Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007428.1 Hibiscus syriacus cultivar Beakdansim tig00020138_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: 917797
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 5
Found at i:415217 original size:155 final size:154
Alignment explanation
Indices: 414936--415261 Score: 607
Period size: 155 Copynumber: 2.1 Consensus size: 154
414926 CTTGTCTATC
*
414936 ACATAAGGAGTTGGATCAACATCACTTTTTTTCGCGATTCTACCATATAAGAAGTTGGATTATCA
1 ACATAAGGAGTTGGATCAACATCACTTTTTTTCGCGATTCTACCATATAAGAAGTCGGATTATCA
* *
415001 TAATGCTTTTGTTCAATTACGTCATAGAAGAAGGTGGATCAATGTTTCCTTTTTTGCTCGATTCC
66 TAATGCTTTTGTTCAATTACATCATAGAAGAAGGTGGATCAATGTTTCCTGTTTTGCTCGATTCC
415066 ATCACATAAGGAGTTGGATCCATA
131 ATCACATAAGGAGTTGGATCCATA
415090 ACATAAGGAGTTGGATCAACATCACTTTTTTTTCGCGATTCTACCATATAAGAAGTCGGATTATC
1 ACATAAGGAGTTGGATCAACATCAC-TTTTTTTCGCGATTCTACCATATAAGAAGTCGGATTATC
415155 ATAATGCTTTTGTTCAATTACATCATAGAAGAAGGTGGATCAATGTTTCCTGTTTTGCTCGATTC
65 ATAATGCTTTTGTTCAATTACATCATAGAAGAAGGTGGATCAATGTTTCCTGTTTTGCTCGATTC
*
415220 TATCACATAAGGAGTTGGATCCATA
130 CATCACATAAGGAGTTGGATCCATA
415245 ACATAAGGAGTTGGATC
1 ACATAAGGAGTTGGATC
415262 TGCATCGACC
Statistics
Matches: 167, Mismatches: 4, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
154 25 0.15
155 142 0.85
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.35
Consensus pattern (154 bp):
ACATAAGGAGTTGGATCAACATCACTTTTTTTCGCGATTCTACCATATAAGAAGTCGGATTATCA
TAATGCTTTTGTTCAATTACATCATAGAAGAAGGTGGATCAATGTTTCCTGTTTTGCTCGATTCC
ATCACATAAGGAGTTGGATCCATA
Found at i:417253 original size:21 final size:22
Alignment explanation
Indices: 417222--417270 Score: 82
Period size: 21 Copynumber: 2.3 Consensus size: 22
417212 TCCTTGTTTT
*
417222 GCTTGATTCCATCACATAAGGA
1 GCTTGAATCCATCACATAAGGA
417244 G-TTGAATCCATCACATAAGGA
1 GCTTGAATCCATCACATAAGGA
417265 GCTTGA
1 GCTTGA
417271 TCTGCATCGA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 20 0.80
22 5 0.20
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.27
Consensus pattern (22 bp):
GCTTGAATCCATCACATAAGGA
Found at i:430647 original size:37 final size:36
Alignment explanation
Indices: 430604--430692 Score: 92
Period size: 36 Copynumber: 2.4 Consensus size: 36
430594 TTTTCTTTCG
430604 AAACAAAGTGTCGTCTCACTAGAGACAATTT-TCTTAA
1 AAACAAA-TGTCGTCTCACTAGAGACAATTTCTCTT-A
* * ** *
430641 AAACAAATTTTGTCTTGCTTGAGACAATTTCTCTTA
1 AAACAAATGTCGTCTCACTAGAGACAATTTCTCTTA
430677 AAACAAAT-TCCGTCTC
1 AAACAAATGT-CGTCTC
430693 TCCTGAGTCA
Statistics
Matches: 43, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
35 1 0.02
36 31 0.72
37 11 0.26
ACGTcount: A:0.35, C:0.20, G:0.11, T:0.34
Consensus pattern (36 bp):
AAACAAATGTCGTCTCACTAGAGACAATTTCTCTTA
Found at i:430705 original size:36 final size:36
Alignment explanation
Indices: 430625--430708 Score: 100
Period size: 36 Copynumber: 2.3 Consensus size: 36
430615 CGTCTCACTA
** *
430625 GAGACAATTTTCTTAAAAACAAATTTTGTCTTGCTT
1 GAGACAATTTTCTTAAAAACAAATTCCGTCTTGCCT
430661 GAGACAATTTCTCTT-AAAACAAATTCCGTCTCT-CCT
1 GAGACAATTT-TCTTAAAAACAAATTCCGTCT-TGCCT
*
430697 GAGTCAATTTTC
1 GAGACAATTTTC
430709 CCTTGAGATG
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
35 2 0.05
36 35 0.83
37 5 0.12
ACGTcount: A:0.31, C:0.20, G:0.11, T:0.38
Consensus pattern (36 bp):
GAGACAATTTTCTTAAAAACAAATTCCGTCTTGCCT
Found at i:431008 original size:65 final size:65
Alignment explanation
Indices: 430955--431248 Score: 392
Period size: 65 Copynumber: 4.5 Consensus size: 65
430945 TTCAAACAAG
** *
430955 TTTTGTCTCTCTTGAGACAATTTCTCTTGAAACAAAGATCTTTGAGATTGTTTCCCTTGAAACGA
1 TTTTGTCTCTCTTGAGACAATTTCTCTTGAAAC-ATCATCTTTGAGATCGTTTCCCTTGAAACGA
431020 A
65 A
* * * * **
431021 TTTTGTCTCTCTTAAGAGAGTTTCTCTTGAAACATCATCTTTGAGATCATTTCCCTTGAATTGAA
1 TTTTGTCTCTCTTGAGACAATTTCTCTTGAAACATCATCTTTGAGATCGTTTCCCTTGAAACGAA
* * * * *
431086 TTTTGTCTCTCTTGATATAGA-TTCACTTGAAGCATCATCTTTGAGATCGTTTCCCTTGAATCGA
1 TTTTGTCTCTCTTGAGACA-ATTTCTCTTGAAACATCATCTTTGAGATCGTTTCCCTTGAAACGA
431150 A
65 A
* *
431151 TTTTTTCTCTCTTGAGACAATTTCTCTTGAAACATCATATTTGAGATCGTTTCCCTTGAAACGAA
1 TTTTGTCTCTCTTGAGACAATTTCTCTTGAAACATCATCTTTGAGATCGTTTCCCTTGAAACGAA
** *
431216 TTTTGTCTCTCTTGAGATGATTTCTCTTAAAAC
1 TTTTGTCTCTCTTGAGACAATTTCTCTTGAAAC
431249 CATTATCCCT
Statistics
Matches: 198, Mismatches: 28, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
64 1 0.01
65 167 0.84
66 30 0.15
ACGTcount: A:0.25, C:0.19, G:0.14, T:0.42
Consensus pattern (65 bp):
TTTTGTCTCTCTTGAGACAATTTCTCTTGAAACATCATCTTTGAGATCGTTTCCCTTGAAACGAA
Found at i:431567 original size:83 final size:83
Alignment explanation
Indices: 431396--431590 Score: 239
Period size: 83 Copynumber: 2.3 Consensus size: 83
431386 GATGGCAAGT
* * * * * *
431396 CGTCCTCTTCACGTAGGAACCGTGTTATCCACTGACCAGATCTCCTTATCACGTATGAGTCGTGT
1 CGTCCTCGTCACGTAGGAACCGTGTTATCCACCGACCAGATCTCCTCATCACGTAGGAGCCGCGT
*
431461 CAACCTTAAATAACCAAT
66 CAACCTTAAATAACCAAC
* * **
431479 TGTCCTCGTCACGTCGGAATTGT-TTCATCCACCGACCAGATCTCCTCATCACGTAGGAGCCGCG
1 CGTCCTCGTCACGTAGGAACCGTGTT-ATCCACCGACCAGATCTCCTCATCACGTAGGAGCCGCG
*
431543 TCAACCTTAGATAACCAAC
65 TCAACCTTAAATAACCAAC
* * *
431562 CGTCCTCATCGCATAGGAACCGTGTTATC
1 CGTCCTCGTCACGTAGGAACCGTGTTATC
431591 ATCATCCTTA
Statistics
Matches: 91, Mismatches: 19, Indels: 4
0.80 0.17 0.04
Matches are distributed among these distances:
82 2 0.02
83 87 0.96
84 2 0.02
ACGTcount: A:0.25, C:0.31, G:0.17, T:0.27
Consensus pattern (83 bp):
CGTCCTCGTCACGTAGGAACCGTGTTATCCACCGACCAGATCTCCTCATCACGTAGGAGCCGCGT
CAACCTTAAATAACCAAC
Found at i:431722 original size:134 final size:137
Alignment explanation
Indices: 431481--431812 Score: 420
Period size: 134 Copynumber: 2.4 Consensus size: 137
431471 TAACCAATTG
* * * * *
431481 TCCTCGTCACGTCGGAATTGTTTCATCCACCGACCAGATCTCCTCATCACGTAGGAGCCGCGTCA
1 TCCTCATCACGTAGGAATTGTGTCATCCACCGACCAGATCTCCTCATCACGTAGAAGCCGCATCA
* * *
431546 ACCTTAGATAACCAACCGTCCTCATCGCATAGGAACCGTGTTAT-C-ATCATCCTTAAA-AATGG
66 ACCTTAGATAACCAACCATCCTCATCGCATAGGAACCATGTTATCCAATCATCCCTAAAGAA-GG
* *
431608 TC-AGCCA
130 CCAAGACA
* * * *
431615 TCCTCATCGCGTAGGAATTGTGTCATCAATCGACCAGATCTCCTCATCACGTATAAGCCGCATCA
1 TCCTCATCACGTAGGAATTGTGTCATCCACCGACCAGATCTCCTCATCACGTAGAAGCCGCATCA
** * *
431680 ACCTTAGATAACCAGTCATCCTCATCGCGTAGGAACCATGTTATCACCAATTATCCCTAAAGAAG
66 ACCTTAGATAACCAACCATCCTCATCGCATAGGAACCATGTTAT--CCAATCATCCCTAAAGAAG
*
431745 GCCAAGACG
129 GCCAAGACA
* *
431754 TCCTCATCACGTAGGAATAGTGTCATCCACCGACCATATCTCCTCATCACGTAGAAGCC
1 TCCTCATCACGTAGGAATTGTGTCATCCACCGACCAGATCTCCTCATCACGTAGAAGCC
431813 ATGTCACCCA
Statistics
Matches: 167, Mismatches: 25, Indels: 7
0.84 0.13 0.04
Matches are distributed among these distances:
134 95 0.57
137 1 0.01
138 13 0.08
139 58 0.35
ACGTcount: A:0.28, C:0.31, G:0.17, T:0.24
Consensus pattern (137 bp):
TCCTCATCACGTAGGAATTGTGTCATCCACCGACCAGATCTCCTCATCACGTAGAAGCCGCATCA
ACCTTAGATAACCAACCATCCTCATCGCATAGGAACCATGTTATCCAATCATCCCTAAAGAAGGC
CAAGACA
Found at i:431878 original size:139 final size:139
Alignment explanation
Indices: 431480--431879 Score: 323
Period size: 139 Copynumber: 2.9 Consensus size: 139
431470 ATAACCAATT
* * * * * * * *
431480 GTCCTCGTCACGTCGGAATTGTTTCATCCACCGACCAGATCTCCTCATCACGTAGGAGCCGCGTC
1 GTCCTCATCACGTAGGAATAGTGTCATCAACCGACCAGATCTCCTCATCACGTAGAAGCCACATC
* ** * * * * * * *
431545 AACCTTAGATAACCAACCGTCCTCATCGCATAGGAACCGTG-T--TATC-ATCAT-CCTTAAA-A
66 AACCATAGATAACCAGTCATCCTCATCACGTAGGAACCATGCTACCACCAATTATACC-TAAAGA
* *
431604 ATGGTC-AGCC
130 A-GGCCAAGAC
* * * * * *
431614 ATCCTCATCGCGTAGGAATTGTGTCATCAATCGACCAGATCTCCTCATCACGTATAAGCCGCATC
1 GTCCTCATCACGTAGGAATAGTGTCATCAACCGACCAGATCTCCTCATCACGTAGAAGCCACATC
* * * * *
431679 AACCTTAGATAACCAGTCATCCTCATCGCGTAGGAACCATGTTATCACCAATTATCCCTAAAGAA
66 AACCATAGATAACCAGTCATCCTCATCACGTAGGAACCATGCTACCACCAATTATACCTAAAGAA
431744 GGCCAAGAC
131 GGCCAAGAC
* * **
431753 GTCCTCATCACGTAGGAATAGTGTCATCCACCGACCATATCTCCTCATCACGTAGAAGCCATGTC
1 GTCCTCATCACGTAGGAATAGTGTCATCAACCGACCAGATCTCCTCATCACGTAGAAGCCACATC
* *** * * *
431818 ACCCATAGATGGTCA-TACTTCCTCATCACGTAGGAACCGTGCTACCTCCAAATT-TACCTAAA
66 AACCATAGATAACCAGT-CATCCTCATCACGTAGGAACCATGCTACCACC-AATTATACCTAAA
431880 AATTACCAGA
Statistics
Matches: 215, Mismatches: 42, Indels: 13
0.80 0.16 0.05
Matches are distributed among these distances:
134 91 0.42
135 1 0.00
137 2 0.01
138 12 0.06
139 105 0.49
140 4 0.02
ACGTcount: A:0.28, C:0.31, G:0.16, T:0.24
Consensus pattern (139 bp):
GTCCTCATCACGTAGGAATAGTGTCATCAACCGACCAGATCTCCTCATCACGTAGAAGCCACATC
AACCATAGATAACCAGTCATCCTCATCACGTAGGAACCATGCTACCACCAATTATACCTAAAGAA
GGCCAAGAC
Found at i:432073 original size:3 final size:3
Alignment explanation
Indices: 432065--432095 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
432055 ATTTTGTTAA
432065 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
432096 GAGGCCAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:435194 original size:31 final size:29
Alignment explanation
Indices: 435124--435195 Score: 83
Period size: 29 Copynumber: 2.4 Consensus size: 29
435114 GTTGCATTGT
435124 TTATACCATTGAACTTTCAATTTTGTCAA
1 TTATACCATTGAACTTTCAATTTTGTCAA
* * *
435153 TAATAACATTGAACTTT-GATTTTCGTTTCAA
1 TTATACCATTGAACTTTCAATTTT-G--TCAA
435184 TTATACCATTGA
1 TTATACCATTGA
435196 GTCGTTAAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
28 5 0.14
29 16 0.46
31 14 0.40
ACGTcount: A:0.32, C:0.15, G:0.08, T:0.44
Consensus pattern (29 bp):
TTATACCATTGAACTTTCAATTTTGTCAA
Found at i:436242 original size:20 final size:21
Alignment explanation
Indices: 436210--436302 Score: 66
Period size: 21 Copynumber: 4.4 Consensus size: 21
436200 TTATATTCTT
*
436210 TTAAAATTTGTATTTATTTAC
1 TTAAAATTTGTATATATTTAC
*
436231 TTAAAA-TTGTATATATTT-T
1 TTAAAATTTGTATATATTTAC
* * *
436250 TTAGATATTTTTTATATTTTTTA-
1 TTA-A-AATTTGTATA-TATTTAC
* *
436273 TTAAAAATTTGTATTTATTTTC
1 TT-AAAATTTGTATATATTTAC
436295 TTAAAATT
1 TTAAAATT
436303 ATATATACTT
Statistics
Matches: 55, Mismatches: 10, Indels: 14
0.70 0.13 0.18
Matches are distributed among these distances:
19 3 0.05
20 12 0.22
21 17 0.31
22 15 0.27
23 7 0.13
24 1 0.02
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.60
Consensus pattern (21 bp):
TTAAAATTTGTATATATTTAC
Found at i:436298 original size:22 final size:22
Alignment explanation
Indices: 436212--436300 Score: 78
Period size: 22 Copynumber: 4.1 Consensus size: 22
436202 ATATTCTTTT
*
436212 AAAATTTGTATTTATTTACTT-
1 AAAATTTGTATTTATTTTCTTA
*
436233 AAAA-TTGTATATATTTT-TTA
1 AAAATTTGTATTTATTTTCTTA
* * * *
436253 GATATTTTTTATATT-TTTTATTA
1 -AAAATTTGTAT-TTATTTTCTTA
436276 AAAATTTGTATTTATTTTCTTA
1 AAAATTTGTATTTATTTTCTTA
436298 AAA
1 AAA
436301 TTATATATAC
Statistics
Matches: 52, Mismatches: 10, Indels: 11
0.71 0.14 0.15
Matches are distributed among these distances:
19 2 0.04
20 11 0.21
21 8 0.15
22 27 0.52
23 4 0.08
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.58
Consensus pattern (22 bp):
AAAATTTGTATTTATTTTCTTA
Found at i:437004 original size:24 final size:24
Alignment explanation
Indices: 436983--437036 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
436973 AACCATAAGG
436983 AACGTACCACAAGAGCTGATAAAA
1 AACGTACCACAAGAGCTGATAAAA
** * *
437007 AACGTGTCACAAGAGCAGAGAGAAA
1 AACGTACCACAAGAGCTGATA-AAA
437032 AACGT
1 AACGT
437037 GTCACAATGA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
24 17 0.68
25 8 0.32
ACGTcount: A:0.48, C:0.19, G:0.22, T:0.11
Consensus pattern (24 bp):
AACGTACCACAAGAGCTGATAAAA
Found at i:437038 original size:25 final size:24
Alignment explanation
Indices: 436990--437043 Score: 81
Period size: 25 Copynumber: 2.2 Consensus size: 24
436980 AGGAACGTAC
* *
436990 CACAAGAGCTGATAAAAAACGTGT
1 CACAAGAGCAGAGAAAAAACGTGT
437014 CACAAGAGCAGAGAGAAAAACGTGT
1 CACAAGAGCAGAGA-AAAAACGTGT
437039 CACAA
1 CACAA
437044 TGATATATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
24 12 0.44
25 15 0.56
ACGTcount: A:0.48, C:0.19, G:0.22, T:0.11
Consensus pattern (24 bp):
CACAAGAGCAGAGAAAAAACGTGT
Found at i:441591 original size:21 final size:20
Alignment explanation
Indices: 441562--441601 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
441552 ACTAAAATAA
441562 AAATAAAAAAATGCGAAAACC
1 AAATAAAAAAATGC-AAAACC
*
441583 AAATTAAAAAATGCAAAAC
1 AAATAAAAAAATGCAAAAC
441602 TTGATTTCAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.68, C:0.12, G:0.07, T:0.12
Consensus pattern (20 bp):
AAATAAAAAAATGCAAAACC
Found at i:442648 original size:15 final size:16
Alignment explanation
Indices: 442620--442660 Score: 59
Period size: 17 Copynumber: 2.6 Consensus size: 16
442610 GGCATTCAGG
442620 CTATATAA-ATAAT-A
1 CTATATAATATAATAA
442634 CTATATAATATAATAA
1 CTATATAATATAATAA
442650 CATATATAATA
1 C-TATATAATA
442661 AACTTCACTC
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.33
15 5 0.21
16 2 0.08
17 9 0.38
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.37
Consensus pattern (16 bp):
CTATATAATATAATAA
Found at i:442661 original size:15 final size:14
Alignment explanation
Indices: 442620--442658 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 14
442610 GGCATTCAGG
442620 CTATATAAATAATA
1 CTATATAAATAATA
442634 CTATATAATATAATAA
1 CTATATAA-ATAAT-A
442650 CATATATAA
1 C-TATATAA
442659 TAAACTTCAC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 8 0.36
15 5 0.23
16 2 0.09
17 7 0.32
ACGTcount: A:0.56, C:0.08, G:0.00, T:0.36
Consensus pattern (14 bp):
CTATATAAATAATA
Found at i:443084 original size:46 final size:45
Alignment explanation
Indices: 443031--443182 Score: 123
Period size: 44 Copynumber: 3.4 Consensus size: 45
443021 TAGATTACTT
443031 CACTACTCTTCCTTGAAGATTTCATACTTTGCTGAAAAATCTGTTC
1 CACTACTCTTCCTTGAAGATTTCATA-TTTGCTGAAAAATCTGTTC
** * * * * * *
443077 CACTACTCTT--TTGTGGAGTTCAGATTTG-TGATTGAATTTTATTC
1 CACTACTCTTCCTTGAAGATTTCATATTTGCTGA--AAAATCTGTTC
* * * *
443121 CACAACCCTTCCTTGGAG-TTTGATATTTTGCTGAAAAATCTGTTC
1 CACTACTCTTCCTTGAAGATTTCATA-TTTGCTGAAAAATCTGTTC
*
443166 CACTACTCTTCCGTGAA
1 CACTACTCTTCCTTGAA
443183 AACGAATTGA
Statistics
Matches: 77, Mismatches: 23, Indels: 13
0.68 0.20 0.12
Matches are distributed among these distances:
42 3 0.04
43 4 0.05
44 25 0.32
45 24 0.31
46 18 0.23
47 3 0.04
ACGTcount: A:0.24, C:0.22, G:0.14, T:0.40
Consensus pattern (45 bp):
CACTACTCTTCCTTGAAGATTTCATATTTGCTGAAAAATCTGTTC
Found at i:443531 original size:191 final size:190
Alignment explanation
Indices: 443192--443555 Score: 448
Period size: 191 Copynumber: 1.9 Consensus size: 190
443182 AAACGAATTG
* * * *
443192 AGAATCTAATTTCAATACTCTTCCGTGAAGATCAGACTCACCATTGGATTACTTCATTACTCTTC
1 AGAATCTAATTTCAATACTCTTCCGCGAAGATCAGACTCACAATTGAATTACTTCACTACTCTTC
* * * * *
443257 CGTGAAGATTTCATACTTCGCTGAAATATCCGTTCCACTACTCTTTGTGGAAAGTGAATTTTGTT
66 CGTGAAGATTTCATACTTCGCTGAAAAATCCGTTCCACTACTCTTTGTGGAAACTAAACTTTGGT
* *
443322 ATTGTTTTTTGGTTTTGCTTCACTACTCTTCCGTGAAGTTTGAAAATGATTGACTTGACA
131 ATTGTTTCTTGCTTTTGCTTCACTACTCTTCCGTGAAGTTTGAAAATGATTGACTTGACA
* * * * *
443382 AGAATCTAATTTCACTACTCTTCCGCGAATATTAGATTCA-AAGTTGAATTTTCTTCCACTACTC
1 AGAATCTAATTTCAATACTCTTCCGCGAAGATCAGACTCACAA-TTGAA-TTACTT-CACTACTC
* * * *
443446 TTCCGTGGAG-TTTGATACTTTGCTGAAAAATCTGTTCCACTACTCTTTTGTGG-AACTCAAACT
63 TTCCGTGAAGATTTCATACTTCGCTGAAAAATCCGTTCCACTACTC-TTTGTGGAAACT-AAACT
* * *
443509 TTGGTCTTG-TTCTTGCTTTTGCTTCACTATTCTTCTGTGAAGTTTGA
126 TTGGTATTGTTTCTTGCTTTTGCTTCACTACTCTTCCGTGAAGTTTGA
443556 TTTGACTTGA
Statistics
Matches: 146, Mismatches: 23, Indels: 9
0.82 0.13 0.05
Matches are distributed among these distances:
189 1 0.01
190 39 0.27
191 73 0.50
192 33 0.23
ACGTcount: A:0.24, C:0.20, G:0.15, T:0.41
Consensus pattern (190 bp):
AGAATCTAATTTCAATACTCTTCCGCGAAGATCAGACTCACAATTGAATTACTTCACTACTCTTC
CGTGAAGATTTCATACTTCGCTGAAAAATCCGTTCCACTACTCTTTGTGGAAACTAAACTTTGGT
ATTGTTTCTTGCTTTTGCTTCACTACTCTTCCGTGAAGTTTGAAAATGATTGACTTGACA
Found at i:444746 original size:15 final size:15
Alignment explanation
Indices: 444726--444760 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
444716 TGTAATCACA
444726 TGATGGACAGAACAG
1 TGATGGACAGAACAG
444741 TGATGGACAGAACAG
1 TGATGGACAGAACAG
444756 TGATG
1 TGATG
444761 TACGATCAAC
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:0.37, C:0.11, G:0.34, T:0.17
Consensus pattern (15 bp):
TGATGGACAGAACAG
Found at i:444996 original size:40 final size:40
Alignment explanation
Indices: 444949--445051 Score: 134
Period size: 40 Copynumber: 2.6 Consensus size: 40
444939 TTTTTGTCTG
* *
444949 AAATGGGCCTTCAGTATGCCCCATATTTTATTTCTGACTA
1 AAATGGGCCTTCAGTATGCCCCACATTTTATTTCTAACTA
* * * *
444989 AAATGGGCCTTTAGCATGCCCTACATTTTATTTCTAACTG
1 AAATGGGCCTTCAGTATGCCCCACATTTTATTTCTAACTA
* *
445029 AAATAGGCCTTCAATATGCCCCA
1 AAATGGGCCTTCAGTATGCCCCA
445052 ACCTTTGCTG
Statistics
Matches: 52, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 52 1.00
ACGTcount: A:0.27, C:0.24, G:0.15, T:0.34
Consensus pattern (40 bp):
AAATGGGCCTTCAGTATGCCCCACATTTTATTTCTAACTA
Found at i:450860 original size:20 final size:21
Alignment explanation
Indices: 450821--450867 Score: 69
Period size: 20 Copynumber: 2.2 Consensus size: 21
450811 ACTAAAATAA
450821 AAATATAAAAAATGCGAAAACC
1 AAAT-TAAAAAATGCGAAAACC
450843 AAATTAAAAAATGC-AAAACC
1 AAATTAAAAAATGCGAAAACC
*
450863 TAATT
1 AAATT
450868 TCGGGACCAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 10 0.42
21 10 0.42
22 4 0.17
ACGTcount: A:0.62, C:0.13, G:0.06, T:0.19
Consensus pattern (21 bp):
AAATTAAAAAATGCGAAAACC
Found at i:451839 original size:15 final size:16
Alignment explanation
Indices: 451811--451851 Score: 59
Period size: 17 Copynumber: 2.6 Consensus size: 16
451801 GGCCTTCGAG
451811 CTATATAA-ATAATAA
1 CTATATAATATAATAA
451826 -TATATAATATAATAA
1 CTATATAATATAATAA
451841 CGTATATAATA
1 C-TATATAATA
451852 AATGTCACTC
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 7 0.30
15 7 0.30
17 9 0.39
ACGTcount: A:0.56, C:0.05, G:0.02, T:0.37
Consensus pattern (16 bp):
CTATATAATATAATAA
Found at i:452616 original size:77 final size:77
Alignment explanation
Indices: 452479--452624 Score: 213
Period size: 77 Copynumber: 1.9 Consensus size: 77
452469 TCGATTCAAT
* * * *
452479 TAGAACGGGAGGAAGCATCACACTTTCGATTCAAGTAAAATGAAAGGAGGCATAACACTTTTGAT
1 TAGAACGGAAGGAAGCATCACACTTTCGATTCAAGTAAAACGAAAAGAGGCATAACACTTTCGAT
452544 TCTCGTCAAAAG
66 TCTCGTCAAAAG
* * *
452556 TAGAACGGAAGGAAGCATCACACTTTCGTTTCAAGTAGAACGAAAAGAGGCATGGA-ACTTTCGA
1 TAGAACGGAAGGAAGCATCACACTTTCGATTCAAGTAAAACGAAAAGAGGCAT-AACACTTTCGA
452620 TTCTC
65 TTCTC
452625 AAAGACAGAA
Statistics
Matches: 61, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
77 60 0.98
78 1 0.02
ACGTcount: A:0.36, C:0.18, G:0.23, T:0.23
Consensus pattern (77 bp):
TAGAACGGAAGGAAGCATCACACTTTCGATTCAAGTAAAACGAAAAGAGGCATAACACTTTCGAT
TCTCGTCAAAAG
Found at i:454082 original size:20 final size:20
Alignment explanation
Indices: 454043--454101 Score: 61
Period size: 19 Copynumber: 3.1 Consensus size: 20
454033 TACAGACTCT
*
454043 TAACTT-ATTTAAGA-TTCA
1 TAACTTAATTTCAGATTTCA
454061 TAACTTAATTTCAGATTTCA
1 TAACTTAATTTCAGATTTCA
** *
454081 TAGTTTATTTTCA-ATTTCA
1 TAACTTAATTTCAGATTTCA
454100 TA
1 TA
454102 GCCAATTCAT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
18 6 0.17
19 15 0.43
20 14 0.40
ACGTcount: A:0.34, C:0.12, G:0.05, T:0.49
Consensus pattern (20 bp):
TAACTTAATTTCAGATTTCA
Found at i:464498 original size:20 final size:21
Alignment explanation
Indices: 464445--464506 Score: 63
Period size: 20 Copynumber: 2.9 Consensus size: 21
464435 TTCCCCTGTG
464445 GGGGGGAATCGGTTCCCCTTCAAA
1 GGGGGG-ATCGGTT-CCC-TCAAA
* *
464469 GGGGGAATCGGTTCCCTC-AT
1 GGGGGGATCGGTTCCCTCAAA
*
464489 GGGGGGATCGATTCCCTC
1 GGGGGGATCGGTTCCCTC
464507 TGCACCAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
20 17 0.50
21 2 0.06
22 3 0.09
23 7 0.21
24 5 0.15
ACGTcount: A:0.16, C:0.26, G:0.35, T:0.23
Consensus pattern (21 bp):
GGGGGGATCGGTTCCCTCAAA
Found at i:468359 original size:22 final size:21
Alignment explanation
Indices: 468317--468356 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
468307 GAGTTTATTT
*
468317 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
468338 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
468357 ACAATTTATC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:470249 original size:20 final size:20
Alignment explanation
Indices: 470201--470255 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 20
470191 TTGGAGCGTG
* *
470201 GGGGAATCAGTACCCCCTAT
1 GGGGAATCGGTTCCCCCTAT
470221 GGGGAATCGGTTCCCCCTAT
1 GGGGAATCGGTTCCCCCTAT
470241 GGGGAATCGGTTCCC
1 GGGGAATCGGTTCCC
470256 TAAGTGTAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.18, C:0.29, G:0.31, T:0.22
Consensus pattern (20 bp):
GGGGAATCGGTTCCCCCTAT
Found at i:475338 original size:40 final size:40
Alignment explanation
Indices: 475270--475351 Score: 137
Period size: 40 Copynumber: 2.0 Consensus size: 40
475260 GCAAAAGAGG
*
475270 GAGCACTATATTTCTAGGAAATTTTCTATGTTAGTGGAGA
1 GAGCACTATATTTCTAGGAAATTGTCTATGTTAGTGGAGA
* *
475310 GAGCACTATATTTTTAGGGAATTGTCTATGTTAGTGGAGA
1 GAGCACTATATTTCTAGGAAATTGTCTATGTTAGTGGAGA
475350 GA
1 GA
475352 CAAAAAAATA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.29, C:0.09, G:0.26, T:0.37
Consensus pattern (40 bp):
GAGCACTATATTTCTAGGAAATTGTCTATGTTAGTGGAGA
Found at i:476632 original size:307 final size:306
Alignment explanation
Indices: 476046--476655 Score: 1159
Period size: 307 Copynumber: 2.0 Consensus size: 306
476036 GGTGGCCAAA
*
476046 CGTTGGCCATAGAGCCTTTTAGAGTGAAGAAGCGGCGCTAAGGGGATATTAACAATTGAAAACTA
1 CGTTGGCCATAGACCCTTTTAGAGTGAAGAAGCGGCGCTAAGGGGATATTAACAATTGAAAACTA
476111 GGGTTCAGTTTTATCCAATATTTTATATATATATTAATGCATAAAATGGTAACAAATGAGGGTTA
66 GGGTTCAGTTTTATCCAATATTTTATATATATATTAATGCATAAAATGGTAACAAATGAGGGTTA
476176 AGTGCGTATAAAAAAAACAAAGAAAGTTTGCTTTTCAGAATCCAACCAAACCCACATGAATTGGT
131 AGTGCGTATAAAAAAAACAAAGAAAGTTTGCTTTTCAGAATCCAACCAAACCCACATGAATTGGT
476241 CTTTGGGGGGTAAACTATTTCTATAGTCCTTCAAATATTATGGGTAAATTCTTTCCTTAATCTTT
196 CTTTGGGGGGTAAACTATTTCTATAGTCCTTCAAATATTATGGGTAAATTCTTTCCTTAATCTTT
476306 TAGTTTTGATGCGTTATTCACTTCAGTCCATTCTT-TGTGAATTGGT
261 TAGTTTTGATGCGTTATTCACTTCAGTCCATTCTTGTGT-AATTGGT
* *
476352 CGTTGGCCTTAGACCCTTTTAGAGTGAAGAAGCGGCGTTAAGGGGATATTAACAATTGAAAACTA
1 CGTTGGCCATAGACCCTTTTAGAGTGAAGAAGCGGCGCTAAGGGGATATTAACAATTGAAAACTA
476417 GGGTTCAGTTTTATCCAATATTTTATATATATATTAATGCATAAAATGGTAACAAATGAGGGTTA
66 GGGTTCAGTTTTATCCAATATTTTATATATATATTAATGCATAAAATGGTAACAAATGAGGGTTA
*
476482 AGTGCGTATAAAAAAAAACAAAGAAAGTTTGCTTTTCAGAATCCAACCAAACCCACGTGAATTGG
131 AGTGCGTAT-AAAAAAAACAAAGAAAGTTTGCTTTTCAGAATCCAACCAAACCCACATGAATTGG
476547 TCTTTGGGGGGTAAACTATTTCTATAGTCCTTCAAATATTATGGGTAAATTCTTTCCTTAATCTT
195 TCTTTGGGGGGTAAACTATTTCTATAGTCCTTCAAATATTATGGGTAAATTCTTTCCTTAATCTT
476612 TTAGTTTTGATGCGTTATTCACTTCAGTCCATTCTTGTGTAATT
260 TTAGTTTTGATGCGTTATTCACTTCAGTCCATTCTTGTGTAATT
476656 CCATCTTAAT
Statistics
Matches: 298, Mismatches: 4, Indels: 3
0.98 0.01 0.01
Matches are distributed among these distances:
306 136 0.46
307 159 0.53
308 3 0.01
ACGTcount: A:0.32, C:0.14, G:0.19, T:0.35
Consensus pattern (306 bp):
CGTTGGCCATAGACCCTTTTAGAGTGAAGAAGCGGCGCTAAGGGGATATTAACAATTGAAAACTA
GGGTTCAGTTTTATCCAATATTTTATATATATATTAATGCATAAAATGGTAACAAATGAGGGTTA
AGTGCGTATAAAAAAAACAAAGAAAGTTTGCTTTTCAGAATCCAACCAAACCCACATGAATTGGT
CTTTGGGGGGTAAACTATTTCTATAGTCCTTCAAATATTATGGGTAAATTCTTTCCTTAATCTTT
TAGTTTTGATGCGTTATTCACTTCAGTCCATTCTTGTGTAATTGGT
Found at i:479714 original size:3 final size:3
Alignment explanation
Indices: 479706--479759 Score: 108
Period size: 3 Copynumber: 18.0 Consensus size: 3
479696 ACTTGGCCTG
479706 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
479754 TAT TAT
1 TAT TAT
479760 ACAAACTAGT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:480623 original size:3 final size:3
Alignment explanation
Indices: 480615--480644 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
480605 AATGTCTCAA
480615 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
480645 TCTTGAATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:486840 original size:19 final size:20
Alignment explanation
Indices: 486816--486856 Score: 75
Period size: 19 Copynumber: 2.1 Consensus size: 20
486806 AACAGGTAAC
486816 AAATTTGACAAAAT-GATTA
1 AAATTTGACAAAATCGATTA
486835 AAATTTGACAAAATCGATTA
1 AAATTTGACAAAATCGATTA
486855 AA
1 AA
486857 TATAACATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 14 0.67
20 7 0.33
ACGTcount: A:0.54, C:0.07, G:0.10, T:0.29
Consensus pattern (20 bp):
AAATTTGACAAAATCGATTA
Found at i:488480 original size:19 final size:20
Alignment explanation
Indices: 488448--488489 Score: 68
Period size: 19 Copynumber: 2.1 Consensus size: 20
488438 CATTTGGACC
*
488448 CTACAAGGGTGTTTTATTGG
1 CTACAAGGGGGTTTTATTGG
488468 CTAC-AGGGGGTTTTATTGG
1 CTACAAGGGGGTTTTATTGG
488487 CTA
1 CTA
488490 TGCAGTCAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 17 0.81
20 4 0.19
ACGTcount: A:0.19, C:0.12, G:0.31, T:0.38
Consensus pattern (20 bp):
CTACAAGGGGGTTTTATTGG
Found at i:489626 original size:226 final size:226
Alignment explanation
Indices: 489199--491367 Score: 2930
Period size: 226 Copynumber: 9.6 Consensus size: 226
489189 TAACAAATAA
* * * *
489199 AGTAATTAATCGGTTATGTTATCGTCGGATTTCTAAGGCTCAATTAGCTTAAACTTTGGTAACGT
1 AGTAATTAACCGGTTATGTTATCGTCGGATTTCTAAGGCTCCATCAGCTTAAACTTTGGTAACAT
*
489264 TTTAGGCGTTACCTAATATGTTGATAATATTGATAACAAATT--GTAATTAACCTATTTTGTTAT
66 TTTAGGCGTTACCTAATATGTTGATAATACTGATAACAAATTAAGTAATTAACCTATTTTGTTAT
** * * * *
489327 CGTTGGATTTCTAATGCCCCATCAGCTTTAAAAAGGCACTACCTATTACGATACATAAGAGCTAC
131 CGTCAGATTTCTAAGGCCCCATCAGCTTTAAAAAGGCGCTACCTATTACGTTACATAAGCGCTAC
* * *
489392 CTAATATGTTATTATTCTAGATAGTGTTTCC
196 CTAATATGTTATTATGCTTGATAATGTTTCC
* * **
489423 AGTAATTAACCAGTTATGTTATTGTCATATTTCTAAGGCTCCATCAGCTTAAACTTTGGTATA-A
1 AGTAATTAACCGGTTATGTTATCGTCGGATTTCTAAGGCTCCATCAGCTTAAACTTTGGTA-ACA
* * * *
489487 TTTTAGGCATTACCTTATATGTTGA-AGATACTGATAAAAAATAAAGTAATTAACCTATTTTGTT
65 TTTTAGGCGTTACCTAATATGTTGATA-ATACTGATAACAAATTAAGTAATTAACCTATTTTGTT
* * * ***
489551 GTCGTCATATTTTTAAGGCCCCATCAGCTTTAAAAATATGCTACCTATTACGTTACATAAGCGCT
129 ATCGTCAGATTTCTAAGGCCCCATCAGCTTTAAAAAGGCGCTACCTATTACGTTACATAAGCGCT
*
489616 ACCCAATATGTTATTATGCTTGATAATGTTTCC
194 ACCTAATATGTTATTATGCTTGATAATGTTTCC
* *
489649 AGTAATTAACCGGTTATTTTATCGTCTGATTTCTAAGGCTCCATCAGCTTAAACTTTGGTAACAT
1 AGTAATTAACCGGTTATGTTATCGTCGGATTTCTAAGGCTCCATCAGCTTAAACTTTGGTAACAT
* * *
489714 TTTTGGTGTTACCTAATATGTTGATAATACTGATAACAAATTAAGTAATTAATCTATTTTGTTAT
66 TTTAGGCGTTACCTAATATGTTGATAATACTGATAACAAATTAAGTAATTAACCTATTTTGTTAT
* * * * * * *
489779 CGTCGGATTTCTAAGGCCCTATCAGCTTTGAAAATGCACTACCTATTACATTACATAAGCACTAC
131 CGTCAGATTTCTAAGGCCCCATCAGCTTTAAAAAGGCGCTACCTATTACGTTACATAAGCGCTAC
*
489844 CTAATATGTTATTATGCTTGATAATGTTTCG
196 CTAATATGTTATTATGCTTGATAATGTTTCC
* * * * * *
489875 AGTAATTAATCGGTTATATTATCATCAGATTTCTACGGCTCCATCAGCTAAAACTTTGGTAACA-
1 AGTAATTAACCGGTTATGTTATCGTCGGATTTCTAAGGCTCCATCAGCTTAAACTTTGGTAACAT
* * *
489939 TTTAGGCGTTACATAATATGTTGATAGTACTGATAACCAAATTAAGTAATTAAGCTATTTTGTTA
66 TTTAGGCGTTACCTAATATGTTGATAATACTGATAA-CAAATTAAGTAATTAACCTATTTTGTTA
* * * *
490004 TCGTTAGATTTCTAAGGCCCCATCAGCTTTAAAAAGGCGTTACCTATTGCGTTACATAAGCTCTA
130 TCGTCAGATTTCTAAGGCCCCATCAGCTTTAAAAAGGCGCTACCTATTACGTTACATAAGCGCTA
*
490069 CCTAATATGTTATTATACTTGATAATGTTTCC
195 CCTAATATGTTATTATGCTTGATAATGTTTCC
* * *
490101 AGTAATTAACCGGTTATGCTATCGTCGGATTTGTAAGGCTCCTTCAGCTTAAACTTTGGTAACAT
1 AGTAATTAACCGGTTATGTTATCGTCGGATTTCTAAGGCTCCATCAGCTTAAACTTTGGTAACAT
* *
490166 TTTAGGCGTTACCTAATATGTTGATAATACTGATAACAAA-TATGTAATAAACCTATTTTGTTAT
66 TTTAGGCGTTACCTAATATGTTGATAATACTGATAACAAATTAAGTAATTAACCTATTTTGTTAT
* * * *
490230 CGTC-GAATTTCTAAGGCCCAATCAGCTTTAAAAAGACGTTAACTATTACGTTACATAAGCGCTA
131 CGTCAG-ATTTCTAAGGCCCCATCAGCTTTAAAAAGGCGCTACCTATTACGTTACATAAGCGCTA
*
490294 CCTAATATGTTATTATGCTTGATAATGTTTAC
195 CCTAATATGTTATTATGCTTGATAATGTTTCC
* * * * **
490326 AGTAATTAACCAGTTATGTTATCGTCGGGTTTATAAGGCTCCAT-AACATTAATTTTTGGTAACA
1 AGTAATTAACCGGTTATGTTATCGTCGGATTTCTAAGGCTCCATCAGC-TTAAACTTTGGTAACA
** * *
490390 TTTTAGGCAATACCTAATATGTTGATAATACTGATAACAAATTAAATAATTAACATA-TTTGTTA
65 TTTTAGGCGTTACCTAATATGTTGATAATACTGATAACAAATTAAGTAATTAACCTATTTTGTTA
** * * * * **
490454 TCGTC-GAATTTCTAAGGTACCATTAGCTTTAAAAAAGTGCTACTTATTTTGTTACATAAGCGCT
130 TCGTCAG-ATTTCTAAGGCCCCATCAGCTTTAAAAAGGCGCTACCTATTACGTTACATAAGCGCT
490518 ACCTAATATGTTATTATGCTTGATAATGTTTCC
194 ACCTAATATGTTATTATGCTTGATAATGTTTCC
*
490551 AGTAATTAACCGGTTATGTTATCGTCGGATTTCTAAGGCTCCGTCAGCTTAAACTTTGGTAACAT
1 AGTAATTAACCGGTTATGTTATCGTCGGATTTCTAAGGCTCCATCAGCTTAAACTTTGGTAACAT
* * * *
490616 TTTAGGCATTACCT-A-AT-TTGTTAATACTAATGAA-AAATTAAGTAATTAATCTATTTTGTTA
66 TTTAGGCGTTACCTAATATGTTGATAATACTGAT-AACAAATTAAGTAATTAACCTATTTTGTTA
* * ** * * * *
490677 TCGGCGGATTTCTAAGGCCCTGTCATCTTTAAAAAGGTGCTACCTATTACGTTACATAAACACTA
130 TCGTCAGATTTCTAAGGCCCCATCAGCTTTAAAAAGGCGCTACCTATTACGTTACATAAGCGCTA
*
490742 CCTAATATGTTATTATGTTTGATAATGTTTCC
195 CCTAATATGTTATTATGCTTGATAATGTTTCC
*
490774 AGTAATTAACCGGTTATGTTATTGTCGGATTTCTAAGGCTCCATCAGCTTAAACTTTGGTAACAT
1 AGTAATTAACCGGTTATGTTATCGTCGGATTTCTAAGGCTCCATCAGCTTAAACTTTGGTAACAT
* * * * **
490839 TTTAGGTGTTACCTTATATGTTGATAATACTGATTAGAAATTAAGTAATTAATTTATTTTGTTAT
66 TTTAGGCGTTACCTAATATGTTGATAATACTGATAACAAATTAAGTAATTAACCTATTTTGTTAT
* * * * *
490904 CGTCAGATTTCTAAGGCCCCATCAACTTTAAAAAGGCACTACCTATTACATTACATAAGTGGTAC
131 CGTCAGATTTCTAAGGCCCCATCAGCTTTAAAAAGGCGCTACCTATTACGTTACATAAGCGCTAC
**
490969 CTAATATGTTATTATGCTTGATAATGTTTTA
196 CTAATATGTTATTATGCTTGATAATGTTTCC
* * * *
491000 AGTAATTAATCGGTTATGTTATCGTTGGATTTCTAAAGCTCCATCAGCTTAAACTTTGATAACAT
1 AGTAATTAACCGGTTATGTTATCGTCGGATTTCTAAGGCTCCATCAGCTTAAACTTTGGTAACAT
* *
491065 TTTAGGCGTTACATAATATGTTGATAATACTAATAACAAATTAAGTAATTAACCTATTTTGTTAT
66 TTTAGGCGTTACCTAATATGTTGATAATACTGATAACAAATTAAGTAATTAACCTATTTTGTTAT
* * * * * *
491130 CGTCGGATTTCTACA-GCCCCATCAACTTTTAAAAGGCGTTACCTATTACGTTACATAAGCTCTG
131 CGTCAGATTTCTA-AGGCCCCATCAGCTTTAAAAAGGCGCTACCTATTACGTTACATAAGCGCTA
491194 CCTAATATGTTATTATGCTTGATAATGTTTCC
195 CCTAATATGTTATTATGCTTGATAATGTTTCC
* * * * * * * * *
491226 AATAGTTAATCGGTTATGCTT-TCTTCGGATTTGTAAGGCTCCTTTAGCTTAAGCTTTGGCAACA
1 AGTAATTAACCGGTTATG-TTATCGTCGGATTTCTAAGGCTCCATCAGCTTAAACTTTGGTAACA
* *
491290 TTTTAGGCATTACCTAATATGTTGATAATACTGATAACAAATTATGTAATTAACCTATTTTGTTA
65 TTTTAGGCGTTACCTAATATGTTGATAATACTGATAACAAATTAAGTAATTAACCTATTTTGTTA
491355 TCGTCAGATTTCT
130 TCGTCAGATTTCT
491368 TAAAAGGCAT
Statistics
Matches: 1708, Mismatches: 216, Indels: 40
0.87 0.11 0.02
Matches are distributed among these distances:
222 28 0.02
223 168 0.10
224 96 0.06
225 395 0.23
226 983 0.58
227 38 0.02
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.39
Consensus pattern (226 bp):
AGTAATTAACCGGTTATGTTATCGTCGGATTTCTAAGGCTCCATCAGCTTAAACTTTGGTAACAT
TTTAGGCGTTACCTAATATGTTGATAATACTGATAACAAATTAAGTAATTAACCTATTTTGTTAT
CGTCAGATTTCTAAGGCCCCATCAGCTTTAAAAAGGCGCTACCTATTACGTTACATAAGCGCTAC
CTAATATGTTATTATGCTTGATAATGTTTCC
Found at i:490027 original size:452 final size:452
Alignment explanation
Indices: 489199--492314 Score: 4054
Period size: 452 Copynumber: 7.0 Consensus size: 452
489189 TAACAAATAA
* * * *
489199 AGTAATTAATCGGTTATGTTATCGTCGGATTTCTAAGGCTCAATTAGCTTAAACTTTGGTAACGT
1 AGTAATTAACCGGTTATGTTATCGTCGGATTTCTAAGGCTCCATCAGCTTAAACTTTGGTAACAT
*
489264 TTTAGGCGTTACCTAATATGTTGATAATATTGATAACAAATT--GTAATTAACCTATTTTGTTAT
66 TTTAGGCGTTACCTAATATGTTGATAATACTGATAACAAATTAAGTAATTAACCTATTTTGTTAT
* * * *
489327 CGTTGGATTTCTAATGCCCCATCAGCTTTAAAAAGGCACTACCTATTACGATACATAAG-AGCTA
131 CGTCGGATTTCTAAGGCCCCATCAGCTTTAAAAAGGCGCTACCTATTACGTTACATAAGCA-CTA
* * * * * **
489391 CCTAATATGTTATTATTCTAGATAGTGTTTCCAGTAATTAACCAGTTATGTTATTGTCATATTTC
195 CCTAATATGTTATTATGCTTGATAATGTTTCCAGTAATTAACCGGTTATGTTATCGTCGGATTTC
*
489456 TAAGGCTCCATCAGCTTAAACTTTGGTATA-ATTTTAGGCATTACCTTATATGTTGA-AGATACT
260 TAAGGCTCCATCAGCTTAAACTTTGGTA-ACATTTTAGGCATTACCTAATATGTTGATA-ATACT
* * * * *
489519 GATAAAAAATAAAGTAATTAACCTATTTTGTTGTCGTCATATTTTTAAGGCCCCATCAGCTTTAA
323 GATAACAAATTAAGTAATTAACCTATTTTGTTATCGTCAGATTTCTAAGGCCCCATCAGCTTTAA
* * *
489584 AAATATGCTACCTATTACGTTACATAAGCGCTACCCAATATGTTATTATGCTTGATAATGTTTCC
388 AAAGACGCTACCTATTACGTTACATAAGCGCTACCTAATATGTTATTATGCTTGATAATGTTTCC
* *
489649 AGTAATTAACCGGTTATTTTATCGTCTGATTTCTAAGGCTCCATCAGCTTAAACTTTGGTAACAT
1 AGTAATTAACCGGTTATGTTATCGTCGGATTTCTAAGGCTCCATCAGCTTAAACTTTGGTAACAT
* * *
489714 TTTTGGTGTTACCTAATATGTTGATAATACTGATAACAAATTAAGTAATTAATCTATTTTGTTAT
66 TTTAGGCGTTACCTAATATGTTGATAATACTGATAACAAATTAAGTAATTAACCTATTTTGTTAT
* * * * *
489779 CGTCGGATTTCTAAGGCCCTATCAGCTTTGAAAATGCACTACCTATTACATTACATAAGCACTAC
131 CGTCGGATTTCTAAGGCCCCATCAGCTTTAAAAAGGCGCTACCTATTACGTTACATAAGCACTAC
* * * * *
489844 CTAATATGTTATTATGCTTGATAATGTTTCGAGTAATTAATCGGTTATATTATCATCAGATTTCT
196 CTAATATGTTATTATGCTTGATAATGTTTCCAGTAATTAACCGGTTATGTTATCGTCGGATTTCT
* * * * *
489909 ACGGCTCCATCAGCTAAAACTTTGGTAACA-TTTAGGCGTTACATAATATGTTGATAGTACTGAT
261 AAGGCTCCATCAGCTTAAACTTTGGTAACATTTTAGGCATTACCTAATATGTTGATAATACTGAT
* *
489973 AACCAAATTAAGTAATTAAGCTATTTTGTTATCGTTAGATTTCTAAGGCCCCATCAGCTTTAAAA
326 AA-CAAATTAAGTAATTAACCTATTTTGTTATCGTCAGATTTCTAAGGCCCCATCAGCTTTAAAA
* * * * *
490038 AGGCGTTACCTATTGCGTTACATAAGCTCTACCTAATATGTTATTATACTTGATAATGTTTCC
390 AGACGCTACCTATTACGTTACATAAGCGCTACCTAATATGTTATTATGCTTGATAATGTTTCC
* * *
490101 AGTAATTAACCGGTTATGCTATCGTCGGATTTGTAAGGCTCCTTCAGCTTAAACTTTGGTAACAT
1 AGTAATTAACCGGTTATGTTATCGTCGGATTTCTAAGGCTCCATCAGCTTAAACTTTGGTAACAT
* *
490166 TTTAGGCGTTACCTAATATGTTGATAATACTGATAACAAA-TATGTAATAAACCTATTTTGTTAT
66 TTTAGGCGTTACCTAATATGTTGATAATACTGATAACAAATTAAGTAATTAACCTATTTTGTTAT
* * * * * *
490230 CGTCGAATTTCTAAGGCCCAATCAGCTTTAAAAAGACGTTAACTATTACGTTACATAAGCGCTAC
131 CGTCGGATTTCTAAGGCCCCATCAGCTTTAAAAAGGCGCTACCTATTACGTTACATAAGCACTAC
* * * *
490295 CTAATATGTTATTATGCTTGATAATGTTTACAGTAATTAACCAGTTATGTTATCGTCGGGTTTAT
196 CTAATATGTTATTATGCTTGATAATGTTTCCAGTAATTAACCGGTTATGTTATCGTCGGATTTCT
* ** *
490360 AAGGCTCCAT-AACATTAATTTTTGGTAACATTTTAGGCAATACCTAATATGTTGATAATACTGA
261 AAGGCTCCATCAGC-TTAAACTTTGGTAACATTTTAGGCATTACCTAATATGTTGATAATACTGA
* * ** *
490424 TAACAAATTAAATAATTAACATA-TTTGTTATCGTC-GAATTTCTAAGGTACCATTAGCTTTAAA
325 TAACAAATTAAGTAATTAACCTATTTTGTTATCGTCAG-ATTTCTAAGGCCCCATCAGCTTTAAA
* * **
490487 AA-AGTGCTACTTATTTTGTTACATAAGCGCTACCTAATATGTTATTATGCTTGATAATGTTTCC
389 AAGA-CGCTACCTATTACGTTACATAAGCGCTACCTAATATGTTATTATGCTTGATAATGTTTCC
*
490551 AGTAATTAACCGGTTATGTTATCGTCGGATTTCTAAGGCTCCGTCAGCTTAAACTTTGGTAACAT
1 AGTAATTAACCGGTTATGTTATCGTCGGATTTCTAAGGCTCCATCAGCTTAAACTTTGGTAACAT
* * * *
490616 TTTAGGCATTACCT-A-AT-TTGTTAATACTAATGAA-AAATTAAGTAATTAATCTATTTTGTTA
66 TTTAGGCGTTACCTAATATGTTGATAATACTGAT-AACAAATTAAGTAATTAACCTATTTTGTTA
* ** * * *
490677 TCGGCGGATTTCTAAGGCCCTGTCATCTTTAAAAAGGTGCTACCTATTACGTTACATAAACACTA
130 TCGTCGGATTTCTAAGGCCCCATCAGCTTTAAAAAGGCGCTACCTATTACGTTACATAAGCACTA
* *
490742 CCTAATATGTTATTATGTTTGATAATGTTTCCAGTAATTAACCGGTTATGTTATTGTCGGATTTC
195 CCTAATATGTTATTATGCTTGATAATGTTTCCAGTAATTAACCGGTTATGTTATCGTCGGATTTC
** *
490807 TAAGGCTCCATCAGCTTAAACTTTGGTAACATTTTAGGTGTTACCTTATATGTTGATAATACTGA
260 TAAGGCTCCATCAGCTTAAACTTTGGTAACATTTTAGGCATTACCTAATATGTTGATAATACTGA
* * ** *
490872 TTAGAAATTAAGTAATTAATTTATTTTGTTATCGTCAGATTTCTAAGGCCCCATCAACTTTAAAA
325 TAACAAATTAAGTAATTAACCTATTTTGTTATCGTCAGATTTCTAAGGCCCCATCAGCTTTAAAA
* * * * * **
490937 AGGCACTACCTATTACATTACATAAGTGGTACCTAATATGTTATTATGCTTGATAATGTTTTA
390 AGACGCTACCTATTACGTTACATAAGCGCTACCTAATATGTTATTATGCTTGATAATGTTTCC
* * * *
491000 AGTAATTAATCGGTTATGTTATCGTTGGATTTCTAAAGCTCCATCAGCTTAAACTTTGATAACAT
1 AGTAATTAACCGGTTATGTTATCGTCGGATTTCTAAGGCTCCATCAGCTTAAACTTTGGTAACAT
* *
491065 TTTAGGCGTTACATAATATGTTGATAATACTAATAACAAATTAAGTAATTAACCTATTTTGTTAT
66 TTTAGGCGTTACCTAATATGTTGATAATACTGATAACAAATTAAGTAATTAACCTATTTTGTTAT
* * * * *
491130 CGTCGGATTTCTACA-GCCCCATCAACTTTTAAAAGGCGTTACCTATTACGTTACATAAGCTCTG
131 CGTCGGATTTCTA-AGGCCCCATCAGCTTTAAAAAGGCGCTACCTATTACGTTACATAAGCACTA
* * * *
491194 CCTAATATGTTATTATGCTTGATAATGTTTCCAATAGTTAATCGGTTATGCTT-TCTTCGGATTT
195 CCTAATATGTTATTATGCTTGATAATGTTTCCAGTAATTAACCGGTTATG-TTATCGTCGGATTT
* * * * *
491258 GTAAGGCTCCTTTAGCTTAAGCTTTGGCAACATTTTAGGCATTACCTAATATGTTGATAATACTG
259 CTAAGGCTCCATCAGCTTAAACTTTGGTAACATTTTAGGCATTACCTAATATGTTGATAATACTG
*
491323 ATAACAAATTATGTAATTAACCTATTTTGTTATCGTCAGA--T-T---------T---C-TT-AA
324 ATAACAAATTAAGTAATTAACCTATTTTGTTATCGTCAGATTTCTAAGGCCCCATCAGCTTTAAA
* ** * * *
491371 AAGGCATTACCTATTACGCTACATAAGCTCTGCCTAATATGTTATTATGCTTGATAATGTTTCC
389 AAGACGCTACCTATTACGTTACATAAGCGCTACCTAATATGTTATTATGCTTGATAATGTTTCC
* * * * * * * *
491435 AATAATTAATCGGTTATGCTATCGTCGGATTTGTAAAGCTCCTTCAGCTTAAGCTTTGGCAACAT
1 AGTAATTAACCGGTTATGTTATCGTCGGATTTCTAAGGCTCCATCAGCTTAAACTTTGGTAACAT
* *
491500 TTTAGGCATTACCTAATATGTTGATAATACTGATAACAAATTATGTAATTAACCTATTTTGTTAT
66 TTTAGGCGTTACCTAATATGTTGATAATACTGATAACAAATTAAGTAATTAACCTATTTTGTTAT
* * * *
491565 CGTCGGATTTTTAAGGCCCCATCAGTTTTAAAAAGTCGCTACCTATTACGTTACATAAGCGCTAC
131 CGTCGGATTTCTAAGGCCCCATCAGCTTTAAAAAGGCGCTACCTATTACGTTACATAAGCACTAC
* * * *
491630 CTAATATG---TTA---TT-ATAATGTTTCCTGTAATTAACCAGATATGTTATCGTCGGATTTAT
196 CTAATATGTTATTATGCTTGATAATGTTTCCAGTAATTAACCGGTTATGTTATCGTCGGATTTCT
* * ** ** *
491688 AAGGTTCCATAAAATTAATTTTTGGTAACATTTTAGGCGTTACCTAATATGTTGATAATACTGAT
261 AAGGCTCCATCAGCTTAAACTTTGGTAACATTTTAGGCATTACCTAATATGTTGATAATACTGAT
* * *
491753 AACAAATTAAGTAATTAACATATTTTGTTATCGTCGGATTTCTAAGGTCCCATCAGCTTTAAAAA
326 AACAAATTAAGTAATTAACCTATTTTGTTATCGTCAGATTTCTAAGGCCCCATCAGCTTTAAAAA
* * *
491818 GACGTTACCTATTTCGTTACATAAGCGCTACCTAATATGTTATTATGATTGATAATGTTTCC
391 GACGCTACCTATTACGTTACATAAGCGCTACCTAATATGTTATTATGCTTGATAATGTTTCC
* * * * * *
491880 AGTAATTAACAGGTTATGTTATCATCGGATTTTTAAGGCTCCATCAGGTTAAACTTAGGTAA-AA
1 AGTAATTAACCGGTTATGTTATCGTCGGATTTCTAAGGCTCCATCAGCTTAAACTTTGGTAACAT
* * *
491944 TTTAGGCGTTTCCTAATATGTTGATAATATTGATAACAAATTAAGTAATTAACCTATTTTTTTAT
66 TTTAGGCGTTACCTAATATGTTGATAATACTGATAACAAATTAAGTAATTAACCTATTTTGTTAT
* * ** * * *
492009 TGTCGGATTACTAAGATCCCATCAGCTTTAAAAAGGCGCTACCTATGACATTACATAAGCGCTAC
131 CGTCGGATTTCTAAGGCCCCATCAGCTTTAAAAAGGCGCTACCTATTACGTTACATAAGCACTAC
* ***
492074 CTAATATGTTATTATGCTTGATAATGTTTCCAATAATTATTTGGTTATGTTATCGTCGGATTTCT
196 CTAATATGTTATTATGCTTGATAATGTTTCCAGTAATTAACCGGTTATGTTATCGTCGGATTTCT
* * * * *
492139 AAGGC-CGCATCAACTTAAACTTTGGTAACATTTTAAGCATTA-CTAATATGTTGATAAAATTGT
261 AAGGCTC-CATCAGCTTAAACTTTGGTAACATTTTAGGCATTACCTAATATGTTGATAATACTGA
*
492202 TAACAAATTAAGTAATTAACCTATTTTGTTATCGTCAGATTTCTAAGGTCCCATCAGCTTTAAAA
325 TAACAAATTAAGTAATTAACCTATTTTGTTATCGTCAGATTTCTAAGGCCCCATCAGCTTTAAAA
* * *
492267 ATG-CGCTACTTATTACGTTACATAAACGCTACGTAATATGTTATTATG
390 A-GACGCTACCTATTACGTTACATAAGCGCTACCTAATATGTTATTATG
492315 TTTTTCCAGT
Statistics
Matches: 2316, Mismatches: 300, Indels: 100
0.85 0.11 0.04
Matches are distributed among these distances:
427 2 0.00
428 125 0.05
429 2 0.00
430 1 0.00
431 1 0.00
432 3 0.00
434 1 0.00
435 238 0.10
436 2 0.00
437 1 0.00
440 2 0.00
443 1 0.00
444 127 0.05
445 109 0.05
447 18 0.01
448 210 0.09
449 163 0.07
450 392 0.17
451 277 0.12
452 637 0.28
453 4 0.00
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.38
Consensus pattern (452 bp):
AGTAATTAACCGGTTATGTTATCGTCGGATTTCTAAGGCTCCATCAGCTTAAACTTTGGTAACAT
TTTAGGCGTTACCTAATATGTTGATAATACTGATAACAAATTAAGTAATTAACCTATTTTGTTAT
CGTCGGATTTCTAAGGCCCCATCAGCTTTAAAAAGGCGCTACCTATTACGTTACATAAGCACTAC
CTAATATGTTATTATGCTTGATAATGTTTCCAGTAATTAACCGGTTATGTTATCGTCGGATTTCT
AAGGCTCCATCAGCTTAAACTTTGGTAACATTTTAGGCATTACCTAATATGTTGATAATACTGAT
AACAAATTAAGTAATTAACCTATTTTGTTATCGTCAGATTTCTAAGGCCCCATCAGCTTTAAAAA
GACGCTACCTATTACGTTACATAAGCGCTACCTAATATGTTATTATGCTTGATAATGTTTCC
Found at i:491518 original size:209 final size:208
Alignment explanation
Indices: 491156--491578 Score: 765
Period size: 209 Copynumber: 2.0 Consensus size: 208
491146 CCCCATCAAC
* *
491156 TTTTAAAAGGCGTTACCTATTACGTTACATAAGCTCTGCCTAATATGTTATTATGCTTGATAATG
1 TTTTAAAAGGCATTACCTATTACGCTACATAAGCTCTGCCTAATATGTTATTATGCTTGATAATG
* * * * *
491221 TTTCCAATAGTTAATCGGTTATGCTTTCTTCGGATTTGTAAGGCTCCTTTAGCTTAAGCTTTGGC
66 TTTCCAATAATTAATCGGTTATGCTATCGTCGGATTTGTAAAGCTCCTTCAGCTTAAGCTTTGGC
491286 AACATTTTAGGCATTACCTAATATGTTGATAATACTGATAACAAATTATGTAATTAACCTATTTT
131 AACATTTTAGGCATTACCTAATATGTTGATAATACTGATAACAAATTATGTAATTAACCTATTTT
491351 GTTATCGTCAGAT
196 GTTATCGTCAGAT
491364 TTCTTAAAAGGCATTACCTATTACGCTACATAAGCTCTGCCTAATATGTTATTATGCTTGATAAT
1 TT-TTAAAAGGCATTACCTATTACGCTACATAAGCTCTGCCTAATATGTTATTATGCTTGATAAT
491429 GTTTCCAATAATTAATCGGTTATGCTATCGTCGGATTTGTAAAGCTCCTTCAGCTTAAGCTTTGG
65 GTTTCCAATAATTAATCGGTTATGCTATCGTCGGATTTGTAAAGCTCCTTCAGCTTAAGCTTTGG
491494 CAACATTTTAGGCATTACCTAATATGTTGATAATACTGATAACAAATTATGTAATTAACCTATTT
130 CAACATTTTAGGCATTACCTAATATGTTGATAATACTGATAACAAATTATGTAATTAACCTATTT
*
491559 TGTTATCGTCGGAT
195 TGTTATCGTCAGAT
491573 TTTTAA
1 TTTTAA
491579 GGCCCCATCA
Statistics
Matches: 206, Mismatches: 8, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
208 6 0.03
209 200 0.97
ACGTcount: A:0.29, C:0.16, G:0.15, T:0.40
Consensus pattern (208 bp):
TTTTAAAAGGCATTACCTATTACGCTACATAAGCTCTGCCTAATATGTTATTATGCTTGATAATG
TTTCCAATAATTAATCGGTTATGCTATCGTCGGATTTGTAAAGCTCCTTCAGCTTAAGCTTTGGC
AACATTTTAGGCATTACCTAATATGTTGATAATACTGATAACAAATTATGTAATTAACCTATTTT
GTTATCGTCAGAT
Found at i:492625 original size:20 final size:21
Alignment explanation
Indices: 492602--492709 Score: 75
Period size: 20 Copynumber: 5.3 Consensus size: 21
492592 TTACAATTTT
492602 ATAA-TATTTATGATTTTTAA
1 ATAATTATTTATGATTTTTAA
* * *
492622 ATAATTATTTTTTACAATTTT--
1 ATAATTA-TTTAT-GATTTTTAA
* *
492643 ATAA-TAGTTATGGTTTTTAA
1 ATAATTATTTATGATTTTTAA
*
492663 ATAATTATTT-TGCATTTTAAA
1 ATAATTATTTATG-ATTTTTAA
* *
492684 ATAACTA-TTATAATTTTTAA
1 ATAATTATTTATGATTTTTAA
492704 ATAATT
1 ATAATT
492710 CTATTTTTAT
Statistics
Matches: 65, Mismatches: 15, Indels: 16
0.68 0.16 0.17
Matches are distributed among these distances:
18 4 0.06
19 3 0.05
20 26 0.40
21 23 0.35
22 4 0.06
23 5 0.08
ACGTcount: A:0.39, C:0.03, G:0.05, T:0.54
Consensus pattern (21 bp):
ATAATTATTTATGATTTTTAA
Found at i:492638 original size:41 final size:41
Alignment explanation
Indices: 492587--492673 Score: 156
Period size: 41 Copynumber: 2.1 Consensus size: 41
492577 ATATTTTATA
*
492587 ATTTTTTACAATTTTATAATATTTATGATTTTTAAATAATT
1 ATTTTTTACAATTTTATAATAGTTATGATTTTTAAATAATT
*
492628 ATTTTTTACAATTTTATAATAGTTATGGTTTTTAAATAATT
1 ATTTTTTACAATTTTATAATAGTTATGATTTTTAAATAATT
492669 ATTTT
1 ATTTT
492674 GCATTTTAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 44 1.00
ACGTcount: A:0.34, C:0.02, G:0.05, T:0.59
Consensus pattern (41 bp):
ATTTTTTACAATTTTATAATAGTTATGATTTTTAAATAATT
Found at i:492931 original size:11 final size:11
Alignment explanation
Indices: 492887--492932 Score: 51
Period size: 11 Copynumber: 4.3 Consensus size: 11
492877 ATAATATCAA
492887 TTTAAAATGA-
1 TTTAAAATGAT
*
492897 TTAAAAATGAT
1 TTTAAAATGAT
492908 TTTATAAA-GAT
1 TTTA-AAATGAT
*
492919 TTTAAAATAAT
1 TTTAAAATGAT
492930 TTT
1 TTT
492933 GAATGTATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
10 12 0.40
11 15 0.50
12 3 0.10
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.46
Consensus pattern (11 bp):
TTTAAAATGAT
Found at i:495228 original size:26 final size:25
Alignment explanation
Indices: 495198--495246 Score: 71
Period size: 26 Copynumber: 1.9 Consensus size: 25
495188 TTATGTTAAA
*
495198 ATAATAAATTTACAAAGATTTTAGGG
1 ATAATAAACTTACAAA-ATTTTAGGG
*
495224 ATAATAAACTTATAAAATTTTAG
1 ATAATAAACTTACAAAATTTTAG
495247 AAACAAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 7 0.33
26 14 0.67
ACGTcount: A:0.49, C:0.04, G:0.10, T:0.37
Consensus pattern (25 bp):
ATAATAAACTTACAAAATTTTAGGG
Found at i:500423 original size:6 final size:6
Alignment explanation
Indices: 500414--500441 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
500404 TTTAATAATT
500414 ATAAAA ATAAAA ATAAAA ATAAAA ATAA
1 ATAAAA ATAAAA ATAAAA ATAAAA ATAA
500442 TAAAAATCCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (6 bp):
ATAAAA
Found at i:501981 original size:18 final size:18
Alignment explanation
Indices: 501958--501998 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
501948 ACCCGTCACA
* *
501958 ACCCGACCCGTTGACCTG
1 ACCCGACCCGATGACCCG
*
501976 ACCCGATCCGATGACCCG
1 ACCCGACCCGATGACCCG
501994 ACCCG
1 ACCCG
501999 TTGACCGTTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.20, C:0.46, G:0.22, T:0.12
Consensus pattern (18 bp):
ACCCGACCCGATGACCCG
Found at i:504572 original size:29 final size:24
Alignment explanation
Indices: 504451--504562 Score: 154
Period size: 24 Copynumber: 4.7 Consensus size: 24
504441 TTCTATTATA
* * *
504451 ATACCTGACCTGGATTCTGATCAG
1 ATACTTGACCTGGATTTTGATCTG
*
504475 ATACTTGACCTGGATTCTGATC-G
1 ATACTTGACCTGGATTTTGATCTG
*
504498 AATACTTGACCTGAATTTTGATCTG
1 -ATACTTGACCTGGATTTTGATCTG
504523 ATACTTGACCTGGATTTTGATCTG
1 ATACTTGACCTGGATTTTGATCTG
*
504547 ATATTTGACCTGGATT
1 ATACTTGACCTGGATT
504563 ATGTTTTGAT
Statistics
Matches: 81, Mismatches: 5, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
23 1 0.01
24 79 0.98
25 1 0.01
ACGTcount: A:0.24, C:0.19, G:0.20, T:0.38
Consensus pattern (24 bp):
ATACTTGACCTGGATTTTGATCTG
Found at i:504743 original size:2 final size:2
Alignment explanation
Indices: 504736--504768 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
504726 CGGATGGGGG
504736 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
504769 TTTAAAAAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:510810 original size:23 final size:22
Alignment explanation
Indices: 510766--510848 Score: 96
Period size: 23 Copynumber: 3.8 Consensus size: 22
510756 TTTGGTGCAG
*
510766 AGGGAATCGATACCCCCTTGAA
1 AGGGAATCGATTCCCCCTTGAA
510788 AGGGAATCGATTCCCCCTCTGAA
1 AGGGAATCGATTCCCCCT-TGAA
* * *
510811 GGGGAACCGATTCCCCC-TGTA
1 AGGGAATCGATTCCCCCTTGAA
* *
510832 GGGGAATCGATACCCCC
1 AGGGAATCGATTCCCCC
510849 CTGGGGTTCT
Statistics
Matches: 54, Mismatches: 6, Indels: 3
0.86 0.10 0.05
Matches are distributed among these distances:
21 18 0.33
22 17 0.31
23 19 0.35
ACGTcount: A:0.25, C:0.31, G:0.25, T:0.18
Consensus pattern (22 bp):
AGGGAATCGATTCCCCCTTGAA
Found at i:510836 original size:21 final size:21
Alignment explanation
Indices: 510767--510848 Score: 92
Period size: 21 Copynumber: 3.8 Consensus size: 21
510757 TTGGTGCAGA
* *
510767 GGGAATCGATACCCCCTTGAAA
1 GGGAATCGATTCCCCC-TGAAG
510789 GGGAATCGATTCCCCCTCTGAAG
1 GGGAATCGATT-CCCC-CTGAAG
* *
510812 GGGAACCGATTCCCCCTGTAG
1 GGGAATCGATTCCCCCTGAAG
*
510833 GGGAATCGATACCCCC
1 GGGAATCGATTCCCCC
510849 CTGGGGTTCT
Statistics
Matches: 52, Mismatches: 6, Indels: 5
0.83 0.10 0.08
Matches are distributed among these distances:
21 19 0.37
22 14 0.27
23 18 0.35
24 1 0.02
ACGTcount: A:0.24, C:0.32, G:0.26, T:0.18
Consensus pattern (21 bp):
GGGAATCGATTCCCCCTGAAG
Found at i:510851 original size:22 final size:22
Alignment explanation
Indices: 510767--510851 Score: 100
Period size: 22 Copynumber: 3.9 Consensus size: 22
510757 TTGGTGCAGA
* *
510767 GGGAATCGATACCCCCTTGAAA
1 GGGAATCGATACCCCCCTGAAG
*
510789 GGGAATCGATTCCCCCTCTGAAG
1 GGGAATCGATACCCCC-CTGAAG
* * *
510812 GGGAACCGAT-TCCCCCTGTAG
1 GGGAATCGATACCCCCCTGAAG
510833 GGGAATCGATACCCCCCTG
1 GGGAATCGATACCCCCCTG
510852 GGGTTCTATT
Statistics
Matches: 53, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
21 14 0.26
22 26 0.49
23 13 0.25
ACGTcount: A:0.24, C:0.32, G:0.26, T:0.19
Consensus pattern (22 bp):
GGGAATCGATACCCCCCTGAAG
Found at i:512758 original size:17 final size:16
Alignment explanation
Indices: 512729--512794 Score: 64
Period size: 16 Copynumber: 4.1 Consensus size: 16
512719 CATTTTGGAT
*
512729 ATTTTGGAATGTTTGA
1 ATTTTGGATTGTTTGA
512745 ATTTGTGGATTGTTTG-
1 ATTT-TGGATTGTTTGA
* *
512761 ACTTTGAATTTGTTTGA
1 ATTTTGGA-TTGTTTGA
512778 ATTTATGGA-TGTTTGA
1 ATTT-TGGATTGTTTGA
512794 A
1 A
512795 CTTATATTTC
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
15 3 0.07
16 22 0.54
17 13 0.32
18 3 0.07
ACGTcount: A:0.23, C:0.02, G:0.24, T:0.52
Consensus pattern (16 bp):
ATTTTGGATTGTTTGA
Found at i:515118 original size:55 final size:55
Alignment explanation
Indices: 514213--515105 Score: 1113
Period size: 55 Copynumber: 16.2 Consensus size: 55
514203 CAACAGAATA
* * * *
514213 ATAGGACTCGAACAATCTT-TGACAAACGGGTATGTTCCCTATTCTTTCAGGGAGT
1 ATAGGACTCGAACAATCTTCAG-CAAACGTGTCTGCTCCCTATTCTTTCAGGGAGT
** * * * * *
514268 ATAAAACTCAAACAATATTCAGCAAACGTGTCCGTTCCTTATTCTTTCAGGGAGT
1 ATAGGACTCGAACAATCTTCAGCAAACGTGTCTGCTCCCTATTCTTTCAGGGAGT
* *
514323 ATAGGACTCGAACAATCTTTAGCAAACGTGTCTGCTCCCTATTCTTTCACGGAGT
1 ATAGGACTCGAACAATCTTCAGCAAACGTGTCTGCTCCCTATTCTTTCAGGGAGT
* * * *
514378 ATAGGACTCGAACAATCTTTAGTAAACATGTCTGCTTCCTATTCTTTCAGGGAGT
1 ATAGGACTCGAACAATCTTCAGCAAACGTGTCTGCTCCCTATTCTTTCAGGGAGT
* *
514433 ATAGGACTCGAACAATCTTTAGCAAACATGTCTGCTCCCTATTCTTTCAGGGAGT
1 ATAGGACTCGAACAATCTTCAGCAAACGTGTCTGCTCCCTATTCTTTCAGGGAGT
** * ** * *
514488 ATAGGACTTAAACCATCTTCATAAAACGTGTTTGCTCCCTATTCTTTCAGTGAGT
1 ATAGGACTCGAACAATCTTCAGCAAACGTGTCTGCTCCCTATTCTTTCAGGGAGT
* * * *** * *
514543 ATAGGACTCGAACAATCTTCAGTAAACTTATCCAATCTCTATTCTTTCAGGGACT
1 ATAGGACTCGAACAATCTTCAGCAAACGTGTCTGCTCCCTATTCTTTCAGGGAGT
* * * * * *
514598 ATAGAACTCGAATAATCTTCAGCAAACGTGTATGCTTCCTATTATTTCAGGGATT
1 ATAGGACTCGAACAATCTTCAGCAAACGTGTCTGCTCCCTATTCTTTCAGGGAGT
* * * * * **
514653 ATAGGACTCCATCAATCTTCAGTAAATGTGTCTACTCTATATTCTTTCAGGGAGT
1 ATAGGACTCGAACAATCTTCAGCAAACGTGTCTGCTCCCTATTCTTTCAGGGAGT
* * * *
514708 GTAGGACTCAAACAATCTTCAGCAAACATGTCTGCTCTCTATTCTTTCAGGGAGT
1 ATAGGACTCGAACAATCTTCAGCAAACGTGTCTGCTCCCTATTCTTTCAGGGAGT
*
514763 ATAGGACTCGAACAATCTTCAGCAAATGTGTCTGCTCCCTATTCTTTCAGGGAGT
1 ATAGGACTCGAACAATCTTCAGCAAACGTGTCTGCTCCCTATTCTTTCAGGGAGT
* * *
514818 ATAAGACTCAAACAATCTTCAGCAAACGTGTATGCTCCCTATTCTTTCAGGGAGT
1 ATAGGACTCGAACAATCTTCAGCAAACGTGTCTGCTCCCTATTCTTTCAGGGAGT
* * *
514873 ATAGGACTCGAGCAATCTTCAGCAAACGTGTATGCTCCCTATTATTTCAGGGAGT
1 ATAGGACTCGAACAATCTTCAGCAAACGTGTCTGCTCCCTATTCTTTCAGGGAGT
* * *
514928 ATAGGACTTGAACAATCTTCAGAAAACGTGTCTTCTCCCTATTCTTTCAGGGAGT
1 ATAGGACTCGAACAATCTTCAGCAAACGTGTCTGCTCCCTATTCTTTCAGGGAGT
* * * * *
514983 ATAGGACTCAAACAATCTTCAGCATACGTGTCTACTCCATATTCTTTTAGGGAGT
1 ATAGGACTCGAACAATCTTCAGCAAACGTGTCTGCTCCCTATTCTTTCAGGGAGT
* * ** * *
515038 ATAGGACTCGAACCATGTTCATAAAACGTGTCTTCTCTCTATTCTTTCAGGGAGT
1 ATAGGACTCGAACAATCTTCAGCAAACGTGTCTGCTCCCTATTCTTTCAGGGAGT
*
515093 ATAAGACTCGAAC
1 ATAGGACTCGAAC
515106 CATATTCATA
Statistics
Matches: 719, Mismatches: 118, Indels: 2
0.86 0.14 0.00
Matches are distributed among these distances:
55 718 1.00
56 1 0.00
ACGTcount: A:0.28, C:0.22, G:0.17, T:0.32
Consensus pattern (55 bp):
ATAGGACTCGAACAATCTTCAGCAAACGTGTCTGCTCCCTATTCTTTCAGGGAGT
Found at i:515213 original size:37 final size:37
Alignment explanation
Indices: 515159--515272 Score: 144
Period size: 37 Copynumber: 3.1 Consensus size: 37
515149 ATCAGACTCG
* * *
515159 AGATTGATTTG-CTTCACTATTGTTTCGTGAAGGCTTA
1 AGATTGATTTGTC-TCACTACTCTTCCGTGAAGGCTTA
* *
515196 AGATTAATTTGTCTCACTACTCTTCCATGAAGGCTTA
1 AGATTGATTTGTCTCACTACTCTTCCGTGAAGGCTTA
515233 AGA-TGATTTGAT-TCACTACTCTTCCGTGAAGGCTTA
1 AGATTGATTTG-TCTCACTACTCTTCCGTGAAGGCTTA
515269 AGAT
1 AGAT
515273 GGCCCAAAGG
Statistics
Matches: 67, Mismatches: 7, Indels: 6
0.84 0.09 0.08
Matches are distributed among these distances:
36 32 0.48
37 34 0.51
38 1 0.01
ACGTcount: A:0.25, C:0.18, G:0.18, T:0.39
Consensus pattern (37 bp):
AGATTGATTTGTCTCACTACTCTTCCGTGAAGGCTTA
Found at i:515249 original size:36 final size:35
Alignment explanation
Indices: 515163--515273 Score: 141
Period size: 36 Copynumber: 3.1 Consensus size: 35
515153 GACTCGAGAT
* * *
515163 TGATTTGCTTCACTATTGTTTCGTGAAGGCTTAAGA
1 TGATTTG-TTCACTACTCTTCCGTGAAGGCTTAAGA
* *
515199 TTAATTTGTCTCACTACTCTTCCATGAAGGCTTAAGA
1 -TGATTTGT-TCACTACTCTTCCGTGAAGGCTTAAGA
515236 TGATTTGATTCACTACTCTTCCGTGAAGGCTTAAGA
1 TGATTTG-TTCACTACTCTTCCGTGAAGGCTTAAGA
515272 TG
1 TG
515274 GCCCAAAGGA
Statistics
Matches: 65, Mismatches: 7, Indels: 5
0.84 0.09 0.06
Matches are distributed among these distances:
36 35 0.54
37 30 0.46
ACGTcount: A:0.24, C:0.18, G:0.19, T:0.39
Consensus pattern (35 bp):
TGATTTGTTCACTACTCTTCCGTGAAGGCTTAAGA
Found at i:515400 original size:37 final size:37
Alignment explanation
Indices: 515359--515473 Score: 178
Period size: 37 Copynumber: 3.1 Consensus size: 37
515349 TACTGATGGC
*
515359 TTGCTTCACTACTCTTCCGTAAAGGCTTAAGATTGAT
1 TTGCTTCACTACTCTTCCGTGAAGGCTTAAGATTGAT
515396 TTGCTTCACTACTCTTCCGTGAAGGCTTAAGATCT-AT
1 TTGCTTCACTACTCTTCCGTGAAGGCTTAAGAT-TGAT
* * *
515433 TTGCTTTAGTACTCTTCCGTGAAGGCTTAAGATTGAC
1 TTGCTTCACTACTCTTCCGTGAAGGCTTAAGATTGAT
515470 TTGC
1 TTGC
515474 CCCAATCTCA
Statistics
Matches: 72, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
36 1 0.01
37 70 0.97
38 1 0.01
ACGTcount: A:0.22, C:0.22, G:0.18, T:0.38
Consensus pattern (37 bp):
TTGCTTCACTACTCTTCCGTGAAGGCTTAAGATTGAT
Found at i:517297 original size:13 final size:13
Alignment explanation
Indices: 517288--517323 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
517278 ATATGACGCG
517288 CATTTATGACACA
1 CATTTATGACACA
*
517301 CATTTATGACAAA
1 CATTTATGACACA
*
517314 AATTTATGAC
1 CATTTATGAC
517324 GTTCATTGAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.42, C:0.17, G:0.08, T:0.33
Consensus pattern (13 bp):
CATTTATGACACA
Found at i:517408 original size:85 final size:85
Alignment explanation
Indices: 517318--517515 Score: 285
Period size: 85 Copynumber: 2.3 Consensus size: 85
517308 GACAAAAATT
517318 TATGACGTT-CATTGAGTGTCATTGAAGCCCCCGTCATAAAT-TAAG-ATGACACACATTTGTGC
1 TATGAC-TTACATTGAGTGTCATTGAAGCCCCCGTCATAAATCT--GTATGACACACATTTGTGC
517380 GTCATAAATTTATGACACGCATG
63 GTCATAAATTTATGACACGCATG
* * * * *
517403 TATGACTTACATTGCGCGTCATTGAAGCCCCCGTCATAAATCTGTTTGACATACATTTGTGTGTC
1 TATGACTTACATTGAGTGTCATTGAAGCCCCCGTCATAAATCTGTATGACACACATTTGTGCGTC
*
517468 TTAAATTTATGACACGCATG
66 ATAAATTTATGACACGCATG
*
517488 TATGACTTACATTGTGTGTCATTGAAGC
1 TATGACTTACATTGAGTGTCATTGAAGC
517516 ACACATCATT
Statistics
Matches: 102, Mismatches: 8, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
84 3 0.03
85 98 0.96
86 1 0.01
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.34
Consensus pattern (85 bp):
TATGACTTACATTGAGTGTCATTGAAGCCCCCGTCATAAATCTGTATGACACACATTTGTGCGTC
ATAAATTTATGACACGCATG
Found at i:519998 original size:39 final size:38
Alignment explanation
Indices: 519955--520036 Score: 137
Period size: 39 Copynumber: 2.1 Consensus size: 38
519945 TCTTTCTTTT
* *
519955 TTTTCCTTTTCGGTGTCCCTTCTCCTTTCTCCTCTTCC
1 TTTTCCTTTGCAGTGTCCCTTCTCCTTTCTCCTCTTCC
519993 GTTTTCCTTTGCAGTGTCCCTTCTCCTTTCTCCTCTTCC
1 -TTTTCCTTTGCAGTGTCCCTTCTCCTTTCTCCTCTTCC
520032 TTTTC
1 TTTTC
520037 AACAAGTTCT
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
38 5 0.12
39 36 0.88
ACGTcount: A:0.01, C:0.38, G:0.09, T:0.52
Consensus pattern (38 bp):
TTTTCCTTTGCAGTGTCCCTTCTCCTTTCTCCTCTTCC
Found at i:523895 original size:15 final size:15
Alignment explanation
Indices: 523861--523900 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
523851 TATGCTTTAT
523861 TTTTCCTTCTTTGACG
1 TTTT-CTTCTTTGACG
523877 -TTTCTTCTTTGACG
1 TTTTCTTCTTTGACG
523891 TTTTCTTCTT
1 TTTTCTTCTT
523901 AGTTGTTGTC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 11 0.48
15 12 0.52
ACGTcount: A:0.05, C:0.23, G:0.10, T:0.62
Consensus pattern (15 bp):
TTTTCTTCTTTGACG
Found at i:531629 original size:14 final size:14
Alignment explanation
Indices: 531610--531639 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
531600 GCTAACATGC
*
531610 ATCAAAAGAAAAAA
1 ATCAAAACAAAAAA
531624 ATCAAAACAAAAAA
1 ATCAAAACAAAAAA
531638 AT
1 AT
531640 GAAGAATCTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.77, C:0.10, G:0.03, T:0.10
Consensus pattern (14 bp):
ATCAAAACAAAAAA
Found at i:533710 original size:27 final size:28
Alignment explanation
Indices: 533673--533728 Score: 87
Period size: 27 Copynumber: 2.0 Consensus size: 28
533663 AATATACATT
533673 TTTAAAGAAACCTAAAAATTTCAAAAAC
1 TTTAAAGAAACCTAAAAATTTCAAAAAC
* *
533701 TTTAAA-AAACCTCAAAATTTTAAAAAC
1 TTTAAAGAAACCTAAAAATTTCAAAAAC
533728 T
1 T
533729 ACAATTTCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
27 20 0.77
28 6 0.23
ACGTcount: A:0.55, C:0.14, G:0.02, T:0.29
Consensus pattern (28 bp):
TTTAAAGAAACCTAAAAATTTCAAAAAC
Found at i:534566 original size:21 final size:22
Alignment explanation
Indices: 534540--534598 Score: 59
Period size: 23 Copynumber: 2.7 Consensus size: 22
534530 ATAATTTACA
534540 TCGAAGTGCCACATA-TTCGTC
1 TCGAAGTGCCACATATTTCGTC
*
534561 TCGAAG-GACCACATAATTTTGTC
1 TCGAAGTG-CCACAT-ATTTCGTC
* *
534584 CCGAAGTACCACATA
1 TCGAAGTGCCACATA
534599 GGTTTGTCCT
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
20 1 0.03
21 12 0.39
22 2 0.06
23 16 0.52
ACGTcount: A:0.31, C:0.27, G:0.17, T:0.25
Consensus pattern (22 bp):
TCGAAGTGCCACATATTTCGTC
Found at i:534594 original size:23 final size:23
Alignment explanation
Indices: 534562--534668 Score: 142
Period size: 23 Copynumber: 4.7 Consensus size: 23
534552 ATATTCGTCT
**
534562 CGAAGGACCACATAATTTTGTCC
1 CGAAGGACCACATAGGTTTGTCC
*
534585 CGAAGTACCACATAGGTTTGTCC
1 CGAAGGACCACATAGGTTTGTCC
* * *
534608 TGAATGACCACATAGTTTTGTCC
1 CGAAGGACCACATAGGTTTGTCC
* *
534631 CGAAGGATCACATAGGTTTGTCA
1 CGAAGGACCACATAGGTTTGTCC
534654 CGAAGGACCACATAG
1 CGAAGGACCACATAG
534669 AACCCTCAAC
Statistics
Matches: 71, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 71 1.00
ACGTcount: A:0.30, C:0.23, G:0.21, T:0.25
Consensus pattern (23 bp):
CGAAGGACCACATAGGTTTGTCC
Found at i:534627 original size:46 final size:46
Alignment explanation
Indices: 534562--534668 Score: 162
Period size: 46 Copynumber: 2.3 Consensus size: 46
534552 ATATTCGTCT
* *
534562 CGAAGGACCACATAATTTTGTCCCGAAGTACCACATAGGTTTGTC-
1 CGAAGGACCACATAGTTTTGTCCCGAAGGACCACATAGGTTTGTCA
* *
534607 CTGAATGACCACATAGTTTTGTCCCGAAGGATCACATAGGTTTGTCA
1 C-GAAGGACCACATAGTTTTGTCCCGAAGGACCACATAGGTTTGTCA
534654 CGAAGGACCACATAG
1 CGAAGGACCACATAG
534669 AACCCTCAAC
Statistics
Matches: 55, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
45 1 0.02
46 53 0.96
47 1 0.02
ACGTcount: A:0.30, C:0.23, G:0.21, T:0.25
Consensus pattern (46 bp):
CGAAGGACCACATAGTTTTGTCCCGAAGGACCACATAGGTTTGTCA
Found at i:537443 original size:21 final size:21
Alignment explanation
Indices: 537417--537460 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
537407 AAAAAAAGTT
537417 TTAACATCTATTTATGAAAAA
1 TTAACATCTATTTATGAAAAA
537438 TTAACATCTATTTATGAAAAA
1 TTAACATCTATTTATGAAAAA
537459 TT
1 TT
537461 TGTTCACTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.45, C:0.09, G:0.05, T:0.41
Consensus pattern (21 bp):
TTAACATCTATTTATGAAAAA
Found at i:539719 original size:24 final size:24
Alignment explanation
Indices: 539691--539739 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
539681 GTTAAAAGAA
*
539691 TGATTGGTTATTTTTCATTTTTCT
1 TGATTGGTTATTTTTCATCTTTCT
539715 TGATTGGTTATTTTTCATCTTTCT
1 TGATTGGTTATTTTTCATCTTTCT
539739 T
1 T
539740 CCTTTTATCT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.12, C:0.10, G:0.12, T:0.65
Consensus pattern (24 bp):
TGATTGGTTATTTTTCATCTTTCT
Found at i:551757 original size:21 final size:21
Alignment explanation
Indices: 551731--551776 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
551721 ATTTACCATG
* *
551731 ATTGCGACCGTCGCGGGCGCT
1 ATTGCGACCATCGCGGACGCT
*
551752 ATTGCGGCCATCGCGGACGCT
1 ATTGCGACCATCGCGGACGCT
551773 ATTG
1 ATTG
551777 ACTGTCTTGG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.13, C:0.30, G:0.35, T:0.22
Consensus pattern (21 bp):
ATTGCGACCATCGCGGACGCT
Found at i:553566 original size:35 final size:36
Alignment explanation
Indices: 553523--553594 Score: 137
Period size: 36 Copynumber: 2.0 Consensus size: 36
553513 AGACAATTGA
553523 GGGGTGGGG-CATAATTGGAAAGATAACTCGAGGAG
1 GGGGTGGGGACATAATTGGAAAGATAACTCGAGGAG
553558 GGGGTGGGGACATAATTGGAAAGATAACTCGAGGAG
1 GGGGTGGGGACATAATTGGAAAGATAACTCGAGGAG
553594 G
1 G
553595 AGGTTATCGA
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
35 9 0.25
36 27 0.75
ACGTcount: A:0.32, C:0.08, G:0.43, T:0.17
Consensus pattern (36 bp):
GGGGTGGGGACATAATTGGAAAGATAACTCGAGGAG
Found at i:560266 original size:63 final size:63
Alignment explanation
Indices: 560167--560315 Score: 280
Period size: 63 Copynumber: 2.4 Consensus size: 63
560157 GACGCCACAT
560167 CTATTTAAATGGAATACTGCAATCTTGAATTTAAAAGATTTGCAACCTATATTATCATTACTA
1 CTATTTAAATGGAATACTGCAATCTTGAATTTAAAAGATTTGCAACCTATATTATCATTACTA
* *
560230 CTATTTAAATGGAATCCTGCAATCTTGAATTTAAAAGTTTTGCAACCTATATTATCATTACTA
1 CTATTTAAATGGAATACTGCAATCTTGAATTTAAAAGATTTGCAACCTATATTATCATTACTA
560293 CTATTTAAATGGAATACTGCAAT
1 CTATTTAAATGGAATACTGCAAT
560316 GATGATGAAT
Statistics
Matches: 83, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
63 83 1.00
ACGTcount: A:0.37, C:0.15, G:0.10, T:0.38
Consensus pattern (63 bp):
CTATTTAAATGGAATACTGCAATCTTGAATTTAAAAGATTTGCAACCTATATTATCATTACTA
Found at i:562075 original size:7 final size:8
Alignment explanation
Indices: 562056--562081 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
562046 ACACCCATTC
562056 AAAAACAG
1 AAAAACAG
562064 AAAAACAG
1 AAAAACAG
562072 AAAAACAG
1 AAAAACAG
562080 AA
1 AA
562082 GACACCCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.77, C:0.12, G:0.12, T:0.00
Consensus pattern (8 bp):
AAAAACAG
Found at i:573458 original size:21 final size:21
Alignment explanation
Indices: 573434--573480 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 21
573424 GGAGTACGGA
573434 GGACGGCGGACA-GCAAGCGAC
1 GGACGGCGGA-AGGCAAGCGAC
*
573455 GGACGGTGGAAGGCAAGCGAC
1 GGACGGCGGAAGGCAAGCGAC
573476 GGACG
1 GGACG
573481 ACGATGGAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 1 0.04
21 23 0.96
ACGTcount: A:0.28, C:0.23, G:0.47, T:0.02
Consensus pattern (21 bp):
GGACGGCGGAAGGCAAGCGAC
Found at i:575029 original size:2 final size:2
Alignment explanation
Indices: 575022--575060 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
575012 CGTCTGATTT
*
575022 TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
575061 ATCTGCAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:575266 original size:38 final size:37
Alignment explanation
Indices: 575146--575308 Score: 161
Period size: 37 Copynumber: 4.3 Consensus size: 37
575136 ATTTTGAAAA
** * * *
575146 TATATAATATAGGGTTTTTAAAGCATTTTG-AAAACC
1 TATATAATATATAGTTTTAAAAACATTTTGAAAAACT
* *
575182 TATATAATATATTGTTTTGAAAATCATTTT-AAAAA-T
1 TATATAATATATAGTTTT-AAAAACATTTTGAAAAACT
575218 ATATATAATATATAGTTTTAAAAAACATTTTGAAAAACT
1 -TATATAATATATAGTTTT-AAAAACATTTTGAAAAACT
* * *
575257 TATACAATATATAATTTTAAAAACATTTTTTGAAAAAAAT
1 TATATAATATATAGTTTTAAAAACA--TTTTG-AAAAACT
575297 TATATAATATAT
1 TATATAATATAT
575309 TTTTATTATA
Statistics
Matches: 107, Mismatches: 12, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
36 16 0.15
37 47 0.44
38 21 0.20
39 6 0.06
40 17 0.16
ACGTcount: A:0.47, C:0.05, G:0.06, T:0.42
Consensus pattern (37 bp):
TATATAATATATAGTTTTAAAAACATTTTGAAAAACT
Found at i:576480 original size:5 final size:5
Alignment explanation
Indices: 576465--576514 Score: 50
Period size: 5 Copynumber: 10.0 Consensus size: 5
576455 GTATTATTAG
* *
576465 TATTAT TATTT TATTT TATTT T-TCTT T-TTT TATTT TATCT CATTT TATTT
1 TATT-T TATTT TATTT TATTT TAT-TT TATTT TATTT TATTT TATTT TATTT
576515 CTGCGATTTA
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
4 4 0.11
5 30 0.79
6 4 0.11
ACGTcount: A:0.18, C:0.06, G:0.00, T:0.76
Consensus pattern (5 bp):
TATTT
Found at i:576537 original size:14 final size:15
Alignment explanation
Indices: 576520--576548 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
576510 TATTTCTGCG
576520 ATTTATTT-TTATTT
1 ATTTATTTCTTATTT
576534 ATTTATTTCTTATTT
1 ATTTATTTCTTATTT
576549 TTAATCTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (15 bp):
ATTTATTTCTTATTT
Found at i:576548 original size:21 final size:23
Alignment explanation
Indices: 576522--576565 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 23
576512 TTTCTGCGAT
*
576522 TTATTTTT-ATTTATT-TATTTC
1 TTATTTTTAATCTATTCTATTTC
576543 TTATTTTTAATCTATTCTATTTC
1 TTATTTTTAATCTATTCTATTTC
576566 ATTTATTCTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 8 0.40
22 6 0.30
23 6 0.30
ACGTcount: A:0.20, C:0.09, G:0.00, T:0.70
Consensus pattern (23 bp):
TTATTTTTAATCTATTCTATTTC
Found at i:579311 original size:95 final size:95
Alignment explanation
Indices: 579141--579400 Score: 274
Period size: 95 Copynumber: 2.7 Consensus size: 95
579131 ATTATATATA
* * * ***
579141 TATATATATACAATAAAGCTTGAGCTATCCCTCTAAAGCAATTGGTTAAACGCTTTAGCTTTATG
1 TATA-ATATACAATAAAACTTGAGCTGTCCCTCTAGAGCAATTGGTTAAACGCCCGAGCTTTATG
*
579206 GATAAGATTCAGCTAGCCTGGTAAAGGTGAT
65 GATAAGATTCAGCTAGCCTGATAAAGGTGAT
* * *
579237 TATAATATACAATAAAACTTGAGTTGTCCCTTTAGAGCAATTGGTTAAACATCCCGA-CTTTATG
1 TATAATATACAATAAAACTTGAGCTGTCCCTCTAGAGCAATTGGTTAAAC-GCCCGAGCTTTATG
* * *
579301 GATAATATTCAGCTAGTCTGATAAAGGTGGT
65 GATAAGATTCAGCTAGCCTGATAAAGGTGAT
* * * * * *
579332 TATAATAT-CTATACAATGATATTAAGCTGTCCCTGTAGAGCAATTGGTTAAATGCCCG-GCTCT
1 TATAATATACAATA-AA--A-CTTGAGCTGTCCCTCTAGAGCAATTGGTTAAACGCCCGAGCTTT
579395 ATGGAT
62 ATGGAT
579401 TCATCTAGCT
Statistics
Matches: 137, Mismatches: 21, Indels: 11
0.81 0.12 0.07
Matches are distributed among these distances:
94 4 0.03
95 85 0.62
96 6 0.04
97 14 0.10
98 28 0.20
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Consensus pattern (95 bp):
TATAATATACAATAAAACTTGAGCTGTCCCTCTAGAGCAATTGGTTAAACGCCCGAGCTTTATGG
ATAAGATTCAGCTAGCCTGATAAAGGTGAT
Found at i:580673 original size:84 final size:83
Alignment explanation
Indices: 580522--582157 Score: 1520
Period size: 84 Copynumber: 19.5 Consensus size: 83
580512 GAAATTGTTG
* * *
580522 GCAGCATAATTCAAGACTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCA
1 GCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTA-ACTCA
* *
580587 GCTCAAAGACACAACATTT
65 GCTCAAAGGCACATCATTT
** * * * * *
580606 GCAATATAGCTCAAGGCGAAAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCGACTAAGCACA
1 GCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTAA-CTCA
*
580671 GCTGC-AAGGCACAACATTT
65 GCT-CAAAGGCACATCATTT
** * * **
580690 GCAGCATAACTCAATACCAGAAGGGTTATCTGCTAACAAAAGACCTTCGAGTTTAACTACACTCA
1 GCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTA-ACTCA
* *
580755 GCTCCAAGACACATCATTT
65 GCTCAAAGGCACATCATTT
* * * * * * *
580774 GCAACATAACTCAAGGCAAGAACGGCTATTTGCCAACAAAAAACCTTCGAGTTCGACTACGCTCA
1 GCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTA-ACTCA
*
580839 GCTCCAAGGCACATCATTT
65 GCTCAAAGGCACATCATTT
* * ** *
580858 GCAGCATAACTCAAGGCTAGAAGGATTATCTGACAGTAAAAGACCTTCGAGTTCGACTACGCTCA
1 GCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTA-ACTCA
*
580923 GCTCCAAGGCACATCATTT
65 GCTCAAAGGCACATCATTT
* * * * * *
580942 GCAGTATAACTCAAGGCTAAAAGGGTTATCTGCCAAGAAAATACCTTCGAGCTCAACTACACTCA
1 GCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTA-ACTCA
*
581007 GCTCCAAGGCACATCATTT
65 GCTCAAAGGCACATCATTT
* * *
581026 GCAGCATAGCTAAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCA
1 GCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTA-ACTCA
* * *
581091 GCTAAAAGACACAACATTT
65 GCTCAAAGGCACATCATTT
* * * * * * * *
581110 ACAGCATAGCTCAAGGCGAGAATGGTTATTTGCCGACAAAAGACCTTCGAGTTTGACTACGCTCA
1 GCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTA-ACTCA
* *
581175 GCTGC-AATGCACAACATTT
65 GCT-CAAAGGCACATCATTT
* * * * ** *
581194 GCAGCATAACTCAAGGCCAGAAAGATTATCTGCCAACAAAAGAACTTCGAGTTTAACTACGCTCA
1 GCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTA-ACTCA
581259 GCTCCAAA-GCACATCATTT
65 GCT-CAAAGGCACATCATTT
** * * ** * * * * *
581278 GCAATATAACTCAAGGCAATAAATGCTATTTGCCAACAAAAGACCTTCGAGATCGACTACGCTTA
1 GCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTA-ACTCA
581343 GCTCCAAA-GCACATCATTT
65 GCT-CAAAGGCACATCATTT
* * * *
581362 GCAGCATAACTCAAGGCTAGAAGGGTTATATGCCAACAAAAGACCTTGGAGTTCGATTACGCTCA
1 GCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTA-ACTCA
* *
581427 ACTCAAAGGCACATTATTT
65 GCTCAAAGGCACATCATTT
** * * * *
581446 GCAATATAACTCAAGGCTAGAAGGATTATCTG-C--C--AAGACCTTCAAGTTCGACTACGCTTA
1 GCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTA-ACTCA
* *
581506 GCTCCAAGGCATATCATTT
65 GCTCAAAGGCACATCATTT
** * * * * * *
581525 GCAATATAACTCAAGGCAAGAAGGGCTATTTGTCAACAAAAGACTTTCGACTTCGACTTCGATTA
1 GCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGA----C--CTTCGAGTTCGACTA
581590 CACTCAGCT-ACAAGGCACAAT-ATTT
60 -ACTCAGCTCA-AAGGCAC-ATCATTT
* * * * * * *
581615 ACAGCATAACTCAATGCTAGAAGGGTTATCTGCAAACCAAAGACCTTCGGGTTCGATTACACTTA
1 GCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTA-ACTCA
* *
581680 GCTCAAGGGAACATCATTT
65 GCTCAAAGGCACATCATTT
* * * * * * *
581699 ACAACATAACTCAAGGCTAGAAGGGTTATCTGTCAA-TAAAGACTTTCAAGTTCGATTACACTCA
1 GCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTA-ACTCA
581763 GCTCAAAGGCACATCATTT
65 GCTCAAAGGCACATCATTT
* * * * ** * *
581782 GCAGCATAGCTTAAGCCGAGAAGGGTTATCTGCCAACCAAAA-ACCTTCGAGTTAAATTACATTC
1 GCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAA-CAAAAGACCTTCGAGTTCGACTA-ACTC
* *
581846 AACTCAAAGGCACATAATTT
64 AGCTCAAAGGCACATCATTT
* * * * *
581866 GCAGCATAACTCAAGACAAGAAGGGTTATCTGCCAACAAAAAACCTTCGAGTTTGATTACACTCA
1 GCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTA-ACTCA
* *
581931 GCTGAAGGGCACATCATTT
65 GCTCAAAGGCACATCATTT
** ** * * * *
581950 ATAATATAACTCAAGGCTAGAAGGGTTATCTGTCAAC-AAAGACCTTC-ATATTCGATTGCACTC
1 GCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGA-GTTCGACT-AACTC
* *
582013 AACTCAAAGACACATCATTT
64 AGCTCAAAGGCACATCATTT
* * *
582033 GCAGCATAACTCAAGGCTAGAAAGGTTATCTGCCAACAAAAGACCTGCGAGTTCGATTACACTCA
1 GCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTA-ACTCA
*
582098 GCTCAAATGCACATCATTT
65 GCTCAAAGGCACATCATTT
* * * **
582117 ACAGCATATCTCAAGGCAAGAAGGGTTATCTATCAACAAAA
1 GCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAA
582158 TTGTCGAGTT
Statistics
Matches: 1293, Mismatches: 229, Indels: 60
0.82 0.14 0.04
Matches are distributed among these distances:
79 65 0.05
80 1 0.00
81 1 0.00
82 2 0.00
83 149 0.12
84 1000 0.77
85 9 0.01
86 1 0.00
88 1 0.00
90 62 0.05
91 2 0.00
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.23
Consensus pattern (83 bp):
GCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTAACTCAG
CTCAAAGGCACATCATTT
Found at i:580810 original size:168 final size:168
Alignment explanation
Indices: 580522--582157 Score: 1681
Period size: 168 Copynumber: 9.7 Consensus size: 168
580512 GAAATTGTTG
* *
580522 GCAGCATAATTCAAGACTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCA
1 GCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCA
* * * * *
580587 GCTCAAAGACACAACATTTGCAATATAGCTCAAGGCGAA-AAGGGCTATCTGCCAACAAAAGACC
66 GCTCAAAGGCACATCATTTGCAACATAACTCAAGGC-AAGAAGGGTTATCTGCCAACAAAAGACC
* * *
580651 TTCGAGTTCGACTAAGCACAGCTGCAAGGCACAACATTT
130 TTCGAGTTCGACTAAGCTCAGCTCCAAGGCACATCATTT
** * * ** *
580690 GCAGCATAACTCAATACCAGAAGGGTTATCTGCTAACAAAAGACCTTCGAGTTTAACTACACTCA
1 GCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCA
* * * * * *
580755 GCTCCAAGACACATCATTTGCAACATAACTCAAGGCAAGAACGGCTATTTGCCAACAAAAAACCT
66 GCTCAAAGGCACATCATTTGCAACATAACTCAAGGCAAGAAGGGTTATCTGCCAACAAAAGACCT
*
580820 TCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTT
131 TCGAGTTCGACTAAGCTCAGCTCCAAGGCACATCATTT
* * ** * *
580858 GCAGCATAACTCAAGGCTAGAAGGATTATCTGACAGTAAAAGACCTTCGAGTTCGACTACGCTCA
1 GCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCA
* ** * *
580923 GCTCCAAGGCACATCATTTGCAGTATAACTCAAGGCTAA-AAGGGTTATCTGCCAAGAAAATACC
66 GCTCAAAGGCACATCATTTGCAACATAACTCAAGGC-AAGAAGGGTTATCTGCCAACAAAAGACC
* *
580987 TTCGAGCTCAACTACA-CTCAGCTCCAAGGCACATCATTT
130 TTCGAGTTCGACTA-AGCTCAGCTCCAAGGCACATCATTT
* *
581026 GCAGCATAGCTAAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCA
1 GCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCA
* * * * * * * * * *
581091 GCTAAAAGACACAACATTTACAGCATAGCTCAAGGCGAGAATGGTTATTTGCCGACAAAAGACCT
66 GCTCAAAGGCACATCATTTGCAACATAACTCAAGGCAAGAAGGGTTATCTGCCAACAAAAGACCT
* * * * *
581156 TCGAGTTTGACTACGCTCAGCTGCAATGCACAACATTT
131 TCGAGTTCGACTAAGCTCAGCTCCAAGGCACATCATTT
* * * * ** * *
581194 GCAGCATAACTCAAGGCCAGAAAGATTATCTGCCAACAAAAGAACTTCGAGTTTAACTACGCTCA
1 GCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCA
* * ** * *
581259 GCTCCAAA-GCACATCATTTGCAATATAACTCAAGGCAATAAATGCTATTTGCCAACAAAAGACC
66 GCT-CAAAGGCACATCATTTGCAACATAACTCAAGGCAAGAAGGGTTATCTGCCAACAAAAGACC
* * * *
581323 TTCGAGATCGACTACGCTTAGCTCCAAAGCACATCATTT
130 TTCGAGTTCGACTAAGCTCAGCTCCAAGGCACATCATTT
* * *
581362 GCAGCATAACTCAAGGCTAGAAGGGTTATATGCCAACAAAAGACCTTGGAGTTCGATTACGCTCA
1 GCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCA
* * * * *
581427 ACTCAAAGGCACATTATTTGCAATATAACTCAAGGCTAGAAGGATTATCTG-C--C--AAGACCT
66 GCTCAAAGGCACATCATTTGCAACATAACTCAAGGCAAGAAGGGTTATCTGCCAACAAAAGACCT
* * * *
581487 TCAAGTTCGACTACGCTTAGCTCCAAGGCATATCATTT
131 TCGAGTTCGACTAAGCTCAGCTCCAAGGCACATCATTT
** * * * * *
581525 GCAATATAACTCAAGGCAAGAAGGGCTATTTGTCAACAAAAGACTTTCGACTTCGACTTCGATTA
1 GCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGA----C--CTTCGAGTTCGATTA
* * * * * *
581590 CACTCAGCT-ACAAGGCACAAT-ATTTACAGCATAACTCAATGCTAGAAGGGTTATCTGCAAACC
60 CACTCAGCTCA-AAGGCAC-ATCATTTGCAACATAACTCAAGGCAAGAAGGGTTATCTGCCAACA
* * * *
581653 AAAGACCTTCGGGTTCGATTACA-CTTAGCT-CAAGGGAACATCATTT
123 AAAGACCTTCGAGTTCGACTA-AGCTCAGCTCCAA-GGCACATCATTT
* * * * * *
581699 ACAACATAACTCAAGGCTAGAAGGGTTATCTGTCAA-TAAAGACTTTCAAGTTCGATTACACTCA
1 GCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCA
* * * * *
581763 GCTCAAAGGCACATCATTTGCAGCATAGCTTAAGCCGAGAAGGGTTATCTGCCAACCAAAA-ACC
66 GCTCAAAGGCACATCATTTGCAACATAACTCAAGGCAAGAAGGGTTATCTGCCAA-CAAAAGACC
** * * * * *
581827 TTCGAGTTAAATTACA-TTCAACTCAAAGGCACATAATTT
130 TTCGAGTTCGACTA-AGCTCAGCTCCAAGGCACATCATTT
* * * *
581866 GCAGCATAACTCAAGACAAGAAGGGTTATCTGCCAACAAAAAACCTTCGAGTTTGATTACACTCA
1 GCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCA
* * ** * * *
581931 GCTGAAGGGCACATCATTTATAATATAACTCAAGGCTAGAAGGGTTATCTGTCAAC-AAAGACCT
66 GCTCAAAGGCACATCATTTGCAACATAACTCAAGGCAAGAAGGGTTATCTGCCAACAAAAGACCT
* * * * * *
581995 TC-ATATTCGATTGCA-CTCAACTCAAAGACACATCATTT
131 TCGA-GTTCGACT-AAGCTCAGCTCCAAGGCACATCATTT
* *
582033 GCAGCATAACTCAAGGCTAGAAAGGTTATCTGCCAACAAAAGACCTGCGAGTTCGATTACACTCA
1 GCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCA
* * * * **
582098 GCTCAAATGCACATCATTTACAGCATATCTCAAGGCAAGAAGGGTTATCTATCAACAAAA
66 GCTCAAAGGCACATCATTTGCAACATAACTCAAGGCAAGAAGGGTTATCTGCCAACAAAA
582158 TTGTCGAGTT
Statistics
Matches: 1227, Mismatches: 210, Indels: 62
0.82 0.14 0.04
Matches are distributed among these distances:
163 78 0.06
165 1 0.00
166 6 0.00
167 270 0.22
168 732 0.60
169 64 0.05
170 2 0.00
172 1 0.00
173 8 0.01
174 65 0.05
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.23
Consensus pattern (168 bp):
GCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCA
GCTCAAAGGCACATCATTTGCAACATAACTCAAGGCAAGAAGGGTTATCTGCCAACAAAAGACCT
TCGAGTTCGACTAAGCTCAGCTCCAAGGCACATCATTT
Found at i:581477 original size:504 final size:500
Alignment explanation
Indices: 580522--582157 Score: 1935
Period size: 504 Copynumber: 3.2 Consensus size: 500
580512 GAAATTGTTG
* *
580522 GCAGCATAATTCAAGACTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCA
1 GCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCA
* * ** * *
580587 GCTCAAAGACACAACATTTGCAATATAGCTCAAGGCGAAAAGGGCTATCTGCCAACAAAAGACCT
66 GCTAAAAGACACAACATTTACAGCATAGCTCAAGGCGAGAAGGGTTATCTGCCAACAAAAGACCT
* * **
580652 TCGAGTTCGACTAAGCACAGCTGCAAGGCACAACATTTGCAGCATAACTCAATACCAGAAGGGTT
131 TCGAGTTCGACTACGCTCAGCTGCAAGGCACAACATTTGCAGCATAACTCAAGGCCAGAAGGGTT
* *
580717 ATCTGCTAACAAAAGACCTTCGAGTTTAACTACACTCAGCTCC-AAGACACATCATTTGCAACAT
196 ATCTGCCAACAAAAGAACTTCGAGTTTAACTACACTCAGCTCCAAAG-CACATCATTTGCAACAT
* *
580781 AACTCAAGGCAAGAACGGCTATTTGCCAACAAAAAACCTTCGAGTTCGACTACGCTCAGCTCCAA
260 AACTCAAGGCAAGAAAGGCTATTTGCCAAC-AAAAACCTTCGAGTTCGACTACGCTTAGCTCCAA
* * * **
580846 GGCACATCATTTGCAGCATAACTCAAGGCTAGAAGGATTATCTGACAGTAAAAGACCTTCGAGTT
324 AGCACATCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTT
* * * *
580911 CGACTACGCTCAGCTCCAAGGCACATCATTTGCAGTATAACTCAAGGCTAAAAGGGTTATCTGCC
389 CGATTACGCTCAGCTCAAAGGCACATCATTTGCAATATAACTCAAGGCTAGAAGGGTTATCTGCC
* *
580976 AAGAAAATACCTTCGAGCTCAACTACACTCAGCTCCAAGGCACATCATTT
454 AAG-AAA-ACCTTC-AGTTCGACTACACTCAGCTCCAAGGCACATCATTT
* *
581026 GCAGCATAGCTAAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCA
1 GCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCA
* * *
581091 GCTAAAAGACACAACATTTACAGCATAGCTCAAGGCGAGAATGGTTATTTGCCGACAAAAGACCT
66 GCTAAAAGACACAACATTTACAGCATAGCTCAAGGCGAGAAGGGTTATCTGCCAACAAAAGACCT
* * * *
581156 TCGAGTTTGACTACGCTCAGCTGCAATGCACAACATTTGCAGCATAACTCAAGGCCAGAAAGATT
131 TCGAGTTCGACTACGCTCAGCTGCAAGGCACAACATTTGCAGCATAACTCAAGGCCAGAAGGGTT
* *
581221 ATCTGCCAACAAAAGAACTTCGAGTTTAACTACGCTCAGCTCCAAAGCACATCATTTGCAATATA
196 ATCTGCCAACAAAAGAACTTCGAGTTTAACTACACTCAGCTCCAAAGCACATCATTTGCAACATA
* * *
581286 ACTCAAGGCAATAAATGCTATTTGCCAACAAAAGACCTTCGAGATCGACTACGCTTAGCTCCAAA
261 ACTCAAGGCAAGAAAGGCTATTTGCCAACAAAA-ACCTTCGAGTTCGACTACGCTTAGCTCCAAA
* *
581351 GCACATCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATATGCCAACAAAAGACCTTGGAGTTC
325 GCACATCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTC
* * *
581416 GATTACGCTCAACTCAAAGGCACATTATTTGCAATATAACTCAAGGCTAGAAGGATTATCTGCCA
390 GATTACGCTCAGCTCAAAGGCACATCATTTGCAATATAACTCAAGGCTAGAAGGGTTATCTGCCA
* * *
581481 AG---ACCTTCAAGTTCGACTACGCTTAGCTCCAAGGCATATCATTT
455 AGAAAACCTTC-AGTTCGACTACACTCAGCTCCAAGGCACATCATTT
** * * * * *
581525 GCAATATAACTCAAGGCAAGAAGGGCTATTTGTCAACAAAAGACTTTCGACTTCGACTTCGATTA
1 GCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGA----C--CTTCGAGTTCGATTA
* * * * * * * *
581590 CACTCAGCTACAAGGCACAATATTTACAGCATAACTCAATGCTAGAAGGGTTATCTGCAAACCAA
60 CACTCAGCTAAAAGACACAACATTTACAGCATAGCTCAAGGCGAGAAGGGTTATCTGCCAACAAA
* * * * * * * * *
581655 AGACCTTCGGGTTCGATTACACTTAGCT-CAAGGGAACATCATTTACAACATAACTCAAGGCTAG
125 AGACCTTCGAGTTCGACTACGCTCAGCTGCAA-GGCACAACATTTGCAGCATAACTCAAGGCCAG
* * * ** *
581719 AAGGGTTATCTGTCAA-TAAAG-ACTTTCAAGTTCGATTACACTCAGCT-CAAAGGCACATCATT
189 AAGGGTTATCTGCCAACAAAAGAAC-TTCGAGTTTAACTACACTCAGCTCCAAA-GCACATCATT
* * * * * * * * ** * *
581781 TGCAGCATAGCTTAAGCCGAGAAGGGTTATCTGCCAACCAAAAACCTTCGAGTTAAATTAC-ATT
252 TGCAACATAACTCAAGGCAAGAAAGGCTATTTGCCAA-CAAAAACCTTCGAGTTCGACTACGCTT
* * * * *
581845 CAACT-CAAAGGCACATAATTTGCAGCATAACTCAAGACAAGAAGGGTTATCTGCCAACAAAAAA
316 -AGCTCCAAA-GCACATCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGA
* * * * **
581909 CCTTCGAGTTTGATTACACTCAGCTGAAGGGCACATCATTTATAATATAACTCAAGGCTAGAAGG
379 CCTTCGAGTTCGATTACGCTCAGCTCAAAGGCACATCATTTGCAATATAACTCAAGGCTAGAAGG
* * * * * * * *
581974 GTTATCTGTCAACAAAGACCTTCATATTCGATTGCACTCAACTCAAAGACACATCATTT
444 GTTATCTGCCAAGAAA-ACCTTCA-GTTCGACTACACTCAGCTCCAAGGCACATCATTT
* *
582033 GCAGCATAACTCAAGGCTAGAAAGGTTATCTGCCAACAAAAGACCTGCGAGTTCGATTACACTCA
1 GCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCA
* * * * **
582098 GCTCAAATG-CACATCATTTACAGCATATCTCAAGGCAAGAAGGGTTATCTATCAACAAAA
66 GCT-AAAAGACACAACATTTACAGCATAGCTCAAGGCGAGAAGGGTTATCTGCCAACAAAA
582158 TTGTCGAGTT
Statistics
Matches: 959, Mismatches: 153, Indels: 42
0.83 0.13 0.04
Matches are distributed among these distances:
499 71 0.07
502 64 0.07
503 20 0.02
504 598 0.62
505 138 0.14
507 1 0.00
508 67 0.07
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.23
Consensus pattern (500 bp):
GCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCA
GCTAAAAGACACAACATTTACAGCATAGCTCAAGGCGAGAAGGGTTATCTGCCAACAAAAGACCT
TCGAGTTCGACTACGCTCAGCTGCAAGGCACAACATTTGCAGCATAACTCAAGGCCAGAAGGGTT
ATCTGCCAACAAAAGAACTTCGAGTTTAACTACACTCAGCTCCAAAGCACATCATTTGCAACATA
ACTCAAGGCAAGAAAGGCTATTTGCCAACAAAAACCTTCGAGTTCGACTACGCTTAGCTCCAAAG
CACATCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCG
ATTACGCTCAGCTCAAAGGCACATCATTTGCAATATAACTCAAGGCTAGAAGGGTTATCTGCCAA
GAAAACCTTCAGTTCGACTACACTCAGCTCCAAGGCACATCATTT
Found at i:582800 original size:41 final size:41
Alignment explanation
Indices: 582723--582800 Score: 95
Period size: 41 Copynumber: 1.9 Consensus size: 41
582713 AATGTTTTTG
* **
582723 AAATACATATAATATATATAGTTTTGAAAATGATTTTTTAA
1 AAATACATATAATATATATAGTTTTAAAAACCATTTTTTAA
* *
582764 AAATATATATAATATATA-ATTTTTAAAAAACCATTTT
1 AAATACATATAATATATATAGTTTT-AAAAACCATTTT
582801 GAAAATATAT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
40 5 0.16
41 26 0.84
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.44
Consensus pattern (41 bp):
AAATACATATAATATATATAGTTTTAAAAACCATTTTTTAA
Found at i:585258 original size:3 final size:3
Alignment explanation
Indices: 585245--585281 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
585235 ATGCAATTTA
*
585245 TAT TA- TAT TAT TAT TAG TA- TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
585282 ACGTTTTTGT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
2 4 0.13
3 27 0.87
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:585267 original size:14 final size:14
Alignment explanation
Indices: 585248--585274 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
585238 CAATTTATAT
585248 TATATTATTATTAG
1 TATATTATTATTAG
585262 TATATTATTATTA
1 TATATTATTATTA
585275 TTATTATACG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (14 bp):
TATATTATTATTAG
Found at i:585272 original size:17 final size:17
Alignment explanation
Indices: 585250--585282 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
585240 ATTTATATTA
585250 TATTATTATTAGTATAT
1 TATTATTATTAGTATAT
*
585267 TATTATTATTATTATA
1 TATTATTATTAGTATA
585283 CGTTTTTGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (17 bp):
TATTATTATTAGTATAT
Found at i:586499 original size:17 final size:18
Alignment explanation
Indices: 586479--586528 Score: 70
Period size: 17 Copynumber: 2.9 Consensus size: 18
586469 TTTCTACGTA
586479 TATTTTTATT-TATTTTT
1 TATTTTTATTCTATTTTT
586496 TATTTTT-TTCCTATTTTT
1 TATTTTTATT-CTATTTTT
586514 TA-TTTTATTCTATTT
1 TATTTTTATTCTATTT
586529 CATTTCTTCT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
16 2 0.07
17 17 0.57
18 11 0.37
ACGTcount: A:0.16, C:0.06, G:0.00, T:0.78
Consensus pattern (18 bp):
TATTTTTATTCTATTTTT
Found at i:586502 original size:18 final size:18
Alignment explanation
Indices: 586489--586528 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
586479 TATTTTTATT
586489 TATTTTTTATTTTTTTCC
1 TATTTTTTATTTTTTTCC
*
586507 TATTTTTTATTTTATT-C
1 TATTTTTTATTTTTTTCC
586524 TATTT
1 TATTT
586529 CATTTCTTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 6 0.29
18 15 0.71
ACGTcount: A:0.15, C:0.07, G:0.00, T:0.78
Consensus pattern (18 bp):
TATTTTTTATTTTTTTCC
Found at i:586527 original size:28 final size:28
Alignment explanation
Indices: 586439--586528 Score: 85
Period size: 33 Copynumber: 3.0 Consensus size: 28
586429 TTTTATTAAA
586439 TTTTT-CTATTTTTTATTTTA-TCTCATT
1 TTTTTCCTATTTTTTATTTTATTCT-ATT
* *
586466 TTGTTTCTACGTATATTTTTATTTATTTTTTATT
1 TT-TTTC--C-TAT-TTTTTATTT-TATTCTATT
586500 TTTTTCCTATTTTTTATTTTATTCTATT
1 TTTTTCCTATTTTTTATTTTATTCTATT
586528 T
1 T
586529 CATTTCTTCT
Statistics
Matches: 51, Mismatches: 4, Indels: 15
0.73 0.06 0.21
Matches are distributed among these distances:
27 2 0.04
28 11 0.22
29 9 0.18
30 3 0.06
31 2 0.04
32 3 0.06
33 13 0.25
34 6 0.12
35 2 0.04
ACGTcount: A:0.16, C:0.09, G:0.02, T:0.73
Consensus pattern (28 bp):
TTTTTCCTATTTTTTATTTTATTCTATT
Found at i:598596 original size:18 final size:17
Alignment explanation
Indices: 598573--598611 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
598563 TTATTTGAGG
*
598573 TATTTTACTATTGATTAT
1 TATTTTAATATT-ATTAT
*
598591 TATTTTAATATTATTTT
1 TATTTTAATATTATTAT
598608 TATT
1 TATT
598612 AATATATGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.67
Consensus pattern (17 bp):
TATTTTAATATTATTAT
Found at i:598649 original size:48 final size:50
Alignment explanation
Indices: 598574--598682 Score: 141
Period size: 49 Copynumber: 2.2 Consensus size: 50
598564 TATTTGAGGT
* * * *
598574 ATTTTACTATTGATTATTATTTTAATATTATTTTTAT-TAATATATGTTA
1 ATTTTACGATTGATTATTATGTTAATATTATTTTTATATAATATATATCA
* *
598623 ATTTTACGATTG-TTGTTATGTTAATATTATTTTTATATTATATATATCA
1 ATTTTACGATTGATTATTATGTTAATATTATTTTTATATAATATATATCA
*
598672 TTTTTACGATT
1 ATTTTACGATT
598683 TATGATCATA
Statistics
Matches: 52, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
48 22 0.42
49 30 0.58
ACGTcount: A:0.30, C:0.04, G:0.06, T:0.60
Consensus pattern (50 bp):
ATTTTACGATTGATTATTATGTTAATATTATTTTTATATAATATATATCA
Found at i:600516 original size:18 final size:18
Alignment explanation
Indices: 600493--600528 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
600483 GCACTGGTAA
600493 GTTTTATTTTCAACATTT
1 GTTTTATTTTCAACATTT
600511 GTTTTATTTTCAACATTT
1 GTTTTATTTTCAACATTT
600529 ATGTAATGAT
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:0.22, C:0.11, G:0.06, T:0.61
Consensus pattern (18 bp):
GTTTTATTTTCAACATTT
Found at i:602086 original size:3 final size:3
Alignment explanation
Indices: 602078--602121 Score: 56
Period size: 3 Copynumber: 15.0 Consensus size: 3
602068 TTTAATTACA
*
602078 TAT TAT TAT TAT TAT TAT TAT TAT TA- TAT T-G TAT TAT ATAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT
602122 AAAATATACA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
2 3 0.08
3 30 0.83
4 3 0.08
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:603480 original size:32 final size:34
Alignment explanation
Indices: 603434--603519 Score: 104
Period size: 37 Copynumber: 2.5 Consensus size: 34
603424 GAAAATATTA
* *
603434 TAACGAATTCAATTTAA-T-AACAATCTACTAAG
1 TAACTAATTTAATTTAACTAAACAATCTACTAAG
*
603466 TAACTAATTTAATTTAATCTAAAAATAATCTACTAAG
1 TAACTAATTTAATTTAA-CT--AAACAATCTACTAAG
603503 TAACTAATTTAATTTAA
1 TAACTAATTTAATTTAA
603520 ACAAGTAAAA
Statistics
Matches: 46, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
32 15 0.33
34 1 0.02
37 30 0.65
ACGTcount: A:0.48, C:0.12, G:0.03, T:0.37
Consensus pattern (34 bp):
TAACTAATTTAATTTAACTAAACAATCTACTAAG
Found at i:603824 original size:15 final size:15
Alignment explanation
Indices: 603793--603865 Score: 62
Period size: 15 Copynumber: 4.8 Consensus size: 15
603783 TGACTTTAAC
603793 TTTC-TTCTCTTCT-T
1 TTTCTTTCT-TTCTCT
603807 TTTCTTTCTTTCTCT
1 TTTCTTTCTTTCTCT
*
603822 TTTCTTTTTTTCTTCCT
1 TTTCTTTCTTTC-T-CT
*
603839 CTTCTTTC-TTCTCT
1 TTTCTTTCTTTCTCT
*
603853 CCTTCTTTCTTTC
1 -TTTCTTTCTTTC
603866 ATCTCGGTAT
Statistics
Matches: 50, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
14 10 0.20
15 25 0.50
16 7 0.14
17 8 0.16
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (15 bp):
TTTCTTTCTTTCTCT
Found at i:603846 original size:21 final size:20
Alignment explanation
Indices: 603792--603865 Score: 61
Period size: 19 Copynumber: 3.9 Consensus size: 20
603782 CTGACTTTAA
603792 CTTTCTTCTCTTC-TT-TTT
1 CTTTCTTCTCTTCTTTCTTT
603810 CTTTCTT-TC-TCTTTTCTTT
1 CTTTCTTCTCTTC-TTTCTTT
*
603829 TTTTCTTCCTCTTCTTTC-TT
1 CTTTCTT-CTCTTCTTTCTTT
*
603849 CTCTCCTTCT-TTCTTTC
1 CT-TTCTTCTCTTCTTTC
603866 ATCTCGGTAT
Statistics
Matches: 46, Mismatches: 3, Indels: 13
0.74 0.05 0.21
Matches are distributed among these distances:
16 2 0.04
17 2 0.04
18 9 0.20
19 16 0.35
20 5 0.11
21 10 0.22
22 2 0.04
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (20 bp):
CTTTCTTCTCTTCTTTCTTT
Found at i:603865 original size:19 final size:17
Alignment explanation
Indices: 603792--603870 Score: 65
Period size: 17 Copynumber: 4.6 Consensus size: 17
603782 CTGACTTTAA
*
603792 CTTTCTTCTCTTCTTTTT
1 CTTTCTTCTC-TCCTTTT
603810 CTTTCTT-TCT-CTTTT
1 CTTTCTTCTCTCCTTTT
* *
603825 CTTT-TTTTCTTCCTCTT
1 CTTTCTTCTC-TCCTTTT
603842 CTTTCTTCTCTCCTTCTTT
1 CTTTCTTCTCTCC-T-TTT
*
603861 CTTTCATCTC
1 CTTTCTTCTC
603871 GGTATAACCC
Statistics
Matches: 50, Mismatches: 5, Indels: 11
0.76 0.08 0.17
Matches are distributed among these distances:
14 2 0.04
15 10 0.20
16 2 0.04
17 13 0.26
18 12 0.24
19 11 0.22
ACGTcount: A:0.01, C:0.32, G:0.00, T:0.67
Consensus pattern (17 bp):
CTTTCTTCTCTCCTTTT
Found at i:605061 original size:22 final size:23
Alignment explanation
Indices: 605019--605062 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
605009 AAATCAAAAT
*
605019 ATTTAACTTTTAATTTCATATCG
1 ATTTAAATTTTAATTTCATATCG
605042 ATTTAAATTTTAA-TTCATATC
1 ATTTAAATTTTAATTTCATATC
605063 AATTACATCA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.34, C:0.11, G:0.02, T:0.52
Consensus pattern (23 bp):
ATTTAAATTTTAATTTCATATCG
Found at i:607203 original size:12 final size:11
Alignment explanation
Indices: 607186--607211 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
607176 TACGAAATCC
607186 AAAAAAAAAAG
1 AAAAAAAAAAG
607197 AAAAAAAAAAG
1 AAAAAAAAAAG
607208 AAAA
1 AAAA
607212 TACATTGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAG
Found at i:614560 original size:40 final size:40
Alignment explanation
Indices: 614513--614608 Score: 138
Period size: 40 Copynumber: 2.4 Consensus size: 40
614503 ACAAGTTCCA
* *
614513 AAATCGCAACACAAATAGTTAAATCGCAACGATAATATGT
1 AAATCGCAACGCAAATAGGTAAATCGCAACGATAATATGT
* * *
614553 AATTCGCAACGCGAATAGGTAAATCGCAATGATAATATGT
1 AAATCGCAACGCAAATAGGTAAATCGCAACGATAATATGT
*
614593 AAATCACAACGCAAAT
1 AAATCGCAACGCAAAT
614609 TCTCCAAATT
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 48 1.00
ACGTcount: A:0.46, C:0.18, G:0.15, T:0.22
Consensus pattern (40 bp):
AAATCGCAACGCAAATAGGTAAATCGCAACGATAATATGT
Found at i:614589 original size:20 final size:20
Alignment explanation
Indices: 614513--614603 Score: 85
Period size: 20 Copynumber: 4.5 Consensus size: 20
614503 ACAAGTTCCA
* *
614513 AAATCGCAAC-ACAAATAGTT
1 AAATCGCAACGA-TAATAGGT
*
614533 AAATCGCAACGATAATATGT
1 AAATCGCAACGATAATAGGT
* **
614553 AATTCGCAACGCGAATAGGT
1 AAATCGCAACGATAATAGGT
* *
614573 AAATCGCAATGATAATATGT
1 AAATCGCAACGATAATAGGT
*
614593 AAATCACAACG
1 AAATCGCAACG
614604 CAAATTCTCC
Statistics
Matches: 56, Mismatches: 14, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
20 55 0.98
21 1 0.02
ACGTcount: A:0.45, C:0.18, G:0.15, T:0.22
Consensus pattern (20 bp):
AAATCGCAACGATAATAGGT
Found at i:614727 original size:20 final size:20
Alignment explanation
Indices: 614702--614754 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
614692 TTTTTCAAAT
614702 TCGCAACGCGAATAGGTAAA
1 TCGCAACGCGAATAGGTAAA
** *
614722 TCGCAACGATAATATGTAAA
1 TCGCAACGCGAATAGGTAAA
614742 TCGCAACGCGAAT
1 TCGCAACGCGAAT
614755 TCTCCAAATT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.40, C:0.21, G:0.21, T:0.19
Consensus pattern (20 bp):
TCGCAACGCGAATAGGTAAA
Found at i:614817 original size:146 final size:146
Alignment explanation
Indices: 614553--614841 Score: 461
Period size: 146 Copynumber: 2.0 Consensus size: 146
614543 GATAATATGT
*
614553 AATTCGCAACGCGAATAGGTAAATCGCAATGATAATATGTAAATCACAACGCAAATTCTCCAAAT
1 AATTCGCAACGCGAATAGGTAAATCGCAACGATAATATGTAAATCACAACGCAAATTCTCCAAAT
* * * * * * *
614618 TTGTAACTCGAATTTCGCAACGCTAATTACCGATATAGGTAATTAGTATTGCGAAAACGAAATTC
66 TCGCAACTCGAATTTCGCAACACCAATTACCGATATAGATAATAAGCATTGCGAAAACGAAATTC
*
614683 GAGTTGCGATTTTTCA
131 CAGTTGCGATTTTTCA
* *
614699 AATTCGCAACGCGAATAGGTAAATCGCAACGATAATATGTAAATCGCAACGCGAATTCTCCAAAT
1 AATTCGCAACGCGAATAGGTAAATCGCAACGATAATATGTAAATCACAACGCAAATTCTCCAAAT
*
614764 TCGCAACTCGAATTTCGCAACACCAATTACCGATATAGATAATAAGCGTTGCGAAAACGAAATTC
66 TCGCAACTCGAATTTCGCAACACCAATTACCGATATAGATAATAAGCATTGCGAAAACGAAATTC
*
614829 CCGTTGCGATTTT
131 CAGTTGCGATTTT
614842 GGAGAATCGC
Statistics
Matches: 130, Mismatches: 13, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
146 130 1.00
ACGTcount: A:0.37, C:0.20, G:0.17, T:0.27
Consensus pattern (146 bp):
AATTCGCAACGCGAATAGGTAAATCGCAACGATAATATGTAAATCACAACGCAAATTCTCCAAAT
TCGCAACTCGAATTTCGCAACACCAATTACCGATATAGATAATAAGCATTGCGAAAACGAAATTC
CAGTTGCGATTTTTCA
Found at i:614909 original size:20 final size:21
Alignment explanation
Indices: 614884--615023 Score: 89
Period size: 20 Copynumber: 6.9 Consensus size: 21
614874 TGCGATTTTC
614884 CAAATTCGCAACGCGAA-AGT
1 CAAATTCGCAACGCGAATAGT
*
614904 CAAATTCGCAATGCGAATAGT
1 CAAATTCGCAACGCGAATAGT
* **
614925 TAAA-TCGCAACGATAATATGT
1 CAAATTCGCAACGCGAATA-GT
*
614946 --AATTCACAACGCGAATAGGT
1 CAAATTCGCAACGCGAATA-GT
**
614966 -AAA-TCGCAACGATAATATGT
1 CAAATTCGCAACGCGAATA-GT
* **
614986 -AAA-TCACAACGCGAATTCT
1 CAAATTCGCAACGCGAATAGT
*
615005 CCAAATTCGCAACTCGAAT
1 -CAAATTCGCAACGCGAAT
615024 TTCGCAACAC
Statistics
Matches: 93, Mismatches: 20, Indels: 12
0.74 0.16 0.10
Matches are distributed among these distances:
19 3 0.03
20 66 0.71
21 13 0.14
22 11 0.12
ACGTcount: A:0.41, C:0.21, G:0.16, T:0.22
Consensus pattern (21 bp):
CAAATTCGCAACGCGAATAGT
Found at i:614950 original size:40 final size:40
Alignment explanation
Indices: 614906--615001 Score: 156
Period size: 40 Copynumber: 2.4 Consensus size: 40
614896 GCGAAAGTCA
* * *
614906 AATTCGCAATGCGAATAGTTAAATCGCAACGATAATATGT
1 AATTCACAACGCGAATAGGTAAATCGCAACGATAATATGT
614946 AATTCACAACGCGAATAGGTAAATCGCAACGATAATATGT
1 AATTCACAACGCGAATAGGTAAATCGCAACGATAATATGT
*
614986 AAATCACAACGCGAAT
1 AATTCACAACGCGAAT
615002 TCTCCAAATT
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 52 1.00
ACGTcount: A:0.43, C:0.18, G:0.17, T:0.23
Consensus pattern (40 bp):
AATTCACAACGCGAATAGGTAAATCGCAACGATAATATGT
Found at i:615081 original size:20 final size:20
Alignment explanation
Indices: 615056--615104 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
615046 TAGGTAATTA
615056 GCGTTGCGAAAACAAAATAC
1 GCGTTGCGAAAACAAAATAC
* *
615076 GCGTTGCAAAAACAAAATTC
1 GCGTTGCGAAAACAAAATAC
615096 GCGTTGCGA
1 GCGTTGCGA
615105 TTTTCCAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.39, C:0.20, G:0.22, T:0.18
Consensus pattern (20 bp):
GCGTTGCGAAAACAAAATAC
Found at i:615148 original size:20 final size:20
Alignment explanation
Indices: 615125--615162 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
615115 TCACAACGCG
615125 AATAGGTAAATCGCAACGAT
1 AATAGGTAAATCGCAACGAT
*
615145 AATATGTAAATCGCAACG
1 AATAGGTAAATCGCAACG
615163 TGAATTCTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.45, C:0.16, G:0.18, T:0.21
Consensus pattern (20 bp):
AATAGGTAAATCGCAACGAT
Found at i:628781 original size:27 final size:27
Alignment explanation
Indices: 628751--628811 Score: 113
Period size: 27 Copynumber: 2.3 Consensus size: 27
628741 ATTTTGGTAT
628751 GATTCTAAGAATCAAAGGCATTTGAGA
1 GATTCTAAGAATCAAAGGCATTTGAGA
*
628778 GATTATAAGAATCAAAGGCATTTGAGA
1 GATTCTAAGAATCAAAGGCATTTGAGA
628805 GATTCTA
1 GATTCTA
628812 GATGTTATAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.41, C:0.10, G:0.21, T:0.28
Consensus pattern (27 bp):
GATTCTAAGAATCAAAGGCATTTGAGA
Found at i:629180 original size:95 final size:95
Alignment explanation
Indices: 629058--629277 Score: 316
Period size: 95 Copynumber: 2.3 Consensus size: 95
629048 TGATGAGGAG
*
629058 GTATCGATACCATGGTGAGGGTATCGATACCAAGTAACATCGAACCTAATTTTGGTATCGATACC
1 GTATCGATACCATGGTGAGGGTATCGATACCAAGGAACATCGAACCTAATTTTGGTATCGATACC
* *
629123 AGAAGGGGGTATAGGTACCCTAGCATAGTA
66 AGAAGGGGGTATAGGTACCATAGCAGAGTA
* *
629153 GTATCGATACCATGGTGAGGGTATCGATACCAAGGCACATCGAAGCTAATTTTGGTATCGATACC
1 GTATCGATACCATGGTGAGGGTATCGATACCAAGGAACATCGAACCTAATTTTGGTATCGATACC
* * * * * *
629218 GGAATGGGGTATCGTTACCATAGTAGGGTA
66 AGAAGGGGGTATAGGTACCATAGCAGAGTA
*
629248 GTATCGATACCATGGT-ATAGGTATCGATAC
1 GTATCGATACCATGGTGA-GGGTATCGATAC
629278 TGAAGGGCCA
Statistics
Matches: 112, Mismatches: 12, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
94 1 0.01
95 111 0.99
ACGTcount: A:0.30, C:0.17, G:0.26, T:0.26
Consensus pattern (95 bp):
GTATCGATACCATGGTGAGGGTATCGATACCAAGGAACATCGAACCTAATTTTGGTATCGATACC
AGAAGGGGGTATAGGTACCATAGCAGAGTA
Found at i:629664 original size:54 final size:54
Alignment explanation
Indices: 629602--630049 Score: 596
Period size: 54 Copynumber: 8.3 Consensus size: 54
629592 GAGTATCCAA
* * *
629602 TAGGCACTAAGTATGCATTTCACATAATTCATCCTATGTGGATGAATAACAGTT
1 TAGGCACTAAGTGTGCATTTCACAGAATTCATCCTATGTGGATGAATAACCGTT
* *
629656 TAGGCACTAAGTGTGCATTTCACGGAATTCATCATATGTGGATGAATAACCGTT
1 TAGGCACTAAGTGTGCATTTCACAGAATTCATCCTATGTGGATGAATAACCGTT
* * * **
629710 TTGGCACTAAGTGTGCATTTCACGGAATTCATCTTATGTGGATGAAT-ACTATT
1 TAGGCACTAAGTGTGCATTTCACAGAATTCATCCTATGTGGATGAATAACCGTT
* *
629763 TTGGCACTAAGTGTGCATTTCAC-GAAATTCATCCTATGTGGATGAATAATCGTT
1 TAGGCACTAAGTGTGCATTTCACAG-AATTCATCCTATGTGGATGAATAACCGTT
* * *
629817 TCGACACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTT
1 TAGGCACTAAGTGTGCATTTCACAGAATTCATCCTATGTGGATGAATAACCGTT
* * * * *
629871 TCGACACTAAGTGTGCATTTTACAGAATTCATCTTATGTAGATGAATAACCGTT
1 TAGGCACTAAGTGTGCATTTCACAGAATTCATCCTATGTGGATGAATAACCGTT
* * * *
629925 TCGGTACTAAGTGTGCATTTCACGGAATTCATCTTATGTGGATGAATAACCGTT
1 TAGGCACTAAGTGTGCATTTCACAGAATTCATCCTATGTGGATGAATAACCGTT
* *
629979 TCA-GCACTAAGTGTGCATTTCACAGAATTCATCCTATGAGGATGAATATCCGTT
1 T-AGGCACTAAGTGTGCATTTCACAGAATTCATCCTATGTGGATGAATAACCGTT
* * *
630033 TCGGTACTAGGTGTGCA
1 TAGGCACTAAGTGTGCA
630050 AGGTGTAGAA
Statistics
Matches: 355, Mismatches: 34, Indels: 10
0.89 0.09 0.03
Matches are distributed among these distances:
52 1 0.00
53 48 0.14
54 305 0.86
55 1 0.00
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.34
Consensus pattern (54 bp):
TAGGCACTAAGTGTGCATTTCACAGAATTCATCCTATGTGGATGAATAACCGTT
Found at i:630856 original size:13 final size:13
Alignment explanation
Indices: 630838--630862 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
630828 CAGACTTCTC
630838 TTCTTCTTCTTCA
1 TTCTTCTTCTTCA
630851 TTCTTCTTCTTC
1 TTCTTCTTCTTC
630863 CCCGTGAGAC
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:0.04, C:0.32, G:0.00, T:0.64
Consensus pattern (13 bp):
TTCTTCTTCTTCA
Found at i:632186 original size:23 final size:23
Alignment explanation
Indices: 632142--632209 Score: 64
Period size: 23 Copynumber: 3.0 Consensus size: 23
632132 CATCTTATAT
* * *
632142 GGCACTACGGTACGATTATACGC
1 GGCACTTCGGTGCAATTATACGC
* *
632165 GGCACTTCGGTGCAATTCTACGT
1 GGCACTTCGGTGCAATTATACGC
* * *
632188 TGCACTTTGGTGCATTTATACG
1 GGCACTTCGGTGCAATTATACG
632210 AGCTGTGATG
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.21, C:0.24, G:0.25, T:0.31
Consensus pattern (23 bp):
GGCACTTCGGTGCAATTATACGC
Found at i:635049 original size:10 final size:10
Alignment explanation
Indices: 635034--635059 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
635024 TCTCTTCTTT
635034 TTCTTCATTC
1 TTCTTCATTC
635044 TTCTTCATTC
1 TTCTTCATTC
635054 TTCTTC
1 TTCTTC
635060 TTCCCCGTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.08, C:0.31, G:0.00, T:0.62
Consensus pattern (10 bp):
TTCTTCATTC
Found at i:636328 original size:23 final size:23
Alignment explanation
Indices: 636297--636354 Score: 80
Period size: 23 Copynumber: 2.5 Consensus size: 23
636287 TCTTATATGT
*
636297 CACTACGGTGTAATTCTACGCGG
1 CACTACGGTGCAATTCTACGCGG
* *
636320 CACTCCGGTGCAATTCTACGTGG
1 CACTACGGTGCAATTCTACGCGG
*
636343 CACTTCGGTGCA
1 CACTACGGTGCA
636355 TTTATACTAG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.19, C:0.29, G:0.26, T:0.26
Consensus pattern (23 bp):
CACTACGGTGCAATTCTACGCGG
Found at i:638074 original size:133 final size:137
Alignment explanation
Indices: 637686--638103 Score: 569
Period size: 138 Copynumber: 3.1 Consensus size: 137
637676 GTCATAGGTG
* * ** *
637686 CATTTCGACATA-AATTGTATATAATGGTTATCGATCGATTTTGTGTAATGCATAATGGTGTATT
1 CATTTCGACATACAATTATGTATAAAAGTTATCGATCGATTTTGTGTAATGCATAATGGTGCATT
* * * *
637750 TTCGTATCAGTACTATGTATACTTTCGGCACTAGATGTGCAACCATGGTATTCATAACGAGTTTG
66 TTCGTATCAGTAC-ATGTGTACTTTCGTCACTAGGTGTGCAACCATGGTATTCATAATGAGTTTG
*
637815 TGAATTAT
130 TGAATTAC
* * * *
637823 CATTTCGACATACAATTATGTTTAAAAGTTATTGATAGATTTTGTGTAATACATAATGGTGCATT
1 CATTTCGACATACAATTATGTATAAAAGTTATCGATCGATTTTGTGTAATGCATAATGGTGCATT
*
637888 TTTGTATCAGTACTATGTGTACTTTCGAT-ACTAGGTGTGCAACCATGGTATTCATAATGAGTTT
66 TTCGTATCAGTAC-ATGTGTACTTTCG-TCACTAGGTGTGCAACCATGGTATTCATAATGAGTTT
637952 GTGAATTA-
129 GTGAATTAC
* * *
637960 CATTTTGACATACAATTATGTATAAAAGTTATCGATCGATTTT-TTTAATGCAT-ATGTTGCATT
1 CATTTCGACATACAATTATGTATAAAAGTTATCGATCGATTTTGTGTAATGCATAATGGTGCATT
* * *
638023 TTCATATCAGTAC-TGTGTACTTTCGTCACTAGGTGTGCAACCATGGAATTCATAATGAGTTTAT
66 TTCGTATCAGTACATGTGTACTTTCGTCACTAGGTGTGCAACCATGGTATTCATAATGAGTTTGT
638087 GAATTAC
131 GAATTAC
*
638094 CATTTTGACA
1 CATTTCGACA
638104 CTATGTGTGC
Statistics
Matches: 252, Mismatches: 25, Indels: 11
0.88 0.09 0.04
Matches are distributed among these distances:
132 1 0.00
133 53 0.21
134 10 0.04
135 20 0.08
136 8 0.03
137 51 0.20
138 109 0.43
ACGTcount: A:0.29, C:0.13, G:0.17, T:0.40
Consensus pattern (137 bp):
CATTTCGACATACAATTATGTATAAAAGTTATCGATCGATTTTGTGTAATGCATAATGGTGCATT
TTCGTATCAGTACATGTGTACTTTCGTCACTAGGTGTGCAACCATGGTATTCATAATGAGTTTGT
GAATTAC
Found at i:638112 original size:53 final size:53
Alignment explanation
Indices: 638049--638151 Score: 152
Period size: 53 Copynumber: 1.9 Consensus size: 53
638039 GTACTTTCGT
638049 CACTAGGTGTGCAACCATGGAATTCATAATGAGTTTATGAATTACCATTTTGA
1 CACTAGGTGTGCAACCATGGAATTCATAATGAGTTTATGAATTACCATTTTGA
* ** * * *
638102 CACTATGTGTGCATTCATGGAATTTATAATGAGTTTGTGAATTTCCATTT
1 CACTAGGTGTGCAACCATGGAATTCATAATGAGTTTATGAATTACCATTT
638152 CGGCACTTAG
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
53 44 1.00
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.39
Consensus pattern (53 bp):
CACTAGGTGTGCAACCATGGAATTCATAATGAGTTTATGAATTACCATTTTGA
Found at i:643177 original size:35 final size:35
Alignment explanation
Indices: 643135--643241 Score: 121
Period size: 34 Copynumber: 3.1 Consensus size: 35
643125 TTAATATGTG
*
643135 TTTGATAATTGTAAAACATCTGATATCTATAAATA
1 TTTGATAACTGTAAAACATCTGATATCTATAAATA
* * *
643170 TTTGATAAGTGT-AATCA-CATGATATCTGTAAATA
1 TTTGATAACTGTAAAACATC-TGATATCTATAAATA
* *
643204 TTTGATAACTG-AAAATCATTTGATAACTATAAATA
1 TTTGATAACTGTAAAA-CATCTGATATCTATAAATA
643239 TTT
1 TTT
643242 AGAATTCATC
Statistics
Matches: 60, Mismatches: 8, Indels: 8
0.79 0.11 0.11
Matches are distributed among these distances:
33 1 0.02
34 30 0.50
35 29 0.48
ACGTcount: A:0.41, C:0.08, G:0.10, T:0.40
Consensus pattern (35 bp):
TTTGATAACTGTAAAACATCTGATATCTATAAATA
Found at i:643209 original size:17 final size:17
Alignment explanation
Indices: 643135--643241 Score: 81
Period size: 17 Copynumber: 6.2 Consensus size: 17
643125 TTAATATGTG
* *
643135 TTTGATAATTGTAAAACA
1 TTTGATAACTGT-AAATA
* * *
643153 TCTGATATCTATAAATA
1 TTTGATAACTGTAAATA
*
643170 TTTGATAAGTGT-AATCA
1 TTTGATAACTGTAAAT-A
** *
643187 CATGATATCTGTAAATA
1 TTTGATAACTGTAAATA
*
643204 TTTGATAACTGAAAATCA
1 TTTGATAACTGTAAAT-A
*
643222 TTTGATAACTATAAATA
1 TTTGATAACTGTAAATA
643239 TTT
1 TTT
643242 AGAATTCATC
Statistics
Matches: 67, Mismatches: 19, Indels: 7
0.72 0.20 0.08
Matches are distributed among these distances:
16 3 0.04
17 38 0.57
18 26 0.39
ACGTcount: A:0.41, C:0.08, G:0.10, T:0.40
Consensus pattern (17 bp):
TTTGATAACTGTAAATA
Found at i:649704 original size:26 final size:26
Alignment explanation
Indices: 649668--649717 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
649658 AGAAAAAGAA
649668 GACCCACAACTAAATAAATAAATACT
1 GACCCACAACTAAATAAATAAATACT
649694 GACCCACAACTAAATAAATAAATA
1 GACCCACAACTAAATAAATAAATA
649718 GCTATGAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.56, C:0.22, G:0.04, T:0.18
Consensus pattern (26 bp):
GACCCACAACTAAATAAATAAATACT
Found at i:661699 original size:61 final size:60
Alignment explanation
Indices: 661613--661751 Score: 183
Period size: 61 Copynumber: 2.3 Consensus size: 60
661603 ATATACATTA
* * * * *
661613 TTAATAATGATTTAATGATTAACTACTAATGATTTAATAATATAATGATTTGA-TTTAATGCT
1 TTAATAATTATTAAAT-TTTAACTACTAATGATTTAAT-A-ATAATGATTTAACTTTAATGAT
661675 TTAATAATTATTAAATTTTAACTACTAATGATTTAATAATAATGATTTAACTTTAATGAT
1 TTAATAATTATTAAATTTTAACTACTAATGATTTAATAATAATGATTTAACTTTAATGAT
*
661735 TTATTAATTA-TAAATTT
1 TTAATAATTATTAAATTT
661752 AATAATGATT
Statistics
Matches: 70, Mismatches: 6, Indels: 5
0.86 0.07 0.06
Matches are distributed among these distances:
59 18 0.26
60 18 0.26
61 20 0.29
62 14 0.20
ACGTcount: A:0.42, C:0.04, G:0.06, T:0.47
Consensus pattern (60 bp):
TTAATAATTATTAAATTTTAACTACTAATGATTTAATAATAATGATTTAACTTTAATGAT
Found at i:661719 original size:14 final size:14
Alignment explanation
Indices: 661625--661757 Score: 65
Period size: 14 Copynumber: 9.1 Consensus size: 14
661615 AATAATGATT
*
661625 TAATGA-TTAACTAC
1 TAATGATTTAA-TAA
661639 TAATGATTTAATAATA
1 TAATGATTTAAT-A-A
* *
661655 TAATGATTTGAT-T
1 TAATGATTTAATAA
*
661668 TAATGCTTTAATAA
1 TAATGATTTAATAA
* * *
661682 TTATTAAATTTTAACTAC
1 -TAAT-GA-TTTAA-TAA
661700 TAATGATTTAATAA
1 TAATGATTTAATAA
*
661714 TAATGATTTAACT-T
1 TAATGATTTAA-TAA
*
661728 TAATGATTTATTAA
1 TAATGATTTAATAA
* *
661742 TTATAAATTTAATAA
1 TAAT-GATTTAATAA
661757 T
1 T
661758 GATTTATTAA
Statistics
Matches: 89, Mismatches: 19, Indels: 21
0.69 0.15 0.16
Matches are distributed among these distances:
13 11 0.12
14 33 0.37
15 23 0.26
16 12 0.13
17 8 0.09
18 2 0.02
ACGTcount: A:0.43, C:0.05, G:0.06, T:0.47
Consensus pattern (14 bp):
TAATGATTTAATAA
Found at i:661751 original size:29 final size:28
Alignment explanation
Indices: 661639--661771 Score: 112
Period size: 29 Copynumber: 4.6 Consensus size: 28
661629 GATTAACTAC
*
661639 TAATGATTTAATAA-TATAATGATTTGATT
1 TAATGATTTAATAATTATAA--ATTTAATT
* *
661668 TAATGCTTTAATAATTATTAAATTTTAACTAC
1 TAATGATTTAATAATTA-TAAA-TTTAA-T-T
* *
661700 TAATGATTTAATAATAAT-GATTTAACTT
1 TAATGATTTAATAATTATAAATTTAA-TT
*
661728 TAATGATTTATTAATTATAAATTTAA--
1 TAATGATTTAATAATTATAAATTTAATT
*
661754 TAATGATTTATTAATTAT
1 TAATGATTTAATAATTAT
661772 TAATATGATA
Statistics
Matches: 88, Mismatches: 10, Indels: 15
0.78 0.09 0.13
Matches are distributed among these distances:
26 18 0.20
28 16 0.18
29 27 0.31
30 7 0.08
31 5 0.06
32 15 0.17
ACGTcount: A:0.42, C:0.03, G:0.06, T:0.49
Consensus pattern (28 bp):
TAATGATTTAATAATTATAAATTTAATT
Found at i:661799 original size:26 final size:26
Alignment explanation
Indices: 661728--661847 Score: 99
Period size: 26 Copynumber: 4.8 Consensus size: 26
661718 GATTTAACTT
* *
661728 TAATGATTTATTAATTATAAATTTAA
1 TAATGATTTATTAATTATTAATATAA
*
661754 TAATGATTTATTAATTATTAATATGA
1 TAATGATTTATTAATTATTAATATAA
* * *
661780 TAATGATTTAGTAATGATTACTACTAA
1 TAATGATTTATTAATTATTAATA-TAA
*
661807 TGAA--A-TTA-TAATAATT-AT-TAA
1 T-AATGATTTATTAATTATTAATATAA
* *
661828 TCATGATTTACTAATTATTA
1 TAATGATTTATTAATTATTA
661848 TTAATTTAAT
Statistics
Matches: 76, Mismatches: 11, Indels: 15
0.75 0.11 0.15
Matches are distributed among these distances:
20 1 0.01
21 4 0.05
22 1 0.01
23 4 0.05
24 14 0.18
25 3 0.04
26 44 0.58
27 3 0.04
28 2 0.03
ACGTcount: A:0.43, C:0.03, G:0.07, T:0.47
Consensus pattern (26 bp):
TAATGATTTATTAATTATTAATATAA
Found at i:662018 original size:13 final size:13
Alignment explanation
Indices: 661978--662023 Score: 60
Period size: 13 Copynumber: 3.7 Consensus size: 13
661968 TAATGAAATT
*
661978 ATAATAATTACTA
1 ATAATTATTACTA
*
661991 ATAATGATT--TA
1 ATAATTATTACTA
662002 ATAATTATTACTA
1 ATAATTATTACTA
662015 ATAATTATT
1 ATAATTATT
662024 TAATAGTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
11 10 0.34
13 19 0.66
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (13 bp):
ATAATTATTACTA
Done.