Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008459.1 Hibiscus syriacus cultivar Beakdansim tig00111272_pilon, 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: 632685
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 4
Found at i:357778 original size:25 final size:25
Alignment explanation
Indices: 357733--357803 Score: 67
Period size: 25 Copynumber: 2.8 Consensus size: 25
357723 TTTGTTATTA
*
357733 TTTTATTTAT-TTAATATTTTTCTC
1 TTTTATTTATATTTATATTTTTCTC
*
357757 TTTTGATTTATATTTATATTTTGTCTA
1 TTTT-ATTTATATTTATATTTT-TCTC
*
357784 TTATT-TTTAT-TTTACATTTT
1 TT-TTATTTATATTTATATTTT
357804 GATTTATTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
24 4 0.10
25 15 0.38
26 14 0.35
27 5 0.12
28 2 0.05
ACGTcount: A:0.21, C:0.06, G:0.03, T:0.70
Consensus pattern (25 bp):
TTTTATTTATATTTATATTTTTCTC
Found at i:357804 original size:25 final size:25
Alignment explanation
Indices: 357763--357821 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 25
357753 TCTCTTTTGA
*
357763 TTTATATTTATATTTTG-TCTATTATT
1 TTTAT-TTTACATTTTGATCTATT-TT
*
357789 TTTATTTTACATTTTGATTTATTTT
1 TTTATTTTACATTTTGATCTATTTT
*
357814 TTTCTTTT
1 TTTATTTT
357822 TCTTTTATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
25 19 0.66
26 10 0.34
ACGTcount: A:0.19, C:0.05, G:0.03, T:0.73
Consensus pattern (25 bp):
TTTATTTTACATTTTGATCTATTTT
Found at i:369483 original size:18 final size:18
Alignment explanation
Indices: 369460--369499 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
369450 CTATATCGGT
*
369460 AATTAATAATAATAACAA
1 AATTAATAAAAATAACAA
*
369478 AATTAATAAAAATAATAA
1 AATTAATAAAAATAACAA
369496 AATT
1 AATT
369500 TTCAATTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.30
Consensus pattern (18 bp):
AATTAATAAAAATAACAA
Found at i:371228 original size:6 final size:6
Alignment explanation
Indices: 371219--371251 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
371209 ATTCATATTC
371219 TTATAA TTATAA TTATAA TTATAA TTATAA TTA
1 TTATAA TTATAA TTATAA TTATAA TTATAA TTA
371252 ATTAATTAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
TTATAA
Found at i:371259 original size:8 final size:9
Alignment explanation
Indices: 371244--371276 Score: 50
Period size: 10 Copynumber: 3.7 Consensus size: 9
371234 TAATTATAAT
371244 TATAATTAA
1 TATAATTAA
371253 T-TAATTAA
1 TATAATTAA
371261 TATAATATAA
1 TATAAT-TAA
371271 TATAAT
1 TATAAT
371277 AATTTATGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 8 0.36
9 5 0.23
10 9 0.41
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (9 bp):
TATAATTAA
Found at i:371261 original size:18 final size:18
Alignment explanation
Indices: 371222--371280 Score: 54
Period size: 18 Copynumber: 3.3 Consensus size: 18
371212 CATATTCTTA
371222 TAATTATAATT-A-TAATT
1 TAATTATAATTAATTAA-T
371239 ATAATTATAATTAATTAAT
1 -TAATTATAATTAATTAAT
371258 TAA-TATAATATAATATAA-
1 TAATTATAAT-TAAT-TAAT
371276 TAATT
1 TAATT
371281 TATGTTTACA
Statistics
Matches: 36, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
17 6 0.17
18 21 0.58
19 6 0.17
20 3 0.08
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TAATTATAATTAATTAAT
Found at i:372058 original size:169 final size:172
Alignment explanation
Indices: 371763--372104 Score: 663
Period size: 169 Copynumber: 2.0 Consensus size: 172
371753 AACTTTCTCT
371763 AATTATCATACTAACACGAGTCTGATTAAGTTCGGAATCTATTTTTTGATAGCTCAAAGTCAATA
1 AATTATCATACTAACACGAGTCTGATTAAGTTCGGAATCTATTTTTTGATAGCTCAAAGTCAATA
371828 ACTTTAACAATTAGATTCTCAAATCTCACATTATTTAAATATCGATTTTTATATATTTAATATAG
66 ACTTTAACAATTAGATTCTCAAATCTCACATTATTTAAATATCGATTTTTATATATTTAATATAG
371893 TCTTTTAAACATGAACTTATTGAGTGATAGAAAACAATACCC
131 TCTTTTAAACATGAACTTATTGAGTGATAGAAAACAATACCC
371935 AATTATCATACT-A-ACGAGTCTGATTAAGTTCGGAATCTATTTTTTGATAGCTCAAAGTCAATA
1 AATTATCATACTAACACGAGTCTGATTAAGTTCGGAATCTATTTTTTGATAGCTCAAAGTCAATA
371998 AC-TTAACAATTAGATTCTCAAATCTCACATTATTTAAATATCGATTTTTATATATTTAATATAG
66 ACTTTAACAATTAGATTCTCAAATCTCACATTATTTAAATATCGATTTTTATATATTTAATATAG
372062 TCTTTTAAACATGAACTTATTGAGTGATAGAAAACAATACCC
131 TCTTTTAAACATGAACTTATTGAGTGATAGAAAACAATACCC
372104 A
1 A
372105 TGCACGTGTG
Statistics
Matches: 170, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
169 105 0.62
170 52 0.31
171 1 0.01
172 12 0.07
ACGTcount: A:0.38, C:0.14, G:0.10, T:0.38
Consensus pattern (172 bp):
AATTATCATACTAACACGAGTCTGATTAAGTTCGGAATCTATTTTTTGATAGCTCAAAGTCAATA
ACTTTAACAATTAGATTCTCAAATCTCACATTATTTAAATATCGATTTTTATATATTTAATATAG
TCTTTTAAACATGAACTTATTGAGTGATAGAAAACAATACCC
Found at i:374037 original size:57 final size:57
Alignment explanation
Indices: 373943--374132 Score: 335
Period size: 57 Copynumber: 3.3 Consensus size: 57
373933 CACCTGAATA
373943 TGGAATTATGATCAACATCATAATTCTAGCAATAAGAAAATAAGAATGTATGTTTTC
1 TGGAATTATGATCAACATCATAATTCTAGCAATAAGAAAATAAGAATGTATGTTTTC
* * * *
374000 TGGAATTATGATCAACATCACAATTCTATCAAAAAGAAAACAAGAATGTATGTTTTC
1 TGGAATTATGATCAACATCATAATTCTAGCAATAAGAAAATAAGAATGTATGTTTTC
*
374057 TGGAATTATGATCAACATCATAATTCTAGCAATAAGAAAATAAGAATGTATGCTTTC
1 TGGAATTATGATCAACATCATAATTCTAGCAATAAGAAAATAAGAATGTATGTTTTC
374114 TGGAATTATGATCAACATC
1 TGGAATTATGATCAACATC
374133 TACTCCAAGC
Statistics
Matches: 124, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
57 124 1.00
ACGTcount: A:0.42, C:0.13, G:0.14, T:0.32
Consensus pattern (57 bp):
TGGAATTATGATCAACATCATAATTCTAGCAATAAGAAAATAAGAATGTATGTTTTC
Found at i:379475 original size:14 final size:13
Alignment explanation
Indices: 379427--379474 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
379417 CTACAAAAAA
*
379427 GTTTTTTCTTTTAT
1 GTTTTTTGTTTT-T
*
379441 GATTTTTGGTTTTT
1 G-TTTTTTGTTTTT
*
379455 GGTTTTTGTTTTT
1 GTTTTTTGTTTTT
379468 GTTTTTT
1 GTTTTTT
379475 TATTTTATTT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
13 16 0.57
14 3 0.11
15 9 0.32
ACGTcount: A:0.04, C:0.02, G:0.17, T:0.77
Consensus pattern (13 bp):
GTTTTTTGTTTTT
Found at i:379499 original size:19 final size:18
Alignment explanation
Indices: 379464--379506 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
379454 TGGTTTTTGT
*
379464 TTTTGTTTTTTTATTTTA
1 TTTTGTTTTTTCATTTTA
*
379482 TTTTGTTATTTTCCTTTTA
1 TTTTGTT-TTTTCATTTTA
*
379501 ATTTGT
1 TTTTGT
379507 GGAATGAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 7 0.33
19 14 0.67
ACGTcount: A:0.12, C:0.05, G:0.07, T:0.77
Consensus pattern (18 bp):
TTTTGTTTTTTCATTTTA
Found at i:381866 original size:14 final size:14
Alignment explanation
Indices: 381848--381895 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
381838 TCGTTCGTCT
* *
381848 ATTTATGTTGGTTT
1 ATTTATGTTAGTTC
*
381862 ATTTATATTAGTTC
1 ATTTATGTTAGTTC
* *
381876 GTTTATGTTCGTTC
1 ATTTATGTTAGTTC
381890 ATTTAT
1 ATTTAT
381896 ATTCAACAGA
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.19, C:0.06, G:0.15, T:0.60
Consensus pattern (14 bp):
ATTTATGTTAGTTC
Found at i:382143 original size:24 final size:24
Alignment explanation
Indices: 382116--382168 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
382106 TTTACATTTG
* *
382116 TTTATGTTCATTCGTTTTTGTTCA
1 TTTATGTTCATTCATTTGTGTTCA
* *
382140 TTTACGTTCATTCATTTGTGTTCG
1 TTTATGTTCATTCATTTGTGTTCA
382164 TTTAT
1 TTTAT
382169 CACTTTAACG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.13, C:0.13, G:0.13, T:0.60
Consensus pattern (24 bp):
TTTATGTTCATTCATTTGTGTTCA
Found at i:382625 original size:34 final size:34
Alignment explanation
Indices: 382583--382650 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
382573 ACAACTTATA
382583 GGTCCACAGTGGACCGAATAATGAATACAAAGTT
1 GGTCCACAGTGGACCGAATAATGAATACAAAGTT
382617 GGTCCACAGTGGACCGAATAATGAATACAAAGTT
1 GGTCCACAGTGGACCGAATAATGAATACAAAGTT
382651 CAAAGAAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.38, C:0.18, G:0.24, T:0.21
Consensus pattern (34 bp):
GGTCCACAGTGGACCGAATAATGAATACAAAGTT
Found at i:391472 original size:32 final size:32
Alignment explanation
Indices: 391431--391529 Score: 198
Period size: 32 Copynumber: 3.1 Consensus size: 32
391421 AACTAAAATC
391431 TTATGATTTGTCATAGAGAGATCAAGATTTCA
1 TTATGATTTGTCATAGAGAGATCAAGATTTCA
391463 TTATGATTTGTCATAGAGAGATCAAGATTTCA
1 TTATGATTTGTCATAGAGAGATCAAGATTTCA
391495 TTATGATTTGTCATAGAGAGATCAAGATTTCA
1 TTATGATTTGTCATAGAGAGATCAAGATTTCA
391527 TTA
1 TTA
391530 GGGTTTTGAT
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 67 1.00
ACGTcount: A:0.34, C:0.09, G:0.18, T:0.38
Consensus pattern (32 bp):
TTATGATTTGTCATAGAGAGATCAAGATTTCA
Found at i:393766 original size:103 final size:103
Alignment explanation
Indices: 393587--393789 Score: 352
Period size: 103 Copynumber: 2.0 Consensus size: 103
393577 ACTAAGAAGA
393587 TTTATCACGGCAGGGGTAAATAAAAGTAGTTTAACATACATAAAATAATATTTTTGACAATTTTA
1 TTTATCACGGCAGGGGTAAATAAAAGTAGTTTAACATACATAAAATAATATTTTTGACAATTTTA
*
393652 CGACTAAGCTGAAGTTATAGTGGCATAAAAACAACTGG
66 CAACTAAGCTGAAGTTATAGTGGCATAAAAACAACTGG
* * * * *
393690 TTTATCATGGCAGGGGTAAATAAAAGTAGTTTAACATACATAACATATTGTTTTTGACACTTTTA
1 TTTATCACGGCAGGGGTAAATAAAAGTAGTTTAACATACATAAAATAATATTTTTGACAATTTTA
393755 CAACTAAGCTGAAGTTATAGTGGCATAAAAACAAC
66 CAACTAAGCTGAAGTTATAGTGGCATAAAAACAAC
393790 GTAAAGTGGA
Statistics
Matches: 94, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
103 94 1.00
ACGTcount: A:0.40, C:0.12, G:0.17, T:0.31
Consensus pattern (103 bp):
TTTATCACGGCAGGGGTAAATAAAAGTAGTTTAACATACATAAAATAATATTTTTGACAATTTTA
CAACTAAGCTGAAGTTATAGTGGCATAAAAACAACTGG
Found at i:395920 original size:21 final size:17
Alignment explanation
Indices: 395870--395914 Score: 83
Period size: 17 Copynumber: 2.7 Consensus size: 17
395860 AACTTAATTA
395870 TCAAT-TATAATTTAGG
1 TCAATATATAATTTAGG
395886 TCAATATATAATTTAGG
1 TCAATATATAATTTAGG
395903 TCAATATATAAT
1 TCAATATATAAT
395915 AAATTTTATT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
16 5 0.18
17 23 0.82
ACGTcount: A:0.42, C:0.07, G:0.09, T:0.42
Consensus pattern (17 bp):
TCAATATATAATTTAGG
Found at i:403721 original size:2 final size:2
Alignment explanation
Indices: 403714--403749 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
403704 ATCACGATTG
403714 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
403750 TCCCTATGTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:407904 original size:15 final size:16
Alignment explanation
Indices: 407860--407906 Score: 60
Period size: 16 Copynumber: 3.0 Consensus size: 16
407850 ATTCATACAT
*
407860 AGCATCTGAATCATTC
1 AGCATTTGAATCATTC
*
407876 AGTATTTGAATCATTC
1 AGCATTTGAATCATTC
*
407892 AGCGTTT-AATCATTC
1 AGCATTTGAATCATTC
407907 TGAAGTAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
15 8 0.30
16 19 0.70
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.38
Consensus pattern (16 bp):
AGCATTTGAATCATTC
Found at i:407999 original size:19 final size:20
Alignment explanation
Indices: 407962--408000 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
407952 TATTTACTTT
*
407962 TTTAAAAAGTCATTTTTAAAC
1 TTTAAAAAG-CATTCTTAAAC
407983 TTTAAAAA-CATTCTTAAA
1 TTTAAAAAGCATTCTTAAA
408001 GGAATAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
21 8 0.47
ACGTcount: A:0.46, C:0.10, G:0.03, T:0.41
Consensus pattern (20 bp):
TTTAAAAAGCATTCTTAAAC
Found at i:408186 original size:19 final size:18
Alignment explanation
Indices: 408153--408188 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
408143 AGAAAAAAAA
*
408153 TAAAAAAAATACTTAATT
1 TAAAAAAAAAACTTAATT
408171 TAAAAAAAAAAGCTTAAT
1 TAAAAAAAAAA-CTTAAT
408189 ACAAAAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.64, C:0.06, G:0.03, T:0.28
Consensus pattern (18 bp):
TAAAAAAAAAACTTAATT
Found at i:408715 original size:15 final size:15
Alignment explanation
Indices: 408674--408725 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
408664 CATATAAGTT
**
408674 AATAATTTTGATAAA
1 AATAATTTTTTTAAA
**
408689 AATAA-TAATTTAAA
1 AATAATTTTTTTAAA
408703 AATAATTTTTTTAAA
1 AATAATTTTTTTAAA
408718 AATTAATT
1 AA-TAATT
408726 AAATCTAATA
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
14 10 0.34
15 14 0.48
16 5 0.17
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (15 bp):
AATAATTTTTTTAAA
Found at i:411275 original size:19 final size:20
Alignment explanation
Indices: 411224--411277 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 20
411214 AAACATTAAG
*
411224 GAAAGTTTCGAAACTCTTGA
1 GAAAGTTTCGAAACTCATGA
* *
411244 GATAGTTTTGAAACTACAT-A
1 GAAAGTTTCGAAACT-CATGA
411264 -AAAGTTTCGAAACT
1 GAAAGTTTCGAAACT
411278 TTTTGGGCTA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
19 12 0.43
20 14 0.50
21 2 0.07
ACGTcount: A:0.39, C:0.13, G:0.17, T:0.31
Consensus pattern (20 bp):
GAAAGTTTCGAAACTCATGA
Found at i:412848 original size:3 final size:3
Alignment explanation
Indices: 412840--412876 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
412830 CTTTCTTTCT
412840 TTC TTC TTC TTC TTC -TC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
412877 ATTACCTGTT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:412860 original size:17 final size:16
Alignment explanation
Indices: 412836--412873 Score: 67
Period size: 17 Copynumber: 2.3 Consensus size: 16
412826 CTTACTTTCT
412836 TTCTTTCTTCTTCTTC
1 TTCTTTCTTCTTCTTC
412852 TTCTCTTCTTCTTCTTC
1 TTCT-TTCTTCTTCTTC
412869 TTCTT
1 TTCTT
412874 CTTATTACCT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 5 0.24
17 16 0.76
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (16 bp):
TTCTTTCTTCTTCTTC
Found at i:415193 original size:2 final size:2
Alignment explanation
Indices: 415186--415210 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
415176 GAAAAATTCA
415186 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
415211 AAATACCTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:415899 original size:16 final size:16
Alignment explanation
Indices: 415869--415901 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
415859 TAAAATATTC
415869 TATAATAATATAAAAT
1 TATAATAATATAAAAT
415885 TATAA-AATATCAAAAT
1 TATAATAATAT-AAAAT
415901 T
1 T
415902 TATTATATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (16 bp):
TATAATAATATAAAAT
Found at i:418501 original size:21 final size:21
Alignment explanation
Indices: 418477--418554 Score: 66
Period size: 21 Copynumber: 3.7 Consensus size: 21
418467 CCTTCAGGAT
418477 ATATATGTAATCCTTTGGAAC
1 ATATATGTAATCCTTTGGAAC
* * * * *
418498 ATATATGCAGTTCTTCGGGAC
1 ATATATGTAATCCTTTGGAAC
* ** *
418519 ATATATTTGGTCCTTTGGAAT
1 ATATATGTAATCCTTTGGAAC
*
418540 ATATATGTGATCCTT
1 ATATATGTAATCCTT
418555 AAGGAGTGGT
Statistics
Matches: 43, Mismatches: 14, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
21 43 1.00
ACGTcount: A:0.27, C:0.14, G:0.18, T:0.41
Consensus pattern (21 bp):
ATATATGTAATCCTTTGGAAC
Found at i:418599 original size:19 final size:21
Alignment explanation
Indices: 418560--418603 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
418550 TCCTTAAGGA
418560 GTGGTCATTCTGGACATATAT
1 GTGGTCATTCTGGACATATAT
* *
418581 GTGGTCATTCGGGATATATAT
1 GTGGTCATTCTGGACATATAT
418602 GT
1 GT
418604 ATATATGGGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.23, C:0.11, G:0.27, T:0.39
Consensus pattern (21 bp):
GTGGTCATTCTGGACATATAT
Found at i:420705 original size:189 final size:189
Alignment explanation
Indices: 420385--420762 Score: 756
Period size: 189 Copynumber: 2.0 Consensus size: 189
420375 TGCGGGAAGA
420385 AACTTAATGGAACGGTTTATGGGAGTTCGTGTGGGCAGCCGTGGAGGTACATTAGCTGGGATGGA
1 AACTTAATGGAACGGTTTATGGGAGTTCGTGTGGGCAGCCGTGGAGGTACATTAGCTGGGATGGA
420450 ATACACTTCACTGAGGCAACCAACTTGTGGGTTGCGAATCGCATTTTTAATGGATCTTTCTCCGA
66 ATACACTTCACTGAGGCAACCAACTTGTGGGTTGCGAATCGCATTTTTAATGGATCTTTCTCCGA
420515 TCCACAGGTTTCTATCAACAATGCTTGTCACCGGTCATGACTATAGGTGCAATCCCTTG
131 TCCACAGGTTTCTATCAACAATGCTTGTCACCGGTCATGACTATAGGTGCAATCCCTTG
420574 AACTTAATGGAACGGTTTATGGGAGTTCGTGTGGGCAGCCGTGGAGGTACATTAGCTGGGATGGA
1 AACTTAATGGAACGGTTTATGGGAGTTCGTGTGGGCAGCCGTGGAGGTACATTAGCTGGGATGGA
420639 ATACACTTCACTGAGGCAACCAACTTGTGGGTTGCGAATCGCATTTTTAATGGATCTTTCTCCGA
66 ATACACTTCACTGAGGCAACCAACTTGTGGGTTGCGAATCGCATTTTTAATGGATCTTTCTCCGA
420704 TCCACAGGTTTCTATCAACAATGCTTGTCACCGGTCATGACTATAGGTGCAATCCCTTG
131 TCCACAGGTTTCTATCAACAATGCTTGTCACCGGTCATGACTATAGGTGCAATCCCTTG
420763 TATCTGTAAT
Statistics
Matches: 189, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
189 189 1.00
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.30
Consensus pattern (189 bp):
AACTTAATGGAACGGTTTATGGGAGTTCGTGTGGGCAGCCGTGGAGGTACATTAGCTGGGATGGA
ATACACTTCACTGAGGCAACCAACTTGTGGGTTGCGAATCGCATTTTTAATGGATCTTTCTCCGA
TCCACAGGTTTCTATCAACAATGCTTGTCACCGGTCATGACTATAGGTGCAATCCCTTG
Found at i:421039 original size:12 final size:12
Alignment explanation
Indices: 421022--421046 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
421012 GTCAAATAAT
421022 TTAGGCATCAAA
1 TTAGGCATCAAA
421034 TTAGGCATCAAA
1 TTAGGCATCAAA
421046 T
1 T
421047 GGTGCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.16, G:0.16, T:0.28
Consensus pattern (12 bp):
TTAGGCATCAAA
Found at i:425240 original size:12 final size:12
Alignment explanation
Indices: 425223--425247 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
425213 GTCAAATAAT
425223 TTAGGCACCAAA
1 TTAGGCACCAAA
425235 TTAGGCACCAAA
1 TTAGGCACCAAA
425247 T
1 T
425248 GGTGCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.24, G:0.16, T:0.20
Consensus pattern (12 bp):
TTAGGCACCAAA
Found at i:428972 original size:21 final size:19
Alignment explanation
Indices: 428946--428984 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
428936 AAATGGGTAA
428946 TGTTTTCTGTGTTTTGTGTTC
1 TGTTTTCTG-GTTTT-TGTTC
*
428967 TGTTTTTTGGTTTTTGTT
1 TGTTTTCTGGTTTTTGTT
428985 GGGAGTGATG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 5 0.29
21 8 0.47
ACGTcount: A:0.00, C:0.05, G:0.23, T:0.72
Consensus pattern (19 bp):
TGTTTTCTGGTTTTTGTTC
Found at i:438230 original size:2 final size:2
Alignment explanation
Indices: 438223--438253 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
438213 GAAATCTAAG
438223 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 T
438254 TTAATGATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:449062 original size:21 final size:22
Alignment explanation
Indices: 449015--449067 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
449005 AGAAATTGCA
449015 CCGAAGTG-CCACATAGAATGTC
1 CCGAAG-GACCACATAGAATGTC
*
449037 TCGAAGGACCACATAG-ATGTC
1 CCGAAGGACCACATAGAATGTC
449058 CCGAAGGACC
1 CCGAAGGACC
449068 GCGTAGATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 15 0.54
22 13 0.46
ACGTcount: A:0.32, C:0.28, G:0.25, T:0.15
Consensus pattern (22 bp):
CCGAAGGACCACATAGAATGTC
Found at i:449175 original size:44 final size:44
Alignment explanation
Indices: 449127--449216 Score: 101
Period size: 44 Copynumber: 2.0 Consensus size: 44
449117 ATACCTTGTT
* *
449127 TCACATAAAC-TATTAATCACATAGATCATGTCTCATAGCATATA
1 TCACATAAACATA-TAATCACATAGATCATATCGCATAGCATATA
*** * *
449171 TCACATGTGCATATAATCACATATATCATATCGCATAGCTTATA
1 TCACATAAACATATAATCACATAGATCATATCGCATAGCATATA
449215 TC
1 TC
449217 TTGTTCTCAT
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
44 36 0.95
45 2 0.05
ACGTcount: A:0.38, C:0.21, G:0.08, T:0.33
Consensus pattern (44 bp):
TCACATAAACATATAATCACATAGATCATATCGCATAGCATATA
Found at i:449252 original size:16 final size:17
Alignment explanation
Indices: 449223--449255 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
449213 TATCTTGTTC
449223 TCATATGTTCACATAGA
1 TCATATGTTCACATAGA
449240 TCATATG-TCACATAGA
1 TCATATGTTCACATAGA
449256 ATAACATGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.36, C:0.18, G:0.12, T:0.33
Consensus pattern (17 bp):
TCATATGTTCACATAGA
Found at i:453332 original size:25 final size:27
Alignment explanation
Indices: 453278--453332 Score: 62
Period size: 26 Copynumber: 2.1 Consensus size: 27
453268 TGACCGATTG
*
453278 ATATTATAACTGAAAAAGTCAAAAAGA
1 ATATTATAACTGAAAAAGTCAAAAAAA
*
453305 ATATTA-AATTGAAAAA-T-AAAAATAA
1 ATATTATAACTGAAAAAGTCAAAAA-AA
453330 ATA
1 ATA
453333 GAGAGAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
24 5 0.20
25 5 0.20
26 9 0.36
27 6 0.24
ACGTcount: A:0.64, C:0.04, G:0.07, T:0.25
Consensus pattern (27 bp):
ATATTATAACTGAAAAAGTCAAAAAAA
Found at i:453396 original size:20 final size:21
Alignment explanation
Indices: 453357--453397 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
453347 TAAAAAAGGT
453357 AAATAAATAAAATAAGTAAAA
1 AAATAAATAAAATAAGTAAAA
* *
453378 AAATAAA-AATATAATTAAAA
1 AAATAAATAAAATAAGTAAAA
453398 GGGAAGATAA
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:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (21 bp):
AAATAAATAAAATAAGTAAAA
Found at i:453968 original size:19 final size:19
Alignment explanation
Indices: 453944--453982 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
453934 TCGAATGCAT
453944 TCCATGCACCGATGCACTC
1 TCCATGCACCGATGCACTC
*
453963 TCCATGCATCGATGCACTC
1 TCCATGCACCGATGCACTC
453982 T
1 T
453983 GAATATTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.38, G:0.15, T:0.26
Consensus pattern (19 bp):
TCCATGCACCGATGCACTC
Found at i:453999 original size:65 final size:63
Alignment explanation
Indices: 453881--454089 Score: 210
Period size: 65 Copynumber: 3.2 Consensus size: 63
453871 TATTCAAAGG
* *
453881 CATGCACCGATGCA-TCAGTCCATGCATCGATGCATCGATGAAT-TAATT-GAACATCGAATGCA
1 CATGCACCGATGCACTC--TCCATGCATCGATGCATC--TGAATAT-TTTCAAACATCGAATGCA
*
453943 TTC
61 TTT
453946 CATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAAAACATCGAATGCATTT
1 CATGCACCGATGCACTCTCCATGCATCGATGCA-TCTGAATATTTTC-AAACATCGAATGCATTT
* * ** * **
454011 GATGCATCGATGCACAAGT-CATGCATCGATGCATCAGGCTATTTTTCAAACATCGAATGCATTT
1 CATGCACCGATGCAC-TCTCCATGCATCGATGCATCTGAATA-TTTTCAAACATCGAATGCATTT
*
454075 CATGCATCGATGCAC
1 CATGCACCGATGCAC
454090 ACTTGGTGCA
Statistics
Matches: 126, Mismatches: 11, Indels: 15
0.83 0.07 0.10
Matches are distributed among these distances:
63 7 0.06
64 53 0.42
65 63 0.50
66 3 0.02
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.28
Consensus pattern (63 bp):
CATGCACCGATGCACTCTCCATGCATCGATGCATCTGAATATTTTCAAACATCGAATGCATTT
Found at i:454082 original size:64 final size:66
Alignment explanation
Indices: 453930--454090 Score: 213
Period size: 65 Copynumber: 2.5 Consensus size: 66
453920 GAATTAATTG
* * * *
453930 AACATCGAATGCATTCCATGCACCGATGCAC-TCTCCATGCATCGATGCACTCTGAATATTTTCA
1 AACATCGAATGCATTTCATGCATCGATGCACAACTCCATGCATCGATGCACTCAGAATATTTTCA
453994 A
66 A
* * **
453995 AACATCGAATGCATTTGATGCATCGATGCACAAGT-CATGCATCGATGCA-TCAGGCTATTTTTC
1 AACATCGAATGCATTTCATGCATCGATGCACAACTCCATGCATCGATGCACTCAGAATA-TTTTC
454058 -A
65 AA
454059 AACATCGAATGCATTTCATGCATCGATGCACA
1 AACATCGAATGCATTTCATGCATCGATGCACA
454091 CTTGGTGCAC
Statistics
Matches: 85, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
64 37 0.44
65 47 0.55
66 1 0.01
ACGTcount: A:0.30, C:0.25, G:0.16, T:0.28
Consensus pattern (66 bp):
AACATCGAATGCATTTCATGCATCGATGCACAACTCCATGCATCGATGCACTCAGAATATTTTCA
A
Found at i:454105 original size:64 final size:64
Alignment explanation
Indices: 453930--454110 Score: 220
Period size: 64 Copynumber: 2.8 Consensus size: 64
453920 GAATTAATTG
* * * * *
453930 AACATCGAATGCATTCCATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAA
1 AACATCGAATGCATTTCATGCATCGATGCACACTTCATGCATCGATGCA-TCAGAATATTTTCAA
* ** **
453995 AACATCGAATGCATTTGATGCATCGATGCACAAGTCATGCATCGATGCATCAGGCTATTTTTC-A
1 AACATCGAATGCATTTCATGCATCGATGCACACTTCATGCATCGATGCATCAGAATA-TTTTCAA
** *
454059 AACATCGAATGCATTTCATGCATCGATGCACACTTGGTGCACCGATGCATCA
1 AACATCGAATGCATTTCATGCATCGATGCACACTTCATGCATCGATGCATCA
454111 AGTGTTCCAA
Statistics
Matches: 99, Mismatches: 16, Indels: 3
0.84 0.14 0.03
Matches are distributed among these distances:
64 52 0.53
65 47 0.47
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.28
Consensus pattern (64 bp):
AACATCGAATGCATTTCATGCATCGATGCACACTTCATGCATCGATGCATCAGAATATTTTCAA
Found at i:458273 original size:30 final size:30
Alignment explanation
Indices: 457854--458256 Score: 779
Period size: 30 Copynumber: 13.4 Consensus size: 30
457844 TCCGAAGGAC
457854 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
457884 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
457914 CTATCCAGAGGTCATAAAGATCCTCAGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
457944 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
457974 CTATCCAGAGGTCATAAAGATCCTCAGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
458004 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
458034 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
458064 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
458094 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
458124 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
458154 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
458184 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
458214 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
458244 CTATCCATAGGTC
1 CTATCCAGAGGTC
458257 CCGAAGAACC
Statistics
Matches: 368, Mismatches: 5, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
30 368 1.00
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.24
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:458296 original size:31 final size:31
Alignment explanation
Indices: 458242--458334 Score: 98
Period size: 31 Copynumber: 3.0 Consensus size: 31
458232 GATCCTCGGT
* *
458242 AACTATCCATAGGTCCCGAAGAACCTAGGTA
1 AACTATCCATATGTCCCGAAGAACATAGGTA
* **
458273 AACTATCCATATGTTCCTTAGAACATAGGTA
1 AACTATCCATATGTCCCGAAGAACATAGGTA
* * *
458304 TACTGTCCATATGTCTCGAA-AGACATAGGTA
1 AACTATCCATATGTCCCGAAGA-ACATAGGTA
458335 GTTCTTTGAC
Statistics
Matches: 50, Mismatches: 11, Indels: 2
0.79 0.17 0.03
Matches are distributed among these distances:
30 1 0.02
31 49 0.98
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.27
Consensus pattern (31 bp):
AACTATCCATATGTCCCGAAGAACATAGGTA
Found at i:462874 original size:30 final size:30
Alignment explanation
Indices: 462575--462857 Score: 539
Period size: 30 Copynumber: 9.4 Consensus size: 30
462565 TCCGAAGGAC
462575 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
462605 TTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
462635 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
462665 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
462695 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
462725 CTATCCAGAGTTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
462755 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
462785 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
462815 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
462845 CTATCCATAGGTC
1 CTATCCAGAGGTC
462858 CCGAAGAACC
Statistics
Matches: 248, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 248 1.00
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.24
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:462897 original size:31 final size:31
Alignment explanation
Indices: 462843--462935 Score: 89
Period size: 31 Copynumber: 3.0 Consensus size: 31
462833 GATCCTCGGT
* *
462843 AACTATCCATAGGTCCCGAAGAACCTAGGTA
1 AACTATCCATATGTCCCGAAGAACATAGGTA
* **
462874 AACTATCCATATGTTCCTTAGAACATAGGTA
1 AACTATCCATATGTCCCGAAGAACATAGGTA
* * * *
462905 TACTGTACATATGTCTCGAA-AGACATAGGTA
1 AACTATCCATATGTCCCGAAGA-ACATAGGTA
462936 GTTCTTTGAC
Statistics
Matches: 49, Mismatches: 12, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
30 1 0.02
31 48 0.98
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.27
Consensus pattern (31 bp):
AACTATCCATATGTCCCGAAGAACATAGGTA
Found at i:463298 original size:2 final size:2
Alignment explanation
Indices: 463286--463338 Score: 99
Period size: 2 Copynumber: 27.0 Consensus size: 2
463276 TACACAACTC
463286 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
463327 AT AT AT AT AT AT
1 AT AT AT AT AT AT
463339 TGTAACATGT
Statistics
Matches: 50, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 49 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:464451 original size:2 final size:2
Alignment explanation
Indices: 464444--464485 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
464434 ATCCTTATCC
464444 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
464486 CATTTAATTA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:468944 original size:21 final size:21
Alignment explanation
Indices: 468902--468945 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
468892 ACCCCGGGAG
*
468902 CTAGTTCTTCACGAGCTGCTC
1 CTAGTTCTTCACGAGCTCCTC
* *
468923 CTAGTTCTTCTCGTGCTCCTC
1 CTAGTTCTTCACGAGCTCCTC
468944 CT
1 CT
468946 CCTCCTCCAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.09, C:0.36, G:0.16, T:0.39
Consensus pattern (21 bp):
CTAGTTCTTCACGAGCTCCTC
Found at i:470006 original size:19 final size:19
Alignment explanation
Indices: 469962--470013 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 19
469952 AATTAATTGA
469962 ACATCGAATGCA-T-TCCAT
1 ACATCG-ATGCACTCTCCAT
* *
469980 GCACCGATGCACTCTCCAT
1 ACATCGATGCACTCTCCAT
469999 ACATCGATGCACTCT
1 ACATCGATGCACTCT
470014 GAATATTTTC
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
17 5 0.18
18 5 0.18
19 18 0.64
ACGTcount: A:0.27, C:0.35, G:0.13, T:0.25
Consensus pattern (19 bp):
ACATCGATGCACTCTCCAT
Found at i:470105 original size:64 final size:63
Alignment explanation
Indices: 469912--470121 Score: 226
Period size: 65 Copynumber: 3.3 Consensus size: 63
469902 TATTCAAAGG
* * * *
469912 CATGCATCGATGCATCAGTCCATGCATCGATGCATCGATGAATTAATT-GAACATCGAATGCATT
1 CATGCATCGATGCA-CAGTCCATGCATCGATGCATC-AGGTATT-TTTAAAACATCGAATGCATT
*
469976 C
63 T
* ** * * * *
469977 CATGCACCGATGCACTCTCCATACATCGATGCACTCTGAATATTTTCAAAACATCGAATGCATTT
1 CATGCATCGATGCACAGTCCATGCATCGATGCA-TCAG-GTATTTTTAAAACATCGAATGCATTT
*
470042 GATGCATCGATGCACAAGT-CATGCATCGATGCATCAGGCTATTTTTAAAACATCGAATGCATTT
1 CATGCATCGATGCAC-AGTCCATGCATCGATGCATCAGG-TATTTTTAAAACATCGAATGCATTT
470106 CATGCATCGATGCACA
1 CATGCATCGATGCACA
470122 CTTGGTGCAC
Statistics
Matches: 119, Mismatches: 21, Indels: 12
0.78 0.14 0.08
Matches are distributed among these distances:
63 1 0.01
64 58 0.49
65 59 0.50
66 1 0.01
ACGTcount: A:0.31, C:0.24, G:0.17, T:0.28
Consensus pattern (63 bp):
CATGCATCGATGCACAGTCCATGCATCGATGCATCAGGTATTTTTAAAACATCGAATGCATTT
Found at i:470136 original size:64 final size:64
Alignment explanation
Indices: 469912--470141 Score: 223
Period size: 64 Copynumber: 3.6 Consensus size: 64
469902 TATTCAAAGG
* * * *
469912 CATGCATCGATGCATCAGTCCATGCATCGATGCATCGATGAAT-TAATT--GAACATCGAATGCA
1 CATGCATCGATGCA-CACTTCATGCATCGATGCATC-A-GAATAT-TTTCAAAACATCGAATGCA
*
469974 TTC
62 TTT
* * * * *
469977 CATGCACCGATGCACTCTCCATACATCGATGCACTCTGAATATTTTCAAAACATCGAATGCATTT
1 CATGCATCGATGCACACTTCATGCATCGATGCA-TCAGAATATTTTCAAAACATCGAATGCATTT
* ** ** *
470042 GATGCATCGATGCACAAGTCATGCATCGATGCATCAGGCTATTTTTAAAACATCGAATGCATTT
1 CATGCATCGATGCACACTTCATGCATCGATGCATCAGAATATTTTCAAAACATCGAATGCATTT
** *
470106 CATGCATCGATGCACACTTGGTGCACCGATGCATCA
1 CATGCATCGATGCACACTTCATGCATCGATGCATCA
470142 AGTGTTCCAA
Statistics
Matches: 136, Mismatches: 25, Indels: 9
0.80 0.15 0.05
Matches are distributed among these distances:
63 6 0.04
64 74 0.54
65 56 0.41
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.28
Consensus pattern (64 bp):
CATGCATCGATGCACACTTCATGCATCGATGCATCAGAATATTTTCAAAACATCGAATGCATTT
Found at i:472696 original size:84 final size:83
Alignment explanation
Indices: 472451--472862 Score: 373
Period size: 85 Copynumber: 4.8 Consensus size: 83
472441 TGTCATCGAA
* * * * * * * *
472451 CTGAATGGAATCAAACTCGACA-GTTTTTGTTGACAGATAGCTTTTCTCGACTTAAGATATGTTG
1 CTGAATGTAATCGAACTCGA-AGGTCTTTGTTGACAGATAGC-CTTCTCGCCTTGAGCTATGCTG
*
472515 TAAATTTGACATGCCCTTGAG
64 TAAATTTGATATG-CCTTGAG
** * * * * * * * *
472536 CAAAAAGAAATCGAACTCGAAGATATTTGTTGATAGATAACCCTTCTCGCCTTGAGTTATGCTAT
1 CTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGAT-AGCCTTCTCGCCTTGAGCTATGCTGT
*
472601 AAATTTAATATGTCCTTGAG
65 AAATTTGATATG-CCTTGAG
* * *
472621 CTGAATGTAATCAAACTCAAAGGTCTTTGTTGACAGATAGCCTTATCGCCTTGAGCTATGCTGTA
1 CTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAGCCTTCTCGCCTTGAGCTATGCTGTA
* *
472686 AATTTGATATGCATTTGAC
66 AATTTGATATGC-CTTGAG
* * *
472705 CTGAATGTAACCGAACTCGAAGGTCTTTGTTG-CTGGAAGATAACCCTTCTCGCCTTGAGCTATA
1 CTGAATGTAATCGAACTCGAAGGTCTTTGTTGAC----AGAT-AGCCTTCTCGCCTTGAGCTATG
472769 CTGTAAATTTGATATGCCATTGAG
61 CTGTAAATTTGATATGCC-TTGAG
* *
472793 CTGAATATAATCGAACTCGAAGG--TTTGTTGCTAGCAGATAGTCATTCTCGCCTTGAGCTATGC
1 CTGAATGTAATCGAACTCGAAGGTCTTTGTTG--A-CAGATAG-CCTTCTCGCCTTGAGCTATGC
*
472856 TGCAAAT
62 TGTAAAT
472863 AGTGTAACAC
Statistics
Matches: 265, Mismatches: 48, Indels: 27
0.78 0.14 0.08
Matches are distributed among these distances:
83 2 0.01
84 67 0.25
85 92 0.35
86 38 0.14
87 4 0.02
88 61 0.23
90 1 0.00
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Consensus pattern (83 bp):
CTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAGCCTTCTCGCCTTGAGCTATGCTGTA
AATTTGATATGCCTTGAG
Found at i:472782 original size:88 final size:87
Alignment explanation
Indices: 472494--472862 Score: 362
Period size: 84 Copynumber: 4.3 Consensus size: 87
472484 CAGATAGCTT
* * * * * * ** * * *
472494 TTCTCGACTTAAGATATGTTGTAAATTTGACATGCCCTTGAGCAAAAAGAAATCGAACTCGAAGA
1 TTCTCGCCTTGAGCTATGCTGTAAATTTGATATGCCATTGAGCTGAATGTAATCGAACTCGAAGG
* *
472559 TATTTGTTGAT--AGATAACCC
66 TCTTTGTTGCTGAAGATAACCC
* * * * *
472579 TTCTCGCCTTGAGTTATGCTATAAATTTAATATGTCC-TTGAGCTGAATGTAATCAAACTCAAAG
1 TTCTCGCCTTGAGCTATGCTGTAAATTTGATATG-CCATTGAGCTGAATGTAATCGAACTCGAAG
*
472643 GTCTTTG-T--TGACAGAT-AGCC
65 GTCTTTGTTGCTGA-AGATAACCC
* * *
472663 TTATCGCCTTGAGCTATGCTGTAAATTTGATATG-CATTTGACCTGAATGTAACCGAACTCGAAG
1 TTCTCGCCTTGAGCTATGCTGTAAATTTGATATGCCA-TTGAGCTGAATGTAATCGAACTCGAAG
472727 GTCTTTGTTGCTGGAAGATAACCC
65 GTCTTTGTTGCT-GAAGATAACCC
* *
472751 TTCTCGCCTTGAGCTATACTGTAAATTTGATATGCCATTGAGCTGAATATAATCGAACTCGAAGG
1 TTCTCGCCTTGAGCTATGCTGTAAATTTGATATGCCATTGAGCTGAATGTAATCGAACTCGAAGG
* ** *
472816 --TTTGTTGCTAGCAGATAGTCA
66 TCTTTGTTGCT-GAAGATAACCC
*
472837 TTCTCGCCTTGAGCTATGCTGCAAAT
1 TTCTCGCCTTGAGCTATGCTGTAAAT
472863 AGTGTAACAC
Statistics
Matches: 235, Mismatches: 37, Indels: 23
0.80 0.13 0.08
Matches are distributed among these distances:
82 2 0.01
84 64 0.27
85 58 0.25
86 42 0.18
87 5 0.02
88 62 0.26
89 2 0.01
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Consensus pattern (87 bp):
TTCTCGCCTTGAGCTATGCTGTAAATTTGATATGCCATTGAGCTGAATGTAATCGAACTCGAAGG
TCTTTGTTGCTGAAGATAACCC
Found at i:472794 original size:172 final size:168
Alignment explanation
Indices: 472451--472862 Score: 441
Period size: 172 Copynumber: 2.4 Consensus size: 168
472441 TGTCATCGAA
* * * * * * * *
472451 CTGAATGGAATCAAACTCGACAGTTTTTGTTGACAGATAGCTTTTCTCGACTTAAGATATGTTGT
1 CTGAATGTAATCAAACTC-AAAGGTTTTGTTGACAGATAGC-ATTCTCGCCTTGAGCTATGCTGT
* * *
472516 AAATTTGACATGCCCTTGAGCAAAAAGAAATCGAACTCGAAGATATTTGTTGATAGATAACCCTT
64 AAATTTGACATGCACTTGACCAAAAAGAAACCGAACTCGAAGATATTTGTTGATAGATAACCCTT
* *
472581 CTCGCCTTGAGTTATGCTATAAATTTAATATGTCCTTGAG
129 CTCGCCTTGAGCTATACTATAAATTTAATATGTCCTTGAG
* *
472621 CTGAATGTAATCAAACTCAAAGGTCTTTGTTGACAGATAGCCTTATCGCCTTGAGCTATGCTGTA
1 CTGAATGTAATCAAACTCAAAGGT-TTTGTTGACAGATAGCATTCTCGCCTTGAGCTATGCTGTA
* * ** * * * * *
472686 AATTTGATATGCATTTGACCTGAATGTAACCGAACTCGAAGGTCTTTGTTGCTGGAAGATAACCC
65 AATTTGACATGCACTTGACCAAAAAGAAACCGAACTCGAAGATATTTGTTGAT---AGATAACCC
* *
472751 TTCTCGCCTTGAGCTATACTGTAAATTTGATATG-CCATTGAG
127 TTCTCGCCTTGAGCTATACTATAAATTTAATATGTCC-TTGAG
* * *
472793 CTGAATATAATCGAACTCGAAGG-TTTGTTGCTAGCAGATAGTCATTCTCGCCTTGAGCTATGCT
1 CTGAATGTAATCAAACTCAAAGGTTTTGTTG--A-CAGATAG-CATTCTCGCCTTGAGCTATGCT
*
472857 GCAAAT
62 GTAAAT
472863 AGTGTAACAC
Statistics
Matches: 202, Mismatches: 31, Indels: 14
0.82 0.13 0.06
Matches are distributed among these distances:
169 63 0.31
170 40 0.20
171 2 0.01
172 65 0.32
173 7 0.03
174 25 0.12
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Consensus pattern (168 bp):
CTGAATGTAATCAAACTCAAAGGTTTTGTTGACAGATAGCATTCTCGCCTTGAGCTATGCTGTAA
ATTTGACATGCACTTGACCAAAAAGAAACCGAACTCGAAGATATTTGTTGATAGATAACCCTTCT
CGCCTTGAGCTATACTATAAATTTAATATGTCCTTGAG
Found at i:474196 original size:21 final size:21
Alignment explanation
Indices: 474171--474211 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
474161 GGCACTGTAT
474171 ATTTGTCCCGAAGAACCACTG
1 ATTTGTCCCGAAGAACCACTG
*
474192 ATTTGTCCCGAAGGACCACT
1 ATTTGTCCCGAAGAACCACT
474212 CCTTAAGAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.27, C:0.29, G:0.20, T:0.24
Consensus pattern (21 bp):
ATTTGTCCCGAAGAACCACTG
Found at i:479202 original size:2 final size:2
Alignment explanation
Indices: 479195--479221 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
479185 TTTCTAATGA
479195 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
479222 GCGTTCACTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:479221 original size:49 final size:49
Alignment explanation
Indices: 479149--479244 Score: 192
Period size: 49 Copynumber: 2.0 Consensus size: 49
479139 CTTCATTATC
479149 TATATATATATATATATATATATAGCGTTCACTAGATTTCTAATGAATA
1 TATATATATATATATATATATATAGCGTTCACTAGATTTCTAATGAATA
479198 TATATATATATATATATATATATAGCGTTCACTAGATTTCTAATGAA
1 TATATATATATATATATATATATAGCGTTCACTAGATTTCTAATGAA
479245 ATTACTTCTA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 47 1.00
ACGTcount: A:0.41, C:0.08, G:0.08, T:0.43
Consensus pattern (49 bp):
TATATATATATATATATATATATAGCGTTCACTAGATTTCTAATGAATA
Found at i:479589 original size:21 final size:18
Alignment explanation
Indices: 479527--479600 Score: 96
Period size: 18 Copynumber: 3.9 Consensus size: 18
479517 ACTGTATATT
479527 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
*
479545 TATCCCGAACGG-CCACTA
1 TGTCCCGAA-GGACCACTA
479563 TGTCCCGAAGGACCACTGA
1 TGTCCCGAAGGACCACT-A
479582 TTTGTCCCGAAGGACCACT
1 --TGTCCCGAAGGACCACT
479601 CCTGAAGAAC
Statistics
Matches: 49, Mismatches: 2, Indels: 7
0.84 0.03 0.12
Matches are distributed among these distances:
17 2 0.04
18 27 0.55
19 3 0.06
21 17 0.35
ACGTcount: A:0.26, C:0.34, G:0.22, T:0.19
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:486968 original size:23 final size:24
Alignment explanation
Indices: 486942--487005 Score: 67
Period size: 23 Copynumber: 2.6 Consensus size: 24
486932 CTAAAATTTT
*
486942 AAAAAAATGAATAACTAAAATG-A
1 AAAAAAATGAATAACTAAAAAGAA
** *
486965 AAAAAAATGCTTAAATTAAAAAGAA
1 AAAAAAATGAAT-AACTAAAAAGAA
486990 AAAAAGAATGAATAAC
1 AAAAA-AATGAATAAC
487006 CAGAAATGTA
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
23 10 0.32
24 8 0.26
25 8 0.26
26 5 0.16
ACGTcount: A:0.69, C:0.05, G:0.09, T:0.17
Consensus pattern (24 bp):
AAAAAAATGAATAACTAAAAAGAA
Found at i:494647 original size:2 final size:2
Alignment explanation
Indices: 494640--494680 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
494630 TTAAATTTTA
*
494640 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AA AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
494681 TTTTGTTTCG
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:498030 original size:29 final size:29
Alignment explanation
Indices: 497988--498045 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
497978 CAAGTAACAC
497988 GATGGTTCAGTGTAATAAAAGATTATGTG
1 GATGGTTCAGTGTAATAAAAGATTATGTG
498017 GATGGTTCAGTGTAATAAAAGATTATGTG
1 GATGGTTCAGTGTAATAAAAGATTATGTG
498046 TAGGCTGGGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.34, C:0.03, G:0.28, T:0.34
Consensus pattern (29 bp):
GATGGTTCAGTGTAATAAAAGATTATGTG
Found at i:502111 original size:22 final size:22
Alignment explanation
Indices: 502070--502112 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
502060 TTTTATAAGC
*
502070 AATATTGAAAACAAATTAATTA
1 AATATTGAAAACAAAATAATTA
502092 AATATT-AAAACACAAATAATT
1 AATATTGAAAACA-AAATAATT
502113 TTATGGTATC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.60, C:0.07, G:0.02, T:0.30
Consensus pattern (22 bp):
AATATTGAAAACAAAATAATTA
Found at i:512768 original size:22 final size:22
Alignment explanation
Indices: 512742--512783 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
512732 TATAAATAAA
512742 TATTTAAACTATGTTTTTTAGG
1 TATTTAAACTATGTTTTTTAGG
* *
512764 TATTTAAATTATTTTTTTTA
1 TATTTAAACTATGTTTTTTA
512784 TCAAATTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.29, C:0.02, G:0.07, T:0.62
Consensus pattern (22 bp):
TATTTAAACTATGTTTTTTAGG
Found at i:514876 original size:24 final size:24
Alignment explanation
Indices: 514848--514895 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
514838 CCTTATTACT
*
514848 TTTATACTTTTCTTCAATTTAGAC
1 TTTATACTTTTCATCAATTTAGAC
514872 TTTATACTTTTCATCAATTTAGAC
1 TTTATACTTTTCATCAATTTAGAC
514896 ATAATTAGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.27, C:0.17, G:0.04, T:0.52
Consensus pattern (24 bp):
TTTATACTTTTCATCAATTTAGAC
Found at i:516004 original size:29 final size:29
Alignment explanation
Indices: 515962--516050 Score: 169
Period size: 29 Copynumber: 3.1 Consensus size: 29
515952 CGAGCTAGGG
*
515962 GTAGGTCGTCATGCCTTCCGGGCGACCTT
1 GTAGGTCGCCATGCCTTCCGGGCGACCTT
515991 GTAGGTCGCCATGCCTTCCGGGCGACCTT
1 GTAGGTCGCCATGCCTTCCGGGCGACCTT
516020 GTAGGTCGCCATGCCTTCCGGGCGACCTT
1 GTAGGTCGCCATGCCTTCCGGGCGACCTT
516049 GT
1 GT
516051 CTCCGCTTGC
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 59 1.00
ACGTcount: A:0.10, C:0.33, G:0.31, T:0.26
Consensus pattern (29 bp):
GTAGGTCGCCATGCCTTCCGGGCGACCTT
Found at i:516129 original size:27 final size:27
Alignment explanation
Indices: 516098--516149 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
516088 ATTCCTGCAC
516098 GTCCCCTACTGCTCCCCGCTGCATGTA
1 GTCCCCTACTGCTCCCCGCTGCATGTA
*
516125 GTCCCCTCCTGCTCCCCGCTGCATG
1 GTCCCCTACTGCTCCCCGCTGCATG
516150 CCGCTGCATA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.08, C:0.48, G:0.19, T:0.25
Consensus pattern (27 bp):
GTCCCCTACTGCTCCCCGCTGCATGTA
Found at i:516570 original size:22 final size:22
Alignment explanation
Indices: 516542--516583 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
516532 ATTAATTAGT
*
516542 TTGTTAGTTTAGGGTTATATGA
1 TTGTTAGTTTAAGGTTATATGA
*
516564 TTGTTAGTTTAAGTTTATAT
1 TTGTTAGTTTAAGGTTATAT
516584 AAATAAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.24, C:0.00, G:0.21, T:0.55
Consensus pattern (22 bp):
TTGTTAGTTTAAGGTTATATGA
Found at i:516657 original size:44 final size:45
Alignment explanation
Indices: 516601--516685 Score: 113
Period size: 45 Copynumber: 1.9 Consensus size: 45
516591 AAATTATTAA
*
516601 TTAGTATGTAGTTATAGTTAAA-AA-TAATTAATTAGTTTGTTTTG
1 TTAGTATGTAGTTATA-TAAAACAATTAATTAATTAGTTTGTTTTG
*
516645 TTAGTCAT-TAGTTATATAAAACAATTATTTAATTAGTTTGT
1 TTAGT-ATGTAGTTATATAAAACAATTAATTAATTAGTTTGT
516686 GTTAGTTAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
43 4 0.11
44 15 0.42
45 17 0.47
ACGTcount: A:0.35, C:0.02, G:0.13, T:0.49
Consensus pattern (45 bp):
TTAGTATGTAGTTATATAAAACAATTAATTAATTAGTTTGTTTTG
Found at i:516900 original size:16 final size:16
Alignment explanation
Indices: 516868--516914 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
516858 TTTAAAAAGT
*
516868 TTAGTTTGTTAGT-TTA
1 TTAGTTTATTA-TATTA
516884 TTAGTTTATTATATTA
1 TTAGTTTATTATATTA
*
516900 TAAG-TTATTATATTA
1 TTAGTTTATTATATTA
516915 AATTTTTTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 12 0.43
16 16 0.57
ACGTcount: A:0.30, C:0.00, G:0.11, T:0.60
Consensus pattern (16 bp):
TTAGTTTATTATATTA
Found at i:520306 original size:14 final size:13
Alignment explanation
Indices: 520240--520309 Score: 56
Period size: 14 Copynumber: 5.3 Consensus size: 13
520230 TATAATGATT
520240 ATTAGTATCAAATC
1 ATTAGTAT-AAATC
* *
520254 ATTATTATAATTTC
1 ATTAGTATAA-ATC
*
520268 ATTACTAGT-AATC
1 ATTAGTA-TAAATC
520281 ATTAG--TAAATC
1 ATTAGTATAAATC
520292 ATTAGTATCAAATC
1 ATTAGTAT-AAATC
520306 ATTA
1 ATTA
520310 AATATTAATA
Statistics
Matches: 45, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
10 1 0.02
11 9 0.20
13 9 0.20
14 25 0.56
15 1 0.02
ACGTcount: A:0.41, C:0.11, G:0.06, T:0.41
Consensus pattern (13 bp):
ATTAGTATAAATC
Found at i:520316 original size:21 final size:22
Alignment explanation
Indices: 520286--520330 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
520276 TAATCATTAG
*
520286 TAAATCATTAGT-ATCAAATCAT
1 TAAATCATTAATAAT-AAATCAT
520308 TAAAT-ATTAATAATAAATCAT
1 TAAATCATTAATAATAAATCAT
520329 TA
1 TA
520331 TTAATAATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.51, C:0.09, G:0.02, T:0.38
Consensus pattern (22 bp):
TAAATCATTAATAATAAATCAT
Found at i:520348 original size:24 final size:23
Alignment explanation
Indices: 520301--520358 Score: 75
Period size: 24 Copynumber: 2.6 Consensus size: 23
520291 CATTAGTATC
*
520301 AAATCATTA--AATATTAATAAT
1 AAATCATTATTAATAATAATAAT
*
520322 AAATCATTATTAATAATAATTACT
1 AAATCATTATTAATAATAA-TAAT
520346 AAATCATTATTAA
1 AAATCATTATTAA
520359 ATCATTAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
21 9 0.28
23 7 0.22
24 16 0.50
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (23 bp):
AAATCATTATTAATAATAATAAT
Found at i:520391 original size:26 final size:26
Alignment explanation
Indices: 520351--520449 Score: 118
Period size: 26 Copynumber: 4.0 Consensus size: 26
520341 TTACTAAATC
*
520351 ATTATTAAATCATTA--AT-ATCATT
1 ATTATCAAATCATTATTATAATCATT
*
520374 ATTATCAAATCATTATTATAATGATT
1 ATTATCAAATCATTATTATAATCATT
*
520400 ATTA-CTAAATCATTATTATAATGATT
1 ATTATC-AAATCATTATTATAATCATT
*
520426 ATTATCAAATCATTACTA-AATCAT
1 ATTATCAAATCATTATTATAATCAT
520450 CAGTACATTA
Statistics
Matches: 67, Mismatches: 4, Indels: 8
0.85 0.05 0.10
Matches are distributed among these distances:
23 14 0.21
25 8 0.12
26 44 0.66
27 1 0.01
ACGTcount: A:0.43, C:0.10, G:0.02, T:0.44
Consensus pattern (26 bp):
ATTATCAAATCATTATTATAATCATT
Found at i:520483 original size:11 final size:11
Alignment explanation
Indices: 520249--520533 Score: 108
Period size: 11 Copynumber: 23.6 Consensus size: 11
520239 TATTAGTATC
520249 AAATCATTATT
1 AAATCATTATT
*
520260 ATAATTTCATTACT
1 A-AA--TCATTATT
*
520274 AGTAATCATTAGT
1 A--AATCATTATT
520287 AAATCATTAGTAT
1 AAATCATTA-T-T
520300 CAAATCATTA--
1 -AAATCATTATT
* * *
520310 AATATTAATAAT
1 AA-ATCATTATT
520322 AAATCATTATT
1 AAATCATTATT
* *
520333 AATAATAATTACT
1 -A-AATCATTATT
520346 AAATCATTATT
1 AAATCATTATT
*
520357 AAATCATTAAT
1 AAATCATTATT
* * *
520368 ATCATTATTATC
1 A-AATCATTATT
520380 AAATCATTATT
1 AAATCATTATT
*
520391 ATAATGATTATTACT
1 A-AATCATTA-T--T
520406 AAATCATTATT
1 AAATCATTATT
*
520417 ATAATGATTATTAT
1 A-AATCATTA-T-T
*
520431 CAAATCATTACT
1 -AAATCATTATT
* *
520443 AAATCATCAGT
1 AAATCATTATT
* * *
520454 ACATTAAATATT
1 A-AATCATTATT
520466 AAAATCATTATT
1 -AAATCATTATT
520478 AAATCATTATTGT
1 AAATCATTA-T-T
*
520491 CTAAT-ATTATT
1 -AAATCATTATT
520502 AAATCATTATTAT
1 AAATCATTA-T-T
*
520515 CAAATCATTACT
1 -AAATCATTATT
520527 AAATCAT
1 AAATCAT
520534 ATAATTATTA
Statistics
Matches: 206, Mismatches: 38, Indels: 60
0.68 0.12 0.20
Matches are distributed among these distances:
9 2 0.01
10 8 0.04
11 75 0.36
12 44 0.21
13 27 0.13
14 44 0.21
15 6 0.03
ACGTcount: A:0.45, C:0.11, G:0.02, T:0.42
Consensus pattern (11 bp):
AAATCATTATT
Found at i:520485 original size:27 final size:26
Alignment explanation
Indices: 520455--520546 Score: 75
Period size: 24 Copynumber: 3.5 Consensus size: 26
520445 ATCATCAGTA
520455 CATTAAATATTAAAATCATTATTAAAT
1 CATT-AATATTAAAATCATTATTAAAT
**
520482 CATT-AT-TGTCTAAT-ATTATTAAAT
1 CATTAATAT-TAAAATCATTATTAAAT
* * *
520506 CATTATTA-TCAAATCATTACTAAAT
1 CATTAATATTAAAATCATTATTAAAT
520531 CATATAATTATTAAAA
1 CAT-TAA-TATTAAAA
520547 AATCCTATGT
Statistics
Matches: 51, Mismatches: 7, Indels: 13
0.72 0.10 0.18
Matches are distributed among these distances:
24 20 0.39
25 19 0.37
26 2 0.04
27 6 0.12
28 4 0.08
ACGTcount: A:0.47, C:0.10, G:0.01, T:0.42
Consensus pattern (26 bp):
CATTAATATTAAAATCATTATTAAAT
Found at i:520500 original size:24 final size:25
Alignment explanation
Indices: 520467--520533 Score: 100
Period size: 24 Copynumber: 2.7 Consensus size: 25
520457 TTAAATATTA
*
520467 AAATCATTATTAAATCATTATTGTC
1 AAATCATTATTAAATCATTATTATC
*
520492 TAAT-ATTATTAAATCATTATTATC
1 AAATCATTATTAAATCATTATTATC
*
520516 AAATCATTACTAAATCAT
1 AAATCATTATTAAATCAT
520534 ATAATTATTA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
24 22 0.59
25 15 0.41
ACGTcount: A:0.43, C:0.12, G:0.01, T:0.43
Consensus pattern (25 bp):
AAATCATTATTAAATCATTATTATC
Found at i:520514 original size:14 final size:14
Alignment explanation
Indices: 520495--520524 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
520485 TATTGTCTAA
*
520495 TATTATTAAATCAT
1 TATTATCAAATCAT
520509 TATTATCAAATCAT
1 TATTATCAAATCAT
520523 TA
1 TA
520525 CTAAATCATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.43, C:0.10, G:0.00, T:0.47
Consensus pattern (14 bp):
TATTATCAAATCAT
Found at i:520798 original size:11 final size:11
Alignment explanation
Indices: 520784--520946 Score: 80
Period size: 11 Copynumber: 13.4 Consensus size: 11
520774 ATTATTAATG
520784 ATTAAATCATT
1 ATTAAATCATT
520795 ATTACAATTTCATT
1 ATTA-AA--TCATT
520809 ATTATTAATCATT
1 ATTA--AATCATT
520822 ACTT-AATCATT
1 A-TTAAATCATT
520833 AATATCAAATCATT
1 -AT-T-AAATCATT
* *
520847 A--AATATTAAT
1 ATTAA-ATCATT
*
520857 AATAAATCATT
1 ATTAAATCATT
*
520868 ATTAATAATAATT
1 ATT-A-AATCATT
*
520881 ACTAAATCATTATT
1 ATTAAATC---ATT
520895 ATTAAATCATT
1 ATTAAATCATT
*
520906 ATTATAATGATT
1 ATTA-AATCATT
520918 ATTGCTAAATCATT
1 A-T--TAAATCATT
520932 ATTAAATCATT
1 ATTAAATCATT
520943 ATTA
1 ATTA
520947 TGGTTAATTG
Statistics
Matches: 119, Mismatches: 12, Indels: 42
0.69 0.07 0.24
Matches are distributed among these distances:
9 2 0.02
10 5 0.04
11 41 0.34
12 15 0.13
13 17 0.14
14 35 0.29
15 4 0.03
ACGTcount: A:0.45, C:0.09, G:0.01, T:0.45
Consensus pattern (11 bp):
ATTAAATCATT
Found at i:520817 original size:35 final size:35
Alignment explanation
Indices: 520774--520910 Score: 98
Period size: 38 Copynumber: 3.7 Consensus size: 35
520764 AAATTAAATC
*
520774 ATTATTAATGATTAAATCATTATTA-CAATTTCATT-
1 ATTATTAAT-ATTAAATCATTATTATCAA-ATCATTA
*
520809 ATTATTAATCATTACTTAATCATTAATATCAAATCATTA
1 ATTATTAAT-ATTA---AATCATTATTATCAAATCATTA
* * * * *
520848 AATATTAATAATAAATCATTATTAATAATAATTACTAA
1 ATTATTAATATTAAATCATTATT-ATCA-AATCA-TTA
* *
520886 ATCATTATTATTAAATCATTATTAT
1 ATTATTAATATTAAATCATTATTAT
520911 AATGATTATT
Statistics
Matches: 81, Mismatches: 13, Indels: 14
0.75 0.12 0.13
Matches are distributed among these distances:
35 22 0.27
36 3 0.04
37 6 0.07
38 39 0.48
39 11 0.14
ACGTcount: A:0.45, C:0.09, G:0.01, T:0.45
Consensus pattern (35 bp):
ATTATTAATATTAAATCATTATTATCAAATCATTA
Found at i:520848 original size:21 final size:20
Alignment explanation
Indices: 520824--520879 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 20
520814 TAATCATTAC
520824 TTAATCATTAAT-ATCAAATCA
1 TTAAT-ATTAATAAT-AAATCA
520845 TTAAATATTAATAATAAATCA
1 TT-AATATTAATAATAAATCA
* *
520866 TTATTAATAATAAT
1 TTAATATTAATAAT
520880 TACTAAATCA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
20 10 0.32
21 16 0.52
22 5 0.16
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (20 bp):
TTAATATTAATAATAAATCA
Found at i:520871 original size:24 final size:25
Alignment explanation
Indices: 520844--520895 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 25
520834 ATATCAAATC
*
520844 ATTAAATATTAA-TAATAAATCATT
1 ATTAAATAATAATTAATAAATCATT
*
520868 ATT-AATAATAATTACTAAATCATT
1 ATTAAATAATAATTAATAAATCATT
520892 ATTA
1 ATTA
520896 TTAAATCATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 7 0.29
24 17 0.71
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (25 bp):
ATTAAATAATAATTAATAAATCATT
Found at i:520913 original size:37 final size:39
Alignment explanation
Indices: 520846--520947 Score: 117
Period size: 37 Copynumber: 2.7 Consensus size: 39
520836 ATCAAATCAT
* *
520846 TAAAT-ATTAATAATAAATCATTATTAATAAT-A-ATTAC
1 TAAATCATTATTATTAAATCATTATT-ATAATGATATTAC
*
520883 TAAATCATTATTATTAAATCATTATTATAATGATTATTGC
1 TAAATCATTATTATTAAATCATTATTATAATGA-TATTAC
520923 TAAATC---ATTATTAAATCATTATTAT
1 TAAATCATTATTATTAAATCATTATTAT
520948 GGTTAATTGC
Statistics
Matches: 58, Mismatches: 3, Indels: 8
0.84 0.04 0.12
Matches are distributed among these distances:
37 29 0.50
38 19 0.33
40 10 0.17
ACGTcount: A:0.46, C:0.07, G:0.02, T:0.45
Consensus pattern (39 bp):
TAAATCATTATTATTAAATCATTATTATAATGATATTAC
Found at i:520946 original size:14 final size:14
Alignment explanation
Indices: 520784--520947 Score: 80
Period size: 14 Copynumber: 12.1 Consensus size: 14
520774 ATTATTAATG
520784 ATTAAATCATTATT
1 ATTAAATCATTATT
* *
520798 A-CAATTTCATTATT
1 ATTAA-ATCATTATT
520812 ATT-AATCATTA--
1 ATTAAATCATTATT
* *
520823 CTT-AATCATTAAT
1 ATTAAATCATTATT
* *
520836 ATCAAATCATTAAAT
1 ATTAAATCATT-ATT
* *
520851 ATTAATAATAAATCATT
1 ATT-A-AAT-CATTATT
* *
520868 ATT-AATAATAATT
1 ATTAAATCATTATT
*
520881 ACTAAATCATTATT
1 ATTAAATCATTATT
520895 ATTAAATCATTATT
1 ATTAAATCATTATT
*
520909 A-T-AATGATTATT
1 ATTAAATCATTATT
**
520921 GCTAAATC---ATT
1 ATTAAATCATTATT
520932 ATTAAATCATTATT
1 ATTAAATCATTATT
520946 AT
1 AT
520948 GGTTAATTGC
Statistics
Matches: 114, Mismatches: 21, Indels: 30
0.69 0.13 0.18
Matches are distributed among these distances:
11 19 0.17
12 9 0.08
13 19 0.17
14 51 0.45
15 5 0.04
16 1 0.01
17 8 0.07
18 2 0.02
ACGTcount: A:0.45, C:0.09, G:0.01, T:0.45
Consensus pattern (14 bp):
ATTAAATCATTATT
Found at i:521181 original size:14 final size:14
Alignment explanation
Indices: 521111--521185 Score: 52
Period size: 14 Copynumber: 5.6 Consensus size: 14
521101 TCACTCCATT
*
521111 AAATCATTAGTATC
1 AAATCATTACTATC
*
521125 AAATCATTATTAT-
1 AAATCATTACTATC
* * *
521138 AATTTCATGATTA-C
1 AA-ATCATTACTATC
*
521152 TAATCATTAC---C
1 AAATCATTACTATC
521163 AAATCATTACTATC
1 AAATCATTACTATC
521177 AAATCATTA
1 AAATCATTA
521186 AATATTAATA
Statistics
Matches: 48, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
11 10 0.21
13 7 0.15
14 31 0.65
ACGTcount: A:0.43, C:0.16, G:0.03, T:0.39
Consensus pattern (14 bp):
AAATCATTACTATC
Found at i:521228 original size:46 final size:46
Alignment explanation
Indices: 521168--521277 Score: 170
Period size: 46 Copynumber: 2.4 Consensus size: 46
521158 TTACCAAATC
*
521168 ATTACTATCAAATCATTAAATATTAATAATAATTTCATGATTACT-
1 ATTATTATCAAATCATTAAATATTAATAATAATTTCATGATTACTA
*
521213 ATTCATTATCAAATCATTAAATATTAATAATAATTTCATTATTACTA
1 ATT-ATTATCAAATCATTAAATATTAATAATAATTTCATGATTACTA
521260 ATTATTA-CTAAATCATTA
1 ATTATTATC-AAATCATTA
521278 CTATCAAATC
Statistics
Matches: 60, Mismatches: 2, Indels: 5
0.90 0.03 0.07
Matches are distributed among these distances:
45 4 0.07
46 53 0.88
47 3 0.05
ACGTcount: A:0.45, C:0.11, G:0.01, T:0.44
Consensus pattern (46 bp):
ATTATTATCAAATCATTAAATATTAATAATAATTTCATGATTACTA
Found at i:521273 original size:106 final size:108
Alignment explanation
Indices: 521136--521419 Score: 414
Period size: 106 Copynumber: 2.7 Consensus size: 108
521126 AATCATTATT
*
521136 ATAATTTCATGATTACTAATCATTACCAAATCATTACTATCAAATCATTAAATATTAATAATAAT
1 ATAATTTCATTATTACTAATCATTACCAAATCATTACTATCAAATCATTAAATATTAATAATAAT
521201 TTCATGATTACT-AT-TCATTATCAAATCATTAAATATTAATA
66 TTCATGATTACTAATATCATTATCAAATCATTAAATATTAATA
* *
521242 ATAATTTCATTATTACTAATTATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAAT
1 ATAATTTCATTATTACTAATCATTACCAAATCATTACTATCAAATCATTAAATATTAATAATAAT
* *
521307 TTCATTATTACTAATCATTATTATCAAATCATTAAATATTAATA
66 TTCATGATTACTAAT-ATCATTATCAAATCATTAAATATTAATA
521351 ATAATTTCATTATTACTAATCA-T------T-A-T--TATCAAATCATTAAATATTAATAATAAT
1 ATAATTTCATTATTACTAATCATTACCAAATCATTACTATCAAATCATTAAATATTAATAATAAT
*
521405 TTCATTATTACTAAT
66 TTCATGATTACTAAT
521420 CATGACTAAA
Statistics
Matches: 169, Mismatches: 6, Indels: 14
0.89 0.03 0.07
Matches are distributed among these distances:
98 43 0.25
100 1 0.01
101 1 0.01
102 1 0.01
106 73 0.43
107 2 0.01
108 1 0.01
109 47 0.28
ACGTcount: A:0.44, C:0.12, G:0.01, T:0.43
Consensus pattern (108 bp):
ATAATTTCATTATTACTAATCATTACCAAATCATTACTATCAAATCATTAAATATTAATAATAAT
TTCATGATTACTAATATCATTATCAAATCATTAAATATTAATA
Found at i:521326 original size:13 final size:13
Alignment explanation
Indices: 521308--521389 Score: 50
Period size: 13 Copynumber: 6.5 Consensus size: 13
521298 AATAATAATT
521308 TCATTATTACTAA
1 TCATTATTACTAA
521321 TCATTATTA-TCAA
1 TCATTATTACT-AA
*
521334 --ATCATTA--AA
1 TCATTATTACTAA
* *
521343 T-ATTAATAATAA
1 TCATTATTACTAA
521355 TTTCATTATTACTAA
1 --TCATTATTACTAA
*
521370 TCATTATTATCAAA
1 TCATTATTA-CTAA
521384 TCATTA
1 TCATTA
521390 AATATTAATA
Statistics
Matches: 55, Mismatches: 6, Indels: 15
0.72 0.08 0.20
Matches are distributed among these distances:
9 2 0.04
10 5 0.09
11 6 0.11
12 3 0.05
13 20 0.36
14 10 0.18
15 9 0.16
ACGTcount: A:0.43, C:0.12, G:0.00, T:0.45
Consensus pattern (13 bp):
TCATTATTACTAA
Found at i:521332 original size:49 final size:49
Alignment explanation
Indices: 521164--521422 Score: 362
Period size: 49 Copynumber: 5.1 Consensus size: 49
521154 ATCATTACCA
* *
521164 AATCATTACTATCAAATCATTAAATATTAATAATAATTTCATGATTACT
1 AATCATTATTATCAAATCATTAAATATTAATAATAATTTCATTATTACT
*
521213 -AT--TCATTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATTATTACT
1 AATCATTATTATCAAATCATTAAATATTAATAAT-A----A-T-TT-C--ATTATTACT
*
521269 AAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACT
1 -AATCATTATTATCAAATCATTAAATATTAATAATAATTTCATTATTACT
521319 AATCATTATTATCAAATCATTAAATATTAATAATAATTTCATTATTACT
1 AATCATTATTATCAAATCATTAAATATTAATAATAATTTCATTATTACT
521368 AATCATTATTATCAAATCATTAAATATTAATAATAATTTCATTATTACT
1 AATCATTATTATCAAATCATTAAATATTAATAATAATTTCATTATTACT
521417 AATCAT
1 AATCAT
521423 GACTAAATAA
Statistics
Matches: 190, Mismatches: 6, Indels: 28
0.85 0.03 0.12
Matches are distributed among these distances:
46 27 0.14
47 1 0.01
48 2 0.01
49 103 0.54
50 9 0.05
51 1 0.01
52 2 0.01
53 4 0.02
54 2 0.01
55 1 0.01
56 8 0.04
58 2 0.01
59 1 0.01
60 27 0.14
ACGTcount: A:0.45, C:0.11, G:0.00, T:0.44
Consensus pattern (49 bp):
AATCATTATTATCAAATCATTAAATATTAATAATAATTTCATTATTACT
Found at i:522964 original size:2 final size:2
Alignment explanation
Indices: 522959--523001 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
522949 TCTACAAATA
522959 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
523001 A
1 A
523002 GATTAAATAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:523246 original size:17 final size:17
Alignment explanation
Indices: 523191--523251 Score: 59
Period size: 17 Copynumber: 3.4 Consensus size: 17
523181 CTAATATAAA
*
523191 TTAAACAAAATATTTTT
1 TTAAACACAATATTTTT
* *
523208 TTAAAACAACACTAAATATTT
1 TT-AAAC-ACA--ATATTTTT
523229 TTAAACACAATATTTTT
1 TTAAACACAATATTTTT
523246 TTAAAC
1 TTAAAC
523252 GGGAATAAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 8
0.73 0.10 0.17
Matches are distributed among these distances:
17 14 0.40
18 4 0.11
19 5 0.14
20 4 0.11
21 8 0.23
ACGTcount: A:0.48, C:0.11, G:0.00, T:0.41
Consensus pattern (17 bp):
TTAAACACAATATTTTT
Found at i:523343 original size:14 final size:14
Alignment explanation
Indices: 523324--523350 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
523314 ACACATACAC
523324 AACAACAAAAAATG
1 AACAACAAAAAATG
523338 AACAACAAAAAAT
1 AACAACAAAAAAT
523351 AATAAATTAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.74, C:0.15, G:0.04, T:0.07
Consensus pattern (14 bp):
AACAACAAAAAATG
Found at i:523521 original size:5 final size:5
Alignment explanation
Indices: 523511--523541 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
523501 AATTAATTTT
*
523511 ATATA ATATA ATATA ATATA TTATA ATATA A
1 ATATA ATATA ATATA ATATA ATATA ATATA A
523542 CTTAAACTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (5 bp):
ATATA
Found at i:523792 original size:28 final size:28
Alignment explanation
Indices: 523761--523814 Score: 108
Period size: 28 Copynumber: 1.9 Consensus size: 28
523751 ATAATCTAAT
523761 ATATAACTTAAACTAACAAACTAATATA
1 ATATAACTTAAACTAACAAACTAATATA
523789 ATATAACTTAAACTAACAAACTAATA
1 ATATAACTTAAACTAACAAACTAATA
523815 ATTTATACTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.57, C:0.15, G:0.00, T:0.28
Consensus pattern (28 bp):
ATATAACTTAAACTAACAAACTAATATA
Found at i:523821 original size:28 final size:28
Alignment explanation
Indices: 523757--523821 Score: 105
Period size: 28 Copynumber: 2.3 Consensus size: 28
523747 TTATATAATC
523757 TAATATATAACTTAAACTAACAAACTAA
1 TAATATATAACTTAAACTAACAAACTAA
523785 T-ATAATATAACTTAAACTAACAAACTAA
1 TAAT-ATATAACTTAAACTAACAAACTAA
*
523813 TAATTTATA
1 TAATATATA
523822 CTAACAAACT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
27 2 0.06
28 30 0.88
29 2 0.06
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.32
Consensus pattern (28 bp):
TAATATATAACTTAAACTAACAAACTAA
Found at i:523824 original size:21 final size:21
Alignment explanation
Indices: 523791--523839 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
523781 CTAATATAAT
523791 ATAACTTAAACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
* *
523812 ATAATTTATACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
523833 ATTAACT
1 A-TAACT
523840 AAATTTATGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.31
Consensus pattern (21 bp):
ATAACTTAAACTAACAAACTA
Found at i:525385 original size:17 final size:14
Alignment explanation
Indices: 525344--525387 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 14
525334 TTAAAAAGTA
*
525344 TTAATAATATATTT
1 TTAATAAAATATTT
525358 TTAATAAAATATTT
1 TTAATAAAATATTT
525372 TATATATAAAAATATT
1 T-TA-AT-AAAATATT
525388 AACAATGAGT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
14 14 0.54
15 2 0.08
16 2 0.08
17 8 0.31
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TTAATAAAATATTT
Found at i:535296 original size:171 final size:171
Alignment explanation
Indices: 535011--535356 Score: 647
Period size: 171 Copynumber: 2.0 Consensus size: 171
535001 TAATTTGAAG
*
535011 ATTAAATTGAAATGTCAAAAGATTTGAGGATTAATTCAAAATAATAATCATAATTTGAAGTTAAA
1 ATTAAATTGAAATGTCAAAAGATTTGAGGATTAATTCAAAATAAAAATCATAATTTGAAGTTAAA
535076 ATTAAAATATTAAAAAATATGAGAAAATTTTAAATTTTAAAATTAATTTAAAATAAAAAGTATAA
66 ATTAAAATATTAAAAAATATGAGAAAATTTTAAATTTTAAAATTAATTTAAAATAAAAAGTATAA
*
535141 TTTAAAGGAGTATGGTGCAATTAACTAAAACTATGCCCTTT
131 TTTAAAGGAGTAGGGTGCAATTAACTAAAACTATGCCCTTT
*
535182 ATTAAATTGAAATGTCAAAAGATTTGAGGTTTAATTCAAAATAAAAATCATAATTTGAAGTTAAA
1 ATTAAATTGAAATGTCAAAAGATTTGAGGATTAATTCAAAATAAAAATCATAATTTGAAGTTAAA
*
535247 ATTAAAATATTAAAAAATATGAGAAAATTTTAAATTTTAAAATTAATTTAAAATAAAGAGTATAA
66 ATTAAAATATTAAAAAATATGAGAAAATTTTAAATTTTAAAATTAATTTAAAATAAAAAGTATAA
*
535312 TTTAAAGGAGTAGGGTGCAATTAACTAAAACTATTCCCTTT
131 TTTAAAGGAGTAGGGTGCAATTAACTAAAACTATGCCCTTT
535353 ATTA
1 ATTA
535357 GTCTTTCCAT
Statistics
Matches: 170, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
171 170 1.00
ACGTcount: A:0.49, C:0.05, G:0.11, T:0.35
Consensus pattern (171 bp):
ATTAAATTGAAATGTCAAAAGATTTGAGGATTAATTCAAAATAAAAATCATAATTTGAAGTTAAA
ATTAAAATATTAAAAAATATGAGAAAATTTTAAATTTTAAAATTAATTTAAAATAAAAAGTATAA
TTTAAAGGAGTAGGGTGCAATTAACTAAAACTATGCCCTTT
Found at i:544905 original size:226 final size:229
Alignment explanation
Indices: 544502--544921 Score: 603
Period size: 226 Copynumber: 1.8 Consensus size: 229
544492 TTCCATAAAC
* *
544502 TCCTATCAAAGGCTGAACACTTGGTCCTTTTTTCCATGATCCTTCTGCAACATAAAGCATTACAG
1 TCCTATCAAAGGCAGAACACTAGGTCCTTTTTTCCATGATCCTTCTGCAACATAAAGCATTACAG
* * * **
544567 AGATTATTCTAGCACATTGTTGCTTAGGGTGCAAGGCAAATTCTAGATGCTAGAACCTTTAGATT
66 AGATTATTCTAGCACATTCTTGATTAGGGTGCAAGGCAAATTATAGACACTAGAACCTTTAGATT
** * * * *
544632 GCTCAAGATGCAAGGCACAAGAAAATGCACACACATGAGCGAGGTAAGG-GCAATATCTCTGAGA
131 GCTCAAGACACAAGGCACAAGAAAAGGCACACACATGAGCAAGGTAAGGCACAATATCTATGAGA
544696 GTATAACAATAGTACCCCCTATAAAGTCTTATGA
196 GTATAACAATAGTACCCCCTATAAAGTCTTATGA
* *
544730 TCCTATCAAAGGCAGAACACTAGGTCC-TTTTTCCTTGATCCTTCTGCAACATAAAGCATTATAG
1 TCCTATCAAAGGCAGAACACTAGGTCCTTTTTTCCATGATCCTTCTGCAACATAAAGCATTACAG
* * *
544794 AGATTATTCTAGCACTTTCTT-ATTAGGGTGCAAGGCAAATTATAGGCACTAGAACCTTTATATT
66 AGATTATTCTAGCACATTCTTGATTAGGGTGCAAGGCAAATTATAGACACTAGAACCTTTAGATT
** * * * *
544858 GCTTGAGGCACAAGGCACGAGAAAAGGCACTCGCATGAGCAAGGTAAGGCACAATATCTATGAG
131 GCTCAAGACACAAGGCACAAGAAAAGGCACACACATGAGCAAGGTAAGGCACAATATCTATGAG
544922 TGTGTATCTT
Statistics
Matches: 167, Mismatches: 24, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
226 76 0.46
227 66 0.40
228 25 0.15
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.27
Consensus pattern (229 bp):
TCCTATCAAAGGCAGAACACTAGGTCCTTTTTTCCATGATCCTTCTGCAACATAAAGCATTACAG
AGATTATTCTAGCACATTCTTGATTAGGGTGCAAGGCAAATTATAGACACTAGAACCTTTAGATT
GCTCAAGACACAAGGCACAAGAAAAGGCACACACATGAGCAAGGTAAGGCACAATATCTATGAGA
GTATAACAATAGTACCCCCTATAAAGTCTTATGA
Found at i:553019 original size:21 final size:22
Alignment explanation
Indices: 552985--553032 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
552975 TTATTAATTG
*
552985 TAATCTACCACTAAGACATGAT
1 TAATCTACAACTAAGACATGAT
* *
553007 TAATC-ACAACTAAGATATGGT
1 TAATCTACAACTAAGACATGAT
553028 TAATC
1 TAATC
553033 GTAAATGGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 18 0.78
22 5 0.22
ACGTcount: A:0.42, C:0.19, G:0.10, T:0.29
Consensus pattern (22 bp):
TAATCTACAACTAAGACATGAT
Found at i:553869 original size:30 final size:31
Alignment explanation
Indices: 553833--553894 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
553823 CCCGAAGGAC
*
553833 CAGTCCATA-GATCCGAAGAACCTAGGTAAA
1 CAGTCCATATGATCCGAAGAACATAGGTAAA
*
553863 CAGTCCATATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGATCCGAAGAACATAGGTAAA
553894 C
1 C
553895 CCTCGACCCT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 9 0.31
31 20 0.69
ACGTcount: A:0.39, C:0.23, G:0.19, T:0.19
Consensus pattern (31 bp):
CAGTCCATATGATCCGAAGAACATAGGTAAA
Found at i:554659 original size:64 final size:64
Alignment explanation
Indices: 554551--554771 Score: 277
Period size: 64 Copynumber: 3.5 Consensus size: 64
554541 TAATGAAGGT
* * * * * *
554551 ATGCATCGATGCACTACTGATGCATCGGTGCATAAAATGTATTCGATGTTGT-ATTATTACTGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCATGAATTGCATTCGATGTT-TCATTATTAATGGG
554615 ATGCATCGATGCACTACTTATGCATCGATGCATGAATTGCATTCGATGTTTCATTATTAATGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCATGAATTGCATTCGATGTTTCATTATTAATGGG
* * **
554679 ATGCATCGATGCACTACTTATGCATCGATGCACGAATTGCATTCGATGTATTTATT-TTAA-AAG
1 ATGCATCGATGCACTACTTATGCATCGATGCATGAATTGCATTCGATGT-TTCATTATTAATGGG
* * *
554742 AGTGCATCGATGCACTTCCTGTGCATCGAT
1 A-TGCATCGATGCACTACTTATGCATCGAT
554772 ACACCTTTAA
Statistics
Matches: 141, Mismatches: 13, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
63 3 0.02
64 133 0.94
65 5 0.04
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.34
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTATGCATCGATGCATGAATTGCATTCGATGTTTCATTATTAATGGG
Found at i:555641 original size:2 final size:2
Alignment explanation
Indices: 555634--555664 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
555624 AAAATTAAAT
555634 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 T
555665 TCTTTTTGCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:556648 original size:25 final size:25
Alignment explanation
Indices: 556610--556659 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
556600 AAGAAGTTAT
556610 GTTAAAAAAATTTA-GGGAGTGCGAA
1 GTTAAAAAAATTTAGGGGA-TGCGAA
* *
556635 GTTATAAAATTTTAGGGGATGCGAA
1 GTTAAAAAAATTTAGGGGATGCGAA
556660 ATTTAATAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 18 0.82
26 4 0.18
ACGTcount: A:0.40, C:0.04, G:0.28, T:0.28
Consensus pattern (25 bp):
GTTAAAAAAATTTAGGGGATGCGAA
Found at i:557815 original size:10 final size:11
Alignment explanation
Indices: 557789--557822 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
557779 TTAAATGCCA
557789 ATTTTTAAATT
1 ATTTTTAAATT
*
557800 ATTTTTAAGTT
1 ATTTTTAAATT
*
557811 ATTTTAAAATT
1 ATTTTTAAATT
557822 A
1 A
557823 AAAATATTGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (11 bp):
ATTTTTAAATT
Found at i:560402 original size:16 final size:16
Alignment explanation
Indices: 560381--560421 Score: 73
Period size: 16 Copynumber: 2.6 Consensus size: 16
560371 CCTTTCGGGA
560381 ATTCTTATTTCAGTAG
1 ATTCTTATTTCAGTAG
560397 ATTCTTATTTCAGTAG
1 ATTCTTATTTCAGTAG
*
560413 ATCCTTATT
1 ATTCTTATT
560422 GTACCACATA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.24, C:0.15, G:0.10, T:0.51
Consensus pattern (16 bp):
ATTCTTATTTCAGTAG
Found at i:575557 original size:20 final size:21
Alignment explanation
Indices: 575508--575554 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
575498 TAGTTTGACC
575508 AAAAAATAATTTAAATACCTA
1 AAAAAATAATTTAAATACCTA
*
575529 AAAAAATAATTTAGATACCTA
1 AAAAAATAATTTAAATACCTA
575550 AAAAA
1 AAAAA
575555 TAACATAGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.64, C:0.09, G:0.02, T:0.26
Consensus pattern (21 bp):
AAAAAATAATTTAAATACCTA
Found at i:585228 original size:13 final size:13
Alignment explanation
Indices: 585196--585228 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
585186 AAATAATTTC
585196 TTTA-AAATATAT
1 TTTATAAATATAT
585208 TGTTATAAATATAT
1 T-TTATAAATATAT
585222 TTTATAA
1 TTTATAA
585229 TTTTAGATTG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 1 0.05
13 9 0.47
14 9 0.47
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (13 bp):
TTTATAAATATAT
Found at i:587666 original size:26 final size:26
Alignment explanation
Indices: 587637--587703 Score: 107
Period size: 26 Copynumber: 2.6 Consensus size: 26
587627 ATTAGACGCG
587637 TGTATATTTATTATTAATTAGAAACA
1 TGTATATTTATTATTAATTAGAAACA
* * *
587663 TGTATATTTATTCTTAATTAGACACG
1 TGTATATTTATTATTAATTAGAAACA
587689 TGTATATTTATTATT
1 TGTATATTTATTATT
587704 TAAATGTAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 37 1.00
ACGTcount: A:0.34, C:0.06, G:0.09, T:0.51
Consensus pattern (26 bp):
TGTATATTTATTATTAATTAGAAACA
Found at i:590108 original size:24 final size:25
Alignment explanation
Indices: 590040--590109 Score: 83
Period size: 24 Copynumber: 2.8 Consensus size: 25
590030 TATAAACGTC
590040 AAATACTATGAATAATATTATTTATTA
1 AAATA-TA-GAATAATATTATTTATTA
*
590067 AAATA-ATAATAATATTATTT-TTA
1 AAATATAGAATAATATTATTTATTA
590090 AAATATTAGAATAAT-TTATT
1 AAATA-TAGAATAATATTATT
590110 CAATATTATT
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
23 8 0.21
24 18 0.46
25 8 0.21
27 5 0.13
ACGTcount: A:0.50, C:0.01, G:0.03, T:0.46
Consensus pattern (25 bp):
AAATATAGAATAATATTATTTATTA
Found at i:590266 original size:22 final size:22
Alignment explanation
Indices: 590235--590391 Score: 59
Period size: 24 Copynumber: 6.6 Consensus size: 22
590225 ATGAAAATAT
*
590235 TAATATTATTATAATATTAAAA
1 TAATAATATTATAATATTAAAA
* *
590257 TAATAATATTGTATTATATTTTAAA
1 TAATAATA-T-TATAATA-TTAAAA
*
590282 CAATATATATTA-AATATTCAACAA
1 TAATA-ATATTATAATATT-AA-AA
** *
590306 TTCAATAATATTATTTTTATTAAAT
1 -T-AATAATATTA-TAATATTAAAA
* * * *
590331 TATTAAATAATATTAATTTTATTAA
1 TAAT-AATATTA-TAATATTA-AAA
590356 TAATAA-ATTATATATTATTAAAA
1 TAATAATATTATA-A-TATTAAAA
590379 TAA-AAGTATTATA
1 TAATAA-TATTATA
590392 TTATACATTA
Statistics
Matches: 98, Mismatches: 21, Indels: 30
0.66 0.14 0.20
Matches are distributed among these distances:
22 13 0.13
23 16 0.16
24 35 0.36
25 21 0.21
26 9 0.09
27 4 0.04
ACGTcount: A:0.50, C:0.03, G:0.01, T:0.46
Consensus pattern (22 bp):
TAATAATATTATAATATTAAAA
Found at i:590326 original size:27 final size:27
Alignment explanation
Indices: 590296--590355 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
590286 ATATATTAAA
* * *
590296 TATTCAACAATTCAATAATATTATTTT
1 TATTAAACAATTAAATAATATTAATTT
**
590323 TATTAAATTATTAAATAATATTAATTT
1 TATTAAACAATTAAATAATATTAATTT
590350 TATTAA
1 TATTAA
590356 TAATAAATTA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (27 bp):
TATTAAACAATTAAATAATATTAATTT
Found at i:590346 original size:18 final size:18
Alignment explanation
Indices: 590323--590380 Score: 57
Period size: 18 Copynumber: 3.1 Consensus size: 18
590313 ATATTATTTT
590323 TATTAA-ATTATTAAATAA
1 TATTAATATTATT-AATAA
*
590341 TATTAATTTTATTAATAA
1 TATTAATATTATTAATAA
590359 TAAATTATATATTATTAA-AA
1 T--ATTA-ATATTATTAATAA
590379 TA
1 TA
590381 AAAGTATTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
18 13 0.38
19 5 0.15
20 7 0.21
21 9 0.26
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (18 bp):
TATTAATATTATTAATAA
Found at i:593491 original size:22 final size:24
Alignment explanation
Indices: 593466--593515 Score: 68
Period size: 22 Copynumber: 2.1 Consensus size: 24
593456 TTATTTCAAC
593466 TATTTTAAAATAA-TTAAATAT-T
1 TATTTTAAAATAACTTAAATATAT
*
593488 TATTTTAAAGTAAGCTTAAATATAT
1 TATTTTAAAATAA-CTTAAATATAT
593513 TAT
1 TAT
593516 GAAAACACAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
22 12 0.50
24 8 0.33
25 4 0.17
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (24 bp):
TATTTTAAAATAACTTAAATATAT
Found at i:593770 original size:40 final size:38
Alignment explanation
Indices: 593693--593784 Score: 107
Period size: 40 Copynumber: 2.4 Consensus size: 38
593683 GATTTTTATT
* *
593693 TATTTAT-ATATATATATATTTGCAAATGTTTTTGAAA
1 TATTTATAATATATATATATTTGAAAAGGTTTTTGAAA
593730 TATTTATAATATATATA-ATTTTGAAAACGGTTTTTGGAAA
1 TATTTATAATATATATATA-TTTGAAAA-GGTTTTT-GAAA
* *
593770 TATATATAACATATA
1 TATTTATAATATATA
593785 GTTTTTAAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
37 8 0.17
38 16 0.34
39 6 0.13
40 17 0.36
ACGTcount: A:0.41, C:0.03, G:0.09, T:0.47
Consensus pattern (38 bp):
TATTTATAATATATATATATTTGAAAAGGTTTTTGAAA
Found at i:593803 original size:38 final size:34
Alignment explanation
Indices: 593772--594180 Score: 334
Period size: 36 Copynumber: 11.5 Consensus size: 34
593762 TTTGGAAATA
* *
593772 TATATAACATATAGTTTTTAAAAAATATTTTGAAAA-
1 TATATAATATATAG-TTTT--AAAACATTTTGAAAAC
593808 TATATAATATATAGTTTTTAAAACATTTTGAAAAC
1 TATATAATATATAG-TTTTAAAACATTTTGAAAAC
* * *
593843 TCATATAATATATAGTTTTGAAATCATTATGAAAATA
1 T-ATATAATATATAGTTTT-AAAACATTTTGAAAA-C
*
593880 TATATAATATATATTTTTTTTAAAACATTTTGAAAAAC
1 TATATAATATATA---GTTTTAAAACATTTTG-AAAAC
*
593918 TTATATAATATATAGTTTTGAAATCATTTTGAAAA-
1 -TATATAATATATAGTTTT-AAAACATTTTGAAAAC
593953 TATACATAATATATAGTTTTTTAAAACATTTTGAAAAAC
1 TAT--ATAATATATAG--TTTTAAAACATTTTG-AAAAC
593992 TTATATAATATATAGTTTTAAAAACATTTTTTGAAAAC
1 -TATATAATATATAGTTTT-AAAACA--TTTTGAAAAC
594030 T-TAT-ATATATAGTTTTAAAAACATTTTGGAAAAC
1 TATATAATATATAGTTTT-AAAACATTTT-GAAAAC
* *
594064 TTATATAATAT-T-TTTTTGAAATCATTTTGAAAAC
1 -TATATAATATATAGTTTT-AAAACATTTTGAAAAC
* * *** *
594098 AATATAATATATAGTTTTGAATTTTTTTTAAAA-
1 TATATAATATATAGTTTTAAAACATTTTGAAAAC
* *
594131 -ATATAATATATAGTTTAAAAAATATTTTTG-AAA-
1 TATATAATATATAGTTT-TAAAACA-TTTTGAAAAC
*
594164 TATATATTATATAGTTT
1 TATATAATATATAGTTT
594181 ATTTTATAAT
Statistics
Matches: 317, Mismatches: 27, Indels: 60
0.78 0.07 0.15
Matches are distributed among these distances:
32 16 0.05
33 19 0.06
34 60 0.19
35 42 0.13
36 86 0.27
37 32 0.10
38 33 0.10
39 26 0.08
40 3 0.01
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.45
Consensus pattern (34 bp):
TATATAATATATAGTTTTAAAACATTTTGAAAAC
Found at i:593849 original size:74 final size:71
Alignment explanation
Indices: 593794--594115 Score: 422
Period size: 74 Copynumber: 4.5 Consensus size: 71
593784 AGTTTTTAAA
*
593794 AAAT-ATTTTGAAAATATATAATATATAGTTTTTAAAACATTTTG-AAAACTCATATAATATATA
1 AAATCATTTTGAAAATATATAATATATAGTTTTTAAAACATTTTGAAAAACTTATATAATATATA
593857 GTTTTG
66 GTTTTG
* *
593863 AAATCATTATGAAAATATATATAATATATATTTTTTTTAAAACATTTTGAAAAACTTATATAATA
1 AAATCATTTTG-AAA-ATATATAATATATA--GTTTTTAAAACATTTTGAAAAACTTATATAATA
593928 TATAGTTTTG
62 TATAGTTTTG
593938 AAATCATTTTGAAAATATACATAATATATAGTTTTTTAAAACATTTTGAAAAACTTATATAATAT
1 AAATCATTTTGAAAATAT--ATAATATATAG-TTTTTAAAACATTTTGAAAAACTTATATAATAT
*
594003 ATAGTTTTA
63 ATAGTTTTG
* * *
594012 AAAACATTTTTTGAAAACT-TAT-ATATATAGTTTTAAAAACATTTTGGAAAACTTATATAATAT
1 AAATCA--TTTTGAAAA-TATATAATATATAGTTTTTAAAACATTTTGAAAAACTTATATAATAT
*
594075 -T-TTTTTG
63 ATAGTTTTG
*
594082 AAATCATTTTGAAAACAATATAATATATAGTTTT
1 AAATCATTTTGAAAA-TATATAATATATAGTTTT
594116 GAATTTTTTT
Statistics
Matches: 226, Mismatches: 13, Indels: 27
0.85 0.05 0.10
Matches are distributed among these distances:
68 10 0.04
69 7 0.03
70 26 0.12
71 4 0.02
72 45 0.20
73 12 0.05
74 67 0.30
75 44 0.19
76 10 0.04
77 1 0.00
ACGTcount: A:0.45, C:0.05, G:0.06, T:0.44
Consensus pattern (71 bp):
AAATCATTTTGAAAATATATAATATATAGTTTTTAAAACATTTTGAAAAACTTATATAATATATA
GTTTTG
Found at i:594165 original size:32 final size:33
Alignment explanation
Indices: 593994--594181 Score: 100
Period size: 34 Copynumber: 5.5 Consensus size: 33
593984 TGAAAAACTT
593994 ATATAATATATAGTTTTAAAAACAT-TTTTTGAAAA
1 ATATAATATATAG-TTTAAAAA-ATATTTTT-AAAA
* * * *
594029 CT-TATATATATAGTTTTAAAAACATTTTGGAAAA
1 ATATA-ATATATAGTTTAAAAAATATTTT-TAAAA
*** *
594063 CTTATATAATAT-T--TTTTTGAAATCATTTTGAAAACA
1 ---ATATAATATATAGTTTAAAAAAT-ATTTT-TAAA-A
** * *
594099 ATATAATATATAGTTT-TGAATTTTTTTTAAAA
1 ATATAATATATAGTTTAAAAAATATTTTTAAAA
*
594131 ATATAATATATAGTTTAAAAAATATTTTTGAAAT
1 ATATAATATATAGTTTAAAAAATATTTTT-AAAA
*
594165 ATATATTATATAGTTTA
1 ATATAATATATAGTTTA
594182 TTTTATAATA
Statistics
Matches: 121, Mismatches: 18, Indels: 29
0.72 0.11 0.17
Matches are distributed among these distances:
32 17 0.14
33 21 0.17
34 48 0.40
35 23 0.19
36 5 0.04
37 5 0.04
38 2 0.02
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.46
Consensus pattern (33 bp):
ATATAATATATAGTTTAAAAAATATTTTTAAAA
Found at i:594454 original size:16 final size:15
Alignment explanation
Indices: 594433--594463 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
594423 TGGCCGCCGA
594433 TATCCTGGGACTGACC
1 TATCCTGGGAC-GACC
594449 TATCCTGGGACGACC
1 TATCCTGGGACGACC
594464 GACCTCACAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.19, C:0.32, G:0.26, T:0.23
Consensus pattern (15 bp):
TATCCTGGGACGACC
Found at i:595396 original size:21 final size:22
Alignment explanation
Indices: 595367--595416 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
595357 CTTTTGATAT
595367 TTTTA-TTA-TTATTATTTT-CC
1 TTTTATTTATTTATT-TTTTCCC
595387 TTTTATTTATTTATTTTTTCCC
1 TTTTATTTATTTATTTTTTCCC
*
595409 TTTGATTT
1 TTTTATTT
595417 TTTTGTTATG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
20 5 0.19
21 7 0.27
22 14 0.54
ACGTcount: A:0.16, C:0.10, G:0.02, T:0.72
Consensus pattern (22 bp):
TTTTATTTATTTATTTTTTCCC
Done.