Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A04
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: 81554553
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2322942 characters in sequence are not A, C, G, or T
File 173 of 253
Found at i:56172099 original size:43 final size:43
Alignment explanation
Indices: 56172031--56172202 Score: 120
Period size: 43 Copynumber: 4.0 Consensus size: 43
56172021 AAAGTTCGTA
* * *
56172031 CAATGCCAACGTCCGAGACGTAGTCTTACATGTAATCAAATAT
1 CAATGCCAACGTCCCAGACGTAGTCTTACACGAAATCAAATAT
*
56172074 CAATGCC-ACTGTCCCAGACAG-AGTCTTACACGAAATCAAACA-
1 CAATGCCAAC-GTCCCAGAC-GTAGTCTTACACGAAATCAAATAT
* * * * * * *
56172116 CGATGTCGATGTACCAGACAT-GATCTTACACGTAAATCTCAA-AT
1 CAATGCCAACGTCCCAGACGTAG-TCTTACACG-AAATC-AAATAT
* * * * *
56172160 CGATGCTAACGTCCCAGACGTGGTCCTACATGAAATCAAATAT
1 CAATGCCAACGTCCCAGACGTAGTCTTACACGAAATCAAATAT
56172203 TGAAATCCTA
Statistics
Matches: 100, Mismatches: 19, Indels: 20
0.72 0.14 0.14
Matches are distributed among these distances:
41 1 0.01
42 26 0.26
43 47 0.47
44 25 0.25
45 1 0.01
ACGTcount: A:0.35, C:0.26, G:0.16, T:0.23
Consensus pattern (43 bp):
CAATGCCAACGTCCCAGACGTAGTCTTACACGAAATCAAATAT
Found at i:56180789 original size:43 final size:43
Alignment explanation
Indices: 56180669--56180825 Score: 169
Period size: 43 Copynumber: 3.7 Consensus size: 43
56180659 TGTGTTCTCG
* *
56180669 TGTAAGACCACGTTTGGGATGTTGGCATCGACT-TATGATTTACA
1 TGTAAGACCACGTCTGGGATGTTGGCATCGA-TATTTGATTT-CA
* * * * *
56180713 TGTAAGACCATGTCTGAGACGTTGGCAT-TATATTTGATTTCG
1 TGTAAGACCACGTCTGGGATGTTGGCATCGATATTTGATTTCA
*
56180755 TGTAAGACC-CTGTCTGGGATAGTT-GCATCGATATTTGATTACA
1 TGTAAGACCAC-GTCTGGGAT-GTTGGCATCGATATTTGATTTCA
*
56180798 TGTAAGACCACGTCTGGGACGTTGGCAT
1 TGTAAGACCACGTCTGGGATGTTGGCAT
56180826 TGTACGAGCT
Statistics
Matches: 93, Mismatches: 14, Indels: 13
0.77 0.12 0.11
Matches are distributed among these distances:
42 25 0.27
43 43 0.46
44 25 0.27
ACGTcount: A:0.24, C:0.17, G:0.25, T:0.34
Consensus pattern (43 bp):
TGTAAGACCACGTCTGGGATGTTGGCATCGATATTTGATTTCA
Found at i:56180824 original size:85 final size:86
Alignment explanation
Indices: 56180666--56180826 Score: 231
Period size: 85 Copynumber: 1.9 Consensus size: 86
56180656 ATATGTGTTC
* *
56180666 TCGTGTAAGACCACGTTTGGGATGTTGGCATCGACTTATGATTTACATGTAAGACCATGTCTGAG
1 TCGTGTAAGACCACGTCTGGGATGTTGGCATCGACTTATGATTTACATGTAAGACCACGTCTGAG
56180731 ACGTTGGCATTATATTTGATT
66 ACGTTGGCATTATATTTGATT
*
56180752 TCGTGTAAGACC-CTGTCTGGGATAGTT-GCATCGA-TATTTGA-TTACATGTAAGACCACGTCT
1 TCGTGTAAGACCAC-GTCTGGGAT-GTTGGCATCGACT-TATGATTTACATGTAAGACCACGTCT
*
56180813 GGGACGTTGGCATT
63 GAGACGTTGGCATT
56180827 GTACGAGCTT
Statistics
Matches: 68, Mismatches: 4, Indels: 7
0.86 0.05 0.09
Matches are distributed among these distances:
85 34 0.50
86 31 0.46
87 3 0.04
ACGTcount: A:0.24, C:0.17, G:0.25, T:0.34
Consensus pattern (86 bp):
TCGTGTAAGACCACGTCTGGGATGTTGGCATCGACTTATGATTTACATGTAAGACCACGTCTGAG
ACGTTGGCATTATATTTGATT
Found at i:56183151 original size:15 final size:16
Alignment explanation
Indices: 56183124--56183154 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
56183114 GGATTTTAAC
56183124 CCATATAACAAAATGG
1 CCATATAACAAAATGG
56183140 CCATAT-ACAAAATGG
1 CCATATAACAAAATGG
56183155 AATAATATAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.48, C:0.19, G:0.13, T:0.19
Consensus pattern (16 bp):
CCATATAACAAAATGG
Found at i:56183782 original size:48 final size:49
Alignment explanation
Indices: 56183707--56184019 Score: 345
Period size: 48 Copynumber: 6.5 Consensus size: 49
56183697 AAAGTACCAA
* * * * *
56183707 GCCATGTCCCCGACATGGTCTTGCATGAATC-CACATACCATCACCGAT
1 GCCATGTCCCAGACATGGTCTTACATGAAGCACACATATCATCGCCGAT
* * *
56183755 GCCATGTCCCCGACATGGTCTTACATGAATC-CACATATCATCGCTGAT
1 GCCATGTCCCAGACATGGTCTTACATGAAGCACACATATCATCGCCGAT
* *
56183803 GCCATGTCCCAGACATGGTCTTACACTG--GCACACATATCATCACTGAT
1 GCCATGTCCCAGACATGGTCTTACA-TGAAGCACACATATCATCGCCGAT
* * * *
56183851 GCCATGTCCCAGACATGGTCTTACA-CAGGAACATATATCATCGCCGAT
1 GCCATGTCCCAGACATGGTCTTACATGAAGCACACATATCATCGCCGAT
* * *
56183899 GCCATGTCCCAGACATGGTCTTACA-CAAGCACATATATCATCGCTGAT
1 GCCATGTCCCAGACATGGTCTTACATGAAGCACACATATCATCGCCGAT
* * * *
56183947 GCCATGTCCCAGACATGGTTTTACACTG--GCACATATACCATCGTCGAT
1 GCCATGTCCCAGACATGGTCTTACA-TGAAGCACACATATCATCGCCGAT
* *
56183995 GTCATGTCCCAAACATGGTCTTACA
1 GCCATGTCCCAGACATGGTCTTACA
56184020 CAGGCACATT
Statistics
Matches: 236, Mismatches: 23, Indels: 12
0.87 0.08 0.04
Matches are distributed among these distances:
47 1 0.00
48 233 0.99
49 2 0.01
ACGTcount: A:0.27, C:0.31, G:0.17, T:0.25
Consensus pattern (49 bp):
GCCATGTCCCAGACATGGTCTTACATGAAGCACACATATCATCGCCGAT
Found at i:56183971 original size:144 final size:144
Alignment explanation
Indices: 56183745--56184028 Score: 428
Period size: 144 Copynumber: 2.0 Consensus size: 144
56183735 ATCCACATAC
* * *
56183745 CATCACCGATGCCATGTCCCCGACATGGTCTTACATGAATCCACATATCATCGCTGATGCCATGT
1 CATCACCGATGCCATGTCCCAGACATGGTCTTACATCAAGCCACATATCATCGCTGATGCCATGT
* *
56183810 CCCAGACATGGTCTTACACTGGCACACATATCATCACT-GATGCCATGTCCCAGACATGGTCTTA
66 CCCAGACATGGTCTTACACTGGCACACATACCATC-CTCGATGCCATGTCCCAAACATGGTCTTA
56183874 CACAGGAACATATAT
130 CACAGGAACATATAT
* *
56183889 CATCGCCGATGCCATGTCCCAGACATGGTCTTACA-CAAGCACATATATCATCGCTGATGCCATG
1 CATCACCGATGCCATGTCCCAGACATGGTCTTACATCAAGC-CACATATCATCGCTGATGCCATG
* * * *
56183953 TCCCAGACATGGTTTTACACTGGCACATATACCATCGTCGATGTCATGTCCCAAACATGGTCTTA
65 TCCCAGACATGGTCTTACACTGGCACACATACCATCCTCGATGCCATGTCCCAAACATGGTCTTA
*
56184018 CACAGGCACAT
130 CACAGGAACAT
56184029 TTAGCACGGT
Statistics
Matches: 126, Mismatches: 12, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
143 4 0.03
144 122 0.97
ACGTcount: A:0.27, C:0.30, G:0.17, T:0.25
Consensus pattern (144 bp):
CATCACCGATGCCATGTCCCAGACATGGTCTTACATCAAGCCACATATCATCGCTGATGCCATGT
CCCAGACATGGTCTTACACTGGCACACATACCATCCTCGATGCCATGTCCCAAACATGGTCTTAC
ACAGGAACATATAT
Found at i:56184020 original size:48 final size:48
Alignment explanation
Indices: 56183752--56184028 Score: 378
Period size: 48 Copynumber: 5.8 Consensus size: 48
56183742 TACCATCACC
* * ** *
56183752 GATGCCATGTCCCCGACATGGTCTTACATGAATC-CACATATCATCGCT
1 GATGCCATGTCCCAGACATGGTCTTACA-CAGGCACATATATCATCGCT
* * *
56183800 GATGCCATGTCCCAGACATGGTCTTACACTGGCACACATATCATCACT
1 GATGCCATGTCCCAGACATGGTCTTACACAGGCACATATATCATCGCT
* *
56183848 GATGCCATGTCCCAGACATGGTCTTACACAGGAACATATATCATCGCC
1 GATGCCATGTCCCAGACATGGTCTTACACAGGCACATATATCATCGCT
*
56183896 GATGCCATGTCCCAGACATGGTCTTACACAAGCACATATATCATCGCT
1 GATGCCATGTCCCAGACATGGTCTTACACAGGCACATATATCATCGCT
* * *
56183944 GATGCCATGTCCCAGACATGGTTTTACACTGGCACATATACCATCG-T
1 GATGCCATGTCCCAGACATGGTCTTACACAGGCACATATATCATCGCT
* *
56183991 CGATGTCATGTCCCAAACATGGTCTTACACAGGCACAT
1 -GATGCCATGTCCCAGACATGGTCTTACACAGGCACAT
56184029 TTAGCACGGT
Statistics
Matches: 205, Mismatches: 22, Indels: 4
0.89 0.10 0.02
Matches are distributed among these distances:
47 2 0.01
48 203 0.99
ACGTcount: A:0.27, C:0.30, G:0.18, T:0.25
Consensus pattern (48 bp):
GATGCCATGTCCCAGACATGGTCTTACACAGGCACATATATCATCGCT
Found at i:56189463 original size:24 final size:25
Alignment explanation
Indices: 56189417--56189463 Score: 62
Period size: 24 Copynumber: 1.9 Consensus size: 25
56189407 ACATTTCAAT
56189417 ATAAGTCACATTAAATAAAAACACA
1 ATAAGTCACATTAAATAAAAACACA
*
56189442 ATAA-TCA-ATTAACATAATAACA
1 ATAAGTCACATTAA-ATAAAAACA
56189464 TGCTCGATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 5 0.25
24 11 0.55
25 4 0.20
ACGTcount: A:0.60, C:0.15, G:0.02, T:0.23
Consensus pattern (25 bp):
ATAAGTCACATTAAATAAAAACACA
Found at i:56196025 original size:22 final size:22
Alignment explanation
Indices: 56195997--56196053 Score: 87
Period size: 22 Copynumber: 2.6 Consensus size: 22
56195987 TACTAGGCTC
56195997 ACACGCCCGTGTGGTCCAAGGG
1 ACACGCCCGTGTGGTCCAAGGG
* *
56196019 ACACGCCCGTGTGGTTCGAGGG
1 ACACGCCCGTGTGGTCCAAGGG
*
56196041 ACACACCCGTGTG
1 ACACGCCCGTGTG
56196054 ACCCTAAGAC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.18, C:0.32, G:0.35, T:0.16
Consensus pattern (22 bp):
ACACGCCCGTGTGGTCCAAGGG
Found at i:56198367 original size:50 final size:48
Alignment explanation
Indices: 56198248--56198564 Score: 195
Period size: 46 Copynumber: 6.7 Consensus size: 48
56198238 GGTAAAGTGC
* *
56198248 CGATGCCATGTCTCAGACATGGTCTTACATTGGCTATCATCTTCGAGG
1 CGATGCCATGTCTCAGACATGGTCTTACACTAGCTATCATCTTCGAGG
* * *
56198296 CTGATGCCATGTC-CTAAACATGGTCTTACACTAGCTCTCA-CATAATC-ATGT
1 C-GATGCCATGTCTC-AGACATGGTCTTACACTAGCTATCATC-T--TCGA-GG
* *
56198347 CGATGCCATGTCTCAGACATGGTCTTACACTAAC-A-CATC-TCGTAGC
1 CGATGCCATGTCTCAGACATGGTCTTACACTAGCTATCATCTTCG-AGG
* * * * *
56198393 CGATG-CATGTCCCAG-CAT-GTCTTATACTGGCT-TACGTC-CCGAGG
1 CGATGCCATGTCTCAGACATGGTCTTACACTAGCTAT-CATCTTCGAGG
* * * *
56198437 CTGATG-CATGTCTTAGACAT-GTCTTACACTAGC-ACTCGTC-TCAATGC
1 C-GATGCCATGTCTCAGACATGGTCTTACACTAGCTA-TCATCTTCGA-GG
* ** *
56198484 CGATGCCATGTC-CTAGACATGGTCTTACACTAGCTCTCATAAT-GTGG
1 CGATGCCATGTCTC-AGACATGGTCTTACACTAGCTATCATCTTCGAGG
*
56198531 CCGATG-CATGTCCCAGACAT-GTCTTACACTAGCT
1 -CGATGCCATGTCTCAGACATGGTCTTACACTAGCT
56198565 CACACAAATG
Statistics
Matches: 214, Mismatches: 30, Indels: 52
0.72 0.10 0.18
Matches are distributed among these distances:
43 10 0.05
44 6 0.03
45 28 0.13
46 44 0.21
47 29 0.14
48 27 0.13
49 35 0.16
50 30 0.14
51 5 0.02
ACGTcount: A:0.23, C:0.28, G:0.19, T:0.29
Consensus pattern (48 bp):
CGATGCCATGTCTCAGACATGGTCTTACACTAGCTATCATCTTCGAGG
Found at i:56198539 original size:94 final size:93
Alignment explanation
Indices: 56198246--56198563 Score: 285
Period size: 94 Copynumber: 3.4 Consensus size: 93
56198236 TGGGTAAAGT
* * *
56198246 GCCGATGCCATGTCTCAGACATGGTCTTACATTGGCTATCATCTTCG-AGGCTGATGCCATGTCC
1 GCCGATG-CATGTCTCAGACAT-GTCTTACACTAGC-A-CATC-TCGTA-GCCGATGCCATGTCC
* *
56198310 TAAACATGGTCTTACACTAGCTCTCACATAATCAT-
60 TAGACATGGTCTTACACTAGCTCT-ACATAAT-GTG
* * *
56198345 GTCGATGCCATGTCTCAGACATGGTCTTACACTAACACATCTCGTAGCCGATG-CATGTCCCAG-
1 GCCGATG-CATGTCTCAGACAT-GTCTTACACTAGCACATCTCGTAGCCGATGCCATGTCCTAGA
* * * *** *
56198408 CAT-GTCTTATACTGGCT-TACGTCCCGAG
64 CATGGTCTTACACTAGCTCTACATAATGTG
* *
56198436 GCTGATGCATGTCTTAGACATGTCTTACACTAGCAC-TCGTC-TCAATGCCGATGCCATGTCCTA
1 GCCGATGCATGTCTCAGACATGTCTTACACTAGCACATC-TCGT--A-GCCGATGCCATGTCCTA
56198499 GACATGGTCTTACACTAGCTCT-CATAATGTG
62 GACATGGTCTTACACTAGCTCTACATAATGTG
*
56198530 GCCGATGCATGTCCCAGACATGTCTTACACTAGC
1 GCCGATGCATGTCTCAGACATGTCTTACACTAGC
56198564 TCACACAAAT
Statistics
Matches: 179, Mismatches: 30, Indels: 25
0.76 0.13 0.11
Matches are distributed among these distances:
88 3 0.02
89 16 0.09
90 14 0.08
91 15 0.08
92 10 0.06
93 15 0.08
94 50 0.28
95 9 0.05
96 9 0.05
97 5 0.03
98 1 0.01
99 32 0.18
ACGTcount: A:0.23, C:0.28, G:0.19, T:0.29
Consensus pattern (93 bp):
GCCGATGCATGTCTCAGACATGTCTTACACTAGCACATCTCGTAGCCGATGCCATGTCCTAGACA
TGGTCTTACACTAGCTCTACATAATGTG
Found at i:56198546 original size:139 final size:141
Alignment explanation
Indices: 56198246--56198556 Score: 341
Period size: 139 Copynumber: 2.2 Consensus size: 141
56198236 TGGGTAAAGT
* * * * *
56198246 GCCGATGCCATGTCTCAGACATGGTCTTACATTGGC-TATCATCTTCGAGGCTGATGCCATGTCC
1 GCCGATG-CATGTCCCAGACAT-GTCTTATACTGGCTTA-CGTC-CCGAGGCTGATGCCATGTCC
* *
56198310 TAAACATGGTCTTACACTAGCTCTCACATAATCATGTCGATGCCATGTCTCAGACATGGTCTTAC
62 TAAACATGGTCTTACACTAGCACTCACATAA-CATGCCGATGCCATGTCTCAGACATGGTCTTAC
56198375 ACTAACACATCTCGTA
126 ACTAACACATCTCGTA
* *
56198391 GCCGATGCATGTCCCAG-CATGTCTTATACTGGCTTACGTCCCGAGGCTGATG-CATGTCTTAGA
1 GCCGATGCATGTCCCAGACATGTCTTATACTGGCTTACGTCCCGAGGCTGATGCCATGTCCTAAA
* *
56198454 CAT-GTCTTACACTAGCACTCGTC-TCA-ATGCCGATGCCATGTC-CTAGACATGGTCTTACACT
66 CATGGTCTTACACTAGCACTC-ACATAACATGCCGATGCCATGTCTC-AGACATGGTCTTACACT
* * * *
56198515 AGCTC-TCATAATGTG
129 AACACATC-T--CGTA
56198530 GCCGATGCATGTCCCAGACATGTCTTA
1 GCCGATGCATGTCCCAGACATGTCTTA
56198557 CACTAGCTCA
Statistics
Matches: 144, Mismatches: 15, Indels: 19
0.81 0.08 0.11
Matches are distributed among these distances:
136 3 0.02
137 36 0.25
139 37 0.26
140 22 0.15
141 11 0.08
142 14 0.10
143 5 0.03
144 9 0.06
145 7 0.05
ACGTcount: A:0.23, C:0.28, G:0.20, T:0.29
Consensus pattern (141 bp):
GCCGATGCATGTCCCAGACATGTCTTATACTGGCTTACGTCCCGAGGCTGATGCCATGTCCTAAA
CATGGTCTTACACTAGCACTCACATAACATGCCGATGCCATGTCTCAGACATGGTCTTACACTAA
CACATCTCGTA
Found at i:56202112 original size:31 final size:29
Alignment explanation
Indices: 56202072--56202177 Score: 106
Period size: 31 Copynumber: 3.5 Consensus size: 29
56202062 GATATTAAAT
*
56202072 TTAATTTAATACTTATCTAAATAGTATTTTA
1 TTAATTTAATA-TTATCTAGATA-TATTTTA
* * **
56202103 TTAAATTAATATTA-ATATGATATATTAAA
1 TTAATTTAATATTATCTA-GATATATTTTA
56202132 TTTAATTTAATATTTATCTAGATAATATTTTA
1 -TTAATTTAATA-TTATCTAGAT-ATATTTTA
56202164 TTAATTTAATATTA
1 TTAATTTAATATTA
56202178 ATGTGATTAA
Statistics
Matches: 61, Mismatches: 9, Indels: 11
0.75 0.11 0.14
Matches are distributed among these distances:
29 7 0.11
30 19 0.31
31 27 0.44
32 8 0.13
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.52
Consensus pattern (29 bp):
TTAATTTAATATTATCTAGATATATTTTA
Found at i:56202115 original size:61 final size:61
Alignment explanation
Indices: 56202050--56202179 Score: 215
Period size: 61 Copynumber: 2.1 Consensus size: 61
56202040 ATTTATCTAG
*
56202050 ATATTAATATGAGATATTAAATTTAATTTAATACTTATCTAAATAGTATTTTATTAAATTA
1 ATATTAATATGAGATATTAAATTTAATTTAATACTTATCTAAATAATATTTTATTAAATTA
* * * *
56202111 ATATTAATATGATATATTAAATTTAATTTAATATTTATCTAGATAATATTTTATTAATTTA
1 ATATTAATATGAGATATTAAATTTAATTTAATACTTATCTAAATAATATTTTATTAAATTA
56202172 ATATTAAT
1 ATATTAAT
56202180 GTGATTAAAT
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
61 64 1.00
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.50
Consensus pattern (61 bp):
ATATTAATATGAGATATTAAATTTAATTTAATACTTATCTAAATAATATTTTATTAAATTA
Found at i:56207397 original size:12 final size:12
Alignment explanation
Indices: 56207380--56207405 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
56207370 ATACGTCTGG
56207380 TTGTCAAGTTCA
1 TTGTCAAGTTCA
56207392 TTGTCAAGTTCA
1 TTGTCAAGTTCA
56207404 TT
1 TT
56207406 AAACAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.15, G:0.15, T:0.46
Consensus pattern (12 bp):
TTGTCAAGTTCA
Found at i:56208410 original size:13 final size:14
Alignment explanation
Indices: 56208378--56208407 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
56208368 TAAAGACTAA
*
56208378 TTTATTTTTATTTT
1 TTTAATTTTATTTT
56208392 TTTAATTTTATTTT
1 TTTAATTTTATTTT
56208406 TT
1 TT
56208408 AATAGAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (14 bp):
TTTAATTTTATTTT
Found at i:56209024 original size:34 final size:34
Alignment explanation
Indices: 56208981--56209084 Score: 199
Period size: 34 Copynumber: 3.1 Consensus size: 34
56208971 CGAAACAAAG
*
56208981 AAAAAACATGTTGAGAGACAAGTAATTCTAATCT
1 AAAAAACATGTTGAGAGACAAGTAACTCTAATCT
56209015 AAAAAACATGTTGAGAGACAAGTAACTCTAATCT
1 AAAAAACATGTTGAGAGACAAGTAACTCTAATCT
56209049 AAAAAACATGTTGAGAGACAAGTAACTCTAATCT
1 AAAAAACATGTTGAGAGACAAGTAACTCTAATCT
56209083 AA
1 AA
56209085 GAGTCCCAAT
Statistics
Matches: 69, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
34 69 1.00
ACGTcount: A:0.48, C:0.13, G:0.14, T:0.24
Consensus pattern (34 bp):
AAAAAACATGTTGAGAGACAAGTAACTCTAATCT
Found at i:56217174 original size:43 final size:44
Alignment explanation
Indices: 56217126--56217215 Score: 130
Period size: 43 Copynumber: 2.1 Consensus size: 44
56217116 AACTTTGTTT
* *
56217126 TTAGTTTACC-ACTTAAACTCTGATTAGTGCAGGTTATTTTAA-A
1 TTAGTTT-CCTACTTAAACTCTCATTAATGCAGGTTATTTTAATA
*
56217169 TTAGTTTCCTACTTAAACTCTCATTAATGTAGGTTATTTTAATA
1 TTAGTTTCCTACTTAAACTCTCATTAATGCAGGTTATTTTAATA
56217213 TTA
1 TTA
56217216 TTTGGCCTAC
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
42 2 0.05
43 36 0.86
44 4 0.10
ACGTcount: A:0.30, C:0.13, G:0.11, T:0.46
Consensus pattern (44 bp):
TTAGTTTCCTACTTAAACTCTCATTAATGCAGGTTATTTTAATA
Found at i:56219708 original size:51 final size:51
Alignment explanation
Indices: 56219648--56219749 Score: 195
Period size: 51 Copynumber: 2.0 Consensus size: 51
56219638 GAACAATCGC
*
56219648 TCCCCTAATAGTAATCAGCAAAAAAGGAATTGTTAGATGAAAGATAATTAT
1 TCCCCTAATAGTAATCAACAAAAAAGGAATTGTTAGATGAAAGATAATTAT
56219699 TCCCCTAATAGTAATCAACAAAAAAGGAATTGTTAGATGAAAGATAATTAT
1 TCCCCTAATAGTAATCAACAAAAAAGGAATTGTTAGATGAAAGATAATTAT
56219750 AACAGAGAGA
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 50 1.00
ACGTcount: A:0.46, C:0.12, G:0.15, T:0.27
Consensus pattern (51 bp):
TCCCCTAATAGTAATCAACAAAAAAGGAATTGTTAGATGAAAGATAATTAT
Found at i:56225962 original size:5 final size:5
Alignment explanation
Indices: 56225952--56225976 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
56225942 TTTTTCTTGC
56225952 AATTT AATTT AATTT AATTT AATTT
1 AATTT AATTT AATTT AATTT AATTT
56225977 TTATTATTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
AATTT
Found at i:56231508 original size:47 final size:47
Alignment explanation
Indices: 56231437--56232410 Score: 1592
Period size: 47 Copynumber: 20.6 Consensus size: 47
56231427 CCCTTCGGGA
* * * * * *
56231437 CTTATCATATTTATACACTTTCACATTCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
56231484 CCTATCACATATATACACTTTCACATTCATCACATTGGCCATTCA-GC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATT-AGGC
*
56231531 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
56231578 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
56231625 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
56231672 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
56231719 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
**
56231768 CTTATCACATATATATTCTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
56231815 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
56231862 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
56231909 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATT-CGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
56231957 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
56232004 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
56232051 CTTATCACATATATACATTTTCACATTCATCACTTCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
56232098 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
56232147 CTTATCACATATATATACTTTCACATTCATCACATCGGCCATTAGAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
56232194 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
56232241 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
56232288 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
56232337 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
56232384 CTTATCACATATATACACTTTCACATT
1 CTTATCACATATATACACTTTCACATT
56232411 TATTCAAATA
Statistics
Matches: 866, Mismatches: 50, Indels: 22
0.92 0.05 0.02
Matches are distributed among these distances:
46 34 0.04
47 655 0.76
48 10 0.01
49 167 0.19
ACGTcount: A:0.29, C:0.29, G:0.08, T:0.34
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:56231515 original size:25 final size:25
Alignment explanation
Indices: 56231487--56231565 Score: 85
Period size: 25 Copynumber: 3.3 Consensus size: 25
56231477 ACTCGGCCCT
56231487 ATCACATATATACACTTTCACATTC
1 ATCACATATATACACTTTCACATTC
** * *
56231512 ATCACAT-T-GGC-CATTCAGCCTT-
1 ATCACATATATACACTTTCA-CATTC
56231534 ATCACATATATACACTTTCACATTC
1 ATCACATATATACACTTTCACATTC
56231559 ATCACAT
1 ATCACAT
56231566 CGGCCATTCG
Statistics
Matches: 41, Mismatches: 8, Indels: 10
0.69 0.14 0.17
Matches are distributed among these distances:
22 12 0.29
23 5 0.12
24 5 0.12
25 19 0.46
ACGTcount: A:0.33, C:0.29, G:0.04, T:0.34
Consensus pattern (25 bp):
ATCACATATATACACTTTCACATTC
Found at i:56231817 original size:190 final size:190
Alignment explanation
Indices: 56231437--56232410 Score: 1731
Period size: 190 Copynumber: 5.1 Consensus size: 190
56231427 CCCTTCGGGA
* * * * * * * *
56231437 CTTATCATATTTATACACTTTCACATTCATCACGTTGGCCACTCGGCCCTATCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACAC
*
56231502 TTTCACATTCATCACATTGGCCATTCA-GCCTTATCAC--ATATATACACTTTCACATTCATCAC
66 TTTCACATTCATCACATCGGCCATT-AGGCCTTATCACATATATATACACTTTCACATTCATCAC
*
56231564 ATCGGCCATTCGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
130 ATTGGCCATTCGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
56231625 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACAC
56231690 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACA
66 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACA
**
56231755 TTGGCCATTCGGCCTTATCACATATATATTCTTTCACATTCATCACATCGGCCATTAGGC
131 TTGGCCATTCGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
56231815 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACAC
56231880 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACA
66 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACA
56231945 TTGGCCATTC-GCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
131 TTGGCCATTCGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
56232004 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGACCTTATCACATATATACAT
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACAC
*
56232069 TTTCACATTCATCACTTCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACA
66 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACA
* *
56232134 TTGGCCATTCGGCCTTATCACATATATATACTTTCACATTCATCACATCGGCCATTAGAC
131 TTGGCCATTCGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
56232194 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACAC
56232259 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACA
66 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACA
56232324 TTGGCCATTCGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
131 TTGGCCATTCGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
56232384 CTTATCACATATATACACTTTCACATT
1 CTTATCACATATATACACTTTCACATT
56232411 TATTCAAATA
Statistics
Matches: 752, Mismatches: 30, Indels: 6
0.95 0.04 0.01
Matches are distributed among these distances:
187 1 0.00
188 91 0.12
189 181 0.24
190 479 0.64
ACGTcount: A:0.29, C:0.29, G:0.08, T:0.34
Consensus pattern (190 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACAC
TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACA
TTGGCCATTCGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:56236227 original size:30 final size:30
Alignment explanation
Indices: 56236193--56236252 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
56236183 AATGACTTAA
56236193 CCAAGTCTATAAACATCAAGTATGTACACT
1 CCAAGTCTATAAACATCAAGTATGTACACT
56236223 CCAAGTCTATAAACATCAAGTATGTACACT
1 CCAAGTCTATAAACATCAAGTATGTACACT
56236253 TTTAAACATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.40, C:0.23, G:0.10, T:0.27
Consensus pattern (30 bp):
CCAAGTCTATAAACATCAAGTATGTACACT
Found at i:56236515 original size:40 final size:40
Alignment explanation
Indices: 56236464--56236802 Score: 549
Period size: 40 Copynumber: 8.5 Consensus size: 40
56236454 CCTTCAGGGT
* * *
56236464 TTAGCACGGATATATCACTAGCATGAATGCTCTTCGGAAC
1 TTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGAAC
*
56236504 TTAGTCCGGATACATCACTAGCACGAATGCTCTTC-GAGAC
1 TTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGA-AC
*
56236544 TTAGCCCGGATACATCACTAGCACGAATGCTCTTCGAAAC
1 TTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGAAC
*
56236584 TTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGGAC
1 TTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGAAC
*
56236624 TTAGCCCAGATACATCACTAGCACGAATGCTCTTC-GAGAC
1 TTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGA-AC
*
56236664 TTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGGAC
1 TTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGAAC
56236704 TTAGCCCGGATACATCACTAGCACGAATGCTCTTC-GAGAC
1 TTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGA-AC
*
56236744 TTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGGAC
1 TTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGAAC
56236784 TTAGCCCGGATACATCACT
1 TTAGCCCGGATACATCACT
56236803 CTCAATTCTC
Statistics
Matches: 279, Mismatches: 14, Indels: 12
0.91 0.05 0.04
Matches are distributed among these distances:
39 4 0.01
40 272 0.97
41 3 0.01
ACGTcount: A:0.27, C:0.29, G:0.20, T:0.24
Consensus pattern (40 bp):
TTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGAAC
Found at i:56238288 original size:47 final size:47
Alignment explanation
Indices: 56238217--56238621 Score: 675
Period size: 47 Copynumber: 8.6 Consensus size: 47
56238207 CCCTTCGGGA
* * * * * *
56238217 CTTATCATATTTATACACTTTCACATTCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
56238264 CCTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
56238311 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
56238358 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
56238405 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
56238452 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
56238499 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
56238548 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
56238595 CTTATCACATATATACACTTTCACATT
1 CTTATCACATATATACACTTTCACATT
56238622 TATTCAAATA
Statistics
Matches: 342, Mismatches: 14, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
47 297 0.87
49 45 0.13
ACGTcount: A:0.29, C:0.30, G:0.08, T:0.34
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:56238295 original size:25 final size:25
Alignment explanation
Indices: 56238267--56238345 Score: 76
Period size: 25 Copynumber: 3.3 Consensus size: 25
56238257 ACTCGGCCCT
56238267 ATCACATATATACACTTTCACATTC
1 ATCACATATATACACTTTCACATTC
** * * *
56238292 ATCACAT-T-GGC-CATTCGGCCTT-
1 ATCACATATATACACTTTC-ACATTC
56238314 ATCACATATATACACTTTCACATTC
1 ATCACATATATACACTTTCACATTC
56238339 ATCACAT
1 ATCACAT
56238346 CGGCCATTCG
Statistics
Matches: 39, Mismatches: 10, Indels: 10
0.66 0.17 0.17
Matches are distributed among these distances:
22 11 0.28
23 5 0.13
24 5 0.13
25 18 0.46
ACGTcount: A:0.32, C:0.29, G:0.05, T:0.34
Consensus pattern (25 bp):
ATCACATATATACACTTTCACATTC
Found at i:56242466 original size:27 final size:26
Alignment explanation
Indices: 56242418--56242477 Score: 75
Period size: 27 Copynumber: 2.3 Consensus size: 26
56242408 GCGAGGCTGC
*
56242418 CAGATATTGTGACGAAGTCACCAGATA
1 CAGATATTGTGACGAAGCCACCAGA-A
* * *
56242445 CAGATATTGTGGCTAGGCCACCAGAA
1 CAGATATTGTGACGAAGCCACCAGAA
56242471 CAGATAT
1 CAGATAT
56242478 ATATATATGT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 8 0.28
27 21 0.72
ACGTcount: A:0.35, C:0.20, G:0.23, T:0.22
Consensus pattern (26 bp):
CAGATATTGTGACGAAGCCACCAGAA
Found at i:56242490 original size:33 final size:32
Alignment explanation
Indices: 56242439--56242502 Score: 83
Period size: 33 Copynumber: 2.0 Consensus size: 32
56242429 ACGAAGTCAC
* *
56242439 CAGATACAGATATTGTGGCTAGGCCACCAGAA
1 CAGATACAGATATTGTGGCGAAGCCACCAGAA
* *
56242471 CAGATATATATATATGTGGCGAAGCCACCAGA
1 CAGATACAGATAT-TGTGGCGAAGCCACCAGA
56242503 TTGCAGTGAG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
32 11 0.41
33 16 0.59
ACGTcount: A:0.36, C:0.20, G:0.23, T:0.20
Consensus pattern (32 bp):
CAGATACAGATATTGTGGCGAAGCCACCAGAA
Found at i:56246403 original size:16 final size:17
Alignment explanation
Indices: 56246372--56246411 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
56246362 ACCCAAAATT
*
56246372 AAATCAAAATATAAAAA
1 AAATAAAAATATAAAAA
*
56246389 TAATAAAAATA-AAAAA
1 AAATAAAAATATAAAAA
56246405 AAATAAA
1 AAATAAA
56246412 CTAACTTAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
16 11 0.55
17 9 0.45
ACGTcount: A:0.80, C:0.03, G:0.00, T:0.17
Consensus pattern (17 bp):
AAATAAAAATATAAAAA
Found at i:56246832 original size:27 final size:26
Alignment explanation
Indices: 56246784--56246843 Score: 75
Period size: 27 Copynumber: 2.3 Consensus size: 26
56246774 GCGAGGCTGC
*
56246784 CAGATATTGTGACGAAGTCACCAGATA
1 CAGATATTGTGACGAAGCCACCAGA-A
* * *
56246811 CAGATATTGTGGCTAGGCCACCAGAA
1 CAGATATTGTGACGAAGCCACCAGAA
56246837 CAGATAT
1 CAGATAT
56246844 ATATATGTGG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 8 0.28
27 21 0.72
ACGTcount: A:0.35, C:0.20, G:0.23, T:0.22
Consensus pattern (26 bp):
CAGATATTGTGACGAAGCCACCAGAA
Found at i:56254990 original size:13 final size:13
Alignment explanation
Indices: 56254972--56254996 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
56254962 GTAAGTGATT
56254972 TTGATGATTTTTC
1 TTGATGATTTTTC
56254985 TTGATGATTTTT
1 TTGATGATTTTT
56254997 ATACTTTTAA
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:0.16, C:0.04, G:0.16, T:0.64
Consensus pattern (13 bp):
TTGATGATTTTTC
Found at i:56255774 original size:48 final size:46
Alignment explanation
Indices: 56255719--56256086 Score: 229
Period size: 46 Copynumber: 7.8 Consensus size: 46
56255709 TATGAAAACC
*
56255719 AGTGTAAGACCATGTCTGGCACATGGCATCGGCATTGAGACGAGAGCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGAGA-GAGAG-T
* * * *
56255767 AGTGTAAGA-CATGTTTGGGACAT-GCATCGGCCTCGAGATGTA-AGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGAGA-G-AGAG-T
* * *
56255813 AGTATAAGA-CATGTCTGGGACAT-GCATCGGC-TACGAGAG-GTGTT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCAT-TGAGAGAGAG-T
* * *
56255857 AGTGTAAGACCATGTTTGGGACATGGCATCGACACGTAT-AGAG-GTGT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCA--T-TGAGAGAGAGT
* * * * *
56255904 GAGTATAAGACCATGTCTGGGACATGGCATCAGTATGGATATGTGAGAGCT
1 -AGTGTAAGACCATGTCTGGGACATGGCATCGGCATTG--A-GAGAGAG-T
* * * * ** *
56255955 AGTGTAAGACCATGTTTGGGACATGGCATTGGCCTCGATTTTGATAGT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGA--GAGAGAGT
*
56256003 CAGTGTAAGACCATGT-TCGGGACATGGCATCGAC-TTGATG-GATGAGT
1 -AGTGTAAGACCATGTCT-GGGACATGGCATCGGCATTGA-GAGA-GAGT
*
56256050 CAGTGTAAGACCATGTCTGGGATATGGCATCGGCATT
1 -AGTGTAAGACCATGTCTGGGACATGGCATCGGCATT
56256087 ATACCCTATG
Statistics
Matches: 260, Mismatches: 39, Indels: 42
0.76 0.11 0.12
Matches are distributed among these distances:
44 9 0.03
45 15 0.06
46 61 0.23
47 48 0.18
48 55 0.21
49 39 0.15
50 32 0.12
51 1 0.00
ACGTcount: A:0.26, C:0.17, G:0.31, T:0.26
Consensus pattern (46 bp):
AGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGAGAGAGAGT
Found at i:56255821 original size:46 final size:46
Alignment explanation
Indices: 56255676--56255887 Score: 182
Period size: 46 Copynumber: 4.6 Consensus size: 46
56255666 GTGTGCTAGC
* * * * *
56255676 GTAAGACATGTCTGGGACATGCATCGACCAC-ATTATGAAAACCAGT
1 GTAAGACATGTCTGGGACATGCATCGGCCTCGA-GATGTAAGCCAGT
* * * * *
56255722 GTAAGACCATGTCTGGCACATGGCATCGGCATTGAGACG-AGAGCTAGT
1 GTAAGA-CATGTCTGGGACAT-GCATCGGCCTCGAGATGTA-AGCCAGT
*
56255770 GTAAGACATGTTTGGGACATGCATCGGCCTCGAGATGTAAGCCAGT
1 GTAAGACATGTCTGGGACATGCATCGGCCTCGAGATGTAAGCCAGT
* * **
56255816 ATAAGACATGTCTGGGACATGCATCGG-CTACGAGAGGT--GTTAGT
1 GTAAGACATGTCTGGGACATGCATCGGCCT-CGAGATGTAAGCCAGT
*
56255860 GTAAGACCATGTTTGGGACATGGCATCG
1 GTAAGA-CATGTCTGGGACAT-GCATCG
56255888 ACACGTATAG
Statistics
Matches: 136, Mismatches: 22, Indels: 16
0.78 0.13 0.09
Matches are distributed among these distances:
44 9 0.07
45 15 0.11
46 64 0.47
47 27 0.20
48 20 0.15
49 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.29, T:0.23
Consensus pattern (46 bp):
GTAAGACATGTCTGGGACATGCATCGGCCTCGAGATGTAAGCCAGT
Found at i:56256999 original size:13 final size:13
Alignment explanation
Indices: 56256969--56256993 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
56256959 ATGATTAAAG
56256969 TATAATATAATAA
1 TATAATATAATAA
56256982 TATAATATAATA
1 TATAATATAATA
56256994 TAATAAAGTA
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:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
TATAATATAATAA
Found at i:56257042 original size:13 final size:14
Alignment explanation
Indices: 56257007--56257044 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
56256997 TAAAGTAATT
*
56257007 AAATAAAACAAATA
1 AAATAAAAGAAATA
*
56257021 AAATAAAAGAAA-G
1 AAATAAAAGAAATA
56257034 AAATAAAAGAA
1 AAATAAAAGAA
56257045 CAAATGAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 11 0.50
14 11 0.50
ACGTcount: A:0.79, C:0.03, G:0.08, T:0.11
Consensus pattern (14 bp):
AAATAAAAGAAATA
Found at i:56258903 original size:20 final size:20
Alignment explanation
Indices: 56258878--56258918 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
56258868 GCCCTATGGC
56258878 CATGTCCCAAGCCACACGGG
1 CATGTCCCAAGCCACACGGG
*
56258898 CATGTCCCAGGCCACACGGG
1 CATGTCCCAAGCCACACGGG
56258918 C
1 C
56258919 GTGTGCCCCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.22, C:0.41, G:0.27, T:0.10
Consensus pattern (20 bp):
CATGTCCCAAGCCACACGGG
Found at i:56265195 original size:27 final size:27
Alignment explanation
Indices: 56265171--56265473 Score: 302
Period size: 27 Copynumber: 11.2 Consensus size: 27
56265161 TTAGTTTACC
56265171 AAATTACCAAAATACCCTTGGTTTATA
1 AAATTACCAAAATACCCTTGGTTTATA
* *
56265198 AAATCACCAAAATACTCC-TGGTTTGTA
1 AAATTACCAAAATAC-CCTTGGTTTATA
* *
56265225 AAATTACCAAAATACCTTTGGTTTACA
1 AAATTACCAAAATACCCTTGGTTTATA
* *
56265252 AAATTACCAAAATACCCTTAGTTTGTA
1 AAATTACCAAAATACCCTTGGTTTATA
*
56265279 AAATTACTAAAATACCCTTGGTTTATA
1 AAATTACCAAAATACCCTTGGTTTATA
*
56265306 AAATTACCAAAATACCCTTGGTTTGTA
1 AAATTACCAAAATACCCTTGGTTTATA
* * *
56265333 AAATTATCAAAATACCCTTAGTTTGTA
1 AAATTACCAAAATACCCTTGGTTTATA
* * * *
56265360 AAATTACCAAAATACCATTGATTTGTG
1 AAATTACCAAAATACCCTTGGTTTATA
** * *** *
56265387 AAATTACTGAAATACCCTCGACCTGTA
1 AAATTACCAAAATACCCTTGGTTTATA
*** * ** *
56265414 AAATTATTGAAATACCCTCGACTTGTA
1 AAATTACCAAAATACCCTTGGTTTATA
* *
56265441 AAATTACCAAAGTACCCTTGATTTATA
1 AAATTACCAAAATACCCTTGGTTTATA
*
56265468 GAATTA
1 AAATTA
56265474 TCGTTTTACC
Statistics
Matches: 235, Mismatches: 39, Indels: 4
0.85 0.14 0.01
Matches are distributed among these distances:
26 1 0.00
27 232 0.99
28 2 0.01
ACGTcount: A:0.40, C:0.18, G:0.09, T:0.33
Consensus pattern (27 bp):
AAATTACCAAAATACCCTTGGTTTATA
Found at i:56265236 original size:54 final size:54
Alignment explanation
Indices: 56265171--56265473 Score: 347
Period size: 54 Copynumber: 5.6 Consensus size: 54
56265161 TTAGTTTACC
*
56265171 AAATTACCAAAATACCCTTGGTTTATAAAATCACCAAAATACTCC-TGGTTTGTA
1 AAATTACCAAAATACCCTTGGTTTATAAAATTACCAAAATAC-CCTTGGTTTGTA
* * *
56265225 AAATTACCAAAATACCTTTGGTTTACAAAATTACCAAAATACCCTTAGTTTGTA
1 AAATTACCAAAATACCCTTGGTTTATAAAATTACCAAAATACCCTTGGTTTGTA
*
56265279 AAATTACTAAAATACCCTTGGTTTATAAAATTACCAAAATACCCTTGGTTTGTA
1 AAATTACCAAAATACCCTTGGTTTATAAAATTACCAAAATACCCTTGGTTTGTA
* * * * * *
56265333 AAATTATCAAAATACCCTTAGTTTGTAAAATTACCAAAATACCATTGATTTGTG
1 AAATTACCAAAATACCCTTGGTTTATAAAATTACCAAAATACCCTTGGTTTGTA
** * *** * *** * **
56265387 AAATTACTGAAATACCCTCGACCTGTAAAATTATTGAAATACCCTCGACTTGTA
1 AAATTACCAAAATACCCTTGGTTTATAAAATTACCAAAATACCCTTGGTTTGTA
* * *
56265441 AAATTACCAAAGTACCCTTGATTTATAGAATTA
1 AAATTACCAAAATACCCTTGGTTTATAAAATTA
56265474 TCGTTTTACC
Statistics
Matches: 210, Mismatches: 38, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
53 2 0.01
54 208 0.99
ACGTcount: A:0.40, C:0.18, G:0.09, T:0.33
Consensus pattern (54 bp):
AAATTACCAAAATACCCTTGGTTTATAAAATTACCAAAATACCCTTGGTTTGTA
Found at i:56265526 original size:27 final size:27
Alignment explanation
Indices: 56265496--56266068 Score: 819
Period size: 27 Copynumber: 21.3 Consensus size: 27
56265486 CGATTTACAA
* *
56265496 AATTACCGAAATACACTTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
56265523 AATTACCAAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
56265550 AATTATC-AAAGTACCCCTGTAGGGTAG
1 AATTACCGAAA-TACCCCTGTAGGGTAG
*
56265577 AATTACCGAAATACCCCTGTAAGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
56265604 AATTACCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
56265631 AATTATCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
56265658 AATTACCGAAATACCCTTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
56265685 AATTACCGGAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
56265712 AATTACCGGAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
56265739 AATTACCGGAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
56265766 AATTACCGGAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
56265793 AATTACC-AGAATACCCCTGTAAGGTAG
1 AATTACCGA-AATACCCCTGTAGGGTAG
*
56265820 AATTATCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
56265847 AATTACTGAAATACCCCTATAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
56265874 AATTACCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
** * *
56265901 AATTACTAAAATACCCCTGTATGGTGG
1 AATTACCGAAATACCCCTGTAGGGTAG
56265928 AATTACCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
**
56265955 AATTATTGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
56265982 AATTATCGAAATACCCTTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
** * *
56266009 AATTACTAAAATACCCCTGTAGAGTGG
1 AATTACCGAAATACCCCTGTAGGGTAG
* * * * *
56266036 AATTATCGAGATA-CCTTGTGGGGTAA
1 AATTACCGAAATACCCCTGTAGGGTAG
56266062 AATTACC
1 AATTACC
56266069 ATTTTGCCCC
Statistics
Matches: 493, Mismatches: 49, Indels: 9
0.89 0.09 0.02
Matches are distributed among these distances:
26 17 0.03
27 472 0.96
28 4 0.01
ACGTcount: A:0.34, C:0.20, G:0.22, T:0.25
Consensus pattern (27 bp):
AATTACCGAAATACCCCTGTAGGGTAG
Found at i:56266547 original size:22 final size:22
Alignment explanation
Indices: 56266495--56266548 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
56266485 TTAAAGCCTT
* *
56266495 CTGATTATGGCTCTGTGTCAAC
1 CTGATTATGGCTCTATGCCAAC
*
56266517 CT-ACATATGGCTCTATGCCAAC
1 CTGA-TTATGGCTCTATGCCAAC
56266539 CTGATTATGG
1 CTGATTATGG
56266549 TTGTGTACCA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
21 1 0.04
22 24 0.92
23 1 0.04
ACGTcount: A:0.22, C:0.24, G:0.20, T:0.33
Consensus pattern (22 bp):
CTGATTATGGCTCTATGCCAAC
Found at i:56266748 original size:27 final size:27
Alignment explanation
Indices: 56266718--56266819 Score: 127
Period size: 27 Copynumber: 3.8 Consensus size: 27
56266708 ATTCTGTTAA
* *
56266718 GTGGCTTTGCCACATTATCTGTTTCTG
1 GTGGCTCTGCCACAATATCTGTTTCTG
*
56266745 GTGGCTATGCCACAAATATCTG-TTCTG
1 GTGGCTCTGCCAC-AATATCTGTTTCTG
56266772 GTGGCTCTGCCACAATATCTGTATT-TG
1 GTGGCTCTGCCACAATATCTGT-TTCTG
* *
56266799 GTGACTCTGTCACAATATCTG
1 GTGGCTCTGCCACAATATCTG
56266820 ATAACTGAGC
Statistics
Matches: 67, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
26 8 0.12
27 50 0.75
28 9 0.13
ACGTcount: A:0.19, C:0.23, G:0.22, T:0.37
Consensus pattern (27 bp):
GTGGCTCTGCCACAATATCTGTTTCTG
Found at i:56266994 original size:6 final size:6
Alignment explanation
Indices: 56266979--56267038 Score: 61
Period size: 6 Copynumber: 9.8 Consensus size: 6
56266969 ATTATGTTAC
* *
56266979 CTGATA CTGATT CTGATT CTGATT CTG-TCAC CTGATT CTGATT CTGATT
1 CTGATT CTGATT CTGATT CTGATT CTGAT--T CTGATT CTGATT CTGATT
56267028 CT-AGTT CTGAT
1 CTGA-TT CTGAT
56267039 AATGTTTCTT
Statistics
Matches: 46, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
5 2 0.04
6 39 0.85
7 4 0.09
8 1 0.02
ACGTcount: A:0.18, C:0.20, G:0.17, T:0.45
Consensus pattern (6 bp):
CTGATT
Found at i:56267036 original size:31 final size:31
Alignment explanation
Indices: 56266956--56267029 Score: 103
Period size: 31 Copynumber: 2.4 Consensus size: 31
56266946 TTGCATTCAC
* * *
56266956 ATTCTGATTTTTGATTATGTTACCTGATACTG
1 ATTCTGA-TTCTGATTCTGTCACCTGATACTG
*
56266988 ATTCTGATTCTGATTCTGTCACCTGATTCTG
1 ATTCTGATTCTGATTCTGTCACCTGATACTG
56267019 ATTCTGATTCT
1 ATTCTGATTCT
56267030 AGTTCTGATA
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
31 31 0.82
32 7 0.18
ACGTcount: A:0.19, C:0.18, G:0.15, T:0.49
Consensus pattern (31 bp):
ATTCTGATTCTGATTCTGTCACCTGATACTG
Found at i:56271805 original size:16 final size:17
Alignment explanation
Indices: 56271784--56271819 Score: 65
Period size: 16 Copynumber: 2.2 Consensus size: 17
56271774 CCTTTGGAGG
56271784 CTTTCTTCTT-CTTTTT
1 CTTTCTTCTTGCTTTTT
56271800 CTTTCTTCTTGCTTTTT
1 CTTTCTTCTTGCTTTTT
56271817 CTT
1 CTT
56271820 GAAATCTCTC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 10 0.53
17 9 0.47
ACGTcount: A:0.00, C:0.25, G:0.03, T:0.72
Consensus pattern (17 bp):
CTTTCTTCTTGCTTTTT
Found at i:56273397 original size:18 final size:19
Alignment explanation
Indices: 56273356--56273400 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 19
56273346 GTTAAAAAGG
56273356 TTATTTTT-ATTTTGATTC
1 TTATTTTTCATTTTGATTC
* *
56273374 TCATTTTTCATTTTTATT-
1 TTATTTTTCATTTTGATTC
56273392 TTATTTTTC
1 TTATTTTTC
56273401 TTTAACTAGA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 15 0.65
19 8 0.35
ACGTcount: A:0.16, C:0.09, G:0.02, T:0.73
Consensus pattern (19 bp):
TTATTTTTCATTTTGATTC
Found at i:56273889 original size:21 final size:21
Alignment explanation
Indices: 56273863--56273904 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
56273853 CCATATGGCT
56273863 GTGTCCCTTGGGCACACGGGC
1 GTGTCCCTTGGGCACACGGGC
56273884 GTGTCCCTTGGGCACACGGGC
1 GTGTCCCTTGGGCACACGGGC
56273905 ACGTGAGTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.10, C:0.33, G:0.38, T:0.19
Consensus pattern (21 bp):
GTGTCCCTTGGGCACACGGGC
Found at i:56277111 original size:50 final size:50
Alignment explanation
Indices: 56276980--56277269 Score: 219
Period size: 50 Copynumber: 5.8 Consensus size: 50
56276970 AACCAAAGCT
* * * *
56276980 ATCTGGTACGCATAGTAGCCTACACTTAGTACTACACATGTGACC-AACA
1 ATCTGATACACATAGTAGCCTGCACTTAGTACTACACACGTGACCTAACA
* * * *
56277029 ATCT-AGTAAACGTAGTAGCCTGCACTTGGTACTACACACATGACCTAAGC-
1 ATCTGA-TACACATAGTAGCCTGCACTTAGTACTACACACGTGACCTAA-CA
* * * * **
56277079 ATCTGATACACGTAGTAGCCTGTACTTAGTACTACACACATGA-TTGAAGTT
1 ATCTGATACACATAGTAGCCTGCACTTAGTACTACACACGTGACCT-AA-CA
* * * * * * * * *
56277130 GTCGGGTACGCATAATAGCCTGCACTTAGTACTGCACATGCGACCTAACT
1 ATCTGATACACATAGTAGCCTGCACTTAGTACTACACACGTGACCTAACA
* * *
56277180 ATCTGGTACACATAGTAGCCTACACTTAGTACTACACACGTGACCTAAAACC
1 ATCTGATACACATAGTAGCCTGCACTTAGTACTACACACGTGACCT--AACA
* * * * *
56277232 ATCTTAAATACATAGTAGCCTACACATAGTACTACACA
1 ATCTGATACACATAGTAGCCTGCACTTAGTACTACACA
56277270 TGTGTTCTCA
Statistics
Matches: 192, Mismatches: 40, Indels: 15
0.78 0.16 0.06
Matches are distributed among these distances:
49 37 0.19
50 82 0.43
51 36 0.19
52 37 0.19
ACGTcount: A:0.33, C:0.26, G:0.16, T:0.26
Consensus pattern (50 bp):
ATCTGATACACATAGTAGCCTGCACTTAGTACTACACACGTGACCTAACA
Found at i:56283647 original size:20 final size:20
Alignment explanation
Indices: 56283619--56283662 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
56283609 ACCAAATTTG
*
56283619 CAACTTACCATAATCTTTCA
1 CAACATACCATAATCTTTCA
*
56283639 CAACATACCATAGTCTTTCA
1 CAACATACCATAATCTTTCA
56283659 CAAC
1 CAAC
56283663 TTAAACCACT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.36, C:0.32, G:0.02, T:0.30
Consensus pattern (20 bp):
CAACATACCATAATCTTTCA
Found at i:56283835 original size:41 final size:43
Alignment explanation
Indices: 56283727--56283843 Score: 148
Period size: 41 Copynumber: 2.8 Consensus size: 43
56283717 ATACCAATGA
* **
56283727 CATATCCCAAATATGGTCTTACATGGGATCTCATATCAATGGC
1 CATATCCCAAATATGGTCTTACACGAAATCTCATATCAATGGC
* * **
56283770 AATAGCCCAGCTATGGTCTTACACGAAATCTCATATC-AT-GC
1 CATATCCCAAATATGGTCTTACACGAAATCTCATATCAATGGC
*
56283811 CATATCCCAAATATGGTCTTACACGTAATCTCA
1 CATATCCCAAATATGGTCTTACACGAAATCTCA
56283844 ACTAACCCTA
Statistics
Matches: 62, Mismatches: 12, Indels: 2
0.82 0.16 0.03
Matches are distributed among these distances:
41 30 0.48
42 2 0.03
43 30 0.48
ACGTcount: A:0.32, C:0.26, G:0.14, T:0.29
Consensus pattern (43 bp):
CATATCCCAAATATGGTCTTACACGAAATCTCATATCAATGGC
Found at i:56287327 original size:40 final size:40
Alignment explanation
Indices: 56287279--56287541 Score: 386
Period size: 40 Copynumber: 6.6 Consensus size: 40
56287269 CTACTTGCTC
* *
56287279 AATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACC
1 AATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACA
*
56287319 AATGCCTTCGGGACTTAGCCCGGATATAGTAGCTCGCACA
1 AATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACA
* *
56287359 AATGCCTTCGGGACTTAGCCCGGATGTAATAACTCGCACA
1 AATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACA
* *
56287399 AATGCCTTCGGGACTTAGCCCGGATGTAATAACTCGCACA
1 AATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACA
*
56287439 AATGCCTTTGGGACTTAGCCCGGATATAGTAACTCGCACA
1 AATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACA
* * * *
56287479 AATGCCTTCGGGACTTAGCCTGGA-ACCAGTCACTAG-AGCA
1 AATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCA-CA
56287519 AATGCCTTCGGGACTTAGCCCGG
1 AATGCCTTCGGGACTTAGCCCGG
56287542 TTATCATCCG
Statistics
Matches: 206, Mismatches: 15, Indels: 4
0.92 0.07 0.02
Matches are distributed among these distances:
39 2 0.01
40 204 0.99
ACGTcount: A:0.26, C:0.28, G:0.24, T:0.22
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACA
Found at i:56295468 original size:39 final size:39
Alignment explanation
Indices: 56295369--56295662 Score: 346
Period size: 40 Copynumber: 7.5 Consensus size: 39
56295359 AAGCCAAGTA
* * * *
56295369 CCTTCGGGATTTA-ACCGGATATAGCT-ACTTGCTCAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAATG
*
56295407 CCTTC-GGACATAGCCCGGATATAGTAACTCGCACAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAATG
*
56295445 CCTTCGGGACTTAGCCCGGATATAGTAGCTCGCACAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAATG
* * *
56295484 CCTTCGGGACTTAGCCCGGATGTAATAACTCGCAAAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGC-ACAATG
* * *
56295524 CCTTCGGGACTTAGCCCGGATGTAATAACTTGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCAC-AATG
56295564 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCAC-AATG
* * *
56295604 CCTTCGGGACTTAGCCCGGA-ACCAATCACTAGCGCA-AATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACT--CGCACAATG
*
56295644 CATTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
56295663 TTATCATCCG
Statistics
Matches: 228, Mismatches: 20, Indels: 14
0.87 0.08 0.05
Matches are distributed among these distances:
37 6 0.03
38 30 0.13
39 63 0.28
40 125 0.55
42 4 0.02
ACGTcount: A:0.26, C:0.28, G:0.23, T:0.23
Consensus pattern (39 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAATG
Found at i:56309855 original size:17 final size:17
Alignment explanation
Indices: 56309829--56309868 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
56309819 AAACATATCC
56309829 GATAAAACCCAATAAAT
1 GATAAAACCCAATAAAT
*
56309846 GATAATACCCAATAAAT
1 GATAAAACCCAATAAAT
56309863 GATAAA
1 GATAAA
56309869 TGATAAAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.57, C:0.15, G:0.07, T:0.20
Consensus pattern (17 bp):
GATAAAACCCAATAAAT
Found at i:56329131 original size:148 final size:148
Alignment explanation
Indices: 56328863--56329152 Score: 535
Period size: 148 Copynumber: 2.0 Consensus size: 148
56328853 GGTCTCATGT
*
56328863 GCATCAGTGCCCGAAAAGGTTATGATTATTATGTGACTTTCATCAATGACTATTCTCGATATGGA
1 GCATCAGTGCCCGAAAAGGTTATGATTATTATGTGACTTTCATCAAGGACTATTCTCGATATGGA
*
56328928 TATGTTTATCTAATGCACCACAAAAACAAACCTTTGATAAATTTTGAGAGTTTCGTGCTGAAGTA
66 TATGTTCATCTAATGCACCACAAAAACAAACCTTTGATAAATTTTGAGAGTTTCGTGCTGAAGTA
56328993 GAAAAGCAATTATTATGA
131 GAAAAGCAATTATTATGA
* *
56329011 GCATCAGTGCCCGAAGAGGTTATGATTATTATGTGACTTTCATCGAGGACTATTCTCGATATGGA
1 GCATCAGTGCCCGAAAAGGTTATGATTATTATGTGACTTTCATCAAGGACTATTCTCGATATGGA
*
56329076 TATGTTCATCTAATGCACCGCAAAAACAAACCTTTGATAAATTTTGAGAGTTTCGTGCTGAAGTA
66 TATGTTCATCTAATGCACCACAAAAACAAACCTTTGATAAATTTTGAGAGTTTCGTGCTGAAGTA
56329141 GAAAAGCAATTA
131 GAAAAGCAATTA
56329153 GGTTTATCTA
Statistics
Matches: 137, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
148 137 1.00
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Consensus pattern (148 bp):
GCATCAGTGCCCGAAAAGGTTATGATTATTATGTGACTTTCATCAAGGACTATTCTCGATATGGA
TATGTTCATCTAATGCACCACAAAAACAAACCTTTGATAAATTTTGAGAGTTTCGTGCTGAAGTA
GAAAAGCAATTATTATGA
Found at i:56334929 original size:43 final size:43
Alignment explanation
Indices: 56334858--56334985 Score: 184
Period size: 43 Copynumber: 3.0 Consensus size: 43
56334848 AACATATCAT
* * * * *
56334858 TTCACTGGCATTACGCCTGCTAGACACGAAGGCCCGAATACAA
1 TTCACCGGCATAAAGCCTACTAGGCACGAAGGCCCGAATACAA
56334901 TTCACCGGCATAAAGCCTACTAGGCACGAAGGCCCGAATACAA
1 TTCACCGGCATAAAGCCTACTAGGCACGAAGGCCCGAATACAA
* **
56334944 ATCACCGGCACGAAGCCTACTAGGCACGAAGGCCCGAATACA
1 TTCACCGGCATAAAGCCTACTAGGCACGAAGGCCCGAATACA
56334986 CATCACCTAC
Statistics
Matches: 77, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 77 1.00
ACGTcount: A:0.33, C:0.31, G:0.22, T:0.14
Consensus pattern (43 bp):
TTCACCGGCATAAAGCCTACTAGGCACGAAGGCCCGAATACAA
Found at i:56334991 original size:43 final size:42
Alignment explanation
Indices: 56334872--56335010 Score: 188
Period size: 43 Copynumber: 3.2 Consensus size: 42
56334862 CTGGCATTAC
* * **
56334872 GCCTGCTAGACACGAAGGCCCGAATACAATTCACCGGCATAAA
1 GCCTACTAGGCACGAAGGCCCGAATACAA-TCACCGGCACGAA
56334915 GCCTACTAGGCACGAAGGCCCGAATACAAATCACCGGCACGAA
1 GCCTACTAGGCACGAAGGCCCGAATAC-AATCACCGGCACGAA
**
56334958 GCCTACTAGGCACGAAGGCCCGAATACACATCACCTACACGAA
1 GCCTACTAGGCACGAAGGCCCGAATACA-ATCACCGGCACGAA
*
56335001 GCCTGCTAGG
1 GCCTACTAGG
56335011 ATTTAACCCG
Statistics
Matches: 87, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
42 1 0.01
43 84 0.97
44 2 0.02
ACGTcount: A:0.33, C:0.32, G:0.22, T:0.12
Consensus pattern (42 bp):
GCCTACTAGGCACGAAGGCCCGAATACAATCACCGGCACGAA
Found at i:56335054 original size:38 final size:38
Alignment explanation
Indices: 56334995--56335102 Score: 162
Period size: 38 Copynumber: 2.8 Consensus size: 38
56334985 ACATCACCTA
* *
56334995 CACGAAGCCTGCTAGGATTTAACCCGGATATATTACTAG
1 CACGAAGCCTAC-AGGATTTAACCCGGATATATTACCAG
*
56335034 TACGAAGCCTACAGGATTTAACCCGGATATATTACCAG
1 CACGAAGCCTACAGGATTTAACCCGGATATATTACCAG
**
56335072 CACGAAGCCTATGGGATTTAACCCGGATATA
1 CACGAAGCCTACAGGATTTAACCCGGATATA
56335103 ATTCCAACAT
Statistics
Matches: 63, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
38 53 0.84
39 10 0.16
ACGTcount: A:0.32, C:0.23, G:0.20, T:0.24
Consensus pattern (38 bp):
CACGAAGCCTACAGGATTTAACCCGGATATATTACCAG
Found at i:56340648 original size:43 final size:43
Alignment explanation
Indices: 56340587--56340768 Score: 258
Period size: 43 Copynumber: 4.2 Consensus size: 43
56340577 CTGGCATTAC
**
56340587 GCCTGCTAGGCACGAAGGCCCGAATACACGTCACCGGCACAAA
1 GCCTGCTAGGCACGAAGGCCCGAATACAATTCACCGGCACAAA
* *
56340630 GCCTGCTAGACACGAAGGCCCGAATACAATTCACCGGCATAAA
1 GCCTGCTAGGCACGAAGGCCCGAATACAATTCACCGGCACAAA
* *
56340673 GCCTACTAGGCACGAAGGCCCGAATACAATTCACCGGCACGAA
1 GCCTGCTAGGCACGAAGGCCCGAATACAATTCACCGGCACAAA
* ** *
56340716 GCCTACTAGGCACGAAGGCCCGAATACACA-TCACCTACACGAA
1 GCCTGCTAGGCACGAAGGCCCGAATACA-ATTCACCGGCACAAA
56340759 GCCTGCTAGG
1 GCCTGCTAGG
56340769 ATTTAACCCG
Statistics
Matches: 127, Mismatches: 11, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
43 126 0.99
44 1 0.01
ACGTcount: A:0.32, C:0.33, G:0.23, T:0.12
Consensus pattern (43 bp):
GCCTGCTAGGCACGAAGGCCCGAATACAATTCACCGGCACAAA
Found at i:56340813 original size:38 final size:38
Alignment explanation
Indices: 56340753--56340860 Score: 162
Period size: 38 Copynumber: 2.8 Consensus size: 38
56340743 ACATCACCTA
* * *
56340753 CACGAAGCCTGCTAGGATTTAACCCGGATATATTACTAG
1 CACGAAGCCTAC-GGGATTTAACCCGGATATATTACCAG
*
56340792 TACGAAGCCTACGGGATTTAACCCGGATATATTACCAG
1 CACGAAGCCTACGGGATTTAACCCGGATATATTACCAG
*
56340830 CACGAAGCCTATGGGATTTAACCCGGATATA
1 CACGAAGCCTACGGGATTTAACCCGGATATA
56340861 ATTCCAACAT
Statistics
Matches: 63, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
38 53 0.84
39 10 0.16
ACGTcount: A:0.31, C:0.23, G:0.21, T:0.24
Consensus pattern (38 bp):
CACGAAGCCTACGGGATTTAACCCGGATATATTACCAG
Found at i:56346417 original size:43 final size:43
Alignment explanation
Indices: 56346349--56346525 Score: 284
Period size: 43 Copynumber: 4.1 Consensus size: 43
56346339 CTGGCATTAC
* *
56346349 GCCTGCTAGGCACGAAGGCCCGAATACACGTCACCGGCACAAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
* * *
56346392 GCCTGCTAGGCACGAAAGCCAGAATACACTTCACCGGCACGAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
*
56346435 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCTGCACGAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
*
56346478 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCAGC-CGAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
56346520 GCCTGC
1 GCCTGC
56346526 GAGGATTTAA
Statistics
Matches: 125, Mismatches: 9, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
42 10 0.08
43 115 0.92
ACGTcount: A:0.30, C:0.35, G:0.24, T:0.11
Consensus pattern (43 bp):
GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
Found at i:56346638 original size:38 final size:38
Alignment explanation
Indices: 56346510--56346621 Score: 181
Period size: 38 Copynumber: 2.9 Consensus size: 38
56346500 AATACACATC
56346510 ACCAGC-CGAAGCCTGCGAGGATTTAACCCGGATATATT
1 ACCAGCACGAAGCCTGCG-GGATTTAACCCGGATATATT
* *
56346548 ACCAGTACGAAGCCTGCGGGATTTAATCCGGATATATT
1 ACCAGCACGAAGCCTGCGGGATTTAACCCGGATATATT
*
56346586 ACCAGCACGAAGCCTACGGGATTTAACCCGGATATA
1 ACCAGCACGAAGCCTGCGGGATTTAACCCGGATATA
56346622 ATTCCAGGAT
Statistics
Matches: 68, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
38 57 0.84
39 11 0.16
ACGTcount: A:0.30, C:0.25, G:0.23, T:0.21
Consensus pattern (38 bp):
ACCAGCACGAAGCCTGCGGGATTTAACCCGGATATATT
Found at i:56355458 original size:39 final size:40
Alignment explanation
Indices: 56355403--56355559 Score: 187
Period size: 40 Copynumber: 4.0 Consensus size: 40
56355393 CTGTCTAGCG
*
56355403 TGTTTCTG-TTGGATTAGCTCTTATGAGCTTCTCTCTGGAAA
1 TGTTTC-GATTGGATTAGCTCTTATGAGCTTCTATCTGG-AA
* * * *
56355444 T-TTT-G-TCTGTATTAGCTCTTATGAGGTTCTGTCTGGCA
1 TGTTTCGAT-TGGATTAGCTCTTATGAGCTTCTATCTGGAA
*
56355482 TGTTTCGATTGGATTAGCTCTTATGAGCTTCTATCTGGCA
1 TGTTTCGATTGGATTAGCTCTTATGAGCTTCTATCTGGAA
* *
56355522 TGTTTCAATTGGATTAGCTCTTATGAACTTCTATCTGG
1 TGTTTCGATTGGATTAGCTCTTATGAGCTTCTATCTGG
56355560 TGTGTTCGGT
Statistics
Matches: 103, Mismatches: 9, Indels: 9
0.85 0.07 0.07
Matches are distributed among these distances:
38 4 0.04
39 29 0.28
40 68 0.66
41 2 0.02
ACGTcount: A:0.17, C:0.17, G:0.22, T:0.45
Consensus pattern (40 bp):
TGTTTCGATTGGATTAGCTCTTATGAGCTTCTATCTGGAA
Found at i:56358523 original size:40 final size:40
Alignment explanation
Indices: 56358468--56358590 Score: 176
Period size: 40 Copynumber: 3.1 Consensus size: 40
56358458 TGTTATACTC
56358468 TCTGTCT-GACGTGTTTCAATTGGATTAGCTCTTATGAGCT
1 TCTGTCTAG-CGTGTTTCAATTGGATTAGCTCTTATGAGCT
* * * * *
56358508 TCTGTTTAGCGTGTTTCGATTTGATTAGCTCTTATGACCA
1 TCTGTCTAGCGTGTTTCAATTGGATTAGCTCTTATGAGCT
*
56358548 TCTGTCTAGCGTGTTTCAGTTGGATTAGCTCTTATGAGCT
1 TCTGTCTAGCGTGTTTCAATTGGATTAGCTCTTATGAGCT
56358588 TCT
1 TCT
56358591 ATCTGGTATG
Statistics
Matches: 71, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
40 70 0.99
41 1 0.01
ACGTcount: A:0.16, C:0.18, G:0.22, T:0.44
Consensus pattern (40 bp):
TCTGTCTAGCGTGTTTCAATTGGATTAGCTCTTATGAGCT
Found at i:56362776 original size:12 final size:12
Alignment explanation
Indices: 56362759--56362785 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
56362749 GTATTTTGTG
56362759 TACCGCCACTGT
1 TACCGCCACTGT
56362771 TACCGCCACTGT
1 TACCGCCACTGT
56362783 TAC
1 TAC
56362786 TGTTACTGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.19, C:0.41, G:0.15, T:0.26
Consensus pattern (12 bp):
TACCGCCACTGT
Found at i:56362789 original size:6 final size:6
Alignment explanation
Indices: 56362778--56362803 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
56362768 TGTTACCGCC
56362778 ACTGTT ACTGTT ACTGTT ACTGTT AC
1 ACTGTT ACTGTT ACTGTT ACTGTT AC
56362804 CCTTACGGTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.19, C:0.19, G:0.15, T:0.46
Consensus pattern (6 bp):
ACTGTT
Found at i:56362991 original size:18 final size:18
Alignment explanation
Indices: 56362934--56362993 Score: 59
Period size: 18 Copynumber: 3.3 Consensus size: 18
56362924 GACTATCTGC
* *
56362934 TACTGAATAATTGACTGT
1 TACTGAATAAATGACTAT
* *
56362952 TACAGAATAAACGACTGA-
1 TACTGAATAAATGACT-AT
*
56362970 TACTGAATAAATGAATAT
1 TACTGAATAAATGACTAT
56362988 TACTGA
1 TACTGA
56362994 TTAACCGATT
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
17 1 0.03
18 32 0.97
ACGTcount: A:0.43, C:0.12, G:0.15, T:0.30
Consensus pattern (18 bp):
TACTGAATAAATGACTAT
Found at i:56374949 original size:24 final size:28
Alignment explanation
Indices: 56374880--56374978 Score: 86
Period size: 28 Copynumber: 3.7 Consensus size: 28
56374870 AAATAGAGTG
* *
56374880 TATAATATAATTTACA-AATAAAAT-ATA
1 TATAATATAATATATATAATAAAATCA-A
*
56374907 TAATAATATAA-ATCCTATAAT-AAAT-AA
1 T-ATAATATAATAT-ATATAATAAAATCAA
*
56374934 TATAA-A-AATATATATAATAAAATCTA
1 TATAATATAATATATATAATAAAATCAA
56374960 TATAATATAATATATATAA
1 TATAATATAATATATATAA
56374979 GAAAGATAGA
Statistics
Matches: 59, Mismatches: 5, Indels: 15
0.75 0.06 0.19
Matches are distributed among these distances:
24 8 0.14
25 7 0.12
26 10 0.17
27 5 0.08
28 26 0.44
29 3 0.05
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (28 bp):
TATAATATAATATATATAATAAAATCAA
Found at i:56374950 original size:21 final size:22
Alignment explanation
Indices: 56374895--56374978 Score: 66
Period size: 21 Copynumber: 3.9 Consensus size: 22
56374885 TATAATTTAC
*
56374895 AAATAAAATATAT-AATAATAT
1 AAATAATATATATAAATAATAT
**
56374916 AAATCCTATA-ATAAATAATAT
1 AAATAATATATATAAATAATAT
* *
56374937 AAA-AATATATATAATAAAATCT
1 AAATAATATATATAA-ATAATAT
* *
56374959 ATATAATATAATATATATAA
1 AAATAATAT-ATATAAATAA
56374979 GAAAGATAGA
Statistics
Matches: 48, Mismatches: 10, Indels: 8
0.73 0.15 0.12
Matches are distributed among these distances:
20 6 0.12
21 22 0.46
22 7 0.15
23 8 0.17
24 5 0.10
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.35
Consensus pattern (22 bp):
AAATAATATATATAAATAATAT
Found at i:56374961 original size:14 final size:14
Alignment explanation
Indices: 56374896--56375143 Score: 107
Period size: 14 Copynumber: 17.9 Consensus size: 14
56374886 ATAATTTACA
56374896 AATAAAATATATAAT
1 AATAAAATATAT-AT
**
56374911 AATATAAAT-CCTAT
1 AATA-AAATATATAT
56374925 AAT-AAATA-ATAT
1 AATAAAATATATAT
56374937 -A-AAAATATATAT
1 AATAAAATATATAT
*
56374949 AATAAAATCTATAT
1 AATAAAATATATAT
*
56374963 AATATAATATATAT
1 AATAAAATATATAT
* *
56374977 AAGAAAGATAGATAT
1 AATAAA-ATATATAT
*
56374992 TATAAGGAATAATATAT
1 AATAA--AAT-ATATAT
56375009 AATAAAATATAGTAT
1 AATAAAATATA-TAT
*
56375024 -GTAGTAAA-A-ATA-
1 AATA--AAATATATAT
* *
56375036 CAT-AAATAAATAT
1 AATAAAATATATAT
*
56375049 AATGAAATATGATAT
1 AATAAAATAT-ATAT
* *
56375064 GAT-AAAGA-ATAT
1 AATAAAATATATAT
56375076 AATAATAATA-ATAT
1 AATAA-AATATATAT
* *
56375090 AAT-AAGTAT-TTT
1 AATAAAATATATAT
*
56375102 TATAAAA-ATATAGT
1 AATAAAATATATA-T
56375116 AATATAAATAATATAT
1 AATA-AAAT-ATATAT
56375132 AAT-AAATATATA
1 AATAAAATATATA
56375144 ACATATAGTA
Statistics
Matches: 178, Mismatches: 27, Indels: 58
0.68 0.10 0.22
Matches are distributed among these distances:
10 3 0.02
11 7 0.04
12 29 0.16
13 16 0.09
14 64 0.36
15 31 0.17
16 13 0.07
17 15 0.08
ACGTcount: A:0.59, C:0.02, G:0.06, T:0.34
Consensus pattern (14 bp):
AATAAAATATATAT
Found at i:56375123 original size:16 final size:16
Alignment explanation
Indices: 56375071--56375135 Score: 59
Period size: 16 Copynumber: 4.2 Consensus size: 16
56375061 TATGATAAAG
56375071 AATAT-AATAATA-AT
1 AATATAAATAATATAT
56375085 AATAT-AATAAGTAT-T
1 AATATAAATAA-TATAT
**
56375100 TTTATAAA-AATATAGT
1 AATATAAATAATATA-T
56375116 AATATAAATAATATAT
1 AATATAAATAATATAT
56375132 AATA
1 AATA
56375136 AATATATAAC
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
14 13 0.32
15 8 0.20
16 14 0.34
17 6 0.15
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.38
Consensus pattern (16 bp):
AATATAAATAATATAT
Found at i:56375139 original size:11 final size:10
Alignment explanation
Indices: 56374897--56375161 Score: 74
Period size: 10 Copynumber: 26.4 Consensus size: 10
56374887 TAATTTACAA
56374897 ATAA-AATAT
1 ATAATAATAT
56374906 ATAATAATAT
1 ATAATAATAT
**
56374916 A-AATCCTAT
1 ATAATAATAT
56374925 AATAAATAATAT
1 -AT-AATAATAT
*
56374937 A-AAAATATAT
1 ATAATA-ATAT
*
56374947 ATAATAAAAT
1 ATAATAATAT
*
56374957 CT-AT-ATAAT
1 ATAATAAT-AT
56374966 ATAAT-ATAT
1 ATAATAATAT
* *
56374975 ATAAGAA-AG
1 ATAATAATAT
*
56374984 ATAGATATTAT
1 ATA-ATAATAT
*
56374995 AAGGAATAATAT
1 -A-TAATAATAT
*
56375007 ATAATAAAAT
1 ATAATAATAT
* *
56375017 ATAGT-ATGT
1 ATAATAATAT
* *
56375026 AGTAAAAATAC
1 A-TAATAATAT
56375037 ATAAATAA-AT
1 AT-AATAATAT
56375047 ATAATGAA-AT
1 ATAAT-AATAT
*
56375057 ATGAT-ATGAT
1 ATAATAAT-AT
*
56375067 A-AAGAATAT
1 ATAATAATAT
56375076 AATAATAATAAT
1 -ATAATAAT-AT
56375088 ATAATAAGTATT
1 ATAATAA-TA-T
* * *
56375100 TTTATAAAAAT
1 ATAAT-AATAT
*
56375111 ATAGTAATAT
1 ATAATAATAT
56375121 A-AATAATAT
1 ATAATAATAT
56375130 ATAATAA-AT
1 ATAATAATAT
*
56375139 AT-ATAACAT
1 ATAATAATAT
* *
56375148 ATAGTAAAAT
1 ATAATAATAT
56375158 ATAA
1 ATAA
56375162 ATATAACAGA
Statistics
Matches: 184, Mismatches: 43, Indels: 57
0.65 0.15 0.20
Matches are distributed among these distances:
8 6 0.03
9 53 0.29
10 72 0.39
11 29 0.16
12 21 0.11
13 3 0.02
ACGTcount: A:0.59, C:0.02, G:0.06, T:0.34
Consensus pattern (10 bp):
ATAATAATAT
Found at i:56377719 original size:40 final size:40
Alignment explanation
Indices: 56377634--56377817 Score: 216
Period size: 40 Copynumber: 4.7 Consensus size: 40
56377624 GCTACTCGTT
*
56377634 CAAATGCCTTCGGGACATAGCCC-G-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
*
56377673 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * *
56377713 CCAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * * * *
56377752 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
56377793 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
56377818 CCATGCACAT
Statistics
Matches: 124, Mismatches: 15, Indels: 11
0.83 0.10 0.07
Matches are distributed among these distances:
38 2 0.02
39 53 0.43
40 56 0.45
41 13 0.10
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:56377744 original size:79 final size:79
Alignment explanation
Indices: 56377636--56377817 Score: 217
Period size: 79 Copynumber: 2.3 Consensus size: 79
56377626 TACTCGTTCA
* **
56377636 AATGCCTTCGGGACATAGCCCGTTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGGAT
1 AATGCCTTCGGGACTTAGCCCGGAATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCCGGAT
* *
56377700 TTAGTAAC-TCGCACC
65 ATAGTAACTTAGCA-C
* **
56377715 AATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCGGAT
1 AATGCCTTCGGGACTTAGCCCGGAA-TAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGAT
* *
56377779 ATGGTCACTTAGCAC
65 ATAGTAACTTAGCAC
*
56377794 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAGCCCGGA
56377818 CCATGCACAT
Statistics
Matches: 88, Mismatches: 11, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
78 12 0.14
79 61 0.69
80 15 0.17
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (79 bp):
AATGCCTTCGGGACTTAGCCCGGAATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGATA
TAGTAACTTAGCAC
Found at i:56377750 original size:39 final size:40
Alignment explanation
Indices: 56377634--56377817 Score: 207
Period size: 39 Copynumber: 4.7 Consensus size: 40
56377624 GCTACTCGTT
* **
56377634 CAAATGCCTTCGGGACATAGCCCGTTA-TAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
* *
56377673 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
* *
56377713 CCAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
* * * *
56377752 CAAATGCCTTC-GGATCTTAGTCCGG-ATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGAAT-TAGTAAC-TCGCA
56377793 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
56377818 CCATGCACAT
Statistics
Matches: 122, Mismatches: 16, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
38 2 0.02
39 56 0.46
40 53 0.43
41 11 0.09
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
Found at i:56379660 original size:39 final size:38
Alignment explanation
Indices: 56379609--56379778 Score: 166
Period size: 39 Copynumber: 4.3 Consensus size: 38
56379599 GGACTAAGAT
56379609 CCGAA-GCATTTGTGCGAGATACAAGTTCCGGGTTAAG-C
1 CCGAAGGCATTTGTGCGAGATACAA--TCCGGGTTAAGTC
*
56379647 CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAAGTC
1 CCGAAGGCATTTGTGCGAGATAC--AATCCGGGTT-AAGTC
* * *
56379688 CCGAAGGCATTCGTGCGAGTTATTAATCCGGGTTAAGTC
1 CCGAAGGCATTTGTGCGAGATA-CAATCCGGGTTAAGTC
* * * * *
56379727 CCGAAGGCA-TTGTGTGAGTTACTAAAACCGGGCTATGTC
1 CCGAAGGCATTTGTGCGAGATAC--AATCCGGGTTAAGTC
56379766 CCGAAGGCATTTG
1 CCGAAGGCATTTG
56379779 AACGAGGAGC
Statistics
Matches: 112, Mismatches: 11, Indels: 16
0.81 0.08 0.12
Matches are distributed among these distances:
38 15 0.13
39 59 0.53
40 16 0.14
41 22 0.20
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.25
Consensus pattern (38 bp):
CCGAAGGCATTTGTGCGAGATACAATCCGGGTTAAGTC
Found at i:56379692 original size:79 final size:78
Alignment explanation
Indices: 56379556--56379778 Score: 204
Period size: 79 Copynumber: 2.8 Consensus size: 78
56379546 ATGAATGCTG
* * * * * * *
56379556 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTA-AGTGAATATATCCGGACTAAGAT-CCGAA-GCAT
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGA-T-ACTAAAACCGGGCTAAG-TCCCGAAGGCAT
56379618 TTGTGCGAGATA-CAA
63 TTGTGCGAGATATCAA
* * *
56379633 GTTCCGGGTTAAG-CCCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAAGTCCCGAAGGCA
1 --TCCGGGTTAAGTCCCGAAGG-CATTGTGCGAGATACTAAAACCGGGCT-AAGTCCCGAAGGCA
* * *
56379697 TTCGTGCGAGTTATTAA
62 TTTGTGCGAGATATCAA
* * *
56379714 TCCGGGTTAAGTCCCGAAGGCATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTTG
56379779 AACGAGGAGC
Statistics
Matches: 121, Mismatches: 16, Indels: 15
0.80 0.11 0.10
Matches are distributed among these distances:
78 35 0.29
79 61 0.50
80 23 0.19
81 2 0.02
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.26
Consensus pattern (78 bp):
TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTTG
TGCGAGATATCAA
Found at i:56379796 original size:79 final size:80
Alignment explanation
Indices: 56379635--56379811 Score: 193
Period size: 78 Copynumber: 2.2 Consensus size: 80
56379625 AGATACAAGT
* * *
56379635 TCCGGGTTAAG-CCCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAAGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAAGTCCCGAAGGCATT
** * *
56379699 CGTGCGAGTTATTAA
66 CGAACGAGTGACTAA
* * *
56379714 TCCGGGTTAAGTCCCGAAGG-CATTGTGTGAGTTACTAAAACCGGGCT-ATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAAGTCCCGAAGGCATT
*
56379777 TGAACGAG-GAGCTATA
66 CGAACGAGTGA-CTA-A
*
56379793 TCC-GGTTAAATCCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
56379812 TACGTGATTT
Statistics
Matches: 83, Mismatches: 12, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
77 1 0.01
78 37 0.45
79 37 0.45
80 8 0.10
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.24
Consensus pattern (80 bp):
TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAAGTCCCGAAGGCATT
CGAACGAGTGACTAA
Found at i:56389017 original size:78 final size:81
Alignment explanation
Indices: 56388876--56389057 Score: 223
Period size: 78 Copynumber: 2.3 Consensus size: 81
56388866 TACTCGTTCA
* *
56388876 AATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGA
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGA
* *
56388940 TTTAGTAAC-TCGCACC
66 TATAGTAACTTAGCA-C
**
56388956 AATGCCTTCGGG-CTTAGCCCGGAAT-TAGT-ACTCGCACAAATGCCTTC-GGATCTTAGTCCGG
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGG
* *
56389017 ATATGGTCACTTAGCAC
65 ATATAGTAACTTAGCAC
*
56389034 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAGCCCGGA
56389058 CATCATTCGA
Statistics
Matches: 89, Mismatches: 9, Indels: 9
0.83 0.08 0.08
Matches are distributed among these distances:
77 3 0.03
78 45 0.51
79 28 0.31
80 13 0.15
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (81 bp):
AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGA
TATAGTAACTTAGCAC
Found at i:56389057 original size:40 final size:40
Alignment explanation
Indices: 56388855--56389057 Score: 229
Period size: 40 Copynumber: 5.1 Consensus size: 40
56388845 CGGAATTTAA
** *
56388855 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
56388895 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
56388935 CCGGATTTAGTAACTCGCACCAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
56388974 CCGGA-ATTAGT-ACTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
56389013 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
56389053 CCGGA
1 CCGGA
56389058 CATCATTCGA
Statistics
Matches: 140, Mismatches: 15, Indels: 16
0.82 0.09 0.09
Matches are distributed among these distances:
37 2 0.01
38 17 0.12
39 28 0.20
40 82 0.59
41 11 0.08
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:56391329 original size:43 final size:42
Alignment explanation
Indices: 56391208--56391338 Score: 163
Period size: 43 Copynumber: 3.0 Consensus size: 42
56391198 AATCACTGCA
* * * *
56391208 AAAGATCATGTTCTTTAGCAGCGTCTGTAGTAAAAGCGCTGCT
1 AAAGATCATGTTCTTTAGCAGCGTTTGT-GAAAAAGTGCCGCT
* * *
56391251 AAAAATCATGTTCTTTAGCGGCGTTTGTGATAAAAGTGCCACT
1 AAAGATCATGTTCTTTAGCAGCGTTTGTGA-AAAAGTGCCGCT
*
56391294 AAAGATCATGTTCTTTAGCAGCATTTGTGGAAAAAGTGCCGCT
1 AAAGATCATGTTCTTTAGCAGCGTTTGT-GAAAAAGTGCCGCT
56391337 AA
1 AA
56391339 CATTAACAGA
Statistics
Matches: 75, Mismatches: 11, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
42 1 0.01
43 72 0.96
44 2 0.03
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.31
Consensus pattern (42 bp):
AAAGATCATGTTCTTTAGCAGCGTTTGTGAAAAAGTGCCGCT
Found at i:56395561 original size:26 final size:26
Alignment explanation
Indices: 56395532--56395639 Score: 180
Period size: 26 Copynumber: 4.2 Consensus size: 26
56395522 TGGTACAAAT
56395532 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
56395558 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
56395584 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
56395610 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
56395636 TGAT
1 TGAT
56395640 GGGCATTTCA
Statistics
Matches: 75, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 75 1.00
ACGTcount: A:0.33, C:0.07, G:0.23, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:56402506 original size:26 final size:26
Alignment explanation
Indices: 56402438--56402574 Score: 184
Period size: 26 Copynumber: 5.2 Consensus size: 26
56402428 GTGGCCAAAT
* *
56402438 TGATAATGGGTTAGGTAAATGGTACAAA
1 TGATAATGGGTTAGGTAAAT-GTTC-CA
*
56402466 TTGATAATGGGTTAGGTAAATGTTCAA
1 -TGATAATGGGTTAGGTAAATGTTCCA
* * *
56402493 TGATAATGGATTAGGTAAATATTCCT
1 TGATAATGGGTTAGGTAAATGTTCCA
56402519 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
56402545 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
56402571 TGAT
1 TGAT
56402575 GGGCATTTCA
Statistics
Matches: 99, Mismatches: 9, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
26 74 0.75
27 2 0.02
28 3 0.03
29 20 0.20
ACGTcount: A:0.34, C:0.06, G:0.25, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:56406594 original size:9 final size:9
Alignment explanation
Indices: 56406580--56406605 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
56406570 GCAGAAGGAC
56406580 AATTTTGAA
1 AATTTTGAA
56406589 AATTTTGAA
1 AATTTTGAA
56406598 AATTTTGA
1 AATTTTGA
56406606 TCTCTCATAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.42, C:0.00, G:0.12, T:0.46
Consensus pattern (9 bp):
AATTTTGAA
Found at i:56407167 original size:22 final size:23
Alignment explanation
Indices: 56407130--56407202 Score: 80
Period size: 22 Copynumber: 3.2 Consensus size: 23
56407120 TTACGGTTAC
56407130 TTAAGTGTTCTAAATAGATTTAA
1 TTAAGTGTTCTAAATAGATTTAA
* *
56407153 TTCA-TGTT-TATAATATGA-TTAC
1 TTAAGTGTTCTA-AATA-GATTTAA
56407175 TTAAGTGTTCTAAATAGATTTAA
1 TTAAGTGTTCTAAATAGATTTAA
56407198 GTTAA
1 -TTAA
56407203 ATTTCAATTC
Statistics
Matches: 40, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
21 2 0.05
22 16 0.40
23 16 0.40
24 6 0.15
ACGTcount: A:0.37, C:0.05, G:0.12, T:0.45
Consensus pattern (23 bp):
TTAAGTGTTCTAAATAGATTTAA
Found at i:56407183 original size:23 final size:23
Alignment explanation
Indices: 56407126--56407196 Score: 85
Period size: 23 Copynumber: 3.1 Consensus size: 23
56407116 TAAATTACGG
56407126 TTACTTAAGTGTTCTAAATAGAT
1 TTACTTAAGTGTTCTAAATAGAT
* *
56407149 TTAATTCA-TGTT-TATAATATGA-
1 TTACTTAAGTGTTCTA-AATA-GAT
56407171 TTACTTAAGTGTTCTAAATAGAT
1 TTACTTAAGTGTTCTAAATAGAT
56407194 TTA
1 TTA
56407197 AGTTAAATTT
Statistics
Matches: 39, Mismatches: 4, Indels: 10
0.74 0.08 0.19
Matches are distributed among these distances:
21 2 0.05
22 16 0.41
23 19 0.49
24 2 0.05
ACGTcount: A:0.35, C:0.07, G:0.11, T:0.46
Consensus pattern (23 bp):
TTACTTAAGTGTTCTAAATAGAT
Found at i:56407556 original size:21 final size:20
Alignment explanation
Indices: 56407532--56407570 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
56407522 TTCTTTTATT
56407532 TATTTATAATTTGTTTATTAC
1 TATTTAT-ATTTGTTTATTAC
*
56407553 TATTTATGTTTGTTTATT
1 TATTTATATTTGTTTATT
56407571 TATAAGAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.23, C:0.03, G:0.08, T:0.67
Consensus pattern (20 bp):
TATTTATATTTGTTTATTAC
Found at i:56412969 original size:21 final size:21
Alignment explanation
Indices: 56412943--56412983 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
56412933 AGACGAGCAA
* *
56412943 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
56412964 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
56412984 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:56416536 original size:32 final size:32
Alignment explanation
Indices: 56416500--56416560 Score: 122
Period size: 32 Copynumber: 1.9 Consensus size: 32
56416490 AGAAAATTAA
56416500 AAAATTTCTAAAATTTTAACACGATTGAAGCT
1 AAAATTTCTAAAATTTTAACACGATTGAAGCT
56416532 AAAATTTCTAAAATTTTAACACGATTGAA
1 AAAATTTCTAAAATTTTAACACGATTGAA
56416561 AATTAAAGGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.46, C:0.11, G:0.08, T:0.34
Consensus pattern (32 bp):
AAAATTTCTAAAATTTTAACACGATTGAAGCT
Found at i:56417076 original size:13 final size:13
Alignment explanation
Indices: 56417058--56417085 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
56417048 AATTAAAATA
56417058 ATTCGCAGCATTT
1 ATTCGCAGCATTT
56417071 ATTCGCAGCATTT
1 ATTCGCAGCATTT
56417084 AT
1 AT
56417086 GGGAAAAACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.25, C:0.21, G:0.14, T:0.39
Consensus pattern (13 bp):
ATTCGCAGCATTT
Found at i:56417126 original size:41 final size:41
Alignment explanation
Indices: 56417081--56417158 Score: 104
Period size: 41 Copynumber: 1.9 Consensus size: 41
56417071 ATTCGCAGCA
*
56417081 TTTATGGGAAAAACACT-GCTATTGCTTTACCTTTTGCGGCG
1 TTTATGAGAAAAAC-CTCGCTATTGCTTTACCTTTTGCGGCG
* * *
56417122 TTTATGAGAAAAACGTCGTTATTGCTTTACTTTTTGC
1 TTTATGAGAAAAACCTCGCTATTGCTTTACCTTTTGC
56417159 AAACGCAGCT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
40 1 0.03
41 31 0.97
ACGTcount: A:0.23, C:0.17, G:0.19, T:0.41
Consensus pattern (41 bp):
TTTATGAGAAAAACCTCGCTATTGCTTTACCTTTTGCGGCG
Found at i:56418717 original size:22 final size:23
Alignment explanation
Indices: 56418675--56418717 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
56418665 TATATGAGAT
*
56418675 TAGTTAAAATATTTTACATATGA
1 TAGTTAAAATAGTTTACATATGA
*
56418698 TAGTTAAATTAGTTTA-ATAT
1 TAGTTAAAATAGTTTACATAT
56418718 TAGTAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 4 0.22
23 14 0.78
ACGTcount: A:0.42, C:0.02, G:0.09, T:0.47
Consensus pattern (23 bp):
TAGTTAAAATAGTTTACATATGA
Found at i:56420033 original size:26 final size:26
Alignment explanation
Indices: 56420000--56420052 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
56419990 TCAATCAAAG
56420000 AGTTAGAAACGAAATATATAATTAAA
1 AGTTAGAAACGAAATATATAATTAAA
56420026 AGTTAGAAACGAAATATATAATTAAA
1 AGTTAGAAACGAAATATATAATTAAA
56420052 A
1 A
56420053 CAAATGCAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.58, C:0.04, G:0.11, T:0.26
Consensus pattern (26 bp):
AGTTAGAAACGAAATATATAATTAAA
Found at i:56423237 original size:24 final size:25
Alignment explanation
Indices: 56423191--56423238 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
56423181 ATTTTGGCAT
*
56423191 ATCTGAATCTGATATCTGTATCTAA
1 ATCTGAAACTGATATCTGTATCTAA
*
56423216 ATCTGAAACTGA-GTCTGTATCTA
1 ATCTGAAACTGATATCTGTATCTA
56423239 TTTCTGATTG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 10 0.48
25 11 0.52
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.38
Consensus pattern (25 bp):
ATCTGAAACTGATATCTGTATCTAA
Found at i:56424817 original size:23 final size:25
Alignment explanation
Indices: 56424787--56424832 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
56424777 ATAGATAAAC
56424787 AATATA-TT-TCTTTATGATAATTA
1 AATATATTTATCTTTATGATAATTA
*
56424810 AATATATTTATTTTTATGATAAT
1 AATATATTTATCTTTATGATAAT
56424833 ATTTATGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 2 0.10
25 12 0.60
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.54
Consensus pattern (25 bp):
AATATATTTATCTTTATGATAATTA
Found at i:56425877 original size:35 final size:35
Alignment explanation
Indices: 56425838--56425911 Score: 148
Period size: 35 Copynumber: 2.1 Consensus size: 35
56425828 CTTAATATCG
56425838 AAACTCAATCAATTGAACTAAAATAGCCTTTTTAA
1 AAACTCAATCAATTGAACTAAAATAGCCTTTTTAA
56425873 AAACTCAATCAATTGAACTAAAATAGCCTTTTTAA
1 AAACTCAATCAATTGAACTAAAATAGCCTTTTTAA
56425908 AAAC
1 AAAC
56425912 ATATAATTGA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.47, C:0.18, G:0.05, T:0.30
Consensus pattern (35 bp):
AAACTCAATCAATTGAACTAAAATAGCCTTTTTAA
Found at i:56427484 original size:19 final size:20
Alignment explanation
Indices: 56427447--56427487 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
56427437 TACAATGCAA
*
56427447 TTCAATTTCATATTGAATAT
1 TTCAATTTCATATTCAATAT
*
56427467 TTCAATTT-TTATTCAATAT
1 TTCAATTTCATATTCAATAT
56427486 TT
1 TT
56427488 GCCTAAATTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.32, C:0.10, G:0.02, T:0.56
Consensus pattern (20 bp):
TTCAATTTCATATTCAATAT
Found at i:56427850 original size:6 final size:6
Alignment explanation
Indices: 56427827--56427898 Score: 56
Period size: 6 Copynumber: 11.2 Consensus size: 6
56427817 AAGCTGTGGG
* * *
56427827 TTCTTCT TTCTTT CTCTTT TTCTTT TTCTTT CTTTTTGT TTCGTTT TGCTTTT
1 TTCTT-T TTCTTT TTCTTT TTCTTT TTCTTT -TTCTT-T TTC-TTT TTC-TTT
56427880 TTCTTT CTT-TTT TTCTTT T
1 TTCTTT -TTCTTT TTCTTT T
56427899 ATTACTATAA
Statistics
Matches: 53, Mismatches: 7, Indels: 11
0.75 0.10 0.15
Matches are distributed among these distances:
5 2 0.04
6 27 0.51
7 21 0.40
8 3 0.06
ACGTcount: A:0.00, C:0.18, G:0.04, T:0.78
Consensus pattern (6 bp):
TTCTTT
Found at i:56429476 original size:40 final size:40
Alignment explanation
Indices: 56429387--56429523 Score: 184
Period size: 41 Copynumber: 3.4 Consensus size: 40
56429377 CGTTTTACCA
* * * *
56429387 AAAACACCGCTAAAAATAGAGCAATAGCGGCGTTTTTTGTT
1 AAAACACCGCTAAAAACAGAGCATTAGCGGCG-CTTTTGAT
* *
56429428 AAAACGCCGCTAAAAACAGAGCATTAGCGGCGCTTTTGGT
1 AAAACACCGCTAAAAACAGAGCATTAGCGGCGCTTTTGAT
* *
56429468 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTCGAT
1 AAAACACCGCTAAAAA-CAGAGCATTAGCGGCGCTTTTGAT
56429509 AAAACACCGCTAAAA
1 AAAACACCGCTAAAA
56429524 GTCATATAAT
Statistics
Matches: 87, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
40 22 0.25
41 65 0.75
ACGTcount: A:0.37, C:0.23, G:0.20, T:0.20
Consensus pattern (40 bp):
AAAACACCGCTAAAAACAGAGCATTAGCGGCGCTTTTGAT
Found at i:56429626 original size:17 final size:17
Alignment explanation
Indices: 56429578--56429627 Score: 52
Period size: 17 Copynumber: 3.0 Consensus size: 17
56429568 ACTAATCTAT
56429578 AACCCCTAAAACACT--A
1 AACCCCT-AAACACTAAA
*
56429594 AACCTCTAAATC-CTAAA
1 AACCCCTAAA-CACTAAA
56429611 AACCCCTAAACACTAAA
1 AACCCCTAAACACTAAA
56429628 CTATAACCTC
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
15 5 0.18
16 8 0.29
17 15 0.54
ACGTcount: A:0.50, C:0.34, G:0.00, T:0.16
Consensus pattern (17 bp):
AACCCCTAAACACTAAA
Found at i:56438226 original size:26 final size:26
Alignment explanation
Indices: 56438170--56438276 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
56438160 ATGAAATTCC
56438170 ATCATGGAACATTTACCTAA-CCATT
1 ATCATGGAACATTTACCTAACCCATT
*
56438195 ATCATGGAATATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
*
56438221 ATCATGAAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
56438247 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
56438273 ATCA
1 ATCA
56438277 ATTTGTATCA
Statistics
Matches: 77, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
25 19 0.25
26 58 0.75
ACGTcount: A:0.36, C:0.25, G:0.07, T:0.32
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:56441412 original size:6 final size:6
Alignment explanation
Indices: 56441372--56441425 Score: 56
Period size: 6 Copynumber: 8.7 Consensus size: 6
56441362 GTTTAATCTA
* *
56441372 ATTTTT ATTATTT A-TTTT AGTTTTG ATTCTAT ATTTTT ATTTTT ATTTTT
1 ATTTTT ATT-TTT ATTTTT A-TTTTT ATT-TTT ATTTTT ATTTTT ATTTTT
56441422 ATTT
1 ATTT
56441426 GATAATGAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
5 4 0.10
6 24 0.60
7 12 0.30
ACGTcount: A:0.20, C:0.02, G:0.04, T:0.74
Consensus pattern (6 bp):
ATTTTT
Found at i:56441461 original size:20 final size:20
Alignment explanation
Indices: 56441436--56441480 Score: 90
Period size: 20 Copynumber: 2.2 Consensus size: 20
56441426 GATAATGAAT
56441436 TTTAATAGAAAATTTTTATA
1 TTTAATAGAAAATTTTTATA
56441456 TTTAATAGAAAATTTTTATA
1 TTTAATAGAAAATTTTTATA
56441476 TTTAA
1 TTTAA
56441481 ATCATGGACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.51
Consensus pattern (20 bp):
TTTAATAGAAAATTTTTATA
Found at i:56445928 original size:49 final size:49
Alignment explanation
Indices: 56445855--56446049 Score: 248
Period size: 49 Copynumber: 3.9 Consensus size: 49
56445845 TAGCCGAAGC
* *
56445855 TATCTGGTACGCATAGTAGCCTGCACTTAGTACTACACATGTGACCAAT
1 TATCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGACCAAT
* * *
56445904 AATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGATCACAGT
1 TATCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGA-C-CAAT
* * * * *
56445955 TTTC-GAGTACGCATAGTAGCCTGCACTTAGTACCACACATGCGACCAAT
1 TATCTG-GTACACATAGTAGCCTGCACTTAGTACTACACACGTGACCAAT
* *
56446004 TATCCGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACC
1 TATCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGACC
56446050 TCACAATAGT
Statistics
Matches: 123, Mismatches: 19, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
49 81 0.66
50 4 0.03
51 38 0.31
ACGTcount: A:0.28, C:0.27, G:0.19, T:0.26
Consensus pattern (49 bp):
TATCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGACCAAT
Found at i:56445974 original size:100 final size:100
Alignment explanation
Indices: 56445861--56446047 Score: 338
Period size: 100 Copynumber: 1.9 Consensus size: 100
56445851 AAGCTATCTG
* * *
56445861 GTACGCATAGTAGCCTGCACTTAGTACTACACATGTGACCAATAATCTGGTACACGTAGTAGCCT
1 GTACGCATAGTAGCCTGCACTTAGTACCACACATGCGACCAATAATCCGGTACACGTAGTAGCCT
56445926 GCACTTAGTACTACACACGTGATCACAGTTTTCGA
66 GCACTTAGTACTACACACGTGATCACAGTTTTCGA
*
56445961 GTACGCATAGTAGCCTGCACTTAGTACCACACATGCGACCAATTATCCGGTACACGTAGTAGCCT
1 GTACGCATAGTAGCCTGCACTTAGTACCACACATGCGACCAATAATCCGGTACACGTAGTAGCCT
56446026 GCACTTAGTACTACACACGTGA
66 GCACTTAGTACTACACACGTGA
56446048 CCTCACAATA
Statistics
Matches: 83, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
100 83 1.00
ACGTcount: A:0.29, C:0.27, G:0.19, T:0.25
Consensus pattern (100 bp):
GTACGCATAGTAGCCTGCACTTAGTACCACACATGCGACCAATAATCCGGTACACGTAGTAGCCT
GCACTTAGTACTACACACGTGATCACAGTTTTCGA
Found at i:56447201 original size:34 final size:34
Alignment explanation
Indices: 56447158--56447225 Score: 127
Period size: 34 Copynumber: 2.0 Consensus size: 34
56447148 TTGGTATACA
*
56447158 CGTCCATGGTGAAGAATATGAACAAAATTGGCTT
1 CGTCCATGGTGAAGAAGATGAACAAAATTGGCTT
56447192 CGTCCATGGTGAAGAAGATGAACAAAATTGGCTT
1 CGTCCATGGTGAAGAAGATGAACAAAATTGGCTT
56447226 TTAATTTTGT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.35, C:0.15, G:0.25, T:0.25
Consensus pattern (34 bp):
CGTCCATGGTGAAGAAGATGAACAAAATTGGCTT
Found at i:56448048 original size:41 final size:40
Alignment explanation
Indices: 56447966--56448087 Score: 154
Period size: 41 Copynumber: 3.0 Consensus size: 40
56447956 TGATACTTTG
* * * *
56447966 CTCAAAAACGCCGCTGTTGCTTACCTTTTGCGGCGTTTTT
1 CTCATAAACGCCGCTATTGCTTACTTTTTGCGGTGTTTTT
*
56448006 CTCATAAACGCCGCTATTGCTTGACTTTTTGTGGTGTTTTT
1 CTCATAAACGCCGCTATTGCTT-ACTTTTTGCGGTGTTTTT
* * *
56448047 CTCATAAACGCAGCTACTGCTTTACTTATTGCGGTGTTTTT
1 CTCATAAACGCCGCTATTGC-TTACTTTTTGCGGTGTTTTT
56448088 TCGTTAGCGC
Statistics
Matches: 71, Mismatches: 9, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
40 20 0.28
41 49 0.69
42 2 0.03
ACGTcount: A:0.16, C:0.23, G:0.19, T:0.42
Consensus pattern (40 bp):
CTCATAAACGCCGCTATTGCTTACTTTTTGCGGTGTTTTT
Found at i:56452455 original size:18 final size:19
Alignment explanation
Indices: 56452420--56452457 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
56452410 TATATTTTTG
56452420 TAATATAATTTTTCTATTT
1 TAATATAATTTTTCTATTT
56452439 TAATATAATTTTT-TATTT
1 TAATATAATTTTTCTATTT
56452457 T
1 T
56452458 TTAATTTAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.66
Consensus pattern (19 bp):
TAATATAATTTTTCTATTT
Found at i:56452458 original size:19 final size:20
Alignment explanation
Indices: 56452415--56452458 Score: 65
Period size: 19 Copynumber: 2.2 Consensus size: 20
56452405 TTTTTTATAT
56452415 TTTTGTAATATAATTTTTCTA
1 TTTT-TAATATAATTTTTCTA
56452436 -TTTTAATATAATTTTT-TA
1 TTTTTAATATAATTTTTCTA
56452454 TTTTT
1 TTTTT
56452459 TAATTTAGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 2 0.09
19 17 0.77
20 3 0.14
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.68
Consensus pattern (20 bp):
TTTTTAATATAATTTTTCTA
Found at i:56452934 original size:21 final size:22
Alignment explanation
Indices: 56452900--56452940 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
56452890 TCCTTCCGCA
*
56452900 ATAAAAATATTAATTAAATTGT
1 ATAAAAATAATAATTAAATTGT
56452922 ATAAAAA-AATAATTAAATT
1 ATAAAAATAATAATTAAATT
56452941 AAACATCGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (22 bp):
ATAAAAATAATAATTAAATTGT
Found at i:56453146 original size:15 final size:16
Alignment explanation
Indices: 56453126--56453160 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
56453116 ATCAATTTAA
*
56453126 TTTAATTTTATATT-T
1 TTTAATATTATATTAT
56453141 TTTAATATTATATTAT
1 TTTAATATTATATTAT
56453157 TTTA
1 TTTA
56453161 TAAAAATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 13 0.72
16 5 0.28
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (16 bp):
TTTAATATTATATTAT
Found at i:56453383 original size:15 final size:17
Alignment explanation
Indices: 56453346--56453381 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
56453336 ACTACTTAAC
56453346 TTTTCAATATTTAATTT
1 TTTTCAATATTTAATTT
56453363 TTTTCAATATTT-ATTT
1 TTTTCAATATTTAATTT
56453379 TTT
1 TTT
56453382 CAGTTTATCA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 7 0.37
17 12 0.63
ACGTcount: A:0.25, C:0.06, G:0.00, T:0.69
Consensus pattern (17 bp):
TTTTCAATATTTAATTT
Found at i:56456042 original size:15 final size:16
Alignment explanation
Indices: 56456015--56456044 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
56456005 ATTTTTACGA
56456015 TAAAATAATAATAAAT
1 TAAAATAATAATAAAT
56456031 TAAAAT-ATAATAAA
1 TAAAATAATAATAAA
56456045 GTAGTAGAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
TAAAATAATAATAAAT
Found at i:56457430 original size:6 final size:6
Alignment explanation
Indices: 56457383--56457444 Score: 54
Period size: 6 Copynumber: 9.7 Consensus size: 6
56457373 CAATATATAC
* *
56457383 TTTTAT TTATAT TTATATAT ATTATTAT TTTT-T GTTTAAT TTTTAT TTTTAT
1 TTTTAT TTTTAT TT-T-TAT -TT-TTAT TTTTAT -TTTTAT TTTTAT TTTTAT
56457435 TTTTAT TTTT
1 TTTTAT TTTT
56457445 TTCAAACGTA
Statistics
Matches: 47, Mismatches: 4, Indels: 10
0.77 0.07 0.16
Matches are distributed among these distances:
5 1 0.02
6 33 0.70
7 3 0.06
8 6 0.13
9 4 0.09
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.76
Consensus pattern (6 bp):
TTTTAT
Found at i:56459796 original size:105 final size:102
Alignment explanation
Indices: 56459687--56459883 Score: 254
Period size: 105 Copynumber: 1.9 Consensus size: 102
56459677 ACACTCGTAG
* ** *
56459687 TGCCATAACCCAGTTATGTTCTTATCA-TCAGGATGTCATAGCCCAGCTATGGTCTTAC-TCTTA
1 TGCCATAACCCAGTTATGGTCTTATCACT-AAAATGCCATAGCCCAGCTATGGTCTTACAT-TTA
*
56459750 GACATATATTGCCATGGTCCAACTATGGTCTTACATTCACGA
64 -ACA-AT-TTGCCATGGTCCAACCATGGTCTTACATTCACGA
* * *
56459792 TGCCATAACCTAGTTATGGTCTTTTCACTAAAATGCCATAGCCCAGTTATGGTCTTACATTTAAC
1 TGCCATAACCCAGTTATGGTCTTATCACTAAAATGCCATAGCCCAGCTATGGTCTTACATTTAAC
*
56459857 ACTTTGCCATGGTCCAACCATGGTCTT
66 AATTTGCCATGGTCCAACCATGGTCTT
56459884 GTTCGTCAAT
Statistics
Matches: 81, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
102 23 0.28
103 1 0.01
104 3 0.04
105 52 0.64
106 2 0.02
ACGTcount: A:0.25, C:0.25, G:0.16, T:0.34
Consensus pattern (102 bp):
TGCCATAACCCAGTTATGGTCTTATCACTAAAATGCCATAGCCCAGCTATGGTCTTACATTTAAC
AATTTGCCATGGTCCAACCATGGTCTTACATTCACGA
Found at i:56459810 original size:33 final size:32
Alignment explanation
Indices: 56459773--56459852 Score: 88
Period size: 33 Copynumber: 2.4 Consensus size: 32
56459763 ATGGTCCAAC
** *
56459773 TATGGTCTTACATTCACGATGCCATAACCTAGT
1 TATGGTCTTACATT-AAAATGCCATAACCCAGT
* * *
56459806 TATGGTCTTTTCACTAAAATGCCATAGCCCAGT
1 TATGGTC-TTACATTAAAATGCCATAACCCAGT
56459839 TATGGTCTTACATT
1 TATGGTCTTACATT
56459853 TAACACTTTG
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
32 5 0.13
33 28 0.74
34 5 0.13
ACGTcount: A:0.26, C:0.23, G:0.15, T:0.36
Consensus pattern (32 bp):
TATGGTCTTACATTAAAATGCCATAACCCAGT
Found at i:56465129 original size:13 final size:12
Alignment explanation
Indices: 56465113--56465178 Score: 59
Period size: 13 Copynumber: 5.6 Consensus size: 12
56465103 TATATTTTTC
56465113 CTAAATATTATCA
1 CTAAATA-TATCA
56465126 CTAAATA-ATC-
1 CTAAATATATCA
56465136 CTAAATATAATCA
1 CTAAATAT-ATCA
*
56465149 CTAAATA-AT-T
1 CTAAATATATCA
*
56465159 GTAAATATTATCA
1 CTAAATA-TATCA
56465172 CTAAATA
1 CTAAATA
56465179 ATTCAAAATT
Statistics
Matches: 43, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
10 13 0.30
11 5 0.12
12 5 0.12
13 20 0.47
ACGTcount: A:0.50, C:0.14, G:0.02, T:0.35
Consensus pattern (12 bp):
CTAAATATATCA
Found at i:56465181 original size:23 final size:23
Alignment explanation
Indices: 56465113--56465187 Score: 114
Period size: 23 Copynumber: 3.3 Consensus size: 23
56465103 TATATTTTTC
*
56465113 CTAAATATTATCACTAAATAATC
1 CTAAATATTATCACTAAATAATT
*
56465136 CTAAATATAATCACTAAATAATT
1 CTAAATATTATCACTAAATAATT
*
56465159 GTAAATATTATCACTAAATAATT
1 CTAAATATTATCACTAAATAATT
*
56465182 CAAAAT
1 CTAAAT
56465188 TTAAAAATCA
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.51, C:0.13, G:0.01, T:0.35
Consensus pattern (23 bp):
CTAAATATTATCACTAAATAATT
Found at i:56465210 original size:18 final size:18
Alignment explanation
Indices: 56465189--56465227 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
56465179 ATTCAAAATT
56465189 TAAAAATCAAAATTAAAC
1 TAAAAATCAAAATTAAAC
* * *
56465207 TAAAGATTAAACTTAAAC
1 TAAAAATCAAAATTAAAC
56465225 TAA
1 TAA
56465228 TTACACAGTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.62, C:0.10, G:0.03, T:0.26
Consensus pattern (18 bp):
TAAAAATCAAAATTAAAC
Found at i:56467067 original size:46 final size:48
Alignment explanation
Indices: 56466995--56467219 Score: 200
Period size: 46 Copynumber: 4.7 Consensus size: 48
56466985 TTATTTGTGT
* *
56466995 GCCAATGTAAGACATGTCTGGGACAT-GCATCGGCCTTGAGATGTA-A
1 GCCAGTGTAAGACATGTCTGGGACATGGCATCGGCCTCGAGATGTAGA
56467041 GCCAGTGTAAGACATGTCTGGGACAT-GCATCGG-CTACGAGATGT---
1 GCCAGTGTAAGACATGTCTGGGACATGGCATCGGCCT-CGAGATGTAGA
* * * *
56467085 GTCAGTGAAAGACCATGTCTGGGACATGGCATCGGCAC-CTATATGTGAGA
1 GCCAGTGTAAGA-CATGTCTGGGACATGGCATCGGC-CTCGAGATGT-AGA
* * ** *
56467135 GCTAGTGTAAGACTATGTTTGGGACATGGTGTCGGCCTC--GATTTAGATA
1 GCCAGTGTAAGAC-ATGTCTGGGACATGGCATCGGCCTCGAGATGTAG--A
*
56467184 GTCAGTGTAAGACCATGTCTGGGACATGGCATCGGC
1 GCCAGTGTAAGA-CATGTCTGGGACATGGCATCGGC
56467220 ATTATACCCT
Statistics
Matches: 146, Mismatches: 19, Indels: 25
0.77 0.10 0.13
Matches are distributed among these distances:
44 10 0.07
45 16 0.11
46 52 0.36
47 2 0.01
48 4 0.03
49 32 0.22
50 30 0.21
ACGTcount: A:0.25, C:0.19, G:0.31, T:0.25
Consensus pattern (48 bp):
GCCAGTGTAAGACATGTCTGGGACATGGCATCGGCCTCGAGATGTAGA
Found at i:56469281 original size:44 final size:44
Alignment explanation
Indices: 56469218--56469304 Score: 174
Period size: 44 Copynumber: 2.0 Consensus size: 44
56469208 AAGTTCTCGG
56469218 TTTAGTCCCGAATCGATTTTGATGAATGTTTTGGGTTTCGTATT
1 TTTAGTCCCGAATCGATTTTGATGAATGTTTTGGGTTTCGTATT
56469262 TTTAGTCCCGAATCGATTTTGATGAATGTTTTGGGTTTCGTAT
1 TTTAGTCCCGAATCGATTTTGATGAATGTTTTGGGTTTCGTAT
56469305 ACCCAAATAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.18, C:0.11, G:0.23, T:0.47
Consensus pattern (44 bp):
TTTAGTCCCGAATCGATTTTGATGAATGTTTTGGGTTTCGTATT
Done.