Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A05
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: 100714657
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 3970000 characters in sequence are not A, C, G, or T
File 178 of 318
Found at i:55869088 original size:33 final size:33
Alignment explanation
Indices: 55869050--55869117 Score: 127
Period size: 33 Copynumber: 2.1 Consensus size: 33
55869040 GGTATTTTGG
55869050 TAATTTTACAAACTAGGGGTATTTTAGTAATTT
1 TAATTTTACAAACTAGGGGTATTTTAGTAATTT
*
55869083 TAATTTTACAAACTAGGGGTATTTTGGTAATTT
1 TAATTTTACAAACTAGGGGTATTTTAGTAATTT
55869116 TA
1 TA
55869118 CTGATCGAGG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.32, C:0.06, G:0.16, T:0.46
Consensus pattern (33 bp):
TAATTTTACAAACTAGGGGTATTTTAGTAATTT
Found at i:55869130 original size:60 final size:60
Alignment explanation
Indices: 55869027--55869143 Score: 182
Period size: 60 Copynumber: 1.9 Consensus size: 60
55869017 ATTTTAGTAA
*
55869027 TTTACAAACTAGGGGTATTTTGGTAATTTTACAAACTAGGGGTATTTTAGTAATTTTAAT
1 TTTACAAACTAGGGGTATTTTGGTAATTTTACAAACGAGGGGTATTTTAGTAATTTTAAT
* * *
55869087 TTTACAAACTAGGGGTATTTTGGTAATTTTACTGATCGA-GGGTATTTTGGTAATTTT
1 TTTACAAACTAGGGGTATTTTGGTAATTTTAC-AAACGAGGGGTATTTTAGTAATTTT
55869144 GTAAACCAAG
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
60 49 0.94
61 3 0.06
ACGTcount: A:0.28, C:0.07, G:0.21, T:0.44
Consensus pattern (60 bp):
TTTACAAACTAGGGGTATTTTGGTAATTTTACAAACGAGGGGTATTTTAGTAATTTTAAT
Found at i:55869161 original size:87 final size:86
Alignment explanation
Indices: 55868943--55869171 Score: 267
Period size: 87 Copynumber: 2.7 Consensus size: 86
55868933 AGTATTTCGA
* * *
55868943 TAATTTCACAAATC-AGTGGTATTTTGGTAATTTTACAAGCCAAGGGTATTTT-G-----GTAAT
1 TAATTT-ACAAA-CGAGGGGTATTTTGGTAATTTTACAAACCAAGGGTATTTTAGTAATTTTAAT
55869001 TTTACAAACTAGGGGTATTTTAG
64 TTTACAAACTAGGGGTATTTTAG
* * *
55869024 TAATTTACAAACTAGGGGTATTTTGGTAATTTTACAAACTAGGGGTATTTTAGTAATTTTAATTT
1 TAATTTACAAACGAGGGGTATTTTGGTAATTTTACAAACCAAGGGTATTTTAGTAATTTTAATTT
*
55869089 TACAAACTAGGGGTATTTTGG
66 TACAAACTAGGGGTATTTTAG
* * **
55869110 TAATTTTACTGATCGA-GGGTATTTTGGTAATTTTGTAAACCAAGGGTATTTTAGTAATTTTA
1 TAA-TTTAC-AAACGAGGGGTATTTTGGTAATTTTACAAACCAAGGGTATTTTAGTAATTTTA
55869172 TAAATCGAGG
Statistics
Matches: 126, Mismatches: 13, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
79 1 0.01
80 39 0.31
81 7 0.06
86 29 0.23
87 47 0.37
88 3 0.02
ACGTcount: A:0.31, C:0.08, G:0.20, T:0.42
Consensus pattern (86 bp):
TAATTTACAAACGAGGGGTATTTTGGTAATTTTACAAACCAAGGGTATTTTAGTAATTTTAATTT
TACAAACTAGGGGTATTTTAG
Found at i:55869182 original size:27 final size:27
Alignment explanation
Indices: 55869163--55869506 Score: 562
Period size: 27 Copynumber: 12.7 Consensus size: 27
55869153 GGGTATTTTA
* *
55869163 GTAATTTTATAAATCGAGGGTAAAACG
1 GTAATTCTATAAATCGAGGGTAAAATG
*
55869190 GTAATTCTGTAAATCGAGGGTAAAATG
1 GTAATTCTATAAATCGAGGGTAAAATG
* *
55869217 ATAATTCTATAAATCGAGGGTAAAACG
1 GTAATTCTATAAATCGAGGGTAAAATG
*
55869244 GTAATTCTATAAATCGAGGGTAAAACG
1 GTAATTCTATAAATCGAGGGTAAAATG
55869271 GTAATTCTATAAATCGAGGGTAAAATG
1 GTAATTCTATAAATCGAGGGTAAAATG
* *
55869298 ATAATTCTATAAATCGAGGGTAAAACG
1 GTAATTCTATAAATCGAGGGTAAAATG
*
55869325 GTAATTCTATAAATCGAGAGTAAAATG
1 GTAATTCTATAAATCGAGGGTAAAATG
*
55869352 GTAATTCTGTAAATCGAGGGTAAAATG
1 GTAATTCTATAAATCGAGGGTAAAATG
55869379 GTAATTCTATAAATCGAGGGTAAAATG
1 GTAATTCTATAAATCGAGGGTAAAATG
55869406 GTAATTCTATAAATCGAGGGTAAAATG
1 GTAATTCTATAAATCGAGGGTAAAATG
*
55869433 GTAATTTTATAAATCGAGGGTAAAATG
1 GTAATTCTATAAATCGAGGGTAAAATG
*
55869460 GTAATTCTATAAATCGAGGGTAAAACG
1 GTAATTCTATAAATCGAGGGTAAAATG
* *
55869487 GTAATTCTACAAATTGAGGG
1 GTAATTCTATAAATCGAGGG
55869507 CATTTTAGTA
Statistics
Matches: 296, Mismatches: 21, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 296 1.00
ACGTcount: A:0.41, C:0.08, G:0.22, T:0.29
Consensus pattern (27 bp):
GTAATTCTATAAATCGAGGGTAAAATG
Found at i:55876346 original size:17 final size:18
Alignment explanation
Indices: 55876310--55876347 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
55876300 ACTAAGACAT
55876310 ATTAAACACAAACAATAA
1 ATTAAACACAAACAATAA
55876328 ATTAAGACAC-AAC-ATAA
1 ATTAA-ACACAAACAATAA
55876345 ATT
1 ATT
55876348 TGACTGTAGC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 7 0.37
18 8 0.42
19 4 0.21
ACGTcount: A:0.61, C:0.16, G:0.03, T:0.21
Consensus pattern (18 bp):
ATTAAACACAAACAATAA
Found at i:55876657 original size:20 final size:19
Alignment explanation
Indices: 55876628--55876666 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
55876618 CTAGCTCAAC
55876628 GAGCTAAATTAAGCTCAAAT
1 GAGCTAAATTAAGCT-AAAT
* *
55876648 GAGCTGAATTGAGCTAAAT
1 GAGCTAAATTAAGCTAAAT
55876667 AGAGATCGAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.41, C:0.13, G:0.21, T:0.26
Consensus pattern (19 bp):
GAGCTAAATTAAGCTAAAT
Found at i:55886707 original size:53 final size:54
Alignment explanation
Indices: 55886617--55886813 Score: 209
Period size: 55 Copynumber: 3.6 Consensus size: 54
55886607 AACTTACCAT
* * * *
55886617 TGCCATGTCTTGACATGGTCTTACGTGGTATCCTTGCCTTAT-GAGCTCACTAT
1 TGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAGAGCTTACTAA
* * * *
55886670 TGCCATGCCTTGGCATGGTCTTACATGGGATCTTTGCCTTATAGTAGTTTA-TCAA
1 TGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAG-AGCTTACT-AA
* * * * * * *
55886725 TGCCATGTCTTGAAATGGTCTTACATGATTTCCTTGCCTTGTAGAACTTACCAA
1 TGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAGAGCTTACTAA
* *
55886779 TGCCATGCCTTGGCATGGTCTTACTTGGTATCCTT
1 TGCCATGCCTTGACATGGTCTTACATGGTATCCTT
55886814 AGACCTTAAT
Statistics
Matches: 115, Mismatches: 25, Indels: 7
0.78 0.17 0.05
Matches are distributed among these distances:
53 37 0.32
54 37 0.32
55 41 0.36
ACGTcount: A:0.19, C:0.23, G:0.20, T:0.38
Consensus pattern (54 bp):
TGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAGAGCTTACTAA
Found at i:55889921 original size:44 final size:44
Alignment explanation
Indices: 55889866--55889950 Score: 125
Period size: 44 Copynumber: 1.9 Consensus size: 44
55889856 TATGTATGAG
* *
55889866 GCATCTGAGCTCATTGAGTTGGTCCAAGTTCATTATGGATGTGA
1 GCATCCGAGCTCATTGAGTTGGTCCAAGTTCATTATAGATGTGA
* **
55889910 GCATCCGAGCTCGTTGAGTTGGTCTGAGTTCATTATAGATG
1 GCATCCGAGCTCATTGAGTTGGTCCAAGTTCATTATAGATG
55889951 CGGTACATGT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 36 1.00
ACGTcount: A:0.21, C:0.16, G:0.28, T:0.34
Consensus pattern (44 bp):
GCATCCGAGCTCATTGAGTTGGTCCAAGTTCATTATAGATGTGA
Found at i:55894918 original size:48 final size:48
Alignment explanation
Indices: 55894837--55894960 Score: 133
Period size: 48 Copynumber: 2.6 Consensus size: 48
55894827 CATGTCCCAG
* * * *
55894837 ACATGGT-TTACACTGGCTCACATGTCAAGGCCGATACCATATTCAAA
1 ACATGGTCTTACACTAGCTCTCATCTCAAGGCCGATACCATATCCAAA
* * * * * *
55894884 ACATGGTCTTACACTAGCTCTCGTCTCAATGCCGATGCCATGTCCCAG
1 ACATGGTCTTACACTAGCTCTCATCTCAAGGCCGATACCATATCCAAA
* *
55894932 ACATGGTCTTACACTTGCTCTCATATCAA
1 ACATGGTCTTACACTAGCTCTCATCTCAA
55894961 CCAAATGTCA
Statistics
Matches: 63, Mismatches: 13, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
47 7 0.11
48 56 0.89
ACGTcount: A:0.27, C:0.29, G:0.16, T:0.28
Consensus pattern (48 bp):
ACATGGTCTTACACTAGCTCTCATCTCAAGGCCGATACCATATCCAAA
Found at i:55898523 original size:18 final size:18
Alignment explanation
Indices: 55898500--55898535 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
55898490 CTACAGTAAG
55898500 GAAGGGTGTGGTTACACA
1 GAAGGGTGTGGTTACACA
55898518 GAAGGGTGTGGTTACACA
1 GAAGGGTGTGGTTACACA
55898536 CCTTTTTCGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.11, G:0.39, T:0.22
Consensus pattern (18 bp):
GAAGGGTGTGGTTACACA
Found at i:55900084 original size:44 final size:44
Alignment explanation
Indices: 55900034--55900122 Score: 169
Period size: 44 Copynumber: 2.0 Consensus size: 44
55900024 GCTGCTAGAG
*
55900034 ACACTAGTGATAATCGGCTATAGTAGAGTTTTACTCAATTTCAT
1 ACACTAGTGATAATCGGCTATAGTAGAATTTTACTCAATTTCAT
55900078 ACACTAGTGATAATCGGCTATAGTAGAATTTTACTCAATTTCAT
1 ACACTAGTGATAATCGGCTATAGTAGAATTTTACTCAATTTCAT
55900122 A
1 A
55900123 AATTTGCATT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.36
Consensus pattern (44 bp):
ACACTAGTGATAATCGGCTATAGTAGAATTTTACTCAATTTCAT
Found at i:55900673 original size:28 final size:28
Alignment explanation
Indices: 55900636--55900713 Score: 120
Period size: 28 Copynumber: 2.8 Consensus size: 28
55900626 TCAAATATGG
* *
55900636 CACTCAGTGTACGAAATATTGAGAATGA
1 CACTTAGTGTGCGAAATATTGAGAATGA
* *
55900664 CGCTTAGTGTGCGAGATATTGAGAATGA
1 CACTTAGTGTGCGAAATATTGAGAATGA
55900692 CACTTAGTGTGCGAAATATTGA
1 CACTTAGTGTGCGAAATATTGA
55900714 ATGATTCAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 44 1.00
ACGTcount: A:0.33, C:0.13, G:0.26, T:0.28
Consensus pattern (28 bp):
CACTTAGTGTGCGAAATATTGAGAATGA
Found at i:55902206 original size:47 final size:47
Alignment explanation
Indices: 55901957--55902280 Score: 210
Period size: 47 Copynumber: 7.0 Consensus size: 47
55901947 AACATGGGAT
* *
55901957 ATATTGCCGATGCCGTGTCCCAGACATGGTCTTACACTGGCTCTCAT-
1 ATATGGCCGATGCCATGTCCCAGACAT-GTCTTACACTGGCTCTCATA
* * ** *
55902004 ATGTGCGTGCTGATG-CATGTCCCAGACATGTCTTACACCAG--CACA-A
1 ATAT--G-GCCGATGCCATGTCCCAGACATGTCTTACACTGGCTCTCATA
* * * * * * *
55902050 CTCTTAGCCGATG-CGTGTCCCAGACACGTCTCACACTGGCTAACT-GT-
1 AT-ATGGCCGATGCCATGTCCCAGACATGTCTTACACTGGCT--CTCATA
** * *
55902097 CGA-GGCCGATG-CATGTCCCAGACATGTCTTACTCT-GCACTCA-A
1 ATATGGCCGATGCCATGTCCCAGACATGTCTTACACTGGCTCTCATA
55902140 CAT-TGTGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATA
1 -ATATG-GCCGATGCCATGTCCCAGACAT-GTCTTACACTGGCTCTCATA
* * * * *
55902189 ATATGGCTGAAG-CATGTCCCAGACATGTCTTACACTAGCCCTCATCT
1 ATATGGCCGATGCCATGTCCCAGACATGTCTTACACTGGCTCTCAT-A
* *
55902236 AGAT-GCCGATGCCATGTCCTAGACATGGTCTTACACTGGCTCTCA
1 ATATGGCCGATGCCATGTCCCAGACAT-GTCTTACACTGGCTCTCA
55902281 AATCACCCAA
Statistics
Matches: 212, Mismatches: 42, Indels: 45
0.71 0.14 0.15
Matches are distributed among these distances:
42 2 0.01
44 30 0.14
45 34 0.16
46 40 0.19
47 44 0.21
48 40 0.19
49 16 0.08
50 6 0.03
ACGTcount: A:0.22, C:0.31, G:0.21, T:0.27
Consensus pattern (47 bp):
ATATGGCCGATGCCATGTCCCAGACATGTCTTACACTGGCTCTCATA
Found at i:55902261 original size:94 final size:92
Alignment explanation
Indices: 55901961--55902280 Score: 341
Period size: 94 Copynumber: 3.5 Consensus size: 92
55901951 TGGGATATAT
* *
55901961 TGCCGATGCCGTGTCCCAGACATGGTCTTACACTGGCTCTCATATGTGCGTGCTGATGCATGTCC
1 TGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATATAT--G-GCTGATGCATGTCC
* * *
55902026 CAGACATGTCTTACACCAGCAC-AACTCTTA
63 CAGACATGTCTTACACTAGCACTCA-TCTGA
* * * * ** *
55902056 -GCCGATG-CGTGTCCCAGACA-CGTCTCACACTGGCTAACT-GTCGA-GGCCGATGCATGTCCC
1 TGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCT--CTCATATATGGCTGATGCATGTCCC
* *
55902116 AGACATGTCTTACTCT-GCACTCAACATTG-
64 AGACATGTCTTACACTAGCACTCATC--TGA
*
55902145 TGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATATGGCTGAAGCATGTCCCA
1 TGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCAT-ATATGGCTGATGCATGTCCCA
*
55902210 GACATGTCTTACACTAGCCCTCATCTAGA
65 GACATGTCTTACACTAGCACTCATCT-GA
*
55902239 TGCCGATGCCATGTCCTAGACATGGTCTTACACTGGCTCTCA
1 TGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCA
55902281 AATCACCCAA
Statistics
Matches: 187, Mismatches: 24, Indels: 29
0.78 0.10 0.12
Matches are distributed among these distances:
88 5 0.03
89 29 0.16
90 11 0.06
91 13 0.07
92 28 0.15
93 44 0.24
94 57 0.30
ACGTcount: A:0.22, C:0.31, G:0.21, T:0.26
Consensus pattern (92 bp):
TGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATATATGGCTGATGCATGTCCCAG
ACATGTCTTACACTAGCACTCATCTGA
Found at i:55908729 original size:30 final size:30
Alignment explanation
Indices: 55908674--55908731 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
55908664 CATGGCCATG
* *
55908674 ACACACGCCCATGGGTGTGAGCCGTGTGTC
1 ACACACGCCCATGGGTCTGACCCGTGTGTC
* *
55908704 ACACACGCCCATGTGTCTTACCCGTGTG
1 ACACACGCCCATGGGTCTGACCCGTGTG
55908732 GACAAATTAG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.17, C:0.33, G:0.28, T:0.22
Consensus pattern (30 bp):
ACACACGCCCATGGGTCTGACCCGTGTGTC
Found at i:55909555 original size:91 final size:94
Alignment explanation
Indices: 55909395--55909716 Score: 304
Period size: 94 Copynumber: 3.4 Consensus size: 94
55909385 GGGATATATT
* *
55909395 GCCGATGCCGTGTCCCAGACATGGTCTTACACTGGCTCTCATATGTGCGTGCTGATGCATGTCCT
1 GCCGATGCCGTGTCCCAGACATGGTCTTACACTGGCTCTCATATGTGCGGGCCGATGCATGTCCT
55909460 AGACATGTCTTACACTAGCACAACTCTTA
66 AGACATGTCTTACACTAGCACAACTCTTA
* * *
55909489 GCCGATG-CGTGTCCTAGACAT-GTCTTACACTGGCTGTC-TCTGT-CGAGGCCGATGCATGT-C
1 GCCGATGCCGTGTCCCAGACATGGTCTTACACTGGCTCTCATATGTGCG-GGCCGATGCATGTCC
* * *
55909549 TCAGACATGTCTTACTCTGGCACTTATCTCTGT-
65 T-AGACATGTCTTACACTAGCAC--AACTCT-TA
** * * * * *
55909582 GCCGACACCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATAT---TGCTGACGCATGTCC
1 GCCGATGCCGTGTCCCAGACATGGTCTTACACTGGCTCTCAT-ATGTGCGGGCCGATGCATGTCC
* ** *
55909644 CAGACATGTCTTACACTAGC-CCTCGTCTGGA
65 TAGACATGTCTTACACTAGCACAAC-TCT-TA
* *
55909675 TGCTGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCA
1 -GCCGATGCCGTGTCCCAGACATGGTCTTACACTGGCTCTCA
55909717 AATCACCCAT
Statistics
Matches: 189, Mismatches: 26, Indels: 26
0.78 0.11 0.11
Matches are distributed among these distances:
90 4 0.02
91 36 0.19
92 20 0.11
93 24 0.13
94 85 0.45
95 17 0.09
96 1 0.01
97 2 0.01
ACGTcount: A:0.20, C:0.30, G:0.21, T:0.29
Consensus pattern (94 bp):
GCCGATGCCGTGTCCCAGACATGGTCTTACACTGGCTCTCATATGTGCGGGCCGATGCATGTCCT
AGACATGTCTTACACTAGCACAACTCTTA
Found at i:55909641 original size:47 final size:47
Alignment explanation
Indices: 55909405--55909716 Score: 173
Period size: 47 Copynumber: 6.7 Consensus size: 47
55909395 GCCGATGCCG
* *
55909405 TGTCCCAGACATGGTCTTACACTGGCTCTCATATGTGCGTGCTGATG-CA
1 TGTCCCAGACATGGTCTTACACTGGCTCTCATA--TG-ATGCTGACGCCA
* * * * * * * * *
55909454 TGTCCTAGACAT-GTCTTACACTAGCAC-AACTCTTA-GCCGATG-CG
1 TGTCCCAGACATGGTCTTACACTGGCTCTCA-TATGATGCTGACGCCA
* * * * *
55909498 TGTCCTAGACAT-GTCTTACACTGGCTGTCTC-TGTCGAGGCCGATG-CA
1 TGTCCCAGACATGGTCTTACACTGGC--TCTCATAT-GATGCTGACGCCA
* * * * * * *
55909545 TGTCTCAGACAT-GTCTTACTCTGGCACTTATCTCTG-TGCCGACACCA
1 TGTCCCAGACATGGTCTTACACTGGCTCTCA--TATGATGCTGACGCCA
55909592 TGTCCCAGACATGGTCTTACACTGGCTCTCATAAT-ATTGCTGACG-CA
1 TGTCCCAGACATGGTCTTACACTGGCTCTCAT-ATGA-TGCTGACGCCA
* * * * *
55909639 TGTCCCAGACAT-GTCTTACACTAGCCCTCGTCTGGATGCTGATGCCA
1 TGTCCCAGACATGGTCTTACACTGGCTCTCATAT-GATGCTGACGCCA
55909686 TGTCCCAGACATGGTCTTACACTGGCTCTCA
1 TGTCCCAGACATGGTCTTACACTGGCTCTCA
55909717 AATCACCCAT
Statistics
Matches: 206, Mismatches: 39, Indels: 37
0.73 0.14 0.13
Matches are distributed among these distances:
44 31 0.15
45 5 0.02
46 32 0.16
47 75 0.36
48 52 0.25
49 11 0.05
ACGTcount: A:0.20, C:0.29, G:0.21, T:0.29
Consensus pattern (47 bp):
TGTCCCAGACATGGTCTTACACTGGCTCTCATATGATGCTGACGCCA
Found at i:55914542 original size:24 final size:24
Alignment explanation
Indices: 55914514--55914568 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 24
55914504 TTAATACATG
55914514 CATTACTTAAAACGACCCAAAATT
1 CATTACTTAAAACGACCCAAAATT
* *
55914538 CATTACTCAAAATGACCCAAAATT
1 CATTACTTAAAACGACCCAAAATT
55914562 CA-TACTT
1 CATTACTT
55914569 GGGTAAAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
23 4 0.14
24 24 0.86
ACGTcount: A:0.44, C:0.25, G:0.04, T:0.27
Consensus pattern (24 bp):
CATTACTTAAAACGACCCAAAATT
Found at i:55915775 original size:40 final size:40
Alignment explanation
Indices: 55915713--55915796 Score: 98
Period size: 40 Copynumber: 2.1 Consensus size: 40
55915703 TGACATATCG
*
55915713 GCTAAATATGGCACTCAATGTGCGGTTCG-GTATAGCTTCA
1 GCTAAATATGGCACTCAATGTGCGATTCGAG-ATAGCTTCA
* * * * *
55915753 GCTAAATTTGGCATTTAGTGTGCGATTTGAGATAGCTTCA
1 GCTAAATATGGCACTCAATGTGCGATTCGAGATAGCTTCA
55915793 GCTA
1 GCTA
55915797 TGTACAACAC
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
40 36 0.97
41 1 0.03
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (40 bp):
GCTAAATATGGCACTCAATGTGCGATTCGAGATAGCTTCA
Found at i:55915863 original size:28 final size:28
Alignment explanation
Indices: 55915832--55915899 Score: 118
Period size: 28 Copynumber: 2.4 Consensus size: 28
55915822 TCAAATATGG
*
55915832 CACTTAGTGTGCGAAATATTGCGAATGA
1 CACTTAGTGTGCGAAATATTGAGAATGA
*
55915860 CACTTAGTGTGCGAGATATTGAGAATGA
1 CACTTAGTGTGCGAAATATTGAGAATGA
55915888 CACTTAGTGTGC
1 CACTTAGTGTGC
55915900 AAAAAAATCG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.29
Consensus pattern (28 bp):
CACTTAGTGTGCGAAATATTGAGAATGA
Found at i:55917915 original size:45 final size:45
Alignment explanation
Indices: 55917851--55917936 Score: 136
Period size: 45 Copynumber: 1.9 Consensus size: 45
55917841 CCAAAACATG
*
55917851 TGTCACAAATTTCACGAACTCAAACCACAACTCAATGAGTTTGGA
1 TGTCACAAATATCACGAACTCAAACCACAACTCAATGAGTTTGGA
* * *
55917896 TGTCACATATATCATGAACTCAGACCACAACTCAATGAGTT
1 TGTCACAAATATCACGAACTCAAACCACAACTCAATGAGTT
55917937 CAGATTACAT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 37 1.00
ACGTcount: A:0.37, C:0.24, G:0.13, T:0.26
Consensus pattern (45 bp):
TGTCACAAATATCACGAACTCAAACCACAACTCAATGAGTTTGGA
Found at i:55922612 original size:16 final size:16
Alignment explanation
Indices: 55922591--55922625 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
55922581 ATCAAAAGAG
55922591 TAAAATTTATTAAAAT
1 TAAAATTTATTAAAAT
55922607 TAAAATTTATTAAAAT
1 TAAAATTTATTAAAAT
55922623 TAA
1 TAA
55922626 TTATCTTGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
TAAAATTTATTAAAAT
Found at i:55933802 original size:24 final size:23
Alignment explanation
Indices: 55933761--55933805 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
55933751 TTAAACTAAA
*
55933761 TTCTTTTTTATTTCTTTTAATAT
1 TTCTTTTTTATTTATTTTAATAT
*
55933784 TTCTTTTTTTTGTTATTTTAAT
1 TTCTTTTTTAT-TTATTTTAAT
55933806 TGTAAATTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.16, C:0.07, G:0.02, T:0.76
Consensus pattern (23 bp):
TTCTTTTTTATTTATTTTAATAT
Found at i:55936120 original size:19 final size:19
Alignment explanation
Indices: 55936083--55936120 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
55936073 ATTCACATGT
*
55936083 TTTAAATATATATATATAA
1 TTTAAATATATATAAATAA
55936102 TTTAAAGTATAT-TAAATAA
1 TTTAAA-TATATATAAATAA
55936121 GCATAACTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (19 bp):
TTTAAATATATATAAATAA
Found at i:55936407 original size:11 final size:11
Alignment explanation
Indices: 55936391--55936415 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
55936381 AAATGTTTAG
55936391 GTATATAATAT
1 GTATATAATAT
55936402 GTATATAATAT
1 GTATATAATAT
55936413 GTA
1 GTA
55936416 CATGACTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.00, G:0.12, T:0.44
Consensus pattern (11 bp):
GTATATAATAT
Found at i:55937071 original size:26 final size:26
Alignment explanation
Indices: 55937035--55937094 Score: 93
Period size: 26 Copynumber: 2.3 Consensus size: 26
55937025 TTTCTCGAAT
*
55937035 CGAGTCGAGTGAGATGGAATTCAAAA
1 CGAGTCGAGTGAGATGAAATTCAAAA
*
55937061 CGAGTCGAGTGAGATGAAATTCAAAT
1 CGAGTCGAGTGAGATGAAATTCAAAA
*
55937087 CGAATCGA
1 CGAGTCGA
55937095 ATCGAATATA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.38, C:0.13, G:0.28, T:0.20
Consensus pattern (26 bp):
CGAGTCGAGTGAGATGAAATTCAAAA
Found at i:55938201 original size:19 final size:19
Alignment explanation
Indices: 55938179--55938215 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
55938169 AAAATTGGAG
* *
55938179 TTTGGGGGGAAGTAAAAGT
1 TTTGGGGGAAAGCAAAAGT
55938198 TTTGGGGGAAAGCAAAAG
1 TTTGGGGGAAAGCAAAAG
55938216 GAAAAAAGTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.35, C:0.03, G:0.41, T:0.22
Consensus pattern (19 bp):
TTTGGGGGAAAGCAAAAGT
Found at i:55938226 original size:27 final size:28
Alignment explanation
Indices: 55938192--55938250 Score: 102
Period size: 28 Copynumber: 2.1 Consensus size: 28
55938182 GGGGGGAAGT
55938192 AAAAGTTTTGGGG-GAAAGCAAAAGGAA
1 AAAAGTTTTGGGGAGAAAGCAAAAGGAA
*
55938219 AAAAGTTTTGGGGAGAAAGTAAAAGGAA
1 AAAAGTTTTGGGGAGAAAGCAAAAGGAA
55938247 AAAA
1 AAAA
55938251 AATTTGTGGG
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
27 13 0.43
28 17 0.57
ACGTcount: A:0.53, C:0.02, G:0.31, T:0.15
Consensus pattern (28 bp):
AAAAGTTTTGGGGAGAAAGCAAAAGGAA
Found at i:55938256 original size:28 final size:27
Alignment explanation
Indices: 55938198--55938256 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 27
55938188 AAGTAAAAGT
**
55938198 TTTGGGGGAAAGCAAAAGGAAAAAAGT
1 TTTGGGGGAAAGCAAAAGGAAAAAAAA
*
55938225 TTTGGGGAGAAAGTAAAAGGAAAAAAAA
1 TTTGGGG-GAAAGCAAAAGGAAAAAAAA
55938253 TTTG
1 TTTG
55938257 TGGGTTTGGA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
27 7 0.25
28 21 0.75
ACGTcount: A:0.49, C:0.02, G:0.31, T:0.19
Consensus pattern (27 bp):
TTTGGGGGAAAGCAAAAGGAAAAAAAA
Found at i:55938304 original size:82 final size:79
Alignment explanation
Indices: 55938163--55938323 Score: 223
Period size: 82 Copynumber: 2.0 Consensus size: 79
55938153 ACATAAATTT
* *
55938163 GAAAAAAAAATTGGAGTTTGGGGGGAAGTAAAAGTTTTGGGGGAAAGCAAAAGGAAAAAAGTTTT
1 GAAAAAAAAATTGGAGTTTGGAGGGAAGTAAAAGTTTTGGGGGAAAACAAAAGGAAAAAAGTTTT
55938228 GGGGAGAAAGTAAAAG
66 -GGG-GAAAGTAAAAG
* * * *
55938244 GAAAAAAAATTTGTGGGTTTGGAGGGAAGTAACAGTTTTGGGGAGAAAATAAAAGGAAAAAAGTT
1 GAAAAAAAAATTG-GAGTTTGGAGGGAAGTAAAAGTTTTGGGG-GAAAACAAAAGGAAAAAAGTT
*
55938309 TTGTGGAAAGTAAAA
64 TTGGGGAAAGTAAAA
55938324 TTTTTAAGAA
Statistics
Matches: 71, Mismatches: 7, Indels: 4
0.87 0.09 0.05
Matches are distributed among these distances:
81 22 0.31
82 28 0.39
83 21 0.30
ACGTcount: A:0.45, C:0.01, G:0.32, T:0.21
Consensus pattern (79 bp):
GAAAAAAAAATTGGAGTTTGGAGGGAAGTAAAAGTTTTGGGGGAAAACAAAAGGAAAAAAGTTTT
GGGGAAAGTAAAAG
Found at i:55938414 original size:28 final size:28
Alignment explanation
Indices: 55938370--55938431 Score: 90
Period size: 28 Copynumber: 2.2 Consensus size: 28
55938360 AAGGGGAAGT
* *
55938370 AAAAGTTTTAGGGAGAAAGTAAAAGGAA
1 AAAAGTCTTAGGGAGAAAATAAAAGGAA
55938398 AAAAGTCTT-GGGAAGAAAATAAAAGGAA
1 AAAAGTCTTAGGG-AGAAAATAAAAGGAA
55938426 AAAAGT
1 AAAAGT
55938432 TTTGAGGGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
27 3 0.10
28 28 0.90
ACGTcount: A:0.56, C:0.02, G:0.26, T:0.16
Consensus pattern (28 bp):
AAAAGTCTTAGGGAGAAAATAAAAGGAA
Found at i:55938826 original size:16 final size:16
Alignment explanation
Indices: 55938802--55938842 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
55938792 TACTTTGGTT
*
55938802 GGCTATAATGAAATAG
1 GGCTGTAATGAAATAG
*
55938818 GGCTGTAATGGAATAG
1 GGCTGTAATGAAATAG
*
55938834 AGCTGTAAT
1 GGCTGTAAT
55938843 AAGTAATTCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.37, C:0.07, G:0.29, T:0.27
Consensus pattern (16 bp):
GGCTGTAATGAAATAG
Found at i:55939179 original size:12 final size:12
Alignment explanation
Indices: 55939147--55939189 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
55939137 AAAAATCAAA
55939147 ATATAT-AATACT
1 ATATATAAATA-T
*
55939159 ATA-AAAAATAT
1 ATATATAAATAT
55939170 ATATATAAATAT
1 ATATATAAATAT
55939182 ATATATAA
1 ATATATAA
55939190 TACAAGCAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
11 5 0.19
12 22 0.81
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.37
Consensus pattern (12 bp):
ATATATAAATAT
Found at i:55939182 original size:21 final size:19
Alignment explanation
Indices: 55939144--55939182 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 19
55939134 TTAAAAAATC
*
55939144 AAAATATATAATACTATAA
1 AAAATATATAATAATATAA
55939163 AAAATATATATATAAATATA
1 AAAATATATA-AT-AATATA
55939183 TATATAATAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 10 0.59
20 2 0.12
21 5 0.29
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (19 bp):
AAAATATATAATAATATAA
Found at i:55943874 original size:40 final size:40
Alignment explanation
Indices: 55943819--55944036 Score: 334
Period size: 40 Copynumber: 5.5 Consensus size: 40
55943809 CGGATGATAA
* *
55943819 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-T
55943859 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
55943899 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* * *
55943939 TCGGGCTAGGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
55943979 CCGGGCTAAGTCCCGAAGGCATTTGAGCGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
*
55944019 CC-GGCTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
55944037 TACTTGGTTT
Statistics
Matches: 166, Mismatches: 10, Indels: 5
0.92 0.06 0.03
Matches are distributed among these distances:
39 17 0.10
40 148 0.89
41 1 0.01
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:55947749 original size:11 final size:11
Alignment explanation
Indices: 55947733--55947757 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
55947723 TGAGGTAGAA
55947733 ATTATTATTTT
1 ATTATTATTTT
55947744 ATTATTATTTT
1 ATTATTATTTT
55947755 ATT
1 ATT
55947758 TTCTACAGCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (11 bp):
ATTATTATTTT
Found at i:55955916 original size:12 final size:12
Alignment explanation
Indices: 55955899--55955923 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
55955889 ATGTAAGTGA
55955899 TCTTGATGATTT
1 TCTTGATGATTT
55955911 TCTTGATGATTT
1 TCTTGATGATTT
55955923 T
1 T
55955924 TACATTTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.08, G:0.16, T:0.60
Consensus pattern (12 bp):
TCTTGATGATTT
Found at i:55965662 original size:33 final size:33
Alignment explanation
Indices: 55965619--55965688 Score: 131
Period size: 33 Copynumber: 2.1 Consensus size: 33
55965609 AATTAGCATA
55965619 ATTATAATCAAGTATTTTAGGCTTAGCTTACTC
1 ATTATAATCAAGTATTTTAGGCTTAGCTTACTC
*
55965652 ATTATCATCAAGTATTTTAGGCTTAGCTTACTC
1 ATTATAATCAAGTATTTTAGGCTTAGCTTACTC
55965685 ATTA
1 ATTA
55965689 GCATTCTTAC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.30, C:0.16, G:0.11, T:0.43
Consensus pattern (33 bp):
ATTATAATCAAGTATTTTAGGCTTAGCTTACTC
Found at i:55968091 original size:31 final size:31
Alignment explanation
Indices: 55968047--55968125 Score: 122
Period size: 31 Copynumber: 2.5 Consensus size: 31
55968037 TTTAACGGTT
* * *
55968047 ACTGGACCAAAGCCTTTTCATAAATCATATC
1 ACTGGGCCGAAGCCTTTTAATAAATCATATC
55968078 ACTGGGCCGAAGCCTTTTAATAAATCATATC
1 ACTGGGCCGAAGCCTTTTAATAAATCATATC
*
55968109 ACTCGGCCGAAGCCTTT
1 ACTGGGCCGAAGCCTTT
55968126 ACTGTAAACG
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.30, C:0.27, G:0.15, T:0.28
Consensus pattern (31 bp):
ACTGGGCCGAAGCCTTTTAATAAATCATATC
Found at i:55968196 original size:42 final size:42
Alignment explanation
Indices: 55968149--55968240 Score: 148
Period size: 42 Copynumber: 2.2 Consensus size: 42
55968139 TGGCCCTTAG
* ** *
55968149 GCCCATTTCAATATCACATGTAATGTCAATGGATGTATGCAA
1 GCCCATTTCAATATCACATGAAATACCAATGAATGTATGCAA
55968191 GCCCATTTCAATATCACATGAAATACCAATGAATGTATGCAA
1 GCCCATTTCAATATCACATGAAATACCAATGAATGTATGCAA
55968233 GCCCATTT
1 GCCCATTT
55968241 GGGGAGACTA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.35, C:0.22, G:0.14, T:0.29
Consensus pattern (42 bp):
GCCCATTTCAATATCACATGAAATACCAATGAATGTATGCAA
Found at i:55968405 original size:25 final size:26
Alignment explanation
Indices: 55968377--55968457 Score: 78
Period size: 25 Copynumber: 3.2 Consensus size: 26
55968367 GGAGGCCTAG
* *
55968377 CCTTTTTTAAT-AACTTGGGCAAAGC
1 CCTTTTCTAATAAACTGGGGCAAAGC
* *
55968402 CC-TTTCTGATAAACTGGGGCAGAGC
1 CCTTTTCTAATAAACTGGGGCAAAGC
** *
55968427 CCTTTTC-GGTAAACTGGGGCAGAGC
1 CCTTTTCTAATAAACTGGGGCAAAGC
55968452 CCTTTT
1 CCTTTT
55968458 AGCACTTCCT
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
24 6 0.12
25 39 0.80
26 4 0.08
ACGTcount: A:0.22, C:0.23, G:0.23, T:0.31
Consensus pattern (26 bp):
CCTTTTCTAATAAACTGGGGCAAAGC
Found at i:55969407 original size:27 final size:27
Alignment explanation
Indices: 55969381--55969511 Score: 86
Period size: 27 Copynumber: 4.7 Consensus size: 27
55969371 ATCTACAAAC
*
55969381 CAAGGGTATTTCAGTAATTTTGTAAAC
1 CAAGGGTATTTCAGTAATTTTGTAAAT
** *
55969408 CAATAGTATTCCTA-TAATTTT-TAAAAAAGT
1 CAAGGGTATTTC-AGTAATTTTGT---AAA-T
**
55969438 CAAGGGTATTTTTGTAATTTTGTAAAT
1 CAAGGGTATTTCAGTAATTTTGTAAAT
* ** **
55969465 CAGGGGTATTTTGGTAATTTTACAAAT
1 CAAGGGTATTTCAGTAATTTTGTAAAT
**
55969492 TGAGGGTATTTCAGTAATTT
1 CAAGGGTATTTCAGTAATTT
55969512 CTCAAACCAG
Statistics
Matches: 79, Mismatches: 18, Indels: 14
0.71 0.16 0.13
Matches are distributed among these distances:
26 1 0.01
27 55 0.70
28 4 0.05
29 3 0.04
30 15 0.19
31 1 0.01
ACGTcount: A:0.33, C:0.08, G:0.18, T:0.42
Consensus pattern (27 bp):
CAAGGGTATTTCAGTAATTTTGTAAAT
Found at i:55969526 original size:27 final size:26
Alignment explanation
Indices: 55969495--55969566 Score: 72
Period size: 27 Copynumber: 2.7 Consensus size: 26
55969485 TACAAATTGA
55969495 GGGTATTTCAGTAATTTCTCAAACCAG
1 GGGTATTTCAGTAATTTCTCAAA-CAG
* ** * **
55969522 TGGTATTTTGGTAATTTTATCCTACAG
1 GGGTATTTCAGTAA-TTTCTCAAACAG
55969549 GGGTATTTCAGTAATTTC
1 GGGTATTTCAGTAATTTC
55969567 ACAATCGAGG
Statistics
Matches: 34, Mismatches: 10, Indels: 3
0.72 0.21 0.06
Matches are distributed among these distances:
26 3 0.09
27 25 0.74
28 6 0.18
ACGTcount: A:0.25, C:0.14, G:0.19, T:0.42
Consensus pattern (26 bp):
GGGTATTTCAGTAATTTCTCAAACAG
Found at i:55969577 original size:27 final size:26
Alignment explanation
Indices: 55969462--55969577 Score: 65
Period size: 27 Copynumber: 4.3 Consensus size: 26
55969452 TAATTTTGTA
** *
55969462 AATCAGGGGTATTTTGGTAATTTTAC
1 AATCAGGGGTATTTCAGTAATTTCAC
* *
55969488 AAAT-TGAGGGTATTTCAGTAATTTCTC
1 -AATCAG-GGGTATTTCAGTAATTTCAC
* * ** *
55969515 AAACCAGTGGTATTTTGGTAATTTTATC
1 -AATCAGGGGTATTTCAGTAATTTCA-C
*
55969543 -CTACAGGGGTATTTCAGTAATTTCAC
1 AAT-CAGGGGTATTTCAGTAATTTCAC
55969569 AATCGAGGG
1 AATC-AGGG
55969578 TAAAACAGAA
Statistics
Matches: 64, Mismatches: 19, Indels: 12
0.67 0.20 0.13
Matches are distributed among these distances:
26 3 0.05
27 59 0.92
28 2 0.03
ACGTcount: A:0.28, C:0.12, G:0.22, T:0.38
Consensus pattern (26 bp):
AATCAGGGGTATTTCAGTAATTTCAC
Found at i:55969603 original size:27 final size:27
Alignment explanation
Indices: 55969569--55969660 Score: 105
Period size: 27 Copynumber: 3.4 Consensus size: 27
55969559 GTAATTTCAC
55969569 AATCGAGGGTAAAACAGAAATTTTGTA
1 AATCGAGGGTAAAACAGAAATTTTGTA
* ** *
55969596 AATTGAGGGTAAAATGGTAATTTTGTA
1 AATCGAGGGTAAAACAGAAATTTTGTA
* *
55969623 AATCGAGGGTAAAAC-GATAATTCTATA
1 AATCGAGGGTAAAACAGA-AATTTTGTA
*
55969650 AGTCGAGGGTA
1 AATCGAGGGTA
55969661 CTTTGGTAAT
Statistics
Matches: 54, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
26 1 0.02
27 53 0.98
ACGTcount: A:0.40, C:0.07, G:0.25, T:0.28
Consensus pattern (27 bp):
AATCGAGGGTAAAACAGAAATTTTGTA
Found at i:55969683 original size:54 final size:53
Alignment explanation
Indices: 55969559--55969684 Score: 130
Period size: 54 Copynumber: 2.3 Consensus size: 53
55969549 GGGTATTTCA
* * * *
55969559 GTAATTTCACAATCGAGGGTAAAACAGAAATTTTGTAAATTGAGGGTAAAATG
1 GTAATTTTACAATCGAGGGTAAAACAGAAATTCTATAAATCGAGGGTAAAATG
* ***
55969612 GTAATTTTGTA-AATCGAGGGTAAAAC-GATAATTCTATAAGTCGAGGGTACTTTG
1 GTAA-TTT-TACAATCGAGGGTAAAACAGA-AATTCTATAAATCGAGGGTAAAATG
55969666 GTAATTTTACAAGTCGAGG
1 GTAATTTTACAA-TCGAGG
55969685 ATATTTCAGT
Statistics
Matches: 60, Mismatches: 8, Indels: 9
0.78 0.10 0.12
Matches are distributed among these distances:
52 2 0.03
53 11 0.18
54 46 0.77
55 1 0.02
ACGTcount: A:0.37, C:0.09, G:0.24, T:0.31
Consensus pattern (53 bp):
GTAATTTTACAATCGAGGGTAAAACAGAAATTCTATAAATCGAGGGTAAAATG
Found at i:55969696 original size:27 final size:27
Alignment explanation
Indices: 55969640--55969699 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 27
55969630 GGTAAAACGA
* * * *
55969640 TAATTCTATAAGTCGAGGGTACTTTGG
1 TAATTTTACAAGTCGAGGATACTTTAG
55969667 TAATTTTACAAGTCGAGGATA-TTTCAG
1 TAATTTTACAAGTCGAGGATACTTT-AG
55969694 TAATTT
1 TAATTT
55969700 GGTAAACTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 3 0.11
27 25 0.89
ACGTcount: A:0.30, C:0.10, G:0.20, T:0.40
Consensus pattern (27 bp):
TAATTTTACAAGTCGAGGATACTTTAG
Found at i:55975217 original size:37 final size:37
Alignment explanation
Indices: 55975159--55975229 Score: 115
Period size: 37 Copynumber: 1.9 Consensus size: 37
55975149 TAGCTCGAAT
* *
55975159 AATCCCCACATGTAGTTATCGGGTCTTACCCGGACAA
1 AATCCCCACACGTAGTCATCGGGTCTTACCCGGACAA
*
55975196 AATCTCCACACGTAGTCATCGGGTCTTACCCGGA
1 AATCCCCACACGTAGTCATCGGGTCTTACCCGGA
55975230 ATATATTTCC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.25, C:0.31, G:0.20, T:0.24
Consensus pattern (37 bp):
AATCCCCACACGTAGTCATCGGGTCTTACCCGGACAA
Found at i:55975422 original size:48 final size:48
Alignment explanation
Indices: 55975362--55976139 Score: 1254
Period size: 48 Copynumber: 16.2 Consensus size: 48
55975352 CGGCCACAAT
* *
55975362 ATATACACATCTCATACATATTTCACATTAGCCATTCGACTTTACCAC
1 ATATACATATCTCATACATATTTCACATTAGCCATTCGGCTTTACCAC
*
55975410 ATATACATATCTCATACATATTTCACATTAGCCATTCGGATTTACCAC
1 ATATACATATCTCATACATATTTCACATTAGCCATTCGGCTTTACCAC
*
55975458 ATAT--ATATCTCATACATATTTCATATTAGCCATTCGGCTTTACCAC
1 ATATACATATCTCATACATATTTCACATTAGCCATTCGGCTTTACCAC
* ** *
55975504 ATATATATATCTCATACATATTTCATGTTAGCCATTCGACTTTACCAC
1 ATATACATATCTCATACATATTTCACATTAGCCATTCGGCTTTACCAC
*
55975552 ATATACATATCTCATACATATTTCACATTAACCATTCGGCTTTACCAC
1 ATATACATATCTCATACATATTTCACATTAGCCATTCGGCTTTACCAC
*
55975600 ATATACATATCTCATACATATTTCACATTAGCCATTCGGATTTACCAC
1 ATATACATATCTCATACATATTTCACATTAGCCATTCGGCTTTACCAC
**
55975648 ATATACATATCTCATACATATTTCATGTTAGCCATTCGGCTTTACCAC
1 ATATACATATCTCATACATATTTCACATTAGCCATTCGGCTTTACCAC
* ** *
55975696 ATATATATATCTCATACATATTTCATGTTAGCCATTCGACTTTACCAC
1 ATATACATATCTCATACATATTTCACATTAGCCATTCGGCTTTACCAC
55975744 ATATACATATCTCATACATATTTCACATTAGCCATTCGGCTTTACCAC
1 ATATACATATCTCATACATATTTCACATTAGCCATTCGGCTTTACCAC
55975792 ATATACATATCTCATACATATTTCACATTAGCCATTCGGCTTTACCAC
1 ATATACATATCTCATACATATTTCACATTAGCCATTCGGCTTTACCAC
* * *
55975840 ATATATATATCTCATACATATTTCACATTAGCCATTCGGATTTACCATAT
1 ATATACATATCTCATACATATTTCACATTAGCCATTCGGCTTTACC--AC
* **
55975890 ATATATATATCTCATACATATTTCATGTTAGCCATTCGGCTTTACCAC
1 ATATACATATCTCATACATATTTCACATTAGCCATTCGGCTTTACCAC
*
55975938 ATATACATATCTCATACATATTTCACATTAGCCATTCGGATTTACCAC
1 ATATACATATCTCATACATATTTCACATTAGCCATTCGGCTTTACCAC
* *
55975986 ATATATATATCTCATACATATTTCATATTAGCCATTCGGCTTTACCAC
1 ATATACATATCTCATACATATTTCACATTAGCCATTCGGCTTTACCAC
* **
55976034 ATATATATATCTCATACATATTTCATGTTAGCCATTCGGCTTTACCAC
1 ATATACATATCTCATACATATTTCACATTAGCCATTCGGCTTTACCAC
55976082 ATATACATATCTCATACATATTTCACATTAGCCATTCGGCTTTACCAC
1 ATATACATATCTCATACATATTTCACATTAGCCATTCGGCTTTACCAC
* *
55976130 ACATATATAT
1 ATATACATAT
55976140 ATTTATCTTG
Statistics
Matches: 683, Mismatches: 43, Indels: 8
0.93 0.06 0.01
Matches are distributed among these distances:
46 44 0.06
48 595 0.87
50 44 0.06
ACGTcount: A:0.32, C:0.25, G:0.06, T:0.37
Consensus pattern (48 bp):
ATATACATATCTCATACATATTTCACATTAGCCATTCGGCTTTACCAC
Found at i:55979361 original size:13 final size:13
Alignment explanation
Indices: 55979343--55979372 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
55979333 ATAACTCAAC
55979343 GAATACTCTAATA
1 GAATACTCTAATA
55979356 GAATACTCTAATA
1 GAATACTCTAATA
55979369 GAAT
1 GAAT
55979373 TCTCAAGCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.47, C:0.13, G:0.10, T:0.30
Consensus pattern (13 bp):
GAATACTCTAATA
Found at i:55981756 original size:43 final size:43
Alignment explanation
Indices: 55981667--55981758 Score: 114
Period size: 43 Copynumber: 2.1 Consensus size: 43
55981657 TTGCAATTGT
* *
55981667 GTGTAAGACCATGTCAGGGACATTAGCATCGTTATGCTATTAC
1 GTGTAACACCATGTCAGGGACATTAGCATCGTTATGATATTAC
* * * *
55981710 GTGTAACACCATGTCTGGGACATTGGCATTGTTAT-ATGATTTC
1 GTGTAACACCATGTCAGGGACATTAGCATCGTTATGAT-ATTAC
55981753 GTGTAA
1 GTGTAA
55981759 AACCCTATTT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
42 1 0.02
43 41 0.98
ACGTcount: A:0.26, C:0.16, G:0.24, T:0.34
Consensus pattern (43 bp):
GTGTAACACCATGTCAGGGACATTAGCATCGTTATGATATTAC
Found at i:55987508 original size:27 final size:27
Alignment explanation
Indices: 55987478--55987589 Score: 138
Period size: 27 Copynumber: 4.1 Consensus size: 27
55987468 AGGAAGCGTC
*
55987478 CTGGTGGCTATGCCACAATTATCTGAT
1 CTGGTGGCTCTGCCACAATTATCTGAT
*
55987505 CTGGTGGCTCTGCCACATATT-TCTGTT
1 CTGGTGGCTCTGCCACA-ATTATCTGAT
*
55987532 CTGGTGGCTCTGCCACGATTATCTGTAT
1 CTGGTGGCTCTGCCACAATTATCTG-AT
* * *
55987560 CTGGTGACTCTGTCAC-ATTATCTGTT
1 CTGGTGGCTCTGCCACAATTATCTGAT
55987586 CTGG
1 CTGG
55987590 CAGCCATGCT
Statistics
Matches: 75, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
26 8 0.11
27 49 0.65
28 18 0.24
ACGTcount: A:0.15, C:0.24, G:0.23, T:0.38
Consensus pattern (27 bp):
CTGGTGGCTCTGCCACAATTATCTGAT
Found at i:55987584 original size:54 final size:54
Alignment explanation
Indices: 55987478--55987589 Score: 163
Period size: 54 Copynumber: 2.1 Consensus size: 54
55987468 AGGAAGCGTC
* *
55987478 CTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATTTCTGTT
1 CTGGTGGCTATGCCACAATTATCTGATCTGGTGACTCTGCCACATATATCTGTT
* * *
55987532 CTGGTGGCTCTGCCACGATTATCTGTATCTGGTGACTCTGTCACAT-TATCTGTT
1 CTGGTGGCTATGCCACAATTATCTG-ATCTGGTGACTCTGCCACATATATCTGTT
55987586 CTGG
1 CTGG
55987590 CAGCCATGCT
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
54 34 0.65
55 18 0.35
ACGTcount: A:0.15, C:0.24, G:0.23, T:0.38
Consensus pattern (54 bp):
CTGGTGGCTATGCCACAATTATCTGATCTGGTGACTCTGCCACATATATCTGTT
Found at i:55988633 original size:11 final size:10
Alignment explanation
Indices: 55988605--55988638 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
55988595 AGGCTGTAAG
55988605 TATTCTGAAT
1 TATTCTGAAT
*
55988615 TTTTCTGAAT
1 TATTCTGAAT
55988625 ATATTCTGAAT
1 -TATTCTGAAT
55988636 TAT
1 TAT
55988639 CTGTCTGTAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
10 12 0.57
11 9 0.43
ACGTcount: A:0.29, C:0.09, G:0.09, T:0.53
Consensus pattern (10 bp):
TATTCTGAAT
Found at i:55994109 original size:40 final size:40
Alignment explanation
Indices: 55994052--55994242 Score: 305
Period size: 40 Copynumber: 4.8 Consensus size: 40
55994042 AGGGATTTAA
**
55994052 CCGGATATAGCT-ACTCGCTTAAATGCCTTCGGGACTTAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
*
55994092 CCGGATATAGTAGCTCGCACAAATGCCTTCGGGACTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
55994132 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
55994172 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
55994212 CCGGA-ATTAGTCACTAGCACAAATGCCTTCG
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCG
55994243 TTATCATCCG
Statistics
Matches: 143, Mismatches: 6, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
39 2 0.01
40 141 0.99
ACGTcount: A:0.26, C:0.28, G:0.23, T:0.24
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:55998837 original size:27 final size:27
Alignment explanation
Indices: 55998797--55998902 Score: 126
Period size: 27 Copynumber: 3.9 Consensus size: 27
55998787 AGGAAGCGTC
*
55998797 CTGGTGGCTATGCCACAATTATCTGAT
1 CTGGTGGCTCTGCCACAATTATCTGAT
*
55998824 CTGGTGGCTCTGCCACATATT-TCTGTT
1 CTGGTGGCTCTGCCACA-ATTATCTGAT
* *
55998851 CTGGTGGCTCTGCTACGATTATCTGTAT
1 CTGGTGGCTCTGCCACAATTATCTG-AT
* *
55998879 CTGGTGACTCTGTCAC-ATTATCTG
1 CTGGTGGCTCTGCCACAATTATCTG
55998903 TCCTGGCAGC
Statistics
Matches: 68, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
26 3 0.04
27 48 0.71
28 17 0.25
ACGTcount: A:0.16, C:0.24, G:0.23, T:0.38
Consensus pattern (27 bp):
CTGGTGGCTCTGCCACAATTATCTGAT
Found at i:55998903 original size:54 final size:54
Alignment explanation
Indices: 55998794--55998908 Score: 151
Period size: 54 Copynumber: 2.1 Consensus size: 54
55998784 TGGAGGAAGC
* *
55998794 GTCCTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATTTCT
1 GTCCTGGTGGCTATGCCACAATTATCTGATCTGGTGACTCTGCCACATATATCT
* * * * *
55998848 GTTCTGGTGGCTCTGCTACGATTATCTGTATCTGGTGACTCTGTCACAT-TATCT
1 GTCCTGGTGGCTATGCCACAATTATCTG-ATCTGGTGACTCTGCCACATATATCT
55998902 GTCCTGG
1 GTCCTGG
55998909 CAGCCATGCT
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
54 34 0.65
55 18 0.35
ACGTcount: A:0.15, C:0.24, G:0.23, T:0.37
Consensus pattern (54 bp):
GTCCTGGTGGCTATGCCACAATTATCTGATCTGGTGACTCTGCCACATATATCT
Found at i:56009744 original size:47 final size:47
Alignment explanation
Indices: 56009690--56009785 Score: 151
Period size: 47 Copynumber: 2.0 Consensus size: 47
56009680 GTTGAATTTA
56009690 AAGCTTGTTAAATTTG-CTCTTAATATTT-TCGGATAAGTTACTTAGTT
1 AAGCTTGTTAAATTTGCCT-TTAATATTTCT-GGATAAGTTACTTAGTT
*
56009737 AAGCTTGTTAAATTTTCCTTTAATATTTCTGGATAAGTTACTTAGTT
1 AAGCTTGTTAAATTTGCCTTTAATATTTCTGGATAAGTTACTTAGTT
56009784 AA
1 AA
56009786 AGAAAATTTT
Statistics
Matches: 46, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
47 43 0.93
48 3 0.07
ACGTcount: A:0.29, C:0.10, G:0.14, T:0.47
Consensus pattern (47 bp):
AAGCTTGTTAAATTTGCCTTTAATATTTCTGGATAAGTTACTTAGTT
Found at i:56010662 original size:45 final size:45
Alignment explanation
Indices: 56010598--56010771 Score: 253
Period size: 45 Copynumber: 3.9 Consensus size: 45
56010588 TCGTACAGTA
* *
56010598 CTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCAGTGAGATG
1 CTATTCGGGCCTTCGAGCCTAGCAGGCTATAATGCCGGTGAGATG
* * *
56010643 CTATTCAGGCCTTCGAGCCTAGCAGGCTATAATACCGGTGAGATA
1 CTATTCGGGCCTTCGAGCCTAGCAGGCTATAATGCCGGTGAGATG
* *
56010688 CTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAAATG
1 CTATTCGGGCCTTCGAGCCTAGCAGGCTATAATGCCGGTGAGATG
* *
56010733 ATA-TC-GGCCTTCGAGCCTAGTAGGCTATAATGCCGGTGA
1 CTATTCGGGCCTTCGAGCCTAGCAGGCTATAATGCCGGTGA
56010772 ATGAATTCAG
Statistics
Matches: 116, Mismatches: 13, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
43 32 0.28
44 2 0.02
45 82 0.71
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.26
Consensus pattern (45 bp):
CTATTCGGGCCTTCGAGCCTAGCAGGCTATAATGCCGGTGAGATG
Found at i:56028502 original size:47 final size:47
Alignment explanation
Indices: 56028448--56028590 Score: 250
Period size: 47 Copynumber: 3.0 Consensus size: 47
56028438 GTTGAATTTA
56028448 AAGCTTGTTAAATTTGCTCTTAATATTTTCGGATAAGTTACTTAGTT
1 AAGCTTGTTAAATTTGCTCTTAATATTTTCGGATAAGTTACTTAGTT
56028495 AAGCTTGTTAAATTTGCTCTTAATATTTTCGGATAAGTTACTTAGTT
1 AAGCTTGTTAAATTTGCTCTTAATATTTTCGGATAAGTTACTTAGTT
* * * *
56028542 AAGCTTGTTAAATTTGCCCTTAATATTTCCAGATAAGGTACTTAGTT
1 AAGCTTGTTAAATTTGCTCTTAATATTTTCGGATAAGTTACTTAGTT
56028589 AA
1 AA
56028591 AGAAAATTTT
Statistics
Matches: 92, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 92 1.00
ACGTcount: A:0.29, C:0.12, G:0.15, T:0.44
Consensus pattern (47 bp):
AAGCTTGTTAAATTTGCTCTTAATATTTTCGGATAAGTTACTTAGTT
Found at i:56029469 original size:45 final size:45
Alignment explanation
Indices: 56029393--56029567 Score: 233
Period size: 45 Copynumber: 3.9 Consensus size: 45
56029383 TATCGTATAG
* * *
56029393 TACTATTCGAGCCTTTTGAGCCTAGTAGGCTATAATGCCGGGGTGA
1 TACTATTCGAGCC-TTTGAGCCTAGCAGGCTATAATGCCGGTGAGA
* *
56029439 TACTATTCGAGCCTTTGAGCCTAACAGGCTATAATGCCAGTGAGA
1 TACTATTCGAGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGA
* ** *
56029484 TACTATTCGGGCCTTCAAGCCTAGCAGGCTATAATGCCTGTGAGA
1 TACTATTCGAGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGA
* * *
56029529 TACTATCCGGGCCTTTGAGCCTAGCTGGCTATAATGCCG
1 TACTATTCGAGCCTTTGAGCCTAGCAGGCTATAATGCCG
56029568 ATGAAATGAT
Statistics
Matches: 114, Mismatches: 15, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
45 101 0.89
46 13 0.11
ACGTcount: A:0.23, C:0.23, G:0.25, T:0.28
Consensus pattern (45 bp):
TACTATTCGAGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGA
Found at i:56034997 original size:28 final size:28
Alignment explanation
Indices: 56034957--56035027 Score: 90
Period size: 28 Copynumber: 2.5 Consensus size: 28
56034947 GATGTCTCGT
56034957 ACACTAAGTGCCATACTCAATATCTT-GC
1 ACACTAAGTGCCATACTCAATAT-TTGGC
* * *
56034985 ACACCAAGTGCCATTCTTAATATTTGGC
1 ACACTAAGTGCCATACTCAATATTTGGC
*
56035013 ACAGTAAGTGCCATA
1 ACACTAAGTGCCATA
56035028 TACATATAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
27 2 0.06
28 34 0.94
ACGTcount: A:0.32, C:0.25, G:0.14, T:0.28
Consensus pattern (28 bp):
ACACTAAGTGCCATACTCAATATTTGGC
Found at i:56037252 original size:46 final size:47
Alignment explanation
Indices: 56037146--56037268 Score: 149
Period size: 46 Copynumber: 2.6 Consensus size: 47
56037136 TGTCTTCGAC
* * * *
56037146 ATGGACTTACATGAATTATTCCTGTCTTCAATGCCATATATATATCTAAT
1 ATGGACTTACATGACTCATTCCTGTCTCCAAAGCC--A-ATATATCTAAT
* *
56037196 ATGGGCTTACATGACTCATTCCTGTCTCCAAAGCC-ATATATCTGAT
1 ATGGACTTACATGACTCATTCCTGTCTCCAAAGCCAATATATCTAAT
*
56037242 ATGGACTTACATGACTCATTTCTGTCT
1 ATGGACTTACATGACTCATTCCTGTCT
56037269 TGTCGTGTCC
Statistics
Matches: 65, Mismatches: 8, Indels: 4
0.84 0.10 0.05
Matches are distributed among these distances:
46 35 0.54
50 30 0.46
ACGTcount: A:0.28, C:0.22, G:0.13, T:0.37
Consensus pattern (47 bp):
ATGGACTTACATGACTCATTCCTGTCTCCAAAGCCAATATATCTAAT
Found at i:56041590 original size:46 final size:47
Alignment explanation
Indices: 56041484--56041606 Score: 149
Period size: 46 Copynumber: 2.6 Consensus size: 47
56041474 TGTCTTCGAC
* * * *
56041484 ATGGACTTACATGAATTATTCCTGTCTTCAATGCCATATATATATCTAAT
1 ATGGACTTACATGACTCATTCCTGTCTCCAAAGCC--A-ATATATCTAAT
* *
56041534 ATGGGCTTACATGACTCATTCCTGTCTCCAAAGCC-ATATATCTGAT
1 ATGGACTTACATGACTCATTCCTGTCTCCAAAGCCAATATATCTAAT
*
56041580 ATGGACTTACATGACTCATTTCTGTCT
1 ATGGACTTACATGACTCATTCCTGTCT
56041607 TGTCATGTCC
Statistics
Matches: 65, Mismatches: 8, Indels: 4
0.84 0.10 0.05
Matches are distributed among these distances:
46 35 0.54
50 30 0.46
ACGTcount: A:0.28, C:0.22, G:0.13, T:0.37
Consensus pattern (47 bp):
ATGGACTTACATGACTCATTCCTGTCTCCAAAGCCAATATATCTAAT
Found at i:56046163 original size:42 final size:41
Alignment explanation
Indices: 56046116--56046455 Score: 218
Period size: 42 Copynumber: 7.7 Consensus size: 41
56046106 TCTTTTACTT
56046116 GATGCCATAGT-CCA-ACTATGGTCTTACACAAAGTCTCATATC
1 GATGCCATA-TACCAGAC-ATGGTCTTACACAAA-TCTCATATC
* * *
56046158 GATGCCATGTACCAGACATGGTCTTATACGAAATCACATATC
1 GATGCCATATACCAGACATGGTCTTACAC-AAATCTCATATC
*** * *
56046200 GATGCTGCAT-CCTAGACATGGTCTTACATGAAATCTCATACC
1 GATGCCATATACC-AGACATGGTCTTACA-CAAATCTCATATC
* * * *
56046242 GAAGCCATATCCCAGATATGGTCTTACACATAATCTCATAGC
1 GATGCCATATACCAGACATGGTCTTACACA-AATCTCATATC
*
56046284 GATGCCGATATCATATCCTAGATATGGTCTTACACAAGATCTCATATCGAAGC
1 GATGCC---AT-ATA-CC-AGACATGGTCTTACACAA-ATCTCATAT-----C
* *
56046337 TGATGCCATATCCCAGATATGGTCTTACACAAGATCTCATATTGATGC
1 -GATGCCATATACCAGACATGGTCTTACACAA-ATCTC--A-T-AT-C
* * *
56046385 TGATGCCATATCCCAGATATGGTCTTACACAGTATCTCATATC
1 -GATGCCATATACCAGACATGGTCTTACACA-AATCTCATATC
* * *
56046428 GATGCCATGTCCCATACATGGTCTTACA
1 GATGCCATATACCAGACATGGTCTTACA
56046456 TGTATCACAG
Statistics
Matches: 247, Mismatches: 26, Indels: 50
0.76 0.08 0.15
Matches are distributed among these distances:
41 4 0.02
42 120 0.49
43 8 0.03
44 2 0.01
45 3 0.01
46 3 0.01
47 3 0.01
48 87 0.35
49 2 0.01
50 3 0.01
51 3 0.01
52 2 0.01
53 1 0.00
54 6 0.02
ACGTcount: A:0.30, C:0.25, G:0.16, T:0.29
Consensus pattern (41 bp):
GATGCCATATACCAGACATGGTCTTACACAAATCTCATATC
Found at i:56046287 original size:84 final size:83
Alignment explanation
Indices: 56046133--56046455 Score: 261
Period size: 96 Copynumber: 3.6 Consensus size: 83
56046123 TAGTCCAACT
* * * * * *
56046133 ATGGTCTTACACAAAGTCTCATATCGATGCCATGTACCAGACATGGTCTTATACGAAATCACATA
1 ATGGTCTTACACAAA-TCTCATACCGATGCCATATCCCAGATATGGTCTTACAC-AAATCTCATA
56046198 TCGATGCTGC-ATCCTAGAC
64 TCGATGCTGCAATCCTAGAC
* *
56046217 ATGGTCTTACATGAAATCTCATACCGAAGCCATATCCCAGATATGGTCTTACACATAATCTCATA
1 ATGGTCTTACA-CAAATCTCATACCGATGCCATATCCCAGATATGGTCTTACACA-AATCTCATA
* * *
56046282 GCGATGCCGATATCATATCCTAGAT
64 TCGATG-C--T-GCA-ATCCTAGAC
56046307 ATGGTCTTACACAAGATCTCATATCGAAGCTGATGCCATATCCCAGATATGGTCTTACACAAGAT
1 ATGGTCTTACACAA-ATCTCATA-C----C-GATGCCATATCCCAGATATGGTCTTACACAA-AT
* * *
56046372 CTCATATTGATGCTGATGCCATATCCCAGAT
58 CTCATATCGATGC---TG-CA-ATCCTAGAC
* * * * *
56046403 ATGGTCTTACACAGTATCTCATATCGATGCCATGTCCCATACATGGTCTTACA
1 ATGGTCTTACACA-AATCTCATACCGATGCCATATCCCAGATATGGTCTTACA
56046456 TGTATCACAG
Statistics
Matches: 198, Mismatches: 22, Indels: 32
0.79 0.09 0.13
Matches are distributed among these distances:
83 1 0.01
84 56 0.28
85 4 0.02
87 1 0.01
88 1 0.01
89 2 0.01
90 52 0.26
91 2 0.01
95 3 0.02
96 76 0.38
ACGTcount: A:0.30, C:0.25, G:0.16, T:0.29
Consensus pattern (83 bp):
ATGGTCTTACACAAATCTCATACCGATGCCATATCCCAGATATGGTCTTACACAAATCTCATATC
GATGCTGCAATCCTAGAC
Found at i:56046314 original size:48 final size:48
Alignment explanation
Indices: 56046240--56046433 Score: 275
Period size: 48 Copynumber: 4.0 Consensus size: 48
56046230 AAATCTCATA
* *
56046240 CCGAAGCCATATCCCAGATATGGTCTTACACATA-ATCTCATAGCGATG
1 CCGATGCCATATCCCAGATATGGTCTTACACA-AGATCTCATATCGATG
** * *
56046288 CCGATATCATATCCTAGATATGGTCTTACACAAGATCTCATATCGAAG
1 CCGATGCCATATCCCAGATATGGTCTTACACAAGATCTCATATCGATG
* *
56046336 CTGATGCCATATCCCAGATATGGTCTTACACAAGATCTCATATTGATG
1 CCGATGCCATATCCCAGATATGGTCTTACACAAGATCTCATATCGATG
*
56046384 CTGATGCCATATCCCAGATATGGTCTTACAC-AGTATCTCATATCGATG
1 CCGATGCCATATCCCAGATATGGTCTTACACAAG-ATCTCATATCGATG
56046432 CC
1 CC
56046434 ATGTCCCATA
Statistics
Matches: 130, Mismatches: 14, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
47 3 0.02
48 127 0.98
ACGTcount: A:0.30, C:0.25, G:0.16, T:0.29
Consensus pattern (48 bp):
CCGATGCCATATCCCAGATATGGTCTTACACAAGATCTCATATCGATG
Found at i:56047884 original size:52 final size:52
Alignment explanation
Indices: 56047826--56047976 Score: 162
Period size: 52 Copynumber: 2.9 Consensus size: 52
56047816 GACGAAAAAG
*
56047826 ATGTGAT-ATGTGCTTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTACA
1 ATGTGATCATGTG-TTCCGTATAAGACCATAGCTGGGCTATGGCATCGATACA
* * * ***
56047878 ATGTGATCCAAGT-TCCCATATAAGACCATAGCTGGGCTATGGCATCGATGTG
1 ATGTGAT-CATGTGTTCCGTATAAGACCATAGCTGGGCTATGGCATCGATACA
* * * *
56047930 ATGTGATAATGTGATTCTGTATAAGACCATATCTGGGATATGGCATC
1 ATGTGATCATGTG-TTCCGTATAAGACCATAGCTGGGCTATGGCATC
56047977 AGTATGTTAT
Statistics
Matches: 81, Mismatches: 14, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
51 3 0.04
52 47 0.58
53 28 0.35
54 3 0.04
ACGTcount: A:0.27, C:0.18, G:0.25, T:0.30
Consensus pattern (52 bp):
ATGTGATCATGTGTTCCGTATAAGACCATAGCTGGGCTATGGCATCGATACA
Found at i:56062811 original size:53 final size:52
Alignment explanation
Indices: 56062663--56062863 Score: 186
Period size: 52 Copynumber: 4.0 Consensus size: 52
56062653 TGACGGAATA
* * *
56062663 GATGTGATATGTGCTTCCATATAAGACCATAGCTGGGCTATGGCATCGGTAC
1 GATGTGATATGTGATTCCGTATAAGACCATATCTGGGCTATGGCATCGGTAC
* * **
56062715 AATGTGAT-T-CGAGTTCCCGTATAAGACCATAGT-TGGGCTATGGCATCGGTGT
1 GATGTGATATGTGA-TT-CCGTATAAGACCATA-TCTGGGCTATGGCATCGGTAC
*
56062767 GATGTGATAATGTGATTCCGTATAAGACCATATCTGGGATATGGCATCGGT--
1 GATGTGAT-ATGTGATTCCGTATAAGACCATATCTGGGCTATGGCATCGGTAC
* ** * *
56062818 -ATGT--TATGTGATT-CGTGTAAGACCATGGCAGGGCTATGGCTTCGGT
1 GATGTGATATGTGATTCCGTATAAGACCATATCTGGGCTATGGCATCGGT
56062864 GTGTGATGTG
Statistics
Matches: 126, Mismatches: 16, Indels: 20
0.78 0.10 0.12
Matches are distributed among these distances:
46 27 0.21
47 8 0.06
48 1 0.01
50 5 0.04
51 3 0.02
52 46 0.37
53 31 0.25
54 3 0.02
55 2 0.02
ACGTcount: A:0.24, C:0.16, G:0.29, T:0.31
Consensus pattern (52 bp):
GATGTGATATGTGATTCCGTATAAGACCATATCTGGGCTATGGCATCGGTAC
Found at i:56062856 original size:46 final size:47
Alignment explanation
Indices: 56062670--56062873 Score: 160
Period size: 46 Copynumber: 4.1 Consensus size: 47
56062660 ATAGATGTGA
* * *
56062670 TATGTGCTTCCATATAAGACCATAGCTGGGCTATGGCATCGGTACAATGT
1 TATGTGATTCCGTATAAGACCATAGCAGGGCTATGGCATCGGT---ATGT
* **
56062720 GAT-TCGAGTTCCCGTATAAGACCATAGTTGGGCTATGGCATCGGTGTGATGT
1 TATGT-GA-TT-CCGTATAAGACCATAGCAGGGCTATGGCATC-G-GT-ATGT
* * *
56062772 GATAATGTGATTCCGTATAAGACCATATCTGGGATATGGCATCGGTATGT
1 --T-ATGTGATTCCGTATAAGACCATAGCAGGGCTATGGCATCGGTATGT
* * * *
56062822 TATGTGATT-CGTGTAAGACCATGGCAGGGCTATGGCTTCGGTGTGT
1 TATGTGATTCCGTATAAGACCATAGCAGGGCTATGGCATCGGTATGT
*
56062868 GATGTG
1 TATGTG
56062874 TGACAATGCG
Statistics
Matches: 128, Mismatches: 17, Indels: 22
0.77 0.10 0.13
Matches are distributed among these distances:
46 35 0.27
47 8 0.06
48 1 0.01
49 1 0.01
50 7 0.05
51 4 0.03
52 34 0.27
53 29 0.23
54 4 0.03
55 4 0.03
56 1 0.01
ACGTcount: A:0.23, C:0.16, G:0.29, T:0.31
Consensus pattern (47 bp):
TATGTGATTCCGTATAAGACCATAGCAGGGCTATGGCATCGGTATGT
Found at i:56065247 original size:46 final size:46
Alignment explanation
Indices: 56065197--56065369 Score: 183
Period size: 46 Copynumber: 3.7 Consensus size: 46
56065187 TGGTTGAGCA
*
56065197 TCCGAACTCGTTGAGTTGAGTCCGGGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * * *
56065243 TCCGAACTTGTTGAGTTGAGTCCGAGTTC-GTGA--AATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
* *
56065288 CATCTGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
56065336 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
56065370 GGGGCGGGTT
Statistics
Matches: 102, Mismatches: 16, Indels: 18
0.75 0.12 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
45 3 0.03
46 58 0.57
47 27 0.26
48 3 0.03
50 3 0.03
51 2 0.02
ACGTcount: A:0.21, C:0.20, G:0.28, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:56065353 original size:93 final size:93
Alignment explanation
Indices: 56065194--56065364 Score: 288
Period size: 93 Copynumber: 1.8 Consensus size: 93
56065184 GGATGGTTGA
* * * *
56065194 GCATCCGAACTCGTTGAGTTGAGTCCGGGTTCACTTATGGATGCGAATGTCCGAACTTGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
56065259 TGAGTCCGAGTTCGTGAAATGTAACTAG
66 TGAGTCCGAGTTCGTGAAATGTAACTAG
* *
56065287 GCATCTGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
56065352 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
56065365 ACTTAGGGGC
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.21, C:0.20, G:0.29, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAAATGTAACTAG
Found at i:56068356 original size:15 final size:15
Alignment explanation
Indices: 56068336--56068391 Score: 78
Period size: 15 Copynumber: 3.7 Consensus size: 15
56068326 GTATCTTGGG
56068336 TTTCTTTATTCTGGA
1 TTTCTTTATTCTGGA
*
56068351 TTTCTTTATTCTGTA
1 TTTCTTTATTCTGGA
*
56068366 TTTCTCTA-TCTTGGA
1 TTTCTTTATTC-TGGA
56068381 TTTCTTTATTC
1 TTTCTTTATTC
56068392 GGTTTCCTTG
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
14 2 0.06
15 31 0.89
16 2 0.06
ACGTcount: A:0.12, C:0.16, G:0.09, T:0.62
Consensus pattern (15 bp):
TTTCTTTATTCTGGA
Found at i:56070846 original size:46 final size:46
Alignment explanation
Indices: 56070796--56070962 Score: 175
Period size: 46 Copynumber: 3.6 Consensus size: 46
56070786 TTGAGCATCT
56070796 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCC
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCC
* * *
56070842 GAACTCGTTGAGTTGAGTCCGAG-T---TTGTGAAATG-TAACTAGGCATCC
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATG-GATGCGAA-T--G--TCC
*
56070889 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG-CC
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCC
* *
56070934 TGAGCTCGTTGAGTTGAGTCTGAGTTCAC
1 -GAACTCGTTGAGTTGAGTCCGAGTTCAC
56070963 CTAGGGGCGG
Statistics
Matches: 100, Mismatches: 9, Indels: 24
0.75 0.07 0.18
Matches are distributed among these distances:
42 6 0.06
43 4 0.04
45 4 0.04
46 49 0.49
47 26 0.26
48 2 0.02
50 3 0.03
51 6 0.06
ACGTcount: A:0.22, C:0.19, G:0.29, T:0.30
Consensus pattern (46 bp):
GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCC
Found at i:56070949 original size:93 final size:93
Alignment explanation
Indices: 56070790--56070959 Score: 288
Period size: 93 Copynumber: 1.8 Consensus size: 93
56070780 GGATGGTTGA
* *
56070790 GCATCTGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAGT
56070855 TGAGTCCGAGTTTGTGAAATGTAACTAG
66 TGAGTCCGAGTTTGTGAAATGTAACTAG
*
56070883 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG-CCTGAGCTCGTTGAG
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCC-GAACTCGTTGAG
*
56070947 TTGAGTCTGAGTT
65 TTGAGTCCGAGTT
56070960 CACCTAGGGG
Statistics
Matches: 72, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
92 2 0.03
93 70 0.97
ACGTcount: A:0.22, C:0.19, G:0.29, T:0.31
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAGT
TGAGTCCGAGTTTGTGAAATGTAACTAG
Found at i:56075010 original size:13 final size:13
Alignment explanation
Indices: 56074992--56075016 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
56074982 CTCGGCAGGG
56074992 ACACGCCCGTGTA
1 ACACGCCCGTGTA
56075005 ACACGCCCGTGT
1 ACACGCCCGTGT
56075017 GTGATTATTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.40, G:0.24, T:0.16
Consensus pattern (13 bp):
ACACGCCCGTGTA
Found at i:56085119 original size:28 final size:28
Alignment explanation
Indices: 56085064--56085120 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
56085054 ATCCTAGATG
* * *
56085064 TCCCGTACACTAAGTGTCATACTCAATA
1 TCCCGCACACCAAGTGCCATACTCAATA
* *
56085092 TCCCGCACACCAAGTGCCATTCTTAATA
1 TCCCGCACACCAAGTGCCATACTCAATA
56085120 T
1 T
56085121 TTTTCACACT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.30, C:0.32, G:0.11, T:0.28
Consensus pattern (28 bp):
TCCCGCACACCAAGTGCCATACTCAATA
Found at i:56087865 original size:14 final size:14
Alignment explanation
Indices: 56087846--56087875 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
56087836 AAAGTTTCAG
56087846 ATACAGAACTAGCT
1 ATACAGAACTAGCT
56087860 ATACAGAACTAGCT
1 ATACAGAACTAGCT
56087874 AT
1 AT
56087876 GTATGAGTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.43, C:0.20, G:0.13, T:0.23
Consensus pattern (14 bp):
ATACAGAACTAGCT
Found at i:56092517 original size:15 final size:16
Alignment explanation
Indices: 56092492--56092521 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
56092482 TTATATTTGT
56092492 TTTTATTTAAAAATAA
1 TTTTATTTAAAAATAA
56092508 TTTT-TTTAAAAATA
1 TTTTATTTAAAAATA
56092522 CACTAAATGC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TTTTATTTAAAAATAA
Found at i:56092741 original size:13 final size:14
Alignment explanation
Indices: 56092714--56092742 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
56092704 GTTGGGTAAG
56092714 TTTTTTTTAAGGTT
1 TTTTTTTTAAGGTT
56092728 TTTTTTTTAA-GTT
1 TTTTTTTTAAGGTT
56092741 TT
1 TT
56092743 GGTAATGGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.33
14 10 0.67
ACGTcount: A:0.14, C:0.00, G:0.10, T:0.76
Consensus pattern (14 bp):
TTTTTTTTAAGGTT
Found at i:56095250 original size:5 final size:5
Alignment explanation
Indices: 56095240--56095286 Score: 94
Period size: 5 Copynumber: 9.4 Consensus size: 5
56095230 TTTTTTCCAT
56095240 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TA
1 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TA
56095287 ATCAAACTAC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 42 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TATTA
Found at i:56098308 original size:40 final size:40
Alignment explanation
Indices: 56098241--56098417 Score: 225
Period size: 40 Copynumber: 4.5 Consensus size: 40
56098231 ACCCAAGTAT
*
56098241 CTTCGGGAT-TTAG-CCGGATATAACAACTCGCACAAATGC
1 CTTCGGG-TCTTAGCCCGGATATAGCAACTCGCACAAATGC
56098280 CTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGC
1 CTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGC
* * * *
56098320 CTTCGGGTCTTAGCCTGGATATAATC-ACTAGCATAAATGC
1 CTTCGGGTCTTAGCCCGGATAT-AGCAACTCGCACAAATGC
* * *
56098360 CTTCGGGACATAGCCCGGATATAGCAACTCGCACGAATGC
1 CTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGC
* *
56098400 CTTCGGATCTTAGTCCGG
1 CTTCGGGTCTTAGCCCGG
56098418 TTATCATCCG
Statistics
Matches: 118, Mismatches: 16, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
38 1 0.01
39 13 0.11
40 102 0.86
41 2 0.02
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.24
Consensus pattern (40 bp):
CTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGC
Found at i:56098374 original size:80 final size:79
Alignment explanation
Indices: 56098241--56098417 Score: 250
Period size: 80 Copynumber: 2.2 Consensus size: 79
56098231 ACCCAAGTAT
* * *
56098241 CTTCGGGAT-TTAGCCGGATATAACAACTCGCACAAATGCCTTCGGGTCTTAGCCCGGATATAGC
1 CTTCGGG-TCTTAGCCGGATATAACAACTAGCACAAATGCCTTCGGGACATAGCCCGGATATAGC
56098305 AACTCGCACAAATGC
65 AACTCGCACAAATGC
*
56098320 CTTCGGGTCTTAGCCTGGATATAATC-ACTAGCATAAATGCCTTCGGGACATAGCCCGGATATAG
1 CTTCGGGTCTTAGCC-GGATATAA-CAACTAGCACAAATGCCTTCGGGACATAGCCCGGATATAG
*
56098384 CAACTCGCACGAATGC
64 CAACTCGCACAAATGC
*
56098400 CTTCGGATCTTAGTCCGG
1 CTTCGGGTCTTAG-CCGG
56098418 TTATCATCCG
Statistics
Matches: 88, Mismatches: 6, Indels: 7
0.87 0.06 0.07
Matches are distributed among these distances:
78 1 0.01
79 13 0.15
80 71 0.81
81 3 0.03
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.24
Consensus pattern (79 bp):
CTTCGGGTCTTAGCCGGATATAACAACTAGCACAAATGCCTTCGGGACATAGCCCGGATATAGCA
ACTCGCACAAATGC
Found at i:56108755 original size:46 final size:45
Alignment explanation
Indices: 56108700--56108907 Score: 197
Period size: 46 Copynumber: 4.5 Consensus size: 45
56108690 CGAACTCATG
* * *
56108700 GAGTTGAGTCCAGGTTCACTTATGGATGCAAACGTCCGAACTCATT
1 GAGTTGAGTCGA-GTTCACTTATGGATGCAAACGTCCGAGCTCGTT
* * * *
56108746 GAGTTGAGTCTGAGTTC-GTGA--GATGTAACTAGGCATCCGAGCTCGTT
1 GAGTTGAGTC-GAGTTCACTTATGGATGCAA--A--CGTCCGAGCTCGTT
* * * *
56108793 GAGTTAAGTCTGAGTTCACTTATCGAAGCGAACGTCCGAGCTCGTT
1 GAGTTGAGTC-GAGTTCACTTATGGATGCAAACGTCCGAGCTCGTT
* *
56108839 GAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTT
1 GAGTTGAGT-CGAGTTCACTTATGGATGCAAACGTCCGAGCTCGTT
56108885 GAGTTGAGTTCGAGTTCACTTAT
1 GAGTTGAG-TCGAGTTCACTTAT
56108908 AGGCGGGTTA
Statistics
Matches: 134, Mismatches: 18, Indels: 20
0.78 0.10 0.12
Matches are distributed among these distances:
43 6 0.04
45 3 0.02
46 88 0.66
47 30 0.22
48 3 0.02
50 4 0.03
ACGTcount: A:0.23, C:0.20, G:0.28, T:0.29
Consensus pattern (45 bp):
GAGTTGAGTCGAGTTCACTTATGGATGCAAACGTCCGAGCTCGTT
Found at i:56108894 original size:51 final size:46
Alignment explanation
Indices: 56108782--56108907 Score: 198
Period size: 46 Copynumber: 2.7 Consensus size: 46
56108772 AACTAGGCAT
* * *
56108782 CCGAGCTCGTTGAGTTAAGTCTGAGTTCACTTATCGAAGCGAACGT
1 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATCGAAGCGAACGC
* *
56108828 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
1 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATCGAAGCGAACGC
*
56108874 CCGAGCTCGTTGAGTTGAGTTCGAGTTCACTTAT
1 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTAT
56108908 AGGCGGGTTA
Statistics
Matches: 74, Mismatches: 6, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
46 74 1.00
ACGTcount: A:0.21, C:0.22, G:0.28, T:0.29
Consensus pattern (46 bp):
CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATCGAAGCGAACGC
Found at i:56111532 original size:30 final size:29
Alignment explanation
Indices: 56111496--56111552 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 29
56111486 ATAGTATTGT
*
56111496 ATCTTGGGTTTATTTATTCTGGGTTTCTCA
1 ATCTTGGATTTATTTATT-TGGGTTTCTCA
* *
56111526 ATCTTGGATTTCTTTATTTGGTTTTCT
1 ATCTTGGATTTATTTATTTGGGTTTCT
56111553 TGTTATCTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 8 0.33
30 16 0.67
ACGTcount: A:0.12, C:0.12, G:0.18, T:0.58
Consensus pattern (29 bp):
ATCTTGGATTTATTTATTTGGGTTTCTCA
Found at i:56114334 original size:46 final size:46
Alignment explanation
Indices: 56114282--56114502 Score: 216
Period size: 46 Copynumber: 4.8 Consensus size: 46
56114272 AATATTTGAG
*
56114282 CATCCGAACTCGTTGAATTGAGTCCGAGTTCACTTATGGATGCGAA
1 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA
* * * * *
56114328 CATCCGAACTCGTTGAGTTGAGTTCGAGTTC-GTGA--GATGTAACTAGG
1 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG---CGA-A
* * * **
56114375 CATCCGAGCTCGTTGAGTTGAGTCTGAGTTTACTTATGGATATGAA
1 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA
* * *
56114421 CGTCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCAAA
1 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA
* * *
56114467 C-GCTCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTA
1 CATC-CGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
56114503 AGGGCGGGTT
Statistics
Matches: 139, Mismatches: 28, Indels: 16
0.76 0.15 0.09
Matches are distributed among these distances:
43 4 0.03
45 3 0.02
46 99 0.71
47 28 0.20
48 2 0.01
50 3 0.02
ACGTcount: A:0.23, C:0.20, G:0.27, T:0.30
Consensus pattern (46 bp):
CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA
Found at i:56114440 original size:93 final size:93
Alignment explanation
Indices: 56114281--56114451 Score: 261
Period size: 93 Copynumber: 1.8 Consensus size: 93
56114271 AAATATTTGA
* *
56114281 GCATCCGAACTCGTTGAATTGAGTCCGAGTTCACTTATGGATGCGAACATCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAATTGAGTCCGAGTTCACTTATGGATACGAACATCCGAACTCATTGAGT
*
56114346 TGAGTTCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* * * * * *
56114374 GCATCCGAGCTCGTTGAGTTGAGTCTGAGTTTACTTATGGATATGAACGTCCGAACTCATTGAGT
1 GCATCCGAACTCGTTGAATTGAGTCCGAGTTCACTTATGGATACGAACATCCGAACTCATTGAGT
56114439 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
56114452 ACTTATGGAT
Statistics
Matches: 69, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
93 69 1.00
ACGTcount: A:0.23, C:0.19, G:0.27, T:0.30
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAATTGAGTCCGAGTTCACTTATGGATACGAACATCCGAACTCATTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:56117888 original size:16 final size:17
Alignment explanation
Indices: 56117867--56117913 Score: 71
Period size: 16 Copynumber: 2.9 Consensus size: 17
56117857 TATGTAACGC
56117867 CCCAAAAATCCCGAAA-
1 CCCAAAAATCCCGAAAT
*
56117883 CCCAAAAATCCTGAAAT
1 CCCAAAAATCCCGAAAT
56117900 CCC-AAAATCCCGAA
1 CCCAAAAATCCCGAA
56117914 CTTTCTTTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
16 25 0.89
17 3 0.11
ACGTcount: A:0.47, C:0.36, G:0.06, T:0.11
Consensus pattern (17 bp):
CCCAAAAATCCCGAAAT
Found at i:56119641 original size:27 final size:27
Alignment explanation
Indices: 56119611--56119956 Score: 395
Period size: 27 Copynumber: 12.8 Consensus size: 27
56119601 ATTACCAAAG
* *
56119611 TACCCTTGATTTATAGAATTACCGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
*
56119638 TACCCTCGATTTACAGAATTACTGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
* * *
56119665 TACCCTCAATTTATAAAATTACCGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
*
56119692 TACCCTCGATTTATAGAATTACCGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
* * *
56119719 TACCCTTGATTTACAGAATTATCATTT
1 TACCCTCGATTTACAGAATTACCGTTT
* * ***
56119746 TATCCTCGATTTATAGAATTATTATTT
1 TACCCTCGATTTACAGAATTACCGTTT
*
56119773 TATCCTCGATTTACAGAATTACCGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
* **
56119800 TACCCTCGATTTATAGAATTATTGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
*
56119827 TACCCTCGATTTACAAAATTACCGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
* * *
56119854 TACTCTCGATTTACAAAATTACTGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
* * * *
56119881 CACCTTCGGTTTACAGAATTACCATTT
1 TACCCTCGATTTACAGAATTACCGTTT
* **
56119908 TACCCTCAATTTACAGAATTATTGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
* * *
56119935 TACCTTCAATTTATAGAATTAC
1 TACCCTCGATTTACAGAATTAC
56119957 TAAAATACCC
Statistics
Matches: 271, Mismatches: 48, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 271 1.00
ACGTcount: A:0.29, C:0.20, G:0.09, T:0.43
Consensus pattern (27 bp):
TACCCTCGATTTACAGAATTACCGTTT
Found at i:56119978 original size:27 final size:27
Alignment explanation
Indices: 56119948--56120037 Score: 135
Period size: 27 Copynumber: 3.3 Consensus size: 27
56119938 CTTCAATTTA
56119948 TAGAATTACTAAAATACCCCTGTAGGG
1 TAGAATTACTAAAATACCCCTGTAGGG
56119975 TAGAATTACTAAAATACCCCTGTAGGG
1 TAGAATTACTAAAATACCCCTGTAGGG
* * * *
56120002 TAGAATTACTGAGATACCCTTGTGGGG
1 TAGAATTACTAAAATACCCCTGTAGGG
*
56120029 TAAAATTAC
1 TAGAATTAC
56120038 CATTTTGCCC
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 58 1.00
ACGTcount: A:0.36, C:0.17, G:0.20, T:0.28
Consensus pattern (27 bp):
TAGAATTACTAAAATACCCCTGTAGGG
Found at i:56120303 original size:28 final size:27
Alignment explanation
Indices: 56120263--56120372 Score: 150
Period size: 27 Copynumber: 4.0 Consensus size: 27
56120253 GGAGGAAGCG
56120263 TTCTGGTGGCTATGCCACAAATATCTGT
1 TTCTGGTGGCTATGCCAC-AATATCTGT
56120291 TTCTGGTGGCTATGCCACAAATATCTG-
1 TTCTGGTGGCTATGCCAC-AATATCTGT
*
56120318 TTCTGGTGGCTCTGCCACAATATCTGT
1 TTCTGGTGGCTATGCCACAATATCTGT
* * * *
56120345 ATCTGGTGACTCTGTCACAATATCTGT
1 TTCTGGTGGCTATGCCACAATATCTGT
56120372 T
1 T
56120373 GACCGATCGA
Statistics
Matches: 76, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
26 8 0.11
27 41 0.54
28 27 0.36
ACGTcount: A:0.20, C:0.23, G:0.21, T:0.36
Consensus pattern (27 bp):
TTCTGGTGGCTATGCCACAATATCTGT
Found at i:56120512 original size:22 final size:22
Alignment explanation
Indices: 56120480--56120538 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 22
56120470 CCCGTAATTG
*
56120480 ATGGCTCTGTGCCAACCTAAAT
1 ATGGCTTTGTGCCAACCTAAAT
* * * *
56120502 ATGGCTTTGTGCCATCTTGACT
1 ATGGCTTTGTGCCAACCTAAAT
*
56120524 ATGGCTTCGTGCCAA
1 ATGGCTTTGTGCCAA
56120539 ACGTATTTAC
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.20, C:0.25, G:0.22, T:0.32
Consensus pattern (22 bp):
ATGGCTTTGTGCCAACCTAAAT
Found at i:56120902 original size:6 final size:6
Alignment explanation
Indices: 56120893--56120983 Score: 78
Period size: 6 Copynumber: 14.8 Consensus size: 6
56120883 TTGCATTCAC
* * *
56120893 ATTCTG ATTCTG ATTCTG -TCACCTA ATTCTG ATTCTG ATTCTA ATTCTG
1 ATTCTG ATTCTG ATTCTG AT--TCTG ATTCTG ATTCTG ATTCTG ATTCTG
* * *
56120942 ATTCTG -TCACCTG ATTCTG ATTCTG ATTCTC ATTTTG ATTCT
1 ATTCTG AT--TCTG ATTCTG ATTCTG ATTCTG ATTCTG ATTCT
56120984 AGTTCTGGTA
Statistics
Matches: 67, Mismatches: 12, Indels: 12
0.74 0.13 0.13
Matches are distributed among these distances:
5 2 0.03
6 58 0.87
7 5 0.07
8 2 0.03
ACGTcount: A:0.19, C:0.21, G:0.12, T:0.48
Consensus pattern (6 bp):
ATTCTG
Found at i:56120923 original size:19 final size:19
Alignment explanation
Indices: 56120899--56120966 Score: 95
Period size: 19 Copynumber: 3.6 Consensus size: 19
56120889 TCACATTCTG
56120899 ATTCTGATTCTGTCACCTA
1 ATTCTGATTCTGTCACCTA
*
56120918 ATTCTGATTCTG--ATTCTA
1 ATTCTGATTCTGTCA-CCTA
*
56120936 ATTCTGATTCTGTCACCTG
1 ATTCTGATTCTGTCACCTA
56120955 ATTCTGATTCTG
1 ATTCTGATTCTG
56120967 ATTCTCATTT
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
17 1 0.02
18 15 0.35
19 26 0.60
20 1 0.02
ACGTcount: A:0.19, C:0.22, G:0.13, T:0.46
Consensus pattern (19 bp):
ATTCTGATTCTGTCACCTA
Found at i:56120943 original size:37 final size:37
Alignment explanation
Indices: 56120893--56120983 Score: 146
Period size: 37 Copynumber: 2.5 Consensus size: 37
56120883 TTGCATTCAC
*
56120893 ATTCTGATTCTGATTCTGTCACCTAATTCTGATTCTG
1 ATTCTAATTCTGATTCTGTCACCTAATTCTGATTCTG
*
56120930 ATTCTAATTCTGATTCTGTCACCTGATTCTGATTCTG
1 ATTCTAATTCTGATTCTGTCACCTAATTCTGATTCTG
* *
56120967 ATTCTCATTTTGATTCT
1 ATTCTAATTCTGATTCT
56120984 AGTTCTGGTA
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 50 1.00
ACGTcount: A:0.19, C:0.21, G:0.12, T:0.48
Consensus pattern (37 bp):
ATTCTAATTCTGATTCTGTCACCTAATTCTGATTCTG
Found at i:56122441 original size:29 final size:28
Alignment explanation
Indices: 56122388--56122495 Score: 110
Period size: 29 Copynumber: 3.8 Consensus size: 28
56122378 CATGACTATG
*
56122388 AATGTGACTGGGCCTAAT-GGTCCATATA
1 AATGTGATTGGGCCTAATAGG-CCATATA
*
56122416 AATGTGATTTGGGCCGAATAGGCCATATA
1 AATGTGA-TTGGGCCTAATAGGCCATATA
* * * *
56122445 CAGGTGATTTGGGCCTAATGGGCCATATG
1 AATGTGA-TTGGGCCTAATAGGCCATATA
* *
56122474 AATATGATTGGGCTTAATAGGC
1 AATGTGATTGGGCCTAATAGGC
56122496 AGATACAGGT
Statistics
Matches: 66, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
28 20 0.30
29 44 0.67
30 2 0.03
ACGTcount: A:0.28, C:0.15, G:0.29, T:0.29
Consensus pattern (28 bp):
AATGTGATTGGGCCTAATAGGCCATATA
Found at i:56122464 original size:58 final size:56
Alignment explanation
Indices: 56122396--56122505 Score: 148
Period size: 58 Copynumber: 1.9 Consensus size: 56
56122386 TGAATGTGAC
* * *
56122396 TGGGCCTAATGGTCCATATAAATGTGATTTGGGCCGAATAGGCCATATACAGGTGATT
1 TGGGCCTAATGGGCCATATAAATATGA-TTGGGCCGAATAGG-CAGATACAGGTGATT
* **
56122454 TGGGCCTAATGGGCCATATGAATATGATTGGGCTTAATAGGCAGATACAGGT
1 TGGGCCTAATGGGCCATATAAATATGATTGGGCCGAATAGGCAGATACAGGT
56122506 ATGTGAAATT
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
56 10 0.22
57 12 0.26
58 24 0.52
ACGTcount: A:0.28, C:0.15, G:0.29, T:0.28
Consensus pattern (56 bp):
TGGGCCTAATGGGCCATATAAATATGATTGGGCCGAATAGGCAGATACAGGTGATT
Found at i:56123608 original size:17 final size:18
Alignment explanation
Indices: 56123575--56123609 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
56123565 GTTTAAGAAG
56123575 GGTTTTCAATGAAAACAC
1 GGTTTTCAATGAAAACAC
*
56123593 GGTTTTCACT-AAAACAC
1 GGTTTTCAATGAAAACAC
56123610 TTCAATGTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.37, C:0.20, G:0.14, T:0.29
Consensus pattern (18 bp):
GGTTTTCAATGAAAACAC
Found at i:56127430 original size:51 final size:51
Alignment explanation
Indices: 56127375--56127474 Score: 121
Period size: 51 Copynumber: 2.0 Consensus size: 51
56127365 CTACCACATA
** * *
56127375 ACATGTAA-CACATCCATAATGAACTTGGACCTCTCAACGAGCTCGGATGTT
1 ACATG-AATCACATCCATAATGAACTCAGACCACTCAACGAGCTCAGATGTT
* * *
56127426 ACATGAATCCCATCTATTATGAACTCAGACCACTCAACGAGCTCAGATG
1 ACATGAATCACATCCATAATGAACTCAGACCACTCAACGAGCTCAGATG
56127475 CTCGCATCCA
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
50 2 0.05
51 39 0.95
ACGTcount: A:0.33, C:0.27, G:0.16, T:0.24
Consensus pattern (51 bp):
ACATGAATCACATCCATAATGAACTCAGACCACTCAACGAGCTCAGATGTT
Found at i:56129674 original size:21 final size:20
Alignment explanation
Indices: 56129650--56129691 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
56129640 AACTAGGATA
*
56129650 AATAGACATGTTACTATTATG
1 AATAGA-ATGTTACCATTATG
*
56129671 AATAGATTGTTACCATTATG
1 AATAGAATGTTACCATTATG
56129691 A
1 A
56129692 GCTTAATTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.38
Consensus pattern (20 bp):
AATAGAATGTTACCATTATG
Found at i:56132795 original size:41 final size:41
Alignment explanation
Indices: 56132680--56132797 Score: 112
Period size: 41 Copynumber: 2.8 Consensus size: 41
56132670 CATACCAATT
* *
56132680 CCATATCCTAGATATGGTCTTACATGAGATCTCATATTGATG
1 CCATATCCTAGATATGGTCTTACACGA-ATCTCATATCGATG
* * * * * *
56132722 CCAAAAGCCTAGCTATGGTCTGACACAAAATCTGAT-TCGATG
1 CC-ATATCCTAGATATGGTCTTACAC-GAATCTCATATCGATG
*
56132764 CCATATCCCAGATATGGTCTTACACGTAATCTCA
1 CCATATCCTAGATATGGTCTTACACG-AATCTCA
56132798 ACTAACCTTA
Statistics
Matches: 58, Mismatches: 15, Indels: 7
0.73 0.19 0.09
Matches are distributed among these distances:
41 24 0.41
42 9 0.16
43 24 0.41
44 1 0.02
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.30
Consensus pattern (41 bp):
CCATATCCTAGATATGGTCTTACACGAATCTCATATCGATG
Found at i:56147595 original size:33 final size:33
Alignment explanation
Indices: 56147558--56147661 Score: 104
Period size: 33 Copynumber: 3.2 Consensus size: 33
56147548 AGAAACAGTC
* *
56147558 CAGTAACAGTTAGGCCTTAGCCCATTACAGTAA
1 CAGTAACAGTTGGGCCTAAGCCCATTACAGTAA
* * *
56147591 CAGTAGCAGTCTGGGCCTGAGCCCA-GACAGTAA
1 CAGTAACAGT-TGGGCCTAAGCCCATTACAGTAA
** *
56147624 CAGTATTAGTGGGGCCTAAGCCCATTACAG-AA
1 CAGTAACAGTTGGGCCTAAGCCCATTACAGTAA
56147656 TCAGTA
1 -CAGTA
56147662 CAATATGCAA
Statistics
Matches: 59, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
32 14 0.24
33 33 0.56
34 12 0.20
ACGTcount: A:0.31, C:0.24, G:0.24, T:0.21
Consensus pattern (33 bp):
CAGTAACAGTTGGGCCTAAGCCCATTACAGTAA
Found at i:56152694 original size:20 final size:20
Alignment explanation
Indices: 56152669--56152720 Score: 104
Period size: 20 Copynumber: 2.6 Consensus size: 20
56152659 GTGTAGTCAC
56152669 ACACACCCGTGTGGCTTGGG
1 ACACACCCGTGTGGCTTGGG
56152689 ACACACCCGTGTGGCTTGGG
1 ACACACCCGTGTGGCTTGGG
56152709 ACACACCCGTGT
1 ACACACCCGTGT
56152721 CCTCAGCCTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.17, C:0.33, G:0.31, T:0.19
Consensus pattern (20 bp):
ACACACCCGTGTGGCTTGGG
Found at i:56157013 original size:42 final size:42
Alignment explanation
Indices: 56156966--56157086 Score: 129
Period size: 43 Copynumber: 2.9 Consensus size: 42
56156956 CACATAGTGC
* *
56156966 CATATCAATGCCATGTCCTAGATATGGTCTGACATGAGATCT
1 CATATCAATGCCATGTCCTAGATATGGTCTGACACGAAATCT
* *
56157008 CATATCAATGCCAATAG--CTCAGCTATGGTCTTACACGAAATCT
1 CATATCAATGCC-AT-GTCCT-AGATATGGTCTGACACGAAATCT
* * * *
56157051 CATATCGATGCCATATCCCAGATATGGTCTTACACG
1 CATATCAATGCCATGTCCTAGATATGGTCTGACACG
56157087 TAACCTCAAC
Statistics
Matches: 66, Mismatches: 8, Indels: 10
0.79 0.10 0.12
Matches are distributed among these distances:
42 32 0.48
43 33 0.50
44 1 0.02
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.29
Consensus pattern (42 bp):
CATATCAATGCCATGTCCTAGATATGGTCTGACACGAAATCT
Found at i:56157051 original size:43 final size:42
Alignment explanation
Indices: 56156966--56157086 Score: 145
Period size: 42 Copynumber: 2.9 Consensus size: 42
56156956 CACATAGTGC
* * * *
56156966 CATATCAATGCCAT-GTCCTAGATATGGTCTGACATGAGATCT
1 CATATCAATGCCATAG-CCCAGATATGGTCTTACACGAAATCT
* *
56157008 CATATCAATGCCAATAGCTCAGCTATGGTCTTACACGAAATCT
1 CATATCAATGCC-ATAGCCCAGATATGGTCTTACACGAAATCT
* *
56157051 CATATCGATGCCATATCCCAGATATGGTCTTACACG
1 CATATCAATGCCATAGCCCAGATATGGTCTTACACG
56157087 TAACCTCAAC
Statistics
Matches: 67, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
42 33 0.49
43 33 0.49
44 1 0.01
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.29
Consensus pattern (42 bp):
CATATCAATGCCATAGCCCAGATATGGTCTTACACGAAATCT
Found at i:56161319 original size:39 final size:40
Alignment explanation
Indices: 56161219--56161403 Score: 191
Period size: 40 Copynumber: 4.7 Consensus size: 40
56161209 TTGAATGATG
* * *
56161219 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAC-CAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAT
* * *
56161258 ATCCGGACTAGGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAT
*
56161299 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
* * *
56161338 TCTGGGTTAAGTCCCGAAGGCAATTGTGCGAGTTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
* *
56161377 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
56161404 AACGAGTAGC
Statistics
Matches: 120, Mismatches: 19, Indels: 12
0.79 0.13 0.08
Matches are distributed among these distances:
39 35 0.29
40 75 0.62
41 10 0.08
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
Found at i:56161425 original size:79 final size:79
Alignment explanation
Indices: 56161272--56161436 Score: 192
Period size: 79 Copynumber: 2.1 Consensus size: 79
56161262 GGACTAGGAT
* * **
56161272 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
* *
56161337 ATCTGGGTTAAGTC
66 ATCTCGGTTAAATC
* *
56161351 CCGAAGGCAATTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCAATTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
* *
56161414 TATATC-CGGTTAAATT
63 TAAATCTCGGTTAAATC
56161430 CCGAAGG
1 CCGAAGG
56161437 TACGTGATTT
Statistics
Matches: 73, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
78 2 0.03
79 47 0.64
80 24 0.33
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCTCGGTTAAATC
Found at i:56169070 original size:23 final size:23
Alignment explanation
Indices: 56169044--56169094 Score: 102
Period size: 23 Copynumber: 2.2 Consensus size: 23
56169034 AAACCCGAAA
56169044 GAATGAAAAAGGATAGAATACCT
1 GAATGAAAAAGGATAGAATACCT
56169067 GAATGAAAAAGGATAGAATACCT
1 GAATGAAAAAGGATAGAATACCT
56169090 GAATG
1 GAATG
56169095 CTTACACTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.51, C:0.08, G:0.24, T:0.18
Consensus pattern (23 bp):
GAATGAAAAAGGATAGAATACCT
Found at i:56173442 original size:28 final size:29
Alignment explanation
Indices: 56173385--56173461 Score: 86
Period size: 28 Copynumber: 2.7 Consensus size: 29
56173375 AAAAAATAGA
* * * *
56173385 CACTAAGGCTCACAAAT-ACATATCCTGC
1 CACTAAGGCTCACATATAACAGATACAGC
56173413 CACTAAGGCTCACATATAACAGA-ACAGC
1 CACTAAGGCTCACATATAACAGATACAGC
* *
56173441 CACCAAGGCTCGCATATAACA
1 CACTAAGGCTCACATATAACA
56173462 AAATTTTCCA
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
28 38 0.90
29 4 0.10
ACGTcount: A:0.39, C:0.31, G:0.13, T:0.17
Consensus pattern (29 bp):
CACTAAGGCTCACATATAACAGATACAGC
Found at i:56173825 original size:55 final size:56
Alignment explanation
Indices: 56173761--56173866 Score: 169
Period size: 56 Copynumber: 1.9 Consensus size: 56
56173751 TTTTCATATG
56173761 CCATATGATGCCATAGCAA-ATGGCTAGGCCTTACACTATATGGACTTCTCATTCC
1 CCATATGATGCCATAGCAATATGGCTAGGCCTTACACTATATGGACTTCTCATTCC
* ** *
56173816 CCATATGATGCCTTATTAATATGGCTAGGCCTTACACTATATGGTCTTCTC
1 CCATATGATGCCATAGCAATATGGCTAGGCCTTACACTATATGGACTTCTC
56173867 TTGCCATGGC
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
55 16 0.35
56 30 0.65
ACGTcount: A:0.25, C:0.25, G:0.16, T:0.33
Consensus pattern (56 bp):
CCATATGATGCCATAGCAATATGGCTAGGCCTTACACTATATGGACTTCTCATTCC
Found at i:56181240 original size:42 final size:42
Alignment explanation
Indices: 56181194--56181279 Score: 154
Period size: 42 Copynumber: 2.0 Consensus size: 42
56181184 CATCAGACCT
*
56181194 TATACTTAACTCAAGGGAAGTCTCCCTATCTTCCTTTAGCCC
1 TATACTTAACTCAACGGAAGTCTCCCTATCTTCCTTTAGCCC
*
56181236 TATACTTAACTCAACGGAAGTCTCCCTATCTTCCTTTAGTCC
1 TATACTTAACTCAACGGAAGTCTCCCTATCTTCCTTTAGCCC
56181278 TA
1 TA
56181280 CTCTCCTGAA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.24, C:0.30, G:0.10, T:0.35
Consensus pattern (42 bp):
TATACTTAACTCAACGGAAGTCTCCCTATCTTCCTTTAGCCC
Found at i:56185276 original size:27 final size:27
Alignment explanation
Indices: 56185216--56185276 Score: 68
Period size: 27 Copynumber: 2.3 Consensus size: 27
56185206 CCCTTGTGAT
* *
56185216 GTAAAATTACCATAATGCCCCTGTAGG
1 GTAAAATTACCATAATACCCCTATAGG
** *
56185243 GTAAAATTACTGTAATACCCCTATATG
1 GTAAAATTACCATAATACCCCTATAGG
*
56185270 GTGAAAT
1 GTAAAAT
56185277 GGTGATTCTG
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.30
Consensus pattern (27 bp):
GTAAAATTACCATAATACCCCTATAGG
Found at i:56185315 original size:27 final size:27
Alignment explanation
Indices: 56185285--56185352 Score: 100
Period size: 27 Copynumber: 2.5 Consensus size: 27
56185275 ATGGTGATTC
*
56185285 TGCCATTATGTGATAAAATGACTGTTT
1 TGCCCTTATGTGATAAAATGACTGTTT
* **
56185312 TGCCCTTATGTGGTAGGATGACTGTTT
1 TGCCCTTATGTGATAAAATGACTGTTT
56185339 TGCCCTTATGTGAT
1 TGCCCTTATGTGAT
56185353 GTATATTTAT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.21, C:0.15, G:0.24, T:0.41
Consensus pattern (27 bp):
TGCCCTTATGTGATAAAATGACTGTTT
Found at i:56185791 original size:32 final size:32
Alignment explanation
Indices: 56185720--56185791 Score: 90
Period size: 32 Copynumber: 2.2 Consensus size: 32
56185710 CCAAGGCCCT
* * * *
56185720 AACTGATATTGATTCTGATATGGGCTAGACCC
1 AACTGATAGTGATTCTAAGATGGGCTAGACAC
*
56185752 AACTGATAGTGATTCTAAGATGGGCTAGGCAC
1 AACTGATAGTGATTCTAAGATGGGCTAGACAC
*
56185784 AATTGATA
1 AACTGATA
56185792 CTATGATGGG
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.32, C:0.15, G:0.24, T:0.29
Consensus pattern (32 bp):
AACTGATAGTGATTCTAAGATGGGCTAGACAC
Found at i:56196222 original size:25 final size:25
Alignment explanation
Indices: 56196188--56196259 Score: 108
Period size: 25 Copynumber: 2.9 Consensus size: 25
56196178 CTCTTTTAAT
56196188 AACTAGGGCAAAGCCCTTTTTGATA
1 AACTAGGGCAAAGCCCTTTTTGATA
* *
56196213 AACTAGGGCAAAGCCCTTTTCGGTA
1 AACTAGGGCAAAGCCCTTTTTGATA
* *
56196238 AACTGGGGCAAAGCTCTTTTTG
1 AACTAGGGCAAAGCCCTTTTTG
56196260 CACTTCCTCT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 42 1.00
ACGTcount: A:0.28, C:0.21, G:0.24, T:0.28
Consensus pattern (25 bp):
AACTAGGGCAAAGCCCTTTTTGATA
Found at i:56196330 original size:21 final size:21
Alignment explanation
Indices: 56196305--56196355 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
56196295 TATAATGAGT
* *
56196305 ATATCATGTGCATCTGATAAC
1 ATATCATGTGCATATCATAAC
* *
56196326 ATATCATGCGCATATCATATC
1 ATATCATGTGCATATCATAAC
56196347 ATATCATGT
1 ATATCATGT
56196356 ATATCAAAAG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.33, C:0.20, G:0.12, T:0.35
Consensus pattern (21 bp):
ATATCATGTGCATATCATAAC
Found at i:56196435 original size:25 final size:24
Alignment explanation
Indices: 56196392--56196439 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
56196382 ATAATGAATC
* * *
56196392 CCTAGGGGTACAATGGTCACTTTTA
1 CCTAGGGGCAAAATAGTCA-TTTTA
56196417 CCTAGGGGCAAAATAGTCATTTT
1 CCTAGGGGCAAAATAGTCATTTT
56196440 CATATTTTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 4 0.20
25 16 0.80
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.31
Consensus pattern (24 bp):
CCTAGGGGCAAAATAGTCATTTTA
Found at i:56207419 original size:24 final size:25
Alignment explanation
Indices: 56207392--56207469 Score: 86
Period size: 25 Copynumber: 3.2 Consensus size: 25
56207382 GCTTAGCCTC
56207392 TTTTAAT-AACTGGGGCAAAGCCCT
1 TTTTAATAAACTGGGGCAAAGCCCT
* *
56207416 TTTTGATAAACTGGGGCCAAGCCCT
1 TTTTAATAAACTGGGGCAAAGCCCT
* * * * *
56207441 TTTCAGTAAACTAGGCCAAAGCTCT
1 TTTTAATAAACTGGGGCAAAGCCCT
56207466 TTTT
1 TTTT
56207470 GCACTTCCTC
Statistics
Matches: 43, Mismatches: 10, Indels: 1
0.80 0.19 0.02
Matches are distributed among these distances:
24 6 0.14
25 37 0.86
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.32
Consensus pattern (25 bp):
TTTTAATAAACTGGGGCAAAGCCCT
Found at i:56207541 original size:21 final size:21
Alignment explanation
Indices: 56207516--56207564 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
56207506 TATAATGAGT
* *
56207516 ATATCATGTGCATCTCATAAC
1 ATATCATGCGCATATCATAAC
* *
56207537 ATATCATGCGCATATTATATC
1 ATATCATGCGCATATCATAAC
56207558 ATATCAT
1 ATATCAT
56207565 ATCATATCAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.35, C:0.20, G:0.08, T:0.37
Consensus pattern (21 bp):
ATATCATGCGCATATCATAAC
Done.