Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032253.1 Gossypioides kirkii chromosome KI_11
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: 55708359
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2600 characters in sequence are not A, C, G, or T
File 51 of 182
Found at i:17366511 original size:19 final size:19
Alignment explanation
Indices: 17366489--17366528 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
17366479 TTTAAAATGT
*
17366489 TTAAATTAAATTTTTACAA
1 TTAAATTAAATTCTTACAA
*
17366508 TTAATTTAAATTCTTACAA
1 TTAAATTAAATTCTTACAA
17366527 TT
1 TT
17366529 TAAAATCTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.07, G:0.00, T:0.50
Consensus pattern (19 bp):
TTAAATTAAATTCTTACAA
Found at i:17366655 original size:17 final size:16
Alignment explanation
Indices: 17366629--17366662 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
17366619 TTACACTTCG
17366629 ATTTTAAATTTCAATTT
1 ATTTTAAATTTC-ATTT
*
17366646 ATTTTCAATTTCATTT
1 ATTTTAAATTTCATTT
17366662 A
1 A
17366663 AACTTAAGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.32, C:0.09, G:0.00, T:0.59
Consensus pattern (16 bp):
ATTTTAAATTTCATTT
Found at i:17366733 original size:12 final size:12
Alignment explanation
Indices: 17366714--17366767 Score: 51
Period size: 12 Copynumber: 4.7 Consensus size: 12
17366704 TTAATTTCGA
17366714 ATTT-AACTTTC
1 ATTTCAACTTTC
*
17366725 ATTTCAACTTTA
1 ATTTCAACTTTC
*
17366737 ATTTCAA-TTTT
1 ATTTCAACTTTC
*
17366748 ATTT-AATTTTC
1 ATTTCAACTTTC
17366759 AATTTCAAC
1 -ATTTCAAC
17366768 CAAACCTTGC
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
10 2 0.06
11 14 0.40
12 17 0.49
13 2 0.06
ACGTcount: A:0.31, C:0.15, G:0.00, T:0.54
Consensus pattern (12 bp):
ATTTCAACTTTC
Found at i:17369428 original size:33 final size:33
Alignment explanation
Indices: 17369391--17369455 Score: 121
Period size: 33 Copynumber: 2.0 Consensus size: 33
17369381 GCAGAGATTT
17369391 TCGATCTCAAAGGGGCAATAAATTTCTATCATG
1 TCGATCTCAAAGGGGCAATAAATTTCTATCATG
*
17369424 TCGATCTCAAAGGGGCAATAAATTTCTGTCAT
1 TCGATCTCAAAGGGGCAATAAATTTCTATCAT
17369456 TATCCCTAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.31
Consensus pattern (33 bp):
TCGATCTCAAAGGGGCAATAAATTTCTATCATG
Found at i:17369952 original size:56 final size:57
Alignment explanation
Indices: 17369884--17370021 Score: 154
Period size: 56 Copynumber: 2.4 Consensus size: 57
17369874 TTTGGGTACA
* * *
17369884 AAAAAGGTGGTGTCGATCATGTGTTGACAAACACCC-AAAAATATTTTTCGG-ACCAG
1 AAAAAGG-GGTGTCGACCATGGGATGACAAACACCCAAAAAATATTTTTCGGTACCAG
* * * *
17369940 AAAAAGTGGGTGTCGACCATGGGATGATAAACACCCGAAAAAAATATTTTTGGGTATCTG
1 AAAAAG-GGGTGTCGACCATGGGATGACAAACACCC--AAAAAATATTTTTCGGTACCAG
17370000 AAAAAGAGGGTGTCGACCATGG
1 AAAAAG-GGGTGTCGACCATGG
17370022 TTTGGTAGAT
Statistics
Matches: 69, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
56 30 0.43
57 1 0.01
59 14 0.20
60 24 0.35
ACGTcount: A:0.36, C:0.15, G:0.25, T:0.23
Consensus pattern (57 bp):
AAAAAGGGGTGTCGACCATGGGATGACAAACACCCAAAAAATATTTTTCGGTACCAG
Found at i:17370480 original size:21 final size:21
Alignment explanation
Indices: 17370430--17370480 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
17370420 TTCTTGGATA
17370430 CCTGGCCAACTTCAAGAAATT
1 CCTGGCCAACTTCAAGAAATT
* *
17370451 CTTGACCAACTTCAAGAAATT
1 CCTGGCCAACTTCAAGAAATT
17370472 CCTGGCCAA
1 CCTGGCCAA
17370481 GTCGTCTCGG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.33, C:0.29, G:0.14, T:0.24
Consensus pattern (21 bp):
CCTGGCCAACTTCAAGAAATT
Found at i:17371705 original size:60 final size:60
Alignment explanation
Indices: 17371586--17371752 Score: 209
Period size: 60 Copynumber: 2.8 Consensus size: 60
17371576 CTTTTTTTGG
* *
17371586 GTGTCGGTCATGGCTTGGCAAACACCCAAAAA-A--TTTTTTT-GTATCTGAAAAAGGGA
1 GTGTCGGCCATGGCTTGGCAGACACCCAAAAATATTTTTTTTTCGTATCTGAAAAAGGGA
* *
17371642 GTGTCGGCCATGGCTTGACAGATACCCAAAAATATTTTTTTTTCGTATCT-AGAAAAGGGA
1 GTGTCGGCCATGGCTTGGCAGACACCCAAAAATATTTTTTTTTCGTATCTGA-AAAAGGGA
* *
17371702 GTGTCGGCCATGGCTTGGCAGACATCCAAAAAAATAATTTTTTATTCGTAT
1 GTGTCGGCCATGGCTTGGCAGACA-CC-CAAAAAT-ATTTTTTTTTCGTAT
17371753 TTTTTGGGTG
Statistics
Matches: 95, Mismatches: 8, Indels: 9
0.85 0.07 0.08
Matches are distributed among these distances:
56 28 0.29
57 1 0.01
59 8 0.08
60 36 0.38
61 2 0.02
62 6 0.06
63 14 0.15
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.31
Consensus pattern (60 bp):
GTGTCGGCCATGGCTTGGCAGACACCCAAAAATATTTTTTTTTCGTATCTGAAAAAGGGA
Found at i:17377197 original size:22 final size:21
Alignment explanation
Indices: 17377172--17377212 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
17377162 AATTAATTTG
*
17377172 GATATTCGATATTTATTTTTTT
1 GATATTCGAGATTT-TTTTTTT
*
17377194 GATATTTGAGATTTTTTTT
1 GATATTCGAGATTTTTTTT
17377213 CCTTGGTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.22, C:0.02, G:0.12, T:0.63
Consensus pattern (21 bp):
GATATTCGAGATTTTTTTTTT
Found at i:17379237 original size:58 final size:58
Alignment explanation
Indices: 17379129--17379238 Score: 130
Period size: 58 Copynumber: 1.9 Consensus size: 58
17379119 TTAATATAAC
* * * * *** *
17379129 ATTTGGTACTTTAGCTTGACACTTTTTCCTAATTTGGTATTTAAATTTTTTTGACTCA
1 ATTTGGTACCTGAACTTGACAATTTTTCCTAATTTGGTACCCAAACTTTTTTGACTCA
* *
17379187 ATTTGGTACCTGAACTTGACAATTTTTTCTAATTTGGTACCCAAGCTTTTTT
1 ATTTGGTACCTGAACTTGACAATTTTTCCTAATTTGGTACCCAAACTTTTTT
17379239 CAGATTCAAT
Statistics
Matches: 42, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
58 42 1.00
ACGTcount: A:0.23, C:0.15, G:0.13, T:0.49
Consensus pattern (58 bp):
ATTTGGTACCTGAACTTGACAATTTTTCCTAATTTGGTACCCAAACTTTTTTGACTCA
Found at i:17388836 original size:29 final size:29
Alignment explanation
Indices: 17388799--17388859 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 29
17388789 TATTTATTTT
* *
17388799 ATAATTAATTTAAATTTTATAAT-ATAAAA
1 ATAAATAATTTAAA-TTTAAAATGATAAAA
17388828 ATAAATAATTTAAATTTAAAATGATAAAA
1 ATAAATAATTTAAATTTAAAATGATAAAA
17388857 ATA
1 ATA
17388860 CTTAAAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 7 0.24
29 22 0.76
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (29 bp):
ATAAATAATTTAAATTTAAAATGATAAAA
Found at i:17394264 original size:21 final size:20
Alignment explanation
Indices: 17394211--17394265 Score: 58
Period size: 21 Copynumber: 2.7 Consensus size: 20
17394201 TTAATCAAAA
17394211 GATGAAAACTTAAATTTAAT
1 GATGAAAACTTAAATTTAAT
* * *
17394231 AACCGAGAA-TTAAATATTAAT
1 GA-TGAAAACTTAAAT-TTAAT
17394252 GATGAAAACTTAAA
1 GATGAAAACTTAAA
17394266 ACTATTTTTT
Statistics
Matches: 26, Mismatches: 6, Indels: 5
0.70 0.16 0.14
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.53, C:0.07, G:0.11, T:0.29
Consensus pattern (20 bp):
GATGAAAACTTAAATTTAAT
Found at i:17398263 original size:53 final size:53
Alignment explanation
Indices: 17398143--17398439 Score: 461
Period size: 53 Copynumber: 5.6 Consensus size: 53
17398133 TCATATTTGG
*
17398143 TAACTCATGATGACACAGAGTCATCGGACCTTTAATCCGT-ATAGGATTCATA
1 TAACTCACGATGACACAGAGTCATCGGACCTTTAATCCGTAATAGGATTCATA
* *
17398195 TAACTCACGATGACACAGATTCATCGGACCTTTAATCCTTAATAGGATTCATA
1 TAACTCACGATGACACAGAGTCATCGGACCTTTAATCCGTAATAGGATTCATA
*
17398248 TAACTCACGATGACACAGAGTCATCGGATCTTTAATCCGTAATAGGATTCATA
1 TAACTCACGATGACACAGAGTCATCGGACCTTTAATCCGTAATAGGATTCATA
* * * * *
17398301 TAACTCATGATGACACAAAGTCATCGGACCTTTAATCCATACTAGGATCCATA
1 TAACTCACGATGACACAGAGTCATCGGACCTTTAATCCGTAATAGGATTCATA
* * *
17398354 TAACTCACAATGATACAGAGTCATCAGACCTTTAATCCGTAATAGGATTCATA
1 TAACTCACGATGACACAGAGTCATCGGACCTTTAATCCGTAATAGGATTCATA
* *
17398407 TAACTCACAATGACACAAAGTCATCGGACCTTT
1 TAACTCACGATGACACAGAGTCATCGGACCTTT
17398440 TTGTATTTAC
Statistics
Matches: 221, Mismatches: 23, Indels: 1
0.90 0.09 0.00
Matches are distributed among these distances:
52 37 0.17
53 184 0.83
ACGTcount: A:0.35, C:0.23, G:0.14, T:0.28
Consensus pattern (53 bp):
TAACTCACGATGACACAGAGTCATCGGACCTTTAATCCGTAATAGGATTCATA
Found at i:17402137 original size:24 final size:23
Alignment explanation
Indices: 17402074--17402137 Score: 58
Period size: 24 Copynumber: 2.7 Consensus size: 23
17402064 TTAGAATTCA
* ** *
17402074 AAAAAATATAAAATTATTTTTTT
1 AAAAATTATAAAATTAAATTATT
17402097 AAAAATTA-AAATCATTAAATTATT
1 AAAAATTATAAA--ATTAAATTATT
17402121 AAAAATGTATAAAATTA
1 AAAAAT-TATAAAATTA
17402138 TAAGAAAATA
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
22 3 0.09
23 7 0.21
24 18 0.55
25 2 0.06
26 3 0.09
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.39
Consensus pattern (23 bp):
AAAAATTATAAAATTAAATTATT
Found at i:17402423 original size:25 final size:24
Alignment explanation
Indices: 17402367--17402423 Score: 64
Period size: 24 Copynumber: 2.3 Consensus size: 24
17402357 CATTATGCCT
17402367 ATTATTTAATATAATTTGTTAGTA
1 ATTATTTAATATAATTTGTTAGTA
*
17402391 CTTATTTAA-A-AATATATGTTAGATA
1 ATTATTTAATATAAT-T-TGTTAG-TA
17402416 ATTATTTA
1 ATTATTTA
17402424 TTGCGATATT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
22 3 0.11
23 2 0.07
24 14 0.50
25 9 0.32
ACGTcount: A:0.40, C:0.02, G:0.07, T:0.51
Consensus pattern (24 bp):
ATTATTTAATATAATTTGTTAGTA
Found at i:17405100 original size:31 final size:31
Alignment explanation
Indices: 17405065--17405134 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 31
17405055 ATTACATAAT
* *
17405065 AATCATTAAATTAATTAGAA-ATTTTTATTTA
1 AATCACTAAATTAATTA-AATATTTTTATATA
* *
17405096 AATCACTAAATTATTTAAATTTTTTTATATA
1 AATCACTAAATTAATTAAATATTTTTATATA
17405127 AATCACTA
1 AATCACTA
17405135 TATTGTTACA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
30 2 0.06
31 32 0.94
ACGTcount: A:0.44, C:0.07, G:0.01, T:0.47
Consensus pattern (31 bp):
AATCACTAAATTAATTAAATATTTTTATATA
Found at i:17405150 original size:31 final size:31
Alignment explanation
Indices: 17405086--17405150 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
17405076 TAATTAGAAA
* *
17405086 TTTTTATTTAAATCACTAAATTATTTAAATT
1 TTTTTATATAAATCACTAAATTAGTTAAATT
* *
17405117 TTTTTATATAAATCACTATATT-GTTACATT
1 TTTTTATATAAATCACTAAATTAGTTAAATT
17405147 TTTT
1 TTTT
17405151 AAAATCTAGT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
30 10 0.33
31 20 0.67
ACGTcount: A:0.34, C:0.08, G:0.02, T:0.57
Consensus pattern (31 bp):
TTTTTATATAAATCACTAAATTAGTTAAATT
Found at i:17410720 original size:11 final size:12
Alignment explanation
Indices: 17410687--17410745 Score: 50
Period size: 11 Copynumber: 4.9 Consensus size: 12
17410677 ATATTAGTTA
17410687 ATAATAATAA-T
1 ATAATAATAATT
*
17410698 ATAATACTAATT
1 ATAATAATAATT
17410710 A-AATAATAATTT
1 ATAATAATAA-TT
* *
17410722 ATATTATTATATT
1 ATAATAATA-ATT
*
17410735 ATAATATTAAT
1 ATAATAATAAT
17410746 AAATTAAAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
11 16 0.41
12 7 0.18
13 15 0.38
14 1 0.03
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.46
Consensus pattern (12 bp):
ATAATAATAATT
Found at i:17416843 original size:11 final size:12
Alignment explanation
Indices: 17416810--17416868 Score: 50
Period size: 11 Copynumber: 4.9 Consensus size: 12
17416800 ATATTAGTTA
17416810 ATAATAATAA-T
1 ATAATAATAATT
*
17416821 ATAATACTAATT
1 ATAATAATAATT
17416833 A-AATAATAATTT
1 ATAATAATAA-TT
* *
17416845 ATATTATTATATT
1 ATAATAATA-ATT
*
17416858 ATAATATTAAT
1 ATAATAATAAT
17416869 AAATTAAAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
11 16 0.41
12 7 0.18
13 15 0.38
14 1 0.03
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.46
Consensus pattern (12 bp):
ATAATAATAATT
Found at i:17417599 original size:27 final size:26
Alignment explanation
Indices: 17417536--17417616 Score: 92
Period size: 27 Copynumber: 3.0 Consensus size: 26
17417526 CCATTAACTC
17417536 GACCTGTTGACCTAACCCATTGACTTT
1 GACCTGTTGACC-AACCCATTGACTTT
17417563 GATCC-GTTGACTCAACCCATTGACTTT
1 GA-CCTGTTGAC-CAACCCATTGACTTT
* * *
17417590 GACCTATTGACCCGACCTATTGACTTT
1 GACCTGTTGA-CCAACCCATTGACTTT
17417617 ATTGTTAACT
Statistics
Matches: 47, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
26 2 0.04
27 41 0.87
28 4 0.09
ACGTcount: A:0.22, C:0.30, G:0.15, T:0.33
Consensus pattern (26 bp):
GACCTGTTGACCAACCCATTGACTTT
Found at i:17418549 original size:167 final size:167
Alignment explanation
Indices: 17418273--17418577 Score: 583
Period size: 167 Copynumber: 1.8 Consensus size: 167
17418263 ATTGCAATTG
17418273 AGACTGAGATATATGTTATCATACCATTGTGTGCTCATGGGTTAGGATTGTACGGTAGAAAACGT
1 AGACTGAGATATATGTTATCATACCATTGTGTGCTCATGGGTTAGGATTGTACGGTAGAAAACGT
* *
17418338 GGTAATCACCCTTTCAAATGGTTAATAGTAAAATCACACTGTTATTGATGAGGATTGGTTGGGGA
66 GGTAATCACCCTTTCAAATGGTTAATAGTAAAACCACACTGTTATTGATGACGATTGGTTGGGGA
17418403 GGGGTTCTATGTGCTCATACCATTGTGTGCTCAAACC
131 GGGGTTCTATGTGCTCATACCATTGTGTGCTCAAACC
*
17418440 AGACTGAGATATATGTTATCATACCATTGTGTGCTCATGGGTTAGGATTGTACGGTAGAAGACGT
1 AGACTGAGATATATGTTATCATACCATTGTGTGCTCATGGGTTAGGATTGTACGGTAGAAAACGT
17418505 GGTAATCACCCTTTCAAATGGTTAATAGTAAAACCACACTGTTATTGATGACGATTGGTTGGGGA
66 GGTAATCACCCTTTCAAATGGTTAATAGTAAAACCACACTGTTATTGATGACGATTGGTTGGGGA
17418570 GGGGTTCT
131 GGGGTTCT
17418578 GGGGAACCTC
Statistics
Matches: 135, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
167 135 1.00
ACGTcount: A:0.28, C:0.14, G:0.26, T:0.32
Consensus pattern (167 bp):
AGACTGAGATATATGTTATCATACCATTGTGTGCTCATGGGTTAGGATTGTACGGTAGAAAACGT
GGTAATCACCCTTTCAAATGGTTAATAGTAAAACCACACTGTTATTGATGACGATTGGTTGGGGA
GGGGTTCTATGTGCTCATACCATTGTGTGCTCAAACC
Found at i:17421546 original size:26 final size:26
Alignment explanation
Indices: 17421515--17421565 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
17421505 TGGAAAGCAT
17421515 TAGAATAACACATAATGATCAAGAAG
1 TAGAATAACACATAATGATCAAGAAG
*
17421541 TAGAATAACATATAATGATCAAGAA
1 TAGAATAACACATAATGATCAAGAA
17421566 ATATGTCTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.55, C:0.10, G:0.14, T:0.22
Consensus pattern (26 bp):
TAGAATAACACATAATGATCAAGAAG
Found at i:17421875 original size:17 final size:17
Alignment explanation
Indices: 17421855--17421887 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
17421845 TGTAGCATTT
17421855 TTTGAAAGC-TTTAAAAA
1 TTTGAAA-CTTTTAAAAA
17421872 TTTGAAACTTTTAAAA
1 TTTGAAACTTTTAAAA
17421888 GAAGTTATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 1 0.07
17 14 0.93
ACGTcount: A:0.45, C:0.06, G:0.09, T:0.39
Consensus pattern (17 bp):
TTTGAAACTTTTAAAAA
Found at i:17422613 original size:22 final size:23
Alignment explanation
Indices: 17422570--17422615 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 23
17422560 TAATATTTTA
*
17422570 AATTGAAGAAAAAATATCAAATT
1 AATTGAAGAAAAAATATAAAATT
17422593 AATTGAA-AAAATAA-ATAAAATT
1 AATTGAAGAAAA-AATATAAAATT
17422615 A
1 A
17422616 TTTTAATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 12 0.57
23 9 0.43
ACGTcount: A:0.65, C:0.02, G:0.07, T:0.26
Consensus pattern (23 bp):
AATTGAAGAAAAAATATAAAATT
Found at i:17424522 original size:20 final size:21
Alignment explanation
Indices: 17424497--17424535 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
17424487 AAATACTTTT
*
17424497 TTCTAAATA-TCTAAATGAGA
1 TTCTAAAAAGTCTAAATGAGA
17424517 TTCTAAAAAGTCTAAATGA
1 TTCTAAAAAGTCTAAATGA
17424536 TTTATTCAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.46, C:0.10, G:0.10, T:0.33
Consensus pattern (21 bp):
TTCTAAAAAGTCTAAATGAGA
Found at i:17425014 original size:16 final size:16
Alignment explanation
Indices: 17424987--17425056 Score: 79
Period size: 16 Copynumber: 4.4 Consensus size: 16
17424977 TTTGGTTCGC
*
17424987 TGTAATGGAATAGAGA
1 TGTAATGAAATAGAGA
*
17425003 TATAATGAAATAGA-A
1 TGTAATGAAATAGAGA
*
17425018 CTGTAATGAAATAGAGC
1 -TGTAATGAAATAGAGA
* *
17425035 TGTAATGGAATAGAGC
1 TGTAATGAAATAGAGA
17425051 TGTAAT
1 TGTAAT
17425057 CAATAATTCA
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
15 1 0.02
16 46 0.98
ACGTcount: A:0.44, C:0.04, G:0.24, T:0.27
Consensus pattern (16 bp):
TGTAATGAAATAGAGA
Found at i:17425031 original size:32 final size:32
Alignment explanation
Indices: 17424986--17425056 Score: 97
Period size: 32 Copynumber: 2.2 Consensus size: 32
17424976 GTTTGGTTCG
*
17424986 CTGTAATGGAATAGAGATATAATGAAATAGAA
1 CTGTAATGAAATAGAGATATAATGAAATAGAA
* * * *
17425018 CTGTAATGAAATAGAGCTGTAATGGAATAGAG
1 CTGTAATGAAATAGAGATATAATGAAATAGAA
17425050 CTGTAAT
1 CTGTAAT
17425057 CAATAATTCA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.44, C:0.06, G:0.24, T:0.27
Consensus pattern (32 bp):
CTGTAATGAAATAGAGATATAATGAAATAGAA
Found at i:17425295 original size:58 final size:56
Alignment explanation
Indices: 17425226--17425371 Score: 179
Period size: 58 Copynumber: 2.5 Consensus size: 56
17425216 AATTTTAATG
*
17425226 ATTATTATTAAATATAATTTAATAAAAATAT-TAATTTATTTAATTATATTTTAACATA
1 ATTATTATTAAATATAATTTAATAAAAATATGTAATTTA-ATAA-TAT-TTTTAACATA
* *
17425284 ATTATTATTAAATACAATTTAATAAAATAATATGTAATTTAATAATATTTTTAATATA
1 ATTATTATTAAATATAATTTAAT-AAA-AATATGTAATTTAATAATATTTTTAACATA
*
17425342 ATTATTATTAAAATATGAA-TTAGTAAAAAT
1 ATTATTATT-AAATAT-AATTTAATAAAAAT
17425372 TATAATATAT
Statistics
Matches: 78, Mismatches: 5, Indels: 11
0.83 0.05 0.12
Matches are distributed among these distances:
57 3 0.04
58 43 0.55
59 15 0.19
60 10 0.13
61 7 0.09
ACGTcount: A:0.50, C:0.01, G:0.02, T:0.47
Consensus pattern (56 bp):
ATTATTATTAAATATAATTTAATAAAAATATGTAATTTAATAATATTTTTAACATA
Found at i:17434128 original size:25 final size:25
Alignment explanation
Indices: 17434098--17434147 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
17434088 TATTTTAGAA
17434098 AATTTTAACATTCTTGATAGTAAAT
1 AATTTTAACATTCTTGATAGTAAAT
**
17434123 AATTTTAGTATTCTTGATAGTAAAT
1 AATTTTAACATTCTTGATAGTAAAT
17434148 TATTAATTAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.38, C:0.06, G:0.10, T:0.46
Consensus pattern (25 bp):
AATTTTAACATTCTTGATAGTAAAT
Found at i:17443123 original size:24 final size:25
Alignment explanation
Indices: 17443084--17443133 Score: 75
Period size: 24 Copynumber: 2.0 Consensus size: 25
17443074 TAAGTGTGAG
*
17443084 ACTAAAAATAAAGTTTAACTGAAAA
1 ACTAAAAATAAAGTTTAACTAAAAA
*
17443109 ACTAAAAA-AATGTTTAACTAAAAA
1 ACTAAAAATAAAGTTTAACTAAAAA
17443133 A
1 A
17443134 AAGAAAAACG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 15 0.65
25 8 0.35
ACGTcount: A:0.62, C:0.08, G:0.06, T:0.24
Consensus pattern (25 bp):
ACTAAAAATAAAGTTTAACTAAAAA
Found at i:17443140 original size:24 final size:24
Alignment explanation
Indices: 17443087--17443141 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 24
17443077 GTGTGAGACT
*
17443087 AAAAATAAA-GTTTAACTGAAAAA
1 AAAAAAAAATGTTTAACTGAAAAA
**
17443110 CTAAAAAAATGTTTAACT-AAAAA
1 AAAAAAAAATGTTTAACTGAAAAA
*
17443133 AAAGAAAAA
1 AAAAAAAAA
17443142 CGAGACATAA
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
23 17 0.68
24 8 0.32
ACGTcount: A:0.67, C:0.05, G:0.07, T:0.20
Consensus pattern (24 bp):
AAAAAAAAATGTTTAACTGAAAAA
Found at i:17452308 original size:2 final size:2
Alignment explanation
Indices: 17452301--17452346 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
17452291 TTAAACATAA
17452301 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
17452343 AT AT
1 AT AT
17452347 TTAATTTTAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17454455 original size:16 final size:16
Alignment explanation
Indices: 17454434--17454464 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
17454424 CCATCAACAA
17454434 ATTAAACCAAAATATT
1 ATTAAACCAAAATATT
*
17454450 ATTAAACCCAAATAT
1 ATTAAACCAAAATAT
17454465 AATTCATTCT
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:0.55, C:0.16, G:0.00, T:0.29
Consensus pattern (16 bp):
ATTAAACCAAAATATT
Found at i:17454495 original size:57 final size:58
Alignment explanation
Indices: 17454432--17454549 Score: 168
Period size: 57 Copynumber: 2.1 Consensus size: 58
17454422 ATCCATCAAC
*
17454432 AAATTAAACCAAAATATTATTAAACCCAAATATAA-TTCATTCTTCAAA-AACACTTAT
1 AAATTAAACCAAAATATTATTAAACCCAAATATAATTTCATTCTT-AAATAACACTAAT
* * * *
17454489 AAATTAAACCCAAATATTTTTAAACTCAAATATAATTTTATTCTTAAATAACACTAAT
1 AAATTAAACCAAAATATTATTAAACCCAAATATAATTTCATTCTTAAATAACACTAAT
17454547 AAA
1 AAA
17454550 CAACTCCTTT
Statistics
Matches: 54, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
57 35 0.65
58 19 0.35
ACGTcount: A:0.51, C:0.15, G:0.00, T:0.34
Consensus pattern (58 bp):
AAATTAAACCAAAATATTATTAAACCCAAATATAATTTCATTCTTAAATAACACTAAT
Found at i:17455332 original size:29 final size:29
Alignment explanation
Indices: 17455298--17455355 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
17455288 AACTAAAAAA
17455298 TTAAATGCTAAAAAATAAATA-TTAAAATT
1 TTAAAT-CTAAAAAATAAATACTTAAAATT
* * *
17455327 TTAAATCTTAAATATAATTACTTAAAATT
1 TTAAATCTAAAAAATAAATACTTAAAATT
17455356 AATTATGGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 11 0.44
29 14 0.56
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.40
Consensus pattern (29 bp):
TTAAATCTAAAAAATAAATACTTAAAATT
Found at i:17464284 original size:37 final size:38
Alignment explanation
Indices: 17464233--17464317 Score: 111
Period size: 37 Copynumber: 2.3 Consensus size: 38
17464223 AATAAACTTT
* *
17464233 TAATCCTAGCCCTAGATATAAA-CCTAAAGAG-ATCTTA
1 TAATCCTAGCCCTAGATATAAATCCTAAAG-GTAACTAA
* *
17464270 TAATCCTAGTCCTAGATTTAAATCCTAAAGGTAACTAA
1 TAATCCTAGCCCTAGATATAAATCCTAAAGGTAACTAA
17464308 TAATCCTAGC
1 TAATCCTAGC
17464318 TATCTATCTA
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
37 21 0.51
38 20 0.49
ACGTcount: A:0.39, C:0.21, G:0.11, T:0.29
Consensus pattern (38 bp):
TAATCCTAGCCCTAGATATAAATCCTAAAGGTAACTAA
Found at i:17464370 original size:16 final size:15
Alignment explanation
Indices: 17464336--17464374 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 15
17464326 TATATGTCTA
*
17464336 ATAAT-AAATAAGAC
1 ATAATAAAATAACAC
17464350 ATAATAAAATAACATC
1 ATAATAAAATAACA-C
17464366 ATAATAAAA
1 ATAATAAAA
17464375 AAGCTTACAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 5 0.23
15 7 0.32
16 10 0.45
ACGTcount: A:0.67, C:0.08, G:0.03, T:0.23
Consensus pattern (15 bp):
ATAATAAAATAACAC
Found at i:17467459 original size:20 final size:20
Alignment explanation
Indices: 17467434--17467486 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 20
17467424 ATTGAATCGA
*
17467434 TTTTATAATTTTTT-AATAT
1 TTTTATAATTTTTTCAAAAT
*
17467453 TTTT-TATTTTTTTTCAAAAT
1 TTTTATA-ATTTTTTCAAAAT
*
17467473 TTTAATAATTTTTT
1 TTTTATAATTTTTT
17467487 TGTTTTGAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
18 2 0.07
19 10 0.37
20 13 0.48
21 2 0.07
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (20 bp):
TTTTATAATTTTTTCAAAAT
Found at i:17468602 original size:19 final size:20
Alignment explanation
Indices: 17468556--17468619 Score: 69
Period size: 19 Copynumber: 3.1 Consensus size: 20
17468546 TTTATAATTT
17468556 TTTTTAAAAATATAAATTTTGAAA
1 TTTTTAAAAAT-T--ATTTTG-AA
*
17468580 TTTTTATAAA-TATTTTGAA
1 TTTTTAAAAATTATTTTGAA
17468599 -TTTTAAAAATTATTTTGAA
1 TTTTTAAAAATTATTTTGAA
17468618 TT
1 TT
17468620 ACTTTGTAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
18 8 0.22
19 11 0.31
20 7 0.19
22 1 0.03
24 9 0.25
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (20 bp):
TTTTTAAAAATTATTTTGAA
Found at i:17469976 original size:3 final size:3
Alignment explanation
Indices: 17469968--17469994 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
17469958 TTTAGGGTTT
17469968 AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA
17469995 GAATATACAA
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):
AGA
Found at i:17470041 original size:17 final size:18
Alignment explanation
Indices: 17470008--17470041 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
17469998 TATACAAATA
17470008 TTTCATTTACGAATTTTC
1 TTTCATTTACGAATTTTC
*
17470026 TTTCCTTTAC-AATTTT
1 TTTCATTTACGAATTTT
17470042 AAAGAAGCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.21, C:0.18, G:0.03, T:0.59
Consensus pattern (18 bp):
TTTCATTTACGAATTTTC
Found at i:17471999 original size:12 final size:12
Alignment explanation
Indices: 17471982--17472020 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
17471972 AAATGGGAGA
17471982 TGAAGAAGATAG
1 TGAAGAAGATAG
*
17471994 TGAAGAAGAAAG
1 TGAAGAAGATAG
17472006 ATGAAGAAGATAG
1 -TGAAGAAGATAG
17472019 TG
1 TG
17472021 TGACGGCCGG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
12 13 0.54
13 11 0.46
ACGTcount: A:0.51, C:0.00, G:0.33, T:0.15
Consensus pattern (12 bp):
TGAAGAAGATAG
Found at i:17481665 original size:29 final size:30
Alignment explanation
Indices: 17481632--17481690 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
17481622 AGTCCAAAAG
17481632 TTTCAC-AAATTTACG-AATTAGA-CCTTAAA
1 TTTCACAAAATTT-CGAAATTA-ATCCTTAAA
17481661 TTTCACAAAATTTCGAAATTAATCCTTAAA
1 TTTCACAAAATTTCGAAATTAATCCTTAAA
17481691 ATCACTAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
29 9 0.33
30 18 0.67
ACGTcount: A:0.42, C:0.17, G:0.05, T:0.36
Consensus pattern (30 bp):
TTTCACAAAATTTCGAAATTAATCCTTAAA
Found at i:17481695 original size:29 final size:29
Alignment explanation
Indices: 17481634--17481701 Score: 70
Period size: 30 Copynumber: 2.3 Consensus size: 29
17481624 TCCAAAAGTT
*
17481634 TCACAAATTTACGAATTAGACCTTAAATT
1 TCACAAATTTACGAATTAGACCTTAAATA
17481663 TCACAAAATTT-CGAAATTA-ATCCTTAAA-A
1 TCAC-AAATTTACG-AATTAGA-CCTTAAATA
17481692 TCACTAAATT
1 TCAC-AAATT
17481702 CACAATTTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
29 16 0.47
30 18 0.53
ACGTcount: A:0.44, C:0.18, G:0.04, T:0.34
Consensus pattern (29 bp):
TCACAAATTTACGAATTAGACCTTAAATA
Found at i:17495560 original size:2 final size:2
Alignment explanation
Indices: 17495548--17495577 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
17495538 AAATCATAGC
*
17495548 CT CT TT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
17495578 TCTTTCTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
CT
Found at i:17497487 original size:20 final size:19
Alignment explanation
Indices: 17497441--17497489 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
17497431 ATTACAAAAT
* *
17497441 AATTCAAAATAATTTTTAA
1 AATTCAAAATAATTATAAA
*
17497460 AATTCAAAATACTTATAAA
1 AATTCAAAATAATTATAAA
17497479 AATTTCAAAAT
1 AA-TTCAAAAT
17497490 TTATATTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 18 0.69
20 8 0.31
ACGTcount: A:0.55, C:0.08, G:0.00, T:0.37
Consensus pattern (19 bp):
AATTCAAAATAATTATAAA
Found at i:17497951 original size:13 final size:13
Alignment explanation
Indices: 17497923--17497959 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
17497913 TCATATTTCA
17497923 TTATATAAATTAT
1 TTATATAAATTAT
17497936 TTATAATAAATT-T
1 TTAT-ATAAATTAT
17497949 TTA-ATAAATTA
1 TTATATAAATTA
17497960 AAAATATTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
11 7 0.32
13 8 0.36
14 7 0.32
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (13 bp):
TTATATAAATTAT
Found at i:17498069 original size:17 final size:18
Alignment explanation
Indices: 17498049--17498089 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 18
17498039 TATGATTAGA
17498049 AAATTTACA-TATA-TAAT
1 AAATTTA-ATTATATTAAT
*
17498066 AAATATAATTATATTAAT
1 AAATTTAATTATATTAAT
17498084 AAATTT
1 AAATTT
17498090 TACTTTTTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
16 1 0.05
17 10 0.50
18 9 0.45
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (18 bp):
AAATTTAATTATATTAAT
Found at i:17512292 original size:3 final size:3
Alignment explanation
Indices: 17512286--17512316 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
17512276 ACCATCATTT
17512286 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
17512317 ATACAACATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:17513366 original size:30 final size:30
Alignment explanation
Indices: 17513332--17513395 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
17513322 AAAAGGTCCT
17513332 TAAACTATCCAAAAATTACATTTTAACCCC
1 TAAACTATCCAAAAATTACATTTTAACCCC
* * * * *
17513362 TAAACTTTTCTAAAATTATATTTTAACCCT
1 TAAACTATCCAAAAATTACATTTTAACCCC
17513392 TAAA
1 TAAA
17513396 ATTTTTCAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.42, C:0.20, G:0.00, T:0.38
Consensus pattern (30 bp):
TAAACTATCCAAAAATTACATTTTAACCCC
Found at i:17513407 original size:60 final size:60
Alignment explanation
Indices: 17513343--17513499 Score: 183
Period size: 61 Copynumber: 2.6 Consensus size: 60
17513333 AAACTATCCA
* *
17513343 AAAATTACATTTTAACCC-CTAAACTTTTCTAAAATTATATTTT-AACCCTTAAAATTTTTC
1 AAAATTACATTTTAACCCTC-AAACTTTT-TAAAATTATATTTTGAACCCCTAAAATTTTCC
* * * *
17513403 AAAATTATATTTTAACCCTCAAACTTTTTCAAAATCATATTTTGACCCCCTAAACTTTTCC
1 AAAATTACATTTTAACCCTCAAACTTTTT-AAAATTATATTTTGAACCCCTAAAATTTTCC
* * *
17513464 AAAATCACATATTAACCCTCAAACTTCTATAAAATT
1 AAAATTACATTTTAACCCTCAAACTT-TTTAAAATT
17513500 TCATTTTCAT
Statistics
Matches: 82, Mismatches: 11, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
59 1 0.01
60 37 0.45
61 42 0.51
62 2 0.02
ACGTcount: A:0.39, C:0.22, G:0.01, T:0.39
Consensus pattern (60 bp):
AAAATTACATTTTAACCCTCAAACTTTTTAAAATTATATTTTGAACCCCTAAAATTTTCC
Found at i:17513488 original size:30 final size:30
Alignment explanation
Indices: 17513343--17513489 Score: 161
Period size: 30 Copynumber: 4.9 Consensus size: 30
17513333 AAACTATCCA
* *
17513343 AAAATTACATTTTAACCC-CTAAACTTTTCT
1 AAAATTATATTTTAACCCTC-AAACTTTTCC
* * *
17513373 AAAATTATATTTTAACCCTTAAAATTTTTC
1 AAAATTATATTTTAACCCTCAAACTTTTCC
*
17513403 AAAATTATATTTTAACCCTCAAACTTTTTC
1 AAAATTATATTTTAACCCTCAAACTTTTCC
* * *
17513433 AAAATCATATTTTGACCCCCTAAACTTTTCC
1 AAAATTATATTTTAACCCTC-AAACTTTTCC
* * *
17513464 AAAATCACATATTAACCCTCAAACTT
1 AAAATTATATTTTAACCCTCAAACTT
17513490 CTATAAAATT
Statistics
Matches: 100, Mismatches: 15, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
30 75 0.75
31 25 0.25
ACGTcount: A:0.38, C:0.22, G:0.01, T:0.39
Consensus pattern (30 bp):
AAAATTATATTTTAACCCTCAAACTTTTCC
Found at i:17515108 original size:49 final size:50
Alignment explanation
Indices: 17515031--17515615 Score: 454
Period size: 49 Copynumber: 11.8 Consensus size: 50
17515021 ACAAAGCATT
** *
17515031 AAGGGAAAGATTTAAGCCATAACGGCGAATCCAGTA-CGCGAAGATAATG
1 AAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGATAATG
* * ** * * *
17515080 GAGGGAAAGGTTTAAGTTGCAACAGCGAA-CCTTGTACCTCAGAAG--AATG
1 AAGGGAAAGATTTAAGCCGCAACGGCGAATCC-AGTACCAC-GAAGATAATG
* * * *
17515129 AAAGGAAAGATTTAAGCCGCAATGGCAAATCCAGTACCATGAAGATAATG
1 AAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGATAATG
* * * * ** * * * *
17515179 GAGGGAAAGGTTTAAGTCGTAAC-GATAAACCTTGTACCTCAGAAG--CATG
1 AAGGGAAAGATTTAAGCCGCAACGGCGAATCC-AGTACCAC-GAAGATAATG
** *
17515228 AAGGGAAAGATTTAAGCTACAACGGCGAATCCAGTACCACGAAGATGAT-
1 AAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGATAATG
* * * * *
17515277 AGAGGGAAATG-TTTAAGTCGCAATGGCGAA-CCTTGTACCTCAGAAG--CATG
1 A-AGGGAAA-GATTTAAGCCGCAACGGCGAATCC-AGTACCAC-GAAGATAATG
*
17515327 AAGGGAAAGATTTAAGCCGTAACGGCGAATCCAGTACCACGAAGATAATG
1 AAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGATAATG
* * * ** * * *
17515377 GAGGGAAAGGTTTTAGTTGTAACGGCGAA-CCTTGTACCTC--AGAATAATG
1 AAGGGAAAGATTTAAGCCGCAACGGCGAATCC-AGTACCACGAAG-ATAATG
* *
17515426 AAGGGAAAGATTTAAGCTGCAACGGCGAATCCAGTACCACGAAGATGAT-
1 AAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGATAATG
* * * **
17515475 AAGGGAAAGGTTTAAGTCGCAACGGCG-ATCCTTGTACCTTGAA-A-ACATG
1 AAGGGAAAGATTTAAGCCGCAACGGCGAATCC-AGTACCACGAAGATA-ATG
* *
17515524 AAGGGAAAGATTTAAGCCGTAACGGCGAATCCAGTATCACGAAGATAATTG
1 AAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGATAA-TG
*
17515575 -AGGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCACGA
1 AAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGA
17515616 TGACATTGTA
Statistics
Matches: 414, Mismatches: 90, Indels: 63
0.73 0.16 0.11
Matches are distributed among these distances:
48 24 0.06
49 221 0.53
50 151 0.36
51 18 0.04
ACGTcount: A:0.37, C:0.17, G:0.26, T:0.19
Consensus pattern (50 bp):
AAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGATAATG
Found at i:17515210 original size:99 final size:99
Alignment explanation
Indices: 17515031--17515611 Score: 781
Period size: 99 Copynumber: 5.9 Consensus size: 99
17515021 ACAAAGCATT
** *
17515031 AAGGGAAAGATTTAAGCCATAACGGCGAATCCAGTA-CGCGAAGATAATGGAGGGAAAGGTTTAA
1 AAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGATAATGGAGGGAAAGGTTTAA
* *
17515095 GTTGCAACAGCGAACCTTGTACCTCAGAAGAATG
66 GTCGCAACGGCGAACCTTGTACCTCAGAAGAATG
* * * *
17515129 AAAGGAAAGATTTAAGCCGCAATGGCAAATCCAGTACCATGAAGATAATGGAGGGAAAGGTTTAA
1 AAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGATAATGGAGGGAAAGGTTTAA
* *** *
17515194 GTCGTAACGATAAACCTTGTACCTCAGAAGCATG
66 GTCGCAACGGCGAACCTTGTACCTCAGAAGAATG
** * * *
17515228 AAGGGAAAGATTTAAGCTACAACGGCGAATCCAGTACCACGAAGATGATAGAGGGAAATGTTTAA
1 AAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGATAATGGAGGGAAAGGTTTAA
* *
17515293 GTCGCAATGGCGAACCTTGTACCTCAGAAGCATG
66 GTCGCAACGGCGAACCTTGTACCTCAGAAGAATG
* *
17515327 AAGGGAAAGATTTAAGCCGTAACGGCGAATCCAGTACCACGAAGATAATGGAGGGAAAGGTTTTA
1 AAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGATAATGGAGGGAAAGGTTTAA
* * *
17515392 GTTGTAACGGCGAACCTTGTACCTCAGAATAATG
66 GTCGCAACGGCGAACCTTGTACCTCAGAAGAATG
* * *
17515426 AAGGGAAAGATTTAAGCTGCAACGGCGAATCCAGTACCACGAAGATGAT-AAGGGAAAGGTTTAA
1 AAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGATAATGGAGGGAAAGGTTTAA
* * *
17515490 GTCGCAACGGCGATCCTTGTACCT-TGAAAACATG
66 GTCGCAACGGCGAACCTTGTACCTCAGAAGA-ATG
* * * *
17515524 AAGGGAAAGATTTAAGCCGTAACGGCGAATCCAGTATCACGAAGATAATTGAGGGAAAGATTTAA
1 AAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGATAATGGAGGGAAAGGTTTAA
* * *
17515589 GCCGCAACGGCGAATCTAGTACC
66 GTCGCAACGGCGAACCTTGTACC
17515612 ACGATGACAT
Statistics
Matches: 420, Mismatches: 60, Indels: 5
0.87 0.12 0.01
Matches are distributed among these distances:
97 4 0.01
98 113 0.27
99 303 0.72
ACGTcount: A:0.37, C:0.17, G:0.26, T:0.19
Consensus pattern (99 bp):
AAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGATAATGGAGGGAAAGGTTTAA
GTCGCAACGGCGAACCTTGTACCTCAGAAGAATG
Found at i:17516222 original size:16 final size:16
Alignment explanation
Indices: 17516201--17516232 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
17516191 GCCCTAAATA
17516201 CCCAAATACACCCAAG
1 CCCAAATACACCCAAG
*
17516217 CCCAAATACACTCAAG
1 CCCAAATACACCCAAG
17516233 GTTTGAAACC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.44, C:0.41, G:0.06, T:0.09
Consensus pattern (16 bp):
CCCAAATACACCCAAG
Found at i:17516329 original size:11 final size:11
Alignment explanation
Indices: 17516281--17516336 Score: 58
Period size: 11 Copynumber: 4.7 Consensus size: 11
17516271 CCGTCACTGT
17516281 CACGTCAGCACC
1 CACGTCAGCA-C
17516293 GTCACGTCAGCATC
1 --CACGTCAGCA-C
*
17516307 CATGTCAGCAC
1 CACGTCAGCAC
*
17516318 CACGTCATCAC
1 CACGTCAGCAC
17516329 CACGTCAG
1 CACGTCAG
17516337 TCACGTGACC
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
11 17 0.46
12 9 0.24
14 11 0.30
ACGTcount: A:0.25, C:0.41, G:0.18, T:0.16
Consensus pattern (11 bp):
CACGTCAGCAC
Found at i:17516432 original size:18 final size:18
Alignment explanation
Indices: 17516369--17516434 Score: 71
Period size: 18 Copynumber: 3.7 Consensus size: 18
17516359 ACCATTGATT
* *
17516369 GCTCCTCTGCCTGAGACT
1 GCTCCTCTGCCCGAGACC
*
17516387 GCTCCTCTCCCCGAGACC
1 GCTCCTCTGCCCGAGACC
* *
17516405 -CTTCTGCTGCCCGAGGCC
1 GCTCCT-CTGCCCGAGACC
17516423 GCTCCTCTGCCC
1 GCTCCTCTGCCC
17516435 AAGGACCTCC
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
17 4 0.10
18 31 0.79
19 4 0.10
ACGTcount: A:0.08, C:0.48, G:0.21, T:0.23
Consensus pattern (18 bp):
GCTCCTCTGCCCGAGACC
Found at i:17532389 original size:158 final size:158
Alignment explanation
Indices: 17532099--17532431 Score: 443
Period size: 158 Copynumber: 2.1 Consensus size: 158
17532089 GTAACCATAT
* * * *
17532099 ATGCTCACACGAGCTGTGAAATAGGTTTGCTCACATGAGCTGTGGGTTGAGATATGGGGCTACAT
1 ATGCTCACACGAGCTGTGAAATAGGTTTGCTCACACGAGCTGTGGGTCGAGATATGAGGCTACAC
* * * * ** *
17532164 GATGCTGCTCACACGAGCTGTGGCAGAACTATAATAAATGTTGGACCTCAGCCATCGGTAGGACA
66 GATACTGCTCACACGAGCTGTGGCAGAACCACAACAAATGCAGGACCTCAACCATCGGTAGGACA
* *
17532229 TCTAAGACCAGCACTCATATAATATGTA
131 TCTAAGACCAGCACCCATATAACATGTA
* * * * *
17532257 ATGCTCACACGAGCTGTGAAATGGGTTTGCTCACACGAGCTGTGGGTCGAGATGTTAGGTTACCC
1 ATGCTCACACGAGCTGTGAAATAGGTTTGCTCACACGAGCTGTGGGTCGAGATATGAGGCTACAC
* * * *
17532322 GATATTGCTCACACGAGCTGTGG-AGAATCCGCAACCAATGCAGGACCTCAACCATCGGTAGGGC
66 GATACTGCTCACACGAGCTGTGGCAGAA-CCACAACAAATGCAGGACCTCAACCATCGGTAGGAC
*
17532386 ATCTAAGACTAGCACCCATATAACATGTA
130 ATCTAAGACCAGCACCCATATAACATGTA
17532415 ATGCTCACACGAGCTGT
1 ATGCTCACACGAGCTGT
17532432 AACTGTAACA
Statistics
Matches: 151, Mismatches: 23, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
157 4 0.03
158 147 0.97
ACGTcount: A:0.28, C:0.23, G:0.25, T:0.24
Consensus pattern (158 bp):
ATGCTCACACGAGCTGTGAAATAGGTTTGCTCACACGAGCTGTGGGTCGAGATATGAGGCTACAC
GATACTGCTCACACGAGCTGTGGCAGAACCACAACAAATGCAGGACCTCAACCATCGGTAGGACA
TCTAAGACCAGCACCCATATAACATGTA
Found at i:17536431 original size:2 final size:2
Alignment explanation
Indices: 17536424--17536457 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
17536414 ATAATGTTTA
17536424 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
17536458 TTGTTACAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17537518 original size:7 final size:7
Alignment explanation
Indices: 17537506--17537532 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
17537496 GGAGGAGTGG
17537506 AGGAAGT
1 AGGAAGT
17537513 AGGAAGT
1 AGGAAGT
17537520 AGGAAGT
1 AGGAAGT
17537527 AGGAAG
1 AGGAAG
17537533 GAAAGTGGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.44, C:0.00, G:0.44, T:0.11
Consensus pattern (7 bp):
AGGAAGT
Found at i:17544425 original size:17 final size:18
Alignment explanation
Indices: 17544405--17544439 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
17544395 TTAGGTGGGT
17544405 TTTAAATATA-TTTTAAA
1 TTTAAATATAGTTTTAAA
*
17544422 TTTAAATTTAGTTTTAAA
1 TTTAAATATAGTTTTAAA
17544440 ATTGAGATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (18 bp):
TTTAAATATAGTTTTAAA
Found at i:17546413 original size:30 final size:31
Alignment explanation
Indices: 17546343--17546414 Score: 94
Period size: 30 Copynumber: 2.4 Consensus size: 31
17546333 CTGTTCAGAG
* * * *
17546343 ATTATA-TTTTGACCCCCAAACTTTTCTAAA
1 ATTATATTTTTAACCCCAAAACTTTCCAAAA
17546373 ATTATATTTTTAACCCCAAAAC-TTCCAAAA
1 ATTATATTTTTAACCCCAAAACTTTCCAAAA
17546403 ATTATATTTTTA
1 ATTATATTTTTA
17546415 CCTCGAACTT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
30 24 0.65
31 13 0.35
ACGTcount: A:0.38, C:0.19, G:0.01, T:0.42
Consensus pattern (31 bp):
ATTATATTTTTAACCCCAAAACTTTCCAAAA
Found at i:17546440 original size:58 final size:57
Alignment explanation
Indices: 17546380--17546531 Score: 205
Period size: 58 Copynumber: 2.6 Consensus size: 57
17546370 AAAATTATAT
* *
17546380 TTTTAACCCCAAAACTTCCAAAAATTATATTTTTACCTCGAACTTTTAAAAATCCCA
1 TTTTAACCCCGAAACTTCCAAAAATTATATTTTTACCTCAAACTTTTAAAAATCCCA
* ** * *
17546437 TTTTGACCTTGAAACTTCCAAAAATTATAATTTTACCCTCAAATTTTTAAAAATCCCA
1 TTTTAACCCCGAAACTTCCAAAAATTATATTTTTA-CCTCAAACTTTTAAAAATCCCA
* * *
17546495 TTTTAATCCCGAAACTTCTAAAAATTACATTTTTACC
1 TTTTAACCCCGAAACTTCCAAAAATTATATTTTTACC
17546532 CCTGGATGTC
Statistics
Matches: 80, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
57 32 0.40
58 48 0.60
ACGTcount: A:0.38, C:0.22, G:0.03, T:0.38
Consensus pattern (57 bp):
TTTTAACCCCGAAACTTCCAAAAATTATATTTTTACCTCAAACTTTTAAAAATCCCA
Found at i:17546525 original size:29 final size:28
Alignment explanation
Indices: 17546366--17546532 Score: 88
Period size: 29 Copynumber: 5.8 Consensus size: 28
17546356 CCCCAAACTT
* *
17546366 TTCT-AAAATTATATTTTTAACCCCAAAAC
1 TTCTAAAAATTACA-TTTTAA-CCCGAAAC
* * *
17546395 TTCCAAAAATTATATTTTTACCTCG-AAC
1 TTCTAAAAATTACATTTTAACC-CGAAAC
* ** * *
17546423 TTTTAAAAATCCCATTTTGACCTTGAAAC
1 TTCTAAAAATTACATTTTAACC-CGAAAC
* * * *
17546452 TTCCAAAAATTATAATTTT-ACCCTCAAAT
1 TTCTAAAAATTA-CATTTTAACCC-GAAAC
* **
17546481 TTTTAAAAATCCCATTTTAATCCCGAAAC
1 TTCTAAAAATTACATTTTAA-CCCGAAAC
*
17546510 TTCTAAAAATTACATTTTTACCC
1 TTCTAAAAATTACATTTTAACCC
17546533 CTGGATGTCC
Statistics
Matches: 102, Mismatches: 29, Indels: 15
0.70 0.20 0.10
Matches are distributed among these distances:
28 31 0.30
29 54 0.53
30 17 0.17
ACGTcount: A:0.38, C:0.22, G:0.02, T:0.38
Consensus pattern (28 bp):
TTCTAAAAATTACATTTTAACCCGAAAC
Found at i:17546532 original size:58 final size:57
Alignment explanation
Indices: 17546343--17546532 Score: 202
Period size: 58 Copynumber: 3.3 Consensus size: 57
17546333 CTGTTCAGAG
* * * *** *
17546343 ATTATATTTTGACCCCCAAACTTTTCTAAAATTATATTTTTAACCCCAAAACTTCCAAAA
1 ATTATATTTTTACCCTCAAACTTTT-AAAAATCCCA-TTTTAA-CCCGAAACTTCCAAAA
* * *
17546403 ATTATATTTTTA-CCTCGAACTTTTAAAAATCCCATTTTGACCTTGAAACTTCCAAAA
1 ATTATATTTTTACCCTCAAACTTTTAAAAATCCCATTTTAACC-CGAAACTTCCAAAA
* * *
17546460 ATTATAATTTTACCCTCAAATTTTTAAAAATCCCATTTTAATCCCGAAACTTCTAAAA
1 ATTATATTTTTACCCTCAAACTTTTAAAAATCCCATTTTAA-CCCGAAACTTCCAAAA
*
17546518 ATTACATTTTTACCC
1 ATTATATTTTTACCC
17546533 CTGGATGTCC
Statistics
Matches: 109, Mismatches: 18, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
56 2 0.02
57 28 0.26
58 56 0.51
59 12 0.11
60 11 0.10
ACGTcount: A:0.37, C:0.22, G:0.03, T:0.38
Consensus pattern (57 bp):
ATTATATTTTTACCCTCAAACTTTTAAAAATCCCATTTTAACCCGAAACTTCCAAAA
Found at i:17546588 original size:59 final size:59
Alignment explanation
Indices: 17546502--17546650 Score: 146
Period size: 59 Copynumber: 2.5 Consensus size: 59
17546492 CCATTTTAAT
*
17546502 CCCGAAAC-TTCTAAAAATTA-CATTTTTACCCCT-GGATGTCCAAAAACTCCATTTTTGA
1 CCCGAAACTTTC-AAAAATTACCA-TTTTACCCCTCGGATGTCAAAAAACTCCATTTTTGA
* * * * *
17546560 CCCCGAAACTTTCAAAAATTACCGTTTTA-CTCTCGGATGTCAAAAAATTTCGTTTTTGA
1 -CCCGAAACTTTCAAAAATTACCATTTTACCCCTCGGATGTCAAAAAACTCCATTTTTGA
* * *
17546619 TCC-TAATTTTCCAAAAATTACCATTTTACCCC
1 CCCGAAACTTT-CAAAAATTACCATTTTACCCC
17546651 CGAATGTTTA
Statistics
Matches: 74, Mismatches: 11, Indels: 10
0.78 0.12 0.11
Matches are distributed among these distances:
57 5 0.07
58 21 0.28
59 44 0.59
60 4 0.05
ACGTcount: A:0.32, C:0.26, G:0.08, T:0.35
Consensus pattern (59 bp):
CCCGAAACTTTCAAAAATTACCATTTTACCCCTCGGATGTCAAAAAACTCCATTTTTGA
Found at i:17546747 original size:29 final size:29
Alignment explanation
Indices: 17546691--17546752 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 29
17546681 ATATTTTTCC
* *
17546691 AAAATTACCATTTTTCCCTTCAGAGTCCT
1 AAAATTACCATTTTACCCTTCAGAGTCCA
*
17546720 AAAATTACCATTTTACCC-TCGAGTGTCCA
1 AAAATTACCATTTTACCCTTC-AGAGTCCA
17546749 AAAA
1 AAAA
17546753 GTCTCATTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 2 0.07
29 27 0.93
ACGTcount: A:0.34, C:0.26, G:0.08, T:0.32
Consensus pattern (29 bp):
AAAATTACCATTTTACCCTTCAGAGTCCA
Found at i:17552396 original size:18 final size:18
Alignment explanation
Indices: 17552364--17552398 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
17552354 AAAAGAGAAA
**
17552364 AAGAAGAAACGCAAAAAC
1 AAGAAGAAAAACAAAAAC
17552382 AAGAAGAAAAACAAAAA
1 AAGAAGAAAAACAAAAA
17552399 TTGAAAAAGG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.74, C:0.11, G:0.14, T:0.00
Consensus pattern (18 bp):
AAGAAGAAAAACAAAAAC
Found at i:17554305 original size:201 final size:201
Alignment explanation
Indices: 17553955--17555011 Score: 1350
Period size: 201 Copynumber: 5.2 Consensus size: 201
17553945 AACAACAAGA
* * * *
17553955 CGGTAATCTTCCTGATGAGATACAGAGAAGTATACCAACTCGACGCTCGATTTGAGCAAAT-TAT
1 CGGTCATCTTCCTGATGAGATACAGAGAAGTAGACCAACTCAACGCTCGATGTGAGCAAATCT-T
* * * * * * *
17554019 CAAACCCCACCTTCCTGATGAGACATTGAGAAACAGGTCGAAGCAATAAATTGGTTAGCTTCCTG
65 CGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGTAATAAAATGGTTAGCTTCCTG
* *
17554084 ATGAGATACTAAGAAGTGGACCAAATTCGTCTTCTTGATGAGATACAGAGAAGCGAATTGAAACA
130 ATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGAATTGAAACA
17554149 AGTGAGG
195 AGTGAGG
* * * **
17554156 CGGTCATCTTCCTAATGAGATACAGAGAAGTATACCAACTCAACGCTCAATACGAGCAAATCTTC
1 CGGTCATCTTCCTGATGAGATACAGAGAAGTAGACCAACTCAACGCTCGATGTGAGCAAATCTTC
* *
17554221 GAACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGTAATTAAATGGTTAGCTTCCTGA
66 GAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGTAATAAAATGGTTAGCTTCCTGA
* * *
17554286 TGAGATACTAAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGTGGATTGAAACAA
131 TGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGAATTGAAACAA
*
17554351 GTGATG
196 GTGAGG
* * *
17554357 CGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCTACGCTCGATGTGAGCAAA
1 CGGTCATCTTCCTGATGAGATACAGAGAAGTAGACCAACTC--A---ACGCTCGATGTGAGCAAA
* * *
17554422 TCTTCAAACCCTA-CTTCCTGATGAGATACTGAGAAGCAGGTCGAACTAATAAAATGGTTAGCTT
61 TCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGTAATAAAATGGTTAGCTT
* *
17554486 CCTGATGAGATACTGAGAAGTAGACCAAATTCGTCTTCCTAATGAGATACAGAGAAGCGAATTGA
126 CCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGAATTGA
17554551 AACAAGTGAGG
191 AACAAGTGAGG
* * **
17554562 CGGTCATCTTCCTGATGAGATACAGAGAAGTACG-CCAACTCGAGGCTTAATGCT-AGCAAATCT
1 CGGTCATCTTCCTGATGAGATACAGAGAAGTA-GACCAACTCAACGCTCGATG-TGAGCAAATCT
* *
17554625 TCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCTT
64 TCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGTAATAAAATGGTTAGCTTCCT
* *
17554690 GATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCGGATGAGATACAGAGAAGTGAATTGAAAC
129 GATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGAATTGAAAC
** *
17554755 AAACGATG
194 AAGTGAGG
* * * * *
17554763 CAGTCATCTTTCTAATGAGATACTGAGAAGAAGACCGAA-TCAAACCCATGCTCGATGTGAGCAA
1 CGGTCATCTTCCTGATGAGATACAGAGAAGTAGACC-AACTC-AA--C--GCTCGATGTGAGCAA
* *
17554827 ATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAACGGGTCGAAGTAATAAAATGGTTAGCT
60 ATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGTAATAAAATGGTTAGCT
* * * * * * * **
17554892 TCCTGATGAGGTACTGAGAAGTGAACCAAATCCGTCTTCCTGATGAAACACAGAGAAGTGGATCA
125 TCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGAATTG
* *
17554957 AAATAAGTGATG
190 AAACAAGTGAGG
* * * * * *
17554969 CGGTAATCTTCTTGATGAGATTCTGAGAAGAAGACCAAATCAA
1 CGGTCATCTTCCTGATGAGATACAGAGAAGTAGACCAACTCAA
17555012 TGAAACCAGA
Statistics
Matches: 752, Mismatches: 86, Indels: 32
0.86 0.10 0.04
Matches are distributed among these distances:
200 25 0.03
201 367 0.49
202 4 0.01
203 1 0.00
205 159 0.21
206 196 0.26
ACGTcount: A:0.35, C:0.19, G:0.23, T:0.23
Consensus pattern (201 bp):
CGGTCATCTTCCTGATGAGATACAGAGAAGTAGACCAACTCAACGCTCGATGTGAGCAAATCTTC
GAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGTAATAAAATGGTTAGCTTCCTGA
TGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGAATTGAAACAA
GTGAGG
Found at i:17554783 original size:406 final size:406
Alignment explanation
Indices: 17553997--17554998 Score: 1488
Period size: 406 Copynumber: 2.5 Consensus size: 406
17553987 TACCAACTCG
* * *
17553997 ACGCTCGATTTGAGCAAAT-TATCAAACCCCACCTTCCTGATGAGACATTGAGAAACAGGTCGAA
1 ACGCTCGATGTGAGCAAATCT-TCAAACCCCACCTTCCTGATGAGATACTGAGAAACAGGTCGAA
* * *
17554061 GC-AATAAATTGGTTAGCTTCCTGATGAGATACTAAGAAGTGGACCAAATTCGTCTTCTTGATGA
65 -CTAATAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGT-GACCAAATTCGTCTTCCTGATGA
* *
17554125 GATACAGAGAAGCGAATTGAAACAAGTGAGGCGGTCATCTTCCTAATGAGATACAGAGAAGTATA
128 GATACAGAGAAGCGAATTGAAACAAGTGAGGCGGTCATCTTCCTGATGAGATACAGAGAAGTACA
17554190 CCAACTCAACGCTCAATACGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAGAAGCA
193 CCAACTCAACGCTCAATACGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAGAAGCA
* *
17554255 GGTCGAAGTAATTAAATGGTTAGCTTCCTGATGAGATACTAAGAAGTGGACCAAATTCGTCTTCC
258 GGTCGAAGCAATAAAATGGTTAGCTTCCTGATGAGATACTAAGAAGTGGACCAAATTCGTCTTCC
* * ** * *
17554320 TGATGAGATACAGAGAAGTGGATTGAAACAAGTGATGCGGTCATCTTCCTGATGAGATACTGAGA
323 GGATGAGATACAGAGAAGTGAATTGAAACAAACGATGCAGTCATCTTCCTAATGAGATACTGAGA
*
17554385 AGAAGACCAAATCAAACCT
388 AGAAGACCAAATCAAACCC
* *
17554404 ACGCTCGATGTGAGCAAATCTTCAAACCCTA-CTTCCTGATGAGATACTGAGAAGCAGGTCGAAC
1 ACGCTCGATGTGAGCAAATCTTCAAACCCCACCTTCCTGATGAGATACTGAGAAACAGGTCGAAC
*
17554468 TAATAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGTAGACCAAATTCGTCTTCCTAATGAGA
66 TAATAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGT-GACCAAATTCGTCTTCCTGATGAGA
*
17554533 TACAGAGAAGCGAATTGAAACAAGTGAGGCGGTCATCTTCCTGATGAGATACAGAGAAGTACGCC
130 TACAGAGAAGCGAATTGAAACAAGTGAGGCGGTCATCTTCCTGATGAGATACAGAGAAGTACACC
* * * * * *
17554598 AACTCGAGGCTTAATGCTAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGG
195 AACTCAACGCTCAATACGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAGAAGCAGG
* *
17554663 TCGAAGCAATAAAATGGTTAGCTTCTTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCGG
260 TCGAAGCAATAAAATGGTTAGCTTCCTGATGAGATACTAAGAAGTGGACCAAATTCGTCTTCCGG
*
17554728 ATGAGATACAGAGAAGTGAATTGAAACAAACGATGCAGTCATCTTTCTAATGAGATACTGAGAAG
325 ATGAGATACAGAGAAGTGAATTGAAACAAACGATGCAGTCATCTTCCTAATGAGATACTGAGAAG
*
17554793 AAGACCGAATCAAACCC
390 AAGACCAAATCAAACCC
* * * * *
17554810 ATGCTCGATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAACGGGTCGAAG
1 ACGCTCGATGTGAGCAAATCTTCAAACCCCACCTTCCTGATGAGATACTGAGAAACAGGTCGAAC
* * *
17554875 TAATAAAATGGTTAGCTTCCTGATGAGGTACTGAGAAGTGAACCAAATCCGTCTTCCTGATGAAA
66 TAATAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGTG-ACCAAATTCGTCTTCCTGATGAGA
* * * ** * * * * * *
17554940 CACAGAGAAGTGGATCAAAATAAGTGATGCGGTAATCTTCTTGATGAGATTCTGAGAAG
130 TACAGAGAAGCGAATTGAAACAAGTGAGGCGGTCATCTTCCTGATGAGATACAGAGAAG
17554999 AAGACCAAAT
Statistics
Matches: 538, Mismatches: 53, Indels: 8
0.90 0.09 0.01
Matches are distributed among these distances:
405 1 0.00
406 372 0.69
407 164 0.30
408 1 0.00
ACGTcount: A:0.34, C:0.19, G:0.23, T:0.23
Consensus pattern (406 bp):
ACGCTCGATGTGAGCAAATCTTCAAACCCCACCTTCCTGATGAGATACTGAGAAACAGGTCGAAC
TAATAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGTGACCAAATTCGTCTTCCTGATGAGAT
ACAGAGAAGCGAATTGAAACAAGTGAGGCGGTCATCTTCCTGATGAGATACAGAGAAGTACACCA
ACTCAACGCTCAATACGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGT
CGAAGCAATAAAATGGTTAGCTTCCTGATGAGATACTAAGAAGTGGACCAAATTCGTCTTCCGGA
TGAGATACAGAGAAGTGAATTGAAACAAACGATGCAGTCATCTTCCTAATGAGATACTGAGAAGA
AGACCAAATCAAACCC
Found at i:17555374 original size:6 final size:6
Alignment explanation
Indices: 17555365--17555432 Score: 59
Period size: 6 Copynumber: 11.5 Consensus size: 6
17555355 TTAGGTGGGT
* * *
17555365 TTTAAA TTT-AT TTCTAAA ATTAAA TTT-AC TTTAAA TTTAAA TTTAAA
1 TTTAAA TTTAAA TT-TAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* **
17555412 TTCATT TTTAAA TTTAAA TTT
1 TTTAAA TTTAAA TTTAAA TTT
17555433 TAGTTTTAAA
Statistics
Matches: 47, Mismatches: 12, Indels: 6
0.72 0.18 0.09
Matches are distributed among these distances:
5 7 0.15
6 38 0.81
7 2 0.04
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.54
Consensus pattern (6 bp):
TTTAAA
Found at i:17555404 original size:17 final size:18
Alignment explanation
Indices: 17555365--17555409 Score: 65
Period size: 17 Copynumber: 2.6 Consensus size: 18
17555355 TTAGGTGGGT
*
17555365 TTTAAATTTATTTCTAAA
1 TTTAAATTTACTTCTAAA
*
17555383 ATTAAATTTACTT-TAAA
1 TTTAAATTTACTTCTAAA
17555400 TTTAAATTTA
1 TTTAAATTTA
17555410 AATTCATTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
17 13 0.54
18 11 0.46
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.53
Consensus pattern (18 bp):
TTTAAATTTACTTCTAAA
Found at i:17555423 original size:18 final size:19
Alignment explanation
Indices: 17555400--17555445 Score: 67
Period size: 19 Copynumber: 2.5 Consensus size: 19
17555390 TTACTTTAAA
*
17555400 TTTAAATTTAAA-TTCATT
1 TTTAAATTTAAATTTCAGT
*
17555418 TTTAAATTTAAATTTTAGT
1 TTTAAATTTAAATTTCAGT
17555437 TTTAAATTT
1 TTTAAATTT
17555446 GAGATAATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 12 0.48
19 13 0.52
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (19 bp):
TTTAAATTTAAATTTCAGT
Found at i:17555553 original size:18 final size:18
Alignment explanation
Indices: 17555510--17555554 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
17555500 TTACAAAGTC
*
17555510 TAATTACAAA-AAATGCA
1 TAATTACAAATAAATCCA
17555527 TAATT-CAAATGAAATCCA
1 TAATTACAAAT-AAATCCA
17555545 -AATTACAAAT
1 TAATTACAAAT
17555555 TGGAGCCCAA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
16 4 0.17
17 9 0.38
18 11 0.46
ACGTcount: A:0.56, C:0.13, G:0.04, T:0.27
Consensus pattern (18 bp):
TAATTACAAATAAATCCA
Found at i:17556178 original size:3 final size:3
Alignment explanation
Indices: 17556172--17556224 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
17556162 ATGACTGTTT
17556172 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
17556220 TAA TA
1 TAA TA
17556225 TAACGCCATT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:17557419 original size:30 final size:29
Alignment explanation
Indices: 17557384--17557484 Score: 102
Period size: 30 Copynumber: 3.5 Consensus size: 29
17557374 CTAACTATTC
*
17557384 AAAAATTATATTTTAACCGCT-AAACTTCT
1 AAAAATTACATTTTAACC-CTGAAACTTCT
*
17557413 CTAAAATTACATTTTAACCCTGAAACTTCT
1 -AAAAATTACATTTTAACCCTGAAACTTCT
*
17557443 AAAAATTACATTTGT-A-CCTCG-AACATCT
1 AAAAATTACATTT-TAACCCT-GAAACTTCT
*
17557471 AAAAATTATATTTT
1 AAAAATTACATTTT
17557485 TACTCCCAGA
Statistics
Matches: 63, Mismatches: 5, Indels: 9
0.82 0.06 0.12
Matches are distributed among these distances:
27 1 0.02
28 21 0.33
29 16 0.25
30 25 0.40
ACGTcount: A:0.41, C:0.18, G:0.04, T:0.38
Consensus pattern (29 bp):
AAAAATTACATTTTAACCCTGAAACTTCT
Found at i:17557542 original size:30 final size:29
Alignment explanation
Indices: 17557371--17557548 Score: 89
Period size: 30 Copynumber: 6.1 Consensus size: 29
17557361 ACCCTGTAAG
* * *
17557371 TCCCTAACTATTCAAAAATTATATTTTAAC
1 TCCCAAACT-TTCAAAAATTACATTTTTAC
* * *
17557401 -CGCTAAACTTCTCTAAAATTACATTTTAAC
1 TC-CCAAACTT-TCAAAAATTACATTTTTAC
* *
17557431 -CCTGAAAC-TTCTAAAAATTACATTTGTAC
1 TCC-CAAACTTTC-AAAAATTACATTTTTAC
* * * *
17557460 -CTCGAAC-ATCTAAAAATTATATTTTTAC
1 TCCCAAACTTTC-AAAAATTACATTTTTAC
* * **
17557488 TCCCAGACTTTTAAAAATCCCATTTTTGA-
1 TCCCAAACTTTCAAAAATTACATTTTT-AC
*
17557517 TCCCAAAACTTTCAAAAATTACATTTGTAC
1 TCCC-AAACTTTCAAAAATTACATTTTTAC
17557547 TC
1 TC
17557549 TAAAAATTAC
Statistics
Matches: 112, Mismatches: 27, Indels: 18
0.71 0.17 0.11
Matches are distributed among these distances:
28 23 0.21
29 40 0.36
30 49 0.44
ACGTcount: A:0.37, C:0.22, G:0.04, T:0.37
Consensus pattern (29 bp):
TCCCAAACTTTCAAAAATTACATTTTTAC
Found at i:17558162 original size:95 final size:96
Alignment explanation
Indices: 17558024--17558196 Score: 251
Period size: 95 Copynumber: 1.8 Consensus size: 96
17558014 CAATATTCTT
* * * ** *
17558024 TTATTTCGAGTTTCGAAAATTTGTGCTTTCACTTACTAGGTGCAATTTTTCTTCAAATTGAAATA
1 TTATTTCGAGTTTCGAAAATTTGCGCCTTAACTTACTAGGTGCAACCTTTCTTCAAATCGAAATA
*
17558089 ATCGAATATCCTTAATCGAGGCAATGTTTCC
66 ATCGAACATCCTTAATCGAGGCAATGTTTCC
*
17558120 TTATCTTCGA-TTTCG-AAATTTGCGCCTTAACTTACTAGGTGCAACCTTTCTTCAAATCGAGAT
1 TTAT-TTCGAGTTTCGAAAATTTGCGCCTTAACTTACTAGGTGCAACCTTTCTTCAAATCGAAAT
17558183 AATCGAACATCCTT
65 AATCGAACATCCTT
17558197 TTCCAAAATT
Statistics
Matches: 68, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
95 54 0.79
96 9 0.13
97 5 0.07
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.39
Consensus pattern (96 bp):
TTATTTCGAGTTTCGAAAATTTGCGCCTTAACTTACTAGGTGCAACCTTTCTTCAAATCGAAATA
ATCGAACATCCTTAATCGAGGCAATGTTTCC
Found at i:17558730 original size:21 final size:21
Alignment explanation
Indices: 17558684--17558726 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
17558674 CGTCTTCTTT
*
17558684 ATTA-TTATTATTTATATTTA
1 ATTATTTATTATTGATATTTA
17558704 ATTATTTATTA-TGATATTTA
1 ATTATTTATTATTGATATTTA
17558724 ATT
1 ATT
17558727 TATTGATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 15 0.71
21 6 0.29
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (21 bp):
ATTATTTATTATTGATATTTA
Found at i:17558849 original size:19 final size:19
Alignment explanation
Indices: 17558831--17558872 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
17558821 TTTAATTTTA
*
17558831 ATTTTAATT-TTTTTATTT
1 ATTTTAATTATTGTTATTT
*
17558849 ATTTAAATTATTGTTATTT
1 ATTTTAATTATTGTTATTT
17558868 ATTTT
1 ATTTT
17558873 CATGCCATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.71
Consensus pattern (19 bp):
ATTTTAATTATTGTTATTT
Found at i:17559219 original size:23 final size:24
Alignment explanation
Indices: 17559193--17559253 Score: 58
Period size: 23 Copynumber: 2.7 Consensus size: 24
17559183 TATATTATTA
17559193 ATTAATTAATATT-TATTGTCATT
1 ATTAATTAATATTATATTGTCATT
*
17559216 ATT-ATT-ATGATTATATTGTTATT
1 ATTAATTAAT-ATTATATTGTCATT
* *
17559239 -TTATTTAATACTATA
1 ATTAATTAATATTATA
17559254 ATTATATTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
21 2 0.06
22 8 0.26
23 19 0.61
24 2 0.06
ACGTcount: A:0.34, C:0.03, G:0.05, T:0.57
Consensus pattern (24 bp):
ATTAATTAATATTATATTGTCATT
Found at i:17568001 original size:49 final size:48
Alignment explanation
Indices: 17567912--17568369 Score: 251
Period size: 49 Copynumber: 9.3 Consensus size: 48
17567902 GCAACGATAG
* * *
17567912 ACCTTACACCTT-AAACTTGAAGAGGAATAGCTTTAAGCCGCGAA-GGCGA
1 ACCTAACACCTTAAAAC-TGAAGAGG-ATAGATTGAAGCCGC-AACGGCGA
** * *
17567961 ACCTAATGCCTTCAAGCTGAAGAGAGATAGATTGAAGCCGCAACGGCGA
1 ACCTAACACCTTAAAACTGAAGAG-GATAGATTGAAGCCGCAACGGCGA
* * * * * *
17568010 ATCTAACACCTTAAAACTGAAGTGGGATAGGTTGAAGTCGCAATGACGA
1 ACCTAACACCTTAAAACTGAAG-AGGATAGATTGAAGCCGCAACGGCGA
* * * *
17568059 ACCTAACACCCTAAAAC-CAAGGAGGGA-AGGTTGAAGCCGCAACGGCGG
1 ACCTAACACCTTAAAACTGAA-GA-GGATAGATTGAAGCCGCAACGGCGA
* * * * * *
17568107 ACCTTACACCTTAAAACAGAAGAGGGATAGGTTGAAGCCACAACGACGG
1 ACCTAACACCTTAAAACTGAAGA-GGATAGATTGAAGCCGCAACGGCGA
* ** * * * * *
17568156 ACCTAACACATTAAAAACCAAATAGGGAAAGATTGAAGTCACAACGTCGA
1 ACCTAACACCTT-AAAACTGAAGA-GGATAGATTGAAGCCGCAACGGCGA
* * ** * * * * *
17568206 ATCTTACACCTTAAAACAAAAGAGGAATAGGTTGAAGTCGCGATGACGA
1 ACCTAACACCTTAAAACTGAAGAGG-ATAGATTGAAGCCGCAACGGCGA
** * * * * * *
17568255 ACCTAATGCCTTAAAATTGAAGAGGGATAGATTGAAACCACGACGACGG
1 ACCTAACACCTTAAAACTGAAGA-GGATAGATTGAAGCCGCAACGGCGA
* * * * *
17568304 ATCTAACACCTTGAAA-TCAAAGAGGGAACAGATTGAAGCCGCAACGACGA
1 ACCTAACACCTTAAAACT-GAAGA-GG-ATAGATTGAAGCCGCAACGGCGA
* *
17568354 ATCTTACACCTTAAAA
1 ACCTAACACCTTAAAA
17568370 AAAAGTTAAG
Statistics
Matches: 321, Mismatches: 75, Indels: 25
0.76 0.18 0.06
Matches are distributed among these distances:
48 45 0.14
49 199 0.62
50 77 0.24
ACGTcount: A:0.39, C:0.21, G:0.23, T:0.17
Consensus pattern (48 bp):
ACCTAACACCTTAAAACTGAAGAGGATAGATTGAAGCCGCAACGGCGA
Found at i:17568031 original size:98 final size:98
Alignment explanation
Indices: 17567917--17568369 Score: 376
Period size: 99 Copynumber: 4.6 Consensus size: 98
17567907 GATAGACCTT
* * * * ** * *
17567917 ACACCTT-AAACTTGAAGAGGAATAGCTTTAAGCCGCGAA-GGCGAACCTAATGCCTTCAAGCTG
1 ACACCTTAAAAC-AGAAGAGGAATAGGTTGAAGCCGC-AACGACGAACCTAACACCTTAAAACTG
* *
17567980 AAGAGAGATAGATTGAAGCCGCAACGGCGAATCTA
64 AAGAGGGATAGATTGAAGCCACAACGGCGAATCTA
* * * * * * *
17568015 ACACCTTAAAACTGAAGTGGGATAGGTTGAAGTCGCAATGACGAACCTAACACCCTAAAAC-CAA
1 ACACCTTAAAACAGAAGAGGAATAGGTTGAAGCCGCAACGACGAACCTAACACCTTAAAACTGAA
* * * * *
17568079 GGAGGGA-AGGTTGAAGCCGCAACGGCGGACCTT
66 -GAGGGATAGATTGAAGCCACAACGGCGAATCTA
* * * * **
17568112 ACACCTTAAAACAGAAGAGGGATAGGTTGAAGCCACAACGACGGACCTAACACATTAAAAACCAA
1 ACACCTTAAAACAGAAGAGGAATAGGTTGAAGCCGCAACGACGAACCTAACACCTT-AAAACTGA
* * * * *
17568177 ATAGGGAAAGATTGAAGTCACAACGTCGAATCTT
65 AGAGGGATAGATTGAAGCCACAACGGCGAATCTA
* * * * ** *
17568211 ACACCTTAAAACAAAAGAGGAATAGGTTGAAGTCGCGATGACGAACCTAATGCCTTAAAATTGAA
1 ACACCTTAAAACAGAAGAGGAATAGGTTGAAGCCGCAACGACGAACCTAACACCTTAAAACTGAA
* * * *
17568276 GAGGGATAGATTGAAACCACGACGACGGATCTA
66 GAGGGATAGATTGAAGCCACAACGGCGAATCTA
* * * * *
17568309 ACACCTTGAAATCA-AAGAGGGAACAGATTGAAGCCGCAACGACGAATCTTACACCTTAAAA
1 ACACCTT-AAAACAGAAGA-GGAATAGGTTGAAGCCGCAACGACGAACCTAACACCTTAAAA
17568370 AAAAGTTAAG
Statistics
Matches: 283, Mismatches: 64, Indels: 15
0.78 0.18 0.04
Matches are distributed among these distances:
97 74 0.26
98 99 0.35
99 110 0.39
ACGTcount: A:0.39, C:0.21, G:0.23, T:0.17
Consensus pattern (98 bp):
ACACCTTAAAACAGAAGAGGAATAGGTTGAAGCCGCAACGACGAACCTAACACCTTAAAACTGAA
GAGGGATAGATTGAAGCCACAACGGCGAATCTA
Found at i:17568118 original size:97 final size:97
Alignment explanation
Indices: 17567833--17568260 Score: 360
Period size: 97 Copynumber: 4.4 Consensus size: 97
17567823 TCATAGAGTT
* * * * * *
17567833 TGAAGAGGGATAAGTTGAAGTTGCAACGATGGACCTAACACCCTAAAACCAAAGATGGAA-TTTG
1 TGAAGAGGGATAGGTTGAAGTCGCAACGACGAACCTAACACCCTAAAACCAAAGAGGGAAGATTG
* * **
17567897 AATCTGCAAC-GATAGACCTTACACCTT-AAAC
66 AAGCCGCAACGGCGA-ACCTTACACCTTAAAAC
* * * * * ** * * * ** *
17567928 TTGAAGAGGAATAGCTTTAAGCCGCGAA-GGCGAACCTAATGCCTTCAAGCTGAAGAGAGATAGA
1 -TGAAGAGGGATAGGTTGAAGTCGC-AACGACGAACCTAACACCCTAAAACCAAAGAGGGA-AGA
* *
17567992 TTGAAGCCGCAACGGCGAATCTAACACCTTAAAAC
63 TTGAAGCCGCAACGGCGAACCTTACACCTTAAAAC
* * * *
17568027 TGAAGTGGGATAGGTTGAAGTCGCAATGACGAACCTAACACCCTAAAACCAAGGAGGGAAGGTTG
1 TGAAGAGGGATAGGTTGAAGTCGCAACGACGAACCTAACACCCTAAAACCAAAGAGGGAAGATTG
*
17568092 AAGCCGCAACGGCGGACCTTACACCTTAAAAC
66 AAGCCGCAACGGCGAACCTTACACCTTAAAAC
* * * * ** *
17568124 AGAAGAGGGATAGGTTGAAGCCACAACGACGGACCTAACACATTAAAAACCAAATAGGGAAAGAT
1 TGAAGAGGGATAGGTTGAAGTCGCAACGACGAACCTAACACCCT-AAAACCAAAGAGGG-AAGAT
* * * *
17568189 TGAAGTCACAACGTCGAATCTTACACCTTAAAAC
64 TGAAGCCGCAACGGCGAACCTTACACCTTAAAAC
** * * *
17568223 AAAAGAGGAATAGGTTGAAGTCGCGATGACGAACCTAA
1 TGAAGAGGGATAGGTTGAAGTCGCAACGACGAACCTAA
17568261 TGCCTTAAAA
Statistics
Matches: 257, Mismatches: 67, Indels: 13
0.76 0.20 0.04
Matches are distributed among these distances:
96 38 0.15
97 75 0.29
98 74 0.29
99 70 0.27
ACGTcount: A:0.39, C:0.20, G:0.23, T:0.18
Consensus pattern (97 bp):
TGAAGAGGGATAGGTTGAAGTCGCAACGACGAACCTAACACCCTAAAACCAAAGAGGGAAGATTG
AAGCCGCAACGGCGAACCTTACACCTTAAAAC
Found at i:17568282 original size:148 final size:147
Alignment explanation
Indices: 17567833--17568374 Score: 474
Period size: 148 Copynumber: 3.7 Consensus size: 147
17567823 TCATAGAGTT
*** * * * * * *
17567833 TGAAGAGGGATA-AGTTGAAGTTGCAACGATGGACCTAACACCCTAAAACCAAAGATGG-AA-TT
1 TGAAGAGGGATAGA-TTGAAGCCACAACGACGGATCTAACACCTTAAAACCAAATAGGGAAAGAT
* * ** * *
17567895 TGAA-TCTGCAACGA-TAGACCTTACACCTT-AAACTTGAAGAGGAATAGCTTTAAGCCGCGAAG
65 TGAAGTC-GCAACGACGA-ATCTTACACCTTAAAAC-AAAAGAGGAATAGGTTGAAGCCGCGAAG
* *
17567957 GCGAACCTAATGCCTTCAAGC
127 GCGAACCTAATGCCTTAAAAC
* * * * * * * *
17567978 TGAAGAGAGATAGATTGAAGCCGCAACGGCGAATCTAACACCTTAAAACTGAAGT-GGGATAGGT
1 TGAAGAGGGATAGATTGAAGCCACAACGACGGATCTAACACCTTAAAAC-CAAATAGGGAAAGAT
* * * * * * *
17568042 TGAAGTCGCAATGACGAACCTAACACCCTAAAACCAAGGAGGGA-AGGTTGAAGCCGC-AACGGC
65 TGAAGTCGCAACGACGAATCTTACACCTTAAAACAAAAGAGGAATAGGTTGAAGCCGCGAA-GGC
* * **
17568105 GGACCTTACACCTTAAAAC
129 GAACCTAATGCCTTAAAAC
* * * *
17568124 AGAAGAGGGATAGGTTGAAGCCACAACGACGGACCTAACACATTAAAAACCAAATAGGGAAAGAT
1 TGAAGAGGGATAGATTGAAGCCACAACGACGGATCTAACACCTT-AAAACCAAATAGGGAAAGAT
* * * * *
17568189 TGAAGTCACAACGTCGAATCTTACACCTTAAAACAAAAGAGGAATAGGTTGAAGTCGCGATGACG
65 TGAAGTCGCAACGACGAATCTTACACCTTAAAACAAAAGAGGAATAGGTTGAAGCCGCGAAGGCG
*
17568254 AACCTAATGCCTTAAAAT
130 AACCTAATGCCTTAAAAC
* * * * *
17568272 TGAAGAGGGATAGATTGAAACCACGACGACGGATCTAACACCTTGAAATCAAAGAGGGAACAGAT
1 TGAAGAGGGATAGATTGAAGCCACAACGACGGATCTAACACCTTAAAACCAAATAGGGAA-AGAT
*
17568337 TGAAGCCGCAACGACGAATCTTACACCTTAAAA-AAAAG
65 TGAAGTCGCAACGACGAATCTTACACCTTAAAACAAAAG
17568375 TTAAGAGACA
Statistics
Matches: 313, Mismatches: 71, Indels: 24
0.77 0.17 0.06
Matches are distributed among these distances:
145 43 0.14
146 70 0.22
147 92 0.29
148 107 0.34
149 1 0.00
ACGTcount: A:0.39, C:0.20, G:0.23, T:0.18
Consensus pattern (147 bp):
TGAAGAGGGATAGATTGAAGCCACAACGACGGATCTAACACCTTAAAACCAAATAGGGAAAGATT
GAAGTCGCAACGACGAATCTTACACCTTAAAACAAAAGAGGAATAGGTTGAAGCCGCGAAGGCGA
ACCTAATGCCTTAAAAC
Found at i:17571126 original size:40 final size:40
Alignment explanation
Indices: 17571067--17571277 Score: 246
Period size: 40 Copynumber: 5.3 Consensus size: 40
17571057 GCCACGAGCC
* * * * ** *
17571067 TAGCAAGCTATGAGTCGGTGAAATGATTCGGGCTACGACC
1 TAGCAGGCTTTGAGCCGGTGAAGTGATTCAAGCTACGACT
* * *
17571107 TAGTAGGCTTTGAGCCGGTGATGTGATTCAAGCTACGGCT
1 TAGCAGGCTTTGAGCCGGTGAAGTGATTCAAGCTACGACT
* *
17571147 TAGCAAGCTTTGAGCCAGT-AATGTGATTCAAGCTACGACT
1 TAGCAGGCTTTGAGCCGGTGAA-GTGATTCAAGCTACGACT
* *
17571187 TAGCAGGATTTGAGCCGGTGATGTGATTCAAGCTACGACT
1 TAGCAGGCTTTGAGCCGGTGAAGTGATTCAAGCTACGACT
* *
17571227 TAGCAGGCTTTGGGCCGGTGATGTGATTCAAGCTAC-AGCT
1 TAGCAGGCTTTGAGCCGGTGAAGTGATTCAAGCTACGA-CT
17571267 TAGCAGGCTTT
1 TAGCAGGCTTT
17571278 AATCAGTGAG
Statistics
Matches: 147, Mismatches: 21, Indels: 6
0.84 0.12 0.03
Matches are distributed among these distances:
39 2 0.01
40 144 0.98
41 1 0.01
ACGTcount: A:0.24, C:0.19, G:0.29, T:0.27
Consensus pattern (40 bp):
TAGCAGGCTTTGAGCCGGTGAAGTGATTCAAGCTACGACT
Found at i:17572331 original size:43 final size:43
Alignment explanation
Indices: 17572280--17572370 Score: 130
Period size: 43 Copynumber: 2.1 Consensus size: 43
17572270 CAGGCACACA
* * *
17572280 GGTTGGGACATGGTCGTGTGACCTTACTTT-GTACACACACAAG
1 GGTTGGGACACGGTCATGTGACCTTA-TTTCGCACACACACAAG
*
17572323 GGTTGGGACACGGTCATGTGACCTTATTTCGCACACACACACG
1 GGTTGGGACACGGTCATGTGACCTTATTTCGCACACACACAAG
17572366 GGTTG
1 GGTTG
17572371 ATACACGATC
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
42 3 0.07
43 40 0.93
ACGTcount: A:0.22, C:0.23, G:0.29, T:0.26
Consensus pattern (43 bp):
GGTTGGGACACGGTCATGTGACCTTATTTCGCACACACACAAG
Found at i:17572377 original size:43 final size:43
Alignment explanation
Indices: 17572280--17572395 Score: 126
Period size: 43 Copynumber: 2.7 Consensus size: 43
17572270 CAGGCACACA
* * *
17572280 GGTTGGGACATGGTCGTGTGACCTTACTTT-GTACACACACAAG
1 GGTTGAGACACGGTCGTGTGACCTTA-TTTCGCACACACACAAG
* * *
17572323 GGTTGGGACACGGTCATGTGACCTTATTTCGCACACACACACG
1 GGTTGAGACACGGTCGTGTGACCTTATTTCGCACACACACAAG
* * * *
17572366 GGTTGATACACGATCGTGTGTCCCTATTTC
1 GGTTGAGACACGGTCGTGTGACCTTATTTC
17572396 AATTGCTCAC
Statistics
Matches: 62, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
42 3 0.05
43 59 0.95
ACGTcount: A:0.22, C:0.24, G:0.26, T:0.28
Consensus pattern (43 bp):
GGTTGAGACACGGTCGTGTGACCTTATTTCGCACACACACAAG
Found at i:17585225 original size:124 final size:124
Alignment explanation
Indices: 17585071--17585307 Score: 343
Period size: 124 Copynumber: 1.9 Consensus size: 124
17585061 ATGAGAGAAA
* * * * *
17585071 AAATGAGACTGTTTGGGAGTTGAAATAGAAGAAGCAGAAAGATGGCTC-AGTTCTGTCTTAAAAA
1 AAATGAGACTGCTTAGGAATTGAAATAGAAGAAGCAGAAAGACGACTCGA-TTCTGTCTTAAAAA
* * *
17585135 TGTAGTTGCATTTTATT-TTATTATTTTCTATTATACCTCGAATCAACAAATAAGTTCATT
65 TGTAATTGCATTTTATTATT-TTATTTTATATTATACCTCAAATCAACAAATAAGTTCATT
* *
17585195 AAATGAGACTGCTTAGGAATTGAAATAGAAGAAGCAGAAAGACGATTCGATTCTGTCTTGAAAAT
1 AAATGAGACTGCTTAGGAATTGAAATAGAAGAAGCAGAAAGACGACTCGATTCTGTCTTAAAAAT
*
17585260 GTAATTGCATTTTATTATTTTATTTTATATTATACCTTAAATCAACAA
66 GTAATTGCATTTTATTATTTTATTTTATATTATACCTCAAATCAACAA
17585308 TCAGCTCATT
Statistics
Matches: 100, Mismatches: 11, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
124 97 0.97
125 3 0.03
ACGTcount: A:0.37, C:0.11, G:0.16, T:0.36
Consensus pattern (124 bp):
AAATGAGACTGCTTAGGAATTGAAATAGAAGAAGCAGAAAGACGACTCGATTCTGTCTTAAAAAT
GTAATTGCATTTTATTATTTTATTTTATATTATACCTCAAATCAACAAATAAGTTCATT
Found at i:17586322 original size:2 final size:2
Alignment explanation
Indices: 17586315--17586400 Score: 172
Period size: 2 Copynumber: 43.0 Consensus size: 2
17586305 TAAACGAATA
17586315 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
17586357 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
17586399 AT
1 AT
17586401 TTCTAACAAA
Statistics
Matches: 84, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 84 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17588789 original size:13 final size:13
Alignment explanation
Indices: 17588771--17588798 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
17588761 AAAAATCTAG
17588771 AGAAATGATGAAA
1 AGAAATGATGAAA
17588784 AGAAATGATGAAA
1 AGAAATGATGAAA
17588797 AG
1 AG
17588799 GCTATAAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.61, C:0.00, G:0.25, T:0.14
Consensus pattern (13 bp):
AGAAATGATGAAA
Found at i:17590187 original size:6 final size:6
Alignment explanation
Indices: 17590176--17590214 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
17590166 TGATCAAAAT
* * *
17590176 TGAAAG TGAAAG TGAAAG TGAAAT TGGAAT TGAAAG TGA
1 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGA
17590215 TATGAACTGT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.46, C:0.00, G:0.31, T:0.23
Consensus pattern (6 bp):
TGAAAG
Found at i:17591443 original size:32 final size:32
Alignment explanation
Indices: 17591370--17591430 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
17591360 ACACCATGTC
* *
17591370 TATTGATGTGGCAGTGCCACATCATCACCGAG
1 TATTGATGTGACAATGCCACATCATCACCGAG
*
17591402 TATTAATGTGACAATGCCACATCATCACC
1 TATTGATGTGACAATGCCACATCATCACC
17591431 TATTGTTGAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.26
Consensus pattern (32 bp):
TATTGATGTGACAATGCCACATCATCACCGAG
Found at i:17591733 original size:15 final size:16
Alignment explanation
Indices: 17591713--17591745 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
17591703 CTTAATTGAA
*
17591713 AAGCATAGTCT-ACAC
1 AAGCATACTCTAACAC
17591728 AAGCATACTCTAACAC
1 AAGCATACTCTAACAC
17591744 AA
1 AA
17591746 ACTCAATGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.45, C:0.27, G:0.09, T:0.18
Consensus pattern (16 bp):
AAGCATACTCTAACAC
Found at i:17593298 original size:2 final size:2
Alignment explanation
Indices: 17593291--17593334 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
17593281 TTTAAATTAC
17593291 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
17593333 AT
1 AT
17593335 CGGGTCGGGC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17593543 original size:19 final size:19
Alignment explanation
Indices: 17593515--17593553 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
17593505 AAACTTTACA
*
17593515 AATAATTTATATT-AATTTT
1 AATAAATTAT-TTAAATTTT
17593534 AATAAATTATTTAAATTTT
1 AATAAATTATTTAAATTTT
17593553 A
1 A
17593554 TATTTCATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 2 0.11
19 16 0.89
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
AATAAATTATTTAAATTTT
Found at i:17594262 original size:3 final size:3
Alignment explanation
Indices: 17594254--17594280 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
17594244 AACTAGGTCT
17594254 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
17594281 AATAACCATG
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:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:17595697 original size:3 final size:3
Alignment explanation
Indices: 17595689--17595735 Score: 85
Period size: 3 Copynumber: 15.7 Consensus size: 3
17595679 TCACAAATAT
*
17595689 TTA TTA TTA GTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
17595736 TCACAACATA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:17598009 original size:3 final size:3
Alignment explanation
Indices: 17597981--17598032 Score: 50
Period size: 3 Copynumber: 15.7 Consensus size: 3
17597971 CCCATTTCAC
*
17597981 CTT CTT TTT CTT CTT GCTTT CATT CTT CTGGT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT -C-TT C-TT CTT CT--T CTT CTT CTT CTT CTT
17598028 CTT CT
1 CTT CT
17598033 GTCATTCAAG
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
3 32 0.76
4 5 0.12
5 5 0.12
ACGTcount: A:0.02, C:0.29, G:0.06, T:0.63
Consensus pattern (3 bp):
CTT
Found at i:17598026 original size:20 final size:23
Alignment explanation
Indices: 17597989--17598029 Score: 61
Period size: 20 Copynumber: 1.9 Consensus size: 23
17597979 ACCTTCTTTT
17597989 TCTTCTTGCTTTCATTCTTCTGG
1 TCTTCTTGCTTTCATTCTTCTGG
17598012 TCTTCTT-C-TTC-TTCTTCT
1 TCTTCTTGCTTTCATTCTTCT
17598030 TCTGTCATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.39
21 3 0.17
22 1 0.06
23 7 0.39
ACGTcount: A:0.02, C:0.29, G:0.07, T:0.61
Consensus pattern (23 bp):
TCTTCTTGCTTTCATTCTTCTGG
Found at i:17603875 original size:5 final size:5
Alignment explanation
Indices: 17603867--17603892 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
17603857 TTAGATTAGG
17603867 TTTCT TTTCT TTTCT TTTCT TTTCT T
1 TTTCT TTTCT TTTCT TTTCT TTTCT T
17603893 CTTAATTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTCT
Found at i:17604524 original size:14 final size:16
Alignment explanation
Indices: 17604504--17604539 Score: 58
Period size: 14 Copynumber: 2.4 Consensus size: 16
17604494 ATAGAAAGAA
17604504 AGTTTAGTTT-AATTT
1 AGTTTAGTTTAAATTT
17604519 -GTTTAGTTTAAATTT
1 AGTTTAGTTTAAATTT
17604534 AGTTTA
1 AGTTTA
17604540 TAAACAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
14 9 0.47
15 5 0.26
16 5 0.26
ACGTcount: A:0.28, C:0.00, G:0.14, T:0.58
Consensus pattern (16 bp):
AGTTTAGTTTAAATTT
Found at i:17614382 original size:11 final size:11
Alignment explanation
Indices: 17614366--17614392 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
17614356 TTAATATTTA
17614366 AAAATAAAAAT
1 AAAATAAAAAT
17614377 AAAATAAAAAT
1 AAAATAAAAAT
17614388 AAAAT
1 AAAAT
17614393 CAACATTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (11 bp):
AAAATAAAAAT
Found at i:17622669 original size:29 final size:30
Alignment explanation
Indices: 17622602--17622674 Score: 89
Period size: 29 Copynumber: 2.5 Consensus size: 30
17622592 TGAATCTCAA
*
17622602 AATTATAT--ATGAATTTTGATCTGATGTGC
1 AATTATATACATGAATTTTAATCTGA-GTGC
*
17622631 AATTATATACATGAATTTTAATTTG-GTGC
1 AATTATATACATGAATTTTAATCTGAGTGC
*
17622660 AATTATATACGTGAA
1 AATTATATACATGAA
17622675 ACTCTAATTG
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
29 26 0.67
31 13 0.33
ACGTcount: A:0.36, C:0.07, G:0.15, T:0.42
Consensus pattern (30 bp):
AATTATATACATGAATTTTAATCTGAGTGC
Found at i:17622928 original size:29 final size:30
Alignment explanation
Indices: 17622896--17622966 Score: 99
Period size: 29 Copynumber: 2.4 Consensus size: 30
17622886 AAATTAAGAT
*
17622896 TTCATGTATAAAATTACACA-AAATCAAAA
1 TTCATGTATAAAATTACACATAAACCAAAA
* *
17622925 TTCATGTATACAATTACACATTAAACCATAA
1 TTCATGTATAAAATTACACA-TAAACCAAAA
17622956 TTCATGTATAA
1 TTCATGTATAA
17622967 TTTTAGGATT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
29 19 0.53
31 17 0.47
ACGTcount: A:0.48, C:0.15, G:0.04, T:0.32
Consensus pattern (30 bp):
TTCATGTATAAAATTACACATAAACCAAAA
Found at i:17627084 original size:25 final size:23
Alignment explanation
Indices: 17627055--17627100 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
17627045 ATTGGATCCA
17627055 AATTAAATTCTAAAAAGATAATTAG
1 AATTAAA-TCTAAAAA-ATAATTAG
*
17627080 AATTAAATCTAAATAATAATT
1 AATTAAATCTAAAAAATAATT
17627101 TCCTAATTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 7 0.35
25 7 0.35
ACGTcount: A:0.57, C:0.04, G:0.04, T:0.35
Consensus pattern (23 bp):
AATTAAATCTAAAAAATAATTAG
Found at i:17644075 original size:18 final size:18
Alignment explanation
Indices: 17644039--17644079 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
17644029 AAAAATAAAG
*
17644039 AAAAAAAGTATTTTCTTA
1 AAAAAAAGTATTGTCTTA
17644057 AAAAAGAAGTATTGT-TTA
1 AAAAA-AAGTATTGTCTTA
17644075 AAAAA
1 AAAAA
17644080 TAGAAAAATC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 13 0.62
19 8 0.38
ACGTcount: A:0.56, C:0.02, G:0.10, T:0.32
Consensus pattern (18 bp):
AAAAAAAGTATTGTCTTA
Found at i:17647957 original size:58 final size:58
Alignment explanation
Indices: 17647887--17648006 Score: 188
Period size: 58 Copynumber: 2.1 Consensus size: 58
17647877 AAAAGGAATT
* * *
17647887 GTTTATGAGTGTTATTT-AGGAATAAAATTATATTTGAGTTTAAAAATATTTGGGTTTA
1 GTTTATAAGTGTT-TTTGAAGAATAAAATTATATTTGAGTTTAAAAATATTTGAGTTTA
*
17647945 GTTTATAAGTGTTTTTGAAGAATGAAATTATATTTGAGTTTAAAAATATTTGAGTTTA
1 GTTTATAAGTGTTTTTGAAGAATAAAATTATATTTGAGTTTAAAAATATTTGAGTTTA
17648003 GTTT
1 GTTT
17648007 GTTGATGGGT
Statistics
Matches: 57, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
57 3 0.05
58 54 0.95
ACGTcount: A:0.34, C:0.00, G:0.18, T:0.47
Consensus pattern (58 bp):
GTTTATAAGTGTTTTTGAAGAATAAAATTATATTTGAGTTTAAAAATATTTGAGTTTA
Found at i:17648257 original size:23 final size:23
Alignment explanation
Indices: 17648214--17648258 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
17648204 AAAAAAATTC
**
17648214 AACTCGATTCGTTTAACTCGAAT
1 AACTCGATTCGAATAACTCGAAT
*
17648237 AACTCGATTCGAATAATTCGAA
1 AACTCGATTCGAATAACTCGAA
17648259 ATTCGAAATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.36, C:0.20, G:0.13, T:0.31
Consensus pattern (23 bp):
AACTCGATTCGAATAACTCGAAT
Found at i:17649159 original size:17 final size:16
Alignment explanation
Indices: 17649134--17649167 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
17649124 TAATAGCAAG
*
17649134 AAAATGAAAAGAACAAA
1 AAAAAGAAAAGAA-AAA
17649151 AAAAAGAAAAGAAAAA
1 AAAAAGAAAAGAAAAA
17649167 A
1 A
17649168 CTATATCAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.82, C:0.03, G:0.12, T:0.03
Consensus pattern (16 bp):
AAAAAGAAAAGAAAAA
Found at i:17655019 original size:13 final size:13
Alignment explanation
Indices: 17655001--17655050 Score: 55
Period size: 13 Copynumber: 3.7 Consensus size: 13
17654991 TATTTTTTTC
17655001 AATTAAAATTATA
1 AATTAAAATTATA
*
17655014 AATTAAAATAATA
1 AATTAAAATTATA
* *
17655027 ATTTTAAAATTTATC
1 A-ATTAAAA-TTATA
17655042 AATTAAAAT
1 AATTAAAAT
17655051 ATTATTAAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
13 14 0.47
14 12 0.40
15 4 0.13
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (13 bp):
AATTAAAATTATA
Found at i:17655229 original size:2 final size:2
Alignment explanation
Indices: 17655222--17655286 Score: 130
Period size: 2 Copynumber: 32.5 Consensus size: 2
17655212 TAAAATATTT
17655222 TA TA TA TA TA TA TA TA TA 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 TA TA TA TA TA TA
17655264 TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
17655287 TGAAAAGTTA
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:17660005 original size:28 final size:28
Alignment explanation
Indices: 17659952--17660011 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 28
17659942 AAAATTAAAT
* *
17659952 TTTAGGTTCTTAAAAGTTGGAAAAAAAA
1 TTTAGATTCTTAAAAATTGGAAAAAAAA
*
17659980 TTTAGATTCCTTAAAAATTGGTAAAAAAA
1 TTTAGATT-CTTAAAAATTGGAAAAAAAA
17660009 TTT
1 TTT
17660012 TGGACCCTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
28 7 0.25
29 21 0.75
ACGTcount: A:0.45, C:0.05, G:0.13, T:0.37
Consensus pattern (28 bp):
TTTAGATTCTTAAAAATTGGAAAAAAAA
Found at i:17660020 original size:29 final size:28
Alignment explanation
Indices: 17659960--17660050 Score: 92
Period size: 30 Copynumber: 3.1 Consensus size: 28
17659950 ATTTTAGGTT
* * * *
17659960 CTTAAAAGTTGGAAAAAAAATTTAGATTC
1 CTTAAAAATTGGAAAAAAATTTTGGA-CC
17659989 CTTAAAAATTGGTAAAAAAATTTTGGACC
1 CTTAAAAATTGG-AAAAAAATTTTGGACC
* *
17660018 CTTAAAAACTGAAAAACAATATTTTGGACC
1 CTTAAAAATTGGAAAA-AA-ATTTTGGACC
17660048 CTT
1 CTT
17660051 TTCAACCTTG
Statistics
Matches: 53, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
28 4 0.08
29 24 0.45
30 25 0.47
ACGTcount: A:0.45, C:0.12, G:0.12, T:0.31
Consensus pattern (28 bp):
CTTAAAAATTGGAAAAAAATTTTGGACC
Found at i:17668122 original size:51 final size:51
Alignment explanation
Indices: 17667980--17668222 Score: 348
Period size: 51 Copynumber: 4.8 Consensus size: 51
17667970 GTTATAAACG
* * *
17667980 AAAGAGTCCGATGACTAAGTGTCATTGTGAGTAAATGAATCATTTACGGATT
1 AAAG-GTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTCTACGGATT
* *
17668032 AAAGGTCCGAT-ACTAAGGGTCATCGTGAGTAAACGAATCCTCTACGGATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTCTACGGATT
17668082 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAACT-AATCCTCTACGGATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAA-TGAATCCTCTACGGATT
* * *
17668133 AAAGGTCCAATGACTAAGTGTCATCGTGAGTAAATGAATCCAT-GACGAATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCC-TCTACGGATT
* *
17668184 AAAGGTCCGATGACTTAGTGTCATCGTGAGTATATGAAT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAAT
17668223 TTCTATACGG
Statistics
Matches: 174, Mismatches: 13, Indels: 9
0.89 0.07 0.05
Matches are distributed among these distances:
50 46 0.26
51 123 0.71
52 5 0.03
ACGTcount: A:0.33, C:0.16, G:0.23, T:0.28
Consensus pattern (51 bp):
AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTCTACGGATT
Found at i:17669849 original size:2 final size:2
Alignment explanation
Indices: 17669842--17669867 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
17669832 AGGAAGTCAA
17669842 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
17669868 TACGAGGCTT
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:17673452 original size:2 final size:2
Alignment explanation
Indices: 17673445--17673475 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
17673435 ATTTTGATAA
17673445 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 A
17673476 ATAGGTTATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:17673521 original size:26 final size:26
Alignment explanation
Indices: 17673481--17673535 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
17673471 ATATAATAGG
* *
17673481 TTATTAAAATTATATTTACATTAAAA
1 TTATTAAAATCATATTTACAGTAAAA
* *
17673507 TTATTAAGATCATATTTATAGTAAAA
1 TTATTAAAATCATATTTACAGTAAAA
17673533 TTA
1 TTA
17673536 AATTATTTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (26 bp):
TTATTAAAATCATATTTACAGTAAAA
Found at i:17679185 original size:59 final size:59
Alignment explanation
Indices: 17679067--17679374 Score: 345
Period size: 59 Copynumber: 5.2 Consensus size: 59
17679057 TCGCGGGAGC
* * * * *
17679067 AAAATGGTAATTTTCGGTGAAAT-TAGGGTC-AAAAGGGAATTTTGGAAAATTCGAGGGT
1 AAAATGATAATTTTTGGTGAAATCGA-GGTCAAAAATGGAATTTTGGAAAGTTCGAGGGT
* * * *
17679125 AAAATAATAATTTTTGGTGAAATCGAGCTCGAAAATGGAATTTTGGAAAGTTCAAGGGT
1 AAAATGATAATTTTTGGTGAAATCGAGGTCAAAAATGGAATTTTGGAAAGTTCGAGGGT
* * * * *
17679184 AAAATGATAATTTTTGATGAAATCGGGGTTAAAAATGGAATTTTAGAAAGTTCGGGGGGT
1 AAAATGATAATTTTTGGTGAAATCGAGGTCAAAAATGGAATTTTGGAAAGTTC-GAGGGT
* * *
17679244 AAAATGGTAATTTTTGGTGAAATCGAGGGCAAAAATGGAATTTTGGAAAGTTCGGGGGT
1 AAAATGATAATTTTTGGTGAAATCGAGGTCAAAAATGGAATTTTGGAAAGTTCGAGGGT
* * * * * *
17679303 AAAATGGTAA-TTTTGGTGAAATTGGGGTTAAAAATGGAATTTTAGAAAGTT-TAGTGGT
1 AAAATGATAATTTTTGGTGAAATCGAGGTCAAAAATGGAATTTTGGAAAGTTCGAG-GGT
*
17679361 AAAATGGTAATTTT
1 AAAATGATAATTTT
17679375 CGGACAGTCC
Statistics
Matches: 215, Mismatches: 30, Indels: 9
0.85 0.12 0.04
Matches are distributed among these distances:
57 1 0.00
58 72 0.33
59 91 0.42
60 51 0.24
ACGTcount: A:0.37, C:0.04, G:0.28, T:0.32
Consensus pattern (59 bp):
AAAATGATAATTTTTGGTGAAATCGAGGTCAAAAATGGAATTTTGGAAAGTTCGAGGGT
Found at i:17679267 original size:119 final size:117
Alignment explanation
Indices: 17679097--17679374 Score: 385
Period size: 119 Copynumber: 2.4 Consensus size: 117
17679087 AATTAGGGTC
* * * * ** * *
17679097 AAAAGGGAATTTTGGAAAATTCGAGGGTAAAATAATAATTTTTGGTGAAATCGAGCTCGAAAATG
1 AAAATGGAATTTTAGAAAGTTCGGGGGTAAAATGGTAATTTTTGGTGAAATCGAGCGCAAAAATG
17679162 GAATTTTGGAAAGTTCAAGGGTAAAATGATAATTTTTGATGAAATCGGGGTTA
66 GAATTTTGGAAAGTTCAAGGGTAAAATGATAA-TTTTGATGAAATCGGGGTTA
*
17679215 AAAATGGAATTTTAGAAAGTTCGGGGGGTAAAATGGTAATTTTTGGTGAAATCGAGGGCAAAAAT
1 AAAATGGAATTTTAGAAAGTTC-GGGGGTAAAATGGTAATTTTTGGTGAAATCGAGCGCAAAAAT
** * * *
17679280 GGAATTTTGGAAAGTTCGGGGGTAAAATGGTAATTTTGGTGAAATTGGGGTTA
65 GGAATTTTGGAAAGTTCAAGGGTAAAATGATAATTTTGATGAAATCGGGGTTA
** *
17679333 AAAATGGAATTTTAGAAAGTTTAGTGGTAAAATGGTAATTTT
1 AAAATGGAATTTTAGAAAGTTCGGGGGTAAAATGGTAATTTT
17679375 CGGACAGTCC
Statistics
Matches: 142, Mismatches: 17, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
117 18 0.13
118 58 0.41
119 66 0.46
ACGTcount: A:0.37, C:0.04, G:0.28, T:0.32
Consensus pattern (117 bp):
AAAATGGAATTTTAGAAAGTTCGGGGGTAAAATGGTAATTTTTGGTGAAATCGAGCGCAAAAATG
GAATTTTGGAAAGTTCAAGGGTAAAATGATAATTTTGATGAAATCGGGGTTA
Found at i:17679329 original size:29 final size:29
Alignment explanation
Indices: 17679067--17679345 Score: 118
Period size: 29 Copynumber: 9.5 Consensus size: 29
17679057 TCGCGGGAGC
*
17679067 AAAATGGTAATTTTCGGTGAAATT-AGGGT
1 AAAATGGTAATTTT-GGTGAAATTGGGGGT
* * *
17679096 CAAAA-GGGAATTTTGG-AAAATTCGAGGGT
1 -AAAATGGTAATTTTGGTGAAATT-GGGGGT
** * * *
17679125 AAAATAATAATTTTTGGTGAAA-TCGAGCT
1 AAAATGGTAA-TTTTGGTGAAATTGGGGGT
**
17679154 CGAAAATGG-AATTTT-G-GAAAGTTCAAGGGT
1 --AAAATGGTAATTTTGGTGAAA-TT-GGGGGT
* * * *
17679184 AAAATGATAATTTTTGATGAAATCGGGGTT
1 AAAATGGTAA-TTTTGGTGAAATTGGGGGT
*
17679214 AAAAATGG-AATTTT--AGAAAGTTCGGGGGGT
1 -AAAATGGTAATTTTGGTGAAA-TT--GGGGGT
* **
17679244 AAAATGGTAATTTTTGGTGAAATCGAGGGCA
1 AAAATGGTAA-TTTTGGTGAAATTG-GGGGT
17679275 AAAATGG-AATTTT-G-GAAAGTTCGGGGGT
1 AAAATGGTAATTTTGGTGAAA-TT-GGGGGT
*
17679303 AAAATGGTAATTTTGGTGAAATTGGGGTT
1 AAAATGGTAATTTTGGTGAAATTGGGGGT
17679332 AAAAATGG-AATTTT
1 -AAAATGGTAATTTT
17679346 AGAAAGTTTA
Statistics
Matches: 186, Mismatches: 34, Indels: 59
0.67 0.12 0.21
Matches are distributed among these distances:
27 17 0.09
28 26 0.14
29 57 0.31
30 44 0.24
31 33 0.18
32 5 0.03
33 4 0.02
ACGTcount: A:0.37, C:0.04, G:0.28, T:0.31
Consensus pattern (29 bp):
AAAATGGTAATTTTGGTGAAATTGGGGGT
Done.