Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000907.1 Hibiscus syriacus cultivar Beakdansim tig00001799_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 656280
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 4
Found at i:339 original size:19 final size:20
Alignment explanation
Indices: 308--353 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
298 CGATATAACA
308 GGTAAAAATATGAT-AAACC
1 GGTAAAAATATGATAAAACC
327 GGTAACAAA-ATGATAAAACC
1 GGTAA-AAATATGATAAAACC
347 GGTAAAA
1 GGTAAAA
354 TAATACCGGA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 12 0.48
20 13 0.52
ACGTcount: A:0.54, C:0.11, G:0.17, T:0.17
Consensus pattern (20 bp):
GGTAAAAATATGATAAAACC
Found at i:2615 original size:21 final size:21
Alignment explanation
Indices: 2568--2630 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
2558 AAGACAATCA
* *
2568 AGAGTCGAAGAGAAACTTGATC
1 AGAGTCGAAGAGAAACTCGA-G
*
2590 A-AGTCGTAGAGAAACTCGAG
1 AGAGTCGAAGAGAAACTCGAG
* *
2610 AGAGTCGAAGATACACTCGAG
1 AGAGTCGAAGAGAAACTCGAG
2631 GAATAAGGGG
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
20 1 0.03
21 32 0.94
22 1 0.03
ACGTcount: A:0.40, C:0.16, G:0.29, T:0.16
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTCGAG
Found at i:2705 original size:32 final size:32
Alignment explanation
Indices: 2664--2724 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
2654 AAATAGATGG
*
2664 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGTGA
* *
2696 AGTGGTGAAAGAAGTTGGGGTGTTAAGGG
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGG
2725 GTGATATTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.30, C:0.00, G:0.48, T:0.23
Consensus pattern (32 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGTGA
Found at i:4534 original size:19 final size:19
Alignment explanation
Indices: 4510--4558 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
4500 AATGTCGAGT
4510 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
4529 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
*
4548 TATTTTTGTAT
1 TAATTTTGTAT
4559 GTGAATATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.31, C:0.02, G:0.10, T:0.57
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:5089 original size:198 final size:199
Alignment explanation
Indices: 4680--6233 Score: 2990
Period size: 198 Copynumber: 7.9 Consensus size: 199
4670 ATGGCCACAG
*
4680 GGTGCACCCATAAAGTGTCGATCCATATATAAAAAAGTGTCAATCCCAAAATCATCGAACCCAAA
1 GGTGCACCCATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCGAACCCAAA
4745 AGTATAATGTAATATGTAA-TTTTCAATCTAACCGGTACAATTATACCGG-TTTATGAGAGAATA
65 AGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATA
4808 TGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAATGGAA
130 TGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAATGGAA
4873 AACAA
195 AACAA
4878 GGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAA
1 GGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAA
4943 GTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAT
66 GTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAT
5008 GTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAATGGAAA
131 GTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAATGGAAA
5073 ACAA
196 ACAA
5077 GGTGCA-CCATAAAGTGTCGATCC--ATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAA
1 GGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAA
*
5139 GTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATATCGGTTTTATGAGAGAATAT
66 GTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAT
5204 GTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAATGGAAA
131 GTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAATGGAAA
5269 ACAA
196 ACAA
5273 GGTGCACCCATAAAGTGTCGATCCATATAT-AAAAGTGTCGATCCCAAAATCATCGAACCCAAAA
1 GGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAA
5337 GTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAT
66 GTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAT
5402 GTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAATGGAAA
131 GTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAATGGAAA
5467 ACAA
196 ACAA
5471 GGTGCACCCATAAAGTGTCGATCCATATAT-AAAAGTGTCGATCCCAAAATCATCGAACCCAAAA
1 GGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAA
5535 GTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAT
66 GTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAT
5600 GTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAATGG-AA
131 GTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAATGGAAA
5664 ACAA
196 ACAA
5668 GGTGCACCCATAAAGTGTCGATCCATATAT-AAAAGTGTCGATCCCAAAATCATCGAACCCAAAA
1 GGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAA
5732 GTATAATGTAATATGTAATTTTTCAATCTAACC-GTACAATTATACCGGTTTTATGAGAG-ATAT
66 GTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAT
5795 GTCTAAATAATGTGTCGACACT-ATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAATGGAAA
131 GTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAATGGAAA
5859 ACAA
196 ACAA
5863 GGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCC-AAA
1 GGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAA
5927 GTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAT
66 GTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAT
5992 GTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAATGGAAA
131 GTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAATGGAAA
6057 ACAA
196 ACAA
6061 GGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAA
1 GGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAA
6126 GTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAT
66 GTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAT
6191 GTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACT
131 GTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACT
6234 AATTTAAATA
Statistics
Matches: 1342, Mismatches: 3, Indels: 21
0.98 0.00 0.02
Matches are distributed among these distances:
194 39 0.03
195 98 0.07
196 260 0.19
197 198 0.15
198 542 0.40
199 205 0.15
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.31
Consensus pattern (199 bp):
GGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAA
GTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAT
GTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAATGGAAA
ACAA
Found at i:5434 original size:394 final size:397
Alignment explanation
Indices: 4680--6233 Score: 2970
Period size: 394 Copynumber: 3.9 Consensus size: 397
4670 ATGGCCACAG
*
4680 GGTGCACCCATAAAGTGTCGATCCATATATAAAAAAGTGTCAATCCCAAAATCATCGAACCCAAA
1 GGTGCACCCATAAAGTGTCGATCCA-ATAT-AAAAAGTGTCGATCCCAAAATCATCGAACCCAAA
4745 AGTATAATGTAATATGTAA-TTTTCAATCTAACCGGTACAATTATACCGG-TTTATGAGAGAATA
64 AGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATA
4808 TGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAATGGAA
129 TGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAATGGAA
4873 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
194 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
4938 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
259 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
5003 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
324 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
5068 GGAAAACAA
389 GGAAAACAA
5077 GGTGCA-CCATAAAGTGTCGATCC-ATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAG
1 GGTGCACCCATAAAGTGTCGATCCAATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAG
*
5140 TATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATATCGGTTTTATGAGAGAATATG
66 TATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATG
5205 TCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAATGGAAAA
131 TCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAATGGAAAA
5270 CAAGGTGCACCCATAAAGTGTCGATCCATATAT-AAAAGTGTCGATCCCAAAATCATCGAACCCA
196 CAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCA
5334 AAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAA
261 AAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAA
5399 TATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAATGG
326 TATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAATGG
5464 AAAACAA
391 AAAACAA
5471 GGTGCACCCATAAAGTGTCGATCC-ATATATAAAAGTGTCGATCCCAAAATCATCGAACCCAAAA
1 GGTGCACCCATAAAGTGTCGATCCAATATA-AAAAGTGTCGATCCCAAAATCATCGAACCCAAAA
5535 GTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAT
65 GTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAT
5600 GTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAATGG-AA
130 GTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAATGGAAA
5664 ACAAGGTGCACCCATAAAGTGTCGATCCATATAT-AAAAGTGTCGATCCCAAAATCATCGAACCC
195 ACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCC
5728 AAAAGTATAATGTAATATGTAATTTTTCAATCTAACC-GTACAATTATACCGGTTTTATGAGAG-
260 AAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGA
5791 ATATGTCTAAATAATGTGTCGACACT-ATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAATG
325 ATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAATG
5855 GAAAACAA
390 GAAAACAA
5863 GGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCC-AAA
1 GGTGCACCCATAAAGTGTCGATCCA-ATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAA
5927 GTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAT
65 GTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAT
5992 GTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAATGGAAA
130 GTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAATGGAAA
6057 ACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCC
195 ACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCC
6122 AAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGA
260 AAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGA
6187 ATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACT
325 ATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACT
6234 AATTTAAATA
Statistics
Matches: 1143, Mismatches: 3, Indels: 22
0.98 0.00 0.02
Matches are distributed among these distances:
392 200 0.17
393 144 0.13
394 305 0.27
395 265 0.23
396 203 0.18
397 26 0.02
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.31
Consensus pattern (397 bp):
GGTGCACCCATAAAGTGTCGATCCAATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAG
TATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATG
TCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAATGGAAAA
CAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCA
AAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAA
TATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAATGG
AAAACAA
Found at i:6201 original size:789 final size:790
Alignment explanation
Indices: 4680--6233 Score: 2978
Period size: 789 Copynumber: 2.0 Consensus size: 790
4670 ATGGCCACAG
4680 GGTGCACCCATAAAGTGTCGATCCATATATAAAAAAGTGTCAATCCCAAAATCATCGAACCCAAA
1 GGTGCACCCATAAAGTGTCGATCCATATAT-AAAAAGTGTCAATCCCAAAATCATCGAACCCAAA
4745 AGTATAATGTAATATGTAATTTTCAATCTAACCGGTACAATTATACCGGTTTATGAGAGAATATG
65 AGTATAATGTAATATGTAATTTTCAATCTAACCGGTACAATTATACCGGTTTATGAGAGAATATG
4810 TCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAATGGAAAA
130 TCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAATGGAAAA
4875 CAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCA
195 CAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCA
4940 AAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAA
260 AAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAA
5005 TATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAATGG
325 TATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAATGG
5070 AAAACAAGGTGCACCATAAAGTGTCGATCCATATAAAAAGTGTCGATCCCAAAATCATCGAACCC
390 AAAACAAGGTGCACCATAAAGTGTCGATCCATATAAAAAGTGTCGATCCCAAAATCATCGAACCC
*
5135 AAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATATCGGTTTTATGAGAGA
455 AAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGA
5200 ATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAATG
520 ATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAATG
5265 GAAAACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAGTGTCGATCCCAAAATCATCGAA
585 GAAAACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAGTGTCGATCCCAAAATCATCGAA
5330 CCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAG
650 CCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAG
5395 AGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGA
715 AGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGA
5460 ATGGAAAACAA
780 ATGGAAAACAA
*
5471 GGTGCACCCATAAAGTGTCGATCCATATAT-AAAAGTGTCGATCCCAAAATCATCGAACCCAAAA
1 GGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCAATCCCAAAATCATCGAACCCAAAA
5535 GTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAT
66 GTATAATGTAATATGTAA-TTTTCAATCTAACCGGTACAATTATACCGG-TTTATGAGAGAATAT
5600 GTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAATGG-AA
129 GTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAATGGAAA
5664 ACAAGGTGCACCCATAAAGTGTCGATCCATATAT-AAAAGTGTCGATCCCAAAATCATCGAACCC
194 ACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCC
5728 AAAAGTATAATGTAATATGTAATTTTTCAATCTAACC-GTACAATTATACCGGTTTTATGAGAG-
259 AAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGA
5791 ATATGTCTAAATAATGTGTCGACACT-ATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAATG
324 ATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAATG
5855 GAAAACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGA
389 GAAAACAAGGTGCA-CCATAAAGTGTCGATCC--ATATAAAAAGTGTCGATCCCAAAATCATCGA
5920 ACCC-AAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGA
451 ACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGA
5984 GAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATG
516 GAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATG
6049 AATGGAAAACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCA
581 AATGGAAAACAAGGTGCACCCATAAAGTGTCGATCCATATAT-AAAAGTGTCGATCCCAAAATCA
6114 TCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTT
645 TCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTT
6179 ATGAGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACT
710 ATGAGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACT
6234 AATTTAAATA
Statistics
Matches: 755, Mismatches: 2, Indels: 14
0.98 0.00 0.02
Matches are distributed among these distances:
786 52 0.07
787 43 0.06
788 192 0.25
789 295 0.39
790 66 0.09
791 107 0.14
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.31
Consensus pattern (790 bp):
GGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCAATCCCAAAATCATCGAACCCAAAA
GTATAATGTAATATGTAATTTTCAATCTAACCGGTACAATTATACCGGTTTATGAGAGAATATGT
CTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAATGGAAAAC
AAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAA
AAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAAT
ATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAATGGA
AAACAAGGTGCACCATAAAGTGTCGATCCATATAAAAAGTGTCGATCCCAAAATCATCGAACCCA
AAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAA
TATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAATGG
AAAACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAGTGTCGATCCCAAAATCATCGAAC
CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGA
GAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAA
TGGAAAACAA
Found at i:7709 original size:3 final size:3
Alignment explanation
Indices: 7701--7775 Score: 78
Period size: 3 Copynumber: 25.0 Consensus size: 3
7691 TGAAGCTGAC
* * * ** * *
7701 GAT GAT GAT GAT GAT GAC GAT GAA GCT GGC GAT GAA GAT GAT GAC GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
*
7749 GAT GAT GAT GAT GAT GAA GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT
7776 CCAAACAAGT
Statistics
Matches: 57, Mismatches: 15, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.35, C:0.05, G:0.35, T:0.25
Consensus pattern (3 bp):
GAT
Found at i:9562 original size:182 final size:183
Alignment explanation
Indices: 8973--9663 Score: 1205
Period size: 181 Copynumber: 3.8 Consensus size: 183
8963 CAAAGTTTTC
* ** * *
8973 ACACTTTTTAATATTGTGTATGTACTTTATGTCCAGAATGAAAG-AAAATGTGTCGATACCATTT
1 ACACTTTCTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTT
* *
9037 AAAAAAGTGTCG--ATTGAAAAAACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAA
66 AAAAAAGTGTCGACATT---TACACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAA
*
9100 TATAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
128 TATAACCGGTATAAAAATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
9156 ACACTTTCTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTT
1 ACACTTTCTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTT
9221 -AAAAAGTGTCGACATTTACACATCGGAACCCAGA-TTATAATGTAATAGATAATTTTGTAATAT
66 AAAAAAGTGTCGACATTTACACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAATAT
*
9284 AACCGGTATAAAAATATCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
131 AACCGGTATAAAAATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
9337 ACACTTTCTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTT
1 ACACTTTCTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTT
*
9402 -AAAAAGTGTCGACATTTACACATCGGAACCCATATTTATAATGTAATAGATAATTTTGTAATAT
66 AAAAAAGTGTCGACATTTACACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAATAT
*
9466 AACCGGTATAAAAATACCGGTTTTATGAGCGAATAGGTCTACAACCTTTATCG
131 AACCGGTATAAAAATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
*
9519 ACACTTTCTAATATTGTGTCGGTACTTTATGTTCAGATTGGAAGAAAAATGTGTCGATACCATTT
1 ACACTTTCTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTT
9584 AAAAAAGTGTCGACATTTACACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAATAT
66 AAAAAAGTGTCGACATTTACACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAATAT
9649 AACCGGTATAAAAAT
131 AACCGGTATAAAAAT
9664 GTGTCGATAC
Statistics
Matches: 489, Mismatches: 14, Indels: 10
0.95 0.03 0.02
Matches are distributed among these distances:
181 178 0.36
182 160 0.33
183 128 0.26
184 20 0.04
185 3 0.01
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.33
Consensus pattern (183 bp):
ACACTTTCTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTT
AAAAAAGTGTCGACATTTACACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAATAT
AACCGGTATAAAAATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
Found at i:9695 original size:22 final size:23
Alignment explanation
Indices: 9659--9701 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
9649 AACCGGTATA
9659 AAAATGTGTCGATACCTTTTTAT
1 AAAATGTGTCGATACCTTTTTAT
* *
9682 AAAA-GTGTCTATACTTTTTT
1 AAAATGTGTCGATACCTTTTT
9702 CACTGTGGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.30, C:0.12, G:0.12, T:0.47
Consensus pattern (23 bp):
AAAATGTGTCGATACCTTTTTAT
Found at i:12857 original size:23 final size:23
Alignment explanation
Indices: 12826--12888 Score: 92
Period size: 22 Copynumber: 2.8 Consensus size: 23
12816 ATAGGTAAAC
*
12826 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* *
12849 ATATAATGTAATAGGTA-TCGTT
1 ATATAATGTAATAGGTAGCCCTT
12871 ATATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
12889 TGGTTATATT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
22 20 0.56
23 16 0.44
ACGTcount: A:0.37, C:0.06, G:0.21, T:0.37
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:12875 original size:22 final size:23
Alignment explanation
Indices: 12826--12897 Score: 101
Period size: 23 Copynumber: 3.2 Consensus size: 23
12816 ATAGGTAAAC
* * *
12826 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGTCGTT
12849 ATATAATGTAATAGGTA-TCGTT
1 ATATAATGTAATAGGTAGTCGTT
*
12871 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGTCGTT
12894 ATAT
1 ATAT
12898 TGTAAAGTGT
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
22 20 0.45
23 24 0.55
ACGTcount: A:0.35, C:0.06, G:0.21, T:0.39
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGTCGTT
Found at i:13279 original size:20 final size:20
Alignment explanation
Indices: 13256--13308 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
13246 TAAACATATG
13256 ATGTAATAGGTAGCCCTTAT
1 ATGTAATAGGTAGCCCTTAT
* **
13276 ATGTAATAGGTATCGTTTAT
1 ATGTAATAGGTAGCCCTTAT
13296 ATGTAATAGGTAG
1 ATGTAATAGGTAG
13309 TGGTTATATT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.32, C:0.08, G:0.23, T:0.38
Consensus pattern (20 bp):
ATGTAATAGGTAGCCCTTAT
Found at i:13315 original size:20 final size:20
Alignment explanation
Indices: 13256--13322 Score: 73
Period size: 20 Copynumber: 3.3 Consensus size: 20
13246 TAAACATATG
**
13256 ATGTAATAGGTAGCCCTTAT
1 ATGTAATAGGTAGTGCTTAT
*
13276 ATGTAATAGGTA-TCGTTTAT
1 ATGTAATAGGTAGT-GCTTAT
*
13296 ATGTAATAGGTAGTGGTTAT
1 ATGTAATAGGTAGTGCTTAT
13316 ATTGTAA
1 A-TGTAA
13323 AGTGTCTATC
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
20 34 0.85
21 6 0.15
ACGTcount: A:0.31, C:0.06, G:0.22, T:0.40
Consensus pattern (20 bp):
ATGTAATAGGTAGTGCTTAT
Found at i:13618 original size:25 final size:25
Alignment explanation
Indices: 13584--13634 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
13574 ACAACAAATC
*
13584 AATTAAACATTGTTGTGGGTACATT
1 AATTAAACATTGTTATGGGTACATT
*
13609 AATTGAACATTGTTATGGGTACATT
1 AATTAAACATTGTTATGGGTACATT
13634 A
1 A
13635 TTTGGATTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.33, C:0.08, G:0.20, T:0.39
Consensus pattern (25 bp):
AATTAAACATTGTTATGGGTACATT
Found at i:13904 original size:18 final size:18
Alignment explanation
Indices: 13883--13919 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
13873 GTAATTGGAG
13883 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
13901 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
13919 T
1 T
13920 ATATTTCGGC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:14218 original size:39 final size:39
Alignment explanation
Indices: 14175--14339 Score: 312
Period size: 39 Copynumber: 4.2 Consensus size: 39
14165 TCCGATGCTC
* *
14175 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAATCTCATATGATGCCAAGCAAAAGGAA
14214 ATCAAAATCCAAATCTCATATGATGCCAAGCAAAAGGAA
1 ATCAAAATCCAAATCTCATATGATGCCAAGCAAAAGGAA
14253 ATCAAAATCCAAATCTCATATGATGCCAAGCAAAAGGAA
1 ATCAAAATCCAAATCTCATATGATGCCAAGCAAAAGGAA
14292 ATCAAAATCCAAATCTCATATGATGCCAAGCAAAAGGAA
1 ATCAAAATCCAAATCTCATATGATGCCAAGCAAAAGGAA
14331 ATCAAAATC
1 ATCAAAATC
14340 TACAACTTGA
Statistics
Matches: 124, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 124 1.00
ACGTcount: A:0.48, C:0.21, G:0.13, T:0.18
Consensus pattern (39 bp):
ATCAAAATCCAAATCTCATATGATGCCAAGCAAAAGGAA
Found at i:14774 original size:23 final size:23
Alignment explanation
Indices: 14743--14806 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
14733 ATAGGTAAAC
*
14743 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
14766 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
14789 ATATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
14807 TGGTTATATT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.36, C:0.06, G:0.20, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:14813 original size:23 final size:23
Alignment explanation
Indices: 14743--14815 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
14733 ATAGGTAAAC
* **
14743 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGTGCTT
*
14766 ATATAATGTAATAGGTA-TCGTTT
1 ATATAATGTAATAGGTAGT-GCTT
*
14789 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGTGCTT
14812 ATAT
1 ATAT
14816 TGTAAAGTGT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
23 42 0.98
24 1 0.02
ACGTcount: A:0.34, C:0.05, G:0.21, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGTGCTT
Found at i:15449 original size:14 final size:14
Alignment explanation
Indices: 15425--15498 Score: 68
Period size: 17 Copynumber: 5.3 Consensus size: 14
15415 TGTTTGTCCT
15425 TTTTATT-TATTAA
1 TTTTATTATATTAA
15438 TTTTATTATATT-A
1 TTTTATTATATTAA
15451 --TTATTATATT-A
1 TTTTATTATATTAA
15462 TTATTATTATTATTAGA
1 TT-TTATTA-TATTA-A
15479 TTATTATTATTATTAA
1 TT-TTATTA-TATTAA
15495 TTTT
1 TTTT
15499 TATTTTTCTT
Statistics
Matches: 54, Mismatches: 0, Indels: 12
0.82 0.00 0.18
Matches are distributed among these distances:
11 11 0.20
13 8 0.15
14 10 0.19
15 6 0.11
16 3 0.06
17 16 0.30
ACGTcount: A:0.32, C:0.00, G:0.01, T:0.66
Consensus pattern (14 bp):
TTTTATTATATTAA
Found at i:15452 original size:3 final size:3
Alignment explanation
Indices: 15431--15493 Score: 80
Period size: 3 Copynumber: 22.0 Consensus size: 3
15421 TCCTTTTTAT
15431 TTA TTAA TT- TTA TTA -TA TTA TTA TTA -TA TTA TTA TTA TTA TTA
1 TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
15474 TTA -GA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA
15494 ATTTTTATTT
Statistics
Matches: 53, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
2 7 0.13
3 43 0.81
4 3 0.06
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:15456 original size:20 final size:21
Alignment explanation
Indices: 15431--15493 Score: 85
Period size: 20 Copynumber: 3.0 Consensus size: 21
15421 TCCTTTTTAT
15431 TTATTAATTTTATTA-TATTA
1 TTATTAATTTTATTATTATTA
*
15451 TTATT-ATATTATTATTATTA
1 TTATTAATTTTATTATTATTA
15471 TTATTAGATTATTATTATTATTA
1 TTATTA-ATT-TTATTATTATTA
15494 ATTTTTATTT
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
19 8 0.22
20 15 0.41
22 2 0.05
23 12 0.32
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (21 bp):
TTATTAATTTTATTATTATTA
Found at i:15703 original size:2 final size:2
Alignment explanation
Indices: 15696--15723 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
15686 ATAATGTTTA
15696 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
15724 TTACTTTGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:18907 original size:21 final size:21
Alignment explanation
Indices: 18883--18942 Score: 62
Period size: 21 Copynumber: 3.2 Consensus size: 21
18873 TCAAAGAAAT
18883 ATTTACCAAACTTTGAAAACC
1 ATTTACCAAACTTTGAAAACC
*
18904 ATTT-TCAAA----G-AAA-C
1 ATTTACCAAACTTTGAAAACC
18918 ATTTACCAAACTTTGAAAACC
1 ATTTACCAAACTTTGAAAACC
18939 ATTT
1 ATTT
18943 TTTCAAAGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 14
0.65 0.04 0.30
Matches are distributed among these distances:
14 5 0.17
15 7 0.23
16 1 0.03
19 1 0.03
20 7 0.23
21 9 0.30
ACGTcount: A:0.43, C:0.20, G:0.05, T:0.32
Consensus pattern (21 bp):
ATTTACCAAACTTTGAAAACC
Found at i:18909 original size:35 final size:36
Alignment explanation
Indices: 18849--18977 Score: 167
Period size: 35 Copynumber: 3.7 Consensus size: 36
18839 TATACCAAAC
* *
18849 TTACAAAACTTTGAAAAACATTTTTCAAAGAAATAT
1 TTACCAAACTTTGAAAACCATTTTTCAAAGAAATAT
*
18885 TTACCAAACTTTGAAAACCA-TTTTCAAAGAAACAT
1 TTACCAAACTTTGAAAACCATTTTTCAAAGAAATAT
* **
18920 TTACCAAACTTTGAAAACCATTTTTTCAAAG--TTGG
1 TTACCAAACTTTGAAAACCA-TTTTTCAAAGAAATAT
18955 TTACCAAAC-TTGAAAACCATTTT
1 TTACCAAACTTTGAAAACCATTTT
18978 AATACTTTCA
Statistics
Matches: 84, Mismatches: 7, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
33 4 0.05
34 10 0.12
35 43 0.51
36 18 0.21
37 9 0.11
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.33
Consensus pattern (36 bp):
TTACCAAACTTTGAAAACCATTTTTCAAAGAAATAT
Found at i:19120 original size:27 final size:27
Alignment explanation
Indices: 19082--19138 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
19072 TGCCAACTGA
19082 AGTTGAACACAACTTCAGTTTGTCTGT
1 AGTTGAACACAACTTCAGTTTGTCTGT
19109 AGTTGAACACAACTTCAGTTTGTCTGT
1 AGTTGAACACAACTTCAGTTTGTCTGT
19136 AGT
1 AGT
19139 CACCATCTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.26, C:0.18, G:0.19, T:0.37
Consensus pattern (27 bp):
AGTTGAACACAACTTCAGTTTGTCTGT
Found at i:23091 original size:10 final size:10
Alignment explanation
Indices: 23076--23105 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
23066 ACTATTCACG
23076 TGAATAGTAA
1 TGAATAGTAA
23086 TGAATAGTAA
1 TGAATAGTAA
*
23096 TAAATAGTAA
1 TGAATAGTAA
23106 ACTAGCAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.53, C:0.00, G:0.17, T:0.30
Consensus pattern (10 bp):
TGAATAGTAA
Found at i:23570 original size:35 final size:36
Alignment explanation
Indices: 23503--23610 Score: 155
Period size: 35 Copynumber: 3.0 Consensus size: 36
23493 TATTTTCAAC
* ** *
23503 AAACATCTACCAAACTTTGAAAAATATTTTTCAAAG
1 AAACATTTACCAAACTTTGAAAACCATCTTTCAAAG
23539 AAACATTTACCAAACTTTGAAAACCA-CTTTCAAAG
1 AAACATTTACCAAACTTTGAAAACCATCTTTCAAAG
*
23574 AAACATTTACCAAACTTTGAAAACCATTTTTTCAAAG
1 AAACATTTACCAAACTTTGAAAACCA-TCTTTCAAAG
23611 TTGGTTACCA
Statistics
Matches: 65, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
35 34 0.52
36 23 0.35
37 8 0.12
ACGTcount: A:0.45, C:0.19, G:0.06, T:0.30
Consensus pattern (36 bp):
AAACATTTACCAAACTTTGAAAACCATCTTTCAAAG
Found at i:28944 original size:14 final size:14
Alignment explanation
Indices: 28925--28977 Score: 88
Period size: 14 Copynumber: 3.8 Consensus size: 14
28915 CAAACTTGTT
28925 TGTTTTCTACAGTC
1 TGTTTTCTACAGTC
*
28939 TGTTTTCTACATTC
1 TGTTTTCTACAGTC
*
28953 TGTTTTATACAGTC
1 TGTTTTCTACAGTC
28967 TGTTTTCTACA
1 TGTTTTCTACA
28978 TGGTATCAAG
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 35 1.00
ACGTcount: A:0.17, C:0.19, G:0.11, T:0.53
Consensus pattern (14 bp):
TGTTTTCTACAGTC
Found at i:28965 original size:28 final size:28
Alignment explanation
Indices: 28925--28978 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
28915 CAAACTTGTT
*
28925 TGTTTTCTACAGTCTGTTTTCTACATTC
1 TGTTTTATACAGTCTGTTTTCTACATTC
28953 TGTTTTATACAGTCTGTTTTCTACAT
1 TGTTTTATACAGTCTGTTTTCTACAT
28979 GGTATCAAGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.17, C:0.19, G:0.11, T:0.54
Consensus pattern (28 bp):
TGTTTTATACAGTCTGTTTTCTACATTC
Found at i:33703 original size:14 final size:14
Alignment explanation
Indices: 33684--33736 Score: 81
Period size: 14 Copynumber: 3.8 Consensus size: 14
33674 CAGACTTGTA
33684 TGTTTTCTACAGTT
1 TGTTTTCTACAGTT
33698 TGTTTTCTACA-TT
1 TGTTTTCTACAGTT
*
33711 CTGTTTTATACAGTT
1 -TGTTTTCTACAGTT
33726 TGTTTTCTACA
1 TGTTTTCTACA
33737 ACAAGCTAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
13 2 0.06
14 31 0.89
15 2 0.06
ACGTcount: A:0.17, C:0.15, G:0.11, T:0.57
Consensus pattern (14 bp):
TGTTTTCTACAGTT
Found at i:41644 original size:31 final size:31
Alignment explanation
Indices: 41606--41681 Score: 125
Period size: 31 Copynumber: 2.5 Consensus size: 31
41596 TTAACTCGGG
41606 GTGACCACATCTTAATTAAATAAAAACGAAA
1 GTGACCACATCTTAATTAAATAAAAACGAAA
* *
41637 GTGACCACGTCTTAATTAAATAAAAATGAAA
1 GTGACCACATCTTAATTAAATAAAAACGAAA
*
41668 GTGACCATATCTTA
1 GTGACCACATCTTA
41682 TGCTTTTTAA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.46, C:0.16, G:0.12, T:0.26
Consensus pattern (31 bp):
GTGACCACATCTTAATTAAATAAAAACGAAA
Found at i:49892 original size:29 final size:30
Alignment explanation
Indices: 49831--49903 Score: 112
Period size: 29 Copynumber: 2.5 Consensus size: 30
49821 TACTTTTTTT
*
49831 ATTTAAATATTTAAATTATTTTTTTGATTA
1 ATTTAAATATTTAAATTATTTTTTCGATTA
*
49861 ATTTAAGTATTTAAATTA-TTTTTCGATTA
1 ATTTAAATATTTAAATTATTTTTTCGATTA
*
49890 ATTTAATTATTTAA
1 ATTTAAATATTTAA
49904 CATTTTAACC
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
29 23 0.57
30 17 0.43
ACGTcount: A:0.37, C:0.01, G:0.04, T:0.58
Consensus pattern (30 bp):
ATTTAAATATTTAAATTATTTTTTCGATTA
Found at i:50202 original size:17 final size:19
Alignment explanation
Indices: 50162--50202 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
50152 ATAAAACATG
* *
50162 ATTAGGCATTTATTTTTGT
1 ATTAAGCATTTATTTTTCT
50181 ATTAAGCATTT-TTTTTCT
1 ATTAAGCATTTATTTTTCT
50199 -TTAA
1 ATTAA
50203 CGTCACCTGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
17 4 0.20
18 6 0.30
19 10 0.50
ACGTcount: A:0.24, C:0.07, G:0.10, T:0.59
Consensus pattern (19 bp):
ATTAAGCATTTATTTTTCT
Found at i:54884 original size:20 final size:22
Alignment explanation
Indices: 54859--54902 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 22
54849 AAAAGGGGGA
54859 AACAAA-GAGACG-GAAGAGAG
1 AACAAACGAGACGAGAAGAGAG
54879 AACAAAGCGAGACGAGAAGAGAG
1 AACAAA-CGAGACGAGAAGAGAG
54902 A
1 A
54903 GTGAGAAGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 6 0.29
22 6 0.29
23 9 0.43
ACGTcount: A:0.55, C:0.11, G:0.34, T:0.00
Consensus pattern (22 bp):
AACAAACGAGACGAGAAGAGAG
Found at i:56132 original size:3 final size:3
Alignment explanation
Indices: 56124--56168 Score: 83
Period size: 3 Copynumber: 15.3 Consensus size: 3
56114 AAGTAAGCCT
56124 TTA TTA TTA TTA TTA -TA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
56169 ATATAAATTT
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 39 0.95
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:58087 original size:25 final size:25
Alignment explanation
Indices: 58045--58095 Score: 68
Period size: 24 Copynumber: 2.0 Consensus size: 25
58035 TTTAAATTGA
58045 TATATTTCATATATAATAATTTCTTT
1 TATATTTCATATATAAT-ATTTCTTT
* *
58071 TATATTT-ATTTATAATATTTTTTT
1 TATATTTCATATATAATATTTCTTT
58095 T
1 T
58096 GAATGGTTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 8 0.35
25 8 0.35
26 7 0.30
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.65
Consensus pattern (25 bp):
TATATTTCATATATAATATTTCTTT
Found at i:59985 original size:29 final size:30
Alignment explanation
Indices: 59915--59974 Score: 95
Period size: 29 Copynumber: 2.0 Consensus size: 30
59905 CAATTTAAGG
59915 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAAT-GTTTTTGGACTTGAATTGAATTTA
*
59946 CAAAATGTTTTTGGA-TTTAATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTGAATTTA
59975 TTCAAAGTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 13 0.46
30 9 0.32
31 6 0.21
ACGTcount: A:0.33, C:0.05, G:0.17, T:0.45
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTGAATTGAATTTA
Found at i:60080 original size:21 final size:21
Alignment explanation
Indices: 60054--60154 Score: 111
Period size: 21 Copynumber: 4.8 Consensus size: 21
60044 AGGGTGTCAA
60054 AGTGCATCCATGCACTCCTGC
1 AGTGCATCCATGCACTCCTGC
60075 AGTGCATCCATGCA-TCCCTGC
1 AGTGCATCCATGCACT-CCTGC
60096 AGTGCATCCATGCA--CCTGCAC
1 AGTGCATCCATGCACTCCTG--C
* * *
60117 TAGTACATCGATGCAC-CATGC
1 -AGTGCATCCATGCACTCCTGC
60138 AGTGCATCCATGCACTC
1 AGTGCATCCATGCACTC
60155 AAACACCGAA
Statistics
Matches: 69, Mismatches: 5, Indels: 12
0.80 0.06 0.14
Matches are distributed among these distances:
19 4 0.06
20 14 0.20
21 36 0.52
22 12 0.17
23 3 0.04
ACGTcount: A:0.23, C:0.36, G:0.19, T:0.23
Consensus pattern (21 bp):
AGTGCATCCATGCACTCCTGC
Found at i:60198 original size:20 final size:20
Alignment explanation
Indices: 60173--60240 Score: 82
Period size: 20 Copynumber: 3.4 Consensus size: 20
60163 AATGCAATTA
*
60173 GTGCATCGATGCATCCTTCT
1 GTGCATCGATGCATCCTGCT
**
60193 GTGCATCGATGCATCAAGGCT
1 GTGCATCGATGCATC-CTGCT
* *
60214 GTGTAGCGATGCATCCTGCT
1 GTGCATCGATGCATCCTGCT
60234 GTGCATC
1 GTGCATC
60241 CATGAACGAA
Statistics
Matches: 38, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
20 23 0.61
21 15 0.39
ACGTcount: A:0.18, C:0.26, G:0.26, T:0.29
Consensus pattern (20 bp):
GTGCATCGATGCATCCTGCT
Found at i:60387 original size:20 final size:22
Alignment explanation
Indices: 60349--60388 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
60339 TTTGAGTAGA
60349 AAAATCATCCCCAAACGGCTCC
1 AAAATCATCCCCAAACGGCTCC
60371 AAAA-CATCCCC-AACGGCT
1 AAAATCATCCCCAAACGGCT
60389 ATATACAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.38, C:0.40, G:0.10, T:0.12
Consensus pattern (22 bp):
AAAATCATCCCCAAACGGCTCC
Found at i:62879 original size:34 final size:30
Alignment explanation
Indices: 62841--62909 Score: 95
Period size: 30 Copynumber: 2.2 Consensus size: 30
62831 TTGATATAAC
62841 AATTTAAGGCAAAATGGTTTTTGGACTTGAATTG
1 AATTTAA--CAAAAT-GTTTTTGGACTT-AATTG
62875 AATTT-ACAAAATGTTTTTGGACTTAATTG
1 AATTTAACAAAATGTTTTTGGACTTAATTG
62904 AATTTA
1 AATTTA
62910 TTCAAAGTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
29 10 0.29
30 12 0.35
31 6 0.18
33 1 0.03
34 5 0.15
ACGTcount: A:0.35, C:0.06, G:0.17, T:0.42
Consensus pattern (30 bp):
AATTTAACAAAATGTTTTTGGACTTAATTG
Found at i:62920 original size:29 final size:30
Alignment explanation
Indices: 62850--62909 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
62840 CAATTTAAGG
62850 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAAT-GTTTTTGGACTTGAATTGAATTTA
62881 CAAAATGTTTTTGGACTT-AATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTGAATTTA
62910 TTCAAAGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 12 0.41
31 6 0.21
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTGAATTGAATTTA
Found at i:63015 original size:21 final size:20
Alignment explanation
Indices: 62989--63087 Score: 119
Period size: 21 Copynumber: 4.8 Consensus size: 20
62979 AGGGTGTCAA
62989 AGTGCATCCATGCACCCCTGC
1 AGTGCATCCATGCA-CCCTGC
*
63010 AGTGCATCTATGCATCCCTGC
1 AGTGCATCCATGCA-CCCTGC
63031 AGTGCATCCATGCA-CCTGCAC
1 AGTGCATCCATGCACCCTG--C
* *
63052 TAGTGCATACATGCACCATGC
1 -AGTGCATCCATGCACCCTGC
63073 AGTGCATCCATGCAC
1 AGTGCATCCATGCAC
63088 TCAAACACCG
Statistics
Matches: 68, Mismatches: 6, Indels: 9
0.82 0.07 0.11
Matches are distributed among these distances:
19 4 0.06
20 14 0.21
21 34 0.50
22 13 0.19
23 3 0.04
ACGTcount: A:0.23, C:0.35, G:0.19, T:0.22
Consensus pattern (20 bp):
AGTGCATCCATGCACCCTGC
Found at i:63133 original size:20 final size:20
Alignment explanation
Indices: 63108--63181 Score: 78
Period size: 20 Copynumber: 3.6 Consensus size: 20
63098 AATGCAATTA
*
63108 GTGCATCAATGCATCCTTCT
1 GTGCATCGATGCATCCTTCT
***
63128 GTGCATCGATGCATCAAGGCT
1 GTGCATCGATGCATC-CTTCT
63149 GTGCATCGATGCATCCTGT-T
1 GTGCATCGATGCATCCT-TCT
*
63169 GTGCATCCATGCA
1 GTGCATCGATGCA
63182 CAAAGGCTGC
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
20 27 0.61
21 17 0.39
ACGTcount: A:0.20, C:0.27, G:0.23, T:0.30
Consensus pattern (20 bp):
GTGCATCGATGCATCCTTCT
Found at i:63155 original size:41 final size:41
Alignment explanation
Indices: 63108--63190 Score: 116
Period size: 41 Copynumber: 2.0 Consensus size: 41
63098 AATGCAATTA
*
63108 GTGCATCAATGCATCCT-TCTGTGCATCGATGCATC-AAGGCT
1 GTGCATCAATGCATCCTGT-TGTGCATCCATGCA-CAAAGGCT
*
63149 GTGCATCGATGCATCCTGTTGTGCATCCATGCACAAAGGCT
1 GTGCATCAATGCATCCTGTTGTGCATCCATGCACAAAGGCT
63190 G
1 G
63191 CAATGGCTAG
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
40 1 0.03
41 36 0.95
42 1 0.03
ACGTcount: A:0.22, C:0.27, G:0.24, T:0.28
Consensus pattern (41 bp):
GTGCATCAATGCATCCTGTTGTGCATCCATGCACAAAGGCT
Found at i:63332 original size:20 final size:22
Alignment explanation
Indices: 63294--63333 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
63284 TTTGAGTAGA
63294 AAAATCATCCCCAAACGGCTCC
1 AAAATCATCCCCAAACGGCTCC
63316 AAAA-CATCCCC-AACGGCT
1 AAAATCATCCCCAAACGGCT
63334 ATATACAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.38, C:0.40, G:0.10, T:0.12
Consensus pattern (22 bp):
AAAATCATCCCCAAACGGCTCC
Found at i:68772 original size:18 final size:18
Alignment explanation
Indices: 68718--68772 Score: 56
Period size: 18 Copynumber: 3.0 Consensus size: 18
68708 TTATATAAAA
* *
68718 TATATTTTATTATAATTA
1 TATATTTTATTATATTTT
* * *
68736 TATGTTATATTTGTATTTT
1 TATATTTTA-TTATATTTT
68755 TATATTTTATTATATTTT
1 TATATTTTATTATATTTT
68773 AATTGATATA
Statistics
Matches: 28, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
18 15 0.54
19 13 0.46
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (18 bp):
TATATTTTATTATATTTT
Found at i:71544 original size:177 final size:177
Alignment explanation
Indices: 71248--71613 Score: 671
Period size: 177 Copynumber: 2.1 Consensus size: 177
71238 TAAATACTAT
71248 TTTAATTAAAATAAAAATTATTTTTAATTATTCATTGGAGTAGATGTATAAAATATTTATTGTTT
1 TTTAATTAAAATAAAAATTATTTTTAATTATTCATTGGAGTAGATGTATAAAATATTTATTGTTT
71313 CAAGTATTAAGTGTTGCAACAGAAATTAAATTTAAGTACTTAGATAAAACAAAAAAATCAATATT
66 CAAGTATTAAGTGTTGCAACAGAAATTAAATTTAAGTACTTAGATAAAACAAAAAAATCAATATT
* *
71378 AAATTGAACACTAAAACTATATATTAAATTAAATATTAATGATTATA
131 AAATCGAACACTAAAACTATATATCAAATTAAATATTAATGATTATA
* *
71425 TTTAATTAAAATAAAAATTATTTTTAATTATTTATTGGAGTAGATGTATCAAATATTTATTGTTT
1 TTTAATTAAAATAAAAATTATTTTTAATTATTCATTGGAGTAGATGTATAAAATATTTATTGTTT
71490 CAAGTATTAAGT-TGTGCAACAGAAATTAAATTTAAGTACTTAGATAAAACAAAAAAATCAATAT
66 CAAGTATTAAGTGT-TGCAACAGAAATTAAATTTAAGTACTTAGATAAAACAAAAAAATCAATAT
71554 TAAATCGAACACTAAAACTATATATCAAATTAAATATTAATGATTATA
130 TAAATCGAACACTAAAACTATATATCAAATTAAATATTAATGATTATA
71602 TTTAATATAAAA
1 TTTAAT-TAAAA
71614 AGTACTCCAT
Statistics
Matches: 183, Mismatches: 4, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
176 1 0.01
177 177 0.97
178 5 0.03
ACGTcount: A:0.48, C:0.06, G:0.08, T:0.38
Consensus pattern (177 bp):
TTTAATTAAAATAAAAATTATTTTTAATTATTCATTGGAGTAGATGTATAAAATATTTATTGTTT
CAAGTATTAAGTGTTGCAACAGAAATTAAATTTAAGTACTTAGATAAAACAAAAAAATCAATATT
AAATCGAACACTAAAACTATATATCAAATTAAATATTAATGATTATA
Found at i:72168 original size:12 final size:12
Alignment explanation
Indices: 72151--72186 Score: 72
Period size: 12 Copynumber: 3.0 Consensus size: 12
72141 ATTATATATA
72151 AAATAAAATTTT
1 AAATAAAATTTT
72163 AAATAAAATTTT
1 AAATAAAATTTT
72175 AAATAAAATTTT
1 AAATAAAATTTT
72187 CAATTAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (12 bp):
AAATAAAATTTT
Found at i:73316 original size:18 final size:17
Alignment explanation
Indices: 73293--73337 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
73283 GATTATATAT
73293 TTTAAAATCAATAAATAA
1 TTTAAAATCAA-AAATAA
*
73311 TTTAAAATTTAAAAATAA
1 TTTAAAA-TCAAAAATAA
*
73329 TTAAAAATC
1 TTTAAAATC
73338 CAAGGTGACG
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
17 1 0.04
18 19 0.83
19 3 0.13
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (17 bp):
TTTAAAATCAAAAATAA
Found at i:74546 original size:20 final size:20
Alignment explanation
Indices: 74521--74558 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
74511 TTCGAAATAG
74521 GGAGTGCATCGATACATCAC
1 GGAGTGCATCGATACATCAC
*
74541 GGAGTGCATCGGTACATC
1 GGAGTGCATCGATACATC
74559 CCTTCATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.21
Consensus pattern (20 bp):
GGAGTGCATCGATACATCAC
Found at i:74884 original size:13 final size:12
Alignment explanation
Indices: 74862--74888 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
74852 TTCTTTTAAA
74862 AAATCATTTTTG
1 AAATCATTTTTG
74874 AAATCATTTTTG
1 AAATCATTTTTG
74886 AAA
1 AAA
74889 AATTACTCCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.44
Consensus pattern (12 bp):
AAATCATTTTTG
Found at i:74891 original size:14 final size:14
Alignment explanation
Indices: 74855--74891 Score: 51
Period size: 12 Copynumber: 2.8 Consensus size: 14
74845 TAAGATTTTC
*
74855 TTTTAAAAAATCAT
1 TTTTGAAAAATCAT
74869 TTTTG--AAATCAT
1 TTTTGAAAAATCAT
74881 TTTTGAAAAAT
1 TTTTGAAAAAT
74892 TACTCCCCCT
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
12 12 0.60
14 8 0.40
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.46
Consensus pattern (14 bp):
TTTTGAAAAATCAT
Found at i:76860 original size:21 final size:22
Alignment explanation
Indices: 76808--76880 Score: 85
Period size: 23 Copynumber: 3.3 Consensus size: 22
76798 CATAGCAGAG
76808 TGCATCGATGCACATTCAAGGAA
1 TGCATCGATGCACATTCAAGG-A
* *
76831 TGCATCGATGCACCTTCATGG-
1 TGCATCGATGCACATTCAAGGA
* *
76852 TGTATCGATGCATATTCAAAGGA
1 TGCATCGATGCACATTC-AAGGA
76875 TGCATC
1 TGCATC
76881 AGTACACTCT
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
21 14 0.34
22 3 0.07
23 24 0.59
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27
Consensus pattern (22 bp):
TGCATCGATGCACATTCAAGGA
Found at i:82215 original size:65 final size:64
Alignment explanation
Indices: 82143--82278 Score: 184
Period size: 65 Copynumber: 2.1 Consensus size: 64
82133 ATACTAATTA
* * *
82143 CATTCGATGTTTCA-AAAGAACCAGGAGTGCATCGATGCATGGTTTGTGCATCGGTACATAAAAT
1 CATTCGATGTTTCATAAA-AACCAAGAGTGCATCGATGCATGG-CTGTGCATCGGTACACAAAAT
82207 G
64 G
* ** *
82208 CATTCGATGTTTCATTAAATTCAAGATTGCATCGATGCATGGCTGTGCATCGGTACACAAAATG
1 CATTCGATGTTTCATAAAAACCAAGAGTGCATCGATGCATGGCTGTGCATCGGTACACAAAATG
82272 CATTCGA
1 CATTCGA
82279 AATAGAGAGT
Statistics
Matches: 63, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
64 27 0.43
65 34 0.54
66 2 0.03
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.29
Consensus pattern (64 bp):
CATTCGATGTTTCATAAAAACCAAGAGTGCATCGATGCATGGCTGTGCATCGGTACACAAAATG
Found at i:89597 original size:20 final size:20
Alignment explanation
Indices: 89572--89622 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
89562 CATGCTTGGC
*
89572 ATTAAAAGAAAAATAAAGAA
1 ATTAAAAGAAAAAGAAAGAA
89592 ATTAAAA-AGAAAAGAAAGAA
1 ATTAAAAGA-AAAAGAAAGAA
**
89612 AAGAAAAGAAA
1 ATTAAAAGAAA
89623 GCTTTATTCA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 1 0.04
20 24 0.92
21 1 0.04
ACGTcount: A:0.76, C:0.00, G:0.14, T:0.10
Consensus pattern (20 bp):
ATTAAAAGAAAAAGAAAGAA
Found at i:89613 original size:14 final size:14
Alignment explanation
Indices: 89596--89623 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
89586 AAAGAAATTA
89596 AAAAGAAAAGAAAG
1 AAAAGAAAAGAAAG
89610 AAAAGAAAAGAAAG
1 AAAAGAAAAGAAAG
89624 CTTTATTCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (14 bp):
AAAAGAAAAGAAAG
Found at i:89777 original size:14 final size:14
Alignment explanation
Indices: 89758--89792 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
89748 ATTATACAAG
89758 AAAAATAACTCCTA
1 AAAAATAACTCCTA
89772 AAAAATAACTCCTA
1 AAAAATAACTCCTA
*
89786 ATAAATA
1 AAAAATA
89793 GGAAATGATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.60, C:0.17, G:0.00, T:0.23
Consensus pattern (14 bp):
AAAAATAACTCCTA
Found at i:90132 original size:57 final size:57
Alignment explanation
Indices: 90064--90184 Score: 226
Period size: 57 Copynumber: 2.1 Consensus size: 57
90054 CAAAAGGAAT
90064 AACTAAAAGCAAGTTTAAGCAAAGCATGACATTCCAATAATCCGTTAATATCAATGG
1 AACTAAAAGCAAGTTTAAGCAAAGCATGACATTCCAATAATCCGTTAATATCAATGG
*
90121 AACTAAAAGCAAGTTTAAGCAAAGCATGGCATTCCAATAATCCGTTAATATCAATGG
1 AACTAAAAGCAAGTTTAAGCAAAGCATGACATTCCAATAATCCGTTAATATCAATGG
90178 AAC-AAAA
1 AACTAAAA
90185 TTTACTGCCT
Statistics
Matches: 63, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
56 4 0.06
57 59 0.94
ACGTcount: A:0.45, C:0.17, G:0.14, T:0.23
Consensus pattern (57 bp):
AACTAAAAGCAAGTTTAAGCAAAGCATGACATTCCAATAATCCGTTAATATCAATGG
Found at i:93133 original size:6 final size:6
Alignment explanation
Indices: 92976--93131 Score: 276
Period size: 6 Copynumber: 26.0 Consensus size: 6
92966 CGAGGTACCT
92976 GTTAAA GTTAAA GTTAAA GTTAAA GTTAAA GTTAAA GTTAAA GTTAAA
1 GTTAAA GTTAAA GTTAAA GTTAAA GTTAAA GTTAAA GTTAAA GTTAAA
93024 GTTAAA GTTAAA GTTAAA GTTAAA GTTAAA GTTAAA GTTAAA GTTAAA
1 GTTAAA GTTAAA GTTAAA GTTAAA GTTAAA GTTAAA GTTAAA GTTAAA
* *
93072 GTTAAA GTTAAA GTTAAA GTTAAA GTTAAA GTTAAA ATTAAA ATTAAA
1 GTTAAA GTTAAA GTTAAA GTTAAA GTTAAA GTTAAA GTTAAA GTTAAA
* *
93120 ATTAAA ATTAAA
1 GTTAAA GTTAAA
93132 ATATGCTAAA
Statistics
Matches: 149, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
6 149 1.00
ACGTcount: A:0.53, C:0.00, G:0.14, T:0.33
Consensus pattern (6 bp):
GTTAAA
Found at i:100384 original size:43 final size:42
Alignment explanation
Indices: 100277--100395 Score: 166
Period size: 42 Copynumber: 2.8 Consensus size: 42
100267 TCTTTTGTGG
* * * *
100277 CATTTTTTAAACAAACGCCGTAATAGATCAGTACATTAGTGA
1 CATTTTATATACAAATGCCGCAATAGATCAGTACATTAGTGA
*
100319 CATTTTATATACAAATGCCGCAATAGATCAGTACATTAGTGG
1 CATTTTATATACAAATGCCGCAATAGATCAGTACATTAGTGA
* *
100361 CGATTTTATATACAAATGTCGCAATAGGTCAGTAC
1 C-ATTTTATATACAAATGCCGCAATAGATCAGTAC
100396 GTCTGTTAAA
Statistics
Matches: 69, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
42 38 0.55
43 31 0.45
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.31
Consensus pattern (42 bp):
CATTTTATATACAAATGCCGCAATAGATCAGTACATTAGTGA
Found at i:103516 original size:42 final size:41
Alignment explanation
Indices: 103423--103516 Score: 113
Period size: 42 Copynumber: 2.3 Consensus size: 41
103413 TCAGGCCAGG
103423 TATAT-AT-ATTTAAATTAAATATATAAATATTATATATAT
1 TATATAATAATTTAAATTAAATATATAAATATTATATATAT
* * *
103462 T-TTTAATTTAATTTAAATTAAATTTATTAATATTATATATAT
1 TATATAA--TAATTTAAATTAAATATATAAATATTATATATAT
103504 ATATATAATAATT
1 -TATATAATAATT
103517 ATTTTTAATA
Statistics
Matches: 45, Mismatches: 4, Indels: 9
0.78 0.07 0.16
Matches are distributed among these distances:
38 2 0.04
39 2 0.04
41 1 0.02
42 35 0.78
43 1 0.02
44 4 0.09
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (41 bp):
TATATAATAATTTAAATTAAATATATAAATATTATATATAT
Found at i:103870 original size:42 final size:43
Alignment explanation
Indices: 103824--103943 Score: 138
Period size: 43 Copynumber: 2.8 Consensus size: 43
103814 TATTATAAAC
* *
103824 GCCACTAAAAACAATAGAATTAGCGCCGTTTGTGG-AAAAAAA
1 GCCACTAAAGACAATAGAATTAGCGACGTTTGTGGTAAAAAAA
* *
103866 GCCACTAAAGACAA-ATG-ATCTAACGACGTTTGTGGTAAAAAAC
1 GCCACTAAAGACAATA-GAAT-TAGCGACGTTTGTGGTAAAAAAA
* * *
103909 GCCACTAAAGACAATAAAATTAGCAAAGTTTGTGG
1 GCCACTAAAGACAATAGAATTAGCGACGTTTGTGG
103944 CGAAAAACAC
Statistics
Matches: 65, Mismatches: 8, Indels: 9
0.79 0.10 0.11
Matches are distributed among these distances:
41 3 0.05
42 27 0.42
43 32 0.49
44 3 0.05
ACGTcount: A:0.43, C:0.17, G:0.19, T:0.21
Consensus pattern (43 bp):
GCCACTAAAGACAATAGAATTAGCGACGTTTGTGGTAAAAAAA
Found at i:103917 original size:43 final size:43
Alignment explanation
Indices: 103820--103958 Score: 133
Period size: 43 Copynumber: 3.3 Consensus size: 43
103810 TTTGTATTAT
* * *
103820 AAACGCCACTAAAAAC-AATAGAATTAGCGCCGTTTGTGGAAA
1 AAACGCCACTAAAGACAAATAGAATTAACGACGTTTGTGGAAA
*
103862 AAAAGCCACTAAAGACAAAT-G-ATCTAACGACGTTTGTGGTAAA
1 AAACGCCACTAAAGACAAATAGAAT-TAACGACGTTTGTGG-AAA
* * * * *
103905 AAACGCCACTAAAGAC-AATAAAATTAGCAAAGTTTGTGGCGAA
1 AAACGCCACTAAAGACAAATAGAATTAACGACGTTTGTGG-AAA
*
103948 AAACACCACTA
1 AAACGCCACTA
103959 TAAATCATAA
Statistics
Matches: 80, Mismatches: 12, Indels: 9
0.79 0.12 0.09
Matches are distributed among these distances:
41 2 0.03
42 31 0.39
43 45 0.56
44 2 0.03
ACGTcount: A:0.45, C:0.19, G:0.17, T:0.19
Consensus pattern (43 bp):
AAACGCCACTAAAGACAAATAGAATTAACGACGTTTGTGGAAA
Found at i:104969 original size:31 final size:31
Alignment explanation
Indices: 104933--104991 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
104923 AACTTAAAAG
* * *
104933 AGTTTTGCAATACTGAGATTTAAATAATTTT
1 AGTTTTACAATACTAAAATTTAAATAATTTT
104964 AGTTTTACAATACTAAAATTTAAATAAT
1 AGTTTTACAATACTAAAATTTAAATAAT
104992 CTATACAACT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.42, C:0.07, G:0.08, T:0.42
Consensus pattern (31 bp):
AGTTTTACAATACTAAAATTTAAATAATTTT
Found at i:105067 original size:22 final size:22
Alignment explanation
Indices: 105018--105066 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
105008 ATAAATTATT
* **
105018 TAAAATAAATCAATCTATATTT
1 TAAAATAAATCAATCGATATAA
105040 TAAAATAAATCAATCGATACTAA
1 TAAAATAAATCAATCGATA-TAA
105063 TAAA
1 TAAA
105067 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.10, G:0.02, T:0.33
Consensus pattern (22 bp):
TAAAATAAATCAATCGATATAA
Found at i:105145 original size:22 final size:22
Alignment explanation
Indices: 105072--105145 Score: 62
Period size: 22 Copynumber: 3.2 Consensus size: 22
105062 ATAAATTATT
105072 TAAAATAAATCAATCTATAC-AA
1 TAAAATAAATCAATC-ATACTAA
**
105094 CTACAATAATAAATCAATCCATA-TTT
1 -T--AA-AATAAATCAAT-CATACTAA
105120 TAAAATAAATCAATCATACTAA
1 TAAAATAAATCAATCATACTAA
105142 TAAA
1 TAAA
105146 TTATTTAAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 13
0.71 0.07 0.22
Matches are distributed among these distances:
21 4 0.10
22 16 0.39
23 3 0.07
25 3 0.07
26 14 0.34
27 1 0.02
ACGTcount: A:0.55, C:0.15, G:0.00, T:0.30
Consensus pattern (22 bp):
TAAAATAAATCAATCATACTAA
Found at i:105169 original size:32 final size:31
Alignment explanation
Indices: 105118--105223 Score: 113
Period size: 32 Copynumber: 3.6 Consensus size: 31
105108 CAATCCATAT
*
105118 TTTAAAATAAATCAATCATACTAATAAATTA
1 TTTAAAATAAATCAACCATACTAATAAATTA
*
105149 TTTAAAATAAATC-A--AT--TCAT--A-T-
1 TTTAAAATAAATCAACCATACTAATAAATTA
105171 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAA-CCATACTAATAAATTA
105203 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAA-CCATA
105224 TTTTAAAATA
Statistics
Matches: 63, Mismatches: 2, Indels: 19
0.75 0.02 0.23
Matches are distributed among these distances:
22 13 0.21
23 2 0.03
24 1 0.02
26 5 0.08
28 5 0.08
30 2 0.03
31 14 0.22
32 21 0.33
ACGTcount: A:0.53, C:0.11, G:0.00, T:0.36
Consensus pattern (31 bp):
TTTAAAATAAATCAACCATACTAATAAATTA
Found at i:105175 original size:22 final size:22
Alignment explanation
Indices: 105149--105191 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
105139 TAATAAATTA
*
105149 TTTAAAATAAATCAATTCATAT
1 TTTAAAATAAATCAATCCATAT
105171 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
105192 CTAATAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:105200 original size:22 final size:22
Alignment explanation
Indices: 105151--105199 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
105141 ATAAATTATT
* **
105151 TAAAATAAATCAATTCATATTT
1 TAAAATAAATCAATCCATATAA
105173 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
105196 TAAA
1 TAAA
105200 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:105216 original size:54 final size:54
Alignment explanation
Indices: 105101--105269 Score: 295
Period size: 54 Copynumber: 3.1 Consensus size: 54
105091 CAACTACAAT
105101 AATAAATCAATCCATATTTTAAAATAAATCAAT-CATACTAATAAATTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
*
105154 AATAAATCAATTCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
* *
105208 AATAAATCAATCCATATTTTAAAATAAATCAATCCATAATAATAATTTATTTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTA-TTTAA
105263 AATAAAT
1 AATAAAT
105270 TATTTTAAAA
Statistics
Matches: 110, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
53 32 0.29
54 66 0.60
55 12 0.11
ACGTcount: A:0.53, C:0.11, G:0.00, T:0.37
Consensus pattern (54 bp):
AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
Found at i:105229 original size:22 final size:22
Alignment explanation
Indices: 105203--105245 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
105193 TAATAAATTA
105203 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
105225 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
105246 ATAATAATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:105266 original size:15 final size:15
Alignment explanation
Indices: 105248--105329 Score: 146
Period size: 15 Copynumber: 5.5 Consensus size: 15
105238 AATCCATAAT
*
105248 AATAATTTATTTTAA
1 AATAAATTATTTTAA
105263 AATAAATTATTTTAA
1 AATAAATTATTTTAA
*
105278 AATAAATTATTTTAT
1 AATAAATTATTTTAA
105293 AATAAATTATTTTAA
1 AATAAATTATTTTAA
105308 AATAAATTATTTTAA
1 AATAAATTATTTTAA
105323 AATAAAT
1 AATAAAT
105330 AACCTTATTA
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 64 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
AATAAATTATTTTAA
Found at i:110453 original size:42 final size:42
Alignment explanation
Indices: 110394--110480 Score: 156
Period size: 42 Copynumber: 2.1 Consensus size: 42
110384 CCGAAATCCT
*
110394 GTGTTTGGTTCATGTAATTCGTTTTCCGGAAAATGTTTTCCC
1 GTGTTTGGTTCACGTAATTCGTTTTCCGGAAAATGTTTTCCC
*
110436 GTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGTTTTCCC
1 GTGTTTGGTTCACGTAATTCGTTTTCCGGAAAATGTTTTCCC
110478 GTG
1 GTG
110481 AAACAATAAT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.16, C:0.17, G:0.22, T:0.45
Consensus pattern (42 bp):
GTGTTTGGTTCACGTAATTCGTTTTCCGGAAAATGTTTTCCC
Found at i:110735 original size:26 final size:24
Alignment explanation
Indices: 110673--110735 Score: 60
Period size: 24 Copynumber: 2.6 Consensus size: 24
110663 CATTTTCATC
110673 AAAATAT-TAATTATTAAAATATTT
1 AAAATATAT-ATTATTAAAATATTT
*
110697 AAAATATAT-TTATTAATAT-TTAT
1 AAAATATATATTATTAAAATATT-T
110720 AATAATATAGTATTAT
1 AA-AATATA-TATTAT
110736 ATTTTTAATA
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
22 2 0.06
23 12 0.36
24 13 0.39
25 2 0.06
26 4 0.12
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.48
Consensus pattern (24 bp):
AAAATATATATTATTAAAATATTT
Found at i:110737 original size:22 final size:23
Alignment explanation
Indices: 110690--110750 Score: 65
Period size: 22 Copynumber: 2.8 Consensus size: 23
110680 TAATTATTAA
* *
110690 AATATTTAAAAT-ATAT-TTATT
1 AATATTTATAATAATATAGTATT
110711 AATATTTATAATAATATAGTATT
1 AATATTTATAATAATATAGTATT
* *
110734 -ATATTTTTAATATTATA
1 AATATTTATAATAATATA
110751 TAAAATAATC
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
21 11 0.32
22 19 0.56
23 4 0.12
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (23 bp):
AATATTTATAATAATATAGTATT
Found at i:110766 original size:31 final size:31
Alignment explanation
Indices: 110701--110779 Score: 83
Period size: 31 Copynumber: 2.5 Consensus size: 31
110691 ATATTTAAAA
110701 TATATTTATTAATATTTATAATAATATAGTAT
1 TATATTTATTAATATTTATAATAATATAG-AT
110733 TATATTT-TTAATATTATATAA-AATAATCA-AT
1 TATATTTATTAATATT-TATAATAAT-AT-AGAT
*
110764 TATATTATAATAATAT
1 TATATT-TATTAATAT
110780 AAGATATTAT
Statistics
Matches: 41, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
31 19 0.46
32 15 0.37
33 7 0.17
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (31 bp):
TATATTTATTAATATTTATAATAATATAGAT
Found at i:110849 original size:28 final size:29
Alignment explanation
Indices: 110764--110864 Score: 109
Period size: 28 Copynumber: 3.5 Consensus size: 29
110754 AATAATCAAT
* * * *
110764 TATATTATAATAATATAAGATATTATATTTT
1 TATATT-TAATAATAGAATA-ATTTTATTTA
*
110795 TAT-TTTAATAATATAATAATTTT-TTTA
1 TATATTTAATAATAGAATAATTTTATTTA
110822 TATATTTAATAAT-GAATAATTTTATTTA
1 TATATTTAATAATAGAATAATTTTATTTA
110850 TATATTTAAATAATA
1 TATATTT-AATAATA
110865 TTTTAGTAAA
Statistics
Matches: 62, Mismatches: 4, Indels: 9
0.83 0.05 0.12
Matches are distributed among these distances:
27 15 0.24
28 24 0.39
29 18 0.29
30 2 0.03
31 3 0.05
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (29 bp):
TATATTTAATAATAGAATAATTTTATTTA
Found at i:110994 original size:90 final size:86
Alignment explanation
Indices: 110881--111050 Score: 200
Period size: 90 Copynumber: 1.9 Consensus size: 86
110871 TAAAGATATT
* * * * * *
110881 TAAAATATACTAATTAATATTTTTA-AAATATAA-TATAACACTATTACTTTAATAAATAATTAA
1 TAAAATATACAAATTAATATTTTTATAAATAAAATTATAAAAATAATA-TTTAAT-AATAAATAA
110944 TATAATTTATAATATTTTATTTCAC
64 -ATAATTT-TAATATTTTATTTCAC
*
110969 TAAAATATATCAATATTAATATTTTTATTAATAAAATTATAAAAATAATATTTAATAATAAATAA
1 TAAAATATA-CAA-ATTAATATTTTTATAAATAAAATTATAAAAATAATATTTAATAATAAATAA
*
111034 ATTATTTTAATATTTTA
64 ATAATTTTAATATTTTA
111051 AAATAATGAT
Statistics
Matches: 70, Mismatches: 8, Indels: 8
0.81 0.09 0.09
Matches are distributed among these distances:
88 19 0.27
89 8 0.11
90 21 0.30
91 12 0.17
92 10 0.14
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (86 bp):
TAAAATATACAAATTAATATTTTTATAAATAAAATTATAAAAATAATATTTAATAATAAATAAAT
AATTTTAATATTTTATTTCAC
Found at i:117821 original size:39 final size:39
Alignment explanation
Indices: 117762--117840 Score: 149
Period size: 39 Copynumber: 2.0 Consensus size: 39
117752 ATTATGAAAC
*
117762 TGAGTTATATTATGATTAGGATTAATTATTAGTATTTTA
1 TGAGATATATTATGATTAGGATTAATTATTAGTATTTTA
117801 TGAGATATATTATGATTAGGATTAATTATTAGTATTTTA
1 TGAGATATATTATGATTAGGATTAATTATTAGTATTTTA
117840 T
1 T
117841 TTTATTAGTA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.34, C:0.00, G:0.15, T:0.51
Consensus pattern (39 bp):
TGAGATATATTATGATTAGGATTAATTATTAGTATTTTA
Found at i:122751 original size:39 final size:39
Alignment explanation
Indices: 122708--122788 Score: 128
Period size: 39 Copynumber: 2.1 Consensus size: 39
122698 TGAGTGGGAC
* *
122708 TATGAGTTATATTACGATTAGGATT-ATTAATTATTATTT
1 TATGAGTTATATTACGATTAAGATTAATT-ATTAGTATTT
122747 TATGAGTTATATTACGATTAAGATTAATTATTAGTATTT
1 TATGAGTTATATTACGATTAAGATTAATTATTAGTATTT
122786 TAT
1 TAT
122789 TTTATTAGTA
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
39 36 0.92
40 3 0.08
ACGTcount: A:0.35, C:0.02, G:0.12, T:0.51
Consensus pattern (39 bp):
TATGAGTTATATTACGATTAAGATTAATTATTAGTATTT
Found at i:132946 original size:24 final size:24
Alignment explanation
Indices: 132914--132966 Score: 97
Period size: 24 Copynumber: 2.2 Consensus size: 24
132904 GACACTCTTT
*
132914 TTGTTCTCAAATTCCCTTAAAGAA
1 TTGTTCTCAAATTCCATTAAAGAA
132938 TTGTTCTCAAATTCCATTAAAGAA
1 TTGTTCTCAAATTCCATTAAAGAA
132962 TTGTT
1 TTGTT
132967 TTAGTTTTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.32, C:0.17, G:0.09, T:0.42
Consensus pattern (24 bp):
TTGTTCTCAAATTCCATTAAAGAA
Found at i:135796 original size:15 final size:15
Alignment explanation
Indices: 135776--135829 Score: 54
Period size: 17 Copynumber: 3.4 Consensus size: 15
135766 AACCAAAATG
*
135776 AAAAATCTTTAATTA
1 AAAAATATTTAATTA
135791 AAAAATAATTTTAATTA
1 AAAAAT-A-TTTAATTA
* *
135808 AAATAAAATTTAATAA
1 AAA-AATATTTAATTA
135824 AAAAAT
1 AAAAAT
135830 TTCATTCATA
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
15 8 0.25
16 10 0.31
17 12 0.38
18 2 0.06
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (15 bp):
AAAAATATTTAATTA
Found at i:135805 original size:17 final size:16
Alignment explanation
Indices: 135783--135829 Score: 60
Period size: 17 Copynumber: 2.9 Consensus size: 16
135773 ATGAAAAATC
135783 TTTAATTAAAAAATAA
1 TTTAATTAAAAAATAA
135799 TTTTAATTAAAATAA-AA
1 -TTTAATTAAAA-AATAA
*
135816 TTTAATAAAAAAAT
1 TTTAATTAAAAAAT
135830 TTCATTCATA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
15 2 0.07
16 10 0.37
17 13 0.48
18 2 0.07
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
TTTAATTAAAAAATAA
Found at i:135810 original size:16 final size:16
Alignment explanation
Indices: 135783--135831 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 16
135773 ATGAAAAATC
135783 TTTAATTAAAAAATAAT
1 TTTAATT-AAAAATAAT
*
135800 TTTAATT-AAAATAAAA
1 TTTAATTAAAAAT-AAT
135816 TTTAA-TAAAAA-AAT
1 TTTAATTAAAAATAAT
135830 TT
1 TT
135832 CATTCATATT
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
14 4 0.14
15 6 0.21
16 11 0.39
17 7 0.25
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TTTAATTAAAAATAAT
Found at i:139137 original size:29 final size:29
Alignment explanation
Indices: 139096--139185 Score: 123
Period size: 29 Copynumber: 3.2 Consensus size: 29
139086 AGGGGTGTGT
139096 TGTGTTGTGTGTGTAAGAGATGAAAGGAG
1 TGTGTTGTGTGTGTAAGAGATGAAAGGAG
* *
139125 TGTGTTGTGTGTGTGAGAGATGAAATGA-
1 TGTGTTGTGTGTGTAAGAGATGAAAGGAG
* *
139153 -GT-TTGTGTGTGCAAGAGATTAAAGGAG
1 TGTGTTGTGTGTGTAAGAGATGAAAGGAG
139180 TGTGTT
1 TGTGTT
139186 ATGTATGTTA
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
26 20 0.38
27 2 0.04
28 2 0.04
29 28 0.54
ACGTcount: A:0.26, C:0.01, G:0.39, T:0.34
Consensus pattern (29 bp):
TGTGTTGTGTGTGTAAGAGATGAAAGGAG
Found at i:139183 original size:24 final size:22
Alignment explanation
Indices: 139131--139184 Score: 54
Period size: 24 Copynumber: 2.3 Consensus size: 22
139121 GGAGTGTGTT
*
139131 GTGTGTGTGAGAGATGAAATGA
1 GTGTGTGTGAGAGATGAAAGGA
*
139153 GTTTGTGTGTGCAAGAGATTAAAGGA
1 G--TGTGTGTG--AGAGATGAAAGGA
139179 GTGTGT
1 GTGTGT
139185 TATGTATGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
22 1 0.04
24 13 0.50
26 12 0.46
ACGTcount: A:0.28, C:0.02, G:0.39, T:0.31
Consensus pattern (22 bp):
GTGTGTGTGAGAGATGAAAGGA
Found at i:144718 original size:20 final size:20
Alignment explanation
Indices: 144682--144719 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
144672 ATCCTATTCC
**
144682 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
144702 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
144720 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:144994 original size:23 final size:23
Alignment explanation
Indices: 144933--145090 Score: 84
Period size: 23 Copynumber: 6.5 Consensus size: 23
144923 TTTAATTGAT
* *
144933 AACGAACACAAATGAACGAACATA
1 AACGAACAC-AATAAACAAACATA
* *
144957 AACGAA-AGATGTAAACAAACATA
1 AACGAACACA-ATAAACAAACATA
* *
144980 AATGAATACAATAAACGAACGTTAACGATA
1 AACGAACACAATAAAC--A----AAC-ATA
* *
145010 AACGAACACAATGAACGAACATA
1 AACGAACACAATAAACAAACATA
* *
145033 AACGAACAGATGTAAACAAACATA
1 AACGAACACA-ATAAACAAACATA
* * * * *
145057 AATGAATACAATAAACGAACGTT
1 AACGAACACAATAAACAAACATA
145080 AACGAACACAA
1 AACGAACACAA
145091 ACGAATTAAC
Statistics
Matches: 100, Mismatches: 24, Indels: 21
0.69 0.17 0.14
Matches are distributed among these distances:
22 1 0.01
23 51 0.51
24 28 0.28
25 1 0.01
29 3 0.03
30 16 0.16
ACGTcount: A:0.57, C:0.17, G:0.13, T:0.13
Consensus pattern (23 bp):
AACGAACACAATAAACAAACATA
Found at i:145037 original size:30 final size:30
Alignment explanation
Indices: 144973--145037 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 30
144963 AGATGTAAAC
* * *
144973 AAAC-ATAAATGAATACAATAAACGAACGT
1 AAACGATAAACGAACACAATAAACGAACAT
* *
145002 TAACGATAAACGAACACAATGAACGAACAT
1 AAACGATAAACGAACACAATAAACGAACAT
145032 AAACGA
1 AAACGA
145038 ACAGATGTAA
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
29 3 0.10
30 26 0.90
ACGTcount: A:0.57, C:0.17, G:0.12, T:0.14
Consensus pattern (30 bp):
AAACGATAAACGAACACAATAAACGAACAT
Found at i:145038 original size:10 final size:10
Alignment explanation
Indices: 145023--145138 Score: 51
Period size: 10 Copynumber: 11.2 Consensus size: 10
145013 GAACACAATG
145023 AACGAACATA
1 AACGAACATA
145033 AACGAACAGATGTA
1 AACGAAC--A--TA
*
145047 AACAAACATA
1 AACGAACATA
*
145057 AATGAATACAATA
1 AACG-A-AC-ATA
* *
145070 AACGAACGTT
1 AACGAACATA
*
145080 AACGAACACA
1 AACGAACATA
*
145090 AACG-A-ATT
1 AACGAACATA
145098 AAC--ACAATA
1 AACGAAC-ATA
*
145107 AATGAACATA
1 AACGAACATA
145117 AACGAACATA
1 AACGAACATA
* *
145127 AATGAAAATA
1 AACGAACATA
145137 AA
1 AA
145139 TTTTTTTTCT
Statistics
Matches: 79, Mismatches: 16, Indels: 22
0.68 0.14 0.19
Matches are distributed among these distances:
7 1 0.01
8 4 0.05
9 5 0.06
10 45 0.57
11 5 0.06
12 5 0.06
13 6 0.08
14 8 0.10
ACGTcount: A:0.59, C:0.16, G:0.10, T:0.15
Consensus pattern (10 bp):
AACGAACATA
Found at i:145056 original size:77 final size:77
Alignment explanation
Indices: 144933--145084 Score: 288
Period size: 77 Copynumber: 2.0 Consensus size: 77
144923 TTTAATTGAT
144933 AACGAACACAAATGAACGAACATAAACGAAAGATGTAAACAAACATAAATGAATACAATAAACGA
1 AACGAACACAAATGAACGAACATAAACGAAAGATGTAAACAAACATAAATGAATACAATAAACGA
144998 ACGTTAACGATA
66 ACGTTAACGATA
145010 AACGAACAC-AATGAACGAACATAAACGAACAGATGTAAACAAACATAAATGAATACAATAAACG
1 AACGAACACAAATGAACGAACATAAACGAA-AGATGTAAACAAACATAAATGAATACAATAAACG
145074 AACGTTAACGA
65 AACGTTAACGA
145085 ACACAAACGA
Statistics
Matches: 74, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
76 20 0.27
77 54 0.73
ACGTcount: A:0.57, C:0.16, G:0.13, T:0.14
Consensus pattern (77 bp):
AACGAACACAAATGAACGAACATAAACGAAAGATGTAAACAAACATAAATGAATACAATAAACGA
ACGTTAACGATA
Found at i:145787 original size:2 final size:2
Alignment explanation
Indices: 145780--145805 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
145770 GATGGAAAAC
145780 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
145806 TTCCAGCAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:147953 original size:143 final size:141
Alignment explanation
Indices: 147657--147966 Score: 396
Period size: 143 Copynumber: 2.2 Consensus size: 141
147647 ATATTTTTAT
*
147657 ATTTATAAATAAGATATTTATTTACTTAGAAATATCAGAAAAGGACTTCTAGGTGCTTTAAGACA
1 ATTTATAAATAGGATATTTATTTACTTAGAAATATCAGAAAAGGACTTCTAGGTGCTTTAAGACA
*
147722 GCCCATTTCTTAATATTAAAAAATAAATAAATATTAATAAAATATTTCTCTAAAATAATTAAAAT
66 ACCCATTTCTTAATATTAAAAAATAAATAAATATTAATAAAATATTTCTCTAAAATAATTAAAAT
147787 AAATCATATATA
131 AAA-CATATATA
* * * *
147799 ATTGATAAAATAGGATATTTATTTATTTA-AGAATATCAGAAAATGACTTCTAGGTGCTTTAATA
1 ATTTAT-AAATAGGATATTTATTTACTTAGA-AATATCAGAAAAGGACTTCTAGGTGCTTTAAGA
* * *
147863 TAACTCATTTCTTAATATTAAAAAATAAATAAATATTAA-AATATGACTATTTTTCATAAAAGTA
64 CAACCCATTTCTTAATATTAAAAAATAAATAAATATTAATAA-A--A-TATTTCTC-TAAAA-TA
* *
147927 ATTTATATAAA-AT-TA-A
123 ATTAAAATAAACATATATA
*
147943 ATTTATAAATAGGATTTTTATTTA
1 ATTTATAAATAGGATATTTATTTA
147967 ATATATAAAA
Statistics
Matches: 147, Mismatches: 13, Indels: 15
0.84 0.07 0.09
Matches are distributed among these distances:
142 8 0.05
143 105 0.71
144 6 0.04
145 3 0.02
146 9 0.06
147 5 0.03
148 11 0.07
ACGTcount: A:0.46, C:0.07, G:0.07, T:0.39
Consensus pattern (141 bp):
ATTTATAAATAGGATATTTATTTACTTAGAAATATCAGAAAAGGACTTCTAGGTGCTTTAAGACA
ACCCATTTCTTAATATTAAAAAATAAATAAATATTAATAAAATATTTCTCTAAAATAATTAAAAT
AAACATATATA
Found at i:148053 original size:21 final size:21
Alignment explanation
Indices: 148025--148074 Score: 52
Period size: 22 Copynumber: 2.4 Consensus size: 21
148015 ACTACATAAT
148025 AATA-ATAACA-ATAATAACTA
1 AATATATAACATATAA-AACTA
*
148045 AATATATAAACATATAAAATTA
1 AATATAT-AACATATAAAACTA
148067 AA-ATATAA
1 AATATATAA
148075 ATAAACAATG
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
20 6 0.23
21 6 0.23
22 10 0.38
23 4 0.15
ACGTcount: A:0.66, C:0.06, G:0.00, T:0.28
Consensus pattern (21 bp):
AATATATAACATATAAAACTA
Found at i:149519 original size:3 final size:3
Alignment explanation
Indices: 149511--149587 Score: 77
Period size: 3 Copynumber: 25.0 Consensus size: 3
149501 AATATTTATT
*
149511 TAA TAA TAA TAA TAA TAA TAA TAA TGTA TAA TAA TAA TAAA TAAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA T-AA T-AA TAA
* *
149559 -ATA TAA TAA TAA TAA -AT TAA TAA GAA TAA
1 TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA
149588 AGTTCCTAAA
Statistics
Matches: 63, Mismatches: 6, Indels: 10
0.80 0.08 0.13
Matches are distributed among these distances:
2 2 0.03
3 51 0.81
4 10 0.16
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:149563 original size:23 final size:23
Alignment explanation
Indices: 149511--149581 Score: 94
Period size: 23 Copynumber: 3.1 Consensus size: 23
149501 AATATTTATT
149511 TAATA-ATAATAATAAT-AATAA
1 TAATATATAATAATAATAAATAA
*
149532 TAATGTATAATAATAATAAATAAA
1 TAATATATAATAATAATAAAT-AA
149556 TAA-ATATAATAATAATAAATTAA
1 TAATATATAATAATAATAAA-TAA
149579 TAA
1 TAA
149582 GAATAAAGTT
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
21 4 0.09
22 11 0.25
23 23 0.52
24 6 0.14
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (23 bp):
TAATATATAATAATAATAAATAA
Found at i:149564 original size:20 final size:19
Alignment explanation
Indices: 149519--149588 Score: 74
Period size: 19 Copynumber: 3.7 Consensus size: 19
149509 TTTAATAATA
*
149519 ATAATAATAAT-AATAATGT
1 ATAATAATAATAAATAA-AT
149538 ATAATAATAATAAATAAAT
1 ATAATAATAATAAATAAAT
*
149557 AAATATAATAAT-AATAAAT
1 ATA-ATAATAATAAATAAAT
*
149576 -TAATAAGAATAAA
1 ATAATAATAATAAA
149589 GTTCCTAAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
17 7 0.16
18 3 0.07
19 21 0.48
20 13 0.30
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (19 bp):
ATAATAATAATAAATAAAT
Found at i:158442 original size:34 final size:34
Alignment explanation
Indices: 158380--158450 Score: 83
Period size: 35 Copynumber: 2.1 Consensus size: 34
158370 TATTTGTTAC
*
158380 TTTTTTTAAATTTGAATATTAAAGATAATTATTAA
1 TTTTTTTAAATTTCAATATTAAAGATAA-TATTAA
* *
158415 TTTTTTGTATATTTCAA-ATTAAA-ATAATATTTA
1 TTTTTT-TAAATTTCAATATTAAAGATAATATTAA
158448 TTT
1 TTT
158451 AATTTGAATA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
33 8 0.25
34 4 0.12
35 12 0.38
36 8 0.25
ACGTcount: A:0.39, C:0.01, G:0.04, T:0.55
Consensus pattern (34 bp):
TTTTTTTAAATTTCAATATTAAAGATAATATTAA
Found at i:158670 original size:20 final size:18
Alignment explanation
Indices: 158631--158669 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
158621 AGTGTTATTT
158631 TCTTGAAAAAATTTCTTC
1 TCTTGAAAAAATTTCTTC
158649 TCTTGAAAAAATATT-TTC
1 TCTTGAAAAAAT-TTCTTC
158667 TCT
1 TCT
158670 CATTCTCAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 18 0.90
19 2 0.10
ACGTcount: A:0.33, C:0.15, G:0.05, T:0.46
Consensus pattern (18 bp):
TCTTGAAAAAATTTCTTC
Found at i:160585 original size:20 final size:22
Alignment explanation
Indices: 160541--160592 Score: 67
Period size: 20 Copynumber: 2.5 Consensus size: 22
160531 TATTGATAGT
*
160541 GGTATCGATA-CTGTAAGGGTA
1 GGTATCGATACCTGTAAGGGAA
160562 -GTATCGATACCTGT-A-GGAA
1 GGTATCGATACCTGTAAGGGAA
160581 GGTATCGATACC
1 GGTATCGATACC
160593 CTTAAAATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
19 3 0.11
20 21 0.75
21 4 0.14
ACGTcount: A:0.29, C:0.15, G:0.29, T:0.27
Consensus pattern (22 bp):
GGTATCGATACCTGTAAGGGAA
Found at i:160640 original size:19 final size:20
Alignment explanation
Indices: 160616--160653 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
160606 ATGCCAGATT
*
160616 GGTATCGGTA-CCTTGAAAA
1 GGTATCGATACCCTTGAAAA
160635 GGTATCGATACCCTTGAAA
1 GGTATCGATACCCTTGAAA
160654 CATTGAACCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.26
Consensus pattern (20 bp):
GGTATCGATACCCTTGAAAA
Found at i:161235 original size:21 final size:21
Alignment explanation
Indices: 161209--161276 Score: 68
Period size: 21 Copynumber: 3.2 Consensus size: 21
161199 GTCGAGGGTT
161209 TTATGTGGTCATTCGGGACAA
1 TTATGTGGTCATTCGGGACAA
161230 TTATGTGGT-ACTTCGGTG-CAAA
1 TTATGTGGTCA-TTCGG-GAC-AA
* * *
161252 CTATGTGGTCATTTGGGATAA
1 TTATGTGGTCATTCGGGACAA
161273 TTAT
1 TTAT
161277 ATGGCACTTC
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
20 1 0.03
21 21 0.55
22 15 0.39
23 1 0.03
ACGTcount: A:0.24, C:0.12, G:0.26, T:0.38
Consensus pattern (21 bp):
TTATGTGGTCATTCGGGACAA
Found at i:167358 original size:42 final size:40
Alignment explanation
Indices: 167304--167383 Score: 115
Period size: 42 Copynumber: 1.9 Consensus size: 40
167294 GCATAATTGT
* * *
167304 TAAGGGTTGTATCGATACCTGTTGATAGTGGTATCGATACTC
1 TAAGGGTAGTATCGATACCTGTAG-GA-TGGTATCGATACTC
167346 TAAGGGTAGTATCGATACCTGTAGGATGGTATCGATAC
1 TAAGGGTAGTATCGATACCTGTAGGATGGTATCGATAC
167384 CCTTAAAACA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
40 12 0.34
41 1 0.03
42 22 0.63
ACGTcount: A:0.26, C:0.14, G:0.28, T:0.33
Consensus pattern (40 bp):
TAAGGGTAGTATCGATACCTGTAGGATGGTATCGATACTC
Found at i:167377 original size:20 final size:20
Alignment explanation
Indices: 167312--167384 Score: 67
Period size: 20 Copynumber: 3.5 Consensus size: 20
167302 GTTAAGGGTT
* *
167312 GTATCGATACCTGTTGATAGTG
1 GTATCGATACCTGTAG-GA-TG
* * *
167334 GTATCGATACTCT-AAGGGTA
1 GTATCGATAC-CTGTAGGATG
167354 GTATCGATACCTGTAGGATG
1 GTATCGATACCTGTAGGATG
167374 GTATCGATACC
1 GTATCGATACC
167385 CTTAAAACAT
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
19 2 0.05
20 26 0.63
22 11 0.27
23 2 0.05
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.32
Consensus pattern (20 bp):
GTATCGATACCTGTAGGATG
Found at i:167525 original size:20 final size:21
Alignment explanation
Indices: 167480--167533 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
167470 TACATGCGGA
*
167480 GGTATCGATACCCTTGAAGTGT
1 GGTATCGATACCCTT-AAGGGT
*
167502 GGTATCGGTACCCTT-AGGGT
1 GGTATCGATACCCTTAAGGGT
*
167522 GGTACCGATACC
1 GGTATCGATACC
167534 TCTAAGCATG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 14 0.50
22 14 0.50
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.28
Consensus pattern (21 bp):
GGTATCGATACCCTTAAGGGT
Found at i:168087 original size:21 final size:21
Alignment explanation
Indices: 168042--168090 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
168032 TCGACGGTTT
* * * *
168042 TATGTGGTCCTTCGGGATAAT
1 TATGTGGTCCTCCGGAACAAA
168063 TATGTGGTCCTCCGGAACAAA
1 TATGTGGTCCTCCGGAACAAA
168084 TATGTGG
1 TATGTGG
168091 CACTTCGGTG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.22, C:0.16, G:0.29, T:0.33
Consensus pattern (21 bp):
TATGTGGTCCTCCGGAACAAA
Found at i:175847 original size:24 final size:26
Alignment explanation
Indices: 175820--175869 Score: 77
Period size: 24 Copynumber: 2.0 Consensus size: 26
175810 TAAAATGACT
175820 AAGTAAAAAATTGA-AA-AATAATGA
1 AAGTAAAAAATTGAGAACAATAATGA
*
175844 AAGTAAATAATTGAGAACAATAATGA
1 AAGTAAAAAATTGAGAACAATAATGA
175870 TGCAAGATAG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 13 0.57
25 2 0.09
26 8 0.35
ACGTcount: A:0.62, C:0.02, G:0.14, T:0.22
Consensus pattern (26 bp):
AAGTAAAAAATTGAGAACAATAATGA
Found at i:177676 original size:44 final size:44
Alignment explanation
Indices: 177615--177701 Score: 131
Period size: 44 Copynumber: 2.0 Consensus size: 44
177605 TATCAGTACT
177615 AGTATCGGTACTTTAGTGTATTTTTACACACTAGTATCGATACC
1 AGTATCGGTACTTTAGTGTATTTTTACACACTAGTATCGATACC
* * *
177659 AGTATTGGTA-TTGTAGTGTATTTTTACACATTGGTATCGATAC
1 AGTATCGGTACTT-TAGTGTATTTTTACACACTAGTATCGATAC
177702 ATGTATCAGT
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
43 2 0.05
44 37 0.95
ACGTcount: A:0.26, C:0.14, G:0.18, T:0.41
Consensus pattern (44 bp):
AGTATCGGTACTTTAGTGTATTTTTACACACTAGTATCGATACC
Found at i:178054 original size:17 final size:18
Alignment explanation
Indices: 178034--178075 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
178024 TAAATTTATT
*
178034 TATTTTATCA-TTTTAAA
1 TATTTTATCACTTCTAAA
*
178051 TATTTTTATTACTTCTAAA
1 TA-TTTTATCACTTCTAAA
178070 TATTTT
1 TATTTT
178076 TTAAATTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 2 0.10
18 11 0.52
19 8 0.38
ACGTcount: A:0.31, C:0.07, G:0.00, T:0.62
Consensus pattern (18 bp):
TATTTTATCACTTCTAAA
Found at i:178059 original size:18 final size:19
Alignment explanation
Indices: 178036--178076 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
178026 AATTTATTTA
*
178036 TTTTATCA-TTTTAAATAT
1 TTTTATCACTTCTAAATAT
*
178054 TTTTATTACTTCTAAATAT
1 TTTTATCACTTCTAAATAT
178073 TTTT
1 TTTT
178077 TAAATTTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 7 0.35
19 13 0.65
ACGTcount: A:0.29, C:0.07, G:0.00, T:0.63
Consensus pattern (19 bp):
TTTTATCACTTCTAAATAT
Found at i:180339 original size:27 final size:27
Alignment explanation
Indices: 180270--180333 Score: 128
Period size: 27 Copynumber: 2.4 Consensus size: 27
180260 AAACAGTGTT
180270 GAATGATTCAACATCAAAGTACATTCA
1 GAATGATTCAACATCAAAGTACATTCA
180297 GAATGATTCAACATCAAAGTACATTCA
1 GAATGATTCAACATCAAAGTACATTCA
180324 GAATGATTCA
1 GAATGATTCA
180334 GAATCATTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.44, C:0.17, G:0.12, T:0.27
Consensus pattern (27 bp):
GAATGATTCAACATCAAAGTACATTCA
Found at i:180405 original size:16 final size:16
Alignment explanation
Indices: 180380--180414 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
180370 ATTCATACAG
180380 AGCATATGAATCATTC
1 AGCATATGAATCATTC
*
180396 AGCATTTGAATCATTC
1 AGCATATGAATCATTC
180412 AGC
1 AGC
180415 GCTTAATCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.34, C:0.20, G:0.14, T:0.31
Consensus pattern (16 bp):
AGCATATGAATCATTC
Found at i:180424 original size:15 final size:16
Alignment explanation
Indices: 180386--180426 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
180376 ACAGAGCATA
*
180386 TGAATCATTCAGCATT
1 TGAATCATTCAGCACT
*
180402 TGAATCATTCAGCGCT
1 TGAATCATTCAGCACT
180418 T-AATCATTC
1 TGAATCATTC
180427 TGAAGTAAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 8 0.35
16 15 0.65
ACGTcount: A:0.29, C:0.22, G:0.12, T:0.37
Consensus pattern (16 bp):
TGAATCATTCAGCACT
Found at i:183689 original size:20 final size:20
Alignment explanation
Indices: 183666--183758 Score: 105
Period size: 20 Copynumber: 4.6 Consensus size: 20
183656 TCAGTAGACT
* *
183666 ATCGCAACACGAAATAGAAA
1 ATCGCAACGCGAAATGGAAA
** ** *
183686 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGGAA-A
183707 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
*
183727 ATCGCAATGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
183747 ATCGCAACGCGA
1 ATCGCAACGCGA
183759 TTTTCAGTTG
Statistics
Matches: 59, Mismatches: 13, Indels: 2
0.80 0.18 0.03
Matches are distributed among these distances:
20 44 0.75
21 15 0.25
ACGTcount: A:0.42, C:0.23, G:0.20, T:0.15
Consensus pattern (20 bp):
ATCGCAACGCGAAATGGAAA
Found at i:187364 original size:6 final size:6
Alignment explanation
Indices: 187353--187378 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
187343 TTGAGAGAGA
187353 TCAGGC TCAGGC TCAGGC TCAGGC TC
1 TCAGGC TCAGGC TCAGGC TCAGGC TC
187379 CAGCTCACGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.35, G:0.31, T:0.19
Consensus pattern (6 bp):
TCAGGC
Found at i:190464 original size:19 final size:18
Alignment explanation
Indices: 190423--190466 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
190413 TTCAATATAC
*
190423 ATATAATATAATTTTAAT
1 ATATATTATAATTTTAAT
*
190441 A-ATATTATATTTTTAAT
1 ATATATTATAATTTTAAT
190458 ATTATATTA
1 A-TATATTA
190467 ATATATACTC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 15 0.68
18 1 0.05
19 6 0.27
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
ATATATTATAATTTTAAT
Found at i:190540 original size:17 final size:17
Alignment explanation
Indices: 190514--190573 Score: 52
Period size: 17 Copynumber: 3.4 Consensus size: 17
190504 AAATTTTTAA
190514 ATAA-ATTATTAATAAT
1 ATAATATTATTAATAAT
*
190530 ATAATATTATTAA-ATT
1 ATAATATTATTAATAAT
*
190546 ATTAATAATATGTAATATAT
1 A-TAATATTAT-TAATA-AT
190566 ATATATAT
1 ATA-ATAT
190574 ATATATATTT
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
16 7 0.21
17 16 0.47
18 3 0.09
19 3 0.09
20 5 0.15
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (17 bp):
ATAATATTATTAATAAT
Found at i:190949 original size:29 final size:29
Alignment explanation
Indices: 190894--190949 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
190884 CCTGGAAAAT
* * *
190894 ATAATTCGTTTTACGTAAAATAGTTTTAG
1 ATAATTCATTTTACGTAAAACAATTTTAG
190923 ATAATTCATTTTACGTAAAACAATTTT
1 ATAATTCATTTTACGTAAAACAATTTT
190950 CGGGTAATCT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.38, C:0.09, G:0.09, T:0.45
Consensus pattern (29 bp):
ATAATTCATTTTACGTAAAACAATTTTAG
Done.