Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397274.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_228.0, 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: 2969030
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 66526 characters in sequence are not A, C, G, or T
File 4 of 8
Found at i:1478189 original size:34 final size:34
Alignment explanation
Indices: 1478151--1478497 Score: 212
Period size: 34 Copynumber: 10.2 Consensus size: 34
1478141 CACTAGATGC
*
1478151 TACATGCCAAGGTCAAAACTTCAACACCAAATGT
1 TACATGCCAAGGTCAAAGCTTCAACACCAAATGT
* * * *
1478185 TACATGTCAAGGTCAAAGCTTCACCTCTAAATGT
1 TACATGCCAAGGTCAAAGCTTCAACACCAAATGT
* * *
1478219 TACATGCCAAGGTTAAAGCTTTAACACCAGATGT
1 TACATGCCAAGGTCAAAGCTTCAACACCAAATGT
* ** * * *
1478253 TGCACACCAAGATCAAAGTTTCAGCACCAAATGT
1 TACATGCCAAGGTCAAAGCTTCAACACCAAATGT
* * * * *
1478287 TACATGCCAAGATTAAAGCTTCACCATTC-GATGT
1 TACATGCCAAGGTCAAAGCTTCAACA-CCAAATGT
* * * * * * *
1478321 TACATGCCAAAGTTAAATCTTCACCGCTAGATGT
1 TACATGCCAAGGTCAAAGCTTCAACACCAAATGT
* * * *** ** *
1478355 TATATGCTAAGGTTAAAGCTTCATTGCTGAATAT
1 TACATGCCAAGGTCAAAGCTTCAACACCAAATGT
* *
1478389 TACATGCCAAGGTCAACA-CTTTACCACCAAATGT
1 TACATGCCAAGGTCAA-AGCTTCAACACCAAATGT
* ** * * **
1478423 TACACGTTAAGGTCAAAACTTTAACACTGAATGT
1 TACATGCCAAGGTCAAAGCTTCAACACCAAATGT
* * * * * *
1478457 TATATGTCAAAGTTAAAGCTTCAACACCATATAT
1 TACATGCCAAGGTCAAAGCTTCAACACCAAATGT
1478491 TACATGC
1 TACATGC
1478498 AAAAACTTCC
Statistics
Matches: 236, Mismatches: 73, Indels: 8
0.74 0.23 0.03
Matches are distributed among these distances:
33 1 0.00
34 233 0.99
35 2 0.01
ACGTcount: A:0.36, C:0.22, G:0.14, T:0.28
Consensus pattern (34 bp):
TACATGCCAAGGTCAAAGCTTCAACACCAAATGT
Found at i:1490387 original size:186 final size:187
Alignment explanation
Indices: 1490038--1490389 Score: 498
Period size: 186 Copynumber: 1.9 Consensus size: 187
1490028 TGGTGACAAA
* *
1490038 TTTGTCTATGATCTATCGTGCATGGTTCTTTTGGAGAAGCTGGAATGATAGAGCTTTGTGGTGAT
1 TTTGTCTATGATCTATCGTCCATGGTTCTTTTGGAGAAGCTGGAATGATAGAACTTTGTGGTGAT
* *
1490103 AAAGGTGGCAATCCTCTGAACTGTGCTTCATTACATGTTCCTGGTTTAAAGTAGAGTTGAAGTTC
66 AAAGGTGCCAATCCTCTGAACTGTGATTCATTACATGTTCCTGGTTTAAAGTAGAGTTGAAGTTC
* *
1490168 ATGTGAGGATAACTCTAGAGTCATTTGGAAAGACATATATTAGGTGGTGATAAAGGT
131 AGGTGAGGATAACTCTAGAGTCATATGGAAAGACATATATTAGGTGGTGATAAAGGT
*
1490225 TTTGTCTATGATCTAGT-GTCCATGGTTCTTTTGGAGGAA-CT-GAATGGTAGAACTTTGTGGTG
1 TTTGTCTATGATCTA-TCGTCCATGGTTCTTTTGGA-GAAGCTGGAATGATAGAACTTTGTGGTG
* * * **
1490287 GTAAAGGTGCCAGTCCTCTGAACTGTGATTCATTACATGTTCTTGGTTTCGAGTAGAGTTG-AGA
64 ATAAAGGTGCCAATCCTCTGAACTGTGATTCATTACATGTTCCTGGTTTAAAGTAGAGTTGAAG-
* * *
1490351 TTCAGGTGTGGATGACTCTATAGTCA-ATGAGAAAGACAT
128 TTCAGGTGAGGATAACTCTAGAGTCATATG-GAAAGACAT
1490390 GAAATAGATG
Statistics
Matches: 146, Mismatches: 15, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
185 4 0.03
186 104 0.71
187 34 0.23
188 4 0.03
ACGTcount: A:0.26, C:0.12, G:0.27, T:0.35
Consensus pattern (187 bp):
TTTGTCTATGATCTATCGTCCATGGTTCTTTTGGAGAAGCTGGAATGATAGAACTTTGTGGTGAT
AAAGGTGCCAATCCTCTGAACTGTGATTCATTACATGTTCCTGGTTTAAAGTAGAGTTGAAGTTC
AGGTGAGGATAACTCTAGAGTCATATGGAAAGACATATATTAGGTGGTGATAAAGGT
Found at i:1494122 original size:2 final size:2
Alignment explanation
Indices: 1494115--1494140 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1494105 GTCTCCCTCA
1494115 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
1494141 TGCTTGTGAA
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1505062 original size:12 final size:12
Alignment explanation
Indices: 1505026--1505082 Score: 69
Period size: 12 Copynumber: 4.6 Consensus size: 12
1505016 TGAGCAAAAG
1505026 GATTTATCCTCTT
1 GATTT-TCCTCTT
**
1505039 GATAAATCCTCTT
1 GAT-TTTCCTCTT
1505052 GATTTTCCTCTT
1 GATTTTCCTCTT
*
1505064 GATTATCCTCTT
1 GATTTTCCTCTT
1505076 GATTTTC
1 GATTTTC
1505083 AATTCCAATA
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
12 24 0.65
13 13 0.35
ACGTcount: A:0.18, C:0.23, G:0.09, T:0.51
Consensus pattern (12 bp):
GATTTTCCTCTT
Found at i:1505076 original size:24 final size:25
Alignment explanation
Indices: 1505026--1505082 Score: 89
Period size: 24 Copynumber: 2.3 Consensus size: 25
1505016 TGAGCAAAAG
1505026 GATTTATCCTCTTGATAAATCCTCTT
1 GATTT-TCCTCTTGATAAATCCTCTT
*
1505052 GATTTTCCTCTTGAT-TATCCTCTT
1 GATTTTCCTCTTGATAAATCCTCTT
1505076 GATTTTC
1 GATTTTC
1505083 AATTCCAATA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
24 15 0.50
25 10 0.33
26 5 0.17
ACGTcount: A:0.18, C:0.23, G:0.09, T:0.51
Consensus pattern (25 bp):
GATTTTCCTCTTGATAAATCCTCTT
Found at i:1506258 original size:60 final size:59
Alignment explanation
Indices: 1506185--1506301 Score: 189
Period size: 60 Copynumber: 2.0 Consensus size: 59
1506175 GAATCAAGAC
* *
1506185 AGATATCATAATGAAGGATAATGGGGATCATAAACAGATATGCTTCTTGACTTAGTGAAT
1 AGATATCATAATGAAGGATAATGGGCATCAT-AACAGATATGCTCCTTGACTTAGTGAAT
* *
1506245 AGATATCATAATGAAGTATAATGGGCATCATGACAGATATGCTCCTTGACTTAGTGA
1 AGATATCATAATGAAGGATAATGGGCATCATAACAGATATGCTCCTTGACTTAGTGA
1506302 TATAATTTCT
Statistics
Matches: 53, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
59 24 0.45
60 29 0.55
ACGTcount: A:0.37, C:0.12, G:0.21, T:0.30
Consensus pattern (59 bp):
AGATATCATAATGAAGGATAATGGGCATCATAACAGATATGCTCCTTGACTTAGTGAAT
Found at i:1507889 original size:59 final size:59
Alignment explanation
Indices: 1507795--1507907 Score: 156
Period size: 59 Copynumber: 1.9 Consensus size: 59
1507785 TCATGACAGA
* *
1507795 TATCATAATGAAGGATAATGAGGATCATAATAGATATGATCTTTGACTTAGTGAATAGG
1 TATCATAATGAAGGATAATGAGGATCATAACAGATATGATCCTTGACTTAGTGAATAGG
* * * *
1507854 TATCATAATGAATGATATTG-GCGATCATGACAGATATGCTCCTTGACTTAGTGA
1 TATCATAATGAAGGATAATGAG-GATCATAACAGATATGATCCTTGACTTAGTGA
1507908 TATAATTTCC
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
58 1 0.02
59 46 0.98
ACGTcount: A:0.35, C:0.11, G:0.21, T:0.33
Consensus pattern (59 bp):
TATCATAATGAAGGATAATGAGGATCATAACAGATATGATCCTTGACTTAGTGAATAGG
Found at i:1509845 original size:56 final size:56
Alignment explanation
Indices: 1509737--1509846 Score: 157
Period size: 56 Copynumber: 2.0 Consensus size: 56
1509727 TTGACTCCTG
* * * * *
1509737 ATCCTATGGTGAGATACTTAGTAATATGTCAAACCGTAAAAGACGTTTGAAAGTAA
1 ATCCTATAGTGAGACACTTAGTAATATGTCAAACCGTAAAAGAAGATAGAAAGTAA
* *
1509793 ATCCTATAGTGAGACATTTAGTAATATGTCAAACTGTAAAAGAAGATAGAAAGT
1 ATCCTATAGTGAGACACTTAGTAATATGTCAAACCGTAAAAGAAGATAGAAAGT
1509847 GTCTATGCTA
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
56 47 1.00
ACGTcount: A:0.42, C:0.11, G:0.19, T:0.28
Consensus pattern (56 bp):
ATCCTATAGTGAGACACTTAGTAATATGTCAAACCGTAAAAGAAGATAGAAAGTAA
Found at i:1513368 original size:15 final size:16
Alignment explanation
Indices: 1513348--1513377 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1513338 TAAAAGTAAA
1513348 ATTTTATTTA-TAATT
1 ATTTTATTTACTAATT
1513363 ATTTTATTTACTAAT
1 ATTTTATTTACTAAT
1513378 AGTAATGTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (16 bp):
ATTTTATTTACTAATT
Found at i:1518691 original size:31 final size:31
Alignment explanation
Indices: 1518649--1518708 Score: 111
Period size: 31 Copynumber: 1.9 Consensus size: 31
1518639 GATAGAGTAG
*
1518649 AATATGGGCTGGCCCGGCCCTGCCCATATAA
1 AATATGAGCTGGCCCGGCCCTGCCCATATAA
1518680 AATATGAGCTGGCCCGGCCCTGCCCATAT
1 AATATGAGCTGGCCCGGCCCTGCCCATAT
1518709 TTTTTCAACC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.22, C:0.33, G:0.25, T:0.20
Consensus pattern (31 bp):
AATATGAGCTGGCCCGGCCCTGCCCATATAA
Found at i:1524068 original size:21 final size:21
Alignment explanation
Indices: 1524027--1524070 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
1524017 TTTTTTATTT
1524027 AATTATAAATAAAAATATAAA
1 AATTATAAATAAAAATATAAA
* *
1524048 AATT-TAATTAAACATATTAAA
1 AATTATAAATAAAAATA-TAAA
1524069 AA
1 AA
1524071 AATAAAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (21 bp):
AATTATAAATAAAAATATAAA
Found at i:1537832 original size:24 final size:25
Alignment explanation
Indices: 1537801--1537857 Score: 73
Period size: 24 Copynumber: 2.4 Consensus size: 25
1537791 AATATTAAAA
*
1537801 TAATAATTTATT-TTTTATAAATTT
1 TAATAATTTATTATTATATAAATTT
*
1537825 TAATAA-TTATTATTATATAATTTT
1 TAATAATTTATTATTATATAAATTT
*
1537849 TATTAATTT
1 TAATAATTT
1537858 TAAAAAAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
23 5 0.18
24 21 0.75
25 2 0.07
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (25 bp):
TAATAATTTATTATTATATAAATTT
Found at i:1538073 original size:16 final size:17
Alignment explanation
Indices: 1538054--1538085 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1538044 TTTAGTGTTT
1538054 ATATTT-TTTTAAAAAA
1 ATATTTATTTTAAAAAA
1538070 ATATTTATTTTAAAAA
1 ATATTTATTTTAAAAA
1538086 CTAATAAATC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
ATATTTATTTTAAAAAA
Found at i:1538156 original size:14 final size:15
Alignment explanation
Indices: 1538134--1538166 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
1538124 TTGTAAGGTA
1538134 TTTTATCTTTTT-AT
1 TTTTATCTTTTTAAT
*
1538148 TTTTCTCTTTTTAAT
1 TTTTATCTTTTTAAT
1538163 TTTT
1 TTTT
1538167 TTATTTAAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.12, C:0.09, G:0.00, T:0.79
Consensus pattern (15 bp):
TTTTATCTTTTTAAT
Found at i:1539058 original size:16 final size:15
Alignment explanation
Indices: 1539017--1539059 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 15
1539007 TTTAATATAT
1539017 TATTATTTATATTAAA
1 TATTA-TTATATTAAA
1539033 TATGTA-TATATTACAA
1 TAT-TATTATATTA-AA
1539049 TATTATTATAT
1 TATTATTATAT
1539060 ATTTAAACAT
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
15 9 0.38
16 13 0.54
17 2 0.08
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.53
Consensus pattern (15 bp):
TATTATTATATTAAA
Found at i:1539437 original size:19 final size:19
Alignment explanation
Indices: 1539388--1539429 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
1539378 GACATTAATT
1539388 TAAAATATTATTTTTATAAA
1 TAAAATA-TATTTTTATAAA
*
1539408 TAAAATCTATTTTTATAAA
1 TAAAATATATTTTTATAAA
1539427 TAA
1 TAA
1539430 GAAATATTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 15 0.71
20 6 0.29
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (19 bp):
TAAAATATATTTTTATAAA
Found at i:1540064 original size:34 final size:32
Alignment explanation
Indices: 1540020--1540083 Score: 83
Period size: 34 Copynumber: 1.9 Consensus size: 32
1540010 TTTTTGAAAC
1540020 TCAAGCATAATCTTTAAAATATCTTTTCAAAGAA
1 TCAAGCATAATC-TTAAAATA-CTTTTCAAAGAA
* * *
1540054 TCAAGTATAATCTTACAATACTTTTTAAAG
1 TCAAGCATAATCTTAAAATACTTTTCAAAG
1540084 GAGCAAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
32 9 0.33
33 7 0.26
34 11 0.41
ACGTcount: A:0.42, C:0.14, G:0.06, T:0.38
Consensus pattern (32 bp):
TCAAGCATAATCTTAAAATACTTTTCAAAGAA
Found at i:1541094 original size:2 final size:2
Alignment explanation
Indices: 1541089--1541113 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1541079 AGTTAAAGTG
1541089 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1541114 AACAAAGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1543076 original size:2 final size:2
Alignment explanation
Indices: 1543069--1543098 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1543059 TGAATACTCT
1543069 AG AG 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 AG AG
1543099 GAAGGCATGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1544405 original size:12 final size:12
Alignment explanation
Indices: 1544390--1544416 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
1544380 AGCAAAATAA
1544390 AAATAAAAAAGG
1 AAATAAAAAAGG
1544402 AAATAAAAAAGG
1 AAATAAAAAAGG
1544414 AAA
1 AAA
1544417 AGCAGAAAAA
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:0.78, C:0.00, G:0.15, T:0.07
Consensus pattern (12 bp):
AAATAAAAAAGG
Found at i:1548174 original size:24 final size:24
Alignment explanation
Indices: 1548146--1548213 Score: 118
Period size: 24 Copynumber: 2.8 Consensus size: 24
1548136 TATTGAAGAA
1548146 GGAATGGGGGCATCAGCCCTGAAG
1 GGAATGGGGGCATCAGCCCTGAAG
*
1548170 GGAATGGGAGCATCAGCCCTGAAG
1 GGAATGGGGGCATCAGCCCTGAAG
*
1548194 GGAATGGGGGCATCATCCCT
1 GGAATGGGGGCATCAGCCCT
1548214 AAAACTGAAC
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 41 1.00
ACGTcount: A:0.25, C:0.22, G:0.38, T:0.15
Consensus pattern (24 bp):
GGAATGGGGGCATCAGCCCTGAAG
Found at i:1548249 original size:15 final size:15
Alignment explanation
Indices: 1548229--1548437 Score: 164
Period size: 15 Copynumber: 14.3 Consensus size: 15
1548219 TGAACCCCTG
*
1548229 AAGAAGTATTCCATC
1 AAGAAGTATCCCATC
*
1548244 AAGAAGTATCCCATG
1 AAGAAGTATCCCATC
* * *
1548259 AAGACGTAGCTCATC
1 AAGAAGTATCCCATC
*
1548274 AAGAAGTATCCCATG
1 AAGAAGTATCCCATC
* *
1548289 AAGACA-TAGCTCATC
1 AAGA-AGTATCCCATC
1548304 AAGAAGTATCCCATC
1 AAGAAGTATCCCATC
* *
1548319 AAGAAGTAGCTCATC
1 AAGAAGTATCCCATC
*
1548334 AAGAAAT-TCCCATC
1 AAGAAGTATCCCATC
*
1548348 AAGAAGTCA-CTCATC
1 AAGAAGT-ATCCCATC
*
1548363 AAGAA-AATCCCATC
1 AAGAAGTATCCCATC
* * *
1548377 AAGAATTAGCTCATC
1 AAGAAGTATCCCATC
*
1548392 AAGAAATAT-CC--C
1 AAGAAGTATCCCATC
* * *
1548404 AAGAATTAGCTCATC
1 AAGAAGTATCCCATC
1548419 AAGAA-TATCCCATC
1 AAGAAGTATCCCATC
1548433 AAGAA
1 AAGAA
1548438 TTAGCTCCAA
Statistics
Matches: 150, Mismatches: 35, Indels: 19
0.74 0.17 0.09
Matches are distributed among these distances:
12 8 0.05
13 2 0.01
14 35 0.23
15 104 0.69
16 1 0.01
ACGTcount: A:0.42, C:0.23, G:0.14, T:0.21
Consensus pattern (15 bp):
AAGAAGTATCCCATC
Found at i:1548354 original size:29 final size:30
Alignment explanation
Indices: 1548240--1548467 Score: 271
Period size: 30 Copynumber: 7.9 Consensus size: 30
1548230 AGAAGTATTC
* * *
1548240 CATCAAGAAGTATCCCATGAAGACGTAGCT
1 CATCAAGAAATATCCCATCAAGAAGTAGCT
* *
1548270 CATCAAGAAGTATCCCATGAAGACA-TAGCT
1 CATCAAGAAATATCCCATCAAGA-AGTAGCT
*
1548300 CATCAAGAAGTATCCCATCAAGAAGTAGCT
1 CATCAAGAAATATCCCATCAAGAAGTAGCT
1548330 CATCAAGAAAT-TCCCATCAAGAAGTCA-CT
1 CATCAAGAAATATCCCATCAAGAAGT-AGCT
*
1548359 CATCAAGAAA-ATCCCATCAAGAATTAGCT
1 CATCAAGAAATATCCCATCAAGAAGTAGCT
*
1548388 CATCAAGAAATAT-CC--CAAGAATTAGCT
1 CATCAAGAAATATCCCATCAAGAAGTAGCT
*
1548415 CATCAAG-AATATCCCATCAAGAATTAGCT
1 CATCAAGAAATATCCCATCAAGAAGTAGCT
*
1548444 C--CAAGAAATAT-CCATCCAGAAGTA
1 CATCAAGAAATATCCCATCAAGAAGTA
1548468 CATTCTCAAG
Statistics
Matches: 182, Mismatches: 6, Indels: 23
0.86 0.03 0.11
Matches are distributed among these distances:
26 5 0.03
27 36 0.20
28 6 0.03
29 67 0.37
30 68 0.37
ACGTcount: A:0.42, C:0.24, G:0.14, T:0.21
Consensus pattern (30 bp):
CATCAAGAAATATCCCATCAAGAAGTAGCT
Found at i:1548477 original size:56 final size:57
Alignment explanation
Indices: 1548240--1548478 Score: 226
Period size: 56 Copynumber: 4.1 Consensus size: 57
1548230 AGAAGTATTC
* ** * *
1548240 CATCAAGAAGTATCCCATGAAGACGTAGCTCATCAAGAAGTATCCCATGAAGACA-TAGC-T
1 CATCAAGAA-TATCCCATCAAGAATTAGCTCA-CAAGAAATAT-CCATCAAGA-AGTA-CAT
*
1548300 CATCAAGAAGTATCCCATCAAGAAGTAGCTCATCAAGAAAT-TCCCATCAAGAAGT-CACT
1 CATCAAGAA-TATCCCATCAAGAATTAGCTCA-CAAGAAATAT-CCATCAAGAAGTACA-T
* *
1548359 CATCAAGAAAATCCCATCAAGAATTAGCTCATCAAGAAATATCC--CAAGAATTAGC-T
1 CATCAAGAATATCCCATCAAGAATTAGCTCA-CAAGAAATATCCATCAAGAAGTA-CAT
*
1548415 CATCAAGAATATCCCATCAAGAATTAGCTC-CAAGAAATATCCATCCAGAAGTACATT
1 CATCAAGAATATCCCATCAAGAATTAGCTCACAAGAAATATCCATCAAGAAGTACA-T
1548472 C-TCAAGA
1 CATCAAGA
1548479 TCCCCTTATT
Statistics
Matches: 159, Mismatches: 10, Indels: 24
0.82 0.05 0.12
Matches are distributed among these distances:
54 12 0.08
55 1 0.01
56 50 0.31
57 3 0.02
58 33 0.21
59 22 0.14
60 38 0.24
ACGTcount: A:0.41, C:0.24, G:0.13, T:0.21
Consensus pattern (57 bp):
CATCAAGAATATCCCATCAAGAATTAGCTCACAAGAAATATCCATCAAGAAGTACAT
Found at i:1555322 original size:27 final size:28
Alignment explanation
Indices: 1555250--1555326 Score: 106
Period size: 29 Copynumber: 2.8 Consensus size: 28
1555240 AATTAATTTT
1555250 TATAAAAATTTATTTAAATTAAAATAAAA
1 TATAAAAATTTATTTAAATT-AAATAAAA
1555279 TATAAAAATTTGA-TTAAATGT-AATAAAA
1 TATAAAAATTT-ATTTAAAT-TAAATAAAA
1555307 -ATAAAAATTTATTTAAATTA
1 TATAAAAATTTATTTAAATTA
1555327 TTTTAAATAA
Statistics
Matches: 44, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
26 2 0.05
27 16 0.36
28 7 0.16
29 17 0.39
30 2 0.05
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (28 bp):
TATAAAAATTTATTTAAATTAAATAAAA
Found at i:1557988 original size:28 final size:28
Alignment explanation
Indices: 1557957--1558016 Score: 120
Period size: 28 Copynumber: 2.1 Consensus size: 28
1557947 TTAATTATGG
1557957 TTTTTCAATTTCATTTTTGTTAAAATTA
1 TTTTTCAATTTCATTTTTGTTAAAATTA
1557985 TTTTTCAATTTCATTTTTGTTAAAATTA
1 TTTTTCAATTTCATTTTTGTTAAAATTA
1558013 TTTT
1 TTTT
1558017 AAGTTAAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.27, C:0.07, G:0.03, T:0.63
Consensus pattern (28 bp):
TTTTTCAATTTCATTTTTGTTAAAATTA
Found at i:1564620 original size:21 final size:21
Alignment explanation
Indices: 1564596--1564660 Score: 76
Period size: 21 Copynumber: 3.1 Consensus size: 21
1564586 CACAGTCCTG
*
1564596 AAGGCCATTGCTTTCAATGTC
1 AAGGCCATTGCTTTCAATATC
* * * *
1564617 AAGGCCATTTCCTTCTATCTC
1 AAGGCCATTGCTTTCAATATC
*
1564638 AAGGCCATTGCTCTCAATATC
1 AAGGCCATTGCTTTCAATATC
1564659 AA
1 AA
1564661 TGTCATTCCC
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.26, C:0.28, G:0.14, T:0.32
Consensus pattern (21 bp):
AAGGCCATTGCTTTCAATATC
Found at i:1564673 original size:42 final size:42
Alignment explanation
Indices: 1564596--1564682 Score: 111
Period size: 42 Copynumber: 2.1 Consensus size: 42
1564586 CACAGTCCTG
* * * *
1564596 AAGGCCATTGCTTTCAATGTCAAGGCCATTTCCTTCTATCTC
1 AAGGCCATTGCTCTCAATATCAAGGCCATTCCCTTCAATCTC
* * *
1564638 AAGGCCATTGCTCTCAATATCAATGTCATTCCCTTCAATTTC
1 AAGGCCATTGCTCTCAATATCAAGGCCATTCCCTTCAATCTC
1564680 AAG
1 AAG
1564683 ATCATTTCCT
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.25, C:0.28, G:0.13, T:0.34
Consensus pattern (42 bp):
AAGGCCATTGCTCTCAATATCAAGGCCATTCCCTTCAATCTC
Found at i:1564675 original size:21 final size:21
Alignment explanation
Indices: 1564651--1564708 Score: 55
Period size: 21 Copynumber: 2.8 Consensus size: 21
1564641 GCCATTGCTC
1564651 TCAATATCAATG-TCATTCCCT
1 TCAATATCAA-GATCATTCCCT
* *
1564672 TCAATTTCAAGATCATTTCCT
1 TCAATATCAAGATCATTCCCT
* * *
1564693 TCCATTTCAAGCTCAT
1 TCAATATCAAGATCAT
1564709 GGCCATCATC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
20 1 0.03
21 31 0.97
ACGTcount: A:0.28, C:0.28, G:0.05, T:0.40
Consensus pattern (21 bp):
TCAATATCAAGATCATTCCCT
Found at i:1566167 original size:20 final size:20
Alignment explanation
Indices: 1566138--1566175 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1566128 TTACTTATTA
1566138 CAAATTTATATTT-TTAATT
1 CAAATTTATATTTATTAATT
1566157 CAAATTATATATTTATTAA
1 CAAATT-TATATTTATTAA
1566176 ATAAAAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 6 0.35
20 7 0.41
21 4 0.24
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (20 bp):
CAAATTTATATTTATTAATT
Found at i:1574296 original size:16 final size:15
Alignment explanation
Indices: 1574272--1574301 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
1574262 CATCTTTTAT
1574272 TTTAAATCAAATAAA
1 TTTAAATCAAATAAA
1574287 TTTAACATCAAATAA
1 TTTAA-ATCAAATAA
1574302 TAATAAAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.57, C:0.10, G:0.00, T:0.33
Consensus pattern (15 bp):
TTTAAATCAAATAAA
Found at i:1574419 original size:27 final size:30
Alignment explanation
Indices: 1574371--1574426 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
1574361 TTTAGTTTAA
*
1574371 AATAAAAAATATATGATTTTAA-TTAAATAT
1 AATAAAAAATATAAGA-TTTAATTTAAATAT
1574401 AATAAAAAATA-AAGA-TTAATTTAAAT
1 AATAAAAAATATAAGATTTAATTTAAAT
1574427 TTTTTAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
27 4 0.17
28 6 0.25
29 3 0.12
30 11 0.46
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.36
Consensus pattern (30 bp):
AATAAAAAATATAAGATTTAATTTAAATAT
Found at i:1577718 original size:16 final size:16
Alignment explanation
Indices: 1577693--1577726 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1577683 AAATGATGTA
*
1577693 AAACACTTAAATGTTC
1 AAACACTTAAATATTC
*
1577709 AAACATTTAAATATTC
1 AAACACTTAAATATTC
1577725 AA
1 AA
1577727 TTTTACTTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.15, G:0.03, T:0.32
Consensus pattern (16 bp):
AAACACTTAAATATTC
Found at i:1581891 original size:13 final size:13
Alignment explanation
Indices: 1581881--1581912 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
1581871 TCTGTTTTGT
1581881 ATTTTTTTTTTCA
1 ATTTTTTTTTTCA
1581894 ATTTTTTTTTTC-
1 ATTTTTTTTTTCA
1581906 ATTTTTT
1 ATTTTTT
1581913 AATTAATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 7 0.37
13 12 0.63
ACGTcount: A:0.12, C:0.06, G:0.00, T:0.81
Consensus pattern (13 bp):
ATTTTTTTTTTCA
Found at i:1585560 original size:18 final size:18
Alignment explanation
Indices: 1585492--1585561 Score: 63
Period size: 18 Copynumber: 3.9 Consensus size: 18
1585482 CGTTTAATTA
* *
1585492 ATCGTG-TTAATCCTGTT
1 ATCGTGTTTAAACGTGTT
* * *
1585509 ATCATGTTTAAACGTATAA
1 ATCGTGTTTAAACGTGT-T
*
1585528 AT-GTGTTTAATCGTGTT
1 ATCGTGTTTAAACGTGTT
1585545 ATCGTGTTTAAACGTGT
1 ATCGTGTTTAAACGTGT
1585562 ATACATGACA
Statistics
Matches: 40, Mismatches: 10, Indels: 5
0.73 0.18 0.09
Matches are distributed among these distances:
17 7 0.17
18 31 0.77
19 2 0.05
ACGTcount: A:0.26, C:0.11, G:0.19, T:0.44
Consensus pattern (18 bp):
ATCGTGTTTAAACGTGTT
Found at i:1596638 original size:24 final size:23
Alignment explanation
Indices: 1596609--1596658 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
1596599 TCAAGAAAAT
* * *
1596609 TTAAAAGGAAAATATTGTTTTAA
1 TTAAAAAGAAAACAATGTTTTAA
1596632 TTAAAAAGAAAACAATGTTTTAA
1 TTAAAAAGAAAACAATGTTTTAA
1596655 TTAA
1 TTAA
1596659 TCTCTCAACT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.52, C:0.02, G:0.10, T:0.36
Consensus pattern (23 bp):
TTAAAAAGAAAACAATGTTTTAA
Found at i:1598361 original size:14 final size:16
Alignment explanation
Indices: 1598326--1598361 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
1598316 AATAGAAAAA
1598326 CATTTTAATTGTATAT
1 CATTTTAATTGTATAT
1598342 -ATTTTAATT-TA-AT
1 CATTTTAATTGTATAT
1598355 CATTTTA
1 CATTTTA
1598362 GTTACATTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
13 2 0.11
14 8 0.42
15 9 0.47
ACGTcount: A:0.33, C:0.06, G:0.03, T:0.58
Consensus pattern (16 bp):
CATTTTAATTGTATAT
Found at i:1598522 original size:21 final size:21
Alignment explanation
Indices: 1598498--1598563 Score: 69
Period size: 23 Copynumber: 3.0 Consensus size: 21
1598488 TTGACACGAC
*
1598498 TATTTAATTATATCGTATTTA
1 TATTTAATTATATAGTATTTA
* *
1598519 TATTTACTTATATAGTTATTAA
1 TATTTAATTATATAG-TATTTA
*
1598541 TAATTTATTTATATATGTATTTA
1 T-ATTTAATTATATA-GTATTTA
1598564 AAATTTTAAT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
21 13 0.35
22 6 0.16
23 17 0.46
24 1 0.03
ACGTcount: A:0.35, C:0.03, G:0.05, T:0.58
Consensus pattern (21 bp):
TATTTAATTATATAGTATTTA
Found at i:1603094 original size:4 final size:4
Alignment explanation
Indices: 1603085--1603111 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
1603075 GGCCCTTCTA
1603085 CCTG CCTG CCTG CCTG CCTG CCTG CCT
1 CCTG CCTG CCTG CCTG CCTG CCTG CCT
1603112 TTACCCTTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.00, C:0.52, G:0.22, T:0.26
Consensus pattern (4 bp):
CCTG
Found at i:1604556 original size:17 final size:17
Alignment explanation
Indices: 1604536--1604571 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
1604526 AATTATATTA
1604536 TATAAAATTATGAAACT
1 TATAAAATTATGAAACT
* *
1604553 TATAAAATTGTGAGACT
1 TATAAAATTATGAAACT
1604570 TA
1 TA
1604572 AAGCAAGAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.06, G:0.11, T:0.36
Consensus pattern (17 bp):
TATAAAATTATGAAACT
Found at i:1611945 original size:24 final size:24
Alignment explanation
Indices: 1611910--1611958 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 24
1611900 AGTCACACTG
*
1611910 AATATTCTAGAATGATG-CTATTTA
1 AATATTCAAGAATGA-GACTATTTA
1611934 AATATTCAAGAATGAGACTATTTA
1 AATATTCAAGAATGAGACTATTTA
1611958 A
1 A
1611959 TATAAAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.04
24 22 0.96
ACGTcount: A:0.43, C:0.08, G:0.12, T:0.37
Consensus pattern (24 bp):
AATATTCAAGAATGAGACTATTTA
Found at i:1613245 original size:2 final size:2
Alignment explanation
Indices: 1613238--1613265 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1613228 AAGTTGCACC
1613238 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
1613266 CTTTATTAAG
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:1614507 original size:26 final size:27
Alignment explanation
Indices: 1614463--1614521 Score: 84
Period size: 26 Copynumber: 2.2 Consensus size: 27
1614453 TTCAAGCGCA
* *
1614463 CATGTTGAAAAAAAAATTGGTATACGT
1 CATGTTGAAAAAAAAATTGCTACACGT
*
1614490 CATGTTG-AAAAAAAATTGCTACATGT
1 CATGTTGAAAAAAAAATTGCTACACGT
1614516 CATGTT
1 CATGTT
1614522 TAAGGTGTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
26 22 0.76
27 7 0.24
ACGTcount: A:0.41, C:0.10, G:0.17, T:0.32
Consensus pattern (27 bp):
CATGTTGAAAAAAAAATTGCTACACGT
Found at i:1614628 original size:27 final size:27
Alignment explanation
Indices: 1614571--1614630 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 27
1614561 ACAAAGATTG
* * * *
1614571 TTACATGTTATGTTTAAAAAAACATTC
1 TTACACGTCATGTTGAAAAAAACATTA
1614598 TTACACGTCATGTTGAAAAAAA-AGTTA
1 TTACACGTCATGTTGAAAAAAACA-TTA
1614625 TTACAC
1 TTACAC
1614631 ACTATAATTA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 1 0.04
27 27 0.96
ACGTcount: A:0.42, C:0.13, G:0.10, T:0.35
Consensus pattern (27 bp):
TTACACGTCATGTTGAAAAAAACATTA
Found at i:1614731 original size:28 final size:28
Alignment explanation
Indices: 1614695--1614765 Score: 90
Period size: 28 Copynumber: 2.5 Consensus size: 28
1614685 TAGAGACCTA
*
1614695 GTTATACACCATGTTGCAAAAAAA-AGTT
1 GTTACACACCATGTTG-AAAAAAATAGTT
*
1614723 GTTACACACTATGTTGAAAAAAATAGTT
1 GTTACACACCATGTTGAAAAAAATAGTT
* *
1614751 GTCACACGCCATGTT
1 GTTACACACCATGTT
1614766 TAAGGTGTTT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
27 7 0.19
28 30 0.81
ACGTcount: A:0.38, C:0.17, G:0.15, T:0.30
Consensus pattern (28 bp):
GTTACACACCATGTTGAAAAAAATAGTT
Found at i:1614884 original size:26 final size:26
Alignment explanation
Indices: 1614852--1614909 Score: 80
Period size: 26 Copynumber: 2.2 Consensus size: 26
1614842 AATATTATTA
* *
1614852 TTACATGTCAGATTCAAAAAAAGTTG
1 TTACATGCCAGATTCAAAAAAAATTG
* *
1614878 TTACATGCCATATTGAAAAAAAATTG
1 TTACATGCCAGATTCAAAAAAAATTG
1614904 TTACAT
1 TTACAT
1614910 ACTATGTTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.33
Consensus pattern (26 bp):
TTACATGCCAGATTCAAAAAAAATTG
Found at i:1615062 original size:86 final size:86
Alignment explanation
Indices: 1614901--1615067 Score: 228
Period size: 86 Copynumber: 1.9 Consensus size: 86
1614891 TGAAAAAAAA
* * *
1614901 TTGTTACATACTATGTTTAAGGTATTTAACTCAAAGAGTTTATATTTTAGTAAAATATAAAGATA
1 TTGTTACATACCATGTTTAAGGTATTTAACTCAAAGAGTTTATATCTTAGTAAAATACAAAGATA
*
1614966 GAAAGCAAGTTTCATGTCATG
66 GAAAGCAAGTTGCATGTCATG
* * *
1614987 TTGTTACATGCCATGTTTAAGGTGTTTAATTTC-AAGAGTTTATATCTTAGTAAAATACAAAGAT
1 TTGTTACATACCATGTTTAAGGTATTTAA-CTCAAAGAGTTTATATCTTAGTAAAATACAAAGAT
* **
1615051 AGATATTAAGTTGCATG
65 AGAAAGCAAGTTGCATG
1615068 CCATATTTAA
Statistics
Matches: 70, Mismatches: 10, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
86 68 0.97
87 2 0.03
ACGTcount: A:0.37, C:0.08, G:0.16, T:0.39
Consensus pattern (86 bp):
TTGTTACATACCATGTTTAAGGTATTTAACTCAAAGAGTTTATATCTTAGTAAAATACAAAGATA
GAAAGCAAGTTGCATGTCATG
Found at i:1619381 original size:25 final size:24
Alignment explanation
Indices: 1619347--1619523 Score: 104
Period size: 25 Copynumber: 7.1 Consensus size: 24
1619337 TTGAGAAACA
*
1619347 TGTAATGTTAAAAGGCTTCAGGAT
1 TGTAAGGTTAAAAGGCTTCAGGAT
*
1619371 GTGTAAGGTTAAAAGGTTTCAGGAT
1 -TGTAAGGTTAAAAGGCTTCAGGAT
* * * **
1619396 TGGTTAGGTTCAAAGGTTTCAAAATT
1 T-GTAAGGTTAAAAGGCTTCAGGA-T
* * *
1619422 TGCAAGATTAAAAGGTTTCAGGAT
1 TGTAAGGTTAAAAGGCTTCAGGAT
* *
1619446 TGATAAGGGTAAAA-ACTTTCAGGATT
1 TG-TAAGGTTAAAAGGC-TTCAGGA-T
* * *
1619472 TGTAAAGTTGAAAAAGCTTCAAGAT
1 TGTAAGGTT-AAAAGGCTTCAGGAT
* ** *
1619497 GGGTAAGGCAAAAAGGCTTCAGAAT
1 -TGTAAGGTTAAAAGGCTTCAGGAT
1619522 TG
1 TG
1619524 AGAAGTGTGA
Statistics
Matches: 115, Mismatches: 29, Indels: 17
0.71 0.18 0.11
Matches are distributed among these distances:
24 5 0.04
25 89 0.77
26 20 0.17
27 1 0.01
ACGTcount: A:0.36, C:0.08, G:0.26, T:0.30
Consensus pattern (24 bp):
TGTAAGGTTAAAAGGCTTCAGGAT
Found at i:1619473 original size:50 final size:50
Alignment explanation
Indices: 1619363--1619473 Score: 123
Period size: 50 Copynumber: 2.2 Consensus size: 50
1619353 GTTAAAAGGC
* * * * * * * **
1619363 TTCAGGATGTGTAAGGTTAAAAGGTTTCAGGATTGGTTAGGTTCAAAGGT
1 TTCAGGATTTGCAAGATTAAAAGGTTTCAGGATTGATAAGGGTAAAAACT
**
1619413 TTCAAAATTTGCAAGATTAAAAGGTTTCAGGATTGATAAGGGTAAAAACT
1 TTCAGGATTTGCAAGATTAAAAGGTTTCAGGATTGATAAGGGTAAAAACT
1619463 TTCAGGATTTG
1 TTCAGGATTTG
1619474 TAAAGTTGAA
Statistics
Matches: 48, Mismatches: 13, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
50 48 1.00
ACGTcount: A:0.33, C:0.07, G:0.26, T:0.33
Consensus pattern (50 bp):
TTCAGGATTTGCAAGATTAAAAGGTTTCAGGATTGATAAGGGTAAAAACT
Found at i:1623087 original size:45 final size:45
Alignment explanation
Indices: 1623003--1623091 Score: 110
Period size: 45 Copynumber: 2.0 Consensus size: 45
1622993 GAATGCGTAA
*
1623003 CACGCCATGGTGAGAATATGTGAGACGACATAGAAGGAATATGTG
1 CACGCCATGGTGAGAATATATGAGACGACATAGAAGGAATATGTG
* * *
1623048 CACGGCATGTTGAGAATATATGATAC-AC-TATGAAGGGAATATGT
1 CACGCCATGGTGAGAATATATGAGACGACATA-GAA-GGAATATGT
1623092 AACACAAGAT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
43 2 0.05
44 5 0.13
45 31 0.82
ACGTcount: A:0.36, C:0.12, G:0.28, T:0.24
Consensus pattern (45 bp):
CACGCCATGGTGAGAATATATGAGACGACATAGAAGGAATATGTG
Found at i:1623109 original size:23 final size:23
Alignment explanation
Indices: 1623083--1623165 Score: 107
Period size: 23 Copynumber: 3.6 Consensus size: 23
1623073 CACTATGAAG
1623083 GGAATATGTAACACAAGATGGAA
1 GGAATATGTAACACAAGATGGAA
* **
1623106 GGAATATGTAACAC--GCTCTAAA
1 GGAATATGTAACACAAGAT-GGAA
1623128 GGGAATATGTAACACAAGATGGAA
1 -GGAATATGTAACACAAGATGGAA
1623152 GGAATATGTAACAC
1 GGAATATGTAACAC
1623166 GCTCTAGAGG
Statistics
Matches: 50, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
21 2 0.04
22 2 0.04
23 42 0.84
24 2 0.04
25 2 0.04
ACGTcount: A:0.45, C:0.12, G:0.24, T:0.19
Consensus pattern (23 bp):
GGAATATGTAACACAAGATGGAA
Found at i:1623178 original size:23 final size:23
Alignment explanation
Indices: 1623106--1623190 Score: 89
Period size: 23 Copynumber: 3.7 Consensus size: 23
1623096 CAAGATGGAA
*
1623106 GGAATATGTAACACGCTCTAAAG
1 GGAATATGTAACACGCTCTAGAG
**** * *
1623129 GGAATATGTAACACAAGATGGAA
1 GGAATATGTAACACGCTCTAGAG
1623152 GGAATATGTAACACGCTCTAGAG
1 GGAATATGTAACACGCTCTAGAG
* *
1623175 GGAATATATGACACGC
1 GGAATATGTAACACGC
1623191 CATGATGAGA
Statistics
Matches: 47, Mismatches: 15, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
23 47 1.00
ACGTcount: A:0.40, C:0.15, G:0.25, T:0.20
Consensus pattern (23 bp):
GGAATATGTAACACGCTCTAGAG
Found at i:1623904 original size:23 final size:23
Alignment explanation
Indices: 1623176--1623905 Score: 283
Period size: 23 Copynumber: 31.9 Consensus size: 23
1623166 GCTCTAGAGG
* * *
1623176 GAATATATGACACGCCATGATGA
1 GAATATGTGACATGCCATGGTGA
* * **
1623199 GAATATATGACATGACAT-GAAA
1 GAATATGTGACATGCCATGGTGA
* * * * *
1623221 GGAATATATGACACGACACGTTGA
1 -GAATATGTGACATGCCATGGTGA
*** *
1623245 GAATATGTGACACAACATGGTCA
1 GAATATGTGACATGCCATGGTGA
*
1623268 GAATATGAAAGACA-G-CATGGTGA
1 GAATATG--TGACATGCCATGGTGA
* * * * * *
1623291 GAATATATGACACGCTATAGAGG
1 GAATATGTGACATGCCATGGTGA
*
1623314 GAATATGTGACA--CGATAGGATGA
1 GAATATGTGACATGCCAT-GG-TGA
* *
1623337 GAATATGCGACATGCCATGGAGA
1 GAATATGTGACATGCCATGGTGA
* *
1623360 GAATATGTGACACAG-CATGATGA
1 GAATATGTGACA-TGCCATGGTGA
* * * *
1623383 GAATATGTAAGACGACATGGTGA
1 GAATATGTGACATGCCATGGTGA
* * **
1623406 GAATATGTGAAACGCCAT-GAAA
1 GAATATGTGACATGCCATGGTGA
* * ***
1623428 GGAATATATGAGACAACATGGTGA
1 -GAATATGTGACATGCCATGGTGA
* ** *
1623452 GAATATGTGACACGTTAAGGTGA
1 GAATATGTGACATGCCATGGTGA
* * *
1623475 GTATATGTGACATGCCATGGAGG
1 GAATATGTGACATGCCATGGTGA
* **
1623498 GAATA--TGACACGCCAT-GAAA
1 GAATATGTGACATGCCATGGTGA
*
1623518 TGAATATGTGACATGCCATGG-AA
1 -GAATATGTGACATGCCATGGTGA
* *
1623541 GGAATATGTAACATGCCATAGTGA
1 -GAATATGTGACATGCCATGGTGA
* * * **
1623565 GAATATGTGAGACGACAT-GAAA
1 GAATATGTGACATGCCATGGTGA
* * *
1623587 GGAATATGTTACATGGCATGTTGA
1 -GAATATGTGACATGCCATGGTGA
* **
1623611 GAATATATGACACACCATGGTGA
1 GAATATGTGACATGCCATGGTGA
*** **
1623634 GAATATGTGACATAATATGGAAA
1 GAATATGTGACATGCCATGGTGA
* *
1623657 GAATATGTAAGACA--ACATGATGA
1 GAATATGT--GACATGCCATGGTGA
* * ** * **
1623680 GAATATGTGATACGGAAGGGCCA
1 GAATATGTGACATGCCATGGTGA
* * * *
1623703 GAATATATGATACGCCATAGATG-
1 GAATATGTGACATGCCAT-GGTGA
* * * * *
1623726 GAATATATAAGACGACATGGTGA
1 GAATATGTGACATGCCATGGTGA
1623749 GAATATGTGACATGCCATGGTGA
1 GAATATGTGACATGCCATGGTGA
*
1623772 GAATATGTGAGATGCCATAGG-G-
1 GAATATGTGACATGCCAT-GGTGA
* *
1623794 GAATATGTGAGATGACATGGTGA
1 GAATATGTGACATGCCATGGTGA
* * *
1623817 GAATATGTGCCATGCCATGGAGG
1 GAATATGTGACATGCCATGGTGA
* * *
1623840 GAATATATGACACGCCAT-AT-A
1 GAATATGTGACATGCCATGGTGA
*
1623861 CGAAATATGTGACATGGCATGGTGA
1 -G-AATATGTGACATGCCATGGTGA
* *
1623886 GAATATGTGAAATGACATGG
1 GAATATGTGACATGCCATGG
1623906 AAGGAATATA
Statistics
Matches: 529, Mismatches: 144, Indels: 68
0.71 0.19 0.09
Matches are distributed among these distances:
20 2 0.00
21 27 0.05
22 30 0.06
23 444 0.84
24 14 0.03
25 12 0.02
ACGTcount: A:0.38, C:0.12, G:0.27, T:0.23
Consensus pattern (23 bp):
GAATATGTGACATGCCATGGTGA
Found at i:1623914 original size:46 final size:46
Alignment explanation
Indices: 1622971--1623964 Score: 329
Period size: 46 Copynumber: 21.7 Consensus size: 46
1622961 ATATATTGAA
* * ** *
1622971 AATATGTGACAC-ATTATGGAGGGAATGCGTAACACGCCATGGTGAG
1 AATATGTGACACGA-CATGGATGGAATATGTGACACGCCATGGTGAG
* * * * *
1623017 AATATGTGAGACGACATAGAAGGAATATGTG-CACGGCATGTTGAG
1 AATATGTGACACGACATGGATGGAATATGTGACACGCCATGGTGAG
* * * * * *** *
1623062 AATATATGATAC-ACTATGAAGGGAATATGTAACACAAGATGG-AAGG
1 AATATGTGACACGAC-ATGGATGGAATATGTGACACGCCATGGTGA-G
* * ** * * *** *
1623108 AATATGTAACACG-CTCTAAAGGGAATATGTAACACAAGATGG-AAGG
1 AATATGTGACACGAC-ATGGATGGAATATGTGACACGCCATGGTGA-G
* * * * * *
1623154 AATATGTAACACG-CTCTAGAGGGAATATATGACACGCCATGATGAG
1 AATATGTGACACGAC-ATGGATGGAATATGTGACACGCCATGGTGAG
* * * * * * * *
1623200 AATATATGACATGACATGAAAGGAATATATGACACGACACGTTGAG
1 AATATGTGACACGACATGGATGGAATATGTGACACGCCATGGTGAG
* * *
1623246 AATATGTGACACAACATGG-TCAGAATATGAAAGACA-G-CATGGTGAG
1 AATATGTGACACGACATGGAT-GGAATATG--TGACACGCCATGGTGAG
* * *
1623292 AATATATGACACG-CTATAGAGGGAATATGTGACACG--ATAGGATGAG
1 AATATGTGACACGAC-ATGGATGGAATATGTGACACGCCAT-GG-TGAG
* * * *
1623338 AATATGCGACATGCCATGGA-GAGAATATGTGACACAG-CATGATGAG
1 AATATGTGACACGACATGGATG-GAATATGTGACAC-GCCATGGTGAG
* * * **
1623384 AATATGTAAGACGACATGG-TGAGAATATGTGAAACGCCAT-GAAAGG
1 AATATGTGACACGACATGGATG-GAATATGTGACACGCCATGGTGA-G
* * * ** *
1623430 AATATATGAGACAACATGG-TGAGAATATGTGACACGTTAAGGTGAG
1 AATATGTGACACGACATGGATG-GAATATGTGACACGCCATGGTGAG
* * * * **
1623476 TATATGTGACATGCCATGGAGGGAATA--TGACACGCCAT-GAAATG
1 AATATGTGACACGACATGGATGGAATATGTGACACGCCATGGTGA-G
* * * * * *
1623520 AATATGTGACATGCCATGGAAGGAATATGTAACATGCCATAGTGAG
1 AATATGTGACACGACATGGATGGAATATGTGACACGCCATGGTGAG
* * * * * * *
1623566 AATATGTGAGACGACATGAAAGGAATATGTTACATGGCATGTTGAG
1 AATATGTGACACGACATGGATGGAATATGTGACACGCCATGGTGAG
* **** **
1623612 AATATATGACAC-ACCATGG-TGAGAATATGTGACATAATATGGAAAG
1 AATATGTGACACGA-CATGGATG-GAATATGTGACACGCCATGGTGAG
* * * * ** * **
1623658 AATATGTAAGACAACAT-GATGAGAATATGTGATACGGAAGGGCCAG
1 AATATGTGACACGACATGGATG-GAATATGTGACACGCCATGGTGAG
* * * * * * * *
1623704 AATATATGATACGCCATAGATGGAATATATAAGACGACATGGTGAG
1 AATATGTGACACGACATGGATGGAATATGTGACACGCCATGGTGAG
* * * *
1623750 AATATGTGACATGCCATGG-TGAGAATATGTGAGATGCCATAGG-G-G
1 AATATGTGACACGACATGGATG-GAATATGTGACACGCCAT-GGTGAG
* * * * * *
1623795 AATATGTGAGATGACATGG-TGAGAATATGTGCCATGCCATGGAGGG
1 AATATGTGACACGACATGGATG-GAATATGTGACACGCCATGGTGAG
* * ** * * * *
1623841 AATATATGACACGCCATATACGAAATATGTGACATGGCATGGTGAG
1 AATATGTGACACGACATGGATGGAATATGTGACACGCCATGGTGAG
* * * * * * * *
1623887 AATATGTGAAATGACATGGAAGGAATATATGAGAAGACATGGACG-G
1 AATATGTGACACGACATGGATGGAATATGTGACACGCCATGG-TGAG
* *
1623933 AATATCTGACAC-ACCATAGATGGAATATGTGA
1 AATATGTGACACGA-CATGGATGGAATATGTGA
1623965 AACGACATAA
Statistics
Matches: 722, Mismatches: 186, Indels: 80
0.73 0.19 0.08
Matches are distributed among these distances:
43 2 0.00
44 44 0.06
45 86 0.12
46 563 0.78
47 21 0.03
48 6 0.01
ACGTcount: A:0.39, C:0.12, G:0.27, T:0.22
Consensus pattern (46 bp):
AATATGTGACACGACATGGATGGAATATGTGACACGCCATGGTGAG
Found at i:1623973 original size:23 final size:23
Alignment explanation
Indices: 1623886--1623973 Score: 72
Period size: 23 Copynumber: 3.8 Consensus size: 23
1623876 GGCATGGTGA
* *
1623886 GAATATGTGAAATGACATGGAAG
1 GAATATGTGAAACGACATAGAAG
* * *
1623909 GAATATATGAGAA-GACATGGACG
1 GAATATGTGA-AACGACATAGAAG
* * *
1623932 GAATATCTGACAC-ACCATAGATG
1 GAATATGTGAAACGA-CATAGAAG
1623955 GAATATGTGAAACGACATA
1 GAATATGTGAAACGACATA
1623974 AATTTAAATG
Statistics
Matches: 53, Mismatches: 8, Indels: 8
0.77 0.12 0.12
Matches are distributed among these distances:
22 2 0.04
23 48 0.91
24 3 0.06
ACGTcount: A:0.43, C:0.11, G:0.25, T:0.20
Consensus pattern (23 bp):
GAATATGTGAAACGACATAGAAG
Found at i:1625222 original size:25 final size:26
Alignment explanation
Indices: 1625194--1625250 Score: 80
Period size: 26 Copynumber: 2.2 Consensus size: 26
1625184 AAAAATTTTG
* * *
1625194 TTACACACTGTG-TTCAAAAAAATTA
1 TTACACACCGTGTTTAAAAAAAAATA
1625219 TTACACACCGTGTTTAAAAAAAAATA
1 TTACACACCGTGTTTAAAAAAAAATA
1625245 TTACAC
1 TTACAC
1625251 GATATGCACT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
25 11 0.39
26 17 0.61
ACGTcount: A:0.46, C:0.18, G:0.07, T:0.30
Consensus pattern (26 bp):
TTACACACCGTGTTTAAAAAAAAATA
Found at i:1632059 original size:17 final size:17
Alignment explanation
Indices: 1632035--1632068 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
1632025 AAATAGTAAA
1632035 TTTATAATTAA-AATAT
1 TTTATAATTAATAATAT
1632051 TTTATTAATTAATAATAT
1 TTTA-TAATTAATAATAT
1632069 AAATTATGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 7 0.44
18 5 0.31
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TTTATAATTAATAATAT
Found at i:1634727 original size:27 final size:28
Alignment explanation
Indices: 1634696--1634748 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
1634686 TTAAGAAATT
1634696 ATTTAAATAAA-ATTTTATTTGTATTAC
1 ATTTAAATAAATATTTTATTTGTATTAC
* * *
1634723 ATTTAATTAAATTTTTTATTTTTATT
1 ATTTAAATAAATATTTTATTTGTATT
1634749 TTAAATCAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 10 0.45
28 12 0.55
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (28 bp):
ATTTAAATAAATATTTTATTTGTATTAC
Found at i:1638442 original size:27 final size:29
Alignment explanation
Indices: 1638391--1638444 Score: 85
Period size: 27 Copynumber: 1.9 Consensus size: 29
1638381 TTTGATTTAA
1638391 AATAAAAATATAAAATTTTAATTAAATAT
1 AATAAAAATATAAAATTTTAATTAAATAT
*
1638420 AATAAAAATA-AAAA-TTTATTTAAAT
1 AATAAAAATATAAAATTTTAATTAAAT
1638445 TTTTTTAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 10 0.42
28 4 0.17
29 10 0.42
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (29 bp):
AATAAAAATATAAAATTTTAATTAAATAT
Found at i:1640330 original size:18 final size:18
Alignment explanation
Indices: 1640286--1640332 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
1640276 TATTATTAAA
*
1640286 AACATGATTAAGATATTT
1 AACATCATTAAGATATTT
* * *
1640304 AATACCATTAAGATGTTT
1 AACATCATTAAGATATTT
1640322 AACATCATTAA
1 AACATCATTAA
1640333 ATTAAAATAT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.45, C:0.11, G:0.09, T:0.36
Consensus pattern (18 bp):
AACATCATTAAGATATTT
Found at i:1641907 original size:2 final size:2
Alignment explanation
Indices: 1641900--1641925 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1641890 TATTATATTC
1641900 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
1641926 AAATCTACCC
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:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1642927 original size:82 final size:83
Alignment explanation
Indices: 1642834--1642986 Score: 263
Period size: 82 Copynumber: 1.9 Consensus size: 83
1642824 TTAATCAATA
* *
1642834 ATAATTGTCATACATTGATTTAAGAATAATATATTAATTTTAATAAT-AAAGAATGAAAATTTTG
1 ATAATTATCATAAATTGATTTAAGAATAATATATTAATTTTAATAATAAAAGAATGAAAATTTTG
1642898 AAAGATACTGAACCTTAT
66 AAAGATACTGAACCTTAT
* *
1642916 ATAATTATCATAAATTGATTTAAGAATAATCTATTAATTTTAATAATAAAAGTATGAAAATTTTG
1 ATAATTATCATAAATTGATTTAAGAATAATATATTAATTTTAATAATAAAAGAATGAAAATTTTG
1642981 AAAGAT
66 AAAGAT
1642987 TGAATCTCAT
Statistics
Matches: 66, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
82 44 0.67
83 22 0.33
ACGTcount: A:0.48, C:0.05, G:0.09, T:0.39
Consensus pattern (83 bp):
ATAATTATCATAAATTGATTTAAGAATAATATATTAATTTTAATAATAAAAGAATGAAAATTTTG
AAAGATACTGAACCTTAT
Found at i:1646730 original size:15 final size:15
Alignment explanation
Indices: 1646710--1646740 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
1646700 TTAGAGGGGA
1646710 ATGGTAAGGAAACAC
1 ATGGTAAGGAAACAC
1646725 ATGGTAAGGAAACAC
1 ATGGTAAGGAAACAC
1646740 A
1 A
1646741 CCAGGCAGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.48, C:0.13, G:0.26, T:0.13
Consensus pattern (15 bp):
ATGGTAAGGAAACAC
Found at i:1647518 original size:134 final size:134
Alignment explanation
Indices: 1647322--1647589 Score: 527
Period size: 134 Copynumber: 2.0 Consensus size: 134
1647312 ATTTTTTAAT
1647322 TCAATACAAATCACTTGATTAACTGGAGATTGGTTTGAATTTTTTTTCATTAATGATACAAAAGT
1 TCAATACAAATCACTTGATTAACTGGAGATTGGTTTGAATTTTTTTTCATTAATGATACAAAAGT
*
1647387 TTAAAGAAAATCATTAAATATATATTATAAAATTAAATTAAAATTATGTTTAAATAAGAAACAAT
66 TTAAAGAAAATCATTAAATATATATTATAAAATTAAATTAAAATTATGTTCAAATAAGAAACAAT
1647452 TATA
131 TATA
1647456 TCAATACAAATCACTTGATTAACTGGAGATTGGTTTGAATTTTTTTTCATTAATGATACAAAAGT
1 TCAATACAAATCACTTGATTAACTGGAGATTGGTTTGAATTTTTTTTCATTAATGATACAAAAGT
1647521 TTAAAGAAAATCATTAAATATATATTATAAAATTAAATTAAAATTATGTTCAAATAAGAAACAAT
66 TTAAAGAAAATCATTAAATATATATTATAAAATTAAATTAAAATTATGTTCAAATAAGAAACAAT
1647586 TATA
131 TATA
1647590 CAGTTAAAAG
Statistics
Matches: 133, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
134 133 1.00
ACGTcount: A:0.46, C:0.07, G:0.09, T:0.38
Consensus pattern (134 bp):
TCAATACAAATCACTTGATTAACTGGAGATTGGTTTGAATTTTTTTTCATTAATGATACAAAAGT
TTAAAGAAAATCATTAAATATATATTATAAAATTAAATTAAAATTATGTTCAAATAAGAAACAAT
TATA
Found at i:1648138 original size:30 final size:30
Alignment explanation
Indices: 1648102--1648160 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
1648092 TTGTGTCCAA
* *
1648102 TTTTATTTTGAACAAAATAAACTTTTATGC
1 TTTTATTTTAAACAAAATAAACTATTATGC
**
1648132 TTTTATTTTAAATTAAATAAACTATTATG
1 TTTTATTTTAAACAAAATAAACTATTATG
1648161 ACTAATAGTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.39, C:0.07, G:0.05, T:0.49
Consensus pattern (30 bp):
TTTTATTTTAAACAAAATAAACTATTATGC
Found at i:1654834 original size:95 final size:95
Alignment explanation
Indices: 1654720--1654908 Score: 324
Period size: 95 Copynumber: 2.0 Consensus size: 95
1654710 GTATGTTGTG
*
1654720 GATGTCAATGTTAAACAGATTGTAAAGCTGAAGGAGAAAAAAAATGAAACTTTACACAAAGGATC
1 GATGTCAATGTTAAACAGATTGTAAAGCTAAAGGAGAAAAAAAATGAAACTTTACACAAAGGATC
*
1654785 AGTCTAATAGAGGACCTGATTGAAACTATT
66 AGTCTAACAGAGGACCTGATTGAAACTATT
* * *
1654815 GATGTCACTGTTAAACAGATTGTAAAGCTAAAGGAGATAAAAAATGAAACTTTACATAAAGGATC
1 GATGTCAATGTTAAACAGATTGTAAAGCTAAAGGAGAAAAAAAATGAAACTTTACACAAAGGATC
*
1654880 AGTTTAACAGAGGACCTGATTGAAACTAT
66 AGTCTAACAGAGGACCTGATTGAAACTAT
1654909 GGAAGAGCTC
Statistics
Matches: 88, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
95 88 1.00
ACGTcount: A:0.44, C:0.12, G:0.20, T:0.25
Consensus pattern (95 bp):
GATGTCAATGTTAAACAGATTGTAAAGCTAAAGGAGAAAAAAAATGAAACTTTACACAAAGGATC
AGTCTAACAGAGGACCTGATTGAAACTATT
Found at i:1658527 original size:22 final size:23
Alignment explanation
Indices: 1658501--1658550 Score: 77
Period size: 22 Copynumber: 2.2 Consensus size: 23
1658491 ATGGTTCGTA
1658501 ATATAAAA-TGTTATGAATA-TAT
1 ATATAAAATTG-TATGAATATTAT
1658523 ATATAAAATTGTATGAATATTAT
1 ATATAAAATTGTATGAATATTAT
1658546 ATATA
1 ATATA
1658551 TTTAATTTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
22 16 0.62
23 10 0.38
ACGTcount: A:0.50, C:0.00, G:0.08, T:0.42
Consensus pattern (23 bp):
ATATAAAATTGTATGAATATTAT
Found at i:1659292 original size:19 final size:19
Alignment explanation
Indices: 1659243--1659286 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
1659233 CTTCTTTTTT
1659243 TTTTAATATT-TTAAAAAAA
1 TTTTAA-ATTATTAAAAAAA
1659262 TTTTAAATTATTAAAAAAA
1 TTTTAAATTATTAAAAAAA
1659281 TATTTA
1 T-TTTA
1659287 TTTATTCTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 3 0.13
19 16 0.70
20 4 0.17
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
TTTTAAATTATTAAAAAAA
Found at i:1667696 original size:24 final size:24
Alignment explanation
Indices: 1667669--1667724 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
1667659 AGTTTTAGAG
*
1667669 AAAA-AAAGAAAAAAATAAGAAAGA
1 AAAACAAAGAAAAAAA-AAAAAAGA
*
1667693 AAAACAGAGAAAAAAAAAAAAAGA
1 AAAACAAAGAAAAAAAAAAAAAGA
*
1667717 AACACAAA
1 AAAACAAA
1667725 TAATATATAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
24 17 0.63
25 10 0.37
ACGTcount: A:0.82, C:0.05, G:0.11, T:0.02
Consensus pattern (24 bp):
AAAACAAAGAAAAAAAAAAAAAGA
Found at i:1668373 original size:7 final size:7
Alignment explanation
Indices: 1668361--1668398 Score: 60
Period size: 7 Copynumber: 5.4 Consensus size: 7
1668351 AATATGTCTC
1668361 AAAATGA
1 AAAATGA
1668368 AAAATGA
1 AAAATGA
1668375 AAAATGA
1 AAAATGA
1668382 AAAA-GA
1 AAAATGA
1668388 AGAAATGA
1 A-AAATGA
1668396 AAA
1 AAA
1668399 GATTTTCGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
6 3 0.10
7 23 0.79
8 3 0.10
ACGTcount: A:0.74, C:0.00, G:0.16, T:0.11
Consensus pattern (7 bp):
AAAATGA
Found at i:1671470 original size:10 final size:10
Alignment explanation
Indices: 1671455--1671490 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
1671445 ATTCAGTTAA
*
1671455 TTAATAATAT
1 TTAATAGTAT
1671465 TTAATAGTAT
1 TTAATAGTAT
*
1671475 ATAATAGTAT
1 TTAATAGTAT
1671485 TTAATA
1 TTAATA
1671491 CTATAATATT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (10 bp):
TTAATAGTAT
Found at i:1671485 original size:20 final size:20
Alignment explanation
Indices: 1671456--1671495 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
1671446 TTCAGTTAAT
*
1671456 TAATAATATTTAATAGTATA
1 TAATAATATTTAATACTATA
*
1671476 TAATAGTATTTAATACTATA
1 TAATAATATTTAATACTATA
1671496 ATATTTTGTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.45
Consensus pattern (20 bp):
TAATAATATTTAATACTATA
Found at i:1672971 original size:2 final size:2
Alignment explanation
Indices: 1672960--1672991 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1672950 ATTTTTGGGC
1672960 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1672992 CAAGTAGTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1697737 original size:12 final size:12
Alignment explanation
Indices: 1697701--1697759 Score: 55
Period size: 12 Copynumber: 4.7 Consensus size: 12
1697691 GCTGTCATTG
1697701 TCATCATCGTCA
1 TCATCATCGTCA
* *
1697713 TCCTCTTCGTCA
1 TCATCATCGTCA
*
1697725 TCATCATCTTCA
1 TCATCATCGTCA
*
1697737 TCATTGTCATCGTCT
1 TCA---TCATCGTCA
1697752 TCATCATC
1 TCATCATC
1697760 ATCGTCACTT
Statistics
Matches: 37, Mismatches: 7, Indels: 6
0.74 0.14 0.12
Matches are distributed among these distances:
12 27 0.73
15 10 0.27
ACGTcount: A:0.19, C:0.34, G:0.07, T:0.41
Consensus pattern (12 bp):
TCATCATCGTCA
Found at i:1697763 original size:15 final size:15
Alignment explanation
Indices: 1697704--1697765 Score: 61
Period size: 15 Copynumber: 3.9 Consensus size: 15
1697694 GTCATTGTCA
* *
1697704 TCATCGTCATCCTCT
1 TCATCATCATCGTCT
* *
1697719 TCGTCATCATCATCT
1 TCATCATCATCGTCT
1697734 TCATCATTGTCATCGTCT
1 TCATCA---TCATCGTCT
1697752 TCATCATCATCGTC
1 TCATCATCATCGTC
1697766 ACTTTCTTCA
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
15 25 0.64
18 14 0.36
ACGTcount: A:0.18, C:0.34, G:0.08, T:0.40
Consensus pattern (15 bp):
TCATCATCATCGTCT
Found at i:1697776 original size:18 final size:21
Alignment explanation
Indices: 1697719--1697766 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
1697709 GTCATCCTCT
* *
1697719 TCGTCATCATCATCTTCATCA
1 TCGTCATCGTCTTCTTCATCA
* *
1697740 TTGTCATCGTCTTCATCATCA
1 TCGTCATCGTCTTCTTCATCA
1697761 TCGTCA
1 TCGTCA
1697767 CTTTCTTCAT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.21, C:0.31, G:0.08, T:0.40
Consensus pattern (21 bp):
TCGTCATCGTCTTCTTCATCA
Found at i:1700042 original size:2 final size:2
Alignment explanation
Indices: 1699983--1700027 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
1699973 CAACAAGTTT
1699983 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1700025 TA T
1 TA T
1700028 CTAAAACCTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1707339 original size:38 final size:38
Alignment explanation
Indices: 1707296--1707370 Score: 96
Period size: 38 Copynumber: 2.0 Consensus size: 38
1707286 TCAAATTCTT
1707296 CTTTTCTTTTCTCAAAAATCTATAAGAAAAATCTAATA
1 CTTTTCTTTTCTCAAAAATCTATAAGAAAAATCTAATA
* * * * **
1707334 CTTTTCTTTTTTCTACAATCTGTAAGCGAAATCTAAT
1 CTTTTCTTTTCTCAAAAATCTATAAGAAAAATCTAAT
1707371 GGTATTAAAT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
38 31 1.00
ACGTcount: A:0.35, C:0.17, G:0.05, T:0.43
Consensus pattern (38 bp):
CTTTTCTTTTCTCAAAAATCTATAAGAAAAATCTAATA
Found at i:1713303 original size:15 final size:15
Alignment explanation
Indices: 1713283--1713312 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1713273 ATTGTAGTCT
1713283 CAATTAAAGAAAAGA
1 CAATTAAAGAAAAGA
*
1713298 CAATTAAAGATAAGA
1 CAATTAAAGAAAAGA
1713313 GAAAACAAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.63, C:0.07, G:0.13, T:0.17
Consensus pattern (15 bp):
CAATTAAAGAAAAGA
Found at i:1720042 original size:8 final size:8
Alignment explanation
Indices: 1720029--1720057 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
1720019 TAAATGCTAA
1720029 CATATAGT
1 CATATAGT
1720037 CATATAGT
1 CATATAGT
1720045 CATATAGT
1 CATATAGT
1720053 CATAT
1 CATAT
1720058 GTGTTGCACA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.38, C:0.14, G:0.10, T:0.38
Consensus pattern (8 bp):
CATATAGT
Found at i:1721614 original size:330 final size:339
Alignment explanation
Indices: 1721223--1721834 Score: 857
Period size: 342 Copynumber: 1.8 Consensus size: 339
1721213 ATATTTTTAC
* * *
1721223 TATATATATACTTTAAATATAAATATATATACTTTCTATTTTATGTTAACATTACAAAAATTATA
1 TATATATACACTTTAAATATAAATATATATACTTGCTATTTTATGTTAACATTACAAAAATTAAA
*
1721288 ACTTGTAAAATTATTAATCAT-A-ATATATATACCTTT-TTTTATATAAACTTAT-A-ATAT-AC
66 ACTTATAAAATTATTAATCATAATATATATATACCTTTGTTTTATATAAACTTATAATATATAAC
* * * *
1721347 -AA-ACCTAAAGATAAGCTGTGAGATTAGAATAGTTTTGAAATTTAGTTA-TTTTTTTAATTTAA
131 TAATACCTAAAAAGAAGCTGTGAGATTAGAATAATTTTGAAACTTAGTTATTTTTTTTAATTTAA
* * * *
1721409 TATAATTAAGGACAAACCCATATAATTAATTAAATTAATTCAA-GAAACTATAATTATTAATTAC
196 TATAATTAAAGAAAAACCCATATAATTAATTAAATTAATT-AATAAAACTATAATTATTAATTAA
* *
1721473 CTTGTAACGTCTTTTAATATAACTACTATTATATATATATATATATATACACTAAAATACTTTTA
260 CTTGCAACGTCTTTCAATATAACTACTATTATATATATATATATATATACACTAAAATACTTTTA
1721538 GTGTGTGTGTGTATA
325 GTGTGTGTGTGTATA
* * * *
1721553 TATATATACACTTTAAATATAACTATATTTACTTGCTATTTTGTGTTAACATTATAAAAATTAAA
1 TATATATACACTTTAAATATAAATATATATACTTGCTATTTTATGTTAACATTACAAAAATTAAA
*
1721618 ACTTATAAAATTATTAATTATAATATATATATACCTTTGTTTTATATAAACTTATAATATATAAA
66 ACTTATAAAATTATTAATCATAATATATATATACCTTTGTTTTATATAAACTTATAATATAT-AA
* * *
1721683 CTTAATTATCTAAAAAGGAGTTGTGAGATTAGAATAATTTTGAAACTTAGTTATTTTTTTTAATT
130 C-TAA-TACCTAAAAAGAAGCTGTGAGATTAGAATAATTTTGAAACTTAGTTATTTTTTTTAATT
* * ** * *
1721748 TTATGTAATTAAAGAAAAACTTATATAATTAATTAAATTAATTAATAAAATTATGATTATTAATT
193 TAATATAATTAAAGAAAAACCCATATAATTAATTAAATTAATTAATAAAACTATAATTATTAATT
*
1721813 AACTTGCAATGTCTTTCAATAT
258 AACTTGCAACGTCTTTCAATAT
1721835 CTATACTTTA
Statistics
Matches: 240, Mismatches: 29, Indels: 14
0.85 0.10 0.05
Matches are distributed among these distances:
330 77 0.32
331 1 0.00
332 14 0.06
333 16 0.07
334 1 0.00
335 4 0.02
337 2 0.01
339 2 0.01
341 41 0.17
342 82 0.34
ACGTcount: A:0.42, C:0.08, G:0.07, T:0.44
Consensus pattern (339 bp):
TATATATACACTTTAAATATAAATATATATACTTGCTATTTTATGTTAACATTACAAAAATTAAA
ACTTATAAAATTATTAATCATAATATATATATACCTTTGTTTTATATAAACTTATAATATATAAC
TAATACCTAAAAAGAAGCTGTGAGATTAGAATAATTTTGAAACTTAGTTATTTTTTTTAATTTAA
TATAATTAAAGAAAAACCCATATAATTAATTAAATTAATTAATAAAACTATAATTATTAATTAAC
TTGCAACGTCTTTCAATATAACTACTATTATATATATATATATATATACACTAAAATACTTTTAG
TGTGTGTGTGTATA
Found at i:1722381 original size:15 final size:15
Alignment explanation
Indices: 1722361--1722390 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1722351 AACTGCTCAG
1722361 TTCTTCTTTTATTCC
1 TTCTTCTTTTATTCC
*
1722376 TTCTTCTTTTCTTCC
1 TTCTTCTTTTATTCC
1722391 CTTAGCTAGC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.03, C:0.30, G:0.00, T:0.67
Consensus pattern (15 bp):
TTCTTCTTTTATTCC
Found at i:1724180 original size:21 final size:22
Alignment explanation
Indices: 1724145--1724185 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
1724135 ACTCTAATCT
*
1724145 ATATCAAATAAAAAATAAGCGG
1 ATATCAAATAAAAAAAAAGCGG
*
1724167 ATATTAAA-AAAAAAAAAGC
1 ATATCAAATAAAAAAAAAGC
1724186 TGGAAGCGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.66, C:0.07, G:0.10, T:0.17
Consensus pattern (22 bp):
ATATCAAATAAAAAAAAAGCGG
Found at i:1726329 original size:24 final size:27
Alignment explanation
Indices: 1726300--1726357 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 27
1726290 AATAAACTTT
1726300 TATTTTTTA-TTATA-TTT-AATTAAA
1 TATTTTTTATTTATATTTTAAATTAAA
*
1726324 TA-TTTTTATTTTTATTTTAAATTAAA
1 TATTTTTTATTTATATTTTAAATTAAA
*
1726350 AATTTTTT
1 TATTTTTT
1726358 TATAACTAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
23 6 0.21
24 6 0.21
25 3 0.11
26 8 0.29
27 5 0.18
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (27 bp):
TATTTTTTATTTATATTTTAAATTAAA
Found at i:1727762 original size:19 final size:19
Alignment explanation
Indices: 1727730--1727771 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
1727720 TACCCTCCTC
* *
1727730 TTTATTTATTTATTTTTAA
1 TTTATATATATATTTTTAA
1727749 TTTATATATATATTTTTAA
1 TTTATATATATATTTTTAA
1727768 TTTA
1 TTTA
1727772 ATTTAGTTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (19 bp):
TTTATATATATATTTTTAA
Found at i:1736717 original size:2 final size:2
Alignment explanation
Indices: 1736710--1736734 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1736700 AGCCTCGGGG
1736710 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1736735 GAAAAATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1747129 original size:45 final size:45
Alignment explanation
Indices: 1747078--1747170 Score: 118
Period size: 45 Copynumber: 2.1 Consensus size: 45
1747068 TGCAGGTCCT
* *
1747078 GCACCTTCTCCGATCT-GTTT-CGCCTCAGATCGCACCACCGCAGCC
1 GCACCTTCTCCGATCTAGTTTAC-CCT-AGATCGCACCACCACACCC
* *
1747123 GCACCTTCTCCGTTCTAGTTTACCGTAGATCGCACCACCACACCC
1 GCACCTTCTCCGATCTAGTTTACCCTAGATCGCACCACCACACCC
1747168 GCA
1 GCA
1747171 GATTGCACTC
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
45 35 0.83
46 6 0.14
47 1 0.02
ACGTcount: A:0.18, C:0.43, G:0.16, T:0.23
Consensus pattern (45 bp):
GCACCTTCTCCGATCTAGTTTACCCTAGATCGCACCACCACACCC
Found at i:1751274 original size:6 final size:6
Alignment explanation
Indices: 1751263--1751297 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
1751253 ACTAGTAGCA
* *
1751263 GCTGCT GCTGCT GCTGCC GCTGCC GCTGCC GCTGC
1 GCTGCC GCTGCC GCTGCC GCTGCC GCTGCC GCTGC
1751298 AGCAGCTGAG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.00, C:0.43, G:0.34, T:0.23
Consensus pattern (6 bp):
GCTGCC
Found at i:1758047 original size:23 final size:25
Alignment explanation
Indices: 1758021--1758080 Score: 72
Period size: 23 Copynumber: 2.5 Consensus size: 25
1758011 ATTAACTAAT
1758021 GATTAATTTATTAATT-TAA-AAAA
1 GATTAATTTATTAATTCTAATAAAA
* *
1758044 GATTAATTAATTATTTCTAATAAAA
1 GATTAATTTATTAATTCTAATAAAA
*
1758069 AATT-ATTTATTA
1 GATTAATTTATTA
1758081 TTTTTATATT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
23 14 0.45
24 10 0.32
25 7 0.23
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.47
Consensus pattern (25 bp):
GATTAATTTATTAATTCTAATAAAA
Found at i:1758303 original size:21 final size:21
Alignment explanation
Indices: 1758279--1758323 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
1758269 AAATTTATTT
1758279 AATTTAAAATAAATAT-ATAAA
1 AATTT-AAATAAATATAATAAA
*
1758300 AATTTAATTAAATATAATAAA
1 AATTTAAATAAATATAATAAA
1758321 AAT
1 AAT
1758324 AAATATTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 9 0.41
21 13 0.59
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (21 bp):
AATTTAAATAAATATAATAAA
Found at i:1758305 original size:26 final size:28
Alignment explanation
Indices: 1758275--1758339 Score: 75
Period size: 27 Copynumber: 2.5 Consensus size: 28
1758265 GAAAAAATTT
* *
1758275 ATTTAATTTAAA-ATAA-ATATATAAAA
1 ATTTAATTTAAATATAATAAAAATAAAA
*
1758301 ATTTAA-TTAAATATAATAAAAATAAAT
1 ATTTAATTTAAATATAATAAAAATAAAA
1758328 ATTT-ATTTAAAT
1 ATTTAATTTAAAT
1758340 TTTTTAAAAC
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
25 5 0.15
26 11 0.33
27 17 0.52
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (28 bp):
ATTTAATTTAAATATAATAAAAATAAAA
Found at i:1758324 original size:31 final size:30
Alignment explanation
Indices: 1758267--1758339 Score: 73
Period size: 27 Copynumber: 2.5 Consensus size: 30
1758257 GTTATTGAGA
* *
1758267 AAAAATTTATTTAATTTAAAATAAATATAT
1 AAAAATTTATTAAATATAAAATAAATATAT
1758297 AAAAATTTAATTAAATAT--AATAAA-A-AT
1 AAAAATTT-ATTAAATATAAAATAAATATAT
*
1758324 AAATATTTATTTAAAT
1 AAAAATTTA-TTAAAT
1758340 TTTTTAAAAC
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
26 1 0.03
27 15 0.39
28 1 0.03
29 6 0.16
30 8 0.21
31 7 0.18
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (30 bp):
AAAAATTTATTAAATATAAAATAAATATAT
Found at i:1760696 original size:27 final size:27
Alignment explanation
Indices: 1760665--1760731 Score: 134
Period size: 27 Copynumber: 2.5 Consensus size: 27
1760655 GAAGGATAAG
1760665 AGTGTATTTTTAAACTAATGAAGATTC
1 AGTGTATTTTTAAACTAATGAAGATTC
1760692 AGTGTATTTTTAAACTAATGAAGATTC
1 AGTGTATTTTTAAACTAATGAAGATTC
1760719 AGTGTATTTTTAA
1 AGTGTATTTTTAA
1760732 TCAAATCTCA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.36, C:0.06, G:0.15, T:0.43
Consensus pattern (27 bp):
AGTGTATTTTTAAACTAATGAAGATTC
Found at i:1760914 original size:30 final size:30
Alignment explanation
Indices: 1760879--1760937 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
1760869 GCCTATGTTC
*
1760879 TTTTATTTTGAATCAAACAAGTTCTTATAT
1 TTTTATTTTGAACCAAACAAGTTCTTATAT
* * *
1760909 TTTTATTTTGAGCCAAATAAGTTTTTATA
1 TTTTATTTTGAACCAAACAAGTTCTTATA
1760938 ATTAATGATT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.32, C:0.08, G:0.08, T:0.51
Consensus pattern (30 bp):
TTTTATTTTGAACCAAACAAGTTCTTATAT
Found at i:1761372 original size:19 final size:19
Alignment explanation
Indices: 1761348--1761401 Score: 51
Period size: 19 Copynumber: 2.9 Consensus size: 19
1761338 TGTTAAATTT
1761348 ATTATAAAATATTTAATAA
1 ATTATAAAATATTTAATAA
* *
1761367 ATTATAGTAATATTT-TTAA
1 ATTATA-AAATATTTAATAA
1761386 A-TA-AAAATATATTAAT
1 ATTATAAAATAT-TTAAT
1761402 TATCATTTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 7
0.72 0.10 0.18
Matches are distributed among these distances:
16 5 0.18
17 3 0.11
18 3 0.11
19 10 0.36
20 7 0.25
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (19 bp):
ATTATAAAATATTTAATAA
Found at i:1763470 original size:21 final size:23
Alignment explanation
Indices: 1763444--1763497 Score: 71
Period size: 21 Copynumber: 2.5 Consensus size: 23
1763434 ATAAAAAATA
1763444 AAAATATTATTTA-AAATTTTTT
1 AAAATATTATTTAGAAATTTTTT
*
1763466 -AAATA--ATTCAGAAATTTTTT
1 AAAATATTATTTAGAAATTTTTT
1763486 AAAATATTATTT
1 AAAATATTATTT
1763498 CAATTGCATA
Statistics
Matches: 26, Mismatches: 2, Indels: 7
0.74 0.06 0.20
Matches are distributed among these distances:
19 4 0.15
20 9 0.35
21 10 0.38
23 3 0.12
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (23 bp):
AAAATATTATTTAGAAATTTTTT
Found at i:1763549 original size:20 final size:20
Alignment explanation
Indices: 1763517--1763556 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1763507 AATTTTACTT
*
1763517 ATTTAAAATAAATAAGTAAA
1 ATTTAAAATAAATAAATAAA
1763537 ATTT-AAATAAAATAAATAAA
1 ATTTAAAAT-AAATAAATAAA
1763557 TAATATGCGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.30
Consensus pattern (20 bp):
ATTTAAAATAAATAAATAAA
Found at i:1764555 original size:13 final size:12
Alignment explanation
Indices: 1764532--1764571 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
1764522 ATTCATAAAG
1764532 TTTTAATAATAT
1 TTTTAATAATAT
1764544 TTTTATATAATAT
1 TTTTA-ATAATAT
* *
1764557 TTTAAATATTAT
1 TTTTAATAATAT
1764569 TTT
1 TTT
1764572 AGGATATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
12 14 0.56
13 11 0.44
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (12 bp):
TTTTAATAATAT
Found at i:1768269 original size:24 final size:26
Alignment explanation
Indices: 1768219--1768270 Score: 63
Period size: 28 Copynumber: 2.0 Consensus size: 26
1768209 ATTATAATTC
*
1768219 AAATAAATTTTTATATTTATTTTAAAAT
1 AAATAAATTTTTATA--TATTTAAAAAT
1768247 AAATAAATTTTTATA-A-TTAAAAAT
1 AAATAAATTTTTATATATTTAAAAAT
1768271 TATTTAATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
24 7 0.30
25 1 0.04
28 15 0.65
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (26 bp):
AAATAAATTTTTATATATTTAAAAAT
Found at i:1768561 original size:24 final size:27
Alignment explanation
Indices: 1768510--1768563 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
1768500 GTTTATTTAA
*
1768510 TTAAAAATAATAATATAAATAATTAAT
1 TTAAAAATAATAATATAAATAATAAAT
*
1768537 TTAAAAGTAATAA-A-AAATAA-AAAT
1 TTAAAAATAATAATATAAATAATAAAT
1768561 TTA
1 TTA
1768564 TTCAAATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 6 0.24
25 6 0.24
26 1 0.04
27 12 0.48
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (27 bp):
TTAAAAATAATAATATAAATAATAAAT
Found at i:1772159 original size:19 final size:19
Alignment explanation
Indices: 1772124--1772162 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
1772114 TAATAATAAT
*
1772124 TGATATTTTAATTAATTTA
1 TGATATTTTAATAAATTTA
1772143 TGATCATTTTAA-AAATTTA
1 TGAT-ATTTTAATAAATTTA
1772162 T
1 T
1772163 TTTTTTATCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.38, C:0.03, G:0.05, T:0.54
Consensus pattern (19 bp):
TGATATTTTAATAAATTTA
Found at i:1775173 original size:13 final size:13
Alignment explanation
Indices: 1775155--1775183 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
1775145 GAACAAGAGA
1775155 CGCCCATCTCACG
1 CGCCCATCTCACG
1775168 CGCCCATCTCACG
1 CGCCCATCTCACG
1775181 CGC
1 CGC
1775184 TTTACCCTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.14, C:0.55, G:0.17, T:0.14
Consensus pattern (13 bp):
CGCCCATCTCACG
Found at i:1775626 original size:23 final size:24
Alignment explanation
Indices: 1775577--1775626 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
1775567 AATTAAAAAT
*
1775577 AAAAAATCATAAAAATAAGAAATA
1 AAAAAATCATAAAAATAAGAAAGA
** *
1775601 AAAAAATTGTAAAAAT-GGAAAGA
1 AAAAAATCATAAAAATAAGAAAGA
1775624 AAA
1 AAA
1775627 GGGATCGAGG
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
23 8 0.36
24 14 0.64
ACGTcount: A:0.72, C:0.02, G:0.10, T:0.16
Consensus pattern (24 bp):
AAAAAATCATAAAAATAAGAAAGA
Found at i:1778248 original size:16 final size:16
Alignment explanation
Indices: 1778227--1778257 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1778217 ATTATTTTGT
1778227 AAGAATAGAATAAAAA
1 AAGAATAGAATAAAAA
*
1778243 AAGAATAGAGTAAAA
1 AAGAATAGAATAAAA
1778258 TATTTGGAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.71, C:0.00, G:0.16, T:0.13
Consensus pattern (16 bp):
AAGAATAGAATAAAAA
Found at i:1779364 original size:23 final size:23
Alignment explanation
Indices: 1779292--1779372 Score: 60
Period size: 23 Copynumber: 3.6 Consensus size: 23
1779282 TTTTGTCTTT
* *
1779292 TAATATTAAATATTATTTAATTA
1 TAATATAAAATATTATTAAATTA
*** ** *
1779315 TAATATATGGT-TTGATTATTTTT
1 TAATATAAAATATT-ATTAAATTA
1779338 TAATATAAAATATTATTAAATTA
1 TAATATAAAATATTATTAAATTA
1779361 T-A-ATAAAATATT
1 TAATATAAAATATT
1779373 TTTTTGGGGT
Statistics
Matches: 42, Mismatches: 14, Indels: 6
0.68 0.23 0.10
Matches are distributed among these distances:
21 10 0.24
22 3 0.07
23 27 0.64
24 2 0.05
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.51
Consensus pattern (23 bp):
TAATATAAAATATTATTAAATTA
Found at i:1780399 original size:5 final size:5
Alignment explanation
Indices: 1780389--1780417 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
1780379 CTTTTCATCC
1780389 ATTCA ATTCA ATTCA ATTCA ATTCA ATTC
1 ATTCA ATTCA ATTCA ATTCA ATTCA ATTC
1780418 CCTTCCCCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.38, C:0.21, G:0.00, T:0.41
Consensus pattern (5 bp):
ATTCA
Found at i:1780471 original size:5 final size:5
Alignment explanation
Indices: 1780461--1780485 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
1780451 CATTCATCTC
1780461 TTTCT TTTCT TTTCT TTTCT TTTCT
1 TTTCT TTTCT TTTCT TTTCT TTTCT
1780486 CATCGGATCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTCT
Found at i:1791518 original size:2 final size:2
Alignment explanation
Indices: 1791513--1791542 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1791503 CCCCACGCCC
1791513 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1791543 ACCATTTCTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1801842 original size:18 final size:18
Alignment explanation
Indices: 1801819--1801858 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
1801809 AAATAAGGGT
1801819 ATCATCATAATCATAATC
1 ATCATCATAATCATAATC
* *
1801837 ATCATCATTATCATTATC
1 ATCATCATAATCATAATC
1801855 ATCA
1 ATCA
1801859 CCGTGACTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.40, C:0.23, G:0.00, T:0.38
Consensus pattern (18 bp):
ATCATCATAATCATAATC
Found at i:1803977 original size:45 final size:46
Alignment explanation
Indices: 1803898--1803986 Score: 112
Period size: 45 Copynumber: 2.0 Consensus size: 46
1803888 AAAGGGTGTG
* *
1803898 AGGGGAGCACTGATGCTCCTTGAGGGAGCTTTGATCGG-GCTTCTC
1 AGGGGAGCACCGATGCTCCTTGAAGGAGCTTTGATCGGAGCTTCTC
*
1803943 AGGGGAGCACCGATGCTCCCTT-AAGGAG-TCTTGATGGGAGCTTC
1 AGGGGAGCACCGATGCT-CCTTGAAGGAGCT-TTGATCGGAGCTTC
1803987 GACACTCCTC
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
44 1 0.03
45 28 0.74
46 9 0.24
ACGTcount: A:0.18, C:0.22, G:0.35, T:0.25
Consensus pattern (46 bp):
AGGGGAGCACCGATGCTCCTTGAAGGAGCTTTGATCGGAGCTTCTC
Found at i:1804881 original size:17 final size:18
Alignment explanation
Indices: 1804867--1804900 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
1804857 AATAATAATT
1804867 AATTA-TTAATTATAAAA
1 AATTATTTAATTATAAAA
1804884 AATTATTTAATT-TAAAA
1 AATTATTTAATTATAAAA
1804901 TAAAAATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
AATTATTTAATTATAAAA
Found at i:1805539 original size:29 final size:29
Alignment explanation
Indices: 1805502--1805567 Score: 87
Period size: 29 Copynumber: 2.2 Consensus size: 29
1805492 GCAGAAAATA
1805502 TCAAATAAGCACTTATTCTTTTAATTTGT
1 TCAAATAAGCACTTATTCTTTTAATTTGT
* * * *
1805531 TCAATTAAGCTCTTATTCTTTTATTTTGAG
1 TCAAATAAGCACTTATTCTTTTAATTTG-T
1805561 TCAAATA
1 TCAAATA
1805568 GATTCTTAGT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
29 25 0.81
30 6 0.19
ACGTcount: A:0.30, C:0.14, G:0.08, T:0.48
Consensus pattern (29 bp):
TCAAATAAGCACTTATTCTTTTAATTTGT
Found at i:1808093 original size:16 final size:17
Alignment explanation
Indices: 1808056--1808093 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
1808046 TAATCTCCAC
*
1808056 TAAAATTAGGAGAAAAT
1 TAAAATTAAGAGAAAAT
*
1808073 GAAAATTAAGA-AAAAT
1 TAAAATTAAGAGAAAAT
1808089 TAAAA
1 TAAAA
1808094 ATGAACATTA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
16 9 0.50
17 9 0.50
ACGTcount: A:0.66, C:0.00, G:0.13, T:0.21
Consensus pattern (17 bp):
TAAAATTAAGAGAAAAT
Found at i:1810192 original size:17 final size:17
Alignment explanation
Indices: 1810146--1810193 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 17
1810136 AATACTTATG
1810146 TATAAATTAA--ATATA
1 TATAAATTAATTATATA
*
1810161 TATAATATTTTATTATATA
1 TATAA-A-TTAATTATATA
1810180 TATAAATTAATTAT
1 TATAAATTAATTAT
1810194 GTAAATTATA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
15 5 0.19
16 1 0.04
17 10 0.37
18 1 0.04
19 10 0.37
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TATAAATTAATTATATA
Found at i:1810216 original size:200 final size:205
Alignment explanation
Indices: 1809973--1810595 Score: 778
Period size: 200 Copynumber: 3.0 Consensus size: 205
1809963 TTTATAATTA
* * * * * * *
1809973 TATATATATGAAATTAATGATATAACTTATTTATTATAATGTTTTATATCAAAATTTATATAAAT
1 TATATATATAAAATTAATAATATAAATTATATGTTATAATGTTTTATATCAAAGTTTGTATAAAT
* * *
1810038 AATAACTAATTATAAATAATATGTTATAAAATCTAAAGTGATAGTTAATAAACTTGTTAAGTGTA
66 AATAACTAATTATAAATAATATGTTATAAAATCTAAAGTGATAATTAATAAAGTTATTAAGTGTA
* *
1810103 ATAATATAAATAAAGTTTATTATAAGTTATAGTAATACTTATGTATAAATTAAATATATAT-A-A
131 ATCATATAAATAAAATTTATTATAAGTTATAGTAATACTTATGTATAAATTAAATATATATAATA
1810166 TAT-TTTA-T
196 TATATTTATT
* * *
1810174 TATATATAT-AAATTAATTATGTAAATTATATGTTAAAATGTTTTATATCAAAGTTTGTATAAAT
1 TATATATATAAAATTAATAATATAAATTATATGTTATAATGTTTTATATCAAAGTTTGTATAAAT
* * *
1810238 AACAACTAATTATAAACAATATGTTATAAAATCT-AAGATGATAATTAATAAAGTTATTAAATGT
66 AATAACTAATTATAAATAATATGTTATAAAATCTAAAG-TGATAATTAATAAAGTTATTAAGTGT
*
1810302 AATCATATAAATAAAATTTATTATAAGTTATAGTAATACTTATGTATAAATGAAATATATGTGTA
130 AATCATATAAATAAAATTTATTATAAGTTATAGTAATACTTATGTATAAAT-TAA-ATA----TA
1810367 TATAATATATGACTTTATT
189 TATAATATAT-A-TTTATT
* * * *
1810386 TAATATAGATATAAAATTAATAACATAAGTTTTGTGTTATAATGTTTTATATC--AGTTTGTATA
1 T-ATAT--ATATAAAATTAATAATATAAATTATATGTTATAATGTTTTATATCAAAGTTTGTATA
* * *
1810449 AATAATAACTAATTATAAATAATATATTATAAAATCTAAGGTGATAACTAATAAAGTTATTAAGT
63 AATAATAACTAATTATAAATAATATGTTATAAAATCTAAAGTGATAATTAATAAAGTTATTAAGT
* * ** *
1810514 GTGATCATATAAATAAAATTTATTATAAATTATAGTAATGTTTATGTATAAATTAAATATATGT-
128 GTAATCATATAAATAAAATTTATTATAAGTTATAGTAATACTTATGTATAAATTAAATATATATA
*
1810578 ATATATAATATATT
193 ATATAT-ATTTATT
1810592 TATA
1 TATA
1810596 AAATTATATA
Statistics
Matches: 366, Mismatches: 38, Indels: 32
0.84 0.09 0.07
Matches are distributed among these distances:
199 3 0.01
200 150 0.41
201 11 0.03
202 3 0.01
205 3 0.01
206 11 0.03
207 8 0.02
208 8 0.02
211 4 0.01
212 5 0.01
213 6 0.02
214 115 0.31
215 6 0.02
216 33 0.09
ACGTcount: A:0.47, C:0.03, G:0.08, T:0.42
Consensus pattern (205 bp):
TATATATATAAAATTAATAATATAAATTATATGTTATAATGTTTTATATCAAAGTTTGTATAAAT
AATAACTAATTATAAATAATATGTTATAAAATCTAAAGTGATAATTAATAAAGTTATTAAGTGTA
ATCATATAAATAAAATTTATTATAAGTTATAGTAATACTTATGTATAAATTAAATATATATAATA
TATATTTATT
Found at i:1810577 original size:23 final size:22
Alignment explanation
Indices: 1810532--1810585 Score: 58
Period size: 23 Copynumber: 2.5 Consensus size: 22
1810522 ATAAATAAAA
*
1810532 TTTATTATAAATTATAGTAATG
1 TTTATTATAAATTATAATAATG
1810554 TTTATGTATAAATTA-AATATATG
1 TTTAT-TATAAATTATAATA-ATG
*
1810577 TATA-TATAA
1 TTTATTATAA
1810586 TATATTTATA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
21 5 0.18
22 8 0.29
23 15 0.54
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.48
Consensus pattern (22 bp):
TTTATTATAAATTATAATAATG
Found at i:1810625 original size:18 final size:20
Alignment explanation
Indices: 1810579--1810626 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
1810569 AATATATGTA
1810579 TATATAATATATTTATAAAAT
1 TATAT-ATATATTTATAAAAT
*
1810600 TATATATATATTTATAACAT
1 TATATATATATTTATAAAAT
*
1810620 TTTATAT
1 TATATAT
1810627 TATGAAACAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 20 0.80
21 5 0.20
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (20 bp):
TATATATATATTTATAAAAT
Found at i:1812107 original size:20 final size:20
Alignment explanation
Indices: 1812084--1812122 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1812074 ATCATTAGTA
* *
1812084 ATATATATATTTTAAATATT
1 ATATATATAATATAAATATT
1812104 ATATATATAATATAAATAT
1 ATATATATAATATAAATAT
1812123 ATTTTATATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
ATATATATAATATAAATATT
Found at i:1812123 original size:31 final size:26
Alignment explanation
Indices: 1812088--1812146 Score: 73
Period size: 31 Copynumber: 2.1 Consensus size: 26
1812078 TTAGTAATAT
1812088 ATATATTTTAAATATTATATATATAATATAA
1 ATATATTTT--ATATT-TA-ATATAAT-TAA
1812119 ATATATTTTATATTTAATATAATTAA
1 ATATATTTTATATTTAATATAATTAA
1812145 AT
1 AT
1812147 GTAATGTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
26 5 0.18
27 7 0.25
28 2 0.07
29 5 0.18
31 9 0.32
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (26 bp):
ATATATTTTATATTTAATATAATTAA
Found at i:1812124 original size:22 final size:22
Alignment explanation
Indices: 1812099--1812140 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
1812089 TATATTTTAA
1812099 ATATTATATATATAATATAAAT
1 ATATTATATATATAATATAAAT
* *
1812121 ATATTTTATATTTAATATAA
1 ATATTATATATATAATATAA
1812141 TTAAATGTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
ATATTATATATATAATATAAAT
Done.