Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167893.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_16, 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: 22157061
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 74000 characters in sequence are not A, C, G, or T
File 89 of 113
Found at i:18530202 original size:61 final size:61
Alignment explanation
Indices: 18530107--18530223 Score: 180
Period size: 61 Copynumber: 1.9 Consensus size: 61
18530097 TAATGATTTA
*
18530107 GAAAAATAAATAAAGCTCCTCTAAACAGAAGCTCAATAACTTTGAAAAATAAATAAACTTT
1 GAAAAATAAATAAAGCTCCTATAAACAGAAGCTCAATAACTTTGAAAAATAAATAAACTTT
* * * * *
18530168 GAAAAATAAATAAGGTTCCTATAAGCAGAGGCTCAATAACTTTGAAAAATCAATAA
1 GAAAAATAAATAAAGCTCCTATAAACAGAAGCTCAATAACTTTGAAAAATAAATAA
18530224 GGTTTCTTTA
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
61 50 1.00
ACGTcount: A:0.51, C:0.14, G:0.11, T:0.24
Consensus pattern (61 bp):
GAAAAATAAATAAAGCTCCTATAAACAGAAGCTCAATAACTTTGAAAAATAAATAAACTTT
Found at i:18530223 original size:43 final size:43
Alignment explanation
Indices: 18530162--18530358 Score: 182
Period size: 43 Copynumber: 4.6 Consensus size: 43
18530152 AAAATAAATA
* *
18530162 AACTTTGAAAAATAAATAAGGTTCCTATAAGCAGAGGCTCAAT
1 AACTTTGAAAAATAAATAAGGCTCCTTTAAGCAGAGGCTCAAT
* * * *** *
18530205 AACTTTGAAAAATCAATAAGGTTTCTTTAAATGGAGGATCAAT
1 AACTTTGAAAAATAAATAAGGCTCCTTTAAGCAGAGGCTCAAT
* * * * *
18530248 GACATTGAAAAATAAATAAAGCTCATTTAAGCAGAAGG-TCAAC
1 AACTTTGAAAAATAAATAAGGCTCCTTTAAGCAG-AGGCTCAAT
** * *
18530291 AGTTCTTAAAAAATAAATAAGACTCCTTTAAGCAGAGGCTCAAT
1 AACT-TTGAAAAATAAATAAGGCTCCTTTAAGCAGAGGCTCAAT
*
18530335 AACTTT-AAGAAATAAATAAAGCTC
1 AACTTTGAA-AAATAAATAAGGCTC
18530359 TTGACAATCA
Statistics
Matches: 119, Mismatches: 31, Indels: 8
0.75 0.20 0.05
Matches are distributed among these distances:
42 2 0.02
43 82 0.69
44 35 0.29
ACGTcount: A:0.46, C:0.13, G:0.15, T:0.26
Consensus pattern (43 bp):
AACTTTGAAAAATAAATAAGGCTCCTTTAAGCAGAGGCTCAAT
Found at i:18536836 original size:23 final size:24
Alignment explanation
Indices: 18536792--18536836 Score: 58
Period size: 23 Copynumber: 1.9 Consensus size: 24
18536782 TTTAGGTCAA
*
18536792 TTTAGAAATTTTTGCAAGTTTTAT
1 TTTAGAAATTTTTGCAAATTTTAT
18536816 TTTA-AAATTTTT-CACAATTTT
1 TTTAGAAATTTTTGCA-AATTTT
18536837 GGGTCTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 2 0.11
23 13 0.68
24 4 0.21
ACGTcount: A:0.31, C:0.07, G:0.07, T:0.56
Consensus pattern (24 bp):
TTTAGAAATTTTTGCAAATTTTAT
Found at i:18538224 original size:19 final size:19
Alignment explanation
Indices: 18538202--18538246 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
18538192 CCAAATTTTA
* *
18538202 AGTCTAATTTAAACTCTTC
1 AGTCCAATTCAAACTCTTC
18538221 AGTCCAATTCAAACTCTTC
1 AGTCCAATTCAAACTCTTC
*
18538240 AATCCAA
1 AGTCCAA
18538247 ACAAATAGGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.36, C:0.27, G:0.04, T:0.33
Consensus pattern (19 bp):
AGTCCAATTCAAACTCTTC
Found at i:18540410 original size:211 final size:219
Alignment explanation
Indices: 18540037--18540525 Score: 552
Period size: 211 Copynumber: 2.2 Consensus size: 219
18540027 ATTTGTATTA
* * * * *
18540037 TGATTTTCTTGTATTTATTTTCTCTAAAATCATTATTTTTTAAAATTTATTGA-TCAACCCTTCG
1 TGATTTTCATATATTCATTTTCTTTAAAATCATTATTTATTAAAATTTATTGATTCAACCCTTCG
* * *
18540101 ATTTTGTAATATTTATATTTATATTTTTTACTTTTGATTTTCTTATGACTTATGGTTTTCTATCC
66 A--TTGTAATATTAACATTTATAATTTTTACTTTTGATTTTCTTATGACTTATGGTTTTCTATCC
* *
18540166 CTTTTAAAGGTGAAAGTTATATGAGTGTCTTTCATGTCTTTATTACACTTTTT-TCTCC-CTT-T
129 CTTTTAAAGGTGAAAGTTATATGAGTGTCTTTCATATCTTTATCACACTTTTTCTC-CCACTTGT
* *
18540228 CT-CATATTTCGTGGATTATTGACTTT
193 CTCCATATTACGTGAATTATTGACTTT
* * * *
18540254 TGATTTTCATATATTCATTTTCTTTAAAATCATTATTTGTTAAAATTTATTGATTTAA-CTTTTG
1 TGATTTTCATATATTCATTTTCTTTAAAATCATTATTTATTAAAATTTATTGATTCAACCCTTCG
* * *
18540318 A-T-T-ATA-TAACATTTATAATTTTTACTTTTTATTTTCTTTTGACTTATGGTTTT-TAATCTC
66 ATTGTAATATTAACATTTATAATTTTTACTTTTGATTTTCTTATGACTTATGGTTTTCT-ATCCC
* * *
18540378 TTTTAATGGT-AAGAGTTATATGAGTTTCTTTCATATCTTTATCATACTTTTTCTCCCAATTCTT
130 TTTTAAAGGTGAA-AGTTATATGAGTGTCTTTCATATCTTTATCACACTTTTTCTCCC-A--CTT
* *
18540442 GTTTGCCATATTACTTGAATTATTGACTTT
191 GTCT-CCATATTACGTGAATTATTGACTTT
* * * * *
18540472 TGGTTTTCGTATATTCATTTTCTTCAAAACCATTATCTATTAAAATTTATTGAT
1 TGATTTTCATATATTCATTTTCTTTAAAATCATTATTTATTAAAATTTATTGAT
18540526 CAAATATTTA
Statistics
Matches: 232, Mismatches: 29, Indels: 21
0.82 0.10 0.07
Matches are distributed among these distances:
210 3 0.01
211 92 0.40
212 5 0.02
213 1 0.00
214 1 0.00
215 3 0.01
216 2 0.01
217 53 0.23
218 72 0.31
ACGTcount: A:0.25, C:0.12, G:0.09, T:0.54
Consensus pattern (219 bp):
TGATTTTCATATATTCATTTTCTTTAAAATCATTATTTATTAAAATTTATTGATTCAACCCTTCG
ATTGTAATATTAACATTTATAATTTTTACTTTTGATTTTCTTATGACTTATGGTTTTCTATCCCT
TTTAAAGGTGAAAGTTATATGAGTGTCTTTCATATCTTTATCACACTTTTTCTCCCACTTGTCTC
CATATTACGTGAATTATTGACTTT
Found at i:18540563 original size:23 final size:24
Alignment explanation
Indices: 18540532--18540580 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
18540522 TGATCAAATA
*
18540532 TTTA-GTTTTGTAACATTAT-ATTT
1 TTTATGTTTTATAAC-TTATGATTT
*
18540555 TTTATTTTTTATAACTTATGATTT
1 TTTATGTTTTATAACTTATGATTT
18540579 TT
1 TT
18540581 CATCTTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
23 8 0.36
24 14 0.64
ACGTcount: A:0.24, C:0.04, G:0.06, T:0.65
Consensus pattern (24 bp):
TTTATGTTTTATAACTTATGATTT
Found at i:18540569 original size:24 final size:25
Alignment explanation
Indices: 18540537--18540589 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 25
18540527 AAATATTTAG
* *
18540537 TTTTGTAACATTAT-ATTTTTTAT-T
1 TTTTATAAC-TTATGATTTTTCATCT
18540561 TTTTATAACTTATGATTTTTCATCT
1 TTTTATAACTTATGATTTTTCATCT
18540586 TTTT
1 TTTT
18540590 TAAGGGTCAG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 4 0.16
24 16 0.64
25 5 0.20
ACGTcount: A:0.23, C:0.08, G:0.04, T:0.66
Consensus pattern (25 bp):
TTTTATAACTTATGATTTTTCATCT
Found at i:18542105 original size:249 final size:253
Alignment explanation
Indices: 18541649--18542118 Score: 639
Period size: 249 Copynumber: 1.9 Consensus size: 253
18541639 TATTTACATA
* *** *
18541649 TTATCTTTAAAGAATCAAGTGAACGTAACATTTGCTTCTTTTTCCATTCTTTTCATTGTGCTTGA
1 TTATCTTTAAAGAATCAAGTGAACGTAAAATTTGCTTCTTTTTCCATTCTTTTCAGCATGCTAGA
* *
18541714 TTTTTTTTATAGGAATTTAAAATTTTTGGTAATGTATAAGCTCATTGACAATGAAAGGTGATACT
66 TTTTTTTTATAGGAATTTAAAATCTTT-GTAA-GTATAAGCTCATTGACAATGAAAGGTGACACT
* * * * * *
18541779 TAAATTTCAATGTTTCAATAAAATTTTTATTCCTTTTGTTATCCCATGTTTTTCTCTTTTTTTTT
129 TAAATTTCAATATTTCAATAAAAATTTGATTCATTTTATTATCCCAAGTTTTTCTCTTTTTTTTT
*
18541844 CCCTATTAATTTATTTATTGCTTTTTAAAGAATTTTGATTTCTATTTATTGTTATCCCATC
194 -CCTAATAATTTATTTATTGCTTTTTAAAGAATTTTGATTTCTATTTATTGTTATCCCATC
* ** * *
18541905 TTATTTTTAAAGAATCAAGTTCACGTAAAATTTTCTTCTTTTTCTATTCTTTTCAGCATGCTAGA
1 TTATCTTTAAAGAATCAAGTGAACGTAAAATTTGCTTCTTTTTCCATTCTTTTCAGCATGCTAGA
* *
18541970 TTTTTTTTTATAGGAATTTAAAA-CTTT-T-A-TA-AA-CTCATTGACAATGGAATGTGACACTT
66 -TTTTTTTTATAGGAATTTAAAATCTTTGTAAGTATAAGCTCATTGACAATGAAAGGTGACACTT
*
18542029 AAATTTCAATATTTTAATAAAAATTTGATTCATTTTATTATCCCAAGTTTTTCTCTCTTTTCTTT
130 AAATTTCAATATTTCAATAAAAATTTGATTCATTTTATTATCCCAAGTTTTTCTCT-TTTT-TTT
18542094 T-CTAATAATTTATTTATTGCTTTTT
193 TCCTAATAATTTATTTATTGCTTTTT
18542119 TCTTCATTTC
Statistics
Matches: 189, Mismatches: 22, Indels: 13
0.84 0.10 0.06
Matches are distributed among these distances:
249 95 0.50
250 6 0.03
251 6 0.03
253 1 0.01
254 1 0.01
256 58 0.31
257 22 0.12
ACGTcount: A:0.28, C:0.13, G:0.09, T:0.51
Consensus pattern (253 bp):
TTATCTTTAAAGAATCAAGTGAACGTAAAATTTGCTTCTTTTTCCATTCTTTTCAGCATGCTAGA
TTTTTTTTATAGGAATTTAAAATCTTTGTAAGTATAAGCTCATTGACAATGAAAGGTGACACTTA
AATTTCAATATTTCAATAAAAATTTGATTCATTTTATTATCCCAAGTTTTTCTCTTTTTTTTTCC
TAATAATTTATTTATTGCTTTTTAAAGAATTTTGATTTCTATTTATTGTTATCCCATC
Found at i:18543268 original size:10 final size:11
Alignment explanation
Indices: 18543225--18543267 Score: 54
Period size: 10 Copynumber: 4.0 Consensus size: 11
18543215 ATATCATAAC
18543225 TAAAAATAATTA
1 TAAAAATAA-TA
18543237 TAAAAAT-ATA
1 TAAAAATAATA
*
18543247 TAAAATTAATA
1 TAAAAATAATA
18543258 -AAAAATAATA
1 TAAAAATAATA
18543268 ATTTTATAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
10 17 0.61
11 4 0.14
12 7 0.25
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (11 bp):
TAAAAATAATA
Found at i:18543277 original size:21 final size:21
Alignment explanation
Indices: 18543253--18543293 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
18543243 TATATAAAAT
18543253 TAATAAAAAATAATAATTTTA
1 TAATAAAAAATAATAATTTTA
* * *
18543274 TAATTAAAAATTATTATTTT
1 TAATAAAAAATAATAATTTT
18543294 TATTAATTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (21 bp):
TAATAAAAAATAATAATTTTA
Found at i:18543361 original size:16 final size:16
Alignment explanation
Indices: 18543335--18543376 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
18543325 AATAATATTT
18543335 TAATAACTATAATAAA
1 TAATAACTATAATAAA
* *
18543351 TTATAATTATAATAAA
1 TAATAACTATAATAAA
18543367 TAATAACTAT
1 TAATAACTAT
18543377 TTATATTTTA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (16 bp):
TAATAACTATAATAAA
Found at i:18543398 original size:21 final size:22
Alignment explanation
Indices: 18543368--18543411 Score: 81
Period size: 21 Copynumber: 2.0 Consensus size: 22
18543358 TATAATAAAT
18543368 AATAACTATTTATATTTTAATA
1 AATAACTATTTATATTTTAATA
18543390 AATAA-TATTTATATTTTAATA
1 AATAACTATTTATATTTTAATA
18543411 A
1 A
18543412 GTATAATAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 17 0.77
22 5 0.23
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (22 bp):
AATAACTATTTATATTTTAATA
Found at i:18543425 original size:7 final size:7
Alignment explanation
Indices: 18543405--18543453 Score: 55
Period size: 7 Copynumber: 6.9 Consensus size: 7
18543395 TATTTATATT
18543405 TTAATAA
1 TTAATAA
18543412 GTATAATAA
1 -T-TAATAA
18543421 TTAATAA
1 TTAATAA
18543428 TTAATAA
1 TTAATAA
*
18543435 TTAATTA
1 TTAATAA
*
18543442 TAAATAA
1 TTAATAA
18543449 -TAATA
1 TTAATA
18543454 TTTTATTTTC
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
6 4 0.11
7 24 0.67
8 2 0.06
9 6 0.17
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (7 bp):
TTAATAA
Found at i:18543780 original size:18 final size:16
Alignment explanation
Indices: 18543740--18543782 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
18543730 ACATTTCATT
18543740 TTTTTAATTTTATATA
1 TTTTTAATTTTATATA
*
18543756 TTATTAATTTTATAATTA
1 TTTTTAATTTTAT-A-TA
18543774 TTTTTAATT
1 TTTTTAATT
18543783 ATGGTATCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 12 0.52
17 1 0.04
18 10 0.43
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
TTTTTAATTTTATATA
Found at i:18544125 original size:3 final size:3
Alignment explanation
Indices: 18544119--18544150 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
18544109 ATGATTTAAT
*
18544119 AAC AAC AAC AAC AAC AAT AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
18544151 TAATAATAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.69, C:0.28, G:0.00, T:0.03
Consensus pattern (3 bp):
AAC
Found at i:18544139 original size:18 final size:18
Alignment explanation
Indices: 18544116--18544156 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
18544106 TTGATGATTT
18544116 AATAACAACAACAACAAC
1 AATAACAACAACAACAAC
*
18544134 AATAACAACAACAACAAT
1 AATAACAACAACAACAAC
18544152 AATAA
1 AATAA
18544157 TAATAATAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.68, C:0.22, G:0.00, T:0.10
Consensus pattern (18 bp):
AATAACAACAACAACAAC
Found at i:18544142 original size:15 final size:15
Alignment explanation
Indices: 18544122--18544153 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
18544112 ATTTAATAAC
18544122 AACAACAACAACAAT
1 AACAACAACAACAAT
18544137 AACAACAACAACAAT
1 AACAACAACAACAAT
18544152 AA
1 AA
18544154 TAATAATAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.69, C:0.25, G:0.00, T:0.06
Consensus pattern (15 bp):
AACAACAACAACAAT
Found at i:18544155 original size:3 final size:3
Alignment explanation
Indices: 18544149--18544189 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
18544139 CAACAACAAC
18544149 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
18544190 ATCAATAATT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:18544378 original size:13 final size:13
Alignment explanation
Indices: 18544360--18544384 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
18544350 AAAATTATAC
18544360 TAAAATATTTATT
1 TAAAATATTTATT
18544373 TAAAATATTTAT
1 TAAAATATTTAT
18544385 GCGTTTTTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
TAAAATATTTATT
Found at i:18546419 original size:19 final size:19
Alignment explanation
Indices: 18546392--18546438 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
18546382 CTAAAATATT
18546392 AAATCAAAAATAAAATCAAA
1 AAAT-AAAAATAAAATCAAA
* *
18546412 AAATAAAAATAGAATGAAA
1 AAATAAAAATAAAATCAAA
18546431 AAA-AAAAA
1 AAATAAAAA
18546439 AAACCTGCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 5 0.20
19 16 0.64
20 4 0.16
ACGTcount: A:0.79, C:0.04, G:0.04, T:0.13
Consensus pattern (19 bp):
AAATAAAAATAAAATCAAA
Found at i:18547229 original size:3 final size:3
Alignment explanation
Indices: 18547223--18547316 Score: 60
Period size: 3 Copynumber: 33.0 Consensus size: 3
18547213 AAAAAAGGAA
* * *
18547223 AAT AAT AAAT AA- AAG AAA AAT AAAT AAT AAT AAT AAT AAT CCAT AAT
1 AAT AAT -AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT -AAT AAT
* *
18547270 -AC AAT -GT AAT AAT AAT -AT AAT -AT AAT -AT AAT -AT AAT -AT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
18547311 AAT AAT
1 AAT AAT
18547317 CTAGCATACC
Statistics
Matches: 72, Mismatches: 8, Indels: 22
0.71 0.08 0.22
Matches are distributed among these distances:
2 14 0.19
3 50 0.69
4 8 0.11
ACGTcount: A:0.64, C:0.03, G:0.02, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:18547291 original size:5 final size:5
Alignment explanation
Indices: 18547242--18547352 Score: 82
Period size: 5 Copynumber: 21.2 Consensus size: 5
18547232 TAAAAGAAAA
* *
18547242 ATAA- ATAAT AATAAT AATAAT CCATAAT ACAAT GTAAT AATAAT ATAAT
1 ATAAT ATAAT -ATAAT -ATAAT --ATAAT ATAAT ATAAT -ATAAT ATAAT
* ** **
18547291 ATAAT ATAAT ATAAT ATAAT AATAAT CTAGC ATACC AT-AT CATAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT -ATAAT ATAAT ATAAT ATAAT -ATAAT ATAAT
18547342 ATAAT ATAAT A
1 ATAAT ATAAT A
18547353 CACTATATTA
Statistics
Matches: 88, Mismatches: 12, Indels: 13
0.78 0.11 0.12
Matches are distributed among these distances:
4 4 0.05
5 57 0.65
6 22 0.25
7 5 0.06
ACGTcount: A:0.57, C:0.07, G:0.02, T:0.34
Consensus pattern (5 bp):
ATAAT
Found at i:18547685 original size:55 final size:54
Alignment explanation
Indices: 18547552--18547958 Score: 213
Period size: 55 Copynumber: 7.4 Consensus size: 54
18547542 CTAGTCAAGC
* * * ** ***
18547552 AAATGATCTAGATTGAGCCAAGATTGAACT-TTTAGGATTGAATTGCAAG-CTAGA
1 AAATGATCTGGACTGAGCCAAGATCGAA-TGACTAGGATTGAACCACAAGTCTA-A
* * * * *
18547606 AAATGATATGGATTGAGCCAAGATCGAATGATTGGGATTGAACCTCAAGTCTGAA
1 AAATGATCTGGACTGAGCCAAGATCGAATGACTAGGATTGAACCACAAGTCT-AA
* * * *
18547661 AAATGATCTGGACTGAGTCGAGATCAAATAACTAGGATTGAACCACAAGT-TAGA
1 AAATGATCTGGACTGAGCCAAGATCGAATGACTAGGATTGAACCACAAGTCTA-A
* * * * * * *
18547715 AAGATGATTTAGACTGAACTC-AGATCAAATGACAAGGATTGAACCATAAGTGTAGA
1 AA-ATGATCTGGACTGAGC-CAAGATCGAATGACTAGGATTGAACCACAAGTCTA-A
* * * ** *
18547771 AAACGATCTTGACTGAGCCAAGATTGAGCG-GT-GAGATTGAACCACAAGTC-AA
1 AAATGATCTGGACTGAGCCAAGATCGAATGACTAG-GATTGAACCACAAGTCTAA
* * *
18547823 GAAGATGATCTGGACTGAGCCGAGATCGAATGA-TCAGGATTGAACCATAAAT-TAGGA
1 -AA-ATGATCTGGACTGAGCCAAGATCGAATGACT-AGGATTGAACCACAAGTCTA--A
* * * ** * * **
18547880 AAATGACCTAGATTGAGCTGAGATCAAATGACCAGGATTGAATTACAAGT-TAAAA
1 AAATGATCTGGACTGAGCCAAGATCGAATGACTAGGATTGAACCACAAGTCT--AA
* *
18547935 AAATGATCTAGACCGAGCCAAGAT
1 AAATGATCTGGACTGAGCCAAGAT
18547959 TGAAAATGAG
Statistics
Matches: 274, Mismatches: 59, Indels: 39
0.74 0.16 0.10
Matches are distributed among these distances:
52 1 0.00
53 6 0.02
54 81 0.30
55 173 0.63
56 11 0.04
57 2 0.01
ACGTcount: A:0.39, C:0.14, G:0.23, T:0.23
Consensus pattern (54 bp):
AAATGATCTGGACTGAGCCAAGATCGAATGACTAGGATTGAACCACAAGTCTAA
Found at i:18547864 original size:164 final size:163
Alignment explanation
Indices: 18547641--18547961 Score: 389
Period size: 164 Copynumber: 2.0 Consensus size: 163
18547631 GAATGATTGG
* *
18547641 GATTGAACCTCAAGTCTGAAAAATGATCTGGACTGAGTCGAGATCAAATAACTAGGATTGAACCA
1 GATTGAACCACAAGTC-GAAAAATGATCTGGACTGAGCCGAGATCAAATAACTAGGATTGAACCA
* ** *
18547706 CAAGTTA-GAAAGATGATTTAGACTGAACTCAGATCAAATGACAAGGATTGAACCATAAGTGT-A
65 CAAATTAGGAAA-ATGACCTAGACTGAACTCAGATCAAATGACAAGGATTGAACCACAAGT-TAA
* * *
18547769 GAAAACGATCTTGACTGAGCCAAGATTGAGCGGTGA
128 AAAAACGATCTAGACCGAGCCAAGATTGAGCGGTGA
* *
18547805 GATTGAACCACAAGTC-AAGAAGATGATCTGGACTGAGCCGAGATCGAATGA-TCAGGATTGAAC
1 GATTGAACCACAAGTCGAA-AA-ATGATCTGGACTGAGCCGAGATCAAATAACT-AGGATTGAAC
* * * * * **
18547868 CATAAATTAGGAAAATGACCTAGATTGAGCTGAGATCAAATGACCAGGATTGAATTACAAGTTAA
63 CACAAATTAGGAAAATGACCTAGACTGAACTCAGATCAAATGACAAGGATTGAACCACAAGTTAA
*
18547933 AAAAATGATCTAGACCGAGCCAAGATTGA
128 AAAAACGATCTAGACCGAGCCAAGATTGA
18547962 AAATGAGTAA
Statistics
Matches: 133, Mismatches: 19, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
162 2 0.02
163 4 0.03
164 123 0.92
165 4 0.03
ACGTcount: A:0.40, C:0.15, G:0.23, T:0.22
Consensus pattern (163 bp):
GATTGAACCACAAGTCGAAAAATGATCTGGACTGAGCCGAGATCAAATAACTAGGATTGAACCAC
AAATTAGGAAAATGACCTAGACTGAACTCAGATCAAATGACAAGGATTGAACCACAAGTTAAAAA
AACGATCTAGACCGAGCCAAGATTGAGCGGTGA
Found at i:18547897 original size:109 final size:109
Alignment explanation
Indices: 18547696--18547897 Score: 250
Period size: 109 Copynumber: 1.9 Consensus size: 109
18547686 AAATAACTAG
* *
18547696 GATTGAACCACAAGTTAGAAAGATGATTTAGACTGAACTCAGATCAAATGACAAGGATTGAACCA
1 GATTGAACCACAAGTAAGAAAGATGATCTAGACTGAACTCAGATCAAATGACAAGGATTGAACCA
* * *
18547761 TAAGTGTAGAAAACGATCTTGACTGAGCCAAGATTGAGCGGTGA
66 TAAATGTAGAAAACGACCTAGACTGAGCCAAGATTGAGCGGTGA
* * *
18547805 GATTGAACCACAAGTCAAG-AAGATGATCTGGACTGAGC-CGAGATCGAATGATC-AGGATTGAA
1 GATTGAACCACAAGT-AAGAAAGATGATCTAGACTGAACTC-AGATCAAATGA-CAAGGATTGAA
* *
18547867 CCATAAAT-TAGGAAAATGACCTAGATTGAGC
63 CCATAAATGTA-GAAAACGACCTAGACTGAGC
18547898 TGAGATCAAA
Statistics
Matches: 79, Mismatches: 10, Indels: 8
0.81 0.10 0.08
Matches are distributed among these distances:
108 3 0.04
109 73 0.92
110 3 0.04
ACGTcount: A:0.39, C:0.15, G:0.24, T:0.21
Consensus pattern (109 bp):
GATTGAACCACAAGTAAGAAAGATGATCTAGACTGAACTCAGATCAAATGACAAGGATTGAACCA
TAAATGTAGAAAACGACCTAGACTGAGCCAAGATTGAGCGGTGA
Found at i:18548751 original size:18 final size:18
Alignment explanation
Indices: 18548728--18548766 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
18548718 TAAGTCTTCC
*
18548728 TTTTTTCTCTTTTTTATT
1 TTTTTTATCTTTTTTATT
*
18548746 TTTTTTATTTTTTTTATT
1 TTTTTTATCTTTTTTATT
18548764 TTT
1 TTT
18548767 ATCTTTTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.08, C:0.05, G:0.00, T:0.87
Consensus pattern (18 bp):
TTTTTTATCTTTTTTATT
Found at i:18548774 original size:18 final size:18
Alignment explanation
Indices: 18548737--18548776 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
18548727 CTTTTTTCTC
*
18548737 TTTTTTATTTTTTTTATT
1 TTTTTTATTTTTTCTATT
18548755 TTTTTTATTTTTATCT-TT
1 TTTTTTATTTTT-TCTATT
18548773 TTTT
1 TTTT
18548777 GAACACCTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 18 0.90
19 2 0.10
ACGTcount: A:0.10, C:0.03, G:0.00, T:0.88
Consensus pattern (18 bp):
TTTTTTATTTTTTCTATT
Found at i:18553552 original size:19 final size:18
Alignment explanation
Indices: 18553528--18553578 Score: 66
Period size: 19 Copynumber: 2.7 Consensus size: 18
18553518 TAAAAGAACT
*
18553528 TAAAATATAAAATCAAAAA
1 TAAAATAAAAAAT-AAAAA
18553547 TAAAATCAAAAAATAAAAA
1 TAAAAT-AAAAAATAAAAA
18553566 TAAAATAGAAAAA
1 TAAAATA-AAAAA
18553579 AAACATGCGA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
18 1 0.03
19 22 0.76
20 6 0.21
ACGTcount: A:0.76, C:0.04, G:0.02, T:0.18
Consensus pattern (18 bp):
TAAAATAAAAAATAAAAA
Found at i:18553558 original size:13 final size:13
Alignment explanation
Indices: 18553529--18553564 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
18553519 AAAAGAACTT
*
18553529 AAAATATAAAATC
1 AAAAAATAAAATC
18553542 -AAAAATAAAATC
1 AAAAAATAAAATC
18553554 AAAAAATAAAA
1 AAAAAATAAAA
18553565 ATAAAATAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 11 0.52
13 10 0.48
ACGTcount: A:0.78, C:0.06, G:0.00, T:0.17
Consensus pattern (13 bp):
AAAAAATAAAATC
Found at i:18553570 original size:12 final size:13
Alignment explanation
Indices: 18553529--18553570 Score: 52
Period size: 12 Copynumber: 3.2 Consensus size: 13
18553519 AAAAGAACTT
18553529 AAAATATAAAATCA
1 AAAATA-AAAATCA
18553543 AAAAT-AAAATCAA
1 AAAATAAAAATC-A
18553556 AAAATAAAAAT-A
1 AAAATAAAAATCA
18553568 AAA
1 AAA
18553571 TAGAAAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 10 0.38
13 6 0.23
14 10 0.38
ACGTcount: A:0.79, C:0.05, G:0.00, T:0.17
Consensus pattern (13 bp):
AAAATAAAAATCA
Found at i:18554367 original size:3 final size:3
Alignment explanation
Indices: 18554361--18554494 Score: 63
Period size: 3 Copynumber: 46.3 Consensus size: 3
18554351 AAAGAAAGAA
*
18554361 AAT AAT AA- AAT -AT AAT AAT AAT AAT ATAT TAT AAT AAT AAT ACAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT A-AT
* * ** * *
18554406 AAT -AC AAT -GT AAT AGC AAT -AT AAT ATAT TAT AAT -AT AAT AGT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT
* **
18554448 AAT -CT AAT -AT ACCAT -AT CGT AAT -AT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT A--AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
18554491 AAT A
1 AAT A
18554495 TCACCATATA
Statistics
Matches: 97, Mismatches: 19, Indels: 30
0.66 0.13 0.21
Matches are distributed among these distances:
2 17 0.18
3 71 0.73
4 7 0.07
5 2 0.02
ACGTcount: A:0.57, C:0.05, G:0.03, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:18554383 original size:19 final size:19
Alignment explanation
Indices: 18554361--18554407 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 19
18554351 AAAGAAAGAA
18554361 AATAATAAAATATAATAAT
1 AATAATAAAATATAATAAT
* *
18554380 AATAATATATTATAATAAT
1 AATAATAAAATATAATAAT
18554399 AATACATAA
1 AATA-ATAA
18554408 TACAATGTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
19 21 0.88
20 3 0.12
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (19 bp):
AATAATAAAATATAATAAT
Found at i:18554401 original size:16 final size:16
Alignment explanation
Indices: 18554361--18554495 Score: 72
Period size: 16 Copynumber: 8.7 Consensus size: 16
18554351 AAAGAAAGAA
*
18554361 AATAATAAAATATAAT
1 AATAATAATATATAAT
*
18554377 AATAATAATATATTAT
1 AATAATAATATATAAT
*
18554393 AATAATAATACATAAT
1 AATAATAATATATAAT
* * **
18554409 -ACAAT-GTA-ATAGC
1 AATAATAATATATAAT
*
18554422 AAT-ATAATATATTAT
1 AATAATAATATATAAT
*
18554437 AAT-ATAATAGTA-ATCT
1 AATAATAATA-TATA-AT
*
18554453 AAT-ATACCATATCGTAAT
1 AATAATA--ATAT-ATAAT
18554471 -ATAATAATA-ATAAT
1 AATAATAATATATAAT
18554485 AATAATAATAT
1 AATAATAATAT
18554496 CACCATATAA
Statistics
Matches: 89, Mismatches: 18, Indels: 24
0.68 0.14 0.18
Matches are distributed among these distances:
13 5 0.06
14 9 0.10
15 24 0.27
16 40 0.45
17 3 0.03
18 7 0.08
19 1 0.01
ACGTcount: A:0.56, C:0.05, G:0.03, T:0.36
Consensus pattern (16 bp):
AATAATAATATATAAT
Found at i:18554455 original size:11 final size:11
Alignment explanation
Indices: 18554375--18554495 Score: 56
Period size: 11 Copynumber: 11.2 Consensus size: 11
18554365 ATAAAATATA
*
18554375 ATAATAATAAT
1 ATAATAGTAAT
*
18554386 ATATTA-TAAT
1 ATAATAGTAAT
*
18554396 AATAATACATAAT
1 -ATAATA-GTAAT
*
18554409 ACAAT-GTAAT
1 ATAATAGTAAT
*
18554419 AGCAATA-TAAT
1 A-TAATAGTAAT
*
18554430 ATATTA-TAAT
1 ATAATAGTAAT
18554440 ATAATAGTAAT
1 ATAATAGTAAT
* **
18554451 CTAATA-TACC
1 ATAATAGTAAT
*
18554461 AT-ATCGTAAT
1 ATAATAGTAAT
*
18554471 ATAATAATAAT
1 ATAATAGTAAT
*
18554482 AATAATAATAAT
1 -ATAATAGTAAT
18554494 AT
1 AT
18554496 CACCATATAA
Statistics
Matches: 85, Mismatches: 16, Indels: 18
0.71 0.13 0.15
Matches are distributed among these distances:
9 2 0.02
10 28 0.33
11 36 0.42
12 15 0.18
13 4 0.05
ACGTcount: A:0.55, C:0.06, G:0.03, T:0.36
Consensus pattern (11 bp):
ATAATAGTAAT
Found at i:18558420 original size:16 final size:17
Alignment explanation
Indices: 18558385--18558417 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
18558375 TCAATACTGT
18558385 TAAAAACCAAAAGATAA
1 TAAAAACCAAAAGATAA
*
18558402 TAAAACCCAAAAGATA
1 TAAAAACCAAAAGATA
18558418 TAACCAATGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.67, C:0.15, G:0.06, T:0.12
Consensus pattern (17 bp):
TAAAAACCAAAAGATAA
Found at i:18558627 original size:67 final size:66
Alignment explanation
Indices: 18558432--18558617 Score: 216
Period size: 67 Copynumber: 2.8 Consensus size: 66
18558422 CAATGTTCAT
* * *
18558432 AATTAATAAATAAATATTATTTTTAAAACTGAAGAAATTGAAAAAATAAAGAAAGCAAAAAATGC
1 AATTAAT-AATAAATATTATTTTTAAAATTGAAGAAAATGAAAAAATCAAGAAAGCAAAAAATGC
*
18558497 AT
65 AC
* ** *
18558499 AATTAATTAATAAATATTATTTTTAAAATTCAAGAAAATGAAAAGGTCAAGAAAGCTAAAAA-GA
1 AATTAA-TAATAAATATTATTTTTAAAATTGAAGAAAATGAAAAAATCAAGAAAGCAAAAAATG-
18558563 CAC
64 CAC
* *
18558566 AATTAATAGATAAATATTATTTTT-CAATTGAAGAAAACT-AAAATATCAAGAA
1 AATTAATA-ATAAATATTATTTTTAAAATTGAAGAAAA-TGAAAAAATCAAGAA
18558618 TGCCCAAAAA
Statistics
Matches: 103, Mismatches: 12, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
66 25 0.24
67 77 0.75
68 1 0.01
ACGTcount: A:0.56, C:0.06, G:0.09, T:0.28
Consensus pattern (66 bp):
AATTAATAATAAATATTATTTTTAAAATTGAAGAAAATGAAAAAATCAAGAAAGCAAAAAATGCA
C
Found at i:18559653 original size:21 final size:21
Alignment explanation
Indices: 18559629--18559673 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 21
18559619 TAATTTTGCA
18559629 TTTGTA-TTTGCTAATATATAG
1 TTTGTACTTTG-TAATATATAG
18559650 TTTGTACTGTTTGTAATATATAG
1 TTTGTAC--TTTGTAATATATAG
18559673 T
1 T
18559674 AAAAAATATT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
21 6 0.29
23 11 0.52
24 4 0.19
ACGTcount: A:0.27, C:0.04, G:0.16, T:0.53
Consensus pattern (21 bp):
TTTGTACTTTGTAATATATAG
Found at i:18560442 original size:301 final size:304
Alignment explanation
Indices: 18559928--18560548 Score: 793
Period size: 301 Copynumber: 2.0 Consensus size: 304
18559918 ATACAATATT
* *
18559928 AAATTATAAAATTATCAAAATTTTATAAATTTTATACTACCTAATTATCAAATCAACCATCCAAA
1 AAATAATAAAAATATCAAAATTTTATAAATTTTATACTACCTAATTATCAAATCAACCATCCAAA
* * * ** *
18559993 GCATGGGTGTAAAAAATCTTGTATTATAAATTTTTAAAATTTAATTTGAATCTAAATTGATTTTT
66 GCAT-GGTGTAAAAAACCTAGTATTATAAATTTTTAAAATCTAATCCGAATCTAAATCGATTTTT
* * * * * ** * *** *
18560058 CTTTAAAACGGAACCGATTTGAATTTTTCCTTTGATTTGGTTTGACTCATTGATTTTTTAAATTT
130 CTTTAAAACGAAACCGATCTAAATTCTACCTTTGATTTAATTCGACTCACCAATATTTTAAATTT
*
18560123 AATTTATTTTAGTTTTTATATATTATTTTAATATAATTTTTAATACATTCAAATAAATTTAGATA
195 AATTTATTTTAATTTTTATATATTATTTTAATATAATTTTTAATACATTCAAATAAATTTAGATA
* * *
18560188 TATAATAATTACTTTTA-TTTTATAAAAATTTAAATATATATAAA
260 TAAAATAATTACTTTTATTTTTAAAAAAATTTAAATATATAGAAA
* * * * * * *
18560232 AGATAATAAAAATATCAACATTTTATAAATTTTATACTACCTGATTATGAAATTAACCGTGCAAA
1 AAATAATAAAAATATCAAAATTTTATAAATTTTATACTACCTAATTATCAAATCAACCATCCAAA
* *
18560297 GTACAT-GTGTAAAAAACCTAGTTTTATAAA-TTTTAAAATCTAATCCGAATCTGAATCGATTTT
66 G--CATGGTGTAAAAAACCTAGTATTATAAATTTTTAAAATCTAATCCGAATCTAAATCGATTTT
* * * *
18560360 T-TTTTAATC-AAACTGATCTAAATTCTACCTTTGATTTAATTCGATTCACCAATATTTTAAATT
129 TCTTTAAAACGAAACCGATCTAAATTCTACCTTTGATTTAATTCGACTCACCAATATTTTAAATT
* * * *
18560423 TAATTTATTTTAATTTTTATATATTATTTTGATATAATTTTTAATATATTTAAATAGATTTAGAT
194 TAATTTATTTTAATTTTTATATATTATTTTAATATAATTTTTAATACATTCAAATAAATTTAGAT
* *
18560488 TTAAAATAATTATTTTTATTTTTAAAAAAATTTAAATATATAGAAA
259 ATAAAATAATTACTTTTATTTTTAAAAAAATTTAAATATATAGAAA
18560534 AAATAATAAAAATAT
1 AAATAATAAAAATAT
18560549 ATCATCCAAT
Statistics
Matches: 270, Mismatches: 44, Indels: 8
0.84 0.14 0.02
Matches are distributed among these distances:
301 115 0.43
302 45 0.17
303 29 0.11
304 78 0.29
306 3 0.01
ACGTcount: A:0.41, C:0.08, G:0.06, T:0.45
Consensus pattern (304 bp):
AAATAATAAAAATATCAAAATTTTATAAATTTTATACTACCTAATTATCAAATCAACCATCCAAA
GCATGGTGTAAAAAACCTAGTATTATAAATTTTTAAAATCTAATCCGAATCTAAATCGATTTTTC
TTTAAAACGAAACCGATCTAAATTCTACCTTTGATTTAATTCGACTCACCAATATTTTAAATTTA
ATTTATTTTAATTTTTATATATTATTTTAATATAATTTTTAATACATTCAAATAAATTTAGATAT
AAAATAATTACTTTTATTTTTAAAAAAATTTAAATATATAGAAA
Found at i:18562303 original size:2 final size:2
Alignment explanation
Indices: 18562291--18562323 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
18562281 CTCTTTCCAT
*
18562291 TA TA CA 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
18562324 CTCACAAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:18566352 original size:5 final size:5
Alignment explanation
Indices: 18566342--18566366 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
18566332 GGATGCTTCG
18566342 GTTTT GTTTT GTTTT GTTTT GTTTT
1 GTTTT GTTTT GTTTT GTTTT GTTTT
18566367 TTCTCTTGCT
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:0.00, G:0.20, T:0.80
Consensus pattern (5 bp):
GTTTT
Found at i:18566954 original size:30 final size:30
Alignment explanation
Indices: 18566918--18566977 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
18566908 TTCGTGATTA
* *
18566918 CCTCCACATTATTGCCTAATCAACCTTTGC
1 CCTCCACATCATTACCTAATCAACCTTTGC
*
18566948 CCTCCACATCATTACTTAATCAACCTTTGC
1 CCTCCACATCATTACCTAATCAACCTTTGC
18566978 ATTTGCGCTG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.25, C:0.37, G:0.05, T:0.33
Consensus pattern (30 bp):
CCTCCACATCATTACCTAATCAACCTTTGC
Found at i:18571098 original size:16 final size:16
Alignment explanation
Indices: 18571077--18571110 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
18571067 CATAAATTGG
18571077 TATATTAGACAATGTT
1 TATATTAGACAATGTT
18571093 TATATTAGACAATGTT
1 TATATTAGACAATGTT
18571109 TA
1 TA
18571111 ATTCTTAGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.38, C:0.06, G:0.12, T:0.44
Consensus pattern (16 bp):
TATATTAGACAATGTT
Found at i:18571697 original size:21 final size:21
Alignment explanation
Indices: 18571660--18571711 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
18571650 AAGTATATTA
*
18571660 CAATCATAAGAAGAAATGAA-G
1 CAATCACAAGAAGAAAT-AAGG
18571681 CAATCACAAG-AGAAAATAAGG
1 CAATCACAAGAAG-AAATAAGG
*
18571702 CAACCACAAG
1 CAATCACAAG
18571712 CCTTAGTAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 4 0.15
21 23 0.85
ACGTcount: A:0.56, C:0.17, G:0.17, T:0.10
Consensus pattern (21 bp):
CAATCACAAGAAGAAATAAGG
Found at i:18571924 original size:19 final size:18
Alignment explanation
Indices: 18571878--18571940 Score: 56
Period size: 19 Copynumber: 3.4 Consensus size: 18
18571868 TTGTTGGAGG
* *
18571878 TTTATGGAT-TTTTTGAAT
1 TTTAT-GATGTTTATGAAA
18571896 TTTATAGATGTTTATGAAA
1 TTTAT-GATGTTTATGAAA
* *
18571915 GTTTATGATGTTTGTGTAA
1 -TTTATGATGTTTATGAAA
18571934 TTTATGA
1 TTTATGA
18571941 ATAAATGATG
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
18 15 0.39
19 18 0.47
20 5 0.13
ACGTcount: A:0.27, C:0.00, G:0.19, T:0.54
Consensus pattern (18 bp):
TTTATGATGTTTATGAAA
Found at i:18572302 original size:73 final size:72
Alignment explanation
Indices: 18572163--18572352 Score: 199
Period size: 73 Copynumber: 2.6 Consensus size: 72
18572153 TTTTTTCAAG
* * *
18572163 TTAAAAGTATTATTG-AGGAAATTTTATTACTAAAAAGCAAATAATAATACTTTTACGAATGGAA
1 TTAAAAGTATTATTGAAGG-AATTTTATTA-TAAAAAGAAAATAATAACACTTTTACGAA-GAAA
18572227 TATTTA-GCCA
63 TA-TTACGCCA
* * *
18572237 TTAAATGTGTTATTGAAGGAATTTTATTATAAAAAGAAAATAATAACACTTTTGATGACA-AAAT
1 TTAAAAGTATTATTGAAGGAATTTTATTATAAAAAGAAAATAATAACACTTTT-ACGA-AGAAAT
18572301 ATTACGCCA
64 ATTACGCCA
*
18572310 TTAAAAGTACAATTATAT-ATGGAATTTTATTATAAAAAGAAAA
1 TTAAAAGT---ATTAT-TGAAGGAATTTTATTATAAAAAGAAAA
18572353 AAGTTTTTAG
Statistics
Matches: 99, Mismatches: 9, Indels: 14
0.81 0.07 0.11
Matches are distributed among these distances:
72 3 0.03
73 37 0.37
74 26 0.26
75 4 0.04
76 28 0.28
77 1 0.01
ACGTcount: A:0.47, C:0.07, G:0.12, T:0.35
Consensus pattern (72 bp):
TTAAAAGTATTATTGAAGGAATTTTATTATAAAAAGAAAATAATAACACTTTTACGAAGAAATAT
TACGCCA
Found at i:18572573 original size:48 final size:49
Alignment explanation
Indices: 18572487--18572579 Score: 125
Period size: 48 Copynumber: 1.9 Consensus size: 49
18572477 ATGTATTTTT
* **
18572487 CATGCATCAATATTTATATTTTTACCAATGGCAGTTTTGTTATTTGTCA
1 CATGCATCAATATTTACATTTTTACCAATAACAGTTTTGTTATTTGTCA
* * *
18572536 CATGCA-CAATATTTACATTTTTACTATTAACATTTTTGTTATTT
1 CATGCATCAATATTTACATTTTTACCAATAACAGTTTTGTTATTT
18572580 TCATCATATG
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
48 32 0.84
49 6 0.16
ACGTcount: A:0.28, C:0.14, G:0.09, T:0.49
Consensus pattern (49 bp):
CATGCATCAATATTTACATTTTTACCAATAACAGTTTTGTTATTTGTCA
Found at i:18573612 original size:16 final size:16
Alignment explanation
Indices: 18573586--18573625 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
18573576 TTCCTTGATT
18573586 AAACTAAAAAAAATCAA
1 AAAC-AAAAAAAATCAA
**
18573603 AAACAAAAAAAATTGA
1 AAACAAAAAAAATCAA
18573619 AAACAAA
1 AAACAAA
18573626 TCGAAAAATG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 17 0.81
17 4 0.19
ACGTcount: A:0.78, C:0.10, G:0.03, T:0.10
Consensus pattern (16 bp):
AAACAAAAAAAATCAA
Found at i:18573734 original size:25 final size:25
Alignment explanation
Indices: 18573706--18573756 Score: 59
Period size: 25 Copynumber: 2.0 Consensus size: 25
18573696 CATATTTTAA
*
18573706 TTATGTCA-TTTGTTTTAAATTATTG
1 TTAT-TCATTTTGTTTTAAATAATTG
* *
18573731 TTATTTATTTTGTTTTTAATAATTG
1 TTATTCATTTTGTTTTAAATAATTG
18573756 T
1 T
18573757 AGGACATTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
24 2 0.09
25 20 0.91
ACGTcount: A:0.24, C:0.02, G:0.10, T:0.65
Consensus pattern (25 bp):
TTATTCATTTTGTTTTAAATAATTG
Found at i:18573741 original size:20 final size:18
Alignment explanation
Indices: 18573698--18573741 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 18
18573688 ATTTCATGCA
18573698 TATTTTAATTATGTCATT
1 TATTTTAATTATGTCATT
* *
18573716 TGTTTTAAATTATTGTTATT
1 TATTTT-AATTA-TGTCATT
18573736 TATTTT
1 TATTTT
18573742 GTTTTTAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 5 0.24
19 5 0.24
20 11 0.52
ACGTcount: A:0.25, C:0.02, G:0.07, T:0.66
Consensus pattern (18 bp):
TATTTTAATTATGTCATT
Found at i:18577406 original size:107 final size:106
Alignment explanation
Indices: 18577271--18577482 Score: 284
Period size: 107 Copynumber: 2.0 Consensus size: 106
18577261 TTGTCAGACC
* *
18577271 ATCACTAGTCCAAGTAAACACTAATCCTGGATCCATTCCTTTCAAGCCCATTACTGTGCCTAATC
1 ATCACTAGTCCAAGTAAACACCAATCCTGGATCCATTCCTTTCAAGCCCATTACTATGCCTAATC
* *
18577336 TAGATAATCCT-AAGAAACAAGCA-AAATTGAAAAGGGTTTTCG
66 TAGACAAT-CTAAAG-AACAAG-AGAAACTGAAAAGGGTTTTCG
* * * **
18577378 ATCACTAGTCCAGGTAAACACCAATCCTGGATCCATTCTTTTCGAGCCCATTGTTATGCCTAATC
1 ATCACTAGTCCAAGTAAACACCAATCCTGGATCCATTCCTTTCAAGCCCATTACTATGCCTAATC
*
18577443 TTGACAATCTAAATGAACAAGAGAAACTGAAAAGGGTTTT
66 TAGACAATCTAAA-GAACAAGAGAAACTGAAAAGGGTTTT
18577483 TGATTCTATA
Statistics
Matches: 92, Mismatches: 10, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
106 3 0.03
107 88 0.96
108 1 0.01
ACGTcount: A:0.34, C:0.23, G:0.15, T:0.28
Consensus pattern (106 bp):
ATCACTAGTCCAAGTAAACACCAATCCTGGATCCATTCCTTTCAAGCCCATTACTATGCCTAATC
TAGACAATCTAAAGAACAAGAGAAACTGAAAAGGGTTTTCG
Found at i:18594006 original size:21 final size:21
Alignment explanation
Indices: 18593980--18594021 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
18593970 ATCATAAAAT
*
18593980 AAAAAAATCAAATAAACATAA
1 AAAAAAAACAAATAAACATAA
18594001 AAAAAAAACAAATAAACATAA
1 AAAAAAAACAAATAAACATAA
18594022 TCCCTAGGGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.79, C:0.10, G:0.00, T:0.12
Consensus pattern (21 bp):
AAAAAAAACAAATAAACATAA
Found at i:18595271 original size:3 final size:3
Alignment explanation
Indices: 18595263--18595311 Score: 89
Period size: 3 Copynumber: 16.3 Consensus size: 3
18595253 TAATAAAAAC
*
18595263 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ACA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
18595311 A
1 A
18595312 ATAAATAAAT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:18595479 original size:16 final size:16
Alignment explanation
Indices: 18595451--18595492 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
18595441 TGTTTTTTTT
18595451 TAAATCCCT-CAAACCA
1 TAAA-CCCTCCAAACCA
*
18595467 TAAACCCTCCAAACCT
1 TAAACCCTCCAAACCA
18595483 TAAAACCCTC
1 T-AAACCCTC
18595493 AAAAACCTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
15 4 0.17
16 11 0.48
17 8 0.35
ACGTcount: A:0.40, C:0.40, G:0.00, T:0.19
Consensus pattern (16 bp):
TAAACCCTCCAAACCA
Found at i:18595500 original size:18 final size:17
Alignment explanation
Indices: 18595450--18595506 Score: 64
Period size: 18 Copynumber: 3.4 Consensus size: 17
18595440 ATGTTTTTTT
*
18595450 TTAAATCCCTC-AAACC
1 TTAAAACCCTCAAAACC
* *
18595466 AT-AAACCCTCCAAACC
1 TTAAAACCCTCAAAACC
18595482 TTAAAACCCTCAAAAACC
1 TTAAAACCCTC-AAAACC
18595500 TTAAAAC
1 TTAAAAC
18595507 TTAAAACTCT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
15 7 0.21
16 7 0.21
17 8 0.24
18 12 0.35
ACGTcount: A:0.46, C:0.35, G:0.00, T:0.19
Consensus pattern (17 bp):
TTAAAACCCTCAAAACC
Found at i:18595519 original size:15 final size:15
Alignment explanation
Indices: 18595501--18595535 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
18595491 TCAAAAACCT
18595501 TAAAACTTAAAACTC
1 TAAAACTTAAAACTC
*
18595516 TAAAATTTAAAACTC
1 TAAAACTTAAAACTC
18595531 -AAAAC
1 TAAAAC
18595536 CAAAACCCTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
14 4 0.22
15 14 0.78
ACGTcount: A:0.57, C:0.17, G:0.00, T:0.26
Consensus pattern (15 bp):
TAAAACTTAAAACTC
Found at i:18601830 original size:55 final size:55
Alignment explanation
Indices: 18601743--18601873 Score: 154
Period size: 55 Copynumber: 2.4 Consensus size: 55
18601733 AACTTTCAAA
* *
18601743 ACTTTTCAAAAGGAGATTTTTTATTTAAAAGTTCATTGCCTATCTTTATAGGAGC
1 ACTTTTCAAAAGGAGATTTTTTATTTAAAAGTTCATTACCTATCTTTATAAGAGC
* ** * * ** **
18601798 CCTTTTCAAATTGAGTTTTTTTTTTTTTAAGTTTGTTACCTATCTTTATAAGAGC
1 ACTTTTCAAAAGGAGATTTTTTATTTAAAAGTTCATTACCTATCTTTATAAGAGC
*
18601853 ACTTTTCAAAAAGAGATTTTT
1 ACTTTTCAAAAGGAGATTTTT
18601874 ATAAAGTCAC
Statistics
Matches: 61, Mismatches: 15, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
55 61 1.00
ACGTcount: A:0.28, C:0.12, G:0.12, T:0.47
Consensus pattern (55 bp):
ACTTTTCAAAAGGAGATTTTTTATTTAAAAGTTCATTACCTATCTTTATAAGAGC
Found at i:18601945 original size:50 final size:49
Alignment explanation
Indices: 18601848--18602426 Score: 466
Period size: 50 Copynumber: 11.6 Consensus size: 49
18601838 TATCTTTATA
*
18601848 AGAGCACTTTTCAAAAAGAGATTTTTATAAAGTCACTTGCCTATGTCTAT
1 AGAGCACTTTTCAAAATGAGATTTTT-TAAAGTCACTTGCCTATGTCTAT
* * * * **
18601898 ACGAGAACTTTTCAAAAAGAGATCTTTTCAAGTCACTTGTTTATGTCTAT
1 A-GAGCACTTTTCAAAATGAGATTTTTTAAAGTCACTTGCCTATGTCTAT
* * * *
18601948 AGAAGGACTTTTTAAATTGAGAATTTTTAAAGTCACTTGCCTATGTCTATT
1 AG-AGCACTTTTCAAAATGAGATTTTTTAAAGTCACTTGCCTATGTCTA-T
* * * * *
18601999 AAAGTA-TTGTTCAAATTGAGTTTTTTTAAAGTCACTTGCCTATGTTTAT
1 AGAGCACTT-TTCAAAATGAGATTTTTTAAAGTCACTTGCCTATGTCTAT
* * *
18602048 AGGACCACTTTTGAAAATGAGATTTTTTTAAAGTCACTTGCTTATGTCTAT
1 A-GAGCACTTTTCAAAATGAGA-TTTTTTAAAGTCACTTGCCTATGTCTAT
* * *
18602099 AAGAGCACTTTTCAAAAAGAGATTTTTTAATGTCACTTGTCTATGTCTAT
1 -AGAGCACTTTTCAAAATGAGATTTTTTAAAGTCACTTGCCTATGTCTAT
*
18602149 AGAAGCACTTTT-AAAATTGAGATTTTTTAAAGTCACTT---AATGTCTAT
1 AG-AGCACTTTTCAAAA-TGAGATTTTTTAAAGTCACTTGCCTATGTCTAT
* * *
18602196 AGGTGC-C-ATTC-AAATAGAGATGTTTTTAAAGTCACTTGTCTATG-CTAT
1 A-GAGCACTTTTCAAAAT-GAGAT-TTTTTAAAGTCACTTGCCTATGTCTAT
* * * * *
18602244 AAGAGCACTTTT-TAAATAGAGATTTTTTTTTTTTAAGTCATTTACCTATCT-TCAT
1 -AGAGCACTTTTCAAAAT-GAGA-----TTTTTTAAAGTCACTTGCCTATGTCT-AT
**
18602299 AGGAGCACTTTTC-AAATAGAGATTTTTTGAAAGTCACTTGCCTACATCTAT
1 A-GAGCACTTTTCAAAAT-GAGATTTTTT-AAAGTCACTTGCCTATGTCTAT
* * * *
18602350 AGGACCACTTTTCAAAA-GAAGA-TTTTTAAAGTTACTTGCCTATGTTTAG
1 A-GAGCACTTTTCAAAATG-AGATTTTTTAAAGTCACTTGCCTATGTCTAT
* *
18602399 AGAAGCACTTTTCAAATTAAGATTTTTT
1 AG-AGCACTTTTCAAAATGAGATTTTTT
18602427 TTTTATGAAA
Statistics
Matches: 431, Mismatches: 61, Indels: 74
0.76 0.11 0.13
Matches are distributed among these distances:
44 1 0.00
45 10 0.02
46 16 0.04
47 11 0.03
48 9 0.02
49 49 0.11
50 189 0.44
51 100 0.23
52 5 0.01
54 19 0.04
55 22 0.05
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.40
Consensus pattern (49 bp):
AGAGCACTTTTCAAAATGAGATTTTTTAAAGTCACTTGCCTATGTCTAT
Found at i:18602277 original size:201 final size:197
Alignment explanation
Indices: 18601844--18602386 Score: 553
Period size: 201 Copynumber: 2.7 Consensus size: 197
18601834 TACCTATCTT
* * * * * *
18601844 TATAAGAGCACTTTTCAAAAAGAGATTTTTATAAAGTCACTTGCCTATGTCTATACGAGAACTTT
1 TATAAGACCACTTTTGAAAATGAGATTTTTTTAAAGTCACTTGCCTATGTCTATAAGAGCACTTT
* * * *
18601909 TCAAAAAGAGATCTTTTCAAGTCACTTGTTTATGTCTATAGAAGGACTTTTTAAATTGAGAATTT
66 TCAAAAAGAGAT-TTTTTAAGTCACTTGTCTATGTCTATAGAAGCACTTTTAAAATTGAG-ATTT
* *** * *
18601974 TTAAAGTCACTTGCCTATGTCTATTAAAGTATTGTTCAAATTGAGTTTTTTTAAAGTCACTTGCC
129 TTAAAGTCACTT--CAATGTCTATTAAAGTACCATTCAAATAGAGTGTTTTTAAAGTCACTTGCC
*
18602039 TATGTT
192 TATGTC
* *
18602045 TATAGGACCACTTTTGAAAATGAGATTTTTTTAAAGTCACTTGCTTATGTCTATAAGAGCACTTT
1 TATAAGACCACTTTTGAAAATGAGATTTTTTTAAAGTCACTTGCCTATGTCTATAAGAGCACTTT
18602110 TCAAAAAGAGATTTTTTAATGTCACTTGTCTATGTCTATAGAAGCACTTTTAAAATTGAGATTTT
66 TCAAAAAGAGATTTTTTAA-GTCACTTGTCTATGTCTATAGAAGCACTTTTAAAATTGAGA-TTT
* * *
18602175 TTAAAGTCACTT-AATGTCTA-T-AGGTGCCATTCAAATAGAGATGTTTTTAAAGTCACTTGTCT
129 TTAAAGTCACTTCAATGTCTATTAAAGTACCATTCAAATAGAG-TGTTTTTAAAGTCACTTGCCT
18602237 ATG-C
193 ATGTC
* * * * * * *
18602241 TATAAGAGCACTTTT-TAAATAGAGATTTTTTTTTTTTAAGTCATTTACCTATCT-TCATAGGAG
1 TATAAGACCACTTTTGAAAAT-GAGA----TTTTTTTAAAGTCACTTGCCTATGTCT-ATAAGAG
* * ** * *
18602304 CACTTTTCAAATAGAGATTTTTTGAAAGTCACTTGCCTACATCTATAGGACCACTTTTCAAAA--
60 CACTTTTCAAAAAGAGATTTTTT--AAGTCACTTGTCTATGTCTATAGAAGCACTTTT-AAAATT
*
18602367 GAAGATTTTTAAAGTTACTT
122 G-AGATTTTTAAAGTCACTT
18602387 GCCTATGTTT
Statistics
Matches: 291, Mismatches: 38, Indels: 27
0.82 0.11 0.08
Matches are distributed among these distances:
195 4 0.01
196 30 0.10
197 23 0.08
198 7 0.02
199 1 0.00
200 70 0.24
201 150 0.52
202 6 0.02
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.40
Consensus pattern (197 bp):
TATAAGACCACTTTTGAAAATGAGATTTTTTTAAAGTCACTTGCCTATGTCTATAAGAGCACTTT
TCAAAAAGAGATTTTTTAAGTCACTTGTCTATGTCTATAGAAGCACTTTTAAAATTGAGATTTTT
AAAGTCACTTCAATGTCTATTAAAGTACCATTCAAATAGAGTGTTTTTAAAGTCACTTGCCTATG
TC
Found at i:18602408 original size:49 final size:50
Alignment explanation
Indices: 18602302--18602425 Score: 135
Period size: 49 Copynumber: 2.5 Consensus size: 50
18602292 TCTTCATAGG
* *
18602302 AGCACTTTTCAAATAG-AGATTTTTTGAAAGTCACTTGCCTACATCTATAGG
1 AGCACTTTTCAAA-AGAAGA-TTTTTGAAAGTCACTTGCCTACATCTAGAGA
* * ** *
18602353 ACCACTTTTCAAAAGAAGATTTTT-AAAGTTACTTGCCTATGTTTAGAGA
1 AGCACTTTTCAAAAGAAGATTTTTGAAAGTCACTTGCCTACATCTAGAGA
**
18602402 AGCACTTTTCAAATTAAGATTTTT
1 AGCACTTTTCAAAAGAAGATTTTT
18602426 TTTTTATGAA
Statistics
Matches: 62, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
49 40 0.65
50 7 0.11
51 15 0.24
ACGTcount: A:0.33, C:0.15, G:0.14, T:0.38
Consensus pattern (50 bp):
AGCACTTTTCAAAAGAAGATTTTTGAAAGTCACTTGCCTACATCTAGAGA
Found at i:18603377 original size:144 final size:144
Alignment explanation
Indices: 18603104--18603426 Score: 373
Period size: 144 Copynumber: 2.2 Consensus size: 144
18603094 AAACCTCGAG
* * * * *
18603104 ATCATAATTTAATATTATTTAATGATTTTTGGTGCATTCAAAACCTTAACTGTACCTCATAATGT
1 ATCATATTTTCATATTATTTAATGATTTTTGGTGCATTCAAAACCTTAACAGCACCTCAGAATGT
* * * * ** *
18603169 GTGAAATCACTAAAATACCCTTTAAAGGTATTTTTATAATTTGAGCTTCTTGAGGTTGATTTTTC
66 GTGAAATCACTAAAATACCCTTTAAAGGTAATTTCATAATTTAACCTTCTTGAGGTCAAATTTTC
18603234 ACAA-AATGT-TTCAA
131 ACAACAAT-TCTT-AA
* * * * * **
18603248 ATCATGTTTTTATATTATTTGATGATTTTTGGTTCATTGAAAACCTTGGCAGCACCTCAGAATGT
1 ATCATATTTTCATATTATTTAATGATTTTTGGTGCATTCAAAACCTTAACAGCACCTCAGAATGT
* * *
18603313 GTGAAATTACTAAAATACCTTTTAAAGGTAATTTCATAATTTAACCTT-TTCGATGTCAAATTTT
66 GTGAAATCACTAAAATACCCTTTAAAGGTAATTTCATAATTTAACCTTCTT-GAGGTCAAATTTT
*
18603377 CACAACAATTCTTAG
130 CACAACAATTCTTAA
* *
18603392 ATCTTATTTTCATATTATTTCATGATTTTTGGTGC
1 ATCATATTTTCATATTATTTAATGATTTTTGGTGC
18603427 TTTAAAATTA
Statistics
Matches: 149, Mismatches: 27, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
143 2 0.01
144 142 0.95
145 5 0.03
ACGTcount: A:0.31, C:0.14, G:0.12, T:0.43
Consensus pattern (144 bp):
ATCATATTTTCATATTATTTAATGATTTTTGGTGCATTCAAAACCTTAACAGCACCTCAGAATGT
GTGAAATCACTAAAATACCCTTTAAAGGTAATTTCATAATTTAACCTTCTTGAGGTCAAATTTTC
ACAACAATTCTTAA
Found at i:18605016 original size:9 final size:9
Alignment explanation
Indices: 18605002--18605053 Score: 58
Period size: 9 Copynumber: 6.1 Consensus size: 9
18604992 TCATACCTTG
18605002 TCATGCATA
1 TCATGCATA
18605011 TCATGCAT-
1 TCATGCATA
18605019 TCAT-CATA
1 TCATGCATA
*
18605027 T-AT-TATA
1 TCATGCATA
18605034 TTCATGCATA
1 -TCATGCATA
18605044 TCATGCATA
1 TCATGCATA
18605053 T
1 T
18605054 GTTTTTAAGT
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
7 8 0.22
8 6 0.16
9 20 0.54
10 3 0.08
ACGTcount: A:0.33, C:0.19, G:0.08, T:0.40
Consensus pattern (9 bp):
TCATGCATA
Found at i:18607248 original size:16 final size:16
Alignment explanation
Indices: 18607226--18607281 Score: 51
Period size: 16 Copynumber: 3.2 Consensus size: 16
18607216 CAGCTTTTTC
18607226 TTAAAAATATATTT-TTT
1 TTAAAAA-AT-TTTATTT
18607243 TTAAAAAATTTTATTT
1 TTAAAAAATTTTATTT
*
18607259 TTAAGGAAAATTGATATTT
1 TTAA--AAAATT-TTATTT
18607278 TTAA
1 TTAA
18607282 CTTTTCCTTA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
15 3 0.09
16 9 0.26
17 7 0.21
18 6 0.18
19 9 0.26
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (16 bp):
TTAAAAAATTTTATTT
Found at i:18607329 original size:122 final size:118
Alignment explanation
Indices: 18607139--18607386 Score: 345
Period size: 123 Copynumber: 2.1 Consensus size: 118
18607129 CTTTTATACA
* * *
18607139 AAGAAAATTGATATTTTCAAATTTTTCTTAAAAATGTTTTTTTTTTATTTTTTATTTTCAAGAAA
1 AAGAAAATTGATATTTTCAAATTTTCCTTAAAAATGATTTTTTTTTATATTTTATTTTCAAGAAA
* * *
18607204 AATTGATACTTTCAGCTTTTTCTTAAAAATATATTTTTTTTAAAAAATTTTATTTTT
66 AATTAATACTTTCAACTTTTCCTT-AAAA-ATATTTTTTTT-AAAAATTTTA-TTTT
* * *
18607261 AAGGAAAATTGATATTTTTAACTTTTCCTTAAAAATGATTTTTTTTTA-ATTTTATTTTCAAGAG
1 AA-GAAAATTGATATTTTCAAATTTTCCTTAAAAATGATTTTTTTTTATATTTTATTTTCAAGAA
* *
18607325 AAATTAATACTTTCAACTTTTCCTTTAAAATATTTTTTTTGAAAATTTTATTTT
65 AAATTAATACTTTCAACTTTTCCTTAAAAATATTTTTTTTAAAAATTTTATTTT
18607379 AAGAAAAT
1 AAGAAAAT
18607387 CGTTGAAAAA
Statistics
Matches: 114, Mismatches: 11, Indels: 7
0.86 0.08 0.05
Matches are distributed among these distances:
117 6 0.05
118 6 0.05
119 9 0.08
120 11 0.10
121 3 0.03
122 38 0.33
123 41 0.36
ACGTcount: A:0.35, C:0.06, G:0.06, T:0.52
Consensus pattern (118 bp):
AAGAAAATTGATATTTTCAAATTTTCCTTAAAAATGATTTTTTTTTATATTTTATTTTCAAGAAA
AATTAATACTTTCAACTTTTCCTTAAAAATATTTTTTTTAAAAATTTTATTTT
Found at i:18607343 original size:59 final size:57
Alignment explanation
Indices: 18607139--18607386 Score: 255
Period size: 59 Copynumber: 4.1 Consensus size: 57
18607129 CTTTTATACA
* * * * *
18607139 AAGAAAATTGATATTTTCAAATTTTTCTTAAAAATGTTTTTTTTTTATTTTTTATTTTC
1 AAGAAAATTGATACTTTCAACTTTTCCTTAAAAAT-ATTTTTTTTTA-ATTTTATTTTC
* * *
18607198 AAGAAAAATTGATACTTTCAGCTTTTTCTTAAAAATATATTTTTTTTAAAAAATTTTATTTTT
1 AAG-AAAATTGATACTTTCAACTTTTCCTTAAAAATAT-TTTTTTTT----AATTTTATTTTC
* *
18607261 AAGGAAAATTGATATTTTTAACTTTTCCTTAAAAATGATTTTTTTTTAATTTTATTTTC
1 AA-GAAAATTGATACTTTCAACTTTTCCTTAAAAAT-ATTTTTTTTTAATTTTATTTTC
* * *
18607320 AAGAGAAATTAATACTTTCAACTTTTCCTTTAAAATATTTTTTTTGAAAATTTTATTTT-
1 AAGA-AAATTGATACTTTCAACTTTTCCTTAAAAATATTTTTTTT--TAATTTTATTTTC
18607379 AAGAAAAT
1 AAGAAAAT
18607387 CGTTGAAAAA
Statistics
Matches: 162, Mismatches: 16, Indels: 23
0.81 0.08 0.11
Matches are distributed among these distances:
58 15 0.09
59 48 0.30
60 48 0.30
63 47 0.29
64 4 0.02
ACGTcount: A:0.35, C:0.06, G:0.06, T:0.52
Consensus pattern (57 bp):
AAGAAAATTGATACTTTCAACTTTTCCTTAAAAATATTTTTTTTTAATTTTATTTTC
Found at i:18607573 original size:22 final size:22
Alignment explanation
Indices: 18607508--18607564 Score: 105
Period size: 22 Copynumber: 2.6 Consensus size: 22
18607498 AAACCTTGAT
18607508 GTGGCTCAGCTTCGCTACTAAA
1 GTGGCTCAGCTTCGCTACTAAA
*
18607530 GCGGCTCAGCTTCGCTACTAAA
1 GTGGCTCAGCTTCGCTACTAAA
18607552 GTGGCTCAGCTTC
1 GTGGCTCAGCTTC
18607565 AGGCATAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.19, C:0.30, G:0.25, T:0.26
Consensus pattern (22 bp):
GTGGCTCAGCTTCGCTACTAAA
Found at i:18608737 original size:42 final size:40
Alignment explanation
Indices: 18608672--18608918 Score: 245
Period size: 42 Copynumber: 6.3 Consensus size: 40
18608662 AACAAAGCTT
* * *
18608672 TCTAAACAGAGGCTCAACGACTTTGAAAAAAATAAA-TGCTCC
1 TCTAAACAGAGGCACCACAACTTT---AAAAATAAATTGCTCC
*
18608714 TCTAAACAGAGGCACCACAACTTTGGAAAAATAAATTGCTCT
1 TCTAAACAGAGGCACCACAACTTT--AAAAATAAATTGCTCC
18608756 TCTAAACAGAGGCACCACAAC--T-----TAAATTGCTCC
1 TCTAAACAGAGGCACCACAACTTTAAAAATAAATTGCTCC
18608789 TCTAAACAGAGGCACCACAAC--T-----TAAATTGCTCC
1 TCTAAACAGAGGCACCACAACTTTAAAAATAAATTGCTCC
* *
18608822 TCTAAACAGATGCACCACAACTTTTCAAAATAAATTGCTCC
1 TCTAAACAGAGGCACCACAAC-TTTAAAAATAAATTGCTCC
* *
18608863 TCTAAACAGAGGCAACACAACTTTGAAAAAATAAATTGCTCT
1 TCTAAACAGAGGCACCACAACTTT--AAAAATAAATTGCTCC
18608905 TCTAAACAGAGGCA
1 TCTAAACAGAGGCA
18608919 ACACTTAGAG
Statistics
Matches: 182, Mismatches: 12, Indels: 22
0.84 0.06 0.10
Matches are distributed among these distances:
33 63 0.35
36 1 0.01
40 4 0.02
41 39 0.21
42 75 0.41
ACGTcount: A:0.40, C:0.24, G:0.13, T:0.23
Consensus pattern (40 bp):
TCTAAACAGAGGCACCACAACTTTAAAAATAAATTGCTCC
Found at i:18608787 original size:33 final size:33
Alignment explanation
Indices: 18608745--18608885 Score: 183
Period size: 33 Copynumber: 4.0 Consensus size: 33
18608735 TTTGGAAAAA
*
18608745 TAAATTGCTCTTCTAAACAGAGGCACCACAACT
1 TAAATTGCTCCTCTAAACAGAGGCACCACAACT
18608778 TAAATTGCTCCTCTAAACAGAGGCACCACAACT
1 TAAATTGCTCCTCTAAACAGAGGCACCACAACT
*
18608811 TAAATTGCTCCTCTAAACAGATGCACCACAACTTTT
1 TAAATTGCTCCTCTAAACAGAGGCACCACAAC---T
*
18608847 CAAAATAAATTGCTCCTCTAAACAGAGGCAACACAACT
1 -----TAAATTGCTCCTCTAAACAGAGGCACCACAACT
18608885 T
1 T
18608886 TGAAAAAATA
Statistics
Matches: 96, Mismatches: 4, Indels: 16
0.83 0.03 0.14
Matches are distributed among these distances:
33 64 0.67
36 1 0.01
38 1 0.01
41 30 0.31
ACGTcount: A:0.38, C:0.28, G:0.11, T:0.24
Consensus pattern (33 bp):
TAAATTGCTCCTCTAAACAGAGGCACCACAACT
Found at i:18608868 original size:41 final size:42
Alignment explanation
Indices: 18608811--18608922 Score: 172
Period size: 41 Copynumber: 2.7 Consensus size: 42
18608801 CACCACAACT
* * **
18608811 TAAATTGCTCCTCTAAACAGATGCACCACAACTTT-TCAAAA
1 TAAATTGCTCCTCTAAACAGAGGCAACACAACTTTGAAAAAA
18608852 TAAATTGCTCCTCTAAACAGAGGCAACACAACTTTGAAAAAA
1 TAAATTGCTCCTCTAAACAGAGGCAACACAACTTTGAAAAAA
*
18608894 TAAATTGCTCTTCTAAACAGAGGCAACAC
1 TAAATTGCTCCTCTAAACAGAGGCAACAC
18608923 TTAGAGGCAA
Statistics
Matches: 65, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
41 33 0.51
42 32 0.49
ACGTcount: A:0.41, C:0.24, G:0.11, T:0.24
Consensus pattern (42 bp):
TAAATTGCTCCTCTAAACAGAGGCAACACAACTTTGAAAAAA
Found at i:18608954 original size:55 final size:55
Alignment explanation
Indices: 18608870--18608977 Score: 173
Period size: 55 Copynumber: 2.0 Consensus size: 55
18608860 TCCTCTAAAC
* *
18608870 AGAGGCAACACAACTTTGAAAAAATAAATTGCTCTTCTAAACAGAGGCAACACTT
1 AGAGGCAACACAACTTTGAAAAAATAAATTACTCCTCTAAACAGAGGCAACACTT
*
18608925 AGAGGCAACCACAACTTTG-AAAAATAAATTATTCCTCTAAACAGAGGCAACAC
1 AGAGGCAA-CACAACTTTGAAAAAATAAATTACTCCTCTAAACAGAGGCAACAC
18608978 AACTTTAAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
55 39 0.80
56 10 0.20
ACGTcount: A:0.44, C:0.21, G:0.14, T:0.20
Consensus pattern (55 bp):
AGAGGCAACACAACTTTGAAAAAATAAATTACTCCTCTAAACAGAGGCAACACTT
Found at i:18609341 original size:21 final size:21
Alignment explanation
Indices: 18609315--18609354 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
18609305 AGTTTCACAT
18609315 CTCAAAG-TTTCTCATTTGAAA
1 CTCAAAGATTT-TCATTTGAAA
18609336 CTCAAAGATTTTCATTTGA
1 CTCAAAGATTTTCATTTGA
18609355 GTTCGAAGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.33, C:0.17, G:0.10, T:0.40
Consensus pattern (21 bp):
CTCAAAGATTTTCATTTGAAA
Found at i:18609501 original size:58 final size:58
Alignment explanation
Indices: 18609424--18609540 Score: 171
Period size: 58 Copynumber: 2.0 Consensus size: 58
18609414 GGTTGAAAAT
* * *
18609424 TCACATTCGATAAATTTTGGGTTTCACACCTCAAACATTCTCATTTGAAACCCAAAGA
1 TCACATTCGACAAACTTTGGATTTCACACCTCAAACATTCTCATTTGAAACCCAAAGA
* * **
18609482 TCACATTCGACAAACTTTGGATTTCACACCTCAAAGATTTTCATTTGAAATTCAAAGA
1 TCACATTCGACAAACTTTGGATTTCACACCTCAAACATTCTCATTTGAAACCCAAAGA
18609540 T
1 T
18609541 TCTCCTTTGA
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
58 52 1.00
ACGTcount: A:0.35, C:0.22, G:0.10, T:0.32
Consensus pattern (58 bp):
TCACATTCGACAAACTTTGGATTTCACACCTCAAACATTCTCATTTGAAACCCAAAGA
Found at i:18610698 original size:9 final size:8
Alignment explanation
Indices: 18610686--18610725 Score: 55
Period size: 9 Copynumber: 4.9 Consensus size: 8
18610676 TGAGTCTTCA
18610686 TTTTCTTT
1 TTTTCTTT
18610694 CTTTTCTTT
1 -TTTTCTTT
18610703 TTTT-TTT
1 TTTTCTTT
18610710 TTTTCATTT
1 TTTTC-TTT
18610719 TTTTCTT
1 TTTTCTT
18610726 CCTTCATTCG
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
7 7 0.24
8 6 0.21
9 16 0.55
ACGTcount: A:0.03, C:0.12, G:0.00, T:0.85
Consensus pattern (8 bp):
TTTTCTTT
Found at i:18611638 original size:19 final size:19
Alignment explanation
Indices: 18611614--18611663 Score: 57
Period size: 22 Copynumber: 2.5 Consensus size: 19
18611604 GATAACAAAT
18611614 GAAATCCTATTAC-CTAAAA
1 GAAATCCTATTACTCT-AAA
18611633 GAAATCCTAACATTACTCTAAA
1 GAAATCCT---ATTACTCTAAA
18611655 GAAATCCTA
1 GAAATCCTA
18611664 AAATGACAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
19 9 0.33
22 16 0.59
23 2 0.07
ACGTcount: A:0.46, C:0.22, G:0.06, T:0.26
Consensus pattern (19 bp):
GAAATCCTATTACTCTAAA
Found at i:18611655 original size:22 final size:22
Alignment explanation
Indices: 18611622--18611664 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
18611612 ATGAAATCCT
18611622 ATTACCTAAAAGAAATCCTAAC
1 ATTACCTAAAAGAAATCCTAAC
18611644 ATTACTCT-AAAGAAATCCTAA
1 ATTAC-CTAAAAGAAATCCTAA
18611665 AATGACAAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 18 0.90
23 2 0.10
ACGTcount: A:0.49, C:0.21, G:0.05, T:0.26
Consensus pattern (22 bp):
ATTACCTAAAAGAAATCCTAAC
Found at i:18614693 original size:23 final size:23
Alignment explanation
Indices: 18614667--18614710 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
18614657 TTTTTTTTTT
*
18614667 TATAAAAAAAACTGATGCTTTAA
1 TATAAAAAAAACTGATACTTTAA
* *
18614690 TATAAAGAAAATTGATACTTT
1 TATAAAAAAAACTGATACTTT
18614711 CAACTTTTCT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.50, C:0.07, G:0.09, T:0.34
Consensus pattern (23 bp):
TATAAAAAAAACTGATACTTTAA
Found at i:18615800 original size:3 final size:3
Alignment explanation
Indices: 18615792--18615817 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
18615782 GAATGTCTAC
18615792 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
18615818 ATAAATAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:18616379 original size:41 final size:43
Alignment explanation
Indices: 18616334--18616538 Score: 145
Period size: 43 Copynumber: 4.9 Consensus size: 43
18616324 TTGACTCTGT
* *
18616334 GCAGAAAATGCTTGACTCCCTAA-GG-AGATGTTTGACTATTA
1 GCAGAAAATGCTTGACTCCCCAATGGAAGATGCTTGACTATTA
* **
18616375 GCAGAAAATGGTTGACTCCCCAATGGAAGATGCTTGACTCGTA
1 GCAGAAAATGCTTGACTCCCCAATGGAAGATGCTTGACTATTA
* * ** * * *
18616418 G-ATGAGAAATGTTTAACTCCTTATTGGAAGATGCTTGACTCTCA
1 GCA-GA-AAATGCTTGACTCCCCAATGGAAGATGCTTGACTATTA
* * * *
18616462 GCAGAAAATGCATG--T--CCAATGGAGGATGCATGACTATCA
1 GCAGAAAATGCTTGACTCCCCAATGGAAGATGCTTGACTATTA
* * * * * *
18616501 GAAGAAAATGTTTGACACTCCAGTGGAGGATGCTTGAC
1 GCAGAAAATGCTTGACTCCCCAATGGAAGATGCTTGAC
18616539 ACTCCAATAG
Statistics
Matches: 128, Mismatches: 27, Indels: 16
0.75 0.16 0.09
Matches are distributed among these distances:
39 29 0.23
41 22 0.17
42 3 0.02
43 39 0.30
44 34 0.27
45 1 0.01
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.26
Consensus pattern (43 bp):
GCAGAAAATGCTTGACTCCCCAATGGAAGATGCTTGACTATTA
Found at i:18616559 original size:22 final size:21
Alignment explanation
Indices: 18616506--18616560 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 21
18616496 TATCAGAAGA
* *
18616506 AAATGTTTGACACTCCAGTGG
1 AAATGTTTGACACTCCAATGC
* *
18616527 AGGATGCTTGACACTCCAATAGC
1 A-AATGTTTGACACTCCAAT-GC
18616550 AAATGTTTGAC
1 AAATGTTTGAC
18616561 TGCTCGGTGG
Statistics
Matches: 26, Mismatches: 6, Indels: 3
0.74 0.17 0.09
Matches are distributed among these distances:
21 1 0.04
22 23 0.88
23 2 0.08
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.27
Consensus pattern (21 bp):
AAATGTTTGACACTCCAATGC
Found at i:18619267 original size:8 final size:8
Alignment explanation
Indices: 18619254--18619306 Score: 56
Period size: 8 Copynumber: 6.9 Consensus size: 8
18619244 TTTGACCCTA
18619254 ACATATAT
1 ACATATAT
18619262 ACATATAT
1 ACATATAT
18619270 --ATATAT
1 ACATATAT
*
18619276 ATATATAT
1 ACATATAT
18619284 ACATATAT
1 ACATATAT
* *
18619292 ATAGATAT
1 ACATATAT
*
18619300 AGATATA
1 ACATATA
18619307 GATATGGAGT
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
6 6 0.16
8 32 0.84
ACGTcount: A:0.51, C:0.06, G:0.04, T:0.40
Consensus pattern (8 bp):
ACATATAT
Found at i:18619271 original size:10 final size:10
Alignment explanation
Indices: 18619254--18619300 Score: 58
Period size: 10 Copynumber: 4.7 Consensus size: 10
18619244 TTTGACCCTA
*
18619254 ACATATATAC
1 ACATATATAT
*
18619264 ATATATATAT
1 ACATATATAT
*
18619274 ATATATATAT
1 ACATATATAT
18619284 ACATATATAT
1 ACATATATAT
*
18619294 AGATATA
1 ACATATA
18619301 GATATAGATA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
10 33 1.00
ACGTcount: A:0.51, C:0.06, G:0.02, T:0.40
Consensus pattern (10 bp):
ACATATATAT
Found at i:18619273 original size:6 final size:6
Alignment explanation
Indices: 18619256--18619311 Score: 67
Period size: 6 Copynumber: 9.3 Consensus size: 6
18619246 TGACCCTAAC
* * * *
18619256 ATATAT ACATAT ATATAT ATATAT ATATAC ATATAT ATAGAT ATAGAT
1 ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT
*
18619304 ATAGAT AT
1 ATATAT AT
18619312 GGAGTACTAG
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 45 1.00
ACGTcount: A:0.50, C:0.04, G:0.05, T:0.41
Consensus pattern (6 bp):
ATATAT
Found at i:18619885 original size:49 final size:50
Alignment explanation
Indices: 18619826--18619927 Score: 145
Period size: 49 Copynumber: 2.1 Consensus size: 50
18619816 CTACATATCC
* *
18619826 AAATTATGATTTACCTTTTTCAT-TTTTTGATAAGATTACATTTA-AATGA
1 AAATTATGATTTA-CTTTTTCATCTTTTTGATAAAATTAAATTTATAATGA
**
18619875 AAATTATGATTTACTTTTTTTTCTTTTTGATAAAATTAAATTTATAATGA
1 AAATTATGATTTACTTTTTCATCTTTTTGATAAAATTAAATTTATAATGA
18619925 AAA
1 AAA
18619928 ATAATAGTTA
Statistics
Matches: 47, Mismatches: 4, Indels: 3
0.87 0.07 0.06
Matches are distributed among these distances:
48 7 0.15
49 32 0.68
50 8 0.17
ACGTcount: A:0.37, C:0.06, G:0.07, T:0.50
Consensus pattern (50 bp):
AAATTATGATTTACTTTTTCATCTTTTTGATAAAATTAAATTTATAATGA
Found at i:18620325 original size:27 final size:27
Alignment explanation
Indices: 18620295--18620346 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
18620285 AAAGATTACG
*
18620295 ATAAGATAAAATTAAATAATATTATAA
1 ATAAAATAAAATTAAATAATATTATAA
18620322 ATAAAATAAAATTAAATAATATTAT
1 ATAAAATAAAATTAAATAATATTAT
18620347 TTTATTTATA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (27 bp):
ATAAAATAAAATTAAATAATATTATAA
Found at i:18622291 original size:13 final size:14
Alignment explanation
Indices: 18622258--18622289 Score: 50
Period size: 12 Copynumber: 2.4 Consensus size: 14
18622248 ACTTTTTTAT
18622258 TAAAAATGATCTAA
1 TAAAAATGATCTAA
18622272 TAAAAAT-AT-TAA
1 TAAAAATGATCTAA
18622284 TAAAAA
1 TAAAAA
18622290 ATTCAAATTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 9 0.50
13 2 0.11
14 7 0.39
ACGTcount: A:0.66, C:0.03, G:0.03, T:0.28
Consensus pattern (14 bp):
TAAAAATGATCTAA
Found at i:18622750 original size:30 final size:30
Alignment explanation
Indices: 18622692--18622752 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
18622682 ATCCTTAAAT
* *
18622692 TTTAATTTATATTTAAATAAGCCCTTAACA
1 TTTAATTTATATCTAAATAAGCCATTAACA
* * *
18622722 TTTAATTTGTATCTAATTAAGTCATTAACA
1 TTTAATTTATATCTAAATAAGCCATTAACA
18622752 T
1 T
18622753 AAATCAATTT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.38, C:0.11, G:0.05, T:0.46
Consensus pattern (30 bp):
TTTAATTTATATCTAAATAAGCCATTAACA
Found at i:18622805 original size:30 final size:28
Alignment explanation
Indices: 18622770--18622860 Score: 96
Period size: 29 Copynumber: 3.1 Consensus size: 28
18622760 TTTTTATTTG
*
18622770 AAATAACAATTTACTTAAATACAAATCAAA
1 AAATAA-AATTTATTTAAATACAAAT-AAA
* *
18622800 GAATAAAAGTTTATTTAAATGC-AATAAA
1 AAATAAAA-TTTATTTAAATACAAATAAA
18622828 AATATAAAAATTTATTTAAATA-AAATAAA
1 AA-AT-AAAATTTATTTAAATACAAATAAA
18622857 AAAT
1 AAAT
18622861 TCAAAAACTT
Statistics
Matches: 52, Mismatches: 5, Indels: 10
0.78 0.07 0.15
Matches are distributed among these distances:
28 6 0.12
29 26 0.50
30 20 0.38
ACGTcount: A:0.60, C:0.05, G:0.03, T:0.31
Consensus pattern (28 bp):
AAATAAAATTTATTTAAATACAAATAAA
Found at i:18622867 original size:30 final size:29
Alignment explanation
Indices: 18622777--18622874 Score: 92
Period size: 29 Copynumber: 3.3 Consensus size: 29
18622767 TTGAAATAAC
* *
18622777 AATTTACTTAAATACAAATCAAAGAA-TAAA
1 AATTTATTTAAATA-AAAT-AAAAAATTAAA
* **
18622807 AGTTTATTTAAATGCAAT-AAAAATATAAA
1 AATTTATTTAAATAAAATAAAAAAT-TAAA
18622836 AATTTATTTAAATAAAATAAAAAATTCAAA
1 AATTTATTTAAATAAAATAAAAAATT-AAA
18622866 AACTTTATT
1 AA-TTTATT
18622875 AATATTTTAA
Statistics
Matches: 55, Mismatches: 8, Indels: 9
0.76 0.11 0.12
Matches are distributed among these distances:
27 4 0.07
29 23 0.42
30 22 0.40
31 6 0.11
ACGTcount: A:0.57, C:0.06, G:0.03, T:0.34
Consensus pattern (29 bp):
AATTTATTTAAATAAAATAAAAAATTAAA
Found at i:18623693 original size:2 final size:2
Alignment explanation
Indices: 18623686--18623725 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
18623676 GAACATGGAA
18623686 AG AG AG AG AG 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 AG AG AG AG AG
18623726 CACAACTTTG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:18627339 original size:24 final size:24
Alignment explanation
Indices: 18627307--18627352 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
18627297 TATACCAATA
*
18627307 TGCTTATGTATTTGTATGTTACTG
1 TGCTTATGTATTTATATGTTACTG
18627331 TGCTTATGTATTTATATGTTAC
1 TGCTTATGTATTTATATGTTAC
18627353 CCTTACTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.20, C:0.09, G:0.17, T:0.54
Consensus pattern (24 bp):
TGCTTATGTATTTATATGTTACTG
Found at i:18631994 original size:20 final size:20
Alignment explanation
Indices: 18631969--18632010 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
18631959 TTGTAATAGG
18631969 TTGGTGTCCTTGTTTCTCAA
1 TTGGTGTCCTTGTTTCTCAA
*
18631989 TTGGTGTCCTTGTTTTTCAA
1 TTGGTGTCCTTGTTTCTCAA
18632009 TT
1 TT
18632011 TTTCCTACTC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.10, C:0.17, G:0.19, T:0.55
Consensus pattern (20 bp):
TTGGTGTCCTTGTTTCTCAA
Found at i:18635482 original size:157 final size:155
Alignment explanation
Indices: 18635264--18635577 Score: 533
Period size: 158 Copynumber: 2.0 Consensus size: 155
18635254 TTAGGAAATG
*
18635264 TACACTAAGATTTCGATTTGCAAGTTCTTTTTTTCAAGTTGATGGAATTGTCTTCAACATG-TGT
1 TACACTAAGATTTCGATTTGCAAGTTCTTTTTTTCAAGTTGATGAAATTGTCTTCAACATGTTGT
*
18635328 TTTTTTGGTTTTCTCTATGCTGACCAAAATACCAATTACATCTATGTTTTTCTAAAAAAAAAAAA
66 TTTTTTGGTTTTCTCTATGCTCACCAAAATACCAATTACATCTATGTTTTTC---AAAAAAAAAA
18635393 GTCCTATTTTATGCAATAATTTTCAATA
128 GTCCTATTTTATGCAATAATTTTCAATA
*
18635421 TACACTAAGATTTTCGATTTGCAAGTTCTTTTTTTCAAG-TGATGAAATTGTCTTCAACATGTTT
1 TACACTAAGA-TTTCGATTTGCAAGTTCTTTTTTTCAAGTTGATGAAATTGTCTTCAACATGTTG
*
18635485 TTTTTTTGGTTTTCTCTATGCTCACCAAAATACCAATTACATCTATGTTTTTCCAAAAAAAAAGT
65 TTTTTTTGGTTTTCTCTATGCTCACCAAAATACCAATTACATCTATGTTTTTCAAAAAAAAAAGT
*
18635550 CCTATTTTATGCAATAATTTTTAATA
130 CCTATTTTATGCAATAATTTTCAATA
18635576 TA
1 TA
18635578 ATAGCAATGA
Statistics
Matches: 150, Mismatches: 5, Indels: 6
0.93 0.03 0.04
Matches are distributed among these distances:
155 38 0.25
157 31 0.21
158 81 0.54
ACGTcount: A:0.31, C:0.15, G:0.11, T:0.44
Consensus pattern (155 bp):
TACACTAAGATTTCGATTTGCAAGTTCTTTTTTTCAAGTTGATGAAATTGTCTTCAACATGTTGT
TTTTTTGGTTTTCTCTATGCTCACCAAAATACCAATTACATCTATGTTTTTCAAAAAAAAAAGTC
CTATTTTATGCAATAATTTTCAATA
Found at i:18637776 original size:22 final size:22
Alignment explanation
Indices: 18637751--18637800 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
18637741 ACCACTAAAC
*
18637751 ATAGTATTTTTATGTAACTTGA
1 ATAGTATTTTTAGGTAACTTGA
*
18637773 ATAGTATTTTTGGGTAACTTGA
1 ATAGTATTTTTAGGTAACTTGA
18637795 AT-GTAT
1 ATAGTAT
18637801 GTCTCTTAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
21 4 0.15
22 22 0.85
ACGTcount: A:0.30, C:0.04, G:0.18, T:0.48
Consensus pattern (22 bp):
ATAGTATTTTTAGGTAACTTGA
Found at i:18645194 original size:17 final size:17
Alignment explanation
Indices: 18645172--18645205 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
18645162 AGAGAAGAGA
18645172 TGTGTAGAATGGGATGT
1 TGTGTAGAATGGGATGT
18645189 TGTGTAGAATGGGATGT
1 TGTGTAGAATGGGATGT
18645206 GTTGAGGTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.41, T:0.35
Consensus pattern (17 bp):
TGTGTAGAATGGGATGT
Found at i:18657318 original size:21 final size:22
Alignment explanation
Indices: 18657292--18657343 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
18657282 AGTCTGAAAC
* **
18657292 TTAATTTTAGCTT-TTTTTTTT
1 TTAATTTTACCTTATTTTTAAT
*
18657313 TTAATTTTTCCTTATTTTTAAT
1 TTAATTTTACCTTATTTTTAAT
18657335 TTAATTTTA
1 TTAATTTTA
18657344 ATATATGGTA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
21 11 0.44
22 14 0.56
ACGTcount: A:0.21, C:0.06, G:0.02, T:0.71
Consensus pattern (22 bp):
TTAATTTTACCTTATTTTTAAT
Found at i:18657741 original size:135 final size:135
Alignment explanation
Indices: 18657511--18657759 Score: 372
Period size: 135 Copynumber: 1.8 Consensus size: 135
18657501 AGGTGTTTTA
* * * * * **
18657511 TTTTTACAAATGTCTTATTTGATAAACGATCTTCCAGAATTTTTAGAAAAGCTAATAAGGTGTTT
1 TTTTTACAAATGCCTTATTTGATAAACGATCTTCCAAAATCTTTACAAAAGCAAATAAGGCATTT
18657576 CTTTGAACAAATACCTTATTTGATGTTTTTTCCAACATATTTACAAAGCCCATTCAAATAACGCA
66 CTTTGAACAAATACCTTATTTGATGTTTTTTCCAACATATTTACAAAGCCCATTCAAATAACGCA
18657641 TTTCC
131 TTTCC
* * * **
18657646 TTTTTACAAATGCCTTATTTGATAGACGCTCTTTCAAAATCTTTACAAATTCAAATAAGGCATTT
1 TTTTTACAAATGCCTTATTTGATAAACGATCTTCCAAAATCTTTACAAAAGCAAATAAGGCATTT
*
18657711 CCTTTGAACAAATGCCTTATTTGATGTTTTTTCCAACATATTTACAAAG
66 -CTTTGAACAAATACCTTATTTGATGTTTTTTCCAACATATTTACAAAG
18657760 GCAAATAAGG
Statistics
Matches: 100, Mismatches: 13, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
135 53 0.53
136 47 0.47
ACGTcount: A:0.33, C:0.17, G:0.10, T:0.40
Consensus pattern (135 bp):
TTTTTACAAATGCCTTATTTGATAAACGATCTTCCAAAATCTTTACAAAAGCAAATAAGGCATTT
CTTTGAACAAATACCTTATTTGATGTTTTTTCCAACATATTTACAAAGCCCATTCAAATAACGCA
TTTCC
Found at i:18657896 original size:19 final size:18
Alignment explanation
Indices: 18657858--18657892 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
18657848 CATAATTGGG
18657858 TATATTTAATTAAAAAAT
1 TATATTTAATTAAAAAAT
18657876 TATATTTAATTAAAAAA
1 TATATTTAATTAAAAAA
18657893 ATTAAAATCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
TATATTTAATTAAAAAAT
Found at i:18659763 original size:3 final size:3
Alignment explanation
Indices: 18659757--18659823 Score: 134
Period size: 3 Copynumber: 22.3 Consensus size: 3
18659747 TTGTTGTGAA
18659757 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
18659805 ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT A
18659824 CATTCTATAA
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 64 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:18660166 original size:18 final size:19
Alignment explanation
Indices: 18660143--18660187 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
18660133 TTGTTTTGTT
18660143 TTTATTTATTAT-ATATTA
1 TTTATTTATTATGATATTA
* *
18660161 TTTA-TTATTTTGTTATTA
1 TTTATTTATTATGATATTA
18660179 TTT-TTTATT
1 TTTATTTATT
18660188 TGAATAAATC
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
17 6 0.26
18 17 0.74
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.73
Consensus pattern (19 bp):
TTTATTTATTATGATATTA
Found at i:18660623 original size:14 final size:14
Alignment explanation
Indices: 18660606--18660663 Score: 61
Period size: 14 Copynumber: 4.4 Consensus size: 14
18660596 ATTCTAACAA
18660606 AAAATAATGAAAAT
1 AAAATAATGAAAAT
*
18660620 AAAATAA-AATAAAT
1 AAAATAATGA-AAAT
*
18660634 AAAAT--TGAAATT
1 AAAATAATGAAAAT
18660646 AAAA-AATGAAAAT
1 AAAATAATGAAAAT
18660659 AAAAT
1 AAAAT
18660664 GGAAAAAGAA
Statistics
Matches: 35, Mismatches: 4, Indels: 10
0.71 0.08 0.20
Matches are distributed among these distances:
12 7 0.20
13 12 0.34
14 16 0.46
ACGTcount: A:0.72, C:0.00, G:0.05, T:0.22
Consensus pattern (14 bp):
AAAATAATGAAAAT
Found at i:18660644 original size:20 final size:20
Alignment explanation
Indices: 18660605--18660658 Score: 58
Period size: 20 Copynumber: 2.7 Consensus size: 20
18660595 AATTCTAACA
*
18660605 AAAAATAATGAAAA-TAAAAT
1 AAAAA-AATGAAAATTGAAAT
18660625 AAAATAAAT-AAAATTGAAAT
1 AAAA-AAATGAAAATTGAAAT
*
18660645 TAAAAAATGAAAAT
1 AAAAAAATGAAAAT
18660659 AAAATGGAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
19 8 0.28
20 20 0.69
21 1 0.03
ACGTcount: A:0.72, C:0.00, G:0.06, T:0.22
Consensus pattern (20 bp):
AAAAAAATGAAAATTGAAAT
Found at i:18661539 original size:3 final size:3
Alignment explanation
Indices: 18661533--18661572 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
18661523 AGATAAAAGA
*
18661533 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAC AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
18661573 GTAACAATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:18661577 original size:9 final size:9
Alignment explanation
Indices: 18661533--18661580 Score: 60
Period size: 9 Copynumber: 5.3 Consensus size: 9
18661523 AGATAAAAGA
*
18661533 AATAATAAT
1 AATAATAAC
*
18661542 AATAATAAT
1 AATAATAAC
*
18661551 AATAATAAT
1 AATAATAAC
18661560 AATAATAAC
1 AATAATAAC
*
18661569 AATAGTAAC
1 AATAATAAC
18661578 AAT
1 AAT
18661581 TTAAAATAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 37 1.00
ACGTcount: A:0.65, C:0.04, G:0.02, T:0.29
Consensus pattern (9 bp):
AATAATAAC
Found at i:18666840 original size:142 final size:145
Alignment explanation
Indices: 18666670--18666969 Score: 351
Period size: 144 Copynumber: 2.1 Consensus size: 145
18666660 ACATTAATTG
* * *
18666670 ATGATTTTCTA-TGCATTGAAAACCTTGATCACT-CCTCGAGAAGTATG-AATTACTAAAATACC
1 ATGATTTT-TAGTGCATTGAAAACCTTGAT-ACTACCTCAAAAAGTATGAAAGTACTAAAATACC
** * * *
18666732 CTTATGA-GCATTTTTGTAATTTGAACTTTTCAAGGTCAATTTTTTACAAAAACTTGCAAATAAT
64 CTTAAAAGGCATTCTTGTAATTTGAACTTTCCAAGGTCAATTTCTTACAAAAACTTGCAAATAAT
**
18666796 GTTTTTATAATA-TTTA
129 AATTTTATAATATTTTA
* ** *
18666812 ATGATTTTTAGTGTATTGAAAACCTTGATTGTACCTCAAAAAGTGTGAAAGTACTAAAATACCCT
1 ATGATTTTTAGTGCATTGAAAACCTTGATACTACCTCAAAAAGTATGAAAGTACTAAAATACCCT
* * * * *
18666877 TAAAAGGTATTCTTGTAATTTGACCTTTCCAAGGTCAATTTCTTACAAAAATTTTCATATAATAA
66 TAAAAGGCATTCTTGTAATTTGAACTTTCCAAGGTCAATTTCTTACAAAAACTTGCAAATAATAA
* *
18666942 TTTTATATTATTTTG
131 TTTTATAATATTTTA
18666957 A-GATTTTTAGTGC
1 ATGATTTTTAGTGC
18666970 TTTAAAATTG
Statistics
Matches: 131, Mismatches: 22, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
141 3 0.02
142 36 0.27
143 19 0.15
144 69 0.53
145 4 0.03
ACGTcount: A:0.34, C:0.13, G:0.12, T:0.41
Consensus pattern (145 bp):
ATGATTTTTAGTGCATTGAAAACCTTGATACTACCTCAAAAAGTATGAAAGTACTAAAATACCCT
TAAAAGGCATTCTTGTAATTTGAACTTTCCAAGGTCAATTTCTTACAAAAACTTGCAAATAATAA
TTTTATAATATTTTA
Found at i:18671908 original size:2 final size:2
Alignment explanation
Indices: 18671901--18671932 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
18671891 CCCGTTGGGA
18671901 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
18671933 TTCGAATCAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:18673145 original size:20 final size:19
Alignment explanation
Indices: 18673122--18673159 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
18673112 CAAATGTATT
*
18673122 ATTTAATTATATATTATTTA
1 ATTTAATTAAATA-TATTTA
18673142 ATTTAATTAAATATATTT
1 ATTTAATTAAATATATTT
18673160 TTTCTTTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
ATTTAATTAAATATATTTA
Found at i:18673484 original size:11 final size:11
Alignment explanation
Indices: 18673450--18673488 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
18673440 ATTTGTGGAT
18673450 TTTTAATT-TA
1 TTTTAATTATA
18673460 CTTTTAATTGATA
1 -TTTTAATT-ATA
18673473 TTTTAATTATA
1 TTTTAATTATA
18673484 TTTTA
1 TTTTA
18673489 TTTTTATGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
11 16 0.62
12 8 0.31
13 2 0.08
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.64
Consensus pattern (11 bp):
TTTTAATTATA
Found at i:18673791 original size:18 final size:17
Alignment explanation
Indices: 18673768--18673819 Score: 59
Period size: 18 Copynumber: 2.9 Consensus size: 17
18673758 AATCAGCTTT
18673768 AAAAAAATATTTTTTGCA
1 AAAAAAATATTTTTTG-A
*
18673786 AAAAAATTATATTTTTGA
1 AAAAAAATAT-TTTTTGA
*
18673804 AAAATAAAAATTTTTT
1 AAAA-AAATATTTTTT
18673820 TGTTGTTTGA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
18 19 0.66
19 10 0.34
ACGTcount: A:0.52, C:0.02, G:0.04, T:0.42
Consensus pattern (17 bp):
AAAAAAATATTTTTTGA
Found at i:18673819 original size:19 final size:19
Alignment explanation
Indices: 18673768--18673821 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 19
18673758 AATCAGCTTT
18673768 AAAAAAATATTTTTTGCAAA
1 AAAAAAAT-TTTTTTGCAAA
** *
18673788 AAAATTATATTTTTG-AAA
1 AAAAAAATTTTTTTGCAAA
18673806 AATAAAAATTTTTTTG
1 AA-AAAAATTTTTTTG
18673822 TTGTTTGATT
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
18 5 0.19
19 16 0.59
20 6 0.22
ACGTcount: A:0.50, C:0.02, G:0.06, T:0.43
Consensus pattern (19 bp):
AAAAAAATTTTTTTGCAAA
Found at i:18673913 original size:25 final size:25
Alignment explanation
Indices: 18673871--18673930 Score: 86
Period size: 25 Copynumber: 2.4 Consensus size: 25
18673861 ATTGATAAAG
*
18673871 TTATTAAAATATTAAAAATTATTTA
1 TTATTAAAATATTAAAAATTACTTA
*
18673896 TTATTAATTATATT-AAAATTACTTA
1 TTATTAA-AATATTAAAAATTACTTA
18673921 TTATTAAAAT
1 TTATTAAAAT
18673931 TATCAATATT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
24 2 0.06
25 24 0.77
26 5 0.16
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (25 bp):
TTATTAAAATATTAAAAATTACTTA
Found at i:18673921 original size:15 final size:16
Alignment explanation
Indices: 18673898--18673956 Score: 68
Period size: 15 Copynumber: 3.8 Consensus size: 16
18673888 ATTATTTATT
18673898 ATTAATTA-TATTAAA
1 ATTAATTATTATTAAA
*
18673913 ATTACTTATTATTAAA
1 ATTAATTATTATTAAA
* *
18673929 ATT-ATCAATATTAAA
1 ATTAATTATTATTAAA
*
18673944 AATAATTATTATT
1 ATTAATTATTATT
18673957 TGAATAATAA
Statistics
Matches: 35, Mismatches: 7, Indels: 3
0.78 0.16 0.07
Matches are distributed among these distances:
15 18 0.51
16 17 0.49
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.47
Consensus pattern (16 bp):
ATTAATTATTATTAAA
Found at i:18673925 original size:16 final size:15
Alignment explanation
Indices: 18673902--18673956 Score: 58
Period size: 16 Copynumber: 3.6 Consensus size: 15
18673892 TTTATTATTA
18673902 ATTA-TATTAAAATT
1 ATTATTATTAAAATT
18673916 ACTTATTATTAAAATT
1 A-TTATTATTAAAATT
* * *
18673932 ATCAATATTAAAAATA
1 ATTATTATT-AAAATT
18673948 ATTATTATT
1 ATTATTATT
18673957 TGAATAATAA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
14 1 0.03
15 9 0.27
16 23 0.70
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (15 bp):
ATTATTATTAAAATT
Found at i:18673973 original size:31 final size:31
Alignment explanation
Indices: 18673905--18673973 Score: 77
Period size: 31 Copynumber: 2.2 Consensus size: 31
18673895 ATTATTAATT
* * *
18673905 ATATTAAAATTACTTATTATTAAAATTATCA
1 ATATTAAAAATAATTATTATTAAAATAATCA
**
18673936 ATATTAAAAATAATTATTATTTGAATAAT-A
1 ATATTAAAAATAATTATTATTAAAATAATCA
18673966 ATAATTAA
1 AT-ATTAA
18673974 TATTAAAATA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
30 3 0.09
31 29 0.91
ACGTcount: A:0.52, C:0.03, G:0.01, T:0.43
Consensus pattern (31 bp):
ATATTAAAAATAATTATTATTAAAATAATCA
Found at i:18673983 original size:21 final size:20
Alignment explanation
Indices: 18673944--18673999 Score: 69
Period size: 21 Copynumber: 2.8 Consensus size: 20
18673934 CAATATTAAA
* **
18673944 AATAATTATTATTTGAATAAT
1 AATAATTAATATTAAAAT-AT
18673965 AATAATTAATATTAAAATAT
1 AATAATTAATATTAAAATAT
18673985 AAT-ATTAATATTAAA
1 AATAATTAATATTAAA
18674000 CCCTTAAAAC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
19 12 0.38
20 5 0.16
21 15 0.47
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (20 bp):
AATAATTAATATTAAAATAT
Found at i:18674889 original size:7 final size:7
Alignment explanation
Indices: 18674838--18674888 Score: 63
Period size: 7 Copynumber: 7.6 Consensus size: 7
18674828 TGATTCCCAG
18674838 TTTTAAT
1 TTTTAAT
18674845 TTTTAAT
1 TTTTAAT
18674852 TTTTAAT
1 TTTTAAT
18674859 TTTTAA-
1 TTTTAAT
18674865 TTTT-A-
1 TTTTAAT
18674870 TTTTAAGT
1 TTTTAA-T
*
18674878 TTTTTAT
1 TTTTAAT
18674885 TTTT
1 TTTT
18674889 TTCAAAAATA
Statistics
Matches: 40, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
5 5 0.12
6 5 0.12
7 25 0.62
8 5 0.12
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.75
Consensus pattern (7 bp):
TTTTAAT
Found at i:18675633 original size:6 final size:7
Alignment explanation
Indices: 18675612--18675636 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
18675602 ACTATCCCAT
18675612 AAATAAA
1 AAATAAA
18675619 AAATAAA
1 AAATAAA
18675626 AAATAAA
1 AAATAAA
18675633 AAAT
1 AAAT
18675637 TTGGCATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (7 bp):
AAATAAA
Found at i:18676913 original size:29 final size:29
Alignment explanation
Indices: 18676856--18676913 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
18676846 ATTGAGTAAA
* * *
18676856 AATAAAATATTACAAACTTGATTGGTTAT
1 AATAAAATATTACAAACTTAAATGATTAT
18676885 AATAAAATATTA-AGAACTTAAATGATTAT
1 AATAAAATATTACA-AACTTAAATGATTAT
18676914 TAAATTATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 1 0.04
29 24 0.96
ACGTcount: A:0.50, C:0.05, G:0.09, T:0.36
Consensus pattern (29 bp):
AATAAAATATTACAAACTTAAATGATTAT
Found at i:18680936 original size:30 final size:30
Alignment explanation
Indices: 18680879--18680936 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
18680869 AGCATGCCTG
* *
18680879 TTTTGATAGGGGCTCTGTGGAGCATTCACA
1 TTTTGATAGGGGCTATATGGAGCATTCACA
* * *
18680909 TTTTGGTAGGGGCTATATTGAGTATTCA
1 TTTTGATAGGGGCTATATGGAGCATTCA
18680937 TGTTCTGATA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.21, C:0.12, G:0.29, T:0.38
Consensus pattern (30 bp):
TTTTGATAGGGGCTATATGGAGCATTCACA
Found at i:18690094 original size:20 final size:21
Alignment explanation
Indices: 18690071--18690111 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
18690061 ATAATAATTT
18690071 TATATCAAAATTTAT-TTAAA
1 TATATCAAAATTTATATTAAA
*
18690091 TATATTAAAATTTATATTAAA
1 TATATCAAAATTTATATTAAA
18690112 ATAATATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46
Consensus pattern (21 bp):
TATATCAAAATTTATATTAAA
Found at i:18690108 original size:12 final size:12
Alignment explanation
Indices: 18690069--18690127 Score: 54
Period size: 12 Copynumber: 5.2 Consensus size: 12
18690059 AAATAATAAT
*
18690069 TTTATATCAAAA
1 TTTATATTAAAA
18690081 TTTAT-TT-AAA
1 TTTATATTAAAA
18690091 --TATATTAAAA
1 TTTATATTAAAA
18690101 TTTATATTAAAA
1 TTTATATTAAAA
* *
18690113 TAATATATAAAAA
1 T-TTATATTAAAA
18690126 TT
1 TT
18690128 AAAAATTAAG
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
8 3 0.08
9 2 0.05
10 6 0.16
11 1 0.03
12 16 0.42
13 10 0.26
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.46
Consensus pattern (12 bp):
TTTATATTAAAA
Found at i:18701553 original size:66 final size:63
Alignment explanation
Indices: 18701383--18701704 Score: 229
Period size: 62 Copynumber: 5.2 Consensus size: 63
18701373 TTAAACGCTT
* * * * * * * *
18701383 GATCATTTAAGGCATTTATGTAATCGAACTTCC-TAAATGATCTT-ATTATAAAATTGA-AAAGA
1 GATCAATTAAGGCATTTATGTAACCAAAC-GCCTTAATTGATCTTCTTTATAAATTTTAGAAA-A
* * * * * *
18701445 GATCAATTAAGGCGTTT-GGTTACATAAACGCCTTAATTGATCTTTTTTATAAATTTTATATGAA
1 GATCAATTAAGGCATTTATGTAAC-CAAACGCCTTAATTGATCTTCTTTATAAATTTTAGA--AA
18701509 A
63 A
** * * *
18701510 GATCAATTAAGGTGTTTCATGTAAGCAAACACCTTAATTGATC-TCTTTATAAATTTTGGAAAA
1 GATCAATTAAGGCATTT-ATGTAACCAAACGCCTTAATTGATCTTCTTTATAAATTTTAGAAAA
* *
18701573 GGTCAATTAAGGCATTTATGTAACCAAATGCCTTAATTGATC-TC--TATAAA-TTT-GCAAAA
1 GATCAATTAAGGCATTTATGTAACCAAACGCCTTAATTGATCTTCTTTATAAATTTTAG-AAAA
* * * * *
18701632 GATCAATTAAGGCATTT-GGTTACACAAATGCCTTAATTGATCTTGTTT-TTAATTTATA-AAAA
1 GATCAATTAAGGCATTTATGTAAC-CAAACGCCTTAATTGATCTTCTTTATAAATTT-TAGAAAA
18701694 GAATCAATTAA
1 G-ATCAATTAA
18701705 TTAAGGCATG
Statistics
Matches: 211, Mismatches: 32, Indels: 33
0.76 0.12 0.12
Matches are distributed among these distances:
58 5 0.02
59 41 0.19
60 7 0.03
61 8 0.04
62 60 0.28
63 37 0.18
64 1 0.00
65 31 0.15
66 18 0.09
67 3 0.01
ACGTcount: A:0.37, C:0.12, G:0.13, T:0.37
Consensus pattern (63 bp):
GATCAATTAAGGCATTTATGTAACCAAACGCCTTAATTGATCTTCTTTATAAATTTTAGAAAA
Done.