Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold311
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: 800152
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
File 3 of 7
Found at i:301542 original size:135 final size:136
Alignment explanation
Indices: 301297--301855 Score: 641
Period size: 135 Copynumber: 4.0 Consensus size: 136
301287 GCACCTTTTT
* *
301297 CACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTTCTATCTCTAAGTCC
1 CACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA-CTTTTCT-TCTTTAAGTCC
*
301362 AATGTAGCTGGCCTTGAATCAGCACATTGGCACCTCTAAGTCCAATGTAGCTGGCCTTGAATCAG
64 AATATAGCTGGCCTTGAATCAGCACATTGGCACCTCTAAGTCCAATGTAGCTGGCCTTGAATCAG
301427 CACATTGG
129 CACATTGG
301435 CACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCAC-TTTCTTCTTTAAGTCCAA
1 CACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACTTTTCTTCTTTAAGTCCAA
* * *
301499 TGTAGCTGGCCTTGAATCAGCACATTGGCACCTCTAAGCCCAATATAGCTGGCCTTGAATCAGCA
66 TATAGCTGGCCTTGAATCAGCACATTGGCACCTCTAAGTCCAATGTAGCTGGCCTTGAATCAGCA
*
301564 TATTGG
131 CATTGG
* * * *
301570 CACCTTCTTCTTTAGTCCAATGTAGTTGGCCTTGAATCAGCACATTGGCAC----C-TC--TAAG
1 CA-C--C-T-TTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACTTTTCTTCTTTAAG
* * * *
301628 CCCAAATATAGCTGGCCTTGAATCAGTATATTGGCACCTTCTTCTTTAGTCCAATGTAGCTGGCC
61 TCC-AATATAGCTGGCCTTGAATCAGCACATTGGCA-C--C-TC-TAAGTCCAATGTAGCTGGCC
*
301693 TTGAATCAGCACATTGA
120 TTGAATCAGCACATTGG
* **
301710 CACCTCTAAG-CCTAATATAGCTGGCCTTGAATCAGCATATTGGCACATTTTCCACCTTTAAGTC
1 CACCTTTAAGTCC-AATATAGCTGGCCTTGAATCAGCATATTGGCAC-TTTT-CTTCTTTAAGTC
* *
301774 CAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTTTAAGTTCAATGTAGCTGGC
63 CAATATAGCTGGCCTTGAATCAGCACATTGGCA------CC-TC--TAAGTCCAATGTAGCTGGC
301839 CTTGAATCAGCACATTG
119 CTTGAATCAGCACATTG
301856 ACATCTTTTT
Statistics
Matches: 364, Mismatches: 30, Indels: 45
0.83 0.07 0.10
Matches are distributed among these distances:
134 8 0.02
135 144 0.40
136 10 0.03
137 3 0.01
138 46 0.13
139 4 0.01
140 71 0.20
141 1 0.00
142 1 0.00
143 31 0.09
144 6 0.02
146 3 0.01
147 35 0.10
148 1 0.00
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.31
Consensus pattern (136 bp):
CACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACTTTTCTTCTTTAAGTCCAA
TATAGCTGGCCTTGAATCAGCACATTGGCACCTCTAAGTCCAATGTAGCTGGCCTTGAATCAGCA
CATTGG
Found at i:301913 original size:107 final size:104
Alignment explanation
Indices: 301727--301918 Score: 251
Period size: 107 Copynumber: 1.8 Consensus size: 104
301717 AAGCCTAATA
* * * *
301727 TAGCTGGCCTTGAATCAGCATATTGGCACATTTTCCACCTTTAAGTCCAATATAGCTGGCCTTGA
1 TAGCTGGCCTTGAATCAGCACATTGACACATTTTCCACCTTTAAGCCCAATATAGCTGGCCGTGA
* *
301792 ATCAGCATATTGGCACCTTTTCCATCTTTAAGTTCAATG
66 ATCAACATAGTGGCACCTTTTCCATCTTTAAGTTCAATG
* * *
301831 TAGCTGGCCTTGAATCAGCACATTGACATCTTTTTTCTCATCTTTAAGCCCAATATCA-TTGGCC
1 TAGCTGGCCTTGAATCAGCACATTGACA-C-ATTTTC-CACCTTTAAGCCCAATAT-AGCTGGCC
*
301895 GTGAATCAACATAGTGGCATCTTT
62 GTGAATCAACATAGTGGCACCTTT
301919 ATCAATTTTC
Statistics
Matches: 74, Mismatches: 10, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
104 26 0.35
105 1 0.01
106 5 0.07
107 41 0.55
108 1 0.01
ACGTcount: A:0.25, C:0.24, G:0.16, T:0.35
Consensus pattern (104 bp):
TAGCTGGCCTTGAATCAGCACATTGACACATTTTCCACCTTTAAGCCCAATATAGCTGGCCGTGA
ATCAACATAGTGGCACCTTTTCCATCTTTAAGTTCAATG
Found at i:302091 original size:169 final size:173
Alignment explanation
Indices: 301762--302119 Score: 424
Period size: 169 Copynumber: 2.1 Consensus size: 173
301752 GCACATTTTC
* *
301762 CACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTTTAAGTTC
1 CACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTTT-CATCTTTAAGTCC
* * * *
301827 AATGTAGCTGGCCTTGAATCAGCACATTGACATCTTTTTTCTCATCTTTAAGCCCAATATCATTG
65 AATATAGCTAGCC-TGAATCAGCACATTGACATCCTTTTTCTCATCTTTAAACCCAATATCATTG
* *
301892 GCCGTGAATCAACATAGTGGCATCTTTATCAATTTTC-TCATCTT
129 GCCGTGAATCAACATAGTGGCATCTTTATCAATCTTCATCATCAT
* * *
301936 CATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACC-TTT-ATCTTTAAGTCCA
1 CACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTTTCATCTTTAAGTCCA
* ** * **
301999 ATATCGCTAGCC-GCATATTGGCTC-TT-TTATCCTTTTTCTCATCTTTAAACCCAATATCATTG
66 ATATAGCTAGCCTG-A-ATCAGCACATTGACATCCTTTTTCTCATCTTTAAACCCAATATCATTG
* * * * *
302061 GCCGTGAATCAACGTATTGGTCCT-TTTATCACTCTTCATCCTCAT
129 GCCGTGAATCAACATAGTGG-CATCTTTATCAATCTTCATCATCAT
302106 CACCTTTAAGTCCA
1 CACCTTTAAGTCCA
302120 GTGTGACAGG
Statistics
Matches: 157, Mismatches: 23, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
169 62 0.39
170 23 0.15
171 26 0.17
173 3 0.02
174 43 0.27
ACGTcount: A:0.24, C:0.26, G:0.13, T:0.37
Consensus pattern (173 bp):
CACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTTTCATCTTTAAGTCCA
ATATAGCTAGCCTGAATCAGCACATTGACATCCTTTTTCTCATCTTTAAACCCAATATCATTGGC
CGTGAATCAACATAGTGGCATCTTTATCAATCTTCATCATCAT
Found at i:302861 original size:52 final size:52
Alignment explanation
Indices: 302805--302922 Score: 200
Period size: 52 Copynumber: 2.3 Consensus size: 52
302795 CACTGATCTT
302805 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
* *
302857 TGTATCGGTACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
* *
302909 TATATCGATCCATG
1 TGTATCGATACATG
302923 ACCTTCCTAA
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 61 1.00
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.31
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
Found at i:312464 original size:2 final size:2
Alignment explanation
Indices: 312459--312486 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
312449 TCTTCCTAAC
312459 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
312487 GAAGAAAAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:316104 original size:39 final size:39
Alignment explanation
Indices: 316042--316124 Score: 105
Period size: 39 Copynumber: 2.1 Consensus size: 39
316032 CTAAAAGACT
*
316042 TTAAAGGACATATATCGATATGAA-AGTTCTCACATAACC
1 TTAAAGGACATATATCGACATGAAGA-TTCTCACATAACC
* * * *
316081 TTAATGGACATGTTTCGACATGAAGATTTTCACATAACC
1 TTAAAGGACATATATCGACATGAAGATTCTCACATAACC
316120 TTAAA
1 TTAAA
316125 CGCAGTTTTG
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
39 36 0.97
40 1 0.03
ACGTcount: A:0.39, C:0.17, G:0.13, T:0.31
Consensus pattern (39 bp):
TTAAAGGACATATATCGACATGAAGATTCTCACATAACC
Found at i:316302 original size:78 final size:78
Alignment explanation
Indices: 316129--316310 Score: 188
Period size: 78 Copynumber: 2.3 Consensus size: 78
316119 CTTAAACGCA
* * *
316129 GTTTTGAGGATACTATTACCAAAATAACTTTAATGGATATATTTCGACAAGAAAGTTCCCACATG
1 GTTTTGAGG-TAGTATTACCAAAATAACCTTAATGGATATATTTCGACAAGAAAGTACCCACATG
316194 ACTCTAAGGACTTG
65 ACTCTAAGGACTTG
* * * * * * * * * * *
316208 ATTCTAAGGT-GTTATTATCAAAATGACCTTGATGGATATGTTTTGACACGAAAGTACTCGCATG
1 GTTTTGAGGTAG-TATTACCAAAATAACCTTAATGGATATATTTCGACAAGAAAGTACCCACATG
316272 AC-CTTAAGGACTTG
65 ACTC-TAAGGACTTG
*
316286 GTTTTGAGGTAGTATTACCTAAATA
1 GTTTTGAGGTAGTATTACCAAAATA
316311 CCCTAACGGA
Statistics
Matches: 80, Mismatches: 20, Indels: 7
0.75 0.19 0.07
Matches are distributed among these distances:
77 1 0.01
78 72 0.90
79 7 0.09
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.34
Consensus pattern (78 bp):
GTTTTGAGGTAGTATTACCAAAATAACCTTAATGGATATATTTCGACAAGAAAGTACCCACATGA
CTCTAAGGACTTG
Found at i:316350 original size:78 final size:79
Alignment explanation
Indices: 316268--316421 Score: 177
Period size: 78 Copynumber: 2.0 Consensus size: 79
316258 AAAGTACTCG
* * * * *
316268 CATGACCTTAAGGACTTGGTTTTGAGGTAGTA-TTACCTAAATACCC-TAACGGACATGTTTCAA
1 CATGACCTTAAGAACTCGATTATAAGGTAGTATTTACCTAAATACCCTTAACGGACATGTTTCAA
*
316331 TACTGAAGGTTCCCA
66 TA-TGAAAGTTCCCA
* *** * *
316346 CATGATCTTAAGAACTCGATTATAAGGTAGTATTTTTTTAAATACCCTTAACGGATATGTTTCGA
1 CATGACCTTAAGAACTCGATTATAAGGTAGTATTTACCTAAATACCCTTAACGGACATGTTTCAA
316411 TATGAAAGTTC
66 TATGAAAGTTC
316422 TTACAGGATC
Statistics
Matches: 62, Mismatches: 12, Indels: 3
0.81 0.16 0.04
Matches are distributed among these distances:
78 26 0.42
79 19 0.31
80 17 0.27
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Consensus pattern (79 bp):
CATGACCTTAAGAACTCGATTATAAGGTAGTATTTACCTAAATACCCTTAACGGACATGTTTCAA
TATGAAAGTTCCCA
Found at i:331034 original size:2 final size:2
Alignment explanation
Indices: 331029--331054 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
331019 TTTTTTTCCT
331029 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
331055 GAGAGAGAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:331059 original size:2 final size:2
Alignment explanation
Indices: 331054--331085 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
331044 ATATATATAT
331054 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
331086 TTTATAGTGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:331414 original size:20 final size:19
Alignment explanation
Indices: 331387--331428 Score: 66
Period size: 20 Copynumber: 2.2 Consensus size: 19
331377 ATTATATAAA
*
331387 ATAAAATAATATTTATTAT
1 ATAAAATAAGATTTATTAT
331406 ATAATAATAAGATTTATTAT
1 ATAA-AATAAGATTTATTAT
331426 ATA
1 ATA
331429 TTTAAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (19 bp):
ATAAAATAAGATTTATTAT
Found at i:331830 original size:18 final size:18
Alignment explanation
Indices: 331776--331831 Score: 60
Period size: 18 Copynumber: 3.1 Consensus size: 18
331766 CCCTTTTGCC
* *
331776 TTTAATTTTGTTCAATATT
1 TTTAATTTT-TTTAATAAT
*
331795 TTTAATTTTTTTATTAAT
1 TTTAATTTTTTTAATAAT
331813 TTT-ATTTTTTTACATAAT
1 TTTAATTTTTTTA-ATAAT
331831 T
1 T
331832 ATAAATTTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
17 9 0.28
18 14 0.44
19 9 0.28
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.68
Consensus pattern (18 bp):
TTTAATTTTTTTAATAAT
Found at i:331873 original size:38 final size:35
Alignment explanation
Indices: 331826--331913 Score: 92
Period size: 34 Copynumber: 2.5 Consensus size: 35
331816 ATTTTTTTAC
* * *
331826 ATAATTATAAATTTAATAATTTTTAATTATTATTTAAT
1 ATAAATATAAATTT--TAATATATAATTATT-TTTAAT
*
331864 ATAAATAT-AATTTTAATATATATTTATTTTTAAT
1 ATAAATATAAATTTTAATATATAATTATTTTTAAT
331898 ATAAATAT--ATTTTAAT
1 ATAAATATAAATTTTAAT
331914 TATTTATTAT
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
33 8 0.17
34 14 0.30
35 12 0.26
37 5 0.11
38 7 0.15
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (35 bp):
ATAAATATAAATTTTAATATATAATTATTTTTAAT
Found at i:331880 original size:17 final size:17
Alignment explanation
Indices: 331858--331913 Score: 78
Period size: 17 Copynumber: 3.4 Consensus size: 17
331848 TTAATTATTA
331858 TTTAATATAAATATAAT
1 TTTAATATAAATATAAT
* * *
331875 TTTAATATATATTTATT
1 TTTAATATAAATATAAT
331892 TTTAATATAAATAT-AT
1 TTTAATATAAATATAAT
331908 TTTAAT
1 TTTAAT
331914 TATTTATTAT
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
16 7 0.21
17 26 0.79
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TTTAATATAAATATAAT
Found at i:331898 original size:28 final size:28
Alignment explanation
Indices: 331837--331901 Score: 71
Period size: 28 Copynumber: 2.4 Consensus size: 28
331827 TAATTATAAA
*
331837 TTTAATA-ATTTTTAATTATTATTTAAT
1 TTTAATATAATTTTAATTATTATTTAAT
* * *
331864 ATAAATATAATTTTAA-TATATATTTATT
1 TTTAATATAATTTTAATTAT-TATTTAAT
331892 TTTAATATAA
1 TTTAATATAA
331902 ATATATTTTA
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
27 8 0.27
28 22 0.73
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (28 bp):
TTTAATATAATTTTAATTATTATTTAAT
Found at i:336659 original size:18 final size:17
Alignment explanation
Indices: 336631--336672 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 17
336621 ATGAGTTTCG
336631 AATTTTTTTAAAATTTT
1 AATTTTTTTAAAATTTT
**
336648 AATTTATTTTAATCTTTT
1 AATTT-TTTTAAAATTTT
336666 AATTTTT
1 AATTTTT
336673 ATCTAATTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 7 0.32
18 15 0.68
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (17 bp):
AATTTTTTTAAAATTTT
Found at i:338332 original size:17 final size:16
Alignment explanation
Indices: 338299--338330 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
338289 CTTTTTTATT
338299 ATTTTAATATCATATA
1 ATTTTAATATCATATA
338315 ATTTT-ATAT-ATATA
1 ATTTTAATATCATATA
338329 AT
1 AT
338331 AAAAAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.44
15 4 0.25
16 5 0.31
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (16 bp):
ATTTTAATATCATATA
Found at i:339026 original size:2 final size:2
Alignment explanation
Indices: 339019--339062 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
339009 CGGCTGGCCC
339019 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
339061 AT
1 AT
339063 TTTTATAAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:339516 original size:18 final size:17
Alignment explanation
Indices: 339478--339516 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
339468 AAAAATATAA
339478 TTTTTTATTTTAATCAAT
1 TTTTTTATTTTAA-CAAT
339496 TTTTTTATCTTTAA-AAT
1 TTTTTTAT-TTTAACAAT
339513 TTTT
1 TTTT
339517 AAATAATGGT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 8 0.40
19 5 0.25
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.69
Consensus pattern (17 bp):
TTTTTTATTTTAACAAT
Found at i:339817 original size:19 final size:17
Alignment explanation
Indices: 339787--339823 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
339777 TAACTTCATA
339787 ATAATTAAAAATAGTTTT
1 ATAATTAAAAATA-TTTT
339805 ATAATTAAAAAATATTTT
1 ATAATT-AAAAATATTTT
339823 A
1 A
339824 AGTAAAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (17 bp):
ATAATTAAAAATATTTT
Found at i:343004 original size:2 final size:2
Alignment explanation
Indices: 342997--343035 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
342987 TTGTATTACA
342997 AT AT AT AT AT AT 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 AT AT AT AT AT AT A
343036 CTGTAAAAGT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:343814 original size:2 final size:2
Alignment explanation
Indices: 343807--343864 Score: 62
Period size: 2 Copynumber: 29.0 Consensus size: 2
343797 ATTTTCACTA
* * * * * *
343807 AT AT AT AT AT AT AT AT AT AT AT AT AT AC AC AC AT AT AC AC AC
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
343849 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
343865 CACTATCAAC
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (2 bp):
AT
Found at i:344471 original size:18 final size:17
Alignment explanation
Indices: 344440--344474 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
344430 AACCCCTCCC
*
344440 TTTATTTATTTTTATTT
1 TTTATTTATATTTATTT
344457 TTTATTTTATATTTATTT
1 TTTA-TTTATATTTATTT
344475 ATATTTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (17 bp):
TTTATTTATATTTATTT
Found at i:345958 original size:77 final size:77
Alignment explanation
Indices: 345858--346014 Score: 244
Period size: 77 Copynumber: 2.0 Consensus size: 77
345848 TCTCAATAAA
* *
345858 ATTAAAGGGAACCACATGAAACAACATTCAGTTGGTTTGTTCTTTGAAATTAAATTAGGTTAAAA
1 ATTAAAGGGAACCAAAAGAAACAACATTCAGTTGGTTTGTTCTTTGAAATTAAATTAGGTTAAAA
*
345923 ATTCTTTGATTC
66 ACTCTTTGATTC
* *
345935 ATTAAA-GGAAGCCAAAAGAAACAACATTCAGTTGGTTTGTTCTTTGAAATTAGATTATGTTAAA
1 ATTAAAGGGAA-CCAAAAGAAACAACATTCAGTTGGTTTGTTCTTTGAAATTAAATTAGGTTAAA
*
345999 AACTCTTTGTTTC
65 AACTCTTTGATTC
346012 ATT
1 ATT
346015 GTGAAAAAGA
Statistics
Matches: 73, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
76 4 0.05
77 69 0.95
ACGTcount: A:0.36, C:0.11, G:0.15, T:0.37
Consensus pattern (77 bp):
ATTAAAGGGAACCAAAAGAAACAACATTCAGTTGGTTTGTTCTTTGAAATTAAATTAGGTTAAAA
ACTCTTTGATTC
Found at i:346339 original size:2 final size:2
Alignment explanation
Indices: 346332--346369 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
346322 CACAATCTAA
*
346332 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AG AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
346370 CTAAAAGAAC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:347185 original size:2 final size:2
Alignment explanation
Indices: 347180--347210 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
347170 TTTTTACTCT
347180 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
347211 TCATAAATAA
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:353361 original size:2 final size:2
Alignment explanation
Indices: 353344--353378 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
353334 CCCTTGAAAA
*
353344 AT AT CT AT AT -T 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
353379 TATGACTGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:353431 original size:27 final size:26
Alignment explanation
Indices: 353401--353488 Score: 69
Period size: 27 Copynumber: 3.3 Consensus size: 26
353391 AATTAGTGTC
353401 AAAATCAAATGATATTAATTT-AATTAT
1 AAAAT-AAAT-ATATTAATTTAAATTAT
353428 AAAA-AAAT-TAATTTAAATTTAAATTAT
1 AAAATAAATAT-A-TT-AATTTAAATTAT
353455 AAAATAAA-ATATTTAATTTTTAAATT-T
1 AAAATAAATATA-TTAA--TTTAAATTAT
353482 AAAATAA
1 AAAATAA
353489 TCACTTACTA
Statistics
Matches: 53, Mismatches: 0, Indels: 16
0.77 0.00 0.23
Matches are distributed among these distances:
23 1 0.02
24 1 0.02
25 6 0.11
26 7 0.13
27 26 0.49
28 12 0.23
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (26 bp):
AAAATAAATATATTAATTTAAATTAT
Found at i:353478 original size:21 final size:22
Alignment explanation
Indices: 353444--353487 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
353434 ATTAATTTAA
353444 ATTTAAATTATAAA-ATAAAAT
1 ATTTAAATTATAAATATAAAAT
* * *
353465 ATTTAATTTTTAAATTTAAAAT
1 ATTTAAATTATAAATATAAAAT
353487 A
1 A
353488 ATCACTTACT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
ATTTAAATTATAAATATAAAAT
Found at i:354603 original size:25 final size:26
Alignment explanation
Indices: 354575--354627 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 26
354565 TTTAAATTTA
*
354575 AATATATAAATATTAATATAAA-AAT
1 AATATATAAATAATAATATAAATAAT
* * *
354600 AATATTTTAATAATATTATAAATAAT
1 AATATATAAATAATAATATAAATAAT
354626 AA
1 AA
354628 AACAAAATTT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
25 18 0.78
26 5 0.22
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (26 bp):
AATATATAAATAATAATATAAATAAT
Found at i:357072 original size:16 final size:16
Alignment explanation
Indices: 357029--357072 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 16
357019 TAACTCTAAT
* *
357029 TTTAATATAATCTAAA
1 TTTAAAATAATTTAAA
* *
357045 TATGAAATAATTTAAA
1 TTTAAAATAATTTAAA
357061 TTTAAAATAATT
1 TTTAAAATAATT
357073 CGATATACAA
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (16 bp):
TTTAAAATAATTTAAA
Found at i:357762 original size:16 final size:16
Alignment explanation
Indices: 357720--357770 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
357710 TATGCATCAT
*
357720 TTTCGAGTTTAAGTCA
1 TTTCGAGTTTAGGTCA
* *
357736 TGTC-AGCTTTAGGTTA
1 TTTCGAG-TTTAGGTCA
*
357752 TTTCGAGTTTAGATCA
1 TTTCGAGTTTAGGTCA
357768 TTT
1 TTT
357771 AGATTTAAGT
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
15 2 0.07
16 23 0.85
17 2 0.07
ACGTcount: A:0.22, C:0.12, G:0.20, T:0.47
Consensus pattern (16 bp):
TTTCGAGTTTAGGTCA
Found at i:362327 original size:31 final size:30
Alignment explanation
Indices: 362273--362345 Score: 87
Period size: 31 Copynumber: 2.4 Consensus size: 30
362263 AAGATCTAAT
*
362273 AATTTTAATAATTATAATTATTATTTATCA
1 AATTTTAATAATTATAATTATTATTTATAA
* *
362303 AATTTTAATTAATTA-ATTTAATTATTTTTAA
1 AATTTTAA-TAATTATAATT-ATTATTTATAA
362334 AATTTT-ATAATT
1 AATTTTAATAATT
362346 TAAATTTTAA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
29 5 0.13
30 12 0.32
31 21 0.55
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.56
Consensus pattern (30 bp):
AATTTTAATAATTATAATTATTATTTATAA
Found at i:362350 original size:14 final size:16
Alignment explanation
Indices: 362333--362366 Score: 54
Period size: 14 Copynumber: 2.2 Consensus size: 16
362323 ATTATTTTTA
362333 AAATTTT-ATAATT-T
1 AAATTTTAATAATTAT
362347 AAATTTTAATAATTAT
1 AAATTTTAATAATTAT
362363 AAAT
1 AAAT
362367 CGCCTCTGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 7 0.39
15 6 0.33
16 5 0.28
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
AAATTTTAATAATTAT
Found at i:362352 original size:31 final size:33
Alignment explanation
Indices: 362277--362340 Score: 89
Period size: 34 Copynumber: 2.0 Consensus size: 33
362267 TCTAATAATT
362277 TTAA-TAATTATAATTATTATTTATCAAATTTTAA
1 TTAATTAATT-TAATTATTATTTA-CAAATTTTAA
362311 TTAATTAATTTAATTATT-TTTA-AAATTTTA
1 TTAATTAATTTAATTATTATTTACAAATTTTA
362341 TAATTTAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
31 8 0.28
33 4 0.14
34 12 0.41
35 5 0.17
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (33 bp):
TTAATTAATTTAATTATTATTTACAAATTTTAA
Found at i:362837 original size:25 final size:25
Alignment explanation
Indices: 362775--362838 Score: 65
Period size: 25 Copynumber: 2.5 Consensus size: 25
362765 ATGGCTCATT
* ** *
362775 AATTTTATTTACATATATTTAATTTT
1 AATTTTATTTA-AAATATAAAATTTA
* *
362801 AATTTAACTTAAAATATAAAATTTA
1 AATTTTATTTAAAATATAAAATTTA
362826 AATTTTATTTAAA
1 AATTTTATTTAAA
362839 TTTATTTATT
Statistics
Matches: 30, Mismatches: 8, Indels: 1
0.77 0.21 0.03
Matches are distributed among these distances:
25 21 0.70
26 9 0.30
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (25 bp):
AATTTTATTTAAAATATAAAATTTA
Found at i:363129 original size:21 final size:20
Alignment explanation
Indices: 363103--363154 Score: 61
Period size: 19 Copynumber: 2.5 Consensus size: 20
363093 AAAAAGCTTT
363103 ATTTTTTTATATATAAATTTA
1 ATTTTTTT-TATATAAATTTA
*
363124 A-TTTTTTTATCTAAATTTA
1 ATTTTTTTTATATAAATTTA
363143 ATATTTTATTTA
1 AT-TTTT-TTTA
363155 AATTTTTTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
19 12 0.44
20 6 0.22
21 5 0.19
22 4 0.15
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (20 bp):
ATTTTTTTTATATAAATTTA
Found at i:363138 original size:19 final size:19
Alignment explanation
Indices: 363100--363159 Score: 68
Period size: 18 Copynumber: 3.2 Consensus size: 19
363090 ATTAAAAAGC
*
363100 TTTATTTTTTTATATATAAA
1 TTTAATTTTTT-TATATAAA
*
363120 TTTAATTTTTTTATCTAAA
1 TTTAATTTTTTTATATAAA
* *
363139 TTTAA-TATTTTATTTAAA
1 TTTAATTTTTTTATATAAA
363157 TTT
1 TTT
363160 TTTAAAATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
18 14 0.39
19 12 0.33
20 10 0.28
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (19 bp):
TTTAATTTTTTTATATAAA
Found at i:363163 original size:21 final size:21
Alignment explanation
Indices: 363139--363179 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
363129 TTTATCTAAA
* * *
363139 TTTAATATTTTATTTAAATTT
1 TTTAAAATATTATATAAATTT
363160 TTTAAAATATTATATAAATT
1 TTTAAAATATTATATAAATT
363180 ATCAAAGGTG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
TTTAAAATATTATATAAATTT
Found at i:363423 original size:3 final size:3
Alignment explanation
Indices: 363417--363453 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
363407 TTATTATGGC
363417 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
363454 CGTCTGTGAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:366679 original size:18 final size:18
Alignment explanation
Indices: 366645--366678 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
366635 TACTTTTTAA
366645 TTTATATTTAAATAAAAT
1 TTTATATTTAAATAAAAT
366663 TTTAT-TTTAAATAAAA
1 TTTATATTTAAATAAAA
366679 AATTAATTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TTTATATTTAAATAAAAT
Found at i:366688 original size:17 final size:17
Alignment explanation
Indices: 366650--366688 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
366640 TTTAATTTAT
**
366650 ATTTAAATAAAATTTTA
1 ATTTAAATAAAAAATTA
*
366667 TTTTAAATAAAAAATTA
1 ATTTAAATAAAAAATTA
366684 ATTTA
1 ATTTA
366689 TGTTAAAAAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATTTAAATAAAAAATTA
Found at i:366715 original size:18 final size:17
Alignment explanation
Indices: 366676--366717 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 17
366666 ATTTTAAATA
*
366676 AAAAATTAATTTATGT-T
1 AAAAATTATTTTA-GTAT
366693 AAAAATTATTTTAGTAT
1 AAAAATTATTTTAGTAT
366710 ATAAAATT
1 A-AAAATT
366718 TGTTTGGCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 2 0.09
17 14 0.64
18 6 0.27
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (17 bp):
AAAAATTATTTTAGTAT
Found at i:367089 original size:30 final size:29
Alignment explanation
Indices: 367021--367098 Score: 97
Period size: 29 Copynumber: 2.7 Consensus size: 29
367011 AAAGTTATAA
*
367021 AAAATTTATTT--ATGTATAAATTAAAAGTT
1 AAAATTTATTTGAATG--TAAATTAAAAATT
*
367050 AAAATTTATTTTAATGTAAATTAAAAATT
1 AAAATTTATTTGAATGTAAATTAAAAATT
367079 AAAGATTTATTTGAATGTAA
1 AAA-ATTTATTTGAATGTAA
367099 TAAAAAAATA
Statistics
Matches: 44, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
29 26 0.59
30 15 0.34
31 3 0.07
ACGTcount: A:0.49, C:0.00, G:0.08, T:0.44
Consensus pattern (29 bp):
AAAATTTATTTGAATGTAAATTAAAAATT
Found at i:367506 original size:19 final size:20
Alignment explanation
Indices: 367465--367506 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
367455 TTTTTAAAAA
* *
367465 TAAATATAAATAATTTTAAT
1 TAAATATAAATAATATCAAT
*
367485 TAAATA-AAATAATATCATT
1 TAAATATAAATAATATCAAT
367504 TAA
1 TAA
367507 TTTATTAATA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (20 bp):
TAAATATAAATAATATCAAT
Found at i:369191 original size:26 final size:27
Alignment explanation
Indices: 369132--369195 Score: 71
Period size: 26 Copynumber: 2.4 Consensus size: 27
369122 TTTCACATGT
369132 TATA-TTATTATAATGTTTAACATACTA
1 TATATTTA-TATAATGTTTAACATACTA
* *
369159 TATATTTATATAAT-TTTGACATATTA
1 TATATTTATATAATGTTTAACATACTA
369185 -ATAATTTATAT
1 TAT-ATTTATAT
369196 TATATAAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
25 2 0.06
26 18 0.55
27 10 0.30
28 3 0.09
ACGTcount: A:0.41, C:0.05, G:0.03, T:0.52
Consensus pattern (27 bp):
TATATTTATATAATGTTTAACATACTA
Found at i:369254 original size:16 final size:17
Alignment explanation
Indices: 369233--369265 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
369223 CATATTGTAT
369233 TCATAT-TATTTTTATA
1 TCATATATATTTTTATA
369249 TCATATCATATTTTTAT
1 TCATAT-ATATTTTTAT
369266 TTTTTATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
18 9 0.60
ACGTcount: A:0.30, C:0.09, G:0.00, T:0.61
Consensus pattern (17 bp):
TCATATATATTTTTATA
Found at i:369336 original size:33 final size:34
Alignment explanation
Indices: 369270--369333 Score: 98
Period size: 34 Copynumber: 2.0 Consensus size: 34
369260 TTTTATTTTT
*
369270 TATTTTATATTTTGTGTTATATTCAAAATTATAA
1 TATTTTATATTTTGTGCTATATTCAAAATTATAA
369304 TATTTTATATTTT-TGCTATA-T-AAAATTATA
1 TATTTTATATTTTGTGCTATATTCAAAATTATA
369334 TAACTATAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
31 9 0.31
32 1 0.03
33 6 0.21
34 13 0.45
ACGTcount: A:0.36, C:0.03, G:0.05, T:0.56
Consensus pattern (34 bp):
TATTTTATATTTTGTGCTATATTCAAAATTATAA
Found at i:369902 original size:22 final size:23
Alignment explanation
Indices: 369874--369922 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
369864 ATTATATATC
* *
369874 ATTTTTAAATGTAAAATTTGATA
1 ATTTTAAAATGTAAAATTTAATA
* *
369897 ATTTTAAAATTTAAATTTTAATA
1 ATTTTAAAATGTAAAATTTAATA
369920 ATT
1 ATT
369923 GTAACTTTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (23 bp):
ATTTTAAAATGTAAAATTTAATA
Found at i:370173 original size:22 final size:21
Alignment explanation
Indices: 370142--370188 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
370132 ATAAAAATAA
370142 AAATTT-TAT-TTTTAT-ATT
1 AAATTTATATATTTTATAATT
370160 AATATTTATATATTTTATAATT
1 AA-ATTTATATATTTTATAATT
370182 AAATTTA
1 AAATTTA
370189 AATAAAAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
18 2 0.08
19 4 0.16
20 3 0.12
21 11 0.44
22 5 0.20
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
AAATTTATATATTTTATAATT
Found at i:370247 original size:10 final size:10
Alignment explanation
Indices: 370197--370250 Score: 56
Period size: 10 Copynumber: 5.4 Consensus size: 10
370187 TAAATAAAAA
*
370197 TAATTTTAAT
1 TAATTTAAAT
*
370207 T-ATTTAATAA
1 TAATTTAA-AT
370217 TAATTTAAAT
1 TAATTTAAAT
* *
370227 CAAATTAAAT
1 TAATTTAAAT
370237 TAATTTAAAT
1 TAATTTAAAT
370247 TAAT
1 TAAT
370251 AAAAAAATTA
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
9 5 0.14
10 24 0.69
11 6 0.17
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (10 bp):
TAATTTAAAT
Found at i:370852 original size:2 final size:2
Alignment explanation
Indices: 370847--370874 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
370837 TCTTCATGCT
370847 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
370875 GGAAATTTGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:373472 original size:20 final size:21
Alignment explanation
Indices: 373447--373486 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
373437 AATGCCTTGG
373447 GAGTTTA-AGATCTCGGATTT
1 GAGTTTAGAGATCTCGGATTT
373467 GAGTTTAGAGATCTCGGATT
1 GAGTTTAGAGATCTCGGATT
373487 CGGACAGGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.25, C:0.10, G:0.28, T:0.38
Consensus pattern (21 bp):
GAGTTTAGAGATCTCGGATTT
Found at i:374333 original size:17 final size:16
Alignment explanation
Indices: 374284--374338 Score: 67
Period size: 17 Copynumber: 3.2 Consensus size: 16
374274 TATATTATAA
374284 TTATATTTAA-AATATT
1 TTATATTTAATAAT-TT
374300 TTATATTTATATAAATTT
1 TTATATTTA-AT-AATTT
374318 TTATATTTTAATAATTT
1 TTATA-TTTAATAATTT
374335 TTAT
1 TTAT
374339 TATATAAAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
16 9 0.26
17 10 0.29
18 9 0.26
19 7 0.20
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
TTATATTTAATAATTT
Found at i:374335 original size:34 final size:32
Alignment explanation
Indices: 374284--374346 Score: 83
Period size: 34 Copynumber: 1.9 Consensus size: 32
374274 TATATTATAA
374284 TTATATTTAAAATATTTTATATTTATATAAATTT
1 TTATATTTAAAATATTTT-TA-TTATATAAATTT
*
374318 TTATATTT-TAATAATTTTTATTATATAAA
1 TTATATTTAAAAT-ATTTTTATTATATAAA
374347 ATTAAAAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
32 9 0.33
33 5 0.19
34 13 0.48
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (32 bp):
TTATATTTAAAATATTTTTATTATATAAATTT
Found at i:375188 original size:20 final size:20
Alignment explanation
Indices: 375163--375201 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
375153 TAAATGATGT
375163 TATTTAATTTAAAAAATTTA
1 TATTTAATTTAAAAAATTTA
* *
375183 TATTTATTTTTAAAAATTT
1 TATTTAATTTAAAAAATTT
375202 TTAATAAAAA
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:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
TATTTAATTTAAAAAATTTA
Found at i:377025 original size:21 final size:21
Alignment explanation
Indices: 376970--377025 Score: 51
Period size: 21 Copynumber: 2.7 Consensus size: 21
376960 AATAATATTA
*
376970 AATTTAAAATTAATTTAATTT
1 AATTTAAAATTATTTTAATTT
* ***
376991 AACCTCGTAA-TATTTTAATTT
1 AA-TTTAAAATTATTTTAATTT
377012 AATTTAAAATTATT
1 AATTTAAAATTATT
377026 AAAATTTTAA
Statistics
Matches: 24, Mismatches: 9, Indels: 4
0.65 0.24 0.11
Matches are distributed among these distances:
20 3 0.12
21 18 0.75
22 3 0.12
ACGTcount: A:0.43, C:0.05, G:0.02, T:0.50
Consensus pattern (21 bp):
AATTTAAAATTATTTTAATTT
Found at i:377072 original size:16 final size:16
Alignment explanation
Indices: 377004--377072 Score: 50
Period size: 16 Copynumber: 4.1 Consensus size: 16
376994 CTCGTAATAT
*
377004 TTTAATTTAATTTAAA
1 TTTATTTTAATTTAAA
* **
377020 ATTATTAAAATTTTAAA
1 TTTATTTTAA-TTTAAA
*
377037 TTAATATTTT-ATTATCAA
1 TT--TATTTTAATT-TAAA
377055 TTTATTTTAATTTAAA
1 TTTATTTTAATTTAAA
377071 TT
1 TT
377073 AAAAATTTTA
Statistics
Matches: 39, Mismatches: 9, Indels: 10
0.67 0.16 0.17
Matches are distributed among these distances:
16 17 0.44
17 12 0.31
18 6 0.15
19 4 0.10
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (16 bp):
TTTATTTTAATTTAAA
Found at i:377507 original size:25 final size:23
Alignment explanation
Indices: 377468--377519 Score: 68
Period size: 25 Copynumber: 2.2 Consensus size: 23
377458 TTATTCTGTT
* *
377468 TATTTATATTTTTATATTATAATTA
1 TATTTAAATTATTATATTA-AA-TA
377493 TATTTAAATTATTATATTAAATA
1 TATTTAAATTATTATATTAAATA
377516 TATT
1 TATT
377520 AATTAATAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 6 0.24
24 2 0.08
25 17 0.68
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (23 bp):
TATTTAAATTATTATATTAAATA
Found at i:377519 original size:14 final size:13
Alignment explanation
Indices: 377479--377525 Score: 55
Period size: 13 Copynumber: 3.7 Consensus size: 13
377469 ATTTATATTT
377479 TTATATTATAATTA
1 TTATATTA-AATTA
377493 -TAT-TTAAATTA
1 TTATATTAAATTA
377504 TTATATTAAATATA
1 TTATATTAAAT-TA
377518 TTA-ATTAA
1 TTATATTAA
377526 TAATTTAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
11 5 0.17
12 6 0.20
13 14 0.47
14 5 0.17
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (13 bp):
TTATATTAAATTA
Found at i:377629 original size:31 final size:32
Alignment explanation
Indices: 377567--377634 Score: 86
Period size: 31 Copynumber: 2.2 Consensus size: 32
377557 TTAAGATCAT
* *
377567 ATTATTTTTTATTATATTATTATTATAATTTA
1 ATTATTTTTTATAATAATATTATTATAATTTA
*
377599 ATTATTTTTTA-AATAATATT-TATATTATTTA
1 ATTATTTTTTATAATAATATTAT-TATAATTTA
377630 ATTAT
1 ATTAT
377635 ATTAGGTTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
30 1 0.03
31 20 0.62
32 11 0.34
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (32 bp):
ATTATTTTTTATAATAATATTATTATAATTTA
Found at i:378519 original size:10 final size:10
Alignment explanation
Indices: 378506--378532 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
378496 ATAATTTATT
378506 ATATTTTCTA
1 ATATTTTCTA
378516 ATATTTTCTA
1 ATATTTTCTA
378526 ATATTTT
1 ATATTTT
378533 TATATTTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.63
Consensus pattern (10 bp):
ATATTTTCTA
Found at i:379943 original size:24 final size:25
Alignment explanation
Indices: 379896--379944 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
379886 TTTATATATA
* *
379896 TTTAAATTAAATATAAATATAATTT
1 TTTAAATAAAATATAAATAAAATTT
379921 TTTAAATAAAATATAAA-AAAATTT
1 TTTAAATAAAATATAAATAAAATTT
379945 AAATATATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 6 0.27
25 16 0.73
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (25 bp):
TTTAAATAAAATATAAATAAAATTT
Found at i:381858 original size:22 final size:22
Alignment explanation
Indices: 381830--381882 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
381820 AAAGTAATTA
* *
381830 GGTATATTAGGGGTTACAATAT
1 GGTATATTAGAGATTACAATAT
*
381852 GGTATATTAGAGATTACGATAT
1 GGTATATTAGAGATTACAATAT
*
381874 GCTATATTA
1 GGTATATTA
381883 AAAATAACGA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.34, C:0.06, G:0.23, T:0.38
Consensus pattern (22 bp):
GGTATATTAGAGATTACAATAT
Found at i:381892 original size:22 final size:22
Alignment explanation
Indices: 381848--381893 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
381838 AGGGGTTACA
* * * *
381848 ATATGGTATATTAGAGATTACG
1 ATATGCTATATTAAAAATAACG
381870 ATATGCTATATTAAAAATAACG
1 ATATGCTATATTAAAAATAACG
381892 AT
1 AT
381894 CTGATATCTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.43, C:0.07, G:0.15, T:0.35
Consensus pattern (22 bp):
ATATGCTATATTAAAAATAACG
Found at i:382091 original size:16 final size:16
Alignment explanation
Indices: 382070--382106 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
382060 GTTATTTTCA
*
382070 GGTTCGGGTCATTTTG
1 GGTTCGGGCCATTTTG
382086 GGTTCGGGCCATTTTG
1 GGTTCGGGCCATTTTG
382102 GGTTC
1 GGTTC
382107 AGGTTAATCG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.05, C:0.16, G:0.38, T:0.41
Consensus pattern (16 bp):
GGTTCGGGCCATTTTG
Found at i:382165 original size:53 final size:53
Alignment explanation
Indices: 382085--382188 Score: 156
Period size: 53 Copynumber: 2.0 Consensus size: 53
382075 GGGTCATTTT
* *
382085 GGGTTCGGGCCATTTTGGGTTCAGGTTAATCGGGTTTAACACTT-GGGTTAATC
1 GGGTTCGGGCCATTTTGGATTCAGGTTAATCGAGTTTAACA-TTCGGGTTAATC
* *
382138 GGGTTCGGGTCATTTTGGATTCGGGTTAATCGAGTTTAACATTCGGGTTAA
1 GGGTTCGGGCCATTTTGGATTCAGGTTAATCGAGTTTAACATTCGGGTTAA
382189 ATTAGGTTCA
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
52 2 0.04
53 44 0.96
ACGTcount: A:0.18, C:0.13, G:0.32, T:0.37
Consensus pattern (53 bp):
GGGTTCGGGCCATTTTGGATTCAGGTTAATCGAGTTTAACATTCGGGTTAATC
Found at i:383203 original size:16 final size:16
Alignment explanation
Indices: 383184--383234 Score: 66
Period size: 16 Copynumber: 3.2 Consensus size: 16
383174 GGTGTAGATT
*
383184 ATTTCGGGCTCGGGTC
1 ATTTCGGGTTCGGGTC
* *
383200 ATTTTGGATTCGGGTC
1 ATTTCGGGTTCGGGTC
*
383216 ATTTCAGGTTCGGGTC
1 ATTTCGGGTTCGGGTC
383232 ATT
1 ATT
383235 CTGGATTCAG
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.12, C:0.18, G:0.31, T:0.39
Consensus pattern (16 bp):
ATTTCGGGTTCGGGTC
Found at i:383256 original size:32 final size:32
Alignment explanation
Indices: 383179--383266 Score: 104
Period size: 32 Copynumber: 2.8 Consensus size: 32
383169 TTTTGGGTGT
* * * *
383179 AGATTATTTCGGGCTCGGGTCATTTTGGATTC
1 AGATCATTTCAGGTTCGGGTCATTCTGGATTC
* *
383211 GGGTCATTTCAGGTTCGGGTCATTCTGGATTC
1 AGATCATTTCAGGTTCGGGTCATTCTGGATTC
* *
383243 AGATCATTTCAGGTTTGAGTCATT
1 AGATCATTTCAGGTTCGGGTCATT
383267 TTAGGTTTGG
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
32 46 1.00
ACGTcount: A:0.17, C:0.16, G:0.27, T:0.40
Consensus pattern (32 bp):
AGATCATTTCAGGTTCGGGTCATTCTGGATTC
Found at i:383265 original size:16 final size:16
Alignment explanation
Indices: 383213--383275 Score: 56
Period size: 16 Copynumber: 3.9 Consensus size: 16
383203 TTGGATTCGG
* *
383213 GTCATTTCAGGTTCGG
1 GTCATTTCAGGTTTGA
* * *
383229 GTCA-TTCTGGATTCA
1 GTCATTTCAGGTTTGA
383244 GATCATTTCAGGTTTGA
1 G-TCATTTCAGGTTTGA
*
383261 GTCATTTTAGGTTTG
1 GTCATTTCAGGTTTG
383276 GATCAGTTCG
Statistics
Matches: 36, Mismatches: 9, Indels: 4
0.73 0.18 0.08
Matches are distributed among these distances:
15 7 0.19
16 20 0.56
17 9 0.25
ACGTcount: A:0.17, C:0.14, G:0.25, T:0.43
Consensus pattern (16 bp):
GTCATTTCAGGTTTGA
Found at i:385486 original size:24 final size:25
Alignment explanation
Indices: 385441--385487 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
385431 ATTTTTTAAA
** *
385441 TTTTTATATTTATATTATATATATT
1 TTTTTATAAATATATTAAATATATT
385466 TTTTTATAAATAT-TTAAATATA
1 TTTTTATAAATATATTAAATATA
385488 ATATTTTAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 8 0.42
25 11 0.58
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (25 bp):
TTTTTATAAATATATTAAATATATT
Found at i:385487 original size:14 final size:15
Alignment explanation
Indices: 385470--385501 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
385460 TATATTTTTT
385470 TATAAATA-TTTAAA
1 TATAAATATTTTAAA
385484 TAT-AATATTTTAAA
1 TATAAATATTTTAAA
385498 TATA
1 TATA
385502 TAAAAAAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 3
0.84 0.00 0.16
Matches are distributed among these distances:
13 4 0.25
14 12 0.75
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
TATAAATATTTTAAA
Found at i:385529 original size:17 final size:16
Alignment explanation
Indices: 385475--385545 Score: 58
Period size: 15 Copynumber: 4.4 Consensus size: 16
385465 TTTTTTATAA
*
385475 ATATTTAAATAT-AAT
1 ATATTTAAAAATAAAT
*
385490 AT-TTTAAATATATAAAA
1 ATATTTAAA-A-ATAAAT
*
385507 AAATTTAAAAAGTAAAT
1 ATATTTAAAAA-TAAAT
*
385524 ATATTT-ATAATAAAT
1 ATATTTAAAAATAAAT
385539 ATATTTA
1 ATATTTA
385546 TATTTAATAT
Statistics
Matches: 44, Mismatches: 6, Indels: 11
0.72 0.10 0.18
Matches are distributed among these distances:
14 6 0.14
15 13 0.30
16 6 0.14
17 13 0.30
18 6 0.14
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.42
Consensus pattern (16 bp):
ATATTTAAAAATAAAT
Found at i:386376 original size:21 final size:22
Alignment explanation
Indices: 386350--386392 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
386340 AATTTGATTA
*
386350 ATTTATTTTATATTTA-AATTT
1 ATTTATTATATATTTATAATTT
*
386371 ATTTATTATCTATTTATAATTT
1 ATTTATTATATATTTATAATTT
386393 TAATATTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (22 bp):
ATTTATTATATATTTATAATTT
Found at i:387258 original size:16 final size:15
Alignment explanation
Indices: 387232--387261 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
387222 CCTCGTATCA
387232 TTTTTATTTTATTAT
1 TTTTTATTTTATTAT
387247 TTTTTATATTTATTA
1 TTTTTAT-TTTATTA
387262 AATATTATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (15 bp):
TTTTTATTTTATTAT
Found at i:387274 original size:2 final size:2
Alignment explanation
Indices: 387263--387300 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
387253 TATTTATTAA
387263 AT AT -T AT AT AT 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 AT AT AT AT AT AT A
387301 CACACACACA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:388742 original size:16 final size:16
Alignment explanation
Indices: 388714--388766 Score: 63
Period size: 16 Copynumber: 3.3 Consensus size: 16
388704 TAATTTAAGT
388714 TTTATAATT-TTTTAAA
1 TTTA-AATTATTTTAAA
**
388730 TTTAAATTATTTTTGA
1 TTTAAATTATTTTAAA
*
388746 TTTAAATTATTTTAAT
1 TTTAAATTATTTTAAA
388762 TTTAA
1 TTTAA
388767 GTCGAAAAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
15 4 0.13
16 27 0.87
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (16 bp):
TTTAAATTATTTTAAA
Found at i:389002 original size:16 final size:16
Alignment explanation
Indices: 388966--389010 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
388956 TGTTTAAGTT
*
388966 ATTTCAAATTTGAATA
1 ATTTTAAATTTGAATA
*
388982 ATTTTAAATTTGAATC
1 ATTTTAAATTTGAATA
*
388998 ATTTTAGATTTGA
1 ATTTTAAATTTGA
389011 TTTTTTATCG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.38, C:0.04, G:0.09, T:0.49
Consensus pattern (16 bp):
ATTTTAAATTTGAATA
Found at i:391775 original size:18 final size:16
Alignment explanation
Indices: 391742--391810 Score: 58
Period size: 16 Copynumber: 4.6 Consensus size: 16
391732 ATCTAAATAT
391742 TAAAAAATATAATAAA
1 TAAAAAATATAATAAA
*
391758 TAAAAAAT-TAAT-AT
1 TAAAAAATATAATAAA
*
391772 TAAAATA-AT-ATAAA
1 TAAAAAATATAATAAA
* *
391786 TATAAAAT-TATTAAGA
1 TAAAAAATATAATAA-A
391802 TAAAAAATA
1 TAAAAAATA
391811 AAAAAAAATC
Statistics
Matches: 40, Mismatches: 7, Indels: 11
0.69 0.12 0.19
Matches are distributed among these distances:
13 2 0.05
14 15 0.38
15 7 0.17
16 16 0.40
ACGTcount: A:0.68, C:0.00, G:0.01, T:0.30
Consensus pattern (16 bp):
TAAAAAATATAATAAA
Found at i:391784 original size:28 final size:30
Alignment explanation
Indices: 391737--391810 Score: 89
Period size: 30 Copynumber: 2.5 Consensus size: 30
391727 TACGTATCTA
391737 AATATTAAAAAATATAATAAATAAAAAATT
1 AATATTAAAAAATATAATAAATAAAAAATT
* *
391767 AATATTAAAATAATATAA-ATATAAAATTATT
1 AATATTAAAA-AATATAATAAATAAAA-AATT
*
391798 AAGA-TAAAAAATA
1 AATATTAAAAAATA
391811 AAAAAAAATC
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
29 4 0.10
30 22 0.56
31 13 0.33
ACGTcount: A:0.68, C:0.00, G:0.01, T:0.31
Consensus pattern (30 bp):
AATATTAAAAAATATAATAAATAAAAAATT
Found at i:392362 original size:21 final size:22
Alignment explanation
Indices: 392338--392382 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
392328 GGAACATAAT
* *
392338 ATTTAATTATATTTTTA-TTAA
1 ATTTAATTAAATTTTAATTTAA
392359 ATTTAATTAAATTTTAATTTAA
1 ATTTAATTAAATTTTAATTTAA
392381 AT
1 AT
392383 AAAAATTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 15 0.71
22 6 0.29
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
ATTTAATTAAATTTTAATTTAA
Found at i:392374 original size:11 final size:11
Alignment explanation
Indices: 392339--392382 Score: 54
Period size: 11 Copynumber: 4.0 Consensus size: 11
392329 GAACATAATA
*
392339 TTTAATTATAT
1 TTTAATTAAAT
*
392350 TTTTATTAAA-
1 TTTAATTAAAT
392360 TTTAATTAAAT
1 TTTAATTAAAT
392371 TTTAATTTAAAT
1 TTTAA-TTAAAT
392383 AAAAATTAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
10 9 0.32
11 13 0.46
12 6 0.21
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (11 bp):
TTTAATTAAAT
Found at i:392471 original size:22 final size:22
Alignment explanation
Indices: 392445--392503 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 22
392435 ATTAAATTAA
*
392445 ATTTTATTTTTTAATTATT-TTT
1 ATTTTATTTTTTAA-AATTATTT
** *
392467 ATTTTATAATATAAAATTATTT
1 ATTTTATTTTTTAAAATTATTT
392489 ATTTTATTTTTTAAA
1 ATTTTATTTTTTAAA
392504 TAGTAAAAAA
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
21 3 0.10
22 26 0.90
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (22 bp):
ATTTTATTTTTTAAAATTATTT
Found at i:392516 original size:28 final size:27
Alignment explanation
Indices: 392463--392517 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
392453 TTTTAATTAT
*
392463 TTTTATTTTATAATATAAAATTATTTA
1 TTTTATTTTATAATATAAAATAATTTA
*
392490 TTTTATTTTTTAAATAGTAAAA-AATTTA
1 TTTTATTTTAT-AATA-TAAAATAATTTA
392518 AAAAAATAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 10 0.42
28 9 0.38
29 5 0.21
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (27 bp):
TTTTATTTTATAATATAAAATAATTTA
Found at i:392956 original size:19 final size:20
Alignment explanation
Indices: 392934--392982 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
392924 AAATGATATG
392934 AAATAATATA-AAAAAAATA
1 AAATAATATATAAAAAAATA
* *
392953 AAATATTATATAAAAATATA
1 AAATAATATATAAAAAAATA
*
392973 ACATAA-ATAT
1 AAATAATATAT
392983 TAATAGATCA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
19 13 0.52
20 12 0.48
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (20 bp):
AAATAATATATAAAAAAATA
Found at i:393062 original size:27 final size:27
Alignment explanation
Indices: 393032--393088 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
393022 AATAAATTAT
393032 TAATATTATAAA-AT-TTATATTAATATA
1 TAATATTATAAATATATT-TA-TAATATA
*
393059 TAATATTTTAAATATATTTATAATATA
1 TAATATTATAAATATATTTATAATATA
393086 TAA
1 TAA
393089 AATATACATT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
27 21 0.78
28 4 0.15
29 2 0.07
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (27 bp):
TAATATTATAAATATATTTATAATATA
Found at i:393068 original size:20 final size:20
Alignment explanation
Indices: 393029--393066 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
393019 ATAAATAAAT
393029 TATTAATATTATAAAATTTA
1 TATTAATATTATAAAATTTA
*
393049 TATTAATA-TATAATATTT
1 TATTAATATTATAAAATTT
393067 TAAATATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
TATTAATATTATAAAATTTA
Found at i:393080 original size:20 final size:20
Alignment explanation
Indices: 393057--393094 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
393047 TATATTAATA
* *
393057 TATAATATTTTAAATATATT
1 TATAATATATAAAATATATT
393077 TATAATATATAAAATATA
1 TATAATATATAAAATATA
393095 CATTATTGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
TATAATATATAAAATATATT
Found at i:393564 original size:2 final size:2
Alignment explanation
Indices: 393557--393588 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
393547 TATGGATAGA
393557 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
393589 AGAAAAACAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:396549 original size:2 final size:2
Alignment explanation
Indices: 396537--396567 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
396527 GCAACACATG
*
396537 TA TA TA AA 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
396568 TGAGATTTGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:397455 original size:37 final size:37
Alignment explanation
Indices: 397385--397460 Score: 109
Period size: 37 Copynumber: 2.1 Consensus size: 37
397375 AATATAGGAG
* **
397385 TTGATCTTAAACTTGCAACTTAATGTAATGTAAAGTT
1 TTGATCCTAAACTTGCAACTTAACATAATGTAAAGTT
397422 TTGATCCTAAACTTGCAACTTAACATACA-GTAAAGTT
1 TTGATCCTAAACTTGCAACTTAACATA-ATGTAAAGTT
397459 TT
1 TT
397461 AATTTGCAAC
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
37 34 0.97
38 1 0.03
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.38
Consensus pattern (37 bp):
TTGATCCTAAACTTGCAACTTAACATAATGTAAAGTT
Found at i:397524 original size:30 final size:30
Alignment explanation
Indices: 397436--397526 Score: 112
Period size: 31 Copynumber: 3.0 Consensus size: 30
397426 TCCTAAACTT
* * *
397436 GCAACTTAACATACA-GTAAAGTTTTAATTT
1 GCAACTTAATATA-ATGTAAAGTTTTGATTC
*
397466 GCAACTTAATATAGTGTAAAAGTTTTGATTC
1 GCAACTTAATATAATGT-AAAGTTTTGATTC
*
397497 GCAACTTAATATAATGTAAAGTCTTGATTC
1 GCAACTTAATATAATGTAAAGTTTTGATTC
397527 TAAACTTTTT
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
30 26 0.49
31 27 0.51
ACGTcount: A:0.37, C:0.12, G:0.13, T:0.37
Consensus pattern (30 bp):
GCAACTTAATATAATGTAAAGTTTTGATTC
Found at i:397533 original size:30 final size:31
Alignment explanation
Indices: 397468--397533 Score: 89
Period size: 30 Copynumber: 2.2 Consensus size: 31
397458 TTTAATTTGC
* * *
397468 AACTTAATATAGTGTAAAAGTTTTGATTCGC
1 AACTTAATATAATGTAAAAGTCTTGATTCGA
*
397499 AACTTAATATAATGT-AAAGTCTTGATTCTA
1 AACTTAATATAATGTAAAAGTCTTGATTCGA
397529 AACTT
1 AACTT
397534 TTTAATTATT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
30 17 0.55
31 14 0.45
ACGTcount: A:0.38, C:0.11, G:0.12, T:0.39
Consensus pattern (31 bp):
AACTTAATATAATGTAAAAGTCTTGATTCGA
Found at i:402077 original size:21 final size:21
Alignment explanation
Indices: 402048--402091 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
402038 CTGTTGCATT
*
402048 TGTTCCTGAAT-CTGCTCCATC
1 TGTTCCTG-ATGCTGCTACATC
*
402069 TGTTGCTGATGCTGCTACATC
1 TGTTCCTGATGCTGCTACATC
402090 TG
1 TG
402092 CTCCGTCTGC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 2 0.10
21 18 0.90
ACGTcount: A:0.14, C:0.27, G:0.20, T:0.39
Consensus pattern (21 bp):
TGTTCCTGATGCTGCTACATC
Found at i:403703 original size:42 final size:44
Alignment explanation
Indices: 403651--403746 Score: 146
Period size: 44 Copynumber: 2.2 Consensus size: 44
403641 GATTTATTAA
403651 AACAATTGTTCAATGGCA-TCAAAA-TTTTCAAGTTT-GAATTCTT
1 AACAATTGTTCAATGGCATTCAAAAGTTTTCAAGTTTAG-A-TCTT
403694 AAC-ATTGTTCAATGGCATTCAAAAGTTTTCAAGTTTAGATCTT
1 AACAATTGTTCAATGGCATTCAAAAGTTTTCAAGTTTAGATCTT
403737 AACAATTGTT
1 AACAATTGTT
403747 TTTCTTTTAA
Statistics
Matches: 49, Mismatches: 0, Indels: 7
0.88 0.00 0.12
Matches are distributed among these distances:
42 14 0.29
43 16 0.33
44 18 0.37
45 1 0.02
ACGTcount: A:0.34, C:0.14, G:0.12, T:0.40
Consensus pattern (44 bp):
AACAATTGTTCAATGGCATTCAAAAGTTTTCAAGTTTAGATCTT
Found at i:404251 original size:9 final size:11
Alignment explanation
Indices: 404223--404289 Score: 65
Period size: 11 Copynumber: 6.5 Consensus size: 11
404213 TTAATAGTAT
404223 ATATATTTATA
1 ATATATTTATA
404234 ATATATTTATA
1 ATATATTTATA
404245 A-AT-TTTAT-
1 ATATATTTATA
404253 -TATA-TTATA
1 ATATATTTATA
*
404262 ATTATATTTAAA
1 A-TATATTTATA
*
404274 ATAT-TTTATT
1 ATATATTTATA
404284 ATATAT
1 ATATAT
404290 AAATTTTAAT
Statistics
Matches: 46, Mismatches: 3, Indels: 14
0.73 0.05 0.22
Matches are distributed among these distances:
8 6 0.13
9 5 0.11
10 10 0.22
11 20 0.43
12 5 0.11
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (11 bp):
ATATATTTATA
Found at i:404257 original size:29 final size:31
Alignment explanation
Indices: 404224--404287 Score: 98
Period size: 29 Copynumber: 2.2 Consensus size: 31
404214 TAATAGTATA
*
404224 TATATTTATAA-TATATTTATAA-ATTTTAT
1 TATATTTATAATTATATTTAAAATATTTTAT
404253 TATA-TTATAATTATATTTAAAATATTTTAT
1 TATATTTATAATTATATTTAAAATATTTTAT
404283 TATAT
1 TATAT
404288 ATAAATTTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
28 6 0.19
29 14 0.45
30 11 0.35
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (31 bp):
TATATTTATAATTATATTTAAAATATTTTAT
Found at i:404290 original size:29 final size:28
Alignment explanation
Indices: 404224--404304 Score: 96
Period size: 29 Copynumber: 2.9 Consensus size: 28
404214 TAATAGTATA
*
404224 TATATTTATAATATATTTATAAATTTTAT
1 TATA-TTATAATATATTTAAAAATTTTAT
404253 TATATTATAATTATATTTAAAATATTTTAT
1 TATATTATAA-TATATTTAAAA-ATTTTAT
404283 TATA-TATAA-AT-TTTAATAAATT
1 TATATTATAATATATTTAA-AAATT
404305 AATAATTCGT
Statistics
Matches: 48, Mismatches: 1, Indels: 9
0.83 0.02 0.16
Matches are distributed among these distances:
26 8 0.17
27 4 0.08
28 6 0.12
29 19 0.40
30 11 0.23
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (28 bp):
TATATTATAATATATTTAAAAATTTTAT
Found at i:406405 original size:16 final size:16
Alignment explanation
Indices: 406384--406417 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
406374 ATTGTGTAAG
*
406384 ACTAATTTAGTTTTAC
1 ACTAATTTAATTTTAC
406400 ACTAATTTAATTTTAC
1 ACTAATTTAATTTTAC
406416 AC
1 AC
406418 CCACTTAAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.35, C:0.15, G:0.03, T:0.47
Consensus pattern (16 bp):
ACTAATTTAATTTTAC
Found at i:410158 original size:101 final size:102
Alignment explanation
Indices: 409795--410211 Score: 536
Period size: 102 Copynumber: 4.1 Consensus size: 102
409785 GCATTAGATA
* * * * *
409795 AATAAAATTAGAATAGGGAGGGAATAACCAAGTCCATTGCTCCTAATTAATTGTAGGTATTAAAT
1 AATAAAATTAGAATAGGGATGAAATAACCAAGTCCATTACTCCAAATTAATTGTGGGTATTAAAT
* * *
409860 TAATGAAATTAGAAAAAAAATATTTGAGTTTTAAATT
66 TAATAAAATTAGAAAAAAAGTATTTGAGTATTAAATT
* * * * * *
409897 AACAATATTGGAATAGGGATGGAATAACCAAGTCCATTACTCCAAATTAATT-TCGGGAATCAAA
1 AATAAAATTAGAATAGGGATGAAATAACCAAGTCCATTACTCCAAATTAATTGT-GGGTATTAAA
*
409961 TTAATAAAATTAAAAAAAAAAGTATTTGAGTATTAAATT
65 TTAATAAAATT-AGAAAAAAAGTATTTGAGTATTAAATT
* * * * *
410000 AAGAGAATTAGAATAGGG-T-AGAATAACTAGGTCCATGACTCCAAATTAATTGTGGGTATTAAA
1 AATAAAATTAGAATAGGGATGA-AATAACCAAGTCCATTACTCCAAATTAATTGTGGGTATTAAA
*
410063 TTAATAAAATTAGAAAAAAACTATTTGAGTATTAAATT
65 TTAATAAAATTAGAAAAAAAGTATTTGAGTATTAAATT
* *
410101 AATAAAATTAGAATAGGGATGAAAAAACCAGGTCCATTACTCCAAATTAATTG-GGGTATTAAAT
1 AATAAAATTAGAATAGGGATGAAATAACCAAGTCCATTACTCCAAATTAATTGTGGGTATTAAAT
** * *
410165 TAATAAAATTTTAAAAAAAGTAATTGAGTATTAAAGT
66 TAATAAAATTAGAAAAAAAGTATTTGAGTATTAAATT
410202 AATAAAATTA
1 AATAAAATTA
410212 ATTGTGGGGA
Statistics
Matches: 274, Mismatches: 35, Indels: 13
0.85 0.11 0.04
Matches are distributed among these distances:
101 95 0.35
102 139 0.51
103 40 0.15
ACGTcount: A:0.47, C:0.07, G:0.15, T:0.30
Consensus pattern (102 bp):
AATAAAATTAGAATAGGGATGAAATAACCAAGTCCATTACTCCAAATTAATTGTGGGTATTAAAT
TAATAAAATTAGAAAAAAAGTATTTGAGTATTAAATT
Found at i:410347 original size:5 final size:5
Alignment explanation
Indices: 410339--410370 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
410329 ATTATTTTAA
410339 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AA
410371 TTATAATAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:410846 original size:14 final size:14
Alignment explanation
Indices: 410815--410930 Score: 56
Period size: 14 Copynumber: 8.4 Consensus size: 14
410805 AATCTCTAAC
410815 ATAATTATATAAAT
1 ATAATTATATAAAT
*
410829 ATAATATATTTAAA-
1 ATAAT-TATATAAAT
410843 ATAA-T-TA-AAAT
1 ATAATTATATAAAT
410854 ATAAATTAATATAAAT
1 AT-AATT-ATATAAAT
*
410870 A-AATT-TTTAAA-
1 ATAATTATATAAAT
410881 AT--TTATAT-AAT
1 ATAATTATATAAAT
410892 ATAACTTAT-TAATAT
1 ATAA-TTATATAA-AT
410907 ATTAAAATTTATATAAAT
1 A-T--AA-TTATATAAAT
410925 ATAATT
1 ATAATT
410931 TTTTTTTTCT
Statistics
Matches: 78, Mismatches: 5, Indels: 38
0.64 0.04 0.31
Matches are distributed among these distances:
10 7 0.09
11 8 0.10
12 8 0.10
13 2 0.03
14 20 0.26
15 14 0.18
16 6 0.08
17 1 0.01
18 9 0.12
19 3 0.04
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (14 bp):
ATAATTATATAAAT
Found at i:410903 original size:24 final size:23
Alignment explanation
Indices: 410856--410903 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
410846 ATTAAAATAT
*
410856 AAATTAATATAAATAAATTTTTA
1 AAATTAATATAAATAAATTATTA
* *
410879 AAATTTATATAATATAACTTATTA
1 AAATTAATATAA-ATAAATTATTA
410903 A
1 A
410904 TATATTAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 11 0.52
24 10 0.48
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (23 bp):
AAATTAATATAAATAAATTATTA
Found at i:411121 original size:46 final size:47
Alignment explanation
Indices: 411038--411127 Score: 123
Period size: 48 Copynumber: 1.9 Consensus size: 47
411028 CCCGATTGAT
* *
411038 TTTTTATATAATTTTAATTATATTAAATAATAATTATTTATTTAAATA
1 TTTTTATATAATATAAATTATATTAAATAATAATTATTT-TTTAAATA
411086 TTTTTA-ATAATATAAATATATATT-AA-AATAATTATTTTTTAA
1 TTTTTATATAATATAAAT-TATATTAAATAATAATTATTTTTTAA
411128 TTACAATTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
45 5 0.13
46 11 0.28
47 11 0.28
48 12 0.31
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (47 bp):
TTTTTATATAATATAAATTATATTAAATAATAATTATTTTTTAAATA
Found at i:411442 original size:26 final size:26
Alignment explanation
Indices: 411379--411448 Score: 65
Period size: 26 Copynumber: 2.7 Consensus size: 26
411369 TATTTTTTAA
411379 ATATATATTT-AAAATTAAAATATTTT
1 ATAT-TATTTAAAAATTAAAATATTTT
**
411405 ATATTAAATAAATAATT-AAATATTTT
1 ATATTATTTAAA-AATTAAAATATTTT
*
411431 A-ATTTATTTAAAATTTAA
1 ATA-TTATTTAAAAATTAA
411449 CATACATAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 8
0.73 0.10 0.17
Matches are distributed among these distances:
25 7 0.20
26 24 0.69
27 4 0.11
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (26 bp):
ATATTATTTAAAAATTAAAATATTTT
Found at i:411471 original size:29 final size:31
Alignment explanation
Indices: 411439--411510 Score: 89
Period size: 29 Copynumber: 2.5 Consensus size: 31
411429 TTAATTTATT
* * *
411439 TAAAATTTAACATAC-ATAATT-TATTTTAA
1 TAAAATATAAAATACAATAATTAAATTTTAA
411468 TAAAATATAAAATACAATAATTAAATTTTAA
1 TAAAATATAAAATACAATAATTAAATTTTAA
411499 T-AAATA-AAAATA
1 TAAAATATAAAATA
411511 TATAAAAATT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
29 19 0.50
30 11 0.29
31 8 0.21
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (31 bp):
TAAAATATAAAATACAATAATTAAATTTTAA
Found at i:417375 original size:13 final size:12
Alignment explanation
Indices: 417359--417396 Score: 53
Period size: 13 Copynumber: 3.2 Consensus size: 12
417349 TTGAATTAGT
417359 TTTATATATTATA
1 TTTATATATT-TA
417372 TTTATATATTTA
1 TTTATATATTTA
417384 TTTA-A-ATTTA
1 TTTATATATTTA
417394 TTT
1 TTT
417397 GATTTAAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 8 0.32
11 1 0.04
12 6 0.24
13 10 0.40
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (12 bp):
TTTATATATTTA
Found at i:418004 original size:6 final size:6
Alignment explanation
Indices: 417995--418024 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
417985 AAATGAAAAA
*
417995 TGATTT TGATTT TGATTT TGATTT TAATTT
1 TGATTT TGATTT TGATTT TGATTT TGATTT
418025 GTTGCCTATA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.20, C:0.00, G:0.13, T:0.67
Consensus pattern (6 bp):
TGATTT
Found at i:418619 original size:25 final size:25
Alignment explanation
Indices: 418591--418643 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
418581 ATTTTTTTAA
*
418591 TTTCCTCAACCTTT-TTTTCTTTTTC
1 TTTCCTCAA-CTTTCTTTTCCTTTTC
**
418616 TTTCCTTTACTTTCTTTTCCTTTTC
1 TTTCCTCAACTTTCTTTTCCTTTTC
418641 TTT
1 TTT
418644 ATAAAAACTC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 4 0.17
25 20 0.83
ACGTcount: A:0.06, C:0.26, G:0.00, T:0.68
Consensus pattern (25 bp):
TTTCCTCAACTTTCTTTTCCTTTTC
Found at i:418631 original size:20 final size:20
Alignment explanation
Indices: 418606--418644 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
418596 TCAACCTTTT
*
418606 TTTCTTTTTCTTTCCTTTAC
1 TTTCTTTTCCTTTCCTTTAC
*
418626 TTTCTTTTCCTTTTCTTTA
1 TTTCTTTTCCTTTCCTTTA
418645 TAAAAACTCT
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:0.05, C:0.23, G:0.00, T:0.72
Consensus pattern (20 bp):
TTTCTTTTCCTTTCCTTTAC
Found at i:419019 original size:111 final size:111
Alignment explanation
Indices: 418819--419038 Score: 318
Period size: 111 Copynumber: 2.0 Consensus size: 111
418809 CGAATTTAGA
* * *
418819 TTAATCGAATTTAATACAAATTAATTAATTTTCGATCAATTAAGTTTAACACACGGATTTATCTG
1 TTAATCGAATTTAATACAAATTAATTAACTTTCGATCAATTAAGTTTAACACACAGATTTATCTC
* * * *
418884 TTATGATCATTTTGAGCTTGGATCATTTTGAGATAATTGTTTAAAG
66 TTAAGATCATTTTGAGCTTAGATCATTTTGAAATAATTATTTAAAG
* *
418930 TTAATCGAATTTAATACAAATTAATTAGCTTTCGATCAATTAAGTTT-ACTACACAGATTTATTT
1 TTAATCGAATTTAATACAAATTAATTAACTTTCGATCAATTAAGTTTAAC-ACACAGATTTATCT
*
418994 ACTTAAGAT-ATTTTGAGTTTAGATCATTTTGAAATAATTATTTAA
65 -CTTAAGATCATTTTGAGCTTAGATCATTTTGAAATAATTATTTAA
419039 GTCAAATCAA
Statistics
Matches: 97, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
110 2 0.02
111 89 0.92
112 6 0.06
ACGTcount: A:0.36, C:0.10, G:0.11, T:0.43
Consensus pattern (111 bp):
TTAATCGAATTTAATACAAATTAATTAACTTTCGATCAATTAAGTTTAACACACAGATTTATCTC
TTAAGATCATTTTGAGCTTAGATCATTTTGAAATAATTATTTAAAG
Found at i:419083 original size:16 final size:16
Alignment explanation
Indices: 419047--419089 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
419037 AAGTCAAATC
* *
419047 AAATTCGAATTATTTT
1 AAATTCAAATTATTAT
419063 AAATTCAAATTATTAT
1 AAATTCAAATTATTAT
* *
419079 GAATTTAAATT
1 AAATTCAAATT
419090 TTTTTTATTC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.47
Consensus pattern (16 bp):
AAATTCAAATTATTAT
Found at i:419309 original size:24 final size:25
Alignment explanation
Indices: 419282--419335 Score: 78
Period size: 22 Copynumber: 2.3 Consensus size: 25
419272 TAAAAATAAA
*
419282 TAAAAATAATCTTTTATTTTTAT-T
1 TAAAAATAAGCTTTTATTTTTATAT
419306 T-AAAA-AAGCTTTTATTTTTATAT
1 TAAAAATAAGCTTTTATTTTTATAT
419329 TAAAAAT
1 TAAAAAT
419336 TATTTTATCA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
22 15 0.58
23 6 0.23
24 5 0.19
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.52
Consensus pattern (25 bp):
TAAAAATAAGCTTTTATTTTTATAT
Found at i:419319 original size:22 final size:23
Alignment explanation
Indices: 419292--419334 Score: 79
Period size: 22 Copynumber: 1.9 Consensus size: 23
419282 TAAAAATAAT
419292 CTTTTATTTTTAT-TTAAAAAAG
1 CTTTTATTTTTATATTAAAAAAG
419314 CTTTTATTTTTATATTAAAAA
1 CTTTTATTTTTATATTAAAAA
419335 TTATTTTATC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.37, C:0.05, G:0.02, T:0.56
Consensus pattern (23 bp):
CTTTTATTTTTATATTAAAAAAG
Found at i:419341 original size:23 final size:22
Alignment explanation
Indices: 419293--419343 Score: 66
Period size: 23 Copynumber: 2.3 Consensus size: 22
419283 AAAAATAATC
*
419293 TTTTATTTTTATTTAAAAAAGC
1 TTTTATTTTTATTTAAAAAAGA
**
419315 TTTTATTTTTATATTAAAAATTA
1 TTTTATTTTTAT-TTAAAAAAGA
419338 TTTTAT
1 TTTTAT
419344 CAAAAATATT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
22 12 0.48
23 13 0.52
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (22 bp):
TTTTATTTTTATTTAAAAAAGA
Found at i:421646 original size:39 final size:39
Alignment explanation
Indices: 421597--421677 Score: 153
Period size: 39 Copynumber: 2.1 Consensus size: 39
421587 ATGTCCAGAG
*
421597 CAACATAATGCATTGACCAGGAATTATTAGTTATATATT
1 CAACACAATGCATTGACCAGGAATTATTAGTTATATATT
421636 CAACACAATGCATTGACCAGGAATTATTAGTTATATATT
1 CAACACAATGCATTGACCAGGAATTATTAGTTATATATT
421675 CAA
1 CAA
421678 TATAGAAATT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (39 bp):
CAACACAATGCATTGACCAGGAATTATTAGTTATATATT
Found at i:423285 original size:11 final size:11
Alignment explanation
Indices: 423262--423291 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
423252 AATTATATCC
423262 AAACTTGATTGA
1 AAACTT-ATTGA
423274 AAACTTATTGA
1 AAACTTATTGA
423285 AAACTTA
1 AAACTTA
423292 CATTGAGAGC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 12 0.67
12 6 0.33
ACGTcount: A:0.47, C:0.10, G:0.10, T:0.33
Consensus pattern (11 bp):
AAACTTATTGA
Found at i:423714 original size:25 final size:25
Alignment explanation
Indices: 423680--423729 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
423670 CTTAGTCTGA
423680 CCGTCTGAGGTTAAAAAGCTTTAGG
1 CCGTCTGAGGTTAAAAAGCTTTAGG
423705 CCGTCTGAGGTTAAAAAGCTTTAGG
1 CCGTCTGAGGTTAAAAAGCTTTAGG
423730 TGAACCCTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.28, C:0.16, G:0.28, T:0.28
Consensus pattern (25 bp):
CCGTCTGAGGTTAAAAAGCTTTAGG
Found at i:423849 original size:2 final size:2
Alignment explanation
Indices: 423842--423892 Score: 95
Period size: 2 Copynumber: 26.0 Consensus size: 2
423832 TGTTTATGAG
423842 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
423884 CT CT -T CT CT
1 CT CT CT CT CT
423893 TTTCTAAAGG
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 47 0.98
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
CT
Found at i:427471 original size:23 final size:23
Alignment explanation
Indices: 427440--427506 Score: 64
Period size: 23 Copynumber: 2.9 Consensus size: 23
427430 TTACATTTTT
* *
427440 TATAATATTTAAATTTAAATTTG
1 TATATTATTTAAATTTAAATTTC
* * *
427463 TATATTATTTACA-TAAAATATC
1 TATATTATTTAAATTTAAATTTC
*
427485 TATTATCATTTAAATTTAAATT
1 TA-TATTATTTAAATTTAAATT
427507 AAATAACAAT
Statistics
Matches: 33, Mismatches: 9, Indels: 3
0.73 0.20 0.07
Matches are distributed among these distances:
22 8 0.24
23 20 0.61
24 5 0.15
ACGTcount: A:0.43, C:0.04, G:0.01, T:0.51
Consensus pattern (23 bp):
TATATTATTTAAATTTAAATTTC
Done.