Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007952.1 Hibiscus syriacus cultivar Beakdansim tig00110377_pilon, whole genome shotgun sequence
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: 3169409
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 16
Found at i:518795 original size:2 final size:2
Alignment explanation
Indices: 518788--518864 Score: 136
Period size: 2 Copynumber: 38.5 Consensus size: 2
518778 TTAGGAGTTG
518788 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
518830 TA TA TA TA TA TA TA TA TA TA TA TA TG CA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
518865 GCATCATACG
Statistics
Matches: 71, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 71 1.00
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (2 bp):
TA
Found at i:519825 original size:20 final size:20
Alignment explanation
Indices: 519797--519862 Score: 64
Period size: 20 Copynumber: 3.3 Consensus size: 20
519787 GAACCGGTGT
*
519797 AAACTGACTAAGAACCGACA
1 AAACCGACTAAGAACCGACA
*
519817 AAACCGACTGAA-AACCGATA
1 AAACCGACT-AAGAACCGACA
* *
519837 AAACC-AGCTTAGAACCAACA
1 AAACCGA-CTAAGAACCGACA
519857 AAACCG
1 AAACCG
519863 GCTTGAACCG
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
19 2 0.05
20 33 0.89
21 2 0.05
ACGTcount: A:0.50, C:0.27, G:0.14, T:0.09
Consensus pattern (20 bp):
AAACCGACTAAGAACCGACA
Found at i:519866 original size:20 final size:20
Alignment explanation
Indices: 519807--519872 Score: 71
Period size: 20 Copynumber: 3.4 Consensus size: 20
519797 AAACTGACTA
* *
519807 AGAACCGACAAAACCGACTG
1 AGAACCGACAAAACCGGCTT
* * *
519827 AAAACCGATAAAACCAGCTT
1 AGAACCGACAAAACCGGCTT
*
519847 AGAACCAACAAAACCGGCTT
1 AGAACCGACAAAACCGGCTT
519867 -GAACCG
1 AGAACCG
519873 CCGGTTCTGT
Statistics
Matches: 36, Mismatches: 10, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
19 5 0.14
20 31 0.86
ACGTcount: A:0.45, C:0.29, G:0.17, T:0.09
Consensus pattern (20 bp):
AGAACCGACAAAACCGGCTT
Found at i:528111 original size:13 final size:13
Alignment explanation
Indices: 528093--528136 Score: 63
Period size: 13 Copynumber: 3.5 Consensus size: 13
528083 ATTATTTGAG
528093 ATTGTGAATATTA
1 ATTGTGAATATTA
528106 ATTGTGAATATTA
1 ATTGTGAATATTA
* *
528119 AATGTG-CTATTA
1 ATTGTGAATATTA
528131 ATTGTG
1 ATTGTG
528137 GGAATTAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
12 10 0.36
13 18 0.64
ACGTcount: A:0.34, C:0.02, G:0.18, T:0.45
Consensus pattern (13 bp):
ATTGTGAATATTA
Found at i:528198 original size:2 final size:2
Alignment explanation
Indices: 528191--528249 Score: 109
Period size: 2 Copynumber: 29.5 Consensus size: 2
528181 TGTAAATAAT
528191 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
528233 TA TA TA TA TA TA AA TA T
1 TA TA TA TA TA TA TA TA T
528250 TTACTTTCAT
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:528636 original size:233 final size:236
Alignment explanation
Indices: 528227--528846 Score: 1165
Period size: 233 Copynumber: 2.6 Consensus size: 236
528217 TATATATATA
* *
528227 TATATATATATATATATAAATATTTACTTTCATTTTTATTTATTTTGTAGGTTACATAGAATGGC
1 TATATATATTTATAAATAAATATTTACTTTCATTTTTATTTATTTTGTAGGTTACATAGAATGGC
*
528292 CCAATTGAAAAATATAAAACGAATCGAAAGCCCACAACTCGGCCCAATCCACCAACCCAAAATGA
66 CCAATTGAAAAATATAAAACGAATCGAAGGCCCACAACTCGGCCCAATCCACCAACCCAAAATGA
528357 CCTGAAGTCCTAAAAAATACCCAATTGAATATTAAATGTGCTATTAATTGTGGGAATTAATTGTA
131 CCTGAAGTCCTAAAAAATACCCAATTGAATATTAAATGTGCTATTAATTGTGGGAATTAATTGTA
528422 ATTGTGTTAATTATA-TTATTATAATTAATTTGTAAATAA-
196 ATTGTGTTAATTATATTTATTATAATTAATTTGTAAATAAT
528461 T-TATATATTTATAAATAAATATTTACTTTCATTTTTATTTATTTTGTAGGTTACATAGAATGGC
1 TATATATATTTATAAATAAATATTTACTTTCATTTTTATTTATTTTGTAGGTTACATAGAATGGC
528525 CCAATTGAAAAATATAAAACGAATCGAAGGCCCACAACTCGGCCCAATCCACCAACCCAAAATGA
66 CCAATTGAAAAATATAAAACGAATCGAAGGCCCACAACTCGGCCCAATCCACCAACCCAAAATGA
*
528590 CCTGAAGTCCTAAAAAATACCCAATTGAATATTAAATGTGCTATTAATTGTGGGAATTAATTTTA
131 CCTGAAGTCCTAAAAAATACCCAATTGAATATTAAATGTGCTATTAATTGTGGGAATTAATTGTA
528655 ATTGTGTTAATTATATTTATTATAATTAATTTGTAAATAAT
196 ATTGTGTTAATTATATTTATTATAATTAATTTGTAAATAAT
528696 TATATATATTTATAAATAAATATTTACTTTCATTTTTATTTATTTTGTAGGTTACATAGAATGGC
1 TATATATATTTATAAATAAATATTTACTTTCATTTTTATTTATTTTGTAGGTTACATAGAATGGC
*
528761 CCAATTGAAAAATATAAAACGAATCGAAGGCCCACAACTCGACCCAATCCACCAACCCAAAATGA
66 CCAATTGAAAAATATAAAACGAATCGAAGGCCCACAACTCGGCCCAATCCACCAACCCAAAATGA
*
528826 CCCGAAGTCCTAAAAAATACC
131 CCTGAAGTCCTAAAAAATACC
528847 AGACCCAAGA
Statistics
Matches: 377, Mismatches: 6, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
233 204 0.54
234 25 0.07
235 1 0.00
236 147 0.39
ACGTcount: A:0.40, C:0.15, G:0.11, T:0.34
Consensus pattern (236 bp):
TATATATATTTATAAATAAATATTTACTTTCATTTTTATTTATTTTGTAGGTTACATAGAATGGC
CCAATTGAAAAATATAAAACGAATCGAAGGCCCACAACTCGGCCCAATCCACCAACCCAAAATGA
CCTGAAGTCCTAAAAAATACCCAATTGAATATTAAATGTGCTATTAATTGTGGGAATTAATTGTA
ATTGTGTTAATTATATTTATTATAATTAATTTGTAAATAAT
Found at i:528666 original size:19 final size:20
Alignment explanation
Indices: 528633--528672 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
528623 AAATGTGCTA
528633 TTAATTGTGGGAATTA-ATT
1 TTAATTGTGGGAATTATATT
**
528652 TTAATTGTGTTAATTATATT
1 TTAATTGTGGGAATTATATT
528672 T
1 T
528673 ATTATAATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.30, C:0.00, G:0.15, T:0.55
Consensus pattern (20 bp):
TTAATTGTGGGAATTATATT
Found at i:529194 original size:29 final size:30
Alignment explanation
Indices: 529126--529199 Score: 80
Period size: 29 Copynumber: 2.5 Consensus size: 30
529116 GGCGATTTGA
*
529126 CCTAACTAACACCCTATAGACCTATATTTC
1 CCTAACTAACACCCTATAGACCAATATTTC
** * *
529156 CGGATA-TAACACCGT-TTGACCAATATTTC
1 CCTA-ACTAACACCCTATAGACCAATATTTC
529185 CCTAACTAACACCCT
1 CCTAACTAACACCCT
529200 TTTGGCTGAA
Statistics
Matches: 34, Mismatches: 8, Indels: 5
0.72 0.17 0.11
Matches are distributed among these distances:
28 1 0.03
29 22 0.65
30 10 0.29
31 1 0.03
ACGTcount: A:0.32, C:0.32, G:0.07, T:0.28
Consensus pattern (30 bp):
CCTAACTAACACCCTATAGACCAATATTTC
Found at i:530712 original size:12 final size:12
Alignment explanation
Indices: 530695--530721 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
530685 AAAATTTCGT
530695 TAATCCATTACG
1 TAATCCATTACG
530707 TAATCCATTACG
1 TAATCCATTACG
530719 TAA
1 TAA
530722 GGCAACATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.37, C:0.22, G:0.07, T:0.33
Consensus pattern (12 bp):
TAATCCATTACG
Found at i:530888 original size:23 final size:23
Alignment explanation
Indices: 530829--530889 Score: 56
Period size: 23 Copynumber: 2.7 Consensus size: 23
530819 TAAACGCAAC
* *
530829 AAATGAAT-AAAATGACTATATA
1 AAATAAATAAAAATGACTATAAA
*
530851 AAATAAA-ACATAATGA-TAATAAA
1 AAATAAATA-AAAATGACT-ATAAA
530874 AAATAAATAAAAATGA
1 AAATAAATAAAAATGA
530890 AGGCAAAATA
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
22 7 0.23
23 23 0.74
24 1 0.03
ACGTcount: A:0.67, C:0.03, G:0.07, T:0.23
Consensus pattern (23 bp):
AAATAAATAAAAATGACTATAAA
Found at i:533050 original size:15 final size:15
Alignment explanation
Indices: 533030--533062 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
533020 TTAGCTAGGT
*
533030 GGGCGGATGTGGGGC
1 GGGCGGATGCGGGGC
533045 GGGCGGATGCGGGGC
1 GGGCGGATGCGGGGC
533060 GGG
1 GGG
533063 TAATGTCTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.06, C:0.15, G:0.70, T:0.09
Consensus pattern (15 bp):
GGGCGGATGCGGGGC
Found at i:533367 original size:29 final size:29
Alignment explanation
Indices: 533290--533370 Score: 126
Period size: 29 Copynumber: 2.8 Consensus size: 29
533280 CAACCTTTGC
* * *
533290 CCAATATTTCCTTAATTAAAACCCTTTGA
1 CCAATATTTCCCTAATTAACACCCTTTAA
*
533319 CCAATATTTTCCTAATTAACACCCTTTAA
1 CCAATATTTCCCTAATTAACACCCTTTAA
533348 CCAATATTTCCCTAATTAACACC
1 CCAATATTTCCCTAATTAACACC
533371 TTTTTGTTGA
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 47 1.00
ACGTcount: A:0.35, C:0.28, G:0.01, T:0.36
Consensus pattern (29 bp):
CCAATATTTCCCTAATTAACACCCTTTAA
Found at i:535176 original size:22 final size:21
Alignment explanation
Indices: 535142--535185 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
535132 ATAATTATTT
*
535142 AAAAAATTAAATAAAAATATA
1 AAAAAATTAAATAAAAAAATA
*
535163 AAAAATATTTAATAAAAAAATA
1 AAAAA-ATTAAATAAAAAAATA
535185 A
1 A
535186 TTTTTTATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (21 bp):
AAAAAATTAAATAAAAAAATA
Found at i:536232 original size:29 final size:28
Alignment explanation
Indices: 536200--536337 Score: 102
Period size: 29 Copynumber: 4.8 Consensus size: 28
536190 AATTATTGTT
* *
536200 AGGTGATATTCTGGGAAATATTTCGATAA
1 AGGTGACATT-TGGGAATTATTTCGATAA
* * *
536229 AGGTGACATTT-TGATATTATTTTGAAAAA
1 AGGTGACATTTGGGA-ATTATTTCG-ATAA
* * *
536258 AGGTGATATTATGGGAAATATTTTGA-AA
1 AGGTGACATT-TGGGAATTATTTCGATAA
*
536286 AGGTAACATATTGGGAATTATTTCG-TAAA
1 AGGTGACAT-TTGGGAATTATTTCGAT-AA
*
536315 AGGTGACACTCTGGGAATTATTT
1 AGGTGACA-TTTGGGAATTATTT
536338 TTAAGAAGTG
Statistics
Matches: 87, Mismatches: 14, Indels: 16
0.74 0.12 0.14
Matches are distributed among these distances:
27 2 0.02
28 29 0.33
29 44 0.51
30 10 0.11
31 2 0.02
ACGTcount: A:0.36, C:0.06, G:0.22, T:0.36
Consensus pattern (28 bp):
AGGTGACATTTGGGAATTATTTCGATAA
Found at i:536330 original size:57 final size:58
Alignment explanation
Indices: 536200--536338 Score: 158
Period size: 58 Copynumber: 2.4 Consensus size: 58
536190 AATTATTGTT
* * * *
536200 AGGTGATATTCTGGGAAATATTTCGATAAAGGTGACATTTTGATATTATTTTGAAAAA
1 AGGTGATATTCTGGGAAATATTTTGATAAAGGTAACATTTGGATATTATTTCGAAAAA
* *
536258 AGGTGATATTATGGGAAATATTTTGA-AAAGGTAACATATTGGGA-ATTATTTCG-TAAA
1 AGGTGATATTCTGGGAAATATTTTGATAAAGGTAACAT-TT-GGATATTATTTCGAAAAA
* * *
536315 AGGTGACACTCTGGGAATTATTTT
1 AGGTGATATTCTGGGAAATATTTT
536339 TAAGAAGTGA
Statistics
Matches: 69, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
57 33 0.48
58 34 0.49
59 2 0.03
ACGTcount: A:0.35, C:0.06, G:0.22, T:0.37
Consensus pattern (58 bp):
AGGTGATATTCTGGGAAATATTTTGATAAAGGTAACATTTGGATATTATTTCGAAAAA
Found at i:536361 original size:57 final size:58
Alignment explanation
Indices: 536211--536361 Score: 155
Period size: 57 Copynumber: 2.6 Consensus size: 58
536201 GGTGATATTC
* * * * *
536211 TGGGAAATATTTCGATAAAGGTGACATTTTGA-TATTATTTTGAAAAAAGGTGATATTA
1 TGGGAAATATTTTGA-AAAGGTGACATTTTGAGAATTATTTCGAAAAAAGGTGACACTA
* * * * *
536269 TGGGAAATATTTTGAAAAGGTAACATATTGGGAATTATTTCG-TAAAAGGTGACACTC
1 TGGGAAATATTTTGAAAAGGTGACATTTTGAGAATTATTTCGAAAAAAGGTGACACTA
* *
536326 TGGGAATTATTTTTAAGAA-GTGACATTTTGAGAATT
1 TGGGAAATATTTTGAA-AAGGTGACATTTTGAGAATT
536362 TTCAAATGTT
Statistics
Matches: 76, Mismatches: 15, Indels: 5
0.79 0.16 0.05
Matches are distributed among these distances:
57 52 0.68
58 24 0.32
ACGTcount: A:0.36, C:0.05, G:0.22, T:0.36
Consensus pattern (58 bp):
TGGGAAATATTTTGAAAAGGTGACATTTTGAGAATTATTTCGAAAAAAGGTGACACTA
Found at i:542770 original size:29 final size:28
Alignment explanation
Indices: 542738--542896 Score: 106
Period size: 29 Copynumber: 5.6 Consensus size: 28
542728 AATTATTGTT
* * *
542738 AGGTGATATTCTGAGAAATATTTCGATAA
1 AGGTGACATTATGGGAAATATTTCGA-AA
* * *
542767 AGGTGACATTTTGGGAATTATTTTGAAA
1 AGGTGACATTATGGGAAATATTTCGAAA
*
542795 A-ATGACATTATGGGAAATATTTCGAAAA
1 AGGTGACATTATGGGAAATATTTCG-AAA
** * *
542823 AGGAAACA-TATTGGGAATTATTTTGTAAA
1 AGGTGACATTA-TGGGAAATATTTCG-AAA
* * * **
542852 AGGTGACACTCTGGGAATTATTTAAAAA
1 AGGTGACATTATGGGAAATATTTCGAAA
* *
542880 AAGTGACATTTTGGGAA
1 AGGTGACATTATGGGAA
542897 TTTTCAAATG
Statistics
Matches: 103, Mismatches: 23, Indels: 9
0.76 0.17 0.07
Matches are distributed among these distances:
27 19 0.18
28 26 0.25
29 57 0.55
30 1 0.01
ACGTcount: A:0.39, C:0.06, G:0.22, T:0.33
Consensus pattern (28 bp):
AGGTGACATTATGGGAAATATTTCGAAA
Found at i:542815 original size:56 final size:58
Alignment explanation
Indices: 542752--542898 Score: 183
Period size: 56 Copynumber: 2.6 Consensus size: 58
542742 GATATTCTGA
* *
542752 GAAATATTTCGATAAAGGTGACATTTTGGGAATTATTTTG-AAAA-ATGACATTATGG
1 GAAATATTTCGAAAAAGGTGACATTTTGGGAATTATTTTGTAAAAGATGACACTATGG
** * * *
542808 GAAATATTTCGAAAAAGGAAACATATTGGGAATTATTTTGTAAAAGGTGACACTCTGG
1 GAAATATTTCGAAAAAGGTGACATTTTGGGAATTATTTTGTAAAAGATGACACTATGG
* * *
542866 GAATTATTT-AAAAAAAGTGACATTTTGGGAATT
1 GAAATATTTCGAAAAAGGTGACATTTTGGGAATT
542899 TTCAAATGTT
Statistics
Matches: 76, Mismatches: 13, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
56 36 0.47
57 23 0.30
58 17 0.22
ACGTcount: A:0.39, C:0.06, G:0.21, T:0.33
Consensus pattern (58 bp):
GAAATATTTCGAAAAAGGTGACATTTTGGGAATTATTTTGTAAAAGATGACACTATGG
Found at i:542894 original size:28 final size:28
Alignment explanation
Indices: 542769--542898 Score: 129
Period size: 29 Copynumber: 4.6 Consensus size: 28
542759 TTCGATAAAG
*
542769 GTGACATTTTGGGAATTATTTTGAAAAA
1 GTGACATTTTGGGAATTATTTAGAAAAA
* * *
542797 -TGACATTATGGGAAATATTTCGAAAAA
1 GTGACATTTTGGGAATTATTTAGAAAAA
* * *
542824 G-GAAACATATTGGGAATTATTTTGTAAAAG
1 GTG--ACATTTTGGGAATTATTTAG-AAAAA
* * *
542854 GTGACACTCTGGGAATTATTTAAAAAAA
1 GTGACATTTTGGGAATTATTTAGAAAAA
542882 GTGACATTTTGGGAATT
1 GTGACATTTTGGGAATT
542899 TTCAAATGTT
Statistics
Matches: 81, Mismatches: 16, Indels: 10
0.76 0.15 0.09
Matches are distributed among these distances:
27 25 0.31
28 19 0.23
29 31 0.38
30 5 0.06
31 1 0.01
ACGTcount: A:0.38, C:0.06, G:0.22, T:0.34
Consensus pattern (28 bp):
GTGACATTTTGGGAATTATTTAGAAAAA
Found at i:545346 original size:14 final size:14
Alignment explanation
Indices: 545327--545354 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
545317 TAAAATTGCT
545327 AATGAATTATAGGG
1 AATGAATTATAGGG
545341 AATGAATTATAGGG
1 AATGAATTATAGGG
545355 TGAATTACAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.29, T:0.29
Consensus pattern (14 bp):
AATGAATTATAGGG
Found at i:545360 original size:12 final size:13
Alignment explanation
Indices: 545328--545361 Score: 52
Period size: 14 Copynumber: 2.6 Consensus size: 13
545318 AAAATTGCTA
545328 ATGAATTATAGGG
1 ATGAATTATAGGG
545341 AATGAATTATAGGG
1 -ATGAATTATAGGG
545355 -TGAATTA
1 ATGAATTA
545362 CATATATAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 7 0.35
14 13 0.65
ACGTcount: A:0.41, C:0.00, G:0.26, T:0.32
Consensus pattern (13 bp):
ATGAATTATAGGG
Found at i:548029 original size:40 final size:40
Alignment explanation
Indices: 547974--548173 Score: 328
Period size: 40 Copynumber: 5.0 Consensus size: 40
547964 TGCAGGTTTA
*
547974 TAATACACTTCGGTGTATATGGTGGGCACAACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
*
548014 TAATACACTTCGGTGTATATGGTGGGCATGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
* *
548054 TAATACACTTCGGTGTATTTGGTGGACACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
*
548094 TAATACACTTCGGTGTATATGGTGGGCATGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
*
548134 TAATACACTTTGGTGTATATGGTGGGGGCACGACCTTATG
1 TAATACACTTCGGTGTATATGGT--GGGCACGACCTTATG
548174 CGTAGGACTA
Statistics
Matches: 148, Mismatches: 10, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
40 134 0.91
42 14 0.09
ACGTcount: A:0.23, C:0.16, G:0.27, T:0.34
Consensus pattern (40 bp):
TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
Found at i:548370 original size:91 final size:90
Alignment explanation
Indices: 548254--548540 Score: 429
Period size: 91 Copynumber: 3.2 Consensus size: 90
548244 TGGTATATGG
* *
548254 TTATGGA-ATAATGGCAAGTGTATTGGTAAAATAAGCTTACGAGCTTATGGGATTAAATGGTAAG
1 TTATGGATA-AATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGGGATTAAATGGTAAG
*
548318 TATATTGGTAAAATAAGCTTATGATC
65 TATATTGGTAAAATAAGCTTATGAGC
* *
548344 TTATGGAATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGGGATTTAATGGTATG
1 TTATGG-ATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGGGATTAAATGGTAAG
548409 TATATTGGTAAAATAAGCTTATGAGC
65 TATATTGGTAAAATAAGCTTATGAGC
* * *
548435 TTATGG--AAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTAT-GTAATAAATGGTAGGT
1 TTATGGATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGGGATTAAATGGTAAGT
*
548497 ATATTGGTAAAATAAGCTTACGAGC
66 ATATTGGTAAAATAAGCTTATGAGC
*
548522 TTATAGGATAAATGATAAG
1 TTAT-GGATAAATGGTAAG
548541 AAATTTTATA
Statistics
Matches: 181, Mismatches: 11, Indels: 10
0.90 0.05 0.05
Matches are distributed among these distances:
87 40 0.22
88 42 0.23
90 15 0.08
91 83 0.46
92 1 0.01
ACGTcount: A:0.38, C:0.06, G:0.23, T:0.33
Consensus pattern (90 bp):
TTATGGATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGGGATTAAATGGTAAGT
ATATTGGTAAAATAAGCTTATGAGC
Found at i:548371 original size:45 final size:45
Alignment explanation
Indices: 548254--548540 Score: 404
Period size: 45 Copynumber: 6.4 Consensus size: 45
548244 TGGTATATGG
* *
548254 TTATGGAAT-AATGGCAAGTGTATTGGTAAAATAAGCTTACGAGC
1 TTATGGAATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGC
* * *
548298 TTATGGGATTAAATGGTAAGTATATTGGTAAAATAAGCTTATGATC
1 TTAT-GGAATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGC
548344 TTATGGAATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGC
1 TTATGGAATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGC
* * * *
548389 TTATGGGATTTAATGGTATGTATATTGGTAAAATAAGCTTATGAGC
1 TTAT-GGAATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGC
548435 TTATGG---AAATGGTAAGTATATTGGTAAAATAAGCTTACGAGC
1 TTATGGAATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGC
* *
548477 TTATGTAATAAATGGTAGGTATATTGGTAAAATAAGCTTACGAGC
1 TTATGGAATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGC
*
548522 TTATAGG-ATAAATGATAAG
1 TTAT-GGAATAAATGGTAAG
548541 AAATTTTATA
Statistics
Matches: 216, Mismatches: 20, Indels: 13
0.87 0.08 0.05
Matches are distributed among these distances:
42 38 0.18
44 4 0.02
45 97 0.45
46 77 0.36
ACGTcount: A:0.38, C:0.06, G:0.23, T:0.33
Consensus pattern (45 bp):
TTATGGAATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGC
Found at i:548504 original size:133 final size:135
Alignment explanation
Indices: 548274--548530 Score: 428
Period size: 133 Copynumber: 1.9 Consensus size: 135
548264 ATGGCAAGTG
548274 TATTGGTAAAATAAGCTTACGAGCTTATGGGATTAAATGGTAAGTATATTGGTAAAATAAGCTTA
1 TATTGGTAAAATAAGCTTACGAGCTTATGGG--TAAATGGTAAGTATATTGGTAAAATAAGCTTA
* * *
548339 TGATCTTATGGAATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGGGATTTAATG
64 CGAGCTTATGGAATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATAGGATTTAATG
548404 GTATGTA
129 GTATGTA
*
548411 TATTGGTAAAATAAGCTTATGAGCTTAT-GG-AAATGGTAAGTATATTGGTAAAATAAGCTTACG
1 TATTGGTAAAATAAGCTTACGAGCTTATGGGTAAATGGTAAGTATATTGGTAAAATAAGCTTACG
* *
548474 AGCTTATGTAATAAATGGTAGGTATATTGGTAAAATAAGCTTACGAGCTTATAGGAT
66 AGCTTATGGAATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATAGGAT
548531 AAATGATAAG
Statistics
Matches: 114, Mismatches: 6, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
133 85 0.75
136 2 0.02
137 27 0.24
ACGTcount: A:0.37, C:0.06, G:0.23, T:0.34
Consensus pattern (135 bp):
TATTGGTAAAATAAGCTTACGAGCTTATGGGTAAATGGTAAGTATATTGGTAAAATAAGCTTACG
AGCTTATGGAATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATAGGATTTAATGGT
ATGTA
Found at i:557161 original size:23 final size:23
Alignment explanation
Indices: 557135--557218 Score: 107
Period size: 23 Copynumber: 3.7 Consensus size: 23
557125 CTCGTATAAA
*
557135 TGCACCGAAGTGCCACGTAGAAC
1 TGCACCGAAGTGCCACGTAGAAT
*
557158 TGCACCGAAGTGTCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
*
557181 TGCACC-ATAGTGCCGCGTAGAAT
1 TGCACCGA-AGTGCCACGTAGAAT
* *
557204 TGCATCGTAGTGCCA
1 TGCACCGAAGTGCCA
557219 TATAAGATTG
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
22 1 0.02
23 51 0.98
ACGTcount: A:0.27, C:0.26, G:0.26, T:0.20
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAT
Found at i:557498 original size:7 final size:7
Alignment explanation
Indices: 557486--557514 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
557476 TGTCATATAA
557486 ATCACAT
1 ATCACAT
557493 ATCACAT
1 ATCACAT
557500 ATCACAT
1 ATCACAT
557507 AT-ACAT
1 ATCACAT
557513 AT
1 AT
557515 AGACACATGG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.45, C:0.24, G:0.00, T:0.31
Consensus pattern (7 bp):
ATCACAT
Found at i:560006 original size:31 final size:31
Alignment explanation
Indices: 559964--560038 Score: 114
Period size: 31 Copynumber: 2.4 Consensus size: 31
559954 CGATTACGTC
* *
559964 GGGGACCATATTGCAAATGGACTAAATGTTG
1 GGGGACTATATTGCAAATAGACTAAATGTTG
*
559995 GGGGACTATATTACAAATAGACTAAATGTTG
1 GGGGACTATATTGCAAATAGACTAAATGTTG
*
560026 GGGGACTGTATTG
1 GGGGACTATATTG
560039 TAAGTTTTAA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.32, C:0.11, G:0.29, T:0.28
Consensus pattern (31 bp):
GGGGACTATATTGCAAATAGACTAAATGTTG
Found at i:560374 original size:50 final size:49
Alignment explanation
Indices: 560287--560412 Score: 171
Period size: 50 Copynumber: 2.5 Consensus size: 49
560277 GTAGCAGTAA
* *
560287 AGCGCGCCCCCTGAACCGCGCTATACGCTAATTTGGCGCCACGTGGGTAT
1 AGCGCGCCCCCTG-TCCGCGCTATACGCTAATCTGGCGCCACGTGGGTAT
* * * *
560337 AGCGTGCCCCCTGTCCCGCGATATACGGTGATCTGGCGCCACGTGGGTAT
1 AGCGCGCCCCCTGT-CCGCGCTATACGCTAATCTGGCGCCACGTGGGTAT
560387 AGCGCGCCCCCTGATCCGCGCTATAC
1 AGCGCGCCCCCTG-TCCGCGCTATAC
560413 CTGGGTATCT
Statistics
Matches: 66, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
50 65 0.98
51 1 0.02
ACGTcount: A:0.16, C:0.36, G:0.29, T:0.20
Consensus pattern (49 bp):
AGCGCGCCCCCTGTCCGCGCTATACGCTAATCTGGCGCCACGTGGGTAT
Found at i:560551 original size:10 final size:10
Alignment explanation
Indices: 560536--560574 Score: 53
Period size: 10 Copynumber: 3.9 Consensus size: 10
560526 TTATCACACT
560536 AAATTCTCTC
1 AAATTCTCTC
560546 AAATTCTCT-
1 AAATTCTCTC
560555 AAATTTCTCTC
1 AAA-TTCTCTC
*
560566 AAATACTCT
1 AAATTCTCT
560575 ATCTTTTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
9 3 0.12
10 20 0.77
11 3 0.12
ACGTcount: A:0.33, C:0.26, G:0.00, T:0.41
Consensus pattern (10 bp):
AAATTCTCTC
Found at i:560564 original size:20 final size:19
Alignment explanation
Indices: 560534--560575 Score: 66
Period size: 20 Copynumber: 2.2 Consensus size: 19
560524 TTTTATCACA
*
560534 CTAAATTCTCTCAAATTCT
1 CTAAATTCTCTCAAATACT
560553 CTAAATTTCTCTCAAATACT
1 CTAAA-TTCTCTCAAATACT
560573 CTA
1 CTA
560576 TCTTTTTAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.33, C:0.26, G:0.00, T:0.40
Consensus pattern (19 bp):
CTAAATTCTCTCAAATACT
Found at i:560895 original size:111 final size:111
Alignment explanation
Indices: 560701--561033 Score: 576
Period size: 111 Copynumber: 3.0 Consensus size: 111
560691 TGGAAATCAT
* *
560701 ATATCTCTACACTTTGCTGATACGGTAACATTTTAACATTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCAACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
* *
560766 TATTTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAC
66 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
* *
560812 ATATCTCGACACTTTGCTGATACGGTAATATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCAACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
560877 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
66 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
** *
560923 ATATCTCAACACTTTAATGATACGATAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCAACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
*
560988 TAATTAGTTGATTTATTTAATGCATGATTATTAGAGTAAGAATTAA
66 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
561034 TTTTTGTAAT
Statistics
Matches: 211, Mismatches: 11, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
111 211 1.00
ACGTcount: A:0.37, C:0.08, G:0.11, T:0.45
Consensus pattern (111 bp):
ATATCTCAACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
Found at i:561972 original size:18 final size:18
Alignment explanation
Indices: 561949--561984 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
561939 GCCACTGCAG
561949 CCATATATGATGCCGCAA
1 CCATATATGATGCCGCAA
561967 CCATATATGATGCCGCAA
1 CCATATATGATGCCGCAA
561985 TCTCCTTTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.28, G:0.17, T:0.22
Consensus pattern (18 bp):
CCATATATGATGCCGCAA
Found at i:562342 original size:15 final size:15
Alignment explanation
Indices: 562324--562376 Score: 70
Period size: 15 Copynumber: 3.5 Consensus size: 15
562314 GGATGACGAC
562324 GACGACGATGATGAT
1 GACGACGATGATGAT
* *
562339 GACGACGATGGTGAC
1 GACGACGATGATGAT
*
562354 GACGACGACGATGAT
1 GACGACGATGATGAT
*
562369 GACAACGA
1 GACGACGA
562377 GGAGTCAGAA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 32 1.00
ACGTcount: A:0.34, C:0.19, G:0.34, T:0.13
Consensus pattern (15 bp):
GACGACGATGATGAT
Found at i:562371 original size:18 final size:18
Alignment explanation
Indices: 562315--562376 Score: 76
Period size: 18 Copynumber: 3.6 Consensus size: 18
562305 ACCTGCTCAG
562315 GATGACGACGACGACGAT
1 GATGACGACGACGACGAT
*
562333 GAT---GATGACGACGAT
1 GATGACGACGACGACGAT
*
562348 GGTGACGACGACGACGAT
1 GATGACGACGACGACGAT
*
562366 GATGACAACGA
1 GATGACGACGA
562377 GGAGTCAGAA
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
15 13 0.36
18 23 0.64
ACGTcount: A:0.34, C:0.19, G:0.34, T:0.13
Consensus pattern (18 bp):
GATGACGACGACGACGAT
Found at i:565557 original size:27 final size:27
Alignment explanation
Indices: 565525--565577 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
565515 TGTTAGGGGC
*
565525 GAACTTGAACTTTTAAAATTT-TAGGGT
1 GAACTTGAACTTAT-AAATTTCTAGGGT
565552 GAACTTGAACTTATAAATTTCTAGGG
1 GAACTTGAACTTATAAATTTCTAGGG
565578 GAATCAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 6 0.25
27 18 0.75
ACGTcount: A:0.34, C:0.09, G:0.19, T:0.38
Consensus pattern (27 bp):
GAACTTGAACTTATAAATTTCTAGGGT
Found at i:566801 original size:16 final size:16
Alignment explanation
Indices: 566774--566819 Score: 65
Period size: 16 Copynumber: 2.8 Consensus size: 16
566764 TGACTGACTT
*
566774 TTGACTTTTGACCATAG
1 TTGAC-TTTGACCAGAG
*
566791 TTGACTTTGACCAGCG
1 TTGACTTTGACCAGAG
566807 TTGACTTTGACCA
1 TTGACTTTGACCA
566820 AAATGTCAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
16 22 0.81
17 5 0.19
ACGTcount: A:0.22, C:0.22, G:0.20, T:0.37
Consensus pattern (16 bp):
TTGACTTTGACCAGAG
Found at i:567635 original size:26 final size:27
Alignment explanation
Indices: 567572--567635 Score: 67
Period size: 26 Copynumber: 2.4 Consensus size: 27
567562 TCTGATATTC
* *
567572 AAATGACTGAAATATCTCTGAACCCTA
1 AAATGACTGAAATACCTCTAAACCCTA
* * *
567599 AAAAGATTGAAATACCT-TAAACTCTA
1 AAATGACTGAAATACCTCTAAACCCTA
*
567625 ATATGACTGAA
1 AAATGACTGAA
567636 GTAACCTCGA
Statistics
Matches: 29, Mismatches: 8, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
26 15 0.52
27 14 0.48
ACGTcount: A:0.45, C:0.17, G:0.11, T:0.27
Consensus pattern (27 bp):
AAATGACTGAAATACCTCTAAACCCTA
Found at i:569994 original size:18 final size:18
Alignment explanation
Indices: 569967--570006 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
569957 ATTAACGTAT
569967 TGAC-CCACTGTGAACGA
1 TGACACCACTGTGAACGA
569984 TGACACCACTGTGAACGA
1 TGACACCACTGTGAACGA
570002 TGACA
1 TGACA
570007 TTGTAAAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 4 0.18
18 18 0.82
ACGTcount: A:0.33, C:0.28, G:0.23, T:0.17
Consensus pattern (18 bp):
TGACACCACTGTGAACGA
Found at i:570150 original size:14 final size:12
Alignment explanation
Indices: 570121--570154 Score: 50
Period size: 14 Copynumber: 2.7 Consensus size: 12
570111 AAATATTTAG
570121 AAAATAAATATA
1 AAAATAAATATA
570133 AAAATAAATTACTA
1 AAAATAAA-TA-TA
570147 AAAATAAA
1 AAAATAAA
570155 AATATTATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 8 0.40
13 2 0.10
14 10 0.50
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (12 bp):
AAAATAAATATA
Found at i:570254 original size:29 final size:28
Alignment explanation
Indices: 570222--570288 Score: 104
Period size: 25 Copynumber: 2.5 Consensus size: 28
570212 TTCCAGTTCA
570222 GTGCCTAACGTTTTTTTCGTTCTAGTTTG
1 GTGCCTAACG-TTTTTTCGTTCTAGTTTG
570251 GTGCCTAACG---TTTCGTTCTAGTTTG
1 GTGCCTAACGTTTTTTCGTTCTAGTTTG
570276 GTGCCTAACGTTT
1 GTGCCTAACGTTT
570289 CATTCTGTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
25 25 0.71
29 10 0.29
ACGTcount: A:0.12, C:0.19, G:0.22, T:0.46
Consensus pattern (28 bp):
GTGCCTAACGTTTTTTCGTTCTAGTTTG
Found at i:570264 original size:25 final size:25
Alignment explanation
Indices: 570236--570294 Score: 109
Period size: 25 Copynumber: 2.4 Consensus size: 25
570226 CTAACGTTTT
570236 TTTCGTTCTAGTTTGGTGCCTAACG
1 TTTCGTTCTAGTTTGGTGCCTAACG
570261 TTTCGTTCTAGTTTGGTGCCTAACG
1 TTTCGTTCTAGTTTGGTGCCTAACG
*
570286 TTTCATTCT
1 TTTCGTTCT
570295 GTAACTCAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.12, C:0.20, G:0.20, T:0.47
Consensus pattern (25 bp):
TTTCGTTCTAGTTTGGTGCCTAACG
Found at i:570386 original size:19 final size:18
Alignment explanation
Indices: 570347--570382 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
570337 GCTGTTAACC
570347 CATTAAAAAAGCCACGTG
1 CATTAAAAAAGCCACGTG
570365 CATTAAAAAAGCCACGTG
1 CATTAAAAAAGCCACGTG
570383 GCATATTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.22, G:0.17, T:0.17
Consensus pattern (18 bp):
CATTAAAAAAGCCACGTG
Found at i:571320 original size:19 final size:19
Alignment explanation
Indices: 571294--571341 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 19
571284 TCATTTTAAT
571294 TTATTTTTTATTTGCAAAAA
1 TTATTTTTTATTTGC-AAAA
571314 TTATTTTTTATTTGCAAAA
1 TTATTTTTTATTTGCAAAA
571333 TT-TTTTTTA
1 TTATTTTTTA
571342 ATATAAAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
18 7 0.25
19 6 0.21
20 15 0.54
ACGTcount: A:0.29, C:0.04, G:0.04, T:0.62
Consensus pattern (19 bp):
TTATTTTTTATTTGCAAAA
Found at i:572771 original size:20 final size:22
Alignment explanation
Indices: 572724--572771 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 22
572714 ATTTAGATCT
572724 GAAATAAAAAAATTAAACAAGAA
1 GAAATAAAAAAA-TAAACAAGAA
* *
572747 AAAATAAAATAA-AAACAA-AA
1 GAAATAAAAAAATAAACAAGAA
572767 GAAAT
1 GAAAT
572772 GTTGACACTT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
20 6 0.27
21 6 0.27
23 10 0.45
ACGTcount: A:0.77, C:0.04, G:0.06, T:0.12
Consensus pattern (22 bp):
GAAATAAAAAAATAAACAAGAA
Found at i:579461 original size:31 final size:32
Alignment explanation
Indices: 579423--579507 Score: 136
Period size: 31 Copynumber: 2.7 Consensus size: 32
579413 CCTAAGGTGA
579423 CCTTGGGTAGGCTCTAAGGCCCCAA-ACATTT
1 CCTTGGGTAGGCTCTAAGGCCCCAAGACATTT
*
579454 CCTTGGGTAGGCTCTAAGGCCCCAAGATATTT
1 CCTTGGGTAGGCTCTAAGGCCCCAAGACATTT
* *
579486 CATTGGGTAGGCTCTTAGGCCC
1 CCTTGGGTAGGCTCTAAGGCCC
579508 TAAAGTACTC
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
31 25 0.50
32 25 0.50
ACGTcount: A:0.20, C:0.27, G:0.26, T:0.27
Consensus pattern (32 bp):
CCTTGGGTAGGCTCTAAGGCCCCAAGACATTT
Found at i:579492 original size:32 final size:31
Alignment explanation
Indices: 579425--579542 Score: 137
Period size: 32 Copynumber: 3.7 Consensus size: 31
579415 TAAGGTGACC
* *
579425 TTGGGTAGGCTCTAAGGCCCCAAACATTTCC
1 TTGGGTAGGCTCTAAGGCCCCAAATATTTCA
579456 TTGGGTAGGCTCTAAGGCCCCAAGATATTTCA
1 TTGGGTAGGCTCTAAGGCCCCAA-ATATTTCA
* * * *
579488 TTGGGTAGGCTCTTAGGCCCTAAAGTACTCCA
1 TTGGGTAGGCTCTAAGGCCCCAAA-TATTTCA
* * *
579520 TTAGGCAGGCTCTCAGGCCCCAA
1 TTGGGTAGGCTCTAAGGCCCCAA
579543 GATACTCCCT
Statistics
Matches: 75, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
31 24 0.32
32 51 0.68
ACGTcount: A:0.23, C:0.27, G:0.25, T:0.25
Consensus pattern (31 bp):
TTGGGTAGGCTCTAAGGCCCCAAATATTTCA
Found at i:579549 original size:32 final size:32
Alignment explanation
Indices: 579431--579555 Score: 103
Period size: 32 Copynumber: 3.9 Consensus size: 32
579421 GACCTTGGGT
* * * *
579431 AGGCTCTAAGGCCCCAA-ACATTTCC-TTGGGT
1 AGGCTCTAAGGCCCCAAGATA-CTCCATTAGGC
* * * *
579462 AGGCTCTAAGGCCCCAAGATATTTCATTGGGT
1 AGGCTCTAAGGCCCCAAGATACTCCATTAGGC
* *
579494 AGGCTCTTAGGCCCTAA-AGTACTCCATTAGGC
1 AGGCTCTAAGGCCCCAAGA-TACTCCATTAGGC
* *
579526 AGGCTCTCAGGCCCCAAGATACTCCCTTAG
1 AGGCTCTAAGGCCCCAAGATACTCCATTAG
579556 ATTGGCTCCT
Statistics
Matches: 79, Mismatches: 11, Indels: 7
0.81 0.11 0.07
Matches are distributed among these distances:
31 21 0.27
32 57 0.72
33 1 0.01
ACGTcount: A:0.24, C:0.29, G:0.22, T:0.25
Consensus pattern (32 bp):
AGGCTCTAAGGCCCCAAGATACTCCATTAGGC
Found at i:580133 original size:30 final size:32
Alignment explanation
Indices: 580079--580139 Score: 81
Period size: 30 Copynumber: 2.0 Consensus size: 32
580069 TGGATATTGT
580079 TGAATTCTATTTTTAATATATAAATGATTTTC
1 TGAATTCTATTTTTAATATATAAATGATTTTC
* * *
580111 TGAATTTTA-TTTT-ATCTATAAATTATTTT
1 TGAATTCTATTTTTAATATATAAATGATTTT
580140 ACATTTTTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 14 0.54
31 4 0.15
32 8 0.31
ACGTcount: A:0.33, C:0.05, G:0.05, T:0.57
Consensus pattern (32 bp):
TGAATTCTATTTTTAATATATAAATGATTTTC
Found at i:581309 original size:21 final size:21
Alignment explanation
Indices: 581276--581315 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
581266 AACTACACAG
581276 TACAGAGGATATCGATACTCC
1 TACAGAGGATATCGATACTCC
*
581297 TACAG-GGAGTATCGGTACT
1 TACAGAGGA-TATCGATACT
581316 ACATTTTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.30, C:0.20, G:0.25, T:0.25
Consensus pattern (21 bp):
TACAGAGGATATCGATACTCC
Found at i:585188 original size:65 final size:63
Alignment explanation
Indices: 585062--585271 Score: 214
Period size: 65 Copynumber: 3.3 Consensus size: 63
585052 TTTATCAAAG
* * *
585062 TGATGCACCGATGCACCAATCCATGCA-CTGATGCAC-CATGA-ATTAAATTG-AACATCAAATG
1 TGATGCATCGATGCA-CAA-CCATGCATC-GATGCACTCAGGATATT---TTGAAACATCGAATG
585123 CATT
60 CATT
* * *
585127 TCATGCATCGATGCACATACCATGCATCGATGCACTGAGGAT-TTTATGACAATATCGAATGCAT
1 TGATGCATCGATGCACA-ACCATGCATCGATGCACTCAGGATATTT-TGA-AACATCGAATGCAT
585191 T
63 T
* * *
585192 TGATGCATCGATGCACCAACCATGCATCGATGCACTCTGGCTATTTTGAAACATCGAATGCACT
1 TGATGCATCGATGCA-CAACCATGCATCGATGCACTCAGGATATTTTGAAACATCGAATGCATT
585256 TGATGCATCGATGCAC
1 TGATGCATCGATGCAC
585272 TCTTAGTGCA
Statistics
Matches: 124, Mismatches: 12, Indels: 20
0.79 0.08 0.13
Matches are distributed among these distances:
62 1 0.01
63 3 0.02
64 44 0.35
65 71 0.57
66 5 0.04
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.27
Consensus pattern (63 bp):
TGATGCATCGATGCACAACCATGCATCGATGCACTCAGGATATTTTGAAACATCGAATGCATT
Found at i:585271 original size:17 final size:19
Alignment explanation
Indices: 585243--585291 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
585233 TATTTTGAAA
585243 CATCGAATGCACT-TGA-TG
1 CATCG-ATGCACTCTGAGTG
*
585261 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
*
585280 CACCGATGCACT
1 CATCGATGCACT
585292 AAGGGTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTGAGTG
Found at i:590828 original size:42 final size:44
Alignment explanation
Indices: 590782--590876 Score: 124
Period size: 44 Copynumber: 2.2 Consensus size: 44
590772 TTGTGCTTCA
* * *
590782 TGCATTGATACACC-T-AACAGTGCATCGATGCA-TCCTTGAATG
1 TGCATCGATACACCATGAA-AGTGCACCGATGCACGCCTTGAATG
*
590824 TGCATCGATACACCATGAAGGTGCACCGATGCACGCCTTGAATG
1 TGCATCGATACACCATGAAAGTGCACCGATGCACGCCTTGAATG
590868 TGCATCGAT
1 TGCATCGAT
590877 GCACAAGGCC
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
42 13 0.28
43 13 0.28
44 20 0.43
ACGTcount: A:0.27, C:0.25, G:0.22, T:0.25
Consensus pattern (44 bp):
TGCATCGATACACCATGAAAGTGCACCGATGCACGCCTTGAATG
Found at i:590870 original size:23 final size:23
Alignment explanation
Indices: 590801--590881 Score: 96
Period size: 23 Copynumber: 3.7 Consensus size: 23
590791 ACACCTAACA
*
590801 GTGCATCGATGCA-TCCTTGAAT
1 GTGCATCGATGCACACCTTGAAT
* *
590823 GTGCATCGAT--ACACCATGAAG
1 GTGCATCGATGCACACCTTGAAT
* *
590844 GTGCACCGATGCACGCCTTGAAT
1 GTGCATCGATGCACACCTTGAAT
590867 GTGCATCGATGCACA
1 GTGCATCGATGCACA
590882 AGGCCATGCA
Statistics
Matches: 47, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
20 1 0.02
21 15 0.32
22 10 0.21
23 21 0.45
ACGTcount: A:0.26, C:0.26, G:0.25, T:0.23
Consensus pattern (23 bp):
GTGCATCGATGCACACCTTGAAT
Found at i:594526 original size:18 final size:18
Alignment explanation
Indices: 594503--594537 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
594493 TTCCATCCGG
*
594503 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
594521 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
594538 GTCCTTTCGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:599354 original size:18 final size:18
Alignment explanation
Indices: 599331--599365 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
599321 TTCCATCCGG
*
599331 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
599349 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
599366 GTCCTTTCGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:609023 original size:11 final size:11
Alignment explanation
Indices: 609007--609033 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
608997 CCCACTTTGT
609007 AAAAAAAGAAA
1 AAAAAAAGAAA
609018 AAAAAAAGAAA
1 AAAAAAAGAAA
609029 AAAAA
1 AAAAA
609034 TGAAGTTGTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (11 bp):
AAAAAAAGAAA
Found at i:611399 original size:21 final size:21
Alignment explanation
Indices: 611373--611445 Score: 137
Period size: 21 Copynumber: 3.5 Consensus size: 21
611363 CCGAGAGAAA
611373 ACCGATTCCCTATGAGGGGGT
1 ACCGATTCCCTATGAGGGGGT
*
611394 ACCGATTCCCTATGAGAGGGT
1 ACCGATTCCCTATGAGGGGGT
611415 ACCGATTCCCTATGAGGGGGT
1 ACCGATTCCCTATGAGGGGGT
611436 ACCGATTCCC
1 ACCGATTCCC
611446 CCATGCTCCA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 50 1.00
ACGTcount: A:0.21, C:0.27, G:0.29, T:0.23
Consensus pattern (21 bp):
ACCGATTCCCTATGAGGGGGT
Found at i:613872 original size:20 final size:20
Alignment explanation
Indices: 613828--613872 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
613818 AATGCACTTA
* *
613828 GTGCATCGATGCATCCTGAT
1 GTGCACCGATACATCCTGAT
* *
613848 ATGCACCGATACATCCTGCT
1 GTGCACCGATACATCCTGAT
613868 GTGCA
1 GTGCA
613873 TCCATGCACG
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.22, C:0.29, G:0.22, T:0.27
Consensus pattern (20 bp):
GTGCACCGATACATCCTGAT
Found at i:613960 original size:21 final size:21
Alignment explanation
Indices: 613936--613989 Score: 108
Period size: 21 Copynumber: 2.6 Consensus size: 21
613926 GAAGGGGTAT
613936 CGATGCACCATGATAGTGCAC
1 CGATGCACCATGATAGTGCAC
613957 CGATGCACCATGATAGTGCAC
1 CGATGCACCATGATAGTGCAC
613978 CGATGCACCATG
1 CGATGCACCATG
613990 TTATGGGCAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.28, C:0.30, G:0.24, T:0.19
Consensus pattern (21 bp):
CGATGCACCATGATAGTGCAC
Found at i:617263 original size:20 final size:21
Alignment explanation
Indices: 617235--617332 Score: 114
Period size: 20 Copynumber: 4.7 Consensus size: 21
617225 AGGGTGTCAA
617235 AGTGCATCCATGCACCCCTG-
1 AGTGCATCCATGCACCCCTGC
*
617255 AGTGTATCCATGCACCCCTGC
1 AGTGCATCCATGCACCCCTGC
617276 AGTGCATCCATGCA--CCTGCAC
1 AGTGCATCCATGCACCCCTG--C
* *
617297 TAGTGCATCGATGCA-CCATGC
1 -AGTGCATCCATGCACCCCTGC
617318 AGTGCATCCATGCAC
1 AGTGCATCCATGCAC
617333 TCCATTTCGA
Statistics
Matches: 67, Mismatches: 5, Indels: 11
0.81 0.06 0.13
Matches are distributed among these distances:
19 4 0.06
20 32 0.48
21 15 0.22
22 13 0.19
23 3 0.04
ACGTcount: A:0.22, C:0.36, G:0.20, T:0.21
Consensus pattern (21 bp):
AGTGCATCCATGCACCCCTGC
Found at i:617377 original size:20 final size:20
Alignment explanation
Indices: 617352--617424 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
617342 AAGGAACTTA
617352 GTGCATCGATGCATCCTGAT
1 GTGCATCGATGCATCCTGAT
*
617372 GTGCATCGATGCATCCTGTT
1 GTGCATCGATGCATCCTGAT
* * *
617392 GTGCATCGATACATCTTGCT
1 GTGCATCGATGCATCCTGAT
*
617412 GTGCATCCATGCA
1 GTGCATCGATGCA
617425 CGAAGGCTGC
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.19, C:0.26, G:0.23, T:0.32
Consensus pattern (20 bp):
GTGCATCGATGCATCCTGAT
Found at i:617574 original size:20 final size:22
Alignment explanation
Indices: 617536--617575 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
617526 TTTTTAGTAA
617536 AAAATCATCCCCAAACGGCTCC
1 AAAATCATCCCCAAACGGCTCC
617558 AAAA-CATCCCC-AACGGCT
1 AAAATCATCCCCAAACGGCT
617576 ATATACAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.38, C:0.40, G:0.10, T:0.12
Consensus pattern (22 bp):
AAAATCATCCCCAAACGGCTCC
Found at i:617829 original size:34 final size:32
Alignment explanation
Indices: 617790--617859 Score: 86
Period size: 34 Copynumber: 2.1 Consensus size: 32
617780 TTTTGTAAAG
* *
617790 GGGAAAGGTTCTAGCTTATCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
* *
617824 GGGAAATGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
617856 GGGA
1 GGGA
617860 GTTGTAAGGT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 11 0.34
33 1 0.03
34 20 0.62
ACGTcount: A:0.31, C:0.16, G:0.29, T:0.24
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:619036 original size:19 final size:20
Alignment explanation
Indices: 618997--619036 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
618987 TAAGTGCTAA
*
618997 TGAATTTTAAGATTTTATAT
1 TGAATTTTAAGATTATATAT
619017 TGAATTTTAA-ATTATATAT
1 TGAATTTTAAGATTATATAT
619036 T
1 T
619037 CGATTAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (20 bp):
TGAATTTTAAGATTATATAT
Found at i:621192 original size:15 final size:16
Alignment explanation
Indices: 621172--621204 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
621162 GCTTACCTCC
*
621172 TTCTTCTT-TTCTTCT
1 TTCTTCTTGTCCTTCT
621187 TTCTTCTTGTCCTTCT
1 TTCTTCTTGTCCTTCT
621203 TT
1 TT
621205 TATTCATCAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.00, C:0.27, G:0.03, T:0.70
Consensus pattern (16 bp):
TTCTTCTTGTCCTTCT
Found at i:626275 original size:23 final size:25
Alignment explanation
Indices: 626244--626289 Score: 60
Period size: 23 Copynumber: 1.9 Consensus size: 25
626234 TAATATTCTC
*
626244 ATTTAAATATTAT-ATT-TTTTAAT
1 ATTTAAATAATATGATTATTTTAAT
*
626267 ATTTTAATAATATGATTATTTTA
1 ATTTAAATAATATGATTATTTTA
626290 TTAAGTAGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 11 0.58
24 3 0.16
25 5 0.26
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (25 bp):
ATTTAAATAATATGATTATTTTAAT
Found at i:630761 original size:2 final size:2
Alignment explanation
Indices: 630754--630800 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
630744 GAAAAATCAA
630754 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
630796 AT AT A
1 AT AT A
630801 GTTTTTGGAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:637922 original size:17 final size:17
Alignment explanation
Indices: 637895--637936 Score: 75
Period size: 17 Copynumber: 2.4 Consensus size: 17
637885 GTTGTGGTTA
637895 AAATAAAAAATAATAATT
1 AAAT-AAAAATAATAATT
637913 AAATAAAAATAATAATT
1 AAATAAAAATAATAATT
637930 AAATAAA
1 AAATAAA
637937 CAAATTAAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 20 0.83
18 4 0.17
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (17 bp):
AAATAAAAATAATAATT
Found at i:638609 original size:19 final size:19
Alignment explanation
Indices: 638550--638615 Score: 53
Period size: 19 Copynumber: 3.4 Consensus size: 19
638540 AAACTATTTA
**
638550 AATTAAAATACCTAAAAAAT
1 AATTAAAATA-CTAAAACCT
* *
638570 AATATAATATTA-TAAATCCT
1 AAT-TAA-AATACTAAAACCT
638590 AATTAAAATACTAAAACCT
1 AATTAAAATACTAAAACCT
*
638609 ATTTAAA
1 AATTAAA
638616 CTAAAATACA
Statistics
Matches: 36, Mismatches: 7, Indels: 7
0.72 0.14 0.14
Matches are distributed among these distances:
18 3 0.08
19 16 0.44
20 11 0.31
21 3 0.08
22 3 0.08
ACGTcount: A:0.58, C:0.11, G:0.00, T:0.32
Consensus pattern (19 bp):
AATTAAAATACTAAAACCT
Found at i:638643 original size:64 final size:64
Alignment explanation
Indices: 638518--638712 Score: 182
Period size: 64 Copynumber: 2.9 Consensus size: 64
638508 TAAAACATCT
* * *
638518 TAAATCCTAATTAAAACACTTAAAA-CTATTTAAATTAAAATACCTAAA-A-AATAATATAATAT
1 TAAATCCTAATTAAAATAC-TAAAACCTATTTAAACTAAAATA-C-AAAGATAA-AATAAAATAT
*
638580 -TA
62 AAA
638582 TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACAAAGATAAAGATAAAATATAAA
1 TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACAAAGATAAA-ATAAAATAT--A
638647 AA
63 AA
638649 TAATATCCTAAAACTGAATTAAAATACTAAAAACCTATTTAAACTAAAATACAAAGATAAAATA
1 TAA-AT-C-----CT-AATTAAAATACT-AAAACCTATTTAAACTAAAATACAAAGATAAAATA
638713 TAATGTTTAA
Statistics
Matches: 111, Mismatches: 4, Indels: 21
0.82 0.03 0.15
Matches are distributed among these distances:
62 3 0.03
63 8 0.07
64 44 0.40
67 4 0.04
68 2 0.02
69 1 0.01
74 2 0.02
75 15 0.14
76 32 0.29
ACGTcount: A:0.58, C:0.11, G:0.02, T:0.28
Consensus pattern (64 bp):
TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACAAAGATAAAATAAAATATAAA
Found at i:638700 original size:76 final size:75
Alignment explanation
Indices: 638590--638736 Score: 233
Period size: 76 Copynumber: 1.9 Consensus size: 75
638580 TATAAATCCT
638590 AATTAAAATACTAAAACCTATTTAAACTAAAATACAAAGATAAAGATAAAAT-ATAAAAATAATA
1 AATTAAAATACTAAAACCTATTTAAACTAAAATACAAAGATAAA-ATAAAATGATAAAAATAATA
638654 TCCTAAAACTG
65 TCCTAAAACTG
* * * *
638665 AATTAAAATACTAAAAACCTATTTAAACTAAAATACAAAGATAAAATATAATGTTTAAAATATTA
1 AATTAAAATACT-AAAACCTATTTAAACTAAAATACAAAGATAAAATAAAATGATAAAAATAATA
638730 TCCTAAA
65 TCCTAAA
638737 TTTAAGTTTA
Statistics
Matches: 66, Mismatches: 4, Indels: 3
0.90 0.05 0.04
Matches are distributed among these distances:
75 18 0.27
76 48 0.73
ACGTcount: A:0.59, C:0.10, G:0.03, T:0.28
Consensus pattern (75 bp):
AATTAAAATACTAAAACCTATTTAAACTAAAATACAAAGATAAAATAAAATGATAAAAATAATAT
CCTAAAACTG
Found at i:640362 original size:18 final size:18
Alignment explanation
Indices: 640339--640374 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
640329 GAACCAAATC
640339 TTTTTTTTTTCTGCACTG
1 TTTTTTTTTTCTGCACTG
640357 TTTTTTTTTTCTGCACTG
1 TTTTTTTTTTCTGCACTG
640375 CATTGTTTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.06, C:0.17, G:0.11, T:0.67
Consensus pattern (18 bp):
TTTTTTTTTTCTGCACTG
Found at i:644526 original size:15 final size:15
Alignment explanation
Indices: 644506--644539 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
644496 TTCCTCTTGT
644506 TCTTCCTGATGTGCG
1 TCTTCCTGATGTGCG
*
644521 TCTTCCTGATGTGTG
1 TCTTCCTGATGTGCG
644536 TCTT
1 TCTT
644540 TTTTCTGCTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.06, C:0.24, G:0.24, T:0.47
Consensus pattern (15 bp):
TCTTCCTGATGTGCG
Found at i:646161 original size:21 final size:20
Alignment explanation
Indices: 646124--646162 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
646114 GACTGTGGTG
*
646124 TTTCTGATTTAATAAAAATC
1 TTTCTGATTTAAGAAAAATC
*
646144 TTTCTTGATTTTAGAAAAA
1 TTTC-TGATTTAAGAAAAA
646163 GATAGAATTC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.46
Consensus pattern (20 bp):
TTTCTGATTTAAGAAAAATC
Found at i:646228 original size:17 final size:18
Alignment explanation
Indices: 646197--646231 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
646187 AAGATATATT
646197 AAAAT-AAAATAAATAAA
1 AAAATAAAAATAAATAAA
646214 AAAATAAAAATAATATAA
1 AAAATAAAAATAA-ATAA
646232 TAATAAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 7 0.44
19 4 0.25
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (18 bp):
AAAATAAAAATAAATAAA
Found at i:646320 original size:15 final size:16
Alignment explanation
Indices: 646286--646330 Score: 56
Period size: 15 Copynumber: 2.7 Consensus size: 16
646276 GTTGTGGTTA
646286 AAATAAAAAATAAGAATT
1 AAATAAAAAAT-A-AATT
646304 AAATAAAAAAT-AATT
1 AAATAAAAAATAAATT
646319 AAATAAACAAAT
1 AAATAAA-AAAT
646331 TAAAGAGATT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
15 11 0.42
16 4 0.15
18 11 0.42
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.22
Consensus pattern (16 bp):
AAATAAAAAATAAATT
Found at i:647116 original size:76 final size:75
Alignment explanation
Indices: 646980--647127 Score: 217
Period size: 76 Copynumber: 2.0 Consensus size: 75
646970 TTTTAAATCC
*
646980 TAATTAAAATACTAAAACCTATTTAAACTAAAATACAAAGATAAAGATAAAATATAAAAATAATA
1 TAATTAAAATACTAAAACCTATTTAAACTAAAACACAAAGATAAAGATAAAATATAAAAATAATA
647045 TCCTAAAACT
66 TCCTAAAACT
* * * * *
647055 TAATTAAAATACTAAAAATCTATTTAAACTAAAACACAAAGATAAA-ATATAATGTTTAAAATAT
1 TAATTAAAATACT-AAAACCTATTTAAACTAAAACACAAAGATAAAGATAAAAT-ATAAAAATAA
647119 TATCCTAAA
64 TATCCTAAA
647128 TTTGAGTTTA
Statistics
Matches: 65, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
75 19 0.29
76 46 0.71
ACGTcount: A:0.58, C:0.10, G:0.03, T:0.29
Consensus pattern (75 bp):
TAATTAAAATACTAAAACCTATTTAAACTAAAACACAAAGATAAAGATAAAATATAAAAATAATA
TCCTAAAACT
Found at i:653464 original size:19 final size:19
Alignment explanation
Indices: 653437--653490 Score: 56
Period size: 19 Copynumber: 2.7 Consensus size: 19
653427 TTCATTTCAC
653437 ATTATAATATCATTTAAAA-T
1 ATTA-AATAT-ATTTAAAATT
*
653457 ATTAAATAAAATTTAAAATT
1 ATTAAAT-ATATTTAAAATT
*
653477 ATAAAATATATTTA
1 ATTAAATATATTTA
653491 GGCTTAAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.43
Consensus pattern (19 bp):
ATTAAATATATTTAAAATT
Found at i:654508 original size:15 final size:15
Alignment explanation
Indices: 654488--654522 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
654478 GAGAAAACAC
654488 ATGCATAATTTATTA
1 ATGCATAATTTATTA
654503 ATGCATAATTTATTA
1 ATGCATAATTTATTA
654518 ATGCA
1 ATGCA
654523 ATAGTAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.40, C:0.09, G:0.09, T:0.43
Consensus pattern (15 bp):
ATGCATAATTTATTA
Found at i:654607 original size:27 final size:27
Alignment explanation
Indices: 654576--654627 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
654566 AATATAATAA
*
654576 AACTAAAC-ATGGATAAATAAATAAAAT
1 AACTAAACTAAGG-TAAATAAATAAAAT
*
654603 AACTAAACTAAGGTATATAAATAAA
1 AACTAAACTAAGGTAAATAAATAAA
654628 TACATGAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 19 0.86
28 3 0.14
ACGTcount: A:0.62, C:0.08, G:0.08, T:0.23
Consensus pattern (27 bp):
AACTAAACTAAGGTAAATAAATAAAAT
Found at i:656332 original size:3 final size:3
Alignment explanation
Indices: 656324--656368 Score: 81
Period size: 3 Copynumber: 15.0 Consensus size: 3
656314 TTTTGACTTG
*
656324 TAA TAA TAA TAG TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
656369 ACATAAAAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:657164 original size:227 final size:226
Alignment explanation
Indices: 656763--657654 Score: 1288
Period size: 227 Copynumber: 3.9 Consensus size: 226
656753 TTTGCTTTTG
* * *
656763 AGATAAAACTATCTCGAGTGAGGCAAAATTTGTTTTGTGTTTCAAAGTAAACTATGATAAGCAAG
1 AGATAAAACTACCTCGAGTGAGGCAAAATTTGTTTTGTGTTTCAAGGAAAACTATGATAAGCAAG
* * *
656828 ATGGAATTTTCCTTTAAGAGAAACAATCTAAAAAGATACAAGCAATATGTTCCTTCGTGTTGAGG
66 ATGGAATTTTCCTTTAAGAGAAGCAATATAAAAAGATACAAGCAATATGTTCTTTCGTGTTGAGG
* *
656893 AAGTCTAATCGTTGTCAGATGATGTGACGCTTCAATTAAGAATGTAAAGTTTATTGACGATGTTG
131 AAGTCTAATCGTTGTCAGATGATGTGACGCTTCATTTGAGAATGTAAAGTTT-TTGACGATGTTG
*
656958 TTCCTTCGTGTTGAGGAAGTCTAATTGTTGTC
195 TTCCTTCGTGTTGAGGAAGTCTAATCGTTGTC
656990 AGATAAAACTACCTCGAGTGAGG-AAAATTTTGTTTTGTGTTTCAAGGAAAACTATGATAAGCAA
1 AGATAAAACTACCTCGAGTGAGGCAAAA-TTTGTTTTGTGTTTCAAGGAAAACTATGATAAGCAA
* * * *
657054 GATGGAATTTTCCTTTAAGAGAAGCAATATTAAAAGATACATGCAATATGTTCTTTCATGTTAAG
65 GATGGAATTTTCCTTTAAGAGAAGCAATATAAAAAGATACAAGCAATATGTTCTTTCGTGTTGAG
* * * *
657119 GAAGTCAAATCGTTGTCAGATGCTGTGACACTTTATTTGAGAATGTAAAGTTTTTTTGACGATGT
130 GAAGTCTAATCGTTGTCAGATGATGTGACGCTTCATTTGAGAATGTAAAG--TTTTTGACGATGT
*
657184 TGTTCCTTCGTGTTGAGGAAGTCTAAACGTTGTC
193 TGTTCCTTCGTGTTGAGGAAGTCTAATCGTTGTC
*
657218 AGATAAAA-TAACTCGAGTGAGGCAAAATTTGTTTTGTGTTTCAAGGAAAACTATGATAAGCAAG
1 AGATAAAACTACCTCGAGTGAGGCAAAATTTGTTTTGTGTTTCAAGGAAAACTATGATAAGCAAG
* ** *
657282 ATGGAATTTTCCTTTAAGAGAAGCAATCTAAAAAGATACAAGTGATATATTAC-TTCGTGTTGAG
66 ATGGAATTTTCCTTTAAGAGAAGCAATATAAAAAGATACAAGCAATATGTT-CTTTCGTGTTGAG
* *
657346 GAAGTCTAATCATTGTCAGATGATATGACGCTTCATTTGAGAATGTAAAGTTTGTTGACGATGTT
130 GAAGTCTAATCGTTGTCAGATGATGTGACGCTTCATTTGAGAATGTAAAGTTT-TTGACGATGTT
* * * *
657411 GTTCTTTCGTGTTGATGAATTCTAATCATTGTC
194 GTTCCTTCGTGTTGAGGAAGTCTAATCGTTGTC
* *
657444 AGATAAAACTGCCTCGAGTGAGGCAAAATTTGTTTTGTGTTTCAAGGAAGACTATGATAAGCAAG
1 AGATAAAACTACCTCGAGTGAGGCAAAATTTGTTTTGTGTTTCAAGGAAAACTATGATAAGCAAG
* * * * *
657509 ATGAAATTTTCCTTTAAGAGAAGCAATCA-AAAAAGATACACGCGATATGTTCTTTTGTATTGAG
66 ATGGAATTTTCCTTTAAGAGAAGCAAT-ATAAAAAGATACAAGCAATATGTTCTTTCGTGTTGAG
* * * ** *
657573 GAAGTCTAATCGTTGTTAGATGATGTGATGTTTTTGTTTGAGAAAGTAAAGTGTTTTGACGATGT
130 GAAGTCTAATCGTTGTCAGATGATGTGACG-CTTCATTTGAGAATGTAAAGT-TTTTGACGATGT
657638 TGTTCCTTCGTGGTTGA
193 TGTTCCTTCGT-GTTGA
657655 TCGCTTGTAA
Statistics
Matches: 596, Mismatches: 57, Indels: 22
0.88 0.08 0.03
Matches are distributed among these distances:
225 3 0.01
226 52 0.09
227 439 0.74
228 92 0.15
229 10 0.02
ACGTcount: A:0.32, C:0.11, G:0.22, T:0.35
Consensus pattern (226 bp):
AGATAAAACTACCTCGAGTGAGGCAAAATTTGTTTTGTGTTTCAAGGAAAACTATGATAAGCAAG
ATGGAATTTTCCTTTAAGAGAAGCAATATAAAAAGATACAAGCAATATGTTCTTTCGTGTTGAGG
AAGTCTAATCGTTGTCAGATGATGTGACGCTTCATTTGAGAATGTAAAGTTTTTGACGATGTTGT
TCCTTCGTGTTGAGGAAGTCTAATCGTTGTC
Found at i:668778 original size:25 final size:25
Alignment explanation
Indices: 668749--668803 Score: 85
Period size: 25 Copynumber: 2.2 Consensus size: 25
668739 AATATAAATA
668749 ATGAAATAATTTT-AAATAATGTTTG
1 ATGAAATAATTTTGAAA-AATGTTTG
*
668774 ATGAAATAATTTTGAAAAATTTTTG
1 ATGAAATAATTTTGAAAAATGTTTG
668799 ATGAA
1 ATGAA
668804 GTTTTTTAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
25 25 0.89
26 3 0.11
ACGTcount: A:0.45, C:0.00, G:0.13, T:0.42
Consensus pattern (25 bp):
ATGAAATAATTTTGAAAAATGTTTG
Found at i:671422 original size:14 final size:14
Alignment explanation
Indices: 671403--671431 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
671393 GATAAAGCAA
671403 GAGGAAATTGTTGG
1 GAGGAAATTGTTGG
671417 GAGGAAATTGTTGG
1 GAGGAAATTGTTGG
671431 G
1 G
671432 CAACTAGGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.00, G:0.45, T:0.28
Consensus pattern (14 bp):
GAGGAAATTGTTGG
Found at i:672160 original size:33 final size:33
Alignment explanation
Indices: 672115--672178 Score: 112
Period size: 33 Copynumber: 1.9 Consensus size: 33
672105 AGTTGTTTCT
672115 TGGTTCACTACTTAGTGTTTGAGAGAAACTATG
1 TGGTTCACTACTTAGTGTTTGAGAGAAACTATG
672148 TGGTTCGA-TACTTAGTGTTTGAGAGAAACTA
1 TGGTTC-ACTACTTAGTGTTTGAGAGAAACTA
672179 GGTGAAAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
33 29 0.97
34 1 0.03
ACGTcount: A:0.28, C:0.11, G:0.25, T:0.36
Consensus pattern (33 bp):
TGGTTCACTACTTAGTGTTTGAGAGAAACTATG
Found at i:677679 original size:103 final size:103
Alignment explanation
Indices: 677556--677761 Score: 412
Period size: 103 Copynumber: 2.0 Consensus size: 103
677546 ATTTTTAATG
677556 CAACATTCTAGATTAATTGAAAATGATATTTGTCTGAAAACTAAAATTAGTTACAAGAAGTGTTT
1 CAACATTCTAGATTAATTGAAAATGATATTTGTCTGAAAACTAAAATTAGTTACAAGAAGTGTTT
677621 ACATATTGTTCTATGATAATTGAATAAAATATTAAATT
66 ACATATTGTTCTATGATAATTGAATAAAATATTAAATT
677659 CAACATTCTAGATTAATTGAAAATGATATTTGTCTGAAAACTAAAATTAGTTACAAGAAGTGTTT
1 CAACATTCTAGATTAATTGAAAATGATATTTGTCTGAAAACTAAAATTAGTTACAAGAAGTGTTT
677724 ACATATTGTTCTATGATAATTGAATAAAATATTAAATT
66 ACATATTGTTCTATGATAATTGAATAAAATATTAAATT
677762 AAGTAAAAAA
Statistics
Matches: 103, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
103 103 1.00
ACGTcount: A:0.43, C:0.08, G:0.12, T:0.38
Consensus pattern (103 bp):
CAACATTCTAGATTAATTGAAAATGATATTTGTCTGAAAACTAAAATTAGTTACAAGAAGTGTTT
ACATATTGTTCTATGATAATTGAATAAAATATTAAATT
Found at i:684924 original size:21 final size:20
Alignment explanation
Indices: 684886--684924 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
684876 CGGTTCACCC
684886 CGATTTTCCCGATTTTTAGT
1 CGATTTTCCCGATTTTTAGT
684906 CGATTCTT-CCGATTCTTTA
1 CGATT-TTCCCGATT-TTTA
684925 CCGGTTCTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.15, C:0.23, G:0.13, T:0.49
Consensus pattern (20 bp):
CGATTTTCCCGATTTTTAGT
Found at i:685363 original size:34 final size:34
Alignment explanation
Indices: 685320--685392 Score: 146
Period size: 34 Copynumber: 2.1 Consensus size: 34
685310 CTCTTCCTGT
685320 TTCATCCAATATAACACTATAAATACAAAGTATA
1 TTCATCCAATATAACACTATAAATACAAAGTATA
685354 TTCATCCAATATAACACTATAAATACAAAGTATA
1 TTCATCCAATATAACACTATAAATACAAAGTATA
685388 TTCAT
1 TTCAT
685393 ACATTATTTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 39 1.00
ACGTcount: A:0.48, C:0.18, G:0.03, T:0.32
Consensus pattern (34 bp):
TTCATCCAATATAACACTATAAATACAAAGTATA
Found at i:688983 original size:9 final size:9
Alignment explanation
Indices: 688951--689039 Score: 79
Period size: 10 Copynumber: 9.3 Consensus size: 9
688941 CTGCTGGAAA
*
688951 ACCGGTTTA
1 ACCGGTTTG
*
688960 ACCAGTTTTG
1 ACC-GGTTTG
688970 AACCGGTTTG
1 -ACCGGTTTG
*
688980 ACCGGTTCG
1 ACCGGTTTG
688989 AACCGGTTTG
1 -ACCGGTTTG
*
688999 ACCGGTCTG
1 ACCGGTTTG
689008 AACCGGTTTG
1 -ACCGGTTTG
*
689018 ACCGGTCTG
1 ACCGGTTTG
*
689027 AACCGGGTTG
1 -ACCGGTTTG
689037 ACC
1 ACC
689040 CGACCCGACT
Statistics
Matches: 65, Mismatches: 10, Indels: 10
0.76 0.12 0.12
Matches are distributed among these distances:
9 30 0.46
10 32 0.49
11 3 0.05
ACGTcount: A:0.18, C:0.26, G:0.29, T:0.27
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:688993 original size:19 final size:19
Alignment explanation
Indices: 688968--689039 Score: 119
Period size: 19 Copynumber: 3.8 Consensus size: 19
688958 TAACCAGTTT
688968 TGAACCGGTTTGACCGGT-
1 TGAACCGGTTTGACCGGTC
688986 TCGAACCGGTTTGACCGGTC
1 T-GAACCGGTTTGACCGGTC
689006 TGAACCGGTTTGACCGGTC
1 TGAACCGGTTTGACCGGTC
*
689025 TGAACCGGGTTGACC
1 TGAACCGGTTTGACC
689040 CGACCCGACT
Statistics
Matches: 51, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
18 1 0.02
19 49 0.96
20 1 0.02
ACGTcount: A:0.17, C:0.26, G:0.32, T:0.25
Consensus pattern (19 bp):
TGAACCGGTTTGACCGGTC
Found at i:689014 original size:38 final size:39
Alignment explanation
Indices: 688950--689039 Score: 121
Period size: 38 Copynumber: 2.3 Consensus size: 39
688940 GCTGCTGGAA
* * *
688950 AACCGGTTTAACCAGTTTTGAACCGGTTTGACCGGT-TCG
1 AACCGGTTTGACCAGGTCTGAACCGGTTTGACCGGTCT-G
688989 AACCGGTTTGACC-GGTCTGAACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCAGGTCTGAACCGGTTTGACCGGTCTG
*
689027 AACCGGGTTGACC
1 AACCGGTTTGACC
689040 CGACCCGACT
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
38 33 0.72
39 13 0.28
ACGTcount: A:0.19, C:0.26, G:0.29, T:0.27
Consensus pattern (39 bp):
AACCGGTTTGACCAGGTCTGAACCGGTTTGACCGGTCTG
Found at i:689055 original size:17 final size:17
Alignment explanation
Indices: 689033--689090 Score: 98
Period size: 17 Copynumber: 3.4 Consensus size: 17
689023 TCTGAACCGG
*
689033 GTTGACCCGACCCGACT
1 GTTGACCCGACCCGACC
689050 GTTGACCCGACCCGACC
1 GTTGACCCGACCCGACC
*
689067 GTTTACCCGACCCGACC
1 GTTGACCCGACCCGACC
689084 GTTGACC
1 GTTGACC
689091 GTGACCGTTG
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 38 1.00
ACGTcount: A:0.17, C:0.43, G:0.22, T:0.17
Consensus pattern (17 bp):
GTTGACCCGACCCGACC
Found at i:689092 original size:7 final size:7
Alignment explanation
Indices: 689080--689122 Score: 72
Period size: 7 Copynumber: 6.4 Consensus size: 7
689070 TACCCGACCC
689080 GACCGTT
1 GACCGTT
689087 GACCG-T
1 GACCGTT
689093 GACCGTT
1 GACCGTT
689100 GACCG-T
1 GACCGTT
689106 GACCGTT
1 GACCGTT
689113 GACCGTT
1 GACCGTT
689120 GAC
1 GAC
689123 TTTCTTTGAC
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
6 12 0.35
7 22 0.65
ACGTcount: A:0.16, C:0.30, G:0.30, T:0.23
Consensus pattern (7 bp):
GACCGTT
Found at i:689098 original size:13 final size:13
Alignment explanation
Indices: 689080--689118 Score: 78
Period size: 13 Copynumber: 3.0 Consensus size: 13
689070 TACCCGACCC
689080 GACCGTTGACCGT
1 GACCGTTGACCGT
689093 GACCGTTGACCGT
1 GACCGTTGACCGT
689106 GACCGTTGACCGT
1 GACCGTTGACCGT
689119 TGACTTTCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.15, C:0.31, G:0.31, T:0.23
Consensus pattern (13 bp):
GACCGTTGACCGT
Found at i:689105 original size:20 final size:20
Alignment explanation
Indices: 689080--689122 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 20
689070 TACCCGACCC
689080 GACCGTTGACCGTGACCGTT
1 GACCGTTGACCGTGACCGTT
689100 GACCG-TGACCGTTGACCGTT
1 GACCGTTGACCG-TGACCGTT
689120 GAC
1 GAC
689123 TTTCTTTGAC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.16, C:0.30, G:0.30, T:0.23
Consensus pattern (20 bp):
GACCGTTGACCGTGACCGTT
Found at i:690073 original size:32 final size:31
Alignment explanation
Indices: 690026--690112 Score: 79
Period size: 30 Copynumber: 2.8 Consensus size: 31
690016 ATCATTCTCG
** *
690026 GGTAGGCCCTGCGGCCCTAAGATGTGTTCTTA
1 GGTAGGCCCCACGGCCCTAAGATGT-ATCTTA
* * *
690058 GGTAGGCCCCACGGCCCGAA-ATCTATCTTG
1 GGTAGGCCCCACGGCCCTAAGATGTATCTTA
*
690088 GGTAGGCTCTCA-GGCCCTAAGATGT
1 GGTAGGC-CCCACGGCCCTAAGATGT
690113 TCCCTTAGGG
Statistics
Matches: 44, Mismatches: 9, Indels: 5
0.76 0.16 0.09
Matches are distributed among these distances:
30 18 0.41
31 9 0.20
32 17 0.39
ACGTcount: A:0.18, C:0.28, G:0.30, T:0.24
Consensus pattern (31 bp):
GGTAGGCCCCACGGCCCTAAGATGTATCTTA
Found at i:690104 original size:62 final size:63
Alignment explanation
Indices: 689990--690112 Score: 153
Period size: 62 Copynumber: 2.0 Consensus size: 63
689980 CTAATGTGAC
* ** *
689990 TCTTAGGTAGGCTCTGCGGCCCTGAGATCATTCTCGGGTAGGCCCTGCGGCCCTAAGATGTGT
1 TCTTAGGTAGGCCCCACGGCCCTGAAATCATTCTCGGGTAGGCCCTGCGGCCCTAAGATGTGT
* *
690053 TCTTAGGTAGGCCCCACGGCCC-GAAATC-TATCTTGGGTAGGCTCT-CAGGCCCTAAGATGT
1 TCTTAGGTAGGCCCCACGGCCCTGAAATCAT-TCTCGGGTAGGCCCTGC-GGCCCTAAGATGT
690113 TCCCTTAGGG
Statistics
Matches: 52, Mismatches: 6, Indels: 5
0.83 0.10 0.08
Matches are distributed among these distances:
61 2 0.04
62 31 0.60
63 19 0.37
ACGTcount: A:0.17, C:0.28, G:0.29, T:0.26
Consensus pattern (63 bp):
TCTTAGGTAGGCCCCACGGCCCTGAAATCATTCTCGGGTAGGCCCTGCGGCCCTAAGATGTGT
Found at i:696349 original size:9 final size:9
Alignment explanation
Indices: 696317--696405 Score: 79
Period size: 10 Copynumber: 9.3 Consensus size: 9
696307 CTGCTGGAAA
*
696317 ACCGGTTTA
1 ACCGGTTTG
*
696326 ACCAGTTTTG
1 ACC-GGTTTG
696336 AACCGGTTTG
1 -ACCGGTTTG
*
696346 ACCGGTTCG
1 ACCGGTTTG
696355 AACCGGTTTG
1 -ACCGGTTTG
*
696365 ACCGGTCTG
1 ACCGGTTTG
696374 AACCGGTTTG
1 -ACCGGTTTG
*
696384 ACCGGTCTG
1 ACCGGTTTG
*
696393 AACCGGGTTG
1 -ACCGGTTTG
696403 ACC
1 ACC
696406 CGACCCGACT
Statistics
Matches: 65, Mismatches: 10, Indels: 10
0.76 0.12 0.12
Matches are distributed among these distances:
9 30 0.46
10 32 0.49
11 3 0.05
ACGTcount: A:0.18, C:0.26, G:0.29, T:0.27
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:696359 original size:19 final size:19
Alignment explanation
Indices: 696334--696405 Score: 119
Period size: 19 Copynumber: 3.8 Consensus size: 19
696324 TAACCAGTTT
696334 TGAACCGGTTTGACCGGT-
1 TGAACCGGTTTGACCGGTC
696352 TCGAACCGGTTTGACCGGTC
1 T-GAACCGGTTTGACCGGTC
696372 TGAACCGGTTTGACCGGTC
1 TGAACCGGTTTGACCGGTC
*
696391 TGAACCGGGTTGACC
1 TGAACCGGTTTGACC
696406 CGACCCGACT
Statistics
Matches: 51, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
18 1 0.02
19 49 0.96
20 1 0.02
ACGTcount: A:0.17, C:0.26, G:0.32, T:0.25
Consensus pattern (19 bp):
TGAACCGGTTTGACCGGTC
Found at i:696380 original size:38 final size:39
Alignment explanation
Indices: 696316--696405 Score: 121
Period size: 38 Copynumber: 2.3 Consensus size: 39
696306 GCTGCTGGAA
* * *
696316 AACCGGTTTAACCAGTTTTGAACCGGTTTGACCGGT-TCG
1 AACCGGTTTGACCAGGTCTGAACCGGTTTGACCGGTCT-G
696355 AACCGGTTTGACC-GGTCTGAACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCAGGTCTGAACCGGTTTGACCGGTCTG
*
696393 AACCGGGTTGACC
1 AACCGGTTTGACC
696406 CGACCCGACT
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
38 33 0.72
39 13 0.28
ACGTcount: A:0.19, C:0.26, G:0.29, T:0.27
Consensus pattern (39 bp):
AACCGGTTTGACCAGGTCTGAACCGGTTTGACCGGTCTG
Found at i:696421 original size:17 final size:17
Alignment explanation
Indices: 696399--696473 Score: 123
Period size: 17 Copynumber: 4.4 Consensus size: 17
696389 TCTGAACCGG
*
696399 GTTGACCCGACCCGACT
1 GTTGACCCGACCCGACC
696416 GTTGACCCGACCCGACC
1 GTTGACCCGACCCGACC
*
696433 GTTTACCCGACCCGACC
1 GTTGACCCGACCCGACC
*
696450 GTTTACCCGACCCGACC
1 GTTGACCCGACCCGACC
696467 GTTGACC
1 GTTGACC
696474 GTGACCGTTG
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 55 1.00
ACGTcount: A:0.17, C:0.44, G:0.21, T:0.17
Consensus pattern (17 bp):
GTTGACCCGACCCGACC
Found at i:697423 original size:32 final size:30
Alignment explanation
Indices: 697349--697424 Score: 80
Period size: 30 Copynumber: 2.5 Consensus size: 30
697339 CTAATGTGAC
* *
697349 TCTTAGGTAGGCTCTGCGGCCTGAGATCAT
1 TCTTAGGTAGGCCCTGCGGCCTAAGATCAT
** **
697379 TCTCGGGTAGGCCCTGCGGCCCTAAGATGTGT
1 TCTTAGGTAGGCCCTGCGG-CCTAAGAT-CAT
697411 TCTTAGGTAGGCCC
1 TCTTAGGTAGGCCC
697425 CACGGCCCCG
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
30 16 0.44
31 7 0.19
32 13 0.36
ACGTcount: A:0.14, C:0.26, G:0.32, T:0.28
Consensus pattern (30 bp):
TCTTAGGTAGGCCCTGCGGCCTAAGATCAT
Found at i:700587 original size:15 final size:15
Alignment explanation
Indices: 700569--700599 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
700559 GAAATCGTCA
*
700569 TATCGAGATTACGAG
1 TATCGAGATGACGAG
700584 TATCGAGATGACGAG
1 TATCGAGATGACGAG
700599 T
1 T
700600 TCCATAAGAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.32, C:0.13, G:0.29, T:0.26
Consensus pattern (15 bp):
TATCGAGATGACGAG
Found at i:701539 original size:25 final size:24
Alignment explanation
Indices: 701511--701557 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
701501 TAGTTGAAAG
* *
701511 GTAATTTTTTAACTTTAGTTTTTTA
1 GTAAATTTTTAAATTTA-TTTTTTA
701536 GTAAATTTTTAAATTTATTTTT
1 GTAAATTTTTAAATTTATTTTT
701558 ATCTTTTTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 5 0.25
25 15 0.75
ACGTcount: A:0.28, C:0.02, G:0.06, T:0.64
Consensus pattern (24 bp):
GTAAATTTTTAAATTTATTTTTTA
Found at i:703480 original size:25 final size:27
Alignment explanation
Indices: 703445--703511 Score: 75
Period size: 29 Copynumber: 2.5 Consensus size: 27
703435 AAAAAAATCA
*
703445 AGGTACTTAATTGCA-CA-AAAAAGTT
1 AGGTACCTAATTGCACCATAAAAAGTT
* *
703470 AGTTACCTAATTACACCATTTAAAAAGTT
1 AGGTACCTAATTGCACCA--TAAAAAGTT
703499 AGGTACCTAATTG
1 AGGTACCTAATTG
703512 TATAATTAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
25 12 0.36
26 2 0.06
29 19 0.58
ACGTcount: A:0.40, C:0.15, G:0.13, T:0.31
Consensus pattern (27 bp):
AGGTACCTAATTGCACCATAAAAAGTT
Found at i:703523 original size:29 final size:29
Alignment explanation
Indices: 703461--703528 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 29
703451 TTAATTGCAC
* *
703461 AAAAAAGTTAGTTACCTAATTACACCATT
1 AAAAAAGTTAGGTACCTAATTACACAATT
* ** *
703490 TAAAAAGTTAGGTACCTAATTGTATAATT
1 AAAAAAGTTAGGTACCTAATTACACAATT
703519 AAAAAAGTTA
1 AAAAAAGTTA
703529 AACAACTAAT
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.47, C:0.10, G:0.10, T:0.32
Consensus pattern (29 bp):
AAAAAAGTTAGGTACCTAATTACACAATT
Found at i:704819 original size:42 final size:42
Alignment explanation
Indices: 704760--704876 Score: 171
Period size: 42 Copynumber: 2.8 Consensus size: 42
704750 GGATAATTTG
* * *
704760 TAAATCCTTTGGGTCATCTGTTAGTCTTTCTAGCATGATGCT
1 TAAATCCTTCGGGTCATCTGTCAGTCTTTCGAGCATGATGCT
* * *
704802 TAAATCCTTCGGGTCATCGGTCAATCTTTCGAGCATGACGCT
1 TAAATCCTTCGGGTCATCTGTCAGTCTTTCGAGCATGATGCT
*
704844 TAAATCCTTCGGGTCATCTGTCAGTTTTTCGAG
1 TAAATCCTTCGGGTCATCTGTCAGTCTTTCGAG
704877 TCAGATGATA
Statistics
Matches: 66, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 66 1.00
ACGTcount: A:0.20, C:0.22, G:0.21, T:0.38
Consensus pattern (42 bp):
TAAATCCTTCGGGTCATCTGTCAGTCTTTCGAGCATGATGCT
Found at i:705028 original size:36 final size:36
Alignment explanation
Indices: 704988--705302 Score: 456
Period size: 36 Copynumber: 8.8 Consensus size: 36
704978 TCAATTTTTG
*
704988 AATCTCAACCTTCACAGAAGAGTAGTGAAGTAATGC
1 AATCTCAACCTTCACGGAAGAGTAGTGAAGTAATGC
*
705024 AATCTCAACCTTCACGAAAGAGTAGTGAAGTAATGC
1 AATCTCAACCTTCACGGAAGAGTAGTGAAGTAATGC
*
705060 AATCTCAACCTTCACGAAAGAGTAGTGAAGTAATGC
1 AATCTCAACCTTCACGGAAGAGTAGTGAAGTAATGC
705096 AATCTCAACCTTCACGGAAGAGTAGTGAAGTAATGC
1 AATCTCAACCTTCACGGAAGAGTAGTGAAGTAATGC
* *
705132 AATCTCAACCTTCACGGAAAACTAGTGAAGTAATGC
1 AATCTCAACCTTCACGGAAGAGTAGTGAAGTAATGC
* * *
705168 CAT-TTAGCCTTCACGGAAGAGTAGTGAAGTAATGC
1 AATCTCAACCTTCACGGAAGAGTAGTGAAGTAATGC
* *
705203 AATCTCAACCTTCACGGAAAAGTAGTGAAGAAATGC
1 AATCTCAACCTTCACGGAAGAGTAGTGAAGTAATGC
* *
705239 AAT-TTAGCCTTCACGGAAGAGTAGTGAAGTAAAT-C
1 AATCTCAACCTTCACGGAAGAGTAGTGAAGT-AATGC
* * * *
705274 ATTCTTAGCCTTCACGGAAGAGCAGTGAA
1 AATCTCAACCTTCACGGAAGAGTAGTGAA
705303 TCAAGATTAG
Statistics
Matches: 255, Mismatches: 21, Indels: 6
0.90 0.07 0.02
Matches are distributed among these distances:
35 56 0.22
36 199 0.78
ACGTcount: A:0.37, C:0.19, G:0.21, T:0.23
Consensus pattern (36 bp):
AATCTCAACCTTCACGGAAGAGTAGTGAAGTAATGC
Found at i:705219 original size:71 final size:72
Alignment explanation
Indices: 704988--705302 Score: 449
Period size: 71 Copynumber: 4.4 Consensus size: 72
704978 TCAATTTTTG
* * *
704988 AATCTCAACCTTCACAGAAGAGTAGTGAAGTAATGCAATCTCAACCTTCACGAAAGAGTAGTGAA
1 AATCTCAACCTTCACGGAAAAGTAGTGAAGTAATGCAATCTCAACCTTCACGGAAGAGTAGTGAA
705053 GTAATGC
66 GTAATGC
705060 AATCTCAACCTTCAC-GAAAGAGTAGTGAAGTAATGCAATCTCAACCTTCACGGAAGAGTAGTGA
1 AATCTCAACCTTCACGGAAA-AGTAGTGAAGTAATGCAATCTCAACCTTCACGGAAGAGTAGTGA
705124 AGTAATGC
65 AGTAATGC
* * * *
705132 AATCTCAACCTTCACGGAAAACTAGTGAAGTAATGCCAT-TTAGCCTTCACGGAAGAGTAGTGAA
1 AATCTCAACCTTCACGGAAAAGTAGTGAAGTAATGCAATCTCAACCTTCACGGAAGAGTAGTGAA
705196 GTAATGC
66 GTAATGC
* * *
705203 AATCTCAACCTTCACGGAAAAGTAGTGAAGAAATGCAAT-TTAGCCTTCACGGAAGAGTAGTGAA
1 AATCTCAACCTTCACGGAAAAGTAGTGAAGTAATGCAATCTCAACCTTCACGGAAGAGTAGTGAA
705267 GTAAAT-C
66 GT-AATGC
* * * * *
705274 ATTCTTAGCCTTCACGGAAGAGCAGTGAA
1 AATCTCAACCTTCACGGAAAAGTAGTGAA
705303 TCAAGATTAG
Statistics
Matches: 226, Mismatches: 14, Indels: 7
0.91 0.06 0.03
Matches are distributed among these distances:
71 121 0.54
72 101 0.45
73 4 0.02
ACGTcount: A:0.37, C:0.19, G:0.21, T:0.23
Consensus pattern (72 bp):
AATCTCAACCTTCACGGAAAAGTAGTGAAGTAATGCAATCTCAACCTTCACGGAAGAGTAGTGAA
GTAATGC
Found at i:705467 original size:10 final size:9
Alignment explanation
Indices: 705449--705480 Score: 50
Period size: 8 Copynumber: 3.8 Consensus size: 9
705439 GTTTCCATCT
705449 TATTATATA
1 TATTATATA
705458 TA-TATATA
1 TATTATATA
705466 TATTAT-TA
1 TATTATATA
705474 TATTATA
1 TATTATA
705481 ATTATTACAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
8 16 0.76
9 5 0.24
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (9 bp):
TATTATATA
Found at i:708354 original size:22 final size:20
Alignment explanation
Indices: 708326--708421 Score: 119
Period size: 18 Copynumber: 4.9 Consensus size: 20
708316 GTTCTTAAGG
708326 AGTGGTCCTTCGGGACATATAC
1 AGTGGTCCTTCGGGACA-AT-C
708348 AGTGGTCCTTCGGGAC-AT-
1 AGTGGTCCTTCGGGACAATC
* *
708366 AGTGGTTCTTCGGAACAATC
1 AGTGGTCCTTCGGGACAATC
708386 AGTGGTCCTTCGGGAC-AT-
1 AGTGGTCCTTCGGGACAATC
*
708404 AGTGGTCATTCGGGACAA
1 AGTGGTCCTTCGGGACAA
708422 ATATTCATTG
Statistics
Matches: 66, Mismatches: 5, Indels: 9
0.82 0.06 0.11
Matches are distributed among these distances:
18 29 0.44
19 5 0.08
20 16 0.24
22 16 0.24
ACGTcount: A:0.22, C:0.21, G:0.30, T:0.27
Consensus pattern (20 bp):
AGTGGTCCTTCGGGACAATC
Found at i:708396 original size:38 final size:40
Alignment explanation
Indices: 708326--708416 Score: 141
Period size: 38 Copynumber: 2.3 Consensus size: 40
708316 GTTCTTAAGG
*
708326 AGTGGTCCTTCGGGACATATACAGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGAACATATACAGTGGTCCTTCGGGACAT
*
708366 AGTGGTTCTTCGGAACA-AT-CAGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGAACATATACAGTGGTCCTTCGGGACAT
*
708404 AGTGGTCATTCGG
1 AGTGGTCCTTCGG
708417 GACAAATATT
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
38 30 0.64
39 2 0.04
40 15 0.32
ACGTcount: A:0.20, C:0.21, G:0.31, T:0.29
Consensus pattern (40 bp):
AGTGGTCCTTCGGAACATATACAGTGGTCCTTCGGGACAT
Found at i:714488 original size:19 final size:19
Alignment explanation
Indices: 714464--714528 Score: 121
Period size: 19 Copynumber: 3.4 Consensus size: 19
714454 GAATGCAATT
714464 AGTGCATCGATGCATGAGG
1 AGTGCATCGATGCATGAGG
714483 AGTGCATCGATGCATGAGG
1 AGTGCATCGATGCATGAGG
*
714502 AATGCATCGATGCATGAGG
1 AGTGCATCGATGCATGAGG
714521 AGTGCATC
1 AGTGCATC
714529 AAATGCACCT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 44 1.00
ACGTcount: A:0.28, C:0.17, G:0.34, T:0.22
Consensus pattern (19 bp):
AGTGCATCGATGCATGAGG
Found at i:715298 original size:18 final size:18
Alignment explanation
Indices: 715275--715345 Score: 61
Period size: 18 Copynumber: 3.8 Consensus size: 18
715265 GTTCTTAAGG
715275 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
* * * *
715293 AGTGGTTCTTCAGAATAAT
1 AGTGGTCCTTCGGGA-CAT
* * *
715312 CAATAGTCCTTTGGGACAT
1 -AGTGGTCCTTCGGGACAT
715331 AGTGGTCCTTCGGGA
1 AGTGGTCCTTCGGGA
715346 TAAATATTCA
Statistics
Matches: 37, Mismatches: 14, Indels: 4
0.67 0.25 0.07
Matches are distributed among these distances:
18 24 0.65
19 4 0.11
20 9 0.24
ACGTcount: A:0.23, C:0.18, G:0.28, T:0.31
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:718419 original size:33 final size:33
Alignment explanation
Indices: 718371--718447 Score: 109
Period size: 33 Copynumber: 2.3 Consensus size: 33
718361 AGGAGATGCA
* * *
718371 GGAGCATTAATACCACTGGTTCCAATTCCCAAC
1 GGAGCATTAAAACCACGGGTTCCAATACCCAAC
*
718404 TGAGCATTAAAACCACGGGTTCCAATACCCAAC
1 GGAGCATTAAAACCACGGGTTCCAATACCCAAC
*
718437 GGAGAATTAAA
1 GGAGCATTAAA
718448 GAATAACGAT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.36, C:0.26, G:0.17, T:0.21
Consensus pattern (33 bp):
GGAGCATTAAAACCACGGGTTCCAATACCCAAC
Found at i:724432 original size:20 final size:19
Alignment explanation
Indices: 724370--724432 Score: 65
Period size: 19 Copynumber: 3.3 Consensus size: 19
724360 TATATTATTT
*
724370 TTAAATTATTAATATTAAC
1 TTAAATTATTAATATTAAA
*
724389 TTAAATT-TTAAATTTTAAA
1 TTAAATTATT-AATATTAAA
* *
724408 ATAAATATATTTATATTAAA
1 TTAAAT-TATTAATATTAAA
724428 TTAAA
1 TTAAA
724433 ATGTCAGATA
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
18 2 0.06
19 19 0.54
20 12 0.34
21 2 0.06
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.48
Consensus pattern (19 bp):
TTAAATTATTAATATTAAA
Found at i:736737 original size:17 final size:18
Alignment explanation
Indices: 736704--736737 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
736694 TGAAGAACAA
*
736704 TTTATCAGAGGTTGTTCT
1 TTTATCAGAGATTGTTCT
736722 TTTATCAGA-ATTGTTC
1 TTTATCAGAGATTGTTC
736738 GAAGGGACTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.21, C:0.12, G:0.18, T:0.50
Consensus pattern (18 bp):
TTTATCAGAGATTGTTCT
Found at i:740948 original size:34 final size:34
Alignment explanation
Indices: 740910--740980 Score: 81
Period size: 34 Copynumber: 2.1 Consensus size: 34
740900 AAATGCCATA
*
740910 AAAGAAAAATTATTAA-AAATAAAAACAAAAAAAT
1 AAAGAAAAATTA-TAATAAAGAAAAACAAAAAAAT
* * * *
740944 AAAGATACATTATAATAAAGAAAAAGAAAATAAT
1 AAAGAAAAATTATAATAAAGAAAAACAAAAAAAT
740978 AAA
1 AAA
740981 CCCCAACGGT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
33 3 0.10
34 28 0.90
ACGTcount: A:0.73, C:0.03, G:0.06, T:0.18
Consensus pattern (34 bp):
AAAGAAAAATTATAATAAAGAAAAACAAAAAAAT
Found at i:752127 original size:3 final size:3
Alignment explanation
Indices: 752121--752172 Score: 61
Period size: 3 Copynumber: 17.0 Consensus size: 3
752111 TTATTATTTG
* *
752121 ATA ATA ATA ATA ATA TATA ATA ATA GTA AT- ATA ATA ATA ATA TTA
1 ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
752166 TATA ATA
1 -ATA ATA
752173 TTATTATATA
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
2 2 0.05
3 35 0.83
4 5 0.12
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (3 bp):
ATA
Done.