Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009572.1 Hibiscus syriacus cultivar Beakdansim tig00116937_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2529503
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 13
Found at i:242505 original size:20 final size:20
Alignment explanation
Indices: 242482--242521 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
242472 TTTTATATTC
242482 GTTCGATTATGTTCGCTTGT
1 GTTCGATTATGTTCGCTTGT
* *
242502 GTTCGTTTATGTTCGTTTGT
1 GTTCGATTATGTTCGCTTGT
242522 TTGTATCCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.07, C:0.12, G:0.25, T:0.55
Consensus pattern (20 bp):
GTTCGATTATGTTCGCTTGT
Found at i:242592 original size:31 final size:31
Alignment explanation
Indices: 242556--242614 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
242546 AAAGAACATT
242556 AACAAGTTATATTCCTTAATGAACGAACCTG
1 AACAAGTTATATTCCTTAATGAACGAACCTG
*
242587 AACAAGTTATATTCCTTAATGAATGAAC
1 AACAAGTTATATTCCTTAATGAACGAAC
242615 ACAAATAAGA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.41, C:0.17, G:0.12, T:0.31
Consensus pattern (31 bp):
AACAAGTTATATTCCTTAATGAACGAACCTG
Found at i:246075 original size:156 final size:156
Alignment explanation
Indices: 245269--247396 Score: 2716
Period size: 156 Copynumber: 13.8 Consensus size: 156
245259 AACATTACAA
* * * *
245269 TCAACTCTGTTACAATACATCTTGAATTATCATTAGTGAAAAACCT-AAATGGTCCTTTCCTACT
1 TCAACTTTGTTACAATACATCTTGAATTATCATTAGTGAAAAACATGAAA-GATCCATTCCTACT
* * *
245333 TAAAGGGCGACATGCCTAAAAATACCCGACATACAAC--AAAATACCTTGCATTATGGTACCTAT
65 TAAAGGGTGACATGTCT-AAAATATCCGACATACAACAGAAAATACCTTGCATTATGGTACCTAT
* *
245396 GAAGCATAATTGCATAAGATAATTAAGT
129 GAAGCATAATTGCATAAGCTAATTAGGT
* * * *
245424 TCAACTTTGTTACAATATATCTTGAATTATCAATAGTAAAAAACATGAAAGA-CCATTCCTTCTT
1 TCAACTTTGTTACAATACATCTTGAATTATCATTAGTGAAAAACATGAAAGATCCATTCCTACTT
* * *
245488 AAAGGGCGACATGTCTTAAAATAACCGACATGCAACAG-AAATA-CTTGCATTATGGTACCTATG
66 AAAGGGTGACATGTC-TAAAATATCCGACATACAACAGAAAATACCTTGCATTATGGTACCTATG
245551 AAGCATAATTGCATAAGC---TTAGGTT
130 AAGCATAATTGCATAAGCTAATTAGG-T
* * *
245576 TTAACTTTGTTACAATACATCTTGAATTATCATTAGTGAAAGACAT--CAGATCCATTCC-ACTT
1 TCAACTTTGTTACAATACATCTTGAATTATCATTAGTGAAAAACATGAAAGATCCATTCCTACTT
* * * *
245638 AAAGGGTGACATATCTAAAAT-TCCGACATACAACAGAAAAGACCTTGCATTATAGTACCTACGA
66 AAAGGGTGACATGTCTAAAATATCCGACATACAACAGAAAATACCTTGCATTATGGTACCTATGA
245702 AGCATAATTGCATAAGCTAATTAGGT
131 AGCATAATTGCATAAGCTAATTAGGT
* * * *
245728 TTAACTTTGTTACAACACAT-TTGAATCATCATTAGTGAAAAACATGAAAGATTCATTCCTACTT
1 TCAACTTTGTTACAATACATCTTGAATTATCATTAGTGAAAAACATGAAAGATCCATTCCTACTT
* * * *
245792 AAAGGATGACATGTCTAAAA-ATACC--CATACAACAGAAAATACCTTGCATTACGATGCC--T-
66 AAAGGGTGACATGTCTAAAATAT-CCGACATACAACAGAAAATACCTTGCATTATGGTACCTATG
245851 --GCAT-ATTGCATAAGCTAATTTA-GT
130 AAGCATAATTGCATAAGCTAA-TTAGGT
* * *
245875 TCAACTTTGTTAAAATACATCTTGAATTATCATTAGCGACAAACATGAAAGATCCATTCCTACTT
1 TCAACTTTGTTACAATACATCTTGAATTATCATTAGTGAAAAACATGAAAGATCCATTCCTACTT
*
245940 AAAGGGTGACATGTCTAAAATATCCGACATACAACAGAAAATACCTTGCATTATGGTGCCTATGA
66 AAAGGGTGACATGTCTAAAATATCCGACATACAACAGAAAATACCTTGCATTATGGTACCTATGA
*
246005 AGCATAATTGCATAAGGTAATTAGGT
131 AGCATAATTGCATAAGCTAATTAGGT
* * *
246031 TGAACTTTGTTACAATCCATCTTGAATTATCATTAGTGAAAAACATGAAAGATCCATTCCAACTT
1 TCAACTTTGTTACAATACATCTTGAATTATCATTAGTGAAAAACATGAAAGATCCATTCCTACTT
* * *
246096 AAAGGGTGGCATGTCTAAAAT-TACTCGACATACAACA-TAAATACCTTGCATTAGGGTACCTAT
66 AAAGGGTGACATGTCTAAAATAT-C-CGACATACAACAGAAAATACCTTGCATTATGGTACCTAT
*
246159 GACGCATAATTGCATAAGCTAATTAGGT
129 GAAGCATAATTGCATAAGCTAATTAGGT
* *
246187 TCAACTTTGTTACAATACATCTTGAAATATCATTAATGAAAAACATGAAAGATCCATTCCTACTT
1 TCAACTTTGTTACAATACATCTTGAATTATCATTAGTGAAAAACATGAAAGATCCATTCCTACTT
* * * * *
246252 AAAGGATGACATGCCTAAAAATACCCGACATTCAAAAGAAAATACCTTGCATTATGGTACCTATG
66 AAAGGGTGACATGTCT-AAAATATCCGACATACAACAGAAAATACCTTGCATTATGGTACCTATG
* *
246317 AAACATAATTGCATAAGCTAAATAGGT
130 AAGCATAATTGCATAAGCTAATTAGGT
* * * * *
246344 T--TCTTTGTTACAACACATTTTGAATTATCATTAGTG-CAAACATGAAAGA-CTCATTACTACT
1 TCAACTTTGTTACAATACATCTTGAATTATCATTAGTGAAAAACATGAAAGATC-CATTCCTACT
* * *
246405 TAAAGGATGACATGTCTAAAAATACCCGACATACAACAAAAAATACCTTGCATTACT-GTACC--
65 TAAAGGGTGACATGTCT-AAAATATCCGACATACAACAGAAAATACCTTGCATTA-TGGTACCTA
246467 T---GCATAATTGCATAAGCTAATTAGGT
128 TGAAGCATAATTGCATAAGCTAATTAGGT
* * * *
246493 TCAACTTTGTTACAATACATCTTCAATTATCATTAGCGAAAAACATGATAGATACATTCCTACTT
1 TCAACTTTGTTACAATACATCTTGAATTATCATTAGTGAAAAACATGAAAGATCCATTCCTACTT
* * *
246558 AAAGGGTGACATGTCTAAAAAATCCGACATACAATAGAAAATACCTTGCATTATGTTACCTATGA
66 AAAGGGTGACATGTCTAAAATATCCGACATACAACAGAAAATACCTTGCATTATGGTACCTATGA
* *
246623 AG-ATAATTTCATTAGCTAATTAGGT
131 AGCATAATTGCATAAGCTAATTAGGT
* * * *
246648 TGAACTTTGTTACAATCCATCTTGAATTATCCTTAGTAAAAAAACATGAAAGATCCATTCCTACT
1 TCAACTTTGTTACAATACATCTTGAATTATCATTAGT-GAAAAACATGAAAGATCCATTCCTACT
* * * * * * * *
246713 TAAAGGGAGGCAGGTCT-AATTACCCTACATACAACAGAAAATACCTTACATTATGGCACCTATG
65 TAAAGGGTGACATGTCTAAAATATCCGACATACAACAGAAAATACCTTGCATTATGGTACCTATG
246777 AAGCATAATTGCATAAGCTAATTAGGT
130 AAGCATAATTGCATAAGCTAATTAGGT
* * * * *
246804 TTAACTTTGTTACAATACATCTTGAATTATTATTAGTGAAAAAATATGAAAGATCCATTCCCACC
1 TCAACTTTGTTACAATACATCTTGAATTATCATTAGTG-AAAAACATGAAAGATCCATTCCTACT
*
246869 TAAAGGGTGACATGTCTAAAA-ATTCCTGACATACAACAGAAAAGACCTTGCATTATGGTACCTA
65 TAAAGGGTGACATGTCTAAAATA-TCC-GACATACAACAGAAAATACCTTGCATTATGGTACCTA
*
246933 TGAAGCATAATTGCATAAGCTAATTAAGT
128 TGAAGCATAATTGCATAAGCTAATTAGGT
* * * * *
246962 TTAACTTTGTTACAACACAT-TATGAATTATCGTTAGTGAAAAACATAAAAGATGCATTCCTACT
1 TCAACTTTGTTACAATACATCT-TGAATTATCATTAGTGAAAAACATGAAAGATCCATTCCTACT
* * * *
247026 TAAAGGATTACATGTCTAAAAATACCCGACATACAACAGAAAATACCTTGCATTACGGTACC--T
65 TAAAGGGTGACATGTCT-AAAATATCCGACATACAACAGAAAATACCTTGCATTATGGTACCTAT
247089 ---GCATAATTGCATAAGCTAATTAGGT
129 GAAGCATAATTGCATAAGCTAATTAGGT
* * *
247114 TCAACTTTGTTACAATACATCTTGAATTATCATTAGAG-ACAACATG-AAGATCCATTCCTACTC
1 TCAACTTTGTTACAATACATCTTGAATTATCATTAGTGAAAAACATGAAAGATCCATTCCTACTT
* *
247177 AAAGGGTGACGTGTCTAAAAATATCCAACATACAACAGAAAATACCTTGCATTATGGTACCTATG
66 AAAGGGTGACATGTCT-AAAATATCCGACATACAACAGAAAATACCTTGCATTATGGTACCTATG
* *
247242 AAGCATAATCGCATAAGCTAATTATGT
130 AAGCATAATTGCATAAGCTAATTAGGT
* * *
247269 TGAACTTTGTTACAATCCATCTTGAATTATCATTAGTCAAAAACATGAAAGATCCATTCCTACTT
1 TCAACTTTGTTACAATACATCTTGAATTATCATTAGTGAAAAACATGAAAGATCCATTCCTACTT
* * * * *
247334 AAAGGGTG-GATGTCTAAAATTACCCAACATACAATAGAAAATACCTTCCATTA-GTGTACCTAT
66 AAAGGGTGACATGTCTAAAA-TATCCGACATACAACAGAAAATACCTTGCATTATG-GTACCTAT
247397 TGTAGACACC
Statistics
Matches: 1720, Mismatches: 189, Indels: 127
0.84 0.09 0.06
Matches are distributed among these distances:
147 33 0.02
148 81 0.05
149 36 0.02
150 157 0.09
151 107 0.06
152 157 0.09
153 46 0.03
154 178 0.10
155 247 0.14
156 411 0.24
157 166 0.10
158 100 0.06
159 1 0.00
ACGTcount: A:0.38, C:0.18, G:0.13, T:0.30
Consensus pattern (156 bp):
TCAACTTTGTTACAATACATCTTGAATTATCATTAGTGAAAAACATGAAAGATCCATTCCTACTT
AAAGGGTGACATGTCTAAAATATCCGACATACAACAGAAAATACCTTGCATTATGGTACCTATGA
AGCATAATTGCATAAGCTAATTAGGT
Found at i:246568 original size:618 final size:618
Alignment explanation
Indices: 245269--247396 Score: 3119
Period size: 618 Copynumber: 3.5 Consensus size: 618
245259 AACATTACAA
* * * * *
245269 TCAACTCTGTTACAATACATCTTGAATTATCATTAGTGAAAAACCT-AAATGGTCCTTTCCTACT
1 TCAACTTTGTTACAATACATCTTGAATTATCATTAGCGAAAAACATGAAA-GATCCATTCCTACT
* * *
245333 TAAAGGGCGACATGCCTAAAAATACCCGACATACAAC--AAAATACCTTGCATTATGGTACCTAT
65 TAAAGGGTGACATGTCTAAAAATATCCGACATACAACAGAAAATACCTTGCATTATGGTACCTAT
* * * ** *
245396 GAAGCATAATTGCATAAGATAATTAAGTTCAACTTTGTTACAATATATCTTGAATTATCAATAGT
130 GAAGCATAATTGCATAAGCTAATTAGGTTGAACTTTGTTACAATCCATCTTGAATTATCATTAGT
* * * * *
245461 AAAAAACATGAAAGA-CCATTCCTTCTTAAAGGGCGACATGTCTTAAAA-TAACCGACATGCAAC
195 AAAAAACATGAAAGATCCATTCCTACTTAAAGGGTGGCATGTC-TAAAATTACCCGACATACAAC
*
245524 AG-AAATA-CTTGCATTATGGTACCTATGAAGCATAATTGCATAAGC---TTAGGTTTTAACTTT
259 AGAAAATACCTTGCATTAGGGTACCTATGAAGCATAATTGCATAAGCTAATTAGG-TTTAACTTT
* *
245584 GTTACAATACATCTTGAATTATCATTAGTGAAAGACAT--CAGATCCATTCCACTTAAAGGGTGA
323 GTTACAATACATCTTGAATTATCATTAGTGAAAAACATGAAAGATCCATTCCACTTAAAGGGTGA
* * * *
245647 CATATCT-AAAATTCCGACATACAACAGAAAAGACCTTGCATTATAGTACCTACGAAGCATAATT
388 CATGTCTAAAAATCCCGACATACAACAGAAAAGACCTTGCATTATGGTACCTATGAAGCATAATT
*
245711 GCATAAGCTAATTAGGTTTAACTTTGTTACAACACA-TTTGAATCATCATTAGTGAAAAACATGA
453 GCATAAGCTAATTAGGTTT-ACTTTGTTACAACACATTTTGAATTATCATTAGTGAAAAACATGA
245775 AAGATTCATTCCTACTTAAAGGATGACATGTCTAAAAATA-CC--CATACAACAGAAAATACCTT
517 AAGA-TCATTCCTACTTAAAGGATGACATGTCTAAAAATACCCGACATACAACAGAAAATACCTT
*
245837 GCATTACGATGCCTGCAT-ATTGCATAAGCTAATTTA-GT
581 GCATTACG-TACCTGCATAATTGCATAAGCTAA-TTAGGT
* *
245875 TCAACTTTGTTAAAATACATCTTGAATTATCATTAGCGACAAACATGAAAGATCCATTCCTACTT
1 TCAACTTTGTTACAATACATCTTGAATTATCATTAGCGAAAAACATGAAAGATCCATTCCTACTT
*
245940 AAAGGGTGACATGTCT-AAAATATCCGACATACAACAGAAAATACCTTGCATTATGGTGCCTATG
66 AAAGGGTGACATGTCTAAAAATATCCGACATACAACAGAAAATACCTTGCATTATGGTACCTATG
* *
246004 AAGCATAATTGCATAAGGTAATTAGGTTGAACTTTGTTACAATCCATCTTGAATTATCATTAGTG
131 AAGCATAATTGCATAAGCTAATTAGGTTGAACTTTGTTACAATCCATCTTGAATTATCATTAGTA
* *
246069 AAAAACATGAAAGATCCATTCCAACTTAAAGGGTGGCATGTCTAAAATTACTCGACATACAACA-
196 AAAAACATGAAAGATCCATTCCTACTTAAAGGGTGGCATGTCTAAAATTACCCGACATACAACAG
* * *
246133 TAAATACCTTGCATTAGGGTACCTATGACGCATAATTGCATAAGCTAATTAGGTTCAACTTTGTT
261 AAAATACCTTGCATTAGGGTACCTATGAAGCATAATTGCATAAGCTAATTAGGTTTAACTTTGTT
* * *
246198 ACAATACATCTTGAAATATCATTAATGAAAAACATGAAAGATCCATTCCTACTTAAAGGATGACA
326 ACAATACATCTTGAATTATCATTAGTGAAAAACATGAAAGATCCATTCC-ACTTAAAGGGTGACA
* * * * *
246263 TGCCTAAAAATACCCGACATTCAAAAGAAAATACCTTGCATTATGGTACCTATGAAACATAATTG
390 TGTCTAAAAAT-CCCGACATACAACAGAAAAGACCTTGCATTATGGTACCTATGAAGCATAATTG
* *
246328 CATAAGCTAAATAGGTTT-CTTTGTTACAACACATTTTGAATTATCATTAGTG-CAAACATGAAA
454 CATAAGCTAATTAGGTTTACTTTGTTACAACACATTTTGAATTATCATTAGTGAAAAACATGAAA
* *
246391 GACTCATTACTACTTAAAGGATGACATGTCTAAAAATACCCGACATACAACAAAAAATACCTTGC
519 GA-TCATTCCTACTTAAAGGATGACATGTCTAAAAATACCCGACATACAACAGAAAATACCTTGC
246456 ATTACTGTACCTGCATAATTGCATAAGCTAATTAGGT
583 ATTAC-GTACCTGCATAATTGCATAAGCTAATTAGGT
* * *
246493 TCAACTTTGTTACAATACATCTTCAATTATCATTAGCGAAAAACATGATAGATACATTCCTACTT
1 TCAACTTTGTTACAATACATCTTGAATTATCATTAGCGAAAAACATGAAAGATCCATTCCTACTT
* *
246558 AAAGGGTGACATGTCTAAAAA-ATCCGACATACAATAGAAAATACCTTGCATTATGTTACCTATG
66 AAAGGGTGACATGTCTAAAAATATCCGACATACAACAGAAAATACCTTGCATTATGGTACCTATG
* * *
246622 AAG-ATAATTTCATTAGCTAATTAGGTTGAACTTTGTTACAATCCATCTTGAATTATCCTTAGTA
131 AAGCATAATTGCATAAGCTAATTAGGTTGAACTTTGTTACAATCCATCTTGAATTATCATTAGT-
* * *
246686 AAAAAACATGAAAGATCCATTCCTACTTAAAGGGAGGCAGGTCT--AATTACCCTACATACAACA
195 AAAAAACATGAAAGATCCATTCCTACTTAAAGGGTGGCATGTCTAAAATTACCCGACATACAACA
* * *
246749 GAAAATACCTTACATTATGGCACCTATGAAGCATAATTGCATAAGCTAATTAGGTTTAACTTTGT
260 GAAAATACCTTGCATTAGGGTACCTATGAAGCATAATTGCATAAGCTAATTAGGTTTAACTTTGT
* * *
246814 TACAATACATCTTGAATTATTATTAGTGAAAAAATATGAAAGATCCATTCCCACCTAAAGGGTGA
325 TACAATACATCTTGAATTATCATTAGTG-AAAAACATGAAAGATCCATT-CCACTTAAAGGGTGA
*
246879 CATGTCTAAAAATTCCTGACATACAACAGAAAAGACCTTGCATTATGGTACCTATGAAGCATAAT
388 CATGTCTAAAAA-TCCCGACATACAACAGAAAAGACCTTGCATTATGGTACCTATGAAGCATAAT
* * * *
246944 TGCATAAGCTAATTAAGTTTAACTTTGTTACAACACATTATGAATTATCGTTAGTGAAAAACATA
452 TGCATAAGCTAATTAGGTTT-ACTTTGTTACAACACATTTTGAATTATCATTAGTGAAAAACATG
*
247009 AAAGATGCATTCCTACTTAAAGGATTACATGTCTAAAAATACCCGACATACAACAGAAAATACCT
516 AAAGAT-CATTCCTACTTAAAGGATGACATGTCTAAAAATACCCGACATACAACAGAAAATACCT
247074 TGCATTACGGTACCTGCATAATTGCATAAGCTAATTAGGT
580 TGCATTAC-GTACCTGCATAATTGCATAAGCTAATTAGGT
* * *
247114 TCAACTTTGTTACAATACATCTTGAATTATCATTAGAG-ACAACATG-AAGATCCATTCCTACTC
1 TCAACTTTGTTACAATACATCTTGAATTATCATTAGCGAAAAACATGAAAGATCCATTCCTACTT
* *
247177 AAAGGGTGACGTGTCTAAAAATATCCAACATACAACAGAAAATACCTTGCATTATGGTACCTATG
66 AAAGGGTGACATGTCTAAAAATATCCGACATACAACAGAAAATACCTTGCATTATGGTACCTATG
* * *
247242 AAGCATAATCGCATAAGCTAATTATGTTGAACTTTGTTACAATCCATCTTGAATTATCATTAGTC
131 AAGCATAATTGCATAAGCTAATTAGGTTGAACTTTGTTACAATCCATCTTGAATTATCATTAGTA
* *
247307 AAAAACATGAAAGATCCATTCCTACTTAAAGGGTGG-ATGTCTAAAATTACCCAACATACAATAG
196 AAAAACATGAAAGATCCATTCCTACTTAAAGGGTGGCATGTCTAAAATTACCCGACATACAACAG
* *
247371 AAAATACCTTCCATTAGTGTACCTAT
261 AAAATACCTTGCATTAGGGTACCTAT
247397 TGTAGACACC
Statistics
Matches: 1367, Mismatches: 119, Indels: 57
0.89 0.08 0.04
Matches are distributed among these distances:
605 18 0.01
606 68 0.05
607 106 0.08
608 41 0.03
609 36 0.03
611 43 0.03
612 5 0.00
613 11 0.01
614 78 0.06
615 24 0.02
616 80 0.06
617 176 0.13
618 281 0.21
619 46 0.03
620 118 0.09
621 236 0.17
ACGTcount: A:0.38, C:0.18, G:0.13, T:0.30
Consensus pattern (618 bp):
TCAACTTTGTTACAATACATCTTGAATTATCATTAGCGAAAAACATGAAAGATCCATTCCTACTT
AAAGGGTGACATGTCTAAAAATATCCGACATACAACAGAAAATACCTTGCATTATGGTACCTATG
AAGCATAATTGCATAAGCTAATTAGGTTGAACTTTGTTACAATCCATCTTGAATTATCATTAGTA
AAAAACATGAAAGATCCATTCCTACTTAAAGGGTGGCATGTCTAAAATTACCCGACATACAACAG
AAAATACCTTGCATTAGGGTACCTATGAAGCATAATTGCATAAGCTAATTAGGTTTAACTTTGTT
ACAATACATCTTGAATTATCATTAGTGAAAAACATGAAAGATCCATTCCACTTAAAGGGTGACAT
GTCTAAAAATCCCGACATACAACAGAAAAGACCTTGCATTATGGTACCTATGAAGCATAATTGCA
TAAGCTAATTAGGTTTACTTTGTTACAACACATTTTGAATTATCATTAGTGAAAAACATGAAAGA
TCATTCCTACTTAAAGGATGACATGTCTAAAAATACCCGACATACAACAGAAAATACCTTGCATT
ACGTACCTGCATAATTGCATAAGCTAATTAGGT
Found at i:247457 original size:20 final size:20
Alignment explanation
Indices: 247423--247484 Score: 83
Period size: 20 Copynumber: 3.1 Consensus size: 20
247413 TGACCGGGTT
247423 TTAT-ATTTATATTATTATTA
1 TTATAATTTAT-TTATTATTA
247443 TTATAATTTATTTATTATTA
1 TTATAATTTATTTATTATTA
*
247463 TTAATAATTTCTTTATT-TTA
1 TT-ATAATTTATTTATTATTA
247483 TT
1 TT
247485 TTTTGTAGGA
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
20 20 0.51
21 19 0.49
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (20 bp):
TTATAATTTATTTATTATTA
Found at i:247462 original size:23 final size:21
Alignment explanation
Indices: 247427--247484 Score: 84
Period size: 21 Copynumber: 2.8 Consensus size: 21
247417 CGGGTTTTAT
247427 ATTTATATTATTATTATT-ATA
1 ATTTAT-TTATTATTATTAATA
247448 ATTTATTTATTATTATTAATA
1 ATTTATTTATTATTATTAATA
*
247469 ATTTCTTTATT-TTATT
1 ATTTATTTATTATTATT
247485 TTTTGTAGGA
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
20 16 0.46
21 19 0.54
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.66
Consensus pattern (21 bp):
ATTTATTTATTATTATTAATA
Found at i:252371 original size:105 final size:105
Alignment explanation
Indices: 252256--253069 Score: 1488
Period size: 105 Copynumber: 7.8 Consensus size: 105
252246 CGACTGACTG
* *
252256 CAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGA
1 CAAC-AACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGA
*
252321 CAACGCAAGTTCAACTTCATGACGAAGGGACCGCTGGTTGT
65 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGT
* *
252362 CAACAACAACTTCCCAAATTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGAC
1 CAACAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGAC
252427 AACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGT
66 AACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGT
* *
252467 CAACAACAACTTCCCAAATTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGAC
1 CAACAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGAC
252532 AACGCAAGTTC-ACTTCACGACGAAGGGACCGCTGGTTGT
66 AACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGT
**
252571 CAACAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCGGAC
1 CAACAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGAC
252636 AACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGT
66 AACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGT
* *
252676 CAACAACAACTTCCCAATTTCAGAGCCAATTTTAACTTCACAGCGAAGGATATTGGACTCCAGAC
1 CAACAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGAC
252741 AACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGT
66 AACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGT
*
252781 CAACAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGAC
1 CAACAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGAC
252846 AACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGT
66 AACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGT
*
252886 CAACAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTAGACTCAAGAC
1 CAACAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGAC
252951 AACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGT
66 AACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGT
252991 C-ACAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGAC
1 CAACAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGAC
253055 AACGCAAGTTCAACT
66 AACGCAAGTTCAACT
253070 CCAGACAACG
Statistics
Matches: 692, Mismatches: 15, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
104 177 0.26
105 511 0.74
106 4 0.01
ACGTcount: A:0.33, C:0.27, G:0.19, T:0.21
Consensus pattern (105 bp):
CAACAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGAC
AACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGT
Found at i:252805 original size:314 final size:316
Alignment explanation
Indices: 252256--253418 Score: 1841
Period size: 314 Copynumber: 3.6 Consensus size: 316
252246 CGACTGACTG
*
252256 CAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGA
1 CAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGA
* *
252321 CAACGCAAGTTCAACTTCATGACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCAAATTCAGA
66 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCAATTTCAGA
* *
252386 GTCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGA
131 GCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGA
* *
252451 AGGGACCGCTGGTTGTCAACAACAACTTCCCAAATTCAGAGTCAATTTCAACTTCACAGCGAAGG
196 AGGGACCGCTGGTTGTCAACAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGG
252516 ATATTGGACTCAAGACAACGCAAGTTC-ACTTCACGACGAAGGGACCGCTGGTTGT
261 ATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGT
*
252571 CAAC-AACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCGGA
1 CAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGA
252635 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCAATTTCAGA
66 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCAATTTCAGA
*
252700 GCCAATTTTAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGA
131 GCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGA
252765 AGGGACCGCTGGTTGTCAACAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGG
196 AGGGACCGCTGGTTGTCAACAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGG
*
252830 ATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGT
261 ATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGT
* *
252886 CAAC-AACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTAGACTCAAGA
1 CAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGA
252950 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTC-ACAACAACTTCCCAATTTCAGA
66 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCAATTTCAGA
253014 GCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTCCAGACAAC
131 GCCAATTTCAACTTCACAGCGAAGGATATTGGACTC----C-A-G--A---CAA---C-G-CAA-
* * *
253079 GCAAGTCAACTTCACGACGAAGGGACCACTGGTTGTCAACAACAACTTCCCAATTTCAGAACCAA
179 G---TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCAATTTCAGAGCCAA
*
253144 TTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGAAGAAGGGA
241 TTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGA
*
253209 CAGCTGGTTGT
306 CCGCTGGTTGT
* * *
253220 CAACAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCGAGA
1 CAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGA
* * *
253285 CAACACAAGTTCAACTTCACAACGAAGGGA-CGACTGGTTGTCAACAAACAATTTCCCAATTTCA
66 CAACGCAAGTTCAACTTCACGACGAAGGGACCG-CTGGTTGTCAAC-AACAACTTCCCAATTTCA
* * * * *
253349 GAGCCAATTTTAACTTAACAGCGAAGGATATTGGACTCGAGACAACACAATTTCAACTTCACGAC
129 GAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGAC
253414 GAAGG
194 GAAGG
253419 ATATCCAATT
Statistics
Matches: 790, Mismatches: 33, Indels: 48
0.91 0.04 0.06
Matches are distributed among these distances:
314 329 0.42
315 135 0.17
317 18 0.02
318 1 0.00
319 1 0.00
320 1 0.00
321 3 0.00
322 1 0.00
323 1 0.00
325 3 0.00
326 3 0.00
328 1 0.00
329 2 0.00
330 3 0.00
331 2 0.00
332 1 0.00
334 137 0.17
335 93 0.12
336 2 0.00
337 53 0.07
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.21
Consensus pattern (316 bp):
CAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGA
CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCAATTTCAGA
GCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGA
AGGGACCGCTGGTTGTCAACAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGG
ATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGT
Found at i:253004 original size:419 final size:423
Alignment explanation
Indices: 252226--253418 Score: 1855
Period size: 419 Copynumber: 2.8 Consensus size: 423
252216 TGGTGGTAGC
* * ** *
252226 TCAACTTCAC-AGCGAAGGGGCGACTGACTG-CAACAAACAACTTCTCAATTTCAGAGCCAATTT
1 TCAACTTCACGA-CGAAGGGACCACTGGTTGTCAAC-AACAACTTCCCAATTTCAGAGCCAATTT
*
252289 CAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCATGACGAAGGGACCG
64 CAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCG
* *
252354 CTGGTTGTCAACAACAACTTCCCAAATTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGA
129 CTGGTTGTCAACAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGA
252419 CTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCAA
194 CTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCAA
* *
252484 ATTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACGCAAGTTC-ACTTC
259 TTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTC
252548 ACGACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACA
324 ACGACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACA
252613 GCGAAGGATATTGGACT-C-C-G-GACAACGCAAG
389 GCGAAGGATATTGGACTACGCAGCGACAACGCAAG
* *
252644 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCAATTTCAGAGCCAATTTT
1 -TCAACTTCACGACGAAGGGACCACTGGTTGTCAACAACAACTTCCCAATTTCAGAGCCAATTTC
252709 AACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGC
65 AACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGC
252774 TGGTTGTCAACAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGAC
130 TGGTTGTCAACAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGAC
*
252839 TCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCAAT
195 TCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCAAT
*
252904 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTAGACTCAAGACAACGCAAGTTCAACTTCA
260 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCA
252969 CGACGAAGGGACCGCTGGTTGTC-ACAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAG
325 CGACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAG
253033 CGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTCCAGACAACGCAAG
390 CGAAGGATATTGGACT-------ACGC-AG--------C-GACAACGCAAG
*
253084 TCAACTTCACGACGAAGGGACCACTGGTTGTCAACAACAACTTCCCAATTTCAGAACCAATTTCA
1 TCAACTTCACGACGAAGGGACCACTGGTTGTCAACAACAACTTCCCAATTTCAGAGCCAATTTCA
* * *
253149 ACTTCACAGCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGAAGAAGGGACAGCT
66 ACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCT
* *
253214 GGTTGTCAACAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGAC
131 GGTTGTCAAC-AACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGAC
* * * *
253279 TCGAGACAACACAAGTTCAACTTCACAACGAAGGGA-CGACTGGTTGTCAACAAACAATTTCCCA
195 TCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCG-CTGGTTGTCAAC-AACAACTTCCCA
* * * * *
253343 ATTTCAGAGCCAATTTTAACTTAACAGCGAAGGATATTGGACTCGAGACAACACAATTTCAACTT
258 ATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTT
253408 CACGACGAAGG
323 CACGACGAAGG
253419 ATATCCAATT
Statistics
Matches: 715, Mismatches: 32, Indels: 32
0.92 0.04 0.04
Matches are distributed among these distances:
419 353 0.49
420 34 0.05
427 1 0.00
428 1 0.00
430 1 0.00
439 136 0.19
440 108 0.15
441 81 0.11
ACGTcount: A:0.34, C:0.26, G:0.19, T:0.21
Consensus pattern (423 bp):
TCAACTTCACGACGAAGGGACCACTGGTTGTCAACAACAACTTCCCAATTTCAGAGCCAATTTCA
ACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCT
GGTTGTCAACAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACT
CAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCAATT
TCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCAC
GACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGC
GAAGGATATTGGACTACGCAGCGACAACGCAAG
Found at i:253075 original size:21 final size:20
Alignment explanation
Indices: 253046--253089 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 20
253036 AGGATATTGG
253046 ACTCAAGACAACGCAAGTTCA
1 ACTCAAGACAACGCAAG-TCA
*
253067 ACTCCAGACAACGCAAGTCA
1 ACTCAAGACAACGCAAGTCA
253087 ACT
1 ACT
253090 TCACGACGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 6 0.27
21 16 0.73
ACGTcount: A:0.41, C:0.32, G:0.14, T:0.14
Consensus pattern (20 bp):
ACTCAAGACAACGCAAGTCA
Found at i:253169 original size:125 final size:125
Alignment explanation
Indices: 252942--253194 Score: 463
Period size: 125 Copynumber: 2.0 Consensus size: 125
252932 AGGATATTAG
*
252942 ACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCACAACAACTTCCCAA
1 ACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCACTGGTTGTCACAACAACTTCCCAA
*
253007 TTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACGCAAGTTCA
66 TTTCAGAACCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACGCAAGTTCA
*
253067 ACTCCAGACAACGCAAG-TCAACTTCACGACGAAGGGACCACTGGTTGTCAACAACAACTTCCCA
1 ACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCACTGGTTGTC-ACAACAACTTCCCA
253131 ATTTCAGAACCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACGCAAGTTCA
65 ATTTCAGAACCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACGCAAGTTCA
253192 ACT
1 ACT
253195 TCACGAAGAA
Statistics
Matches: 124, Mismatches: 3, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
124 31 0.25
125 93 0.75
ACGTcount: A:0.35, C:0.28, G:0.17, T:0.20
Consensus pattern (125 bp):
ACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCACTGGTTGTCACAACAACTTCCCAA
TTTCAGAACCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACGCAAGTTCA
Found at i:253260 original size:106 final size:106
Alignment explanation
Indices: 253067--253418 Score: 534
Period size: 106 Copynumber: 3.3 Consensus size: 106
253057 CGCAAGTTCA
* * * *
253067 ACTCCAGACAACGCAAG-TCAACTTCACGACGAAGGGACCA-CTGGTTGTCAAC-AACAACTTCC
1 ACTCGAGACAACACAAGTTCAACTTCACGAAGAAGGGA-CAGCTGGTTGTCAACAAACAATTTCC
*
253129 CAATTTCAGAACCAATTTCAACTTCACAGCGAAGGATATTGG
65 CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
253171 ACTCAAGACAACGCAAGTTCAACTTCACGAAGAAGGGACAGCTGGTTGTCAACAAACAATTTCCC
1 ACTCGAGACAACACAAGTTCAACTTCACGAAGAAGGGACAGCTGGTTGTCAACAAACAATTTCCC
*
253236 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
253277 ACTCGAGACAACACAAGTTCAACTTCAC-AACGAAGGGAC-GACTGGTTGTCAACAAACAATTTC
1 ACTCGAGACAACACAAGTTCAACTTCACGAA-GAAGGGACAG-CTGGTTGTCAACAAACAATTTC
* *
253340 CCAATTTCAGAGCCAATTTTAACTTAACAGCGAAGGATATTGG
64 CCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
253383 ACTCGAGACAACACAATTTCAACTTCACGACGAAGG
1 ACTCGAGACAACACAAGTTCAACTTCACGAAGAAGG
253419 ATATCCAATT
Statistics
Matches: 230, Mismatches: 12, Indels: 10
0.91 0.05 0.04
Matches are distributed among these distances:
104 18 0.08
105 34 0.15
106 177 0.77
107 1 0.00
ACGTcount: A:0.36, C:0.25, G:0.18, T:0.21
Consensus pattern (106 bp):
ACTCGAGACAACACAAGTTCAACTTCACGAAGAAGGGACAGCTGGTTGTCAACAAACAATTTCCC
AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
Found at i:253762 original size:36 final size:36
Alignment explanation
Indices: 253722--253862 Score: 228
Period size: 36 Copynumber: 3.9 Consensus size: 36
253712 CAAAACTAAG
* *
253722 TTTTGTCTCTCTTGAGACGGTTTCTCTTGAAACAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
* *
253758 TTTTGTCTCTCTTGAGACGGTTTCTCTTGAAACAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
* *
253794 TTTTGTCCCTCTTGAGACAGTTTCCCTTGAAATAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
253830 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC
253863 GCCAATCTTT
Statistics
Matches: 99, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 99 1.00
ACGTcount: A:0.22, C:0.21, G:0.16, T:0.41
Consensus pattern (36 bp):
TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
Found at i:254324 original size:20 final size:20
Alignment explanation
Indices: 254290--254351 Score: 83
Period size: 20 Copynumber: 3.1 Consensus size: 20
254280 TGACCGGGTT
254290 TTAT-ATTTATATTATTATTA
1 TTATAATTTAT-TTATTATTA
254310 TTATAATTTATTTATTATTA
1 TTATAATTTATTTATTATTA
*
254330 TTAATAATTTCTTTATT-TTA
1 TT-ATAATTTATTTATTATTA
254350 TT
1 TT
254352 TTTTGTAGGA
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
20 20 0.51
21 19 0.49
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (20 bp):
TTATAATTTATTTATTATTA
Found at i:254329 original size:23 final size:21
Alignment explanation
Indices: 254294--254351 Score: 84
Period size: 21 Copynumber: 2.8 Consensus size: 21
254284 CGGGTTTTAT
254294 ATTTATATTATTATTATT-ATA
1 ATTTAT-TTATTATTATTAATA
254315 ATTTATTTATTATTATTAATA
1 ATTTATTTATTATTATTAATA
*
254336 ATTTCTTTATT-TTATT
1 ATTTATTTATTATTATT
254352 TTTTGTAGGA
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
20 16 0.46
21 19 0.54
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.66
Consensus pattern (21 bp):
ATTTATTTATTATTATTAATA
Found at i:256577 original size:157 final size:157
Alignment explanation
Indices: 256046--257460 Score: 1953
Period size: 157 Copynumber: 9.1 Consensus size: 157
256036 CAGTTCCGAC
** * *
256046 ACCTATGAAGCATAATTGCATAAGCTAATTTTGTTCAACTTTGTTACAATTCATCTTGAATTCTC
1 ACCTATGAAGCATAATTGCATAAGCTAATTAGGTTCAACTTTGTTACAATCCATCTTGAATTATC
* *
256111 ATTAGTGAAAAACATGAAAGATCCATTCCTACTTAAAGGATGACATGCCTAAAAATACCCGACAT
66 ATTAGTGAAAAACATGAAAGATCCATTCCTACTTAAAGGGTGACATGTCTAAAAATACCCGACAT
** *
256176 ACAACCCAAAATACCTTGCAGTATGGT
131 ACAACAGAAAATACCTTGCATTATGGT
* * * * * *
256203 ACCTATGAAGCATAATTGCATAAGCTAATTAAGTTTAACTTTTTTGCAA-CACCTTTTGAATTAT
1 ACCTATGAAGCATAATTGCATAAGCTAATTAGGTTCAACTTTGTTACAATC-CATCTTGAATTAT
* * * *
256267 CATTAGTGAAAAACATGAAAGATTCATTCCTACTTAAAGGATGACATGTCTAAAATTACCCGATA
65 CATTAGTGAAAAACATGAAAGATCCATTCCTACTTAAAGGGTGACATGTCTAAAAATACCCGACA
* **
256332 TGCAACAG-AAATACCTTGCATTACAGT
130 TACAACAGAAAATACCTTGCATTATGGT
* *
256359 ACC--T---GCATAATTGCATAAGCTAATTAGGTTCAACTTTGTTACAATTCATCGTGAATTATC
1 ACCTATGAAGCATAATTGCATAAGCTAATTAGGTTCAACTTTGTTACAATCCATCTTGAATTATC
* * * * *
256419 ATTAGTGACAAACATGATAGATCCATTCGTACTTAAAGGGTGGCATGTCTAAAAATATCCGACAT
66 ATTAGTGAAAAACATGAAAGATCCATTCCTACTTAAAGGGTGACATGTCTAAAAATACCCGACAT
*
256484 ACAACAGAAAATACCTTGTATTATGGT
131 ACAACAGAAAATACCTTGCATTATGGT
* * * * *
256511 AACTATGAAGAATAACTGCATTAGCTAATTAGGTTGAACTTTGTTACAATCCATCTTGAATTATC
1 ACCTATGAAGCATAATTGCATAAGCTAATTAGGTTCAACTTTGTTACAATCCATCTTGAATTATC
* * * *
256576 ATTAGTGAAAAACATGAAAGAACCATTCCTTCTTAAAGGGTGGCATGTCTAAAATTACCCGACAT
66 ATTAGTGAAAAACATGAAAGATCCATTCCTACTTAAAGGGTGACATGTCTAAAAATACCCGACAT
256641 ACAACAGAAAATACCTTGCATTATGGT
131 ACAACAGAAAATACCTTGCATTATGGT
* * * *
256668 ACCTAGGAAGCATAATTGCATAAGCTAATTAGATTTAACTTTGTTACAATACATCTTGAATTATC
1 ACCTATGAAGCATAATTGCATAAGCTAATTAGGTTCAACTTTGTTACAATCCATCTTGAATTATC
* * *
256733 ATTAGTGAAAAACATGAAAGATTCATTCCCACTTAAAGGGTGACATGTCTAAAAATACCTGACAT
66 ATTAGTGAAAAACATGAAAGATCCATTCCTACTTAAAGGGTGACATGTCTAAAAATACCCGACAT
256798 ACAACAGAAAATACCTTGCATTATGGT
131 ACAACAGAAAATACCTTGCATTATGGT
* * * *
256825 ACCTATGAAGCATAATTGCATAAGCTAATTATGTTTAACTTTGTTACAA-CACATTTTTAATTAT
1 ACCTATGAAGCATAATTGCATAAGCTAATTAGGTTCAACTTTGTTACAATC-CATCTTGAATTAT
* *
256889 CATTTGTGAAAAAAACATGAAAGAAT-CATTCCTACTTAAAGGATGACATGTCTAAAAATACCCG
65 CATTAGTG--AAAAACATGAAAG-ATCCATTCCTACTTAAAGGGTGACATGTCTAAAAATACCCG
* *
256953 ACATACAATAGAAAATACCTTGCATTACGGT
127 ACATACAACAGAAAATACCTTGCATTATGGT
* * *
256984 ACC--T---GCATAATTGCATAAGCTAATTAGTTTCAACTTTGTTACAATACAACTTGAATTATC
1 ACCTATGAAGCATAATTGCATAAGCTAATTAGGTTCAACTTTGTTACAATCCATCTTGAATTATC
* * * *
257044 ATTAGCGACATACATGAAAGATCCATTCCTACTTAAAGGGTGACATGTCTAAAAATATCCGACAT
66 ATTAGTGAAAAACATGAAAGATCCATTCCTACTTAAAGGGTGACATGTCTAAAAATACCCGACAT
* * *
257109 ACAACAGAAAGTACTTTGCATTATTGT
131 ACAACAGAAAATACCTTGCATTATGGT
*
257136 ACCTATGAAGCATAATTGCATAAGCTAATTAGGTTGAACTTTGTTACAATCCATCTTGAATTATC
1 ACCTATGAAGCATAATTGCATAAGCTAATTAGGTTCAACTTTGTTACAATCCATCTTGAATTATC
* * *
257201 ATTAGTGAAAAACATTAAAGATCCATTCCTACTTAAAGGGTGGCATGTCTAAAATTACCCGACAT
66 ATTAGTGAAAAACATGAAAGATCCATTCCTACTTAAAGGGTGACATGTCTAAAAATACCCGACAT
* *
257266 ACAACATAAAATACCTTGCATTAGGGT
131 ACAACAGAAAATACCTTGCATTATGGT
* * * *
257293 ACCTATGAAACATAATTTCATAAGCTAATTAGGTTCAACTTTGTTATAATACATCTTGAATTATC
1 ACCTATGAAGCATAATTGCATAAGCTAATTAGGTTCAACTTTGTTACAATCCATCTTGAATTATC
* * * * *
257358 ATTAGTGAAAAACATGATAGATACATTCCTATTTAAAGGATGACATGCCTAAAAATACCCGACAT
66 ATTAGTGAAAAACATGAAAGATCCATTCCTACTTAAAGGGTGACATGTCTAAAAATACCCGACAT
257423 ACAACAGAAAATACCTTGC-TT-TGTGT
131 ACAACAGAAAATACCTTGCATTATG-GT
257449 ACCTATGAAGCA
1 ACCTATGAAGCA
257461 AAAAAGCAGT
Statistics
Matches: 1106, Mismatches: 132, Indels: 41
0.86 0.10 0.03
Matches are distributed among these distances:
151 111 0.10
152 94 0.08
154 56 0.05
155 1 0.00
156 34 0.03
157 728 0.66
159 80 0.07
160 2 0.00
ACGTcount: A:0.38, C:0.18, G:0.14, T:0.31
Consensus pattern (157 bp):
ACCTATGAAGCATAATTGCATAAGCTAATTAGGTTCAACTTTGTTACAATCCATCTTGAATTATC
ATTAGTGAAAAACATGAAAGATCCATTCCTACTTAAAGGGTGACATGTCTAAAAATACCCGACAT
ACAACAGAAAATACCTTGCATTATGGT
Found at i:257140 original size:468 final size:469
Alignment explanation
Indices: 256054--257441 Score: 1981
Period size: 468 Copynumber: 3.0 Consensus size: 469
256044 ACACCTATGA
* * *
256054 AGCATAATTGCATAAGCTAATT-TTGTTCAACTTTGTTACAATTCATCTTGAATTCTCATTAGTG
1 AGCATAATTGCATAAGCTAATTAGT-TTCAACTTTGTTACAATACATCTTGAATTATCATTAGTG
* * **
256118 AAAAACATGAAAGATCCATTCCTACTTAAAGGATGACATGCCTAAAAATACCCGACATACAACCC
65 AAAAACATGAAAGATCCATTCCTACTTAAAGGGTGACATGTCTAAAAATACCCGACATACAACAG
* *
256183 AAAATACCTTGCAGTATGGTACCTATGAAGCATAATTGCATAAGCTAATTA-AGTTTAACTTTTT
130 AAAATACCTTGCATTATGGTACCTATGAAGCATAATTGCATAAGCTAATTAGA-TTTAACTTTGT
* * * * *
256247 TGCAACACCTTTTGAATTATCATTAGTGAAAAACATGAAAGATTCATTCCTACTTAAAGGATGAC
194 TACAATACATCTTGAATTATCATTAGTGAAAAACATGAAAGATTCATTCCTACTTAAAGGGTGAC
* * *
256312 ATGTCTAAAATTACCCGATATGCAACAG-AAATACCTTGCATTACAGTACC--T---GCATAATT
259 ATGTCTAAAATTACCCGACATACAACAGAAAATACCTTGCATTACGGTACCTATGAAGCATAATT
* * *
256371 GCATAAGCTAATTAGGTTCAACTTTGTTACAATTCATCGTGAATTATCATTAGTGACAAACATGA
324 GCATAAGCTAATTAGGTTCAACTTTGTTACAATACATCTTGAATTATCATTAGTGAAAAACATGA
* * * * *
256436 TAGATCCATTCGTACTTAAAGGGTGGCATGTCTAAAAATATCCGACATACAACAGAAAATACCTT
389 TAGATACATTCCTACTTAAAGGATGACATGTCTAAAAATACCCGACATACAACAGAAAATACCTT
* *
256501 GTATTATGGTAACTAT
454 GCATTACGGTAACTAT
* * * * * *
256517 GAAGAATAACTGCATTAGCTAATTAGGTTGAACTTTGTTACAATCCATCTTGAATTATCATTAGT
1 --AGCATAATTGCATAAGCTAATTAGTTTCAACTTTGTTACAATACATCTTGAATTATCATTAGT
* * * *
256582 GAAAAACATGAAAGAACCATTCCTTCTTAAAGGGTGGCATGTCTAAAATTACCCGACATACAACA
64 GAAAAACATGAAAGATCCATTCCTACTTAAAGGGTGACATGTCTAAAAATACCCGACATACAACA
*
256647 GAAAATACCTTGCATTATGGTACCTAGGAAGCATAATTGCATAAGCTAATTAGATTTAACTTTGT
129 GAAAATACCTTGCATTATGGTACCTATGAAGCATAATTGCATAAGCTAATTAGATTTAACTTTGT
*
256712 TACAATACATCTTGAATTATCATTAGTGAAAAACATGAAAGATTCATTCCCACTTAAAGGGTGAC
194 TACAATACATCTTGAATTATCATTAGTGAAAAACATGAAAGATTCATTCCTACTTAAAGGGTGAC
* * *
256777 ATGTCTAAAAATACCTGACATACAACAGAAAATACCTTGCATTATGGTACCTATGAAGCATAATT
259 ATGTCTAAAATTACCCGACATACAACAGAAAATACCTTGCATTACGGTACCTATGAAGCATAATT
* * * * * *
256842 GCATAAGCTAATTATGTTTAACTTTGTTACAACACATTTTTAATTATCATTTGTGAAAAAAACAT
324 GCATAAGCTAATTAGGTTCAACTTTGTTACAATACATCTTGAATTATCATTAGTG--AAAAACAT
* *
256907 GAAAGA-ATCATTCCTACTTAAAGGATGACATGTCTAAAAATACCCGACATACAATAGAAAATAC
387 GATAGATA-CATTCCTACTTAAAGGATGACATGTCTAAAAATACCCGACATACAACAGAAAATAC
*
256971 CTTGCATTACGGT-AC-CT
451 CTTGCATTACGGTAACTAT
* *
256988 -GCATAATTGCATAAGCTAATTAGTTTCAACTTTGTTACAATACAACTTGAATTATCATTAGCGA
1 AGCATAATTGCATAAGCTAATTAGTTTCAACTTTGTTACAATACATCTTGAATTATCATTAGTGA
* * *
257052 CATACATGAAAGATCCATTCCTACTTAAAGGGTGACATGTCTAAAAATATCCGACATACAACAGA
66 AAAACATGAAAGATCCATTCCTACTTAAAGGGTGACATGTCTAAAAATACCCGACATACAACAGA
* * * * *
257117 AAGTACTTTGCATTATTGTACCTATGAAGCATAATTGCATAAGCTAATTAGGTTGAACTTTGTTA
131 AAATACCTTGCATTATGGTACCTATGAAGCATAATTGCATAAGCTAATTAGATTTAACTTTGTTA
* * * *
257182 CAATCCATCTTGAATTATCATTAGTGAAAAACATTAAAGATCCATTCCTACTTAAAGGGTGGCAT
196 CAATACATCTTGAATTATCATTAGTGAAAAACATGAAAGATTCATTCCTACTTAAAGGGTGACAT
* * * *
257247 GTCTAAAATTACCCGACATACAACATAAAATACCTTGCATTAGGGTACCTATGAAACATAATTTC
261 GTCTAAAATTACCCGACATACAACAGAAAATACCTTGCATTACGGTACCTATGAAGCATAATTGC
*
257312 ATAAGCTAATTAGGTTCAACTTTGTTATAATACATCTTGAATTATCATTAGTGAAAAACATGATA
326 ATAAGCTAATTAGGTTCAACTTTGTTACAATACATCTTGAATTATCATTAGTGAAAAACATGATA
* *
257377 GATACATTCCTATTTAAAGGATGACATGCCTAAAAATACCCGACATACAACAGAAAATACCTTGC
391 GATACATTCCTACTTAAAGGATGACATGTCTAAAAATACCCGACATACAACAGAAAATACCTTGC
257442 TTTGTGTACC
Statistics
Matches: 818, Mismatches: 93, Indels: 23
0.88 0.10 0.02
Matches are distributed among these distances:
465 254 0.31
466 92 0.11
467 1 0.00
468 339 0.41
471 56 0.07
472 2 0.00
473 74 0.09
ACGTcount: A:0.38, C:0.18, G:0.14, T:0.31
Consensus pattern (469 bp):
AGCATAATTGCATAAGCTAATTAGTTTCAACTTTGTTACAATACATCTTGAATTATCATTAGTGA
AAAACATGAAAGATCCATTCCTACTTAAAGGGTGACATGTCTAAAAATACCCGACATACAACAGA
AAATACCTTGCATTATGGTACCTATGAAGCATAATTGCATAAGCTAATTAGATTTAACTTTGTTA
CAATACATCTTGAATTATCATTAGTGAAAAACATGAAAGATTCATTCCTACTTAAAGGGTGACAT
GTCTAAAATTACCCGACATACAACAGAAAATACCTTGCATTACGGTACCTATGAAGCATAATTGC
ATAAGCTAATTAGGTTCAACTTTGTTACAATACATCTTGAATTATCATTAGTGAAAAACATGATA
GATACATTCCTACTTAAAGGATGACATGTCTAAAAATACCCGACATACAACAGAAAATACCTTGC
ATTACGGTAACTAT
Found at i:257238 original size:625 final size:621
Alignment explanation
Indices: 256046--257460 Score: 2276
Period size: 625 Copynumber: 2.3 Consensus size: 621
256036 CAGTTCCGAC
* * *
256046 ACCTATGAAGCATAATTGCATAAGCTAATTTTGTTCAACTTTGTTACAATTCATCTTGAATTCTC
1 ACCTATGAAGCATAATTGCATAAGCTAA-TTAGTTCAACTTTGTTACAATACATCTTGAATTATC
*
256111 ATTAGTGAAAAACATGAAAGATCCATTCCTACTTAAAGGATGACATGCCTAAAAATACCCGACAT
65 ATTAGTGAAAAACATGAAAGATACATTCCTACTTAAAGGATGACATGCCTAAAAATACCCGACAT
** *
256176 ACAACCCAAAATACCTTGCAGTATGGTACCTATGAAGCATAATTGCATAAGCTAATTAAGTTTAA
130 ACAACAGAAAATACCTTGCATTATGGTACCTATGAAGCATAATTGCATAAGCTAATTAAGTTTAA
* * * *
256241 CTTTTTTGCAACACCTTTTGAATTATCATTAGTGAAAAACATGAAAGATTCATTCCTACTTAAAG
195 CTTTGTTACAACACATTTTGAATTATCATTAGTGAAAAACATGAAAGAATCATTCCTACTTAAAG
* * *
256306 GATGACATGTCTAAAATTACCCGATATGCAACAGAAATACCTTGCATTACAGTACCTGCATAATT
260 GATGACATGTCTAAAAATACCCGACATACAACAGAAATACCTTGCATTACAGTACCTGCATAATT
* * *
256371 GCATAAGCTAATTAGGTTCAACTTTGTTACAATTCATCGTGAATTATCATTAGTGACAAACATGA
325 GCATAAGCTAATTAGGTTCAACTTTGTTACAATACAACGTGAATTATCATTAGCGACAAACATGA
* * *
256436 TAGATCCATTCGTACTTAAAGGGTGGCATGTCTAAAAATATCCGACATACAACAGAAAATACCTT
390 AAGATCCATTCCTACTTAAAGGGTGACATGTCTAAAAATATCCGACATACAACAGAAAATACCTT
* *
256501 GTATTATGGTAACTATGAAGAATAACTGCATTAGCTAATTAGGTTGAACTTTGTTACAATCCATC
455 GCATTATGGTAACTATGAAGAATAACTGCATAAGCTAATTAGGTTGAACTTTGTTACAATCCATC
*
256566 TTGAATTATCATTAGTGAAAAACATGAAAGAACCATTCCTTCTTAAAGGGTGGCATGTCTAAAAT
520 TTGAATTATCATTAGTGAAAAACATGAAAGAACCATTCCTACTTAAAGGGTGGCATGTCTAAAAT
*
256631 TACCCGACATACAACAGAAAATACCTTGCATTATGGT
585 TACCCGACATACAACAGAAAATACCTTGCATTAGGGT
* *
256668 ACCTAGGAAGCATAATTGCATAAGCTAATTAGATTTAACTTTGTTACAATACATCTTGAATTATC
1 ACCTATGAAGCATAATTGCATAAGCTAATTAG-TTCAACTTTGTTACAATACATCTTGAATTATC
* * * * *
256733 ATTAGTGAAAAACATGAAAGATTCATTCCCACTTAAAGGGTGACATGTCTAAAAATACCTGACAT
65 ATTAGTGAAAAACATGAAAGATACATTCCTACTTAAAGGATGACATGCCTAAAAATACCCGACAT
*
256798 ACAACAGAAAATACCTTGCATTATGGTACCTATGAAGCATAATTGCATAAGCTAATTATGTTTAA
130 ACAACAGAAAATACCTTGCATTATGGTACCTATGAAGCATAATTGCATAAGCTAATTAAGTTTAA
* *
256863 CTTTGTTACAACACATTTTTAATTATCATTTGTGAAAAAAACATGAAAGAATCATTCCTACTTAA
195 CTTTGTTACAACACATTTTGAATTATCATTAGTG--AAAAACATGAAAGAATCATTCCTACTTAA
* *
256928 AGGATGACATGTCTAAAAATACCCGACATACAATAGAAAATACCTTGCATTACGGTACCTGCATA
258 AGGATGACATGTCTAAAAATACCCGACATACAACAG-AAATACCTTGCATTACAGTACCTGCATA
* * *
256993 ATTGCATAAGCTAATTAGTTTCAACTTTGTTACAATACAACTTGAATTATCATTAGCGACATACA
322 ATTGCATAAGCTAATTAGGTTCAACTTTGTTACAATACAACGTGAATTATCATTAGCGACAAACA
*
257058 TGAAAGATCCATTCCTACTTAAAGGGTGACATGTCTAAAAATATCCGACATACAACAGAAAGTAC
387 TGAAAGATCCATTCCTACTTAAAGGGTGACATGTCTAAAAATATCCGACATACAACAGAAAATAC
* * * * *
257123 TTTGCATTATTGTACCTATGAAGCATAATTGCATAAGCTAATTAGGTTGAACTTTGTTACAATCC
452 CTTGCATTATGGTAACTATGAAGAATAACTGCATAAGCTAATTAGGTTGAACTTTGTTACAATCC
* *
257188 ATCTTGAATTATCATTAGTGAAAAACATTAAAGATCCATTCCTACTTAAAGGGTGGCATGTCTAA
517 ATCTTGAATTATCATTAGTGAAAAACATGAAAGAACCATTCCTACTTAAAGGGTGGCATGTCTAA
*
257253 AATTACCCGACATACAACATAAAATACCTTGCATTAGGGT
582 AATTACCCGACATACAACAGAAAATACCTTGCATTAGGGT
* * *
257293 ACCTATGAAACATAATTTCATAAGCTAATTAGGTTCAACTTTGTTATAATACATCTTGAATTATC
1 ACCTATGAAGCATAATTGCATAAGCTAATTA-GTTCAACTTTGTTACAATACATCTTGAATTATC
* *
257358 ATTAGTGAAAAACATGATAGATACATTCCTATTTAAAGGATGACATGCCTAAAAATACCCGACAT
65 ATTAGTGAAAAACATGAAAGATACATTCCTACTTAAAGGATGACATGCCTAAAAATACCCGACAT
257423 ACAACAGAAAATACCTTGC-TT-TGTGTACCTATGAAGCA
130 ACAACAGAAAATACCTTGCATTATG-GTACCTATGAAGCA
257461 AAAAAGCAGT
Statistics
Matches: 728, Mismatches: 59, Indels: 10
0.91 0.07 0.01
Matches are distributed among these distances:
621 3 0.00
622 206 0.28
623 2 0.00
624 76 0.10
625 440 0.60
626 1 0.00
ACGTcount: A:0.38, C:0.18, G:0.14, T:0.31
Consensus pattern (621 bp):
ACCTATGAAGCATAATTGCATAAGCTAATTAGTTCAACTTTGTTACAATACATCTTGAATTATCA
TTAGTGAAAAACATGAAAGATACATTCCTACTTAAAGGATGACATGCCTAAAAATACCCGACATA
CAACAGAAAATACCTTGCATTATGGTACCTATGAAGCATAATTGCATAAGCTAATTAAGTTTAAC
TTTGTTACAACACATTTTGAATTATCATTAGTGAAAAACATGAAAGAATCATTCCTACTTAAAGG
ATGACATGTCTAAAAATACCCGACATACAACAGAAATACCTTGCATTACAGTACCTGCATAATTG
CATAAGCTAATTAGGTTCAACTTTGTTACAATACAACGTGAATTATCATTAGCGACAAACATGAA
AGATCCATTCCTACTTAAAGGGTGACATGTCTAAAAATATCCGACATACAACAGAAAATACCTTG
CATTATGGTAACTATGAAGAATAACTGCATAAGCTAATTAGGTTGAACTTTGTTACAATCCATCT
TGAATTATCATTAGTGAAAAACATGAAAGAACCATTCCTACTTAAAGGGTGGCATGTCTAAAATT
ACCCGACATACAACAGAAAATACCTTGCATTAGGGT
Found at i:261954 original size:295 final size:294
Alignment explanation
Indices: 261386--261974 Score: 747
Period size: 295 Copynumber: 2.0 Consensus size: 294
261376 ACCCAAGAGT
* *
261386 CACCTTAGGTCCATAAGAAATTATCATTCAGTGCTCAACCTATACAAGGAATTACCAATAGCGAT
1 CACCTTAGGTCCATAAGAAATTATCATTCAGTGCTCAACCTATACAAGGAATTACCAACAGCGAC
* * * * * **
261451 TGAACCTGTCAGTGTCTTCAGTTATACCAGAGCCCAAAGTACCCCGTATAAAAATAATGTCAGAC
66 TAAACATGCCAGTGTCTTCAGTCATACCAAAGCCCAAAGTACCCAATATAAAAATAATGTCAGAC
* * * * * *
261516 TGTAAATAGAGATAAAAATCAGAGCAGAGATCATAGATCATATCGAAAATCATATATCATAACAT
131 TATAAATAGAGATAAAAATCAGAGCAGAGATCATAGATCATATAGAAAATCAGAGATCAGAACAA
* *
261581 ATATCAAAGTTCAGAATAGAAATCAGAGGTCAGCTTGTATTTCAGATAACAGAGACATGCTTTTA
196 ATATCAAAGTTCAAAATAGAAATCAGAGGTCAGCCTGTATTTCAGATAACAGAGACATGCTTTTA
* *
261646 AAATCAGAGAAAACATTCGTATGACCAGGGAACA
261 AAATCAGAGAAAACATACGTATGACCAAGGAACA
* * * * * * *
261680 CACCTTAGTTCCATAAGAAATTTTCAGTT-GGTGTTGAACCTATACAAGTAATTACCAGCAGCGA
1 CACCTTAGGTCCATAAGAAATTATCA-TTCAGTGCTCAACCTATACAAGGAATTACCAACAGCGA
*
261744 CTAAACATGCCAGTGTCTTCAGTCATACCAAAGTCTCAGAA-TA-CCAATATAAAAATAAT-TCT
65 CTAAACATGCCAGTGTCTTCAGTCATACCAAAG-CCCA-AAGTACCCAATATAAAAATAATGTC-
* * *
261806 AGTCTATAAATAGAGATAAAAAATCAGAGCAGAGGTCATAGATCATATA-AGAAATCAGAGATTA
127 AGACTATAAATAGAGAT-AAAAATCAGAGCAGAGATCATAGATCATATAGA-AAATCAGAGATCA
* * * * * *
261870 GAACAAATATCTATGTTTAAAATAGAAATCAGAGGTCAGCCTGTATTTCATATAACAGAGGCGTG
190 GAACAAATATCAAAGTTCAAAATAGAAATCAGAGGTCAGCCTGTATTTCAGATAACAGAGACATG
* *
261935 CTTTTAAAATCATAGAAAACATACGTATGATCAAGGAACA
255 CTTTTAAAATCAGAGAAAACATACGTATGACCAAGGAACA
261975 TACTCGAGGT
Statistics
Matches: 251, Mismatches: 38, Indels: 11
0.84 0.13 0.04
Matches are distributed among these distances:
293 2 0.01
294 110 0.44
295 137 0.55
296 2 0.01
ACGTcount: A:0.41, C:0.17, G:0.16, T:0.26
Consensus pattern (294 bp):
CACCTTAGGTCCATAAGAAATTATCATTCAGTGCTCAACCTATACAAGGAATTACCAACAGCGAC
TAAACATGCCAGTGTCTTCAGTCATACCAAAGCCCAAAGTACCCAATATAAAAATAATGTCAGAC
TATAAATAGAGATAAAAATCAGAGCAGAGATCATAGATCATATAGAAAATCAGAGATCAGAACAA
ATATCAAAGTTCAAAATAGAAATCAGAGGTCAGCCTGTATTTCAGATAACAGAGACATGCTTTTA
AAATCAGAGAAAACATACGTATGACCAAGGAACA
Found at i:265413 original size:16 final size:16
Alignment explanation
Indices: 265380--265417 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
265370 GATAAACTGA
265380 TTTATACTTAAGTATT
1 TTTATACTTAAGTATT
265396 TTTAT-CTTAATGT-TT
1 TTTATACTTAA-GTATT
265411 TTTATAC
1 TTTATAC
265418 ACCGCGAGGA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
15 12 0.60
16 8 0.40
ACGTcount: A:0.26, C:0.08, G:0.05, T:0.61
Consensus pattern (16 bp):
TTTATACTTAAGTATT
Found at i:270795 original size:32 final size:33
Alignment explanation
Indices: 270758--270822 Score: 105
Period size: 32 Copynumber: 2.0 Consensus size: 33
270748 TTTTGGTTGA
* *
270758 GTGCAACCTACAATGTTAA-TTTTTTAACATTT
1 GTGCAACCTAAAATATTAATTTTTTTAACATTT
270790 GTGCAACCTAAAATATTAATTTTTTTAACATTT
1 GTGCAACCTAAAATATTAATTTTTTTAACATTT
270823 TCGATTAACA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 17 0.57
33 13 0.43
ACGTcount: A:0.34, C:0.14, G:0.08, T:0.45
Consensus pattern (33 bp):
GTGCAACCTAAAATATTAATTTTTTTAACATTT
Found at i:276797 original size:19 final size:19
Alignment explanation
Indices: 276769--276816 Score: 78
Period size: 19 Copynumber: 2.5 Consensus size: 19
276759 ATTATAGTCG
* *
276769 TGATTATTTTTAAATGAGT
1 TGATTTTTTTTAAATGAGC
276788 TGATTTTTTTTAAATGAGC
1 TGATTTTTTTTAAATGAGC
276807 TGATTTTTTT
1 TGATTTTTTT
276817 AAAAAAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.25, C:0.02, G:0.15, T:0.58
Consensus pattern (19 bp):
TGATTTTTTTTAAATGAGC
Found at i:277809 original size:30 final size:32
Alignment explanation
Indices: 277774--277847 Score: 107
Period size: 30 Copynumber: 2.4 Consensus size: 32
277764 ACCCCAAAAT
* *
277774 TTTAGATAGAATACTA-ATTTGACCTT-TAAC
1 TTTAGATAAAATACTATATTTGACCTTACAAC
*
277804 TTTAGATAAAATACTATTTTTGACCTTACAAC
1 TTTAGATAAAATACTATATTTGACCTTACAAC
277836 TTTAGATAAAAT
1 TTTAGATAAAAT
277848 GTCAATTTGA
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
30 15 0.38
31 9 0.23
32 15 0.38
ACGTcount: A:0.39, C:0.12, G:0.08, T:0.41
Consensus pattern (32 bp):
TTTAGATAAAATACTATATTTGACCTTACAAC
Found at i:278174 original size:2 final size:2
Alignment explanation
Indices: 278167--278218 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
278157 TAGTTTAATT
278167 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
278209 TA TA TA TA TA
1 TA TA TA TA TA
278219 ATAAGTTGTA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:280323 original size:14 final size:15
Alignment explanation
Indices: 280293--280326 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
280283 TTGGGTCAAA
280293 ATATAAAATAAATTT
1 ATATAAAATAAATTT
*
280308 ATATAAATTAAA-TT
1 ATATAAAATAAATTT
280322 ATATA
1 ATATA
280327 TTATAATTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 7 0.39
15 11 0.61
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
ATATAAAATAAATTT
Found at i:280764 original size:34 final size:34
Alignment explanation
Indices: 280699--280764 Score: 82
Period size: 34 Copynumber: 1.9 Consensus size: 34
280689 AGATTTTGAT
*
280699 AAATTATATATTATAATTTTATCAAACTTATAAC
1 AAATTATATATTATAATTTTATCAAAATTATAAC
*
280733 AAATTATA-ATATATAA-TTTCTCAAAAATTATA
1 AAATTATATAT-TATAATTTTATC-AAAATTATA
280765 TAAATTAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
33 7 0.25
34 21 0.75
ACGTcount: A:0.50, C:0.08, G:0.00, T:0.42
Consensus pattern (34 bp):
AAATTATATATTATAATTTTATCAAAATTATAAC
Found at i:280821 original size:18 final size:18
Alignment explanation
Indices: 280798--280850 Score: 72
Period size: 18 Copynumber: 2.9 Consensus size: 18
280788 ATATAAACAT
*
280798 ATTATGATATAGATATAG
1 ATTATGATATATATATAG
*
280816 ATTATGATATATATATAT
1 ATTATGATATATATATAG
280834 ATATAT-ATATATATATA
1 AT-TATGATATATATATA
280851 TGTCCTTATT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
18 29 0.91
19 3 0.09
ACGTcount: A:0.47, C:0.00, G:0.08, T:0.45
Consensus pattern (18 bp):
ATTATGATATATATATAG
Found at i:280829 original size:2 final size:2
Alignment explanation
Indices: 280804--280851 Score: 62
Period size: 2 Copynumber: 24.0 Consensus size: 2
280794 ACATATTATG
* *
280804 AT AT AG AT AT AG AT -T AT GAT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT
280846 AT AT AT
1 AT AT AT
280852 GTCCTTATTT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
1 1 0.03
2 37 0.93
3 2 0.05
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.46
Consensus pattern (2 bp):
AT
Found at i:288762 original size:13 final size:12
Alignment explanation
Indices: 288735--288785 Score: 52
Period size: 13 Copynumber: 4.2 Consensus size: 12
288725 TAATATTGAT
288735 AAATATATATTA
1 AAATATATATTA
*
288747 AAATATGATTTTA
1 AAATAT-ATATTA
288760 AAATA-AT-TTA
1 AAATATATATTA
288770 AAAGTAATATATTA
1 AAA-T-ATATATTA
288784 AA
1 AA
288786 TAGGATTTTA
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
10 6 0.18
11 3 0.09
12 7 0.21
13 12 0.36
14 5 0.15
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (12 bp):
AAATATATATTA
Found at i:290336 original size:3 final size:3
Alignment explanation
Indices: 290313--290392 Score: 88
Period size: 3 Copynumber: 26.0 Consensus size: 3
290303 CTTTTTTATT
* *
290313 TAA TAA TATA TATA TAT TAA TAA TAA TTA TAA TAA TAA TAA TAA TAA
1 TAA TAA TA-A TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
** **
290360 TAA TAA TAA TTT TAA TAA TTT TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
290393 GTAAACTAAA
Statistics
Matches: 64, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
3 57 0.89
4 7 0.11
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (3 bp):
TAA
Found at i:290509 original size:24 final size:24
Alignment explanation
Indices: 290462--290508 Score: 87
Period size: 23 Copynumber: 2.0 Consensus size: 24
290452 AATAGAGCAA
290462 AGACGAATAAAGACAATAATTTTT
1 AGACGAATAAAGACAATAATTTTT
290486 AGACGAA-AAAGACAATAATTTTT
1 AGACGAATAAAGACAATAATTTTT
290509 TCATTTGGCA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 16 0.70
24 7 0.30
ACGTcount: A:0.51, C:0.09, G:0.13, T:0.28
Consensus pattern (24 bp):
AGACGAATAAAGACAATAATTTTT
Found at i:290609 original size:45 final size:46
Alignment explanation
Indices: 290541--290938 Score: 615
Period size: 46 Copynumber: 8.7 Consensus size: 46
290531 GATGAAAATG
* * *
290541 TTGAACACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG-TT
1 TTGAAAACATCAAGCACTGAAGGACTTACAGATGACCCGAAGGTTT
* * * *
290586 TTGAAAACATCATGCACTTAAGGGCTTACAAATGACCCGAAGG-TT
1 TTGAAAACATCAAGCACTGAAGGACTTACAGATGACCCGAAGGTTT
* ** * *
290631 TTGAAAACATCATGCACTGAAGGGTTTATAGATGACCCGGAGG-TT
1 TTGAAAACATCAAGCACTGAAGGACTTACAGATGACCCGAAGGTTT
*
290676 TTGAAAACATCAAGCACTGAAGGACTTACAGATGACTCGAAGG-TT
1 TTGAAAACATCAAGCACTGAAGGACTTACAGATGACCCGAAGGTTT
290721 TTGAAAACATCAAGCACTGAAGGACTTACAGATGACCCGAAGGTTT
1 TTGAAAACATCAAGCACTGAAGGACTTACAGATGACCCGAAGGTTT
290767 TTGAAAACATCAAGCACTGAAGGACTTACAGATGACCCGAAGGTTT
1 TTGAAAACATCAAGCACTGAAGGACTTACAGATGACCCGAAGGTTT
290813 TTGAAAACATCAAGCACTGAAGGACTTACAGATGACCCGAAGGTTT
1 TTGAAAACATCAAGCACTGAAGGACTTACAGATGACCCGAAGGTTT
* *
290859 TTGAAAACATCATGCACTGAAGGACTTACAGATGACTCGAAGGTTT
1 TTGAAAACATCAAGCACTGAAGGACTTACAGATGACCCGAAGGTTT
* *
290905 TTTAAAACATCAAGCACTGAAGGTCTTACAGATG
1 TTGAAAACATCAAGCACTGAAGGACTTACAGATG
290939 TGGGAAACAG
Statistics
Matches: 332, Mismatches: 20, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
45 163 0.49
46 169 0.51
ACGTcount: A:0.35, C:0.19, G:0.22, T:0.24
Consensus pattern (46 bp):
TTGAAAACATCAAGCACTGAAGGACTTACAGATGACCCGAAGGTTT
Found at i:291989 original size:17 final size:16
Alignment explanation
Indices: 291969--292024 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 16
291959 AATATAATGA
291969 AAATAAATAAATAGTAT
1 AAATAAATAAATA-TAT
291986 AAATAAAATAATATATAT
1 AAAT-AAATAA-ATATAT
* *
292004 ATATATATATAATATAT
1 AAATAAATA-AATATAT
292021 AAAT
1 AAAT
292025 GTATGTATAA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
17 17 0.52
18 13 0.39
19 3 0.09
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (16 bp):
AAATAAATAAATATAT
Found at i:292017 original size:19 final size:19
Alignment explanation
Indices: 291993--292043 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
291983 TATAAATAAA
*
291993 ATAATATATATATATATAT
1 ATAATATATAAATATATAT
* *
292012 ATAATATATAAATGTATGT
1 ATAATATATAAATATATAT
292031 ATAATATAATAAA
1 ATAATAT-ATAAA
292044 ATACTAAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 23 0.82
20 5 0.18
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.41
Consensus pattern (19 bp):
ATAATATATAAATATATAT
Found at i:293796 original size:106 final size:106
Alignment explanation
Indices: 293611--294462 Score: 1402
Period size: 106 Copynumber: 8.0 Consensus size: 106
293601 GCATTGTTCC
* * *
293611 GAGTCTAATATCCTCCG-TCGTGAAGTTGAAATTGGCTCTGGAATTGGGAAGTTGTTTATTGACA
1 GAGTCCAATATCCTTCGCT-GTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACA
* *
293675 ACCAGCGGTCCCTTCGTCGTGAATTTGAACTTGCGTTGTCTT
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
293717 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* *
293782 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
293823 GAGTCCAATATCCTTCGCTATGAAGTTGAAATTGACTCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
293888 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
293929 GAGTCCAATATCCTTCGTTGTGAAGTTGGAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
293994 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
**
294035 GAGTCCAATATCCTTATCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
*
294100 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
294141 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
*
294206 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
294247 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTAAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
294312 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
294353 GAGTCCAATATCCTTCGCTTTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* * * * *
294418 ACAGTC-GTCCCTTCTTTGTGAAGTTGAACTTGTGTTGTCTC
66 CCAG-CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
294459 GAGT
1 GAGT
294463 GGCACGATAT
Statistics
Matches: 700, Mismatches: 44, Indels: 4
0.94 0.06 0.01
Matches are distributed among these distances:
106 698 1.00
107 2 0.00
ACGTcount: A:0.22, C:0.18, G:0.25, T:0.34
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:296093 original size:14 final size:14
Alignment explanation
Indices: 296092--296149 Score: 50
Period size: 13 Copynumber: 4.1 Consensus size: 14
296082 TTCTTTCTTT
296092 TTTCTTTTGTT-TTC
1 TTTCTTTT-TTGTTC
296106 -TTCTTTTTTGCTTC
1 TTTCTTTTTTG-TTC
296120 TTTTCTTTTTTGTT-
1 -TTTCTTTTTTGTTC
*
296134 TTTTTCTTTTTGTTC
1 TTTCT-TTTTTGTTC
296149 T
1 T
296150 GATTGAATCT
Statistics
Matches: 37, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
12 2 0.05
13 11 0.30
14 11 0.30
15 3 0.08
16 10 0.27
ACGTcount: A:0.00, C:0.14, G:0.07, T:0.79
Consensus pattern (14 bp):
TTTCTTTTTTGTTC
Found at i:296095 original size:7 final size:7
Alignment explanation
Indices: 296063--296144 Score: 60
Period size: 7 Copynumber: 11.6 Consensus size: 7
296053 TTTTTATCCC
296063 TTTTTC-
1 TTTTTCT
**
296069 TTTTTGA
1 TTTTTCT
*
296076 TTTTTGT
1 TTTTTCT
*
296083 TCTTTCT
1 TTTTTCT
296090 TTTTTCT
1 TTTTTCT
*
296097 TTTGT-T
1 TTTTTCT
*
296103 TTCTTCT
1 TTTTTCT
296110 TTTTTGCT
1 TTTTT-CT
296118 TCTTTTCT
1 T-TTTTCT
*
296126 TTTTTGTT
1 TTTTT-CT
296134 TTTTTCT
1 TTTTTCT
296141 TTTT
1 TTTT
296145 GTTCTGATTG
Statistics
Matches: 60, Mismatches: 11, Indels: 9
0.75 0.14 0.11
Matches are distributed among these distances:
6 9 0.15
7 35 0.58
8 12 0.20
9 4 0.07
ACGTcount: A:0.01, C:0.12, G:0.06, T:0.80
Consensus pattern (7 bp):
TTTTTCT
Found at i:296099 original size:20 final size:20
Alignment explanation
Indices: 296065--296149 Score: 64
Period size: 20 Copynumber: 4.0 Consensus size: 20
296055 TTTATCCCTT
**
296065 TTTCTTTTTGATTTTTGTTC
1 TTTCTTTTTTCTTTTTGTTC
*
296085 TTTCTTTTTTC-TTTTGTTT
1 TTTCTTTTTTCTTTTTGTTC
* *
296104 TCTTCTTTTTTGCTTCTTTTCTTT
1 T-TTCTTTTTT-C-T-TTTTGTTC
*
296128 TTTGTTTTTTTCTTTTTGTTC
1 TTT-CTTTTTTCTTTTTGTTC
296149 T
1 T
296150 GATTGAATCT
Statistics
Matches: 52, Mismatches: 7, Indels: 11
0.74 0.10 0.16
Matches are distributed among these distances:
19 8 0.15
20 18 0.35
21 8 0.15
22 1 0.02
23 3 0.06
24 14 0.27
ACGTcount: A:0.01, C:0.13, G:0.07, T:0.79
Consensus pattern (20 bp):
TTTCTTTTTTCTTTTTGTTC
Found at i:296109 original size:24 final size:23
Alignment explanation
Indices: 296063--296147 Score: 66
Period size: 24 Copynumber: 3.6 Consensus size: 23
296053 TTTTTATCCC
*
296063 TTTTTCTTTTTGATTTTTGTTCTTTCT
1 TTTTTC-TTTTG--TTTTCTTCTTT-T
296090 TTTTTCTTTTGTTTTCTTCTTTT
1 TTTTTCTTTTGTTTTCTTCTTTT
* * *
296113 TTGCTTCTTTTCTTTT-TTGTTTT
1 TT-TTTCTTTTGTTTTCTTCTTTT
*
296136 TTTCT-TTTTGTT
1 TTTTTCTTTTGTT
296148 CTGATTGAAT
Statistics
Matches: 50, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
21 6 0.12
22 1 0.02
23 11 0.22
24 21 0.42
26 5 0.10
27 6 0.12
ACGTcount: A:0.01, C:0.12, G:0.07, T:0.80
Consensus pattern (23 bp):
TTTTTCTTTTGTTTTCTTCTTTT
Found at i:296128 original size:15 final size:15
Alignment explanation
Indices: 296086--296149 Score: 71
Period size: 15 Copynumber: 4.3 Consensus size: 15
296076 TTTTTGTTCT
296086 TTCTTTT-TTCTTTTG
1 TTCTTTTCTT-TTTTG
296101 TT-TTCTTCTTTTTTG
1 TTCTT-TTCTTTTTTG
296116 CTTCTTTTCTTTTTTG
1 -TTCTTTTCTTTTTTG
*
296132 TTTTTTTC-TTTTTG
1 TTCTTTTCTTTTTTG
296146 TTCT
1 TTCT
296150 GATTGAATCT
Statistics
Matches: 43, Mismatches: 2, Indels: 9
0.80 0.04 0.17
Matches are distributed among these distances:
14 11 0.26
15 16 0.37
16 14 0.33
17 2 0.05
ACGTcount: A:0.00, C:0.14, G:0.06, T:0.80
Consensus pattern (15 bp):
TTCTTTTCTTTTTTG
Found at i:296131 original size:31 final size:31
Alignment explanation
Indices: 296086--296144 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
296076 TTTTTGTTCT
296086 TTCTTTTTTCTTTTGTTTTCTTCTTTTTTGC
1 TTCTTTTTTCTTTTGTTTTCTTCTTTTTTGC
*
296117 TTCTTTTCTT-TTTTGTTTTTTTCTTTTT
1 TTCTTTT-TTCTTTTGTTTTCTTCTTTTT
296145 GTTCTGATTG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
31 24 0.92
32 2 0.08
ACGTcount: A:0.00, C:0.14, G:0.05, T:0.81
Consensus pattern (31 bp):
TTCTTTTTTCTTTTGTTTTCTTCTTTTTTGC
Found at i:300940 original size:9 final size:8
Alignment explanation
Indices: 300879--300948 Score: 54
Period size: 9 Copynumber: 8.4 Consensus size: 8
300869 AAAATAATGA
*
300879 AAATAAAT
1 AAATATAT
300887 AAATAGTAT
1 AAATA-TAT
*
300896 AAATA-AA
1 AAATATAT
300903 ATAATATAT
1 A-AATATAT
*
300912 ATATATAAT
1 AAATAT-AT
300921 AAATATAAT
1 AAATAT-AT
300930 AAAT-TAT
1 AAATATAT
300937 ATAATATAT
1 A-AATATAT
300946 AAA
1 AAA
300949 ATACTAATAG
Statistics
Matches: 51, Mismatches: 5, Indels: 12
0.75 0.07 0.18
Matches are distributed among these distances:
7 5 0.10
8 19 0.37
9 27 0.53
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.34
Consensus pattern (8 bp):
AAATATAT
Found at i:300977 original size:21 final size:21
Alignment explanation
Indices: 300900--300977 Score: 68
Period size: 25 Copynumber: 3.4 Consensus size: 21
300890 TAGTATAAAT
300900 AAAATAATATATATATATAATA
1 AAAATAATATATATA-ATAATA
*
300922 AATATAATAAATTATATAATATATA
1 AAAATAAT--A-TATATAATA-ATA
300947 AAATACTAATAGTA-ATAATAATA
1 AAA-A-TAATA-TATATAATAATA
300970 AAAATAAT
1 AAAATAAT
300978 GAAAATAAAT
Statistics
Matches: 47, Mismatches: 3, Indels: 13
0.75 0.05 0.21
Matches are distributed among these distances:
21 4 0.09
22 8 0.17
23 6 0.13
24 10 0.21
25 14 0.30
26 1 0.02
27 4 0.09
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.35
Consensus pattern (21 bp):
AAAATAATATATATAATAATA
Found at i:301705 original size:37 final size:37
Alignment explanation
Indices: 301612--301713 Score: 125
Period size: 37 Copynumber: 2.8 Consensus size: 37
301602 GTTCTTGTGG
* * ** * *
301612 ATCCTATCTTTAGGAGTTTAAATAATAGTAGAACTTT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGCAGAAATTT
*
301649 ATCATATTTTTAGGAGTTTGAATCCTAGCA-AAATTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGCAGAAATT-T
301686 ATCCTATTTTTAGGAGTTTGAATCCTAG
1 ATCCTATTTTTAGGAGTTTGAATCCTAG
301714 TAGGACGAAA
Statistics
Matches: 56, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
36 4 0.07
37 52 0.93
ACGTcount: A:0.31, C:0.13, G:0.15, T:0.41
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGCAGAAATTT
Found at i:302405 original size:54 final size:54
Alignment explanation
Indices: 302347--302489 Score: 184
Period size: 52 Copynumber: 2.7 Consensus size: 54
302337 CTTAAAACAC
302347 TTGACAACACATTCATCATTTCTTGTGGCTTCTGCTCAGATGCTCATAAAACTT
1 TTGACAACACATTCATCATTTCTTGTGGCTTCTGCTCAGATGCTCATAAAACTT
* * * * * *
302401 TTGACAACACATTCA--ATCTCATGTGGTTTCTACCCAGATGTTCATAAAACTT
1 TTGACAACACATTCATCATTTCTTGTGGCTTCTGCTCAGATGCTCATAAAACTT
* *
302453 TTGACAACACATTCCTCTTTTTCTT-TGGCTTCTGCTC
1 TTGACAACACATTCATC-ATTTCTTGTGGCTTCTGCTC
302490 GGATTTCTGG
Statistics
Matches: 73, Mismatches: 13, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
52 45 0.62
54 24 0.33
55 4 0.05
ACGTcount: A:0.24, C:0.25, G:0.12, T:0.38
Consensus pattern (54 bp):
TTGACAACACATTCATCATTTCTTGTGGCTTCTGCTCAGATGCTCATAAAACTT
Found at i:306671 original size:14 final size:16
Alignment explanation
Indices: 306640--306676 Score: 51
Period size: 14 Copynumber: 2.4 Consensus size: 16
306630 CTTGATTCAA
*
306640 TTTTTTTCCTTTTTTC
1 TTTTTTTCCTTTTCTC
306656 TTTTTTT-C-TTTCTC
1 TTTTTTTCCTTTTCTC
306670 TTTTTTT
1 TTTTTTT
306677 ATGAATGCGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 12 0.60
15 1 0.05
16 7 0.35
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (16 bp):
TTTTTTTCCTTTTCTC
Found at i:309620 original size:41 final size:43
Alignment explanation
Indices: 309540--309623 Score: 109
Period size: 41 Copynumber: 2.0 Consensus size: 43
309530 CTGTGCATCA
* *
309540 AACAAAACTTTACATGCAGGGGACAGCTTTCAGTCCTAACTTC
1 AACAAAACTTTACATACAGGGGACAGCTTTCACTCCTAACTTC
* * *
309583 AACAAAAC-TTACATATAGGGGATA-CTTTCCCTCCTAACTTC
1 AACAAAACTTTACATACAGGGGACAGCTTTCACTCCTAACTTC
309624 TTTAAACAAG
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
41 15 0.42
42 13 0.36
43 8 0.22
ACGTcount: A:0.33, C:0.26, G:0.13, T:0.27
Consensus pattern (43 bp):
AACAAAACTTTACATACAGGGGACAGCTTTCACTCCTAACTTC
Found at i:310878 original size:13 final size:13
Alignment explanation
Indices: 310848--310884 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
310838 CGAAATTTAA
*
310848 TAATGAAAATAA-
1 TAATAAAAATAAT
310860 -AATAAAAATAAT
1 TAATAAAAATAAT
310872 TAATAAAAATAAT
1 TAATAAAAATAAT
310885 ATACACATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
11 10 0.45
13 12 0.55
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (13 bp):
TAATAAAAATAAT
Found at i:310894 original size:24 final size:25
Alignment explanation
Indices: 310848--310909 Score: 74
Period size: 24 Copynumber: 2.6 Consensus size: 25
310838 CGAAATTTAA
*
310848 TAATGAAAATAAAATAAAAAT-AAT
1 TAATGAAAATAATATAAAAATAAAT
* * *
310872 TAATAAAAATAATATACACATAAAT
1 TAATGAAAATAATATAAAAATAAAT
310897 T-ATGAAAATAATA
1 TAATGAAAATAATA
310910 AGTATATAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
24 28 0.88
25 4 0.12
ACGTcount: A:0.66, C:0.03, G:0.03, T:0.27
Consensus pattern (25 bp):
TAATGAAAATAATATAAAAATAAAT
Found at i:311878 original size:77 final size:74
Alignment explanation
Indices: 311711--311861 Score: 216
Period size: 75 Copynumber: 2.0 Consensus size: 74
311701 TTAATAGAAA
**
311711 AAAATAAATAAATATTATTTATTAAAATTATATATATGTATTTATGATTAAATACTAATAATATT
1 AAAATAAATAAATATTATTTATTAAAATTATATATA-GTATTTATGATTAAATACTAATAATAAA
*
311776 ATATTAAAAT
65 ACATTAAAAT
311786 AAACATGTAAA-AAATATTATTTATTAAAATTATATATA-TATTTATGATTAAATACTAATAATA
1 AAA-A--TAAATAAATATTATTTATTAAAATTATATATAGTATTTATGATTAAATACTAATAATA
311849 AAACATATAAAAT
63 AAACAT-TAAAAT
311862 TGAAATACAA
Statistics
Matches: 69, Mismatches: 3, Indels: 7
0.87 0.04 0.09
Matches are distributed among these distances:
75 31 0.45
76 7 0.10
77 27 0.39
78 4 0.06
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.41
Consensus pattern (74 bp):
AAAATAAATAAATATTATTTATTAAAATTATATATAGTATTTATGATTAAATACTAATAATAAAA
CATTAAAAT
Found at i:313259 original size:3 final size:3
Alignment explanation
Indices: 313229--313304 Score: 93
Period size: 3 Copynumber: 25.0 Consensus size: 3
313219 CTTTTTTATT
313229 TAA TAA TATA TATA TAA T-A TATA TAA TAA TAA TAA T-A TAA TAA TAA
1 TAA TAA TA-A TA-A TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA
**
313275 TAA TAA TAA TAA TAA TTT TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
313305 GTAAACTGAA
Statistics
Matches: 65, Mismatches: 4, Indels: 8
0.84 0.05 0.10
Matches are distributed among these distances:
2 4 0.06
3 51 0.78
4 10 0.15
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:317843 original size:155 final size:153
Alignment explanation
Indices: 317550--317858 Score: 575
Period size: 155 Copynumber: 2.0 Consensus size: 153
317540 GTGATTGGAT
317550 AAATCATAAGCAATATGACTTATAATCAAATATTAATCAAGAAATCATGTTTTGGACATTTGAAT
1 AAATCATAAGCAATATGACTTATAATCAAATATTAATCAAGAAATCATGTTTTGGACATTTGAAT
317615 TTATTTAAGGCTTAGGGGGTATTATAGGTCTTTAATGAATGAAATTTTACCATTTTCCCTCGATT
66 TTATTTAAGGCTTAGGGGG-ATTATAGGTCTTTAATGAATGAAATTTTACCATTTTCCCTCGATT
317680 TAGCCTTAAGAGATCGATCATTTG
130 TAGCCTTAAGAGATCGATCATTTG
317704 AAATCATAAGCAAATATGACTTATAATCAAATATTAATCAAGAAATCATGTTTTGGACCATTTTG
1 AAATCATAAGC-AATATGACTTATAATCAAATATTAATCAAGAAATCATGTTTTGGA-CA-TTTG
317769 AATTTATTTAAGGCTTAGGGGG-TTATAGGTCTTTAATGAATGAAATTTTACCATTTTCCCTCGA
63 AATTTATTTAAGGCTTAGGGGGATTATAGGTCTTTAATGAATGAAATTTTACCATTTTCCCTCGA
317833 TTTAGCCTTAAGAGATCGATCATTTG
128 TTTAGCCTTAAGAGATCGATCATTTG
317859 CATTTTAATA
Statistics
Matches: 152, Mismatches: 0, Indels: 5
0.97 0.00 0.03
Matches are distributed among these distances:
154 11 0.07
155 113 0.74
156 2 0.01
157 26 0.17
ACGTcount: A:0.34, C:0.13, G:0.16, T:0.38
Consensus pattern (153 bp):
AAATCATAAGCAATATGACTTATAATCAAATATTAATCAAGAAATCATGTTTTGGACATTTGAAT
TTATTTAAGGCTTAGGGGGATTATAGGTCTTTAATGAATGAAATTTTACCATTTTCCCTCGATTT
AGCCTTAAGAGATCGATCATTTG
Found at i:318637 original size:3 final size:3
Alignment explanation
Indices: 318619--318675 Score: 60
Period size: 3 Copynumber: 18.3 Consensus size: 3
318609 AAATCATTAA
* **
318619 ATT ATT TTT AATT ATT ATT ATT ATT AAA ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT -ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
318665 AAT ATAT ATT A
1 ATT AT-T ATT A
318676 CAAGCCCAAA
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
3 39 0.89
4 5 0.11
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:319985 original size:15 final size:15
Alignment explanation
Indices: 319965--320014 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
319955 ATCCATTAGT
319965 TTTTAATATTATTAC
1 TTTTAATATTATTAC
* *
319980 TTTTAAT-TTCTTTC
1 TTTTAATATTATTAC
319994 ATTTTAATTATTATTA-
1 -TTTTAA-TATTATTAC
320010 TTTTA
1 TTTTA
320015 TTTTATTATA
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
14 5 0.18
15 18 0.64
16 1 0.04
17 4 0.14
ACGTcount: A:0.28, C:0.06, G:0.00, T:0.66
Consensus pattern (15 bp):
TTTTAATATTATTAC
Found at i:325361 original size:2 final size:2
Alignment explanation
Indices: 325354--325390 Score: 56
Period size: 2 Copynumber: 18.0 Consensus size: 2
325344 TTATCCTTTA
*
325354 AT AT AT AT CCT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT
325391 CCTTTGTTGT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
2 31 0.97
3 1 0.03
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:328220 original size:114 final size:114
Alignment explanation
Indices: 327889--328227 Score: 538
Period size: 113 Copynumber: 3.0 Consensus size: 114
327879 AAGTGTCATG
* *
327889 TGCTCATAGTAGAAAT-AAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGCTATCTGAT
1 TGCTCATAGTAGAAATAAAG-AGGCCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGAT
*
327953 CTGGTTTGATATGAACCCCAAAACCAATCATTAGATTTGAAAGATGAATT
65 CTGGTTTGGTATGAACCCCAAAACCAATCATTAGATTTGAAAGATGAATT
* *
328003 TGCTCATAGTAGAAATAAGGA-GCCCAATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATC
1 TGCTCATAGTAGAAATAAAGAGGCCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
*
328067 TGGTTTAGTATGAACCCCAAAACCAATCATTAGATTTGAAAGATGAATT
66 TGGTTTGGTATGAACCCCAAAACCAATCATTAGATTTGAAAGATGAATT
*
328116 TGCTCATAGTAGAAATAAAGAGGCCCAATAGCATCTTTTGGAAGTGTTCTTTGAGTTATCTGATC
1 TGCTCATAGTAGAAATAAAGAGGCCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
* * * * * *
328181 TGGTTCGGTAGGAATCCCAGAACCAATCATTGGAATTGAAAGATGAA
66 TGGTTTGGTATGAACCCCAAAACCAATCATTAGATTTGAAAGATGAA
328228 CTGCATGATC
Statistics
Matches: 207, Mismatches: 16, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
113 107 0.52
114 98 0.47
115 2 0.01
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.31
Consensus pattern (114 bp):
TGCTCATAGTAGAAATAAAGAGGCCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
TGGTTTGGTATGAACCCCAAAACCAATCATTAGATTTGAAAGATGAATT
Found at i:330286 original size:54 final size:54
Alignment explanation
Indices: 330199--330304 Score: 158
Period size: 54 Copynumber: 2.0 Consensus size: 54
330189 AATAATTGAG
* * *
330199 AAATCTGAGCAGAAGCCATAGGAAAGGATGAATGTGTTGTCAAATGCTTTACGA
1 AAATCTGAGCAGAAGCCACAAGAAAGGAAGAATGTGTTGTCAAATGCTTTACGA
* * *
330253 AAATCTGAGCAGAAGCTACAAGAAAGGAAGAATGTGTTTTCAAATGTTTTAC
1 AAATCTGAGCAGAAGCCACAAGAAAGGAAGAATGTGTTGTCAAATGCTTTAC
330305 ATCTCGACAG
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
54 46 1.00
ACGTcount: A:0.39, C:0.12, G:0.24, T:0.25
Consensus pattern (54 bp):
AAATCTGAGCAGAAGCCACAAGAAAGGAAGAATGTGTTGTCAAATGCTTTACGA
Found at i:330734 original size:22 final size:22
Alignment explanation
Indices: 330707--330759 Score: 88
Period size: 22 Copynumber: 2.4 Consensus size: 22
330697 CTACACTCTT
*
330707 CAAAGATGATAGATTCTCTTTT
1 CAAAGATGATAGATTCTCTTTC
*
330729 TAAAGATGATAGATTCTCTTTC
1 CAAAGATGATAGATTCTCTTTC
330751 CAAAGATGA
1 CAAAGATGA
330760 AAGCTTTATG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.36
Consensus pattern (22 bp):
CAAAGATGATAGATTCTCTTTC
Found at i:331662 original size:76 final size:76
Alignment explanation
Indices: 331555--331841 Score: 522
Period size: 76 Copynumber: 3.8 Consensus size: 76
331545 CTATTTCCCA
**
331555 CATCTGTAAGT-CTATAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
331619 AGCCTTAGGGT
66 AGCCTTAGGGT
331630 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
331695 AGCCTTAGGGT
66 AGCCTTAGGGT
* *
331706 CATCTGTAAGTTCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGTTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
331771 AACCTTAGGGT
66 AGCCTTAGGGT
331782 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTT
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTT
331842 GTTACTTTGA
Statistics
Matches: 204, Mismatches: 7, Indels: 1
0.96 0.03 0.00
Matches are distributed among these distances:
75 11 0.05
76 193 0.95
ACGTcount: A:0.23, C:0.18, G:0.23, T:0.36
Consensus pattern (76 bp):
CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTAGGGT
Found at i:332066 original size:76 final size:76
Alignment explanation
Indices: 331967--332301 Score: 580
Period size: 76 Copynumber: 4.4 Consensus size: 76
331957 CTATTTCCCA
*
331967 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
332032 AGCCTTAGGGT
66 AACCTTAGGGT
* * *
332043 CATCTATAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGTTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
332108 AACCTTAGGGT
66 AACCTTAGGGT
332119 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCC-AAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
332184 AAACCTTAGGGT
65 AAACCTTAGGGT
* * *
332196 CATCTGTAAATCTTGTAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
332261 AGCCTTAGGGT
66 AACCTTAGGGT
332272 CATCTGTAAGTCCTGCAGTGCATGATGTTT
1 CATCTGTAAGTCCTGCAGTGCATGATGTTT
332302 TTAAGACCTC
Statistics
Matches: 245, Mismatches: 13, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
76 173 0.71
77 72 0.29
ACGTcount: A:0.24, C:0.19, G:0.22, T:0.35
Consensus pattern (76 bp):
CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AACCTTAGGGT
Found at i:332217 original size:153 final size:152
Alignment explanation
Indices: 331967--332301 Score: 580
Period size: 153 Copynumber: 2.2 Consensus size: 152
331957 CTATTTCCCA
*
331967 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
* * *
332032 AGCCTTAGGGTCATCTATAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGTTTTTT
66 AACCTTAGGGTCATCTATAAATCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
332097 GATGTTTTCAAAACCTTAGGGT
131 GATGTTTTCAAAACCTTAGGGT
332119 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCC-AAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
* * **
332184 AAACCTTAGGGTCATCTGTAAATCTTGTAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTT
65 AAACCTTAGGGTCATCTATAAATCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTT
*
332249 TGATGTTTTCAAAGCCTTAGGGT
130 TGATGTTTTCAAAACCTTAGGGT
332272 CATCTGTAAGTCCTGCAGTGCATGATGTTT
1 CATCTGTAAGTCCTGCAGTGCATGATGTTT
332302 TTAAGACCTC
Statistics
Matches: 173, Mismatches: 9, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
152 31 0.18
153 142 0.82
ACGTcount: A:0.24, C:0.19, G:0.22, T:0.35
Consensus pattern (152 bp):
CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AACCTTAGGGTCATCTATAAATCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
GATGTTTTCAAAACCTTAGGGT
Found at i:332471 original size:31 final size:31
Alignment explanation
Indices: 332436--332519 Score: 91
Period size: 31 Copynumber: 2.7 Consensus size: 31
332426 GTAAACATCA
* * *
332436 ATTTTTCATTTTTCTTA-AATTCATTAAAATT
1 ATTTTTAATTATTATTATAATT-ATTAAAATT
*
332467 ATTTTTAATTATTATTATTATTATTAAAATT
1 ATTTTTAATTATTATTATAATTATTAAAATT
* *
332498 ATTATT-ATTATTATTATTATTA
1 ATTTTTAATTATTATTATAATTA
332520 ATATAAATAT
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
30 16 0.34
31 28 0.60
32 3 0.06
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.61
Consensus pattern (31 bp):
ATTTTTAATTATTATTATAATTATTAAAATT
Found at i:332482 original size:3 final size:3
Alignment explanation
Indices: 332464--332519 Score: 76
Period size: 3 Copynumber: 18.3 Consensus size: 3
332454 ATTCATTAAA
* **
332464 ATT ATT TTT AATT ATT ATT ATT ATT ATT AAA ATT ATT ATT ATT ATT
1 ATT ATT ATT -ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
332510 ATT ATT ATT A
1 ATT ATT ATT A
332520 ATATAAATAT
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
3 44 0.96
4 2 0.04
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:333819 original size:15 final size:15
Alignment explanation
Indices: 333796--333850 Score: 51
Period size: 15 Copynumber: 3.7 Consensus size: 15
333786 AATATGATCC
*
333796 ATTAGTTTTAATATT
1 ATTACTTTTAATATT
333811 ATTACTTTTAAT-TT
1 ATTACTTTTAATATT
* *
333825 CTTTCATTTTAATTATT
1 ATTAC-TTTTAA-TATT
333842 ATTA-TTTTA
1 ATTACTTTTA
333851 TTTTATTATT
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
14 5 0.16
15 22 0.69
16 1 0.03
17 4 0.12
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.64
Consensus pattern (15 bp):
ATTACTTTTAATATT
Found at i:335010 original size:19 final size:19
Alignment explanation
Indices: 334967--335021 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 19
334957 GTAGCTAATT
334967 GTAGAAAATCAGAC--TATA
1 GTAGAAAA-CAGACTGTATA
*
334985 GAAAGAAAACAGACTGTATA
1 G-TAGAAAACAGACTGTATA
335005 GTAGAAAACAGACTGTA
1 GTAGAAAACAGACTGTA
335022 GGAAATAGTC
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
18 6 0.19
19 21 0.66
20 5 0.16
ACGTcount: A:0.51, C:0.11, G:0.20, T:0.18
Consensus pattern (19 bp):
GTAGAAAACAGACTGTATA
Found at i:336958 original size:36 final size:35
Alignment explanation
Indices: 336906--336975 Score: 95
Period size: 36 Copynumber: 2.0 Consensus size: 35
336896 ATACCTTCTG
* *
336906 TTTCAGATGCACAGGATCCGAATCTGGTTTTTGGT
1 TTTCAGAGGCACAGGATCCGAATCTGGTTCTTGGT
* *
336941 TTTCAGAGGCAACAGGATCTGAATTTGGTTCTTGG
1 TTTCAGAGGC-ACAGGATCCGAATCTGGTTCTTGG
336976 CGAATGCTAG
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
35 9 0.30
36 21 0.70
ACGTcount: A:0.21, C:0.16, G:0.27, T:0.36
Consensus pattern (35 bp):
TTTCAGAGGCACAGGATCCGAATCTGGTTCTTGGT
Found at i:345088 original size:13 final size:13
Alignment explanation
Indices: 345070--345095 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
345060 AAATTTTGGT
345070 TAGGTCCATCAAA
1 TAGGTCCATCAAA
345083 TAGGTCCATCAAA
1 TAGGTCCATCAAA
345096 CATCACTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.23, G:0.15, T:0.23
Consensus pattern (13 bp):
TAGGTCCATCAAA
Found at i:350323 original size:17 final size:17
Alignment explanation
Indices: 350291--350324 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
350281 ACCATTTGAT
350291 CATGATATTTCAATATG
1 CATGATATTTCAATATG
350308 CATGTATATTTC-ATATG
1 CATG-ATATTTCAATATG
350325 ACATATATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.32, C:0.12, G:0.12, T:0.44
Consensus pattern (17 bp):
CATGATATTTCAATATG
Found at i:350333 original size:18 final size:18
Alignment explanation
Indices: 350295--350333 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
350285 TTTGATCATG
*
350295 ATATTTCAATATGCATGT
1 ATATTTCAATATGCATAT
350313 ATATTTC-ATATGACATAT
1 ATATTTCAATATG-CATAT
350331 ATA
1 ATA
350334 ACAAGCATGC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.38, C:0.10, G:0.08, T:0.44
Consensus pattern (18 bp):
ATATTTCAATATGCATAT
Found at i:353365 original size:21 final size:21
Alignment explanation
Indices: 353340--353384 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
353330 CGCAAATCAG
*
353340 TTTCCAGATTCGCATTGCGAT
1 TTTCCAAATTCGCATTGCGAT
*
353361 TTTCCAAATTCGCGTTGCGAT
1 TTTCCAAATTCGCATTGCGAT
353382 TTT
1 TTT
353385 TCGACTATCG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.18, C:0.22, G:0.18, T:0.42
Consensus pattern (21 bp):
TTTCCAAATTCGCATTGCGAT
Found at i:353434 original size:20 final size:20
Alignment explanation
Indices: 353387--353477 Score: 112
Period size: 20 Copynumber: 4.5 Consensus size: 20
353377 GCGATTTTTC
*
353387 GACTATCGCAATGCGAATAT
1 GACTATCGCAATGCGATTAT
*
353407 GTA-AATCGCAATGCGATTAT
1 G-ACTATCGCAATGCGATTAT
* *
353427 GACTATCGCAATGTGATTCT
1 GACTATCGCAATGCGATTAT
*
353447 GACTATCGCAATGCGATTCT
1 GACTATCGCAATGCGATTAT
*
353467 GACTGTCGCAA
1 GACTATCGCAA
353478 CACAAATGTT
Statistics
Matches: 62, Mismatches: 7, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
19 1 0.02
20 60 0.97
21 1 0.02
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.29
Consensus pattern (20 bp):
GACTATCGCAATGCGATTAT
Found at i:353908 original size:12 final size:13
Alignment explanation
Indices: 353893--353925 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
353883 AAAAGAATAA
353893 GAAGAAA-TCCCC
1 GAAGAAAGTCCCC
353905 GAAGAAAAGTCCCC
1 GAAG-AAAGTCCCC
353919 GAAGAAA
1 GAAGAAA
353926 ATGCAACGGG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 4 0.21
13 6 0.32
14 9 0.47
ACGTcount: A:0.48, C:0.24, G:0.21, T:0.06
Consensus pattern (13 bp):
GAAGAAAGTCCCC
Found at i:353919 original size:14 final size:14
Alignment explanation
Indices: 353900--353926 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
353890 TAAGAAGAAA
353900 TCCCCGAAGAAAAG
1 TCCCCGAAGAAAAG
353914 TCCCCGAAGAAAA
1 TCCCCGAAGAAAA
353927 TGCAACGGGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.30, G:0.19, T:0.07
Consensus pattern (14 bp):
TCCCCGAAGAAAAG
Found at i:356281 original size:140 final size:140
Alignment explanation
Indices: 356029--356298 Score: 486
Period size: 140 Copynumber: 1.9 Consensus size: 140
356019 AAACGTTGTA
*
356029 TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAATAACTTGAGTTTGAACATTGCTA
1 TTATGTGTAAACTTTTAACAATTTCAGTTAGGCATGTATTAATAACTTGAGTTTGAACATTGCTA
* *
356094 TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
66 TGATATGTTCAGTTATTAGCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
356159 TATGTGTATT
131 TATGTGTATT
* * *
356169 TTATGTGTAAACTTTTAACAATTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAATATTGTTA
1 TTATGTGTAAACTTTTAACAATTTCAGTTAGGCATGTATTAATAACTTGAGTTTGAACATTGCTA
356234 TGATATGTTCAGTTATTAGCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
66 TGATATGTTCAGTTATTAGCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
356299 CGCAACGCGA
Statistics
Matches: 124, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
140 124 1.00
ACGTcount: A:0.30, C:0.13, G:0.15, T:0.42
Consensus pattern (140 bp):
TTATGTGTAAACTTTTAACAATTTCAGTTAGGCATGTATTAATAACTTGAGTTTGAACATTGCTA
TGATATGTTCAGTTATTAGCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
TATGTGTATT
Found at i:356294 original size:20 final size:20
Alignment explanation
Indices: 356269--356507 Score: 158
Period size: 20 Copynumber: 12.8 Consensus size: 20
356259 TTACACATTC
356269 ATTTGAATATCGCAACGCGA
1 ATTTGAATATCGCAACGCGA
*
356289 ATTTGACTATCGCAACGCGA
1 ATTTGAATATCGCAACGCGA
* *
356309 ATTTGATTATCGCAACTC-A
1 ATTTGAATATCGCAACGCGA
356328 A----AA-ATCGCAACGCGA
1 ATTTGAATATCGCAACGCGA
*
356343 ATTTGACTATCGCAACGC-A
1 ATTTGAATATCGCAACGCGA
356362 A----AA-ATCGCAACGCGA
1 ATTTGAATATCGCAACGCGA
** *
356377 ATTTGTCTATTGCAACGCGA
1 ATTTGAATATCGCAACGCGA
* *
356397 ATTTGACTATCGCAACG-GTT
1 ATTTGAATATCGCAACGCG-A
*
356417 ATTT-AACTATCACAA--CG-
1 ATTTGAA-TATCGCAACGCGA
*
356434 A---GAAAATCGCAACGCGA
1 ATTTGAATATCGCAACGCGA
* *
356451 ATTTGAGTATCGCAACACGA
1 ATTTGAATATCGCAACGCGA
* * * *
356471 ATTTGATTATCCCAACGGGT
1 ATTTGAATATCGCAACGCGA
*
356491 ATTTGACTATCGCAACG
1 ATTTGAATATCGCAACG
356508 AGAAAATCGC
Statistics
Matches: 170, Mismatches: 27, Indels: 44
0.71 0.11 0.18
Matches are distributed among these distances:
14 25 0.15
15 8 0.05
16 2 0.01
17 2 0.01
19 8 0.05
20 125 0.74
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.26
Consensus pattern (20 bp):
ATTTGAATATCGCAACGCGA
Found at i:356340 original size:34 final size:34
Alignment explanation
Indices: 356297--356542 Score: 183
Period size: 34 Copynumber: 6.9 Consensus size: 34
356287 GAATTTGACT
* *
356297 ATCGCAACGCGAATTTGATTATCGCAACTCAAAA
1 ATCGCAACGCGAATTTGACTATCGCAACGCAAAA
356331 ATCGCAACGCGAATTTGACTATCGCAACGCAAAA
1 ATCGCAACGCGAATTTGACTATCGCAACGCAAAA
* * *
356365 ATCGCAACGCGAATTTGTCTATTGCAACGCGAATTTGACT
1 ATCGCAACGCGAATTTGACTATCGCAACGC-AA----A-A
* * *
356405 ATCGCAACG-GTTATTTAACTATCACAACG-AGAAA
1 ATCGCAACGCG-AATTTGACTATCGCAACGCA-AAA
* * *
356439 ATCGCAACGCGAATTTGAGTATCGCAACACGAATTTGATT
1 ATCGCAACGCGAATTTGACTATCGCAACGC-AA----A-A
* * *
356479 ATCCCAACGGGTATTTGACTATCGCAACG-AGAAA
1 ATCGCAACGCGAATTTGACTATCGCAACGCA-AAA
* * *
356513 ATCGCAAAGCGTATTAGACTATCGCAACGC
1 ATCGCAACGCGAATTTGACTATCGCAACGC
356543 GAATTGACTT
Statistics
Matches: 167, Mismatches: 27, Indels: 35
0.73 0.12 0.15
Matches are distributed among these distances:
34 107 0.64
35 6 0.04
36 1 0.01
38 2 0.01
39 5 0.03
40 46 0.28
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.24
Consensus pattern (34 bp):
ATCGCAACGCGAATTTGACTATCGCAACGCAAAA
Found at i:356409 original size:74 final size:73
Alignment explanation
Indices: 356331--356556 Score: 285
Period size: 74 Copynumber: 3.1 Consensus size: 73
356321 CAACTCAAAA
* * *
356331 ATCGCAACGCGAATTTGACTATCGCAACGCA-AAAATCGCAACGCGAATTTGTCTATTGCAACGC
1 ATCGCAACG-GTATTTGACTATCGCAACG-AGAAAATCGCAACGCGAATTTGACTATCGCAACGC
356395 GAATTTGACT
64 GAATTTGACT
* * * *
356405 ATCGCAACGGTTATTTAACTATCACAACGAGAAAATCGCAACGCGAATTTGAGTATCGCAACACG
1 ATCGCAACGG-TATTTGACTATCGCAACGAGAAAATCGCAACGCGAATTTGACTATCGCAACGCG
*
356470 AATTTGATT
65 AATTTGACT
* * * *
356479 ATCCCAACGGGTATTTGACTATCGCAACGAGAAAATCGCAAAGCGTATTAGACTATCGCAACGCG
1 ATCGCAAC-GGTATTTGACTATCGCAACGAGAAAATCGCAACGCGAATTTGACTATCGCAACGCG
356544 AA-TTGACT
65 AATTTGACT
*
356552 TTCGC
1 ATCGC
356557 GTTGTGATTT
Statistics
Matches: 130, Mismatches: 19, Indels: 7
0.83 0.12 0.04
Matches are distributed among these distances:
73 10 0.08
74 118 0.91
75 2 0.02
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.24
Consensus pattern (73 bp):
ATCGCAACGGTATTTGACTATCGCAACGAGAAAATCGCAACGCGAATTTGACTATCGCAACGCGA
ATTTGACT
Found at i:356487 original size:54 final size:54
Alignment explanation
Indices: 356277--356487 Score: 186
Period size: 54 Copynumber: 3.9 Consensus size: 54
356267 TCATTTGAAT
*
356277 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGATTATCGCAACTCA-AAA
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGATTATCGCAAC-GAGAAA
* * *
356331 ATCGCAACGCGAATTTGACTATCGCAACGC-AA----A-AATCGCAACGCGAATTTGTCT
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGATTATCGCAACGAGAA------A
* * * * *
356385 ATTGCAACGCGAATTTGACTATCGCAACG-GTTATTTAACTATCACAACGAGAAA
1 ATCGCAACGCGAATTTGACTATCGCAACGCG-AATTTGATTATCGCAACGAGAAA
* * *
356439 ATCGCAACGCGAATTTGAGTATCGCAACACGAATTTGATTATCCCAACG
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGATTATCGCAACG
356488 GGTATTTGAC
Statistics
Matches: 125, Mismatches: 17, Indels: 30
0.73 0.10 0.17
Matches are distributed among these distances:
48 10 0.08
49 1 0.01
53 2 0.02
54 98 0.78
55 2 0.02
59 1 0.01
60 11 0.09
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.24
Consensus pattern (54 bp):
ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGATTATCGCAACGAGAAA
Found at i:356556 original size:19 final size:20
Alignment explanation
Indices: 356513--356556 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
356503 CAACGAGAAA
*
356513 ATCGCAAAGCGTATTAGACT
1 ATCGCAAAGCGAATTAGACT
*
356533 ATCGCAACGCGAATT-GACT
1 ATCGCAAAGCGAATTAGACT
*
356552 TTCGC
1 ATCGC
356557 GTTGTGATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (20 bp):
ATCGCAAAGCGAATTAGACT
Found at i:358208 original size:21 final size:21
Alignment explanation
Indices: 358179--358279 Score: 78
Period size: 21 Copynumber: 4.8 Consensus size: 21
358169 GGGAGGGACG
* *
358179 TCTTCAACGATGACAGTGGCC
1 TCTTGAACGATGACAGGGGCC
* ** *
358200 TCTTGAACGGTGGGAGGGGAC
1 TCTTGAACGATGACAGGGGCC
** *
358221 TCTTGAGGGATGATAGGGGCC
1 TCTTGAACGATGACAGGGGCC
**
358242 TCTTGAACGAT-AGGGGAGGCC
1 TCTTGAACGATGACAGG-GGCC
*
358263 TCTTGAATGATGACAGG
1 TCTTGAACGATGACAGG
358280 TGAGTCGGGC
Statistics
Matches: 59, Mismatches: 19, Indels: 3
0.73 0.23 0.04
Matches are distributed among these distances:
20 3 0.05
21 53 0.90
22 3 0.05
ACGTcount: A:0.23, C:0.18, G:0.37, T:0.23
Consensus pattern (21 bp):
TCTTGAACGATGACAGGGGCC
Found at i:358266 original size:42 final size:42
Alignment explanation
Indices: 358187--358279 Score: 107
Period size: 42 Copynumber: 2.2 Consensus size: 42
358177 CGTCTTCAAC
* * *
358187 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGATGGGAGAGGACTCTTGAGG
* * **
358229 GATGATAGGGGCCTCTTGAACGATAGGG-GAGGCCTCTTGAAT
1 GATGACAGGGGCCTCTTGAACGAT-GGGAGAGGACTCTTGAGG
358271 GATGACAGG
1 GATGACAGG
358280 TGAGTCGGGC
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
42 39 0.93
43 3 0.07
ACGTcount: A:0.23, C:0.16, G:0.40, T:0.22
Consensus pattern (42 bp):
GATGACAGGGGCCTCTTGAACGATGGGAGAGGACTCTTGAGG
Found at i:358788 original size:18 final size:19
Alignment explanation
Indices: 358765--358810 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
358755 GAAACTTAAA
358765 ATCGCAACACG-AATGACT
1 ATCGCAACACGAAATGACT
*
358783 ATCGCAACGCGAAAATGACT
1 ATCGCAACACG-AAATGACT
358803 ATCGCAAC
1 ATCGCAAC
358811 GAGAGAATCG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 10 0.40
20 15 0.60
ACGTcount: A:0.39, C:0.28, G:0.17, T:0.15
Consensus pattern (19 bp):
ATCGCAACACGAAATGACT
Found at i:358879 original size:20 final size:20
Alignment explanation
Indices: 358854--358921 Score: 109
Period size: 20 Copynumber: 3.4 Consensus size: 20
358844 GCGATTCTTT
**
358854 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
358874 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
*
358894 TGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
358914 CGTTGCGA
1 CGTTGCGA
358922 AAGTAAACTA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.18, C:0.19, G:0.26, T:0.37
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:358880 original size:34 final size:37
Alignment explanation
Indices: 358836--358921 Score: 97
Period size: 40 Copynumber: 2.3 Consensus size: 37
358826 CGATTTTCAT
*
358836 TTCGCATTGCGAT-TC-TTTC-GTTGCGATAGTCAAA
1 TTCGCGTTGCGATATCATTTCGGTTGCGATAGTCAAA
**
358870 TTCGCGTTGCGATAGTCATTTTCGTGTTGCGATAGTCATT
1 TTCGCGTTGCGATA-TCA-TTTCG-GTTGCGATAGTCAAA
358910 TTCGCGTTGCGA
1 TTCGCGTTGCGA
358922 AAGTAAACTA
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
34 12 0.28
36 2 0.05
38 4 0.09
40 25 0.58
ACGTcount: A:0.16, C:0.20, G:0.24, T:0.40
Consensus pattern (37 bp):
TTCGCGTTGCGATATCATTTCGGTTGCGATAGTCAAA
Found at i:360533 original size:19 final size:19
Alignment explanation
Indices: 360416--360525 Score: 86
Period size: 20 Copynumber: 5.9 Consensus size: 19
360406 TCTGAAACTT
*
360416 AAAATCGCAACACGAAAATG
1 AAAATCGCAACGCG-AAATG
*
360436 AAAATCGCAACACGAAAATG
1 AAAATCGCAACGCG-AAATG
** *
360456 ACTATCGCAACGCGAATTTG
1 AAAATCGCAACGCGAA-ATG
***
360476 TCTATCGCAACGCG--A-G
1 AAAATCGCAACGCGAAATG
360492 --AATCGCAACGCGAAATG
1 AAAATCGCAACGCGAAATG
360509 AAAATCGCAACGCGAAA
1 AAAATCGCAACGCGAAA
360526 CTAAAATCAC
Statistics
Matches: 77, Mismatches: 7, Indels: 13
0.79 0.07 0.13
Matches are distributed among these distances:
14 11 0.14
16 2 0.03
17 1 0.01
19 17 0.22
20 46 0.60
ACGTcount: A:0.44, C:0.24, G:0.19, T:0.14
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATG
Found at i:360948 original size:22 final size:22
Alignment explanation
Indices: 360921--360963 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
360911 GAGATAAACG
360921 GATTTCGTCGGAGATGGGGACT
1 GATTTCGTCGGAGATGGGGACT
360943 GATTTCGTCGGAGATGGGGAC
1 GATTTCGTCGGAGATGGGGAC
360964 GGATGTCGCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.19, C:0.14, G:0.42, T:0.26
Consensus pattern (22 bp):
GATTTCGTCGGAGATGGGGACT
Found at i:361167 original size:20 final size:20
Alignment explanation
Indices: 361137--361254 Score: 137
Period size: 20 Copynumber: 5.9 Consensus size: 20
361127 GCGCTTTGAA
*
361137 AATCGCATTGCGATAGTCAG
1 AATCGCGTTGCGATAGTCAG
* *
361157 CATCGCGTTGCGACAGTCAG
1 AATCGCGTTGCGATAGTCAG
*
361177 AATCGCGTTGCGATAGTCAA
1 AATCGCGTTGCGATAGTCAG
* * *
361197 AATCCCTTTGCGACAGTCAG
1 AATCGCGTTGCGATAGTCAG
* *
361217 AATCGCGTTGTGATAGTCAT
1 AATCGCGTTGCGATAGTCAG
* *
361237 ACTCGCATTGCGATAGTC
1 AATCGCGTTGCGATAGTC
361255 GGAAAATCGC
Statistics
Matches: 80, Mismatches: 18, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 80 1.00
ACGTcount: A:0.25, C:0.24, G:0.25, T:0.26
Consensus pattern (20 bp):
AATCGCGTTGCGATAGTCAG
Found at i:361235 original size:60 final size:60
Alignment explanation
Indices: 361135--361254 Score: 159
Period size: 60 Copynumber: 2.0 Consensus size: 60
361125 TGGCGCTTTG
* * * *
361135 AAAATCGCATTGCGATAGTCAGCATCGCGTTGCGACAGTCAGAATCGCGTTGCGATAGTC
1 AAAATCCCATTGCGACAGTCAGAATCGCGTTGCGACAGTCAGAATCGCATTGCGATAGTC
* * * * *
361195 AAAATCCCTTTGCGACAGTCAGAATCGCGTTGTGATAGTCATACTCGCATTGCGATAGTC
1 AAAATCCCATTGCGACAGTCAGAATCGCGTTGCGACAGTCAGAATCGCATTGCGATAGTC
361255 GGAAAATCGC
Statistics
Matches: 51, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
60 51 1.00
ACGTcount: A:0.27, C:0.23, G:0.24, T:0.26
Consensus pattern (60 bp):
AAAATCCCATTGCGACAGTCAGAATCGCGTTGCGACAGTCAGAATCGCATTGCGATAGTC
Found at i:361903 original size:31 final size:31
Alignment explanation
Indices: 361865--361938 Score: 148
Period size: 31 Copynumber: 2.4 Consensus size: 31
361855 ATTTTTTTTG
361865 TTCATGTTCGTTTATTAAGGAATATAACTTA
1 TTCATGTTCGTTTATTAAGGAATATAACTTA
361896 TTCATGTTCGTTTATTAAGGAATATAACTTA
1 TTCATGTTCGTTTATTAAGGAATATAACTTA
361927 TTCATGTTCGTT
1 TTCATGTTCGTT
361939 CATTTAATAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.28, C:0.11, G:0.14, T:0.47
Consensus pattern (31 bp):
TTCATGTTCGTTTATTAAGGAATATAACTTA
Found at i:361964 original size:10 final size:10
Alignment explanation
Indices: 361949--362022 Score: 50
Period size: 10 Copynumber: 7.6 Consensus size: 10
361939 CATTTAATAA
361949 ATAAACGAAC
1 ATAAACGAAC
361959 ATAAACG-A-
1 ATAAACGAAC
361967 AT--ACGAAC
1 ATAAACGAAC
*
361975 ATAAACCAAC
1 ATAAACGAAC
** *
361985 ACGAAC-ATAA
1 ATAAACGA-AC
361995 ATGAACACGAAC
1 AT-AA-ACGAAC
362007 ATAAACGAAC
1 ATAAACGAAC
362017 ATAAAC
1 ATAAAC
362023 TTTAGAGACC
Statistics
Matches: 49, Mismatches: 7, Indels: 16
0.68 0.10 0.22
Matches are distributed among these distances:
6 3 0.06
7 1 0.02
8 4 0.08
9 2 0.04
10 30 0.61
11 3 0.06
12 5 0.10
13 1 0.02
ACGTcount: A:0.58, C:0.22, G:0.09, T:0.11
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:361974 original size:16 final size:16
Alignment explanation
Indices: 361953--362017 Score: 103
Period size: 16 Copynumber: 4.1 Consensus size: 16
361943 TAATAAATAA
*
361953 ACGAACATAAACGAAT
1 ACGAACATAAACGAAC
*
361969 ACGAACATAAACCAAC
1 ACGAACATAAACGAAC
*
361985 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
362001 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
362017 A
1 A
362018 TAAACTTTAG
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 44 1.00
ACGTcount: A:0.57, C:0.23, G:0.11, T:0.09
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:362266 original size:11 final size:11
Alignment explanation
Indices: 362241--362305 Score: 85
Period size: 11 Copynumber: 5.8 Consensus size: 11
362231 AAATTTCATC
* *
362241 AGCTCGACTCG
1 AGCTCGATTCA
*
362252 AGCTCGATTGA
1 AGCTCGATTCA
*
362263 AGCTCAATTTCA
1 AGCTCGA-TTCA
362275 AGCTCGATTCA
1 AGCTCGATTCA
362286 AGCTCGATTCA
1 AGCTCGATTCA
362297 AGCTCGATT
1 AGCTCGATT
362306 GACCCAATCC
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
11 38 0.81
12 9 0.19
ACGTcount: A:0.26, C:0.26, G:0.20, T:0.28
Consensus pattern (11 bp):
AGCTCGATTCA
Found at i:362279 original size:23 final size:22
Alignment explanation
Indices: 362252--362307 Score: 85
Period size: 23 Copynumber: 2.5 Consensus size: 22
362242 GCTCGACTCG
362252 AGCTCGATTGAAGCTCAATTTCA
1 AGCTCGATTGAAGCTCAA-TTCA
* *
362275 AGCTCGATTCAAGCTCGATTCA
1 AGCTCGATTGAAGCTCAATTCA
362297 AGCTCGATTGA
1 AGCTCGATTGA
362308 CCCAATCCAG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
22 14 0.47
23 16 0.53
ACGTcount: A:0.29, C:0.23, G:0.20, T:0.29
Consensus pattern (22 bp):
AGCTCGATTGAAGCTCAATTCA
Found at i:362290 original size:34 final size:35
Alignment explanation
Indices: 362232--362301 Score: 97
Period size: 34 Copynumber: 2.0 Consensus size: 35
362222 AACTCAAAAA
* *
362232 AATTTCATCAGCTCGACTCGAGCTCGATTGAAGCTC
1 AATTTCA-CAGCTCGACTCAAGCTCGATTCAAGCTC
*
362268 AATTTCA-AGCTCGATTCAAGCTCGATTCAAGCTC
1 AATTTCACAGCTCGACTCAAGCTCGATTCAAGCTC
362302 GATTGACCCA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
34 24 0.77
36 7 0.23
ACGTcount: A:0.27, C:0.27, G:0.17, T:0.29
Consensus pattern (35 bp):
AATTTCACAGCTCGACTCAAGCTCGATTCAAGCTC
Found at i:363545 original size:7 final size:7
Alignment explanation
Indices: 363533--363623 Score: 130
Period size: 7 Copynumber: 13.0 Consensus size: 7
363523 AATTAGATTA
363533 AGGGTTT
1 AGGGTTT
363540 AGGGTTT
1 AGGGTTT
363547 AGGAG-TT
1 AGG-GTTT
*
363554 AGGTTTT
1 AGGGTTT
*
363561 AGTGTTT
1 AGGGTTT
*
363568 ATGGTTT
1 AGGGTTT
*
363575 AGAGTTT
1 AGGGTTT
363582 AGGGTTT
1 AGGGTTT
363589 AGGGTTT
1 AGGGTTT
363596 AGGGTTT
1 AGGGTTT
363603 AGGGTTT
1 AGGGTTT
363610 AGGGTTT
1 AGGGTTT
363617 AGGGTTT
1 AGGGTTT
363624 TTAATAATCA
Statistics
Matches: 74, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
7 73 0.99
8 1 0.01
ACGTcount: A:0.16, C:0.00, G:0.38, T:0.45
Consensus pattern (7 bp):
AGGGTTT
Found at i:363847 original size:10 final size:10
Alignment explanation
Indices: 363788--363831 Score: 70
Period size: 10 Copynumber: 4.4 Consensus size: 10
363778 ATAAATGACT
363788 GAACATAAAC
1 GAACATAAAC
363798 GAACATAAAC
1 GAACATAAAC
*
363808 GAACATAATC
1 GAACATAAAC
*
363818 GAACATAACC
1 GAACATAAAC
363828 GAAC
1 GAAC
363832 GAACATAATC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
10 32 1.00
ACGTcount: A:0.55, C:0.23, G:0.11, T:0.11
Consensus pattern (10 bp):
GAACATAAAC
Found at i:363855 original size:20 final size:20
Alignment explanation
Indices: 363788--363855 Score: 73
Period size: 20 Copynumber: 3.2 Consensus size: 20
363778 ATAAATGACT
* *
363788 GAACATAAACGAACATAAAC
1 GAACATAATCGAACATACAC
363808 GAACATAATCGAACATAACCGAAC
1 GAACATAATCGAACAT-A-C--AC
*
363832 GAACATAATCGAACATTCAC
1 GAACATAATCGAACATACAC
363852 GAAC
1 GAAC
363856 GTAAATGAAC
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
20 21 0.51
21 1 0.02
22 1 0.02
24 18 0.44
ACGTcount: A:0.51, C:0.24, G:0.12, T:0.13
Consensus pattern (20 bp):
GAACATAATCGAACATACAC
Found at i:365245 original size:23 final size:23
Alignment explanation
Indices: 365215--365262 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
365205 CGCTTGATTC
365215 ATGTAAAGTTTATGCATTTAAAT
1 ATGTAAAGTTTATGCATTTAAAT
365238 ATGTAAAGTTTATGCATTTAAAT
1 ATGTAAAGTTTATGCATTTAAAT
365261 AT
1 AT
365263 AGGGGGGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.40, C:0.04, G:0.12, T:0.44
Consensus pattern (23 bp):
ATGTAAAGTTTATGCATTTAAAT
Found at i:367850 original size:10 final size:10
Alignment explanation
Indices: 367837--367861 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
367827 CATGCAAACT
367837 CAAACAAATG
1 CAAACAAATG
367847 CAAACAAATG
1 CAAACAAATG
367857 CAAAC
1 CAAAC
367862 TCAAACTCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.60, C:0.24, G:0.08, T:0.08
Consensus pattern (10 bp):
CAAACAAATG
Found at i:371981 original size:48 final size:48
Alignment explanation
Indices: 371908--372003 Score: 174
Period size: 48 Copynumber: 2.0 Consensus size: 48
371898 CATGCGAAAT
371908 TCGATAGGGTTATGAGAGCTAATTATCCAGAAATTTTATCAGAAGTTG
1 TCGATAGGGTTATGAGAGCTAATTATCCAGAAATTTTATCAGAAGTTG
* *
371956 TCGATAGGGTTATGGGAGCTGATTATCCAGAAATTTTATCAGAAGTTG
1 TCGATAGGGTTATGAGAGCTAATTATCCAGAAATTTTATCAGAAGTTG
372004 ACTGGATGGA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.31, C:0.10, G:0.25, T:0.33
Consensus pattern (48 bp):
TCGATAGGGTTATGAGAGCTAATTATCCAGAAATTTTATCAGAAGTTG
Found at i:375583 original size:33 final size:34
Alignment explanation
Indices: 375544--375631 Score: 119
Period size: 33 Copynumber: 2.7 Consensus size: 34
375534 CAAACTAAAT
375544 GTCTCCAAGATCCC-CATCATCAAACCCGAGCAC
1 GTCTCCAAGATCCCTCATCATCAAACCCGAGCAC
**
375577 GTCTCC-ATCTCCCTCATCATCAAACCCGAGCAC
1 GTCTCCAAGATCCCTCATCATCAAACCCGAGCAC
**
375610 GTCTCC-ATCTCCCTCATCATCA
1 GTCTCCAAGATCCCTCATCATCA
375632 TCAGTCACTC
Statistics
Matches: 52, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
32 5 0.10
33 47 0.90
ACGTcount: A:0.25, C:0.44, G:0.09, T:0.22
Consensus pattern (34 bp):
GTCTCCAAGATCCCTCATCATCAAACCCGAGCAC
Found at i:375594 original size:30 final size:33
Alignment explanation
Indices: 375554--375631 Score: 149
Period size: 33 Copynumber: 2.4 Consensus size: 33
375544 GTCTCCAAGA
375554 TCCC-CATCATCAAACCCGAGCACGTCTCCATC
1 TCCCTCATCATCAAACCCGAGCACGTCTCCATC
375586 TCCCTCATCATCAAACCCGAGCACGTCTCCATC
1 TCCCTCATCATCAAACCCGAGCACGTCTCCATC
375619 TCCCTCATCATCA
1 TCCCTCATCATCA
375632 TCAGTCACTC
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
32 4 0.09
33 41 0.91
ACGTcount: A:0.24, C:0.46, G:0.08, T:0.22
Consensus pattern (33 bp):
TCCCTCATCATCAAACCCGAGCACGTCTCCATC
Found at i:390396 original size:2 final size:2
Alignment explanation
Indices: 390391--390424 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
390381 ATATCCATTC
390391 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
390425 CAAATACACA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:393641 original size:27 final size:27
Alignment explanation
Indices: 393605--393658 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
393595 CTCTATTTAT
393605 TTTTTACCATAGTAGTTGATGTGTCTA
1 TTTTTACCATAGTAGTTGATGTGTCTA
393632 TTTTTACCATAGTAGTTGATGTGTCTA
1 TTTTTACCATAGTAGTTGATGTGTCTA
393659 GCATTAATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.22, C:0.11, G:0.19, T:0.48
Consensus pattern (27 bp):
TTTTTACCATAGTAGTTGATGTGTCTA
Found at i:398617 original size:15 final size:16
Alignment explanation
Indices: 398585--398623 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
398575 CAATTATGTT
398585 AGGGACTTAAACAAAA
1 AGGGACTTAAACAAAA
*
398601 AGGGACTT-AAGAAAA
1 AGGGACTTAAACAAAA
398616 AGAGGACT
1 AG-GGACT
398624 AATGGAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.51, C:0.10, G:0.26, T:0.13
Consensus pattern (16 bp):
AGGGACTTAAACAAAA
Found at i:398910 original size:18 final size:20
Alignment explanation
Indices: 398887--398923 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
398877 TAACTTTTTT
398887 TTAAAA-TAA-TTTAGATAC
1 TTAAAATTAATTTTAGATAC
398905 TTAAAATTAATTTTAGATA
1 TTAAAATTAATTTTAGATA
398924 TAATTTAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
19 3 0.18
20 8 0.47
ACGTcount: A:0.49, C:0.03, G:0.05, T:0.43
Consensus pattern (20 bp):
TTAAAATTAATTTTAGATAC
Found at i:402676 original size:11 final size:11
Alignment explanation
Indices: 402652--402696 Score: 56
Period size: 11 Copynumber: 4.1 Consensus size: 11
402642 TTGGTGCTGG
402652 AAACAAGATAA
1 AAACAAGATAA
* *
402663 AAATAAGATTA
1 AAACAAGATAA
402674 AAACAAGATAA
1 AAACAAGATAA
402685 AGAA-AAGATAA
1 A-AACAAGATAA
402696 A
1 A
402697 TGAATTGCAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
11 27 0.93
12 2 0.07
ACGTcount: A:0.71, C:0.04, G:0.11, T:0.13
Consensus pattern (11 bp):
AAACAAGATAA
Found at i:402680 original size:22 final size:22
Alignment explanation
Indices: 402652--402693 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
402642 TTGGTGCTGG
402652 AAACAAGATAAA-AATAAGATTA
1 AAACAAGATAAAGAA-AAGATTA
402674 AAACAAGATAAAGAAAAGAT
1 AAACAAGATAAAGAAAAGAT
402694 AAATGAATTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.69, C:0.05, G:0.12, T:0.14
Consensus pattern (22 bp):
AAACAAGATAAAGAAAAGATTA
Found at i:403202 original size:25 final size:22
Alignment explanation
Indices: 403173--403218 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
403163 TTTTTAACCC
403173 AATCTTAATTCCTAATAAAATAATA
1 AATC-TAA-TCCTAA-AAAATAATA
*
403198 AATCTAATCCTAAAAGATAAT
1 AATCTAATCCTAAAAAATAAT
403219 GCATCATCCT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 7 0.35
23 6 0.30
24 3 0.15
25 4 0.20
ACGTcount: A:0.52, C:0.13, G:0.02, T:0.33
Consensus pattern (22 bp):
AATCTAATCCTAAAAAATAATA
Found at i:407893 original size:25 final size:22
Alignment explanation
Indices: 407864--407909 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
407854 TTTTTAACCC
407864 AATCTTAATTCCTAATAAAATAATA
1 AATC-TAA-TCCTAA-AAAATAATA
*
407889 AATCTAATCCTAAAAGATAAT
1 AATCTAATCCTAAAAAATAAT
407910 GCATTATCCT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 7 0.35
23 6 0.30
24 3 0.15
25 4 0.20
ACGTcount: A:0.52, C:0.13, G:0.02, T:0.33
Consensus pattern (22 bp):
AATCTAATCCTAAAAAATAATA
Found at i:410675 original size:9 final size:9
Alignment explanation
Indices: 410649--410681 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
410639 TGATACTCGA
410649 TTAAA-TAT
1 TTAAATTAT
410657 TTATAATTAT
1 TTA-AATTAT
410667 TTAAATTAT
1 TTAAATTAT
410676 TTAAAT
1 TTAAAT
410682 AAGATTATCT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 3 0.13
9 14 0.61
10 6 0.26
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (9 bp):
TTAAATTAT
Found at i:414929 original size:53 final size:54
Alignment explanation
Indices: 414785--414946 Score: 159
Period size: 53 Copynumber: 2.9 Consensus size: 54
414775 CCAAAGTGAT
** *
414785 AATG-ATGTAAATTTTATAAGACTAAAATGTTATATAAATCTTTTAATTTTTTTTAA
1 AATGAATGTAAATTTTATAAGACTAAAATACTATATAAATC-TTTAA--ATTTTTAA
* * * *
414841 AATGAA-GAATAATTTGATACATTGTAAATGAAATACTATATAAATCTTTAAATTTTTAA
1 AATGAATGTA-AATTTTATA-A--G--ACTAAAATACTATATAAATCTTTAAATTTTTAA
414900 AAT-AATGTAAATTTTATAAGACTAAAATACTATATAAATCTTTAAAT
1 AATGAATGTAAATTTTATAAGACTAAAATACTATATAAATCTTTAAAT
414947 ACCAAAGACA
Statistics
Matches: 87, Mismatches: 11, Indels: 19
0.74 0.09 0.16
Matches are distributed among these distances:
53 25 0.29
55 1 0.01
56 6 0.07
57 10 0.11
58 11 0.13
59 12 0.14
60 1 0.01
61 5 0.06
62 16 0.18
ACGTcount: A:0.46, C:0.05, G:0.07, T:0.42
Consensus pattern (54 bp):
AATGAATGTAAATTTTATAAGACTAAAATACTATATAAATCTTTAAATTTTTAA
Found at i:423520 original size:19 final size:19
Alignment explanation
Indices: 423496--423538 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
423486 TTTTCATAAA
423496 AAAAAG-AAAAAGAAAAATC
1 AAAAAGCAAAAA-AAAAATC
* *
423515 AAAAAGCCAAAAAAAATTC
1 AAAAAGCAAAAAAAAAATC
423534 AAAAA
1 AAAAA
423539 CTACGAACGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 17 0.81
20 4 0.19
ACGTcount: A:0.77, C:0.09, G:0.07, T:0.07
Consensus pattern (19 bp):
AAAAAGCAAAAAAAAAATC
Found at i:426291 original size:36 final size:36
Alignment explanation
Indices: 426243--426314 Score: 117
Period size: 36 Copynumber: 2.0 Consensus size: 36
426233 TTACCTTCTG
* **
426243 TTTCAGATGCAACAGGATTTGAATCTGGTTCTTGGC
1 TTTCAGAGGCAACAGGATCCGAATCTGGTTCTTGGC
426279 TTTCAGAGGCAACAGGATCCGAATCTGGTTCTTGGC
1 TTTCAGAGGCAACAGGATCCGAATCTGGTTCTTGGC
426315 GAATGCTAGG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.22, C:0.19, G:0.26, T:0.32
Consensus pattern (36 bp):
TTTCAGAGGCAACAGGATCCGAATCTGGTTCTTGGC
Found at i:428121 original size:19 final size:19
Alignment explanation
Indices: 428094--428133 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
428084 GGAATATGGG
428094 CCTCATTTTGAAACCTGGA
1 CCTCATTTTGAAACCTGGA
*
428113 CCTCCTTTTGAAACCTGGA
1 CCTCATTTTGAAACCTGGA
428132 CC
1 CC
428134 GTGTGGGCTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.23, C:0.33, G:0.15, T:0.30
Consensus pattern (19 bp):
CCTCATTTTGAAACCTGGA
Found at i:428443 original size:19 final size:19
Alignment explanation
Indices: 428400--428454 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 19
428390 CTGATACCAT
428400 GTAGAAAATCAGAC--TATA
1 GTAGAAAA-CAGACTGTATA
*
428418 GAAAGAAAACAGACTGTATA
1 G-TAGAAAACAGACTGTATA
428438 GTAGAAAACAGACTGTA
1 GTAGAAAACAGACTGTA
428455 GGAAACAGTC
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
18 6 0.19
19 21 0.66
20 5 0.16
ACGTcount: A:0.51, C:0.11, G:0.20, T:0.18
Consensus pattern (19 bp):
GTAGAAAACAGACTGTATA
Found at i:440524 original size:19 final size:19
Alignment explanation
Indices: 440500--440551 Score: 104
Period size: 19 Copynumber: 2.7 Consensus size: 19
440490 AATGCAATGA
440500 GTGCATCGATGCATGGTAT
1 GTGCATCGATGCATGGTAT
440519 GTGCATCGATGCATGGTAT
1 GTGCATCGATGCATGGTAT
440538 GTGCATCGATGCAT
1 GTGCATCGATGCAT
440552 AAAATGCATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.21, C:0.17, G:0.31, T:0.31
Consensus pattern (19 bp):
GTGCATCGATGCATGGTAT
Found at i:440607 original size:20 final size:20
Alignment explanation
Indices: 440579--440617 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
440569 GAAGAAATTA
440579 ATTGATGCATCGATGCATGG
1 ATTGATGCATCGATGCATGG
* *
440599 ATTGGTGCATCGGTGCATG
1 ATTGATGCATCGATGCATG
440618 CCCTCCAAAA
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:0.21, C:0.15, G:0.33, T:0.31
Consensus pattern (20 bp):
ATTGATGCATCGATGCATGG
Found at i:445922 original size:30 final size:30
Alignment explanation
Indices: 445886--445961 Score: 80
Period size: 30 Copynumber: 2.5 Consensus size: 30
445876 TTTTTAGTGT
445886 TGTATTTGTGTTCGTTTATTTATTTTTGAA
1 TGTATTTGTGTTCGTTTATTTATTTTTGAA
* * ** *
445916 TGTATTTATATTCACTTATTTATTTTTTAA
1 TGTATTTGTGTTCGTTTATTTATTTTTGAA
* * *
445946 GGTGTTAGTGTTCGTT
1 TGTATTTGTGTTCGTT
445962 CGTATAGTGC
Statistics
Matches: 34, Mismatches: 12, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.18, C:0.05, G:0.16, T:0.61
Consensus pattern (30 bp):
TGTATTTGTGTTCGTTTATTTATTTTTGAA
Found at i:449675 original size:27 final size:27
Alignment explanation
Indices: 449611--449688 Score: 79
Period size: 27 Copynumber: 2.9 Consensus size: 27
449601 ACCAAAACTT
* *
449611 AAACCCCAATCCCAGATGACCACCGCC
1 AAACCCCAATGCCAGATGACCACCGAC
* *
449638 AAGCCCCAATGGCA-ATCGACCACCGAC
1 AAACCCCAATGCCAGAT-GACCACCGAC
*
449665 AAACCCCAATGTCAGCA-GACCACC
1 AAACCCCAATGCCAG-ATGACCACC
449689 CTCACATTGT
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
26 2 0.05
27 39 0.93
29 1 0.02
ACGTcount: A:0.35, C:0.44, G:0.14, T:0.08
Consensus pattern (27 bp):
AAACCCCAATGCCAGATGACCACCGAC
Done.