Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007999.1 Hibiscus syriacus cultivar Beakdansim tig00110450_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: 11700749
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 21 of 50
Found at i:5508289 original size:12 final size:12
Alignment explanation
Indices: 5508272--5508297 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
5508262 AAACATTAAA
5508272 AATTAAAAAATT
1 AATTAAAAAATT
5508284 AATTAAAAAATT
1 AATTAAAAAATT
5508296 AA
1 AA
5508298 AAGTTAAAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (12 bp):
AATTAAAAAATT
Found at i:5508306 original size:34 final size:34
Alignment explanation
Indices: 5508233--5508299 Score: 89
Period size: 36 Copynumber: 1.9 Consensus size: 34
5508223 TTATCTAATC
** *
5508233 TTAAAAATAAAAAATAATTTGAAATTTAAAAACA
1 TTAAAAATAAAAAATAATTAAAAAATTAAAAACA
5508267 TTAAAAATTAAAAAATTAATTAAAAAATTAAAA
1 TTAAAAA-TAAAAAA-TAATTAAAAAATTAAAA
5508300 GTTAAAACAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
34 7 0.25
35 7 0.25
36 14 0.50
ACGTcount: A:0.67, C:0.01, G:0.01, T:0.30
Consensus pattern (34 bp):
TTAAAAATAAAAAATAATTAAAAAATTAAAAACA
Found at i:5509294 original size:60 final size:58
Alignment explanation
Indices: 5509206--5509395 Score: 168
Period size: 60 Copynumber: 3.2 Consensus size: 58
5509196 TGCATCACAG
* *
5509206 TCCTCAAAGTATGAC-TCTATTTTAAATTAGTCTCTAAACTTTTAAATATTCCAATTTCA
1 TCCTCAAACTATGACTTC-ATTCTAAATTAGTC-CTAAACTTTTAAATATTCCAATTTCA
* * * *
5509265 TCCTTAAACTATGACTATCATTCTAAATTAGTCCTCAAACTTTTGAATATTTCAATTTTA
1 TCCTCAAACTATGACT-TCATTCTAAATTAGTCCT-AAACTTTTAAATATTCCAATTTCA
* * * * * * * *
5509325 TCCCCAAACTTTAACCTTCATTCTAAACTGGTCCCCAAACTTTTTTAAACATTCCAGTTTCA
1 TCCTCAAACTATGA-CTTCATTCTAAATTAGT-CCTAAAC--TTTTAAATATTCCAATTTCA
5509387 TCC-CAAACT
1 TCCTCAAACT
5509396 TTATGTATAT
Statistics
Matches: 106, Mismatches: 18, Indels: 12
0.78 0.13 0.09
Matches are distributed among these distances:
59 15 0.14
60 61 0.58
61 12 0.11
62 18 0.17
ACGTcount: A:0.32, C:0.24, G:0.05, T:0.39
Consensus pattern (58 bp):
TCCTCAAACTATGACTTCATTCTAAATTAGTCCTAAACTTTTAAATATTCCAATTTCA
Found at i:5509609 original size:29 final size:29
Alignment explanation
Indices: 5509572--5509627 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
5509562 TAGAAAAAAG
*
5509572 TTAATAGTTTAAGGATGAAATTAGAATGT
1 TTAAAAGTTTAAGGATGAAATTAGAATGT
* * *
5509601 TTAAAAGTTTAATGATTAATTTAGAAT
1 TTAAAAGTTTAAGGATGAAATTAGAAT
5509628 AAAAGTCATA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.43, C:0.00, G:0.16, T:0.41
Consensus pattern (29 bp):
TTAAAAGTTTAAGGATGAAATTAGAATGT
Found at i:5509622 original size:60 final size:60
Alignment explanation
Indices: 5509525--5509676 Score: 171
Period size: 60 Copynumber: 2.5 Consensus size: 60
5509515 TGAATTTGGA
* * *
5509525 GATGAAATTGGAATGTTCAAAATTTTGAGGACCAATTTAGAA-AAAAGTTAATAGTTTAAG
1 GATGAAATTGGAATGTTCAAAAGTTTAAGGACCAATTTAGAATAAAAG-TAATAGGTTAAG
* * * ** * *
5509585 GATGAAATTAGAATGTTTAAAAGTTTAATGATTAATTTAGAATAAAAGTCATAGGTTGAG
1 GATGAAATTGGAATGTTCAAAAGTTTAAGGACCAATTTAGAATAAAAGTAATAGGTTAAG
* * *
5509645 GATGAAATTGGAATATGCAAAAATTTAAGGAC
1 GATGAAATTGGAATGTTCAAAAGTTTAAGGAC
5509677 TATTTTAATT
Statistics
Matches: 74, Mismatches: 17, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
60 69 0.93
61 5 0.07
ACGTcount: A:0.44, C:0.04, G:0.20, T:0.32
Consensus pattern (60 bp):
GATGAAATTGGAATGTTCAAAAGTTTAAGGACCAATTTAGAATAAAAGTAATAGGTTAAG
Found at i:5512414 original size:26 final size:26
Alignment explanation
Indices: 5512380--5512446 Score: 82
Period size: 26 Copynumber: 2.5 Consensus size: 26
5512370 ATATTTTTAT
*
5512380 TTTCGTAAAATTTTAT-AGGTTTGTCTA
1 TTTC-TAAAATTTTATAAGCTTT-TCTA
*
5512407 TTTCTAAAATTTTATAAGCTTTTCTC
1 TTTCTAAAATTTTATAAGCTTTTCTA
*
5512433 TTTCTAACATTTTA
1 TTTCTAAAATTTTA
5512447 GAAGTGTCTC
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
26 27 0.75
27 9 0.25
ACGTcount: A:0.27, C:0.12, G:0.07, T:0.54
Consensus pattern (26 bp):
TTTCTAAAATTTTATAAGCTTTTCTA
Found at i:5523908 original size:33 final size:32
Alignment explanation
Indices: 5523864--5523965 Score: 125
Period size: 33 Copynumber: 3.1 Consensus size: 32
5523854 ATGAACATAA
* *
5523864 CATAACATGAACTTTCAAGGTAAGAACTTGTAT
1 CATAACATGAACTTTCATGG-AAGAACTTATAT
*
5523897 CGTAACATGAACTTTCATGGAATGAACTTATAT
1 CATAACATGAACTTTCATGGAA-GAACTTATAT
* *
5523930 CATAACATGAATTTTCATGGCAAGAA-TTATCT
1 CATAACATGAACTTTCATGG-AAGAACTTATAT
5523962 CATA
1 CATA
5523966 TAAATCATAA
Statistics
Matches: 61, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
32 11 0.18
33 48 0.79
34 2 0.03
ACGTcount: A:0.38, C:0.16, G:0.14, T:0.32
Consensus pattern (32 bp):
CATAACATGAACTTTCATGGAAGAACTTATAT
Found at i:5524708 original size:50 final size:50
Alignment explanation
Indices: 5524624--5524813 Score: 197
Period size: 50 Copynumber: 3.8 Consensus size: 50
5524614 ATTATACCAT
* * * *
5524624 TGAACTTATCACATAATTACACCAGTAAAATTTAACACATATCATATCAA
1 TGAACTTAACACATAATTACACTAGTGAACTTTAACACATATCATATCAA
* * * *
5524674 TGAACTTAACATATAATTACACTAGTCAACTTTAACACATA--ATATTAG
1 TGAACTTAACACATAATTACACTAGTGAACTTTAACACATATCATATCAA
* * * * *
5524722 TGAACTTAATACATAATTATAC-ATGTGAACTTAAATACATATCATGTCAA
1 TGAACTTAACACATAATTACACTA-GTGAACTTTAACACATATCATATCAA
* * * *
5524772 TCAACTTAACACATAATTACTCTAGTGAATTTTAACATATAT
1 TGAACTTAACACATAATTACACTAGTGAACTTTAACACATAT
5524814 TTACACTAGT
Statistics
Matches: 112, Mismatches: 24, Indels: 8
0.78 0.17 0.06
Matches are distributed among these distances:
47 1 0.01
48 38 0.34
50 72 0.64
51 1 0.01
ACGTcount: A:0.44, C:0.17, G:0.06, T:0.34
Consensus pattern (50 bp):
TGAACTTAACACATAATTACACTAGTGAACTTTAACACATATCATATCAA
Found at i:5524727 original size:23 final size:22
Alignment explanation
Indices: 5524696--5524738 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
5524686 ATAATTACAC
5524696 TAGTCAACTTTAACACATAATAT
1 TAGTCAAC-TTAACACATAATAT
* *
5524719 TAGTGAACTTAATACATAAT
1 TAGTCAACTTAACACATAAT
5524739 TATACATGTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.44, C:0.14, G:0.07, T:0.35
Consensus pattern (22 bp):
TAGTCAACTTAACACATAATAT
Found at i:5524735 original size:22 final size:24
Alignment explanation
Indices: 5524674--5524762 Score: 74
Period size: 26 Copynumber: 3.6 Consensus size: 24
5524664 ATCATATCAA
* * *
5524674 TGAACTTAACATATAATTACACTAG
1 TGAACTTAATACATAATTATA-TAG
* *
5524699 TCAACTTTAACACATAA-TAT-TAG
1 TGAAC-TTAATACATAATTATATAG
*
5524722 TGAACTTAATACATAATTATACATG
1 TGAACTTAATACATAATTATATA-G
5524747 TGAACTTAAATACATA
1 TGAACTT-AATACATA
5524763 TCATGTCAAT
Statistics
Matches: 53, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
22 10 0.19
23 10 0.19
24 1 0.02
25 14 0.26
26 18 0.34
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.34
Consensus pattern (24 bp):
TGAACTTAATACATAATTATATAG
Found at i:5525228 original size:31 final size:31
Alignment explanation
Indices: 5525193--5525268 Score: 107
Period size: 31 Copynumber: 2.5 Consensus size: 31
5525183 TCAAAAAACA
* *
5525193 TAAGATATGGTTACTTTCATTTTTATTTTAT
1 TAAGATATGGTCACTTTCATTTTTATTTAAT
* *
5525224 TAAGATATGATCATTTTCATTTTTATTTAAT
1 TAAGATATGGTCACTTTCATTTTTATTTAAT
*
5525255 TAAGATGTGGTCAC
1 TAAGATATGGTCAC
5525269 CCCGAGTTAA
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.29, C:0.08, G:0.12, T:0.51
Consensus pattern (31 bp):
TAAGATATGGTCACTTTCATTTTTATTTAAT
Found at i:5527861 original size:19 final size:20
Alignment explanation
Indices: 5527820--5527870 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
5527810 GAAACCCCTT
*
5527820 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
5527840 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
5527859 TGAAGATACATG
1 TGAAAATACATG
5527871 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:5544923 original size:4 final size:4
Alignment explanation
Indices: 5544914--5544939 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
5544904 CATCTAAGAA
5544914 TTAT TTAT TTAT TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TT
5544940 TTCTTATGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTAT
Found at i:5545075 original size:44 final size:44
Alignment explanation
Indices: 5545025--5545124 Score: 112
Period size: 44 Copynumber: 2.3 Consensus size: 44
5545015 ATTCATTTCA
* * * *
5545025 TTATGTGATGGGATCTA-CTAAAAGTGTGACGCTGATCCAACTCC
1 TTATGTGATGGAATCGAGCGAAAAG-GAGACGCTGATCCAACTCC
* * * *
5545069 TTATGTGATGAAATCGAGCGAAATGGAGATGCTGGTCCAACTCC
1 TTATGTGATGGAATCGAGCGAAAAGGAGACGCTGATCCAACTCC
5545113 TTATGTGATGGA
1 TTATGTGATGGA
5545125 TGAACCAAGG
Statistics
Matches: 46, Mismatches: 9, Indels: 2
0.81 0.16 0.04
Matches are distributed among these distances:
44 41 0.89
45 5 0.11
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.29
Consensus pattern (44 bp):
TTATGTGATGGAATCGAGCGAAAAGGAGACGCTGATCCAACTCC
Found at i:5545199 original size:83 final size:84
Alignment explanation
Indices: 5545104--5545258 Score: 240
Period size: 84 Copynumber: 1.9 Consensus size: 84
5545094 GAGATGCTGG
* * * *
5545104 TCCAACTCCTTATGTGATGGATGAACC-AAGGTTGAATAAGTTCTTCTCATTAGGAACTTCTTCT
1 TCCAACTCCTTATATGATGGATGAACCAAAGGTTGAACAAGTTATTCTCATTAGAAACTTCTTCT
5545168 CCCTCATTGGAAATGTTGA
66 CCCTCATTGGAAATGTTGA
* *
5545187 TCCAACTCCTTATATGATGGATGAGCCAAAGGTTGAACAAGTTATTCTCATTAGAAAGTTCTTCT
1 TCCAACTCCTTATATGATGGATGAACCAAAGGTTGAACAAGTTATTCTCATTAGAAACTTCTTCT
*
5545252 CCTTCAT
66 CCCTCAT
5545259 CTGACGAGCT
Statistics
Matches: 64, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
83 25 0.39
84 39 0.61
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.35
Consensus pattern (84 bp):
TCCAACTCCTTATATGATGGATGAACCAAAGGTTGAACAAGTTATTCTCATTAGAAACTTCTTCT
CCCTCATTGGAAATGTTGA
Found at i:5545400 original size:116 final size:117
Alignment explanation
Indices: 5545175--5545420 Score: 327
Period size: 116 Copynumber: 2.1 Consensus size: 117
5545165 TCTCCCTCAT
* * *
5545175 TGGAAATGTTGATCCAACTCCTTATATGATGGATGAGCCAAAGGTTGAACAAGTTATTCTCATTA
1 TGGAAATGCTGATCCAACTCCATATATGATGGATGAGCCAAAGGTCGAACAAGTTATTCTCATTA
* * *
5545240 GAAAGTTCTTCTCCTTCATCTGACGAGCTTTTCTCATCAAGAACCCTTCTAC
66 GAAACTTCTTCTCCTTCATCGGACGAGCTTTTCTCATCAAGAACCCTTCCAC
* * *
5545292 TTGAAATGCTGATCCAACTCCATATGTGATGGATGAGCC-AAGGTCGAACAAGTTCTTCTCATTA
1 TGGAAATGCTGATCCAACTCCATATATGATGGATGAGCCAAAGGTCGAACAAGTTATTCTCATTA
* * * * *
5545356 GGAACTTCTTCTTCC-TCATCGGATGAG-TTCTTCTTATTATGAACCCTTCCAC
66 GAAACTTCTTC-TCCTTCATCGGACGAGCTT-TTCTCATCAAGAACCCTTCCAC
5545408 TGGAAATGCTGAT
1 TGGAAATGCTGAT
5545421 GGGTTTACGC
Statistics
Matches: 112, Mismatches: 15, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
115 2 0.02
116 72 0.64
117 38 0.34
ACGTcount: A:0.27, C:0.22, G:0.17, T:0.33
Consensus pattern (117 bp):
TGGAAATGCTGATCCAACTCCATATATGATGGATGAGCCAAAGGTCGAACAAGTTATTCTCATTA
GAAACTTCTTCTCCTTCATCGGACGAGCTTTTCTCATCAAGAACCCTTCCAC
Found at i:5546543 original size:2 final size:2
Alignment explanation
Indices: 5546536--5546586 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
5546526 TCAGCTTTAT
5546536 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5546578 TA TA TA TA T
1 TA TA TA TA T
5546587 GTGTGTGTGT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5546591 original size:2 final size:2
Alignment explanation
Indices: 5546586--5546610 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5546576 TATATATATA
5546586 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
5546611 ATGTATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:5551019 original size:15 final size:17
Alignment explanation
Indices: 5550999--5551030 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
5550989 CATGAAGGGC
5550999 TAAAAT-TAAA-CACAA
1 TAAAATATAAAGCACAA
5551014 TAAAATATAAAGCACAA
1 TAAAATATAAAGCACAA
5551031 ATTAAAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 4 0.27
17 5 0.33
ACGTcount: A:0.66, C:0.12, G:0.03, T:0.19
Consensus pattern (17 bp):
TAAAATATAAAGCACAA
Found at i:5556088 original size:24 final size:23
Alignment explanation
Indices: 5556046--5556122 Score: 69
Period size: 24 Copynumber: 3.6 Consensus size: 23
5556036 GAATGCAATT
5556046 AATGCATCGATGC--A--TAAGG
1 AATGCATCGATGCAAATGTAAGG
5556065 AATGCATCGATGCAAATGTTAAGG
1 AATGCATCGATGCAAATG-TAAGG
* * *
5556089 GATGCATCGATAC-ACTGT-A-G
1 AATGCATCGATGCAAATGTAAGG
5556109 AATGCATCGATGCA
1 AATGCATCGATGCA
5556123 CTTCAAGGGG
Statistics
Matches: 47, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
19 13 0.28
20 12 0.26
21 2 0.04
22 1 0.02
23 3 0.06
24 16 0.34
ACGTcount: A:0.35, C:0.17, G:0.25, T:0.23
Consensus pattern (23 bp):
AATGCATCGATGCAAATGTAAGG
Found at i:5557695 original size:23 final size:23
Alignment explanation
Indices: 5557665--5557724 Score: 93
Period size: 23 Copynumber: 2.6 Consensus size: 23
5557655 CATTTTATAT
*
5557665 GGCACTTCGGTGCAATTCTACGC
1 GGCACTTCGGTGCAATTCTACAC
*
5557688 GGCACTTCGGTGCAATTCTACAT
1 GGCACTTCGGTGCAATTCTACAC
*
5557711 GGAACTTCGGTGCA
1 GGCACTTCGGTGCA
5557725 TTTATACGAG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.20, C:0.27, G:0.27, T:0.27
Consensus pattern (23 bp):
GGCACTTCGGTGCAATTCTACAC
Found at i:5567990 original size:20 final size:20
Alignment explanation
Indices: 5567965--5568022 Score: 107
Period size: 20 Copynumber: 2.9 Consensus size: 20
5567955 TTCCCCTTGA
5567965 AGTGCATCGATACATTCTAC
1 AGTGCATCGATACATTCTAC
5567985 AGTGCATCGATACATTCTAC
1 AGTGCATCGATACATTCTAC
*
5568005 AGTGCATCGATGCATTCT
1 AGTGCATCGATACATTCT
5568023 TTAACATGTG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.31
Consensus pattern (20 bp):
AGTGCATCGATACATTCTAC
Found at i:5568119 original size:19 final size:19
Alignment explanation
Indices: 5568095--5568146 Score: 95
Period size: 19 Copynumber: 2.7 Consensus size: 19
5568085 TTTAAGGGGG
5568095 TGCATTGATGCACTTCTTA
1 TGCATTGATGCACTTCTTA
5568114 TGCATTGATGCACTTCTTA
1 TGCATTGATGCACTTCTTA
*
5568133 TGCATCGATGCACT
1 TGCATTGATGCACT
5568147 AATTACATTC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.21, C:0.23, G:0.17, T:0.38
Consensus pattern (19 bp):
TGCATTGATGCACTTCTTA
Found at i:5569503 original size:20 final size:20
Alignment explanation
Indices: 5569478--5569564 Score: 156
Period size: 20 Copynumber: 4.3 Consensus size: 20
5569468 AAATCATTTT
5569478 TCAAAATTTCATTTTGATTA
1 TCAAAATTTCATTTTGATTA
5569498 TCAAAATTTCATTTTGATTA
1 TCAAAATTTCATTTTGATTA
*
5569518 TCAAAATTTCATTTTGATTT
1 TCAAAATTTCATTTTGATTA
*
5569538 TCAAAATTTCATTTTGATTT
1 TCAAAATTTCATTTTGATTA
5569558 TCAAAAT
1 TCAAAAT
5569565 CAACTTTGGT
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
20 66 1.00
ACGTcount: A:0.34, C:0.10, G:0.05, T:0.51
Consensus pattern (20 bp):
TCAAAATTTCATTTTGATTA
Found at i:5569577 original size:19 final size:19
Alignment explanation
Indices: 5569530--5569586 Score: 71
Period size: 19 Copynumber: 2.9 Consensus size: 19
5569520 AAAATTTCAT
*
5569530 TTTGATTTTCAAAATTTC-AT
1 TTTGATTTTCAAAA--TCAAC
5569550 TTTGATTTTCAAAATCAAC
1 TTTGATTTTCAAAATCAAC
*
5569569 TTTGGTTTTCAAAATCAA
1 TTTGATTTTCAAAATCAA
5569587 ATCATTTTCA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
18 2 0.06
19 18 0.53
20 14 0.41
ACGTcount: A:0.33, C:0.12, G:0.07, T:0.47
Consensus pattern (19 bp):
TTTGATTTTCAAAATCAAC
Found at i:5571417 original size:21 final size:21
Alignment explanation
Indices: 5571385--5571424 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
5571375 AACTACCCAG
*
5571385 TATAGAGGGTATTGATACTCC
1 TATAGAGGGTATTAATACTCC
5571406 TATAG-GGAGTATTAATACT
1 TATAGAGG-GTATTAATACT
5571425 ACCTTTTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.12
21 15 0.88
ACGTcount: A:0.33, C:0.10, G:0.23, T:0.35
Consensus pattern (21 bp):
TATAGAGGGTATTAATACTCC
Found at i:5571575 original size:44 final size:45
Alignment explanation
Indices: 5571498--5571599 Score: 179
Period size: 44 Copynumber: 2.3 Consensus size: 45
5571488 ACTATGTAAT
*
5571498 GTAGTATCAATACCATTTTTGCATTCTGGAATTTGAGCAACGATG
1 GTAGTATCGATACCATTTTTGCATTCTGGAATTTGAGCAACGATG
*
5571543 GTAGTATCGATACCA-TTTTGCATTCTGGAATTTGAGCAATGATG
1 GTAGTATCGATACCATTTTTGCATTCTGGAATTTGAGCAACGATG
5571587 GTAGTATCGATAC
1 GTAGTATCGATAC
5571600 TACCTTGAGA
Statistics
Matches: 55, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
44 41 0.75
45 14 0.25
ACGTcount: A:0.28, C:0.15, G:0.22, T:0.35
Consensus pattern (45 bp):
GTAGTATCGATACCATTTTTGCATTCTGGAATTTGAGCAACGATG
Found at i:5581644 original size:16 final size:17
Alignment explanation
Indices: 5581612--5581644 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
5581602 AAAATAAATG
*
5581612 AAATTAAAACTATATAA
1 AAATAAAAACTATATAA
5581629 AAATAAAAACTA-ATAA
1 AAATAAAAACTATATAA
5581645 TTTTAAAGCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.70, C:0.06, G:0.00, T:0.24
Consensus pattern (17 bp):
AAATAAAAACTATATAA
Found at i:5582948 original size:3 final size:3
Alignment explanation
Indices: 5582940--5583019 Score: 76
Period size: 3 Copynumber: 26.7 Consensus size: 3
5582930 TCTGGTTTTG
* * * *
5582940 TAA TAA TAA TATT TAT TAA TAA TAA AAA TAAA TAA TAA TAT TAA TAA
1 TAA TAA TAA TA-A TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA
5582987 TAA TAA TAA TAA -ACA -AA TAA -AA TAA TAA TAA TA
1 TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TA
5583020 GTAAATATAA
Statistics
Matches: 66, Mismatches: 6, Indels: 10
0.80 0.07 0.12
Matches are distributed among these distances:
2 4 0.06
3 57 0.86
4 5 0.08
ACGTcount: A:0.65, C:0.01, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:5582964 original size:19 final size:19
Alignment explanation
Indices: 5582940--5583019 Score: 76
Period size: 19 Copynumber: 4.3 Consensus size: 19
5582930 TCTGGTTTTG
** *
5582940 TAATAATAATATTTATTAA
1 TAATAATAATAAATAATAA
*
5582959 TAATAAAAATAAATAATAA
1 TAATAATAATAAATAATAA
*
5582978 TATTAATAAT-AATAATAA
1 TAATAATAATAAATAATAA
5582996 TAA-ACA-AATAAAATAATAA
1 TAATA-ATAAT-AAATAATAA
5583015 TAATA
1 TAATA
5583020 GTAAATATAA
Statistics
Matches: 50, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
17 4 0.08
18 11 0.22
19 34 0.68
20 1 0.02
ACGTcount: A:0.65, C:0.01, G:0.00, T:0.34
Consensus pattern (19 bp):
TAATAATAATAAATAATAA
Found at i:5582970 original size:25 final size:24
Alignment explanation
Indices: 5582941--5582998 Score: 80
Period size: 25 Copynumber: 2.3 Consensus size: 24
5582931 CTGGTTTTGT
*
5582941 AATAATAATATTTATTAATAATAAA
1 AATAATAATA-ATATTAATAATAAA
*
5582966 AATAAATAATAATATTAATAATAAT
1 AAT-AATAATAATATTAATAATAAA
5582991 AATAATAA
1 AATAATAA
5582999 ACAAATAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
24 5 0.17
25 18 0.60
26 7 0.23
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (24 bp):
AATAATAATAATATTAATAATAAA
Found at i:5583485 original size:112 final size:116
Alignment explanation
Indices: 5583346--5583757 Score: 431
Period size: 123 Copynumber: 3.5 Consensus size: 116
5583336 ATCTCTTTCT
* *
5583346 GTGATAGAGTCATGCAAAAGGCTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGA
1 GTGATAGAGTCATACAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGA
* *
5583411 TAAGTTCTTCTCATTATGAACTTTTTCTGGAAA-TGA-TGATCCA-TC-GA
66 TAAGTTCTTCTCATTATGAACTTTCTCTGGAAAGTGACTGATCCACTCTCA
* * * * *
5583458 GTGAT-GAATTCGA-GCGAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTTTTCA
1 GTGATAG-AGTC-ATACAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCA
* * * *
5583521 GATGAGTTCTTCTCATTATGAACTCTCTCTGGAAAAGTTGATGCTGATCTATCTCTTTCT
64 GATAAGTTCTTCTCATTATGAACTTTCTCTGG-AAAG-TGA--CTGATCCA-CTC--TCA
* *
5583581 GTGATAGAGTCATACAAAAGATTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGA
1 GTGATAGAGTCATACAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGA
* * * *
5583646 TAAGTTCTTCTTATTATGAACTTTCTCTGGAAAAATTGATGCTGATCTATCTCCTTCT
66 TAAGTTCTTCTCATTATGAACTTTCTCTGG--AAAGTGA--CTGATCCA-CT-C-TCA
* * * *
5583704 GTGATAGAGTCAAACAAATGGTTGAACAAGCTCTTCTCATTATGAACTTTTTCT
1 GTGATAGAGTCATACAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCT
5583758 GGAAATGATG
Statistics
Matches: 257, Mismatches: 26, Indels: 23
0.84 0.08 0.08
Matches are distributed among these distances:
111 1 0.00
112 83 0.32
113 4 0.02
115 3 0.01
118 6 0.02
120 2 0.01
122 1 0.00
123 151 0.59
124 6 0.02
ACGTcount: A:0.27, C:0.19, G:0.16, T:0.38
Consensus pattern (116 bp):
GTGATAGAGTCATACAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGA
TAAGTTCTTCTCATTATGAACTTTCTCTGGAAAGTGACTGATCCACTCTCA
Found at i:5583622 original size:123 final size:123
Alignment explanation
Indices: 5583474--5583757 Score: 460
Period size: 123 Copynumber: 2.3 Consensus size: 123
5583464 AATTCGAGCG
* * * *
5583474 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTTTTCAGATGAGTTCTTCTCATTA
1 AAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTA
* * *
5583539 TGAACTCTCTCTGGAAAAGTTGATGCTGATCTATCTCTTTCTGTGATAGAGTCATACA
66 TGAACTCTCTCTGGAAAAATTGATGCTGATCTATCTCCTTCTGTGATAGAGTCAAACA
* *
5583597 AAAGATTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTTATTA
1 AAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTA
*
5583662 TGAACTTTCTCTGGAAAAATTGATGCTGATCTATCTCCTTCTGTGATAGAGTCAAACA
66 TGAACTCTCTCTGGAAAAATTGATGCTGATCTATCTCCTTCTGTGATAGAGTCAAACA
* *
5583720 AATGGTTGAACAAGCTCTTCTCATTATGAACTTTTTCT
1 AAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCT
5583758 GGAAATGATG
Statistics
Matches: 148, Mismatches: 13, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
123 148 1.00
ACGTcount: A:0.27, C:0.19, G:0.14, T:0.40
Consensus pattern (123 bp):
AAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTA
TGAACTCTCTCTGGAAAAATTGATGCTGATCTATCTCCTTCTGTGATAGAGTCAAACA
Found at i:5584970 original size:18 final size:18
Alignment explanation
Indices: 5584943--5584977 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
5584933 TATATGAAAC
*
5584943 AAATTGAATTTCAAAAAT
1 AAATTAAATTTCAAAAAT
5584961 AAATTAAATTTCAAAAA
1 AAATTAAATTTCAAAAA
5584978 GATAAACTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.60, C:0.06, G:0.03, T:0.31
Consensus pattern (18 bp):
AAATTAAATTTCAAAAAT
Found at i:5585346 original size:19 final size:19
Alignment explanation
Indices: 5585324--5585361 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
5585314 CTGACCCTCC
*
5585324 TTTTCTATTTCATTATTTT
1 TTTTCTATTTCATCATTTT
*
5585343 TTTTCTTTTTCATCATTTT
1 TTTTCTATTTCATCATTTT
5585362 CATTTTTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.13, C:0.13, G:0.00, T:0.74
Consensus pattern (19 bp):
TTTTCTATTTCATCATTTT
Found at i:5585391 original size:25 final size:24
Alignment explanation
Indices: 5585337--5585391 Score: 56
Period size: 25 Copynumber: 2.2 Consensus size: 24
5585327 TCTATTTCAT
* * **
5585337 TATTTTTTTTCTTTTTCATCATTT
1 TATTTTTTTTCTTCTTCAGCATAA
5585361 TCATTTTTTTTCTTCTTCAAGCATAA
1 T-ATTTTTTTTCTTCTTC-AGCATAA
5585387 TATTT
1 TATTT
5585392 CTTGACAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
24 1 0.04
25 19 0.76
26 5 0.20
ACGTcount: A:0.18, C:0.15, G:0.02, T:0.65
Consensus pattern (24 bp):
TATTTTTTTTCTTCTTCAGCATAA
Found at i:5596453 original size:16 final size:17
Alignment explanation
Indices: 5596421--5596453 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
5596411 AAAATAAATG
*
5596421 AAATTAAAACTATATAA
1 AAATAAAAACTATATAA
5596438 AAATAAAAACTA-ATAA
1 AAATAAAAACTATATAA
5596454 TTTTAAAGCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.70, C:0.06, G:0.00, T:0.24
Consensus pattern (17 bp):
AAATAAAAACTATATAA
Found at i:5596924 original size:14 final size:14
Alignment explanation
Indices: 5596907--5596949 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
5596897 ATCTTCTCAT
*
5596907 TTCTCTCTTTTCTC
1 TTCTCTCTCTTCTC
5596921 TTCTCTCTCTTCTC
1 TTCTCTCTCTTCTC
5596935 TTCTCT-TCTCTCTC
1 TTCTCTCTCT-TCTC
5596949 T
1 T
5596950 AACTGAGAGA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
13 3 0.11
14 24 0.89
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (14 bp):
TTCTCTCTCTTCTC
Found at i:5596946 original size:21 final size:20
Alignment explanation
Indices: 5596898--5596949 Score: 70
Period size: 19 Copynumber: 2.6 Consensus size: 20
5596888 CGAAGGGCCA
* *
5596898 TCTTCTCATTTCTCTCTTTTC
1 TCTTCTC-TCTCTCTCTCTTC
5596919 TCTTCTCTCTCT-TCTCTTC
1 TCTTCTCTCTCTCTCTCTTC
5596938 TCTTCTCTCTCT
1 TCTTCTCTCTCT
5596950 AACTGAGAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 18 0.62
20 4 0.14
21 7 0.24
ACGTcount: A:0.02, C:0.38, G:0.00, T:0.60
Consensus pattern (20 bp):
TCTTCTCTCTCTCTCTCTTC
Found at i:5597762 original size:3 final size:3
Alignment explanation
Indices: 5597754--5597851 Score: 69
Period size: 3 Copynumber: 33.0 Consensus size: 3
5597744 TCCGGTTTTG
* * *
5597754 TAA TAA TAA TATT TAT TAA TAA TAA AAA TAAA TAA TAA T-A TAA TAA
1 TAA TAA TAA TA-A TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA
* * * *
5597800 TAT TAT TAA TAA TAA TTA TAA -ACA -AA TAA -AA TAA TAA TAA TAG
1 TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA
*
5597843 TAA AAA TAA
1 TAA TAA TAA
5597852 AACAAATGGA
Statistics
Matches: 77, Mismatches: 12, Indels: 12
0.76 0.12 0.12
Matches are distributed among these distances:
2 6 0.08
3 66 0.86
4 5 0.06
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:5597775 original size:13 final size:12
Alignment explanation
Indices: 5597757--5597818 Score: 54
Period size: 13 Copynumber: 5.0 Consensus size: 12
5597747 GGTTTTGTAA
5597757 TAATAATATTTAT
1 TAATAATA-TTAT
**
5597770 TAATAATAAAAAT
1 TAATAAT-ATTAT
* *
5597783 AAATAATAATA-
1 TAATAATATTAT
5597794 TAATAATATTAT
1 TAATAATATTAT
5597806 TAATAATAATTAT
1 TAATAAT-ATTAT
5597819 AAACAAATAA
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
11 9 0.22
12 10 0.25
13 20 0.50
14 1 0.03
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (12 bp):
TAATAATATTAT
Found at i:5597797 original size:37 final size:37
Alignment explanation
Indices: 5597775--5597853 Score: 88
Period size: 37 Copynumber: 2.2 Consensus size: 37
5597765 TTTATTAATA
* *
5597775 ATAAAAATAAA-TAATAATATAATAATATTATTAATA
1 ATAAAAATAAACAAATAAAATAATAATATTATTAATA
** * * *
5597811 ATAATTATAAACAAATAAAATAATAATAATAGTAAAA
1 ATAAAAATAAACAAATAAAATAATAATATTATTAATA
5597848 ATAAAA
1 ATAAAA
5597854 CAAATGGATG
Statistics
Matches: 33, Mismatches: 9, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
36 9 0.27
37 24 0.73
ACGTcount: A:0.67, C:0.01, G:0.01, T:0.30
Consensus pattern (37 bp):
ATAAAAATAAACAAATAAAATAATAATATTATTAATA
Found at i:5597827 original size:40 final size:37
Alignment explanation
Indices: 5597754--5597841 Score: 108
Period size: 40 Copynumber: 2.3 Consensus size: 37
5597744 TCCGGTTTTG
*
5597754 TAATAATAATATTTATTAATAATAAAAATAAATAATAA
1 TAATAATAATATTTATTAATAATAAAAACAAATAA-AA
5597792 T-ATAATAATA-TTATTAATAATAATTATAAACAAATAAAA
1 TAATAATAATATTTATTAATAAT-A--A-AAACAAATAAAA
5597831 TAATAATAATA
1 TAATAATAATA
5597842 GTAAAAATAA
Statistics
Matches: 44, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
36 11 0.25
37 10 0.23
38 1 0.02
39 4 0.09
40 18 0.41
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.36
Consensus pattern (37 bp):
TAATAATAATATTTATTAATAATAAAAACAAATAAAA
Found at i:5600223 original size:15 final size:16
Alignment explanation
Indices: 5600203--5600232 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
5600193 TTAAGAAATC
5600203 AATGAAAAT-TATTTT
1 AATGAAAATATATTTT
5600218 AATGAAAATATATTT
1 AATGAAAATATATTT
5600233 AATTATTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (16 bp):
AATGAAAATATATTTT
Found at i:5604028 original size:21 final size:21
Alignment explanation
Indices: 5603999--5604043 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
5603989 ATTCTGACTA
5603999 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
* * *
5604020 TCGCGTTGCGATTTTTCTAAT
1 TCGCATTGCGATTTTCCAAAT
5604041 TCG
1 TCG
5604044 TAATGCGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.18, C:0.22, G:0.18, T:0.42
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:5604233 original size:20 final size:20
Alignment explanation
Indices: 5604045--5604222 Score: 302
Period size: 20 Copynumber: 8.9 Consensus size: 20
5604035 TCTAATTCGT
5604045 AATGCGAATACGTAAATCGC
1 AATGCGAATACGTAAATCGC
* * *
5604065 AATTCGTATACGTAAATCGT
1 AATGCGAATACGTAAATCGC
5604085 AATGCGAATACGTAAATCGC
1 AATGCGAATACGTAAATCGC
*
5604105 AATGCGAATATGTAAATCGC
1 AATGCGAATACGTAAATCGC
5604125 AATGCGAATACGTAAATCGC
1 AATGCGAATACGTAAATCGC
*
5604145 AAAGCGAATACGTAAATCGC
1 AATGCGAATACGTAAATCGC
5604165 AATGCGAATACGTAAATCGC
1 AATGCGAATACGTAAATCGC
5604185 AATGCGAATACGTAAATCGC
1 AATGCGAATACGTAAATCGC
*
5604205 AATGCGAATATGTAAATC
1 AATGCGAATACGTAAATC
5604223 ACAACGTGAA
Statistics
Matches: 147, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 147 1.00
ACGTcount: A:0.40, C:0.18, G:0.19, T:0.22
Consensus pattern (20 bp):
AATGCGAATACGTAAATCGC
Found at i:5604244 original size:60 final size:60
Alignment explanation
Indices: 5604045--5604251 Score: 276
Period size: 60 Copynumber: 3.5 Consensus size: 60
5604035 TCTAATTCGT
* * *
5604045 AATGCGAATAC-GTAAATCGCAATTCGTATACGTAAATCGTAATGCGAATACGTAAATCGC
1 AATGCGAAT-CTGTAAATCGCAATGCGAATACGTAAATCGCAATGCGAATACGTAAATCGC
* *
5604105 AATGCGAATATGTAAATCGCAATGCGAATACGTAAATCGCAAAGCGAATACGTAAATCGC
1 AATGCGAATCTGTAAATCGCAATGCGAATACGTAAATCGCAATGCGAATACGTAAATCGC
* *
5604165 AATGCGAATAC-GTAAATCGCAATGCGAATACGTAAATCGCAATGCGAATATGTAAATCAC
1 AATGCGAAT-CTGTAAATCGCAATGCGAATACGTAAATCGCAATGCGAATACGTAAATCGC
* * *
5604225 AACGTGAATCTG-ACTATCGCAATGCGA
1 AATGCGAATCTGTA-AATCGCAATGCGA
5604252 TTTACATAGC
Statistics
Matches: 131, Mismatches: 12, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
59 2 0.02
60 129 0.98
ACGTcount: A:0.40, C:0.19, G:0.19, T:0.22
Consensus pattern (60 bp):
AATGCGAATCTGTAAATCGCAATGCGAATACGTAAATCGCAATGCGAATACGTAAATCGC
Found at i:5604456 original size:22 final size:22
Alignment explanation
Indices: 5604431--5604496 Score: 105
Period size: 22 Copynumber: 3.0 Consensus size: 22
5604421 GGCGACATCC
5604431 GTCCCCATCTCCGACGAAATCA
1 GTCCCCATCTCCGACGAAATCA
*
5604453 GTCCCCATCTCCGACGATATCA
1 GTCCCCATCTCCGACGAAATCA
* *
5604475 GTCTCCATCTCCGGCGAAATCA
1 GTCCCCATCTCCGACGAAATCA
5604497 TTCACGGTCA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 40 1.00
ACGTcount: A:0.24, C:0.39, G:0.15, T:0.21
Consensus pattern (22 bp):
GTCCCCATCTCCGACGAAATCA
Found at i:5604601 original size:20 final size:20
Alignment explanation
Indices: 5604578--5604615 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
5604568 TGCAATAGTA
5604578 ATTTTCGTGTTGCGATTTTC
1 ATTTTCGTGTTGCGATTTTC
5604598 ATTTTCGTGTTGCGATTT
1 ATTTTCGTGTTGCGATTT
5604616 AAAGTTTCAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.11, C:0.13, G:0.21, T:0.55
Consensus pattern (20 bp):
ATTTTCGTGTTGCGATTTTC
Found at i:5604623 original size:20 final size:20
Alignment explanation
Indices: 5604580--5604623 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
5604570 CAATAGTAAT
** *
5604580 TTTCGTGTTGCGATTTTCAT
1 TTTCGTGTTGCGATTTAAAG
5604600 TTTCGTGTTGCGATTTAAAG
1 TTTCGTGTTGCGATTTAAAG
5604620 TTTC
1 TTTC
5604624 AGAAACTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.14, C:0.14, G:0.20, T:0.52
Consensus pattern (20 bp):
TTTCGTGTTGCGATTTAAAG
Found at i:5606484 original size:20 final size:20
Alignment explanation
Indices: 5606459--5606635 Score: 166
Period size: 20 Copynumber: 9.5 Consensus size: 20
5606449 AGAATAGTTT
5606459 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
5606479 ACTATCGCAACGCGAAAATG
1 ACTATCGCAATGCGAAAATG
* *
5606499 ACTATCGTAA--CG-AGA-G
1 ACTATCGCAATGCGAAAATG
5606515 A--ATCGCAATGCG-AAATG
1 ACTATCGCAATGCGAAAATG
**
5606532 AAAATCGCAA--C-AACAA--
1 ACTATCGCAATGCGAA-AATG
5606548 A--ATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
5606566 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
**
5606586 ACTATCGCAATGCGAATTTG
1 ACTATCGCAATGCGAAAATG
**
5606606 ACTATCGCAATGCGAATTTG
1 ACTATCGCAATGCGAAAATG
5606626 ACTATCGCAA
1 ACTATCGCAA
5606636 CGAAAGAATC
Statistics
Matches: 136, Mismatches: 7, Indels: 28
0.80 0.04 0.16
Matches are distributed among these distances:
14 13 0.10
16 10 0.07
17 8 0.06
18 5 0.04
19 7 0.05
20 93 0.68
ACGTcount: A:0.40, C:0.21, G:0.19, T:0.20
Consensus pattern (20 bp):
ACTATCGCAATGCGAAAATG
Found at i:5606707 original size:20 final size:20
Alignment explanation
Indices: 5606682--5606728 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
5606672 GATTCTCTCG
5606682 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCAAATTCGCA
** *
5606702 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCAAATTCGCA
5606722 TTGCGAT
1 TTGCGAT
5606729 TTTAAGTTTC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.36
Consensus pattern (20 bp):
TTGCGATAGTCAAATTCGCA
Found at i:5607303 original size:21 final size:20
Alignment explanation
Indices: 5607235--5607315 Score: 54
Period size: 21 Copynumber: 3.9 Consensus size: 20
5607225 GGCCTCCCCT
5607235 ATCGTTCAAGAGGCTCCTATC
1 ATCGTTCAAGAGGC-CCTATC
** * **
5607256 ATCCCTCAAGAGTCCCCTCCC
1 ATCGTTCAAGAG-GCCCTATC
* *
5607277 ACCGTTCAAGAGGCCACTGTC
1 ATCGTTCAAGAGGCC-CTATC
*
5607298 ATCGTTTAAGAGGTCCCT
1 ATCGTTCAAGAGG-CCCT
5607316 CCCAACATTC
Statistics
Matches: 44, Mismatches: 13, Indels: 6
0.70 0.21 0.10
Matches are distributed among these distances:
20 2 0.05
21 39 0.89
22 3 0.07
ACGTcount: A:0.22, C:0.35, G:0.19, T:0.25
Consensus pattern (20 bp):
ATCGTTCAAGAGGCCCTATC
Found at i:5607309 original size:42 final size:42
Alignment explanation
Indices: 5607237--5607319 Score: 98
Period size: 42 Copynumber: 2.0 Consensus size: 42
5607227 CCTCCCCTAT
5607237 CGTTCAAGAGGCTCCTATCATCCCTCAAGA-GTCCCCTCCCAC
1 CGTTCAAGAGGCTCCTATCATCCCTCAAGAGGT-CCCTCCCAC
* ** *
5607279 CGTTCAAGAGGC-CACTGTCATCGTTTAAGAGGTCCCTCCCA
1 CGTTCAAGAGGCTC-CTATCATCCCTCAAGAGGTCCCTCCCA
5607320 ACATTCTAGA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
41 1 0.03
42 32 0.91
43 2 0.06
ACGTcount: A:0.22, C:0.37, G:0.18, T:0.23
Consensus pattern (42 bp):
CGTTCAAGAGGCTCCTATCATCCCTCAAGAGGTCCCTCCCAC
Found at i:5608743 original size:13 final size:13
Alignment explanation
Indices: 5608696--5608748 Score: 52
Period size: 14 Copynumber: 3.9 Consensus size: 13
5608686 TTTATTGTTT
5608696 AATTGATTTGTAA
1 AATTGATTTGTAA
*
5608709 AAGATGATTTGTAA
1 AA-TTGATTTGTAA
**
5608723 ATATTGATTTGTTT
1 A-ATTGATTTGTAA
*
5608737 AATTGATGTGTA
1 AATTGATTTGTA
5608749 CATAATTATT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
13 11 0.34
14 20 0.62
15 1 0.03
ACGTcount: A:0.34, C:0.00, G:0.19, T:0.47
Consensus pattern (13 bp):
AATTGATTTGTAA
Found at i:5608873 original size:20 final size:19
Alignment explanation
Indices: 5608848--5608914 Score: 81
Period size: 20 Copynumber: 3.7 Consensus size: 19
5608838 CTATCGCAAA
5608848 TTCGCATTGCGATTTTCATT
1 TTCGCATTGCGATTTTCA-T
5608868 TTCGCATTGCGA--TTCA-
1 TTCGCATTGCGATTTTCAT
*
5608884 --CTCATTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
5608901 TTCGCATTGCGATT
1 TTCGCATTGCGATT
5608915 CTCTCGTTGC
Statistics
Matches: 40, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
14 9 0.22
16 4 0.10
18 4 0.10
19 11 0.28
20 12 0.30
ACGTcount: A:0.16, C:0.22, G:0.16, T:0.45
Consensus pattern (19 bp):
TTCGCATTGCGATTTTCAT
Found at i:5608890 original size:34 final size:34
Alignment explanation
Indices: 5608852--5608947 Score: 131
Period size: 33 Copynumber: 2.9 Consensus size: 34
5608842 CGCAAATTCG
5608852 CATTGCGATTTTCATTTTCGCATTGCGATTCACT
1 CATTGCGATTTTCATTTTCGCATTGCGATTCACT
*
5608886 CATTGCGATTTTCA-TTTCGCATTGCGATTCTCT
1 CATTGCGATTTTCATTTTCGCATTGCGATTCACT
* ** * *
5608919 CGTTGCGATAGTCATTTCCGCGTTGCGAT
1 CATTGCGATTTTCATTTTCGCATTGCGAT
5608948 AGTCAATTCC
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
33 29 0.53
34 26 0.47
ACGTcount: A:0.16, C:0.24, G:0.19, T:0.42
Consensus pattern (34 bp):
CATTGCGATTTTCATTTTCGCATTGCGATTCACT
Found at i:5608944 original size:20 final size:20
Alignment explanation
Indices: 5608919--5609007 Score: 135
Period size: 20 Copynumber: 4.5 Consensus size: 20
5608909 GCGATTCTCT
5608919 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
*
5608939 CGTTGCGATAGTCAATTCCG
1 CGTTGCGATAGTCATTTCCG
5608959 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
*
5608979 TGTTGCGATAGTCATATT-CG
1 CGTTGCGATAGTCAT-TTCCG
*
5608999 CATTGCGAT
1 CGTTGCGAT
5609008 TTCCGCGTTG
Statistics
Matches: 63, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
20 61 0.97
21 2 0.03
ACGTcount: A:0.18, C:0.22, G:0.25, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:5611482 original size:24 final size:24
Alignment explanation
Indices: 5611455--5611501 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
5611445 CAAAATCCGA
5611455 GTATTGACCAAGATCAAAGTTCGG
1 GTATTGACCAAGATCAAAGTTCGG
*
5611479 GTATTGACCAAGATCAAATTTCG
1 GTATTGACCAAGATCAAAGTTCG
5611502 AATACTGACT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.28
Consensus pattern (24 bp):
GTATTGACCAAGATCAAAGTTCGG
Found at i:5611510 original size:24 final size:24
Alignment explanation
Indices: 5611459--5611510 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
5611449 ATCCGAGTAT
** *
5611459 TGACCAAGATCAAAGTTCGGGTAT
1 TGACCAAGATCAAAGTTCGAATAC
*
5611483 TGACCAAGATCAAATTTCGAATAC
1 TGACCAAGATCAAAGTTCGAATAC
5611507 TGAC
1 TGAC
5611511 TAGTACTCAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.25
Consensus pattern (24 bp):
TGACCAAGATCAAAGTTCGAATAC
Found at i:5612362 original size:20 final size:20
Alignment explanation
Indices: 5612337--5612403 Score: 116
Period size: 20 Copynumber: 3.4 Consensus size: 20
5612327 AAATTCAGTA
5612337 TTGCGATAGTCAGAATCTCG
1 TTGCGATAGTCAGAATCTCG
5612357 TTGCGATAGTCAGAATCTCG
1 TTGCGATAGTCAGAATCTCG
* *
5612377 TTGCGATAGTCAGATTCACG
1 TTGCGATAGTCAGAATCTCG
5612397 TTGCGAT
1 TTGCGAT
5612404 TTACGTATTC
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.24, C:0.19, G:0.25, T:0.31
Consensus pattern (20 bp):
TTGCGATAGTCAGAATCTCG
Found at i:5612413 original size:20 final size:20
Alignment explanation
Indices: 5612397--5612523 Score: 182
Period size: 20 Copynumber: 6.3 Consensus size: 20
5612387 CAGATTCACG
*
5612397 TTGCGATTTACGTATTCACA
1 TTGCGATTTACGTATTCGCA
5612417 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTATTCGCA
*
5612437 TTCCGATTTACGTATTCGCA
1 TTGCGATTTACGTATTCGCA
* *
5612457 TTGTGATTTACGTAATCGCA
1 TTGCGATTTACGTATTCGCA
* **
5612477 TTGCGATTTTCCAAATTCGCA
1 TTGCGA-TTTACGTATTCGCA
5612498 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTATTCGCA
5612518 TTGCGA
1 TTGCGA
5612524 ATTAGGAAAA
Statistics
Matches: 93, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
20 77 0.83
21 16 0.17
ACGTcount: A:0.22, C:0.20, G:0.18, T:0.39
Consensus pattern (20 bp):
TTGCGATTTACGTATTCGCA
Found at i:5612512 original size:61 final size:60
Alignment explanation
Indices: 5612401--5612520 Score: 177
Period size: 61 Copynumber: 2.0 Consensus size: 60
5612391 TTCACGTTGC
* **
5612401 GATTTACGTATTCACATTGCGATTTACGTATTCGCATTCCGATTTACGTATTCGCATTGT
1 GATTTACGTAATCACATTGCGATTTACAAATTCGCATTCCGATTTACGTATTCGCATTGT
* * *
5612461 GATTTACGTAATCGCATTGCGATTTTCCAAATTCGCATTGCGATTTACGTATTCGCATTG
1 GATTTACGTAATCACATTGCGA-TTTACAAATTCGCATTCCGATTTACGTATTCGCATTG
5612521 CGAATTAGGA
Statistics
Matches: 53, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
60 20 0.38
61 33 0.62
ACGTcount: A:0.23, C:0.20, G:0.17, T:0.40
Consensus pattern (60 bp):
GATTTACGTAATCACATTGCGATTTACAAATTCGCATTCCGATTTACGTATTCGCATTGT
Found at i:5612967 original size:45 final size:44
Alignment explanation
Indices: 5612836--5613010 Score: 197
Period size: 45 Copynumber: 3.9 Consensus size: 44
5612826 TAATCCAAGA
* * * * *
5612836 CTTTTGATTATTTGGGTTGTCAAAAGTAAAACCAAAGGATTAGTTC
1 CTTTTGATTA-CTGGGTTG-CAAAATTAAAATCAAATGATTAGTTT
* * * **
5612882 CTTCTGATTACTAGGTTGGAAAATTAAAATCAAACAATTAGTTT
1 CTTTTGATTACTGGGTTGCAAAATTAAAATCAAATGATTAGTTT
5612926 CTTTTGATTACTGGGTTGTCAAAATTAAAATCAAATGATTAGTTT
1 CTTTTGATTACTGGGTTG-CAAAATTAAAATCAAATGATTAGTTT
* * *
5612971 CTTTTGATTATTGGGTTGAAAGAATCAAAATCAAATGATT
1 CTTTTGATTACTGGGTTGCAA-AATTAAAATCAAATGATT
5613011 TGGTTACTAA
Statistics
Matches: 110, Mismatches: 17, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
44 38 0.35
45 63 0.57
46 9 0.08
ACGTcount: A:0.35, C:0.10, G:0.17, T:0.38
Consensus pattern (44 bp):
CTTTTGATTACTGGGTTGCAAAATTAAAATCAAATGATTAGTTT
Found at i:5613275 original size:58 final size:57
Alignment explanation
Indices: 5613224--5613363 Score: 187
Period size: 58 Copynumber: 2.4 Consensus size: 57
5613214 TAAACCTTTG
5613224 AATTTATTTTCTTGAGAAT-TTCAAATGATTCTATTTTGTAAAAGAAAATAAATTGTTA
1 AATTTATTTTCTTGAGAATCTT--AATGATTCTATTTTGTAAAAGAAAATAAATTGTTA
* * *
5613282 AATTTATTTTCTTGGGAATCCTTAATGATTCTACCTTT-TAAAAGGAAATAAATTGTTA
1 AATTTATTTTCTTGAGAAT-CTTAATGATTCTA-TTTTGTAAAAGAAAATAAATTGTTA
5613340 AATTTATTTTCTTTG-GAATCTTAA
1 AATTTATTTTC-TTGAGAATCTTAA
5613364 ATAAAGAAAT
Statistics
Matches: 75, Mismatches: 3, Indels: 9
0.86 0.03 0.10
Matches are distributed among these distances:
57 5 0.07
58 62 0.83
59 6 0.08
60 2 0.03
ACGTcount: A:0.36, C:0.08, G:0.11, T:0.46
Consensus pattern (57 bp):
AATTTATTTTCTTGAGAATCTTAATGATTCTATTTTGTAAAAGAAAATAAATTGTTA
Found at i:5613402 original size:43 final size:43
Alignment explanation
Indices: 5613326--5613410 Score: 118
Period size: 43 Copynumber: 2.0 Consensus size: 43
5613316 CTTTTAAAAG
* *
5613326 GAAATAAATTGTTAAATTTATTTTCTTTGGAATCTTAAATAAA
1 GAAATAAATTATTAAATTTATTTTCTTAGGAATCTTAAATAAA
* *
5613369 GAAATAAATTATTGAATTTATTTTC-TAGAGAATCTTTAATAA
1 GAAATAAATTATTAAATTTATTTTCTTAG-GAATCTTAAATAA
5613411 TTCTATTGTG
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
42 2 0.05
43 35 0.95
ACGTcount: A:0.42, C:0.05, G:0.09, T:0.44
Consensus pattern (43 bp):
GAAATAAATTATTAAATTTATTTTCTTAGGAATCTTAAATAAA
Found at i:5613445 original size:101 final size:101
Alignment explanation
Indices: 5613264--5613450 Score: 252
Period size: 101 Copynumber: 1.8 Consensus size: 101
5613254 CTATTTTGTA
* * * * * *
5613264 AAAGAAAATAAATTGTTAAATTTATTTTCTTGGGAATCCTTAATGATTCTACCTTTTAAAAGGAA
1 AAAGAAAATAAATTATTAAATTTATTTTCTAGAGAATCCTTAATAATTCTA-CTTTAAAAACGAA
5613329 ATAAATTGTTAAATTTATTTTCTTTGGAATCTTAAAT
65 ATAAATTGTTAAATTTATTTTCTTTGGAATCTTAAAT
* *
5613366 AAAG-AAATAAATTATTGAATTTATTTTCTAGAGAATCTTTAATAATTCTA-TTGTGAAAAACGA
1 AAAGAAAATAAATTATTAAATTTATTTTCTAGAGAATCCTTAATAATTCTACTT-T-AAAAACGA
*
5613429 AATAAATTGTTGAATTTATTTT
64 AATAAATTGTTAAATTTATTTT
5613451 GTTGAGAATC
Statistics
Matches: 74, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
99 2 0.03
100 1 0.01
101 67 0.91
102 4 0.05
ACGTcount: A:0.40, C:0.06, G:0.11, T:0.43
Consensus pattern (101 bp):
AAAGAAAATAAATTATTAAATTTATTTTCTAGAGAATCCTTAATAATTCTACTTTAAAAACGAAA
TAAATTGTTAAATTTATTTTCTTTGGAATCTTAAAT
Found at i:5613459 original size:58 final size:58
Alignment explanation
Indices: 5613369--5613800 Score: 237
Period size: 58 Copynumber: 7.4 Consensus size: 58
5613359 CTTAAATAAA
* * * *
5613369 GAAATAAATTATTGAATTTATTTTCTAGAGAATCTTTAATAATTCTATTGTGAAAAAC
1 GAAATAAATTGTTGAATTTATTTTCTTGAGAATCTTGAATGATTCTATTGTGAAAAAC
* *
5613427 GAAATAAATTGTTGAATTTATTTTGTTGAGAATCTTGAATGATTCTA-TGCT-TAAAAC
1 GAAATAAATTGTTGAATTTATTTTCTTGAGAATCTTGAATGATTCTATTG-TGAAAAAC
* * * *
5613484 -AATATAAATTGTTGGATTTATATTTTTTTTG-GAAATCTCGAATGATTCTATTATGTAAAAA-
1 GAA-ATAAATTGTT-GAATT-TA-TTTTCTTGAG-AATCTTGAATGATTCTATTGTG-AAAAAC
* * * * *
5613545 GAAATAAATTGTTGAATTTATTTTCTT-AGGAGTCTTGAACG-TGTCCATTTTG-TAAAC
1 GAAATAAATTGTTGAATTTATTTTCTTGA-GAATCTTGAATGAT-TCTATTGTGAAAAAC
** * * * * *
5613602 GGAAATAAATCATTTAATTTATTTTCTTG-GAAAT-TT-ATATGATTATGTTTTGTAAAA-
1 -GAAATAAATTGTTGAATTTATTTTCTTGAG-AATCTTGA-ATGATTCTATTGTGAAAAAC
* * * * * * *
5613659 GAAAATAAATTATTTAATTTATTTTCTAGA-AATCTT-ATATGATTTTGTTTTGTAAAAAG
1 G-AAATAAATTGTTGAATTTATTTTCTTGAGAATCTTGA-ATGATTCTATTGTG-AAAAAC
* * * * * * * * *
5613718 GAAATGAATTATTAAATTTACTTTCTTGAAAATCATGTATAATTCTACTT-TGTAAAAAT
1 GAAATAAATTGTTGAATTTATTTTCTTGAGAATCTTGAATGATTCTA-TTGTG-AAAAAC
* **
5613777 AAAATAAATCATTGAATTTATTTT
1 GAAATAAATTGTTGAATTTATTTT
5613801 ATGGGAATCA
Statistics
Matches: 299, Mismatches: 47, Indels: 55
0.75 0.12 0.14
Matches are distributed among these distances:
56 10 0.03
57 71 0.24
58 126 0.42
59 45 0.15
60 30 0.10
61 11 0.04
62 6 0.02
ACGTcount: A:0.38, C:0.06, G:0.12, T:0.44
Consensus pattern (58 bp):
GAAATAAATTGTTGAATTTATTTTCTTGAGAATCTTGAATGATTCTATTGTGAAAAAC
Found at i:5613665 original size:57 final size:59
Alignment explanation
Indices: 5613604--5613800 Score: 220
Period size: 59 Copynumber: 3.4 Consensus size: 59
5613594 TTGTAAACGG
5613604 AAATAAATCATTTAATTTATTTTCTTGGAAAT-TTATATGATTATGTTTTGT-AAAAGA
1 AAATAAATCATTTAATTTATTTTCTTGGAAATCTTATATGATTATGTTTTGTAAAAAGA
* * * *
5613661 AAATAAATTATTTAATTTATTTTC-TAGAAATCTTATATGATTTTGTTTTGTAAAAAGG
1 AAATAAATCATTTAATTTATTTTCTTGGAAATCTTATATGATTATGTTTTGTAAAAAGA
* * * * * * * * * ** *
5613719 AAATGAATTATTAAATTTACTTTCTTGAAAATCATGTATAATTCTACTTTGTAAAAATA
1 AAATAAATCATTTAATTTATTTTCTTGGAAATCTTATATGATTATGTTTTGTAAAAAGA
*
5613778 AAATAAATCATTGAATTTATTTT
1 AAATAAATCATTTAATTTATTTT
5613801 ATGGGAATCA
Statistics
Matches: 116, Mismatches: 21, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
56 6 0.05
57 41 0.35
58 26 0.22
59 43 0.37
ACGTcount: A:0.40, C:0.05, G:0.09, T:0.46
Consensus pattern (59 bp):
AAATAAATCATTTAATTTATTTTCTTGGAAATCTTATATGATTATGTTTTGTAAAAAGA
Found at i:5613772 original size:59 final size:58
Alignment explanation
Indices: 5613650--5613864 Score: 154
Period size: 58 Copynumber: 3.8 Consensus size: 58
5613640 ATGATTATGT
* * * * * **
5613650 TTTGT-AAAAGAAAATAAATTATTTAATTTATTTTCTAGAAATCTTATATGATTTTGT
1 TTTGTAAAAAGAAAATAAATTATTAAATTTACTTTCTAGAAATCATATATAATTCTAC
* * * *
5613707 TTTGTAAAAAGGAAATGAATTATTAAATTTACTTTCTTGAAAATCATGTATAATTCTAC
1 TTTGTAAAAAGAAAATAAATTATTAAATTTACTTTCTAG-AAATCATATATAATTCTAC
* * * * * * * ** *
5613766 TTTGTAAAAATAAAATAAATCATTGAATTTATTTTATGGGAATCA-AGTATGTTTCTAT
1 TTTGTAAAAAGAAAATAAATTATTAAATTTACTTTCTAGAAATCATA-TATAATTCTAC
**
5613824 TTTGT--AAA-AAAATAAATCGTTAAATTTA-TTTCTTAGAAATC
1 TTTGTAAAAAGAAAATAAATTATTAAATTTACTTTC-TAGAAATC
5613865 TCGACATGTT
Statistics
Matches: 125, Mismatches: 29, Indels: 10
0.76 0.18 0.06
Matches are distributed among these distances:
54 3 0.02
55 24 0.19
56 3 0.02
57 5 0.04
58 46 0.37
59 44 0.35
ACGTcount: A:0.40, C:0.06, G:0.10, T:0.44
Consensus pattern (58 bp):
TTTGTAAAAAGAAAATAAATTATTAAATTTACTTTCTAGAAATCATATATAATTCTAC
Found at i:5615884 original size:17 final size:17
Alignment explanation
Indices: 5615862--5615903 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 17
5615852 TTAATGAACA
*
5615862 TTGTTAGTATGGCTTAG
1 TTGTTAGTATGGATTAG
5615879 TTGTTAGTATGGATTAG
1 TTGTTAGTATGGATTAG
*
5615896 CTGTTAGT
1 TTGTTAGT
5615904 GTGGTACTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.19, C:0.05, G:0.29, T:0.48
Consensus pattern (17 bp):
TTGTTAGTATGGATTAG
Found at i:5616517 original size:19 final size:19
Alignment explanation
Indices: 5616493--5616538 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
5616483 TCAACTTAAT
5616493 AAAAATTATTAAGGTGGTA
1 AAAAATTATTAAGGTGGTA
** *
5616512 AAAAATGGTTATGGTGGTA
1 AAAAATTATTAAGGTGGTA
5616531 AATAAATT
1 AA-AAATT
5616539 TAACCATTTG
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 18 0.82
20 4 0.18
ACGTcount: A:0.46, C:0.00, G:0.22, T:0.33
Consensus pattern (19 bp):
AAAAATTATTAAGGTGGTA
Found at i:5617154 original size:24 final size:24
Alignment explanation
Indices: 5617117--5617172 Score: 105
Period size: 24 Copynumber: 2.4 Consensus size: 24
5617107 AAACAAAAAC
5617117 TAAAA-TTTTTAAAGGCATGGTAT
1 TAAAATTTTTTAAAGGCATGGTAT
5617140 TAAAATTTTTTAAAGGCATGGTAT
1 TAAAATTTTTTAAAGGCATGGTAT
5617164 TAAAATTTT
1 TAAAATTTT
5617173 GAATGGTGAT
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
23 5 0.16
24 27 0.84
ACGTcount: A:0.39, C:0.04, G:0.14, T:0.43
Consensus pattern (24 bp):
TAAAATTTTTTAAAGGCATGGTAT
Found at i:5619118 original size:44 final size:44
Alignment explanation
Indices: 5619051--5619155 Score: 117
Period size: 44 Copynumber: 2.4 Consensus size: 44
5619041 TTCTACTAAT
* * * *
5619051 AAACGCCGCTAAAAGTCAAGTTATGTTGCGGCA-TTT-GTATAC
1 AAACGCCGCTAAAGGTTAAGTTATATAGCGGCATTTTAGTATAC
*
5619093 TAAAACGCCGCTAAAGGTTAGGTTATATAGCGGCATTTTAGTATAC
1 --AAACGCCGCTAAAGGTTAAGTTATATAGCGGCATTTTAGTATAC
5619139 AAACGCCG-TAACAGGTT
1 AAACGCCGCTAA-AGGTT
5619156 CGCCATATAG
Statistics
Matches: 53, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
43 3 0.06
44 41 0.77
45 3 0.06
46 6 0.11
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.28
Consensus pattern (44 bp):
AAACGCCGCTAAAGGTTAAGTTATATAGCGGCATTTTAGTATAC
Found at i:5625398 original size:20 final size:20
Alignment explanation
Indices: 5625375--5625464 Score: 108
Period size: 20 Copynumber: 4.5 Consensus size: 20
5625365 ACATGTTCAA
* * *
5625375 AAATTGCAACGTGAATAGGT
1 AAATCGCAACGCGAATATGT
**
5625395 AAATCGCAACGATAATATGT
1 AAATCGCAACGCGAATATGT
*
5625415 AAATCGCTACGCGAATATGT
1 AAATCGCAACGCGAATATGT
*
5625435 AAATCGCAACGCGAATTTGT
1 AAATCGCAACGCGAATATGT
*
5625455 AAATCACAAC
1 AAATCGCAAC
5625465 ACAGAAGTCA
Statistics
Matches: 60, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 60 1.00
ACGTcount: A:0.41, C:0.18, G:0.18, T:0.23
Consensus pattern (20 bp):
AAATCGCAACGCGAATATGT
Found at i:5625575 original size:27 final size:27
Alignment explanation
Indices: 5625537--5625589 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
5625527 CGATTTCCTA
*
5625537 ATTCGCGACGCGATTTCCTAATTCGCG
1 ATTCGCAACGCGATTTCCTAATTCGCG
**
5625564 ATTCGCAACGCGATTTTGTAATTCGC
1 ATTCGCAACGCGATTTCCTAATTCGC
5625590 AACTCGATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.21, C:0.26, G:0.21, T:0.32
Consensus pattern (27 bp):
ATTCGCAACGCGATTTCCTAATTCGCG
Found at i:5625686 original size:20 final size:20
Alignment explanation
Indices: 5625518--5625689 Score: 146
Period size: 20 Copynumber: 8.2 Consensus size: 20
5625508 GAACTCCATT
*
5625518 TTCGCAACGCGATTTCCTAA
1 TTCGCAACGCGATTTTCTAA
* *
5625538 TTCGCGACGCGATTTCCTAATTCGCGA
1 TTCGCAACGCGATTTTCT-A------A
*
5625565 TTCGCAACGCGATTTTGTAA
1 TTCGCAACGCGATTTTCTAA
*
5625585 TTCGCAACTCGATTTTCCTAA
1 TTCGCAACGCGATTTT-CTAA
*
5625606 TTCGCGACGCGATTTTCTAA
1 TTCGCAACGCGATTTTCTAA
* * * *
5625626 TTCGCGACGCTAATTCCTAA
1 TTCGCAACGCGATTTTCTAA
* * *
5625646 TTCGCGACGCTAATTTCTAA
1 TTCGCAACGCGATTTTCTAA
*
5625666 TTCGCAACGCGATTTTGTAA
1 TTCGCAACGCGATTTTCTAA
5625686 TTCG
1 TTCG
5625690 GAATTAGCGT
Statistics
Matches: 128, Mismatches: 16, Indels: 16
0.80 0.10 0.10
Matches are distributed among these distances:
20 93 0.73
21 18 0.14
26 1 0.01
27 16 0.12
ACGTcount: A:0.23, C:0.26, G:0.17, T:0.34
Consensus pattern (20 bp):
TTCGCAACGCGATTTTCTAA
Found at i:5625799 original size:20 final size:20
Alignment explanation
Indices: 5625684--5625787 Score: 199
Period size: 20 Copynumber: 5.2 Consensus size: 20
5625674 GCGATTTTGT
5625684 AATTCGGAATTAGCGTCGCG
1 AATTCGGAATTAGCGTCGCG
5625704 AATTCGGAATTAGCGTCGCG
1 AATTCGGAATTAGCGTCGCG
*
5625724 AATTCGGAATTAGCGTCGTG
1 AATTCGGAATTAGCGTCGCG
5625744 AATTCGGAATTAGCGTCGCG
1 AATTCGGAATTAGCGTCGCG
5625764 AATTCGGAATTAGCGTCGCG
1 AATTCGGAATTAGCGTCGCG
5625784 AATT
1 AATT
5625788 AGAAAATCGC
Statistics
Matches: 82, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 82 1.00
ACGTcount: A:0.26, C:0.18, G:0.29, T:0.27
Consensus pattern (20 bp):
AATTCGGAATTAGCGTCGCG
Found at i:5625804 original size:20 final size:21
Alignment explanation
Indices: 5625776--5625823 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
5625766 TTCGGAATTA
*
5625776 GCGTCGCGAA-TTAGAAAATC
1 GCGTTGCGAATTTAGAAAATC
*
5625796 GCGTTGCGAATTTGGAAAATC
1 GCGTTGCGAATTTAGAAAATC
5625817 GCGTTGC
1 GCGTTGC
5625824 AAAATTGGAG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 9 0.36
21 16 0.64
ACGTcount: A:0.27, C:0.19, G:0.29, T:0.25
Consensus pattern (21 bp):
GCGTTGCGAATTTAGAAAATC
Found at i:5625807 original size:60 final size:60
Alignment explanation
Indices: 5625684--5625812 Score: 195
Period size: 60 Copynumber: 2.1 Consensus size: 60
5625674 GCGATTTTGT
* * * *
5625684 AATTCGGAATTAGCGTCGCGAATTCGGAATTAGCGTCGCGAATTCGGAATTAGCGTCGTG
1 AATTCGGAATTAGCGTCGCGAATTCGGAATTAGCGTCGCGAATTAGAAAATAGCGTCGCG
* *
5625744 AATTCGGAATTAGCGTCGCGAATTCGGAATTAGCGTCGCGAATTAGAAAATCGCGTTGCG
1 AATTCGGAATTAGCGTCGCGAATTCGGAATTAGCGTCGCGAATTAGAAAATAGCGTCGCG
*
5625804 AATTTGGAA
1 AATTCGGAA
5625813 AATCGCGTTG
Statistics
Matches: 62, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
60 62 1.00
ACGTcount: A:0.28, C:0.17, G:0.29, T:0.26
Consensus pattern (60 bp):
AATTCGGAATTAGCGTCGCGAATTCGGAATTAGCGTCGCGAATTAGAAAATAGCGTCGCG
Found at i:5625815 original size:21 final size:21
Alignment explanation
Indices: 5625776--5625850 Score: 73
Period size: 20 Copynumber: 3.7 Consensus size: 21
5625766 TTCGGAATTA
* *
5625776 GCGTCGCGAA-TTAGAAAATC
1 GCGTTGCGAATTTGGAAAATC
5625796 GCGTTGCGAATTTGGAAAATC
1 GCGTTGCGAATTTGGAAAATC
* * **
5625817 GCGTTGCAAAATTGG-AGTTC
1 GCGTTGCGAATTTGGAAAATC
*
5625837 GCGTTACGAATTTG
1 GCGTTGCGAATTTG
5625851 AAATTCCGTG
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 23 0.51
21 22 0.49
ACGTcount: A:0.28, C:0.16, G:0.28, T:0.28
Consensus pattern (21 bp):
GCGTTGCGAATTTGGAAAATC
Found at i:5625892 original size:20 final size:20
Alignment explanation
Indices: 5625864--5625993 Score: 170
Period size: 20 Copynumber: 6.5 Consensus size: 20
5625854 TTCCGTGTTG
* * *
5625864 TTCCTAATTCGTGATGCTAA
1 TTCCGAATTCGCGACGCTAA
5625884 TTCCGAATTCGCGACGCTAA
1 TTCCGAATTCGCGACGCTAA
5625904 TTTCCGAATTCGCGACGCTAA
1 -TTCCGAATTCGCGACGCTAA
*
5625925 TTCTGAATTCGCGACGCTAA
1 TTCCGAATTCGCGACGCTAA
*
5625945 TTCTGAATTCGCGACGCTAA
1 TTCCGAATTCGCGACGCTAA
* * * *
5625965 TTCCTAATTCACAACGTTAA
1 TTCCGAATTCGCGACGCTAA
5625985 TTCCGAATT
1 TTCCGAATT
5625994 ACAAAATCAC
Statistics
Matches: 99, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
20 79 0.80
21 20 0.20
ACGTcount: A:0.26, C:0.25, G:0.16, T:0.32
Consensus pattern (20 bp):
TTCCGAATTCGCGACGCTAA
Found at i:5625944 original size:61 final size:60
Alignment explanation
Indices: 5625864--5625993 Score: 170
Period size: 61 Copynumber: 2.1 Consensus size: 60
5625854 TTCCGTGTTG
* * * * *
5625864 TTCCTAATTCGTGATGCTAATTCCGAATTCGCGACGCTAATTTCCGAATTCGCGACGCTAA
1 TTCCGAATTCGCGACGCTAATTCCGAATTCGCGACGCTAA-TTCCGAATTCACAACGCTAA
* * * *
5625925 TTCTGAATTCGCGACGCTAATTCTGAATTCGCGACGCTAATTCCTAATTCACAACGTTAA
1 TTCCGAATTCGCGACGCTAATTCCGAATTCGCGACGCTAATTCCGAATTCACAACGCTAA
5625985 TTCCGAATT
1 TTCCGAATT
5625994 ACAAAATCAC
Statistics
Matches: 59, Mismatches: 10, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
60 24 0.41
61 35 0.59
ACGTcount: A:0.26, C:0.25, G:0.16, T:0.32
Consensus pattern (60 bp):
TTCCGAATTCGCGACGCTAATTCCGAATTCGCGACGCTAATTCCGAATTCACAACGCTAA
Found at i:5626043 original size:20 final size:20
Alignment explanation
Indices: 5626016--5626102 Score: 122
Period size: 20 Copynumber: 4.3 Consensus size: 20
5626006 TGCGAATCGC
5626016 GAATTAGGAATTAGCGTC-A
1 GAATTAGGAATTAGCGTCGA
* *
5626035 CGAACTAGGAAATAGCGTCGA
1 -GAATTAGGAATTAGCGTCGA
5626056 GAATTAGGAATTAGCGTCGA
1 GAATTAGGAATTAGCGTCGA
* *
5626076 GAATTAGGAATTAGTGTCGC
1 GAATTAGGAATTAGCGTCGA
5626096 GAATTAG
1 GAATTAG
5626103 AAAATCTCAT
Statistics
Matches: 60, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
20 59 0.98
21 1 0.02
ACGTcount: A:0.36, C:0.11, G:0.29, T:0.24
Consensus pattern (20 bp):
GAATTAGGAATTAGCGTCGA
Found at i:5626129 original size:21 final size:21
Alignment explanation
Indices: 5626094--5626160 Score: 82
Period size: 21 Copynumber: 3.2 Consensus size: 21
5626084 AATTAGTGTC
*
5626094 GCGAA-TTAGAAAATCTCATT
1 GCGAATTTAGAAAATCACATT
*
5626114 GCGAATTTACAAAATCACATT
1 GCGAATTTAGAAAATCACATT
* * *
5626135 GCGAATTTGGAAAATCGCGTT
1 GCGAATTTAGAAAATCACATT
5626156 GCGAA
1 GCGAA
5626161 ATTGGAGTTC
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
20 5 0.12
21 35 0.88
ACGTcount: A:0.37, C:0.16, G:0.19, T:0.27
Consensus pattern (21 bp):
GCGAATTTAGAAAATCACATT
Found at i:5626194 original size:21 final size:20
Alignment explanation
Indices: 5626133--5626206 Score: 85
Period size: 21 Copynumber: 3.6 Consensus size: 20
5626123 CAAAATCACA
*
5626133 TTGCGAATTTGGAAAATCGCG
1 TTGCGAATTT-GAAATTCGCG
* * *
5626154 TTGCGAAATTGGAGTTCGCG
1 TTGCGAATTTGAAATTCGCG
5626174 TTGCGAATTTGAAATTTCGCG
1 TTGCGAATTTGAAA-TTCGCG
*
5626195 TTACGAATTTGA
1 TTGCGAATTTGA
5626207 CTTATGTGTT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 18 0.41
21 26 0.59
ACGTcount: A:0.26, C:0.14, G:0.27, T:0.34
Consensus pattern (20 bp):
TTGCGAATTTGAAATTCGCG
Found at i:5626240 original size:20 final size:20
Alignment explanation
Indices: 5626215--5626266 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
5626205 GACTTATGTG
5626215 TTGCGATTTACAAATTCGCA
1 TTGCGATTTACAAATTCGCA
5626235 TTGCGATTTACAAATTCGCA
1 TTGCGATTTACAAATTCGCA
*
5626255 TTGCAATTTACA
1 TTGCGATTTACA
5626267 TATTATCGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.31, C:0.19, G:0.13, T:0.37
Consensus pattern (20 bp):
TTGCGATTTACAAATTCGCA
Found at i:5626650 original size:82 final size:80
Alignment explanation
Indices: 5626531--5626835 Score: 222
Period size: 82 Copynumber: 3.7 Consensus size: 80
5626521 GTGTTCATGA
* * * * *
5626531 GAAAAATGCCACAATAGGTT-AACCCTACTGCGGCGTTTGTATAAAAATGCCGATAAAGT-TCT-
1 GAAAAACGCCACTATA-GTTGAA-CCTATTGC-GCGTTTGTATAAAAATGCAGCTAAAGTAT-TG
5626593 AATATGTTACGGCATTTATT
62 AAT-TGTTACGGCATTTATT
** *
5626613 GAAAAACGCCACTATAGTTGAACCATATTGCAGCGTTTGTATAAAAACACAGCTAAAGTATTGAC
1 GAAAAACGCCACTATAGTTGAACC-TATTGC-GCGTTTGTATAAAAATGCAGCTAAAGTATTGAA
* *
5626678 TTGTTGCGGCGTTTATT
64 TTGTTACGGCATTTATT
* * * * *
5626695 GAAAAAACACCACTATAGATGGACCTATTGCGACGTTTGTATAAAAATGCTGCTAAAGTACT-AC
1 G-AAAAACGCCACTATAGTTGAACCTATTGCG-CGTTTGTATAAAAATGCAGCTAAAGTATTGA-
* * * * *
5626759 ACTGTTGCGGCGTTTGTC
63 ATTGTTACGGCATTTATT
* * * * * * ** *
5626777 AAAAAACGCCATTATAGATGGACTTATTGCGACATTTGTATAAAAGCGCTGCTAAAGTA
1 GAAAAACGCCACTATAGTTGAACCTATTGCG-CGTTTGTATAAAAATGCAGCTAAAGTA
5626836 CTACTGTGCT
Statistics
Matches: 187, Mismatches: 29, Indels: 15
0.81 0.13 0.06
Matches are distributed among these distances:
81 59 0.32
82 105 0.56
83 23 0.12
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.29
Consensus pattern (80 bp):
GAAAAACGCCACTATAGTTGAACCTATTGCGCGTTTGTATAAAAATGCAGCTAAAGTATTGAATT
GTTACGGCATTTATT
Found at i:5626690 original size:41 final size:41
Alignment explanation
Indices: 5626640--5626783 Score: 109
Period size: 41 Copynumber: 3.5 Consensus size: 41
5626630 TTGAACCATA
* *
5626640 TTGCAGCGTTTGTATAAAAACACAGCTAAAGTATTGACTTG
1 TTGCGGCGTTTGTATAAAAACACAGCTAAAGTATTGACCTG
* * * *
5626681 TTGCGGCGTTTAT-TGAAAAAACACCA-CTATAG-ATGGACCTA
1 TTGCGGCGTTTGTAT--AAAAACA-CAGCTAAAGTATTGACCTG
* ** * *
5626722 TTGCGACGTTTGTATAAAAATGCTGCTAAAGTACT-ACACTG
1 TTGCGGCGTTTGTATAAAAACACAGCTAAAGTATTGAC-CTG
5626763 TTGCGGCGTTTGTCA-AAAAAC
1 TTGCGGCGTTTGT-ATAAAAAC
5626784 GCCATTATAG
Statistics
Matches: 78, Mismatches: 17, Indels: 16
0.70 0.15 0.14
Matches are distributed among these distances:
39 1 0.01
40 13 0.17
41 48 0.62
42 14 0.18
43 2 0.03
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Consensus pattern (41 bp):
TTGCGGCGTTTGTATAAAAACACAGCTAAAGTATTGACCTG
Found at i:5626828 original size:81 final size:81
Alignment explanation
Indices: 5626614--5626839 Score: 258
Period size: 81 Copynumber: 2.8 Consensus size: 81
5626604 GCATTTATTG
* * * * * * *
5626614 AAAAACGCCACTATAGTTGAACCATATTGC-AGCGTTTGTATAAAAACACAGCTAAAGTATTGAC
1 AAAAACACCACTATAGATGGACC-TATTGCGA-CATTTGTATAAAAACGCTGCTAAAGTACT-AC
* * *
5626678 TTGTTGCGGCGTTTATTGA
63 CTGTTGCGGCGTTTAGTCA
* *
5626697 AAAAACACCACTATAGATGGACCTATTGCGACGTTTGTATAAAAATGCTGCTAAAGTACTACACT
1 AAAAACACCACTATAGATGGACCTATTGCGACATTTGTATAAAAACGCTGCTAAAGTACTAC-CT
5626762 GTTGCGGCGTTT-GTCA
65 GTTGCGGCGTTTAGTCA
* * * *
5626778 AAAAACGCCATTATAGATGGACTTATTGCGACATTTGTATAAAAGCGCTGCTAAAGTACTAC
1 AAAAACACCACTATAGATGGACCTATTGCGACATTTGTATAAAAACGCTGCTAAAGTACTAC
5626840 TGTGCTACGC
Statistics
Matches: 125, Mismatches: 16, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
81 60 0.48
82 44 0.35
83 21 0.17
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.29
Consensus pattern (81 bp):
AAAAACACCACTATAGATGGACCTATTGCGACATTTGTATAAAAACGCTGCTAAAGTACTACCTG
TTGCGGCGTTTAGTCA
Found at i:5626854 original size:81 final size:81
Alignment explanation
Indices: 5626696--5626867 Score: 227
Period size: 81 Copynumber: 2.1 Consensus size: 81
5626686 GCGTTTATTG
* *
5626696 AAAAAACACCACTATAGATGGACCTATTGCGACGTTTGTATAAAAATGCTGCTAAAGTACTACAC
1 AAAAAACACCACTATAGATGGACCTATTGCGACATTTGTATAAAAACGCTGCTAAAGTACTACAC
* * *
5626761 TGTTGCGGCGTTTGTC
66 TGCTACGCCGTTTGTC
* * * * **
5626777 AAAAAACGCCATTATAGATGGACTTATTGCGACATTTGTATAAAAGCGCTGCTAAAGTACTACTG
1 AAAAAACACCACTATAGATGGACCTATTGCGACATTTGTATAAAAACGCTGCTAAAGTACTACAC
5626842 TGCTACGCCGTTTGTC
66 TGCTACGCCGTTTGTC
*
5626858 GAAGAAACAC
1 -AAAAAACAC
5626868 TGCTAACGTT
Statistics
Matches: 77, Mismatches: 13, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
81 70 0.91
82 7 0.09
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.27
Consensus pattern (81 bp):
AAAAAACACCACTATAGATGGACCTATTGCGACATTTGTATAAAAACGCTGCTAAAGTACTACAC
TGCTACGCCGTTTGTC
Found at i:5627489 original size:21 final size:23
Alignment explanation
Indices: 5627447--5627490 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 23
5627437 CATTTTAATC
5627447 AAAATATTAATTATTAAATATTT
1 AAAATATTAATTATTAAATATTT
*
5627470 AAAATA-TATTTATT-AATATTT
1 AAAATATTAATTATTAAATATTT
5627491 CTAATAATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 7 0.35
22 7 0.35
23 6 0.30
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (23 bp):
AAAATATTAATTATTAAATATTT
Found at i:5627500 original size:22 final size:23
Alignment explanation
Indices: 5627456--5627518 Score: 60
Period size: 22 Copynumber: 2.8 Consensus size: 23
5627446 CAAAATATTA
*
5627456 ATTATTAAATATTTAAAAT-ATAT
1 ATTATT-AATATTTATAATAATAT
*
5627479 -TTATTAATATTTCTAATAATAT
1 ATTATTAATATTTATAATAATAT
* *
5627501 AATATT-ATATTTTTAATA
1 ATTATTAATATTTATAATA
5627519 TTATCGCGAC
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
21 10 0.29
22 20 0.59
23 4 0.12
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (23 bp):
ATTATTAATATTTATAATAATAT
Found at i:5627764 original size:6 final size:7
Alignment explanation
Indices: 5627745--5627775 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
5627735 TTTAATTACG
5627745 AAAATTT
1 AAAATTT
5627752 AAAATTT
1 AAAATTT
5627759 -AAATTT
1 AAAATTT
5627765 AAAATTT
1 AAAATTT
5627772 AAAA
1 AAAA
5627776 ACATGATTCG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.26
7 17 0.74
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (7 bp):
AAAATTT
Found at i:5627764 original size:13 final size:13
Alignment explanation
Indices: 5627746--5627774 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
5627736 TTAATTACGA
5627746 AAATTTAAAATTT
1 AAATTTAAAATTT
5627759 AAATTTAAAATTT
1 AAATTTAAAATTT
5627772 AAA
1 AAA
5627775 AACATGATTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (13 bp):
AAATTTAAAATTT
Found at i:5627897 original size:23 final size:23
Alignment explanation
Indices: 5627867--5627923 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 23
5627857 CATAAGTATG
5627867 AAATGAATAAAATAAAAAAATAAT
1 AAATGAATAAAA-AAAAAAATAAT
**
5627891 -AATGAATTTAAAAAAAAATAAT
1 AAATGAATAAAAAAAAAAATAAT
*
5627913 AAATAAATAAA
1 AAATGAATAAA
5627924 TCAAGACGGA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
22 11 0.41
23 16 0.59
ACGTcount: A:0.74, C:0.00, G:0.04, T:0.23
Consensus pattern (23 bp):
AAATGAATAAAAAAAAAAATAAT
Found at i:5629299 original size:25 final size:26
Alignment explanation
Indices: 5629258--5629313 Score: 87
Period size: 25 Copynumber: 2.2 Consensus size: 26
5629248 TATTTTTTAA
5629258 AAAACTATATATTATATATATATTTTC
1 AAAACTATATA-TATATATATATTTTC
*
5629285 AAAACTATATA-ATATATATGTTTTC
1 AAAACTATATATATATATATATTTTC
5629310 AAAA
1 AAAA
5629314 ATGTTTTCAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
25 17 0.61
27 11 0.39
ACGTcount: A:0.48, C:0.07, G:0.02, T:0.43
Consensus pattern (26 bp):
AAAACTATATATATATATATATTTTC
Found at i:5629319 original size:12 final size:12
Alignment explanation
Indices: 5629302--5629326 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5629292 TATAATATAT
5629302 ATGTTTTCAAAA
1 ATGTTTTCAAAA
5629314 ATGTTTTCAAAA
1 ATGTTTTCAAAA
5629326 A
1 A
5629327 CTATATATTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (12 bp):
ATGTTTTCAAAA
Found at i:5629331 original size:38 final size:35
Alignment explanation
Indices: 5629280--5629420 Score: 146
Period size: 38 Copynumber: 3.9 Consensus size: 35
5629270 TATATATATA
5629280 TTTTC-AAAACTATATAATATATATGTTTTCAAAAATG
1 TTTTCAAAAACTATAT-AT-TATAT-TTTTCAAAAATG
*
5629317 TTTTCAAAAACTATATATTATA--TTT-AAAATTG
1 TTTTCAAAAACTATATATTATATTTTTCAAAAATG
*
5629349 TTTTCAAAAACTATATATTATATATTTTCGAAAACTG
1 TTTTCAAAAACTATATATTATAT-TTTTC-AAAAATG
* * *
5629386 CTTTCTAAAAATTATATATTATAATTTTCCAAAAA
1 TTTTC-AAAAACTATATATTAT-ATTTTTCAAAAA
5629421 AATTCAAAAA
Statistics
Matches: 90, Mismatches: 6, Indels: 16
0.80 0.05 0.14
Matches are distributed among these distances:
32 28 0.31
33 3 0.03
35 3 0.03
36 4 0.04
37 21 0.23
38 29 0.32
39 2 0.02
ACGTcount: A:0.43, C:0.09, G:0.04, T:0.44
Consensus pattern (35 bp):
TTTTCAAAAACTATATATTATATTTTTCAAAAATG
Found at i:5629356 original size:32 final size:32
Alignment explanation
Indices: 5629310--5629371 Score: 115
Period size: 32 Copynumber: 1.9 Consensus size: 32
5629300 ATATGTTTTC
5629310 AAAAATGTTTTCAAAAACTATATATTATATTT
1 AAAAATGTTTTCAAAAACTATATATTATATTT
*
5629342 AAAATTGTTTTCAAAAACTATATATTATAT
1 AAAAATGTTTTCAAAAACTATATATTATAT
5629372 ATTTTCGAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.44
Consensus pattern (32 bp):
AAAAATGTTTTCAAAAACTATATATTATATTT
Found at i:5629360 original size:70 final size:64
Alignment explanation
Indices: 5629236--5629408 Score: 177
Period size: 70 Copynumber: 2.6 Consensus size: 64
5629226 TATTTAAAAC
* * *
5629236 TGTTTTCAAAAATATTTTTTAAAAAACTATATATTATATATATATTTTCAAAACTATATAATATA
1 TGTTTTCAAAAA-ATGTTTTCAAAAACTATATATTATATAAATATTTTCAAAACTATAT-AT-TA
5629301 TA
63 TA
*
5629303 TGTTTTC-AAAAATGTTTTCAAAAACTATATATTATATTTAAAATTGTTTTCAAAAACTATATAT
1 TGTTTTCAAAAAATGTTTTCAAAAACTATATATTATA--T-AAA-TATTTTC-AAAACTATATAT
5629367 TATA
61 TATA
* * * * *
5629371 TATTTTCGAAAACTGCTTTCTAAAAATTATATATTATA
1 TGTTTTCAAAAAATGTTTTC-AAAAACTATATATTATA
5629409 ATTTTCCAAA
Statistics
Matches: 91, Mismatches: 8, Indels: 11
0.83 0.07 0.10
Matches are distributed among these distances:
65 23 0.25
66 4 0.04
67 8 0.09
68 12 0.13
69 18 0.20
70 26 0.29
ACGTcount: A:0.43, C:0.08, G:0.03, T:0.46
Consensus pattern (64 bp):
TGTTTTCAAAAAATGTTTTCAAAAACTATATATTATATAAATATTTTCAAAACTATATATTATA
Found at i:5630281 original size:163 final size:162
Alignment explanation
Indices: 5630021--5630780 Score: 894
Period size: 163 Copynumber: 4.6 Consensus size: 162
5630011 TGAAAAATAG
* * * * *
5630021 CCCTTCTTGCCTTGAGCTATGCTGTAAATTTGATTTGCCTCTAAGTTGAA-TGTAATCGAACTCG
1 CCCTTCTAGCCTTGAGTTATGCTGTAAA--TGATGTGCCTCTGAGCT-AAGTGTAATCGAACTCG
*
5630085 AAGGTCTTTGTTGGTAGATAACCCTTTTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGC
63 AAGGTC--T-TTGGCAGATAACCCTTTTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGC
*
5630150 TGAGTGTAATCGAACTCAAAGGTCTTTATTGATAGATAA
125 TGAGTGTAATCGAACTCAAAGGTCTTT-TTGACAGATAA
* * * * *
5630189 CCCATCTAGCCTTGAGTTATACTGTAAATGATGTGCCTTTGAGTTAAGTGTAATCGAAGTCGAAG
1 CCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCTCTGAGCTAAGTGTAATCGAACTCGAAG
* * * *
5630254 GACTTTGGCAGATAACCCTTATTGCCTTGAGCTATGATGCAAATGATGTTCCTTTGAGCTGAGTG
66 GTCTTTGGCAGATAACCCTTTTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTG
* * * *
5630319 TAATCGAACGCGAAGGTCTTTTTGTTGGCAGATAT
131 TAATCGAACTCAAAGGTC--TTT-TTGACAGATAA
* * * * * * * *
5630354 CCCTTCTAGCCTTAAGATATACTGCAAATGATGTGCCTATGAGCTGAGTGTAATCAAACTTGAAG
1 CCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCTCTGAGCTAAGTGTAATCGAACTCGAAG
* ** *
5630419 GTCTTTGGCAGATAGCCCTTCTTT-CCTTGAGCTATATTGAAAATGATGTGCCTTTGAGCTGAGT
66 GTCTTTGGCAGATAACCCTT-TTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGT
5630483 GTAATCGAACTCAAAGGTCTTTGTTGACAGATAA
130 GTAATCGAACTCAAAGGTCTTT-TTGACAGATAA
* * * * *
5630517 CCCTTCTATCCTTGAGTTATGCTGTAAATAATGTGCCTTTGAGCTGAGTGTAATCGAACTCCAAG
1 CCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCTCTGAGCTAAGTGTAATCGAACTCGAAG
* * * * *
5630582 GTCTTTGGCAGATAACCCTTTTTTCCTTGAGCTATGCTGTAAATGATATGCCTTTAAGATGAGTG
66 GTCTTTGGCAGATAACCCTTTTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTG
* *
5630647 TAATCAAACTCGAAGGTCTTTTTTGACAGATAA
131 TAATCGAACTCAAAGGTC-TTTTTGACAGATAA
* * * * *
5630680 CCCTTATCGCCTTGAGTTATGTTGTAAATTTGATGTGCCTCTGAGCTAAATGTAATCAAACTCGA
1 CCCTTCTAGCCTTGAGTTATGCTGTAAA--TGATGTGCCTCTGAGCTAAGTGTAATCGAACTCGA
*
5630745 AGGTCTTTGTTGGAAGATAACCCTTTTTGCCTTGAG
64 AGGTC--T-TTGGCAGATAACCCTTTTTGCCTTGAG
5630781 TTATATTGCA
Statistics
Matches: 510, Mismatches: 71, Indels: 22
0.85 0.12 0.04
Matches are distributed among these distances:
162 3 0.01
163 246 0.48
164 4 0.01
165 173 0.34
166 34 0.07
167 1 0.00
168 49 0.10
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.35
Consensus pattern (162 bp):
CCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCTCTGAGCTAAGTGTAATCGAACTCGAAG
GTCTTTGGCAGATAACCCTTTTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTG
TAATCGAACTCAAAGGTCTTTTTGACAGATAA
Found at i:5630516 original size:248 final size:247
Alignment explanation
Indices: 5630006--5630793 Score: 869
Period size: 248 Copynumber: 3.2 Consensus size: 247
5629996 ACTCGACAAT
* * * * * * * *
5630006 TTTGTTGAAAAATAGCCCTTCTTGCCTTGAGCTATGCTGTAAATTTGAT-TTGCCTCTAAGTTGA
1 TTTGTTGACAGATAACCCTTCTTGCCTTGAGCTATGATGCAAA--TGATGTT-CCTTTGAGCTGA
* *
5630070 ATGTAATCGAACTCGAAGGTCTTTGTTGGTAGATAACCCTTTTTGCCTTGAGCTATGCTGCAAAT
63 GTGTAATCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTTTTGCCTTGAGCTATGCTGCAAAT
* * * *
5630135 GATGTGCCTTTGAGCTGAGTGTAATCGAACTCAAAGGTCTTTATTGATAGATAACCCATCTAGCC
128 GATGTGCCTTTGAGCTGAGTGTAATCAAACTCGAAGGTC-TT-TTGACAGATAACCCTTCTAGCC
* * * * *
5630200 TTGAGTTATACTGTAAATGATGTGCCTTTGAGTTAAGTGTAATCGAAGTCGAAGGAC
191 TTGAGTTATATTGAAAATGATGTGCCTTTGAGCTAAGTGTAATCGAACTCGAAGGTC
*
5630257 TTTG--G-CAGATAACCCTTATTGCCTTGAGCTATGATGCAAATGATGTTCCTTTGAGCTGAGTG
1 TTTGTTGACAGATAACCCTTCTTGCCTTGAGCTATGATGCAAATGATGTTCCTTTGAGCTGAGTG
* * * * * * *
5630319 TAATCGAACGCGAAGGTCTTTTTGTTGGCAGATATCCCTTCTAGCCTTAAGATATACTGCAAATG
66 TAATCGAACTCGAAGGTC--TTTGTTGGCAGATAACCCTTTTTGCCTTGAGCTATGCTGCAAATG
* * * * **
5630384 ATGTGCCTATGAGCTGAGTGTAATCAAACTTGAAGGTC-TTTGGCAGATAGCCCTTCTTTCCTTG
129 ATGTGCCTTTGAGCTGAGTGTAATCAAACTCGAAGGTCTTTTGACAGATAACCCTTCTAGCCTTG
* * *
5630448 AGCTATATTGAAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCAAAGGTC
194 AGTTATATTGAAAATGATGTGCCTTTGAGCTAAGTGTAATCGAACTCGAAGGTC
* * * * *
5630502 TTTGTTGACAGATAACCCTTCTAT-CCTTGAGTTATGCTGTAAATAATGTGCCTTTGAGCTGAGT
1 TTTGTTGACAGATAACCCTTCT-TGCCTTGAGCTATGATGCAAATGATGTTCCTTTGAGCTGAGT
* * *
5630566 GTAATCGAACTCCAAGGTC--T-TTGGCAGATAACCCTTTTTTCCTTGAGCTATGCTGTAAATGA
65 GTAATCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTTTTGCCTTGAGCTATGCTGCAAATGA
* * * * *
5630628 TATGCCTTTAAGATGAGTGTAATCAAACTCGAAGGTCTTTTTTGACAGATAACCCTTATCGCCTT
130 TGTGCCTTTGAGCTGAGTGTAATCAAACTCGAAGGTC--TTTTGACAGATAACCCTTCTAGCCTT
* * * * *
5630693 GAGTTATGTTGTAAATTTGATGTGCCTCTGAGCTAAATGTAATCAAACTCGAAGGTC
193 GAGTTATATTG-AAA-ATGATGTGCCTTTGAGCTAAGTGTAATCGAACTCGAAGGTC
* *
5630750 TTTGTTGGA-AGATAACCCTTTTTGCCTTGAGTTAT-ATTGCAAAT
1 TTTGTT-GACAGATAACCCTTCTTGCCTTGAGCTATGA-TGCAAAT
5630794 AGTTTCTTTA
Statistics
Matches: 449, Mismatches: 73, Indels: 33
0.81 0.13 0.06
Matches are distributed among these distances:
243 66 0.15
244 1 0.00
245 69 0.15
246 62 0.14
247 7 0.02
248 236 0.53
249 4 0.01
251 4 0.01
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.35
Consensus pattern (247 bp):
TTTGTTGACAGATAACCCTTCTTGCCTTGAGCTATGATGCAAATGATGTTCCTTTGAGCTGAGTG
TAATCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTTTTGCCTTGAGCTATGCTGCAAATGAT
GTGCCTTTGAGCTGAGTGTAATCAAACTCGAAGGTCTTTTGACAGATAACCCTTCTAGCCTTGAG
TTATATTGAAAATGATGTGCCTTTGAGCTAAGTGTAATCGAACTCGAAGGTC
Found at i:5630716 original size:328 final size:332
Alignment explanation
Indices: 5630005--5630793 Score: 1043
Period size: 328 Copynumber: 2.4 Consensus size: 332
5629995 AACTCGACAA
* * * * * * * * *
5630005 TTTTGTTGAAAAATAGCCCTTCTTGCCTTGAGCTATGCTGTAAATTTGATTTGCCTCTAAGTTGA
1 TTTTGTTGACAGATAACCCTTATAGCCTTGAGATATGCTGTAAATTTGATGTGCCTCTGAGCTGA
* * **
5630070 ATGTAATCGAACTCGAAGGTCTTTGTTGGTAGATAACCCTTTTTGCCTTGAGCTATGCTGCAAAT
66 ATGTAATCAAACTCGAAGGTC-TTGTTGGAAGATAACCCTTTTTGCCTTGAGCTATATTGCAAAT
*
5630135 GATGTGCCTTTGAGCTGAGTGTAATCGAACTCAAAGGTCTTTATTGATAGATAACCCATCTAGCC
130 GATGTGCCTTTGAGCTGAGTGTAATCGAACTCAAAGGTCTTTATTGACAGATAACCCATCTAGCC
* * * *
5630200 TTGAGTTATACTGTAAATGATGTGCCTTTGAGTTAAGTGTAATCGAAGTCGAAGGACTTTGGCAG
195 TTGAGTTATACTGTAAATAATGTGCCTTTGAGCTAAGTGTAATCGAACTCCAAGGACTTTGGCAG
* * * * *
5630265 ATAACCCTTATTGCCTTGAGCTATGATGCAAATGATGTTCCTTTGAGCTGAGTGTAATCGAACGC
260 ATAACCCTTATTGCCTTGAGCTATGATGCAAATGATATGCCTTTAAGATGAGTGTAATCAAACGC
5630330 GAAGGTCT
325 GAAGGTCT
* * * * * * *
5630338 TTTTGTTGGCAGATATCCCTTCTAGCCTTAAGATATACTGCAAA--TGATGTGCCTATGAGCTGA
1 TTTTGTTGACAGATAACCCTTATAGCCTTGAGATATGCTGTAAATTTGATGTGCCTCTGAGCTGA
* * * * *
5630401 GTGTAATCAAACTTGAAGGTC-T-TTGGCAGATAGCCCTTCTTT-CCTTGAGCTATATTGAAAAT
66 ATGTAATCAAACTCGAAGGTCTTGTTGGAAGATAACCCTT-TTTGCCTTGAGCTATATTGCAAAT
* * *
5630463 GATGTGCCTTTGAGCTGAGTGTAATCGAACTCAAAGGTCTTTGTTGACAGATAACCCTTCTATCC
130 GATGTGCCTTTGAGCTGAGTGTAATCGAACTCAAAGGTCTTTATTGACAGATAACCCATCTAGCC
* * *
5630528 TTGAGTTATGCTGTAAATAATGTGCCTTTGAGCTGAGTGTAATCGAACTCCAAGGTCTTTGGCAG
195 TTGAGTTATACTGTAAATAATGTGCCTTTGAGCTAAGTGTAATCGAACTCCAAGGACTTTGGCAG
* * * * *
5630593 ATAACCCTTTTTTCCTTGAGCTATGCTGTAAATGATATGCCTTTAAGATGAGTGTAATCAAACTC
260 ATAACCCTTATTGCCTTGAGCTATGATGCAAATGATATGCCTTTAAGATGAGTGTAATCAAACGC
5630658 GAAGGTC-
325 GAAGGTCT
* * * *
5630665 TTTT-TTGACAGATAACCCTTATCGCCTTGAGTTATGTTGTAAATTTGATGTGCCTCTGAGCTAA
1 TTTTGTTGACAGATAACCCTTATAGCCTTGAGATATGCTGTAAATTTGATGTGCCTCTGAGCTGA
*
5630729 ATGTAATCAAACTCGAAGGTCTTTGTTGGAAGATAACCCTTTTTGCCTTGAGTTATATTGCAAAT
66 ATGTAATCAAACTCGAAGGTC-TTGTTGGAAGATAACCCTTTTTGCCTTGAGCTATATTGCAAAT
5630794 AGTTTCTTTA
Statistics
Matches: 390, Mismatches: 59, Indels: 16
0.84 0.13 0.03
Matches are distributed among these distances:
326 30 0.08
327 4 0.01
328 248 0.64
329 4 0.01
330 4 0.01
331 65 0.17
333 35 0.09
ACGTcount: A:0.26, C:0.17, G:0.21, T:0.35
Consensus pattern (332 bp):
TTTTGTTGACAGATAACCCTTATAGCCTTGAGATATGCTGTAAATTTGATGTGCCTCTGAGCTGA
ATGTAATCAAACTCGAAGGTCTTGTTGGAAGATAACCCTTTTTGCCTTGAGCTATATTGCAAATG
ATGTGCCTTTGAGCTGAGTGTAATCGAACTCAAAGGTCTTTATTGACAGATAACCCATCTAGCCT
TGAGTTATACTGTAAATAATGTGCCTTTGAGCTAAGTGTAATCGAACTCCAAGGACTTTGGCAGA
TAACCCTTATTGCCTTGAGCTATGATGCAAATGATATGCCTTTAAGATGAGTGTAATCAAACGCG
AAGGTCT
Found at i:5634962 original size:85 final size:84
Alignment explanation
Indices: 5634852--5635113 Score: 402
Period size: 85 Copynumber: 3.1 Consensus size: 84
5634842 TTCTTTGAGT
*
5634852 GTCATTGAAGGCCCCGTCATAAATTAAGATGACACACATTTGTACGTCATAAATTTATGACACGC
1 GTCATTGAA-GCCCCGTCATAAATTAAGATGACACACATTTGTGCGTCATAAATTTATGACACGC
5634917 ATGTATGACTTACATTGCGC
65 ATGTATGACTTACATTGCGC
*
5634937 GTTATTGAAGCCCCCGTCATAAATTAAGATGACACACATTTGTGCGTCATAAATTTATGACACGC
1 GTCATTGAAG-CCCCGTCATAAATTAAGATGACACACATTTGTGCGTCATAAATTTATGACACGC
5635002 ATGTATGACTTACATTGCGC
65 ATGTATGACTTACATTGCGC
* * * *
5635022 GTCATTGAAGCCCCGTCATAAATCT--GCTTGACAAACATTTGTGTGTCATAAATTTATGACATG
1 GTCATTGAAGCCCCGTCATAAAT-TAAG-ATGACACACATTTGTGCGTCATAAATTTATGACACG
* *
5635085 CATATATGACTTACATTGCGT
64 CATGTATGACTTACATTGCGC
5635106 GTCATTGA
1 GTCATTGA
5635114 TGCACACGTC
Statistics
Matches: 165, Mismatches: 9, Indels: 7
0.91 0.05 0.04
Matches are distributed among these distances:
83 1 0.01
84 73 0.44
85 91 0.55
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.32
Consensus pattern (84 bp):
GTCATTGAAGCCCCGTCATAAATTAAGATGACACACATTTGTGCGTCATAAATTTATGACACGCA
TGTATGACTTACATTGCGC
Found at i:5635180 original size:2 final size:2
Alignment explanation
Indices: 5635173--5635319 Score: 235
Period size: 2 Copynumber: 74.5 Consensus size: 2
5635163 TTTAGGAAAT
*
5635173 TA TA TA TA TA TA TA TA TA TA -A TA TA AA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
5635214 TA TA TA TA TA TA TG T- TA TA TA TA TG TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
5635255 TA TA TA CA TA TA TA TA TA TA TA TA TA CA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5635297 TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
5635320 TGTAGATTGA
Statistics
Matches: 134, Mismatches: 9, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
1 2 0.01
2 132 0.99
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (2 bp):
TA
Found at i:5638950 original size:2 final size:2
Alignment explanation
Indices: 5638943--5639005 Score: 126
Period size: 2 Copynumber: 31.5 Consensus size: 2
5638933 TCAATCTACA
5638943 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5638985 AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT A
5639006 AATTTCCGAA
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5639155 original size:85 final size:84
Alignment explanation
Indices: 5639066--5639276 Score: 266
Period size: 85 Copynumber: 2.5 Consensus size: 84
5639056 GACGTGTGCA
*
5639066 TCAATGACACGCAATATAAGTCATATATGCGTGTCATAAATTTATGACACACAAATGTATGTCAA
1 TCAATGACACGCAATATAAGTCATATATGCGTGTCATAAATTTATGACACACAAATGTATCTC-A
*
5639131 GC-AGATTTATGGCAGGGGCT
65 GCTA-ATTTATGACAGGGGCT
* * * *
5639151 TCAATGACACGCAATGTAAGTCATATATGCGTGTCATAAATTTATGACGCACAAATGTGTCTCAT
1 TCAATGACACGCAATATAAGTCATATATGCGTGTCATAAATTTATGACACACAAATGTATCTCAG
*
5639216 CTTAATTTATGACGGGGGCT
66 C-TAATTTATGACAGGGGCT
* * *
5639236 TCAATGACACTCAA-AGAACGTCAT-TAATGAGTGTCATAAAT
1 TCAATGACACGCAATATAA-GTCATAT-ATGCGTGTCATAAAT
5639277 GCGCATCATA
Statistics
Matches: 111, Mismatches: 11, Indels: 8
0.85 0.08 0.06
Matches are distributed among these distances:
84 5 0.05
85 105 0.95
86 1 0.01
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.29
Consensus pattern (84 bp):
TCAATGACACGCAATATAAGTCATATATGCGTGTCATAAATTTATGACACACAAATGTATCTCAG
CTAATTTATGACAGGGGCT
Found at i:5640507 original size:27 final size:27
Alignment explanation
Indices: 5640472--5640529 Score: 89
Period size: 27 Copynumber: 2.1 Consensus size: 27
5640462 ATTTTCAAAA
* *
5640472 ATATTTTTTAAAAACTATATATTATAT
1 ATATGTTTTAAAAACTATATAATATAT
*
5640499 ATATGTTTTCAAAACTATATAATATAT
1 ATATGTTTTAAAAACTATATAATATAT
5640526 ATAT
1 ATAT
5640530 ATATATTCAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.48
Consensus pattern (27 bp):
ATATGTTTTAAAAACTATATAATATAT
Found at i:5640526 original size:29 final size:27
Alignment explanation
Indices: 5640472--5640541 Score: 86
Period size: 27 Copynumber: 2.5 Consensus size: 27
5640462 ATTTTCAAAA
* *
5640472 ATATTTTTTAAAAACTATATATTATAT
1 ATATATTTTCAAAACTATATATTATAT
*
5640499 ATATGTTTTCAAAACTATATAATATATAT
1 ATATATTTTCAAAACTATAT-AT-TATAT
*
5640528 ATATATATTCAAAA
1 ATATATTTTCAAAA
5640542 ATGTTTTCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
27 18 0.49
28 2 0.05
29 17 0.46
ACGTcount: A:0.47, C:0.06, G:0.01, T:0.46
Consensus pattern (27 bp):
ATATATTTTCAAAACTATATATTATAT
Found at i:5640527 original size:70 final size:68
Alignment explanation
Indices: 5640452--5640637 Score: 186
Period size: 67 Copynumber: 2.7 Consensus size: 68
5640442 TTTAAAAAAA
*
5640452 ATATATAGATATTTTCAAAAATATTTTTTAAAAACTATATATTATATATATGTTTTC-AAAACTA
1 ATATATA-ATATTTTC-AAAATATTTTTTAAAAACTATATATTATATATATATTTTCAAAAACTA
5640516 TATAAT
64 TA-AAT
* * * *
5640522 ATATATATATATATTCAAAA-ATGTTTTCAAAACTATAT-TTATATTAAAAATATTTTCAAAAAC
1 ATATATA-ATATTTTCAAAATATTTTTTAAAAACTATATATTATA-T--ATATATTTTCAAAAAC
5640585 TATAAAT
62 TATAAAT
* * * *
5640592 -TATAT-ATATTTTTAAAAT-GTTTTCAAAATCTATATATTATATATAT
1 ATATATAATATTTTCAAAATATTTTTTAAAAACTATATATTATATATAT
5640638 TTTAAAAAAT
Statistics
Matches: 96, Mismatches: 14, Indels: 17
0.76 0.11 0.13
Matches are distributed among these distances:
65 3 0.03
67 28 0.29
68 22 0.23
69 9 0.09
70 25 0.26
71 9 0.09
ACGTcount: A:0.46, C:0.06, G:0.02, T:0.46
Consensus pattern (68 bp):
ATATATAATATTTTCAAAATATTTTTTAAAAACTATATATTATATATATATTTTCAAAAACTATA
AAT
Found at i:5640570 original size:28 final size:30
Alignment explanation
Indices: 5640525--5640588 Score: 94
Period size: 30 Copynumber: 2.1 Consensus size: 30
5640515 ATATAATATA
*
5640525 TATATATATATTCAAAAATGTTTTC-AAAAC
1 TATATATATATT-AAAAATATTTTCAAAAAC
*
5640555 TATATTTATATTAAAAATATTTTCAAAAAC
1 TATATATATATTAAAAATATTTTCAAAAAC
5640585 TATA
1 TATA
5640589 AATTATATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
29 11 0.35
30 20 0.65
ACGTcount: A:0.48, C:0.08, G:0.02, T:0.42
Consensus pattern (30 bp):
TATATATATATTAAAAATATTTTCAAAAAC
Found at i:5640580 original size:41 final size:41
Alignment explanation
Indices: 5640501--5640583 Score: 114
Period size: 41 Copynumber: 2.0 Consensus size: 41
5640491 TATTATATAT
* *
5640501 ATGTTTTCAAAACTATATAATATATATATATATATTCAAAA
1 ATGTTTTCAAAACTATATAATATATAAAAATATATTCAAAA
* *
5640542 ATGTTTTCAAAACTATAT-TTATATTAAAAATATTTTCAAAA
1 ATGTTTTCAAAACTATATAATATA-TAAAAATATATTCAAAA
5640583 A
1 A
5640584 CTATAAATTA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
40 4 0.11
41 33 0.89
ACGTcount: A:0.48, C:0.07, G:0.02, T:0.42
Consensus pattern (41 bp):
ATGTTTTCAAAACTATATAATATATAAAAATATATTCAAAA
Found at i:5640609 original size:37 final size:38
Alignment explanation
Indices: 5640567--5640662 Score: 140
Period size: 37 Copynumber: 2.6 Consensus size: 38
5640557 TATTTATATT
*
5640567 AAAAATATTTTCAAAAACTATAAATTATATATATTTT-
1 AAAAATGTTTTCAAAAACTATAAATTATATATATTTTA
* * *
5640604 TAAAATGTTTTCAAAATCTATATATTATATATATTTTA
1 AAAAATGTTTTCAAAAACTATAAATTATATATATTTTA
*
5640642 AAAAATGTTTTCACAAACTAT
1 AAAAATGTTTTCAAAAACTAT
5640663 TTTCTAAATC
Statistics
Matches: 51, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
37 33 0.65
38 18 0.35
ACGTcount: A:0.47, C:0.07, G:0.02, T:0.44
Consensus pattern (38 bp):
AAAAATGTTTTCAAAAACTATAAATTATATATATTTTA
Found at i:5640709 original size:47 final size:50
Alignment explanation
Indices: 5640611--5640709 Score: 132
Period size: 51 Copynumber: 2.0 Consensus size: 50
5640601 TTTTAAAATG
*
5640611 TTTTCAAAATCTATATATTATATATATTTTAAAAAATGTTTTCACAAACTA
1 TTTTCAAAATCTATATA-TATATATATTTTAAAAAACGTTTTCACAAACTA
* * *
5640662 TTTTCTAAATCTATATA-ATATATGTTTT-CAAAACGTTTTCA-AAACTA
1 TTTTCAAAATCTATATATATATATATTTTAAAAAACGTTTTCACAAACTA
5640709 T
1 T
5640710 ATAAAATATA
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
47 7 0.16
48 11 0.25
49 10 0.23
51 16 0.36
ACGTcount: A:0.40, C:0.11, G:0.03, T:0.45
Consensus pattern (50 bp):
TTTTCAAAATCTATATATATATATATTTTAAAAAACGTTTTCACAAACTA
Found at i:5640726 original size:36 final size:37
Alignment explanation
Indices: 5640668--5640767 Score: 107
Period size: 36 Copynumber: 2.7 Consensus size: 37
5640658 ACTATTTTCT
* *
5640668 AAATCTATATAATATATGTTTTCAAAAC-GTTTTC-AA
1 AAAT-TATATAATATATATTTTCAAAACTGCTTTCTAA
* *
5640704 AACTATATAAAATATATATTTTCGAAAACTGCTTTCTAA
1 AAAT-TATATAATATATATTTTC-AAAACTGCTTTCTAA
*
5640743 AAATTATATATTATA-ATTTTCAAAA
1 AAATTATATAATATATATTTTCAAAA
5640768 AATATTTTCA
Statistics
Matches: 53, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
36 23 0.43
37 11 0.21
38 14 0.26
39 5 0.09
ACGTcount: A:0.45, C:0.10, G:0.04, T:0.41
Consensus pattern (37 bp):
AAATTATATAATATATATTTTCAAAACTGCTTTCTAA
Found at i:5640903 original size:23 final size:23
Alignment explanation
Indices: 5640857--5640907 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
5640847 CTGTCTACAA
*
5640857 ATATTATAATAAAATAGTTAATT
1 ATATTATAATAAAATAGATAATT
*
5640880 ATATTATAATAATATAAGAT-ATT
1 ATATTATAATAAAAT-AGATAATT
5640903 ATATT
1 ATATT
5640908 TTTATTTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 22 0.88
24 3 0.12
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (23 bp):
ATATTATAATAAAATAGATAATT
Found at i:5640999 original size:19 final size:18
Alignment explanation
Indices: 5640975--5641043 Score: 52
Period size: 19 Copynumber: 3.6 Consensus size: 18
5640965 ATATTATTAA
5640975 ATTATTAATAATGAATAAT
1 ATTATTAATAAT-AATAAT
* *
5640994 ATTATTTAT-ATATTTAAT
1 ATTATTAATAATA-ATAAT
5641012 ATTAATATAATAATCTAATAAT
1 ATT-AT-TAATAA--TAATAAT
5641034 ATT-TTAATAA
1 ATTATTAATAA
5641044 AGATATTTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 12
0.71 0.07 0.21
Matches are distributed among these distances:
17 1 0.03
18 9 0.22
19 16 0.40
20 4 0.10
21 1 0.03
22 7 0.17
23 2 0.05
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (18 bp):
ATTATTAATAATAATAAT
Found at i:5641064 original size:23 final size:23
Alignment explanation
Indices: 5641038--5641082 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
5641028 AATAATATTT
5641038 TAATAAAGATATTTAAAATATAC
1 TAATAAAGATATTTAAAATATAC
* * *
5641061 TAATTAATATTTTTAAAATATA
1 TAATAAAGATATTTAAAATATA
5641083 ATATAACACT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
TAATAAAGATATTTAAAATATAC
Found at i:5641192 original size:17 final size:18
Alignment explanation
Indices: 5641170--5641207 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
5641160 TTTTAATAAT
5641170 TATAAATAA-TATTTTAA
1 TATAAATAATTATTTTAA
5641187 TATAAATAATTATTTTAA
1 TATAAATAATTATTTTAA
5641205 TAT
1 TAT
5641208 TTAAAAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 9 0.45
18 11 0.55
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TATAAATAATTATTTTAA
Done.