Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008738.1 Hibiscus syriacus cultivar Beakdansim tig00111813_pilon, 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: 90215
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Found at i:359 original size:55 final size:55
Alignment explanation
Indices: 133--755 Score: 810
Period size: 55 Copynumber: 11.8 Consensus size: 55
123 TTATGTGCAA
133 AAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCA-TATATGT-T
1 AAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATGTGT
* * * *
186 -AACTTGAGAAATTCATATTAAGT-GATGAATTTCTGTATGGGCACTATA-ATGT
1 AAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATGTGT
* * * *
238 AAACTTAAGAAATTCATAATAA---GA--ATTTTTCGTATGGACACTATA--TGT
1 AAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATGTGT
* *
286 AAACTTAAGAAATCCATACTAAGTGGATGAATTTCCGTATGGACACTATATGTGT
1 AAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATGTGT
* *
341 AAACTTAAGAAATTCATACTAAGTGGATGAATTTTCGTATGGGTACTATATGTGT
1 AAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATGTGT
396 AAACTTAAGAAATTCATACTAAG-GGATGAATTTCCGTA-GGGCACTATATGTGT
1 AAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATGTGT
* *
449 AAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATTGACACTATATGTGT
1 AAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATGTGT
* *
504 AAACTTAACAAATTCATACTCAGTGGATGAATTTCCGTATGGGCAC--TATGTGT
1 AAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATGTGT
* *
557 TAACTTAAG-AATTC-TACTAAGTGGATGAATTTCCGTATGGGCACTGTATGTGT
1 AAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATGTGT
** **
610 AAACTTAAG-AATTCATACTAA--GGATGAATTTATGTA--GGCGTTATATGTGT
1 AAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATGTGT
** *
660 AAACTTAAG-AATTCATACTAAGTGGATGAATTTATGTATGGGCACTATA-GTGC
1 AAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATGTGT
* * * *
713 AAGCTTAAGAAATCCATACTAAGTGTATGAATTTCTGTATGGG
1 AAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGG
756 AGATATATGT
Statistics
Matches: 508, Mismatches: 42, Indels: 39
0.86 0.07 0.07
Matches are distributed among these distances:
48 23 0.05
49 17 0.03
50 32 0.06
51 53 0.10
52 59 0.12
53 120 0.24
54 72 0.14
55 132 0.26
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.34
Consensus pattern (55 bp):
AAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATGTGT
Found at i:441 original size:108 final size:110
Alignment explanation
Indices: 133--755 Score: 810
Period size: 108 Copynumber: 5.9 Consensus size: 110
123 TTATGTGCAA
*
133 AAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCA-TATATGT-T-AACTTGAGA
1 AAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATGTGTAAACTTAAGA
* * *
195 AATTCATATTAAGT-GATGAATTTCTGTATGGGCACTATA-ATGT
66 AATTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATGTGT
* * * *
238 AAACTTAAGAAATTCATAATAA---GA--ATTTTTCGTATGGACACTATA--TGTAAACTTAAGA
1 AAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATGTGTAAACTTAAGA
* *
296 AATCCATACTAAGTGGATGAATTTCCGTATGGACACTATATGTGT
66 AATTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATGTGT
* *
341 AAACTTAAGAAATTCATACTAAGTGGATGAATTTTCGTATGGGTACTATATGTGTAAACTTAAGA
1 AAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATGTGTAAACTTAAGA
406 AATTCATACTAAG-GGATGAATTTCCGTA-GGGCACTATATGTGT
66 AATTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATGTGT
* * *
449 AAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATTGACACTATATGTGTAAACTTAACA
1 AAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATGTGTAAACTTAAGA
*
514 AATTCATACTCAGTGGATGAATTTCCGTATGGGCAC--TATGTGT
66 AATTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATGTGT
* *
557 TAACTTAAG-AATTC-TACTAAGTGGATGAATTTCCGTATGGGCACTGTATGTGTAAACTTAAG-
1 AAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATGTGTAAACTTAAGA
** **
619 AATTCATACTAA--GGATGAATTTATGTA--GGCGTTATATGTGT
66 AATTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATGTGT
** * *
660 AAACTTAAG-AATTCATACTAAGTGGATGAATTTATGTATGGGCACTATA-GTGCAAGCTTAAGA
1 AAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATGTGTAAACTTAAGA
* * *
723 AATCCATACTAAGTGTATGAATTTCTGTATGGG
66 AATTCATACTAAGTGGATGAATTTCCGTATGGG
756 AGATATATGT
Statistics
Matches: 455, Mismatches: 41, Indels: 41
0.85 0.08 0.08
Matches are distributed among these distances:
99 1 0.00
100 14 0.03
101 27 0.06
102 25 0.05
103 68 0.15
104 42 0.09
105 32 0.07
106 59 0.13
107 5 0.01
108 121 0.27
109 30 0.07
110 31 0.07
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.34
Consensus pattern (110 bp):
AAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATGTGTAAACTTAAGA
AATTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATGTGT
Found at i:1038 original size:67 final size:67
Alignment explanation
Indices: 960--1224 Score: 348
Period size: 67 Copynumber: 4.0 Consensus size: 67
950 AAGATTAATA
* *
960 GCCTAACTGTGCA-TTGACATAAATGTGTCAATTATGCCAGTTAGATAAAAGGCTAAGTGCCTTT
1 GCCTAACTGTGCATTTGACAGAAAT-TGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTT
1024 GAG
65 GAG
1027 GCCTAACTGTGCATTTGACAGAAA---TCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTG
1 GCCTAACTGTGCATTTGACAGAAATTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTG
1089 AG
66 AG
* * *
1091 GCCTAACTGTGCAATTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAATATAG--T
1 GCCTAACTGTGCATTTGACAGAAA-TTGTCAATTATGCCAGTTAGATGAAAGGCTAA-GT-GCCT
1154 TT-AG
63 TTGAG
* * **
1158 GCCTAACTGTGCATTTGACAGAAGATTTTCAATCATGCCAGTTAGATGAAAGATTAA-TGCCTTT
1 GCCTAACTGTGCATTTGACAGAA-ATTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTT
1222 GAG
65 GAG
1225 AAAAAGACTA
Statistics
Matches: 177, Mismatches: 10, Indels: 22
0.85 0.05 0.11
Matches are distributed among these distances:
64 63 0.36
65 1 0.01
66 3 0.02
67 66 0.37
68 42 0.24
69 1 0.01
70 1 0.01
ACGTcount: A:0.32, C:0.16, G:0.23, T:0.29
Consensus pattern (67 bp):
GCCTAACTGTGCATTTGACAGAAATTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTG
AG
Found at i:1129 original size:132 final size:131
Alignment explanation
Indices: 960--1224 Score: 376
Period size: 132 Copynumber: 2.0 Consensus size: 131
950 AAGATTAATA
* * *
960 GCCTAACTGTGCATTGACATAAATGTGTCAATTATGCCAGTTAGATAAAAGGCTAA-GT-GCCTT
1 GCCTAACTGTGCATTGACAGAAAGGTGTCAATTATGCCAGTTAGATAAAAGGCTAATATAG--TT
* *
1023 TGAGGCCTAACTGTGCATTTGACAGAA-A-TCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
64 T-AGGCCTAACTGTGCATTTGACAGAAGATTCAATCATGCCAGTTAGATGAAAGACTAA-TGCCT
1086 TTGAG
127 TTGAG
*
1091 GCCTAACTGTGCAATTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAATATAGTTT
1 GCCTAACTGTGC-ATTGACAGAAAGGTGTCAATTATGCCAGTTAGATAAAAGGCTAATATAGTTT
*
1156 AGGCCTAACTGTGCATTTGACAGAAGATTTTCAATCATGCCAGTTAGATGAAAGATTAATGCCTT
65 AGGCCTAACTGTGCATTTGACAGAAGA--TTCAATCATGCCAGTTAGATGAAAGACTAATGCCTT
1221 TGAG
128 TGAG
1225 AAAAAGACTA
Statistics
Matches: 120, Mismatches: 7, Indels: 11
0.87 0.05 0.08
Matches are distributed among these distances:
131 37 0.31
132 45 0.38
133 1 0.01
134 11 0.09
135 26 0.22
ACGTcount: A:0.32, C:0.16, G:0.23, T:0.29
Consensus pattern (131 bp):
GCCTAACTGTGCATTGACAGAAAGGTGTCAATTATGCCAGTTAGATAAAAGGCTAATATAGTTTA
GGCCTAACTGTGCATTTGACAGAAGATTCAATCATGCCAGTTAGATGAAAGACTAATGCCTTTGA
G
Found at i:1313 original size:45 final size:44
Alignment explanation
Indices: 1255--1379 Score: 162
Period size: 44 Copynumber: 2.8 Consensus size: 44
1245 TGTATAATGT
* *
1255 CGTATAAAAGGCATGAAAGGATGTCATAAATGAAATGTAT-ATAG
1 CGTA-AAAAGGCATGAAAGGATGCCATAAATGAAATGCATAATAG
* * *
1299 TGTAAAAAGGGGCATGAAAGGATGCCCTAAATAAAATGCATAATAG
1 CGTAAAAA--GGCATGAAAGGATGCCATAAATGAAATGCATAATAG
*
1345 CGTATAAAGGCATGAAAGGATGCCATAAATGAAAT
1 CGTAAAAAGGCATGAAAGGATGCCATAAATGAAAT
1380 ACAGGGGTGC
Statistics
Matches: 69, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
43 4 0.06
44 28 0.41
45 27 0.39
46 10 0.14
ACGTcount: A:0.46, C:0.10, G:0.23, T:0.22
Consensus pattern (44 bp):
CGTAAAAAGGCATGAAAGGATGCCATAAATGAAATGCATAATAG
Found at i:2048 original size:83 final size:84
Alignment explanation
Indices: 1939--2105 Score: 311
Period size: 83 Copynumber: 2.0 Consensus size: 84
1929 AAATCTGGAA
1939 ACAAAATTTTACGGGTTTTTAGAAGAAATATTTTAAAAGTGATGTGACATATGTATTTCGTATAC
1 ACAAAATTTTACGGGTTTTTAGAAGAAATATTTTAAAAGTGATGTGACATATGTATTTCGTATAC
2004 -GAAGGGTACACGGAATATG
66 AGAAGGGTACAC-GAATATG
2023 ACAAAATTTTAC-GGTTTTTAGAAGAAATATTTTAAAAGTGATGTGACATATGTATTTCGTATAC
1 ACAAAATTTTACGGGTTTTTAGAAGAAATATTTTAAAAGTGATGTGACATATGTATTTCGTATAC
2087 AGAAGGGTACACGAATATG
66 AGAAGGGTACACGAATATG
2106 GTTGTTACAA
Statistics
Matches: 82, Mismatches: 0, Indels: 3
0.96 0.00 0.04
Matches are distributed among these distances:
83 59 0.72
84 23 0.28
ACGTcount: A:0.38, C:0.08, G:0.20, T:0.34
Consensus pattern (84 bp):
ACAAAATTTTACGGGTTTTTAGAAGAAATATTTTAAAAGTGATGTGACATATGTATTTCGTATAC
AGAAGGGTACACGAATATG
Found at i:2463 original size:7 final size:7
Alignment explanation
Indices: 2451--2494 Score: 54
Period size: 7 Copynumber: 6.4 Consensus size: 7
2441 GTCATTACAA
2451 TAAACCC
1 TAAACCC
2458 TAAACCC
1 TAAACCC
*
2465 TAAA-CT
1 TAAACCC
* *
2471 TAAATCA
1 TAAACCC
2478 TAAACCC
1 TAAACCC
2485 TAAACCC
1 TAAACCC
2492 TAA
1 TAA
2495 TTGTACTTAC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
6 5 0.16
7 27 0.84
ACGTcount: A:0.48, C:0.32, G:0.00, T:0.20
Consensus pattern (7 bp):
TAAACCC
Found at i:7075 original size:16 final size:16
Alignment explanation
Indices: 7054--7092 Score: 78
Period size: 16 Copynumber: 2.4 Consensus size: 16
7044 CATTGATTTA
7054 GCACCAATAATTCACT
1 GCACCAATAATTCACT
7070 GCACCAATAATTCACT
1 GCACCAATAATTCACT
7086 GCACCAA
1 GCACCAA
7093 CAGTGCTTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.38, C:0.33, G:0.08, T:0.21
Consensus pattern (16 bp):
GCACCAATAATTCACT
Found at i:13921 original size:24 final size:23
Alignment explanation
Indices: 13885--13930 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
13875 ATAATCATTT
*
13885 AATAATTTATTATATATTTTTTGA
1 AATAATTTATTAT-TACTTTTTGA
*
13909 AATAATTTTTTATTACTTTTTG
1 AATAATTTATTATTACTTTTTG
13931 TAGTTATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 8 0.40
24 12 0.60
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.61
Consensus pattern (23 bp):
AATAATTTATTATTACTTTTTGA
Found at i:14888 original size:21 final size:19
Alignment explanation
Indices: 14831--14885 Score: 94
Period size: 19 Copynumber: 2.9 Consensus size: 19
14821 TATTGAGTTC
14831 GTATATAAATAATTTTTAA
1 GTATATAAATAATTTTTAA
14850 GTATATAAATAATTTTTAA
1 GTATATAAATAATTTTTAA
14869 GTATAT-AATGAATTTTT
1 GTATATAAAT-AATTTTT
14886 TTACACTGAA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
18 3 0.09
19 32 0.91
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.49
Consensus pattern (19 bp):
GTATATAAATAATTTTTAA
Found at i:18201 original size:26 final size:25
Alignment explanation
Indices: 18171--18235 Score: 76
Period size: 26 Copynumber: 2.5 Consensus size: 25
18161 ATGCAAAAAG
18171 TAATAAAAAATTAATACAATAAAATA
1 TAATAAAAAATTAATA-AATAAAATA
** * *
18197 TAATAAACTATTAAATAATTATAATA
1 TAATAAAAAATT-AATAAATAAAATA
18223 TAATAAAAAATTA
1 TAATAAAAAATTA
18236 GCTTCTAAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
25 1 0.03
26 27 0.84
27 4 0.12
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (25 bp):
TAATAAAAAATTAATAAATAAAATA
Found at i:19940 original size:30 final size:30
Alignment explanation
Indices: 19904--19968 Score: 94
Period size: 30 Copynumber: 2.2 Consensus size: 30
19894 CTTCTATTAG
*
19904 TTCATAAAATAATAGAGCATCCCGTATCAA
1 TTCATAAAATAACAGAGCATCCCGTATCAA
* * *
19934 TTCATAAAATAACGGAGCATCTCGTATCAG
1 TTCATAAAATAACAGAGCATCCCGTATCAA
19964 TTCAT
1 TTCAT
19969 GATACATATG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.38, C:0.20, G:0.12, T:0.29
Consensus pattern (30 bp):
TTCATAAAATAACAGAGCATCCCGTATCAA
Found at i:20885 original size:31 final size:31
Alignment explanation
Indices: 20847--20908 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
20837 CCTCGACAAC
*
20847 TGTCCATAGGTCCCG-AAGAACCTAGGTAAAT
1 TGTCCATAGGTCCCGAAAG-ACATAGGTAAAT
* *
20878 TGTCCATATGTCTCGAAAGACATAGGTAAAT
1 TGTCCATAGGTCCCGAAAGACATAGGTAAAT
20909 CCTCAACTCT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
31 24 0.89
32 3 0.11
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.26
Consensus pattern (31 bp):
TGTCCATAGGTCCCGAAAGACATAGGTAAAT
Found at i:21876 original size:20 final size:20
Alignment explanation
Indices: 21851--21888 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
21841 TTCCCCTTGA
21851 AGTGCATCGATGCATTCTAT
1 AGTGCATCGATGCATTCTAT
*
21871 AGTGCATTGATGCATTCT
1 AGTGCATCGATGCATTCT
21889 TTTAACATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.24, C:0.18, G:0.21, T:0.37
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTAT
Found at i:27614 original size:124 final size:124
Alignment explanation
Indices: 27481--27727 Score: 451
Period size: 124 Copynumber: 2.0 Consensus size: 124
27471 AACAATAGCA
*
27481 TTTTTTTTGTTAAAATGGTGAAAATGTCATTACATTCAAATTCTTAGGTATTAGACAATTCCTAC
1 TTTTTTTTGTTAAAATGGTGAAAATGTCATTACATTCAAATTCTTAGGTATTAGACAATTACTAC
*
27546 CACTTCGGACAAGAATACCCTTA-GGGGTGTTTGGTTCAAAGATTGTGGGATTCCCATT
66 CACTTCAGACAAGAATACCCTTAGGGGGTGTTTGGTTCAAAGATTGTGGGATTCCCATT
*
27604 TTTTTGTTTGTTAAAATGGTGAAAATGTCATTACATTCAAATTCTTAGGTATTAGACAATTACTG
1 TTTTT-TTTGTTAAAATGGTGAAAATGTCATTACATTCAAATTCTTAGGTATTAGACAATTACTA
27669 CCACTTCAGACAAGAATACCCTTAGGGGGTGTTTGGTTCAAAGATTGTGGGATTCCCAT
65 CCACTTCAGACAAGAATACCCTTAGGGGGTGTTTGGTTCAAAGATTGTGGGATTCCCAT
27728 AGGATGGGAA
Statistics
Matches: 119, Mismatches: 3, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
123 5 0.04
124 80 0.67
125 34 0.29
ACGTcount: A:0.29, C:0.15, G:0.19, T:0.37
Consensus pattern (124 bp):
TTTTTTTTGTTAAAATGGTGAAAATGTCATTACATTCAAATTCTTAGGTATTAGACAATTACTAC
CACTTCAGACAAGAATACCCTTAGGGGGTGTTTGGTTCAAAGATTGTGGGATTCCCATT
Found at i:28665 original size:5 final size:5
Alignment explanation
Indices: 28655--28680 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
28645 ATATTATTTT
28655 TTATA TTATA TTATA TTATA TTATA T
1 TTATA TTATA TTATA TTATA TTATA T
28681 ATAAATAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (5 bp):
TTATA
Found at i:48129 original size:36 final size:36
Alignment explanation
Indices: 48088--48163 Score: 134
Period size: 36 Copynumber: 2.1 Consensus size: 36
48078 ATTTTCGGGA
* *
48088 TTTTGCTATTTTTGGCAAAATTCGAATAAATACGAT
1 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACAAT
48124 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACAAT
1 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACAAT
48160 TTTT
1 TTTT
48164 TTTAGCTATA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.33, C:0.11, G:0.13, T:0.43
Consensus pattern (36 bp):
TTTTGCTATTTTTGGCAAAATTCGAATAAAGACAAT
Found at i:50022 original size:15 final size:16
Alignment explanation
Indices: 49992--50024 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
49982 TTGGTTGTCG
49992 ATTGTCGATATTTTTT
1 ATTGTCGATATTTTTT
*
50008 ATTGTC-ATTTTTTTT
1 ATTGTCGATATTTTTT
50023 AT
1 AT
50025 ATTATAGCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.18, C:0.06, G:0.09, T:0.67
Consensus pattern (16 bp):
ATTGTCGATATTTTTT
Found at i:51518 original size:31 final size:31
Alignment explanation
Indices: 51482--51540 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
51472 ATAAAAGTGA
51482 AATTAAATAAAAACAAACGTGACTATATCTT
1 AATTAAATAAAAACAAACGTGACTATATCTT
* *
51513 AATTAAATAAAAGCAAATGTGACTATAT
1 AATTAAATAAAAACAAACGTGACTATAT
51541 GTATATATCT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.53, C:0.10, G:0.08, T:0.29
Consensus pattern (31 bp):
AATTAAATAAAAACAAACGTGACTATATCTT
Found at i:58430 original size:5 final size:5
Alignment explanation
Indices: 58417--58459 Score: 52
Period size: 5 Copynumber: 8.4 Consensus size: 5
58407 GCTTCTCTTC
*
58417 TTTCTT TTTCT TTTC- TTTCT TTTTT TTTCT TTTCT GTTTCT TT
1 TTTC-T TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT -TTTCT TT
58460 GCTGCGTTGT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
4 4 0.12
5 20 0.61
6 9 0.27
ACGTcount: A:0.00, C:0.16, G:0.02, T:0.81
Consensus pattern (5 bp):
TTTCT
Found at i:58432 original size:15 final size:15
Alignment explanation
Indices: 58409--58459 Score: 68
Period size: 15 Copynumber: 3.4 Consensus size: 15
58399 CTCGGTAAGC
*
58409 TTCTCTTCTTTCTTT
1 TTCTTTTCTTTCTTT
58424 TTCTTTTCTTTCTTT
1 TTCTTTTCTTTCTTT
*
58439 TT-TTTTCTTTTCTGT
1 TTCTTTTC-TTTCTTT
58454 TTCTTT
1 TTCTTT
58460 GCTGCGTTGT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
14 5 0.16
15 24 0.75
16 3 0.09
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.78
Consensus pattern (15 bp):
TTCTTTTCTTTCTTT
Found at i:58438 original size:19 final size:20
Alignment explanation
Indices: 58409--58451 Score: 70
Period size: 19 Copynumber: 2.2 Consensus size: 20
58399 CTCGGTAAGC
58409 TTCTCTTCTTTCTTTTTCTT
1 TTCTCTTCTTTCTTTTTCTT
*
58429 TTCT-TTCTTTTTTTTTCTT
1 TTCTCTTCTTTCTTTTTCTT
58448 TTCT
1 TTCT
58452 GTTTCTTTGC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 18 0.82
20 4 0.18
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (20 bp):
TTCTCTTCTTTCTTTTTCTT
Found at i:58945 original size:3 final size:3
Alignment explanation
Indices: 58927--59003 Score: 91
Period size: 3 Copynumber: 25.3 Consensus size: 3
58917 TGTAATATTA
* * * * *
58927 AAT AAT ATAT ATT AAT AAT AAT AAT AAT AAT TAT TAT TAT AAT TAT
1 AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
58973 AAT AAT AAT AAT AAT TAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
59004 TAAATAACAT
Statistics
Matches: 65, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
3 62 0.95
4 3 0.05
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (3 bp):
AAT
Found at i:59272 original size:17 final size:17
Alignment explanation
Indices: 59250--59305 Score: 53
Period size: 17 Copynumber: 3.2 Consensus size: 17
59240 TTGAATAAGC
59250 TCTTCTCATTATGAACT
1 TCTTCTCATTATGAACT
*
59267 TCTTCTTC-TCCTGATG-AGT
1 TCTTC-TCAT--T-ATGAACT
59286 TCTTCTCATTATGAACT
1 TCTTCTCATTATGAACT
59303 TCT
1 TCT
59306 CTGGAAAAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 12
0.69 0.04 0.27
Matches are distributed among these distances:
16 3 0.10
17 12 0.39
18 4 0.13
19 9 0.29
20 3 0.10
ACGTcount: A:0.18, C:0.25, G:0.09, T:0.48
Consensus pattern (17 bp):
TCTTCTCATTATGAACT
Found at i:59456 original size:113 final size:113
Alignment explanation
Indices: 59250--59789 Score: 811
Period size: 113 Copynumber: 4.8 Consensus size: 113
59240 TTGAATAAGC
*
59250 TCTTCTCATTATGAACTTCTTCTT-C-TC--CTGATGAGTTCTTCTCATTATGAACTT-CTCTGG
1 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTGCTCTGG
* * *
59310 AAAAACTGACCCATCAAGTGATGGATTTTAGCAAAAAGCTGAACAAAT
66 AAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAAGCTGAACAAAT
* *
59358 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTAG
1 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTGCTCTGG
**
59423 AAAATTTGATCCATCAAGTGATGGATTTGAGCAAAAAGCTGAACAAAT
66 AAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAAGCTGAACAAAT
* * * **
59471 TCTTCTCATTATGAACTTCTTCTTCCTTCTTTAAATGAGTTCTTCTCATTATGAACTCGAACTGG
1 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTGCTCTGG
* * *
59536 AAAAGCTAATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAAT
66 AAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAAGCTGAACAAAT
* **
59584 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGG
1 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTGCTCTGG
* * * * *
59649 AAAAGATAATCCATCAAGTGATAGATTTGAGCAAAAGGTTGAACAAAT
66 AAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAAGCTGAACAAAT
* *
59697 TCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTCCTCTGG
1 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTGCTCTGG
59762 AAAAGCTGATCCATCAAGTGATGGATTT
66 AAAAGCTGATCCATCAAGTGATGGATTT
59790 AAATCTTTGC
Statistics
Matches: 397, Mismatches: 30, Indels: 5
0.92 0.07 0.01
Matches are distributed among these distances:
108 24 0.06
109 1 0.00
110 2 0.01
112 26 0.07
113 344 0.87
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.36
Consensus pattern (113 bp):
TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTGCTCTGG
AAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAAGCTGAACAAAT
Found at i:60551 original size:167 final size:167
Alignment explanation
Indices: 60273--60666 Score: 630
Period size: 167 Copynumber: 2.3 Consensus size: 167
60263 AAACCAAATT
* * * *
60273 AGATCAGATAACTCAAAGAACACTTCCAAAAGATGCTATTGGGTCTCCTT-ATTTCTTT-CAAAT
1 AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAG-CACATTCA--TCTTTCCAAAT
* * *
60336 TCAATGATTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAG
62 TCAATAACTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAAAAGATGCTATGAG
*
60401 CACATTCCTCTTCCAAATTCAATAACTGGTTTTACCAAACC
127 CACATTCATCTTCCAAATTCAATAACTGGTTTTACCAAACC
60442 AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCCAAATTCAA
1 AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCCAAATTCAA
60507 TAACTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAAAAGATGCTATGAGCACA
66 TAACTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAAAAGATGCTATGAGCACA
* * *
60572 TTCATCTTTCAAATTCAATGATTGGTTTTACCAAACC
131 TTCATCTTCCAAATTCAATAACTGGTTTTACCAAACC
*
60609 AGATCAGATAACTCAAAGGACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCCA
1 AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCCA
60667 GCTAATGTTT
Statistics
Matches: 211, Mismatches: 12, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
166 5 0.02
167 165 0.78
168 4 0.02
169 37 0.18
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.27
Consensus pattern (167 bp):
AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCCAAATTCAA
TAACTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAAAAGATGCTATGAGCACA
TTCATCTTCCAAATTCAATAACTGGTTTTACCAAACC
Found at i:60552 original size:84 final size:84
Alignment explanation
Indices: 60273--60666 Score: 625
Period size: 83 Copynumber: 4.7 Consensus size: 84
60263 AAACCAAATT
* * * *
60273 AGATCAGATAACTCAAAGAACACTTCCAAAAGATGCTATTGGGTCTCCTT-ATTTCTTT-CAAAT
1 AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAG-CACATTCA--TCTTTCCAAAT
* *
60336 TCAATGATTGGTTTTACCAAACC
62 TCAATAACTGGTTTTACCAAACC
*
60359 AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCCTC-TTCCAAATTCAA
1 AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCCAAATTCAA
60423 TAACTGGTTTTACCAAACC
66 TAACTGGTTTTACCAAACC
60442 AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCCAAATTCAA
1 AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCCAAATTCAA
60507 TAACTGGTTTTACCAAACC
66 TAACTGGTTTTACCAAACC
*
60526 AGATCAGATAACTCAAAGAACACTTCCAAAAGATGCTATGAGCACATTCATCTTT-CAAATTCAA
1 AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCCAAATTCAA
* *
60590 TGATTGGTTTTACCAAACC
66 TAACTGGTTTTACCAAACC
*
60609 AGATCAGATAACTCAAAGGACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCCA
1 AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCCA
60667 GCTAATGTTT
Statistics
Matches: 291, Mismatches: 13, Indels: 10
0.93 0.04 0.03
Matches are distributed among these distances:
82 2 0.01
83 158 0.54
84 91 0.31
85 3 0.01
86 37 0.13
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.27
Consensus pattern (84 bp):
AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCCAAATTCAA
TAACTGGTTTTACCAAACC
Found at i:61829 original size:24 final size:23
Alignment explanation
Indices: 61802--61860 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 23
61792 TTGACCCCTC
*
61802 TTTTTCTTTTTCTTTTTTTTTCTT
1 TTTTTCTTTTTCTCTTTTTTT-TT
61826 TTTTTCTTTTCTCTCTTTTTTTTT
1 TTTTTCTTTT-TCTCTTTTTTTTT
*
61850 ATTTT-TTTTTC
1 TTTTTCTTTTTC
61861 ATTAAGCATA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
22 2 0.06
23 4 0.12
24 16 0.50
25 10 0.31
ACGTcount: A:0.02, C:0.14, G:0.00, T:0.85
Consensus pattern (23 bp):
TTTTTCTTTTTCTCTTTTTTTTT
Found at i:71993 original size:9 final size:9
Alignment explanation
Indices: 71979--72003 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
71969 TAAACATGCT
71979 TTTAAATAA
1 TTTAAATAA
71988 TTTAAATAA
1 TTTAAATAA
71997 TTTAAAT
1 TTTAAAT
72004 TTACATGTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (9 bp):
TTTAAATAA
Found at i:74158 original size:14 final size:14
Alignment explanation
Indices: 74136--74185 Score: 64
Period size: 14 Copynumber: 3.4 Consensus size: 14
74126 CTCGGTAAGC
*
74136 TTCTCTTCTTTCTT
1 TTCTTTTCTTTCTT
74150 TTCTTTTCTTTCTT
1 TTCTTTTCTTTCTT
*
74164 TTTTTTTCTTTTCTGT
1 TTCTTTTC-TTTCT-T
74180 TTCTTT
1 TTCTTT
74186 GCTGCGTTGT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
14 20 0.65
15 5 0.16
16 6 0.19
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.78
Consensus pattern (14 bp):
TTCTTTTCTTTCTT
Found at i:74182 original size:6 final size:5
Alignment explanation
Indices: 74144--74185 Score: 59
Period size: 5 Copynumber: 8.4 Consensus size: 5
74134 GCTTCTCTTC
*
74144 TTTCT TTTCT TTTC- TTTCT TTTTT TTTCT TTTCT GTTTCT TT
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT -TTTCT TT
74186 GCTGCGTTGT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
4 4 0.12
5 24 0.73
6 5 0.15
ACGTcount: A:0.00, C:0.17, G:0.02, T:0.81
Consensus pattern (5 bp):
TTTCT
Found at i:74671 original size:3 final size:3
Alignment explanation
Indices: 74653--74716 Score: 56
Period size: 3 Copynumber: 21.0 Consensus size: 3
74643 TGTAATATTA
* * * * * * *
74653 AAT AAT ATAT ATT AAT AAT AAT AAT TAT TAT TAT TAT TAT TAT AAT
1 AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
74699 AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT
74717 TGTAATCACA
Statistics
Matches: 56, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
3 53 0.95
4 3 0.05
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (3 bp):
AAT
Found at i:75926 original size:14 final size:14
Alignment explanation
Indices: 75909--75955 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
75899 GTCTTAGATC
75909 TTAAACCTTAAATT
1 TTAAACCTTAAATT
75923 TT-AACCTTTAAATT
1 TTAAACC-TTAAATT
*
75937 TTAAA-CTCTAAATC
1 TTAAACCT-TAAATT
75951 TTAAA
1 TTAAA
75956 TCTAAACCCT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
13 5 0.17
14 22 0.76
15 2 0.07
ACGTcount: A:0.43, C:0.15, G:0.00, T:0.43
Consensus pattern (14 bp):
TTAAACCTTAAATT
Found at i:78261 original size:51 final size:51
Alignment explanation
Indices: 78154--78286 Score: 137
Period size: 51 Copynumber: 2.6 Consensus size: 51
78144 CACCTTTAGT
* * * * * *
78154 AGTAAAGCGTGCCCCTTGCACCGCGCTATACGATGATTTGGCGCTACGTGG
1 AGTATAGCGCGCCCCCTGCACCGCGCTATACGATGATCTGACACTACGTGG
* *
78205 GGTATAGCGCGCCCCCTGCACCGCGCTATACGGTGATCTGACA-TACACGT-G
1 AGTATAGCGCGCCCCCTGCACCGCGCTATACGATGATCTGACACT--ACGTGG
*
78256 AGTATAGCGCAG-CCCCTGCAACGCGCTATAC
1 AGTATAGCGC-GCCCCCTGCACCGCGCTATAC
78287 TTGGATATCT
Statistics
Matches: 69, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
50 1 0.01
51 63 0.91
52 5 0.07
ACGTcount: A:0.21, C:0.32, G:0.27, T:0.20
Consensus pattern (51 bp):
AGTATAGCGCGCCCCCTGCACCGCGCTATACGATGATCTGACACTACGTGG
Found at i:78454 original size:13 final size:14
Alignment explanation
Indices: 78426--78454 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
78416 ATATTTTATA
78426 ATATTTTTACTATT
1 ATATTTTTACTATT
78440 ATATTTTTACT-TT
1 ATATTTTTACTATT
78453 AT
1 AT
78455 TTAATATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.27
14 11 0.73
ACGTcount: A:0.28, C:0.07, G:0.00, T:0.66
Consensus pattern (14 bp):
ATATTTTTACTATT
Found at i:78654 original size:110 final size:111
Alignment explanation
Indices: 78529--78749 Score: 374
Period size: 110 Copynumber: 2.0 Consensus size: 111
78519 TGGAAATCAT
*
78529 ATATCTCTACACTTTGCTGATAC-AGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTA
1 ATATCTCGACACTTTGCTGATACGA-TAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTA
* *
78593 ATATTTAGTT-ATTTATTTAATGCATGATTATTAGATTAAGAATTAA
65 ATAATTAGTTGATTCATTTAATGCATGATTATTAGATTAAGAATTAA
* *
78639 ATATCTCGACACTTTGTTGATACGATAATATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACGATAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
78704 TAATTAGTTGATTCATTTAATGCATGATTATTAGATTAAGAATTAA
66 TAATTAGTTGATTCATTTAATGCATGATTATTAGATTAAGAATTAA
78750 TTTTTGTAAT
Statistics
Matches: 104, Mismatches: 5, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
110 68 0.65
111 36 0.35
ACGTcount: A:0.37, C:0.08, G:0.10, T:0.46
Consensus pattern (111 bp):
ATATCTCGACACTTTGCTGATACGATAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
TAATTAGTTGATTCATTTAATGCATGATTATTAGATTAAGAATTAA
Found at i:83603 original size:46 final size:45
Alignment explanation
Indices: 83542--83633 Score: 166
Period size: 46 Copynumber: 2.0 Consensus size: 45
83532 ACGCGGTACC
*
83542 TGCCCCGCTATATAAAATTATGTGAGGAGTAAAGGTATGTCGCGG
1 TGCCCCGCTATATAAAATTATGTCAGGAGTAAAGGTATGTCGCGG
83587 TGCCCGCGCTATATAAAATTATGTCAGGAGTAAAGGTATGTCGCGG
1 TGCCC-CGCTATATAAAATTATGTCAGGAGTAAAGGTATGTCGCGG
83633 T
1 T
83634 ACCTGTCCCG
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
45 5 0.11
46 40 0.89
ACGTcount: A:0.28, C:0.16, G:0.28, T:0.27
Consensus pattern (45 bp):
TGCCCCGCTATATAAAATTATGTCAGGAGTAAAGGTATGTCGCGG
Found at i:86377 original size:15 final size:15
Alignment explanation
Indices: 86357--86388 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
86347 ATCAGGCGGA
86357 GAGCCGAATGAATGG
1 GAGCCGAATGAATGG
86372 GAGCCGAATGAATGG
1 GAGCCGAATGAATGG
86387 GA
1 GA
86389 AACCGAAAGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.34, C:0.12, G:0.41, T:0.12
Consensus pattern (15 bp):
GAGCCGAATGAATGG
Found at i:86791 original size:20 final size:20
Alignment explanation
Indices: 86766--86815 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
86756 GATCAACAAA
86766 TTCGCAACGCAAACTCCAAT
1 TTCGCAACGCAAACTCCAAT
* ***
86786 TTCGCAACTCAGTTTCCAAT
1 TTCGCAACGCAAACTCCAAT
86806 TTCGCAACGC
1 TTCGCAACGC
86816 GAATATGTAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.28, C:0.34, G:0.12, T:0.26
Consensus pattern (20 bp):
TTCGCAACGCAAACTCCAAT
Found at i:86830 original size:20 final size:20
Alignment explanation
Indices: 86807--86894 Score: 59
Period size: 20 Copynumber: 4.3 Consensus size: 20
86797 GTTTCCAATT
*
86807 TCGCAACGCGAATATGTAAA
1 TCGCAACGCGAATTTGTAAA
*** * ** *
86827 TCGCGTTGCGATTTTCCAATT
1 TCGCAACGCGAATTTGTAA-A
* *
86848 TCGCAACACGAATCTGTAAA
1 TCGCAACGCGAATTTGTAAA
* *
86868 TCGCAACGCAAATTTATAAA
1 TCGCAACGCGAATTTGTAAA
86888 TCGCAAC
1 TCGCAAC
86895 ACAGAAGTCA
Statistics
Matches: 46, Mismatches: 21, Indels: 2
0.67 0.30 0.03
Matches are distributed among these distances:
20 35 0.76
21 11 0.24
ACGTcount: A:0.34, C:0.24, G:0.16, T:0.26
Consensus pattern (20 bp):
TCGCAACGCGAATTTGTAAA
Found at i:86946 original size:20 final size:20
Alignment explanation
Indices: 86900--87111 Score: 191
Period size: 20 Copynumber: 10.4 Consensus size: 20
86890 GCAACACAGA
* *
86900 AGTC-AATTCGCAACAC-AA
1 AGTCAAATTCGCAACGCGAT
86918 AGTCAAATTCGCAACGCGAT
1 AGTCAAATTCGCAACGCGAT
* *
86938 AGTCTAATTCGTAACGCGAATT
1 AGTCAAATTCGCAACGCG-A-T
* *
86960 TGT-AAA-TCGCAACAC-AT
1 AGTCAAATTCGCAACGCGAT
*
86977 AAGTCAAATTCGCAACGCAAT
1 -AGTCAAATTCGCAACGCGAT
*
86998 AGTCAAATTCGCAATGCGAT
1 AGTCAAATTCGCAACGCGAT
* *
87018 AGTCAAATACGCAATGCGAT
1 AGTCAAATTCGCAACGCGAT
*
87038 AGTCAAATTCGCATTCGCAATGCGAT
1 AGTC-AA-----ATTCGCAACGCGAT
*
87064 AGTCAAATTCGCAATGCGAT
1 AGTCAAATTCGCAACGCGAT
*
87084 AGTCAAATTCGCAACGCGAA
1 AGTCAAATTCGCAACGCGAT
87104 AGTCAAAT
1 AGTCAAAT
87112 GTTTTTACGC
Statistics
Matches: 164, Mismatches: 16, Indels: 26
0.80 0.08 0.13
Matches are distributed among these distances:
17 1 0.01
18 7 0.04
19 14 0.09
20 113 0.69
21 7 0.04
22 3 0.02
25 2 0.01
26 17 0.10
ACGTcount: A:0.38, C:0.22, G:0.17, T:0.23
Consensus pattern (20 bp):
AGTCAAATTCGCAACGCGAT
Found at i:86981 original size:78 final size:80
Alignment explanation
Indices: 86872--87021 Score: 241
Period size: 78 Copynumber: 1.9 Consensus size: 80
86862 TGTAAATCGC
86872 AACGCAAATTTATAAATCGCAACACAGAAGTC-AATTCGCAACACAA-AGTCAAATTCGCAACGC
1 AACGCAAATTTATAAATCGCAACACAGAAGTCAAATTCGCAACACAATAGTCAAATTCGCAACGC
86935 GATAGTCTAATTCGT
66 GATAGTCTAATTCGT
* * * * *
86950 AACGCGAATTTGTAAATCGCAACACATAAGTCAAATTCGCAACGCAATAGTCAAATTCGCAATGC
1 AACGCAAATTTATAAATCGCAACACAGAAGTCAAATTCGCAACACAATAGTCAAATTCGCAACGC
87015 GATAGTC
66 GATAGTC
87022 AAATACGCAA
Statistics
Matches: 65, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
78 29 0.45
79 13 0.20
80 23 0.35
ACGTcount: A:0.40, C:0.23, G:0.15, T:0.22
Consensus pattern (80 bp):
AACGCAAATTTATAAATCGCAACACAGAAGTCAAATTCGCAACACAATAGTCAAATTCGCAACGC
GATAGTCTAATTCGT
Found at i:87063 original size:26 final size:26
Alignment explanation
Indices: 87004--87076 Score: 104
Period size: 26 Copynumber: 3.0 Consensus size: 26
86994 CAATAGTCAA
87004 ATTCGCAATGCGATAGTCAAA-T---
1 ATTCGCAATGCGATAGTCAAATTCGC
87026 A--CGCAATGCGATAGTCAAATTCGC
1 ATTCGCAATGCGATAGTCAAATTCGC
87050 ATTCGCAATGCGATAGTCAAATTCGC
1 ATTCGCAATGCGATAGTCAAATTCGC
87076 A
1 A
87077 ATGCGATAGT
Statistics
Matches: 45, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
20 18 0.40
21 1 0.02
22 1 0.02
24 1 0.02
26 24 0.53
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.25
Consensus pattern (26 bp):
ATTCGCAATGCGATAGTCAAATTCGC
Found at i:87071 original size:46 final size:46
Alignment explanation
Indices: 87004--87096 Score: 177
Period size: 46 Copynumber: 2.0 Consensus size: 46
86994 CAATAGTCAA
87004 ATTCGCAATGCGATAGTCAAATACGCAATGCGATAGTCAAATTCGC
1 ATTCGCAATGCGATAGTCAAATACGCAATGCGATAGTCAAATTCGC
*
87050 ATTCGCAATGCGATAGTCAAATTCGCAATGCGATAGTCAAATTCGC
1 ATTCGCAATGCGATAGTCAAATACGCAATGCGATAGTCAAATTCGC
87096 A
1 A
87097 ACGCGAAAGT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.25
Consensus pattern (46 bp):
ATTCGCAATGCGATAGTCAAATACGCAATGCGATAGTCAAATTCGC
Found at i:87090 original size:66 final size:66
Alignment explanation
Indices: 86984--87111 Score: 211
Period size: 66 Copynumber: 1.9 Consensus size: 66
86974 CATAAGTCAA
* *
86984 ATTCGCAACGCAATAGTCAAATTCGCAATGCGATAGTCAAATACGCAATGCGATAGTCAAATTCG
1 ATTCGCAACGCAATAGTCAAATTCGCAATGCGATAGTCAAATACGCAACGCGAAAGTCAAATTCG
87049 C
66 C
* * *
87050 ATTCGCAATGCGATAGTCAAATTCGCAATGCGATAGTCAAATTCGCAACGCGAAAGTCAAAT
1 ATTCGCAACGCAATAGTCAAATTCGCAATGCGATAGTCAAATACGCAACGCGAAAGTCAAAT
87112 GTTTTTACGC
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
66 57 1.00
ACGTcount: A:0.37, C:0.22, G:0.19, T:0.23
Consensus pattern (66 bp):
ATTCGCAACGCAATAGTCAAATTCGCAATGCGATAGTCAAATACGCAACGCGAAAGTCAAATTCG
C
Found at i:89253 original size:20 final size:20
Alignment explanation
Indices: 89210--89255 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
89200 GTTAGGGGAA
* *
89210 TTACGTGATGAGGTCGTGCT
1 TTACGTCATGAGGTCGTACT
89230 TTACGTCATGAGGTCGGTAC-
1 TTACGTCATGAGGTC-GTACT
89250 TTACGT
1 TTACGT
89256 GAAGATAATG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 20 0.87
21 3 0.13
ACGTcount: A:0.17, C:0.17, G:0.30, T:0.35
Consensus pattern (20 bp):
TTACGTCATGAGGTCGTACT
Found at i:89721 original size:21 final size:21
Alignment explanation
Indices: 89672--89721 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
89662 GCCTCTTATT
* *
89672 GTTCAAGAGGCCCCTCTCATC
1 GTTCAAGAAGCCCCTCTCACC
*
89693 -ATCGAAGAAGCCCCTCTCACC
1 GTTC-AAGAAGCCCCTCTCACC
89714 GTTCAAGA
1 GTTCAAGA
89722 GGTCCCGCCC
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
20 2 0.09
21 19 0.83
22 2 0.09
ACGTcount: A:0.26, C:0.36, G:0.18, T:0.20
Consensus pattern (21 bp):
GTTCAAGAAGCCCCTCTCACC
Done.