Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 113035596
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: 113035596
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 271 characters in sequence are not A, C, G, or T
File 296 of 378
Found at i:89425845 original size:26 final size:26
Alignment explanation
Indices: 89425816--89425922 Score: 155
Period size: 26 Copynumber: 4.2 Consensus size: 26
89425806 TGGTACAAAT
*
89425816 TGATAATAGG-TTAGGTAAATGTTCCA
1 TGATAAT-GGATTAGGTAAATATTCCA
89425842 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGATTAGGTAAATATTCCA
* *
89425868 TGATAATGG-GTAGGTAAATGTTCCA
1 TGATAATGGATTAGGTAAATATTCCA
*
89425893 TGATAATGGTTTAGGTAAATATTCCA
1 TGATAATGGATTAGGTAAATATTCCA
89425919 TGAT
1 TGAT
89425923 GGGCATTTCA
Statistics
Matches: 74, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
25 25 0.34
26 49 0.66
ACGTcount: A:0.35, C:0.07, G:0.22, T:0.36
Consensus pattern (26 bp):
TGATAATGGATTAGGTAAATATTCCA
Found at i:89425889 original size:51 final size:52
Alignment explanation
Indices: 89425816--89425922 Score: 189
Period size: 51 Copynumber: 2.1 Consensus size: 52
89425806 TGGTACAAAT
*
89425816 TGATAATAGGTTAGGTAAATGTTCCATGATAATGGATTAGGTAAATATTCCA
1 TGATAATAGGGTAGGTAAATGTTCCATGATAATGGATTAGGTAAATATTCCA
*
89425868 TGATAAT-GGGTAGGTAAATGTTCCATGATAATGGTTTAGGTAAATATTCCA
1 TGATAATAGGGTAGGTAAATGTTCCATGATAATGGATTAGGTAAATATTCCA
89425919 TGAT
1 TGAT
89425923 GGGCATTTCA
Statistics
Matches: 53, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
51 46 0.87
52 7 0.13
ACGTcount: A:0.35, C:0.07, G:0.22, T:0.36
Consensus pattern (52 bp):
TGATAATAGGGTAGGTAAATGTTCCATGATAATGGATTAGGTAAATATTCCA
Found at i:89427588 original size:27 final size:28
Alignment explanation
Indices: 89427548--89427608 Score: 90
Period size: 27 Copynumber: 2.2 Consensus size: 28
89427538 AGGAAGCGTC
89427548 CTGGTGGCTATGCCACGAT-TATCTG-AT
1 CTGGTGGCTATGCCAC-ATATATCTGTAT
*
89427575 CTGGTGGCTCTGCCACATATATCTGTAT
1 CTGGTGGCTATGCCACATATATCTGTAT
89427603 CTGGTG
1 CTGGTG
89427609 ACTTCGTCAC
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
26 2 0.06
27 21 0.68
28 8 0.26
ACGTcount: A:0.16, C:0.23, G:0.26, T:0.34
Consensus pattern (28 bp):
CTGGTGGCTATGCCACATATATCTGTAT
Found at i:89427619 original size:28 final size:26
Alignment explanation
Indices: 89427548--89427626 Score: 70
Period size: 27 Copynumber: 2.9 Consensus size: 26
89427538 AGGAAGCGTC
* * *
89427548 CTGGTGGCTATGCCACGATTATCTGAT
1 CTGGTGACTCTGCCAC-AATATCTGAT
*
89427575 CTGGTGGCTCTGCCACATATATCTGTAT
1 CTGGTGACTCTGCCACA-ATATCTG-AT
*
89427603 CTGGTGACT-TCGTCACAATATCTG
1 CTGGTGACTCT-GCCACAATATCTG
89427627 GTAGCCTCGC
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
26 1 0.02
27 29 0.64
28 15 0.33
ACGTcount: A:0.19, C:0.24, G:0.23, T:0.34
Consensus pattern (26 bp):
CTGGTGACTCTGCCACAATATCTGAT
Found at i:89432608 original size:55 final size:55
Alignment explanation
Indices: 89432496--89432637 Score: 142
Period size: 55 Copynumber: 2.6 Consensus size: 55
89432486 CAACATGGCT
* ** * * *
89432496 GTGGTCAAACCTGCCAAAACAACACGGGCGTGCGACACGCCCGTCTGGAAGAACC
1 GTGGTCGAACCTGTTAAAACAACACGGGCGTGAGACACGCCCGTCTCGAACAACC
* * * * *
89432551 GTGGGT-GAACCTGTTAAAACAGCACGGGCGTTAGACACGCCCGTGTCTAACACCC
1 GT-GGTCGAACCTGTTAAAACAACACGGGCGTGAGACACGCCCGTCTCGAACAACC
* **
89432606 GTGGTCGAACCTGTCAAATTAACACGGGCGTG
1 GTGGTCGAACCTGTTAAAACAACACGGGCGTG
89432638 GGGCTTTTAT
Statistics
Matches: 69, Mismatches: 16, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
54 3 0.04
55 63 0.91
56 3 0.04
ACGTcount: A:0.27, C:0.29, G:0.28, T:0.16
Consensus pattern (55 bp):
GTGGTCGAACCTGTTAAAACAACACGGGCGTGAGACACGCCCGTCTCGAACAACC
Found at i:89435772 original size:4 final size:4
Alignment explanation
Indices: 89435763--89435787 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
89435753 TGTTCTTAAA
89435763 AAAC AAAC AAAC AAAC AAAC AAAC A
1 AAAC AAAC AAAC AAAC AAAC AAAC A
89435788 TGTATACTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.24, G:0.00, T:0.00
Consensus pattern (4 bp):
AAAC
Found at i:89438313 original size:84 final size:87
Alignment explanation
Indices: 89438168--89438336 Score: 222
Period size: 84 Copynumber: 2.0 Consensus size: 87
89438158 TATTCCAAAT
*
89438168 TTTTATTTTGTTTCCAAAAAAGAGAAATTAAAATTAAATAAAAATTTATTTCGGGATTTATTCCC
1 TTTTATTTTGTTTCC-AAAAAGAGAAATTAAAATTAAATAAAAA-TTATTTCAGGATTTATTCCC
*
89438233 GCCATTTAATAAGATTTTATCTCA
64 GCCATTTAACAAGATTTTATCTCA
* *
89438257 TTTTATTTTGTTTCC-AAAATAG-AATT-AAATTAAAT-AAAA-TATGTTCTAGGATTTATTTCC
1 TTTTATTTTGTTTCCAAAAAGAGAAATTAAAATTAAATAAAAATTAT-TTC-AGGATTTATTCCC
*
89438317 GCCGTTTAACAAGATTTTAT
64 GCCATTTAACAAGATTTTAT
89438337 TTTATTTTGT
Statistics
Matches: 73, Mismatches: 5, Indels: 9
0.84 0.06 0.10
Matches are distributed among these distances:
82 3 0.04
83 3 0.04
84 33 0.45
85 9 0.12
86 4 0.05
87 6 0.08
89 15 0.21
ACGTcount: A:0.37, C:0.11, G:0.09, T:0.43
Consensus pattern (87 bp):
TTTTATTTTGTTTCCAAAAAGAGAAATTAAAATTAAATAAAAATTATTTCAGGATTTATTCCCGC
CATTTAACAAGATTTTATCTCA
Found at i:89438344 original size:84 final size:85
Alignment explanation
Indices: 89438078--89438442 Score: 241
Period size: 89 Copynumber: 4.2 Consensus size: 85
89438068 TTTTTTTTCC
* * * * * *
89438078 TTTATTTTA-TTTATTTCCAAACGAGAAATTAAAGGTAAATAAAATCTGTT-TCAGGATTGATTT
1 TTTATTTTATTTTGTTTCCAAAAGAGAAATTAAA-TTAAATAAAATATGTTCT-AGGATTTATTC
*
89438141 CCGCTG-TT--CAATGATTTTAT
64 CCGCCGTTTAACAA-GATTTTAT
** *
89438161 TCCAAATTTTTATTTTGTTTCCAAAAAAGAGAAATTAAAATTAAATAAAAATTTAT-TTC-GGGA
1 T--TTA-TTTTATTTTGTTTCC--AAAAGAGAAATT-AAATTAAAT-AAAA--TATGTTCTAGGA
* *
89438224 TTTATTCCCGCCATTTAATAAGATTTTAT
57 TTTATTCCCGCCGTTTAACAAGATTTTAT
* * * *
89438253 CTCATTTTATTTTGTTTCCAAAATAG-AATTAAATTAAATAAAATATGTTCTAGGATTTATTTCC
1 TTTATTTTATTTTGTTTCCAAAAGAGAAATTAAATTAAATAAAATATGTTCTAGGATTTATTCCC
89438317 GCCGTTTAACAAGATTTTAT
66 GCCGTTTAACAAGATTTTAT
* ** * * * * *
89438337 TTTATTTTGTTTTATTTTGTTTCCAAATAAAG-ACGT-AATCAAAT-AATTTTGTTTTGGGATTT
1 TTTA-----TTTTATTTTGTTTCCAAA-AGAGAAATTAAATTAAATAAAATATGTTCTAGGATTT
89438399 ATTCCCGCCGTTTAAC-AGATTTTAT
60 ATTCCCGCCGTTTAACAAGATTTTAT
* *
89438424 TTTGATATAATTTTGTTTC
1 TTT-ATTTTATTTTGTTTC
89438443 AGGATTTAAT
Statistics
Matches: 226, Mismatches: 33, Indels: 46
0.74 0.11 0.15
Matches are distributed among these distances:
82 3 0.01
83 16 0.07
84 35 0.15
85 10 0.04
86 9 0.04
87 26 0.12
88 30 0.13
89 56 0.25
90 25 0.11
91 4 0.02
92 10 0.04
93 2 0.01
ACGTcount: A:0.33, C:0.11, G:0.11, T:0.45
Consensus pattern (85 bp):
TTTATTTTATTTTGTTTCCAAAAGAGAAATTAAATTAAATAAAATATGTTCTAGGATTTATTCCC
GCCGTTTAACAAGATTTTAT
Found at i:89438352 original size:89 final size:84
Alignment explanation
Indices: 89438168--89438442 Score: 254
Period size: 89 Copynumber: 3.2 Consensus size: 84
89438158 TATTCCAAAT
89438168 TTTTATTTTGTTTCCAAAAAAGAGAAATTAAAATTAAATAAAAATTTAT-TTC-GGGATTTATTC
1 TTTTATTTTGTTTCC-AAAAA-AG-AATT-AAATTAAAT-AAAA--TATGTTCTGGGATTTATTC
* * * *
89438231 CCGCCATTTAATAAGATTTTATCTCA
59 CCGCCGTTTAACAAGATTTTATTTTA
* * *
89438257 TTTTATTTTGTTTCCAAAATAGAATTAAATTAAATAAAATATGTTCTAGGATTTATTTCCGCCGT
1 TTTTATTTTGTTTCCAAAAAAGAATTAAATTAAATAAAATATGTTCTGGGATTTATTCCCGCCGT
89438322 TTAACAAGATTTTATTTTA
66 TTAACAAGATTTTATTTTA
** * * * *
89438341 TTTTGTTTTATTTTGTTTCCAAATAAAGACGT-AATCAAAT-AATTTTGTTTTGGGATTTATTCC
1 -----TTTTATTTTGTTTCCAAA-AAAGAATTAAATTAAATAAAATATGTTCTGGGATTTATTCC
89438404 CGCCGTTTAAC-AGATTTTATTTTGA
60 CGCCGTTTAACAAGATTTTATTTT-A
* *
89438429 TATAATTTTGTTTC
1 TTTTATTTTGTTTC
89438443 AGGATTTAAT
Statistics
Matches: 159, Mismatches: 18, Indels: 24
0.79 0.09 0.12
Matches are distributed among these distances:
82 3 0.02
83 15 0.09
84 35 0.22
85 9 0.06
86 4 0.03
87 14 0.09
88 34 0.21
89 40 0.25
90 5 0.03
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.47
Consensus pattern (84 bp):
TTTTATTTTGTTTCCAAAAAAGAATTAAATTAAATAAAATATGTTCTGGGATTTATTCCCGCCGT
TTAACAAGATTTTATTTTA
Found at i:89438478 original size:51 final size:51
Alignment explanation
Indices: 89438379--89438480 Score: 125
Period size: 51 Copynumber: 2.0 Consensus size: 51
89438369 ACGTAATCAA
** * * * *
89438379 ATAATTTTGTTTTGGGATTTATTCCCGCCGTTTAACAGATTTTATTTTGAT
1 ATAATTTTGTTTCAGGATTTAATCCCGCCGTTCAACAAATTATATTTTGAT
*
89438430 ATAATTTTGTTTCAGGATTTAATCCTGCCGTTCAACAAAATTAT-TTTTGAT
1 ATAATTTTGTTTCAGGATTTAATCCCGCCGTTCAAC-AAATTATATTTTGAT
89438481 TTTGTTTCAG
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
51 38 0.88
52 5 0.12
ACGTcount: A:0.25, C:0.13, G:0.14, T:0.48
Consensus pattern (51 bp):
ATAATTTTGTTTCAGGATTTAATCCCGCCGTTCAACAAATTATATTTTGAT
Found at i:89441521 original size:63 final size:63
Alignment explanation
Indices: 89441443--89441570 Score: 247
Period size: 63 Copynumber: 2.0 Consensus size: 63
89441433 TGAGTGATGA
*
89441443 ATGAGAAATTGATTCTCAAAGTAAGTTACTTGGAAATATTTGTTGAGGAAAAGAAAAGCTTAG
1 ATGAGAAATTGATTCTCAAAGTAAGTTACTTGGAAATATTTGTTAAGGAAAAGAAAAGCTTAG
89441506 ATGAGAAATTGATTCTCAAAGTAAGTTACTTGGAAATATTTGTTAAGGAAAAGAAAAGCTTAG
1 ATGAGAAATTGATTCTCAAAGTAAGTTACTTGGAAATATTTGTTAAGGAAAAGAAAAGCTTAG
89441569 AT
1 AT
89441571 CCCACATTGG
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
63 64 1.00
ACGTcount: A:0.42, C:0.06, G:0.21, T:0.30
Consensus pattern (63 bp):
ATGAGAAATTGATTCTCAAAGTAAGTTACTTGGAAATATTTGTTAAGGAAAAGAAAAGCTTAG
Found at i:89441869 original size:20 final size:20
Alignment explanation
Indices: 89441840--89441886 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
89441830 ATATATCGTG
89441840 AATT-ATTTGATTCTAAT-C
1 AATTGATTTGATTCTAATCC
*
89441858 AATTTGATTTGATTTTAATCC
1 AA-TTGATTTGATTCTAATCC
89441879 AATTGATT
1 AATTGATT
89441887 CAATTGCTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
18 2 0.08
19 2 0.08
20 18 0.72
21 3 0.12
ACGTcount: A:0.32, C:0.09, G:0.09, T:0.51
Consensus pattern (20 bp):
AATTGATTTGATTCTAATCC
Found at i:89442366 original size:18 final size:18
Alignment explanation
Indices: 89442343--89442377 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
89442333 ATAATTTATC
89442343 TTTATATATAAATATTTA
1 TTTATATATAAATATTTA
* *
89442361 TTTATATTTATATATTT
1 TTTATATATAAATATTT
89442378 TGTTCACTAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
TTTATATATAAATATTTA
Found at i:89444382 original size:144 final size:144
Alignment explanation
Indices: 89444122--89444554 Score: 740
Period size: 144 Copynumber: 3.0 Consensus size: 144
89444112 GCTCAAAAAC
* *
89444122 ACAATTTACCGTTTCTTGTTGGTCAGCTTAATACTCGTGGTTATGTACAAAATTCCATGTCTAAT
1 ACAATTTCCCGTTTCTTGTTGGTCAGCTTAATACTCGTGGTTATGTACAAAATTTCATGTCTAAT
*
89444187 AGAAATTGCATTGTTTTTATATTCTATCACTGGTTAATAGAAAACTTAGATTCCAACAAATTCCA
66 AGAAATTGCATTGTTTTTATATTCTATCACTGGTTAATAGACAACTTAGATTCCAACAAATTCCA
89444252 GACATGCAAAGAAA
131 GACATGCAAAGAAA
* *
89444266 ACAATTTCCCGTTTCTTGTTGGTCAGCTTAATACTCGTGGTTATGTACAAAATTTCATGCCTAAA
1 ACAATTTCCCGTTTCTTGTTGGTCAGCTTAATACTCGTGGTTATGTACAAAATTTCATGTCTAAT
*
89444331 AGATATTGCATTGTTTTTATATTCTATCACTGGTTAATAGACAACTTAGATTCCAACAAATTCCA
66 AGAAATTGCATTGTTTTTATATTCTATCACTGGTTAATAGACAACTTAGATTCCAACAAATTCCA
*
89444396 GACATGCAAAGAAT
131 GACATGCAAAGAAA
*
89444410 ACAATTTCCCGTTTCTTGTTGGTCAGCTTAATACTCGTGGTTATGTACAAAATTTAATGTCTAAT
1 ACAATTTCCCGTTTCTTGTTGGTCAGCTTAATACTCGTGGTTATGTACAAAATTTCATGTCTAAT
* * * *
89444475 AGAAATTGTATTGTTTTTATATTCAATCACTGGTTAATAGACAAATTATATTCCAACAAATTCCA
66 AGAAATTGCATTGTTTTTATATTCTATCACTGGTTAATAGACAACTTAGATTCCAACAAATT-C-
89444540 CAGACATGCAAAGAA
129 CAGACATGCAAAGAA
89444555 TACAGAATAG
Statistics
Matches: 272, Mismatches: 15, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
144 256 0.94
145 1 0.00
146 15 0.06
ACGTcount: A:0.33, C:0.17, G:0.14, T:0.36
Consensus pattern (144 bp):
ACAATTTCCCGTTTCTTGTTGGTCAGCTTAATACTCGTGGTTATGTACAAAATTTCATGTCTAAT
AGAAATTGCATTGTTTTTATATTCTATCACTGGTTAATAGACAACTTAGATTCCAACAAATTCCA
GACATGCAAAGAAA
Found at i:89452137 original size:20 final size:18
Alignment explanation
Indices: 89452112--89452155 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
89452102 AATATGCATA
89452112 TGTTGAAGTGTTTGGTTTTT
1 TGTTGAAGT-TTT-GTTTTT
*
89452132 TGTTG-AGTTTTTTTTTT
1 TGTTGAAGTTTTGTTTTT
89452149 TGTTGAA
1 TGTTGAA
89452156 AAGAAAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 10 0.45
18 4 0.18
19 3 0.14
20 5 0.23
ACGTcount: A:0.11, C:0.00, G:0.25, T:0.64
Consensus pattern (18 bp):
TGTTGAAGTTTTGTTTTT
Found at i:89452553 original size:20 final size:20
Alignment explanation
Indices: 89452511--89452553 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
89452501 AATGCAACTT
* *
89452511 AAACACAAATCTAATCTTCA
1 AAACACAAATATAATCTTAA
89452531 AAACACAAATATAATCTTAA
1 AAACACAAATATAATCTTAA
89452551 AAA
1 AAA
89452554 TTATTTTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.58, C:0.19, G:0.00, T:0.23
Consensus pattern (20 bp):
AAACACAAATATAATCTTAA
Found at i:89454658 original size:24 final size:24
Alignment explanation
Indices: 89454631--89454677 Score: 60
Period size: 26 Copynumber: 1.9 Consensus size: 24
89454621 ATAACAATTT
89454631 TTTTA-CTTAAAAAATATATTATTA
1 TTTTATCTTAAAAAATAT-TTATTA
*
89454655 TTTTATTTTTAAAAAATATTTAT
1 TTTTA-TCTTAAAAAATATTTAT
89454678 ATATATACTG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 5 0.25
25 4 0.20
26 11 0.55
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (24 bp):
TTTTATCTTAAAAAATATTTATTA
Found at i:89455386 original size:38 final size:37
Alignment explanation
Indices: 89455344--89455460 Score: 91
Period size: 38 Copynumber: 3.2 Consensus size: 37
89455334 AAATATTTTG
89455344 TTAGTAATTTATTATAAATTGTTGTGTTTTGTGAGTTT
1 TTAGTAATTTATTATAAATTGTTGTGTTTTGT-AGTTT
* * * * ***
89455382 TTAGTAA--T-GTA-AATTTATTTTGTTAAATA-TTT
1 TTAGTAATTTATTATAAATTGTTGTGTTTTGTAGTTT
* *
89455414 GTTAGCAATTTATTTTAAATTGTTGTGTTTTGTAAGTTT
1 -TTAGTAATTTATTATAAATTGTTGTGTTTTGT-AGTTT
89455453 TTAGTAAT
1 TTAGTAAT
89455461 GTAATTTTAA
Statistics
Matches: 55, Mismatches: 17, Indels: 14
0.64 0.20 0.16
Matches are distributed among these distances:
32 3 0.05
33 7 0.13
34 11 0.20
35 3 0.05
36 2 0.04
37 11 0.20
38 15 0.27
39 3 0.05
ACGTcount: A:0.27, C:0.01, G:0.15, T:0.56
Consensus pattern (37 bp):
TTAGTAATTTATTATAAATTGTTGTGTTTTGTAGTTT
Found at i:89455436 original size:71 final size:72
Alignment explanation
Indices: 89455297--89455469 Score: 267
Period size: 71 Copynumber: 2.4 Consensus size: 72
89455287 TAGTTTAGTA
* * * *
89455297 TTTTGGTGATTTTTTAGTAATATAAAATTATTTTGTTAAATATTTTGTTAGTAATTTATTATAAA
1 TTTT-GTGAGTTTTTAGTAATGTAAATTTATTTTGTTAAATATTTTGTTAGCAATTTATTATAAA
89455362 TTGTTGTG
65 TTGTTGTG
*
89455370 TTTTGTGAGTTTTTAGTAATGTAAATTTATTTTGTTAAATA-TTTGTTAGCAATTTATTTTAAAT
1 TTTTGTGAGTTTTTAGTAATGTAAATTTATTTTGTTAAATATTTTGTTAGCAATTTATTATAAAT
89455434 TGTTGTG
66 TGTTGTG
* *
89455441 TTTTGTAAGTTTTTAGTAATGTAATTTTA
1 TTTTGTGAGTTTTTAGTAATGTAAATTTA
89455470 AAAAAAATTA
Statistics
Matches: 93, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
71 55 0.59
72 34 0.37
73 4 0.04
ACGTcount: A:0.28, C:0.01, G:0.14, T:0.57
Consensus pattern (72 bp):
TTTTGTGAGTTTTTAGTAATGTAAATTTATTTTGTTAAATATTTTGTTAGCAATTTATTATAAAT
TGTTGTG
Found at i:89455722 original size:105 final size:104
Alignment explanation
Indices: 89455520--89455867 Score: 435
Period size: 101 Copynumber: 3.3 Consensus size: 104
89455510 TTATAAATTG
* *
89455520 TTAGTGTTTTGTTATTTTTTAGTAATGTAGTTTCTTTTTAAAAA-AATGTTATAGTTATTTATTT
1 TTAGTGTTTTGTGATTTTTTAGTAATGTA-ATT-TTTTTAAAAATAAT-TT-TA--TATTTATTT
*
89455584 TTTTTAGTAATTTATGTGATTAGG-T-TATAAATTGTTAGTGTTTAGT
60 TGTTT-GTAATTTA--TGATTAGGTTATATAAATTGTTAGTGTTTAGT
* * *
89455630 TTAGGGTTTTGTGAATTTTTCAGTAATGTAATTTTTTTAAAAATAATTTTATAGTTATTTTGTTT
1 TTAGTGTTTTGTG-ATTTTTTAGTAATGTAATTTTTTTAAAAATAATTTTATATTTATTTTGTTT
*
89455695 GTAATTTATGATTAGGTTATATAAATTGTTAGTATTTAGT
65 GTAATTTATGATTAGGTTATATAAATTGTTAGTGTTTAGT
* * **
89455735 TTAGTGTTTTGTGATTTTTTGGTAATGT-A-TTTTTAAAAAATAA-TTTATATTTATTTTGTCAG
1 TTAGTGTTTTGTGATTTTTTAGTAATGTAATTTTTTTAAAAATAATTTTATATTTATTTTGTTTG
*
89455797 TAATTTATGATTAGCTTATATAAATTGTTAGTGTTT-GT
66 TAATTTATGATTAGGTTATATAAATTGTTAGTGTTTAGT
89455835 TTAGTGTTTTGTGATTTTTT--TAATGTAATTTTT
1 TTAGTGTTTTGTGATTTTTTAGTAATGTAATTTTT
89455868 ATATAATGTA
Statistics
Matches: 216, Mismatches: 16, Indels: 22
0.85 0.06 0.09
Matches are distributed among these distances:
98 6 0.03
99 1 0.00
100 26 0.12
101 50 0.23
102 13 0.06
103 9 0.04
104 14 0.06
105 40 0.19
106 12 0.06
108 2 0.01
109 12 0.06
110 16 0.07
111 15 0.07
ACGTcount: A:0.27, C:0.01, G:0.15, T:0.57
Consensus pattern (104 bp):
TTAGTGTTTTGTGATTTTTTAGTAATGTAATTTTTTTAAAAATAATTTTATATTTATTTTGTTTG
TAATTTATGATTAGGTTATATAAATTGTTAGTGTTTAGT
Found at i:89458783 original size:47 final size:47
Alignment explanation
Indices: 89458713--89458885 Score: 283
Period size: 47 Copynumber: 3.7 Consensus size: 47
89458703 CCCTTCGGGA
* *
89458713 CTTATCACATTTATACACTTTCACATCCATCACATTGGCCATTTGGC
1 CTTATCACATATATACACTTTCACATCCATCACATTGGCCATTCGGC
* *
89458760 CTTATCACATATATACACCTTCACATCCATCACATCGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATCCATCACATTGGCCATTCGGC
* *
89458807 CTTATCACATATATACACATTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATCCATCACATTGGCCATTCGGC
*
89458854 CTTATCACATATATACACTTTCACATTCATCA
1 CTTATCACATATATACACTTTCACATCCATCA
89458886 ATTTCATCAT
Statistics
Matches: 118, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 118 1.00
ACGTcount: A:0.29, C:0.31, G:0.07, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATCCATCACATTGGCCATTCGGC
Found at i:89458860 original size:22 final size:22
Alignment explanation
Indices: 89458788--89458863 Score: 64
Period size: 22 Copynumber: 3.3 Consensus size: 22
89458778 CTTCACATCC
*
89458788 ATCACATCGGCCATTCGGCCTT
1 ATCACATTGGCCATTCGGCCTT
** * *
89458810 ATCACATATATACACATTC-ACATT
1 ATCACAT-T-GGC-CATTCGGCCTT
89458834 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
89458857 ATCACAT
1 ATCACAT
89458864 ATATACACTT
Statistics
Matches: 40, Mismatches: 9, Indels: 10
0.68 0.15 0.17
Matches are distributed among these distances:
22 19 0.47
23 4 0.10
24 5 0.12
25 12 0.30
ACGTcount: A:0.28, C:0.32, G:0.11, T:0.30
Consensus pattern (22 bp):
ATCACATTGGCCATTCGGCCTT
Found at i:89462358 original size:28 final size:28
Alignment explanation
Indices: 89462326--89462419 Score: 82
Period size: 28 Copynumber: 3.3 Consensus size: 28
89462316 TTCACGCACT
* *
89462326 TAGTGCCCACTGACCGATCTCGCACACA
1 TAGTGCCCAATGACAGATCTCGCACACA
* * *
89462354 TAGTGCTCAGTTGA-AGAACTCGCACACA
1 TAGTGCCCA-ATGACAGATCTCGCACACA
* * * *
89462382 CAGTGCCTCAATTACTGATTTCGCACACA
1 TAGTGCC-CAATGACAGATCTCGCACACA
89462411 TAGTGCCCA
1 TAGTGCCCA
89462420 TATTCATTCG
Statistics
Matches: 51, Mismatches: 12, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
28 29 0.57
29 22 0.43
ACGTcount: A:0.28, C:0.32, G:0.18, T:0.22
Consensus pattern (28 bp):
TAGTGCCCAATGACAGATCTCGCACACA
Found at i:89462607 original size:43 final size:43
Alignment explanation
Indices: 89462548--89462773 Score: 371
Period size: 43 Copynumber: 5.3 Consensus size: 43
89462538 CCTTGCTCGA
** * **
89462548 ATCACCGGCATTAAGCCTGCTAGGCGCGAAAACCCGAATACAT
1 ATCACCGGCACAAAGCCTGCTAGGCACGAAGGCCCGAATACAT
* * *
89462591 ATTATCGGCACAAAGCCTGCTAGGCACGAAGGCCTGAATACAT
1 ATCACCGGCACAAAGCCTGCTAGGCACGAAGGCCCGAATACAT
*
89462634 ATCATCGGCACAAAGCCTGCTAGGCACGAAGGCCCGAATACAT
1 ATCACCGGCACAAAGCCTGCTAGGCACGAAGGCCCGAATACAT
89462677 ATCACCGGCACAAAGCCTGCTAGGCACGAAGGCCCGAATACAT
1 ATCACCGGCACAAAGCCTGCTAGGCACGAAGGCCCGAATACAT
89462720 ATCACCGGCACAAAGCCTGCTAGGCACGAAGGCCCGAATACAT
1 ATCACCGGCACAAAGCCTGCTAGGCACGAAGGCCCGAATACAT
89462763 ATCACCGGCAC
1 ATCACCGGCAC
89462774 GAATGCTCTT
Statistics
Matches: 172, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
43 172 1.00
ACGTcount: A:0.32, C:0.31, G:0.23, T:0.14
Consensus pattern (43 bp):
ATCACCGGCACAAAGCCTGCTAGGCACGAAGGCCCGAATACAT
Found at i:89464782 original size:47 final size:47
Alignment explanation
Indices: 89464712--89464884 Score: 283
Period size: 47 Copynumber: 3.7 Consensus size: 47
89464702 CCCTTCGGGA
* *
89464712 CTTATCACATTTATACACTTTCACATCCATCACATTGGCCATTTGGC
1 CTTATCACATATATACACTTTCACATCCATCACATTGGCCATTCGGC
* *
89464759 CTTATCACATATATACACCTTCACATCCATCACATCGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATCCATCACATTGGCCATTCGGC
* *
89464806 CTTATCACATATATACACATTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATCCATCACATTGGCCATTCGGC
*
89464853 CTTATCACATATATACACTTTCACATTCATCA
1 CTTATCACATATATACACTTTCACATCCATCA
89464885 ATTTCATCAT
Statistics
Matches: 118, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 118 1.00
ACGTcount: A:0.29, C:0.31, G:0.07, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATCCATCACATTGGCCATTCGGC
Found at i:89464859 original size:22 final size:22
Alignment explanation
Indices: 89464787--89464862 Score: 64
Period size: 22 Copynumber: 3.3 Consensus size: 22
89464777 CTTCACATCC
*
89464787 ATCACATCGGCCATTCGGCCTT
1 ATCACATTGGCCATTCGGCCTT
** * *
89464809 ATCACATATATACACATTC-ACATT
1 ATCACAT-T-GGC-CATTCGGCCTT
89464833 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
89464856 ATCACAT
1 ATCACAT
89464863 ATATACACTT
Statistics
Matches: 40, Mismatches: 9, Indels: 10
0.68 0.15 0.17
Matches are distributed among these distances:
22 19 0.47
23 4 0.10
24 5 0.12
25 12 0.30
ACGTcount: A:0.28, C:0.32, G:0.11, T:0.30
Consensus pattern (22 bp):
ATCACATTGGCCATTCGGCCTT
Found at i:89468436 original size:40 final size:40
Alignment explanation
Indices: 89468339--89468518 Score: 168
Period size: 40 Copynumber: 4.5 Consensus size: 40
89468329 TCGAATGGTG
* *
89468339 TCCGGGCTAAGTCCCGAAGGCTTTTGTGCTA-AGTGACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTG--AGAGTTACTAAA
* *
89468380 TCCGGG-TCAACTCCCGAAGGCATTTGTGAGAGTTACCAAA
1 TCCGGGCT-AAGTCCCGAAGGCATTTGTGAGAGTTACTAAA
* * * * *
89468420 ACCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGAGAGTTACTAAA
* * * * *
89468460 TCCGGGCTAATTCCCGAAGGCAATTGTGCGAATCACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGAGAGTTACTA-AA
*
89468501 -CCGGGCTATGTCCCGAAG
1 TCCGGGCTAAGTCCCGAAG
89468519 ACAATCGAGC
Statistics
Matches: 115, Mismatches: 20, Indels: 9
0.80 0.14 0.06
Matches are distributed among these distances:
39 1 0.01
40 87 0.76
41 27 0.23
ACGTcount: A:0.26, C:0.24, G:0.26, T:0.24
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGAGAGTTACTAAA
Found at i:89468479 original size:80 final size:80
Alignment explanation
Indices: 89468340--89468532 Score: 208
Period size: 80 Copynumber: 2.4 Consensus size: 80
89468330 CGAATGGTGT
* * * *
89468340 CCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGTGACTAAATCCGGGTCAACTCCCGAAGGCATTT
1 CCGGGCTAAGTCCCGAAGGCATTCGTGC-GAGTGACTAAATCCGGGTCAACTCCCGAAGGCAATT
* *
89468405 GTGAGAGTTACCAAAA
65 GTGAGAATCACCAAAA
* * * *
89468421 CCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGG-CTAATTCCCGAAGGCAATT
1 CCGGGCTAAGTCCCGAAGGCATTCGTGCGAGTGACTAAATCCGGGTC-AACTCCCGAAGGCAATT
* * *
89468485 GTGCGAATCACTATAA
65 GTGAGAATCACCAAAA
* * * *
89468501 CCGGGCTATGTCCCGAAGACAATCGAGCGAGT
1 CCGGGCTAAGTCCCGAAGGCATTCGTGCGAGT
89468533 CGCTATATCC
Statistics
Matches: 93, Mismatches: 18, Indels: 3
0.82 0.16 0.03
Matches are distributed among these distances:
79 1 0.01
80 67 0.72
81 25 0.27
ACGTcount: A:0.27, C:0.24, G:0.26, T:0.23
Consensus pattern (80 bp):
CCGGGCTAAGTCCCGAAGGCATTCGTGCGAGTGACTAAATCCGGGTCAACTCCCGAAGGCAATTG
TGAGAATCACCAAAA
Found at i:89468539 original size:40 final size:40
Alignment explanation
Indices: 89468461--89468544 Score: 98
Period size: 40 Copynumber: 2.1 Consensus size: 40
89468451 GTTATTAAAT
* * *
89468461 CCGGGCTAATTCCCGAAGGCAATTGTGCGAATCACTATAA
1 CCGGGCTAATTCCCGAAGACAATCGAGCGAATCACTATAA
* * *
89468501 CCGGGCT-ATGTCCCGAAGACAATCGAGCGAGTCGCTATAT
1 CCGGGCTAAT-TCCCGAAGACAATCGAGCGAATCACTATAA
89468541 CCGG
1 CCGG
89468545 TTAAATTCCG
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
39 2 0.05
40 35 0.95
ACGTcount: A:0.26, C:0.27, G:0.26, T:0.20
Consensus pattern (40 bp):
CCGGGCTAATTCCCGAAGACAATCGAGCGAATCACTATAA
Found at i:89476515 original size:40 final size:40
Alignment explanation
Indices: 89476419--89476597 Score: 189
Period size: 40 Copynumber: 4.5 Consensus size: 40
89476409 CGAATGGTGT
* * * *
89476419 CCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGTGACTAAAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAAA
* *
89476460 CCGGG-TCAACTCCCGAAGGCATTTGTGCGAGTTACCAAAA
1 CCGGGCT-AAGTCCCGAAGGCATTTGTGCGAGTTACTAAAA
* * * *
89476500 CCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAA
* * * * *
89476540 CCGGGCTAATTCCCGAAGGCAATTGTGCGAATCACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAA
*
89476580 CCGGGCTATGTCCCGAAG
1 CCGGGCTAAGTCCCGAAG
89476598 ACAATCGAGC
Statistics
Matches: 114, Mismatches: 22, Indels: 5
0.81 0.16 0.04
Matches are distributed among these distances:
40 89 0.78
41 25 0.22
ACGTcount: A:0.26, C:0.25, G:0.26, T:0.23
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAA
Found at i:89476558 original size:80 final size:80
Alignment explanation
Indices: 89476419--89476611 Score: 217
Period size: 80 Copynumber: 2.4 Consensus size: 80
89476409 CGAATGGTGT
* * * *
89476419 CCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGTGACTAAATCCGGGTCAACTCCCGAAGGCATTT
1 CCGGGCTAAGTCCCGAAGGCATTCGTGC-GAGTGACTAAATCCGGGTCAACTCCCGAAGGCAATT
* *
89476484 GTGCGAGTTACCAAAA
65 GTGCGAATCACCAAAA
* * * *
89476500 CCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGG-CTAATTCCCGAAGGCAATT
1 CCGGGCTAAGTCCCGAAGGCATTCGTGCGAGTGACTAAATCCGGGTC-AACTCCCGAAGGCAATT
* *
89476564 GTGCGAATCACTATAA
65 GTGCGAATCACCAAAA
* * * *
89476580 CCGGGCTATGTCCCGAAGACAATCGAGCGAGT
1 CCGGGCTAAGTCCCGAAGGCATTCGTGCGAGT
89476612 CGCTATATCC
Statistics
Matches: 94, Mismatches: 17, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
79 1 0.01
80 68 0.72
81 25 0.27
ACGTcount: A:0.26, C:0.24, G:0.26, T:0.23
Consensus pattern (80 bp):
CCGGGCTAAGTCCCGAAGGCATTCGTGCGAGTGACTAAATCCGGGTCAACTCCCGAAGGCAATTG
TGCGAATCACCAAAA
Found at i:89476618 original size:40 final size:40
Alignment explanation
Indices: 89476540--89476623 Score: 98
Period size: 40 Copynumber: 2.1 Consensus size: 40
89476530 GTTATTAAAT
* * *
89476540 CCGGGCTAATTCCCGAAGGCAATTGTGCGAATCACTATAA
1 CCGGGCTAATTCCCGAAGACAATCGAGCGAATCACTATAA
* * *
89476580 CCGGGCT-ATGTCCCGAAGACAATCGAGCGAGTCGCTATAT
1 CCGGGCTAAT-TCCCGAAGACAATCGAGCGAATCACTATAA
89476620 CCGG
1 CCGG
89476624 TTAAATTCCG
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
39 2 0.05
40 35 0.95
ACGTcount: A:0.26, C:0.27, G:0.26, T:0.20
Consensus pattern (40 bp):
CCGGGCTAATTCCCGAAGACAATCGAGCGAATCACTATAA
Found at i:89479491 original size:39 final size:40
Alignment explanation
Indices: 89479328--89479492 Score: 151
Period size: 39 Copynumber: 4.2 Consensus size: 40
89479318 AAATTGAATG
* * * **
89479328 ATATCCGGGCTAAG-CCCGAAGACAATTATGCTG-GAAATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGC-GAGTGATT
* * * **
89479367 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGATT
* * *
89479407 ATATCCGGGCTAAG-GCCGAAGGCATTCGTGCGAGTTATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGATT
*
89479446 CTATCCGGGCTAAGACCCGAAGGCATTTGTGC-ACGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGA-GTGATT
89479486 A-ATCCGG
1 ATATCCGG
89479493 TTATATTCCG
Statistics
Matches: 101, Mismatches: 21, Indels: 8
0.78 0.16 0.06
Matches are distributed among these distances:
39 51 0.50
40 50 0.50
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.24
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGATT
Found at i:89484049 original size:40 final size:40
Alignment explanation
Indices: 89483967--89484131 Score: 144
Period size: 40 Copynumber: 4.2 Consensus size: 40
89483957 AAATTGAATG
* * ** *
89483967 ATATCCGGGCTAAG-CCCGAAGACAATTATGCTG-GAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGC-GAGTGACT
* * *
89484006 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGTGACT
* *
89484046 ATATCCGGGCT-A-ACCCGAAGGC-ATTCGTGCGAGTTATT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCGAGTGACT
* * *
89484084 CTATCCGGGCTAAGACCCGAAGGCATTTGTGC-ACGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCGA-GTGACT
89484124 ATATCCGG
1 ATATCCGG
89484132 TTATATTCCG
Statistics
Matches: 102, Mismatches: 17, Indels: 13
0.77 0.13 0.10
Matches are distributed among these distances:
37 3 0.03
38 28 0.27
39 16 0.16
40 53 0.52
41 2 0.02
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGTGACT
Found at i:89491989 original size:40 final size:40
Alignment explanation
Indices: 89491923--89492089 Score: 169
Period size: 40 Copynumber: 4.2 Consensus size: 40
89491913 AAATTGAATG
* * *
89491923 ATATCCGGGCTAAG-CCCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* * ***
89491962 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
*
89492002 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGC-GAGTTATT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTG-GTAATT
* * ** *
89492042 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCACGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
89492082 ATATCCGG
1 ATATCCGG
89492090 TTATATTCCG
Statistics
Matches: 105, Mismatches: 18, Indels: 9
0.80 0.14 0.07
Matches are distributed among these distances:
39 16 0.15
40 87 0.83
41 2 0.02
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
Found at i:89497825 original size:45 final size:45
Alignment explanation
Indices: 89497761--89497930 Score: 199
Period size: 45 Copynumber: 3.8 Consensus size: 45
89497751 TATCGTACGG
* * *
89497761 TACTATTCAGG-CCTTTGAGCCTAGCAGGCTATGATGCCAGTGAGA
1 TACTATTC-GGACCTTCGAGCCTAGCAGGCTATAATGCCGGTGAGA
* *
89497806 TACTATTCGGACTTTTGAGCCTAGCAGGCTATAATGCCGGTGAGA
1 TACTATTCGGACCTTCGAGCCTAGCAGGCTATAATGCCGGTGAGA
*
89497851 TACTATTC-GAGCCTTCGAGCCTAGCAGGCTATAATGCCGGTGAAA
1 TACTATTCGGA-CCTTCGAGCCTAGCAGGCTATAATGCCGGTGAGA
* *
89497896 TGA-TATT-GG-GCTTCGAGCCTAGCAGGC-AAAATGCC
1 T-ACTATTCGGACCTTCGAGCCTAGCAGGCTATAATGCC
89497931 AGTGGATGAA
Statistics
Matches: 113, Mismatches: 8, Indels: 11
0.86 0.06 0.08
Matches are distributed among these distances:
42 7 0.06
43 17 0.15
44 4 0.04
45 84 0.74
46 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.26, T:0.26
Consensus pattern (45 bp):
TACTATTCGGACCTTCGAGCCTAGCAGGCTATAATGCCGGTGAGA
Found at i:89512717 original size:93 final size:93
Alignment explanation
Indices: 89512605--89512776 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
89512595 CGCCCATAAG
* *
89512605 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
89512670 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
*
89512698 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
89512763 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
89512777 TCAACCATCC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:89512773 original size:46 final size:46
Alignment explanation
Indices: 89512598--89512773 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
89512588 TGTAACCCGC
* * *
89512598 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* *
89512644 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
*
89512694 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
89512737 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
89512774 TGCTCAACCA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 63 0.57
47 29 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.20
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:89524978 original size:41 final size:43
Alignment explanation
Indices: 89524876--89525012 Score: 154
Period size: 43 Copynumber: 3.2 Consensus size: 43
89524866 TGTGTTCTCA
* *
89524876 TGTAAGACCATGTTTGGGACGTTGGCATCGATATGTGGTTACG
1 TGTAAGACCATGTTTGGGACATTGGCATCGATATGTGATTACG
* * * *
89524919 AGTAAGACCATGTCTGGGACATTAGCATCG-TATTTGATT-CG
1 TGTAAGACCATGTTTGGGACATTGGCATCGATATGTGATTACG
* * * *
89524960 TGTAAGACCCTGTTTGGGACAGTGGCATCGATATGAGA-TAGCA
1 TGTAAGACCATGTTTGGGACATTGGCATCGATATGTGATTA-CG
89525003 TGTAAGACCA
1 TGTAAGACCA
89525013 CATCTAGGAT
Statistics
Matches: 76, Mismatches: 15, Indels: 6
0.78 0.15 0.06
Matches are distributed among these distances:
41 28 0.37
42 12 0.16
43 36 0.47
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.29
Consensus pattern (43 bp):
TGTAAGACCATGTTTGGGACATTGGCATCGATATGTGATTACG
Found at i:89527526 original size:15 final size:15
Alignment explanation
Indices: 89527506--89527535 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
89527496 TTATCTTTTG
89527506 TTAACTTGATTAATA
1 TTAACTTGATTAATA
*
89527521 TTAACTTGTTTAATA
1 TTAACTTGATTAATA
89527536 CTGGGATAAA
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:0.37, C:0.07, G:0.07, T:0.50
Consensus pattern (15 bp):
TTAACTTGATTAATA
Found at i:89528352 original size:16 final size:16
Alignment explanation
Indices: 89528327--89528357 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
89528317 TAGTGTGTCA
*
89528327 ATTTTTAATTATTTTT
1 ATTTTAAATTATTTTT
89528343 ATTTTAAATTATTTT
1 ATTTTAAATTATTTT
89528358 GTTATTAATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
ATTTTAAATTATTTTT
Found at i:89528981 original size:12 final size:12
Alignment explanation
Indices: 89528964--89529005 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
89528954 TTAACATAGC
89528964 AGTAGATGTAGA
1 AGTAGATGTAGA
*
89528976 AGTAGACGTAGA
1 AGTAGATGTAGA
**
89528988 AACAGATGTAGA
1 AGTAGATGTAGA
89529000 AGTAGA
1 AGTAGA
89529006 ATTGACCAAT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.45, C:0.05, G:0.31, T:0.19
Consensus pattern (12 bp):
AGTAGATGTAGA
Found at i:89531327 original size:22 final size:22
Alignment explanation
Indices: 89531298--89531381 Score: 116
Period size: 22 Copynumber: 3.9 Consensus size: 22
89531288 CTTGGCACAG
89531298 GGGC-ACACGCCCGTGTGAGAA
1 GGGCAACACGCCCGTGTGAGAA
* *
89531319 GGGCAACACTCCTGTGTGAGAA
1 GGGCAACACGCCCGTGTGAGAA
*
89531341 GGGCAACACGCCCGTGTGGGAA
1 GGGCAACACGCCCGTGTGAGAA
* *
89531363 TGGCAACATGCCCGTGTGA
1 GGGCAACACGCCCGTGTGA
89531382 CCAATCAACA
Statistics
Matches: 54, Mismatches: 8, Indels: 1
0.86 0.13 0.02
Matches are distributed among these distances:
21 4 0.07
22 50 0.93
ACGTcount: A:0.24, C:0.26, G:0.36, T:0.14
Consensus pattern (22 bp):
GGGCAACACGCCCGTGTGAGAA
Found at i:89532681 original size:46 final size:45
Alignment explanation
Indices: 89532534--89532751 Score: 194
Period size: 46 Copynumber: 4.7 Consensus size: 45
89532524 AAGGCAAGGT
* *
89532534 GCCGATGCCATGTCCCAGACACTGTCTTACACTAGCACTCGTCTTG-T-
1 GCCGATG-CATGTCCCAGACA-TGTCTTACACT-G-GCTCGTCTCGATG
* * * *
89532581 GTCGATGCCATGTCCCAGACATGGTCTTACACTGACTATCATCTC-ATA
1 GCCGATG-CATGTCCCAGACAT-GTCTTACACTGGC--TCGTCTCGATG
*
89532629 GTCGATGCATGTCCCAGACATGTCTTACACTGGCTTACGTCTCGA-G
1 GCCGATGCATGTCCCAGACATGTCTTACACTGGC-T-CGTCTCGATG
* **
89532675 GCCGATGCATGTCCCGGACATGTCTTACACTGGCTC-TCATAATATG
1 GCCGATGCATGTCCCAGACATGTCTTACACTGGCTCGTC-T-CGATG
*
89532721 GCTGATGCATGTCCCAGACATGTCTTACACT
1 GCCGATGCATGTCCCAGACATGTCTTACACT
89532752 AACCCTCAAT
Statistics
Matches: 148, Mismatches: 13, Indels: 21
0.81 0.07 0.12
Matches are distributed among these distances:
43 2 0.01
44 2 0.01
45 5 0.03
46 81 0.55
47 51 0.34
48 7 0.05
ACGTcount: A:0.22, C:0.30, G:0.20, T:0.28
Consensus pattern (45 bp):
GCCGATGCATGTCCCAGACATGTCTTACACTGGCTCGTCTCGATG
Found at i:89532742 original size:92 final size:93
Alignment explanation
Indices: 89532536--89532752 Score: 255
Period size: 92 Copynumber: 2.3 Consensus size: 93
89532526 GGCAAGGTGC
* * *
89532536 CGATGCCATGTCCCAGACACTGTCTTACACTAGCACTCGTCTTGTGTCGATGCCATGTCCCAGAC
1 CGATG-CATGTCCCAGACA-TGTCTTACACTAGCACTCGTCTCGGGCCGATGCCATGTCCCAGAC
*
89532601 ATGGTCTTACACTGACTATCATCTCATAGT
64 ATGGTCTTACACTGACTATCATATCATAGT
* * *
89532631 CGATGCATGTCCCAGACATGTCTTACACTGGC-TTACGTCTCGAGGCCGATG-CATGTCCCGGAC
1 CGATGCATGTCCCAGACATGTCTTACACTAGCACT-CGTCTCG-GGCCGATGCCATGTCCCAGAC
* * *
89532694 AT-GTCTTACACTGGCTCTCATA--ATATGG
64 ATGGTCTTACACTGACTATCATATCATA-GT
89532722 CTGATGCATGTCCCAGACATGTCTTACACTA
1 C-GATGCATGTCCCAGACATGTCTTACACTA
89532753 ACCCTCAATA
Statistics
Matches: 107, Mismatches: 11, Indels: 11
0.83 0.09 0.09
Matches are distributed among these distances:
90 3 0.03
91 2 0.02
92 46 0.43
93 32 0.30
94 19 0.18
95 5 0.05
ACGTcount: A:0.22, C:0.29, G:0.20, T:0.29
Consensus pattern (93 bp):
CGATGCATGTCCCAGACATGTCTTACACTAGCACTCGTCTCGGGCCGATGCCATGTCCCAGACAT
GGTCTTACACTGACTATCATATCATAGT
Found at i:89536060 original size:101 final size:101
Alignment explanation
Indices: 89535880--89536074 Score: 230
Period size: 101 Copynumber: 1.9 Consensus size: 101
89535870 GTTGTAAGAG
* * * * *
89535880 TTAAGATTCGCACCTCGAACCACATGAGCCCCACTAGTTCTGCGAGTGTAAAGGCCGTCACACCA
1 TTAAGATCCGCACCTCGAACCACATAAGACCCACTAGTTCTGCGAGTGCAAAGGCCGCCACACCA
89535945 AACATGGGTCGAGGGAA-CGACCCAATGATTAAGGAT
66 AACATGGGTCGAGGGAAGC-ACCCAATGATTAAGGAT
* * * * * * * *
89535981 TTAAGATCCGCAGCTCGAGCCACATAAGATCCACTAGTTTTGTGGGTGCGAAGGCCGCCACACTA
1 TTAAGATCCGCACCTCGAACCACATAAGACCCACTAGTTCTGCGAGTGCAAAGGCCGCCACACCA
* * *
89536046 GACATGGTTTGAGGGAAGCACCCAATGAT
66 AACATGGGTCGAGGGAAGCACCCAATGAT
89536075 CGAATAGAGT
Statistics
Matches: 77, Mismatches: 16, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
101 76 0.99
102 1 0.01
ACGTcount: A:0.29, C:0.26, G:0.25, T:0.20
Consensus pattern (101 bp):
TTAAGATCCGCACCTCGAACCACATAAGACCCACTAGTTCTGCGAGTGCAAAGGCCGCCACACCA
AACATGGGTCGAGGGAAGCACCCAATGATTAAGGAT
Found at i:89539145 original size:39 final size:39
Alignment explanation
Indices: 89539102--89539378 Score: 339
Period size: 39 Copynumber: 7.2 Consensus size: 39
89539092 TGTTTTTGAG
*
89539102 TATTGCGATATATGCTTAAATGTTATGTGATTATATGTA
1 TATTGTGATATATGCTTAAATGTTATGTGATTATATGTA
*
89539141 TATTGTGATATATGCTTAAATGTTTTGTGATTATATG-A
1 TATTGTGATATATGCTTAAATGTTATGTGATTATATGTA
*
89539179 GTATTGTGATATATGCTTAAATGTTATGTAATTATATGTA
1 -TATTGTGATATATGCTTAAATGTTATGTGATTATATGTA
* * **
89539219 TATTGTGATATATGCTTGAATGTTATATGATTATA-CAA
1 TATTGTGATATATGCTTAAATGTTATGTGATTATATGTA
* * * *
89539257 GTATTATGATTTATGTTTAAATATTATGTGATTATATGTA
1 -TATTGTGATATATGCTTAAATGTTATGTGATTATATGTA
* * **
89539297 TATTATGATATATGTTTAAATGTTATGTGATTATA-CAA
1 TATTGTGATATATGCTTAAATGTTATGTGATTATATGTA
* *
89539335 GTATTGTGATATATGTTTAAATATTATGTGA-T-TATGTA
1 -TATTGTGATATATGCTTAAATGTTATGTGATTATATGTA
89539373 TATTGT
1 TATTGT
89539379 AACAACCCAA
Statistics
Matches: 207, Mismatches: 25, Indels: 14
0.84 0.10 0.06
Matches are distributed among these distances:
37 8 0.04
38 5 0.02
39 192 0.93
40 2 0.01
ACGTcount: A:0.32, C:0.03, G:0.17, T:0.49
Consensus pattern (39 bp):
TATTGTGATATATGCTTAAATGTTATGTGATTATATGTA
Found at i:89539227 original size:78 final size:78
Alignment explanation
Indices: 89539100--89539378 Score: 409
Period size: 78 Copynumber: 3.6 Consensus size: 78
89539090 AATGTTTTTG
* *
89539100 AGTATTGCGATATATGCTTAAATGTTATGTGATTATATGTATATTGTGATATATGCTTAAATGTT
1 AGTATTGTGATATATGCTTAAATATTATGTGATTATATGTATATTGTGATATATGCTTAAATGTT
* **
89539165 TTGTGATTATATG
66 ATGTGATTATACA
* * *
89539178 AGTATTGTGATATATGCTTAAATGTTATGTAATTATATGTATATTGTGATATATGCTTGAATGTT
1 AGTATTGTGATATATGCTTAAATATTATGTGATTATATGTATATTGTGATATATGCTTAAATGTT
*
89539243 ATATGATTATACA
66 ATGTGATTATACA
* * * * *
89539256 AGTATTATGATTTATGTTTAAATATTATGTGATTATATGTATATTATGATATATGTTTAAATGTT
1 AGTATTGTGATATATGCTTAAATATTATGTGATTATATGTATATTGTGATATATGCTTAAATGTT
89539321 ATGTGATTATACA
66 ATGTGATTATACA
*
89539334 AGTATTGTGATATATGTTTAAATATTATGTGA-T-TATGTATATTGT
1 AGTATTGTGATATATGCTTAAATATTATGTGATTATATGTATATTGT
89539379 AACAACCCAA
Statistics
Matches: 182, Mismatches: 19, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
76 11 0.06
77 1 0.01
78 170 0.93
ACGTcount: A:0.32, C:0.03, G:0.17, T:0.48
Consensus pattern (78 bp):
AGTATTGTGATATATGCTTAAATATTATGTGATTATATGTATATTGTGATATATGCTTAAATGTT
ATGTGATTATACA
Found at i:89550361 original size:16 final size:16
Alignment explanation
Indices: 89550337--89550392 Score: 76
Period size: 16 Copynumber: 3.5 Consensus size: 16
89550327 TTATTTTTGG
89550337 ATATAAATAGTAAATA
1 ATATAAATAGTAAATA
*
89550353 ATATTAATAGTAAATA
1 ATATAAATAGTAAATA
* *
89550369 ACATGAATAGTAAATA
1 ATATAAATAGTAAATA
*
89550385 ACATAAAT
1 ATATAAAT
89550393 TATCTAAAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 36 1.00
ACGTcount: A:0.59, C:0.04, G:0.07, T:0.30
Consensus pattern (16 bp):
ATATAAATAGTAAATA
Found at i:89550527 original size:39 final size:39
Alignment explanation
Indices: 89550473--89550726 Score: 395
Period size: 39 Copynumber: 6.5 Consensus size: 39
89550463 GTGTTACATA
89550473 TATTGTGATATATGCTTAAATGTTATGTGATTATATGAG
1 TATTGTGATATATGCTTAAATGTTATGTGATTATATGAG
* *
89550512 TATTGTGACATATGCTTAAATGTTATATGATTATATGTA-
1 TATTGTGATATATGCTTAAATGTTATGTGATTATATG-AG
89550551 TATTGTGATATATGCTTAAATGTTATGTGATTATATGAG
1 TATTGTGATATATGCTTAAATGTTATGTGATTATATGAG
*
89550590 TATTGTGACATATGCTTAAATGTTATGTGATTATATGTA-
1 TATTGTGATATATGCTTAAATGTTATGTGATTATATG-AG
*
89550629 TATTGTGATATATGCATAAATGTTATGTGATTATATGAG
1 TATTGTGATATATGCTTAAATGTTATGTGATTATATGAG
* * *
89550668 TATTGTGATATATGCTTGAATGTTAGGTGATTATATGTG
1 TATTGTGATATATGCTTAAATGTTATGTGATTATATGAG
* *
89550707 TAATATGATATATGCTTAAA
1 TATTGTGATATATGCTTAAA
89550727 AATGAGTATG
Statistics
Matches: 197, Mismatches: 14, Indels: 8
0.90 0.06 0.04
Matches are distributed among these distances:
38 2 0.01
39 193 0.98
40 2 0.01
ACGTcount: A:0.32, C:0.04, G:0.19, T:0.45
Consensus pattern (39 bp):
TATTGTGATATATGCTTAAATGTTATGTGATTATATGAG
Found at i:89550563 original size:24 final size:23
Alignment explanation
Indices: 89550554--89550666 Score: 60
Period size: 23 Copynumber: 5.6 Consensus size: 23
89550544 ATATGTATAT
*
89550554 TGTGA-TATATGCTTAAATGTTA
1 TGTGATTATATGATTAAATGTTA
*
89550576 TGTGATTATATGAGT--A---T-
1 TGTGATTATATGATTAAATGTTA
* *
89550593 TGTGA-CATATGCTTAAATGTTA
1 TGTGATTATATGATTAAATGTTA
*
89550615 TGTGATTATATG--T--AT-AT-
1 TGTGATTATATGATTAAATGTTA
89550632 TGTGA-TATATGCA-TAAATGTTA
1 TGTGATTATATG-ATTAAATGTTA
89550654 TGTGATTATATGA
1 TGTGATTATATGA
89550667 GTATTGTGAT
Statistics
Matches: 68, Mismatches: 8, Indels: 30
0.64 0.08 0.28
Matches are distributed among these distances:
16 12 0.18
17 10 0.15
18 4 0.06
19 2 0.03
20 2 0.03
21 4 0.06
22 16 0.24
23 18 0.26
ACGTcount: A:0.32, C:0.04, G:0.19, T:0.45
Consensus pattern (23 bp):
TGTGATTATATGATTAAATGTTA
Found at i:89550600 original size:78 final size:78
Alignment explanation
Indices: 89550471--89550726 Score: 440
Period size: 78 Copynumber: 3.3 Consensus size: 78
89550461 GGGTGTTACA
89550471 TATATTGTGATATATGCTTAAATGTTATGTGATTATATGAGTATTGTGACATATGCTTAAATGTT
1 TATATTGTGATATATGCTTAAATGTTATGTGATTATATGAGTATTGTGACATATGCTTAAATGTT
*
89550536 ATATGATTATATG
66 ATGTGATTATATG
89550549 TATATTGTGATATATGCTTAAATGTTATGTGATTATATGAGTATTGTGACATATGCTTAAATGTT
1 TATATTGTGATATATGCTTAAATGTTATGTGATTATATGAGTATTGTGACATATGCTTAAATGTT
89550614 ATGTGATTATATG
66 ATGTGATTATATG
* * *
89550627 TATATTGTGATATATGCATAAATGTTATGTGATTATATGAGTATTGTGATATATGCTTGAATGTT
1 TATATTGTGATATATGCTTAAATGTTATGTGATTATATGAGTATTGTGACATATGCTTAAATGTT
*
89550692 AGGTGATTATATG
66 ATGTGATTATATG
* * *
89550705 TGTAATATGATATATGCTTAAA
1 TATATTGTGATATATGCTTAAA
89550727 AATGAGTATG
Statistics
Matches: 169, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
78 169 1.00
ACGTcount: A:0.32, C:0.04, G:0.19, T:0.45
Consensus pattern (78 bp):
TATATTGTGATATATGCTTAAATGTTATGTGATTATATGAGTATTGTGACATATGCTTAAATGTT
ATGTGATTATATG
Found at i:89552419 original size:46 final size:46
Alignment explanation
Indices: 89552369--89552541 Score: 183
Period size: 46 Copynumber: 3.7 Consensus size: 46
89552359 TGGTTGAGCA
89552369 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * *
89552415 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--AATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
* *
89552460 CATCCGAACTGGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * *
89552508 CCCGAGCTCATTGAGTTGAGTCTGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
89552542 GGGGCGGGTT
Statistics
Matches: 103, Mismatches: 15, Indels: 18
0.76 0.11 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
45 3 0.03
46 58 0.56
47 28 0.27
48 3 0.03
50 3 0.03
51 2 0.02
ACGTcount: A:0.23, C:0.20, G:0.28, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:89552525 original size:93 final size:93
Alignment explanation
Indices: 89552366--89552536 Score: 288
Period size: 93 Copynumber: 1.8 Consensus size: 93
89552356 GGATGGTTGA
* * *
89552366 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCATTGAGT
89552431 TGAGTCCGAGTTCGTGAAATGTAACTAG
66 TGAGTCCGAGTTCGTGAAATGTAACTAG
* *
89552459 GCATCCGAACTGGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCATTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCATTGAGT
*
89552524 TGAGTCTGAGTTC
66 TGAGTCCGAGTTC
89552537 ACTTAGGGGC
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:0.20, G:0.29, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCATTGAGT
TGAGTCCGAGTTCGTGAAATGTAACTAG
Found at i:89556684 original size:20 final size:20
Alignment explanation
Indices: 89556631--89556687 Score: 66
Period size: 20 Copynumber: 3.0 Consensus size: 20
89556621 AAAATTTTAC
89556631 AAACAA-AAATAT-AATATT
1 AAACAATAAATATAAATATT
* *
89556649 AAACATTAAATCTAAATATT
1 AAACAATAAATATAAATATT
89556669 AAA-AATAACATATAAATAT
1 AAACAATAA-ATATAAATAT
89556688 ATAATATAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
18 5 0.16
19 9 0.28
20 18 0.56
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.30
Consensus pattern (20 bp):
AAACAATAAATATAAATATT
Found at i:89556930 original size:153 final size:151
Alignment explanation
Indices: 89556625--89556933 Score: 365
Period size: 153 Copynumber: 2.0 Consensus size: 151
89556615 ACAAACAAAA
** * *
89556625 TTTTACAAACAAAAATATAATATTAAACATTAAATCTAAATATTAAAAATAACATATAAATATAT
1 TTTTACAAACAAAAATATAATATTAAACATTAAATCTAAATAACAAAAATAAAATATAAAAATAT
* * *
89556690 AATATAAAAAAAATATTACAAACTAAAAAAAAACATACCTTAAAACTATTATGATTTATCCCTAA
66 AATATAAAAAAAATATTACAAAC--AAAAAAAACATACCTTAAAACTATCATAAATTATCCCTAA
89556755 AAACTCCAAAAACAAACAATTTT
129 AAACTCCAAAAACAAACAATTTT
* *
89556778 TTTTACAAACAAAAATATAATCTTAAATATTAAATCTAAACATCAACAATAAATTAAAATATAAA
1 TTTTACAAACAAAAATATAATATTAAACATTAAATCT-AA-AT-AACAA-AAA-TAAAATATAAA
** * * * *
89556843 AATATAATATACAAATTATTATTACAAAC-AATAAAACATACCTTAAAACTATCATAAATTCTCT
61 AATATAATATA-AAAAAAATATTACAAACAAAAAAAACATACCTTAAAACTATCATAAATTATCC
* *
89556907 CT-AGAACTCC-AACACAAAC-ATTTT
125 CTAAAAACTCCAAAAACAAACAATTTT
89556931 TTT
1 TTT
89556934 CTCCCACAAC
Statistics
Matches: 133, Mismatches: 17, Indels: 12
0.82 0.10 0.07
Matches are distributed among these distances:
153 43 0.32
154 10 0.08
155 9 0.07
156 34 0.26
157 3 0.02
158 20 0.15
159 14 0.11
ACGTcount: A:0.55, C:0.14, G:0.01, T:0.31
Consensus pattern (151 bp):
TTTTACAAACAAAAATATAATATTAAACATTAAATCTAAATAACAAAAATAAAATATAAAAATAT
AATATAAAAAAAATATTACAAACAAAAAAAACATACCTTAAAACTATCATAAATTATCCCTAAAA
ACTCCAAAAACAAACAATTTT
Found at i:89557543 original size:30 final size:29
Alignment explanation
Indices: 89557500--89557556 Score: 69
Period size: 30 Copynumber: 1.9 Consensus size: 29
89557490 AAATAACCTA
*
89557500 TTTTTGTAATTAATCTAAATTTTATAAATT
1 TTTTTGTAATTAATAT-AATTTTATAAATT
** *
89557530 TTTTTGTTTTTAATATTATTTTATAAA
1 TTTTTGTAATTAATATAATTTTATAAA
89557557 ATAAACGGAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
29 10 0.43
30 13 0.57
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.61
Consensus pattern (29 bp):
TTTTTGTAATTAATATAATTTTATAAATT
Found at i:89558176 original size:3 final size:3
Alignment explanation
Indices: 89558170--89558206 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
89558160 ATCATCGTTG
89558170 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
89558207 CTGTCTTCTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:89566463 original size:54 final size:52
Alignment explanation
Indices: 89566371--89566473 Score: 129
Period size: 54 Copynumber: 1.9 Consensus size: 52
89566361 TTAGAAACAA
* *
89566371 CAAAACTTAATTAATTTAACTATATTTAATAATAATT-AAAATTTTAAAATT
1 CAAAACTTAATGAATTTAACTACATTTAATAATAATTAAAAATTTTAAAATT
*
89566422 CAAAACTTAATGAATTTAATAACTACATTTAATCAA-GATTAAAAATTTTAAA
1 CAAAACTTAATGAA-TT--TAACTACATTTAAT-AATAATTAAAAATTTTAAA
89566474 TTAAAAATCA
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
51 13 0.30
52 2 0.05
54 16 0.36
55 13 0.30
ACGTcount: A:0.51, C:0.08, G:0.02, T:0.39
Consensus pattern (52 bp):
CAAAACTTAATGAATTTAACTACATTTAATAATAATTAAAAATTTTAAAATT
Found at i:89566493 original size:16 final size:14
Alignment explanation
Indices: 89566459--89566514 Score: 60
Period size: 14 Copynumber: 3.9 Consensus size: 14
89566449 TTTAATCAAG
* *
89566459 ATTAAAAATTTTAA
1 ATTAAAAATATAAA
89566473 ATTAAAAATCATAATA
1 ATTAAAAAT-ATAA-A
*
89566489 ATTAAAAATATCAA
1 ATTAAAAATATAAA
89566503 ATT-AAAATATAA
1 ATTAAAAATATAA
89566515 TGTTTATCTC
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
13 8 0.22
14 13 0.36
15 5 0.14
16 10 0.28
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.34
Consensus pattern (14 bp):
ATTAAAAATATAAA
Found at i:89566694 original size:5 final size:5
Alignment explanation
Indices: 89566680--89566713 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
89566670 ATAAACTTCC
* *
89566680 AAAAT TAAAT AAAAT AGAAT AAAAT AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
89566714 ACTATCTCAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (5 bp):
AAAAT
Found at i:89571721 original size:20 final size:21
Alignment explanation
Indices: 89571682--89571722 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
89571672 ACTTGTATAA
* *
89571682 CTATCATCAAACATTCAAAAT
1 CTATCATCAAAAAATCAAAAT
89571703 CTATCAT-AAAAAATCAAAAT
1 CTATCATCAAAAAATCAAAAT
89571723 AATCATGTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.54, C:0.20, G:0.00, T:0.27
Consensus pattern (21 bp):
CTATCATCAAAAAATCAAAAT
Found at i:89578110 original size:30 final size:30
Alignment explanation
Indices: 89578076--89578136 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
89578066 TTTCCGAGCC
* *
89578076 TAGGGGCAAAATCATAATTTTGCAAAGGTT
1 TAGGGGCAAAATCATAATTTTGAAAAAGTT
**
89578106 TAGGGGCAAAATTGTAATTTTGAAAAAGTT
1 TAGGGGCAAAATCATAATTTTGAAAAAGTT
89578136 T
1 T
89578137 GAGTTAGGGA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.38, C:0.07, G:0.23, T:0.33
Consensus pattern (30 bp):
TAGGGGCAAAATCATAATTTTGAAAAAGTT
Found at i:89578768 original size:47 final size:46
Alignment explanation
Indices: 89578650--89578982 Score: 222
Period size: 54 Copynumber: 6.8 Consensus size: 46
89578640 ATTGACGGTT
* *
89578650 AAGGATACCATGTAAGACCATGTCAAGACATGGCATTGGTA-AGGC
1 AAGGATACCATGTAAGACCATGTCAAGACATGGCATTGGCATAGAC
* * * *
89578695 AAGGATCCCGTGTAAGACCATGTCAAGACATGGCATCGGCATTGAC
1 AAGGATACCATGTAAGACCATGTCAAGACATGGCATTGGCATAGAC
** **
89578741 TAAGGACT-CCATGTAAGACCACATCAAGATGTGGCATTGGCACTAAGAC
1 -AAGGA-TACCATGTAAGACCATGTCAAGACATGGCATTGGCA-T-AGAC
*** * *
89578790 AAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGGTA-AGAT
1 AAGGATACCATGTAAGACCATGTCAAG-ACATGGCA-TTGGCATAGAC
* * *
89578837 AAGGATATCATGTAAGACCATGTCAAGGCATGGCATTGATAAGTTCTATAAGGC
1 AAGGATACCATGTAAGACCATGTCAAGACATGGCATTG----G--C-AT-AGAC
* * * * *
89578891 AAGGAAATCATGTAAGACCATGCCAAGGCATGGCATTGATAAGTTCTATAAGGC
1 AAGGATACCATGTAAGACCATGTCAAGACATGGCATTG----G--C-AT-AGAC
* *
89578945 AAGGAAATCATGTAAGACCATGTCAAGACATGGCATTG
1 AAGGATACCATGTAAGACCATGTCAAGACATGGCATTG
89578983 ATAAGTTAAT
Statistics
Matches: 237, Mismatches: 34, Indels: 25
0.80 0.11 0.08
Matches are distributed among these distances:
45 40 0.17
46 9 0.04
47 60 0.25
48 22 0.09
49 10 0.04
50 5 0.02
52 1 0.00
54 90 0.38
ACGTcount: A:0.35, C:0.18, G:0.25, T:0.23
Consensus pattern (46 bp):
AAGGATACCATGTAAGACCATGTCAAGACATGGCATTGGCATAGAC
Found at i:89578863 original size:95 final size:92
Alignment explanation
Indices: 89578649--89578879 Score: 243
Period size: 95 Copynumber: 2.5 Consensus size: 92
89578639 AATTGACGGT
* * *
89578649 TAAGGATACCATGTAAGACCATGTCAAGACATGGCATTGGTAAGGCAAGGATCCCGTGTAAGACC
1 TAAGGATACCATGTAAGACCATGTCAAGACATGGCATTGGTAAGACAAGGATACCATGTAAGACC
*
89578714 ATGTCAAGACATGGCATCGGCATTGAC
66 ATGTCAAGACATGGCATCGGCATAGAC
** **
89578741 TAAGGACT-CCATGTAAGACCACATCAAGATGTGGCATTGGCACTAAGACAAGGATACCATGTAA
1 TAAGGA-TACCATGTAAGACCATGTCAAGACATGGCATTGG---TAAGACAAGGATACCATGTAA
*** * *
89578805 GACCATGTTTGGAACATGGCATTTGGTA-AGA-
62 GACCATGTCAAG-ACATGGCA-TCGGCATAGAC
* * *
89578836 TAAGGATATCATGTAAGACCATGTCAAGGCATGGCATTGATAAG
1 TAAGGATACCATGTAAGACCATGTCAAGACATGGCATTGGTAAG
89578880 TTCTATAAGG
Statistics
Matches: 112, Mismatches: 20, Indels: 14
0.77 0.14 0.10
Matches are distributed among these distances:
92 38 0.34
93 1 0.01
94 1 0.01
95 58 0.52
96 10 0.09
97 4 0.04
ACGTcount: A:0.34, C:0.18, G:0.25, T:0.23
Consensus pattern (92 bp):
TAAGGATACCATGTAAGACCATGTCAAGACATGGCATTGGTAAGACAAGGATACCATGTAAGACC
ATGTCAAGACATGGCATCGGCATAGAC
Found at i:89578889 original size:25 final size:25
Alignment explanation
Indices: 89578861--89578945 Score: 66
Period size: 25 Copynumber: 3.2 Consensus size: 25
89578851 AGACCATGTC
89578861 AAGGCATGGCATTGATAAGTTCTAT
1 AAGGCATGGCATTGATAAGTTCTAT
* * * *
89578886 AAGGCAAGGAAATCATG-TAAG-ACCAT
1 AAGGCATGG-CAT--TGATAAGTTCTAT
89578912 GCCAAGGCATGGCATTGATAAGTTCTAT
1 ---AAGGCATGGCATTGATAAGTTCTAT
89578940 AAGGCA
1 AAGGCA
89578946 AGGAAATCAT
Statistics
Matches: 44, Mismatches: 8, Indels: 16
0.65 0.12 0.24
Matches are distributed among these distances:
25 14 0.32
26 7 0.16
27 8 0.18
28 7 0.16
29 8 0.18
ACGTcount: A:0.36, C:0.15, G:0.25, T:0.24
Consensus pattern (25 bp):
AAGGCATGGCATTGATAAGTTCTAT
Found at i:89578901 original size:54 final size:54
Alignment explanation
Indices: 89578837--89579098 Score: 366
Period size: 54 Copynumber: 4.9 Consensus size: 54
89578827 TTGGTAAGAT
89578837 AAGGATATCATGTAAGACCATGTCAAGGCATGGCATTGATAAGTTCTATAAGGC
1 AAGGATATCATGTAAGACCATGTCAAGGCATGGCATTGATAAGTTCTATAAGGC
* *
89578891 AAGGAAATCATGTAAGACCATGCCAAGGCATGGCATTGATAAGTTCTATAAGGC
1 AAGGATATCATGTAAGACCATGTCAAGGCATGGCATTGATAAGTTCTATAAGGC
* * *
89578945 AAGGAAATCATGTAAGACCATGTCAAGACATGGCATTGATAAGTTAATATAAGGC
1 AAGGATATCATGTAAGACCATGTCAAGGCATGGCATTGATAAGTT-CTATAAGGC
** * *
89579000 AAAGG-TCCCATGTAAGACCATGCCAAGGCATGGCATTGGTAAGTT-TATAAGGC
1 -AAGGATATCATGTAAGACCATGTCAAGGCATGGCATTGATAAGTTCTATAAGGC
* * * * *
89579053 AAGGATACCACGTAAGACCATGTCAAGACATGGCAATGGTAAGTTC
1 AAGGATATCATGTAAGACCATGTCAAGGCATGGCATTGATAAGTTC
89579099 AAAAAGGAAA
Statistics
Matches: 188, Mismatches: 16, Indels: 8
0.89 0.08 0.04
Matches are distributed among these distances:
52 4 0.02
53 43 0.23
54 95 0.51
55 42 0.22
56 4 0.02
ACGTcount: A:0.37, C:0.16, G:0.24, T:0.23
Consensus pattern (54 bp):
AAGGATATCATGTAAGACCATGTCAAGGCATGGCATTGATAAGTTCTATAAGGC
Found at i:89590484 original size:25 final size:21
Alignment explanation
Indices: 89590438--89590477 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
89590428 AAAGCCTCTG
89590438 GGGTTTAAGAGAAAACTAAAT
1 GGGTTTAAGAGAAAACTAAAT
89590459 GGGTTTAAGAGAAAACTAA
1 GGGTTTAAGAGAAAACTAA
89590478 CCCAATGCAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.47, C:0.05, G:0.25, T:0.23
Consensus pattern (21 bp):
GGGTTTAAGAGAAAACTAAAT
Found at i:89597376 original size:232 final size:232
Alignment explanation
Indices: 89596970--89597437 Score: 767
Period size: 232 Copynumber: 2.0 Consensus size: 232
89596960 AAATTTTATT
* * * * *
89596970 AGACCATCATCAGAAAAAAGTTTGGGATTGAATCTCCCGTATTTTTTAAACGTATTCAAGGTGGT
1 AGACCATCATCAGAAAAAAGTTTGGGATTGAATCTCCCGCAATTTTGAAACATATTCAAGGTGAT
* *
89597035 ATATGTGAAGTCATTCATCCACCATGTGGACCATTCAAAAATTTTATGGGTTTGATAGATACATC
66 ATATGTGAAATCATTCATCCACCATGTGGACCATTCAAAAATGTTATGGGTTTGATAGATACATC
* *
89597100 TACTATGTGGTCATATGTGTGTTTATTATTAACTCACAATCTGGCGTTTGTGATACTACTTGCTT
131 TACTAGGTGGTCATATGTGTGTTTATTATTAACTCACAATCTGGCGTTTGTGATACTACGTGCTT
*
89597165 AAATAATTTGAATAAGAGCATAATGATTATGCAATCA
196 AAATAATTTGAATAAGAGCATAATGATTATACAATCA
*
89597202 AGACCATCA-CTATAAAAAAGTTTGGGATTGAATCTCCCGCAATTTTGAAACATATTCAAGGTGA
1 AGACCATCATC-AGAAAAAAGTTTGGGATTGAATCTCCCGCAATTTTGAAACATATTCAAGGTGA
* * *
89597266 TATATGTGAAATCATTCATCCACCATGTGGACCATTCAAATATGTTATGGTTTTGATAGATGCAT
65 TATATGTGAAATCATTCATCCACCATGTGGACCATTCAAAAATGTTATGGGTTTGATAGATACAT
*
89597331 CTACTAGGTGGTCATATGTGTGTTTATTATTGACTCACAATCTGGCGTTTGTGATACTACGTGCT
130 CTACTAGGTGGTCATATGTGTGTTTATTATTAACTCACAATCTGGCGTTTGTGATACTACGTGCT
* *
89597396 TAAATAATTTGACTAAGAGCATAATGATTATATAATCA
195 TAAATAATTTGAATAAGAGCATAATGATTATACAATCA
89597434 AGAC
1 AGAC
89597438 TATCCGTCTT
Statistics
Matches: 218, Mismatches: 17, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
231 1 0.00
232 217 1.00
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Consensus pattern (232 bp):
AGACCATCATCAGAAAAAAGTTTGGGATTGAATCTCCCGCAATTTTGAAACATATTCAAGGTGAT
ATATGTGAAATCATTCATCCACCATGTGGACCATTCAAAAATGTTATGGGTTTGATAGATACATC
TACTAGGTGGTCATATGTGTGTTTATTATTAACTCACAATCTGGCGTTTGTGATACTACGTGCTT
AAATAATTTGAATAAGAGCATAATGATTATACAATCA
Found at i:89608338 original size:93 final size:93
Alignment explanation
Indices: 89608231--89608401 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 93
89608221 GCCCCTAAGT
* *
89608231 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
89608296 CGAGTTCGGATGCCTAGCTACATTTCAC
66 CGAGTTCGGATGCCTAGCTACATTTCAC
*
89608324 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
89608389 CGAGTTCGGATGC
66 CGAGTTCGGATGC
89608402 TCAACCATCC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.21
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGCTACATTTCAC
Found at i:89608398 original size:46 final size:45
Alignment explanation
Indices: 89608226--89608398 Score: 215
Period size: 46 Copynumber: 3.8 Consensus size: 45
89608216 AACCCGCCCC
* *
89608226 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGAC-TTCGCATCCA
* * *
89608272 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGC-TACA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA--CTTCGCATCCA
* *
89608318 TTTCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 --TAAGTGAACTCGGACTCAACTCAACGAGTTCGGAC-TTCGCATCCA
89608365 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
89608399 TGCTCAACCA
Statistics
Matches: 108, Mismatches: 12, Indels: 14
0.81 0.09 0.10
Matches are distributed among these distances:
45 3 0.03
46 67 0.62
47 35 0.32
48 3 0.03
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.21
Consensus pattern (45 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACTTCGCATCCA
Found at i:89609945 original size:46 final size:46
Alignment explanation
Indices: 89609877--89610092 Score: 195
Period size: 46 Copynumber: 4.6 Consensus size: 46
89609867 GTGCAGATTC
* * * * *
89609877 CATGTCCCAAAGATGGTCTTACACTAACTATCATCTCGTA-GCCGATG
1 CATGTCCCAGACAT-GTCTTACACTAGCTCTCATCTC-AAGGCCGATG
** * * *
89609924 CATGTCGTAGACATGTCTTACACTAGCT-TACGTCTCAAGGCCAATA
1 CATGTCCCAGACATGTCTTACACTAGCTCT-CATCTCAAGGCCGATG
* *
89609970 CATGTCCCAGACATGTCTTACACTAGCTCTCGTCTCAATGCCGATG
1 CATGTCCCAGACATGTCTTACACTAGCTCTCATCTCAAGGCCGATG
** * **
89610016 CCATGTCTGAGACATTGTCTTACACTAGCTCTCATAAT-GTGGCCGATG
1 -CATGTCCCAGACA-TGTCTTACACTAGCTCTCAT-CTCAAGGCCGATG
*
89610064 CATGTCCCAGACATGTCTTACATTAGCTC
1 CATGTCCCAGACATGTCTTACACTAGCTC
89610093 ACACACAAAT
Statistics
Matches: 139, Mismatches: 24, Indels: 13
0.79 0.14 0.07
Matches are distributed among these distances:
45 2 0.01
46 77 0.55
47 33 0.24
48 26 0.19
49 1 0.01
ACGTcount: A:0.25, C:0.28, G:0.18, T:0.29
Consensus pattern (46 bp):
CATGTCCCAGACATGTCTTACACTAGCTCTCATCTCAAGGCCGATG
Found at i:89612011 original size:21 final size:21
Alignment explanation
Indices: 89611986--89612030 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
89611976 TGTCATCGAA
*
89611986 AACCTATTTCCTTCTAATTCT
1 AACCTATTTCCTTCTAATTAT
*
89612007 AACCTATTTGCTTCTAATTAT
1 AACCTATTTCCTTCTAATTAT
89612028 AAC
1 AAC
89612031 ACAAGCTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.29, C:0.24, G:0.02, T:0.44
Consensus pattern (21 bp):
AACCTATTTCCTTCTAATTAT
Found at i:89614367 original size:30 final size:30
Alignment explanation
Indices: 89614333--89614393 Score: 106
Period size: 30 Copynumber: 2.0 Consensus size: 30
89614323 TCCATTTTCT
89614333 CCGTTTTCT-GCCCGTTTCTTGCTCTTTTTA
1 CCGTTTT-TGGCCCGTTTCTTGCTCTTTTTA
89614363 CCGTTTTTGGCCCGTTTCTTGCTCTTTTTA
1 CCGTTTTTGGCCCGTTTCTTGCTCTTTTTA
89614393 C
1 C
89614394 TCTTTTATGC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 1 0.03
30 29 0.97
ACGTcount: A:0.03, C:0.30, G:0.15, T:0.52
Consensus pattern (30 bp):
CCGTTTTTGGCCCGTTTCTTGCTCTTTTTA
Found at i:89628287 original size:68 final size:68
Alignment explanation
Indices: 89628159--89628345 Score: 171
Period size: 68 Copynumber: 2.8 Consensus size: 68
89628149 CTTTACAAGC
* * * * * * *** *
89628159 TGCCATAGCTGAGCTATGGTCTTACACCAT-ATGATCCCAAGTTTATTATCTTGGCGGACTCCAT
1 TGCCATAGCCGAGCTATGGTCTAACA-CATCATGAACCCATGTTTAATGTCTCAACAGACTCCAT
89628223 -ATGT
65 GA-GT
* * * *
89628227 TTCCATAGTCGAGCTATGGTCTAACATATCATGAACCCATGTTTAATGTCTCAACAGACTCTATG
1 TGCCATAGCCGAGCTATGGTCTAACACATCATGAACCCATGTTTAATGTCTCAACAGACTCCATG
89628292 AGT
66 AGT
* * * **
89628295 TGCTATAGCCTAGCTATGGTCTTACACATTTTGAACCCATGTTTAATGTCT
1 TGCCATAGCCGAGCTATGGTCTAACACATCATGAACCCATGTTTAATGTCT
89628346 TGGAGGACTT
Statistics
Matches: 95, Mismatches: 22, Indels: 4
0.79 0.18 0.03
Matches are distributed among these distances:
67 2 0.02
68 92 0.97
69 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.17, T:0.35
Consensus pattern (68 bp):
TGCCATAGCCGAGCTATGGTCTAACACATCATGAACCCATGTTTAATGTCTCAACAGACTCCATG
AGT
Found at i:89630665 original size:15 final size:16
Alignment explanation
Indices: 89630647--89630679 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
89630637 TTTGATAGTT
89630647 AATT-AAAAAGGACTA
1 AATTGAAAAAGGACTA
*
89630662 AATTGAAAAAGGAGTA
1 AATTGAAAAAGGACTA
89630678 AA
1 AA
89630680 ACTTGTTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.61, C:0.03, G:0.18, T:0.18
Consensus pattern (16 bp):
AATTGAAAAAGGACTA
Found at i:89631868 original size:33 final size:33
Alignment explanation
Indices: 89631826--89631901 Score: 98
Period size: 33 Copynumber: 2.3 Consensus size: 33
89631816 TGTATAAGTG
* * * *
89631826 TAAGACCATAGTTGGGCGATGACATCTTGATGA
1 TAAGACCATAGCTAGGCGATGACATCCTAATGA
* *
89631859 TAAGACCATAGCTAGGCTATGGCATCCTAATGA
1 TAAGACCATAGCTAGGCGATGACATCCTAATGA
89631892 TAAGACCATA
1 TAAGACCATA
89631902 ACTGGGTTAT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.34, C:0.18, G:0.22, T:0.25
Consensus pattern (33 bp):
TAAGACCATAGCTAGGCGATGACATCCTAATGA
Found at i:89631900 original size:105 final size:101
Alignment explanation
Indices: 89631687--89631879 Score: 244
Period size: 105 Copynumber: 1.9 Consensus size: 101
89631677 ATTGACAGAA
* * * *
89631687 AAGACCATGGTTGAACCATGGCAATGTTTGAATGTAAGACCATAGTTGGGCTATGGCATTTTAAT
1 AAGACCATGGTTGAACCATGGCAATGTATGAATGTAAGACCATAGTTGGGCGATGACATCTTAAT
* *
89631752 GAAAAGACCATAACTGGGTTATGACGCCTTGAACAT
66 GAAAAGACCATAACTAGGCTATGACGCCTTGAACAT
*
89631788 AAGACCATGGTTGGACCATGGCAGTATATGTAT-AAGTGTAAGACCATAGTTGGGCGATGACATC
1 AAGACCATGGTTGAACCATGGC---A-ATGTATGAA-TGTAAGACCATAGTTGGGCGATGACATC
* * *
89631852 TTGATGATAAGACCATAGCTAGGCTATG
61 TTAATGAAAAGACCATAACTAGGCTATG
89631880 GCATCCTAAT
Statistics
Matches: 77, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
101 21 0.27
104 3 0.04
105 53 0.69
ACGTcount: A:0.32, C:0.16, G:0.25, T:0.27
Consensus pattern (101 bp):
AAGACCATGGTTGAACCATGGCAATGTATGAATGTAAGACCATAGTTGGGCGATGACATCTTAAT
GAAAAGACCATAACTAGGCTATGACGCCTTGAACAT
Found at i:89631975 original size:30 final size:30
Alignment explanation
Indices: 89631922--89631978 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
89631912 GGCATTGCAA
*
89631922 GTGTAAGACCATAGCAGGGCTATGGCAATT
1 GTGTAAGACCATAGCAGGACTATGGCAATT
**
89631952 GTGTAAGACCATAGTTGGACTATGGCA
1 GTGTAAGACCATAGCAGGACTATGGCA
89631979 TCAAGAAAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.30, C:0.16, G:0.30, T:0.25
Consensus pattern (30 bp):
GTGTAAGACCATAGCAGGACTATGGCAATT
Found at i:89641624 original size:44 final size:44
Alignment explanation
Indices: 89641570--89641679 Score: 123
Period size: 46 Copynumber: 2.4 Consensus size: 44
89641560 CATGTCTCAA
89641570 ACATGGTCTTACACTAGCTCAACTC-ATAGTCGATGCATGCCCCAG
1 ACAT-GTCTTACACTAGCTCAACTCGA-AGTCGATGCATGCCCCAG
* * * * **
89641615 GCATGTCTTACACTGGCTTACATCTCGAAGTTGATGCATGTTCCAG
1 ACATGTCTTACACTAGC-T-CAACTCGAAGTCGATGCATGCCCCAG
89641661 ACATGTCTTACACTAGCTC
1 ACATGTCTTACACTAGCTC
89641680 TTGTCTCAAT
Statistics
Matches: 54, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
44 13 0.24
45 5 0.09
46 35 0.65
47 1 0.02
ACGTcount: A:0.25, C:0.28, G:0.18, T:0.29
Consensus pattern (44 bp):
ACATGTCTTACACTAGCTCAACTCGAAGTCGATGCATGCCCCAG
Found at i:89641711 original size:47 final size:45
Alignment explanation
Indices: 89641651--89641779 Score: 129
Period size: 47 Copynumber: 2.8 Consensus size: 45
89641641 GAAGTTGATG
* *
89641651 CATGTTCCAGACATGTCTTACACTAGCTCTTGTC-TCAA-T-GCCAATGT
1 CATGTCCCAGACATGTCTTACACTAGCTC---TCAT-AAGTGGCCAA-CT
* *
89641698 CATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGTGGCCGACT
1 CATGTCCCAGACAT-GTCTTACACTAGCTCTCATAA-GTGGCCAACT
*
89641745 CATGTCCCAGACATGTCTTACACTAGCTCACATAA
1 CATGTCCCAGACATGTCTTACACTAGCTCTCATAA
89641780 CCCATACGTC
Statistics
Matches: 71, Mismatches: 6, Indels: 11
0.81 0.07 0.12
Matches are distributed among these distances:
45 4 0.06
46 20 0.28
47 29 0.41
48 18 0.25
ACGTcount: A:0.25, C:0.29, G:0.16, T:0.29
Consensus pattern (45 bp):
CATGTCCCAGACATGTCTTACACTAGCTCTCATAAGTGGCCAACT
Found at i:89644159 original size:7 final size:7
Alignment explanation
Indices: 89644142--89644185 Score: 54
Period size: 7 Copynumber: 6.1 Consensus size: 7
89644132 TTTTCTTTTC
89644142 TTTTTAA
1 TTTTTAA
89644149 -TTTTAA
1 TTTTTAA
89644155 TTTTTAA
1 TTTTTAA
*
89644162 TTTTCTATT
1 TTTT-TA-A
89644171 TTTTTAA
1 TTTTTAA
89644178 TTTTTAA
1 TTTTTAA
89644185 T
1 T
89644186 CAAATCTCAA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
6 6 0.19
7 18 0.56
8 4 0.12
9 4 0.12
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (7 bp):
TTTTTAA
Found at i:89646928 original size:31 final size:31
Alignment explanation
Indices: 89646866--89646928 Score: 74
Period size: 31 Copynumber: 2.0 Consensus size: 31
89646856 AAATCATCAT
** *
89646866 TAAAATATTCAATAATTATATTTATTTTTAA
1 TAAAATATAAAATAATTATATTAATTTTTAA
*
89646897 TAAAATATAAAATTATT-TATTAATTTATTAA
1 TAAAATATAAAATAATTATATTAATTT-TTAA
89646928 T
1 T
89646929 GATGTGTTCT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
30 8 0.30
31 19 0.70
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.51
Consensus pattern (31 bp):
TAAAATATAAAATAATTATATTAATTTTTAA
Found at i:89648790 original size:28 final size:28
Alignment explanation
Indices: 89648747--89648808 Score: 97
Period size: 28 Copynumber: 2.2 Consensus size: 28
89648737 GCTCGCGAAG
89648747 TGGGTCACAAGCATTCCACCTCACAAGA
1 TGGGTCACAAGCATTCCACCTCACAAGA
* * *
89648775 TGGGTCACAAGTATTCCACCTCGCGAGA
1 TGGGTCACAAGCATTCCACCTCACAAGA
89648803 TGGGTC
1 TGGGTC
89648809 GTCAGGGTCA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.26, C:0.29, G:0.24, T:0.21
Consensus pattern (28 bp):
TGGGTCACAAGCATTCCACCTCACAAGA
Found at i:89650325 original size:31 final size:31
Alignment explanation
Indices: 89650290--89650469 Score: 254
Period size: 31 Copynumber: 5.8 Consensus size: 31
89650280 CTTGTCACTT
* * *
89650290 GTAGCCGAAGCTACCACTATTCACTGATTAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAA
* *
89650321 GTAGCCGGAGCTACCATTTTTCACTGATCAA
1 GTAGCCGAAGCTACCACTTTTCACTGATCAA
*
89650352 GTAGCCGAAGCTACCACTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAA
*
89650383 GTAGCC-AGAGCTACCATTTTTCACTGATCAA
1 GTAGCCGA-AGCTACCACTTTTCACTGATCAA
*
89650414 GTAGTCGAAGCTACCACTTTTCACTGATCAA
1 GTAGCCGAAGCTACCACTTTTCACTGATCAA
* *
89650445 GTAACCGAAACTACCACTTTTCACT
1 GTAGCCGAAGCTACCACTTTTCACT
89650470 TGTCATTTGT
Statistics
Matches: 132, Mismatches: 15, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
30 1 0.01
31 130 0.98
32 1 0.01
ACGTcount: A:0.28, C:0.27, G:0.17, T:0.28
Consensus pattern (31 bp):
GTAGCCGAAGCTACCACTTTTCACTGATCAA
Found at i:89650551 original size:50 final size:51
Alignment explanation
Indices: 89650449--89650573 Score: 180
Period size: 50 Copynumber: 2.5 Consensus size: 51
89650439 GATCAAGTAA
* * * *
89650449 CCGAAACTACCACTTTTCACTTGTCATTTGTCATTGACCAGATAAGTCTAG
1 CCGAAGCTATCACTTATCACTTGTCACTTGTCATTGACCAGATAAGTCTAG
* * *
89650500 CCGAAGCTATCACTTATCACTT-TCACTTGTCCTTGATCAGATAAGTGTAG
1 CCGAAGCTATCACTTATCACTTGTCACTTGTCATTGACCAGATAAGTCTAG
89650550 CCGAAGCTATCACTTATCACTTGT
1 CCGAAGCTATCACTTATCACTTGT
89650574 TGCCATGGTC
Statistics
Matches: 66, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
50 46 0.70
51 20 0.30
ACGTcount: A:0.26, C:0.26, G:0.14, T:0.34
Consensus pattern (51 bp):
CCGAAGCTATCACTTATCACTTGTCACTTGTCATTGACCAGATAAGTCTAG
Found at i:89654291 original size:16 final size:16
Alignment explanation
Indices: 89654270--89654311 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
89654260 TAACTAAATT
89654270 ATATAATTTCATGA-TA
1 ATATAATTTCAT-ATTA
*
89654286 ATATAATGTCATATTA
1 ATATAATTTCATATTA
89654302 ATAATAATTT
1 AT-ATAATTT
89654312 TATTATTATA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
15 1 0.05
16 15 0.68
17 6 0.27
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (16 bp):
ATATAATTTCATATTA
Found at i:89660878 original size:64 final size:63
Alignment explanation
Indices: 89660778--89660906 Score: 213
Period size: 64 Copynumber: 2.0 Consensus size: 63
89660768 CTATGCAGAA
* *
89660778 AGCTAATGAATGAGAAAGTAGTAACATTGGCACTATTGTAAGGATTACAAGTGACAAAAGTTG
1 AGCTAATGAATGAGAAAGTAGTAACATTAGCACTATTGTAAGGATTACAACTGACAAAAGTTG
* *
89660841 AGCTAATGAATGAGAAAAGTAGTAACATTAGTACTATTGTAAGGATTAGAACTGACAAAAGTTG
1 AGCTAATGAATGAG-AAAGTAGTAACATTAGCACTATTGTAAGGATTACAACTGACAAAAGTTG
89660905 AG
1 AG
89660907 AGTTTGATAA
Statistics
Matches: 61, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
63 14 0.23
64 47 0.77
ACGTcount: A:0.43, C:0.09, G:0.23, T:0.26
Consensus pattern (63 bp):
AGCTAATGAATGAGAAAGTAGTAACATTAGCACTATTGTAAGGATTACAACTGACAAAAGTTG
Found at i:89662588 original size:262 final size:259
Alignment explanation
Indices: 89661768--89662668 Score: 898
Period size: 263 Copynumber: 3.5 Consensus size: 259
89661758 ACAAAGGATA
* * * * * **
89661768 AAATAACATAA-ATTAGTTCAACCAATTATTATATACGGGGTATTTTCCTCGCATATCAAAAATA
1 AAATAACATAAGA-TAGTTCAACCAATTATTATACACTGTGTATTTTCCTAGCACATC-AAAGCA
* *
89661832 ACTTCCACAACAT-AGTGCCATCTCACCTTGTCATTACCTTATATATATAT-TCTAAGAGTGTAT
64 ACTTCCACAACATGA-TGCCACCTCACCTTGTCGTTACCTTATATATAT-TCTCTAAGAGTGTAT
* *
89661895 CATAT-T-AAATATTGATTTTTTCAATTTTACGAT-ATGCAACATTATTTATCAAGAGTATAACT
127 CATATATAAAAAATTGAGTTTTTCAATTTTAC-ATGATGCAACATTATTTATCAAGAGTATAACT
* * * * * * *
89661957 -CTGACGTAGTGAAGCAAAACTTCTTAAATCTCATTAACCTTATAGAGATTTGATAAACTGGCAG
191 GC-GAAGTAGTGAAACAGAACTCCTAAAATCTCATTATCCTTATAGGGATTTGATAAACTGGCAG
*
89662021 GCTAT
255 GCGAT
* *
89662026 AAATAACATAAGATAATTCAACCAATTATTATACACTGTGTATTTTTCCTA-CACATTGAAAGCA
1 AAATAACATAAGATAGTTCAACCAATTATTATACACTGTGTA-TTTTCCTAGCACA-TCAAAGCA
* * * * *
89662090 ACTTCCACAACATGGTGCCACCTAACCTTGTCGTTACCTTAAATATATTCTCTAAGAGTATATTA
64 ACTTCCACAACATGATGCCACCTCACCTTGTCGTTACCTTATATATATTCTCTAAGAGTGTATCA
*
89662155 TAT-TAAAAAATTGAGATTTTTTCAATTTTAC-TAGATACAACATTATTTATCAAGAGTATAACT
129 TATATAAAAAATTGAG--TTTTTCAATTTTACAT-GATGCAACATTATTTATCAAGAGTATAACT
* ** **
89662218 GTGAAGTAGTGAAATGGAACTCCTTAAAAATCTCATTAAT-CTTATAGAGG-TTTGATAAACTAA
191 GCGAAGTAGTGAAACAGAACTCC-T-AAAATCTCATT-ATCCTTATAG-GGATTTGATAAACTGG
*
89662281 CAGGCAAT
252 CAGGCGAT
* * *
89662289 AAATAACATAAGATAGTTCAACCAATTGTTATACACTGTGTATCTTCC-AGCACATCATAAGCAG
1 AAATAACATAAGATAGTTCAACCAATTATTATACACTGTGTATTTTCCTAGCACATCA-AAGCAA
* * * *** *
89662353 CTGCCACAACGTGATGTCACCTCACCTCACCGTTACATTATATATATTCTCTAAGAGTGTATCAT
65 CTTCCACAACATGATGCCACCTCACCTTGTCGTTACCTTATATATATTCTCTAAGAGTGTATCAT
* * *
89662418 ATTAATAAAAAATTGAGTTTTTCAATTTTGCATGATGCAACATTATATATCAAGTA-TATAATTG
130 A-T-ATAAAAAATTGAGTTTTTCAATTTTACATGATGCAACATTATTTATCAAG-AGTATAACTG
* * * * * *
89662482 CGAAGTAGTGAAACAGAACTCCTCAAGTCTCAGTATCCTCATAGGGATTTGATAAACTGGCCGAC
192 CGAAGTAGTGAAACAGAACTCCTAAAATCTCATTATCCTTATAGGGATTTGATAAACTGGCAGGC
89662547 GAT
257 GAT
** * *
89662550 AAATTAACATAA-ATTAGTTCAACCAATTATTATACACTGCATACTTTTCC-CGCACAACAAAAG
1 AAA-TAACATAAGA-TAGTTCAACCAATTATTATACACTGTGTA-TTTTCCTAGCACATC-AAAG
** ** * * * * *
89662613 CAACTTCCACAATGTGGGGCCACTTCACATTGCCGTTACATAATATATATTCTCTA
62 CAACTTCCACAACATGATGCCACCTCACCTTGTCGTTACCTTATATATATTCTCTA
89662669 GGGCAACTCG
Statistics
Matches: 533, Mismatches: 82, Indels: 51
0.80 0.12 0.08
Matches are distributed among these distances:
257 1 0.00
258 102 0.19
259 18 0.03
260 4 0.01
261 94 0.18
262 104 0.20
263 193 0.36
264 5 0.01
265 12 0.02
ACGTcount: A:0.36, C:0.18, G:0.12, T:0.33
Consensus pattern (259 bp):
AAATAACATAAGATAGTTCAACCAATTATTATACACTGTGTATTTTCCTAGCACATCAAAGCAAC
TTCCACAACATGATGCCACCTCACCTTGTCGTTACCTTATATATATTCTCTAAGAGTGTATCATA
TATAAAAAATTGAGTTTTTCAATTTTACATGATGCAACATTATTTATCAAGAGTATAACTGCGAA
GTAGTGAAACAGAACTCCTAAAATCTCATTATCCTTATAGGGATTTGATAAACTGGCAGGCGAT
Found at i:89668481 original size:20 final size:20
Alignment explanation
Indices: 89668458--89668502 Score: 58
Period size: 19 Copynumber: 2.3 Consensus size: 20
89668448 TTTTAGGTTG
89668458 GTTTTGGACTT-TTTTGATTT
1 GTTTTGGACTTGTTTT-ATTT
*
89668478 G-TTTGGGCTTGTTTTATTT
1 GTTTTGGACTTGTTTTATTT
89668497 GTTTTG
1 GTTTTG
89668503 TTTTTTCGGG
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
19 13 0.59
20 9 0.41
ACGTcount: A:0.07, C:0.04, G:0.24, T:0.64
Consensus pattern (20 bp):
GTTTTGGACTTGTTTTATTT
Found at i:89673358 original size:46 final size:45
Alignment explanation
Indices: 89673308--89673482 Score: 203
Period size: 46 Copynumber: 3.8 Consensus size: 45
89673298 TGGTTGAGCA
89673308 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
* * * *
89673354 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGAATGTAACTAG-GCA-
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACT-TATG-GA-T-GCGAAG
*
89673400 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
* * *
89673446 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
89673483 GCGGGTTACA
Statistics
Matches: 110, Mismatches: 11, Indels: 16
0.80 0.08 0.12
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 2 0.02
46 98 0.89
47 2 0.02
48 3 0.03
49 1 0.01
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.29
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAG
Found at i:89673462 original size:92 final size:92
Alignment explanation
Indices: 89673305--89673475 Score: 306
Period size: 92 Copynumber: 1.9 Consensus size: 92
89673295 GGATGGTTGA
* *
89673305 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
89673370 TGAGTCCGAGTTCGTGAATGTAACTAG
66 TGAGTCCGAGTTCGTGAATGTAACTAG
* *
89673397 GCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
89673462 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
89673476 CTTATGGGCG
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
92 75 1.00
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.28
Consensus pattern (92 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAATGTAACTAG
Found at i:89680890 original size:46 final size:46
Alignment explanation
Indices: 89680840--89681015 Score: 182
Period size: 46 Copynumber: 3.8 Consensus size: 46
89680830 TGGTTGAGCA
89680840 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * *
89680886 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--AATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
* *
89680931 CATCC-AAGCTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAACG
1 --TCCGAA-CTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
89680979 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
89681016 GCGGGTTACA
Statistics
Matches: 105, Mismatches: 14, Indels: 22
0.74 0.10 0.16
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
45 3 0.03
46 62 0.59
47 26 0.25
48 3 0.03
50 3 0.03
51 2 0.02
ACGTcount: A:0.21, C:0.20, G:0.29, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:89680996 original size:93 final size:93
Alignment explanation
Indices: 89680837--89681008 Score: 292
Period size: 93 Copynumber: 1.8 Consensus size: 93
89680827 GGATGGTTGA
* *
89680837 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
89680902 TGAGTCCGAGTTCGTGAAATGTAACTAG
66 TGAGTCCGAGTTCGTGAAATGTAACTAG
* *
89680930 GCATCC-AAGCTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAG
1 GCATCCGAA-CTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
89680994 TTGAGTCCGAGTTCG
65 TTGAGTCCGAGTTCG
89681009 CTTATGGGCG
Statistics
Matches: 74, Mismatches: 4, Indels: 2
0.93 0.05 0.03
Matches are distributed among these distances:
92 2 0.03
93 72 0.97
ACGTcount: A:0.22, C:0.21, G:0.29, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAAATGTAACTAG
Found at i:89690488 original size:329 final size:329
Alignment explanation
Indices: 89689890--89690550 Score: 1286
Period size: 329 Copynumber: 2.0 Consensus size: 329
89689880 GGTGTTGTCG
89689890 ACAGTCTATTCTTCTCCACCAAACGAATCAGTGTTCTCCTTGATGATTCCAATTATCTTTTATGG
1 ACAGTCTATTCTTCTCCACCAAACGAATCAGTGTTCTCCTTGATGATTCCAATTATCTTTTATGG
89689955 CAGTAACAGGTCCTTTTGGCTGTTAAAACTTACAAGCTTCAACGGTTTCTTGATCTTAGTACTGT
66 CAGTAACAGGTCCTTTTGGCTGTTAAAACTTACAAGCTTCAACGGTTTCTTGATCTTAGTACTGT
89690020 TTCACCATCTCAAGTCATTATAGAAGAGGATGGTGTGACTCAAGAAAATGTTGAGTTTACTCGGT
131 TTCACCATCTCAAGTCATTATAGAAGAGGATGGTGTGACTCAAGAAAATGTTGAGTTTACTCGGT
* *
89690085 TTGAACAGCAAGATAGTACCATTGCTTCTTAGCTTTTGTCTTTGGTGAGTCAATCTGTTTTACCT
196 TTGAACAACAAGATAGTACCATTGCTTCTTAGCTTTTATCTTTGGTGAGTCAATCTGTTTTACCT
89690150 CATCTTATTGGCTTGGATACAAGTGCCCAAATTTGGAATGCTATTGTGTCTCTCTATGGCAGTAA
261 CATCTTATTGGCTTGGATACAAGTGCCCAAATTTGGAATGCTATTGTGTCTCTCTATGGCAGTAA
89690215 AACT
326 AACT
89690219 ACAGTCTATTCTTCTCCACCAAACGAATCAGTGTTCTCCTTGATGATTCCAATTATCTTTTATGG
1 ACAGTCTATTCTTCTCCACCAAACGAATCAGTGTTCTCCTTGATGATTCCAATTATCTTTTATGG
89690284 CAGTAACAGGTCCTTTTGGCTGTTAAAACTTACAAGCTTCAACGGTTTCTTGATCTTAGTACTGT
66 CAGTAACAGGTCCTTTTGGCTGTTAAAACTTACAAGCTTCAACGGTTTCTTGATCTTAGTACTGT
89690349 TTCACCATCTCAAGTCATTATAGAAGAGGATGGTGTGACTCAAGAAAATGTTGAGTTTACTCGGT
131 TTCACCATCTCAAGTCATTATAGAAGAGGATGGTGTGACTCAAGAAAATGTTGAGTTTACTCGGT
*
89690414 TTGAACAACAAGATAGTACCATTGCTTCTTGGCTTTTATCTTTGGTGAGTCAATCTGTTTTACCT
196 TTGAACAACAAGATAGTACCATTGCTTCTTAGCTTTTATCTTTGGTGAGTCAATCTGTTTTACCT
*
89690479 CATCTTATTGGCTTGGATACAAGTGCCCAAATTTGGAATGCTATTGTGTCTCTCTATGGTAGTAA
261 CATCTTATTGGCTTGGATACAAGTGCCCAAATTTGGAATGCTATTGTGTCTCTCTATGGCAGTAA
89690544 AACT
326 AACT
89690548 ACA
1 ACA
89690551 TCTCGACTGA
Statistics
Matches: 328, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
329 328 1.00
ACGTcount: A:0.26, C:0.19, G:0.18, T:0.36
Consensus pattern (329 bp):
ACAGTCTATTCTTCTCCACCAAACGAATCAGTGTTCTCCTTGATGATTCCAATTATCTTTTATGG
CAGTAACAGGTCCTTTTGGCTGTTAAAACTTACAAGCTTCAACGGTTTCTTGATCTTAGTACTGT
TTCACCATCTCAAGTCATTATAGAAGAGGATGGTGTGACTCAAGAAAATGTTGAGTTTACTCGGT
TTGAACAACAAGATAGTACCATTGCTTCTTAGCTTTTATCTTTGGTGAGTCAATCTGTTTTACCT
CATCTTATTGGCTTGGATACAAGTGCCCAAATTTGGAATGCTATTGTGTCTCTCTATGGCAGTAA
AACT
Found at i:89703894 original size:24 final size:23
Alignment explanation
Indices: 89703867--89703913 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
89703857 AAAAAATCTT
* *
89703867 AAAATATTTAAAAATTACAAAAAA
1 AAAAAATTTAAAAAATA-AAAAAA
89703891 AAAAAATTTAAAAAATAAAAAAA
1 AAAAAATTTAAAAAATAAAAAAA
89703914 TATTTAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 6 0.29
24 15 0.71
ACGTcount: A:0.77, C:0.02, G:0.00, T:0.21
Consensus pattern (23 bp):
AAAAAATTTAAAAAATAAAAAAA
Found at i:89703896 original size:17 final size:16
Alignment explanation
Indices: 89703876--89703940 Score: 60
Period size: 17 Copynumber: 3.9 Consensus size: 16
89703866 TAAAATATTT
89703876 AAAAATTACAAAAAAAA
1 AAAAATTA-AAAAAAAA
*
89703893 AAAATTTAAAAAATAAA
1 AAAAATTAAAAAA-AAA
* *
89703910 AAAATATT-TAAAAATA
1 AAAA-ATTAAAAAAAAA
*
89703926 TAAAATTAAAAAAAA
1 AAAAATTAAAAAAAA
89703941 TATATTTATA
Statistics
Matches: 38, Mismatches: 7, Indels: 7
0.73 0.13 0.13
Matches are distributed among these distances:
15 3 0.08
16 15 0.39
17 18 0.47
18 2 0.05
ACGTcount: A:0.77, C:0.02, G:0.00, T:0.22
Consensus pattern (16 bp):
AAAAATTAAAAAAAAA
Found at i:89703897 original size:16 final size:16
Alignment explanation
Indices: 89703876--89703938 Score: 58
Period size: 16 Copynumber: 3.8 Consensus size: 16
89703866 TAAAATATTT
89703876 AAAAATTACAAAAA-AA
1 AAAAATTA-AAAAATAA
89703892 AAAAATTTAAAAAATAAA
1 AAAAA-TTAAAAAAT-AA
*
89703910 AAAATATTTAAAAAT-A
1 AAAA-ATTAAAAAATAA
*
89703926 TAAAATTAAAAAA
1 AAAAATTAAAAAA
89703939 AATATATTTA
Statistics
Matches: 40, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
15 8 0.20
16 14 0.35
17 3 0.08
18 14 0.35
19 1 0.03
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (16 bp):
AAAAATTAAAAAATAA
Found at i:89703912 original size:18 final size:18
Alignment explanation
Indices: 89703876--89703930 Score: 69
Period size: 19 Copynumber: 3.1 Consensus size: 18
89703866 TAAAATATTT
*
89703876 AAAAA-TTACAAAA-AAA
1 AAAAATTTAAAAAATAAA
89703892 AAAAATTTAAAAAATAAA
1 AAAAATTTAAAAAATAAA
89703910 AAAATATTTAAAAATATAAA
1 AAAA-ATTTAAAAA-ATAAA
89703930 A
1 A
89703931 TTAAAAAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
16 5 0.15
17 7 0.21
18 7 0.21
19 9 0.26
20 6 0.18
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (18 bp):
AAAAATTTAAAAAATAAA
Found at i:89703912 original size:19 final size:20
Alignment explanation
Indices: 89703888--89703930 Score: 70
Period size: 19 Copynumber: 2.2 Consensus size: 20
89703878 AAATTACAAA
89703888 AAAAAAAAATTTAAAAA-AT
1 AAAAAAAAATTTAAAAATAT
*
89703907 AAAAAAATATTTAAAAATAT
1 AAAAAAAAATTTAAAAATAT
89703927 AAAA
1 AAAA
89703931 TTAAAAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 16 0.73
20 6 0.27
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (20 bp):
AAAAAAAAATTTAAAAATAT
Found at i:89703929 original size:27 final size:28
Alignment explanation
Indices: 89703892--89703948 Score: 73
Period size: 27 Copynumber: 2.0 Consensus size: 28
89703882 TACAAAAAAA
*
89703892 AAAAATTTAAAA-AATAAAAAA-ATATTT
1 AAAAATATAAAATAA-AAAAAATATATTT
89703919 AAAAATATAAAATTAAAAAAAATATATTT
1 AAAAATATAAAA-TAAAAAAAATATATTT
89703948 A
1 A
89703949 TAGCATACGA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
27 11 0.42
28 6 0.23
29 9 0.35
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (28 bp):
AAAAATATAAAATAAAAAAAATATATTT
Found at i:89704238 original size:31 final size:30
Alignment explanation
Indices: 89704203--89704281 Score: 72
Period size: 31 Copynumber: 2.6 Consensus size: 30
89704193 GATCCTTTAG
*
89704203 AATTTATGAAAAATTTAATTAGC-CCT-CTCCA
1 AATTT-TGAAAAATTTAATTA-CACCTCCT-AA
* * *
89704234 AATTTTGTAAATTTTCATTACACCTCCTAA
1 AATTTTGAAAAATTTAATTACACCTCCTAA
89704264 AATTTTTGAAAAATTTAA
1 AA-TTTTGAAAAATTTAA
89704282 CCAGGTCTTT
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
29 1 0.03
30 18 0.47
31 19 0.50
ACGTcount: A:0.39, C:0.15, G:0.05, T:0.41
Consensus pattern (30 bp):
AATTTTGAAAAATTTAATTACACCTCCTAA
Found at i:89705624 original size:19 final size:18
Alignment explanation
Indices: 89705605--89705702 Score: 99
Period size: 19 Copynumber: 5.2 Consensus size: 18
89705595 AACAAGGATA
89705605 AAATAAAATAAAATGTAT
1 AAATAAAATAAAATGTAT
* *
89705623 AAAT-AAATGATATAGTAGAT
1 AAATAAAATAAAAT-GT--AT
** *
89705643 TGATAAAATAAAATATAT
1 AAATAAAATAAAATGTAT
89705661 AAATAAAAATAAAATGTAT
1 AAAT-AAAATAAAATGTAT
89705680 AAATAAAAATAAAATGTAT
1 AAAT-AAAATAAAATGTAT
89705699 AAAT
1 AAAT
89705703 TTTAAGTGCT
Statistics
Matches: 65, Mismatches: 10, Indels: 9
0.77 0.12 0.11
Matches are distributed among these distances:
17 7 0.11
18 10 0.15
19 36 0.55
20 5 0.08
21 7 0.11
ACGTcount: A:0.64, C:0.00, G:0.07, T:0.29
Consensus pattern (18 bp):
AAATAAAATAAAATGTAT
Found at i:89707888 original size:53 final size:53
Alignment explanation
Indices: 89707808--89707912 Score: 147
Period size: 53 Copynumber: 2.0 Consensus size: 53
89707798 TTATAGAACA
* * * * * *
89707808 ATCAAATGGAGTAGTTAAATTCTACAAGAATTCTCTTTTATTCATGTGATTGG
1 ATCAAATAGAGGAGCTAAATTCTACAAGAACTCTATTTTATTCATGTAATTGG
*
89707861 ATCAAATAGAGGAGCTAAATTTTACAAGAACTCTATTTTATTCATGTAATTG
1 ATCAAATAGAGGAGCTAAATTCTACAAGAACTCTATTTTATTCATGTAATTG
89707913 AAACTATAAA
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
53 45 1.00
ACGTcount: A:0.35, C:0.11, G:0.15, T:0.38
Consensus pattern (53 bp):
ATCAAATAGAGGAGCTAAATTCTACAAGAACTCTATTTTATTCATGTAATTGG
Found at i:89708306 original size:25 final size:25
Alignment explanation
Indices: 89708252--89708307 Score: 71
Period size: 25 Copynumber: 2.2 Consensus size: 25
89708242 GTAGCTTTCT
89708252 TTCAAATTTATCAATAAATTTTGAC
1 TTCAAATTTATCAATAAATTTTGAC
*
89708277 TTCAAATTT-TCAAGTCAACTTTTGAC
1 TTCAAATTTATCAA-T-AAATTTTGAC
89708303 -TCAAA
1 TTCAAA
89708308 ATTTGTGTGT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
24 4 0.14
25 15 0.54
26 9 0.32
ACGTcount: A:0.38, C:0.16, G:0.05, T:0.41
Consensus pattern (25 bp):
TTCAAATTTATCAATAAATTTTGAC
Found at i:89714546 original size:53 final size:52
Alignment explanation
Indices: 89714395--89714549 Score: 190
Period size: 52 Copynumber: 3.0 Consensus size: 52
89714385 TGACGGAAAA
*
89714395 GATGTGATATGT-ACTTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTGC
1 GATGTGATATGTGA-TTCCGTATAAGACCATATCTGGGCTATGGCATCGGTGC
* * * * *
89714447 AATGTGAT-TCGAGATCCCATATAAGACCATAGT-TGGGCTATGGCATCGGTGT
1 GATGTGATAT-GTGATTCCGTATAAGACCATA-TCTGGGCTATGGCATCGGTGC
*
89714499 GATGTGATAATGTGATTCCGTATAAGACCATATCTGGGATATGGCATCGGT
1 GATGTGAT-ATGTGATTCCGTATAAGACCATATCTGGGCTATGGCATCGGT
89714550 ATGTCATGTG
Statistics
Matches: 86, Mismatches: 11, Indels: 11
0.80 0.10 0.10
Matches are distributed among these distances:
51 1 0.01
52 49 0.57
53 35 0.41
54 1 0.01
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.30
Consensus pattern (52 bp):
GATGTGATATGTGATTCCGTATAAGACCATATCTGGGCTATGGCATCGGTGC
Found at i:89714588 original size:46 final size:47
Alignment explanation
Indices: 89714409--89714605 Score: 126
Period size: 46 Copynumber: 4.0 Consensus size: 47
89714399 TGATATGTAC
* * * *
89714409 TTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTGCAATGTGATTCGAGA
1 TTCCGTATAAGACCATAGCAGGGATATGGCATCGGT---ATGTCA-T-GTGA
* * ** * *
89714461 TCCCATATAAGACCATAGTTGGGCTATGGCATCGGTGTGATGTGATAATGTGA
1 TTCCGTATAAGACCATAGCAGGGATATGGCATC-G-GT-A--TG-TCATGTGA
* *
89714514 TTCCGTATAAGACCATATCTGGGATATGGCATCGGTATGTCATGTGA
1 TTCCGTATAAGACCATAGCAGGGATATGGCATCGGTATGTCATGTGA
* * * * * *
89714561 -TCCGTGTAAGACCATGGCAGGGCTATGGCTTCGGTGTGTGATGTG
1 TTCCGTATAAGACCATAGCAGGGATATGGCATCGGTATGTCATGTG
89714606 TGACAATGTA
Statistics
Matches: 120, Mismatches: 20, Indels: 16
0.77 0.13 0.10
Matches are distributed among these distances:
46 37 0.31
47 7 0.06
48 2 0.02
50 1 0.01
51 2 0.02
52 32 0.27
53 32 0.27
54 5 0.04
55 2 0.02
ACGTcount: A:0.23, C:0.17, G:0.30, T:0.29
Consensus pattern (47 bp):
TTCCGTATAAGACCATAGCAGGGATATGGCATCGGTATGTCATGTGA
Found at i:89715368 original size:20 final size:20
Alignment explanation
Indices: 89715343--89715380 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
89715333 ACCCCATAGG
89715343 CAGGCCACACGGGAATGTCC
1 CAGGCCACACGGGAATGTCC
*
89715363 CAGGCCACACGGGCATGT
1 CAGGCCACACGGGAATGT
89715381 GCCCTTATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.24, C:0.34, G:0.32, T:0.11
Consensus pattern (20 bp):
CAGGCCACACGGGAATGTCC
Found at i:89721825 original size:52 final size:53
Alignment explanation
Indices: 89721762--89721900 Score: 178
Period size: 52 Copynumber: 2.7 Consensus size: 53
89721752 ATATGTACTT
*
89721762 CTGTATAAGACCATAGCTGGGCTATGGCATCGGTACAATGTG-ATTCGAGA-TC
1 CTGTATAAGACCATAGCTGGGCTATGGCATCGGTACAATGTGAAAT-GAGATTC
*** *
89721814 CTGTATAAGACCATAGCTGGGCTATGGCATCGGTGTGATGTGAAATGTGATTC
1 CTGTATAAGACCATAGCTGGGCTATGGCATCGGTACAATGTGAAATGAGATTC
*
89721867 C-GTATAAGACCATATCT-GGCATATGGCATCGGTA
1 CTGTATAAGACCATAGCTGGGC-TATGGCATCGGTA
89721901 TGTTATGTGA
Statistics
Matches: 77, Mismatches: 7, Indels: 6
0.86 0.08 0.07
Matches are distributed among these distances:
51 3 0.04
52 69 0.90
53 5 0.06
ACGTcount: A:0.27, C:0.18, G:0.27, T:0.28
Consensus pattern (53 bp):
CTGTATAAGACCATAGCTGGGCTATGGCATCGGTACAATGTGAAATGAGATTC
Found at i:89730171 original size:68 final size:68
Alignment explanation
Indices: 89730099--89730252 Score: 172
Period size: 67 Copynumber: 2.3 Consensus size: 68
89730089 CATCATGTGT
* * * * *
89730099 ACAAGAGAGCTACAAGATATTATGATGTAGCTAGGTCGTATGGGT-GATACTA-TG-TGTACACC
1 ACAAGAGAGCTAC-AGATA-TAT-ATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACC
89730161 ATGTAG
63 ATGTAG
* * *
89730167 ACAAGAGAGCTAC-GAGATATATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATG
1 ACAAGAGAGCTACAGATATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATG
89730231 TAG
66 TAG
89730234 ACAAGAGAGCTACGAGATA
1 ACAAGAGAGCTAC-AGATA
89730253 AACTGGCTAG
Statistics
Matches: 72, Mismatches: 9, Indels: 9
0.80 0.10 0.10
Matches are distributed among these distances:
64 19 0.26
65 7 0.10
66 5 0.07
67 25 0.35
68 13 0.18
69 3 0.04
ACGTcount: A:0.34, C:0.16, G:0.28, T:0.23
Consensus pattern (68 bp):
ACAAGAGAGCTACAGATATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATG
TAG
Found at i:89731406 original size:2 final size:2
Alignment explanation
Indices: 89731399--89731431 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
89731389 TCATGAGATG
89731399 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
89731432 GACTAGTCTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:89732336 original size:4 final size:4
Alignment explanation
Indices: 89732329--89733707 Score: 2758
Period size: 4 Copynumber: 344.8 Consensus size: 4
89732319 TTACTACTAA
89732329 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
89732377 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
89732425 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
89732473 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
89732521 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
89732569 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
89732617 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
89732665 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
89732713 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
89732761 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
89732809 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
89732857 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
89732905 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
89732953 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
89733001 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
89733049 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
89733097 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
89733145 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
89733193 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
89733241 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
89733289 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
89733337 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
89733385 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
89733433 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
89733481 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
89733529 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
89733577 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
89733625 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
89733673 TATG TATG TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TATG TAT
89733708 ATTAAGAACA
Statistics
Matches: 1375, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 1375 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:89741928 original size:2 final size:2
Alignment explanation
Indices: 89741921--89741950 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
89741911 ACTTTAATAC
*
89741921 AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
89741951 CCCTTTCAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:89744402 original size:40 final size:40
Alignment explanation
Indices: 89744342--89744501 Score: 257
Period size: 40 Copynumber: 4.0 Consensus size: 40
89744332 CACATCATCG
* *
89744342 GCACGAATGCCCTTCAGGACTTAGCCCGGATGTAACACCA
1 GCACGAATGCTCTTCGGGACTTAGCCCGGATGTAACACCA
*
89744382 GCACAAATGCTCTTCGGGACTTAGCCCGGATGTAACACCA
1 GCACGAATGCTCTTCGGGACTTAGCCCGGATGTAACACCA
*
89744422 GCACGAATGCTCTTCGGGACTTAGCCTGGATGTAACACCA
1 GCACGAATGCTCTTCGGGACTTAGCCCGGATGTAACACCA
* * *
89744462 ACACGAATGCTCTTCGGAACTTAGCCCGGATATAACACCA
1 GCACGAATGCTCTTCGGGACTTAGCCCGGATGTAACACCA
89744502 TTTCCCATAC
Statistics
Matches: 111, Mismatches: 9, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
40 111 1.00
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.20
Consensus pattern (40 bp):
GCACGAATGCTCTTCGGGACTTAGCCCGGATGTAACACCA
Found at i:89746603 original size:2 final size:2
Alignment explanation
Indices: 89746596--89746625 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
89746586 ACTTTAATAC
*
89746596 AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
89746626 CCCTTTCAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:89748552 original size:5 final size:5
Alignment explanation
Indices: 89748542--89748609 Score: 50
Period size: 6 Copynumber: 12.8 Consensus size: 5
89748532 TATGTCTTTC
* *
89748542 AAAAT AAAAT --AAT AAAAGT GAAAT GAAAAT AAAAAT AAAAAT CAAAAGA
1 AAAAT AAAAT AAAAT AAAA-T AAAAT -AAAAT -AAAAT -AAAAT -AAAA-T
89748591 AAAAT AAAAT AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAA
89748610 ATAAGAGTAA
Statistics
Matches: 52, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
3 3 0.06
5 22 0.42
6 27 0.52
ACGTcount: A:0.76, C:0.01, G:0.06, T:0.16
Consensus pattern (5 bp):
AAAAT
Found at i:89748577 original size:12 final size:12
Alignment explanation
Indices: 89748562--89748611 Score: 52
Period size: 11 Copynumber: 4.3 Consensus size: 12
89748552 AATAAAAGTG
89748562 AAATGAAAATAA
1 AAATGAAAATAA
* *
89748574 AAATAAAAATCA
1 AAATGAAAATAA
89748586 AAA-GAAAA-ATA
1 AAATGAAAATA-A
89748597 AAAT-AAAATAA
1 AAATGAAAATAA
89748608 AAAT
1 AAAT
89748612 AAGAGTAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
11 17 0.55
12 14 0.45
ACGTcount: A:0.78, C:0.02, G:0.04, T:0.16
Consensus pattern (12 bp):
AAATGAAAATAA
Found at i:89748588 original size:7 final size:6
Alignment explanation
Indices: 89748562--89748629 Score: 68
Period size: 6 Copynumber: 11.5 Consensus size: 6
89748552 AATAAAAGTG
* * *
89748562 AAATGA AAATAA AAATAA AAATCA AAAGAA AAAT-A AAAT-A AAATAA
1 AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA
* *
89748608 AAATAA GAGTAA ATAATAA AAA
1 AAATAA AAATAA A-AATAA AAA
89748630 AAAGAGGATT
Statistics
Matches: 51, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
5 10 0.20
6 36 0.71
7 5 0.10
ACGTcount: A:0.76, C:0.01, G:0.06, T:0.16
Consensus pattern (6 bp):
AAATAA
Found at i:89748592 original size:23 final size:23
Alignment explanation
Indices: 89748542--89748604 Score: 65
Period size: 23 Copynumber: 2.7 Consensus size: 23
89748532 TATGTCTTTC
* * *
89748542 AAAATAAAATAATAAAAGTGAAATG
1 AAAAT-AAA-AATAAAAATCAAAAG
89748567 AAAATAAAAATAAAAATCAAAAG
1 AAAATAAAAATAAAAATCAAAAG
89748590 AAAA-ATAAAATAAAA
1 AAAATA-AAAATAAAA
89748605 TAAAAATAAG
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
22 1 0.03
23 25 0.74
24 3 0.09
25 5 0.15
ACGTcount: A:0.76, C:0.02, G:0.06, T:0.16
Consensus pattern (23 bp):
AAAATAAAAATAAAAATCAAAAG
Found at i:89748604 original size:29 final size:29
Alignment explanation
Indices: 89748542--89748632 Score: 91
Period size: 29 Copynumber: 3.1 Consensus size: 29
89748532 TATGTCTTTC
*
89748542 AAAATAAAATAATAAAAGT-GAAATGAAAATA
1 AAAAT-AAA-AATAAAAGTAAAAAT-AAAATA
89748573 AAAATAAAAATCAAAAG-AAAAATAAAAT-
1 AAAATAAAAAT-AAAAGTAAAAATAAAATA
*
89748601 AAAATAAAAATAAGAGTAAATAATAAAA-A
1 AAAATAAAAATAAAAGTAAA-AATAAAATA
89748630 AAA
1 AAA
89748633 GAGGATTCAA
Statistics
Matches: 53, Mismatches: 2, Indels: 12
0.79 0.03 0.18
Matches are distributed among these distances:
27 4 0.08
28 14 0.26
29 18 0.34
30 12 0.23
31 5 0.09
ACGTcount: A:0.76, C:0.01, G:0.07, T:0.16
Consensus pattern (29 bp):
AAAATAAAAATAAAAGTAAAAATAAAATA
Done.