Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr7
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: 55462051
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2780933 characters in sequence are not A, C, G, or T
File 144 of 163
Found at i:47328716 original size:7 final size:8
Alignment explanation
Indices: 47328692--47328724 Score: 57
Period size: 8 Copynumber: 4.0 Consensus size: 8
47328682 TTTAAATATA
47328692 TTAATTTTT
1 TTAA-TTTT
47328701 TTAATTTT
1 TTAATTTT
47328709 TTAATTTT
1 TTAATTTT
47328717 TTAATTTT
1 TTAATTTT
47328725 AATCTTTCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 20 0.83
9 4 0.17
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (8 bp):
TTAATTTT
Found at i:47331860 original size:16 final size:16
Alignment explanation
Indices: 47331839--47331878 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
47331829 CGTTTGGTTC
47331839 GCTGTAATGGAATAGA
1 GCTGTAATGGAATAGA
*
47331855 GCTGTAACGGAATAGA
1 GCTGTAATGGAATAGA
*
47331871 GTTGTAAT
1 GCTGTAAT
47331879 TCAATTGTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.35, C:0.07, G:0.30, T:0.28
Consensus pattern (16 bp):
GCTGTAATGGAATAGA
Found at i:47333201 original size:52 final size:53
Alignment explanation
Indices: 47333098--47333203 Score: 187
Period size: 52 Copynumber: 2.0 Consensus size: 53
47333088 ATATGTATGG
*
47333098 TAGTTTTTGTGTATATCTCTTTCTTTTTTAATTAGGAGATTAGATGCTAAAGT
1 TAGTTTTTGTGTATATATCTTTCTTTTTTAATTAGGAGATTAGATGCTAAAGT
*
47333151 TAGTTTTTGTGTATATATCTTTC-TTTTTAATTAGGAGATTAGATGTTAAAGT
1 TAGTTTTTGTGTATATATCTTTCTTTTTTAATTAGGAGATTAGATGCTAAAGT
47333203 T
1 T
47333204 TAGGAGATAA
Statistics
Matches: 51, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
52 29 0.57
53 22 0.43
ACGTcount: A:0.25, C:0.06, G:0.17, T:0.52
Consensus pattern (53 bp):
TAGTTTTTGTGTATATATCTTTCTTTTTTAATTAGGAGATTAGATGCTAAAGT
Found at i:47337778 original size:52 final size:53
Alignment explanation
Indices: 47337676--47337781 Score: 205
Period size: 52 Copynumber: 2.0 Consensus size: 53
47337666 ATATGTATGG
47337676 TAGTTTTTGTGTATATCTCTTTCTTTTTTAATTAGGAGATTAGATGCTAAAGT
1 TAGTTTTTGTGTATATCTCTTTCTTTTTTAATTAGGAGATTAGATGCTAAAGT
47337729 TAGTTTTTGTGTATATCTCTTTC-TTTTTAATTAGGAGATTAGATGCTAAAGT
1 TAGTTTTTGTGTATATCTCTTTCTTTTTTAATTAGGAGATTAGATGCTAAAGT
47337781 T
1 T
47337782 TAGGAGATAA
Statistics
Matches: 53, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 30 0.57
53 23 0.43
ACGTcount: A:0.25, C:0.08, G:0.17, T:0.51
Consensus pattern (53 bp):
TAGTTTTTGTGTATATCTCTTTCTTTTTTAATTAGGAGATTAGATGCTAAAGT
Found at i:47338234 original size:63 final size:63
Alignment explanation
Indices: 47338161--47338280 Score: 213
Period size: 63 Copynumber: 1.9 Consensus size: 63
47338151 CATGGATATT
* *
47338161 TTCTTATCACATCAAGAATGAGGTGTATCTTAATAGAGTTTGAATTACCAAATTTAAGTTATA
1 TTCTTATCACATCAAGAATGAGGTGCAACTTAATAGAGTTTGAATTACCAAATTTAAGTTATA
*
47338224 TTCTTATCACATCGAGAATGAGGTGCAACTTAATAGAGTTTGAATTACCAAATTTAA
1 TTCTTATCACATCAAGAATGAGGTGCAACTTAATAGAGTTTGAATTACCAAATTTAA
47338281 CTTTTAAATC
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
63 54 1.00
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.36
Consensus pattern (63 bp):
TTCTTATCACATCAAGAATGAGGTGCAACTTAATAGAGTTTGAATTACCAAATTTAAGTTATA
Found at i:47338919 original size:15 final size:15
Alignment explanation
Indices: 47338899--47338934 Score: 56
Period size: 15 Copynumber: 2.4 Consensus size: 15
47338889 TGAAAAAGTT
47338899 AAAGAAAATACGAA-A
1 AAAGAAAATAC-AAGA
47338914 AAAGAAAATACAAGA
1 AAAGAAAATACAAGA
47338929 AAAGAA
1 AAAGAA
47338935 TAAACAGATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 2 0.10
15 18 0.90
ACGTcount: A:0.75, C:0.06, G:0.14, T:0.06
Consensus pattern (15 bp):
AAAGAAAATACAAGA
Found at i:47339685 original size:17 final size:18
Alignment explanation
Indices: 47339645--47339689 Score: 56
Period size: 17 Copynumber: 2.5 Consensus size: 18
47339635 TTATAGTTTA
47339645 TATATATTTTATATACATT
1 TATAT-TTTTATATACATT
* *
47339664 CATATTTTTATA-ATATT
1 TATATTTTTATATACATT
47339681 TATATTTTT
1 TATATTTTT
47339690 CATGTTTTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
17 12 0.52
18 7 0.30
19 4 0.17
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.62
Consensus pattern (18 bp):
TATATTTTTATATACATT
Found at i:47344291 original size:15 final size:15
Alignment explanation
Indices: 47344273--47344316 Score: 63
Period size: 15 Copynumber: 2.9 Consensus size: 15
47344263 AAAGAGATGT
47344273 GAAAAAATAAAAATG
1 GAAAAAATAAAAATG
47344288 G-AAAAATGAAAAATG
1 GAAAAAAT-AAAAATG
*
47344303 GAAAAAGTAAAAAT
1 GAAAAAATAAAAAT
47344317 AGAGAGGCTA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
14 6 0.23
15 15 0.58
16 5 0.19
ACGTcount: A:0.70, C:0.00, G:0.16, T:0.14
Consensus pattern (15 bp):
GAAAAAATAAAAATG
Found at i:47346260 original size:133 final size:133
Alignment explanation
Indices: 47345833--47346958 Score: 1413
Period size: 133 Copynumber: 8.5 Consensus size: 133
47345823 NNNNNNNNNN
*
47345833 GAGTACATTTTGAAGCCAG--ATTCTACTTCCCTGGACAGCAGTGGAATAGATTGAAGATTTCAT
1 GAGTACA--TTGAAGCCAGTAATTCTACTTCCCTGGACAGCAGTGGAATAGATTGAAGATTTCAG
* * * *
47345896 ATCTTGTCTCCCTAAGCAGTAG--TG-G-AGGAGATCAAAGATGGCAGATTTTACCTCC-CTGTG
64 ATCTTGCCTTCCT--GCA-TAGACAGCGAAGCAGATCAAAGATGGCAGATTTTACCTCCTC-GTG
*
47345956 GCTACAGTG
125 GTTACAGTG
*
47345965 GAGTACATTGAAGCCAGTAATTCTACTTCCCTGGACAGCAATGGAATAGATTGAAGATTTCAGAT
1 GAGTACATTGAAGCCAGTAATTCTACTTCCCTGGACAGCAGTGGAATAGATTGAAGATTTCAGAT
* * * * * *
47346030 CCTGTCTCCCTAAGCAGTAG--TG-G-AGTAGATCAAAAATGGCAGATTTTACCTTCCT-GTGGT
66 CTTGCCTTCCT--GCA-TAGACAGCGAAGCAGATCAAAGATGGCAGATTTTACC-TCCTCGTGGT
47346090 TACAGTG
127 TACAGTG
*
47346097 GAGTACATTGAAGCCAGTAATTCTACTTCCCTAGG-CAGCAGTGGAATAGATTGAAGATTTTAGA
1 GAGTACATTGAAGCCAGTAATTCTACTTCCCT-GGACAGCAGTGGAATAGATTGAAGATTTCAGA
* *
47346161 TCTTACCTTCCTGCATAGACAGCGAAGCAGATCGAAGATGGCAGATTTTACCTCCTCGTGGTTAC
65 TCTTGCCTTCCTGCATAGACAGCGAAGCAGATCAAAGATGGCAGATTTTACCTCCTCGTGGTTAC
47346226 AGTG
130 AGTG
* *
47346230 GAGTACATTGAAGCCAATAATTCTACTTCCCTGGACAGCAGCGGAATAGATTGAAGATTTCAGAT
1 GAGTACATTGAAGCCAGTAATTCTACTTCCCTGGACAGCAGTGGAATAGATTGAAGATTTCAGAT
* * * *
47346295 CTTGTCTCCCTAAGCAGTAG--TG-G-AGCAGATCAAAAAT-G--GATTTTACCTCC-CTGTGGT
66 CTTGCCTTCCT--GCA-TAGACAGCGAAGCAGATCAAAGATGGCAGATTTTACCTCCTC-GTGGT
47346352 TACAGTG
127 TACAGTG
* * *
47346359 GAGTACATTGAAGCCAGTAACTCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTTAGAT
1 GAGTACATTGAAGCCAGTAATTCTACTTCCCTGGACAGCAGTGGAATAGATTGAAGATTTCAGAT
* * * * *
47346424 ATTGCCTTCCTGCATAGACAGCGAAGCAGATCGAAGATGACGGATTTTACCTCTTCGTGGTTACA
66 CTTGCCTTCCTGCATAGACAGCGAAGCAGATCAAAGATGGCAGATTTTACCTCCTCGTGGTTACA
47346489 GTG
131 GTG
*
47346492 GAGTACATTGAAGCCAGTAATTCTACTTCCCTAGG-CAGCAGTGGAATAGATTGAAGATTTTAGA
1 GAGTACATTGAAGCCAGTAATTCTACTTCCCT-GGACAGCAGTGGAATAGATTGAAGATTTCAGA
* * * * *
47346556 TCTTACCTTCCTGCATAGACAGCGAAGCAGATCGAGGATGGCGGATTTTACCTCCTCGTGGTTAT
65 TCTTGCCTTCCTGCATAGACAGCGAAGCAGATCAAAGATGGCAGATTTTACCTCCTCGTGGTTAC
*
47346621 AGTA
130 AGTG
*
47346625 GAGTACATTGAAGCCAGTAATTCTACTTCCCTGGACAGTAGTGGAATAGATTGAAGATTTCAGAT
1 GAGTACATTGAAGCCAGTAATTCTACTTCCCTGGACAGCAGTGGAATAGATTGAAGATTTCAGAT
* * * * * * *
47346690 CTTGTC-TCCT-TA-AGCAGTAGTGGAGCAGGTCAAAGATAGCAGATTTTACCTCC-CTGTGGTT
66 CTTGCCTTCCTGCATAG-A-CAGCGAAGCAGATCAAAGATGGCAGATTTTACCTCCTC-GTGGTT
47346751 ACAGTG
128 ACAGTG
* * *
47346757 GAGTACATTGAAGCCAGTAATTCTACTTCTCTGGATAGCAGTGGAATAGATTGAAGATTTTAGAT
1 GAGTACATTGAAGCCAGTAATTCTACTTCCCTGGACAGCAGTGGAATAGATTGAAGATTTCAGAT
* * * *
47346822 ATTGCCTTCCTGCATAGACAACGAAGCAGATCGAAGATGGCAGATTTTACCTCTTCGTGGTTACA
66 CTTGCCTTCCTGCATAGACAGCGAAGCAGATCAAAGATGGCAGATTTTACCTCCTCGTGGTTACA
47346887 GTG
131 GTG
* *
47346890 GAGTACATTGAAGCCAGTAATTCTACTTCTCTGGATAGCAGTGGAATAGATTGAAGATTTCAGAT
1 GAGTACATTGAAGCCAGTAATTCTACTTCCCTGGACAGCAGTGGAATAGATTGAAGATTTCAGAT
47346955 CTTG
66 CTTG
47346959 TCTCCCCGAG
Statistics
Matches: 884, Mismatches: 78, Indels: 63
0.86 0.08 0.06
Matches are distributed among these distances:
126 3 0.00
127 3 0.00
128 2 0.00
129 96 0.11
130 27 0.03
131 5 0.01
132 304 0.34
133 429 0.49
134 7 0.01
135 5 0.01
136 3 0.00
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.29
Consensus pattern (133 bp):
GAGTACATTGAAGCCAGTAATTCTACTTCCCTGGACAGCAGTGGAATAGATTGAAGATTTCAGAT
CTTGCCTTCCTGCATAGACAGCGAAGCAGATCAAAGATGGCAGATTTTACCTCCTCGTGGTTACA
GTG
Found at i:47347023 original size:265 final size:264
Alignment explanation
Indices: 47345833--47347024 Score: 1441
Period size: 265 Copynumber: 4.5 Consensus size: 264
47345823 NNNNNNNNNN
*
47345833 GAGTACATTTTGAAGCCAG--ATTCTACTTCCCTGGACAGCAGTGGAATAGATTGAAGATTTCAT
1 GAGTACA--TTGAAGCCAGTAATTCTACTTCCCTGGACAGCAGTGGAATAGATTGAAGATTTCAG
* * * * *
47345896 ATCTTGTCTCCCTAAGCAGTAGTGGAGGAGATCAAAGATGGCAGATTTTACCTCCCTGTGGCTAC
64 ATCTTGTCTCCCTGAGCAGTAGTGGAGCAGATCAAAGATAGCAGATTTTACCTCCTTGTGGTTAC
*
47345961 AGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGACAGCAATGGAATAGATTGAAGATTTC
129 AGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGACAGCAGTGGAATAGATTGAAGATTTC
* * * * *
47346026 AGATCCTGTCTCCCTAAGCAGTAGTGGAGTAGATCAAAAATGGCAGATTTTACCT-TCCTGTGGT
194 AGATCTTGCCTCCCTAAGCAG-AGCGAAGCAGATCAAAAATGGCAGATTTTACCTCTCCTGTGGT
47346090 TACAGTG
258 TACAGTG
*
47346097 GAGTACATTGAAGCCAGTAATTCTACTTCCCTAGG-CAGCAGTGGAATAGATTGAAGATTTTAGA
1 GAGTACATTGAAGCCAGTAATTCTACTTCCCT-GGACAGCAGTGGAATAGATTGAAGATTTCAGA
** * * * * * * * *
47346161 TCTTACCTTCCTGCA-TAGACAGCGAAGCAGATCGAAGATGGCAGATTTTACCTCCTCGTGGTTA
65 TCTTGTCTCCCTG-AGCAG-TAGTGGAGCAGATCAAAGATAGCAGATTTTACCTCCTTGTGGTTA
* *
47346225 CAGTGGAGTACATTGAAGCCAATAATTCTACTTCCCTGGACAGCAGCGGAATAGATTGAAGATTT
128 CAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGACAGCAGTGGAATAGATTGAAGATTT
* * *
47346290 CAGATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATCAAAAAT-G--GATTTTACCTC-CCTGTGG
193 CAGATCTTGCCTCCCTAAGCAG-AGCGAAGCAGATCAAAAATGGCAGATTTTACCTCTCCTGTGG
47346351 TTACAGTG
257 TTACAGTG
* * *
47346359 GAGTACATTGAAGCCAGTAACTCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTTAGAT
1 GAGTACATTGAAGCCAGTAATTCTACTTCCCTGGACAGCAGTGGAATAGATTGAAGATTTCAGAT
* * * * * * * * *
47346424 ATTGCCTTCCTGCA-TAGACAGCGAAGCAGATCGAAGAT-GACGGATTTTACCT-CTTCGTGGTT
66 CTTGTCTCCCTG-AGCAG-TAGTGGAGCAGATCAAAGATAG-CAGATTTTACCTCCTT-GTGGTT
47346486 ACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTAGG-CAGCAGTGGAATAGATTGAAGAT
127 ACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCT-GGACAGCAGTGGAATAGATTGAAGAT
* * * * * ** *
47346550 TTTAGATCTTACCTTCCTGCATAG-ACAGCGAAGCAGATCGAGGATGGCGGATTTTA-C-CTCCT
191 TTCAGATCTTGCCTCCCT--A-AGCAGAGCGAAGCAGATCAAAAATGGCAGATTTTACCTCTCCT
* *
47346612 CGTGGTTATAGTA
253 -GTGGTTACAGTG
*
47346625 GAGTACATTGAAGCCAGTAATTCTACTTCCCTGGACAGTAGTGGAATAGATTGAAGATTTCAGAT
1 GAGTACATTGAAGCCAGTAATTCTACTTCCCTGGACAGCAGTGGAATAGATTGAAGATTTCAGAT
* * * *
47346690 CTTGTCTCCTTAAGCAGTAGTGGAGCAGGTCAAAGATAGCAGATTTTACCTCCCTGTGGTTACAG
66 CTTGTCTCCCTGAGCAGTAGTGGAGCAGATCAAAGATAGCAGATTTTACCTCCTTGTGGTTACAG
* * *
47346755 TGGAGTACATTGAAGCCAGTAATTCTACTTCTCTGGATAGCAGTGGAATAGATTGAAGATTTTAG
131 TGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGACAGCAGTGGAATAGATTGAAGATTTCAG
* * * * *
47346820 ATATTGCCTTCCTGCATAGACA-A-CGAAGCAGATCGAAGATGGCAGATTTTACCTCTTC-GTGG
196 ATCTTGCCTCCCT--A-AG-CAGAGCGAAGCAGATCAAAAATGGCAGATTTTACCTCTCCTGTGG
47346882 TTACAGTG
257 TTACAGTG
* *
47346890 GAGTACATTGAAGCCAGTAATTCTACTTCTCTGGATAGCAGTGGAATAGATTGAAGATTTCAGAT
1 GAGTACATTGAAGCCAGTAATTCTACTTCCCTGGACAGCAGTGGAATAGATTGAAGATTTCAGAT
* * ** *
47346955 CTTGTCTCCCCGAGCAGTAGTGGAGCAGGTCAAAGATAGCAGATTTTACCTCCTTGAAGTTGCAG
66 CTTGTCTCCCTGAGCAGTAGTGGAGCAGATCAAAGATAGCAGATTTTACCTCCTTGTGGTTACAG
47347020 TGGAG
131 TGGAG
47347025 CAGACTCCTT
Statistics
Matches: 827, Mismatches: 75, Indels: 51
0.87 0.08 0.05
Matches are distributed among these distances:
261 5 0.01
262 222 0.27
263 16 0.02
264 65 0.08
265 423 0.51
266 92 0.11
267 4 0.00
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.29
Consensus pattern (264 bp):
GAGTACATTGAAGCCAGTAATTCTACTTCCCTGGACAGCAGTGGAATAGATTGAAGATTTCAGAT
CTTGTCTCCCTGAGCAGTAGTGGAGCAGATCAAAGATAGCAGATTTTACCTCCTTGTGGTTACAG
TGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGACAGCAGTGGAATAGATTGAAGATTTCAG
ATCTTGCCTCCCTAAGCAGAGCGAAGCAGATCAAAAATGGCAGATTTTACCTCTCCTGTGGTTAC
AGTG
Found at i:47347130 original size:398 final size:390
Alignment explanation
Indices: 47345843--47347008 Score: 1233
Period size: 395 Copynumber: 3.0 Consensus size: 390
47345833 GAGTACATTT
* ** * *** * **
47345843 TGAAGCCAGATTCTACTTCCCTGGACAGCAGTGGAATAGATTGAAGATTTCATATCTTGTCTCCC
1 TGAAGCCAGAATCTACTTAACTGGACAG-AGTGGAATAGATTGAAAACCACAGATCTCATCT-CC
* * * * * *
47345908 T-AAGCAGTAGTGGAGGAGATCAAAGATGGCAGATTTTACCTCCCTGTGGCTACAGTGGAGTACA
64 TAAAGCAGTAGAGCAGCAGGTCAAAGATAGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACA
* * * ** *
47345972 TTGAAGCCAGTAATTCTACTTCCCTGGACAGCAATGGAATAGATTGAAGATTTCAGATCCTGTCT
129 TTGAAGCCAGTAACTCTACTTCCCTGGACAGCAGTGGAATAGATTGAAGATTTTAGATATTGCCT
* * * * * * * *
47346037 CCCT--A-AG-CAGTAGTGGAGTAGATCAAAAATGGCAGATTTTACCT-TCCTGTGGTTACAGTG
194 TCCTGCATAGACA--A-CGAAGCAGATCGAAGATGACAGATTTTACCTCTTC-GTGGTTACAGTG
*
47346097 GAGTACATTGAAGCCAGTAATTCTACTTCCCTAGGCAGCAGTGGAATAGATTGAAGATTTTAGAT
255 GAGTACATTGAAGCCAGTAATTCTACTTCCCTAGGCAGCAGTGGAATAGATTGAAGATTTCAGAT
* * * * * *
47346162 CTTACCTTCCTGCATAGACAGCGAAGCAGATCGAAGATGGCAGATTTTACCTCCTCGTGGTTACA
320 CTTACCTCCCCGCACAGACAGCGAAGCAGATCAAAGATAGCAGATTTTACCTCCTC-TGG-TATA
*
47346227 GTGGAGTACAT
383 GT--A-TACAG
* ** * * *** **
47346238 TGAAGCCAATAATTCTACTTCCCTGGACAGCAGCGGAATAGATTGAAGATTTCAGATCTTGTCTC
1 TGAAGCC-AGAA-TCTACTTAACTGGACAG-AGTGGAATAGATTGAAAACCACAGATCTCATCT-
* * * *
47346303 CCT-AAGCAGTAGTGGAGCAGATCAAAAAT-G--GATTTTACCTCCCTGTGGTTACAGTGGAGTA
62 CCTAAAGCAGTAGAGCAGCAGGTCAAAGATAGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTA
*
47346364 CATTGAAGCCAGTAACTCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTTAGATATTGC
127 CATTGAAGCCAGTAACTCTACTTCCCTGGACAGCAGTGGAATAGATTGAAGATTTTAGATATTGC
* *
47346429 CTTCCTGCATAGACAGCGAAGCAGATCGAAGATGACGGATTTTACCTCTTCGTGGTTACAGTGGA
192 CTTCCTGCATAGACAACGAAGCAGATCGAAGATGACAGATTTTACCTCTTCGTGGTTACAGTGGA
*
47346494 GTACATTGAAGCCAGTAATTCTACTTCCCTAGGCAGCAGTGGAATAGATTGAAGATTTTAGATCT
257 GTACATTGAAGCCAGTAATTCTACTTCCCTAGGCAGCAGTGGAATAGATTGAAGATTTCAGATCT
* * * * * * *
47346559 TACCTTCCTGCATAGACAGCGAAGCAGATCGAGGATGGCGGATTTTACCTCCTCGTGGTTATAGT
322 TACCTCCCCGCACAGACAGCGAAGCAGATCAAAGATAGCAGATTTTACCTCCTC-TGG-TATAGT
*
47346624 AGAGTACAT
385 --A-TACAG
** * *** **
47346633 TGAAGCCAGTAATTCTACTTCCCTGGACAGTAGTGGAATAGATTGAAGATTTCAGATCTTGTCTC
1 TGAAGCCAG-AA-TCTACTTAACTGGACAG-AGTGGAATAGATTGAAAACCACAGATCTCATCTC
* * *
47346698 CTTAAGCAGTAGTGGAGCAGGTCAAAGATAGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTAC
63 CTAAAGCAGTAGAGCAGCAGGTCAAAGATAGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTAC
* * *
47346763 ATTGAAGCCAGTAATTCTACTTCTCTGGATAGCAGTGGAATAGATTGAAGATTTTAGATATTGCC
128 ATTGAAGCCAGTAACTCTACTTCCCTGGACAGCAGTGGAATAGATTGAAGATTTTAGATATTGCC
*
47346828 TTCCTGCATAGACAACGAAGCAGATCGAAGATGGCAGATTTTACCTCTTCGTGGTTACAGTGGAG
193 TTCCTGCATAGACAACGAAGCAGATCGAAGATGACAGATTTTACCTCTTCGTGGTTACAGTGGAG
* *
47346893 TACATTGAAGCCAGTAATTCTACTTCTCT-GGATAGCAGTGGAATAGATTGAAGATTTCAGATCT
258 TACATTGAAGCCAGTAATTCTACTTCCCTAGG-CAGCAGTGGAATAGATTGAAGATTTCAGATCT
** * * * *
47346957 TGTCTCCCCG-AGCAG-TAGTGGAGCAGGTCAAAGATAGCAGATTTTACCTCCT
322 TACCTCCCCGCA-CAGACAGCGAAGCAGATCAAAGATAGCAGATTTTACCTCCT
47347009 TGAAGTTGCA
Statistics
Matches: 701, Mismatches: 56, Indels: 26
0.90 0.07 0.03
Matches are distributed among these distances:
394 97 0.14
395 263 0.38
396 7 0.01
397 111 0.16
398 223 0.32
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.29
Consensus pattern (390 bp):
TGAAGCCAGAATCTACTTAACTGGACAGAGTGGAATAGATTGAAAACCACAGATCTCATCTCCTA
AAGCAGTAGAGCAGCAGGTCAAAGATAGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATT
GAAGCCAGTAACTCTACTTCCCTGGACAGCAGTGGAATAGATTGAAGATTTTAGATATTGCCTTC
CTGCATAGACAACGAAGCAGATCGAAGATGACAGATTTTACCTCTTCGTGGTTACAGTGGAGTAC
ATTGAAGCCAGTAATTCTACTTCCCTAGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTACC
TCCCCGCACAGACAGCGAAGCAGATCAAAGATAGCAGATTTTACCTCCTCTGGTATAGTATACAG
Found at i:47347846 original size:15 final size:15
Alignment explanation
Indices: 47347826--47347861 Score: 56
Period size: 15 Copynumber: 2.4 Consensus size: 15
47347816 TGAAAAAGTT
47347826 AAAGAAAATACGAA-A
1 AAAGAAAATAC-AAGA
47347841 AAAGAAAATACAAGA
1 AAAGAAAATACAAGA
47347856 AAAGAA
1 AAAGAA
47347862 TAAACAGATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 2 0.10
15 18 0.90
ACGTcount: A:0.75, C:0.06, G:0.14, T:0.06
Consensus pattern (15 bp):
AAAGAAAATACAAGA
Found at i:47348612 original size:17 final size:18
Alignment explanation
Indices: 47348572--47348615 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
47348562 TTATAGTTTA
47348572 TATATATTTTATATACATT
1 TATAT-TTTTATATACATT
* *
47348591 CATATTTTTATA-ATATT
1 TATATTTTTATATACATT
47348608 TATATTTT
1 TATATTTT
47348616 CATGTTTTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 11 0.50
18 7 0.32
19 4 0.18
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (18 bp):
TATATTTTTATATACATT
Found at i:47348633 original size:22 final size:24
Alignment explanation
Indices: 47348596--47348640 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 24
47348586 ACATTCATAT
*
47348596 TTTTATAATATTTATATTTTCATG
1 TTTTATAATATTTATATGTTCATG
47348620 TTTTA-AA-ATTTATATGTTCAT
1 TTTTATAATATTTATATGTTCAT
47348641 ACATTTTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 13 0.65
23 2 0.10
24 5 0.25
ACGTcount: A:0.31, C:0.04, G:0.04, T:0.60
Consensus pattern (24 bp):
TTTTATAATATTTATATGTTCATG
Found at i:47350078 original size:383 final size:383
Alignment explanation
Indices: 47349371--47350132 Score: 1506
Period size: 383 Copynumber: 2.0 Consensus size: 383
47349361 TGGTACCGAT
*
47349371 TTTTGGGCGTTACGAGGGTGCTAACCCTTCCTCGTGCGTAACTGACTCCCGAACCCGTTTTCTTA
1 TTTTGGGCGTTACGAGGGTGCTAACCCTTCCTCCTGCGTAACTGACTCCCGAACCCGTTTTCTTA
47349436 AATTTCGTAGACCAGAATCGTTTTTAAGGTGAGCCGATCACACCTCAATAAAGGATCGGTGGCGA
66 AATTTCGTAGACCAGAATCGTTTTTAAGGTGAGCCGATCACACCTCAATAAAGGATCGGTGGCGA
47349501 CTCCAATTCTTGTTTTTTAAAGTCGACAACTAAATTTTTGTTTTCAAAAAATGGTTTCGACAAAC
131 CTCCAATTCTTGTTTTTTAAAGTCGACAACTAAATTTTTGTTTTCAAAAAATGGTTTCGACAAAC
47349566 ATGTTTTCCAATATAGAATTTTAAGAAGCAATTAAACGATTCATAGGACCAAAGAGCCCCGACAA
196 ATGTTTTCCAATATAGAATTTTAAGAAGCAATTAAACGATTCATAGGACCAAAGAGCCCCGACAA
47349631 CAAAATACTAGTAAGCATAATTAATACAAGTTACAATGAAGCCTATCATATCGGAGGTGGAGCAA
261 CAAAATACTAGTAAGCATAATTAATACAAGTTACAATGAAGCCTATCATATCGGAGGTGGAGCAA
47349696 GTTCATCTTCACCCTCCCATGATTCCTTGATATCAGAGTCATCAATATCTTCATTCGA
326 GTTCATCTTCACCCTCCCATGATTCCTTGATATCAGAGTCATCAATATCTTCATTCGA
*
47349754 TTTTGGGCGTTGCGAGGGTGCTAACCCTTCCTCCTGCGTAACTGACTCCCGAACCCGTTTTCTTA
1 TTTTGGGCGTTACGAGGGTGCTAACCCTTCCTCCTGCGTAACTGACTCCCGAACCCGTTTTCTTA
47349819 AATTTCGTAGACCAGAATCGTTTTTAAGGTGAGCCGATCACACCTCAATAAAGGATCGGTGGCGA
66 AATTTCGTAGACCAGAATCGTTTTTAAGGTGAGCCGATCACACCTCAATAAAGGATCGGTGGCGA
47349884 CTCCAATTCTTGTTTTTTAAAGTCGACAACTAAATTTTTGTTTTCAAAAAATGGTTTCGACAAAC
131 CTCCAATTCTTGTTTTTTAAAGTCGACAACTAAATTTTTGTTTTCAAAAAATGGTTTCGACAAAC
47349949 ATGTTTTCCAATATAGAATTTTAAGAAGCAATTAAACGATTCATAGGACCAAAGAGCCCCGACAA
196 ATGTTTTCCAATATAGAATTTTAAGAAGCAATTAAACGATTCATAGGACCAAAGAGCCCCGACAA
47350014 CAAAATACTAGTAAGCATAATTAATACAAGTTACAATGAAGCCTATCATATCGGAGGTGGAGCAA
261 CAAAATACTAGTAAGCATAATTAATACAAGTTACAATGAAGCCTATCATATCGGAGGTGGAGCAA
47350079 GTTCATCTTCACCCTCCCATGATTCCTTGATATCAGAGTCATCAATATCTTCAT
326 GTTCATCTTCACCCTCCCATGATTCCTTGATATCAGAGTCATCAATATCTTCAT
47350133 CATCCCATTT
Statistics
Matches: 377, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
383 377 1.00
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.30
Consensus pattern (383 bp):
TTTTGGGCGTTACGAGGGTGCTAACCCTTCCTCCTGCGTAACTGACTCCCGAACCCGTTTTCTTA
AATTTCGTAGACCAGAATCGTTTTTAAGGTGAGCCGATCACACCTCAATAAAGGATCGGTGGCGA
CTCCAATTCTTGTTTTTTAAAGTCGACAACTAAATTTTTGTTTTCAAAAAATGGTTTCGACAAAC
ATGTTTTCCAATATAGAATTTTAAGAAGCAATTAAACGATTCATAGGACCAAAGAGCCCCGACAA
CAAAATACTAGTAAGCATAATTAATACAAGTTACAATGAAGCCTATCATATCGGAGGTGGAGCAA
GTTCATCTTCACCCTCCCATGATTCCTTGATATCAGAGTCATCAATATCTTCATTCGA
Found at i:47369814 original size:19 final size:19
Alignment explanation
Indices: 47369776--47369813 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
47369766 TGAAAATAAC
*
47369776 ATGTTTAATATATAGATAT
1 ATGTTTAATAAATAGATAT
47369795 ATGTTTAA-AAATAG-TAT
1 ATGTTTAATAAATAGATAT
47369812 AT
1 AT
47369814 AATAAATAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 5 0.28
18 5 0.28
19 8 0.44
ACGTcount: A:0.45, C:0.00, G:0.11, T:0.45
Consensus pattern (19 bp):
ATGTTTAATAAATAGATAT
Found at i:47374299 original size:91 final size:92
Alignment explanation
Indices: 47374144--47374331 Score: 360
Period size: 91 Copynumber: 2.1 Consensus size: 92
47374134 GTTGAATAGC
47374144 AAAGTTTAAGATTTTTCATGTTTTGAATTCAAACCTTACTTGAATATTTTTCTTTAATTTAAAGT
1 AAAGTTTAAGATTTTTCATGTTTTGAATTCAAACCTTACTTGAATATTTTTCTTTAATTTAAAGT
*
47374209 TG-TTTTTTTAATAATTTTTATAAAAA
66 TGTTTTTTTTAATAAATTTTATAAAAA
47374235 AAAGTTTAAGATTTTTCATGTTTTGAATTCAAACCTTACTTGAATATTTTTCTTTAATTTAAAGT
1 AAAGTTTAAGATTTTTCATGTTTTGAATTCAAACCTTACTTGAATATTTTTCTTTAATTTAAAGT
47374300 TGTTTTTTTTAATAAATTTTATAAAAA
66 TGTTTTTTTTAATAAATTTTATAAAAA
47374327 AAAGT
1 AAAGT
47374332 ATGAAAATAG
Statistics
Matches: 95, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
91 67 0.71
92 28 0.29
ACGTcount: A:0.35, C:0.06, G:0.08, T:0.51
Consensus pattern (92 bp):
AAAGTTTAAGATTTTTCATGTTTTGAATTCAAACCTTACTTGAATATTTTTCTTTAATTTAAAGT
TGTTTTTTTTAATAAATTTTATAAAAA
Found at i:47382415 original size:73 final size:73
Alignment explanation
Indices: 47382335--47382472 Score: 204
Period size: 73 Copynumber: 1.9 Consensus size: 73
47382325 AACAGGGAGT
* * * * * *
47382335 GTGCTTTATTTGGAGATTGACATCTTTGTCTTTTTTTATTGTCATAATATTTTCTTGTGGGATTT
1 GTGCTTTAATGGGAGATTGACATCTTTGTCCTTTTTAATTGTCATAATATTTTCTCGTGAGATTT
47382400 ATCATTGC
66 ATCATTGC
* *
47382408 GTGCTTTAATGGGAGTTTGTCATCTTTGTCCTTTTTAATTGTCATAATATTTTCTCGTGAGATTT
1 GTGCTTTAATGGGAGATTGACATCTTTGTCCTTTTTAATTGTCATAATATTTTCTCGTGAGATTT
47382473 TGTTGTTTCC
Statistics
Matches: 57, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
73 57 1.00
ACGTcount: A:0.18, C:0.12, G:0.18, T:0.52
Consensus pattern (73 bp):
GTGCTTTAATGGGAGATTGACATCTTTGTCCTTTTTAATTGTCATAATATTTTCTCGTGAGATTT
ATCATTGC
Found at i:47384058 original size:75 final size:75
Alignment explanation
Indices: 47383967--47384246 Score: 421
Period size: 75 Copynumber: 3.8 Consensus size: 75
47383957 ATTGAATATA
* *
47383967 AAGGGGGTTGCTAAGTGCT-AGTTTCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTA
1 AAGGGGGTTGCTAAGTGCTGA-TTCCCCGACTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTA
47384031 TCTTAAATGTG
65 TCTTAAATGTG
* * * *
47384042 AAAGGGGTTGCTAAGTGTTGATTCCCCGACTCATTGGTGGTTGTTAAGTGCTGATTCCACTGTAT
1 AAGGGGGTTGCTAAGTGCTGATTCCCCGACTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTAT
47384107 CTTAAATGTG
66 CTTAAATGTG
*
47384117 AAGGGGGTTGCTAAGTGCTGATTCCCC--C-GA--GG-GGTTGCTAAGTGCTGATTCCACCGTAT
1 AAGGGGGTTGCTAAGTGCTGATTCCCCGACTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTAT
47384176 CTTAAATGTG
66 CTTAAATGTG
* *
47384186 AAGGGGGTTGCTAAGTGCTGATTCCCCGACTCATTGGTGATTGCTAAGTGCTGAATCCACC
1 AAGGGGGTTGCTAAGTGCTGATTCCCCGACTCATTGGTGGTTGCTAAGTGCTGATTCCACC
47384247 AATAACAGAT
Statistics
Matches: 184, Mismatches: 14, Indels: 14
0.87 0.07 0.07
Matches are distributed among these distances:
69 62 0.34
70 2 0.01
71 1 0.01
72 2 0.01
73 1 0.01
74 2 0.01
75 113 0.61
76 1 0.01
ACGTcount: A:0.21, C:0.19, G:0.28, T:0.32
Consensus pattern (75 bp):
AAGGGGGTTGCTAAGTGCTGATTCCCCGACTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTAT
CTTAAATGTG
Found at i:47384064 original size:42 final size:41
Alignment explanation
Indices: 47384005--47384141 Score: 155
Period size: 42 Copynumber: 3.5 Consensus size: 41
47383995 ATTCATTGGT
47384005 GGTTGCTAAGTGCTGATTCCACCGTATCTTAAATGTGAAAGG
1 GGTTGCTAAGTGCTGATTCCACCGTATCTTAAATGTG-AAGG
* * *
47384047 GGTTGCTAAGTGTTGATTCC-CCG-A-C-T-CAT-TG--GT
1 GGTTGCTAAGTGCTGATTCCACCGTATCTTAAATGTGAAGG
* *
47384080 GGTTGTTAAGTGCTGATTCCACTGTATCTTAAATGTGAAGGG
1 GGTTGCTAAGTGCTGATTCCACCGTATCTTAAATGTGAA-GG
47384122 GGTTGCTAAGTGCTGATTCC
1 GGTTGCTAAGTGCTGATTCC
47384142 CCCGAGGGGT
Statistics
Matches: 77, Mismatches: 9, Indels: 18
0.74 0.09 0.17
Matches are distributed among these distances:
33 19 0.25
34 2 0.03
35 1 0.01
36 3 0.04
37 3 0.04
38 3 0.04
39 3 0.04
40 1 0.01
41 3 0.04
42 39 0.51
ACGTcount: A:0.21, C:0.17, G:0.28, T:0.34
Consensus pattern (41 bp):
GGTTGCTAAGTGCTGATTCCACCGTATCTTAAATGTGAAGG
Found at i:47393858 original size:163 final size:163
Alignment explanation
Indices: 47393581--47393900 Score: 550
Period size: 163 Copynumber: 2.0 Consensus size: 163
47393571 TTGTTTTCCT
*
47393581 ATAATTTTAACTGCATATATGCAAGACATTAGCTTTTGATTGTTTCAACCATTAGATTTATCAAT
1 ATAATTTTAACTACATATATGCAAGACATTAGCTTTTGATTGTTTCAACCATTAGATTTATCAAT
* * *
47393646 TATGTCTTTAGTACTTAATTATTACGTGTCAGTTTCATTAGTATGGGATGCCGATAATGATTTTT
66 TATGTCTTTACTACTTAATTATTACGTGTCAGTTTCATTAGTATGGGATGCCAATAATAATTTTT
* * *
47393711 TTATGTGTATGAATGCAAATTTTTATGCCGATA
131 TTATGTGAATGAAAGCAAATGTTTATGCCGATA
* *
47393744 ATAATTTTAACTACATATATGCAAGACATTAGCTTTTGATTGTTTCAACCATTAGATTTTTCGAT
1 ATAATTTTAACTACATATATGCAAGACATTAGCTTTTGATTGTTTCAACCATTAGATTTATCAAT
*
47393809 TATGTCTTTACTACTTAATTATTACGTGTCAGTTTCATTAGTTTGGGATGCCAATAATAATTTTT
66 TATGTCTTTACTACTTAATTATTACGTGTCAGTTTCATTAGTATGGGATGCCAATAATAATTTTT
47393874 TTATGTGAATGAAAGCAAATGTTTATG
131 TTATGTGAATGAAAGCAAATGTTTATG
47393901 TGACTGCTTG
Statistics
Matches: 147, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
163 147 1.00
ACGTcount: A:0.30, C:0.12, G:0.15, T:0.44
Consensus pattern (163 bp):
ATAATTTTAACTACATATATGCAAGACATTAGCTTTTGATTGTTTCAACCATTAGATTTATCAAT
TATGTCTTTACTACTTAATTATTACGTGTCAGTTTCATTAGTATGGGATGCCAATAATAATTTTT
TTATGTGAATGAAAGCAAATGTTTATGCCGATA
Found at i:47400706 original size:92 final size:92
Alignment explanation
Indices: 47400549--47400733 Score: 370
Period size: 92 Copynumber: 2.0 Consensus size: 92
47400539 GCAATTATGA
47400549 TCGGATTATCTTGAGAACATATTGTGAGGATTGATAAAAGCATGTTAATAAATTGCTTAGTATTT
1 TCGGATTATCTTGAGAACATATTGTGAGGATTGATAAAAGCATGTTAATAAATTGCTTAGTATTT
47400614 ACATACCAACTTACTAAACTATATAGC
66 ACATACCAACTTACTAAACTATATAGC
47400641 TCGGATTATCTTGAGAACATATTGTGAGGATTGATAAAAGCATGTTAATAAATTGCTTAGTATTT
1 TCGGATTATCTTGAGAACATATTGTGAGGATTGATAAAAGCATGTTAATAAATTGCTTAGTATTT
47400706 ACATACCAACTTACTAAACTATATAGC
66 ACATACCAACTTACTAAACTATATAGC
47400733 T
1 T
47400734 TACCCCATTC
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
92 93 1.00
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.35
Consensus pattern (92 bp):
TCGGATTATCTTGAGAACATATTGTGAGGATTGATAAAAGCATGTTAATAAATTGCTTAGTATTT
ACATACCAACTTACTAAACTATATAGC
Found at i:47401390 original size:18 final size:19
Alignment explanation
Indices: 47401353--47401396 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 19
47401343 TTATATATTT
* *
47401353 TAATATATTATAAATTACA
1 TAATATATTAAAAATAACA
47401372 TAATATA-TAAAAATAACA
1 TAATATATTAAAAATAACA
47401390 TAATATA
1 TAATATA
47401397 AAGTATTGTG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 16 0.70
19 7 0.30
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (19 bp):
TAATATATTAAAAATAACA
Found at i:47408436 original size:18 final size:19
Alignment explanation
Indices: 47408391--47408439 Score: 57
Period size: 18 Copynumber: 2.6 Consensus size: 19
47408381 GAATATTTAC
*
47408391 ATAAAAATTAAACTAAGTAA
1 ATAAAAA-TAAACTAAATAA
47408411 A-AACAAATAAA-TAAATAA
1 ATAA-AAATAAACTAAATAA
47408429 ATAAAAATAAA
1 ATAAAAATAAA
47408440 AACAAAACTT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
18 14 0.54
19 8 0.31
20 4 0.15
ACGTcount: A:0.73, C:0.04, G:0.02, T:0.20
Consensus pattern (19 bp):
ATAAAAATAAACTAAATAA
Found at i:47424635 original size:126 final size:126
Alignment explanation
Indices: 47424410--47424667 Score: 403
Period size: 126 Copynumber: 2.0 Consensus size: 126
47424400 ACAAATGCAT
* * * *
47424410 ATTACTCAATTGATGATCTAAAACTGGGTAAGCAGGTGAGGCACTTCCCGAATTTGCTGCTAAGG
1 ATTACTCAACTGATGATCTAAAACCGGGTAAGCACGTGAAGCACTTCCCGAATTTGCTGCTAAGG
* * *
47424475 AACTTGTACTGTCTTGCCTGTTATGACCAGAGAAGCTATTGTGTGTGGAGAGGAGCTCGGA
66 AACTTGTACTGTCTTGCCGGTTATGACCAGAGAAGCTAATGTGTGTGGAGAGGAGCTCAGA
* *
47424536 ATTACTCAACTGATGATC-CAAACGCGGGTAAAG-ACGTGAAGCACTTCCCGTATTTGCTGCTAA
1 ATTACTCAACTGATGATCTAAAAC-CGGGT-AAGCACGTGAAGCACTTCCCGAATTTGCTGCTAA
47424599 GGAACTTGTACTGTCTTGCCGGTTATGACCAGAGAAGCTAATGTGTGTGGAGAGGAGCTCAGA
64 GGAACTTGTACTGTCTTGCCGGTTATGACCAGAGAAGCTAATGTGTGTGGAGAGGAGCTCAGA
47424662 ATTACT
1 ATTACT
47424668 TTCAGGAGGA
Statistics
Matches: 121, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
125 4 0.03
126 114 0.94
127 3 0.02
ACGTcount: A:0.27, C:0.19, G:0.27, T:0.28
Consensus pattern (126 bp):
ATTACTCAACTGATGATCTAAAACCGGGTAAGCACGTGAAGCACTTCCCGAATTTGCTGCTAAGG
AACTTGTACTGTCTTGCCGGTTATGACCAGAGAAGCTAATGTGTGTGGAGAGGAGCTCAGA
Found at i:47424742 original size:42 final size:42
Alignment explanation
Indices: 47424673--47424757 Score: 125
Period size: 42 Copynumber: 2.0 Consensus size: 42
47424663 TTACTTTCAG
* * * *
47424673 GAGGAGTATATTGTGCAGGTTGTTGATAAGAGGAGGATGATT
1 GAGGAGGATATTGTGAAGGCTGCTGATAAGAGGAGGATGATT
*
47424715 GAGGAGGATATTGTGAAGGCTGCTGATAAGTGGAGGATGATT
1 GAGGAGGATATTGTGAAGGCTGCTGATAAGAGGAGGATGATT
47424757 G
1 G
47424758 CGGGTTACTT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.28, C:0.04, G:0.40, T:0.28
Consensus pattern (42 bp):
GAGGAGGATATTGTGAAGGCTGCTGATAAGAGGAGGATGATT
Found at i:47427111 original size:39 final size:37
Alignment explanation
Indices: 47427038--47427113 Score: 91
Period size: 36 Copynumber: 2.0 Consensus size: 37
47427028 GATTATTAAT
*
47427038 ATAAATAATAAATAATTTAATTTTTTTAACATAATTA
1 ATAAATAATAAATAATTTAATTTTCTTAACATAATTA
* *
47427075 ATAAA-AATATATAATTTAATATAATTCTTAATATAATTA
1 ATAAATAATAAATAATTTAAT-T--TTCTTAACATAATTA
47427114 TTCTTATATG
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
36 14 0.42
37 6 0.18
39 13 0.39
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (37 bp):
ATAAATAATAAATAATTTAATTTTCTTAACATAATTA
Found at i:47430922 original size:18 final size:18
Alignment explanation
Indices: 47430895--47430929 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
47430885 GGAAATGGAG
47430895 CCCCACCCAATAAGGGGT
1 CCCCACCCAATAAGGGGT
*
47430913 CCCCATCCAATAAGGGG
1 CCCCACCCAATAAGGGG
47430930 ACCACATTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.29, C:0.37, G:0.23, T:0.11
Consensus pattern (18 bp):
CCCCACCCAATAAGGGGT
Found at i:47437577 original size:3 final size:3
Alignment explanation
Indices: 47437569--47437604 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
47437559 GAGGAATTTT
47437569 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
47437605 GTTTACACTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:47443464 original size:45 final size:42
Alignment explanation
Indices: 47443387--47443471 Score: 136
Period size: 42 Copynumber: 2.0 Consensus size: 42
47443377 TTACTTTCAG
*
47443387 GAGGAGGATATTGTGCAGGTTGTTGATAAGAGGATGATGATT
1 GAGGAGGATATTGTGCAGGCTGTTGATAAGAGGATGATGATT
*
47443429 GAGGAGGATATTGTGCAGGCTGTTGATAAGTA-GAGGATGATT
1 GAGGAGGATATTGTGCAGGCTGTTGATAAG-AGGATGATGATT
47443471 G
1 G
47443472 CGGATTAATT
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
42 39 0.98
43 1 0.03
ACGTcount: A:0.28, C:0.04, G:0.39, T:0.29
Consensus pattern (42 bp):
GAGGAGGATATTGTGCAGGCTGTTGATAAGAGGATGATGATT
Found at i:47452414 original size:16 final size:16
Alignment explanation
Indices: 47452393--47452462 Score: 104
Period size: 16 Copynumber: 4.4 Consensus size: 16
47452383 TTTGGTTCGC
* *
47452393 TGTATTGGATTAGAGG
1 TGTAATGGAATAGAGG
* *
47452409 TGTATTGGATTAGAGG
1 TGTAATGGAATAGAGG
47452425 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
47452441 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
47452457 TGTAAT
1 TGTAAT
47452463 AGCAAATCAA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 52 1.00
ACGTcount: A:0.31, C:0.00, G:0.36, T:0.33
Consensus pattern (16 bp):
TGTAATGGAATAGAGG
Found at i:47452546 original size:39 final size:43
Alignment explanation
Indices: 47452441--47452550 Score: 129
Period size: 45 Copynumber: 2.6 Consensus size: 43
47452431 GGAATAGAGG
47452441 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTT--A
* * ***
47452486 TGTAATGGAATAGAGGCGTAATAG-TAATCTTGTGTTTGG-T-
1 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTA
47452526 TG-AATGGAATAGAGGTGTAATAGCA
1 TGTAATGGAATAGAGGTGTAATAGCA
47452551 TAATGGAAAA
Statistics
Matches: 57, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
39 20 0.35
40 2 0.04
43 1 0.02
44 11 0.19
45 23 0.40
ACGTcount: A:0.34, C:0.05, G:0.29, T:0.32
Consensus pattern (43 bp):
TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTA
Found at i:47460058 original size:13 final size:13
Alignment explanation
Indices: 47460040--47460064 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
47460030 GAATGATATT
47460040 TTGATGATATAAA
1 TTGATGATATAAA
47460053 TTGATGATATAA
1 TTGATGATATAA
47460065 TTGTGGTACC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.16, T:0.40
Consensus pattern (13 bp):
TTGATGATATAAA
Found at i:47460746 original size:24 final size:25
Alignment explanation
Indices: 47460719--47460771 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 25
47460709 GTGCTTTCTG
47460719 ATTAAGTGCTCTTCG-GAGCTTCCC
1 ATTAAGTGCTCTTCGTGAGCTTCCC
*
47460743 ATTAAGTGCTCTTTGTGAGCTTCCC
1 ATTAAGTGCTCTTCGTGAGCTTCCC
47460768 ATTA
1 ATTA
47460772 TTAAGCCCGA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
24 14 0.52
25 13 0.48
ACGTcount: A:0.19, C:0.25, G:0.19, T:0.38
Consensus pattern (25 bp):
ATTAAGTGCTCTTCGTGAGCTTCCC
Found at i:47468832 original size:3 final size:3
Alignment explanation
Indices: 47468824--47468876 Score: 97
Period size: 3 Copynumber: 17.3 Consensus size: 3
47468814 ATGCTAATGC
47468824 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TTAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA
47468870 TAA TAA T
1 TAA TAA T
47468877 TCACACGTGC
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 46 0.94
4 3 0.06
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:47476755 original size:11 final size:12
Alignment explanation
Indices: 47476739--47476770 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
47476729 CCCTTTTAAA
47476739 ATTTAAAAATT-
1 ATTTAAAAATTC
47476750 ATTTAAAAATTC
1 ATTTAAAAATTC
47476762 A-TTAAAAAT
1 ATTTAAAAAT
47476771 AAACAAAAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 19 0.95
12 1 0.05
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (12 bp):
ATTTAAAAATTC
Found at i:47482354 original size:284 final size:284
Alignment explanation
Indices: 47481844--47482541 Score: 1192
Period size: 284 Copynumber: 2.5 Consensus size: 284
47481834 GAAGGAAACA
* *
47481844 AAAACCTAATATAATAAATAAATAAATAAAACTAAAAACTCCTATTGCAATAAAAGCGTTCATAT
1 AAAACCTGATATAATAAATAAATAAATAAAACTAAAAACTCCTATTGCAATAAAAGCGTCCATAT
*
47481909 CATTACTCCCCTTCTCCGAGTTGAGCTTGTCCTCAAGCTCAAATTCAGAATAAACTT-AAGAACT
66 CATTACTCCCCTTCTCAGAGTTGAGCTTGTCCTCAAGCTCAAATTCAGAATAAACTTCAA-AACT
*
47481973 TATCCTCTTTAATTCATATTGGTAGCCTTTTATAGACCGTTAATAACAAAGGAAAGAGTCCTAAT
130 TATCCTCTTTAATTCATATTGGCAGCCTTTTATAGACCGTTAATAACAAAGGAAAGAGTCCTAAT
*
47482038 TAACATAAAATAGAATTCTTAACTTAGAGTTTATTAAGGAAACAAAAACCTAATATAATAAAGAA
195 TAACATAAAATAGAATTCTTAACTTAGAGTTTATGAAGGAAACAAAAACCTAATATAATAAAGAA
47482103 AATAAGTAAAACTAAAACTCTTAAT
260 AATAAGTAAAACTAAAACTCTTAAT
*
47482128 AAAACCTGATATAATAAATAAATAAATAAAACTAAAAACACCTATTGCAATAAAAGCGTCCATAT
1 AAAACCTGATATAATAAATAAATAAATAAAACTAAAAACTCCTATTGCAATAAAAGCGTCCATAT
*
47482193 CATTACTCCCCTTCTCGGAGTTGAGCTTGTCCTCAAGCTCAAATTCAGAATAAACTTCAAAACTT
66 CATTACTCCCCTTCTCAGAGTTGAGCTTGTCCTCAAGCTCAAATTCAGAATAAACTTCAAAACTT
* * *
47482258 ATCCTCTTTAATTCATATTGGCAGCCTTTTATAGACTGTTAATAACAATGGAAAGAGTCTTAATT
131 ATCCTCTTTAATTCATATTGGCAGCCTTTTATAGACCGTTAATAACAAAGGAAAGAGTCCTAATT
* *
47482323 GACATAAAATAGAATT-TCTAACTTAGAGTTTATGAAGGAAACAAAAACCTAATATAATAGAGAA
196 AACATAAAATAGAATTCT-TAACTTAGAGTTTATGAAGGAAACAAAAACCTAATATAATAAAGAA
47482387 AATAAGTAAAACTAAAACTCTTAAT
260 AATAAGTAAAACTAAAACTCTTAAT
*
47482412 AAAACTTG--AT-AT-AATAAATAAATAAAACTAAAAACTCCTATTGCAATAAAAGCGTCCATAT
1 AAAACCTGATATAATAAATAAATAAATAAAACTAAAAACTCCTATTGCAATAAAAGCGTCCATAT
* * *
47482473 CATTACTCCCCTTCTCAGAGTTGAGCTTGTCCTCAAGTTGAAATTCAGAATAAACTTCAGAACTT
66 CATTACTCCCCTTCTCAGAGTTGAGCTTGTCCTCAAGCTCAAATTCAGAATAAACTTCAAAACTT
47482538 ATCC
131 ATCC
47482542 AAAATCATCT
Statistics
Matches: 395, Mismatches: 17, Indels: 8
0.94 0.04 0.02
Matches are distributed among these distances:
280 113 0.29
281 2 0.01
282 2 0.01
283 1 0.00
284 275 0.70
285 2 0.01
ACGTcount: A:0.43, C:0.17, G:0.10, T:0.29
Consensus pattern (284 bp):
AAAACCTGATATAATAAATAAATAAATAAAACTAAAAACTCCTATTGCAATAAAAGCGTCCATAT
CATTACTCCCCTTCTCAGAGTTGAGCTTGTCCTCAAGCTCAAATTCAGAATAAACTTCAAAACTT
ATCCTCTTTAATTCATATTGGCAGCCTTTTATAGACCGTTAATAACAAAGGAAAGAGTCCTAATT
AACATAAAATAGAATTCTTAACTTAGAGTTTATGAAGGAAACAAAAACCTAATATAATAAAGAAA
ATAAGTAAAACTAAAACTCTTAAT
Found at i:47485618 original size:18 final size:17
Alignment explanation
Indices: 47485595--47485636 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 17
47485585 TTTAGCGAAC
47485595 AAAAATATATAAATATA
1 AAAAATATATAAATATA
* *
47485612 AACAAATATTTATATATA
1 AA-AAATATATAAATATA
47485630 AAAAATA
1 AAAAATA
47485637 AAATAAATTG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 7 0.32
18 15 0.68
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (17 bp):
AAAAATATATAAATATA
Found at i:47487589 original size:38 final size:38
Alignment explanation
Indices: 47487536--47487609 Score: 130
Period size: 38 Copynumber: 1.9 Consensus size: 38
47487526 CAATGGTGTG
*
47487536 ATATGTGCTATTGTGTAAGACCATATCTGGGATATGAC
1 ATATGTGCTACTGTGTAAGACCATATCTGGGATATGAC
*
47487574 ATATGTGCTACTGTGTAAGACTATATCTGGGATATG
1 ATATGTGCTACTGTGTAAGACCATATCTGGGATATG
47487610 GAATCAATGT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.28, C:0.12, G:0.24, T:0.35
Consensus pattern (38 bp):
ATATGTGCTACTGTGTAAGACCATATCTGGGATATGAC
Found at i:47490252 original size:12 final size:12
Alignment explanation
Indices: 47490221--47490256 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
47490211 TAATTTCTAA
* *
47490221 TATATATATATA
1 TATATATGTATG
47490233 TATATATGTATG
1 TATATATGTATG
47490245 TATATATGTATG
1 TATATATGTATG
47490257 AGAAAATTGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.50
Consensus pattern (12 bp):
TATATATGTATG
Found at i:47490566 original size:3 final size:3
Alignment explanation
Indices: 47490558--47490606 Score: 53
Period size: 3 Copynumber: 15.7 Consensus size: 3
47490548 TTACAATATC
* * *
47490558 AAT AAT AAT AAAT AAT AAT AAAT AAT AAT GAT AAT AAT GAT AAA AAT
1 AAT AAT AAT -AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT
47490605 AA
1 AA
47490607 AAATTTTAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
3 32 0.84
4 6 0.16
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:47490573 original size:10 final size:10
Alignment explanation
Indices: 47490558--47490610 Score: 65
Period size: 10 Copynumber: 5.3 Consensus size: 10
47490548 TTACAATATC
47490558 AATAATAATA
1 AATAATAATA
47490568 AATAATAATA
1 AATAATAATA
47490578 AATAATAATGA
1 AATAATAAT-A
*
47490589 TAATAATGATA
1 -AATAATAATA
47490600 AA-AATAA-A
1 AATAATAATA
47490608 AAT
1 AAT
47490611 TTTAAAAAAC
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
8 3 0.08
9 4 0.11
10 21 0.55
11 2 0.05
12 8 0.21
ACGTcount: A:0.68, C:0.00, G:0.04, T:0.28
Consensus pattern (10 bp):
AATAATAATA
Found at i:47491831 original size:37 final size:39
Alignment explanation
Indices: 47491781--47491875 Score: 113
Period size: 41 Copynumber: 2.4 Consensus size: 39
47491771 ATAAGGTGAA
* *
47491781 ACCCAGTGTCTCATCG-GCTAAACCGAAG-TAAATTGGC
1 ACCCAGTGTCTCATCGAACTAAACCGAAGATAAATTGAC
* * *
47491818 ACCCAGTGCCTCATCGAATTAATCCGAAGTAATAAATTGAC
1 ACCCAGTGTCTCATCGAACTAAACCGAAG--ATAAATTGAC
47491859 ACCCAGTGTCTCATCGA
1 ACCCAGTGTCTCATCGA
47491876 CTAGAAGTTG
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
37 15 0.31
38 9 0.19
41 24 0.50
ACGTcount: A:0.32, C:0.27, G:0.18, T:0.23
Consensus pattern (39 bp):
ACCCAGTGTCTCATCGAACTAAACCGAAGATAAATTGAC
Found at i:47492811 original size:3 final size:3
Alignment explanation
Indices: 47492803--47492859 Score: 107
Period size: 3 Copynumber: 19.3 Consensus size: 3
47492793 TCATTTACTT
47492803 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
47492851 AT- ATA ATA A
1 ATA ATA ATA A
47492860 GTATAATTTA
Statistics
Matches: 53, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 51 0.96
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:47495661 original size:2 final size:2
Alignment explanation
Indices: 47495650--47495687 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
47495640 AATCAGAAAA
47495650 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
47495688 TTAGCTGTGT
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 32 0.94
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:47496642 original size:3 final size:3
Alignment explanation
Indices: 47496636--47496681 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
47496626 ATTACTGGGG
47496636 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
47496682 TATTACTACT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:47503708 original size:21 final size:21
Alignment explanation
Indices: 47503684--47503727 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
47503674 TAGATCTAAT
*
47503684 TAAATAGAAAAGATA-ATTAAA
1 TAAATA-AAAAGATACAATAAA
*
47503705 TAAATAAAATGATACAATAAA
1 TAAATAAAAAGATACAATAAA
47503726 TA
1 TA
47503728 CTGAATTTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.66, C:0.02, G:0.07, T:0.25
Consensus pattern (21 bp):
TAAATAAAAAGATACAATAAA
Found at i:47506308 original size:14 final size:14
Alignment explanation
Indices: 47506289--47506323 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
47506279 ATCTGTGTCA
**
47506289 TAATTAATTTTTAT
1 TAATTAATTTAAAT
47506303 TAATTAATTTAAAT
1 TAATTAATTTAAAT
47506317 TAATTAA
1 TAATTAA
47506324 GAGATAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (14 bp):
TAATTAATTTAAAT
Found at i:47507852 original size:31 final size:30
Alignment explanation
Indices: 47507817--47507885 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 30
47507807 ATACACGAGC
* *
47507817 TTTGATTTAATGTGTAATGTTATACA-TGAAT
1 TTTGATTTAATGCG--ATGTTATACATTAAAT
* *
47507848 TTTGATTTTATGCGATTTTATACATTAAAT
1 TTTGATTTAATGCGATGTTATACATTAAAT
47507878 TTTGATTT
1 TTTGATTT
47507886 GATTAAATTT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
29 9 0.27
30 12 0.36
31 12 0.36
ACGTcount: A:0.29, C:0.04, G:0.13, T:0.54
Consensus pattern (30 bp):
TTTGATTTAATGCGATGTTATACATTAAAT
Found at i:47507896 original size:30 final size:29
Alignment explanation
Indices: 47507836--47507896 Score: 68
Period size: 30 Copynumber: 2.1 Consensus size: 29
47507826 ATGTGTAATG
* * **
47507836 TTATACATGAATTTTGATTTTATGCGATT
1 TTATACATAAATTTTGATTTGATGAAATT
*
47507865 TTATACATTAAATTTTGATTTGATTAAATT
1 TTATACA-TAAATTTTGATTTGATGAAATT
47507895 TT
1 TT
47507897 TAGAAATTAC
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
29 7 0.27
30 19 0.73
ACGTcount: A:0.31, C:0.05, G:0.10, T:0.54
Consensus pattern (29 bp):
TTATACATAAATTTTGATTTGATGAAATT
Found at i:47509567 original size:22 final size:22
Alignment explanation
Indices: 47509517--47509560 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
47509507 TGGTTGACCA
47509517 CCTTTTGTCTTGTTATTAGTAC
1 CCTTTTGTCTTGTTATTAGTAC
47509539 CCTTTTGTCTTGTTATTAGTAC
1 CCTTTTGTCTTGTTATTAGTAC
47509561 ATCTTTGGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.14, C:0.18, G:0.14, T:0.55
Consensus pattern (22 bp):
CCTTTTGTCTTGTTATTAGTAC
Found at i:47515736 original size:23 final size:23
Alignment explanation
Indices: 47515704--47515753 Score: 93
Period size: 23 Copynumber: 2.2 Consensus size: 23
47515694 GTTTCAATTT
47515704 TAAC-TTGTTTCTCCACTTCACC
1 TAACTTTGTTTCTCCACTTCACC
47515726 TAACTTTGTTTCTCCACTTCACC
1 TAACTTTGTTTCTCCACTTCACC
47515749 TAACT
1 TAACT
47515754 AAAGTTTGTC
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 4 0.15
23 23 0.85
ACGTcount: A:0.20, C:0.34, G:0.04, T:0.42
Consensus pattern (23 bp):
TAACTTTGTTTCTCCACTTCACC
Found at i:47528083 original size:19 final size:18
Alignment explanation
Indices: 47528054--47528097 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
47528044 AATTCAAAAT
*
47528054 AAATTT-TAAAATTC-TA
1 AAATTTATAAAAATCTTA
47528070 AATATTTATAAAAATCTTA
1 AA-ATTTATAAAAATCTTA
47528089 AAATTTATA
1 AAATTTATA
47528098 TTTTAAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
16 2 0.08
17 4 0.17
18 14 0.58
19 4 0.17
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (18 bp):
AAATTTATAAAAATCTTA
Found at i:47528122 original size:25 final size:25
Alignment explanation
Indices: 47528074--47528122 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
47528064 ATTCTAAATA
* *
47528074 TTTATAAAAATCTTAAAATTTATAT
1 TTTATAAAAATCTAAAAATATATAT
47528099 TTTA-AAAAATCTAAAGAATATATA
1 TTTATAAAAATCTAAA-AATATATA
47528123 AAGAAAGTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 10 0.48
25 11 0.52
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.41
Consensus pattern (25 bp):
TTTATAAAAATCTAAAAATATATAT
Found at i:47531385 original size:33 final size:33
Alignment explanation
Indices: 47531336--47531402 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
47531326 AAGTAGAGGG
* *
47531336 ACTAAATTATTGAAAATAAAAGTACAGGGACTA
1 ACTAAATTATTAAAAATAAAAGTACAAGGACTA
* *
47531369 ACTAAATTCTTAAAAATAAAAGTATAAGGACTA
1 ACTAAATTATTAAAAATAAAAGTACAAGGACTA
47531402 A
1 A
47531403 ATTCCAAATT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.54, C:0.09, G:0.12, T:0.25
Consensus pattern (33 bp):
ACTAAATTATTAAAAATAAAAGTACAAGGACTA
Found at i:47531406 original size:29 final size:29
Alignment explanation
Indices: 47531324--47531406 Score: 85
Period size: 33 Copynumber: 2.7 Consensus size: 29
47531314 TTCAAATTTG
* * *
47531324 AAAAGTAGAGGGACTAAATTATTGAAAAT
1 AAAAGTACAGGGACTAAATTCTTAAAAAT
47531353 AAAAGTACAGGGACTAACTAAATTCTTAAAAAT
1 AAAAGTACAGGG----ACTAAATTCTTAAAAAT
* *
47531386 AAAAGTATAAGGACTAAATTC
1 AAAAGTACAGGGACTAAATTC
47531407 CAAATTTATG
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
29 20 0.44
33 25 0.56
ACGTcount: A:0.52, C:0.08, G:0.16, T:0.24
Consensus pattern (29 bp):
AAAAGTACAGGGACTAAATTCTTAAAAAT
Found at i:47532529 original size:614 final size:614
Alignment explanation
Indices: 47531362--47532590 Score: 2458
Period size: 614 Copynumber: 2.0 Consensus size: 614
47531352 TAAAAGTACA
47531362 GGGACTAACTAAATTCTTAAAAATAAAAGTATAAGGACTAAATTCCAAATTTATGAAGAGTACAT
1 GGGACTAACTAAATTCTTAAAAATAAAAGTATAAGGACTAAATTCCAAATTTATGAAGAGTACAT
47531427 GGATTTATGGTATGTATATTTTAACCTTTATACTACAAAACATTTATTATTAATATATCTATAAT
66 GGATTTATGGTATGTATATTTTAACCTTTATACTACAAAACATTTATTATTAATATATCTATAAT
47531492 TGTAATAAATTTTTATTATTAAAATATTAATATTTATTATTTTCAATAATTTTCTGTTGACCAAA
131 TGTAATAAATTTTTATTATTAAAATATTAATATTTATTATTTTCAATAATTTTCTGTTGACCAAA
47531557 TTGTTTTCTATGAAACAAACACAGAAAAATGCAGAAAATATTTTTTTGTAAATCATTTTACAGTG
196 TTGTTTTCTATGAAACAAACACAGAAAAATGCAGAAAATATTTTTTTGTAAATCATTTTACAGTG
47531622 AAACAAACGAAGCCTCAAGCACAAAGACGAAGTGTTATTATTTATGGGATTAATATCTTCCCCTT
261 AAACAAACGAAGCCTCAAGCACAAAGACGAAGTGTTATTATTTATGGGATTAATATCTTCCCCTT
47531687 AGTATCTTCTTGTCTCATTTTCATCCTCATCAAGGAAAAGCATTAGAAAATAGATACTCTGATTG
326 AGTATCTTCTTGTCTCATTTTCATCCTCATCAAGGAAAAGCATTAGAAAATAGATACTCTGATTG
47531752 TCGGTATAATTAAACTCCAAACCCACTCCATCAATTTAACATATCAGATTTCTAGCCTTTTGAAA
391 TCGGTATAATTAAACTCCAAACCCACTCCATCAATTTAACATATCAGATTTCTAGCCTTTTGAAA
47531817 TTAAAATTTCTAGGAATTATAAAAATGAGATGCTGTCGTCATATATTCCGGATGGTAATAAATAG
456 TTAAAATTTCTAGGAATTATAAAAATGAGATGCTGTCGTCATATATTCCGGATGGTAATAAATAG
47531882 ATGGAGTGGAGTTAGGTAAAAATAATCAATTGATTTGAGCAACTACTACCAGTTTAGTTGGGTAG
521 ATGGAGTGGAGTTAGGTAAAAATAATCAATTGATTTGAGCAACTACTACCAGTTTAGTTGGGTAG
47531947 TTACCATAGCGCATTTACTCTTCATAAAT
586 TTACCATAGCGCATTTACTCTTCATAAAT
47531976 GGGACTAACTAAATTCTTAAAAATAAAAGTATAAGGACTAAATTCCAAATTTATGAAGAGTACAT
1 GGGACTAACTAAATTCTTAAAAATAAAAGTATAAGGACTAAATTCCAAATTTATGAAGAGTACAT
47532041 GGATTTATGGTATGTATATTTTAACCTTTATACTACAAAACATTTATTATTAATATATCTATAAT
66 GGATTTATGGTATGTATATTTTAACCTTTATACTACAAAACATTTATTATTAATATATCTATAAT
47532106 TGTAATAAATTTTTATTATTAAAATATTAATATTTATTATTTTCAATAATTTTCTGTTGACCAAA
131 TGTAATAAATTTTTATTATTAAAATATTAATATTTATTATTTTCAATAATTTTCTGTTGACCAAA
47532171 TTGTTTTCTATGAAACAAACACAGAAAAATGCAGAAAATATTTTTTTGTAAATCATTTTACAGTG
196 TTGTTTTCTATGAAACAAACACAGAAAAATGCAGAAAATATTTTTTTGTAAATCATTTTACAGTG
47532236 AAACAAACGAAGCCTCAAGCACAAAGACGAAGTGTTATTATTTATGGGATTAATATCTTCCCCTT
261 AAACAAACGAAGCCTCAAGCACAAAGACGAAGTGTTATTATTTATGGGATTAATATCTTCCCCTT
47532301 AGTATCTTCTTGTCTCATTTTCATCCTCATCAAGGAAAAGCATTAGAAAATAGATACTCTGATTG
326 AGTATCTTCTTGTCTCATTTTCATCCTCATCAAGGAAAAGCATTAGAAAATAGATACTCTGATTG
47532366 TCGGTATAATTAAACTCCAAACCCACTCCATCAATTTAACATATCAGATTTCTAGCCTTTTGAAA
391 TCGGTATAATTAAACTCCAAACCCACTCCATCAATTTAACATATCAGATTTCTAGCCTTTTGAAA
47532431 TTAAAATTTCTAGGAATTATAAAAATGAGATGCTGTCGTCATATATTCCGGATGGTAATAAATAG
456 TTAAAATTTCTAGGAATTATAAAAATGAGATGCTGTCGTCATATATTCCGGATGGTAATAAATAG
47532496 ATGGAGTGGAGTTAGGTAAAAATAATCAATTGATTTGAGCAACTACTACCAGTTTAGTTGGGTAG
521 ATGGAGTGGAGTTAGGTAAAAATAATCAATTGATTTGAGCAACTACTACCAGTTTAGTTGGGTAG
47532561 TTACCATAGCGCATTTACTCTTCATAAAT
586 TTACCATAGCGCATTTACTCTTCATAAAT
47532590 G
1 G
47532591 CTGCAACTCA
Statistics
Matches: 615, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
614 615 1.00
ACGTcount: A:0.37, C:0.14, G:0.13, T:0.36
Consensus pattern (614 bp):
GGGACTAACTAAATTCTTAAAAATAAAAGTATAAGGACTAAATTCCAAATTTATGAAGAGTACAT
GGATTTATGGTATGTATATTTTAACCTTTATACTACAAAACATTTATTATTAATATATCTATAAT
TGTAATAAATTTTTATTATTAAAATATTAATATTTATTATTTTCAATAATTTTCTGTTGACCAAA
TTGTTTTCTATGAAACAAACACAGAAAAATGCAGAAAATATTTTTTTGTAAATCATTTTACAGTG
AAACAAACGAAGCCTCAAGCACAAAGACGAAGTGTTATTATTTATGGGATTAATATCTTCCCCTT
AGTATCTTCTTGTCTCATTTTCATCCTCATCAAGGAAAAGCATTAGAAAATAGATACTCTGATTG
TCGGTATAATTAAACTCCAAACCCACTCCATCAATTTAACATATCAGATTTCTAGCCTTTTGAAA
TTAAAATTTCTAGGAATTATAAAAATGAGATGCTGTCGTCATATATTCCGGATGGTAATAAATAG
ATGGAGTGGAGTTAGGTAAAAATAATCAATTGATTTGAGCAACTACTACCAGTTTAGTTGGGTAG
TTACCATAGCGCATTTACTCTTCATAAAT
Found at i:47533851 original size:33 final size:33
Alignment explanation
Indices: 47533802--47533868 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
47533792 AAGTAGAGGG
* *
47533802 ACTAAATTATTGAAAATAAAAGTACAGGGACTA
1 ACTAAATTATTAAAAATAAAAGTACAAGGACTA
* *
47533835 ACTAAATTCTTAAAAATAAAAGTATAAGGACTA
1 ACTAAATTATTAAAAATAAAAGTACAAGGACTA
47533868 A
1 A
47533869 ATTCCAAATT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.54, C:0.09, G:0.12, T:0.25
Consensus pattern (33 bp):
ACTAAATTATTAAAAATAAAAGTACAAGGACTA
Found at i:47533872 original size:29 final size:29
Alignment explanation
Indices: 47533790--47533872 Score: 85
Period size: 33 Copynumber: 2.7 Consensus size: 29
47533780 TTCAAATTTG
* * *
47533790 AAAAGTAGAGGGACTAAATTATTGAAAAT
1 AAAAGTACAGGGACTAAATTCTTAAAAAT
47533819 AAAAGTACAGGGACTAACTAAATTCTTAAAAAT
1 AAAAGTACAGGG----ACTAAATTCTTAAAAAT
* *
47533852 AAAAGTATAAGGACTAAATTC
1 AAAAGTACAGGGACTAAATTC
47533873 CAAATTTATG
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
29 20 0.44
33 25 0.56
ACGTcount: A:0.52, C:0.08, G:0.16, T:0.24
Consensus pattern (29 bp):
AAAAGTACAGGGACTAAATTCTTAAAAAT
Found at i:47539467 original size:5 final size:5
Alignment explanation
Indices: 47539454--47539484 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
47539444 GGCTGGCTGG
*
47539454 GTGCA GTGCT GTGCT GTGCT GTGCT GTGCT G
1 GTGCT GTGCT GTGCT GTGCT GTGCT GTGCT G
47539485 CTAACCCCCC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.03, C:0.19, G:0.42, T:0.35
Consensus pattern (5 bp):
GTGCT
Found at i:47540975 original size:12 final size:12
Alignment explanation
Indices: 47540958--47540983 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
47540948 CCCAACAATC
47540958 CCAACTCCAGCA
1 CCAACTCCAGCA
47540970 CCAACTCCAGCA
1 CCAACTCCAGCA
47540982 CC
1 CC
47540984 GATACCGGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.54, G:0.08, T:0.08
Consensus pattern (12 bp):
CCAACTCCAGCA
Found at i:47554004 original size:28 final size:28
Alignment explanation
Indices: 47553972--47554070 Score: 93
Period size: 28 Copynumber: 3.8 Consensus size: 28
47553962 AGTTAATGAT
*
47553972 ATTAAACTAATTAGTAACATTGAAATAC
1 ATTAAACTAATTAATAACATTGAAATAC
* **
47554000 ATTAAGCTAATT-AT-ACA-T-AACCAC
1 ATTAAACTAATTAATAACATTGAAATAC
* * *
47554024 -GT-AACTAATTAATTACTTTGAAATAC
1 ATTAAACTAATTAATAACATTGAAATAC
47554050 ATTAAACTAATTAATAACATT
1 ATTAAACTAATTAATAACATT
47554071 ATAAAAATAT
Statistics
Matches: 53, Mismatches: 12, Indels: 12
0.69 0.16 0.16
Matches are distributed among these distances:
22 7 0.13
23 3 0.06
24 6 0.11
25 2 0.04
26 7 0.13
27 2 0.04
28 26 0.49
ACGTcount: A:0.47, C:0.13, G:0.05, T:0.34
Consensus pattern (28 bp):
ATTAAACTAATTAATAACATTGAAATAC
Found at i:47561223 original size:20 final size:20
Alignment explanation
Indices: 47561198--47561235 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
47561188 CAGTCTGTGA
47561198 TTTTATTA-ATTTTCTACTAC
1 TTTTATTATATTTT-TACTAC
47561218 TTTTATTATATTTTTACT
1 TTTTATTATATTTTTACT
47561236 TAAAACTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.24, C:0.11, G:0.00, T:0.66
Consensus pattern (20 bp):
TTTTATTATATTTTTACTAC
Found at i:47576355 original size:14 final size:14
Alignment explanation
Indices: 47576327--47576377 Score: 50
Period size: 14 Copynumber: 3.5 Consensus size: 14
47576317 TTAATCAAAT
47576327 ATAAATAA-GTAATA
1 ATAAATAATGT-ATA
47576341 ATAAATAATGTATA
1 ATAAATAATGTATA
* *
47576355 ATTTAAATTATTTATA
1 A--TAAATAATGTATA
47576371 ATAAATA
1 ATAAATA
47576378 TGGTTTATTT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
14 17 0.55
15 2 0.06
16 12 0.39
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (14 bp):
ATAAATAATGTATA
Found at i:47577188 original size:12 final size:11
Alignment explanation
Indices: 47577159--47577187 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
47577149 CGAAAAATAA
47577159 TTAAAAATACT
1 TTAAAAATACT
47577170 TTAAAAATACT
1 TTAAAAATACT
47577181 TTAAAAA
1 TTAAAAA
47577188 AATTATAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.34
Consensus pattern (11 bp):
TTAAAAATACT
Found at i:47601094 original size:20 final size:21
Alignment explanation
Indices: 47601063--47601120 Score: 75
Period size: 20 Copynumber: 2.8 Consensus size: 21
47601053 AAACTATAAT
*
47601063 TTTTGTAGTTTTTGTAAA-TA
1 TTTTGAAGTTTTTGTAAATTA
*
47601083 TTTTGAA-TTTTTGAAAATTA
1 TTTTGAAGTTTTTGTAAATTA
47601103 TTTTGAATGTTTTTGTAA
1 TTTTGAA-GTTTTTGTAA
47601121 TTTTTGTTGA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
19 9 0.28
20 15 0.47
22 8 0.25
ACGTcount: A:0.28, C:0.00, G:0.14, T:0.59
Consensus pattern (21 bp):
TTTTGAAGTTTTTGTAAATTA
Found at i:47605888 original size:108 final size:109
Alignment explanation
Indices: 47605684--47605901 Score: 420
Period size: 108 Copynumber: 2.0 Consensus size: 109
47605674 TACCGAAATG
47605684 GGCCATTTTCCCCAAAATCGCGTCCACGTTAGCGCGATGTCAGGGGACGTGTTAGCAAATCGCGT
1 GGCCATTTTCCCCAAAATCGCGTCCACGTTAGCGCGATGTCAGGGGACGTGTTAGCAAATCGCGT
*
47605749 GGACGTCAGCGCGTTTTGCTGATGTGTTAGAAAATCGCGTCCTC
66 GGACGTCAGCGCGTTTTGCTGATGTGGTAGAAAATCGCGTCCTC
47605793 GGCCATTTT-CCCAAAATCGCGTCCACGTTAGCGCGATGTCAGGGGACGTGTTAGCAAATCGCGT
1 GGCCATTTTCCCCAAAATCGCGTCCACGTTAGCGCGATGTCAGGGGACGTGTTAGCAAATCGCGT
47605857 GGACGTCAGCGCGTTTTGCTGATGTGGTAGAAAATCGCGTCCTC
66 GGACGTCAGCGCGTTTTGCTGATGTGGTAGAAAATCGCGTCCTC
47605901 G
1 G
47605902 TAGGCGCGAT
Statistics
Matches: 108, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
108 99 0.92
109 9 0.08
ACGTcount: A:0.20, C:0.25, G:0.29, T:0.25
Consensus pattern (109 bp):
GGCCATTTTCCCCAAAATCGCGTCCACGTTAGCGCGATGTCAGGGGACGTGTTAGCAAATCGCGT
GGACGTCAGCGCGTTTTGCTGATGTGGTAGAAAATCGCGTCCTC
Found at i:47606109 original size:33 final size:33
Alignment explanation
Indices: 47606059--47606133 Score: 98
Period size: 34 Copynumber: 2.2 Consensus size: 33
47606049 AAACTAATCC
* *
47606059 TCTCTCAAATTTCCTCTC-AATTTCTTCTAAATT
1 TCTCTC-AATTTCCTCTCAAATTCCTTCAAAATT
*
47606092 TCCTCTCAATTTGCTCTCAAATTCCTTCAAAATT
1 T-CTCTCAATTTCCTCTCAAATTCCTTCAAAATT
47606126 TCTCTCAA
1 TCTCTCAA
47606134 ATCCATATTT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
33 18 0.49
34 19 0.51
ACGTcount: A:0.25, C:0.29, G:0.01, T:0.44
Consensus pattern (33 bp):
TCTCTCAATTTCCTCTCAAATTCCTTCAAAATT
Found at i:47606116 original size:22 final size:22
Alignment explanation
Indices: 47606059--47606135 Score: 97
Period size: 22 Copynumber: 3.5 Consensus size: 22
47606049 AAACTAATCC
47606059 TCTCTCAAATTTCCTCTCAATT
1 TCTCTCAAATTTCCTCTCAATT
47606081 TCT-TCTAAATTTCCTCTCAATT
1 TCTCTC-AAATTTCCTCTCAATT
47606103 TGCTCTCAAA-TTCCT-TCAAAATT
1 T-CTCTCAAATTTCCTCTC--AATT
47606126 TCTCTCAAAT
1 TCTCTCAAAT
47606136 CCATATTTAT
Statistics
Matches: 49, Mismatches: 0, Indels: 11
0.82 0.00 0.18
Matches are distributed among these distances:
21 4 0.08
22 33 0.67
23 10 0.20
24 2 0.04
ACGTcount: A:0.26, C:0.29, G:0.01, T:0.44
Consensus pattern (22 bp):
TCTCTCAAATTTCCTCTCAATT
Found at i:47606135 original size:11 final size:11
Alignment explanation
Indices: 47606059--47606135 Score: 72
Period size: 11 Copynumber: 6.9 Consensus size: 11
47606049 AAACTAATCC
47606059 TCTCTCAAATT
1 TCTCTCAAATT
47606070 TCCTCTC-AATT
1 T-CTCTCAAATT
47606081 TCT-TCTAAATT
1 TCTCTC-AAATT
47606092 TCCTCTC-AATT
1 T-CTCTCAAATT
47606103 TGCTCTCAAATT
1 T-CTCTCAAATT
*
47606115 CCT-TCAAAATT
1 TCTCTC-AAATT
47606126 TCTCTCAAAT
1 TCTCTCAAAT
47606136 CCATATTTAT
Statistics
Matches: 55, Mismatches: 3, Indels: 16
0.74 0.04 0.22
Matches are distributed among these distances:
9 2 0.04
10 4 0.07
11 34 0.62
12 13 0.24
13 2 0.04
ACGTcount: A:0.26, C:0.29, G:0.01, T:0.44
Consensus pattern (11 bp):
TCTCTCAAATT
Found at i:47607075 original size:31 final size:31
Alignment explanation
Indices: 47607020--47607082 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 31
47607010 TATATATTAA
** *
47607020 TTTTAAAATAATAATATGAAATTTTTAATTT
1 TTTTAAAATAATAATAAAAAATTTTCAATTT
47607051 TTTTAAAA-AATAATAAAAACATTTTCAATTT
1 TTTTAAAATAATAATAAAAA-ATTTTCAATTT
47607082 T
1 T
47607083 AAATTTGACA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 9 0.32
31 19 0.68
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.48
Consensus pattern (31 bp):
TTTTAAAATAATAATAAAAAATTTTCAATTT
Found at i:47609108 original size:51 final size:54
Alignment explanation
Indices: 47609004--47609108 Score: 137
Period size: 54 Copynumber: 2.0 Consensus size: 54
47608994 AATTCGAAAA
* * *
47609004 AAAAAGTTATTAGGGTTTAGGAGGAAGTTAAAATTTTGGGGGAAAATTAAAAGG
1 AAAAAGTTATTAGGGTTTAGGAGGAAGATAAAATTTTGGAGGAAAAGTAAAAGG
*
47609058 AAAAAGTTTTTAGGGTTT-GG-GGAA-ATAAAATTTTTGGAGG-AAAGTAAAAGG
1 AAAAAGTTATTAGGGTTTAGGAGGAAGATAAAA-TTTTGGAGGAAAAGTAAAAGG
47609109 GTTTGACTTT
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
51 15 0.33
52 12 0.26
53 2 0.04
54 17 0.37
ACGTcount: A:0.42, C:0.00, G:0.30, T:0.29
Consensus pattern (54 bp):
AAAAAGTTATTAGGGTTTAGGAGGAAGATAAAATTTTGGAGGAAAAGTAAAAGG
Found at i:47614195 original size:41 final size:40
Alignment explanation
Indices: 47614139--47614224 Score: 109
Period size: 41 Copynumber: 2.1 Consensus size: 40
47614129 AGGATATGTT
* * *
47614139 GTTTTTGGAGAGAGAAGTGAAAATACGTCTTACATGACGC
1 GTTTTTGGAGAGAGAAATAAAAATACGTCTTACAGGACGC
** *
47614179 GTTTTTAGGAGAGAGAAATAAAAATGTGTCTTATAGGACGC
1 GTTTTT-GGAGAGAGAAATAAAAATACGTCTTACAGGACGC
47614220 GTTTT
1 GTTTT
47614225 CAGGGTAACG
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
40 6 0.15
41 33 0.85
ACGTcount: A:0.33, C:0.09, G:0.27, T:0.31
Consensus pattern (40 bp):
GTTTTTGGAGAGAGAAATAAAAATACGTCTTACAGGACGC
Found at i:47621348 original size:131 final size:131
Alignment explanation
Indices: 47621192--47621430 Score: 365
Period size: 131 Copynumber: 1.8 Consensus size: 131
47621182 TTCTTATTCC
* *
47621192 TAATTTAAAACATGTTAAATTATAATACAATATACATGA-ATATTTAATTTAAAGCACATTAAAT
1 TAATTTAAAACA-GTTAAATTATAATACAATATACAT-ACAAATTTAATTTAAAACACATTAAAT
** * *
47621256 TATAATACAATATACATGCATATTTAATTTAAAATACCTTAAATTATAATACAATATACATGCAT
64 TATAATACAATATACAAACATATTTAATTTAAAACACATTAAATTATAATACAATATACATGCAT
47621321 ATT
129 ATT
* *
47621324 TAATTTAAACACA-TTAAATTATAATACAATATACATACAAATTTATTTTAAAACAGATTAAATT
1 TAATTTAAA-ACAGTTAAATTATAATACAATATACATACAAATTTAATTTAAAACACATTAAATT
47621388 ATAATACAATATACAAACATATTTAATTTAAAACACATTAAAT
65 ATAATACAATATACAAACATATTTAATTTAAAACACATTAAAT
47621431 GAAATAAATT
Statistics
Matches: 97, Mismatches: 8, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
130 1 0.01
131 84 0.87
132 9 0.09
133 3 0.03
ACGTcount: A:0.51, C:0.10, G:0.03, T:0.37
Consensus pattern (131 bp):
TAATTTAAAACAGTTAAATTATAATACAATATACATACAAATTTAATTTAAAACACATTAAATTA
TAATACAATATACAAACATATTTAATTTAAAACACATTAAATTATAATACAATATACATGCATAT
T
Found at i:47621385 original size:87 final size:86
Alignment explanation
Indices: 47621192--47621430 Score: 361
Period size: 87 Copynumber: 2.7 Consensus size: 86
47621182 TTCTTATTCC
*
47621192 TAATTTAAAACATGTTAAATTATAATACAATATACATGAATATTTAATTTAAAGCACATTAAATT
1 TAATTTAAAACA-GTTAAATTATAATACAATATACATGCATATTTAATTTAAA-CACATTAAATT
* *
47621257 ATAATACAATATACATGCATATT
64 ATAATACAATATACATACAAATT
* *
47621280 TAATTTAAAATACCTTAAATTATAATACAATATACATGCATATTTAATTTAAACACATTAAATTA
1 TAATTTAAAACA-GTTAAATTATAATACAATATACATGCATATTTAATTTAAACACATTAAATTA
47621345 TAATACAATATACATACAAATT
65 TAATACAATATACATACAAATT
* **
47621367 TATTTTAAAACAGATTAAATTATAATACAATATACAAACATATTTAATTTAAAACACATTAAAT
1 TAATTTAAAACAG-TTAAATTATAATACAATATACATGCATATTTAATTT-AAACACATTAAAT
47621431 GAAATAAATT
Statistics
Matches: 138, Mismatches: 11, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
87 76 0.55
88 62 0.45
ACGTcount: A:0.51, C:0.10, G:0.03, T:0.37
Consensus pattern (86 bp):
TAATTTAAAACAGTTAAATTATAATACAATATACATGCATATTTAATTTAAACACATTAAATTAT
AATACAATATACATACAAATT
Found at i:47621428 original size:44 final size:44
Alignment explanation
Indices: 47621192--47621430 Score: 356
Period size: 44 Copynumber: 5.5 Consensus size: 44
47621182 TTCTTATTCC
**
47621192 TAATTTAAAACATGTTAAATTATAATACAATATACATGA-ATATT
1 TAATTTAAAACACATTAAATTATAATACAATATACAT-ACATATT
* *
47621236 TAATTTAAAGCACATTAAATTATAATACAATATACATGCATATT
1 TAATTTAAAACACATTAAATTATAATACAATATACATACATATT
* * *
47621280 TAATTTAAAATACCTTAAATTATAATACAATATACATGCATATT
1 TAATTTAAAACACATTAAATTATAATACAATATACATACATATT
*
47621324 TAATTT-AAACACATTAAATTATAATACAATATACATACAAATT
1 TAATTTAAAACACATTAAATTATAATACAATATACATACATATT
* * *
47621367 TATTTTAAAACAGATTAAATTATAATACAATATACAAACATATT
1 TAATTTAAAACACATTAAATTATAATACAATATACATACATATT
47621411 TAATTTAAAACACATTAAAT
1 TAATTTAAAACACATTAAAT
47621431 GAAATAAATT
Statistics
Matches: 176, Mismatches: 17, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
43 38 0.22
44 138 0.78
ACGTcount: A:0.51, C:0.10, G:0.03, T:0.37
Consensus pattern (44 bp):
TAATTTAAAACACATTAAATTATAATACAATATACATACATATT
Found at i:47621504 original size:27 final size:26
Alignment explanation
Indices: 47621474--47621558 Score: 74
Period size: 26 Copynumber: 3.4 Consensus size: 26
47621464 AAAAAAAACG
47621474 TAAATTAAAATGGA-AAGAAAGATAATT
1 TAAA-TAAAATGGAGAA-AAAGATAATT
*
47621501 TAAATGAAAT-GAGAAAAA-A-AA--
1 TAAATAAAATGGAGAAAAAGATAATT
* *
47621522 TAAATTTAAATGGATAAAAAGATAATT
1 TAAA-TAAAATGGAGAAAAAGATAATT
47621549 TAAATAAAAT
1 TAAATAAAAT
47621559 TGAAATGAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 15
0.71 0.06 0.23
Matches are distributed among these distances:
21 4 0.09
22 5 0.11
23 9 0.19
24 2 0.04
25 7 0.15
26 12 0.26
27 8 0.17
ACGTcount: A:0.62, C:0.00, G:0.12, T:0.26
Consensus pattern (26 bp):
TAAATAAAATGGAGAAAAAGATAATT
Found at i:47621505 original size:21 final size:21
Alignment explanation
Indices: 47621476--47621553 Score: 59
Period size: 21 Copynumber: 3.4 Consensus size: 21
47621466 AAAAAACGTA
*
47621476 AATTAAAATGGA-AAGAAAGAT
1 AATTTAAATGGAGAA-AAAGAT
*
47621497 AATTTAAATGAAATGAGAAAAAAAAT
1 AATTTAAATG----GAG-AAAAAGAT
*
47621523 AAATTTAAATGGATAAAAAGAT
1 -AATTTAAATGGAGAAAAAGAT
47621545 AATTTAAAT
1 AATTTAAAT
47621554 AAAATTGAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 14
0.72 0.06 0.22
Matches are distributed among these distances:
21 18 0.39
22 7 0.15
23 2 0.04
25 2 0.04
26 5 0.11
27 12 0.26
ACGTcount: A:0.62, C:0.00, G:0.13, T:0.26
Consensus pattern (21 bp):
AATTTAAATGGAGAAAAAGAT
Found at i:47621524 original size:26 final size:27
Alignment explanation
Indices: 47621481--47621533 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
47621471 ACGTAAATTA
*
47621481 AAATGGAAAGAAAGAT-AATTTAAATG
1 AAATGGAAAGAAAAATAAATTTAAATG
47621507 AAATGAGAAA-AAAAATAAATTTAAATG
1 AAATG-GAAAGAAAAATAAATTTAAATG
47621534 GATAAAAAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 10 0.42
27 14 0.58
ACGTcount: A:0.62, C:0.00, G:0.15, T:0.23
Consensus pattern (27 bp):
AAATGGAAAGAAAAATAAATTTAAATG
Found at i:47621570 original size:48 final size:48
Alignment explanation
Indices: 47621463--47621558 Score: 140
Period size: 48 Copynumber: 2.0 Consensus size: 48
47621453 AAATTAATAT
*
47621463 GAAAAAAAACGTAAATTAAAATGGAAAGAAAGATAATTTAAATGAAATGA
1 GAAAAAAAA--TAAATTAAAATGGAAAGAAAGATAATTTAAATAAAATGA
*
47621513 GAAAAAAAATAAATTTAAATGGATAA-AAAGATAATTTAAATAAAAT
1 GAAAAAAAATAAATTAAAATGGA-AAGAAAGATAATTTAAATAAAAT
47621559 TGAAATGAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
48 32 0.74
49 2 0.05
50 9 0.21
ACGTcount: A:0.64, C:0.01, G:0.12, T:0.23
Consensus pattern (48 bp):
GAAAAAAAATAAATTAAAATGGAAAGAAAGATAATTTAAATAAAATGA
Found at i:47621603 original size:17 final size:16
Alignment explanation
Indices: 47621550--47621608 Score: 57
Period size: 17 Copynumber: 3.6 Consensus size: 16
47621540 AAGATAATTT
47621550 AAAT-AAAATTGAAATG
1 AAATGAAAA-TGAAATG
*
47621566 AAAATGAAAATGAAATA
1 -AAATGAAAATGAAATG
*
47621583 AAATGGAAATAGAAATG
1 AAATGAAAAT-GAAATG
*
47621600 AAATCAAAA
1 AAATGAAAA
47621609 AAAAAGTTGA
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
16 9 0.26
17 22 0.63
18 4 0.11
ACGTcount: A:0.66, C:0.02, G:0.14, T:0.19
Consensus pattern (16 bp):
AAATGAAAATGAAATG
Found at i:47621834 original size:21 final size:21
Alignment explanation
Indices: 47621810--47621849 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
47621800 TTTAAATTGA
47621810 GAAAAAATTTAAATAAAATAT
1 GAAAAAATTTAAATAAAATAT
*
47621831 GAAAAATTTTAAATAAAAT
1 GAAAAAATTTAAATAAAAT
47621850 GTAATTGAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (21 bp):
GAAAAAATTTAAATAAAATAT
Found at i:47622006 original size:21 final size:21
Alignment explanation
Indices: 47621982--47622045 Score: 94
Period size: 21 Copynumber: 3.0 Consensus size: 21
47621972 TTAGGAAAAT
47621982 TAAATTTAAATGGAAATGAAA
1 TAAATTTAAATGGAAATGAAA
* *
47622003 TAAATTTAAATGGAAAAT-TAT
1 TAAATTTAAATGG-AAATGAAA
47622024 TAAATTTAAATGGAAATGAAA
1 TAAATTTAAATGGAAATGAAA
47622045 T
1 T
47622046 GAAAAAAAGA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
20 4 0.11
21 29 0.78
22 4 0.11
ACGTcount: A:0.55, C:0.00, G:0.12, T:0.33
Consensus pattern (21 bp):
TAAATTTAAATGGAAATGAAA
Found at i:47626673 original size:89 final size:90
Alignment explanation
Indices: 47626561--47626845 Score: 378
Period size: 90 Copynumber: 3.2 Consensus size: 90
47626551 ATTCTAGAAT
* * * * *
47626561 ATTAATACACAAAAATATAAAATTCAAAC-AAAAATAATAC-GCACTAAATTAAATTTAAACACC
1 ATTAATGCACGAAAATTTTAAATTCAAACTAAATATAATACAG-ACTAAATTAAATTTAAACACC
*
47626624 CAACAAACTACAAATAGATAGGTTAA
65 CAACAAACTACAAATAGATAGGTAAA
* * * *
47626650 ATTAATGTACGAAAATTTTAAATTCAAACTACATATTATACAGACTAAATTAAATTTAAATACCC
1 ATTAATGCACGAAAATTTTAAATTCAAACTAAATATAATACAGACTAAATTAAATTTAAACACCC
*
47626715 AACAAACTACAAACAGAT-GGATAAA
66 AACAAACTACAAATAGATAGG-TAAA
* * * * *
47626740 ATTAGTGCACGAAATTTTTAAATTCAAACTATATATAACACAGACTAAATTAAATTTAAACACCT
1 ATTAATGCACGAAAATTTTAAATTCAAACTAAATATAATACAGACTAAATTAAATTTAAACACCC
47626805 AACAAACTACAAATAGATAGGTAAA
66 AACAAACTACAAATAGATAGGTAAA
*
47626830 ATTAATACACGAAAAT
1 ATTAATGCACGAAAAT
47626846 ATAAAAATGA
Statistics
Matches: 169, Mismatches: 23, Indels: 7
0.85 0.12 0.04
Matches are distributed among these distances:
89 26 0.15
90 140 0.83
91 3 0.02
ACGTcount: A:0.53, C:0.15, G:0.06, T:0.26
Consensus pattern (90 bp):
ATTAATGCACGAAAATTTTAAATTCAAACTAAATATAATACAGACTAAATTAAATTTAAACACCC
AACAAACTACAAATAGATAGGTAAA
Found at i:47627656 original size:104 final size:105
Alignment explanation
Indices: 47627544--47627841 Score: 352
Period size: 104 Copynumber: 2.8 Consensus size: 105
47627534 CCTAAAGTAA
*
47627544 AAAAAAAAAGTGCATTAGGAGTGAAAAAATGTACTTGGTGTCGGCCATCTACTTGCCAGCACACA
1 AAAAAAAAAGTGCATTAGGAGTGAAAAAATGTACTTGGTG-CGGCCATCTACTTGCCAGCACTCA
* *
47627609 AATTTTTTTAAATGACACTGATGTCGGCCATCAGTGT-CCC
65 ATTTTTTTTAAATGACACTGATGCCGGCCATCAGTGTCCCC
* * * *
47627649 -AAAAAAAAGTGCATTGGGAGTCG-AAAAATATACTTGGTGCCGACTATCTACTTGCCAGCACTC
1 AAAAAAAAAGTGCATTAGGAGT-GAAAAAATGTACTTGGTG-CGGCCATCTACTTGCCAGCACTC
* *
47627712 AATTTTTTCTTAAATGACACTGGTGCCGGTCATCAGTGTCCCC
64 AATTTTTT-TTAAATGACACTGATGCCGGCCATCAGTGTCCCC
** ** *
47627755 AAAAAAAAAGGTGCCCTAGGAGCCAAAAAAATGTACTTGGTGCTGGCCATCTA-TTGGCCAACAC
1 AAAAAAAAA-GTGCATTAGGAG-TGAAAAAATGTACTTGGTGC-GGCCATCTACTT-GCCAGCAC
*
47627819 TCGATTTTTTTTAAAATGACACT
62 TCAATTTTTTTT-AAATGACACT
47627842 AGTACCGACC
Statistics
Matches: 163, Mismatches: 20, Indels: 16
0.82 0.10 0.08
Matches are distributed among these distances:
104 62 0.38
105 28 0.17
106 3 0.02
107 8 0.05
108 14 0.09
109 48 0.29
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.27
Consensus pattern (105 bp):
AAAAAAAAAGTGCATTAGGAGTGAAAAAATGTACTTGGTGCGGCCATCTACTTGCCAGCACTCAA
TTTTTTTTAAATGACACTGATGCCGGCCATCAGTGTCCCC
Found at i:47627894 original size:109 final size:104
Alignment explanation
Indices: 47627543--47627913 Score: 349
Period size: 109 Copynumber: 3.5 Consensus size: 104
47627533 TCCTAAAGTA
* * * *
47627543 AAAAAAAAAAGTGCATTAGGAG-TGAAAAAATGTACTTGGTGTCGGCCATCTACTTGCCAGCACA
1 AAAAAAAAAAGTGCCTTAGGAGCCG-AAAAATGTACTTGGTGCCGGCCATCTACTTGCCAGCACT
*
47627607 CAAATTTTTTTAAATGACACTGATGT-CGGCCATCAGTGTCC
65 CAATTTTTTTTAAATGACACT-A-GTCCGGCCATCAGTGTCC
* * * * * * *
47627648 -CAAAAAAAAGTGCATTGGGAGTCGAAAAATATACTTGGTGCCGACTATCTACTTGCCAGCACTC
1 AAAAAAAAAAGTGCCTTAGGAGCCGAAAAATGTACTTGGTGCCGGCCATCTACTTGCCAGCACTC
* *
47627712 AATTTTTTCTTAAATGACACTGGTGCCGGTCATCAGTGTCCCC
66 AATTTTTT-TTAAATGACACTAGT-CCGGCCATCAGTGT--CC
* * * * *
47627755 AAAAAAAAAGGTGCCCTAGGAGCCAAAAAAATGTACTTGGTGCTGGCCATCTA-TTGGCCAACAC
1 AAAAAAAAAAGTGCCTTAGGAGCC-GAAAAATGTACTTGGTGCCGGCCATCTACTT-GCCAGCAC
* * *
47627819 TCGATTTTTTTTAAAATGACACTAGTACCGACCATCAATGTCC
64 TCAATTTTTTTT-AAATGACACTAGT-CCGGCCATCAGTGTCC
*
47627862 AAAAGTAAAAAAAGTGCCTTTGG-GCCGGAAAAATGTA-TCTGGTGCCGGCCAT
1 -AAA--AAAAAAAGTGCCTTAGGAGCC-GAAAAATGTACT-TGGTGCCGGCCAT
47627914 TACATGGTCA
Statistics
Matches: 217, Mismatches: 35, Indels: 24
0.79 0.13 0.09
Matches are distributed among these distances:
103 2 0.01
104 61 0.28
105 25 0.12
107 4 0.02
108 25 0.12
109 86 0.40
110 14 0.06
ACGTcount: A:0.33, C:0.21, G:0.20, T:0.26
Consensus pattern (104 bp):
AAAAAAAAAAGTGCCTTAGGAGCCGAAAAATGTACTTGGTGCCGGCCATCTACTTGCCAGCACTC
AATTTTTTTTAAATGACACTAGTCCGGCCATCAGTGTCC
Found at i:47639188 original size:2 final size:2
Alignment explanation
Indices: 47639181--47639215 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
47639171 NNNNNNNNTC
47639181 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
47639216 CAATAAAAGA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:47648188 original size:24 final size:24
Alignment explanation
Indices: 47648152--47648204 Score: 97
Period size: 24 Copynumber: 2.2 Consensus size: 24
47648142 ATTTGTAAAC
*
47648152 TCTGGTAATGCTCTGTAACCCTGT
1 TCTGGTAACGCTCTGTAACCCTGT
47648176 TCTGGTAACGCTCTGTAACCCTGT
1 TCTGGTAACGCTCTGTAACCCTGT
47648200 TCTGG
1 TCTGG
47648205 CAACAGATTC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.15, C:0.26, G:0.23, T:0.36
Consensus pattern (24 bp):
TCTGGTAACGCTCTGTAACCCTGT
Found at i:47656762 original size:16 final size:18
Alignment explanation
Indices: 47656730--47656765 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
47656720 TGTAATGTTT
47656730 TATATTATGTTATATTTA
1 TATATTATGTTATATTTA
47656748 TATATTAT-TTA-ATTTA
1 TATATTATGTTATATTTA
47656764 TA
1 TA
47656766 ACACATAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 7 0.39
17 3 0.17
18 8 0.44
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (18 bp):
TATATTATGTTATATTTA
Found at i:47662194 original size:3 final size:3
Alignment explanation
Indices: 47662186--47662213 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
47662176 AACGGATTCT
47662186 ACC ACC ACC ACC ACC ACC ACC ACC ACC A
1 ACC ACC ACC ACC ACC ACC ACC ACC ACC A
47662214 TCGATAGAGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.36, C:0.64, G:0.00, T:0.00
Consensus pattern (3 bp):
ACC
Found at i:47665174 original size:15 final size:15
Alignment explanation
Indices: 47665157--47665189 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 15
47665147 AAGGTATAAT
47665157 AAAATATTAAAAAATA
1 AAAAT-TTAAAAAATA
47665173 AAAATTTAAAAAATA
1 AAAATTTAAAAAATA
47665188 AA
1 AA
47665190 GACATATATC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (15 bp):
AAAATTTAAAAAATA
Found at i:47671212 original size:207 final size:207
Alignment explanation
Indices: 47670857--47671272 Score: 814
Period size: 207 Copynumber: 2.0 Consensus size: 207
47670847 CAAGGTCAAG
47670857 TACAACTCTGATGGCTCGGTTGAAAGATTTAAAGCCAGACTTGTTAGGAAGGGTTATACTCAGCA
1 TACAACTCTGATGGCTCGGTTGAAAGATTTAAAGCCAGACTTGTTAGGAAGGGTTATACTCAGCA
47670922 GGCAGGTTTTTTATTTTCACGACACTTTCCCCTGTTGCAAAGCAAGTCACAATTTGCACGGTCAT
66 GGCAGGTTTTTTATTTTCACGACACTTTCCCCTGTTGCAAAGCAAGTCACAATTTGCACGGTCAT
47670987 TGCTCTTGCTGTATAGTTTGGTTGGCCCTTGTTTCAAATGGATGCCTATAATGCAAGGAGATTTA
131 TGCTCTTGCTGTATAGTTTGGTTGGCCCTTGTTTCAAATGGATGCCTATAATGCAAGGAGATTTA
47671052 CATGAGAAGATT
196 CATGAGAAGATT
47671064 TACAACTCTGATGGCTCGGTTGAAAGATTTAAAGCCAGACTTGTTAGGAAGGGTTATACTCAGCA
1 TACAACTCTGATGGCTCGGTTGAAAGATTTAAAGCCAGACTTGTTAGGAAGGGTTATACTCAGCA
*
47671129 GGCAGGTTTTTTATTTTCACGACACTTTCCCCTGTTGCGAAGCAAGTCACAATTTGCACGGTCAT
66 GGCAGGTTTTTTATTTTCACGACACTTTCCCCTGTTGCAAAGCAAGTCACAATTTGCACGGTCAT
47671194 TGCTCTTGCTGTATAGTTTGGTTGGCCCTTGTTTCAAATGGATGCCTATAATGCAAGGAGATTTA
131 TGCTCTTGCTGTATAGTTTGGTTGGCCCTTGTTTCAAATGGATGCCTATAATGCAAGGAGATTTA
*
47671259 CATGAGAAGGTT
196 CATGAGAAGATT
47671271 TA
1 TA
47671273 TATGACTCTT
Statistics
Matches: 207, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
207 207 1.00
ACGTcount: A:0.26, C:0.18, G:0.23, T:0.33
Consensus pattern (207 bp):
TACAACTCTGATGGCTCGGTTGAAAGATTTAAAGCCAGACTTGTTAGGAAGGGTTATACTCAGCA
GGCAGGTTTTTTATTTTCACGACACTTTCCCCTGTTGCAAAGCAAGTCACAATTTGCACGGTCAT
TGCTCTTGCTGTATAGTTTGGTTGGCCCTTGTTTCAAATGGATGCCTATAATGCAAGGAGATTTA
CATGAGAAGATT
Found at i:47678767 original size:4 final size:4
Alignment explanation
Indices: 47678758--47678786 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
47678748 ATTTTCAAGT
47678758 TACA TACA TACA TACA TACA TACA TACA T
1 TACA TACA TACA TACA TACA TACA TACA T
47678787 CATTTTTTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.48, C:0.24, G:0.00, T:0.28
Consensus pattern (4 bp):
TACA
Found at i:47680376 original size:76 final size:76
Alignment explanation
Indices: 47680277--47680494 Score: 366
Period size: 76 Copynumber: 2.9 Consensus size: 76
47680267 TTAACTTAGT
* * *
47680277 TCTT-TTATAACTAGAGAAGTTATAAATTAATATATAGTAAAATTGTACTTTGGCCCCCATAAAA
1 TCTTCTTATAAATAAAGAAATTATAAATTAATATATAGTAAAATTGTACTTTGGCCCCCATAAAA
47680341 ATTTTTTCTAG
66 ATTTTTTCTAG
47680352 TCTTCTTATAAATAAAGAAATTATAAATTAATATATAGTAAAATTGTACTTTGGCCCCCATAAAA
1 TCTTCTTATAAATAAAGAAATTATAAATTAATATATAGTAAAATTGTACTTTGGCCCCCATAAAA
47680417 ATTTTTTCTAG
66 ATTTTTTCTAG
** **
47680428 TCTTCTTATAAATAAAGAAATTATAAATTAATATATAGTAAAATTACACTTTAACCCCCATAAAA
1 TCTTCTTATAAATAAAGAAATTATAAATTAATATATAGTAAAATTGTACTTTGGCCCCCATAAAA
47680493 AT
66 AT
47680495 GAAATGATTT
Statistics
Matches: 135, Mismatches: 7, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
75 4 0.03
76 131 0.97
ACGTcount: A:0.42, C:0.12, G:0.07, T:0.38
Consensus pattern (76 bp):
TCTTCTTATAAATAAAGAAATTATAAATTAATATATAGTAAAATTGTACTTTGGCCCCCATAAAA
ATTTTTTCTAG
Found at i:47690785 original size:6 final size:6
Alignment explanation
Indices: 47690774--47690819 Score: 92
Period size: 6 Copynumber: 7.7 Consensus size: 6
47690764 ATATCATATT
47690774 ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA ATTA
1 ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA ATTA
47690820 GAAAATAAAC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 40 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (6 bp):
ATTAAA
Found at i:47691884 original size:21 final size:22
Alignment explanation
Indices: 47691860--47691912 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
47691850 AAAAAAATTA
47691860 AAATAAAAGAAAAG-ATAA-AAG
1 AAATAAAA-AAAAGTATAACAAG
**
47691881 AAATTCAAAAAAGTATAACAAG
1 AAATAAAAAAAAGTATAACAAG
47691903 AAATAAAAAA
1 AAATAAAAAA
47691913 TAATAATTGT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 5 0.19
21 10 0.38
22 11 0.42
ACGTcount: A:0.74, C:0.04, G:0.09, T:0.13
Consensus pattern (22 bp):
AAATAAAAAAAAGTATAACAAG
Found at i:47702590 original size:6 final size:6
Alignment explanation
Indices: 47702565--47702607 Score: 56
Period size: 6 Copynumber: 7.5 Consensus size: 6
47702555 TTTAGTTGAT
47702565 AAAT-A AAAT-A AAAT-A AAATAA AAATAA AAATAAA AAATAA AAA
1 AAATAA AAATAA AAATAA AAATAA AAATAA AAAT-AA AAATAA AAA
47702608 AACATAATAA
Statistics
Matches: 36, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
5 14 0.39
6 16 0.44
7 6 0.17
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AAATAA
Found at i:47702606 original size:5 final size:5
Alignment explanation
Indices: 47702565--47702599 Score: 52
Period size: 5 Copynumber: 6.6 Consensus size: 5
47702555 TTTAGTTGAT
47702565 AAATA AAATA AAATA AAATAA AAATAA AAATA AAA
1 AAATA AAATA AAATA AAAT-A AAAT-A AAATA AAA
47702600 AATAAAAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 18 0.62
6 11 0.38
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (5 bp):
AAATA
Found at i:47702614 original size:10 final size:9
Alignment explanation
Indices: 47702563--47702614 Score: 52
Period size: 10 Copynumber: 5.4 Consensus size: 9
47702553 AATTTAGTTG
*
47702563 ATAAATAAA
1 ATAAAAAAA
47702572 ATAAAATAAA
1 ATAAAA-AAA
47702582 ATAAAAATAA
1 ATAAAAA-AA
47702592 A-AATAAAAA
1 ATAA-AAAAA
47702601 ATAAAAAAA
1 ATAAAAAAA
47702610 CATAA
1 -ATAA
47702615 TAACAAAATT
Statistics
Matches: 37, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
9 16 0.43
10 21 0.57
ACGTcount: A:0.81, C:0.02, G:0.00, T:0.17
Consensus pattern (9 bp):
ATAAAAAAA
Found at i:47702617 original size:13 final size:12
Alignment explanation
Indices: 47702563--47702609 Score: 51
Period size: 13 Copynumber: 3.8 Consensus size: 12
47702553 AATTTAGTTG
47702563 ATAAATAAAATAAA
1 ATAAA-AAAA-AAA
*
47702577 AT-AAAATAAAA
1 ATAAAAAAAAAA
47702588 ATAAAAATAAAAA
1 ATAAAAA-AAAAA
47702601 ATAAAAAAA
1 ATAAAAAAA
47702610 CATAATAACA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
11 5 0.17
12 9 0.31
13 13 0.45
14 2 0.07
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (12 bp):
ATAAAAAAAAAA
Found at i:47705425 original size:17 final size:17
Alignment explanation
Indices: 47705405--47705456 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 17
47705395 GGCAAGCACC
47705405 AACAGAGAAAAAACAAA
1 AACAGAGAAAAAACAAA
*
47705422 AACAGAGCAAAATAA-AGA
1 AACAGAG-AAAA-AACAAA
*
47705440 AACAAAGAAACAAACAA
1 AACAGAGAAA-AAACAA
47705457 TCAAATGCCT
Statistics
Matches: 28, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
17 12 0.43
18 14 0.50
19 2 0.07
ACGTcount: A:0.73, C:0.13, G:0.12, T:0.02
Consensus pattern (17 bp):
AACAGAGAAAAAACAAA
Found at i:47716264 original size:13 final size:13
Alignment explanation
Indices: 47716222--47716273 Score: 61
Period size: 13 Copynumber: 4.0 Consensus size: 13
47716212 AAAGATGAAA
47716222 ACTTGATG-AAAG
1 ACTTGATGAAAAG
* * *
47716234 ACTTAATTAAAAAC
1 ACTTGA-TGAAAAG
47716248 ACTTGATGAAAAG
1 ACTTGATGAAAAG
47716261 ACTTGATGAAAAG
1 ACTTGATGAAAAG
47716274 CTTAAAAAGA
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
12 5 0.16
13 19 0.59
14 8 0.25
ACGTcount: A:0.48, C:0.10, G:0.17, T:0.25
Consensus pattern (13 bp):
ACTTGATGAAAAG
Found at i:47716272 original size:26 final size:24
Alignment explanation
Indices: 47716215--47716299 Score: 68
Period size: 23 Copynumber: 3.5 Consensus size: 24
47716205 GTATTCCAAA
47716215 GATG-AAAACTTGATGAAAGACTT
1 GATGAAAAACTTGATGAAAGACTT
* *
47716238 AATTAAAAACACTTGATGAAAAGACTT
1 GA-TGAAAA-ACTTGATG-AAAGACTT
* *
47716265 GATGAAAAGCTT-A-AAAAGAACTT
1 GATGAAAAACTTGATGAAAG-ACTT
*
47716288 GATGCAAAACTT
1 GATGAAAAACTT
47716300 AATAAAAAAA
Statistics
Matches: 49, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
22 4 0.08
23 15 0.31
24 2 0.04
25 6 0.12
26 13 0.27
27 9 0.18
ACGTcount: A:0.48, C:0.11, G:0.16, T:0.25
Consensus pattern (24 bp):
GATGAAAAACTTGATGAAAGACTT
Found at i:47716283 original size:22 final size:23
Alignment explanation
Indices: 47716256--47716301 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
47716246 ACACTTGATG
47716256 AAAAG-ACTTGATG-AAAAGCTTA
1 AAAAGAACTTGATGCAAAA-CTTA
47716278 AAAAGAACTTGATGCAAAACTTA
1 AAAAGAACTTGATGCAAAACTTA
47716301 A
1 A
47716302 TAAAAAAAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 5 0.23
23 13 0.59
24 4 0.18
ACGTcount: A:0.52, C:0.11, G:0.15, T:0.22
Consensus pattern (23 bp):
AAAAGAACTTGATGCAAAACTTA
Found at i:47716925 original size:19 final size:19
Alignment explanation
Indices: 47716883--47716926 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
47716873 ATATATATTT
47716883 TTATTTTTATTTTTTATAA
1 TTATTTTTATTTTTTATAA
*
47716902 ATATTTTATATTTTTTA-AA
1 TTATTTT-TATTTTTTATAA
47716921 TTATTT
1 TTATTT
47716927 ATTGATGTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 13 0.59
20 9 0.41
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (19 bp):
TTATTTTTATTTTTTATAA
Found at i:47716927 original size:18 final size:19
Alignment explanation
Indices: 47716883--47716928 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
47716873 ATATATATTT
*
47716883 TTATTTTTATTTTTTATAA
1 TTATTTATATTTTTTATAA
*
47716902 ATATTTTATATTTTTTA-AA
1 TTA-TTTATATTTTTTATAA
47716921 TTATTTAT
1 TTATTTAT
47716929 TGATGTGACA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
18 5 0.22
19 6 0.26
20 12 0.52
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (19 bp):
TTATTTATATTTTTTATAA
Found at i:47734012 original size:3 final size:3
Alignment explanation
Indices: 47733952--47733995 Score: 72
Period size: 3 Copynumber: 14.7 Consensus size: 3
47733942 GCCCAAAGTA
47733952 AAT AAT AAT AAT AAT AAT AAT AA- ATAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AA
47733996 ATCTTATCCA
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
2 1 0.03
3 37 0.95
4 1 0.03
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:47739002 original size:2 final size:2
Alignment explanation
Indices: 47738995--47739032 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
47738985 TCCAATGTAA
*
47738995 AT AT AT AT AT AT AT AT AT AT AT TT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
47739033 GTATGCAGTT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:47740027 original size:21 final size:21
Alignment explanation
Indices: 47740001--47740071 Score: 70
Period size: 21 Copynumber: 3.3 Consensus size: 21
47739991 ATTAATAGCA
*
47740001 AATATAATTAACAGACCCATT
1 AATATAATTAACATACCCATT
** *** *
47740022 AATATAAAAAACATTAATAATA
1 AATATAATTAACA-TACCCATT
47740044 AATATAATTAACATACCCATT
1 AATATAATTAACATACCCATT
47740065 AATATAA
1 AATATAA
47740072 AAAAATTAAT
Statistics
Matches: 36, Mismatches: 13, Indels: 2
0.71 0.25 0.04
Matches are distributed among these distances:
21 22 0.61
22 14 0.39
ACGTcount: A:0.56, C:0.13, G:0.01, T:0.30
Consensus pattern (21 bp):
AATATAATTAACATACCCATT
Found at i:47740087 original size:42 final size:42
Alignment explanation
Indices: 47739981--47740088 Score: 171
Period size: 43 Copynumber: 2.5 Consensus size: 42
47739971 CTCTTAATAT
**
47739981 TATATAAAAAATTAATAGCAAATATAATTAACAGACCCATTAA
1 TATA-AAAAAATTAATAATAAATATAATTAACAGACCCATTAA
*
47740024 TATAAAAAACATTAATAATAAATATAATTAACATACCCATTAA
1 TATAAAAAA-ATTAATAATAAATATAATTAACAGACCCATTAA
47740067 TATAAAAAAATTAATAATAAAT
1 TATAAAAAAATTAATAATAAAT
47740089 GTATACTAAA
Statistics
Matches: 61, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
42 18 0.30
43 43 0.70
ACGTcount: A:0.59, C:0.09, G:0.02, T:0.30
Consensus pattern (42 bp):
TATAAAAAAATTAATAATAAATATAATTAACAGACCCATTAA
Found at i:47742949 original size:17 final size:17
Alignment explanation
Indices: 47742915--47742960 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 17
47742905 ATATGTAAAA
47742915 TAAATAATTAAGAATATATT
1 TAAATAA-TAA-AATATA-T
47742935 TAAA-AATAAAATATAT
1 TAAATAATAAAATATAT
47742951 TAAATAATAA
1 TAAATAATAA
47742961 TTCAAAAATC
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
16 5 0.20
17 11 0.44
18 3 0.12
19 2 0.08
20 4 0.16
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (17 bp):
TAAATAATAAAATATAT
Found at i:47742967 original size:28 final size:27
Alignment explanation
Indices: 47742911--47742974 Score: 69
Period size: 28 Copynumber: 2.3 Consensus size: 27
47742901 ATGTATATGT
*
47742911 AAAAT-AAATAATTAAGAATATATTTA
1 AAAATAAAATAATTAAGAATATATTCA
*
47742937 AAAATAAAATATATTAAATAATA-ATTCA
1 AAAATAAAATA-ATT-AAGAATATATTCA
47742965 AAAATCAAAA
1 AAAAT-AAAA
47742975 CTATGTTTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
26 5 0.16
27 5 0.16
28 12 0.38
29 10 0.31
ACGTcount: A:0.66, C:0.03, G:0.02, T:0.30
Consensus pattern (27 bp):
AAAATAAAATAATTAAGAATATATTCA
Found at i:47743000 original size:26 final size:27
Alignment explanation
Indices: 47742964--47743017 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
47742954 ATAATAATTC
47742964 AAAAATCAAAACTAT-GTTTATATTAA
1 AAAAATCAAAACTATAGTTTATATTAA
* * *
47742990 AAAAATTAAAAGTATATTTTATATTAA
1 AAAAATCAAAACTATAGTTTATATTAA
47743017 A
1 A
47743018 TTATAAAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
26 13 0.54
27 11 0.46
ACGTcount: A:0.56, C:0.04, G:0.04, T:0.37
Consensus pattern (27 bp):
AAAAATCAAAACTATAGTTTATATTAA
Found at i:47752202 original size:13 final size:13
Alignment explanation
Indices: 47752184--47752216 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
47752174 TATTTGGGCT
47752184 TTGGGTTTAAGTA
1 TTGGGTTTAAGTA
47752197 TTGGGTTTAAGTA
1 TTGGGTTTAAGTA
*
47752210 TTAGGTT
1 TTGGGTT
47752217 AGGATTGTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.21, C:0.00, G:0.30, T:0.48
Consensus pattern (13 bp):
TTGGGTTTAAGTA
Found at i:47752328 original size:13 final size:13
Alignment explanation
Indices: 47752290--47752328 Score: 64
Period size: 12 Copynumber: 3.2 Consensus size: 13
47752280 CTGTGGACTA
47752290 TTTAA-ATTTGGT
1 TTTAATATTTGGT
47752302 TTTAATATTT-GT
1 TTTAATATTTGGT
47752314 TTTAATATTTGGT
1 TTTAATATTTGGT
47752327 TT
1 TT
47752329 GGGCCCTAGG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
12 17 0.68
13 8 0.32
ACGTcount: A:0.23, C:0.00, G:0.13, T:0.64
Consensus pattern (13 bp):
TTTAATATTTGGT
Found at i:47756798 original size:190 final size:191
Alignment explanation
Indices: 47756474--47756858 Score: 763
Period size: 190 Copynumber: 2.0 Consensus size: 191
47756464 AAATTTAATT
47756474 ATAAAAATATAAAATTGTACTTTTTAAAATGAAGCAAAAGATTTATAAAAAAAAAATAACTGAAA
1 ATAAAAATATAAAATTGTACTTTTTAAAATGAAGCAAAAGATTTATAAAAAAAAAATAACTGAAA
47756539 TTGATGTTTTCAAAATTTCACTTTTTTTTTCAATTACGAATGATGTATGCTTTCTGCTCAAACAT
66 TTGATGTTTTCAAAATTTCACTTTTTTTTTCAATTACGAATGATGTATGCTTTCTGCTCAAACAT
47756604 TTTTATTAAATATCTTTATATTTATTTTATTAAAAATGAACTGTTCATCCAAATATTTTTC
131 TTTTATTAAATATCTTTATATTTATTTTATTAAAAATGAACTGTTCATCCAAATATTTTTC
47756665 ATAAAAATAT-AAATTGTACTTTTTAAAATGAAGCAAAAGATTTATAAAAAAAAAATAACTGAAA
1 ATAAAAATATAAAATTGTACTTTTTAAAATGAAGCAAAAGATTTATAAAAAAAAAATAACTGAAA
47756729 TTGATGTTTTCAAAATTTCACTTTTTTTTTCAATTACGAATGATGTATGCTTTCTGCTCAAACAT
66 TTGATGTTTTCAAAATTTCACTTTTTTTTTCAATTACGAATGATGTATGCTTTCTGCTCAAACAT
47756794 TTTTATTAAATATCTTTATATTTATTTTATTAAAAATGAACTGTTCATCCAAATATTTTTC
131 TTTTATTAAATATCTTTATATTTATTTTATTAAAAATGAACTGTTCATCCAAATATTTTTC
47756855 ATAA
1 ATAA
47756859 GATTTGAAAA
Statistics
Matches: 194, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
190 184 0.95
191 10 0.05
ACGTcount: A:0.41, C:0.10, G:0.07, T:0.42
Consensus pattern (191 bp):
ATAAAAATATAAAATTGTACTTTTTAAAATGAAGCAAAAGATTTATAAAAAAAAAATAACTGAAA
TTGATGTTTTCAAAATTTCACTTTTTTTTTCAATTACGAATGATGTATGCTTTCTGCTCAAACAT
TTTTATTAAATATCTTTATATTTATTTTATTAAAAATGAACTGTTCATCCAAATATTTTTC
Found at i:47766134 original size:3 final size:3
Alignment explanation
Indices: 47766128--47766158 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
47766118 TGATAGTAAC
47766128 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
47766159 GTACTAACTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:47766864 original size:13 final size:13
Alignment explanation
Indices: 47766828--47766873 Score: 53
Period size: 13 Copynumber: 3.7 Consensus size: 13
47766818 TGTTAATAGT
47766828 TAAA-AAAAATG-
1 TAAAGAAAAATGA
47766839 T-AAGAAAACATGA
1 TAAAGAAAA-ATGA
47766852 TAAAGAAAAATGA
1 TAAAGAAAAATGA
*
47766865 TAAATAAAA
1 TAAAGAAAA
47766874 GGAGTAAATC
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
10 2 0.07
11 5 0.17
12 3 0.10
13 13 0.43
14 7 0.23
ACGTcount: A:0.70, C:0.02, G:0.11, T:0.17
Consensus pattern (13 bp):
TAAAGAAAAATGA
Found at i:47776833 original size:20 final size:20
Alignment explanation
Indices: 47776804--47776842 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
47776794 CATTAAATTT
*
47776804 GAAATGAAAAATAAGATAAG
1 GAAATGAAAAAAAAGATAAG
*
47776824 GAAATTAAAAAAAAGATAA
1 GAAATGAAAAAAAAGATAA
47776843 CAAGATCAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.69, C:0.00, G:0.15, T:0.15
Consensus pattern (20 bp):
GAAATGAAAAAAAAGATAAG
Found at i:47779847 original size:23 final size:23
Alignment explanation
Indices: 47779819--47779909 Score: 82
Period size: 23 Copynumber: 4.1 Consensus size: 23
47779809 GTGTGAACTT
47779819 TTCATATTCAAGTCTCTTCACTC
1 TTCATATTCAAGTCTCTTCACTC
* * * * *
47779842 TTCATA---ATGTGT-GTAACTT
1 TTCATATTCAAGTCTCTTCACTC
* *
47779861 TTCATCTTCAAGTCTATTCACTC
1 TTCATATTCAAGTCTCTTCACTC
*
47779884 TTCATATTCAAGCCTCTTCACTC
1 TTCATATTCAAGTCTCTTCACTC
47779907 TTC
1 TTC
47779910 TAACTTTTCA
Statistics
Matches: 50, Mismatches: 14, Indels: 8
0.69 0.19 0.11
Matches are distributed among these distances:
19 9 0.18
20 4 0.08
22 4 0.08
23 33 0.66
ACGTcount: A:0.22, C:0.27, G:0.07, T:0.44
Consensus pattern (23 bp):
TTCATATTCAAGTCTCTTCACTC
Done.