTAGTAACAATTAA
66 TAAATTTACA-TAATTTGATAATTTTACTAACAATTAA
16905595 TACAATTATC
Statistics
Matches: 91, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
117 90 0.99
118 1 0.01
ACGTcount: A:0.39, C:0.09, G:0.10, T:0.42
Consensus pattern (117 bp):
TTAACAATGTTACATTCACATAATGTTAGATTTGAAAAAATGTTTTGACTGGTACTAAAAATTAA
TAAATTTACATAATTTGATAATTTTACTAACAATTAACATAATTTTTTTGAC
Found at i:16908847 original size:125 final size:125
Alignment explanation
Indices: 16908625--16908990 Score: 552
Period size: 126 Copynumber: 2.9 Consensus size: 125
16908615 CCTAAACATG
* *
16908625 CTACTGTAGCAAAATCGCGTCCACGACGGCGCTATTTCACAAATTCTTCTCAAATAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGACGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
* * *
16908690 TAGAAGCGATTTTACACTATTTGCTCAGAAACGTCAACTCAAAATTATTTCTTCCGGGAC
66 TAAAAGCGATTTTATACTATTTGCTCAGAAACGTCAAATCAAAATTATTTCTTCCGGGAC
* * *
16908750 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATATCACAAATTCTTCTCAAATAGCATCCTAC
1 CTACTGTAGCAAAAGCGCGTCCACGACGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
* * ** *
16908815 TACAAGCGATTTTATACTATTTGCTCAAAAACGTCAAAAAAATAATTATTTCTTCCGTGAC
66 TAAAAGCGATTTTATACTATTTGCTCAGAAACGTCAAATCAA-AATTATTTCTTCCGGGAC
* * *
16908876 CTATTGTAGCAAAAGCGCGTCCACGATGGCGCGATTTCATAAATTCTTCTCAAATAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGACGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
* * *
16908941 TAAAAGCGATTTTATACTATTTGATCAGAAACGTCAAGTCGAAATTATTT
66 TAAAAGCGATTTTATACTATTTGCTCAGAAACGTCAAATCAAAATTATTT
16908991 ATTTCAGGAC
Statistics
Matches: 216, Mismatches: 24, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
125 104 0.48
126 112 0.52
ACGTcount: A:0.32, C:0.23, G:0.15, T:0.29
Consensus pattern (125 bp):
CTACTGTAGCAAAAGCGCGTCCACGACGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
TAAAAGCGATTTTATACTATTTGCTCAGAAACGTCAAATCAAAATTATTTCTTCCGGGAC
Found at i:16918186 original size:16 final size:18
Alignment explanation
Indices: 16918154--16918188 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
16918144 GTAGAGAGAA
16918154 AATAATGTTATATTAAAT
1 AATAATGTTATATTAAAT
16918172 AATAAT-TTA-ATTAAAT
1 AATAATGTTATATTAAAT
16918188 A
1 A
16918189 TGAAATGTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.47
17 3 0.18
18 6 0.35
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (18 bp):
AATAATGTTATATTAAAT
Found at i:16920618 original size:40 final size:39
Alignment explanation
Indices: 16920574--16920708 Score: 130
Period size: 40 Copynumber: 3.4 Consensus size: 39
16920564 ACCAGTTTGG
* *
16920574 CACCCAGTGCCTCATCGGATAATTCGAAGTAATAAGTAGA
1 CACCCAGTGCCTCATCGGATAATCCGAAGTAATAA-TTGA
* * * * *
16920614 CACCCAGTGTCTCATCAGCTAAACCGAAGT-A-AATTGG
1 CACCCAGTGCCTCATCGGATAATCCGAAGTAATAATTGA
* * *
16920651 CACTCAGTGCCTCATCGAATTAATCCGAAGTAGTAAATTGA
1 CACCCAGTGCCTCATCGGA-TAATCCGAAGTAAT-AATTGA
*
16920692 CACCCAGTGTCTCATCG
1 CACCCAGTGCCTCATCG
16920709 ACTCGAAGTC
Statistics
Matches: 74, Mismatches: 17, Indels: 7
0.76 0.17 0.07
Matches are distributed among these distances:
37 16 0.22
38 12 0.16
39 1 0.01
40 25 0.34
41 20 0.27
ACGTcount: A:0.32, C:0.26, G:0.19, T:0.24
Consensus pattern (39 bp):
CACCCAGTGCCTCATCGGATAATCCGAAGTAATAATTGA
Found at i:16920700 original size:41 final size:40
Alignment explanation
Indices: 16920574--16920709 Score: 127
Period size: 41 Copynumber: 3.5 Consensus size: 40
16920564 ACCAGTTTGG
* * * * *
16920574 CACCCAGTGCCTCATCGGATAATTCGAAGTAATAAGTAGA
1 CACCCAGTGCCTCATCGAATAATCCGAAGTAGTAAATTGA
* * * *
16920614 CACCCAGTGTCTCATC-AGCTAAACCG-A--AGTAAATTGG
1 CACCCAGTGCCTCATCGA-ATAATCCGAAGTAGTAAATTGA
*
16920651 CACTCAGTGCCTCATCGAATTAATCCGAAGTAGTAAATTGA
1 CACCCAGTGCCTCATCGAA-TAATCCGAAGTAGTAAATTGA
*
16920692 CACCCAGTGTCTCATCGA
1 CACCCAGTGCCTCATCGA
16920710 CTCGAAGTCG
Statistics
Matches: 74, Mismatches: 16, Indels: 11
0.73 0.16 0.11
Matches are distributed among these distances:
37 20 0.27
38 7 0.09
39 2 0.03
40 20 0.27
41 25 0.34
ACGTcount: A:0.32, C:0.26, G:0.18, T:0.24
Consensus pattern (40 bp):
CACCCAGTGCCTCATCGAATAATCCGAAGTAGTAAATTGA
Found at i:16921562 original size:21 final size:21
Alignment explanation
Indices: 16921538--16921596 Score: 55
Period size: 21 Copynumber: 2.8 Consensus size: 21
16921528 TCCTTCTTTC
16921538 TTTTCTTTCTTTTTCTCCGTG
1 TTTTCTTTCTTTTTCTCCGTG
* *** * *
16921559 TTTTGTTTGACTTTCTCTGTT
1 TTTTCTTTCTTTTTCTCCGTG
16921580 TCTTTCTTTCTTTTTCT
1 T-TTTCTTTCTTTTTCT
16921597 ATTTCCTTTT
Statistics
Matches: 27, Mismatches: 10, Indels: 1
0.71 0.26 0.03
Matches are distributed among these distances:
21 16 0.59
22 11 0.41
ACGTcount: A:0.02, C:0.20, G:0.08, T:0.69
Consensus pattern (21 bp):
TTTTCTTTCTTTTTCTCCGTG
Found at i:16922069 original size:59 final size:60
Alignment explanation
Indices: 16922006--16922119 Score: 160
Period size: 59 Copynumber: 1.9 Consensus size: 60
16921996 TTTTTTGTCA
*
16922006 AATTTGGTACTTTAACTTGACACTTTTT-CCTAATTTGGTACCTAAACT-TTTTTAGGCCG
1 AATTTGGTACTTGAACTTGACA-TTTTTCCCTAATTTGGTACCTAAACTATTTTTAGGCCG
* * *
16922065 AATTTGGTACTTGAACTTGGCATTTTTCCCCTAGTTTGGTACCTAAGCTATTTTT
1 AATTTGGTACTTGAACTTGACATTTTT-CCCTAATTTGGTACCTAAACTATTTTT
16922120 TAGGTTCAAT
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
58 5 0.10
59 20 0.42
60 18 0.38
61 5 0.10
ACGTcount: A:0.22, C:0.18, G:0.15, T:0.45
Consensus pattern (60 bp):
AATTTGGTACTTGAACTTGACATTTTTCCCTAATTTGGTACCTAAACTATTTTTAGGCCG
Found at i:16922671 original size:31 final size:28
Alignment explanation
Indices: 16922602--16922675 Score: 85
Period size: 28 Copynumber: 2.5 Consensus size: 28
16922592 CCAACTTTTA
*
16922602 AAAAATTGTCAAGTTTAGGTACCAAATT
1 AAAAAGTGTCAAGTTTAGGTACCAAATT
* * *
16922630 AAGAAGTGTCAAGTTTGGGTACTAAATT
1 AAAAAGTGTCAAGTTTAGGTACCAAATT
16922658 AGGAAAAAGTGTCAAGTT
1 ---AAAAAGTGTCAAGTT
16922676 CATATACCAA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
28 24 0.63
31 14 0.37
ACGTcount: A:0.41, C:0.08, G:0.22, T:0.30
Consensus pattern (28 bp):
AAAAAGTGTCAAGTTTAGGTACCAAATT
Found at i:16923895 original size:2 final size:2
Alignment explanation
Indices: 16923879--16923912 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
16923869 GAAAAACTTA
*
16923879 AT AT AA AT A- AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
16923913 AGAGTTGAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:16924106 original size:26 final size:26
Alignment explanation
Indices: 16924067--16924127 Score: 95
Period size: 26 Copynumber: 2.3 Consensus size: 26
16924057 TAGGTTAATT
* *
16924067 TTAAAATAAGTAATATGTAAAATAAC
1 TTAAAATAAATAATATATAAAATAAC
*
16924093 TTAAAATAAATAATATATAAAGTAAC
1 TTAAAATAAATAATATATAAAATAAC
16924119 TTAAAATAA
1 TTAAAATAA
16924128 TTAGTCTTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.61, C:0.03, G:0.05, T:0.31
Consensus pattern (26 bp):
TTAAAATAAATAATATATAAAATAAC
Found at i:16924175 original size:21 final size:21
Alignment explanation
Indices: 16924146--16924185 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
16924136 ATAAGTTAGG
16924146 TTAAAATAATAAATAAAAGGT
1 TTAAAATAATAAATAAAAGGT
* **
16924167 TTAATATAATCTATAAAAG
1 TTAAAATAATAAATAAAAG
16924186 AGAAAATTGG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.57, C:0.03, G:0.07, T:0.33
Consensus pattern (21 bp):
TTAAAATAATAAATAAAAGGT
Found at i:16924253 original size:2 final size:2
Alignment explanation
Indices: 16924248--16924308 Score: 90
Period size: 2 Copynumber: 31.5 Consensus size: 2
16924238 ATATAAAGTG
16924248 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
16924290 A- AA AC AT AT AT -T AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT A
16924309 AAGGTTTTAA
Statistics
Matches: 55, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
1 2 0.04
2 53 0.96
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:16924259 original size:18 final size:16
Alignment explanation
Indices: 16924236--16924310 Score: 89
Period size: 16 Copynumber: 4.6 Consensus size: 16
16924226 TTAAAATAAC
16924236 ATATATAAAGTGATATAT
1 ATATATAAA-T-ATATAT
*
16924254 ATATATATATATATAT
1 ATATATAAATATATAT
*
16924270 ATATATATATATATAT
1 ATATATAAATATATAT
*
16924286 ATATA-AAACATATATT
1 ATATATAAATATATA-T
16924302 ATATATAAA
1 ATATATAAA
16924311 GGTTTTAAAA
Statistics
Matches: 52, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
15 7 0.13
16 33 0.63
17 4 0.08
18 8 0.15
ACGTcount: A:0.53, C:0.01, G:0.03, T:0.43
Consensus pattern (16 bp):
ATATATAAATATATAT
Found at i:16930409 original size:29 final size:31
Alignment explanation
Indices: 16930357--16930424 Score: 81
Period size: 29 Copynumber: 2.3 Consensus size: 31
16930347 ATAGTTGAAC
*
16930357 CTAAATT-TTGGAATTTGAAAAGTA-AAGAAA
1 CTAAATTCTTGGAATGTGAAAAGTATAA-AAA
*
16930387 CTAAATTCTTGGAA-GT-AAAAGTATAATAA
1 CTAAATTCTTGGAATGTGAAAAGTATAAAAA
16930416 CTAAATTCT
1 CTAAATTCT
16930425 AAATTATCAA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
29 18 0.53
30 10 0.29
31 6 0.18
ACGTcount: A:0.47, C:0.07, G:0.13, T:0.32
Consensus pattern (31 bp):
CTAAATTCTTGGAATGTGAAAAGTATAAAAA
Found at i:16932040 original size:24 final size:21
Alignment explanation
Indices: 16932013--16932060 Score: 69
Period size: 24 Copynumber: 2.1 Consensus size: 21
16932003 AACTTTTTAA
16932013 AAATAAAATCTAAAAATATATAAC
1 AAATAAAAT-TAAAAA-ATAT-AC
16932037 AAATAAAATTAAAAAATATAC
1 AAATAAAATTAAAAAATATAC
16932058 AAA
1 AAA
16932061 AAAGATAGTC
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
21 5 0.21
22 4 0.17
23 6 0.25
24 9 0.38
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.23
Consensus pattern (21 bp):
AAATAAAATTAAAAAATATAC
Found at i:16932450 original size:51 final size:51
Alignment explanation
Indices: 16932344--16932450 Score: 128
Period size: 51 Copynumber: 2.1 Consensus size: 51
16932334 TTTGTTATTT
* * * *
16932344 TATTTTCAATTTATATATATTCTTTATATTTATTTCAAATTTATATTTTTT
1 TATTTTCAATTTATATATATACATTATATTTATTTCAAATTTATATTTATA
* *
16932395 TATTTTCAATTTATATATATACATTA-ATTT-TTTGAAGTTTTATGATTTATA
1 TATTTTCAATTTATATATATACATTATATTTATTTCAA-ATTTAT-ATTTATA
16932446 TATTT
1 TATTT
16932451 CTTATATTTT
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
49 5 0.10
50 9 0.19
51 34 0.71
ACGTcount: A:0.31, C:0.05, G:0.03, T:0.62
Consensus pattern (51 bp):
TATTTTCAATTTATATATATACATTATATTTATTTCAAATTTATATTTATA
Found at i:16932986 original size:2 final size:2
Alignment explanation
Indices: 16932979--16933012 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
16932969 TAAGATCATA
16932979 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
16933013 AATCAGTTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16944301 original size:12 final size:13
Alignment explanation
Indices: 16944284--16944314 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
16944274 AGAAATAGTG
16944284 AAATTGGA-TTTT
1 AAATTGGAGTTTT
16944296 AAATTGGAGTTTT
1 AAATTGGAGTTTT
16944309 AAATTG
1 AAATTG
16944315 AAAGATATGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 8 0.44
13 10 0.56
ACGTcount: A:0.35, C:0.00, G:0.19, T:0.45
Consensus pattern (13 bp):
AAATTGGAGTTTT
Found at i:16948349 original size:13 final size:13
Alignment explanation
Indices: 16948333--16948374 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 13
16948323 AATACACATG
16948333 AATTTATATATAA
1 AATTTATATATAA
*
16948346 AATTTAGATTATAAA
1 AATTTATA-TAT-AA
16948361 AATTTATATA-AA
1 AATTTATATATAA
16948373 AA
1 AA
16948375 AATATATAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
12 4 0.16
13 7 0.28
14 5 0.20
15 9 0.36
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (13 bp):
AATTTATATATAA
Found at i:16950181 original size:44 final size:44
Alignment explanation
Indices: 16950118--16950621 Score: 306
Period size: 44 Copynumber: 11.6 Consensus size: 44
16950108 GGGTCTACTT
*
16950118 CACTGCAACTTCAGGGAGATAAGATTATCGGCTTTAATCTCCTC
1 CACTGCAACTTCAGGGAGATAAGATTATCGGCTTTAATCTGCTC
* ** ** * * *
16950162 CACTGCATCTTCAGGGAGATAAGATCTGCCATCTTCAGTTTGC-C
1 CACTGCAACTTCAGGGAGATAAGAT-TATCGGCTTTAATCTGCTC
* *** *
16950206 TCACTGCAACTTCA-GGAGGATAAGACTTGTTTAC-TTAGTCTGCTC
1 -CACTGCAACTTCAGGGA-GATAAGA-TTATCGGCTTTAATCTGCTC
* * * * * *
16950251 CACTACAACTTCAGGGAGATAAGACTA---GATGTGATCTG-TT
1 CACTGCAACTTCAGGGAGATAAGATTATCGGCTTTAATCTGCTC
* * * * * *
16950291 CTCTGTAACTTCAGAGAGATAAGATCCA-AGGTTTTAATCTGCTC
1 CACTGCAACTTCAGGGAGATAAGAT-TATCGGCTTTAATCTGCTC
*
16950335 CACTGCAACTTCAGGGAGATAGGATTATCGGCTTTAATCTGCTC
1 CACTGCAACTTCAGGGAGATAAGATTATCGGCTTTAATCTGCTC
* * *
16950379 CACTGTAACTTCAGGGAGATAAGATT-T-GCCATCTTCAGTCTGC-C
1 CACTGCAACTTCAGGGAGATAAGATTATCGGC-T-TT-AATCTGCTC
* * *** *
16950423 TCACTGCAACTTTA-GGAGGATAAGACTTGTTTAC-TTAGTCTGCTC
1 -CACTGCAACTTCAGGGA-GATAAGA-TTATCGGCTTTAATCTGCTC
* * **
16950468 CACTGCAACTTCAGGGAGATAAGACTA---GATGCAATCTGCT-
1 CACTGCAACTTCAGGGAGATAAGATTATCGGCTTTAATCTGCTC
** * * * * * *
16950508 CTTTGCAACTTCAGAGAGGTAAGATCCA-AGGTTTTAATCCGCTC
1 CACTGCAACTTCAGGGAGATAAGAT-TATCGGCTTTAATCTGCTC
* * *
16950552 CACTGCAACTTAAGGGAGATAGGATTATCAGCTTTAATCTGCTC
1 CACTGCAACTTCAGGGAGATAAGATTATCGGCTTTAATCTGCTC
*
16950596 CACTGCAACTTCAGGGATATAAGATT
1 CACTGCAACTTCAGGGAGATAAGATT
16950622 TGCCATCTTC
Statistics
Matches: 350, Mismatches: 82, Indels: 56
0.72 0.17 0.11
Matches are distributed among these distances:
40 41 0.12
41 14 0.04
42 2 0.01
43 23 0.07
44 200 0.57
45 65 0.19
46 3 0.01
47 1 0.00
48 1 0.00
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (44 bp):
CACTGCAACTTCAGGGAGATAAGATTATCGGCTTTAATCTGCTC
Found at i:16950493 original size:217 final size:217
Alignment explanation
Indices: 16950118--16950795 Score: 1158
Period size: 217 Copynumber: 3.1 Consensus size: 217
16950108 GGGTCTACTT
* * * *
16950118 CACTGCAACTTCAGGGAGATAAGATTATCGGCTTTAATCTCCTCCACTGCATCTTCAGGGAGATA
1 CACTGCAACTTAAGGGAGATAGGATTATCGGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATA
* *
16950183 AGATCTGCCATCTTCAGTTTGCCTCACTGCAACTTCAGGAGGATAAGACTTGTTTACTTAGTCTG
66 AGATTTGCCATCTTCAGTCTGCCTCACTGCAACTTCAGGAGGATAAGACTTGTTTACTTAGTCTG
* * * * *
16950248 CTCCACTACAACTTCAGGGAGATAAGACTAGATGTGATCTGTTCTCTGTAACTTCAGAGAGATAA
131 CTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGTTCTTTGCAACTTCAGAGAGGTAA
*
16950313 GATCCAAGGTTTTAATCTGCTC
196 GATCCAAGGTTTTAATCCGCTC
* *
16950335 CACTGCAACTTCAGGGAGATAGGATTATCGGCTTTAATCTGCTCCACTGTAACTTCAGGGAGATA
1 CACTGCAACTTAAGGGAGATAGGATTATCGGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATA
*
16950400 AGATTTGCCATCTTCAGTCTGCCTCACTGCAACTTTAGGAGGATAAGACTTGTTTACTTAGTCTG
66 AGATTTGCCATCTTCAGTCTGCCTCACTGCAACTTCAGGAGGATAAGACTTGTTTACTTAGTCTG
* *
16950465 CTCCACTGCAACTTCAGGGAGATAAGACTAGATGCAATCTGCTCTTTGCAACTTCAGAGAGGTAA
131 CTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGTTCTTTGCAACTTCAGAGAGGTAA
16950530 GATCCAAGGTTTTAATCCGCTC
196 GATCCAAGGTTTTAATCCGCTC
* *
16950552 CACTGCAACTTAAGGGAGATAGGATTATCAGCTTTAATCTGCTCCACTGCAACTTCAGGGATATA
1 CACTGCAACTTAAGGGAGATAGGATTATCGGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATA
*
16950617 AGATTTGCCATCTTCAGTCTGCCTCACAGCAACTTCAGGAGGATAAGACTTGTTTACTTAGTCTG
66 AGATTTGCCATCTTCAGTCTGCCTCACTGCAACTTCAGGAGGATAAGACTTGTTTACTTAGTCTG
* *
16950682 CTCCACTGCAATTTTAGGGAGATAAGACTAGATGCGATCTGTTCTTTGCAACTTCAGAGAGGTAA
131 CTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGTTCTTTGCAACTTCAGAGAGGTAA
16950747 GATCCAAGGTTTTAATCCGCTC
196 GATCCAAGGTTTTAATCCGCTC
16950769 CACTGCAACTTAAGGGAGATAGGATTA
1 CACTGCAACTTAAGGGAGATAGGATTA
16950796 CTGGCCACCG
Statistics
Matches: 436, Mismatches: 25, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
217 436 1.00
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.30
Consensus pattern (217 bp):
CACTGCAACTTAAGGGAGATAGGATTATCGGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATA
AGATTTGCCATCTTCAGTCTGCCTCACTGCAACTTCAGGAGGATAAGACTTGTTTACTTAGTCTG
CTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGTTCTTTGCAACTTCAGAGAGGTAA
GATCCAAGGTTTTAATCCGCTC
Found at i:16950706 original size:44 final size:43
Alignment explanation
Indices: 16950118--16950710 Score: 301
Period size: 44 Copynumber: 13.6 Consensus size: 43
16950108 GGGTCTACTT
* ** *
16950118 CACTGCAACTTCAGGGAGATAAGA-TTATCGGCTTTAATCTCCTC
1 CACTGCAACTTCAGGGAGATAAGACTTGT-TAC-TTAATCTGCTC
* ** * *
16950162 CACTGCATCTTCAGGGAGATAAGA-TCTGCCATCTTCAGTTTGC-C
1 CACTGCAACTTCAGGGAGATAAGACT-TGTTA-CTT-AATCTGCTC
*
16950206 TCACTGCAACTTCA-GGAGGATAAGACTTGTTTACTTAGTCTGCTC
1 -CACTGCAACTTCAGGGA-GATAAGACTTG-TTACTTAATCTGCTC
* * * *
16950251 CACTACAACTTCAGGGAGATAAGACTAG--A-TGTGATCTG-TT
1 CACTGCAACTTCAGGGAGATAAGACTTGTTACT-TAATCTGCTC
* * * **
16950291 CTCTGTAACTTCAGAGAGATAAGATCCAAGGTT--TTAATCTGCTC
1 CACTGCAACTTCAGGGAGATAAGA--C-TTGTTACTTAATCTGCTC
* * **
16950335 CACTGCAACTTCAGGGAGATAGGA-TTATCGGCTTTAATCTGCTC
1 CACTGCAACTTCAGGGAGATAAGACTTGT-TAC-TTAATCTGCTC
* * ** *
16950379 CACTGTAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGC-C
1 CACTGCAACTTCAGGGAGATAAGACTTGTTA-CTT-AATCTGCTC
* *
16950423 TCACTGCAACTTTA-GGAGGATAAGACTTGTTTACTTAGTCTGCTC
1 -CACTGCAACTTCAGGGA-GATAAGACTTG-TTACTTAATCTGCTC
* * *
16950468 CACTGCAACTTCAGGGAGATAAGACTAGATGC--AATCTGCT-
1 CACTGCAACTTCAGGGAGATAAGACTTGTTACTTAATCTGCTC
** * * ** *
16950508 CTTTGCAACTTCAGAGAGGTAAGATCCAAGGTT--TTAATCCGCTC
1 CACTGCAACTTCAGGGAGATAAGA--C-TTGTTACTTAATCTGCTC
* * * *
16950552 CACTGCAACTTAAGGGAGATAGGA-TTATCAGCTTTAATCTGCTC
1 CACTGCAACTTCAGGGAGATAAGACTTGTTA-C-TTAATCTGCTC
* * ** *
16950596 CACTGCAACTTCAGGGATATAAGATTTGCCATCTTCAGTCTGC-C
1 CACTGCAACTTCAGGGAGATAAGACTTGTTA-CTT-AATCTGCTC
* *
16950640 TCACAGCAACTTCA-GGAGGATAAGACTTGTTTACTTAGTCTGCTC
1 -CACTGCAACTTCAGGGA-GATAAGACTTG-TTACTTAATCTGCTC
* *
16950685 CACTGCAATTTTAGGGAGATAAGACT
1 CACTGCAACTTCAGGGAGATAAGACT
16950711 AGATGCGATC
Statistics
Matches: 420, Mismatches: 84, Indels: 90
0.71 0.14 0.15
Matches are distributed among these distances:
40 44 0.10
41 13 0.03
42 2 0.00
43 18 0.04
44 229 0.55
45 110 0.26
46 4 0.01
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.30
Consensus pattern (43 bp):
CACTGCAACTTCAGGGAGATAAGACTTGTTACTTAATCTGCTC
Done.