Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A13
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: 109233746
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2708888 characters in sequence are not A, C, G, or T
File 164 of 332
Found at i:54169188 original size:40 final size:40
Alignment explanation
Indices: 54169133--54169278 Score: 163
Period size: 40 Copynumber: 3.6 Consensus size: 40
54169123 AGCTCCTGTT
* * *
54169133 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTATCTTGCA
1 CAAATGCCTTCGGGACATAACCCGGATT-TAGTAACTCGCA
*
54169173 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* * *
54169213 CAAATGCCATCGGGACTTAAACCCAGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACAT-AACCCGGATTTAGTAACTCGCA
* *
54169254 CCAAATG-CATC-GGACTTAACCCGGA
1 -CAAATGCCTTCGGGACATAACCCGGA
54169279 ACATTCTACA
Statistics
Matches: 96, Mismatches: 7, Indels: 7
0.87 0.06 0.06
Matches are distributed among these distances:
39 7 0.07
40 56 0.58
41 27 0.28
42 6 0.06
ACGTcount: A:0.29, C:0.27, G:0.20, T:0.23
Consensus pattern (40 bp):
CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
Found at i:54176493 original size:39 final size:40
Alignment explanation
Indices: 54176390--54176606 Score: 273
Period size: 39 Copynumber: 5.5 Consensus size: 40
54176380 GCTCCTCGTT
* *
54176390 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
54176430 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
54176470 CAAATGCC-TCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * *
54176509 CAAATGCCATC-GGACTTAACCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
** * * * *
54176548 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
54176589 CAAA-GCCTTCGGGACTTA
1 CAAATGCCTTCGGGACTTA
54176607 GCCGGACACC
Statistics
Matches: 159, Mismatches: 13, Indels: 10
0.87 0.07 0.05
Matches are distributed among these distances:
39 78 0.49
40 68 0.43
41 13 0.08
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:54176493 original size:79 final size:80
Alignment explanation
Indices: 54176390--54176606 Score: 282
Period size: 79 Copynumber: 2.7 Consensus size: 80
54176380 GCTCCTCGTT
*
54176390 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
*
54176455 ATTTAGTAACTCGCA
66 AATTAGTAACTCGCA
* *
54176470 CAAATGCC-TCGGGACTTAACCCGGATT-TAGTAACTCGCACAAATGCCATC-GGACTTAACCCG
1 CAAATGCCTTCGGGACTTAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCG
*
54176532 GAATTAGTATCTCGCA
65 GAATTAGTAACTCGCA
* * * * *
54176548 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTA
1 CAAATGCCTTCGGGA-CTTAGCCCGGTTATAGTAAC-TCGCACAAATGCCTTCGGGACTTA
54176607 GCCGGACACC
Statistics
Matches: 119, Mismatches: 12, Indels: 12
0.83 0.08 0.08
Matches are distributed among these distances:
78 38 0.32
79 56 0.47
80 25 0.21
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (80 bp):
CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
AATTAGTAACTCGCA
Found at i:54180151 original size:43 final size:43
Alignment explanation
Indices: 54179950--54180150 Score: 262
Period size: 43 Copynumber: 4.7 Consensus size: 43
54179940 ATATCGTACA
* * *
54179950 ATGCCAAGGTCCCAGACGTGGTCATACATGTAATCACATATCG
1 ATGCCAACGTCCCAGACGTGGTCTTACACGTAATCACATATCG
* * * * *
54179993 ATGTC-ACTGTCCCAAACAG-GGTCTTAGACGTAATCGCATATCA
1 ATGCCAAC-GTCCCAGAC-GTGGTCTTACACGTAATCACATATCG
*
54180036 ATGCCAACGTCCCAGACGTGGTCTTACACGTTATCACATATCG
1 ATGCCAACGTCCCAGACGTGGTCTTACACGTAATCACATATCG
* *
54180079 ATGCCAACATCCCAGACGTGGTCTTACACATAATCACATATCG
1 ATGCCAACGTCCCAGACGTGGTCTTACACGTAATCACATATCG
*
54180122 ATGCCAATGTCCCAGACGTGGTCTTACAC
1 ATGCCAACGTCCCAGACGTGGTCTTACAC
54180151 ACACACACAT
Statistics
Matches: 135, Mismatches: 19, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
42 2 0.01
43 130 0.96
44 3 0.02
ACGTcount: A:0.29, C:0.28, G:0.18, T:0.24
Consensus pattern (43 bp):
ATGCCAACGTCCCAGACGTGGTCTTACACGTAATCACATATCG
Found at i:54183429 original size:19 final size:19
Alignment explanation
Indices: 54183405--54183446 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
54183395 CATCCGTTTA
*
54183405 AACAGTACTTCATCCATAT
1 AACAGTAATTCATCCATAT
*
54183424 AACAGTAATTCATCCTTAT
1 AACAGTAATTCATCCATAT
54183443 AACA
1 AACA
54183447 CATAGCTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.40, C:0.24, G:0.05, T:0.31
Consensus pattern (19 bp):
AACAGTAATTCATCCATAT
Found at i:54198879 original size:40 final size:40
Alignment explanation
Indices: 54198842--54198971 Score: 140
Period size: 40 Copynumber: 3.3 Consensus size: 40
54198832 GCTACTCGTT
* *
54198842 CAAATTCCTTCAGGACATAGCCC-GATTATAGTAACTCGCA
1 CAAATGCCTTCAGGACATAACCCGGATT-TAGTAACTCGCA
* *
54198882 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCAGGACATAACCCGGATTTAGTAACTCGCA
* * * * *
54198922 CCAATGCCTTC-GGGCTTAGA-CCGGAATTAGTAGCTCGCA
1 CAAATGCCTTCAGGACATA-ACCCGGATTTAGTAACTCGCA
54198961 CAAATGCCTTC
1 CAAATGCCTTC
54198972 GGATCTTAGT
Statistics
Matches: 79, Mismatches: 9, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
39 33 0.42
40 42 0.53
41 4 0.05
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCAGGACATAACCCGGATTTAGTAACTCGCA
Found at i:54198959 original size:39 final size:40
Alignment explanation
Indices: 54198870--54198973 Score: 158
Period size: 39 Copynumber: 2.6 Consensus size: 40
54198860 AGCCCGATTA
*
54198870 TAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATT
1 TAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAAT
*
54198910 TAGTAACTCGCACCAATGCCTTCGGG-CTTAGA-CCGGAAT
1 TAGTAACTCGCACAAATGCCTTCGGGACTTA-ACCCGGAAT
*
54198949 TAGTAGCTCGCACAAATGCCTTCGG
1 TAGTAACTCGCACAAATGCCTTCGG
54198974 ATCTTAGTCC
Statistics
Matches: 59, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
39 33 0.56
40 26 0.44
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
TAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAAT
Found at i:54199010 original size:79 final size:80
Alignment explanation
Indices: 54198870--54199020 Score: 191
Period size: 79 Copynumber: 1.9 Consensus size: 80
54198860 AGCCCGATTA
* * *
54198870 TAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACCAATGCCTTCGG
1 TAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATATAGTAACTAGCACCAAAGCCTTCGG
54198935 G-CTTAGACCGGAAT
66 GACTTAGACCGGAAT
* ** * *
54198949 TAGTAGCTCGCACAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA-CAAAGCCTTC
1 TAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGGATATAGTAAC-TAGCACCAAAGCCTTC
54199012 GGGACTTAG
64 GGGACTTAG
54199021 CCCAGACATC
Statistics
Matches: 61, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
78 3 0.05
79 49 0.80
80 9 0.15
ACGTcount: A:0.26, C:0.26, G:0.23, T:0.25
Consensus pattern (80 bp):
TAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATATAGTAACTAGCACCAAAGCCTTCGG
GACTTAGACCGGAAT
Found at i:54202540 original size:15 final size:17
Alignment explanation
Indices: 54202522--54202553 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
54202512 TAGCATAGTT
54202522 TACCAAA-TCA-ATTCA
1 TACCAAACTCACATTCA
54202537 TACCAAACTCACATTCA
1 TACCAAACTCACATTCA
54202554 CAAGTATCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 3 0.20
17 5 0.33
ACGTcount: A:0.44, C:0.31, G:0.00, T:0.25
Consensus pattern (17 bp):
TACCAAACTCACATTCA
Found at i:54206901 original size:26 final size:26
Alignment explanation
Indices: 54206842--54206948 Score: 180
Period size: 26 Copynumber: 4.2 Consensus size: 26
54206832 TGAAATGCCC
*
54206842 ATCATGGAACATTTACCTAAACC-TT
1 ATCATGGAACATTTACCTAACCCATT
54206867 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
54206893 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
54206919 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
54206945 ATCA
1 ATCA
54206949 ATTTGTACCA
Statistics
Matches: 76, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
25 22 0.29
26 54 0.71
ACGTcount: A:0.36, C:0.24, G:0.07, T:0.33
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:54213919 original size:26 final size:26
Alignment explanation
Indices: 54213888--54213995 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
54213878 TGAAATGCCC
*
54213888 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
54213914 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
54213940 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
54213966 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
54213992 ATCA
1 ATCA
54213996 ATTTGTACCA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.36, C:0.24, G:0.07, T:0.32
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:54216636 original size:22 final size:23
Alignment explanation
Indices: 54216611--54216657 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
54216601 ATTTTGTTCA
*
54216611 ATTTTAACTT-TTATTTAAAAAT
1 ATTTTAACTTGTTATATAAAAAT
* *
54216633 ATTTTAATTTGTTATATGAAAAT
1 ATTTTAACTTGTTATATAAAAAT
54216656 AT
1 AT
54216658 ATTATCAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 9 0.43
23 12 0.57
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.53
Consensus pattern (23 bp):
ATTTTAACTTGTTATATAAAAAT
Found at i:54216967 original size:107 final size:107
Alignment explanation
Indices: 54216783--54216977 Score: 293
Period size: 107 Copynumber: 1.8 Consensus size: 107
54216773 GAAAAGGAAT
* *
54216783 ACAATTGACATTGGAGTGTTGGACAGGTGTCATGTAAAATATAGAGGGATTAGAATTGATATTCA
1 ACAATTGACATTGGAGTATTGGACAGGTGTCATGTAAAATATAAAGGGATTAGAATTGATATTCA
* * *
54216848 ACCATTAGCTTCTCATGTCAAAAGAAGAACAAGAAGAAGAAA
66 ACCACTACCTTCTCATGCCAAAAGAAGAACAAGAAGAAGAAA
* *
54216890 ACAATTGACATTGGAGTATTGGACAGGTGTCATGTAAAA-AGTAAAGGGTTTAGAATTGATATTT
1 ACAATTGACATTGGAGTATTGGACAGGTGTCATGTAAAATA-TAAAGGGATTAGAATTGATATTC
* *
54216954 GATCACTACCTTCTCATGCCAAAA
65 AACCACTACCTTCTCATGCCAAAA
54216978 AAAATTAAAA
Statistics
Matches: 78, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
106 1 0.01
107 77 0.99
ACGTcount: A:0.38, C:0.12, G:0.22, T:0.28
Consensus pattern (107 bp):
ACAATTGACATTGGAGTATTGGACAGGTGTCATGTAAAATATAAAGGGATTAGAATTGATATTCA
ACCACTACCTTCTCATGCCAAAAGAAGAACAAGAAGAAGAAA
Found at i:54217460 original size:27 final size:27
Alignment explanation
Indices: 54217430--54217484 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
54217420 TAAAAAAGAA
54217430 GGAATATTACCCCAACACAAAGCGTTG
1 GGAATATTACCCCAACACAAAGCGTTG
54217457 GGAATATTACCCCAACACAAAGCGTTG
1 GGAATATTACCCCAACACAAAGCGTTG
54217484 G
1 G
54217485 TAGGAACCAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.18
Consensus pattern (27 bp):
GGAATATTACCCCAACACAAAGCGTTG
Found at i:54219754 original size:106 final size:106
Alignment explanation
Indices: 54219558--54219754 Score: 261
Period size: 106 Copynumber: 1.9 Consensus size: 106
54219548 ACATAATTAG
* * *
54219558 GAGAAAAAATTGAGAATGCAAAAACTATAGAAAAAAATATAGCATCAAAATAATTGAACTGACAT
1 GAGAAAAAATTGAGAATGCAAAAACTAAAGAAAAAAATATAGCATCAAAATAATTAAACTAACAT
* ** **
54219623 GCTATACAAATTATTTATATGAAAAATGTGTATAGTTAAGA
66 ACTATACAAATTATACATACCAAAAATGTGTATAGTTAAGA
* * **
54219664 GAGAAAAAATTGAGAATGCAAAAATTAAATAAAAAAAGTA-AGCATGGAAATAATTAAACTAACA
1 GAGAAAAAATTGAGAATGCAAAAACTAAAGAAAAAAA-TATAGCATCAAAATAATTAAACTAACA
*
54219728 TACTGTACAAATTATACATACCAAAAA
65 TACTATACAAATTATACATACCAAAAA
54219755 AAAATTAAAG
Statistics
Matches: 77, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
106 75 0.97
107 2 0.03
ACGTcount: A:0.55, C:0.09, G:0.13, T:0.24
Consensus pattern (106 bp):
GAGAAAAAATTGAGAATGCAAAAACTAAAGAAAAAAATATAGCATCAAAATAATTAAACTAACAT
ACTATACAAATTATACATACCAAAAATGTGTATAGTTAAGA
Found at i:54221251 original size:20 final size:20
Alignment explanation
Indices: 54221224--54221265 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
54221214 TGGAGAGAAT
* *
54221224 TTTTTTTTTTGA-GTTTGGG
1 TTTTGTTTTTGAGGTTTGAG
54221243 TTTTGTTTTTGAGGTTTGAG
1 TTTTGTTTTTGAGGTTTGAG
54221263 TTT
1 TTT
54221266 GTATGTTTAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 11 0.55
20 9 0.45
ACGTcount: A:0.07, C:0.00, G:0.26, T:0.67
Consensus pattern (20 bp):
TTTTGTTTTTGAGGTTTGAG
Found at i:54226262 original size:40 final size:40
Alignment explanation
Indices: 54226203--54226414 Score: 268
Period size: 40 Copynumber: 5.3 Consensus size: 40
54226193 CATTTGAATG
*
54226203 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
* *
54226243 TTATCCGGGTTAAGACCCGAAGGCATTTGTGCTAGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
* *
54226283 TTATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGA-T
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAG-TGATT
* * *
54226323 ATATCCGGGCTAAGACCCGAAGGAATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAG-TGATT
* * * * *
54226363 ATACCCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
54226403 ATATCC-GGCTAA
1 ATATCCGGGCTAA
54226415 ATTCCGAAGA
Statistics
Matches: 153, Mismatches: 16, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
39 7 0.05
40 143 0.93
41 3 0.02
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.28
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
Found at i:54228969 original size:22 final size:22
Alignment explanation
Indices: 54228941--54228984 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
54228931 TAGATCAAGA
54228941 AAGAAATAAATTGGATTTAGAT
1 AAGAAATAAATTGGATTTAGAT
54228963 AAGAAATAAATTGGATTTAGAT
1 AAGAAATAAATTGGATTTAGAT
54228985 CGGGGAAATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.18, T:0.32
Consensus pattern (22 bp):
AAGAAATAAATTGGATTTAGAT
Found at i:54229296 original size:55 final size:55
Alignment explanation
Indices: 54229231--54229340 Score: 150
Period size: 55 Copynumber: 2.0 Consensus size: 55
54229221 GAGATGTAAT
* * *
54229231 TACATGTAAGACCATGCCTGGGACATTGGCATTG-TATTATGATTACGTGTAAGAC
1 TACATGTAAGAACATGCCTGGGACATTGGCATCGTTA-TATGATTACATGTAAGAC
* * *
54229286 TACATGTAAGAATATGTCTGGGACATTGGCATCGTTATATGATTTCATGTAAGAC
1 TACATGTAAGAACATGCCTGGGACATTGGCATCGTTATATGATTACATGTAAGAC
54229341 CATGTCTGGG
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
55 46 0.96
56 2 0.04
ACGTcount: A:0.30, C:0.15, G:0.23, T:0.33
Consensus pattern (55 bp):
TACATGTAAGAACATGCCTGGGACATTGGCATCGTTATATGATTACATGTAAGAC
Found at i:54229349 original size:43 final size:43
Alignment explanation
Indices: 54229287--54229386 Score: 146
Period size: 43 Copynumber: 2.3 Consensus size: 43
54229277 GTGTAAGACT
** * *
54229287 ACATGTAAGAATATGTCTGGGACATTGGCATCGTTATATGATT
1 ACATGTAAGACCATGTCTGGGACATTGGCATCGATATATGATA
* *
54229330 TCATGTAAGACCATGTCTGGGACATTGGCATCGATATGTGATA
1 ACATGTAAGACCATGTCTGGGACATTGGCATCGATATATGATA
54229373 ACATGTAAGACCAT
1 ACATGTAAGACCAT
54229387 ATCTAGGATA
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 50 1.00
ACGTcount: A:0.31, C:0.15, G:0.23, T:0.31
Consensus pattern (43 bp):
ACATGTAAGACCATGTCTGGGACATTGGCATCGATATATGATA
Found at i:54230888 original size:24 final size:24
Alignment explanation
Indices: 54230837--54230886 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
54230827 ACAGCGTAAG
*
54230837 AAATCTAACTAGTTTGGATTTAAT
1 AAATCTAACTAGTTTGGATTCAAT
54230861 AAATCTAACTAGTTTGGATTC-AT
1 AAATCTAACTAGTTTGGATTCAAT
54230884 AAA
1 AAA
54230887 ATAGTAGTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
23 5 0.20
24 20 0.80
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.38
Consensus pattern (24 bp):
AAATCTAACTAGTTTGGATTCAAT
Found at i:54235166 original size:12 final size:12
Alignment explanation
Indices: 54235151--54235175 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
54235141 TAGCTTCATT
54235151 TTTCACCCAAAA
1 TTTCACCCAAAA
54235163 TTTCACCCAAAA
1 TTTCACCCAAAA
54235175 T
1 T
54235176 CTGTACTTGA
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:0.40, C:0.32, G:0.00, T:0.28
Consensus pattern (12 bp):
TTTCACCCAAAA
Found at i:54238789 original size:48 final size:48
Alignment explanation
Indices: 54238725--54238872 Score: 208
Period size: 48 Copynumber: 3.1 Consensus size: 48
54238715 TTGATGTACA
*
54238725 AGATATATATATGTGGTAAAGCCGAATGGCTAATGTAAAATATGTATG
1 AGATATATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATG
* *
54238773 AGATATATATATGTGGTAAAGTCGAAAGGCTAATGTGAAATATGTATG
1 AGATATATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATG
** ** *
54238821 AGCCATGCATATGTGATAAAGCC-AATTGGCTAATGTGAAATATGTATG
1 AGATATATATATGTGGTAAAGCCGAA-TGGCTAATGTGAAATATGTATG
54238869 AGAT
1 AGAT
54238873 GTGTATATAT
Statistics
Matches: 87, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
47 2 0.02
48 85 0.98
ACGTcount: A:0.39, C:0.07, G:0.24, T:0.30
Consensus pattern (48 bp):
AGATATATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATG
Found at i:54240841 original size:40 final size:40
Alignment explanation
Indices: 54240786--54241061 Score: 437
Period size: 40 Copynumber: 6.9 Consensus size: 40
54240776 TTCAGTATGT
* *
54240786 TATATCCGAGCTAAGTCTCGAAGAGCATTCGTGCTGGTGA
1 TATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGA
*
54240826 TATATCCAGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGA
1 TATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGA
* *
54240866 TGTATTCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGA
1 TATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGA
* *
54240906 TATATTCGGGCTAAGTCCCGAAGAGCATTCATGCTGGTGA
1 TATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGA
*
54240946 TGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGA
1 TATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGA
* *
54240986 TATATCCGGGCTAAGTCCTGAAGAGCATTTGTGCTGGTGA
1 TATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGA
* *
54241026 TGTATCCGGGCTAAGCCCCGAAG-GCATTCGTGCTGG
1 TATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGG
54241062 GACAAAATTC
Statistics
Matches: 218, Mismatches: 18, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
39 12 0.06
40 206 0.94
ACGTcount: A:0.22, C:0.21, G:0.30, T:0.26
Consensus pattern (40 bp):
TATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGA
Found at i:54241443 original size:57 final size:59
Alignment explanation
Indices: 54241337--54241451 Score: 180
Period size: 57 Copynumber: 2.0 Consensus size: 59
54241327 TGTGCGAATG
*
54241337 ATTAGAGGCACTGTGTGTGCAAATTCTTTTAACCGAGCACTATGTGTGCGAAATCGGTA
1 ATTAGAGGCACTGTGTGTGCAAATTCTTTCAACCGAGCACTATGTGTGCGAAATCGGTA
* * *
54241396 ATTA-AGGCACTGTGTGTGCGAGTTC-TTCAACCGAGCACTATGTGTGCGAGATCGGT
1 ATTAGAGGCACTGTGTGTGCAAATTCTTTCAACCGAGCACTATGTGTGCGAAATCGGT
54241452 TAGTGGGCAC
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
57 29 0.56
58 19 0.37
59 4 0.08
ACGTcount: A:0.24, C:0.18, G:0.28, T:0.30
Consensus pattern (59 bp):
ATTAGAGGCACTGTGTGTGCAAATTCTTTCAACCGAGCACTATGTGTGCGAAATCGGTA
Found at i:54245205 original size:48 final size:48
Alignment explanation
Indices: 54245108--54245207 Score: 164
Period size: 48 Copynumber: 2.1 Consensus size: 48
54245098 CAAGATATAT
* *
54245108 ATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGCCATGC
1 ATATGTGGTAAAGCCAAATGGCTAATGTGAAATATGTATGAGACATGC
**
54245156 ATATGTGGTAAAGCCAAATGGCTAATGTGAAATATGTATGAGATGTGC
1 ATATGTGGTAAAGCCAAATGGCTAATGTGAAATATGTATGAGACATGC
54245204 ATAT
1 ATAT
54245208 ATATTGTGGC
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.35, C:0.10, G:0.26, T:0.29
Consensus pattern (48 bp):
ATATGTGGTAAAGCCAAATGGCTAATGTGAAATATGTATGAGACATGC
Found at i:54253196 original size:15 final size:15
Alignment explanation
Indices: 54253176--54253215 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
54253166 GGAGCCTAGA
54253176 ATAAAGAAAT-CATAG
1 ATAAAGAAATCCAT-G
54253191 ATAAAGAAATCCATG
1 ATAAAGAAATCCATG
*
54253206 ATAAGGAAAT
1 ATAAAGAAAT
54253216 ATAAATTACA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 20 0.87
16 3 0.13
ACGTcount: A:0.57, C:0.07, G:0.15, T:0.20
Consensus pattern (15 bp):
ATAAAGAAATCCATG
Found at i:54267181 original size:8 final size:8
Alignment explanation
Indices: 54267168--54267192 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
54267158 CCTTGCCCTT
54267168 CTCACATG
1 CTCACATG
54267176 CTCACATG
1 CTCACATG
54267184 CTCACATG
1 CTCACATG
54267192 C
1 C
54267193 CACTTTCCTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.40, G:0.12, T:0.24
Consensus pattern (8 bp):
CTCACATG
Found at i:54275094 original size:30 final size:30
Alignment explanation
Indices: 54275049--54275110 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 30
54275039 CTTAATAAGT
*
54275049 AAATACCTCTAAAATAATAACAAAATTAAC
1 AAATACCTCTAAAATAAAAACAAAATTAAC
* *
54275079 AAATGCCTTTAAAATAAAAACAAAATTAAC
1 AAATACCTCTAAAATAAAAACAAAATTAAC
54275109 AA
1 AA
54275111 TAAAATAAGT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.61, C:0.15, G:0.02, T:0.23
Consensus pattern (30 bp):
AAATACCTCTAAAATAAAAACAAAATTAAC
Found at i:54277728 original size:30 final size:30
Alignment explanation
Indices: 54277692--54277750 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
54277682 CTTAACAAGC
54277692 AAATGCCTCTAAAATAATAAAAAAATTAAG
1 AAATGCCTCTAAAATAATAAAAAAATTAAG
* *
54277722 AAATGCCTTTAAAATAATAACAAAATTAA
1 AAATGCCTCTAAAATAATAAAAAAATTAA
54277751 CAATAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.59, C:0.10, G:0.05, T:0.25
Consensus pattern (30 bp):
AAATGCCTCTAAAATAATAAAAAAATTAAG
Found at i:54279429 original size:27 final size:27
Alignment explanation
Indices: 54279385--54279473 Score: 124
Period size: 27 Copynumber: 3.3 Consensus size: 27
54279375 AAAAATAGTC
* * * *
54279385 ATTTTACCCTATAGGGGTATGTCGATC
1 ATTTTACACTACAAGGGTATGTCGATA
*
54279412 ATTTTACACTACAAGGGTATGTCGGTA
1 ATTTTACACTACAAGGGTATGTCGATA
*
54279439 ATTTTACACTACAAGGGTATTTCGATA
1 ATTTTACACTACAAGGGTATGTCGATA
54279466 ATTTTACA
1 ATTTTACA
54279474 AATCGGGGGT
Statistics
Matches: 55, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 55 1.00
ACGTcount: A:0.29, C:0.16, G:0.18, T:0.37
Consensus pattern (27 bp):
ATTTTACACTACAAGGGTATGTCGATA
Found at i:54279483 original size:27 final size:27
Alignment explanation
Indices: 54279399--54279701 Score: 262
Period size: 27 Copynumber: 11.3 Consensus size: 27
54279389 TACCCTATAG
* * * *
54279399 GGGTATGTCGATCATTTTAC-ACTACAA
1 GGGTATTTCGATAATTTTACAAAT-CGA
* * * *
54279426 GGGTATGTCGGTAATTTTAC-ACTACAA
1 GGGTATTTCGATAATTTTACAAAT-CGA
*
54279453 GGGTATTTCGATAATTTTACAAATCGG
1 GGGTATTTCGATAATTTTACAAATCGA
* *
54279480 GGGTGTTTCGACAATTTTACAAATCGA
1 GGGTATTTCGATAATTTTACAAATCGA
*
54279507 GGGTATTT-TAGTAATTTTACAAATCGA
1 GGGTATTTCGA-TAATTTTACAAATCGA
*
54279534 GGGTGTTTCGATAATTTTACAAATCGA
1 GGGTATTTCGATAATTTTACAAATCGA
* * * *
54279561 GGGTTTTTTGGTAATTTCACAAATCTG-
1 GGGTATTTCGATAATTTTACAAATC-GA
* *
54279588 GGGTATTTAGGTAATTTTACAAATCGA
1 GGGTATTTCGATAATTTTACAAATCGA
* * ** *
54279615 GGGTATTT-TAGTAATTTCACACCT-AA
1 GGGTATTTCGA-TAATTTTACAAATCGA
*
54279641 GGGTATTTCGGTAATTTTACAAATC-A
1 GGGTATTTCGATAATTTTACAAATCGA
*
54279667 GAGGTATTTCGGTAA-TTTACAAATCGA
1 G-GGTATTTCGATAATTTTACAAATCGA
54279694 GGGTATTT
1 GGGTATTT
54279702 TAGTAATTTC
Statistics
Matches: 233, Mismatches: 33, Indels: 21
0.81 0.11 0.07
Matches are distributed among these distances:
26 40 0.17
27 189 0.81
28 4 0.02
ACGTcount: A:0.30, C:0.12, G:0.21, T:0.37
Consensus pattern (27 bp):
GGGTATTTCGATAATTTTACAAATCGA
Found at i:54280060 original size:28 final size:28
Alignment explanation
Indices: 54280027--54280118 Score: 148
Period size: 28 Copynumber: 3.3 Consensus size: 28
54280017 TGGCCCCTTT
* * *
54280027 AGGCCCAATCTCGTTCACATGGCCCATC
1 AGGCCCAATCACATTCATATGGCCCATC
54280055 AGGCCCAATCACATTCATATGGCCCATC
1 AGGCCCAATCACATTCATATGGCCCATC
*
54280083 AGACCCAATCACATTCATATGGCCCATC
1 AGGCCCAATCACATTCATATGGCCCATC
54280111 AGGCCCAA
1 AGGCCCAA
54280119 CTACTTTCCA
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 59 1.00
ACGTcount: A:0.28, C:0.37, G:0.15, T:0.20
Consensus pattern (28 bp):
AGGCCCAATCACATTCATATGGCCCATC
Found at i:54282955 original size:27 final size:27
Alignment explanation
Indices: 54282928--54283124 Score: 177
Period size: 27 Copynumber: 7.3 Consensus size: 27
54282918 TAAAATAGTC
* * * *
54282928 ATTTTACCCTACAGGGGTATGTCGGTC
1 ATTTTACACTACAAGGGTATTTCGGTA
54282955 ATTTTACACTACAAGGGTATTTCGGTA
1 ATTTTACACTACAAGGGTATTTCGGTA
*
54282982 ATTTTACACTACAAGGGTATTTCGATA
1 ATTTTACACTACAAGGGTATTTCGGTA
* * **
54283009 ATTTTACA-AATCAATGGTATTTTAGTA
1 ATTTTACACTA-CAAGGGTATTTCGGTA
* * *
54283036 ATTTTACA-AATCGAGGGTATTTCGATA
1 ATTTTACACTA-CAAGGGTATTTCGGTA
* *
54283063 ATTTTACA-AATCGAGGGTATTTCGGTA
1 ATTTTACACTA-CAAGGGTATTTCGGTA
* * *
54283090 ATTTTACA-AATCAAGGGTGTTTCAGTA
1 ATTTTACACTA-CAAGGGTATTTCGGTA
54283117 ATTTTACA
1 ATTTTACA
54283125 AATTGAGGGT
Statistics
Matches: 150, Mismatches: 19, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
26 1 0.01
27 149 0.99
ACGTcount: A:0.31, C:0.13, G:0.18, T:0.38
Consensus pattern (27 bp):
ATTTTACACTACAAGGGTATTTCGGTA
Found at i:54283053 original size:81 final size:81
Alignment explanation
Indices: 54282968--54283362 Score: 492
Period size: 81 Copynumber: 4.9 Consensus size: 81
54282958 TTACACTACA
* * * * * *
54282968 AGGGTATTTCGGTAATTTTAC-ACTACAAGGGTATTTCGATAATTTTACAAATCAATGGTATTTT
1 AGGGTATTTCGATAATTTTACAAAT-CAGGGGTATTTCGGTAATTTTACAAATCAAGGGTATTTC
54283032 AGTAATTTTACAAATCG
65 AGTAATTTTACAAATCG
*
54283049 AGGGTATTTCGATAATTTTACAAATC-GAGGGTATTTCGGTAATTTTACAAATCAAGGGTGTTTC
1 AGGGTATTTCGATAATTTTACAAATCAG-GGGTATTTCGGTAATTTTACAAATCAAGGGTATTTC
*
54283113 AGTAATTTTACAAATTG
65 AGTAATTTTACAAATCG
* * * * * * ** * *
54283130 AGGGTGTTTCAATAATTTCAAAAATTAGGGGTATTTAGGTAATTTTACAAATTGAGGTTATTTTA
1 AGGGTATTTCGATAATTTTACAAATCAGGGGTATTTCGGTAATTTTACAAATCAAGGGTATTTCA
54283195 GTAATTTT-CATAATCG
66 GTAATTTTACA-AATCG
* * * *
54283211 AGGGTAGTTCGGTAATTTTACAAATCAGGGGTATTTTGGTAATTTTACAAATCGAGGGTATTTCA
1 AGGGTATTTCGATAATTTTACAAATCAGGGGTATTTCGGTAATTTTACAAATCAAGGGTATTTCA
* *
54283276 ATAATTTCAC-AATCG
66 GTAATTTTACAAATCG
* * *
54283291 AGGGTATTTCGATAATTTTACAAATCGGGGGTATTTCGATAATTTTACAAAGCAAGGGTATTTCA
1 AGGGTATTTCGATAATTTTACAAATCAGGGGTATTTCGGTAATTTTACAAATCAAGGGTATTTCA
54283356 GTAATTT
66 GTAATTT
54283363 CTCTTTATTA
Statistics
Matches: 268, Mismatches: 41, Indels: 11
0.84 0.13 0.03
Matches are distributed among these distances:
80 71 0.26
81 193 0.72
82 4 0.01
ACGTcount: A:0.32, C:0.10, G:0.19, T:0.39
Consensus pattern (81 bp):
AGGGTATTTCGATAATTTTACAAATCAGGGGTATTTCGGTAATTTTACAAATCAAGGGTATTTCA
GTAATTTTACAAATCG
Found at i:54283125 original size:27 final size:27
Alignment explanation
Indices: 54282968--54283362 Score: 396
Period size: 27 Copynumber: 14.7 Consensus size: 27
54282958 TTACACTACA
* * *
54282968 AGGGTATTTCGGTAATTTTAC-ACTACA
1 AGGGTATTTCAGTAATTTTACAAAT-CG
*
54282995 AGGGTATTTC-GATAATTTTACAAATCA
1 AGGGTATTTCAG-TAATTTTACAAATCG
* *
54283022 ATGGTATTTTAGTAATTTTACAAATCG
1 AGGGTATTTCAGTAATTTTACAAATCG
54283049 AGGGTATTTC-GATAATTTTACAAATCG
1 AGGGTATTTCAG-TAATTTTACAAATCG
* *
54283076 AGGGTATTTCGGTAATTTTACAAATCA
1 AGGGTATTTCAGTAATTTTACAAATCG
* *
54283103 AGGGTGTTTCAGTAATTTTACAAATTG
1 AGGGTATTTCAGTAATTTTACAAATCG
* * * * *
54283130 AGGGTGTTTCAATAATTTCAAAAAT-T
1 AGGGTATTTCAGTAATTTTACAAATCG
*
54283156 AGGGGTATTT-AGGTAATTTTACAAATTG
1 A-GGGTATTTCA-GTAATTTTACAAATCG
* *
54283184 AGGTTATTTTAGTAATTTT-CATAATCG
1 AGGGTATTTCAGTAATTTTACA-AATCG
* *
54283211 AGGGTAGTTCGGTAATTTTACAAATC-
1 AGGGTATTTCAGTAATTTTACAAATCG
**
54283237 AGGGGTATTTTGGTAATTTTACAAATCG
1 A-GGGTATTTCAGTAATTTTACAAATCG
* *
54283265 AGGGTATTTCAATAATTTCAC-AATCG
1 AGGGTATTTCAGTAATTTTACAAATCG
54283291 AGGGTATTTC-GATAATTTTACAAATCG
1 AGGGTATTTCAG-TAATTTTACAAATCG
* * *
54283318 GGGGTATTTC-GATAATTTTACAAAGCA
1 AGGGTATTTCAG-TAATTTTACAAATCG
54283345 AGGGTATTTCAGTAATTT
1 AGGGTATTTCAGTAATTT
54283363 CTCTTTATTA
Statistics
Matches: 314, Mismatches: 38, Indels: 32
0.82 0.10 0.08
Matches are distributed among these distances:
26 30 0.10
27 274 0.87
28 10 0.03
ACGTcount: A:0.32, C:0.10, G:0.19, T:0.39
Consensus pattern (27 bp):
AGGGTATTTCAGTAATTTTACAAATCG
Found at i:54283710 original size:28 final size:28
Alignment explanation
Indices: 54283679--54283766 Score: 122
Period size: 28 Copynumber: 3.1 Consensus size: 28
54283669 TGGCCCCTTT
* * * *
54283679 AGGCCCAATCTCGTTCACATGGCCCATT
1 AGGCCCAATCACATTCATATGGCCCATC
*
54283707 AGGCCCAATCACATTCATATGTCCCATC
1 AGGCCCAATCACATTCATATGGCCCATC
*
54283735 AGGCTCAATCACATTCATATGGCCCATC
1 AGGCCCAATCACATTCATATGGCCCATC
54283763 AGGC
1 AGGC
54283767 TCAACTACTT
Statistics
Matches: 53, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 53 1.00
ACGTcount: A:0.26, C:0.34, G:0.16, T:0.24
Consensus pattern (28 bp):
AGGCCCAATCACATTCATATGGCCCATC
Found at i:54298823 original size:42 final size:42
Alignment explanation
Indices: 54298692--54298846 Score: 134
Period size: 42 Copynumber: 3.7 Consensus size: 42
54298682 TACTACACCA
* * * *
54298692 ATGCCATATCCCATATATGGTCTTACATGGGATCTCAT-ATCG
1 ATGCCATACCCCAGATATGGTCTTACACGAGATCTCATAAT-G
* * * * * * *
54298734 ATGCTCATACCCTA-ACTATGGTCTTACAAGAAATATCACATTA
1 ATGC-CATACCCCAGA-TATGGTCTTACACGAGATCTCATAATG
*
54298777 ATGCCATACCCCAGATATTGTCTTACACGAGATCTCATAATG
1 ATGCCATACCCCAGATATGGTCTTACACGAGATCTCATAATG
* * *
54298819 ATGCCATATCCTAGATATGGACTTACAC
1 ATGCCATACCCCAGATATGGTCTTACAC
54298847 ATAGCCTCGA
Statistics
Matches: 88, Mismatches: 21, Indels: 8
0.75 0.18 0.07
Matches are distributed among these distances:
42 57 0.65
43 30 0.34
44 1 0.01
ACGTcount: A:0.32, C:0.25, G:0.14, T:0.30
Consensus pattern (42 bp):
ATGCCATACCCCAGATATGGTCTTACACGAGATCTCATAATG
Found at i:54307458 original size:40 final size:40
Alignment explanation
Indices: 54307399--54307610 Score: 268
Period size: 40 Copynumber: 5.3 Consensus size: 40
54307389 CATTTGAATG
*
54307399 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
* *
54307439 TTATCCGGGTTAAGACCCGAAGGCATTTGTGCTAGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
* *
54307479 TTATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGA-T
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAG-TGATT
* * *
54307519 ATATCCGGGCTAAGACCCGAAGGCATTTGTCCGAGTTG-CT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAG-TGATT
* * * * *
54307559 ATACCCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
54307599 ATATCC-GGCTAA
1 ATATCCGGGCTAA
54307611 ATTCCGAAGA
Statistics
Matches: 153, Mismatches: 16, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
39 7 0.05
40 143 0.93
41 3 0.02
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.28
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
Found at i:54313655 original size:53 final size:53
Alignment explanation
Indices: 54313481--54313684 Score: 160
Period size: 53 Copynumber: 3.8 Consensus size: 53
54313471 AGGGTTTAAG
* * * * * *
54313481 GATACCAAGTAAGACCTTGCCAATG-CATGGAATTGGTAAGTTTTACAAGGCAAG
1 GATACCACGTAAGACCATGCCAA-GACATGGAAATGGTAAG-TTCATAAGGCAAA
* * * ** * * * *
54313535 GAAATCATGTAAGACCATGTGAAGACAT-GACATTGATAAACTACTATAAGGCAAA
1 GATACCACGTAAGACCATGCCAAGACATGGA-AATGGT-AAGTTC-ATAAGGCAAA
* * * * *
54313590 GATCCCATGTAAGACCATGCCAAGGCATGGAAATGGTGAGTTCATAAGGCAAG
1 GATACCACGTAAGACCATGCCAAGACATGGAAATGGTAAGTTCATAAGGCAAA
*
54313643 GATACCACGTAAGACCATGTCAAGACATGGAAATGGTAAGTT
1 GATACCACGTAAGACCATGCCAAGACATGGAAATGGTAAGTT
54313685 TAAAAAGGAA
Statistics
Matches: 116, Mismatches: 29, Indels: 11
0.74 0.19 0.07
Matches are distributed among these distances:
53 49 0.42
54 29 0.25
55 36 0.31
56 2 0.02
ACGTcount: A:0.38, C:0.17, G:0.24, T:0.22
Consensus pattern (53 bp):
GATACCACGTAAGACCATGCCAAGACATGGAAATGGTAAGTTCATAAGGCAAA
Found at i:54314362 original size:21 final size:21
Alignment explanation
Indices: 54314336--54314376 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
54314326 GACTAACTTA
54314336 GAGTGACTTCGTGATCCCCTG
1 GAGTGACTTCGTGATCCCCTG
*
54314357 GAGTGACTTTGTGATCCCCT
1 GAGTGACTTCGTGATCCCCT
54314377 ATTCCAACTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.15, C:0.27, G:0.27, T:0.32
Consensus pattern (21 bp):
GAGTGACTTCGTGATCCCCTG
Found at i:54333644 original size:93 final size:93
Alignment explanation
Indices: 54333537--54333707 Score: 272
Period size: 93 Copynumber: 1.8 Consensus size: 93
54333527 GCCCATAAGT
* * * * *
54333537 GAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCATCCATAAGTGAACTCGGGCTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAA
*
54333602 TGAGCTT-GGATGCCTAGTTACATCTCTC
66 CGAG-TTCGGATGCCTAGTTACATCTCTC
54333630 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAA
54333695 CGAGTTCGGATGC
66 CGAGTTCGGATGC
54333708 TCAACCATCC
Statistics
Matches: 71, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
92 2 0.03
93 69 0.97
ACGTcount: A:0.27, C:0.29, G:0.22, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCTC
Found at i:54333704 original size:46 final size:46
Alignment explanation
Indices: 54333529--54333704 Score: 180
Period size: 46 Copynumber: 3.8 Consensus size: 46
54333519 TGTAACCCGC
* *
54333529 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* * *
54333575 CCATAAGTGAACTCGGGCTCAACTCAATGAGCTT-GG--ATGC-CTAGTT
1 CCATAAGTGAACTCGGACTCAACTCAACGAG-TTCGGACATTCGC-A--T
* *** *
54333621 ACATCTCTCGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
1 CCATAAGT-GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
54333668 CCATAAGTGAACTCAGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
54333705 TGCTCAACCA
Statistics
Matches: 103, Mismatches: 18, Indels: 18
0.74 0.13 0.13
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
46 64 0.62
47 30 0.29
49 4 0.04
50 1 0.01
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.22
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:54335971 original size:29 final size:29
Alignment explanation
Indices: 54335938--54335996 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
54335928 CCTTAACTCA
54335938 AACTTTTGAAAAATTACAATTTTGCCCCT
1 AACTTTTGAAAAATTACAATTTTGCCCCT
* * * *
54335967 AACTTTTGCATATTTACACTTTTGCCCCT
1 AACTTTTGAAAAATTACAATTTTGCCCCT
54335996 A
1 A
54335997 GGCTCAGGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.29, C:0.24, G:0.07, T:0.41
Consensus pattern (29 bp):
AACTTTTGAAAAATTACAATTTTGCCCCT
Found at i:54340225 original size:30 final size:30
Alignment explanation
Indices: 54340189--54340249 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
54340179 TCCTTAACTC
54340189 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
54340219 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
54340249 A
1 A
54340250 GGCTCAGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACAATTTTGCCCCT
Found at i:54352559 original size:54 final size:54
Alignment explanation
Indices: 54352477--54352591 Score: 221
Period size: 54 Copynumber: 2.1 Consensus size: 54
54352467 GATTGCCTCA
54352477 CAGTATCAACAAGTTATCTCAGTATTTTGTGACTAGAAATACTTTAAGTTATGG
1 CAGTATCAACAAGTTATCTCAGTATTTTGTGACTAGAAATACTTTAAGTTATGG
54352531 CAGTATCAACAAGTTATCTCAGTATTTTGTGACTAGAAATACTTTAAGTTATGG
1 CAGTATCAACAAGTTATCTCAGTATTTTGTGACTAGAAATACTTTAAGTTATGG
54352585 CATGTAT
1 CA-GTAT
54352592 AGGGACTTGA
Statistics
Matches: 60, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
54 56 0.93
55 4 0.07
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (54 bp):
CAGTATCAACAAGTTATCTCAGTATTTTGTGACTAGAAATACTTTAAGTTATGG
Found at i:54353084 original size:71 final size:71
Alignment explanation
Indices: 54353000--54353137 Score: 260
Period size: 71 Copynumber: 1.9 Consensus size: 71
54352990 ATATGTATAG
54353000 ATTTTCATTATAAATAAACAAAAACATTA-TCTGATATCTTTATAATGAGATAATTGATTTTTAG
1 ATTTTCATTATAAATAAACAAAAACATTATTC-GATATCTTTATAATGAGATAATTGATTTTTAG
54353064 TGAGTCT
65 TGAGTCT
54353071 ATTTTCATTATAAATAAACAAAAACATTATTCGATATCTTTATAATGAGATAATTGATTTTTAGT
1 ATTTTCATTATAAATAAACAAAAACATTATTCGATATCTTTATAATGAGATAATTGATTTTTAGT
54353136 GA
66 GA
54353138 AGAGAGGTTA
Statistics
Matches: 66, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
71 64 0.97
72 2 0.03
ACGTcount: A:0.41, C:0.08, G:0.09, T:0.42
Consensus pattern (71 bp):
ATTTTCATTATAAATAAACAAAAACATTATTCGATATCTTTATAATGAGATAATTGATTTTTAGT
GAGTCT
Found at i:54361258 original size:46 final size:46
Alignment explanation
Indices: 54361205--54361341 Score: 184
Period size: 46 Copynumber: 3.0 Consensus size: 46
54361195 TATATAAACA
* * * *
54361205 CATCTCATACATATCTCACATTAGCCATTTAGCTTTACCACATATC
1 CATCTCATACACATTTCGCATTAGCCATTCAGCTTTACCACATATC
* *
54361251 CATCTCATACACGTTTCGCATTAGCCATTCAGCTTTACCTCATATC
1 CATCTCATACACATTTCGCATTAGCCATTCAGCTTTACCACATATC
* * **
54361297 CATCTCATACACATTTCGTATTAGCCATTCGGCTTCGCCACATAT
1 CATCTCATACACATTTCGCATTAGCCATTCAGCTTTACCACATAT
54361342 ATACACTTCC
Statistics
Matches: 79, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
46 79 1.00
ACGTcount: A:0.26, C:0.31, G:0.08, T:0.34
Consensus pattern (46 bp):
CATCTCATACACATTTCGCATTAGCCATTCAGCTTTACCACATATC
Found at i:54361386 original size:47 final size:47
Alignment explanation
Indices: 54361355--54361834 Score: 816
Period size: 47 Copynumber: 10.2 Consensus size: 47
54361345 CACTTCCACG
* ** *
54361355 TTCATCTCATTGGCCATTCTACCTTATCACATATATGCATGTTTACA
1 TTCATCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACA
*
54361402 TTCATCACATTGGCCATTCGGCCTTATCACATATTTGCATGTTCACA
1 TTCATCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACA
*
54361449 TTCATCACATTGGCCATTCGGCCTTATCACACATATGCATGTTCACA
1 TTCATCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACA
*
54361496 TTCATCACATTGGCCATTCGGCCTTATCACACATATGCATGTTCACA
1 TTCATCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACA
* *
54361543 TTCATCACATTGGTCATTCGGCCTTATCACACATATGCATGTTCACA
1 TTCATCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACA
*
54361590 TTCATCACATTGGCCATTCGGCCTTATCACATATTTGCATGTTCACA
1 TTCATCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACA
*
54361637 TTCATCACATTGGCCATTCGGCCTTATCACACATATGCATGTTCACA
1 TTCATCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACA
*
54361684 TTCATCACATTGGCCATTCGGCCTTATCACATATTTGCATGTTCACA
1 TTCATCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACA
*
54361731 TTCATCACATTGGCCATTCGGCCTTATCACATATTTGCATGTTCACA
1 TTCATCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACA
* * *
54361778 TTCATCACATTGGCCATTCGACTTTATCACACATATGCATGTTCACA
1 TTCATCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACA
54361825 TTCATCACAT
1 TTCATCACAT
54361835 AAAATCCTAA
Statistics
Matches: 414, Mismatches: 19, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 414 1.00
ACGTcount: A:0.25, C:0.28, G:0.12, T:0.35
Consensus pattern (47 bp):
TTCATCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACA
Found at i:54361692 original size:25 final size:25
Alignment explanation
Indices: 54361474--54361598 Score: 76
Period size: 23 Copynumber: 5.2 Consensus size: 25
54361464 ATTCGGCCTT
54361474 ATCACACATATGCATGTTCACATTC
1 ATCACACATATGCATGTTCACATTC
* *
54361499 AT--CACAT-TGGCCA--TTCGGCCTT-
1 ATCACACATAT-G-CATGTTC-ACATTC
54361521 ATCACACATATGCATGTTCACATTC
1 ATCACACATATGCATGTTCACATTC
* *
54361546 AT--CACAT-TGGTCA--TTCGGCCTT-
1 ATCACACATAT-G-CATGTTC-ACATTC
54361568 ATCACACATATGCATGTTCACATTC
1 ATCACACATATGCATGTTCACATTC
54361593 ATCACA
1 ATCACA
54361599 TTGGCCATTC
Statistics
Matches: 74, Mismatches: 8, Indels: 36
0.63 0.07 0.31
Matches are distributed among these distances:
22 12 0.16
23 22 0.30
24 22 0.30
25 18 0.24
ACGTcount: A:0.28, C:0.29, G:0.11, T:0.32
Consensus pattern (25 bp):
ATCACACATATGCATGTTCACATTC
Found at i:54361866 original size:141 final size:138
Alignment explanation
Indices: 54361578--54361866 Score: 409
Period size: 141 Copynumber: 2.1 Consensus size: 138
54361568 ATCACACATA
54361578 TGCATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATTTGCATGTTCACATTCATC
1 TGCATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATTTGCATGTTCACATTCATC
* * * ***
54361643 ACATTGGCCATTCGGCCTTATCACACATATGCATGTTCACATTCATCACATTGGCC-ATTCGGCC
66 ACATTGGCCATTCGGCCTTATCACACATATGCATGTTCACATTCATCACATAGTCCTAATC-AAA
*
54361707 TTATCACATATT
130 ATAT-A-A-ATT
54361719 TGCATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATTTGCATGTTCACATTCATC
1 TGCATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATTTGCATGTTCACATTCATC
* * *
54361784 ACATTGGCCATTCGACTTTATCACACATATGCATGTTCACATTCATCACATAAAATCCTAAATCA
66 ACATTGGCCATTCGGCCTTATCACACATATGCATGTTCACATTCATCACAT--AGTCCT-AATCA
54361849 AAATATAAATT
128 AAATATAAATT
*
54361860 TTCATGT
1 TGCATGT
54361867 ATTCACATCA
Statistics
Matches: 133, Mismatches: 11, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
141 123 0.92
142 1 0.01
143 3 0.02
144 3 0.02
145 3 0.02
ACGTcount: A:0.28, C:0.26, G:0.11, T:0.35
Consensus pattern (138 bp):
TGCATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATTTGCATGTTCACATTCATC
ACATTGGCCATTCGGCCTTATCACACATATGCATGTTCACATTCATCACATAGTCCTAATCAAAA
TATAAATT
Found at i:54366147 original size:21 final size:21
Alignment explanation
Indices: 54366123--54366166 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
54366113 AAAATCACTT
*
54366123 AACAA-AATTTATAAATCTATC
1 AACAAGAATTCAT-AATCTATC
*
54366144 AACAAGCATTCATAATCTATC
1 AACAAGAATTCATAATCTATC
54366165 AA
1 AA
54366167 GAAACTTCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.50, C:0.18, G:0.02, T:0.30
Consensus pattern (21 bp):
AACAAGAATTCATAATCTATC
Found at i:54366181 original size:21 final size:21
Alignment explanation
Indices: 54366135--54366178 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
54366125 CAAAATTTAT
*
54366135 AAATCTATCAACAAGCATTCA
1 AAATCTATCAACAAACATTCA
* *
54366156 TAATCTATCAAGAAAC-TTCA
1 AAATCTATCAACAAACATTCA
54366176 AAA
1 AAA
54366179 ATCATACATA
Statistics
Matches: 19, Mismatches: 4, Indels: 1
0.79 0.17 0.04
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.50, C:0.20, G:0.05, T:0.25
Consensus pattern (21 bp):
AAATCTATCAACAAACATTCA
Found at i:54367922 original size:25 final size:25
Alignment explanation
Indices: 54367888--54367956 Score: 93
Period size: 25 Copynumber: 2.8 Consensus size: 25
54367878 GGATTGCAAG
*
54367888 GAAAGCCTTTGTGGTGAATCTTTTA
1 GAAAGCCTTTGTGGTGAATCCTTTA
** *
54367913 GAAAGCCTTTGTGGAAAATCCTTTG
1 GAAAGCCTTTGTGGTGAATCCTTTA
*
54367938 GAAAGCCTTTATGGTGAAT
1 GAAAGCCTTTGTGGTGAAT
54367957 TCTCTGGAAA
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 37 1.00
ACGTcount: A:0.28, C:0.13, G:0.25, T:0.35
Consensus pattern (25 bp):
GAAAGCCTTTGTGGTGAATCCTTTA
Found at i:54367964 original size:25 final size:25
Alignment explanation
Indices: 54367887--54367966 Score: 90
Period size: 25 Copynumber: 3.2 Consensus size: 25
54367877 CGGATTGCAA
54367887 GGAAAGCCTTTGTGGTGAA-TCTTTT
1 GGAAAGCCTTTGTGGTGAATTC-TTT
* ** *
54367912 AGAAAGCCTTTGTGGAAAATCCTTT
1 GGAAAGCCTTTGTGGTGAATTCTTT
* *
54367937 GGAAAGCCTTTATGGTGAATTCTCT
1 GGAAAGCCTTTGTGGTGAATTCTTT
54367962 GGAAA
1 GGAAA
54367967 ATCAGCAGAG
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
25 43 0.98
26 1 0.02
ACGTcount: A:0.28, C:0.14, G:0.25, T:0.34
Consensus pattern (25 bp):
GGAAAGCCTTTGTGGTGAATTCTTT
Found at i:54368119 original size:25 final size:25
Alignment explanation
Indices: 54368085--54368138 Score: 90
Period size: 25 Copynumber: 2.2 Consensus size: 25
54368075 GGATTTCATG
*
54368085 GAAAGCCTTTGTGGCGAATCCTCTA
1 GAAAGCCTTTGTGGCAAATCCTCTA
*
54368110 GAAAGCCTTTGTGGCAAATTCTCTA
1 GAAAGCCTTTGTGGCAAATCCTCTA
54368135 GAAA
1 GAAA
54368139 ATTTGTAAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (25 bp):
GAAAGCCTTTGTGGCAAATCCTCTA
Found at i:54369491 original size:27 final size:26
Alignment explanation
Indices: 54369461--54369524 Score: 74
Period size: 27 Copynumber: 2.4 Consensus size: 26
54369451 TATCATACAT
*
54369461 GTCACTTCATATCGTAGGGGCATATCA
1 GTCACTTCATA-CATAGGGGCATATCA
* * *
54369488 GTCATTTTACCACATAGGGGCATATCA
1 GTCACTTCA-TACATAGGGGCATATCA
54369515 GTCACTTCAT
1 GTCACTTCAT
54369525 CAATTTGGGG
Statistics
Matches: 29, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
27 28 0.97
28 1 0.03
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.31
Consensus pattern (26 bp):
GTCACTTCATACATAGGGGCATATCA
Found at i:54369670 original size:17 final size:18
Alignment explanation
Indices: 54369638--54369672 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
54369628 CTATGATGCG
54369638 GGCCCATGTGGGCCCACA
1 GGCCCATGTGGGCCCACA
*
54369656 GGCCCGTGT-GGCCCACA
1 GGCCCATGTGGGCCCACA
54369673 AAGCCCAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.14, C:0.40, G:0.34, T:0.11
Consensus pattern (18 bp):
GGCCCATGTGGGCCCACA
Found at i:54375423 original size:40 final size:40
Alignment explanation
Indices: 54375341--54375558 Score: 239
Period size: 40 Copynumber: 5.5 Consensus size: 40
54375331 AAGCCAAGTA
* * * *
54375341 CCTTCGGGATTTA-ACCGGATATAGCT-ACTCGCTC-AATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCACACAAATG
* *
54375379 CCTTCGGGACATAGCCCGGATATAGTAACTCACACCAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCACACAAATG
* *
54375419 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATT
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCACACAAATG
* * * *
54375459 CCTTCGGGACTTAGCCCGGATGTAATAACTCGCACAAACG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCACACAAATG
* *
54375499 CCTTCGGGACTTAGCCC-GAAACTAGTCACT-AGCACAAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCA-CAC-AAATG
54375540 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
54375559 TTATCATCCA
Statistics
Matches: 154, Mismatches: 19, Indels: 10
0.84 0.10 0.05
Matches are distributed among these distances:
38 12 0.08
39 18 0.12
40 102 0.66
41 21 0.14
42 1 0.01
ACGTcount: A:0.27, C:0.29, G:0.22, T:0.22
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCACACAAATG
Found at i:54377523 original size:26 final size:26
Alignment explanation
Indices: 54377463--54377526 Score: 74
Period size: 26 Copynumber: 2.5 Consensus size: 26
54377453 TACATCGTTT
* * *
54377463 CTCACACAAGCTATGAAATGAGTCTA
1 CTCACACGAGCTATGAAATGAGCCAA
* *
54377489 CTTACACGAGCTATGAAATGGGCCAA
1 CTCACACGAGCTATGAAATGAGCCAA
*
54377515 CTCATACGAGCT
1 CTCACACGAGCT
54377527 GTGGGTCAGA
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.34, C:0.25, G:0.19, T:0.22
Consensus pattern (26 bp):
CTCACACGAGCTATGAAATGAGCCAA
Found at i:54380497 original size:49 final size:49
Alignment explanation
Indices: 54380420--54380664 Score: 285
Period size: 49 Copynumber: 4.9 Consensus size: 49
54380410 TAGCCGAAGC
* *
54380420 TATCTGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAAT
1 TATCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGCGACCAAT
* * * *
54380469 TATAC-GGTACACGTAGTAGCCTACACTTAGTACTACACACGTGACCTAAC
1 TAT-CTGGTACACATAGTAGCCTGCACTTAGTACTACACACGCGACC-AAT
* * * * *
54380519 CATCTGATACACGTAGTAGCCTGCACTTAGTACTACACACGTGATCGAAGT
1 TATCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGCGA-CCAA-T
* * * *
54380570 TTTCAGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAAT
1 TATCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGCGACCAAT
* * *
54380619 TATCTGGTACACATAGTAGCCTACACTTAGTATTACACACGTGACC
1 TATCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGCGACC
54380665 TCACAATAGC
Statistics
Matches: 164, Mismatches: 27, Indels: 10
0.82 0.13 0.05
Matches are distributed among these distances:
49 80 0.49
50 47 0.29
51 37 0.23
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.26
Consensus pattern (49 bp):
TATCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGCGACCAAT
Found at i:54381346 original size:30 final size:30
Alignment explanation
Indices: 54381312--54381371 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
54381302 CTTTAATACG
54381312 AACTTTGGCAAAATTACTA-TTTTGCCCCTA
1 AACTTTGGCAAAATTAC-ACTTTTGCCCCTA
* * *
54381342 AACTTTTGCATAATTACACTTTTTCCCCTA
1 AACTTTGGCAAAATTACACTTTTGCCCCTA
54381372 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 1 0.04
30 25 0.96
ACGTcount: A:0.28, C:0.25, G:0.07, T:0.40
Consensus pattern (30 bp):
AACTTTGGCAAAATTACACTTTTGCCCCTA
Found at i:54390983 original size:43 final size:42
Alignment explanation
Indices: 54390919--54390999 Score: 117
Period size: 43 Copynumber: 1.9 Consensus size: 42
54390909 TCTGAACTCA
* **
54390919 TTCACCAGCATTTCGCCTGCTAGGCTTGAAGCCCGATATCAT
1 TTCACCAGCATTTAGCCTGCTAGGCCCGAAGCCCGATATCAT
*
54390961 TTCACCAGTATTATAGCCTGCTAGGCCCGAAGCCCGATA
1 TTCACCAGCATT-TAGCCTGCTAGGCCCGAAGCCCGATA
54391000 ATATTATTCA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
42 11 0.32
43 23 0.68
ACGTcount: A:0.23, C:0.31, G:0.20, T:0.26
Consensus pattern (42 bp):
TTCACCAGCATTTAGCCTGCTAGGCCCGAAGCCCGATATCAT
Found at i:54392675 original size:14 final size:15
Alignment explanation
Indices: 54392646--54392675 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
54392636 CAAAATTTAG
54392646 ACATGATACTTTCAC
1 ACATGATACTTTCAC
54392661 ACATGATAC-TTCAC
1 ACATGATACTTTCAC
54392675 A
1 A
54392676 TATAATAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.37, C:0.27, G:0.07, T:0.30
Consensus pattern (15 bp):
ACATGATACTTTCAC
Found at i:54393605 original size:52 final size:52
Alignment explanation
Indices: 54393543--54393647 Score: 183
Period size: 52 Copynumber: 2.0 Consensus size: 52
54393533 TCTTTCATTC
* *
54393543 ATGGTCTTACTCATCATACTTAGCTACCCTAACATCTTTCATCTATGGTTTT
1 ATGGTATTACTCATCATACTTAGCTACCATAACATCTTTCATCTATGGTTTT
*
54393595 ATGGTATTACTCATCATACTTGGCTACCATAACATCTTTCATCTATGGTTTT
1 ATGGTATTACTCATCATACTTAGCTACCATAACATCTTTCATCTATGGTTTT
54393647 A
1 A
54393648 CACCGACTAC
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 50 1.00
ACGTcount: A:0.25, C:0.23, G:0.10, T:0.42
Consensus pattern (52 bp):
ATGGTATTACTCATCATACTTAGCTACCATAACATCTTTCATCTATGGTTTT
Found at i:54397135 original size:48 final size:48
Alignment explanation
Indices: 54397083--54397180 Score: 151
Period size: 48 Copynumber: 2.0 Consensus size: 48
54397073 TCTGAGTATG
* * *
54397083 TGCCTGTGTAAGACCATGTCTGGGACACGGCATCGGTGATAATATGTA
1 TGCCTATGTAAGACCATGTCTGGGACACGGCATCAGCGATAATATGTA
* *
54397131 TGCCTATGTAAGACCATGTTTGGGACATGGCATCAGCGATAATATGTA
1 TGCCTATGTAAGACCATGTCTGGGACACGGCATCAGCGATAATATGTA
54397179 TG
1 TG
54397181 TGTGACAGCC
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
48 45 1.00
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.29
Consensus pattern (48 bp):
TGCCTATGTAAGACCATGTCTGGGACACGGCATCAGCGATAATATGTA
Found at i:54399131 original size:40 final size:39
Alignment explanation
Indices: 54399074--54399260 Score: 168
Period size: 39 Copynumber: 4.7 Consensus size: 39
54399064 TTGAATGATG
*
54399074 TCCGGGCTAAG-TCCCGAAGGC-TTTGTGCTAAG-TGACCATA
1 TCCGGACTAAGAT-CCGAAGGCATTTGTGC-AAGAT-ACCA-A
* *
54399114 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAA
1 TCCGGACTAAGATCCGAAGGCATTTGTGCAAGATACCAA
* *
54399153 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAA
1 TCCGGACTAAGATCCGAAGGCATTTGTGCAAGATACCAA
* * * * *
54399192 TTCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 -TCCGGACTAAGATCCGAAGGCATTTGTGCAAGATAC-CAA
**
54399232 TCCGGGTTAAG-TCCCGAAGGCATTTGTGC
1 TCCGGACTAAGAT-CCGAAGGCATTTGTGC
54399261 GAATTACTAT
Statistics
Matches: 132, Mismatches: 9, Indels: 12
0.86 0.06 0.08
Matches are distributed among these distances:
39 72 0.55
40 51 0.39
41 9 0.07
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (39 bp):
TCCGGACTAAGATCCGAAGGCATTTGTGCAAGATACCAA
Found at i:54399234 original size:79 final size:79
Alignment explanation
Indices: 54399074--54399297 Score: 253
Period size: 79 Copynumber: 2.8 Consensus size: 79
54399064 TTGAATGATG
* * * * * *
54399074 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGAT-CCGAAGGCAT
1 TCCGGACTAAGTCCCGAAGGCATTTGTGCGAA-TTACTATAACCGGGCTAAG-TCCCGAAGGCAT
54399137 TTGTGCGAGATACTAA
64 TTGTGCGAGATACTAA
*
54399153 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGA-TACTA-ATTCCGGGCTAAG-CCCGAAGGCA
1 TCCGGACTAAG-TCCCGAAGGCATTTGTGCGA-ATTACTATA-ACCGGGCTAAGTCCCGAAGGCA
*
54399214 TTTGTGCGAGTTACTAAA
63 TTTGTGCGAGATACT-AA
** *
54399232 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAATTACTATAACCGGGCTATGTCCCGAAGGCATTT
1 TCCGGACTAAGTCCCGAAGGCATTTGTGCGAATTACTATAACCGGGCTAAGTCCCGAAGGCATTT
54399297 G
66 G
54399298 AACGAGGAGC
Statistics
Matches: 125, Mismatches: 10, Indels: 19
0.81 0.06 0.12
Matches are distributed among these distances:
78 26 0.21
79 74 0.59
80 24 0.19
81 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (79 bp):
TCCGGACTAAGTCCCGAAGGCATTTGTGCGAATTACTATAACCGGGCTAAGTCCCGAAGGCATTT
GTGCGAGATACTAA
Found at i:54399261 original size:40 final size:40
Alignment explanation
Indices: 54399074--54399297 Score: 262
Period size: 40 Copynumber: 5.7 Consensus size: 40
54399064 TTGAATGATG
* * * *
54399074 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* *
54399114 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACT-AA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
* * *
54399153 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
54399193 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
54399232 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAATTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
54399273 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
54399298 AACGAGGAGC
Statistics
Matches: 164, Mismatches: 14, Indels: 12
0.86 0.07 0.06
Matches are distributed among these distances:
39 73 0.45
40 81 0.49
41 10 0.06
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:54399319 original size:79 final size:77
Alignment explanation
Indices: 54399081--54399330 Score: 233
Period size: 79 Copynumber: 3.2 Consensus size: 77
54399071 ATGTCCGGGC
* * * *
54399081 TAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGAT-CCGAAGGCATTTGTGCG
1 TAAGTCCCGAAGGCATTTGTGCGAA-TTACTATATCCGGGCTAAG-TCCCGAAGGCATTTGTGCG
* *
54399144 AGATACTAATCCGGAC
64 AG-GACTAATCCGG-T
54399160 TAAGAT-CCGAAGGCATTTGTGCGAGA-TACTA-ATTCCGGGCTAAG-CCCGAAGGCATTTGTGC
1 TAAG-TCCCGAAGGCATTTGTGCGA-ATTACTATA-TCCGGGCTAAGTCCCGAAGGCATTTGTGC
*
54399221 GAGTTACTAAATCCGGGT
63 GAG-GACT-AATCC-GGT
* * **
54399239 TAAGTCCCGAAGGCATTTGTGCGAATTACTATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG
1 TAAGTCCCGAAGGCATTTGTGCGAATTACTATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAG
54399304 GAGCTATATCCGGT
66 GA-CTA-ATCCGGT
* *
54399318 TAAATTCCGAAGG
1 TAAGTCCCGAAGG
54399331 TACGTGATTT
Statistics
Matches: 145, Mismatches: 13, Indels: 26
0.79 0.07 0.14
Matches are distributed among these distances:
78 26 0.18
79 82 0.57
80 36 0.25
81 1 0.01
ACGTcount: A:0.28, C:0.21, G:0.26, T:0.25
Consensus pattern (77 bp):
TAAGTCCCGAAGGCATTTGTGCGAATTACTATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAG
GACTAATCCGGT
Found at i:54402473 original size:40 final size:38
Alignment explanation
Indices: 54402339--54402525 Score: 241
Period size: 39 Copynumber: 4.8 Consensus size: 38
54402329 ATTTGAATGA
* *
54402339 TATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGATTT
1 TATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGA--T
* *
54402379 TATCCGGG-TAAGACCCGAAGGCATTTATGCTAGTGAT
1 TATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGAT
*
54402416 TTTCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGAT
1 TATCCGGGCTAAGACCCGAAGGCATTTGTGCGAG-TGAT
*
54402455 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCT
1 -TATCCGGGCTAAGACCCGAAGGCATTTGTGCGAG-TGAT
* * *
54402495 TACCCGGGTTAAGACCCGAAGGCAATTGTGC
1 TATCCGGGCTAAGACCCGAAGGCATTTGTGC
54402526 TTGTGGTTAT
Statistics
Matches: 134, Mismatches: 10, Indels: 7
0.89 0.07 0.05
Matches are distributed among these distances:
37 8 0.06
38 23 0.17
39 58 0.43
40 45 0.34
ACGTcount: A:0.23, C:0.21, G:0.29, T:0.27
Consensus pattern (38 bp):
TATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGAT
Found at i:54410758 original size:40 final size:40
Alignment explanation
Indices: 54410699--54410910 Score: 268
Period size: 40 Copynumber: 5.3 Consensus size: 40
54410689 CATTTGAATG
*
54410699 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
* * *
54410739 TTATCCGGGTTAAGACCCGAAGGCATTTATGCTAGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
* *
54410779 TTATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGA-T
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAG-TGATT
* *
54410819 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAG-TGATT
* * * * *
54410859 ATACCCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
54410899 ATATCC-GGCTAA
1 ATATCCGGGCTAA
54410911 ATTCCGAAGA
Statistics
Matches: 153, Mismatches: 16, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
39 7 0.05
40 143 0.93
41 3 0.02
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.28
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
Found at i:54412356 original size:50 final size:50
Alignment explanation
Indices: 54412276--54412415 Score: 235
Period size: 50 Copynumber: 2.8 Consensus size: 50
54412266 TGTTGCAGTA
* * *
54412276 TGCCTGTGTAAGACCATGTCTAGGACATGGCATTGGCGATAATATATATG
1 TGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCGATAATATATATG
*
54412326 TGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGTGATAATATATATG
1 TGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCGATAATATATATG
*
54412376 TGCCAGTGTAAGATCATGTCTGGGACATGGCATCGGCGAT
1 TGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCGAT
54412416 GATGTGTGGA
Statistics
Matches: 84, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
50 84 1.00
ACGTcount: A:0.26, C:0.17, G:0.29, T:0.28
Consensus pattern (50 bp):
TGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCGATAATATATATG
Found at i:54416281 original size:39 final size:38
Alignment explanation
Indices: 54416229--54416302 Score: 94
Period size: 39 Copynumber: 1.9 Consensus size: 38
54416219 ATGCCAACGT
* * *
54416229 CCCAGACATGGTCTTACATGTAATCAAATATCGATGCCG
1 CCCAGACAGGGTCTTACACGAAATCAAATAT-GATGCCG
* *
54416268 CCCAGATAGGGTCTTACACGAAATCATATATGATG
1 CCCAGACAGGGTCTTACACGAAATCAAATATGATG
54416303 TCAATGTCCC
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
38 4 0.13
39 26 0.87
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.26
Consensus pattern (38 bp):
CCCAGACAGGGTCTTACACGAAATCAAATATGATGCCG
Found at i:54418264 original size:37 final size:36
Alignment explanation
Indices: 54418213--54418320 Score: 107
Period size: 37 Copynumber: 2.9 Consensus size: 36
54418203 ATTCCAAAAA
*
54418213 TAATATTATTTTAATAGTTTAATATTAAATTTAAT-T
1 TAATATTATCTTAATAGTTTAATATT-AATTTAATAT
*
54418249 TAATACTTATCTTAATAGTATT-TTATTAATTTAATAT
1 TAATA-TTATCTTAATAGT-TTAATATTAATTTAATAT
*
54418286 TAACCTAATTATCTTAA-ATTTTAAT-TTAATTTAAT
1 TAA--T-ATTATCTTAATAGTTTAATATTAATTTAAT
54418321 GTTTAAATAT
Statistics
Matches: 61, Mismatches: 4, Indels: 13
0.78 0.05 0.17
Matches are distributed among these distances:
36 13 0.21
37 32 0.52
38 5 0.08
39 10 0.16
40 1 0.02
ACGTcount: A:0.40, C:0.05, G:0.02, T:0.54
Consensus pattern (36 bp):
TAATATTATCTTAATAGTTTAATATTAATTTAATAT
Found at i:54427112 original size:20 final size:18
Alignment explanation
Indices: 54427088--54427134 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 18
54427078 ATTCTCATTG
*
54427088 AATTAATAAAATTATACTT
1 AATTAATAAAAATATA-TT
54427107 AGATT-ATAAAAATATATT
1 A-ATTAATAAAAATATATT
*
54427125 ATTTAATAAA
1 AATTAATAAA
54427135 TTTAAAATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
17 2 0.08
18 8 0.33
19 11 0.46
20 3 0.12
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (18 bp):
AATTAATAAAAATATATT
Found at i:54428007 original size:26 final size:26
Alignment explanation
Indices: 54427978--54428030 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
54427968 TTGTTTTCCA
54427978 TCTTTTATCCAATTATTCTCATTAAT
1 TCTTTTATCCAATTATTCTCATTAAT
54428004 TCTTTTATCCAATTATTCTCATTAAT
1 TCTTTTATCCAATTATTCTCATTAAT
54428030 T
1 T
54428031 TTTCCATACT
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:0.26, C:0.19, G:0.00, T:0.55
Consensus pattern (26 bp):
TCTTTTATCCAATTATTCTCATTAAT
Found at i:54441343 original size:29 final size:30
Alignment explanation
Indices: 54441281--54441343 Score: 76
Period size: 29 Copynumber: 2.1 Consensus size: 30
54441271 ATATTTATAT
* **
54441281 ATAAATAGATTTAAAAAGAAATGTACAATC
1 ATAAATAGATTTAAAAAGAAATATACAAAA
54441311 ATAAATAGATTT-AAAAGAAA-ATACATAAA
1 ATAAATAGATTTAAAAAGAAATATACA-AAA
54441340 ATAA
1 ATAA
54441344 TATAAAATCA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
28 4 0.14
29 13 0.45
30 12 0.41
ACGTcount: A:0.62, C:0.05, G:0.08, T:0.25
Consensus pattern (30 bp):
ATAAATAGATTTAAAAAGAAATATACAAAA
Found at i:54441461 original size:21 final size:20
Alignment explanation
Indices: 54441437--54441475 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
54441427 TTTTATAACG
54441437 AAACAATATAAATGATATACA
1 AAACAATATAAAT-ATATACA
*
54441458 AAACAATATATATATATA
1 AAACAATATAAATATATA
54441476 TATATATGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.62, C:0.08, G:0.03, T:0.28
Consensus pattern (20 bp):
AAACAATATAAATATATACA
Found at i:54442062 original size:12 final size:12
Alignment explanation
Indices: 54442045--54442072 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
54442035 GGATCTTCAT
54442045 GGGTAGTGGATC
1 GGGTAGTGGATC
54442057 GGGTAGTGGATC
1 GGGTAGTGGATC
54442069 GGGT
1 GGGT
54442073 TGAAACGTGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.14, C:0.07, G:0.54, T:0.25
Consensus pattern (12 bp):
GGGTAGTGGATC
Found at i:54444210 original size:19 final size:19
Alignment explanation
Indices: 54444169--54444210 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
54444159 GTAAAAATCT
*
54444169 AATGCAGATGATGCAATGC
1 AATGCAAATGATGCAATGC
*
54444188 AATGCAAATGCATGGAATG-
1 AATGCAAATG-ATGCAATGC
54444207 AATG
1 AATG
54444211 TAAAAGAAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 13 0.65
20 7 0.35
ACGTcount: A:0.40, C:0.12, G:0.26, T:0.21
Consensus pattern (19 bp):
AATGCAAATGATGCAATGC
Found at i:54444726 original size:275 final size:275
Alignment explanation
Indices: 54444235--54444788 Score: 966
Period size: 275 Copynumber: 2.0 Consensus size: 275
54444225 GTGTTGATTT
*
54444235 TAAATTCAATTCTATTAGAACAACTTTTCTAGAAAACAAATTCCTTTACATAAAACAGATTACAT
1 TAAATTCAATTCTATTAGAACAACTTTTCTAGAAAAAAAATTCCTTTACATAAAACAGATTACAT
54444300 ATACGGCATTAACTTCATATTCTAGGCGAAGTCACCGATCCCTTTTCTTCGTAAAAGTCAAATCA
66 ATACGGCATTAACTTCATATTCTAGGCGAAGTCACCGATCCCTTTTCTTCGTAAAAGTCAAATCA
* *
54444365 GCCAAGCTTCCAATAAATGCATCCACTAGCTCCTTTTTGCTTGATCCAGGCTTCAACTTATTGTC
131 GCCAAGCTTCCAATAAATGCATCCACTAGCTCCTTTTTGCTTGATCCAGACTGCAACTTATTGTC
* * *
54444430 CTTGCGATGTTGATTAGCTCCTTTAAGAAAGTCGGGACGCGACGGCTCTTGAATAATCTTTATCA
196 CTTGCGATGTTGATTAGCTCCTTTAAGAAAGTCGGGACACGACGACTCTCGAATAATCTTTATCA
*
54444495 TCTTGAATCCTCAGG
261 GCTTGAATCCTCAGG
54444510 TAAATTCAATTCTATTAGAACAACTTTTCTAGAAAAAAAATTCCTTTACATAAAACAGATTACAT
1 TAAATTCAATTCTATTAGAACAACTTTTCTAGAAAAAAAATTCCTTTACATAAAACAGATTACAT
* * *
54444575 ATACGGCCTTGACTTCATATTCTAGGCGAAGTCATCGATCCCTTTTCTTCGTAAAAGTCAAATC-
66 ATACGGCATTAACTTCATATTCTAGGCGAAGTCACCGATCCCTTTTCTTCGTAAAAGTCAAATCA
* * *
54444639 GTGCAAGCTTCCAATAAATGCATCCACTAGCTCCTTTTTGCTTGATCCAGACTGCGACTTGTTGT
131 G-CCAAGCTTCCAATAAATGCATCCACTAGCTCCTTTTTGCTTGATCCAGACTGCAACTTATTGT
*
54444704 CCTTGCGATGTTGATTAGCTCCTTTAAGAAAGTCGGGACATGACGACTCTCGAATAATCTTTATC
195 CCTTGCGATGTTGATTAGCTCCTTTAAGAAAGTCGGGACACGACGACTCTCGAATAATCTTTATC
54444769 AGCTTGAATCCTCAGG
260 AGCTTGAATCCTCAGG
54444785 TAAA
1 TAAA
54444789 ATCTTGTTTT
Statistics
Matches: 264, Mismatches: 14, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
274 1 0.00
275 263 1.00
ACGTcount: A:0.30, C:0.22, G:0.15, T:0.33
Consensus pattern (275 bp):
TAAATTCAATTCTATTAGAACAACTTTTCTAGAAAAAAAATTCCTTTACATAAAACAGATTACAT
ATACGGCATTAACTTCATATTCTAGGCGAAGTCACCGATCCCTTTTCTTCGTAAAAGTCAAATCA
GCCAAGCTTCCAATAAATGCATCCACTAGCTCCTTTTTGCTTGATCCAGACTGCAACTTATTGTC
CTTGCGATGTTGATTAGCTCCTTTAAGAAAGTCGGGACACGACGACTCTCGAATAATCTTTATCA
GCTTGAATCCTCAGG
Found at i:54446970 original size:23 final size:20
Alignment explanation
Indices: 54446933--54446978 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 20
54446923 TTTTATAACG
*
54446933 AAACAATATAAATGATATACA
1 AAACAATATAAATGA-ATAAA
54446954 AAACAATATATATATGAATAAA
1 AAACAATATA-A-ATGAATAAA
54446976 AAA
1 AAA
54446979 TATACATAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 10 0.45
22 8 0.36
23 4 0.18
ACGTcount: A:0.65, C:0.07, G:0.04, T:0.24
Consensus pattern (20 bp):
AAACAATATAAATGAATAAA
Found at i:54448487 original size:14 final size:15
Alignment explanation
Indices: 54448468--54448496 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
54448458 TTGGACTTTA
54448468 ATTTTGGTTT-TTTT
1 ATTTTGGTTTATTTT
54448482 ATTTTGGTTTATTTT
1 ATTTTGGTTTATTTT
54448497 GTTTATTTGG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.10, C:0.00, G:0.14, T:0.76
Consensus pattern (15 bp):
ATTTTGGTTTATTTT
Found at i:54448505 original size:18 final size:17
Alignment explanation
Indices: 54448475--54448513 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
54448465 TTAATTTTGG
54448475 TTTTTTTATTTTGGTTT
1 TTTTTTTATTTTGGTTT
54448492 ATTTTGTTTA-TTTGGTTT
1 -TTTT-TTTATTTTGGTTT
54448510 TTTT
1 TTTT
54448514 AGGCCCGGGC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 4 0.20
18 12 0.60
19 4 0.20
ACGTcount: A:0.08, C:0.00, G:0.13, T:0.79
Consensus pattern (17 bp):
TTTTTTTATTTTGGTTT
Found at i:54451750 original size:22 final size:22
Alignment explanation
Indices: 54451725--54451772 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
54451715 AATTAATTCT
54451725 AAATAAAATTTA-ATTAA-CAATA
1 AAAT-AAATTTATATTAATCAA-A
*
54451747 AAATTAATTTATATTAATCAAA
1 AAATAAATTTATATTAATCAAA
54451769 AAAT
1 AAAT
54451773 GAGATAAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
21 6 0.26
22 14 0.61
23 3 0.13
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.35
Consensus pattern (22 bp):
AAATAAATTTATATTAATCAAA
Found at i:54453240 original size:17 final size:19
Alignment explanation
Indices: 54453214--54453250 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 19
54453204 AAGTAGGCAA
54453214 AAAAAAATTA-T-TAATTT
1 AAAAAAATTAGTATAATTT
*
54453231 AAAAAGATTAGTATAATTT
1 AAAAAAATTAGTATAATTT
54453250 A
1 A
54453251 GATACCATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 9 0.53
18 1 0.06
19 7 0.41
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (19 bp):
AAAAAAATTAGTATAATTT
Found at i:54458683 original size:15 final size:15
Alignment explanation
Indices: 54458635--54458684 Score: 73
Period size: 15 Copynumber: 3.3 Consensus size: 15
54458625 TTTATCAAAT
54458635 TTATATTGATTGAAA
1 TTATATTGATTGAAA
* * *
54458650 TCATTTTGATTGAAT
1 TTATATTGATTGAAA
54458665 TTATATTGATTGAAA
1 TTATATTGATTGAAA
54458680 TTATA
1 TTATA
54458685 ATATATATAT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.36, C:0.02, G:0.12, T:0.50
Consensus pattern (15 bp):
TTATATTGATTGAAA
Found at i:54459347 original size:18 final size:19
Alignment explanation
Indices: 54459326--54459366 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
54459316 AATGAAATGA
54459326 GAAATTGA-AT-TGAGAATT
1 GAAATTGAGATATGAG-ATT
54459344 GAAATTGAGATATGAGATT
1 GAAATTGAGATATGAGATT
54459363 GAAA
1 GAAA
54459367 ATATGAACCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 9 0.43
20 4 0.19
ACGTcount: A:0.46, C:0.00, G:0.24, T:0.29
Consensus pattern (19 bp):
GAAATTGAGATATGAGATT
Found at i:54464071 original size:29 final size:30
Alignment explanation
Indices: 54464033--54464091 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
54464023 CTGATAATAA
54464033 CATAGCCATGT-CCAGACATGGTCTTACAT
1 CATAGCCATGTCCCAGACATGGTCTTACAT
54464062 CATAGCCATGTCCCAGACATGGTCTTACAT
1 CATAGCCATGTCCCAGACATGGTCTTACAT
54464092 GTGGATGTGA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 11 0.38
30 18 0.62
ACGTcount: A:0.27, C:0.29, G:0.17, T:0.27
Consensus pattern (30 bp):
CATAGCCATGTCCCAGACATGGTCTTACAT
Found at i:54464184 original size:50 final size:50
Alignment explanation
Indices: 54464121--54464320 Score: 265
Period size: 50 Copynumber: 3.9 Consensus size: 50
54464111 ATGATCGTCT
* *
54464121 GGTGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTC
1 GGTGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTC
* * *
54464171 GGTGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTC
1 GGTGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTC
* *
54464221 GGTGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAA
1 GGTGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTC---ATC-T-C
* *
54464276 GGATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 GG-TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCT
54464321 TTACCCAAAT
Statistics
Matches: 131, Mismatches: 13, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
50 87 0.66
53 2 0.02
54 1 0.01
55 2 0.02
56 39 0.30
ACGTcount: A:0.20, C:0.30, G:0.24, T:0.26
Consensus pattern (50 bp):
GGTGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTC
Found at i:54464235 original size:100 final size:103
Alignment explanation
Indices: 54464115--54464320 Score: 321
Period size: 100 Copynumber: 2.0 Consensus size: 103
54464105 GTCTTCATGA
* *
54464115 TCGTCTGGTGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTC-ATC-T-CGG-TGC
1 TCGTCTGGTGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGGATGC
54464176 CAACGCCATGTCCCAGACATGGTCTTACATGGGACCTC
66 CAACGCCATGTCCCAGACATGGTCTTACATGGGACCTC
54464214 TCGTCTCGGTGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGGA
1 TCGTCT-GGTGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCA--ATCTTAAGGA
* *
54464279 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTC
63 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTC
54464320 T
1 T
54464321 TTACCCAAAT
Statistics
Matches: 96, Mismatches: 4, Indels: 7
0.90 0.04 0.07
Matches are distributed among these distances:
99 6 0.06
100 44 0.46
103 3 0.03
104 1 0.01
105 2 0.02
106 40 0.42
ACGTcount: A:0.19, C:0.31, G:0.24, T:0.26
Consensus pattern (103 bp):
TCGTCTGGTGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGGATGC
CAACGCCATGTCCCAGACATGGTCTTACATGGGACCTC
Found at i:54464436 original size:13 final size:13
Alignment explanation
Indices: 54464415--54464446 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
54464405 GCTTGGATCA
*
54464415 TCATCAAATAAAT
1 TCATAAAATAAAT
54464428 TCATAAAATAAAT
1 TCATAAAATAAAT
54464441 TCATAA
1 TCATAA
54464447 TTGCTGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:54471366 original size:50 final size:50
Alignment explanation
Indices: 54471302--54471501 Score: 247
Period size: 50 Copynumber: 3.9 Consensus size: 50
54471292 TCATCGATGT
* *
54471302 GGTGCCCATTCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTC
1 GGTGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTC
* * *
54471352 GGTGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTC
1 GGTGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTC
* * *
54471402 GGTGCCCATGCCATGTCCCAGACATAGTCTTACAGGGGACCTCTCATGATCTTAA
1 GGTGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTC---ATC-T-C
* * *
54471457 GGATGCCAATGCCATGTCCTAGACATGGTCTTACATGGGATCTCT
1 GG-TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCT
54471502 TTACCCAAAT
Statistics
Matches: 128, Mismatches: 16, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
50 86 0.67
53 2 0.02
54 1 0.01
55 2 0.02
56 37 0.29
ACGTcount: A:0.20, C:0.30, G:0.23, T:0.26
Consensus pattern (50 bp):
GGTGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTC
Found at i:54471422 original size:100 final size:104
Alignment explanation
Indices: 54471302--54471501 Score: 300
Period size: 100 Copynumber: 1.9 Consensus size: 104
54471292 TCATCGATGT
* * *
54471302 GGTGCCCATTCCATGTCCCAGACATGGTCTTACAGGGGACCTCTC-ATC-T-CGG-TGCCAACGC
1 GGTGCCCATGCCATGTCCCAGACATAGTCTTACAGGGGACCTCTCAATCTTAAGGATGCCAACGC
54471363 CATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTC
66 CATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTC
*
54471402 GGTGCCCATGCCATGTCCCAGACATAGTCTTACAGGGGACCTCTCATGATCTTAAGGATGCCAAT
1 GGTGCCCATGCCATGTCCCAGACATAGTCTTACAGGGGACCTCTCA--ATCTTAAGGATGCCAAC
* *
54471467 GCCATGTCCTAGACATGGTCTTACATGGGATCTCT
64 GCCATGTCCCAGACATGGTCTTACATGGGACCTCT
54471502 TTACCCAAAT
Statistics
Matches: 88, Mismatches: 6, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
100 43 0.49
103 3 0.03
104 1 0.01
105 2 0.02
106 39 0.44
ACGTcount: A:0.20, C:0.30, G:0.23, T:0.26
Consensus pattern (104 bp):
GGTGCCCATGCCATGTCCCAGACATAGTCTTACAGGGGACCTCTCAATCTTAAGGATGCCAACGC
CATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTC
Found at i:54471617 original size:13 final size:13
Alignment explanation
Indices: 54471596--54471627 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
54471586 GCTTGGATCA
*
54471596 TCATCAAATAAAT
1 TCATAAAATAAAT
54471609 TCATAAAATAAAT
1 TCATAAAATAAAT
54471622 TCATAA
1 TCATAA
54471628 TTGCTGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:54474005 original size:15 final size:15
Alignment explanation
Indices: 54473957--54474006 Score: 73
Period size: 15 Copynumber: 3.3 Consensus size: 15
54473947 TTTGTCAAAT
54473957 TTATATTGATTGAAA
1 TTATATTGATTGAAA
* * *
54473972 TCATTTTGATTGAAT
1 TTATATTGATTGAAA
54473987 TTATATTGATTGAAA
1 TTATATTGATTGAAA
54474002 TTATA
1 TTATA
54474007 ATATATATAT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.36, C:0.02, G:0.12, T:0.50
Consensus pattern (15 bp):
TTATATTGATTGAAA
Found at i:54474661 original size:18 final size:19
Alignment explanation
Indices: 54474640--54474680 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
54474630 AATGAAATGA
54474640 GAAATTGA-AT-TGAGAATT
1 GAAATTGAGATATGAG-ATT
54474658 GAAATTGAGATATGAGATT
1 GAAATTGAGATATGAGATT
54474677 GAAA
1 GAAA
54474681 ATATGAACCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 9 0.43
20 4 0.19
ACGTcount: A:0.46, C:0.00, G:0.24, T:0.29
Consensus pattern (19 bp):
GAAATTGAGATATGAGATT
Found at i:54475990 original size:49 final size:49
Alignment explanation
Indices: 54475825--54476062 Score: 305
Period size: 49 Copynumber: 4.8 Consensus size: 49
54475815 TGAGGTTGCA
* * *
54475825 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGAAAATTGTGATCACG
1 TGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAATTG-G-TCACG
* * * **
54475876 TGTGTAGTACTAAGTTCAGGCTACTACGTGTATCAGATGGTTAGGTCACG
1 TGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAATT-GGTCACG
*
54475926 TGTGTAGTACTAAGTGCAGGCTACTATGTGTACCGGATAATTGGTCACG
1 TGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAATTGGTCACG
* * * * *
54475975 TGTGTAGTACTAAGTGCAGACTACTACGTGTACCGGATAATTGGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAATTGGTCACG
* *
54476024 TGTGTAGTACTATGTGCAGGCTACTATGCGTACCAGATA
1 TGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATA
54476063 GCTTTGGCTA
Statistics
Matches: 163, Mismatches: 23, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
49 86 0.53
50 41 0.25
51 35 0.21
52 1 0.01
ACGTcount: A:0.26, C:0.18, G:0.27, T:0.30
Consensus pattern (49 bp):
TGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAATTGGTCACG
Found at i:54482481 original size:58 final size:57
Alignment explanation
Indices: 54482373--54482483 Score: 154
Period size: 58 Copynumber: 1.9 Consensus size: 57
54482363 AAGAATGTTA
* *
54482373 TTAAATTATATATTTTTTTATTAAATTATATTTAATAATAATTATGTTAAAATATGG
1 TTAAACTATATATTTTTTTATTAAATTATATTTAATAATAATTATATTAAAATATGG
*
54482430 TTAAACTATTTATTATTTTTATTAAATTAT-TTTAAATAATAATCT-TATTAAAAT
1 TTAAACTATATATT-TTTTTATTAAATTATATTT-AATAATAAT-TATATTAAAAT
54482484 TTAATAACAA
Statistics
Matches: 48, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
57 15 0.31
58 32 0.67
59 1 0.02
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.53
Consensus pattern (57 bp):
TTAAACTATATATTTTTTTATTAAATTATATTTAATAATAATTATATTAAAATATGG
Found at i:54482681 original size:16 final size:16
Alignment explanation
Indices: 54482651--54482721 Score: 72
Period size: 16 Copynumber: 4.4 Consensus size: 16
54482641 TTGAATTACT
*
54482651 AATTACAACTCTATTTC
1 AATTACAGCTCTA-TTC
*
54482668 -ATTACAGCTTTATTC
1 AATTACAGCTCTATTC
* *
54482683 AATTACAGCTCCATCC
1 AATTACAGCTCTATTC
*
54482699 AATTACAGCCCTATTC
1 AATTACAGCTCTATTC
*
54482715 CATTACA
1 AATTACA
54482722 ATGAACCAAA
Statistics
Matches: 44, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
15 3 0.07
16 41 0.93
ACGTcount: A:0.32, C:0.28, G:0.04, T:0.35
Consensus pattern (16 bp):
AATTACAGCTCTATTC
Found at i:54483146 original size:22 final size:21
Alignment explanation
Indices: 54483111--54483151 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
54483101 AGAAGAAAAG
54483111 AAAACCAAAATTGTCCAGAAA
1 AAAACCAAAATTGTCCAGAAA
* *
54483132 AAAACTCAAATTTGTGCAGA
1 AAAAC-CAAAATTGTCCAGA
54483152 GATTTGAAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.51, C:0.17, G:0.12, T:0.20
Consensus pattern (21 bp):
AAAACCAAAATTGTCCAGAAA
Found at i:54485608 original size:22 final size:22
Alignment explanation
Indices: 54485571--54485617 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 22
54485561 CTTTGATCAC
54485571 ATACAAAATTTACATTCA-CAA
1 ATACAAAATTTACATTCAGCAA
* *
54485592 ATACCAAATTTACCATTTAGCAA
1 ATACAAAATTTA-CATTCAGCAA
54485615 ATA
1 ATA
54485618 GCATCATAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 11 0.50
22 5 0.23
23 6 0.27
ACGTcount: A:0.49, C:0.19, G:0.02, T:0.30
Consensus pattern (22 bp):
ATACAAAATTTACATTCAGCAA
Found at i:54491394 original size:7 final size:7
Alignment explanation
Indices: 54491382--54491407 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
54491372 TTTGATTTTG
54491382 TTCTTAT
1 TTCTTAT
54491389 TTCTTAT
1 TTCTTAT
54491396 TTCTTAT
1 TTCTTAT
54491403 TTCTT
1 TTCTT
54491408 CTTTATCCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.12, C:0.15, G:0.00, T:0.73
Consensus pattern (7 bp):
TTCTTAT
Found at i:54491803 original size:25 final size:25
Alignment explanation
Indices: 54491745--54491794 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
54491735 TTATAAAATG
*
54491745 TATGAAACGACGTCGTTTTAAGCCA
1 TATGAAATGACGTCGTTTTAAGCCA
54491770 TATGAAATGACGTCGTTTTAAGCCA
1 TATGAAATGACGTCGTTTTAAGCCA
54491795 ATCTCAATGG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30
Consensus pattern (25 bp):
TATGAAATGACGTCGTTTTAAGCCA
Found at i:54492466 original size:16 final size:18
Alignment explanation
Indices: 54492400--54492463 Score: 67
Period size: 21 Copynumber: 3.3 Consensus size: 18
54492390 GTACTTTATG
54492400 TATATTATTTAT-TCATATA
1 TATATTATTT-TGT-ATATA
54492419 TATATTATTTTGTATATCA
1 TATATTATTTTGTATAT-A
*
54492438 TTTATATTGTTTTGTATATA
1 --TATATTATTTTGTATATA
54492458 TATATT
1 TATATT
54492464 TTTACACTTA
Statistics
Matches: 40, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
18 11 0.28
19 12 0.30
20 1 0.03
21 16 0.40
ACGTcount: A:0.31, C:0.03, G:0.05, T:0.61
Consensus pattern (18 bp):
TATATTATTTTGTATATA
Found at i:54499192 original size:30 final size:30
Alignment explanation
Indices: 54499126--54499193 Score: 109
Period size: 30 Copynumber: 2.3 Consensus size: 30
54499116 GTCGAAACAC
* * *
54499126 ATTCTCATGCATATTGATTTAATCTCACAA
1 ATTCTCGTGCATATTAACTTAATCTCACAA
54499156 ATTCTCGTGCATATTAACTTAATCTCACAA
1 ATTCTCGTGCATATTAACTTAATCTCACAA
54499186 ATTCTCGT
1 ATTCTCGT
54499194 TCGTAATTCG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.31, C:0.22, G:0.07, T:0.40
Consensus pattern (30 bp):
ATTCTCGTGCATATTAACTTAATCTCACAA
Found at i:54501597 original size:30 final size:30
Alignment explanation
Indices: 54501553--54501609 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
54501543 GACGAGCTTT
*
54501553 GGGGCCAAAGTGTAAATATGTGAAAGTTTA
1 GGGGCAAAAGTGTAAATATGTGAAAGTTTA
* * *
54501583 GGGGCAAAATTGTAATTTTGTGAAAGT
1 GGGGCAAAAGTGTAAATATGTGAAAGT
54501610 ATGATTTATG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.35, C:0.05, G:0.30, T:0.30
Consensus pattern (30 bp):
GGGGCAAAAGTGTAAATATGTGAAAGTTTA
Found at i:54502032 original size:50 final size:50
Alignment explanation
Indices: 54501944--54502057 Score: 151
Period size: 50 Copynumber: 2.3 Consensus size: 50
54501934 AGATCCCGTA
* * *
54501944 TAAGACCATATCT--GGGATATGGCATTGGCATCGATATGTGAACCTATG
1 TAAGACCATGTCTGGGGGACATGGCATTGGCATCGATATGTGAACCCATG
* * *
54501992 TAAGACCATGTCTGGGGGACATGGCATTGGCATTGTTATGTGATCCCATG
1 TAAGACCATGTCTGGGGGACATGGCATTGGCATCGATATGTGAACCCATG
*
54502042 TAAGACCATGTTTGGG
1 TAAGACCATGTCTGGG
54502058 ACAGGACGCC
Statistics
Matches: 57, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
48 12 0.21
50 45 0.79
ACGTcount: A:0.25, C:0.17, G:0.28, T:0.30
Consensus pattern (50 bp):
TAAGACCATGTCTGGGGGACATGGCATTGGCATCGATATGTGAACCCATG
Found at i:54509489 original size:48 final size:48
Alignment explanation
Indices: 54509418--54509671 Score: 241
Period size: 48 Copynumber: 5.4 Consensus size: 48
54509408 GGGTTAATGA
* * * * ** * *
54509418 GATCCCGTATAAGACCATATCTGGGATATGGCATCAGCATCAATAAGT
1 GATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGATATGT
* * *
54509466 GATCCCATGTAATACCATGTCTGGGACATGTCATTGGCATCGTTATGT
1 GATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGATATGT
** * *
54509514 GATCTTATGTAAGACTATGTCTGGGACATGGCATTGGCATCGATATGA
1 GATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGATATGT
* *** * *
54509562 GAACATTGTGTAAGACCATAG-CTGGG-C-T---ATTGGCTTCAATATGT
1 GATC-CCATGTAAGACCAT-GTCTGGGACATGGCATTGGCATCGATATGT
*
54509606 GATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGATAAGT
1 GATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGATATGT
*
54509654 GGTCCCATGTAAGACCAT
1 GATCCCATGTAAGACCAT
54509672 ATCCGGGATT
Statistics
Matches: 166, Mismatches: 32, Indels: 16
0.78 0.15 0.07
Matches are distributed among these distances:
42 1 0.01
43 16 0.10
44 17 0.10
45 1 0.01
47 1 0.01
48 112 0.67
49 17 0.10
50 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.29
Consensus pattern (48 bp):
GATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGATATGT
Found at i:54511756 original size:43 final size:43
Alignment explanation
Indices: 54511696--54511860 Score: 192
Period size: 43 Copynumber: 3.9 Consensus size: 43
54511686 AAAGCTCATA
* * *
54511696 CAATGCC-ATATCCCAGACATGGTCATACATGTTATCATATAT
1 CAATGCCAATGTCCCAGACATGGTCTTACATGTAATCATATAT
* * *
54511738 CAATGCCAACGTCCCAGACGTGGTCTTACATGAAATCATATAAT
1 CAATGCCAATGTCCCAGACATGGTCTTACATGTAATCATAT-AT
** * *
54511782 -GGTGCCAATGTCCCCGACATGGTCTTACATGTAATCACA-AT
1 CAATGCCAATGTCCCAGACATGGTCTTACATGTAATCATATAT
*
54511823 ACAATGCTAATGTCCCAGACATGGTCTTACATGTAATC
1 -CAATGCCAATGTCCCAGACATGGTCTTACATGTAATC
54511861 TCATCTCAAT
Statistics
Matches: 102, Mismatches: 17, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
41 2 0.02
42 7 0.07
43 91 0.89
44 2 0.02
ACGTcount: A:0.32, C:0.25, G:0.16, T:0.28
Consensus pattern (43 bp):
CAATGCCAATGTCCCAGACATGGTCTTACATGTAATCATATAT
Found at i:54515440 original size:48 final size:48
Alignment explanation
Indices: 54515222--54515441 Score: 189
Period size: 48 Copynumber: 4.6 Consensus size: 48
54515212 CATAGTAGGG
* * * * * *
54515222 TGCCAATGCCATATCCCGGATATGGTCTTATATGGGACCACTTATAGA
1 TGCCAATGCCATATCCCAGACATGGTCTTACATGGGATCACATATCGA
** *
54515270 TGCCAATGCCATGCCCCAGACATGGTCTTACATGGGATCACACAT--A
1 TGCCAATGCCATATCCCAGACATGGTCTTACATGGGATCACATATCGA
* * * ** * *
54515316 T-CGAA-GCCGATAGCCCAGCCATGGTCTTACATAATGCTCTCATATCGA
1 TGCCAATGCC-ATATCCCAGACATGGTCTTACAT-GGGATCACATATCGA
* *
54515364 TGCCAATGCCATGTCCTGAGA-ATGGTCTTACATGGGATCACATATCGA
1 TGCCAATGCCATATCC-CAGACATGGTCTTACATGGGATCACATATCGA
* * *
54515412 TGCCGATGCCATATCCCAGATATTGTCTTA
1 TGCCAATGCCATATCCCAGACATGGTCTTA
54515442 TACGGGATGT
Statistics
Matches: 134, Mismatches: 30, Indels: 16
0.74 0.17 0.09
Matches are distributed among these distances:
44 3 0.02
45 23 0.17
46 9 0.07
47 3 0.02
48 72 0.54
49 19 0.14
50 5 0.04
ACGTcount: A:0.27, C:0.26, G:0.20, T:0.27
Consensus pattern (48 bp):
TGCCAATGCCATATCCCAGACATGGTCTTACATGGGATCACATATCGA
Found at i:54520745 original size:16 final size:16
Alignment explanation
Indices: 54520724--54520756 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
54520714 CTCACGCTCG
54520724 TATTCAGTTACACTCA
1 TATTCAGTTACACTCA
*
54520740 TATTCAGTTACAGTCA
1 TATTCAGTTACACTCA
54520756 T
1 T
54520757 TCTACCTTGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.30, C:0.21, G:0.09, T:0.39
Consensus pattern (16 bp):
TATTCAGTTACACTCA
Found at i:54522990 original size:48 final size:48
Alignment explanation
Indices: 54522667--54522991 Score: 311
Period size: 48 Copynumber: 6.8 Consensus size: 48
54522657 CATAGTAGGG
* * * * * * *
54522667 TGCCAATGCCATATCTCGGATATGGTCTTACATGGGACCACTTATCGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCACATAACGA
* * * * *
54522715 TGCCAATGCCATGCCCCAGACATTGTCTTACATGAGATCACA-CA-TA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCACATAACGA
* * ** ** *
54522761 T-CGAA-GCCGATAG-CCCAG-CTATGGTCTTACACGATACTTTCATATCGA
1 TGCCAATGCC-AT-GTCCCAGAC-ATGGTCTTACATGGGA-TCACATAACGA
*
54522809 TGCCAATGCCATGTCCCAGACATGGTCTTACATTGGATCACATAACGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCACATAACGA
54522857 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCACATAACGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCACATAACGA
* * * * *
54522905 TGCTAATACCATGTCCTAGACATGGTCTTACATGGGATCAAATATCGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCACATAACGA
* * * *
54522953 TGCCGATGCCATATCCCAGATATGGTCTTATATGGGATC
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATC
54522992 TCATCAACTC
Statistics
Matches: 225, Mismatches: 42, Indels: 20
0.78 0.15 0.07
Matches are distributed among these distances:
44 4 0.02
45 23 0.10
46 6 0.03
48 166 0.74
49 22 0.10
50 4 0.02
ACGTcount: A:0.28, C:0.26, G:0.19, T:0.27
Consensus pattern (48 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCACATAACGA
Found at i:54525214 original size:18 final size:18
Alignment explanation
Indices: 54525191--54525230 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
54525181 TCAAGAATAC
54525191 TTTATCA-TCAACTTGAAA
1 TTTATCATTCAA-TTGAAA
*
54525209 TTTATCATTGAATTGAAA
1 TTTATCATTCAATTGAAA
54525227 TTTA
1 TTTA
54525231 ATATCTTTAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 17 0.85
19 3 0.15
ACGTcount: A:0.38, C:0.10, G:0.07, T:0.45
Consensus pattern (18 bp):
TTTATCATTCAATTGAAA
Found at i:54532345 original size:46 final size:46
Alignment explanation
Indices: 54532253--54532381 Score: 186
Period size: 46 Copynumber: 2.8 Consensus size: 46
54532243 TGTAACCCGC
* * * * * *
54532253 CCATAAGCGAACTCAGACTCAACTCAATGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* *
54532299 CCATGAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
54532345 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
54532382 TGCTCAACCA
Statistics
Matches: 74, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 74 1.00
ACGTcount: A:0.29, C:0.28, G:0.22, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:54535660 original size:105 final size:100
Alignment explanation
Indices: 54535482--54535673 Score: 260
Period size: 105 Copynumber: 1.9 Consensus size: 100
54535472 GACAGATAAT
*
54535482 ACCATGGTTGGACAATGGCAATATTTAAATGTAAGACCATAGCTGGGCTATGGCATTTCAGTGAA
1 ACCATGGTTGGACAATGACAATATTTAAATGTAAGACCATAGCTGGGCTATGGCATTTCAGTGAA
54535547 AAGACCATAACTGGATTATGGCACCGTGAACGTAAG
66 AAGACCATAACTGG-TTATGGCACCGTGAACGTAAG
* * * *
54535583 ACCATGGTTGGACCATGACAGTATATGTATAAGTGTAAGACCATATCTGGGCTATGGCATCTTGA
1 ACCATGGTTGGACAATGACA--ATAT-T-TAAATGTAAGACCATAGCTGGGCTATGGCAT-TTCA
* *
54535648 -TGATAAGACCATAATTGGTTATGGCA
61 GTGAAAAGACCATAACTGGTTATGGCA
54535674 TTATGAGTGT
Statistics
Matches: 79, Mismatches: 7, Indels: 7
0.85 0.08 0.08
Matches are distributed among these distances:
101 18 0.23
103 4 0.05
104 9 0.11
105 45 0.57
106 3 0.04
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.27
Consensus pattern (100 bp):
ACCATGGTTGGACAATGACAATATTTAAATGTAAGACCATAGCTGGGCTATGGCATTTCAGTGAA
AAGACCATAACTGGTTATGGCACCGTGAACGTAAG
Found at i:54547804 original size:43 final size:42
Alignment explanation
Indices: 54547688--54547835 Score: 136
Period size: 43 Copynumber: 3.5 Consensus size: 42
54547678 TATCCTAGAT
* * * * * * *
54547688 ATGGTCTTACATGTTATCACATATCAATGCCACTGTGCCAGAT
1 ATGGTCTTACACGTAATCA-TTAACAATGCCAATGTCCCAGAC
* * *
54547731 AGGGTCTTACACGAAATCGATTAACGATGCCAATGTCCCAGAC
1 ATGGTCTTACACGTAATC-ATTAACAATGCCAATGTCCCAGAC
*
54547774 ATGGTCTTACACGTAATC-TTAATACAATGCCAATGTCCCAAAC
1 ATGGTCTTACACGTAATCATT-A-ACAATGCCAATGTCCCAGAC
* *
54547817 ATGGTTTTACATGTAATCA
1 ATGGTCTTACACGTAATCA
54547836 CATCTCAATA
Statistics
Matches: 85, Mismatches: 16, Indels: 7
0.79 0.15 0.06
Matches are distributed among these distances:
41 2 0.02
42 1 0.01
43 81 0.95
44 1 0.01
ACGTcount: A:0.32, C:0.23, G:0.16, T:0.29
Consensus pattern (42 bp):
ATGGTCTTACACGTAATCATTAACAATGCCAATGTCCCAGAC
Found at i:54558152 original size:25 final size:25
Alignment explanation
Indices: 54558120--54558189 Score: 95
Period size: 25 Copynumber: 2.8 Consensus size: 25
54558110 CTGTACATGT
54558120 ATGCTCACACGAGCTGTGAATCAAA
1 ATGCTCACACGAGCTGTGAATCAAA
* * * *
54558145 ATGTTCACACAAGCTGTGAATTAGA
1 ATGCTCACACGAGCTGTGAATCAAA
*
54558170 ATGCTCACACGAGCTATGAA
1 ATGCTCACACGAGCTGTGAA
54558190 AGTAGGCCTG
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 38 1.00
ACGTcount: A:0.36, C:0.21, G:0.20, T:0.23
Consensus pattern (25 bp):
ATGCTCACACGAGCTGTGAATCAAA
Found at i:54559729 original size:46 final size:45
Alignment explanation
Indices: 54559626--54559793 Score: 160
Period size: 46 Copynumber: 3.6 Consensus size: 45
54559616 CACATTATGA
*
54559626 AAGCTAGTGTAAGACCATGTCTGGGACATGGCATCAGCATTGAGATG
1 AAGCTAGTGTAAGA-CATGTCTGGGACAT-GCATCAGCATCGAGATG
* * * *
54559673 AGTGCTAGTGTAGGACATGTCTGGGACATGCATCTGCCTCGAGATG
1 A-AGCTAGTGTAAGACATGTCTGGGACATGCATCAGCATCGAGATG
* * * *
54559719 TAAGCCAGTGTAAGACATGTTTGGGACATGCGTCAGTTAT-GAGATG
1 -AAGCTAGTGTAAGACATGTCTGGGACATGCATCAG-CATCGAGATG
*
54559765 ATAG-TCAGTGTAAGACCATGTTTGGGACA
1 A-AGCT-AGTGTAAGA-CATGTCTGGGACA
54559794 CGGCATCAAC
Statistics
Matches: 101, Mismatches: 14, Indels: 12
0.80 0.11 0.09
Matches are distributed among these distances:
45 1 0.01
46 59 0.58
47 30 0.30
48 11 0.11
ACGTcount: A:0.27, C:0.16, G:0.30, T:0.26
Consensus pattern (45 bp):
AAGCTAGTGTAAGACATGTCTGGGACATGCATCAGCATCGAGATG
Done.