Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D10
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: 67973905
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.32
Warning! 1760000 characters in sequence are not A, C, G, or T
File 187 of 228
Found at i:55743849 original size:13 final size:13
Alignment explanation
Indices: 55743831--55743855 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
55743821 TTTTAGTTTT
55743831 ATTGGGTTGGGTA
1 ATTGGGTTGGGTA
55743844 ATTGGGTTGGGT
1 ATTGGGTTGGGT
55743856 TGGATAATTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.12, C:0.00, G:0.48, T:0.40
Consensus pattern (13 bp):
ATTGGGTTGGGTA
Found at i:55745189 original size:20 final size:22
Alignment explanation
Indices: 55745137--55745191 Score: 57
Period size: 20 Copynumber: 2.7 Consensus size: 22
55745127 AACTATAACA
*
55745137 AAATAAAAATATATTAAATTATT
1 AAATATAAATATATTAAA-TATT
55745160 AAATAT---TATATTAAA-A-T
1 AAATATAAATATATTAAATATT
55745177 AAATATAAATATATT
1 AAATATAAATATATT
55745192 TTTAAAAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 9
0.74 0.03 0.24
Matches are distributed among these distances:
17 7 0.25
18 1 0.04
20 15 0.54
23 5 0.18
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
AAATATAAATATATTAAATATT
Found at i:55745641 original size:26 final size:25
Alignment explanation
Indices: 55745575--55745641 Score: 61
Period size: 24 Copynumber: 2.8 Consensus size: 25
55745565 CACGACCATA
* *
55745575 TTAT-TTTTTTATTTTTTTAAATAT
1 TTATATTTTATATATTTTTAAATAT
*
55745599 TTATATTATAT-TA-TTTT-AATAT
1 TTATATTTTATATATTTTTAAATAT
55745621 TTAATAATTTTATATATTTTT
1 TT-AT-ATTTTATATATTTTT
55745642 TATTTATTGA
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
22 7 0.21
23 6 0.18
24 11 0.32
25 6 0.18
26 4 0.12
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (25 bp):
TTATATTTTATATATTTTTAAATAT
Found at i:55745662 original size:26 final size:27
Alignment explanation
Indices: 55745604--55745664 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
55745594 AATATTTATA
*
55745604 TTATATTATTTTAATATTTAATAATTT
1 TTATATTATTTTAATATTGAATAATTT
*
55745631 TATATATT-TTTTATTTATTGAA-AATTT
1 T-TATATTATTTTA-ATATTGAATAATTT
55745658 TTATATT
1 TTATATT
55745665 CATCTTAACA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
26 6 0.20
27 12 0.40
28 12 0.40
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (27 bp):
TTATATTATTTTAATATTGAATAATTT
Found at i:55746624 original size:12 final size:12
Alignment explanation
Indices: 55746607--55746632 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
55746597 CAAAACAGGC
55746607 TTTTAGCGGCGT
1 TTTTAGCGGCGT
55746619 TTTTAGCGGCGT
1 TTTTAGCGGCGT
55746631 TT
1 TT
55746633 GGATAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.15, G:0.31, T:0.46
Consensus pattern (12 bp):
TTTTAGCGGCGT
Found at i:55746848 original size:73 final size:72
Alignment explanation
Indices: 55746701--55746869 Score: 185
Period size: 73 Copynumber: 2.3 Consensus size: 72
55746691 AAAAAAAGTA
* * * * *
55746701 TTAGCGGCATTTTTGAGCAAAGCGCCGCAAATAACCTAAGACCAACAACGCCGTTTTCTGAGCTT
1 TTAGCGGCGTTTTTG-GAAAAGCGCCGCAAAAAACCCAAGACCAACAACGCCGTTTTCTGAACTT
** *
55746766 TTGGGGAT
65 TCAGAGAT
* * * *
55746774 TTAGCGGCGCTTTTGGAAAAGCGCCGCAAAAAAACCCAAGCCCAACGATGCCGTTTTCTGAACTT
1 TTAGCGGCGTTTTTGGAAAAGCGCCGC-AAAAAACCCAAGACCAACAACGCCGTTTTCTGAACTT
55746839 TCAGAGAT
65 TCAGAGAT
* * *
55746847 TTAGTGGCGTTTTTCGTAAAGCG
1 TTAGCGGCGTTTTTGGAAAAGCG
55746870 TCGCTAAAGG
Statistics
Matches: 79, Mismatches: 16, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
72 11 0.14
73 68 0.86
ACGTcount: A:0.27, C:0.23, G:0.24, T:0.26
Consensus pattern (72 bp):
TTAGCGGCGTTTTTGGAAAAGCGCCGCAAAAAACCCAAGACCAACAACGCCGTTTTCTGAACTTT
CAGAGAT
Found at i:55747299 original size:279 final size:279
Alignment explanation
Indices: 55746873--55747639 Score: 1183
Period size: 279 Copynumber: 2.8 Consensus size: 279
55746863 TAAAGCGTCG
55746873 CTAAAGGTAAGCAATAGCGGCGTTTCCTATAAAAACGCCGCAAAAAATAAATCAATTTATAAAAA
1 CTAAAGGTAAGCAATAGCGGCGTTTCCTATAAAAACGCCGCAAAAAATAAATCAATTTATAAAAA
*
55746938 ATAAAAAAAATTTAGAATAGCAAAGCGGCGTCGTTTTGTTCAAAATGAAAAAATTTTGCGGCGCT
66 AT-AAAAAAATTTAGAATAGCAAAACGGCGTCGTTTTGTTCAAAATGAAAAAATTTTGCGGCGCT
*
55747003 TTATATGAAGCGCCGCTAAAGGTAAGCAATAGCGGCGTTTTCTATAAAAACGCCGCAAAAAATAA
130 TTATAAGAAGCGCCGCTAAAGGTAAGCAATAGCGGCGTTTTCTATAAAAACGCCGCAAAAAATAA
55747068 ATCAATTTAT-AAAAAAATAAAAAAAAT-TTAGAATAGCAAAACGGCGTCGTTTTGTTCAAAATG
195 ATCAATTTATAAAAAAAAT-AAAAAAATGTTAGAATAGCAAAACGGCGTCGTTTTGTTCAAAATG
55747131 AAAAAATTTTGCGGCGC-T-T-
259 -AAAAATTTTGCGGCGCTTATA
*
55747150 CTTAAGGTAAGCAATAGCGGCGTTTCCTATAAAAACGCCGCAAAAAATAAATCAATTTATAAAAA
1 CTAAAGGTAAGCAATAGCGGCGTTTCCTATAAAAACGCCGCAAAAAATAAATCAATTTAT--AAA
55747215 AAATAAAAAAATTTTAGAATAGCAAAACGGCGTCGTTTTGTTCAAAATGAAAAAATTTTGCGGCG
64 AAATAAAAAAA-TTTAGAATAGCAAAACGGCGTCGTTTTGTTCAAAATGAAAAAATTTTGCGGCG
55747280 CTTTATAAGAAGCGCCGCTAAAGGTAAGCAATAGCGGCGTTTTCTATAAAAACGCCGCAAAAAAT
128 CTTTATAAGAAGCGCCGCTAAAGGTAAGCAATAGCGGCGTTTTCTATAAAAACGCCGCAAAAAAT
* * *
55747345 AAATCAACTTATAAAAAAAATAAAAAATTGTTAGAATAGCAAAACGGCGTCGTTTTTTTCAAAAT
193 AAATCAATTTATAAAAAAAATAAAAAAATGTTAGAATAGCAAAACGGCGTCGTTTTGTTCAAAAT
55747410 GAAAAATTTTGCGGCGCTTTATAAGAA
258 GAAAAATTTTGCGGCGC-TTAT----A
*
55747437 GCGCCGCTAAAGGTAAGCAATAGCGGCGTTTCCTATATAAACGCCGC-AAAAATAAATCAATTTA
1 ------CTAAAGGTAAGCAATAGCGGCGTTTCCTATAAAAACGCCGCAAAAAATAAATCAATTTA
55747501 T-----A-AAAAAAATTTAGAATAGCAAAACGGCGTCGTTTTGTTCAAAATG-AAAAATTTTGCG
60 TAAAAAATAAAAAAATTTAGAATAGCAAAACGGCGTCGTTTTGTTCAAAATGAAAAAATTTTGCG
*
55747559 GCGCTTTATAAGAAGCGCCGCTAAAGGTAAGCAATAGCGGCG---T-TA-GAAAACGCCGCAAAA
125 GCGCTTTATAAGAAGCGCCGCTAAAGGTAAGCAATAGCGGCGTTTTCTATAAAAACGCCGCAAAA
55747619 AATAAATCAATTTATAAAAAA
190 AATAAATCAATTTATAAAAAA
55747640 TTTCCCAAAT
Statistics
Matches: 461, Mismatches: 10, Indels: 38
0.91 0.02 0.07
Matches are distributed among these distances:
277 93 0.20
278 9 0.02
279 158 0.34
280 43 0.09
281 1 0.00
282 55 0.12
283 37 0.08
284 7 0.02
285 1 0.00
292 18 0.04
293 39 0.08
ACGTcount: A:0.43, C:0.15, G:0.17, T:0.25
Consensus pattern (279 bp):
CTAAAGGTAAGCAATAGCGGCGTTTCCTATAAAAACGCCGCAAAAAATAAATCAATTTATAAAAA
ATAAAAAAATTTAGAATAGCAAAACGGCGTCGTTTTGTTCAAAATGAAAAAATTTTGCGGCGCTT
TATAAGAAGCGCCGCTAAAGGTAAGCAATAGCGGCGTTTTCTATAAAAACGCCGCAAAAAATAAA
TCAATTTATAAAAAAAATAAAAAAATGTTAGAATAGCAAAACGGCGTCGTTTTGTTCAAAATGAA
AAATTTTGCGGCGCTTATA
Found at i:55747456 original size:146 final size:145
Alignment explanation
Indices: 55747153--55747639 Score: 804
Period size: 147 Copynumber: 3.4 Consensus size: 145
55747143 GGCGCTTCTT
55747153 AAGGTAAGCAATAGCGGCGTTTCCTATAAAAACGCCGCAAAAAATAAATCAATTTATAAAAAAAA
1 AAGGTAAGCAATAGCGGCGTTTCCTATAAAAACGCCGCAAAAAATAAATCAATTTATAAAAAAAA
55747218 TAAAAAAATTTTAGAATAGCAAAACGGCGTCGTTTTGTTCAAAATGAAAAAATTTTGCGGCGCTT
66 T-AAAAAATTTTAGAATAGCAAAACGGCGTCGTTTTGTTCAAAATG-AAAAATTTTGCGGCGCTT
55747283 TATAAGAAGCGCCGCTA
129 TATAAGAAGCGCCGCTA
* *
55747300 AAGGTAAGCAATAGCGGCGTTTTCTATAAAAACGCCGCAAAAAATAAATCAACTTATAAAAAAAA
1 AAGGTAAGCAATAGCGGCGTTTCCTATAAAAACGCCGCAAAAAATAAATCAATTTATAAAAAAAA
*
55747365 TAAAAAATTGTTAGAATAGCAAAACGGCGTCGTTTTTTTCAAAATGAAAAATTTTGCGGCGCTTT
66 TAAAAAATT-TTAGAATAGCAAAACGGCGTCGTTTTGTTCAAAATGAAAAATTTTGCGGCGCTTT
55747430 ATAAGAAGCGCCGCTA
130 ATAAGAAGCGCCGCTA
*
55747446 AAGGTAAGCAATAGCGGCGTTTCCTATATAAACGCCGC-AAAAATAAATCAATTTAT------AA
1 AAGGTAAGCAATAGCGGCGTTTCCTATAAAAACGCCGCAAAAAATAAATCAATTTATAAAAAAAA
55747504 -AAAAAA-TTTAGAATAGCAAAACGGCGTCGTTTTGTTCAAAATGAAAAATTTTGCGGCGCTTTA
66 TAAAAAATTTTAGAATAGCAAAACGGCGTCGTTTTGTTCAAAATGAAAAATTTTGCGGCGCTTTA
55747567 TAAGAAGCGCCGCTA
131 TAAGAAGCGCCGCTA
*
55747582 AAGGTAAGCAATAGCGGCG--T--TA-GAAAACGCCGCAAAAAATAAATCAATTTATAAAAAA
1 AAGGTAAGCAATAGCGGCGTTTCCTATAAAAACGCCGCAAAAAATAAATCAATTTATAAAAAA
55747640 TTTCCCAAAT
Statistics
Matches: 323, Mismatches: 9, Indels: 25
0.90 0.03 0.07
Matches are distributed among these distances:
131 9 0.03
132 20 0.06
134 1 0.00
136 89 0.28
137 1 0.00
138 6 0.02
139 2 0.01
145 17 0.05
146 79 0.24
147 99 0.31
ACGTcount: A:0.43, C:0.15, G:0.17, T:0.24
Consensus pattern (145 bp):
AAGGTAAGCAATAGCGGCGTTTCCTATAAAAACGCCGCAAAAAATAAATCAATTTATAAAAAAAA
TAAAAAATTTTAGAATAGCAAAACGGCGTCGTTTTGTTCAAAATGAAAAATTTTGCGGCGCTTTA
TAAGAAGCGCCGCTA
Found at i:55747517 original size:136 final size:138
Alignment explanation
Indices: 55747153--55747639 Score: 727
Period size: 136 Copynumber: 3.5 Consensus size: 138
55747143 GGCGCTTCTT
55747153 AAGGTAAGCAATAGCGGCGTTTCCTATAAAAACGCCGCAAAAAATAAATCAATTTATAAAAAAAA
1 AAGGTAAGCAATAGCGGCGTTTCCTATAAAAACGCCGCAAAAAATAAATCAATTTAT-------A
55747218 TAAAAAAATTTTAGAATAGCAAAACGGCGTCGTTTTGTTCAAAATGAAAAAATTTTGCGGCGCTT
59 -AAAAAAATTTTAGAATAGCAAAACGGCGTCGTTTTGTTCAAAATG-AAAAATTTTGCGGCGCTT
55747283 TATAAGAAGCGCCGCTA
122 TATAAGAAGCGCCGCTA
* *
55747300 AAGGTAAGCAATAGCGGCGTTTTCTATAAAAACGCCGCAAAAAATAAATCAACTTATAAAAAAAA
1 AAGGTAAGCAATAGCGGCGTTTCCTATAAAAACGCCGCAAAAAATAAATCAA-TT-T----ATAA
*
55747365 TAAAAAATTGTTAGAATAGCAAAACGGCGTCGTTTTTTTCAAAATGAAAAATTTTGCGGCGCTTT
60 -AAAAAATT-TTAGAATAGCAAAACGGCGTCGTTTTGTTCAAAATGAAAAATTTTGCGGCGCTTT
55747430 ATAAGAAGCGCCGCTA
123 ATAAGAAGCGCCGCTA
*
55747446 AAGGTAAGCAATAGCGGCGTTTCCTATATAAACGCCGC-AAAAATAAATCAATTTATAAAAAAAA
1 AAGGTAAGCAATAGCGGCGTTTCCTATAAAAACGCCGCAAAAAATAAATCAATTTATAAAAAAAA
55747510 -TTTAGAATAGCAAAACGGCGTCGTTTTGTTCAAAATGAAAAATTTTGCGGCGCTTTATAAGAAG
66 TTTTAGAATAGCAAAACGGCGTCGTTTTGTTCAAAATGAAAAATTTTGCGGCGCTTTATAAGAAG
55747574 CGCCGCTA
131 CGCCGCTA
*
55747582 AAGGTAAGCAATAGCGGCG--T--TA-GAAAACGCCGCAAAAAATAAATCAATTTATAAAAAA
1 AAGGTAAGCAATAGCGGCGTTTCCTATAAAAACGCCGCAAAAAATAAATCAATTTATAAAAAA
55747640 TTTCCCAAAT
Statistics
Matches: 322, Mismatches: 9, Indels: 33
0.88 0.02 0.09
Matches are distributed among these distances:
131 9 0.03
132 26 0.08
134 1 0.00
136 89 0.28
137 1 0.00
138 6 0.02
139 3 0.01
143 1 0.00
144 2 0.01
145 14 0.04
146 80 0.25
147 86 0.27
148 2 0.01
149 1 0.00
153 1 0.00
ACGTcount: A:0.43, C:0.15, G:0.17, T:0.24
Consensus pattern (138 bp):
AAGGTAAGCAATAGCGGCGTTTCCTATAAAAACGCCGCAAAAAATAAATCAATTTATAAAAAAAA
TTTTAGAATAGCAAAACGGCGTCGTTTTGTTCAAAATGAAAAATTTTGCGGCGCTTTATAAGAAG
CGCCGCTA
Found at i:55748233 original size:14 final size:15
Alignment explanation
Indices: 55748205--55748237 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
55748195 AAGTTTTATA
55748205 GATTATGGAATTAGG
1 GATTATGGAATTAGG
55748220 GATTATGG-ATTAGG
1 GATTATGGAATTAGG
55748234 GATT
1 GATT
55748238 CTGATTTAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.30, C:0.00, G:0.33, T:0.36
Consensus pattern (15 bp):
GATTATGGAATTAGG
Found at i:55748289 original size:13 final size:13
Alignment explanation
Indices: 55748260--55748309 Score: 66
Period size: 13 Copynumber: 3.8 Consensus size: 13
55748250 TTAATGTGAT
*
55748260 TTAAGGTTTATGGG
1 TTAAGGGTTA-GGG
55748274 TTAAGGGTTAGGG
1 TTAAGGGTTAGGG
55748287 TTAAGGGTTA-GG
1 TTAAGGGTTAGGG
*
55748299 TTAGGGGTTAG
1 TTAAGGGTTAG
55748310 ATGTTAATAG
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
12 11 0.33
13 13 0.39
14 9 0.27
ACGTcount: A:0.22, C:0.00, G:0.42, T:0.36
Consensus pattern (13 bp):
TTAAGGGTTAGGG
Found at i:55748306 original size:12 final size:12
Alignment explanation
Indices: 55748272--55748309 Score: 58
Period size: 12 Copynumber: 3.1 Consensus size: 12
55748262 AAGGTTTATG
55748272 GGTTAAGGGTTA
1 GGTTAAGGGTTA
55748284 GGGTTAAGGGTTA
1 -GGTTAAGGGTTA
*
55748297 GGTTAGGGGTTA
1 GGTTAAGGGTTA
55748309 G
1 G
55748310 ATGTTAATAG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 12 0.50
13 12 0.50
ACGTcount: A:0.21, C:0.00, G:0.47, T:0.32
Consensus pattern (12 bp):
GGTTAAGGGTTA
Found at i:55748612 original size:7 final size:7
Alignment explanation
Indices: 55748602--55748655 Score: 65
Period size: 7 Copynumber: 7.7 Consensus size: 7
55748592 GATTTAAGGT
55748602 TTAGGGG
1 TTAGGGG
*
55748609 TTAGTGG
1 TTAGGGG
55748616 TTAGGGG
1 TTAGGGG
55748623 TTAGGGG
1 TTAGGGG
* *
55748630 TTAAGAG
1 TTAGGGG
55748637 TTAGGGAG
1 TTAGGG-G
55748645 TTA-GGG
1 TTAGGGG
55748651 TTAGG
1 TTAGG
55748656 ACTTAAGGAT
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
6 4 0.10
7 31 0.79
8 4 0.10
ACGTcount: A:0.20, C:0.00, G:0.48, T:0.31
Consensus pattern (7 bp):
TTAGGGG
Found at i:55749001 original size:19 final size:18
Alignment explanation
Indices: 55748972--55749025 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 18
55748962 GGACCAAATT
*
55748972 ATAAGAAATAAAATTAAA
1 ATAAAAAATAAAATTAAA
* *
55748990 ATACAAAAATAAAAATGAA
1 ATA-AAAAATAAAATTAAA
55749009 ATAAAAACACTAAAATT
1 ATAAAAA-A-TAAAATT
55749026 TTTAATTTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
18 7 0.24
19 16 0.55
20 6 0.21
ACGTcount: A:0.70, C:0.06, G:0.04, T:0.20
Consensus pattern (18 bp):
ATAAAAAATAAAATTAAA
Found at i:55749084 original size:47 final size:48
Alignment explanation
Indices: 55749010--55749108 Score: 173
Period size: 47 Copynumber: 2.1 Consensus size: 48
55749000 AAAAATGAAA
* *
55749010 TAAAAACACTAAAATTTTTAATTTTATCTAATTTTTATAAATATTACT
1 TAAAAACACTAAAATTTATAAATTTATCTAATTTTTATAAATATTACT
55749058 TAAAAA-ACTAAAATTTATAAATTTATCTAATTTTTATAAATATTACT
1 TAAAAACACTAAAATTTATAAATTTATCTAATTTTTATAAATATTACT
55749105 TAAA
1 TAAA
55749109 CAAAACTATG
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
47 43 0.88
48 6 0.12
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.45
Consensus pattern (48 bp):
TAAAAACACTAAAATTTATAAATTTATCTAATTTTTATAAATATTACT
Found at i:55749449 original size:16 final size:15
Alignment explanation
Indices: 55749428--55749467 Score: 55
Period size: 16 Copynumber: 2.7 Consensus size: 15
55749418 TGGTTGAAAT
55749428 ATTTATTCCCCTCCAA
1 ATTTATTCCCCTCC-A
*
55749444 ATTTATTCCCCTTCA
1 ATTTATTCCCCTCCA
55749459 ATTT-TTCCC
1 ATTTATTCCC
55749468 ATACCCGAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 5 0.22
15 5 0.22
16 13 0.57
ACGTcount: A:0.20, C:0.35, G:0.00, T:0.45
Consensus pattern (15 bp):
ATTTATTCCCCTCCA
Found at i:55753879 original size:43 final size:43
Alignment explanation
Indices: 55753831--55754039 Score: 303
Period size: 43 Copynumber: 4.9 Consensus size: 43
55753821 GCTTTTATCA
* *
55753831 AAAGCGTCGCTAAAGATCATGTTTTTTAGCGGCGTTTGTGGTT
1 AAAGCGCCGCTAAAGATCATGTTCTTTAGCGGCGTTTGTGGTT
* * *
55753874 AAAGCGTCGCTAAAGATCATGTTCTTTAGCGGCATTTGTGTTT
1 AAAGCGCCGCTAAAGATCATGTTCTTTAGCGGCGTTTGTGGTT
* * *
55753917 AAAGCGCCGCTAAAGATCATGTTCTTTAGCAGCGTTTGCGGGT
1 AAAGCGCCGCTAAAGATCATGTTCTTTAGCGGCGTTTGTGGTT
*
55753960 AAGGCGCCGCTAAAGATCATGTTCTTTAGCGGCGTTTGTAGG-T
1 AAAGCGCCGCTAAAGATCATGTTCTTTAGCGGCGTTTGT-GGTT
* *
55754003 AAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTT
1 AAAGCGCCGCTAAAGATCATGTTCTTTAGCGGCGTTT
55754040 TGCCTCATAA
Statistics
Matches: 150, Mismatches: 15, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
43 148 0.99
44 2 0.01
ACGTcount: A:0.23, C:0.18, G:0.27, T:0.32
Consensus pattern (43 bp):
AAAGCGCCGCTAAAGATCATGTTCTTTAGCGGCGTTTGTGGTT
Found at i:55754519 original size:24 final size:24
Alignment explanation
Indices: 55754470--55754520 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
55754460 AATCCTAAGA
* ** *
55754470 AAATTTTATTAATTATTTTTATTT
1 AAATTTAATTAATTATCATTACTT
55754494 AAATTTAATTAATTATCATTACTT
1 AAATTTAATTAATTATCATTACTT
55754518 AAA
1 AAA
55754521 AAGTTTTAAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.55
Consensus pattern (24 bp):
AAATTTAATTAATTATCATTACTT
Found at i:55758968 original size:15 final size:15
Alignment explanation
Indices: 55758948--55758979 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
55758938 CTTGACAGCC
55758948 ATCTCCATTCCGGAT
1 ATCTCCATTCCGGAT
55758963 ATCTCCATTCCGGAT
1 ATCTCCATTCCGGAT
55758978 AT
1 AT
55758980 AGCTATCTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.22, C:0.31, G:0.12, T:0.34
Consensus pattern (15 bp):
ATCTCCATTCCGGAT
Found at i:55759152 original size:14 final size:13
Alignment explanation
Indices: 55759122--55759178 Score: 53
Period size: 13 Copynumber: 4.4 Consensus size: 13
55759112 ATATGTTTCG
55759122 TAATTTTATAATA
1 TAATTTTATAATA
* *
55759135 TAATTTTTTCAATT
1 TAATTTTAT-AATA
*
55759149 TAA-TTCATAATA
1 TAATTTTATAATA
* *
55759161 TAATTGTATAATT
1 TAATTTTATAATA
55759174 TAATT
1 TAATT
55759179 GGTCATTAAA
Statistics
Matches: 34, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
12 6 0.18
13 22 0.65
14 6 0.18
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.54
Consensus pattern (13 bp):
TAATTTTATAATA
Found at i:55759159 original size:26 final size:25
Alignment explanation
Indices: 55759129--55759178 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 25
55759119 TCGTAATTTT
* *
55759129 ATAATATAATTTTTTCAATTTAATTC
1 ATAATATAATTGTAT-AATTTAATTC
55759155 ATAATATAATTGTATAATTTAATT
1 ATAATATAATTGTATAATTTAATT
55759179 GGTCATTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 9 0.41
26 13 0.59
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.52
Consensus pattern (25 bp):
ATAATATAATTGTATAATTTAATTC
Found at i:55759625 original size:29 final size:33
Alignment explanation
Indices: 55759578--55759637 Score: 92
Period size: 30 Copynumber: 1.9 Consensus size: 33
55759568 ATCTTAATCA
55759578 ATAAATAATATTTCATTTA-ATTTAAAATAAAT
1 ATAAATAATATTTCATTTATATTTAAAATAAAT
55759610 ATAAAT-AT-TTTC-TTTATATTTAAAATAA
1 ATAAATAATATTTCATTTATATTTAAAATAA
55759638 CTTTCTCAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
29 4 0.15
30 15 0.56
31 2 0.07
32 6 0.22
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (33 bp):
ATAAATAATATTTCATTTATATTTAAAATAAAT
Found at i:55760391 original size:25 final size:25
Alignment explanation
Indices: 55760362--55760422 Score: 65
Period size: 24 Copynumber: 2.5 Consensus size: 25
55760352 AAAAATATAT
55760362 TAAATTATTAAATAT-TATATTAAAA
1 TAAATTA-TAAATATATATATTAAAA
* *
55760387 TAAA-TATAAATATATTTTTTAAAA
1 TAAATTATAAATATATATATTAAAA
*
55760411 -AAATTAAAAATA
1 TAAATTATAAATA
55760423 ATAATATGTG
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
23 10 0.32
24 17 0.55
25 4 0.13
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (25 bp):
TAAATTATAAATATATATATTAAAA
Found at i:55760400 original size:20 final size:22
Alignment explanation
Indices: 55760348--55760402 Score: 57
Period size: 20 Copynumber: 2.7 Consensus size: 22
55760338 AACTATAACA
*
55760348 AAATAAAAATATATTAAATTATT
1 AAATATAAATATATTAAA-TATT
55760371 AAATAT---TATATTAAA-A-T
1 AAATATAAATATATTAAATATT
55760388 AAATATAAATATATT
1 AAATATAAATATATT
55760403 TTTTAAAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 9
0.74 0.03 0.24
Matches are distributed among these distances:
17 7 0.25
18 1 0.04
20 15 0.54
23 5 0.18
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
AAATATAAATATATTAAATATT
Found at i:55770267 original size:12 final size:12
Alignment explanation
Indices: 55770250--55770290 Score: 64
Period size: 12 Copynumber: 3.4 Consensus size: 12
55770240 TTTGTCTTCC
55770250 ATTTGAGTTTTT
1 ATTTGAGTTTTT
55770262 ATTTGAGTTTTT
1 ATTTGAGTTTTT
**
55770274 ATTTGCTTTTTT
1 ATTTGAGTTTTT
55770286 ATTTG
1 ATTTG
55770291 CTTTATTAGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.15, C:0.02, G:0.15, T:0.68
Consensus pattern (12 bp):
ATTTGAGTTTTT
Found at i:55770291 original size:12 final size:12
Alignment explanation
Indices: 55770257--55770294 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
55770247 TCCATTTGAG
**
55770257 TTTTTATTTGAG
1 TTTTTATTTGCT
55770269 TTTTTATTTGCT
1 TTTTTATTTGCT
55770281 TTTTTATTTGCT
1 TTTTTATTTGCT
55770293 TT
1 TT
55770295 ATTAGTTGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.11, C:0.05, G:0.11, T:0.74
Consensus pattern (12 bp):
TTTTTATTTGCT
Found at i:55773232 original size:22 final size:22
Alignment explanation
Indices: 55773207--55773320 Score: 90
Period size: 22 Copynumber: 5.2 Consensus size: 22
55773197 TTCTTATTCC
*
55773207 TAATTTAAAACACGTTAAATTA
1 TAATTTAAAACACATTAAATTA
* * * * *
55773229 TAATATAATATACATGCATATT-
1 TAATTTAAAACACAT-TAAATTA
55773251 TAATTTAAAACACATTAAATTA
1 TAATTTAAAACACATTAAATTA
** * *
55773273 TAATACAATATACA-TACATATT-
1 TAATTTAAAACACATTA-A-ATTA
55773295 TAATTTAAAACACATTAAATTA
1 TAATTTAAAACACATTAAATTA
55773317 TAAT
1 TAAT
55773321 ACAATATACA
Statistics
Matches: 67, Mismatches: 19, Indels: 12
0.68 0.19 0.12
Matches are distributed among these distances:
21 9 0.13
22 49 0.73
23 9 0.13
ACGTcount: A:0.51, C:0.10, G:0.02, T:0.38
Consensus pattern (22 bp):
TAATTTAAAACACATTAAATTA
Found at i:55773255 original size:44 final size:44
Alignment explanation
Indices: 55773207--55773358 Score: 259
Period size: 44 Copynumber: 3.5 Consensus size: 44
55773197 TTCTTATTCC
* * *
55773207 TAATTTAAAACACGTTAAATTATAATATAATATACATGCATATT
1 TAATTTAAAACACATTAAATTATAATACAATATACATACATATT
55773251 TAATTTAAAACACATTAAATTATAATACAATATACATACATATT
1 TAATTTAAAACACATTAAATTATAATACAATATACATACATATT
*
55773295 TAATTTAAAACACATTAAATTATAATACAATATACATACATGTT
1 TAATTTAAAACACATTAAATTATAATACAATATACATACATATT
*
55773339 TATTTTAAAACACATTAAAT
1 TAATTTAAAACACATTAAAT
55773359 ATATTAATTC
Statistics
Matches: 103, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 103 1.00
ACGTcount: A:0.50, C:0.11, G:0.02, T:0.38
Consensus pattern (44 bp):
TAATTTAAAACACATTAAATTATAATACAATATACATACATATT
Found at i:55773681 original size:18 final size:18
Alignment explanation
Indices: 55773658--55773724 Score: 93
Period size: 18 Copynumber: 3.8 Consensus size: 18
55773648 AAGTGAAATG
55773658 AATATGAAATGAAAATAA
1 AATATGAAATGAAAATAA
*
55773676 AATATGAAATG-AAATGA
1 AATATGAAATGAAAATAA
55773693 AATATGAAATGAAAATAA
1 AATATGAAATGAAAATAA
*
55773711 AGTAT-AAATTGAAA
1 AATATGAAA-TGAAA
55773725 TGAAATAAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
17 19 0.43
18 25 0.57
ACGTcount: A:0.63, C:0.00, G:0.13, T:0.24
Consensus pattern (18 bp):
AATATGAAATGAAAATAA
Found at i:55773701 original size:35 final size:35
Alignment explanation
Indices: 55773645--55773731 Score: 133
Period size: 35 Copynumber: 2.5 Consensus size: 35
55773635 TAAAATGTGA
*
55773645 ATAAAGTGAAATG-AATATGAAATGAAAATAAAAT
1 ATAAATTGAAATGAAATATGAAATGAAAATAAAAT
*
55773679 ATGAAA-TGAAATGAAATATGAAATGAAAATAAAGT
1 AT-AAATTGAAATGAAATATGAAATGAAAATAAAAT
55773714 ATAAATTGAAATGAAATA
1 ATAAATTGAAATGAAATA
55773732 AATTACAATC
Statistics
Matches: 49, Mismatches: 1, Indels: 5
0.89 0.02 0.09
Matches are distributed among these distances:
34 12 0.24
35 37 0.76
ACGTcount: A:0.61, C:0.00, G:0.15, T:0.24
Consensus pattern (35 bp):
ATAAATTGAAATGAAATATGAAATGAAAATAAAAT
Found at i:55773846 original size:23 final size:24
Alignment explanation
Indices: 55773820--55773871 Score: 79
Period size: 23 Copynumber: 2.2 Consensus size: 24
55773810 CAAATTTAGA
55773820 TGAAATGAAATGAGAAATGAAAG-
1 TGAAATGAAATGAGAAATGAAAGT
* *
55773843 TGAAATGAATTTAGAAATGAAAGT
1 TGAAATGAAATGAGAAATGAAAGT
55773867 TGAAA
1 TGAAA
55773872 ATTGAAATTG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
23 21 0.81
24 5 0.19
ACGTcount: A:0.54, C:0.00, G:0.23, T:0.23
Consensus pattern (24 bp):
TGAAATGAAATGAGAAATGAAAGT
Found at i:55773871 original size:12 final size:11
Alignment explanation
Indices: 55773820--55773895 Score: 64
Period size: 12 Copynumber: 6.5 Consensus size: 11
55773810 CAAATTTAGA
55773820 TGAAATGAAAT
1 TGAAATGAAAT
* *
55773831 GAGAAATGAAAG
1 -TGAAATGAAAT
*
55773843 TGAAATGAATT
1 TGAAATGAAAT
55773854 TAGAAATGAAAGT
1 T-GAAATGAAA-T
55773867 TGAAAATTGAAAT
1 TG-AAA-TGAAAT
55773880 TGAAATTGAAA-
1 TGAAA-TGAAAT
55773891 TGAAA
1 TGAAA
55773896 AAAGAAAAAT
Statistics
Matches: 54, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
11 14 0.26
12 27 0.50
13 8 0.15
14 5 0.09
ACGTcount: A:0.54, C:0.00, G:0.21, T:0.25
Consensus pattern (11 bp):
TGAAATGAAAT
Found at i:55775501 original size:58 final size:58
Alignment explanation
Indices: 55775421--55775548 Score: 186
Period size: 58 Copynumber: 2.2 Consensus size: 58
55775411 ACGGACTAAA
*
55775421 TTAAATTTAAACACCCAACAAACTACAAACAGATGGGTAAAATTAATATGCA-AAAATT
1 TTAAATTTAAACACCCAACAAACTACAAACAGATGGGTAAAATTAATAT-AAGAAAATT
* * * *
55775479 TTAAATTTAAACACTCATCAAACTACAAATAGATGGGTAAAATTAATGTAAGAAAATT
1 TTAAATTTAAACACCCAACAAACTACAAACAGATGGGTAAAATTAATATAAGAAAATT
*
55775537 TTAAATTCAAAC
1 TTAAATTTAAAC
55775549 TATATATAAT
Statistics
Matches: 63, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
57 1 0.02
58 62 0.98
ACGTcount: A:0.51, C:0.13, G:0.09, T:0.27
Consensus pattern (58 bp):
TTAAATTTAAACACCCAACAAACTACAAACAGATGGGTAAAATTAATATAAGAAAATT
Found at i:55775581 original size:90 final size:90
Alignment explanation
Indices: 55775479--55775667 Score: 272
Period size: 90 Copynumber: 2.1 Consensus size: 90
55775469 TGCAAAAATT
* * * * **
55775479 TTAAATTTAAACACTCATCAAACTACAAATAGATGGGTAAAATTAATGTA-AGAAAATTTTAAAT
1 TTAAATTTAAACACCCAACAAACTACAAACAGATAGGTAAAATTAATACACA-AAAATTTTAAAT
*
55775543 TCAAACTATATATAATACAAAATAAA
65 TCAAACTACATATAATACAAAATAAA
55775569 TTAAATTTAAACACCCAACAAACTACAAACAGATAGGTAAAATTAATACACAAAAATTTTAAATT
1 TTAAATTTAAACACCCAACAAACTACAAACAGATAGGTAAAATTAATACACAAAAATTTTAAATT
** *
55775634 CAAACTACATATAATACGGACTAAA
66 CAAACTACATATAATACAAAATAAA
55775659 TTAAATTTA
1 TTAAATTTA
55775668 TAGATACAAA
Statistics
Matches: 88, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
90 87 0.99
91 1 0.01
ACGTcount: A:0.53, C:0.13, G:0.06, T:0.29
Consensus pattern (90 bp):
TTAAATTTAAACACCCAACAAACTACAAACAGATAGGTAAAATTAATACACAAAAATTTTAAATT
CAAACTACATATAATACAAAATAAA
Found at i:55780532 original size:42 final size:41
Alignment explanation
Indices: 55780464--55780593 Score: 201
Period size: 42 Copynumber: 3.2 Consensus size: 41
55780454 GGGCATGAAA
*
55780464 GTGC-ATTCAGGAGTACCGAAGTACAAACAGGGGCACGTAT
1 GTGCAATTCAGGGGTACCGAAGTACAAACAGGGGCACGTAT
*
55780504 GTGCAATTCAGGGGGTACCAAAGTACAAACAGGGGCACGTAT
1 GTGCAATTCA-GGGGTACCGAAGTACAAACAGGGGCACGTAT
* *
55780546 GTGCAATTCAAGGGCACCGAA-TACAAACAGGGGCACGTAT
1 GTGCAATTCAGGGGTACCGAAGTACAAACAGGGGCACGTAT
55780586 GTGCAATT
1 GTGCAATT
55780594 TACAATATTC
Statistics
Matches: 83, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
40 31 0.37
41 13 0.16
42 39 0.47
ACGTcount: A:0.33, C:0.20, G:0.29, T:0.18
Consensus pattern (41 bp):
GTGCAATTCAGGGGTACCGAAGTACAAACAGGGGCACGTAT
Found at i:55780810 original size:13 final size:14
Alignment explanation
Indices: 55780784--55780814 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
55780774 TCTAAATAAA
55780784 TAATTATATTCAAT
1 TAATTATATTCAAT
55780798 TAATTAT-TTCAAT
1 TAATTATATTCAAT
55780811 TAAT
1 TAAT
55780815 CATAAACATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.59
14 7 0.41
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (14 bp):
TAATTATATTCAAT
Found at i:55788899 original size:14 final size:13
Alignment explanation
Indices: 55788866--55788900 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
55788856 GATTATTGTT
*
55788866 TTTATTTCGTTTA
1 TTTATTTTGTTTA
55788879 TTTATTTTGTTTA
1 TTTATTTTGTTTA
55788892 TATTATTTT
1 T-TTATTTT
55788901 TTATGCCATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 13 0.65
14 7 0.35
ACGTcount: A:0.17, C:0.03, G:0.06, T:0.74
Consensus pattern (13 bp):
TTTATTTTGTTTA
Found at i:55800792 original size:44 final size:44
Alignment explanation
Indices: 55800743--55801457 Score: 221
Period size: 44 Copynumber: 16.2 Consensus size: 44
55800733 AAGGTTGAAG
* *
55800743 ATCTTATCTCCCTAAGCAGCAGTGGAGCAGATCGAAGACGGCGA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACGGCGA
* ** *
55800787 ATCTTATCTTTCC-AAG-A-TAGTGGGAAGCAGATTTG-AG-CCACCA
1 ATCTTATC-TCCCTAAGCAGTAGT-GG-AGCAGA-TTGAAGACGGCGA
* * * * ** * *
55800830 AGCCTTGTCTCCCTGAGCAGCAGTGGAAAAGGTTGAAGA-GTG-TA
1 A-TCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACG-GCGA
* *
55800874 GATCTTATCTCCCTAAAGCAGTAGTAGAGCAGATCGAAGACGGCGA
1 -ATCTTATCTCCCT-AAGCAGTAGTGGAGCAGATTGAAGACGGCGA
* * ** *
55800920 ATCTTATCTTTCC-AAG-A-TAGTGGGAAGCAGATTTAAG-CCACCA
1 ATCTTATC-TCCCTAAGCAGTAGT-GG-AGCAGATTGAAGACGGCGA
* * * * * * *
55800963 AGCCTTGTCTCCCTGAGCAGCAGTGGAGAAGGTTGAAGA-GTG-AA
1 A-TCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACG-GCGA
*
55801007 GATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGA
1 -ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACGGCGA
* * ** *
55801052 ATCTTATCTTTCC-AAG-A-TAGTGGGAAGCAGATTTAAG-CCACCA
1 ATCTTATC-TCCCTAAGCAGTAGT-GG-AGCAGATTGAAGACGGCGA
* * * * * ** *
55801095 AGCCTTGTCTCCCTGAGCAGTAGTGGAGAAGGTTGAAGATTG-TA
1 A-TCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACGGCGA
* * *
55801139 GATCTTATCTCCCTAAGCAGTAGTAGAGCAGATCGAAGACGGTGA
1 -ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACGGCGA
* ** *
55801184 ATCTTATCTTTCC-AAG-A-TAGTGGGAAGCAGATTTG-AG-CCACCA
1 ATCTTATC-TCCCTAAGCAGTAGT-GG-AGCAGA-TTGAAGACGGCGA
* * * ** * *
55801227 AGCCTTGTCTCCCTGAGCA-TCAGTGGAAAAGGTTGAAGA-GTG-TA
1 A-TCTTATCTCCCTAAGCAGT-AGTGGAGCAGATTGAAGACG-GCGA
* * * *
55801271 GATCTTATCTCCCTAAAGCAGTAGTGGAGCAGATCGAAAATGACGA
1 -ATCTTATCTCCCT-AAGCAGTAGTGGAGCAGATTGAAGACGGCGA
** * ** *
55801317 ATCTTATCTTTCTAAG-A-TAGTAGGAAGCAGATTTAAG-CCACCA
1 ATCTTATCTCCCTAAGCAGTAGT-GG-AGCAGATTGAAGACGGCGA
* * * * *****
55801360 AGCCTTATCTCCCTAAGCAGTAGCGGAGAAGGTTGAAG-TTTATA
1 A-TCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACGGCGA
* * * *
55801404 GATCTTATCTCCCTGAGTAGTAGTGGAGCAGATCGAAGACGGCAA
1 -ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACGGCGA
55801449 ATCTTATCT
1 ATCTTATCT
55801458 TTCCAAGATA
Statistics
Matches: 472, Mismatches: 139, Indels: 120
0.65 0.19 0.16
Matches are distributed among these distances:
42 19 0.04
43 50 0.11
44 286 0.61
45 93 0.20
46 24 0.05
ACGTcount: A:0.30, C:0.20, G:0.25, T:0.25
Consensus pattern (44 bp):
ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACGGCGA
Found at i:55801087 original size:132 final size:132
Alignment explanation
Indices: 55800700--55801484 Score: 1208
Period size: 132 Copynumber: 6.0 Consensus size: 132
55800690 ACCGGTGAAA
* *
55800700 CACCAAGCATTGTCTCCCTGAGCAGTAGTGGAGAAGG-T------TGAAGATCTTATCTCCCTAA
1 CACCAAGCCTTGTCTCCCTGAGCAGCAGTGGAGAAGGTTGAAGAGTGAAGATCTTATCTCCCTAA
* *
55800758 GCAGCAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTGA
66 GCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAA
55800823 GC
131 GC
* *
55800825 CACCAAGCCTTGTCTCCCTGAGCAGCAGTGGAAAAGGTTGAAGAGTGTAGATCTTATCTCCCTAA
1 CACCAAGCCTTGTCTCCCTGAGCAGCAGTGGAGAAGGTTGAAGAGTGAAGATCTTATCTCCCT-A
*
55800890 AGCAGTAGTAGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTA
65 AGCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTA
55800955 AGC
130 AGC
55800958 CACCAAGCCTTGTCTCCCTGAGCAGCAGTGGAGAAGGTTGAAGAGTGAAGATCTTATCTCCCTAA
1 CACCAAGCCTTGTCTCCCTGAGCAGCAGTGGAGAAGGTTGAAGAGTGAAGATCTTATCTCCCTAA
55801023 GCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAA
66 GCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAA
55801088 GC
131 GC
* * *
55801090 CACCAAGCCTTGTCTCCCTGAGCAGTAGTGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAA
1 CACCAAGCCTTGTCTCCCTGAGCAGCAGTGGAGAAGGTTGAAGAGTGAAGATCTTATCTCCCTAA
* * *
55801155 GCAGTAGTAGAGCAGATCGAAGACGGTGAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTGA
66 GCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAA
55801220 GC
131 GC
* * *
55801222 CACCAAGCCTTGTCTCCCTGAGCATCAGTGGAAAAGGTTGAAGAGTGTAGATCTTATCTCCCTAA
1 CACCAAGCCTTGTCTCCCTGAGCAGCAGTGGAGAAGGTTGAAGAGTGAAGATCTTATCTCCCT-A
* * * * *
55801287 AGCAGTAGTGGAGCAGATCGAAAATGACGAATCTTATCTTTCTAAGATAGTAGGAAGCAGATTTA
65 AGCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTA
55801352 AGC
130 AGC
* * * * * * *
55801355 CACCAAGCCTTATCTCCCTAAGCAGTAGCGGAGAAGGTTGAAG-TTTATAGATCTTATCTCCCTG
1 CACCAAGCCTTGTCTCCCTGAGCAGCAGTGGAGAAGGTTGAAGAGTGA-AGATCTTATCTCCCTA
* * *
55801419 AGTAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGTAGATTTA
65 AGCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTA
55801484 A
130 A
55801485 TTCACCAAAT
Statistics
Matches: 604, Mismatches: 46, Indels: 13
0.91 0.07 0.02
Matches are distributed among these distances:
125 34 0.06
126 1 0.00
132 329 0.54
133 240 0.40
ACGTcount: A:0.30, C:0.20, G:0.26, T:0.25
Consensus pattern (132 bp):
CACCAAGCCTTGTCTCCCTGAGCAGCAGTGGAGAAGGTTGAAGAGTGAAGATCTTATCTCCCTAA
GCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAA
GC
Found at i:55801292 original size:265 final size:264
Alignment explanation
Indices: 55800700--55801484 Score: 1251
Period size: 265 Copynumber: 3.0 Consensus size: 264
55800690 ACCGGTGAAA
* * *
55800700 CACCAAGCATTGTCTCCCTGAGCAGTAGTGGAGAAGG-T------TGAAGATCTTATCTCCCTAA
1 CACCAAGCCTTGTCTCCCTGAGCAGCAGTGGAAAAGGTTGAAGAGTGAAGATCTTATCTCCCTAA
* *
55800758 GCAGCAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTGA
66 GCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAA
* * *
55800823 GCCACCAAGCCTTGTCTCCCTGAGCAGCAGTGGAAAAGGTTGAAGAGTGTAGATCTTATCTCCCT
131 GCCACCAAGCCTTGTCTCCCTGAGCAGTAGTGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCT
55800888 AAAGCAGTAGTAGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATAGTGGGAAGCAGATT
196 -AAGCAGTAGTAGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATAGTGGGAAGCAGATT
55800953 TAAGC
260 TAAGC
*
55800958 CACCAAGCCTTGTCTCCCTGAGCAGCAGTGGAGAAGGTTGAAGAGTGAAGATCTTATCTCCCTAA
1 CACCAAGCCTTGTCTCCCTGAGCAGCAGTGGAAAAGGTTGAAGAGTGAAGATCTTATCTCCCTAA
55801023 GCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAA
66 GCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAA
55801088 GCCACCAAGCCTTGTCTCCCTGAGCAGTAGTGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCT
131 GCCACCAAGCCTTGTCTCCCTGAGCAGTAGTGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCT
*
55801153 AAGCAGTAGTAGAGCAGATCGAAGACGGTGAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTT
196 AAGCAGTAGTAGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTT
*
55801218 GAGC
261 AAGC
* *
55801222 CACCAAGCCTTGTCTCCCTGAGCATCAGTGGAAAAGGTTGAAGAGTGTAGATCTTATCTCCCTAA
1 CACCAAGCCTTGTCTCCCTGAGCAGCAGTGGAAAAGGTTGAAGAGTGAAGATCTTATCTCCCT-A
* * * * *
55801287 AGCAGTAGTGGAGCAGATCGAAAATGACGAATCTTATCTTTCTAAGATAGTAGGAAGCAGATTTA
65 AGCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTA
* * * * *
55801352 AGCCACCAAGCCTTATCTCCCTAAGCAGTAGCGGAGAAGGTTGAAGTTTATAGATCTTATCTCCC
130 AGCCACCAAGCCTTGTCTCCCTGAGCAGTAGTGGAGAAGGTTGAAGATTGTAGATCTTATCTCCC
* * * * *
55801417 TGAGTAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGTAGATT
195 TAAGCAGTAGTAGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATAGTGGGAAGCAGATT
55801482 TAA
260 TAA
55801485 TTCACCAAAT
Statistics
Matches: 490, Mismatches: 29, Indels: 9
0.93 0.05 0.02
Matches are distributed among these distances:
258 35 0.07
259 1 0.00
264 127 0.26
265 327 0.67
ACGTcount: A:0.30, C:0.20, G:0.26, T:0.25
Consensus pattern (264 bp):
CACCAAGCCTTGTCTCCCTGAGCAGCAGTGGAAAAGGTTGAAGAGTGAAGATCTTATCTCCCTAA
GCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAA
GCCACCAAGCCTTGTCTCCCTGAGCAGTAGTGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCT
AAGCAGTAGTAGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTT
AAGC
Found at i:55801474 original size:397 final size:390
Alignment explanation
Indices: 55800700--55801484 Score: 1302
Period size: 397 Copynumber: 2.0 Consensus size: 390
55800690 ACCGGTGAAA
55800700 CACCAAGCATTGTCTCCCTGAGCAGTAGTGGAGAAGGTTGAAGATCTTATCTCCCTAAGCAGCAG
1 CACCAAGCATTGTCTCCCTGAGCAGTAGTGGAGAAGGTTGAAGATCTTATCTCCCTAAGCAGCAG
*
55800765 TGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTGAGCCACCA
66 TAGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTGAGCCACCA
55800830 AGCCTTGTCTCCCTGAGCAGCAGTGGAAAAGGTTGAAGAGTGTAGATCTTATCTCCCTAAAGCAG
131 AGCCTTGTCTCCCTGAGCAGCAGTGGAAAAGGTTGAAGAGTGTAGATCTTATCTCCCTAAAGCAG
* * *
55800895 TAGTAGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCA
196 TAGTAGAGCAGATCGAAAACGACGAATCTTATCTTTCCAAGATAGTAGGAAGCAGATTTAAGCCA
* * *
55800960 CCAAGCCTTGTCTCCCTGAGCAGCAGTGGAGAAGGTTGAAGAGTGAAGATCTTATCTCCCTAAGC
261 CCAAGCCTTATCTCCCTAAGCAGCAGCGGAGAAGGTTGAAGAGTGAAGATCTTATCTCCCTAAGC
*
55801025 AGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGC
326 AGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGC
*
55801090 CACCAAGCCTTGTCTCCCTGAGCAGTAGTGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAA
1 CACCAAGCATTGTCTCCCTGAGCAGTAGTGGAGAAGGTT---GA----AGATCTTATCTCCCTAA
* *
55801155 GCAGTAGTAGAGCAGATCGAAGACGGTGAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTGA
59 GCAGCAGTAGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTGA
*
55801220 GCCACCAAGCCTTGTCTCCCTGAGCATCAGTGGAAAAGGTTGAAGAGTGTAGATCTTATCTCCCT
124 GCCACCAAGCCTTGTCTCCCTGAGCAGCAGTGGAAAAGGTTGAAGAGTGTAGATCTTATCTCCCT
* * *
55801285 AAAGCAGTAGTGGAGCAGATCGAAAATGACGAATCTTATCTTTCTAAGATAGTAGGAAGCAGATT
189 AAAGCAGTAGTAGAGCAGATCGAAAACGACGAATCTTATCTTTCCAAGATAGTAGGAAGCAGATT
* * *
55801350 TAAGCCACCAAGCCTTATCTCCCTAAGCAGTAGCGGAGAAGGTTGAAG-TTTATAGATCTTATCT
254 TAAGCCACCAAGCCTTATCTCCCTAAGCAGCAGCGGAGAAGGTTGAAGAGTGA-AGATCTTATCT
* * *
55801414 CCCTGAGTAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGTAG
318 CCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAG
55801479 ATTTAA
383 ATTTAA
55801485 TTCACCAAAT
Statistics
Matches: 366, Mismatches: 21, Indels: 9
0.92 0.05 0.02
Matches are distributed among these distances:
390 38 0.10
393 2 0.01
396 2 0.01
397 324 0.89
ACGTcount: A:0.30, C:0.20, G:0.26, T:0.25
Consensus pattern (390 bp):
CACCAAGCATTGTCTCCCTGAGCAGTAGTGGAGAAGGTTGAAGATCTTATCTCCCTAAGCAGCAG
TAGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTGAGCCACCA
AGCCTTGTCTCCCTGAGCAGCAGTGGAAAAGGTTGAAGAGTGTAGATCTTATCTCCCTAAAGCAG
TAGTAGAGCAGATCGAAAACGACGAATCTTATCTTTCCAAGATAGTAGGAAGCAGATTTAAGCCA
CCAAGCCTTATCTCCCTAAGCAGCAGCGGAGAAGGTTGAAGAGTGAAGATCTTATCTCCCTAAGC
AGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGC
Found at i:55803419 original size:14 final size:13
Alignment explanation
Indices: 55803386--55803420 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
55803376 GATTATTGTT
*
55803386 TTTATTTCGTTTA
1 TTTATTTTGTTTA
55803399 TTTATTTTGTTTA
1 TTTATTTTGTTTA
55803412 TATTATTTT
1 T-TTATTTT
55803421 TTATGCCATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 13 0.65
14 7 0.35
ACGTcount: A:0.17, C:0.03, G:0.06, T:0.74
Consensus pattern (13 bp):
TTTATTTTGTTTA
Found at i:55806944 original size:161 final size:154
Alignment explanation
Indices: 55806664--55807176 Score: 423
Period size: 155 Copynumber: 3.3 Consensus size: 154
55806654 AAATGTATAA
* * *
55806664 TTCATGTTGGACATGTTTAGAATGGA-ATTTATCTTGAAAATGAGCTTAATTTGGTTATTGTTAA
1 TTCATGTTGGACATGTTTAGAATGGATA-TGATCTTGAAAATGAGCTTACTTTGGTTATTGTCAA
* *
55806728 ATGTCAGTCATTTTGGTAACCGGATGATAACCCTTTTTGTAATTACTTATAAAGAAGAAACTAGA
65 ATGTCAGTCA-TTTGGTAACCAGATGATAACCCTATTTGTAATTACTTAT--A-AAG--A--AGA
**
55806793 GTTTTAAGGTTAGTGGGT-AATATGAAGTAAAT
122 GTTTTAAGGCCAGTGGGTGAATATGAAGTAAAT
* * *
55806825 TTCATGTTGGACATGATTAGAATGGATATGATCTCGAAAATGGGCTTACTTTGGTTATTGTCAAA
1 TTCATGTTGGACATGTTTAGAATGGATATGATCTTGAAAATGAGCTTACTTTGGTTATTGTCAAA
* ** * *
55806890 TGTCAGTCATTTGAGTAACCAGATGA-CA-CCTGGATTTGTGGTTGCTTGTAAAGAAGAGTTTTA
66 TGTCAGTCATTTG-GTAACCAGATGATAACCCT--ATTTGTAATTACTTATAAAGAAGAGTTTTA
* * *
55806953 AGGCCAGTGGGTGATTTTTAAGTAAAT
128 AGGCCAGTGGGTGAATATGAAGTAAAT
** * * *
55806980 TTCATGTTGGACATGTTTACTACGGATATGATCTTGAAAACGAG-TCTACTTTGGTTATCGTCAA
1 TTCATGTTGGACATGTTTAGAATGGATATGATCTTGAAAATGAGCT-TACTTTGGTTATTGTCAA
* * * * * ** *
55807044 ATTTCAGTTATTTGGGTAACCTGACGAT-A-TCTAATTTTGTGGTTACGTATAAAGAAGTGGAAG
65 ATGTCAGTCATTT-GGTAACCAGATGATAACCCT-A-TTTGTAATTACTTATAAAGAA---G-AG
* * * *
55807107 TTTTAATGTCAATGGGTG-ATATAAAGTAAAT
123 TTTTAAGGCCAGTGGGTGAATATGAAGTAAAT
* * * *
55807138 TTTATGTTGGCCATAG-TTAGAATGGACATCATCTTGAAA
1 TTCATGTTGGACAT-GTTTAGAATGGATATGATCTTGAAA
55807177 CACATTATAA
Statistics
Matches: 290, Mismatches: 48, Indels: 31
0.79 0.13 0.08
Matches are distributed among these distances:
154 21 0.07
155 107 0.37
156 2 0.01
158 44 0.15
159 22 0.08
160 5 0.02
161 88 0.30
162 1 0.00
ACGTcount: A:0.31, C:0.10, G:0.22, T:0.37
Consensus pattern (154 bp):
TTCATGTTGGACATGTTTAGAATGGATATGATCTTGAAAATGAGCTTACTTTGGTTATTGTCAAA
TGTCAGTCATTTGGTAACCAGATGATAACCCTATTTGTAATTACTTATAAAGAAGAGTTTTAAGG
CCAGTGGGTGAATATGAAGTAAAT
Found at i:55814762 original size:21 final size:21
Alignment explanation
Indices: 55814665--55814754 Score: 117
Period size: 21 Copynumber: 4.3 Consensus size: 21
55814655 GACGTTGCTA
*
55814665 TGCTTCCCTTGCTGCAGCCTC
1 TGCTTCCCTCGCTGCAGCCTC
**
55814686 TGCTTCCCTCGCTTTAGCCTC
1 TGCTTCCCTCGCTGCAGCCTC
*
55814707 TGCTTCCCTCGCTGCAGCCTG
1 TGCTTCCCTCGCTGCAGCCTC
* * *
55814728 TACTTCTCTCGCTGCCGCCTC
1 TGCTTCCCTCGCTGCAGCCTC
55814749 TGCTTC
1 TGCTTC
55814755 TCTTGCTGTC
Statistics
Matches: 58, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 58 1.00
ACGTcount: A:0.04, C:0.43, G:0.18, T:0.34
Consensus pattern (21 bp):
TGCTTCCCTCGCTGCAGCCTC
Found at i:55814835 original size:66 final size:66
Alignment explanation
Indices: 55814745--55814891 Score: 183
Period size: 66 Copynumber: 2.2 Consensus size: 66
55814735 CTCGCTGCCG
* * *
55814745 CCTCTGCTTCTCTTGCTGTCGCATCTACTTTAAGCTGCT-GCTGGAGTTCTTCATA-CTTTCGTT
1 CCTCAGCTTCTCTCGCTGTCGCATCTACTTTAAGCTG-TAGCTGGAGTTCTTCACATCTTT-GTT
55814808 GAA
64 GAA
* * * *
55814811 CCTCAGCTTCTCTCGCTG-CTGCATCTGCTTTCAGTTGTAGCTGGAGTTCTTCACATCTTTTTTG
1 CCTCAGCTTCTCTCGCTGTC-GCATCTACTTTAAGCTGTAGCTGGAGTTCTTCACATCTTTGTTG
55814875 AA
65 AA
55814877 CCTCAGCTTCTCTCG
1 CCTCAGCTTCTCTCG
55814892 ATGTTGCCTC
Statistics
Matches: 71, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
65 2 0.03
66 65 0.92
67 4 0.06
ACGTcount: A:0.13, C:0.29, G:0.18, T:0.40
Consensus pattern (66 bp):
CCTCAGCTTCTCTCGCTGTCGCATCTACTTTAAGCTGTAGCTGGAGTTCTTCACATCTTTGTTGA
A
Found at i:55814907 original size:66 final size:66
Alignment explanation
Indices: 55814784--55814914 Score: 183
Period size: 66 Copynumber: 2.0 Consensus size: 66
55814774 TTAAGCTGCT
* * * *
55814784 GCTGGAGTTCTTCATACTTTCGTTGAACCTCAGCTTCTCTCGCTGCTGCATCTGCTTTCAGTTGT
1 GCTGGAGTTCTTCACACTTTCGTTGAACCTCAGCTTCTCTCGATGCTGCATCCGCTTTAAGTTGT
55814849 A
66 A
* * *
55814850 GCTGGAGTTCTTCACATCTTT-TTTGAACCTCAGCTTCTCTCGATGTTGCCTCCGCTTTAAGTTG
1 GCTGGAGTTCTTCACA-CTTTCGTTGAACCTCAGCTTCTCTCGATGCTGCATCCGCTTTAAGTTG
55814914 T
65 T
55814915 GTAATTTGCT
Statistics
Matches: 57, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
66 53 0.93
67 4 0.07
ACGTcount: A:0.14, C:0.27, G:0.19, T:0.40
Consensus pattern (66 bp):
GCTGGAGTTCTTCACACTTTCGTTGAACCTCAGCTTCTCTCGATGCTGCATCCGCTTTAAGTTGT
A
Found at i:55820364 original size:16 final size:16
Alignment explanation
Indices: 55820343--55820386 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 16
55820333 ACTAAGCTAC
55820343 GTAAGTTATGTATTAT
1 GTAAGTTATGTATTAT
*
55820359 GTAAGTTATTTATTAT
1 GTAAGTTATGTATTAT
* *
55820375 GAAAATTATGTA
1 GTAAGTTATGTA
55820387 AGTTGTAGTA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.48
Consensus pattern (16 bp):
GTAAGTTATGTATTAT
Found at i:55820424 original size:9 final size:9
Alignment explanation
Indices: 55820412--55820495 Score: 68
Period size: 9 Copynumber: 9.8 Consensus size: 9
55820402 CAAATTATGC
55820412 TATGTAAGT
1 TATGTAAGT
*
55820421 TATGTATGT
1 TATGTAAGT
** *
55820430 CGTATAAGT
1 TATGTAAGT
55820439 TATGTAAG-
1 TATGTAAGT
55820447 T-TGTAAGT
1 TATGTAAGT
55820455 TATGTAAGT
1 TATGTAAGT
*
55820464 TAT-TTA-T
1 TATGTAAGT
* *
55820471 TATGAAAAT
1 TATGTAAGT
*
55820480 TAAGTAAGT
1 TATGTAAGT
55820489 TATGTAA
1 TATGTAA
55820496 TTTACGAATA
Statistics
Matches: 56, Mismatches: 15, Indels: 8
0.71 0.19 0.10
Matches are distributed among these distances:
7 10 0.18
8 5 0.09
9 41 0.73
ACGTcount: A:0.36, C:0.01, G:0.19, T:0.44
Consensus pattern (9 bp):
TATGTAAGT
Found at i:55820455 original size:16 final size:16
Alignment explanation
Indices: 55820414--55820544 Score: 70
Period size: 16 Copynumber: 7.8 Consensus size: 16
55820404 AATTATGCTA
*
55820414 TGTAAGTTATGTATGT
1 TGTAAGTTATGTAAGT
*
55820430 CGTATAAGTTATGTAAGT
1 --TGTAAGTTATGTAAGT
55820448 TGTAAGTTATGTAAGT
1 TGTAAGTTATGTAAGT
* * * *
55820464 TATTTA-TTATGAAAAT
1 T-GTAAGTTATGTAAGT
*
55820480 TAAGTAAGTTATGTAATT
1 T--GTAAGTTATGTAAGT
** *
55820498 TACGAATAA-TTA-AAAAAT
1 T--G--TAAGTTATGTAAGT
55820516 TGTAAGTTATGTAAGT
1 TGTAAGTTATGTAAGT
55820532 TGTAAGTTATGTA
1 TGTAAGTTATGTA
55820545 TAATATTAAT
Statistics
Matches: 88, Mismatches: 18, Indels: 16
0.72 0.15 0.13
Matches are distributed among these distances:
14 3 0.03
15 3 0.03
16 42 0.48
17 5 0.06
18 29 0.33
19 3 0.03
20 3 0.03
ACGTcount: A:0.37, C:0.02, G:0.18, T:0.43
Consensus pattern (16 bp):
TGTAAGTTATGTAAGT
Found at i:55820577 original size:34 final size:37
Alignment explanation
Indices: 55820538--55820619 Score: 116
Period size: 38 Copynumber: 2.3 Consensus size: 37
55820528 AAGTTGTAAG
55820538 TTATGTATA-A-T-ATTAATTAACTAAGTTATGCAAT
1 TTATGTATATATTAATTAATTAACTAAGTTATGCAAT
* *
55820572 TTATGTATAATATTAATTAATTAATTAAGTTATGTAAT
1 TTATGTAT-ATATTAATTAATTAACTAAGTTATGCAAT
55820610 TTATGTATAT
1 TTATGTATAT
55820620 TAACTAATTA
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
34 8 0.19
35 1 0.02
36 1 0.02
37 3 0.07
38 29 0.69
ACGTcount: A:0.40, C:0.02, G:0.09, T:0.49
Consensus pattern (37 bp):
TTATGTATATATTAATTAATTAACTAAGTTATGCAAT
Found at i:55820628 original size:31 final size:31
Alignment explanation
Indices: 55820587--55820994 Score: 205
Period size: 31 Copynumber: 13.7 Consensus size: 31
55820577 TATAATATTA
55820587 ATTAATTAATTAAGTTATGTAATTTATGTAT
1 ATTAATTAATTAAGTTATGTAATTTATGTAT
* *
55820618 ATTAACTAATTAAGTTTTGTAATTTATG-ACT
1 ATTAATTAATTAAGTTATGTAATTTATGTA-T
** *
55820649 AATTAAAAAATGTAAGTTATGTAAGTTATG--T
1 -ATTAATTAAT-TAAGTTATGTAATTTATGTAT
* * *
55820680 A--AGTT--GTAAGTTATGT-ATAATAT-TA-
1 ATTAATTAATTAAGTTATGTAAT-TTATGTAT
* * * * * *
55820705 ATTAACTAAGTTATGTAAT-TTATGTAT-CAT
1 ATTAATTAA-TTAAGTTATGTAATTTATGTAT
* **
55820735 ATTAA-T--GTAAGTTATGTAACATATGTATAAT
1 ATTAATTAATTAAGTTATGTAATTTATG--T-AT
*
55820766 ATTAATTAACTAAGTTATGTAATTTATGTAT
1 ATTAATTAATTAAGTTATGTAATTTATGTAT
*
55820797 CA-T-ATTAATGTAAGTTATGTAACTTATGTAT
1 -ATTAATTAAT-TAAGTTATGTAATTTATGTAT
55820828 ATTAATTAATTAAGTTATGTAATTTATG---
1 ATTAATTAATTAAGTTATGTAATTTATGTAT
55820856 --T-A-TAATTAAGTTATGTAATTTATGTAT
1 ATTAATTAATTAAGTTATGTAATTTATGTAT
* * * *
55820883 AAT-ATTAATGTAAGTTATGT-A--TAAGAAC
1 ATTAATTAAT-TAAGTTATGTAATTTATGTAT
55820911 A-TAA--AATTAAGTTATGTAATTTATGTAT
1 ATTAATTAATTAAGTTATGTAATTTATGTAT
* * *
55820939 AAT-ATTAATGTATGTTATGTAATTTATGAAT
1 ATTAATTAAT-TAAGTTATGTAATTTATGTAT
**
55820970 AATTAAAAAAATGTAAGTTATGTAA
1 -ATT-AATTAAT-TAAGTTATGTAA
55820995 GTTGTAAGCT
Statistics
Matches: 290, Mismatches: 44, Indels: 83
0.70 0.11 0.20
Matches are distributed among these distances:
24 23 0.08
25 25 0.09
26 11 0.04
27 8 0.03
28 13 0.04
29 9 0.03
30 29 0.10
31 105 0.36
32 19 0.07
33 16 0.06
34 32 0.11
ACGTcount: A:0.41, C:0.02, G:0.12, T:0.45
Consensus pattern (31 bp):
ATTAATTAATTAAGTTATGTAATTTATGTAT
Found at i:55820672 original size:9 final size:9
Alignment explanation
Indices: 55820658--55820881 Score: 86
Period size: 9 Copynumber: 25.6 Consensus size: 9
55820648 TAATTAAAAA
55820658 ATGTAAGTT
1 ATGTAAGTT
55820667 ATGTAAGTT
1 ATGTAAGTT
55820676 ATGTAAG-T
1 ATGTAAGTT
55820684 -TGTAAGTT
1 ATGTAAGTT
*
55820692 ATGTATA-AT
1 ATGTA-AGTT
55820701 AT-TAA-TT
1 ATGTAAGTT
**
55820708 AACTAAGTT
1 ATGTAAGTT
*
55820717 ATGTAATTT
1 ATGTAAGTT
*
55820726 ATGTATCATATT
1 ATGTA--A-GTT
55820738 AATGTAAGTT
1 -ATGTAAGTT
**
55820748 ATGTAACAT
1 ATGTAAGTT
*
55820757 ATGTATA-AT
1 ATGTA-AGTT
55820766 AT-TAA-TT
1 ATGTAAGTT
**
55820773 AACTAAGTT
1 ATGTAAGTT
*
55820782 ATGTAATTT
1 ATGTAAGTT
*
55820791 ATGTATCATATT
1 ATGTA--A-GTT
55820803 AATGTAAGTT
1 -ATGTAAGTT
*
55820813 ATGTAACTT
1 ATGTAAGTT
55820822 ATGT-A--T
1 ATGTAAGTT
55820828 AT-TAA-TT
1 ATGTAAGTT
55820835 AAT-TAAGTT
1 -ATGTAAGTT
*
55820844 ATGTAATTT
1 ATGTAAGTT
*
55820853 ATGT-A-TA
1 ATGTAAGTT
55820860 AT-TAAGTT
1 ATGTAAGTT
*
55820868 ATGTAATTT
1 ATGTAAGTT
55820877 ATGTA
1 ATGTA
55820882 TAATATTAAT
Statistics
Matches: 169, Mismatches: 22, Indels: 48
0.71 0.09 0.20
Matches are distributed among these distances:
5 1 0.01
6 5 0.03
7 17 0.10
8 24 0.14
9 98 0.58
10 6 0.04
11 4 0.02
12 4 0.02
13 10 0.06
ACGTcount: A:0.38, C:0.03, G:0.13, T:0.46
Consensus pattern (9 bp):
ATGTAAGTT
Found at i:55820689 original size:16 final size:18
Alignment explanation
Indices: 55820658--55820881 Score: 86
Period size: 16 Copynumber: 12.8 Consensus size: 18
55820648 TAATTAAAAA
55820658 ATGTAAGTTATGTAAGTT
1 ATGTAAGTTATGTAAGTT
55820676 ATGTAAG-T-TGTAAGTT
1 ATGTAAGTTATGTAAGTT
*
55820692 ATGTATA-ATAT-TAA-TT
1 ATGTA-AGTTATGTAAGTT
** *
55820708 AACTAAGTTATGTAATTT
1 ATGTAAGTTATGTAAGTT
*
55820726 ATGTATCATATTAATGTAAGTT
1 ATGTA--A-GTT-ATGTAAGTT
** *
55820748 ATGTAACATATGTATA-AT
1 ATGTAAGTTATGTA-AGTT
**
55820766 AT-TAA-TTAACTAAGTT
1 ATGTAAGTTATGTAAGTT
* *
55820782 ATGTAATTTATGTATCATATT
1 ATGTAAGTTATGTA--A-GTT
*
55820803 AATGTAAGTTATGTAACTT
1 -ATGTAAGTTATGTAAGTT
55820822 ATGT-A--TAT-TAA-TT
1 ATGTAAGTTATGTAAGTT
*
55820835 AAT-TAAGTTATGTAATTT
1 -ATGTAAGTTATGTAAGTT
*
55820853 ATGT-A-TAAT-TAAGTT
1 ATGTAAGTTATGTAAGTT
*
55820868 ATGTAATTTATGTA
1 ATGTAAGTTATGTA
55820882 TAATATTAAT
Statistics
Matches: 156, Mismatches: 22, Indels: 56
0.67 0.09 0.24
Matches are distributed among these distances:
13 3 0.02
14 6 0.04
15 14 0.09
16 35 0.22
17 25 0.16
18 35 0.22
19 4 0.03
20 4 0.03
21 4 0.03
22 26 0.17
ACGTcount: A:0.38, C:0.03, G:0.13, T:0.46
Consensus pattern (18 bp):
ATGTAAGTTATGTAAGTT
Found at i:55820749 original size:22 final size:21
Alignment explanation
Indices: 55820715--55820904 Score: 101
Period size: 22 Copynumber: 8.8 Consensus size: 21
55820705 ATTAACTAAG
55820715 TTATGTAATTTATGTATCATA
1 TTATGTAATTTATGTATCATA
* *
55820736 TTAATGTAAGTTATGTAACATA
1 TT-ATGTAATTTATGTATCATA
*
55820758 TGTA--TAATATTAAT-TAAC-TAA
1 T-TATGTAAT-TT-ATGTATCAT-A
55820779 GTTATGTAATTTATGTATCATA
1 -TTATGTAATTTATGTATCATA
* *
55820801 TTAATGTAAGTTATGTA--A-C
1 TT-ATGTAATTTATGTATCATA
* *
55820820 TTATGTATATTAAT-TAATTA-A
1 TTATGTA-ATTTATGT-ATCATA
*
55820841 GTTATGTAATTTATGTATAATTAA
1 -TTATGTAATTTATGTATCA-T-A
*
55820865 GTTATGTAATTTATGTATAATA
1 -TTATGTAATTTATGTATCATA
*
55820887 TTAATGTAAGTTATGTAT
1 TT-ATGTAATTTATGTAT
55820905 AAGAACATAA
Statistics
Matches: 136, Mismatches: 12, Indels: 41
0.72 0.06 0.22
Matches are distributed among these distances:
18 6 0.04
19 7 0.05
20 5 0.04
21 26 0.19
22 64 0.47
23 7 0.05
24 21 0.15
ACGTcount: A:0.38, C:0.03, G:0.12, T:0.48
Consensus pattern (21 bp):
TTATGTAATTTATGTATCATA
Found at i:55820764 original size:65 final size:65
Alignment explanation
Indices: 55820691--55820858 Score: 297
Period size: 65 Copynumber: 2.6 Consensus size: 65
55820681 AGTTGTAAGT
55820691 TATGTATAATATTAATTAACTAAGTTATGTAATTTATGTATCATATTAATGTAAGTTATGTAACA
1 TATGTATAATATTAATTAACTAAGTTATGTAATTTATGTATCATATTAATGTAAGTTATGTAACA
*
55820756 TATGTATAATATTAATTAACTAAGTTATGTAATTTATGTATCATATTAATGTAAGTTATGTAACT
1 TATGTATAATATTAATTAACTAAGTTATGTAATTTATGTATCATATTAATGTAAGTTATGTAACA
*
55820821 TATG--T-ATATTAATTAATTAAGTTATGTAATTTATGTAT
1 TATGTATAATATTAATTAACTAAGTTATGTAATTTATGTAT
55820859 AATTAAGTTA
Statistics
Matches: 101, Mismatches: 2, Indels: 3
0.95 0.02 0.03
Matches are distributed among these distances:
62 32 0.32
63 1 0.01
65 68 0.67
ACGTcount: A:0.39, C:0.04, G:0.11, T:0.47
Consensus pattern (65 bp):
TATGTATAATATTAATTAACTAAGTTATGTAATTTATGTATCATATTAATGTAAGTTATGTAACA
Found at i:55820774 original size:152 final size:148
Alignment explanation
Indices: 55820516--55820903 Score: 427
Period size: 152 Copynumber: 2.6 Consensus size: 148
55820506 ATTAAAAAAT
*
55820516 TGTAAGTTATGTAAGTTGTAAGTTATGTATAATATTAATTAACTAAGTTATGCAATTTATGTATA
1 TGTAAGTTATGTAAGTTGTAAGTTATGTATAATATTAATTAACTAAGTTATGTAATTTATGTATA
** * *
55820581 ATATTAAT-TAA-TTAAT-TAAGTTATGTAATTTATGTATATTAACTAATTAAGTTTTGTAATTT
66 ATATTAATGTAAGTT-ATGTAACATATGTAATATATGTATATTAAC----TAAGTTATGTAATTT
*
55820643 ATG-ACTAATTAAAAAATGTAAGTTA
126 ATGTA-TCA-T-AAAAATGTAAGTTA
*
55820668 TGTAAGTTATGTAAGTTGTAAGTTATGTATAATATTAATTAACTAAGTTATGTAATTTATGTATC
1 TGTAAGTTATGTAAGTTGTAAGTTATGTATAATATTAATTAACTAAGTTATGTAATTTATGTATA
55820733 ATATTAATGTAAGTTATGTAACATATGT-ATAATAT-TA-ATTAACTAAGTTATGTAATTTATGT
66 ATATTAATGTAAGTTATGTAACATATGTAAT-ATATGTATATTAACTAAGTTATGTAATTTATGT
**
55820795 ATCATATTAATGTAAGTTA
130 ATCATAAAAATGTAAGTTA
* * * * *
55820814 TGTAACTTATGTATA-TTAATTAA-TTAAGTTATGTAAT-TTATGTATAATTAAGTTATGTAATT
1 TGTAAGTTATGTA-AGTT--GTAAGTTATG-TA--TAATATTA-AT-TAACTAAGTTATGTAATT
55820876 TATGTATAATATTAATGTAAGTTATGTA
58 TATGTATAATATTAATGTAAGTTATGTA
55820904 TAAGAACATA
Statistics
Matches: 208, Mismatches: 15, Indels: 27
0.83 0.06 0.11
Matches are distributed among these distances:
146 26 0.12
147 6 0.03
148 24 0.12
149 4 0.02
150 5 0.02
151 44 0.21
152 77 0.37
153 9 0.04
154 13 0.06
ACGTcount: A:0.39, C:0.03, G:0.12, T:0.46
Consensus pattern (148 bp):
TGTAAGTTATGTAAGTTGTAAGTTATGTATAATATTAATTAACTAAGTTATGTAATTTATGTATA
ATATTAATGTAAGTTATGTAACATATGTAATATATGTATATTAACTAAGTTATGTAATTTATGTA
TCATAAAAATGTAAGTTA
Found at i:55820866 original size:24 final size:24
Alignment explanation
Indices: 55820834--55820906 Score: 107
Period size: 24 Copynumber: 3.1 Consensus size: 24
55820824 GTATATTAAT
55820834 TAATTAAGTTATGTAATTTATGTA
1 TAATTAAGTTATGTAATTTATGTA
55820858 TAATTAAGTTATGTAATTTATGTA
1 TAATTAAGTTATGTAATTTATGTA
*
55820882 TAA-T-A-TTAATGTAAGTTATGTA
1 TAATTAAGTT-ATGTAATTTATGTA
55820904 TAA
1 TAA
55820907 GAACATAAAA
Statistics
Matches: 47, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
21 2 0.04
22 17 0.36
23 1 0.02
24 27 0.57
ACGTcount: A:0.40, C:0.00, G:0.12, T:0.48
Consensus pattern (24 bp):
TAATTAAGTTATGTAATTTATGTA
Found at i:55820934 original size:56 final size:55
Alignment explanation
Indices: 55820807--55820960 Score: 202
Period size: 56 Copynumber: 2.8 Consensus size: 55
55820797 CATATTAATG
* * *** ** *
55820807 TAAGTTATGTAACTTATGTATATTAATTAAT-TAAGTTATGTAATTTATGTATAAT
1 TAAGTTATGTAATTTATGTATAAT-ATTAATGTAAGTTATGTAAAGAACATAAAAT
55820862 TAAGTTATGTAATTTATGTATAATATTAATGTAAGTTATGTATAAGAACATAAAAT
1 TAAGTTATGTAATTTATGTATAATATTAATGTAAGTTATGTA-AAGAACATAAAAT
*
55820918 TAAGTTATGTAATTTATGTATAATATTAATGTATGTTATGTAA
1 TAAGTTATGTAATTTATGTATAATATTAATGTAAGTTATGTAA
55820961 TTTATGAATA
Statistics
Matches: 88, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
54 6 0.07
55 34 0.39
56 48 0.55
ACGTcount: A:0.40, C:0.01, G:0.12, T:0.46
Consensus pattern (55 bp):
TAAGTTATGTAATTTATGTATAATATTAATGTAAGTTATGTAAAGAACATAAAAT
Found at i:55820984 original size:56 final size:56
Alignment explanation
Indices: 55820813--55820993 Score: 169
Period size: 56 Copynumber: 3.2 Consensus size: 56
55820803 AATGTAAGTT
* * * ***
55820813 ATGTAACTTATGTATATTAATTAAT-TAAGTTATGTAATTTATGTATAATT-AAGTT
1 ATGTAATTTATGTATAAT-ATTAATGTAAGTTATGTAATTTATGAATAATTAAAAAA
* *
55820868 ATGTAATTTATGTATAATATTAATGTAAGTTATGT-A--TAAGAA-CA-TAAAATTAA
1 ATGTAATTTATGTATAATATTAATGTAAGTTATGTAATTTATGAATAATTAAAA--AA
*
55820921 GTTATGTAATTTATGTATAATATTAATGTATGTTATGTAATTTATGAATAATTAAAAAA
1 ---ATGTAATTTATGTATAATATTAATGTAAGTTATGTAATTTATGAATAATTAAAAAA
*
55820980 ATGTAAGTTATGTA
1 ATGTAATTTATGTA
55820994 AGTTGTAAGC
Statistics
Matches: 102, Mismatches: 12, Indels: 23
0.74 0.09 0.17
Matches are distributed among these distances:
50 1 0.01
51 3 0.03
52 4 0.04
54 7 0.07
55 26 0.25
56 47 0.46
57 1 0.01
59 7 0.07
60 1 0.01
61 5 0.05
ACGTcount: A:0.42, C:0.01, G:0.12, T:0.45
Consensus pattern (56 bp):
ATGTAATTTATGTATAATATTAATGTAAGTTATGTAATTTATGAATAATTAAAAAA
Found at i:55821061 original size:142 final size:138
Alignment explanation
Indices: 55820776--55821051 Score: 297
Period size: 142 Copynumber: 1.9 Consensus size: 138
55820766 ATTAATTAAC
* * **
55820776 TAAGTTATGTAATTTATGTATCATATTAATGTAAGTTATGTAACTTATGTATATTAATTAATTAA
1 TAAGTTATGTAATTTATGTATAATATTAATGTAAGTTATGTAACTTATGAATATTAAAAAATTAA
* * * *
55820841 GTTATGTAATTTATGTATAATTAAGTTATGTAATTTATGTATAATATTAATGTAAGTTATGTATA
66 GTTATGTAATTTAAGTATAATTAAGTAATGTAATTTATGTATAATATTAATGTAAGCTAAGTATA
55820906 AGAACATAAAAT
131 AG---AT-AAAT
* *
55820918 TAAGTTATGTAATTTATGTATAATATTAATGTATGTTATGTAATTTATGAATAATTAAAAAAATG
1 TAAGTTATGTAATTTATGTATAATATTAATGTAAGTTATGTAACTTATGAAT-ATT-AAAAAAT-
* *
55820983 TAAGTTATGTAAGTTGTAAGCTGTAAGTTATGTAAGTTGTCAA-TTATGTATAATATTAAT-TAA
63 TAAGTTATGTAA-TT-TAAG-TATAA-TTAAGTAA--TGT-AATTTATGTATAATATTAATGTAA
55821046 -CTAAGT
121 GCTAAGT
55821052 TATGTAATTA
Statistics
Matches: 112, Mismatches: 12, Indels: 13
0.82 0.09 0.09
Matches are distributed among these distances:
142 48 0.43
143 3 0.03
144 5 0.04
145 12 0.11
146 2 0.02
147 3 0.03
148 4 0.04
149 10 0.09
150 3 0.03
151 20 0.18
152 2 0.02
ACGTcount: A:0.40, C:0.02, G:0.13, T:0.45
Consensus pattern (138 bp):
TAAGTTATGTAATTTATGTATAATATTAATGTAAGTTATGTAACTTATGAATATTAAAAAATTAA
GTTATGTAATTTAAGTATAATTAAGTAATGTAATTTATGTATAATATTAATGTAAGCTAAGTATA
AGATAAAT
Found at i:55825927 original size:41 final size:40
Alignment explanation
Indices: 55825863--55826264 Score: 263
Period size: 41 Copynumber: 9.8 Consensus size: 40
55825853 TTTTGTTACT
* * *
55825863 ATTAGCGGCGCTTAGATACAAACGCCGCTGAAGA-CAAGAGA
1 ATTAGCGGCGC-TAGTTAAAAACGCCGCTAAAGATC-AGAGA
* * *
55825904 ATTAGTGGCGCTCAGTTAAAAACGCCGCTAAAGATCCGAGT
1 ATTAGCGGCGCT-AGTTAAAAACGCCGCTAAAGATCAGAGA
* * * *
55825945 ATTAGCGGCGCTTGTATAAAAACGCCGTTAAAGATCCGAGC
1 ATTAGCGGCGCTAGT-TAAAAACGCCGCTAAAGATCAGAGA
** * *
55825986 ATTAGCGGCGCATAGACAAAAACGCCGCTAAAGATCCGAGC
1 ATTAGCGGCGC-TAGTTAAAAACGCCGCTAAAGATCAGAGA
** * *
55826027 ATTAGCGGCGCGTAGACAAAAACGCCGCTAAAGATCCGAGC
1 ATTAGCGGCGC-TAGTTAAAAACGCCGCTAAAGATCAGAGA
**** *
55826068 ATTAGCGGCGCATACACGAAAACGCCGCTAAAGACTC-GAGC
1 ATTAGCGGCGC-TAGTTAAAAACGCCGCTAAAGA-TCAGAGA
* ** * *
55826109 ATTAGCGGCCCCTAGACAAAAACGCCGCTAAAGATCCGAGC
1 ATTAGCGG-CGCTAGTTAAAAACGCCGCTAAAGATCAGAGA
* **** * * *
55826150 ATTAGCGGTGCCTACACGAAAACGCTGCTAGAGACTC-GAGC
1 ATTAGCGGCG-CTAGTTAAAAACGCCGCTAAAGA-TCAGAGA
* ** *
55826191 ATTAGCTGCGCCTAGACAAAAACGCCGCTAAAGATCCA-AGC
1 ATTAGCGGCG-CTAGTTAAAAACGCCGCTAAAGAT-CAGAGA
***
55826232 ATTAGCGGCGCTTACACAAAAACGCCGCTAAAG
1 ATTAGCGGCGC-TAGTTAAAAACGCCGCTAAAG
55826265 GTTTAAAAAA
Statistics
Matches: 314, Mismatches: 35, Indels: 24
0.84 0.09 0.06
Matches are distributed among these distances:
40 7 0.02
41 298 0.95
42 9 0.03
ACGTcount: A:0.34, C:0.26, G:0.24, T:0.15
Consensus pattern (40 bp):
ATTAGCGGCGCTAGTTAAAAACGCCGCTAAAGATCAGAGA
Found at i:55826007 original size:82 final size:81
Alignment explanation
Indices: 55825921--55826264 Score: 485
Period size: 82 Copynumber: 4.2 Consensus size: 81
55825911 GCGCTCAGTT
* * * *
55825921 AAAAACGCCGCTAAAGA-TCCGAGTATTAGCGGCGCTTGTATAAAAACGCCGTTAAAGATCCGAG
1 AAAAACGCCGCTAAAGACT-CGAGCATTAGCGGCGCTAG-ACAAAAACGCCGCTAAAGATCCGAG
*
55825985 CATTAGCGGCGCATAGAC
64 CATTAGCGGCGCATACAC
55826003 AAAAACGCCGCTAAAGA-TCCGAGCATTAGCGGCGCGTAGACAAAAACGCCGCTAAAGATCCGAG
1 AAAAACGCCGCTAAAGACT-CGAGCATTAGCGGCGC-TAGACAAAAACGCCGCTAAAGATCCGAG
55826067 CATTAGCGGCGCATACAC
64 CATTAGCGGCGCATACAC
* *
55826085 GAAAACGCCGCTAAAGACTCGAGCATTAGCGGCCCCTAGACAAAAACGCCGCTAAAGATCCGAGC
1 AAAAACGCCGCTAAAGACTCGAGCATTAGCGG-CGCTAGACAAAAACGCCGCTAAAGATCCGAGC
* *
55826150 ATTAGCGGTGCCTACAC
65 ATTAGCGGCGCATACAC
* * * * *
55826167 GAAAACGCTGCTAGAGACTCGAGCATTAGCTGCGCCTAGACAAAAACGCCGCTAAAGATCCAAGC
1 AAAAACGCCGCTAAAGACTCGAGCATTAGCGGCG-CTAGACAAAAACGCCGCTAAAGATCCGAGC
*
55826232 ATTAGCGGCGCTTACAC
65 ATTAGCGGCGCATACAC
55826249 AAAAACGCCGCTAAAG
1 AAAAACGCCGCTAAAG
55826265 GTTTAAAAAA
Statistics
Matches: 239, Mismatches: 19, Indels: 8
0.90 0.07 0.03
Matches are distributed among these distances:
81 1 0.00
82 233 0.97
83 5 0.02
ACGTcount: A:0.35, C:0.27, G:0.24, T:0.15
Consensus pattern (81 bp):
AAAAACGCCGCTAAAGACTCGAGCATTAGCGGCGCTAGACAAAAACGCCGCTAAAGATCCGAGCA
TTAGCGGCGCATACAC
Found at i:55826090 original size:123 final size:122
Alignment explanation
Indices: 55825863--55826264 Score: 477
Period size: 123 Copynumber: 3.3 Consensus size: 122
55825853 TTTTGTTACT
* * * * * * **
55825863 ATTAGCGGCGCTTAGATACAAACGCCGCTGAAGA-CAAGAGAATTAGTGGCGCTCAGTTAAAAAC
1 ATTAGCGGCGCTTAGACAAAAACGCCGCTAAAGATC-CGAGCATTAGCGGCGCT-AGACAAAAAC
* * ** * *
55825927 GCCGCTAAAGATCCGAGTATTAGCGGCGCTTGTATAAAAACGCCGTTAAAGATCCGAGC
64 GCCGCTAAAGATCCGAGCATTAGCGGCGCATACACAAAAACGCCGCTAAAGATCCGAGC
*
55825986 ATTAGCGGCGCATAGACAAAAACGCCGCTAAAGATCCGAGCATTAGCGGCGCGTAGACAAAAACG
1 ATTAGCGGCGCTTAGACAAAAACGCCGCTAAAGATCCGAGCATTAGCGGCGC-TAGACAAAAACG
*
55826051 CCGCTAAAGATCCGAGCATTAGCGGCGCATACACGAAAACGCCGCTAAAGA-CTCGAGC
65 CCGCTAAAGATCCGAGCATTAGCGGCGCATACACAAAAACGCCGCTAAAGATC-CGAGC
* * * * *
55826109 ATTAGCGGCCCCTAGACAAAAACGCCGCTAAAGATCCGAGCATTAGCGGTGCCTACACGAAAACG
1 ATTAGCGGCGCTTAGACAAAAACGCCGCTAAAGATCCGAGCATTAGCGGCG-CTAGACAAAAACG
* * * * * *
55826174 CTGCTAGAGA-CTCGAGCATTAGCTGCGCCTAGACAAAAACGCCGCTAAAGATCCAAGC
65 CCGCTAAAGATC-CGAGCATTAGCGGCGCATACACAAAAACGCCGCTAAAGATCCGAGC
*
55826232 ATTAGCGGCGCTTACACAAAAACGCCGCTAAAG
1 ATTAGCGGCGCTTAGACAAAAACGCCGCTAAAG
55826265 GTTTAAAAAA
Statistics
Matches: 242, Mismatches: 31, Indels: 12
0.85 0.11 0.04
Matches are distributed among these distances:
122 2 0.01
123 236 0.98
124 4 0.02
ACGTcount: A:0.34, C:0.26, G:0.24, T:0.15
Consensus pattern (122 bp):
ATTAGCGGCGCTTAGACAAAAACGCCGCTAAAGATCCGAGCATTAGCGGCGCTAGACAAAAACGC
CGCTAAAGATCCGAGCATTAGCGGCGCATACACAAAAACGCCGCTAAAGATCCGAGC
Found at i:55829047 original size:17 final size:17
Alignment explanation
Indices: 55829025--55829069 Score: 56
Period size: 16 Copynumber: 2.7 Consensus size: 17
55829015 AAAAAGTATT
55829025 TTAAAAATATTTTAAAA
1 TTAAAAATATTTTAAAA
*
55829042 TTAAAAA-AATTTAAAA
1 TTAAAAATATTTTAAAA
* *
55829058 ATAAATATATTT
1 TTAAAAATATTT
55829070 ATTATATCGG
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
16 13 0.57
17 10 0.43
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
TTAAAAATATTTTAAAA
Found at i:55829829 original size:25 final size:25
Alignment explanation
Indices: 55829780--55829829 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
55829770 AGTTATATAA
* * *
55829780 TATCCAAACAATAACAAGATAATAG
1 TATCAAAACAACAACAAAATAATAG
55829805 TATCAAAACAACAACAAAATAATAG
1 TATCAAAACAACAACAAAATAATAG
55829830 CAAAACGATA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.60, C:0.16, G:0.06, T:0.18
Consensus pattern (25 bp):
TATCAAAACAACAACAAAATAATAG
Found at i:55833293 original size:23 final size:22
Alignment explanation
Indices: 55833250--55833296 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
55833240 ACTGTACATG
55833250 TAAATAAAAATTAGAACTTTTT
1 TAAATAAAAATTAGAACTTTTT
55833272 TAAATAAAAATTAGAACTTTTT
1 TAAATAAAAATTAGAACTTTTT
55833294 TAA
1 TAA
55833297 TCATTTTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.40
Consensus pattern (22 bp):
TAAATAAAAATTAGAACTTTTT
Found at i:55834146 original size:7 final size:7
Alignment explanation
Indices: 55834136--55834170 Score: 61
Period size: 7 Copynumber: 4.9 Consensus size: 7
55834126 ATTAAAAATA
55834136 TATATTT
1 TATATTT
55834143 TATATTT
1 TATATTT
55834150 TATATTT
1 TATATTT
55834157 TATATTT
1 TATATTT
55834164 TAATATT
1 T-ATATT
55834171 GTATGTAGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 22 0.81
8 5 0.19
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (7 bp):
TATATTT
Found at i:55835971 original size:68 final size:68
Alignment explanation
Indices: 55835816--55835961 Score: 204
Period size: 68 Copynumber: 2.1 Consensus size: 68
55835806 GTTTTGCTTA
* * * * **
55835816 CATAAGAGTCATCGGT-TAATCACTTTTCTTAGAAAGTAAAGTTAAATATCAGTATAGGATAATA
1 CATAAGAGTCAT-AGTCTAATTATTTTTCTTAGAAAGTAAAGTTAAAAATCAACATAGGATAATA
55835880 ATTC
65 ATTC
* *
55835884 CATAAGAGTCATAGTCTAATTATTTTTCTTATAAAGTAAAGTTAAAAATCAACATATGATAATAA
1 CATAAGAGTCATAGTCTAATTATTTTTCTTAGAAAGTAAAGTTAAAAATCAACATAGGATAATAA
55835949 TTC
66 TTC
55835952 CATAAGAGTC
1 CATAAGAGTC
55835962 TTGATCTAAT
Statistics
Matches: 69, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
67 2 0.03
68 67 0.97
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.34
Consensus pattern (68 bp):
CATAAGAGTCATAGTCTAATTATTTTTCTTAGAAAGTAAAGTTAAAAATCAACATAGGATAATAA
TTC
Found at i:55842576 original size:42 final size:41
Alignment explanation
Indices: 55842476--55842639 Score: 211
Period size: 42 Copynumber: 4.0 Consensus size: 41
55842466 GTTAATATTT
* * *
55842476 TAAGCACCGCTAAAGAACACGGTCTTTAGCGGTGTTTTTTC
1 TAAGCGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTC
* * *
55842517 CAAGCGCCTCTAAAGAACATGGTCCTTAGCGGCGTTTCTTTC
1 TAAGCGCCGCTAAAGAACATGGTCTTTAGCGGCGTTT-TTTC
** *
55842559 TAAGCGCCGCTAAAGAACATTATCTTTAGCTGCGTTTTTTAC
1 TAAGCGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTT-C
* *
55842601 TAAGCGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTTT
1 TAAGCGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTT
55842640 ATACAAAAGC
Statistics
Matches: 105, Mismatches: 16, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
41 34 0.32
42 71 0.68
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.32
Consensus pattern (41 bp):
TAAGCGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTC
Found at i:55842634 original size:84 final size:83
Alignment explanation
Indices: 55842476--55842634 Score: 219
Period size: 83 Copynumber: 1.9 Consensus size: 83
55842466 GTTAATATTT
* * *
55842476 TAAGCACCGCTAAAGAACACGGTCTTTAGCGGTGTTTTTTCCAAGCGCCTCTAAAGAACATGGTC
1 TAAGCACCGCTAAAGAACACGATCTTTAGCGGCGTTTTTTCCAAGCGCCGCTAAAGAACATGGTC
55842541 CTTAGCGGCGTTTCTTTC
66 CTTAGCGGCGTTTCTTTC
* ** * * *
55842559 TAAGCGCCGCTAAAGAACATTATCTTTAGCTGCGTTTTTTACTAAGCGCCGCTAAAGAACATGTT
1 TAAGCACCGCTAAAGAACACGATCTTTAGCGGCGTTTTTT-CCAAGCGCCGCTAAAGAACATGGT
*
55842624 CTTTAGCGGCG
65 CCTTAGCGGCG
55842635 CTTTTATACA
Statistics
Matches: 65, Mismatches: 10, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
83 34 0.52
84 31 0.48
ACGTcount: A:0.25, C:0.24, G:0.21, T:0.30
Consensus pattern (83 bp):
TAAGCACCGCTAAAGAACACGATCTTTAGCGGCGTTTTTTCCAAGCGCCGCTAAAGAACATGGTC
CTTAGCGGCGTTTCTTTC
Found at i:55842981 original size:21 final size:21
Alignment explanation
Indices: 55842955--55843025 Score: 99
Period size: 21 Copynumber: 3.4 Consensus size: 21
55842945 TTTTGCTCTG
55842955 CTCTGCTTCTCC-CGCTGCAGC
1 CTCTGCTTC-CCTCGCTGCAGC
55842976 CTCTGCTTCCCTCGCTGCAGC
1 CTCTGCTTCCCTCGCTGCAGC
* * *
55842997 CGCTGCTTCCCTCGCTGCCGT
1 CTCTGCTTCCCTCGCTGCAGC
55843018 CTCTGCTT
1 CTCTGCTT
55843026 TAAGTTGTAG
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
20 2 0.04
21 43 0.96
ACGTcount: A:0.03, C:0.46, G:0.20, T:0.31
Consensus pattern (21 bp):
CTCTGCTTCCCTCGCTGCAGC
Found at i:55846657 original size:16 final size:16
Alignment explanation
Indices: 55846613--55846722 Score: 88
Period size: 19 Copynumber: 6.9 Consensus size: 16
55846603 GATTTTAGTA
55846613 AAGTATATATTCCAGC
1 AAGTATATATTCCAGC
55846629 AAGTGGAATATATTCCAGC
1 AAGT---ATATATTCCAGC
**
55846648 AAGTATATATT-TGGC
1 AAGTATATATTCCAGC
*
55846663 ---CATATATTCCAGC
1 AAGTATATATTCCAGC
55846676 AAG--TATATTCCAGC
1 AAGTATATATTCCAGC
*
55846690 AACTGGAATATATTCCAGC
1 AA---GTATATATTCCAGC
55846709 AAGTATATATTCCA
1 AAGTATATATTCCA
55846723 AAGTTATAGT
Statistics
Matches: 76, Mismatches: 6, Indels: 24
0.72 0.06 0.23
Matches are distributed among these distances:
12 7 0.09
13 2 0.03
14 13 0.17
15 2 0.03
16 22 0.29
17 1 0.01
19 29 0.38
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.31
Consensus pattern (16 bp):
AAGTATATATTCCAGC
Found at i:55846682 original size:14 final size:14
Alignment explanation
Indices: 55846637--55846716 Score: 63
Period size: 14 Copynumber: 5.4 Consensus size: 14
55846627 GCAAGTGGAA
55846637 TATATTCCAGCAAG
1 TATATTCCAGCAAG
*** *
55846651 TATATATTTGGCCA-
1 TATAT-TCCAGCAAG
55846665 TATATTCCAGCAAG
1 TATATTCCAGCAAG
55846679 TATATTCCAGCAACTGG
1 TATATTCCAGCAA---G
55846696 AATATATTCCAGCAAG
1 --TATATTCCAGCAAG
55846712 TATAT
1 TATAT
55846717 ATTCCAAAGT
Statistics
Matches: 51, Mismatches: 8, Indels: 14
0.70 0.11 0.19
Matches are distributed among these distances:
13 4 0.08
14 28 0.55
15 4 0.08
16 1 0.02
17 1 0.02
19 13 0.25
ACGTcount: A:0.35, C:0.19, G:0.14, T:0.33
Consensus pattern (14 bp):
TATATTCCAGCAAG
Found at i:55848003 original size:15 final size:15
Alignment explanation
Indices: 55847968--55848000 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
55847958 TCTAAGCTGC
55847968 TAAACCTTTAAACCT
1 TAAACCTTTAAACCT
*
55847983 TAAACC-TTAAATCT
1 TAAACCTTTAAACCT
55847997 TAAA
1 TAAA
55848001 ACCAATAACC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.45, C:0.21, G:0.00, T:0.33
Consensus pattern (15 bp):
TAAACCTTTAAACCT
Found at i:55848645 original size:20 final size:21
Alignment explanation
Indices: 55848608--55848664 Score: 53
Period size: 20 Copynumber: 2.8 Consensus size: 21
55848598 CCAAACTCTC
** * *
55848608 AAACCCTAAACCGAAAACACT
1 AAACCCTAAATTGTAAACACA
* *
55848629 AAA-CCTACATTGTAAACTCA
1 AAACCCTAAATTGTAAACACA
55848649 AAACCCTAAATTGTAA
1 AAACCCTAAATTGTAA
55848665 TCCAAAAATA
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
20 14 0.50
21 14 0.50
ACGTcount: A:0.49, C:0.26, G:0.05, T:0.19
Consensus pattern (21 bp):
AAACCCTAAATTGTAAACACA
Found at i:55849084 original size:114 final size:114
Alignment explanation
Indices: 55848781--55849485 Score: 683
Period size: 115 Copynumber: 6.2 Consensus size: 114
55848771 CCAAAACTCT
* * * * * * * * * *
55848781 GTTAAGATATTTTGCGGTGCTTTCAAAACAGCGCCACTAACAATATGCTTTCGCGGCGGTTTCCT
1 GTTAAGATATTTTGCGGCGCATCCACAA-AGCGCCGCTAATACTATCCTTTAGCGGCGTTTTCCT
* * * ** *
55848846 GTAAGTGCCACAAATTTTAGTATACATCAAGACCAAAACGTTGCGTTTTG
65 ATAAGCGCCACTAATTCAAGTATACATCAAGACCAAAACGCTGCGTTTTG
* * *
55848896 GTTAAGGTATTTTGCGGCGCTATCCACAAATCGCCGCTAATACTATGCTTTAGCGGCG-TTTCAC
1 GTTAAGATATTTTGCGGCGC-ATCCACAAAGCGCCGCTAATACTATCCTTTAGCGGCGTTTTC-C
** *
55848960 CGTAAGCGCCAATAATTCAAGTATACATTC-AGACCAAAACGCTGCGTTTTG
64 TATAAGCGCCACTAATTCAAGTATACA-TCAAGACCAAAACGCTGCGTTTTG
* * *
55849011 GTTCAA-ATATTTTGCGGCACATCCAAAAAGCGCCGCTAATACTATCCTTTAGCGGCGTTTTCCA
1 GTT-AAGATATTTTGCGGCGCATCCACAAAGCGCCGCTAATACTATCCTTTAGCGGCGTTTTCCT
** * * *
55849075 ATAAGCGCCACTAACGCTAA-CATACCTCAAGACCAAAACTCTGCGTTTTG
65 ATAAGCGCCACTAATTC-AAGTATACATCAAGACCAAAACGCTGCGTTTTG
* ** * *
55849125 GTTAAGATATTTTGCGGCGCTTTTACCAAAGCGCCGCTAATACTATCCTTTAACGGCGTTTTACT
1 GTTAAGATATTTTGCGGCGCATCCA-CAAAGCGCCGCTAATACTATCCTTTAGCGGCGTTTTCCT
* * *
55849190 ATAAGCGCCACTAATTCTAGTATACATCAAGACCAAAACGTTGTGTTTTG
65 ATAAGCGCCACTAATTCAAGTATACATCAAGACCAAAACGCTGCGTTTTG
* * * ** * * *
55849240 GTTAAGATATTTTGCGACGCCAGCCACGACTCGCCGCTAATACTATGCTTTAGCGACGTTTTCGG
1 GTTAAGATATTTTGCGGCG-CATCCACAAAGCGCCGCTAATACTATCCTTTAGCGGCGTTTTC-C
* * * *
55849305 TA-AA-CGCCACTAATTCTAGTATA-AGCAAGACTAAAACGATGCGTTTTG
64 TATAAGCGCCACTAATTCAAGTATACATCAAGACCAAAACGCTGCGTTTTG
* * * * * * * *
55849353 GTTCAGATATTTCGCGGTGCTTTCAAAAAGCGCCGCTAATACTAT-CTATTTGTGGCGTTTTCCT
1 GTTAAGATATTTTGCGGCGCATCCACAAAGCGCCGCTAATACTATCCT-TTAGCGGCGTTTTCCT
* * *
55849417 ATAAGCGCCACTAATTCTAA-CATACCTCAAGACC-AAACTCTGCGTTTTG
65 ATAAGCGCCACTAATTC-AAGTATACATCAAGACCAAAACGCTGCGTTTTG
*
55849466 GTTAAGATATTTTGCAGCGC
1 GTTAAGATATTTTGCGGCGC
55849486 TATGCTTTAA
Statistics
Matches: 484, Mismatches: 89, Indels: 36
0.79 0.15 0.06
Matches are distributed among these distances:
111 4 0.01
112 32 0.07
113 84 0.17
114 121 0.25
115 230 0.48
116 13 0.03
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.30
Consensus pattern (114 bp):
GTTAAGATATTTTGCGGCGCATCCACAAAGCGCCGCTAATACTATCCTTTAGCGGCGTTTTCCTA
TAAGCGCCACTAATTCAAGTATACATCAAGACCAAAACGCTGCGTTTTG
Found at i:55849315 original size:229 final size:227
Alignment explanation
Indices: 55848867--55849480 Score: 688
Period size: 229 Copynumber: 2.7 Consensus size: 227
55848857 AAATTTTAGT
* * * *
55848867 ATACATCAAGACCAAAACGTTGCGTTTTGGTTAAGGTATTTTGCGGCGC-TATCCACAAATCGCC
1 ATACATCAAGACCAAAAC-TTGCGTTTTGGTTAAGATATTTTGCGGCGCTTTTAC-CAAAGCGCC
* ** * *
55848931 GCTAATACTATGCTTTAGCGGCGTTTCACCGTAAGCGCCAATAATTCAAGTATACATTC-AGACC
64 GCTAATACTAT-CTTTAGCGGCGTTTTACTATAAGCGCCACTAATTCTAGTATACA-TCAAGACC
* *
55848995 AAAACGCTGCGTTTTGGTTCAA-ATATTTTGCGGCACATCCAAAAAGCGCCGCTAATACTATCCT
127 AAAACGTTGCGTTTTGGTT-AAGATATTTTGCGGCACAGCCAAAAAGCGCCGCTAATACTATCCT
* *
55849059 TTAGCGGCGTTTTCCAATAAGCGCCACTAACGCTAAC
191 TTAGCGACGTTTTCCAATAAACGCCACTAACGCTAAC
*
55849096 ATACCTCAAGACCAAAACTCTGCGTTTTGGTTAAGATATTTTGCGGCGCTTTTACCAAAGCGCCG
1 ATACATCAAGACCAAAACT-TGCGTTTTGGTTAAGATATTTTGCGGCGCTTTTACCAAAGCGCCG
*
55849161 CTAATACTATCCTTTAACGGCGTTTTACTATAAGCGCCACTAATTCTAGTATACATCAAGACCAA
65 CTAATACTAT-CTTTAGCGGCGTTTTACTATAAGCGCCACTAATTCTAGTATACATCAAGACCAA
* ** ** *
55849226 AACGTTGTGTTTTGGTTAAGATATTTTGCGACGC-CAGCCACGACTCGCCGCTAATACTATGCTT
129 AACGTTGCGTTTTGGTTAAGATATTTTGCG--GCACAGCCAAAAAGCGCCGCTAATACTATCCTT
** ** **
55849290 TAGCGACGTTTT-CGGTAAACGCCACTAATTCTAGT
192 TAGCGACGTTTTCCAATAAACGCCACTAACGCTAAC
* * * * * * * *
55849325 ATA-AGCAAGACTAAAACGATGCGTTTTGGTTCAGATATTTCGCGGTGCTTTCA-AAAAGCGCCG
1 ATACATCAAGACCAAAAC-TTGCGTTTTGGTTAAGATATTTTGCGGCGCTTTTACCAAAGCGCCG
* * * ** *
55849388 CTAATACTATCTATTTGTGGCGTTTTCCTATAAGCGCCACTAATTCTAACATACCTCAAGACC-A
65 CTAATACTATCT-TTAGCGGCGTTTTACTATAAGCGCCACTAATTCTAGTATACATCAAGACCAA
55849452 AAC-TCTGCGTTTTGGTTAAGATATTTTGC
129 AACGT-TGCGTTTTGGTTAAGATATTTTGC
55849481 AGCGCTATGC
Statistics
Matches: 331, Mismatches: 45, Indels: 21
0.83 0.11 0.05
Matches are distributed among these distances:
225 1 0.00
226 29 0.09
227 62 0.19
228 46 0.14
229 153 0.46
230 38 0.11
231 2 0.01
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.30
Consensus pattern (227 bp):
ATACATCAAGACCAAAACTTGCGTTTTGGTTAAGATATTTTGCGGCGCTTTTACCAAAGCGCCGC
TAATACTATCTTTAGCGGCGTTTTACTATAAGCGCCACTAATTCTAGTATACATCAAGACCAAAA
CGTTGCGTTTTGGTTAAGATATTTTGCGGCACAGCCAAAAAGCGCCGCTAATACTATCCTTTAGC
GACGTTTTCCAATAAACGCCACTAACGCTAAC
Found at i:55849632 original size:204 final size:204
Alignment explanation
Indices: 55849309--55849691 Score: 488
Period size: 205 Copynumber: 1.9 Consensus size: 204
55849299 TTTCGGTAAA
* * * * *
55849309 CGCCACTAATTCTAGTATAAGCAAGACTAAAACGATGCGTTTTGGTTCAGATATTTCGCGGTGCT
1 CGCCACTAATTCTAGGATAAGCAAGACCAAAACGATGCGTTTCGGTTAAGATATTTCGCGGCGCT
* * *
55849374 TTCAAAAAGCGCCGCTAATACTATCTATTTGTGGCGTTTTCCTATAAGCGCCACTAATTCTAACA
66 TTCAAAAAGCGCCGCTAATAC-AGCTATTAGCGGCGTTTTCCTATAAGCGCCACTAATTCTAACA
* * * * *
55849439 TACCTCAAGAC-CAAACTCTGCGTTTTGGTTAAGATATTTTGCAGCGCTATGCTTTAACGGCATT
130 TACATCAAGACAAAAACGCTGCATTTTGGTTAAGAGATTTTGCAGCGCTATGCTTTAACGGCATT
55849503 TTCCCTTAAG
195 TTCCCTTAAG
* * *
55849513 CGCCACTAATTCTAGGATACATCAAGACCGAAACGATGCGTTTCGGTTAAGATATTTTTGCGGCG
1 CGCCACTAATTCTAGGATA-AGCAAGACCAAAACGATGCGTTTCGGTTAAGATA-TTTCGCGGCG
* *
55849578 CATTTCGCAAAA-CGCCGCTAATAC-GCT-TTAGCGGCGTTTT-CTCATAATCGCCACTAATTCT
64 C-TTTC-AAAAAGCGCCGCTAATACAGCTATTAGCGGCGTTTTCCT-ATAAGCGCCACTAATTCT
** *
55849639 AGTATACATCAAGACAAAAACGCTGCATTTTGGTTAAGAGATTTTGCGGCGCT
126 AACATACATCAAGACAAAAACGCTGCATTTTGGTTAAGAGATTTTGCAGCGCT
55849692 CTGTGGTAAA
Statistics
Matches: 152, Mismatches: 21, Indels: 11
0.83 0.11 0.06
Matches are distributed among these distances:
203 2 0.01
204 58 0.38
205 63 0.41
206 9 0.06
207 16 0.11
208 4 0.03
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.31
Consensus pattern (204 bp):
CGCCACTAATTCTAGGATAAGCAAGACCAAAACGATGCGTTTCGGTTAAGATATTTCGCGGCGCT
TTCAAAAAGCGCCGCTAATACAGCTATTAGCGGCGTTTTCCTATAAGCGCCACTAATTCTAACAT
ACATCAAGACAAAAACGCTGCATTTTGGTTAAGAGATTTTGCAGCGCTATGCTTTAACGGCATTT
TCCCTTAAG
Found at i:55851559 original size:8 final size:8
Alignment explanation
Indices: 55851548--55851590 Score: 52
Period size: 8 Copynumber: 5.5 Consensus size: 8
55851538 AATATTTATA
55851548 AAAATTCT
1 AAAATTCT
55851556 AAAATT-T
1 AAAATTCT
* * *
55851563 ATATTTAT
1 AAAATTCT
55851571 AAAATTCT
1 AAAATTCT
55851579 AAAATTCT
1 AAAATTCT
55851587 AAAA
1 AAAA
55851591 ATATATATAT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
7 5 0.17
8 24 0.83
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (8 bp):
AAAATTCT
Found at i:55851578 original size:23 final size:24
Alignment explanation
Indices: 55851539--55851584 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 24
55851529 AAATTAAAAA
55851539 ATATTTATAAAAATTCTAAAATTT
1 ATATTTATAAAAATTCTAAAATTT
55851563 ATATTTAT-AAAATTCTAAAATT
1 ATATTTATAAAAATTCTAAAATT
55851585 CTAAAAATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 14 0.64
24 8 0.36
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (24 bp):
ATATTTATAAAAATTCTAAAATTT
Found at i:55853532 original size:40 final size:39
Alignment explanation
Indices: 55853473--55853566 Score: 152
Period size: 40 Copynumber: 2.4 Consensus size: 39
55853463 CAATTCAAAC
*
55853473 AAAATTAAATTCAAACCATAAAATTAATCAACATATAAA
1 AAAATTAAATTCAAACCATAAAATCAATCAACATATAAA
*
55853512 AAAACTTAAATTCAAACCATAAAATCAATCGACATATAAA
1 AAAA-TTAAATTCAAACCATAAAATCAATCAACATATAAA
55853552 AAAATTTAAATTCAA
1 AAAA-TTAAATTCAA
55853567 TCTTGAAATA
Statistics
Matches: 51, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
39 4 0.08
40 47 0.92
ACGTcount: A:0.60, C:0.14, G:0.01, T:0.26
Consensus pattern (39 bp):
AAAATTAAATTCAAACCATAAAATCAATCAACATATAAA
Found at i:55854760 original size:21 final size:21
Alignment explanation
Indices: 55854731--55854773 Score: 52
Period size: 20 Copynumber: 2.0 Consensus size: 21
55854721 ACAATATTAA
*
55854731 AAACATTTTTTTTAAATTCATC
1 AAACA-TTTTATTAAATTCATC
*
55854753 AAAC-TTTTATTAAATTTATC
1 AAACATTTTATTAAATTCATC
55854773 A
1 A
55854774 CAAATAATTG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 15 0.79
22 4 0.21
ACGTcount: A:0.40, C:0.12, G:0.00, T:0.49
Consensus pattern (21 bp):
AAACATTTTATTAAATTCATC
Found at i:55854855 original size:19 final size:18
Alignment explanation
Indices: 55854823--55854859 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
55854813 TATATTTATA
55854823 AAATTTATTATTTATTTT
1 AAATTTATTATTTATTTT
*
55854841 AAATTTGATTCTTTATTTT
1 AAATTT-ATTATTTATTTT
55854860 TATAATATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.65
Consensus pattern (18 bp):
AAATTTATTATTTATTTT
Found at i:55856434 original size:15 final size:16
Alignment explanation
Indices: 55856409--55856442 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
55856399 TAAATATAAT
55856409 TTTATTATTTTAATAG
1 TTTATTATTTTAATAG
55856425 TTTA-TATTTTAATAG
1 TTTATTATTTTAATAG
55856440 TTT
1 TTT
55856443 TGGATCGGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 14 0.78
16 4 0.22
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (16 bp):
TTTATTATTTTAATAG
Found at i:55856513 original size:15 final size:15
Alignment explanation
Indices: 55856488--55856524 Score: 56
Period size: 15 Copynumber: 2.4 Consensus size: 15
55856478 ATAATACAAT
55856488 TTTATTATTTTAATAA
1 TTTA-TATTTTAATAA
*
55856504 TTTATATTTTTATAA
1 TTTATATTTTAATAA
55856519 TTTATA
1 TTTATA
55856525 AATAATTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 16 0.80
16 4 0.20
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (15 bp):
TTTATATTTTAATAA
Found at i:55856515 original size:80 final size:80
Alignment explanation
Indices: 55856358--55856513 Score: 253
Period size: 80 Copynumber: 2.0 Consensus size: 80
55856348 TATTTCTTTA
*
55856358 AGTTTTAGGTCGAAATTAAATTATATATTTTTACGATAATATAAATATAATTTTATTATTTTAAT
1 AGTTTTAGGTCGAAATTAAATTATATATTTTTACGATAATATAAATACAATTTTATTATTTTAAT
*
55856423 AGTTTATATTTTAAT
66 AATTTATATTTTAAT
* *
55856438 AGTTTT-GGATCGGAATTAAATTATATATTTTTAGGATAATAT-AATACAATTTTATTATTTTAA
1 AGTTTTAGG-TCGAAATTAAATTATATATTTTTACGATAATATAAATACAATTTTATTATTTTAA
55856501 TAATTTATATTTT
65 TAATTTATATTTT
55856514 TATAATTTAT
Statistics
Matches: 71, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
79 34 0.48
80 37 0.52
ACGTcount: A:0.38, C:0.03, G:0.08, T:0.51
Consensus pattern (80 bp):
AGTTTTAGGTCGAAATTAAATTATATATTTTTACGATAATATAAATACAATTTTATTATTTTAAT
AATTTATATTTTAAT
Found at i:55859828 original size:95 final size:95
Alignment explanation
Indices: 55859570--55860040 Score: 377
Period size: 95 Copynumber: 5.0 Consensus size: 95
55859560 AGGGATTAGT
** * * * * * * *
55859570 GCTTTAATCTACTCCACTGTAACTTCAGGGAGATTAGACTCGCATCTACAATTTACTCCACTGCA
1 GCTTTAATCTGTTCCACTGCAACTTCAGGGAAATAAGATTCGCATCTTCAATCTGCTCCACTGCA
* * *
55859635 ACTTTC-GGGAGATAATATTTGTAATTTGTA
66 AC-TTCAAGGAGATAAGATTTGTAACTTGTA
* * * * * *
55859665 GCCTTAATCTGTTTCACTGCAACTTTAAGGAAATAATATTCGCATCTTCAATCTGCTCCACTACA
1 GCTTTAATCTGTTCCACTGCAACTTCAGGGAAATAAGATTCGCATCTTCAATCTGCTCCACTGCA
* * *
55859730 ACTTCAAAGAGATTAGATTTGTAACTCGTA
66 ACTTCAAGGAGATAAGATTTGTAACTTGTA
* *
55859760 GCTTTGATCTGTTCCACTGCAACTTCAGGGAAATAAGATTCGCATCTTCAATCTGCTCCACTGTA
1 GCTTTAATCTGTTCCACTGCAACTTCAGGGAAATAAGATTCGCATCTTCAATCTGCTCCACTGCA
* * * *
55859825 ACTTTAGGGAGGTAAGACTTGTAAC-T-T-
66 ACTTCAAGGAGATAAGATTTGTAACTTGTA
* * ** * * * * * *
55859852 -C---AACCCGCCCCACTGTAACTTCAGAGAGATAATATTTGCCATAATGACTTCAATCT-ATCC
1 GCTTTAATCTGTTCCACTGCAACTTCAGGGAAATAAGATTCG-C---AT--CTTCAATCTGCT-C
* * * *
55859912 CACTGCAACTTC-AGGGGTATAGGATTTGTGATTTGTA
59 CACTGCAACTTCAAGGAG-ATAAGATTTGTAACTTGTA
* * * * *
55859949 GCTTTAATCTATTCCACTACAACTTCAGGGAAATGAGATTCGCATATTCAATCTGCTCCACTGTA
1 GCTTTAATCTGTTCCACTGCAACTTCAGGGAAATAAGATTCGCATCTTCAATCTGCTCCACTGCA
55860014 ACTTCAAGGAGATAAGATTTGTAACTT
66 ACTTCAAGGAGATAAGATTTGTAACTT
55860041 CAAGGAGATA
Statistics
Matches: 283, Mismatches: 75, Indels: 36
0.72 0.19 0.09
Matches are distributed among these distances:
88 27 0.10
89 1 0.00
91 1 0.00
92 2 0.01
93 5 0.02
94 32 0.11
95 180 0.64
96 6 0.02
97 2 0.01
98 1 0.00
100 1 0.00
101 25 0.09
ACGTcount: A:0.29, C:0.22, G:0.16, T:0.33
Consensus pattern (95 bp):
GCTTTAATCTGTTCCACTGCAACTTCAGGGAAATAAGATTCGCATCTTCAATCTGCTCCACTGCA
ACTTCAAGGAGATAAGATTTGTAACTTGTA
Found at i:55859841 original size:44 final size:44
Alignment explanation
Indices: 55859766--55859875 Score: 114
Period size: 44 Copynumber: 2.5 Consensus size: 44
55859756 CGTAGCTTTG
* * *
55859766 ATCTGTTCCACTGCAACTTCAGGGAAATAAGA-TTCGCATCTTCA
1 ATCTGCTCCACTGTAACTTCAGGGAAATAAGACTT-GCAACTTCA
* ** *
55859810 ATCTGCTCCACTGTAACTTTAGGGAGGTAAGACTTGTAACTTCA
1 ATCTGCTCCACTGTAACTTCAGGGAAATAAGACTTGCAACTTCA
* * *
55859854 ACCCGCCCCACTGTAACTTCAG
1 ATCTGCTCCACTGTAACTTCAG
55859876 AGAGATAATA
Statistics
Matches: 54, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
44 52 0.96
45 2 0.04
ACGTcount: A:0.27, C:0.27, G:0.17, T:0.28
Consensus pattern (44 bp):
ATCTGCTCCACTGTAACTTCAGGGAAATAAGACTTGCAACTTCA
Found at i:55860037 original size:23 final size:23
Alignment explanation
Indices: 55860010--55860066 Score: 114
Period size: 23 Copynumber: 2.5 Consensus size: 23
55860000 TCTGCTCCAC
55860010 TGTAACTTCAAGGAGATAAGATT
1 TGTAACTTCAAGGAGATAAGATT
55860033 TGTAACTTCAAGGAGATAAGATT
1 TGTAACTTCAAGGAGATAAGATT
55860056 TGTAACTTCAA
1 TGTAACTTCAA
55860067 TCTGCCCCAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.39, C:0.11, G:0.19, T:0.32
Consensus pattern (23 bp):
TGTAACTTCAAGGAGATAAGATT
Found at i:55860138 original size:162 final size:163
Alignment explanation
Indices: 55859898--55860192 Score: 427
Period size: 162 Copynumber: 1.8 Consensus size: 163
55859888 TGCCATAATG
* * * *
55859898 ACTTCAATCTATCCCACTGCAACTTCAGGGGTATAGGATTTGTGATTTGTAGCTTTAATCTATTC
1 ACTTCAATCTACCCCACTGCAACTTCAGGGGTATACGATTTGTAATTTGTAGCCTTAATCTATTC
* * *
55859963 CACTACAACTTCAGGGAAATGAGATTCGC-ATATTCAATCTGCTCCACTGTAACTTCA-AGGAGA
66 CACTACAACTTCAGGAAAATAAGATTCGCTATATTCAATCTGCTCCACTGCAACTTCAGA-GAGA
55860026 TAAGATTTGTAACTTCAAGGAGATAAGATTTGTA
130 TAAGATTTGTAACTTCAAGGAGATAAGATTTGTA
* * *
55860060 ACTTCAATCTGCCCCACTGCAACTTCAGGAGG-ATCCGATTTGTAATTTGTAGCCTTAATCTGTT
1 ACTTCAATCTACCCCACTGCAACTTCAGG-GGTATACGATTTGTAATTTGTAGCCTTAATCTATT
* *
55860124 CCAC-AGCAACTTCAGGAAAATAAGATTCGCTATCTTCAGTCTGCTCCACTGCAACTTCAGAGAG
65 CCACTA-CAACTTCAGGAAAATAAGATTCGCTATATTCAATCTGCTCCACTGCAACTTCAGAGAG
55860188 ATAAG
129 ATAAG
55860193 GTTTATAGCT
Statistics
Matches: 117, Mismatches: 12, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
161 1 0.01
162 80 0.68
163 35 0.30
164 1 0.01
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.31
Consensus pattern (163 bp):
ACTTCAATCTACCCCACTGCAACTTCAGGGGTATACGATTTGTAATTTGTAGCCTTAATCTATTC
CACTACAACTTCAGGAAAATAAGATTCGCTATATTCAATCTGCTCCACTGCAACTTCAGAGAGAT
AAGATTTGTAACTTCAAGGAGATAAGATTTGTA
Found at i:55872714 original size:22 final size:22
Alignment explanation
Indices: 55872688--55872761 Score: 87
Period size: 22 Copynumber: 3.3 Consensus size: 22
55872678 AAATAAATAT
55872688 TTAAATAAAGAAAATATAAACA
1 TTAAATAAAGAAAATATAAACA
* * *
55872710 TTAAATAATACGAACA-ACAAATA
1 TTAAATAA-A-GAAAATATAAACA
55872733 TTTAAATAAAGAAAATATAAACA
1 -TTAAATAAAGAAAATATAAACA
55872756 TTAAAT
1 TTAAAT
55872762 CTTTTAACAT
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
22 18 0.43
23 12 0.29
24 12 0.29
ACGTcount: A:0.64, C:0.07, G:0.04, T:0.26
Consensus pattern (22 bp):
TTAAATAAAGAAAATATAAACA
Found at i:55876070 original size:41 final size:41
Alignment explanation
Indices: 55876016--55876099 Score: 141
Period size: 41 Copynumber: 2.0 Consensus size: 41
55876006 ATTGGTTCCC
*
55876016 TTTGGGATTATTAGAGCCAGTTTAATAAAATAAGTAGACCT
1 TTTGGGATTATTAGAGCAAGTTTAATAAAATAAGTAGACCT
* *
55876057 TTTGGGATTATTAGAGTAAGTTTAATCAAATAAGTAGACCT
1 TTTGGGATTATTAGAGCAAGTTTAATAAAATAAGTAGACCT
55876098 TT
1 TT
55876100 CTGTTATTCT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.36, C:0.08, G:0.19, T:0.37
Consensus pattern (41 bp):
TTTGGGATTATTAGAGCAAGTTTAATAAAATAAGTAGACCT
Found at i:55877970 original size:6 final size:6
Alignment explanation
Indices: 55877959--55877989 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
55877949 GCTCAATCTC
55877959 TATTTT TATTTT TATTTT TATTTT TATTTT T
1 TATTTT TATTTT TATTTT TATTTT TATTTT T
55877990 CAATAATTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TATTTT
Found at i:55879453 original size:30 final size:30
Alignment explanation
Indices: 55879413--55879473 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
55879403 AATCACCATC
* * *
55879413 ATTTTATTTTATTTTATTTTTTACATTTTT
1 ATTTGATTTTAGTTTATTTTATACATTTTT
* *
55879443 ATTTGATTTTAGTTTGTTTTATACTTTTTT
1 ATTTGATTTTAGTTTATTTTATACATTTTT
55879473 A
1 A
55879474 AATTATTGTT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.20, C:0.03, G:0.05, T:0.72
Consensus pattern (30 bp):
ATTTGATTTTAGTTTATTTTATACATTTTT
Found at i:55882861 original size:8 final size:8
Alignment explanation
Indices: 55882838--55882899 Score: 74
Period size: 9 Copynumber: 7.6 Consensus size: 8
55882828 AGTGGAGGCA
*
55882838 AAAAAAAT
1 AAAAAAAC
55882846 AATAAAAAC
1 AA-AAAAAC
55882855 AATAAAAAC
1 AA-AAAAAC
55882864 AAAAAAAC
1 AAAAAAAC
55882872 --AAAAAC
1 AAAAAAAC
55882878 AATAAAAAC
1 AA-AAAAAC
55882887 AAAAAAAC
1 AAAAAAAC
55882895 AAAAA
1 AAAAA
55882900 CAAAAGAAAA
Statistics
Matches: 49, Mismatches: 1, Indels: 8
0.84 0.02 0.14
Matches are distributed among these distances:
6 6 0.12
8 19 0.39
9 24 0.49
ACGTcount: A:0.84, C:0.10, G:0.00, T:0.06
Consensus pattern (8 bp):
AAAAAAAC
Found at i:55882869 original size:17 final size:17
Alignment explanation
Indices: 55882838--55882896 Score: 79
Period size: 17 Copynumber: 3.6 Consensus size: 17
55882828 AGTGGAGGCA
*
55882838 AAAAAAATAATAAAAAC
1 AAAAAAACAATAAAAAC
55882855 AATAAAAACAA-AAAAAC
1 AA-AAAAACAATAAAAAC
55882872 --AAAAACAATAAAAAC
1 AAAAAAACAATAAAAAC
55882887 AAAAAAACAA
1 AAAAAAACAA
55882897 AAACAAAAGA
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
14 8 0.22
15 6 0.16
17 16 0.43
18 7 0.19
ACGTcount: A:0.83, C:0.10, G:0.00, T:0.07
Consensus pattern (17 bp):
AAAAAAACAATAAAAAC
Found at i:55882875 original size:14 final size:15
Alignment explanation
Indices: 55882858--55882904 Score: 71
Period size: 14 Copynumber: 3.3 Consensus size: 15
55882848 TAAAAACAAT
55882858 AAAAACAA-AAAAAC
1 AAAAACAACAAAAAC
*
55882872 AAAAACAATAAAAAC
1 AAAAACAACAAAAAC
55882887 AAAAA-AACAAAAAC
1 AAAAACAACAAAAAC
55882901 AAAA
1 AAAA
55882905 GAAAAAATCT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
14 20 0.65
15 11 0.35
ACGTcount: A:0.85, C:0.13, G:0.00, T:0.02
Consensus pattern (15 bp):
AAAAACAACAAAAAC
Found at i:55882875 original size:23 final size:23
Alignment explanation
Indices: 55882840--55882902 Score: 108
Period size: 23 Copynumber: 2.7 Consensus size: 23
55882830 TGGAGGCAAA
*
55882840 AAAAATAATAAAAACAATAAAAAC
1 AAAAA-AACAAAAACAATAAAAAC
55882864 AAAAAAACAAAAACAATAAAAAC
1 AAAAAAACAAAAACAATAAAAAC
55882887 AAAAAAACAAAAACAA
1 AAAAAAACAAAAACAA
55882903 AAGAAAAAAT
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
23 33 0.87
24 5 0.13
ACGTcount: A:0.83, C:0.11, G:0.00, T:0.06
Consensus pattern (23 bp):
AAAAAAACAAAAACAATAAAAAC
Found at i:55882882 original size:32 final size:31
Alignment explanation
Indices: 55882840--55882899 Score: 102
Period size: 32 Copynumber: 1.9 Consensus size: 31
55882830 TGGAGGCAAA
*
55882840 AAAAATAATAAAAACAATAAAAACAAAAAAAC
1 AAAAACAATAAAAACAA-AAAAACAAAAAAAC
55882872 AAAAACAATAAAAACAAAAAAACAAAAA
1 AAAAACAATAAAAACAAAAAAACAAAAA
55882900 CAAAAGAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
31 11 0.41
32 16 0.59
ACGTcount: A:0.83, C:0.10, G:0.00, T:0.07
Consensus pattern (31 bp):
AAAAACAATAAAAACAAAAAAACAAAAAAAC
Found at i:55883366 original size:13 final size:13
Alignment explanation
Indices: 55883350--55883399 Score: 57
Period size: 14 Copynumber: 3.8 Consensus size: 13
55883340 TCACTTGAAA
*
55883350 AAAAAACAAAAAC
1 AAAAAAGAAAAAC
*
55883363 -AAAAAGAAAAAA
1 AAAAAAGAAAAAC
55883375 AGAAAAAGAAAAAC
1 A-AAAAAGAAAAAC
*
55883389 GAAAAAGAAAA
1 AAAAAAGAAAA
55883400 GAGAAAAAGA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
12 10 0.32
13 10 0.32
14 11 0.35
ACGTcount: A:0.84, C:0.06, G:0.10, T:0.00
Consensus pattern (13 bp):
AAAAAAGAAAAAC
Found at i:55883374 original size:20 final size:21
Alignment explanation
Indices: 55883349--55883394 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 21
55883339 TTCACTTGAA
55883349 AAAAAAACAAAAACAAAAA-G
1 AAAAAAACAAAAACAAAAACG
* *
55883369 AAAAAAAGAAAAAGAAAAACG
1 AAAAAAACAAAAACAAAAACG
55883390 AAAAA
1 AAAAA
55883395 GAAAAGAGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 17 0.74
21 6 0.26
ACGTcount: A:0.85, C:0.07, G:0.09, T:0.00
Consensus pattern (21 bp):
AAAAAAACAAAAACAAAAACG
Found at i:55883380 original size:6 final size:6
Alignment explanation
Indices: 55883347--55883410 Score: 67
Period size: 6 Copynumber: 10.2 Consensus size: 6
55883337 ACTTCACTTG
* *
55883347 AAAA-A AAAACA AAAACA AAAAGAAA AAAAGA AAAAGA AAAACGA AAAAGA
1 AAAAGA AAAAGA AAAAGA AAAAG--A AAAAGA AAAAGA AAAA-GA AAAAGA
55883397 AAAGAGA AAAAGA A
1 AAA-AGA AAAAGA A
55883411 GAGGCCAAAG
Statistics
Matches: 53, Mismatches: 1, Indels: 9
0.84 0.02 0.14
Matches are distributed among these distances:
5 4 0.08
6 31 0.58
7 12 0.23
8 6 0.11
ACGTcount: A:0.83, C:0.05, G:0.12, T:0.00
Consensus pattern (6 bp):
AAAAGA
Found at i:55883387 original size:26 final size:26
Alignment explanation
Indices: 55883347--55883410 Score: 87
Period size: 26 Copynumber: 2.5 Consensus size: 26
55883337 ACTTCACTTG
*
55883347 AAAA-AAAAACAAAAAC-AAAAAGAAA
1 AAAAGAAAAAGAAAAACGAAAAAG-AA
55883372 AAAAGAAAAAGAAAAACGAAAAAGAA
1 AAAAGAAAAAGAAAAACGAAAAAGAA
*
55883398 AAGAGAAAAAGAA
1 AAAAGAAAAAGAA
55883411 GAGGCCAAAG
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
25 4 0.11
26 25 0.71
27 6 0.17
ACGTcount: A:0.83, C:0.05, G:0.12, T:0.00
Consensus pattern (26 bp):
AAAAGAAAAAGAAAAACGAAAAAGAA
Found at i:55883405 original size:13 final size:12
Alignment explanation
Indices: 55883347--55883410 Score: 67
Period size: 13 Copynumber: 5.1 Consensus size: 12
55883337 ACTTCACTTG
*
55883347 AAAA-AAAAACA
1 AAAAGAAAAAGA
*
55883358 AAAACAAAAAGAAA
1 AAAAGAAAAAG--A
55883372 AAAAGAAAAAGA
1 AAAAGAAAAAGA
55883384 AAAACGAAAAAGA
1 AAAA-GAAAAAGA
55883397 AAAGAGAAAAAGA
1 AAA-AGAAAAAGA
55883410 A
1 A
55883411 GAGGCCAAAG
Statistics
Matches: 46, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
11 4 0.09
12 10 0.22
13 20 0.43
14 12 0.26
ACGTcount: A:0.83, C:0.05, G:0.12, T:0.00
Consensus pattern (12 bp):
AAAAGAAAAAGA
Found at i:55883750 original size:45 final size:47
Alignment explanation
Indices: 55883682--55883769 Score: 117
Period size: 45 Copynumber: 1.9 Consensus size: 47
55883672 TTCATTTTAT
* *
55883682 TCATCTTTGTATTTTTGACAAAATACGCCATCTTGATTAATTTATTC
1 TCATCTTTGTATTCTAGACAAAATACGCCATCTTGATTAATTTATTC
** *
55883729 TCAT-TTTGTATTCTAGA-AAAATTTGCTATCTTGATTAATTT
1 TCATCTTTGTATTCTAGACAAAATACGCCATCTTGATTAATTT
55883770 GTTCATTTAG
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
45 21 0.58
46 11 0.31
47 4 0.11
ACGTcount: A:0.28, C:0.14, G:0.09, T:0.49
Consensus pattern (47 bp):
TCATCTTTGTATTCTAGACAAAATACGCCATCTTGATTAATTTATTC
Found at i:55884661 original size:134 final size:134
Alignment explanation
Indices: 55884497--55884768 Score: 490
Period size: 134 Copynumber: 2.0 Consensus size: 134
55884487 GAGCTGGTTA
* *
55884497 AAGATTGCAGATCTTGCCTTCCTGTATTTGGCAGCGAAGCAGATCGAAGATGGCAGATTTTACCT
1 AAGATTGCAGATCTTCCCTTCCTGTATTTGGCAGCGAAGCAGATCAAAGATGGCAGATTTTACCT
* * *
55884562 CCTTGACTACAGTGGAGTACATTGAAGCCGATAATTCTATCTCCCTGTATTTGGCAGTGGAATAG
66 CCCTGACTACAGTGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATTTGGCAGTAGAATAG
*
55884627 ATTG
131 AGTG
55884631 AAGATTGCAGATCTTCCCTTCCTGTATTTGGCAGCGAAGCAGATCAAAGATGGCAGATTTTACCT
1 AAGATTGCAGATCTTCCCTTCCTGTATTTGGCAGCGAAGCAGATCAAAGATGGCAGATTTTACCT
55884696 CCCTGACTACAGTGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATTTGGCAGTAGAATAG
66 CCCTGACTACAGTGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATTTGGCAGTAGAATAG
55884761 AGTG
131 AGTG
55884765 AAGA
1 AAGA
55884769 AAACCAGATC
Statistics
Matches: 132, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
134 132 1.00
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.29
Consensus pattern (134 bp):
AAGATTGCAGATCTTCCCTTCCTGTATTTGGCAGCGAAGCAGATCAAAGATGGCAGATTTTACCT
CCCTGACTACAGTGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATTTGGCAGTAGAATAG
AGTG
Found at i:55885058 original size:130 final size:131
Alignment explanation
Indices: 55884857--55885286 Score: 463
Period size: 130 Copynumber: 3.3 Consensus size: 131
55884847 CGAAAGAAAC
* ** *
55884857 CAGATCTTATCTCCCTAAGCAATAGTAGAGCAGGTCGAAGATGGCGGATTTTACCTCCCCAATTA
1 CAGATCTTATCTCCCTAAGCAATAGTGGAGCAGGTCGAAGATGGCGGATTTTACCTCCCTGACTA
* * * *****
55884922 CGGTGGAGTACATTAAAGCCAGTAGTTCTATCTCCCTG-GGCAACAGTGGAATAGAGTGAAGATT
66 CAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGATTTGGCAGTGGAATAGAGTGAAGATT
55884986 A
131 A
*
55884987 CAGATCTTATCTCCCTAAGCAATAGTGGAGCAGGTCGAAGATGGCGGATTTTACCTCCTTGACTA
1 CAGATCTTATCTCCCTAAGCAATAGTGGAGCAGGTCGAAGATGGCGGATTTTACCTCCCTGACTA
* * *
55885052 CAGTGGAGTACATTGAAGTC-GATAATTCTATCTCACTGTATTTGGCAGTGGAATAGATTGAAGA
66 CAGTGGAGTACATTGAAGCCAG-TAATTCTATCTCCCTG-ATTTGGCAGTGGAATAGAGTGAAGA
*
55885116 TTG
129 TTA
** * * * * * * * *
55885119 CAGATCTTGCCTTCCT--GTATTTGGCAGCGAAGCAGATCAAAGATGGCAGATTTTACCTCCCTG
1 CAGATCTTATCTCCCTAAGCA-AT---AGTGGAGCAGGTCGAAGATGGCGGATTTTACCTCCCTG
* * *
55885182 ACTACAGTGGAGTACATTGAAGCCAATAACTCTATCTCCCTGTATTTGGCAGTAGAATAGAGTGA
62 ACTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTG-ATTTGGCAGTGGAATAGAGTGA
**
55885247 AGAAAA
126 AGATTA
*
55885253 CCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAG
1 -CAGATCTTATCTCCCTAAGCAATAGTGGAGCAG
55885287 ATCACATCAA
Statistics
Matches: 245, Mismatches: 44, Indels: 19
0.80 0.14 0.06
Matches are distributed among these distances:
129 1 0.00
130 93 0.38
131 1 0.00
132 33 0.13
133 8 0.03
134 93 0.38
135 13 0.05
136 1 0.00
137 2 0.01
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.27
Consensus pattern (131 bp):
CAGATCTTATCTCCCTAAGCAATAGTGGAGCAGGTCGAAGATGGCGGATTTTACCTCCCTGACTA
CAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGATTTGGCAGTGGAATAGAGTGAAGATT
A
Found at i:55885364 original size:44 final size:41
Alignment explanation
Indices: 55885249--55885366 Score: 150
Period size: 40 Copynumber: 2.8 Consensus size: 41
55885239 TAGAGTGAAG
55885249 AAAACCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATC
1 AAAACCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATC
* * *
55885290 ACATCAAG-TCTTATCTCCCTAAGCAGTAGTGGAGCAGA-C
1 AAAACCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATC
*
55885329 GAAAGAAACCAGATCTTATCTCCCTAAGCAATAGTGGA
1 ---A-AAACCAGATCTTATCTCCCTAAGCAGTAGTGGA
55885367 ACAGGTCGAA
Statistics
Matches: 65, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
39 1 0.02
40 30 0.46
41 5 0.08
42 1 0.02
43 4 0.06
44 24 0.37
ACGTcount: A:0.35, C:0.24, G:0.19, T:0.22
Consensus pattern (41 bp):
AAAACCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATC
Found at i:55885442 original size:481 final size:480
Alignment explanation
Indices: 55884534--55885802 Score: 1928
Period size: 481 Copynumber: 2.7 Consensus size: 480
55884524 TTGGCAGCGA
* *
55884534 AGCAGATCGAAGATGGCAGATTTTACCTCCTTGACTACAGTGGAGTACATTGAAGCCGATAATTC
1 AGCAGGTCGAAGATGGCGGATTTTACCTCCTTGACTACAGTGGAGTACATTGAAG-CGATAATTC
*
55884599 TATCTCCCTGTATTTGGCAGTGGAATAGATTGAAGATTGCAGATCTTCCCTTCCTGTATTTGGCA
65 TATCTCCCTGTATTTGGCAGTGGAATAGATTGAAGATTGCAGATCTTACCTTCCTGTATTTGGCA
55884664 GCGAAGCAGATCAAAGATGGCAGATTTTACCTCCCTGACTACAGTGGAGTACATTGAAGCCGATA
130 GCGAAGCAGATCAAAGATGGCAGATTTTACCTCCCTGACTACAGTGGAGTACATTGAAGCCGATA
*
55884729 ACTCTATCTCCCTGTATTTGGCAGTAGAATAGAGTGAAGAAAACCAGATCATATCTCCCTAAGCA
195 ACTCTATCTCCCTGTATTTGGCAGTAGAATAGAGTGAAGAAAACCAGATCTTATCTCCCTAAGCA
*
55884794 GTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGTAGTAGTAGAGCAGACGAAAGAAACCA
260 GTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGTAGTAGTGGAGCAGACGAAAGAAACCA
* **
55884859 GATCTTATCTCCCTAAGCAATAGTAGAGCAGGTCGAAGATGGCGGATTTTACCTCCCCAATTACG
325 GATCTTATCTCCCTAAGCAATAGTAGAACAGGTCGAAGATGGCAAATTTTACCTCCCCAATTACG
55884924 GTGGAGTACATTAAAGCCAGTAGTTCTATCTCCCTGGGCAACAGTGGAATAGAGTGAAGATTACA
390 GTGGAGTACATTAAAGCCAGTAGTTCTATCTCCCTGGGCAACAGTGGAATAGAGTGAAGATTACA
55884989 GATCTTATCTCCCTAAGCAATAGTGG
455 GATCTTATCTCCCTAAGCAATAGTGG
55885015 AGCAGGTCGAAGATGGCGGATTTTACCTCCTTGACTACAGTGGAGTACATTGAAGTCGATAATTC
1 AGCAGGTCGAAGATGGCGGATTTTACCTCCTTGACTACAGTGGAGTACATTGAAG-CGATAATTC
* *
55885080 TATCTCACTGTATTTGGCAGTGGAATAGATTGAAGATTGCAGATCTTGCCTTCCTGTATTTGGCA
65 TATCTCCCTGTATTTGGCAGTGGAATAGATTGAAGATTGCAGATCTTACCTTCCTGTATTTGGCA
*
55885145 GCGAAGCAGATCAAAGATGGCAGATTTTACCTCCCTGACTACAGTGGAGTACATTGAAGCCAATA
130 GCGAAGCAGATCAAAGATGGCAGATTTTACCTCCCTGACTACAGTGGAGTACATTGAAGCCGATA
55885210 ACTCTATCTCCCTGTATTTGGCAGTAGAATAGAGTGAAGAAAACCAGATCTTATCTCCCTAAGCA
195 ACTCTATCTCCCTGTATTTGGCAGTAGAATAGAGTGAAGAAAACCAGATCTTATCTCCCTAAGCA
*
55885275 GTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAGTAGTGGAGCAGACGAAAGAAACCA
260 GTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGTAGTAGTGGAGCAGACGAAAGAAACCA
* * *
55885340 GATCTTATCTCCCTAAGCAATAGTGGAACAGGTCGAAGATGGCAAATTTTACCTCTCCTATTACG
325 GATCTTATCTCCCTAAGCAATAGTAGAACAGGTCGAAGATGGCAAATTTTACCTCCCCAATTACG
55885405 GTGGAGTACATTAAAGCCAGTAGTTCTATCTCCCTGGGCAACAGTGGAATAGAGTGAAGATTACA
390 GTGGAGTACATTAAAGCCAGTAGTTCTATCTCCCTGGGCAACAGTGGAATAGAGTGAAGATTACA
*
55885470 GATCTTATCTCCCTAGGCAATAGTGG
455 GATCTTATCTCCCTAAGCAATAGTGG
* * * * * *
55885496 AGCAGGTCGAAGATGGTGGATTTTACCTCAC-TGATTACGGTGGAGTACATTAAAGCCAGTAGTT
1 AGCAGGTCGAAGATGGCGGATTTTACCTC-CTTGACTACAGTGGAGTACATTGAAGCGA-TAATT
***** * * * * * *
55885560 CTATCTCCCTG--GGCAACAGTGGAATAGAGTGAAGATTACAGATCTTATCTCCCTAAGCA-AT-
64 CTATCTCCCTGTATTTGGCAGTGGAATAGATTGAAGATTGCAGATCTTACCTTCCT--GTATTTG
* * * * * * * *
55885621 --AGTGGAGCAGGTCGAAGATGGCGGATTTTACCTCCCTGATTACGGTGGAGTACATTGAAGCTG
127 GCAGCGAAGCAGATCAAAGATGGCAGATTTTACCTCCCTGACTACAGTGGAGTACATTGAAGCCG
* ** ***** * **
55885684 GTAGTTCTATCTCCCTG--GGCAACAGTGGAATAGAGTGAAGAGCA-CAGATCTTATCTCCCTAA
192 ATAACTCTATCTCCCTGTATTTGGCAGTAGAATAGAGTGAAGAAAACCAGATCTTATCTCCCTAA
* *
55885746 GTAGTAGTGGAGCAGATCACATCCAGTCTTATCTCCCTAAGTAGTAGTGGAGCAGAC
257 GCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGTAGTAGTGGAGCAGAC
55885803 TAAAAACACA
Statistics
Matches: 726, Mismatches: 58, Indels: 15
0.91 0.07 0.02
Matches are distributed among these distances:
474 72 0.10
475 19 0.03
477 68 0.09
479 33 0.05
480 3 0.00
481 530 0.73
482 1 0.00
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.26
Consensus pattern (480 bp):
AGCAGGTCGAAGATGGCGGATTTTACCTCCTTGACTACAGTGGAGTACATTGAAGCGATAATTCT
ATCTCCCTGTATTTGGCAGTGGAATAGATTGAAGATTGCAGATCTTACCTTCCTGTATTTGGCAG
CGAAGCAGATCAAAGATGGCAGATTTTACCTCCCTGACTACAGTGGAGTACATTGAAGCCGATAA
CTCTATCTCCCTGTATTTGGCAGTAGAATAGAGTGAAGAAAACCAGATCTTATCTCCCTAAGCAG
TAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGTAGTAGTGGAGCAGACGAAAGAAACCAG
ATCTTATCTCCCTAAGCAATAGTAGAACAGGTCGAAGATGGCAAATTTTACCTCCCCAATTACGG
TGGAGTACATTAAAGCCAGTAGTTCTATCTCCCTGGGCAACAGTGGAATAGAGTGAAGATTACAG
ATCTTATCTCCCTAAGCAATAGTGG
Found at i:55885481 original size:44 final size:44
Alignment explanation
Indices: 55885431--55885743 Score: 151
Period size: 44 Copynumber: 7.2 Consensus size: 44
55885421 CCAGTAGTTC
* *
55885431 TATCTCCCTGGGCAACAGTGGAATAGAGTGAAGATTACAGATCT
1 TATCTCCCTGGGCAACAGTGGAGTAGAGTGAAGATGACAGATCT
* * * *** *
55885475 TATCTCCCTAGGCAATAGTGGAGCAG-GTCGAAGATGGTGGATTT
1 TATCTCCCTGGGCAACAGTGGAGTAGAGT-GAAGATGACAGATCT
* * *** * * * *
55885519 TACCTCACT-GATTACGGTGGAGTACA-TTAA-A-GCCAGTAGT-T
1 TATCTCCCTGGGCAACAGTGGAGTAGAGTGAAGATGACAG-A-TCT
* *
55885560 CTATCTCCCTGGGCAACAGTGGAATAGAGTGAAGATTACAGATCT
1 -TATCTCCCTGGGCAACAGTGGAGTAGAGTGAAGATGACAGATCT
** * * * * *
55885605 TATCTCCCTAAGCAATAGTGGAGCAG-GTCGAAGATGGCGGATTT
1 TATCTCCCTGGGCAACAGTGGAGTAGAGT-GAAGATGACAGATCT
* *** * * * * ** *
55885649 TACCTCCCT-GATTACGGTGGAGTACATTGAAGCTGGTAGTTC-
1 TATCTCCCTGGGCAACAGTGGAGTAGAGTGAAGATGACAGATCT
*
55885691 TATCTCCCTGGGCAACAGTGGAATAGAGTGAAGA-GCACAGATCT
1 TATCTCCCTGGGCAACAGTGGAGTAGAGTGAAGATG-ACAGATCT
55885735 TATCTCCCT
1 TATCTCCCT
55885744 AAGTAGTAGT
Statistics
Matches: 185, Mismatches: 69, Indels: 30
0.65 0.24 0.11
Matches are distributed among these distances:
40 2 0.01
41 3 0.02
42 19 0.10
43 62 0.34
44 93 0.50
45 3 0.02
46 3 0.02
ACGTcount: A:0.28, C:0.20, G:0.26, T:0.27
Consensus pattern (44 bp):
TATCTCCCTGGGCAACAGTGGAGTAGAGTGAAGATGACAGATCT
Found at i:55885496 original size:130 final size:130
Alignment explanation
Indices: 55885338--55885760 Score: 713
Period size: 130 Copynumber: 3.3 Consensus size: 130
55885328 CGAAAGAAAC
* **
55885338 CAGATCTTATCTCCCTAAGCAATAGTGGAACAGGTCGAAGATGGCAAATTTTACCTCTCCT-ATT
1 CAGATCTTATCTCCCTAAGCAATAGTGGAGCAGGTCGAAGATGGCGGATTTTACCTC-CCTGATT
55885402 ACGGTGGAGTACATTAAAGCCAGTAGTTCTATCTCCCTGGGCAACAGTGGAATAGAGTGAAGATT
65 ACGGTGGAGTACATTAAAGCCAGTAGTTCTATCTCCCTGGGCAACAGTGGAATAGAGTGAAGATT
55885467 A
130 A
* * *
55885468 CAGATCTTATCTCCCTAGGCAATAGTGGAGCAGGTCGAAGATGGTGGATTTTACCTCACTGATTA
1 CAGATCTTATCTCCCTAAGCAATAGTGGAGCAGGTCGAAGATGGCGGATTTTACCTCCCTGATTA
55885533 CGGTGGAGTACATTAAAGCCAGTAGTTCTATCTCCCTGGGCAACAGTGGAATAGAGTGAAGATTA
66 CGGTGGAGTACATTAAAGCCAGTAGTTCTATCTCCCTGGGCAACAGTGGAATAGAGTGAAGATTA
55885598 CAGATCTTATCTCCCTAAGCAATAGTGGAGCAGGTCGAAGATGGCGGATTTTACCTCCCTGATTA
1 CAGATCTTATCTCCCTAAGCAATAGTGGAGCAGGTCGAAGATGGCGGATTTTACCTCCCTGATTA
* ** **
55885663 CGGTGGAGTACATTGAAGCTGGTAGTTCTATCTCCCTGGGCAACAGTGGAATAGAGTGAAGAGCA
66 CGGTGGAGTACATTAAAGCCAGTAGTTCTATCTCCCTGGGCAACAGTGGAATAGAGTGAAGATTA
* *
55885728 CAGATCTTATCTCCCTAAGTAGTAGTGGAGCAG
1 CAGATCTTATCTCCCTAAGCAATAGTGGAGCAG
55885761 ATCACATCCA
Statistics
Matches: 276, Mismatches: 16, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
129 2 0.01
130 274 0.99
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.26
Consensus pattern (130 bp):
CAGATCTTATCTCCCTAAGCAATAGTGGAGCAGGTCGAAGATGGCGGATTTTACCTCCCTGATTA
CGGTGGAGTACATTAAAGCCAGTAGTTCTATCTCCCTGGGCAACAGTGGAATAGAGTGAAGATTA
Found at i:55887437 original size:30 final size:30
Alignment explanation
Indices: 55887397--55887457 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
55887387 AATCACCATC
* * *
55887397 ATTTTATTTTATTTTATTTTTTACATTTTT
1 ATTTGATTTTAGTTTATTTTATACATTTTT
* *
55887427 ATTTGATTTTAGTTTGTTTTATACTTTTTT
1 ATTTGATTTTAGTTTATTTTATACATTTTT
55887457 A
1 A
55887458 AATTATTGTT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.20, C:0.03, G:0.05, T:0.72
Consensus pattern (30 bp):
ATTTGATTTTAGTTTATTTTATACATTTTT
Found at i:55888827 original size:16 final size:15
Alignment explanation
Indices: 55888793--55888840 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
55888783 TTAATAAATT
* *
55888793 AAAAAATTAAGTGTT
1 AAAAAATTAAATGTG
55888808 AAAAAATTAAATAGTG
1 AAAAAATTAAAT-GTG
55888824 -AAAAATTAAATGCTG
1 AAAAAATTAAATG-TG
55888839 AA
1 AA
55888841 TTTAAGTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
14 1 0.04
15 24 0.86
16 3 0.11
ACGTcount: A:0.58, C:0.02, G:0.12, T:0.27
Consensus pattern (15 bp):
AAAAAATTAAATGTG
Found at i:55890538 original size:24 final size:24
Alignment explanation
Indices: 55890511--55890557 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
55890501 AAACTCATTT
55890511 ATATATT-ATTACTTTATATATTAC
1 ATATATTCATT-CTTTATATATTAC
* *
55890535 ATATTTTCATTTTTTATATATTA
1 ATATATTCATTCTTTATATATTA
55890558 TTTATTCCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 17 0.85
25 3 0.15
ACGTcount: A:0.34, C:0.06, G:0.00, T:0.60
Consensus pattern (24 bp):
ATATATTCATTCTTTATATATTAC
Found at i:55890684 original size:15 final size:16
Alignment explanation
Indices: 55890654--55890686 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
55890644 TTTTCCCTTA
55890654 TTATTCATTTTCAAAT
1 TTATTCATTTTCAAAT
*
55890670 TTATT-ATTTTTAAAT
1 TTATTCATTTTCAAAT
55890685 TT
1 TT
55890687 TTTTACATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.30, C:0.06, G:0.00, T:0.64
Consensus pattern (16 bp):
TTATTCATTTTCAAAT
Found at i:55892226 original size:15 final size:16
Alignment explanation
Indices: 55892200--55892234 Score: 63
Period size: 15 Copynumber: 2.2 Consensus size: 16
55892190 AAAATATAAT
55892200 AATATAATAAGGAATA
1 AATATAATAAGGAATA
55892216 AATATAA-AAGGAATA
1 AATATAATAAGGAATA
55892231 AATA
1 AATA
55892235 CAAGCATGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 12 0.63
16 7 0.37
ACGTcount: A:0.66, C:0.00, G:0.11, T:0.23
Consensus pattern (16 bp):
AATATAATAAGGAATA
Found at i:55894314 original size:18 final size:20
Alignment explanation
Indices: 55894291--55894330 Score: 57
Period size: 18 Copynumber: 2.1 Consensus size: 20
55894281 GAAAGAAATT
55894291 TTATTTATTT-TTCAAA-AA
1 TTATTTATTTGTTCAAATAA
*
55894309 TTATTTTTTTGTTCAAATAA
1 TTATTTATTTGTTCAAATAA
55894329 TT
1 TT
55894331 GTTGGATTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 9 0.47
19 6 0.32
20 4 0.21
ACGTcount: A:0.33, C:0.05, G:0.03, T:0.60
Consensus pattern (20 bp):
TTATTTATTTGTTCAAATAA
Found at i:55895761 original size:19 final size:19
Alignment explanation
Indices: 55895737--55895885 Score: 96
Period size: 18 Copynumber: 8.1 Consensus size: 19
55895727 CACGAGATTT
55895737 TTTTTTGAAAACACGAAAA
1 TTTTTTGAAAACACGAAAA
* *
55895756 TTTTTT-AGAAATACGAGAA
1 TTTTTTGA-AAACACGAAAA
* * *
55895775 -TCTTAG-AAATACGAAAA
1 TTTTTTGAAAACACGAAAA
*
55895792 -TTTTTGAAAACACGGAAA
1 TTTTTTGAAAACACGAAAA
* * *
55895810 -TCTTT-AAAATACGAGAAT
1 TTTTTTGAAAACACGA-AAA
* **
55895828 TTTTTTTAAAACACAGAATT
1 TTTTTTGAAAACAC-GAAAA
55895848 TTTTTTGAAAACACGAAAA
1 TTTTTTGAAAACACGAAAA
* *
55895867 -TTGTTGAAAACACAAAAA
1 TTTTTTGAAAACACGAAAA
55895885 T
1 T
55895886 ATTGATAAAT
Statistics
Matches: 101, Mismatches: 21, Indels: 16
0.73 0.15 0.12
Matches are distributed among these distances:
17 21 0.21
18 35 0.35
19 22 0.22
20 21 0.21
21 2 0.02
ACGTcount: A:0.46, C:0.10, G:0.11, T:0.32
Consensus pattern (19 bp):
TTTTTTGAAAACACGAAAA
Found at i:55895782 original size:17 final size:17
Alignment explanation
Indices: 55895760--55895827 Score: 59
Period size: 17 Copynumber: 3.9 Consensus size: 17
55895750 CGAAAATTTT
55895760 TTAGAAATACGAGAATC
1 TTAGAAATACGAGAATC
* *
55895777 TTAGAAATACGAAAATT
1 TTAGAAATACGAGAATC
* *
55895794 TTTGAAAACACG-GAAATC
1 TTAG-AAATACGAG-AATC
55895812 TTTA-AAATACGAGAAT
1 -TTAGAAATACGAGAAT
55895828 TTTTTTTAAA
Statistics
Matches: 39, Mismatches: 8, Indels: 8
0.71 0.15 0.15
Matches are distributed among these distances:
17 27 0.69
18 10 0.26
19 2 0.05
ACGTcount: A:0.49, C:0.10, G:0.15, T:0.26
Consensus pattern (17 bp):
TTAGAAATACGAGAATC
Found at i:55895812 original size:35 final size:36
Alignment explanation
Indices: 55895744--55895831 Score: 101
Period size: 35 Copynumber: 2.5 Consensus size: 36
55895734 TTTTTTTTTG
* * *
55895744 AAAACACGAAAATTTTTTAGAAATACGAGAATC-TT
1 AAAATACGAAAATTTTTGAGAAACACGAGAATCTTT
55895779 AGAAATACGAAAATTTTTGA-AAACACG-GAAATCTTT
1 A-AAATACGAAAATTTTTGAGAAACACGAG-AATCTTT
*
55895815 AAAATACGAGAATTTTT
1 AAAATACGAAAATTTTT
55895832 TTTAAAACAC
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
34 1 0.02
35 26 0.57
36 19 0.41
ACGTcount: A:0.48, C:0.10, G:0.12, T:0.30
Consensus pattern (36 bp):
AAAATACGAAAATTTTTGAGAAACACGAGAATCTTT
Done.