Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A03
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: 108673976
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.31
Warning! 5040000 characters in sequence are not A, C, G, or T
File 64 of 333
Found at i:19137553 original size:23 final size:23
Alignment explanation
Indices: 19137523--19137568 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
19137513 AGTGACTGAA
19137523 TGTTTGAAGCTTTAAAAATGGCT
1 TGTTTGAAGCTTTAAAAATGGCT
19137546 TGTTTGAAGCTTTAAAAATGGCT
1 TGTTTGAAGCTTTAAAAATGGCT
19137569 ATTCTTGCCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.30, C:0.09, G:0.22, T:0.39
Consensus pattern (23 bp):
TGTTTGAAGCTTTAAAAATGGCT
Found at i:19158652 original size:16 final size:16
Alignment explanation
Indices: 19158626--19158670 Score: 65
Period size: 16 Copynumber: 2.8 Consensus size: 16
19158616 TAATTAGTAA
19158626 AAAAGAATATATACAT
1 AAAAGAATATATACAT
*
19158642 AATAA-AATATATATAT
1 AA-AAGAATATATACAT
19158658 AAAAGAATATATA
1 AAAAGAATATATA
19158671 AGAAAAATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
15 2 0.08
16 22 0.85
17 2 0.08
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.29
Consensus pattern (16 bp):
AAAAGAATATATACAT
Found at i:19163663 original size:42 final size:42
Alignment explanation
Indices: 19163615--19163727 Score: 113
Period size: 42 Copynumber: 2.7 Consensus size: 42
19163605 ACTGAGATTC
* * *
19163615 CGTATAAGACCATATCTCGGATATGGCATCGATGTG-TGATTT
1 CGTATAAGACCATATCTAGGATATGGCATCAATATGAT-ATTT
* * *
19163657 TGTATAAGACCATGT-TAAGGACATGGCATCAATATGATATTT
1 CGTATAAGACCATATCT-AGGATATGGCATCAATATGATATTT
* * *
19163699 CATGTAAGACCATATCTGGGATATGGCAT
1 CGTATAAGACCATATCTAGGATATGGCAT
19163728 TGATACGGTA
Statistics
Matches: 56, Mismatches: 12, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
41 1 0.02
42 53 0.95
43 2 0.04
ACGTcount: A:0.31, C:0.15, G:0.22, T:0.32
Consensus pattern (42 bp):
CGTATAAGACCATATCTAGGATATGGCATCAATATGATATTT
Found at i:19169847 original size:29 final size:29
Alignment explanation
Indices: 19169795--19169850 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
19169785 ATTGAGATCC
*
19169795 GAACTCATTGAGTTGTGGTCCGAGTTCGT
1 GAACTCATTGAGTTGCGGTCCGAGTTCGT
* * *
19169824 GAACTCGTTGAGTTGCGTTTCGAGTTC
1 GAACTCATTGAGTTGCGGTCCGAGTTC
19169851 ACCTATGGAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.16, C:0.18, G:0.30, T:0.36
Consensus pattern (29 bp):
GAACTCATTGAGTTGCGGTCCGAGTTCGT
Found at i:19169924 original size:46 final size:46
Alignment explanation
Indices: 19169824--19169950 Score: 148
Period size: 46 Copynumber: 2.7 Consensus size: 46
19169814 CCGAGTTCGT
* * * *
19169824 GAACTCGTTGAGTTGCGTTTCGAGTTCACCTATGGATGCAAGCATCT
1 GAACTCGTTGAGTTGCGTTCCGAGTTCA-TTATGGATGCAAGCACCC
* *
19169871 GAACTCGTTGAGTTGTGTTCCGTGTTCATTATGGATGCGAA-CACCC
1 GAACTCGTTGAGTTGCGTTCCGAGTTCATTATGGATGC-AAGCACCC
* * *
19169917 GAGCTCGTTGAGCTGCGTTGCGAGTTCATTATGG
1 GAACTCGTTGAGTTGCGTTCCGAGTTCATTATGG
19169951 GTGAGATTAT
Statistics
Matches: 68, Mismatches: 11, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
46 41 0.60
47 27 0.40
ACGTcount: A:0.19, C:0.20, G:0.28, T:0.32
Consensus pattern (46 bp):
GAACTCGTTGAGTTGCGTTCCGAGTTCATTATGGATGCAAGCACCC
Found at i:19175278 original size:20 final size:20
Alignment explanation
Indices: 19175253--19175293 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
19175243 TATTCTCTAA
19175253 AAAGTTTCAATTATGTAATG
1 AAAGTTTCAATTATGTAATG
*
19175273 AAAGTTTCAATTATTTAATG
1 AAAGTTTCAATTATGTAATG
19175293 A
1 A
19175294 GGTAAGGGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.41, C:0.05, G:0.12, T:0.41
Consensus pattern (20 bp):
AAAGTTTCAATTATGTAATG
Found at i:19178591 original size:15 final size:15
Alignment explanation
Indices: 19178573--19178610 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
19178563 AAATTGTTTC
19178573 TTCAAATTTTAAGTT
1 TTCAAATTTTAAGTT
*
19178588 TTCAAAATTTAAGTT
1 TTCAAATTTTAAGTT
*
19178603 TTTAAATT
1 TTCAAATT
19178611 ATTTTCCTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.37, C:0.05, G:0.05, T:0.53
Consensus pattern (15 bp):
TTCAAATTTTAAGTT
Found at i:19178605 original size:16 final size:16
Alignment explanation
Indices: 19178568--19178605 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
19178558 ATCAAAAATT
*
19178568 GTTTCTTCAAATTTTAA
1 GTTT-TTCAAAATTTAA
19178585 G-TTTTCAAAATTTAA
1 GTTTTTCAAAATTTAA
19178600 GTTTTT
1 GTTTTT
19178606 AAATTATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 12 0.63
16 6 0.32
17 1 0.05
ACGTcount: A:0.29, C:0.08, G:0.08, T:0.55
Consensus pattern (16 bp):
GTTTTTCAAAATTTAA
Found at i:19179932 original size:19 final size:19
Alignment explanation
Indices: 19179905--19179943 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
19179895 GTTTTATCTA
* * *
19179905 TTTTGTTTTTTATTTTTTC
1 TTTTCTTTTCTATATTTTC
19179924 TTTTCTTTTCTATATTTTC
1 TTTTCTTTTCTATATTTTC
19179943 T
1 T
19179944 ATATTTGGAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.08, C:0.10, G:0.03, T:0.79
Consensus pattern (19 bp):
TTTTCTTTTCTATATTTTC
Found at i:19181897 original size:34 final size:34
Alignment explanation
Indices: 19181859--19181932 Score: 148
Period size: 34 Copynumber: 2.2 Consensus size: 34
19181849 ATTATATGAA
19181859 TTAAGACATGAAACTATATGAATATCCTTGTAAG
1 TTAAGACATGAAACTATATGAATATCCTTGTAAG
19181893 TTAAGACATGAAACTATATGAATATCCTTGTAAG
1 TTAAGACATGAAACTATATGAATATCCTTGTAAG
19181927 TTAAGA
1 TTAAGA
19181933 TGAGTAATAG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 40 1.00
ACGTcount: A:0.42, C:0.11, G:0.15, T:0.32
Consensus pattern (34 bp):
TTAAGACATGAAACTATATGAATATCCTTGTAAG
Found at i:19182405 original size:15 final size:16
Alignment explanation
Indices: 19182373--19182407 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
19182363 TTAAGTTAAA
*
19182373 GAAAGTAGATGCAATG
1 GAAAGTAGATGAAATG
19182389 GAAAGTA-ATGAAATG
1 GAAAGTAGATGAAATG
19182404 GAAA
1 GAAA
19182408 TGAAATAAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 11 0.61
16 7 0.39
ACGTcount: A:0.51, C:0.03, G:0.29, T:0.17
Consensus pattern (16 bp):
GAAAGTAGATGAAATG
Found at i:19185334 original size:42 final size:42
Alignment explanation
Indices: 19185273--19185463 Score: 172
Period size: 42 Copynumber: 4.5 Consensus size: 42
19185263 TCAAAAGCTT
* * * *
19185273 AATAGAAGCTCATGAGAGCTAAACAAAAACCCATAAGGGTTG
1 AATAGAAGCTCATAAGAGCTAAACAAAAACTCATAAGAGTTA
* * *
19185315 AGTAGAAGCTCGTAAGAGCTGAAA-AAAAACTCATATGAGTTA
1 AATAGAAGCTCATAAGAGCT-AAACAAAAACTCATAAGAGTTA
* * * *
19185357 AACAGAAGCTCATAAGAGCTTAACAGAAACTCATAAGAGTTT
1 AATAGAAGCTCATAAGAGCTAAACAAAAACTCATAAGAGTTA
* * * *
19185399 AATAGAAGCTTGA-AAGAGCTGAACGAAAACTCATATGCA-TTA
1 AATAGAAGC-TCATAAGAGCTAAACAAAAACTCATAAG-AGTTA
* **
19185441 AACAGAAGCTTGTAAGAGCTAAA
1 AATAGAAGCTCATAAGAGCTAAA
19185464 TGGAAAGTAA
Statistics
Matches: 119, Mismatches: 25, Indels: 10
0.77 0.16 0.06
Matches are distributed among these distances:
41 3 0.03
42 110 0.92
43 6 0.05
ACGTcount: A:0.46, C:0.15, G:0.20, T:0.20
Consensus pattern (42 bp):
AATAGAAGCTCATAAGAGCTAAACAAAAACTCATAAGAGTTA
Found at i:19185370 original size:21 final size:20
Alignment explanation
Indices: 19185251--19185408 Score: 86
Period size: 21 Copynumber: 7.7 Consensus size: 20
19185241 TGAGTATATC
19185251 GTTAACAGAAGCTCA-AA-A
1 GTTAACAGAAGCTCATAAGA
* *
19185269 GCTTAATAGAAGCTCATGAGA
1 G-TTAACAGAAGCTCATAAGA
* * * * *
19185290 GCTAAACAAAAACCCATAAGG
1 G-TTAACAGAAGCTCATAAGA
** *
19185311 GTTGAGTAGAAGCTCGTAAGA
1 GTT-AACAGAAGCTCATAAGA
* * * * *
19185332 GCTGAAAAAAAACTCATATGA
1 G-TTAACAGAAGCTCATAAGA
19185353 GTTAAACAGAAGCTCATAAGA
1 GTT-AACAGAAGCTCATAAGA
*
19185374 GCTTAACAGAAACTCATAAGA
1 G-TTAACAGAAGCTCATAAGA
*
19185395 GTTTAATAGAAGCT
1 G-TTAACAGAAGCT
19185409 TGAAAGAGCT
Statistics
Matches: 100, Mismatches: 33, Indels: 11
0.69 0.23 0.08
Matches are distributed among these distances:
18 1 0.01
19 13 0.13
20 3 0.03
21 80 0.80
22 3 0.03
ACGTcount: A:0.45, C:0.15, G:0.20, T:0.20
Consensus pattern (20 bp):
GTTAACAGAAGCTCATAAGA
Found at i:19185417 original size:84 final size:84
Alignment explanation
Indices: 19185276--19185463 Score: 243
Period size: 84 Copynumber: 2.2 Consensus size: 84
19185266 AAAGCTTAAT
* * * *
19185276 AGAAGCTCATGAGAGCTAAACAAAAACCCATAAGGGTTGAGTAGAAGCTCGTAAGAGCTGAAAAA
1 AGAAGCTCATAAGAGCTAAACAAAAACCCATAAGAGTTGAATAGAAGCTCGAAAGAGCTGAAAAA
19185341 AAACTCATATG-AGTTAAAC
66 AAACTCATATGCA-TTAAAC
* * * * * **
19185360 AGAAGCTCATAAGAGCTTAACAGAAACTCATAAGAGTTTAATAGAAGCTTGAAAGAGCTGAACGA
1 AGAAGCTCATAAGAGCTAAACAAAAACCCATAAGAGTTGAATAGAAGCTCGAAAGAGCTGAAAAA
19185425 AAACTCATATGCATTAAAC
66 AAACTCATATGCATTAAAC
**
19185444 AGAAGCTTGTAAGAGCTAAA
1 AGAAGCTCATAAGAGCTAAA
19185464 TGGAAAGTAA
Statistics
Matches: 89, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
84 88 0.99
85 1 0.01
ACGTcount: A:0.45, C:0.15, G:0.20, T:0.20
Consensus pattern (84 bp):
AGAAGCTCATAAGAGCTAAACAAAAACCCATAAGAGTTGAATAGAAGCTCGAAAGAGCTGAAAAA
AAACTCATATGCATTAAAC
Found at i:19192223 original size:24 final size:23
Alignment explanation
Indices: 19192191--19192240 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 23
19192181 CGATGCCACA
*
19192191 CAGGCGTGTGGTCGCCCGTGTGG
1 CAGGCGTGTGGTAGCCCGTGTGG
* *
19192214 CAGGCCGTGTGGTAGGCTGTGTGG
1 CAGG-CGTGTGGTAGCCCGTGTGG
19192238 CAG
1 CAG
19192241 TACACAGCCA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 4 0.17
24 19 0.83
ACGTcount: A:0.08, C:0.22, G:0.48, T:0.22
Consensus pattern (23 bp):
CAGGCGTGTGGTAGCCCGTGTGG
Found at i:19192230 original size:12 final size:12
Alignment explanation
Indices: 19192195--19192237 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
19192185 GCCACACAGG
* *
19192195 CGTGTGGTCGCC
1 CGTGTGGTAGGC
*
19192207 CGTGTGGCAGGC
1 CGTGTGGTAGGC
19192219 CGTGTGGTAGGC
1 CGTGTGGTAGGC
*
19192231 TGTGTGG
1 CGTGTGG
19192238 CAGTACACAG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.05, C:0.21, G:0.49, T:0.26
Consensus pattern (12 bp):
CGTGTGGTAGGC
Found at i:19192568 original size:13 final size:13
Alignment explanation
Indices: 19192550--19192574 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19192540 CTTAGACCCT
19192550 TGATTATGTGATC
1 TGATTATGTGATC
19192563 TGATTATGTGAT
1 TGATTATGTGAT
19192575 GTATGTATTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.04, G:0.24, T:0.48
Consensus pattern (13 bp):
TGATTATGTGATC
Found at i:19196315 original size:27 final size:26
Alignment explanation
Indices: 19196285--19196356 Score: 81
Period size: 29 Copynumber: 2.6 Consensus size: 26
19196275 TATGATTAAA
19196285 AGAAACAAATATTTATGGTGAAAGAAG
1 AGAAA-AAATATTTATGGTGAAAGAAG
*
19196312 AGAAAAAATTATTTATATGGTGAAAGGAG
1 AGAAAAAA-TA-TT-TATGGTGAAAGAAG
*
19196341 AGAGAAAATTATTTAT
1 AGA-AAAAATATTTAT
19196357 TCATCTTCCT
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
26 3 0.08
27 10 0.26
28 4 0.10
29 18 0.46
30 4 0.10
ACGTcount: A:0.50, C:0.01, G:0.21, T:0.28
Consensus pattern (26 bp):
AGAAAAAATATTTATGGTGAAAGAAG
Found at i:19196342 original size:29 final size:29
Alignment explanation
Indices: 19196298--19196356 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
19196288 AACAAATATT
19196298 TATGGTGAAAGAAGAGAAAAAATTATTTA
1 TATGGTGAAAGAAGAGAAAAAATTATTTA
* *
19196327 TATGGTGAAAGGAGAGAGAAAATTATTTA
1 TATGGTGAAAGAAGAGAAAAAATTATTTA
19196356 T
1 T
19196357 TCATCTTCCT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.24, T:0.29
Consensus pattern (29 bp):
TATGGTGAAAGAAGAGAAAAAATTATTTA
Found at i:19196791 original size:14 final size:14
Alignment explanation
Indices: 19196772--19196800 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
19196762 GAAAGTTACA
19196772 ATATCTTTGATTTT
1 ATATCTTTGATTTT
19196786 ATATCTTTGATTTT
1 ATATCTTTGATTTT
19196800 A
1 A
19196801 GGGACTAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.24, C:0.07, G:0.07, T:0.62
Consensus pattern (14 bp):
ATATCTTTGATTTT
Found at i:19199178 original size:46 final size:46
Alignment explanation
Indices: 19199122--19199297 Score: 180
Period size: 46 Copynumber: 3.8 Consensus size: 46
19199112 TGGTTGAGCA
*
19199122 TCCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * *
19199168 TCCGAACTCGTTGAGTTGAGTCTGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
19199213 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* ** * *
19199261 CCCGAGTTCATTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
19199298 GCGGGTTACA
Statistics
Matches: 107, Mismatches: 14, Indels: 18
0.77 0.10 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 60 0.56
47 28 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.21, C:0.19, G:0.29, T:0.31
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:19199278 original size:93 final size:93
Alignment explanation
Indices: 19199119--19199290 Score: 281
Period size: 93 Copynumber: 1.8 Consensus size: 93
19199109 GGATGGTTGA
* * * *
19199119 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCATTGAGT
*
19199184 TGAGTCTGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
**
19199212 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGTTCATTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCATTGAGT
19199277 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
19199291 CTTATGGGCG
Statistics
Matches: 72, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.30
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCATTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:19213020 original size:3 final size:3
Alignment explanation
Indices: 19213012--19213041 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
19213002 CTACAATCGG
*
19213012 TTA TTA TTA TTA TTA TTA TTA TTT TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
19213042 CTACATAAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:19216815 original size:7 final size:7
Alignment explanation
Indices: 19216788--19216828 Score: 57
Period size: 7 Copynumber: 5.9 Consensus size: 7
19216778 TAATTGAATT
19216788 TATTTTA
1 TATTTTA
*
19216795 TA-TCTA
1 TATTTTA
19216801 TAATTTTA
1 T-ATTTTA
19216809 TATTTTA
1 TATTTTA
19216816 TATTTTA
1 TATTTTA
19216823 TATTTT
1 TATTTT
19216829 TTTGCATATA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
6 4 0.13
7 22 0.73
8 4 0.13
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.68
Consensus pattern (7 bp):
TATTTTA
Found at i:19225004 original size:24 final size:25
Alignment explanation
Indices: 19224977--19225025 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
19224967 TGAAGTGAAA
19224977 GGTAAATGATATTA-TGAATAATTT
1 GGTAAATGATATTAGTGAATAATTT
* *
19225001 GGTAGATGATTTTATGTGAATAATT
1 GGTAAATGATATTA-GTGAATAATT
19225026 GCAAGTAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 12 0.57
26 9 0.43
ACGTcount: A:0.37, C:0.00, G:0.20, T:0.43
Consensus pattern (25 bp):
GGTAAATGATATTAGTGAATAATTT
Found at i:19227249 original size:34 final size:34
Alignment explanation
Indices: 19227206--19227270 Score: 112
Period size: 34 Copynumber: 1.9 Consensus size: 34
19227196 GAGTTAGGCT
*
19227206 GATCGGTGCTTAGGAGCCCCTCGGTGACCACGCG
1 GATCGGTGCTGAGGAGCCCCTCGGTGACCACGCG
*
19227240 GATCGGTGCTGCGGAGCCCCTCGGTGACCAC
1 GATCGGTGCTGAGGAGCCCCTCGGTGACCAC
19227271 ATGTTCGAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.14, C:0.34, G:0.35, T:0.17
Consensus pattern (34 bp):
GATCGGTGCTGAGGAGCCCCTCGGTGACCACGCG
Found at i:19232509 original size:46 final size:46
Alignment explanation
Indices: 19232459--19232632 Score: 194
Period size: 46 Copynumber: 3.8 Consensus size: 46
19232449 GTTGAGCATT
19232459 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTC
1 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTC
* * * *
19232505 CGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--AATG-TAACTAGGCATC
1 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G--TC
* * *
19232552 CGAACTTGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCC
1 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTC
* *
19232598 CGAGCTCCTTGAGTTGAGTCCGAGTTCACTTATGG
1 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
19232633 GCGGGTTACA
Statistics
Matches: 105, Mismatches: 14, Indels: 18
0.77 0.10 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
45 3 0.03
46 60 0.57
47 28 0.27
48 3 0.03
50 3 0.03
51 2 0.02
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.29
Consensus pattern (46 bp):
CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTC
Found at i:19232618 original size:93 final size:93
Alignment explanation
Indices: 19232454--19232624 Score: 288
Period size: 93 Copynumber: 1.8 Consensus size: 93
19232444 GGATGGTTGA
* * * *
19232454 GCATTCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCCTTGAGT
19232519 TGAGTCCGAGTTCGTGAAATGTAACTAG
66 TGAGTCCGAGTTCGTGAAATGTAACTAG
* *
19232547 GCATCCGAACTTGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCCTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCCTTGAGT
19232612 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
19232625 ACTTATGGGC
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCCTTGAGT
TGAGTCCGAGTTCGTGAAATGTAACTAG
Found at i:19239596 original size:46 final size:46
Alignment explanation
Indices: 19239544--19239719 Score: 180
Period size: 46 Copynumber: 3.8 Consensus size: 46
19239534 TGGTTGAGCA
*
19239544 TCCGAACTCGTTGAGTTGAGTCAGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * * *
19239590 TTCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--AATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
* *
19239635 CATCCGAACTCGTTGAGTTGAATCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
19239683 CCCGAGCTCGTTGAGTTGAGTCTGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
19239720 GCGGGTTACA
Statistics
Matches: 104, Mismatches: 17, Indels: 18
0.75 0.12 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
45 3 0.03
46 60 0.58
47 27 0.26
48 3 0.03
50 3 0.03
51 2 0.02
ACGTcount: A:0.23, C:0.19, G:0.28, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:19239700 original size:93 final size:93
Alignment explanation
Indices: 19239541--19239711 Score: 279
Period size: 93 Copynumber: 1.8 Consensus size: 93
19239531 GGATGGTTGA
* * **
19239541 GCATCCGAACTCGTTGAGTTGAGTCAGAGTTCACTTATGGATGCGAATGTTCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAATCAGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
19239606 TGAGTCCGAGTTCGTGAAATGTAACTAG
66 TGAGTCCGAGTTCGTGAAATGTAACTAG
* *
19239634 GCATCCGAACTCGTTGAGTTGAATCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAATCAGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
*
19239699 TGAGTCTGAGTTC
66 TGAGTCCGAGTTC
19239712 ACTTATGGGC
Statistics
Matches: 71, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 71 1.00
ACGTcount: A:0.23, C:0.20, G:0.28, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAATCAGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAAATGTAACTAG
Found at i:19242600 original size:12 final size:12
Alignment explanation
Indices: 19242580--19242612 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
19242570 AACACCACAC
*
19242580 GGCCATGTGGTA
1 GGCCGTGTGGTA
19242592 GGCCGTGTGGTA
1 GGCCGTGTGGTA
19242604 GGCCGTGTG
1 GGCCGTGTG
19242613 ATCGACGAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.09, C:0.18, G:0.48, T:0.24
Consensus pattern (12 bp):
GGCCGTGTGGTA
Found at i:19247338 original size:14 final size:15
Alignment explanation
Indices: 19247319--19247353 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
19247309 ATTTATTGAC
19247319 ATATTTCT-ATAAAA
1 ATATTTCTAATAAAA
*
19247333 ATATTTTTAATAAAA
1 ATATTTCTAATAAAA
19247348 ATATTT
1 ATATTT
19247354 TCATTCACTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 7 0.37
15 12 0.63
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (15 bp):
ATATTTCTAATAAAA
Found at i:19247621 original size:77 final size:77
Alignment explanation
Indices: 19247533--19247679 Score: 195
Period size: 77 Copynumber: 1.9 Consensus size: 77
19247523 AACTTAAATA
* * ** * * *
19247533 AAAAAAAGCAATTAAGCCTCTCTTTTTTTTTACTCAATTGAGCACTTGAACTTTCAAAATGCATC
1 AAAAAAAGCAATTAAACCACTAGTTTTTTTCACTCAATTGAGCACTCGAACTTTCAAAATGCATA
19247598 AAAAAGGCCATC
66 AAAAAGGCCATC
* * * *
19247610 AAAAAAGGCAATTAAACCACTAGTTTTTTTCACTCAATTGGGTACTCGAATTTTCAAAATGCATA
1 AAAAAAAGCAATTAAACCACTAGTTTTTTTCACTCAATTGAGCACTCGAACTTTCAAAATGCATA
19247675 AAAAA
66 AAAAA
19247680 AACCTTCAAA
Statistics
Matches: 59, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
77 59 1.00
ACGTcount: A:0.40, C:0.18, G:0.11, T:0.31
Consensus pattern (77 bp):
AAAAAAAGCAATTAAACCACTAGTTTTTTTCACTCAATTGAGCACTCGAACTTTCAAAATGCATA
AAAAAGGCCATC
Found at i:19247801 original size:18 final size:18
Alignment explanation
Indices: 19247750--19247801 Score: 52
Period size: 18 Copynumber: 2.8 Consensus size: 18
19247740 AATATATAAA
*
19247750 AATAATAAATAATAACTTTT
1 AATAA-AAAT-ATAAATTTT
*
19247770 -ATAAAATTATTAAATTTT
1 AATAAAAATA-TAAATTTT
19247788 AATAAAAATATAAA
1 AATAAAAATATAAA
19247802 AAAATTTGGA
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
17 1 0.04
18 14 0.52
19 12 0.44
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (18 bp):
AATAAAAATATAAATTTT
Found at i:19248094 original size:29 final size:28
Alignment explanation
Indices: 19248060--19248182 Score: 92
Period size: 28 Copynumber: 4.4 Consensus size: 28
19248050 TATATTTTGA
*
19248060 ATAATTTTCTTATGATTTTATTAAATATT
1 ATAATTTTTTTATGATTTTA-TAAATATT
* *
19248089 ATAATTTTTTTAT-ATTTCTATATATTTT
1 ATAATTTTTTTATGATTT-TATAAATATT
* *
19248117 ATAATTTTTTTACGATTTTTGTAAA-ATT
1 ATAATTTTTTTATGA-TTTTATAAATATT
* * * * *
19248145 TTATATTTCTATAT-ATTTTATAATTTTT
1 ATA-ATTTTTTTATGATTTTATAAATATT
19248173 AT-ATTTTTTT
1 ATAATTTTTTT
19248183 CTAATTTTTA
Statistics
Matches: 72, Mismatches: 17, Indels: 13
0.71 0.17 0.13
Matches are distributed among these distances:
26 6 0.08
27 7 0.10
28 30 0.42
29 26 0.36
30 3 0.04
ACGTcount: A:0.30, C:0.03, G:0.02, T:0.64
Consensus pattern (28 bp):
ATAATTTTTTTATGATTTTATAAATATT
Found at i:19248160 original size:57 final size:56
Alignment explanation
Indices: 19248040--19248182 Score: 141
Period size: 57 Copynumber: 2.5 Consensus size: 56
19248030 TTACGAAATT
* * * * *
19248040 TATATTTATTTATATTTTGAATAATTTTCTTATGATTTTATTAAATATTATAATTTTTT
1 TATATTT-TATATATTTT--ATAATTTTTTTACGATTTTATTAAATATTATAATTTCTA
*
19248099 TATATTTCTATATATTTTATAATTTTTTTACGATTTT-TGTAAA-ATTTTATATTTCTA
1 TATATTT-TATATATTTTATAATTTTTTTACGATTTTAT-TAAATATTATA-ATTTCTA
19248156 TATATTTTATA-ATTTT-TATATTTTTTT
1 TATATTTTATATATTTTATA-ATTTTTTT
19248183 CTAATTTTTA
Statistics
Matches: 74, Mismatches: 7, Indels: 10
0.81 0.08 0.11
Matches are distributed among these distances:
54 2 0.03
55 13 0.18
56 10 0.14
57 33 0.45
59 16 0.22
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.64
Consensus pattern (56 bp):
TATATTTTATATATTTTATAATTTTTTTACGATTTTATTAAATATTATAATTTCTA
Found at i:19249963 original size:17 final size:18
Alignment explanation
Indices: 19249930--19249968 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 18
19249920 CTTTCTTTGA
19249930 TTTTCTTTTTCTCCATTT
1 TTTTCTTTTTCTCCATTT
19249948 TTTTCTTTGTT-T-CATTT
1 TTTTCTTT-TTCTCCATTT
19249965 TTTT
1 TTTT
19249969 TATAGTTAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 9 0.45
18 9 0.45
19 2 0.10
ACGTcount: A:0.05, C:0.15, G:0.03, T:0.77
Consensus pattern (18 bp):
TTTTCTTTTTCTCCATTT
Found at i:19251180 original size:14 final size:14
Alignment explanation
Indices: 19251161--19251195 Score: 70
Period size: 14 Copynumber: 2.5 Consensus size: 14
19251151 TTAGCCTCAG
19251161 ACCCCACAGTTACC
1 ACCCCACAGTTACC
19251175 ACCCCACAGTTACC
1 ACCCCACAGTTACC
19251189 ACCCCAC
1 ACCCCAC
19251196 CTACATCACT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.29, C:0.54, G:0.06, T:0.11
Consensus pattern (14 bp):
ACCCCACAGTTACC
Found at i:19257552 original size:26 final size:26
Alignment explanation
Indices: 19257512--19257620 Score: 182
Period size: 26 Copynumber: 4.2 Consensus size: 26
19257502 ATGAAATTCC
*
19257512 TATCATGGAACATTTACCTAACCCAT
1 TATCATGAAACATTTACCTAACCCAT
* * *
19257538 TATAATGGAACATTTACCTAACCTAT
1 TATCATGAAACATTTACCTAACCCAT
19257564 TATCATGAAACATTTACCTAACCCAT
1 TATCATGAAACATTTACCTAACCCAT
19257590 TATCATGAAACATTTACCTAACCCAT
1 TATCATGAAACATTTACCTAACCCAT
19257616 TATCA
1 TATCA
19257621 ATTTGTATCA
Statistics
Matches: 78, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 78 1.00
ACGTcount: A:0.38, C:0.25, G:0.06, T:0.32
Consensus pattern (26 bp):
TATCATGAAACATTTACCTAACCCAT
Found at i:19258449 original size:269 final size:269
Alignment explanation
Indices: 19257957--19258450 Score: 814
Period size: 269 Copynumber: 1.8 Consensus size: 269
19257947 CGTTACATAA
* * *
19257957 AGTTTTACATTTTATTCAATTTAGTCTCTGAATTCGAAATAGCAATAACTTCCAATTCCTAACCT
1 AGTTTTACATTTTATTCAATTTAGTCCCTAAATTCAAAATAGCAATAACTTCCAATTCCTAACCT
* *
19258022 CAGTTTAAAATTTGACTTCAAATACATTCATTAGGGACCTTCTACTTTCTATTTATACTGAAATT
66 CAGTTTAAAATCTGACTTCAAATACATTCATTAGGGACCTTCTACTTTCTATTTATACTAAAATT
* * * * *
19258087 TCATAACAGTTTCACATTTTATTCACTTTAGTCCATATGTGCAAAACTAACAATTAAATGTTACA
131 TCACAACAATTTCACATTTTATTCACTTTAATCCATATGTACAAAACTAACAATTAAATGTCACA
*
19258152 ATTTAGTCTTTTTCATAATCTAAGCTTAAATATTTTTCAAGAAATCAACAAAGGAAACTTTCTAA
196 ATCTAGTCTTTTTCATAATCTAAGCTTAAATATTTTTCAAGAAATCAACAAAGGAAACTTTCTAA
19258217 AGCTTTATC
261 AGCTTTATC
* *
19258226 AGTTTTATATTTTATTCAATTTAGTCCCTAAATTCAAAATAGCAATAACTTCCAATTCCTGACCT
1 AGTTTTACATTTTATTCAATTTAGTCCCTAAATTCAAAATAGCAATAACTTCCAATTCCTAACCT
19258291 C-GATTTAAAATCTGACTTCAAATACATTCATTAGGGACAC-TCTACTTTCTATTTATACTAAAA
66 CAG-TTTAAAATCTGACTTCAAATACATTCATTAGGGAC-CTTCTACTTTCTATTTATACTAAAA
19258354 TTTCACAACAATTTCACATTTTATTCACTTTAATCCATATGTACAAAACTAACAATTAAATGTCA
129 TTTCACAACAATTTCACATTTTATTCACTTTAATCCATATGTACAAAACTAACAATTAAATGTCA
*
19258419 CAATCTAGTCTTTTTTTATAATCT-AGCTTAAA
194 CAATCTAGTC-TTTTTCATAATCTAAGCTTAAA
19258451 ATATATCAAT
Statistics
Matches: 208, Mismatches: 14, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
268 1 0.00
269 194 0.93
270 13 0.06
ACGTcount: A:0.35, C:0.18, G:0.07, T:0.39
Consensus pattern (269 bp):
AGTTTTACATTTTATTCAATTTAGTCCCTAAATTCAAAATAGCAATAACTTCCAATTCCTAACCT
CAGTTTAAAATCTGACTTCAAATACATTCATTAGGGACCTTCTACTTTCTATTTATACTAAAATT
TCACAACAATTTCACATTTTATTCACTTTAATCCATATGTACAAAACTAACAATTAAATGTCACA
ATCTAGTCTTTTTCATAATCTAAGCTTAAATATTTTTCAAGAAATCAACAAAGGAAACTTTCTAA
AGCTTTATC
Found at i:19258777 original size:19 final size:20
Alignment explanation
Indices: 19258748--19258792 Score: 58
Period size: 19 Copynumber: 2.3 Consensus size: 20
19258738 CACATAATTA
*
19258748 AATTAATTTAAT-CATACTTT
1 AATTAACTTAATCCAT-CTTT
19258768 -ATTAACTTAATCCATCTTT
1 AATTAACTTAATCCATCTTT
19258787 AATTAA
1 AATTAA
19258793 TAAAAGTGGA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
19 14 0.64
20 8 0.36
ACGTcount: A:0.40, C:0.13, G:0.00, T:0.47
Consensus pattern (20 bp):
AATTAACTTAATCCATCTTT
Found at i:19261365 original size:41 final size:42
Alignment explanation
Indices: 19261307--19261467 Score: 186
Period size: 41 Copynumber: 3.8 Consensus size: 42
19261297 AGGGTTACTA
* * * * *
19261307 AGACTACGTGTAAGACCATATCTGGGATATGACATCAATATG
1 AGACTACATGTAAGACCATAGCTAGGATATGGCATCGATATG
19261349 AGACTAC-TGTAAGACCATAGCTAGGATATGGCATCGATATG
1 AGACTACATGTAAGACCATAGCTAGGATATGGCATCGATATG
* *
19261390 AGACCT-CATGTAAGACCATAGCT-GAGCTATTGGCAACGATATG
1 AGA-CTACATGTAAGACCATAGCTAG-GATA-TGGCATCGATATG
*
19261433 AG-CTCACATGTAAGACCATATCTAGGATATGGCAT
1 AGACT-ACATGTAAGACCATAGCTAGGATATGGCAT
19261468 TGGTACGGTA
Statistics
Matches: 103, Mismatches: 9, Indels: 14
0.82 0.07 0.11
Matches are distributed among these distances:
41 37 0.36
42 32 0.31
43 33 0.32
44 1 0.01
ACGTcount: A:0.34, C:0.19, G:0.22, T:0.25
Consensus pattern (42 bp):
AGACTACATGTAAGACCATAGCTAGGATATGGCATCGATATG
Found at i:19268778 original size:19 final size:19
Alignment explanation
Indices: 19268754--19268791 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
19268744 TTGTGATTGC
*
19268754 CCCTTGAACGTATTCGACA
1 CCCTTGAACGTAGTCGACA
19268773 CCCTTGAACGTAGTCGACA
1 CCCTTGAACGTAGTCGACA
19268792 AAGTTTCGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.26, C:0.32, G:0.18, T:0.24
Consensus pattern (19 bp):
CCCTTGAACGTAGTCGACA
Found at i:19268915 original size:42 final size:42
Alignment explanation
Indices: 19268866--19269064 Score: 190
Period size: 42 Copynumber: 4.8 Consensus size: 42
19268856 TTAGGGTTAC
19268866 TAAGACTACGTGTAAGACCATATCTGGGATATGACATCAATA
1 TAAGACTACGTGTAAGACCATATCTGGGATATGACATCAATA
* * *
19268908 AAAGACTACGTGTAAGACCATATCTGGGATATGGCATCGATA
1 TAAGACTACGTGTAAGACCATATCTGGGATATGACATCAATA
* * * * * * * **
19268950 TAAGACTTCGTGGACGACTATAGCTGGGCTATTGGCATTGATA
1 TAAGACTACGTGTAAGACCATATCTGGGATA-TGACATCAATA
* * * *
19268993 TGAGA-TCACATATAAGACCATATTTGGGATATGACATCAATA
1 TAAGACT-ACGTGTAAGACCATATCTGGGATATGACATCAATA
* *
19269035 TGAGACTACGTGTATGA-C--ATCTGGGATATG
1 TAAGACTACGTGTAAGACCATATCTGGGATATG
19269065 GCATTGGTAC
Statistics
Matches: 126, Mismatches: 28, Indels: 9
0.77 0.17 0.06
Matches are distributed among these distances:
39 11 0.09
41 1 0.01
42 84 0.67
43 30 0.24
ACGTcount: A:0.34, C:0.16, G:0.23, T:0.28
Consensus pattern (42 bp):
TAAGACTACGTGTAAGACCATATCTGGGATATGACATCAATA
Found at i:19269898 original size:11 final size:11
Alignment explanation
Indices: 19269882--19269907 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
19269872 AAATCTGATG
19269882 TTTTAAAATTA
1 TTTTAAAATTA
19269893 TTTTAAAATTA
1 TTTTAAAATTA
19269904 TTTT
1 TTTT
19269908 TGTTGTTTAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (11 bp):
TTTTAAAATTA
Found at i:19270617 original size:43 final size:43
Alignment explanation
Indices: 19270569--19270737 Score: 148
Period size: 43 Copynumber: 4.0 Consensus size: 43
19270559 ATTAAGATGT
*
19270569 GATTACATGTAAGACCATGTCTGGGACATTGGCATTGTACTGA
1 GATTACATGTAAGACCATGTCTGGGACATTGGCATCGTACTGA
** * *
19270612 GATTACATGTAAGACCATGTCTGGGACATTAACATCGTTAAT-C
1 GATTACATGTAAGACCATGTCTGGGACATTGGCATCG-TACTGA
* * * * * *
19270655 TATTTCATGTAAGACCCTGTCTGGGATAGTGGCATCG-ACATGT
1 GATTACATGTAAGACCATGTCTGGGACATTGGCATCGTAC-TGA
* * * *
19270698 GA-TAGCATGTAAGATCATATCTGGGATA-TGGCATTGTACT
1 GATTA-CATGTAAGACCATGTCTGGGACATTGGCATCGTACT
19270738 AGCTTATGTG
Statistics
Matches: 101, Mismatches: 20, Indels: 11
0.77 0.15 0.08
Matches are distributed among these distances:
41 1 0.01
42 10 0.10
43 87 0.86
44 3 0.03
ACGTcount: A:0.28, C:0.17, G:0.24, T:0.31
Consensus pattern (43 bp):
GATTACATGTAAGACCATGTCTGGGACATTGGCATCGTACTGA
Found at i:19280917 original size:25 final size:26
Alignment explanation
Indices: 19280862--19280911 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 26
19280852 TCAAATTAAC
* *
19280862 TATTAATTTTTAAATTTAATGTAAAA
1 TATTAATATTTAAATTAAATGTAAAA
*
19280888 TATTAATATTT-AATTAAATTTAAA
1 TATTAATATTTAAATTAAATGTAAA
19280912 CAATTATTGA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 11 0.52
26 10 0.48
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (26 bp):
TATTAATATTTAAATTAAATGTAAAA
Found at i:19281767 original size:19 final size:19
Alignment explanation
Indices: 19281743--19281787 Score: 81
Period size: 19 Copynumber: 2.4 Consensus size: 19
19281733 CTCGGAAGCG
19281743 GATCTCCCTCAAGATCGAA
1 GATCTCCCTCAAGATCGAA
19281762 GATCTCCCTCAAGATCGAA
1 GATCTCCCTCAAGATCGAA
*
19281781 TATCTCC
1 GATCTCC
19281788 ATTTAATTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.29, C:0.33, G:0.13, T:0.24
Consensus pattern (19 bp):
GATCTCCCTCAAGATCGAA
Found at i:19285017 original size:42 final size:42
Alignment explanation
Indices: 19284959--19285039 Score: 135
Period size: 42 Copynumber: 1.9 Consensus size: 42
19284949 TCCTAATTGA
*
19284959 AAAATAATTCTCTTATTCTAATAAACTACTAAAACATAAGGG
1 AAAATAATTCCCTTATTCTAATAAACTACTAAAACATAAGGG
* *
19285001 AAAATAATTCCCTTATTCTAATAAATTACTAAAAGATAA
1 AAAATAATTCCCTTATTCTAATAAACTACTAAAACATAA
19285040 AATAAAATAT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.49, C:0.14, G:0.05, T:0.32
Consensus pattern (42 bp):
AAAATAATTCCCTTATTCTAATAAACTACTAAAACATAAGGG
Found at i:19285047 original size:42 final size:42
Alignment explanation
Indices: 19284959--19285052 Score: 127
Period size: 42 Copynumber: 2.3 Consensus size: 42
19284949 TCCTAATTGA
* **
19284959 AAAATAATTCTCTTATTCTAATAAACTACTAAAACATAAGGG
1 AAAATAATTCCCTTATTCTAATAAACTACTAAAACATAAAAG
* * *
19285001 AAAATAATTCCCTTATTCTAATAAATTACTAAAAGATAAAAT
1 AAAATAATTCCCTTATTCTAATAAACTACTAAAACATAAAAG
19285043 AAAAT-ATTCC
1 AAAATAATTCC
19285053 TAGAATACGA
Statistics
Matches: 46, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
41 5 0.11
42 41 0.89
ACGTcount: A:0.50, C:0.14, G:0.04, T:0.32
Consensus pattern (42 bp):
AAAATAATTCCCTTATTCTAATAAACTACTAAAACATAAAAG
Found at i:19293144 original size:18 final size:20
Alignment explanation
Indices: 19293114--19293165 Score: 63
Period size: 18 Copynumber: 2.7 Consensus size: 20
19293104 AAAATTATTA
*
19293114 AAATATTATAAAATTTTA-G
1 AAATATGATAAAATTTTATG
*
19293133 AAA-ATGATAAAAATTTATG
1 AAATATGATAAAATTTTATG
*
19293152 AAATATTATAAAAT
1 AAATATGATAAAAT
19293166 AATAAAAATT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
18 12 0.44
19 7 0.26
20 8 0.30
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.37
Consensus pattern (20 bp):
AAATATGATAAAATTTTATG
Found at i:19293155 original size:9 final size:10
Alignment explanation
Indices: 19293102--19293210 Score: 68
Period size: 10 Copynumber: 11.1 Consensus size: 10
19293092 TGTTTAAGCT
19293102 TAAAA-ATTA
1 TAAAATATTA
19293111 TTAAAATATTA
1 -TAAAATATTA
*
19293122 TAAAATTTTA
1 TAAAATATTA
*
19293132 GAAAATGA-TA
1 TAAAAT-ATTA
19293142 -AAAAT-TTA
1 TAAAATATTA
*
19293150 TGAAATATTA
1 TAAAATATTA
*
19293160 TAAAATAATA
1 TAAAATATTA
19293170 -AAAATTATTA
1 TAAAA-TATTA
*
19293180 GAAAA-ATTAA
1 TAAAATATT-A
* * *
19293190 TTACATGTTA
1 TAAAATATTA
19293200 TAAAATATTA
1 TAAAATATTA
19293210 T
1 T
19293211 TAATACATTA
Statistics
Matches: 76, Mismatches: 14, Indels: 18
0.70 0.13 0.17
Matches are distributed among these distances:
8 2 0.03
9 16 0.21
10 48 0.63
11 10 0.13
ACGTcount: A:0.57, C:0.01, G:0.05, T:0.38
Consensus pattern (10 bp):
TAAAATATTA
Found at i:19296519 original size:14 final size:14
Alignment explanation
Indices: 19296483--19296512 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
19296473 TATTTTCAAT
*
19296483 TTACTATTATATTA
1 TTACTATTTTATTA
19296497 TTACTATTTTATTA
1 TTACTATTTTATTA
19296511 TT
1 TT
19296513 GTTATTTAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.63
Consensus pattern (14 bp):
TTACTATTTTATTA
Found at i:19297156 original size:14 final size:14
Alignment explanation
Indices: 19297137--19297179 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
19297127 CAAAACATTG
19297137 TTAAAATAATTTTT
1 TTAAAATAATTTTT
*
19297151 TTAAAATAATATTT
1 TTAAAATAATTTTT
* *
19297165 TGATAATTAATTTTT
1 TTA-AAATAATTTTT
19297180 ATTTATTTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
14 15 0.62
15 9 0.38
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (14 bp):
TTAAAATAATTTTT
Found at i:19297814 original size:23 final size:22
Alignment explanation
Indices: 19297757--19297826 Score: 74
Period size: 23 Copynumber: 3.3 Consensus size: 22
19297747 AAAAGTAAAA
*
19297757 TAAATTCAAATCATATATAT-T
1 TAAATTCAAATAATATATATCT
*
19297778 TCAATT--AATAATATATATCT
1 TAAATTCAAATAATATATATCT
* *
19297798 TAATATTCAAATTATATTTATCT
1 TAA-ATTCAAATAATATATATCT
19297821 TAAATT
1 TAAATT
19297827 TAATATTTAT
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
19 11 0.28
20 3 0.08
21 8 0.20
22 3 0.08
23 15 0.38
ACGTcount: A:0.44, C:0.09, G:0.00, T:0.47
Consensus pattern (22 bp):
TAAATTCAAATAATATATATCT
Found at i:19297871 original size:20 final size:21
Alignment explanation
Indices: 19297833--19297875 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 21
19297823 AATTTAATAT
*
19297833 TTATCATAAAGATAAATGTTA
1 TTATCATAAAGAGAAATGTTA
19297854 TTATCATAAA-AGAAATGTTA
1 TTATCATAAAGAGAAATGTTA
19297874 TT
1 TT
19297876 TAATTTTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.47, C:0.05, G:0.09, T:0.40
Consensus pattern (21 bp):
TTATCATAAAGAGAAATGTTA
Found at i:19299271 original size:23 final size:22
Alignment explanation
Indices: 19299239--19299285 Score: 67
Period size: 23 Copynumber: 2.1 Consensus size: 22
19299229 CAGAAAGTGT
*
19299239 AATATTTTTATAAAATAATTAA
1 AATATTTTTAGAAAATAATTAA
*
19299261 AATATGTTTTAGAAAATATTTAA
1 AATAT-TTTTAGAAAATAATTAA
19299284 AA
1 AA
19299286 CTTTAAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 5 0.23
23 17 0.77
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (22 bp):
AATATTTTTAGAAAATAATTAA
Found at i:19299300 original size:19 final size:19
Alignment explanation
Indices: 19299268--19299304 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
19299258 TAAAATATGT
19299268 TTTAGAAAATATTTAAAAC
1 TTTAGAAAATATTTAAAAC
19299287 TTTA-AAAATAATTTAAAA
1 TTTAGAAAAT-ATTTAAAA
19299305 TAATTTAGGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.38
Consensus pattern (19 bp):
TTTAGAAAATATTTAAAAC
Found at i:19300599 original size:51 final size:51
Alignment explanation
Indices: 19300518--19300634 Score: 180
Period size: 51 Copynumber: 2.3 Consensus size: 51
19300508 CGGATCACAT
* *
19300518 TTATCACTTGTCACTTGTCACTGGTCAGATAAGTGTAGCTAAAACTACCAC
1 TTATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAACTACAAC
* * **
19300569 TTATCACTTGTCACTTGTCACTGATTAGATAAGTGTAGCTGAGGCTACAAC
1 TTATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAACTACAAC
19300620 TTATCACTTGTCACT
1 TTATCACTTGTCACT
19300635 GATCAGAAGT
Statistics
Matches: 60, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
51 60 1.00
ACGTcount: A:0.27, C:0.22, G:0.16, T:0.34
Consensus pattern (51 bp):
TTATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAACTACAAC
Found at i:19305021 original size:46 final size:46
Alignment explanation
Indices: 19304973--19305138 Score: 155
Period size: 46 Copynumber: 3.6 Consensus size: 46
19304963 TCCGAACTCG
* *
19304973 TTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCC-GGACTCG
1 TTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCAAG-CTCA
* *
19305019 TTGAGTTGAGTCCGAG-T---TTGTGAGATG-TAACTAGGTATCCAAGCTCA
1 TTGAGTTGAGTCCGAGTTCACTTATG-GATGCGAAC---G--TCCAAGCTCA
* * *
19305066 TTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACATTCGAGCTCA
1 TTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCAAGCTCA
*
19305112 TTGAGTTGAGTCTGAGTTCACTTATGG
1 TTGAGTTGAGTCCGAGTTCACTTATGG
19305139 GCGGGTTAGA
Statistics
Matches: 98, Mismatches: 10, Indels: 24
0.74 0.08 0.18
Matches are distributed among these distances:
42 7 0.07
43 4 0.04
45 2 0.02
46 50 0.51
47 22 0.22
48 2 0.02
50 4 0.04
51 7 0.07
ACGTcount: A:0.22, C:0.17, G:0.28, T:0.32
Consensus pattern (46 bp):
TTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCAAGCTCA
Found at i:19308883 original size:14 final size:14
Alignment explanation
Indices: 19308864--19308897 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
19308854 TAAAACCAAG
19308864 ACCAATCCAAATCA
1 ACCAATCCAAATCA
**
19308878 ACCAATCCATTTCA
1 ACCAATCCAAATCA
19308892 ACCAAT
1 ACCAAT
19308898 TTGATACCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.44, C:0.35, G:0.00, T:0.21
Consensus pattern (14 bp):
ACCAATCCAAATCA
Found at i:19310537 original size:43 final size:44
Alignment explanation
Indices: 19310476--19310577 Score: 161
Period size: 44 Copynumber: 2.3 Consensus size: 44
19310466 ATTAGTGACA
*
19310476 AGTGACAAGTGATAAGTGGTAGC-CTAACTACACTTATCTGATC
1 AGTGACAAGTGATAAGTGGTAGCTCTAACTACACTTATCTAATC
* * *
19310519 AGTGACGAGTGATAAGTGGTAGCTTTAGCTACACTTATCTAATC
1 AGTGACAAGTGATAAGTGGTAGCTCTAACTACACTTATCTAATC
19310563 AGTGACAAGTGATAA
1 AGTGACAAGTGATAA
19310578 ATGTGATCTG
Statistics
Matches: 53, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
43 22 0.42
44 31 0.58
ACGTcount: A:0.33, C:0.16, G:0.23, T:0.28
Consensus pattern (44 bp):
AGTGACAAGTGATAAGTGGTAGCTCTAACTACACTTATCTAATC
Found at i:19313831 original size:27 final size:27
Alignment explanation
Indices: 19313801--19313854 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
19313791 TTTTTCATCC
19313801 ATATTTATAATATTA-AC-CATAAATAAA
1 ATATTT-TAAT-TTATACACATAAATAAA
*
19313828 ATATTTTAATTTATACATATAAATAAA
1 ATATTTTAATTTATACACATAAATAAA
19313855 TTCGCGCATC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
25 3 0.12
26 6 0.25
27 15 0.62
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.41
Consensus pattern (27 bp):
ATATTTTAATTTATACACATAAATAAA
Found at i:19329281 original size:13 final size:13
Alignment explanation
Indices: 19329263--19329288 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
19329253 TTTTATTTTA
19329263 TAATATTTTAAAT
1 TAATATTTTAAAT
19329276 TAATATTTTAAAT
1 TAATATTTTAAAT
19329289 GTTTTATAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
TAATATTTTAAAT
Found at i:19329376 original size:81 final size:82
Alignment explanation
Indices: 19329276--19329483 Score: 203
Period size: 81 Copynumber: 2.5 Consensus size: 82
19329266 TATTTTAAAT
19329276 TAATATTTTAAATGTTTTATAATATATGTTTATTCAAACGTCTTGTTT-TTGAAAT-TTTTTTAA
1 TAATATTTTAAA--TTTTATAATATATGTTTATTCAAACGT-TTGTTTATTGAAATATTTTTT-A
19329339 AATGGTTTATTATTTATTTTA
62 AATGGTTTATTATTTATTTTA
** * *
19329360 TAATATTTTAAATTTATATTTTAAATGTTT-TAT-AATA--TTTGTTTATTTAAATATTTTTTAA
1 TAATATTTTAAATTT-TATAATATATGTTTAT-TCAA-ACGTTTGTTTATTGAAATATTTTTTAA
* * *
19329421 TTTGTTTATTATTTGTTTTA
63 ATGGTTTATTATTTATTTTA
* * *
19329441 TAATATTATAAATGTTTTATAATATTTATTTATTCAAACGTTT
1 TAATATTTTAAA--TTTTATAATATATGTTTATTCAAACGTTT
19329484 TTAAATAAAT
Statistics
Matches: 100, Mismatches: 13, Indels: 22
0.74 0.10 0.16
Matches are distributed among these distances:
80 6 0.06
81 37 0.37
82 23 0.23
83 19 0.19
84 15 0.15
ACGTcount: A:0.32, C:0.02, G:0.06, T:0.59
Consensus pattern (82 bp):
TAATATTTTAAATTTTATAATATATGTTTATTCAAACGTTTGTTTATTGAAATATTTTTTAAATG
GTTTATTATTTATTTTA
Found at i:19329423 original size:16 final size:17
Alignment explanation
Indices: 19329388--19329419 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
19329378 TTTTAAATGT
19329388 TTTATAATATTTGTTTA
1 TTTATAATATTTGTTTA
19329405 TTTA-AATATTT-TTTA
1 TTTATAATATTTGTTTA
19329420 ATTTGTTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 4 0.27
16 7 0.47
17 4 0.27
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (17 bp):
TTTATAATATTTGTTTA
Found at i:19329606 original size:44 final size:44
Alignment explanation
Indices: 19329552--19329718 Score: 123
Period size: 44 Copynumber: 4.0 Consensus size: 44
19329542 ATTTGTTTAT
19329552 TATTA-AAAAAAATTAAATAAACAAATATTATAAAACATTTAAAA
1 TATTATAAAAAAA-TAAATAAACAAATATTATAAAACATTTAAAA
19329596 TATTATAAAAAAATAAGA-AAACAAATA--AT-AAAC------AA
1 TATTATAAAAAAATAA-ATAAACAAATATTATAAAACATTTAAAA
* * *
19329631 -ATTA-AAAAAATGTTTAAATAAAGAAATATTATAAAACAATTAAAA
1 TATTATAAAAAA---ATAAATAAACAAATATTATAAAACATTTAAAA
*
19329676 TATTATAAAACAAAT-AATAAAC-AAT-TTAAAAAACAATTTAAAA
1 TATTATAAAA-AAATAAATAAACAAATATTATAAAAC-ATTTAAAA
19329719 AAACCGTTTG
Statistics
Matches: 98, Mismatches: 6, Indels: 39
0.69 0.04 0.27
Matches are distributed among these distances:
33 6 0.06
34 4 0.04
35 3 0.03
36 11 0.11
38 2 0.02
39 4 0.04
41 4 0.04
42 10 0.10
43 10 0.10
44 23 0.23
45 11 0.11
46 4 0.04
47 4 0.04
48 2 0.02
ACGTcount: A:0.66, C:0.05, G:0.02, T:0.27
Consensus pattern (44 bp):
TATTATAAAAAAATAAATAAACAAATATTATAAAACATTTAAAA
Found at i:19329640 original size:80 final size:81
Alignment explanation
Indices: 19329553--19329760 Score: 271
Period size: 80 Copynumber: 2.6 Consensus size: 81
19329543 TTTGTTTATT
19329553 ATTAAAAAAAA--TTAAATAAACAAATATTATAAAACATTTAAAATATTATAAAA-AAATAAGAA
1 ATTAAAAAAAAGTTTAAATAAACAAATATTATAAAACATTTAAAATATTATAAAACAAATAA-AA
*
19329615 AACAA-ATAATAAACAA
65 AACAATATAAAAAACAA
* * * *
19329631 ATTAAAAAAATGTTTAAATAAAGAAATATTATAAAACAATTAAAATATTATAAAACAAATAATAA
1 ATTAAAAAAAAGTTTAAATAAACAAATATTATAAAACATTTAAAATATTATAAAACAAATAAAAA
*
19329696 ACAATTTAAAAAACAA
66 ACAATATAAAAAACAA
* * * * *
19329712 TTTAAAAAAACCGTTTGAATAAATAGATATTATAAAACATTTAAAATAT
1 ATTAAAAAAA-AGTTTAAATAAACAAATATTATAAAACATTTAAAATAT
19329761 AAATTTTAAA
Statistics
Matches: 113, Mismatches: 12, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
78 10 0.09
80 46 0.41
81 24 0.21
82 33 0.29
ACGTcount: A:0.64, C:0.05, G:0.03, T:0.28
Consensus pattern (81 bp):
ATTAAAAAAAAGTTTAAATAAACAAATATTATAAAACATTTAAAATATTATAAAACAAATAAAAA
ACAATATAAAAAACAA
Found at i:19329722 original size:13 final size:12
Alignment explanation
Indices: 19329694--19329720 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
19329684 AACAAATAAT
19329694 AAACAATTTAAA
1 AAACAATTTAAA
19329706 AAACAATTTAAA
1 AAACAATTTAAA
19329718 AAA
1 AAA
19329721 ACCGTTTGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.70, C:0.07, G:0.00, T:0.22
Consensus pattern (12 bp):
AAACAATTTAAA
Found at i:19329796 original size:15 final size:15
Alignment explanation
Indices: 19329767--19329796 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
19329757 ATATAAATTT
*
19329767 TAAATATTATAAAAA
1 TAAATATTAAAAAAA
19329782 TAAATATTAAAAAAA
1 TAAATATTAAAAAAA
19329797 AGGAAAATGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (15 bp):
TAAATATTAAAAAAA
Found at i:19338830 original size:10 final size:10
Alignment explanation
Indices: 19338815--19338843 Score: 51
Period size: 9 Copynumber: 3.0 Consensus size: 10
19338805 ATTGCTTGTT
19338815 TGAATAGAAA
1 TGAATAGAAA
19338825 TGAATAG-AA
1 TGAATAGAAA
19338834 TGAATAGAAA
1 TGAATAGAAA
19338844 AAGAGAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.50
10 9 0.50
ACGTcount: A:0.59, C:0.00, G:0.21, T:0.21
Consensus pattern (10 bp):
TGAATAGAAA
Found at i:19339679 original size:53 final size:54
Alignment explanation
Indices: 19339621--19339731 Score: 197
Period size: 53 Copynumber: 2.1 Consensus size: 54
19339611 AAGAAAAGAA
19339621 AATTTCCATTTTCACCCTAAAAGGAAAACTTTTTCTAGTTCTATGTTTTGATT-
1 AATTTCCATTTTCACCCTAAAAGGAAAACTTTTTCTAGTTCTATGTTTTGATTC
* *
19339674 AATTTCTATTTTCACCCTGAAAGGAAAACTTTTTCTAGTTCTATGTTTTGATTC
1 AATTTCCATTTTCACCCTAAAAGGAAAACTTTTTCTAGTTCTATGTTTTGATTC
19339728 AATT
1 AATT
19339732 GGTTCAAGCC
Statistics
Matches: 55, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
53 51 0.93
54 4 0.07
ACGTcount: A:0.28, C:0.16, G:0.10, T:0.46
Consensus pattern (54 bp):
AATTTCCATTTTCACCCTAAAAGGAAAACTTTTTCTAGTTCTATGTTTTGATTC
Found at i:19341846 original size:19 final size:19
Alignment explanation
Indices: 19341822--19341859 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
19341812 GACACACGCC
19341822 TGTGTTCTAGGTCGTGTAG
1 TGTGTTCTAGGTCGTGTAG
*
19341841 TGTGTTCTAGGTTGTGTAG
1 TGTGTTCTAGGTCGTGTAG
19341860 CACACATGGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.11, C:0.08, G:0.37, T:0.45
Consensus pattern (19 bp):
TGTGTTCTAGGTCGTGTAG
Found at i:19348357 original size:28 final size:28
Alignment explanation
Indices: 19348297--19348358 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
19348287 ATTCTCTGTC
*
19348297 TAAAAACAACCTATTCTCATAAATATAA
1 TAAAAACAACCTAATCTCATAAATATAA
* * *
19348325 AAAAAACAACCTAAAT-TCATAAATTTTA
1 TAAAAACAACCT-AATCTCATAAATATAA
19348353 TAAAAA
1 TAAAAA
19348359 AAATGACATA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
28 26 0.93
29 2 0.07
ACGTcount: A:0.58, C:0.15, G:0.00, T:0.27
Consensus pattern (28 bp):
TAAAAACAACCTAATCTCATAAATATAA
Found at i:19352842 original size:19 final size:19
Alignment explanation
Indices: 19352810--19352858 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 19
19352800 TAATTCAATG
* *
19352810 GACATGTAACTCTTGACAT
1 GACATGAAAATCTTGACAT
* *
19352829 GGCATGAAAATCTTGAGAT
1 GACATGAAAATCTTGACAT
*
19352848 GATATGAAAAT
1 GACATGAAAAT
19352859 GACTGGAGAG
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.39, C:0.12, G:0.20, T:0.29
Consensus pattern (19 bp):
GACATGAAAATCTTGACAT
Found at i:19357955 original size:46 final size:46
Alignment explanation
Indices: 19357847--19357973 Score: 148
Period size: 46 Copynumber: 2.7 Consensus size: 46
19357837 GCCACATTAT
* * * *
19357847 GAGAACCATTGTAAGACCATGTCTGGGACATGGCATTGGCATTGAGAC
1 GAGAGCCAGTGTAAGA-CATGTCTGGGACAT-GCATTAGCATCGAGAC
* * *
19357895 GAGAGCTAGTGTAAGACATGTCTGGGACATGCATTAGCCTCGAGAT
1 GAGAGCCAGTGTAAGACATGTCTGGGACATGCATTAGCATCGAGAC
*
19357941 GTA-AGCCAGTGTAAGACATGTTTGGGACATGCA
1 G-AGAGCCAGTGTAAGACATGTCTGGGACATGCA
19357974 GCGGCTACGA
Statistics
Matches: 69, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
46 41 0.59
47 15 0.22
48 13 0.19
ACGTcount: A:0.29, C:0.17, G:0.30, T:0.24
Consensus pattern (46 bp):
GAGAGCCAGTGTAAGACATGTCTGGGACATGCATTAGCATCGAGAC
Found at i:19365706 original size:46 final size:46
Alignment explanation
Indices: 19365527--19365735 Score: 185
Period size: 46 Copynumber: 4.5 Consensus size: 46
19365517 TTTGTGCACT
* * ** *
19365527 AGTGTAAGACATGTCTGAGACATGCATTGGCCACATTATGAAAGCC
1 AGTGTAAGACATGTCTGGGACATGCATTGGCTACAAGATGTAAGCC
* ** * *
19365573 ATTGTAAGACCATGTCTGGGACATAGCATTGGC-ATTGAGACG-AGAGCT
1 AGTGTAAGA-CATGTCTGGGACAT-GCATTGGCTA-CAAGATGTA-AGCC
* * * * *
19365621 AGTGTAAGACATGTTTGGGACTTGCATCAGCCT-CGAGATGTAAGCC
1 AGTGTAAGACATGTCTGGGACATGCAT-TGGCTACAAGATGTAAGCC
*
19365667 AGTGTAAGACATGTCTGGGACATGCATTGGCTACAAGATGT--GTC
1 AGTGTAAGACATGTCTGGGACATGCATTGGCTACAAGATGTAAGCC
19365711 AGTGTAAGACTATGTCTGGGACATG
1 AGTGTAAGAC-ATGTCTGGGACATG
19365736 GCATCGACAC
Statistics
Matches: 132, Mismatches: 22, Indels: 19
0.76 0.13 0.11
Matches are distributed among these distances:
44 12 0.09
45 17 0.13
46 52 0.39
47 30 0.23
48 21 0.16
ACGTcount: A:0.29, C:0.17, G:0.28, T:0.26
Consensus pattern (46 bp):
AGTGTAAGACATGTCTGGGACATGCATTGGCTACAAGATGTAAGCC
Found at i:19374234 original size:20 final size:20
Alignment explanation
Indices: 19374186--19374236 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 20
19374176 TTTTTGCTAT
*
19374186 TTTATTATTAAATTAATTAC
1 TTTATTATTATATTAATTAC
19374206 TTTA--A-TATATT-ATTAC
1 TTTATTATTATATTAATTAC
19374222 TATTATTATTATATT
1 T-TTATTATTATATT
19374237 TCTATTTATA
Statistics
Matches: 26, Mismatches: 1, Indels: 8
0.74 0.03 0.23
Matches are distributed among these distances:
16 6 0.23
17 8 0.31
18 1 0.04
19 1 0.04
20 10 0.38
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (20 bp):
TTTATTATTATATTAATTAC
Found at i:19374372 original size:15 final size:14
Alignment explanation
Indices: 19374341--19374377 Score: 56
Period size: 15 Copynumber: 2.6 Consensus size: 14
19374331 AAAACTTTAG
*
19374341 TTATTATTATATTA
1 TTATTATTATATCA
19374355 TTATTATTAATATCA
1 TTATTATT-ATATCA
19374370 TTATTATT
1 TTATTATT
19374378 TTTTAAACTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 8 0.38
15 13 0.62
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (14 bp):
TTATTATTATATCA
Found at i:19376138 original size:29 final size:29
Alignment explanation
Indices: 19376095--19376152 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
19376085 ATTATTTGAG
* *
19376095 AAGCTGTTAATGAAGCTAACAAGCATCAC
1 AAGCCGTTAACGAAGCTAACAAGCATCAC
19376124 AAGCCGTTAACGAAGCTAACAAGCATCAC
1 AAGCCGTTAACGAAGCTAACAAGCATCAC
19376153 GGGGATAAGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.41, C:0.24, G:0.17, T:0.17
Consensus pattern (29 bp):
AAGCCGTTAACGAAGCTAACAAGCATCAC
Found at i:19415940 original size:89 final size:88
Alignment explanation
Indices: 19415724--19415984 Score: 240
Period size: 89 Copynumber: 3.0 Consensus size: 88
19415714 TTATGGCAGG
* * * * *
19415724 CCTTATCTCCCTGAAGTTGTAGTGGAGCAGGTTAAAAGTTA-CAAATCTCAACTCCCCGAAGTTA
1 CCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTT-GAAGATAGCAAATCTTAACTCCCTGAAGTTA
* * *
19415788 TAGTGGAGTAGATTGAAG-TTAGA
65 TAGTAGAGCAGATTAAAGCTTAGA
* * * ** * * ** * * *
19415811 TCTTATCTCTCTGATGTTGCAGTGGAATAGATCGGGGATAGCAAATCTTACCTCTCTGAAGTTAC
1 CCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGATAGCAAATCTTAACTCCCTGAAGTTAT
19415876 AGTAGAGCAGATTAAAGCCATTA-A
66 AGTAGAGCAGATTAAAG-C-TTAGA
* ** *
19415900 CCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGATAGCAAATTTTATTTCCCTGAAGTTGT
1 CCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGATAGCAAATCTTAACTCCCTGAAGTTAT
* *
19415965 AGTAGAACAGATTTAAGCTT
66 AGTAGAGCAGATTAAAGCTT
19415985 CAAGTTACAA
Statistics
Matches: 133, Mismatches: 37, Indels: 8
0.75 0.21 0.04
Matches are distributed among these distances:
86 3 0.02
87 60 0.45
88 1 0.01
89 66 0.50
90 3 0.02
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.31
Consensus pattern (88 bp):
CCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGATAGCAAATCTTAACTCCCTGAAGTTAT
AGTAGAGCAGATTAAAGCTTAGA
Found at i:19416171 original size:45 final size:46
Alignment explanation
Indices: 19416098--19416355 Score: 129
Period size: 45 Copynumber: 5.6 Consensus size: 46
19416088 AATCCCATAC
* *
19416098 CCCTGAAGTTGCAATGG-GATGGATTGAAGA-AATCAAGTCTTATCT
1 CCCTGAAGTTGCAGTGGAG-TAGATTGAAGACAATCAAGTCTTATCT
* * * * * *
19416143 CCCTGAAGTTGCAGTGGAGTAGACTGAAGATAGTGAA-TCTCATTT
1 CCCTGAAGTTGCAGTGGAGTAGATTGAAGACAATCAAGTCTTATCT
* * ** * *
19416188 CCTTGAAGTTGTAGTGGAACAGATT-AAGATTACAAGTTACAAATCTGATC-
1 CCCTGAAGTTGCAGTGGAGTAGATTGAAG---ACAA--T-CAAGTCTTATCT
* *
19416238 CCCTGAAGTTGCAGTGGAGTAGATTGAAGA-AAGCGAGT-TTCATCT
1 CCCTGAAGTTGCAGTGGAGTAGATTGAAGACAATCAAGTCTT-ATCT
* * * * * * * *
19416283 CCCTGAAGTTGTAGTAGAGCAAATTAAAG-CTA-CAAATCTAATCT
1 CCCTGAAGTTGCAGTGGAGTAGATTGAAGACAATCAAGTCTTATCT
* * * *
19416327 CTCTAAAGATGCAGTGGAGCAGATTGAAG
1 CCCTGAAGTTGCAGTGGAGTAGATTGAAG
19416356 CGAAAATTCC
Statistics
Matches: 158, Mismatches: 41, Indels: 29
0.69 0.18 0.13
Matches are distributed among these distances:
43 1 0.01
44 38 0.24
45 77 0.49
46 5 0.03
47 4 0.03
48 1 0.01
49 1 0.01
50 23 0.15
51 8 0.05
ACGTcount: A:0.33, C:0.16, G:0.24, T:0.28
Consensus pattern (46 bp):
CCCTGAAGTTGCAGTGGAGTAGATTGAAGACAATCAAGTCTTATCT
Found at i:19416224 original size:89 final size:89
Alignment explanation
Indices: 19416131--19416355 Score: 218
Period size: 95 Copynumber: 2.5 Consensus size: 89
19416121 TTGAAGAAAT
* * * * *
19416131 CAAGTCTTATCTCCCTGAAGTTGCAGTGGAGTAGACTGAAGATAGTGAATCTCATTTCCTTGAAG
1 CAAGTCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAGAAAGCGAATCTCATCTCCCTGAAG
* *
19416196 TTGTAGTGGAACAGATTAAGATTACAAGTTA
66 TTGTAGTAGAAC-----AA-ATTA-AAGCTA
* * * *
19416227 CAAATCTGATC-CCCTGAAGTTGCAGTGGAGTAGATTGAAGAAAGCGAGTTTCATCTCCCTGAAG
1 CAAGTCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAGAAAGCGAATCTCATCTCCCTGAAG
*
19416291 TTGTAGTAGAGCAAATTAAAGCTA
66 TTGTAGTAGAACAAATTAAAGCTA
* * * * * *
19416315 CAAATCTAATCTCTCTAAAGATGCAGTGGAGCAGATTGAAG
1 CAAGTCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAG
19416356 CGAAAATTCC
Statistics
Matches: 111, Mismatches: 17, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
88 15 0.14
89 29 0.26
90 2 0.02
95 56 0.50
96 9 0.08
ACGTcount: A:0.33, C:0.16, G:0.23, T:0.28
Consensus pattern (89 bp):
CAAGTCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAGAAAGCGAATCTCATCTCCCTGAAG
TTGTAGTAGAACAAATTAAAGCTA
Found at i:19416317 original size:95 final size:95
Alignment explanation
Indices: 19416143--19416317 Score: 235
Period size: 95 Copynumber: 1.8 Consensus size: 95
19416133 AGTCTTATCT
* * * * *
19416143 CCCTGAAGTTGCAGTGGAGTAGACTGAAGATAGTGAATCTCATTTCCTTGAAGTTGTAGTGGAAC
1 CCCTGAAGTTGCAGTGGAGTAGACTGAAGAAAGCGAATCTCATCTCCCTGAAGTTGTAGTAGAAC
* *
19416208 AGATTAAGATTACAAGTTACAAATCTGATC
66 AAATTAAGACTACAAGTTACAAATCTGATC
* * * *
19416238 CCCTGAAGTTGCAGTGGAGTAGATTGAAGAAAGCGAGTTTCATCTCCCTGAAGTTGTAGTAGAGC
1 CCCTGAAGTTGCAGTGGAGTAGACTGAAGAAAGCGAATCTCATCTCCCTGAAGTTGTAGTAGAAC
19416303 AAATTAA-AGCTACAA
66 AAATTAAGA-CTACAA
19416318 ATCTAATCTC
Statistics
Matches: 68, Mismatches: 11, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
94 1 0.01
95 67 0.99
ACGTcount: A:0.33, C:0.15, G:0.24, T:0.27
Consensus pattern (95 bp):
CCCTGAAGTTGCAGTGGAGTAGACTGAAGAAAGCGAATCTCATCTCCCTGAAGTTGTAGTAGAAC
AAATTAAGACTACAAGTTACAAATCTGATC
Found at i:19416995 original size:15 final size:15
Alignment explanation
Indices: 19416958--19416997 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 15
19416948 AAAAAGGTGA
19416958 TTTTTTA-TTC-TGT
1 TTTTTTATTTCATGT
*
19416971 TTTTCT-TTTCATGT
1 TTTTTTATTTCATGT
19416985 TTTTTTATTTCAT
1 TTTTTTATTTCAT
19416998 TTATGTTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
13 8 0.36
14 8 0.36
15 6 0.27
ACGTcount: A:0.10, C:0.10, G:0.05, T:0.75
Consensus pattern (15 bp):
TTTTTTATTTCATGT
Found at i:19417723 original size:17 final size:18
Alignment explanation
Indices: 19417680--19417725 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 18
19417670 TTCTCTATTT
*
19417680 TATTATTAAATTAATTAA
1 TATTATTATATTAATTAA
* *
19417698 T-TTAATATATT-ATTAC
1 TATTATTATATTAATTAA
19417714 TATTATTATATT
1 TATTATTATATT
19417726 TCTATTTATA
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
16 5 0.22
17 17 0.74
18 1 0.04
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (18 bp):
TATTATTATATTAATTAA
Found at i:19417865 original size:15 final size:14
Alignment explanation
Indices: 19417834--19417870 Score: 56
Period size: 15 Copynumber: 2.6 Consensus size: 14
19417824 AAAACTATAG
*
19417834 TTATTATTATATTA
1 TTATTATTATATCA
19417848 TTATTATTAATATCA
1 TTATTATT-ATATCA
19417863 TTATTATT
1 TTATTATT
19417871 TTTTAAACTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 8 0.38
15 13 0.62
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (14 bp):
TTATTATTATATCA
Found at i:19419453 original size:22 final size:22
Alignment explanation
Indices: 19419442--19419484 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
19419432 TCTCTCTATT
19419442 TTGCTACCATTTTACTATTATG
1 TTGCTACCATTTTACTATTATG
* *
19419464 TTGCTACTATTTTATTATTAT
1 TTGCTACCATTTTACTATTAT
19419485 TGTTTGGATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.23, C:0.14, G:0.07, T:0.56
Consensus pattern (22 bp):
TTGCTACCATTTTACTATTATG
Found at i:19421453 original size:72 final size:72
Alignment explanation
Indices: 19421372--19421519 Score: 296
Period size: 72 Copynumber: 2.1 Consensus size: 72
19421362 ATTACCTAAT
19421372 TATAACATTATATTAGTTGGGACTATGAACTCTTTTAGCAATTATGTGGACTTCAAATCAAAACA
1 TATAACATTATATTAGTTGGGACTATGAACTCTTTTAGCAATTATGTGGACTTCAAATCAAAACA
19421437 AAAGTTA
66 AAAGTTA
19421444 TATAACATTATATTAGTTGGGACTATGAACTCTTTTAGCAATTATGTGGACTTCAAATCAAAACA
1 TATAACATTATATTAGTTGGGACTATGAACTCTTTTAGCAATTATGTGGACTTCAAATCAAAACA
19421509 AAAGTTA
66 AAAGTTA
19421516 TATA
1 TATA
19421520 TCACTACTTA
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
72 76 1.00
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.35
Consensus pattern (72 bp):
TATAACATTATATTAGTTGGGACTATGAACTCTTTTAGCAATTATGTGGACTTCAAATCAAAACA
AAAGTTA
Found at i:19426600 original size:28 final size:29
Alignment explanation
Indices: 19426530--19426601 Score: 80
Period size: 27 Copynumber: 2.6 Consensus size: 29
19426520 TATAATTCAA
*
19426530 CAAATTCAAA-AT-AAATAATACTTTTTT
1 CAAATTTAAATATAAAATAATACTTTTTT
* *
19426557 TAAATTTAAATTTAAAAT-ATA-TTTTTT
1 CAAATTTAAATATAAAATAATACTTTTTT
19426584 CAAATTTAAATAATAAAA
1 CAAATTTAAAT-ATAAAA
19426602 ATTAAAAATT
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
27 24 0.65
28 9 0.24
29 4 0.11
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (29 bp):
CAAATTTAAATATAAAATAATACTTTTTT
Found at i:19427770 original size:29 final size:29
Alignment explanation
Indices: 19427727--19427789 Score: 83
Period size: 29 Copynumber: 2.2 Consensus size: 29
19427717 TGGTATTGAT
* *
19427727 ATTTTTAATAATTTTTTTTATAATTTTATA
1 ATTTTTAATAATTTTTTTAAAAATTTTA-A
*
19427757 ATTTTT-ATGATTTTTTTAAAAATTTTAA
1 ATTTTTAATAATTTTTTTAAAAATTTTAA
19427785 ATTTT
1 ATTTT
19427790 AAAGTTAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
28 6 0.20
29 18 0.60
30 6 0.20
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (29 bp):
ATTTTTAATAATTTTTTTAAAAATTTTAA
Found at i:19432814 original size:166 final size:166
Alignment explanation
Indices: 19432540--19432871 Score: 646
Period size: 166 Copynumber: 2.0 Consensus size: 166
19432530 TACTATGTTC
*
19432540 CTACTCTCAGTGGTCCATAATTATATCTTTTATTTTCTTTATGTTTGTATTTACTTTAGGGAATG
1 CTACTCTCAGTGGTCCATAATTATATCTTTTATTTTCTTTATGTTTGCATTTACTTTAGGGAATG
*
19432605 TAACAAATTTGGTAGGGCAGACTTCTAAACACCTCTATTGATCTTTTATTTTATAATAACCATCA
66 TAACAAATTTGGTAGGGCAGACTTCTAAACACCTCTATTGATCTTTTATTTCATAATAACCATCA
19432670 TAAACATACGTGGATTTTAAATCAGAATCTATCTAT
131 TAAACATACGTGGATTTTAAATCAGAATCTATCTAT
19432706 CTACTCTCAGTGGTCCATAATTATATCTTTTATTTTCTTTATGTTTGCATTTACTTTAGGGAATG
1 CTACTCTCAGTGGTCCATAATTATATCTTTTATTTTCTTTATGTTTGCATTTACTTTAGGGAATG
19432771 TAACAAATTTGGTAGGGCAGACTTCTAAACACCTCTATTGATCTTTTATTTCATAATAACCATCA
66 TAACAAATTTGGTAGGGCAGACTTCTAAACACCTCTATTGATCTTTTATTTCATAATAACCATCA
19432836 TAAACATACGTGGATTTTAAATCAGAATCTATCTAT
131 TAAACATACGTGGATTTTAAATCAGAATCTATCTAT
19432872 TCATGTTGTC
Statistics
Matches: 164, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
166 164 1.00
ACGTcount: A:0.30, C:0.16, G:0.12, T:0.42
Consensus pattern (166 bp):
CTACTCTCAGTGGTCCATAATTATATCTTTTATTTTCTTTATGTTTGCATTTACTTTAGGGAATG
TAACAAATTTGGTAGGGCAGACTTCTAAACACCTCTATTGATCTTTTATTTCATAATAACCATCA
TAAACATACGTGGATTTTAAATCAGAATCTATCTAT
Found at i:19434080 original size:20 final size:20
Alignment explanation
Indices: 19434055--19434097 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
19434045 TTACTAACGG
19434055 AGTAAGAAAAAAACTCCACA
1 AGTAAGAAAAAAACTCCACA
19434075 AGTAAGAAAAAAACTCCACA
1 AGTAAGAAAAAAACTCCACA
19434095 AGT
1 AGT
19434098 GCATTTAGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.58, C:0.19, G:0.12, T:0.12
Consensus pattern (20 bp):
AGTAAGAAAAAAACTCCACA
Found at i:19439141 original size:46 final size:46
Alignment explanation
Indices: 19439044--19439168 Score: 162
Period size: 46 Copynumber: 2.7 Consensus size: 46
19439034 TTTGAGAGCC
* *
19439044 AGTGTAAGACCATGTTTAGGACATGACATCGGCATTGAGACGAGTGCT
1 AGTGTAAGA-CATGTTTAGGACATG-CATCGGCATCGAGACGAATGCT
* * *
19439092 AGTGTAAGACATGTCTAGGACATGCATCGGCCTCGAGACGTAAT-TT
1 AGTGTAAGACATGTTTAGGACATGCATCGGCATCGAGACG-AATGCT
*
19439138 AGTGTAAGACATGTTTGGGACATGCATCGGC
1 AGTGTAAGACATGTTTAGGACATGCATCGGC
19439169 TACGAGATCT
Statistics
Matches: 69, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
46 44 0.64
47 16 0.23
48 9 0.13
ACGTcount: A:0.28, C:0.18, G:0.29, T:0.26
Consensus pattern (46 bp):
AGTGTAAGACATGTTTAGGACATGCATCGGCATCGAGACGAATGCT
Found at i:19439175 original size:46 final size:46
Alignment explanation
Indices: 19439044--19439214 Score: 149
Period size: 46 Copynumber: 3.7 Consensus size: 46
19439034 TTTGAGAGCC
* *
19439044 AGTGTAAGACCATGTTTAGGACATGACATCGGC-ATTGAGACG-AGTGCT
1 AGTGTAAGACCATGTTTAGGACATG-CATCGGCTA-CGAGACGTA-T-TT
*
19439092 AGTGTAAGA-CATGTCTAGGACATGCATCGGCCT-CGAGACGTAATTT
1 AGTGTAAGACCATGTTTAGGACATGCATCGG-CTACGAGACGT-ATTT
* * *
19439138 AGTGTAAGA-CATGTTTGGGACATGCATCGGCTACGAGATC-T-GTC
1 AGTGTAAGACCATGTTTAGGACATGCATCGGCTACGAGA-CGTATTT
* *
19439182 AGTGTAAGACCATGTATGGGACATGGCATCGGC
1 AGTGTAAGACCATGTTTAGGACAT-GCATCGGC
19439215 ACCTTACCCC
Statistics
Matches: 107, Mismatches: 8, Indels: 18
0.80 0.06 0.14
Matches are distributed among these distances:
44 10 0.09
45 15 0.14
46 55 0.51
47 17 0.16
48 10 0.09
ACGTcount: A:0.27, C:0.18, G:0.29, T:0.25
Consensus pattern (46 bp):
AGTGTAAGACCATGTTTAGGACATGCATCGGCTACGAGACGTATTT
Found at i:19443527 original size:79 final size:81
Alignment explanation
Indices: 19443391--19443575 Score: 227
Period size: 79 Copynumber: 2.3 Consensus size: 81
19443381 TTGAATGATG
* *
19443391 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAAT
19443455 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * * **
19443470 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
19443532 ATTGTGCGAGTTACTATA
64 ATTGTGCGAGATACTATA
* *
19443550 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
19443576 AACGAGTAGC
Statistics
Matches: 91, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 1 0.01
79 57 0.63
80 33 0.36
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAAT
TGTGCGAGATACTATA
Found at i:19443589 original size:40 final size:40
Alignment explanation
Indices: 19443392--19443575 Score: 207
Period size: 40 Copynumber: 4.6 Consensus size: 40
19443382 TGAATGATGT
* * * *
19443392 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* * *
19443432 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
19443472 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
* *
19443510 TCCGGGTTAAGTCCCGAAGGCAATTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
19443551 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
19443576 AACGAGTAGC
Statistics
Matches: 124, Mismatches: 13, Indels: 14
0.82 0.09 0.09
Matches are distributed among these distances:
39 35 0.28
40 79 0.64
41 10 0.08
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:19443597 original size:79 final size:79
Alignment explanation
Indices: 19443444--19443598 Score: 199
Period size: 79 Copynumber: 2.0 Consensus size: 79
19443434 GGACTAAGAT
* * **
19443444 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
19443509 ATCCGGGTTAAGTC
66 ATCCGGGTTAAGTC
* *
19443523 CCGAAGGCAATTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCAATTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
*
19443586 TATATCC-GGTTAA
63 TAAATCCGGGTTAA
19443599 ATTTCGAAGG
Statistics
Matches: 66, Mismatches: 7, Indels: 6
0.84 0.09 0.08
Matches are distributed among these distances:
78 2 0.03
79 39 0.59
80 25 0.38
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAGTC
Found at i:19460002 original size:14 final size:14
Alignment explanation
Indices: 19459983--19460009 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
19459973 GCATAGGAAC
19459983 TTTATTTTACTTTA
1 TTTATTTTACTTTA
19459997 TTTATTTTACTTT
1 TTTATTTTACTTT
19460010 GTTAAAATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.19, C:0.07, G:0.00, T:0.74
Consensus pattern (14 bp):
TTTATTTTACTTTA
Found at i:19470842 original size:21 final size:21
Alignment explanation
Indices: 19470818--19470868 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
19470808 CAATTATCCC
19470818 AAATTAATCACCTAAAAAAAT
1 AAATTAATCACCTAAAAAAAT
*
19470839 AAATTAATCACCTAAAATAAT
1 AAATTAATCACCTAAAAAAAT
19470860 AAATTAATC
1 AAATTAATC
19470869 TAACTCACTC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.59, C:0.14, G:0.00, T:0.27
Consensus pattern (21 bp):
AAATTAATCACCTAAAAAAAT
Found at i:19470952 original size:14 final size:14
Alignment explanation
Indices: 19470933--19470961 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
19470923 TCTTGAATGC
19470933 CTCCTACTAAGATT
1 CTCCTACTAAGATT
19470947 CTCCTACTAAGATT
1 CTCCTACTAAGATT
19470961 C
1 C
19470962 CACGAGAAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.31, G:0.07, T:0.34
Consensus pattern (14 bp):
CTCCTACTAAGATT
Found at i:19475926 original size:22 final size:22
Alignment explanation
Indices: 19475901--19475944 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
19475891 AATTATTAAC
19475901 ATAACGAATTTTAATAAATTTT
1 ATAACGAATTTTAATAAATTTT
** * *
19475923 ATAATTAATTTTCATTAATTTT
1 ATAACGAATTTTAATAAATTTT
19475945 GGTTAATTTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.41, C:0.05, G:0.02, T:0.52
Consensus pattern (22 bp):
ATAACGAATTTTAATAAATTTT
Found at i:19478656 original size:5 final size:5
Alignment explanation
Indices: 19478642--19478670 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
19478632 AAATCATATA
19478642 ATTTT A-TTT ATTTT ATTTT ATTTT ATTTT
1 ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT
19478671 TTACTAAACC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 19 0.83
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (5 bp):
ATTTT
Found at i:19479729 original size:23 final size:22
Alignment explanation
Indices: 19479703--19479750 Score: 53
Period size: 22 Copynumber: 2.1 Consensus size: 22
19479693 CAATTTCATC
19479703 CTAATCTAAATT-CACTTCCTTTT
1 CTAA-CTAAATTACACTT-CTTTT
* *
19479726 CTAACTCAATTATACTTCTTTT
1 CTAACTAAATTACACTTCTTTT
19479748 CTA
1 CTA
19479751 CTTAATTTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
22 14 0.64
23 8 0.36
ACGTcount: A:0.27, C:0.25, G:0.00, T:0.48
Consensus pattern (22 bp):
CTAACTAAATTACACTTCTTTT
Found at i:19480406 original size:32 final size:30
Alignment explanation
Indices: 19480369--19480441 Score: 85
Period size: 32 Copynumber: 2.3 Consensus size: 30
19480359 ATTATTTAAT
* *
19480369 TAATAAATATCT-TTTAACTTAATAATAATAAG
1 TAATAAATATCTATCT-ACTT-A-AATAAAAAG
19480401 TAATAAATATCTATCTACTTAAATAAAAAG
1 TAATAAATATCTATCTACTTAAATAAAAAG
19480431 TAAATAAATAT
1 T-AATAAATAT
19480442 TTATGTTACA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
30 9 0.24
31 10 0.27
32 16 0.43
33 2 0.05
ACGTcount: A:0.53, C:0.07, G:0.03, T:0.37
Consensus pattern (30 bp):
TAATAAATATCTATCTACTTAAATAAAAAG
Found at i:19481614 original size:38 final size:38
Alignment explanation
Indices: 19481563--19481658 Score: 113
Period size: 40 Copynumber: 2.5 Consensus size: 38
19481553 CCATCTCCAT
* *
19481563 CCAACCC-ATCACACCATGTGGGGATAGAATCGACCCAC
1 CCAACCCTA-CACACCATATGGGGATAGAATCAACCCAC
** *
19481601 CCAACCCTACACACCAAGTATGGGGATTTAATCAACCCAT
1 CCAACCCTACACACC-A-TATGGGGATAGAATCAACCCAC
19481641 CCAACCCTACACACCATA
1 CCAACCCTACACACCATA
19481659 AGGAACCACA
Statistics
Matches: 50, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
38 15 0.30
39 3 0.06
40 32 0.64
ACGTcount: A:0.34, C:0.38, G:0.12, T:0.16
Consensus pattern (38 bp):
CCAACCCTACACACCATATGGGGATAGAATCAACCCAC
Found at i:19481639 original size:40 final size:40
Alignment explanation
Indices: 19481581--19481656 Score: 116
Period size: 40 Copynumber: 1.9 Consensus size: 40
19481571 TCACACCATG
*
19481581 TGGGGATAGAATCGACCCACCCAACCCTACACACCAAGTA
1 TGGGGATAGAATCAACCCACCCAACCCTACACACCAAGTA
** *
19481621 TGGGGATTTAATCAACCCATCCAACCCTACACACCA
1 TGGGGATAGAATCAACCCACCCAACCCTACACACCA
19481657 TAAGGAACCA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 32 1.00
ACGTcount: A:0.34, C:0.36, G:0.14, T:0.16
Consensus pattern (40 bp):
TGGGGATAGAATCAACCCACCCAACCCTACACACCAAGTA
Found at i:19487788 original size:51 final size:51
Alignment explanation
Indices: 19487710--19487837 Score: 220
Period size: 51 Copynumber: 2.5 Consensus size: 51
19487700 AAATGATGAT
*
19487710 GAAAAAAAAGAGAAAGAAAAAAAGCTCTCATGTTGTTCTTGGCCGAATAGAA
1 GAAAGAAAA-AGAAAGAAAAAAAGCTCTCATGTTGTTCTTGGCCGAATAGAA
19487762 GAAAGAAAAAGAAAGAAAAAAAGCTCTCATGTTGTTCTTGGCCGAATAGAA
1 GAAAGAAAAAGAAAGAAAAAAAGCTCTCATGTTGTTCTTGGCCGAATAGAA
* *
19487813 GAAAGAAAAAGAAGGAAAAAGAGCT
1 GAAAGAAAAAGAAAGAAAAAAAGCT
19487838 TTGAGGAAAT
Statistics
Matches: 73, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
51 65 0.89
52 8 0.11
ACGTcount: A:0.51, C:0.10, G:0.23, T:0.16
Consensus pattern (51 bp):
GAAAGAAAAAGAAAGAAAAAAAGCTCTCATGTTGTTCTTGGCCGAATAGAA
Found at i:19496429 original size:23 final size:22
Alignment explanation
Indices: 19496403--19496450 Score: 53
Period size: 22 Copynumber: 2.1 Consensus size: 22
19496393 CAATTTAATC
19496403 CTAATCTAAATT-CACTTCCTTTT
1 CTAA-CTAAATTACACTT-CTTTT
* *
19496426 CTAACTCAATTATACTTCTTTT
1 CTAACTAAATTACACTTCTTTT
19496448 CTA
1 CTA
19496451 CTTACTTTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
22 14 0.64
23 8 0.36
ACGTcount: A:0.27, C:0.25, G:0.00, T:0.48
Consensus pattern (22 bp):
CTAACTAAATTACACTTCTTTT
Found at i:19496908 original size:32 final size:30
Alignment explanation
Indices: 19496872--19496944 Score: 101
Period size: 32 Copynumber: 2.3 Consensus size: 30
19496862 ATTATTTAAT
*
19496872 TAATAAATATCTATTAACTTAATAATAATAAG
1 TAATAAATATCTATTAACTT-A-AATAAAAAG
*
19496904 TAATAAATATCTATTTACTTAAATAAAAAG
1 TAATAAATATCTATTAACTTAAATAAAAAG
19496934 TAATTAAATAT
1 TAA-TAAATAT
19496945 TTATGTTACA
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
30 11 0.29
31 8 0.21
32 19 0.50
ACGTcount: A:0.53, C:0.05, G:0.03, T:0.38
Consensus pattern (30 bp):
TAATAAATATCTATTAACTTAAATAAAAAG
Found at i:19503075 original size:48 final size:48
Alignment explanation
Indices: 19503017--19503337 Score: 319
Period size: 48 Copynumber: 6.7 Consensus size: 48
19503007 TATGTGTGGT
19503017 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCATGATATGAGAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCATGATATGAGAGCC
* * * * * * *
19503065 AGTGTAAGACCATGTTTGGAACATAGCATTGGCGATGTTGTGAGAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCATGATATGAGAGCC
* *
19503113 AGTGTAAGACCATGTCTGGGACATGGCATCGG-CATTGATATGTGCA-CT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCA-TGATATGAG-AGCC
* * * * ** * *
19503161 AGTGTAAAACCATGTCTGGGGCATGGTATCAGCCACAACATAAGAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCATGATATGAGAGCC
* * * * *
19503209 AGTGTAAGACCATGTCTGGGATATGGCATCGG-TATTGAGACGAGAGCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCA-TGATATGAGAGCC
* * *
19503257 AGTGTAAGACCATGTCTGGGACATGGCATTGGCC-TCAACATGTA-AGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCAT-GATATG-AGAGCC
* *
19503305 AGTGTAAGACCATGTTTGGAACATGGCATCGGC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGC
19503338 AATTTACCCT
Statistics
Matches: 217, Mismatches: 48, Indels: 16
0.77 0.17 0.06
Matches are distributed among these distances:
47 4 0.02
48 209 0.96
49 4 0.02
ACGTcount: A:0.28, C:0.19, G:0.30, T:0.24
Consensus pattern (48 bp):
AGTGTAAGACCATGTCTGGGACATGGCATCGGCCATGATATGAGAGCC
Found at i:19503309 original size:144 final size:144
Alignment explanation
Indices: 19503016--19503334 Score: 358
Period size: 144 Copynumber: 2.2 Consensus size: 144
19503006 ATATGTGTGG
* ** * * *
19503016 TAGTGTAAGACCATGTCTGGGACATGGCATCGGCCATGATATGAGAGCCAGTGTAAGACCATGTT
1 TAGTGTAAGACCATGTCTGGGACATGGCATCAGCCACAACATAAGAGCCAGTGTAAGACCATGTC
* * *
19503081 TGGAACATAGCATTGGCGATGTTGTGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGC
66 TGGAACATAGCATCGGCGATGTAGCGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGC
** *
19503146 ATTGATATGTGCAC
131 ATCAACATGTGCAC
* * *
19503160 TAGTGTAAAACCATGTCTGGGGCATGGTATCAGCCACAACATAAGAGCCAGTGTAAGACCATGTC
1 TAGTGTAAGACCATGTCTGGGACATGGCATCAGCCACAACATAAGAGCCAGTGTAAGACCATGTC
* * * * * *
19503225 TGGGATATGGCATCGG-TAT-TGAGACGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATTG
66 TGGAACATAGCATCGGCGATGT-AG-CGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCG
*
19503288 GCCTCAACATGTAAGC-C
129 GCATCAACATGT--GCAC
* *
19503305 -AGTGTAAGACCATGTTTGGAACATGGCATC
1 TAGTGTAAGACCATGTCTGGGACATGGCATC
19503335 GGCAATTTAC
Statistics
Matches: 144, Mismatches: 27, Indels: 8
0.80 0.15 0.04
Matches are distributed among these distances:
142 1 0.01
143 3 0.02
144 137 0.95
145 1 0.01
146 2 0.01
ACGTcount: A:0.28, C:0.19, G:0.29, T:0.24
Consensus pattern (144 bp):
TAGTGTAAGACCATGTCTGGGACATGGCATCAGCCACAACATAAGAGCCAGTGTAAGACCATGTC
TGGAACATAGCATCGGCGATGTAGCGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGC
ATCAACATGTGCAC
Found at i:19522626 original size:46 final size:46
Alignment explanation
Indices: 19522559--19522651 Score: 177
Period size: 46 Copynumber: 2.0 Consensus size: 46
19522549 TTTTTATGGA
*
19522559 ATGTTTTTTCGGATGTTATTAAGCATGTTGATAATAAATTGAGTTT
1 ATGTTTTTTCAGATGTTATTAAGCATGTTGATAATAAATTGAGTTT
19522605 ATGTTTTTTCAGATGTTATTAAGCATGTTGATAATAAATTGAGTTT
1 ATGTTTTTTCAGATGTTATTAAGCATGTTGATAATAAATTGAGTTT
19522651 A
1 A
19522652 ATTAAAGTAA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.30, C:0.04, G:0.18, T:0.47
Consensus pattern (46 bp):
ATGTTTTTTCAGATGTTATTAAGCATGTTGATAATAAATTGAGTTT
Found at i:19526868 original size:27 final size:26
Alignment explanation
Indices: 19526833--19526887 Score: 69
Period size: 26 Copynumber: 2.1 Consensus size: 26
19526823 ATTTTAAAAT
19526833 ATAAAAAAA-TATTTCAAAAAAT-TATA
1 ATAAAAAAATTA-TT-AAAAAATATATA
19526859 ATAAATAAAATTATTAAAAAATATATA
1 ATAAA-AAAATTATTAAAAAATATATA
19526886 AT
1 AT
19526888 TTTTAAAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
26 12 0.46
27 12 0.46
28 2 0.08
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (26 bp):
ATAAAAAAATTATTAAAAAATATATA
Found at i:19526883 original size:25 final size:22
Alignment explanation
Indices: 19526828--19526883 Score: 58
Period size: 25 Copynumber: 2.4 Consensus size: 22
19526818 AAAAAATTTT
*
19526828 AAAATATAAAAAAATATTTCAA
1 AAAATATAAAAAAAAATTTCAA
*
19526850 AAAATTATAATAAATAAAATTATTAA
1 AAAA-TATAA-AAA-AAAATT-TCAA
19526876 AAAATATA
1 AAAATATA
19526884 TAATTTTTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
22 4 0.14
23 5 0.18
24 3 0.11
25 9 0.32
26 7 0.25
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (22 bp):
AAAATATAAAAAAAAATTTCAA
Found at i:19526888 original size:18 final size:19
Alignment explanation
Indices: 19526867--19526915 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
19526857 TAATAAATAA
*
19526867 AATTATTAAAAAAT-ATAT
1 AATTTTTAAAAAATGATAT
* *
19526885 AATTTTTAAAATATGTTAT
1 AATTTTTAAAAAATGATAT
19526904 AATTTTTAAAAA
1 AATTTTTAAAAA
19526916 TAATAACGTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
18 12 0.46
19 14 0.54
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (19 bp):
AATTTTTAAAAAATGATAT
Found at i:19539050 original size:17 final size:16
Alignment explanation
Indices: 19539024--19539058 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
19539014 ATTTTTCTAT
*
19539024 AAAAATTAAAAATTCA
1 AAAAATTAAAAATACA
19539040 AAAATATTAAAAATACA
1 AAAA-ATTAAAAATACA
19539057 AA
1 AA
19539059 GTTCCAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.23
Consensus pattern (16 bp):
AAAAATTAAAAATACA
Found at i:19552012 original size:16 final size:16
Alignment explanation
Indices: 19551991--19552029 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
19551981 GTAGATTGGC
*
19551991 AAAAGCCGAAATGCCG
1 AAAAGCCGAAATGCCA
* *
19552007 AAAAGCTGAAATGTCA
1 AAAAGCCGAAATGCCA
19552023 AAAAGCC
1 AAAAGCC
19552030 AAAAGTTTGG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.49, C:0.21, G:0.21, T:0.10
Consensus pattern (16 bp):
AAAAGCCGAAATGCCA
Found at i:19554483 original size:17 final size:17
Alignment explanation
Indices: 19554461--19554493 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
19554451 GTGATATTAA
*
19554461 TAATAAAATAAATAAAG
1 TAATAAAAGAAATAAAG
19554478 TAATAAAAGAAATAAA
1 TAATAAAAGAAATAAA
19554494 ATGCGAGATG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.73, C:0.00, G:0.06, T:0.21
Consensus pattern (17 bp):
TAATAAAAGAAATAAAG
Found at i:19555278 original size:27 final size:28
Alignment explanation
Indices: 19555226--19555278 Score: 65
Period size: 28 Copynumber: 1.9 Consensus size: 28
19555216 AATTTTAAGA
* *
19555226 AAAAAAAGTCATTTGCTTTTCTTTTTTT
1 AAAAAAAGTCATTTGCTCTTCATTTTTT
19555254 AAAAAAAGTTC-TTT-CTCTTCATTTT
1 AAAAAAAG-TCATTTGCTCTTCATTTT
19555279 CTCTCTAGGC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
27 9 0.41
28 11 0.50
29 2 0.09
ACGTcount: A:0.30, C:0.13, G:0.06, T:0.51
Consensus pattern (28 bp):
AAAAAAAGTCATTTGCTCTTCATTTTTT
Done.