Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032253.1 Gossypioides kirkii chromosome KI_11
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: 55708359
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2600 characters in sequence are not A, C, G, or T
File 86 of 182
Found at i:27174383 original size:17 final size:17
Alignment explanation
Indices: 27174361--27174394 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
27174351 CCTCAGTCAC
27174361 ATAAAGAAAAGAGAAAA
1 ATAAAGAAAAGAGAAAA
*
27174378 ATAAAGAAAAGGGAAAA
1 ATAAAGAAAAGAGAAAA
27174395 GAAGGAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.74, C:0.00, G:0.21, T:0.06
Consensus pattern (17 bp):
ATAAAGAAAAGAGAAAA
Found at i:27187858 original size:15 final size:16
Alignment explanation
Indices: 27187829--27187878 Score: 61
Period size: 15 Copynumber: 3.2 Consensus size: 16
27187819 AGTCACGTAT
27187829 AAAA-AAAGAAGAAGA
1 AAAAGAAAGAAGAAGA
27187844 AAAAGAAAGAA-AAGA
1 AAAAGAAAGAAGAAGA
*
27187859 AAAAGAGAA-AAGCAGA
1 AAAAGA-AAGAAGAAGA
27187875 AAAA
1 AAAA
27187879 TATATATATT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
15 16 0.52
16 15 0.48
ACGTcount: A:0.78, C:0.02, G:0.20, T:0.00
Consensus pattern (16 bp):
AAAAGAAAGAAGAAGA
Found at i:27192628 original size:18 final size:18
Alignment explanation
Indices: 27192583--27192629 Score: 76
Period size: 19 Copynumber: 2.6 Consensus size: 18
27192573 ACTAAGTCAC
27192583 TTGGTATTAGATATATAA
1 TTGGTATTAGATATATAA
*
27192601 TTGTGTATTAGATATATGA
1 TTG-GTATTAGATATATAA
27192620 TTGGTATTAG
1 TTGGTATTAG
27192630 TGTTAGTGAG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
18 10 0.37
19 17 0.63
ACGTcount: A:0.32, C:0.00, G:0.21, T:0.47
Consensus pattern (18 bp):
TTGGTATTAGATATATAA
Found at i:27202553 original size:14 final size:14
Alignment explanation
Indices: 27202518--27202547 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
27202508 GTAAACCATC
*
27202518 CAAGACAAGTACTT
1 CAAGACAAGTACGT
27202532 CAAGACAAGTACGT
1 CAAGACAAGTACGT
27202546 CA
1 CA
27202548 CAACAATATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.43, C:0.23, G:0.17, T:0.17
Consensus pattern (14 bp):
CAAGACAAGTACGT
Found at i:27204773 original size:106 final size:107
Alignment explanation
Indices: 27204652--27204873 Score: 356
Period size: 108 Copynumber: 2.1 Consensus size: 107
27204642 TTTACTGAAT
* *
27204652 ATAATTTAACGTAATTATAATTATTAATTATAATGCTTTCGTTAAATATT-AAAACATGAAAGTT
1 ATAATTTAACATAATTATAATTATTAATTATAATGATTTCGTTAAATATTAAAAACATGAAAGTT
*
27204716 AATATCCTTTTGGAAAGGATATAATGTTTTAATAAACCTTCA
66 AATATCCTTTTGGAAAGGATATAATATTTTAATAAACCTTCA
* * *
27204758 ATAATTTAACATAATTATAATTTTTAATTATAATGATTTTGTTAAATATTAAAAAACATGGAAGT
1 ATAATTTAACATAATTATAATTATTAATTATAATGATTTCGTTAAATATT-AAAAACATGAAAGT
*
27204823 TAATATCCTTTTGGAAAGGATATAATATTTTAATAAACCTTCC
65 TAATATCCTTTTGGAAAGGATATAATATTTTAATAAACCTTCA
27204866 ATATATTT
1 ATA-ATTT
27204874 TTTAAAAGAA
Statistics
Matches: 106, Mismatches: 7, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
106 46 0.43
108 56 0.53
109 4 0.04
ACGTcount: A:0.42, C:0.08, G:0.09, T:0.42
Consensus pattern (107 bp):
ATAATTTAACATAATTATAATTATTAATTATAATGATTTCGTTAAATATTAAAAACATGAAAGTT
AATATCCTTTTGGAAAGGATATAATATTTTAATAAACCTTCA
Found at i:27204935 original size:122 final size:127
Alignment explanation
Indices: 27204802--27205047 Score: 340
Period size: 122 Copynumber: 2.0 Consensus size: 127
27204792 GATTTTGTTA
* * * **
27204802 AATATTAAAAAACATGGAAGTTAATATCCTTTTGGAAAGGATATAATATTTTAATAAACCTTCCA
1 AATATTAAAAAACATAGAAGTTAATATCCTTTTGAAAAGGACATAATATTAAAATAAACCTTCCA
* * *
27204867 TATATTT-TTTAAA-AGA-ATATTTCCATTTTAATATGAGATATTATA-TAAAAGGAAATTG
66 CATATTTCTCTAAAGAGATATATTTCCATTTTAATATGAGATATTAAATTAAAAGGAAATTG
* * *
27204925 AATATT-AAAAACATATAAGTTAATATCCTTTTGAAAAGGACATAATGTTAAAATAAATCTTCCA
1 AATATTAAAAAACATAGAAGTTAATATCCTTTTGAAAAGGACATAATATTAAAATAAACCTTCCA
* *
27204989 CATATTTCTCTAAAGATATATATTTTCATTTTAATATGAGATATTAAATTAAAAGGAAA
66 CATATTTCTCTAAAGAGATATATTTCCATTTTAATATGAGATATTAAATTAAAAGGAAA
27205048 AATAGAGTAT
Statistics
Matches: 106, Mismatches: 13, Indels: 5
0.85 0.10 0.04
Matches are distributed among these distances:
122 56 0.53
123 11 0.10
124 2 0.02
125 27 0.25
126 10 0.09
ACGTcount: A:0.45, C:0.08, G:0.09, T:0.37
Consensus pattern (127 bp):
AATATTAAAAAACATAGAAGTTAATATCCTTTTGAAAAGGACATAATATTAAAATAAACCTTCCA
CATATTTCTCTAAAGAGATATATTTCCATTTTAATATGAGATATTAAATTAAAAGGAAATTG
Found at i:27207495 original size:18 final size:18
Alignment explanation
Indices: 27207468--27207504 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
27207458 TGTGAAACCC
*
27207468 CTCCCCATGTAGTGCAAA
1 CTCCCAATGTAGTGCAAA
*
27207486 CTCCCAATGTATTGCAAA
1 CTCCCAATGTAGTGCAAA
27207504 C
1 C
27207505 CCTTATGTAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.30, C:0.32, G:0.14, T:0.24
Consensus pattern (18 bp):
CTCCCAATGTAGTGCAAA
Found at i:27207527 original size:18 final size:18
Alignment explanation
Indices: 27207504--27207538 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
27207494 GTATTGCAAA
27207504 CCCTTATGTAGTGTGAAT
1 CCCTTATGTAGTGTGAAT
27207522 CCCTTATGTAGTGTGAA
1 CCCTTATGTAGTGTGAA
27207539 CTCCACATGT
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:0.23, C:0.17, G:0.23, T:0.37
Consensus pattern (18 bp):
CCCTTATGTAGTGTGAAT
Found at i:27207600 original size:53 final size:53
Alignment explanation
Indices: 27207470--27207601 Score: 126
Period size: 53 Copynumber: 2.5 Consensus size: 53
27207460 TGAAACCCCT
* ** * * *
27207470 CCCCATGTAGTGCAAACTCCCA-ATGTATTGCAAACCCTTATGTAGTGTGAATC
1 CCCCATGCAGTGTGAAC-CCCACATGTAATGCAAACCCTCATGTAGTGCGAATC
** * *
27207523 CCTTATGTAGTGTGAACTCCACATGTAATGCAAACCCTCATGTAGTGCGAA-C
1 CCCCATGCAGTGTGAACCCCACATGTAATGCAAACCCTCATGTAGTGCGAATC
27207575 CCCCATGCA-TGTGGAACCCCTACATGT
1 CCCCATGCAGTGT-GAACCCC-ACATGT
27207602 GCAAACCCCC
Statistics
Matches: 64, Mismatches: 12, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
51 3 0.05
52 16 0.25
53 45 0.70
ACGTcount: A:0.27, C:0.28, G:0.18, T:0.27
Consensus pattern (53 bp):
CCCCATGCAGTGTGAACCCCACATGTAATGCAAACCCTCATGTAGTGCGAATC
Found at i:27208188 original size:27 final size:27
Alignment explanation
Indices: 27208158--27208222 Score: 96
Period size: 27 Copynumber: 2.4 Consensus size: 27
27208148 CCCTAGGTGA
*
27208158 GTGAACCCTATGTGCGAGCCCCTAAGT
1 GTGAACCCTATGTGCGAACCCCTAAGT
*
27208185 GTGAACCC-ATTGTGCGAACCCCTAGGT
1 GTGAACCCTA-TGTGCGAACCCCTAAGT
27208212 GTGAACCCTAT
1 GTGAACCCTAT
27208223 ATGTGCTAAC
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
26 1 0.03
27 32 0.94
28 1 0.03
ACGTcount: A:0.23, C:0.29, G:0.25, T:0.23
Consensus pattern (27 bp):
GTGAACCCTATGTGCGAACCCCTAAGT
Found at i:27208219 original size:14 final size:14
Alignment explanation
Indices: 27208140--27208219 Score: 56
Period size: 14 Copynumber: 5.7 Consensus size: 14
27208130 AACCATACAT
*
27208140 GTGTGAATCCCTAG
1 GTGTGAACCCCTAG
*
27208154 GTGAGTGAA-CCCTAT
1 GT--GTGAACCCCTAG
* * *
27208169 GTGCGAGCCCCTAA
1 GTGTGAACCCCTAG
* *
27208183 GTGTGAACCCAT-T
1 GTGTGAACCCCTAG
*
27208196 GTGCGAACCCCTAG
1 GTGTGAACCCCTAG
27208210 GTGTGAACCC
1 GTGTGAACCC
27208220 TATATGTGCT
Statistics
Matches: 50, Mismatches: 12, Indels: 8
0.71 0.17 0.11
Matches are distributed among these distances:
13 13 0.26
14 25 0.50
15 7 0.14
16 5 0.10
ACGTcount: A:0.23, C:0.28, G:0.28, T:0.23
Consensus pattern (14 bp):
GTGTGAACCCCTAG
Found at i:27211217 original size:20 final size:19
Alignment explanation
Indices: 27211178--27211219 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
27211168 AATAGTTAAA
*
27211178 AAAAATTAAAACTTTGTTT
1 AAAAATTAAAACTTTCTTT
*
27211197 AAAAATTTAAACTTTTCTTT
1 AAAAATTAAAAC-TTTCTTT
27211217 AAA
1 AAA
27211220 TGACTAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 11 0.55
20 9 0.45
ACGTcount: A:0.48, C:0.07, G:0.02, T:0.43
Consensus pattern (19 bp):
AAAAATTAAAACTTTCTTT
Found at i:27211465 original size:292 final size:297
Alignment explanation
Indices: 27210960--27211630 Score: 846
Period size: 292 Copynumber: 2.3 Consensus size: 297
27210950 AATAAAAAGT
* * * *
27210960 TTTCTTTTTTTTAAAACAAAATCATTACTTTTCTTAAAAAT-CAAAATTTCTATTTCAAAATAGT
1 TTTCTTTTTTTT-AAAGAAAATCATTACTTTTCTTAAAACTCCAAACTTT-TATTTCGAAATAG-
* * * * *
27211024 TTAAAAAAA-TCAAATTTTGTTTAAAAACTTAAACTTTTCTCTTTTAAAATGCCTAAAAAAATAT
63 TTAAAAAAATTAAAACTTTGCTTAAAAACTTAAACTTTTCTCTTTTAAAATGACTAAAAAAATAG
* * * *
27211088 ATTTTTATTTTTAAAAATCTAAACTTCCTTTTTTTTAAAAAAACACTAATTTATTTAAAAATCTA
128 AGTTATATTTTTAAAAATCTAAACTTCCTTTTTTTAAAAAAAACACTAATTTATTTAAAAATCCA
* * * * *
27211153 AATTTTTATTTCAAAAATAGTTAAAAAAAATTAAAACTTTGTTTAAAAATTTAAAC-TTTTCTTT
193 AACTTTCATTGCAAAAATAGTT-AAAAAAATCAAAACTTTATTTAAAAATTTAAACTTTTTCTTT
*
27211217 -AAATGACTAAAAAACATATTTTTATTTTTAAAAATCTAAAC
257 AAAATGACTAAAAAACAGATTTTTA-TTTTAAAAATCTAAAC
* *
27211258 -TT-TTTTTTTT-ATGAAAATCACTA-TTTTCTTAAAACTCCAAACTTTTATTTCGAAATAGTTA
1 TTTCTTTTTTTTAAAGAAAATCATTACTTTTCTTAAAACTCCAAACTTTTATTTCGAAATAGTTA
* * *
27211319 AAAAAATTTAAAACTTTGCTTAAAAATTTAAACTTTT-TC-TTTAAAATGATTAAAAAAATAGGG
66 AAAAAA-TTAAAACTTTGCTTAAAAACTTAAACTTTTCTCTTTTAAAATGACTAAAAAAATAGAG
* * *
27211382 TTATA-TTTTAAAAATCTAAACTTTCTTTTTTTAAAAAAAAATCACT-ATTTTTCTTAAAACTCC
130 TTATATTTTTAAAAATCTAAACTTCCTTTTTTT-AAAAAAAA-CACTAATTTAT-TTAAAAATCC
*
27211445 AAACTTTCATTGC-GAAATAGTTAAAAAAATCAAAACTTTATTTAAAAATTTAAACTTTTTCTTT
192 AAACTTTCATTGCAAAAATAGTTAAAAAAATCAAAACTTTATTTAAAAATTTAAACTTTTTCTTT
*
27211509 AAAATGACTAAAAAACCGATTTTTATTTTAAAAATCTAAAC
257 AAAATGACTAAAAAACAGATTTTTATTTTAAAAATCTAAAC
* * *
27211550 TTTCTTTTTTTTAAAAAAGAAAATCATTATTTTTCTTAAAACTCAAAACTTTTATTTCGAAATTG
1 TTTCTTTTTTTT---AAAGAAAATCATTACTTTTCTTAAAACTCCAAACTTTTATTTCGAAATAG
*
27211615 TTAAAAAAATGAAAAC
63 TTAAAAAAATTAAAAC
27211631 ATTTCCCAAG
Statistics
Matches: 324, Mismatches: 34, Indels: 30
0.84 0.09 0.08
Matches are distributed among these distances:
291 57 0.18
292 76 0.23
293 72 0.22
294 50 0.15
296 8 0.02
297 2 0.01
298 17 0.05
299 42 0.13
ACGTcount: A:0.44, C:0.11, G:0.03, T:0.42
Consensus pattern (297 bp):
TTTCTTTTTTTTAAAGAAAATCATTACTTTTCTTAAAACTCCAAACTTTTATTTCGAAATAGTTA
AAAAAATTAAAACTTTGCTTAAAAACTTAAACTTTTCTCTTTTAAAATGACTAAAAAAATAGAGT
TATATTTTTAAAAATCTAAACTTCCTTTTTTTAAAAAAAACACTAATTTATTTAAAAATCCAAAC
TTTCATTGCAAAAATAGTTAAAAAAATCAAAACTTTATTTAAAAATTTAAACTTTTTCTTTAAAA
TGACTAAAAAACAGATTTTTATTTTAAAAATCTAAAC
Found at i:27212034 original size:3 final size:3
Alignment explanation
Indices: 27212026--27212056 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
27212016 CATGAAATCC
27212026 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
27212057 GATGATGATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:27212061 original size:3 final size:3
Alignment explanation
Indices: 27212055--27212080 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
27212045 AATAATAATA
27212055 ATG ATG ATG ATG ATG ATG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG AT
27212081 AATTTGGGCC
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:0.35, C:0.00, G:0.31, T:0.35
Consensus pattern (3 bp):
ATG
Found at i:27212591 original size:42 final size:42
Alignment explanation
Indices: 27212544--27213160 Score: 702
Period size: 42 Copynumber: 14.5 Consensus size: 42
27212534 GAACCCCTAG
* *
27212544 CCTAGGCCTCTAAATGCAATGAAAAGTAAATGCACTTCCACA
1 CCTAGGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACA
* *
27212586 CCTAGGCCTTTAAATGCGATGAAAAGTAAATGGACCTCCACA
1 CCTAGGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACA
* * * *
27212628 CCTGGGCCTCTAACTGCATTGAAAAATAAATGGACCTCCACA
1 CCTAGGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACA
* * **
27212670 CCAAGGCCTCTGGCTCTAAATGCGATGAAAAGTAAATGGACCTTTACA
1 CCTAGG---C---CTCTAAATGCAATGAAAAGTAAATGGACCTCCACA
* *
27212718 CCTAGGCCTCTAAATGTAATGAAAAGTAAATGGACCTCAACA
1 CCTAGGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACA
* * * **
27212760 CCTAGGCCTTTAAATGTAATGAAGAGTAAATGGACCTCCATG
1 CCTAGGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACA
*
27212802 CCTAGGCCTCTAAATGCAATGAAAAGTAAATAGACCTCCACA
1 CCTAGGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACA
* *
27212844 CCT-GAGCCTCTAAATGCTATGAAAAGTAAAGGGACCTCCACA
1 CCTAG-GCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACA
* *
27212886 CTTAGACCTCTAAATGCAATGAAAAGTAAATGGACCTCCACA
1 CCTAGGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACA
* * * * * * *
27212928 CCTGGGACTCTAAATGCGACGAAAAGCAAATAGACCTCTACA
1 CCTAGGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACA
** ** *
27212970 CCT-GAGCCTAAAAATGTGATGAAAAGTAAATGGGCCTCCACA
1 CCTAG-GCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACA
* * * * *
27213012 CATGGGCCTCTAAGTGCTATGAAAAGTAAATGGGCCTCCACA
1 CCTAGGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACA
* *
27213054 CCT-GGACCTCTAAATGCAAGGAAAAGTAAATGAACCTCCACA
1 CCTAGG-CCTCTAAATGCAATGAAAAGTAAATGGACCTCCACA
* * *
27213096 TCTGGGCCTCTAAATGTAATGAAAAGTAAATGGACCTCCACA
1 CCTAGGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACA
27213138 CCT-GAGCCTCTAAATGCAATGAA
1 CCTAG-GCCTCTAAATGCAATGAA
27213161 TGCTTTCCTT
Statistics
Matches: 485, Mismatches: 77, Indels: 26
0.82 0.13 0.04
Matches are distributed among these distances:
41 5 0.01
42 440 0.91
43 4 0.01
45 2 0.00
48 34 0.07
ACGTcount: A:0.37, C:0.24, G:0.18, T:0.21
Consensus pattern (42 bp):
CCTAGGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACA
Found at i:27213574 original size:1 final size:1
Alignment explanation
Indices: 27213568--27213654 Score: 66
Period size: 1 Copynumber: 87.0 Consensus size: 1
27213558 TCTCTCTCTA
* * * * * * * * *
27213568 TTTTTTTCTTCTTTTTTTTTTTGTTTTTTTTCTCTTTTTCTTTTTTTCTCTTTTTCTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * *
27213633 CTTTTTTTTTTTGTGTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTT
27213655 CTTGATTTAA
Statistics
Matches: 62, Mismatches: 24, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
1 62 1.00
ACGTcount: A:0.00, C:0.10, G:0.03, T:0.86
Consensus pattern (1 bp):
T
Found at i:27213602 original size:40 final size:41
Alignment explanation
Indices: 27213558--27213639 Score: 105
Period size: 40 Copynumber: 2.0 Consensus size: 41
27213548 TCTCTTGCTC
27213558 TCTCTCTCTATTTTTTTCTTCTTTTT-TTTTTTGTT-TTTTT
1 TCTCTCTCTATTTTTTTC-TCTTTTTCTTTTTTGTTCTTTTT
* * * *
27213598 TCTCTTTTTCTTTTTTTCTCTTTTTCTTTTTTTTTCTTTTT
1 TCTCTCTCTATTTTTTTCTCTTTTTCTTTTTTGTTCTTTTT
27213639 T
1 T
27213640 TTTTTGTGTT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
39 7 0.19
40 23 0.64
41 6 0.17
ACGTcount: A:0.01, C:0.16, G:0.01, T:0.82
Consensus pattern (41 bp):
TCTCTCTCTATTTTTTTCTCTTTTTCTTTTTTGTTCTTTTT
Found at i:27213654 original size:16 final size:16
Alignment explanation
Indices: 27213562--27213644 Score: 87
Period size: 16 Copynumber: 4.9 Consensus size: 16
27213552 TTGCTCTCTC
27213562 TCTCTATTTTTTTCTTCTT
1 TCTCT-TTTTTTT-TT-TT
* *
27213581 TTTTTTTTTGTTTTTTT
1 TCTCTTTTT-TTTTTTT
*
27213598 TCTCTTTTTCTTTTTT
1 TCTCTTTTTTTTTTTT
27213614 TCTCTTTTTCTTTTTTT
1 TCTCTTTTT-TTTTTTT
27213631 T-TCTTTTTTTTTTT
1 TCTCTTTTTTTTTTT
27213645 GTGTTTTTTT
Statistics
Matches: 56, Mismatches: 6, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
15 6 0.11
16 22 0.39
17 16 0.29
18 6 0.11
19 6 0.11
ACGTcount: A:0.01, C:0.13, G:0.01, T:0.84
Consensus pattern (16 bp):
TCTCTTTTTTTTTTTT
Found at i:27218384 original size:4 final size:4
Alignment explanation
Indices: 27218375--27218422 Score: 69
Period size: 4 Copynumber: 12.0 Consensus size: 4
27218365 AGCGAATTAG
* * *
27218375 TGAA TGAA TGCA TGAA TGAA TGAA CGAA TGAA TGAA TGAA TGAT TGAA
1 TGAA TGAA TGAA TGAA TGAA TGAA TGAA TGAA TGAA TGAA TGAA TGAA
27218423 ATTAGGGCAC
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
4 38 1.00
ACGTcount: A:0.46, C:0.04, G:0.25, T:0.25
Consensus pattern (4 bp):
TGAA
Found at i:27220664 original size:22 final size:22
Alignment explanation
Indices: 27220612--27220667 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
27220602 GGAAGAAAAA
27220612 AAATCAGTAAAAAATAGTCAAAT
1 AAATCA-TAAAAAATAGTCAAAT
* * *
27220635 GAAGCATAAAAAAT-GTGAAAT
1 AAATCATAAAAAATAGTCAAAT
27220656 CAAATCATAAAA
1 -AAATCATAAAA
27220668 CATTGCGAAC
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
21 6 0.22
22 17 0.63
23 4 0.15
ACGTcount: A:0.61, C:0.09, G:0.11, T:0.20
Consensus pattern (22 bp):
AAATCATAAAAAATAGTCAAAT
Found at i:27221283 original size:23 final size:20
Alignment explanation
Indices: 27221239--27221283 Score: 54
Period size: 23 Copynumber: 2.1 Consensus size: 20
27221229 ATTAGAAAAT
*
27221239 TAAATAAATTAATGCACGAA
1 TAAATAAATTAATGCACAAA
27221259 TAAATAAATCTAATATGCACAAA
1 TAAATAAAT-T-A-ATGCACAAA
27221282 TA
1 TA
27221284 CTAAAAAACC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 9 0.43
21 1 0.05
22 1 0.05
23 10 0.48
ACGTcount: A:0.56, C:0.11, G:0.07, T:0.27
Consensus pattern (20 bp):
TAAATAAATTAATGCACAAA
Found at i:27229081 original size:49 final size:50
Alignment explanation
Indices: 27229000--27229335 Score: 226
Period size: 49 Copynumber: 6.8 Consensus size: 50
27228990 TTCGTTACAG
* * * *
27229000 CTTCAATCTGTTCCCTCTTTAG-TTTTAGGGTGTTAGATCTATCC-TTGCGA
1 CTTCAATCT-ATCCCTCTTTAGATTTTAAGGTGTTAGATCCA-CCATTACGA
* * *
27229050 CTTCAATCTATCCCT-TTTCGATTTTAAGGTGTTAGGTCTCTATCATT--GTA
1 CTTCAATCTATCCCTCTTTAGATTTTAAGGTGTTAGATC-C-ACCATTACG-A
* * * *
27229100 GCTTCAACCTATCCCTCTTTAG-TTTTAAAGTGTAAGATCCACCATTACGG
1 -CTTCAATCTATCCCTCTTTAGATTTTAAGGTGTTAGATCCACCATTACGA
* * * * *
27229150 CTTCAATATTTCCTTCTTT-GATTTTAGGGTGTTAGATCCACCATTACGG
1 CTTCAATCTATCCCTCTTTAGATTTTAAGGTGTTAGATCCACCATTACGA
* * * ** *
27229199 CTTCAATCCATCCCTCTTT-GATTTTAAGGTGTAAGGTCCGTCATTGA-GG
1 CTTCAATCTATCCCTCTTTAGATTTTAAGGTGTTAGATCCACCATT-ACGA
* * ** * * *
27229248 CTTCAACCTATCCCTCTTCAG-TTTTAAGGCATAAGATCCACCATTGCGG
1 CTTCAATCTATCCCTCTTTAGATTTTAAGGTGTTAGATCCACCATTACGA
* * * * *
27229297 CTCCAACCTTTCCCTCTTCA-ATTTTAGGGTGTTAGATCC
1 CTTCAATCTATCCCTCTTTAGATTTTAAGGTGTTAGATCC
27229336 CTATTAAGAA
Statistics
Matches: 228, Mismatches: 44, Indels: 29
0.76 0.15 0.10
Matches are distributed among these distances:
48 5 0.02
49 173 0.76
50 14 0.06
51 32 0.14
52 4 0.02
ACGTcount: A:0.21, C:0.24, G:0.16, T:0.39
Consensus pattern (50 bp):
CTTCAATCTATCCCTCTTTAGATTTTAAGGTGTTAGATCCACCATTACGA
Found at i:27229309 original size:147 final size:149
Alignment explanation
Indices: 27229010--27229335 Score: 419
Period size: 147 Copynumber: 2.2 Consensus size: 149
27229000 CTTCAATCTG
* * * * *
27229010 TTCCCTCTTTAGTTTTAGGGTGTTAGATCTATCCTTGCGACTTCAATCTATCCCTTTTCGATTTT
1 TTCCCTCTTCAATTTTAGGGTGTTAGATCCATCCTTACGACTTCAATCCATCCCTTTTCGATTTT
* * **
27229075 AAGGTGTTAGGTCTCTATCATTGTAGCTTCAACCTATCCCTCTTTAGTTTTAAAGTGTAAGATCC
66 AAGGTGTAAGGTCTCTATCATTGTAGCTTCAACCTATCCCTCTTCAGTTTTAAAGCATAAGATCC
* *
27229140 ACCATTACGGCTTCAATAT
131 ACCATTACGGCTCCAACAT
* ** *
27229159 TTCCTTCTTTGATTTTAGGGTGTTAGATCCA-CCATTACGGCTTCAATCCATCCCTCTTT-GATT
1 TTCCCTCTTCAATTTTAGGGTGTTAGATCCATCC-TTACGACTTCAATCCATCCCT-TTTCGATT
* *
27229222 TTAAGGTGTAAGGTC-C-GTCATTG-AGGCTTCAACCTATCCCTCTTCAGTTTTAAGGCATAAGA
64 TTAAGGTGTAAGGTCTCTATCATTGTA-GCTTCAACCTATCCCTCTTCAGTTTTAAAGCATAAGA
* *
27229284 TCCACCATTGCGGCTCCAACCT
128 TCCACCATTACGGCTCCAACAT
27229306 TTCCCTCTTCAATTTTAGGGTGTTAGATCC
1 TTCCCTCTTCAATTTTAGGGTGTTAGATCC
27229336 CTATTAAGAA
Statistics
Matches: 154, Mismatches: 20, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
146 1 0.01
147 84 0.55
148 3 0.02
149 63 0.41
150 3 0.02
ACGTcount: A:0.21, C:0.24, G:0.16, T:0.39
Consensus pattern (149 bp):
TTCCCTCTTCAATTTTAGGGTGTTAGATCCATCCTTACGACTTCAATCCATCCCTTTTCGATTTT
AAGGTGTAAGGTCTCTATCATTGTAGCTTCAACCTATCCCTCTTCAGTTTTAAAGCATAAGATCC
ACCATTACGGCTCCAACAT
Found at i:27239785 original size:21 final size:22
Alignment explanation
Indices: 27239747--27239788 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
27239737 ATAAATTTTA
27239747 TTTTAATATTATGGGTTTAGGG
1 TTTTAATATTATGGGTTTAGGG
*
27239769 TTTTTATATTA-GGGTTTAGG
1 TTTTAATATTATGGGTTTAGG
27239789 ATTTAAGGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.21, C:0.00, G:0.26, T:0.52
Consensus pattern (22 bp):
TTTTAATATTATGGGTTTAGGG
Found at i:27244458 original size:46 final size:46
Alignment explanation
Indices: 27244406--27244503 Score: 153
Period size: 46 Copynumber: 2.1 Consensus size: 46
27244396 CTATTTTTTT
27244406 GTGCAAGTCATTTTTTCTGCAC-ACGTATTCTTTACCTACATTATTG
1 GTGCAAGTCATTTTTTCTGCACGA-GTATTCTTTACCTACATTATTG
* * *
27244452 GTGCAAGTTATTTTTTCTGCACGAGTATTTTTTGCCTACATTATTG
1 GTGCAAGTCATTTTTTCTGCACGAGTATTCTTTACCTACATTATTG
27244498 GTGCAA
1 GTGCAA
27244504 ATAATGTTTT
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
46 47 0.98
47 1 0.02
ACGTcount: A:0.21, C:0.18, G:0.16, T:0.44
Consensus pattern (46 bp):
GTGCAAGTCATTTTTTCTGCACGAGTATTCTTTACCTACATTATTG
Found at i:27248129 original size:9 final size:9
Alignment explanation
Indices: 27248114--27248145 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
27248104 GATAATGATT
27248114 AAAATTTTA
1 AAAATTTTA
*
27248123 CAAATTTTA
1 AAAATTTTA
27248132 AAAATTTTA
1 AAAATTTTA
27248141 AAAAT
1 AAAAT
27248146 ATGAGACCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (9 bp):
AAAATTTTA
Found at i:27254311 original size:16 final size:17
Alignment explanation
Indices: 27254284--27254316 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
27254274 ATAAAAAATT
*
27254284 TTAAAAATTAATTAAAA
1 TTAAAAATTAATGAAAA
27254301 TTAAAAA-TAATGAAAA
1 TTAAAAATTAATGAAAA
27254317 ATATCTATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (17 bp):
TTAAAAATTAATGAAAA
Found at i:27254836 original size:21 final size:22
Alignment explanation
Indices: 27254812--27254852 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
27254802 TTTTGATTGT
27254812 TGTTTTAATGCTGTT-TTTTAC
1 TGTTTTAATGCTGTTATTTTAC
* *
27254833 TGTTTTGATGTTGTTATTTT
1 TGTTTTAATGCTGTTATTTT
27254853 TGTTGCTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.12, C:0.05, G:0.17, T:0.66
Consensus pattern (22 bp):
TGTTTTAATGCTGTTATTTTAC
Found at i:27254852 original size:24 final size:21
Alignment explanation
Indices: 27254825--27254897 Score: 67
Period size: 21 Copynumber: 3.2 Consensus size: 21
27254815 TTTAATGCTG
27254825 TTTTTTACTGTTTTGATGTTGTTA
1 TTTTTT-CTGTTTT--TGTTGTTA
*
27254849 TTTTTGTTGCTATTTTTGTTGTTA
1 -TTTT-TT-CTGTTTTTGTTGTTA
27254873 TTTTTGT-TGTTTTTGTTGTTA
1 TTTTT-TCTGTTTTTGTTGTTA
27254894 TTTT
1 TTTT
27254898 ACTGTTATTT
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
21 17 0.40
22 1 0.02
23 5 0.12
24 8 0.19
25 4 0.09
26 8 0.19
ACGTcount: A:0.08, C:0.03, G:0.16, T:0.73
Consensus pattern (21 bp):
TTTTTTCTGTTTTTGTTGTTA
Found at i:27254862 original size:12 final size:12
Alignment explanation
Indices: 27254841--27254939 Score: 107
Period size: 12 Copynumber: 8.6 Consensus size: 12
27254831 ACTGTTTTGA
27254841 TGTTGTTATTTT
1 TGTTGTTATTTT
*
27254853 TGTTGCTATTTT
1 TGTTGTTATTTT
27254865 TGTTGTTATTTT
1 TGTTGTTATTTT
27254877 TGTTG---TTTT
1 TGTTGTTATTTT
27254886 TGTTGTTA-TTT
1 TGTTGTTATTTT
**
27254897 TACTGTTATTTT
1 TGTTGTTATTTT
*
27254909 TGTTGCTATTTT
1 TGTTGTTATTTT
* *
27254921 GGCTGTTATTTT
1 TGTTGTTATTTT
*
27254933 AGTTGTT
1 TGTTGTT
27254940 TGGATGTTAT
Statistics
Matches: 71, Mismatches: 12, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
9 9 0.13
11 9 0.13
12 53 0.75
ACGTcount: A:0.09, C:0.04, G:0.18, T:0.69
Consensus pattern (12 bp):
TGTTGTTATTTT
Found at i:27254867 original size:21 final size:22
Alignment explanation
Indices: 27254841--27254939 Score: 94
Period size: 23 Copynumber: 4.3 Consensus size: 22
27254831 ACTGTTTTGA
27254841 TGTTGTTATTTTTGTTGCTATTTT
1 TGTTGTTATTTTTGTTG-TA-TTT
27254865 TGTTGTTATTTTTGTTGT-TTT
1 TGTTGTTATTTTTGTTGTATTT
*
27254886 TGTTGTTATTTTACTGTTAT-TTT
1 TGTTGTTATTTT--TGTTGTATTT
* * *
27254909 TGTTGCTATTTTGGCTGTTATTT
1 TGTTGTTATTTTTGTTG-TATTT
27254932 TAGTTGTT
1 T-GTTGTT
27254940 TGGATGTTAT
Statistics
Matches: 64, Mismatches: 6, Indels: 10
0.80 0.08 0.12
Matches are distributed among these distances:
21 17 0.27
22 1 0.02
23 24 0.38
24 22 0.34
ACGTcount: A:0.09, C:0.04, G:0.18, T:0.69
Consensus pattern (22 bp):
TGTTGTTATTTTTGTTGTATTT
Found at i:27254886 original size:56 final size:56
Alignment explanation
Indices: 27254826--27254940 Score: 142
Period size: 56 Copynumber: 2.1 Consensus size: 56
27254816 TTAATGCTGT
** * * *
27254826 TTTTTACTGTT-TTGATGTTGTTATTTTTGTTGCTATTTTTGTTGTTATTTTTGTTG
1 TTTTTACTGTTATT-ATACTGTTATTTTTGTTGCTATTTTGGCTGTTATTTTAGTTG
** *
27254882 TTTTTGTTGTTATTTTACTGTTATTTTTGTTGCTATTTTGGCTGTTATTTTAGTTG
1 TTTTTACTGTTATTATACTGTTATTTTTGTTGCTATTTTGGCTGTTATTTTAGTTG
27254938 TTT
1 TTT
27254941 GGATGTTATT
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
56 48 0.96
57 2 0.04
ACGTcount: A:0.10, C:0.04, G:0.17, T:0.69
Consensus pattern (56 bp):
TTTTTACTGTTATTATACTGTTATTTTTGTTGCTATTTTGGCTGTTATTTTAGTTG
Found at i:27254954 original size:56 final size:56
Alignment explanation
Indices: 27254844--27254952 Score: 166
Period size: 56 Copynumber: 2.0 Consensus size: 56
27254834 GTTTTGATGT
* * * * *
27254844 TGTTATTTTTGTTGCTATTTTTGTTGTTATTTTTGTTGTTTTTGTTGTTATTTTAC
1 TGTTATTTTTGTTGCTATTTTGGCTGTTATTTTAGTTGTTTTGGATGTTATTTTAC
27254900 TGTTATTTTTGTTGCTATTTTGGCTGTTATTTTAGTTG-TTTGGATGTTATTTT
1 TGTTATTTTTGTTGCTATTTTGGCTGTTATTTTAGTTGTTTTGGATGTTATTTT
27254953 TATGTCTTTT
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
55 13 0.27
56 35 0.73
ACGTcount: A:0.10, C:0.04, G:0.18, T:0.68
Consensus pattern (56 bp):
TGTTATTTTTGTTGCTATTTTGGCTGTTATTTTAGTTGTTTTGGATGTTATTTTAC
Found at i:27255130 original size:21 final size:21
Alignment explanation
Indices: 27255088--27255131 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
27255078 ATTTATTTAT
* *
27255088 TTTTTAATGTTTGTTTTAATA
1 TTTTTAATGTTTATTTGAATA
27255109 TTTTTAA-GTTTATTTGATATA
1 TTTTTAATGTTTATTTGA-ATA
27255130 TT
1 TT
27255132 ATATATTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.25, C:0.00, G:0.09, T:0.66
Consensus pattern (21 bp):
TTTTTAATGTTTATTTGAATA
Found at i:27256085 original size:9 final size:9
Alignment explanation
Indices: 27256060--27256250 Score: 82
Period size: 9 Copynumber: 20.0 Consensus size: 9
27256050 TACTAAAAGT
27256060 TTATAAAAA
1 TTATAAAAA
*
27256069 CTTGTAAAAA
1 -TTATAAAAA
*
27256079 TTATAAAAC
1 TTATAAAAA
27256088 TTA-AAAAA
1 TTATAAAAA
27256096 TTATAAAAA
1 TTATAAAAA
27256105 TTCATAAAAA
1 TT-ATAAAAA
* *
27256115 CCTATAAATA
1 -TTATAAAAA
*
27256125 TTACAAAAA
1 TTATAAAAA
27256134 CTTATAAAAAAAA
1 -TTAT---AAAAA
* *
27256147 TTTTAAATA
1 TTATAAAAA
* * * *
27256156 CTACATATAG
1 TTATA-AAAA
*
27256166 TTATAAAAC
1 TTATAAAAA
27256175 TTATAAAAA
1 TTATAAAAA
27256184 TTCATAATAAGA
1 TT-ATAA-AA-A
27256196 TTA-AATAAA
1 TTATAA-AAA
*
27256205 TTAGAAAAA
1 TTATAAAAA
*
27256214 ATAT-AAAA
1 TTATAAAAA
* *
27256222 TTTTAATATCA
1 TTATAA-A-AA
*
27256233 TTATAAAAT
1 TTATAAAAA
27256242 TTATAAAAA
1 TTATAAAAA
27256251 CTCATTTATT
Statistics
Matches: 134, Mismatches: 32, Indels: 31
0.68 0.16 0.16
Matches are distributed among these distances:
8 13 0.10
9 59 0.44
10 41 0.31
11 10 0.07
12 6 0.04
13 5 0.04
ACGTcount: A:0.59, C:0.06, G:0.02, T:0.33
Consensus pattern (9 bp):
TTATAAAAA
Found at i:27256096 original size:17 final size:18
Alignment explanation
Indices: 27256060--27256103 Score: 63
Period size: 17 Copynumber: 2.4 Consensus size: 18
27256050 TACTAAAAGT
*
27256060 TTATAAAAACTTGTAAAAA
1 TTAT-AAAACTTGAAAAAA
27256079 TTATAAAACTT-AAAAAA
1 TTATAAAACTTGAAAAAA
27256096 TTATAAAA
1 TTATAAAA
27256104 ATTCATAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 13 0.54
18 7 0.29
19 4 0.17
ACGTcount: A:0.61, C:0.05, G:0.02, T:0.32
Consensus pattern (18 bp):
TTATAAAACTTGAAAAAA
Found at i:27256114 original size:20 final size:19
Alignment explanation
Indices: 27256060--27256143 Score: 84
Period size: 19 Copynumber: 4.5 Consensus size: 19
27256050 TACTAAAAGT
*
27256060 TTATAAAAACTTGTAAAAA-
1 TTATAAAAA-TTATAAAAAC
*
27256079 TTATAAAACTTA-AAAAA-
1 TTATAAAAATTATAAAAAC
27256096 TTATAAAAATTCATAAAAAC
1 TTATAAAAATT-ATAAAAAC
* * *
27256116 CTATAAATATTACAAAAAC
1 TTATAAAAATTATAAAAAC
27256135 TTATAAAAA
1 TTATAAAAA
27256144 AAATTTTAAA
Statistics
Matches: 54, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
17 15 0.28
18 3 0.06
19 27 0.50
20 9 0.17
ACGTcount: A:0.61, C:0.08, G:0.01, T:0.30
Consensus pattern (19 bp):
TTATAAAAATTATAAAAAC
Found at i:27259226 original size:39 final size:39
Alignment explanation
Indices: 27259172--27259252 Score: 153
Period size: 39 Copynumber: 2.1 Consensus size: 39
27259162 CATATCACAT
27259172 GTATGGGGATAGGACGATATTGAAAGGAGAAAGATTATG
1 GTATGGGGATAGGACGATATTGAAAGGAGAAAGATTATG
*
27259211 GTATGGGGATAGGACGATATTGAAAGGAGAAAGATTCTG
1 GTATGGGGATAGGACGATATTGAAAGGAGAAAGATTATG
27259250 GTA
1 GTA
27259253 GTTTAATGAT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.37, C:0.04, G:0.36, T:0.23
Consensus pattern (39 bp):
GTATGGGGATAGGACGATATTGAAAGGAGAAAGATTATG
Found at i:27259728 original size:23 final size:23
Alignment explanation
Indices: 27259702--27259749 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
27259692 AAATAATTGC
27259702 TTTACACTTTATTATTTCAATAT
1 TTTACACTTTATTATTTCAATAT
27259725 TTTACACTTTATTATTTCAATAT
1 TTTACACTTTATTATTTCAATAT
27259748 TT
1 TT
27259750 GGACTATATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.29, C:0.12, G:0.00, T:0.58
Consensus pattern (23 bp):
TTTACACTTTATTATTTCAATAT
Found at i:27259762 original size:22 final size:23
Alignment explanation
Indices: 27259702--27259762 Score: 79
Period size: 23 Copynumber: 2.7 Consensus size: 23
27259692 AAATAATTGC
*
27259702 TTTACACTTTATTATTTCAATAT
1 TTTACACTATATTATTTCAATAT
*
27259725 TTTACACTTTATTATTTCAATA-
1 TTTACACTATATTATTTCAATAT
**
27259747 TTTGGACTATATTATT
1 TTTACACTATATTATT
27259763 ATTATTTTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
22 13 0.37
23 22 0.63
ACGTcount: A:0.30, C:0.11, G:0.03, T:0.56
Consensus pattern (23 bp):
TTTACACTATATTATTTCAATAT
Found at i:27261675 original size:30 final size:30
Alignment explanation
Indices: 27261599--27261678 Score: 83
Period size: 30 Copynumber: 2.7 Consensus size: 30
27261589 ATTGAATAGT
* *
27261599 AAGTAGAG-GACTGTTTTGTCACTTTTTGAT
1 AAGTTGAGTGACTGTTTTGTCACTTTTT-AC
* * *
27261629 AACTTTAGTGATTGTTTTGTCACATTTTT-C
1 AAGTTGAGTGACTGTTTTGTCAC-TTTTTAC
27261659 AAGTTGAGTGACTGTTTTGT
1 AAGTTGAGTGACTGTTTTGT
27261679 TAAATGTAAC
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
30 22 0.55
31 13 0.32
32 5 0.12
ACGTcount: A:0.21, C:0.10, G:0.21, T:0.47
Consensus pattern (30 bp):
AAGTTGAGTGACTGTTTTGTCACTTTTTAC
Found at i:27264269 original size:74 final size:74
Alignment explanation
Indices: 27264146--27264411 Score: 254
Period size: 74 Copynumber: 3.6 Consensus size: 74
27264136 GACACAAAAG
* * * * * **
27264146 CCTGCTAGGAACATAGCTCGATAAAACCAGCAGAAAAACTGCTAGGCACATAGCTTGATAACACT
1 CCTGCTAGGAACATAGCCCGATAACACCGGCACAAAGACTGCTAGGCACATAGCCAGATAACACT
27264211 GGCACAAAC
66 GGCACAAAC
* * * * * *
27264220 CCTGCTAGGGACATAGCCCGATAACACCGGTACAAAGACTGCTAAGCACATGGCCCGATAACACC
1 CCTGCTAGGAACATAGCCCGATAACACCGGCACAAAGACTGCTAGGCACATAGCCAGATAACACT
*
27264285 GGCATAAAC
66 GGCACAAAC
* * * * * *
27264294 CCTGCTAGGCACATGGCCCGATAACAACGGCATAAAGCCTGCTAGGCACAAAGCCAGATAACACT
1 CCTGCTAGGAACATAGCCCGATAACACCGGCACAAAGACTGCTAGGCACATAGCCAGATAACACT
27264359 -G-AC--A-
66 GGCACAAAC
* * * * * *
27264363 CGTGCTAGGCATAAAGCCCGATAACACCGGCACAGAGGCCTGCTAGGCA
1 CCTGCTAGGAACATAGCCCGATAACACCGGCACA-AAGACTGCTAGGCA
27264412 TAAAGCTCGA
Statistics
Matches: 159, Mismatches: 32, Indels: 6
0.81 0.16 0.03
Matches are distributed among these distances:
69 28 0.18
70 14 0.09
72 1 0.01
73 1 0.01
74 115 0.72
ACGTcount: A:0.35, C:0.29, G:0.22, T:0.14
Consensus pattern (74 bp):
CCTGCTAGGAACATAGCCCGATAACACCGGCACAAAGACTGCTAGGCACATAGCCAGATAACACT
GGCACAAAC
Found at i:27264318 original size:37 final size:37
Alignment explanation
Indices: 27264146--27264411 Score: 227
Period size: 37 Copynumber: 7.3 Consensus size: 37
27264136 GACACAAAAG
* * * * * *
27264146 CCTGCTAGGAACATAGCTCGATAAAACCAGCAGAAAA
1 CCTGCTAGGCACATAGCCCGATAACACCGGCACAAAC
* ** *
27264183 ACTGCTAGGCACATAGCTTGATAACACTGGCACAAAC
1 CCTGCTAGGCACATAGCCCGATAACACCGGCACAAAC
* * *
27264220 CCTGCTAGGGACATAGCCCGATAACACCGGTACAAAG
1 CCTGCTAGGCACATAGCCCGATAACACCGGCACAAAC
* * * *
27264257 ACTGCTAAGCACATGGCCCGATAACACCGGCATAAAC
1 CCTGCTAGGCACATAGCCCGATAACACCGGCACAAAC
* * * *
27264294 CCTGCTAGGCACATGGCCCGATAACAACGGCATAAAG
1 CCTGCTAGGCACATAGCCCGATAACACCGGCACAAAC
* * *
27264331 CCTGCTAGGCACAAAGCCAGATAACA-CTG-AC--A-
1 CCTGCTAGGCACATAGCCCGATAACACCGGCACAAAC
* * * **
27264363 CGTGCTAGGCATAAAGCCCGATAACACCGGCACAGAGG
1 CCTGCTAGGCACATAGCCCGATAACACCGGCACA-AAC
27264401 CCTGCTAGGCA
1 CCTGCTAGGCA
27264412 TAAAGCTCGA
Statistics
Matches: 186, Mismatches: 37, Indels: 11
0.79 0.16 0.05
Matches are distributed among these distances:
32 23 0.12
33 3 0.02
34 2 0.01
35 1 0.01
36 2 0.01
37 145 0.78
38 10 0.05
ACGTcount: A:0.35, C:0.29, G:0.22, T:0.14
Consensus pattern (37 bp):
CCTGCTAGGCACATAGCCCGATAACACCGGCACAAAC
Found at i:27264639 original size:36 final size:36
Alignment explanation
Indices: 27264592--27264663 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
27264582 AAGACGATTA
27264592 CCCGGTGACCCCACCTTATTTTTCTATCAACGGTTG
1 CCCGGTGACCCCACCTTATTTTTCTATCAACGGTTG
27264628 CCCGGTGACCCCACCTTATTTTTCTATCAACGGTTG
1 CCCGGTGACCCCACCTTATTTTTCTATCAACGGTTG
27264664 ACAATCGATC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.17, C:0.33, G:0.17, T:0.33
Consensus pattern (36 bp):
CCCGGTGACCCCACCTTATTTTTCTATCAACGGTTG
Found at i:27265817 original size:92 final size:92
Alignment explanation
Indices: 27265712--27265896 Score: 361
Period size: 92 Copynumber: 2.0 Consensus size: 92
27265702 ACATTCACAT
*
27265712 AATCATGCTTTAATTGGCACCAAGTGATACTATTCTAATCTAATAACTCAAGCAATTCTATCAAA
1 AATCATGCTTTAATTGGCACCAAGTGATACTATTCAAATCTAATAACTCAAGCAATTCTATCAAA
27265777 CATTTCAATCCCATAAAAATAAACCAG
66 CATTTCAATCCCATAAAAATAAACCAG
27265804 AATCATGCTTTAATTGGCACCAAGTGATACTATTCAAATCTAATAACTCAAGCAATTCTATCAAA
1 AATCATGCTTTAATTGGCACCAAGTGATACTATTCAAATCTAATAACTCAAGCAATTCTATCAAA
27265869 CATTTCAATCCCATAAAAATAAACCAG
66 CATTTCAATCCCATAAAAATAAACCAG
27265896 A
1 A
27265897 TTTGAATGGC
Statistics
Matches: 92, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
92 92 1.00
ACGTcount: A:0.42, C:0.22, G:0.08, T:0.29
Consensus pattern (92 bp):
AATCATGCTTTAATTGGCACCAAGTGATACTATTCAAATCTAATAACTCAAGCAATTCTATCAAA
CATTTCAATCCCATAAAAATAAACCAG
Found at i:27270263 original size:25 final size:27
Alignment explanation
Indices: 27270232--27270281 Score: 77
Period size: 25 Copynumber: 1.9 Consensus size: 27
27270222 TCTCATCCCA
27270232 ATTTTACCCC-AATAAAA-TTATGACG
1 ATTTTACCCCTAATAAAATTTATGACG
*
27270257 ATTTTACCCCTGATAAAATTTATGA
1 ATTTTACCCCTAATAAAATTTATGA
27270282 GAAAATATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 10 0.45
26 6 0.27
27 6 0.27
ACGTcount: A:0.38, C:0.18, G:0.08, T:0.36
Consensus pattern (27 bp):
ATTTTACCCCTAATAAAATTTATGACG
Found at i:27271192 original size:22 final size:24
Alignment explanation
Indices: 27271149--27271193 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 24
27271139 TGGTAATATG
27271149 TTTTGATATAACAAATTAAAGTGT
1 TTTTGATATAACAAATTAAAGTGT
*
27271173 TTTTGA-ATAA-AAGTTAAAGTG
1 TTTTGATATAACAAATTAAAGTG
27271194 AGAAATTTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 10 0.50
23 4 0.20
24 6 0.30
ACGTcount: A:0.42, C:0.02, G:0.16, T:0.40
Consensus pattern (24 bp):
TTTTGATATAACAAATTAAAGTGT
Found at i:27271434 original size:20 final size:20
Alignment explanation
Indices: 27271409--27271456 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
27271399 TATTGATTTG
** *
27271409 GTATCGATACTTTTCATAAA
1 GTATCGATAAATTCCATAAA
*
27271429 GTATCGATAAATTCCATCAA
1 GTATCGATAAATTCCATAAA
27271449 GTATCGAT
1 GTATCGAT
27271457 GTTCCTGTTC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.35, C:0.17, G:0.12, T:0.35
Consensus pattern (20 bp):
GTATCGATAAATTCCATAAA
Found at i:27274278 original size:37 final size:35
Alignment explanation
Indices: 27274233--27274302 Score: 90
Period size: 37 Copynumber: 1.9 Consensus size: 35
27274223 TTCCAAAAAT
27274233 AATATTATTTTAA-AAT-TTTAATATTAAATTTAATTC
1 AATATTATTTTAATAATATTT--TATT-AATTTAATTC
27274269 AATACTTATTTTAATAATATTTTATTAATTTAAT
1 AATA-TTATTTTAATAATATTTTATTAATTTAAT
27274303 ATTAAAGTGA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
36 12 0.39
37 13 0.42
38 3 0.10
39 3 0.10
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (35 bp):
AATATTATTTTAATAATATTTTATTAATTTAATTC
Found at i:27274308 original size:62 final size:64
Alignment explanation
Indices: 27274242--27274441 Score: 191
Period size: 62 Copynumber: 3.1 Consensus size: 64
27274232 TAATATTATT
27274242 TTAAAATTTTAATATTAAATTTAAT-TCAATACTTATTTTA-AT-AATATTTTATTAATTTAATA
1 TTAAAATTTTAATATTAAATTTAATAT-AATACTTATTTTAGATAAATATTTTATTAATTTAATA
*
27274304 TTAAAGTGATTATATTAATATTAAATTTAATATAATATTTATCTTGTAGATAAATATTTTATT-A
1 TTAAA---A-T-T-TTAATATTAAATTTAATATAATACTTAT-TT-TAGATAAATATTTTATTAA
27274368 TTT--TA
58 TTTAATA
* * * * ** *
27274373 ATAAGA-TTTAATATTAAATTTAATGTATTACTTA-TCAAGATAAATATTATATTAATTTAATA
1 TTAAAATTTTAATATTAAATTTAATATAATACTTATTTTAGATAAATATTTTATTAATTTAATA
27274435 TTAAAAT
1 TTAAAAT
27274442 GATTAAGTTT
Statistics
Matches: 112, Mismatches: 11, Indels: 29
0.74 0.07 0.19
Matches are distributed among these distances:
59 15 0.13
60 5 0.04
62 35 0.31
63 1 0.01
65 1 0.01
66 2 0.02
67 1 0.01
68 25 0.22
69 8 0.07
70 2 0.02
71 6 0.05
72 11 0.10
ACGTcount: A:0.44, C:0.03, G:0.04, T:0.50
Consensus pattern (64 bp):
TTAAAATTTTAATATTAAATTTAATATAATACTTATTTTAGATAAATATTTTATTAATTTAATA
Found at i:27297903 original size:13 final size:14
Alignment explanation
Indices: 27297885--27297914 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
27297875 GTCAATGCAA
27297885 TCAGA-GTTAAATG
1 TCAGAGGTTAAATG
27297898 TCAGAGGTTAAATG
1 TCAGAGGTTAAATG
27297912 TCA
1 TCA
27297915 ATGTACTGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.31
14 11 0.69
ACGTcount: A:0.37, C:0.10, G:0.23, T:0.30
Consensus pattern (14 bp):
TCAGAGGTTAAATG
Found at i:27302212 original size:14 final size:14
Alignment explanation
Indices: 27302193--27302220 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
27302183 GATTATTCAC
27302193 ATTATTTTAAACCT
1 ATTATTTTAAACCT
27302207 ATTATTTTAAACCT
1 ATTATTTTAAACCT
27302221 TGTGAGCCAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.14, G:0.00, T:0.50
Consensus pattern (14 bp):
ATTATTTTAAACCT
Found at i:27305013 original size:16 final size:16
Alignment explanation
Indices: 27304992--27305033 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 16
27304982 TGCTAAAACA
27304992 AATAAAATGCAGA-GAC
1 AATAAAATGCA-ATGAC
27305008 AATAAAAATGCAATGAC
1 AAT-AAAATGCAATGAC
27305025 AATTAAAAT
1 AA-TAAAAT
27305034 AAATGCTTGC
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
16 4 0.17
17 18 0.78
18 1 0.04
ACGTcount: A:0.60, C:0.10, G:0.12, T:0.19
Consensus pattern (16 bp):
AATAAAATGCAATGAC
Found at i:27328795 original size:42 final size:42
Alignment explanation
Indices: 27328683--27328910 Score: 227
Period size: 42 Copynumber: 5.4 Consensus size: 42
27328673 CAAAGTCATA
* *
27328683 AGTCTTCCTTTCAAAC--AATCTTATGCTC-TACC-GAGTCAT-
1 AGTCTTCCTTT-AAACATAATCTCATGCTCAT-CCTGAGACATG
* *
27328722 AGGTCTTCCTTTTTAAACATAATCTCTTGCTCATCCTGAGTCATG
1 A-GTCTTCC--TTTAAACATAATCTCATGCTCATCCTGAGACATG
*
27328767 AGTCTTCCTTTAAACATAATCTCATGCTCAT-CTCGAGACAGG
1 AGTCTTCCTTTAAACATAATCTCATGCTCATCCT-GAGACATG
* *
27328809 AGTCTTCCTTTAAACATACTCTCATGCTCATCTTGAGACATG
1 AGTCTTCCTTTAAACATAATCTCATGCTCATCCTGAGACATG
* * *
27328851 AGTCTTCCTTTAAACATACTCTCATTCTCCTTCC-GAGACATG
1 AGTCTTCCTTTAAACATAATCTCATGCT-CATCCTGAGACATG
* *
27328893 AGTGTTCCATTTATACAT
1 AGTCTTCC-TTTAAACAT
27328911 CAAGTGATTC
Statistics
Matches: 164, Mismatches: 13, Indels: 20
0.83 0.07 0.10
Matches are distributed among these distances:
39 1 0.01
40 7 0.04
41 6 0.04
42 110 0.67
43 24 0.15
44 15 0.09
45 1 0.01
ACGTcount: A:0.25, C:0.26, G:0.12, T:0.36
Consensus pattern (42 bp):
AGTCTTCCTTTAAACATAATCTCATGCTCATCCTGAGACATG
Found at i:27332049 original size:126 final size:126
Alignment explanation
Indices: 27331824--27332076 Score: 488
Period size: 126 Copynumber: 2.0 Consensus size: 126
27331814 GTTTTATCAA
27331824 TAAGCATCCATCAATGCCTAATATAAAAGTACTTTAATTATCCTAGTAAAATATAGATAATTATA
1 TAAGCATCCATCAATGCCTAATATAAAAGTACTTTAATTATCCTAGTAAAATATAGATAATTATA
27331889 ATGAGAGCATACAATTTCCATATCTATTCATGCATAGAGTTGTTTAAATCACATAGGGCTT
66 ATGAGAGCATACAATTTCCATATCTATTCATGCATAGAGTTGTTTAAATCACATAGGGCTT
27331950 TAAGCATCCATCAATGCCTAATATAAAAGTACTTTAATTATCCTAGTAAAATATAGATAATTATA
1 TAAGCATCCATCAATGCCTAATATAAAAGTACTTTAATTATCCTAGTAAAATATAGATAATTATA
* *
27332015 ATGAGAGCATATAATTTCCATATTTATTCATGCATAGAGTTGTTTAAATCACATAGGGCTT
66 ATGAGAGCATACAATTTCCATATCTATTCATGCATAGAGTTGTTTAAATCACATAGGGCTT
27332076 T
1 T
27332077 TCGGCTTGTA
Statistics
Matches: 125, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
126 125 1.00
ACGTcount: A:0.39, C:0.14, G:0.12, T:0.35
Consensus pattern (126 bp):
TAAGCATCCATCAATGCCTAATATAAAAGTACTTTAATTATCCTAGTAAAATATAGATAATTATA
ATGAGAGCATACAATTTCCATATCTATTCATGCATAGAGTTGTTTAAATCACATAGGGCTT
Found at i:27339085 original size:17 final size:17
Alignment explanation
Indices: 27339055--27339093 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
27339045 TAAAACAAAC
27339055 AAAATGCAGAGACAATA
1 AAAATGCAGAGACAATA
*
27339072 AAAATGCA-ATGACAATT
1 AAAATGCAGA-GACAATA
27339089 AAAAT
1 AAAAT
27339094 AAATGCATGC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 1 0.05
17 19 0.95
ACGTcount: A:0.59, C:0.10, G:0.13, T:0.18
Consensus pattern (17 bp):
AAAATGCAGAGACAATA
Found at i:27345695 original size:18 final size:18
Alignment explanation
Indices: 27345662--27345696 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
27345652 AGCTTGTGGT
*
27345662 TGCATCTGGTTATATGAC
1 TGCATCTGATTATATGAC
*
27345680 TGCATCTGATTTTATGA
1 TGCATCTGATTATATGA
27345697 TCTCATTTGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.23, C:0.14, G:0.20, T:0.43
Consensus pattern (18 bp):
TGCATCTGATTATATGAC
Found at i:27366465 original size:51 final size:51
Alignment explanation
Indices: 27366399--27366630 Score: 347
Period size: 51 Copynumber: 4.5 Consensus size: 51
27366389 GAATCTATAA
* * * * *
27366399 ACTCACGATGACACTTAATCATCTGACCTTTAATCCATACAGGATTCATTT
1 ACTCATGATGACACTTAGTCATCGGACCGTTAATCCATAAAGGATTCATTT
* * *
27366450 ACTCATGATGGCACTTAGTCATCAGACCGTTAATCCATAAATGATTCATTT
1 ACTCATGATGACACTTAGTCATCGGACCGTTAATCCATAAAGGATTCATTT
* *
27366501 ACTCATGATGACACTTAGCCATCGGACCGTTAATCCATAATGGATTCATTT
1 ACTCATGATGACACTTAGTCATCGGACCGTTAATCCATAAAGGATTCATTT
* *
27366552 ACTCATGATGACACTTAGTCATTGGACCATTAATCCATAAAGGATTCATTT
1 ACTCATGATGACACTTAGTCATCGGACCGTTAATCCATAAAGGATTCATTT
*
27366603 ACTCACGATGACACTTAGTCATCGGACC
1 ACTCATGATGACACTTAGTCATCGGACC
27366631 CTTTCGTTTA
Statistics
Matches: 163, Mismatches: 18, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
51 163 1.00
ACGTcount: A:0.31, C:0.24, G:0.14, T:0.31
Consensus pattern (51 bp):
ACTCATGATGACACTTAGTCATCGGACCGTTAATCCATAAAGGATTCATTT
Found at i:27373777 original size:51 final size:51
Alignment explanation
Indices: 27373651--27373780 Score: 206
Period size: 51 Copynumber: 2.5 Consensus size: 51
27373641 GAATCTATAA
* * * *
27373651 ACTCACGATGACACATAGTCATCGAACCTTTAATCCATACAGGATTCATTT
1 ACTCACGATGACACTTAGTCATCGGACCATTAATCCATAAAGGATTCATTT
* *
27373702 ACTGATGATGACACTTAGTCATCGGACCATTAATCCATAAAGGATTCATTT
1 ACTCACGATGACACTTAGTCATCGGACCATTAATCCATAAAGGATTCATTT
27373753 ACTCACGATGACACTTAGTCATCGGACC
1 ACTCACGATGACACTTAGTCATCGGACC
27373781 CTTTCGTTTA
Statistics
Matches: 71, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
51 71 1.00
ACGTcount: A:0.32, C:0.25, G:0.15, T:0.28
Consensus pattern (51 bp):
ACTCACGATGACACTTAGTCATCGGACCATTAATCCATAAAGGATTCATTT
Found at i:27379802 original size:24 final size:24
Alignment explanation
Indices: 27379770--27379896 Score: 131
Period size: 24 Copynumber: 5.5 Consensus size: 24
27379760 CAAGCATGCA
27379770 AACTACCGATACTTCTATACATAC
1 AACTACCGATACTTCTATACATAC
** **
27379794 AACTACCGATAC-TC-GCA-ATTT
1 AACTACCGATACTTCTATACATAC
*
27379815 AACTATCGATACTTCTATACATAC
1 AACTACCGATACTTCTATACATAC
* **
27379839 AACTACCGATAC-T-TACA-ATTT
1 AACTACCGATACTTCTATACATAC
*
27379860 AACTACTGATACTTCTATACATAC
1 AACTACCGATACTTCTATACATAC
27379884 AACTACCGATACT
1 AACTACCGATACT
27379897 CACAATTTAA
Statistics
Matches: 79, Mismatches: 18, Indels: 12
0.72 0.17 0.11
Matches are distributed among these distances:
21 26 0.33
22 7 0.09
23 7 0.09
24 39 0.49
ACGTcount: A:0.37, C:0.27, G:0.06, T:0.31
Consensus pattern (24 bp):
AACTACCGATACTTCTATACATAC
Found at i:27379804 original size:45 final size:45
Alignment explanation
Indices: 27379770--27379916 Score: 235
Period size: 45 Copynumber: 3.3 Consensus size: 45
27379760 CAAGCATGCA
*
27379770 AACTACCGATACTTCTATACATACAACTACCGATACTCGCAATTT
1 AACTACCGATACTTCTATACATACAACTACCGATACTAGCAATTT
*
27379815 AACTATCGATACTTCTATACATACAACTACCGATACTTA-CAATTT
1 AACTACCGATACTTCTATACATACAACTACCGATAC-TAGCAATTT
*
27379860 AACTACTGATACTTCTATACATACAACTACCGATACTCA-CAATTT
1 AACTACCGATACTTCTATACATACAACTACCGATACT-AGCAATTT
27379905 AACTACCGATAC
1 AACTACCGATAC
27379917 AACTCAAGTC
Statistics
Matches: 95, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
44 1 0.01
45 93 0.98
46 1 0.01
ACGTcount: A:0.37, C:0.27, G:0.05, T:0.30
Consensus pattern (45 bp):
AACTACCGATACTTCTATACATACAACTACCGATACTAGCAATTT
Found at i:27379865 original size:21 final size:21
Alignment explanation
Indices: 27379794--27379916 Score: 93
Period size: 21 Copynumber: 5.6 Consensus size: 21
27379784 CTATACATAC
**
27379794 AACTACCGATACTCGCAATTT
1 AACTACCGATACTTACAATTT
* * **
27379815 AACTATCGATACTTCTATACATAC
1 AACTACCGATAC-T-TACA-ATTT
27379839 AACTACCGATACTTACAATTT
1 AACTACCGATACTTACAATTT
* * **
27379860 AACTACTGATACTTCTATACATAC
1 AACTACCGATAC-T-TACA-ATTT
*
27379884 AACTACCGATACTCACAATTT
1 AACTACCGATACTTACAATTT
27379905 AACTACCGATAC
1 AACTACCGATAC
27379917 AACTCAAGTC
Statistics
Matches: 77, Mismatches: 19, Indels: 12
0.71 0.18 0.11
Matches are distributed among these distances:
21 38 0.49
22 7 0.09
23 6 0.08
24 26 0.34
ACGTcount: A:0.37, C:0.27, G:0.06, T:0.30
Consensus pattern (21 bp):
AACTACCGATACTTACAATTT
Found at i:27380608 original size:51 final size:51
Alignment explanation
Indices: 27380545--27380670 Score: 243
Period size: 51 Copynumber: 2.5 Consensus size: 51
27380535 GAATCTGTAA
*
27380545 ACTCACGATGACACTTAGTCATCGGACCTTTAATCCATAAAGGATTCATTT
1 ACTCACGATGACACTTAGTCATCGGACCGTTAATCCATAAAGGATTCATTT
27380596 ACTCACGATGACACTTAGTCATCGGACCGTTAATCCATAAAGGATTCATTT
1 ACTCACGATGACACTTAGTCATCGGACCGTTAATCCATAAAGGATTCATTT
27380647 ACTCACGATGACACTTAGTCATCG
1 ACTCACGATGACACTTAGTCATCG
27380671 AACCCTTTCG
Statistics
Matches: 74, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
51 74 1.00
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.29
Consensus pattern (51 bp):
ACTCACGATGACACTTAGTCATCGGACCGTTAATCCATAAAGGATTCATTT
Found at i:27382438 original size:20 final size:19
Alignment explanation
Indices: 27382406--27382443 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
27382396 TCGTCGTTTC
27382406 TATCTTTCACATTTCCAAT
1 TATCTTTCACATTTCCAAT
*
27382425 TATCGTTTCTCATTTCCAA
1 TATC-TTTCACATTTCCAA
27382444 CAATCATTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.24, C:0.26, G:0.03, T:0.47
Consensus pattern (19 bp):
TATCTTTCACATTTCCAAT
Found at i:27392384 original size:15 final size:15
Alignment explanation
Indices: 27392354--27392387 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
27392344 TTTTATATTA
**
27392354 AATTTTAATTTGATG
1 AATTTTAATTAAATG
27392369 AATTTTAATTAAATG
1 AATTTTAATTAAATG
27392384 AATT
1 AATT
27392388 AAAAGTTAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (15 bp):
AATTTTAATTAAATG
Found at i:27393785 original size:27 final size:27
Alignment explanation
Indices: 27393705--27393899 Score: 207
Period size: 27 Copynumber: 7.3 Consensus size: 27
27393695 CATGGTCAAA
* *
27393705 ATTCTGTATTTGGCTCAAATGAGTGAT
1 ATTCTGTATCTGGCTCAAATGAGCGAT
*
27393732 ATTCTGTATCTAG-TCAAATGAGCGAT
1 ATTCTGTATCTGGCTCAAATGAGCGAT
* * *
27393758 ATTTTGTATTTGGCTCGAATGAGCGAT
1 ATTCTGTATCTGGCTCAAATGAGCGAT
* *
27393785 ATTCTATATCTGGCTCTAATGAGCGAT
1 ATTCTGTATCTGGCTCAAATGAGCGAT
27393812 ATTCTGTATCTGGCTCAAATGCA-CGAT
1 ATTCTGTATCTGGCTCAAATG-AGCGAT
* * ** *
27393839 ACTCTGTATCTAGCTTGAAT-ACGTGAT
1 ATTCTGTATCTGGCTCAAATGA-GCGAT
* * *
27393866 ATTCTGTATTTGGCTCGAATGAGTGAT
1 ATTCTGTATCTGGCTCAAATGAGCGAT
27393893 ATTCTGT
1 ATTCTGT
27393900 TATTTTTGAA
Statistics
Matches: 141, Mismatches: 22, Indels: 10
0.82 0.13 0.06
Matches are distributed among these distances:
25 1 0.01
26 22 0.16
27 116 0.82
28 2 0.01
ACGTcount: A:0.25, C:0.15, G:0.21, T:0.38
Consensus pattern (27 bp):
ATTCTGTATCTGGCTCAAATGAGCGAT
Found at i:27393826 original size:54 final size:54
Alignment explanation
Indices: 27393705--27393899 Score: 236
Period size: 54 Copynumber: 3.6 Consensus size: 54
27393695 CATGGTCAAA
* *
27393705 ATTCTGTATTTGGCTCAAATGAGTGATATTCTGTATCTAG-TCAAATGAGCGAT
1 ATTCTGTATTTGGCTCAAATGAGCGATATTCTGTATCTAGCTCTAATGAGCGAT
* * * *
27393758 ATTTTGTATTTGGCTCGAATGAGCGATATTCTATATCTGGCTCTAATGAGCGAT
1 ATTCTGTATTTGGCTCAAATGAGCGATATTCTGTATCTAGCTCTAATGAGCGAT
* * *
27393812 ATTCTGTATCTGGCTCAAATGCA-CGATACTCTGTATCTAGCT-TGAAT-ACGTGAT
1 ATTCTGTATTTGGCTCAAATG-AGCGATATTCTGTATCTAGCTCT-AATGA-GCGAT
* *
27393866 ATTCTGTATTTGGCTCGAATGAGTGATATTCTGT
1 ATTCTGTATTTGGCTCAAATGAGCGATATTCTGT
27393900 TATTTTTGAA
Statistics
Matches: 120, Mismatches: 17, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
53 38 0.32
54 81 0.68
55 1 0.01
ACGTcount: A:0.25, C:0.15, G:0.21, T:0.38
Consensus pattern (54 bp):
ATTCTGTATTTGGCTCAAATGAGCGATATTCTGTATCTAGCTCTAATGAGCGAT
Found at i:27393880 original size:81 final size:80
Alignment explanation
Indices: 27393705--27393899 Score: 241
Period size: 81 Copynumber: 2.4 Consensus size: 80
27393695 CATGGTCAAA
* * * *
27393705 ATTCTGTATTTGGCTCAAATGAGTGATATTCTGTATCTAGTCAAATGAGCGATATTTTGTATTTG
1 ATTCTGTATTTGGCTCAAATGAGTGATATTCTGTATCTAGTCAAATGAGCGATACTCTGTATCTA
27393770 GCTCGAATGAGCGAT
66 GCTCGAATGAGCGAT
* * * * *
27393785 ATTCTATATCTGGCTCTAATGAGCGATATTCTGTATCTGGCTCAAATGCA-CGATACTCTGTATC
1 ATTCTGTATTTGGCTCAAATGAGTGATATTCTGTATCTAG-TCAAATG-AGCGATACTCTGTATC
* *
27393849 TAGCTTGAAT-ACGTGAT
64 TAGCTCGAATGA-GCGAT
*
27393866 ATTCTGTATTTGGCTCGAATGAGTGATATTCTGT
1 ATTCTGTATTTGGCTCAAATGAGTGATATTCTGT
27393900 TATTTTTGAA
Statistics
Matches: 97, Mismatches: 15, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
80 36 0.37
81 60 0.62
82 1 0.01
ACGTcount: A:0.25, C:0.15, G:0.21, T:0.38
Consensus pattern (80 bp):
ATTCTGTATTTGGCTCAAATGAGTGATATTCTGTATCTAGTCAAATGAGCGATACTCTGTATCTA
GCTCGAATGAGCGAT
Found at i:27396260 original size:24 final size:24
Alignment explanation
Indices: 27396231--27396324 Score: 125
Period size: 24 Copynumber: 3.9 Consensus size: 24
27396221 CACAGACAAC
**
27396231 TTAGCTCACACGAGCCCAGAATGG
1 TTAGCTCTTACGAGCCCAGAATGG
* *
27396255 TCAGCTCTTATGAGCCCAGAATGG
1 TTAGCTCTTACGAGCCCAGAATGG
* * *
27396279 TTAGCTCTTATGATCCCAAAATGG
1 TTAGCTCTTACGAGCCCAGAATGG
27396303 TTAGCTCTTACGAGCCCAGAAT
1 TTAGCTCTTACGAGCCCAGAAT
27396325 CAGAATGATG
Statistics
Matches: 60, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 60 1.00
ACGTcount: A:0.28, C:0.26, G:0.21, T:0.26
Consensus pattern (24 bp):
TTAGCTCTTACGAGCCCAGAATGG
Found at i:27396356 original size:27 final size:27
Alignment explanation
Indices: 27396308--27396382 Score: 89
Period size: 27 Copynumber: 2.7 Consensus size: 27
27396298 AATGGTTAGC
* *
27396308 TCTTACGAGCCCAGAATCAGAATGA-TGA
1 TCTTTCGAG-CCAGAATCAGAATAACT-A
* *
27396336 TCTTTCGAGCCAGAATTAGAATAACTC
1 TCTTTCGAGCCAGAATCAGAATAACTA
27396363 TCTTTCGAGCCAGAATCAGA
1 TCTTTCGAGCCAGAATCAGA
27396383 TTACTCCTCA
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
27 32 0.78
28 9 0.22
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.25
Consensus pattern (27 bp):
TCTTTCGAGCCAGAATCAGAATAACTA
Found at i:27406933 original size:20 final size:19
Alignment explanation
Indices: 27406892--27406936 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
27406882 ATAGTTTTCA
**
27406892 TGCATTTTTATTTTGTCAT
1 TGCATTTTTATTAAGTCAT
*
27406911 TGCATTTTTATTAAGTTAGT
1 TGCATTTTTATTAAGTCA-T
27406931 TGCATT
1 TGCATT
27406937 GTCATTGAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 15 0.68
20 7 0.32
ACGTcount: A:0.20, C:0.09, G:0.13, T:0.58
Consensus pattern (19 bp):
TGCATTTTTATTAAGTCAT
Found at i:27409184 original size:52 final size:52
Alignment explanation
Indices: 27409106--27409211 Score: 185
Period size: 52 Copynumber: 2.0 Consensus size: 52
27409096 AGTATTAACA
* *
27409106 ATTTTAGTGTGCAGATCTAACTTAATTGCACTGACATCTTTACTTACATTTC
1 ATTTTAGTGTGCAAATCTAACTTAATTGCACTGACATCTTTACTCACATTTC
*
27409158 ATTTTAGTGTGCAAATCTGACTTAATTGCACTGACATCTTTACTCACATTTC
1 ATTTTAGTGTGCAAATCTAACTTAATTGCACTGACATCTTTACTCACATTTC
27409210 AT
1 AT
27409212 CTAATTTTAG
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.27, C:0.20, G:0.11, T:0.42
Consensus pattern (52 bp):
ATTTTAGTGTGCAAATCTAACTTAATTGCACTGACATCTTTACTCACATTTC
Found at i:27414054 original size:12 final size:12
Alignment explanation
Indices: 27414037--27414077 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
27414027 TGTAGAAGAC
27414037 ATAAAATAAAAG
1 ATAAAATAAAAG
*
27414049 ATAAAATAAAAT
1 ATAAAATAAAAG
27414061 AGT-AAATAAAAG
1 A-TAAAATAAAAG
27414073 A-AAAA
1 ATAAAA
27414078 GCTTGAGTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
11 3 0.12
12 21 0.84
13 1 0.04
ACGTcount: A:0.76, C:0.00, G:0.07, T:0.17
Consensus pattern (12 bp):
ATAAAATAAAAG
Found at i:27415795 original size:12 final size:13
Alignment explanation
Indices: 27415765--27415795 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
27415755 TAATAATTAT
*
27415765 TAAAAAATAAGAA
1 TAAAAAATAACAA
27415778 TAAAAAATAACAA
1 TAAAAAATAACAA
27415791 TAAAA
1 TAAAA
27415796 TAAAAAGAGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.77, C:0.03, G:0.03, T:0.16
Consensus pattern (13 bp):
TAAAAAATAACAA
Found at i:27419706 original size:19 final size:19
Alignment explanation
Indices: 27419647--27419706 Score: 54
Period size: 19 Copynumber: 3.2 Consensus size: 19
27419637 AGACTGTCGC
*
27419647 TGCATAAATATTCTTCAAT
1 TGCATAAGTATTCTTCAAT
* *
27419666 TGCATCCAG-A-ACTATC-AT
1 TGCAT-AAGTATTCT-TCAAT
27419684 TGCATAAGTATTCTTCAAT
1 TGCATAAGTATTCTTCAAT
27419703 TGCA
1 TGCA
27419707 CCCAGGAATG
Statistics
Matches: 31, Mismatches: 5, Indels: 10
0.67 0.11 0.22
Matches are distributed among these distances:
17 2 0.06
18 12 0.39
19 16 0.52
20 1 0.03
ACGTcount: A:0.33, C:0.20, G:0.10, T:0.37
Consensus pattern (19 bp):
TGCATAAGTATTCTTCAAT
Found at i:27419725 original size:37 final size:36
Alignment explanation
Indices: 27419629--27419725 Score: 113
Period size: 37 Copynumber: 2.6 Consensus size: 36
27419619 ATTTCCGGAA
*
27419629 TGCACCCAAGACTGTCGCTGCATAAATATTCTTCAAT
1 TGCACCC-AGAATGTCGCTGCATAAATATTCTTCAAT
* * ** *
27419666 TGCATCCAGAACTATCATTGCATAAGTATTCTTCAAT
1 TGCACCCAGAA-TGTCGCTGCATAAATATTCTTCAAT
27419703 TGCACCCAGGAATGTCGCTGCAT
1 TGCACCCA-GAATGTCGCTGCAT
27419726 GAACATGTCC
Statistics
Matches: 48, Mismatches: 10, Indels: 4
0.77 0.16 0.06
Matches are distributed among these distances:
36 3 0.06
37 42 0.88
38 3 0.06
ACGTcount: A:0.29, C:0.26, G:0.15, T:0.30
Consensus pattern (36 bp):
TGCACCCAGAATGTCGCTGCATAAATATTCTTCAAT
Found at i:27419744 original size:26 final size:26
Alignment explanation
Indices: 27419715--27419767 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
27419705 CACCCAGGAA
*
27419715 TGTCGCTGCATGAACATGTCCAGAAT
1 TGTCGCTGCATGAACATGTCAAGAAT
*
27419741 TGTCGCTGCATGAACGTGTCAAGAAT
1 TGTCGCTGCATGAACATGTCAAGAAT
27419767 T
1 T
27419768 ACGCCCAGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.26, C:0.21, G:0.25, T:0.28
Consensus pattern (26 bp):
TGTCGCTGCATGAACATGTCAAGAAT
Found at i:27420131 original size:26 final size:26
Alignment explanation
Indices: 27420091--27420143 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
27420081 AGAGGAGAGT
*
27420091 AAGAGAGCAAGTCGAGTAGCCTAGAC
1 AAGAGAGCAAATCGAGTAGCCTAGAC
27420117 AAGAGAGCAAATCGAGTAGCCTAGAC
1 AAGAGAGCAAATCGAGTAGCCTAGAC
27420143 A
1 A
27420144 TAGTATTCTC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.42, C:0.19, G:0.28, T:0.11
Consensus pattern (26 bp):
AAGAGAGCAAATCGAGTAGCCTAGAC
Found at i:27420614 original size:16 final size:16
Alignment explanation
Indices: 27420593--27420623 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
27420583 TTATGGATCC
27420593 CATTTTACCTTTATTA
1 CATTTTACCTTTATTA
*
27420609 CATTTTATCTTTATT
1 CATTTTACCTTTATT
27420624 TTCACATTAT
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:0.23, C:0.16, G:0.00, T:0.61
Consensus pattern (16 bp):
CATTTTACCTTTATTA
Found at i:27424567 original size:15 final size:15
Alignment explanation
Indices: 27424512--27424567 Score: 51
Period size: 15 Copynumber: 3.7 Consensus size: 15
27424502 TCTCCATTTC
* *
27424512 CTTTTTCTTCTTCAG
1 CTTTTCCTTCTTCAT
*
27424527 CTTTCTCCTTC-TCTT
1 CTTT-TCCTTCTTCAT
* *
27424542 CTGTGCCTTCTTCAT
1 CTTTTCCTTCTTCAT
27424557 CTTTTCCTTCT
1 CTTTTCCTTCT
27424568 CCTTCTTCTT
Statistics
Matches: 31, Mismatches: 8, Indels: 4
0.72 0.19 0.09
Matches are distributed among these distances:
14 5 0.16
15 21 0.68
16 5 0.16
ACGTcount: A:0.04, C:0.34, G:0.05, T:0.57
Consensus pattern (15 bp):
CTTTTCCTTCTTCAT
Found at i:27424572 original size:18 final size:18
Alignment explanation
Indices: 27424551--27424585 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
27424541 TCTGTGCCTT
27424551 CTTCATCTTTTCCTTCTC
1 CTTCATCTTTTCCTTCTC
* *
27424569 CTTCTTCTTTTTCTTCT
1 CTTCATCTTTTCCTTCT
27424586 AGACCCACAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.03, C:0.34, G:0.00, T:0.63
Consensus pattern (18 bp):
CTTCATCTTTTCCTTCTC
Found at i:27424575 original size:24 final size:26
Alignment explanation
Indices: 27424516--27424577 Score: 65
Period size: 30 Copynumber: 2.3 Consensus size: 26
27424506 CATTTCCTTT
27424516 TTCTTCTTCAGCTTTCTCCTTCTCTTC
1 TTCTTCTTCAGCTTTCTCCTTCTC-TC
*
27424543 TGTGCCTTCTTCATCTTT-TCCTTCTC-C
1 T-T--CTTCTTCAGCTTTCTCCTTCTCTC
27424570 TTCTTCTT
1 TTCTTCTT
27424578 TTTCTTCTAG
Statistics
Matches: 31, Mismatches: 1, Indels: 9
0.76 0.02 0.22
Matches are distributed among these distances:
24 6 0.19
26 1 0.03
27 3 0.10
28 1 0.03
29 8 0.26
30 12 0.39
ACGTcount: A:0.03, C:0.35, G:0.05, T:0.56
Consensus pattern (26 bp):
TTCTTCTTCAGCTTTCTCCTTCTCTC
Found at i:27442386 original size:27 final size:27
Alignment explanation
Indices: 27442356--27442549 Score: 169
Period size: 27 Copynumber: 7.2 Consensus size: 27
27442346 ATCTTGCTTA
* *
27442356 AATGAGTGATATTTTGTATTTGGCTCG
1 AATGAGCGATATTCTGTATTTGGCTCG
*
27442383 AATGAACGATATTCTGTATTTGGCTCG
1 AATGAGCGATATTCTGTATTTGGCTCG
*
27442410 AATGAACGATATTCTGTATTTGGCTCG
1 AATGAGCGATATTCTGTATTTGGCTCG
* * *
27442437 AATGAGCGATATTCTGTATATGTCTCA
1 AATGAGCGATATTCTGTATTTGGCTCG
* * * * * *
27442464 AATGCGTGATATTTTTTATCTAGCTC-
1 AATGAGCGATATTCTGTATTTGGCTCG
** *
27442490 ACATGCA-CGATATTCTGTATCCGACTCG
1 A-ATG-AGCGATATTCTGTATTTGGCTCG
* * *
27442518 AATGCA-CGATATTCTATCTCTGGCTCG
1 AATG-AGCGATATTCTGTATTTGGCTCG
27442545 AATGA
1 AATGA
27442550 ATGCTATTAT
Statistics
Matches: 139, Mismatches: 25, Indels: 7
0.81 0.15 0.04
Matches are distributed among these distances:
26 2 0.01
27 136 0.98
28 1 0.01
ACGTcount: A:0.26, C:0.17, G:0.20, T:0.37
Consensus pattern (27 bp):
AATGAGCGATATTCTGTATTTGGCTCG
Found at i:27442428 original size:54 final size:54
Alignment explanation
Indices: 27442363--27442550 Score: 189
Period size: 54 Copynumber: 3.5 Consensus size: 54
27442353 TTAAATGAGT
* * * * *
27442363 GATATTTTGTATTTGGCTCGAATGAACGATATTCTGTATTTGGCTCGAATGAAC
1 GATATTCTGTATCTGGCTCGAATGAACGATATTCTGTATATGACTCGAATGCAC
* * * * **
27442417 GATATTCTGTATTTGGCTCGAATGAGCGATATTCTGTATATGTCTCAAATGCGT
1 GATATTCTGTATCTGGCTCGAATGAACGATATTCTGTATATGACTCGAATGCAC
* * * * **
27442471 GATATTTTTTATCTAGCTC-ACATGCACGATATTCTGTATCCGACTCGAATGCAC
1 GATATTCTGTATCTGGCTCGA-ATGAACGATATTCTGTATATGACTCGAATGCAC
* *
27442525 GATATTCTATCTCTGGCTCGAATGAA
1 GATATTCTGTATCTGGCTCGAATGAA
27442551 TGCTATTATG
Statistics
Matches: 107, Mismatches: 25, Indels: 4
0.79 0.18 0.03
Matches are distributed among these distances:
53 1 0.01
54 105 0.98
55 1 0.01
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.37
Consensus pattern (54 bp):
GATATTCTGTATCTGGCTCGAATGAACGATATTCTGTATATGACTCGAATGCAC
Found at i:27459182 original size:17 final size:17
Alignment explanation
Indices: 27459162--27459217 Score: 55
Period size: 17 Copynumber: 3.3 Consensus size: 17
27459152 ATTGTCATTA
27459162 CATTTTTATTGTCTCTG
1 CATTTTTATTGTCTCTG
27459179 CA-TTTTACTTGT-TCTCG
1 CATTTTTA-TTGTCTCT-G
*
27459196 CATTTTCATTGTCGT-TG
1 CATTTTTATTGTC-TCTG
27459213 CATTT
1 CATTT
27459218 CCATTAATAT
Statistics
Matches: 33, Mismatches: 1, Indels: 10
0.75 0.02 0.23
Matches are distributed among these distances:
16 8 0.24
17 19 0.58
18 5 0.15
19 1 0.03
ACGTcount: A:0.12, C:0.20, G:0.12, T:0.55
Consensus pattern (17 bp):
CATTTTTATTGTCTCTG
Found at i:27464577 original size:15 final size:14
Alignment explanation
Indices: 27464554--27464613 Score: 66
Period size: 15 Copynumber: 4.1 Consensus size: 14
27464544 TTTCATTTAT
*
27464554 TATCCTTTCGAATA
1 TATCCTTTCAAATA
27464568 TATCCTTTTCAAATA
1 TATCC-TTTCAAATA
* *
27464583 TATCCATTCAGATA
1 TATCCTTTCAAATA
*
27464597 TAACCTTTTCAAATA
1 TATCC-TTTCAAATA
27464612 TA
1 TA
27464614 CTTTCGGATA
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
14 16 0.42
15 22 0.58
ACGTcount: A:0.35, C:0.20, G:0.03, T:0.42
Consensus pattern (14 bp):
TATCCTTTCAAATA
Found at i:27464612 original size:27 final size:29
Alignment explanation
Indices: 27464565--27464629 Score: 80
Period size: 27 Copynumber: 2.3 Consensus size: 29
27464555 ATCCTTTCGA
* *
27464565 ATATATCCTTTTCAAATATATCCATTCAG
1 ATATAACCTTTTCAAATATATACATTCAG
* *
27464594 ATATAACCTTTTC-AA-ATATACTTTCGG
1 ATATAACCTTTTCAAATATATACATTCAG
27464621 ATATAACCT
1 ATATAACCT
27464630 AATCAATGAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
27 18 0.56
28 2 0.06
29 12 0.38
ACGTcount: A:0.35, C:0.20, G:0.05, T:0.40
Consensus pattern (29 bp):
ATATAACCTTTTCAAATATATACATTCAG
Found at i:27464635 original size:27 final size:28
Alignment explanation
Indices: 27464593--27464653 Score: 79
Period size: 29 Copynumber: 2.2 Consensus size: 28
27464583 TATCCATTCA
**
27464593 GATATAACCTTTTCAA-ATATACTTTCG
1 GATATAACCTAATCAAGATATACTTTCG
*
27464620 GATATAACCTAATCAATGATATCCTTTCG
1 GATATAACCTAATCAA-GATATACTTTCG
27464649 GATAT
1 GATAT
27464654 CTCTTTTCAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 14 0.48
29 15 0.52
ACGTcount: A:0.34, C:0.18, G:0.10, T:0.38
Consensus pattern (28 bp):
GATATAACCTAATCAAGATATACTTTCG
Found at i:27464642 original size:56 final size:55
Alignment explanation
Indices: 27464582--27464845 Score: 139
Period size: 56 Copynumber: 4.8 Consensus size: 55
27464572 CTTTTCAAAT
*
27464582 ATATCCATTCAGATATAAC-CTTTTCA-AATATACTTTCGGATATAACCTAATCAATG
1 ATATCC-TTCAGATAT--CTCTTTTCATAATATACTTACGGATATAACCTAATCAATG
* * * ** *
27464638 ATATCCTTTCGGATATCTCTTTTCATACTATTCTTACGGATATAACCTTTTCATTG
1 ATATCC-TTCAGATATCTCTTTTCATAATATACTTACGGATATAACCTAATCAATG
* * * ** *
27464694 ATATCCTTGCAGATATCCCTTTT--TAATAATA-TT-CGCATAT-TCCTTTTCATTG
1 ATATCCTT-CAGATATCTCTTTTCATAAT-ATACTTACGGATATAACCTAATCAATG
* * * * * * ** * *
27464746 ATATCCTTGCGGATATCCCTTTTTAATAATATCCTTACGGGTAT-TCCTTTTCATTA
1 ATATCCTT-CAGATATCTC-TTTTCATAATATACTTACGGATATAACCTAATCAATG
* * * *
27464802 ATATCCCTGCGGATATCCCTTTTCAATAATATCCTTACGGATAT
1 ATAT-CCTTCAGATATCTCTTTTC-ATAATATACTTACGGATAT
27464846 TCCTTTTCAT
Statistics
Matches: 175, Mismatches: 22, Indels: 22
0.80 0.10 0.10
Matches are distributed among these distances:
52 29 0.17
53 10 0.06
54 8 0.05
55 21 0.12
56 104 0.59
57 3 0.02
ACGTcount: A:0.27, C:0.22, G:0.09, T:0.42
Consensus pattern (55 bp):
ATATCCTTCAGATATCTCTTTTCATAATATACTTACGGATATAACCTAATCAATG
Found at i:27464714 original size:28 final size:28
Alignment explanation
Indices: 27464638--27464928 Score: 250
Period size: 28 Copynumber: 10.5 Consensus size: 28
27464628 CTAATCAATG
* *
27464638 ATATCCTTTCGGATATCTCTTTTCA-TA
1 ATATCCTTGCGGATATCCCTTTTCATTA
* * * * *
27464665 CTATTCTTACGGATATAACCTTTTCATTG
1 ATATCCTTGCGGATAT-CCCTTTTCATTA
* * *
27464694 ATATCCTTGCAGATATCCCTTTTTAATA
1 ATATCCTTGCGGATATCCCTTTTCATTA
* * *
27464722 ATA---TT-CGCATATTCCTTTTCATTG
1 ATATCCTTGCGGATATCCCTTTTCATTA
* *
27464746 ATATCCTTGCGGATATCCCTTTTTAATA
1 ATATCCTTGCGGATATCCCTTTTCATTA
* * *
27464774 ATATCCTTACGGGTATTCCTTTTCATTA
1 ATATCCTTGCGGATATCCCTTTTCATTA
* *
27464802 ATATCCCTGCGGATATCCCTTTTCAATA
1 ATATCCTTGCGGATATCCCTTTTCATTA
* * *
27464830 ATATCCTTACGGATATTCCTTTTCATTG
1 ATATCCTTGCGGATATCCCTTTTCATTA
* * *
27464858 ATATCCTTGCTGATATTCCTTTTCATTG
1 ATATCCTTGCGGATATCCCTTTTCATTA
* * * *
27464886 ATACCCTTGCGGATATCTCTTCTCAATA
1 ATATCCTTGCGGATATCCCTTTTCATTA
* *
27464914 ATATCTTTACGGATA
1 ATATCCTTGCGGATA
27464929 AAGAAATCAA
Statistics
Matches: 206, Mismatches: 52, Indels: 11
0.77 0.19 0.04
Matches are distributed among these distances:
24 16 0.08
25 2 0.01
27 15 0.07
28 160 0.78
29 13 0.06
ACGTcount: A:0.24, C:0.22, G:0.10, T:0.44
Consensus pattern (28 bp):
ATATCCTTGCGGATATCCCTTTTCATTA
Found at i:27464795 original size:108 final size:111
Alignment explanation
Indices: 27464636--27464880 Score: 318
Period size: 108 Copynumber: 2.2 Consensus size: 111
27464626 ACCTAATCAA
* * * * * *
27464636 TGATATCCTTTCGGATATCTC-TTTTCATACTATTCTTACGGATATAACCTTTTCATTGATATCC
1 TGATATCCTTGCGGATATCCCTTTTTAATAATATCCTTACGGATATAACCTTTTCATTAATATCC
* *
27464700 TTGCAGATATCCCTTTTTAATAATA-TT-CGCATATTCCTTTTCAT
66 CTGCAGATATCCCTTTTCAATAATACTTACGCATATTCCTTTTCAT
* *
27464744 TGATATCCTTGCGGATATCCCTTTTTAATAATATCCTTACGGGTAT-TCCTTTTCATTAATATCC
1 TGATATCCTTGCGGATATCCCTTTTTAATAATATCCTTACGGATATAACCTTTTCATTAATATCC
* *
27464808 CTGCGGATATCCCTTTTCAATAATATCCTTACGGATATTCCTTTTCAT
66 CTGCAGATATCCCTTTTCAATAATA--CTTACGCATATTCCTTTTCAT
* *
27464856 TGATATCCTTGCTGATATTCCTTTT
1 TGATATCCTTGCGGATATCCCTTTT
27464881 CATTGATACC
Statistics
Matches: 118, Mismatches: 14, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
108 57 0.48
109 20 0.17
111 2 0.02
112 39 0.33
ACGTcount: A:0.23, C:0.22, G:0.10, T:0.45
Consensus pattern (111 bp):
TGATATCCTTGCGGATATCCCTTTTTAATAATATCCTTACGGATATAACCTTTTCATTAATATCC
CTGCAGATATCCCTTTTCAATAATACTTACGCATATTCCTTTTCAT
Found at i:27464847 original size:56 final size:56
Alignment explanation
Indices: 27464636--27464901 Score: 326
Period size: 56 Copynumber: 4.8 Consensus size: 56
27464626 ACCTAATCAA
* * * * *
27464636 TGATATCCTTTCGGATATCTCTTTTC-ATACTATTCTTACGGATATAACCTTTTCAT
1 TGATATCCTTGCGGATATCCCTTTTCAATAATATCCTTACGGATAT-TCCTTTTCAT
* * *
27464692 TGATATCCTTGCAGATATCCCTTTTTAATAATA---TT-CGCATATTCCTTTTCAT
1 TGATATCCTTGCGGATATCCCTTTTCAATAATATCCTTACGGATATTCCTTTTCAT
* *
27464744 TGATATCCTTGCGGATATCCCTTTTTAATAATATCCTTACGGGTATTCCTTTTCAT
1 TGATATCCTTGCGGATATCCCTTTTCAATAATATCCTTACGGATATTCCTTTTCAT
* *
27464800 TAATATCCCTGCGGATATCCCTTTTCAATAATATCCTTACGGATATTCCTTTTCAT
1 TGATATCCTTGCGGATATCCCTTTTCAATAATATCCTTACGGATATTCCTTTTCAT
* * * * * *
27464856 TGATATCCTTGCTGATATTCCTTTTCATTGATACCCTTGCGGATAT
1 TGATATCCTTGCGGATATCCCTTTTCAATAATATCCTTACGGATAT
27464902 CTCTTCTCAA
Statistics
Matches: 183, Mismatches: 22, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
52 41 0.22
53 6 0.03
54 2 0.01
55 2 0.01
56 127 0.69
57 5 0.03
ACGTcount: A:0.23, C:0.22, G:0.11, T:0.44
Consensus pattern (56 bp):
TGATATCCTTGCGGATATCCCTTTTCAATAATATCCTTACGGATATTCCTTTTCAT
Found at i:27468620 original size:36 final size:36
Alignment explanation
Indices: 27468533--27468768 Score: 172
Period size: 36 Copynumber: 6.6 Consensus size: 36
27468523 TCGATGGAGA
* * * * *
27468533 GCTTACGTCTCGATTAGAGCGTAATGCTATGTGAGT
1 GCTTACATCTCGGTTAGAGCGTATTGCTATGTAATT
* ** *
27468569 GCATATGTTTCGGTTAGAGCGTATTGCTATGTAATT
1 GCTTACATCTCGGTTAGAGCGTATTGCTATGTAATT
* * * * *
27468605 GCTTACATCTTGGTTAGAGTGTAATGTTAAG-AGATT
1 GCTTACATCTCGGTTAGAGCGTATTGCTATGTA-ATT
* * ** * * *
27468641 TCTTACATCTCGATTAGAGAATAATGCTATGTGATC
1 GCTTACATCTCGGTTAGAGCGTATTGCTATGTAATT
* * **
27468677 GCATACGTCTTAGTTAGAGCGTATTGCTATGTAATT
1 GCTTACATCTCGGTTAGAGCGTATTGCTATGTAATT
*
27468713 GCTTACATCTCGATTAGAGCGTAATT-CTAAT-TAATT
1 GCTTACATCTCGGTTAGAGCGT-ATTGCT-ATGTAATT
**
27468749 GCTTATGTCTCGGTTAGAGC
1 GCTTACATCTCGGTTAGAGC
27468769 ATAAGGCCAT
Statistics
Matches: 152, Mismatches: 44, Indels: 8
0.75 0.22 0.04
Matches are distributed among these distances:
35 1 0.01
36 146 0.96
37 5 0.03
ACGTcount: A:0.25, C:0.14, G:0.22, T:0.38
Consensus pattern (36 bp):
GCTTACATCTCGGTTAGAGCGTATTGCTATGTAATT
Found at i:27468760 original size:108 final size:108
Alignment explanation
Indices: 27468533--27468772 Score: 308
Period size: 108 Copynumber: 2.2 Consensus size: 108
27468523 TCGATGGAGA
* * *
27468533 GCTTACGTCTCGATTAGAGCGTAATGCTATGTGAGTGCATATGTTTCGGTTAGAGCGTATTGCTA
1 GCTTACGTCTCGATTAGAGCATAATGCTATGTGAGTGCATACGTTTCAGTTAGAGCGTATTGCTA
* * *
27468598 TGTAATTGCTTACATCTTGGTTAGAGTGTAATGTTAAGAGATT
66 TGTAATTGCTTACATCTCGATTAGAGCGTAATGTTAAGAGATT
* * *
27468641 TCTTACATCTCGATTAGAGAATAATGCTATGTGA-TCGCATACGTCTT-AGTTAGAGCGTATTGC
1 GCTTACGTCTCGATTAGAGCATAATGCTATGTGAGT-GCATACGT-TTCAGTTAGAGCGTATTGC
*
27468704 TATGTAATTGCTTACATCTCGATTAGAGCGTAAT-TCTAATTA-ATT
64 TATGTAATTGCTTACATCTCGATTAGAGCGTAATGT-TAA-GAGATT
* *
27468749 GCTTATGTCTCGGTTAGAGCATAA
1 GCTTACGTCTCGATTAGAGCATAA
27468773 GGCCATTTCA
Statistics
Matches: 113, Mismatches: 15, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
107 2 0.02
108 108 0.96
109 3 0.03
ACGTcount: A:0.26, C:0.14, G:0.22, T:0.38
Consensus pattern (108 bp):
GCTTACGTCTCGATTAGAGCATAATGCTATGTGAGTGCATACGTTTCAGTTAGAGCGTATTGCTA
TGTAATTGCTTACATCTCGATTAGAGCGTAATGTTAAGAGATT
Found at i:27471946 original size:72 final size:72
Alignment explanation
Indices: 27471863--27472000 Score: 240
Period size: 72 Copynumber: 1.9 Consensus size: 72
27471853 GTTTTGTAAG
*
27471863 TGCATATGTCTCGATTAGAGCGTATTGCTATGTAATTGCTTACGTCTCGGTTAGAGCGTAATGCT
1 TGCATATGTCTCGATTAGAGCGTATTGCTATGTAATTGCTTACGTCTCAGTTAGAGCGTAATGCT
27471928 ATGCGAT
66 ATGCGAT
* * *
27471935 TGCATATGTCTCGGTTATAGCGTATTGCTATGTAATTGCTTACGTCTTAGTTAGAGCGTAATGCT
1 TGCATATGTCTCGATTAGAGCGTATTGCTATGTAATTGCTTACGTCTCAGTTAGAGCGTAATGCT
27472000 A
66 A
27472001 ATTAATCGCT
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
72 62 1.00
ACGTcount: A:0.22, C:0.16, G:0.24, T:0.38
Consensus pattern (72 bp):
TGCATATGTCTCGATTAGAGCGTATTGCTATGTAATTGCTTACGTCTCAGTTAGAGCGTAATGCT
ATGCGAT
Found at i:27472012 original size:36 final size:36
Alignment explanation
Indices: 27471829--27472027 Score: 186
Period size: 36 Copynumber: 5.5 Consensus size: 36
27471819 CGATGGAGAT
* * * * * *
27471829 CTTACGTTTCTGTTAGAGCGTGATGTTTTGTAAGTG
1 CTTACGTCTCAGTTAGAGCGTAATGCTATGTAATTG
* * *
27471865 CATATGTCTC-GATTAGAGCGTATTGCTATGTAATTG
1 CTTACGTCTCAG-TTAGAGCGTAATGCTATGTAATTG
* **
27471901 CTTACGTCTCGGTTAGAGCGTAATGCTATGCGATTG
1 CTTACGTCTCAGTTAGAGCGTAATGCTATGTAATTG
* * * * *
27471937 CATATGTCTCGGTTATAGCGTATTGCTATGTAATTG
1 CTTACGTCTCAGTTAGAGCGTAATGCTATGTAATTG
* *
27471973 CTTACGTCTTAGTTAGAGCGTAATGCTAAT-TAATCG
1 CTTACGTCTCAGTTAGAGCGTAATGCT-ATGTAATTG
*
27472009 CTTATGTCTCAGTTAGAGC
1 CTTACGTCTCAGTTAGAGC
27472028 ATAAGGCCAT
Statistics
Matches: 132, Mismatches: 28, Indels: 6
0.80 0.17 0.04
Matches are distributed among these distances:
35 1 0.01
36 128 0.97
37 3 0.02
ACGTcount: A:0.22, C:0.16, G:0.24, T:0.39
Consensus pattern (36 bp):
CTTACGTCTCAGTTAGAGCGTAATGCTATGTAATTG
Found at i:27472015 original size:72 final size:72
Alignment explanation
Indices: 27471829--27472027 Score: 231
Period size: 72 Copynumber: 2.8 Consensus size: 72
27471819 CGATGGAGAT
* * * * * * *
27471829 CTTACGTTTCTGTTAGAGCGTGATGTTTTGTAAGT-GCATATGTCTCGATTAGAGCGTATTGCTA
1 CTTACGTCTCAGTTAGAGCGTAATGCTATGCAA-TCGCATATGTCTCGGTTAGAGCGTATTGCTA
27471893 TGTAATTG
65 TGTAATTG
* * * *
27471901 CTTACGTCTCGGTTAGAGCGTAATGCTATGCGATTGCATATGTCTCGGTTATAGCGTATTGCTAT
1 CTTACGTCTCAGTTAGAGCGTAATGCTATGCAATCGCATATGTCTCGGTTAGAGCGTATTGCTAT
27471966 GTAATTG
66 GTAATTG
* * * *
27471973 CTTACGTCTTAGTTAGAGCGTAATGCTAAT-TAATCGCTTATGTCTCAGTTAGAGC
1 CTTACGTCTCAGTTAGAGCGTAATGCT-ATGCAATCGCATATGTCTCGGTTAGAGC
27472028 ATAAGGCCAT
Statistics
Matches: 108, Mismatches: 17, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
71 1 0.01
72 105 0.97
73 2 0.02
ACGTcount: A:0.22, C:0.16, G:0.24, T:0.39
Consensus pattern (72 bp):
CTTACGTCTCAGTTAGAGCGTAATGCTATGCAATCGCATATGTCTCGGTTAGAGCGTATTGCTAT
GTAATTG
Found at i:27473238 original size:13 final size:14
Alignment explanation
Indices: 27473220--27473250 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
27473210 TATTTTAATT
27473220 AAAATTTCAAA-CA
1 AAAATTTCAAACCA
27473233 AAAATTTCAAACCA
1 AAAATTTCAAACCA
27473247 AAAA
1 AAAA
27473251 AACACACCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.65
14 6 0.35
ACGTcount: A:0.65, C:0.16, G:0.00, T:0.19
Consensus pattern (14 bp):
AAAATTTCAAACCA
Found at i:27475022 original size:23 final size:24
Alignment explanation
Indices: 27474996--27475045 Score: 75
Period size: 23 Copynumber: 2.1 Consensus size: 24
27474986 AGAACAGAAT
27474996 AGAACACCATCCAAGCAGAT-AAC
1 AGAACACCATCCAAGCAGATAAAC
* *
27475019 AGAACACCGTCGAAGCAGATAAAC
1 AGAACACCATCCAAGCAGATAAAC
27475043 AGA
1 AGA
27475046 GAGCGAAGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 18 0.75
24 6 0.25
ACGTcount: A:0.48, C:0.26, G:0.18, T:0.08
Consensus pattern (24 bp):
AGAACACCATCCAAGCAGATAAAC
Found at i:27476587 original size:29 final size:28
Alignment explanation
Indices: 27476467--27476580 Score: 133
Period size: 29 Copynumber: 4.0 Consensus size: 28
27476457 TACCTTTCCG
27476467 ACCTTTTCAATTATTATCCTTTCGGATATA
1 ACCTTTTCAA-TA-TATCCTTTCGGATATA
* * *
27476497 TCCTTTTCAAATATATCC-ATCTAGATATA
1 ACCTTTTC-AATATATCCTTTC-GGATATA
27476526 ACCTTTTCAA-ATATCCTTTCGGATATA
1 ACCTTTTCAATATATCCTTTCGGATATA
*
27476553 ACTTTTTCAATGATATCCTTTCGGATAT
1 ACCTTTTCAAT-ATATCCTTTCGGATAT
27476581 CTCTTTTCAT
Statistics
Matches: 72, Mismatches: 7, Indels: 11
0.80 0.08 0.12
Matches are distributed among these distances:
27 21 0.29
28 6 0.08
29 34 0.47
30 9 0.12
31 2 0.03
ACGTcount: A:0.29, C:0.20, G:0.07, T:0.44
Consensus pattern (28 bp):
ACCTTTTCAATATATCCTTTCGGATATA
Found at i:27476719 original size:28 final size:28
Alignment explanation
Indices: 27476638--27476719 Score: 92
Period size: 28 Copynumber: 2.9 Consensus size: 28
27476628 TGCAAGTATC
* *
27476638 CCTTTTCAATAATATCCTTGCGCATATT
1 CCTTTTCAATAATATCATTGCGGATATT
* * *
27476666 CCTTTTCATTGATATCATTGCAGATATT
1 CCTTTTCAATAATATCATTGCGGATATT
* * *
27476694 CCTTCTCAATAATATCTTTACGGATA
1 CCTTTTCAATAATATCATTGCGGATA
27476720 AAGAAATCAA
Statistics
Matches: 43, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
28 43 1.00
ACGTcount: A:0.27, C:0.22, G:0.09, T:0.43
Consensus pattern (28 bp):
CCTTTTCAATAATATCATTGCGGATATT
Found at i:27478314 original size:13 final size:13
Alignment explanation
Indices: 27478296--27478320 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
27478286 TTTATTTTCT
27478296 TTTTGCTGTTATA
1 TTTTGCTGTTATA
27478309 TTTTGCTGTTAT
1 TTTTGCTGTTAT
27478321 CTTCCCTAAT
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:0.12, C:0.08, G:0.16, T:0.64
Consensus pattern (13 bp):
TTTTGCTGTTATA
Found at i:27479302 original size:20 final size:21
Alignment explanation
Indices: 27479279--27479319 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
27479269 AAAAATCTTT
27479279 TAAATTACAA-AAAA-TATAAA
1 TAAATTA-AATAAAATTATAAA
27479299 TAAATTAAATAAAATTATAAA
1 TAAATTAAATAAAATTATAAA
27479320 CACATATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 2 0.11
20 11 0.58
21 6 0.32
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.29
Consensus pattern (21 bp):
TAAATTAAATAAAATTATAAA
Found at i:27480240 original size:8 final size:9
Alignment explanation
Indices: 27480218--27480248 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
27480208 AAAAAAAGTA
27480218 ATTTTTTAT
1 ATTTTTTAT
27480227 ATTTTTTAT
1 ATTTTTTAT
27480236 ATTTTTTA-
1 ATTTTTTAT
27480244 ATTTT
1 ATTTT
27480249 GTAACTTATA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 5 0.23
9 17 0.77
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (9 bp):
ATTTTTTAT
Found at i:27480291 original size:8 final size:8
Alignment explanation
Indices: 27480278--27480320 Score: 59
Period size: 8 Copynumber: 5.1 Consensus size: 8
27480268 GGTATTTTAA
27480278 ATAATTTT
1 ATAATTTT
27480286 ATAATTTT
1 ATAATTTT
27480294 ATAATTTTT
1 ATAA-TTTT
27480303 ATAATTTTT
1 ATAA-TTTT
*
27480312 AAAATTTT
1 ATAATTTT
27480320 A
1 A
27480321 CTTTTTAAAG
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
8 17 0.52
9 16 0.48
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (8 bp):
ATAATTTT
Found at i:27480304 original size:9 final size:9
Alignment explanation
Indices: 27480278--27480319 Score: 61
Period size: 9 Copynumber: 4.9 Consensus size: 9
27480268 GGTATTTTAA
27480278 ATAA-TTTT
1 ATAATTTTT
27480286 ATAA-TTTT
1 ATAATTTTT
27480294 ATAATTTTT
1 ATAATTTTT
27480303 ATAATTTTT
1 ATAATTTTT
*
27480312 AAAATTTT
1 ATAATTTT
27480320 ACTTTTTAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
8 12 0.38
9 20 0.62
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (9 bp):
ATAATTTTT
Found at i:27480304 original size:17 final size:16
Alignment explanation
Indices: 27480278--27480320 Score: 59
Period size: 17 Copynumber: 2.6 Consensus size: 16
27480268 GGTATTTTAA
27480278 ATAATTTTATAATTTT
1 ATAATTTTATAATTTT
27480294 ATAATTTTTATAATTTTT
1 ATAA-TTTTATAA-TTTT
*
27480312 AAAATTTTA
1 ATAATTTTA
27480321 CTTTTTAAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 4 0.17
17 13 0.54
18 7 0.29
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
ATAATTTTATAATTTT
Found at i:27481358 original size:22 final size:22
Alignment explanation
Indices: 27481332--27481374 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
27481322 TCTCTCTATT
27481332 TTGCTACCATTTCACTATTATG
1 TTGCTACCATTTCACTATTATG
* * *
27481354 TTGCTACTATTTTATTATTAT
1 TTGCTACCATTTCACTATTAT
27481375 TATTTGAATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.23, C:0.16, G:0.07, T:0.53
Consensus pattern (22 bp):
TTGCTACCATTTCACTATTATG
Found at i:27481536 original size:21 final size:21
Alignment explanation
Indices: 27481480--27481538 Score: 59
Period size: 25 Copynumber: 2.7 Consensus size: 21
27481470 AAGCATACAT
27481480 ATTTTTAAA-ATTTATTTTCA
1 ATTTTTAAATATTTATTTTCA
27481500 ATTTGTTGAAATATATTTATTTT-A
1 ATTT-TT--AA-ATATTTATTTTCA
27481524 ATATTTTAAATATTT
1 AT-TTTTAAATATTT
27481539 TTAGTATATT
Statistics
Matches: 33, Mismatches: 0, Indels: 11
0.75 0.00 0.25
Matches are distributed among these distances:
20 4 0.12
21 8 0.24
22 2 0.06
23 2 0.06
24 6 0.18
25 11 0.33
ACGTcount: A:0.36, C:0.02, G:0.03, T:0.59
Consensus pattern (21 bp):
ATTTTTAAATATTTATTTTCA
Found at i:27481725 original size:46 final size:46
Alignment explanation
Indices: 27481656--27481747 Score: 139
Period size: 46 Copynumber: 2.0 Consensus size: 46
27481646 CCGATCGGAT
* *
27481656 TTAAACAAAATTTTAAGCCTATTTTCAAGCCGAACTTGAACTTAAC
1 TTAAACAAAATTTTAAGCCTATTTTCAAGCCGAACTTAAACCTAAC
* **
27481702 TTAAACAAAATTTTAAGCTTATTTTTGAGCCGAACTTAAACCTAAC
1 TTAAACAAAATTTTAAGCCTATTTTCAAGCCGAACTTAAACCTAAC
27481748 AAACGGGCTT
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 41 1.00
ACGTcount: A:0.39, C:0.18, G:0.09, T:0.34
Consensus pattern (46 bp):
TTAAACAAAATTTTAAGCCTATTTTCAAGCCGAACTTAAACCTAAC
Found at i:27487689 original size:19 final size:21
Alignment explanation
Indices: 27487646--27487696 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
27487636 ATTTTAAATA
*
27487646 AAATATAAATA-TAATTTTCTT
1 AAATATAAAAAGTAATTTTC-T
27487667 AAATA-AAAAAGTAATTTTC-
1 AAATATAAAAAGTAATTTTCT
27487686 AAATATAAAAA
1 AAATATAAAAA
27487697 ACATAAGAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
19 5 0.19
20 9 0.33
21 13 0.48
ACGTcount: A:0.59, C:0.04, G:0.02, T:0.35
Consensus pattern (21 bp):
AAATATAAAAAGTAATTTTCT
Found at i:27489923 original size:50 final size:50
Alignment explanation
Indices: 27489860--27490027 Score: 214
Period size: 50 Copynumber: 3.3 Consensus size: 50
27489850 TAATAAAATA
* *
27489860 ATGCATTATGTAACTCTCATGTTTGTTAAGTATGCATTATAAATAATGAC
1 ATGCATTATGTAACTCTCATGTTAGTTAAGTATGCATCATAAATAATGAC
* *
27489910 ATGCATTATGTAACTCTCATGTTAGTTAAGTTTGCATCATAAATTATGAC
1 ATGCATTATGTAACTCTCATGTTAGTTAAGTATGCATCATAAATAATGAC
* * *
27489960 ATGCATTACGTAACTCTCATGTTAGTTAAAGCT-TACATCATTAAATTAA-GTC
1 ATGCATTATGTAACTCTCATGTTAGTT-AAG-TATGCATCA-TAAA-TAATGAC
*
27490012 ATGCATTAAGTAACTC
1 ATGCATTATGTAACTC
27490028 ATTTGTTCAT
Statistics
Matches: 105, Mismatches: 9, Indels: 6
0.88 0.08 0.05
Matches are distributed among these distances:
50 72 0.69
51 9 0.09
52 22 0.21
53 2 0.02
ACGTcount: A:0.34, C:0.15, G:0.13, T:0.38
Consensus pattern (50 bp):
ATGCATTATGTAACTCTCATGTTAGTTAAGTATGCATCATAAATAATGAC
Found at i:27490202 original size:55 final size:55
Alignment explanation
Indices: 27490155--27490264 Score: 202
Period size: 55 Copynumber: 2.0 Consensus size: 55
27490145 AGTTATAGTG
*
27490155 TGTTTATTTTCATAAATAAATATGTGTATCTCTAGTTAATTGATAAGTTGAATAA
1 TGTTTATTTTCATAAATAAAAATGTGTATCTCTAGTTAATTGATAAGTTGAATAA
*
27490210 TGTTTATTTTCATAAATAAAAATGTGTGTCTCTAGTTAATTGATAAGTTGAATAA
1 TGTTTATTTTCATAAATAAAAATGTGTATCTCTAGTTAATTGATAAGTTGAATAA
27490265 GAATGTGAAA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
55 53 1.00
ACGTcount: A:0.36, C:0.05, G:0.14, T:0.45
Consensus pattern (55 bp):
TGTTTATTTTCATAAATAAAAATGTGTATCTCTAGTTAATTGATAAGTTGAATAA
Found at i:27491467 original size:27 final size:28
Alignment explanation
Indices: 27491434--27491517 Score: 107
Period size: 27 Copynumber: 3.0 Consensus size: 28
27491424 TCTCAAAATT
*
27491434 AGAAAAAAATTGAAATATTGTAAAAAAG
1 AGAAAAAAATTGAAATATTGAAAAAAAG
** *
27491462 AG-AAAATTTTGAAATATTAAAAAAAAG
1 AGAAAAAAATTGAAATATTGAAAAAAAG
27491489 AGAAAAAAAATTTGAAATATTGAAAAAAA
1 AG-AAAAAAA-TTGAAATATTGAAAAAAA
27491518 TTGAAGTAAA
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
27 23 0.50
28 2 0.04
29 4 0.09
30 17 0.37
ACGTcount: A:0.65, C:0.00, G:0.12, T:0.23
Consensus pattern (28 bp):
AGAAAAAAATTGAAATATTGAAAAAAAG
Found at i:27493466 original size:20 final size:20
Alignment explanation
Indices: 27493441--27493482 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
27493431 AGATTGAGAG
27493441 AAGAAAAAAAGAAGT-AGAAA
1 AAGAAAAAAA-AAGTGAGAAA
*
27493461 AAGAAAAAGAAAGTGAGAAA
1 AAGAAAAAAAAAGTGAGAAA
27493481 AA
1 AA
27493483 AAGAGAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.74, C:0.00, G:0.21, T:0.05
Consensus pattern (20 bp):
AAGAAAAAAAAAGTGAGAAA
Found at i:27493469 original size:18 final size:20
Alignment explanation
Indices: 27493446--27493482 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
27493436 GAGAGAAGAA
27493446 AAAAAG-AAGT-AGAAAAAG
1 AAAAAGAAAGTGAGAAAAAG
27493464 AAAAAGAAAGTGAGAAAAA
1 AAAAAGAAAGTGAGAAAAA
27493483 AAGAGAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
19 4 0.24
20 7 0.41
ACGTcount: A:0.73, C:0.00, G:0.22, T:0.05
Consensus pattern (20 bp):
AAAAAGAAAGTGAGAAAAAG
Found at i:27493489 original size:18 final size:18
Alignment explanation
Indices: 27493438--27493490 Score: 56
Period size: 18 Copynumber: 2.9 Consensus size: 18
27493428 GAGAGATTGA
27493438 GAGAAGAAAAAAAG-AAGT
1 GAGAA-AAAAAAAGAAAGT
27493456 -AGAAAAAGAAAAAGAAAGT
1 GAG-AAAA-AAAAAGAAAGT
*
27493475 GAGAAAAAAAGAGAAA
1 GAGAAAAAAAAAGAAA
27493491 AAGAATTTGA
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
17 4 0.13
18 16 0.53
19 8 0.27
20 2 0.07
ACGTcount: A:0.72, C:0.00, G:0.25, T:0.04
Consensus pattern (18 bp):
GAGAAAAAAAAAGAAAGT
Found at i:27493494 original size:24 final size:23
Alignment explanation
Indices: 27493458--27493504 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
27493448 AAAGAAGTAG
27493458 AAAAAGAAAAAGAAAGTGAGAAA
1 AAAAAGAAAAAGAAAGTGAGAAA
**
27493481 AAAAGAGAAAAAGAATTTGAGAAA
1 AAAA-AGAAAAAGAAAGTGAGAAA
27493505 GTGGAAGGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 4 0.19
24 17 0.81
ACGTcount: A:0.70, C:0.00, G:0.21, T:0.09
Consensus pattern (23 bp):
AAAAAGAAAAAGAAAGTGAGAAA
Found at i:27494663 original size:50 final size:50
Alignment explanation
Indices: 27494597--27494815 Score: 253
Period size: 50 Copynumber: 4.3 Consensus size: 50
27494587 TTCATAAAGT
* *
27494597 CATGTATTGTGTAACTCTCATATTAGTTAAGTATACATCATAAATAATGA
1 CATGCATTATGTAACTCTCATATTAGTTAAGTATACATCATAAATAATGA
* * * *
27494647 CATGCATTATGTAACTCTCATATTAGTTAAGTATAAATTATCAATAAAGA
1 CATGCATTATGTAACTCTCATATTAGTTAAGTATACATCATAAATAATGA
* * * *
27494697 CATGCATTATGTAACTCTCATGTTAGTTAAGTTTTCATCATAAATCATGA
1 CATGCATTATGTAACTCTCATATTAGTTAAGTATACATCATAAATAATGA
* * * *
27494747 CATGCATTATGTAACTC-CAATGTTAGTTAAAGTTTGCATCATTAAATTAA-GT
1 CATGCATTATGTAACTCTC-ATATTAGTT-AAGTATACATCA-TAAA-TAATGA
*
27494799 CATGCATTAAGTAACTC
1 CATGCATTATGTAACTC
27494816 ATTTGTTCAT
Statistics
Matches: 147, Mismatches: 18, Indels: 6
0.86 0.11 0.04
Matches are distributed among these distances:
49 1 0.01
50 112 0.76
51 11 0.07
52 21 0.14
53 2 0.01
ACGTcount: A:0.37, C:0.14, G:0.12, T:0.37
Consensus pattern (50 bp):
CATGCATTATGTAACTCTCATATTAGTTAAGTATACATCATAAATAATGA
Done.