Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 ID=Chr13-JGI_221_v2.0
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: 58321163
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 747533 characters in sequence are not A, C, G, or T
File 147 of 199
Found at i:44195433 original size:71 final size:71
Alignment explanation
Indices: 44195317--44195459 Score: 207
Period size: 71 Copynumber: 2.0 Consensus size: 71
44195307 TGAACAAGGG
* ** * *
44195317 GAAATTGTTATAGCCCTACCTTAAGGATGACACGTGGCAGAACGAATGACAACCTGACAAGAGCC
1 GAAATTGTTATACCCCTACCCCAAGGATGACACATGGCAGAACGAATGACAACCTGACAAGAACC
44195382 CAGGTA
66 CAGGTA
* *
44195388 GAAATTGTTATACCCCTACCCCAAGGATGACACATGGC-GAAACGAATGACGACCTGACAATAAC
1 GAAATTGTTATACCCCTACCCCAAGGATGACACATGGCAG-AACGAATGACAACCTGACAAGAAC
44195452 CCAGGTA
65 CCAGGTA
44195459 G
1 G
44195460 GCCCCCTAGT
Statistics
Matches: 64, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
70 1 0.02
71 63 0.98
ACGTcount: A:0.36, C:0.24, G:0.22, T:0.17
Consensus pattern (71 bp):
GAAATTGTTATACCCCTACCCCAAGGATGACACATGGCAGAACGAATGACAACCTGACAAGAACC
CAGGTA
Found at i:44200239 original size:8 final size:8
Alignment explanation
Indices: 44200226--44200264 Score: 51
Period size: 8 Copynumber: 4.8 Consensus size: 8
44200216 GTTTCTTTGC
44200226 TTGCTTAG
1 TTGCTTAG
44200234 TTGCTTAG
1 TTGCTTAG
* *
44200242 TTTCTTTG
1 TTGCTTAG
44200250 TTTGCTTAG
1 -TTGCTTAG
44200259 TTGCTT
1 TTGCTT
44200265 CAATTATCTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
8 20 0.77
9 6 0.23
ACGTcount: A:0.08, C:0.13, G:0.21, T:0.59
Consensus pattern (8 bp):
TTGCTTAG
Found at i:44200247 original size:25 final size:25
Alignment explanation
Indices: 44200213--44200264 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
44200203 TATATACGAG
44200213 TTAGTTTCTTTGCTTGCTTAGTTGC
1 TTAGTTTCTTTGCTTGCTTAGTTGC
*
44200238 TTAGTTTCTTTGTTTGCTTAGTTGC
1 TTAGTTTCTTTGCTTGCTTAGTTGC
44200263 TT
1 TT
44200265 CAATTATCTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.08, C:0.13, G:0.19, T:0.60
Consensus pattern (25 bp):
TTAGTTTCTTTGCTTGCTTAGTTGC
Found at i:44202572 original size:15 final size:15
Alignment explanation
Indices: 44202535--44202586 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 15
44202525 TTAAATTAAG
* **
44202535 TTAATTAATAAAAAT
1 TTAATTAATTAAACC
* *
44202550 TTATTTAATTAAGCC
1 TTAATTAATTAAACC
*
44202565 TTAATTAATTAAATC
1 TTAATTAATTAAACC
44202580 TTAATTA
1 TTAATTA
44202587 CAATTAACCA
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.46, C:0.06, G:0.02, T:0.46
Consensus pattern (15 bp):
TTAATTAATTAAACC
Found at i:44209835 original size:66 final size:66
Alignment explanation
Indices: 44209715--44209848 Score: 146
Period size: 66 Copynumber: 2.0 Consensus size: 66
44209705 ATTTTGAAGC
* * * *** * *
44209715 TGTAGCTGGAGTTCGTCATATTTTCTTATTGCCTCTACTTCCCTTGTTGTTGCC-TCTGCTTTAA
1 TGTAGCTGGAGTTCATCATACTTTCTTATAGCCTCTACTTCCCTCAATGCTGCCTTC-ACTTTAA
44209779 GT
65 GT
* *
44209781 TGTAGCTGGAGTTCATCATACTTTCTT-TGAGCCTCTATTTCTCTCAATGCTGCCTTCACTTTAA
1 TGTAGCTGGAGTTCATCATACTTTCTTAT-AGCCTCTACTTCCCTCAATGCTGCCTTCACTTTAA
44209845 GT
65 GT
44209847 TG
1 TG
44209849 AGCAATTTGC
Statistics
Matches: 56, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
65 1 0.02
66 53 0.95
67 2 0.04
ACGTcount: A:0.15, C:0.23, G:0.17, T:0.45
Consensus pattern (66 bp):
TGTAGCTGGAGTTCATCATACTTTCTTATAGCCTCTACTTCCCTCAATGCTGCCTTCACTTTAAG
T
Found at i:44212585 original size:24 final size:24
Alignment explanation
Indices: 44212555--44212637 Score: 107
Period size: 24 Copynumber: 3.4 Consensus size: 24
44212545 CTAACCATTC
44212555 ATGAAAAGATTCTATGAATAACTT
1 ATGAAAAGATTCTATGAATAACTT
* *
44212579 ATTAAAAGATTC-ATGAA-AAGATT
1 ATGAAAAGATTCTATGAATAA-CTT
44212602 CATGAAAAGATTCTATGAATAACTT
1 -ATGAAAAGATTCTATGAATAACTT
44212627 ATGAACAAGAT
1 ATGAA-AAGAT
44212638 CTCAAGACTT
Statistics
Matches: 50, Mismatches: 4, Indels: 9
0.79 0.06 0.14
Matches are distributed among these distances:
22 2 0.04
23 7 0.14
24 27 0.54
25 12 0.24
26 2 0.04
ACGTcount: A:0.48, C:0.08, G:0.13, T:0.30
Consensus pattern (24 bp):
ATGAAAAGATTCTATGAATAACTT
Found at i:44212599 original size:12 final size:12
Alignment explanation
Indices: 44212551--44212620 Score: 81
Period size: 12 Copynumber: 5.8 Consensus size: 12
44212541 TACCCTAACC
44212551 ATTCATGAAAAG
1 ATTCATGAAAAG
44212563 ATTCTATGAATAA-
1 ATTC-ATGAA-AAG
* *
44212576 CTT-ATTAAAAG
1 ATTCATGAAAAG
44212587 ATTCATGAAAAG
1 ATTCATGAAAAG
44212599 ATTCATGAAAAG
1 ATTCATGAAAAG
44212611 ATTCTATGAA
1 ATTC-ATGAA
44212621 TAACTTATGA
Statistics
Matches: 49, Mismatches: 4, Indels: 9
0.79 0.06 0.15
Matches are distributed among these distances:
10 2 0.04
11 6 0.12
12 27 0.55
13 12 0.24
14 2 0.04
ACGTcount: A:0.47, C:0.09, G:0.13, T:0.31
Consensus pattern (12 bp):
ATTCATGAAAAG
Found at i:44213932 original size:191 final size:193
Alignment explanation
Indices: 44213596--44213982 Score: 665
Period size: 191 Copynumber: 2.0 Consensus size: 193
44213586 GGGGATGAAG
* *
44213596 GTCACGTCGAATTCCCATGTCAACTAGATCAAGTCAAATTTAAAGATTGTCTTTCAATTTTCTAT
1 GTCACATCGAATTCCCATGTCAACTAGATCAAGTCAAATCTAAAGATTGTCTTTCAATTTTCTAT
*
44213661 CGACATTTAGAATTGTCCCGATGATGTTCTCGCAAGCATTCTTTTCAATATGCATGACATCAAGA
66 CGACATTTAGAATTGTCCCGATGATGTTCTCGCAAACATTCTTTTCAATATGCATGACATCAAGA
44213726 TTGTGTCGCAAAATGTGATGC-TCTTAATAAGGTAACTCAAAAAAA-AC-T-TTTTTTTCCACAA
131 TTGTGTCGCAAAATGTGATGCTTC-TAATAAGGTAACT-AAAAAAATACTTCTTTTTTTCCACAA
* *
44213787 GTCACATCGAATTCCCATGTCAACTAGATCAAGTCAACTCTGAAGATTGTCTTTCAATTTTCTAT
1 GTCACATCGAATTCCCATGTCAACTAGATCAAGTCAAATCTAAAGATTGTCTTTCAATTTTCTAT
*
44213852 CGACATTTAGAATTGTCCCGATGATGTTCTTGCAAACATTCTTTTCAATATGCATGACATCAAGA
66 CGACATTTAGAATTGTCCCGATGATGTTCTCGCAAACATTCTTTTCAATATGCATGACATCAAGA
*
44213917 TTGTGTCGTAAAATGTGATGCTTCTAATAAGGTAACTAAAAAAATACTTCTTTTTTTCCACAA
131 TTGTGTCGCAAAATGTGATGCTTCTAATAAGGTAACTAAAAAAATACTTCTTTTTTTCCACAA
44213980 GTC
1 GTC
44213983 TGCCTCATTA
Statistics
Matches: 185, Mismatches: 7, Indels: 6
0.93 0.04 0.03
Matches are distributed among these distances:
190 7 0.04
191 159 0.86
192 3 0.02
193 16 0.09
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.35
Consensus pattern (193 bp):
GTCACATCGAATTCCCATGTCAACTAGATCAAGTCAAATCTAAAGATTGTCTTTCAATTTTCTAT
CGACATTTAGAATTGTCCCGATGATGTTCTCGCAAACATTCTTTTCAATATGCATGACATCAAGA
TTGTGTCGCAAAATGTGATGCTTCTAATAAGGTAACTAAAAAAATACTTCTTTTTTTCCACAA
Found at i:44217811 original size:23 final size:23
Alignment explanation
Indices: 44217781--44217827 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
44217771 ATGTGTTTAG
44217781 GAGATCTACAATACTTTGTCGAT
1 GAGATCTACAATACTTTGTCGAT
44217804 GAGATCTACAATACTTTGTCGAT
1 GAGATCTACAATACTTTGTCGAT
44217827 G
1 G
44217828 CCCCAAGATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (23 bp):
GAGATCTACAATACTTTGTCGAT
Found at i:44219001 original size:6 final size:6
Alignment explanation
Indices: 44218959--44219040 Score: 58
Period size: 6 Copynumber: 13.7 Consensus size: 6
44218949 TCTTCTCTCT
* * * * **
44218959 TTTTCA TTTTCA TTTTGA CTTTGA CTTTGA TTTTGA TTTTGA TTTTTC
1 TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA
* * * *
44219007 TTCTT-T TTTTGT TTTTGA TCTTGA TTTTGC TTTT
1 TT-TTGA TTTTGA TTTTGA TTTTGA TTTTGA TTTT
44219041 TTTTTTGTGC
Statistics
Matches: 64, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
5 2 0.03
6 60 0.94
7 2 0.03
ACGTcount: A:0.11, C:0.10, G:0.11, T:0.68
Consensus pattern (6 bp):
TTTTGA
Found at i:44219023 original size:30 final size:30
Alignment explanation
Indices: 44218984--44219048 Score: 94
Period size: 30 Copynumber: 2.2 Consensus size: 30
44218974 TGACTTTGAC
* * *
44218984 TTTGATTTTGATTTTGATTTTTCTTCTTTT
1 TTTGTTTTTGATCTTGATTTTGCTTCTTTT
*
44219014 TTTGTTTTTGATCTTGATTTTGCTTTTTTT
1 TTTGTTTTTGATCTTGATTTTGCTTCTTTT
44219044 TTTGT
1 TTTGT
44219049 GCTTGAATCT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.08, C:0.06, G:0.12, T:0.74
Consensus pattern (30 bp):
TTTGTTTTTGATCTTGATTTTGCTTCTTTT
Found at i:44227323 original size:59 final size:59
Alignment explanation
Indices: 44227260--44227394 Score: 225
Period size: 59 Copynumber: 2.3 Consensus size: 59
44227250 TATGATTATC
* *
44227260 ATTATTATGAAATATGATTATTTATTTAATTAATCGAAAATTAATTAATTATTCATAAA
1 ATTATTATGAAATATGATTATTTATTTAATAAATCAAAAATTAATTAATTATTCATAAA
* * *
44227319 ATTATTATGAAATATGATTATTTATTTAATAAATTAAAAATTAATTAATTATTCGTATA
1 ATTATTATGAAATATGATTATTTATTTAATAAATCAAAAATTAATTAATTATTCATAAA
44227378 ATTATTATGAAATATGA
1 ATTATTATGAAATATGA
44227395 CCCAGCTTTT
Statistics
Matches: 71, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
59 71 1.00
ACGTcount: A:0.46, C:0.02, G:0.06, T:0.46
Consensus pattern (59 bp):
ATTATTATGAAATATGATTATTTATTTAATAAATCAAAAATTAATTAATTATTCATAAA
Found at i:44231039 original size:41 final size:41
Alignment explanation
Indices: 44230994--44231087 Score: 109
Period size: 41 Copynumber: 2.3 Consensus size: 41
44230984 TTCCTCTACC
** * *
44230994 TTTTGCGGCATTTATGTGAAAAACGCCACTATTGCTTTATA
1 TTTTGCGGCATTTATAAGAAAAACGCCACTAGTGCTGTATA
* * *
44231035 TTTTGCGGCGTTTATAAGAAAAATGCCACTAGTGGTGTATA
1 TTTTGCGGCATTTATAAGAAAAACGCCACTAGTGCTGTATA
*
44231076 -TTTGCGGTATTT
1 TTTTGCGGCATTT
44231088 TCAGTCAAAA
Statistics
Matches: 44, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
40 10 0.23
41 34 0.77
ACGTcount: A:0.26, C:0.14, G:0.21, T:0.39
Consensus pattern (41 bp):
TTTTGCGGCATTTATAAGAAAAACGCCACTAGTGCTGTATA
Found at i:44237482 original size:14 final size:13
Alignment explanation
Indices: 44237459--44237490 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
44237449 TTTCTAAATT
44237459 ATACAAAAATATG
1 ATACAAAAATATG
44237472 ATACAAAAA-AT-
1 ATACAAAAATATG
44237483 ATACAAAA
1 ATACAAAA
44237491 TAACGCATGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 8 0.42
12 2 0.11
13 9 0.47
ACGTcount: A:0.69, C:0.09, G:0.03, T:0.19
Consensus pattern (13 bp):
ATACAAAAATATG
Found at i:44237486 original size:11 final size:12
Alignment explanation
Indices: 44237454--44237490 Score: 51
Period size: 11 Copynumber: 3.2 Consensus size: 12
44237444 TTTATTTTCT
44237454 AAAT-TATACAA
1 AAATATATACAA
44237465 AAATATGATACAA
1 AAATAT-ATACAA
44237478 AAA-ATATACAA
1 AAATATATACAA
44237489 AA
1 AA
44237491 TAACGCATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 12 0.50
12 3 0.12
13 9 0.38
ACGTcount: A:0.68, C:0.08, G:0.03, T:0.22
Consensus pattern (12 bp):
AAATATATACAA
Found at i:44249425 original size:15 final size:15
Alignment explanation
Indices: 44249405--44249439 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
44249395 CGTCTTTCTC
44249405 CTCTTTTCTTTCTTT
1 CTCTTTTCTTTCTTT
44249420 CTCTTTTCTTTCTTT
1 CTCTTTTCTTTCTTT
44249435 -TCTTT
1 CTCTTT
44249440 CCTATTTAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 5 0.25
15 15 0.75
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (15 bp):
CTCTTTTCTTTCTTT
Found at i:44261911 original size:16 final size:16
Alignment explanation
Indices: 44261890--44261938 Score: 89
Period size: 16 Copynumber: 3.1 Consensus size: 16
44261880 TTCGCTGTAT
44261890 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
44261906 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
*
44261922 TGGAATAGAGACGTAA
1 TGGAATAGAGGCGTAA
44261938 T
1 T
44261939 AGCAAATCAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.39, C:0.06, G:0.35, T:0.20
Consensus pattern (16 bp):
TGGAATAGAGGCGTAA
Found at i:44262189 original size:16 final size:16
Alignment explanation
Indices: 44262152--44262193 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
44262142 TTAATCATAT
*
44262152 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
44262168 TT-AAATATATTATAA
1 TTAAAATATATTATAA
44262183 TTAAAATATAT
1 TTAAAATATAT
44262194 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:44262200 original size:14 final size:15
Alignment explanation
Indices: 44262161--44262202 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
44262151 TTTAAACATA
*
44262161 ATTATTATTAAATAT
1 ATTATAATTAAATAT
44262176 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
44262190 A-TATAATTTAATA
1 ATTATAATTAAATA
44262203 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:44262252 original size:61 final size:60
Alignment explanation
Indices: 44262187--44262507 Score: 229
Period size: 61 Copynumber: 5.3 Consensus size: 60
44262177 TTATAATTAA
44262187 AATATATAAT-TTAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTCAAATCAT
1 AATATATAATATT-ATAAAATTCTTAATAATCAATATTCTTATATGAATTTACT-AAATCAT
* * * * * * * *
44262248 AATATATGATACTATAAAATATAATTTAA-CAT-AATAATTATTAAAT--ATATTA-T-AATTAA
1 AATATATAATATTATAAAAT-T--CTTAATAATCAAT-ATTCTTATATGAAT-TTACTAAATCAT
*
44262307 AATATATAAT-TTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCAT
1 AATATATAATATT-ATAAAATTCTTAATAATCAATATTCTTATATGAATTTACT-AAATCAT
* * * * * * * * *
44262368 AATATATGATACTATAAAA-T-ATAATTTAA-C-ATAATTATTAT-TAAATATATTATAATTAA
1 AATATATAATATTATAAAATTCTTAA--TAATCAAT-ATTCTTATATGAATTTACTA-AATCAT
*
44262427 AATATATAAT-TTAATAAAAGTCTTAATAATCAATATTCTTATATGAATTTACTAAAGTCAT
1 AATATATAATATT-ATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTAAA-TCAT
*
44262488 AATATATGATATTATAAAAT
1 AATATATAATATTATAAAAT
44262508 ATAATTTAAA
Statistics
Matches: 196, Mismatches: 37, Indels: 54
0.68 0.13 0.19
Matches are distributed among these distances:
56 4 0.02
57 10 0.05
58 10 0.05
59 57 0.29
60 19 0.10
61 71 0.36
62 11 0.06
63 10 0.05
64 4 0.02
ACGTcount: A:0.49, C:0.06, G:0.02, T:0.42
Consensus pattern (60 bp):
AATATATAATATTATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTAAATCAT
Found at i:44262368 original size:120 final size:120
Alignment explanation
Indices: 44262150--44262546 Score: 690
Period size: 120 Copynumber: 3.3 Consensus size: 120
44262140 ACTTAATCAT
*
44262150 ATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
1 ATTT-AACATAATAATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
44262215 ATCAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATA
65 ATCAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATA
44262271 ATTTAACATAATAATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAA
1 ATTTAACATAATAATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAA
*
44262336 TTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATA
66 TCAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATA
* *
44262391 ATTTAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAAGTCTTAATAA
1 ATTTAACATAATAATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAA
*
44262456 TCAATATTCTTATATGAATTTACT-AAAGTCATAATATATGATATTATAAAATATA
66 TCAATATTCTTATATGAATTTACTCAAA-TCATAATATATGATACTATAAAATATA
* *
44262511 ATTTAAAATAATTAA-TATTAAATATATTTTAATTAA
1 ATTTAACATAA-TAATTATTAAATATATTATAATTAA
44262547 TATTAAATAG
Statistics
Matches: 265, Mismatches: 9, Indels: 5
0.95 0.03 0.02
Matches are distributed among these distances:
119 3 0.01
120 256 0.97
121 6 0.02
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (120 bp):
ATTTAACATAATAATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAA
TCAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATA
Found at i:44262431 original size:16 final size:16
Alignment explanation
Indices: 44262387--44262433 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
44262377 TACTATAAAA
*
44262387 TATAATTTAACATA-AT
1 TATAA-TTAAAATATAT
*
44262403 TATTATT-AAATATAT
1 TATAATTAAAATATAT
44262418 TATAATTAAAATATAT
1 TATAATTAAAATATAT
44262434 AATTTAATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
14 4 0.15
15 10 0.38
16 12 0.46
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (16 bp):
TATAATTAAAATATAT
Found at i:44262493 original size:59 final size:57
Alignment explanation
Indices: 44262190--44262493 Score: 164
Period size: 59 Copynumber: 5.1 Consensus size: 57
44262180 TAATTAAAAT
44262190 ATATAATTTAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTCAAATCATA
1 ATATAATTTAATAAAA-TCTTAATAATCAATATTCTTATATGAATTTACT-AAATCATA
* * * * *
44262249 ATAT-ATGATACTATAAAAT-ATAATTTAA-CATAATAATTATTAAAT-ATATTATAATTAAA--
1 ATATAAT-TTA--ATAAAATCTTAA--TAATC--AAT-ATTCTTATATGA-ATT-T-ACTAAATC
44262308 AT-
55 ATA
*
44262310 ATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCATA
1 ATATAATTTAATAAAA-TCTTAATAATCAATATTCTTATATGAATTTACT-AAATCATA
* * * * * * * *
44262369 ATAT-ATGATACTATAAAAT-ATAATTTAA-C-ATAATTATTAT-TAAATATATTATAATTAAAA
1 ATATAAT-TTA--ATAAAATCTTAA--TAATCAAT-ATTCTTATATGAATTTACTA-AA-TCATA
44262429 TATATAATTTAATAAAAGTCTTAATAATCAATATTCTTATATGAATTTACTAAAGTCATA
1 -ATATAATTTAATAAAA-TCTTAATAATCAATATTCTTATATGAATTTACTAAA-TCATA
44262489 ATATA
1 ATATA
44262494 TGATATTATA
Statistics
Matches: 181, Mismatches: 29, Indels: 70
0.65 0.10 0.25
Matches are distributed among these distances:
55 2 0.01
56 4 0.02
57 11 0.06
58 11 0.06
59 52 0.29
60 28 0.15
61 46 0.25
62 10 0.06
63 11 0.06
64 4 0.02
65 2 0.01
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.42
Consensus pattern (57 bp):
ATATAATTTAATAAAATCTTAATAATCAATATTCTTATATGAATTTACTAAATCATA
Found at i:44267361 original size:49 final size:49
Alignment explanation
Indices: 44267214--44267365 Score: 171
Period size: 49 Copynumber: 3.0 Consensus size: 49
44267204 ACTCGTCCAT
* * *
44267214 CTGAAACACCATTTATGGGCAAGCCACCATTGGTTTGTAGATAAACTACCA
1 CTGAAACA-C-TTTATGGACAAGCCACCATTGATTTGCAGATAAACTACCA
* * * * *
44267265 CTGATAACACTTTGTGGACAAGACACCATTGATATACAGATATACTACCA
1 CTGA-AACACTTTATGGACAAGCCACCATTGATTTGCAGATAAACTACCA
* *
44267315 CTGAAACACTTTATGGACAAGCCACC-TCTAATTTGCAAATAAACTACCA
1 CTGAAACACTTTATGGACAAGCCACCAT-TGATTTGCAGATAAACTACCA
44267364 CT
1 CT
44267366 TACTTCCATC
Statistics
Matches: 84, Mismatches: 15, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
48 1 0.01
49 38 0.45
50 36 0.43
51 5 0.06
52 4 0.05
ACGTcount: A:0.36, C:0.24, G:0.14, T:0.26
Consensus pattern (49 bp):
CTGAAACACTTTATGGACAAGCCACCATTGATTTGCAGATAAACTACCA
Found at i:44268694 original size:30 final size:31
Alignment explanation
Indices: 44268658--44268716 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
44268648 GTAAATACTC
* **
44268658 AAAAATTTGAGGGATTAA-AGTGCAAATAAG
1 AAAAATTTGAAGGACCAATAGTGCAAATAAG
44268688 AAAAATTTGAAGGACCAATAGTGCAAATA
1 AAAAATTTGAAGGACCAATAGTGCAAATA
44268717 TTTTAAGGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 15 0.60
31 10 0.40
ACGTcount: A:0.51, C:0.07, G:0.20, T:0.22
Consensus pattern (31 bp):
AAAAATTTGAAGGACCAATAGTGCAAATAAG
Found at i:44268994 original size:8 final size:8
Alignment explanation
Indices: 44268981--44269009 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
44268971 TTTTAAATGA
44268981 TATTTTAT
1 TATTTTAT
44268989 TATTTTAT
1 TATTTTAT
44268997 TATTTTAT
1 TATTTTAT
44269005 TATTT
1 TATTT
44269010 AGTATATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (8 bp):
TATTTTAT
Found at i:44270158 original size:2 final size:2
Alignment explanation
Indices: 44270151--44270192 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
44270141 ATGAGGAGGA
44270151 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
44270193 GAATATTCAG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:44275672 original size:39 final size:40
Alignment explanation
Indices: 44275598--44275673 Score: 102
Period size: 39 Copynumber: 1.9 Consensus size: 40
44275588 TATCTGTATT
* *
44275598 CTGTATCTGGTATGGGCCAAGGCCCTAATGTATTCTGATA
1 CTGTATCTGGAATGGGCCAAGGCCCAAATGTATTCTGATA
*
44275638 CTGTATCT-GAATGGGCTAAGGCCCAAACTG-ATTCTG
1 CTGTATCTGGAATGGGCCAAGGCCCAAA-TGTATTCTG
44275674 TTATGGGCAC
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
39 22 0.69
40 10 0.31
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.30
Consensus pattern (40 bp):
CTGTATCTGGAATGGGCCAAGGCCCAAATGTATTCTGATA
Found at i:44287351 original size:21 final size:20
Alignment explanation
Indices: 44287318--44287361 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
44287308 GCTTCAGTTG
* *
44287318 AAAACCCCGAACCCTTTTAGA
1 AAAACCCCAAACCCTATTA-A
*
44287339 AAAACCCTAAACCCTATTAA
1 AAAACCCCAAACCCTATTAA
44287359 AAA
1 AAA
44287362 CACTAATATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.48, C:0.30, G:0.05, T:0.18
Consensus pattern (20 bp):
AAAACCCCAAACCCTATTAA
Found at i:44287386 original size:17 final size:16
Alignment explanation
Indices: 44287353--44287397 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
44287343 CCCTAAACCC
* *
44287353 TATTAAAAACACT-AA
1 TATTAAAAATATTAAA
44287368 TATTAAAAAATATTAAA
1 TATT-AAAAATATTAAA
44287385 TATTAAAAATATT
1 TATTAAAAATATT
44287398 TAAACCCAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
15 4 0.15
16 16 0.62
17 6 0.23
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (16 bp):
TATTAAAAATATTAAA
Found at i:44287401 original size:17 final size:17
Alignment explanation
Indices: 44287366--44287397 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
44287356 TAAAAACACT
44287366 AATATTAAAAAATATTA
1 AATATTAAAAAATATTA
44287383 AATATT-AAAAATATT
1 AATATTAAAAAATATT
44287398 TAAACCCAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
AATATTAAAAAATATTA
Found at i:44310224 original size:49 final size:49
Alignment explanation
Indices: 44310151--44310254 Score: 154
Period size: 49 Copynumber: 2.1 Consensus size: 49
44310141 TCATGTGTTA
* * *
44310151 TAATTTTATAAAGTGTTGAGCTTTTAATTTATGATATTGAACTTAATTT
1 TAATTTTATAAAGTATTGAGCTTTTAATTCATGATATTAAACTTAATTT
* * *
44310200 TAATTTTGTAAAGTATTGATCTTTTGATTCATGATATTAAACTTAATTT
1 TAATTTTATAAAGTATTGAGCTTTTAATTCATGATATTAAACTTAATTT
44310249 TAATTT
1 TAATTT
44310255 ATTTTTTTAA
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
49 49 1.00
ACGTcount: A:0.33, C:0.05, G:0.11, T:0.52
Consensus pattern (49 bp):
TAATTTTATAAAGTATTGAGCTTTTAATTCATGATATTAAACTTAATTT
Found at i:44311655 original size:21 final size:21
Alignment explanation
Indices: 44311614--44311656 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
44311604 AATAAAGTAG
*
44311614 ATTATATATTATTTTTATAGT
1 ATTATATATTATATTTATAGT
44311635 ATTATATATTATGATTT-TAGT
1 ATTATATATTAT-ATTTATAGT
44311656 A
1 A
44311657 AATTCAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 17 0.85
22 3 0.15
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.58
Consensus pattern (21 bp):
ATTATATATTATATTTATAGT
Found at i:44311735 original size:29 final size:27
Alignment explanation
Indices: 44311673--44311808 Score: 90
Period size: 26 Copynumber: 5.1 Consensus size: 27
44311663 AATAAGAATA
*
44311673 ATTATATTAAGAATTTTATTAAATTAT
1 ATTATAATAAGAATTTTATTAAATTAT
*
44311700 ATT-TAATAATAATTATT-TTAAATTAT
1 ATTATAATAAGAATT-TTATTAAATTAT
* * *
44311726 ATT-TTATAA-TATTATATATT--ATGAT
1 ATTATAATAAGAATT-T-TATTAAATTAT
* *
44311751 TTTAGTAATTAAGATTTTTATTAAATTAT
1 ATTA-TAA-TAAGAATTTTATTAAATTAT
*
44311780 ATT-TAATAATAATTATT-TTAAATTAT
1 ATTATAATAAGAATT-TTATTAAATTAT
44311806 ATT
1 ATT
44311809 TTATAGTATT
Statistics
Matches: 86, Mismatches: 13, Indels: 21
0.72 0.11 0.17
Matches are distributed among these distances:
25 11 0.13
26 45 0.52
27 18 0.21
28 4 0.05
29 8 0.09
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (27 bp):
ATTATAATAAGAATTTTATTAAATTAT
Found at i:44311774 original size:80 final size:79
Alignment explanation
Indices: 44311678--44311837 Score: 284
Period size: 80 Copynumber: 2.0 Consensus size: 79
44311668 GAATAATTAT
44311678 ATTAAGAATTTTATTAAATTATATTTAATAATAATTATTTTAAATTATATTTTATAATATTATAT
1 ATTAAGAATTTTATTAAATTATATTTAATAATAATTATTTTAAATTATATTTTATAATATTATAT
*
44311743 ATTATGATTTTAGTA
66 ATTAT-AATTTAGTA
* *
44311758 ATTAAGATTTTTATTAAATTATATTTAATAATAATTATTTTAAATTATATTTTATAGTATTATAT
1 ATTAAGAATTTTATTAAATTATATTTAATAATAATTATTTTAAATTATATTTTATAATATTATAT
44311823 ATTATAATTTAGTA
66 ATTATAATTTAGTA
44311837 A
1 A
44311838 ATTCATATAA
Statistics
Matches: 77, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
79 9 0.12
80 68 0.88
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (79 bp):
ATTAAGAATTTTATTAAATTATATTTAATAATAATTATTTTAAATTATATTTTATAATATTATAT
ATTATAATTTAGTA
Found at i:44311886 original size:31 final size:29
Alignment explanation
Indices: 44311850--44312047 Score: 116
Period size: 26 Copynumber: 7.0 Consensus size: 29
44311840 TCATATAAGA
44311850 ATATTTAATATTAAGAATTTTATTAAATTAT
1 ATATTTAATATT-A-AATTTTATTAAATTAT
* * *
44311881 ATATTT-TTATTAAATTATATTTAA-TA-
1 ATATTTAATATTAAATTTTATTAAATTAT
* * *
44311907 ATACTT-ATTTTAAATTATATT---TTAT
1 ATATTTAATATTAAATTTTATTAAATTAT
*
44311932 AGTA-TTATATATTATAATTTTAGTAAATTA-
1 A-TATTTA-ATATTA-AATTTTATTAAATTAT
44311962 ATATTTAATATTAAGAATTTTATTAAATTAT
1 ATATTTAATATT-A-AATTTTATTAAATTAT
* * *
44311993 ATATTT-TTATTAAATTATATTTAA-TA-
1 ATATTTAATATTAAATTTTATTAAATTAT
* * *
44312019 ATAATT-ATGTTAAATTATGATTAAATTAT
1 ATATTTAATATTAAATT-TTATTAAATTAT
44312048 TCATTATTTA
Statistics
Matches: 132, Mismatches: 20, Indels: 32
0.72 0.11 0.17
Matches are distributed among these distances:
24 2 0.02
25 3 0.02
26 33 0.25
27 14 0.11
28 29 0.22
29 9 0.07
30 27 0.20
31 15 0.11
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.54
Consensus pattern (29 bp):
ATATTTAATATTAAATTTTATTAAATTAT
Found at i:44312006 original size:112 final size:114
Alignment explanation
Indices: 44311730--44312036 Score: 457
Period size: 112 Copynumber: 2.7 Consensus size: 114
44311720 AATTATATTT
* * *
44311730 TATAATA-TTATATATTATG-ATTTTAGT-AATTA-AGATTTTTATTAAATTATATTTAATAATA
1 TATAATATTTA-ATATTAAGAATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATA
44311791 ATTATTTTAAATTATATTTTATAGTATTATATATTATAATTTAGTAAATTCA
65 ATTATTTTAAATTATATTTTATAGTATTATATATTATAATTTAGTAAA-T-A
44311843 TATAAGAATATTTAATATTAAGAATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAA
1 TAT---AATATTTAATATTAAGAATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAA
*
44311908 TACTTATTTTAAATTATATTTTATAGTATTATATATTATAATTTTAGT-AA-A
63 TAATTATTTTAAATTATATTTTATAGTATTATATATTATAA-TTTAGTAAATA
44311959 T-TAATATTTAATATTAAGAATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAA
1 TATAATATTTAATATTAAGAATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAA
*
44312023 TTATGTTAAATTAT
66 TTATTTTAAATTAT
44312037 GATTAAATTA
Statistics
Matches: 180, Mismatches: 6, Indels: 17
0.89 0.03 0.08
Matches are distributed among these distances:
112 74 0.41
113 3 0.02
115 1 0.01
116 13 0.07
117 10 0.06
118 5 0.03
119 68 0.38
120 6 0.03
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.53
Consensus pattern (114 bp):
TATAATATTTAATATTAAGAATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAA
TTATTTTAAATTATATTTTATAGTATTATATATTATAATTTAGTAAATA
Found at i:44314537 original size:6 final size:6
Alignment explanation
Indices: 44314515--44314549 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
44314505 TATTTTTTTA
*
44314515 ATATTT A-ATTA ATATTT ATATTT ATATTT ATATTT
1 ATATTT ATATTT ATATTT ATATTT ATATTT ATATTT
44314550 CATCAGACAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
5 4 0.15
6 22 0.85
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (6 bp):
ATATTT
Found at i:44314873 original size:15 final size:15
Alignment explanation
Indices: 44314853--44314887 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
44314843 AGTCCCTAGA
* *
44314853 GTTTTTTAGTTTAGG
1 GTTTTTAAGGTTAGG
44314868 GTTTTTAAGGTTAGG
1 GTTTTTAAGGTTAGG
44314883 GTTTT
1 GTTTT
44314888 GTTAAAATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.14, C:0.00, G:0.29, T:0.57
Consensus pattern (15 bp):
GTTTTTAAGGTTAGG
Found at i:44314902 original size:21 final size:21
Alignment explanation
Indices: 44314878--44314951 Score: 58
Period size: 21 Copynumber: 3.5 Consensus size: 21
44314868 GTTTTTAAGG
44314878 TTAGGGTTTTGTTAAAATAAT
1 TTAGGGTTTTGTTAAAATAAT
** *** ***
44314899 TTAGGGTCATGTTTGTAGGGT
1 TTAGGGTTTTGTTAAAATAAT
*
44314920 TTAGGGTTTTATTAAAATAAT
1 TTAGGGTTTTGTTAAAATAAT
*
44314941 TTAGGGCTTTG
1 TTAGGGTTTTG
44314952 GATTTTAAGA
Statistics
Matches: 34, Mismatches: 19, Indels: 0
0.64 0.36 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.26, C:0.03, G:0.26, T:0.46
Consensus pattern (21 bp):
TTAGGGTTTTGTTAAAATAAT
Found at i:44315073 original size:34 final size:34
Alignment explanation
Indices: 44315025--44315090 Score: 105
Period size: 34 Copynumber: 1.9 Consensus size: 34
44315015 GTAAGATTTT
*
44315025 AAATAAATTAAATTAGGGTTTAGTGTTTTTAAGA
1 AAATAAATTAAATTAAGGTTTAGTGTTTTTAAGA
* *
44315059 AAATTAATTAAATTAAGGTTTAGTTTTTTTAA
1 AAATAAATTAAATTAAGGTTTAGTGTTTTTAA
44315091 AATAATATTG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.41, C:0.00, G:0.14, T:0.45
Consensus pattern (34 bp):
AAATAAATTAAATTAAGGTTTAGTGTTTTTAAGA
Found at i:44315489 original size:120 final size:120
Alignment explanation
Indices: 44315326--44315696 Score: 381
Period size: 120 Copynumber: 3.0 Consensus size: 120
44315316 TGTTTCTGAA
*
44315326 CAAATAATGTCAAAAACGCTTCAAGCAGGATGCACTGTCAGCAAAATTAATGAAAAAAGCTCTCA
1 CAAATAATGTCAAAAACGCTTCAAGAAGGATGCACTGTCAGCAAAATTAATGAAAAAAGCTCTCA
44315391 CGAGGACGCTCTTTTTCTACAGTAGTTCATGTTTGGCCTTAGGCTATAAATAAGT
66 CGAGGACGCTCTTTTTCTACAGTAGTTCATGTTTGGCCTTAGGCTATAAATAAGT
* * * * *
44315446 CGAATAATGTCAAAAACGCTTCAAGAAGGATGCACGGTTAGCAAAATTACTGAAAAAAGCTCCCA
1 CAAATAATGTCAAAAACGCTTCAAGAAGGATGCACTGTCAGCAAAATTAATGAAAAAAGCTCTCA
* * * **** **** ** **
44315511 CGTGGATGCTCTTTTTCTACAGTGGTTTCTAAAAAAATAAATTTGAGAAGACGGT-TCTGAA--
66 CGAGGACGCTCTTTTTCTACAGTAG-TTC---ATGTTTGGCCTT-AG--G-CTATAAAT-AAGT
* * *
44315572 CAAATAGTGTCAAAAACGCTTCAAGCAA-TATGCACTGTCAGCAAAATTAATGAAAAAAACTCTC
1 CAAATAATGTCAAAAACGCTTCAAG-AAGGATGCACTGTCAGCAAAATTAATGAAAAAAGCTCTC
* * *
44315636 ACAAGGACGCTCTTTTTCTACAGTAGTTCATGTTTGGCCTTAGGATATAAATGAGT
65 ACGAGGACGCTCTTTTTCTACAGTAGTTCATGTTTGGCCTTAGGCTATAAATAAGT
44315692 CAAAT
1 CAAAT
44315697 TTTATTCTTA
Statistics
Matches: 191, Mismatches: 47, Indels: 26
0.72 0.18 0.10
Matches are distributed among these distances:
118 2 0.01
119 2 0.01
120 86 0.45
121 5 0.03
122 4 0.02
124 4 0.02
125 5 0.03
126 75 0.39
127 4 0.02
128 4 0.02
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.27
Consensus pattern (120 bp):
CAAATAATGTCAAAAACGCTTCAAGAAGGATGCACTGTCAGCAAAATTAATGAAAAAAGCTCTCA
CGAGGACGCTCTTTTTCTACAGTAGTTCATGTTTGGCCTTAGGCTATAAATAAGT
Found at i:44315571 original size:246 final size:245
Alignment explanation
Indices: 44315203--44315692 Score: 737
Period size: 246 Copynumber: 2.0 Consensus size: 245
44315193 GGTCTGAATA
* * * * * * *
44315203 AATAGTGTGAAAAACGCTTCAAGCAGGATTCACTATCAGTAAAATTACTGAAAAAACTCTCACGT
1 AATAATGTCAAAAACGCTTCAAGAAGGATGCACGATCAGCAAAATTACTGAAAAAACTCCCACGT
* * * * * * *
44315268 GGACGTTTTTTTTCTGCAGTAGTTCCTGAAAAAATAATTTTGAGAAGATGTTTCTGAACAAATAA
66 GGACGCTCTTTTTCTACAGTAGTTCCTAAAAAAATAAATTTGAGAAGACGGTTCTGAACAAATAA
* * *
44315333 TGTCAAAAACGCTTCAAGCAGGATGCACTGTCAGCAAAATTAATGAAAAAAGCTCTCACGAGGAC
131 TGTCAAAAACGCTTCAAGCAAGATGCACTGTCAGCAAAATTAATGAAAAAAACTCTCACAAGGAC
*
44315398 GCTCTTTTTCTACAGTAGTTCATGTTTGGCCTTAGGCTATAAATAAGTCG
196 GCTCTTTTTCTACAGTAGTTCATGTTTGGCCTTAGGATATAAATAAGTCG
* *
44315448 AATAATGTCAAAAACGCTTCAAGAAGGATGCACGGTTAGCAAAATTACTGAAAAAAGCTCCCACG
1 AATAATGTCAAAAACGCTTCAAGAAGGATGCACGATCAGCAAAATTACTGAAAAAA-CTCCCACG
* * *
44315513 TGGATGCTCTTTTTCTACAGTGGTTTCTAAAAAAATAAATTTGAGAAGACGGTTCTGAACAAATA
65 TGGACGCTCTTTTTCTACAGTAGTTCCTAAAAAAATAAATTTGAGAAGACGGTTCTGAACAAATA
* *
44315578 GTGTCAAAAACGCTTCAAGCAATATGCACTGTCAGCAAAATTAATGAAAAAAACTCTCACAAGGA
130 ATGTCAAAAACGCTTCAAGCAAGATGCACTGTCAGCAAAATTAATGAAAAAAACTCTCACAAGGA
*
44315643 CGCTCTTTTTCTACAGTAGTTCATGTTTGGCCTTAGGATATAAATGAGTC
195 CGCTCTTTTTCTACAGTAGTTCATGTTTGGCCTTAGGATATAAATAAGTC
44315693 AAATTTTATT
Statistics
Matches: 218, Mismatches: 26, Indels: 1
0.89 0.11 0.00
Matches are distributed among these distances:
245 48 0.22
246 170 0.78
ACGTcount: A:0.36, C:0.17, G:0.18, T:0.28
Consensus pattern (245 bp):
AATAATGTCAAAAACGCTTCAAGAAGGATGCACGATCAGCAAAATTACTGAAAAAACTCCCACGT
GGACGCTCTTTTTCTACAGTAGTTCCTAAAAAAATAAATTTGAGAAGACGGTTCTGAACAAATAA
TGTCAAAAACGCTTCAAGCAAGATGCACTGTCAGCAAAATTAATGAAAAAAACTCTCACAAGGAC
GCTCTTTTTCTACAGTAGTTCATGTTTGGCCTTAGGATATAAATAAGTCG
Found at i:44319398 original size:139 final size:139
Alignment explanation
Indices: 44319148--44319420 Score: 422
Period size: 139 Copynumber: 2.0 Consensus size: 139
44319138 AATCGAGTGA
* * *
44319148 AAGTGGTAAAATGAATACTTACCGAATCGAGCGAGTTCAATCGTCGAGCACGATTGAGGCATAAA
1 AAGTGGCAAAACGAATACTTACCGAATCGAGCGAGTTCAATCGTCGAGCACGATGGAGGCATAAA
* * * *
44319213 AGAAATCAAAAGAAAAGAGAGAGGAAACAATGAAAGTTCAGTAGAAAAGATGTAAATAAGCGTCA
66 AGAAATCAAAAGAAAAGAGAGAGGAAACAATGAAAATTCAGCAGAAAAGAGGTAAATAAACGTCA
44319278 GAACGATAG
131 GAACGATAG
*
44319287 AAGTGGCAAAACGAATACTTACCGAATCGAGCGAGTTCCATCGTCGAGCACGATGGAGGCATAAA
1 AAGTGGCAAAACGAATACTTACCGAATCGAGCGAGTTCAATCGTCGAGCACGATGGAGGCATAAA
** * *
44319352 AGAAATCAAAAGAAAATG-GAGAGGAAACAATGAAAATTTGGCAGAAAAGGGGTGAATAAACGTC
66 AGAAATCAAAAGAAAA-GAGAGAGGAAACAATGAAAATTCAGCAGAAAAGAGGTAAATAAACGTC
44319416 AGAAC
130 AGAAC
44319421 AATGGAAGAA
Statistics
Matches: 121, Mismatches: 12, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
139 120 0.99
140 1 0.01
ACGTcount: A:0.45, C:0.14, G:0.25, T:0.16
Consensus pattern (139 bp):
AAGTGGCAAAACGAATACTTACCGAATCGAGCGAGTTCAATCGTCGAGCACGATGGAGGCATAAA
AGAAATCAAAAGAAAAGAGAGAGGAAACAATGAAAATTCAGCAGAAAAGAGGTAAATAAACGTCA
GAACGATAG
Found at i:44319713 original size:12 final size:11
Alignment explanation
Indices: 44319698--44319803 Score: 56
Period size: 11 Copynumber: 10.4 Consensus size: 11
44319688 AAAAAATTAA
44319698 AAAAAGTATTTT
1 AAAAA-TATTTT
44319710 AAAAATATTTT
1 AAAAATATTTT
44319721 --AAA-A--TT
1 AAAAATATTTT
* *
44319727 AAAAA-AATTA
1 AAAAATATTTT
44319737 AAAAAGTATTTT
1 AAAAA-TATTTT
44319749 AAAAA-ATTTT
1 AAAAATATTTT
44319759 --AAA-A-TTT
1 AAAAATATTTT
*
44319766 AAAAA-ATTTAA
1 AAAAATATTT-T
44319777 AAAAAGTATTTT
1 AAAAA-TATTTT
*
44319789 AAAAGTATTTT
1 AAAAATATTTT
44319800 AAAA
1 AAAA
44319804 TTAAAAAAAT
Statistics
Matches: 76, Mismatches: 6, Indels: 25
0.71 0.06 0.23
Matches are distributed among these distances:
6 2 0.03
7 3 0.04
8 9 0.12
9 7 0.09
10 13 0.17
11 21 0.28
12 17 0.22
13 4 0.05
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:44319739 original size:8 final size:9
Alignment explanation
Indices: 44319721--44319781 Score: 50
Period size: 9 Copynumber: 6.4 Consensus size: 9
44319711 AAAATATTTT
44319721 AAAATTAAA
1 AAAATTAAA
44319730 AAAATTAAA
1 AAAATTAAA
*
44319739 AAAGTATTTTAA
1 AAA--A-TTAAA
**
44319751 AAAATTTTA
1 AAAATTAAA
*
44319760 AAATTTAAA
1 AAAATTAAA
*
44319769 AAATTTAAA
1 AAAATTAAA
44319778 AAAA
1 AAAA
44319782 GTATTTTAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
9 34 0.79
10 1 0.02
11 1 0.02
12 7 0.16
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (9 bp):
AAAATTAAA
Found at i:44319754 original size:40 final size:40
Alignment explanation
Indices: 44319673--44319820 Score: 230
Period size: 39 Copynumber: 3.7 Consensus size: 40
44319663 ACCAAAAATT
44319673 TATTTTAAAAATTAAAAAAAATTAAAAAAAGTATTTTAAAAA
1 TATTTT-AAAATT-AAAAAAATTAAAAAAAGTATTTTAAAAA
44319715 TATTTTAAAATTAAAAAAATT-AAAAAAGTATTTTAAAAA
1 TATTTTAAAATTAAAAAAATTAAAAAAAGTATTTTAAAAA
* *
44319754 -ATTTTAAAATTTAAAAAATTTAAAAAAAGTATTTTAAAAG
1 TATTTTAAAA-TTAAAAAAATTAAAAAAAGTATTTTAAAAA
44319794 TATTTTAAAATTAAAAAAA-TAAAAAAA
1 TATTTTAAAATTAAAAAAATTAAAAAAA
44319821 TAATAAAAAT
Statistics
Matches: 100, Mismatches: 3, Indels: 9
0.89 0.03 0.08
Matches are distributed among these distances:
38 9 0.09
39 36 0.36
40 34 0.34
41 15 0.15
42 6 0.06
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (40 bp):
TATTTTAAAATTAAAAAAATTAAAAAAAGTATTTTAAAAA
Found at i:44319755 original size:30 final size:27
Alignment explanation
Indices: 44319710--44319822 Score: 83
Period size: 27 Copynumber: 4.3 Consensus size: 27
44319700 AAAGTATTTT
44319710 AAAAATATTTTAAAATTAAAAAAATTA
1 AAAAATATTTTAAAATTAAAAAAATTA
** *
44319737 AAAAAGTATTTTAAAAAATT-TTAAAATTT
1 AAAAA-TATTTT--AAAATTAAAAAAATTA
** * *
44319766 AAAAA-A-TTTAAAA--AAAGTATTTT
1 AAAAATATTTTAAAATTAAAAAAATTA
* *
44319789 AAAAGTATTTTAAAATTAAAAAAATAA
1 AAAAATATTTTAAAATTAAAAAAATTA
44319816 AAAAATA
1 AAAAATA
44319823 ATAAAAATAT
Statistics
Matches: 63, Mismatches: 15, Indels: 16
0.67 0.16 0.17
Matches are distributed among these distances:
23 8 0.13
24 5 0.08
25 7 0.11
26 3 0.05
27 17 0.27
28 6 0.10
29 11 0.17
30 6 0.10
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.34
Consensus pattern (27 bp):
AAAAATATTTTAAAATTAAAAAAATTA
Found at i:44319777 original size:79 final size:80
Alignment explanation
Indices: 44319674--44319820 Score: 251
Period size: 79 Copynumber: 1.9 Consensus size: 80
44319664 CCAAAAATTT
*
44319674 ATTTTAAAAATTAAAAAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAATTAAAAAAATTAAA
1 ATTTTAAAAATTAAAAAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAATTAAAAAAATAAAA
44319739 AAAGTATTTTAAAAA
66 AAAGTATTTTAAAAA
* * *
44319754 ATTTT-AAAATTTAAAAAATTTAAAAAAAGTATTTTAAAAGTATTTTAAAATTAAAAAAATAAAA
1 ATTTTAAAAATTAAAAAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAATTAAAAAAATAAAA
44319818 AAA
66 AAA
44319821 TAATAAAAAT
Statistics
Matches: 63, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
79 58 0.92
80 5 0.08
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (80 bp):
ATTTTAAAAATTAAAAAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAATTAAAAAAATAAAA
AAAGTATTTTAAAAA
Found at i:44330331 original size:4 final size:4
Alignment explanation
Indices: 44330198--44330311 Score: 228
Period size: 4 Copynumber: 28.5 Consensus size: 4
44330188 TTAAAACGCA
44330198 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
44330246 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
44330294 ATGT ATGT ATGT ATGT AT
1 ATGT ATGT ATGT ATGT AT
44330312 ATCCTAAAAT
Statistics
Matches: 110, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 110 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:44330340 original size:20 final size:20
Alignment explanation
Indices: 44330301--44330341 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
44330291 TGTATGTATG
* *
44330301 TATGTATGTATATCCTAAAA
1 TATGTATGTATATACAAAAA
44330321 TATGTATGTATATACAAAAA
1 TATGTATGTATATACAAAAA
44330341 T
1 T
44330342 CAAAAGCTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.44, C:0.07, G:0.10, T:0.39
Consensus pattern (20 bp):
TATGTATGTATATACAAAAA
Found at i:44330505 original size:8 final size:8
Alignment explanation
Indices: 44330489--44330602 Score: 90
Period size: 9 Copynumber: 13.4 Consensus size: 8
44330479 TTAAGCTATT
44330489 ATATAATA
1 ATATAATA
*
44330497 ATATGATA
1 ATATAATA
*
44330505 AGTAGCAATA
1 A-TA-TAATA
44330515 ATATAAGT-
1 ATATAA-TA
*
44330523 A-GTAATA
1 ATATAATA
44330530 ATAATAATA
1 AT-ATAATA
44330539 ATAATAATA
1 AT-ATAATA
44330548 ATAATAATA
1 AT-ATAATA
44330557 ATAATAATA
1 AT-ATAATA
44330566 ATAATAATA
1 AT-ATAATA
44330575 ATAATAATA
1 AT-ATAATA
44330584 ATAGTAATA
1 ATA-TAATA
44330593 ATA-AATA
1 ATATAATA
44330600 ATA
1 ATA
44330603 AAAGATGATA
Statistics
Matches: 93, Mismatches: 6, Indels: 15
0.82 0.05 0.13
Matches are distributed among these distances:
6 1 0.01
7 11 0.12
8 12 0.13
9 65 0.70
10 4 0.04
ACGTcount: A:0.61, C:0.01, G:0.05, T:0.32
Consensus pattern (8 bp):
ATATAATA
Found at i:44330517 original size:3 final size:3
Alignment explanation
Indices: 44330511--44330603 Score: 143
Period size: 3 Copynumber: 30.7 Consensus size: 3
44330501 GATAAGTAGC
*
44330511 AAT AAT -AT AAGT AGT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
44330556 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AGT AAT AAT AAAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT
44330602 AA
1 AA
44330604 AAGATGATAA
Statistics
Matches: 83, Mismatches: 4, Indels: 6
0.89 0.04 0.06
Matches are distributed among these distances:
2 2 0.02
3 76 0.92
4 5 0.06
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:44330520 original size:15 final size:15
Alignment explanation
Indices: 44330502--44330532 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
44330492 TAATAATATG
44330502 ATAAGTAGCAATAAT
1 ATAAGTAGCAATAAT
*
44330517 ATAAGTAGTAATAAT
1 ATAAGTAGCAATAAT
44330532 A
1 A
44330533 ATAATAATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.55, C:0.03, G:0.13, T:0.29
Consensus pattern (15 bp):
ATAAGTAGCAATAAT
Found at i:44331817 original size:44 final size:44
Alignment explanation
Indices: 44331755--44332521 Score: 305
Period size: 44 Copynumber: 17.5 Consensus size: 44
44331745 TTCGGTTCGT
* *
44331755 TCCACTGTAATCTTAGGGAGATAAGATCCTTTATTTTAATCCGC
1 TCCACTGTAATCTCAGGGAGATAAGATCCTTTATTTCAATCCGC
* * * * *
44331799 TTCACTGTAATCTCAGGGAGATAGGAT--TACTAGCTTCAATCTGC
1 TCCACTGTAATCTCAGGGAGATAAGATCCT-TTA-TTTCAATCCGC
* ** ** *
44331843 TCCGCTGTAATCTCAGGGAGATAAGAT-CTGAAATTCTTCGGTCTGC
1 TCCACTGTAATCTCAGGGAGATAAGATCCT-TTA-T-TTCAATCCGC
* * * * * *
44331889 TCCACTGTAATATCAGGGAGATAA-AACC-TGA-TGCGATCCAC
1 TCCACTGTAATCTCAGGGAGATAAGATCCTTTATTTCAATCCGC
** *
44331930 TCTGCTGTAA-CTTCAGAGAGATAAGATCCTTTA-TTCTAATCCGC
1 TCCACTGTAATC-TCAGGGAGATAAGATCCTTTATTTC-AATCCGC
* * * * *
44331974 TCCACTGTAATCTTAGGGAGATAGGAT--TACTAGCTTCAATCTGC
1 TCCACTGTAATCTCAGGGAGATAAGATCCT-TTA-TTTCAATCCGC
* * * * * **
44332018 TCCGCTGTAATCTCAGGAAGATAAGAT-C-TGA-TGCGATCTAC
1 TCCACTGTAATCTCAGGGAGATAAGATCCTTTATTTCAATCCGC
* * * * * *
44332059 TCTACTATAA-CTTCAGAGATATAAGATCATTTATTTTAATCCGC
1 TCCACTGTAATC-TCAGGGAGATAAGATCCTTTATTTCAATCCGC
* * * * *
44332103 TTCACTGTAATCTCAGGGAGATAGGAT--TACTAGCTTCAATCTGC
1 TCCACTGTAATCTCAGGGAGATAAGATCCT-TTA-TTTCAATCCGC
* * *** *
44332147 TCCGCTGTAATCTCAGGGAGATAAGATCTTTTACGATCTTTGGTCTGC
1 TCCACTGTAATCTCAGGGAGATAAGATCCTTT---AT-TTCAATCCGC
* * * * *
44332195 TCCACTGTAATCTCAAGGAGATAAGA-CC-TGA-TGCGATCCAC
1 TCCACTGTAATCTCAGGGAGATAAGATCCTTTATTTCAATCCGC
** * * *
44332236 TCTGCTGTAA-CTTCAGAGAGATAAGATCCTTTATTTTAATCCAC
1 TCCACTGTAATC-TCAGGGAGATAAGATCCTTTATTTCAATCCGC
** * * *
44332280 TCCACTGTAATCTCATAGAGATAGGAT--TACTAGTTTCAATCTGC
1 TCCACTGTAATCTCAGGGAGATAAGATCCT-TTA-TTTCAATCCGC
* ** ** *
44332324 TCCGCTGTAATCTCAGGGAGATAAGAT-CTGAAATTCTTCGGTCTGC
1 TCCACTGTAATCTCAGGGAGATAAGATCCT-TTA-T-TTCAATCCGC
* * * * *
44332370 TCCACTGTGATCTCAGGGAGATAAGA-CC-TGA-TGCGATCCAC
1 TCCACTGTAATCTCAGGGAGATAAGATCCTTTATTTCAATCCGC
** ** * *
44332411 TCTGCTGTAA-CTTCAGATAGATAAGATCCTTTATTTTAATCCAC
1 TCCACTGTAATC-TCAGGGAGATAAGATCCTTTATTTCAATCCGC
* * * * *
44332455 TCTACTGTAATCTCAGGGAGATAGGAT--TACTAGCTTCAATCTGC
1 TCCACTGTAATCTCAGGGAGATAAGATCCT-TTA-TTTCAATCCGC
*
44332499 TCCGCTGTAATCTCAGGGAGATA
1 TCCACTGTAATCTCAGGGAGATA
44332522 GGATTTGTAA
Statistics
Matches: 534, Mismatches: 145, Indels: 88
0.70 0.19 0.11
Matches are distributed among these distances:
40 3 0.01
41 101 0.19
42 12 0.02
43 22 0.04
44 283 0.53
45 14 0.03
46 66 0.12
47 1 0.00
48 32 0.06
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (44 bp):
TCCACTGTAATCTCAGGGAGATAAGATCCTTTATTTCAATCCGC
Found at i:44331905 original size:46 final size:45
Alignment explanation
Indices: 44331679--44332395 Score: 284
Period size: 44 Copynumber: 16.3 Consensus size: 45
44331669 CCTACTGCTT
* * *
44331679 AGGGAGATAAGA-CT-AATGCCTTAAATCTGCTCCACTGTAACCTC
1 AGGGAGATAAGATCTAAAT-TCTTCAATCTGCTCCACTGTAATCTC
* ** * *
44331723 AAGGAGATAAGATCTGAAATTCTTCGGT-TCGTTCCACTGTAATCTT
1 AGGGAGATAAGATCT-AAATTCTTCAATCT-GCTCCACTGTAATCTC
** * *
44331769 AGGGAGATAAGATCCTTTATT-TT-AATCCGCTTCACTGTAATCTC
1 AGGGAGATAAGAT-CTAAATTCTTCAATCTGCTCCACTGTAATCTC
* * * *
44331813 AGGGAGATAGGAT-T-ACTAGCTTCAATCTGCTCCGCTGTAATCTC
1 AGGGAGATAAGATCTAAAT-TCTTCAATCTGCTCCACTGTAATCTC
** *
44331857 AGGGAGATAAGATCTGAAATTCTTCGGTCTGCTCCACTGTAATATC
1 AGGGAGATAAGATCT-AAATTCTTCAATCTGCTCCACTGTAATCTC
* * * * * * *
44331903 AGGGAGATAAAACCT-GATGCGATCCA-CT-CT--GCTGTAA-CTTC
1 AGGGAGATAAGATCTAAATTC-TTCAATCTGCTCCACTGTAATC-TC
* ** * *
44331944 AGAGAGATAAGATCCTTTATTC-T-AATCCGCTCCACTGTAATCTT
1 AGGGAGATAAGAT-CTAAATTCTTCAATCTGCTCCACTGTAATCTC
* * * *
44331988 AGGGAGATAGGAT-T-ACTAGCTTCAATCTGCTCCGCTGTAATCTC
1 AGGGAGATAAGATCTAAAT-TCTTCAATCTGCTCCACTGTAATCTC
* * * * * * *
44332032 AGGAAGATAAGATCT-GA---TGCGATCTACTCTACTATAA-CTTC
1 AGGGAGATAAGATCTAAATTCTTCAATCTGCTCCACTGTAATC-TC
* * ** * *
44332073 AGAGATATAAGATCATTTATT-TT-AATCCGCTTCACTGTAATCTC
1 AGGGAGATAAGATC-TAAATTCTTCAATCTGCTCCACTGTAATCTC
* * * *
44332117 AGGGAGATAGGAT-T-ACTAGCTTCAATCTGCTCCGCTGTAATCTC
1 AGGGAGATAAGATCTAAAT-TCTTCAATCTGCTCCACTGTAATCTC
* ***
44332161 AGGGAGATAAGATCTTTTACGA-TCTTTGGTCTGCTCCACTGTAATCTC
1 AGGGAGATAAGATC---TA-AATTCTTCAATCTGCTCCACTGTAATCTC
* * * * * * *
44332209 AAGGAGATAAGACCT-GATGCGATCCA-CT-CT--GCTGTAA-CTTC
1 AGGGAGATAAGATCTAAATTC-TTCAATCTGCTCCACTGTAATC-TC
* ** **
44332250 AGAGAGATAAGATCCTTTATT-TT-AATCCACTCCACTGTAATCTC
1 AGGGAGATAAGAT-CTAAATTCTTCAATCTGCTCCACTGTAATCTC
** * * * *
44332294 ATAGAGATAGGAT-TACTAGT-TTCAATCTGCTCCGCTGTAATCTC
1 AGGGAGATAAGATCTA-AATTCTTCAATCTGCTCCACTGTAATCTC
** *
44332338 AGGGAGATAAGATCTGAAATTCTTCGGTCTGCTCCACTGTGATCTC
1 AGGGAGATAAGATCT-AAATTCTTCAATCTGCTCCACTGTAATCTC
44332384 AGGGAGATAAGA
1 AGGGAGATAAGA
44332396 CCTGATGCGA
Statistics
Matches: 490, Mismatches: 128, Indels: 108
0.67 0.18 0.15
Matches are distributed among these distances:
40 4 0.01
41 70 0.14
42 14 0.03
43 22 0.04
44 222 0.45
45 18 0.04
46 99 0.20
47 7 0.01
48 34 0.07
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.31
Consensus pattern (45 bp):
AGGGAGATAAGATCTAAATTCTTCAATCTGCTCCACTGTAATCTC
Found at i:44332185 original size:129 final size:129
Alignment explanation
Indices: 44331884--44332175 Score: 467
Period size: 129 Copynumber: 2.3 Consensus size: 129
44331874 AATTCTTCGG
* * * * * * *
44331884 TCTGCTCCACTGTAATATCAGGGAGATAAAACCTGATGCGATCCACTCTGCTGTAACTTCAGAGA
1 TCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGATGCGATCTACTCTACTATAACTTCAGAGA
* *
44331949 GATAAGATCCTTTATTCTAATCCGCTCCACTGTAATCTTAGGGAGATAGGATTACTAGCTTCAA
66 GATAAGATCATTTATTCTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAA
*
44332013 TCTGCTCCGCTGTAATCTCAGGAAGATAAGATCTGATGCGATCTACTCTACTATAACTTCAGAGA
1 TCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGATGCGATCTACTCTACTATAACTTCAGAGA
* * *
44332078 TATAAGATCATTTATTTTAATCCGCTTCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAA
66 GATAAGATCATTTATTCTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAA
44332142 TCTGCTCCGCTGTAATCTCAGGGAGATAAGATCT
1 TCTGCTCCGCTGTAATCTCAGGGAGATAAGATCT
44332176 TTTACGATCT
Statistics
Matches: 149, Mismatches: 14, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
129 149 1.00
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.31
Consensus pattern (129 bp):
TCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGATGCGATCTACTCTACTATAACTTCAGAGA
GATAAGATCATTTATTCTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAA
Found at i:44332303 original size:306 final size:304
Alignment explanation
Indices: 44331775--44332354 Score: 1000
Period size: 306 Copynumber: 1.9 Consensus size: 304
44331765 TCTTAGGGAG
*
44331775 ATAAGATCCTTTATTTTAATCCGCTTCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATC
1 ATAAGATCATTTATTTTAATCCGCTTCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATC
*
44331840 TGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAAATTCTTCGGTCTGCTCCACTGTAATATCAG
66 TGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAAATTCTTCGGTCTGCTCCACTGTAATATCAA
44331905 GGAGATAAAACCTGATGCGATCCACTCTGCTGTAACTTCAGAGAGATAAGATCCTTTATTCTAAT
131 GGAGATAAAACCTGATGCGATCCACTCTGCTGTAACTTCAGAGAGATAAGATCCTTTATTCTAAT
* * *
44331970 CCGCTCCACTGTAATCTTAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGG
196 CCACTCCACTGTAATCTCAGAGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGG
44332035 AAGATAAGATCTGATGCGATCTACTCTACTATAACTTCAGAGAT
261 AAGATAAGATCTGATGCGATCTACTCTACTATAACTTCAGAGAT
44332079 ATAAGATCATTTATTTTAATCCGCTTCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATC
1 ATAAGATCATTTATTTTAATCCGCTTCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATC
* * * *
44332144 TGCTCCGCTGTAATCTCAGGGAGATAAGATCTTTTACGA-TCTTTGGTCTGCTCCACTGTAATCT
66 TGCTCCGCTGTAATCTCAGGGAGATAAGATC--TGA-AATTCTTCGGTCTGCTCCACTGTAATAT
* *
44332208 CAAGGAGATAAGACCTGATGCGATCCACTCTGCTGTAACTTCAGAGAGATAAGATCCTTTATTTT
128 CAAGGAGATAAAACCTGATGCGATCCACTCTGCTGTAACTTCAGAGAGATAAGATCCTTTATTCT
* *
44332273 AATCCACTCCACTGTAATCTCATAGAGATAGGATTACTAGTTTCAATCTGCTCCGCTGTAATCTC
193 AATCCACTCCACTGTAATCTCAGAGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTC
*
44332338 AGGGAGATAAGATCTGA
258 AGGAAGATAAGATCTGA
44332355 AATTCTTCGG
Statistics
Matches: 259, Mismatches: 14, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
304 95 0.37
306 163 0.63
307 1 0.00
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.32
Consensus pattern (304 bp):
ATAAGATCATTTATTTTAATCCGCTTCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATC
TGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAAATTCTTCGGTCTGCTCCACTGTAATATCAA
GGAGATAAAACCTGATGCGATCCACTCTGCTGTAACTTCAGAGAGATAAGATCCTTTATTCTAAT
CCACTCCACTGTAATCTCAGAGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGG
AAGATAAGATCTGATGCGATCTACTCTACTATAACTTCAGAGAT
Found at i:44332452 original size:175 final size:176
Alignment explanation
Indices: 44332013--44332521 Score: 806
Period size: 175 Copynumber: 2.9 Consensus size: 176
44332003 CTAGCTTCAA
* * * * * *
44332013 TCTGCTCCGCTGTAATCTCAGGAAGATAAGATCTGATGCGATCTACTCTACTATAACTTCAGAGA
1 TCTGCTCCACTGTAATCTCAGGGAGATAAGACCTGATGCGATCCACTCTGCTGTAACTTCAGAGA
* * * *
44332078 TATAAGATCATTTATTTTAATCCGCTTCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAAT
66 GATAAGATCCTTTATTTTAATCCACTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAAT
* * *
44332143 CTGCTCCGCTGTAATCTCAGGGAGATAAGATCTTTTACGATCTTTGG
131 CTGCTCCGCTGTAATCTCAGGGAGATAAGATC-TTGACAATCTTCGG
*
44332190 TCTGCTCCACTGTAATCTCAAGGAGATAAGACCTGATGCGATCCACTCTGCTGTAACTTCAGAGA
1 TCTGCTCCACTGTAATCTCAGGGAGATAAGACCTGATGCGATCCACTCTGCTGTAACTTCAGAGA
** *
44332255 GATAAGATCCTTTATTTTAATCCACTCCACTGTAATCTCATAGAGATAGGATTACTAGTTTCAAT
66 GATAAGATCCTTTATTTTAATCCACTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAAT
44332320 CTGCTCCGCTGTAATCTCAGGGAGATAAGATC-TGA-AATTCTTCGG
131 CTGCTCCGCTGTAATCTCAGGGAGATAAGATCTTGACAA-TCTTCGG
* *
44332365 TCTGCTCCACTGTGATCTCAGGGAGATAAGACCTGATGCGATCCACTCTGCTGTAACTTCAGATA
1 TCTGCTCCACTGTAATCTCAGGGAGATAAGACCTGATGCGATCCACTCTGCTGTAACTTCAGAGA
*
44332430 GATAAGATCCTTTATTTTAATCCACTCTACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAAT
66 GATAAGATCCTTTATTTTAATCCACTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAAT
44332495 CTGCTCCGCTGTAATCTCAGGGAGATA
131 CTGCTCCGCTGTAATCTCAGGGAGATA
44332522 GGATTTGTAA
Statistics
Matches: 307, Mismatches: 24, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
174 1 0.00
175 158 0.51
177 148 0.48
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.32
Consensus pattern (176 bp):
TCTGCTCCACTGTAATCTCAGGGAGATAAGACCTGATGCGATCCACTCTGCTGTAACTTCAGAGA
GATAAGATCCTTTATTTTAATCCACTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAAT
CTGCTCCGCTGTAATCTCAGGGAGATAAGATCTTGACAATCTTCGG
Found at i:44332618 original size:50 final size:50
Alignment explanation
Indices: 44332567--44332725 Score: 167
Period size: 50 Copynumber: 3.2 Consensus size: 50
44332557 GCCATTATGG
* *
44332567 CTTTAATCTTTTTAACTGCAATG-CTGGGATAGCAAGATTCACTGATGTGG
1 CTTTAATCTTTTTAACTGCAATGCCAGGGA-AGCAAGATTCACTGATGTGA
** ** ** * * * * *
44332617 CTTTAATCTGCTCCACTGCACCGCCAGGGAAGTAGGATTCGCCGCTGTGA
1 CTTTAATCTTTTTAACTGCAATGCCAGGGAAGCAAGATTCACTGATGTGA
* *
44332667 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACTGATGTGA
1 CTTTAATCTTTTTAACTGCAATGCCAGGGAAGCAAGATTCACTGATGTGA
44332717 CTTTAATCT
1 CTTTAATCT
44332726 GTTCCACTGC
Statistics
Matches: 82, Mismatches: 26, Indels: 2
0.75 0.24 0.02
Matches are distributed among these distances:
50 77 0.94
51 5 0.06
ACGTcount: A:0.25, C:0.21, G:0.22, T:0.33
Consensus pattern (50 bp):
CTTTAATCTTTTTAACTGCAATGCCAGGGAAGCAAGATTCACTGATGTGA
Found at i:44332721 original size:100 final size:100
Alignment explanation
Indices: 44332542--44332756 Score: 315
Period size: 100 Copynumber: 2.1 Consensus size: 100
44332532 CTCGTAACCT
** * * *
44332542 GGGAAAGTAAGATTCGCCATTATGGCTTTAATCTTTTTAACTGCAATGCTGGGATAGCAAGATTC
1 GGGAAA-TAAGATTCGCCGCTGTGACTTTAATCTTTTTAACTGCAATGCGGGGATAGCAAGATTC
*
44332607 ACTGATGTGGCTTTAATCTGCTCCACTGCACCGCCA
65 ACTGATGTGACTTTAATCTGCTCCACTGCACCGCCA
* *
44332643 GGGAAGTAGGATTCGCCGCTGTGACTTTAATCTTTTTAACTGCAATGTCGGGGA-AGCAAGATTC
1 GGGAAATAAGATTCGCCGCTGTGACTTTAATCTTTTTAACTGCAATG-CGGGGATAGCAAGATTC
* *
44332707 ACTGATGTGACTTTAATCTGTTCCACTGCACCGCCT
65 ACTGATGTGACTTTAATCTGCTCCACTGCACCGCCA
44332743 GGGAAATAAGATTC
1 GGGAAATAAGATTC
44332757 TTGATTTCAC
Statistics
Matches: 101, Mismatches: 12, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
100 91 0.90
101 10 0.10
ACGTcount: A:0.26, C:0.21, G:0.23, T:0.30
Consensus pattern (100 bp):
GGGAAATAAGATTCGCCGCTGTGACTTTAATCTTTTTAACTGCAATGCGGGGATAGCAAGATTCA
CTGATGTGACTTTAATCTGCTCCACTGCACCGCCA
Found at i:44332747 original size:50 final size:50
Alignment explanation
Indices: 44332590--44332756 Score: 172
Period size: 50 Copynumber: 3.3 Consensus size: 50
44332580 AACTGCAATG
* *
44332590 CTGGGATAGCAAGATTCACTGATGTGGCTTTAATCTGCTCCACTGCACCGC
1 CTGGGA-AGCAAGATTCACTGATGTGACTTTAATCTGTTCCACTGCACCGC
* * * * * * * ** ** *
44332641 CAGGGAAGTAGGATTCGCCGCTGTGACTTTAATCTTTTTAACTGCAATGT
1 CTGGGAAGCAAGATTCACTGATGTGACTTTAATCTGTTCCACTGCACCGC
*
44332691 CGGGGAAGCAAGATTCACTGATGTGACTTTAATCTGTTCCACTGCACCGC
1 CTGGGAAGCAAGATTCACTGATGTGACTTTAATCTGTTCCACTGCACCGC
**
44332741 CTGGGAAATAAGATTC
1 CTGGGAAGCAAGATTC
44332757 TTGATTTCAC
Statistics
Matches: 87, Mismatches: 29, Indels: 1
0.74 0.25 0.01
Matches are distributed among these distances:
50 82 0.94
51 5 0.06
ACGTcount: A:0.25, C:0.23, G:0.24, T:0.29
Consensus pattern (50 bp):
CTGGGAAGCAAGATTCACTGATGTGACTTTAATCTGTTCCACTGCACCGC
Found at i:44334010 original size:13 final size:14
Alignment explanation
Indices: 44333978--44334010 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
44333968 TTAGCCTCTC
44333978 CATTTTTCATTTTT
1 CATTTTTCATTTTT
44333992 CA-TTTTCATTTTT
1 CATTTTTCATTTTT
44334005 -ATTTTT
1 CATTTTT
44334011 TTTACTCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 1 0.06
13 15 0.83
14 2 0.11
ACGTcount: A:0.15, C:0.12, G:0.00, T:0.73
Consensus pattern (14 bp):
CATTTTTCATTTTT
Found at i:44334011 original size:7 final size:7
Alignment explanation
Indices: 44333978--44334010 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
44333968 TTAGCCTCTC
44333978 CATTTTT
1 CATTTTT
44333985 CATTTTT
1 CATTTTT
44333992 CA-TTTT
1 CATTTTT
44333998 CATTTTT
1 CATTTTT
44334005 -ATTTTT
1 CATTTTT
44334011 TTTACTCAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
6 12 0.48
7 13 0.52
ACGTcount: A:0.15, C:0.12, G:0.00, T:0.73
Consensus pattern (7 bp):
CATTTTT
Found at i:44334899 original size:25 final size:27
Alignment explanation
Indices: 44334871--44334929 Score: 68
Period size: 25 Copynumber: 2.2 Consensus size: 27
44334861 CTTTTCCTTC
44334871 TTTTTATTTTAT-TTTTGATTT-TTCT
1 TTTTTATTTTATCTTTTGATTTGTTCT
* * *
44334896 TTTTTTTTTTCTGCTTTTGATTTGTTTT
1 TTTTTATTTTAT-CTTTTGATTTGTTCT
44334924 TTTTTA
1 TTTTTA
44334930 ATTGGATCTG
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
25 10 0.37
27 9 0.33
28 8 0.30
ACGTcount: A:0.08, C:0.05, G:0.07, T:0.80
Consensus pattern (27 bp):
TTTTTATTTTATCTTTTGATTTGTTCT
Found at i:44335495 original size:10 final size:10
Alignment explanation
Indices: 44335480--44335505 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
44335470 TACTCCAAGT
44335480 TTTTTTTTGC
1 TTTTTTTTGC
44335490 TTTTTTTTGC
1 TTTTTTTTGC
44335500 TTTTTT
1 TTTTTT
44335506 CATTTCGCAT
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:0.00, C:0.08, G:0.08, T:0.85
Consensus pattern (10 bp):
TTTTTTTTGC
Found at i:44342358 original size:3 final size:3
Alignment explanation
Indices: 44342352--44342418 Score: 84
Period size: 3 Copynumber: 21.7 Consensus size: 3
44342342 GATAAGTAGC
44342352 AAT AAT -AT AAGT AAT AAT AAT AAT -AT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
44342396 ATAT AAT ATAT AAT AAAT AAT AA
1 A-AT AAT A-AT AAT -AAT AAT AA
44342419 AAGATGATAA
Statistics
Matches: 58, Mismatches: 0, Indels: 12
0.83 0.00 0.17
Matches are distributed among these distances:
2 4 0.07
3 42 0.72
4 12 0.21
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:44342382 original size:14 final size:14
Alignment explanation
Indices: 44342363--44342418 Score: 78
Period size: 14 Copynumber: 3.9 Consensus size: 14
44342353 ATAATATAAG
44342363 TAATAATAATAATA
1 TAATAATAATAATA
44342377 TAATAATAATAATAA
1 TAATAATAATAAT-A
44342392 TAATATATAAT-ATA
1 TAATA-ATAATAATA
44342406 TAATAAATAATAA
1 TAAT-AATAATAA
44342419 AAGATGATAA
Statistics
Matches: 38, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
14 23 0.61
15 10 0.26
16 5 0.13
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (14 bp):
TAATAATAATAATA
Found at i:44342418 original size:33 final size:33
Alignment explanation
Indices: 44342329--44342418 Score: 96
Period size: 33 Copynumber: 2.7 Consensus size: 33
44342319 TTTAAGCTAT
* * **
44342329 TATATAATAATATGATAAGTAGCAATAATATAAG
1 TATATAAT-ATATAATAAATAATAATAATATAAG
44342363 TA-ATAATA-ATAATATAATAATAATAATAATAA-
1 TATATAATATATAATA-AATAATAATAAT-ATAAG
44342395 TATATAATATATAATAAATAATAA
1 TATATAATATATAATAAATAATAA
44342419 AAGATGATAA
Statistics
Matches: 48, Mismatches: 4, Indels: 9
0.79 0.07 0.15
Matches are distributed among these distances:
31 5 0.10
32 12 0.25
33 23 0.48
34 8 0.17
ACGTcount: A:0.60, C:0.01, G:0.04, T:0.34
Consensus pattern (33 bp):
TATATAATATATAATAAATAATAATAATATAAG
Found at i:44343797 original size:26 final size:26
Alignment explanation
Indices: 44343744--44343811 Score: 111
Period size: 26 Copynumber: 2.6 Consensus size: 26
44343734 ATAAAAAATA
*
44343744 ACCAAAATATTATAACTTTTTTTATTT
1 ACCAAAATATTATAA-ATTTTTTATTT
44343771 ACCAAAATATTATAAATTTTTTATTT
1 ACCAAAATATTATAAATTTTTTATTT
44343797 ACCAAAATA-TATAAA
1 ACCAAAATATTATAAA
44343812 AAAACAGAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
25 6 0.15
26 19 0.47
27 15 0.38
ACGTcount: A:0.46, C:0.10, G:0.00, T:0.44
Consensus pattern (26 bp):
ACCAAAATATTATAAATTTTTTATTT
Found at i:44343882 original size:27 final size:27
Alignment explanation
Indices: 44343852--44343930 Score: 113
Period size: 27 Copynumber: 2.9 Consensus size: 27
44343842 GGCCAATCAC
*
44343852 ATTGGCGGCACCAAAGGTGCCAAAGAG
1 ATTGGCGGCACCAATGGTGCCAAAGAG
* *
44343879 ATTGGCGGCACCAATGGTGCCAATGTG
1 ATTGGCGGCACCAATGGTGCCAAAGAG
* *
44343906 ATTGGTGGCACCAATGGTACCAAAG
1 ATTGGCGGCACCAATGGTGCCAAAG
44343931 GACTAAAATG
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 46 1.00
ACGTcount: A:0.29, C:0.22, G:0.32, T:0.18
Consensus pattern (27 bp):
ATTGGCGGCACCAATGGTGCCAAAGAG
Found at i:44344586 original size:18 final size:19
Alignment explanation
Indices: 44344547--44344642 Score: 133
Period size: 19 Copynumber: 5.2 Consensus size: 19
44344537 ATTTTATATT
44344547 TTAAATGAAAATAGAGTTA
1 TTAAATGAAAATAGAGTTA
* *
44344566 TTAAATGAGAATAG-TTTA
1 TTAAATGAAAATAGAGTTA
44344584 TTAAATGAAAATAGAGTTA
1 TTAAATGAAAATAGAGTTA
* *
44344603 TTAAATGAGAATAG-TTTA
1 TTAAATGAAAATAGAGTTA
*
44344621 TTAAATTAAAATAGAGTTA
1 TTAAATGAAAATAGAGTTA
44344640 TTA
1 TTA
44344643 CTTAATTAGA
Statistics
Matches: 66, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
18 31 0.47
19 35 0.53
ACGTcount: A:0.49, C:0.00, G:0.15, T:0.36
Consensus pattern (19 bp):
TTAAATGAAAATAGAGTTA
Found at i:44344588 original size:37 final size:37
Alignment explanation
Indices: 44344547--44344642 Score: 183
Period size: 37 Copynumber: 2.6 Consensus size: 37
44344537 ATTTTATATT
44344547 TTAAATGAAAATAGAGTTATTAAATGAGAATAGTTTA
1 TTAAATGAAAATAGAGTTATTAAATGAGAATAGTTTA
44344584 TTAAATGAAAATAGAGTTATTAAATGAGAATAGTTTA
1 TTAAATGAAAATAGAGTTATTAAATGAGAATAGTTTA
*
44344621 TTAAATTAAAATAGAGTTATTA
1 TTAAATGAAAATAGAGTTATTA
44344643 CTTAATTAGA
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.49, C:0.00, G:0.15, T:0.36
Consensus pattern (37 bp):
TTAAATGAAAATAGAGTTATTAAATGAGAATAGTTTA
Found at i:44345030 original size:27 final size:27
Alignment explanation
Indices: 44344946--44345031 Score: 127
Period size: 27 Copynumber: 3.2 Consensus size: 27
44344936 TTTTAGTCCT
*
44344946 TTGGCACCATTGGTGCCGCCAATCACA
1 TTGGCACCATTGGTGCCGCCAATCTCA
*
44344973 TTGGCACCATTGGTGCCGCCAATCTCT
1 TTGGCACCATTGGTGCCGCCAATCTCA
* * *
44345000 TTGGCACCTTTGGTGCCGCCAATGTGA
1 TTGGCACCATTGGTGCCGCCAATCTCA
44345027 TTGGC
1 TTGGC
44345032 CTGATCAGGC
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 53 1.00
ACGTcount: A:0.16, C:0.30, G:0.26, T:0.28
Consensus pattern (27 bp):
TTGGCACCATTGGTGCCGCCAATCTCA
Found at i:44345099 original size:27 final size:28
Alignment explanation
Indices: 44345069--44345123 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
44345059 TTGTTTTTTG
*
44345069 TTTTTTTGGT-ATATTTTGGTAAATAAA
1 TTTTTTTGATAATATTTTGGTAAATAAA
*
44345096 TTTTTTTTATAATATTTTGGTAAATAAA
1 TTTTTTTGATAATATTTTGGTAAATAAA
44345124 AAAAGTTATA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 8 0.32
28 17 0.68
ACGTcount: A:0.33, C:0.00, G:0.11, T:0.56
Consensus pattern (28 bp):
TTTTTTTGATAATATTTTGGTAAATAAA
Found at i:44347721 original size:12 final size:12
Alignment explanation
Indices: 44347704--44347728 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
44347694 TGATCTCTTT
44347704 AAGATGCATGCA
1 AAGATGCATGCA
44347716 AAGATGCATGCA
1 AAGATGCATGCA
44347728 A
1 A
44347729 TGAAATGTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.16, G:0.24, T:0.16
Consensus pattern (12 bp):
AAGATGCATGCA
Found at i:44348003 original size:314 final size:313
Alignment explanation
Indices: 44347402--44348021 Score: 1177
Period size: 314 Copynumber: 2.0 Consensus size: 313
44347392 TAATGAATGA
44347402 AAAGATGCATGCAATGAAATGTAATGTAATATGATGCATGAATGCAAAAAGAGGCATTGATATTG
1 AAAGATGCATGCAATGAAATGTAATGTAATATGATGCATGAATGCAAAAAGAGGCATTGATATTG
44347467 ATTCAATTCTATTAGAACAAATTTACTAGAAAATAAATCTCTTTACATAAAACGGATATTTATAT
66 ATTCAATTCTATTAGAACAAATTTACTAGAAAATAAATCTCTTTACATAAAACGGATATTTATAT
44347532 ACGACCTTGTCCTAATACTCGAAGTAAAGACATCGATCCATTCTCCTCAAATCCATATGTTAAGA
131 ACGACCTTGTCCTAATACTCGAAGTAAAGACATCGATCCATTCTCCTCAAATCCATATGTTAAGA
*
44347597 TTGAATCTCGAAAACTCTTCAAAGGGGCACCTCCTCTATCTCCTTTTTGCTTGATCCGAGCCGTG
196 TTGAATCTCAAAAACTCTTCAAAGGGGCACCTCCTCTATCTCCTTTTTGCTTGATCCGAGCCGTG
*
44347662 ACCCATTGATCACTAATCCTCGTGATGCTCATTGATCTCTTTAAGATGCATGC
261 ACCCATTGACCACTAATCCTCGTGATGCTCATTGATCTCTTTAAGATGCATGC
*
44347715 AAAGATGCATGCAATGAAATGTAATGTAATGTAGATGCATGAATGCAAAAAGAGGCATTGATATT
1 AAAGATGCATGCAATGAAATGTAATGTAATAT-GATGCATGAATGCAAAAAGAGGCATTGATATT
* *
44347780 GATTCAATTCTATTTGAACAACTTTACTAGAAAATAAATCTCTTTACATAAAACGGATATTTATA
65 GATTCAATTCTATTAGAACAAATTTACTAGAAAATAAATCTCTTTACATAAAACGGATATTTATA
44347845 TACGACCTTGTCCTAATACTCGAAGTAAAGACATCGATCCATTCTCCTCAAATCCATATGTTAAG
130 TACGACCTTGTCCTAATACTCGAAGTAAAGACATCGATCCATTCTCCTCAAATCCATATGTTAAG
*
44347910 ATTGAATCTCAAAAACTCTTCAAAGGGGCACCTCCTCTATCTTCTTTTTGCTTGATCCGAGCCGT
195 ATTGAATCTCAAAAACTCTTCAAAGGGGCACCTCCTCTATCTCCTTTTTGCTTGATCCGAGCCGT
44347975 GACCCATTGACCACTAATCCTCGTGATGCTCATTGATCTCTTTAAGA
260 GACCCATTGACCACTAATCCTCGTGATGCTCATTGATCTCTTTAAGA
44348022 AAGTTGGCGT
Statistics
Matches: 300, Mismatches: 6, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
313 31 0.10
314 269 0.90
ACGTcount: A:0.34, C:0.20, G:0.15, T:0.31
Consensus pattern (313 bp):
AAAGATGCATGCAATGAAATGTAATGTAATATGATGCATGAATGCAAAAAGAGGCATTGATATTG
ATTCAATTCTATTAGAACAAATTTACTAGAAAATAAATCTCTTTACATAAAACGGATATTTATAT
ACGACCTTGTCCTAATACTCGAAGTAAAGACATCGATCCATTCTCCTCAAATCCATATGTTAAGA
TTGAATCTCAAAAACTCTTCAAAGGGGCACCTCCTCTATCTCCTTTTTGCTTGATCCGAGCCGTG
ACCCATTGACCACTAATCCTCGTGATGCTCATTGATCTCTTTAAGATGCATGC
Found at i:44349863 original size:33 final size:33
Alignment explanation
Indices: 44349792--44349863 Score: 76
Period size: 33 Copynumber: 2.2 Consensus size: 33
44349782 ATTATGTAAA
* * *
44349792 AAAAATATGAATGCATGTATAATTTTAAGTTAT
1 AAAAATAAGAATGCATATATAATTATAAGTTAT
*
44349825 GAAAATAAGAAATGCATATA-AATTATAGAG-TAT
1 AAAAATAAG-AATGCATATATAATTATA-AGTTAT
44349858 AAAAAT
1 AAAAAT
44349864 GTATATAAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
33 21 0.66
34 11 0.34
ACGTcount: A:0.53, C:0.03, G:0.12, T:0.32
Consensus pattern (33 bp):
AAAAATAAGAATGCATATATAATTATAAGTTAT
Found at i:44352429 original size:110 final size:112
Alignment explanation
Indices: 44352219--44352430 Score: 331
Period size: 111 Copynumber: 1.9 Consensus size: 112
44352209 GTTAATAGCC
** *
44352219 GGTATCAGAATACGAGAAAAAGTTTAAAAATTTTTTTTTGGTGGTGGCCTGCCAATGGCCGACAC
1 GGTATCAGAATACGAGAAAAAGTTTAAAAAAGTTTTTTAGGTGGTGGCCTGCCAATGGCCGACAC
*
44352284 CACCTTTTTTGTGGGAATTTTTTTTTACTTTTTTCGTGTCAAAAGAA
66 CACCTTTTTTGTGAGAATTTTTTTTTACTTTTTTCGTGTCAAAAGAA
* * *
44352331 GGTATCAGTATACGA-AAAAAG-TTAAAAAAGTTTTTTAGGTTGGTGGCCTGCCCATGGCCGGCA
1 GGTATCAGAATACGAGAAAAAGTTTAAAAAAGTTTTTTAGG-TGGTGGCCTGCCAATGGCCGACA
44352394 CCACCTTTTTTGTGAG-ATTTTTTTTTACTTTTTTCGT
65 CCACCTTTTTTGTGAGAATTTTTTTTTACTTTTTTCGT
44352431 ATACTGATAC
Statistics
Matches: 92, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
110 36 0.39
111 42 0.46
112 14 0.15
ACGTcount: A:0.25, C:0.15, G:0.21, T:0.39
Consensus pattern (112 bp):
GGTATCAGAATACGAGAAAAAGTTTAAAAAAGTTTTTTAGGTGGTGGCCTGCCAATGGCCGACAC
CACCTTTTTTGTGAGAATTTTTTTTTACTTTTTTCGTGTCAAAAGAA
Found at i:44352515 original size:92 final size:94
Alignment explanation
Indices: 44352410--44352690 Score: 293
Period size: 110 Copynumber: 2.9 Consensus size: 94
44352400 TTTTTGTGAG
*
44352410 ATTTTTTTTTACTTTTTTCGTATACTGATACCTGCTATTGACACGACAAAA-GT-AAAAAAAAA-
1 ATTTTTTTTTACTTTTTTCATATACTGATACCTGCTATTGACACGA-AAAATGTAAAAAAAAAAT
44352472 TCCCACAAAAAAGGTGGCAGGACACCACCA
65 TCCCACAAAAAAGGTGGCAGGACACCACCA
* *
44352502 ATTTTTTTTTACTTTTTTCATATACTGATACCTTCTTTTGACACGAAAAATGTAAAAAAAAAATT
1 ATTTTTTTTTACTTTTTTCATATACTGATACCTGCTATTGACACGAAAAATGTAAAAAAAAAA-T
44352567 TCCCACAAAAAAGGTGGTGCCGGCCATTGGCAGGTCACCACCAA
65 TCCCACAAAAAA---GGT---GG-CA--GG-A---CACCACC-A
* * * * * *
44352611 AATTTTTTTTAACTTTTTTCGTATACTAATACCTTCTTTTGACAGGAAAAA-GT-AAAAAAAAAT
1 -ATTTTTTTTTACTTTTTTCATATACTGATACCTGCTATTGACACGAAAAATGTAAAAAAAAAAT
44352674 TCCCACAAAAAAGGTGG
65 TCCCACAAAAAAGGTGG
44352691 TGTCGGCCAT
Statistics
Matches: 163, Mismatches: 7, Indels: 29
0.82 0.04 0.15
Matches are distributed among these distances:
91 4 0.02
92 45 0.28
93 9 0.06
95 12 0.07
98 3 0.02
101 4 0.02
102 2 0.01
104 5 0.03
105 1 0.01
107 13 0.08
108 16 0.10
109 3 0.02
110 46 0.28
ACGTcount: A:0.37, C:0.19, G:0.13, T:0.32
Consensus pattern (94 bp):
ATTTTTTTTTACTTTTTTCATATACTGATACCTGCTATTGACACGAAAAATGTAAAAAAAAAATT
CCCACAAAAAAGGTGGCAGGACACCACCA
Found at i:44352701 original size:107 final size:108
Alignment explanation
Indices: 44352486--44352740 Score: 369
Period size: 110 Copynumber: 2.4 Consensus size: 108
44352476 ACAAAAAAGG
* * *
44352486 TGGCAGGACACCACC-AATTTTTTTTTACTTTTTTCATATACTGATACCTTCTTTTGACACGAAA
1 TGGCAGG-CACCACCAAATTTTTTTTAACTTTTTTCGTATACTAATACCTTCTTTTGACACGAAA
44352550 AATGTAAAAAAAAAATTTCCCACAAAAAAGGTGGTGCCGGCCAT
65 AATGTAAAAAAAAAATTTCCCACAAAAAAGGTGGTGCCGGCCAT
*
44352594 TGGCAGGTCACCACCAAAATTTTTTTTAACTTTTTTCGTATACTAATACCTTCTTTTGACAGGAA
1 TGGCAGG-CACCACC-AAATTTTTTTTAACTTTTTTCGTATACTAATACCTTCTTTTGACACGAA
*
44352659 AAA-GT-AAAAAAAAA-TTCCCACAAAAAAGGTGGTGTCGGCCAT
64 AAATGTAAAAAAAAAATTTCCCACAAAAAAGGTGGTGCCGGCCAT
44352701 TGGCAGG--CCACCACAATTTTTTTTATACTTTTTCTCGTAT
1 TGGCAGGCACCACCA-AATTTTTTTTA-ACTTTTT-TCGTAT
44352741 TCTGGTACCG
Statistics
Matches: 136, Mismatches: 6, Indels: 12
0.88 0.04 0.08
Matches are distributed among these distances:
103 1 0.01
104 16 0.12
105 7 0.05
106 6 0.04
107 34 0.25
108 23 0.17
109 2 0.01
110 47 0.35
ACGTcount: A:0.33, C:0.20, G:0.14, T:0.33
Consensus pattern (108 bp):
TGGCAGGCACCACCAAATTTTTTTTAACTTTTTTCGTATACTAATACCTTCTTTTGACACGAAAA
ATGTAAAAAAAAAATTTCCCACAAAAAAGGTGGTGCCGGCCAT
Found at i:44353958 original size:22 final size:21
Alignment explanation
Indices: 44353910--44353958 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 21
44353900 AACTAAATCC
*
44353910 TTTCTCTCAATTTCTCTTTAA
1 TTTCTCTCAAATTCTCTTTAA
44353931 TATTCTCTCAAATTC-CTTTCAAA
1 T-TTCTCTCAAATTCTCTTT--AA
44353954 TTTCT
1 TTTCT
44353959 ATTTAAAAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
21 5 0.21
22 16 0.67
23 3 0.12
ACGTcount: A:0.22, C:0.24, G:0.00, T:0.53
Consensus pattern (21 bp):
TTTCTCTCAAATTCTCTTTAA
Found at i:44355705 original size:30 final size:30
Alignment explanation
Indices: 44355639--44355711 Score: 76
Period size: 30 Copynumber: 2.4 Consensus size: 30
44355629 GACGACGACG
44355639 CAGGCCCATCAACGAGGCCCAGAAATTCAC
1 CAGGCCCATCAACGAGGCCCAGAAATTCAC
* * * * *
44355669 CCGGCCCATCATC-AGCGCCCATAATTTCAT
1 CAGGCCCATCAACGAG-GCCCAGAAATTCAC
*
44355699 CAGGCCCAGCAAC
1 CAGGCCCATCAAC
44355712 AGCACCGACA
Statistics
Matches: 34, Mismatches: 8, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
29 2 0.06
30 32 0.94
ACGTcount: A:0.29, C:0.40, G:0.18, T:0.14
Consensus pattern (30 bp):
CAGGCCCATCAACGAGGCCCAGAAATTCAC
Found at i:44356306 original size:49 final size:49
Alignment explanation
Indices: 44356252--44356470 Score: 384
Period size: 49 Copynumber: 4.5 Consensus size: 49
44356242 GTTTATATTA
44356252 ATGTAATAAAATACAAAATAGTTTATTTTGAATAATTTGATATTATTTG
1 ATGTAATAAAATACAAAATAGTTTATTTTGAATAATTTGATATTATTTG
44356301 ATGTAATAAAATACAAAATAGTTTATTTTGAATAATTTGATATTATTTG
1 ATGTAATAAAATACAAAATAGTTTATTTTGAATAATTTGATATTATTTG
44356350 ATGTAATAAAATACAAAATAGTTTATTTTGAATAATTTGATATTATTTG
1 ATGTAATAAAATACAAAATAGTTTATTTTGAATAATTTGATATTATTTG
* * * *
44356399 ATGTAATAAAATACATAATAGTTTATTTTCAATATTTTGATATTATTTC
1 ATGTAATAAAATACAAAATAGTTTATTTTGAATAATTTGATATTATTTG
* *
44356448 ATTTAATAAAATATAAAATAGTT
1 ATGTAATAAAATACAAAATAGTT
44356471 AATATTCTTA
Statistics
Matches: 163, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 163 1.00
ACGTcount: A:0.43, C:0.03, G:0.09, T:0.45
Consensus pattern (49 bp):
ATGTAATAAAATACAAAATAGTTTATTTTGAATAATTTGATATTATTTG
Found at i:44356327 original size:29 final size:29
Alignment explanation
Indices: 44356294--44356377 Score: 78
Period size: 29 Copynumber: 3.2 Consensus size: 29
44356284 TAATTTGATA
44356294 TTATTTGATGTAATAAAATACAAAATAGT
1 TTATTTGATGTAATAAAATACAAAATAGT
***
44356323 TTATTT--TG-AAT--AAT--TTGATA--
1 TTATTTGATGTAATAAAATACAAAATAGT
44356343 TTATTTGATGTAATAAAATACAAAATAGT
1 TTATTTGATGTAATAAAATACAAAATAGT
44356372 TTATTT
1 TTATTT
44356378 TGAATAATTT
Statistics
Matches: 40, Mismatches: 6, Indels: 18
0.62 0.09 0.28
Matches are distributed among these distances:
20 6 0.15
22 5 0.12
23 3 0.08
24 3 0.08
25 3 0.08
26 3 0.08
27 5 0.12
29 12 0.30
ACGTcount: A:0.43, C:0.02, G:0.10, T:0.45
Consensus pattern (29 bp):
TTATTTGATGTAATAAAATACAAAATAGT
Found at i:44359847 original size:124 final size:124
Alignment explanation
Indices: 44359668--44360078 Score: 583
Period size: 124 Copynumber: 3.3 Consensus size: 124
44359658 CCCAAACATG
* * *
44359668 CTACTGTAGCAAAAACGCGTCCACGTGGGAGCGATTTCAGAAAATT-TTCTTATAAAGCATCTTG
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGAGCGATTTCAG-AAATTCTTCTAATAAAGCATCCTG
* *
44359732 CTTGAAGCATTTTTATACTATTTGCACAAAAACGTCAACTAGAAATTATTTTTTCAGGAC
65 CTTCAAGCATTTTTATACTATTTGCTCAAAAACGTCAACTAGAAATTATTTTTTCAGGAC
* * *
44359792 CTACTGTAGCAAAAGCGCATCTACGTGGGAGCGATTTCAGAAATTCTTCTAATAAAGCATCCTAC
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGAGCGATTTCAGAAATTCTTCTAATAAAGCATCCTGC
* * * * ** *
44359857 TTCAAGCGTTTTTATACAATTTACTCAGAAATTTCAACTTGAAATTATTTTTTCAGGAC
66 TTCAAGCATTTTTATACTATTTGCTCAAAAACGTCAACTAGAAATTATTTTTTCAGGAC
* * *
44359916 CTACTGTAGCAAAATCGCGTCCACGTGGGAGCGATTTCAGAAATTCTTTTGATAAAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGAGCGATTTCAGAAATTCTTCTAATAAAGCATCCTGC
* *
44359981 TTCAAGCGTTTTTTATACTATTTGCTCATAAACGTCAACTCA-AAATTATTTTTTCAGGAC
66 TTCAAGC-ATTTTTATACTATTTGCTCAAAAACGTCAACT-AGAAATTATTTTTTCAGGAC
* *
44360041 CTACTGTAGCAAAAGCGCGTCCTCGTGAGAGCGATTTC
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGAGCGATTTC
44360079 CTTAATAAAT
Statistics
Matches: 253, Mismatches: 31, Indels: 5
0.88 0.11 0.02
Matches are distributed among these distances:
123 5 0.02
124 169 0.67
125 79 0.31
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.33
Consensus pattern (124 bp):
CTACTGTAGCAAAAGCGCGTCCACGTGGGAGCGATTTCAGAAATTCTTCTAATAAAGCATCCTGC
TTCAAGCATTTTTATACTATTTGCTCAAAAACGTCAACTAGAAATTATTTTTTCAGGAC
Found at i:44360288 original size:21 final size:22
Alignment explanation
Indices: 44360248--44360290 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
44360238 CCCTAAAAAT
*
44360248 CCTAAAAATCCTAAACCCTAAC
1 CCTAAAAATCCTAAAACCTAAC
44360270 CCTAAAAATCC-AAAACCTAAC
1 CCTAAAAATCCTAAAACCTAAC
44360291 GTGGGGAGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.49, C:0.35, G:0.00, T:0.16
Consensus pattern (22 bp):
CCTAAAAATCCTAAAACCTAAC
Found at i:44360771 original size:2 final size:2
Alignment explanation
Indices: 44360764--44360856 Score: 121
Period size: 2 Copynumber: 50.0 Consensus size: 2
44360754 NNNNNNNNNN
44360764 TA TA TA TA TA GTA TA TA TA -A TA -A TA -A TA TA -A TA -A TA TA
1 TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
44360802 TA TA -A TA -A TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
44360841 TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA
44360857 ACATTGCATA
Statistics
Matches: 82, Mismatches: 0, Indels: 18
0.82 0.00 0.18
Matches are distributed among these distances:
1 8 0.10
2 72 0.88
3 2 0.02
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (2 bp):
TA
Found at i:44363734 original size:79 final size:75
Alignment explanation
Indices: 44363651--44363807 Score: 201
Period size: 75 Copynumber: 2.0 Consensus size: 75
44363641 TTCATACATT
*
44363651 AATCCATCAACATATT-TAATTTCATAACAAAATATAAAT-TGTAAGCTAAATTAAATCTATATT
1 AATCCATCAACATATTATAATGT-ATAA-AAAAT-T-AATGTGTAA-C-AAATTAAATCTATATT
44363714 TATAACAGTATACTAA
60 TATAACAGTATACTAA
* * * *
44363730 AATCCATCAACATATTATAATGTGTTAGAAATTAATGTGTTACAAATTAAATCTATATTTATAAC
1 AATCCATCAACATATTATAATGTATAAAAAATTAATGTGTAACAAATTAAATCTATATTTATAAC
44363795 AGTATACTAA
66 AGTATACTAA
44363805 AAT
1 AAT
44363808 TTAAAAGTTC
Statistics
Matches: 71, Mismatches: 5, Indels: 8
0.85 0.06 0.10
Matches are distributed among these distances:
75 35 0.49
76 4 0.06
77 5 0.07
78 4 0.06
79 18 0.25
80 5 0.07
ACGTcount: A:0.46, C:0.11, G:0.06, T:0.36
Consensus pattern (75 bp):
AATCCATCAACATATTATAATGTATAAAAAATTAATGTGTAACAAATTAAATCTATATTTATAAC
AGTATACTAA
Found at i:44363767 original size:15 final size:15
Alignment explanation
Indices: 44363747--44363779 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
44363737 CAACATATTA
*
44363747 TAATGTGTTAGAAAT
1 TAATGTGTTACAAAT
44363762 TAATGTGTTACAAAT
1 TAATGTGTTACAAAT
44363777 TAA
1 TAA
44363780 ATCTATATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.42, C:0.03, G:0.15, T:0.39
Consensus pattern (15 bp):
TAATGTGTTACAAAT
Found at i:44363840 original size:13 final size:13
Alignment explanation
Indices: 44363818--44363855 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
44363808 TTAAAAGTTC
*
44363818 AAACATTATATTA
1 AAACAATATATTA
44363831 AAACAATATATTA
1 AAACAATATATTA
44363844 AAA-AAGTATATT
1 AAACAA-TATATT
44363856 TATAATAGTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 2 0.09
13 21 0.91
ACGTcount: A:0.58, C:0.05, G:0.03, T:0.34
Consensus pattern (13 bp):
AAACAATATATTA
Found at i:44365122 original size:42 final size:42
Alignment explanation
Indices: 44365034--44365160 Score: 129
Period size: 38 Copynumber: 3.1 Consensus size: 42
44365024 CATAACAGCA
** * ** * *
44365034 AAAATAAAAAACACAACCATTAACAG-AACACCATTAACAGC
1 AAAATAAAAAACACAACCATTAACAGCATTAACAGCAAAATC
44365075 AAAAATAAAAAACACAACCATTAACAGCATTAACAGCAAAATC
1 -AAAATAAAAAACACAACCATTAACAGCATTAACAGCAAAATC
* *
44365118 AAAAT--CATA-AC-ACCATTAACAGCATTAACAGCAAAATC
1 AAAATAAAAAACACAACCATTAACAGCATTAACAGCAAAATC
44365156 AAAAT
1 AAAAT
44365161 TAACAGCAAA
Statistics
Matches: 75, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
38 32 0.43
39 2 0.03
40 2 0.03
42 31 0.41
43 8 0.11
ACGTcount: A:0.58, C:0.22, G:0.05, T:0.15
Consensus pattern (42 bp):
AAAATAAAAAACACAACCATTAACAGCATTAACAGCAAAATC
Found at i:44365142 original size:38 final size:36
Alignment explanation
Indices: 44365060--44365160 Score: 139
Period size: 38 Copynumber: 2.7 Consensus size: 36
44365050 CCATTAACAG
* * * *
44365060 AACACCATTAACAGCAAAAATAAAAAACACAACCATT
1 AACAGCATTAACAGC-AAAATCAAAATCAAAACCATT
44365097 AACAGCATTAACAGCAAAATCAAAATCATAACACCATT
1 AACAGCATTAACAGCAAAATCAAAATCA-AA-ACCATT
44365135 AACAGCATTAACAGCAAAATCAAAAT
1 AACAGCATTAACAGCAAAATCAAAAT
44365161 TAACAGCAAA
Statistics
Matches: 58, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
36 11 0.19
37 15 0.26
38 32 0.55
ACGTcount: A:0.56, C:0.23, G:0.05, T:0.16
Consensus pattern (36 bp):
AACAGCATTAACAGCAAAATCAAAATCAAAACCATT
Found at i:44365162 original size:18 final size:18
Alignment explanation
Indices: 44365103--44365178 Score: 82
Period size: 18 Copynumber: 4.1 Consensus size: 18
44365093 CATTAACAGC
44365103 ATTAACAGCAAAATCAAA
1 ATTAACAGCAAAATCAAA
* * **
44365121 ATCATAACACCATTAA-CAGC
1 AT--TAACAGCA-AAATCAAA
44365141 ATTAACAGCAAAATCAAA
1 ATTAACAGCAAAATCAAA
44365159 ATTAACAGCAAAATCAAA
1 ATTAACAGCAAAATCAAA
44365177 AT
1 AT
44365179 CAGAACACCA
Statistics
Matches: 46, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
17 2 0.04
18 31 0.67
20 11 0.24
21 2 0.04
ACGTcount: A:0.57, C:0.20, G:0.05, T:0.18
Consensus pattern (18 bp):
ATTAACAGCAAAATCAAA
Found at i:44365170 original size:56 final size:56
Alignment explanation
Indices: 44365103--44365216 Score: 219
Period size: 56 Copynumber: 2.0 Consensus size: 56
44365093 CATTAACAGC
*
44365103 ATTAACAGCAAAATCAAAATCATAACACCATTAACAGCATTAACAGCAAAATCAAA
1 ATTAACAGCAAAATCAAAATCAGAACACCATTAACAGCATTAACAGCAAAATCAAA
44365159 ATTAACAGCAAAATCAAAATCAGAACACCATTAACAGCATTAACAGCAAAATCAAA
1 ATTAACAGCAAAATCAAAATCAGAACACCATTAACAGCATTAACAGCAAAATCAAA
44365215 AT
1 AT
44365217 CAGAACACCA
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 57 1.00
ACGTcount: A:0.55, C:0.21, G:0.06, T:0.18
Consensus pattern (56 bp):
ATTAACAGCAAAATCAAAATCAGAACACCATTAACAGCATTAACAGCAAAATCAAA
Found at i:44365210 original size:38 final size:38
Alignment explanation
Indices: 44365159--44365335 Score: 150
Period size: 38 Copynumber: 5.0 Consensus size: 38
44365149 CAAAATCAAA
44365159 ATTAACAGCAAAATCAAAATCAGAACACCATTAACAGC
1 ATTAACAGCAAAATCAAAATCAGAACACCATTAACAGC
*
44365197 ATTAACAGCAAAATCAAAATCAGAACACCATTAACAAC
1 ATTAACAGCAAAATCAAAATCAGAACACCATTAACAGC
* * * ** *
44365235 -TGAA-TGACTAGGT--TAA-CAGAACACCATT-A-A-C
1 ATTAACAG-CAAAATCAAAATCAGAACACCATTAACAGC
* * *
44365266 ---AACA--AAAAT-AAAA-AACACCACCATTAACAGC
1 ATTAACAGCAAAATCAAAATCAGAACACCATTAACAGC
44365297 ATTAACAGCAAAATCAAAATCAGAACACCATTAACAGC
1 ATTAACAGCAAAATCAAAATCAGAACACCATTAACAGC
44365335 A
1 A
44365336 AAAATCAAAA
Statistics
Matches: 108, Mismatches: 18, Indels: 26
0.71 0.12 0.17
Matches are distributed among these distances:
27 2 0.02
28 11 0.10
29 3 0.03
30 1 0.01
31 2 0.02
32 1 0.01
33 1 0.01
34 16 0.15
35 2 0.02
36 6 0.06
37 10 0.09
38 53 0.49
ACGTcount: A:0.53, C:0.23, G:0.08, T:0.16
Consensus pattern (38 bp):
ATTAACAGCAAAATCAAAATCAGAACACCATTAACAGC
Found at i:44365328 original size:29 final size:30
Alignment explanation
Indices: 44365291--44365348 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 30
44365281 CACCACCATT
*
44365291 AACAGCATTAACAGC-AAAATCAAAATCAG
1 AACACCATTAACAGCAAAAATCAAAATCAG
44365320 AACACCATTAACAGCAAAAATCAAAATCA
1 AACACCATTAACAGCAAAAATCAAAATCA
44365349 CAACCAACAT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 14 0.52
30 13 0.48
ACGTcount: A:0.57, C:0.22, G:0.07, T:0.14
Consensus pattern (30 bp):
AACACCATTAACAGCAAAAATCAAAATCAG
Found at i:44365676 original size:20 final size:21
Alignment explanation
Indices: 44365639--44365682 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
44365629 AATGGGAAAG
* * *
44365639 TTAAAACTAATAATAAATT-T
1 TTAAAAATAAAAAAAAATTAT
44365659 TTAAAAATAAAAAAAAATTAT
1 TTAAAAATAAAAAAAAATTAT
44365680 TTA
1 TTA
44365683 GATCCGGGCC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 16 0.80
21 4 0.20
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.36
Consensus pattern (21 bp):
TTAAAAATAAAAAAAAATTAT
Found at i:44367283 original size:11 final size:11
Alignment explanation
Indices: 44367207--44367285 Score: 63
Period size: 12 Copynumber: 7.0 Consensus size: 11
44367197 TTAACTTTAT
*
44367207 TATTATTATTA
1 TATTATCATTA
*
44367218 TTATTATTATTA
1 -TATTATCATTA
*
44367230 TTATTATTATTA
1 -TATTATCATTA
*
44367242 TTATTATTATTA
1 -TATTATCATTA
44367254 TTATTATCA-T-
1 -TATTATCATTA
44367264 TATTATCATTA
1 TATTATCATTA
*
44367275 TATTTTCATTA
1 TATTATCATTA
44367286 ATAATTATTA
Statistics
Matches: 63, Mismatches: 2, Indels: 5
0.90 0.03 0.07
Matches are distributed among these distances:
9 8 0.13
10 1 0.02
11 11 0.17
12 43 0.68
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (11 bp):
TATTATCATTA
Found at i:44367295 original size:3 final size:3
Alignment explanation
Indices: 44367203--44367275 Score: 128
Period size: 3 Copynumber: 24.3 Consensus size: 3
44367193 CTTGTTAACT
44367203 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
44367251 TTA TTA TTA TCA TTA TTA TCA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
44367276 ATTTTCATTA
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 66 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:44368004 original size:110 final size:108
Alignment explanation
Indices: 44367725--44368264 Score: 757
Period size: 110 Copynumber: 5.0 Consensus size: 108
44367715 TCAAAAAAGG
* * * *
44367725 AAAATATTTCAAAATAAGGTAATATTTTGCGTTTGGAAATTCGAGGAACGTGTCCTAAGGTACTA
1 AAAAT-TTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTG
* * *
44367790 GGTTTCGATTTCTCGTTCGAACAAATGACTTAATATTCTTTTCA
65 GGTTTCGATTTCTCGTTCGACCAAATGACTAAATATCCTTTTCA
*
44367834 AAAATTTTCAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGG
1 AAAATTTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGG
* *
44367899 GTTTCAATTTCTCGTTCGACCAAAT-AGCTAAATATCCTTTTAA
66 GTTTCGATTTCTCGTTCGACCAAATGA-CTAAATATCCTTTTCA
* *
44367942 AAAACTTTTCAAAAATAAGACAATGTTTTGCATTTGGAAATTCGAGGAACGTGCCCTAAGGTACT
1 AAAA-TTTTC-AAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACT
* *
44368007 GGGTTTCGATTTCTCGTTCGACCAAATGACTTAATATCTTTTTCA
64 GGGTTTCGATTTCTCGTTCGACCAAATGACTAAATATCCTTTTCA
* *
44368052 AAAATTTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTACTG
1 AAAATTTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAG-GAACGTGCCCTAAGGTACTG
* * *
44368117 GGTGTCGATTTTTCTCGTTCAACCAAAT-AGCTAAGTATCCTTTTCA
65 GGTTTCGA--TTTCTCGTTCGACCAAATGA-CTAAATATCCTTTTCA
* *
44368163 AAAA-TTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGGAACGTGCTCTAAGGTGCTGG
1 AAAATTTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGG
*
44368227 GTTTCGATTTCTCG-TCTAACCAAATTGAC-AAATATCCT
66 GTTTCGATTTCTCGTTC-GACCAAA-TGACTAAATATCCT
44368265 CTTGAATTTT
Statistics
Matches: 390, Mismatches: 30, Indels: 24
0.88 0.07 0.05
Matches are distributed among these distances:
106 2 0.01
107 23 0.06
108 132 0.34
109 64 0.16
110 134 0.34
111 35 0.09
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.34
Consensus pattern (108 bp):
AAAATTTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGG
GTTTCGATTTCTCGTTCGACCAAATGACTAAATATCCTTTTCA
Found at i:44368177 original size:218 final size:215
Alignment explanation
Indices: 44367725--44368241 Score: 802
Period size: 218 Copynumber: 2.4 Consensus size: 215
44367715 TCAAAAAAGG
* * * * *
44367725 AAAATATTTCAAAATAAGGTAATATTTTGCGTTTGGAAATTCGAGGAACGTGTCCTAAGGTACTA
1 AAAAAATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTG
44367790 GGTTTCGATTTCTCGTTCGAACAAATGACTTAATATTCTTTTCAAAAATTTTCAAAATAAGGCAA
66 GGTTTCGATTTCTCGTTCGAACAAATGACTTAATATTCTTTTCAAAAATTTTCAAAATAAGGCAA
* * * *
44367855 TATTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGGGTTTCAATTTCTCGTTCGACC
131 TATTTTGCGTTTGGAAATTCGAGAAACATGCCCTAAGGTACTGGGTGTCAATTTCTCGTTCAACC
44367920 AAATAGCTAAATATCCTTTT
196 AAATAGCTAAATATCCTTTT
* *
44367940 AAAAAACTTTTCAAAAATAAGACAATGTTTTGCATTTGGAAATTCGAGGAACGTGCCCTAAGGTA
1 AAAAAA--TTTC-AAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTA
*
44368005 CTGGGTTTCGATTTCTCGTTCGACCAAATGACTTAATA-TCTTTTTCAAAAATTTTCAAAATAAG
63 CTGGGTTTCGATTTCTCGTTCGAACAAATGACTTAATATTC-TTTTCAAAAATTTTCAAAATAAG
* *
44368069 GCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTACTGGGTGTCGATTTTTCTCG
127 GCAATATTTTGCGTTTGGAAATTCGAG-AAACATGCCCTAAGGTACTGGGTGTC-A-ATTTCTCG
*
44368134 TTCAACCAAATAGCTAAGTATCCTTTT
189 TTCAACCAAATAGCTAAATATCCTTTT
* * *
44368161 CAAAAATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGGAACGTGCTCTAAGGTGCTG
1 AAAAAATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTG
44368226 GGTTTCGATTTCTCGT
66 GGTTTCGATTTCTCGT
44368242 CTAACCAAAT
Statistics
Matches: 275, Mismatches: 20, Indels: 11
0.90 0.07 0.04
Matches are distributed among these distances:
215 5 0.02
217 6 0.02
218 199 0.72
219 27 0.10
220 1 0.00
221 37 0.13
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.34
Consensus pattern (215 bp):
AAAAAATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTG
GGTTTCGATTTCTCGTTCGAACAAATGACTTAATATTCTTTTCAAAAATTTTCAAAATAAGGCAA
TATTTTGCGTTTGGAAATTCGAGAAACATGCCCTAAGGTACTGGGTGTCAATTTCTCGTTCAACC
AAATAGCTAAATATCCTTTT
Found at i:44374169 original size:23 final size:24
Alignment explanation
Indices: 44374138--44374182 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
44374128 CTTGATTCTC
**
44374138 ATTCTATCAATCTCAATATCATCA
1 ATTCTATCAATCAAAATATCATCA
44374162 ATTC-ATCAATCAAAATATCAT
1 ATTCTATCAATCAAAATATCAT
44374183 TTCATACATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.42, C:0.22, G:0.00, T:0.36
Consensus pattern (24 bp):
ATTCTATCAATCAAAATATCATCA
Found at i:44375087 original size:19 final size:16
Alignment explanation
Indices: 44375063--44375104 Score: 50
Period size: 15 Copynumber: 2.5 Consensus size: 16
44375053 CCTCAAAACA
44375063 TAATTAAACATAATTAATT
1 TAATTAAAC-T-ATT-ATT
44375082 TAATT-AACTATTATT
1 TAATTAAACTATTATT
44375097 TAATTAAA
1 TAATTAAA
44375105 ATTAAACTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
15 8 0.36
16 5 0.23
17 1 0.05
18 3 0.14
19 5 0.23
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (16 bp):
TAATTAAACTATTATT
Found at i:44376396 original size:5 final size:5
Alignment explanation
Indices: 44376386--44376410 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
44376376 TAGCTTATTA
44376386 TTTAT TTTAT TTTAT TTTAT TTTAT
1 TTTAT TTTAT TTTAT TTTAT TTTAT
44376411 GCATTTATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTAT
Found at i:44380605 original size:23 final size:23
Alignment explanation
Indices: 44380579--44380626 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
44380569 TTTTGAGTAA
44380579 TTTAA-TTT-TTTCTTTTCTGTTCT
1 TTTAACTTTCTTTCTTTT-T-TTCT
44380602 TTTAACTTTCTTTCTTTTTTTCT
1 TTTAACTTTCTTTCTTTTTTTCT
44380625 TT
1 TT
44380627 ATTTTTCATT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
23 11 0.48
24 4 0.17
25 8 0.35
ACGTcount: A:0.08, C:0.15, G:0.02, T:0.75
Consensus pattern (23 bp):
TTTAACTTTCTTTCTTTTTTTCT
Found at i:44381771 original size:17 final size:17
Alignment explanation
Indices: 44381729--44381771 Score: 77
Period size: 17 Copynumber: 2.5 Consensus size: 17
44381719 TCAGATTTTA
*
44381729 TTTTGAAGCCAAAATTT
1 TTTTGAAGTCAAAATTT
44381746 TTTTGAAGTCAAAATTT
1 TTTTGAAGTCAAAATTT
44381763 TTTTGAAGT
1 TTTTGAAGT
44381772 AGATTTACGA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.33, C:0.07, G:0.14, T:0.47
Consensus pattern (17 bp):
TTTTGAAGTCAAAATTT
Found at i:44382356 original size:31 final size:32
Alignment explanation
Indices: 44382320--44382384 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
44382310 CTTAGATAAT
44382320 TTTAAAGAG-TTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTTATTAGGATTCAATTACTC
44382351 TTTAAAGAGTTTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTTATTAGGATTCAATTACTC
44382383 TT
1 TT
44382385 GTAATTTGCC
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 9 0.27
32 24 0.73
ACGTcount: A:0.31, C:0.09, G:0.12, T:0.48
Consensus pattern (32 bp):
TTTAAAGAGTTTTTATTAGGATTCAATTACTC
Found at i:44382693 original size:3 final size:3
Alignment explanation
Indices: 44382685--44382716 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
44382675 ATCTATCCTT
44382685 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
44382717 TAACTAATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:44382966 original size:13 final size:13
Alignment explanation
Indices: 44382937--44382965 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
44382927 AAGAAGAAGC
44382937 AAAACGCGCAAAA
1 AAAACGCGCAAAA
44382950 AAAAC-CGCAAAA
1 AAAACGCGCAAAA
44382962 AAAA
1 AAAA
44382966 AAGTTGCCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.69, C:0.21, G:0.10, T:0.00
Consensus pattern (13 bp):
AAAACGCGCAAAA
Found at i:44388998 original size:3 final size:3
Alignment explanation
Indices: 44388990--44389042 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
44388980 ATCTATCCTT
44388990 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
44389038 TTA TT
1 TTA TT
44389043 TAACTAATTA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:44395038 original size:20 final size:23
Alignment explanation
Indices: 44395013--44395057 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 23
44395003 AATTTTTTTC
44395013 AACA-TTAATTT-TTAT-TCAAA
1 AACATTTAATTTGTTATATCAAA
44395033 AACATTTTAATTTGTTATATCAAA
1 AACA-TTTAATTTGTTATATCAAA
44395057 A
1 A
44395058 CATGTTATCA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
20 4 0.19
22 7 0.33
23 4 0.19
24 6 0.29
ACGTcount: A:0.44, C:0.09, G:0.02, T:0.44
Consensus pattern (23 bp):
AACATTTAATTTGTTATATCAAA
Found at i:44403567 original size:52 final size:50
Alignment explanation
Indices: 44403455--44403569 Score: 115
Period size: 52 Copynumber: 2.3 Consensus size: 50
44403445 CATATTGTGG
* * * *
44403455 GTTAAATTTGTTAAATTTGTATCAAATGAAAGAATGTGTAAGTATCGTGA
1 GTTAAATTTATTAAATTTGGATCAAATGAAAGAATGTGTAAATATCGAGA
* * * * *
44403505 GCTAATTTTATTAAATTTGAGATCAAATTGATAA-AATGTGTAAATTTTGAGT
1 GTTAAATTTATTAAATTTG-GATCAAA-TGA-AAGAATGTGTAAATATCGAGA
44403557 GTTAAATTTATTA
1 GTTAAATTTATTA
44403570 TTAAATTTAT
Statistics
Matches: 51, Mismatches: 11, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
50 16 0.31
51 6 0.12
52 27 0.53
53 2 0.04
ACGTcount: A:0.38, C:0.03, G:0.17, T:0.42
Consensus pattern (50 bp):
GTTAAATTTATTAAATTTGGATCAAATGAAAGAATGTGTAAATATCGAGA
Found at i:44412820 original size:5 final size:5
Alignment explanation
Indices: 44412802--44412855 Score: 62
Period size: 5 Copynumber: 11.4 Consensus size: 5
44412792 ATGTTTTAAA
*
44412802 TATAT TA-A- TATAT TATAT TATAT TATAA TA-AT TATAT TATAT TAT-T
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
44412848 ATATAT TA
1 -TATAT TA
44412856 AATAAACTAA
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
3 2 0.05
4 6 0.14
5 33 0.79
6 1 0.02
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (5 bp):
TATAT
Found at i:44412837 original size:19 final size:20
Alignment explanation
Indices: 44412807--44412855 Score: 82
Period size: 19 Copynumber: 2.5 Consensus size: 20
44412797 TTAAATATAT
44412807 TAATATATTATATTATATTA
1 TAATATATTATATTATATTA
44412827 TAATA-ATTATATTATATTA
1 TAATATATTATATTATATTA
*
44412846 TTATATATTA
1 TAATATATTA
44412856 AATAAACTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 18 0.67
20 9 0.33
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
TAATATATTATATTATATTA
Found at i:44412837 original size:24 final size:23
Alignment explanation
Indices: 44412802--44412846 Score: 72
Period size: 24 Copynumber: 1.9 Consensus size: 23
44412792 ATGTTTTAAA
*
44412802 TATATTAATATATTATATTATAT
1 TATAATAATATATTATATTATAT
44412825 TATAATAATTATATTATATTAT
1 TATAATAA-TATATTATATTAT
44412847 TATATATTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (23 bp):
TATAATAATATATTATATTATAT
Found at i:44413081 original size:22 final size:22
Alignment explanation
Indices: 44413042--44413089 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
44413032 AAATAAAAGA
44413042 AAAAGAAACAAAAGAAGA-ACAG
1 AAAAGAAACAAAAGAAGAGAC-G
*
44413064 AAAAGAAAC-AGAGAAAGAGACG
1 AAAAGAAACAAAAG-AAGAGACG
44413086 AAAA
1 AAAA
44413090 TAGGGGAAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
21 3 0.13
22 18 0.78
23 2 0.09
ACGTcount: A:0.71, C:0.08, G:0.21, T:0.00
Consensus pattern (22 bp):
AAAAGAAACAAAAGAAGAGACG
Found at i:44413480 original size:23 final size:24
Alignment explanation
Indices: 44413445--44413489 Score: 67
Period size: 23 Copynumber: 1.9 Consensus size: 24
44413435 AATATGGCAA
44413445 GAAATTAAGTAGAAAAG-AAGTAT
1 GAAATTAAGTAGAAAAGTAAGTAT
44413468 GAAA-TAAGCTAGAAAAGTAAGT
1 GAAATTAAG-TAGAAAAGTAAGT
44413490 GAGCTTAGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 4 0.20
23 12 0.60
24 4 0.20
ACGTcount: A:0.56, C:0.02, G:0.22, T:0.20
Consensus pattern (24 bp):
GAAATTAAGTAGAAAAGTAAGTAT
Found at i:44416134 original size:23 final size:23
Alignment explanation
Indices: 44416108--44416204 Score: 124
Period size: 23 Copynumber: 4.2 Consensus size: 23
44416098 ATAAGTGCCA
*
44416108 CACTGATATGTAGCCAAAACTAC
1 CACTGATATGTAGCCAAAGCTAC
44416131 CACTGATATGTAGCCAAAGCTAC
1 CACTGATATGTAGCCAAAGCTAC
**
44416154 CACTG-TAATGTAGCCGTAGCTAC
1 CACTGAT-ATGTAGCCAAAGCTAC
* * *
44416177 CACTGAAATGTAACCTAAGCTAC
1 CACTGATATGTAGCCAAAGCTAC
44416200 CACTG
1 CACTG
44416205 GTCAATAACA
Statistics
Matches: 65, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
22 1 0.02
23 64 0.98
ACGTcount: A:0.34, C:0.27, G:0.16, T:0.23
Consensus pattern (23 bp):
CACTGATATGTAGCCAAAGCTAC
Found at i:44418899 original size:24 final size:24
Alignment explanation
Indices: 44418872--44418925 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
44418862 TTCAAAGCTT
* *
44418872 TCAAAGAAAAGATAGAGTTTCTTC
1 TCAAAGAAAAGATAGACTTTCTAC
* **
44418896 TCAAAGCATCGATAGACTTTCTAC
1 TCAAAGAAAAGATAGACTTTCTAC
44418920 TCAAAG
1 TCAAAG
44418926 CATCAGCAAC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.39, C:0.19, G:0.15, T:0.28
Consensus pattern (24 bp):
TCAAAGAAAAGATAGACTTTCTAC
Done.