Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011744.1 Kokia drynarioides strain JFW-HI SEQ_126738, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 444708
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Warning! 121 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:233021 original size:10 final size:9
Alignment explanation
Indices: 233007--233124 Score: 58
Period size: 10 Copynumber: 12.3 Consensus size: 9
232997 TTTTTACGAA
233007 TTTTATATT
1 TTTTATATT
233016 TCTTTATATT
1 T-TTTATATT
*
233026 TTGTATATT
1 TTTTATATT
* **
233035 TTTTTTACAA
1 TTTTATA-TT
* **
233045 CTTTATAAAA
1 TTTTAT-ATT
233055 TTTTATAATT
1 TTTTAT-ATT
*
233065 TTTTTTATAT
1 TTTTATAT-T
* *
233075 TTCTATATA
1 TTTTATATT
233084 TTTTATAATT
1 TTTTAT-ATT
*
233094 TTTTACGA-T
1 TTTTA-TATT
233103 TTTTATATT
1 TTTTATATT
233112 TTTTAATATT
1 TTTT-ATATT
233122 TTT
1 TTT
233125 ATTAAAATTT
Statistics
Matches: 83, Mismatches: 18, Indels: 15
0.72 0.16 0.13
Matches are distributed among these distances:
8 1 0.01
9 31 0.37
10 50 0.60
11 1 0.01
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.67
Consensus pattern (9 bp):
TTTTATATT
Found at i:233039 original size:29 final size:28
Alignment explanation
Indices: 233007--233124 Score: 73
Period size: 29 Copynumber: 4.1 Consensus size: 28
232997 TTTTTACGAA
233007 TTTTATATTTCTTTATATTTTGTATATTT
1 TTTTATATTTCTTTATATTTT-TATATTT
*** *
233036 TTTT-TACAACTTTATAAAATTTTATAATTTT
1 TTTTATATTTCTTTAT--ATTTTTAT-A-TTT
* *
233067 TTTTATATTTCTATATA-TTTTATAATT
1 TTTTATATTTCTTTATATTTTTATATTT
*
233094 TTTTACGA-TT-TTTATATTTTTTAATATTT
1 TTTTA-TATTTCTTTATA-TTTTT-ATATTT
233123 TT
1 TT
233125 ATTAAAATTT
Statistics
Matches: 68, Mismatches: 12, Indels: 18
0.69 0.12 0.18
Matches are distributed among these distances:
26 5 0.07
27 9 0.13
28 14 0.21
29 20 0.29
30 6 0.09
31 7 0.10
32 7 0.10
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.67
Consensus pattern (28 bp):
TTTTATATTTCTTTATATTTTTATATTT
Found at i:233364 original size:88 final size:88
Alignment explanation
Indices: 233230--233411 Score: 221
Period size: 88 Copynumber: 2.1 Consensus size: 88
233220 GCTTGAGGGT
*
233230 CTTTTTTATATATTTTAAAAGTTCAAGTACTCAATTGAGTGAAAAAAAAAAAACGA-CTTAA-TG
1 CTTTTTTATATATTTTAAAAGTTCAAGTACTCAAATGAGTGAAAAAAAAAAAACGAGCTTAATTG
233293 ACTTTTTTTAA-AAAGATTTGATAG-
66 -CTTTTTTTAAGAAAG-TTTGA-AGA
* * * * * *
233317 CTTTTTTGATGTATTTTGAAAGTTCAAGTA-TCCAAATGTGTGTAAAAAAAAAGAGGAGCTTAAT
1 CTTTTTT-ATATATTTTAAAAGTTCAAGTACT-CAAATGAGTGAAAAAAAAAAAACGAGCTTAAT
233381 TGCTTTTTTTAAGAAAGTTTGAAGA
64 TGCTTTTTTTAAGAAAGTTTGAAGA
233406 CTTTTT
1 CTTTTT
233412 ACACCCTTAA
Statistics
Matches: 82, Mismatches: 7, Indels: 10
0.83 0.07 0.10
Matches are distributed among these distances:
87 8 0.10
88 42 0.51
89 26 0.32
90 6 0.07
ACGTcount: A:0.38, C:0.08, G:0.15, T:0.40
Consensus pattern (88 bp):
CTTTTTTATATATTTTAAAAGTTCAAGTACTCAAATGAGTGAAAAAAAAAAAACGAGCTTAATTG
CTTTTTTTAAGAAAGTTTGAAGA
Found at i:237563 original size:17 final size:17
Alignment explanation
Indices: 237541--237574 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
237531 CTTTAATGAG
237541 GGTTTAAAGGAGCTAGA
1 GGTTTAAAGGAGCTAGA
*
237558 GGTTTAAAGGAGTTAGA
1 GGTTTAAAGGAGCTAGA
237575 CATCCACTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.35, C:0.03, G:0.35, T:0.26
Consensus pattern (17 bp):
GGTTTAAAGGAGCTAGA
Found at i:243819 original size:21 final size:21
Alignment explanation
Indices: 243773--243832 Score: 70
Period size: 21 Copynumber: 2.9 Consensus size: 21
243763 TGCCCCTCTT
**
243773 TGCACTTTGGTGCCCCTG-AA
1 TGCACTTCCGTGCCCCTGTAA
*
243793 TGCAC-TCCGATGCCCCTGTAT
1 TGCACTTCCG-TGCCCCTGTAA
243814 TGCACTTCCGTGCCCCTGT
1 TGCACTTCCGTGCCCCTGT
243833 GTGTTTAATC
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
19 2 0.06
20 13 0.38
21 15 0.44
22 4 0.12
ACGTcount: A:0.12, C:0.37, G:0.22, T:0.30
Consensus pattern (21 bp):
TGCACTTCCGTGCCCCTGTAA
Found at i:251022 original size:12 final size:12
Alignment explanation
Indices: 251005--251029 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
250995 AATATGAAAC
251005 GAATAATTAATT
1 GAATAATTAATT
251017 GAATAATTAATT
1 GAATAATTAATT
251029 G
1 G
251030 TGAAATTATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.00, G:0.12, T:0.40
Consensus pattern (12 bp):
GAATAATTAATT
Found at i:251648 original size:30 final size:29
Alignment explanation
Indices: 251597--251653 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 29
251587 AATACAATGA
* *
251597 CTAAAATTAATCAATTTAAAATTATAAACG
1 CTAAAATTAATCAAATCAAAA-TATAAACG
*
251627 CTAAAATTAATTAAATCAAAATATAAA
1 CTAAAATTAATCAAATCAAAATATAAA
251654 ATACTAAATC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 6 0.25
30 18 0.75
ACGTcount: A:0.58, C:0.09, G:0.02, T:0.32
Consensus pattern (29 bp):
CTAAAATTAATCAAATCAAAATATAAACG
Found at i:254483 original size:21 final size:20
Alignment explanation
Indices: 254446--254485 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
254436 TACATTACAG
* *
254446 TTTTAAAAAATATTAATTTC
1 TTTTAAAAAAAACTAATTTC
254466 TTTTAGAAAAAAACTAATTT
1 TTTTA-AAAAAAACTAATTT
254486 TATAAAATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (20 bp):
TTTTAAAAAAAACTAATTTC
Found at i:265778 original size:33 final size:32
Alignment explanation
Indices: 265661--265922 Score: 202
Period size: 33 Copynumber: 7.9 Consensus size: 32
265651 TTTCGTATTG
* ** *
265661 TGCCATAGTCCAACTATGGTCTTACATGTGTAT
1 TGCCATAGCCCAACTATGGTCTTACATCAG-AA
* * *
265694 TGTCAT-GGCCAAGCTATGGTCTTACATTCATAA
1 TGCCATAGCCCAA-CTATGGTCTTACA-TCAGAA
* * * **
265727 TGGCAAAACCCAGTTATGGTCTTAACATCAGAA
1 TGCCATAGCCCAACTATGGTCTT-ACATCAGAA
* *
265760 TGCCATAGTCTAACTATGGTCTTATCATCAGAA
1 TGCCATAGCCCAACTATGGTCTTA-CATCAGAA
* *
265793 TGTCATAGCCCAACTATGGTCTTACATCCATATACA
1 TGCCATAGCCCAACTATGGTCTTACAT-C--AGA-A
* * * *
265829 CTGCCATGGTCCAACCATGGTCTTACGTCAGAA
1 -TGCCATAGCCCAACTATGGTCTTACATCAGAA
* * *
265862 TGCCAAAGACCAGCTATGGTCTTATCATCAGAA
1 TGCCATAGCCCAACTATGGTCTTA-CATCAGAA
*
265895 TGCCATAGCCCAGCTATGGTCTTACATC
1 TGCCATAGCCCAACTATGGTCTTACATC
265923 TATATACACT
Statistics
Matches: 180, Mismatches: 38, Indels: 23
0.75 0.16 0.10
Matches are distributed among these distances:
32 32 0.18
33 113 0.63
34 9 0.05
35 2 0.01
36 2 0.01
37 22 0.12
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.29
Consensus pattern (32 bp):
TGCCATAGCCCAACTATGGTCTTACATCAGAA
Found at i:265881 original size:69 final size:71
Alignment explanation
Indices: 265760--265890 Score: 176
Period size: 69 Copynumber: 1.9 Consensus size: 71
265750 AACATCAGAA
* * * * *
265760 TGCCATAGTCTAACTATGGTCTTATCATCAGAATGTCATAGCCCAACTATGGTCTTA-CATCCAT
1 TGCCATAGTCCAACCATGGTCTTATCATCAGAATGCCAAAGACCAACTATGGTCTTATCATCCAT
265824 ATACAC
66 ATACAC
* * *
265830 TGCCATGGTCCAACCATGGTCTTA-CGTCAGAATGCCAAAGACCAGCTATGGTCTTATCATC
1 TGCCATAGTCCAACCATGGTCTTATCATCAGAATGCCAAAGACCAACTATGGTCTTATCATC
265891 AGAATGCCAT
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
69 27 0.52
70 25 0.48
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.29
Consensus pattern (71 bp):
TGCCATAGTCCAACCATGGTCTTATCATCAGAATGCCAAAGACCAACTATGGTCTTATCATCCAT
ATACAC
Found at i:265883 original size:102 final size:102
Alignment explanation
Indices: 265742--265965 Score: 349
Period size: 102 Copynumber: 2.2 Consensus size: 102
265732 AAACCCAGTT
* * * * *
265742 ATGGTCTTAACATCAGAATGCCATAGTCTAACTATGGTCTTATCATCAGAATGTCATAGCCCAAC
1 ATGGTCTT-ACGTCAGAATGCCAAAGACCAACTATGGTCTTATCATCAGAATGCCATAGCCCAAC
265807 TATGGTCTTACATCCATATACACTGCCATGGTCCAACC
65 TATGGTCTTACATCCATATACACTGCCATGGTCCAACC
* *
265845 ATGGTCTTACGTCAGAATGCCAAAGACCAGCTATGGTCTTATCATCAGAATGCCATAGCCCAGCT
1 ATGGTCTTACGTCAGAATGCCAAAGACCAACTATGGTCTTATCATCAGAATGCCATAGCCCAACT
* *
265910 ATGGTCTTACATCTATATACACTTCCATGGTCCAACC
66 ATGGTCTTACATCCATATACACTGCCATGGTCCAACC
*
265947 ATGGTCTTACGTCATAATG
1 ATGGTCTTACGTCAGAATG
265966 TAGCTTGTCT
Statistics
Matches: 111, Mismatches: 10, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
102 103 0.93
103 8 0.07
ACGTcount: A:0.29, C:0.26, G:0.16, T:0.29
Consensus pattern (102 bp):
ATGGTCTTACGTCAGAATGCCAAAGACCAACTATGGTCTTATCATCAGAATGCCATAGCCCAACT
ATGGTCTTACATCCATATACACTGCCATGGTCCAACC
Found at i:269024 original size:16 final size:17
Alignment explanation
Indices: 269003--269059 Score: 57
Period size: 18 Copynumber: 3.4 Consensus size: 17
268993 GATAGAGGAC
269003 TAAATT-AAAAATTGTA
1 TAAATTGAAAAATTGTA
*
269019 TAAATTGTAAAATTGTA
1 TAAATTGAAAAATTGTA
*
269036 -AAATTGTATAAATTTGTA
1 TAAATTG-A-AAAATTGTA
269054 -AAATTG
1 TAAATTG
269060 TATACTGTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
16 12 0.34
17 9 0.26
18 14 0.40
ACGTcount: A:0.49, C:0.00, G:0.11, T:0.40
Consensus pattern (17 bp):
TAAATTGAAAAATTGTA
Found at i:269033 original size:8 final size:8
Alignment explanation
Indices: 269010--269061 Score: 77
Period size: 8 Copynumber: 6.1 Consensus size: 8
269000 GACTAAATTA
269010 AAAATTGT
1 AAAATTGT
269018 ATAAATTGT
1 A-AAATTGT
269027 AAAATTGT
1 AAAATTGT
269035 AAAATTGT
1 AAAATTGT
269043 ATAAATTTGT
1 A-AAA-TTGT
269053 AAAATTGT
1 AAAATTGT
269061 A
1 A
269062 TACTGTTATG
Statistics
Matches: 41, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
8 22 0.54
9 14 0.34
10 5 0.12
ACGTcount: A:0.48, C:0.00, G:0.12, T:0.40
Consensus pattern (8 bp):
AAAATTGT
Found at i:269038 original size:25 final size:26
Alignment explanation
Indices: 269010--269061 Score: 97
Period size: 25 Copynumber: 2.0 Consensus size: 26
269000 GACTAAATTA
269010 AAAATTGTATAAA-TTGTAAAATTGT
1 AAAATTGTATAAATTTGTAAAATTGT
269035 AAAATTGTATAAATTTGTAAAATTGT
1 AAAATTGTATAAATTTGTAAAATTGT
269061 A
1 A
269062 TACTGTTATG
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 13 0.50
26 13 0.50
ACGTcount: A:0.48, C:0.00, G:0.12, T:0.40
Consensus pattern (26 bp):
AAAATTGTATAAATTTGTAAAATTGT
Found at i:269047 original size:18 final size:18
Alignment explanation
Indices: 269010--269063 Score: 76
Period size: 18 Copynumber: 3.1 Consensus size: 18
269000 GACTAAATTA
269010 AAAATTGTATAAATTG--T
1 AAAATTGTA-AAATTGTAT
269027 AAAATTGTAAAATTGTAT
1 AAAATTGTAAAATTGTAT
*
269045 AAATTTGTAAAATTGTAT
1 AAAATTGTAAAATTGTAT
269063 A
1 A
269064 CTGTTATGCA
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
16 6 0.18
17 9 0.26
18 19 0.56
ACGTcount: A:0.48, C:0.00, G:0.11, T:0.41
Consensus pattern (18 bp):
AAAATTGTAAAATTGTAT
Found at i:269185 original size:22 final size:22
Alignment explanation
Indices: 269157--269346 Score: 134
Period size: 22 Copynumber: 8.6 Consensus size: 22
269147 TATTAAGTTT
*
269157 TTTGCACTACGGTGCTTACTGA
1 TTTGCACTACGGTGCCTACTGA
* *
269179 TTTGCACTATGGTGCCTATTG-
1 TTTGCACTACGGTGCCTACTGA
** *
269200 TTTGGCACTACTATGCCTATTGA
1 TTT-GCACTACGGTGCCTACTGA
269223 TTTGCACTACGGTGCCTACT-A
1 TTTGCACTACGGTGCCTACTGA
* *
269244 TTTTGCACTACGATGCCTAATGA
1 -TTTGCACTACGGTGCCTACTGA
* *** * *
269267 TTTACACTATAATGCTTATTGA
1 TTTGCACTACGGTGCCTACTGA
* * * * *
269289 TTCGTAGTTCGGTGTCTACT-A
1 TTTGCACTACGGTGCCTACTGA
*
269310 TTTTACACTACGGTGCCTACTGA
1 -TTTGCACTACGGTGCCTACTGA
* *
269333 TTCGCACTTCGGTG
1 TTTGCACTACGGTG
269347 TGTAACACCC
Statistics
Matches: 126, Mismatches: 36, Indels: 12
0.72 0.21 0.07
Matches are distributed among these distances:
21 5 0.04
22 116 0.92
23 5 0.04
ACGTcount: A:0.20, C:0.22, G:0.19, T:0.38
Consensus pattern (22 bp):
TTTGCACTACGGTGCCTACTGA
Found at i:269275 original size:66 final size:67
Alignment explanation
Indices: 269157--269334 Score: 193
Period size: 66 Copynumber: 2.7 Consensus size: 67
269147 TATTAAGTTT
* * * *
269157 TTTGCACTACGGTGCTTACTGA-TTTGCACTATGGTGCCTATTG-TTTGGCACTACT-ATGCCTA
1 TTTGCACTACGGTGCCTACT-ATTTTGCACTACGGTGCCTAATGATTTGACACTA-TAATGCCTA
269219 TTGA
64 TTGA
* *
269223 TTTGCACTACGGTGCCTACTATTTTGCACTACGATGCCTAATGATTT-ACACTATAATGCTTATT
1 TTTGCACTACGGTGCCTACTATTTTGCACTACGGTGCCTAATGATTTGACACTATAATGCCTATT
269287 GA
66 GA
* * * * * * *
269289 TTCGTAGTTCGGTGTCTACTATTTTACACTACGGTGCCTACTGATT
1 TTTGCACTACGGTGCCTACTATTTTGCACTACGGTGCCTAATGATT
269335 CGCACTTCGG
Statistics
Matches: 95, Mismatches: 14, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
65 2 0.02
66 90 0.95
67 3 0.03
ACGTcount: A:0.21, C:0.21, G:0.19, T:0.39
Consensus pattern (67 bp):
TTTGCACTACGGTGCCTACTATTTTGCACTACGGTGCCTAATGATTTGACACTATAATGCCTATT
GA
Found at i:269658 original size:21 final size:21
Alignment explanation
Indices: 269634--269687 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
269624 CTTGTGCTAG
269634 TTCTACCGATACAAGT-ATAAC
1 TTCTACCGATACAAGTCAT-AC
* *
269655 TTCTACTGATACAAGTCATGC
1 TTCTACCGATACAAGTCATAC
*
269676 ATCTACCGATAC
1 TTCTACCGATAC
269688 TAACAACTCT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 26 0.93
22 2 0.07
ACGTcount: A:0.33, C:0.26, G:0.11, T:0.30
Consensus pattern (21 bp):
TTCTACCGATACAAGTCATAC
Found at i:272923 original size:22 final size:22
Alignment explanation
Indices: 272887--272956 Score: 97
Period size: 22 Copynumber: 3.2 Consensus size: 22
272877 CACCGCAACA
272887 TAAATCAGTAGGCATCGTAGTG
1 TAAATCAGTAGGCATCGTAGTG
*
272909 TAGAA-CAGTAAGCATCGTAGTG
1 TA-AATCAGTAGGCATCGTAGTG
* *
272931 CAAATCAGTAGGCACCGTAGTG
1 TAAATCAGTAGGCATCGTAGTG
272953 TAAA
1 TAAA
272957 ATAATTATTA
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
21 2 0.05
22 37 0.90
23 2 0.05
ACGTcount: A:0.36, C:0.16, G:0.26, T:0.23
Consensus pattern (22 bp):
TAAATCAGTAGGCATCGTAGTG
Found at i:273200 original size:26 final size:23
Alignment explanation
Indices: 273162--273208 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 23
273152 TCAAATTCAC
273162 ACCAATATAATTCGATTAATCATA
1 ACCAATATAATTC-ATTAATCATA
*
273186 ACCAAGTATCAATTCATTTATCA
1 ACCAA-TAT-AATTCATTAATCA
273209 AAATTCCTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 5 0.25
25 10 0.50
26 5 0.25
ACGTcount: A:0.43, C:0.19, G:0.04, T:0.34
Consensus pattern (23 bp):
ACCAATATAATTCATTAATCATA
Found at i:275275 original size:14 final size:15
Alignment explanation
Indices: 275256--275293 Score: 53
Period size: 14 Copynumber: 2.6 Consensus size: 15
275246 ACTAACTTTT
275256 AATTCAATAATT-AA
1 AATTCAATAATTCAA
275270 AATTC-ATCAATTCAA
1 AATTCAAT-AATTCAA
275285 AATTCAATA
1 AATTCAATA
275294 CAAAAATTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
13 2 0.10
14 9 0.43
15 8 0.38
16 2 0.10
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.34
Consensus pattern (15 bp):
AATTCAATAATTCAA
Found at i:283532 original size:19 final size:20
Alignment explanation
Indices: 283508--283559 Score: 79
Period size: 21 Copynumber: 2.6 Consensus size: 20
283498 TCTCAAACGA
*
283508 TCTTACGAGCTAG-TATCGC
1 TCTTACGAGCCAGATATCGC
283527 TCTTACGAGCCAGTATATCGC
1 TCTTACGAGCCAG-ATATCGC
283548 TCTTACGAGCCA
1 TCTTACGAGCCA
283560 ATACAGTAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 12 0.40
21 18 0.60
ACGTcount: A:0.23, C:0.29, G:0.19, T:0.29
Consensus pattern (20 bp):
TCTTACGAGCCAGATATCGC
Found at i:284943 original size:26 final size:26
Alignment explanation
Indices: 284873--284947 Score: 80
Period size: 26 Copynumber: 2.8 Consensus size: 26
284863 TTTATTCTAC
* *
284873 TAAAATTTTGACAATTTTTA-CTCTCGA
1 TAAAATTTTGACGA-TTTTACCCCT-GA
*
284900 TAAAATTTTGGCGATTTTACCCCTGA
1 TAAAATTTTGACGATTTTACCCCTGA
* *
284926 TAAAATTTTGATGTTTTTACCC
1 TAAAATTTTGACGATTTTACCC
284948 TCAACAGAAT
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
26 26 0.63
27 15 0.37
ACGTcount: A:0.29, C:0.16, G:0.11, T:0.44
Consensus pattern (26 bp):
TAAAATTTTGACGATTTTACCCCTGA
Found at i:285331 original size:16 final size:16
Alignment explanation
Indices: 285292--285331 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
285282 GTCCAAATTT
*
285292 CCAATTAAACCCAAAC
1 CCAATTACACCCAAAC
285308 CCAATTACACCCAAAC
1 CCAATTACACCCAAAC
*
285324 CTAATTAC
1 CCAATTAC
285332 CCAACAAGCC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.45, C:0.38, G:0.00, T:0.17
Consensus pattern (16 bp):
CCAATTACACCCAAAC
Found at i:286470 original size:28 final size:28
Alignment explanation
Indices: 286421--286514 Score: 127
Period size: 29 Copynumber: 3.2 Consensus size: 28
286411 GAATGTCCCT
286421 AAACTTTTTAAAAATTTGATTTTAACCCC
1 AAACTTTTTAAAAATTT-ATTTTAACCCC
*
286450 AAACTTTTTAAAAATTTATTTTTAACCTC
1 AAACTTTTTAAAAATTTA-TTTTAACCCC
*
286479 AAACTTTTT-AAAATTACATTTTAACCCC
1 AAACTTTTTAAAAATT-TATTTTAACCCC
286507 TAAACTTT
1 -AAACTTT
286515 CTCAAATTCA
Statistics
Matches: 59, Mismatches: 3, Indels: 6
0.87 0.04 0.09
Matches are distributed among these distances:
28 16 0.27
29 43 0.73
ACGTcount: A:0.38, C:0.17, G:0.01, T:0.44
Consensus pattern (28 bp):
AAACTTTTTAAAAATTTATTTTAACCCC
Found at i:286521 original size:29 final size:30
Alignment explanation
Indices: 286417--286624 Score: 151
Period size: 30 Copynumber: 7.0 Consensus size: 30
286407 CTCAGAATGT
* **
286417 CCCTAAACTTTTTAAAAATTTGATTTTAAC
1 CCCTAAACTTTCTAAAAATTACATTTTAAC
* *
286447 CCC-AAACTTTTTAAAAATTTA-TTTTTAAC
1 CCCTAAACTTTCTAAAAA-TTACATTTTAAC
* *
286476 CTC-AAACTTT-TTAAAATTACATTTTAAC
1 CCCTAAACTTTCTAAAAATTACATTTTAAC
* *
286504 CCCTAAACTTTCT-CAAATTCACATTTTGAC
1 CCCTAAACTTTCTAAAAATT-ACATTTTAAC
* * * *
286534 CCCCAAACCTTTC-CAAAATCACATTTTAAT
1 CCCTAAA-CTTTCTAAAAATTACATTTTAAC
* * *
286564 CCTTGAACTTTCTAAAAATTACATTTTGA-
1 CCCTAAACTTTCTAAAAATTACATTTTAAC
* * * *
286593 CCCTTAATTTTTTCCAAAATTACATTTTAAC
1 CCCTAAACTTTCT-AAAAATTACATTTTAAC
286624 C
1 C
286625 TTAAATTCTT
Statistics
Matches: 143, Mismatches: 25, Indels: 19
0.76 0.13 0.10
Matches are distributed among these distances:
27 3 0.02
28 14 0.10
29 56 0.39
30 60 0.42
31 10 0.07
ACGTcount: A:0.35, C:0.23, G:0.02, T:0.40
Consensus pattern (30 bp):
CCCTAAACTTTCTAAAAATTACATTTTAAC
Found at i:286573 original size:60 final size:59
Alignment explanation
Indices: 286439--286629 Score: 172
Period size: 60 Copynumber: 3.2 Consensus size: 59
286429 TAAAAATTTG
** * * * * * **
286439 ATTTTAACCCCAAACTTTTTAAAAATT-TATTTTTAACCTCAAA-CTTTTTAAAATTAC
1 ATTTTAACCTTAAACTTTCTAAAAATTACATTTTGACCCCCAAACCTTTCCAAAATTAC
* * *
286496 ATTTTAACCCCTAAACTTTCT-CAAATTCACATTTTGACCCCCAAACCTTTCCAAAATCAC
1 ATTTTAA-CCTTAAACTTTCTAAAAATT-ACATTTTGACCCCCAAACCTTTCCAAAATTAC
* ** ***
286556 ATTTTAATCCTTGAACTTTCTAAAAATTACATTTTGACCCTTAATTTTTTCCAAAATTAC
1 ATTTTAA-CCTTAAACTTTCTAAAAATTACATTTTGACCCCCAAACCTTTCCAAAATTAC
286616 ATTTTAACCTTAAA
1 ATTTTAACCTTAAA
286630 TTCTTCGAAA
Statistics
Matches: 108, Mismatches: 21, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
57 12 0.11
58 11 0.10
59 18 0.17
60 62 0.57
61 5 0.05
ACGTcount: A:0.36, C:0.23, G:0.02, T:0.40
Consensus pattern (59 bp):
ATTTTAACCTTAAACTTTCTAAAAATTACATTTTGACCCCCAAACCTTTCCAAAATTAC
Found at i:290435 original size:25 final size:25
Alignment explanation
Indices: 290402--290498 Score: 106
Period size: 25 Copynumber: 3.9 Consensus size: 25
290392 GAAGGAGCGT
* * *
290402 TATTCTGACTAGCTCGTCTAAGCAA
1 TATTATGACTGGCTCGTCTGAGCAA
* **
290427 TATTATGACTGGCTCGTATGAGTGA
1 TATTATGACTGGCTCGTCTGAGCAA
*
290452 TATTATGACTGGCTCG-CATGAGCTA
1 TATTATGACTGGCTCGTC-TGAGCAA
*
290477 TATTATGACTGGCTCGTATGAG
1 TATTATGACTGGCTCGTCTGAG
290499 TNNNNNNNNN
Statistics
Matches: 60, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
25 60 1.00
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.34
Consensus pattern (25 bp):
TATTATGACTGGCTCGTCTGAGCAA
Found at i:290467 original size:50 final size:50
Alignment explanation
Indices: 290402--290499 Score: 144
Period size: 50 Copynumber: 2.0 Consensus size: 50
290392 GAAGGAGCGT
*
290402 TATTCTGACTAGCTCGTC-TAAGCAATATTATGACTGGCTCGTATGAGTGA
1 TATTATGACTAGCTCG-CATAAGCAATATTATGACTGGCTCGTATGAGTGA
* * *
290452 TATTATGACTGGCTCGCATGAGCTATATTATGACTGGCTCGTATGAGT
1 TATTATGACTAGCTCGCATAAGCAATATTATGACTGGCTCGTATGAGT
290500 NNNNNNNNNN
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
49 1 0.02
50 42 0.98
ACGTcount: A:0.24, C:0.17, G:0.23, T:0.35
Consensus pattern (50 bp):
TATTATGACTAGCTCGCATAAGCAATATTATGACTGGCTCGTATGAGTGA
Found at i:290617 original size:25 final size:25
Alignment explanation
Indices: 290522--290691 Score: 139
Period size: 25 Copynumber: 6.8 Consensus size: 25
290512 NNNNNNNNNN
* *
290522 ATTGGCTCGTCTGAGCGATATTATT
1 ATTGGCTCGTATGAGCGATATTATG
*
290547 ATTGGCTCGTCTGAGCGATATTATG
1 ATTGGCTCGTATGAGCGATATTATG
*
290572 ATTGGCTCGTATAAGCGATATTATG
1 ATTGGCTCGTATGAGCGATATTATG
* * *
290597 ATTGGCTCATATGAGCAATATCCA--
1 ATTGGCTCGTATGAGCGATAT-TATG
* * * * *
290621 ACTAGCTCGTCTGAGCGATATTCTA
1 ATTGGCTCGTATGAGCGATATTATG
* * * *
290646 ACTGGCTTGTAGGAGCGATATTTTG
1 ATTGGCTCGTATGAGCGATATTATG
* *
290671 -TCTAGCTCGTAAGAGCGATAT
1 AT-TGGCTCGTATGAGCGATAT
290692 ACTATCAGGG
Statistics
Matches: 117, Mismatches: 24, Indels: 8
0.79 0.16 0.05
Matches are distributed among these distances:
24 16 0.14
25 100 0.85
26 1 0.01
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (25 bp):
ATTGGCTCGTATGAGCGATATTATG
Found at i:294696 original size:27 final size:27
Alignment explanation
Indices: 294595--294701 Score: 83
Period size: 27 Copynumber: 4.0 Consensus size: 27
294585 TATAATTCTC
* *
294595 TGGGACAATAAACAC-AGAGTAGTCCAC
1 TGGGACAATAAACACGAG-GTAATCCAT
* *
294622 TGGGATAGTAAACACGAGGTAATCC-T
1 TGGGACAATAAACACGAGGTAATCCAT
* * * *
294648 CTAGGACATTAAATACGGGGTAATCCAT
1 -TGGGACAATAAACACGAGGTAATCCAT
* * *
294676 TGGGATAATATACACGAGGTAGTCCA
1 TGGGACAATAAACACGAGGTAATCCA
294702 CCAGGATATT
Statistics
Matches: 61, Mismatches: 16, Indels: 6
0.73 0.19 0.07
Matches are distributed among these distances:
27 58 0.95
28 3 0.05
ACGTcount: A:0.36, C:0.18, G:0.24, T:0.21
Consensus pattern (27 bp):
TGGGACAATAAACACGAGGTAATCCAT
Found at i:294722 original size:54 final size:54
Alignment explanation
Indices: 294597--294722 Score: 126
Period size: 54 Copynumber: 2.3 Consensus size: 54
294587 TAATTCTCTG
* * * * * * *
294597 GGACAATAAACACAGAGTAGTCCACTGGGATAGTAAACACGAGGTAATCCTCTA
1 GGACATTAAACACGGGGTAATCCACTGGGATAATAAACACGAGGTAATCCACCA
* * * *
294651 GGACATTAAATACGGGGTAATCCATTGGGATAATATACACGAGGTAGTCCACCA
1 GGACATTAAACACGGGGTAATCCACTGGGATAATAAACACGAGGTAATCCACCA
* * *
294705 GGATATTTAACATGGGGT
1 GGACATTAAACACGGGGT
294723 TAAGTCGCAA
Statistics
Matches: 57, Mismatches: 15, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
54 57 1.00
ACGTcount: A:0.36, C:0.17, G:0.25, T:0.22
Consensus pattern (54 bp):
GGACATTAAACACGGGGTAATCCACTGGGATAATAAACACGAGGTAATCCACCA
Found at i:299399 original size:6 final size:7
Alignment explanation
Indices: 299382--299408 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
299372 ATCAAATATT
299382 TTTTTTA
1 TTTTTTA
299389 TTTTTTA
1 TTTTTTA
299396 TTTTTTA
1 TTTTTTA
299403 TTTTTT
1 TTTTTT
299409 TCAACAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.11, C:0.00, G:0.00, T:0.89
Consensus pattern (7 bp):
TTTTTTA
Found at i:300409 original size:24 final size:21
Alignment explanation
Indices: 300352--300410 Score: 64
Period size: 24 Copynumber: 2.6 Consensus size: 21
300342 GAAGTCTCAC
300352 AAATAAAAATAAAAACAACTAA
1 AAAT-AAAATAAAAACAACTAA
*
300374 AAATGAACATAAAAGTACAACTAA
1 AAAT-AAAATAAAA--ACAACTAA
300398 AAATAATAATAAA
1 AAATAA-AATAAA
300411 TGACACATCA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
22 12 0.39
23 2 0.06
24 17 0.55
ACGTcount: A:0.71, C:0.08, G:0.03, T:0.17
Consensus pattern (21 bp):
AAATAAAATAAAAACAACTAA
Found at i:303700 original size:11 final size:12
Alignment explanation
Indices: 303684--303712 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
303674 ATTTCCCACA
303684 AAAAAGT-GATC
1 AAAAAGTAGATC
303695 AAAAAGTAGATC
1 AAAAAGTAGATC
303707 AAAAAG
1 AAAAAG
303713 AAAAAAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 7 0.41
12 10 0.59
ACGTcount: A:0.62, C:0.07, G:0.17, T:0.14
Consensus pattern (12 bp):
AAAAAGTAGATC
Found at i:308866 original size:44 final size:44
Alignment explanation
Indices: 308692--308956 Score: 158
Period size: 44 Copynumber: 6.2 Consensus size: 44
308682 CAGGTTTATA
* * * * **
308692 AGTCTTCCTTTGTAAACA-A-TCTTATGCTC-TACCAAGGCATA
1 AGTCTTCCTTTTTAAACATATTCTCATGCTCATTCCAAGTCACG
* * * * * *
308733 AGTCTTCCTTTTCAAATATAATCTCACGCTCATTCCGAGAT-ATG
1 AGTCTTCCTTTTTAAACATATTCTCATGCTCATTCCAAG-TCACG
* ** * *
308777 AGTCTT-C-TTTTAAACATAATT-ACATTTTCA-TCC-TGATACATG
1 AGTCTTCCTTTTTAAACAT-ATTCTCATGCTCATTCCAAG-T-CACG
* *
308819 AGTCTTCCTTTTTAAACATATTCTCATTCTCGTTCCAAGTCACG
1 AGTCTTCCTTTTTAAACATATTCTCATGCTCATTCCAAGTCACG
* * * * *
308863 AGTCTTCC--GTTAGACTTATTCTCATGCTCATTCTAAGAT-ATG
1 AGTCTTCCTTTTTAAACATATTCTCATGCTCATTCCAAG-TCACG
* * *
308905 AGTCATCCTTTTTAAACATATTCTCGTGCTCATTCCGAGTCACG
1 AGTCTTCCTTTTTAAACATATTCTCATGCTCATTCCAAGTCACG
308949 AGTCTTCC
1 AGTCTTCC
308957 ATTTATACAT
Statistics
Matches: 170, Mismatches: 38, Indels: 29
0.72 0.16 0.12
Matches are distributed among these distances:
40 3 0.02
41 18 0.11
42 55 0.32
43 17 0.10
44 72 0.42
45 4 0.02
46 1 0.01
ACGTcount: A:0.26, C:0.25, G:0.11, T:0.38
Consensus pattern (44 bp):
AGTCTTCCTTTTTAAACATATTCTCATGCTCATTCCAAGTCACG
Found at i:308866 original size:86 final size:86
Alignment explanation
Indices: 308733--308956 Score: 209
Period size: 86 Copynumber: 2.6 Consensus size: 86
308723 CCAAGGCATA
* * * * * * * **
308733 AGTCTTCCTTTTCAAATATAATCTCACGCTCATTCCGAGAT-ATGAGTCTTCTTTTAAACATAAT
1 AGTCATCCTTTTTAAACATATTCTCATGCTCATTCCAAG-TCACGAGTCTTCCGTTAAAC-TAAT
** * *
308797 T-ACATTTTCATCCTGATACATG
64 TCACATGCTCATCCTAAGACATG
* * * * *
308819 AGTCTTCCTTTTTAAACATATTCTCATTCTCGTTCCAAGTCACGAGTCTTCCGTTAGACTTATTC
1 AGTCATCCTTTTTAAACATATTCTCATGCTCATTCCAAGTCACGAGTCTTCCGTTAAACTAATTC
* * *
308884 TCATGCTCATTCTAAGATATG
66 ACATGCTCATCCTAAGACATG
* *
308905 AGTCATCCTTTTTAAACATATTCTCGTGCTCATTCCGAGTCACGAGTCTTCC
1 AGTCATCCTTTTTAAACATATTCTCATGCTCATTCCAAGTCACGAGTCTTCC
308957 ATTTATACAT
Statistics
Matches: 112, Mismatches: 24, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
85 5 0.04
86 107 0.96
ACGTcount: A:0.25, C:0.25, G:0.11, T:0.39
Consensus pattern (86 bp):
AGTCATCCTTTTTAAACATATTCTCATGCTCATTCCAAGTCACGAGTCTTCCGTTAAACTAATTC
ACATGCTCATCCTAAGACATG
Found at i:314957 original size:21 final size:21
Alignment explanation
Indices: 314933--314986 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
314923 CTTGTGATAG
314933 TTCTACCGATACAAATCTA-AC
1 TTCTACCGATACAAAT-TATAC
* * * *
314954 TTCTACCAAAACAAGTTATGC
1 TTCTACCGATACAAATTATAC
314975 TTCTACCGATAC
1 TTCTACCGATAC
314987 TAAAAACTCT
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
20 2 0.08
21 24 0.92
ACGTcount: A:0.35, C:0.28, G:0.07, T:0.30
Consensus pattern (21 bp):
TTCTACCGATACAAATTATAC
Found at i:315685 original size:41 final size:40
Alignment explanation
Indices: 315620--315716 Score: 97
Period size: 41 Copynumber: 2.4 Consensus size: 40
315610 AGTCGTAAAA
* ** *
315620 CTTCCTCTTTAAATGATCTCATACTTTAC-AGGTTCATAAGT
1 CTTCCTTTTTAAACAATCTCATACTCTACGAGG--CATAAGT
*
315661 CTTCCTTTTTAAACAATCTTATACTCTACTGAGGCATAAGT
1 CTTCCTTTTTAAACAATCTCATACTCTAC-GAGGCATAAGT
* *
315702 TTTCCTTTTCAAACA
1 CTTCCTTTTTAAACA
315717 TAATCTCACT
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
41 44 0.94
43 3 0.06
ACGTcount: A:0.28, C:0.23, G:0.08, T:0.41
Consensus pattern (40 bp):
CTTCCTTTTTAAACAATCTCATACTCTACGAGGCATAAGT
Found at i:315751 original size:44 final size:43
Alignment explanation
Indices: 315703--315895 Score: 144
Period size: 42 Copynumber: 4.5 Consensus size: 43
315693 GGCATAAGTT
* *
315703 TTCCTTTTCAAACATAATCTCACTT-TCATTCTAAGACTTGAGTC
1 TTCCTTTT-AAACATAATCTCA-TTCTCATCCTAAGACATGAGTC
* * *
315747 TTCC-TTTAAACAAAATATCATTCTCATCCTGAGACATGAGTC
1 TTCCTTTTAAACATAATCTCATTCTCATCCTAAGACATGAGTC
* * * * * *
315789 TTCCTTTTTAAACATATTCTCATACTCGTTCC-GAGTCACGAGTC
1 TTCC-TTTTAAACATAATCTCATTCTC-ATCCTAAGACATGAGTC
* * * * *
315833 TTCC-TTTAAACTTATTCTCATGCTTATTCC-GAGACATGAGTC
1 TTCCTTTTAAACATAATCTCATTCTCA-TCCTAAGACATGAGTC
*
315875 TTCCTTTTTAAACATATTCTC
1 TTCC-TTTTAAACATAATCTC
315896 GTGCTTATTC
Statistics
Matches: 123, Mismatches: 19, Indels: 14
0.79 0.12 0.09
Matches are distributed among these distances:
41 2 0.02
42 66 0.54
43 3 0.02
44 49 0.40
45 3 0.02
ACGTcount: A:0.26, C:0.25, G:0.09, T:0.40
Consensus pattern (43 bp):
TTCCTTTTAAACATAATCTCATTCTCATCCTAAGACATGAGTC
Found at i:315787 original size:42 final size:41
Alignment explanation
Indices: 315736--315895 Score: 158
Period size: 42 Copynumber: 3.7 Consensus size: 41
315726 TTTCATTCTA
* * * * *
315736 AGACTTGAGTCTTCCTTTAAACAAAATATCATTCTCATCCTG
1 AGACATGAGTCTTCCTTTAAACATATTCTCATACTCATCC-G
*
315778 AGACATGAGTCTTCCTTTTTAAACATATTCTCATACTCGTTCCG
1 AGACATGAGTCTTCC--TTTAAACATATTCTCATACTC-ATCCG
* * * * *
315822 AGTCACGAGTCTTCCTTTAAACTTATTCTCATGCTTATTCCG
1 AGACATGAGTCTTCCTTTAAACATATTCTCATACTCA-TCCG
315864 AGACATGAGTCTTCCTTTTTAAACATATTCTC
1 AGACATGAGTCTTCC--TTTAAACATATTCTC
315896 GTGCTTATTC
Statistics
Matches: 97, Mismatches: 15, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
42 49 0.51
44 45 0.46
45 3 0.03
ACGTcount: A:0.26, C:0.24, G:0.11, T:0.39
Consensus pattern (41 bp):
AGACATGAGTCTTCCTTTAAACATATTCTCATACTCATCCG
Found at i:315794 original size:86 final size:87
Alignment explanation
Indices: 315689--315927 Score: 232
Period size: 86 Copynumber: 2.8 Consensus size: 87
315679 TTATACTCTA
* * * * * * * **
315689 CTGAGGCATAAGTTTTCCTTTTCAAACATAATCTCACT-TTCATTCTAAGACTTGAGTCTTCCTT
1 CTGAGACATGAGTCTTCCTTTTTAAACATATTCTCA-TACTCATTCCAAGACACGAGTCTTCCTT
*
315753 TAAACAAAATATCATTCTCA-TC
65 TAAACAAAATATCATGCTCATTC
* * *
315775 CTGAGACATGAGTCTTCCTTTTTAAACATATTCTCATACTCGTTCCGAGTCACGAGTCTTCCTTT
1 CTGAGACATGAGTCTTCCTTTTTAAACATATTCTCATACTCATTCCAAGACACGAGTCTTCCTTT
** * * *
315840 AAACTTATTCTCATGCTTATTC
66 AAACAAAATATCATGCTCATTC
* * * * *
315862 C-GAGACATGAGTCTTCCTTTTTAAACATATTCTCGTGCTTATTCCAAGTCACGAGTATTCCATT
1 CTGAGACATGAGTCTTCCTTTTTAAACATATTCTCATACTCATTCCAAGACACGAGTCTTCC-TT
315926 TA
65 TA
315928 TATATCAAAT
Statistics
Matches: 126, Mismatches: 24, Indels: 5
0.81 0.15 0.03
Matches are distributed among these distances:
85 1 0.01
86 118 0.94
87 7 0.06
ACGTcount: A:0.26, C:0.24, G:0.11, T:0.39
Consensus pattern (87 bp):
CTGAGACATGAGTCTTCCTTTTTAAACATATTCTCATACTCATTCCAAGACACGAGTCTTCCTTT
AAACAAAATATCATGCTCATTC
Found at i:315901 original size:44 final size:44
Alignment explanation
Indices: 315777--315906 Score: 183
Period size: 44 Copynumber: 3.0 Consensus size: 44
315767 TTCTCATCCT
* **
315777 GAGACATGAGTCTTCCTTTTTAAACATATTCTCATACTCGTTCC
1 GAGACATGAGTCTTCCTTTTTAAACATATTCTCATGCTTATTCC
* * *
315821 GAGTCACGAGTCTTCC--TTTAAACTTATTCTCATGCTTATTCC
1 GAGACATGAGTCTTCCTTTTTAAACATATTCTCATGCTTATTCC
*
315863 GAGACATGAGTCTTCCTTTTTAAACATATTCTCGTGCTTATTCC
1 GAGACATGAGTCTTCCTTTTTAAACATATTCTCATGCTTATTCC
315907 AAGTCACGAG
Statistics
Matches: 74, Mismatches: 10, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
42 36 0.49
44 38 0.51
ACGTcount: A:0.23, C:0.25, G:0.12, T:0.40
Consensus pattern (44 bp):
GAGACATGAGTCTTCCTTTTTAAACATATTCTCATGCTTATTCC
Found at i:317796 original size:17 final size:17
Alignment explanation
Indices: 317771--317809 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
317761 CGGTAATTCT
317771 TTAAACTATCGAA-CTTA
1 TTAAACTAT-GAAGCTTA
*
317788 TTAAGCTATGAAGCTTA
1 TTAAACTATGAAGCTTA
317805 TTAAA
1 TTAAA
317810 GATGTTGTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
16 3 0.16
17 16 0.84
ACGTcount: A:0.41, C:0.13, G:0.10, T:0.36
Consensus pattern (17 bp):
TTAAACTATGAAGCTTA
Found at i:318392 original size:21 final size:21
Alignment explanation
Indices: 318349--318424 Score: 82
Period size: 21 Copynumber: 3.6 Consensus size: 21
318339 AGAGTTTTTA
* *
318349 GTATCGGTAGAAGTAAT-ATTT
1 GTATCGGTAGAAG-AGTCACTT
* *
318370 GTTTCGATAGAAGAGTCACTT
1 GTATCGGTAGAAGAGTCACTT
**
318391 GTATCGGTAGAACTGTCACTT
1 GTATCGGTAGAAGAGTCACTT
318412 GTATCGGTAGAAG
1 GTATCGGTAGAAG
318425 TCTGCACTAT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 2 0.04
21 43 0.96
ACGTcount: A:0.29, C:0.12, G:0.26, T:0.33
Consensus pattern (21 bp):
GTATCGGTAGAAGAGTCACTT
Found at i:324264 original size:2 final size:2
Alignment explanation
Indices: 324257--324291 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
324247 TTTCGATGAG
* *
324257 TC TC TC TC TC CC TC TC TC TC TC CC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
324292 TTCCTTATAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.54, G:0.00, T:0.46
Consensus pattern (2 bp):
TC
Found at i:324274 original size:12 final size:12
Alignment explanation
Indices: 324257--324290 Score: 68
Period size: 12 Copynumber: 2.8 Consensus size: 12
324247 TTTCGATGAG
324257 TCTCTCTCTCCC
1 TCTCTCTCTCCC
324269 TCTCTCTCTCCC
1 TCTCTCTCTCCC
324281 TCTCTCTCTC
1 TCTCTCTCTC
324291 TTTCCTTATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.00, C:0.56, G:0.00, T:0.44
Consensus pattern (12 bp):
TCTCTCTCTCCC
Found at i:331309 original size:18 final size:18
Alignment explanation
Indices: 331270--331312 Score: 63
Period size: 17 Copynumber: 2.4 Consensus size: 18
331260 CATAATTATC
331270 ATAATT-TTTATAAAATT
1 ATAATTATTTATAAAATT
331287 ATAATTATTT-TAAAATAT
1 ATAATTATTTATAAAAT-T
331305 ATAATTAT
1 ATAATTAT
331313 CATAAATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
17 12 0.50
18 12 0.50
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
ATAATTATTTATAAAATT
Found at i:331318 original size:18 final size:17
Alignment explanation
Indices: 331279--331318 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
331269 CATAATTTTT
*
331279 ATAAAATTATAATTATT
1 ATAAAATTATAATTATC
*
331296 TTAAAATATATAATTATC
1 ATAAAAT-TATAATTATC
331314 ATAAA
1 ATAAA
331319 TTTTTTAATT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (17 bp):
ATAAAATTATAATTATC
Found at i:331835 original size:27 final size:29
Alignment explanation
Indices: 331805--331867 Score: 76
Period size: 27 Copynumber: 2.2 Consensus size: 29
331795 TGGTAAATTT
* *
331805 TTTTTTACCTTTAAAAA-TATAAAA-AAA
1 TTTTTAACCCTTAAAAATTATAAAATAAA
*
331832 TTTTGAACCCTTAAAAATTATAAAATAAA
1 TTTTTAACCCTTAAAAATTATAAAATAAA
*
331861 ATTTTAA
1 TTTTTAA
331868 GCCTCTTTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
27 14 0.48
28 7 0.24
29 8 0.28
ACGTcount: A:0.51, C:0.08, G:0.02, T:0.40
Consensus pattern (29 bp):
TTTTTAACCCTTAAAAATTATAAAATAAA
Found at i:334160 original size:224 final size:224
Alignment explanation
Indices: 333770--334218 Score: 880
Period size: 224 Copynumber: 2.0 Consensus size: 224
333760 ATATTCCATT
*
333770 ACACATTAATTATTTTTTTTATGAATTACAAGAAAAGGGTAAAACCCTAATAACAATACGACTAA
1 ACACATTAATTATTTTTTTTATGAATTACAAGAAAAGGGTAAAACCCTAACAACAATACGACTAA
*
333835 TACGAATTGAATTCAAATTATATTTAGGACAATAAATATTTTTAACCATCAAGTAAACATTAATC
66 TACGAATTGAATTCAAATTATATTTAGGACAATAAATACTTTTAACCATCAAGTAAACATTAATC
333900 ATATTTTCCATCAATTAGTATAGAGCCAACTTAGTTTAATTATTGACATAGATATGATAATTTGA
131 ATATTTTCCATCAATTAGTATAGAGCCAACTTAGTTTAATTATTGACATAGATATGATAATTTGA
333965 AACTCTTTTTCTTTGTATAGATTCAATAG
196 AACTCTTTTTCTTTGTATAGATTCAATAG
333994 ACACATTAATTATTTTTTTTATGAATTACAAGAAAAGGGTAAAACCCTAACAACAATACGACTAA
1 ACACATTAATTATTTTTTTTATGAATTACAAGAAAAGGGTAAAACCCTAACAACAATACGACTAA
334059 TACGAATTGAATTCAAATTATATTTAGGACAATAAATACTTTTAACCATCAAGTAAACATTAATC
66 TACGAATTGAATTCAAATTATATTTAGGACAATAAATACTTTTAACCATCAAGTAAACATTAATC
334124 ATATTTTCCATCAATTAGTATAGAGCCAACTTAGTTTAATTATTGACATAGATATGATAATTTGA
131 ATATTTTCCATCAATTAGTATAGAGCCAACTTAGTTTAATTATTGACATAGATATGATAATTTGA
334189 AACTCTTTTTCTTTGTATAGATTCAATAG
196 AACTCTTTTTCTTTGTATAGATTCAATAG
334218 A
1 A
334219 TTGAGAATCA
Statistics
Matches: 223, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
224 223 1.00
ACGTcount: A:0.41, C:0.13, G:0.10, T:0.37
Consensus pattern (224 bp):
ACACATTAATTATTTTTTTTATGAATTACAAGAAAAGGGTAAAACCCTAACAACAATACGACTAA
TACGAATTGAATTCAAATTATATTTAGGACAATAAATACTTTTAACCATCAAGTAAACATTAATC
ATATTTTCCATCAATTAGTATAGAGCCAACTTAGTTTAATTATTGACATAGATATGATAATTTGA
AACTCTTTTTCTTTGTATAGATTCAATAG
Found at i:334789 original size:23 final size:22
Alignment explanation
Indices: 334762--334812 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 22
334752 TAAAAATTTT
*
334762 AATTTAATT-TTTTAAAAATTAC
1 AATTTAATTATTAT-AAAATTAC
334784 ACATTT-ATTATTATAAAATTAC
1 A-ATTTAATTATTATAAAATTAC
334806 AATTTAA
1 AATTTAA
334813 CTTCGTCTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
21 4 0.16
22 14 0.56
23 7 0.28
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (22 bp):
AATTTAATTATTATAAAATTAC
Found at i:336163 original size:29 final size:30
Alignment explanation
Indices: 336130--336212 Score: 84
Period size: 29 Copynumber: 2.9 Consensus size: 30
336120 TTAATAACAT
336130 AATAAAAATATAATTATAGTATTAAAT-AA
1 AATAAAAATATAATTATAGTATTAAATGAA
* * * *
336159 AATAACAATATAATCATAGTAAT-AATGAC
1 AATAAAAATATAATTATAGTATTAAATGAA
*
336188 AATAAATAT-TAATTA-AGTATATAAA
1 AATAAAAATATAATTATAGTAT-TAAA
336213 CAACAATATA
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
27 4 0.09
28 9 0.21
29 30 0.70
ACGTcount: A:0.59, C:0.04, G:0.05, T:0.33
Consensus pattern (30 bp):
AATAAAAATATAATTATAGTATTAAATGAA
Found at i:336237 original size:17 final size:16
Alignment explanation
Indices: 336205--336238 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
336195 ATTAATTAAG
336205 TATATAAACAACAATA
1 TATATAAACAACAATA
*
336221 TATATATAACAATAATA
1 TATATA-AACAACAATA
336238 T
1 T
336239 GGAAAATTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.59, C:0.09, G:0.00, T:0.32
Consensus pattern (16 bp):
TATATAAACAACAATA
Found at i:338174 original size:17 final size:17
Alignment explanation
Indices: 338148--338186 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
338138 ATATGCGCAC
*
338148 TTGTATGAGA-AATGTGA
1 TTGTACGAGATAAT-TGA
338165 TTGTACGAGATAATTGA
1 TTGTACGAGATAATTGA
338182 TTGTA
1 TTGTA
338187 TGAAGATTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 17 0.85
18 3 0.15
ACGTcount: A:0.33, C:0.03, G:0.26, T:0.38
Consensus pattern (17 bp):
TTGTACGAGATAATTGA
Found at i:340591 original size:21 final size:21
Alignment explanation
Indices: 340560--340618 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 21
340550 ATAGTACAGA
*
340560 CTTCTATCGATACAAGTGA-T
1 CTTCTACCGATACAAGTGACT
* *
340580 AGTTCTACCGATACAACTGACT
1 -CTTCTACCGATACAAGTGACT
*
340602 CTTCTACCGATGCAAGT
1 CTTCTACCGATACAAGT
340619 CTTACTTCTA
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
21 30 0.97
22 1 0.03
ACGTcount: A:0.29, C:0.25, G:0.15, T:0.31
Consensus pattern (21 bp):
CTTCTACCGATACAAGTGACT
Found at i:343032 original size:48 final size:49
Alignment explanation
Indices: 342932--343074 Score: 125
Period size: 48 Copynumber: 3.0 Consensus size: 49
342922 TACACCATTT
* * * * * *
342932 GTGGACAAGCCACCACATAGA-TAGCAATGAACGACCACATAA-CACATC
1 GTGGATAAGCCACCAAATAGATTAACGAT-AACAACCACATAATCGCATC
*
342980 GTGGATGAA-CCA-CAACATA-ATTAACGATAACAACCACATAATCGCATT
1 GTGGAT-AAGCCACCAA-ATAGATTAACGATAACAACCACATAATCGCATC
* ***
343028 GTGGATAAGCCACCAAATAGATTACCGATAATGGCCACATAATCGCA
1 GTGGATAAGCCACCAAATAGATTAACGATAACAACCACATAATCGCA
343075 GTTAAACTGC
Statistics
Matches: 77, Mismatches: 11, Indels: 13
0.76 0.11 0.13
Matches are distributed among these distances:
47 17 0.22
48 32 0.42
49 28 0.36
ACGTcount: A:0.41, C:0.25, G:0.16, T:0.17
Consensus pattern (49 bp):
GTGGATAAGCCACCAAATAGATTAACGATAACAACCACATAATCGCATC
Found at i:345725 original size:27 final size:26
Alignment explanation
Indices: 345695--345789 Score: 68
Period size: 27 Copynumber: 3.5 Consensus size: 26
345685 ATGCTTAATT
*
345695 CTCGGTTAGAGCGTAATGCCGTTATAG
1 CTCGGGTAGAGCGTAATGCC-TTATAG
*
345722 CTCGGGTAGAGCTTTGGACATG-CTTAT-G
1 CTCGGGTAGAGC---GTA-ATGCCTTATAG
** *
345750 TCTCGATTAGAGCGTAATACCATTATAG
1 -CTCGGGTAGAGCGTAATGCC-TTATAG
345778 CTCGGGTAGAGC
1 CTCGGGTAGAGC
345790 TTTGGACATG
Statistics
Matches: 52, Mismatches: 8, Indels: 16
0.68 0.11 0.21
Matches are distributed among these distances:
25 2 0.04
26 3 0.06
27 25 0.48
28 2 0.04
29 14 0.27
30 3 0.06
31 3 0.06
ACGTcount: A:0.23, C:0.19, G:0.28, T:0.29
Consensus pattern (26 bp):
CTCGGGTAGAGCGTAATGCCTTATAG
Found at i:345754 original size:29 final size:29
Alignment explanation
Indices: 345722--345817 Score: 76
Period size: 29 Copynumber: 3.4 Consensus size: 29
345712 GCCGTTATAG
345722 CTCGGGTAGAGCTTTGGACATGCTTATGT
1 CTCGGGTAGAGCTTTGGACATGCTTATGT
** * *
345751 CTCGATTAGAGC---GTA-ATACCATTATAG-
1 CTCGGGTAGAGCTTTGGACAT-GC-TTAT-GT
*
345778 CTCGGGTAGAGCTTTGGACATGCTTACGT
1 CTCGGGTAGAGCTTTGGACATGCTTATGT
*
345807 CTCGGTTAGAG
1 CTCGGGTAGAG
345818 TGTAATGCTA
Statistics
Matches: 49, Mismatches: 10, Indels: 16
0.65 0.13 0.21
Matches are distributed among these distances:
25 2 0.04
26 3 0.06
27 14 0.29
28 2 0.04
29 23 0.47
30 3 0.06
31 2 0.04
ACGTcount: A:0.22, C:0.19, G:0.28, T:0.31
Consensus pattern (29 bp):
CTCGGGTAGAGCTTTGGACATGCTTATGT
Found at i:345760 original size:56 final size:56
Alignment explanation
Indices: 345607--345836 Score: 279
Period size: 56 Copynumber: 4.1 Consensus size: 56
345597 TTAACTCACA
* *
345607 TATAGCTCGGGTAGAGC-TCCGATC-TGCTTATGTCTCGGTTAGAGTGTAATGCCAT
1 TATAGCTCGGGTAGAGCTTTCGA-CATGCTTATGTCTCGGTTAGAGCGTAATGCCAT
** * * * *
345662 TGCAGCTCGAGTAAAG-ATTCGACATGCTTAAT-TCTCGGTTAGAGCGTAATGCCGT
1 TATAGCTCGGGTAGAGCTTTCGACATGCTT-ATGTCTCGGTTAGAGCGTAATGCCAT
* * *
345717 TATAGCTCGGGTAGAGCTTTGGACATGCTTATGTCTCGATTAGAGCGTAATACCAT
1 TATAGCTCGGGTAGAGCTTTCGACATGCTTATGTCTCGGTTAGAGCGTAATGCCAT
* * * *
345773 TATAGCTCGGGTAGAGCTTTGGACATGCTTACGTCTCGGTTAGAGTGTAATGCTAT
1 TATAGCTCGGGTAGAGCTTTCGACATGCTTATGTCTCGGTTAGAGCGTAATGCCAT
345829 TATAGCTC
1 TATAGCTC
345837 AAGTAGGAAA
Statistics
Matches: 149, Mismatches: 21, Indels: 9
0.83 0.12 0.05
Matches are distributed among these distances:
54 1 0.01
55 56 0.38
56 92 0.62
ACGTcount: A:0.23, C:0.19, G:0.26, T:0.32
Consensus pattern (56 bp):
TATAGCTCGGGTAGAGCTTTCGACATGCTTATGTCTCGGTTAGAGCGTAATGCCAT
Found at i:356539 original size:80 final size:80
Alignment explanation
Indices: 356406--356561 Score: 244
Period size: 80 Copynumber: 1.9 Consensus size: 80
356396 GGCACAAACC
*
356406 GTTGGTTAATCCAACTAGAGCTGGGCTCACTTATCGTAGTTTATCTGCTAGGCAAT-GGGTGCCA
1 GTTGGTTAATCCAACTAGAGCTGGGCTCACTTATCGCAGTTTATCTGCTAGGC-ATCGGGTGCCA
356470 TGAATTGACGGACTTT
65 TGAATTGACGGACTTT
* * *
356486 GTTGGTTAATCTAACTAGAGTTGGGCTCACTTATCGCGGTTTAATC-GCTAGGCATCGGGTGCCA
1 GTTGGTTAATCCAACTAGAGCTGGGCTCACTTATCGCAGTTT-ATCTGCTAGGCATCGGGTGCCA
356550 TGAATTGACGGA
65 TGAATTGACGGA
356562 AATTATGAAT
Statistics
Matches: 70, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
79 2 0.03
80 65 0.93
81 3 0.04
ACGTcount: A:0.22, C:0.19, G:0.28, T:0.31
Consensus pattern (80 bp):
GTTGGTTAATCCAACTAGAGCTGGGCTCACTTATCGCAGTTTATCTGCTAGGCATCGGGTGCCAT
GAATTGACGGACTTT
Found at i:359131 original size:40 final size:41
Alignment explanation
Indices: 359087--359173 Score: 113
Period size: 41 Copynumber: 2.1 Consensus size: 41
359077 ATGGGCTGGT
*
359087 ACACGGGCATGTGT-CAGGTATGTGTATACTGTTCTGAGGC
1 ACACGGGCATGTGTCCAGGTATGTGTATACTATTCTGAGGC
* * * * *
359127 ACACGAGCATGTGTCCGGGTGTGTGTATACTATTTTGGGGC
1 ACACGGGCATGTGTCCAGGTATGTGTATACTATTCTGAGGC
359168 ACACGG
1 ACACGG
359174 CCTGACACAT
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
40 13 0.33
41 26 0.67
ACGTcount: A:0.20, C:0.18, G:0.33, T:0.29
Consensus pattern (41 bp):
ACACGGGCATGTGTCCAGGTATGTGTATACTATTCTGAGGC
Found at i:359148 original size:93 final size:94
Alignment explanation
Indices: 359051--359223 Score: 240
Period size: 93 Copynumber: 1.9 Consensus size: 94
359041 TGTGTGTCAA
* * ** *
359051 GGTGTGTGTATACTATTTAGAGGCACATGGGCTGGTACACGGGCATGTG-TCAGGTATGTGTATA
1 GGTGTGTGTATACTATTTAGAGGCACACGGCCTGACACACGGGCATGTGCTAAGGTATGTGTATA
*
359115 CTGTTCTGAGGCACACGAGCATGTGTCCG
66 CTGTTCTAAGGCACACGAGCATGTGTCCG
* * * * *
359144 GGTGTGTGTATACTATTTTGGGGCACACGGCCTGACACATGGGCTTGTGCTAAGGTGTGTGTATA
1 GGTGTGTGTATACTATTTAGAGGCACACGGCCTGACACACGGGCATGTGCTAAGGTATGTGTATA
359209 CTGTTCTAAGGCACA
66 CTGTTCTAAGGCACA
359224 TGGGCTGACA
Statistics
Matches: 68, Mismatches: 11, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
93 41 0.60
94 27 0.40
ACGTcount: A:0.20, C:0.17, G:0.32, T:0.30
Consensus pattern (94 bp):
GGTGTGTGTATACTATTTAGAGGCACACGGCCTGACACACGGGCATGTGCTAAGGTATGTGTATA
CTGTTCTAAGGCACACGAGCATGTGTCCG
Found at i:359152 original size:52 final size:53
Alignment explanation
Indices: 359040--359152 Score: 117
Period size: 52 Copynumber: 2.2 Consensus size: 53
359030 AGTTGTAGGA
* * *
359040 GTGTGTGTCAAGGTGTGTGTATACTATTTAGAGGCACATGGGCTGGTACACGG
1 GTGTGTGTCAAGGTATGTGTATACTATTTAGAGGCACACGAGCTGGTACACGG
** *
359093 GCATGTGTC-AGGTATGTGTATACTGTTCT-GAGGCACACGAGCATGTGT-C-CGG
1 GTGTGTGTCAAGGTATGTGTATACTATT-TAGAGGCACACGAGC-TG-GTACACGG
359145 GTGTGTGT
1 GTGTGTGT
359153 ATACTATTTT
Statistics
Matches: 49, Mismatches: 8, Indels: 7
0.77 0.12 0.11
Matches are distributed among these distances:
52 36 0.73
53 11 0.22
54 2 0.04
ACGTcount: A:0.19, C:0.15, G:0.35, T:0.31
Consensus pattern (53 bp):
GTGTGTGTCAAGGTATGTGTATACTATTTAGAGGCACACGAGCTGGTACACGG
Found at i:359202 original size:53 final size:53
Alignment explanation
Indices: 359144--359260 Score: 144
Period size: 53 Copynumber: 2.2 Consensus size: 53
359134 CATGTGTCCG
* ** * *
359144 GGTGTGTGTATACTATTTTGGGGCACACGGCCTGACACATGGGCTTGTGCTAA
1 GGTGTGTGTATACTATTCTAAGGCACACGGCCTGACAAATGGGCGTGTGCTAA
* * * * *
359197 GGTGTGTGTATACTGTTCTAAGGCACATGGGCTGACAAATGGGCGTGTGTTAG
1 GGTGTGTGTATACTATTCTAAGGCACACGGCCTGACAAATGGGCGTGTGCTAA
359250 GGTGTGTGTAT
1 GGTGTGTGTAT
359261 TGTTTTGAGA
Statistics
Matches: 54, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
53 54 1.00
ACGTcount: A:0.19, C:0.15, G:0.35, T:0.32
Consensus pattern (53 bp):
GGTGTGTGTATACTATTCTAAGGCACACGGCCTGACAAATGGGCGTGTGCTAA
Found at i:361416 original size:18 final size:18
Alignment explanation
Indices: 361376--361427 Score: 56
Period size: 18 Copynumber: 3.0 Consensus size: 18
361366 TTTTCAGTTG
*
361376 TAATTAATTTAAAATT-TT
1 TAATTAA-TTAAATTTATT
*
361394 CAATTAATTAAATTTATT
1 TAATTAATTAAATTTATT
361412 TAATTAA--AAATTTATT
1 TAATTAATTAAATTTATT
361428 CTCATCCCAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
16 9 0.30
17 7 0.23
18 14 0.47
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (18 bp):
TAATTAATTAAATTTATT
Found at i:365870 original size:19 final size:19
Alignment explanation
Indices: 365838--365874 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
365828 TCTTTTTAAC
365838 ATTTCATTTTTTCTCTCAA
1 ATTTCATTTTTTCTCTCAA
365857 ATTTC-TTTTATTCTCTCA
1 ATTTCATTTT-TTCTCTCA
365875 TATTCTCTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.19, C:0.22, G:0.00, T:0.59
Consensus pattern (19 bp):
ATTTCATTTTTTCTCTCAA
Found at i:369382 original size:26 final size:26
Alignment explanation
Indices: 369353--369447 Score: 156
Period size: 26 Copynumber: 3.7 Consensus size: 26
369343 GTATTTGTGA
*
369353 TGCTCACACGAGCTGTGAAATAGGCT
1 TGCTCACACGAGCTATGAAATAGGCT
369379 TGCTCACACGAGCTATGAAATAGG-T
1 TGCTCACACGAGCTATGAAATAGGCT
*
369404 CTGCTCACACGAGCTATGAAATAGGCC
1 -TGCTCACACGAGCTATGAAATAGGCT
369431 TGCTCACACGAGCTATG
1 TGCTCACACGAGCTATG
369448 GGTCAAGATG
Statistics
Matches: 65, Mismatches: 2, Indels: 4
0.92 0.03 0.06
Matches are distributed among these distances:
25 1 0.02
26 64 0.98
ACGTcount: A:0.28, C:0.25, G:0.24, T:0.22
Consensus pattern (26 bp):
TGCTCACACGAGCTATGAAATAGGCT
Found at i:372623 original size:25 final size:26
Alignment explanation
Indices: 372594--372646 Score: 72
Period size: 25 Copynumber: 2.0 Consensus size: 26
372584 GAAAAAAAAA
*
372594 AAAACAAAGCAAAAGA-AATTTTTTT
1 AAAACAAAGCAAAAAAGAATTTTTTT
*
372619 AAAACAAGGCAAAAAATGAATTTTTTT
1 AAAACAAAGCAAAAAA-GAATTTTTTT
372646 A
1 A
372647 GATTTTTTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 14 0.58
27 10 0.42
ACGTcount: A:0.55, C:0.08, G:0.09, T:0.28
Consensus pattern (26 bp):
AAAACAAAGCAAAAAAGAATTTTTTT
Found at i:379500 original size:34 final size:34
Alignment explanation
Indices: 379457--379524 Score: 118
Period size: 34 Copynumber: 2.0 Consensus size: 34
379447 ATTCAAGGAG
* *
379457 AAAGAACATGGCAAAGATTATGAAAAGTTTATAT
1 AAAGAACATGACAAAGATTATCAAAAGTTTATAT
379491 AAAGAACATGACAAAGATTATCAAAAGTTTATAT
1 AAAGAACATGACAAAGATTATCAAAAGTTTATAT
379525 CTACCTTGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.51, C:0.07, G:0.15, T:0.26
Consensus pattern (34 bp):
AAAGAACATGACAAAGATTATCAAAAGTTTATAT
Found at i:384591 original size:18 final size:18
Alignment explanation
Indices: 384543--384597 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 18
384533 GTATTGAGGC
*
384543 AGAA-GAAGAAGAAAGAAA
1 AGAAGGAAGAA-AAAGAAG
* * *
384561 AAAAGAAAAAAAAAGAAG
1 AGAAGGAAGAAAAAGAAG
384579 AGAAGGAAGAAAAAGAAG
1 AGAAGGAAGAAAAAGAAG
384597 A
1 A
384598 AGATGTTGCC
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
18 25 0.86
19 4 0.14
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (18 bp):
AGAAGGAAGAAAAAGAAG
Found at i:387163 original size:24 final size:24
Alignment explanation
Indices: 387129--387175 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
387119 ATTCATCTTT
*
387129 TATTAATTTGCTCTGAC-ATTTTA
1 TATTAATTTGCACTGACAATTTTA
387152 TATTACATTTGCACTGACAATTTT
1 TATTA-ATTTGCACTGACAATTTT
387176 TACTCTTAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 5 0.24
24 11 0.52
25 5 0.24
ACGTcount: A:0.28, C:0.15, G:0.09, T:0.49
Consensus pattern (24 bp):
TATTAATTTGCACTGACAATTTTA
Found at i:388198 original size:19 final size:19
Alignment explanation
Indices: 388171--388207 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
388161 ATAAGAATAG
388171 AAATCTGTGAGCTATCCAT
1 AAATCTGTGAGCTATCCAT
* *
388190 AAATGTGTGAGCTGTCCA
1 AAATCTGTGAGCTATCCA
388208 CTCTAGTATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.30
Consensus pattern (19 bp):
AAATCTGTGAGCTATCCAT
Found at i:391213 original size:101 final size:100
Alignment explanation
Indices: 391080--392252 Score: 906
Period size: 101 Copynumber: 11.7 Consensus size: 100
391070 TCAATATAAT
** * * * ** *
391080 ATCAAATATTATATCCCTGAAGATGCAATGGATCAAATTAGAACTATAATAGCAAATCTTTATCT
1 ATCAAATCCTATATCCCTGAAGTTACAGTGGATCGGATTAGAACTACAATAGCAAATCTTTATCT
* * *
391145 CCCTAAAGTTACAATAGAGCAAGATGAAGCTATCAC
66 CCCTAAAGTTGCAGTGGAGCAAGATGAAGCTA-CAC
* * * * * * *
391181 GTCAAATCCTATATCCCTGAAGATGCAGTGGATGGGATTAGAACAACAGTAGCATATCTTTATCT
1 ATCAAATCCTATATCCCTGAAGTTACAGTGGATCGGATTAGAACTACAATAGCAAATCTTTATCT
* * * * *
391246 TCTTGAAGTTACAGTGGAGCAAGAGGAAGCTACCAC
66 CCCTAAAGTTGCAGTGGAGCAAGATGAAGCTA-CAC
* * * * * * * *
391282 ATCAAATCCTACATCCCTGAAGATGCAATGAATCAGATTAGAACTACAGTAGCAAATCTTGATCT
1 ATCAAATCCTATATCCCTGAAGTTACAGTGGATCGGATTAGAACTACAATAGCAAATCTTTATCT
*
391347 CCCTAAAGTTGTAGTGGAGCAAGATGAAGCTACCAC
66 CCCTAAAGTTGCAGTGGAGCAAGATGAAGCTA-CAC
* * * * * * * **
391383 ACCAAATCTTATATCCATGAAGTTACAGTGGATCAGATTAAAACGACAGTAAAAAATCTTTATCT
1 ATCAAATCCTATATCCCTGAAGTTACAGTGGATCGGATTAGAACTACAATAGCAAATCTTTATCT
* * *
391448 CTC-AGAAGTTGCAGTAGAGCAAGATAAAGCTACAAC
66 CCCTA-AAGTTGCAGTGGAGCAAGATGAAGCTAC-AC
* * * ** * * * *
391484 ATCAAGTCTTATATCCCTGAAATTGTAGTGGATCGAATTAAAAAATACAATAGAAAATCTTTATC
1 ATCAAATCCTATATCCCTGAAGTTACAGTGGATCGGATT-AGAACTACAATAGCAAATCTTTATC
** *
391549 TCCCCGAAGTTGTAGTGGAGCAAGATGAAGCTACGAC
65 TCCCTAAAGTTGCAGTGGAGCAAGATGAAGCTAC-AC
** * * * *
391586 ATCAAATCCTATATCATTGAAGTTACA-TTGATTGAATTA-AAGTTACGAA-AGCAAATCTTTAT
1 ATCAAATCCTATATCCCTGAAGTTACAGTGGATCGGATTAGAA-CTAC-AATAGCAAATCTTTAT
* * * * *
391648 CTCTCTGAAGTTGCAATGGAGCAAGATGAAGCTATAAA
64 CTCCCTAAAGTTGCAGTGGAGCAAGATGAAGCTA-CAC
* * ** * * *
391686 ATCAAATCTTATATCCCTAAAGTTGTAGTGGATCGGATT-GAAGCAACAAAAACAAATC-TTATC
1 ATCAAATCCTATATCCCTGAAGTTACAGTGGATCGGATTAGAA-CTACAATAGCAAATCTTTATC
* * * * *
391749 TCTCTGAA-TATGCAATGGAGCAAGATGAAGTTAAGAC
65 TCCCTAAAGT-TGCAGTGGAGCAAGATGAAGCT-ACAC
* * *
391786 ATCAAATCCTATATCCTTGAAGTTATAGTGGATCGGATTA-AAGCTACAAAAGCAAATC-TTATC
1 ATCAAATCCTATATCCCTGAAGTTACAGTGGATCGGATTAGAA-CTACAATAGCAAATCTTTATC
* *
391849 TCCCTAAAGTTGTAGTGGAGCAAGATAAAGCTACAAC
65 TCCCTAAAGTTGCAGTGGAGCAAGATGAAGCTAC-AC
* * * * * *
391886 ATCAAATCTTATATCCTTGAAGTTACAGTGGACCAG-TTTGAAGCTACGAA-AGTAAATC-TTAT
1 ATCAAATCCTATATCCCTGAAGTTACAGTGGATCGGATTAGAA-CTAC-AATAGCAAATCTTTAT
*** * *
391948 CTTTTTAAAGTTGCAATGGAGCAACATGAAGCTACA-
64 CTCCCTAAAGTTGCAGTGGAGCAAGATGAAGCTACAC
* * * * *
391984 ATACCAAATCTTATAACCTTGAAGTTACAGTGGATCAGATT-GAAGCTATAGA-AGCAAATC-TT
1 AT--CAAATCCTATATCCCTGAAGTTACAGTGGATCGGATTAGAA-CTACA-ATAGCAAATCTTT
*** * * *
392046 ATCTCCCTAAAAACGTAGTAGAGCAAGATGAAGTTACAAC
62 ATCTCCCTAAAGTTGCAGTGGAGCAAGATGAAGCTAC-AC
* * * * * *
392086 ATCAAATCCTATATCCCTGAAGTTACAG-GGATCGGATTGAAAATTACAGTAACAAGTATTTATC
1 ATCAAATCCTATATCCCTGAAGTTACAGTGGATCGGATT-AGAACTACAATAGCAAATCTTTATC
* *
392150 TCCTTAAAGTTGCATTGGAGCAAGATGAAGCTACGAC
65 TCCCTAAAGTTGCAGTGGAGCAAGATGAAGCTAC-AC
* * ** * * *
392187 ATTAAATCCTATATCCCTTAAGTTGTAATGGATCAGATT-GAAGCTACAAAAGCAAATCTTTATC
1 ATCAAATCCTATATCCCTGAAGTTACAGTGGATCGGATTAGAA-CTACAATAGCAAATCTTTATC
392251 TC
65 TC
392253 TCAGAAGTTA
Statistics
Matches: 869, Mismatches: 174, Indels: 58
0.79 0.16 0.05
Matches are distributed among these distances:
98 2 0.00
99 17 0.02
100 375 0.43
101 393 0.45
102 82 0.09
ACGTcount: A:0.38, C:0.18, G:0.17, T:0.27
Consensus pattern (100 bp):
ATCAAATCCTATATCCCTGAAGTTACAGTGGATCGGATTAGAACTACAATAGCAAATCTTTATCT
CCCTAAAGTTGCAGTGGAGCAAGATGAAGCTACAC
Found at i:391413 original size:50 final size:50
Alignment explanation
Indices: 391080--392351 Score: 429
Period size: 50 Copynumber: 25.3 Consensus size: 50
391070 TCAATATAAT
* * * * * *
391080 ATCAAATATTATATCCCTGAAGATGCAATGGATCAA-ATTAGAA-CTATAAT
1 ATCAAATCTTATATCCCTGAAGTTGCAGTGGAGCAAGA-T-GAAGCTACAAC
* * * * * *
391130 AGCAAATCTTTATCTCCCTAAAGTTACAATAGAGCAAGATGAAGCTATC-AC
1 ATCAAATC-TTATATCCCTGAAGTTGCAGTGGAGCAAGATGAAGCTA-CAAC
* * * * * *
391181 GTCAAATCCTATATCCCTGAAGATGCAGTGGATG--GGAT-TAG-AACAAC
1 ATCAAATCTTATATCCCTGAAGTTGCAGTGGA-GCAAGATGAAGCTACAAC
* * * * *
391228 AGTAGCATATCTT-TATCTTCTTGAAGTTACAGTGGAGCAAGAGGAAGCTACCAC
1 A-T--CAAATCTTATATC--CCTGAAGTTGCAGTGGAGCAAGATGAAGCTACAAC
* * * * * * **
391282 ATCAAATCCTACATCCCTGAAGATGCAATGAATC-AGATTAGAA-CTACAGT
1 ATCAAATCTTATATCCCTGAAGTTGCAGTGGAGCAAGA-T-GAAGCTACAAC
* * * * *
391332 AGCAAATCTTGATCTCCCTAAAGTTGTAGTGGAGCAAGATGAAGCTACCAC
1 ATCAAATCTT-ATATCCCTGAAGTTGCAGTGGAGCAAGATGAAGCTACAAC
* * * * * * * **
391383 ACCAAATCTTATATCCATGAAGTTACAGTGGATC-AGATTAAAACGACAGT
1 ATCAAATCTTATATCCCTGAAGTTGCAGTGGAGCAAGA-TGAAGCTACAAC
** * * *
391433 AAAAAATCTT-TATCTCTCAGAAGTTGCAGTAGAGCAAGATAAAGCTACAAC
1 ATCAAATCTTATATC-C-CTGAAGTTGCAGTGGAGCAAGATGAAGCTACAAC
* * * * * * ** *
391484 ATCAAGTCTTATATCCCTGAAATTGTAGTGGATCGAA-TTAAAAAATACAAT
1 ATCAAATCTTATATCCCTGAAGTTGCAGTGGAGC-AAGAT-GAAGCTACAAC
** * * * *
391535 AGAAAATCTTTATCTCCCCGAAGTTGTAGTGGAGCAAGATGAAGCTACGAC
1 ATCAAATC-TTATATCCCTGAAGTTGCAGTGGAGCAAGATGAAGCTACAAC
* ** * * * * *
391586 ATCAAATCCTATATCATTGAAGTTACA-TTGATTG-AA-TTAAAGTTACGAA-
1 ATCAAATCTTATATCCCTGAAGTTGCAGTGGA--GCAAGATGAAGCTAC-AAC
* * * *
391635 AGCAAATCTT-TATCTCTCTGAAGTTGCAATGGAGCAAGATGAAGCTATAAA
1 ATCAAATCTTATATC-C-CTGAAGTTGCAGTGGAGCAAGATGAAGCTACAAC
* * * * * *
391686 ATCAAATCTTATATCCCTAAAGTTGTAGTGGATC-GGATTGAAGCAACAAA
1 ATCAAATCTTATATCCCTGAAGTTGCAGTGGAGCAAGA-TGAAGCTACAAC
* * * * *
391736 AACAAATCTTATCTCTCTGAA-TATGCAATGGAGCAAGATGAAGTTA-AGAC
1 ATCAAATCTTATATCCCTGAAGT-TGCAGTGGAGCAAGATGAAGCTACA-AC
* * ** * * * *
391786 ATCAAATCCTATATCCTTGAAGTTATAGTGGATC-GGATTAAAGCTACAAA
1 ATCAAATCTTATATCCCTGAAGTTGCAGTGGAGCAAGA-TGAAGCTACAAC
* * * * *
391836 AGCAAATCTTATCTCCCTAAAGTTGTAGTGGAGCAAGATAAAGCTACAAC
1 ATCAAATCTTATATCCCTGAAGTTGCAGTGGAGCAAGATGAAGCTACAAC
* * * *
391886 ATCAAATCTTATATCCTTGAAGTTACAGTGGA-CCAGTTTGAAGCTACGAA-
1 ATCAAATCTTATATCCCTGAAGTTGCAGTGGAGCAAG-ATGAAGCTAC-AAC
* *** * * * *
391936 AGT-AAATCTTATCTTTTTAAAGTTGCAATGGAGCAACATGAAGCTACAAT
1 A-TCAAATCTTATATCCCTGAAGTTGCAGTGGAGCAAGATGAAGCTACAAC
* * * * * *
391986 ACCAAATCTTATAACCTTGAAGTTACAGTGGATC-AGATTGAAGCTATAGA-
1 ATCAAATCTTATATCCCTGAAGTTGCAGTGGAGCAAGA-TGAAGCTACA-AC
* * * *** * * *
392036 AGCAAATCTTATCTCCCTAAAAACGTAGTAGAGCAAGATGAAGTTACAAC
1 ATCAAATCTTATATCCCTGAAGTTGCAGTGGAGCAAGATGAAGCTACAAC
* * * * ** **
392086 ATCAAATCCTATATCCCTGAAGTTACAG-GGATC-GGATTGAAAATTACAGT
1 ATCAAATCTTATATCCCTGAAGTTGCAGTGGAGCAAGA-TG-AAGCTACAAC
* * * * * *
392136 AACAAGTAT-TTATCTCCTTAAAGTTGCATTGGAGCAAGATGAAGCTACGAC
1 ATCAA--ATCTTATATCCCTGAAGTTGCAGTGGAGCAAGATGAAGCTACAAC
* * * * * * *
392187 ATTAAATCCTATATCCCTTAAGTTGTAATGGATC-AGATTGAAGCTACAAA
1 ATCAAATCTTATATCCCTGAAGTTGCAGTGGAGCAAGA-TGAAGCTACAAC
* * * ** * *
392237 AGCAAATCTT-TATCTCTCAGAAGTTACAGTAAATCGAA-TTGAAGCTAC-AC
1 ATCAAATCTTATATC-C-CTGAAGTTGCAGTGGAGC-AAGATGAAGCTACAAC
* * * * * *
392287 AAGT-AAATCTTATCTCCTTGAAGGTGCAATAGAGCAAGATGAAGTTA-AGAC
1 -A-TCAAATCTTATATCCCTGAAGTTGCAGTGGAGCAAGATGAAGCTACA-AC
*
392338 ATCAAATCCTATAT
1 ATCAAATCTTATAT
392352 ATAACACTCC
Statistics
Matches: 864, Mismatches: 281, Indels: 154
0.67 0.22 0.12
Matches are distributed among these distances:
46 1 0.00
47 3 0.00
48 9 0.01
49 67 0.08
50 486 0.56
51 233 0.27
52 54 0.06
53 6 0.01
54 5 0.01
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.27
Consensus pattern (50 bp):
ATCAAATCTTATATCCCTGAAGTTGCAGTGGAGCAAGATGAAGCTACAAC
Found at i:392261 original size:101 final size:100
Alignment explanation
Indices: 391080--392266 Score: 896
Period size: 100 Copynumber: 11.8 Consensus size: 100
391070 TCAATATAAT
** * * * * *
391080 ATCAAATATTATATCCCTGAAGATGCAATGGATCAAATTAGAA-CTATAATAGCAAATCTTTATC
1 ATCAAATCCTATATCCCTGAAGTTGCAGTGGATCAGATT-GAAGCTACAAAAGCAAATCTTTATC
* * * *
391144 TCCCTAAAGTTACAATAGAGCAAGATGAAGCTATC-AC
65 TCTC-AAAGTTGCAGTGGAGCAAGATGAAGCTA-CAAC
* * ** * ** *
391181 GTCAAATCCTATATCCCTGAAGATGCAGTGGATGGGATTAGAA-CAACAGTAGCATATCTTTATC
1 ATCAAATCCTATATCCCTGAAGTTGCAGTGGATCAGATT-GAAGCTACAAAAGCAAATCTTTATC
** * * *
391245 TTCTTGAAGTTACAGTGGAGCAAGAGGAAGCTACCAC
65 -TCTCAAAGTTGCAGTGGAGCAAGATGAAGCTACAAC
* * * * ** *
391282 ATCAAATCCTACATCCCTGAAGATGCAATGAATCAGATTAGAA-CTACAGTAGCAAATCTTGATC
1 ATCAAATCCTATATCCCTGAAGTTGCAGTGGATCAGATT-GAAGCTACAAAAGCAAATCTTTATC
* * *
391346 TCCCTAAAGTTGTAGTGGAGCAAGATGAAGCTACCAC
65 TCTC-AAAGTTGCAGTGGAGCAAGATGAAGCTACAAC
* * * * * * *
391383 ACCAAATCTTATATCCATGAAGTTACAGTGGATCAGATTAAAACGACAGTAAA--AAATCTTTAT
1 ATCAAATCCTATATCCCTGAAGTTGCAGTGGATCAGATTGAAGCTACA--AAAGCAAATCTTTAT
* *
391446 CTCTCAGAAGTTGCAGTAGAGCAAGATAAAGCTACAAC
64 CTCTCA-AAGTTGCAGTGGAGCAAGATGAAGCTACAAC
* * * * * ** * *
391484 ATCAAGTCTTATATCCCTGAAATTGTAGTGGATC-GAATTAAAAAATACAATAGAAAATCTTTAT
1 ATCAAATCCTATATCCCTGAAGTTGCAGTGGATCAG-ATT-GAAGCTACAAAAGCAAATCTTTAT
* * * *
391548 CTCCCCGAAGTTGTAGTGGAGCAAGATGAAGCTACGAC
64 CT-CTCAAAGTTGCAGTGGAGCAAGATGAAGCTACAAC
** * * * * * *
391586 ATCAAATCCTATATCATTGAAGTTACA-TTGAT-TGAATTAAAGTTACGAAAGCAAATCTTTATC
1 ATCAAATCCTATATCCCTGAAGTTGCAGTGGATCAG-ATTGAAGCTACAAAAGCAAATCTTTATC
* * * *
391649 TCTCTGAAGTTGCAATGGAGCAAGATGAAGCTATAAA
65 TCTC-AAAGTTGCAGTGGAGCAAGATGAAGCTACAAC
* * * * * *
391686 ATCAAATCTTATATCCCTAAAGTTGTAGTGGATCGGATTGAAGCAACAAAAACAAATC-TTATCT
1 ATCAAATCCTATATCCCTGAAGTTGCAGTGGATCAGATTGAAGCTACAAAAGCAAATCTTTATCT
* * *
391750 CTCTGAA-TATGCAATGGAGCAAGATGAAGTTA-AGAC
66 CTC-AAAGT-TGCAGTGGAGCAAGATGAAGCTACA-AC
* ** * *
391786 ATCAAATCCTATATCCTTGAAGTTATAGTGGATCGGATTAAAGCTACAAAAGCAAATC-TTATCT
1 ATCAAATCCTATATCCCTGAAGTTGCAGTGGATCAGATTGAAGCTACAAAAGCAAATCTTTATCT
* * *
391850 CCCTAAAGTTGTAGTGGAGCAAGATAAAGCTACAAC
66 CTC-AAAGTTGCAGTGGAGCAAGATGAAGCTACAAC
* * * * * * *
391886 ATCAAATCTTATATCCTTGAAGTTACAGTGGACCAGTTTGAAGCTACGAAAGTAAATC-TTATCT
1 ATCAAATCCTATATCCCTGAAGTTGCAGTGGATCAGATTGAAGCTACAAAAGCAAATCTTTATC-
* * * * *
391950 TTTTAAAGTTGCAATGGAGCAACATGAAGCTACAAT
65 TCTCAAAGTTGCAGTGGAGCAAGATGAAGCTACAAC
* * * * * * *
391986 ACCAAATCTTATAACCTTGAAGTTACAGTGGATCAGATTGAAGCTATAGAAGCAAATC-TTATCT
1 ATCAAATCCTATATCCCTGAAGTTGCAGTGGATCAGATTGAAGCTACAAAAGCAAATCTTTATCT
* *** * * *
392050 CCCTAAAAACGTAGTAGAGCAAGATGAAGTTACAAC
66 CTC-AAAGTTGCAGTGGAGCAAGATGAAGCTACAAC
* * ** * * *
392086 ATCAAATCCTATATCCCTGAAGTTACAG-GGATCGGATTGAAAATTACAGTAA-CAAGTATTTAT
1 ATCAAATCCTATATCCCTGAAGTTGCAGTGGATCAGATTG-AAGCTACA-AAAGCAAATCTTTAT
* * *
392149 CTCCTTAAAGTTGCATTGGAGCAAGATGAAGCTACGAC
64 CT-CTCAAAGTTGCAGTGGAGCAAGATGAAGCTACAAC
* * * *
392187 ATTAAATCCTATATCCCTTAAGTTGTAATGGATCAGATTGAAGCTACAAAAGCAAATCTTTATCT
1 ATCAAATCCTATATCCCTGAAGTTGCAGTGGATCAGATTGAAGCTACAAAAGCAAATCTTTATCT
*
392252 CTCAGAAGTTACAGT
66 CTCA-AAGTTGCAGT
392267 AAATCGAATT
Statistics
Matches: 874, Mismatches: 183, Indels: 58
0.78 0.16 0.05
Matches are distributed among these distances:
99 15 0.02
100 395 0.45
101 381 0.44
102 80 0.09
103 3 0.00
ACGTcount: A:0.38, C:0.18, G:0.17, T:0.27
Consensus pattern (100 bp):
ATCAAATCCTATATCCCTGAAGTTGCAGTGGATCAGATTGAAGCTACAAAAGCAAATCTTTATCT
CTCAAAGTTGCAGTGGAGCAAGATGAAGCTACAAC
Found at i:398433 original size:44 final size:43
Alignment explanation
Indices: 398385--398471 Score: 156
Period size: 44 Copynumber: 2.0 Consensus size: 43
398375 CTACCTCCAC
398385 CCACTTTGCTCCTTATTAGAGCAAAATAAAAAAAATTTGTTTG
1 CCACTTTGCTCCTTATTAGAGCAAAATAAAAAAAATTTGTTTG
*
398428 NCCACTTTGCTCCTTATTAGAGCAAAATAAAAAAATTTTGTTTG
1 -CCACTTTGCTCCTTATTAGAGCAAAATAAAAAAAATTTGTTTG
398472 ATGAAGCTTT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.36, C:0.16, G:0.11, T:0.36
Consensus pattern (43 bp):
CCACTTTGCTCCTTATTAGAGCAAAATAAAAAAAATTTGTTTG
Found at i:402556 original size:17 final size:19
Alignment explanation
Indices: 402509--402556 Score: 52
Period size: 17 Copynumber: 2.8 Consensus size: 19
402499 TAATTGTCAT
*
402509 TACATTTT-TATTG-TCTC
1 TACATTTTACATTGTTCTC
402526 TACATTTTAC-TTGTTCTC
1 TACATTTTACATTGTTCTC
402544 -ACA-TTTACATTGT
1 TACATTTTACATTGT
402557 AGTTGCATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
16 5 0.19
17 18 0.67
18 4 0.15
ACGTcount: A:0.21, C:0.19, G:0.06, T:0.54
Consensus pattern (19 bp):
TACATTTTACATTGTTCTC
Found at i:407800 original size:80 final size:79
Alignment explanation
Indices: 407667--407826 Score: 196
Period size: 80 Copynumber: 2.0 Consensus size: 79
407657 TGGATCCGAT
** * ** *
407667 TAAAGCTATGAAAGCAAATCTTATCTTCGTAAAGTTACAATAGAGCAAGATGAAGTTATGACATC
1 TAAAGCTACAAAAGCAAATCTTATCTTCGTAAAGTTACAATAGAGCAAAATGAAGTTACAACACC
407732 AAATCCTATATCCC
66 AAATCCTATATCCC
* * * *
407746 TAAAGCTACAAAAGTAAATCTTTATCTGTC-TAAAGTTATAGTGGAGCAAAATGAAGTTACAACA
1 TAAAGCTACAAAAGCAAATC-TTATCT-TCGTAAAGTTACAATAGAGCAAAATGAAGTTACAACA
*
407810 CCAAATTCTATATCCC
64 CCAAATCCTATATCCC
407826 T
1 T
407827 GAAGTTGTAG
Statistics
Matches: 68, Mismatches: 11, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
79 17 0.25
80 49 0.72
81 2 0.03
ACGTcount: A:0.41, C:0.17, G:0.13, T:0.29
Consensus pattern (79 bp):
TAAAGCTACAAAAGCAAATCTTATCTTCGTAAAGTTACAATAGAGCAAAATGAAGTTACAACACC
AAATCCTATATCCC
Found at i:407838 original size:50 final size:49
Alignment explanation
Indices: 407778--408707 Score: 423
Period size: 50 Copynumber: 18.6 Consensus size: 49
407768 TATCTGTCTA
* * * *
407778 AAGTTATAGTGGAGCAAAATGAAGTTACAACACCAAATTCTATATCCCTG
1 AAGTTGTAGTGGAGCAAGATGAAGCTACAACAGCAAA-TCTATATCCCTG
* * *
407828 AAGTTGTAGTGGATC-AGATTAAAGCTACAGA-AGCAAAT-TTTATCTCCATG
1 AAGTTGTAGTGGAGCAAGA-TGAAGCTACA-ACAGCAAATCTATATC-CC-TG
* * * * * *
407878 AAGATGCAGCGGAGCAAGATGAAGTTACAACATCAAATCCTATATCCTTG
1 AAGTTGTAGTGGAGCAAGATGAAGCTACAACAGCAAAT-CTATATCCCTG
** * * * * * * *
407928 AAGTTACAG-GGATC-GGCTTATACCTACCAA-AGAAAATCT-TATCTTCCTA
1 AAGTTGTAGTGGAGCAAGATGA-AGCTA-CAACAGCAAATCTATATC--CCTG
* * * * * *
407977 AAGCTGAAGTGGAGCAAGATGAAGCTACGACATCAAATTTTATATCCTTG
1 AAGTTGTAGTGGAGCAAGATGAAGCTACAACAGCAAA-TCTATATCCCTG
* * * *
408027 AAGTTGCAGTGGATC-AGATTGAAGCTACGAA-AGTAAATCTTTATCTCTCTG
1 AAGTTGTAGTGGAGCAAGA-TGAAGCTAC-AACAGCAAATCTATATC-C-CTG
* *
408078 AAG-TGTTAGTAGAGCAAGATGAAGCTACAACA-CTAAATCTTATATCCCTA
1 AAGTTG-TAGTGGAGCAAGATGAAGCTACAACAGC-AAATC-TATATCCCTG
* * * *
408128 AAGTTGTAGTGGATC-TGATTGAAGTTAC-ACAAGCAAATCTTATCTCCCTG
1 AAGTTGTAGTGGAGCAAGA-TGAAGCTACAAC-AGCAAATC-TATATCCCTG
** * * * * **
408178 AAGACGCAATGGAGCAAGATGAAGTTACAACATCAAATCTTATATCCCAA
1 AAGTTGTAGTGGAGCAAGATGAAGCTACAACAGCAAATC-TATATCCCTG
* * * * *
408228 AAGTTGCAG-GGATCGAA-TTAAAGCTACAA-AGCAAATCT-TATCTTCCTA
1 AAGTTGTAGTGGAGC-AAGATGAAGCTACAACAGCAAATCTATATC--CCTG
* * *
408276 AAGTTGAAGTGGAGCAAGATGAAGCTACGAC-GTCAAATCCTATATCCTTG
1 AAGTTGTAGTGGAGCAAGATGAAGCTACAACAG-CAAAT-CTATATCCCTG
* * * *
408326 AAGTTGTAGTGGATC-GGATTGAAGCTACGAA-AGTAAATCTTTATCTCTCTG
1 AAGTTGTAGTGGAGCAAGA-TGAAGCTAC-AACAGCAAATCTATATC-C-CTG
* * * *
408377 AAGTTGCAATAGAGCAAGATGAAGCTACAACATCAAATCCTATATCCCTG
1 AAGTTGTAGTGGAGCAAGATGAAGCTACAACAGCAAAT-CTATATCCCTG
* ** * * * * *
408427 AATTTGTAGTGGTTC-GGATTGAAGCTACAAAAGTAAATCTTTATCTCTCTA
1 AAGTTGTAGTGGAGCAAGA-TGAAGCTACAACAGCAAATCTATATC-C-CTG
* * *
408478 AAGTTGTAATGGAGCAAGATGAAGCAACAACACCAAATCTTATATCCCTG
1 AAGTTGTAGTGGAGCAAGATGAAGCTACAACAGCAAATC-TATATCCCTG
* * * *
408528 AAGTTGTAGTGGATC-GGATTGAAGCTACAAAAGCAAATCTTATCTCCCTG
1 AAGTTGTAGTGGAGCAAGA-TGAAGCTACAACAGCAAATC-TATATCCCTG
** * ** ** * *
408578 AAGATT-CCGTAGAGCAAGATGAAATTATGACATCAGATCCTATATCCCTG
1 AAG-TTGTAGTGGAGCAAGATGAAGCTACAACAGCAAAT-CTATATCCCTG
* * * * ** * * * *
408628 AAGTTGCAGTGGATC-AGACTTAAACTACATTAACAATTCCTAGATCCTTG
1 AAGTTGTAGTGGAGCAAGA-TGAAGCTACAACAGCAAAT-CTATATCCCTG
* * *
408678 AAGTTGCAGTGGAGCAAGATAAAGATACAA
1 AAGTTGTAGTGGAGCAAGATGAAGCTACAA
408708 TGTCAAATCC
Statistics
Matches: 653, Mismatches: 166, Indels: 122
0.69 0.18 0.13
Matches are distributed among these distances:
46 4 0.01
47 5 0.01
48 30 0.05
49 91 0.14
50 372 0.57
51 115 0.18
52 36 0.06
ACGTcount: A:0.36, C:0.18, G:0.19, T:0.27
Consensus pattern (49 bp):
AAGTTGTAGTGGAGCAAGATGAAGCTACAACAGCAAATCTATATCCCTG
Found at i:408121 original size:101 final size:99
Alignment explanation
Indices: 407748--408642 Score: 853
Period size: 101 Copynumber: 8.9 Consensus size: 99
407738 TATATCCCTA
* * * * * * *
407748 AAGCTACAAAAGTAAATCTTTATCTGTCTAAAGTTATAGTGGAGCAAAATGAAGTTACAACACCA
1 AAGCTAC-AAAGCAAATCTTTATCTCTCTGAAGTT-CAGTGGAGCAAGATGAAGCTACAACATCA
* *
407813 AAT-TCTATATCCCTGAAGTTGTAGTGGATCAGATTA
64 AATCT-TATATCCCTGAAGTTGTAGTGGATCGGATTG
* * *
407849 AAGCTACAGAAGCAAAT-TTTATCTC-CATGAAGATGCAGCGGAGCAAGATGAAGTTACAACATC
1 AAGCTACA-AAGCAAATCTTTATCTCTC-TGAAG-TTCAGTGGAGCAAGATGAAGCTACAACATC
* * ** *
407912 AAATCCTATATCCTTGAAGTTACAG-GGATCGGCTT-
63 AAATCTTATATCCCTGAAGTTGTAGTGGATCGGATTG
* * * ** *
407947 ATACCTACCAAAGAAAATC-TTATCT-TCCTAAAGCTGAAGTGGAGCAAGATGAAGCTACGACAT
1 A-AGCTA-CAAAGCAAATCTTTATCTCT-CTGAAG-TTCAGTGGAGCAAGATGAAGCTACAACAT
* * * *
408010 CAAATTTTATATCCTTGAAGTTGCAGTGGATCAGATTG
62 CAAATCTTATATCCCTGAAGTTGTAGTGGATCGGATTG
* * *
408048 AAGCTACGAAAGTAAATCTTTATCTCTCTGAAGTGTTAGTAGAGCAAGATGAAGCTACAACA-CT
1 AAGCTAC-AAAGCAAATCTTTATCTCTCTGAAGT-TCAGTGGAGCAAGATGAAGCTACAACATC-
* *
408112 AAATCTTATATCCCTAAAGTTGTAGTGGATCTGATTG
63 AAATCTTATATCCCTGAAGTTGTAGTGGATCGGATTG
* * ** * *
408149 AAGTTACACAAGCAAATC-TTATCTCCCTGAAGACGCAATGGAGCAAGATGAAGTTACAACATCA
1 AAGCTACA-AAGCAAATCTTTATCTCTCTGAAG-TTCAGTGGAGCAAGATGAAGCTACAACATCA
** * * *
408213 AATCTTATATCCCAAAAGTTGCAG-GGATCGAATTA
64 AATCTTATATCCCTGAAGTTGTAGTGGATCGGATTG
* * * *
408248 AAGCTACAAAGCAAATC-TTATCT-TCCTAAAGTTGAAGTGGAGCAAGATGAAGCTACGACGTCA
1 AAGCTACAAAGCAAATCTTTATCTCT-CTGAAGTT-CAGTGGAGCAAGATGAAGCTACAACATCA
* *
408311 AATCCTATATCCTTGAAGTTGTAGTGGATCGGATTG
64 AATCTTATATCCCTGAAGTTGTAGTGGATCGGATTG
* * *
408347 AAGCTACGAAAGTAAATCTTTATCTCTCTGAAGTTGCAATAGAGCAAGATGAAGCTACAACATCA
1 AAGCTAC-AAAGCAAATCTTTATCTCTCTGAAGTT-CAGTGGAGCAAGATGAAGCTACAACATCA
* * *
408412 AATCCTATATCCCTGAATTTGTAGTGGTTCGGATTG
64 AATCTTATATCCCTGAAGTTGTAGTGGATCGGATTG
* * * * * *
408448 AAGCTACAAAAGTAAATCTTTATCTCTCTAAAGTTGTAATGGAGCAAGATGAAGCAACAACACCA
1 AAGCTAC-AAAGCAAATCTTTATCTCTCTGAAGTT-CAGTGGAGCAAGATGAAGCTACAACATCA
408513 AATCTTATATCCCTGAAGTTGTAGTGGATCGGATTG
64 AATCTTATATCCCTGAAGTTGTAGTGGATCGGATTG
* * * ** **
408549 AAGCTACAAAAGCAAATC-TTATCTCCCTGAAGATTCCGTAGAGCAAGATGAAATTATGACATCA
1 AAGCTAC-AAAGCAAATCTTTATCTCTCTGAAG-TTCAGTGGAGCAAGATGAAGCTACAACATCA
* * *
408613 GATCCTATATCCCTGAAGTTGCAGTGGATC
64 AATCTTATATCCCTGAAGTTGTAGTGGATC
408643 AGACTTAAAC
Statistics
Matches: 663, Mismatches: 105, Indels: 53
0.81 0.13 0.06
Matches are distributed among these distances:
98 64 0.10
99 110 0.17
100 208 0.31
101 279 0.42
102 2 0.00
ACGTcount: A:0.36, C:0.18, G:0.19, T:0.27
Consensus pattern (99 bp):
AAGCTACAAAGCAAATCTTTATCTCTCTGAAGTTCAGTGGAGCAAGATGAAGCTACAACATCAAA
TCTTATATCCCTGAAGTTGTAGTGGATCGGATTG
Found at i:408534 original size:400 final size:400
Alignment explanation
Indices: 407787--408656 Score: 1121
Period size: 400 Copynumber: 2.2 Consensus size: 400
407777 AAAGTTATAG
* * *
407787 TGGAGCAAAATGAAGTTACAACACCAAAT-TCTATATCCCTGAAGTTGTAGTGGATC-AGATTAA
1 TGGAGCAAGATGAAGTTACAACATCAAATCT-TATATCCCTGAAGTTGCAGTGGATCGA-ATTAA
* * * *
407850 AGCTACAGAAGCAAATTTTATCTCCATGAAGATGCAGCGGAGCAAGATGAAGTTACAACATCAAA
64 AGCTACAGAAGCAAATCTTATCTCCATAAAGATGAAGCGGAGCAAGATGAAGCTACAACATCAAA
*
407915 TCCTATATCCTTGAAGTTACAGGGATCGGCTTATACCTACCAAAGAAAATCTTATCTTCCTAAAG
129 TCCTATATCCTTGAAGTTACAGGGATCGGATTATACCTACCAAAGAAAATCTTATCTTCCTAAAG
* * ** *
407980 CTGAAGTGGAGCAAGATGAAGCTACGACATCAAATTTTATATCCTTGAAGTTGCAGTGGATCAGA
194 CTGAAGTAGAGCAAGATGAAGCTACAACATCAAATCCTATATCCCTGAAGTTGCAGTGGATCAGA
* * * *
408045 TTGAAGCTACGAAAGTAAATCTTTATCTCTCTGAAGTGTTAGTAGAGCAAGATGAAGCTACAACA
259 TTGAAGCTACAAAAGTAAATCTTTATCTCTCTAAAGTGTTAATAGAGCAAGATGAAGCAACAACA
* * * *
408110 CTAAATCTTATATCCCTAAAGTTGTAGTGGATCTGATTGAAGTTACACAAGCAAATCTTATCTCC
324 CCAAATCTTATATCCCTAAAGTTGTAGTGGATCGGATTGAAGCTACAAAAGCAAATCTTATCTCC
408175 CTGAAGACGCAA
389 CTGAAGACGCAA
**
408187 TGGAGCAAGATGAAGTTACAACATCAAATCTTATATCCCAAAAGTTGCAG-GGATCGAATTAAAG
1 TGGAGCAAGATGAAGTTACAACATCAAATCTTATATCCCTGAAGTTGCAGTGGATCGAATTAAAG
* * * *
408251 CTACA-AAGCAAATCTTATCTTCC-TAAAGTTGAAGTGGAGCAAGATGAAGCTACGACGTCAAAT
66 CTACAGAAGCAAATCTTATC-TCCATAAAGATGAAGCGGAGCAAGATGAAGCTACAACATCAAAT
** * * * *
408314 CCTATATCCTTGAAGTTGTAGTGGATCGGATTGA-AGCTACGAAAGTAAATCTTTATC-TCTCTG
130 CCTATATCCTTGAAGTTACAG-GGATCGGATT-ATACCTACCAAAGAAAATC-TTATCTTC-CTA
* * * *
408377 AAGTTGCAA-TAGAGCAAGATGAAGCTACAACATCAAATCCTATATCCCTGAATTTGTAGTGGTT
191 AAGCTG-AAGTAGAGCAAGATGAAGCTACAACATCAAATCCTATATCCCTGAAGTTGCAGTGGAT
* *
408441 CGGATTGAAGCTACAAAAGTAAATCTTTATCTCTCTAAAGT-TGTAATGGAGCAAGATGAAGCAA
255 CAGATTGAAGCTACAAAAGTAAATCTTTATCTCTCTAAAGTGT-TAATAGAGCAAGATGAAGCAA
*
408505 CAACACCAAATCTTATATCCCTGAAGTTGTAGTGGATCGGATTGAAGCTACAAAAGCAAATCTTA
319 CAACACCAAATCTTATATCCCTAAAGTTGTAGTGGATCGGATTGAAGCTACAAAAGCAAATCTTA
** **
408570 TCTCCCTGAAGATTCCG
384 TCTCCCTGAAGACGCAA
* * ** * * *
408587 TAGAGCAAGATGAAATTATGACATCAGATCCTATATCCCTGAAGTTGCAGTGGATCAGACTTAAA
1 TGGAGCAAGATGAAGTTACAACATCAAATCTTATATCCCTGAAGTTGCAGTGGATC-GAATTAAA
408652 -CTACA
65 GCTACA
408657 TTAACAATTC
Statistics
Matches: 406, Mismatches: 53, Indels: 21
0.85 0.11 0.04
Matches are distributed among these distances:
398 65 0.16
399 46 0.11
400 275 0.68
401 13 0.03
402 7 0.02
ACGTcount: A:0.36, C:0.18, G:0.19, T:0.27
Consensus pattern (400 bp):
TGGAGCAAGATGAAGTTACAACATCAAATCTTATATCCCTGAAGTTGCAGTGGATCGAATTAAAG
CTACAGAAGCAAATCTTATCTCCATAAAGATGAAGCGGAGCAAGATGAAGCTACAACATCAAATC
CTATATCCTTGAAGTTACAGGGATCGGATTATACCTACCAAAGAAAATCTTATCTTCCTAAAGCT
GAAGTAGAGCAAGATGAAGCTACAACATCAAATCCTATATCCCTGAAGTTGCAGTGGATCAGATT
GAAGCTACAAAAGTAAATCTTTATCTCTCTAAAGTGTTAATAGAGCAAGATGAAGCAACAACACC
AAATCTTATATCCCTAAAGTTGTAGTGGATCGGATTGAAGCTACAAAAGCAAATCTTATCTCCCT
GAAGACGCAA
Found at i:409101 original size:14 final size:15
Alignment explanation
Indices: 409073--409104 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
409063 CTAAATATTT
409073 AAAAGTCCAATTTAC
1 AAAAGTCCAATTTAC
409088 AAAAGTCC-ATTTAC
1 AAAAGTCCAATTTAC
409102 AAA
1 AAA
409105 GTAGAAGGCC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.50, C:0.19, G:0.06, T:0.25
Consensus pattern (15 bp):
AAAAGTCCAATTTAC
Found at i:409105 original size:13 final size:14
Alignment explanation
Indices: 409069--409106 Score: 53
Period size: 13 Copynumber: 2.8 Consensus size: 14
409059 TGGCCTAAAT
409069 ATTTA-AAAGTCCA
1 ATTTACAAAGTCCA
409082 ATTTACAAAAGTCC-
1 ATTTAC-AAAGTCCA
409096 ATTTACAAAGT
1 ATTTACAAAGT
409107 AGAAGGCCCA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 10 0.43
14 6 0.26
15 7 0.30
ACGTcount: A:0.45, C:0.16, G:0.08, T:0.32
Consensus pattern (14 bp):
ATTTACAAAGTCCA
Found at i:411785 original size:29 final size:28
Alignment explanation
Indices: 411752--411819 Score: 91
Period size: 29 Copynumber: 2.4 Consensus size: 28
411742 AATTTAATCC
**
411752 TTTTTTTAATTTAGCTTTTTATTTTCTA
1 TTTTTTTAATTTAGCTTTAAATTTTCTA
* *
411780 TATTTTTCAATTTAGCTTTAAATTTTTTA
1 T-TTTTTTAATTTAGCTTTAAATTTTCTA
411809 TTTTTTTAATT
1 TTTTTTTAATT
411820 CAATCCTTTA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
28 10 0.29
29 24 0.71
ACGTcount: A:0.22, C:0.06, G:0.03, T:0.69
Consensus pattern (28 bp):
TTTTTTTAATTTAGCTTTAAATTTTCTA
Found at i:412010 original size:17 final size:17
Alignment explanation
Indices: 411990--412031 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
411980 TTTTACATTT
411990 ATTGTTATTTTTATTAC
1 ATTGTTATTTTTATTAC
* * *
412007 ATTGTCATATTTATTTC
1 ATTGTTATTTTTATTAC
412024 ATT-TTATT
1 ATTGTTATT
412032 ATGTTTCATC
Statistics
Matches: 20, Mismatches: 5, Indels: 1
0.77 0.19 0.04
Matches are distributed among these distances:
16 3 0.15
17 17 0.85
ACGTcount: A:0.24, C:0.07, G:0.05, T:0.64
Consensus pattern (17 bp):
ATTGTTATTTTTATTAC
Found at i:415184 original size:69 final size:70
Alignment explanation
Indices: 415108--415241 Score: 207
Period size: 70 Copynumber: 1.9 Consensus size: 70
415098 ATTACATCAT
* * * *
415108 CCTACAATTACAT-TAAAAAAGTTATATTACTCCTCCACCACACCCAATTACACATACGAAAAGT
1 CCTACAATTACATAAAAAAAAGTGATATTACTCCACCACCACACCCAATTACACATACAAAAAGT
415172 GACAA
66 GACAA
* *
415177 CCTACAATTACATAAAAAAAAGTGATATTAGTCCACCACCACACCCATTTACACATACAAAAAGT
1 CCTACAATTACATAAAAAAAAGTGATATTACTCCACCACCACACCCAATTACACATACAAAAAGT
415242 TACATGAGTT
Statistics
Matches: 58, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
69 13 0.22
70 45 0.78
ACGTcount: A:0.45, C:0.27, G:0.06, T:0.22
Consensus pattern (70 bp):
CCTACAATTACATAAAAAAAAGTGATATTACTCCACCACCACACCCAATTACACATACAAAAAGT
GACAA
Found at i:425219 original size:18 final size:20
Alignment explanation
Indices: 425193--425236 Score: 58
Period size: 19 Copynumber: 2.3 Consensus size: 20
425183 TTTTTCATTT
425193 TTTTCTTCTC-C-TCTTTCTC
1 TTTTCTTCTCACAT-TTTCTC
425212 TTTT-TTCTCACATTTTCTC
1 TTTTCTTCTCACATTTTCTC
425231 TTTTCT
1 TTTTCT
425237 ACCTCATTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
18 5 0.23
19 15 0.68
20 2 0.09
ACGTcount: A:0.05, C:0.30, G:0.00, T:0.66
Consensus pattern (20 bp):
TTTTCTTCTCACATTTTCTC
Found at i:426102 original size:12 final size:12
Alignment explanation
Indices: 426077--426110 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
426067 TGCATATTTA
426077 TATGAAA-TTT-
1 TATGAAATTTTG
426087 TATGAAATTTTG
1 TATGAAATTTTG
426099 TATGAAATTTTG
1 TATGAAATTTTG
426111 CATGTTAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 7 0.32
11 3 0.14
12 12 0.55
ACGTcount: A:0.35, C:0.00, G:0.15, T:0.50
Consensus pattern (12 bp):
TATGAAATTTTG
Found at i:427975 original size:2 final size:2
Alignment explanation
Indices: 427968--427996 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
427958 AATGATTGTG
427968 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
427997 CTACTCAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:430264 original size:52 final size:52
Alignment explanation
Indices: 430136--430265 Score: 152
Period size: 52 Copynumber: 2.5 Consensus size: 52
430126 AAATTAATGA
* * * * * *
430136 ACTGGCTCGTAAAAGCGATAAACTGAACTGGCTCGTAAGATCGATATATTGT
1 ACTGGCTCGTAAGAGCGATATACTGAACTAGCTCGGAAGAGCGATATATTAT
* ** * *
430188 ACTGGCTCGAAAGAGAAATATACTGTACTAGCTTGGAAGAGCGATATATTAT
1 ACTGGCTCGTAAGAGCGATATACTGAACTAGCTCGGAAGAGCGATATATTAT
*
430240 ACTGGCTCGTAAGAGCGATTTACTGA
1 ACTGGCTCGTAAGAGCGATATACTGA
430266 CTGGGCTAGG
Statistics
Matches: 62, Mismatches: 16, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
52 62 1.00
ACGTcount: A:0.33, C:0.16, G:0.24, T:0.27
Consensus pattern (52 bp):
ACTGGCTCGTAAGAGCGATATACTGAACTAGCTCGGAAGAGCGATATATTAT
Found at i:430272 original size:26 final size:26
Alignment explanation
Indices: 430136--430269 Score: 135
Period size: 26 Copynumber: 5.2 Consensus size: 26
430126 AAATTAATGA
* * *
430136 ACTGGCTCGTAAAAGCGATAAACTGA
1 ACTGGCTCGTAAGAGCGATATACTGT
* *
430162 ACTGGCTCGTAAGATCGATATATTGT
1 ACTGGCTCGTAAGAGCGATATACTGT
* **
430188 ACTGGCTCGAAAGAGAAATATACTGT
1 ACTGGCTCGTAAGAGCGATATACTGT
* * * * *
430214 ACTAGCTTGGAAGAGCGATATATTAT
1 ACTGGCTCGTAAGAGCGATATACTGT
*
430240 ACTGGCTCGTAAGAGCGATTTACTG-
1 ACTGGCTCGTAAGAGCGATATACTGT
430265 ACTGG
1 ACTGG
430270 GCTAGGATAA
Statistics
Matches: 85, Mismatches: 23, Indels: 1
0.78 0.21 0.01
Matches are distributed among these distances:
25 5 0.06
26 80 0.94
ACGTcount: A:0.32, C:0.16, G:0.25, T:0.27
Consensus pattern (26 bp):
ACTGGCTCGTAAGAGCGATATACTGT
Found at i:430373 original size:26 final size:26
Alignment explanation
Indices: 430316--430374 Score: 73
Period size: 26 Copynumber: 2.3 Consensus size: 26
430306 TATTGTATTG
* * *
430316 GCTCGGAGGAGTGATATACTGAACTG
1 GCTCGTAGGAGCGATATACTGAACTA
* *
430342 GATCGTAGGAGCGATATACTGAGCTA
1 GCTCGTAGGAGCGATATACTGAACTA
430368 GCTCGTA
1 GCTCGTA
430375 AGAAAGATAT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.27, C:0.17, G:0.32, T:0.24
Consensus pattern (26 bp):
GCTCGTAGGAGCGATATACTGAACTA
Found at i:432679 original size:58 final size:58
Alignment explanation
Indices: 432561--432680 Score: 154
Period size: 58 Copynumber: 2.1 Consensus size: 58
432551 ACGCATCAAC
* * *
432561 AAACTAAACCCAAATAATTTTAAACCGAAATATAATTTCATTCTTCAAAAACACTCAT
1 AAACTAAACCAAAATAATTTTAAACCGAAATATAATTTCATTCCTCAAAAACACTAAT
* * *
432619 AAACTAAACCAAAATATTTTTAAACTC-AAATATAATTTTATTCCT-AAATATCACTAAT
1 AAACTAAACCAAAATAATTTTAAAC-CGAAATATAATTTCATTCCTCAAA-AACACTAAT
432677 AAAC
1 AAAC
432681 AACTCTTTTT
Statistics
Matches: 54, Mismatches: 6, Indels: 4
0.84 0.09 0.06
Matches are distributed among these distances:
57 3 0.06
58 50 0.93
59 1 0.02
ACGTcount: A:0.49, C:0.18, G:0.01, T:0.32
Consensus pattern (58 bp):
AAACTAAACCAAAATAATTTTAAACCGAAATATAATTTCATTCCTCAAAAACACTAAT
Found at i:440631 original size:150 final size:146
Alignment explanation
Indices: 440375--440651 Score: 335
Period size: 150 Copynumber: 1.9 Consensus size: 146
440365 TTTGTCAGTT
*
440375 AAAAAATACAATTTTTTGTGTTGGCCATCAAATGGCCGACACCCCTTTTTCTCGAAAAAAAAATT
1 AAAAAATACAATTTTTGGTGTTGGCCATCAAATGGCCGACACCCCTTTTTCTCGAAAAAAAAATT
*** * * *
440440 ACCTTTTGCAATTGTCGACACCCCCTTTTTCTCGAGAAAAAATTTTCAAAATTTTTTGGTGTTGG
66 AAAATTTGCAATGGCCGACACCCCCTTTTTCTCGAGAAAAAA-ATT--AAATTTTTTGGTGTTGG
440505 GGCACCCCCTTTTCTCGAA
128 GGCACCCCCTTTTCTCGAA
*** **
440524 AAAAAATTAC-ATTTTTGGGTGTTGGCCATTGCATGGCCGACACCCCTTTTTCTCGAAAAAAATT
1 AAAAAA-TACAATTTTT-GGTGTTGGCCATCAAATGGCCGACACCCCTTTTTCTCGAAAAAAAAA
* * *
440588 TTCAAAATTTGC-ATGGCCGACACCCCCTTTTTATTTG-GTAAAAAATTAAATTTTTTGGTGTTG
64 TT-AAAATTTGCAATGGCCGACACCCCCTTTTT-CTCGAGAAAAAAATTAAATTTTTTGGTGTTG
440651 G
127 G
440652 TCATGTAATG
Statistics
Matches: 109, Mismatches: 15, Indels: 10
0.81 0.11 0.07
Matches are distributed among these distances:
147 17 0.16
149 14 0.13
150 70 0.64
151 8 0.07
ACGTcount: A:0.29, C:0.21, G:0.16, T:0.35
Consensus pattern (146 bp):
AAAAAATACAATTTTTGGTGTTGGCCATCAAATGGCCGACACCCCTTTTTCTCGAAAAAAAAATT
AAAATTTGCAATGGCCGACACCCCCTTTTTCTCGAGAAAAAAATTAAATTTTTTGGTGTTGGGGC
ACCCCCTTTTCTCGAA
Done.