Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A11
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: 114316535
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4920000 characters in sequence are not A, C, G, or T
File 130 of 356
Found at i:41460633 original size:16 final size:15
Alignment explanation
Indices: 41460614--41460648 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
41460604 TAATTTAGCC
*
41460614 ATTTTTTTATTTTAA
1 ATTTTGTTATTTTAA
41460629 TATTTTGTTATTTTAA
1 -ATTTTGTTATTTTAA
41460645 ATTT
1 ATTT
41460649 AATTTTTACA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 4 0.22
16 14 0.78
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (15 bp):
ATTTTGTTATTTTAA
Found at i:41463110 original size:43 final size:43
Alignment explanation
Indices: 41463044--41463200 Score: 153
Period size: 43 Copynumber: 3.7 Consensus size: 43
41463034 AACTCGTACA
* *
41463044 ATGCCAATGTCCCAAACATGGTCTTACATGTAATCAAATATTG
1 ATGCCACTGTCCCAGACATGGTCTTACATGTAATCAAATATTG
*
41463087 ATGCCACTGTCCCAGACAAGGTCTTACATG-AAGTCAAATA-TG
1 ATGCCACTGTCCCAGACATGGTCTTACATGTAA-TCAAATATTG
* * * *
41463129 ATGCTGA-TGTCCTAGACATGGTCTTACACGTAAATCTCAA-ATTG
1 ATGC-CACTGTCCCAGACATGGTCTTACATGT-AATC-AAATATTG
**
41463173 ATGCCAAC-GTCCCAGATGTGGTCTTACA
1 ATGCC-ACTGTCCCAGACATGGTCTTACA
41463201 CAAAATCACA
Statistics
Matches: 94, Mismatches: 12, Indels: 15
0.78 0.10 0.12
Matches are distributed among these distances:
42 28 0.30
43 38 0.40
44 28 0.30
ACGTcount: A:0.31, C:0.23, G:0.18, T:0.28
Consensus pattern (43 bp):
ATGCCACTGTCCCAGACATGGTCTTACATGTAATCAAATATTG
Found at i:41470321 original size:20 final size:20
Alignment explanation
Indices: 41470293--41470331 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
41470283 CTAAGAACTA
41470293 TGTGATCTGAGCTCATGATT
1 TGTGATCTGAGCTCATGATT
* *
41470313 TGTGGTCTGAGTTCATGAT
1 TGTGATCTGAGCTCATGAT
41470332 ATATATGACA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.13, G:0.28, T:0.41
Consensus pattern (20 bp):
TGTGATCTGAGCTCATGATT
Found at i:41492431 original size:15 final size:15
Alignment explanation
Indices: 41492408--41492469 Score: 72
Period size: 15 Copynumber: 4.1 Consensus size: 15
41492398 CATGAAAACT
*
41492408 AAGATAAAGAAGTCC
1 AAGATAAAGAAATCC
*
41492423 AAGACAAAGAAATCC
1 AAGATAAAGAAATCC
*
41492438 TAGATAAAGAAATCC
1 AAGATAAAGAAATCC
*
41492453 AAGAGACAA-AAATCC
1 AAGATA-AAGAAATCC
41492468 AA
1 AA
41492470 TATACAATAT
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
15 38 0.95
16 2 0.05
ACGTcount: A:0.58, C:0.16, G:0.15, T:0.11
Consensus pattern (15 bp):
AAGATAAAGAAATCC
Found at i:41507115 original size:25 final size:26
Alignment explanation
Indices: 41507087--41507161 Score: 84
Period size: 26 Copynumber: 2.9 Consensus size: 26
41507077 CTAGAGGCCT
41507087 AGCCTCTTTTAAT-AACTGGGGCAAA
1 AGCCTCTTTTAATAAACTGGGGCAAA
*
41507112 AGCCAT-TTTTGATAAACTGGGGCAAA
1 AGCC-TCTTTTAATAAACTGGGGCAAA
**
41507138 AGCC-CTTTTCGGTAAACTGGGGCA
1 AGCCTCTTTT-AATAAACTGGGGCA
41507162 TAGCCCTTTT
Statistics
Matches: 44, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
25 14 0.32
26 30 0.68
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (26 bp):
AGCCTCTTTTAATAAACTGGGGCAAA
Found at i:41507166 original size:25 final size:26
Alignment explanation
Indices: 41507100--41507171 Score: 101
Period size: 26 Copynumber: 2.8 Consensus size: 26
41507090 CTCTTTTAAT
* *
41507100 AACTGGGGCAAAAGCCATTTTTGATA
1 AACTGGGGCAAAAGCCCTTTTCGATA
*
41507126 AACTGGGGCAAAAGCCCTTTTCGGTA
1 AACTGGGGCAAAAGCCCTTTTCGATA
*
41507152 AACTGGGGC-ATAGCCCTTTT
1 AACTGGGGCAAAAGCCCTTTT
41507172 GCACTTCCTC
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
25 10 0.24
26 32 0.76
ACGTcount: A:0.28, C:0.21, G:0.25, T:0.26
Consensus pattern (26 bp):
AACTGGGGCAAAAGCCCTTTTCGATA
Found at i:41509490 original size:3 final size:3
Alignment explanation
Indices: 41509484--41509508 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
41509474 TTACTACTAT
41509484 TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA T
41509509 TTCATAAACA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:41519678 original size:29 final size:29
Alignment explanation
Indices: 41519593--41519700 Score: 128
Period size: 29 Copynumber: 3.8 Consensus size: 29
41519583 TATCAGATAC
* *
41519593 TAGGCCC-AATCTCATTCATATGACCCAT
1 TAGGCCCAAATCACATTCATATGACCTAT
* *
41519621 TAGGCCCAAATCATATTCGTATGACCTAT
1 TAGGCCCAAATCACATTCATATGACCTAT
* **
41519650 TAGGCCCAAATCACATTCATACGGTCTAT
1 TAGGCCCAAATCACATTCATATGACCTAT
* *
41519679 TAGCCCCAAATCACAGTCATAT
1 TAGGCCCAAATCACATTCATAT
41519701 TCATGCTTTC
Statistics
Matches: 67, Mismatches: 12, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
28 7 0.10
29 60 0.90
ACGTcount: A:0.31, C:0.29, G:0.12, T:0.28
Consensus pattern (29 bp):
TAGGCCCAAATCACATTCATATGACCTAT
Found at i:41523600 original size:40 final size:40
Alignment explanation
Indices: 41523505--41523723 Score: 275
Period size: 40 Copynumber: 5.5 Consensus size: 40
41523495 TGGATGATAA
* * *
41523505 CCGGGCTAAGTCCCGAAGGTATTT-TGCGCTAGTGACT-TGTT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCG--AGTTACTAT-AT
* *
41523546 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTATTACAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
41523586 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
41523626 CCGGGCTAAGTCCCGAAGGCATTGGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* * *
41523666 CCGGGCTATGTCCCGAAGGCATTCGAGCGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
* *
41523706 CC-GGTTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
41523724 TACTTGGCTT
Statistics
Matches: 161, Mismatches: 14, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
39 15 0.09
40 119 0.74
41 23 0.14
42 4 0.02
ACGTcount: A:0.22, C:0.23, G:0.29, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:41531676 original size:40 final size:40
Alignment explanation
Indices: 41531574--41531831 Score: 277
Period size: 40 Copynumber: 6.5 Consensus size: 40
41531564 GTATGATAAT
* * * * **
41531574 CGGGATAAGTCCCGAAGGCAGTTTGCGCTAGTGACTAGTTC
1 CGGGCTAAGTCCCGAAGGCA-TTTGTGCGAGTTACTACATC
* * *
41531615 TGGGCAAAGTCCCGAAGGCATTTGTGCGAGTTATTACATC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTACATC
* * *
41531655 CGGGCTAAGTCCCAAAGGCATTTGTACGAGTTATTACATC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTACATC
* * *
41531695 CGAGCTAAGTCACGAAGGCATTTGTGCGAGTTACTATATC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTACATC
* *
41531735 CGGGCTAAGTCCCGAAGGCATTGGTGCGAGTTACTATATC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTACATC
* * * *
41531775 CGGGCTATGTCCCGAAGGCATTCGAGCGAG-TAGCTATATC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTACATC
* *
41531815 C-GGTTAAATCCCGAAGG
1 CGGGCTAAGTCCCGAAGG
41531832 TACTTGGCTT
Statistics
Matches: 188, Mismatches: 28, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
39 15 0.08
40 156 0.83
41 17 0.09
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTACATC
Found at i:41540266 original size:20 final size:20
Alignment explanation
Indices: 41540241--41540278 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
41540231 ATCATGTCTG
41540241 GGACATTGGCATTGTATTAA
1 GGACATTGGCATTGTATTAA
41540261 GGACATTGGCATTGTATT
1 GGACATTGGCATTGTATT
41540279 GAGATTACAT
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:0.26, C:0.11, G:0.26, T:0.37
Consensus pattern (20 bp):
GGACATTGGCATTGTATTAA
Found at i:41541500 original size:12 final size:12
Alignment explanation
Indices: 41541485--41541521 Score: 65
Period size: 12 Copynumber: 3.1 Consensus size: 12
41541475 GGCTAGTACA
41541485 CGGGCGGGTGGC
1 CGGGCGGGTGGC
41541497 CGGGCGGGTGGC
1 CGGGCGGGTGGC
*
41541509 CGGGCGTGTGGC
1 CGGGCGGGTGGC
41541521 C
1 C
41541522 AAGTCAGTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.00, C:0.27, G:0.62, T:0.11
Consensus pattern (12 bp):
CGGGCGGGTGGC
Found at i:41561585 original size:15 final size:14
Alignment explanation
Indices: 41561535--41561583 Score: 62
Period size: 15 Copynumber: 3.4 Consensus size: 14
41561525 AATAAAACAG
41561535 AGAAAGAAATGAAAA
1 AGAAAGAAA-GAAAA
*
41561550 AGAGAGAAAGAAGAA
1 AGAAAGAAAGAA-AA
*
41561565 GGAAAGAAAGAAAA
1 AGAAAGAAAGAAAA
41561579 AGAAA
1 AGAAA
41561584 AGGGAAATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
14 9 0.31
15 20 0.69
ACGTcount: A:0.71, C:0.00, G:0.27, T:0.02
Consensus pattern (14 bp):
AGAAAGAAAGAAAA
Found at i:41567864 original size:21 final size:22
Alignment explanation
Indices: 41567825--41567878 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
41567815 TTTAGAAGTT
* *
41567825 ATAATAATATAATATAATAAAAC
1 ATAAGAATA-AATAAAATAAAAC
41567848 ATAA-AATAAATAAAATAAAAC
1 ATAAGAATAAATAAAATAAAAC
*
41567869 AAAAGAATAA
1 ATAAGAATAA
41567879 GAACAAAGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 15 0.54
22 9 0.32
23 4 0.14
ACGTcount: A:0.72, C:0.04, G:0.02, T:0.22
Consensus pattern (22 bp):
ATAAGAATAAATAAAATAAAAC
Found at i:41571507 original size:20 final size:20
Alignment explanation
Indices: 41571465--41571507 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
41571455 CATGGATGTA
*
41571465 TATGCTAGAAATTAGAAATT
1 TATGCTAGAAAATAGAAATT
*
41571485 TATGGTAGAAAAT-GAAATAT
1 TATGCTAGAAAATAGAAAT-T
41571505 TAT
1 TAT
41571508 TGATAGATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.47, C:0.02, G:0.16, T:0.35
Consensus pattern (20 bp):
TATGCTAGAAAATAGAAATT
Found at i:41571591 original size:20 final size:20
Alignment explanation
Indices: 41571566--41571610 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
41571556 AGGGACTAAA
* *
41571566 ATGAAAAGTTGTAAAATTTG
1 ATGAAAAATTATAAAATTTG
*
41571586 ATGAAAAATTATAAAATTTT
1 ATGAAAAATTATAAAATTTG
41571606 ATGAA
1 ATGAA
41571611 TACATGTGCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.51, C:0.00, G:0.13, T:0.36
Consensus pattern (20 bp):
ATGAAAAATTATAAAATTTG
Found at i:41573313 original size:46 final size:45
Alignment explanation
Indices: 41573263--41573429 Score: 198
Period size: 46 Copynumber: 3.7 Consensus size: 45
41573253 GTTGGCATCC
41573263 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCG
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-GTCCG
* * * *
41573309 AACTCGTTGAGTTGAGTCCGAGTTC-GTGAATGTAACTAG-GCA-TCCG
1 AACTCGTTGAGTTGAGTCCGAGTTCACT-TATG-GA-T-GCGAAGTCCG
*
41573355 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCG
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-GTCCG
*
41573401 AGCTCGTTGAGTTGAGT-CGAGTTCACTTA
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTA
41573430 GGGCGGGTTA
Statistics
Matches: 103, Mismatches: 10, Indels: 17
0.79 0.08 0.13
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 14 0.14
46 79 0.77
47 2 0.02
48 3 0.03
49 1 0.01
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.29
Consensus pattern (45 bp):
AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAGTCCG
Found at i:41573407 original size:92 final size:90
Alignment explanation
Indices: 41573256--41573424 Score: 293
Period size: 92 Copynumber: 1.9 Consensus size: 90
41573246 CTAGGATGTT
* *
41573256 GGCATCCAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GGCATCCAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
41573321 TGAGTCCGAGTTCGTGAATGTAACTA
66 TGAGT-CGAGTTCGTGAATGTAACTA
*
41573347 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAG
1 GGCATCC-AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
41573412 TTGAGTCGAGTTC
65 TTGAGTCGAGTTC
41573425 ACTTAGGGCG
Statistics
Matches: 74, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
91 14 0.19
92 60 0.81
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.28
Consensus pattern (90 bp):
GGCATCCAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCGAGTTCGTGAATGTAACTA
Found at i:41580788 original size:46 final size:46
Alignment explanation
Indices: 41580738--41580910 Score: 183
Period size: 46 Copynumber: 3.7 Consensus size: 46
41580728 TGTTTGGGCA
*
41580738 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTAAATG
* * *
41580784 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTAA--ATG
* * * * *
41580829 CATCCAAACTCGTTGAGTTGAGCCCGAGTTCATTTATGGGTGTGAAT-
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTAAATG
*
41580876 TCCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 T-CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
41580911 GGGGCGGGTT
Statistics
Matches: 104, Mismatches: 15, Indels: 16
0.77 0.11 0.12
Matches are distributed among these distances:
43 6 0.06
45 5 0.05
46 58 0.56
47 27 0.26
48 3 0.03
50 5 0.05
ACGTcount: A:0.22, C:0.20, G:0.27, T:0.31
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTAAATG
Found at i:41580893 original size:93 final size:93
Alignment explanation
Indices: 41580734--41580905 Score: 265
Period size: 93 Copynumber: 1.8 Consensus size: 93
41580724 AGGATGTTTG
* *
41580734 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAG
1 GGCATCCAAACTCGTTGAGTTGAGCCCGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAG
41580799 TTGAGTCCGAGTTCGTGAGATGTAACTA
66 TTGAGTCCGAGTTCGTGAGATGTAACTA
* * ** *
41580827 GGCATCCAAACTCGTTGAGTTGAGCCCGAGTTCATTTATGGGTGTGAAT-TCCCGAGCTCGTTGA
1 GGCATCCAAACTCGTTGAGTTGAGCCCGAGTTCACTTATGGATGCAAATGT-CCGAACTCGTTGA
41580891 GTTGAGTCCGAGTTC
65 GTTGAGTCCGAGTTC
41580906 ACTTAGGGGC
Statistics
Matches: 71, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
92 1 0.01
93 70 0.99
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.30
Consensus pattern (93 bp):
GGCATCCAAACTCGTTGAGTTGAGCCCGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAG
TTGAGTCCGAGTTCGTGAGATGTAACTA
Found at i:41583222 original size:40 final size:41
Alignment explanation
Indices: 41583087--41583272 Score: 243
Period size: 41 Copynumber: 4.6 Consensus size: 41
41583077 TACTCGAATG
*
41583087 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGCGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGCGACT
*
41583128 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGCGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGCGACT
* * *
41583169 ACATCCGGACTAAGAT-CCAAAGGCATTTGTGCT-AGCGACT
1 ATATCCGGGCTAAG-TCCCGAAGGCATTTGTGCTAAGCGACT
* * * *
41583209 ATATCCAGGCTAAGTCCCGAAGGCATTTATGCT-AGTGACC
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGCGACT
* *
41583249 ATATCCGGGTTAAGACCCGAAGGC
1 ATATCCGGGCTAAGTCCCGAAGGC
41583273 CTTGTGCGAG
Statistics
Matches: 129, Mismatches: 14, Indels: 5
0.87 0.09 0.03
Matches are distributed among these distances:
39 1 0.01
40 59 0.46
41 68 0.53
42 1 0.01
ACGTcount: A:0.26, C:0.25, G:0.25, T:0.24
Consensus pattern (41 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGCGACT
Found at i:41583227 original size:81 final size:82
Alignment explanation
Indices: 41583089--41583242 Score: 231
Period size: 81 Copynumber: 1.9 Consensus size: 82
41583079 CTCGAATGAT
* * * * *
41583089 ATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGCGACTATATCCGGGCTAAGTCCCGAAGGCTT
1 ATCCGGACTAAGTCCCAAAGGCATTTGTGCTAAGCGACTATATCCAGGCTAAGTCCCGAAGGCAT
*
41583154 TTGTGCTAAGCGACTAC
66 TTATGCTAAGCGACTAC
41583171 ATCCGGACTAAGAT-CCAAAGGCATTTGTGCT-AGCGACTATATCCAGGCTAAGTCCCGAAGGCA
1 ATCCGGACTAAG-TCCCAAAGGCATTTGTGCTAAGCGACTATATCCAGGCTAAGTCCCGAAGGCA
41583234 TTTATGCTA
65 TTTATGCTA
41583243 GTGACCATAT
Statistics
Matches: 65, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 38 0.58
82 26 0.40
83 1 0.02
ACGTcount: A:0.25, C:0.25, G:0.25, T:0.25
Consensus pattern (82 bp):
ATCCGGACTAAGTCCCAAAGGCATTTGTGCTAAGCGACTATATCCAGGCTAAGTCCCGAAGGCAT
TTATGCTAAGCGACTAC
Found at i:41587012 original size:23 final size:23
Alignment explanation
Indices: 41586983--41587063 Score: 126
Period size: 23 Copynumber: 3.5 Consensus size: 23
41586973 ACGTTTACCG
41586983 CTATTAGCAGCTTTGCTGCATTA
1 CTATTAGCAGCTTTGCTGCATTA
* *
41587006 CTGTTAGCATCTTTGCTGCATTA
1 CTATTAGCAGCTTTGCTGCATTA
* *
41587029 CTTTTAGCAGCTTTGATGCATTA
1 CTATTAGCAGCTTTGCTGCATTA
41587052 CTATTAGCAGCT
1 CTATTAGCAGCT
41587064 ACGCTGCGAT
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 52 1.00
ACGTcount: A:0.21, C:0.21, G:0.17, T:0.41
Consensus pattern (23 bp):
CTATTAGCAGCTTTGCTGCATTA
Found at i:41587236 original size:28 final size:29
Alignment explanation
Indices: 41587191--41587268 Score: 77
Period size: 33 Copynumber: 2.6 Consensus size: 29
41587181 ATACTATTTT
* *
41587191 GGGCATAGGCCCACACTG-TTACTACATA
1 GGGCTTAGGCCCAGACTGATTACTACATA
* *
41587219 GGGCTTAGGCCTAGACTGAACTATTACTGCATA
1 GGGCTTAGGCCCAGACTG----ATTACTACATA
41587252 GGGCTTAGGCCCAGACT
1 GGGCTTAGGCCCAGACT
41587269 ATACTGTTAT
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
28 15 0.38
33 25 0.62
ACGTcount: A:0.26, C:0.26, G:0.26, T:0.23
Consensus pattern (29 bp):
GGGCTTAGGCCCAGACTGATTACTACATA
Found at i:41587252 original size:33 final size:33
Alignment explanation
Indices: 41587209--41587303 Score: 111
Period size: 33 Copynumber: 2.9 Consensus size: 33
41587199 GCCCACACTG
* *
41587209 TTACTACATAGGGCTTAGGCCTAGACTGA-ACTA
1 TTACTGCATAGGGCTTAGGCCCAGACT-ATACTA
*
41587242 TTACTGCATAGGGCTTAGGCCCAGACTATACTG
1 TTACTGCATAGGGCTTAGGCCCAGACTATACTA
* * * *
41587275 TTATTGAATAGGGCTTAGGCGCAAACTAT
1 TTACTGCATAGGGCTTAGGCCCAGACTAT
41587304 TACTGTATGC
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
32 1 0.02
33 53 0.98
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.28
Consensus pattern (33 bp):
TTACTGCATAGGGCTTAGGCCCAGACTATACTA
Found at i:41589248 original size:25 final size:25
Alignment explanation
Indices: 41589220--41589281 Score: 70
Period size: 25 Copynumber: 2.5 Consensus size: 25
41589210 ACGTCTGTTG
* * * *
41589220 CATCATCGTTGATAGTCTTCTGCTA
1 CATCACCGTTGATAGTCCTCTACAA
**
41589245 CATCACCGTCAATAGTCCTCTACAA
1 CATCACCGTTGATAGTCCTCTACAA
41589270 CATCACCGTTGA
1 CATCACCGTTGA
41589282 AAATCCTTCG
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.26, C:0.31, G:0.13, T:0.31
Consensus pattern (25 bp):
CATCACCGTTGATAGTCCTCTACAA
Found at i:41598286 original size:49 final size:49
Alignment explanation
Indices: 41598109--41598303 Score: 205
Period size: 49 Copynumber: 3.9 Consensus size: 49
41598099 ACTATTGTGA
* *
41598109 GGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTAGC-GAATAATT
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAG-ATAATT
* * * * * *
41598158 GGTCGCATGTGTAATACTAAGTGCAGGCTATTATGCGTACCCA-AAAACTGT
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTA-CCAGATAA-T-T
* * * *
41598209 GATCACGTGTGTAGTACTAAGTGCAGGCTACTACATGTACCAGATTATT
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
* * *
41598258 GGTCACATGTGTAGTACTAAGTGTAGGCTACTATGCGTACCAGATA
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATA
41598304 GCTTCGGCTA
Statistics
Matches: 116, Mismatches: 25, Indels: 10
0.77 0.17 0.07
Matches are distributed among these distances:
49 76 0.66
50 6 0.05
51 34 0.29
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.29
Consensus pattern (49 bp):
GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
Found at i:41598286 original size:100 final size:100
Alignment explanation
Indices: 41598111--41598298 Score: 297
Period size: 100 Copynumber: 1.9 Consensus size: 100
41598101 TATTGTGAGG
* * *
41598111 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTAGCGAATAATTGGTCGCATGTGTAATACT
1 TCACGTGTGTAGTACTAAGTGCAGGCTACTACATGTACCGAATAATTGGTCACATGTGTAATACT
*
41598176 AAGTGCAGGCTATTATGCGTACCCAAAAACTGTGA
66 AAGTGCAGGCTACTATGCGTACCCAAAAACTGTGA
* *
41598211 TCACGTGTGTAGTACTAAGTGCAGGCTACTACATGTACC-AGATTATTGGTCACATGTGTAGTAC
1 TCACGTGTGTAGTACTAAGTGCAGGCTACTACATGTACCGA-ATAATTGGTCACATGTGTAATAC
*
41598275 TAAGTGTAGGCTACTATGCGTACC
65 TAAGTGCAGGCTACTATGCGTACC
41598299 AGATAGCTTC
Statistics
Matches: 80, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
99 1 0.01
100 79 0.99
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.29
Consensus pattern (100 bp):
TCACGTGTGTAGTACTAAGTGCAGGCTACTACATGTACCGAATAATTGGTCACATGTGTAATACT
AAGTGCAGGCTACTATGCGTACCCAAAAACTGTGA
Found at i:41601130 original size:59 final size:59
Alignment explanation
Indices: 41600949--41601279 Score: 513
Period size: 59 Copynumber: 5.6 Consensus size: 59
41600939 GAGGTGTTAC
* *
41600949 AATAATTTTATGAATAATTGATTAATTTTCAATTAATTAAATAAATAATCATATTTCAT
1 AATAATTCTATGAATAATTAATTAATTTTCAATTAATTAAATAAATAATCATATTTCAT
* *
41601008 AATAATTCTATGAATAATTAATTAATTTT-TATTAAATAAATAAATAATCATATTTCAT
1 AATAATTCTATGAATAATTAATTAATTTTCAATTAATTAAATAAATAATCATATTTCAT
* * * * *
41601066 AATAATTTTACGAATAATTAATTAATTTTCAATTAATTAATTAATTAATCATATTGCAT
1 AATAATTCTATGAATAATTAATTAATTTTCAATTAATTAAATAAATAATCATATTTCAT
* ** *
41601125 AATAATTCTATGAATAATTGATTAATTTTTTATTAAATAAATAAATAATCATATTTCAT
1 AATAATTCTATGAATAATTAATTAATTTTCAATTAATTAAATAAATAATCATATTTCAT
*
41601184 AATAATTTTATGAATAATTAATTAATTTTCAATTTAA-TAAATAAATAATCATATTTCAT
1 AATAATTCTATGAATAATTAATTAATTTTCAA-TTAATTAAATAAATAATCATATTTCAT
41601243 AATAATTCTATGAATAATTAATTAATTTTCAATTAAT
1 AATAATTCTATGAATAATTAATTAATTTTCAATTAAT
41601280 CATTCATTTA
Statistics
Matches: 244, Mismatches: 25, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
58 58 0.24
59 182 0.75
60 4 0.02
ACGTcount: A:0.46, C:0.05, G:0.03, T:0.46
Consensus pattern (59 bp):
AATAATTCTATGAATAATTAATTAATTTTCAATTAATTAAATAAATAATCATATTTCAT
Found at i:41601213 original size:118 final size:118
Alignment explanation
Indices: 41600949--41601271 Score: 569
Period size: 118 Copynumber: 2.7 Consensus size: 118
41600939 GAGGTGTTAC
*
41600949 AATAATTTTATGAATAATTGATTAATTTTCAATTAATTAAATAAATAATCATATTTCATAATAAT
1 AATAATTTTATGAATAATTAATTAATTTTCAATTAATTAAATAAATAATCATATTTCATAATAAT
41601014 TCTATGAATAATTAATTAA-TTTTTATTAAATAAATAAATAATCATATTTCAT
66 TCTATGAATAATTAATTAATTTTTTATTAAATAAATAAATAATCATATTTCAT
* * * *
41601066 AATAATTTTACGAATAATTAATTAATTTTCAATTAATTAATTAATTAATCATATTGCATAATAAT
1 AATAATTTTATGAATAATTAATTAATTTTCAATTAATTAAATAAATAATCATATTTCATAATAAT
*
41601131 TCTATGAATAATTGATTAATTTTTTATTAAATAAATAAATAATCATATTTCAT
66 TCTATGAATAATTAATTAATTTTTTATTAAATAAATAAATAATCATATTTCAT
41601184 AATAATTTTATGAATAATTAATTAATTTTCAATTTAA-TAAATAAATAATCATATTTCATAATAA
1 AATAATTTTATGAATAATTAATTAATTTTCAA-TTAATTAAATAAATAATCATATTTCATAATAA
41601248 TTCTATGAATAATTAATTAATTTT
65 TTCTATGAATAATTAATTAATTTT
41601272 CAATTAATCA
Statistics
Matches: 193, Mismatches: 11, Indels: 3
0.93 0.05 0.01
Matches are distributed among these distances:
117 78 0.40
118 111 0.58
119 4 0.02
ACGTcount: A:0.46, C:0.05, G:0.03, T:0.46
Consensus pattern (118 bp):
AATAATTTTATGAATAATTAATTAATTTTCAATTAATTAAATAAATAATCATATTTCATAATAAT
TCTATGAATAATTAATTAATTTTTTATTAAATAAATAAATAATCATATTTCAT
Found at i:41604940 original size:43 final size:43
Alignment explanation
Indices: 41604871--41605027 Score: 147
Period size: 43 Copynumber: 3.7 Consensus size: 43
41604861 TTCTCTCATG
* * * *
41604871 AACGCCGCTAAAGATCATGGTATTTAGCGGCGCTTCTACTAAA
1 AACGCCACTAAAGAACATGATCTTTAGCGGCGCTTCTACTAAA
* * *
41604914 AACGCCACTAAAGAACATAATCTTTAGCAGCACTTCT-CATAAA
1 AACGCCACTAAAGAACATGATCTTTAGCGGCGCTTCTAC-TAAA
** * * * * *
41604957 AACGCTGCTAAAGAACATGATATTTAGTGGCGTTTGTA-AAAA
1 AACGCCACTAAAGAACATGATCTTTAGCGGCGCTTCTACTAAA
*
41604999 AAGCGCCACTATAGAACATGATCTTTAGC
1 AA-CGCCACTAAAGAACATGATCTTTAGC
41605028 AGCATTTGTA
Statistics
Matches: 89, Mismatches: 22, Indels: 6
0.76 0.19 0.05
Matches are distributed among these distances:
42 6 0.07
43 83 0.93
ACGTcount: A:0.36, C:0.21, G:0.17, T:0.25
Consensus pattern (43 bp):
AACGCCACTAAAGAACATGATCTTTAGCGGCGCTTCTACTAAA
Found at i:41605036 original size:43 final size:42
Alignment explanation
Indices: 41604911--41605069 Score: 147
Period size: 43 Copynumber: 3.7 Consensus size: 42
41604901 CGCTTCTACT
* * * *
41604911 AAAAACGCCACTAAAGAACATAATCTTTAGCAGCACTTCTCAT
1 AAAAACGCCACTAAAGAACATGATCTTTAGCAGCATTTGT-AA
** * ** *
41604954 AAAAACGCTGCTAAAGAACATGATATTTAGTGGCGTTTGTAA
1 AAAAACGCCACTAAAGAACATGATCTTTAGCAGCATTTGTAA
*
41604996 AAAAAGCGCCACTATAGAACATGATCTTTAGCAGCATTTGTAGA
1 AAAAA-CGCCACTAAAGAACATGATCTTTAGCAGCATTTGTA-A
* * * * *
41605040 AAAAGCGCCGCCAAAGATCATGTTCTTTAG
1 AAAAACGCCACTAAAGAACATGATCTTTAG
41605070 TGGCATTTTT
Statistics
Matches: 91, Mismatches: 23, Indels: 4
0.77 0.19 0.03
Matches are distributed among these distances:
42 6 0.07
43 80 0.88
44 5 0.05
ACGTcount: A:0.38, C:0.19, G:0.17, T:0.25
Consensus pattern (42 bp):
AAAAACGCCACTAAAGAACATGATCTTTAGCAGCATTTGTAA
Found at i:41605056 original size:86 final size:86
Alignment explanation
Indices: 41604871--41605073 Score: 239
Period size: 86 Copynumber: 2.4 Consensus size: 86
41604861 TTCTCTCATG
* * *
41604871 AACGCCGCTAAAGATCATGGTATTTAGCGGCGCTTCTACTAAAAACGCCACTAAAGAACATAATC
1 AACGCCGCTAAAGATCATGATATTTAGTGGCGCTTCTACAAAAAACGCCACTAAAGAACATAATC
*
41604936 TTTAGCAGCACTTCTCATAAA
66 TTTAGCAGCACTTCTCAGAAA
* * * * * *
41604957 AACGCTGCTAAAGAACATGATATTTAGTGGCGTTTGTA-AAAAAAGCGCCACTATAGAACATGAT
1 AACGCCGCTAAAGATCATGATATTTAGTGGCGCTTCTACAAAAAA-CGCCACTAAAGAACATAAT
* *
41605021 CTTTAGCAGCATTTGT-AGAAA
65 CTTTAGCAGCACTTCTCAGAAA
* * *
41605042 AAGCGCCGCCAAAGATCATGTTCTTTAGTGGC
1 AA-CGCCGCTAAAGATCATGATATTTAGTGGC
41605074 ATTTTTGCGA
Statistics
Matches: 98, Mismatches: 17, Indels: 4
0.82 0.14 0.03
Matches are distributed among these distances:
85 11 0.11
86 87 0.89
ACGTcount: A:0.35, C:0.21, G:0.19, T:0.26
Consensus pattern (86 bp):
AACGCCGCTAAAGATCATGATATTTAGTGGCGCTTCTACAAAAAACGCCACTAAAGAACATAATC
TTTAGCAGCACTTCTCAGAAA
Found at i:41605076 original size:43 final size:43
Alignment explanation
Indices: 41604954--41605108 Score: 134
Period size: 43 Copynumber: 3.6 Consensus size: 43
41604944 CACTTCTCAT
* * * * * *
41604954 AAAAA-CGCTGCTAAAGAACATGATATTTAGTGGCGTTTGTAA
1 AAAAAGCGCCGCTAAAGATCATGTTCTTTAGTGGCATTTGTAG
* * * * **
41604996 AAAAAGCGCCACTATAGAACATGATCTTTAGCAGCATTTGTAG
1 AAAAAGCGCCGCTAAAGATCATGTTCTTTAGTGGCATTTGTAG
* *
41605039 AAAAAGCGCCGCCAAAGATCATGTTCTTTAGTGGCATTT-TTG
1 AAAAAGCGCCGCTAAAGATCATGTTCTTTAGTGGCATTTGTAG
* * *
41605081 CGAGAAGCACCGCTAAAGATCATGTTCT
1 -AAAAAGCGCCGCTAAAGATCATGTTCT
41605109 ATAGCGACAT
Statistics
Matches: 91, Mismatches: 20, Indels: 3
0.80 0.18 0.03
Matches are distributed among these distances:
42 7 0.08
43 84 0.92
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.27
Consensus pattern (43 bp):
AAAAAGCGCCGCTAAAGATCATGTTCTTTAGTGGCATTTGTAG
Found at i:41606148 original size:30 final size:30
Alignment explanation
Indices: 41606108--41606166 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
41606098 CCAAAATGAG
*
41606108 AAATTTCAAAAAATAATAATGA-ATTAGTAT
1 AAATTGCAAAAAATAA-AATGATATTAGTAT
* *
41606138 AAATTGCAAAATATAAAATTATATTAGTA
1 AAATTGCAAAAAATAAAATGATATTAGTA
41606167 ACTAATAACA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 4 0.16
30 21 0.84
ACGTcount: A:0.56, C:0.03, G:0.07, T:0.34
Consensus pattern (30 bp):
AAATTGCAAAAAATAAAATGATATTAGTAT
Found at i:41608582 original size:16 final size:16
Alignment explanation
Indices: 41608561--41608592 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
41608551 AATAAACAAG
*
41608561 TAAAGACTTTTAAATT
1 TAAAGACTATTAAATT
41608577 TAAAGACTATTAAATT
1 TAAAGACTATTAAATT
41608593 CTAAGGTAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.41
Consensus pattern (16 bp):
TAAAGACTATTAAATT
Found at i:41614745 original size:48 final size:48
Alignment explanation
Indices: 41614511--41614754 Score: 232
Period size: 48 Copynumber: 5.1 Consensus size: 48
41614501 ATATGGCATC
* * * *
41614511 GGCATCGGCATCGATATGTGATCCCATGTAAGACCATGTTTGAGACAT
1 GGCATTGGCATCTATATGTGATCCCATGTAAGACCATGTCTGGGACAT
*
41614559 GGCATTGGCATCGT-TATGTGATCCCATGTAAGACCATGTTTGGGACAT
1 GGCATTGGCATC-TATATGTGATCCCATGTAAGACCATGTCTGGGACAT
* * * * *
41614607 GGCATTGGCATCGATATGAGAACATCGTGTAAGACCATAG-CTGGG-CTAT
1 GGCATTGGCATCTATATGTGATC-CCATGTAAGACCAT-GTCTGGGAC-AT
* * * *
41614656 CGGC-TTCG-A--TATGTGTGATCCCATGAAAGACAATGTCTGGGACAT
1 -GGCATTGGCATCTATATGTGATCCCATGTAAGACCATGTCTGGGACAT
* * * *
41614701 GGCATTGGCATCTATAAGTGGTCCCATGTAAGACCATATCTGGGATAT
1 GGCATTGGCATCTATATGTGATCCCATGTAAGACCATGTCTGGGACAT
41614749 GGCATT
1 GGCATT
41614755 TGCACCCTAC
Statistics
Matches: 158, Mismatches: 26, Indels: 24
0.76 0.12 0.12
Matches are distributed among these distances:
44 4 0.03
45 20 0.13
46 9 0.06
48 100 0.63
49 21 0.13
50 4 0.03
ACGTcount: A:0.26, C:0.19, G:0.27, T:0.28
Consensus pattern (48 bp):
GGCATTGGCATCTATATGTGATCCCATGTAAGACCATGTCTGGGACAT
Found at i:41617344 original size:17 final size:17
Alignment explanation
Indices: 41617305--41617358 Score: 56
Period size: 17 Copynumber: 3.1 Consensus size: 17
41617295 TGGATTACTG
*
41617305 AAATCAAATGATATAGAGC
1 AAATAAAATGATAT-G-GC
*
41617324 -AATAAATTGATATGGC
1 AAATAAAATGATATGGC
*
41617340 AAATAAAATGATGTGGC
1 AAATAAAATGATATGGC
41617357 AA
1 AA
41617359 TTCACAGAGA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
16 2 0.07
17 17 0.57
18 11 0.37
ACGTcount: A:0.50, C:0.07, G:0.19, T:0.24
Consensus pattern (17 bp):
AAATAAAATGATATGGC
Found at i:41618198 original size:16 final size:16
Alignment explanation
Indices: 41618162--41618201 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
41618152 CTCACGCTAA
**
41618162 TTCTGTTTTCTCTTTTT
1 TTCT-TTTTCTCTTTGC
41618179 TTCTTTTTCTCTTTGC
1 TTCTTTTTCTCTTTGC
41618195 TTCTTTT
1 TTCTTTT
41618202 ATTGGGTAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 17 0.81
17 4 0.19
ACGTcount: A:0.00, C:0.20, G:0.05, T:0.75
Consensus pattern (16 bp):
TTCTTTTTCTCTTTGC
Found at i:41620860 original size:14 final size:14
Alignment explanation
Indices: 41620841--41620870 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
41620831 CACTATGTGT
41620841 GTGAGTATTCCCGA
1 GTGAGTATTCCCGA
*
41620855 GTGAGTATTCTCGA
1 GTGAGTATTCCCGA
41620869 GT
1 GT
41620871 ATCTGATGTA
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:0.20, C:0.17, G:0.30, T:0.33
Consensus pattern (14 bp):
GTGAGTATTCCCGA
Found at i:41629333 original size:37 final size:37
Alignment explanation
Indices: 41629283--41629361 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
41629273 TTATTACGAA
* *
41629283 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCTCCACACGAAGTCATCGG
* *
41629320 GTCTTACCCGGACAAAATTTCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCTCCACACGAAGTCATCGG
41629357 GTCTT
1 GTCTT
41629362 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.27
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCTCCACACGAAGTCATCGG
Found at i:41629549 original size:47 final size:47
Alignment explanation
Indices: 41629480--41630077 Score: 1038
Period size: 47 Copynumber: 12.7 Consensus size: 47
41629470 CCCTTCGGGA
41629480 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
41629527 CTTATCACATATATACACTTTCACATTTATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
41629574 CTTATCACACATATACACTTTCACATTCATCACATCGACTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
41629621 CTTATCACACATATACACTTTCACATTCATCACATC-GCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
41629667 CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
41629714 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
41629761 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
41629808 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
41629855 CTTATTACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
41629902 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
41629949 CTTATCACACATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
41629996 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
41630043 CTTATCTCATATATGCA-TGTTCACATCCATCACAT
1 CTTATCACATATATACACT-TTCACATTCATCACAT
41630078 AGAATCCTAA
Statistics
Matches: 528, Mismatches: 21, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
46 45 0.09
47 483 0.91
ACGTcount: A:0.30, C:0.29, G:0.08, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:41633447 original size:40 final size:40
Alignment explanation
Indices: 41633390--41633572 Score: 194
Period size: 40 Copynumber: 4.6 Consensus size: 40
41633380 CCAGCATGAT
* * *
41633390 TGCTCTTCAGGATTTAGCACGGATATATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
* *
41633430 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCATGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
* * * *
41633470 TGCTCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACCAA
1 TGCTCTTCGGGACTTAGCCCGGATATA-TCACTAGCACGAA
* *
41633511 TGC-CTTC-GGATCTTAGTCCGGATATGGTCACTTAGCAC-AA
1 TGCTCTTCGGGA-CTTAGCCCGGATAT-ATCAC-TAGCACGAA
*
41633551 AGC-CTTCGGGACTTAGCCCGGA
1 TGCTCTTCGGGACTTAGCCCGGA
41633573 CATCATTCGA
Statistics
Matches: 120, Mismatches: 18, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
39 3 0.03
40 97 0.81
41 20 0.17
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (40 bp):
TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
Found at i:41633918 original size:29 final size:29
Alignment explanation
Indices: 41633879--41633957 Score: 106
Period size: 29 Copynumber: 2.7 Consensus size: 29
41633869 CTTAATAATC
*
41633879 AACCACGCACACTTAGTGCCATGTACTTT-A
1 AACC-CGCACACTTAGTGCCATGCA-TTTCA
*
41633909 AACTCGCACACTTAGTGCCATGCATTTCA
1 AACCCGCACACTTAGTGCCATGCATTTCA
*
41633938 AGCCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
41633958 ATCTCACAAC
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
28 3 0.07
29 38 0.86
30 3 0.07
ACGTcount: A:0.28, C:0.33, G:0.15, T:0.24
Consensus pattern (29 bp):
AACCCGCACACTTAGTGCCATGCATTTCA
Found at i:41634000 original size:43 final size:43
Alignment explanation
Indices: 41633939--41634084 Score: 283
Period size: 43 Copynumber: 3.4 Consensus size: 43
41633929 TGCATTTCAA
41633939 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
1 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
41633982 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
1 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
*
41634025 GTCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
1 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
41634068 GCCCGCACACTTAGTGC
1 GCCCGCACACTTAGTGC
41634085 TGAAAACCAA
Statistics
Matches: 101, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 101 1.00
ACGTcount: A:0.27, C:0.35, G:0.15, T:0.23
Consensus pattern (43 bp):
GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
Found at i:41635681 original size:47 final size:47
Alignment explanation
Indices: 41635603--41636404 Score: 1047
Period size: 47 Copynumber: 16.7 Consensus size: 47
41635593 CCCTTCCGGA
* ** * * * * *
41635603 CTTATCACATTTAGGCACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
41635650 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
41635697 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
41635744 CTTATTACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
41635791 CTTATCACATATATACACTTTCACATTCAACACATCGGCTATAAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * **
41635838 CTTATCACACATATACACTTTCACATTCATCACATCGGCTATTAGAA
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* ** ** **
41635885 C--ATCGGCCAT-TAGGC-CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGG
1 CTTATC--ACATATATACACTT-TCAC--AT-T-CA---TCACA-TCGGC-CAT---TA----GG
41635946 C
47 C
* *
41635947 CTTATCACACATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
41635994 CTTATCACATATATACACTTTCACATTCATCACATCGGTCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
41636041 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
41636088 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
41636135 CTTATTACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
** *
41636182 CTTATCACACGTATACACTTTCACATTCATCACATCGGCGATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
41636229 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
41636276 CTTATCACACATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
41636323 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
41636370 CTTATCTCATATATGCA-TGTTCACATCCATCACAT
1 CTTATCACATATATACACT-TTCACATTCATCACAT
41636405 AGAATCCTAA
Statistics
Matches: 669, Mismatches: 62, Indels: 48
0.86 0.08 0.06
Matches are distributed among these distances:
45 6 0.01
46 8 0.01
47 608 0.91
48 2 0.00
49 1 0.00
50 2 0.00
53 5 0.01
54 5 0.01
55 5 0.01
56 5 0.01
59 2 0.00
60 1 0.00
61 2 0.00
62 4 0.01
63 7 0.01
64 6 0.01
ACGTcount: A:0.29, C:0.29, G:0.09, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:41635857 original size:141 final size:141
Alignment explanation
Indices: 41635603--41636404 Score: 1201
Period size: 141 Copynumber: 5.6 Consensus size: 141
41635593 CCCTTCCGGA
* ** * * * * * * *
41635603 CTTATCACATTTAGGCACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
41635668 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
66 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
41635733 GGCCATTAGGC
131 GGCCATTAGGC
*
41635744 CTTATTACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
* * * *
41635809 TTTCACATTCAACACATCGGCTATAAGGCCTTATCACACATATACACTTTCACATTCATCACATC
66 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACA-T--T--CAT-
41635874 GGCTATTAGAACATCGGCCATTAGGC
125 --C-------ACATCGGCCATTAGGC
*
41635900 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACACATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
*
41635965 TTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
66 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
*
41636030 GGTCATTAGGC
131 GGCCATTAGGC
41636041 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
*
41636106 TTTCACATTCATCACATCGGCCATTAGGCCTTATTACATATATACACTTTCACATTCATCACATC
66 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
*
41636171 GGCTATTAGGC
131 GGCCATTAGGC
** *
41636182 CTTATCACACGTATACACTTTCACATTCATCACATCGGCGATTAGGCCTTATCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
*
41636247 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACACATATACACTTTCACATTCATCACATC
66 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
*
41636312 GGCTATTAGGC
131 GGCCATTAGGC
* *
41636323 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCTCATATATGCA-
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
*
41636387 TGTTCACATCCATCACAT
66 T-TTCACATTCATCACAT
41636405 AGAATCCTAA
Statistics
Matches: 608, Mismatches: 37, Indels: 32
0.90 0.05 0.05
Matches are distributed among these distances:
140 1 0.00
141 465 0.76
142 1 0.00
144 1 0.00
146 3 0.00
148 1 0.00
149 1 0.00
151 3 0.00
153 1 0.00
155 1 0.00
156 130 0.21
ACGTcount: A:0.29, C:0.29, G:0.09, T:0.32
Consensus pattern (141 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
GGCCATTAGGC
Found at i:41635901 original size:62 final size:62
Alignment explanation
Indices: 41635822--41635944 Score: 210
Period size: 62 Copynumber: 2.0 Consensus size: 62
41635812 CACATTCAAC
* *
41635822 ACATCGGCTATAAGGCCTTATCACACATATACACTTTCACATTCATCACATCGGCTATTAGA
1 ACATCGGCCATAAGGCCTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGA
* *
41635884 ACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAG
1 ACATCGGCCATAAGGCCTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAG
41635945 GCCTTATCAC
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
62 57 1.00
ACGTcount: A:0.31, C:0.28, G:0.11, T:0.29
Consensus pattern (62 bp):
ACATCGGCCATAAGGCCTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGA
Found at i:41635907 original size:109 final size:109
Alignment explanation
Indices: 41635775--41635991 Score: 407
Period size: 109 Copynumber: 2.0 Consensus size: 109
41635765 CACATTCATC
*
41635775 ACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCAACACATCGGCTATAAGGCCT
1 ACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCAACACATCGGCCATAAGGCCT
41635840 TATCACACATATACACTTTCACATTCATCACATCGGCTATTAGA
66 TATCACACATATACACTTTCACATTCATCACATCGGCTATTAGA
* *
41635884 ACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCT
1 ACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCAACACATCGGCCATAAGGCCT
41635949 TATCACACATATACACTTTCACATTCATCACATCGGCTATTAG
66 TATCACACATATACACTTTCACATTCATCACATCGGCTATTAG
41635992 GCCTTATCAC
Statistics
Matches: 105, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
109 105 1.00
ACGTcount: A:0.31, C:0.29, G:0.10, T:0.30
Consensus pattern (109 bp):
ACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCAACACATCGGCCATAAGGCCT
TATCACACATATACACTTTCACATTCATCACATCGGCTATTAGA
Found at i:41638808 original size:19 final size:19
Alignment explanation
Indices: 41638784--41638826 Score: 86
Period size: 19 Copynumber: 2.3 Consensus size: 19
41638774 TAGTTTGCAT
41638784 TCAAACATATGTCTAAATA
1 TCAAACATATGTCTAAATA
41638803 TCAAACATATGTCTAAATA
1 TCAAACATATGTCTAAATA
41638822 TCAAA
1 TCAAA
41638827 TGGAACAGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.49, C:0.16, G:0.05, T:0.30
Consensus pattern (19 bp):
TCAAACATATGTCTAAATA
Found at i:41642005 original size:57 final size:58
Alignment explanation
Indices: 41641917--41642054 Score: 165
Period size: 57 Copynumber: 2.4 Consensus size: 58
41641907 CATATAACAG
* ** * * *
41641917 GATTACCAGTCCAGGCTAAATCCTTTTTGTAATATATGCTC-AGAAGAGCTTA-ATTAA
1 GATTACCAGTCCAGCCTAAATCCTAATTGTAACATATGCTCGAG-AGAGATTATATCAA
* *
41641974 GATTACCAGTCCAGCCTAATTCCTAATTGTAACATATGCTCGAGAGGGATTATATCAA
1 GATTACCAGTCCAGCCTAAATCCTAATTGTAACATATGCTCGAGAGAGATTATATCAA
41642032 GATTACCAGTCCAAG-CTAAATCC
1 GATTACCAGTCC-AGCCTAAATCC
41642055 CGTTAGCAAC
Statistics
Matches: 69, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
57 42 0.61
58 25 0.36
59 2 0.03
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.30
Consensus pattern (58 bp):
GATTACCAGTCCAGCCTAAATCCTAATTGTAACATATGCTCGAGAGAGATTATATCAA
Found at i:41649668 original size:45 final size:45
Alignment explanation
Indices: 41649619--41649791 Score: 168
Period size: 45 Copynumber: 3.8 Consensus size: 45
41649609 ACTAGAAACG
* * * *
41649619 AGTAAGACCTTGACTGAAAGACATTATGGCATCACGATTCTATCA
1 AGTAAGACCATGACTGAAAGAAACTATGGCATCACAATTCTATCA
* * *
41649664 AGTAAGACCATGACTAAAAGAAAGTATGGCATCACAATTCTATCG
1 AGTAAGACCATGACTGAAAGAAACTATGGCATCACAATTCTATCA
** * * **
41649709 AGTAAGACCAT-AGCTGAAAGATGCTATGGCATCACAAATCAAAGA
1 AGTAAGACCATGA-CTGAAAGAAACTATGGCATCACAATTCTATCA
* ** * *
41649754 AATAAGACCATGGTTGAAAGACACTATGGCAACACAAT
1 AGTAAGACCATGACTGAAAGAAACTATGGCATCACAAT
41649792 AGAAAATGAA
Statistics
Matches: 104, Mismatches: 22, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
44 1 0.01
45 103 0.99
ACGTcount: A:0.42, C:0.18, G:0.18, T:0.21
Consensus pattern (45 bp):
AGTAAGACCATGACTGAAAGAAACTATGGCATCACAATTCTATCA
Found at i:41649824 original size:46 final size:46
Alignment explanation
Indices: 41649754--41649902 Score: 194
Period size: 46 Copynumber: 3.3 Consensus size: 46
41649744 AAATCAAAGA
* *
41649754 AATAAGACCATGGTTGAAAGACACTATGGCAACACAATAGAAAATG
1 AATAAGACCATGGTTGAAAGACACTATGACAACACAACAGAAAATG
* * * *
41649800 AATAAAACCATGGTTGAAATACACTATGACAACACGACGGAAAATG
1 AATAAGACCATGGTTGAAAGACACTATGACAACACAACAGAAAATG
* * *
41649846 AATAAGACCATGGTTGAAAGACACTATGACATCA-AGAC-GAGAATA
1 AATAAGACCATGGTTGAAAGACACTATGACAACACA-ACAGAAAATG
41649891 AATAAGACCATG
1 AATAAGACCATG
41649903 ACCGAAGACA
Statistics
Matches: 90, Mismatches: 12, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
45 17 0.19
46 73 0.81
ACGTcount: A:0.48, C:0.16, G:0.19, T:0.17
Consensus pattern (46 bp):
AATAAGACCATGGTTGAAAGACACTATGACAACACAACAGAAAATG
Found at i:41651299 original size:18 final size:18
Alignment explanation
Indices: 41651276--41651314 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
41651266 TTTTGATGCC
41651276 TTGTTGATGTGTGTTATT
1 TTGTTGATGTGTGTTATT
41651294 TTGTTGATGTGTGTTATT
1 TTGTTGATGTGTGTTATT
41651312 TTG
1 TTG
41651315 ACAATGTGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.10, C:0.00, G:0.28, T:0.62
Consensus pattern (18 bp):
TTGTTGATGTGTGTTATT
Found at i:41651321 original size:18 final size:18
Alignment explanation
Indices: 41651282--41651323 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
41651272 TGCCTTGTTG
***
41651282 ATGTGTGTTATTTTGTTG
1 ATGTGTGTTATTTTGACA
41651300 ATGTGTGTTATTTTGACA
1 ATGTGTGTTATTTTGACA
41651318 ATGTGT
1 ATGTGT
41651324 TAATGAATGT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.17, C:0.02, G:0.26, T:0.55
Consensus pattern (18 bp):
ATGTGTGTTATTTTGACA
Found at i:41654472 original size:28 final size:27
Alignment explanation
Indices: 41654406--41654473 Score: 84
Period size: 28 Copynumber: 2.4 Consensus size: 27
41654396 ACTCTTTTAA
*
41654406 AATTTGAAATTTAGTCTTTATATTTTT
1 AATTTAAAATTTAGTCTTTATATTTTT
*
41654433 ATTTTAAGAATTTAGTCTTT-TATGTTTT
1 AATTTAA-AATTTAGTCTTTATAT-TTTT
41654461 AGATTTAAAATTT
1 A-ATTTAAAATTT
41654474 TATATCCATT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
27 8 0.23
28 22 0.63
29 5 0.14
ACGTcount: A:0.31, C:0.03, G:0.09, T:0.57
Consensus pattern (27 bp):
AATTTAAAATTTAGTCTTTATATTTTT
Found at i:41655832 original size:6 final size:6
Alignment explanation
Indices: 41655823--41655847 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
41655813 TATAACTTAG
41655823 CGCTCT CGCTCT CGCTCT CGCTCT C
1 CGCTCT CGCTCT CGCTCT CGCTCT C
41655848 TTTTATTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.52, G:0.16, T:0.32
Consensus pattern (6 bp):
CGCTCT
Found at i:41655882 original size:6 final size:6
Alignment explanation
Indices: 41655866--41655907 Score: 50
Period size: 6 Copynumber: 6.8 Consensus size: 6
41655856 TTCAGAGAAG
*
41655866 AAAAG- AAAAGAA AAAGAGA AAAAGA AAAAGA AAAAGA GAAAG
1 AAAAGA AAAAG-A AAA-AGA AAAAGA AAAAGA AAAAGA AAAAG
41655908 GGGGAATGGA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
5 5 0.15
6 19 0.58
7 7 0.21
8 2 0.06
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (6 bp):
AAAAGA
Found at i:41655890 original size:14 final size:13
Alignment explanation
Indices: 41655871--41655906 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 13
41655861 AGAAGAAAAG
41655871 AAAAGAAAAAGAGA
1 AAAAGAAAAAGA-A
41655885 AAAAGAAAAAGAA
1 AAAAGAAAAAGAA
41655898 AAAGAGAAA
1 AAA-AGAAA
41655907 GGGGGAATGG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 4 0.19
14 17 0.81
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (13 bp):
AAAAGAAAAAGAA
Found at i:41655896 original size:20 final size:19
Alignment explanation
Indices: 41655866--41655906 Score: 73
Period size: 20 Copynumber: 2.1 Consensus size: 19
41655856 TTCAGAGAAG
41655866 AAAAGAAAAGAAAAAGAGA
1 AAAAGAAAAGAAAAAGAGA
41655885 AAAAGAAAAAGAAAAAGAGA
1 AAAAG-AAAAGAAAAAGAGA
41655905 AA
1 AA
41655907 GGGGGAATGG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (19 bp):
AAAAGAAAAGAAAAAGAGA
Found at i:41675265 original size:38 final size:39
Alignment explanation
Indices: 41675138--41675514 Score: 561
Period size: 38 Copynumber: 9.7 Consensus size: 39
41675128 CGCAAACAAC
* * * *
41675138 TTGCCTTCGGGTCTTAACCCGGACATATGAACTTGCCTAA
1 TTGCCTTCGGGTCTTAGCCCGGATATAT-AACTCGCATAA
*
41675178 TTGCCTTCGGGTCTTAGCCCAGATATAT--CGTCCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATAAC-T-CGCATAA
* * *
41675217 TTGCCTTCGGGTCATAGCCCGGACATATAACT-GCCTAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATAACTCGCATAA
*
41675255 TTGCCTTCGGGTCTTAGCCCGGATATCGT--CTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATAT-ATAACTCGCATAA
*
41675293 TTGCCTTCGGGTCATAGCCCGGATAT-TAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATAACTCGCATAA
41675331 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATAT-AACTCGCATAA
41675371 TTGCCTTCGGGTCTTAGCCCGGATAT-TAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATAACTCGCATAA
41675409 TTGCCTTCGGGTCTTAGCCCGGATATATAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATAACTCGCATAA
*
41675448 TTGCCTTCGGGTCATAGCCCGGATATATAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATAACTCGCATAA
41675487 TTGCCTTCGGGTCTTAGCCCGGATATAT
1 TTGCCTTCGGGTCTTAGCCCGGATATAT
41675515 CCAATGCTCA
Statistics
Matches: 309, Mismatches: 17, Indels: 23
0.89 0.05 0.07
Matches are distributed among these distances:
36 1 0.00
37 3 0.01
38 131 0.42
39 110 0.36
40 63 0.20
41 1 0.00
ACGTcount: A:0.21, C:0.27, G:0.21, T:0.30
Consensus pattern (39 bp):
TTGCCTTCGGGTCTTAGCCCGGATATATAACTCGCATAA
Found at i:41675391 original size:78 final size:78
Alignment explanation
Indices: 41675138--41675515 Score: 568
Period size: 78 Copynumber: 4.9 Consensus size: 78
41675128 CGCAAACAAC
* * * * * *
41675138 TTGCCTTCGGGTCTTAACCCGGACATATGAACTTGCCTAATTGCCTTCGGGTCTTAGCCCAGATA
1 TTGCCTTCGGGTCATAGCCCGG--ATATTAACTCGCATAATTGCCTTCGGGTCTTAGCCCGGATA
**
41675203 TATCGTC-CGCATAA
64 TATCAACTCGCATAA
* *
41675217 TTGCCTTCGGGTCATAGCCCGGACATATAACT-GCCTAATTGCCTTCGGGTCTTAGCCCGG--AT
1 TTGCCTTCGGGTCATAGCCCGGATAT-TAACTCGCATAATTGCCTTCGGGTCTTAGCCCGGATAT
**
41675279 ATCGTCTCGCATAA
65 ATCAACTCGCATAA
41675293 TTGCCTTCGGGTCATAGCCCGGATATTAACTCGCATAATTGCCTTCGGGTCTTAGCCCGGATATA
1 TTGCCTTCGGGTCATAGCCCGGATATTAACTCGCATAATTGCCTTCGGGTCTTAGCCCGGATATA
41675358 TCAACTCGCATAA
66 TCAACTCGCATAA
*
41675371 TTGCCTTCGGGTCTTAGCCCGGATATTAACTCGCATAATTGCCTTCGGGTCTTAGCCCGGATATA
1 TTGCCTTCGGGTCATAGCCCGGATATTAACTCGCATAATTGCCTTCGGGTCTTAGCCCGGATATA
41675436 T-AACTCGCATAA
66 TCAACTCGCATAA
41675448 TTGCCTTCGGGTCATAGCCCGGATATATAACTCGCATAATTGCCTTCGGGTCTTAGCCCGGATAT
1 TTGCCTTCGGGTCATAGCCCGGATAT-TAACTCGCATAATTGCCTTCGGGTCTTAGCCCGGATAT
41675513 ATC
65 ATC
41675516 CAATGCTCAT
Statistics
Matches: 281, Mismatches: 11, Indels: 14
0.92 0.04 0.05
Matches are distributed among these distances:
75 13 0.05
76 59 0.21
77 66 0.23
78 123 0.44
79 20 0.07
ACGTcount: A:0.21, C:0.27, G:0.21, T:0.30
Consensus pattern (78 bp):
TTGCCTTCGGGTCATAGCCCGGATATTAACTCGCATAATTGCCTTCGGGTCTTAGCCCGGATATA
TCAACTCGCATAA
Found at i:41675396 original size:116 final size:114
Alignment explanation
Indices: 41675138--41675512 Score: 556
Period size: 116 Copynumber: 3.2 Consensus size: 114
41675128 CGCAAACAAC
* * * *
41675138 TTGCCTTCGGGTCTTAACCCGGACATATGAACTTGCCTAATTGCCTTCGGGTCTTAGCCCAGATA
1 TTGCCTTCGGGTCTTAGCCCGG--ATATG-ACTCGCATAATTGCCTTCGGGTCTTAGCCCGGATA
* * *
41675203 -TATCGTCCGCATAATTGCCTTCGGGTCATAGCCCGGACATATAACT-GCCTAA
63 TTAAC-T-CGCATAATTGCCTTCGGGTCATAGCCCGGATATATAACTCGCATAA
* *
41675255 TTGCCTTCGGGTCTTAGCCCGGATATCGTCTCGCATAATTGCCTTCGGGTCATAGCCCGGATATT
1 TTGCCTTCGGGTCTTAGCCCGGATAT-GACTCGCATAATTGCCTTCGGGTCTTAGCCCGGATATT
*
41675320 AACTCGCATAATTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
65 AACTCGCATAATTGCCTTCGGGTCATAGCCCGGATATAT-AACTCGCATAA
*
41675371 TTGCCTTCGGGTCTTAGCCCGGATATTAACTCGCATAATTGCCTTCGGGTCTTAGCCCGGATATA
1 TTGCCTTCGGGTCTTAGCCCGGATA-TGACTCGCATAATTGCCTTCGGGTCTTAGCCCGGATAT-
41675436 TAACTCGCATAATTGCCTTCGGGTCATAGCCCGGATATATAACTCGCATAA
64 TAACTCGCATAATTGCCTTCGGGTCATAGCCCGGATATATAACTCGCATAA
41675487 TTGCCTTCGGGTCTTAGCCCGGATAT
1 TTGCCTTCGGGTCTTAGCCCGGATAT
41675513 ATCCAATGCT
Statistics
Matches: 238, Mismatches: 14, Indels: 14
0.89 0.05 0.05
Matches are distributed among these distances:
114 33 0.14
115 40 0.17
116 104 0.44
117 61 0.26
ACGTcount: A:0.21, C:0.27, G:0.21, T:0.30
Consensus pattern (114 bp):
TTGCCTTCGGGTCTTAGCCCGGATATGACTCGCATAATTGCCTTCGGGTCTTAGCCCGGATATTA
ACTCGCATAATTGCCTTCGGGTCATAGCCCGGATATATAACTCGCATAA
Found at i:41677783 original size:22 final size:22
Alignment explanation
Indices: 41677755--41677819 Score: 87
Period size: 22 Copynumber: 3.0 Consensus size: 22
41677745 GCAAATACAT
*
41677755 TTGGCACACAGCCATAATCAGG
1 TTGGCACAAAGCCATAATCAGG
* *
41677777 TTGGCACAGAGCCAT-ATGTAGG
1 TTGGCACAAAGCCATAAT-CAGG
41677799 TTGGCACAAAGCCATAATCAG
1 TTGGCACAAAGCCATAATCAG
41677820 AATAATTGGC
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
21 2 0.05
22 33 0.89
23 2 0.05
ACGTcount: A:0.32, C:0.23, G:0.25, T:0.20
Consensus pattern (22 bp):
TTGGCACAAAGCCATAATCAGG
Found at i:41678256 original size:27 final size:27
Alignment explanation
Indices: 41678208--41678348 Score: 147
Period size: 27 Copynumber: 5.2 Consensus size: 27
41678198 GGGCAAAATG
* * ** * *
41678208 GTAATTTTACCCCACAAAGGTATCTCG
1 GTAATTCTACCCTACAGGGGTATTTCA
* *
41678235 GTAATTCTACCCTATAGGGGTATTTTA
1 GTAATTCTACCCTACAGGGGTATTTCA
* * * *
41678262 ATATTTCTACCCTACAAGGGTATTTCG
1 GTAATTCTACCCTACAGGGGTATTTCA
* *
41678289 GTAATTCTACCATACAGGGGTGTTTCA
1 GTAATTCTACCCTACAGGGGTATTTCA
41678316 GTAATTCTACCCTACAGGGGTATTTCA
1 GTAATTCTACCCTACAGGGGTATTTCA
*
41678343 ATAATT
1 GTAATT
41678349 TTGTAAATCA
Statistics
Matches: 91, Mismatches: 23, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
27 91 1.00
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.35
Consensus pattern (27 bp):
GTAATTCTACCCTACAGGGGTATTTCA
Found at i:41678339 original size:54 final size:54
Alignment explanation
Indices: 41678208--41678341 Score: 169
Period size: 54 Copynumber: 2.5 Consensus size: 54
41678198 GGGCAAAATG
* * * * * * *
41678208 GTAATTTTACCCCACAAAGGTATCTCGGTAATTCTACCCTATAGGGGTATTTTA
1 GTAATTCTACCCTACAAGGGTATTTCGGTAATTCTACCATACAGGGGTATTTCA
* * *
41678262 ATATTTCTACCCTACAAGGGTATTTCGGTAATTCTACCATACAGGGGTGTTTCA
1 GTAATTCTACCCTACAAGGGTATTTCGGTAATTCTACCATACAGGGGTATTTCA
*
41678316 GTAATTCTACCCTACAGGGGTATTTC
1 GTAATTCTACCCTACAAGGGTATTTC
41678342 AATAATTTTG
Statistics
Matches: 67, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
54 67 1.00
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.35
Consensus pattern (54 bp):
GTAATTCTACCCTACAAGGGTATTTCGGTAATTCTACCATACAGGGGTATTTCA
Found at i:41686645 original size:40 final size:40
Alignment explanation
Indices: 41686551--41686695 Score: 193
Period size: 40 Copynumber: 3.6 Consensus size: 40
41686541 TACTCGAATG
*
41686551 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGCGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCT-AGCGACT
* *
41686592 ACATCCGGACTAAGAT-CCGAAGGCATTTGTGCTAGCGACT
1 ATATCCGGGCTAAG-TCCCGAAGGCATTTGTGCTAGCGACT
* * *
41686632 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGACC
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGCGACT
* *
41686672 ATATCCGGGTTAAGACCCGAAGGC
1 ATATCCGGGCTAAGTCCCGAAGGC
41686696 CTTGTGCGAG
Statistics
Matches: 92, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
39 1 0.01
40 62 0.67
41 28 0.30
42 1 0.01
ACGTcount: A:0.26, C:0.25, G:0.26, T:0.23
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGCGACT
Found at i:41689490 original size:16 final size:17
Alignment explanation
Indices: 41689469--41689509 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
41689459 TATACCATTC
41689469 TCAAAT-ACAAAGCATA
1 TCAAATAACAAAGCATA
*
41689485 TCAAATAATAAAGCATA
1 TCAAATAACAAAGCATA
*
41689502 TCATATAA
1 TCAAATAA
41689510 TACATATACC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 6 0.27
17 16 0.73
ACGTcount: A:0.56, C:0.15, G:0.05, T:0.24
Consensus pattern (17 bp):
TCAAATAACAAAGCATA
Found at i:41689499 original size:17 final size:17
Alignment explanation
Indices: 41689477--41689511 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
41689467 TCTCAAATAC
41689477 AAAGCATATCAAATAAT
1 AAAGCATATCAAATAAT
*
41689494 AAAGCATATCATATAAT
1 AAAGCATATCAAATAAT
41689511 A
1 A
41689512 CATATACCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.57, C:0.11, G:0.06, T:0.26
Consensus pattern (17 bp):
AAAGCATATCAAATAAT
Found at i:41696400 original size:68 final size:67
Alignment explanation
Indices: 41696328--41696477 Score: 171
Period size: 67 Copynumber: 2.2 Consensus size: 67
41696318 CATCATGTGT
* * * *
41696328 ACAAGAGAGCTACAAGACATTATGATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACC
1 ACAAGAGAGCTAC--GACA-TAT-ATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACC
41696390 ATGTAG
62 ATGTAG
** * *
41696396 ACAAGAGAGCTACGGGATATATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGT
1 ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT
41696461 AG
66 AG
41696463 ACAAGAGAGCTACGA
1 ACAAGAGAGCTACGA
41696478 GATAAACTGG
Statistics
Matches: 70, Mismatches: 9, Indels: 7
0.81 0.10 0.08
Matches are distributed among these distances:
64 20 0.29
65 7 0.10
66 4 0.06
67 26 0.37
68 13 0.19
ACGTcount: A:0.33, C:0.17, G:0.29, T:0.21
Consensus pattern (67 bp):
ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT
AG
Found at i:41696433 original size:64 final size:64
Alignment explanation
Indices: 41696352--41696535 Score: 185
Period size: 67 Copynumber: 2.8 Consensus size: 64
41696342 AGACATTATG
* *
41696352 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
* * * * * *
41696416 ATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACCATGTAGACAAGAGAGCTACGAGAT
41696481 AA
63 AA
* * * * *
41696483 ACTG--GCTAGGTCACATGGGTGGTACTAAGTGTTCACCATAT-GTACAAGAGAGC
1 A-TGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAG-ACAAGAGAGC
41696536 CGAACTATAT
Statistics
Matches: 97, Mismatches: 18, Indels: 11
0.77 0.14 0.09
Matches are distributed among these distances:
62 1 0.01
63 18 0.19
64 21 0.22
65 8 0.08
66 16 0.16
67 31 0.32
68 2 0.02
ACGTcount: A:0.30, C:0.17, G:0.29, T:0.23
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:41700959 original size:43 final size:42
Alignment explanation
Indices: 41700898--41701012 Score: 117
Period size: 43 Copynumber: 2.7 Consensus size: 42
41700888 GATGCCACTG
*
41700898 CCCAGACAGGGTCTTACACGAAATCACATA-ATGATGCAAATGT
1 CCCAGACATGGTCTTACACGAAATCACATACA--ATGCAAATGT
* * *
41700941 CCTAGACGTGGTCTTACAC-ATAATCACAATACAATGCCAATGT
1 CCCAGACATGGTCTTACACGA-AATCAC-ATACAATGCAAATGT
* * *
41700984 CCCAGATATGGTCTTACATGTAATCACAT
1 CCCAGACATGGTCTTACACGAAATCACAT
41701013 CTCGCTAATC
Statistics
Matches: 59, Mismatches: 9, Indels: 9
0.77 0.12 0.12
Matches are distributed among these distances:
42 3 0.05
43 52 0.88
44 3 0.05
45 1 0.02
ACGTcount: A:0.35, C:0.24, G:0.16, T:0.25
Consensus pattern (42 bp):
CCCAGACATGGTCTTACACGAAATCACATACAATGCAAATGT
Found at i:41712059 original size:29 final size:30
Alignment explanation
Indices: 41712022--41712093 Score: 78
Period size: 29 Copynumber: 2.5 Consensus size: 30
41712012 ATCAACCGCG
* * *
41712022 CACAATTAGTGCCATGTAC-TTTAAACTCA
1 CACACTTAGTGCCATGTACATTGAAACCCA
*
41712051 CACACTTAGTG-C-TGTACAATTGAAACCCG
1 CACACTTAGTGCCATGTAC-ATTGAAACCCA
41712080 CACACTTAGTGCCA
1 CACACTTAGTGCCA
41712094 ATCTCATGAC
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
27 5 0.14
28 1 0.03
29 28 0.80
30 1 0.03
ACGTcount: A:0.32, C:0.28, G:0.14, T:0.26
Consensus pattern (30 bp):
CACACTTAGTGCCATGTACATTGAAACCCA
Found at i:41718705 original size:40 final size:40
Alignment explanation
Indices: 41718622--41718963 Score: 458
Period size: 40 Copynumber: 8.6 Consensus size: 40
41718612 TTGAATGCTG
* * * * * *
41718622 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAA
* * * * *
41718662 TCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTATTAAA
41718702 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
41718742 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
41718782 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
*
41718822 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* *
41718862 TCCGGGTTAAGT-CCGAAGGCATTCGTGCAAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
41718901 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
41718940 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
41718964 TGAACGAGGA
Statistics
Matches: 277, Mismatches: 21, Indels: 9
0.90 0.07 0.03
Matches are distributed among these distances:
39 71 0.26
40 198 0.71
41 8 0.03
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.27
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
Found at i:41726108 original size:40 final size:40
Alignment explanation
Indices: 41726025--41726367 Score: 476
Period size: 40 Copynumber: 8.6 Consensus size: 40
41726015 TTGAATGCTG
* * * * * *
41726025 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAA
* * * * *
41726065 TCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTATTAAA
41726105 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
41726145 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
41726185 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
*
41726225 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
*
41726265 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
41726305 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
41726344 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
41726368 TGAACGAGGA
Statistics
Matches: 281, Mismatches: 19, Indels: 7
0.92 0.06 0.02
Matches are distributed among these distances:
39 35 0.12
40 238 0.85
41 8 0.03
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.27
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
Found at i:41730066 original size:29 final size:29
Alignment explanation
Indices: 41730001--41730068 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
41729991 TAATCAACCG
41730001 CGCACACTTAGTGCCATGCACTTTAAACT
1 CGCACACTTAGTGCCATGCACTTTAAACT
* * **
41730030 CACGCACTTAGTGCCATGCA-TTTCAAGTT
1 CGCACACTTAGTGCCATGCACTTT-AAACT
41730059 CGCACACTTA
1 CGCACACTTA
41730069 CCTTTTCCGC
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
28 3 0.09
29 29 0.91
ACGTcount: A:0.26, C:0.31, G:0.15, T:0.28
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCACTTTAAACT
Found at i:41730211 original size:29 final size:30
Alignment explanation
Indices: 41730177--41730248 Score: 96
Period size: 29 Copynumber: 2.5 Consensus size: 30
41730167 ATCAACCGCG
*
41730177 CACACTTAGTGCCATGTAC-TTTAAACTCA
1 CACACTTAGTGCCATGTACATTTAAACCCA
*
41730206 CACACTTAGTG-C-TGTACAATTTAAACCCG
1 CACACTTAGTGCCATGTAC-ATTTAAACCCA
41730235 CACACTTAGTGCCA
1 CACACTTAGTGCCA
41730249 ATCTCATGAC
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
27 5 0.14
28 1 0.03
29 30 0.81
30 1 0.03
ACGTcount: A:0.31, C:0.29, G:0.12, T:0.28
Consensus pattern (30 bp):
CACACTTAGTGCCATGTACATTTAAACCCA
Found at i:41730239 original size:174 final size:173
Alignment explanation
Indices: 41729929--41730242 Score: 486
Period size: 174 Copynumber: 1.8 Consensus size: 173
41729919 CAAAATTGAC
* * * *
41729929 TCGCACCCTTCATGTAAATAATTTATATAAAATATATATTGGGTTGCACACATAATGTTTAGTAA
1 TCGCACCCTTAATGTAAATAATTTATAGAAAATATATATTGGGTTGCACACATAATGCTTAATAA
* * ***
41729994 TCAACCGCGCACACTTAGTGCCATGCACTTTAAACTCACGCACTTAGTGCCATGCATTTCAAGTT
66 TCAACCGCGCACACTTAGTGCCATGCACTTTAAACTCACACACTTAGTGCCATACATTTCAAACC
41730059 CGCACACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAG
131 CGCACACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAG
*
41730102 TCGCACCCTTAATGTAAATAATTTATAGAAAATATATATTGGGTTCGCACACATAGTGCTTAATA
1 TCGCACCCTTAATGTAAATAATTTATAGAAAATATATATTGGGTT-GCACACATAATGCTTAATA
* **
41730167 ATCAACCGCGCACACTTAGTGCCATGTACTTTAAACTCACACACTTAGTGCTGTACAATTT-AAA
65 ATCAACCGCGCACACTTAGTGCCATGCACTTTAAACTCACACACTTAGTGCCATAC-ATTTCAAA
41730231 CCCGCACACTTA
129 CCCGCACACTTA
41730243 GTGCCAATCT
Statistics
Matches: 126, Mismatches: 13, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
173 43 0.34
174 79 0.63
175 4 0.03
ACGTcount: A:0.32, C:0.24, G:0.14, T:0.30
Consensus pattern (173 bp):
TCGCACCCTTAATGTAAATAATTTATAGAAAATATATATTGGGTTGCACACATAATGCTTAATAA
TCAACCGCGCACACTTAGTGCCATGCACTTTAAACTCACACACTTAGTGCCATACATTTCAAACC
CGCACACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAG
Found at i:41732973 original size:27 final size:27
Alignment explanation
Indices: 41732932--41733020 Score: 99
Period size: 27 Copynumber: 3.3 Consensus size: 27
41732922 AACCATATAT
*
41732932 CACATAGGGGCAAAACAGTCATTTTAC
1 CACATAAGGGCAAAACAGTCATTTTAC
* * *
41732959 CATATAAGGGCAAAATAGTCATTTTAT
1 CACATAAGGGCAAAACAGTCATTTTAC
* * *
41732986 AACCTAAGGG-AATAACAGTCATCTTAC
1 CACATAAGGGCAA-AACAGTCATTTTAC
41733013 CACATAAG
1 CACATAAG
41733021 CGGTTATAGG
Statistics
Matches: 49, Mismatches: 12, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
26 2 0.04
27 47 0.96
ACGTcount: A:0.40, C:0.19, G:0.16, T:0.25
Consensus pattern (27 bp):
CACATAAGGGCAAAACAGTCATTTTAC
Found at i:41734016 original size:25 final size:27
Alignment explanation
Indices: 41733926--41734020 Score: 158
Period size: 27 Copynumber: 3.6 Consensus size: 27
41733916 TATAACCATA
* *
41733926 TATCACATAGGGGCAAAACAGTCATTT
1 TATCACATAAGGGCAAAATAGTCATTT
41733953 TATCACATAAGGGCAAAATAGTCATTT
1 TATCACATAAGGGCAAAATAGTCATTT
41733980 TATCACATAAGGGCAAAATAGTCA-TT
1 TATCACATAAGGGCAAAATAGTCATTT
41734006 T-TCACATAAGGGCAA
1 TATCACATAAGGGCAA
41734021 TGTGACAGCC
Statistics
Matches: 66, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
25 14 0.21
26 3 0.05
27 49 0.74
ACGTcount: A:0.40, C:0.17, G:0.17, T:0.26
Consensus pattern (27 bp):
TATCACATAAGGGCAAAATAGTCATTT
Found at i:41735751 original size:79 final size:81
Alignment explanation
Indices: 41735615--41735799 Score: 227
Period size: 79 Copynumber: 2.3 Consensus size: 81
41735605 TTGAATGATG
*
41735615 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
41735679 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * * **
41735694 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
41735756 TTTGTGCGAGTTACTATA
64 TTTGTGCGAGATACTATA
* * *
41735774 ACCGGGCTATGTCCCGAAGGTATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
41735800 AACGAGTAGC
Statistics
Matches: 91, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 1 0.01
79 58 0.64
80 32 0.35
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
TGTGCGAGATACTATA
Found at i:41735806 original size:40 final size:40
Alignment explanation
Indices: 41735615--41735799 Score: 225
Period size: 40 Copynumber: 4.7 Consensus size: 40
41735605 TTGAATGATG
* * * *
41735615 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
41735655 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
41735695 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
41735734 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
* *
41735775 -CCGGGCTATGTCCCGAAGGTATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
41735800 AACGAGTAGC
Statistics
Matches: 126, Mismatches: 14, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
39 35 0.28
40 81 0.64
41 10 0.08
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:41735821 original size:79 final size:79
Alignment explanation
Indices: 41735668--41735832 Score: 201
Period size: 79 Copynumber: 2.1 Consensus size: 79
41735658 GGACTAAGAT
* **
41735668 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
*
41735733 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* * *
41735747 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGTATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
* *
41735810 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
41735826 CCGAAGG
1 CCGAAGG
41735833 TACGTGATTT
Statistics
Matches: 74, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
78 2 0.03
79 48 0.65
80 24 0.32
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:41738148 original size:27 final size:27
Alignment explanation
Indices: 41738118--41738221 Score: 122
Period size: 27 Copynumber: 3.9 Consensus size: 27
41738108 CACGTAGTGC
* *
41738118 CAAAACAGTCATTTTACCGCATAATGG
1 CAAAACAGTCATTTTACCACATAAGGG
* * *
41738145 CAAAATAGACATTTTATCACATAAGGG
1 CAAAACAGTCATTTTACCACATAAGGG
*
41738172 CAAAACAATCATTTT--CACATAAGGG
1 CAAAACAGTCATTTTACCACATAAGGG
* *
41738197 AAAAACAGTCATCTTACCACATAAG
1 CAAAACAGTCATTTTACCACATAAG
41738222 CGGGTCTAGG
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
25 22 0.34
27 42 0.66
ACGTcount: A:0.43, C:0.20, G:0.12, T:0.24
Consensus pattern (27 bp):
CAAAACAGTCATTTTACCACATAAGGG
Found at i:41738195 original size:25 final size:25
Alignment explanation
Indices: 41738161--41738208 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
41738151 AGACATTTTA
*
41738161 TCACATAAGGGCAAAACAATCATTT
1 TCACATAAGGGAAAAACAATCATTT
*
41738186 TCACATAAGGGAAAAACAGTCAT
1 TCACATAAGGGAAAAACAATCAT
41738209 CTTACCACAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.46, C:0.19, G:0.15, T:0.21
Consensus pattern (25 bp):
TCACATAAGGGAAAAACAATCATTT
Found at i:41738332 original size:10 final size:10
Alignment explanation
Indices: 41738317--41738342 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
41738307 ATAGGCCTAA
41738317 GGCCCAGGTG
1 GGCCCAGGTG
41738327 GGCCCAGGTG
1 GGCCCAGGTG
41738337 GGCCCA
1 GGCCCA
41738343 TATTCCTGTG
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:0.12, C:0.35, G:0.46, T:0.08
Consensus pattern (10 bp):
GGCCCAGGTG
Found at i:41738781 original size:27 final size:27
Alignment explanation
Indices: 41738743--41738796 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
41738733 AATGGAGCCT
41738743 AATGGAGTTCCCAAACTAACCATAGTC
1 AATGGAGTTCCCAAACTAACCATAGTC
*
41738770 AATGGAGTTCCCTAACTAACCATAGTC
1 AATGGAGTTCCCAAACTAACCATAGTC
41738797 TCCTTTCCTG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.35, C:0.26, G:0.15, T:0.24
Consensus pattern (27 bp):
AATGGAGTTCCCAAACTAACCATAGTC
Found at i:41741677 original size:27 final size:27
Alignment explanation
Indices: 41741645--41741780 Score: 157
Period size: 27 Copynumber: 5.1 Consensus size: 27
41741635 ATCACTTAAA
* *
41741645 GGCAAAACAGTCATTTTACCACATAAG
1 GGCAAAATAGTCATTTTACCATATAAG
* * *
41741672 GTCAAAATAGTTATTTTACTATATAAG
1 GGCAAAATAGTCATTTTACCATATAAG
*
41741699 GGCAAAATAGTCATTTTATCATATAAG
1 GGCAAAATAGTCATTTTACCATATAAG
* * * *
41741726 GCCAAAATAGTCATTCTATCACAT-AG
1 GGCAAAATAGTCATTTTACCATATAAG
* *
41741752 GGCAAAACAGTCATCTTACCATATAAG
1 GGCAAAATAGTCATTTTACCATATAAG
41741779 GG
1 GG
41741781 GGTCTAGGTA
Statistics
Matches: 90, Mismatches: 18, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
26 20 0.22
27 70 0.78
ACGTcount: A:0.40, C:0.17, G:0.15, T:0.29
Consensus pattern (27 bp):
GGCAAAATAGTCATTTTACCATATAAG
Found at i:41741775 original size:53 final size:54
Alignment explanation
Indices: 41741645--41741779 Score: 175
Period size: 54 Copynumber: 2.5 Consensus size: 54
41741635 ATCACTTAAA
* * * * *
41741645 GGCAAAACAGTCATTTTACCACATAAGGTCAAAATAGTTATTTTACTATATAAG
1 GGCAAAACAGTCATTTTACCATATAAGGCCAAAATAGTCATTCTACTACATAAG
* *
41741699 GGCAAAATAGTCATTTTATCATATAAGGCCAAAATAGTCATTCTA-TCACAT-AG
1 GGCAAAACAGTCATTTTACCATATAAGGCCAAAATAGTCATTCTACT-ACATAAG
*
41741752 GGCAAAACAGTCATCTTACCATATAAGG
1 GGCAAAACAGTCATTTTACCATATAAGG
41741780 GGGTCTAGGT
Statistics
Matches: 70, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
53 28 0.40
54 42 0.60
ACGTcount: A:0.40, C:0.17, G:0.14, T:0.29
Consensus pattern (54 bp):
GGCAAAACAGTCATTTTACCATATAAGGCCAAAATAGTCATTCTACTACATAAG
Found at i:41741915 original size:18 final size:17
Alignment explanation
Indices: 41741888--41741921 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
41741878 CATTACGCGG
41741888 GCCTAGGTGGGCCCACAT
1 GCCTAGGT-GGCCCACAT
*
41741906 GCCTATGTGGCCCACA
1 GCCTAGGTGGCCCACA
41741922 ACTCTCAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.18, C:0.35, G:0.29, T:0.18
Consensus pattern (17 bp):
GCCTAGGTGGCCCACAT
Found at i:41744696 original size:50 final size:50
Alignment explanation
Indices: 41744599--41744769 Score: 243
Period size: 50 Copynumber: 3.4 Consensus size: 50
41744589 TCAGGTTGCC
* * * *
41744599 GAAGCTACCACTTTTCACTTGTCATTTGTCCTTGATCAGATAAGTGTAGCT
1 GAAGCTATCACTTATCACTT-TCACTTGTTCTTGATCAGATAAGTGTAGCT
*
41744650 GAAGCTATCACTTATCACTTTCACTTGTTCTTGATCAGATAAGTGTAGCC
1 GAAGCTATCACTTATCACTTTCACTTGTTCTTGATCAGATAAGTGTAGCT
* * * *
41744700 GGAGCTATCACTTATCAGTTTCACTTGTTCTTGATCAGATAATTATAGCT
1 GAAGCTATCACTTATCACTTTCACTTGTTCTTGATCAGATAAGTGTAGCT
*
41744750 AAAGCTATCACTTATCACTT
1 GAAGCTATCACTTATCACTT
41744770 GTTGCCATGG
Statistics
Matches: 107, Mismatches: 13, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
50 89 0.83
51 18 0.17
ACGTcount: A:0.26, C:0.21, G:0.15, T:0.37
Consensus pattern (50 bp):
GAAGCTATCACTTATCACTTTCACTTGTTCTTGATCAGATAAGTGTAGCT
Found at i:41752014 original size:20 final size:20
Alignment explanation
Indices: 41751989--41752027 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
41751979 GAGGTCCTTA
41751989 TGTGGTTAATATGCCATTTT
1 TGTGGTTAATATGCCATTTT
41752009 TGTGGTTAATATGCCATTT
1 TGTGGTTAATATGCCATTT
41752028 ACATAGTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.21, C:0.10, G:0.21, T:0.49
Consensus pattern (20 bp):
TGTGGTTAATATGCCATTTT
Found at i:41752036 original size:20 final size:20
Alignment explanation
Indices: 41751993--41752038 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
41751983 TCCTTATGTG
*** *
41751993 GTTAATATGCCATTTTTGTG
1 GTTAATATGCCATTTACATA
41752013 GTTAATATGCCATTTACATA
1 GTTAATATGCCATTTACATA
41752033 GTTAAT
1 GTTAAT
41752039 GGACATTAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.28, C:0.11, G:0.15, T:0.46
Consensus pattern (20 bp):
GTTAATATGCCATTTACATA
Found at i:41753150 original size:43 final size:43
Alignment explanation
Indices: 41752993--41753151 Score: 128
Period size: 43 Copynumber: 3.7 Consensus size: 43
41752983 TATGTGTTTT
* ** *
41752993 CGTGTAAGACCACGTTTGGGATTTTGGCATCGACTTA-TGATTTA
1 CGTGTAAGACCACGTTTAGGACGTTGGCATCGA-TAATTGA-TTA
* * * * *
41753037 CGTGTAAGACCACGTATAGGACGTAGGTATC-ATACTTGATTT
1 CGTGTAAGACCACGTTTAGGACGTTGGCATCGATAATTGATTA
* * *
41753079 TGTGTAAGACC-CTGTCTAGGATAG-TGGCATCGATAATTGATTA
1 CGTGTAAGACCAC-GTTTAGGA-CGTTGGCATCGATAATTGATTA
* *
41753122 CATGTAAGACCACGTTTGGGACGTTGGCAT
1 CGTGTAAGACCACGTTTAGGACGTTGGCAT
41753152 TGTACGAGCT
Statistics
Matches: 88, Mismatches: 21, Indels: 13
0.72 0.17 0.11
Matches are distributed among these distances:
41 1 0.01
42 26 0.30
43 35 0.40
44 26 0.30
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.32
Consensus pattern (43 bp):
CGTGTAAGACCACGTTTAGGACGTTGGCATCGATAATTGATTA
Found at i:41754487 original size:34 final size:34
Alignment explanation
Indices: 41754448--41754558 Score: 143
Period size: 34 Copynumber: 3.3 Consensus size: 34
41754438 AAATAAATGT
* *
41754448 ATATATATTCACCTTCGGTTATATCAAACCATAC
1 ATATATATTCACCTTCGGTTATACCAAGCCATAC
* *
41754482 ATATATATTCA-CTTTGGATTATACCAAGCTATAC
1 ATATATATTCACCTTCGG-TTATACCAAGCCATAC
* * *
41754516 ATATATAATCACCTTCGATTATGCCAAGCCATAC
1 ATATATATTCACCTTCGGTTATACCAAGCCATAC
41754550 ATATATATT
1 ATATATATT
41754559 TATGTACTTC
Statistics
Matches: 65, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
33 5 0.08
34 56 0.86
35 4 0.06
ACGTcount: A:0.36, C:0.21, G:0.07, T:0.36
Consensus pattern (34 bp):
ATATATATTCACCTTCGGTTATACCAAGCCATAC
Found at i:41757250 original size:27 final size:27
Alignment explanation
Indices: 41757203--41757343 Score: 129
Period size: 27 Copynumber: 5.2 Consensus size: 27
41757193 GGGCAAAATG
* ** *
41757203 GTAATTTTACCCTGTAAGGGTATCTCA
1 GTAATTCTACCCTACAAGGGTATTTCA
* *
41757230 ATAATTCTACCCTACAGGGGTATTTCA
1 GTAATTCTACCCTACAAGGGTATTTCA
* * * * **
41757257 GTATTTCTACCCAAGAAAGGTATTTTG
1 GTAATTCTACCCTACAAGGGTATTTCA
* * *
41757284 GTAATTCTACCCTATAGGGGTATTTCG
1 GTAATTCTACCCTACAAGGGTATTTCA
* *
41757311 GTAATTCTACCTTACAAGGGTATTTCT
1 GTAATTCTACCCTACAAGGGTATTTCA
41757338 GTAATT
1 GTAATT
41757344 TTGTAAATCG
Statistics
Matches: 90, Mismatches: 24, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
27 90 1.00
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.38
Consensus pattern (27 bp):
GTAATTCTACCCTACAAGGGTATTTCA
Found at i:41757333 original size:54 final size:54
Alignment explanation
Indices: 41757231--41757343 Score: 147
Period size: 54 Copynumber: 2.1 Consensus size: 54
41757221 GGTATCTCAA
* *
41757231 TAATTCTACCCTACAGGGGTATTTCAGTATTTCTACCCAAGAAAGGTATTT-TGG
1 TAATTCTACCCTACAGGGGTATTTCAGTAATTCTACCCAACAAAGGTATTTCT-G
* * ** *
41757285 TAATTCTACCCTATAGGGGTATTTCGGTAATTCTACCTTACAAGGGTATTTCTG
1 TAATTCTACCCTACAGGGGTATTTCAGTAATTCTACCCAACAAAGGTATTTCTG
41757339 TAATT
1 TAATT
41757344 TTGTAAATCG
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
54 50 0.98
55 1 0.02
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.38
Consensus pattern (54 bp):
TAATTCTACCCTACAGGGGTATTTCAGTAATTCTACCCAACAAAGGTATTTCTG
Found at i:41757357 original size:27 final size:27
Alignment explanation
Indices: 41757327--41757560 Score: 143
Period size: 27 Copynumber: 8.7 Consensus size: 27
41757317 CTACCTTACA
* **
41757327 AGGGTATTTCTGTAATTTTGTAAATCG
1 AGGGTATTTCAGTAATTTTACAAATCG
*** * **
41757354 AGGGTAAAACAGTAATTCTGTAAATCG
1 AGGGTATTTCAGTAATTTTACAAATCG
* * *
41757381 ATGGTACTTT-GGTAATTTTACAAGTCG
1 AGGGTA-TTTCAGTAATTTTACAAATCG
* **
41757408 AGGGTATTTTAGTAATTTTACAGGTCG
1 AGGGTATTTCAGTAATTTTACAAATCG
* *
41757435 AGGGTATTTCAGTAATTTCACAAAT-T
1 AGGGTATTTCAGTAATTTTACAAATCG
** *
41757461 AGGGGTATTTTGGTAATTTTACAAA-CT
1 A-GGGTATTTCAGTAATTTTACAAATCG
* * *
41757488 AGGGGTATTTTAGTAATTTTATAAA-CT
1 A-GGGTATTTCAGTAATTTTACAAATCG
** * *
41757515 AGGGGTATTTTGGTAATTTTACAAACCA
1 A-GGGTATTTCAGTAATTTTACAAATCG
**
41757543 AGGGTATTTTGGTAATTT
1 AGGGTATTTCAGTAATTT
41757561 GGTAAACTAA
Statistics
Matches: 172, Mismatches: 30, Indels: 10
0.81 0.14 0.05
Matches are distributed among these distances:
26 4 0.02
27 166 0.97
28 2 0.01
ACGTcount: A:0.30, C:0.08, G:0.22, T:0.40
Consensus pattern (27 bp):
AGGGTATTTCAGTAATTTTACAAATCG
Found at i:41757567 original size:27 final size:27
Alignment explanation
Indices: 41757383--41757560 Score: 189
Period size: 27 Copynumber: 6.6 Consensus size: 27
41757373 GTAAATCGAT
* * *
41757383 GGTACTTTGGTAATTTTAC-AAGTCGAG
1 GGTATTTTGGTAATTTTACAAACTAG-G
* ** *
41757410 GGTATTTTAGTAATTTTAC-AGGTCGAG
1 GGTATTTTGGTAATTTTACAAACTAG-G
** * *
41757437 GGTATTTCAGTAATTTCACAAATTAGG
1 GGTATTTTGGTAATTTTACAAACTAGG
41757464 GGTATTTTGGTAATTTTACAAACTAGG
1 GGTATTTTGGTAATTTTACAAACTAGG
* *
41757491 GGTATTTTAGTAATTTTATAAACTAGG
1 GGTATTTTGGTAATTTTACAAACTAGG
* *
41757518 GGTATTTTGGTAATTTTACAAACCAAG
1 GGTATTTTGGTAATTTTACAAACTAGG
41757545 GGTATTTTGGTAATTT
1 GGTATTTTGGTAATTT
41757561 GGTAAACTAA
Statistics
Matches: 132, Mismatches: 18, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
27 129 0.98
28 3 0.02
ACGTcount: A:0.29, C:0.08, G:0.22, T:0.41
Consensus pattern (27 bp):
GGTATTTTGGTAATTTTACAAACTAGG
Found at i:41759526 original size:6 final size:6
Alignment explanation
Indices: 41759515--41759562 Score: 62
Period size: 6 Copynumber: 7.8 Consensus size: 6
41759505 TATCGGAACT
*
41759515 AGAATC AGAATC AGAATC AGAATC AGGTAA-C AGAATC AAAATC AGAAT
1 AGAATC AGAATC AGAATC AGAATC A-G-AATC AGAATC AGAATC AGAAT
41759563 GTGAATGCAA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
5 2 0.05
6 30 0.81
7 3 0.08
8 2 0.05
ACGTcount: A:0.52, C:0.15, G:0.17, T:0.17
Consensus pattern (6 bp):
AGAATC
Found at i:41760097 original size:27 final size:27
Alignment explanation
Indices: 41759957--41760089 Score: 178
Period size: 27 Copynumber: 5.0 Consensus size: 27
41759947 GGGGCAAAAT
* *
41759957 GGTAATT-TACCCTGCAAGGGTATCTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* * *
41759983 GGTAGTTCTATCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* *
41760010 GGTATTTCTACCCTACAAGGGTATTTT
1 GGTAATTCTACCCTACAAGGGTATTTC
*
41760037 GGTAATTCTACCCTATAAGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
*
41760064 GGTAATTCTACCTTACAAGGGTATTT
1 GGTAATTCTACCCTACAAGGGTATTT
41760090 TTGTAATTTT
Statistics
Matches: 92, Mismatches: 14, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
26 6 0.07
27 86 0.93
ACGTcount: A:0.23, C:0.19, G:0.21, T:0.37
Consensus pattern (27 bp):
GGTAATTCTACCCTACAAGGGTATTTC
Found at i:41760111 original size:27 final size:27
Alignment explanation
Indices: 41760025--41760368 Score: 293
Period size: 27 Copynumber: 12.7 Consensus size: 27
41760015 TTCTACCCTA
* **
41760025 CAAGGGTATTTTGGTAATTCTACCCTAT
1 CAAGGGTATTTTGGTAATTTTA-CAAAT
* * **
41760053 -AAGGGTATTTCGGTAATTCTAC-CTT
1 CAAGGGTATTTTGGTAATTTTACAAAT
* **
41760078 ACAAGGGTATTTTTGTAATTTTGTAAAT
1 -CAAGGGTATTTTGGTAATTTTACAAAT
* *** * **
41760106 CGAGGGTAAAATGGTAATTCTGTAAAT
1 CAAGGGTATTTTGGTAATTTTACAAAT
* *
41760133 -AGAGGGTACTTTGGTAATTTTACAAGT
1 CA-AGGGTATTTTGGTAATTTTACAAAT
* * **
41760160 CGAGGGTATTTTAGTAATTTTACAGGT
1 CAAGGGTATTTTGGTAATTTTACAAAT
* ** *
41760187 CGAGGGTATTTCAGTAATTTCACAAAT
1 CAAGGGTATTTTGGTAATTTTACAAAT
*
41760214 CAGGGGTATTTTGGTAATTTTACAAA-
1 CAAGGGTATTTTGGTAATTTTACAAAT
*
41760240 CTAAGGGTATTTTGGTAATTTTACAAAC
1 C-AAGGGTATTTTGGTAATTTTACAAAT
* *
41760268 CAAGGGTATTTTGGTAATTTTATAAAC
1 CAAGGGTATTTTGGTAATTTTACAAAT
* *
41760295 CAATGGTATTTTAGTAATTTTACAAA-
1 CAAGGGTATTTTGGTAATTTTACAAAT
*
41760321 CTAAGGGTATTTTGGTAATTTTACAAAC
1 C-AAGGGTATTTTGGTAATTTTACAAAT
*
41760349 CAGGGGTATTTTGGTAATTT
1 CAAGGGTATTTTGGTAATTT
41760369 GGTAAACTAA
Statistics
Matches: 262, Mismatches: 45, Indels: 19
0.80 0.14 0.06
Matches are distributed among these distances:
25 1 0.00
26 3 0.01
27 255 0.97
28 3 0.01
ACGTcount: A:0.31, C:0.10, G:0.21, T:0.39
Consensus pattern (27 bp):
CAAGGGTATTTTGGTAATTTTACAAAT
Found at i:41764860 original size:25 final size:25
Alignment explanation
Indices: 41764832--41764879 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
41764822 CAAAATGTTG
* * *
41764832 ATCGGTATGCTCTCACAAGCTATAA
1 ATCGATATGCTCACACAAACTATAA
41764857 ATCGATATGCTCACACAAACTAT
1 ATCGATATGCTCACACAAACTAT
41764880 GGGTTGGAAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.35, C:0.25, G:0.12, T:0.27
Consensus pattern (25 bp):
ATCGATATGCTCACACAAACTATAA
Found at i:41768163 original size:55 final size:53
Alignment explanation
Indices: 41768036--41768175 Score: 147
Period size: 53 Copynumber: 2.6 Consensus size: 53
41768026 ATTAGGGTTT
* * ** * *
41768036 AAGGATACCAAGTAAGACCATG-CCAAGGCATGGCATTGGTAAGTATTACAAGC
1 AAGGATACCATGTAAGACCATGTCC-AGACATGGCATTGCAAACTACTACAAGC
* * * *
41768089 AAGGAAATCATGTAAGACCATGTCCAGACATGGCATTGACAAACTGCTATAAGGC
1 AAGGATACCATGTAAGACCATGTCCAGACATGGCATTG-CAAACTACTACAA-GC
*
41768144 AAGGATACCATGTAAGACCATGTCAAGACATG
1 AAGGATACCATGTAAGACCATGTCCAGACATG
41768176 ACAATGGTAA
Statistics
Matches: 71, Mismatches: 13, Indels: 4
0.81 0.15 0.05
Matches are distributed among these distances:
53 31 0.44
54 9 0.13
55 31 0.44
ACGTcount: A:0.39, C:0.19, G:0.23, T:0.19
Consensus pattern (53 bp):
AAGGATACCATGTAAGACCATGTCCAGACATGGCATTGCAAACTACTACAAGC
Found at i:41769639 original size:25 final size:25
Alignment explanation
Indices: 41769611--41769683 Score: 110
Period size: 25 Copynumber: 2.9 Consensus size: 25
41769601 CCTCTTTTAA
41769611 TAACTGGGGCAAAGCCCTTTTTGAT
1 TAACTGGGGCAAAGCCCTTTTTGAT
* *
41769636 TAACTGGGGCAAAGCCCTTTTCGGT
1 TAACTGGGGCAAAGCCCTTTTTGAT
* *
41769661 AAACTAGGGCAAAGCCCTTTTTG
1 TAACTGGGGCAAAGCCCTTTTTG
41769684 CACTTCCTTC
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 43 1.00
ACGTcount: A:0.25, C:0.22, G:0.25, T:0.29
Consensus pattern (25 bp):
TAACTGGGGCAAAGCCCTTTTTGAT
Found at i:41769767 original size:21 final size:20
Alignment explanation
Indices: 41769729--41769787 Score: 64
Period size: 21 Copynumber: 2.9 Consensus size: 20
41769719 TATAATGAAT
* *
41769729 ATATCTTGTGCATCTCATCAC
1 ATATCATGT-CATATCATCAC
**
41769750 ATATCATGTACATATCATGTC
1 ATATCATGT-CATATCATCAC
41769771 ATATCATGTCATATCAT
1 ATATCATGTCATATCAT
41769788 GTATATCAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
20 8 0.24
21 25 0.76
ACGTcount: A:0.31, C:0.22, G:0.08, T:0.39
Consensus pattern (20 bp):
ATATCATGTCATATCATCAC
Found at i:41769773 original size:10 final size:10
Alignment explanation
Indices: 41769749--41769795 Score: 78
Period size: 10 Copynumber: 4.7 Consensus size: 10
41769739 CATCTCATCA
41769749 CATATCATGT
1 CATATCATGT
41769759 ACATATCATGT
1 -CATATCATGT
41769770 CATATCATGT
1 CATATCATGT
41769780 CATATCATGT
1 CATATCATGT
41769790 -ATATCA
1 CATATCA
41769796 AAATCTCATG
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
9 6 0.17
10 20 0.56
11 10 0.28
ACGTcount: A:0.34, C:0.19, G:0.09, T:0.38
Consensus pattern (10 bp):
CATATCATGT
Found at i:41771680 original size:10 final size:10
Alignment explanation
Indices: 41771667--41771698 Score: 50
Period size: 9 Copynumber: 3.4 Consensus size: 10
41771657 AAATTTTACC
41771667 AAATTCTCGA
1 AAATTCTCGA
41771677 AAATTC-CGA
1 AAATTCTCGA
41771686 AAATTCT-GA
1 AAATTCTCGA
41771695 AAAT
1 AAAT
41771699 CAGGGTGTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 15 0.71
10 6 0.29
ACGTcount: A:0.47, C:0.16, G:0.09, T:0.28
Consensus pattern (10 bp):
AAATTCTCGA
Found at i:41777686 original size:25 final size:25
Alignment explanation
Indices: 41777658--41777730 Score: 101
Period size: 25 Copynumber: 2.9 Consensus size: 25
41777648 CCTCTTTTAA
41777658 TAACTGGGGCAAAGCCCTTTTTGAT
1 TAACTGGGGCAAAGCCCTTTTTGAT
* * * *
41777683 TAACTGGGTCAAAGCCCTTCTCGGT
1 TAACTGGGGCAAAGCCCTTTTTGAT
*
41777708 AAACTGGGGCAAAGCCCTTTTTG
1 TAACTGGGGCAAAGCCCTTTTTG
41777731 CACTTCCGCC
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 40 1.00
ACGTcount: A:0.23, C:0.23, G:0.25, T:0.29
Consensus pattern (25 bp):
TAACTGGGGCAAAGCCCTTTTTGAT
Found at i:41777812 original size:11 final size:10
Alignment explanation
Indices: 41777796--41777832 Score: 58
Period size: 10 Copynumber: 3.7 Consensus size: 10
41777786 CATCTCATAA
41777796 CATATCATGT
1 CATATCATGT
41777806 GCATATCATGT
1 -CATATCATGT
41777817 CATATCATGT
1 CATATCATGT
41777827 -ATATCA
1 CATATCA
41777833 AAATCTCATG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
9 6 0.23
10 10 0.38
11 10 0.38
ACGTcount: A:0.32, C:0.19, G:0.11, T:0.38
Consensus pattern (10 bp):
CATATCATGT
Found at i:41777820 original size:21 final size:21
Alignment explanation
Indices: 41777762--41777826 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 21
41777752 ACCCAACCCA
* * *
41777762 TGCATATAATGAATATATCTTG
1 TGCATATCAT-AACATATCATG
*
41777784 TGCATCTCATAACATATCATG
1 TGCATATCATAACATATCATG
**
41777805 TGCATATCATGTCATATCATG
1 TGCATATCATAACATATCATG
41777826 T
1 T
41777827 ATATCAAAAT
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
21 28 0.78
22 8 0.22
ACGTcount: A:0.32, C:0.17, G:0.12, T:0.38
Consensus pattern (21 bp):
TGCATATCATAACATATCATG
Found at i:41786129 original size:53 final size:53
Alignment explanation
Indices: 41786066--41786168 Score: 170
Period size: 53 Copynumber: 1.9 Consensus size: 53
41786056 GTTAGAGTGC
* * *
41786066 GAATTTGATGTTGTCGTACGTAAATAAATGATCAGCATGTCATTAAACATTGG
1 GAATTTGATGTTGCCATACGTAAATAAATGATCAGCATGTCATAAAACATTGG
*
41786119 GAATTTGATGTTGCCATAGGTAAATAAATGATCAGCATGTCATAAAACAT
1 GAATTTGATGTTGCCATACGTAAATAAATGATCAGCATGTCATAAAACAT
41786169 AAGAATTAGG
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
53 46 1.00
ACGTcount: A:0.37, C:0.12, G:0.19, T:0.32
Consensus pattern (53 bp):
GAATTTGATGTTGCCATACGTAAATAAATGATCAGCATGTCATAAAACATTGG
Found at i:41786798 original size:53 final size:53
Alignment explanation
Indices: 41786700--41786804 Score: 122
Period size: 53 Copynumber: 2.0 Consensus size: 53
41786690 ATAAACTACG
* * * *
41786700 ATAAGGCAAAGATCCCATGTAAGACCATGCCAAGGAATGGCAATGGTGAGTTC
1 ATAAGGCAAAGATACCACGTAAGACCATGCCAAGGAATGGAAATGGTCAGTTC
* * * *
41786753 ATAAGGCAAGGATATCACGTAAGACCCTGTCAA-GACATGGAAATGGTCAGTT
1 ATAAGGCAAAGATACCACGTAAGACCATGCCAAGGA-ATGGAAATGGTCAGTT
41786805 TAAAAAGGAA
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
52 2 0.05
53 41 0.95
ACGTcount: A:0.36, C:0.18, G:0.26, T:0.20
Consensus pattern (53 bp):
ATAAGGCAAAGATACCACGTAAGACCATGCCAAGGAATGGAAATGGTCAGTTC
Found at i:41800873 original size:17 final size:17
Alignment explanation
Indices: 41800851--41800883 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
41800841 GTTTTTTTTA
41800851 TTAAAGGATT-GAATTGG
1 TTAAAGG-TTAGAATTGG
41800868 TTAAAGGTTAGAATTG
1 TTAAAGGTTAGAATTG
41800884 ATAGGGAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 2 0.13
17 13 0.87
ACGTcount: A:0.36, C:0.00, G:0.27, T:0.36
Consensus pattern (17 bp):
TTAAAGGTTAGAATTGG
Found at i:41805019 original size:62 final size:62
Alignment explanation
Indices: 41804922--41805047 Score: 243
Period size: 62 Copynumber: 2.0 Consensus size: 62
41804912 CCTAACACGA
41804922 TTCAAATGATACAACAATTTGTTCAATTTAATGGTTTGCAGGATGAGGATCCAAACAATCAC
1 TTCAAATGATACAACAATTTGTTCAATTTAATGGTTTGCAGGATGAGGATCCAAACAATCAC
*
41804984 TTCAAATGATACAACAATTTGTTCAATTTGATGGTTTGCAGGATGAGGATCCAAACAATCAC
1 TTCAAATGATACAACAATTTGTTCAATTTAATGGTTTGCAGGATGAGGATCCAAACAATCAC
41805046 TT
1 TT
41805048 GGCGAATTTT
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
62 63 1.00
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.32
Consensus pattern (62 bp):
TTCAAATGATACAACAATTTGTTCAATTTAATGGTTTGCAGGATGAGGATCCAAACAATCAC
Found at i:41809763 original size:21 final size:20
Alignment explanation
Indices: 41809739--41809781 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
41809729 ATAGGAGAGT
*
41809739 AAAAAGAGTGAAAAATGGGCC
1 AAAAAGAGAG-AAAATGGGCC
*
41809760 AAAAATAGAGAAAATGGGCC
1 AAAAAGAGAGAAAATGGGCC
41809780 AA
1 AA
41809782 CATGGGAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.56, C:0.09, G:0.26, T:0.09
Consensus pattern (20 bp):
AAAAAGAGAGAAAATGGGCC
Found at i:41811177 original size:52 final size:53
Alignment explanation
Indices: 41811094--41811288 Score: 167
Period size: 52 Copynumber: 3.6 Consensus size: 53
41811084 TTCCTTTTTA
* * * * *
41811094 AACTTACCATTGCCATGTCTTGACATGGTCTTGCGTGGTATCTTTG-CTTATG
1 AACTCACCATTGCCATGCCTTGACATGGTCTTACATGGGATCTTTGCCTTATG
41811146 AACTCACCATTGCCATGCCTTGACATGGTCTTACATGGGATCTTTGCCTTATCG
1 AACTCACCATTGCCATGCCTTGACATGGTCTTACATGGGATCTTTGCCTTAT-G
** * * * * * *** * * *
41811200 TAGTTTATCAATGCCATGTCTTGACATGGTCTTACAAGATTTCCTTGCCTTGTAA
1 -AACTCACCATTGCCATGCCTTGACATGGTCTTACATGGGATCTTTGCCTTAT-G
* * *
41811255 AACTTACCAATGCCATGCCTTGGCATGGTCTTAC
1 AACTCACCATTGCCATGCCTTGACATGGTCTTAC
41811289 TTGGTATCCT
Statistics
Matches: 116, Mismatches: 24, Indels: 4
0.81 0.17 0.03
Matches are distributed among these distances:
52 41 0.35
53 5 0.04
54 30 0.26
55 40 0.34
ACGTcount: A:0.21, C:0.24, G:0.18, T:0.36
Consensus pattern (53 bp):
AACTCACCATTGCCATGCCTTGACATGGTCTTACATGGGATCTTTGCCTTATG
Found at i:41811404 original size:23 final size:23
Alignment explanation
Indices: 41811374--41811420 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
41811364 TCATTTCTCC
41811374 ATCAATTCTTGCTTGAATCATTA
1 ATCAATTCTTGCTTGAATCATTA
*
41811397 ATCAATTCTTTCTTGAATCATTA
1 ATCAATTCTTGCTTGAATCATTA
41811420 A
1 A
41811421 GGAATAAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.32, C:0.17, G:0.06, T:0.45
Consensus pattern (23 bp):
ATCAATTCTTGCTTGAATCATTA
Found at i:41813245 original size:45 final size:44
Alignment explanation
Indices: 41813170--41813335 Score: 181
Period size: 45 Copynumber: 3.7 Consensus size: 44
41813160 ATGGTTGAAG
** * * * * *
41813170 GATGCCATAGTGTCTTTTAG-TCATGATCTTATTCGTCTAATTCAT
1 GATGCCATAACGTCTTTCAGCT-ATGGTCTTACTCGT-TAAATCGT
* *
41813215 GATGCCATAGCGTCTTTCAGCTATGGTCTTACTCATTAGAATCGT
1 GATGCCATAACGTCTTTCAGCTATGGTCTTACTCGTTA-AATCGT
*
41813260 GATGCCATAACGTCTTTTAGCTATGGTCTTACTCGTTAAAATCGT
1 GATGCCATAACGTCTTTCAGCTATGGTCTTACTCGTT-AAATCGT
* *
41813305 GATGACATAACGTCTTTCAGCTATAGTCTTA
1 GATGCCATAACGTCTTTCAGCTATGGTCTTA
41813336 TTCAGTCCCG
Statistics
Matches: 105, Mismatches: 13, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
44 2 0.02
45 101 0.96
46 2 0.02
ACGTcount: A:0.24, C:0.20, G:0.17, T:0.39
Consensus pattern (44 bp):
GATGCCATAACGTCTTTCAGCTATGGTCTTACTCGTTAAATCGT
Found at i:41813323 original size:90 final size:90
Alignment explanation
Indices: 41813170--41813335 Score: 219
Period size: 90 Copynumber: 1.8 Consensus size: 90
41813160 ATGGTTGAAG
** * * * *
41813170 GATGCCATAGTGTCTTTTAGTCATGATCTTATTCGTCTAATTCATGATGCCATAGCGTCTTTCAG
1 GATGCCATAACGTCTTTTAGTCATGATCTTACTCGTCTAAATCATGATGACATAACGTCTTTCAG
*
41813235 CTATGGTCTTACTCATTAGAATCGT
66 CTATAGTCTTACTCATTAGAATCGT
* *
41813260 GATGCCATAACGTCTTTTAG-CTATGGTCTTACTCGT-TAAAATCGTGATGACATAACGTCTTTC
1 GATGCCATAACGTCTTTTAGTC-ATGATCTTACTCGTCT-AAATCATGATGACATAACGTCTTTC
41813323 AGCTATAGTCTTA
64 AGCTATAGTCTTA
41813336 TTCAGTCCCG
Statistics
Matches: 65, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
89 2 0.03
90 63 0.97
ACGTcount: A:0.24, C:0.20, G:0.17, T:0.39
Consensus pattern (90 bp):
GATGCCATAACGTCTTTTAGTCATGATCTTACTCGTCTAAATCATGATGACATAACGTCTTTCAG
CTATAGTCTTACTCATTAGAATCGT
Done.