Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D02
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: 67659327
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 461372 characters in sequence are not A, C, G, or T
File 71 of 216
Found at i:21340445 original size:62 final size:59
Alignment explanation
Indices: 21340304--21340447 Score: 143
Period size: 62 Copynumber: 2.4 Consensus size: 59
21340294 CCTCTAATCC
*
21340304 TAATAACTAAC-ACAATAATAATATATTTTATATACAAAATAATACTAACTAAAATTAT
1 TAATAACTAACTATAATAATAATATATTTTATATACAAAATAATACTAACTAAAATTAT
* * * * *
21340362 TAATAACTAACTATAAAAATAATACTAGTTTT-TTTACTAACAATAATACTAAGTAACA-TCT
1 TAATAACTAACTATAATAATAATA-TA-TTTTATATAC-AA-AATAATACTAACTAAAATTAT
*
21340423 TAATACCTTAA-TAATAATAATAATA
1 TAATAAC-TAACT-ATAATAATAATA
21340448 ATAATAATAA
Statistics
Matches: 71, Mismatches: 8, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
58 11 0.15
59 10 0.14
60 6 0.08
61 15 0.21
62 29 0.41
ACGTcount: A:0.52, C:0.11, G:0.01, T:0.35
Consensus pattern (59 bp):
TAATAACTAACTATAATAATAATATATTTTATATACAAAATAATACTAACTAAAATTAT
Found at i:21340911 original size:16 final size:16
Alignment explanation
Indices: 21340892--21340925 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
21340882 TTTTTTTTCC
21340892 TGTTCTTTTA-TTTTTT
1 TGTT-TTTTAGTTTTTT
21340908 TGTTTTTTAGTTTTTT
1 TGTTTTTTAGTTTTTT
21340924 TG
1 TG
21340926 ATATATTTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.06, C:0.03, G:0.12, T:0.79
Consensus pattern (16 bp):
TGTTTTTTAGTTTTTT
Found at i:21340958 original size:28 final size:28
Alignment explanation
Indices: 21340926--21340994 Score: 122
Period size: 28 Copynumber: 2.5 Consensus size: 28
21340916 AGTTTTTTTG
21340926 ATATATTTTGGTAAATAAAAAAAATTAT
1 ATATATTTTGGTAAATAAAAAAAATTAT
*
21340954 ATATATTTTGATAAATAAAAAAAATTAT
1 ATATATTTTGGTAAATAAAAAAAATTAT
21340982 A-ATATTTTGGTAA
1 ATATATTTTGGTAA
21340995 TTTTTATTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
27 11 0.28
28 28 0.72
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.41
Consensus pattern (28 bp):
ATATATTTTGGTAAATAAAAAAAATTAT
Found at i:21351338 original size:53 final size:53
Alignment explanation
Indices: 21351254--21351465 Score: 246
Period size: 53 Copynumber: 4.0 Consensus size: 53
21351244 AAATGGCATT
* * * * * *
21351254 GAAGACCATATCATGTAAGATCGTAATTGGTGGGTTATGACACCATAAGAAAA
1 GAAGACCATATCATGTAAGATCATAACTGGTAGGTTATGACATCATATGGAAA
** *
21351307 GAAGACCATATCATGTAAGATTGTAACTGGTGGGTTATGACATCATATGGAAA
1 GAAGACCATATCATGTAAGATCATAACTGGTAGGTTATGACATCATATGGAAA
** * *
21351360 GAAGACCATATTGTGTTAGACCATAACTGGTAGGTTATTG-CATCATATGGAAA
1 GAAGACCATATCATGTAAGATCATAACTGGTAGGTTA-TGACATCATATGGAAA
* * * * *
21351413 GAATACCATATCGTGTAAGATCATAACTGATAGGTTATGGCATTATATGGAAA
1 GAAGACCATATCATGTAAGATCATAACTGGTAGGTTATGACATCATATGGAAA
21351466 ATTTAAGGAA
Statistics
Matches: 139, Mismatches: 18, Indels: 4
0.86 0.11 0.02
Matches are distributed among these distances:
52 2 0.01
53 135 0.97
54 2 0.01
ACGTcount: A:0.37, C:0.12, G:0.23, T:0.28
Consensus pattern (53 bp):
GAAGACCATATCATGTAAGATCATAACTGGTAGGTTATGACATCATATGGAAA
Found at i:21354253 original size:12 final size:12
Alignment explanation
Indices: 21354238--21354269 Score: 55
Period size: 12 Copynumber: 2.6 Consensus size: 12
21354228 ATCTTGAGGC
21354238 AAAAAGAAGAAG
1 AAAAAGAAGAAG
21354250 AAAAAGAAGAAG
1 AAAAAGAAGAAG
21354262 AAGAAAGA
1 AA-AAAGA
21354270 TATGGTAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 14 0.74
13 5 0.26
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (12 bp):
AAAAAGAAGAAG
Found at i:21369254 original size:16 final size:16
Alignment explanation
Indices: 21369232--21369273 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
21369222 CAATGAAAAG
*
21369232 GTTGAAAAGGATGTTA
1 GTTGAAAAGGATATTA
*
21369248 TTTGAAAAGGATATTA
1 GTTGAAAAGGATATTA
*
21369264 GATGAAAAGG
1 GTTGAAAAGG
21369274 TTCAAAAGGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.43, C:0.00, G:0.29, T:0.29
Consensus pattern (16 bp):
GTTGAAAAGGATATTA
Found at i:21369269 original size:41 final size:40
Alignment explanation
Indices: 21369224--21369300 Score: 127
Period size: 41 Copynumber: 1.9 Consensus size: 40
21369214 TTTCGAATCA
* *
21369224 ATGAAAAGGTTGAAAAGGATGTTATTTGAAAAGGATATTAG
1 ATGAAAAGGTTCAAAAGGATGTTATCTG-AAAGGATATTAG
21369265 ATGAAAAGGTTCAAAAGGATGTTATCTGAAAGGATA
1 ATGAAAAGGTTCAAAAGGATGTTATCTGAAAGGATA
21369301 ACAAATGAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
40 8 0.24
41 26 0.76
ACGTcount: A:0.44, C:0.03, G:0.26, T:0.27
Consensus pattern (40 bp):
ATGAAAAGGTTCAAAAGGATGTTATCTGAAAGGATATTAG
Found at i:21371139 original size:85 final size:83
Alignment explanation
Indices: 21370998--21371199 Score: 296
Period size: 85 Copynumber: 2.4 Consensus size: 83
21370988 CTAAAAACAT
* *
21370998 TGTGGTTTATTCATGAACCAAGTGGCAGTTTTTAATCTGCAAATATGTTGTGCACCCACAACAAG
1 TGTGGTTTAATCATGAACCAAGTGGCAGTTTTTAATCTGCAAATATGTTGTGCACCCAAAACAAG
*
21371063 TGGCAGTAACTGCAAGTA
66 TGGCAGTAACTGCAAATA
* * *
21371081 TGTGGTTTAATCATAAACCAAGTGGGAGTTTGTTTAATCTGCAAATATGTTGTGCACCCAAAATA
1 TGTGGTTTAATCATGAACCAAGTGGCAG-TT-TTTAATCTGCAAATATGTTGTGCACCCAAAACA
*
21371146 AGTTGCAGTAACTGCAAATA
64 AGTGGCAGTAACTGCAAATA
* *
21371166 TGTGGTTCAATCACGAACCAAGTGGCAGCTTTTT
1 TGTGGTTTAATCATGAACCAAGTGGCAG-TTTTT
21371200 TGCAAATGTT
Statistics
Matches: 105, Mismatches: 12, Indels: 3
0.88 0.10 0.03
Matches are distributed among these distances:
83 25 0.24
84 5 0.05
85 75 0.71
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31
Consensus pattern (83 bp):
TGTGGTTTAATCATGAACCAAGTGGCAGTTTTTAATCTGCAAATATGTTGTGCACCCAAAACAAG
TGGCAGTAACTGCAAATA
Found at i:21384045 original size:595 final size:605
Alignment explanation
Indices: 21382079--21386317 Score: 6224
Period size: 595 Copynumber: 7.1 Consensus size: 605
21382069 TGTGGATCCA
* *
21382079 TTGACCAAGT-CGCTCATTTTATTCTTGTTCAGATGAACTACTCTCTGCAAAAGTTAGTGAAGCT
1 TTGACCAAGTCCGCTCATTTTATTCCTGTTCAGATGGACTACTCTCTGCAAAAGTTAGTGAAGCT
*
21382143 CTACATTTCTGAGATTGTAAGAATGCATGGGGTTCCAATTTCAATAATCTCTGATATGAATCCTC
66 CTACATTTCTGAGATTGTAAG-A-GCATGGGGTTCCAATTTCAATAATCTCTGATATGGATCCTC
* *
21382208 TCTTCACTTCACAGTTCTAGAAGAAACTTCATAAGGCTCTGGGTTCGAGATTGGACTTCAGTACT
129 TCTTCACTTCACGGTTCTAGAAGAAACTTCACAAGGC-CTGGGTTCGAGATTGGACTTCAGTACT
* *
21382273 GCGTTCCATCCTCAGACCGATGGTCCATTTGAGAGGGTGATTCATTTACTAGAGGATATGATTTG
193 GCGTTCCATCCTCAGACCGATGGTCAATTTGAGAGGGTGATTCATATACTAGAGGATATGATTTG
* * *
21382338 GAGCTATTTGATTTATTTCTGCGGTAGTTGGGAGGATTTTTTACCGTTAGTTGAGTTCGCCTACA
258 GAGCTATGTGATTTATTTCTGAGGTAGTTGAGAGGATTTTTTACCGTTAGTTGAGTTCGCCTACA
21382403 ATAACAGTTTCCAATCTAGCATCTAGATGGCACCTTACGAGGCTCTATATGGTCATAAGTGTCAT
323 ATAACAGTTTCCAATCTAGCATCTAGATGGCACCTTACGAGGCTCTATATGGTCATAAGTGTCAT
* *
21382468 ACTCTGTTATATTAGATTGAG-T-GGTTAGCGACGGGTTTTGGGTCCTGAGTTGGTTT-CGAGAC
388 ACTCTGTTATATTAGACTGAGTTGGGTGAGCGACGGGTTTTGGGTCCTGAGTTGGTTTCCGAGAC
21382530 TGAAGATAATGTTAGACTAATTTGGGATCGTCTGAAGGCGTCTTCTGATAGATAGAAGTCTTATG
453 TGAAGATAATGTTAGACTAATTTGGGATCGTCTGAAGGCGTCTTCTGATAGATAGAAGTCTTATG
* *
21382595 CAAATATGAAAATCAGAGATAT-AAGTACTCTATGGGGGACATTGTATTTCTTAAGGT-TCTCCG
518 CAAATCTGAAAATCAGAGATATCAAGTACTCTATGGGGGACTTTGTATTTCTTAAGGTATCTCCG
*
21382658 TGGAAAAAGGTTCTACGGTTCAG
583 TGGAAAAAGGTTCTACGGTTCGG
* *
21382681 TTGACCAAGTCCGCACATTTTATTCCTGTTCAG-TGAACTACTCTCTGCAAAAGTTAGTGAAGCT
1 TTGACCAAGTCCGCTCATTTTATTCCTGTTCAGATGGACTACTCTCTGCAAAAGTTAGTGAAGCT
* * *
21382745 CAACATTTCTGAGACTGTAAGAATGCATGGGGTTCAAATTTCAATAATCTCTGATATGGATCCTC
66 CTACATTTCTGAGATTGTAAG-A-GCATGGGGTTCCAATTTCAATAATCTCTGATATGGATCCTC
21382810 TCTTCACTTCACGGTTCTAGAAGAAACTTCACAAGGCTCTGGGTTCGAGATTGGACTTCAGTACT
129 TCTTCACTTCACGGTTCTAGAAGAAACTTCACAAGGC-CTGGGTTCGAGATTGGACTTCAGTACT
21382875 GCGTTCCATCCTCAGACCGATGGTCAATTT--GAGGGTGATTCATATACTAGAGGATATGATTTG
193 GCGTTCCATCCTCAGACCGATGGTCAATTTGAGAGGGTGATTCATATACTAGAGGATATGATTTG
* * * *
21382938 GAGCTATGTGATTTATTTTTGCGGTAGTTGGGAGGATTTTTTACCATTAGTTGAGTTCGCCTACA
258 GAGCTATGTGATTTATTTCTGAGGTAGTTGAGAGGATTTTTTACCGTTAGTTGAGTTCGCCTACA
* *
21383003 ATAACAGTTTCCAATCTAGCATCTAGATGGAACCTTAC---GCTCTATATGGTCATAAGTGCCAT
323 ATAACAGTTTCCAATCTAGCATCTAGATGGCACCTTACGAGGCTCTATATGGTCATAAGTGTCAT
*
21383065 ACTCTGTTATATTAGACTGAGTTGGGTGAGCGACGGGTTTTGGGTCCTGAGTTGGTTTTCGAGAC
388 ACTCTGTTATATTAGACTGAGTTGGGTGAGCGACGGGTTTTGGGTCCTGAGTTGGTTTCCGAGAC
21383130 TGAAGATAATGTTAGACTAATTTGGGATCGTCTGAAGGCGTCTTCTGATAGATAGAAGTCTTATG
453 TGAAGATAATGTTAGACTAATTTGGGATCGTCTGAAGGCGTCTTCTGATAGATAGAAGTCTTATG
21383195 CAAATCTGAAAATCAGAGATATCAAGTACTCTATGAGGGG-CTTTGTA----TTAAGGTATCTCC
518 CAAATCTGAAAATCAGAGATATCAAGTACTCTATG-GGGGACTTTGTATTTCTTAAGGTATCTCC
21383255 GTGGAAAAAGGTTCTACGGTTCGG
582 GTGGAAAAAGGTTCTACGGTTCGG
*
21383279 TTG----AGTCCGCTCATTTTATTCCTGTTCAG--GGACTACTCTCTGTAAAAGTTAGTGAAGCT
1 TTGACCAAGTCCGCTCATTTTATTCCTGTTCAGATGGACTACTCTCTGCAAAAGTTAGTGAAGCT
* * * *
21383338 GTACATTTCTGAGACTGTAAGACTGTATGGGGTTCCAATTTCAATAATCTCTAATATGGATCCTC
66 CTACATTTCTGAGATTGTAAGA--GCATGGGGTTCCAATTTCAATAATCTCTGATATGGATCCTC
* * *
21383403 TCTTCACTTCACAGTTCTAGATGAAACTTCACAAGGCTCTGGGTTCGAGACTGGACTTCAGTACT
129 TCTTCACTTCACGGTTCTAGAAGAAACTTCACAAGGC-CTGGGTTCGAGATTGGACTTCAGTACT
*
21383468 GCGTTCCATCCTCAGACCGATGGTCAATTTGAGAGGGTGAATCATATACTAGAGGATATGATTTG
193 GCGTTCCATCCTCAGACCGATGGTCAATTTGAGAGGGTGATTCATATACTAGAGGATATGATTTG
* *
21383533 GAGCTATGTGATTTATTTCTAAGGTAGTTGAGAGGA-TTTTTACCGTTAGTTGAGTTCGCCTATA
258 GAGCTATGTGATTTATTTCTGAGGTAGTTGAGAGGATTTTTTACCGTTAGTTGAGTTCGCCTACA
* * * * *
21383597 ATAACAGTTTCCAGTCTAGCATCTAGATGGCACCTTATGAGACTCTATATGGTCATAAGTGCCGT
323 ATAACAGTTTCCAATCTAGCATCTAGATGGCACCTTACGAGGCTCTATATGGTCATAAGTGTCAT
21383662 ACTCTGTTATATTAGACTGAGTTGGGTGAGCGACGGGTTTT-GGTCCTGAGTTGGTTTCCGAGAC
388 ACTCTGTTATATTAGACTGAGTTGGGTGAGCGACGGGTTTTGGGTCCTGAGTTGGTTTCCGAGAC
* * *
21383726 TGAATATAATGCTAGACTAATTTGGGATCGT-TGAAGGCGTTTTCTGATAGATAGAAGTCTTATG
453 TGAAGATAATGTTAGACTAATTTGGGATCGTCTGAAGGCGTCTTCTGATAGATAGAAGTCTTATG
* *
21383790 CAAATCTGAAAATTAGAGATATCAAGTACTCTAT-GGGGACTTTGTATTTCTTAAGGTATCTCTG
518 CAAATCTGAAAATCAGAGATATCAAGTACTCTATGGGGGACTTTGTATTTCTTAAGGTATCTCCG
*
21383854 TGGAAAAAGGTTCTATGGTTCGG
583 TGGAAAAAGGTTCTACGGTTCGG
* **
21383877 TTGACCAAGTCTGCTCATTTTATTCCTGTTCAGATGGACTACTCTCTGCAAAAGTTAGTGAAAAT
1 TTGACCAAGTCCGCTCATTTTATTCCTGTTCAGATGGACTACTCTCTGCAAAAGTTAGTGAAGCT
21383942 CTACA-TTCTGAGATTGTAAGA-C-T-GGGTTCCAATTT-AATAATCTCTGATATGGATCCTCTC
66 CTACATTTCTGAGATTGTAAGAGCATGGGGTTCCAATTTCAATAATCTCTGATATGGATCCTCTC
* * *
21384002 TTCGCTTCACGGTTCTAGAAAAAACTTCACAAGG-CTAGGTTCGAGATTGGACTTCAGTACTGCG
131 TTCACTTCACGGTTCTAGAAGAAACTTCACAAGGCCTGGGTTCGAGATTGGACTTCAGTACTGCG
* *
21384066 TTCCATCCTCAGACCGATGGTCACTTTGAGAGGGTGATTC----ACTAGAGGATTTGATTTGGAG
196 TTCCATCCTCAGACCGATGGTCAATTTGAGAGGGTGATTCATATACTAGAGGATATGATTTGGAG
* * *
21384127 CTA--TGATTTATTTCTGA-GTAGTTG-GACGATTTTTTACTGTTAGTTGAGTTCGCCTACAA-G
261 CTATGTGATTTATTTCTGAGGTAGTTGAGAGGATTTTTTACCGTTAGTTGAGTTCGCCTACAATA
*
21384187 ATAGTTTCCAATCTAGCATCTAGATGGCACCTTACGAGGCTCTATATGGTCATAAGTGTCATACT
326 ACAGTTTCCAATCTAGCATCTAGATGGCACCTTACGAGGCTCTATATGGTCATAAGTGTCATACT
*
21384252 CTGTTATATTAGACTGAG-TGTGGTGAGCGAC-GGTTTTGGGACCTGAGTTGGTTTCCGAGACTG
391 CTGTTATATTAGACTGAGTTG-GGTGAGCGACGGGTTTTGGGTCCTGAGTTGGTTTCCGAGACTG
21384315 AAGATAATGTTAGACTAATTT-GGATCGTCTGAAGGCGTCTTCTGATAGATAGAAGTCTTATGCA
455 AAGATAATGTTAGACTAATTTGGGATCGTCTGAAGGCGTCTTCTGATAGATAGAAGTCTTATGCA
21384379 AATCTGAAAATCAGAGATATCAAGTACTCTATGGGGGACTTTGTATTTCTTAAGGTATCTCCGTG
520 AATCTGAAAATCAGAGATATCAAGTACTCTATGGGGGACTTTGTATTTCTTAAGGTATCTCCGTG
*
21384444 GAAAAAGGTTCTACAGTTCGG
585 GAAAAAGGTTCTACGGTTCGG
* *
21384465 TTGACCAAGTCCGCTCATTTTATTCCTATTCAGATGGACAACTCTCTGC-AAAGTTAGTGAAGCT
1 TTGACCAAGTCCGCTCATTTTATTCCTGTTCAGATGGACTACTCTCTGCAAAAGTTAGTGAAGCT
* *
21384529 CTACATTTCTGAGATTGT-AGACTGCAT-GGGTTCTAATTTCAATAATCTCT-ATATGGATCCCC
66 CTACATTTCTGAGATTGTAAGA--GCATGGGGTTCCAATTTCAATAATCTCTGATATGGATCCTC
* * * *
21384591 TCTTCACTTCACGGTTCAAGAAGAAACTTCACAAAGCTCTGGGTTCGAGATTGAACTTCAATACT
129 TCTTCACTTCACGGTTCTAGAAGAAACTTCACAAGGC-CTGGGTTCGAGATTGGACTTCAGTACT
*
21384656 GCGTTCCATCCTCAGACCGATGGTCAATTTGAAAGGGTGATTCATATACTAGAGG--ATGATTTG
193 GCGTTCCATCCTCAGACCGATGGTCAATTTGAGAGGGTGATTCATATACTAGAGGATATGATTTG
* *
21384719 GAGCTATGAGATTTATTTCTGAGGTAGTTGAGAGGATTTTTTTATCGTTAGTTGAGTTCGCCTAC
258 GAGCTATGTGATTTATTTCTGAGGTAGTTGAGAGGA-TTTTTTACCGTTAGTTGAGTTCGCCTAC
21384784 AATAACAGTTTCCAATCTAGCATCTAGATGGCACCTTACGAGGCTCTATATGGTCATAAGTGTCA
322 AATAACAGTTTCCAATCTAGCATCTAGATGGCACCTTACGAGGCTCTATATGGTCATAAGTGTCA
* *
21384849 TACTCTGTTATATTAGATTTAGTTGGGT-AGCGACGGGTTTTGGGTCCTGAGTTGGTTTCCGAGA
387 TACTCTGTTATATTAGACTGAGTTGGGTGAGCGACGGGTTTTGGGTCCTGAGTTGGTTTCCGAGA
* *
21384913 CTGAAGAGAATGTTAGACTAATTTGGGATCGTCTGAAGGCGTCTTCTGATAGATAGAAGTCCTAT
452 CTGAAGATAATGTTAGACTAATTTGGGATCGTCTGAAGGCGTCTTCTGATAGATAGAAGTCTTAT
* ** * *
21384978 GCAAATCTAAAAATCAGAGATATCAAGTACTCTAT-GATGACTTTGTATTTCTTAAGGTAACTAC
517 GCAAATCTGAAAATCAGAGATATCAAGTACTCTATGGGGGACTTTGTATTTCTTAAGGTATCTCC
*
21385042 GT---AAAAGGTTCTATGGTTCGG
582 GTGGAAAAAGGTTCTACGGTTCGG
*
21385063 TTGACCAAGTCCGCTCATTTTATTCCTGTTCAGATGGACTACTCTCTGTAAAAGTTAGTGAAGCT
1 TTGACCAAGTCCGCTCATTTTATTCCTGTTCAGATGGACTACTCTCTGCAAAAGTTAGTGAAGCT
* *
21385128 CTACATTCCTGAGATTGT-AGA-CTTGGGGTTGCCAATTTCAATAATCTCTGATATGGATCCTCT
66 CTACATTTCTGAGATTGTAAGAGCATGGGGTT-CCAATTTCAATAATCTCTGATATGGATCCTCT
*
21385191 CTTCACTTCACGGTTCTAGAA-AATCTTCACAAGGCTCTGGGTTCGAGA-TGGACTTCAGTACTG
130 CTTCACTTCACGGTTCTAGAAGAAACTTCACAAGGC-CTGGGTTCGAGATTGGACTTCAGTACTG
*
21385254 CGTTCCATCCTCAGACCGATGGTCAATTTGAGAGGGTGATT-GTATACTAGAGGATATGATTT-G
194 CGTTCCATCCTCAGACCGATGGTCAATTTGAGAGGGTGATTCATATACTAGAGGATATGATTTGG
* * **
21385317 AGCTATGAGATTTATTTCTGAGGTAGTTGAGA-GATTTTTTATCGTTAGTTGAGCACGCCTACAA
259 AGCTATGTGATTTATTTCTGAGGTAGTTGAGAGGATTTTTTACCGTTAGTTGAGTTCGCCTACAA
*
21385381 TAATAGTTTCCAATCTAGCATCTAGATGGCACCTTACGAGGCTCTATATGGTCATAAGTGTCATA
324 TAACAGTTTCCAATCTAGCATCTAGATGGCACCTTACGAGGCTCTATATGGTCATAAGTGTCATA
21385446 CT-TGTTATATTAGACTGA-----GT-AGCGAC---TTTTGGGTCCTGAGTTGGTTTCCGAGACT
389 CTCTGTTATATTAGACTGAGTTGGGTGAGCGACGGGTTTTGGGTCCTGAGTTGGTTTCCGAGACT
21385501 GAAGATAATGTTAGACTAATTTGGGATCGTCTGAAGGCGTCTTCTGATAGATAGAAGTCTTATGC
454 GAAGATAATGTTAGACTAATTTGGGATCGTCTGAAGGCGTCTTCTGATAGATAGAAGTCTTATGC
21385566 AAATCTGAAAAATC-----TATCATAGTA-TCTATGGGGGACTTTGTATTTCTTAAGGTATCTCC
519 AAATCTG-AAAATCAGAGATATCA-AGTACTCTATGGGGGACTTTGTATTTCTTAAGGTATCTCC
*
21385625 GTGGAAAAAGGTTCTACAGTTC--
582 GTGGAAAAAGGTTCTACGGTTCGG
* *
21385647 -TGACCAAGTCCGCTAATTTTATTCCTGTTCAGATGGACTACTCTCTGCAAAAGTTAGTGAAGTT
1 TTGACCAAGTCCGCTCATTTTATTCCTGTTCAGATGGACTACTCTCTGCAAAAGTTAGTGAAGCT
* *
21385711 CTATATTTCTGAGATTGTAAGACGCATGGGGTTCCAATTTCAATAATGAAGTTCTATTTTCTGAG
66 CTACATTTCTGAGATTGTAAGA-GCATGGGGTTCCAATTTC---AAT-AA--TC-----TCTGAT
* * * * *
21385776 ATTGTAAGACTGCATGGGTTCCAATTTCAATATCTCTGGATCTCTCACTTCACTTAAAGAAACTT
119 A-TG---GA-T-CCT---CT-C---TTCACT-TCAC-GG---T-T--C-T-A---GAAGAAACTT
* *
21385841 CACAA-TCTCTAGGTTCGAGATT-GACTTCA-TACTGCGTTCCATCCTCAGACCGATGGTCAATT
158 CACAAGGC-CTGGGTTCGAGATTGGACTTCAGTACTGCGTTCCATCCTCAGACCGATGGTCAATT
* * *
21385903 TGAAAGGGTGATTCATATACTAGAGGATATGATTTGGAGATATTTGATTTATTTCTGAGGTAGTT
222 TGAGAGGGTGATTCATATACTAGAGGATATGATTTGGAGCTATGTGATTTATTTCTGAGGTAGTT
21385968 G-GAGGATTTTTTACCGTTAGTTGAGTTCGCCTAC-A-AACAGTTTCCAATCTAGCATCTAGATG
287 GAGAGGATTTTTTACCGTTAGTTGAGTTCGCCTACAATAACAGTTTCCAATCTAGCATCTAGATG
*
21386030 GCACCTTACAAGGCTCTATATGGTCATAAGTGTCATACTCTGTTATATTAGACT-A-TTGGGTGA
352 GCACCTTACGAGGCTCTATATGGTCATAAGTGTCATACTCTGTTATATTAGACTGAGTTGGGTGA
* * * *
21386093 GCAACGGGTTTTGGGTCCTGGGTTGGTTTCCGAGACTAAAGATAATGTTTGACTAA-TT-GGATC
417 GCGACGGGTTTTGGGTCCTGAGTTGGTTTCCGAGACTGAAGATAATGTTAGACTAATTTGGGATC
21386156 GTCTGAAGGCGTCTTCTGATAGATAGAAGTCTTATGCAAATCTGAAAATCAG-GATATCAAGTAC
482 GTCTGAAGGCGTCTTCTGATAGATAGAAGTCTTATGCAAATCTGAAAATCAGAGATATCAAGTAC
21386220 -CTATGGGGGACTTTGTATTTCTTAAGGTATCTCCGTGGAAAAAGGTTCTACGGTT---
547 TCTATGGGGGACTTTGTATTTCTTAAGGTATCTCCGTGGAAAAAGGTTCTACGGTTCGG
* *
21386275 TGGACTCAAGTCCGCTAATTTTATTCCTGTTCAGATGGACTAC
1 TTGAC-CAAGTCCGCTCATTTTATTCCTGTTCAGATGGACTAC
21386318 CTGATGGACC
Statistics
Matches: 3334, Mismatches: 180, Indels: 218
0.89 0.05 0.06
Matches are distributed among these distances:
582 10 0.00
583 108 0.03
584 3 0.00
585 8 0.00
586 136 0.04
587 226 0.07
588 145 0.04
589 23 0.01
590 1 0.00
591 80 0.02
592 11 0.00
593 247 0.07
594 107 0.03
595 302 0.09
596 72 0.02
597 281 0.08
598 201 0.06
599 105 0.03
600 259 0.08
601 180 0.05
602 300 0.09
603 35 0.01
604 31 0.01
605 1 0.00
606 1 0.00
609 5 0.00
610 3 0.00
611 2 0.00
614 1 0.00
615 1 0.00
617 1 0.00
618 1 0.00
619 1 0.00
621 110 0.03
622 59 0.02
623 65 0.02
625 2 0.00
626 11 0.00
627 49 0.01
628 2 0.00
629 106 0.03
630 42 0.01
ACGTcount: A:0.26, C:0.17, G:0.23, T:0.34
Consensus pattern (605 bp):
TTGACCAAGTCCGCTCATTTTATTCCTGTTCAGATGGACTACTCTCTGCAAAAGTTAGTGAAGCT
CTACATTTCTGAGATTGTAAGAGCATGGGGTTCCAATTTCAATAATCTCTGATATGGATCCTCTC
TTCACTTCACGGTTCTAGAAGAAACTTCACAAGGCCTGGGTTCGAGATTGGACTTCAGTACTGCG
TTCCATCCTCAGACCGATGGTCAATTTGAGAGGGTGATTCATATACTAGAGGATATGATTTGGAG
CTATGTGATTTATTTCTGAGGTAGTTGAGAGGATTTTTTACCGTTAGTTGAGTTCGCCTACAATA
ACAGTTTCCAATCTAGCATCTAGATGGCACCTTACGAGGCTCTATATGGTCATAAGTGTCATACT
CTGTTATATTAGACTGAGTTGGGTGAGCGACGGGTTTTGGGTCCTGAGTTGGTTTCCGAGACTGA
AGATAATGTTAGACTAATTTGGGATCGTCTGAAGGCGTCTTCTGATAGATAGAAGTCTTATGCAA
ATCTGAAAATCAGAGATATCAAGTACTCTATGGGGGACTTTGTATTTCTTAAGGTATCTCCGTGG
AAAAAGGTTCTACGGTTCGG
Found at i:21385783 original size:52 final size:53
Alignment explanation
Indices: 21385704--21385807 Score: 185
Period size: 52 Copynumber: 2.0 Consensus size: 53
21385694 CAAAAGTTAG
21385704 TGAAGTTCTATATTTCTGAGATTGTAAGAC-GCATGGGGTTCCAATTTCAATAA
1 TGAAGTTCTATATTTCTGAGATTGTAAGACTGCAT-GGGTTCCAATTTCAATAA
21385757 TGAAGTTCTAT-TTTCTGAGATTGTAAGACTGCATGGGTTCCAATTTCAATA
1 TGAAGTTCTATATTTCTGAGATTGTAAGACTGCATGGGTTCCAATTTCAATA
21385808 TCTCTGGATC
Statistics
Matches: 50, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
52 35 0.70
53 15 0.30
ACGTcount: A:0.29, C:0.13, G:0.20, T:0.38
Consensus pattern (53 bp):
TGAAGTTCTATATTTCTGAGATTGTAAGACTGCATGGGTTCCAATTTCAATAA
Found at i:21415499 original size:8 final size:8
Alignment explanation
Indices: 21415486--21415512 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
21415476 TGGACTATCG
21415486 ATTCAATC
1 ATTCAATC
21415494 ATTCAATC
1 ATTCAATC
21415502 ATTCAATC
1 ATTCAATC
21415510 ATT
1 ATT
21415513 TAAACCAACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.37, C:0.22, G:0.00, T:0.41
Consensus pattern (8 bp):
ATTCAATC
Found at i:21424824 original size:24 final size:24
Alignment explanation
Indices: 21424793--21424840 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
21424783 AATGCATTCA
* *
21424793 TTTGAATTT-TGGAAATTTTATGT
1 TTTGAATTTATGAAAATTGTATGT
21424816 TTTGCAATTTATGAAAATTGTATGT
1 TTTG-AATTTATGAAAATTGTATGT
21424841 GACTATAGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 4 0.19
24 5 0.24
25 12 0.57
ACGTcount: A:0.29, C:0.02, G:0.17, T:0.52
Consensus pattern (24 bp):
TTTGAATTTATGAAAATTGTATGT
Found at i:21429880 original size:12 final size:11
Alignment explanation
Indices: 21429859--21429998 Score: 57
Period size: 12 Copynumber: 11.7 Consensus size: 11
21429849 ATGCAGCTTT
*
21429859 CAGATACAATCA
1 CAGATGCAAT-A
*
21429871 CAGATGCAATTC
1 CAGATGCAA-TA
21429883 CAGA-GACAAATA
1 CAGATG-C-AATA
21429895 CAGATGCAGATA
1 CAGATGCA-ATA
**
21429907 CAGACCCAGATA
1 CAGATGCA-ATA
*
21429919 CAGATACAGATA
1 CAGATGCA-ATA
*
21429931 CAGATGCGGATA
1 CAGATGC-AATA
*
21429943 CAGATGCAAACA
1 CAGATGC-AATA
*
21429955 CAGATTCAGATA
1 CAGATGCA-ATA
* *
21429967 CAAATGCAGACA
1 CAGATGCA-ATA
* *
21429979 CAGATTCAGTTA
1 CAGATGCA-ATA
21429991 CAGATGCA
1 CAGATGCA
21429999 GACACCAATC
Statistics
Matches: 99, Mismatches: 22, Indels: 14
0.73 0.16 0.10
Matches are distributed among these distances:
11 3 0.03
12 92 0.93
13 4 0.04
ACGTcount: A:0.44, C:0.21, G:0.19, T:0.16
Consensus pattern (11 bp):
CAGATGCAATA
Found at i:21429910 original size:24 final size:24
Alignment explanation
Indices: 21429870--21429934 Score: 69
Period size: 24 Copynumber: 2.7 Consensus size: 24
21429860 AGATACAATC
* *
21429870 ACAGATGCA-ATTCCAGAGACAAAT
1 ACAGATGCAGA-TACAGACACAAAT
* *
21429894 ACAGATGCAGATACAGACCCAGAT
1 ACAGATGCAGATACAGACACAAAT
*
21429918 ACAGATACAGATACAGA
1 ACAGATGCAGATACAGA
21429935 TGCGGATACA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
24 34 0.97
25 1 0.03
ACGTcount: A:0.46, C:0.22, G:0.18, T:0.14
Consensus pattern (24 bp):
ACAGATGCAGATACAGACACAAAT
Found at i:21429942 original size:24 final size:24
Alignment explanation
Indices: 21429892--21430003 Score: 125
Period size: 24 Copynumber: 4.7 Consensus size: 24
21429882 CCAGAGACAA
* *
21429892 ATACAGATGCAGATACAGACCCAG
1 ATACAGATGCAGACACAGATCCAG
* * * *
21429916 ATACAGATACAGATACAGATGCGG
1 ATACAGATGCAGACACAGATCCAG
* *
21429940 ATACAGATGCAAACACAGATTCAG
1 ATACAGATGCAGACACAGATCCAG
* *
21429964 ATACAAATGCAGACACAGATTCAG
1 ATACAGATGCAGACACAGATCCAG
*
21429988 TTACAGATGCAGACAC
1 ATACAGATGCAGACAC
21430004 CAATCCTACC
Statistics
Matches: 75, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 75 1.00
ACGTcount: A:0.43, C:0.21, G:0.20, T:0.16
Consensus pattern (24 bp):
ATACAGATGCAGACACAGATCCAG
Found at i:21429947 original size:18 final size:18
Alignment explanation
Indices: 21429892--21429983 Score: 85
Period size: 18 Copynumber: 5.1 Consensus size: 18
21429882 CCAGAGACAA
21429892 ATACAGATGCAGATACAG
1 ATACAGATGCAGATACAG
** *
21429910 ACCCAGATACAGATACAG
1 ATACAGATGCAGATACAG
*
21429928 ATACAGATGCGGATACAG
1 ATACAGATGCAGATACAG
* * ** *
21429946 ATGCAAACACAGATTCAG
1 ATACAGATGCAGATACAG
* *
21429964 ATACAAATGCAGACACAG
1 ATACAGATGCAGATACAG
21429982 AT
1 AT
21429984 TCAGTTACAG
Statistics
Matches: 56, Mismatches: 18, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
18 56 1.00
ACGTcount: A:0.45, C:0.21, G:0.20, T:0.15
Consensus pattern (18 bp):
ATACAGATGCAGATACAG
Found at i:21433316 original size:8 final size:8
Alignment explanation
Indices: 21433299--21433339 Score: 50
Period size: 8 Copynumber: 5.2 Consensus size: 8
21433289 AGATACAATA
*
21433299 TTTTTCAT
1 TTTTTAAT
21433307 TTTTTAAT
1 TTTTTAAT
21433315 TTTTTAA-
1 TTTTTAAT
21433322 TTTTT-AT
1 TTTTTAAT
21433329 TTGTTTAAT
1 TT-TTTAAT
21433338 TT
1 TT
21433340 ATTTTAAATT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
6 1 0.03
7 7 0.24
8 17 0.59
9 4 0.14
ACGTcount: A:0.20, C:0.02, G:0.02, T:0.76
Consensus pattern (8 bp):
TTTTTAAT
Found at i:21433325 original size:15 final size:15
Alignment explanation
Indices: 21433307--21433339 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
21433297 TATTTTTCAT
21433307 TTTTTAATTT-TTTAA
1 TTTTT-ATTTGTTTAA
21433322 TTTTTATTTGTTTAA
1 TTTTTATTTGTTTAA
21433337 TTT
1 TTT
21433340 ATTTTAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (15 bp):
TTTTTATTTGTTTAA
Found at i:21438838 original size:32 final size:32
Alignment explanation
Indices: 21438798--21438921 Score: 158
Period size: 32 Copynumber: 3.9 Consensus size: 32
21438788 ATAAGTATAA
* *
21438798 TAATATGATTGGCACAAAGCCATCAGTAGCAG
1 TAATATGATCGGCACAAAGCCATCAGTAACAG
* * * **
21438830 TGATATGATCAGCACACAGCCATCAGTAATGG
1 TAATATGATCGGCACAAAGCCATCAGTAACAG
* *
21438862 TAATATGATCGGTACAAAGCCATCAGTAACGG
1 TAATATGATCGGCACAAAGCCATCAGTAACAG
*
21438894 TAATATAATCGGCACAAAGCCATCAGTA
1 TAATATGATCGGCACAAAGCCATCAGTA
21438922 GCATCGTAGA
Statistics
Matches: 78, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 78 1.00
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.22
Consensus pattern (32 bp):
TAATATGATCGGCACAAAGCCATCAGTAACAG
Found at i:21438884 original size:64 final size:64
Alignment explanation
Indices: 21438798--21438921 Score: 176
Period size: 64 Copynumber: 1.9 Consensus size: 64
21438788 ATAAGTATAA
* * * * *
21438798 TAATATGATTGGCACAAAGCCATCAGTAGCAGTGATATGATCAGCACACAGCCATCAGTAATGG
1 TAATATGATCGGCACAAAGCCATCAGTAACAGTAATATAATCAGCACAAAGCCATCAGTAATGG
* * *
21438862 TAATATGATCGGTACAAAGCCATCAGTAACGGTAATATAATCGGCACAAAGCCATCAGTA
1 TAATATGATCGGCACAAAGCCATCAGTAACAGTAATATAATCAGCACAAAGCCATCAGTA
21438922 GCATCGTAGA
Statistics
Matches: 52, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
64 52 1.00
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.22
Consensus pattern (64 bp):
TAATATGATCGGCACAAAGCCATCAGTAACAGTAATATAATCAGCACAAAGCCATCAGTAATGG
Found at i:21439116 original size:11 final size:11
Alignment explanation
Indices: 21439100--21439145 Score: 56
Period size: 11 Copynumber: 4.0 Consensus size: 11
21439090 CAGAATGAGT
21439100 CATACAAATCA
1 CATACAAATCA
21439111 CATACAAATCA
1 CATACAAATCA
*
21439122 GTCATACTAATCA
1 --CATACAAATCA
*
21439135 CAGACAAATCA
1 CATACAAATCA
21439146 ATCATTTACA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
11 20 0.67
13 10 0.33
ACGTcount: A:0.50, C:0.26, G:0.04, T:0.20
Consensus pattern (11 bp):
CATACAAATCA
Found at i:21439133 original size:24 final size:24
Alignment explanation
Indices: 21439097--21439150 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
21439087 GCTCAGAATG
*
21439097 AGTCATACAAATCACATACAAATC
1 AGTCATACAAATCACAGACAAATC
*
21439121 AGTCATACTAATCACAGACAAATC
1 AGTCATACAAATCACAGACAAATC
*
21439145 AATCAT
1 AGTCAT
21439151 TTACATCACG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.48, C:0.24, G:0.06, T:0.22
Consensus pattern (24 bp):
AGTCATACAAATCACAGACAAATC
Found at i:21439158 original size:24 final size:24
Alignment explanation
Indices: 21439107--21439179 Score: 85
Period size: 24 Copynumber: 3.0 Consensus size: 24
21439097 AGTCATACAA
* * *
21439107 ATCACATACAAATCAGTCATACTA-
1 ATCACAGACAAATCAATCAT-TTAC
21439131 ATCACAGACAAATCAATCATTTAC
1 ATCACAGACAAATCAATCATTTAC
* *
21439155 ATCACGGACAAATAAATCATTTAC
1 ATCACAGACAAATCAATCATTTAC
21439179 A
1 A
21439180 CTCGAGGGGA
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
23 2 0.05
24 41 0.95
ACGTcount: A:0.47, C:0.23, G:0.05, T:0.25
Consensus pattern (24 bp):
ATCACAGACAAATCAATCATTTAC
Found at i:21439228 original size:27 final size:27
Alignment explanation
Indices: 21439194--21439576 Score: 217
Period size: 27 Copynumber: 14.3 Consensus size: 27
21439184 AGGGGAAAAA
* *
21439194 GTCA-TTTACCCTTCAAGGGCATTACG
1 GTCATTTTACCCTTCAAGGGTATTTCG
*
21439220 GTAATTTTA-CCTT-ACAGTGGTATTTCG
1 GTCATTTTACCCTTCA-AG-GGTATTTCG
* * *
21439247 GTCATTTAACCC-T-ATGGGGTATTACG
1 GTCATTTTACCCTTCA-AGGGTATTTCG
* * * * * *
21439273 GTCATTTTACTCTACAGGGGCATTACA
1 GTCATTTTACCCTTCAAGGGTATTTCG
* ** *
21439300 GTTATTTTACCCTAT-GGGGGTTTTTCG
1 GTCATTTTACCCT-TCAAGGGTATTTCG
* * *
21439327 GT-ATTTTACCCTACAGGGGTATTACG
1 GTCATTTTACCCTTCAAGGGTATTTCG
*
21439353 GTCATTTTA-CCTATCAAGGGTATTTTG
1 GTCATTTTACCCT-TCAAGGGTATTTCG
* * * *
21439380 ATAATTTTACCCATCGAGGGTATTTCG
1 GTCATTTTACCCTTCAAGGGTATTTCG
* * *
21439407 GTCATTTTACCCATCAGGGGTATTTTG
1 GTCATTTTACCCTTCAAGGGTATTTCG
* * * * **
21439434 ATAATTTTACCCATCGAGGGTATTTTA
1 GTCATTTTACCCTTCAAGGGTATTTCG
* * * *
21439461 GTCATTTTACCCATCGAGGATAATTCG
1 GTCATTTTACCCTTCAAGGGTATTTCG
* *
21439488 GTCATTTTACCCTTCAAGGGTAATTCA
1 GTCATTTTACCCTTCAAGGGTATTTCG
* * **
21439515 ATCATTTTACCCTACGGGGGTAATTT-G
1 GTCATTTTACCCTTCAAGGGT-ATTTCG
* * *
21439542 GTCATTTTACCCCCTCAGGGGTAATTCG
1 GTCATTTTA-CCCTTCAAGGGTATTTCG
*
21439570 ATCATTT
1 GTCATTT
21439577 AACAAATATT
Statistics
Matches: 277, Mismatches: 66, Indels: 26
0.75 0.18 0.07
Matches are distributed among these distances:
25 1 0.00
26 51 0.18
27 201 0.73
28 24 0.09
ACGTcount: A:0.23, C:0.20, G:0.20, T:0.38
Consensus pattern (27 bp):
GTCATTTTACCCTTCAAGGGTATTTCG
Found at i:21439282 original size:80 final size:79
Alignment explanation
Indices: 21439194--21439430 Score: 232
Period size: 80 Copynumber: 3.0 Consensus size: 79
21439184 AGGGGAAAAA
*
21439194 GTCA-TTTACCCTTCAAGGGCATTACGGTAATTTTACCTTACAGTGGTATTTCGGTCATTTAACC
1 GTCATTTTACCCTTCAAGGGCATTACGGTAATTTTACC-TACAG-GGTATTTCGGTCATTTTACC
*
21439258 CTA-TGGGGTATTACG
64 CTACAGGGGTATTACG
* * * * * ** *
21439273 GTCATTTTACTCTACAGGGGCATTACAGTTATTTTACCCTATGGGGGTTTTTCGGT-ATTTTACC
1 GTCATTTTACCCTTCAAGGGCATTACGGTAATTTTA-CCTA-CAGGGTATTTCGGTCATTTTACC
21439337 CTACAGGGGTATTACG
64 CTACAGGGGTATTACG
* ** * *
21439353 GTCATTTTA-CCTATCAAGGGTATTTTGATAATTTTACCCATCGAGGGTATTTCGGTCATTTTAC
1 GTCATTTTACCCT-TCAAGGGCATTACGGTAATTTTACCTA-C-AGGGTATTTCGGTCATTTTAC
21439417 CC-ATCAGGGGTATT
63 CCTA-CAGGGGTATT
21439431 TTGATAATTT
Statistics
Matches: 127, Mismatches: 23, Indels: 14
0.77 0.14 0.09
Matches are distributed among these distances:
79 20 0.16
80 85 0.67
81 22 0.17
ACGTcount: A:0.22, C:0.19, G:0.21, T:0.38
Consensus pattern (79 bp):
GTCATTTTACCCTTCAAGGGCATTACGGTAATTTTACCTACAGGGTATTTCGGTCATTTTACCCT
ACAGGGGTATTACG
Found at i:21439360 original size:53 final size:53
Alignment explanation
Indices: 21439218--21439445 Score: 191
Period size: 53 Copynumber: 4.3 Consensus size: 53
21439208 AAGGGCATTA
* * * * * *
21439218 CGGTAATTTTACCTTACAGTGGTATTTCGGTCATTTAACCCTATGGGGTATTA
1 CGGTAATTTTACCCTACAGGGGTATTACGGTCATTTTACCCTATGGGGTTTTT
* * * * *
21439271 CGGTCATTTTACTCTACAGGGGCATTACAGTTATTTTACCCTATGGGGGTTTTT
1 CGGTAATTTTACCCTACAGGGGTATTACGGTCATTTTACCCTAT-GGGGTTTTT
*
21439325 CGGT-ATTTTACCCTACAGGGGTATTACGGTCATTTTA-CCTATCAAGGGTATTTT
1 CGGTAATTTTACCCTACAGGGGTATTACGGTCATTTTACCCTAT--GGGGT-TTTT
* *
21439379 -GATAATTTTACCC-ATC-GAGGGTATTTCGGTCATTTTACCC-ATCAGGGGTATTTT
1 CGGTAATTTTACCCTA-CAG-GGGTATTACGGTCATTTTACCCTAT--GGGGT-TTTT
*
21439433 -GATAATTTTACCC
1 CGGTAATTTTACCC
21439446 ATCGAGGGTA
Statistics
Matches: 148, Mismatches: 20, Indels: 13
0.82 0.11 0.07
Matches are distributed among these distances:
52 5 0.03
53 72 0.49
54 69 0.47
55 2 0.01
ACGTcount: A:0.22, C:0.18, G:0.20, T:0.39
Consensus pattern (53 bp):
CGGTAATTTTACCCTACAGGGGTATTACGGTCATTTTACCCTATGGGGTTTTT
Found at i:21439442 original size:81 final size:80
Alignment explanation
Indices: 21439238--21439526 Score: 257
Period size: 81 Copynumber: 3.6 Consensus size: 80
21439228 ACCTTACAGT
* * * * * * **
21439238 GGTATTTCGGTCATTTAACCCT-ATGGGGTATTACGGTCATTTTACTC-TACAGGGGCATTACAG
1 GGTATTTCGGTCATTTTACCCTCA-GGGGTATTACGATAATTTTACCCAT-CAAGGGTATTTTAG
* *
21439301 TTATTTTACCCTAT-GGG
64 TAATTTTACCC-ATCGAG
* * * *
21439318 GGTTTTTCGGT-ATTTTACCCTACAGGGGTATTACGGTCATTTTACCTATCAAGGGTATTTT-GA
1 GGTATTTCGGTCATTTTACCCT-CAGGGGTATTACGATAATTTTACCCATCAAGGGTATTTTAG-
21439381 TAATTTTACCCATCGAG
64 TAATTTTACCCATCGAG
** *
21439398 GGTATTTCGGTCATTTTACCCATCAGGGGTATTTTGATAATTTTACCCATCGAGGGTATTTTAGT
1 GGTATTTCGGTCATTTTACCC-TCAGGGGTATTACGATAATTTTACCCATCAAGGGTATTTTAGT
*
21439463 CATTTTACCCATCGAG
65 AATTTTACCCATCGAG
* * * * *
21439479 GATAATTCGGTCATTTTACCCTTCAAGGGTAATT-CAATCATTTTACCC
1 GGTATTTCGGTCATTTTACCC-TCAGGGGT-ATTACGATAATTTTACCC
21439527 TACGGGGGTA
Statistics
Matches: 175, Mismatches: 25, Indels: 17
0.81 0.12 0.08
Matches are distributed among these distances:
79 12 0.07
80 61 0.35
81 97 0.55
82 5 0.03
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.39
Consensus pattern (80 bp):
GGTATTTCGGTCATTTTACCCTCAGGGGTATTACGATAATTTTACCCATCAAGGGTATTTTAGTA
ATTTTACCCATCGAG
Found at i:21439536 original size:81 final size:81
Alignment explanation
Indices: 21439323--21439553 Score: 265
Period size: 81 Copynumber: 2.9 Consensus size: 81
21439313 ATGGGGGTTT
* * * *
21439323 TTCGGT-ATTTTACCCTACAGGGGT-ATTACGGTCATTTTA-CCTATCAAGGGTATTTTGATAAT
1 TTCGGTCATTTTACCCTTCAGGGGTAATT-CGATCATTTTACCCTATCGAGGGTATTTTG-TCAT
* *
21439385 TTTACCCATCGAGGGTAT
64 TTTACCCATCGAGGATAA
* * * *
21439403 TTCGGTCATTTTACCCATCAGGGGTATTTTGATAATTTTACCC-ATCGAGGGTATTTTAGTCATT
1 TTCGGTCATTTTACCCTTCAGGGGTAATTCGATCATTTTACCCTATCGAGGGTATTTT-GTCATT
21439467 TTACCCATCGAGGATAA
65 TTACCCATCGAGGATAA
* * * *
21439484 TTCGGTCATTTTACCCTTCAAGGGTAATTCAATCATTTTACCCTA-CGGGGGTAATTTGGTCATT
1 TTCGGTCATTTTACCCTTCAGGGGTAATTCGATCATTTTACCCTATCGAGGGT-ATTTTGTCATT
21439548 TTACCC
65 TTACCC
21439554 CCTCAGGGGT
Statistics
Matches: 127, Mismatches: 18, Indels: 11
0.81 0.12 0.07
Matches are distributed among these distances:
80 6 0.05
81 111 0.87
82 10 0.08
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.39
Consensus pattern (81 bp):
TTCGGTCATTTTACCCTTCAGGGGTAATTCGATCATTTTACCCTATCGAGGGTATTTTGTCATTT
TACCCATCGAGGATAA
Found at i:21442005 original size:41 final size:41
Alignment explanation
Indices: 21441989--21442183 Score: 354
Period size: 41 Copynumber: 4.8 Consensus size: 41
21441979 CTTATAGCTT
* *
21441989 GATTCAGATCACCGGCACGTAGCCTGCTAGGTTTATAACCT
1 GATTCAAATCACCGGCACGTAGCCTGCTAGGTTTATAACCC
21442030 GATTCAAATCACCGGCACGTAGCCTGCTAGGTTTATAACCC
1 GATTCAAATCACCGGCACGTAGCCTGCTAGGTTTATAACCC
21442071 GATTCAAATCACCGGCACGTAGCCTGCTAGGTTTATAACCC
1 GATTCAAATCACCGGCACGTAGCCTGCTAGGTTTATAACCC
*
21442112 GATTCAAATCACCGGCACGTAGCCTGCTAAGTTTATAACCC
1 GATTCAAATCACCGGCACGTAGCCTGCTAGGTTTATAACCC
*
21442153 GATTCAAATCACCGACACGTAGCCTGCTAGG
1 GATTCAAATCACCGGCACGTAGCCTGCTAGG
21442184 CGCTTAGCCT
Statistics
Matches: 149, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 149 1.00
ACGTcount: A:0.27, C:0.29, G:0.20, T:0.24
Consensus pattern (41 bp):
GATTCAAATCACCGGCACGTAGCCTGCTAGGTTTATAACCC
Found at i:21443757 original size:16 final size:19
Alignment explanation
Indices: 21443722--21443760 Score: 57
Period size: 16 Copynumber: 2.2 Consensus size: 19
21443712 TATGTTTTGT
21443722 TTTATTATATTATACATTA
1 TTTATTATATTATACATTA
21443741 TTTATTA-ATT-TAC-TTA
1 TTTATTATATTATACATTA
21443757 TTTA
1 TTTA
21443761 ACCTTTAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 7 0.35
17 3 0.15
18 3 0.15
19 7 0.35
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (19 bp):
TTTATTATATTATACATTA
Found at i:21449804 original size:41 final size:41
Alignment explanation
Indices: 21449788--21449982 Score: 345
Period size: 41 Copynumber: 4.8 Consensus size: 41
21449778 CTTATAGCTT
* *
21449788 GATTCAGATCACCGGCACGTAGCCTGCTAGGTTTATAACCT
1 GATTCAAATCACCGGCACGTAGCCTGCTAGGTTTATAACCC
*
21449829 GATTCAAATCACTGGCACGTAGCCTGCTAGGTTTATAACCC
1 GATTCAAATCACCGGCACGTAGCCTGCTAGGTTTATAACCC
21449870 GATTCAAATCACCGGCACGTAGCCTGCTAGGTTTATAACCC
1 GATTCAAATCACCGGCACGTAGCCTGCTAGGTTTATAACCC
* *
21449911 GATTCAAATCACCGGCACGTAGCCTACTAGGTTTATAACTC
1 GATTCAAATCACCGGCACGTAGCCTGCTAGGTTTATAACCC
21449952 GATTCAAATCACCGGCACGTAGCCTGCTAGG
1 GATTCAAATCACCGGCACGTAGCCTGCTAGG
21449983 CGCTTAGCCT
Statistics
Matches: 147, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 147 1.00
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.25
Consensus pattern (41 bp):
GATTCAAATCACCGGCACGTAGCCTGCTAGGTTTATAACCC
Found at i:21450630 original size:12 final size:12
Alignment explanation
Indices: 21450613--21450638 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
21450603 TTTTAGCATT
21450613 ATATATATATAC
1 ATATATATATAC
21450625 ATATATATATAC
1 ATATATATATAC
21450637 AT
1 AT
21450639 GCTTATTCGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.08, G:0.00, T:0.42
Consensus pattern (12 bp):
ATATATATATAC
Found at i:21451565 original size:16 final size:19
Alignment explanation
Indices: 21451530--21451568 Score: 57
Period size: 16 Copynumber: 2.2 Consensus size: 19
21451520 TATGTTTTGT
21451530 TTTATTATATTATACATTA
1 TTTATTATATTATACATTA
21451549 TTTATTA-ATT-TAC-TTA
1 TTTATTATATTATACATTA
21451565 TTTA
1 TTTA
21451569 ACCTTTAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 7 0.35
17 3 0.15
18 3 0.15
19 7 0.35
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (19 bp):
TTTATTATATTATACATTA
Found at i:21452025 original size:41 final size:41
Alignment explanation
Indices: 21451906--21452048 Score: 137
Period size: 41 Copynumber: 3.5 Consensus size: 41
21451896 GGTTGTTACA
* ** *
21451906 GCCTAGCAGGCTTTATGCCGGTGAATTATAGCAGGCTTTAT
1 GCCTAGCAGGCTTTATGCCGGTGTATTATAATAAGCTTTAT
** * * *
21451947 GCCTAGCAGGCTTCGTGCCGGTGTATCAT-ATCTAGCTTTGT
1 GCCTAGCAGGCTTTATGCCGGTGTATTATAAT-AAGCTTTAT
* *
21451988 GCCTAGAAGGCTTTATGCCGGTGTATTTTAATAAGCTTTAT
1 GCCTAGCAGGCTTTATGCCGGTGTATTATAATAAGCTTTAT
* *
21452029 ACATCA-CAGGCTTTATGCCG
1 GCCT-AGCAGGCTTTATGCCG
21452049 ATGTGGTATC
Statistics
Matches: 80, Mismatches: 19, Indels: 6
0.76 0.18 0.06
Matches are distributed among these distances:
41 77 0.96
42 3 0.04
ACGTcount: A:0.21, C:0.21, G:0.24, T:0.34
Consensus pattern (41 bp):
GCCTAGCAGGCTTTATGCCGGTGTATTATAATAAGCTTTAT
Found at i:21456112 original size:41 final size:41
Alignment explanation
Indices: 21456044--21456204 Score: 173
Period size: 41 Copynumber: 3.9 Consensus size: 41
21456034 TGAAAATAAG
* * *
21456044 ATGTTTCAGACTTTACGTCCAAG-AGGCTTGATGCCGATGAA
1 ATGTTTCAGACTTTATGT-CTAGCAGGCTTGATGCCGGTGAA
21456085 ATGTTTCAGACTTTATGTCTAGCAGGCTTGATGCCGGTGAA
1 ATGTTTCAGACTTTATGTCTAGCAGGCTTGATGCCGGTGAA
* ** *
21456126 TTACTTCAGACTTTATGTCTATCAGGCTTTG-TGCCGGTGAA
1 ATGTTTCAGACTTTATGTCTAGCAGGC-TTGATGCCGGTGAA
* * * * * *
21456167 ATGTATCGGGCTTTGTGCCTAGCAGGCTTTATGCCGGT
1 ATGTTTCAGACTTTATGTCTAGCAGGCTTGATGCCGGT
21456205 TTTTTATACA
Statistics
Matches: 100, Mismatches: 17, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
40 5 0.05
41 92 0.92
42 3 0.03
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.34
Consensus pattern (41 bp):
ATGTTTCAGACTTTATGTCTAGCAGGCTTGATGCCGGTGAA
Found at i:21456167 original size:82 final size:82
Alignment explanation
Indices: 21456048--21456204 Score: 199
Period size: 82 Copynumber: 1.9 Consensus size: 82
21456038 AATAAGATGT
* * *
21456048 TTCAGACTTTACGTCCAAGAGGCTTGATGCCGATGAAATGTTTCAGACTTTATGTCTAGCAGGCT
1 TTCAGACTTTACGTCCAACAGGCTTGATGCCGATGAAATGTATCAGACTTTATGCCTAGCAGGCT
21456113 TGATGCCGGTGAATTAC
66 TGATGCCGGTGAATTAC
* * * * * * *
21456130 TTCAGACTTTATGTCTATCAGGCTTTG-TGCCGGTGAAATGTATCGGGCTTTGTGCCTAGCAGGC
1 TTCAGACTTTACGTCCAACAGGC-TTGATGCCGATGAAATGTATCAGACTTTATGCCTAGCAGGC
*
21456194 TTTATGCCGGT
65 TTGATGCCGGT
21456205 TTTTTATACA
Statistics
Matches: 63, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
82 60 0.95
83 3 0.05
ACGTcount: A:0.20, C:0.20, G:0.26, T:0.34
Consensus pattern (82 bp):
TTCAGACTTTACGTCCAACAGGCTTGATGCCGATGAAATGTATCAGACTTTATGCCTAGCAGGCT
TGATGCCGGTGAATTAC
Found at i:21460259 original size:79 final size:80
Alignment explanation
Indices: 21460123--21460346 Score: 287
Period size: 79 Copynumber: 2.8 Consensus size: 80
21460113 TTGAATGATG
* * * * *
21460123 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGAT-CCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGCTAAG-TCCCGAAGGCAT
*
21460186 TTGTGCGAGATACTAAT
64 TTGTGCGAGATACTAAA
* *
21460203 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGCTAAGTCCCGAAGGCATTT
*
21460267 GTGCGAGTTACTAAA
66 GTGCGAGATACTAAA
* *
21460282 TCC-GGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA-CCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AATCCGGGCTAAGTCCCGAAGGCATT
21460345 TG
65 TG
21460347 AACGAGTAGC
Statistics
Matches: 127, Mismatches: 13, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
78 7 0.06
79 101 0.80
80 19 0.15
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGCTAAGTCCCGAAGGCATTT
GTGCGAGATACTAAA
Found at i:21460353 original size:79 final size:78
Alignment explanation
Indices: 21460130--21460379 Score: 274
Period size: 79 Copynumber: 3.2 Consensus size: 78
21460120 ATGTCCGGGC
* * * * *
21460130 TAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGAT-CCGAAGGCATTTGTGCG
1 TAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAACCGGGCTAAG-TCCCGAAGGCATTTGTGCG
* *
21460193 AGATACTAATTCCGGGC
64 AG-TACTAAATCC-GGT
* *
21460210 TAAG-CCCGAAGGCATTGGTGCGAGTTACTA-AATCCGGGTTAAGTCCCGAAGGCATTTGTGCGA
1 TAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA-CCGGGCTAAGTCCCGAAGGCATTTGTGCGA
21460273 GTTACTAAATCCGGT
65 G-TACTAAATCCGGT
* **
21460288 TAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG
1 TAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAG
*
21460353 TAGCTATATCCGGT
66 TA-CTAAATCCGGT
* *
21460367 TAAATTCCGAAGG
1 TAAGTCCCGAAGG
21460380 TATGTGATTT
Statistics
Matches: 146, Mismatches: 18, Indels: 13
0.82 0.10 0.07
Matches are distributed among these distances:
78 10 0.07
79 124 0.85
80 12 0.08
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (78 bp):
TAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAG
TACTAAATCCGGT
Found at i:21460360 original size:40 final size:40
Alignment explanation
Indices: 21460123--21460346 Score: 287
Period size: 40 Copynumber: 5.7 Consensus size: 40
21460113 TTGAATGATG
* * * *
21460123 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
21460163 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
21460203 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
21460242 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
21460282 TCC-GGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
21460322 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
21460347 AACGAGTAGC
Statistics
Matches: 163, Mismatches: 15, Indels: 12
0.86 0.08 0.06
Matches are distributed among these distances:
39 70 0.43
40 85 0.52
41 8 0.05
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:21468478 original size:39 final size:40
Alignment explanation
Indices: 21468377--21468519 Score: 154
Period size: 39 Copynumber: 3.6 Consensus size: 40
21468367 TTGAATGATG
* *
21468377 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTA-AGTGAC-CAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAT
*
21468416 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAT
* *
21468457 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAA-
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
*
21468495 TCCGGGTTAAGTCCCGAAGGCATTT
1 TCCGGGCTAAGTCCCGAAGGCATTT
21468520 ACTTTCTTAG
Statistics
Matches: 89, Mismatches: 8, Indels: 13
0.81 0.07 0.12
Matches are distributed among these distances:
38 10 0.11
39 36 0.40
40 30 0.34
41 12 0.13
42 1 0.01
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.24
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:21480494 original size:8 final size:8
Alignment explanation
Indices: 21480471--21480509 Score: 51
Period size: 8 Copynumber: 4.5 Consensus size: 8
21480461 AAAACAACAC
21480471 ATAATATA
1 ATAATATA
21480479 TATAAATATA
1 -AT-AATATA
21480489 ATAATATA
1 ATAATATA
21480497 ATAATAATA
1 ATAAT-ATA
21480506 ATAA
1 ATAA
21480510 AGAAAGATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
8 11 0.39
9 11 0.39
10 6 0.21
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (8 bp):
ATAATATA
Found at i:21482789 original size:21 final size:21
Alignment explanation
Indices: 21482765--21482804 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
21482755 TTAGTCACTC
* *
21482765 TAAATTAAATTTAAAAATAGA
1 TAAAATAAATCTAAAAATAGA
21482786 TAAAATAAATCTAAAAATA
1 TAAAATAAATCTAAAAATA
21482805 TAATATTAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.30
Consensus pattern (21 bp):
TAAAATAAATCTAAAAATAGA
Found at i:21489854 original size:27 final size:27
Alignment explanation
Indices: 21489823--21489881 Score: 82
Period size: 27 Copynumber: 2.2 Consensus size: 27
21489813 TCATTGACTG
*
21489823 TCTTTGTAATTTGTTCATTTAATCTCA
1 TCTTTGTAATTTCTTCATTTAATCTCA
* **
21489850 TCTTTTTTGTTTCTTCATTTAATCTCA
1 TCTTTGTAATTTCTTCATTTAATCTCA
21489877 TCTTT
1 TCTTT
21489882 TTTATTTTTG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.17, C:0.17, G:0.05, T:0.61
Consensus pattern (27 bp):
TCTTTGTAATTTCTTCATTTAATCTCA
Found at i:21491020 original size:85 final size:85
Alignment explanation
Indices: 21490898--21491057 Score: 266
Period size: 85 Copynumber: 1.9 Consensus size: 85
21490888 ACCAAGTGGC
* * * * *
21490898 AGTTTGTTTAATTTGTAAATATGTTGTGCACCTACAACAAGTGGCAATAACTGCAAGTATGTGGT
1 AGTTTATTTAATCTGTAAATATGTTGTACACCCACAACAAGTGGCAATAACTGCAAATATGTGGT
21490963 TCGATCACGAACTAAATGGT
66 TCGATCACGAACTAAATGGT
21490983 AGTTTATTTAATCTGTAAATATGTTGTACACCCACAACAAGTGGCAATAACTGCAAATATGTGGT
1 AGTTTATTTAATCTGTAAATATGTTGTACACCCACAACAAGTGGCAATAACTGCAAATATGTGGT
*
21491048 TCGATTACGA
66 TCGATCACGA
21491058 GCCAAGAGGC
Statistics
Matches: 69, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
85 69 1.00
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.33
Consensus pattern (85 bp):
AGTTTATTTAATCTGTAAATATGTTGTACACCCACAACAAGTGGCAATAACTGCAAATATGTGGT
TCGATCACGAACTAAATGGT
Found at i:21506245 original size:20 final size:20
Alignment explanation
Indices: 21506201--21506278 Score: 75
Period size: 20 Copynumber: 3.9 Consensus size: 20
21506191 TCAATACCAA
* * *
21506201 GATAAAGGTTTCAATACTAT
1 GATAAAAGTATCAATACTTT
* * *
21506221 AATAAAAATATCGATACTTT
1 GATAAAAGTATCAATACTTT
* *
21506241 GATAAATGTGTCAATACTTT
1 GATAAAAGTATCAATACTTT
*
21506261 GAGAAAAGTATCAATACT
1 GATAAAAGTATCAATACT
21506279 ATAAGCAATG
Statistics
Matches: 44, Mismatches: 14, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.44, C:0.10, G:0.13, T:0.33
Consensus pattern (20 bp):
GATAAAAGTATCAATACTTT
Found at i:21506278 original size:40 final size:40
Alignment explanation
Indices: 21506201--21506278 Score: 93
Period size: 40 Copynumber: 1.9 Consensus size: 40
21506191 TCAATACCAA
* * *
21506201 GATAAAGGTTTCAATACTATAATAAAAATATCGATACTTT
1 GATAAAGGTGTCAATACTATAAGAAAAATATCAATACTTT
* * * *
21506241 GATAAATGTGTCAATACTTTGAGAAAAGTATCAATACT
1 GATAAAGGTGTCAATACTATAAGAAAAATATCAATACT
21506279 ATAAGCAATG
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
40 31 1.00
ACGTcount: A:0.44, C:0.10, G:0.13, T:0.33
Consensus pattern (40 bp):
GATAAAGGTGTCAATACTATAAGAAAAATATCAATACTTT
Found at i:21506291 original size:20 final size:20
Alignment explanation
Indices: 21506211--21506291 Score: 54
Period size: 20 Copynumber: 4.0 Consensus size: 20
21506201 GATAAAGGTT
* **
21506211 TCAATACTATAATAAAAATA
1 TCAATACTATAAGAAATGTA
* * * * *
21506231 TCGATACTTTGATAAATGTG
1 TCAATACTATAAGAAATGTA
* * *
21506251 TCAATACTTTGAGAAAAGTA
1 TCAATACTATAAGAAATGTA
*
21506271 TCAATACTATAAGCAATGTA
1 TCAATACTATAAGAAATGTA
21506291 T
1 T
21506292 AGATACTTTA
Statistics
Matches: 47, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.44, C:0.11, G:0.11, T:0.33
Consensus pattern (20 bp):
TCAATACTATAAGAAATGTA
Found at i:21508933 original size:27 final size:27
Alignment explanation
Indices: 21508903--21509108 Score: 241
Period size: 27 Copynumber: 7.6 Consensus size: 27
21508893 CACCGAGAAT
* * *
21508903 CCATAAGGTAAAATGATCGAAATACCC
1 CCATAGGGTAAAATGACCAAAATACCC
* *
21508930 CCATATGGTAAAATAACCAAAATACCC
1 CCATAGGGTAAAATGACCAAAATACCC
* * *
21508957 CTATAAGGTAAAATTACCAAAATACCC
1 CCATAGGGTAAAATGACCAAAATACCC
* *
21508984 CTATAGGGAAAAATGACCAAAATACCC
1 CCATAGGGTAAAATGACCAAAATACCC
* * *
21509011 CTATAGGGTAAAATGATCGAAATACCC
1 CCATAGGGTAAAATGACCAAAATACCC
* *
21509038 TCATAGGGTAAAATGATCAAAATACCC
1 CCATAGGGTAAAATGACCAAAATACCC
* **
21509065 CCATAGGATAAAATGACTGAAATACCC
1 CCATAGGGTAAAATGACCAAAATACCC
*
21509092 CTATAGGGTAAAATGAC
1 CCATAGGGTAAAATGAC
21509109 TGTTATACCC
Statistics
Matches: 156, Mismatches: 23, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 156 1.00
ACGTcount: A:0.45, C:0.21, G:0.14, T:0.20
Consensus pattern (27 bp):
CCATAGGGTAAAATGACCAAAATACCC
Found at i:21508997 original size:54 final size:54
Alignment explanation
Indices: 21508905--21509108 Score: 268
Period size: 54 Copynumber: 3.8 Consensus size: 54
21508895 CCGAGAATCC
* * * *
21508905 ATAAGGTAAAATGATCGAAATACCCCCATATGGTAAAATAACCAAAATACCCCT
1 ATAAGGTAAAATGACCGAAATACCCCTATAGGGTAAAATGACCAAAATACCCCT
* * *
21508959 ATAAGGTAAAATTACCAAAATACCCCTATAGGGAAAAATGACCAAAATACCCCT
1 ATAAGGTAAAATGACCGAAATACCCCTATAGGGTAAAATGACCAAAATACCCCT
* * * *
21509013 ATAGGGTAAAATGATCGAAATA-CCCTCATAGGGTAAAATGATCAAAATACCCCC
1 ATAAGGTAAAATGACCGAAATACCCCT-ATAGGGTAAAATGACCAAAATACCCCT
*
21509067 AT-AGGATAAAATGACTGAAATACCCCTATAGGGTAAAATGAC
1 ATAAGG-TAAAATGACCGAAATACCCCTATAGGGTAAAATGAC
21509109 TGTTATACCC
Statistics
Matches: 129, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
53 6 0.05
54 119 0.92
55 4 0.03
ACGTcount: A:0.46, C:0.20, G:0.14, T:0.20
Consensus pattern (54 bp):
ATAAGGTAAAATGACCGAAATACCCCTATAGGGTAAAATGACCAAAATACCCCT
Found at i:21513089 original size:45 final size:41
Alignment explanation
Indices: 21513015--21513137 Score: 106
Period size: 45 Copynumber: 2.9 Consensus size: 41
21513005 ATATGTGGTC
** *
21513015 TCGTGTAAGACCACATCTGGGACGATGGCATCGATATATGTGAT
1 TCGTGTAAGACCATGTCTAGGAC-ATGGCATCGATAT-T-TGAT
*
21513059 TATGTGTAAGACCATGTCTAGGACATTGGCATCG-TATTTGAT
1 T-CGTGTAAGACCATGTCTAGGACA-TGGCATCGATATTTGAT
* * *
21513101 TCGTGCAAGACCCTGTC-CGAGACAGTGGCATCGATAT
1 TCGTGTAAGACCATGTCTAG-GACA-TGGCATCGATAT
21513138 GAGATAGCAT
Statistics
Matches: 66, Mismatches: 9, Indels: 10
0.78 0.11 0.12
Matches are distributed among these distances:
40 1 0.02
41 25 0.38
42 8 0.12
43 1 0.02
44 5 0.08
45 26 0.39
ACGTcount: A:0.26, C:0.20, G:0.26, T:0.28
Consensus pattern (41 bp):
TCGTGTAAGACCATGTCTAGGACATGGCATCGATATTTGAT
Found at i:21515245 original size:35 final size:35
Alignment explanation
Indices: 21515194--21515264 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
21515184 GAATAGAAGA
*
21515194 TAAGATGAATGGCAAAGCATACACATGTTTTGTAC
1 TAAGATGAATGCCAAAGCATACACATGTTTTGTAC
21515229 TAAGATGAATGCCAAAGCATACACATGTTTTGTAC
1 TAAGATGAATGCCAAAGCATACACATGTTTTGTAC
21515264 T
1 T
21515265 TAAATGGGAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.37, C:0.15, G:0.18, T:0.30
Consensus pattern (35 bp):
TAAGATGAATGCCAAAGCATACACATGTTTTGTAC
Found at i:21520690 original size:27 final size:27
Alignment explanation
Indices: 21520659--21520836 Score: 187
Period size: 27 Copynumber: 6.6 Consensus size: 27
21520649 TAAATTGTAC
*
21520659 AGCACTAAGTGTGTGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
21520686 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
21520712 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
21520740 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* * *
21520768 AGCACTAAGTGTACGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
21520795 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
21520822 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
21520837 GACTCAATAT
Statistics
Matches: 126, Mismatches: 22, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
27 104 0.83
28 22 0.17
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:21520773 original size:82 final size:81
Alignment explanation
Indices: 21520660--21520815 Score: 215
Period size: 82 Copynumber: 1.9 Consensus size: 81
21520650 AAATTGTACA
* * * *
21520660 GCACTAAGTGTGTGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTACGAAATGAATACGTA-GCACTAAGTG
21520724 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
21520741 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTACGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTACGAAATGAATACGTAGCACTAAGTG
*
21520806 TGCGAGTTGA
65 TGCGAATTGA
21520816 TTATATAGCA
Statistics
Matches: 65, Mismatches: 8, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
81 14 0.22
82 50 0.77
83 1 0.02
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTACGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:21520827 original size:82 final size:81
Alignment explanation
Indices: 21520656--21520836 Score: 211
Period size: 82 Copynumber: 2.2 Consensus size: 81
21520646 GATTAAATTG
* * * *
21520656 TACAGCACTAAGTGTGTGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTACGAAATGAATACGATGCACTAA
21520721 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
21520737 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTACGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTACGAAATGAATACGAT-GCACT
* **
21520801 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
21520819 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
21520837 GACTCAATAT
Statistics
Matches: 82, Mismatches: 16, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
81 17 0.21
82 65 0.79
ACGTcount: A:0.28, C:0.15, G:0.27, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTACGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:21527964 original size:27 final size:27
Alignment explanation
Indices: 21527933--21528110 Score: 196
Period size: 27 Copynumber: 6.6 Consensus size: 27
21527923 TAAATTGTAC
21527933 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
21527960 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
21527986 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
21528014 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
21528042 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
21528069 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
* *
21528096 AGTACTGAGTGTGCG
1 AGCACTAAGTGTGCG
21528111 GACTCAATAT
Statistics
Matches: 128, Mismatches: 20, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
27 105 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:21528047 original size:82 final size:81
Alignment explanation
Indices: 21527934--21528089 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
21527924 AAATTGTACA
* *
21527934 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
21527998 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
21528015 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
21528080 TGCGAGTTGA
65 TGCGAATTGA
21528090 TTATATAGTA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:21546768 original size:20 final size:20
Alignment explanation
Indices: 21546693--21546766 Score: 98
Period size: 20 Copynumber: 3.8 Consensus size: 20
21546683 CAAAAATTAC
21546693 AAAAAATTCAAAATAATTTT
1 AAAAAATTCAAAATAATTTT
*
21546713 CAAAAATTCAAAATAATTTT
1 AAAAAATTCAAAATAATTTT
**
21546733 -AAATTTTCAAAAT-ATTTAT
1 AAAAAATTCAAAATAATTT-T
21546752 AAAAAATTCAAAATA
1 AAAAAATTCAAAATA
21546767 TTGTATTTTT
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
18 4 0.09
19 12 0.26
20 30 0.65
ACGTcount: A:0.58, C:0.07, G:0.00, T:0.35
Consensus pattern (20 bp):
AAAAAATTCAAAATAATTTT
Found at i:21546773 original size:25 final size:25
Alignment explanation
Indices: 21546745--21546793 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
21546735 ATTTTCAAAA
21546745 TATTTATAAAAAATTCA-AAATATTG
1 TATTTATAAAAAATT-ATAAATATTG
*
21546770 TATTTTTAAAAAATTATAAATATT
1 TATTTATAAAAAATTATAAATATT
21546794 ACAAAAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 1 0.05
25 21 0.95
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (25 bp):
TATTTATAAAAAATTATAAATATTG
Found at i:21549431 original size:42 final size:42
Alignment explanation
Indices: 21549385--21549466 Score: 164
Period size: 42 Copynumber: 2.0 Consensus size: 42
21549375 AATAAAAGAA
21549385 AGGAAAAAAGGAACAAGCATACAAATTATAGAATGATTTACT
1 AGGAAAAAAGGAACAAGCATACAAATTATAGAATGATTTACT
21549427 AGGAAAAAAGGAACAAGCATACAAATTATAGAATGATTTA
1 AGGAAAAAAGGAACAAGCATACAAATTATAGAATGATTTA
21549467 TTAATAGGCA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.54, C:0.09, G:0.17, T:0.21
Consensus pattern (42 bp):
AGGAAAAAAGGAACAAGCATACAAATTATAGAATGATTTACT
Found at i:21555379 original size:3 final size:3
Alignment explanation
Indices: 21555373--21555424 Score: 104
Period size: 3 Copynumber: 17.3 Consensus size: 3
21555363 AGCAGGACTT
21555373 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
21555421 TTA T
1 TTA T
21555425 CATCATCATC
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:21559593 original size:30 final size:32
Alignment explanation
Indices: 21559556--21559636 Score: 123
Period size: 30 Copynumber: 2.6 Consensus size: 32
21559546 AAATATATAT
21559556 TTTTTTTATTTTTAAAAATA-TTTTAAAATAC
1 TTTTTTTATTTTTAAAAATATTTTTAAAATAC
21559587 -TTTTTTATTTTT-AAAATATTTTTAAAATAC
1 TTTTTTTATTTTTAAAAATATTTTTAAAATAC
21559617 TTTTTTTAATTTTCTAAAAA
1 TTTTTTT-ATTTT-TAAAAA
21559637 AAAATTTGGT
Statistics
Matches: 45, Mismatches: 0, Indels: 7
0.87 0.00 0.13
Matches are distributed among these distances:
29 6 0.13
30 23 0.51
31 6 0.13
32 5 0.11
33 1 0.02
34 4 0.09
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (32 bp):
TTTTTTTATTTTTAAAAATATTTTTAAAATAC
Found at i:21577109 original size:23 final size:24
Alignment explanation
Indices: 21577065--21577108 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
21577055 AATTGATAAT
*
21577065 TTTTATATTATTTTTAAATTTTAA
1 TTTTATATTATTTTCAAATTTTAA
21577089 TTTTA-ATTA-TTTCAAATTTT
1 TTTTATATTATTTTCAAATTTT
21577109 TTTGCATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 10 0.53
23 4 0.21
24 5 0.26
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (24 bp):
TTTTATATTATTTTCAAATTTTAA
Found at i:21578283 original size:18 final size:18
Alignment explanation
Indices: 21578260--21578294 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
21578250 AACATGATTT
21578260 AAATAA-ATAATCAAATAG
1 AAATAAGAT-ATCAAATAG
21578278 AAATAAGATATCAAATA
1 AAATAAGATATCAAATA
21578295 CAATCAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.66, C:0.06, G:0.06, T:0.23
Consensus pattern (18 bp):
AAATAAGATATCAAATAG
Found at i:21585579 original size:12 final size:12
Alignment explanation
Indices: 21585564--21585607 Score: 74
Period size: 12 Copynumber: 3.8 Consensus size: 12
21585554 AAACCGAGCC
21585564 ATAAATATTTTT
1 ATAAATATTTTT
21585576 ATAAATA--TTT
1 ATAAATATTTTT
21585586 ATAAATATTTTT
1 ATAAATATTTTT
21585598 ATAAATATTT
1 ATAAATATTT
21585608 ACGGAGTGTC
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
10 10 0.33
12 20 0.67
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (12 bp):
ATAAATATTTTT
Found at i:21585588 original size:10 final size:10
Alignment explanation
Indices: 21585573--21585608 Score: 54
Period size: 10 Copynumber: 3.4 Consensus size: 10
21585563 CATAAATATT
21585573 TTTATAAATA
1 TTTATAAATA
21585583 TTTATAAATA
1 TTTATAAATA
21585593 TTTTTATAAATA
1 --TTTATAAATA
21585605 TTTA
1 TTTA
21585609 CGGAGTGTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
10 14 0.58
12 10 0.42
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (10 bp):
TTTATAAATA
Found at i:21585592 original size:22 final size:22
Alignment explanation
Indices: 21585564--21585608 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
21585554 AAACCGAGCC
21585564 ATAAATATTTTTATAAATATTT
1 ATAAATATTTTTATAAATATTT
21585586 ATAAATATTTTTATAAATATTT
1 ATAAATATTTTTATAAATATTT
21585608 A
1 A
21585609 CGGAGTGTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
ATAAATATTTTTATAAATATTT
Found at i:21587007 original size:24 final size:24
Alignment explanation
Indices: 21586980--21587045 Score: 78
Period size: 24 Copynumber: 2.7 Consensus size: 24
21586970 CTTGCTTGAA
* * *
21586980 CTTCCCGATATTGGCTTATATGAG
1 CTTCCCGTTATTGGCTCATAGGAG
* *
21587004 CTTCCCGTTAATGGCTCATCGGAG
1 CTTCCCGTTATTGGCTCATAGGAG
21587028 CTTCCCGTTATATGGCTC
1 CTTCCCGTTAT-TGGCTC
21587046 GAAAAAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
24 29 0.83
25 6 0.17
ACGTcount: A:0.17, C:0.27, G:0.21, T:0.35
Consensus pattern (24 bp):
CTTCCCGTTATTGGCTCATAGGAG
Found at i:21589117 original size:16 final size:16
Alignment explanation
Indices: 21589096--21589132 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
21589086 AAATTGGGCC
21589096 ATGAATGCCATATGAT
1 ATGAATGCCATATGAT
21589112 ATGAATGCCATATGAT
1 ATGAATGCCATATGAT
21589128 ATGAA
1 ATGAA
21589133 ATGTTTTCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.41, C:0.11, G:0.19, T:0.30
Consensus pattern (16 bp):
ATGAATGCCATATGAT
Found at i:21594467 original size:37 final size:35
Alignment explanation
Indices: 21594398--21594475 Score: 88
Period size: 37 Copynumber: 2.2 Consensus size: 35
21594388 GTGACACAAG
*
21594398 TTTAGCTCGGACAAGTAACCTGATGTCATTATAAATA
1 TTTAGCCCGGACAAGTAACCTGATGTCATTAT--ATA
*
21594435 TTTAGCCCGGACAAGTAAGCTGACATG-C-TTATATA
1 TTTAGCCCGGACAAGTAACCTG--ATGTCATTATATA
21594470 TTTAGC
1 TTTAGC
21594476 TCGTACGACC
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
35 9 0.24
37 24 0.65
38 1 0.03
39 3 0.08
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (35 bp):
TTTAGCCCGGACAAGTAACCTGATGTCATTATATA
Found at i:21600179 original size:12 final size:12
Alignment explanation
Indices: 21600162--21600215 Score: 71
Period size: 11 Copynumber: 4.8 Consensus size: 12
21600152 AACTAATCCT
21600162 CTCTCAAATTTC
1 CTCTCAAATTTC
21600174 CTCTC-AATTTC
1 CTCTCAAATTTC
21600185 CTCTCAAA-TTC
1 CTCTCAAATTTC
21600196 CT-TCAAAATTT-
1 CTCTC-AAATTTC
21600207 CTCTCAAAT
1 CTCTCAAAT
21600216 CCATATTTAA
Statistics
Matches: 38, Mismatches: 0, Indels: 9
0.81 0.00 0.19
Matches are distributed among these distances:
10 2 0.05
11 25 0.66
12 11 0.29
ACGTcount: A:0.28, C:0.31, G:0.00, T:0.41
Consensus pattern (12 bp):
CTCTCAAATTTC
Found at i:21603961 original size:124 final size:124
Alignment explanation
Indices: 21603663--21604037 Score: 608
Period size: 124 Copynumber: 3.0 Consensus size: 124
21603653 CCCAAACATG
* **
21603663 CTACTGTAGCAAAAGCGCGTCCACGCGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCTTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCAGC
*
21603728 TAGAAGCGATTTTATACTATTTGCTTAGAAACGTC-AAAAAAATTATTTCTTCCATGAC
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAATTATTTCTTCCATGAC
* *
21603786 CTACTGTAGCAAAAGCGTGTCCACGAGGGTGCGATTTCACAAATTCTTCTCAAATAGCATCCAGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCAGC
* *
21603851 TAGAAGCGATTTTATACTATTTCCTCAGAAACGTCAAAAAAAATTATTTTTTCCATGAC
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAATTATTTCTTCCATGAC
*
21603910 CTACTGTAGCAAAAGCCCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCAGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCAGC
* *** *
21603975 TAGAAGCGATTTTATACTATTTGATCAGAAACGTCAACTCGAAATTATTTCTTCCAGGAC
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAA-AAAAAATTATTTCTTCCATGAC
21604035 CTA
1 CTA
21604038 AAAACCCTAA
Statistics
Matches: 232, Mismatches: 18, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
123 93 0.40
124 119 0.51
125 20 0.09
ACGTcount: A:0.32, C:0.23, G:0.16, T:0.29
Consensus pattern (124 bp):
CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCAGC
TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAATTATTTCTTCCATGAC
Found at i:21604983 original size:5 final size:5
Alignment explanation
Indices: 21604973--21604998 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
21604963 GTGAAAGTGA
21604973 ATTTT ATTTT ATTTT ATTTT ATTTT A
1 ATTTT ATTTT ATTTT ATTTT ATTTT A
21604999 GCTTCCGGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (5 bp):
ATTTT
Found at i:21611609 original size:16 final size:16
Alignment explanation
Indices: 21611552--21611609 Score: 55
Period size: 16 Copynumber: 3.6 Consensus size: 16
21611542 ATAAAAAATA
*
21611552 ATTTTTTATATA-TAT
1 ATTTTTTAAATACTAT
21611567 ATTTTTATAAATACTAT
1 ATTTTT-TAAATACTAT
* * **
21611584 ATATTATAAATTTTAT
1 ATTTTTTAAATACTAT
21611600 ATTTTTTAAA
1 ATTTTTTAAA
21611610 CATAATCAAC
Statistics
Matches: 34, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
15 6 0.18
16 21 0.62
17 7 0.21
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.59
Consensus pattern (16 bp):
ATTTTTTAAATACTAT
Found at i:21616297 original size:11 final size:11
Alignment explanation
Indices: 21616258--21616312 Score: 56
Period size: 11 Copynumber: 4.8 Consensus size: 11
21616248 TTTAAACGTT
21616258 TTTTCTTTTTCC
1 TTTTC-TTTTCC
* **
21616270 TCTTCCCTTCTC
1 TTTTCTTTTC-C
21616282 TTTTCTTTTCC
1 TTTTCTTTTCC
21616293 TTTTCTTTTCC
1 TTTTCTTTTCC
*
21616304 TTTTGTTTT
1 TTTTCTTTT
21616313 TTTATATATC
Statistics
Matches: 35, Mismatches: 7, Indels: 3
0.78 0.16 0.07
Matches are distributed among these distances:
11 23 0.66
12 12 0.34
ACGTcount: A:0.00, C:0.27, G:0.02, T:0.71
Consensus pattern (11 bp):
TTTTCTTTTCC
Found at i:21616299 original size:16 final size:17
Alignment explanation
Indices: 21616260--21616307 Score: 55
Period size: 16 Copynumber: 2.9 Consensus size: 17
21616250 TAAACGTTTT
*
21616260 TTCT-TTTTCCTCTTCCC
1 TTCTCTTTTCCT-TTTCC
21616277 TTCTCTTTT-CTTTTCC
1 TTCTCTTTTCCTTTTCC
*
21616293 TTTTCTTTTCCTTTT
1 TTCTCTTTTCCTTTT
21616308 GTTTTTTTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
16 12 0.44
17 11 0.41
18 4 0.15
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (17 bp):
TTCTCTTTTCCTTTTCC
Found at i:21619685 original size:15 final size:15
Alignment explanation
Indices: 21619665--21619696 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
21619655 TTCAGTGCTG
21619665 TCAGAAACAATGGTT
1 TCAGAAACAATGGTT
21619680 TCAGAAACAATGGTT
1 TCAGAAACAATGGTT
21619695 TC
1 TC
21619697 GGGGCCACCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.38, C:0.16, G:0.19, T:0.28
Consensus pattern (15 bp):
TCAGAAACAATGGTT
Found at i:21621667 original size:19 final size:21
Alignment explanation
Indices: 21621612--21621667 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 21
21621602 ATCTTTTCTT
*
21621612 TTTTTTTCATTCTTCTTCCCA
1 TTTTTTTCATCCTTCTTCCCA
* *
21621633 TTTCTTTCCAACCTTC-TCCC-
1 TTT-TTTTCATCCTTCTTCCCA
*
21621653 TTTTTTTCATGCTTC
1 TTTTTTTCATCCTTC
21621668 CATCCTGACC
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
19 9 0.32
20 3 0.11
21 7 0.25
22 9 0.32
ACGTcount: A:0.09, C:0.32, G:0.02, T:0.57
Consensus pattern (21 bp):
TTTTTTTCATCCTTCTTCCCA
Found at i:21622057 original size:15 final size:15
Alignment explanation
Indices: 21622032--21622071 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
21622022 TTTTGATTGT
21622032 TTCTT-TTGTTCTCG
1 TTCTTGTTGTTCTCG
*
21622046 TTCTTGTTGTTCTTG
1 TTCTTGTTGTTCTCG
21622061 TTCTTGTTGTT
1 TTCTTGTTGTT
21622072 GTGTCTGTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 5 0.21
15 19 0.79
ACGTcount: A:0.00, C:0.15, G:0.17, T:0.68
Consensus pattern (15 bp):
TTCTTGTTGTTCTCG
Found at i:21623482 original size:5 final size:5
Alignment explanation
Indices: 21623467--21623500 Score: 59
Period size: 5 Copynumber: 6.6 Consensus size: 5
21623457 ACAAAAACAC
21623467 TTTCTT TTTCT TTTCT TTTCT TTTCT TTTCT TTT
1 TTTC-T TTTCT TTTCT TTTCT TTTCT TTTCT TTT
21623501 TTGGGTGATT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 24 0.86
6 4 0.14
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTCT
Found at i:21623604 original size:21 final size:21
Alignment explanation
Indices: 21623564--21623604 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
21623554 ATAAAGTAGA
*
21623564 TTATATATTATTTTTATAGTG
1 TTATATATTATATTTATAGTG
21623585 TTATATATTATGATTT-TAGT
1 TTATATATTAT-ATTTATAGT
21623605 ATATTTATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.29, C:0.00, G:0.10, T:0.61
Consensus pattern (21 bp):
TTATATATTATATTTATAGTG
Found at i:21623647 original size:17 final size:18
Alignment explanation
Indices: 21623622--21623667 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
21623612 TATAAGAATA
*
21623622 ATTATATTA-AGAATTTT
1 ATTAAATTATAGAATTTT
* *
21623639 ATTAAATTATATATTTTT
1 ATTAAATTATAGAATTTT
21623657 ATTAAATTATA
1 ATTAAATTATA
21623668 TTTAATAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
17 8 0.32
18 17 0.68
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.54
Consensus pattern (18 bp):
ATTAAATTATAGAATTTT
Found at i:21623915 original size:45 final size:44
Alignment explanation
Indices: 21623826--21623916 Score: 139
Period size: 44 Copynumber: 2.0 Consensus size: 44
21623816 ATTACATCAT
21623826 CATTCCATTCAACCAAACACAAGAATACTATTACAGTTCTATTC
1 CATTCCATTCAACCAAACACAAGAATACTATTACAGTTCTATTC
* *
21623870 CATTCCATTCAACCAAACA-ATTGAATTACTATTACTGTTCTATTC
1 CATTCCATTCAACCAAACACA-AGAA-TACTATTACAGTTCTATTC
21623915 CA
1 CA
21623917 ATACAGCTCT
Statistics
Matches: 43, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
43 1 0.02
44 22 0.51
45 20 0.47
ACGTcount: A:0.36, C:0.26, G:0.04, T:0.33
Consensus pattern (44 bp):
CATTCCATTCAACCAAACACAAGAATACTATTACAGTTCTATTC
Found at i:21623929 original size:16 final size:16
Alignment explanation
Indices: 21623908--21623954 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
21623898 CTATTACTGT
21623908 TCTATTCCAATACAGC
1 TCTATTCCAATACAGC
*
21623924 TCTATT-CAATTATAGC
1 TCTATTCCAA-TACAGC
* *
21623940 TTTATTCCATTACAG
1 TCTATTCCAATACAG
21623955 TGAACCAAAC
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
15 3 0.12
16 20 0.80
17 2 0.08
ACGTcount: A:0.30, C:0.23, G:0.06, T:0.40
Consensus pattern (16 bp):
TCTATTCCAATACAGC
Found at i:21624979 original size:35 final size:35
Alignment explanation
Indices: 21624939--21625008 Score: 99
Period size: 35 Copynumber: 2.0 Consensus size: 35
21624929 GGTGTATGCT
21624939 TTTAAATGACCAAAATTGGTAT-G-TGTTAATGTATC
1 TTTAAATGACCAAAA-TGGTATGGTTGTT-ATGTATC
*
21624974 TTTAAATGGCCAAAATGGTATGGTTGTTATGTATC
1 TTTAAATGACCAAAATGGTATGGTTGTTATGTATC
21625009 AATTATGTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
34 6 0.19
35 22 0.69
36 4 0.12
ACGTcount: A:0.31, C:0.09, G:0.20, T:0.40
Consensus pattern (35 bp):
TTTAAATGACCAAAATGGTATGGTTGTTATGTATC
Found at i:21626102 original size:20 final size:21
Alignment explanation
Indices: 21626069--21626114 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
21626059 TAGGGCGGCT
* * *
21626069 AAGGCTGAATAATAATGACTA
1 AAGGTTGAATAATAATAAATA
21626090 AAGGTTGAA-AATAATAAATA
1 AAGGTTGAATAATAATAAATA
21626110 AAGGT
1 AAGGT
21626115 GATATTTATA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 14 0.64
21 8 0.36
ACGTcount: A:0.52, C:0.04, G:0.20, T:0.24
Consensus pattern (21 bp):
AAGGTTGAATAATAATAAATA
Found at i:21630641 original size:40 final size:40
Alignment explanation
Indices: 21630585--21630803 Score: 224
Period size: 40 Copynumber: 5.5 Consensus size: 40
21630575 TTGATTCAAT
* * * *
21630585 GTACCAGAGTATAAACAGGGGCACGTAAGTGCATTTAGGG
1 GTACCAAAGTACAAATAGGGGCACGTAAGTGCAATTAGGG
* * * *
21630625 GTACCGAAGTACAAACAGAGGCACGTATGTGCAATTA-GG
1 GTACCAAAGTACAAATAGGGGCACGTAAGTGCAATTAGGG
* * * *
21630664 GTACCAAAGTACAAATAGAGGAACGTGAGTGCAATCAGGG
1 GTACCAAAGTACAAATAGGGGCACGTAAGTGCAATTAGGG
* ** *
21630704 GTACAAAAGTACAAATAGGCACACGTAAGTGCATTTAGGG
1 GTACCAAAGTACAAATAGGGGCACGTAAGTGCAATTAGGG
* ** * * *
21630744 GTACCGAAGTATGAATAGGGGCACATAAGGGCAATTAAGG
1 GTACCAAAGTACAAATAGGGGCACGTAAGTGCAATTAGGG
*
21630784 GTACTAAAGTACAAATAGGG
1 GTACCAAAGTACAAATAGGG
21630804 ACACATAAAT
Statistics
Matches: 144, Mismatches: 34, Indels: 2
0.80 0.19 0.01
Matches are distributed among these distances:
39 33 0.23
40 111 0.77
ACGTcount: A:0.38, C:0.15, G:0.29, T:0.18
Consensus pattern (40 bp):
GTACCAAAGTACAAATAGGGGCACGTAAGTGCAATTAGGG
Found at i:21642536 original size:15 final size:17
Alignment explanation
Indices: 21642498--21642538 Score: 52
Period size: 15 Copynumber: 2.6 Consensus size: 17
21642488 TACTTTTAAG
21642498 CATAT-ATCACATTACA
1 CATATAATCACATTACA
21642514 CATATAATCACA-TA-A
1 CATATAATCACATTACA
*
21642529 CATTTAATCA
1 CATATAATCA
21642539 TATACCACAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
15 10 0.43
16 7 0.30
17 6 0.26
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (17 bp):
CATATAATCACATTACA
Found at i:21642634 original size:41 final size:39
Alignment explanation
Indices: 21642495--21642621 Score: 182
Period size: 39 Copynumber: 3.3 Consensus size: 39
21642485 ATTTACTTTT
* * *
21642495 AAGCATATATCACATTACACATATAATCACATAACATTT
1 AAGCATATATCACAATACTCATATAATCACATAACATTC
* * * **
21642534 AATCATATACCACAATACTCATATAATTACATAATGTTC
1 AAGCATATATCACAATACTCATATAATCACATAACATTC
21642573 AAGCATATATCACAATACTCATATAATCACATAACATTC
1 AAGCATATATCACAATACTCATATAATCACATAACATTC
21642612 AAGCATATAT
1 AAGCATATAT
21642622 ATCGCAATAC
Statistics
Matches: 75, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
39 75 1.00
ACGTcount: A:0.46, C:0.20, G:0.03, T:0.31
Consensus pattern (39 bp):
AAGCATATATCACAATACTCATATAATCACATAACATTC
Found at i:21642702 original size:16 final size:15
Alignment explanation
Indices: 21642667--21642709 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
21642657 ACATAATGGT
* *
21642667 CACATGTCATATAAA
1 CACATATCATAAAAA
21642682 CACATATCATAAAACA
1 CACATATCATAAAA-A
21642698 CACATATTCATA
1 CACATA-TCATA
21642710 GTTTAAGATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 12 0.50
16 7 0.29
17 5 0.21
ACGTcount: A:0.49, C:0.23, G:0.02, T:0.26
Consensus pattern (15 bp):
CACATATCATAAAAA
Found at i:21654779 original size:31 final size:31
Alignment explanation
Indices: 21654741--21654804 Score: 110
Period size: 31 Copynumber: 2.1 Consensus size: 31
21654731 TGATCATCTG
*
21654741 AGGGTGGTCTTACAGATACTTCGTGAAAAGT
1 AGGGTGGTCCTACAGATACTTCGTGAAAAGT
*
21654772 AGGGTGGTCCTGCAGATACTTCGTGAAAAGT
1 AGGGTGGTCCTACAGATACTTCGTGAAAAGT
21654803 AG
1 AG
21654805 TTTTTCGTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.28, C:0.14, G:0.31, T:0.27
Consensus pattern (31 bp):
AGGGTGGTCCTACAGATACTTCGTGAAAAGT
Found at i:21664498 original size:23 final size:20
Alignment explanation
Indices: 21664471--21664524 Score: 63
Period size: 23 Copynumber: 2.5 Consensus size: 20
21664461 TTGACGAAAA
*
21664471 TTAATTTTTTCCATCAAGTTAT
1 TTAATTTTTTCC-TCAAATT-T
*
21664493 GTTAATTTATTCCTCAAATTT
1 -TTAATTTTTTCCTCAAATTT
21664514 TTAATTTTTTC
1 TTAATTTTTTC
21664525 TTAACTATGT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 10 0.36
21 1 0.04
22 6 0.21
23 11 0.39
ACGTcount: A:0.26, C:0.13, G:0.04, T:0.57
Consensus pattern (20 bp):
TTAATTTTTTCCTCAAATTT
Found at i:21668055 original size:16 final size:16
Alignment explanation
Indices: 21668034--21668066 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
21668024 CTCAGTGGAG
21668034 TTATTTTGACTATATC
1 TTATTTTGACTATATC
21668050 TTATTTTGACTATATC
1 TTATTTTGACTATATC
21668066 T
1 T
21668067 CAATTAGCGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.24, C:0.12, G:0.06, T:0.58
Consensus pattern (16 bp):
TTATTTTGACTATATC
Found at i:21677715 original size:113 final size:113
Alignment explanation
Indices: 21677517--21677744 Score: 384
Period size: 113 Copynumber: 2.0 Consensus size: 113
21677507 GATCACAAGT
21677517 TTCTGTTTACAAAATTTTAAGAGTCTCATGATCTTTAAAACCATTTCTCCAATAGCCTTTTAACT
1 TTCTGTTTACAAAATTTTAAGAGTCTCATGATCTTTAAAACCATTTCTCCAATAGCCTTTTAACT
* ***
21677582 TCTGTACCATGTTGTCAGACAACAAAACTTACTCAATAAAGTTTTGAG
66 TCTATACCACACTGTCAGACAACAAAACTTACTCAATAAAGTTTTGAG
**
21677630 TTCTGTTTATGAAATTTTAAGAGTCTCATGATCTTTAAAACCATTTCTCCAATAGCCTTTTAACT
1 TTCTGTTTACAAAATTTTAAGAGTCTCATGATCTTTAAAACCATTTCTCCAATAGCCTTTTAACT
* *
21677695 TCTATACCACACTGTGAGACAACAAAACTTACTCAGTAAAGTTTTGAG
66 TCTATACCACACTGTCAGACAACAAAACTTACTCAATAAAGTTTTGAG
21677743 TT
1 TT
21677745 AAAACTTATG
Statistics
Matches: 107, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
113 107 1.00
ACGTcount: A:0.32, C:0.19, G:0.11, T:0.37
Consensus pattern (113 bp):
TTCTGTTTACAAAATTTTAAGAGTCTCATGATCTTTAAAACCATTTCTCCAATAGCCTTTTAACT
TCTATACCACACTGTCAGACAACAAAACTTACTCAATAAAGTTTTGAG
Found at i:21681575 original size:21 final size:22
Alignment explanation
Indices: 21681546--21681591 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
21681536 TTTATCCAAC
*
21681546 GTTACGTTTTGAG-TTTTTAGG
1 GTTACGTTTTAAGATTTTTAGG
*
21681567 GTTAGGTTTTAAGATTTTTAGG
1 GTTACGTTTTAAGATTTTTAGG
21681589 GTT
1 GTT
21681592 TTAAAGAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 11 0.50
22 11 0.50
ACGTcount: A:0.17, C:0.02, G:0.28, T:0.52
Consensus pattern (22 bp):
GTTACGTTTTAAGATTTTTAGG
Found at i:21684360 original size:13 final size:13
Alignment explanation
Indices: 21684342--21684372 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
21684332 GCCATGTATG
21684342 GTGCAGTAAGGTA
1 GTGCAGTAAGGTA
21684355 GTGCAGTAAGGTA
1 GTGCAGTAAGGTA
21684368 GTGCA
1 GTGCA
21684373 AGAAATTAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.29, C:0.10, G:0.39, T:0.23
Consensus pattern (13 bp):
GTGCAGTAAGGTA
Found at i:21684971 original size:19 final size:18
Alignment explanation
Indices: 21684947--21685024 Score: 56
Period size: 18 Copynumber: 4.3 Consensus size: 18
21684937 ATCTAACATT
21684947 TTGTTAGTCAAATTATTAA
1 TTGTTA-TCAAATTATTAA
*
21684966 TTG-T-T-AATTGTATTAA
1 TTGTTATCAAAT-TATTAA
* *
21684982 TTGTTACTAAAATTATCAAA
1 TTGTTA-TCAAATTAT-TAA
*
21685002 TT-ATATCAAATTATTAA
1 TTGTTATCAAATTATTAA
21685019 TTGTTA
1 TTGTTA
21685025 GTACCAGTCA
Statistics
Matches: 45, Mismatches: 7, Indels: 15
0.67 0.10 0.22
Matches are distributed among these distances:
15 3 0.07
16 10 0.22
17 5 0.11
18 11 0.24
19 9 0.20
20 7 0.16
ACGTcount: A:0.38, C:0.05, G:0.08, T:0.49
Consensus pattern (18 bp):
TTGTTATCAAATTATTAA
Found at i:21684986 original size:35 final size:35
Alignment explanation
Indices: 21684947--21685138 Score: 95
Period size: 35 Copynumber: 5.2 Consensus size: 35
21684937 ATCTAACATT
*
21684947 TTGTTAGTCAAATTATTAATTGTTAATTGTATTAA
1 TTGTTAGTCAAATTATTAATTGTTAAATGTATTAA
* * * *
21684982 TTGTTACTAAAATTATCAAATTATATCAAAT-TATTAA
1 TTGTTAGTCAAATTAT-TAATTGT-T-AAATGTATTAA
* * * ** *
21685019 TTGTTAGTACCAGTCAAAATATT--TTGTAAAATCTAACATT
1 TTG-T--T---AGTCAAATTATTAATTGTTAAATGTATTA-A
*
21685059 TTGTTAGTCAAATTATTAATTGTTAATTGTATTAA
1 TTGTTAGTCAAATTATTAATTGTTAAATGTATTAA
* * * *
21685094 TTGTTACTAAAATTATCAAATTATATCAAAT-TATTAA
1 TTGTTAGTCAAATTAT-TAATTGT-T-AAATGTATTAA
21685131 TTGTTAGT
1 TTGTTAGT
21685139 ACCAGTCAAA
Statistics
Matches: 114, Mismatches: 27, Indels: 30
0.67 0.16 0.18
Matches are distributed among these distances:
34 11 0.10
35 28 0.25
36 20 0.18
37 25 0.22
38 11 0.10
39 4 0.04
40 7 0.06
43 8 0.07
ACGTcount: A:0.39, C:0.07, G:0.08, T:0.46
Consensus pattern (35 bp):
TTGTTAGTCAAATTATTAATTGTTAAATGTATTAA
Found at i:21685014 original size:53 final size:53
Alignment explanation
Indices: 21684954--21685136 Score: 199
Period size: 53 Copynumber: 3.3 Consensus size: 53
21684944 ATTTTGTTAG
21684954 TCAAATTATTAATTGTTAATTGTATTAATTGTTACTAAAATTATCAAATTATA
1 TCAAATTATTAATTGTTAATTGTATTAATTGTTACTAAAATTATCAAATTATA
** * ** * ** *
21685007 TCAAATTATTAATTGTTAGTACCAGTCA-AAATAT-TTTGTAAAATCTAACATTTTGTTA
1 TCAAATTATTAATTGTTA--A-TTGT-ATTAAT-TGTTACTAAAAT-TATCAAATT-ATA
21685065 GTCAAATTATTAATTGTTAATTGTATTAATTGTTACTAAAATTATCAAATTATA
1 -TCAAATTATTAATTGTTAATTGTATTAATTGTTACTAAAATTATCAAATTATA
21685119 TCAAATTATTAATTGTTA
1 TCAAATTATTAATTGTTA
21685137 GTACCAGTCA
Statistics
Matches: 102, Mismatches: 18, Indels: 20
0.73 0.13 0.14
Matches are distributed among these distances:
53 36 0.35
54 2 0.02
55 9 0.09
56 26 0.25
57 9 0.09
58 2 0.02
59 18 0.18
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.46
Consensus pattern (53 bp):
TCAAATTATTAATTGTTAATTGTATTAATTGTTACTAAAATTATCAAATTATA
Found at i:21685022 original size:37 final size:38
Alignment explanation
Indices: 21684976--21685136 Score: 100
Period size: 37 Copynumber: 4.3 Consensus size: 38
21684966 TTGTTAATTG
21684976 TATTAATTGTTACTAAAATTATCAAATTATATCAAAT-
1 TATTAATTGTTACTAAAATTATCAAATTATATCAAATC
* * * * * * * *
21685013 TATTAATTGTTAGTACCAGTCA-AAATATTTTGTAAAATC
1 TATTAATTGTTACTA-AAATTATCAA-ATTATATCAAATC
** * * * * * * *
21685052 TAACATTTTGTTAGTCAAATTAT-TAATTGT-T-AATTG
1 TATTA-ATTGTTACTAAAATTATCAAATTATATCAAATC
21685088 TATTAATTGTTACTAAAATTATCAAATTATATCAAAT-
1 TATTAATTGTTACTAAAATTATCAAATTATATCAAATC
21685125 TATTAATTGTTA
1 TATTAATTGTTA
21685137 GTACCAGTCA
Statistics
Matches: 89, Mismatches: 27, Indels: 16
0.67 0.20 0.12
Matches are distributed among these distances:
35 14 0.16
36 11 0.12
37 30 0.34
38 19 0.21
39 7 0.08
40 8 0.09
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.45
Consensus pattern (38 bp):
TATTAATTGTTACTAAAATTATCAAATTATATCAAATC
Found at i:21685083 original size:19 final size:18
Alignment explanation
Indices: 21685059--21685136 Score: 56
Period size: 18 Copynumber: 4.3 Consensus size: 18
21685049 ATCTAACATT
21685059 TTGTTAGTCAAATTATTAA
1 TTGTTA-TCAAATTATTAA
*
21685078 TTG-T-T-AATTGTATTAA
1 TTGTTATCAAAT-TATTAA
* *
21685094 TTGTTACTAAAATTATCAAA
1 TTGTTA-TCAAATTAT-TAA
*
21685114 TT-ATATCAAATTATTAA
1 TTGTTATCAAATTATTAA
21685131 TTGTTA
1 TTGTTA
21685137 GTACCAGTCA
Statistics
Matches: 45, Mismatches: 7, Indels: 15
0.67 0.10 0.22
Matches are distributed among these distances:
15 3 0.07
16 10 0.22
17 5 0.11
18 11 0.24
19 9 0.20
20 7 0.16
ACGTcount: A:0.38, C:0.05, G:0.08, T:0.49
Consensus pattern (18 bp):
TTGTTATCAAATTATTAA
Found at i:21685110 original size:112 final size:112
Alignment explanation
Indices: 21684913--21685238 Score: 589
Period size: 112 Copynumber: 2.9 Consensus size: 112
21684903 ATATTTTTTT
* *
21684913 GTACCAATCAAAACATTTTGTAAAATCTAACATTTTGTTAGTCAAATTATTAATTGTTAATTGTA
1 GTACCAGTCAAAATATTTTGTAAAATCTAACATTTTGTTAGTCAAATTATTAATTGTTAATTGTA
21684978 TTAATTGTTACTAAAATTATCAAATTATATCAAATTATTAATTGTTA
66 TTAATTGTTACTAAAATTATCAAATTATATCAAATTATTAATTGTTA
21685025 GTACCAGTCAAAATATTTTGTAAAATCTAACATTTTGTTAGTCAAATTATTAATTGTTAATTGTA
1 GTACCAGTCAAAATATTTTGTAAAATCTAACATTTTGTTAGTCAAATTATTAATTGTTAATTGTA
21685090 TTAATTGTTACTAAAATTATCAAATTATATCAAATTATTAATTGTTA
66 TTAATTGTTACTAAAATTATCAAATTATATCAAATTATTAATTGTTA
*
21685137 GTACCAGTCAAAATATTTTGTAAAATCTAACATTTTGTTAGTCAAATTAATAATTGTTAATTGTA
1 GTACCAGTCAAAATATTTTGTAAAATCTAACATTTTGTTAGTCAAATTATTAATTGTTAATTGTA
* * * *
21685202 TTAATTTTTATTAAATTTATCAAATTATATCATATTA
66 TTAATTGTTACTAAAATTATCAAATTATATCAAATTA
21685239 GGGTTAAGGT
Statistics
Matches: 207, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
112 207 1.00
ACGTcount: A:0.40, C:0.08, G:0.07, T:0.45
Consensus pattern (112 bp):
GTACCAGTCAAAATATTTTGTAAAATCTAACATTTTGTTAGTCAAATTATTAATTGTTAATTGTA
TTAATTGTTACTAAAATTATCAAATTATATCAAATTATTAATTGTTA
Found at i:21685296 original size:22 final size:22
Alignment explanation
Indices: 21685266--21685317 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
21685256 TTTGTTAAGA
*
21685266 TTAGAGTTTTTAAGTTAAGGGT
1 TTAGAGTTTTTAAGTTAAAGGT
*
21685288 TTAGGGTTTTTAAGTTAAAGG-
1 TTAGAGTTTTTAAGTTAAAGGT
21685309 TTAGAGTTT
1 TTAGAGTTT
21685318 AGGGTTAGGG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 8 0.30
22 19 0.70
ACGTcount: A:0.27, C:0.00, G:0.27, T:0.46
Consensus pattern (22 bp):
TTAGAGTTTTTAAGTTAAAGGT
Found at i:21685366 original size:12 final size:12
Alignment explanation
Indices: 21685346--21685385 Score: 71
Period size: 12 Copynumber: 3.3 Consensus size: 12
21685336 AGGGTTTGTC
*
21685346 AATTAAATTATA
1 AATTTAATTATA
21685358 AATTTAATTATA
1 AATTTAATTATA
21685370 AATTTAATTATA
1 AATTTAATTATA
21685382 AATT
1 AATT
21685386 ATAAATTTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (12 bp):
AATTTAATTATA
Found at i:21685400 original size:7 final size:7
Alignment explanation
Indices: 21685349--21685397 Score: 61
Period size: 7 Copynumber: 7.4 Consensus size: 7
21685339 GTTTGTCAAT
21685349 TAAATTA
1 TAAATTA
21685356 TAAATT-
1 TAAATTA
21685362 T-AATTA
1 TAAATTA
21685368 TAAATT-
1 TAAATTA
21685374 T-AATTA
1 TAAATTA
21685380 TAAATTA
1 TAAATTA
21685387 TAAATTTA
1 TAAA-TTA
21685395 TAA
1 TAA
21685398 TTTTTTAATA
Statistics
Matches: 37, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
5 8 0.22
6 4 0.11
7 19 0.51
8 6 0.16
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (7 bp):
TAAATTA
Found at i:21685921 original size:18 final size:18
Alignment explanation
Indices: 21685895--21685937 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
21685885 GACTCGGAAA
* * *
21685895 AGGAAACATATAAGGGTT
1 AGGATACATAAAAGGGCT
21685913 AGGATACATAAAAGGGCT
1 AGGATACATAAAAGGGCT
21685931 AGGATAC
1 AGGATAC
21685938 GCACCTGGCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.44, C:0.09, G:0.28, T:0.19
Consensus pattern (18 bp):
AGGATACATAAAAGGGCT
Found at i:21687013 original size:41 final size:41
Alignment explanation
Indices: 21686968--21687130 Score: 197
Period size: 41 Copynumber: 4.0 Consensus size: 41
21686958 GTTTTTATAA
* *
21686968 AAGCGCCGCTAATGCTTTGGTCTTTAGCGATGTTTTTGGAG
1 AAGCGCCGCTAATGCTTAGGTCTTTAGCGACGTTTTTGGAG
* *
21687009 AAGCGCCGCTAATGCTTAGGGCTTTAGCGGCGTTTTTGGAG
1 AAGCGCCGCTAATGCTTAGGTCTTTAGCGACGTTTTTGGAG
* *
21687050 AAGCGCCGCTAATG-TTCTGGTCTTTAAC-AGCGTTTTTGG-G
1 AAGCGCCGCTAATGCTT-AGGTCTTTAGCGA-CGTTTTTGGAG
* * *
21687090 AAAGCGCCGCTAATGCTCAGGTCTTTAGTGGCGTTTTTGGA
1 -AAGCGCCGCTAATGCTTAGGTCTTTAGCGACGTTTTTGGA
21687131 AAACGTTTTT
Statistics
Matches: 103, Mismatches: 13, Indels: 11
0.81 0.10 0.09
Matches are distributed among these distances:
40 3 0.03
41 99 0.96
42 1 0.01
ACGTcount: A:0.18, C:0.19, G:0.30, T:0.33
Consensus pattern (41 bp):
AAGCGCCGCTAATGCTTAGGTCTTTAGCGACGTTTTTGGAG
Found at i:21687085 original size:82 final size:82
Alignment explanation
Indices: 21686945--21687133 Score: 258
Period size: 82 Copynumber: 2.3 Consensus size: 82
21686935 CGACCTTTCG
** * *
21686945 GGGCTTTAGTGGCGTTTTTATAAAAGCGCCGCTAATGCTTTGGTCTTTAGCGATGTTTTT-GGAG
1 GGGCTTTAGTGGCGTTTTTGGAAAAGCGCCGCTAATGCTTTGGTCTTTAACGACGTTTTTGGGA-
*
21687009 AAGCGCCGCTAATGCTTA
65 AAGCGCCGCTAATGCTCA
* *
21687027 GGGCTTTAGCGGCGTTTTTGGAGAAGCGCCGCTAATG-TTCTGGTCTTTAAC-AGCGTTTTTGGG
1 GGGCTTTAGTGGCGTTTTTGGAAAAGCGCCGCTAATGCTT-TGGTCTTTAACGA-CGTTTTTGGG
21687090 AAAGCGCCGCTAATGCTCA
64 AAAGCGCCGCTAATGCTCA
*
21687109 GGTCTTTAGTGGCGTTTTTGGAAAA
1 GGGCTTTAGTGGCGTTTTTGGAAAA
21687134 CGTTTTTAAG
Statistics
Matches: 94, Mismatches: 10, Indels: 6
0.85 0.09 0.05
Matches are distributed among these distances:
81 3 0.03
82 88 0.94
83 3 0.03
ACGTcount: A:0.19, C:0.17, G:0.30, T:0.34
Consensus pattern (82 bp):
GGGCTTTAGTGGCGTTTTTGGAAAAGCGCCGCTAATGCTTTGGTCTTTAACGACGTTTTTGGGAA
AGCGCCGCTAATGCTCA
Found at i:21688178 original size:42 final size:43
Alignment explanation
Indices: 21688112--21688286 Score: 185
Period size: 42 Copynumber: 4.1 Consensus size: 43
21688102 AGGTTATGTT
* ** * * * *
21688112 TTTAGCGGCGTTTTTGCTAGAAGCGTCGCTAAAAGT-TTGATC
1 TTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTCTTGGTC
* * *
21688154 TATAGTGGCGTTTGTGAGAAAAGCGTCGCTAAAGGTCTTGGTC
1 TTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTCTTGGTC
* * * *
21688197 TTTAGCGGCATTTTTG-GAAAAAGCACCGCTAAAGGTATTGGTC
1 TTTAGCGGCGTTTGTGAG-AAAAGCGCCGCTAAAGGTCTTGGTC
*
21688240 TTTAGCGGCGTTTGTGA-AAAAGCGCCACTAAAGGTCTTGGTC
1 TTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTCTTGGTC
21688282 TTTAG
1 TTTAG
21688287 TGGCATTTTT
Statistics
Matches: 110, Mismatches: 20, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
42 57 0.52
43 53 0.48
ACGTcount: A:0.24, C:0.16, G:0.28, T:0.32
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTCTTGGTC
Found at i:21688261 original size:85 final size:85
Alignment explanation
Indices: 21688138--21688296 Score: 239
Period size: 85 Copynumber: 1.9 Consensus size: 85
21688128 CTAGAAGCGT
* * *
21688138 CGCTAAAAGTTTGATCTATAGTGGCGTTTGTGAGAAAAGCGTCGCTAAAGGTCTTGGTCTTTAGC
1 CGCTAAAAGTTTGATCTATAGCGGCGTTTGTGAGAAAAGCGCCACTAAAGGTCTTGGTCTTTAGC
21688203 GGCATTTTTGGAAAAAGCAC
66 GGCATTTTTGGAAAAAGCAC
* * *
21688223 CGCTAAAGGTATTGGTCTTTAGCGGCGTTTGTGA-AAAAGCGCCACTAAAGGTCTTGGTCTTTAG
1 CGCTAAAAGT-TTGATCTATAGCGGCGTTTGTGAGAAAAGCGCCACTAAAGGTCTTGGTCTTTAG
*
21688287 TGGCATTTTT
65 CGGCATTTTT
21688297 TTTATAAAAA
Statistics
Matches: 66, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
85 46 0.70
86 20 0.30
ACGTcount: A:0.25, C:0.16, G:0.27, T:0.33
Consensus pattern (85 bp):
CGCTAAAAGTTTGATCTATAGCGGCGTTTGTGAGAAAAGCGCCACTAAAGGTCTTGGTCTTTAGC
GGCATTTTTGGAAAAAGCAC
Found at i:21689428 original size:51 final size:51
Alignment explanation
Indices: 21689367--21689464 Score: 153
Period size: 51 Copynumber: 1.9 Consensus size: 51
21689357 AAATAATTAA
21689367 AAATAGGGATTTAAGAGAAATTTA-AGAGGAAATTGAGAGCAAATTGAAATT
1 AAATAGGGATTTAAGAGAAATTTAGA-AGGAAATTGAGAGCAAATTGAAATT
* * *
21689418 AAATATGGATTTGAGAGAAATTTGGAAGGAAATTGAGAGCAAATTGA
1 AAATAGGGATTTAAGAGAAATTTAGAAGGAAATTGAGAGCAAATTGA
21689465 GAGGAAATTG
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
51 42 0.98
52 1 0.02
ACGTcount: A:0.47, C:0.02, G:0.26, T:0.26
Consensus pattern (51 bp):
AAATAGGGATTTAAGAGAAATTTAGAAGGAAATTGAGAGCAAATTGAAATT
Found at i:21689453 original size:22 final size:22
Alignment explanation
Indices: 21689428--21689490 Score: 69
Period size: 22 Copynumber: 2.8 Consensus size: 22
21689418 AAATATGGAT
21689428 TTGAGAGAAATTTG-GAAGGAAA
1 TTGAGAGAAATTTGAG-AGGAAA
21689450 TTGAGAGCAAA-TTGAGAGGAAA
1 TTGAGAG-AAATTTGAGAGGAAA
21689472 TTGAGA-AAATAATTGAGAG
1 TTGAGAGAAAT--TTGAGAG
21689491 AGGATTAGTT
Statistics
Matches: 36, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
20 3 0.08
22 22 0.61
23 11 0.31
ACGTcount: A:0.46, C:0.02, G:0.30, T:0.22
Consensus pattern (22 bp):
TTGAGAGAAATTTGAGAGGAAA
Found at i:21697669 original size:23 final size:23
Alignment explanation
Indices: 21697639--21697684 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
21697629 CCGCAAATAA
*
21697639 AAAATAAA-CCCAATTTTATAAAT
1 AAAATAAAGCCAAATTTTA-AAAT
21697662 AAAATAAAGCCAAATTTTAAAAT
1 AAAATAAAGCCAAATTTTAAAAT
21697685 GTCCACAGTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 12 0.57
24 9 0.43
ACGTcount: A:0.59, C:0.11, G:0.02, T:0.28
Consensus pattern (23 bp):
AAAATAAAGCCAAATTTTAAAAT
Found at i:21711198 original size:44 final size:44
Alignment explanation
Indices: 21711130--21711365 Score: 156
Period size: 44 Copynumber: 5.1 Consensus size: 44
21711120 TAGATCGCAT
*
21711130 CAGATTGAAGCTAGAAATCTTATCTCCCTGAGATTACAGCGGAG
1 CAGATTGAAGCTAGAAATCCTATCTCCCTGAGATTACAGCGGAG
* *
21711174 CAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAG
1 CAGATTGAAGCTAGAAATCCTATCTCCCTGAGATTACAGCGGAG
** * * *
21711218 C-GAATT-AAAATA-AAGGATCTTATCTCTCTGA-AGTTACAGTAGAGTAGATCGGAT
1 CAG-ATTGAAGCTAGAA--ATCCTATCTCCCTGAGA-TTAC--------AG--CGGAG
* * * *
21711272 CAGATTGAATCCAGAAATCTTATCTCCCTAAGATTACAGCGGAG
1 CAGATTGAAGCTAGAAATCCTATCTCCCTGAGATTACAGCGGAG
* * * * *
21711316 TAGATTGAATCCAGTAATCCTATCTCCCTGAGATTACAGTGGAG
1 CAGATTGAAGCTAGAAATCCTATCTCCCTGAGATTACAGCGGAG
*
21711360 CGGATT
1 CAGATT
21711366 AAAATAAAGG
Statistics
Matches: 151, Mismatches: 23, Indels: 36
0.72 0.11 0.17
Matches are distributed among these distances:
42 1 0.01
43 6 0.04
44 109 0.72
46 2 0.01
52 2 0.01
54 24 0.16
55 5 0.03
56 2 0.01
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.28
Consensus pattern (44 bp):
CAGATTGAAGCTAGAAATCCTATCTCCCTGAGATTACAGCGGAG
Found at i:21711288 original size:142 final size:142
Alignment explanation
Indices: 21711030--21711416 Score: 643
Period size: 142 Copynumber: 2.7 Consensus size: 142
21711020 GGCAGTGGTA
* *
21711030 GAGCAGACTGAAGCTACTAATCCTATCTCCCTGAGATTACAGTGGAGCGGATT-AAATAAAGGAT
1 GAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGAT
* *
21711094 CTTATCTCTTTGAAGTTACAGTAGAGTAGATCGCATCAGATTGAAGCTAGAAATCTTATCTCCCT
66 CTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAGATTGAAGCCAGAAATCTTATCTCCCT
*
21711159 GAGATTACAGCG
131 AAGATTACAGCG
*
21711171 GAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAGCGAATTAAAATAAAGGAT
1 GAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGAT
* *
21711236 CTTATCTCTCTGAAGTTACAGTAGAGTAGATCGGATCAGATTGAATCCAGAAATCTTATCTCCCT
66 CTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAGATTGAAGCCAGAAATCTTATCTCCCT
21711301 AAGATTACAGCG
131 AAGATTACAGCG
* * *
21711313 GAGTAGATTGAATCCAGTAATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGAT
1 GAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGAT
*
21711378 CTTATCTCTCTGAAGTTACAGTAGAG-AGGATCGTATCAG
66 CTTATCTCTCTGAAGTTACAGTAGAGTA-GATCGCATCAG
21711417 GTCTTATCTC
Statistics
Matches: 231, Mismatches: 13, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
141 51 0.22
142 180 0.78
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.28
Consensus pattern (142 bp):
GAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGAT
CTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAGATTGAAGCCAGAAATCTTATCTCCCT
AAGATTACAGCG
Found at i:21711438 original size:41 final size:44
Alignment explanation
Indices: 21711336--21711440 Score: 110
Period size: 44 Copynumber: 2.5 Consensus size: 44
21711326 CCAGTAATCC
* *
21711336 TATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCT
1 TATCTCCCTGAGATTACAGTAGAGAGGATTAAAATAAAGGATCT
* *** *
21711380 TATCTCTCTGA-AGTTACAGTAGAGAGGA-TCGTAT-CAGG-TCT
1 TATCTCCCTGAGA-TTACAGTAGAGAGGATTAAAATAAAGGATCT
21711421 TATCTCCCTGAGATTACAGT
1 TATCTCCCTGAGATTACAGT
21711441 GGAATAGACA
Statistics
Matches: 51, Mismatches: 8, Indels: 7
0.77 0.12 0.11
Matches are distributed among these distances:
41 20 0.39
42 4 0.08
43 4 0.08
44 23 0.45
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.30
Consensus pattern (44 bp):
TATCTCCCTGAGATTACAGTAGAGAGGATTAAAATAAAGGATCT
Found at i:21727460 original size:12 final size:12
Alignment explanation
Indices: 21727443--21727472 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
21727433 CTGCACATGC
21727443 CCATGTGCTAGG
1 CCATGTGCTAGG
*
21727455 CCATGTGTTAGG
1 CCATGTGCTAGG
21727467 CCATGT
1 CCATGT
21727473 AACTCACTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.17, C:0.23, G:0.30, T:0.30
Consensus pattern (12 bp):
CCATGTGCTAGG
Found at i:21744644 original size:107 final size:108
Alignment explanation
Indices: 21744464--21744665 Score: 255
Period size: 107 Copynumber: 1.9 Consensus size: 108
21744454 TAGTTTTTTC
*
21744464 TTAAGAATGTATTGGCCATTTTGATGCGAAAAGCGATGACAACCCAAGCACCTCACCCCAGTTAC
1 TTAAGAATGTATTGGCCATTTTGATGCGAAAAGCGATGACAACCCAAGCACCCCACCCCAGTTAC
*
21744529 TTAACCCAACACACTCCT-ATTTTATTATTATATATTTTTTGG
66 TCAACCCAACACACTCCTAATTTTATTATTATATATTTTTTGG
* * ** * * ***
21744571 TTAAGAATGTTTTGGCCCTTTTGATGCGAAGTG-GAATGACACCCCAAGTACCCCACCTTGGTTA
1 TTAAGAATGTATTGGCCATTTTGATGCGAAAAGCG-ATGACAACCCAAGCACCCCACCCCAGTTA
* * *
21744635 CTCAGCCCAACACACTCTTAATTTTTTTATT
65 CTCAACCCAACACACTCCTAATTTTATTATT
21744666 TAATTCTAGT
Statistics
Matches: 79, Mismatches: 14, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
106 1 0.01
107 68 0.86
108 10 0.13
ACGTcount: A:0.28, C:0.24, G:0.14, T:0.33
Consensus pattern (108 bp):
TTAAGAATGTATTGGCCATTTTGATGCGAAAAGCGATGACAACCCAAGCACCCCACCCCAGTTAC
TCAACCCAACACACTCCTAATTTTATTATTATATATTTTTTGG
Found at i:21746002 original size:30 final size:30
Alignment explanation
Indices: 21745966--21746024 Score: 118
Period size: 30 Copynumber: 2.0 Consensus size: 30
21745956 AAGATTCGAT
21745966 AACAAGAAAGTGAATCTTGATTTTCTTGAA
1 AACAAGAAAGTGAATCTTGATTTTCTTGAA
21745996 AACAAGAAAGTGAATCTTGATTTTCTTGA
1 AACAAGAAAGTGAATCTTGATTTTCTTGA
21746025 TTTGAGCCCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.39, C:0.10, G:0.17, T:0.34
Consensus pattern (30 bp):
AACAAGAAAGTGAATCTTGATTTTCTTGAA
Found at i:21746709 original size:9 final size:9
Alignment explanation
Indices: 21746695--21746723 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
21746685 ATTAACATGC
21746695 AAGAAAATA
1 AAGAAAATA
21746704 AAGAAAATA
1 AAGAAAATA
21746713 AAGAAAATA
1 AAGAAAATA
21746722 AA
1 AA
21746724 ATAAAATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.79, C:0.00, G:0.10, T:0.10
Consensus pattern (9 bp):
AAGAAAATA
Found at i:21746731 original size:19 final size:20
Alignment explanation
Indices: 21746695--21746749 Score: 71
Period size: 19 Copynumber: 2.9 Consensus size: 20
21746685 ATTAACATGC
*
21746695 AAGAAAAT-AAAGAAAATA-
1 AAGAAAATAAAATAAAATAT
21746713 AAGAAAATAAAATAAAATAT
1 AAGAAAATAAAATAAAATAT
*
21746733 AA-AATATAAAATAAAAT
1 AAGAAAATAAAATAAAAT
21746750 TGGCTTGCAT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
18 8 0.24
19 23 0.70
20 2 0.06
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.18
Consensus pattern (20 bp):
AAGAAAATAAAATAAAATAT
Done.