Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 ID=Chr09-JGI_221_v2.0
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: 70713020
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1142373 characters in sequence are not A, C, G, or T
File 208 of 226
Found at i:65637999 original size:20 final size:20
Alignment explanation
Indices: 65637976--65638020 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
65637966 AAGATGTTCA
65637976 ATAATCCAATAAGAAATTCT
1 ATAATCCAATAAGAAATTCT
***
65637996 ATAATTTTATAAGAAATTCT
1 ATAATCCAATAAGAAATTCT
65638016 ATAAT
1 ATAAT
65638021 TTTTAATAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.49, C:0.09, G:0.04, T:0.38
Consensus pattern (20 bp):
ATAATCCAATAAGAAATTCT
Found at i:65638020 original size:40 final size:40
Alignment explanation
Indices: 65637944--65638020 Score: 91
Period size: 40 Copynumber: 1.9 Consensus size: 40
65637934 TTATAATATG
* * **
65637944 ATAAGAGATTCAATAATGTTGTAAGATGTTCAATAATCCA
1 ATAAGAAATTCAATAATGTTATAAGAAATTCAATAATCCA
* * *
65637984 ATAAGAAATTCTATAATTTTATAAGAAATTCTATAAT
1 ATAAGAAATTCAATAATGTTATAAGAAATTCAATAAT
65638021 TTTTAATAAT
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
40 30 1.00
ACGTcount: A:0.45, C:0.08, G:0.10, T:0.36
Consensus pattern (40 bp):
ATAAGAAATTCAATAATGTTATAAGAAATTCAATAATCCA
Found at i:65638021 original size:20 final size:20
Alignment explanation
Indices: 65637984--65638023 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
65637974 CAATAATCCA
65637984 ATAAGAAATTCTATAATTTT
1 ATAAGAAATTCTATAATTTT
65638004 ATAAGAAATTCTATAATTTT
1 ATAAGAAATTCTATAATTTT
65638024 TAATAATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (20 bp):
ATAAGAAATTCTATAATTTT
Found at i:65638032 original size:30 final size:30
Alignment explanation
Indices: 65637996--65638052 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
65637986 AAGAAATTCT
*
65637996 ATAATTTTATAA-GAAATTCTATAATTTTTA
1 ATAATTTTA-AAGGAAATTCAATAATTTTTA
*
65638026 ATAATTTTAAAGGAGATTCAATAATTT
1 ATAATTTTAAAGGAAATTCAATAATTT
65638053 ACAAAATTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 2 0.08
30 22 0.92
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.46
Consensus pattern (30 bp):
ATAATTTTAAAGGAAATTCAATAATTTTTA
Found at i:65639132 original size:11 final size:11
Alignment explanation
Indices: 65639102--65639133 Score: 57
Period size: 10 Copynumber: 3.0 Consensus size: 11
65639092 AAAAGAAAAA
65639102 ATTATAAAATT
1 ATTATAAAATT
65639113 ATT-TAAAATT
1 ATTATAAAATT
65639123 ATTATAAAATT
1 ATTATAAAATT
65639134 TTAACATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 10 0.50
11 10 0.50
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (11 bp):
ATTATAAAATT
Found at i:65639302 original size:19 final size:19
Alignment explanation
Indices: 65639278--65639341 Score: 53
Period size: 19 Copynumber: 3.5 Consensus size: 19
65639268 GTAGATTATG
65639278 AATTTTTAAATTTTTTAAT
1 AATTTTTAAATTTTTTAAT
** *
65639297 AATTTTCGAA-GTTTTAAT
1 AATTTTTAAATTTTTTAAT
* * *
65639315 ATTTTTTGAGTTTTTTAAT
1 AATTTTTAAATTTTTTAAT
65639334 --TTTTTAAA
1 AATTTTTAAA
65639342 AATTTTCTTA
Statistics
Matches: 35, Mismatches: 9, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
17 6 0.17
18 14 0.40
19 15 0.43
ACGTcount: A:0.31, C:0.02, G:0.06, T:0.61
Consensus pattern (19 bp):
AATTTTTAAATTTTTTAAT
Found at i:65639329 original size:18 final size:20
Alignment explanation
Indices: 65639288--65639338 Score: 56
Period size: 18 Copynumber: 2.8 Consensus size: 20
65639278 AATTTTTAAA
*
65639288 TTTTTTAATAATTTTCGAAG
1 TTTTTTAATATTTTTCGAAG
*
65639308 --TTTTAATATTTTTTG-AG
1 TTTTTTAATATTTTTCGAAG
65639325 TTTTTTAAT-TTTTT
1 TTTTTTAATATTTTT
65639339 AAAAATTTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
17 2 0.07
18 18 0.67
19 7 0.26
ACGTcount: A:0.24, C:0.02, G:0.08, T:0.67
Consensus pattern (20 bp):
TTTTTTAATATTTTTCGAAG
Found at i:65647272 original size:21 final size:21
Alignment explanation
Indices: 65647247--65647287 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
65647237 TCAAACATGG
*
65647247 CCGTGTGGCTA-TCTCACACAT
1 CCGTGTGACTACTC-CACACAT
65647268 CCGTGTGACTACTCCACACA
1 CCGTGTGACTACTCCACACA
65647288 CCTGTGTATC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.22, C:0.37, G:0.17, T:0.24
Consensus pattern (21 bp):
CCGTGTGACTACTCCACACAT
Found at i:65647308 original size:147 final size:147
Alignment explanation
Indices: 65647041--65647343 Score: 455
Period size: 147 Copynumber: 2.1 Consensus size: 147
65647031 CCTACAGTGG
* *
65647041 TCACACGCCGTCTGTCCAGAACGTTTGATAGAGCCTAGACTGTATGGCTCCAAACATGGCTATGT
1 TCACACGCCGTCTGTCCAGAACGTTTGATAGAGCCCAGACTGTATGGCTCCAAACATGGCCATGT
* * *
65647106 GGTTATCCGACACGCCCGTGTGACTACTCCACACACCCATGTGTCCAACCGTGTGCTTACCCGTG
66 GGCTATCCGACACACCCGTGTGACTACTCCACACACCCATGTATCCAACCGTGTGCTTACCCGTG
65647171 TAACTCACAGACTTGAC
131 TAACTCACAGACTTGAC
* * * *
65647188 TCACACGTCGTGTGTCCAGAACGTTTGATAGAGCCCAGACTGTATGGCTTCAAACATGGCCGTGT
1 TCACACGCCGTCTGTCCAGAACGTTTGATAGAGCCCAGACTGTATGGCTCCAAACATGGCCATGT
* ** *
65647253 GGCTATCTC-ACACATCCGTGTGACTACTCCACACACCTGTGTATCCAACTGTGTGCTTACCCGT
66 GGCTATC-CGACACACCCGTGTGACTACTCCACACACCCATGTATCCAACCGTGTGCTTACCCGT
* *
65647317 GTAACTCACTGACTTGGC
130 GTAACTCACAGACTTGAC
65647335 TCACACGCC
1 TCACACGCC
65647344 CGTGTCTCAG
Statistics
Matches: 139, Mismatches: 16, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
147 138 0.99
148 1 0.01
ACGTcount: A:0.22, C:0.31, G:0.21, T:0.25
Consensus pattern (147 bp):
TCACACGCCGTCTGTCCAGAACGTTTGATAGAGCCCAGACTGTATGGCTCCAAACATGGCCATGT
GGCTATCCGACACACCCGTGTGACTACTCCACACACCCATGTATCCAACCGTGTGCTTACCCGTG
TAACTCACAGACTTGAC
Found at i:65652132 original size:90 final size:90
Alignment explanation
Indices: 65651973--65652224 Score: 258
Period size: 90 Copynumber: 2.8 Consensus size: 90
65651963 ATAAGCTCAT
* * ** * * *
65651973 TGCTCTTAATAAGTTCATAGCCCAAATTTTGGGTGGTCTTGCT-AGGACGGACTTGATGAATTCA
1 TGCTCTTAATGAGTTCATAACCCAAGCTTTGGGTGGTCCTACTGA-GACGGACTTGATGAACTCA
* *
65652037 CCGAATTTATAAGATGAAG-TACTAGA
65 CCGAATTTATAAGAT-AAGCCACTAAA
* * *
65652063 TGCTCTTAATGAGTTCATAACCCATGGTTTGGGTGGTCCTATTGAGACGGACTTGATGAAC-CTA
1 TGCTCTTAATGAGTTCATAACCCAAGCTTTGGGTGGTCCTACTGAGACGGACTTGATGAACTC-A
* *
65652127 TCGAATTTATAGGATAAGCCACTAAA
65 CCGAATTTATAAGATAAGCCACTAAA
* * * * * * *
65652153 TGTTCTTAATGAATTCATATCCCAAGCTTTAGGTGGTCCTAGTGAGACAGACTTGATGAATTCAC
1 TGCTCTTAATGAGTTCATAACCCAAGCTTTGGGTGGTCCTACTGAGACGGACTTGATGAACTCAC
*
65652218 TGAATTT
66 CGAATTT
65652225 TTAAACTGAG
Statistics
Matches: 134, Mismatches: 24, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
89 4 0.03
90 128 0.96
91 2 0.01
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.33
Consensus pattern (90 bp):
TGCTCTTAATGAGTTCATAACCCAAGCTTTGGGTGGTCCTACTGAGACGGACTTGATGAACTCAC
CGAATTTATAAGATAAGCCACTAAA
Found at i:65653149 original size:66 final size:64
Alignment explanation
Indices: 65652994--65653237 Score: 224
Period size: 66 Copynumber: 3.8 Consensus size: 64
65652984 TTTTAAGTGT
* ** * * *
65652994 TTAATTAAGGTTTATGGTTTATTAAATTAGGGTTTTGGATTTTATTATT-T--TTAAGTATGTA
1 TTAATTAAGGTTTAAGGTTTATTAAATTAGGGTTAAGGATTTTATTATTATGGTTTAGTGTTTA
* * *
65653055 TTAATTAGGGTTTTAAGGTTTGTTAAATTATGGTTAAGGATTTTATTATTATGGTCATTAGTGTT
1 TTAATTAAGG-TTTAAGGTTTATTAAATTAGGGTTAAGGATTTTATTATTATGGT--TTAGTGTT
*
65653120 TG
63 TA
* * * * * *
65653122 TTAATTAGGGTTTATGGTTTGTTAAATTAGGGTTAATGATTTTATTATGAGGGTTTTTAGTGTTT
1 TTAATTAAGGTTTAAGGTTTATTAAATTAGGGTTAAGGATTTTATTATTATGG--TTTAGTGTTT
65653187 A
64 A
* * * * * *
65653188 TAAATTAAGGTTTAAAGTTTATTAATTTAAGATTAATGATTTTATTATTA
1 TTAATTAAGGTTTAAGGTTTATTAAATTAGGGTTAAGGATTTTATTATTA
65653238 GAGTTTTAGG
Statistics
Matches: 150, Mismatches: 25, Indels: 11
0.81 0.13 0.06
Matches are distributed among these distances:
61 9 0.06
62 34 0.23
63 1 0.01
65 1 0.01
66 88 0.59
67 16 0.11
68 1 0.01
ACGTcount: A:0.29, C:0.00, G:0.19, T:0.52
Consensus pattern (64 bp):
TTAATTAAGGTTTAAGGTTTATTAAATTAGGGTTAAGGATTTTATTATTATGGTTTAGTGTTTA
Found at i:65653152 original size:22 final size:22
Alignment explanation
Indices: 65652991--65653155 Score: 71
Period size: 21 Copynumber: 7.7 Consensus size: 22
65652981 GGGTTTTAAG
* *
65652991 TGTTTAATTAAGGTTTATGGTT
1 TGTTAAATTAGGGTTTATGGTT
* *
65653013 TATTAAATTAGGGTTT-TGGAT
1 TGTTAAATTAGGGTTTATGGTT
** * *
65653034 T-TT--ATTA-TTTTTA-AGTA
1 TGTTAAATTAGGGTTTATGGTT
* *
65653051 TGTATTAATTAGGGTTTTAAGGTT
1 TGT-TAAATTAGGG-TTTATGGTT
* * *
65653075 TGTTAAATTATGG-TTAAGGAT
1 TGTTAAATTAGGGTTTATGGTT
* *
65653096 T-TTATTATTATGGTCATTA-GTGTT
1 TGTTA-AATTAGGGT--TTATG-GTT
65653120 TGTT-AATTAGGGTTTATGGTT
1 TGTTAAATTAGGGTTTATGGTT
65653141 TGTTAAATTAGGGTT
1 TGTTAAATTAGGGTT
65653156 AATGATTTTA
Statistics
Matches: 107, Mismatches: 20, Indels: 32
0.67 0.13 0.20
Matches are distributed among these distances:
17 5 0.05
18 5 0.05
19 1 0.01
20 5 0.05
21 34 0.32
22 24 0.22
23 20 0.19
24 11 0.10
25 2 0.02
ACGTcount: A:0.25, C:0.01, G:0.22, T:0.52
Consensus pattern (22 bp):
TGTTAAATTAGGGTTTATGGTT
Found at i:65653786 original size:36 final size:36
Alignment explanation
Indices: 65653739--65653810 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
65653729 TTTCAGAAGA
65653739 ATAGAAGTTCATAGGGAAGACATAAGTTGGAGCAAT
1 ATAGAAGTTCATAGGGAAGACATAAGTTGGAGCAAT
*
65653775 ATAGAAGTTCATAGGGAAGGCATAAGTTGGAGCAAT
1 ATAGAAGTTCATAGGGAAGACATAAGTTGGAGCAAT
65653811 GGTACTATTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.40, C:0.08, G:0.29, T:0.22
Consensus pattern (36 bp):
ATAGAAGTTCATAGGGAAGACATAAGTTGGAGCAAT
Found at i:65660192 original size:50 final size:50
Alignment explanation
Indices: 65660086--65660327 Score: 200
Period size: 50 Copynumber: 4.7 Consensus size: 50
65660076 GGGAATGAGA
* * *
65660086 TCCCATGTAAGACCATGTCTGGGACATGGAATTGGCATCATTGAGATTATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C-CT-AG---ATGAGAAG
* * *
65660142 TCCCATGTAAGAGCATGTCTGGGACATGGCGTTGGCACCTAGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCTAGATGAGAAG
* * * * * *
65660192 T-CCTTCGTAAGACCATGTTTGGGACATGGCATGGGCACCGATATGAGAAC
1 TCCCAT-GTAAGACCATGTCTGGGACATGGCATTGGCACCTAGATGAGAAG
* * * * * * * *
65660242 TCTCATGTAAGACCATATCTGGGATATGGCATTGGCA-GTACAAGAAAAA
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCTAGATGAGAAG
* * *
65660291 TCACATGTAAGACCATGTCTGGGACATGACTTTGGCA
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
65660328 TATTATTATC
Statistics
Matches: 154, Mismatches: 30, Indels: 11
0.79 0.15 0.06
Matches are distributed among these distances:
49 41 0.27
50 73 0.47
51 2 0.01
53 2 0.01
54 1 0.01
55 1 0.01
56 34 0.22
ACGTcount: A:0.29, C:0.19, G:0.28, T:0.25
Consensus pattern (50 bp):
TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCTAGATGAGAAG
Found at i:65666498 original size:16 final size:17
Alignment explanation
Indices: 65666474--65666506 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
65666464 CAAAATCTAA
*
65666474 CCATTTTAACC-TAAAT
1 CCATGTTAACCATAAAT
65666490 CCATGTTAACCATAAAT
1 CCATGTTAACCATAAAT
65666507 GCAAGGGACC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.39, C:0.24, G:0.03, T:0.33
Consensus pattern (17 bp):
CCATGTTAACCATAAAT
Found at i:65675934 original size:12 final size:12
Alignment explanation
Indices: 65675917--65675944 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
65675907 CAATTAAATG
65675917 AATTCTATAATT
1 AATTCTATAATT
65675929 AATTCTATAATT
1 AATTCTATAATT
65675941 AATT
1 AATT
65675945 TAATTCAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (12 bp):
AATTCTATAATT
Found at i:65678925 original size:24 final size:26
Alignment explanation
Indices: 65678874--65678942 Score: 72
Period size: 27 Copynumber: 2.7 Consensus size: 26
65678864 ACATATATTC
**
65678874 TCAATTCAATCACAATTTCTCACACTT
1 TCAATTCAATCA-TTTTTCTCACACTT
65678901 TCAATTCAATCATTTTTC-CAC-CTT
1 TCAATTCAATCATTTTTCTCACACTT
*
65678925 TCAA-TCAATAATTATTTC
1 TCAATTCAATCATT-TTTC
65678943 ACAAATTCAC
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
23 8 0.21
24 11 0.29
25 3 0.08
26 4 0.11
27 12 0.32
ACGTcount: A:0.32, C:0.26, G:0.00, T:0.42
Consensus pattern (26 bp):
TCAATTCAATCATTTTTCTCACACTT
Found at i:65679110 original size:18 final size:18
Alignment explanation
Indices: 65679087--65679133 Score: 69
Period size: 18 Copynumber: 2.6 Consensus size: 18
65679077 CTCCCACTCA
65679087 TAATAATAATAGT-AATAC
1 TAATAATAATA-TAAATAC
65679105 TAATAATAATATAAATAC
1 TAATAATAATATAAATAC
*
65679123 TAATATTAATA
1 TAATAATAATA
65679134 CTTACCTCAC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
17 1 0.04
18 26 0.96
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.36
Consensus pattern (18 bp):
TAATAATAATATAAATAC
Found at i:65679134 original size:12 final size:12
Alignment explanation
Indices: 65679087--65679135 Score: 53
Period size: 12 Copynumber: 4.1 Consensus size: 12
65679077 CTCCCACTCA
* *
65679087 TAATAATAATAG
1 TAATATTAATAC
* *
65679099 TAATACTAATAA
1 TAATATTAATAC
*
65679111 TAATATAAATAC
1 TAATATTAATAC
65679123 TAATATTAATAC
1 TAATATTAATAC
65679135 T
1 T
65679136 TACCTCACAT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 31 1.00
ACGTcount: A:0.55, C:0.06, G:0.02, T:0.37
Consensus pattern (12 bp):
TAATATTAATAC
Found at i:65680055 original size:14 final size:14
Alignment explanation
Indices: 65680036--65680081 Score: 83
Period size: 14 Copynumber: 3.3 Consensus size: 14
65680026 TATTTAAAAT
65680036 ATAATAATAATTTA
1 ATAATAATAATTTA
*
65680050 ATAATACTAATTTA
1 ATAATAATAATTTA
65680064 ATAATAATAATTTA
1 ATAATAATAATTTA
65680078 ATAA
1 ATAA
65680082 CATTTTTTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 30 1.00
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (14 bp):
ATAATAATAATTTA
Found at i:65681219 original size:43 final size:43
Alignment explanation
Indices: 65681171--65681267 Score: 108
Period size: 43 Copynumber: 2.3 Consensus size: 43
65681161 TTGACATCAC
***
65681171 AGTGCATCATCGAATAAACCTAAA-CAAAT-ATATTGGCACACAT
1 AGTGCATCATCGAATAAACC-AAAGC-AATCATACCAGCACACAT
* * *
65681214 AGTGCATAATCGGATAAACCAAAGCAATCATACCAGTACACAT
1 AGTGCATCATCGAATAAACCAAAGCAATCATACCAGCACACAT
65681257 AGTGCATCATC
1 AGTGCATCATC
65681268 AGACAAGTCG
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
42 6 0.13
43 39 0.87
ACGTcount: A:0.42, C:0.23, G:0.13, T:0.22
Consensus pattern (43 bp):
AGTGCATCATCGAATAAACCAAAGCAATCATACCAGCACACAT
Found at i:65681282 original size:43 final size:42
Alignment explanation
Indices: 65681208--65681402 Score: 110
Period size: 42 Copynumber: 4.6 Consensus size: 42
65681198 ATATATTGGC
* * *
65681208 ACACATAGTGCATAATCGGATAAACCAAAGC-AATCATACCAG
1 ACACATAGTGCATCATCAGACAAACCAAAGCAAAT-ATACCAG
** * *
65681250 TACACATAGTGCATCATCAGACAAGTCGAAGCAAATATACTAG
1 -ACACATAGTGCATCATCAGACAAACCAAAGCAAATATACCAG
* ** *** *
65681293 -CACGTAAGTGCATCATCAGATGAATTGAAGCAAATATACTAG
1 ACACAT-AGTGCATCATCAGACAAACCAAAGCAAATATACCAG
* * * * * *
65681335 -TACATAAGTGAATCATCGGATAAACCAAAACAAATATACTAG
1 ACACAT-AGTGCATCATCAGACAAACCAAAGCAAATATACCAG
* * *
65681377 -CACGTAAGTACATCATCAGATAAACC
1 ACACAT-AGTGCATCATCAGACAAACC
65681403 GAAGTATAAA
Statistics
Matches: 124, Mismatches: 26, Indels: 5
0.80 0.17 0.03
Matches are distributed among these distances:
41 4 0.03
42 86 0.69
43 31 0.25
44 3 0.02
ACGTcount: A:0.44, C:0.21, G:0.15, T:0.21
Consensus pattern (42 bp):
ACACATAGTGCATCATCAGACAAACCAAAGCAAATATACCAG
Found at i:65681306 original size:42 final size:41
Alignment explanation
Indices: 65681257--65681396 Score: 154
Period size: 42 Copynumber: 3.3 Consensus size: 41
65681247 CAGTACACAT
65681257 AGTGCATCATCAGACAAGTCGAAGCAAATATACTAGCACGTA
1 AGTGCATCATCAGACAA-TCGAAGCAAATATACTAGCACGTA
* * * *
65681299 AGTGCATCATCAGATGAATTGAAGCAAATATACTAGTACATA
1 AGTGCATCATCAGA-CAATCGAAGCAAATATACTAGCACGTA
* * * * * *
65681341 AGTGAATCATCGGATAAACCAAAACAAATATACTAGCACGTA
1 AGTGCATCATCAGA-CAATCGAAGCAAATATACTAGCACGTA
*
65681383 AGTACATCATCAGA
1 AGTGCATCATCAGA
65681397 TAAACCGAAG
Statistics
Matches: 81, Mismatches: 16, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
42 79 0.98
43 2 0.02
ACGTcount: A:0.44, C:0.19, G:0.16, T:0.21
Consensus pattern (41 bp):
AGTGCATCATCAGACAATCGAAGCAAATATACTAGCACGTA
Found at i:65681338 original size:85 final size:84
Alignment explanation
Indices: 65681235--65681397 Score: 211
Period size: 84 Copynumber: 1.9 Consensus size: 84
65681225 GGATAAACCA
* ** * *
65681235 AAGCAATCATACCAGTACACATAGTGCATCATCAGACAAGTCGAAGCAAATATACTAGCACGTAA
1 AAGCAATCATACCAGTACACA-AGTGAATCATCAGACAAACCAAAACAAATATACTAGCACGTAA
*
65681300 GTGCATCATCAGATGAATTG
65 GTACATCATCAGATGAATTG
* * * *
65681320 AAGCAAAT-ATACTAGTACATAAGTGAATCATCGGATAAACCAAAACAAATATACTAGCACGTAA
1 AAGC-AATCATACCAGTACACAAGTGAATCATCAGACAAACCAAAACAAATATACTAGCACGTAA
65681384 GTACATCATCAGAT
65 GTACATCATCAGAT
65681398 AAACCGAAGT
Statistics
Matches: 67, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
84 49 0.73
85 15 0.22
86 3 0.04
ACGTcount: A:0.44, C:0.20, G:0.15, T:0.21
Consensus pattern (84 bp):
AAGCAATCATACCAGTACACAAGTGAATCATCAGACAAACCAAAACAAATATACTAGCACGTAAG
TACATCATCAGATGAATTG
Found at i:65685828 original size:22 final size:22
Alignment explanation
Indices: 65685803--65685844 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
65685793 ACTTTTGAAG
65685803 GGGAAGGGGATGATGATGATGA
1 GGGAAGGGGATGATGATGATGA
* *
65685825 GGGACGGTGATGATGATGAT
1 GGGAAGGGGATGATGATGAT
65685845 TTTAAAATCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.29, C:0.02, G:0.48, T:0.21
Consensus pattern (22 bp):
GGGAAGGGGATGATGATGATGA
Found at i:65685866 original size:20 final size:20
Alignment explanation
Indices: 65685838--65685877 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
65685828 ACGGTGATGA
*
65685838 TGATGATTTTAAAATCATTT
1 TGATAATTTTAAAATCATTT
65685858 TGATAATTTTAAAATCATTT
1 TGATAATTTTAAAATCATTT
65685878 GCTGATGTGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.38, C:0.05, G:0.07, T:0.50
Consensus pattern (20 bp):
TGATAATTTTAAAATCATTT
Found at i:65692116 original size:16 final size:16
Alignment explanation
Indices: 65692095--65692127 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
65692085 ACTATAGTGG
*
65692095 AATGAGTTTATGATTA
1 AATGAGTTTATAATTA
65692111 AATGAGTTTATAATTA
1 AATGAGTTTATAATTA
65692127 A
1 A
65692128 TAGTCAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.42, C:0.00, G:0.15, T:0.42
Consensus pattern (16 bp):
AATGAGTTTATAATTA
Found at i:65694554 original size:18 final size:17
Alignment explanation
Indices: 65694529--65694564 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
65694519 TTAAAAATTC
*
65694529 ATATTTTTTTATTTTTA
1 ATATTTTTTTAATTTTA
65694546 ATATATTTTTTAATTTTA
1 ATAT-TTTTTTAATTTTA
65694564 A
1 A
65694565 AATACATAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (17 bp):
ATATTTTTTTAATTTTA
Found at i:65704218 original size:13 final size:13
Alignment explanation
Indices: 65704200--65704224 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
65704190 TTTTATTTAT
65704200 TTATTCCCACCGA
1 TTATTCCCACCGA
65704213 TTATTCCCACCG
1 TTATTCCCACCG
65704225 GCCGAATGTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.40, G:0.08, T:0.32
Consensus pattern (13 bp):
TTATTCCCACCGA
Found at i:65704369 original size:6 final size:6
Alignment explanation
Indices: 65704354--65704383 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
65704344 TGTTGTTCAA
*
65704354 TTCCTT TTCCTC TTCCTC TTCCTC TTCCTC
1 TTCCTC TTCCTC TTCCTC TTCCTC TTCCTC
65704384 CCCTTTTGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (6 bp):
TTCCTC
Found at i:65706510 original size:64 final size:64
Alignment explanation
Indices: 65706441--65706718 Score: 465
Period size: 64 Copynumber: 4.4 Consensus size: 64
65706431 AAATAAAATA
*
65706441 AAAATTGGATCATTACATATAATCAAGTAAACAAATTGATTAAAAAACATATGGATAATATATT
1 AAAATTGGATCATTAGATATAATCAAGTAAACAAATTGATTAAAAAACATATGGATAATATATT
* *
65706505 AAAATTGGATCATTACATATAGTCAAGTAAACAAATTGATTAAAAAACATATGGATAATATATT
1 AAAATTGGATCATTAGATATAATCAAGTAAACAAATTGATTAAAAAACATATGGATAATATATT
* * *
65706569 AAAATTGAATCATTAGATATAATCAAGTAAACAACTTGATTAAAAAACATATGGGTAATATATT
1 AAAATTGGATCATTAGATATAATCAAGTAAACAAATTGATTAAAAAACATATGGATAATATATT
*
65706633 --AATTGGATCATTAGATATAATCAAGTAAACAACTTGATTAAAAAACATATGGATAATATATT
1 AAAATTGGATCATTAGATATAATCAAGTAAACAAATTGATTAAAAAACATATGGATAATATATT
65706695 --AATTGGATCATTAGATATAATCAA
1 AAAATTGGATCATTAGATATAATCAA
65706719 CTTGATTCTA
Statistics
Matches: 206, Mismatches: 8, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
62 84 0.41
64 122 0.59
ACGTcount: A:0.50, C:0.08, G:0.11, T:0.32
Consensus pattern (64 bp):
AAAATTGGATCATTAGATATAATCAAGTAAACAAATTGATTAAAAAACATATGGATAATATATT
Found at i:65709324 original size:44 final size:41
Alignment explanation
Indices: 65709276--65709384 Score: 98
Period size: 44 Copynumber: 2.6 Consensus size: 41
65709266 AGTATTATAT
65709276 ATTATGATTTTAGTAAATTCATATAAGAATAAGAATT-TTATTAA
1 ATTAT-ATTTTAGTAAATT-ATAT-AGAATAAGAATTATT-TTAA
* ** *
65709320 ATTATATATTATTATTAAATTATATTTAATAATAATTATTTTAA
1 A-T-TATATT-TTAGTAAATTATATAGAATAAGAATTATTTTAA
65709364 ATTATATTTTAGT--ATTATATA
1 ATTATATTTTAGTAAATTATATA
65709385 TTATGATTTT
Statistics
Matches: 55, Mismatches: 6, Indels: 13
0.74 0.08 0.18
Matches are distributed among these distances:
39 7 0.13
41 4 0.07
42 6 0.11
43 1 0.02
44 15 0.27
45 10 0.18
46 12 0.22
ACGTcount: A:0.44, C:0.01, G:0.05, T:0.50
Consensus pattern (41 bp):
ATTATATTTTAGTAAATTATATAGAATAAGAATTATTTTAA
Found at i:65709363 original size:26 final size:28
Alignment explanation
Indices: 65709309--65709372 Score: 87
Period size: 28 Copynumber: 2.4 Consensus size: 28
65709299 TAAGAATAAG
* * *
65709309 AATTTTATTAAATTATATATTATTATTA
1 AATTATATTTAATAATATATTATTATTA
65709337 AATTATATTTAATAATA-ATTATT-TTA
1 AATTATATTTAATAATATATTATTATTA
65709363 AATTATATTT
1 AATTATATTT
65709373 TAGTATTATA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
26 13 0.39
27 6 0.18
28 14 0.42
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (28 bp):
AATTATATTTAATAATATATTATTATTA
Found at i:65709442 original size:108 final size:106
Alignment explanation
Indices: 65709222--65709469 Score: 311
Period size: 100 Copynumber: 2.4 Consensus size: 106
65709212 AATAAAATAG
65709222 ATTA-TAAATTATATTTAATAATAATTATTTAAATTATATTTTATAGTATTATATATTATGATTT
1 ATTATTAAATTATATTTAATAATAATTATTTAAATTATATTTTATAGTATTATATATTATGATTT
65709286 TAGTAAATTCATATAAGAATAAGAATTTTATTAAATTATATATT
66 TAGTAAATTCATATAAGAAT---AATTTTATTAAATTATATATT
65709330 ATTATTAAATTATATTTAATAATAATTATTTTAAATTATA-TTT-TAGTATTATATATTATGATT
1 ATTATTAAATTATATTTAATAATAATTA-TTTAAATTATATTTTATAGTATTATATATTATGA--
*
65709393 TTATTAGTAAATTCATATAAGAAT-A-TTTATT--A--ACA-ATT
63 TT-TTAGTAAATTCATATAAGAATAATTTTATTAAATTATATATT
* * *
65709431 -TTATTAAATTATATTTTATAACAATTATGTTAAAATATA
1 ATTATTAAATTATATTTAATAATAATTAT-TTAAATTATA
65709470 ATTAAATTAT
Statistics
Matches: 130, Mismatches: 4, Indels: 20
0.84 0.03 0.13
Matches are distributed among these distances:
99 1 0.01
100 34 0.26
101 3 0.02
102 2 0.02
104 1 0.01
106 6 0.05
107 1 0.01
108 22 0.17
109 26 0.20
110 13 0.10
111 21 0.16
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.50
Consensus pattern (106 bp):
ATTATTAAATTATATTTAATAATAATTATTTAAATTATATTTTATAGTATTATATATTATGATTT
TAGTAAATTCATATAAGAATAATTTTATTAAATTATATATT
Found at i:65709463 original size:26 final size:27
Alignment explanation
Indices: 65709418--65709469 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 27
65709408 TATAAGAATA
* *
65709418 TTTATTAACAATTTTATTAAATTATAT
1 TTTATTAACAATTATATTAAAATATAT
*
65709445 TTTA-TAACAATTATGTTAAAATATA
1 TTTATTAACAATTATATTAAAATATA
65709470 ATTAAATTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 18 0.82
27 4 0.18
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.50
Consensus pattern (27 bp):
TTTATTAACAATTATATTAAAATATAT
Found at i:65709636 original size:39 final size:41
Alignment explanation
Indices: 65709591--65709696 Score: 126
Period size: 44 Copynumber: 2.5 Consensus size: 41
65709581 TTTCCTTATG
* *
65709591 CTATTACACCTCTATTCCATTCAACCAAACACAAGAA-TAC
1 CTATTACGCCTCTATTCCATTCAACCAAACAAAAGAATTAC
65709631 C-ATTACGCCTCTATTCCATTACATTCAACCAAACAAAAGAATTAC
1 CTATTACGCCTCTATT-C----CATTCAACCAAACAAAAGAATTAC
*
65709676 CTATTACGCCTCTATTACATT
1 CTATTACGCCTCTATTCCATT
65709697 ACGCCTCTAT
Statistics
Matches: 56, Mismatches: 3, Indels: 13
0.78 0.04 0.18
Matches are distributed among these distances:
39 13 0.23
40 2 0.04
41 4 0.07
44 19 0.34
45 4 0.07
46 14 0.25
ACGTcount: A:0.37, C:0.30, G:0.04, T:0.29
Consensus pattern (41 bp):
CTATTACGCCTCTATTCCATTCAACCAAACAAAAGAATTAC
Found at i:65709671 original size:44 final size:46
Alignment explanation
Indices: 65709608--65709698 Score: 150
Period size: 46 Copynumber: 2.0 Consensus size: 46
65709598 ACCTCTATTC
* *
65709608 CATTCAACCAAACACAAGAA-TACC-ATTACGCCTCTATTCCATTA
1 CATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTACATTA
65709652 CATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTACATTA
1 CATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTACATTA
65709698 C
1 C
65709699 GCCTCTATTC
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
44 19 0.44
45 4 0.09
46 20 0.47
ACGTcount: A:0.40, C:0.30, G:0.04, T:0.26
Consensus pattern (46 bp):
CATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTACATTA
Found at i:65709699 original size:16 final size:16
Alignment explanation
Indices: 65709678--65709714 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
65709668 AGAATTACCT
65709678 ATTACGCCTCTATTAC
1 ATTACGCCTCTATTAC
*
65709694 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTAC
65709710 ATTAC
1 ATTAC
65709715 AGCGAACCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.24, C:0.32, G:0.05, T:0.38
Consensus pattern (16 bp):
ATTACGCCTCTATTAC
Found at i:65710766 original size:22 final size:22
Alignment explanation
Indices: 65710741--65710798 Score: 116
Period size: 22 Copynumber: 2.6 Consensus size: 22
65710731 CTAATATTTC
65710741 CTCTCAATTTCCTTCCAAAATT
1 CTCTCAATTTCCTTCCAAAATT
65710763 CTCTCAATTTCCTTCCAAAATT
1 CTCTCAATTTCCTTCCAAAATT
65710785 CTCTCAATTTCCTT
1 CTCTCAATTTCCTT
65710799 TCTTTAAAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.24, C:0.33, G:0.00, T:0.43
Consensus pattern (22 bp):
CTCTCAATTTCCTTCCAAAATT
Found at i:65711951 original size:7 final size:7
Alignment explanation
Indices: 65711939--65711963 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
65711929 AGTCGATTGA
65711939 TATTTAG
1 TATTTAG
65711946 TATTTAG
1 TATTTAG
65711953 TATTTAG
1 TATTTAG
65711960 TATT
1 TATT
65711964 ATGTATTATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (7 bp):
TATTTAG
Found at i:65712639 original size:18 final size:18
Alignment explanation
Indices: 65712613--65712647 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
65712603 AAGTGCGTTT
*
65712613 CCTAGCCCTTATATGTAC
1 CCTAACCCTTATATGTAC
65712631 CCTAACCCTTATATGTA
1 CCTAACCCTTATATGTA
65712648 TCCTTTCCCG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.31, G:0.09, T:0.34
Consensus pattern (18 bp):
CCTAACCCTTATATGTAC
Found at i:65713158 original size:25 final size:25
Alignment explanation
Indices: 65713124--65713261 Score: 173
Period size: 25 Copynumber: 5.7 Consensus size: 25
65713114 TATTTTGATA
65713124 TTATTTGATGTAATAAAATAGAAGT
1 TTATTTGATGTAATAAAATAGAAGT
65713149 TTATTTGATGTAATAAAATAGAAGT
1 TTATTTGATGTAATAAAATAGAAGT
*
65713174 TTATTTGATGTAATAAAATAGAAAT
1 TTATTTGATGTAATAAAATAGAAGT
** *
65713199 TT-TTTCGA-GT--T-ACTTTG-A-T
1 TTATTT-GATGTAATAAAATAGAAGT
65713218 ATTATTTGATGTAATAAAATAGAAGT
1 -TTATTTGATGTAATAAAATAGAAGT
65713244 TTATTTGATGTAATAAAA
1 TTATTTGATGTAATAAAA
65713262 ATCCTAACCT
Statistics
Matches: 97, Mismatches: 7, Indels: 18
0.80 0.06 0.15
Matches are distributed among these distances:
19 1 0.01
20 5 0.05
21 8 0.08
22 1 0.01
23 1 0.01
24 8 0.08
25 72 0.74
26 1 0.01
ACGTcount: A:0.41, C:0.01, G:0.14, T:0.43
Consensus pattern (25 bp):
TTATTTGATGTAATAAAATAGAAGT
Found at i:65713222 original size:95 final size:94
Alignment explanation
Indices: 65713080--65713261 Score: 303
Period size: 95 Copynumber: 1.9 Consensus size: 94
65713070 TATTTTGAAA
* *
65713080 TTATTTTATGTAAAAAAAAAAGAAATTTTTGAGTTATTTTGATATTATTTGATGTAATAAAATAG
1 TTATTTGATGTAAAAAAAAAAGAAATTTTTGAGTTACTTTGATATTATTTGATGTAATAAAATAG
65713145 AAGTTTATTTGATGTAATAAAATAGAAGT
66 AAGTTTATTTGATGTAATAAAATAGAAGT
* *
65713174 TTATTTGATGT-AATAAAATAGAAATTTTTTCGAGTTACTTTGATATTATTTGATGTAATAAAAT
1 TTATTTGATGTAAAAAAAAAAGAAA-TTTTT-GAGTTACTTTGATATTATTTGATGTAATAAAAT
65713238 AGAAGTTTATTTGATGTAATAAAA
64 AGAAGTTTATTTGATGTAATAAAA
65713262 ATCCTAACCT
Statistics
Matches: 82, Mismatches: 4, Indels: 3
0.92 0.04 0.03
Matches are distributed among these distances:
93 11 0.13
94 15 0.18
95 56 0.68
ACGTcount: A:0.42, C:0.01, G:0.14, T:0.43
Consensus pattern (94 bp):
TTATTTGATGTAAAAAAAAAAGAAATTTTTGAGTTACTTTGATATTATTTGATGTAATAAAATAG
AAGTTTATTTGATGTAATAAAATAGAAGT
Found at i:65713238 original size:45 final size:44
Alignment explanation
Indices: 65713073--65713251 Score: 164
Period size: 45 Copynumber: 3.9 Consensus size: 44
65713063 TTTTGAATAT
* * * * *
65713073 TTTGAAATTATTTTATGTAAAAAAAAAAGAAA-TTTTTGAGTTAT
1 TTTGATATTATTTGATGT-AATAAAATAGAAATTTTTTGAGTTAA
*
65713117 TTTGATATTATTTGATGTAATAAAATAGAAGTTTATTTGATGTAATAAA
1 TTTGATATTATTTGATGTAATAAAATAGAAATTT-TTTGA-GT--T-AA
* * *
65713166 ATAGA-AGTTTATTTGATGTAATAAAATAGAAATTTTTTCGAGTTAC
1 TTTGATA--TTATTTGATGTAATAAAATAGAAATTTTTT-GAGTTAA
*
65713212 TTTGATATTATTTGATGTAATAAAATAGAAGTTTATTTGA
1 TTTGATATTATTTGATGTAATAAAATAGAAATTT-TTTGA
65713252 TGTAATAAAA
Statistics
Matches: 111, Mismatches: 13, Indels: 21
0.77 0.09 0.14
Matches are distributed among these distances:
43 10 0.09
44 18 0.16
45 33 0.30
46 9 0.08
47 2 0.02
48 2 0.02
49 9 0.08
50 28 0.25
ACGTcount: A:0.41, C:0.01, G:0.14, T:0.44
Consensus pattern (44 bp):
TTTGATATTATTTGATGTAATAAAATAGAAATTTTTTGAGTTAA
Found at i:65713309 original size:23 final size:23
Alignment explanation
Indices: 65713257--65713571 Score: 232
Period size: 23 Copynumber: 13.6 Consensus size: 23
65713247 TTTGATGTAA
* *
65713257 TAAAAATCCTAACCTAATTTAAC
1 TAAAAACCCTAACCTAATTTAAT
*** *
65713280 CCTAAACCTTAACCTAATTTAAT
1 TAAAAACCCTAACCTAATTTAAT
65713303 TAAAAACCCTAACCCTAACCTAATTTAAT
1 T--AAA----AACCCTAACCTAATTTAAT
65713332 TAAAAACCCTAACCTAATTTAA-
1 TAAAAACCCTAACCTAATTTAAT
65713354 TACAAAACCCTAACCTAATTTAAT
1 TA-AAAACCCTAACCTAATTTAAT
*
65713378 TAAAAATCCTAAACC----TTAACT
1 TAAAAACCCT-AACCTAATTTAA-T
*
65713399 TAAAAACCCTAAACCTTAA-CT--T
1 TAAAAACCCT-AACC-TAATTTAAT
65713421 TAAAAACCCTAACCTAATTTAA-
1 TAAAAACCCTAACCTAATTTAAT
65713443 TACAAAACCCTAACCTAATTTAAT
1 TA-AAAACCCTAACCTAATTTAAT
65713467 TAAAAACCCTAAACC----TTAACT
1 TAAAAACCCT-AACCTAATTTAA-T
* *
65713488 TAAAAACTCTAAACCTTAA-CT--T
1 TAAAAACCCT-AACC-TAATTTAAT
65713510 TAAAAACCCTAACCTAATTTAA-
1 TAAAAACCCTAACCTAATTTAAT
**
65713532 TACAAAACCCTAACCTAAACCCTAAT
1 TA-AAAACCCTAACCT-AA-TTTAAT
65713558 TAAAAACCCTAACC
1 TAAAAACCCTAACC
65713572 CTAACCTAAT
Statistics
Matches: 240, Mismatches: 20, Indels: 62
0.75 0.06 0.19
Matches are distributed among these distances:
20 14 0.06
21 40 0.17
22 27 0.11
23 103 0.43
24 14 0.06
25 18 0.08
26 2 0.01
27 3 0.01
29 19 0.08
ACGTcount: A:0.47, C:0.26, G:0.00, T:0.27
Consensus pattern (23 bp):
TAAAAACCCTAACCTAATTTAAT
Found at i:65713323 original size:29 final size:29
Alignment explanation
Indices: 65713277--65713345 Score: 120
Period size: 29 Copynumber: 2.3 Consensus size: 29
65713267 AACCTAATTT
*
65713277 AACCCTAAACCTTAACCTAATTTAATTAAA
1 AACCCT-AACCCTAACCTAATTTAATTAAA
65713307 AACCCTAACCCTAACCTAATTTAATTAAA
1 AACCCTAACCCTAACCTAATTTAATTAAA
65713336 AACCCTAACC
1 AACCCTAACC
65713346 TAATTTAATA
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
29 32 0.84
30 6 0.16
ACGTcount: A:0.45, C:0.29, G:0.00, T:0.26
Consensus pattern (29 bp):
AACCCTAACCCTAACCTAATTTAATTAAA
Found at i:65713368 original size:29 final size:28
Alignment explanation
Indices: 65713277--65713368 Score: 104
Period size: 29 Copynumber: 3.4 Consensus size: 28
65713267 AACCTAATTT
*
65713277 AACCCTAAACCTTAACCTAATTTAATTAAA
1 AACCCT-AACCCTAACCTAATTTAA-TAAA
*
65713307 AACCCTAACCCTAACCTAATTTAAT-TA
1 AACCCTAACCCTAACCTAATTTAATAAA
65713334 AA----AACCCTAACCTAATTTAATACAA
1 AACCCTAACCCTAACCTAATTTAATA-AA
65713359 AACCCTAACC
1 AACCCTAACC
65713369 TAATTTAATT
Statistics
Matches: 53, Mismatches: 3, Indels: 13
0.77 0.04 0.19
Matches are distributed among these distances:
23 19 0.36
25 3 0.06
27 3 0.06
28 1 0.02
29 21 0.40
30 6 0.11
ACGTcount: A:0.46, C:0.28, G:0.00, T:0.26
Consensus pattern (28 bp):
AACCCTAACCCTAACCTAATTTAATAAA
Found at i:65713403 original size:21 final size:21
Alignment explanation
Indices: 65713373--65713521 Score: 146
Period size: 21 Copynumber: 6.9 Consensus size: 21
65713363 CTAACCTAAT
*
65713373 TTAA-TTAAAAATCCTAAACC
1 TTAACTTAAAAACCCTAAACC
65713393 TTAACTTAAAAACCCTAAACC
1 TTAACTTAAAAACCCTAAACC
65713414 TTAACTTTAAAAACCCT-AACC
1 TTAAC-TTAAAAACCCTAAACC
*
65713435 -TAATTTAATACAAAACCCT-AACC
1 TTAA-CT--TA-AAAACCCTAAACC
65713458 TAATTTAA-TTAAAAACCCTAAACC
1 ----TTAACTTAAAAACCCTAAACC
*
65713482 TTAACTTAAAAACTCTAAACC
1 TTAACTTAAAAACCCTAAACC
65713503 TTAACTTTAAAAACCCTAA
1 TTAAC-TTAAAAACCCTAA
65713522 CCTAATTTAA
Statistics
Matches: 111, Mismatches: 4, Indels: 26
0.79 0.03 0.18
Matches are distributed among these distances:
20 12 0.11
21 44 0.40
22 25 0.23
23 20 0.18
24 6 0.05
26 1 0.01
28 3 0.03
ACGTcount: A:0.48, C:0.24, G:0.00, T:0.28
Consensus pattern (21 bp):
TTAACTTAAAAACCCTAAACC
Found at i:65713434 original size:89 final size:89
Alignment explanation
Indices: 65713331--65713569 Score: 424
Period size: 89 Copynumber: 2.7 Consensus size: 89
65713321 CCTAATTTAA
*
65713331 TTAAAAACCCTAACCTAATTTAATACAAAACCCTAACCTAATTTAATTAAAAATCCTAAACCTTA
1 TTAAAAACCCTAACCTAATTTAATACAAAACCCTAACCTAATTTAATTAAAAACCCTAAACCTTA
65713396 ACTTAAAAACCCTAAACCTTAACT
66 ACTTAAAAACCCTAAACCTTAACT
65713420 TTAAAAACCCTAACCTAATTTAATACAAAACCCTAACCTAATTTAATTAAAAACCCTAAACCTTA
1 TTAAAAACCCTAACCTAATTTAATACAAAACCCTAACCTAATTTAATTAAAAACCCTAAACCTTA
*
65713485 ACTTAAAAACTCTAAACCTTAACT
66 ACTTAAAAACCCTAAACCTTAACT
**
65713509 TTAAAAACCCTAACCTAATTTAATACAAAACCCTAACCTAAACCCTAATTAAAAACCCTAA
1 TTAAAAACCCTAACCTAATTTAATACAAAACCCTAACCT-AA-TTTAATTAAAAACCCTAA
65713570 CCCTAACCTA
Statistics
Matches: 144, Mismatches: 4, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
89 126 0.88
90 2 0.01
91 16 0.11
ACGTcount: A:0.48, C:0.26, G:0.00, T:0.27
Consensus pattern (89 bp):
TTAAAAACCCTAACCTAATTTAATACAAAACCCTAACCTAATTTAATTAAAAACCCTAAACCTTA
ACTTAAAAACCCTAAACCTTAACT
Found at i:65713478 original size:112 final size:111
Alignment explanation
Indices: 65713313--65713571 Score: 327
Period size: 112 Copynumber: 2.3 Consensus size: 111
65713303 TAAAAACCCT
65713313 AACCCTAACCTAATTTAATTAAAAACCCTAACCTAATTTAATACAAAACCCT-AACCTAATTTAA
1 AACCCTAACCTAATTTAATTAAAAACCCTAACCTAATTTAATACAAAACCCTAAACC----TTAA
65713377 -TTAAAAA-TCCTAAACCTTAAC-TTAAAAACCCTAAACCTTAACTT-TA-AA
62 CTTAAAAACT-CTAAACCTTAACTTTAAAAACCCT-AACC-TAACTTATACAA
65713425 AACCCTAACCTAATTTAA-TACAAAACCCTAACCTAATTTAATTA-AAAACCCTAAACCTTAACT
1 AACCCTAACCTAATTTAATTA-AAAACCCTAACCTAATTTAA-TACAAAACCCTAAACCTTAACT
*
65713488 TAAAAACTCTAAACCTTAACTTTAAAAACCCTAACCTAATTTAATACAA
64 TAAAAACTCTAAACCTTAACTTTAAAAACCCTAACCTAACTT-ATACAA
**
65713537 AACCCTAACCTAAACCCTAATTAAAAACCCTAACC
1 AACCCTAACCT-AA-TTTAATTAAAAACCCTAACC
65713572 CTAACCTAAT
Statistics
Matches: 132, Mismatches: 3, Indels: 22
0.84 0.02 0.14
Matches are distributed among these distances:
109 9 0.07
110 23 0.17
111 16 0.12
112 59 0.45
113 8 0.06
114 15 0.11
115 2 0.02
ACGTcount: A:0.47, C:0.26, G:0.00, T:0.27
Consensus pattern (111 bp):
AACCCTAACCTAATTTAATTAAAAACCCTAACCTAATTTAATACAAAACCCTAAACCTTAACTTA
AAAACTCTAAACCTTAACTTTAAAAACCCTAACCTAACTTATACAA
Found at i:65713541 original size:66 final size:67
Alignment explanation
Indices: 65713313--65713576 Score: 246
Period size: 66 Copynumber: 3.9 Consensus size: 67
65713303 TAAAAACCCT
* *
65713313 AACCCTAACCTAATTTAATTAAAAACCCT-AACC-TAATTTAATACAAAACCCTAACCTAATTTA
1 AACCCTAACCTAATTTAATTAAAAACCCTAAACCTTAACTT--TA-AAAACCCTAACCTAACTT-
65713376 ATTA-AA
62 A-TACAA
* *
65713382 AATCCTAAACC----TTAACTTAAAAACCCTAAACCTTAACTTTAAAAACCCTAACCTAATTTAA
1 AACCCT-AACCTAATTTAA-TTAAAAACCCTAAACCTTAACTTTAAAAACCCTAACCTAACTT-A
65713443 TACAA
63 TACAA
*
65713448 AACCCTAACCTAATTTAATTAAAAACCCTAAACCTTAAC-TTAAAAACTCTAAACCTTAACTT-T
1 AACCCTAACCTAATTTAATTAAAAACCCTAAACCTTAACTTTAAAAACCCT-AACC-TAACTTAT
65713511 A-AA
64 ACAA
*
65713514 AACCCTAACCTAATTTAA-TACAAAACCCT-AACCTAAACCCTAATTAAAAACCCTAACCCTAAC
1 AACCCTAACCTAATTTAATTA-AAAACCCTAAACCTTAA--CT--TTAAAAACCCTAA-CCTAAC
65713577 CTAATTTAAT
Statistics
Matches: 170, Mismatches: 7, Indels: 36
0.80 0.03 0.17
Matches are distributed among these distances:
65 15 0.09
66 59 0.35
67 26 0.15
68 29 0.17
69 25 0.15
70 16 0.09
ACGTcount: A:0.47, C:0.27, G:0.00, T:0.27
Consensus pattern (67 bp):
AACCCTAACCTAATTTAATTAAAAACCCTAAACCTTAACTTTAAAAACCCTAACCTAACTTATAC
AA
Found at i:65713552 original size:29 final size:29
Alignment explanation
Indices: 65713514--65713906 Score: 541
Period size: 29 Copynumber: 13.6 Consensus size: 29
65713504 TAACTTTAAA
65713514 AACCCTAACCTAATTTAA-TACAAAACCCT
1 AACCCTAACCTAATTTAATTA-AAAACCCT
*
65713543 AA-CCTAAACC----CTAATTAAAAACCCT
1 AACCCT-AACCTAATTTAATTAAAAACCCT
*
65713568 AACCCTAACCTAATTTAATTAAAGACCCT
1 AACCCTAACCTAATTTAATTAAAAACCCT
* *
65713597 AACCCTAACCAAATTTAATTAAAGACCCT
1 AACCCTAACCTAATTTAATTAAAAACCCT
* * *
65713626 AACCCTAATCTAAATTAATTAAAGACCCT
1 AACCCTAACCTAATTTAATTAAAAACCCT
65713655 AACCCTAACCTAATTTAATTAAAAACCCT
1 AACCCTAACCTAATTTAATTAAAAACCCT
*
65713684 AACCTAATTAACCT-ATATTAATTAAAAACCCT
1 AACC---CTAACCTAAT-TTAATTAAAAACCCT
*
65713716 AACCCTAATCTAATTTAATTAAAAACCCT
1 AACCCTAACCTAATTTAATTAAAAACCCT
*
65713745 AACCCTAACCTAATTTAATTAAAAACCTT
1 AACCCTAACCTAATTTAATTAAAAACCCT
*
65713774 AACCCTAACCTAATTTAATTAAAAAACCT
1 AACCCTAACCTAATTTAATTAAAAACCCT
*
65713803 ACCCCTAACCTAATTTAATTAAAAACCCT
1 AACCCTAACCTAATTTAATTAAAAACCCT
*
65713832 AACCCTAACATAATTTAATTAAAAACCCT
1 AACCCTAACCTAATTTAATTAAAAACCCT
65713861 AACCCTAACCTAATTTAATTAAAAACCCT
1 AACCCTAACCTAATTTAATTAAAAACCCT
**
65713890 AA-CCTAAATTAATTTAA
1 AACCCTAACCTAATTTAA
65713907 AACCCTAAAC
Statistics
Matches: 328, Mismatches: 24, Indels: 25
0.87 0.06 0.07
Matches are distributed among these distances:
25 17 0.05
26 5 0.02
28 16 0.05
29 261 0.80
30 2 0.01
31 2 0.01
32 25 0.08
ACGTcount: A:0.46, C:0.26, G:0.01, T:0.28
Consensus pattern (29 bp):
AACCCTAACCTAATTTAATTAAAAACCCT
Found at i:65713919 original size:23 final size:23
Alignment explanation
Indices: 65713805--65713924 Score: 96
Period size: 29 Copynumber: 4.7 Consensus size: 23
65713795 AAAAACCTAC
*
65713805 CCCTAACCTAATTTAATTAAAAA
1 CCCTAACCTAAATTAATTAAAAA
65713828 CCCTAACCCTAACATAATTTAATTAAAAA
1 CCCTAA-CCT---A-AA-TTAATTAAAAA
65713857 CCCTAACCCTAACCTAATTTAATTAAAAA
1 CCCTAA-CCT-A---AA-TTAATTAAAAA
*
65713886 CCCTAACCTAAATTAATTTAAAA
1 CCCTAACCTAAATTAATTAAAAA
* *
65713909 CCCTAAACTAAGTTAA
1 CCCTAACCTAAATTAA
65713925 CAATGTTACA
Statistics
Matches: 84, Mismatches: 5, Indels: 16
0.80 0.05 0.15
Matches are distributed among these distances:
23 30 0.36
24 5 0.06
27 3 0.04
28 4 0.05
29 42 0.50
ACGTcount: A:0.47, C:0.24, G:0.01, T:0.28
Consensus pattern (23 bp):
CCCTAACCTAAATTAATTAAAAA
Found at i:65714075 original size:116 final size:116
Alignment explanation
Indices: 65713921--65714274 Score: 645
Period size: 116 Copynumber: 3.1 Consensus size: 116
65713911 CTAAACTAAG
* * * * *
65713921 TTAACAATGTTACATTCACGTAATGTCAGATTTGGAAAAATGTTTTGACTGGTACTAACAATTAA
1 TTAATAATTTTACATTCACATAATGTTAGATTTGGAAAAATGTTTTGATTGGTACTAACAATTAA
65713986 TAATTTTACATAATTTGATAATTTTACTAACCATTAATACAATTTTTTGAC
66 TAATTTTACATAATTTGATAATTTTACTAACCATTAATACAATTTTTTGAC
*
65714037 TTAATAATTTTGCATTCACATAATGTTAGATTTGGAAAAATGTTTTGATTGGTACTAACAATTAA
1 TTAATAATTTTACATTCACATAATGTTAGATTTGGAAAAATGTTTTGATTGGTACTAACAATTAA
65714102 TAATTTTACATAATTTGATAATTTTACTAACCATTAATACAATTTTTTGAC
66 TAATTTTACATAATTTGATAATTTTACTAACCATTAATACAATTTTTTGAC
65714153 TTAATAATTTTACATTCACATAATGTTAGATTTGGAAAAATGTTTTGATTGGTACTAACAATTAA
1 TTAATAATTTTACATTCACATAATGTTAGATTTGGAAAAATGTTTTGATTGGTACTAACAATTAA
*
65714218 TAATTTTATATAATTTGATAATTTTACTAACCATTAATACAATTTTTTGAC
66 TAATTTTACATAATTTGATAATTTTACTAACCATTAATACAATTTTTTGAC
65714269 TTAATA
1 TTAATA
65714275 CAATTTATCA
Statistics
Matches: 230, Mismatches: 8, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
116 230 1.00
ACGTcount: A:0.38, C:0.10, G:0.09, T:0.43
Consensus pattern (116 bp):
TTAATAATTTTACATTCACATAATGTTAGATTTGGAAAAATGTTTTGATTGGTACTAACAATTAA
TAATTTTACATAATTTGATAATTTTACTAACCATTAATACAATTTTTTGAC
Found at i:65714291 original size:17 final size:18
Alignment explanation
Indices: 65714250--65714291 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
65714240 TTTACTAACC
* *
65714250 ATTAATACAATTTTTTGA
1 ATTAATACAATTTTATCA
*
65714268 CTTAATACAA-TTTATCA
1 ATTAATACAATTTTATCA
65714285 ATTAATA
1 ATTAATA
65714292 ATTTCACAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.43, C:0.10, G:0.02, T:0.45
Consensus pattern (18 bp):
ATTAATACAATTTTATCA
Found at i:65717671 original size:125 final size:123
Alignment explanation
Indices: 65717304--65717655 Score: 535
Period size: 125 Copynumber: 2.8 Consensus size: 123
65717294 CCCAAACATG
* *
65717304 CTACTGTAGCAAAAGCGCGTCCACGAAGGCGTGATTTCACAAATTCTTCTCAAATAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
*
65717369 TAGAAGCGATTTTATACTATTTGCTCAAAAACGTCGAAAAAAATTTATTTCTTACATGAC
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTC-AAAAAAA-TTATTTCTTACATGAC
* * *
65717429 CTACTGTAGCAAAAGCACGTCCACGAGGCCGCGATTTCACAAATTCTTCTCAAATAGCATCCTAC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
** * *
65717494 TAGAAGCGATTTTATACTATTTGCTCAGAAATATAAAAAAATAATTATTTCTT-CTGTGAC
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACGT-CAAAAA-AATTATTTCTTAC-ATGAC
*
65717554 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATATAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
**
65717619 TAGAAGCGATTTTATACTATTTTATCAGAAACGTCAA
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAA
65717656 CTCGAAATTA
Statistics
Matches: 205, Mismatches: 19, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
124 3 0.01
125 200 0.98
126 2 0.01
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.30
Consensus pattern (123 bp):
CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAATTATTTCTTACATGAC
Found at i:65718935 original size:17 final size:17
Alignment explanation
Indices: 65718913--65718946 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
65718903 ATATTTATCA
65718913 ATAAAATAAAAATAATT
1 ATAAAATAAAAATAATT
65718930 ATAAAATAAAAATAATT
1 ATAAAATAAAAATAATT
65718947 TTTTTAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
ATAAAATAAAAATAATT
Found at i:65719889 original size:347 final size:348
Alignment explanation
Indices: 65719253--65719908 Score: 1278
Period size: 347 Copynumber: 1.9 Consensus size: 348
65719243 CCTTTTTCCG
65719253 GGAAATCACGTCCACGTCAGCGCGACTTGCTGACTTGGACGCGATTTCCTGGCACCACGTATCAT
1 GGAAATCACGTCCACGTCAGCGCGACTTGCTGACTTGGACGCGATTTCCTGGCACCACGTATCAT
65719318 GTTCCGGGGGACGCGATTTTGCCGATTTTCCCACGTTATGTTTTTTTGGCTTTTAGGGTTTAGGG
66 GTTCCGGGGGACGCGATTTTGCCGATTTTCCCACGTTATGTTTTTTTGGCTTTTAGGGTTTAGGG
*
65719383 TTAAGACTTTTTAGTGTTTTTAGGTCCTGGAATAAATAATTTCGAGTTGACGTTTCTGATCAAAT
131 TTAAGACTTTTTAGTGTTTTTAGGTCCTCGAATAAATAATTTCGAGTTGACGTTTCTGATCAAAT
65719448 AGTATAAAATCACTTCTAGCAAGATGCTATTTGAGAAGAATTTATGAAATCACGCCCTCGTGGAC
196 AGTATAAAATCACTTCTAGCAAGATGCTATTTGAGAAGAATTTATGAAATCACGCCCTCGTGGAC
65719513 GCGCTTTTGCTACAGTAGGTCACGGAAGAAATAATTATTTTTTTGACGTAATCACGTCCACGTCA
261 GCGCTTTTGCTACAGTAGGTCACGGAAGAAATAATTATTTTTTTGACGTAATCACGTCCACGTCA
65719578 GCGCGATGTCAGGGTATGCGCCA
326 GCGCGATGTCAGGGTATGCGCCA
*
65719601 GGAAATCGCGTCCACGTCAGCGCGACTTGCTGACTTGGACGCGATTTCCTGGCACCACGTATCAT
1 GGAAATCACGTCCACGTCAGCGCGACTTGCTGACTTGGACGCGATTTCCTGGCACCACGTATCAT
65719666 GTTCCGGGGGACGCGATTTTGCCGATTTTCCCACGTTATG-TTTTTTGGCTTTTAGGGTTTAGGG
66 GTTCCGGGGGACGCGATTTTGCCGATTTTCCCACGTTATGTTTTTTTGGCTTTTAGGGTTTAGGG
65719730 TTAAGACTTTTTAGTGTTTTTAGGTCCTCGAATAAATAATTTCGAGTTGACGTTTCTGATCAAAT
131 TTAAGACTTTTTAGTGTTTTTAGGTCCTCGAATAAATAATTTCGAGTTGACGTTTCTGATCAAAT
*
65719795 AGTATAAAATCGCTTCTAGCAAGATGCTATTTGAGAAGAATTTATGAAATCACGCCCTCGTGGAC
196 AGTATAAAATCACTTCTAGCAAGATGCTATTTGAGAAGAATTTATGAAATCACGCCCTCGTGGAC
65719860 GCGCTTTTGCTACAGTAGGTCACGGAAGAAATAATTATTTTTTTGACGT
261 GCGCTTTTGCTACAGTAGGTCACGGAAGAAATAATTATTTTTTTGACGT
65719909 TTTTGAGCAA
Statistics
Matches: 305, Mismatches: 3, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
347 201 0.66
348 104 0.34
ACGTcount: A:0.24, C:0.19, G:0.23, T:0.33
Consensus pattern (348 bp):
GGAAATCACGTCCACGTCAGCGCGACTTGCTGACTTGGACGCGATTTCCTGGCACCACGTATCAT
GTTCCGGGGGACGCGATTTTGCCGATTTTCCCACGTTATGTTTTTTTGGCTTTTAGGGTTTAGGG
TTAAGACTTTTTAGTGTTTTTAGGTCCTCGAATAAATAATTTCGAGTTGACGTTTCTGATCAAAT
AGTATAAAATCACTTCTAGCAAGATGCTATTTGAGAAGAATTTATGAAATCACGCCCTCGTGGAC
GCGCTTTTGCTACAGTAGGTCACGGAAGAAATAATTATTTTTTTGACGTAATCACGTCCACGTCA
GCGCGATGTCAGGGTATGCGCCA
Found at i:65720090 original size:125 final size:125
Alignment explanation
Indices: 65719750--65720128 Score: 546
Period size: 126 Copynumber: 3.0 Consensus size: 125
65719740 TTAGTGTTTT
* * *
65719750 TAGGTCCTC-GAATAAATAATTTCGAGTTGACGTTTCTGATCAAATAGTATAAAATCGCTTCTAG
1 TAGGTCC-CGGAAGAAATAATTTTGAGTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAG
* *
65719814 CAAGATGCTATTTGAGAAGAATTTATGAAATCACGCCCTCGTGGACGCGCTTTTGCTACAG
65 CAAGATGCTATTTGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAG
* *** * *
65719875 TAGGTCACGGAAGAAATAATTATTTTTTTGACGTTTTTGAGCAAATAGTATAAAATCGCTTGTAG
1 TAGGTCCCGGAAGAAATAATT-TTGAGTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAG
* *
65719940 CAAGATGCTATTTGAGAAGAATTTGTGATATCGCGCCCTCGTGGATGCGCTTTTGCTACAG
65 CAAGATGCTATTTGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAG
* * *
65720001 TAGGTCCCGGAAGAAATAATTTTGAGTTGACATTTCTGAGCAAATAGTGTAAAATCGCTTCTCGC
1 TAGGTCCCGGAAGAAATAATTTTGAGTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGC
* * *
65720066 AGGATGCTATTTGAGAA-AATTTTGTGAAATCGCGCCATCGTGGACGCGTTTTTGCTACAG
66 AAGATGCTATTTGAGAAGAA-TTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAG
65720126 TAG
1 TAG
65720129 CATGTTTGGG
Statistics
Matches: 224, Mismatches: 27, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
124 3 0.01
125 108 0.48
126 113 0.50
ACGTcount: A:0.29, C:0.16, G:0.22, T:0.32
Consensus pattern (125 bp):
TAGGTCCCGGAAGAAATAATTTTGAGTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGC
AAGATGCTATTTGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAG
Found at i:65723391 original size:23 final size:23
Alignment explanation
Indices: 65723356--65723467 Score: 80
Period size: 23 Copynumber: 4.6 Consensus size: 23
65723346 CATTGTTAAC
* * *
65723356 TTAGTTTAGGGTTTTTAAATAAT
1 TTAGGTTAGGGTTTTGAAATAAA
* *
65723379 TTAGGTTAAGGTTTTGAATTAAA
1 TTAGGTTAGGGTTTTGAAATAAA
* *
65723402 TTAGGTTAGGGTTAGGGTCTTTAATTAAA
1 TTAGGTTAGGG-T----T-TTGAAATAAA
* *
65723431 TTAGGATTAGGGTTTTTAATTAAA
1 TTAGG-TTAGGGTTTTGAAATAAA
65723455 TTAGGTTAGGGTT
1 TTAGGTTAGGGTT
65723468 AGGGTATTTA
Statistics
Matches: 75, Mismatches: 7, Indels: 14
0.78 0.07 0.15
Matches are distributed among these distances:
23 36 0.48
24 16 0.21
25 1 0.01
28 1 0.01
29 15 0.20
30 6 0.08
ACGTcount: A:0.29, C:0.01, G:0.24, T:0.46
Consensus pattern (23 bp):
TTAGGTTAGGGTTTTGAAATAAA
Found at i:65723427 original size:29 final size:29
Alignment explanation
Indices: 65723382--65723568 Score: 194
Period size: 29 Copynumber: 6.6 Consensus size: 29
65723372 AAATAATTTA
* *
65723382 GGTTAAGGTTTTGAATTAAATTAGGTTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
*
65723411 GGTTAGGGTCTTTAATTAAATTAGG--A-
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
65723437 --TTAGGGTTTTTAATTAAATTAGGTTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
* * *
65723464 GGTTAGGGTATTTAATT--A-GAGTTTA-
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
*
65723489 GGTTAGGGTTTTTAATAAAATTAGGATTAG
1 GGTTAGGGTTTTTAATTAAATTAGG-TTAG
*
65723519 GGTTTTTAAGGTTTTTAATTAAATTAGGTTAG
1 GG---TTAGGGTTTTTAATTAAATTAGGTTAG
*
65723551 GGTTAGGGTATTTAATTA
1 GGTTAGGGTTTTTAATTA
65723569 GGATTAGGGT
Statistics
Matches: 130, Mismatches: 15, Indels: 26
0.76 0.09 0.15
Matches are distributed among these distances:
24 22 0.17
25 15 0.12
26 6 0.05
27 3 0.02
28 2 0.02
29 53 0.41
30 2 0.02
32 6 0.05
33 21 0.16
ACGTcount: A:0.30, C:0.01, G:0.26, T:0.44
Consensus pattern (29 bp):
GGTTAGGGTTTTTAATTAAATTAGGTTAG
Found at i:65723434 original size:24 final size:25
Alignment explanation
Indices: 65723361--65723527 Score: 130
Period size: 24 Copynumber: 6.5 Consensus size: 25
65723351 TTAACTTAGT
*
65723361 TTAGGGTTTTTAAATAAT-TTA-GG
1 TTAGGGTTTTTAATTAATATTAGGG
* *
65723384 TTAAGGTTTTGAATTAAATTAGGTTAGGG
1 TTAGGGTTTTTAATT-AA-TA--TTAGGG
* *
65723413 TTAGGGTCTTTAATTAA-ATTAGGA
1 TTAGGGTTTTTAATTAATATTAGGG
65723437 TTAGGGTTTTTAATTAAATTAGGTTAGGG
1 TTAGGGTTTTTAATT-AA-TA--TTAGGG
*
65723466 TTAGGGTATTTAATTAGAGT-TTA-GG
1 TTAGGGTTTTTAATTA-A-TATTAGGG
* *
65723491 TTAGGGTTTTTAA-TAAAATTAGGA
1 TTAGGGTTTTTAATTAATATTAGGG
65723515 TTAGGGTTTTTAA
1 TTAGGGTTTTTAA
65723528 GGTTTTTAAT
Statistics
Matches: 116, Mismatches: 14, Indels: 27
0.74 0.09 0.17
Matches are distributed among these distances:
23 16 0.14
24 37 0.32
25 17 0.15
26 4 0.03
27 1 0.01
28 6 0.05
29 35 0.30
ACGTcount: A:0.31, C:0.01, G:0.25, T:0.44
Consensus pattern (25 bp):
TTAGGGTTTTTAATTAATATTAGGG
Found at i:65723458 original size:53 final size:52
Alignment explanation
Indices: 65723361--65723554 Score: 244
Period size: 53 Copynumber: 3.6 Consensus size: 52
65723351 TTAACTTAGT
* * * *
65723361 TTAGGGTTTTTAAATAATTTAGGTTAAGGTTTTGAATTAAATTAGGTTAGGG
1 TTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGG
*
65723413 TTAGGGTCTTTAATTAAATTAGGATTAGGGTTTTTAATTAAATTAGGTTAGGG
1 TTAGGGTTTTTAATTAAATTAGG-TTAGGGTTTTTAATTAAATTAGGTTAGGG
* * *
65723466 TTAGGGTATTTAATTAGAGTTTAGGTTAGGGTTTTTAATAAAATTAGGATTAGGG
1 TTAGGGTTTTTAATTA-A-ATTAGGTTAGGGTTTTTAATTAAATTAGG-TTAGGG
*
65723521 TTTTTAAGGTTTTTAATTAAATTAGGTTAGGGTT
1 ---TTAGGGTTTTTAATTAAATTAGGTTAGGGTT
65723555 AGGGTATTTA
Statistics
Matches: 124, Mismatches: 11, Indels: 10
0.86 0.08 0.07
Matches are distributed among these distances:
52 20 0.16
53 42 0.34
54 23 0.19
55 11 0.09
56 13 0.10
57 1 0.01
58 14 0.11
ACGTcount: A:0.30, C:0.01, G:0.25, T:0.45
Consensus pattern (52 bp):
TTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGG
Found at i:65723575 original size:19 final size:19
Alignment explanation
Indices: 65723547--65723589 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
65723537 TTAAATTAGG
*
65723547 TTAGGGTTAGGGTATTTAA
1 TTAGGATTAGGGTATTTAA
*
65723566 TTAGGATTAGGGTTTTTAA
1 TTAGGATTAGGGTATTTAA
65723585 TTAGG
1 TTAGG
65723590 GTTTTTAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.26, C:0.00, G:0.30, T:0.44
Consensus pattern (19 bp):
TTAGGATTAGGGTATTTAA
Found at i:65723587 original size:13 final size:13
Alignment explanation
Indices: 65723571--65723613 Score: 77
Period size: 13 Copynumber: 3.3 Consensus size: 13
65723561 TTTAATTAGG
65723571 ATTAGGGTTTTTA
1 ATTAGGGTTTTTA
65723584 ATTAGGGTTTTTA
1 ATTAGGGTTTTTA
*
65723597 ATTAGGGTTTTGA
1 ATTAGGGTTTTTA
65723610 ATTA
1 ATTA
65723614 ATTTAGGTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
13 29 1.00
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.51
Consensus pattern (13 bp):
ATTAGGGTTTTTA
Found at i:65723607 original size:12 final size:12
Alignment explanation
Indices: 65723571--65723675 Score: 66
Period size: 12 Copynumber: 8.1 Consensus size: 12
65723561 TTTAATTAGG
65723571 ATTAGGGTTTTTA
1 ATTAGGG-TTTTA
65723584 ATTAGGGTTTTTA
1 ATTAGGG-TTTTA
65723597 ATTAGGGTTTTGA
1 ATTAGGGTTTT-A
* **
65723610 ATTAATTTAGGTTTGG
1 ATT-A---GGGTTTTA
* ***
65723626 GTTAGGGTTAGG
1 ATTAGGGTTTTA
*
65723638 GTTAGGGTTTTTA
1 ATTAGGG-TTTTA
65723651 ATTAGGGTTTTA
1 ATTAGGGTTTTA
65723663 ATTAGGGTTTTA
1 ATTAGGGTTTTA
65723675 A
1 A
65723676 ATTAATTTAG
Statistics
Matches: 76, Mismatches: 10, Indels: 13
0.77 0.10 0.13
Matches are distributed among these distances:
12 35 0.46
13 32 0.42
14 1 0.01
15 1 0.01
16 2 0.03
17 5 0.07
ACGTcount: A:0.23, C:0.00, G:0.29, T:0.49
Consensus pattern (12 bp):
ATTAGGGTTTTA
Found at i:65723657 original size:13 final size:13
Alignment explanation
Indices: 65723639--65723679 Score: 66
Period size: 13 Copynumber: 3.2 Consensus size: 13
65723629 AGGGTTAGGG
65723639 TTAGGGTTTTTAA
1 TTAGGGTTTTTAA
65723652 TTAGGG-TTTTAA
1 TTAGGGTTTTTAA
*
65723664 TTAGGGTTTTAAA
1 TTAGGGTTTTTAA
65723677 TTA
1 TTA
65723680 ATTTAGGTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
12 12 0.46
13 14 0.54
ACGTcount: A:0.27, C:0.00, G:0.22, T:0.51
Consensus pattern (13 bp):
TTAGGGTTTTTAA
Found at i:65723715 original size:28 final size:28
Alignment explanation
Indices: 65723664--65723728 Score: 103
Period size: 28 Copynumber: 2.3 Consensus size: 28
65723654 AGGGTTTTAA
65723664 TTAGGGTTTTAAATTAATTTAGGTTAGGG
1 TTAGGG-TTTAAATTAATTTAGGTTAGGG
* *
65723693 TTAGGGTTTGAATTAATTTAGGTTATGG
1 TTAGGGTTTAAATTAATTTAGGTTAGGG
65723721 TTAGGGTT
1 TTAGGGTT
65723729 AGGGTTTTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
28 28 0.82
29 6 0.18
ACGTcount: A:0.25, C:0.00, G:0.29, T:0.46
Consensus pattern (28 bp):
TTAGGGTTTAAATTAATTTAGGTTAGGG
Found at i:65723804 original size:13 final size:13
Alignment explanation
Indices: 65723788--65723822 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
65723778 GGATTAGGGT
*
65723788 TTAGGGTTTTTAA
1 TTAGGGTTTTGAA
*
65723801 TTAGAGTTTTGAA
1 TTAGGGTTTTGAA
65723814 TTAGGGTTT
1 TTAGGGTTT
65723823 AGGTTATGGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.23, C:0.00, G:0.26, T:0.51
Consensus pattern (13 bp):
TTAGGGTTTTGAA
Found at i:65723851 original size:18 final size:18
Alignment explanation
Indices: 65723814--65723851 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
65723804 GAGTTTTGAA
*
65723814 TTAGGGTTTAGGTTATGG
1 TTAGGGTTTAGGTTAGGG
65723832 TTAGGG-TTAGGTTTAGGG
1 TTAGGGTTTAGG-TTAGGG
65723850 TT
1 TT
65723852 TTTAATTAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.16, C:0.00, G:0.39, T:0.45
Consensus pattern (18 bp):
TTAGGGTTTAGGTTAGGG
Found at i:65733667 original size:19 final size:19
Alignment explanation
Indices: 65733645--65733691 Score: 67
Period size: 19 Copynumber: 2.5 Consensus size: 19
65733635 ATTGGAACGT
* *
65733645 AAAGTGCATATTGGCGCAC
1 AAAGTGCATACTGGCACAC
*
65733664 AAAGCGCATACTGGCACAC
1 AAAGTGCATACTGGCACAC
65733683 AAAGTGCAT
1 AAAGTGCAT
65733692 CTTGACGTGT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.36, C:0.23, G:0.23, T:0.17
Consensus pattern (19 bp):
AAAGTGCATACTGGCACAC
Found at i:65740879 original size:22 final size:22
Alignment explanation
Indices: 65740851--65740903 Score: 65
Period size: 22 Copynumber: 2.4 Consensus size: 22
65740841 GTCATGTCTA
65740851 GTCTCGAGACATA-AGGC-CATTT
1 GTCTCGAGACATACA--CTCATTT
*
65740873 GTCTCGAGATATACACTCATTT
1 GTCTCGAGACATACACTCATTT
65740895 GTCTCGAGA
1 GTCTCGAGA
65740904 TAGGATAACT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
21 1 0.04
22 26 0.93
23 1 0.04
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.30
Consensus pattern (22 bp):
GTCTCGAGACATACACTCATTT
Found at i:65744190 original size:6 final size:6
Alignment explanation
Indices: 65744179--65744217 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
65744169 AAAATAGCCC
* *
65744179 TAAAAT TAAAAT TAAAAT TAAAAT TAAAAA TATAAT TAA
1 TAAAAT TAAAAT TAAAAT TAAAAT TAAAAT TAAAAT TAA
65744218 GTACTAAGTC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (6 bp):
TAAAAT
Found at i:65746097 original size:21 final size:21
Alignment explanation
Indices: 65746072--65746111 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
65746062 TACCCCCTAA
65746072 ATCCCTTAA-TTAACTCCCCTT
1 ATCCC-TAATTTAACTCCCCTT
*
65746093 ATCCCTAATTTCACTCCCC
1 ATCCCTAATTTAACTCCCC
65746112 AACCGTTCAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.23, C:0.42, G:0.00, T:0.35
Consensus pattern (21 bp):
ATCCCTAATTTAACTCCCCTT
Found at i:65749219 original size:17 final size:17
Alignment explanation
Indices: 65749197--65749231 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
65749187 ATCTTGTGGC
65749197 AAAAAGAAAAGAAAGAG
1 AAAAAGAAAAGAAAGAG
65749214 AAAAAGAAAAGAAAGAG
1 AAAAAGAAAAGAAAGAG
65749231 A
1 A
65749232 TGATAAAACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (17 bp):
AAAAAGAAAAGAAAGAG
Found at i:65756115 original size:111 final size:110
Alignment explanation
Indices: 65755723--65756343 Score: 924
Period size: 109 Copynumber: 5.6 Consensus size: 110
65755713 AAATTTTTCT
* * * *
65755723 AAATGAGGCAATATTTAGCGTTTGGGAAATTCGAGAAAACATGCCCTAAGGTGTTGGGTGTCGAT
1 AAATAAGGCAATGTTTTGCGTTTGGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGAT
*
65755788 TTTTCTCGTTCAACCAAATGGCTTAATATCCTTTTAAAAATTTTA
66 TTTTCTCGTTCAACCAAATGGCTAAATATCCTTTTAAAAATTTTA
*
65755833 AAATAAGGCAATGTTTTGCGTTTGAGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGAT
1 AAATAAGGCAATGTTTTGCGTTTGGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGAT
*
65755898 TTTTCTCGTTCAACCAAATGGCTCAATATCCTTTTAAAAA-TTTA
66 TTTTCTCGTTCAACCAAATGGCTAAATATCCTTTTAAAAATTTTA
* *
65755942 AAATAAGGCAATGTTTTGCATTTGGGAAATTCGAGAAAACGTGCCCTAAGGTGCTGGGTGTCGAT
1 AAATAAGGCAATGTTTTGCGTTTGGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGAT
* *
65756007 TTTCCTCGTTCAACCAAATGGCTTAATATCCTTTTAAAAATTTTTA
66 TTTTCTCGTTCAACCAAATGGCTAAATATCCTTTTAAAAA-TTTTA
65756053 AAATAAGGCAATGTTTTGCGTTTGGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGAT
1 AAATAAGGCAATGTTTTGCGTTTGGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGAT
*
65756118 TTTTCTCATTCAACCAAATGGCTAAATATCCTTTTAAAATATTTTCA
66 TTTTCTCGTTCAACCAAATGGCTAAATATCCTTTTAAAA-ATTTT-A
* * *
65756165 AAATCAGGCAATGTTTTGCGTTTGGGAAATTCGAGAAAACATGCCCTAAGGTGCTAGGTGTTGAT
1 AAATAAGGCAATGTTTTGCGTTTGGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGAT
* * **
65756230 TTTTCTCATTCAACCAAATGACTAAATATCCTTTTAAAAATTTCG
66 TTTTCTCGTTCAACCAAATGGCTAAATATCCTTTTAAAAATTTTA
* * * * * * * * * *
65756275 AAGTAAGGTAATATTTTACGTTT-GGAAA-TCTAAGGAAACGTGCCCTAATGCGCTGGGTTTCGA
1 AAATAAGGCAATGTTTTGCGTTTGGGAAATTC-GAGAAAACATGCCCTAAGGTGCTGGGTGTCGA
65756338 TTTTTC
65 TTTTTC
65756344 CATTTGACCA
Statistics
Matches: 471, Mismatches: 35, Indels: 11
0.91 0.07 0.02
Matches are distributed among these distances:
108 2 0.00
109 139 0.30
110 117 0.25
111 111 0.24
112 102 0.22
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.34
Consensus pattern (110 bp):
AAATAAGGCAATGTTTTGCGTTTGGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGAT
TTTTCTCGTTCAACCAAATGGCTAAATATCCTTTTAAAAATTTTA
Found at i:65756818 original size:41 final size:41
Alignment explanation
Indices: 65756756--65756926 Score: 222
Period size: 41 Copynumber: 4.2 Consensus size: 41
65756746 ATTATTGCTG
*
65756756 AATTGCACATATGTGCTCC-TGTTTGTACTTCGGTACCCCTA
1 AATTGCACATACGTGC-CCTTGTTTGTACTTCGGTACCCCTA
*
65756797 AATTGAACATACGTGTCCC-TGTTTGTACTTCGGTACCCCTA
1 AATTGCACATACGTG-CCCTTGTTTGTACTTCGGTACCCCTA
* * * *
65756838 AATTGCACATATGTGCCCTTATTTGTACTTCAGTACCCCTG
1 AATTGCACATACGTGCCCTTGTTTGTACTTCGGTACCCCTA
* * *
65756879 AATTGCACATACGTGCCCTTTTTTATACTTCGGTACCTCTA
1 AATTGCACATACGTGCCCTTGTTTGTACTTCGGTACCCCTA
65756920 AA-TGCAC
1 AATTGCAC
65756927 TTTTTTCCTG
Statistics
Matches: 115, Mismatches: 13, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
40 8 0.07
41 106 0.92
42 1 0.01
ACGTcount: A:0.22, C:0.27, G:0.15, T:0.36
Consensus pattern (41 bp):
AATTGCACATACGTGCCCTTGTTTGTACTTCGGTACCCCTA
Found at i:65764322 original size:33 final size:33
Alignment explanation
Indices: 65764280--65764472 Score: 173
Period size: 33 Copynumber: 5.7 Consensus size: 33
65764270 ATGTGAAGGG
65764280 GGTTGCTAAGTGCTGATTCCCCGACTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGACTCATTGGT
*
65764313 GGTTGCTAAGTGCTGATT-CCC--C-CA-AGG-
1 GGTTGCTAAGTGCTGATTCCCCGACTCATTGGT
65764340 GGTTGCTAAGTGCTGATTCCCCGACTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGACTCATTGGT
* * *
65764373 GGTTGCTAAGTGCTGATCCCACCGTATCTTAAATGTGAAAGG
1 GGTTGCTAAGTGCTGATTCC-CCG-A-C-T-CAT-TG---GT
** * *
65764415 GGTTGCTAAGTTTTGATTCCCCGAATCACTGGT
1 GGTTGCTAAGTGCTGATTCCCCGACTCATTGGT
*
65764448 GGTTGCTAAGTGCTGAATCCACCGA
1 GGTTGCTAAGTGCTGATTCC-CCGA
65764473 TAACGGACAA
Statistics
Matches: 129, Mismatches: 15, Indels: 31
0.74 0.09 0.18
Matches are distributed among these distances:
27 18 0.14
28 5 0.04
29 2 0.02
30 2 0.02
31 2 0.02
32 5 0.04
33 55 0.43
34 7 0.05
35 1 0.01
36 3 0.02
37 2 0.02
38 3 0.02
39 2 0.02
40 1 0.01
41 3 0.02
42 18 0.14
ACGTcount: A:0.20, C:0.23, G:0.27, T:0.31
Consensus pattern (33 bp):
GGTTGCTAAGTGCTGATTCCCCGACTCATTGGT
Found at i:65764370 original size:135 final size:135
Alignment explanation
Indices: 65764178--65764463 Score: 464
Period size: 135 Copynumber: 2.1 Consensus size: 135
65764168 ATATAAAGGG
*
65764178 GGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTATTGATTCCCCGAATCATTGGTGGTTG
1 GGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTACTGATTCCCCGAATCATTGGTGGTTG
* * * * * *
65764243 TTAAGTGCTGATTCCATCGTATTTTAAATGTGAAGGGGGTTGCTAAGTGCTGATTCCCCGACTCA
66 CTAAGTGCTGATCCCACCGTATCTTAAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCGAATCA
*
65764308 TTGGT
131 CTGGT
* *
65764313 GGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGCTGATTCCCCGACTCATTGGTGGTTG
1 GGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTACTGATTCCCCGAATCATTGGTGGTTG
**
65764378 CTAAGTGCTGATCCCACCGTATCTTAAATGTGAAAGGGGTTGCTAAGTTTTGATTCCCCGAATCA
66 CTAAGTGCTGATCCCACCGTATCTTAAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCGAATCA
65764443 CTGGT
131 CTGGT
65764448 GGTTGCTAAGTGCTGA
1 GGTTGCTAAGTGCTGA
65764464 ATCCACCGAT
Statistics
Matches: 139, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
135 139 1.00
ACGTcount: A:0.20, C:0.20, G:0.28, T:0.33
Consensus pattern (135 bp):
GGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTACTGATTCCCCGAATCATTGGTGGTTG
CTAAGTGCTGATCCCACCGTATCTTAAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCGAATCA
CTGGT
Found at i:65769477 original size:22 final size:22
Alignment explanation
Indices: 65769433--65769482 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
65769423 GGGTCATGTC
*
65769433 TTGTCTCAAGACATAAGACCAT
1 TTGTCTCAAGACATAACACCAT
*
65769455 TTGTCTCAAGATAT-ACACTCAT
1 TTGTCTCAAGACATAACAC-CAT
*
65769477 TCGTCT
1 TTGTCT
65769483 TGAGATAGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 3 0.12
22 21 0.88
ACGTcount: A:0.30, C:0.24, G:0.12, T:0.34
Consensus pattern (22 bp):
TTGTCTCAAGACATAACACCAT
Found at i:65777217 original size:24 final size:23
Alignment explanation
Indices: 65777172--65777217 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 23
65777162 TACCTTTTCA
**
65777172 TTATACTTTATTTTGATTAATTT
1 TTATACTTTATTTTGAAAAATTT
*
65777195 TTATAACTTTATTTTTAAAAATT
1 TTAT-ACTTTATTTTGAAAAATT
65777218 CGATTTTCGT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 4 0.21
24 15 0.79
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.61
Consensus pattern (23 bp):
TTATACTTTATTTTGAAAAATTT
Found at i:65780538 original size:2 final size:2
Alignment explanation
Indices: 65780531--65780555 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
65780521 ATACCTAACC
65780531 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
65780556 CCATTCCAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:65789888 original size:9 final size:9
Alignment explanation
Indices: 65789851--65789892 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
65789841 ACTCATAACC
65789851 ATAAAAA-A
1 ATAAAAATA
*
65789859 ATAAAACTA
1 ATAAAAATA
*
65789868 AGTAATAATA
1 A-TAAAAATA
65789878 ATAAAAATA
1 ATAAAAATA
65789887 ATAAAA
1 ATAAAA
65789893 GTCAACAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
8 6 0.21
9 15 0.54
10 7 0.25
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.21
Consensus pattern (9 bp):
ATAAAAATA
Found at i:65790017 original size:33 final size:33
Alignment explanation
Indices: 65789975--65790095 Score: 122
Period size: 33 Copynumber: 3.5 Consensus size: 33
65789965 CATTAAGAGG
*
65789975 AATAAAAATAA-CAAACAGAATGAAATAAATAAA
1 AATAAAAATAAGAAAACA-AATGAAATAAATAAA
*
65790008 AATAAAAATAAGAAAACACATGATAATAAATATAA
1 AATAAAAATAAGAAAACAAATGA-AATAAATA-AA
65790043 TAATAATATAAATAAGAATAACAAAT-AAATAAATAAA
1 -AAT-A-A-AAATAAGAA-AACAAATGAAATAAATAAA
65790080 AAT-AAAATAAGGAAAA
1 AATAAAAATAA-GAAAA
65790096 AGAAGGGGAA
Statistics
Matches: 76, Mismatches: 3, Indels: 19
0.78 0.03 0.19
Matches are distributed among these distances:
32 8 0.11
33 19 0.25
34 13 0.17
35 2 0.03
36 6 0.08
37 3 0.04
38 9 0.12
39 10 0.13
40 6 0.08
ACGTcount: A:0.71, C:0.04, G:0.06, T:0.19
Consensus pattern (33 bp):
AATAAAAATAAGAAAACAAATGAAATAAATAAA
Found at i:65790048 original size:15 final size:15
Alignment explanation
Indices: 65790030--65790089 Score: 54
Period size: 15 Copynumber: 4.1 Consensus size: 15
65790020 AAAACACATG
65790030 ATAATAAATATAATA
1 ATAATAAATATAATA
*
65790045 ATAATATAA-ATAAGA
1 ATAATA-AATATAATA
*
65790060 ATAACAAATA-AATAA
1 ATAATAAATATAAT-A
*
65790075 ATAA-AAATAAAATA
1 ATAATAAATATAATA
65790089 A
1 A
65790090 GGAAAAAGAA
Statistics
Matches: 38, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
14 11 0.29
15 25 0.66
16 2 0.05
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.25
Consensus pattern (15 bp):
ATAATAAATATAATA
Found at i:65790063 original size:21 final size:19
Alignment explanation
Indices: 65790032--65790089 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 19
65790022 AACACATGAT
*
65790032 AATAAATATAATAATAATATA
1 AATAAAAATAA-AATAA-ATA
*
65790053 AATAAGAATAACAAATAAATA
1 AATAAAAAT-A-AAATAAATA
65790074 AATAAAAATAAAATAA
1 AATAAAAATAAAATAA
65790090 GGAAAAAGAA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
19 6 0.19
20 1 0.03
21 18 0.56
22 6 0.19
23 1 0.03
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.24
Consensus pattern (19 bp):
AATAAAAATAAAATAAATA
Found at i:65796902 original size:2 final size:2
Alignment explanation
Indices: 65796895--65796933 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
65796885 TAAGCTTAAT
65796895 TA TA TA TA TA 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 TA TA TA TA TA T
65796934 GAAAGTTAGT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:65797136 original size:16 final size:17
Alignment explanation
Indices: 65797105--65797138 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
65797095 CCATTATCTT
*
65797105 TTTTTTCCATTATTTAA
1 TTTTTTCCACTATTTAA
65797122 TTTTTTCCACT-TTTAA
1 TTTTTTCCACTATTTAA
65797138 T
1 T
65797139 CGTAGCTCAA
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:0.21, C:0.15, G:0.00, T:0.65
Consensus pattern (17 bp):
TTTTTTCCACTATTTAA
Found at i:65810162 original size:20 final size:20
Alignment explanation
Indices: 65810139--65810177 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
65810129 TTTATATTTA
65810139 TTTTTAAAGATTTTT-TTAAT
1 TTTTTAAA-ATTTTTGTTAAT
*
65810159 TTTTTAGAATTTTTGTTAA
1 TTTTTAAAATTTTTGTTAA
65810178 GAAAACTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.28, C:0.00, G:0.08, T:0.64
Consensus pattern (20 bp):
TTTTTAAAATTTTTGTTAAT
Found at i:65810742 original size:27 final size:28
Alignment explanation
Indices: 65810705--65810758 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 28
65810695 CATTAAAGTT
65810705 AAAAAAAGAATTTCAATTA-TCCCAAAA
1 AAAAAAAGAATTTCAATTATTCCCAAAA
65810732 AAAAAAAGAATTTCAATTATTCCCAAA
1 AAAAAAAGAATTTCAATTATTCCCAAA
65810759 TTTTAATTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
27 19 0.73
28 7 0.27
ACGTcount: A:0.57, C:0.15, G:0.04, T:0.24
Consensus pattern (28 bp):
AAAAAAAGAATTTCAATTATTCCCAAAA
Found at i:65812878 original size:10 final size:10
Alignment explanation
Indices: 65812859--65812888 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
65812849 AGGTGGTTGG
65812859 TTAGTGGGAT
1 TTAGTGGGAT
*
65812869 TTAGTAGGAT
1 TTAGTGGGAT
65812879 TTAGTGGGAT
1 TTAGTGGGAT
65812889 ATGGGTAGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.23, C:0.00, G:0.37, T:0.40
Consensus pattern (10 bp):
TTAGTGGGAT
Found at i:65813580 original size:36 final size:36
Alignment explanation
Indices: 65813539--65813616 Score: 93
Period size: 36 Copynumber: 2.2 Consensus size: 36
65813529 TTTTTGCAGC
* * *
65813539 CGTGTGGAGAACATGGCCATATGAAATCATGCATGT
1 CGTGTGGAGAACACGACCATATGAAATCATGCAGGT
* * * *
65813575 CGTGTGGGGCACACGACCATGTGAAATCATGTAGGT
1 CGTGTGGAGAACACGACCATATGAAATCATGCAGGT
65813611 CGTGTG
1 CGTGTG
65813617 AGTAAACTGT
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.26, C:0.18, G:0.32, T:0.24
Consensus pattern (36 bp):
CGTGTGGAGAACACGACCATATGAAATCATGCAGGT
Found at i:65813665 original size:36 final size:36
Alignment explanation
Indices: 65813625--65813726 Score: 141
Period size: 36 Copynumber: 2.8 Consensus size: 36
65813615 TGAGTAAACT
* * *
65813625 GTGTGAGGCACACGACCATGTGAAATCATGTAGTCC
1 GTGTGAGGCACACGACCGTGTGAAATCATATAGGCC
65813661 GTGTGAGGCACACGACCGTGTGAAATCATATAGGCC
1 GTGTGAGGCACACGACCGTGTGAAATCATATAGGCC
* * **
65813697 TTGTGGGGCACACGGTCGTGTGAAATCATA
1 GTGTGAGGCACACGACCGTGTGAAATCATA
65813727 CAGATCGTGT
Statistics
Matches: 59, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 59 1.00
ACGTcount: A:0.26, C:0.21, G:0.30, T:0.23
Consensus pattern (36 bp):
GTGTGAGGCACACGACCGTGTGAAATCATATAGGCC
Found at i:65822550 original size:38 final size:37
Alignment explanation
Indices: 65822484--65822563 Score: 97
Period size: 38 Copynumber: 2.1 Consensus size: 37
65822474 TCATGGAACG
* * * *
65822484 GTTATCTACTAGTCCTTTGGGGCCACACTGTGACGAC
1 GTTATCTACTAGTCCTTTAGAGACACACTATGACGAC
* *
65822521 AGTTATCTACTAGTCCTTTAGAGAGACACTATGATGAC
1 -GTTATCTACTAGTCCTTTAGAGACACACTATGACGAC
65822559 GTTAT
1 GTTAT
65822564 ATAGATCCCT
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
37 5 0.14
38 31 0.86
ACGTcount: A:0.25, C:0.21, G:0.21, T:0.33
Consensus pattern (37 bp):
GTTATCTACTAGTCCTTTAGAGACACACTATGACGAC
Found at i:65824525 original size:28 final size:28
Alignment explanation
Indices: 65824428--65824509 Score: 146
Period size: 28 Copynumber: 2.9 Consensus size: 28
65824418 AAAACATATA
* *
65824428 AAAATGGAAGCCTTTATCGCAATCTATG
1 AAAATGGAAGCCTTTGTGGCAATCTATG
65824456 AAAATGGAAGCCTTTGTGGCAATCTATG
1 AAAATGGAAGCCTTTGTGGCAATCTATG
65824484 AAAATGGAAGCCTTTGTGGCAATCTA
1 AAAATGGAAGCCTTTGTGGCAATCTA
65824510 AGGAAAGGAA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 52 1.00
ACGTcount: A:0.34, C:0.16, G:0.22, T:0.28
Consensus pattern (28 bp):
AAAATGGAAGCCTTTGTGGCAATCTATG
Found at i:65825595 original size:66 final size:66
Alignment explanation
Indices: 65825525--65825656 Score: 246
Period size: 66 Copynumber: 2.0 Consensus size: 66
65825515 GATAACTAAA
* *
65825525 AAAATTGGAACAACCTTATGTGTAAATAGGAAACCTATCCTGGCATTATAAAAGTTGAAAATAGA
1 AAAATTGGAACAACCTTATGTGTAAATAGGAAACCTATCCTAGCATTATAAAAGTTAAAAATAGA
65825590 T
66 T
65825591 AAAATTGGAACAACCTTATGTGTAAATAGGAAACCTATCCTAGCATTATAAAAGTTAAAAATAGA
1 AAAATTGGAACAACCTTATGTGTAAATAGGAAACCTATCCTAGCATTATAAAAGTTAAAAATAGA
65825656 T
66 T
65825657 CAATATAGAT
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 64 1.00
ACGTcount: A:0.45, C:0.12, G:0.15, T:0.27
Consensus pattern (66 bp):
AAAATTGGAACAACCTTATGTGTAAATAGGAAACCTATCCTAGCATTATAAAAGTTAAAAATAGA
T
Found at i:65825910 original size:18 final size:17
Alignment explanation
Indices: 65825870--65825912 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
65825860 AATACTTTAA
*
65825870 ATAT-AAAATTATAAAT
1 ATATAAAAATAATAAAT
*
65825886 GTATAAAAATAATATAAT
1 ATATAAAAATAATA-AAT
65825904 ATATAAAAA
1 ATATAAAAA
65825913 AACTGCCACG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 3 0.14
17 8 0.36
18 11 0.50
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (17 bp):
ATATAAAAATAATAAAT
Found at i:65830112 original size:15 final size:15
Alignment explanation
Indices: 65830076--65830118 Score: 50
Period size: 16 Copynumber: 2.8 Consensus size: 15
65830066 ACAAAAAATG
* *
65830076 TATAAAATTATTAAA
1 TATAAAAATATAAAA
65830091 TATTAAAAATATAAAA
1 TA-TAAAAATATAAAA
*
65830107 TATAAATATATA
1 TATAAAAATATA
65830119 TTTTTTAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
15 11 0.46
16 13 0.54
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
TATAAAAATATAAAA
Found at i:65832270 original size:59 final size:59
Alignment explanation
Indices: 65832204--65832329 Score: 139
Period size: 59 Copynumber: 2.1 Consensus size: 59
65832194 AACTATGTAT
* * **
65832204 ATAACCAACAAAAC-ATACCTAAAACATAATCATTATTTACCAT-TTAAAACCGTACCTAA
1 ATAACCAACAAAACAAT-CATAAAACATAATCATTATTTACCATCAT-AAACCACACCTAA
* * * * *
65832263 ATAACCAACCAATCAATCATAGAACATATTCATTATTTGCCATCATAAACCACACCTAA
1 ATAACCAACAAAACAATCATAAAACATAATCATTATTTACCATCATAAACCACACCTAA
65832322 ATAACCAA
1 ATAACCAA
65832330 TACATAATCA
Statistics
Matches: 56, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
59 53 0.95
60 3 0.05
ACGTcount: A:0.48, C:0.25, G:0.02, T:0.25
Consensus pattern (59 bp):
ATAACCAACAAAACAATCATAAAACATAATCATTATTTACCATCATAAACCACACCTAA
Found at i:65833102 original size:41 final size:41
Alignment explanation
Indices: 65833037--65833183 Score: 145
Period size: 41 Copynumber: 3.5 Consensus size: 41
65833027 CAATGTTTCA
* * *
65833037 CACACTAAATGCCATCGCATAGCCGAAGCTAT-TATAATCTCG
1 CACACTAAGTGCCAT-ACATAGCCGAAGCTATCT-CAATCTCG
* * *
65833079 CACACTAAGTGTCTTACATAGCCGAAGCTATCTCAGTCTCG
1 CACACTAAGTGCCATACATAGCCGAAGCTATCTCAATCTCG
* *
65833120 CACACTAAGTGCCATAAATAGCCGAATTAGCTATCTCAA-ATCG
1 CACACTAAGTGCCATACATAGCCG-A--AGCTATCTCAATCTCG
* *
65833163 CACACTAAGTGCTAAACATAG
1 CACACTAAGTGCCATACATAG
65833184 TCGATTAATC
Statistics
Matches: 87, Mismatches: 14, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
41 42 0.48
42 14 0.16
43 21 0.24
44 10 0.11
ACGTcount: A:0.34, C:0.27, G:0.15, T:0.24
Consensus pattern (41 bp):
CACACTAAGTGCCATACATAGCCGAAGCTATCTCAATCTCG
Found at i:65850596 original size:539 final size:539
Alignment explanation
Indices: 65849579--65850656 Score: 2039
Period size: 539 Copynumber: 2.0 Consensus size: 539
65849569 TGTTTGTGAC
65849579 TGTCGCACTTTCACTGGTGGTCGTGGCAGGTGTTGTCGCCCACGAGTTCAATGTTAGATTTGTGG
1 TGTCGCACTTTCACTGGTGGTCGTGGCAGGTGTTGTCGCCCACGAGTTCAATGTTAGATTTGTGG
65849644 CAGATTTGGTCACGTGGCTCAATGGTGGCTTTACCATTTTAATCACAAATATGATAATTCTCCTT
66 CAGATTTGGTCACGTGGCTCAATGGTGGCTTTACCATTTTAATCACAAATATGATAATTCTCCTT
65849709 TGGCGACGAATCCAGCGCCAGTGACCTGTGCTGTGTATGGCTCGATTGCGGGGTTTTGTATGCCT
131 TGGCGACGAATCCAGCGCCAGTGACCTGTGCTGTGTATGGCTCGATTGCGGGGTTTTGTATGCCT
*
65849774 ACGGAGAGTACTCACGGTGGTCATGGTGGCTTTACTTTTCCCTGGCTGTTCCTGGTCAGGTCGAG
196 ACGGAGAGTACTCACAGTGGTCATGGTGGCTTTACTTTTCCCTGGCTGTTCCTGGTCAGGTCGAG
*
65849839 TCGTATTTGCCAATGGTGTCACCGGGGTTCGACCTAGGTGGTTGGTGGGGTTATGCTCCTTCTCA
261 TCGTATTTGCCAATGGTGTCACCGGGGTTCGACCTAGGTGGTTGGTGGGGTTATGCTCCTTCCCA
*
65849904 TGCGACCACCTGAATGAAGATCCCTAGGGCTTCTACTAACTCTCTTACTGTGTGGGATAATAATG
326 TGCGACCACCTGAATGAAGATCCCTAAGGCTTCTACTAACTCTCTTACTGTGTGGGATAATAATG
65849969 CAGGCCATCATTTTGGGCCACTTGGAGGCGTTACTAGGCCAATAGGGGCAGACCAAGCTTCTGGG
391 CAGGCCATCATTTTGGGCCACTTGGAGGCGTTACTAGGCCAATAGGGGCAGACCAAGCTTCTGGG
65850034 CCATGCACTGGTGCGGCTAGGACGATTTCTACAGGCTTTGGTTATGGGTCTATTGCGTCAAATCA
456 CCATGCACTGGTGCGGCTAGGACGATTTCTACAGGCTTTGGTTATGGGTCTATTGCGTCAAATCA
65850099 GCAGGTTGGGCCTGGTCAT
521 GCAGGTTGGGCCTGGTCAT
65850118 TGTCGCACTTTCACTGGTGGTCGTGGCAGGTGTTGTCGCCCACGAGTTCAATGTTAGATTTGTGG
1 TGTCGCACTTTCACTGGTGGTCGTGGCAGGTGTTGTCGCCCACGAGTTCAATGTTAGATTTGTGG
* *
65850183 CAGATTTGGTCACGTGGCTCAATGGTGGCTTTACCATTTTAATCGCAAATATGATAATTCTCTTT
66 CAGATTTGGTCACGTGGCTCAATGGTGGCTTTACCATTTTAATCACAAATATGATAATTCTCCTT
*
65850248 TGGCGACGAATCCAGCGCCAGTGACCTGTGCTGTGTATGGCTCGATTGTGGGGTTTTGTATGCCT
131 TGGCGACGAATCCAGCGCCAGTGACCTGTGCTGTGTATGGCTCGATTGCGGGGTTTTGTATGCCT
* * *
65850313 ACGGAGAGTACTCATAGTGGTCATGGTGGCTTTACTTTTCCTTGGTTGTTCCTGGTCAGGTCGAG
196 ACGGAGAGTACTCACAGTGGTCATGGTGGCTTTACTTTTCCCTGGCTGTTCCTGGTCAGGTCGAG
*
65850378 TCGTATTTGCCAATGGTGTCATCGGGGTTCGACCTAGGTGGTTGGTGGGGTTATGCTCCTTCCCA
261 TCGTATTTGCCAATGGTGTCACCGGGGTTCGACCTAGGTGGTTGGTGGGGTTATGCTCCTTCCCA
65850443 TGCGACCACCTGAATGAAGATCCCTAAGGCTTCTACTAACTCTCTTACTGTGTGGGATAATAATG
326 TGCGACCACCTGAATGAAGATCCCTAAGGCTTCTACTAACTCTCTTACTGTGTGGGATAATAATG
*
65850508 CAGGCCATCATTTTGGGCCACTTGGAGGCGTTACTGGGCCAATAGGGGCAGACCAAGCTTCTGGG
391 CAGGCCATCATTTTGGGCCACTTGGAGGCGTTACTAGGCCAATAGGGGCAGACCAAGCTTCTGGG
*
65850573 CCATGCGCTGGTGCGGCTAGGACGATTTCTACAGGCTTTGGTTATGGGTCTATTGCGTCAAATCA
456 CCATGCACTGGTGCGGCTAGGACGATTTCTACAGGCTTTGGTTATGGGTCTATTGCGTCAAATCA
*
65850638 GTAGGTTGGGCCTGGTCAT
521 GCAGGTTGGGCCTGGTCAT
65850657 GGTGGTATCG
Statistics
Matches: 526, Mismatches: 13, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
539 526 1.00
ACGTcount: A:0.18, C:0.22, G:0.29, T:0.31
Consensus pattern (539 bp):
TGTCGCACTTTCACTGGTGGTCGTGGCAGGTGTTGTCGCCCACGAGTTCAATGTTAGATTTGTGG
CAGATTTGGTCACGTGGCTCAATGGTGGCTTTACCATTTTAATCACAAATATGATAATTCTCCTT
TGGCGACGAATCCAGCGCCAGTGACCTGTGCTGTGTATGGCTCGATTGCGGGGTTTTGTATGCCT
ACGGAGAGTACTCACAGTGGTCATGGTGGCTTTACTTTTCCCTGGCTGTTCCTGGTCAGGTCGAG
TCGTATTTGCCAATGGTGTCACCGGGGTTCGACCTAGGTGGTTGGTGGGGTTATGCTCCTTCCCA
TGCGACCACCTGAATGAAGATCCCTAAGGCTTCTACTAACTCTCTTACTGTGTGGGATAATAATG
CAGGCCATCATTTTGGGCCACTTGGAGGCGTTACTAGGCCAATAGGGGCAGACCAAGCTTCTGGG
CCATGCACTGGTGCGGCTAGGACGATTTCTACAGGCTTTGGTTATGGGTCTATTGCGTCAAATCA
GCAGGTTGGGCCTGGTCAT
Found at i:65862679 original size:120 final size:120
Alignment explanation
Indices: 65862456--65862693 Score: 415
Period size: 120 Copynumber: 2.0 Consensus size: 120
65862446 AGACTATTAT
*
65862456 AGAAATATATTAAAGTTTGGTCTAATAATTTTATTTAATTGATAGTTAATTAAGGTACAAGTGTA
1 AGAAATATATTAAAGCTTGGTCTAATAATTTTATTTAATTGATAGTTAATTAAGGTACAAGTGTA
* * *
65862521 ATGATCATAAAGTTAGTGATATCAAAAAGTGCAGTTTTAGAACCCCATTTTCAAA
66 ATGATCATAAAGTTAGTGATATCAAAAAGTACAATTTTAGAACACCATTTTCAAA
*
65862576 AGAAATATATTAAAGCTTGTTCTAATAATTTTATTTAATTGATAGTTAATTAAGGTACAAGTGTA
1 AGAAATATATTAAAGCTTGGTCTAATAATTTTATTTAATTGATAGTTAATTAAGGTACAAGTGTA
65862641 ATGATCATAAAGTTAGTGATATCGAAAAA-TACAATTTTAGAACACCATTTTCA
66 ATGATCATAAAGTTAGTGATATC-AAAAAGTACAATTTTAGAACACCATTTTCA
65862694 TAAACTGAGA
Statistics
Matches: 112, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
120 107 0.96
121 5 0.04
ACGTcount: A:0.41, C:0.08, G:0.14, T:0.37
Consensus pattern (120 bp):
AGAAATATATTAAAGCTTGGTCTAATAATTTTATTTAATTGATAGTTAATTAAGGTACAAGTGTA
ATGATCATAAAGTTAGTGATATCAAAAAGTACAATTTTAGAACACCATTTTCAAA
Found at i:65864832 original size:22 final size:22
Alignment explanation
Indices: 65864801--65864883 Score: 78
Period size: 22 Copynumber: 3.8 Consensus size: 22
65864791 AATTGGTTGA
*
65864801 GTTTGGTTAGTTGATGAACTAT
1 GTTTGATTAGTTGATGAACTAT
* * *
65864823 GTTTGCTTAGTTGATG-AGTTT
1 GTTTGATTAGTTGATGAACTAT
* **
65864844 GTGTTTATTAAATGATGAACTAT
1 GT-TTGATTAGTTGATGAACTAT
*
65864867 GTTTGTTTAGTTGATGA
1 GTTTGATTAGTTGATGA
65864884 GTACATAGGT
Statistics
Matches: 46, Mismatches: 13, Indels: 4
0.73 0.21 0.06
Matches are distributed among these distances:
21 5 0.11
22 36 0.78
23 5 0.11
ACGTcount: A:0.23, C:0.04, G:0.25, T:0.48
Consensus pattern (22 bp):
GTTTGATTAGTTGATGAACTAT
Found at i:65864883 original size:25 final size:25
Alignment explanation
Indices: 65864812--65864883 Score: 59
Period size: 25 Copynumber: 3.1 Consensus size: 25
65864802 TTTGGTTAGT
*
65864812 TGATGAACTATGTTTGCTTAGTTGA
1 TGATGAACTATGTTTGTTTAGTTGA
* *
65864837 TGA-G---T-T-TGTGTTTA-TTAAA
1 TGATGAACTATGTTTGTTTAGTT-GA
65864856 TGATGAACTATGTTTGTTTAGTTGA
1 TGATGAACTATGTTTGTTTAGTTGA
65864881 TGA
1 TGA
65864884 GTACATAGGT
Statistics
Matches: 34, Mismatches: 5, Indels: 16
0.62 0.09 0.29
Matches are distributed among these distances:
18 2 0.06
19 10 0.29
20 2 0.06
21 1 0.03
23 1 0.03
24 2 0.06
25 14 0.41
26 2 0.06
ACGTcount: A:0.25, C:0.04, G:0.24, T:0.47
Consensus pattern (25 bp):
TGATGAACTATGTTTGTTTAGTTGA
Found at i:65874343 original size:29 final size:28
Alignment explanation
Indices: 65874279--65874343 Score: 67
Period size: 29 Copynumber: 2.2 Consensus size: 28
65874269 AATATACCCG
* ***
65874279 TTTTCTCATTTTAGTACCTAAACTTTTT
1 TTTTCTCAATTTAGTACCTAAACTTCAA
*
65874307 TTTGTCTCAATTTAGTACCTAAAGTATCAA
1 TTT-TCTCAATTTAGTACCTAAACT-TCAA
65874337 TTTTCTC
1 TTTTCTC
65874344 TACTTTTAGT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
28 3 0.10
29 23 0.77
30 4 0.13
ACGTcount: A:0.25, C:0.18, G:0.06, T:0.51
Consensus pattern (28 bp):
TTTTCTCAATTTAGTACCTAAACTTCAA
Found at i:65874484 original size:7 final size:7
Alignment explanation
Indices: 65874474--65874531 Score: 52
Period size: 7 Copynumber: 8.4 Consensus size: 7
65874464 TTTAAATTAA
65874474 AAATATT
1 AAATATT
65874481 AAAT-TT
1 AAATATT
*
65874487 AAAGTA-A
1 AAA-TATT
65874494 AAATA-T
1 AAATATT
65874500 AAAT-TT
1 AAATATT
65874506 ATAATATT
1 A-AATATT
65874514 AAATATT
1 AAATATT
65874521 AAAATATT
1 -AAATATT
65874529 AAA
1 AAA
65874532 AAAGACTTTT
Statistics
Matches: 43, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
6 13 0.30
7 20 0.47
8 10 0.23
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (7 bp):
AAATATT
Found at i:65874502 original size:19 final size:20
Alignment explanation
Indices: 65874463--65874506 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
65874453 AATTAGGTTT
*
65874463 ATTTAAATTAAAAATATTAA
1 ATTTAAAGTAAAAATATTAA
65874483 ATTTAAAGTAAAAATA-TAA
1 ATTTAAAGTAAAAATATTAA
65874502 ATTTA
1 ATTTA
65874507 TAATATTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 8 0.35
20 15 0.65
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (20 bp):
ATTTAAAGTAAAAATATTAA
Found at i:65874683 original size:23 final size:24
Alignment explanation
Indices: 65874656--65874701 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
65874646 ATTGATTATA
65874656 AATTTTGT-TAAAAGTTTAAAATT
1 AATTTTGTATAAAAGTTTAAAATT
* *
65874679 AATTTTTTATAAAATTTTAAAAT
1 AATTTTGTATAAAAGTTTAAAAT
65874702 ATATAATTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (24 bp):
AATTTTGTATAAAAGTTTAAAATT
Found at i:65874787 original size:25 final size:21
Alignment explanation
Indices: 65874690--65874799 Score: 77
Period size: 21 Copynumber: 5.1 Consensus size: 21
65874680 ATTTTTTATA
*
65874690 AAATTT-TAAAATATATAATTAT
1 AAATTTATAAAAAAT-TAATT-T
**
65874712 AAATTT-T-AAAAATTAAAAAT
1 AAATTTATAAAAAATT-AATTT
*
65874732 AAA-ATATAAAAAATTAATTT
1 AAATTTATAAAAAATTAATTT
65874752 AAATTTATAAAAAATTATATTTT
1 AAATTTATAAAAAATTA-A-TTT
*
65874775 AGAATTTTATAAAAAA-TATTTT
1 A-AA-TTTATAAAAAATTAATTT
65874797 AAA
1 AAA
65874800 AATATTTTAA
Statistics
Matches: 72, Mismatches: 8, Indels: 17
0.74 0.08 0.18
Matches are distributed among these distances:
19 1 0.01
20 12 0.17
21 28 0.39
22 12 0.17
23 4 0.06
24 4 0.06
25 11 0.15
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (21 bp):
AAATTTATAAAAAATTAATTT
Found at i:65874793 original size:22 final size:20
Alignment explanation
Indices: 65874736--65874799 Score: 65
Period size: 22 Copynumber: 2.9 Consensus size: 20
65874726 AAAAATAAAA
*
65874736 TATAAAAAATTAATTTAAATT
1 TATAAAAAA-TATTTTAAATT
65874757 TATAAAAAATTATATTTTAGAATTT
1 TAT-AAAAA--ATATTTTA-AA-TT
65874782 TATAAAAAATATTTTAAA
1 TATAAAAAATATTTTAAA
65874800 AATATTTTAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
21 5 0.14
22 13 0.35
23 6 0.16
24 8 0.22
25 5 0.14
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.44
Consensus pattern (20 bp):
TATAAAAAATATTTTAAATT
Found at i:65874802 original size:11 final size:11
Alignment explanation
Indices: 65874786--65874813 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
65874776 GAATTTTATA
65874786 AAAAATATTTT
1 AAAAATATTTT
65874797 AAAAATATTTT
1 AAAAATATTTT
65874808 AAAAAT
1 AAAAAT
65874814 TTTATATGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:65881237 original size:11 final size:11
Alignment explanation
Indices: 65881221--65881259 Score: 51
Period size: 11 Copynumber: 3.4 Consensus size: 11
65881211 ACTACTATAT
65881221 ATTACTATTAA
1 ATTACTATTAA
*
65881232 ATTACTACTCTAT
1 ATTACTA-T-TAA
65881245 ATTACTATTAA
1 ATTACTATTAA
65881256 ATTA
1 ATTA
65881260 AGTTAGAGCG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
11 13 0.54
12 2 0.08
13 9 0.38
ACGTcount: A:0.41, C:0.13, G:0.00, T:0.46
Consensus pattern (11 bp):
ATTACTATTAA
Found at i:65881245 original size:24 final size:24
Alignment explanation
Indices: 65881210--65881259 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
65881200 GGATCAACCC
65881210 TACTACTATATATTACTATTAAAT
1 TACTACTATATATTACTATTAAAT
*
65881234 TACTACTCTATATTACTATTAAAT
1 TACTACTATATATTACTATTAAAT
65881258 TA
1 TA
65881260 AGTTAGAGCG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.40, C:0.14, G:0.00, T:0.46
Consensus pattern (24 bp):
TACTACTATATATTACTATTAAAT
Found at i:65881250 original size:13 final size:12
Alignment explanation
Indices: 65881210--65881251 Score: 50
Period size: 13 Copynumber: 3.4 Consensus size: 12
65881200 GGATCAACCC
65881210 TACTACTATATAT
1 TACTACT-TATAT
*
65881223 TACTA-TTAAAT
1 TACTACTTATAT
65881234 TACTACTCTATAT
1 TACTACT-TATAT
65881247 TACTA
1 TACTA
65881252 TTAAATTAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
11 9 0.36
12 2 0.08
13 14 0.56
ACGTcount: A:0.38, C:0.17, G:0.00, T:0.45
Consensus pattern (12 bp):
TACTACTTATAT
Found at i:65885679 original size:24 final size:24
Alignment explanation
Indices: 65885635--65885684 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
65885625 CGCAATAAAG
*
65885635 AATTTAAAAATTATCAAAAATCAA
1 AATTTAAAAAGTATCAAAAATCAA
* *
65885659 AATTATAAAAAGT-TCATAAATTAA
1 AATT-TAAAAAGTATCAAAAATCAA
65885683 AA
1 AA
65885685 AAAAAACATG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
24 15 0.68
25 7 0.32
ACGTcount: A:0.62, C:0.06, G:0.02, T:0.30
Consensus pattern (24 bp):
AATTTAAAAAGTATCAAAAATCAA
Found at i:65889563 original size:22 final size:23
Alignment explanation
Indices: 65889520--65889563 Score: 54
Period size: 22 Copynumber: 1.9 Consensus size: 23
65889510 AACTTGGTCA
* *
65889520 TTTTCCTATAAAAATAAGTTTTTT
1 TTTTCCTAT-AAAACAACTTTTTT
65889544 TTTTCCTAT-AAACAACTTTT
1 TTTTCCTATAAAACAACTTTT
65889564 AAAGCGTAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 9 0.50
24 9 0.50
ACGTcount: A:0.32, C:0.14, G:0.02, T:0.52
Consensus pattern (23 bp):
TTTTCCTATAAAACAACTTTTTT
Found at i:65889763 original size:26 final size:26
Alignment explanation
Indices: 65889733--65889802 Score: 70
Period size: 29 Copynumber: 2.5 Consensus size: 26
65889723 ATACATATCT
65889733 AATTATTTATATTTAGTCA-TATAATA
1 AATTATTTATATTTA-TCATTATAATA
* *
65889759 AATTATTAATATAATTTATTATTTTAATA
1 AATTATT--TAT-ATTTATCATTATAATA
65889788 AATTATTTAATATTT
1 AATTATTT-ATATTT
65889803 CAATTTTATT
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
26 7 0.19
27 5 0.14
28 7 0.19
29 18 0.49
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (26 bp):
AATTATTTATATTTATCATTATAATA
Found at i:65889772 original size:16 final size:16
Alignment explanation
Indices: 65889751--65889800 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 16
65889741 ATATTTAGTC
65889751 ATATAATAAATTATTA
1 ATATAATAAATTATTA
65889767 ATATAAT---TTATTA
1 ATATAATAAATTATTA
* *
65889780 TTTTAATAAATTATTTA
1 ATATAATAAATTA-TTA
65889797 ATAT
1 ATAT
65889801 TTCAATTTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 7
0.70 0.11 0.19
Matches are distributed among these distances:
13 11 0.42
16 10 0.38
17 5 0.19
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
ATATAATAAATTATTA
Found at i:65889776 original size:29 final size:30
Alignment explanation
Indices: 65889743--65889800 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
65889733 AATTATTTAT
65889743 ATTTAGTCA-TATAATAAATTA-TTAATATA
1 ATTTA-TCATTATAATAAATTATTTAATATA
* *
65889772 ATTTATTATTTTAATAAATTATTTAATAT
1 ATTTATCATTATAATAAATTATTTAATAT
65889801 TTCAATTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 2 0.08
29 16 0.64
30 7 0.28
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (30 bp):
ATTTATCATTATAATAAATTATTTAATATA
Found at i:65889829 original size:19 final size:19
Alignment explanation
Indices: 65889807--65889862 Score: 57
Period size: 19 Copynumber: 3.2 Consensus size: 19
65889797 ATATTTCAAT
65889807 TTTATTTTAATAATAAATA
1 TTTATTTTAATAATAAATA
** *
65889826 TTTATTACAATTATAAATA
1 TTTATTTTAATAATAAATA
65889845 --TA--TTAATAATAAATA
1 TTTATTTTAATAATAAATA
65889860 TTT
1 TTT
65889863 TGTAGTATAA
Statistics
Matches: 29, Mismatches: 6, Indels: 6
0.71 0.15 0.15
Matches are distributed among these distances:
15 10 0.34
17 3 0.10
19 16 0.55
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (19 bp):
TTTATTTTAATAATAAATA
Done.