Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold197
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: 573162
ACGTcount: A:0.30, C:0.16, G:0.15, T:0.31
Warning! 46325 characters in sequence are not A, C, G, or T
File 4 of 5
Found at i:360353 original size:27 final size:27
Alignment explanation
Indices: 360313--360396 Score: 70
Period size: 27 Copynumber: 3.2 Consensus size: 27
360303 AAACGTTTTA
*
360313 AAAAAATT-ATAAAACAAAAAAATTAT
1 AAAAAATTAAAAAAACAAAAAAATTAT
**
360339 AAAAAATTAAAAAAATTAAAAAATTGA-
1 AAAAAATTAAAAAAACAAAAAAATT-AT
*
360366 AAAAAA--AAGAAAACCTAAAAAAATT-T
1 AAAAAATTAA-AAAAAC-AAAAAAATTAT
360392 AAAAA
1 AAAAA
360397 CGTTTTAAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 10
0.75 0.10 0.16
Matches are distributed among these distances:
25 2 0.04
26 17 0.36
27 27 0.57
28 1 0.02
ACGTcount: A:0.75, C:0.04, G:0.02, T:0.19
Consensus pattern (27 bp):
AAAAAATTAAAAAAACAAAAAAATTAT
Found at i:360369 original size:10 final size:9
Alignment explanation
Indices: 360310--360444 Score: 86
Period size: 8 Copynumber: 15.0 Consensus size: 9
360300 TAAAAACGTT
360310 TTAAAAAAA
1 TTAAAAAAA
*
360319 TT-ATAAAA
1 TTAAAAAAA
*
360327 -CAAAAAAA
1 TTAAAAAAA
360335 TTATAAAAAA
1 TTA-AAAAAA
360345 TTAAAAAAA
1 TTAAAAAAA
360354 TT-AAAAAA
1 TTAAAAAAA
360362 TTGAAAAAAA
1 TT-AAAAAAA
*
360372 --AAGAAAAC
1 TTAA-AAAAA
*
360380 CTAAAAAAA
1 TTAAAAAAA
**
360389 TTTAAAAACGTT
1 -TTAAAAA--AA
360401 TTAAAAAAA
1 TTAAAAAAA
*
360410 TT-GAAAAA
1 TTAAAAAAA
*
360418 -TAAAAAAT
1 TTAAAAAAA
360426 TATAAAAAAA
1 T-TAAAAAAA
360436 TTAAAAAAA
1 TTAAAAAAA
360445 ATTAGGCTCA
Statistics
Matches: 97, Mismatches: 15, Indels: 28
0.69 0.11 0.20
Matches are distributed among these distances:
7 3 0.03
8 31 0.32
9 25 0.26
10 31 0.32
11 7 0.07
ACGTcount: A:0.72, C:0.03, G:0.03, T:0.22
Consensus pattern (9 bp):
TTAAAAAAA
Found at i:360445 original size:10 final size:10
Alignment explanation
Indices: 360328--360448 Score: 64
Period size: 10 Copynumber: 13.0 Consensus size: 10
360318 ATTATAAAAC
360328 AAAAAAATTA
1 AAAAAAATTA
*
360338 TAAAAAATT-
1 AAAAAAATTA
360347 AAAAAAATT-
1 AAAAAAATTA
*
360356 -AAAAAATTG
1 AAAAAAATTA
360365 AAAAAAA--A
1 AAAAAAATTA
* **
360373 AGAAAACCTA
1 AAAAAAATTA
*
360383 AAAAAATTTA
1 AAAAAAATTA
*** *
360393 AAAACGTTTT
1 AAAAAAATTA
360403 AAAAAAATT-
1 AAAAAAATTA
*
360412 -GAAAAA-T-
1 AAAAAAATTA
360419 -AAAAAATTA
1 AAAAAAATTA
360428 TAAAAAAATTA
1 -AAAAAAATTA
360439 AAAAAAATTA
1 AAAAAAATTA
360449 GGCTCACCCC
Statistics
Matches: 87, Mismatches: 16, Indels: 16
0.73 0.13 0.13
Matches are distributed among these distances:
7 6 0.07
8 19 0.22
9 8 0.09
10 45 0.52
11 9 0.10
ACGTcount: A:0.72, C:0.02, G:0.03, T:0.22
Consensus pattern (10 bp):
AAAAAAATTA
Found at i:360871 original size:135 final size:133
Alignment explanation
Indices: 360653--360923 Score: 348
Period size: 135 Copynumber: 2.0 Consensus size: 133
360643 CTTATTTTTG
* * * *
360653 TATATTATTAATATTTAATTTTATATAGTTACTATACTTCATGTTATTGTATTGCTATATAAATA
1 TATATTATTAATATTTAAGTTTATAAAGTTACTATACTTCATGTTATTATATTACTATATAAATA
* * * * * * *
360718 TTAATTTATATTATTAAATTATGTTATTAATACATTTA-TTCTATATTCAGTACATGTAATACAT
66 TCAATTTATATTACTAAATTATATTATTAATAAATTTACTTC-ACATTCAGTAAATGTAACACAT
360782 ACTA
130 ACTA
** *
360786 TATATTATTAATATTTAAGTTTATAAAGTTATCATATACTTTGTGTTATTATATTATTATATAAA
1 TATATTATTAATATTTAAGTTTATAAAGTTA-C-TATACTTCATGTTATTATATTACTATATAAA
* *
360851 TATCAATTGT-TATTACTAAATTATATTATTAATAAATTTACTTCACGTTTAGTAAATGTAACAC
64 TATCAATT-TATATTACTAAATTATATTATTAATAAATTTACTTCACATTCAGTAAATGTAACAC
360915 ATACTA
128 ATACTA
360921 TAT
1 TAT
360924 TCACTATACA
Statistics
Matches: 118, Mismatches: 16, Indels: 6
0.84 0.11 0.04
Matches are distributed among these distances:
133 29 0.25
134 1 0.01
135 84 0.71
136 4 0.03
ACGTcount: A:0.38, C:0.07, G:0.06, T:0.49
Consensus pattern (133 bp):
TATATTATTAATATTTAAGTTTATAAAGTTACTATACTTCATGTTATTATATTACTATATAAATA
TCAATTTATATTACTAAATTATATTATTAATAAATTTACTTCACATTCAGTAAATGTAACACATA
CTA
Found at i:361936 original size:11 final size:11
Alignment explanation
Indices: 361922--361964 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
361912 TTTTATTTAA
361922 TAATATATTAT
1 TAATATATTAT
361933 TAATATAATTAT
1 TAATAT-ATTAT
361945 ATAATA-ATTAT
1 -TAATATATTAT
*
361956 AAATATATT
1 TAATATATT
361965 TTCATAAATT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
10 4 0.14
11 14 0.50
12 5 0.18
13 5 0.18
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (11 bp):
TAATATATTAT
Found at i:361989 original size:17 final size:17
Alignment explanation
Indices: 361954--361995 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 17
361944 TATAATAATT
361954 ATAAATATATTTTCATAA
1 ATAAA-ATATTTTCATAA
*
361972 ATTAAATATTTT-ATTAA
1 ATAAAATATTTTCA-TAA
361989 ATAAAAT
1 ATAAAAT
361996 CATATCACTA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
16 1 0.05
17 16 0.76
18 4 0.19
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (17 bp):
ATAAAATATTTTCATAA
Found at i:362196 original size:14 final size:15
Alignment explanation
Indices: 362168--362204 Score: 58
Period size: 14 Copynumber: 2.5 Consensus size: 15
362158 ATAAGTTTTG
362168 AATTTTTTTAAATTTA
1 AATTTTTTT-AATTTA
362184 AATTTTTTT-ATTTA
1 AATTTTTTTAATTTA
362198 AATTTTT
1 AATTTTT
362205 AATTTTTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 12 0.57
16 9 0.43
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (15 bp):
AATTTTTTTAATTTA
Found at i:362203 original size:13 final size:14
Alignment explanation
Indices: 362171--362209 Score: 53
Period size: 13 Copynumber: 2.8 Consensus size: 14
362161 AGTTTTGAAT
362171 TTTTTTAAATTTAAA
1 TTTTTT-AATTTAAA
*
362186 TTTTTTTATTTAAA
1 TTTTTTAATTTAAA
362200 -TTTTTAATTT
1 TTTTTTAATTT
362210 TTAAATTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
13 9 0.41
14 7 0.32
15 6 0.27
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (14 bp):
TTTTTTAATTTAAA
Found at i:368227 original size:38 final size:38
Alignment explanation
Indices: 368185--368344 Score: 153
Period size: 38 Copynumber: 4.2 Consensus size: 38
368175 GCAATTTATG
368185 AACAAAAACCACTATAT-TAAACCAGTGGCATGGTTCGA
1 AACAAAAACCACTAT-TCTAAACCAGTGGCATGGTTCGA
* * *** *
368223 AACAAAAATCACTATTTTAAATTGGTGGCACGGTTCGA
1 AACAAAAACCACTATTCTAAACCAGTGGCATGGTTCGA
* **
368261 AACAAAAATCGTTATTCTAAACCAGTGGCATGGTTCGA
1 AACAAAAACCACTATTCTAAACCAGTGGCATGGTTCGA
** * * * *
368299 AATGAAAACCGCTATTCTTAATCGGTGGCATGGTTC-A
1 AACAAAAACCACTATTCTAAACCAGTGGCATGGTTCGA
368336 ATACAAAAA
1 A-ACAAAAA
368345 TCATTATTTT
Statistics
Matches: 99, Mismatches: 21, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
37 3 0.03
38 96 0.97
ACGTcount: A:0.39, C:0.18, G:0.17, T:0.26
Consensus pattern (38 bp):
AACAAAAACCACTATTCTAAACCAGTGGCATGGTTCGA
Found at i:368366 original size:38 final size:38
Alignment explanation
Indices: 368185--368366 Score: 138
Period size: 38 Copynumber: 4.8 Consensus size: 38
368175 GCAATTTATG
*
368185 AACAAAAACCACTATAT-TAAACC-AGTGGCATGGTTCGA
1 AACAAAAATCACTAT-TCTAAACCGA-TGGCATGGTTCGA
* ** * *
368223 AACAAAAATCACTATTTTAAATTGGTGGCACGGTTCGA
1 AACAAAAATCACTATTCTAAACCGATGGCATGGTTCGA
**
368261 AACAAAAATCGTTATTCTAAACC-AGTGGCATGGTTCGA
1 AACAAAAATCACTATTCTAAACCGA-TGGCATGGTTCGA
** * * * * *
368299 AATGAAAACCGCTATTCTTAATCGGTGGCATGGTTC-A
1 AACAAAAATCACTATTCTAAACCGATGGCATGGTTCGA
* * *
368336 ATACAAAAATCATTATTTTTAACCGATGGCA
1 A-ACAAAAATCACTATTCTAAACCGATGGCA
368367 CGATTTGAAA
Statistics
Matches: 112, Mismatches: 27, Indels: 10
0.75 0.18 0.07
Matches are distributed among these distances:
37 3 0.03
38 109 0.97
ACGTcount: A:0.37, C:0.18, G:0.17, T:0.27
Consensus pattern (38 bp):
AACAAAAATCACTATTCTAAACCGATGGCATGGTTCGA
Found at i:368366 original size:76 final size:76
Alignment explanation
Indices: 368185--368352 Score: 207
Period size: 76 Copynumber: 2.2 Consensus size: 76
368175 GCAATTTATG
* * * *
368185 AACAAAAACCACTATAT-TAAACCAGTGGCATGGTTCGAAACAAAAATCACTATTTTAAATTGGT
1 AACAAAAATCATTAT-TCTAAACCAGTGGCATGGTTCGAAACAAAAACCACTATTTTAAATCGGT
368249 GGCACGGTTCGA
65 GGCACGGTTCGA
* ** *
368261 AACAAAAATCGTTATTCTAAACCAGTGGCATGGTTCGAAATGAAAACCGCTATTCTT-AATCGGT
1 AACAAAAATCATTATTCTAAACCAGTGGCATGGTTCGAAACAAAAACCACTATT-TTAAATCGGT
*
368325 GGCATGGTTC-A
65 GGCACGGTTCGA
368336 ATACAAAAATCATTATT
1 A-ACAAAAATCATTATT
368353 TTTAACCGAT
Statistics
Matches: 79, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
75 3 0.04
76 74 0.94
77 2 0.03
ACGTcount: A:0.38, C:0.18, G:0.17, T:0.27
Consensus pattern (76 bp):
AACAAAAATCATTATTCTAAACCAGTGGCATGGTTCGAAACAAAAACCACTATTTTAAATCGGTG
GCACGGTTCGA
Found at i:368913 original size:21 final size:22
Alignment explanation
Indices: 368880--368920 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
368870 ATATATATCT
368880 AAAAATCATAATTTAACTAACTA
1 AAAAATCATAATTTAA-TAACTA
368903 AAAAAT-A-AATTTAATAAC
1 AAAAATCATAATTTAATAAC
368921 GTACAACTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.22
21 7 0.39
22 1 0.06
23 6 0.33
ACGTcount: A:0.61, C:0.10, G:0.00, T:0.29
Consensus pattern (22 bp):
AAAAATCATAATTTAATAACTA
Found at i:369193 original size:20 final size:20
Alignment explanation
Indices: 369170--369221 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 20
369160 AAATAGAGAT
*
369170 AAATTTATAAATATATATTA
1 AAATTTATAAAAATATATTA
* * *
369190 AAATATGTAAAAATTTATTA
1 AAATTTATAAAAATATATTA
*
369210 AAATTAATAAAA
1 AAATTTATAAAA
369222 CTAAAATTTT
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (20 bp):
AAATTTATAAAAATATATTA
Found at i:369244 original size:21 final size:21
Alignment explanation
Indices: 369220--369260 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
369210 AAATTAATAA
*
369220 AACTAAA-ATTTTATTATTTTT
1 AACTAAATATATT-TTATTTTT
369241 AACTAAATATATTTTATTTT
1 AACTAAATATATTTTATTTT
369261 AAGCTGAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.56
Consensus pattern (21 bp):
AACTAAATATATTTTATTTTT
Found at i:375641 original size:38 final size:38
Alignment explanation
Indices: 375586--375724 Score: 122
Period size: 38 Copynumber: 3.7 Consensus size: 38
375576 AACACCAACC
* * * *
375586 ACTATTTTAAACTGGTGGTACGGTTTGAAACGAAAACT
1 ACTATTTTAAACCGGTGGCACGATTCGAAACGAAAACT
*
375624 ACTATTTTAAACCGGTGGCACGATTCGAAACGAAAATT
1 ACTATTTTAAACCGGTGGCACGATTCGAAACGAAAACT
* * * * *
375662 ACTATTCTT-AATCGGTGACACGGTTC-AATACAAAAACC
1 ACTATT-TTAAACCGGTGGCACGATTCGAA-ACGAAAACT
* *
375700 ATTATTCTT-AACCGGTGACACGATT
1 ACTATT-TTAAACCGGTGGCACGATT
375725 TAAAACCGGT
Statistics
Matches: 85, Mismatches: 14, Indels: 4
0.83 0.14 0.04
Matches are distributed among these distances:
37 2 0.02
38 81 0.95
39 2 0.02
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (38 bp):
ACTATTTTAAACCGGTGGCACGATTCGAAACGAAAACT
Found at i:430984 original size:15 final size:16
Alignment explanation
Indices: 430964--430993 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
430954 GTGCCTGGAG
430964 ACCTTT-AGTTTTTGT
1 ACCTTTCAGTTTTTGT
430979 ACCTTTCAGTTTTTG
1 ACCTTTCAGTTTTTG
430994 ACAATTCTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.13, C:0.17, G:0.13, T:0.57
Consensus pattern (16 bp):
ACCTTTCAGTTTTTGT
Found at i:433241 original size:11 final size:12
Alignment explanation
Indices: 433216--433260 Score: 54
Period size: 12 Copynumber: 3.6 Consensus size: 12
433206 ACCTTCTCTT
* *
433216 AAAAAAAAGCGA
1 AAAAAAAAACAA
433228 AAAAAAAAACAA
1 AAAAAAAAACAA
433240 AAAAACAAAACAA
1 AAAAA-AAAACAA
433253 AAGAAAAA
1 AA-AAAAA
433261 GAGAGAAAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
12 15 0.52
13 11 0.38
14 3 0.10
ACGTcount: A:0.84, C:0.09, G:0.07, T:0.00
Consensus pattern (12 bp):
AAAAAAAAACAA
Found at i:434525 original size:28 final size:28
Alignment explanation
Indices: 434439--434525 Score: 79
Period size: 28 Copynumber: 3.1 Consensus size: 28
434429 CGCCTTCTCC
434439 TTTCAAAGCCCACACAAGTTGGTGGCAT
1 TTTCAAAGCCCACACAAGTTGGTGGCAT
* * * * ** *
434467 TTTC-TAGTCCTCAAAGAGCAGGAT-GCCT
1 TTTCAAAGCCCACACA-AGTTGG-TGGCAT
434495 TTTCAAAGCCCACACAAGTTGGTGGCAT
1 TTTCAAAGCCCACACAAGTTGGTGGCAT
434523 TTT
1 TTT
434526 TTAGTCCTCA
Statistics
Matches: 41, Mismatches: 14, Indels: 8
0.65 0.22 0.13
Matches are distributed among these distances:
27 8 0.20
28 25 0.61
29 8 0.20
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.29
Consensus pattern (28 bp):
TTTCAAAGCCCACACAAGTTGGTGGCAT
Found at i:434647 original size:55 final size:55
Alignment explanation
Indices: 434258--434995 Score: 783
Period size: 55 Copynumber: 13.0 Consensus size: 55
434248 GATGCCTGTT
* * * *
434258 CCTTTTAAAGCTCACACAAGTTGGTGGCAC-CTTCAGTCCTCAAAGAGCAGGATGCTTTT
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGA--C---A
* * *
434317 CTTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCCCAAAGAGCAGGACG
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACTTTT-CAGTCCTCAAAGAGCAGGACA
* *
434372 CCTTTTCTTTTAAAGCCCACACAAGTTAGTGGCAC-CTTCAGTCCTCAAAGAGCAGGACGCCTTC
1 CC-TTTC----AAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGA------C
*
434436 T
55 A
**
434437 CCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCTAGTCCTCAAAGAGCAGGATG
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTC-AGTCCTCAAAGAGCAGGACA
* * ***
434492 CCTTTTCAAAGCCCACACAAGTTGGTGGCATTTTTTAGTCCTCAAAGAGCATGATGTTTTTT
1 CC-TTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCA-G--G---ACA
* * * *
434554 CTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCCCAAGGAGCAGGACA
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACA
434609 CCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAGGACA
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACTTTT-CAGTCCTCAAAGAGCAGGACA
* *
434664 CCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGATGCTTTTT
1 CCT-TTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGA--C----A
* * * *
434725 CTTTTCAAAGCCTACACGAGTTGGTGGCACTTTTCAGTCC-CTAAGAGCAGGACA
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACA
434779 CCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAGGACA
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACTTTT-CAGTCCTCAAAGAGCAGGACA
* * *
434834 CCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACG
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACA
* * * *
434889 TCTTTCAAAGCCCATACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACG
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACA
* *
434944 CCTTTCAAAGCCCACACGAGTTGGTGGCACTTTTTAGTCCTC-AAGAGCAGGA
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGA
434996 TACACTTTAT
Statistics
Matches: 588, Mismatches: 54, Indels: 79
0.82 0.07 0.11
Matches are distributed among these distances:
53 4 0.01
54 45 0.08
55 245 0.42
56 54 0.09
57 6 0.01
58 3 0.01
59 47 0.08
60 81 0.14
61 94 0.16
62 2 0.00
64 4 0.01
65 3 0.01
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (55 bp):
CCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACA
Found at i:434846 original size:225 final size:221
Alignment explanation
Indices: 434232--434995 Score: 905
Period size: 225 Copynumber: 3.3 Consensus size: 221
434222 TCCGCTTTTT
* * *
434232 AGTCCTCAAAGAGCAGGATGCCTGTTCCTTTTAAAGCTCACACAAGTTGGTGGCAC-CTTCAGTC
1 AGTCCTCAAAGAGCAGGATGCC---T--TTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTC
434296 CTCAAAGAGCAGGATGCTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCCCAA
61 CTCAAAGAGCAGGA--C---TCTTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCCCAA
* * *
434361 AGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTAGTGGCACCTTCAGTCCTCAAAGAGCA
121 AGAGCAGGAC-AC----CTTTTAAAGCCCACACAAGTTGGTGGCACTTTCAGTCCTCAAAGAGCA
* *
434426 GGACGCCTTCTCCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTC
181 GGAC-AC--CT-C-TTCAAAGCCCACACAAGTTGGTGGCACCTTTC
* *
434471 TAGTCCTCAAAGAGCAGGATGCCTTTTCAAAGCCCACACAAGTTGGTGGCATTTTTTAGTCCTCA
1 -AGTCCTCAAAGAGCAGGATGCCTTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCA
** * *
434536 AAGAGCATGATGTTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTT-CAGTCCCCAAGG
65 AAGAGCA-G--G---ACTCTTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCCCAAAG
* *
434600 AGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACAC
123 AGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCACTTT-CAGTCCTCAAAGAGCAGGACAC
434665 CTCTT-AAAGCCCACACAAGTTGGTGGCACCTTTC
187 CTCTTCAAAGCCCACACAAGTTGGTGGCACCTTTC
* *
434699 AGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCTACACGAGTTGGTGGCACTTTTCAGTC
1 AGTCCTCAAAGAGCAGGATGC-----CTTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTC
* * * *
434764 C-CTAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGC
61 CTCAAAGAGCAGGACTCTTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCCCAAAGAGC
**
434828 AGGACACCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGTCT-
126 AGGACACCTTTTAAAGCCCACACAAGTTGGTGGCA-CTTTCAGTCCTCAAAGAGCAGGACACCTC
*
434892 TTCAAAGCCCATACAAGTTGGTGGCACCTTTC
190 TTCAAAGCCCACACAAGTTGGTGGCACCTTTC
* * *
434924 AGTCCTCAAAGAGCAGGACGCC-TTTCAAAGCCCACACGAGTTGGTGGCACTTTTTAGTCCTC-A
1 AGTCCTCAAAGAGCAGGATGCCTTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAA
434987 AGAGCAGGA
66 AGAGCAGGA
434996 TACACTTTAT
Statistics
Matches: 469, Mismatches: 36, Indels: 59
0.83 0.06 0.10
Matches are distributed among these distances:
219 46 0.10
220 2 0.00
224 5 0.01
225 145 0.31
226 3 0.01
227 44 0.09
228 7 0.01
229 1 0.00
230 3 0.01
231 8 0.02
232 65 0.14
233 20 0.04
235 25 0.05
236 18 0.04
237 51 0.11
238 3 0.01
239 1 0.00
240 22 0.05
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.25
Consensus pattern (221 bp):
AGTCCTCAAAGAGCAGGATGCCTTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAA
AGAGCAGGACTCTTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCCCAAAGAGCAGGAC
ACCTTTTAAAGCCCACACAAGTTGGTGGCACTTTCAGTCCTCAAAGAGCAGGACACCTCTTCAAA
GCCCACACAAGTTGGTGGCACCTTTC
Found at i:434865 original size:29 final size:29
Alignment explanation
Indices: 434777--434867 Score: 73
Period size: 29 Copynumber: 3.2 Consensus size: 29
434767 AAGAGCAGGA
*
434777 CACCTTTCAAAGCCCACACAAGTTGGTGG
1 CACCTTTTAAAGCCCACACAAGTTGGTGG
** * * * **
434806 CA--TTTTCCAGTCCTCA-AAG-AGCAGG
1 CACCTTTTAAAGCCCACACAAGTTGGTGG
434831 ACACCTTTTAAAGCCCACACAAGTTGGTGG
1 -CACCTTTTAAAGCCCACACAAGTTGGTGG
434861 CACCTTT
1 CACCTTT
434868 CAGTCCTCAA
Statistics
Matches: 42, Mismatches: 15, Indels: 10
0.63 0.22 0.15
Matches are distributed among these distances:
25 3 0.07
26 5 0.12
27 9 0.21
28 10 0.24
29 12 0.29
30 3 0.07
ACGTcount: A:0.27, C:0.30, G:0.19, T:0.24
Consensus pattern (29 bp):
CACCTTTTAAAGCCCACACAAGTTGGTGG
Found at i:435808 original size:19 final size:18
Alignment explanation
Indices: 435784--435880 Score: 88
Period size: 19 Copynumber: 5.8 Consensus size: 18
435774 TTTCAGTGAT
435784 TTGTATCGATACATAAGTG
1 TTGTATCGATACA-AAGTG
435803 TTGTATCGATAC-AA---
1 TTGTATCGATACAAAGTG
435817 -TGTATCGATACACAAGTG
1 TTGTATCGATACA-AAGTG
435835 TTGTATCGATAC-AA---
1 TTGTATCGATACAAAGTG
435849 -TGTATCGATACACAAGTG
1 TTGTATCGATACA-AAGTG
*
435867 ATGTATCGATACAA
1 TTGTATCGATACAA
435881 TGTATCGCTA
Statistics
Matches: 66, Mismatches: 0, Indels: 25
0.73 0.00 0.27
Matches are distributed among these distances:
13 22 0.33
15 4 0.06
17 4 0.06
18 1 0.02
19 35 0.53
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.32
Consensus pattern (18 bp):
TTGTATCGATACAAAGTG
Found at i:435822 original size:13 final size:13
Alignment explanation
Indices: 435804--435893 Score: 63
Period size: 13 Copynumber: 6.0 Consensus size: 13
435794 ACATAAGTGT
435804 TGTATCGATACAA
1 TGTATCGATACAA
435817 TGTATCGATACACAA
1 TGTATCGAT--ACAA
435832 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
435849 TGTATCGATACACAAGTGA
1 TGTATCGAT--AC-A---A
435868 TGTATCGATACAA
1 TGTATCGATACAA
*
435881 TGTATCGCTACAA
1 TGTATCGATACAA
435894 AGCTACTACC
Statistics
Matches: 64, Mismatches: 1, Indels: 24
0.72 0.01 0.27
Matches are distributed among these distances:
13 31 0.48
15 6 0.09
16 2 0.03
17 6 0.09
19 19 0.30
ACGTcount: A:0.36, C:0.17, G:0.18, T:0.30
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:435826 original size:32 final size:32
Alignment explanation
Indices: 435785--435892 Score: 189
Period size: 32 Copynumber: 3.4 Consensus size: 32
435775 TTCAGTGATT
*
435785 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACACAAGTGTTGTATCGATACAA
435817 TGTATCGATACACAAGTGTTGTATCGATACAA
1 TGTATCGATACACAAGTGTTGTATCGATACAA
*
435849 TGTATCGATACACAAGTGATGTATCGATACAA
1 TGTATCGATACACAAGTGTTGTATCGATACAA
*
435881 TGTATCGCTACA
1 TGTATCGATACA
435893 AAGCTACTAC
Statistics
Matches: 73, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
32 73 1.00
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.31
Consensus pattern (32 bp):
TGTATCGATACACAAGTGTTGTATCGATACAA
Found at i:438359 original size:51 final size:52
Alignment explanation
Indices: 438302--438424 Score: 171
Period size: 51 Copynumber: 2.4 Consensus size: 52
438292 CAATTCTCCG
* *
438302 CAATCGGGGATA-TCCCAACTCCGATTTTATTTTC-AAAACACTAA-TTTTCTA
1 CAATCGGGGATACT-CCAACTCCGATTTTATTTCCAAAAACACCAATTTTTC-A
*
438353 TAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTTTCA
1 CAATCGGGGATACTCCAACTCCGATTTTATTTCC-AAAAACACCAATTTTTCA
438406 CAATCGGGGATACTCCAAC
1 CAATCGGGGATACTCCAAC
438425 CCGTTAATCA
Statistics
Matches: 64, Mismatches: 4, Indels: 6
0.86 0.05 0.08
Matches are distributed among these distances:
51 30 0.47
52 1 0.02
53 28 0.44
54 5 0.08
ACGTcount: A:0.33, C:0.25, G:0.11, T:0.31
Consensus pattern (52 bp):
CAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAATTTTTCA
Found at i:438416 original size:53 final size:51
Alignment explanation
Indices: 438302--438424 Score: 169
Period size: 53 Copynumber: 2.4 Consensus size: 51
438292 CAATTCTCCG
* *
438302 CAATCGGGGATA-TCCCAACTCCGATTTTATTTTCAAAACACTAATTTTCTA
1 CAATCGGGGATACT-CCAACTCCGATTTTATTTCCAAAACACCAATTTTCTA
*
438353 TAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTT-TCA
1 CAATCGGGGATACTCCAACTCCGATTTTATTTCC--AAAACACCAATTTTCT-A
438406 CAATCGGGGATACTCCAAC
1 CAATCGGGGATACTCCAAC
438425 CCGTTAATCA
Statistics
Matches: 64, Mismatches: 4, Indels: 6
0.86 0.05 0.08
Matches are distributed among these distances:
51 30 0.47
52 2 0.03
53 32 0.50
ACGTcount: A:0.33, C:0.25, G:0.11, T:0.31
Consensus pattern (51 bp):
CAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAACACCAATTTTCTA
Found at i:438446 original size:79 final size:78
Alignment explanation
Indices: 438355--438499 Score: 204
Period size: 79 Copynumber: 1.8 Consensus size: 78
438345 ATTTTCTATA
*
438355 ATCGGGGATACTCCAA-CTCCGATTTTATTTCCAAAAAACACCAATTTTTC-ACAATCGGGGATA
1 ATCGGGGATACTCCAACCT-CGATTTTATTTCC--AAAACACCAATTTTCCTACAATCGGGGATA
438418 CTCCAACCCGTTAATC
63 CTCCAACCCGTTAATC
* * **
438434 ATCGGGGATACTCCAACCTCGATTTTATTTTCAAAACACTAATTTTCCTTTAATCGGGGATACTC
1 ATCGGGGATACTCCAACCTCGATTTTATTTCCAAAACACCAATTTTCCTACAATCGGGGATACTC
438499 C
66 C
438500 GACTCCGATT
Statistics
Matches: 59, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
77 14 0.24
78 15 0.25
79 28 0.47
80 2 0.03
ACGTcount: A:0.30, C:0.26, G:0.13, T:0.31
Consensus pattern (78 bp):
ATCGGGGATACTCCAACCTCGATTTTATTTCCAAAACACCAATTTTCCTACAATCGGGGATACTC
CAACCCGTTAATC
Found at i:438491 original size:52 final size:52
Alignment explanation
Indices: 438434--438558 Score: 146
Period size: 52 Copynumber: 2.4 Consensus size: 52
438424 CCCGTTAATC
* * **
438434 ATCGGGGATACTCCAACCTCGATTTTATTTTC-AAAACACTAATTTTCCTTTA
1 ATCGGGGATACTCCAACCTCGATTTTATTTCCAAAAACACCAATTTTCC-ACA
* * *
438486 ATCGGGGATACTCCGA-CTCCGATTTTATTTCCAAAAACACCAATTTTTCACC
1 ATCGGGGATACTCCAACCT-CGATTTTATTTCCAAAAACACCAATTTTCCACA
*
438538 ATCGAGGATACTCCAACCTCG
1 ATCGGGGATACTCCAACCTCG
438559 TTATTTCATC
Statistics
Matches: 61, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
51 2 0.03
52 43 0.70
53 16 0.26
ACGTcount: A:0.29, C:0.27, G:0.12, T:0.32
Consensus pattern (52 bp):
ATCGGGGATACTCCAACCTCGATTTTATTTCCAAAAACACCAATTTTCCACA
Found at i:438547 original size:130 final size:133
Alignment explanation
Indices: 438304--438583 Score: 455
Period size: 130 Copynumber: 2.1 Consensus size: 133
438294 ATTCTCCGCA
438304 ATCGGGGATA-TCCCAA-CTCCGATTTTATTTTCAAAACACTAATTTTCTATAATCGGGGATACT
1 ATCGGGGATACT-CCAACCTCCGATTTTATTTTCAAAACACTAATTTTCTATAATCGGGGATACT
*
438367 CCAACTCCGATTTTATTTCCAAAAAACACCAATTTTTCACAATCGGGGATACTCCAACC-CGTTA
65 CCAACTCCGATTTTATTTCCAAAAAACACCAATTTTTCACAATCGAGGATACTCCAACCTCGTTA
438431 -ATC
130 TATC
*
438434 ATCGGGGATACTCCAACCT-CGATTTTATTTTCAAAACACTAATTTTCCTTTAATCGGGGATACT
1 ATCGGGGATACTCCAACCTCCGATTTTATTTTCAAAACACTAATTTT-CTATAATCGGGGATACT
* *
438498 CCGACTCCGATTTTATTTCC-AAAAACACCAATTTTTCACCATCGAGGATACTCCAACCTCGTTA
65 CCAACTCCGATTTTATTTCCAAAAAACACCAATTTTTCACAATCGAGGATACTCCAACCTCGTTA
*
438562 TTTC
130 TATC
438566 ATCGGGGATACTCCAACC
1 ATCGGGGATACTCCAACC
438584 CCGTTACCTC
Statistics
Matches: 140, Mismatches: 5, Indels: 8
0.92 0.03 0.05
Matches are distributed among these distances:
130 77 0.55
131 43 0.31
132 20 0.14
ACGTcount: A:0.30, C:0.26, G:0.12, T:0.32
Consensus pattern (133 bp):
ATCGGGGATACTCCAACCTCCGATTTTATTTTCAAAACACTAATTTTCTATAATCGGGGATACTC
CAACTCCGATTTTATTTCCAAAAAACACCAATTTTTCACAATCGAGGATACTCCAACCTCGTTAT
ATC
Found at i:438566 original size:31 final size:28
Alignment explanation
Indices: 438537--438614 Score: 88
Period size: 28 Copynumber: 2.8 Consensus size: 28
438527 AATTTTTCAC
*
438537 CATCGAGGATACTCCAACCTCGTTATTT
1 CATCGAGGATACTCCAACCCCGTTATTT
* **
438565 CATCGGGGATACTCCAACCCCGTTACCT
1 CATCGAGGATACTCCAACCCCGTTATTT
438593 C--CGAGGGGATACTCCAACCCCG
1 CATCGA--GGATACTCCAACCCCG
438615 GCTTTATTCC
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
26 2 0.05
28 41 0.95
ACGTcount: A:0.23, C:0.36, G:0.19, T:0.22
Consensus pattern (28 bp):
CATCGAGGATACTCCAACCCCGTTATTT
Found at i:438717 original size:79 final size:79
Alignment explanation
Indices: 438568--438772 Score: 216
Period size: 79 Copynumber: 2.6 Consensus size: 79
438558 GTTATTTCAT
**
438568 CGGGGATACTCCAACCCCGTTACCTCCGAGGGGATACTCCAACCCCGGCTTTATTCCCAAAATAC
1 CGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGCTTTATTCCCAAAATAC
* *
438633 TGATTTCTCATAAT
66 TGATTTCTCACAAC
* * * ** * ** *
438647 TGGGGATACTCCAACCCCGTTATTTCTGAGGGGATACTCCAATCCCGATTTTTTTTTC-TAAT-C
1 CGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGCTTTATTCCCAAAATAC
438710 ATCGATTTCTCACAAC
66 -T-GATTTCTCACAAC
* * * **
438726 CGGGGATACTCCAGCCCCGTTATTTTCAAGGGGACCCTCCAACCCCG
1 CGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCG
438773 TTATTATCTC
Statistics
Matches: 103, Mismatches: 21, Indels: 4
0.80 0.16 0.03
Matches are distributed among these distances:
77 1 0.01
78 4 0.04
79 98 0.95
ACGTcount: A:0.23, C:0.32, G:0.18, T:0.28
Consensus pattern (79 bp):
CGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGCTTTATTCCCAAAATAC
TGATTTCTCACAAC
Found at i:439883 original size:20 final size:19
Alignment explanation
Indices: 439858--439911 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 19
439848 CTACCACTGT
439858 TTGTATCGATACATG-GCATA
1 TTGTATCGATACATGAG-A-A
439878 TTGTATCGATACATGAAGAA
1 TTGTATCGATACATG-AGAA
439898 TTGTATCGATACAT
1 TTGTATCGATACAT
439912 TGTTCCAAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 30 0.94
21 1 0.03
22 1 0.03
ACGTcount: A:0.33, C:0.13, G:0.19, T:0.35
Consensus pattern (19 bp):
TTGTATCGATACATGAGAA
Found at i:442174 original size:19 final size:21
Alignment explanation
Indices: 442131--442182 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
442121 TTCAATAATT
*
442131 TGTATCGATACATTCAGTAAA
1 TGTATCGATACATTAAGTAAA
442152 TGTATCGATACA-TAAGT-AA
1 TGTATCGATACATTAAGTAAA
442171 TGTATCGATACA
1 TGTATCGATACA
442183 GTGTATCGCT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 14 0.47
20 4 0.13
21 12 0.40
ACGTcount: A:0.38, C:0.13, G:0.15, T:0.33
Consensus pattern (21 bp):
TGTATCGATACATTAAGTAAA
Found at i:442232 original size:13 final size:13
Alignment explanation
Indices: 442214--442239 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
442204 GCCAAGGAAA
442214 TGTATCGATACAT
1 TGTATCGATACAT
442227 TGTATCGATACAT
1 TGTATCGATACAT
442240 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:444654 original size:51 final size:51
Alignment explanation
Indices: 444598--444836 Score: 300
Period size: 51 Copynumber: 4.6 Consensus size: 51
444588 TTAAGTTTAT
* * * *
444598 CAATTTTTCATAATCGAGGATACTTCAACCCCGGTTTTA-TTTCTAAAACAC
1 CAATTTTCCACAATCGGGGATACTTCAACCCCGATTTTATTTTC-AAAACAC
* * * *
444649 TAATTTTCCACAATCGGGGATACTTTAACTCCGATTTTATTTTCGAAACAC
1 CAATTTTCCACAATCGGGGATACTTCAACCCCGATTTTATTTTCAAAACAC
*
444700 CAATTTTCCACAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACAC
1 CAATTTTCCACAATCGGGGATACTTCAACCCCGATTTTATTTTCAAAACAC
** * * * *
444751 CAATTTTCCTTTAATAGGGGATACTCCAACTCCGATTTTATTTCCAAAAACAC
1 CAATTTTCC-ACAATCGGGGATACTTCAACCCCGATTTTATTTTC-AAAACAC
*
444804 CAATTTTTCACAATCGGGGATACTTCAACCCCG
1 CAATTTTCCACAATCGGGGATACTTCAACCCCG
444837 CTAATCATCG
Statistics
Matches: 161, Mismatches: 24, Indels: 5
0.85 0.13 0.03
Matches are distributed among these distances:
51 93 0.58
52 53 0.33
53 15 0.09
ACGTcount: A:0.31, C:0.26, G:0.11, T:0.33
Consensus pattern (51 bp):
CAATTTTCCACAATCGGGGATACTTCAACCCCGATTTTATTTTCAAAACAC
Found at i:445017 original size:79 final size:80
Alignment explanation
Indices: 444843--445018 Score: 266
Period size: 80 Copynumber: 2.2 Consensus size: 80
444833 CCCGCTAATC
*
444843 ATCGGGGATACTCCGACCCCGTTATTTTCGAGGGGATACTCCAACCCCCAGTTTTATTTCTAAAA
1 ATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCCAGTTTTATTTCTAAAA
** *
444908 CATCAAATTTTTATA
66 CATCAAATTTCCACA
*
444923 ATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCGAA-CCCCAGTTTTATTTCTAAAA
1 ATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCCAGTTTTATTTCTAAAA
*
444987 CA-CCAATTCTCCACA
66 CATCAAATT-TCCACA
*
445002 ATCGGGGATATTCCAAC
1 ATCGGGGATACTCCAAC
445019 TCCGATTTTA
Statistics
Matches: 88, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
78 5 0.06
79 41 0.47
80 42 0.48
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.30
Consensus pattern (80 bp):
ATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCCAGTTTTATTTCTAAAA
CATCAAATTTCCACA
Found at i:445031 original size:51 final size:51
Alignment explanation
Indices: 444956--445069 Score: 140
Period size: 51 Copynumber: 2.2 Consensus size: 51
444946 ATTTTCGAGG
* * * *
444956 GGATACTCGAAC-CCCAGTTTTATTTCTAAAACACCAATTCTCCACAATCGG
1 GGATACTCCAACTCCGA-TTTTATTTCCAAAACACCAATTCTCCACAATCGA
* * * *
445007 GGATATTCCAACTCCGATTTTATTTCCAAAACACTAATTTTTCACAATCGA
1 GGATACTCCAACTCCGATTTTATTTCCAAAACACCAATTCTCCACAATCGA
445058 GGATACTCCAAC
1 GGATACTCCAAC
445070 CTCGTTATTT
Statistics
Matches: 53, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
51 50 0.94
52 3 0.06
ACGTcount: A:0.32, C:0.27, G:0.11, T:0.30
Consensus pattern (51 bp):
GGATACTCCAACTCCGATTTTATTTCCAAAACACCAATTCTCCACAATCGA
Found at i:445090 original size:28 final size:28
Alignment explanation
Indices: 445058--445129 Score: 94
Period size: 28 Copynumber: 2.6 Consensus size: 28
445048 TCACAATCGA
* *
445058 GGATACTCCAACCTCGTTATTTCATC-A-G
1 GGATACTCCAACCCCGTTACTTC--CGAGG
445086 GGATACTCCAACCCCGTTACTTCCGAGG
1 GGATACTCCAACCCCGTTACTTCCGAGG
445114 GGATACTCCAACCCCG
1 GGATACTCCAACCCCG
445130 GCTTTATTTC
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
26 1 0.03
27 1 0.03
28 38 0.95
ACGTcount: A:0.24, C:0.35, G:0.18, T:0.24
Consensus pattern (28 bp):
GGATACTCCAACCCCGTTACTTCCGAGG
Found at i:445136 original size:107 final size:107
Alignment explanation
Indices: 445005--445208 Score: 250
Period size: 107 Copynumber: 1.9 Consensus size: 107
444995 CTCCACAATC
* * * *
445005 GGGGATATTCCAACTCCGATTTTATTTCCAAAACACTAATTTTTCACAATCGAGGATACTCCAA-
1 GGGGATACTCCAACCCCGACTTTATTTCCAAAACACTAATTTCTCACAATCGAGGATACTCCAAC
*
445069 CCTCGTTA-TTTCATCAGGGATACTCCAACCCCGTTACTTCCGA
66 CCT-ATTATTTTCA-CAGGGATACTCCAACCCCGTTACTTCCGA
* * * * * * *
445112 GGGGATACTCCAACCCCGGCTTTATTTCCAAAATATTGATTTCTCATAATTGGGGATACTCCAAC
1 GGGGATACTCCAACCCCGACTTTATTTCCAAAACACTAATTTCTCACAATCGAGGATACTCCAAC
* *
445177 CCTATTATTTTCACGGGGATACTCCAATCCCG
66 CCTATTATTTTCACAGGGATACTCCAACCCCG
445209 ACTTTATTTT
Statistics
Matches: 81, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
107 73 0.90
108 8 0.10
ACGTcount: A:0.27, C:0.27, G:0.15, T:0.31
Consensus pattern (107 bp):
GGGGATACTCCAACCCCGACTTTATTTCCAAAACACTAATTTCTCACAATCGAGGATACTCCAAC
CCTATTATTTTCACAGGGATACTCCAACCCCGTTACTTCCGA
Found at i:445244 original size:237 final size:238
Alignment explanation
Indices: 444714--445341 Score: 682
Period size: 237 Copynumber: 2.6 Consensus size: 238
444704 TTTCCACAAT
* * * *
444714 CGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCCTTTAATAGGGGATACTCCA
1 CGGGGATACTCCAA-CCCGATTTTATTTTTAAAACACCAATTTT-CTATAATCGGGGATATTCCA
* * * *
444779 ACTCCGATTTTATTTCCAAAAACACCAATTTTTCACAATCGGGGATACTTCAACCCCGCTA-ATC
64 ACTCCGATTTTATTTCC-AAAACACTAATTTTTCACAATCGGGGATACTCCAACCCCGTTATTTC
* * * * * *
444843 ATCGGGGATACTCCGACCCCGTTATTTTCGAGGGGATACTCCAACCCCCAGTTTTATTTCTAAAA
128 ATCAGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCCAGCTTTATTTCCAAAA
* *
444908 CATCAAATTTTTATAATCGGGGATACTCCAACCCCGTTATTTTCGA
193 CATCAAATTTTCATAATCGGGGATACTCCAACCCCATTATTTTCGA
* * * * * *
444954 -GGGGATACTCGAACCCCAGTTTTATTTCTAAAACACCAATTCTCCACAATCGGGGATATTCCAA
1 CGGGGATACTCCAACCCGA-TTTTATTTTTAAAACACCAATTTTCTATAATCGGGGATATTCCAA
* *
445018 CTCCGATTTTATTTCCAAAACACTAATTTTTCACAATCGAGGATACTCCAACCTCGTTATTTCAT
65 CTCCGATTTTATTTCCAAAACACTAATTTTTCACAATCGGGGATACTCCAACCCCGTTATTTCAT
* *
445083 CAGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAA-CCCCGGCTTTATTTCCAAAATA
130 CAGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCCAGCTTTATTTCCAAAACA
** * *
445147 T-TGATTTCTCATAATTGGGGATACTCCAACCCTATTATTTTC-A
195 TCAAATTT-TCATAATCGGGGATACTCCAACCCCATTATTTTCGA
* * ** * *
445190 CGGGGATACTCCAATCCCGACTTTATTTTTGAAACGTCTATTTTCTATAATCGGGGACACTT-CA
1 CGGGGATACTCCAA-CCCGATTTTATTTTTAAAACACCAATTTTCTATAATCGGGGATA-TTCCA
** * * ** * *
445254 ACCTTTG-TCTTATTTCTAAATTA-TCGATTTTTCACAATCGGGGATTCTCCAACCCCGTTATTT
64 A-CTCCGATTTTATTTCCAAAACACT-AATTTTTCACAATCGGGGATACTCCAACCCCGTTATTT
*
445317 --TCAAGGGGATACTCCAACTCCGTTA
127 CATC-A-GGGATACTCCAACCCCGTTA
445342 TTATCTCCAA
Statistics
Matches: 325, Mismatches: 53, Indels: 23
0.81 0.13 0.06
Matches are distributed among these distances:
235 2 0.01
236 7 0.02
237 196 0.60
238 87 0.27
239 33 0.10
ACGTcount: A:0.27, C:0.26, G:0.14, T:0.32
Consensus pattern (238 bp):
CGGGGATACTCCAACCCGATTTTATTTTTAAAACACCAATTTTCTATAATCGGGGATATTCCAAC
TCCGATTTTATTTCCAAAACACTAATTTTTCACAATCGGGGATACTCCAACCCCGTTATTTCATC
AGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCCAGCTTTATTTCCAAAACAT
CAAATTTTCATAATCGGGGATACTCCAACCCCATTATTTTCGA
Found at i:450548 original size:13 final size:13
Alignment explanation
Indices: 450530--450587 Score: 56
Period size: 13 Copynumber: 4.9 Consensus size: 13
450520 CATACAATTT
450530 ATTGTATCGATAC
1 ATTGTATCGATAC
450543 ATTGTATCGATAC
1 ATTGTATCGATAC
*
450556 AATGT-T--AT--
1 ATTGTATCGATAC
450564 -TTGTATCGATAC
1 ATTGTATCGATAC
*
450576 AATGTATCGATA
1 ATTGTATCGATA
450588 TATGGGTTAC
Statistics
Matches: 36, Mismatches: 3, Indels: 12
0.71 0.06 0.24
Matches are distributed among these distances:
7 3 0.08
8 1 0.03
10 4 0.11
12 1 0.03
13 27 0.75
ACGTcount: A:0.33, C:0.12, G:0.16, T:0.40
Consensus pattern (13 bp):
ATTGTATCGATAC
Found at i:450573 original size:33 final size:31
Alignment explanation
Indices: 450513--450587 Score: 114
Period size: 33 Copynumber: 2.4 Consensus size: 31
450503 AAAAACCCAG
*
450513 ATGTATCCATACAATTTATTGTATCGATACA
1 ATGTATCGATACAATTTATTGTATCGATACA
*
450544 TTGTATCGATACAATGTTATTTGTATCGATACA
1 ATGTATCGATACAAT-TTA-TTGTATCGATACA
450577 ATGTATCGATA
1 ATGTATCGATA
450588 TATGGGTTAC
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
31 13 0.33
32 3 0.08
33 23 0.59
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.40
Consensus pattern (31 bp):
ATGTATCGATACAATTTATTGTATCGATACA
Found at i:453115 original size:19 final size:19
Alignment explanation
Indices: 453072--453144 Score: 76
Period size: 20 Copynumber: 3.7 Consensus size: 19
453062 AACTCTTGTA
*
453072 TGTATCGATACAT-TATGCTT
1 TGTATCGATACATGT-T-CAT
453092 TGTATCGATACATGTTCAT
1 TGTATCGATACATGTTCAT
**
453111 TGTATCGATACATGCACAAT
1 TGTATCGATACATGTTC-AT
*
453131 TGTATTGATACATG
1 TGTATCGATACATG
453145 AAATTGGCAG
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
19 17 0.36
20 29 0.62
21 1 0.02
ACGTcount: A:0.29, C:0.15, G:0.16, T:0.40
Consensus pattern (19 bp):
TGTATCGATACATGTTCAT
Found at i:454015 original size:19 final size:20
Alignment explanation
Indices: 453993--454047 Score: 53
Period size: 19 Copynumber: 2.8 Consensus size: 20
453983 ATTATAATAT
453993 TTTTATATTTTTAAT-AAAA
1 TTTTATATTTTTAATAAAAA
*
454012 TTTTAT-TTAATT-ATAAAAA
1 TTTTATATT-TTTAATAAAAA
454031 TTTTATTAATTTTTAAT
1 TTTTA-T-ATTTTTAAT
454048 TTTAATTATT
Statistics
Matches: 28, Mismatches: 2, Indels: 9
0.72 0.05 0.23
Matches are distributed among these distances:
18 4 0.14
19 17 0.61
20 1 0.04
21 2 0.07
22 4 0.14
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
TTTTATATTTTTAATAAAAA
Found at i:454086 original size:44 final size:47
Alignment explanation
Indices: 453983--454092 Score: 111
Period size: 44 Copynumber: 2.4 Consensus size: 47
453973 TTTGTATATC
* *
453983 ATTATAATATTTTTATATTTTTAATAAAATTTTATTTAATTATAAAAAT
1 ATTATAA-ATTTTTATATTTTTAAT-AAATTTCATTTAATTAGAAAAAT
* * *
454032 TTTATTAATTTTTA-A-TTTTAAT-TATTTCATTTAATT-GAAAAAT
1 ATTATAAATTTTTATATTTTTAATAAATTTCATTTAATTAGAAAAAT
*
454075 AATTATAAATTTTAATAT
1 -ATTATAAATTTTTATAT
454093 ATTTGATTAT
Statistics
Matches: 50, Mismatches: 8, Indels: 9
0.75 0.12 0.13
Matches are distributed among these distances:
43 6 0.12
44 23 0.46
45 1 0.02
46 7 0.14
47 1 0.02
48 7 0.14
49 5 0.10
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.55
Consensus pattern (47 bp):
ATTATAAATTTTTATATTTTTAATAAATTTCATTTAATTAGAAAAAT
Found at i:455898 original size:2 final size:2
Alignment explanation
Indices: 455891--455926 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
455881 ACATTATTCT
455891 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
455927 TAACCAATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:457992 original size:19 final size:20
Alignment explanation
Indices: 457959--458002 Score: 56
Period size: 19 Copynumber: 2.2 Consensus size: 20
457949 AATTTTTTTA
457959 ATTTAAAAAAATAAA-AAATT
1 ATTT-AAAAAATAAATAAATT
*
457979 ATTTAAAAATTAAATAAATT
1 ATTTAAAAAATAAATAAATT
457999 -TTTA
1 ATTTA
458003 TATATATATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 13 0.59
20 9 0.41
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
ATTTAAAAAATAAATAAATT
Found at i:458042 original size:20 final size:20
Alignment explanation
Indices: 458019--458068 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
458009 TATTTAAATG
* *
458019 TTTATATGTAAATATCTAAA
1 TTTATATGCAAATATCAAAA
458039 TTTATATGCAAATATCAAAA
1 TTTATATGCAAATATCAAAA
*
458059 TTTACATGCA
1 TTTATATGCA
458069 TTTATATGGG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.44, C:0.10, G:0.06, T:0.40
Consensus pattern (20 bp):
TTTATATGCAAATATCAAAA
Found at i:464278 original size:19 final size:19
Alignment explanation
Indices: 464235--464285 Score: 79
Period size: 19 Copynumber: 2.7 Consensus size: 19
464225 TTTTAAGAGC
464235 TAGTTATTAA--TTATTAT
1 TAGTTATTAATTTTATTAT
464252 TGAGTTATTAATTTTATTAT
1 T-AGTTATTAATTTTATTAT
464272 TAGTTATTAATTTT
1 TAGTTATTAATTTT
464286 GTAACTAGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
17 1 0.03
18 9 0.29
19 13 0.42
20 8 0.26
ACGTcount: A:0.31, C:0.00, G:0.08, T:0.61
Consensus pattern (19 bp):
TAGTTATTAATTTTATTAT
Found at i:464294 original size:19 final size:19
Alignment explanation
Indices: 464234--464295 Score: 58
Period size: 19 Copynumber: 3.3 Consensus size: 19
464224 CTTTTAAGAG
464234 CTAGTTATTAATTATTAT--
1 CTAGTTATTAATT-TTATAA
*
464252 -TGAGTTATTAATTTTATTA
1 CT-AGTTATTAATTTTATAA
* *
464271 TTAGTTATTAATTTTGTAA
1 CTAGTTATTAATTTTATAA
464290 CTAGTT
1 CTAGTT
464296 GAATTTTGTT
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
17 5 0.14
18 11 0.30
19 20 0.54
20 1 0.03
ACGTcount: A:0.31, C:0.03, G:0.10, T:0.56
Consensus pattern (19 bp):
CTAGTTATTAATTTTATAA
Found at i:466306 original size:27 final size:26
Alignment explanation
Indices: 466259--466310 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 26
466249 TTAATAATTA
466259 TAATTTTTTTACATTAAATAAATAAT
1 TAATTTTTTTACATTAAATAAATAAT
*
466285 TAATTATTTTTA-ATTATTATAAATAA
1 TAATT-TTTTTACATTA-AATAAATAA
466311 AGTATAAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 9 0.39
27 14 0.61
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (26 bp):
TAATTTTTTTACATTAAATAAATAAT
Found at i:468587 original size:33 final size:33
Alignment explanation
Indices: 468550--468614 Score: 112
Period size: 33 Copynumber: 2.0 Consensus size: 33
468540 TGGAGATGAA
468550 ATTTATCTTTAATATTATTAAATTAAAAATAAT
1 ATTTATCTTTAATATTATTAAATTAAAAATAAT
* *
468583 ATTTATCTTTAATATTGTTAAATTTAAAATAA
1 ATTTATCTTTAATATTATTAAATTAAAAATAA
468615 AAAATACTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.46, C:0.03, G:0.02, T:0.49
Consensus pattern (33 bp):
ATTTATCTTTAATATTATTAAATTAAAAATAAT
Found at i:468937 original size:17 final size:16
Alignment explanation
Indices: 468910--468969 Score: 61
Period size: 18 Copynumber: 3.6 Consensus size: 16
468900 ATTATTAACA
468910 TTATAAATTAATATATTT
1 TTAT-AATTAA-ATATTT
468928 TTATAATTAAATTAATTT
1 TTATAATTAAA-T-ATTT
*
468946 TAATAA--AAATATTT
1 TTATAATTAAATATTT
468960 TTATAATTAA
1 TTATAATTAA
468970 TACGTAGTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 9 0.25
15 1 0.03
16 6 0.17
17 7 0.19
18 13 0.36
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TTATAATTAAATATTT
Found at i:469128 original size:3 final size:3
Alignment explanation
Indices: 469120--469147 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
469110 ATAAGTTAAA
469120 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
469148 TTGTTTAACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:469951 original size:25 final size:25
Alignment explanation
Indices: 469917--469968 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
469907 ATGTGATGAG
*
469917 TTATTTTTTAGTTTTTAA-TTTTTAT
1 TTATATTTTAG-TTTTAATTTTTTAT
469942 TTATATTTTAGTTTTAATTTTTTAT
1 TTATATTTTAGTTTTAATTTTTTAT
469967 TT
1 TT
469969 TAAATAATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 6 0.24
25 19 0.76
ACGTcount: A:0.21, C:0.00, G:0.04, T:0.75
Consensus pattern (25 bp):
TTATATTTTAGTTTTAATTTTTTAT
Found at i:472555 original size:21 final size:19
Alignment explanation
Indices: 472531--472570 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 19
472521 TTTAAATTAC
472531 TATTAATAATAAAAATATTTT
1 TATTAA-AATAAAAA-ATTTT
*
472552 TATTTAAATAAAAAATTTT
1 TATTAAAATAAAAAATTTT
472571 AAAATTTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 5 0.28
20 8 0.44
21 5 0.28
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
TATTAAAATAAAAAATTTT
Found at i:473447 original size:11 final size:11
Alignment explanation
Indices: 473431--473461 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
473421 TAAATTTTAT
*
473431 TTTTTACTTAA
1 TTTTTAATTAA
473442 TTTTTAATTAA
1 TTTTTAATTAA
473453 TTTTTAATT
1 TTTTTAATT
473462 TTTTATAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (11 bp):
TTTTTAATTAA
Found at i:474545 original size:2 final size:2
Alignment explanation
Indices: 474538--474567 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
474528 TAGTCTACAA
474538 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
474568 GAAGCCATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:474852 original size:26 final size:25
Alignment explanation
Indices: 474822--474886 Score: 67
Period size: 27 Copynumber: 2.5 Consensus size: 25
474812 ATACTAAAAT
* * *
474822 AAAATAAAAATCAATTAAAATAGTTA
1 AAAATAAAAA-AAATTAAAATAATCA
*
474848 AAAATTAAAACAAAATTAAATTAATCA
1 AAAA-TAAAA-AAAATTAAAATAATCA
474875 AAAATAAAAAAA
1 AAAATAAAAAAA
474887 TCTACAAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
25 3 0.09
26 9 0.27
27 20 0.61
28 1 0.03
ACGTcount: A:0.71, C:0.05, G:0.02, T:0.23
Consensus pattern (25 bp):
AAAATAAAAAAAATTAAAATAATCA
Found at i:478009 original size:21 final size:21
Alignment explanation
Indices: 477975--478022 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
477965 CTGATTTTTT
*
477975 AAAATTTATATTTAAAAATTAA
1 AAAATTAATATTTAAAAA-TAA
*
477997 AAAATTAAT-TTTAAATATAA
1 AAAATTAATATTTAAAAATAA
478017 AAAATT
1 AAAATT
478023 TAAAATTTCT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 9 0.38
21 7 0.29
22 8 0.33
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
AAAATTAATATTTAAAAATAA
Found at i:478025 original size:21 final size:23
Alignment explanation
Indices: 477975--478030 Score: 66
Period size: 21 Copynumber: 2.6 Consensus size: 23
477965 CTGATTTTTT
477975 AAAATTT-ATATTTAAAAATTAA
1 AAAATTTAATATTTAAAAATTAA
*
477997 AAAA-TTAAT-TTTAAATA-TAA
1 AAAATTTAATATTTAAAAATTAA
*
478017 AAAATTTAAAATTT
1 AAAATTTAATATTT
478031 CTTGTTAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
20 7 0.24
21 13 0.45
22 9 0.31
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (23 bp):
AAAATTTAATATTTAAAAATTAA
Found at i:480182 original size:4 final size:4
Alignment explanation
Indices: 480175--480215 Score: 66
Period size: 4 Copynumber: 10.5 Consensus size: 4
480165 GATGTTATAT
*
480175 ATAG ATAG ATA- ATAG ATAG ATAG ATAG ATAG ATAT ATAG AT
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG AT
480216 GCAAAGGTGA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
3 3 0.09
4 31 0.91
ACGTcount: A:0.51, C:0.00, G:0.20, T:0.29
Consensus pattern (4 bp):
ATAG
Found at i:483635 original size:13 final size:13
Alignment explanation
Indices: 483617--483647 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
483607 ACATTTCTTC
483617 ATGTATCGATACA
1 ATGTATCGATACA
483630 ATGTATCGATACA
1 ATGTATCGATACA
*
483643 TTGTA
1 ATGTA
483648 CCATGTATCG
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:0.35, C:0.13, G:0.16, T:0.35
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:483635 original size:33 final size:33
Alignment explanation
Indices: 483597--483739 Score: 119
Period size: 33 Copynumber: 4.0 Consensus size: 33
483587 GTTACAAGTT
483597 ATGTATCGATACATT-T-CTTCATGTATCGATACA
1 ATGTATCGATACATTGTAC--CATGTATCGATACA
483630 ATGTATCGATACATTGTACCATGTATCGATACAA
1 ATGTATCGATACATTGTACCATGTATCGATAC-A
* * * **
483664 ATAGTGATAGGGTAGCTACTGCCAGTTTCATGTATCGATACA
1 AT-GT-AT-CGATA-C-A-T---TGTACCATGTATCGATACA
483706 ATGTATCGATACATTGTACCATGTATCGATACA
1 ATGTATCGATACATTGTACCATGTATCGATACA
483739 A
1 A
483740 ATAGTAATAG
Statistics
Matches: 88, Mismatches: 10, Indels: 24
0.72 0.08 0.20
Matches are distributed among these distances:
33 45 0.51
34 4 0.05
35 3 0.03
36 3 0.03
37 4 0.05
38 2 0.02
39 4 0.05
40 3 0.03
41 2 0.02
42 3 0.03
43 15 0.17
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Consensus pattern (33 bp):
ATGTATCGATACATTGTACCATGTATCGATACA
Found at i:483711 original size:13 final size:13
Alignment explanation
Indices: 483693--483723 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
483683 TGCCAGTTTC
483693 ATGTATCGATACA
1 ATGTATCGATACA
483706 ATGTATCGATACA
1 ATGTATCGATACA
*
483719 TTGTA
1 ATGTA
483724 CCATGTATCG
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:0.35, C:0.13, G:0.16, T:0.35
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:483740 original size:76 final size:76
Alignment explanation
Indices: 483614--483783 Score: 331
Period size: 76 Copynumber: 2.2 Consensus size: 76
483604 GATACATTTC
*
483614 TTCATGTATCGATACAATGTATCGATACATTGTACCATGTATCGATACAAATAGTGATAGGGTAG
1 TTCATGTATCGATACAATGTATCGATACATTGTACCATGTATCGATACAAATAGTAATAGGGTAG
483679 CTACTGCCAGT
66 CTACTGCCAGT
483690 TTCATGTATCGATACAATGTATCGATACATTGTACCATGTATCGATACAAATAGTAATAGGGTAG
1 TTCATGTATCGATACAATGTATCGATACATTGTACCATGTATCGATACAAATAGTAATAGGGTAG
483755 CTACTGCCAGT
66 CTACTGCCAGT
483766 TTCATGTATCGATACAAT
1 TTCATGTATCGATACAAT
483784 TTGGCCATGT
Statistics
Matches: 93, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
76 93 1.00
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Consensus pattern (76 bp):
TTCATGTATCGATACAATGTATCGATACATTGTACCATGTATCGATACAAATAGTAATAGGGTAG
CTACTGCCAGT
Found at i:483808 original size:13 final size:13
Alignment explanation
Indices: 483790--483816 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
483780 CAATTTGGCC
483790 ATGTATCGATACA
1 ATGTATCGATACA
483803 ATGTATCGATACA
1 ATGTATCGATACA
483816 A
1 A
483817 AGCAACATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:484385 original size:18 final size:18
Alignment explanation
Indices: 484362--484420 Score: 52
Period size: 18 Copynumber: 3.3 Consensus size: 18
484352 TTTTTCTCCT
484362 CTTAAAAATATTCTCCCC
1 CTTAAAAATATTCTCCCC
* **
484380 CTTAAACGAT-TATCT-CTT
1 CTTAAA-AATAT-TCTCCCC
484398 CTTAAAAA-ATTCTCCCC
1 CTTAAAAATATTCTCCCC
484415 CTTAAA
1 CTTAAA
484421 CGATTATCTT
Statistics
Matches: 31, Mismatches: 6, Indels: 9
0.67 0.13 0.20
Matches are distributed among these distances:
16 3 0.10
17 9 0.29
18 14 0.45
19 5 0.16
ACGTcount: A:0.34, C:0.29, G:0.02, T:0.36
Consensus pattern (18 bp):
CTTAAAAATATTCTCCCC
Found at i:484414 original size:35 final size:36
Alignment explanation
Indices: 484356--484429 Score: 132
Period size: 35 Copynumber: 2.1 Consensus size: 36
484346 TTTTCGTTTT
484356 TCTCCTCTTAAAAATATTCTCCCCCTTAAACGATTA
1 TCTCCTCTTAAAAATATTCTCCCCCTTAAACGATTA
*
484392 TCTCTTCTTAAAAA-ATTCTCCCCCTTAAACGATTA
1 TCTCCTCTTAAAAATATTCTCCCCCTTAAACGATTA
484427 TCT
1 TCT
484430 TCTCCCCCTT
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
35 24 0.65
36 13 0.35
ACGTcount: A:0.30, C:0.30, G:0.03, T:0.38
Consensus pattern (36 bp):
TCTCCTCTTAAAAATATTCTCCCCCTTAAACGATTA
Found at i:484864 original size:21 final size:21
Alignment explanation
Indices: 484838--484894 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
484828 AAATTATCCA
484838 AATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTGTAG
* *
484859 AATGTATTGATACATTTGTGG
1 AATGTATCGATACATTTGTAG
484880 AATGTATCGATACAT
1 AATGTATCGATACAT
484895 CCTACAAATG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.33, C:0.09, G:0.19, T:0.39
Consensus pattern (21 bp):
AATGTATCGATACATTTGTAG
Found at i:484974 original size:19 final size:19
Alignment explanation
Indices: 484950--485017 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
484940 AATTCAACAA
484950 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
484969 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
484984 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
485001 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
485018 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:484989 original size:13 final size:13
Alignment explanation
Indices: 484971--484995 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
484961 ACATAAGTTT
484971 TGTATCGATACAA
1 TGTATCGATACAA
484984 TGTATCGATACA
1 TGTATCGATACA
484996 TAAGTATTGT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:484993 original size:32 final size:32
Alignment explanation
Indices: 484952--485014 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
484942 TTCAACAATT
*
484952 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
484984 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
485015 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:485075 original size:13 final size:13
Alignment explanation
Indices: 485057--485082 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
485047 CATTTTTCTG
485057 TGTATCGATACAT
1 TGTATCGATACAT
485070 TGTATCGATACAT
1 TGTATCGATACAT
485083 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:485079 original size:33 final size:33
Alignment explanation
Indices: 485037--485103 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
485027 GCCAAGGAAA
***
485037 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
485070 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
485103 T
1 T
485104 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:487499 original size:51 final size:51
Alignment explanation
Indices: 487444--487819 Score: 261
Period size: 51 Copynumber: 7.4 Consensus size: 51
487434 AATTCTCCAC
* *
487444 AATCGGGGATATTCCAACTCCGATTTTATTTTCAAACCACTAATTTTCTAT
1 AATCGGGGATACTCCAACTCCGATTTTATTTTCAAAACACTAATTTTCTAT
* * * *
487495 AATCGGGGATACTCCAACTCCGATTTTATTTCCAAAA-AATACCAATTTCTTCAC
1 AATCGGGGATACTCCAACTCCGATTTTATTTTCAAAACACTA--ATTTTC-T-AT
* *** * * * * *
487549 AATCGGGGATACTCCAACCCCG--GGGATATTCCAACCCCGTTA-TTTC--T
1 AATCGGGGATACTCCAACTCCGATTTTATTTTCAAAACAC-TAATTTTCTAT
* * * * * * *
487596 GA--GAGGATACTCCAACCCCGACTTTATTTTCAAAATATTGATTTT-TCAT
1 AATCGGGGATACTCCAACTCCGATTTTATTTTCAAAACACTAATTTTCT-AT
* * * * *
487645 AATCGGGGATACTCCAACCCCGGTTTTA-TTGCTAAAACACTAATTTTTCCAC
1 AATCGGGGATACTCCAACTCCGATTTTATTTTC-AAAACACTAA-TTTTCTAT
* *
487697 AATCGGGGATATTCCAACTCCAATTTTATTTTCAAAACACTAATTTTCTAT
1 AATCGGGGATACTCCAACTCCGATTTTATTTTCAAAACACTAATTTTCTAT
* * * * *
487748 AATCGGGGATACTCCAACTCTGATTTTATTTCCAAAA-AATACCAATTTCTTCAC
1 AATCGGGGATACTCCAACTCCGATTTTATTTTCAAAACACTA--ATTTTC-T-AT
487802 AATCGGGGATACTCCAAC
1 AATCGGGGATACTCCAAC
487820 CCCGTTAATC
Statistics
Matches: 249, Mismatches: 54, Indels: 41
0.72 0.16 0.12
Matches are distributed among these distances:
45 17 0.07
46 2 0.01
47 11 0.04
49 2 0.01
50 9 0.04
51 105 0.42
52 56 0.22
53 5 0.02
54 42 0.17
ACGTcount: A:0.31, C:0.24, G:0.12, T:0.33
Consensus pattern (51 bp):
AATCGGGGATACTCCAACTCCGATTTTATTTTCAAAACACTAATTTTCTAT
Found at i:487574 original size:17 final size:17
Alignment explanation
Indices: 487552--487587 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
487542 TCTTCACAAT
487552 CGGGGATACTCCAACCC
1 CGGGGATACTCCAACCC
*
487569 CGGGGATATTCCAACCC
1 CGGGGATACTCCAACCC
487586 CG
1 CG
487588 TTATTTCTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.22, C:0.39, G:0.25, T:0.14
Consensus pattern (17 bp):
CGGGGATACTCCAACCC
Found at i:487732 original size:103 final size:105
Alignment explanation
Indices: 487600--487822 Score: 274
Period size: 103 Copynumber: 2.1 Consensus size: 105
487590 ATTTCTGAGA
* * * *
487600 GGATACTCCAACCCCGACTTTATTTTCAAAATATTGATTTT-TCATAATCGGGGATACTCCAACC
1 GGATACTCCAACCCCAACTTTATTTTCAAAACACTAATTTTCT-ATAATCGGGGATACTCCAACC
* * * *
487664 CCGGTTTTA-TTGC-TAAAACACTAATTT-TTCCACAATCGG
65 CCGATTTTATTTCCAAAAAACACCAATTTCTT-CACAATCGG
* * * *
487703 GGATATTCCAACTCCAATTTTATTTTCAAAACACTAATTTTCTATAATCGGGGATACTCCAACTC
1 GGATACTCCAACCCCAACTTTATTTTCAAAACACTAATTTTCTATAATCGGGGATACTCCAACCC
* *
487768 TGATTTTATTTCCAAAAAATACCAATTTCTTCACAATCGG
66 CGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGG
487808 GGATACTCCAACCCC
1 GGATACTCCAACCCC
487823 GTTAATCATC
Statistics
Matches: 100, Mismatches: 16, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
103 61 0.61
104 4 0.04
105 33 0.33
106 2 0.02
ACGTcount: A:0.31, C:0.25, G:0.11, T:0.34
Consensus pattern (105 bp):
GGATACTCCAACCCCAACTTTATTTTCAAAACACTAATTTTCTATAATCGGGGATACTCCAACCC
CGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGG
Found at i:487837 original size:27 final size:28
Alignment explanation
Indices: 487803--487878 Score: 109
Period size: 27 Copynumber: 2.8 Consensus size: 28
487793 TTTCTTCACA
487803 ATCGGGGATACTCCAACCCCGTTA-ATC
1 ATCGGGGATACTCCAACCCCGTTATATC
*
487830 ATCGGGGATACTCCAACCCCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTATATC
***
487858 CGAGGGGATACTCCAACCCCG
1 ATCGGGGATACTCCAACCCCG
487879 GCTTTATTCC
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
27 24 0.55
28 20 0.45
ACGTcount: A:0.24, C:0.34, G:0.21, T:0.21
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTATATC
Found at i:487952 original size:28 final size:29
Alignment explanation
Indices: 487912--487966 Score: 85
Period size: 28 Copynumber: 1.9 Consensus size: 29
487902 TCTCATAATT
487912 GGGGATACTCCAACCCCG-TTATTTTCGA
1 GGGGATACTCCAACCCCGATTATTTTCGA
* *
487940 GGGGATACTCCAATCCCGATTTTTTTC
1 GGGGATACTCCAACCCCGATTATTTTC
487967 TAATCATCGA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 17 0.71
29 7 0.29
ACGTcount: A:0.20, C:0.27, G:0.20, T:0.33
Consensus pattern (29 bp):
GGGGATACTCCAACCCCGATTATTTTCGA
Found at i:488014 original size:77 final size:78
Alignment explanation
Indices: 487832--488034 Score: 248
Period size: 77 Copynumber: 2.6 Consensus size: 78
487822 CGTTAATCAT
* *
487832 CGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGCTTTATTCCCAAAATAT
1 CGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCC-GATTTATTCCCAAAATAT
* * *
487897 TGATTTCTCATAAT
65 CGATTTCTCACAAC
* * ** *
487911 TGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAATCCCGATTT-TTTTC-TAATCAT
1 CGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGATTTATTCCCAAAAT-AT
487974 CGATTTCTCACAAC
65 CGATTTCTCACAAC
* * * *
487988 CGGGGATACTCCAGCCCCGTTATTTTCAAGGGAACACTCCAACCCCG
1 CGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCG
488035 TTATTATCTC
Statistics
Matches: 107, Mismatches: 16, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
76 3 0.03
77 57 0.53
78 4 0.04
79 43 0.40
ACGTcount: A:0.24, C:0.30, G:0.17, T:0.29
Consensus pattern (78 bp):
CGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGATTTATTCCCAAAATATC
GATTTCTCACAAC
Found at i:492456 original size:24 final size:23
Alignment explanation
Indices: 492406--492457 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 23
492396 TATTTTTTTT
* * * *
492406 ATTTTTTAAAACAAATAAAGATC
1 ATTTTTTAAAAAAAAAAAACATA
492429 ATTTTTTAAAAAAAAAAAACATA
1 ATTTTTTAAAAAAAAAAAACATA
*
492452 AATTTT
1 ATTTTT
492458 GAACTTTTCT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.56, C:0.06, G:0.02, T:0.37
Consensus pattern (23 bp):
ATTTTTTAAAAAAAAAAAACATA
Found at i:492603 original size:2 final size:2
Alignment explanation
Indices: 492596--492626 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
492586 GATTTTCAAA
*
492596 AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
492627 AATAAAATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:493019 original size:17 final size:17
Alignment explanation
Indices: 492997--493032 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
492987 CATTTCATAT
* *
492997 TTTTTCTTTTTTTTTTC
1 TTTTTCTTTCTTTCTTC
493014 TTTTTCTTTCTTTCTTC
1 TTTTTCTTTCTTTCTTC
493031 TT
1 TT
493033 CATCTTCCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (17 bp):
TTTTTCTTTCTTTCTTC
Found at i:494324 original size:32 final size:32
Alignment explanation
Indices: 494275--494717 Score: 717
Period size: 32 Copynumber: 13.8 Consensus size: 32
494265 AAAATGGTGA
* * *
494275 TTTGAAAAGGGTTGCCACTGACTTGCGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* *
494307 TTTTAAATGGGTTGCCACCGACTTGCGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* * *
494339 TTTTAAATGGGTTGCCACCAACTTGTGGGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
**
494371 TTTGAAACAGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
494403 TTTGAAATGGGTTGCCACCTACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
494435 TTT-AGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGA-AATGGGTTGCCACCGACTTGTGTGGGC
494467 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
494499 TTTGAAATGGGTTGCCATCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
494531 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
494563 TTTGAAATGGGTTGCCACTGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
494595 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
494627 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
494659 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* *
494691 TTTGGAATGGGTTGCCACCGATTTGTG
1 TTTGAAATGGGTTGCCACCGACTTGTG
494718 AATTTAAAAG
Statistics
Matches: 388, Mismatches: 21, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
31 1 0.00
32 386 0.99
33 1 0.00
ACGTcount: A:0.16, C:0.19, G:0.34, T:0.32
Consensus pattern (32 bp):
TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
Found at i:494769 original size:27 final size:27
Alignment explanation
Indices: 494703--495494 Score: 1129
Period size: 27 Copynumber: 28.9 Consensus size: 27
494693 TGGAATGGGT
* * * *
494703 TGCCACCGATTTGTGAATTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
494730 ATGCCACGGAGTTGTGGACTTAAAAGGG
1 -TGCCACGGAGTTGTGGACTTAAAAGGG
494758 TGCCACGGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
494785 ATGCCACGGAGTTGTGGACTTAAAAGGG
1 -TGCCACGGAGTTGTGGACTTAAAAGGG
* *
494813 TGCCACAGAGTTGTGGACTAAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
*
494840 TGCCACAGAGTTGTGGACTTTAAAAGGG
1 TGCCACGGAGTTGTGGAC-TTAAAAGGG
* * *
494868 TGCCACAGAGTTGTGGACTTAAAAAAGA
1 TGCCACGGAGTTGTGGACTT-AAAAGGG
* * *
494896 TGCCACAGAGTTATGGACTTAAAAAGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
494923 TGCCACGGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
* *
494950 TGCTACGGAGTTGTGGTCTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
494977 TGCCACGGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
* * **
495004 ATGCCATGGAGTTATGGACTTAAAAGAA
1 -TGCCACGGAGTTGTGGACTTAAAAGGG
*
495032 TGCCACAGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
495059 TGCCACGGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
*
495086 TGCCACGGAGTTGTGGTA-TTAAAAGGAA
1 TGCCACGGAGTTGTGG-ACTTAAAAGG-G
*
495114 TGCCACAGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
495141 TGCCACGGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
495168 TGCCACGGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
*
495195 TGCCACGGAGTTGTGGTA-TTAAAAGGAA
1 TGCCACGGAGTTGTGG-ACTTAAAAGG-G
*
495223 TGCCACAGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
495250 TGCCACGGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
*
495277 TGCCACGGAGTTGTGGACTTAAAAGGAA
1 TGCCACGGAGTTGTGGACTTAAAAGG-G
**
495305 TGCCATAGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
*
495332 TGCCACGGAGTTGTGGACTAAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
* *
495359 TACCACGGAGTTGTGGATTTTAAAAGGG
1 TGCCACGGAGTTGTGGA-CTTAAAAGGG
*
495387 TGCCACAGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
*
495414 TACCACGGAGTTGTGGACTTTAAAAGGG
1 TGCCACGGAGTTGTGGAC-TTAAAAGGG
* *
495442 TGCCACAGAGTTGTGGACTTAAAAGGA
1 TGCCACGGAGTTGTGGACTTAAAAGGG
* *
495469 TGTCACAGAGTTGTGGACTTTAAAAG
1 TGCCACGGAGTTGTGGAC-TTAAAAG
495495 AAAATGCCAC
Statistics
Matches: 695, Mismatches: 55, Indels: 28
0.89 0.07 0.04
Matches are distributed among these distances:
27 445 0.64
28 250 0.36
ACGTcount: A:0.30, C:0.14, G:0.33, T:0.23
Consensus pattern (27 bp):
TGCCACGGAGTTGTGGACTTAAAAGGG
Found at i:494772 original size:55 final size:54
Alignment explanation
Indices: 494703--495494 Score: 1129
Period size: 55 Copynumber: 14.5 Consensus size: 54
494693 TGGAATGGGT
* * * *
494703 TGCCACCGATTTGTGAATTTAAAAGGGATGCCACGGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG-TGCCACGGAGTTGTGGACTTAAAAGGG
494758 TGCCACGGAGTTGTGGACTTAAAAGGGATGCCACGGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG-TGCCACGGAGTTGTGGACTTAAAAGGG
* * *
494813 TGCCACAGAGTTGTGGACTAAAAAGGGTGCCACAGAGTTGTGGACTTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGAC-TTAAAAGGG
* * * * * *
494868 TGCCACAGAGTTGTGGACTTAAAAAAGATGCCACAGAGTTATGGACTTAAAAAGG
1 TGCCACGGAGTTGTGGACTT-AAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGG
* *
494923 TGCCACGGAGTTGTGGACTTAAAAGGGTGCTACGGAGTTGTGGTCTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGG
* * **
494977 TGCCACGGAGTTGTGGACTTAAAAGGGATGCCATGGAGTTATGGACTTAAAAGAA
1 TGCCACGGAGTTGTGGACTTAAAAGGG-TGCCACGGAGTTGTGGACTTAAAAGGG
*
495032 TGCCACAGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGG
* *
495086 TGCCACGGAGTTGTGGTA-TTAAAAGGAATGCCACAGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGG-ACTTAAAAGG-GTGCCACGGAGTTGTGGACTTAAAAGGG
495141 TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGG
* *
495195 TGCCACGGAGTTGTGGTA-TTAAAAGGAATGCCACAGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGG-ACTTAAAAGG-GTGCCACGGAGTTGTGGACTTAAAAGGG
*
495250 TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGAA
1 TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGG-G
** *
495305 TGCCATAGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTAAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGG
* * *
495359 TACCACGGAGTTGTGGATTTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGA-CTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGG
* * *
495414 TACCACGGAGTTGTGGACTTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGA
1 TGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGG
* *
495469 TGTCACAGAGTTGTGGACTTTAAAAG
1 TGCCACGGAGTTGTGGAC-TTAAAAG
495495 AAAATGCCAC
Statistics
Matches: 669, Mismatches: 56, Indels: 24
0.89 0.07 0.03
Matches are distributed among these distances:
54 208 0.31
55 439 0.66
56 22 0.03
ACGTcount: A:0.30, C:0.14, G:0.33, T:0.23
Consensus pattern (54 bp):
TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGG
Found at i:494837 original size:82 final size:81
Alignment explanation
Indices: 494703--495494 Score: 1147
Period size: 82 Copynumber: 9.6 Consensus size: 81
494693 TGGAATGGGT
* * * * *
494703 TGCCACCGATTTGTGAATTTAAAAGGGATGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAG
1 TGCCACGGAGTTGTGGACTTAAAAGGG-TGCCACAGAGTTGTGGACTTAAAAGGGTGCCACGGAG
494768 TTGTGGACTTAAAAGGG
65 TTGTGGACTTAAAAGGG
* *
494785 ATGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTAAAAAGGGTGCCACAGAG
1 -TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGGTGCCACGGAG
494850 TTGTGGACTTTAAAAGGG
65 TTGTGGAC-TTAAAAGGG
* * * * *
494868 TGCCACAGAGTTGTGGACTTAAAAAAGATGCCACAGAGTTATGGACTTAAAAAGGTGCCACGGAG
1 TGCCACGGAGTTGTGGACTT-AAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGGTGCCACGGAG
494933 TTGTGGACTTAAAAGGG
65 TTGTGGACTTAAAAGGG
* * * *
494950 TGCTACGGAGTTGTGGTCTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGATGCCATGGAG
1 TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGG-TGCCACGGAG
* **
495015 TTATGGACTTAAAAGAA
65 TTGTGGACTTAAAAGGG
* *
495032 TGCCACAGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGT
1 TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGGTGCCACGGAGT
*
495097 TGTGGTA-TTAAAAGGAA
66 TGTGG-ACTTAAAAGG-G
* *
495114 TGCCACAGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGT
1 TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGGTGCCACGGAGT
495179 TGTGGACTTAAAAGGG
66 TGTGGACTTAAAAGGG
*
495195 TGCCACGGAGTTGTGGTA-TTAAAAGGAATGCCACAGAGTTGTGGACTTAAAAGGGTGCCACGGA
1 TGCCACGGAGTTGTGG-ACTTAAAAGG-GTGCCACAGAGTTGTGGACTTAAAAGGGTGCCACGGA
495259 GTTGTGGACTTAAAAGGG
64 GTTGTGGACTTAAAAGGG
* *
495277 TGCCACGGAGTTGTGGACTTAAAAGGAATGCCATAGAGTTGTGGACTTAAAAGGGTGCCACGGAG
1 TGCCACGGAGTTGTGGACTTAAAAGG-GTGCCACAGAGTTGTGGACTTAAAAGGGTGCCACGGAG
*
495342 TTGTGGACTAAAAAGGG
65 TTGTGGACTTAAAAGGG
* * *
495359 TACCACGGAGTTGTGGATTTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGGTACCACGGAG
1 TGCCACGGAGTTGTGGA-CTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGGTGCCACGGAG
495424 TTGTGGACTTTAAAAGGG
65 TTGTGGAC-TTAAAAGGG
* * *
495442 TGCCACAGAGTTGTGGACTTAAAAGGATGTCACAGAGTTGTGGACTTTAAAAG
1 TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGAC-TTAAAAG
495495 AAAATGCCAC
Statistics
Matches: 648, Mismatches: 49, Indels: 24
0.90 0.07 0.03
Matches are distributed among these distances:
81 75 0.12
82 457 0.71
83 116 0.18
ACGTcount: A:0.30, C:0.14, G:0.33, T:0.23
Consensus pattern (81 bp):
TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGGTGCCACGGAGT
TGTGGACTTAAAAGGG
Found at i:496564 original size:13 final size:13
Alignment explanation
Indices: 496546--496571 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
496536 AGGGTGAAAA
496546 GGTTTTTTTTTTT
1 GGTTTTTTTTTTT
496559 GGTTTTTTTTTTT
1 GGTTTTTTTTTTT
496572 TTTTTAGGAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.00, C:0.00, G:0.15, T:0.85
Consensus pattern (13 bp):
GGTTTTTTTTTTT
Found at i:502795 original size:23 final size:24
Alignment explanation
Indices: 502744--502795 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 24
502734 TATTTTTTTT
* * *
502744 ATTTTTTAAAACAAATAAAGATCA
1 ATTTTTTAAAACAAAAAAACATAA
*
502768 TTTTTTTAAAA-AAAAAAACATAA
1 ATTTTTTAAAACAAAAAAACATAA
502791 ATTTT
1 ATTTT
502796 GAACTTTTCT
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
23 13 0.57
24 10 0.43
ACGTcount: A:0.54, C:0.06, G:0.02, T:0.38
Consensus pattern (24 bp):
ATTTTTTAAAACAAAAAAACATAA
Found at i:503343 original size:10 final size:10
Alignment explanation
Indices: 503330--503359 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
503320 CCATTTCATA
503330 TTTTTTCTTT
1 TTTTTTCTTT
503340 TTTTTTCTTT
1 TTTTTTCTTT
*
503350 TTCTTTCTTT
1 TTTTTTCTTT
503360 CTTCTTCATC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (10 bp):
TTTTTTCTTT
Found at i:503352 original size:16 final size:17
Alignment explanation
Indices: 503331--503365 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
503321 CATTTCATAT
*
503331 TTTTTCTTT-TTTTTTC
1 TTTTTCTTTCTTTCTTC
503347 TTTTTCTTTCTTTCTTC
1 TTTTTCTTTCTTTCTTC
503364 TT
1 TT
503366 CATCTTCCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (17 bp):
TTTTTCTTTCTTTCTTC
Found at i:510744 original size:19 final size:19
Alignment explanation
Indices: 510699--510755 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
510689 CTGCCAGTTT
**
510699 CATGTATCGATACAATTTGGC
1 CATGTATCGATACAA--TGAA
510720 CATGTATCGATACAATGAA
1 CATGTATCGATACAATGAA
510739 CATGTATCGATACAATG
1 CATGTATCGATACAATG
510756 TATCGATACA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 19 0.56
21 15 0.44
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.30
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:510758 original size:13 final size:13
Alignment explanation
Indices: 510740--510766 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
510730 TACAATGAAC
510740 ATGTATCGATACA
1 ATGTATCGATACA
510753 ATGTATCGATACA
1 ATGTATCGATACA
510766 A
1 A
510767 AGCAGCATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:510762 original size:32 final size:33
Alignment explanation
Indices: 510721--510783 Score: 101
Period size: 32 Copynumber: 1.9 Consensus size: 33
510711 CAATTTGGCC
*
510721 ATGTATCGATACAATG-AACATGTATCGATACA
1 ATGTATCGATACAAAGCAACATGTATCGATACA
*
510753 ATGTATCGATACAAAGCAGCATGTATCGATA
1 ATGTATCGATACAAAGCAACATGTATCGATA
510784 GATCTGGGTG
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
32 15 0.54
33 13 0.46
ACGTcount: A:0.40, C:0.16, G:0.17, T:0.27
Consensus pattern (33 bp):
ATGTATCGATACAAAGCAACATGTATCGATACA
Found at i:515348 original size:2 final size:2
Alignment explanation
Indices: 515341--515376 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
515331 CTATAGACTT
*
515341 TA TA TA TA -A TG 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 TA TA T
515377 CATACTACTC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:515976 original size:11 final size:11
Alignment explanation
Indices: 515948--516007 Score: 54
Period size: 11 Copynumber: 5.5 Consensus size: 11
515938 AATAATTATG
515948 TATAAA-AT-A
1 TATAAATATAA
*
515957 TAAAAATATAA
1 TATAAATATAA
515968 TATAAATATAA
1 TATAAATATAA
515979 TATATTTAATA-AA
1 TATA---AATATAA
*
515992 TATAAAAATAA
1 TATAAATATAA
516003 TATAA
1 TATAA
516008 TAATATTATA
Statistics
Matches: 42, Mismatches: 3, Indels: 10
0.76 0.05 0.18
Matches are distributed among these distances:
9 5 0.12
10 5 0.12
11 22 0.52
13 6 0.14
14 4 0.10
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (11 bp):
TATAAATATAA
Found at i:515980 original size:24 final size:24
Alignment explanation
Indices: 515953--516018 Score: 80
Period size: 24 Copynumber: 2.8 Consensus size: 24
515943 TTATGTATAA
* *
515953 AATATAAAAATATAATATAAATAT
1 AATATAATAATATAATATAAAAAT
*
515977 AATATATTTAATA-AATATAAAAAT
1 AATATA-ATAATATAATATAAAAAT
*
516001 AATATAATAATATTATAT
1 AATATAATAATATAATAT
516019 TACGTGTTTA
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
23 5 0.14
24 26 0.74
25 4 0.11
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (24 bp):
AATATAATAATATAATATAAAAAT
Found at i:516005 original size:48 final size:49
Alignment explanation
Indices: 515922--516018 Score: 117
Period size: 48 Copynumber: 2.0 Consensus size: 49
515912 GATTTACAAA
* * *
515922 AAATAAAATTATATTTAATAATTATGTATAAAATATAAAAATATAATAT
1 AAATAAAATTATATTTAATAAATATGAAAAAAATATAAAAATATAATAT
* * *
515971 AAATATAA-TATATTTAATAAATAT-AAAAATAATATAATAATATTATAT
1 AAATAAAATTATATTTAATAAATATGAAAAA-AATATAAAAATATAATAT
516019 TACGTGTTTA
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
47 3 0.07
48 31 0.76
49 7 0.17
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (49 bp):
AAATAAAATTATATTTAATAAATATGAAAAAAATATAAAAATATAATAT
Found at i:525507 original size:19 final size:21
Alignment explanation
Indices: 525471--525513 Score: 54
Period size: 19 Copynumber: 2.1 Consensus size: 21
525461 TTAGTTTATG
525471 TCAATATAATTAAATAA-TTA
1 TCAATATAATTAAATAATTTA
**
525491 TCAA-ATAATTATTTAATTTA
1 TCAATATAATTAAATAATTTA
525511 TCA
1 TCA
525514 TAGATAACTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 10 0.50
20 10 0.50
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (21 bp):
TCAATATAATTAAATAATTTA
Found at i:532803 original size:2 final size:2
Alignment explanation
Indices: 532796--532820 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
532786 TATATTTTAA
532796 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
532821 ATAATTTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:533542 original size:19 final size:18
Alignment explanation
Indices: 533516--533551 Score: 63
Period size: 19 Copynumber: 1.9 Consensus size: 18
533506 ATTCAAATCA
533516 ATTTAATTAATTAATTTT
1 ATTTAATTAATTAATTTT
533534 ATTTGAATTAATTAATTT
1 ATTT-AATTAATTAATTT
533552 GAAATTTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (18 bp):
ATTTAATTAATTAATTTT
Found at i:533557 original size:15 final size:15
Alignment explanation
Indices: 533515--533554 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
533505 GATTCAAATC
533515 AATTTAA-TT-AATT
1 AATTTAATTTGAATT
*
533528 AATTTTATTTGAATT
1 AATTTAATTTGAATT
533543 AA-TTAATTTGAA
1 AATTTAATTTGAA
533555 ATTTATTGGT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
13 6 0.26
14 11 0.48
15 6 0.26
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (15 bp):
AATTTAATTTGAATT
Found at i:533742 original size:24 final size:23
Alignment explanation
Indices: 533699--533743 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 23
533689 TATATAACCA
*
533699 TTTTATTATATATTATATAATAT
1 TTTTATTATATATTAAATAATAT
533722 TTTTATT-TATAATATAAATAAT
1 TTTTATTATAT-AT-TAAATAAT
533744 TTTATGTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 3 0.16
23 9 0.47
24 7 0.37
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (23 bp):
TTTTATTATATATTAAATAATAT
Found at i:535414 original size:2 final size:2
Alignment explanation
Indices: 535407--535437 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
535397 TTTATCCTTA
535407 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
535438 CAAACTTAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:535514 original size:60 final size:62
Alignment explanation
Indices: 535444--535562 Score: 145
Period size: 62 Copynumber: 2.0 Consensus size: 62
535434 TATACAAACT
* * * * *
535444 TAAAACCCCAAACCTAATTTTTTCT-TT-GGTAG-TAGCTATTCTTATTTTCGTTAGCATTAG
1 TAAAAACCCAAAACTAATTTTTTCTCTTCGGTAGCCA-CAATTCTTATTTTCCTTAGCATTAG
**
535504 TAAAAACCCAAAACTTTTTTTTTCTCTTCGGTAGCCACAATTCTTATTTTCCTTAGCAT
1 TAAAAACCCAAAACTAATTTTTTCTCTTCGGTAGCCACAATTCTTATTTTCCTTAGCAT
535563 CGGGAAAAAT
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
60 21 0.43
61 2 0.04
62 25 0.51
63 1 0.02
ACGTcount: A:0.27, C:0.21, G:0.09, T:0.43
Consensus pattern (62 bp):
TAAAAACCCAAAACTAATTTTTTCTCTTCGGTAGCCACAATTCTTATTTTCCTTAGCATTAG
Found at i:535848 original size:23 final size:24
Alignment explanation
Indices: 535799--535848 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
535789 TAGTAGTTCC
* *
535799 TATAGTTTTGTATTTAGAATATGA
1 TATAGTTTTGTATTGAGAATATAA
535823 TATAGTTGTTG-ATTGA-AATATAA
1 TATAGTT-TTGTATTGAGAATATAA
535846 TAT
1 TAT
535849 TACTGTAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
23 9 0.39
24 11 0.48
25 3 0.13
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.48
Consensus pattern (24 bp):
TATAGTTTTGTATTGAGAATATAA
Found at i:536364 original size:13 final size:13
Alignment explanation
Indices: 536346--536371 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
536336 ACACAAGTTT
536346 TGTATCGATACAA
1 TGTATCGATACAA
536359 TGTATCGATACAA
1 TGTATCGATACAA
536372 AACTACTCTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:543044 original size:21 final size:21
Alignment explanation
Indices: 543018--543094 Score: 102
Period size: 21 Copynumber: 3.7 Consensus size: 21
543008 AAAAAATTCA
543018 AATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTGTAG
*
543039 AATGTATCGATACATTTGTGG
1 AATGTATCGATACATTTGTAG
* * *
543060 AATGTATTGATACA-TTCTACA
1 AATGTATCGATACATTTGTA-G
543081 AATGTATCGATACA
1 AATGTATCGATACA
543095 GGGTCCCAAT
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
20 3 0.06
21 46 0.94
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.36
Consensus pattern (21 bp):
AATGTATCGATACATTTGTAG
Found at i:543154 original size:19 final size:19
Alignment explanation
Indices: 543130--543197 Score: 67
Period size: 19 Copynumber: 3.9 Consensus size: 19
543120 AATTCAACAA
543130 TTTGTATCGATACATAAAT
1 TTTGTATCGATACATAAAT
*
543149 TTTGTATCGATGC---AA-
1 TTTGTATCGATACATAAAT
*
543164 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAAT
*
543181 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
543198 TTAGCTACTG
Statistics
Matches: 40, Mismatches: 3, Indels: 12
0.73 0.05 0.22
Matches are distributed among these distances:
13 10 0.25
16 3 0.08
19 27 0.68
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAAT
Found at i:543255 original size:13 final size:13
Alignment explanation
Indices: 543237--543262 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
543227 CATTTTTCTG
543237 TGTATCGATACAT
1 TGTATCGATACAT
543250 TGTATCGATACAT
1 TGTATCGATACAT
543263 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:543274 original size:33 final size:33
Alignment explanation
Indices: 543217--543279 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 33
543207 GCCAAGGAAA
***
543217 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
543250 TGTATCGATACATGGATCTTTGTATCGATA
1 TGTATCGATACATGGATCTGTGTATCGATA
543280 TATTTGGAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.25, C:0.14, G:0.17, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:545807 original size:28 final size:27
Alignment explanation
Indices: 545740--545812 Score: 92
Period size: 27 Copynumber: 2.7 Consensus size: 27
545730 CTTCACAATC
* *
545740 GGGGACACTCCAACCCCGTTAATCATC
1 GGGGATACTCCAACCCCGTTAATCATA
* **
545767 GGGGATACTCCAACCCCGTTATTTTTGA
1 GGGGATACTCCAACCCCGTTAATCAT-A
545795 GGGGATACTCCAACCCCG
1 GGGGATACTCCAACCCCG
545813 ACTTTATTTC
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
27 22 0.55
28 18 0.45
ACGTcount: A:0.23, C:0.33, G:0.22, T:0.22
Consensus pattern (27 bp):
GGGGATACTCCAACCCCGTTAATCATA
Found at i:545858 original size:51 final size:50
Alignment explanation
Indices: 545796--545964 Score: 176
Period size: 52 Copynumber: 3.3 Consensus size: 50
545786 TATTTTTGAG
* ***
545796 GGGATACTCCAACCCCGACTTTATTTCCAAAATATTGATTTTTCATAATC
1 GGGATACTCCAACCCCGATTTTATTTCCAAAATACCAATTTTTCATAATC
* * * * *
545846 AGGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTTCCTTCAATC
1 -GGGATACTCCAACCCCGATTTTATTTCCAAAATACCAATTTTTCAT-AATC
* ** *
545898 GGGGATACTCAAACATCGATTTTATTTCCAAAAATACCAATTTTTCACAATC
1 -GGGATACTCCAACCCCGATTTTATTTCC-AAAATACCAATTTTTCATAATC
545950 GAGGATACTCCAACC
1 G-GGATACTCCAACC
545965 TCGTTATTTC
Statistics
Matches: 94, Mismatches: 21, Indels: 5
0.78 0.17 0.04
Matches are distributed among these distances:
51 38 0.40
52 42 0.45
53 14 0.15
ACGTcount: A:0.32, C:0.25, G:0.11, T:0.32
Consensus pattern (50 bp):
GGGATACTCCAACCCCGATTTTATTTCCAAAATACCAATTTTTCATAATC
Found at i:545983 original size:28 final size:28
Alignment explanation
Indices: 545947--546028 Score: 96
Period size: 28 Copynumber: 2.9 Consensus size: 28
545937 ATTTTTCACA
* *
545947 ATCGAGGATACTCCAACCTCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTATTTC
*
545975 ATCGGGGATACTCCAACCCCGTTACTTC
1 ATCGGGGATACTCCAACCCCGTTATTTC
*
546003 --CGAGGGAACACTCCAACCCCGTTATT
1 ATCG-GGG-ATACTCCAACCCCGTTATT
546029 ATCTCCAAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
26 2 0.04
27 3 0.06
28 42 0.89
ACGTcount: A:0.24, C:0.33, G:0.17, T:0.26
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTATTTC
Found at i:546018 original size:211 final size:211
Alignment explanation
Indices: 545631--546023 Score: 569
Period size: 211 Copynumber: 1.9 Consensus size: 211
545621 AATTCTCCAC
* * * * *
545631 AATCGGGGATATTCCAACTCCGATTTTATTTTCAAAACACTAATTTTCTATAATCGGGTATACTC
1 AATCAGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGATACTC
* *
545696 CAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGGGGACACTCCAACCCCGTTA
66 AAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGACACTCCAACCCCGTTA
* ** * *
545761 ATCATCGGGGATACTCCAACCCCGTTATTTTTGAGGGGATACTCCAACCCCGACTTTATTTCCAA
131 ATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGAACACTCCAACCCCGACTTTATTTCCAA
545826 AATATTGATTTTTCAT
196 AATATTGATTTTTCAT
*
545842 AATCAGGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTTCCT-TCAATCGGGGATAC
1 AATCAGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTT-CTAT-AATCGGGGATAC
* * *
545906 TCAAACAT-CGATTTTATTTCC-AAAAATACCAATTT-TTCACAATCGAGGATACTCCAACCTCG
64 TCAAAC-TCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGACACTCCAACCCCG
*
545968 TTATTTCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGAACACTCCAACCCCG
128 TTA-ATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGAACACTCCAACCCCG
546024 TTATTATCTC
Statistics
Matches: 161, Mismatches: 17, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
210 27 0.17
211 102 0.63
212 31 0.19
213 1 0.01
ACGTcount: A:0.30, C:0.27, G:0.13, T:0.31
Consensus pattern (211 bp):
AATCAGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGATACTC
AAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGACACTCCAACCCCGTTA
ATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGAACACTCCAACCCCGACTTTATTTCCAA
AATATTGATTTTTCAT
Found at i:549353 original size:638 final size:638
Alignment explanation
Indices: 548136--549403 Score: 2482
Period size: 638 Copynumber: 2.0 Consensus size: 638
548126 ACAGTCACTA
*
548136 ATTCATTTTCCTTGTTGTTGTTCTTTATCATGCATTCATTATTTCATCATACTCATCGTCATCGT
1 ATTCATTTTCCTTGTTGCTGTTCTTTATCATGCATTCATTATTTCATCATACTCATCGTCATCGT
548201 GGGACAATTGGCCATTGGTTCAGTGTTCACCAAGGGGCGTTGATCATGGAGCAACAATCCACTTC
66 GGGACAATTGGCCATTGGTTCAGTGTTCACCAAGGGGCGTTGATCATGGAGCAACAATCCACTTC
548266 AGACTTAAAACCTTTTGAGGAAGTCCGAGCATGGTCAGAACGTCGACAGTGTGAAGATGGAGACA
131 AGACTTAAAACCTTTTGAGGAAGTCCGAGCATGGTCAGAACGTCGACAGTGTGAAGATGGAGACA
548331 TCCTTAAACCGGGATATGTCTTGATGACGCACGAAAGTATCAAGATAGGATATCACCAAAATGAT
196 TCCTTAAACCGGGATATGTCTTGATGACGCACGAAAGTATCAAGATAGGATATCACCAAAATGAT
548396 TGGCAGGATCTAGAGACCATCTGGGCTAGTTGGGACAACGCCAAAAGAGAGTCTTTTACCAAGAG
261 TGGCAGGATCTAGAGACCATCTGGGCTAGTTGGGACAACGCCAAAAGAGAGTCTTTTACCAAGAG
548461 ATATGGGGATATCGCTCTTTTGCTCCAAGTCCGCATGGATGTCAATTTATTGCAAGCGGCCTCGC
326 ATATGGGGATATCGCTCTTTTGCTCCAAGTCCGCATGGATGTCAATTTATTGCAAGCGGCCTCGC
548526 AGTTCTAGAACTCGGCATATCGGTGTTTCACTTTTAATCGTGAGGACATGGTTCCAACTGTTGAC
391 AGTTCTAGAACTCGGCATATCGGTGTTTCACTTTTAATCGTGAGGACATGGTTCCAACTGTTGAC
548591 GAGTATACTGCGTTACTCAACATCGAGAAGGCTCAAACTGATAGGGTGTACTACAAGGCTTTGAA
456 GAGTATACTGCGTTACTCAACATCGAGAAGGCTCAAACTGATAGGGTGTACTACAAGGCTTTGAA
548656 CCCCCCGACCTTCAAAAAAAGGTTGGCCCAGATCGTAGGAGCACCAGAACCATGGATCGAGAGCC
521 CCCCCCGACCTTCAAAAAAAGGTTGGCCCAGATCGTAGGAGCACCAGAACCATGGATCGAGAGCC
548721 ATATTAAGAAAAAAGGGAACGGCGAATGCATTTCATGGGTCAGTCACTAATTC
586 ATATTAAGAAAAAAGGGAACGGCGAATGCATTTCATGGGTCAGTCACTAATTC
548774 ATTCATTTTCCTTGTTGCTGTTCTTTATCATGCATTCATTATTTCATCATACTCATCGTCATCGT
1 ATTCATTTTCCTTGTTGCTGTTCTTTATCATGCATTCATTATTTCATCATACTCATCGTCATCGT
*
548839 GGGACAATTGGCCATTGGTTCAGTGTTCACCAAGGGGTGTTGATCATGGAGCAACAATCCACTTC
66 GGGACAATTGGCCATTGGTTCAGTGTTCACCAAGGGGCGTTGATCATGGAGCAACAATCCACTTC
*
548904 AGACTTAAAACCTTTTGAGGAAGTCTGAGCATGGTCAGAACGTCGACAGTGTGAAGATGGAGACA
131 AGACTTAAAACCTTTTGAGGAAGTCCGAGCATGGTCAGAACGTCGACAGTGTGAAGATGGAGACA
*
548969 TCCTTAAATCGGGATATGTCTTGATGACGCACGAAAGTATCAAGATAGGATATCACCAAAATGAT
196 TCCTTAAACCGGGATATGTCTTGATGACGCACGAAAGTATCAAGATAGGATATCACCAAAATGAT
549034 TGGCAGGATCTAGAGACCATCTGGGCTAGTTGGGACAACGCCAAAAGAGAGTCTTTTACCAAGAG
261 TGGCAGGATCTAGAGACCATCTGGGCTAGTTGGGACAACGCCAAAAGAGAGTCTTTTACCAAGAG
549099 ATATGGGGATATCGCTCTTTTGCTCCAAGTCCGCATGGATGTCAATTTATTGCAAGCGGCCTCGC
326 ATATGGGGATATCGCTCTTTTGCTCCAAGTCCGCATGGATGTCAATTTATTGCAAGCGGCCTCGC
549164 AGTTCTAGAACTCGGCATATCGGTGTTTCACTTTTAATCGTGAGGACATGGTTCCAACTGTTGAC
391 AGTTCTAGAACTCGGCATATCGGTGTTTCACTTTTAATCGTGAGGACATGGTTCCAACTGTTGAC
*
549229 GAGTATACTGCGTTACTCAACATCGAGAAGGCTCAAACTGATAGGGTGTACTGCAAGGCTTTGAA
456 GAGTATACTGCGTTACTCAACATCGAGAAGGCTCAAACTGATAGGGTGTACTACAAGGCTTTGAA
*
549294 CCCCCCGACCTTCAAGAAAAGGTTGGCCCAGATCGTAGGAGCACCAGAACCATGGATCGAGAGCC
521 CCCCCCGACCTTCAAAAAAAGGTTGGCCCAGATCGTAGGAGCACCAGAACCATGGATCGAGAGCC
549359 ATATTAAGAAAAAAGGGAACGGCGAATGCATTTCATGGGTCAGTC
586 ATATTAAGAAAAAAGGGAACGGCGAATGCATTTCATGGGTCAGTC
549404 TAAAAGAAGT
Statistics
Matches: 624, Mismatches: 6, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
638 624 1.00
ACGTcount: A:0.28, C:0.21, G:0.24, T:0.27
Consensus pattern (638 bp):
ATTCATTTTCCTTGTTGCTGTTCTTTATCATGCATTCATTATTTCATCATACTCATCGTCATCGT
GGGACAATTGGCCATTGGTTCAGTGTTCACCAAGGGGCGTTGATCATGGAGCAACAATCCACTTC
AGACTTAAAACCTTTTGAGGAAGTCCGAGCATGGTCAGAACGTCGACAGTGTGAAGATGGAGACA
TCCTTAAACCGGGATATGTCTTGATGACGCACGAAAGTATCAAGATAGGATATCACCAAAATGAT
TGGCAGGATCTAGAGACCATCTGGGCTAGTTGGGACAACGCCAAAAGAGAGTCTTTTACCAAGAG
ATATGGGGATATCGCTCTTTTGCTCCAAGTCCGCATGGATGTCAATTTATTGCAAGCGGCCTCGC
AGTTCTAGAACTCGGCATATCGGTGTTTCACTTTTAATCGTGAGGACATGGTTCCAACTGTTGAC
GAGTATACTGCGTTACTCAACATCGAGAAGGCTCAAACTGATAGGGTGTACTACAAGGCTTTGAA
CCCCCCGACCTTCAAAAAAAGGTTGGCCCAGATCGTAGGAGCACCAGAACCATGGATCGAGAGCC
ATATTAAGAAAAAAGGGAACGGCGAATGCATTTCATGGGTCAGTCACTAATTC
Found at i:553383 original size:17 final size:17
Alignment explanation
Indices: 553361--553396 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
553351 AACAGAGGTA
*
553361 AAAAGGAAGGCAAAGTC
1 AAAAGGAAGCCAAAGTC
*
553378 AAAAGGAAGCCACAGTC
1 AAAAGGAAGCCAAAGTC
553395 AA
1 AA
553397 GAATCGATGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.53, C:0.17, G:0.25, T:0.06
Consensus pattern (17 bp):
AAAAGGAAGCCAAAGTC
Found at i:559079 original size:15 final size:15
Alignment explanation
Indices: 559059--559136 Score: 61
Period size: 15 Copynumber: 5.1 Consensus size: 15
559049 CTTCTCTTCA
*
559059 AAAAAAAAGCAAAAG
1 AAAAAAAAGAAAAAG
559074 AAAAAAAAAGGAAAAA-
1 -AAAAAAAA-GAAAAAG
* *
559090 AACAAAACA-AAAAAC
1 AA-AAAAAAGAAAAAG
*
559105 AAAACAAAGAAAAAG
1 AAAAAAAAGAAAAAG
* *
559120 AGAGAAAAGAAAAAG
1 AAAAAAAAGAAAAAG
559135 AA
1 AA
559137 CCTGCTTAAG
Statistics
Matches: 49, Mismatches: 9, Indels: 9
0.73 0.13 0.13
Matches are distributed among these distances:
14 9 0.18
15 22 0.45
16 13 0.27
17 5 0.10
ACGTcount: A:0.81, C:0.06, G:0.13, T:0.00
Consensus pattern (15 bp):
AAAAAAAAGAAAAAG
Found at i:559087 original size:11 final size:10
Alignment explanation
Indices: 559069--559136 Score: 50
Period size: 10 Copynumber: 6.7 Consensus size: 10
559059 AAAAAAAAGC
559069 AAAAGAAAAA
1 AAAAGAAAAA
559079 AAAAGGAAAAA
1 AAAA-GAAAAA
*
559090 AACAA-AACAA
1 AA-AAGAAAAA
*
559100 AAAA-CAAAA
1 AAAAGAAAAA
*
559109 CAAAGAAAAA
1 AAAAGAAAAA
* *
559119 GAGAGAAAAGA
1 AAAAGAAAA-A
559130 AAAAGAA
1 AAAAGAA
559137 CCTGCTTAAG
Statistics
Matches: 45, Mismatches: 9, Indels: 7
0.74 0.15 0.11
Matches are distributed among these distances:
9 8 0.18
10 21 0.47
11 14 0.31
12 2 0.04
ACGTcount: A:0.81, C:0.06, G:0.13, T:0.00
Consensus pattern (10 bp):
AAAAGAAAAA
Done.