Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001129.1 Hibiscus syriacus cultivar Beakdansim tig00002237_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: 21326069
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 24 of 89
Found at i:5142145 original size:149 final size:149
Alignment explanation
Indices: 5141895--5142209 Score: 578
Period size: 149 Copynumber: 2.1 Consensus size: 149
5141885 TATAATTGCA
5141895 CCGAAGTG-CCGCGTAGAATTGCACCGTAGTGCCATATAACAATGTCCATAAGGACCACATATTA
1 CCGAAG-GACCGCGTAGAATTGCACCGTAGTGCCATATAACAATGTCCATAAGGACCACATATTA
5141959 TTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTT
65 TTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTT
* *
5142024 CCACAGAATATATATATATC
130 CCAAAGAATATACATATATC
*
5142044 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTAT
1 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAACAATGTCCATAAGGACCACATATTAT
5142109 TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
66 TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
*
5142174 CAAAGAATATACATATGTC
131 CAAAGAATATACATATATC
5142193 CCGAAGGACCGCGTAGA
1 CCGAAGGACCGCGTAGA
5142210 CCCTCGAATC
Statistics
Matches: 161, Mismatches: 4, Indels: 2
0.96 0.02 0.01
Matches are distributed among these distances:
148 1 0.01
149 160 0.99
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.27
Consensus pattern (149 bp):
CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAACAATGTCCATAAGGACCACATATTAT
TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
CAAAGAATATACATATATC
Found at i:5147790 original size:31 final size:31
Alignment explanation
Indices: 5147732--5147796 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 31
5147722 AAAAAAAATA
* *
5147732 TAAGATTTGATCACTTTTATTTTGTTTTAAT
1 TAAGATTTGATCACTTTCATTTCGTTTTAAT
* *
5147763 TAAGATTT-AGTCACTTTCGTTTCGTTTTAGT
1 TAAGATTTGA-TCACTTTCATTTCGTTTTAAT
5147794 TAA
1 TAA
5147797 CATGTGGTCA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 1 0.03
31 28 0.97
ACGTcount: A:0.25, C:0.09, G:0.12, T:0.54
Consensus pattern (31 bp):
TAAGATTTGATCACTTTCATTTCGTTTTAAT
Found at i:5147978 original size:31 final size:31
Alignment explanation
Indices: 5147943--5148013 Score: 106
Period size: 31 Copynumber: 2.3 Consensus size: 31
5147933 TGTACACTTT
*
5147943 TGGTCACTTACGTTATCATGTTATTAAGTTG
1 TGGTCACTTACATTATCATGTTATTAAGTTG
* * *
5147974 TGGTCACTTACATTATGATTTTATTAAGTTT
1 TGGTCACTTACATTATCATGTTATTAAGTTG
5148005 TGGTCACTT
1 TGGTCACTT
5148014 GGACGTTGAA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.23, C:0.13, G:0.17, T:0.48
Consensus pattern (31 bp):
TGGTCACTTACATTATCATGTTATTAAGTTG
Found at i:5149207 original size:15 final size:15
Alignment explanation
Indices: 5149181--5149218 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
5149171 TAAATTTTAA
5149181 TTAAATTATTTAATAT
1 TTAAATTATTTAAT-T
5149197 TTAAA-TATTTAATT
1 TTAAATTATTTAATT
*
5149211 TTATATTA
1 TTAAATTA
5149219 AAATTAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
14 5 0.25
15 10 0.50
16 5 0.25
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
TTAAATTATTTAATT
Found at i:5149241 original size:26 final size:25
Alignment explanation
Indices: 5149178--5149241 Score: 67
Period size: 26 Copynumber: 2.5 Consensus size: 25
5149168 TTCTAAATTT
* *
5149178 TAATTAAATTAT-TTAATATTTAAA
1 TAATTAAATTATATTAAAATTAAAA
* *
5149202 TATTTAATTTTATATTAAAATTAAAA
1 TAATTAA-ATTATATTAAAATTAAAA
5149228 TAATTAAATATATA
1 TAATTAAAT-TATA
5149242 CATGCAATTA
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
24 6 0.19
25 5 0.16
26 20 0.65
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (25 bp):
TAATTAAATTATATTAAAATTAAAA
Found at i:5150199 original size:183 final size:184
Alignment explanation
Indices: 5149927--5150272 Score: 622
Period size: 183 Copynumber: 1.9 Consensus size: 184
5149917 AACAGTTTCT
5149927 AATTAATTTAAATAATATATAATTATAAAATAAAAATTTTATATAAATTTTTTAATTAATTAATA
1 AATTAATTTAAATAATATATAATTATAAAATAAAAATTTTATATAAATTTTTTAATTAATTAATA
*
5149992 TTGATATAGGTTTAAAAATTATTGAATATT-AATTATTAATTGGGTTTTAAATGGTTTGGGCTGA
66 TTGATATAGGTTTAAAAATTATTGAATATTAAATTATTAATTGAGTTTTAAATGGTTTGGGCTGA
* *
5150056 GTTCTTATGTTATATATAATATATTTAATATTTTTTAATTCAAAAAAAAATTAC
131 GCTCATATGTTATATATAATATATTTAATATTTTTTAATTCAAAAAAAAATTAC
5150110 AATTAATTTAAATAATATATAATTATAAAATAAAAATTTTATATAAATTTTTTAATTAATTAATA
1 AATTAATTTAAATAATATATAATTATAAAATAAAAATTTTATATAAATTTTTTAATTAATTAATA
* * * *
5150175 TTGATTTAGGTTTAAAAGTTATTGAATCTTAAATTATTAATTGAGTTTTAAATGGTTTGGGTTGA
66 TTGATATAGGTTTAAAAATTATTGAATATTAAATTATTAATTGAGTTTTAAATGGTTTGGGCTGA
5150240 GCTCATATGTTATATATAATATATTTAATATTT
131 GCTCATATGTTATATATAATATATTTAATATTT
5150273 AAAATTTAAC
Statistics
Matches: 155, Mismatches: 7, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
183 92 0.59
184 63 0.41
ACGTcount: A:0.42, C:0.02, G:0.09, T:0.47
Consensus pattern (184 bp):
AATTAATTTAAATAATATATAATTATAAAATAAAAATTTTATATAAATTTTTTAATTAATTAATA
TTGATATAGGTTTAAAAATTATTGAATATTAAATTATTAATTGAGTTTTAAATGGTTTGGGCTGA
GCTCATATGTTATATATAATATATTTAATATTTTTTAATTCAAAAAAAAATTAC
Found at i:5154981 original size:143 final size:144
Alignment explanation
Indices: 5154683--5154981 Score: 373
Period size: 143 Copynumber: 2.1 Consensus size: 144
5154673 CCCAACAAAT
*
5154683 ATATCACTG-AAACGTTACTGAAGATGATCAATTGGGAACTGAAAAGTTTATGTCATTATGCATT
1 ATATCACTGAAAAGGTTACTGAAGATGATCAATTGGGAACTGAAAAGTTTATGTCATTATGCATT
* ** * * *
5154747 ATTTTGCATATGAGAAATGCATGTTTTCCTTATATGAAGTGATATATCAGAACTGAAAAGTTTTT
66 AGTTTGCATATGAGAAATGCACATTTTCCTGATATGAAGTGATATAGCAGAACTGAAAAGTTTTC
5154812 TGAAATAAGATAAC
131 TGAAATAAGATAAC
* *
5154826 ATATCACT-AAAAGGTTTA-TGAAGA-GAATTAATTGGGAACTGAAATA-TTTAT-TCCATTTTG
1 ATATCACTGAAAAGG-TTACTGAAGATG-ATCAATTGGGAACTGAAA-AGTTTATGT-CATTATG
*
5154886 CATTAGTTTGTC-TAT-AGGAAATGCACATTTTTCTGATATGAAGTGATAT-GCAGAACTGAAAA
62 CATTAGTTTG-CATATGA-GAAATGCACATTTTCCTGATATGAAGTGATATAGCAGAACTGAAAA
* *
5154948 GTTTTCTGATATAAGATGAC
125 GTTTTCTGAAATAAGATAAC
5154968 ATATCACTGAAAAG
1 ATATCACTGAAAAG
5154982 TTGCTGTCAC
Statistics
Matches: 136, Mismatches: 12, Indels: 16
0.83 0.07 0.10
Matches are distributed among these distances:
142 40 0.29
143 91 0.67
144 5 0.04
ACGTcount: A:0.37, C:0.10, G:0.18, T:0.35
Consensus pattern (144 bp):
ATATCACTGAAAAGGTTACTGAAGATGATCAATTGGGAACTGAAAAGTTTATGTCATTATGCATT
AGTTTGCATATGAGAAATGCACATTTTCCTGATATGAAGTGATATAGCAGAACTGAAAAGTTTTC
TGAAATAAGATAAC
Found at i:5159041 original size:10 final size:11
Alignment explanation
Indices: 5159002--5159074 Score: 55
Period size: 11 Copynumber: 6.8 Consensus size: 11
5158992 CACCCGCACC
*
5159002 AACATATAAATT
1 AACATATTAA-T
*
5159014 ACCATATTAAT
1 AACATATTAAT
5159025 AACATATT-AT
1 AACATATTAAT
*
5159035 AATATA-T-A-
1 AACATATTAAT
*
5159043 AACATATAAATT
1 AACATATTAA-T
*
5159055 ACCATATTAAT
1 AACATATTAAT
5159066 AACATATTA
1 AACATATTA
5159075 TAAAATATAT
Statistics
Matches: 48, Mismatches: 9, Indels: 9
0.73 0.14 0.14
Matches are distributed among these distances:
8 5 0.10
9 2 0.04
10 8 0.17
11 17 0.35
12 16 0.33
ACGTcount: A:0.53, C:0.11, G:0.00, T:0.36
Consensus pattern (11 bp):
AACATATTAAT
Found at i:5159048 original size:41 final size:41
Alignment explanation
Indices: 5159002--5159083 Score: 155
Period size: 41 Copynumber: 2.0 Consensus size: 41
5158992 CACCCGCACC
*
5159002 AACATATAAATTACCATATTAATAACATATTATAATATATA
1 AACATATAAATTACCATATTAATAACATATTATAAAATATA
5159043 AACATATAAATTACCATATTAATAACATATTATAAAATATA
1 AACATATAAATTACCATATTAATAACATATTATAAAATATA
5159084 TATAAACACA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.55, C:0.10, G:0.00, T:0.35
Consensus pattern (41 bp):
AACATATAAATTACCATATTAATAACATATTATAAAATATA
Found at i:5160069 original size:45 final size:45
Alignment explanation
Indices: 5160020--5160258 Score: 252
Period size: 45 Copynumber: 5.3 Consensus size: 45
5160010 TCATCTTTTT
*
5160020 GAGAAAGTCGAA-AAGGACAACACCAAAAGATTGACTCCTCTTCGC
1 GAGAAAGTC-AAGAAGGACAACACCAAAAGATTGACTCCTCTTCAC
* * *
5160065 GAGAAAGTCAAGAAGGACAATACTAAAATATTGACTCCTCTTCAC
1 GAGAAAGTCAAGAAGGACAACACCAAAAGATTGACTCCTCTTCAC
* * * *
5160110 GAGAAAGTCAAGGAA-GACACCACTAAAATATTGACTCATCTTCAC
1 GAGAAAGTCAA-GAAGGACAACACCAAAAGATTGACTCCTCTTCAC
* * * *
5160155 GAGAAAGTCAAGAAAGACATCACCGAAAGATT-ATCTCCTCTTCGC
1 GAGAAAGTCAAGAAGGACAACACCAAAAGATTGA-CTCCTCTTCAC
*** **
5160200 GAGAAAGTCAAGAAGGACGAA-ATTGAAAGATTGACTTTTCTTCAC
1 GAGAAAGTCAAGAAGGAC-AACACCAAAAGATTGACTCCTCTTCAC
*
5160245 GAGAAAATCAAGAA
1 GAGAAAGTCAAGAA
5160259 TAACATTGAA
Statistics
Matches: 167, Mismatches: 21, Indels: 12
0.83 0.10 0.06
Matches are distributed among these distances:
44 6 0.04
45 156 0.93
46 5 0.03
ACGTcount: A:0.42, C:0.20, G:0.18, T:0.20
Consensus pattern (45 bp):
GAGAAAGTCAAGAAGGACAACACCAAAAGATTGACTCCTCTTCAC
Found at i:5160203 original size:135 final size:135
Alignment explanation
Indices: 5160005--5160256 Score: 348
Period size: 135 Copynumber: 1.9 Consensus size: 135
5159995 TACTGAAAAG
*** *
5160005 TTGACTCATCTTTTTGAGAAAGTCGAAAAGGACAACACCAAAAGATTGACTCCTCTTCGCGAGAA
1 TTGACTCATCTTCACGAGAAAGTCGAAAAAGACAACACCAAAAGATTGACTCCTCTTCGCGAGAA
* *
5160070 AGTCAAGAAGGAC-AATACTAAAATATTGACTCCTCTTCACGAGAAAGTCAAGGAAGACACCACT
66 AGTCAAGAAGGACGAA-ACTAAAAGATTGACTCCTCTTCACGAGAAAATCAAGGAAGACACCACT
5160134 AAAATA
130 AAAATA
* *
5160140 TTGACTCATCTTCACGAGAAAGTC-AAGAAAGACATCACCGAAAGATT-ATCTCCTCTTCGCGAG
1 TTGACTCATCTTCACGAGAAAGTCGAA-AAAGACAACACCAAAAGATTGA-CTCCTCTTCGCGAG
* * **
5160203 AAAGTCAAGAAGGACGAAATTGAAAGATTGACTTTTCTTCACGAGAAAATCAAG
64 AAAGTCAAGAAGGACGAAACTAAAAGATTGACTCCTCTTCACGAGAAAATCAAG
5160257 AATAACATTG
Statistics
Matches: 102, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
134 3 0.03
135 97 0.95
136 2 0.02
ACGTcount: A:0.40, C:0.20, G:0.18, T:0.22
Consensus pattern (135 bp):
TTGACTCATCTTCACGAGAAAGTCGAAAAAGACAACACCAAAAGATTGACTCCTCTTCGCGAGAA
AGTCAAGAAGGACGAAACTAAAAGATTGACTCCTCTTCACGAGAAAATCAAGGAAGACACCACTA
AAATA
Found at i:5160322 original size:38 final size:37
Alignment explanation
Indices: 5160225--5160621 Score: 362
Period size: 38 Copynumber: 10.2 Consensus size: 37
5160215 GACGAAATTG
* * *
5160225 AAAGATTGACTTTTCTTCACGAGAAAATCAAGAATAAC
1 AAAGATTGAC-TCTCTTCACGAGGAAGTCAAGAATAAC
** *
5160263 ATTGAAAGATCAACTTCTCTTCACGAGGAAGTCAAGAATAAA
1 ----AAAGATTGAC-TCTCTTCACGAGGAAGTCAAGAATAAC
* * *
5160305 AAAGATTTACTCATCTTCACGAGGGAGTCAAGAATAAA
1 AAAGATTGACTC-TCTTCACGAGGAAGTCAAGAATAAC
* *
5160343 AAAGATTAACTTCTCTTCACGAGGAAGTCAATAATAAC
1 AAAGATTGAC-TCTCTTCACGAGGAAGTCAAGAATAAC
* * *
5160381 AAAGATTGACTCCTCTTCGCGAGGGAGTCAGGAATAAC
1 AAAGATTGACT-CTCTTCACGAGGAAGTCAAGAATAAC
* * *
5160419 AAATAATGACTTCTCTTCACGAGGAATTCAAGAATAAC
1 AAAGATTGAC-TCTCTTCACGAGGAAGTCAAGAATAAC
*
5160457 AAAGATTGATTGACTCCTCTTCACGAGGAAGTCAAGAATAAT
1 -AA-A--GATTGACT-CTCTTCACGAGGAAGTCAAGAATAAC
* * * *
5160499 GAAGATTGACCTCTCTTCACAAGGAAGTCGAGAATAAT
1 AAAGATTGA-CTCTCTTCACGAGGAAGTCAAGAATAAC
* * *
5160537 AGAGATTGAATTCTCTTCACGAGGAAGTCAATAATAAC
1 AAAGATTG-ACTCTCTTCACGAGGAAGTCAAGAATAAC
* * * * *
5160575 AAATATTAACTCTTCTTCACGAGGGAGTTAGGAATAAC
1 AAAGATTGACTC-TCTTCACGAGGAAGTCAAGAATAAC
5160613 AAAGATTGA
1 AAAGATTGA
5160622 ATTCTTGTAA
Statistics
Matches: 295, Mismatches: 48, Indels: 28
0.80 0.13 0.08
Matches are distributed among these distances:
37 6 0.02
38 216 0.73
39 8 0.03
40 2 0.01
41 2 0.01
42 61 0.21
ACGTcount: A:0.40, C:0.17, G:0.18, T:0.25
Consensus pattern (37 bp):
AAAGATTGACTCTCTTCACGAGGAAGTCAAGAATAAC
Found at i:5160370 original size:76 final size:76
Alignment explanation
Indices: 5160225--5160621 Score: 400
Period size: 76 Copynumber: 5.1 Consensus size: 76
5160215 GACGAAATTG
** * * *
5160225 AAAGATTGACTTTTCTTCACGAGAAAATCAAGAATAACATTGAAAGATCAACTTCTCTTCACGAG
1 AAAGATTGACTCCTCTTCACGAGGAAGTCAAGAATAAC----AAAGATTAACTTCTCTTCACGAG
5160290 GAAGTCAAGAATAAA
62 GAAGTCAAGAATAAA
* * * *
5160305 AAAGATTTACTCATCTTCACGAGGGAGTCAAGAATAAAAAAGATTAACTTCTCTTCACGAGGAAG
1 AAAGATTGACTCCTCTTCACGAGGAAGTCAAGAATAACAAAGATTAACTTCTCTTCACGAGGAAG
* *
5160370 TCAATAATAAC
66 TCAAGAATAAA
* * * * * * *
5160381 AAAGATTGACTCCTCTTCGCGAGGGAGTCAGGAATAACAAATAATGACTTCTCTTCACGAGGAAT
1 AAAGATTGACTCCTCTTCACGAGGAAGTCAAGAATAACAAAGATTAACTTCTCTTCACGAGGAAG
5160446 TCAAGAATAACA
66 TCAAGAATAA-A
** * * *
5160458 AAGATTGATTGACTCCTCTTCACGAGGAAGTCAAGAATAATGAAGATTGACCTCTCTTCACAAGG
1 AA-A--GATTGACTCCTCTTCACGAGGAAGTCAAGAATAACAAAGATTAACTTCTCTTCACGAGG
* *
5160523 AAGTCGAGAATAAT
63 AAGTCAAGAATAAA
* * * * * *
5160537 AGAGATTGAATTCTCTTCACGAGGAAGTCAATAATAACAAATATTAAC-TCTTCTTCACGAGGGA
1 AAAGATTGACTCCTCTTCACGAGGAAGTCAAGAATAACAAAGATTAACTTC-TCTTCACGAGGAA
* * *
5160601 GTTAGGAATAAC
65 GTCAAGAATAAA
5160613 AAAGATTGA
1 AAAGATTGA
5160622 ATTCTTGTAA
Statistics
Matches: 264, Mismatches: 48, Indels: 14
0.81 0.15 0.04
Matches are distributed among these distances:
75 2 0.01
76 165 0.62
77 2 0.01
78 2 0.01
79 1 0.00
80 92 0.35
ACGTcount: A:0.40, C:0.17, G:0.18, T:0.25
Consensus pattern (76 bp):
AAAGATTGACTCCTCTTCACGAGGAAGTCAAGAATAACAAAGATTAACTTCTCTTCACGAGGAAG
TCAAGAATAAA
Found at i:5160518 original size:194 final size:194
Alignment explanation
Indices: 5160231--5160615 Score: 531
Period size: 194 Copynumber: 2.0 Consensus size: 194
5160221 ATTGAAAGAT
* ** *
5160231 TGACTTTTCTTCACGAGAAAATCAAGAATAACATTGAAAGATCAACTTCTCTTCACGAGGAAGTC
1 TGACTTCTCTTCACGAGAAAATCAAGAATAACAAAGAAAGATCAACTCCTCTTCACGAGGAAGTC
* * *
5160296 AAGAATAAAAAAGATTTACTCATCTTCACGAGGGAGTCAAGAATAAAAAAGATT-AACTTCTCTT
66 AAGAATAAAAAAGATTGACTCATCTTCACAAGGAAGTCAAGAATAAAAAAGATTGAA-TTCTCTT
* *
5160360 CACGAGGAAGTCAATAATAACAAAGATTGACTCCTCTTCGCGAGGGAGTCAGGAATAACAAATAA
130 CACGAGGAAGTCAATAATAACAAAGATTAACTCCTCTTCACGAGGGAGTCAGGAATAACAAATAA
* * ** **
5160425 TGACTTCTCTTCACGAGGAATTCAAGAATAACAAAGATTGATTGACTCCTCTTCACGAGGAAGTC
1 TGACTTCTCTTCACGAGAAAATCAAGAATAACAAAGAAAGATCAACTCCTCTTCACGAGGAAGTC
** * * *
5160490 AAGAATAATGAAGATTGACCTC-TCTTCACAAGGAAGTCGAGAATAATAGAGATTGAATTCTCTT
66 AAGAATAAAAAAGATTGA-CTCATCTTCACAAGGAAGTCAAGAATAAAAAAGATTGAATTCTCTT
* * *
5160554 CACGAGGAAGTCAATAATAACAAATATTAACTCTTCTTCACGAGGGAGTTAGGAATAACAAA
130 CACGAGGAAGTCAATAATAACAAAGATTAACTCCTCTTCACGAGGGAGTCAGGAATAACAAA
5160616 GATTGAATTC
Statistics
Matches: 166, Mismatches: 23, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
194 161 0.97
195 5 0.03
ACGTcount: A:0.40, C:0.17, G:0.18, T:0.25
Consensus pattern (194 bp):
TGACTTCTCTTCACGAGAAAATCAAGAATAACAAAGAAAGATCAACTCCTCTTCACGAGGAAGTC
AAGAATAAAAAAGATTGACTCATCTTCACAAGGAAGTCAAGAATAAAAAAGATTGAATTCTCTTC
ACGAGGAAGTCAATAATAACAAAGATTAACTCCTCTTCACGAGGGAGTCAGGAATAACAAATAA
Found at i:5167545 original size:95 final size:96
Alignment explanation
Indices: 5167375--5167558 Score: 241
Period size: 95 Copynumber: 1.9 Consensus size: 96
5167365 GTTGAGGCAA
* * *
5167375 TATCGATACCATGGTAAGAGTATTGATACCAAACATACATCAAATCTAATTTTGGTATCGATACT
1 TATCGATACCATGGTAAGAGTATCGATACCAAACATACATCAAACCTAATTTTGGTATCGATACG
*
5167440 GTAAGGGGGTATCAGTACCTTAGTAAGGTAG
66 GTAAGGGGGTATCAGTACCATAGTAAGGTAG
* * * *
5167471 TATCGATACTATGGTAAGGGTATCGATACCATGA-A-ACATCGAACCTAATTTTGGTATCGATAT
1 TATCGATACCATGGTAAGAGTATCGATACCA-AACATACATCAAACCTAATTTTGGTATCGATA-
5167534 CAGGT-A-GGGGTATCAGTACCATAGT
64 C-GGTAAGGGGGTATCAGTACCATAGT
5167559 GTAGAAGTAT
Statistics
Matches: 77, Mismatches: 8, Indels: 7
0.84 0.09 0.08
Matches are distributed among these distances:
95 43 0.56
96 31 0.40
97 3 0.04
ACGTcount: A:0.33, C:0.15, G:0.22, T:0.30
Consensus pattern (96 bp):
TATCGATACCATGGTAAGAGTATCGATACCAAACATACATCAAACCTAATTTTGGTATCGATACG
GTAAGGGGGTATCAGTACCATAGTAAGGTAG
Found at i:5167589 original size:20 final size:20
Alignment explanation
Indices: 5167543--5167594 Score: 54
Period size: 20 Copynumber: 2.5 Consensus size: 20
5167533 TCAGGTAGGG
*
5167543 GTATCAGTACCATAGTGTAGAA
1 GTATCAGTA-C-TAGGGTAGAA
5167565 GTATCAGTACTAGGGTAGTAA
1 GTATCAGTACTAGGGTAG-AA
5167586 -TATCA-TACT
1 GTATCAGTACT
5167595 TCAGAACCAT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
19 4 0.14
20 12 0.43
21 3 0.11
22 9 0.32
ACGTcount: A:0.35, C:0.13, G:0.21, T:0.31
Consensus pattern (20 bp):
GTATCAGTACTAGGGTAGAA
Found at i:5168068 original size:45 final size:45
Alignment explanation
Indices: 5168005--5168498 Score: 688
Period size: 45 Copynumber: 11.0 Consensus size: 45
5167995 TGAAAATACT
* *
5168005 AATGCATATGGGTGCATTATCAATAGAAAAGTATACTACAGTTGA
1 AATGCATATGGGTGCATTATCAACAGAAAAGTATACTATAGTTGA
* * * *
5168050 AATGTATTTGGGTACATTATCAACAGAAAAGTATATTATAGTTGA
1 AATGCATATGGGTGCATTATCAACAGAAAAGTATACTATAGTTGA
* * * *
5168095 AATGTATATGGGTACAATATCAACATAAAAGTATACTATAGTTGA
1 AATGCATATGGGTGCATTATCAACAGAAAAGTATACTATAGTTGA
*
5168140 AATTCATATGGGTGCATTATCAACAGAAAAGTATACTATAGTTGA
1 AATGCATATGGGTGCATTATCAACAGAAAAGTATACTATAGTTGA
*
5168185 AATGCATATGGGTGCATTATCAACAGAAAAGTATACTATATTTGA
1 AATGCATATGGGTGCATTATCAACAGAAAAGTATACTATAGTTGA
*
5168230 AATGCATATGGGTGCATTATCAACATAAAAGTATACTATAGTTGA
1 AATGCATATGGGTGCATTATCAACAGAAAAGTATACTATAGTTGA
* *
5168275 AATGCATATGGGTGCATTATCAACAAAAAAGTATACTATATTTGA
1 AATGCATATGGGTGCATTATCAACAGAAAAGTATACTATAGTTGA
* *
5168320 AATGCATATGGGTGCATTATCAACATTAAAA-TATATTATAGTTGA
1 AATGCATATGGGTGCATTATCAACA-GAAAAGTATACTATAGTTGA
** *
5168365 AATGCATATGGGTGCATTATCAACCA-AAAAGTATGTTGTAGTTGA
1 AATGCATATGGGTGCATTATCAA-CAGAAAAGTATACTATAGTTGA
* * *
5168410 AATGTATATGGGTACATTATCAAGAGAAAAAGTATACTATAGTTGA
1 AATGCATATGGGTGCATTATCAACAG-AAAAGTATACTATAGTTGA
* * * *
5168456 AATAG-ATGTGGGTGTATTATCAACATAAAAGTATGCTATAGTT
1 AAT-GCATATGGGTGCATTATCAACAGAAAAGTATACTATAGTT
5168499 TAAAGAGCAT
Statistics
Matches: 405, Mismatches: 38, Indels: 12
0.89 0.08 0.03
Matches are distributed among these distances:
44 5 0.01
45 358 0.88
46 41 0.10
47 1 0.00
ACGTcount: A:0.40, C:0.10, G:0.18, T:0.32
Consensus pattern (45 bp):
AATGCATATGGGTGCATTATCAACAGAAAAGTATACTATAGTTGA
Found at i:5169030 original size:38 final size:38
Alignment explanation
Indices: 5168969--5169264 Score: 328
Period size: 38 Copynumber: 7.6 Consensus size: 38
5168959 GGTGTTACAA
5168969 TTCTCTTCACGAGGAAGTCAAGAATAACAAAGATTGAC
1 TTCTCTTCACGAGGAAGTCAAGAATAACAAAGATTGAC
* *
5169007 TTCTTTTCACGA-GAGAGTTAAGAATAACAAAGGTTGATTGAC
1 TTCTCTTCACGAGGA-AGTCAAGAATAACAAA----GATTGAC
* *
5169049 -TCATCTTTACGAGGAAGTCAGGAATAACAAAGATT-AC
1 TTC-TCTTCACGAGGAAGTCAAGAATAACAAAGATTGAC
* * * *
5169086 TTAACTTTTCTTCACCAGGGAGTCAAGAATAACGAAGATTAAC
1 TT--C---TCTTCACGAGGAAGTCAAGAATAACAAAGATTGAC
* * * *
5169129 CTCTCTTCATGAGGAAGTCAAGAATAACATAGATTGAA
1 TTCTCTTCACGAGGAAGTCAAGAATAACAAAGATTGAC
* *
5169167 TTCTCTTCACAAGGAAGTCAAGAATAACAAAGATTGAA
1 TTCTCTTCACGAGGAAGTCAAGAATAACAAAGATTGAC
*
5169205 TTCTCTTCACGAGAAAGTCAAGAATAACAAAGATTGAC
1 TTCTCTTCACGAGGAAGTCAAGAATAACAAAGATTGAC
*
5169243 TTCTCTTCACGAGAAAGTCAAG
1 TTCTCTTCACGAGGAAGTCAAG
5169265 TTGAAGCTTA
Statistics
Matches: 218, Mismatches: 27, Indels: 26
0.80 0.10 0.10
Matches are distributed among these distances:
37 4 0.02
38 150 0.69
40 1 0.00
41 3 0.01
42 55 0.25
43 5 0.02
ACGTcount: A:0.39, C:0.17, G:0.18, T:0.26
Consensus pattern (38 bp):
TTCTCTTCACGAGGAAGTCAAGAATAACAAAGATTGAC
Found at i:5171478 original size:2 final size:2
Alignment explanation
Indices: 5171471--5171542 Score: 144
Period size: 2 Copynumber: 36.0 Consensus size: 2
5171461 AAATTTATTG
5171471 TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA
5171513 TA 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 TA
5171543 ATCGCCTTTA
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 70 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5185909 original size:17 final size:17
Alignment explanation
Indices: 5185865--5185913 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
5185855 AAGTAATGAA
5185865 AATAAGAAAATATGAAAG
1 AATAAGAAAAT-TGAAAG
* *
5185883 AATACG-AAATTGAAAT
1 AATAAGAAAATTGAAAG
*
5185899 AGTAAGAAAATTGAA
1 AATAAGAAAATTGAA
5185914 GATAACATAC
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
16 9 0.35
17 12 0.46
18 5 0.19
ACGTcount: A:0.61, C:0.02, G:0.16, T:0.20
Consensus pattern (17 bp):
AATAAGAAAATTGAAAG
Found at i:5186069 original size:18 final size:18
Alignment explanation
Indices: 5186036--5186078 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
5186026 TACTTTGCAA
*
5186036 CTTTCTTTACTTTTTCTT
1 CTTTCTTTAATTTTTCTT
5186054 -TTTCTTTGAATTTTTCTT
1 CTTTCTTT-AATTTTTCTT
5186072 CTTTCTT
1 CTTTCTT
5186079 GTTGCTTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 7 0.32
18 9 0.41
19 6 0.27
ACGTcount: A:0.07, C:0.19, G:0.02, T:0.72
Consensus pattern (18 bp):
CTTTCTTTAATTTTTCTT
Found at i:5194341 original size:16 final size:16
Alignment explanation
Indices: 5194292--5194342 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
5194282 ATAAAATCGT
5194292 TTTATATT-TATATAAA
1 TTTATATTATATA-AAA
5194308 TTTA-A-TATATTAATAA
1 TTTATATTATA-TAA-AA
5194324 TTTATATTATATAAAA
1 TTTATATTATATAAAA
5194340 TTT
1 TTT
5194343 CGAATATTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 10
0.75 0.00 0.25
Matches are distributed among these distances:
14 1 0.03
15 4 0.13
16 17 0.57
17 4 0.13
18 4 0.13
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TTTATATTATATAAAA
Found at i:5198183 original size:2 final size:2
Alignment explanation
Indices: 5198176--5198211 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
5198166 GCATTCATTC
5198176 TA TA TA TA 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 TA TA TA TA
5198212 ACTCAAACAC
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):
TA
Found at i:5198487 original size:2 final size:2
Alignment explanation
Indices: 5198480--5198518 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
5198470 CCTAACTGTT
5198480 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5198519 GGCGACCTTG
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5206003 original size:6 final size:6
Alignment explanation
Indices: 5205983--5206016 Score: 52
Period size: 6 Copynumber: 5.7 Consensus size: 6
5205973 AATTTGGCCT
5205983 ATAAGAA AT-AAA ATAAAA ATAAAA ATAAAA ATAA
1 ATAA-AA ATAAAA ATAAAA ATAAAA ATAAAA ATAA
5206017 TAGTAATAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
5 4 0.15
6 20 0.77
7 2 0.08
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (6 bp):
ATAAAA
Found at i:5206535 original size:133 final size:134
Alignment explanation
Indices: 5206202--5206841 Score: 736
Period size: 133 Copynumber: 4.8 Consensus size: 134
5206192 ACTGTTGCTA
* * * * *
5206202 TAGGGTAGATCAGA-TCGAGAAACA-TTGATTCA-TTCCACTGTTCTTCAGGGAATATTGAATCG
1 TAGGGGAGATCAGACTCGAGAAATATTTGATCCACTT-CACTGCTCTTCAGGGAAGATTGAATCG
** * *
5206264 AAAATGATTTACTTCATTGCTCTTCAGGAAGACCAAATCTGAAAGAAGAAGCGTATGCTCCACTA
65 AACTTGATTTGCTTCACTGCTCTTCAGGAAGACCAAATCTGAAAGAAGAAGCGTATGCTCCACTA
5206329 CTCTT
130 CTCTT
* * * * *
5206334 TAGGGGAGATCACACTCGAGAAATATTTCATCCGCTTCACTGCTCTTTAGGGAAGATTGAATCTA
1 TAGGGGAGATCAGACTCGAGAAATATTTGATCCACTTCACTGCTCTTCAGGGAAGATTGAATCGA
* * * *
5206399 ACTTGATTTACTTCACTGATCTTCAGGAAGACCAAATCTGAAAGAAGAAGCGTTTACTCCA-TAC
66 ACTTGATTTGCTTCACTGCTCTTCAGGAAGACCAAATCTGAAAGAAGAAGCGTATGCTCCACTAC
5206463 TCTT
131 TCTT
* * * *
5206467 TAGGGGAGATCAGACTCGAGAAGTCTTTGATCTACTTTACTGCTCTTCAGGGAAGATTGAATCGA
1 TAGGGGAGATCAGACTCGAGAAATATTTGATCCACTTCACTGCTCTTCAGGGAAGATTGAATCGA
* ** *
5206532 ACTTAATTTGCTTTGCTGCTCTTCAGGAAGACCAAATATGAAAGAAGAAGCGTATGCTCCACTAC
66 ACTTGATTTGCTTCACTGCTCTTCAGGAAGACCAAATCTGAAAGAAGAAGCGTATGCTCCACTAC
5206597 TCTT
131 TCTT
* * * * * *
5206601 TAGGGGAGATCAGGCCCAATAAATCTTTGATCCACTTCACTTCTCTTCAGGGAAGATTGAATCGA
1 TAGGGGAGATCAGACTCGAGAAATATTTGATCCACTTCACTGCTCTTCAGGGAAGATTGAATCGA
* * * * ** * ***
5206666 ACTTGATTTGCTTC-GTGCTCTTCAGGAAGACGAAATATTAAAGAAGAAGAATCTGCTTTGCTAC
66 ACTTGATTTGCTTCACTGCTCTTCAGGAAGACCAAATCTGAAAGAAGAAGCGTATGCTCCACTAC
5206730 TCTT
131 TCTT
* * * ** * *
5206734 TAGGGGAGATCAAACTCGAGAAAAAATTGATCCACTTCACTAATCTTTAGGGAAGATTAAATCTG
1 TAGGGGAGATCAGACTCGAGAAATATTTGATCCACTTCACTGCTCTTCAGGGAAGATTGAATC-G
* * * *
5206799 AA-TCGATTTGTTTCACTGCTCTTTAGGAATACCAAATCT-AAAG
65 AACTTGATTTGCTTCACTGCTCTTCAGGAAGACCAAATCTGAAAG
5206842 GATTGACTGC
Statistics
Matches: 431, Mismatches: 71, Indels: 11
0.84 0.14 0.02
Matches are distributed among these distances:
132 12 0.03
133 235 0.55
134 182 0.42
135 2 0.00
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.30
Consensus pattern (134 bp):
TAGGGGAGATCAGACTCGAGAAATATTTGATCCACTTCACTGCTCTTCAGGGAAGATTGAATCGA
ACTTGATTTGCTTCACTGCTCTTCAGGAAGACCAAATCTGAAAGAAGAAGCGTATGCTCCACTAC
TCTT
Found at i:5206733 original size:267 final size:267
Alignment explanation
Indices: 5206238--5206755 Score: 707
Period size: 267 Copynumber: 1.9 Consensus size: 267
5206228 GATTCATTCC
* * * * *
5206238 ACTGTTCTTCAGGGAATATTGAATCGAAAATGATTTACTTCATTGCTCTTCAGGAAGACCAAATC
1 ACTGCTCTTCAGGGAAGATTGAATCGAAAATAATTTACTTCACTGCTCTTCAGGAAGACCAAATA
* * *
5206303 TGAAAGAAGAAGCGTATGCTCCACTACTCTTTAGGGGAGATCACACTCGAGAAATATTTCATCCG
66 TGAAAGAAGAAGCGTATGCTCCACTACTCTTTAGGGGAGATCACACCCAAGAAATATTTCATCCA
* *
5206368 CTTCACTGCTCTTTAGGGAAGATTGAATCTAACTTGATTTACTTCACTGATCTTCAGGAAGACCA
131 CTTCACTGCTCTTCAGGGAAGATTGAATCGAACTTGATTTACTTCACTGATCTTCAGGAAGACCA
* ** * *
5206433 AATCTGAAAGAAGAAGCGTTTACTCCATACTCTTTAGGGGAGATCAGACTCGAGAAGTCTTTGAT
196 AATATGAAAGAAGAAGAATCTACTCCATACTCTTTAGGGGAGATCAAACTCGAGAAGTCTTTGAT
5206498 CTACTTT
261 CTACTTT
** * **
5206505 ACTGCTCTTCAGGGAAGATTGAATCGAACTTAATTTGCTTTGCTGCTCTTCAGGAAGACCAAATA
1 ACTGCTCTTCAGGGAAGATTGAATCGAAAATAATTTACTTCACTGCTCTTCAGGAAGACCAAATA
** * * *
5206570 TGAAAGAAGAAGCGTATGCTCCACTACTCTTTAGGGGAGATCAGGCCCAATAAATCTTTGATCCA
66 TGAAAGAAGAAGCGTATGCTCCACTACTCTTTAGGGGAGATCACACCCAAGAAATATTTCATCCA
* * * * *
5206635 CTTCACTTCTCTTCAGGGAAGATTGAATCGAACTTGATTTGCTTC-GTGCTCTTCAGGAAGACGA
131 CTTCACTGCTCTTCAGGGAAGATTGAATCGAACTTGATTTACTTCACTGATCTTCAGGAAGACCA
* * *
5206699 AATATTAAAGAAGAAGAATCTGCTTTGC-TACTCTTTAGGGGAGATCAAACTCGAGAA
196 AATATGAAAGAAGAAGAATCTAC--TCCATACTCTTTAGGGGAGATCAAACTCGAGAA
5206756 AAAATTGATC
Statistics
Matches: 216, Mismatches: 33, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
266 33 0.15
267 181 0.84
268 2 0.01
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.30
Consensus pattern (267 bp):
ACTGCTCTTCAGGGAAGATTGAATCGAAAATAATTTACTTCACTGCTCTTCAGGAAGACCAAATA
TGAAAGAAGAAGCGTATGCTCCACTACTCTTTAGGGGAGATCACACCCAAGAAATATTTCATCCA
CTTCACTGCTCTTCAGGGAAGATTGAATCGAACTTGATTTACTTCACTGATCTTCAGGAAGACCA
AATATGAAAGAAGAAGAATCTACTCCATACTCTTTAGGGGAGATCAAACTCGAGAAGTCTTTGAT
CTACTTT
Found at i:5206788 original size:267 final size:267
Alignment explanation
Indices: 5206276--5206835 Score: 696
Period size: 267 Copynumber: 2.1 Consensus size: 267
5206266 AATGATTTAC
* *
5206276 TTCATTGCTCTTCAGGAAGACCAAATCTGAAAGAAGAAGCGTATGCTCCACTACTCTTTAGGGGA
1 TTCACTGCTCTTCAGGAAGACCAAATATGAAAGAAGAAGCGTATGCTCCACTACTCTTTAGGGGA
* * * * *
5206341 GATCACACTCGAGAAATATTTCATCCGCTTCACTGCTCTTTAGGGAAGATTGAATCTAACTTGAT
66 GATCACACCCAAGAAATATTTCATCCACTTCACTGCTCTTCAGGGAAGATTGAATCGAACTTGAT
* ** *
5206406 TTACTTCACTGATCTTCAGGAAGACCAAATCTGAAAGAAGAAGCGTTTACTCCATACTCTTTAGG
131 TTACTTCACTGATCTTCAGGAAGACCAAATATGAAAGAAGAAGAATCTACTCCATACTCTTTAGG
* **** * * ** *
5206471 GGAGATCAGACTCGAGAAGTCTTTGATCTACTTTACTGCTCTTCAGGGAAGATTGAATC-GAACT
196 GGAGATCAAACTCGAGAAAAAATTGATCCACTTCACTAATCTTCAGGGAAGATTAAATCTGAA-T
*
5206535 TAATTTGCT
260 CAATTTG-T
*
5206544 TT-GCTGCTCTTCAGGAAGACCAAATATGAAAGAAGAAGCGTATGCTCCACTACTCTTTAGGGGA
1 TTCACTGCTCTTCAGGAAGACCAAATATGAAAGAAGAAGCGTATGCTCCACTACTCTTTAGGGGA
** * * * *
5206608 GATCAGGCCCAATAAATCTTTGATCCACTTCACTTCTCTTCAGGGAAGATTGAATCGAACTTGAT
66 GATCACACCCAAGAAATATTTCATCCACTTCACTGCTCTTCAGGGAAGATTGAATCGAACTTGAT
* * * * * * *
5206673 TTGCTTC-GTGCTCTTCAGGAAGACGAAATATTAAAGAAGAAGAATCTGCTTTGC-TACTCTTTA
131 TTACTTCACTGATCTTCAGGAAGACCAAATATGAAAGAAGAAGAATCTAC--TCCATACTCTTTA
*
5206736 GGGGAGATCAAACTCGAGAAAAAATTGATCCACTTCACTAATCTTTAGGGAAGATTAAATCTGAA
194 GGGGAGATCAAACTCGAGAAAAAATTGATCCACTTCACTAATCTTCAGGGAAGATTAAATCTGAA
*
5206801 TCGATTTGT
259 TCAATTTGT
* *
5206810 TTCACTGCTCTTTAGGAATACCAAAT
1 TTCACTGCTCTTCAGGAAGACCAAAT
5206836 CTAAAGGATT
Statistics
Matches: 247, Mismatches: 41, Indels: 9
0.83 0.14 0.03
Matches are distributed among these distances:
266 36 0.15
267 204 0.83
268 7 0.03
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.30
Consensus pattern (267 bp):
TTCACTGCTCTTCAGGAAGACCAAATATGAAAGAAGAAGCGTATGCTCCACTACTCTTTAGGGGA
GATCACACCCAAGAAATATTTCATCCACTTCACTGCTCTTCAGGGAAGATTGAATCGAACTTGAT
TTACTTCACTGATCTTCAGGAAGACCAAATATGAAAGAAGAAGAATCTACTCCATACTCTTTAGG
GGAGATCAAACTCGAGAAAAAATTGATCCACTTCACTAATCTTCAGGGAAGATTAAATCTGAATC
AATTTGT
Found at i:5206927 original size:38 final size:38
Alignment explanation
Indices: 5206885--5207298 Score: 384
Period size: 38 Copynumber: 10.8 Consensus size: 38
5206875 AGAACACTTA
* * *
5206885 AAAGACTGACTCCTCTTCACGAGAAAGTCAAGGATAAC
1 AAAGATTGACTCCTCTTCACGAGGAAGTCAAGAATAAC
* * *
5206923 AAAGATTGACTTCTCTTCACGAGAAAGTCAAGAATAAA
1 AAAGATTGACTCCTCTTCACGAGGAAGTCAAGAATAAC
* * * * **
5206961 AAAGATTGATTCCTCTACGCGAGGGAGTCGGGAATAAC
1 AAAGATTGACTCCTCTTCACGAGGAAGTCAAGAATAAC
* * * * *
5206999 AAAGATTGATTTCTCTTTATGAGGAAGTTAAGAATAAC
1 AAAGATTGACTCCTCTTCACGAGGAAGTCAAGAATAAC
* ** * *
5207037 AAAGATTGGCTCCTCTTCGTGAGGGAGTCAGGAATAAC
1 AAAGATTGACTCCTCTTCACGAGGAAGTCAAGAATAAC
*
5207075 AGAGATTGACTCC-C-TCACGAGGAAGTCAAGAATAAC
1 AAAGATTGACTCCTCTTCACGAGGAAGTCAAGAATAAC
* * ** *
5207111 AAAGATTGACTTCTTTTCGTGA-GAGAGTAAAGAATAAC
1 AAAGATTGACTCCTCTTCACGAGGA-AGTCAAGAATAAC
* * * * *
5207149 AAAGATTAACTTCTCTTCATGATGAAGTGAAGAATAAC
1 AAAGATTGACTCCTCTTCACGAGGAAGTCAAGAATAAC
* * * * *
5207187 AAATATTGACTCCTCTTCGCAAGGGAGTCAGGAATAAC
1 AAAGATTGACTCCTCTTCACGAGGAAGTCAAGAATAAC
* * *
5207225 AAAGATTGACTTCTCTGCACGAGGAAGTCAAGAATGACAATG
1 AAAGATTGACTCCTCTTCACGAGGAAGTCAAGAAT---AA-C
*
5207267 AAAGATTGACTCCTCTTCACGAGGGAGTCAAG
1 AAAGATTGACTCCTCTTCACGAGGAAGTCAAG
5207299 TTGAAGCTTC
Statistics
Matches: 301, Mismatches: 67, Indels: 12
0.79 0.18 0.03
Matches are distributed among these distances:
36 29 0.10
37 3 0.01
38 236 0.78
39 2 0.01
41 2 0.01
42 29 0.10
ACGTcount: A:0.37, C:0.17, G:0.22, T:0.24
Consensus pattern (38 bp):
AAAGATTGACTCCTCTTCACGAGGAAGTCAAGAATAAC
Found at i:5206975 original size:76 final size:76
Alignment explanation
Indices: 5206884--5207296 Score: 463
Period size: 76 Copynumber: 5.4 Consensus size: 76
5206874 GAGAACACTT
* * ** *
5206884 AAAAGACTGACTCCTCTTCACGAGAAAGTCAAGG-ATAACAAAGATTGACTTCTCTTCACGAGAA
1 AAAAGATTGACTCCTCTTCGCGAGGGAGTC-AGGAATAACAAAGATTGACTTCTCTTCACGAGGA
5206948 AGTCAAGAATAA
65 AGTCAAGAATAA
* * * * * *
5206960 AAAAGATTGATTCCTCTACGCGAGGGAGTCGGGAATAACAAAGATTGATTTCTCTTTATGAGGAA
1 AAAAGATTGACTCCTCTTCGCGAGGGAGTCAGGAATAACAAAGATTGACTTCTCTTCACGAGGAA
*
5207025 GTTAAGAATAA
66 GTCAAGAATAA
* * * * *
5207036 CAAAGATTGGCTCCTCTTCGTGAGGGAGTCAGGAATAACAGAGATTGAC-TC-CCTCACGAGGAA
1 AAAAGATTGACTCCTCTTCGCGAGGGAGTCAGGAATAACAAAGATTGACTTCTCTTCACGAGGAA
5207099 GTCAAGAATAA
66 GTCAAGAATAA
* * * * * * * * * *
5207110 CAAAGATTGACTTCTTTTCGTGAGAGAGTAAAGAATAACAAAGATTAACTTCTCTTCATGATGAA
1 AAAAGATTGACTCCTCTTCGCGAGGGAGTCAGGAATAACAAAGATTGACTTCTCTTCACGAGGAA
*
5207175 GTGAAGAATAA
66 GTCAAGAATAA
* * * *
5207186 CAAATATTGACTCCTCTTCGCAAGGGAGTCAGGAATAACAAAGATTGACTTCTCTGCACGAGGAA
1 AAAAGATTGACTCCTCTTCGCGAGGGAGTCAGGAATAACAAAGATTGACTTCTCTTCACGAGGAA
5207251 GTCAAGAATGACA
66 GTCAAGAAT-A-A
*
5207264 ATGAAAGATTGACTCCTCTTCACGAGGGAGTCA
1 A--AAAGATTGACTCCTCTTCGCGAGGGAGTCA
5207297 AGTTGAAGCT
Statistics
Matches: 277, Mismatches: 53, Indels: 10
0.81 0.16 0.03
Matches are distributed among these distances:
74 60 0.22
75 6 0.02
76 182 0.66
77 1 0.00
78 1 0.00
80 27 0.10
ACGTcount: A:0.37, C:0.17, G:0.22, T:0.24
Consensus pattern (76 bp):
AAAAGATTGACTCCTCTTCGCGAGGGAGTCAGGAATAACAAAGATTGACTTCTCTTCACGAGGAA
GTCAAGAATAA
Found at i:5207163 original size:150 final size:151
Alignment explanation
Indices: 5206885--5207264 Score: 460
Period size: 150 Copynumber: 2.5 Consensus size: 151
5206875 AGAACACTTA
* * * ** * *
5206885 AAAGACTGACTCCTCTTCACGAGAAAGTCAAGG-ATAACAAAGATTGACTTCTCTTCACGAGAAA
1 AAAGATTGACTCCTCTTCGCAAGGGAGTC-AGGAATAACAAAGATTGACTTC-CCTCACGAGGAA
* * *** * *
5206949 GTCAAGAATAAAAAAGATTGATTCCTCTACGCGAGGGAGTCGGGAATAACAAAGATTGATTTCTC
64 GTCAAGAATAACAAAGATTGATTCCTCTACGCGAGAGAGTAAAGAATAACAAAGATTAACTTCTC
* *
5207014 TTTATGAGGAAGTTAAGAATAAC
129 TTCATGAGGAAGTGAAGAATAAC
* ** *
5207037 AAAGATTGGCTCCTCTTCGTGAGGGAGTCAGGAATAACAGAGATTGAC-TCCCTCACGAGGAAGT
1 AAAGATTGACTCCTCTTCGCAAGGGAGTCAGGAATAACAAAGATTGACTTCCCTCACGAGGAAGT
* * *
5207101 CAAGAATAACAAAGATTGACTT-CTTTTCGTGAGAGAGTAAAGAATAACAAAGATTAACTTCTCT
66 CAAGAATAACAAAGATTGA-TTCCTCTACGCGAGAGAGTAAAGAATAACAAAGATTAACTTCTCT
*
5207165 TCATGATGAAGTGAAGAATAAC
130 TCATGAGGAAGTGAAGAATAAC
* *
5207187 AAATATTGACTCCTCTTCGCAAGGGAGTCAGGAATAACAAAGATTGACTTCTCTGCACGAGGAAG
1 AAAGATTGACTCCTCTTCGCAAGGGAGTCAGGAATAACAAAGATTGACTTCCCT-CACGAGGAAG
*
5207252 TCAAGAATGACAA
65 TCAAGAATAACAA
5207265 TGAAAGATTG
Statistics
Matches: 195, Mismatches: 29, Indels: 8
0.84 0.12 0.03
Matches are distributed among these distances:
150 125 0.64
151 11 0.06
152 59 0.30
ACGTcount: A:0.38, C:0.17, G:0.21, T:0.24
Consensus pattern (151 bp):
AAAGATTGACTCCTCTTCGCAAGGGAGTCAGGAATAACAAAGATTGACTTCCCTCACGAGGAAGT
CAAGAATAACAAAGATTGATTCCTCTACGCGAGAGAGTAAAGAATAACAAAGATTAACTTCTCTT
CATGAGGAAGTGAAGAATAAC
Found at i:5219212 original size:10 final size:10
Alignment explanation
Indices: 5219197--5219232 Score: 72
Period size: 10 Copynumber: 3.6 Consensus size: 10
5219187 TTACTACTTT
5219197 TATTTCACTC
1 TATTTCACTC
5219207 TATTTCACTC
1 TATTTCACTC
5219217 TATTTCACTC
1 TATTTCACTC
5219227 TATTTC
1 TATTTC
5219233 CTTACTAGTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 26 1.00
ACGTcount: A:0.19, C:0.28, G:0.00, T:0.53
Consensus pattern (10 bp):
TATTTCACTC
Found at i:5221228 original size:122 final size:122
Alignment explanation
Indices: 5221010--5221252 Score: 434
Period size: 122 Copynumber: 2.0 Consensus size: 122
5221000 TCCTTGGATA
*
5221010 GTTTTGAGGCCACAATCATCGTAGTAGGGCAAGGTGTAGCATTCTTCATACCAACCTTCTCCAAT
1 GTTTTGAGGCCACAATCATCGTAGTAGGGCAAGGTATAGCATTCTTCATACCAACCTTCTCCAAT
5221075 AATTCAAGAATAAATTTCTTTTGACTAAGCACAATGACCCCATCACACCACTTCACT
66 AATTCAAGAATAAATTTCTTTTGACTAAGCACAATGACCCCATCACACCACTTCACT
5221132 GTTTTGAGGCCACAATCATCAG-AGTAGGGCAAGGTATAGCATTCTTCATACCAACCTTCTCCAA
1 GTTTTGAGGCCACAATCATC-GTAGTAGGGCAAGGTATAGCATTCTTCATACCAACCTTCTCCAA
* * *
5221196 TAATTCAAGAATAAATTTCTTTTGACTGAGCACAGTGGCCCCATCACACCACTTCAC
65 TAATTCAAGAATAAATTTCTTTTGACTAAGCACAATGACCCCATCACACCACTTCAC
5221253 CTCAATCCCA
Statistics
Matches: 116, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
122 115 0.99
123 1 0.01
ACGTcount: A:0.31, C:0.26, G:0.15, T:0.28
Consensus pattern (122 bp):
GTTTTGAGGCCACAATCATCGTAGTAGGGCAAGGTATAGCATTCTTCATACCAACCTTCTCCAAT
AATTCAAGAATAAATTTCTTTTGACTAAGCACAATGACCCCATCACACCACTTCACT
Found at i:5221895 original size:21 final size:20
Alignment explanation
Indices: 5221834--5221886 Score: 61
Period size: 21 Copynumber: 2.6 Consensus size: 20
5221824 TGGCTCAAAT
*
5221834 GATCAATCCCTTCGAAAAAG
1 GATCGATCCCTTCGAAAAAG
* * *
5221854 GATCGATCTCTTTGACCAAAG
1 GATCGATCCCTTCGA-AAAAG
5221875 GATCGATCCCTT
1 GATCGATCCCTT
5221887 GGATAAAAGT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 12 0.44
21 15 0.56
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.26
Consensus pattern (20 bp):
GATCGATCCCTTCGAAAAAG
Found at i:5222751 original size:34 final size:32
Alignment explanation
Indices: 5222698--5222767 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 32
5222688 CCTTACAAAC
*
5222698 TCCCTAGTTTTTCCGGGCTAAACTAGAACCTT
1 TCCCTAGTTTTACCGGGCTAAACTAGAACCTT
*
5222730 TCCCTAGCTTTTACACGGGCTAACCTAGAACCTT
1 TCCCTAG-TTTTAC-CGGGCTAAACTAGAACCTT
5222764 TCCC
1 TCCC
5222768 CATTACAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 22 0.65
ACGTcount: A:0.21, C:0.33, G:0.14, T:0.31
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGCTAAACTAGAACCTT
Found at i:5223076 original size:21 final size:21
Alignment explanation
Indices: 5223050--5223091 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
5223040 CCAGAATGGG
*
5223050 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
5223071 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
5223092 ATATTCAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:5223226 original size:15 final size:15
Alignment explanation
Indices: 5223206--5223262 Score: 53
Period size: 15 Copynumber: 3.5 Consensus size: 15
5223196 ACCATGCAGG
5223206 GGGGAATCTGTACCC
1 GGGGAATCTGTACCC
5223221 GGGGAATC-GATACCCC
1 GGGGAATCTG-TA-CCC
*
5223237 TGGGGGGAATCTGTTCCC
1 ---GGGGAATCTGTACCC
5223255 GGGGAATC
1 GGGGAATC
5223263 GATACCCCTT
Statistics
Matches: 35, Mismatches: 1, Indels: 12
0.73 0.02 0.25
Matches are distributed among these distances:
14 1 0.03
15 18 0.51
16 3 0.09
18 3 0.09
19 9 0.26
20 1 0.03
ACGTcount: A:0.19, C:0.25, G:0.37, T:0.19
Consensus pattern (15 bp):
GGGGAATCTGTACCC
Found at i:5223244 original size:34 final size:35
Alignment explanation
Indices: 5223204--5223289 Score: 156
Period size: 34 Copynumber: 2.5 Consensus size: 35
5223194 AAACCATGCA
5223204 GGGGGGAATCTGTACCCGGGGAATCGATACCCC-T
1 GGGGGGAATCTGTACCCGGGGAATCGATACCCCTT
*
5223238 GGGGGGAATCTGTTCCCGGGGAATCGATACCCCTT
1 GGGGGGAATCTGTACCCGGGGAATCGATACCCCTT
5223273 GGGGGGAATCTGTACCC
1 GGGGGGAATCTGTACCC
5223290 CTTGACAATA
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
34 32 0.65
35 17 0.35
ACGTcount: A:0.19, C:0.26, G:0.36, T:0.20
Consensus pattern (35 bp):
GGGGGGAATCTGTACCCGGGGAATCGATACCCCTT
Found at i:5223293 original size:20 final size:19
Alignment explanation
Indices: 5223221--5223291 Score: 64
Period size: 20 Copynumber: 3.9 Consensus size: 19
5223211 ATCTGTACCC
5223221 GGGGAATCGATACCCCTGG
1 GGGGAATCGATACCCCTGG
*
5223240 GGGGAATCTG-T-TCCC---
1 GGGGAATC-GATACCCCTGG
5223255 GGGGAATCGATACCCCTTGG
1 GGGGAATCGATACCCC-TGG
5223275 GGGGAATCTG-TACCCCT
1 GGGGAATC-GATACCCCT
5223292 TGACAATATG
Statistics
Matches: 42, Mismatches: 2, Indels: 16
0.70 0.03 0.27
Matches are distributed among these distances:
14 1 0.02
15 9 0.21
16 3 0.07
18 3 0.07
19 10 0.24
20 15 0.36
21 1 0.02
ACGTcount: A:0.18, C:0.27, G:0.34, T:0.21
Consensus pattern (19 bp):
GGGGAATCGATACCCCTGG
Found at i:5225251 original size:3 final size:3
Alignment explanation
Indices: 5225243--5225283 Score: 57
Period size: 3 Copynumber: 14.0 Consensus size: 3
5225233 TACATCCTCA
* *
5225243 TTC TTC TTC TTC TTC TTC TTC TTC TTG TTT TTC TTC -TC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
5225284 CCTTTCTTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
2 2 0.06
3 32 0.94
ACGTcount: A:0.00, C:0.29, G:0.02, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:5226651 original size:21 final size:21
Alignment explanation
Indices: 5226625--5226666 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
5226615 CCAGAATGGG
5226625 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
5226646 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
5226667 ATATTCAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.29, C:0.29, G:0.19, T:0.24
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:5226800 original size:15 final size:15
Alignment explanation
Indices: 5226780--5226836 Score: 53
Period size: 15 Copynumber: 3.5 Consensus size: 15
5226770 AACCATGCAG
5226780 GGGGAATCTGTACCC
1 GGGGAATCTGTACCC
5226795 GGGGAATC-GATACCCC
1 GGGGAATCTG-TA-CCC
*
5226811 TGGGGGGAATCTGTTCCC
1 ---GGGGAATCTGTACCC
5226829 GGGGAATC
1 GGGGAATC
5226837 GATACCCCAT
Statistics
Matches: 35, Mismatches: 1, Indels: 12
0.73 0.02 0.25
Matches are distributed among these distances:
14 1 0.03
15 18 0.51
16 3 0.09
18 3 0.09
19 9 0.26
20 1 0.03
ACGTcount: A:0.19, C:0.25, G:0.37, T:0.19
Consensus pattern (15 bp):
GGGGAATCTGTACCC
Found at i:5226819 original size:19 final size:19
Alignment explanation
Indices: 5226779--5226870 Score: 69
Period size: 19 Copynumber: 5.3 Consensus size: 19
5226769 AAACCATGCA
5226779 GGGGGAATCTG-TA-CCC-
1 GGGGGAATCTGATACCCCT
5226795 -GGGGAATC-GATACCCCT
1 GGGGGAATCTGATACCCCT
*
5226812 GGGGGGAATCTG-T-TCCC-
1 -GGGGGAATCTGATACCCCT
5226829 -GGGGAATC-GATACCCCAT
1 GGGGGAATCTGATACCCC-T
* *
5226847 GGGGGAATCTGTTCCCCCT
1 GGGGGAATCTGATACCCCT
5226866 GGGGG
1 GGGGG
5226871 GGGAATCTGT
Statistics
Matches: 60, Mismatches: 4, Indels: 21
0.71 0.05 0.25
Matches are distributed among these distances:
14 2 0.03
15 19 0.32
16 6 0.10
18 3 0.05
19 23 0.38
20 7 0.12
ACGTcount: A:0.17, C:0.26, G:0.37, T:0.20
Consensus pattern (19 bp):
GGGGGAATCTGATACCCCT
Found at i:5226859 original size:34 final size:34
Alignment explanation
Indices: 5226779--5226862 Score: 143
Period size: 34 Copynumber: 2.5 Consensus size: 34
5226769 AAACCATGCA
*
5226779 GGGGGAATCTGTACCCGGGGAATCGATACCCCTG
1 GGGGGAATCTGTTCCCGGGGAATCGATACCCCTG
5226813 GGGGGAATCTGTTCCCGGGGAATCGATACCCCAT-
1 GGGGGAATCTGTTCCCGGGGAATCGATACCCC-TG
5226847 GGGGGAATCTGTTCCC
1 GGGGGAATCTGTTCCC
5226863 CCTGGGGGGG
Statistics
Matches: 48, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
34 47 0.98
35 1 0.02
ACGTcount: A:0.19, C:0.26, G:0.35, T:0.20
Consensus pattern (34 bp):
GGGGGAATCTGTTCCCGGGGAATCGATACCCCTG
Found at i:5226875 original size:22 final size:22
Alignment explanation
Indices: 5226847--5226889 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
5226837 GATACCCCAT
*
5226847 GGGGGAATCTGTTCCCCCTGGG
1 GGGGGAATCTGTACCCCCTGGG
5226869 GGGGGAATCTGTACCCCCTGG
1 GGGGGAATCTGTACCCCCTGG
5226890 ACAATCTGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.12, C:0.28, G:0.40, T:0.21
Consensus pattern (22 bp):
GGGGGAATCTGTACCCCCTGGG
Found at i:5229306 original size:21 final size:21
Alignment explanation
Indices: 5229267--5229322 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 21
5229257 TCCCTTAGAG
* * **
5229267 AAAGGATCGATCTCTTTGACC
1 AAAGGATCGATCCCCTTGAAA
*
5229288 AAAGTATCGATCCCCTTGAAA
1 AAAGGATCGATCCCCTTGAAA
5229309 AAAGGATCGATCCC
1 AAAGGATCGATCCC
5229323 TTAGACAACT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (21 bp):
AAAGGATCGATCCCCTTGAAA
Found at i:5229349 original size:30 final size:29
Alignment explanation
Indices: 5229313--5229389 Score: 127
Period size: 30 Copynumber: 2.6 Consensus size: 29
5229303 TTGAAAAAAG
*
5229313 GATCGATCCCTTAGACAACTGTGAGTTTGA
1 GATCGATCCCTT-GACAACAGTGAGTTTGA
5229343 GATCGATCCCTTGGACAACAGTGAGTTTGA
1 GATCGATCCCTT-GACAACAGTGAGTTTGA
5229373 GATCGATCCCTTGACAA
1 GATCGATCCCTTGACAA
5229390 AATGATCGAT
Statistics
Matches: 45, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 5 0.11
30 40 0.89
ACGTcount: A:0.27, C:0.22, G:0.23, T:0.27
Consensus pattern (29 bp):
GATCGATCCCTTGACAACAGTGAGTTTGA
Found at i:5229398 original size:20 final size:21
Alignment explanation
Indices: 5229372--5229425 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
5229362 AGTGAGTTTG
5229372 AGATCGATCCCTTGA-CAAAA
1 AGATCGATCCCTTGAGCAAAA
* * *
5229392 TGATCGATCCCTCGAGGAAAA
1 AGATCGATCCCTTGAGCAAAA
5229413 AGATCGATCCCTT
1 AGATCGATCCCTT
5229426 TGGTATAACG
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 13 0.46
21 15 0.54
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.22
Consensus pattern (21 bp):
AGATCGATCCCTTGAGCAAAA
Found at i:5231528 original size:20 final size:21
Alignment explanation
Indices: 5231489--5231528 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
5231479 GAAGCTTTAA
* *
5231489 GATCATCAATTTTCTTTTGAT
1 GATCATCAATTTACTCTTGAT
5231510 GATCATC-ATTTACTCTTGA
1 GATCATCAATTTACTCTTGA
5231529 AAGTAAATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.25, C:0.17, G:0.10, T:0.47
Consensus pattern (21 bp):
GATCATCAATTTACTCTTGAT
Found at i:5236355 original size:24 final size:20
Alignment explanation
Indices: 5236323--5236378 Score: 58
Period size: 20 Copynumber: 2.6 Consensus size: 20
5236313 GCACAGGTAG
5236323 TGCATCGATGCACCTGGTAAGGAA
1 TGCATCGATGCA-CT-GT-A-GAA
* *
5236347 TGCATCGATACACTGTAGAG
1 TGCATCGATGCACTGTAGAA
5236367 TGCATCGATGCA
1 TGCATCGATGCA
5236379 TACCTTCATT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 13 0.45
21 1 0.03
22 2 0.07
23 2 0.07
24 11 0.38
ACGTcount: A:0.29, C:0.21, G:0.27, T:0.23
Consensus pattern (20 bp):
TGCATCGATGCACTGTAGAA
Found at i:5236942 original size:18 final size:18
Alignment explanation
Indices: 5236912--5236982 Score: 97
Period size: 18 Copynumber: 3.8 Consensus size: 18
5236902 AGGGATAATC
5236912 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
* * *
5236930 AGCGGTTCTTCGGAACAAT
1 AGTGGTCCTTCGGGAC-AT
5236949 CAGTGGTCCTTCGGGACAT
1 -AGTGGTCCTTCGGGACAT
5236968 AGTGGTCCTTCGGGA
1 AGTGGTCCTTCGGGA
5236983 TAAATATTCA
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
18 28 0.62
19 4 0.09
20 13 0.29
ACGTcount: A:0.18, C:0.23, G:0.32, T:0.27
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:5236959 original size:38 final size:38
Alignment explanation
Indices: 5236908--5236980 Score: 128
Period size: 38 Copynumber: 1.9 Consensus size: 38
5236898 GTCGAGGGAT
*
5236908 AATCAGTGGTCCTTCGGGACATAGCGGTTCTTCGGAAC
1 AATCAGTGGTCCTTCGGGACATAGCGGTCCTTCGGAAC
*
5236946 AATCAGTGGTCCTTCGGGACATAGTGGTCCTTCGG
1 AATCAGTGGTCCTTCGGGACATAGCGGTCCTTCGG
5236981 GATAAATATT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
38 33 1.00
ACGTcount: A:0.19, C:0.23, G:0.30, T:0.27
Consensus pattern (38 bp):
AATCAGTGGTCCTTCGGGACATAGCGGTCCTTCGGAAC
Found at i:5238829 original size:12 final size:12
Alignment explanation
Indices: 5238808--5238840 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
5238798 GGCTACACAG
5238808 AGAGGAAGAGGT
1 AGAGGAAGAGGT
*
5238820 AGAGGTAGAGGT
1 AGAGGAAGAGGT
5238832 AGAGGAAGA
1 AGAGGAAGA
5238841 AGTCAGTCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.48, T:0.09
Consensus pattern (12 bp):
AGAGGAAGAGGT
Found at i:5243195 original size:24 final size:20
Alignment explanation
Indices: 5243163--5243218 Score: 58
Period size: 20 Copynumber: 2.6 Consensus size: 20
5243153 GCACAGGTAG
5243163 TGCATCGATGCACCTGGTAAGGAA
1 TGCATCGATGCA-CT-GT-A-GAA
* *
5243187 TGCATCGATACACTGTAGAG
1 TGCATCGATGCACTGTAGAA
5243207 TGCATCGATGCA
1 TGCATCGATGCA
5243219 TACCTTCATT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 13 0.45
21 1 0.03
22 2 0.07
23 2 0.07
24 11 0.38
ACGTcount: A:0.29, C:0.21, G:0.27, T:0.23
Consensus pattern (20 bp):
TGCATCGATGCACTGTAGAA
Found at i:5243775 original size:18 final size:20
Alignment explanation
Indices: 5243748--5243801 Score: 69
Period size: 18 Copynumber: 2.8 Consensus size: 20
5243738 GTCGAGGGAA
5243748 AATCAGTGGTCCTTCGG-G-
1 AATCAGTGGTCCTTCGGAGC
*
5243766 ATAT-AGTGGTTCTTCGGAGC
1 A-ATCAGTGGTCCTTCGGAGC
5243786 AATCAGTGGTCCTTCG
1 AATCAGTGGTCCTTCG
5243802 AGACAAATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
18 13 0.43
19 5 0.17
20 12 0.40
ACGTcount: A:0.19, C:0.20, G:0.30, T:0.31
Consensus pattern (20 bp):
AATCAGTGGTCCTTCGGAGC
Found at i:5245904 original size:30 final size:30
Alignment explanation
Indices: 5245847--5245904 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
5245837 ATTTTAAATT
* * *
5245847 TTTTTTATAAATATTTACTTTTCAAAAACA
1 TTTTTCATAAATATTGAATTTTCAAAAACA
* *
5245877 TTTTTCATATATATTGAATTTTTAAAAA
1 TTTTTCATAAATATTGAATTTTCAAAAA
5245905 TTTTCTAAAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.40, C:0.07, G:0.02, T:0.52
Consensus pattern (30 bp):
TTTTTCATAAATATTGAATTTTCAAAAACA
Found at i:5256140 original size:32 final size:32
Alignment explanation
Indices: 5256086--5256146 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
5256076 TTAAAAATTT
*
5256086 AGGTACTAAAATGAAATAAAAAGTTAACAGAC
1 AGGTACTAAAATGAAATAAAAAGTAAACAGAC
5256118 AGGTACTAAAATGAAACT-AAAAGTAAACA
1 AGGTACTAAAATGAAA-TAAAAAGTAAACA
5256147 TTAGGTATGG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
32 26 0.96
33 1 0.04
ACGTcount: A:0.57, C:0.10, G:0.15, T:0.18
Consensus pattern (32 bp):
AGGTACTAAAATGAAATAAAAAGTAAACAGAC
Found at i:5256537 original size:15 final size:15
Alignment explanation
Indices: 5256517--5256547 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
5256507 GTTTGTTAAA
*
5256517 ACAGAATGGTTTAGC
1 ACAGAATGATTTAGC
5256532 ACAGAATGATTTAGC
1 ACAGAATGATTTAGC
5256547 A
1 A
5256548 GTCTGAATGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.39, C:0.13, G:0.23, T:0.26
Consensus pattern (15 bp):
ACAGAATGATTTAGC
Found at i:5256852 original size:17 final size:18
Alignment explanation
Indices: 5256822--5256882 Score: 88
Period size: 18 Copynumber: 3.4 Consensus size: 18
5256812 TCTCGACAGT
5256822 GGATGAATCGACCGAAGGA
1 GGATGAA-CGACCGAAGGA
*
5256841 GG-TGAACGACCGAAGAA
1 GGATGAACGACCGAAGGA
*
5256858 GGATGAACGACCGAATGA
1 GGATGAACGACCGAAGGA
5256876 GGATGAA
1 GGATGAA
5256883 TCGATTGCAG
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
17 12 0.32
18 24 0.63
19 2 0.05
ACGTcount: A:0.39, C:0.15, G:0.36, T:0.10
Consensus pattern (18 bp):
GGATGAACGACCGAAGGA
Found at i:5264263 original size:24 final size:24
Alignment explanation
Indices: 5264236--5264289 Score: 108
Period size: 24 Copynumber: 2.2 Consensus size: 24
5264226 AATGGCATGC
5264236 GATATTCTCTAATAAACTATATGT
1 GATATTCTCTAATAAACTATATGT
5264260 GATATTCTCTAATAAACTATATGT
1 GATATTCTCTAATAAACTATATGT
5264284 GATATT
1 GATATT
5264290 GCACCAAACT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.37, C:0.11, G:0.09, T:0.43
Consensus pattern (24 bp):
GATATTCTCTAATAAACTATATGT
Found at i:5265202 original size:22 final size:22
Alignment explanation
Indices: 5265174--5265231 Score: 91
Period size: 22 Copynumber: 2.6 Consensus size: 22
5265164 CAAATATTAA
5265174 AAAAAATTAAATATAAAATACT
1 AAAAAATTAAATATAAAATACT
*
5265196 AAAAAATTAAA-ATTAAATTACT
1 AAAAAATTAAATA-TAAAATACT
5265218 AAAAAATTAAATAT
1 AAAAAATTAAATAT
5265232 GTATATTAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
21 1 0.03
22 31 0.94
23 1 0.03
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.29
Consensus pattern (22 bp):
AAAAAATTAAATATAAAATACT
Found at i:5265214 original size:33 final size:34
Alignment explanation
Indices: 5265132--5265215 Score: 91
Period size: 33 Copynumber: 2.5 Consensus size: 34
5265122 TAATTTTCAG
* ** * *
5265132 AAAATAAAAATTATTTTAAATATAAAATTCTTCA
1 AAAATTAAAATTAAATTAAATATAAAATACTTAA
* *
5265166 AATATTAAAA-AAAATTAAATATAAAATAC-TAA
1 AAAATTAAAATTAAATTAAATATAAAATACTTAA
5265198 AAAATTAAAATTAAATTA
1 AAAATTAAAATTAAATTA
5265216 CTAAAAAATT
Statistics
Matches: 40, Mismatches: 9, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
32 11 0.28
33 21 0.52
34 8 0.20
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (34 bp):
AAAATTAAAATTAAATTAAATATAAAATACTTAA
Found at i:5265241 original size:21 final size:20
Alignment explanation
Indices: 5265174--5265243 Score: 61
Period size: 22 Copynumber: 3.2 Consensus size: 20
5265164 CAAATATTAA
*
5265174 AAAAAATTAAATATAAAATACT
1 AAAAAATTAAATAT--TATACT
5265196 AAAAAATTAAA-ATTAAATTACT
1 AAAAAATTAAATATT--A-TACT
*
5265218 AAAAAATTAAATATGTATATT
1 AAAAAATTAAATAT-TATACT
5265239 AAAAA
1 AAAAA
5265244 TACTAAAATT
Statistics
Matches: 41, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
21 11 0.27
22 27 0.66
23 2 0.05
24 1 0.02
ACGTcount: A:0.66, C:0.03, G:0.01, T:0.30
Consensus pattern (20 bp):
AAAAAATTAAATATTATACT
Found at i:5271785 original size:20 final size:21
Alignment explanation
Indices: 5271749--5271787 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
5271739 GTTACTCCAG
5271749 GTAATTAACTCTGTAACTCTT
1 GTAATTAACTCTGTAACTCTT
*
5271770 GTAATT-ACTTTGTAACTC
1 GTAATTAACTCTGTAACTC
5271788 CAGTTAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.28, C:0.18, G:0.10, T:0.44
Consensus pattern (21 bp):
GTAATTAACTCTGTAACTCTT
Found at i:5271795 original size:21 final size:21
Alignment explanation
Indices: 5271736--5271796 Score: 61
Period size: 20 Copynumber: 2.9 Consensus size: 21
5271726 AGCATAAATG
*
5271736 TTTGTTACTCCAGGTAATTAAC
1 TTTGTAACTCCA-GTAATTAAC
* **
5271758 TCTGTAACTCTTGTAATT-AC
1 TTTGTAACTCCAGTAATTAAC
5271778 TTTGTAACTCCAGTTAATT
1 TTTGTAACTCCAG-TAATT
5271797 TTGACATTTA
Statistics
Matches: 31, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
20 12 0.39
21 11 0.35
22 8 0.26
ACGTcount: A:0.26, C:0.18, G:0.11, T:0.44
Consensus pattern (21 bp):
TTTGTAACTCCAGTAATTAAC
Found at i:5272523 original size:21 final size:21
Alignment explanation
Indices: 5272499--5272546 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
5272489 CTCAAGTGTT
5272499 GATACTCTACATAAGGGTATC
1 GATACTCTACATAAGGGTATC
*
5272520 GATACTCTATATAAGGGTATC
1 GATACTCTACATAAGGGTATC
*
5272541 AATACT
1 GATACT
5272547 GCTATAACAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Consensus pattern (21 bp):
GATACTCTACATAAGGGTATC
Found at i:5284226 original size:124 final size:124
Alignment explanation
Indices: 5284006--5284255 Score: 455
Period size: 124 Copynumber: 2.0 Consensus size: 124
5283996 CAACCGTTCA
*
5284006 TGTTCGATTAGAAATGCCATGGCGCATTCAAAGAGTTGAAGTAAAGACTTATCTCTGCACCGATC
1 TGTTCGATCAGAAATGCCATGGCGCATTCAAAGAGTTGAAGTAAAGACTTATCTCTGCACCGATC
* * * *
5284071 GTAGTTTCCCCAGGTTGGACGGCCGTTCGAATTAATGTGTAATGCAAGTGATTTTATCG
66 GTAGTTCCCCCAGATTGGACGACCGTTCGAATTAATGTGTAATGCAAGTGATTTTACCG
5284130 TGTTCGATCAGAAATGCCATGGCGCATTCAAAGAGTTGAAGTAAAGACTTATCTCTGCACCGATC
1 TGTTCGATCAGAAATGCCATGGCGCATTCAAAGAGTTGAAGTAAAGACTTATCTCTGCACCGATC
5284195 GTAGTTCCCCCAGATTGGACGACCGTTCGAATTAATGTGTAATGCAAGTGATTTTACCG
66 GTAGTTCCCCCAGATTGGACGACCGTTCGAATTAATGTGTAATGCAAGTGATTTTACCG
5284254 TG
1 TG
5284256 GGAGCTGTGC
Statistics
Matches: 121, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
124 121 1.00
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.30
Consensus pattern (124 bp):
TGTTCGATCAGAAATGCCATGGCGCATTCAAAGAGTTGAAGTAAAGACTTATCTCTGCACCGATC
GTAGTTCCCCCAGATTGGACGACCGTTCGAATTAATGTGTAATGCAAGTGATTTTACCG
Found at i:5286302 original size:13 final size:13
Alignment explanation
Indices: 5286284--5286313 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
5286274 GTCATATCTT
*
5286284 CTTTTCACTTTTA
1 CTTTTCACTTCTA
5286297 CTTTTCACTTCTA
1 CTTTTCACTTCTA
5286310 CTTT
1 CTTT
5286314 CTTTCATCTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.13, C:0.27, G:0.00, T:0.60
Consensus pattern (13 bp):
CTTTTCACTTCTA
Found at i:5294997 original size:292 final size:291
Alignment explanation
Indices: 5294474--5295058 Score: 1152
Period size: 292 Copynumber: 2.0 Consensus size: 291
5294464 TGCATTATGT
5294474 CTCTGTCTGGTCATCGATAACCCGATCACATTCCATAGTTACCACATCCTATTTCCAATGAGGAA
1 CTCTGTCTGGTCATCGATAACCCGATCACATTCCATAGTTACCACATCCTATTTCCAATGAGGAA
5294539 TATGAATGGGCTGAAGCAAACCTAAGGAACTTGGTGTTCAGTCTTAACCCGCTGACACACTAGGC
66 TATGAATGGGCTGAAGCAAACCTAAGGAACTTGGTGTTCAGTCTTAACCCGCTGACACACTAGGC
5294604 ATCTAGCAATAAACTCTGACAATTCCCTTTTCATACCCGGCCAATAGAACAATCGTCAAAGCTCT
131 ATCTAGCAATAAACTCTGACAATTCCCTTTTCATACCCGGCCAATAGAACAATCGTCAAAGCTCT
5294669 TGATATATCTTGCTACTGCCTAGGTGTACAGAGAGTGACTACAATGCACCTCATGGAGAATCTTA
196 TGATATATCTTGCTACTGCCTAGGTGTACAGAGAGTGACTACAATGCACCTCATGGAGAATCTTA
5294734 TCGTGCATCTTCAGGTATGCACAACTGACCC
261 TCGTGCATCTTCAGGTATGCACAACTGACCC
5294765 CTCTGTCTGGTCATCGATAACCCGATCACATTCCATAGTTACCACATCCTATTTCCAATGAGGAA
1 CTCTGTCTGGTCATCGATAACCCGATCACATTCCATAGTTACCACATCCTATTTCCAATGAGGAA
*
5294830 TCTGAATGGGCTGAAGCAAACCTAAGGGAACTTGGTGTTCAGTCTTAACCCGCTGACACACTAGG
66 TATGAATGGGCTGAAGCAAACCTAA-GGAACTTGGTGTTCAGTCTTAACCCGCTGACACACTAGG
5294895 CATCTAGCAATAAACTCTGACAATTCCCTTTTCATACCCGGCCAATAGAACAATCGTCAAAGCTC
130 CATCTAGCAATAAACTCTGACAATTCCCTTTTCATACCCGGCCAATAGAACAATCGTCAAAGCTC
5294960 TTGATATATCTTGCTACTGCCTAGGTGTACAGAGAGTGACTACAATGCACCTCATGGAGAATCTT
195 TTGATATATCTTGCTACTGCCTAGGTGTACAGAGAGTGACTACAATGCACCTCATGGAGAATCTT
5295025 ATCGTGCATCTTCAGGTATGCACAACTGACCC
260 ATCGTGCATCTTCAGGTATGCACAACTGACCC
5295057 CT
1 CT
5295059 GAAGTACAAT
Statistics
Matches: 292, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
291 89 0.30
292 203 0.70
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.27
Consensus pattern (291 bp):
CTCTGTCTGGTCATCGATAACCCGATCACATTCCATAGTTACCACATCCTATTTCCAATGAGGAA
TATGAATGGGCTGAAGCAAACCTAAGGAACTTGGTGTTCAGTCTTAACCCGCTGACACACTAGGC
ATCTAGCAATAAACTCTGACAATTCCCTTTTCATACCCGGCCAATAGAACAATCGTCAAAGCTCT
TGATATATCTTGCTACTGCCTAGGTGTACAGAGAGTGACTACAATGCACCTCATGGAGAATCTTA
TCGTGCATCTTCAGGTATGCACAACTGACCC
Found at i:5301762 original size:16 final size:16
Alignment explanation
Indices: 5301738--5301768 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5301728 GTTCTGTGAA
5301738 AGAACCATGGTGTCAC
1 AGAACCATGGTGTCAC
*
5301754 AGAAGCATGGTGTCA
1 AGAACCATGGTGTCA
5301769 AAGAGGCAAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.32, C:0.19, G:0.29, T:0.19
Consensus pattern (16 bp):
AGAACCATGGTGTCAC
Found at i:5302082 original size:22 final size:22
Alignment explanation
Indices: 5302054--5302097 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
5302044 AAACATTCTT
5302054 TTTTTCCTCTCTTTCTTT-TGTC
1 TTTTTCCTCTC-TTCTTTATGTC
*
5302076 TTTTTCCTTTCTTCTTTATGTC
1 TTTTTCCTCTCTTCTTTATGTC
5302098 CTTCTTCATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.02, C:0.25, G:0.05, T:0.68
Consensus pattern (22 bp):
TTTTTCCTCTCTTCTTTATGTC
Found at i:5305394 original size:88 final size:85
Alignment explanation
Indices: 5305279--5305510 Score: 195
Period size: 85 Copynumber: 2.7 Consensus size: 85
5305269 TTTTTAATTA
* * * * * *
5305279 AATTA-AAAGGTAGAAAGTGGGAA-TGAAAAAACTCAGGGGTCTCAATTATAAAGGTAAAAAGTG
1 AATTATAAAGGTAAAAAGT-GAAATTGAAAAAAATCAAGAGCCTCAATTATAAAGGTAAAAA---
*** * *
5305342 AGGTTTA-AAAAAATTAGGGATCTC
62 AGAACTAGAAAAAA-TAGAGACCTC
* * *
5305366 AATTATAAAGGTAAAAAGTGAAATTGAAAAAAATTAAGAGCCTTACTTATAAAGGTAAAAAAGAA
1 AATTATAAAGGTAAAAAGTGAAATTGAAAAAAATCAAGAGCCTCAATTATAAAGGTAAAAAAGAA
5305431 CTAGAAAAAATAGAGACCTC
66 CTAGAAAAAATAGAGACCTC
* * * * * *
5305451 AATTACT-AAGATAAAAAGTGAAATTGAAAAAAATTAGGA-CATCAATAATAAAAGTAAAAA
1 AATTA-TAAAGGTAAAAAGTGAAATTGAAAAAAATCAAGAGCCTCAATTATAAAGGTAAAAA
5305511 TAAGACTAAA
Statistics
Matches: 120, Mismatches: 21, Indels: 11
0.79 0.14 0.07
Matches are distributed among these distances:
84 16 0.13
85 47 0.39
86 7 0.06
87 8 0.07
88 42 0.35
ACGTcount: A:0.53, C:0.07, G:0.18, T:0.22
Consensus pattern (85 bp):
AATTATAAAGGTAAAAAGTGAAATTGAAAAAAATCAAGAGCCTCAATTATAAAGGTAAAAAAGAA
CTAGAAAAAATAGAGACCTC
Found at i:5305400 original size:44 final size:44
Alignment explanation
Indices: 5305279--5305510 Score: 192
Period size: 44 Copynumber: 5.4 Consensus size: 44
5305269 TTTTTAATTA
* * * * **
5305279 AATTA-AAAGGTAGAAAGTGGGAA-TGAAAAAACTCAGGGGTCTC
1 AATTATAAAGGTAAAAAGT-GAAATTGAAAAAAATTAGGGACCTC
** * *
5305322 AATTATAAAGGTAAAAAGTGAGGTTTAAAAAAATTAGGGATCTC
1 AATTATAAAGGTAAAAAGTGAAATTGAAAAAAATTAGGGACCTC
* *
5305366 AATTATAAAGGTAAAAAGTGAAATTGAAAAAAATTA-AGAGCCTT
1 AATTATAAAGGTAAAAAGTGAAATTGAAAAAAATTAGGGA-CCTC
* * * * *
5305410 ACTTATAAAGGTAAAAA-AGAACTAG-AAAAAA-TAGAGACCTC
1 AATTATAAAGGTAAAAAGTGAAATTGAAAAAAATTAGGGACCTC
* *
5305451 AATTACT-AAGATAAAAAGTGAAATTGAAAAAAATTA-GGACATC
1 AATTA-TAAAGGTAAAAAGTGAAATTGAAAAAAATTAGGGACCTC
* *
5305494 AATAATAAAAGTAAAAA
1 AATTATAAAGGTAAAAA
5305511 TAAGACTAAA
Statistics
Matches: 151, Mismatches: 29, Indels: 18
0.76 0.15 0.09
Matches are distributed among these distances:
41 18 0.12
42 16 0.11
43 36 0.24
44 81 0.54
ACGTcount: A:0.53, C:0.07, G:0.18, T:0.22
Consensus pattern (44 bp):
AATTATAAAGGTAAAAAGTGAAATTGAAAAAAATTAGGGACCTC
Found at i:5305480 original size:42 final size:43
Alignment explanation
Indices: 5305319--5305550 Score: 178
Period size: 44 Copynumber: 5.5 Consensus size: 43
5305309 ACTCAGGGGT
** * * *
5305319 CTCAATTATAAAGGTAAAAAGTGAGGTTTAAAAAAATTAGGGAT
1 CTCAATTATAAAGGTAAAAAGTGA-AATTGAAAAAATTAGAGAC
5305363 CTCAATTATAAAGGTAAAAAGTGAAATTGAAAAAAATTA-AGAGC
1 CTCAATTATAAAGGTAAAAAGTGAAATTG-AAAAAATTAGAGA-C
* * * * *
5305407 CTTACTTATAAAGGTAAAAA-AGAACTAGAAAAAA-TAGAGAC
1 CTCAATTATAAAGGTAAAAAGTGAAATTGAAAAAATTAGAGAC
*
5305448 CTCAATTACT-AAGATAAAAAGTGAAATTGAAAAAAATTAG-GAC
1 CTCAATTA-TAAAGGTAAAAAGTGAAATTG-AAAAAATTAGAGAC
* * * * *
5305491 ATCAATAATAAAAGTAAAAA-T-AAGACT-AAAAAATT-GA-AA
1 CTCAATTATAAAGGTAAAAAGTGAA-ATTGAAAAAATTAGAGAC
*
5305530 CTCTAATTATAAAGATAAAAA
1 CTC-AATTATAAAGGTAAAAA
5305551 AATAAAGACC
Statistics
Matches: 151, Mismatches: 26, Indels: 26
0.74 0.13 0.13
Matches are distributed among these distances:
39 4 0.03
40 22 0.15
41 20 0.13
42 19 0.13
43 32 0.21
44 54 0.36
ACGTcount: A:0.56, C:0.07, G:0.14, T:0.23
Consensus pattern (43 bp):
CTCAATTATAAAGGTAAAAAGTGAAATTGAAAAAATTAGAGAC
Found at i:5305545 original size:83 final size:84
Alignment explanation
Indices: 5305363--5305550 Score: 215
Period size: 85 Copynumber: 2.2 Consensus size: 84
5305353 AATTAGGGAT
* * * * * *
5305363 CTCAATTATAAAGGTAAAAAGTGAAATTGAAAAAAATTAAGAGCCTTACTTATAAAGGTAAAAAA
1 CTCAATTATAAAGATAAAAAGTGAAATTGAAAAAAATTAAGAGCATCAATAATAAAAGTAAAAAA
*
5305428 GAACTAGAAAAAATAGAGAC
66 GAACTA-AAAAAATAGAAAC
*
5305448 CTCAATTACT-AAGATAAAAAGTGAAATTGAAAAAAATTAGGA-CATCAATAATAAAAGTAAAAA
1 CTCAATTA-TAAAGATAAAAAGTGAAATTGAAAAAAATTAAGAGCATCAATAATAAAAGTAAAAA
*
5305511 TA-AGACT-AAAAAATTGAAA-
65 -AGA-ACTAAAAAAATAGAAAC
5305530 CTCTAATTATAAAGATAAAAA
1 CTC-AATTATAAAGATAAAAA
5305551 AATAAAGACC
Statistics
Matches: 89, Mismatches: 9, Indels: 12
0.81 0.08 0.11
Matches are distributed among these distances:
82 4 0.04
83 25 0.28
84 17 0.19
85 42 0.47
86 1 0.01
ACGTcount: A:0.57, C:0.08, G:0.12, T:0.22
Consensus pattern (84 bp):
CTCAATTATAAAGATAAAAAGTGAAATTGAAAAAAATTAAGAGCATCAATAATAAAAGTAAAAAA
GAACTAAAAAAATAGAAAC
Found at i:5311539 original size:47 final size:46
Alignment explanation
Indices: 5311443--5311540 Score: 126
Period size: 47 Copynumber: 2.1 Consensus size: 46
5311433 CACGTAGGGG
* *
5311443 TATAGCACGGGGTAGGGGCCGCGCCTTACCTTTAATTCTGATTTATA
1 TATAGCACGGGGTAGGGGCCGCGCCATACCTTTAA-TCTGATTAATA
* *
5311490 TATAGCGCGGGGTAGGGGTCGCGCCATACCTTTAA-CTGATATAATTA
1 TATAGCACGGGGTAGGGGCCGCGCCATACCTTTAATCTGAT-TAA-TA
5311537 TATA
1 TATA
5311541 AGGCGCGGTA
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
45 5 0.11
46 2 0.04
47 38 0.84
ACGTcount: A:0.24, C:0.19, G:0.26, T:0.31
Consensus pattern (46 bp):
TATAGCACGGGGTAGGGGCCGCGCCATACCTTTAATCTGATTAATA
Found at i:5315801 original size:27 final size:27
Alignment explanation
Indices: 5315731--5315801 Score: 79
Period size: 27 Copynumber: 2.6 Consensus size: 27
5315721 AGGTGATGGT
** * *
5315731 GGCGGCGACGGTATCAGGTAAGGGAAT
1 GGCGGCGACGACATCATGTAAGGGAAA
* * *
5315758 GACGGCAACGACATCATGTAATGGAAA
1 GGCGGCGACGACATCATGTAAGGGAAA
5315785 GGCGGCGACGACATCAT
1 GGCGGCGACGACATCAT
5315802 ATATGGCTGT
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.31, C:0.20, G:0.35, T:0.14
Consensus pattern (27 bp):
GGCGGCGACGACATCATGTAAGGGAAA
Found at i:5317507 original size:9 final size:9
Alignment explanation
Indices: 5317495--5317528 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
5317485 TAAGTAAAAT
5317495 ATTAAATAA
1 ATTAAATAA
5317504 ATTAAAT-A
1 ATTAAATAA
*
5317512 CTTAAATAA
1 ATTAAATAA
5317521 ATTAAATA
1 ATTAAATA
5317529 CAAAATATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
8 7 0.32
9 15 0.68
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (9 bp):
ATTAAATAA
Found at i:5317527 original size:17 final size:17
Alignment explanation
Indices: 5317480--5317529 Score: 75
Period size: 17 Copynumber: 3.0 Consensus size: 17
5317470 TGCAAAAAAT
* *
5317480 TTAAATAAGTAAAATA-
1 TTAAATAAATTAAATAC
5317496 TTAAATAAATTAAATAC
1 TTAAATAAATTAAATAC
5317513 TTAAATAAATTAAATAC
1 TTAAATAAATTAAATAC
5317530 AAAATATTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
16 14 0.45
17 17 0.55
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.34
Consensus pattern (17 bp):
TTAAATAAATTAAATAC
Found at i:5319368 original size:60 final size:60
Alignment explanation
Indices: 5319293--5319429 Score: 247
Period size: 60 Copynumber: 2.3 Consensus size: 60
5319283 TATCTTGAAT
*
5319293 TAGTACATAGTGATGATGAGTAATTCTTCTCTTCGGTAAGTGAACAAATGTTGAACTTTC
1 TAGTACATAGTGATGATGAGTAATTCTTCTCTTCGGTAAGTGAAAAAATGTTGAACTTTC
* *
5319353 TATTACATAGTGATGATGAGTAATTCTTCTCTTTGGTAAGTGAAAAAATGTTGAACTTTC
1 TAGTACATAGTGATGATGAGTAATTCTTCTCTTCGGTAAGTGAAAAAATGTTGAACTTTC
5319413 TAGTACATAGTGATGAT
1 TAGTACATAGTGATGAT
5319430 TATGGTGAAT
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
60 73 1.00
ACGTcount: A:0.31, C:0.11, G:0.20, T:0.38
Consensus pattern (60 bp):
TAGTACATAGTGATGATGAGTAATTCTTCTCTTCGGTAAGTGAAAAAATGTTGAACTTTC
Found at i:5321021 original size:312 final size:312
Alignment explanation
Indices: 5320508--5321122 Score: 986
Period size: 312 Copynumber: 2.0 Consensus size: 312
5320498 TGTTTCGTCC
* * *
5320508 ATAATTATTCACGACTTTTTTTCTTTCAAAAGAAATTTTTGTTTTCCTAATTCTTCATAAGAAGC
1 ATAATTATTCACGACTTTTTCTCATTCAAAAGAAATTTTAGTTTTCCTAATTCTTCATAAGAAGC
* * *
5320573 ATTTAAGAAATTATGAATATTATGAAAGTTTTTTAGGAGTTTTCAACTTTTCTAACAATAAGCAA
66 ATTTAAGAAATTATGAATATTATGAAAGTTTATTAGGAGATTTCAACTTTTCTAACAACAAGCAA
* * * *
5320638 AATATCTCAAGTTTATTACAAGATATTTCAATATAACTCTCGAGATAGATCACCTTTTTTCTTTA
131 AATATCTCAAATTTATTACAAGAAACTTCAATATAACTCTCGAGATAGATCACCTCTTTTCTTTA
* * * *
5320703 CTCTACTTAGGGGGGAA-ATTCAAAGAGATTTAATAGCTACAAGAATCTTTTACTAACACTAATG
196 CTCTACTCA-GGGGAAAGATTCAAAGAGATTTAATAGCTACAAGAATCTATTACTAACACTAACG
5320767 TATATCATATTCTTATTCATAATATTCAACATATTAGC-CTAAAGCGGACATCA
260 TATATCATATTCTTATTCATAATATTCAACATATTA-CACTAAAGCGGACATCA
*
5320820 ATAATTATTCATGACTTTTTCTCATTCAAAATG-AATTTTAGTTTTCCTAATTCTTCATAAGAAG
1 ATAATTATTCACGACTTTTTCTCATTCAAAA-GAAATTTTAGTTTTCCTAATTCTTCATAAGAAG
*
5320884 CATTTAAGAAATTATGAATATTATGAAAGTTTATTAGGAGATTTCAACTTTTCTAACAACATG-A
65 CATTTAAGAAATTATGAATATTATGAAAGTTTATTAGGAGATTTCAACTTTTCTAACAACAAGCA
*
5320948 GAAATATCTCAAATTTATTACAAGAAACTTCAATATAACTCTTGAGATAGATCACCTCTTTTCTT
130 -AAATATCTCAAATTTATTACAAGAAACTTCAATATAACTCTCGAGATAGATCACCTCTTTTCTT
* *
5321013 TTCTCTACTCAGGGGAAAGATTCAAAGAGATTTAATAGCTACAAGAATCTATTAGTAACACTAAC
194 TACTCTACTCAGGGGAAAGATTCAAAGAGATTTAATAGCTACAAGAATCTATTACTAACACTAAC
*
5321078 GTCTATCATATTCTTATTCATAATATTCAACATATTACACTAAAG
259 GTATATCATATTCTTATTCATAATATTCAACATATTACACTAAAG
5321123 AGTCCATCAC
Statistics
Matches: 279, Mismatches: 20, Indels: 8
0.91 0.07 0.03
Matches are distributed among these distances:
311 8 0.03
312 270 0.97
313 1 0.00
ACGTcount: A:0.37, C:0.15, G:0.10, T:0.38
Consensus pattern (312 bp):
ATAATTATTCACGACTTTTTCTCATTCAAAAGAAATTTTAGTTTTCCTAATTCTTCATAAGAAGC
ATTTAAGAAATTATGAATATTATGAAAGTTTATTAGGAGATTTCAACTTTTCTAACAACAAGCAA
AATATCTCAAATTTATTACAAGAAACTTCAATATAACTCTCGAGATAGATCACCTCTTTTCTTTA
CTCTACTCAGGGGAAAGATTCAAAGAGATTTAATAGCTACAAGAATCTATTACTAACACTAACGT
ATATCATATTCTTATTCATAATATTCAACATATTACACTAAAGCGGACATCA
Found at i:5321283 original size:111 final size:111
Alignment explanation
Indices: 5321089--5321310 Score: 444
Period size: 111 Copynumber: 2.0 Consensus size: 111
5321079 TCTATCATAT
5321089 TCTTATTCATAATATTCAACATATTACACTAAAGAGTCCATCACATATTTTATTTATTATGCCTA
1 TCTTATTCATAATATTCAACATATTACACTAAAGAGTCCATCACATATTTTATTTATTATGCCTA
5321154 AATTGGGTATTCTACTCAACCAAATTTGTAACACATAATTCGACCC
66 AATTGGGTATTCTACTCAACCAAATTTGTAACACATAATTCGACCC
5321200 TCTTATTCATAATATTCAACATATTACACTAAAGAGTCCATCACATATTTTATTTATTATGCCTA
1 TCTTATTCATAATATTCAACATATTACACTAAAGAGTCCATCACATATTTTATTTATTATGCCTA
5321265 AATTGGGTATTCTACTCAACCAAATTTGTAACACATAATTCGACCC
66 AATTGGGTATTCTACTCAACCAAATTTGTAACACATAATTCGACCC
5321311 GACTCGAAAC
Statistics
Matches: 111, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
111 111 1.00
ACGTcount: A:0.35, C:0.21, G:0.07, T:0.37
Consensus pattern (111 bp):
TCTTATTCATAATATTCAACATATTACACTAAAGAGTCCATCACATATTTTATTTATTATGCCTA
AATTGGGTATTCTACTCAACCAAATTTGTAACACATAATTCGACCC
Found at i:5335292 original size:18 final size:18
Alignment explanation
Indices: 5335238--5335293 Score: 58
Period size: 23 Copynumber: 2.8 Consensus size: 18
5335228 GCGATACTCT
*
5335238 CTCCCTTGGGTATCGGTA
1 CTCCCTTGGGTATCGATA
5335256 CTCCCCTTCCAGTGGTATCGATA
1 CT-CCCTT---G-GGTATCGATA
5335279 CTCCCTTGGGTATCG
1 CTCCCTTGGGTATCG
5335294 GAACCAAATT
Statistics
Matches: 32, Mismatches: 1, Indels: 10
0.74 0.02 0.23
Matches are distributed among these distances:
18 9 0.28
19 6 0.19
22 6 0.19
23 11 0.34
ACGTcount: A:0.12, C:0.32, G:0.23, T:0.32
Consensus pattern (18 bp):
CTCCCTTGGGTATCGATA
Found at i:5337106 original size:10 final size:10
Alignment explanation
Indices: 5337091--5337157 Score: 53
Period size: 10 Copynumber: 6.0 Consensus size: 10
5337081 AAAATGACTG
5337091 TAAACGAACA
1 TAAACGAACA
5337101 TAAACGTACACAA
1 TAAACG-A-AC-A
*
5337114 TAAACGAGCA
1 TAAACGAACA
*
5337124 TAAACAAACA
1 TAAACGAACA
5337134 TAAATGAACGAACA
1 T--A--AACGAACA
5337148 TAAACGAACA
1 TAAACGAACA
5337158 CAATAAATGA
Statistics
Matches: 46, Mismatches: 4, Indels: 14
0.72 0.06 0.22
Matches are distributed among these distances:
10 24 0.52
11 2 0.04
12 5 0.11
13 7 0.15
14 8 0.17
ACGTcount: A:0.58, C:0.19, G:0.10, T:0.12
Consensus pattern (10 bp):
TAAACGAACA
Found at i:5337117 original size:23 final size:23
Alignment explanation
Indices: 5337091--5337174 Score: 105
Period size: 23 Copynumber: 3.6 Consensus size: 23
5337081 AAAATGACTG
*
5337091 TAAACGAACATAAACGTACACAA
1 TAAACGAACATAAACGAACACAA
* * *
5337114 TAAACGAGCATAAACAAACATAAA
1 TAAACGAACATAAACGAACA-CAA
*
5337138 TGAACGAACATAAACGAACACAA
1 TAAACGAACATAAACGAACACAA
*
5337161 TAAATGAACATAAA
1 TAAACGAACATAAA
5337175 TGAAAATAAT
Statistics
Matches: 50, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
23 31 0.62
24 19 0.38
ACGTcount: A:0.60, C:0.18, G:0.10, T:0.13
Consensus pattern (23 bp):
TAAACGAACATAAACGAACACAA
Found at i:5338850 original size:22 final size:22
Alignment explanation
Indices: 5338825--5338867 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
5338815 GCACTAGGAC
*
5338825 GGAAGTGTCTT-AGCACTGATAT
1 GGAAGTGTATTCA-CACTGATAT
5338847 GGAAGTGTATTCACACTGATA
1 GGAAGTGTATTCACACTGATA
5338868 CTAAAGTGCC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 18 0.95
23 1 0.05
ACGTcount: A:0.30, C:0.14, G:0.26, T:0.30
Consensus pattern (22 bp):
GGAAGTGTATTCACACTGATAT
Found at i:5345539 original size:23 final size:23
Alignment explanation
Indices: 5345498--5345569 Score: 73
Period size: 23 Copynumber: 3.3 Consensus size: 23
5345488 AGAATAATTA
*
5345498 TGTCTTTGTG--ACATGTATCTC
1 TGTCTTTGTGACACATTTATCTC
*
5345519 TGT-TATTGTGGCACATTTATCTC
1 TGTCT-TTGTGACACATTTATCTC
*
5345542 TGTCTTTGTGACAAATTT-TCTC
1 TGTCTTTGTGACACATTTATCTC
5345564 TG-CTTT
1 TGTCTTT
5345570 TTGGTAGTTT
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
20 1 0.02
21 12 0.27
22 6 0.14
23 24 0.55
24 1 0.02
ACGTcount: A:0.15, C:0.18, G:0.17, T:0.50
Consensus pattern (23 bp):
TGTCTTTGTGACACATTTATCTC
Found at i:5346375 original size:21 final size:22
Alignment explanation
Indices: 5346332--5346376 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
5346322 TCGTTTATCT
5346332 TTTTAATTTTAAATAATAAAAA
1 TTTTAATTTTAAATAATAAAAA
*
5346354 TTTT-ATTATTAATTAA-AAAAA
1 TTTTAATT-TTAAATAATAAAAA
5346375 TT
1 TT
5346377 AATTTATTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 10 0.48
22 11 0.52
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
TTTTAATTTTAAATAATAAAAA
Found at i:5347426 original size:7 final size:7
Alignment explanation
Indices: 5347416--5347449 Score: 68
Period size: 7 Copynumber: 4.9 Consensus size: 7
5347406 GTTTAAAAAC
5347416 TTTAACT
1 TTTAACT
5347423 TTTAACT
1 TTTAACT
5347430 TTTAACT
1 TTTAACT
5347437 TTTAACT
1 TTTAACT
5347444 TTTAAC
1 TTTAAC
5347450 AAGTTAATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.29, C:0.15, G:0.00, T:0.56
Consensus pattern (7 bp):
TTTAACT
Found at i:5350199 original size:14 final size:14
Alignment explanation
Indices: 5350180--5350207 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
5350170 ACCAAATGAT
5350180 GCCTCACCATTGTG
1 GCCTCACCATTGTG
5350194 GCCTCACCATTGTG
1 GCCTCACCATTGTG
5350208 TTTACATATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.36, G:0.21, T:0.29
Consensus pattern (14 bp):
GCCTCACCATTGTG
Found at i:5357061 original size:14 final size:14
Alignment explanation
Indices: 5357042--5357078 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
5357032 TGCAATAACC
5357042 AGCATTCAAAACTT
1 AGCATTCAAAACTT
5357056 AGCATTCAAAACTT
1 AGCATTCAAAACTT
5357070 AGCATTCAA
1 AGCATTCAA
5357079 GACCTTTATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.43, C:0.22, G:0.08, T:0.27
Consensus pattern (14 bp):
AGCATTCAAAACTT
Found at i:5365444 original size:156 final size:158
Alignment explanation
Indices: 5365160--5365473 Score: 614
Period size: 156 Copynumber: 2.0 Consensus size: 158
5365150 TTGTTGTAGC
5365160 CCTTCCTGAAAATTTGTTTAGGTGGCTATAGAAATGGTATGAGAGAAAATAGGAGGTGGATAGGG
1 CCTTCCTGAAAATTTGTTTAGGTGGCTATAGAAATGGTATGAGAGAAAATAGGAGGTGGATAGGG
5365225 TTTTTTATGATCCCTAAAGTGTGAAAAGATTTTTATTTATAGCCCATCAAGGTCACCTGTCCACC
66 TTTTTTATGATCCCTAAAGTGTGAAAAGATTTTTATTTATAGCCCATCAAGGTCACCTGTCCACC
5365290 -ATAGGAAAATCCCTC-TTTTAATGATA
131 AATAGGAAAATCCCTCTTTTTAATGATA
5365316 CCTTCCTGAAAATTTGTTTAGGTGGCTATAGAAATGGTATGAGAGAAAATAGGAGGTGGATAGGG
1 CCTTCCTGAAAATTTGTTTAGGTGGCTATAGAAATGGTATGAGAGAAAATAGGAGGTGGATAGGG
5365381 TTTTTTATGATCCCTAAAGTGTGAAAAGATTTTTATTTATAGCCCATCAAGGTCACCTGTCCACC
66 TTTTTTATGATCCCTAAAGTGTGAAAAGATTTTTATTTATAGCCCATCAAGGTCACCTGTCCACC
5365446 AATAGGAAAATCCCTCTTTTTAATGATA
131 AATAGGAAAATCCCTCTTTTTAATGATA
5365474 ACTTTTTAAA
Statistics
Matches: 156, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
156 130 0.83
157 15 0.10
158 11 0.07
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.33
Consensus pattern (158 bp):
CCTTCCTGAAAATTTGTTTAGGTGGCTATAGAAATGGTATGAGAGAAAATAGGAGGTGGATAGGG
TTTTTTATGATCCCTAAAGTGTGAAAAGATTTTTATTTATAGCCCATCAAGGTCACCTGTCCACC
AATAGGAAAATCCCTCTTTTTAATGATA
Found at i:5378493 original size:16 final size:16
Alignment explanation
Indices: 5378472--5378504 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
5378462 CACCCTTTTT
5378472 GATAGAAGAAAAGGGA
1 GATAGAAGAAAAGGGA
5378488 GATAGAAGAAAAGGGA
1 GATAGAAGAAAAGGGA
5378504 G
1 G
5378505 GTGCATTTCG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.55, C:0.00, G:0.39, T:0.06
Consensus pattern (16 bp):
GATAGAAGAAAAGGGA
Found at i:5383581 original size:102 final size:102
Alignment explanation
Indices: 5383346--5383581 Score: 258
Period size: 102 Copynumber: 2.3 Consensus size: 102
5383336 CAGGACGAAC
* * ** * *
5383346 AAGTTGGCATATGAATGTCTTCCCCTTGAACTTGAAGGCATTGTGTCATATGGGTTTTGAACAGA
1 AAGTTGGCAGATGAATGTCTTCCCCTTGAACTTGAAGGCATAGTGTCATATAAGTATTAAACAGA
* * * * *
5383411 TTGTTGTGTAGAATGCATCTCCATATTGAGATCGAAC
66 CTGTTATGTACAATGCATCTCCATATTGAGATCAAAA
* * ** * *
5383448 AAGTTGACAGATGAATGCCTTATCCTGGAACTTGAAGGTATAGTGTCATATAAGTATTAAACAGA
1 AAGTTGGCAGATGAATGTCTTCCCCTTGAACTTGAAGGCATAGTGTCATATAAGTATTAAACAGA
* * * *
5383513 CTGTTATGT-CTATGGCATTTCCATGTTGAGGTCAAAA
66 CTGTTATGTACAAT-GCATCTCCATATTGAGATCAAAA
*
5383550 AAGTTGGCAGATGAATGTTTTCCCCTTGAACT
1 AAGTTGGCAGATGAATGTCTTCCCCTTGAACT
5383582 GAAAGGGATG
Statistics
Matches: 106, Mismatches: 27, Indels: 2
0.79 0.20 0.01
Matches are distributed among these distances:
101 2 0.02
102 104 0.98
ACGTcount: A:0.29, C:0.15, G:0.22, T:0.33
Consensus pattern (102 bp):
AAGTTGGCAGATGAATGTCTTCCCCTTGAACTTGAAGGCATAGTGTCATATAAGTATTAAACAGA
CTGTTATGTACAATGCATCTCCATATTGAGATCAAAA
Found at i:5384661 original size:15 final size:15
Alignment explanation
Indices: 5384641--5384669 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
5384631 TTCAATCTAC
5384641 CGAAAGCCCCAAATG
1 CGAAAGCCCCAAATG
5384656 CGAAAGCCCCAAAT
1 CGAAAGCCCCAAAT
5384670 ACATTTAAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.34, G:0.17, T:0.07
Consensus pattern (15 bp):
CGAAAGCCCCAAATG
Found at i:5385437 original size:14 final size:14
Alignment explanation
Indices: 5385418--5385444 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5385408 GTTCGGTTAT
5385418 GTTCATTTATGTTC
1 GTTCATTTATGTTC
5385432 GTTCATTTATGTT
1 GTTCATTTATGTT
5385445 TAACCTAATA
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:0.15, C:0.11, G:0.15, T:0.59
Consensus pattern (14 bp):
GTTCATTTATGTTC
Found at i:5386550 original size:16 final size:16
Alignment explanation
Indices: 5386525--5386565 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
5386515 CCAACGCTTA
*
5386525 TGTTCGTTTATGTTCG
1 TGTTCATTTATGTTCG
5386541 TGTTCATTTATGTTCG
1 TGTTCATTTATGTTCG
5386557 T-TT-ATTTAT
1 TGTTCATTTAT
5386566 TAAATGATCG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 6 0.25
15 2 0.08
16 16 0.67
ACGTcount: A:0.12, C:0.10, G:0.17, T:0.61
Consensus pattern (16 bp):
TGTTCATTTATGTTCG
Found at i:5389235 original size:10 final size:11
Alignment explanation
Indices: 5389216--5389240 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
5389206 ACCGATATTC
5389216 TTTTCTTTTTT
1 TTTTCTTTTTT
5389227 TTTTCTTTTTT
1 TTTTCTTTTTT
5389238 TTT
1 TTT
5389241 AATAAAAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (11 bp):
TTTTCTTTTTT
Found at i:5389292 original size:23 final size:23
Alignment explanation
Indices: 5389266--5389341 Score: 116
Period size: 23 Copynumber: 3.3 Consensus size: 23
5389256 GTATGTGTTA
5389266 CATGTTTATCTCTGTCTTTGTGG
1 CATGTTTATCTCTGTCTTTGTGG
*
5389289 CATGTTTATCTCTGTCTTTGTGA
1 CATGTTTATCTCTGTCTTTGTGG
** *
5389312 CACATTTATCTCTGTTTTTGTGG
1 CATGTTTATCTCTGTCTTTGTGG
5389335 CATGTTT
1 CATGTTT
5389342 TTCAATTTTT
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.12, C:0.17, G:0.18, T:0.53
Consensus pattern (23 bp):
CATGTTTATCTCTGTCTTTGTGG
Found at i:5389918 original size:53 final size:53
Alignment explanation
Indices: 5389861--5389963 Score: 136
Period size: 53 Copynumber: 1.9 Consensus size: 53
5389851 GTGGACACTG
*
5389861 TCAATAAAATATAT-ATCTAATCAAAGAAAACTCAAATTTCAGAGTAGACACCA
1 TCAATAAAATAAATAAT-TAATCAAAGAAAACTCAAATTTCAGAGTAGACACCA
* * * * *
5389914 TCAATAAAATAAATAATTAATCGAAGAAAATTCGAATTTTAGAGTGGACA
1 TCAATAAAATAAATAATTAATCAAAGAAAACTCAAATTTCAGAGTAGACA
5389964 TGTACTAATG
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
53 41 0.95
54 2 0.05
ACGTcount: A:0.50, C:0.13, G:0.11, T:0.26
Consensus pattern (53 bp):
TCAATAAAATAAATAATTAATCAAAGAAAACTCAAATTTCAGAGTAGACACCA
Found at i:5391331 original size:18 final size:18
Alignment explanation
Indices: 5391308--5391346 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
5391298 GCTCTTAAAA
5391308 TTTAAAATTATTATATAT
1 TTTAAAATTATTATATAT
* * *
5391326 TTTAAATTTTTTATGTAT
1 TTTAAAATTATTATATAT
5391344 TTT
1 TTT
5391347 TTTTAAAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (18 bp):
TTTAAAATTATTATATAT
Found at i:5393359 original size:4 final size:4
Alignment explanation
Indices: 5393350--5393446 Score: 55
Period size: 4 Copynumber: 26.0 Consensus size: 4
5393340 AAATAATTAT
* * * *
5393350 TATA TATA TATA TATA TATG TA-A TAT- TA-A TAAA TTTA -ATT TA-A
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
* * * * * *
5393393 TTTA AATA TATA TATA TATA TATA -ATA TTTA TATA TTTA -ATT TAAA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
5393439 TATA TATA
1 TATA TATA
5393447 CCGGCCCGAT
Statistics
Matches: 67, Mismatches: 19, Indels: 14
0.67 0.19 0.14
Matches are distributed among these distances:
3 12 0.18
4 55 0.82
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (4 bp):
TATA
Found at i:5393361 original size:6 final size:6
Alignment explanation
Indices: 5393350--5393446 Score: 55
Period size: 6 Copynumber: 17.3 Consensus size: 6
5393340 AAATAATTAT
* * * *
5393350 TATATA TATATA TATATA TGTA-A TAT-TA -ATAAA TTTA-A TTTA-A
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
* * * * * *
5393393 TTTAAA TATATA TATATA TATATA -ATATT TATATA TTTA-A TTTAAA
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
5393439 TATATA TA
1 TATATA TA
5393447 CCGGCCCGAT
Statistics
Matches: 74, Mismatches: 11, Indels: 12
0.76 0.11 0.12
Matches are distributed among these distances:
4 2 0.03
5 24 0.32
6 48 0.65
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (6 bp):
TATATA
Found at i:5398271 original size:24 final size:25
Alignment explanation
Indices: 5398241--5398292 Score: 70
Period size: 28 Copynumber: 2.0 Consensus size: 25
5398231 AGTTTGACAG
5398241 TTTTTAT-GTTATATAATCCTCATT
1 TTTTTATAGTTATATAATCCTCATT
5398265 TTTTTATAGAAGTTATATAATCCTCATT
1 TTTTTAT---AGTTATATAATCCTCATT
5398293 CATCATCAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
24 7 0.29
28 17 0.71
ACGTcount: A:0.29, C:0.12, G:0.06, T:0.54
Consensus pattern (25 bp):
TTTTTATAGTTATATAATCCTCATT
Found at i:5400889 original size:14 final size:14
Alignment explanation
Indices: 5400870--5400904 Score: 70
Period size: 14 Copynumber: 2.5 Consensus size: 14
5400860 AGAACCAAAC
5400870 TTTTTCTTTTTATT
1 TTTTTCTTTTTATT
5400884 TTTTTCTTTTTATT
1 TTTTTCTTTTTATT
5400898 TTTTTCT
1 TTTTTCT
5400905 ATAACAGGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.06, C:0.09, G:0.00, T:0.86
Consensus pattern (14 bp):
TTTTTCTTTTTATT
Found at i:5406970 original size:11 final size:10
Alignment explanation
Indices: 5406940--5407060 Score: 71
Period size: 9 Copynumber: 12.2 Consensus size: 10
5406930 AATGAGACAT
5406940 AAAAAAGATAG
1 AAAAAAGA-AG
5406951 AAAAGAAAGAATG
1 -AAA-AAAGAA-G
5406964 AAAAAAG-AG
1 AAAAAAGAAG
5406973 AAAAAAG-AG
1 AAAAAAGAAG
5406982 AAAAAATG--G
1 AAAAAA-GAAG
5406991 -AAAAAGAA-
1 AAAAAAGAAG
* *
5406999 AAGAAATAA-
1 AAAAAAGAAG
*
5407008 AAAACAGAAG
1 AAAAAAGAAG
5407018 AAAAAGAGAA-
1 AAAAA-AGAAG
*
5407028 AAAGAAAAAAG
1 AAA-AAAGAAG
5407039 AAAAAA-AAG
1 AAAAAAGAAG
5407048 AAAAAAAGAAG
1 -AAAAAAGAAG
5407059 AA
1 AA
5407061 CGAAGAAAAT
Statistics
Matches: 90, Mismatches: 7, Indels: 26
0.73 0.06 0.21
Matches are distributed among these distances:
7 1 0.01
8 5 0.06
9 32 0.36
10 23 0.26
11 16 0.18
12 7 0.08
13 6 0.07
ACGTcount: A:0.78, C:0.01, G:0.18, T:0.03
Consensus pattern (10 bp):
AAAAAAGAAG
Found at i:5406976 original size:8 final size:8
Alignment explanation
Indices: 5406965--5407057 Score: 66
Period size: 8 Copynumber: 11.2 Consensus size: 8
5406955 GAAAGAATGA
5406965 AAAAAGAG
1 AAAAAGAG
5406973 AAAAAAGAG
1 -AAAAAGAG
5406982 AAAAA-ATGG
1 AAAAAGA--G
*
5406991 AAAAAGAA
1 AAAAAGAG
* *
5406999 AAGAAATAA
1 AA-AAAGAG
5407008 AAAACAGAAG
1 AAAA-AG-AG
5407018 AAAAAGAG
1 AAAAAGAG
5407026 AAAAAGA-
1 AAAAAGAG
5407033 AAAAAGA-
1 AAAAAGAG
*
5407040 AAAAAAAG
1 AAAAAGAG
*
5407048 AAAAAAAG
1 AAAAAGAG
5407056 AA
1 AA
5407058 GAACGAAGAA
Statistics
Matches: 72, Mismatches: 5, Indels: 15
0.78 0.05 0.16
Matches are distributed among these distances:
7 14 0.19
8 28 0.39
9 24 0.33
10 6 0.08
ACGTcount: A:0.80, C:0.01, G:0.17, T:0.02
Consensus pattern (8 bp):
AAAAAGAG
Found at i:5406987 original size:42 final size:42
Alignment explanation
Indices: 5406940--5407069 Score: 103
Period size: 41 Copynumber: 3.1 Consensus size: 42
5406930 AATGAGACAT
*
5406940 AAAAAAGATAGAAAAGAAAG-AATGAAAAA-AG-AGAAAAAAG
1 AAAAAAGATAGAAAAGAAAGAAATAAAAAACAGAAG-AAAAAG
*
5406980 AGAAAAA-ATGGAAAAAGAAAAGAAATAAAAAACAGAAGAAAAAG
1 A-AAAAAGATAG-AAAAG-AAAGAAATAAAAAACAGAAGAAAAAG
* * *
5407024 AGAAAAAGA-A-AAAAGAAA-AAAAAGAAAAAAAGAAGAACGAAG
1 A-AAAAAGATAGAAAAGAAAGAAATA-AAAAACAGAAGAA-AAAG
5407066 AAAA
1 AAAA
5407070 TAGACAGATC
Statistics
Matches: 75, Mismatches: 6, Indels: 17
0.77 0.06 0.17
Matches are distributed among these distances:
40 8 0.11
41 28 0.37
42 13 0.17
43 8 0.11
44 15 0.20
45 3 0.04
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.03
Consensus pattern (42 bp):
AAAAAAGATAGAAAAGAAAGAAATAAAAAACAGAAGAAAAAG
Found at i:5407027 original size:24 final size:24
Alignment explanation
Indices: 5407000--5407069 Score: 81
Period size: 24 Copynumber: 2.9 Consensus size: 24
5406990 GAAAAAGAAA
5407000 AGAAATAA-AAAACAGAAGAAAAAG
1 AGAAA-AAGAAAACAGAAGAAAAAG
* *
5407024 AGAAAAAGAAAAAAGAAAAAAAAG
1 AGAAAAAGAAAACAGAAGAAAAAG
*
5407048 AAAAAAAGAAGAAC-GAAGAAAA
1 AGAAAAAGAA-AACAGAAGAAAA
5407070 TAGACAGATC
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
23 2 0.05
24 35 0.90
25 2 0.05
ACGTcount: A:0.79, C:0.03, G:0.17, T:0.01
Consensus pattern (24 bp):
AGAAAAAGAAAACAGAAGAAAAAG
Found at i:5407033 original size:30 final size:30
Alignment explanation
Indices: 5406949--5407057 Score: 91
Period size: 30 Copynumber: 3.7 Consensus size: 30
5406939 TAAAAAAGAT
* ** *
5406949 AGAAAAGAAAGAATGAAA-AAAGAGAAAAA
1 AGAAAAAAAAGAAAAAAAGAAAAAGAAAAA
* *
5406978 AGAGAAAAAATG-GAAAAAG-AAAAGAAATAA
1 AGA-AAAAAAAGAAAAAAAGAAAAAGAAA-AA
* * *
5407008 A-AAACAGAAGAAAAAGAGAAAAAGAAAAA
1 AGAAAAAAAAGAAAAAAAGAAAAAGAAAAA
5407037 AGAAAAAAAAGAAAAAAAGAA
1 AGAAAAAAAAGAAAAAAAGAA
5407058 GAACGAAGAA
Statistics
Matches: 60, Mismatches: 14, Indels: 11
0.71 0.16 0.13
Matches are distributed among these distances:
28 5 0.08
29 22 0.37
30 33 0.55
ACGTcount: A:0.78, C:0.01, G:0.18, T:0.03
Consensus pattern (30 bp):
AGAAAAAAAAGAAAAAAAGAAAAAGAAAAA
Found at i:5408063 original size:2 final size:2
Alignment explanation
Indices: 5408056--5408099 Score: 56
Period size: 2 Copynumber: 23.0 Consensus size: 2
5408046 ATTTTGTTTT
* *
5408056 TA TA TA TA TA TA TT TA T- TA TT TA T- TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5408096 TA TA
1 TA TA
5408100 ATTTTTGAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
1 2 0.06
2 34 0.94
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (2 bp):
TA
Found at i:5408161 original size:36 final size:35
Alignment explanation
Indices: 5408087--5408186 Score: 92
Period size: 40 Copynumber: 2.7 Consensus size: 35
5408077 TATTATATAT
** *
5408087 ATATATATATATAATTTTTGAAAATGTTTTTGACAAA
1 ATATA-ATATATAATTTTTGAAAAAATTTTCGA-AAA
5408124 ATATAATATATAATTTTTAGAAAACAATTTTCGAAAA
1 ATATAATATATAATTTTT-GAAAA-AATTTTCGAAAA
* *
5408161 TGTATATATTATATAGTTTTTGAAAA
1 ---ATATAATATATAATTTTTGAAAA
5408187 TGGTTTTATA
Statistics
Matches: 53, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
36 13 0.25
37 13 0.25
38 6 0.11
39 5 0.09
40 16 0.30
ACGTcount: A:0.45, C:0.03, G:0.08, T:0.44
Consensus pattern (35 bp):
ATATAATATATAATTTTTGAAAAAATTTTCGAAAA
Found at i:5408204 original size:70 final size:67
Alignment explanation
Indices: 5408124--5408401 Score: 199
Period size: 68 Copynumber: 3.9 Consensus size: 67
5408114 TTTTGACAAA
* *
5408124 ATATAATATATAATTTTT-AGAAAACAATTTTCGAAAATGTATATATTATATAGTTTTTGAAAAT
1 ATATAATATAT-ATTTTTGA-AAAAC-ATTTT-GAAAATATATATATTATATAGTTTTTAAAAAT
5408188 GGTTTT
62 GGTTTT
5408194 ATATAATATATATTTTTGAAAAATCATTTTGAAAATATATATATTATATAGTTTTTAAAAAAACA
1 ATATAATATATATTTTTGAAAAA-CATTTTGAAAATATATATATTATATAGTTTTT---AAAA-A
**
5408259 TTTTTTT
61 TGGTTTT
* *
5408266 AAAAAACTTATATAATATATAGTTTTT-TAAAACATTTTGAAAATATATATATTATATACTTTTT
1 -----A--TATA--ATATATA-TTTTTGAAAAACATTTTGAAAATATATATATTATATAGTTTTT
***
5408330 AAAAAAACATTTT
56 -AAAAATGGTTTT
* * *
5408343 -TA-AAAACTTATAGTTTTT--AAAATATTTTGGAAATATATATATTATATAGTTTTTAAAAA
1 ATATAATA--TATA-TTTTTGAAAAACATTTTGAAAATATATATATTATATAGTTTTTAAAAA
5408402 ATCAGGTTTT
Statistics
Matches: 177, Mismatches: 13, Indels: 40
0.77 0.06 0.17
Matches are distributed among these distances:
66 7 0.04
67 33 0.19
68 36 0.20
69 17 0.10
70 13 0.07
71 3 0.02
72 6 0.03
77 6 0.03
78 5 0.03
79 4 0.02
80 31 0.18
81 11 0.06
82 5 0.03
ACGTcount: A:0.45, C:0.03, G:0.06, T:0.46
Consensus pattern (67 bp):
ATATAATATATATTTTTGAAAAACATTTTGAAAATATATATATTATATAGTTTTTAAAAATGGTT
TT
Found at i:5408235 original size:68 final size:71
Alignment explanation
Indices: 5408083--5408254 Score: 201
Period size: 68 Copynumber: 2.4 Consensus size: 71
5408073 TATTTATTAT
* *
5408083 ATATATATATATATATAATTTTTGAAAATGTTTTTGACAAAATATAATATATAATTTTTAGAAAA
1 ATATATATAT-TATATAGTTTTTGAAAATGGTTTT-----AATATAATATATAATTTTTAGAAAA
5408148 CAATTTTCGAAA
60 CAATTTTCGAAA
*
5408160 ATGTATATATTATATAGTTTTTGAAAATGGTTTT-ATATAATATAT-ATTTTT-GAAAA-ATCAT
1 ATATATATATTATATAGTTTTTGAAAATGGTTTTAATATAATATATAATTTTTAGAAAACA--AT
5408221 TTT-GAAA
64 TTTCGAAA
*
5408228 ATATATATATTATATAGTTTTTAAAAA
1 ATATATATATTATATAGTTTTTGAAAA
5408255 AACATTTTTT
Statistics
Matches: 88, Mismatches: 5, Indels: 13
0.83 0.05 0.12
Matches are distributed among these distances:
67 1 0.01
68 34 0.39
69 11 0.12
70 11 0.12
76 22 0.25
77 9 0.10
ACGTcount: A:0.44, C:0.02, G:0.08, T:0.46
Consensus pattern (71 bp):
ATATATATATTATATAGTTTTTGAAAATGGTTTTAATATAATATATAATTTTTAGAAAACAATTT
TCGAAA
Found at i:5408261 original size:39 final size:39
Alignment explanation
Indices: 5408193--5408569 Score: 210
Period size: 39 Copynumber: 10.1 Consensus size: 39
5408183 AAAATGGTTT
* *
5408193 TATATAATATATA-TTTTTGAAAAATCATTTTGAAAATA
1 TATATAATATATAGTTTTTAAAAAAACATTTTGAAAATA
* * *
5408231 TATATATTATATAGTTTTTAAAAAAACATTTTTTTAAAAAA
1 TATATAATATATAGTTTTTAAAAAAACA--TTTTGAAAATA
*
5408272 CTTATATAATATATAGTTTTT--TAAAACATTTTGAAAATA
1 --TATATAATATATAGTTTTTAAAAAAACATTTTGAAAATA
* *
5408311 TATATATTATATACTTTTTAAAAAAACATTTT-----TA
1 TATATAATATATAGTTTTTAAAAAAACATTTTGAAAATA
* *
5408345 -A-A-AACT-TATAGTTTTT---AAAATATTTTGGAAATA
1 TATATAA-TATATAGTTTTTAAAAAAACATTTTGAAAATA
* *
5408378 TATATATTATATAGTTTTTAAAAAATCAGGTTTTGAAAACATA
1 TATATAATATATAGTTTTTAAAAAAACA--TTTTG-AAA-ATA
* **
5408421 TATATAATATATAATTTTT-TCAAAACATTTTG-AAATCA
1 TATATAATATATAGTTTTTAAAAAAACATTTTGAAAAT-A
* *
5408459 TATA-AA-ATA-AG-TTTT--GAAAACATTTT-TAAA-A
1 TATATAATATATAGTTTTTAAAAAAACATTTTGAAAATA
*
5408490 TATAT-A-ATATAG-TTTT-CAAAAACATTTTGGAAAATA
1 TATATAATATATAGTTTTTAAAAAAACATTTT-GAAAATA
5408526 TAT-T-ATATA-A-TTTTTAAAGGAAAAAACATTTTTGAAAAT-
1 TATATAATATATAGTTTTT--A--AAAAAACA-TTTTGAAAATA
5408565 TATAT
1 TATAT
5408570 TATTTTTATT
Statistics
Matches: 269, Mismatches: 29, Indels: 80
0.71 0.08 0.21
Matches are distributed among these distances:
28 9 0.03
31 19 0.07
32 8 0.03
33 26 0.10
34 7 0.03
35 13 0.05
36 21 0.08
37 21 0.08
38 19 0.07
39 38 0.14
40 19 0.07
41 24 0.09
42 7 0.03
43 38 0.14
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.44
Consensus pattern (39 bp):
TATATAATATATAGTTTTTAAAAAAACATTTTGAAAATA
Found at i:5408298 original size:41 final size:39
Alignment explanation
Indices: 5408192--5408354 Score: 120
Period size: 37 Copynumber: 4.1 Consensus size: 39
5408182 GAAAATGGTT
* ** *
5408192 TTATATAATATATA-TTTTTGAAAA-ATCATTTTGAAAA
1 TTATATAATATATAGTTTTTAAAAACATTTTTTTAAAAA
*
5408229 TATATATATTATATAGTTTTTAAAAAAACATTTTTTTAAAAAA
1 T-TATATAATATATAGTTTTT--AAAAACATTTTTTT-AAAAA
* *
5408272 CTTATATAATATATAGTTTTTTAAAACA---TTTTGAAAA
1 -TTATATAATATATAGTTTTTAAAAACATTTTTTTAAAAA
* * * **
5408309 TATATATATTATATACTTTTTAAAAAAACATTTTTAAAAA
1 T-TATATAATATATAGTTTTTAAAAACATTTTTTTAAAAA
5408349 CTTATA
1 -TTATA
5408355 GTTTTTAAAA
Statistics
Matches: 101, Mismatches: 13, Indels: 21
0.75 0.10 0.16
Matches are distributed among these distances:
36 1 0.01
37 27 0.27
38 16 0.16
39 5 0.05
40 12 0.12
41 11 0.11
42 6 0.06
43 22 0.22
44 1 0.01
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.46
Consensus pattern (39 bp):
TTATATAATATATAGTTTTTAAAAACATTTTTTTAAAAA
Found at i:5408312 original size:80 final size:78
Alignment explanation
Indices: 5408192--5408543 Score: 296
Period size: 67 Copynumber: 4.8 Consensus size: 78
5408182 GAAAATGGTT
*
5408192 TTATATAATATATA-TTTTTGAAAAATCATTTTGAAAATATATATATTATATAGTTTTTAAAAAA
1 TTATATAATATATAGTTTTT-TAAAA-CATTTTGAAAATATATATATTATATAGTTTTTAAAAAA
5408256 ACATTTTTTTAAAAAAC
64 ACA--TTTTTAAAAAAC
*
5408273 TTATATAATATATAGTTTTTTAAAACATTTTGAAAATATATATATTATATACTTTTTAAAAAAAC
1 TTATATAATATATAGTTTTTTAAAACATTTTGAAAATATATATATTATATAGTTTTTAAAAAAAC
5408338 ATTTTT-AAAAAC
66 ATTTTTAAAAAAC
* * *
5408350 --------T-TATAG-TTTTTAAAATATTTTGGAAATATATATATTATATAGTTTTTAAAAAATC
1 TTATATAATATATAGTTTTTTAAAACATTTTGAAAATATATATATTATATAGTTTTTAAAAAAAC
* *
5408405 AGGTTTT-GAAAAC
66 A-TTTTTAAAAAAC
* * *
5408418 ATATATATAATATATAATTTTTTCAAAACATTTTG-AAATCATATA-A-AATA-AG-TTTT--GA
1 -T-TATATAATATATAGTTTTTT-AAAACATTTTGAAAAT-ATATATATTATATAGTTTTTAAAA
5408476 AAACATTTTT--AAAA-
62 AAACATTTTTAAAAAAC
**
5408490 -TATAT-A-ATATAGTTTTCAAAAACATTTTGGAAAATATAT-TA-TATA-A-TTTTTAAA
1 TTATATAATATATAGTTTTTTAAAACATTTT-GAAAATATATATATTATATAGTTTTTAAA
5408544 GGAAAAAACA
Statistics
Matches: 230, Mismatches: 19, Indels: 56
0.75 0.06 0.18
Matches are distributed among these distances:
66 10 0.04
67 69 0.30
68 19 0.08
69 6 0.03
73 4 0.02
74 4 0.02
75 5 0.02
77 10 0.04
78 8 0.03
79 7 0.03
80 50 0.22
81 33 0.14
82 5 0.02
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.45
Consensus pattern (78 bp):
TTATATAATATATAGTTTTTTAAAACATTTTGAAAATATATATATTATATAGTTTTTAAAAAAAC
ATTTTTAAAAAAC
Found at i:5408395 original size:147 final size:147
Alignment explanation
Indices: 5408124--5408543 Score: 404
Period size: 147 Copynumber: 2.9 Consensus size: 147
5408114 TTTTGACAAA
* * * * **
5408124 ATATAATATATAATTTTTAGAAAACAATTTTCGAAAATGTATATATTATATAGTTTTTGAAAATG
1 ATATAATATATAATTTTT-TAAAAC-ATTTT-GAAAATATATATATTATATACTTTTTAAAAACA
*
5408189 GTTTTATATAATATATATTTTTGAAAAATCATTTTGAAAATATATATATTATATAGTTTTTAAAA
63 GTTTTATAAAATATATATTTTT-AAAAATCATTTTGAAAATATATATATTATATAGTTTTTAAAA
** *
5408254 AAACATTTTTTTAAAAAACT-T
127 AAACAGGTTTTGAAAAAA-TAT
* *
5408275 ATATAATATATAGTTTTTTAAAACATTTTGAAAATATATATATTATATACTTTTTAAAAAAACAT
1 ATATAATATATAATTTTTTAAAACATTTTGAAAATATATATATTATATACTTTTT--AAAAACAG
*
5408340 TTTTA-AAAACT-TATAGTTTTT-AAAAT-ATTTTGGAAATATATATATTATATAGTTTTTAAAA
64 TTTTATAAAA-TATATA-TTTTTAAAAATCATTTTGAAAATATATATATTATATAGTTTTTAAAA
* *
5408401 AATCAGGTTTTGAAAACATAT
127 AAACAGGTTTTGAAAAAATAT
** * *
5408422 ATATAATATATAATTTTTTCAAAACATTTTG-AAATCATATA-A--A-ATAAGTTTTGAAAACAT
1 ATATAATATATAATTTTTT-AAAACATTTTGAAAAT-ATATATATTATATACTTTTTAAAAACAG
5408482 TTTTA-AAATATATAATATAGTTTTCAAAAA-CATTTTGGAAAATATAT-TA-TATA-A-TTTTT
64 TTTTATAAA-ATAT-ATAT--TTTT-AAAAATCATTTT-GAAAATATATATATTATATAGTTTTT
5408541 AAA
123 AAA
5408544 GGAAAAAACA
Statistics
Matches: 233, Mismatches: 20, Indels: 39
0.80 0.07 0.13
Matches are distributed among these distances:
142 16 0.07
143 3 0.01
144 18 0.08
145 6 0.03
146 5 0.02
147 82 0.35
148 54 0.23
149 12 0.05
150 20 0.09
151 17 0.07
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.45
Consensus pattern (147 bp):
ATATAATATATAATTTTTTAAAACATTTTGAAAATATATATATTATATACTTTTTAAAAACAGTT
TTATAAAATATATATTTTTAAAAATCATTTTGAAAATATATATATTATATAGTTTTTAAAAAAAC
AGGTTTTGAAAAAATAT
Found at i:5408527 original size:32 final size:31
Alignment explanation
Indices: 5408426--5408539 Score: 108
Period size: 34 Copynumber: 3.6 Consensus size: 31
5408416 ACATATATAT
5408426 AATATATAAT-T--TTTTCAAAACATTTTGA
1 AATATATAATATAGTTTTCAAAACATTTTGA
* * *
5408454 AATCATATAAAATAAGTTTTGAAAACATTTTTAA
1 AAT-ATATAATAT-AGTTTTCAAAACA-TTTTGA
5408488 AATATATAATATAGTTTTCAAAAACATTTTGGAA
1 AATATATAATATAGTTTTC-AAAACATTTT-G-A
* *
5408522 AATATATTATATAATTTT
1 AATATATAATATAGTTTT
5408540 TAAAGGAAAA
Statistics
Matches: 69, Mismatches: 8, Indels: 12
0.78 0.09 0.13
Matches are distributed among these distances:
28 3 0.04
29 6 0.09
30 1 0.01
32 10 0.14
33 24 0.35
34 25 0.36
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.43
Consensus pattern (31 bp):
AATATATAATATAGTTTTCAAAACATTTTGA
Found at i:5408534 original size:34 final size:32
Alignment explanation
Indices: 5408426--5408539 Score: 119
Period size: 33 Copynumber: 3.6 Consensus size: 32
5408416 ACATATATAT
5408426 AATATATAAT-T--TTTTCAAAACATTTTG-A
1 AATATATAATATAGTTTTCAAAACATTTTGAA
* * *
5408454 AATCATATAAAATAAGTTTTGAAAACATTTTTAA
1 AAT-ATATAATAT-AGTTTTCAAAACATTTTGAA
5408488 AATATATAATATAGTTTTCAAAAACATTTTGGAA
1 AATATATAATATAGTTTTC-AAAACATTTT-GAA
* *
5408522 AATATATTATATAATTTT
1 AATATATAATATAGTTTT
5408540 TAAAGGAAAA
Statistics
Matches: 70, Mismatches: 8, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
28 3 0.04
29 6 0.09
30 1 0.01
32 6 0.09
33 32 0.46
34 22 0.31
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.43
Consensus pattern (32 bp):
AATATATAATATAGTTTTCAAAACATTTTGAA
Done.