Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167849.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_12, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 22966848
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 129000 characters in sequence are not A, C, G, or T
File 105 of 129
Found at i:17408066 original size:20 final size:21
Alignment explanation
Indices: 17408043--17408081 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
17408033 TAATTTTTTA
17408043 AAAAAACTT-AAAA-ATTTTCT
1 AAAAAA-TTCAAAATATTTTCT
17408063 AAAAAATTCAAAATATTTT
1 AAAAAATTCAAAATATTTT
17408082 TTGTATTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 2 0.12
20 10 0.59
21 5 0.29
ACGTcount: A:0.56, C:0.08, G:0.00, T:0.36
Consensus pattern (21 bp):
AAAAAATTCAAAATATTTTCT
Found at i:17408211 original size:20 final size:19
Alignment explanation
Indices: 17408173--17408211 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
17408163 TCCCAATTGT
*
17408173 CACATCAATAAGTCAATGC
1 CACATCAATAAGCCAATGC
*
17408192 CACATCAGTAAAGCCAATGC
1 CACATCAAT-AAGCCAATGC
17408212 TATGTCAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.41, C:0.28, G:0.13, T:0.18
Consensus pattern (19 bp):
CACATCAATAAGCCAATGC
Found at i:17408955 original size:28 final size:28
Alignment explanation
Indices: 17408919--17408978 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
17408909 ATTTCTTCAC
** *
17408919 AAAATTTATCTAATTAAAAAAAAAACAA
1 AAAATTTATAAAAATAAAAAAAAAACAA
* *
17408947 AAAATTTATAAAAATGAAAAAAAAATAA
1 AAAATTTATAAAAATAAAAAAAAAACAA
17408975 AAAA
1 AAAA
17408979 AAAACAAAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.73, C:0.03, G:0.02, T:0.22
Consensus pattern (28 bp):
AAAATTTATAAAAATAAAAAAAAAACAA
Found at i:17409436 original size:2 final size:2
Alignment explanation
Indices: 17409429--17409457 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
17409419 TAAACACCTT
17409429 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 T
17409458 GATTGCGAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:17410046 original size:16 final size:17
Alignment explanation
Indices: 17410007--17410049 Score: 63
Period size: 16 Copynumber: 2.6 Consensus size: 17
17409997 TAATTTTTAA
*
17410007 AAATTTTTAAATATGTT
1 AAATTTTTAAATATGTC
17410024 AAA-TTTTAAATAT-TC
1 AAATTTTTAAATATGTC
17410039 AAATTTTTAAA
1 AAATTTTTAAA
17410050 AAAATTTTAG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 4 0.17
16 17 0.71
17 3 0.12
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (17 bp):
AAATTTTTAAATATGTC
Found at i:17410438 original size:12 final size:13
Alignment explanation
Indices: 17410410--17410442 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
17410400 TACAAAAACT
*
17410410 AAAAAATTAGAAG
1 AAAAAATTAGAAA
17410423 AAAAAATTA-AAA
1 AAAAAATTAGAAA
17410435 AAAAAATT
1 AAAAAATT
17410443 GGGACTTAGC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 10 0.53
13 9 0.47
ACGTcount: A:0.76, C:0.00, G:0.06, T:0.18
Consensus pattern (13 bp):
AAAAAATTAGAAA
Found at i:17410493 original size:35 final size:34
Alignment explanation
Indices: 17410423--17410494 Score: 81
Period size: 35 Copynumber: 2.1 Consensus size: 34
17410413 AAATTAGAAG
* * * **
17410423 AAAAAATTAAAAAAAAAATTGGGACTTAGCCAAA
1 AAAAAATTAAAAAAAAAAATGAGACCTAGAAAAA
*
17410457 AAAAAATTGAAAAAAAAAAATGAGACCTATAAAAA
1 AAAAAATT-AAAAAAAAAAATGAGACCTAGAAAAA
17410492 AAA
1 AAA
17410495 TTATGATGAA
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
34 8 0.26
35 23 0.74
ACGTcount: A:0.68, C:0.07, G:0.10, T:0.15
Consensus pattern (34 bp):
AAAAAATTAAAAAAAAAAATGAGACCTAGAAAAA
Found at i:17410817 original size:8 final size:7
Alignment explanation
Indices: 17410801--17410848 Score: 53
Period size: 7 Copynumber: 6.7 Consensus size: 7
17410791 GATTAGTATT
17410801 AAAAAGA
1 AAAAAGA
17410808 AAAAATGA
1 AAAAA-GA
17410816 AAAAAGA
1 AAAAAGA
**
17410823 AAAATTA
1 AAAAAGA
17410830 AATAAA-A
1 AA-AAAGA
17410837 AAAAAGA
1 AAAAAGA
17410844 AAAAA
1 AAAAA
17410849 AATGAATCAC
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
6 3 0.09
7 23 0.66
8 9 0.26
ACGTcount: A:0.83, C:0.00, G:0.08, T:0.08
Consensus pattern (7 bp):
AAAAAGA
Found at i:17412310 original size:20 final size:22
Alignment explanation
Indices: 17412287--17412330 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 22
17412277 TAGATCCTAT
17412287 AAAAATTAAT-ATTTTTA-AAA
1 AAAAATTAATAATTTTTAGAAA
* *
17412307 AAAATTTATTAATTTTTAGAAA
1 AAAAATTAATAATTTTTAGAAA
17412329 AA
1 AA
17412331 GAAAGAGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 8 0.40
21 7 0.35
22 5 0.25
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (22 bp):
AAAAATTAATAATTTTTAGAAA
Found at i:17412607 original size:13 final size:13
Alignment explanation
Indices: 17412586--17412621 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 13
17412576 AAAAAATTTT
17412586 AAAATAAAAAAATAG
1 AAAA-AAAAAAA-AG
17412601 AAAAAAAAAAAAG
1 AAAAAAAAAAAAG
17412614 AAAAAAAA
1 AAAAAAAA
17412622 GGGGGAGCTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 10 0.48
14 7 0.33
15 4 0.19
ACGTcount: A:0.89, C:0.00, G:0.06, T:0.06
Consensus pattern (13 bp):
AAAAAAAAAAAAG
Found at i:17415681 original size:63 final size:63
Alignment explanation
Indices: 17415600--17415722 Score: 140
Period size: 63 Copynumber: 2.0 Consensus size: 63
17415590 ATGATATAAA
* *
17415600 AAAATAAAAAGATTATTTAAAACATTTT-TGCACATAAAACACCTTAAATAATCCTTTTATTAT
1 AAAATAAAAAGATCATTTAAAACATTTTATGCAC-GAAAACACCTTAAATAATCCTTTTATTAT
* * ** * ** *
17415663 AAAATACAAGGATCATTTAAGGCATTTTATGTACGAAAATGCCTTAAATGATCCTTTTAT
1 AAAATAAAAAGATCATTTAAAACATTTTATGCACGAAAACACCTTAAATAATCCTTTTAT
17415723 AAATAAATTA
Statistics
Matches: 49, Mismatches: 10, Indels: 2
0.80 0.16 0.03
Matches are distributed among these distances:
63 45 0.92
64 4 0.08
ACGTcount: A:0.43, C:0.13, G:0.08, T:0.36
Consensus pattern (63 bp):
AAAATAAAAAGATCATTTAAAACATTTTATGCACGAAAACACCTTAAATAATCCTTTTATTAT
Found at i:17415800 original size:13 final size:13
Alignment explanation
Indices: 17415782--17415811 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
17415772 GACAAACGCA
17415782 TTTTTCTAACAAT
1 TTTTTCTAACAAT
*
17415795 TTTTTCTATCAAT
1 TTTTTCTAACAAT
17415808 TTTT
1 TTTT
17415812 GTTACTAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.23, C:0.13, G:0.00, T:0.63
Consensus pattern (13 bp):
TTTTTCTAACAAT
Found at i:17422483 original size:7 final size:7
Alignment explanation
Indices: 17422471--17422501 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
17422461 ACATGCAAAA
17422471 TTTCCTT
1 TTTCCTT
17422478 TTTCCTT
1 TTTCCTT
17422485 TTTCCTT
1 TTTCCTT
17422492 TTTCCTT
1 TTTCCTT
17422499 TTT
1 TTT
17422502 TTTTTTTTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (7 bp):
TTTCCTT
Found at i:17431887 original size:213 final size:214
Alignment explanation
Indices: 17431491--17431904 Score: 611
Period size: 213 Copynumber: 1.9 Consensus size: 214
17431481 TACTACTATT
* *
17431491 ATTGTGTGTATTCAAATATATATCTTTATAATTGTTTTTGATTATATCGTTACAATATCTAATCT
1 ATTGTGTGTATTCAAATATATATC-TTATAATTGTTTTTAATTATATCATTACAATATCTAATCT
* * *
17431556 TACATAATTAAACCAATGTTATTTTTAATTTTATCAAAGTCAATCACATTGCTTATTCAAAATGT
65 CACATAATTAAACCAATGCTATTTTTAATTTTATCAAAGTCAATCACATTGCTCATTCAAAATGT
**
17431621 ACCCTTAGTAAAAAAGAGGCAAATTGAAACTCCTAAAAGAAGTC-AGGAAAAAAAAACGAAAGGA
130 ACCCTTAGTAAAAAAGAGGCAAATTGAAACTCCTAAAAGAAGTCAAAAAAAAAAAAAC-AAAGGA
17431685 ATATATAATTAATACACTGTC
194 ATATATAATTAATACACTGTC
** *
17431706 ATTGTGTGTATTCAAATATATATC-TATCGTTGTTTTTAATTATATCATTATAATATCTAATCTC
1 ATTGTGTGTATTCAAATATATATCTTATAATTGTTTTTAATTATATCATTACAATATCTAATCTC
* *
17431770 ACCTAATTAAACCAATGCTATTTTTAATTTTATTAAAGTCAATCAC-TCTGCTCATTC-AAATGT
66 ACATAATTAAACCAATGCTATTTTTAATTTTATCAAAGTCAATCACAT-TGCTCATTCAAAATGT
** * * *
17431833 ACTTTTAGTAATAAATAGGCAAATTGAAACTCTTAAAAGAAGTCAAAAAAAAAAAAAACAAAGGA
130 ACCCTTAGTAAAAAAGAGGCAAATTGAAACTCCTAAAAGAAGTC-AAAAAAAAAAAAACAAAGGA
17431898 ATATATA
194 ATATATA
17431905 TTTGAGACAA
Statistics
Matches: 179, Mismatches: 17, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
212 46 0.26
213 98 0.55
214 11 0.06
215 24 0.13
ACGTcount: A:0.42, C:0.13, G:0.10, T:0.36
Consensus pattern (214 bp):
ATTGTGTGTATTCAAATATATATCTTATAATTGTTTTTAATTATATCATTACAATATCTAATCTC
ACATAATTAAACCAATGCTATTTTTAATTTTATCAAAGTCAATCACATTGCTCATTCAAAATGTA
CCCTTAGTAAAAAAGAGGCAAATTGAAACTCCTAAAAGAAGTCAAAAAAAAAAAAACAAAGGAAT
ATATAATTAATACACTGTC
Found at i:17432468 original size:21 final size:21
Alignment explanation
Indices: 17432444--17432510 Score: 57
Period size: 21 Copynumber: 3.1 Consensus size: 21
17432434 ATTAGTTTGG
17432444 TAACTTATAATATAATTTTAA
1 TAACTTATAATATAATTTTAA
* * *
17432465 TAAC-TATTGATAAAATTTTGA
1 TAACTTA-TAATATAATTTTAA
*
17432486 TAACCTCT-TAATGTAATTTTAA
1 TAA-CT-TATAATATAATTTTAA
17432508 TAA
1 TAA
17432511 TTAACCTTAT
Statistics
Matches: 35, Mismatches: 7, Indels: 7
0.71 0.14 0.14
Matches are distributed among these distances:
20 2 0.06
21 18 0.51
22 14 0.40
24 1 0.03
ACGTcount: A:0.43, C:0.07, G:0.04, T:0.45
Consensus pattern (21 bp):
TAACTTATAATATAATTTTAA
Found at i:17432857 original size:22 final size:22
Alignment explanation
Indices: 17432838--17432891 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
17432828 ATTGATTTTC
* *
17432838 TACTAAGTTATGAATTATTTAT
1 TACTAAATTATGAATAATTTAT
*
17432860 TACTAAATTATTAATAATTTACT
1 TACTAAATTATGAATAATTTA-T
17432883 T-CTAAATTA
1 TACTAAATTA
17432892 CTGATGATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
22 26 0.93
23 2 0.07
ACGTcount: A:0.41, C:0.07, G:0.04, T:0.48
Consensus pattern (22 bp):
TACTAAATTATGAATAATTTAT
Found at i:17432999 original size:22 final size:22
Alignment explanation
Indices: 17432965--17433076 Score: 107
Period size: 22 Copynumber: 5.0 Consensus size: 22
17432955 ATTATCAATA
17432965 ATTAACTAATTTACTACTAAATT
1 ATTAA-TAATTTACTACTAAATT
* * * * * *
17432988 ATCACTACTTTACAATTAAGTT
1 ATTAATAATTTACTACTAAATT
* * *
17433010 ATTATTGATTTTCTACTAAATT
1 ATTAATAATTTACTACTAAATT
* *
17433032 ATGAATCATTTACTACTAAATT
1 ATTAATAATTTACTACTAAATT
*
17433054 ATTAATAATTTACTTCTAAATT
1 ATTAATAATTTACTACTAAATT
17433076 A
1 A
17433077 CTGATAGTTT
Statistics
Matches: 68, Mismatches: 21, Indels: 1
0.76 0.23 0.01
Matches are distributed among these distances:
22 65 0.96
23 3 0.04
ACGTcount: A:0.39, C:0.12, G:0.03, T:0.46
Consensus pattern (22 bp):
ATTAATAATTTACTACTAAATT
Found at i:17433044 original size:44 final size:44
Alignment explanation
Indices: 17432965--17433240 Score: 139
Period size: 44 Copynumber: 6.0 Consensus size: 44
17432955 ATTATCAATA
* * *
17432965 ATTAACTAATTTACTACTAAATTATCACTACTTTACAATTAAGTT
1 ATTAA-TAATTTACTACTAAATTATCAATACTTTACAACTAAATT
* * * * *
17433010 ATTATTGATTTTCTACTAAATTATGAAT-CATTTACTACTAAATT
1 ATTAATAATTTACTACTAAATTATCAATAC-TTTACAACTAAATT
* * * ***
17433054 ATTAATAATTTACTTCTAAATTA-CTGATAGTTTGTTA-TAAAGTT
1 ATTAATAATTTACTACTAAATTATC-AATACTTTACAACTAAA-TT
* * * * * * *
17433098 A-TAACTGATTTACTATTTAATTTATCAATTATTTATGATAAAATTATCAATA
1 ATTAA-TAATTTACTA-CTAAATTATCAA-TA-CT-T--TACAACTA--AATT
* *
17433150 ATTAACTAATTTACTACTAAATTATCACTGA-TTTACAACTAAGTT
1 ATTAA-TAATTTACTACTAAATTATCAAT-ACTTTACAACTAAATT
* * * *
17433195 ATTATTAATTTACTACTAAGTTATCAATAATTTACATCTAAATT
1 ATTAATAATTTACTACTAAATTATCAATACTTTACAACTAAATT
17433239 AT
1 AT
17433241 CAATGATATA
Statistics
Matches: 173, Mismatches: 40, Indels: 37
0.69 0.16 0.15
Matches are distributed among these distances:
43 9 0.05
44 102 0.59
45 17 0.10
46 3 0.02
47 7 0.04
48 1 0.01
49 1 0.01
50 3 0.02
51 3 0.02
52 12 0.07
53 15 0.09
ACGTcount: A:0.39, C:0.11, G:0.04, T:0.45
Consensus pattern (44 bp):
ATTAATAATTTACTACTAAATTATCAATACTTTACAACTAAATT
Found at i:17433126 original size:185 final size:185
Alignment explanation
Indices: 17432808--17433240 Score: 710
Period size: 185 Copynumber: 2.3 Consensus size: 185
17432798 AATTTATAAA
* * * * *
17432808 TGATTGACAATTAAGTCATCATTGATTTTCTACTAAGTTATGAATTATTTATTACTAAATTATTA
1 TGATTTACAATTAAGTTATTATTGATTTTCTACTAAGTTATGAATAATTTACTACTAAATTATTA
17432873 ATAATTTACTTCTAAATTACTGATGATTTGTTATAAAATTATAACTGATTTACTATTTAATTTAT
66 ATAATTTACTTCTAAATTACTGATGATTTGTTATAAAATTATAACTGATTTACTATTTAATTTAT
17432938 CAATTATTTATGATAAAATTATCAATAATTAACTAATTTACTACTAAATTATCAC
131 CAATTATTTATGATAAAATTATCAATAATTAACTAATTTACTACTAAATTATCAC
* *
17432993 T-ACTTTACAATTAAGTTATTATTGATTTTCTACTAAATTATGAATCATTTACTACTAAATTATT
1 TGA-TTTACAATTAAGTTATTATTGATTTTCTACTAAGTTATGAATAATTTACTACTAAATTATT
*
17433057 AATAATTTACTTCTAAATTACTGAT-AGTTTGTTATAAAGTTATAACTGATTTACTATTTAATTT
65 AATAATTTACTTCTAAATTACTGATGA-TTTGTTATAAAATTATAACTGATTTACTATTTAATTT
17433121 ATCAATTATTTATGATAAAATTATCAATAATTAACTAATTTACTACTAAATTATCAC
129 ATCAATTATTTATGATAAAATTATCAATAATTAACTAATTTACTACTAAATTATCAC
* * * *
17433178 TGATTTACAACTAAGTTATTATTAATTTACTACTAAGTTATCAATAATTTAC-ATCTAAATTAT
1 TGATTTACAATTAAGTTATTATTGATTTTCTACTAAGTTATGAATAATTTACTA-CTAAATTAT
17433241 CAATGATATA
Statistics
Matches: 231, Mismatches: 13, Indels: 8
0.92 0.05 0.03
Matches are distributed among these distances:
184 3 0.01
185 227 0.98
186 1 0.00
ACGTcount: A:0.39, C:0.10, G:0.05, T:0.45
Consensus pattern (185 bp):
TGATTTACAATTAAGTTATTATTGATTTTCTACTAAGTTATGAATAATTTACTACTAAATTATTA
ATAATTTACTTCTAAATTACTGATGATTTGTTATAAAATTATAACTGATTTACTATTTAATTTAT
CAATTATTTATGATAAAATTATCAATAATTAACTAATTTACTACTAAATTATCAC
Found at i:17433184 original size:22 final size:22
Alignment explanation
Indices: 17433156--17433253 Score: 99
Period size: 22 Copynumber: 4.5 Consensus size: 22
17433146 AATAATTAAC
*
17433156 TAATTTACTACTAAATTATCAC
1 TAATTTACTACTAAATTATCAA
* * * * *
17433178 TGATTTACAACTAAGTTATTAT
1 TAATTTACTACTAAATTATCAA
*
17433200 TAATTTACTACTAAGTTATCAA
1 TAATTTACTACTAAATTATCAA
17433222 TAATTTAC-ATCTAAATTATCAA
1 TAATTTACTA-CTAAATTATCAA
* *
17433244 TGATATACTA
1 TAATTTACTA
17433254 TTATGTTATT
Statistics
Matches: 62, Mismatches: 12, Indels: 3
0.81 0.16 0.04
Matches are distributed among these distances:
21 1 0.02
22 60 0.97
23 1 0.02
ACGTcount: A:0.41, C:0.13, G:0.04, T:0.42
Consensus pattern (22 bp):
TAATTTACTACTAAATTATCAA
Found at i:17433262 original size:22 final size:22
Alignment explanation
Indices: 17433236--17433284 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
17433226 TTACATCTAA
17433236 ATTATCAATG-ATATACTATTAT
1 ATTAT-AATGCATATACTATTAT
* * *
17433258 GTTATTATGCATTTACTATTAT
1 ATTATAATGCATATACTATTAT
17433280 ATTAT
1 ATTAT
17433285 TATTGATTTA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 3 0.14
22 19 0.86
ACGTcount: A:0.35, C:0.08, G:0.06, T:0.51
Consensus pattern (22 bp):
ATTATAATGCATATACTATTAT
Found at i:17433293 original size:22 final size:21
Alignment explanation
Indices: 17433243--17433299 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 21
17433233 TAAATTATCA
* *
17433243 ATGATATACTATTATGTTATT
1 ATGATTTACTATTATATTATT
17433264 ATGCATTTACTATTATATTATT
1 ATG-ATTTACTATTATATTATT
*
17433286 ATTGATTTATTATT
1 A-TGATTTACTATT
17433300 TAGTTTTCAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
21 3 0.10
22 26 0.84
23 2 0.06
ACGTcount: A:0.32, C:0.05, G:0.07, T:0.56
Consensus pattern (21 bp):
ATGATTTACTATTATATTATT
Found at i:17433347 original size:22 final size:22
Alignment explanation
Indices: 17433334--17433403 Score: 63
Period size: 22 Copynumber: 3.2 Consensus size: 22
17433324 ATCATCTTAG
17433334 ATTTATTATTAAATTAATCATA
1 ATTTATTATTAAATTAATCATA
* ** *
17433356 ATTTATTATCATGTT-ATTACTA
1 ATTTATTATTAAATTAATCA-TA
**
17433378 ATTTA-TATTAAATTACCCATA
1 ATTTATTATTAAATTAATCATA
17433399 ATTTA
1 ATTTA
17433404 CTGTTAAGTT
Statistics
Matches: 36, Mismatches: 10, Indels: 5
0.71 0.20 0.10
Matches are distributed among these distances:
21 16 0.44
22 20 0.56
ACGTcount: A:0.40, C:0.09, G:0.01, T:0.50
Consensus pattern (22 bp):
ATTTATTATTAAATTAATCATA
Found at i:17433415 original size:43 final size:44
Alignment explanation
Indices: 17433334--17433416 Score: 105
Period size: 43 Copynumber: 1.9 Consensus size: 44
17433324 ATCATCTTAG
* * *
17433334 ATTTATTATTAAATTAATCATAATTTATTATCATGTTATTACTA
1 ATTTATTATTAAATTAACCATAATTTACTATCAAGTTATTACTA
* * *
17433378 ATTTA-TATTAAATTACCCATAATTTACTGTTAAGTTATT
1 ATTTATTATTAAATTAACCATAATTTACTATCAAGTTATT
17433417 TAACTATTAA
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
43 28 0.85
44 5 0.15
ACGTcount: A:0.37, C:0.08, G:0.04, T:0.51
Consensus pattern (44 bp):
ATTTATTATTAAATTAACCATAATTTACTATCAAGTTATTACTA
Found at i:17433934 original size:22 final size:21
Alignment explanation
Indices: 17433905--17434031 Score: 85
Period size: 22 Copynumber: 5.8 Consensus size: 21
17433895 GATTGATAAT
17433905 TAAATTATAAGTTATTTATTAC
1 TAAATTATAA-TTATTTATTAC
* * *
17433927 TAAGTTATTAATGATTTACTAC
1 TAAATTA-TAATTATTTATTAC
* *
17433949 TAAATTATTAATAATTT-TCTTC
1 TAAATTA-TAATTATTTAT-TAC
* * * *
17433971 TAATTTATGAATAATTTATCAT
1 TAAATTAT-AATTATTTATTAC
*
17433993 TAAATTATGAATTATTTATTAT
1 TAAATTAT-AATTATTTATTAC
*
17434015 TAAGTTATAAATTATTT
1 TAAATTAT-AATTATTT
17434032 CTATTAAATT
Statistics
Matches: 85, Mismatches: 16, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
21 1 0.01
22 80 0.94
23 4 0.05
ACGTcount: A:0.39, C:0.05, G:0.05, T:0.51
Consensus pattern (21 bp):
TAAATTATAATTATTTATTAC
Found at i:17433955 original size:44 final size:43
Alignment explanation
Indices: 17433903--17434100 Score: 150
Period size: 44 Copynumber: 4.5 Consensus size: 43
17433893 ATGATTGATA
*
17433903 ATTAAATTATAAGTTATTTATTACTAAGTTATTAATGATTTACT
1 ATTAAATTATAA-TAATTTATTACTAAGTTATTAATGATTTACT
* * * * *
17433947 ACTAAATTATTAATAATTT-TCTTCTAATTTATGAATAATTTA-T
1 ATTAAATTA-TAATAATTTAT-TACTAAGTTATTAATGATTTACT
* * * *
17433990 CATTAAATTATGAATTATTTATTATTAAGTTATAAATTATTT-CT
1 -ATTAAATTAT-AATAATTTATTACTAAGTTATTAATGATTTACT
* ** * ** *
17434034 ATTAAATTGTTGGTGATTTAAAACTAAGTTATTAATGATTTATT
1 ATTAAATT-ATAATAATTTATTACTAAGTTATTAATGATTTACT
*
17434078 ATAAAATTATAACTAATTTATTA
1 ATTAAATTATAA-TAATTTATTA
17434101 TTATTTACCA
Statistics
Matches: 115, Mismatches: 30, Indels: 18
0.71 0.18 0.11
Matches are distributed among these distances:
43 34 0.30
44 77 0.67
45 4 0.03
ACGTcount: A:0.40, C:0.05, G:0.06, T:0.49
Consensus pattern (43 bp):
ATTAAATTATAATAATTTATTACTAAGTTATTAATGATTTACT
Found at i:17434087 original size:22 final size:21
Alignment explanation
Indices: 17433884--17434101 Score: 82
Period size: 22 Copynumber: 10.0 Consensus size: 21
17433874 AAGTATAAAA
* * *
17433884 AAATTATCAATGATTGATAATT
1 AAATTATTAATGATTTATTA-T
*
17433906 AAATTA-TAAGTTATTTATTACT
1 AAATTATTAA-TGATTTATTA-T
* *
17433928 AAGTTATTAATGATTTACTACT
1 AAATTATTAATGATTTATTA-T
* * *
17433950 AAATTATTAATAATTTTCTTCT
1 AAATTATTAATGA-TTTATTAT
* * * *
17433972 AATTTATGAATAATTTATCATT
1 AAATTATTAATGATTTATTA-T
* *
17433994 AAATTATGAATTATTTATTATT
1 AAATTATTAATGATTTATTA-T
* * * *
17434016 AAGTTATAAATTATTT-CTATT
1 AAATTATTAATGATTTATTA-T
* ** **
17434037 AAATTGTTGGTGATTTAAAACT
1 AAATTATTAATGATTTATTA-T
*
17434059 AAGTTATTAATGATTTATTAT
1 AAATTATTAATGATTTATTAT
*
17434080 AAAATTA-TAACTAATTTATTAT
1 -AAATTATTAA-TGATTTATTAT
17434102 TATTTACCAG
Statistics
Matches: 148, Mismatches: 41, Indels: 14
0.73 0.20 0.07
Matches are distributed among these distances:
21 24 0.16
22 117 0.79
23 7 0.05
ACGTcount: A:0.40, C:0.05, G:0.06, T:0.49
Consensus pattern (21 bp):
AAATTATTAATGATTTATTAT
Found at i:17434165 original size:22 final size:22
Alignment explanation
Indices: 17434140--17434198 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 22
17434130 TCAATGATTA
17434140 ACTAATTTATTATTAAATTATC
1 ACTAATTTATTATTAAATTATC
* * * *
17434162 ACTAATTCATAACTAAATTATT
1 ACTAATTTATTATTAAATTATC
* *
17434184 AGTAATTTACTATTA
1 ACTAATTTATTATTA
17434199 CGTTATTAAT
Statistics
Matches: 28, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.42, C:0.10, G:0.02, T:0.46
Consensus pattern (22 bp):
ACTAATTTATTATTAAATTATC
Found at i:17434204 original size:22 final size:22
Alignment explanation
Indices: 17434178--17434302 Score: 87
Period size: 22 Copynumber: 5.8 Consensus size: 22
17434168 TCATAACTAA
* *
17434178 ATTATTAGTAATTTACTATTAC
1 ATTATTAATAATTTACTATTAT
* * **
17434200 GTTATTAATGATTTACTGCTA-
1 ATTATTAATAATTTACTATTAT
* * *
17434221 A--ATTATTAATTTACTACTAA
1 ATTATTAATAATTTACTATTAT
*
17434241 ATTATCAATAATTTACTATTAT
1 ATTATTAATAATTTACTATTAT
*
17434263 ATT-TTTATATATTTACTATTAT
1 ATTATTAATA-ATTTACTATTAT
* * *
17434285 GTTATCATTAATTTACTA
1 ATTATTAATAATTTACTA
17434303 CTTAATTTTA
Statistics
Matches: 79, Mismatches: 19, Indels: 10
0.73 0.18 0.09
Matches are distributed among these distances:
19 15 0.19
20 1 0.01
21 4 0.05
22 56 0.71
23 3 0.04
ACGTcount: A:0.36, C:0.09, G:0.04, T:0.51
Consensus pattern (22 bp):
ATTATTAATAATTTACTATTAT
Found at i:17434225 original size:19 final size:19
Alignment explanation
Indices: 17434203--17434258 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 19
17434193 CTATTACGTT
* *
17434203 ATTAATGATTTACTGCTAA
1 ATTAATAATTTACTACTAA
*
17434222 ATTATTAATTTACTACTAA
1 ATTAATAATTTACTACTAA
17434241 ATTATCAATAATTTACTA
1 A-T-T-AATAATTTACTA
17434259 TTATATTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
19 17 0.57
20 1 0.03
21 1 0.03
22 11 0.37
ACGTcount: A:0.41, C:0.11, G:0.04, T:0.45
Consensus pattern (19 bp):
ATTAATAATTTACTACTAA
Found at i:17434455 original size:22 final size:21
Alignment explanation
Indices: 17434374--17434455 Score: 58
Period size: 22 Copynumber: 3.8 Consensus size: 21
17434364 GTTATTATTG
17434374 ATTTA-TATTAAATTATACATA
1 ATTTATTATTAAATTAT-CATA
* * * *
17434395 ATTTATTATTAAGTGATTACTT
1 ATTTATTATTAAATTATCA-TA
* * **
17434417 ATTAACTATTATGTTATCGATA
1 ATTTATTATTAAATTATC-ATA
17434439 ATTTATTATTAAATTAT
1 ATTTATTATTAAATTAT
17434456 ACTGATATAC
Statistics
Matches: 44, Mismatches: 14, Indels: 5
0.70 0.22 0.08
Matches are distributed among these distances:
21 6 0.14
22 37 0.84
23 1 0.02
ACGTcount: A:0.39, C:0.05, G:0.05, T:0.51
Consensus pattern (21 bp):
ATTTATTATTAAATTATCATA
Found at i:17434501 original size:22 final size:22
Alignment explanation
Indices: 17434476--17434564 Score: 88
Period size: 22 Copynumber: 4.0 Consensus size: 22
17434466 TTTTAAGTTT
*
17434476 TCAATGATTAACTACTAAATTA
1 TCAATGATTTACTACTAAATTA
* * *
17434498 TCAATTACTTACTACTAATTTA
1 TCAATGATTTACTACTAAATTA
* * *
17434520 TCATTTATTTACTACTTAATTA
1 TCAATGATTTACTACTAAATTA
** *
17434542 TTTATGATTTATTACTAAATTA
1 TCAATGATTTACTACTAAATTA
17434564 T
1 T
17434565 TTATAATTTA
Statistics
Matches: 53, Mismatches: 14, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 53 1.00
ACGTcount: A:0.37, C:0.12, G:0.02, T:0.48
Consensus pattern (22 bp):
TCAATGATTTACTACTAAATTA
Found at i:17434565 original size:22 final size:22
Alignment explanation
Indices: 17434486--17434576 Score: 78
Period size: 22 Copynumber: 4.1 Consensus size: 22
17434476 TCAATGATTA
** * *
17434486 ACTACTAAATTATCAATTACTT
1 ACTACTAAATTATTTATAATTT
*
17434508 ACTACTAATTTATCATT-T-ATTT
1 ACTACTAAATTAT--TTATAATTT
* *
17434530 ACTACTTAATTATTTATGATTT
1 ACTACTAAATTATTTATAATTT
*
17434552 ATTACTAAATTATTTATAATTT
1 ACTACTAAATTATTTATAATTT
17434574 ACT
1 ACT
17434577 GTCGTCAATT
Statistics
Matches: 55, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
20 2 0.04
21 1 0.02
22 51 0.93
23 1 0.02
ACGTcount: A:0.36, C:0.12, G:0.01, T:0.51
Consensus pattern (22 bp):
ACTACTAAATTATTTATAATTT
Found at i:17434688 original size:23 final size:23
Alignment explanation
Indices: 17434643--17434688 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
17434633 TTATTGCTAC
**
17434643 TAAGTTATCACTTATTTTTTATT
1 TAAGTTATCACTTATTTAATATT
17434666 TAAGTTATCA-TTGATTTAATATT
1 TAAGTTATCACTT-ATTTAATATT
17434689 ATGTTATTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 2 0.10
23 18 0.90
ACGTcount: A:0.30, C:0.07, G:0.07, T:0.57
Consensus pattern (23 bp):
TAAGTTATCACTTATTTAATATT
Found at i:17434805 original size:22 final size:21
Alignment explanation
Indices: 17434780--17434827 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
17434770 TACTAAAAAG
17434780 TTATCAATT-ATCTACTACTAAA
1 TTATCAATTCATCTACT--TAAA
*
17434802 TTATC-ATTCATTTACTTAAA
1 TTATCAATTCATCTACTTAAA
17434822 TTATCA
1 TTATCA
17434828 TTAATTTACT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
20 9 0.39
21 3 0.13
22 11 0.48
ACGTcount: A:0.38, C:0.17, G:0.00, T:0.46
Consensus pattern (21 bp):
TTATCAATTCATCTACTTAAA
Found at i:17434823 original size:20 final size:20
Alignment explanation
Indices: 17434798--17434837 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
17434788 TATCTACTAC
*
17434798 TAAATTATCATTCATTTACT
1 TAAATTATCATTAATTTACT
17434818 TAAATTATCATTAATTTACT
1 TAAATTATCATTAATTTACT
17434838 AATAAGTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.38, C:0.12, G:0.00, T:0.50
Consensus pattern (20 bp):
TAAATTATCATTAATTTACT
Found at i:17434906 original size:20 final size:20
Alignment explanation
Indices: 17434851--17434898 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
17434841 AAGTTATTGA
17434851 TAATTACAACTAAGTTATAC
1 TAATTACAACTAAGTTATAC
17434871 TAATTACAACTAAGTTATAC
1 TAATTACAACTAAGTTATAC
17434891 TAATTACA
1 TAATTACA
17434899 TTTAAGTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.46, C:0.15, G:0.04, T:0.35
Consensus pattern (20 bp):
TAATTACAACTAAGTTATAC
Found at i:17435326 original size:13 final size:13
Alignment explanation
Indices: 17435298--17435336 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
17435288 TGTCAAAAAT
*
17435298 ATAAAATAAATCAG
1 ATAAAA-AAATAAG
17435312 ATAAAAAAATAAG
1 ATAAAAAAATAAG
*
17435325 ATCAAAAAATAA
1 ATAAAAAAATAA
17435337 AAGTTAAATG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 17 0.74
14 6 0.26
ACGTcount: A:0.72, C:0.05, G:0.05, T:0.18
Consensus pattern (13 bp):
ATAAAAAAATAAG
Found at i:17437280 original size:149 final size:149
Alignment explanation
Indices: 17437067--17437504 Score: 596
Period size: 149 Copynumber: 2.9 Consensus size: 149
17437057 TTGCAATCTT
*
17437067 CATAAAAAATTTCTTTTACTAAAC-AAAAAAAATGATATATTTTTAATTGTTGCTTCATTCTTAT
1 CATAAAAAATTTCTTTTACTAAACGAAAAAATA-G-TATATTTTTAATTGTTGCTTCATTCTTAT
** *
17437131 TACTATCATTCAAAATAACTTTTTTGATATTTTGATGTTAATCTACTTCTCCATTTGGAAAAGAT
64 TACTATCATTCAAAATAACTTTTTTGATATTTTGATGCCAATCTACTTCTCCATTTGGAAAAGAG
* *
17437196 TAAAATATACTTT-GCTTTCTC
129 TAAAAAATA-TTTCGCATTCTC
* * * *
17437217 TATAAAAAATTTCTTTTACTAAACGAAAAGATAGTATATTTTTAATTGTTGCTTTATTTTTATTA
1 CATAAAAAATTTCTTTTACTAAACGAAAAAATAGTATATTTTTAATTGTTGCTTCATTCTTATTA
* * * * * *
17437282 CCATCATTCAAAATAACTATTTTAATATTTTTATGCCAATATAACTTCTCCATTT-GAAAAAAGT
66 CTATCATTCAAAATAACTTTTTTGATATTTTGATGCCAATCT-ACTTCTCCATTTGGAAAAGAGT
17437346 AAAAAATATTTCGCATTCTC
130 AAAAAATATTTCGCATTCTC
* * * *
17437366 CATAAAAAATTTCTTCTACTAAATGAAAAAATAATATATTTTTAATTGTTACTTCATTCTTATTA
1 CATAAAAAATTTCTTTTACTAAACGAAAAAATAGTATATTTTTAATTGTTGCTTCATTCTTATTA
* * *
17437431 CTATTATTCAAAATAACTTTTTTGATATTTTGTTGCCAATCAACTTCTCCATTTGG-AAAGAGTA
66 CTATCATTCAAAATAACTTTTTTGATATTTTGATGCCAATCTACTTCTCCATTTGGAAAAGAGT-
17437495 AAAAAATATT
130 AAAAAATATT
17437505 GTAAGAGATA
Statistics
Matches: 250, Mismatches: 33, Indels: 11
0.85 0.11 0.04
Matches are distributed among these distances:
148 21 0.08
149 187 0.75
150 36 0.14
151 6 0.02
ACGTcount: A:0.37, C:0.13, G:0.06, T:0.43
Consensus pattern (149 bp):
CATAAAAAATTTCTTTTACTAAACGAAAAAATAGTATATTTTTAATTGTTGCTTCATTCTTATTA
CTATCATTCAAAATAACTTTTTTGATATTTTGATGCCAATCTACTTCTCCATTTGGAAAAGAGTA
AAAAATATTTCGCATTCTC
Found at i:17439024 original size:17 final size:16
Alignment explanation
Indices: 17438977--17439024 Score: 55
Period size: 17 Copynumber: 3.0 Consensus size: 16
17438967 TTAATTTTTC
17438977 TTTTATT-TAAAAAA-
1 TTTTATTATAAAAAAT
*
17438991 TTTTATTATACATAAAT
1 TTTTATTATA-AAAAAT
17439008 TTTTATTATATAAAAAT
1 TTTTATTATA-AAAAAT
17439025 ATTAAAATAC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
14 7 0.25
15 2 0.07
16 4 0.14
17 15 0.54
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (16 bp):
TTTTATTATAAAAAAT
Found at i:17439035 original size:33 final size:30
Alignment explanation
Indices: 17438977--17439042 Score: 78
Period size: 33 Copynumber: 2.1 Consensus size: 30
17438967 TTAATTTTTC
* **
17438977 TTTTATTTAAAAAATTTTATTATACATAAAT
1 TTTTATTTAAAAAATATTAAAATACAT-AAT
17439008 TTTTATTATATAAAAATATTAAAATACATAAT
1 TTTTATT-TA-AAAAATATTAAAATACATAAT
17439040 TTT
1 TTT
17439043 AAAAAATAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
31 7 0.23
32 8 0.27
33 15 0.50
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (30 bp):
TTTTATTTAAAAAATATTAAAATACATAAT
Found at i:17440237 original size:16 final size:17
Alignment explanation
Indices: 17440203--17440236 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
17440193 ATATTTTTTT
*
17440203 ATCTAATTATAAAAAAA
1 ATCTAATAATAAAAAAA
17440220 ATCTAATAATAAAAAAA
1 ATCTAATAATAAAAAAA
17440237 TTCATTTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.68, C:0.06, G:0.00, T:0.26
Consensus pattern (17 bp):
ATCTAATAATAAAAAAA
Found at i:17440655 original size:15 final size:16
Alignment explanation
Indices: 17440635--17440665 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
17440625 AATCTGGATG
17440635 ACAACA-AAAAGAAAA
1 ACAACATAAAAGAAAA
17440650 ACAACATAAAAGAAAA
1 ACAACATAAAAGAAAA
17440666 GGGGTGGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.77, C:0.13, G:0.06, T:0.03
Consensus pattern (16 bp):
ACAACATAAAAGAAAA
Found at i:17445100 original size:26 final size:26
Alignment explanation
Indices: 17445081--17445133 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
17445071 TGATGATTTT
*
17445081 TGAAGTACAATAATAGTGATTAAAAC
1 TGAAGTACAATAATAGTGATGAAAAC
*
17445107 TGAAGTACAATAATAGTGATTAAAAC
1 TGAAGTACAATAATAGTGATGAAAAC
17445133 T
1 T
17445134 TATATTTCAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.49, C:0.08, G:0.15, T:0.28
Consensus pattern (26 bp):
TGAAGTACAATAATAGTGATGAAAAC
Found at i:17450608 original size:16 final size:17
Alignment explanation
Indices: 17450587--17450626 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
17450577 TAATTTTTAA
17450587 TATATTT-AAATAAATT
1 TATATTTAAAATAAATT
*
17450603 TATATTTAAAATAATTT
1 TATATTTAAAATAAATT
*
17450620 TTTATTT
1 TATATTT
17450627 TATAATAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 7 0.33
17 14 0.67
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
TATATTTAAAATAAATT
Found at i:17451189 original size:13 final size:12
Alignment explanation
Indices: 17451162--17451209 Score: 55
Period size: 11 Copynumber: 4.1 Consensus size: 12
17451152 AGTAAATTTG
*
17451162 ATAATTTTAAAT
1 ATAATATTAAAT
17451174 ATAATATTATAAT
1 ATAATATTA-AAT
17451187 ATAATA-TAAAT
1 ATAATATTAAAT
*
17451198 AAAATA-TAAAT
1 ATAATATTAAAT
17451209 A
1 A
17451210 AAAAAATAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
11 14 0.42
12 10 0.30
13 9 0.27
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
ATAATATTAAAT
Found at i:17451215 original size:14 final size:15
Alignment explanation
Indices: 17451184--17451222 Score: 53
Period size: 14 Copynumber: 2.6 Consensus size: 15
17451174 ATAATATTAT
17451184 AATATAATATAAATAA
1 AATATAA-ATAAATAA
17451200 AATATAAATAAA-AA
1 AATATAAATAAATAA
*
17451214 AATAAAAAT
1 AATATAAAT
17451223 TTTAATAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 10 0.45
15 5 0.23
16 7 0.32
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (15 bp):
AATATAAATAAATAA
Found at i:17457586 original size:8 final size:8
Alignment explanation
Indices: 17457564--17457594 Score: 53
Period size: 8 Copynumber: 3.8 Consensus size: 8
17457554 ATTCATAAAC
17457564 TAAATATT
1 TAAATATT
17457572 ATAAATATT
1 -TAAATATT
17457581 TAAATATT
1 TAAATATT
17457589 TAAATA
1 TAAATA
17457595 CATAATTTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 14 0.64
9 8 0.36
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (8 bp):
TAAATATT
Found at i:17458934 original size:15 final size:16
Alignment explanation
Indices: 17458914--17458944 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
17458904 TAAGAAATCC
17458914 ATTAAAAGAAA-AAAA
1 ATTAAAAGAAATAAAA
17458929 ATTAAAAGAAATAAAA
1 ATTAAAAGAAATAAAA
17458945 CACTAAAGCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.77, C:0.00, G:0.06, T:0.16
Consensus pattern (16 bp):
ATTAAAAGAAATAAAA
Found at i:17469574 original size:29 final size:29
Alignment explanation
Indices: 17469540--17469634 Score: 99
Period size: 29 Copynumber: 3.3 Consensus size: 29
17469530 GTAATTTTTA
17469540 AAAAATATTTATTATAATTTTTTTAGTTG
1 AAAAATATTTATTATAATTTTTTTAGTTG
* * * * *
17469569 AAAAATATTTGA--AGGAA--TGTTAATTTA
1 AAAAATATTT-ATTA-TAATTTTTTTAGTTG
17469596 AAAAATATTTATTATAATTTTTTTAGTTG
1 AAAAATATTTATTATAATTTTTTTAGTTG
17469625 AAAAATATTT
1 AAAAATATTT
17469635 GAAGGGATGT
Statistics
Matches: 50, Mismatches: 10, Indels: 12
0.69 0.14 0.17
Matches are distributed among these distances:
26 1 0.02
27 18 0.36
28 2 0.04
29 28 0.56
30 1 0.02
ACGTcount: A:0.43, C:0.00, G:0.08, T:0.48
Consensus pattern (29 bp):
AAAAATATTTATTATAATTTTTTTAGTTG
Found at i:17469599 original size:55 final size:56
Alignment explanation
Indices: 17469536--17469686 Score: 277
Period size: 56 Copynumber: 2.7 Consensus size: 56
17469526 TGATGTAATT
17469536 TTTAAAAAATATTTATTATAATTTTTTTAGTTGAAAAATATTTGAAGGAATGTTAA
1 TTTAAAAAATATTTATTATAATTTTTTTAGTTGAAAAATATTTGAAGGAATGTTAA
*
17469592 TTTAAAAAATATTTATTATAATTTTTTTAGTTGAAAAATATTTGAAGGGATGTTAA
1 TTTAAAAAATATTTATTATAATTTTTTTAGTTGAAAAATATTTGAAGGAATGTTAA
*
17469648 TTTAAAAAATATTTATTATAA-TTTTTTAGTTGATAAATA
1 TTTAAAAAATATTTATTATAATTTTTTTAGTTGAAAAATA
17469687 ATTAAATTTT
Statistics
Matches: 93, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
55 17 0.18
56 76 0.82
ACGTcount: A:0.42, C:0.00, G:0.10, T:0.48
Consensus pattern (56 bp):
TTTAAAAAATATTTATTATAATTTTTTTAGTTGAAAAATATTTGAAGGAATGTTAA
Found at i:17469605 original size:27 final size:27
Alignment explanation
Indices: 17469569--17469661 Score: 82
Period size: 27 Copynumber: 3.4 Consensus size: 27
17469559 TTTTTAGTTG
17469569 AAAAATATTTGAAGGAATGTTAATTTA
1 AAAAATATTTGAAGGAATGTTAATTTA
* * * * *
17469596 AAAAATATTT-ATTA-TAATTTTTTTAGTTG
1 AAAAATATTTGA--AGGAA--TGTTAATTTA
*
17469625 AAAAATATTTGAAGGGATGTTAATTTA
1 AAAAATATTTGAAGGAATGTTAATTTA
17469652 AAAAATATTT
1 AAAAATATTT
17469662 ATTATAATTT
Statistics
Matches: 49, Mismatches: 11, Indels: 12
0.68 0.15 0.17
Matches are distributed among these distances:
26 1 0.02
27 28 0.57
28 2 0.04
29 17 0.35
30 1 0.02
ACGTcount: A:0.45, C:0.00, G:0.12, T:0.43
Consensus pattern (27 bp):
AAAAATATTTGAAGGAATGTTAATTTA
Found at i:17470352 original size:14 final size:14
Alignment explanation
Indices: 17470333--17470362 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
17470323 TTATAATTGT
17470333 TTATATATCAATAG
1 TTATATATCAATAG
17470347 TTATATATCAATAG
1 TTATATATCAATAG
17470361 TT
1 TT
17470363 TTTAATTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.47
Consensus pattern (14 bp):
TTATATATCAATAG
Found at i:17473249 original size:111 final size:107
Alignment explanation
Indices: 17473018--17473250 Score: 344
Period size: 111 Copynumber: 2.1 Consensus size: 107
17473008 ATAAAAGGTA
* *
17473018 AAAAATTACAAAAAATTAAAAAACAAACTGTTGAGGAAAAATATAAACTGTGGATCCCGTACCCA
1 AAAAATTAAAAAAAATTAAAAAACAAACTATTGAGGAAAAATATAAACTGTGGATCCCGTACCCA
17473083 AAAAATAAATTAAAAAAATAGAATGTGGACCTATACAACTTT
66 AAAAATAAATTAAAAAAATAGAATGTGGACCTATACAACTTT
** * *
17473125 AAAAATTTTAAAAAA-TATAAAAA-TAACTATTGAGGAAAAATATAAACCTAGGTGTGGATTCCG
1 AAAAATTAAAAAAAATTA-AAAAACAAACTATTGAGGAAAAATATAAA-C----TGTGGATCCCG
17473188 TACCCAAAAAATAAATTAAAAAAATAGAATGTGGACCTATACAACTTT
60 TACCCAAAAAATAAATTAAAAAAATAGAATGTGGACCTATACAACTTT
17473236 AAAAATTAAAAAAAA
1 AAAAATTAAAAAAAA
17473251 AAAGTAGGCC
Statistics
Matches: 113, Mismatches: 7, Indels: 8
0.88 0.05 0.06
Matches are distributed among these distances:
106 23 0.20
107 19 0.17
111 71 0.63
ACGTcount: A:0.55, C:0.11, G:0.11, T:0.24
Consensus pattern (107 bp):
AAAAATTAAAAAAAATTAAAAAACAAACTATTGAGGAAAAATATAAACTGTGGATCCCGTACCCA
AAAAATAAATTAAAAAAATAGAATGTGGACCTATACAACTTT
Found at i:17473568 original size:26 final size:27
Alignment explanation
Indices: 17473530--17473582 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 27
17473520 AAGTTATTTT
17473530 TATTTTTAAAAATT-TTATAATATTTCA
1 TATTTTTAAAAATTATT-TAATATTTCA
* *
17473557 TATTTTT-GAAATTATTTAATTTTTCA
1 TATTTTTAAAAATTATTTAATATTTCA
17473583 AAAAATTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
26 14 0.61
27 9 0.39
ACGTcount: A:0.36, C:0.04, G:0.02, T:0.58
Consensus pattern (27 bp):
TATTTTTAAAAATTATTTAATATTTCA
Found at i:17473637 original size:29 final size:29
Alignment explanation
Indices: 17473574--17473638 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
17473564 GAAATTATTT
*
17473574 AATTTTTCAAAAAATTTTTAAATTCTTAG
1 AATTTTTCAAAAAATTTTTAAATTCTTAA
* * ** *
17473603 AGTTTTTCTAAAAATTTTTAGTTTTTTAA
1 AATTTTTCAAAAAATTTTTAAATTCTTAA
17473632 AATTTTT
1 AATTTTT
17473639 TTATATATTT
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.35, C:0.05, G:0.05, T:0.55
Consensus pattern (29 bp):
AATTTTTCAAAAAATTTTTAAATTCTTAA
Found at i:17473641 original size:19 final size:19
Alignment explanation
Indices: 17473603--17473638 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
17473593 AAATTCTTAG
17473603 AGTTTTTCTAAAAATTTTT
1 AGTTTTTCTAAAAATTTTT
17473622 AGTTTTT-T-AAAATTTTT
1 AGTTTTTCTAAAAATTTTT
17473639 TTATATATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.53
18 1 0.06
19 7 0.41
ACGTcount: A:0.31, C:0.03, G:0.06, T:0.61
Consensus pattern (19 bp):
AGTTTTTCTAAAAATTTTT
Found at i:17473741 original size:17 final size:17
Alignment explanation
Indices: 17473721--17473779 Score: 57
Period size: 17 Copynumber: 3.4 Consensus size: 17
17473711 TAATTTTAAG
17473721 AAAATTTAATTTTTATT
1 AAAATTTAATTTTTATT
* *
17473738 AAAATTTTCATTTTT-TAA
1 AAAA-TTTAATTTTTAT-T
**
17473756 AAAATTGGATTTTTATT
1 AAAATTTAATTTTTATT
17473773 AAAATTT
1 AAAATTT
17473780 TCAAAAATTT
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
17 19 0.58
18 14 0.42
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.54
Consensus pattern (17 bp):
AAAATTTAATTTTTATT
Found at i:17473752 original size:18 final size:18
Alignment explanation
Indices: 17473729--17473782 Score: 65
Period size: 18 Copynumber: 3.1 Consensus size: 18
17473719 AGAAAATTTA
17473729 ATTTTTATTAAAATTTTC
1 ATTTTTATTAAAATTTTC
* * **
17473747 ATTTTT-TAAAAAATTGG
1 ATTTTTATTAAAATTTTC
17473764 ATTTTTATTAAAATTTTC
1 ATTTTTATTAAAATTTTC
17473782 A
1 A
17473783 AAAATTTTCA
Statistics
Matches: 27, Mismatches: 8, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
17 13 0.48
18 14 0.52
ACGTcount: A:0.37, C:0.04, G:0.04, T:0.56
Consensus pattern (18 bp):
ATTTTTATTAAAATTTTC
Found at i:17473768 original size:35 final size:36
Alignment explanation
Indices: 17473714--17473782 Score: 113
Period size: 35 Copynumber: 1.9 Consensus size: 36
17473704 ATTTTTTTAA
*
17473714 TTTTAAGAAAATTTAATTTTTATTAAAATTTTCATT
1 TTTTAAGAAAATTGAATTTTTATTAAAATTTTCATT
*
17473750 TTTTAA-AAAATTGGATTTTTATTAAAATTTTCA
1 TTTTAAGAAAATTGAATTTTTATTAAAATTTTCA
17473783 AAAATTTTCA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
35 25 0.81
36 6 0.19
ACGTcount: A:0.39, C:0.03, G:0.04, T:0.54
Consensus pattern (36 bp):
TTTTAAGAAAATTGAATTTTTATTAAAATTTTCATT
Found at i:17473800 original size:26 final size:26
Alignment explanation
Indices: 17473771--17473835 Score: 76
Period size: 26 Copynumber: 2.5 Consensus size: 26
17473761 TGGATTTTTA
17473771 TTAAAATTTTCAAAAATTTTCAATTT
1 TTAAAATTTTCAAAAATTTTCAATTT
* * * *
17473797 TTAAAATTATCATAATTTTTTAATTT
1 TTAAAATTTTCAAAAATTTTCAATTT
*
17473823 TAAAAATGTTTCA
1 TTAAAAT-TTTCA
17473836 TTTTTTTATT
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
26 28 0.88
27 4 0.12
ACGTcount: A:0.42, C:0.06, G:0.02, T:0.51
Consensus pattern (26 bp):
TTAAAATTTTCAAAAATTTTCAATTT
Found at i:17473958 original size:10 final size:10
Alignment explanation
Indices: 17473902--17474003 Score: 93
Period size: 10 Copynumber: 10.1 Consensus size: 10
17473892 TACTTTATTA
17473902 AAAATTTTTT
1 AAAATTTTTT
*
17473912 AGAAA-TTTTC
1 A-AAATTTTTT
*
17473922 AAAATGTTTT
1 AAAATTTTTT
*
17473932 AGAATTTTTT
1 AAAATTTTTT
*
17473942 GAGAATTTTTT
1 -AAAATTTTTT
17473953 AAAA--TTTT
1 AAAATTTTTT
17473961 AAAATTTTTT
1 AAAATTTTTT
* *
17473971 AGAAGTTTTT
1 AAAATTTTTT
17473981 AAAAGTTTTTTT
1 AAAA--TTTTTT
17473993 AAAATTTTTT
1 AAAATTTTTT
17474003 A
1 A
17474004 TGCTGACGTA
Statistics
Matches: 75, Mismatches: 10, Indels: 14
0.76 0.10 0.14
Matches are distributed among these distances:
8 8 0.11
9 3 0.04
10 42 0.56
11 13 0.17
12 9 0.12
ACGTcount: A:0.37, C:0.01, G:0.08, T:0.54
Consensus pattern (10 bp):
AAAATTTTTT
Found at i:17474124 original size:7 final size:7
Alignment explanation
Indices: 17474114--17474138 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
17474104 ATGAAAATTG
17474114 AAATATC
1 AAATATC
17474121 AAATATC
1 AAATATC
17474128 AAATATC
1 AAATATC
17474135 AAAT
1 AAAT
17474139 TTTATTTTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (7 bp):
AAATATC
Found at i:17476648 original size:30 final size:29
Alignment explanation
Indices: 17476598--17476663 Score: 96
Period size: 30 Copynumber: 2.2 Consensus size: 29
17476588 TTTAAATACA
*
17476598 CCTTTATACTTTTATTGTATCCAAAAAAG
1 CCTTTATACTTTGATTGTATCCAAAAAAG
* *
17476627 GCTTTATACTTTGATTTGTATCCAAATAAG
1 CCTTTATACTTTGA-TTGTATCCAAAAAAG
17476657 CCTTTAT
1 CCTTTAT
17476664 TTCAAATAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
29 12 0.38
30 20 0.62
ACGTcount: A:0.30, C:0.17, G:0.09, T:0.44
Consensus pattern (29 bp):
CCTTTATACTTTGATTGTATCCAAAAAAG
Found at i:17476759 original size:61 final size:57
Alignment explanation
Indices: 17476686--17476820 Score: 139
Period size: 61 Copynumber: 2.3 Consensus size: 57
17476676 AATGATTTAT
* *
17476686 GTTAAG-GTCTTATTTAGGTAT-AAATTAAAAGTTTAAAGGTTTATTTGAATACAAATTAAAG
1 GTTAAGAG-CTTATTTAGGT-TCAAATT-AAAG-ATAAAGGTTTATTTGAATAC-AA-TAAAA
* * *
17476747 GTTAAGAGCTTATTTGGGTTCAAATTAAAGATCAAGGTTTATTTGAATGCAATAAAA
1 GTTAAGAGCTTATTTAGGTTCAAATTAAAGATAAAGGTTTATTTGAATACAATAAAA
*
17476804 ATATAAGAGCTTATTTA
1 GT-TAAGAGCTTATTTA
17476821 AGTAAAGTTG
Statistics
Matches: 64, Mismatches: 7, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
57 5 0.08
58 15 0.23
59 17 0.27
60 5 0.08
61 21 0.33
62 1 0.02
ACGTcount: A:0.40, C:0.05, G:0.17, T:0.38
Consensus pattern (57 bp):
GTTAAGAGCTTATTTAGGTTCAAATTAAAGATAAAGGTTTATTTGAATACAATAAAA
Found at i:17476762 original size:30 final size:30
Alignment explanation
Indices: 17476726--17476819 Score: 86
Period size: 30 Copynumber: 3.2 Consensus size: 30
17476716 GTTTAAAGGT
*
17476726 TTATTTGAATACAAATTAAAGGTTAAGAGC
1 TTATTTGAATACAAATTAAAGATTAAGAGC
** * * *
17476756 TTATTTGGGTTCAAATTAAAGATCAAG-GT
1 TTATTTGAATACAAATTAAAGATTAAGAGC
* *
17476785 TTATTTGAATGC-AA-TAAAAATATAAGAGC
1 TTATTTGAATACAAATTAAAGAT-TAAGAGC
17476814 TTATTT
1 TTATTT
17476820 AAGTAAAGTT
Statistics
Matches: 50, Mismatches: 12, Indels: 5
0.75 0.18 0.07
Matches are distributed among these distances:
27 6 0.12
28 5 0.10
29 17 0.34
30 22 0.44
ACGTcount: A:0.40, C:0.06, G:0.16, T:0.37
Consensus pattern (30 bp):
TTATTTGAATACAAATTAAAGATTAAGAGC
Found at i:17477724 original size:9 final size:8
Alignment explanation
Indices: 17477705--17477755 Score: 59
Period size: 9 Copynumber: 6.1 Consensus size: 8
17477695 TTTTGCTAAT
17477705 AAAAAATA
1 AAAAAATA
17477713 AAAAAAT-
1 AAAAAATA
17477720 AAAAAATGA
1 AAAAAAT-A
*
17477729 AAAAACTTA
1 AAAAA-ATA
17477738 AAAAAATGA
1 AAAAAAT-A
17477747 AAAAAATA
1 AAAAAATA
17477755 A
1 A
17477756 GTAGTTGAGT
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
7 7 0.19
8 10 0.27
9 19 0.51
10 1 0.03
ACGTcount: A:0.80, C:0.02, G:0.04, T:0.14
Consensus pattern (8 bp):
AAAAAATA
Found at i:17478535 original size:12 final size:13
Alignment explanation
Indices: 17478495--17478535 Score: 50
Period size: 12 Copynumber: 3.3 Consensus size: 13
17478485 TTTTGTATTT
*
17478495 TTTATATATTTTA
1 TTTATGTATTTTA
17478508 TTTA-GTATTTTA
1 TTTATGTATTTTA
*
17478520 TTTATGTGTTTT-
1 TTTATGTATTTTA
17478532 TTTA
1 TTTA
17478536 ATAATTTTGC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 15 0.60
13 10 0.40
ACGTcount: A:0.22, C:0.00, G:0.07, T:0.71
Consensus pattern (13 bp):
TTTATGTATTTTA
Found at i:17478788 original size:10 final size:11
Alignment explanation
Indices: 17478760--17478793 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
17478750 TCAAACAAAA
17478760 AATAAAAATTT
1 AATAAAAATTT
17478771 AATAAAAATTT
1 AATAAAAATTT
*
17478782 AATAAAATTTT
1 AATAAAAATTT
17478793 A
1 A
17478794 GAATTAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
AATAAAAATTT
Found at i:17483178 original size:28 final size:28
Alignment explanation
Indices: 17483119--17483187 Score: 90
Period size: 26 Copynumber: 2.5 Consensus size: 28
17483109 TGGATGAAAG
*
17483119 ATAAAAA-AAAAAAAGAAAAAAAATGGG
1 ATAAAAATAAAAAAAGAAAAAAAATGGA
*
17483146 A-AAAAATAAAAAATG-AAAAAAATGGTA
1 ATAAAAATAAAAAAAGAAAAAAAATGG-A
17483173 ATAAAAATAAAAAAA
1 ATAAAAATAAAAAAA
17483188 AAAGAAAGAG
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
26 15 0.42
27 9 0.25
28 12 0.33
ACGTcount: A:0.78, C:0.00, G:0.10, T:0.12
Consensus pattern (28 bp):
ATAAAAATAAAAAAAGAAAAAAAATGGA
Found at i:17483797 original size:22 final size:22
Alignment explanation
Indices: 17483764--17483806 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
17483754 AACTTATGAG
17483764 ATGTGGTCAAAT-GATGAAAATA
1 ATGTGGTCAAATGGAT-AAAATA
17483786 ATGTGGAT-AAATGGATAAAAT
1 ATGTGG-TCAAATGGATAAAAT
17483807 TCATTTTAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.47, C:0.02, G:0.23, T:0.28
Consensus pattern (22 bp):
ATGTGGTCAAATGGATAAAATA
Found at i:17486972 original size:119 final size:119
Alignment explanation
Indices: 17486832--17487186 Score: 429
Period size: 119 Copynumber: 3.0 Consensus size: 119
17486822 TGGTTAATAA
* *
17486832 TAAAAATAATAATTTCAAAAAAAAAAATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCTTTG
1 TAAAAATAA-ATTTTC-AAAAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTT-TTTG
* * * *
17486897 AAAAT-AAGCATTCCAAAAAATATTTTTTGGAAAAAATTGAAAGTATCAATTTTTC-T
63 AAAATAAAG-TTTCTAAAAAATATTTTTGGGAAAAAGTTGAAAGTATCAATTTTTCAT
* *
17486953 TAAAAATAAATTTTCAAAAAAAAATTTTTTTTGAGGAAAAGTTGAAAGTATCAATTTTTTTCGAA
1 TAAAAATAAATTTTCAAAAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTTT-GAA
* *
17487018 ATTAAAGTTTTTAAAAAATATTTTTGGGAAAAAGTTGAAAGTATCAA-TTTTCAT
65 AATAAAGTTTCTAAAAAATATTTTTGGGAAAAAGTTGAAAGTATCAATTTTTCAT
* * * * *
17487072 TAAAAATAAATTTT---TAAAAAAA-AGTTTTAAGGAAAAGTTGAAAGTATCAATTTTTCTCAAA
1 TAAAAATAAATTTTCAAAAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTTTGAAA
* *
17487133 ATTAAAGTTTTCTAAAAAA-ATATTTTGGGGAGAAGTTGAAAGTATCAATTTTTC
66 A-TAAAG-TTTCTAAAAAATAT-TTTTGGGAAAAAGTTGAAAGTATCAATTTTTC
17487187 CTATACAAAA
Statistics
Matches: 206, Mismatches: 21, Indels: 18
0.84 0.09 0.07
Matches are distributed among these distances:
114 3 0.01
115 38 0.18
116 40 0.19
117 5 0.02
118 8 0.04
119 95 0.46
120 8 0.04
121 9 0.04
ACGTcount: A:0.46, C:0.05, G:0.11, T:0.37
Consensus pattern (119 bp):
TAAAAATAAATTTTCAAAAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTTTGAAA
ATAAAGTTTCTAAAAAATATTTTTGGGAAAAAGTTGAAAGTATCAATTTTTCAT
Found at i:17487178 original size:59 final size:60
Alignment explanation
Indices: 17486852--17487186 Score: 343
Period size: 58 Copynumber: 5.7 Consensus size: 60
17486842 AATTTCAAAA
** **
17486852 AAAAAAATATTTTTGAGAAAAAGTTGAAAGTATCAA-TTTTCTTTGAAAAT-AAGCATTC-
1 AAAAAAATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTTC-TCAAAAATAAAGTTTTCT
* * * *
17486910 CAAAAAATATTTTTTG-GAAAAAATTGAAAGTATCAATTTTTCTTAAAAATAAA-TTTTCAA
1 AAAAAAATA-TTTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTCAAAAATAAAGTTTTC-T
* * * * *
17486970 AAAAAAATTTTTTTTGAGGAAAAGTTGAAAGTATCAATTTTTTTCGAAATTAAAGTTTT-T
1 AAAAAAA-TATTTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTCAAAAATAAAGTTTTCT
* *
17487030 -AAAAAATATTTTTGGGAAAAAGTTGAAAGTATCAA-TTTTCATTAAAAATAAA-TTTT-T
1 AAAAAAATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTTC-TCAAAAATAAAGTTTTCT
* * * *
17487087 AAAAAAA-AGTTTTAAGGAAAAGTTGAAAGTATCAATTTTTCTCAAAATTAAAGTTTTCT
1 AAAAAAATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTCAAAAATAAAGTTTTCT
* * *
17487146 AAAAAAATA-TTTTGGGGAGAAGTTGAAAGTATCAATTTTTC
1 AAAAAAATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTTC
17487187 CTATACAAAA
Statistics
Matches: 233, Mismatches: 30, Indels: 27
0.80 0.10 0.09
Matches are distributed among these distances:
57 42 0.18
58 86 0.37
59 56 0.24
60 13 0.06
61 32 0.14
62 4 0.02
ACGTcount: A:0.45, C:0.05, G:0.12, T:0.38
Consensus pattern (60 bp):
AAAAAAATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTCAAAAATAAAGTTTTCT
Found at i:17491854 original size:21 final size:20
Alignment explanation
Indices: 17491824--17491862 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
17491814 TGGATAAAAA
17491824 ATGAGAAAAAAGAAAAAAGG
1 ATGAGAAAAAAGAAAAAAGG
*
17491844 ATGATGAAAAATGAAAAAA
1 ATGA-GAAAAAAGAAAAAA
17491863 TGAAAAAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.69, C:0.00, G:0.21, T:0.10
Consensus pattern (20 bp):
ATGAGAAAAAAGAAAAAAGG
Found at i:17491863 original size:8 final size:8
Alignment explanation
Indices: 17491850--17491875 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
17491840 AAGGATGATG
17491850 AAAAATGA
1 AAAAATGA
17491858 AAAAATGA
1 AAAAATGA
17491866 AAAAATGA
1 AAAAATGA
17491874 AA
1 AA
17491876 CAGGATTCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.77, C:0.00, G:0.12, T:0.12
Consensus pattern (8 bp):
AAAAATGA
Found at i:17493836 original size:42 final size:41
Alignment explanation
Indices: 17493721--17493885 Score: 183
Period size: 41 Copynumber: 4.0 Consensus size: 41
17493711 ATTGTCAATG
* * *
17493721 AGCAATTTATTTTTTCAAAGTTTCGTT-A-CCTCTGTTTAAAGG
1 AGCAATTTA-TTTTTCAAAG--TCGTTGAGCCTCTGATTAGAGA
* * * *
17493763 AGCAATTTACTTTTCAAAGTTGTAGTA-CCTCTAATTAGAGA
1 AGCAATTTATTTTTCAAAGTCGTTG-AGCCTCTGATTAGAGA
* *
17493804 AGCCATTTATTTTTCTAAAGTCGTTGAGCCTCTGATTAGAGG
1 AGCAATTTATTTTTC-AAAGTCGTTGAGCCTCTGATTAGAGA
17493846 AGCAATTTATTTTTCAAAGTCGTTGAGCCTCTGATTAGAG
1 AGCAATTTATTTTTCAAAGTCGTTGAGCCTCTGATTAGAG
17493886 GAGCTTTGAT
Statistics
Matches: 105, Mismatches: 14, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
39 3 0.03
41 59 0.56
42 43 0.41
ACGTcount: A:0.28, C:0.15, G:0.18, T:0.39
Consensus pattern (41 bp):
AGCAATTTATTTTTCAAAGTCGTTGAGCCTCTGATTAGAGA
Found at i:17493877 original size:83 final size:82
Alignment explanation
Indices: 17493725--17493885 Score: 202
Period size: 83 Copynumber: 1.9 Consensus size: 82
17493715 TCAATGAGCA
* *
17493725 ATTTATTTTTTCAAAGTTTCGTTACCTCTGTTTAAAGGAGCAATTTACTTTTCAAAGTTGTAGTA
1 ATTTATTTTTTCAAAG-TTCGTTACCTCTGATTAAAGGAGCAATTTACTTTTCAAAGTCGTAGTA
17493790 CCTCTAATTAGAGAAGCC
65 CCTCTAATTAGAGAAGCC
* * *
17493808 ATTTA-TTTTTCTAAAG-TCGTTGAGCCTCTGATTAGAGGAGCAATTTATTTTTCAAAGTCGTTG
1 ATTTATTTTTTC-AAAGTTCGTT-A-CCTCTGATTAAAGGAGCAATTTACTTTTCAAAGTCGTAG
*
17493871 -AGCCTCTGATTAGAG
63 TA-CCTCTAATTAGAG
17493886 GAGCTTTGAT
Statistics
Matches: 68, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
81 5 0.07
82 8 0.12
83 55 0.81
ACGTcount: A:0.27, C:0.15, G:0.17, T:0.40
Consensus pattern (82 bp):
ATTTATTTTTTCAAAGTTCGTTACCTCTGATTAAAGGAGCAATTTACTTTTCAAAGTCGTAGTAC
CTCTAATTAGAGAAGCC
Found at i:17494061 original size:18 final size:16
Alignment explanation
Indices: 17494012--17494060 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 16
17494002 CAAAATTTAG
17494012 AAAATAAAAAAAAAACA
1 AAAATAAAAAAAAAA-A
17494029 AAAA-ACAAAAAAAATAA
1 AAAATA-AAAAAAAA-AA
17494046 AAAAGTAAAAAAAAA
1 AAAA-TAAAAAAAAA
17494061 TCCAGTTGAG
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
16 1 0.04
17 17 0.61
18 9 0.32
19 1 0.04
ACGTcount: A:0.88, C:0.04, G:0.02, T:0.06
Consensus pattern (16 bp):
AAAATAAAAAAAAAAA
Found at i:17494220 original size:11 final size:11
Alignment explanation
Indices: 17494199--17494240 Score: 50
Period size: 13 Copynumber: 3.7 Consensus size: 11
17494189 AATTGTAAAA
17494199 ATTTTTA-TTC
1 ATTTTTATTTC
17494209 ATTTTTATTTC
1 ATTTTTATTTC
17494220 AGATTTTTATTTC
1 --ATTTTTATTTC
*
17494233 ATATTTAT
1 ATTTTTAT
17494241 CATTTTTTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
10 7 0.25
11 10 0.36
13 11 0.39
ACGTcount: A:0.24, C:0.07, G:0.02, T:0.67
Consensus pattern (11 bp):
ATTTTTATTTC
Found at i:17494227 original size:13 final size:13
Alignment explanation
Indices: 17494209--17494238 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
17494199 ATTTTTATTC
17494209 ATTTTTATTTCAG
1 ATTTTTATTTCAG
*
17494222 ATTTTTATTTCAT
1 ATTTTTATTTCAG
17494235 ATTT
1 ATTT
17494239 ATCATTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.23, C:0.07, G:0.03, T:0.67
Consensus pattern (13 bp):
ATTTTTATTTCAG
Found at i:17497328 original size:14 final size:13
Alignment explanation
Indices: 17497310--17497334 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17497300 ATTTTTCATA
17497310 AAAAAAAATTTTC
1 AAAAAAAATTTTC
17497323 AAAAAAAATTTT
1 AAAAAAAATTTT
17497335 TTTTGAGGAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (13 bp):
AAAAAAAATTTTC
Found at i:17497389 original size:59 final size:58
Alignment explanation
Indices: 17497089--17497595 Score: 492
Period size: 58 Copynumber: 8.7 Consensus size: 58
17497079 ATAATTTCAA
* * *
17497089 AAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTT-TAAATTAAGCTTTTC
1 AAAAAATTTTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAAG-TTTTC
* * * *
17497147 AAAAAATATTTTTG-GAAAAAAGTTGAAAGTATCAATTTTCCTTGAAAAT-AAGCATTCC
1 AAAAAATTTTTTTGAG-GAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAAG-TTTTC
* * * *
17497205 AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCTTTAAAAATAAA-TTTTC
1 AAAAAATTTTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAAGTTTTC
* * * * *
17497262 AAAAAAGGTTTTTTTTTTAGGAAAAGTTGAAAGTATCAATTTTTCAT-AAAAAAAAATTTTC
1 AAAAAA----TTTTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAAGTTTTC
* * *
17497323 AAAAAAAATTTTTTTTGAGGAAAAGTTAAAAGTATCAATTTTCCTTGAAATTAAAGTTTTT
1 --AAAAAA-TTTTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAAGTTTTC
* * * * * *
17497384 AAAAAATATTTTTG-GAGAAAAGTTAAAAGTATCAA-TTTACTTAAAAATAAATTTTTT
1 AAAAAATTTTTTTGAG-GAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAAGTTTTC
** * * * * *
17497441 AAAAAA-AGTTTTGAGAAAAAGTTGAAAGCATCAATTTTTCTCGAAATTAAAGTTTTC
1 AAAAAATTTTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAAGTTTTC
* * *
17497498 AAAAAATTTTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTCGAAATTAAAGTTTTC
1 AAAAAATTTTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAAGTTTTC
* * *
17497556 TAAAAAAATATTTTG-GAAAGAAGTTGAAAGTATCAATTTT
1 -AAAAAATTTTTTTGAGGAA-AAGTTGAAAGTATCAATTTT
17497596 TCCTGTACAA
Statistics
Matches: 383, Mismatches: 48, Indels: 35
0.82 0.10 0.08
Matches are distributed among these distances:
56 22 0.06
57 58 0.15
58 165 0.43
59 45 0.12
60 41 0.11
61 46 0.12
63 6 0.02
ACGTcount: A:0.44, C:0.07, G:0.12, T:0.37
Consensus pattern (58 bp):
AAAAAATTTTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAAGTTTTC
Found at i:17498485 original size:21 final size:21
Alignment explanation
Indices: 17498461--17498580 Score: 100
Period size: 21 Copynumber: 5.7 Consensus size: 21
17498451 TAATCTTTTG
* *
17498461 ATGAGAATTTTTTAATTTTAA
1 ATGAGAATTTTTGAATTTCAA
17498482 ATGAGAATTTTTGAATTTCAA
1 ATGAGAATTTTTGAATTTCAA
* * **
17498503 ATGAGAATATTTGAGTTTTTA
1 ATGAGAATTTTTGAATTTCAA
* * *
17498524 AGGAAGAA-TCTTGAGGTTTCAA
1 ATG-AGAATTTTTGA-ATTTCAA
17498546 ATGAGAATTTTT-AGATTTCAA
1 ATGAGAATTTTTGA-ATTTCAA
* *
17498567 ATGAAAATCTTTGA
1 ATGAGAATTTTTGA
17498581 GATGTGAAAT
Statistics
Matches: 79, Mismatches: 16, Indels: 7
0.77 0.16 0.07
Matches are distributed among these distances:
21 64 0.81
22 15 0.19
ACGTcount: A:0.38, C:0.04, G:0.17, T:0.42
Consensus pattern (21 bp):
ATGAGAATTTTTGAATTTCAA
Found at i:17498581 original size:43 final size:43
Alignment explanation
Indices: 17498461--17498583 Score: 128
Period size: 43 Copynumber: 2.9 Consensus size: 43
17498451 TAATCTTTTG
* *
17498461 ATGAGAATTTTTTA-ATTTTAAATGAGAATTTTTGA-ATTTCAA
1 ATGAGAA-TTTTTAGATTTTAAATGAAAATCTTTGAGATTTCAA
* * * *
17498503 ATGAGAATATTT-GAGTTTTTAAGGAAGAATC-TTGAGGTTTCAA
1 ATGAGAATTTTTAGA-TTTTAAATGAA-AATCTTTGAGATTTCAA
*
17498546 ATGAGAATTTTTAGATTTCAAATGAAAATCTTTGAGAT
1 ATGAGAATTTTTAGATTTTAAATGAAAATCTTTGAGAT
17498584 GTGAAATCTT
Statistics
Matches: 64, Mismatches: 11, Indels: 11
0.74 0.13 0.13
Matches are distributed among these distances:
41 5 0.08
42 23 0.36
43 34 0.53
44 2 0.03
ACGTcount: A:0.37, C:0.04, G:0.17, T:0.41
Consensus pattern (43 bp):
ATGAGAATTTTTAGATTTTAAATGAAAATCTTTGAGATTTCAA
Found at i:17499181 original size:40 final size:40
Alignment explanation
Indices: 17499054--17499345 Score: 295
Period size: 40 Copynumber: 7.4 Consensus size: 40
17499044 TGATTGTCGG
* * * *
17499054 GGAGCTTTTATTTTTCAAAGTTGTTGAGCTTCTAATTAGA
1 GGAGCCTTTATTTTTCAAAGTTATTGAGCCTCTATTTAGA
** *
17499094 TAAG-CTTT-TTTTTTAAAGTTATTGAGCCTCTATTT-GA
1 GGAGCCTTTATTTTTCAAAGTTATTGAGCCTCTATTTAGA
* * * * *
17499131 AGAGCTTTTATTTTTCAAAGTTGTTGAGCTTATATTTAGA
1 GGAGCCTTTATTTTTCAAAGTTATTGAGCCTCTATTTAGA
** * * *
17499171 GGAGCCTTTATTTTTCAAAGTCGTTGAACCTTTAATTAGA
1 GGAGCCTTTATTTTTCAAAGTTATTGAGCCTCTATTTAGA
* * **
17499211 TGAGCCTTTATTTTTCAAAGTTATTGACCCTCTGCTTAGA
1 GGAGCCTTTATTTTTCAAAGTTATTGAGCCTCTATTTAGA
** * *
17499251 GGAGCCTTTTATTTTT-ATTGTTATTAAGCCTCTGTTTAGA
1 GGAGCC-TTTATTTTTCAAAGTTATTGAGCCTCTATTTAGA
* *
17499291 GAAGCCTTTATTTTTCAAAGTTATTGAGCCTCTGTTTAGA
1 GGAGCCTTTATTTTTCAAAGTTATTGAGCCTCTATTTAGA
*
17499331 GGAGCATTTATTTTT
1 GGAGCCTTTATTTTT
17499346 TAAAAATTGT
Statistics
Matches: 207, Mismatches: 40, Indels: 10
0.81 0.16 0.04
Matches are distributed among these distances:
37 4 0.02
38 26 0.13
39 35 0.17
40 133 0.64
41 9 0.04
ACGTcount: A:0.24, C:0.13, G:0.17, T:0.46
Consensus pattern (40 bp):
GGAGCCTTTATTTTTCAAAGTTATTGAGCCTCTATTTAGA
Found at i:17499330 original size:120 final size:119
Alignment explanation
Indices: 17499060--17499345 Score: 326
Period size: 120 Copynumber: 2.4 Consensus size: 119
17499050 TCGGGGAGCT
* * * *
17499060 TTTATTTTTCAAAGTTGTTGAGCTTCTAATTAGATAAG-CTTT-TTTTTTAAAGTTATTGAGCCT
1 TTTATTTTTCAAAGTTGTTGAGCCTCTAATTAGATGAGCCTTTATTTTTCAAAGTTATTGACCCT
* * * * *
17499123 CTATTTGAAGAGCTTTTATTTTTCAAAGTTGTTGAGCTTATATTTAGAGGAGCC
66 CTATTAGAAGAGCTTTTATTTTTCAAAGTTATTAAGCCTATATTTAGAGAAGCC
* * *
17499177 TTTATTTTTCAAAGTCGTTGAACCTTTAATTAGATGAGCCTTTATTTTTCAAAGTTATTGACCCT
1 TTTATTTTTCAAAGTTGTTGAGCCTCTAATTAGATGAGCCTTTATTTTTCAAAGTTATTGACCCT
* * ** * *
17499242 CTGCTTAGAGGAGCCTTTTATTTTT-ATTGTTATTAAGCCTCTGTTTAGAGAAGCC
66 CT-ATTAGAAGAG-CTTTTATTTTTCAAAGTTATTAAGCCTATATTTAGAGAAGCC
* ** * *
17499297 TTTATTTTTCAAAGTTATTGAGCCTCTGTTTAGAGGAGCATTTATTTTT
1 TTTATTTTTCAAAGTTGTTGAGCCTCTAATTAGATGAGCCTTTATTTTT
17499346 TAAAAATTGT
Statistics
Matches: 139, Mismatches: 26, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
117 33 0.24
118 4 0.03
119 21 0.15
120 70 0.50
121 11 0.08
ACGTcount: A:0.24, C:0.13, G:0.16, T:0.47
Consensus pattern (119 bp):
TTTATTTTTCAAAGTTGTTGAGCCTCTAATTAGATGAGCCTTTATTTTTCAAAGTTATTGACCCT
CTATTAGAAGAGCTTTTATTTTTCAAAGTTATTAAGCCTATATTTAGAGAAGCC
Found at i:17499362 original size:41 final size:41
Alignment explanation
Indices: 17499206--17499375 Score: 116
Period size: 40 Copynumber: 4.2 Consensus size: 41
17499196 GAACCTTTAA
* * * * * * *
17499206 TTAGATGAGCCTTTATTTTTCAAAGTTATTG-ACCCTCTGC
1 TTAGAGGAGCATTTATTTTTAAAAATTAGTGAAGCCTCTGT
* *** *
17499246 TTAGAGGAGCCTTTTATTTTT-ATTGTTA-TTAAGCCTCTGT
1 TTAGAGGAG-CATTTATTTTTAAAAATTAGTGAAGCCTCTGT
* * * * *
17499286 TTAGAGAAGCCTTTATTTTTCAAAGTTATTG-AGCCTCTGT
1 TTAGAGGAGCATTTATTTTTAAAAATTAGTGAAGCCTCTGT
* *
17499326 TTAGAGGAGCATTTATTTTTTAAAAATT-GTGAAGCCTTTAT
1 TTAGAGGAGCATTTA-TTTTTAAAAATTAGTGAAGCCTCTGT
17499367 TTAGAGGAG
1 TTAGAGGAG
17499376 TTTTTAGGAA
Statistics
Matches: 105, Mismatches: 19, Indels: 11
0.78 0.14 0.08
Matches are distributed among these distances:
39 11 0.10
40 57 0.54
41 37 0.35
ACGTcount: A:0.25, C:0.13, G:0.18, T:0.44
Consensus pattern (41 bp):
TTAGAGGAGCATTTATTTTTAAAAATTAGTGAAGCCTCTGT
Found at i:17500328 original size:12 final size:12
Alignment explanation
Indices: 17500311--17500350 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
17500301 TTTTTGATAT
17500311 TTTTATTTAGTA
1 TTTTATTTAGTA
*
17500323 TTTTATTTATGTG
1 TTTTATTTA-GTA
17500336 TTTT-TTTAGTA
1 TTTTATTTAGTA
17500347 TTTT
1 TTTT
17500351 TGCATGATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
11 6 0.24
12 13 0.52
13 6 0.24
ACGTcount: A:0.17, C:0.00, G:0.10, T:0.72
Consensus pattern (12 bp):
TTTTATTTAGTA
Found at i:17506723 original size:22 final size:23
Alignment explanation
Indices: 17506684--17506728 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
17506674 AAAAAATTTT
*
17506684 AATTTTTGTTTAATTTGATTTAA
1 AATTTTTGTTTAATTTGAATTAA
17506707 AATTTTT-TATTAA-TTGAATTAA
1 AATTTTTGT-TTAATTTGAATTAA
17506729 TTTAAAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.36, C:0.00, G:0.07, T:0.58
Consensus pattern (23 bp):
AATTTTTGTTTAATTTGAATTAA
Found at i:17522731 original size:42 final size:41
Alignment explanation
Indices: 17522646--17522724 Score: 115
Period size: 42 Copynumber: 1.9 Consensus size: 41
17522636 AGTATAAATG
*
17522646 ATATCTTAATTATATATAAATATAATATTTTTATTAAGTTA
1 ATATCTTAATTATATATAAATATAATAATTTTATTAAGTTA
*
17522687 ATATCTTAAATTATAGTATTAA-ATAATAATTTTATTAA
1 ATATCTT-AATTATA-TATAAATATAATAATTTTATTAA
17522725 TATAATAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
41 7 0.21
42 22 0.65
43 5 0.15
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (41 bp):
ATATCTTAATTATATATAAATATAATAATTTTATTAAGTTA
Found at i:17522762 original size:24 final size:25
Alignment explanation
Indices: 17522707--17522763 Score: 71
Period size: 24 Copynumber: 2.3 Consensus size: 25
17522697 TTATAGTATT
* *
17522707 AAATAATAATTTTATTAATATAATAA
1 AAAT-ATAATTTAAATAATATAATAA
*
17522733 ATATATAATTTAAATAA-ATAATAA
1 AAATATAATTTAAATAATATAATAA
17522757 AAATATA
1 AAATATA
17522764 TTATATATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
24 13 0.48
25 11 0.41
26 3 0.11
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (25 bp):
AAATATAATTTAAATAATATAATAA
Found at i:17524880 original size:35 final size:36
Alignment explanation
Indices: 17524791--17524885 Score: 85
Period size: 35 Copynumber: 2.8 Consensus size: 36
17524781 TGTAAACTTT
*
17524791 ATTTTAA--TAACAAT-AAA-TTTTGAT-TACAAAA
1 ATTTTAATGTAACAATAAAATTTTTGTTGTACAAAA
* * * **
17524822 CTTTTTATGTAACATTATTATTTTTGTTGTA-AAAA
1 ATTTTAATGTAACAATAAAATTTTTGTTGTACAAAA
*
17524857 ATTTTAATGTAACAATAAAATTTTGGTTG
1 ATTTTAATGTAACAATAAAATTTTTGTTG
17524886 CCAAATTTTG
Statistics
Matches: 47, Mismatches: 12, Indels: 6
0.72 0.18 0.09
Matches are distributed among these distances:
31 5 0.11
33 6 0.13
34 1 0.02
35 33 0.70
36 2 0.04
ACGTcount: A:0.40, C:0.05, G:0.08, T:0.46
Consensus pattern (36 bp):
ATTTTAATGTAACAATAAAATTTTTGTTGTACAAAA
Found at i:17536469 original size:15 final size:15
Alignment explanation
Indices: 17536459--17536488 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
17536449 TTTATTTATT
17536459 TACAAAATATTATCA
1 TACAAAATATTATCA
*
17536474 TACAAAATACTATCA
1 TACAAAATATTATCA
17536489 AAATATCATA
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:0.53, C:0.17, G:0.00, T:0.30
Consensus pattern (15 bp):
TACAAAATATTATCA
Found at i:17536562 original size:24 final size:25
Alignment explanation
Indices: 17536488--17536564 Score: 70
Period size: 24 Copynumber: 3.1 Consensus size: 25
17536478 AAATACTATC
**
17536488 AAAATATCATAGAAAAAAATCATGTA
1 AAAATATCATA-ATTAAAATCATGTA
* *
17536514 ATAATATCATAATTAAAAT-AGGTA
1 AAAATATCATAATTAAAATCATGTA
*
17536538 AAAATATGCA-AA-TATAATCATGTA
1 AAAATAT-CATAATTAAAATCATGTA
17536562 AAA
1 AAA
17536565 TAATTATGTA
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
23 5 0.12
24 19 0.45
25 8 0.19
26 10 0.24
ACGTcount: A:0.58, C:0.06, G:0.08, T:0.27
Consensus pattern (25 bp):
AAAATATCATAATTAAAATCATGTA
Found at i:17536630 original size:42 final size:44
Alignment explanation
Indices: 17536578--17536660 Score: 116
Period size: 43 Copynumber: 1.9 Consensus size: 44
17536568 TTATGTAAAT
17536578 AAATAAAATCCA-TAAAAAAATCATGCAAAAA-ATAATAATGAC
1 AAATAAAATCCATTAAAAAAATCATGCAAAAATATAATAATGAC
* * * *
17536620 AAATAAAATCCATTCAAAACATTATGCAAAAATATAGTAAT
1 AAATAAAATCCATTAAAAAAATCATGCAAAAATATAATAAT
17536661 CAAGCAAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
42 12 0.34
43 16 0.46
44 7 0.20
ACGTcount: A:0.60, C:0.12, G:0.05, T:0.23
Consensus pattern (44 bp):
AAATAAAATCCATTAAAAAAATCATGCAAAAATATAATAATGAC
Found at i:17538951 original size:18 final size:18
Alignment explanation
Indices: 17538891--17538972 Score: 51
Period size: 18 Copynumber: 4.3 Consensus size: 18
17538881 ATATAATTGA
*
17538891 GGATGATACATTT-ATGGT
1 GGATAATACATTTGA-GGT
*
17538909 AGGA-AATACATTTTGTGGT
1 -GGATAATACA-TTTGAGGT
**
17538928 AAATAATACATTTGAGGT
1 GGATAATACATTTGAGGT
*
17538946 GGATAATAACCATATGAAGGT
1 GGATAAT-A-CATTTG-AGGT
17538967 GGATAA
1 GGATAA
17538973 CCATGAAGAT
Statistics
Matches: 49, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
18 18 0.37
19 16 0.33
20 5 0.10
21 10 0.20
ACGTcount: A:0.38, C:0.06, G:0.24, T:0.32
Consensus pattern (18 bp):
GGATAATACATTTGAGGT
Found at i:17538953 original size:21 final size:21
Alignment explanation
Indices: 17538929--17538972 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
17538919 TTTTGTGGTA
*
17538929 AATAATACATTTG-AGGTGGAT
1 AATAA-ACATATGAAGGTGGAT
*
17538950 AATAACCATATGAAGGTGGAT
1 AATAAACATATGAAGGTGGAT
17538971 AA
1 AA
17538973 CCATGAAGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.43, C:0.07, G:0.23, T:0.27
Consensus pattern (21 bp):
AATAAACATATGAAGGTGGAT
Found at i:17539343 original size:6 final size:6
Alignment explanation
Indices: 17539292--17539341 Score: 82
Period size: 6 Copynumber: 8.3 Consensus size: 6
17539282 TCAAAATCCG
* *
17539292 CACCAT CACCAT CACCAT CTCCAT CACCAT CACCAT CACCAT CATCAT
1 CACCAT CACCAT CACCAT CACCAT CACCAT CACCAT CACCAT CACCAT
17539340 CA
1 CA
17539342 TCTGAACTTA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 41 1.00
ACGTcount: A:0.32, C:0.48, G:0.00, T:0.20
Consensus pattern (6 bp):
CACCAT
Found at i:17542756 original size:20 final size:21
Alignment explanation
Indices: 17542717--17542757 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
17542707 AACAACAAAA
*
17542717 AAAATTATCAAAATTCATATAC
1 AAAATTAT-AAAATTAATATAC
17542739 AAAATTAT-AAATTAATATA
1 AAAATTATAAAATTAATATA
17542758 TAACACAATC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 10 0.56
22 8 0.44
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.34
Consensus pattern (21 bp):
AAAATTATAAAATTAATATAC
Found at i:17548330 original size:15 final size:15
Alignment explanation
Indices: 17548310--17548357 Score: 66
Period size: 15 Copynumber: 3.4 Consensus size: 15
17548300 GTGGATGGGA
17548310 GATTGGGTGGGGAAG
1 GATTGGGTGGGGAAG
*
17548325 GATTGGAT-GGG-A-
1 GATTGGGTGGGGAAG
17548337 GATTGGGTGGGGAAG
1 GATTGGGTGGGGAAG
17548352 GATTGG
1 GATTGG
17548358 ATGTGGGGGT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
12 7 0.25
13 4 0.14
14 4 0.14
15 13 0.46
ACGTcount: A:0.21, C:0.00, G:0.56, T:0.23
Consensus pattern (15 bp):
GATTGGGTGGGGAAG
Found at i:17548334 original size:27 final size:27
Alignment explanation
Indices: 17548301--17548360 Score: 120
Period size: 27 Copynumber: 2.2 Consensus size: 27
17548291 GGCACATAGG
17548301 TGGATGGGAGATTGGGTGGGGAAGGAT
1 TGGATGGGAGATTGGGTGGGGAAGGAT
17548328 TGGATGGGAGATTGGGTGGGGAAGGAT
1 TGGATGGGAGATTGGGTGGGGAAGGAT
17548355 TGGATG
1 TGGATG
17548361 TGGGGGTTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.22, C:0.00, G:0.55, T:0.23
Consensus pattern (27 bp):
TGGATGGGAGATTGGGTGGGGAAGGAT
Found at i:17548644 original size:20 final size:21
Alignment explanation
Indices: 17548606--17548647 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
17548596 TGTATATGAA
* *
17548606 TTTTGATAATTTTTTTTGTTG
1 TTTTGATAATTTATATTGTTG
17548627 TTTTGAT-ATTTATATTGTTG
1 TTTTGATAATTTATATTGTTG
17548647 T
1 T
17548648 CAATTCTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.17, C:0.00, G:0.14, T:0.69
Consensus pattern (21 bp):
TTTTGATAATTTATATTGTTG
Found at i:17552217 original size:18 final size:18
Alignment explanation
Indices: 17552196--17552274 Score: 65
Period size: 18 Copynumber: 4.6 Consensus size: 18
17552186 CCTCTACTTT
**
17552196 AAATGTATCATTTACCAC
1 AAATGTATCATCCACCAC
**
17552214 AAATGTATCCCCCACCAC
1 AAATGTATCATCCACCAC
*
17552232 AAATGTATCAT---CCTC
1 AAATGTATCATCCACCAC
* * *
17552247 AATTATATCATCCACCTC
1 AAATGTATCATCCACCAC
17552265 AAATGTATCA
1 AAATGTATCA
17552275 AGAACAAAGG
Statistics
Matches: 47, Mismatches: 11, Indels: 6
0.73 0.17 0.09
Matches are distributed among these distances:
15 12 0.26
18 35 0.74
ACGTcount: A:0.37, C:0.29, G:0.05, T:0.29
Consensus pattern (18 bp):
AAATGTATCATCCACCAC
Found at i:17561097 original size:13 final size:13
Alignment explanation
Indices: 17561074--17561174 Score: 51
Period size: 11 Copynumber: 8.3 Consensus size: 13
17561064 ATAAAAATAA
*
17561074 TATAATTTAAATT
1 TATAATATAAATT
*
17561087 TTTAATATAAA-T
1 TATAATATAAATT
17561099 TAT-ATATAAA-T
1 TATAATATAAATT
17561110 T-TAATA-AAA-T
1 TATAATATAAATT
* *
17561120 TAAAATAT-ATTT
1 TATAATATAAATT
* *
17561132 TAT-ATTTAAATA
1 TATAATATAAATT
17561144 TA-AATATAAA-T
1 TATAATATAAATT
17561155 TATTAATAATAAAATT
1 TA-TAAT-AT-AAATT
17561171 TATA
1 TATA
17561175 TTTTACGTAT
Statistics
Matches: 66, Mismatches: 11, Indels: 20
0.68 0.11 0.21
Matches are distributed among these distances:
10 6 0.09
11 22 0.33
12 16 0.24
13 12 0.18
14 2 0.03
15 5 0.08
16 3 0.05
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (13 bp):
TATAATATAAATT
Found at i:17561127 original size:22 final size:22
Alignment explanation
Indices: 17561087--17561155 Score: 70
Period size: 21 Copynumber: 3.1 Consensus size: 22
17561077 AATTTAAATT
*
17561087 TTTAATATAAATTATATATAAA
1 TTTAATATAAATTAAATATAAA
*
17561109 TTTAATA-AAATTAAA-ATATAT
1 TTTAATATAAATTAAATATA-AA
*
17561130 TTTATATTTAAATATAAATATAAA
1 TTTA-ATATAAAT-TAAATATAAA
17561154 TT
1 TT
17561156 ATTAATAATA
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
20 3 0.08
21 12 0.32
22 9 0.24
23 4 0.11
24 7 0.18
25 3 0.08
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
TTTAATATAAATTAAATATAAA
Found at i:17561168 original size:44 final size:44
Alignment explanation
Indices: 17561086--17561179 Score: 104
Period size: 44 Copynumber: 2.1 Consensus size: 44
17561076 TAATTTAAAT
*
17561086 TTTTAATATAAATTATATATAAATTTAATAAAATTAAAA-TATA
1 TTTTAATATAAATTAAATATAAATTTAATAAAATTAAAATTATA
* *
17561129 TTTTATATTTAAATATAAATATAAA-TTATTAATAA-TAAAATTTATA
1 TTTTA-ATATAAAT-TAAATATAAATTTAATAA-AATTAAAA-TTATA
17561175 TTTTA
1 TTTTA
17561180 CGTATATTTA
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
43 5 0.12
44 18 0.42
45 11 0.26
46 9 0.21
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (44 bp):
TTTTAATATAAATTAAATATAAATTTAATAAAATTAAAATTATA
Found at i:17565444 original size:27 final size:29
Alignment explanation
Indices: 17565388--17565445 Score: 68
Period size: 27 Copynumber: 2.1 Consensus size: 29
17565378 TGATGCACAG
*
17565388 ATTTTTTATTATATCTTTTTATAATTTTA
1 ATTTTTTATTATATCTTTTTATAATCTTA
*
17565417 ATTTTTT-TTA-AT-TTTTATATTATCTTA
1 ATTTTTTATTATATCTTTT-TATAATCTTA
17565444 AT
1 AT
17565446 AAAAGAATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
26 4 0.15
27 12 0.46
28 3 0.12
29 7 0.27
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (29 bp):
ATTTTTTATTATATCTTTTTATAATCTTA
Found at i:17570551 original size:20 final size:20
Alignment explanation
Indices: 17570526--17570564 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
17570516 TGACGCCTAC
*
17570526 CAAATAATAGGCATGATATA
1 CAAATAATAGGCATCATATA
*
17570546 CAAATATTAGGCATCATAT
1 CAAATAATAGGCATCATAT
17570565 TAGATGTATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.46, C:0.13, G:0.13, T:0.28
Consensus pattern (20 bp):
CAAATAATAGGCATCATATA
Found at i:17574204 original size:166 final size:167
Alignment explanation
Indices: 17574017--17574553 Score: 449
Period size: 166 Copynumber: 3.3 Consensus size: 167
17574007 ACAAAAATGC
*
17574017 CTTAAATAATCTTTTTATAAAAAAATTAAATGATCCATAATTTAAACAACCAATAATATAATTTT
1 CTTAAATAATC-TTTTATAAAAAAATTAAATGATCCATAATTTAAACAACC-ATAATAT-AGTTT
* * * * * *
17574082 TATTAAATGATCATTTAAGGCATTTTTGTATAT-AAACGTCTTAAACGAT-TTATAA-TTTTTTA
63 TATTAAAAGATCAATTAAGGCATTTTTATAAATAAAACGCCTTAAACGATCCTATAATTTTTTTA
* *
17574144 TA-AAAAG-ATTATTTAAGGTTTTTTTTTGTACAAAAACA-
128 TATAAAAGAATTATTTAA-GTTATTTTATGTACAAAAACAT
* ** * *
17574182 CTTTAAATAATCTTTCTATAAAAAAATAAAATGAGGC-TAAATTTAAATGATCCATAATATAGTT
1 C-TTAAATAATCTTT-TATAAAAAAATTAAATGATCCAT-AATTTAAA-CAACCATAATATAGTT
* * *
17574246 TTATTAAAAGATCAATTAAGGCTTTTTTATAAATAAAATGCCTTAAATGATCCTATAATTTTTTT
62 TTATTAAAAGATCAATTAAGGCATTTTTATAAATAAAACGCCTTAAACGATCCTATAA-TTTTTT
* *
17574311 TATATAAATGAATTATTTAAGTTATTTTATGTACAGAAACAT
126 TATATAAAAGAATTATTTAAGTTATTTTATGTACAAAAACAT
* * *
17574353 CTTAAAAAATCTATTTATAAGAAAATTAAATGATCCATAATTT--A-AACGAT-A-A-A-----A
1 CTTAAATAATCT-TTTATAAAAAAATTAAATGATCCATAATTTAAACAACCATAATATAGTTTTA
* * * * * * *
17574407 --AAAAGATCATTTAAAGCATTTCTATACATAAAACGCCTTAAATGATCTTTTAATTTTTTT-TA
65 TTAAAAGATCAATTAAGGCATTTTTATAAATAAAACGCCTTAAACGATCCTATAATTTTTTTATA
* * * *
17574469 TACACGGATTATTTACGGAGTT-TTTTATATA-AAAATAC--
130 TAAAAGAATTATTTA---AGTTATTTTATGTACAAAA-ACAT
*
17574507 CTTAAATAATCCATTTATAAAAAAATTTAAATGATCCATAATTTAAA
1 CTTAAATAAT-CTTTTATAAAAAAA-TTAAATGATCCATAATTTAAA
17574554 TGTAAAAAAA
Statistics
Matches: 309, Mismatches: 42, Indels: 50
0.77 0.10 0.12
Matches are distributed among these distances:
154 34 0.11
155 29 0.09
156 55 0.18
157 5 0.02
158 1 0.00
163 1 0.00
164 1 0.00
165 38 0.12
166 60 0.19
167 8 0.03
168 1 0.00
169 9 0.03
170 54 0.17
171 13 0.04
ACGTcount: A:0.44, C:0.09, G:0.07, T:0.40
Consensus pattern (167 bp):
CTTAAATAATCTTTTATAAAAAAATTAAATGATCCATAATTTAAACAACCATAATATAGTTTTAT
TAAAAGATCAATTAAGGCATTTTTATAAATAAAACGCCTTAAACGATCCTATAATTTTTTTATAT
AAAAGAATTATTTAAGTTATTTTATGTACAAAAACAT
Found at i:17574669 original size:156 final size:153
Alignment explanation
Indices: 17574286--17574671 Score: 459
Period size: 156 Copynumber: 2.5 Consensus size: 153
17574276 AAATAAAATG
* * * * * *
17574286 CCTTAAATGATCCTATAATTTTTTTTATATAAATGAATTATTTAAGTTATTTTATGTACAGAAAC
1 CCTTAAATGATCCTTTAATTTTTTTTATAT--ATGAATTATTTAAG-AATTTTTTGTATAAAAAT
* * * * * *
17574351 ATCTTAAAAAATCTATTTATAAGAAAATTAAATGATCCATAATTTAAACGATAAAAAAAAGATCA
63 ACCTTAAATAATCCATTTATAAAAAAATTAAATGATCCATAATTTAAACGAAAAAAAAAAAATCA
*
17574416 TTTAAAGCATTTCTATACATAAAACG
128 TTTAAAGCATTTCTATACATAAAACA
* * * * * * *
17574442 CCTTAAATGATCTTTTAATTTTTTTTATACACGGATTATTTACGGAGTTTTTTATATAAAAATAC
1 CCTTAAATGATCCTTTAATTTTTTTTATATATGAATTATTTA-AGAATTTTTTGTATAAAAATAC
*
17574507 CTTAAATAATCCATTTATAAAAAAATTTAAATGATCCATAATTTAAATGTAAAAAAAAAAAATCA
65 CTTAAATAATCCATTTATAAAAAAA-TTAAATGATCCATAATTTAAACG-AAAAAAAAAAAATCA
* * *
17574572 TTT-AAGATATTTCTGTACATAAAATA
128 TTTAAAG-CATTTCTATACATAAAACA
**
17574598 TTTTAAATGATCCTTTAATTTTTTTTATATATGAATTATTTAAGACATTTTTTGTATAAAAATAC
1 CCTTAAATGATCCTTTAATTTTTTTTATATATGAATTATTTAAGA-ATTTTTTGTATAAAAATAC
17574663 CTTAAATAA
65 CTTAAATAA
17574672 AAATAATCTT
Statistics
Matches: 192, Mismatches: 33, Indels: 10
0.82 0.14 0.04
Matches are distributed among these distances:
154 44 0.23
155 28 0.15
156 120 0.62
ACGTcount: A:0.44, C:0.09, G:0.06, T:0.41
Consensus pattern (153 bp):
CCTTAAATGATCCTTTAATTTTTTTTATATATGAATTATTTAAGAATTTTTTGTATAAAAATACC
TTAAATAATCCATTTATAAAAAAATTAAATGATCCATAATTTAAACGAAAAAAAAAAAATCATTT
AAAGCATTTCTATACATAAAACA
Found at i:17576507 original size:21 final size:21
Alignment explanation
Indices: 17576481--17576525 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
17576471 TTTTTTTTAA
17576481 TTTTTTAAATTTT-TAAACTTT
1 TTTTTTAAATTTTGTAAA-TTT
*
17576502 TTTTTTAACTTTTGTAAATTT
1 TTTTTTAAATTTTGTAAATTT
17576523 TTT
1 TTT
17576526 ATTGCTTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.24, C:0.04, G:0.02, T:0.69
Consensus pattern (21 bp):
TTTTTTAAATTTTGTAAATTT
Found at i:17576791 original size:15 final size:15
Alignment explanation
Indices: 17576761--17576802 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 15
17576751 ACGTGTTTTT
17576761 TTTCTTTATTCT-TTA
1 TTTCTTTATT-TATTA
17576776 TTTCTTTATTTATTA
1 TTTCTTTATTTATTA
17576791 TTT-TATTATTTA
1 TTTCT-TTATTTA
17576803 ATAAATATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
14 2 0.08
15 23 0.92
ACGTcount: A:0.19, C:0.07, G:0.00, T:0.74
Consensus pattern (15 bp):
TTTCTTTATTTATTA
Found at i:17578277 original size:179 final size:179
Alignment explanation
Indices: 17577980--17578471 Score: 478
Period size: 182 Copynumber: 2.7 Consensus size: 179
17577970 TTTTTTAAAA
* *
17577980 ATTATTTAAAGTATTTTTTGTTAGAAAATACCTTAAATAATCTCTTAAATAAATCGACTAGCATT
1 ATTATTTAAGGT-TTTTTTGTTA-AAAATACCTTAAATAATCTCTTAAATAAATTGACTAGCATT
* * ** ** * * * * *
17578045 ACTAAAGGCGTCATCTG-GTCAAAACGCCTCAAATAATCATGTTCAATTTTTTTTTTTAGATTAG
64 ATTTAAGATGTTTTCTGATTAAAAACACCTTAAATAATCATATTCAA---TTTTTTTTAGATTAG
** *
17578109 TTAAGACATTTTTTGACAAAAAACGTATTAAATAATCTTGTTT-A-TT-TTTTT-
126 TTAAGACATTTTTT-ACAAAAAACACATTAAATAATATTGTTTAATTTCTTTTTG
17578160 ATTATTTAAGGTTTTTTTGATTAAAAATACCTTAAATAATCTCTTAAATAAATTGACTAGCATTA
1 ATTATTTAAGGTTTTTTTG-TTAAAAATACCTTAAATAATCTCTTAAATAAATTGACTAGCATTA
* ** * * *
17578225 TTTAAGATATTTTCTGATTAAAAACACCTTAAATAATTTTATTTAA-TTTTTTTGGATTATTTAA
65 TTTAAGATGTTTTCTGATTAAAAACACCTTAAATAATCATATTCAATTTTTTTTAGATTAGTTAA
* * * *
17578289 TACATTTTTTACCACAAACACCTTAAATAATATTGTTTAATTTCTTTTTAGG
130 GACATTTTTTACAAAAAACACATTAAATAATATTGTTTAATTTCTTTTT--G
** * * * *
17578341 ATTATTTAAGGTTTTTTTTGCCAAAACACACCTTAAATAATTTCTTAAATAAATTGACAAGTATT
1 ATTATTTAAGG-TTTTTTTGTTAAAA-ATACCTTAAATAATCTCTTAAATAAATTGACTAGCATT
* * * * *
17578406 ATTTAA-AGTGTTTTTTGATTAAAAA-AGCCTTATATAATCATGTTCAATTTTTTTTGGATTATT
64 ATTTAAGA-TGTTTTCTGATTAAAAACA-CCTTAAATAATCATATTCAATTTTTTTTAGATTAGT
17578469 TAA
127 TAA
17578472 AATGACTTAA
Statistics
Matches: 260, Mismatches: 39, Indels: 23
0.81 0.12 0.07
Matches are distributed among these distances:
175 22 0.08
176 26 0.10
177 2 0.01
178 5 0.02
179 57 0.22
180 35 0.13
181 17 0.07
182 78 0.30
183 18 0.07
ACGTcount: A:0.36, C:0.11, G:0.09, T:0.45
Consensus pattern (179 bp):
ATTATTTAAGGTTTTTTTGTTAAAAATACCTTAAATAATCTCTTAAATAAATTGACTAGCATTAT
TTAAGATGTTTTCTGATTAAAAACACCTTAAATAATCATATTCAATTTTTTTTAGATTAGTTAAG
ACATTTTTTACAAAAAACACATTAAATAATATTGTTTAATTTCTTTTTG
Found at i:17578317 original size:58 final size:61
Alignment explanation
Indices: 17578221--17578383 Score: 179
Period size: 58 Copynumber: 2.7 Consensus size: 61
17578211 ATTGACTAGC
* * **
17578221 ATTATTTAAGATATTTTCTGATTAAAAACACCTTAAATAATTTTATTTAA-TT-TTTTT-GG
1 ATTATTTAAGACATTTT-TTACCAAAAACACCTTAAATAATTTTATTTAATTTCTTTTTAGG
* * * *
17578280 ATTATTTAATACATTTTTTACCACAAACACCTTAAATAATATTGTTTAATTTCTTTTTAGG
1 ATTATTTAAGACATTTTTTACCAAAAACACCTTAAATAATTTTATTTAATTTCTTTTTAGG
*** *
17578341 ATTATTTAAGGTTTTTTTTGCCAAAACACACCTTAAATAATTT
1 ATTATTTAAGACATTTTTTACCAAAA-ACACCTTAAATAATTT
17578384 CTTAAATAAA
Statistics
Matches: 85, Mismatches: 15, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
58 26 0.31
59 17 0.20
60 5 0.06
61 22 0.26
62 15 0.18
ACGTcount: A:0.35, C:0.11, G:0.06, T:0.48
Consensus pattern (61 bp):
ATTATTTAAGACATTTTTTACCAAAAACACCTTAAATAATTTTATTTAATTTCTTTTTAGG
Found at i:17579516 original size:18 final size:17
Alignment explanation
Indices: 17579495--17579528 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
17579485 AGTTAAATGT
*
17579495 TTTATTAATAATAAATAA
1 TTTATAAATAA-AAATAA
17579513 TTTATAAATAAAAATA
1 TTTATAAATAAAAATA
17579529 TATAATATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
TTTATAAATAAAAATAA
Found at i:17580152 original size:10 final size:10
Alignment explanation
Indices: 17580108--17580252 Score: 63
Period size: 11 Copynumber: 14.5 Consensus size: 10
17580098 ATTAAAAGAT
17580108 AAATTC-AAA
1 AAATTCTAAA
*
17580117 AAATTTCCAAA
1 AAA-TTCTAAA
*
17580128 ACTATTC-AAA
1 A-AATTCTAAA
17580138 GAAATTCTAAA
1 -AAATTCTAAA
17580149 AAATAAT-TAAA
1 AAAT--TCTAAA
17580160 AAA-T-TAAA
1 AAATTCTAAA
*
17580168 AAATAC-AAA
1 AAATTCTAAA
*
17580177 AAAATCT-AA
1 AAATTCTAAA
* *
17580186 AATTTTTAAA
1 AAATTCTAAA
* *
17580196 AAGTT-TTAA
1 AAATTCTAAA
*
17580205 AAATGCTAAGA
1 AAATTCTAA-A
* *
17580216 TAATTTTGAAA
1 AAATTCT-AAA
17580227 AAATTCTAAA
1 AAATTCTAAA
17580237 AAATTCATAAA
1 AAATTC-TAAA
17580248 AAATT
1 AAATT
17580253 ATAACAAGTT
Statistics
Matches: 103, Mismatches: 18, Indels: 28
0.69 0.12 0.19
Matches are distributed among these distances:
8 8 0.08
9 22 0.21
10 31 0.30
11 38 0.37
12 4 0.04
ACGTcount: A:0.59, C:0.08, G:0.03, T:0.30
Consensus pattern (10 bp):
AAATTCTAAA
Found at i:17580186 original size:19 final size:19
Alignment explanation
Indices: 17580143--17580187 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
17580133 TCAAAGAAAT
17580143 TCTAAAAAATAATTAAAAAA
1 TCTAAAAAATAA-TAAAAAA
17580163 T-TAAAAAATACA-AAAAAA
1 TCTAAAAAATA-ATAAAAAA
17580181 TCTAAAA
1 TCTAAAA
17580188 TTTTTAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
18 7 0.30
19 14 0.61
20 2 0.09
ACGTcount: A:0.71, C:0.07, G:0.00, T:0.22
Consensus pattern (19 bp):
TCTAAAAAATAATAAAAAA
Found at i:17580256 original size:10 final size:10
Alignment explanation
Indices: 17580224--17580278 Score: 58
Period size: 10 Copynumber: 5.4 Consensus size: 10
17580214 GATAATTTTG
*
17580224 AAAAAATTCT
1 AAAAAATTAT
17580234 AAAAAATTCAT
1 AAAAAATT-AT
17580245 AAAAAATTAT
1 AAAAAATTAT
* *
17580255 AACAAGTTATT
1 AAAAAATTA-T
17580266 AAAAAATTA-
1 AAAAAATTAT
17580275 AAAA
1 AAAA
17580279 GAAAATTCTG
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
9 4 0.11
10 17 0.45
11 17 0.45
ACGTcount: A:0.65, C:0.05, G:0.02, T:0.27
Consensus pattern (10 bp):
AAAAAATTAT
Found at i:17580386 original size:17 final size:17
Alignment explanation
Indices: 17580356--17580397 Score: 66
Period size: 18 Copynumber: 2.4 Consensus size: 17
17580346 GTAAACTTAA
*
17580356 AAAATTTCAAAAAATCTC
1 AAAATTTAAAAAAATC-C
17580374 AAAATTTAAAAAAATCC
1 AAAATTTAAAAAAATCC
17580391 AAAATTT
1 AAAATTT
17580398 TTCAAAAAGG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 8 0.35
18 15 0.65
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.29
Consensus pattern (17 bp):
AAAATTTAAAAAAATCC
Found at i:17580404 original size:18 final size:18
Alignment explanation
Indices: 17580355--17580405 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 18
17580345 AGTAAACTTA
*
17580355 AAAAATTTCAAAAAATCTC
1 AAAATTTTC-AAAAATCTC
**
17580374 AAAATTTAAAAAAATC-C
1 AAAATTTTCAAAAATCTC
17580391 AAAATTTTTCAAAAA
1 AAAA-TTTTCAAAAA
17580406 GGTTTTGAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
17 5 0.19
18 15 0.58
19 6 0.23
ACGTcount: A:0.61, C:0.12, G:0.00, T:0.27
Consensus pattern (18 bp):
AAAATTTTCAAAAATCTC
Done.