Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold32
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: 5587194
ACGTcount: A:0.26, C:0.15, G:0.16, T:0.26
Warning! 895791 characters in sequence are not A, C, G, or T
File 3 of 33
Found at i:397156 original size:51 final size:51
Alignment explanation
Indices: 397062--397159 Score: 124
Period size: 51 Copynumber: 1.9 Consensus size: 51
397052 CGAAATAACG
* *** * *
397062 GGGTTGGAGTATCCCCAATTGTGAAAAATTGGTGTTTTGGAAATAAAATTA
1 GGGTTAGAGTATCCCCAATTGTGAAAAATCAATATTTTAGAAATAAAATTA
* *
397113 GGGTTAGAGTATCCCCGATTGTGAGAAATCAATATTTTAGAAATAAA
1 GGGTTAGAGTATCCCCAATTGTGAAAAATCAATATTTTAGAAATAAA
397160 GCCGGGGTTG
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
51 39 1.00
ACGTcount: A:0.36, C:0.09, G:0.23, T:0.32
Consensus pattern (51 bp):
GGGTTAGAGTATCCCCAATTGTGAAAAATCAATATTTTAGAAATAAAATTA
Found at i:397508 original size:72 final size:72
Alignment explanation
Indices: 397419--397557 Score: 242
Period size: 72 Copynumber: 1.9 Consensus size: 72
397409 CGCGCTGTCC
* *
397419 CCCTTTCTAAATTTTGTTTGGGCTAATTTGGAGGTTTCAAAGAGCGGATGAGATACTGTTGGAAA
1 CCCTTTCTAAATTTTGTTTGAGCTAATTTAGAGGTTTCAAAGAGCGGATGAGATACTGTTGGAAA
397484 GACGTCT
66 GACGTCT
* *
397491 CCCTTTCTAAATTTTGTTTGAGCTGATTTAGAGGTTTTAAAGAGCGGATGAGATACTGTTGGAAA
1 CCCTTTCTAAATTTTGTTTGAGCTAATTTAGAGGTTTCAAAGAGCGGATGAGATACTGTTGGAAA
397556 GA
66 GA
397558 TGACTCGATT
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
72 63 1.00
ACGTcount: A:0.27, C:0.12, G:0.26, T:0.35
Consensus pattern (72 bp):
CCCTTTCTAAATTTTGTTTGAGCTAATTTAGAGGTTTCAAAGAGCGGATGAGATACTGTTGGAAA
GACGTCT
Found at i:402099 original size:13 final size:13
Alignment explanation
Indices: 402081--402119 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
402071 ATAATCCCCC
*
402081 TGTATCGATACAG
1 TGTATCGATACAA
402094 TGTATCGATACAA
1 TGTATCGATACAA
*
402107 TGTAGCGATACAA
1 TGTATCGATACAA
402120 AGAATGCTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.36, C:0.15, G:0.21, T:0.28
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:404214 original size:16 final size:16
Alignment explanation
Indices: 404181--404215 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
404171 ATCAATTTCG
404181 TTTGAAGCTTCCTCAT
1 TTTGAAGCTTCCTCAT
*
404197 TTTG-AGCTTCCTCAA
1 TTTGAAGCTTCCTCAT
404212 TTTG
1 TTTG
404216 GACATTTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 14 0.78
16 4 0.22
ACGTcount: A:0.17, C:0.23, G:0.14, T:0.46
Consensus pattern (16 bp):
TTTGAAGCTTCCTCAT
Found at i:405486 original size:79 final size:79
Alignment explanation
Indices: 405375--405581 Score: 236
Period size: 79 Copynumber: 2.6 Consensus size: 79
405365 GAGATAATAA
* * * * * * *
405375 CGGGGTTGGAGTGTTCCCTTGAAAATAACGGGGCTGGAGTATCCCCGGTTGTGAGAAATCGATGA
1 CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAAT-A
*
405440 -TTAGAAAAAAAAAT
65 TTTAGAAAAAAAAAC
* * *
405454 CGGGATTGGAGTATCCCCTCGAAAATAACGGGGTTAGAGTATCCCCAATTATGAGAAATCAATAT
1 CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATAT
* ** * *
405519 TTTGGGAATAAAGC
66 TTAGAAAAAAAAAC
* *
405533 CGGGGTTGGAGTATCCCCTCGGAAGTAACGGGGTTGGAGTATCCCCGAT
1 CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGAT
405582 GAAATAACAA
Statistics
Matches: 106, Mismatches: 21, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
78 1 0.01
79 105 0.99
ACGTcount: A:0.29, C:0.17, G:0.29, T:0.24
Consensus pattern (79 bp):
CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATAT
TTAGAAAAAAAAAC
Found at i:405589 original size:28 final size:28
Alignment explanation
Indices: 405533--405604 Score: 81
Period size: 28 Copynumber: 2.6 Consensus size: 28
405523 GGAATAAAGC
** *
405533 CGGGGTTGGAGTATCCCCTCGGAAGTAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
405561 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
** *
405589 CAAGGTTAGAGTATCC
1 CGGGGTTGGAGTATCC
405605 TCGACTGTGA
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.26, C:0.19, G:0.32, T:0.22
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGAGGAAATAA
Found at i:405860 original size:27 final size:26
Alignment explanation
Indices: 405796--405871 Score: 100
Period size: 27 Copynumber: 2.8 Consensus size: 26
405786 GAAATAAAGT
405796 CGGGGTTGGAGTATCCCCTCGGA-AATAA
1 CGGGGTTGGAGTAT-CCC-C-GATAATAA
*
405824 CGGGGTTGGAGTATCCCCGATGATCAA
1 CGGGGTTGGAGTATCCCCGATAAT-AA
405851 CGGGGTTGGAGTATCCCCGAT
1 CGGGGTTGGAGTATCCCCGAT
405872 TGTGAAGAAA
Statistics
Matches: 45, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
25 2 0.04
26 3 0.07
27 26 0.58
28 14 0.31
ACGTcount: A:0.21, C:0.22, G:0.34, T:0.22
Consensus pattern (26 bp):
CGGGGTTGGAGTATCCCCGATAATAA
Found at i:405953 original size:50 final size:53
Alignment explanation
Indices: 405597--405976 Score: 207
Period size: 52 Copynumber: 7.3 Consensus size: 53
405587 AACAAGGTTA
* * * * *
405597 GAGTATCCTCGACTGTGAA-AAATTGGTATTTTTGAAAATAAAATCGGAGTTG
1 GAGTATCCCCGATTATGAAGAAATTAGTGTTTTTGAAAATAAAATCGGAGTTG
* * * *
405649 GAGTATCCCCGATTA--AAGGAAAATTGGTG-TTTCGAAAATAAAACCGGGGTTG
1 GAGTATCCCCGATTATGAA-G-AAATTAGTGTTTTTGAAAATAAAATCGGAGTTG
* * * * *
405701 GAGTATCCCCGATTGTGGAA-AAATTAGTGTTTTAG-CAATAAAACCGGGGTTG
1 GAGTATCCCCGATTAT-GAAGAAATTAGTGTTTTTGAAAATAAAATCGGAGTTG
* * * * * * *
405753 GAATATCCCCGATTATGAA-AAATCAAT-ATTTTGGAAATAAAGTCGGGGTTG
1 GAGTATCCCCGATTATGAAGAAATTAGTGTTTTTGAAAATAAAATCGGAGTTG
* *** * **** ** * *
405804 GAGTATCCCCTCGGA-AAT-AACGGGGTTGGAGTATCCCCGATGAT-CAA-CGGGGTTG
1 GAGTAT-CCC-C-GATTATGAA-GAAATT--AGTGTTTTTGAAAATAAAATCGGAGTTG
* * *
405859 GAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTG
1 GAGTATCCCCGATTATGAAGAAATTAGTG-TTTTTGAAAATAAAATCGGAGTTG
405913 GAGTAT-CCCGATTAT--AGAAAATTAGTG-TTTTGAAAATAAAATCGGAGTTG
1 GAGTATCCCCGATTATGAAG-AAATTAGTGTTTTTGAAAATAAAATCGGAGTTG
*
405963 GAATATCCCCGATT
1 GAGTATCCCCGATT
405977 GTGGAGAATT
Statistics
Matches: 248, Mismatches: 57, Indels: 47
0.70 0.16 0.13
Matches are distributed among these distances:
50 33 0.13
51 39 0.16
52 103 0.42
53 30 0.12
54 21 0.08
55 16 0.06
56 3 0.01
57 3 0.01
ACGTcount: A:0.32, C:0.13, G:0.26, T:0.29
Consensus pattern (53 bp):
GAGTATCCCCGATTATGAAGAAATTAGTGTTTTTGAAAATAAAATCGGAGTTG
Found at i:408348 original size:13 final size:13
Alignment explanation
Indices: 408330--408355 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
408320 ACAAAGATGC
408330 ATGTATCGATACA
1 ATGTATCGATACA
408343 ATGTATCGATACA
1 ATGTATCGATACA
408356 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:415591 original size:79 final size:77
Alignment explanation
Indices: 415456--415758 Score: 281
Period size: 79 Copynumber: 3.9 Consensus size: 77
415446 AATAAAATTG
* * *
415456 GGGTTGGAGTAT-CTCTGATTACAGAAAATCGGTGTTTTGAAAATAAAGTCGAGGTTGGAGTATA
1 GGGTTGGAGTATCCTC-GATTATAGAAAATCGGTGTTTTAAAAATAAAATCGAGGTTGGAGTAT-
415520 CCCTCGGAAATAATA
64 CCCTCGGAAATAA-A
* *
415535 GGGTTGGAGTATCC-CTGATTATAGAAAATTGGTGTTTTAAAAATAAAATCGGGGTTGGAGTATC
1 GGGTTGGAGTATCCTC-GATTATAGAAAATCGGTGTTTTAAAAATAAAATCGAGGTTGGAGTAT-
* *
415599 CCCTCGAAAATAAC
64 CCCTCGGAAATAAA
* * * * * *** *
415613 GAGGTTAGAGTATCCTCGATTATGGAAAATCGATGCTTTAGAAATAAGGCCGAAGTTGGAGTATC
1 G-GGTTGGAGTATCCTCGATTATAGAAAATCGGTGTTTTAAAAATAAAATCGAGGTTGGAGTATC
*
415678 CC-CGTGAAAATAACG
65 CCTCG-G-AAATAA-A
* ** * * *
415693 GGGTTGGAGTATCCTCGATTGT-GAAAAATTTGTGTTTTAGAAATAAAATTGGGGTTGGAGTATC
1 GGGTTGGAGTATCCTCGATTATAG-AAAATCGGTGTTTTAAAAATAAAATCGAGGTTGGAGTATC
415757 CC
65 CC
415759 CGATTGTGAA
Statistics
Matches: 184, Mismatches: 33, Indels: 14
0.80 0.14 0.06
Matches are distributed among these distances:
77 2 0.01
78 5 0.03
79 174 0.95
80 3 0.02
ACGTcount: A:0.32, C:0.12, G:0.26, T:0.29
Consensus pattern (77 bp):
GGGTTGGAGTATCCTCGATTATAGAAAATCGGTGTTTTAAAAATAAAATCGAGGTTGGAGTATCC
CTCGGAAATAAA
Found at i:415750 original size:158 final size:158
Alignment explanation
Indices: 415457--415759 Score: 384
Period size: 158 Copynumber: 1.9 Consensus size: 158
415447 ATAAAATTGG
* * * * *
415457 GGTTGGAGTATCTCTGATTACAGAAAATCGGTGTTTTGAAAATAAAGTCGAGGTTGGAGTATACC
1 GGTTAGAGTATCTCTGATTACAGAAAATCGATGTTTAGAAAATAAAGCCGAAGTTGGAGTATACC
*
415522 CTCGGAAATAATAGGGTTGGAGTATCCCTGATTATAGAAAATTGGTGTTTTAAAAATAAAATCGG
66 CTCGGAAATAACAGGGTTGGAGTATCCCTGATTATAGAAAATTGGTGTTTTAAAAATAAAATCGG
415587 GGTTGGAGTATCCCCTCGAAAATAACGA
131 GGTTGGAGTATCCCCTCGAAAATAACGA
** *
415615 GGTTAGAGTATC-CTCGATTATGGAAAATCGATGCTTTAG-AAATAAGGCCGAAGTTGGAGTAT-
1 GGTTAGAGTATCTCT-GATTACAGAAAATCGATG-TTTAGAAAATAAAGCCGAAGTTGGAGTATA
* * * *
415677 CCC-CGTGAAAATAACGGGGTTGGAGTAT-CCTCGATTGT-GAAAAATTTGTGTTTTAGAAATAA
64 CCCTCG-G-AAATAACAGGGTTGGAGTATCCCT-GATTATAG-AAAATTGGTGTTTTAAAAATAA
*
415739 AATTGGGGTTGGAGTATCCCC
125 AATCGGGGTTGGAGTATCCCC
415760 GATTGTGAAA
Statistics
Matches: 125, Mismatches: 14, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
156 2 0.02
157 10 0.08
158 109 0.87
159 4 0.03
ACGTcount: A:0.32, C:0.13, G:0.26, T:0.29
Consensus pattern (158 bp):
GGTTAGAGTATCTCTGATTACAGAAAATCGATGTTTAGAAAATAAAGCCGAAGTTGGAGTATACC
CTCGGAAATAACAGGGTTGGAGTATCCCTGATTATAGAAAATTGGTGTTTTAAAAATAAAATCGG
GGTTGGAGTATCCCCTCGAAAATAACGA
Found at i:415861 original size:51 final size:51
Alignment explanation
Indices: 415692--415841 Score: 237
Period size: 51 Copynumber: 2.9 Consensus size: 51
415682 TGAAAATAAC
*
415692 GGGGTTGGAGTATCCTCGATTGTGAAAAATTTGTGTTTTAGAAATAAAATT
1 GGGGTTGGAGTATCCTCGATTGTGAAAAATTAGTGTTTTAGAAATAAAATT
*
415743 GGGGTTGGAGTATCCCCGATTGTGAAAAATTAGTGTTTTAGAAATAAAATT
1 GGGGTTGGAGTATCCTCGATTGTGAAAAATTAGTGTTTTAGAAATAAAATT
* * * * *
415794 GGGGTCGGAGTATCCTCAATTGTGAAAAATCAATATTTTAGAAATAAA
1 GGGGTTGGAGTATCCTCGATTGTGAAAAATTAGTGTTTTAGAAATAAA
415842 GCCGACGTTG
Statistics
Matches: 91, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
51 91 1.00
ACGTcount: A:0.35, C:0.08, G:0.24, T:0.33
Consensus pattern (51 bp):
GGGGTTGGAGTATCCTCGATTGTGAAAAATTAGTGTTTTAGAAATAAAATT
Found at i:424383 original size:13 final size:13
Alignment explanation
Indices: 424365--424389 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
424355 ACAATGAACA
424365 TGTATCGATACAT
1 TGTATCGATACAT
424378 TGTATCGATACA
1 TGTATCGATACA
424390 AAGCAATATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:424387 original size:32 final size:33
Alignment explanation
Indices: 424346--424408 Score: 101
Period size: 32 Copynumber: 1.9 Consensus size: 33
424336 CAATTCTTTA
*
424346 TGTATCGATACAATG-AACATGTATCGATACAT
1 TGTATCGATACAAAGCAACATGTATCGATACAT
*
424378 TGTATCGATACAAAGCAATATGTATCGATAC
1 TGTATCGATACAAAGCAACATGTATCGATAC
424409 TTCTGGGCCT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
32 14 0.50
33 14 0.50
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.30
Consensus pattern (33 bp):
TGTATCGATACAAAGCAACATGTATCGATACAT
Found at i:425177 original size:158 final size:157
Alignment explanation
Indices: 424889--425228 Score: 411
Period size: 158 Copynumber: 2.2 Consensus size: 157
424879 TGTTTGGTAT
* * * *
424889 TTAATTTTGTGTTTTAATTATATAGGGATAAATTTGTAAATTTAGAAATTTTAAAAGGTTTATTT
1 TTAATTTTGTGTTTTAATTATGTAAGGATAAATTTGTAAATTTAGAAAGTTTAAAAGGTTTATTC
* * * * *
424954 GAAAATTTTATTCTAAGGCCAAAAGTGCTTGGACGAATCTTCCTTGAAACTTTTGGATGTTTTTT
66 GAAAATTTTATTCTAAGGCCAAAAGTACTTGGACGAACCTCCCTTGAAACTTTTGCATGTGTTTT
425019 GGATA-CTAATTTCCATTTCTTTGATAC
131 GGA-AGCTAATTTCCATTTCTTTGATAC
* ***
425046 TTAATATTGTGTTTTAATTATGTAAGGACT-AATTT-TCAAATTTAGAAAGTTTAGGGGGGTTTA
1 TTAATTTTGTGTTTTAATTATGTAAGGA-TAAATTTGT-AAATTTAGAAAGTTTA-AAAGGTTTA
* * *
425109 TTCGAAAATTTT-TTACTCAA-GCCAACAGTACTTGGTCGAACCTCCCTTGTAACTTTTGCATGT
63 TTCGAAAATTTTATT-CT-AAGGCCAAAAGTACTTGGACGAACCTCCCTTGAAACTTTTGCATGT
* ** *
425172 GTTTTGTAAGCTAATTTTGATTTCTTTGATGC
126 GTTTTGGAAGCTAATTTCCATTTCTTTGATAC
425204 TTAATTTTGTGTTTTAATTATGTAA
1 TTAATTTTGTGTTTTAATTATGTAA
425229 AGACCTTTTT
Statistics
Matches: 156, Mismatches: 21, Indels: 11
0.83 0.11 0.06
Matches are distributed among these distances:
156 1 0.01
157 48 0.31
158 105 0.67
159 2 0.01
ACGTcount: A:0.29, C:0.10, G:0.16, T:0.45
Consensus pattern (157 bp):
TTAATTTTGTGTTTTAATTATGTAAGGATAAATTTGTAAATTTAGAAAGTTTAAAAGGTTTATTC
GAAAATTTTATTCTAAGGCCAAAAGTACTTGGACGAACCTCCCTTGAAACTTTTGCATGTGTTTT
GGAAGCTAATTTCCATTTCTTTGATAC
Found at i:426127 original size:149 final size:150
Alignment explanation
Indices: 425814--426471 Score: 769
Period size: 150 Copynumber: 4.4 Consensus size: 150
425804 TTTTATGTTA
* * *
425814 TTTTCAAGTCCTTTAAGATCACCGAGCACTTCTAAGTCGATGGTAAACTTTAGGGATATTTTAGC
1 TTTTCAAGTCCCTTAGGATCACCGAGCACTTCTAAGTCGATGGTAAACCTTAGGGATATTTTAGC
* * * * * *
425879 ATTTTCCTCAAAACCTAGTCCTATAAAACAATC-GAGTTTGCTTTTACATC-AAGGTATGAATCA
66 ATTTTCCTCAAAACCTAGTCCTATAAAACTACCAGA-TCTGCTTCTACACCGAAGGTATGAATTA
* *
425942 AGAGTAGGTTTGTTTTTATCT
130 GGAGTAGGTTTATTTTTATCT
* * *
425963 TTTTCAAGTCTCTTAGGATCACCG-GCCACTTCTAAGTTGATGGTAAACCTTAGAGATATTTTAG
1 TTTTCAAGTCCCTTAGGATCACCGAG-CACTTCTAAGTCGATGGTAAACCTTAGGGATATTTTAG
* * * * *
426027 CATTTTCGC-CGAAACCTAGTCTTATAAAACTACCAGGTCTGCTTTTACACCGAAGGTATGAGTT
65 CATTTTC-CTCAAAACCTAGTCCTATAAAACTACCAGATCTGCTTCTACACCGAAGGTATGAATT
*
426091 AGGAGT-GAGTTTGTTTTTATCT
129 AGGAGTAG-GTTTATTTTTATCT
*
426113 TTTTCAA-TCCCTTAGGATCACCGAGCACTTCTAAGTCGATGGTAAATCTTAGGGATATTTTAGC
1 TTTTCAAGTCCCTTAGGATCACCGAGCACTTCTAAGTCGATGGTAAACCTTAGGGATATTTTAGC
* * * * *
426177 ATTTTCCCCAAAACCTAGTCCTATAAAAACTACTAGATTTGCTTCTCCACCAAAGGTATGAATTA
66 ATTTTCCTCAAAACCTAGTCCTAT-AAAACTACCAGATCTGCTTCTACACCGAAGGTATGAATTA
*
426242 GGAGTGGGTTTATTTTTATCT
130 GGAGTAGGTTTATTTTTATCT
* ** * * * *
426263 TTTTCAAGTCCTTTAGGAAT-ATTGACCACTTCTAAGTTGGTGATAAACCTTAGGGATATTTTAG
1 TTTTCAAGTCCCTTAGG-ATCACCGAGCACTTCTAAGTCGATGGTAAACCTTAGGGATATTTTAG
* * * **
426327 CATTTTCCTCGAAACCTAGTCTTATAAAACTACCGAGATC-CCTTCTATGCCGAAGGTATGAATT
65 CATTTTCCTCAAAACCTAGTCCTATAAAACTACC-AGATCTGCTTCTACACCGAAGGTATGAATT
426391 AGGAGTAGGTTTATTTTTATCT
129 AGGAGTAGGTTTATTTTTATCT
* * ***
426413 TTTCCAAGT-CCTCTAGGAT-ATCCGAGCACTTCTATGTCGATGGTAGGTCTTAGGGATAT
1 TTTTCAAGTCCCT-TAGGATCA-CCGAGCACTTCTAAGTCGATGGTAAACCTTAGGGATAT
426472 CCCAATAAAT
Statistics
Matches: 434, Mismatches: 61, Indels: 27
0.83 0.12 0.05
Matches are distributed among these distances:
148 2 0.00
149 173 0.40
150 185 0.43
151 72 0.17
152 2 0.00
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.36
Consensus pattern (150 bp):
TTTTCAAGTCCCTTAGGATCACCGAGCACTTCTAAGTCGATGGTAAACCTTAGGGATATTTTAGC
ATTTTCCTCAAAACCTAGTCCTATAAAACTACCAGATCTGCTTCTACACCGAAGGTATGAATTAG
GAGTAGGTTTATTTTTATCT
Found at i:426382 original size:300 final size:299
Alignment explanation
Indices: 425814--426471 Score: 886
Period size: 300 Copynumber: 2.2 Consensus size: 299
425804 TTTTATGTTA
* *
425814 TTTTCAAGTCCTTTAAGATCACCGAGCACTTCTAAGTCGATGGTAAA-CTTTAGGGATATTTTAG
1 TTTTCAAGTCCCTTAGGATCACCGAGCACTTCTAAGTCGATGGTAAATC-TTAGGGATATTTTAG
* * * *
425878 CATTTTCCTCAAAACCTAGTCCTATAAAACAATCGAGTTTGCTTTTACATCAAGGTATGAATCAA
65 CATTTTCCCCAAAACCTAGTCCTATAAAACAATAGAGTTTGCTTCTACACCAAGGTATGAATCAA
* * *
425943 GAGTAGGTTTGTTTTTATCTTTTTCAAGTCTCTTAGGATCACCGGCCACTTCTAAGTTGATGGTA
130 GAGTAGGTTTATTTTTATCTTTTTCAAGTCTCTTAGGATCACCGACCACTTCTAAGTTGATGATA
* * *
426008 AACCTTAGAGATATTTTAGCATTTTCGCCGAAACCTAGTCTTATAAAACTACCAGGTCTGCTTTT
195 AACCTTAGAGATATTTTAGCATTTTCGCCGAAACCTAGTCTTATAAAACTACCAGATCTCCTTCT
* *
426073 ACACCGAAGGTATGAGTTAGGAGT-GAGTTTGTTTTTATCT
260 ACACCGAAGGTATGAATTAGGAGTAG-GTTTATTTTTATCT
426113 TTTTCAA-TCCCTTAGGATCACCGAGCACTTCTAAGTCGATGGTAAATCTTAGGGATATTTTAGC
1 TTTTCAAGTCCCTTAGGATCACCGAGCACTTCTAAGTCGATGGTAAATCTTAGGGATATTTTAGC
* * *
426177 ATTTTCCCCAAAACCTAGTCCTATAAAAACTACTAGA-TTTGCTTCTCCACCAAAGGTATGAATT
66 ATTTTCCCCAAAACCTAGTCCTAT-AAAAC-AATAGAGTTTGCTTCTACACC-AAGGTATGAATC
* * ** *
426241 AGGAGTGGGTTTATTTTTATCTTTTTCAAGTC-CTTTAGGAAT-ATTGACCACTTCTAAGTTGGT
128 AAGAGTAGGTTTATTTTTATCTTTTTCAAGTCTC-TTAGG-ATCACCGACCACTTCTAAGTTGAT
*
426304 GATAAACCTTAGGGATATTTTAGCATTTTC-CTCGAAACCTAGTCTTATAAAACTACCGAGATC-
191 GATAAACCTTAGAGATATTTTAGCATTTTCGC-CGAAACCTAGTCTTATAAAACTACC-AGATCT
**
426367 CCTTCTATGCCGAAGGTATGAATTAGGAGTAGGTTTATTTTTATCT
254 CCTTCTACACCGAAGGTATGAATTAGGAGTAGGTTTATTTTTATCT
* * **
426413 TTTCCAAGT-CCTCTAGGAT-ATCCGAGCACTTCTATGTCGATGGTAGGTCTTAGGGATAT
1 TTTTCAAGTCCCT-TAGGATCA-CCGAGCACTTCTAAGTCGATGGTAAATCTTAGGGATAT
426472 CCCAATAAAT
Statistics
Matches: 318, Mismatches: 29, Indels: 22
0.86 0.08 0.06
Matches are distributed among these distances:
298 76 0.24
299 26 0.08
300 167 0.53
301 49 0.15
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.36
Consensus pattern (299 bp):
TTTTCAAGTCCCTTAGGATCACCGAGCACTTCTAAGTCGATGGTAAATCTTAGGGATATTTTAGC
ATTTTCCCCAAAACCTAGTCCTATAAAACAATAGAGTTTGCTTCTACACCAAGGTATGAATCAAG
AGTAGGTTTATTTTTATCTTTTTCAAGTCTCTTAGGATCACCGACCACTTCTAAGTTGATGATAA
ACCTTAGAGATATTTTAGCATTTTCGCCGAAACCTAGTCTTATAAAACTACCAGATCTCCTTCTA
CACCGAAGGTATGAATTAGGAGTAGGTTTATTTTTATCT
Found at i:427324 original size:19 final size:19
Alignment explanation
Indices: 427300--427337 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
427290 AGGGATAAGT
*
427300 TGAGTAAGTAATTCACCTC
1 TGAGTAAGCAATTCACCTC
427319 TGAGTAAGCAATTCACCTC
1 TGAGTAAGCAATTCACCTC
427338 GACTTCCCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.32, C:0.24, G:0.16, T:0.29
Consensus pattern (19 bp):
TGAGTAAGCAATTCACCTC
Found at i:431039 original size:15 final size:15
Alignment explanation
Indices: 431019--431052 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
431009 ATTCGACCAC
431019 ATGTACAAATCCTAT
1 ATGTACAAATCCTAT
431034 ATGTACAAATCCTAT
1 ATGTACAAATCCTAT
431049 ATGT
1 ATGT
431053 GGATGTGAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.38, C:0.18, G:0.09, T:0.35
Consensus pattern (15 bp):
ATGTACAAATCCTAT
Found at i:433235 original size:20 final size:20
Alignment explanation
Indices: 433207--433279 Score: 94
Period size: 20 Copynumber: 3.6 Consensus size: 20
433197 ATTTGCCTGC
*
433207 ATGTATCGATACTTTGAATA
1 ATGTATCGATACATTGAATA
* *
433227 ATTTATCGATGCATTGAATA
1 ATGTATCGATACATTGAATA
*
433247 ATGTATCGATACAATG-ATAA
1 ATGTATCGATACATTGAAT-A
433267 ATGTATCGATACA
1 ATGTATCGATACA
433280 ATTTGTAAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
19 2 0.04
20 44 0.96
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGAATA
Found at i:434019 original size:61 final size:61
Alignment explanation
Indices: 433915--434048 Score: 182
Period size: 61 Copynumber: 2.2 Consensus size: 61
433905 AAAGATGACG
* * *
433915 AAGATGAGGAGAGTGATAAAGATGCCAATATGCTTATTCAAGGCCAGCGATATTGGGCAT-A
1 AAGATGAGAAGAGTGATAAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTAGGC-TCA
* *
433976 AAGATGAGAATGA-TGATAAAGGTGCCAATATGCTGATTTAAGGCCAGCGATATTAGGCTCA
1 AAGATGAGAA-GAGTGATAAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTAGGCTCA
*
434037 AAGATGCGAAGA
1 AAGATGAGAAGA
434049 ATGTCAACGT
Statistics
Matches: 65, Mismatches: 6, Indels: 5
0.86 0.08 0.07
Matches are distributed among these distances:
60 3 0.05
61 60 0.92
62 2 0.03
ACGTcount: A:0.37, C:0.13, G:0.28, T:0.22
Consensus pattern (61 bp):
AAGATGAGAAGAGTGATAAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTAGGCTCA
Found at i:434171 original size:52 final size:52
Alignment explanation
Indices: 434105--434559 Score: 239
Period size: 52 Copynumber: 8.7 Consensus size: 52
434095 AGAAGAATGT
* * * **
434105 CAATGTGCTGATTCAAGGCCAGCGACATTAGCCTTAGGAATTTTAAAGATGC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGACTTAGGAATGATAAAGATGC
* * * * * *
434157 CAATATGCTAATTCAAGGTCAACAATATTGGACTTAAAGATGAAAAAGATGATAAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGACTT--AG--G----A-ATGATAAAGATGC
* * * * * * *
434218 CAATATGTTGATTCAAGGCCAACGATATTGGGCTTA-AAGATG-TGAAGAATGT
1 CAATATGCTGATTCAAGGCCAGCGACATTGGACTTAGGA-ATGATAAAG-ATGC
* * * * *
434270 CAATGTGCTGATTCAAGGCCAGCGACATTAGACTTA-AAGATGAGAAAAATGC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGACTTAGGA-ATGATAAAGATGC
* * *
434322 CAATGTGCTGATTCAAGGCCAGCGACATTGGGCTTAGGAATGTTAAAGATGC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGACTTAGGAATGATAAAGATGC
* * * * * *
434374 CAATATGATGATTCAAGGCCAACGATATCGAACTTA--AA-GATGAAA-ATGT
1 CAATATGCTGATTCAAGGCCAGCGACATTGGACTTAGGAATGAT-AAAGATGC
* * * ** * *
434423 CAATGTGCTAATTCAAGGCCAGCGACGTTGGACTTA--AA-GATGGAGGTAC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGACTTAGGAATGATAAAGATGC
* * * * * * * * *
434472 CAATGTGCTAATTTAAAGCCAGCAACATTGGGCTTA-AAGATGGTAAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGACTTAGGA-ATGATAAAGATGC
* * * *
434524 CAATATGCTGATTCAGGGCTAGCAATATTGGACTTA
1 CAATATGCTGATTCAAGGCCAGCGACATTGGACTTA
434560 AAGGTGCCAA
Statistics
Matches: 311, Mismatches: 75, Indels: 34
0.74 0.18 0.08
Matches are distributed among these distances:
48 1 0.00
49 70 0.23
50 6 0.02
51 5 0.02
52 181 0.58
53 3 0.01
54 2 0.01
56 1 0.00
59 1 0.00
60 1 0.00
61 40 0.13
ACGTcount: A:0.35, C:0.16, G:0.24, T:0.25
Consensus pattern (52 bp):
CAATATGCTGATTCAAGGCCAGCGACATTGGACTTAGGAATGATAAAGATGC
Found at i:434198 original size:104 final size:104
Alignment explanation
Indices: 434090--434458 Score: 361
Period size: 104 Copynumber: 3.5 Consensus size: 104
434080 TTAAACTTGC
* *
434090 AGATGAGAAGAATGTCAATGTGCTGATTCAAGGCCAGCGACATTAGCCTTAGGAATTTTAAAGAT
1 AGATGAGAAGAATGTCAATGTGCTGATTCAAGGCCAGCGACATTGGGCTTAGGAATTTTAAAGAT
* * *
434155 GCCAATATGCTAATTCAAGGTCAACAATATTGGACTTAA
66 GCCAATATGCTGATTCAAGGCCAACGATATTGGACTTAA
* * * * *
434194 AGATGAAAAAGATGATAAAGGTGCCAATATGTTGATTCAAGGCCAACGATATTGGGCTTA--AAG
1 AGATG-AGAAGA--AT----GT--CAATGTGCTGATTCAAGGCCAGCGACATTGGGCTTAGGAA-
* * * * * * * *
434257 ATGTGAAGAATGTCAATGTGCTGATTCAAGGCCAGCGACATTAGACTTAA
56 TTTTAAAG-ATGCCAATATGCTGATTCAAGGCCAACGATATTGGACTTAA
* * *
434307 AGATGAGAAAAATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGGCTTAGGAATGTTAAAGAT
1 AGATGAGAAGAATGTCAATGTGCTGATTCAAGGCCAGCGACATTGGGCTTAGGAATTTTAAAGAT
* * *
434372 GCCAATATGATGATTCAAGGCCAACGATATCGAACTTAA
66 GCCAATATGCTGATTCAAGGCCAACGATATTGGACTTAA
* * *
434411 AGAT--GAA-AATGTCAATGTGCTAATTCAAGGCCAGCGACGTTGGACTTA
1 AGATGAGAAGAATGTCAATGTGCTGATTCAAGGCCAGCGACATTGGGCTTA
434459 AAGATGGAGG
Statistics
Matches: 211, Mismatches: 41, Indels: 29
0.75 0.15 0.10
Matches are distributed among these distances:
101 37 0.18
102 3 0.01
104 74 0.35
105 9 0.04
106 3 0.01
107 2 0.01
110 2 0.01
111 4 0.02
112 9 0.04
113 68 0.32
ACGTcount: A:0.36, C:0.15, G:0.24, T:0.25
Consensus pattern (104 bp):
AGATGAGAAGAATGTCAATGTGCTGATTCAAGGCCAGCGACATTGGGCTTAGGAATTTTAAAGAT
GCCAATATGCTGATTCAAGGCCAACGATATTGGACTTAA
Found at i:434313 original size:217 final size:217
Alignment explanation
Indices: 433931--434419 Score: 710
Period size: 217 Copynumber: 2.3 Consensus size: 217
433921 AGGAGAGTGA
* * * * * *
433931 TAAAGATGCCAATATGCTTATTCAAGGCCAGCGATATTGGGCATAAAGATGAGAATGATGATAAA
1 TAAAGATGCCAATATGCTAATTCAAGGCCAACGATATTGGACTTAAAGATGAAAAAGATGATAAA
* *
433996 GGTGCCAATATGCTGATTTAAGGCCAGCGATATTAGGCTCAAAGATGCGAAGAATGTCAACGTAC
66 GGTGCCAATATGCTGATTCAAGGCCAACGATATTAGGCTCAAAGATGCGAAGAATGTCAACGTAC
** * *
434061 TGATTCATAGCCAGCGACATTAAACTTGCAGATGAGAAGAATGTCAATGTGCTGATTCAAGGCCA
131 TGATTCATAGCCAGCGACATTAAACTTAAAGATGAGAAAAATGCCAATGTGCTGATTCAAGGCCA
*
434126 GCGACATTAGCCTTAGGAATTT
196 GCGACATTAGCCTTAGGAATGT
* *
434148 TAAAGATGCCAATATGCTAATTCAAGGTCAACAATATTGGACTTAAAGATGAAAAAGATGATAAA
1 TAAAGATGCCAATATGCTAATTCAAGGCCAACGATATTGGACTTAAAGATGAAAAAGATGATAAA
* * * * * *
434213 GGTGCCAATATGTTGATTCAAGGCCAACGATATTGGGCTTAAAGATGTGAAGAATGTCAATGTGC
66 GGTGCCAATATGCTGATTCAAGGCCAACGATATTAGGCTCAAAGATGCGAAGAATGTCAACGTAC
*
434278 TGATTCA-AGGCCAGCGACATTAGACTTAAAGATGAGAAAAATGCCAATGTGCTGATTCAAGGCC
131 TGATTCATA-GCCAGCGACATTAAACTTAAAGATGAGAAAAATGCCAATGTGCTGATTCAAGGCC
* *
434342 AGCGACATTGGGCTTAGGAATGT
195 AGCGACATTAGCCTTAGGAATGT
* * * *
434365 TAAAGATGCCAATATGATGATTCAAGGCCAACGATATCGAACTTAAAGATGAAAA
1 TAAAGATGCCAATATGCTAATTCAAGGCCAACGATATTGGACTTAAAGATGAAAA
434420 TGTCAATGTG
Statistics
Matches: 241, Mismatches: 30, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
216 1 0.00
217 240 1.00
ACGTcount: A:0.37, C:0.15, G:0.23, T:0.25
Consensus pattern (217 bp):
TAAAGATGCCAATATGCTAATTCAAGGCCAACGATATTGGACTTAAAGATGAAAAAGATGATAAA
GGTGCCAATATGCTGATTCAAGGCCAACGATATTAGGCTCAAAGATGCGAAGAATGTCAACGTAC
TGATTCATAGCCAGCGACATTAAACTTAAAGATGAGAAAAATGCCAATGTGCTGATTCAAGGCCA
GCGACATTAGCCTTAGGAATGT
Found at i:434458 original size:49 final size:49
Alignment explanation
Indices: 434201--434690 Score: 312
Period size: 52 Copynumber: 10.0 Consensus size: 49
434191 TAAAGATGAA
* * * * *
434201 AAAGATGATAAAGGTGCCAATATGTTGATTCAAGGCCAACGATATTGGGCTT
1 AAAGATGA-AAA--TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTT
* *
434253 AAAGATGTGAAGAATGTCAATGTGCTGATTCAAGGCCAGCGACATTAGACTT
1 AAAGA--TGAA-AATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTT
*
434305 AAAGATGAGAAAAATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGGCTT
1 AAAGAT--G-AAAATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTT
* * * * * * *
434357 AGGAATG-TTAAAGATGCCAATATGATGATTCAAGGCCAACGATATCGAACTT
1 A--AA-GATGAAA-ATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTT
* * *
434409 AAAGATGAAAATGTCAATGTGCTAATTCAAGGCCAGCGACGTTGGACTT
1 AAAGATGAAAATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTT
* ** * * * * * *
434458 AAAGATGGAGGTACCAATGTGCTAATTTAAAGCCAGCAACATTGGGCTT
1 AAAGATGAAAATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTT
* * * * * *
434507 AAAGATGGTAAAGGTGCCAATATGCTGATTCAGGGCTAGCAATATTGGACTT
1 AAAGAT-G-AAA-ATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTT
* * *
434559 AAAG--G----TGCCAATGTGCTGATGCAAGGCCAGC-AGCGTTGGGCTT
1 AAAGATGAAAATGCCAATGTGCTGATTCAAGGCCAGCGA-CATTGGACTT
* * * *
434602 AAAG--G----TGACAATATGCTGATTCAAGGCCAGCGATATTAGACTT
1 AAAGATGAAAATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTT
* *
434645 -AAGA--AAAAGGTGCCAATGTGCCGATTCAAGGTCAGCGACATTGGAC
1 AAAGATGAAAA--TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGAC
434691 ATAGAAAGGG
Statistics
Matches: 346, Mismatches: 69, Indels: 50
0.74 0.15 0.11
Matches are distributed among these distances:
42 4 0.01
43 63 0.18
44 1 0.00
48 30 0.09
49 77 0.22
50 8 0.02
51 4 0.01
52 147 0.42
53 3 0.01
54 8 0.02
55 1 0.00
ACGTcount: A:0.34, C:0.16, G:0.26, T:0.24
Consensus pattern (49 bp):
AAAGATGAAAATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTT
Found at i:434576 original size:43 final size:43
Alignment explanation
Indices: 434515--434646 Score: 165
Period size: 43 Copynumber: 3.1 Consensus size: 43
434505 TTAAAGATGG
* *
434515 TAAAGGTGCCAATATGCTGATTCAGGGCTAGCAATATTGGACT
1 TAAAGGTGCCAATATGCTGATTCAAGGCCAGCAATATTGGACT
* * *** *
434558 TAAAGGTGCCAATGTGCTGATGCAAGGCCAGCAGCGTTGGGCT
1 TAAAGGTGCCAATATGCTGATTCAAGGCCAGCAATATTGGACT
* * *
434601 TAAAGGTGACAATATGCTGATTCAAGGCCAGCGATATTAGACT
1 TAAAGGTGCCAATATGCTGATTCAAGGCCAGCAATATTGGACT
434644 TAA
1 TAA
434647 GAAAAAGGTG
Statistics
Matches: 72, Mismatches: 17, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
43 72 1.00
ACGTcount: A:0.30, C:0.17, G:0.27, T:0.25
Consensus pattern (43 bp):
TAAAGGTGCCAATATGCTGATTCAAGGCCAGCAATATTGGACT
Found at i:434863 original size:33 final size:33
Alignment explanation
Indices: 434745--434890 Score: 169
Period size: 32 Copynumber: 4.6 Consensus size: 33
434735 CCAACGACAT
*
434745 TAGGC-TTAGAAGAA-GATGCCACCAACTTGTG
1 TAGGCTTTAGAAGAAGGTTGCCACCAACTTGTG
* * * **
434776 TGGGCTTTTGAA-AAGGTTGCCACCGACTCATG
1 TAGGCTTTAGAAGAAGGTTGCCACCAACTTGTG
*
434808 TGGGCTTT--AAGAAGGGTTGCCACCAACTTGTG
1 TAGGCTTTAGAAGAA-GGTTGCCACCAACTTGTG
*
434840 TAGGCTTTAGAAGAAGGTTGCCACCAGCTTGTG
1 TAGGCTTTAGAAGAAGGTTGCCACCAACTTGTG
434873 TAGGCTTTAGAA-AAGGTT
1 TAGGCTTTAGAAGAAGGTT
434891 TCTCCACTAG
Statistics
Matches: 98, Mismatches: 11, Indels: 11
0.82 0.09 0.09
Matches are distributed among these distances:
30 2 0.02
31 8 0.08
32 54 0.55
33 29 0.30
34 5 0.05
ACGTcount: A:0.26, C:0.18, G:0.29, T:0.27
Consensus pattern (33 bp):
TAGGCTTTAGAAGAAGGTTGCCACCAACTTGTG
Found at i:435029 original size:27 final size:27
Alignment explanation
Indices: 434991--435046 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 27
434981 AAAAAGATTG
*
434991 GGTGCCATGGAGTTATGGACTTAAAAA
1 GGTGCCACGGAGTTATGGACTTAAAAA
* * *
435018 GGTGCCACGGAGTTGTGGGCTTTAAAA
1 GGTGCCACGGAGTTATGGACTTAAAAA
435045 GG
1 GG
435047 AAAAAGTTAC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.27, C:0.12, G:0.36, T:0.25
Consensus pattern (27 bp):
GGTGCCACGGAGTTATGGACTTAAAAA
Found at i:435112 original size:33 final size:32
Alignment explanation
Indices: 435075--435360 Score: 221
Period size: 30 Copynumber: 9.0 Consensus size: 32
435065 GTGGACTGAA
* *
435075 AAGAAAAAAGATGCCACTAAGTCGTGGACTTAG
1 AAGAAAAAAGATGCCACTGAGTCATGGACTT-G
* *
435108 AAGAAAAAAGATGTCACTGAGTCGTGGACTTG
1 AAGAAAAAAGATGCCACTGAGTCATGGACTTG
* * *
435140 GAG-AAGAA-TTGCCACTGAGTCATGGACTTGG
1 AAGAAAAAAGATGCCACTGAGTCATGGACTT-G
*
435171 ATG-AAAAAGAATGCCACTGAGTCATGGACTTGG
1 AAGAAAAAAG-ATGCCACTGAGTCATGGACTT-G
* *
435204 AAGAAAAAAAAGATACCACTAAGTCATGGACTTG
1 AAG--AAAAAAGATGCCACTGAGTCATGGACTTG
* *
435238 --GAGAAGAGATGCCACTGAGTCATGGACTT-
1 AAGAAAAAAGATGCCACTGAGTCATGGACTTG
* * **
435267 TAGGAAGGAGATG-CACTGAGTCATGGACTTTGG
1 AAGAAAAAAGATGCCACTGAGTCATGGAC-TT-G
* * * * *
435300 GAGAAAAAGGATGTCGCTAAGTCATGGACTTG
1 AAGAAAAAAGATGCCACTGAGTCATGGACTTG
* * *
435332 --GAGAAGAGATGCCACTGAGTCGTGGACTT
1 AAGAAAAAAGATGCCACTGAGTCATGGACTT
435361 TTTGGAAAAA
Statistics
Matches: 206, Mismatches: 35, Indels: 27
0.77 0.13 0.10
Matches are distributed among these distances:
30 79 0.38
31 20 0.10
32 5 0.02
33 63 0.31
34 14 0.07
35 19 0.09
36 6 0.03
ACGTcount: A:0.35, C:0.15, G:0.29, T:0.21
Consensus pattern (32 bp):
AAGAAAAAAGATGCCACTGAGTCATGGACTTG
Found at i:443221 original size:20 final size:20
Alignment explanation
Indices: 443196--443342 Score: 150
Period size: 20 Copynumber: 6.8 Consensus size: 20
443186 TTTTACCCAG
443196 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
443216 ATGTATCGATACATTCTGTCTTTTACCCA
1 ATGTATCGATACA-----T-TTTT---CA
*
443245 GATGTATCGATACATTTTTTA
1 -ATGTATCGATACATTTTTCA
443266 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * *
443286 ATGTATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* *
443306 ATGTATCGATACATTCTACA
1 ATGTATCGATACATTTTTCA
443326 ATGTATCGATACATTTT
1 ATGTATCGATACATTTT
443343 GTCTTTTTAC
Statistics
Matches: 106, Mismatches: 11, Indels: 20
0.77 0.08 0.15
Matches are distributed among these distances:
20 80 0.75
21 1 0.01
24 4 0.04
25 2 0.02
26 4 0.04
29 2 0.02
30 13 0.12
ACGTcount: A:0.30, C:0.16, G:0.12, T:0.42
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:443261 original size:50 final size:50
Alignment explanation
Indices: 443186--443280 Score: 181
Period size: 50 Copynumber: 1.9 Consensus size: 50
443176 AAAGTCACAT
443186 TTTTACCCAGATGTATCGATACATTTTTCAATGTATCGATACATTCTGTC
1 TTTTACCCAGATGTATCGATACATTTTTCAATGTATCGATACATTCTGTC
*
443236 TTTTACCCAGATGTATCGATACATTTTTTAATGTATCGATACATT
1 TTTTACCCAGATGTATCGATACATTTTTCAATGTATCGATACATT
443281 TTTCAATGTA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 44 1.00
ACGTcount: A:0.27, C:0.18, G:0.12, T:0.43
Consensus pattern (50 bp):
TTTTACCCAGATGTATCGATACATTTTTCAATGTATCGATACATTCTGTC
Found at i:443890 original size:10 final size:10
Alignment explanation
Indices: 443877--443902 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
443867 CTCCCAAAAG
443877 AAACACCTCC
1 AAACACCTCC
443887 AAACACCTCC
1 AAACACCTCC
443897 AAACAC
1 AAACAC
443903 TTCCTCCTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.46, C:0.46, G:0.00, T:0.08
Consensus pattern (10 bp):
AAACACCTCC
Found at i:446922 original size:17 final size:16
Alignment explanation
Indices: 446896--446947 Score: 50
Period size: 17 Copynumber: 3.1 Consensus size: 16
446886 GTTATAGGTG
* *
446896 AGAAAGAAAGAGGATAA
1 AGAAA-AAAGAAGAAAA
446913 AGAAGAAAAGAAGAAAA
1 AGAA-AAAAGAAGAAAA
*
446930 AGAAAAAAAAAGAGAAA
1 AGAAAAAAGAAGA-AAA
446947 A
1 A
446948 CAAATGAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
16 8 0.27
17 21 0.70
18 1 0.03
ACGTcount: A:0.75, C:0.00, G:0.23, T:0.02
Consensus pattern (16 bp):
AGAAAAAAGAAGAAAA
Found at i:449370 original size:20 final size:20
Alignment explanation
Indices: 449345--449429 Score: 71
Period size: 20 Copynumber: 3.7 Consensus size: 20
449335 TTTTAACTAG
449345 ATGTATCGATACATTGAAAA
1 ATGTATCGATACATTGAAAA
449365 ATGTATCGATACATCTGGGTAAAAAGACAAA
1 ATGTATCGATACAT-T--G-----A-A-A-A
449396 ATGTATCGATACATTGAAAA
1 ATGTATCGATACATTGAAAA
449416 ATGTATCGATACAT
1 ATGTATCGATACAT
449430 CTGGGTACTT
Statistics
Matches: 54, Mismatches: 0, Indels: 22
0.71 0.00 0.29
Matches are distributed among these distances:
20 29 0.54
21 2 0.04
22 1 0.02
23 2 0.04
28 2 0.04
29 1 0.02
30 2 0.04
31 15 0.28
ACGTcount: A:0.44, C:0.12, G:0.16, T:0.28
Consensus pattern (20 bp):
ATGTATCGATACATTGAAAA
Found at i:449450 original size:10 final size:10
Alignment explanation
Indices: 449435--449462 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
449425 TACATCTGGG
449435 TACTTTTCCA
1 TACTTTTCCA
449445 TACTTTTCCA
1 TACTTTTCCA
449455 TACTTTTC
1 TACTTTTC
449463 GCATTCCGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.18, C:0.29, G:0.00, T:0.54
Consensus pattern (10 bp):
TACTTTTCCA
Found at i:452582 original size:20 final size:20
Alignment explanation
Indices: 452557--452612 Score: 103
Period size: 20 Copynumber: 2.8 Consensus size: 20
452547 AATTTGAAGC
*
452557 ATGTATTGATACATTTATTA
1 ATGTATCGATACATTTATTA
452577 ATGTATCGATACATTTATTA
1 ATGTATCGATACATTTATTA
452597 ATGTATCGATACATTT
1 ATGTATCGATACATTT
452613 CCTTAGAAGT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.34, C:0.09, G:0.11, T:0.46
Consensus pattern (20 bp):
ATGTATCGATACATTTATTA
Found at i:452678 original size:19 final size:20
Alignment explanation
Indices: 452650--452703 Score: 56
Period size: 21 Copynumber: 2.7 Consensus size: 20
452640 ATCGATACAT
*
452650 TGTATTGATACAAAACT-TA
1 TGTATCGATACAAAACTGTA
** *
452669 TGTATCGATACATTTACTGTT
1 TGTATCGATACA-AAACTGTA
452690 TGTATCGATACAAA
1 TGTATCGATACAAA
452704 TTATAAAAAT
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
19 11 0.41
20 3 0.11
21 13 0.48
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.39
Consensus pattern (20 bp):
TGTATCGATACAAAACTGTA
Found at i:454200 original size:22 final size:24
Alignment explanation
Indices: 454172--454224 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 24
454162 TTTTAAAAAT
454172 ATAATAAC-TA-AAATTAATAAGA
1 ATAATAACATATAAATTAATAAGA
*
454194 ATAATAACATTATAAATTAATAATA
1 ATAATAACA-TATAAATTAATAAGA
454219 ATAATA
1 ATAATA
454225 TAAGTTTAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
22 8 0.30
24 2 0.07
25 17 0.63
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.32
Consensus pattern (24 bp):
ATAATAACATATAAATTAATAAGA
Found at i:455526 original size:16 final size:16
Alignment explanation
Indices: 455507--455578 Score: 65
Period size: 16 Copynumber: 4.4 Consensus size: 16
455497 ATTCAACGTG
455507 ATTTAAATTTAAAATA
1 ATTTAAATTTAAAATA
* *
455523 ATTTAAAATTAAAACA
1 ATTTAAATTTAAAATA
* *
455539 ATTTAAACTCT-AAATT
1 ATTTAAA-TTTAAAATA
* *
455555 ATTCAAAATTAAAAATA
1 ATT-TAAATTTAAAATA
455572 ATTTAAA
1 ATTTAAA
455579 ATTTTAAAGA
Statistics
Matches: 42, Mismatches: 11, Indels: 6
0.71 0.19 0.10
Matches are distributed among these distances:
16 31 0.74
17 11 0.26
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.38
Consensus pattern (16 bp):
ATTTAAATTTAAAATA
Found at i:455628 original size:16 final size:16
Alignment explanation
Indices: 455607--455639 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
455597 TATCTAACCT
*
455607 AAATTAATTGAATTTA
1 AAATTAATTCAATTTA
455623 AAATTAATTCAATTTA
1 AAATTAATTCAATTTA
455639 A
1 A
455640 TCTTTCAATT
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:0.52, C:0.03, G:0.03, T:0.42
Consensus pattern (16 bp):
AAATTAATTCAATTTA
Found at i:455896 original size:19 final size:20
Alignment explanation
Indices: 455864--455917 Score: 65
Period size: 19 Copynumber: 2.6 Consensus size: 20
455854 TAATATAAAA
455864 TTTTAATTATTTTAAATTAT
1 TTTTAATTATTTTAAATTAT
* *
455884 TTTTATTTA-TTTAATTTAT
1 TTTTAATTATTTTAAATTAT
455903 TTAATTAATTATTTT
1 TT--TTAATTATTTT
455918 TAGTTATAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
19 11 0.39
20 8 0.29
21 6 0.21
22 3 0.11
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (20 bp):
TTTTAATTATTTTAAATTAT
Found at i:456019 original size:20 final size:21
Alignment explanation
Indices: 455993--456040 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 21
455983 TTAAATCTAA
455993 TTATTAATA-ATTTATTATAT
1 TTATTAATATATTTATTATAT
* *
456013 TTTTTAA-ATATTTTTTATAT
1 TTATTAATATATTTATTATAT
456033 TTATTAAT
1 TTATTAAT
456041 GACTAAATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 1 0.04
20 22 0.96
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (21 bp):
TTATTAATATATTTATTATAT
Found at i:456065 original size:16 final size:16
Alignment explanation
Indices: 456044--456088 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
456034 TATTAATGAC
456044 TAAATATTTTATATAT
1 TAAATATTTTATATAT
*
456060 TAAATA-TTTATAATTT
1 TAAATATTTTAT-ATAT
456076 TAAA-ATTTTATAT
1 TAAATATTTTATAT
456089 TTATATATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
15 8 0.31
16 18 0.69
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TAAATATTTTATATAT
Found at i:456095 original size:8 final size:8
Alignment explanation
Indices: 456047--456132 Score: 53
Period size: 7 Copynumber: 11.6 Consensus size: 8
456037 TAATGACTAA
456047 ATAT-TTT
1 ATATATTT
456054 ATATA-TT
1 ATATATTT
*
456061 AAATATTT
1 ATATATTT
456069 ATA-ATTT
1 ATATATTT
*
456076 -TAAAATTT
1 AT-ATATTT
456084 -TATATTT
1 ATATATTT
*
456091 ATATATAT
1 ATATATTT
*
456099 ATATATGT
1 ATATATTT
*
456107 A-AT-TTA
1 ATATATTT
*
456113 ATATATTC
1 ATATATTT
456121 ATA-ATTT
1 ATATATTT
456128 ATATA
1 ATATA
456133 ATATTTATTT
Statistics
Matches: 62, Mismatches: 9, Indels: 15
0.72 0.10 0.17
Matches are distributed among these distances:
6 3 0.05
7 30 0.48
8 29 0.47
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.55
Consensus pattern (8 bp):
ATATATTT
Found at i:456103 original size:16 final size:16
Alignment explanation
Indices: 456084--456140 Score: 55
Period size: 16 Copynumber: 3.6 Consensus size: 16
456074 TTTAAAATTT
*
456084 TATATTTATATATATA
1 TATATTTATATTTATA
*
456100 TATATGTA-ATTTA-A
1 TATATTTATATTTATA
*
456114 TATATTCATAATTTATA
1 TATATTTAT-ATTTATA
456131 TAATATTTAT
1 T-ATATTTAT
456141 TTTGTTAAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
14 7 0.22
15 4 0.12
16 12 0.38
17 2 0.06
18 7 0.22
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (16 bp):
TATATTTATATTTATA
Found at i:458298 original size:14 final size:14
Alignment explanation
Indices: 458279--458319 Score: 64
Period size: 14 Copynumber: 2.9 Consensus size: 14
458269 TAATTGCCAG
*
458279 TTTTCTTTTATTTT
1 TTTTCTTTTATCTT
458293 TTTTCTTTTATCTT
1 TTTTCTTTTATCTT
*
458307 TTATCTTTTATCT
1 TTTTCTTTTATCT
458320 AGAAGGAGCA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.10, C:0.12, G:0.00, T:0.78
Consensus pattern (14 bp):
TTTTCTTTTATCTT
Found at i:458316 original size:7 final size:7
Alignment explanation
Indices: 458282--458319 Score: 58
Period size: 7 Copynumber: 5.4 Consensus size: 7
458272 TTGCCAGTTT
458282 TCTTTTA
1 TCTTTTA
* *
458289 TTTTTTT
1 TCTTTTA
458296 TCTTTTA
1 TCTTTTA
458303 TCTTTTA
1 TCTTTTA
458310 TCTTTTA
1 TCTTTTA
458317 TCT
1 TCT
458320 AGAAGGAGCA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.11, C:0.13, G:0.00, T:0.76
Consensus pattern (7 bp):
TCTTTTA
Found at i:458659 original size:2 final size:2
Alignment explanation
Indices: 458652--458697 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
458642 TCCTCTTTAG
*
458652 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
458694 AT AT
1 AT AT
458698 TTTGCTTTTA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:463972 original size:35 final size:35
Alignment explanation
Indices: 463940--464010 Score: 124
Period size: 35 Copynumber: 2.0 Consensus size: 35
463930 AAAAAATAGG
*
463940 ATAAAATGGGGTACTTAGCTAATAAATAAAATAAA
1 ATAAAATGAGGTACTTAGCTAATAAATAAAATAAA
*
463975 ATAAAATGAGGTACTTAGCTAATAAATAAAACAAA
1 ATAAAATGAGGTACTTAGCTAATAAATAAAATAAA
464010 A
1 A
464011 ATGTCAAAAC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.56, C:0.07, G:0.13, T:0.24
Consensus pattern (35 bp):
ATAAAATGAGGTACTTAGCTAATAAATAAAATAAA
Found at i:464277 original size:3 final size:3
Alignment explanation
Indices: 464269--464302 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
464259 AGCGAAGTTG
464269 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
464303 TTTGCCAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:464951 original size:22 final size:22
Alignment explanation
Indices: 464906--464949 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
464896 TAATAAATAC
* *
464906 TAATTTTATATTATATTTAAAA
1 TAATTTTATATCATAATTAAAA
464928 TAATTTTATATCATAAATTAAA
1 TAATTTTATATCAT-AATTAAA
464950 TATTTAATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (22 bp):
TAATTTTATATCATAATTAAAA
Found at i:465043 original size:19 final size:19
Alignment explanation
Indices: 465019--465058 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
465009 ATTTAAAATA
* *
465019 TTTATATCATATTTATATT
1 TTTATATCATAATCATATT
*
465038 TTTATATTATAATCATATT
1 TTTATATCATAATCATATT
465057 TT
1 TT
465059 ATGTGTTACA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (19 bp):
TTTATATCATAATCATATT
Found at i:467624 original size:2 final size:2
Alignment explanation
Indices: 467617--467652 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
467607 AAAGGTACAA
467617 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
467653 GTTAAACAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:469347 original size:4 final size:4
Alignment explanation
Indices: 469340--469372 Score: 57
Period size: 4 Copynumber: 8.2 Consensus size: 4
469330 TTCTAAGCTC
*
469340 TTTA TTTA TTTA TTTA TTTA TTTT TTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA T
469373 CATCACATTC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (4 bp):
TTTA
Found at i:470889 original size:17 final size:18
Alignment explanation
Indices: 470869--470903 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
470859 TTATATTTTA
*
470869 AAATTTAATAAA-AAATT
1 AAATTTAAAAAATAAATT
470886 AAATTTAAAAAATAAATT
1 AAATTTAAAAAATAAATT
470904 TTTAAAAGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (18 bp):
AAATTTAAAAAATAAATT
Found at i:471536 original size:15 final size:16
Alignment explanation
Indices: 471516--471545 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
471506 AATAAAAAGC
471516 TTTTTATGA-TTTTTA
1 TTTTTATGAGTTTTTA
471531 TTTTTATGAGTTTTT
1 TTTTTATGAGTTTTT
471546 TAAAGATAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.17, C:0.00, G:0.10, T:0.73
Consensus pattern (16 bp):
TTTTTATGAGTTTTTA
Found at i:473313 original size:5 final size:5
Alignment explanation
Indices: 473305--473329 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
473295 TTTATTTTAA
473305 AAAAT AAAAT AAAAT AAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT
473330 TATTTTTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:473353 original size:13 final size:13
Alignment explanation
Indices: 473335--473363 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
473325 AAAATTATTT
473335 TTTAATTTTTATA
1 TTTAATTTTTATA
473348 TTTAATTTTTATA
1 TTTAATTTTTATA
473361 TTT
1 TTT
473364 TTAAATAATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTAATTTTTATA
Found at i:474824 original size:20 final size:20
Alignment explanation
Indices: 474787--474853 Score: 71
Period size: 20 Copynumber: 3.3 Consensus size: 20
474777 TTTTACAATT
* *
474787 TGTATCGATACAATAAGTTAA
1 TGTATCAATAC-ATAAGTGAA
*
474808 TGTATTAATACATAAGTGAA
1 TGTATCAATACATAAGTGAA
* *
474828 TGTATCGATACATAAATGAA
1 TGTATCAATACATAAGTGAA
*
474848 TATATC
1 TGTATC
474854 GATAATAAAA
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
20 30 0.77
21 9 0.23
ACGTcount: A:0.43, C:0.09, G:0.13, T:0.34
Consensus pattern (20 bp):
TGTATCAATACATAAGTGAA
Found at i:474854 original size:20 final size:20
Alignment explanation
Indices: 474815--474862 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
474805 TAATGTATTA
* *
474815 ATACATAAGTGAATGTATCG
1 ATACATAAATGAATATATCG
474835 ATACATAAATGAATATATCG
1 ATACATAAATGAATATATCG
474855 ATA-ATAAA
1 ATACATAAA
474863 ACCTATTAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 5 0.19
20 21 0.81
ACGTcount: A:0.50, C:0.08, G:0.12, T:0.29
Consensus pattern (20 bp):
ATACATAAATGAATATATCG
Found at i:476141 original size:27 final size:27
Alignment explanation
Indices: 476102--476153 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
476092 CCAAATCTAG
*
476102 AATTTACAGGCCA-TCTTTATTTTTTCC
1 AATTTACACGCCATTC-TTATTTTTTCC
476129 AATTTACACGCCATTCTTATTTTTT
1 AATTTACACGCCATTCTTATTTTTT
476154 TTGATAAGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
27 21 0.91
28 2 0.09
ACGTcount: A:0.23, C:0.21, G:0.06, T:0.50
Consensus pattern (27 bp):
AATTTACACGCCATTCTTATTTTTTCC
Found at i:476551 original size:31 final size:28
Alignment explanation
Indices: 476488--476551 Score: 76
Period size: 27 Copynumber: 2.2 Consensus size: 28
476478 AACTTCAATA
*
476488 ATTTAAAAATTAATTATATTAAAGTCAT
1 ATTTAAAAATTAATTATATTAAAATCAT
*
476516 -TTTAAAAAGTTATTTATTATTAATAATCAT
1 ATTTAAAAA-TTAATTA-TATTAA-AATCAT
476546 ATTTAA
1 ATTTAA
476552 CTTAAATATT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
27 8 0.27
28 6 0.20
29 6 0.20
30 5 0.17
31 5 0.17
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (28 bp):
ATTTAAAAATTAATTATATTAAAATCAT
Found at i:476975 original size:13 final size:13
Alignment explanation
Indices: 476957--476984 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
476947 CATTATTCAA
476957 TGTATCGATACAT
1 TGTATCGATACAT
476970 TGTATCGATACAT
1 TGTATCGATACAT
476983 TG
1 TG
476985 ATCTTTTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.39
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:477947 original size:20 final size:20
Alignment explanation
Indices: 477902--477947 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
477892 GTTAATAGCC
*
477902 CATGATTCATGCATTTTAAG
1 CATGTTTCATGCATTTTAAG
477922 CTATGTTTCATGCA-TTTACAG
1 C-ATGTTTCATGCATTTTA-AG
477943 CATGT
1 CATGT
477948 CCAGCACCTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
20 9 0.39
21 14 0.61
ACGTcount: A:0.26, C:0.17, G:0.15, T:0.41
Consensus pattern (20 bp):
CATGTTTCATGCATTTTAAG
Found at i:483878 original size:20 final size:20
Alignment explanation
Indices: 483853--483927 Score: 98
Period size: 20 Copynumber: 3.8 Consensus size: 20
483843 AAAAAGACAA
*
483853 AATGTATCGATACTTTGAAG
1 AATGTATCGATACATTGAAG
*
483873 AATGTATCGATACATTCATAG
1 AATGTATCGATACATTGA-AG
* *
483894 -ATGTATTGATACATTGAAA
1 AATGTATCGATACATTGAAG
483913 AATGTATCGATACAT
1 AATGTATCGATACAT
483928 CTAGGTACTT
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
19 1 0.02
20 44 0.94
21 2 0.04
ACGTcount: A:0.39, C:0.11, G:0.16, T:0.35
Consensus pattern (20 bp):
AATGTATCGATACATTGAAG
Found at i:484919 original size:60 final size:60
Alignment explanation
Indices: 484846--485715 Score: 805
Period size: 60 Copynumber: 14.7 Consensus size: 60
484836 CACTAACTTG
* ** * *
484846 TGTGGGCTTTGAAAAGAGTTGCCACCGGCTCATGGGCTTTGAAAAGAGTTACCACTGGCT
1 TGTGGGCTTTGAAAAGAGTTGCCACCGACTTGTGGGCTTTGAAAAGAGTTGCCACTGACT
* ** *
484906 TGTGGGCTTTGAAAAGA-ATGCCAATGACTTGTGGGCTTTG-AAAG-GGTGCCACTGACT
1 TGTGGGCTTTGAAAAGAGTTGCCACCGACTTGTGGGCTTTGAAAAGAGTTGCCACTGACT
** * *
484963 TGTGGGCTTTGAAAAGAG-TGCCACTAACTTGTGGGCTTT-AAAAG-GGTGCCACTAACT
1 TGTGGGCTTTGAAAAGAGTTGCCACCGACTTGTGGGCTTTGAAAAGAGTTGCCACTGACT
* * * * *
485020 TGTGGGCTTTAAAAAGAG-TGCTACTGACTTGTGGGCTTTGAAAAGAGTTGTCACCGACTT
1 TGTGGGCTTTGAAAAGAGTTGCCACCGACTTGTGGGCTTTGAAAAGAGTTGCCACTGAC-T
* * *
485080 GTGTGGGCTTT-AAAA-AGATGCCACTGACTTGTGGGCTTTG-AAAGAGATGCCACTGACT
1 -TGTGGGCTTTGAAAAGAGTTGCCACCGACTTGTGGGCTTTGAAAAGAGTTGCCACTGACT
* * *
485138 TATGGGCTTTGAAAGGAGTTGCCACCGACTTGTGTGGGCTTTGAAAAGA--TGCCATTGACT
1 TGTGGGCTTTGAAAAGAGTTGCCACCGAC-T-TGTGGGCTTTGAAAAGAGTTGCCACTGACT
* **
485198 TGTGGGCTTTGAAAAGAGTTGCCACCAACTTGTGTGGGCTTTGAAAAGAGTTGCCACCAACTT
1 TGTGGGCTTTGAAAAGAGTTGCCACCGAC-T-TGTGGGCTTTGAAAAGAGTTGCCACTGAC-T
* *
485261 GTGTGGGCTTTGAAAGGAGTTGCCACCGACTTGTGTGGGCTTTGAAAATA--TGCCACTGACT
1 -TGTGGGCTTTGAAAAGAGTTGCCACCGAC-T-TGTGGGCTTTGAAAAGAGTTGCCACTGACT
* * ** *
485322 TGTGGGCTTTGAAAGGAGCTGCCACTAACTTGTGTGGGCTTTGAAAAG-G-TGCCATTGACT
1 TGTGGGCTTTGAAAAGAGTTGCCACCGAC-T-TGTGGGCTTTGAAAAGAGTTGCCACTGACT
* *
485382 TGTGGGCTTTGAAAAGAGTTGCCACCGACTTGTGTGGGCTTTGAAAGGAGTTGCCACCGACTT
1 TGTGGGCTTTGAAAAGAGTTGCCACCGAC-T-TGTGGGCTTTGAAAAGAGTTGCCACTGAC-T
* *
485445 GTGTGGGCTTTGAAAAGA--TGCCACTGACTTGTGGGCTTTG-AAAGAGATGCCACTGACT
1 -TGTGGGCTTTGAAAAGAGTTGCCACCGACTTGTGGGCTTTGAAAAGAGTTGCCACTGACT
* * * *
485503 TGTGGGCTTTGAAAAGAGTTGCCACCAACTTGTGTGGGCTTTG-AAAG-GGTGCCATTGATT
1 TGTGGGCTTTGAAAAGAGTTGCCACCGAC-T-TGTGGGCTTTGAAAAGAGTTGCCACTGACT
* * * * * *
485563 TGTGGGCTTTG-AAAG-GGTGTCACTGACTTGTGGGCTTTG-GAAG-GGTGCCACTGATT
1 TGTGGGCTTTGAAAAGAGTTGCCACCGACTTGTGGGCTTTGAAAAGAGTTGCCACTGACT
* * * * * * * *
485619 TGTGGACTTT-AAAAG-GATGCCACGGAGTTGTGGACTTT-AAAAG-GATGCCACAGAGT
1 TGTGGGCTTTGAAAAGAGTTGCCACCGACTTGTGGGCTTTGAAAAGAGTTGCCACTGACT
* * * *
485675 TGTGGACTTT-AAAAG-GATGCCACGGAGTTGTGGAG-TTTGAA
1 TGTGGGCTTTGAAAAGAGTTGCCACCGACTTGTGG-GCTTTGAA
485716 GAGTCGCAGT
Statistics
Matches: 704, Mismatches: 77, Indels: 61
0.84 0.09 0.07
Matches are distributed among these distances:
56 106 0.15
57 127 0.18
58 22 0.03
59 78 0.11
60 230 0.33
61 39 0.06
62 37 0.05
63 2 0.00
64 63 0.09
ACGTcount: A:0.24, C:0.17, G:0.31, T:0.29
Consensus pattern (60 bp):
TGTGGGCTTTGAAAAGAGTTGCCACCGACTTGTGGGCTTTGAAAAGAGTTGCCACTGACT
Found at i:484946 original size:89 final size:90
Alignment explanation
Indices: 484846--485697 Score: 933
Period size: 89 Copynumber: 9.6 Consensus size: 90
484836 CACTAACTTG
* * ** * ***
484846 TGTGGGCTTTGAAAAGAGTTGCCACCGGCTCATGGGCTTTGAAAAGAGTTACCACTGGC-T-TGT
1 TGTGGGCTTTGAAAAGAGTTGCCACTGACTTGTGGGCTTTGAAAAGAGTTGCCACCAACTTGTGT
*
484909 GGGCTTTGAAAAGAATGCCAATGACT
66 GGGCTTTGAAAAG-ATGCCACTGACT
* *
484935 TGTGGGCTTTG-AAAG-GGTGCCACTGACTTGTGGGCTTTGAAAAGAG-TGCCACTAAC-T-TGT
1 TGTGGGCTTTGAAAAGAGTTGCCACTGACTTGTGGGCTTTGAAAAGAGTTGCCACCAACTTGTGT
* *
484995 GGGCTTT-AAAAGGGTGCCACTAACT
66 GGGCTTTGAAAA-GATGCCACTGACT
* * * *
485020 TGTGGGCTTTAAAAAGAG-TGCTACTGACTTGTGGGCTTTGAAAAGAGTTGTCACCGACTTGTGT
1 TGTGGGCTTTGAAAAGAGTTGCCACTGACTTGTGGGCTTTGAAAAGAGTTGCCACCAACTTGTGT
*
485084 GGGCTTTAAAAAGATGCCACTGACT
66 GGGCTTTGAAAAGATGCCACTGACT
* * * *
485109 TGTGGGCTTTG-AAAGAGATGCCACTGACTTATGGGCTTTGAAAGGAGTTGCCACCGACTTGTGT
1 TGTGGGCTTTGAAAAGAGTTGCCACTGACTTGTGGGCTTTGAAAAGAGTTGCCACCAACTTGTGT
*
485173 GGGCTTTGAAAAGATGCCATTGACT
66 GGGCTTTGAAAAGATGCCACTGACT
**
485198 TGTGGGCTTTGAAAAGAGTTGCCACCAACTTGTGTGGGCTTTGAAAAGAGTTGCCACCAACTTGT
1 TGTGGGCTTTGAAAAGAGTTGCCACTGAC-T-TGTGGGCTTTGAAAAGAGTTGCCACCAACTTGT
* *
485263 GTGGGCTTTGAAAGGAGTTGCCACCGACTT
64 GTGGGCTTTGAAA--AGATGCCACTGAC-T
* * * *
485293 GTGTGGGCTTTGAAAATA--TGCCACTGACTTGTGGGCTTTGAAAGGAGCTGCCACTAACTTGTG
1 -TGTGGGCTTTGAAAAGAGTTGCCACTGACTTGTGGGCTTTGAAAAGAGTTGCCACCAACTTGTG
* *
485356 TGGGCTTTGAAAAGGTGCCATTGACT
65 TGGGCTTTGAAAAGATGCCACTGACT
* * *
485382 TGTGGGCTTTGAAAAGAGTTGCCACCGACTTGTGTGGGCTTTGAAAGGAGTTGCCACCGACTTGT
1 TGTGGGCTTTGAAAAGAGTTGCCACTGAC-T-TGTGGGCTTTGAAAAGAGTTGCCACCAACTTGT
485447 GTGGGCTTTGAAAAGATGCCACTGACT
64 GTGGGCTTTGAAAAGATGCCACTGACT
*
485474 TGTGGGCTTTG-AAAGAGATGCCACTGACTTGTGGGCTTTGAAAAGAGTTGCCACCAACTTGTGT
1 TGTGGGCTTTGAAAAGAGTTGCCACTGACTTGTGGGCTTTGAAAAGAGTTGCCACCAACTTGTGT
* * * *
485538 GGGCTTTGAAAGGGTGCCATTGATT
66 GGGCTTTGAAAAGATGCCACTGACT
* * * * **
485563 TGTGGGCTTTG-AAAG-GGTGTCACTGACTTGTGGGCTTTG-GAAG-GGTGCCACTGA-TT-TGT
1 TGTGGGCTTTGAAAAGAGTTGCCACTGACTTGTGGGCTTTGAAAAGAGTTGCCACCAACTTGTGT
* * *
485622 GGACTTT-AAAAGGATGCCACGGAGT
66 GGGCTTTGAAAA-GATGCCACTGACT
* * * * * *
485647 TGTGGACTTT-AAAAG-GATGCCACAGAGTTGTGGACTTT-AAAAG-GATGCCAC
1 TGTGGGCTTTGAAAAGAGTTGCCACTGACTTGTGGGCTTTGAAAAGAGTTGCCAC
485698 GGAGTTGTGG
Statistics
Matches: 663, Mismatches: 78, Indels: 49
0.84 0.10 0.06
Matches are distributed among these distances:
83 3 0.00
84 59 0.09
85 25 0.04
86 59 0.09
87 37 0.06
88 49 0.07
89 188 0.28
90 38 0.06
91 17 0.03
92 152 0.23
93 1 0.00
94 18 0.03
95 1 0.00
96 16 0.02
ACGTcount: A:0.24, C:0.17, G:0.31, T:0.29
Consensus pattern (90 bp):
TGTGGGCTTTGAAAAGAGTTGCCACTGACTTGTGGGCTTTGAAAAGAGTTGCCACCAACTTGTGT
GGGCTTTGAAAAGATGCCACTGACT
Found at i:485088 original size:32 final size:30
Alignment explanation
Indices: 484846--485715 Score: 814
Period size: 28 Copynumber: 29.4 Consensus size: 30
484836 CACTAACTTG
* *
484846 TGTGGGCTTTGAAAAGAGTTGCCACCGGCT
1 TGTGGGCTTTGAAAAGAGTTGCCACTGACT
** * *
484876 CATGGGCTTTGAAAAGAGTTACCACTGGCT
1 TGTGGGCTTTGAAAAGAGTTGCCACTGACT
* *
484906 TGTGGGCTTTGAAAAGA-ATGCCAATGACT
1 TGTGGGCTTTGAAAAGAGTTGCCACTGACT
*
484935 TGTGGGCTTTG-AAAG-GGTGCCACTGACT
1 TGTGGGCTTTGAAAAGAGTTGCCACTGACT
*
484963 TGTGGGCTTTGAAAAGAG-TGCCACTAACT
1 TGTGGGCTTTGAAAAGAGTTGCCACTGACT
* *
484992 TGTGGGCTTT-AAAAG-GGTGCCACTAACT
1 TGTGGGCTTTGAAAAGAGTTGCCACTGACT
* *
485020 TGTGGGCTTTAAAAAGAG-TGCTACTGACT
1 TGTGGGCTTTGAAAAGAGTTGCCACTGACT
* *
485049 TGTGGGCTTTGAAAAGAGTTGTCACCGACTT
1 TGTGGGCTTTGAAAAGAGTTGCCACTGAC-T
*
485080 GTGTGGGCTTT-AAAA-AGATGCCACTGACT
1 -TGTGGGCTTTGAAAAGAGTTGCCACTGACT
*
485109 TGTGGGCTTTG-AAAGAGATGCCACTGACT
1 TGTGGGCTTTGAAAAGAGTTGCCACTGACT
* * *
485138 TATGGGCTTTGAAAGGAGTTGCCACCGACTT
1 TGTGGGCTTTGAAAAGAGTTGCCACTGAC-T
*
485169 GTGTGGGCTTTGAAAAGA--TGCCATTGACT
1 -TGTGGGCTTTGAAAAGAGTTGCCACTGACT
**
485198 TGTGGGCTTTGAAAAGAGTTGCCACCAACTT
1 TGTGGGCTTTGAAAAGAGTTGCCACTGAC-T
**
485229 GTGTGGGCTTTGAAAAGAGTTGCCACCAACTT
1 -TGTGGGCTTTGAAAAGAGTTGCCACTGAC-T
* *
485261 GTGTGGGCTTTGAAAGGAGTTGCCACCGACTT
1 -TGTGGGCTTTGAAAAGAGTTGCCACTGAC-T
*
485293 GTGTGGGCTTTGAAAATA--TGCCACTGACT
1 -TGTGGGCTTTGAAAAGAGTTGCCACTGACT
* * *
485322 TGTGGGCTTTGAAAGGAGCTGCCACTAACTT
1 TGTGGGCTTTGAAAAGAGTTGCCACTGAC-T
*
485353 GTGTGGGCTTTGAAAAG-G-TGCCATTGACT
1 -TGTGGGCTTTGAAAAGAGTTGCCACTGACT
*
485382 TGTGGGCTTTGAAAAGAGTTGCCACCGACTT
1 TGTGGGCTTTGAAAAGAGTTGCCACTGAC-T
* *
485413 GTGTGGGCTTTGAAAGGAGTTGCCACCGACTT
1 -TGTGGGCTTTGAAAAGAGTTGCCACTGAC-T
485445 GTGTGGGCTTTGAAAAGA--TGCCACTGACT
1 -TGTGGGCTTTGAAAAGAGTTGCCACTGACT
*
485474 TGTGGGCTTTG-AAAGAGATGCCACTGACT
1 TGTGGGCTTTGAAAAGAGTTGCCACTGACT
**
485503 TGTGGGCTTTGAAAAGAGTTGCCACCAACTT
1 TGTGGGCTTTGAAAAGAGTTGCCACTGAC-T
* * *
485534 GTGTGGGCTTTG-AAAG-GGTGCCATTGATT
1 -TGTGGGCTTTGAAAAGAGTTGCCACTGACT
* *
485563 TGTGGGCTTTG-AAAG-GGTGTCACTGACT
1 TGTGGGCTTTGAAAAGAGTTGCCACTGACT
* * *
485591 TGTGGGCTTTG-GAAG-GGTGCCACTGATT
1 TGTGGGCTTTGAAAAGAGTTGCCACTGACT
* * * *
485619 TGTGGACTTT-AAAAG-GATGCCACGGAGT
1 TGTGGGCTTTGAAAAGAGTTGCCACTGACT
* * * *
485647 TGTGGACTTT-AAAAG-GATGCCACAGAGT
1 TGTGGGCTTTGAAAAGAGTTGCCACTGACT
* * * *
485675 TGTGGACTTT-AAAAG-GATGCCACGGAGT
1 TGTGGGCTTTGAAAAGAGTTGCCACTGACT
485703 TGTGGAG-TTTGAA
1 TGTGG-GCTTTGAA
485716 GAGTCGCAGT
Statistics
Matches: 735, Mismatches: 71, Indels: 69
0.84 0.08 0.08
Matches are distributed among these distances:
27 6 0.01
28 257 0.35
29 129 0.18
30 153 0.21
31 15 0.02
32 175 0.24
ACGTcount: A:0.24, C:0.17, G:0.31, T:0.29
Consensus pattern (30 bp):
TGTGGGCTTTGAAAAGAGTTGCCACTGACT
Found at i:487007 original size:17 final size:17
Alignment explanation
Indices: 486977--487027 Score: 61
Period size: 17 Copynumber: 2.9 Consensus size: 17
486967 TTGTTCCCTT
486977 TTTTATTTTGCTTTTGCA
1 TTTT-TTTTGCTTTTGCA
486995 CTTTTTTTT-CTTTT-CA
1 -TTTTTTTTGCTTTTGCA
487011 TTTTTTTGTGCTTTTGC
1 TTTTTTT-TGCTTTTGC
487028 TTTCGACTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
15 7 0.24
16 3 0.10
17 10 0.34
18 5 0.17
19 4 0.14
ACGTcount: A:0.06, C:0.14, G:0.10, T:0.71
Consensus pattern (17 bp):
TTTTTTTTGCTTTTGCA
Found at i:493294 original size:52 final size:52
Alignment explanation
Indices: 493155--493280 Score: 225
Period size: 52 Copynumber: 2.4 Consensus size: 52
493145 AATATGAAAT
493155 TTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGCAAA
1 TTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGCAAA
* *
493207 TTTGCCTGCATGTATTGATGCATTTCATAGTGTATCGATACATCTGGGCAAA
1 TTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGCAAA
*
493259 TTTGCCTGCATGCATCGATACA
1 TTTGCCTGCATGTATCGATACA
493281 AAGATCAGTG
Statistics
Matches: 69, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
52 69 1.00
ACGTcount: A:0.25, C:0.20, G:0.20, T:0.35
Consensus pattern (52 bp):
TTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGCAAA
Found at i:493609 original size:20 final size:22
Alignment explanation
Indices: 493586--493640 Score: 71
Period size: 21 Copynumber: 2.6 Consensus size: 22
493576 ACAATTCAAA
* *
493586 GTATCGATACATGTTG-CA-AT
1 GTATCGATACATGTAGAAATAT
493606 GTATCGATACATG-AGAAATAT
1 GTATCGATACATGTAGAAATAT
493627 GTATCGATACATGT
1 GTATCGATACATGT
493641 CATTGGGAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 1 0.03
20 14 0.47
21 15 0.50
ACGTcount: A:0.35, C:0.13, G:0.20, T:0.33
Consensus pattern (22 bp):
GTATCGATACATGTAGAAATAT
Found at i:495352 original size:12 final size:12
Alignment explanation
Indices: 495320--495353 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
495310 AACCATCAAA
*
495320 GATGAAGAAGAT
1 GATGAAGATGAT
*
495332 GATGAAGATGTT
1 GATGAAGATGAT
495344 GATGAAGATG
1 GATGAAGATG
495354 GTGACTCGGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.35, T:0.24
Consensus pattern (12 bp):
GATGAAGATGAT
Found at i:500061 original size:20 final size:20
Alignment explanation
Indices: 500018--500064 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 20
500008 AAATCTTTTG
500018 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
500039 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
500059 CAAAAT
1 CAAAAT
500065 CAGCATCAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 6 0.26
21 9 0.39
22 8 0.35
ACGTcount: A:0.32, C:0.19, G:0.04, T:0.45
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:502465 original size:15 final size:14
Alignment explanation
Indices: 502445--502486 Score: 59
Period size: 13 Copynumber: 3.0 Consensus size: 14
502435 AGCCAAACTT
502445 GTATCGATACACCAA
1 GTATCGATACA-CAA
*
502460 GTATCGATACA-AT
1 GTATCGATACACAA
502473 GTATCGATACACAA
1 GTATCGATACACAA
502487 AAAATTGTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 12 0.50
14 1 0.04
15 11 0.46
ACGTcount: A:0.40, C:0.21, G:0.14, T:0.24
Consensus pattern (14 bp):
GTATCGATACACAA
Found at i:504761 original size:20 final size:19
Alignment explanation
Indices: 504732--504770 Score: 69
Period size: 20 Copynumber: 2.0 Consensus size: 19
504722 AAGTCAAAAC
504732 CCTTAAATGTATCGATACA
1 CCTTAAATGTATCGATACA
504751 CCTTCAAATGTATCGATACA
1 CCTT-AAATGTATCGATACA
504771 TAATGCACAG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.36, C:0.23, G:0.10, T:0.31
Consensus pattern (19 bp):
CCTTAAATGTATCGATACA
Found at i:504798 original size:13 final size:13
Alignment explanation
Indices: 504780--504804 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
504770 ATAATGCACA
504780 GTATCGATACATT
1 GTATCGATACATT
504793 GTATCGATACAT
1 GTATCGATACAT
504805 GACCAAATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:504817 original size:20 final size:21
Alignment explanation
Indices: 504792--504844 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
504782 ATCGATACAT
*
504792 TGTATCGATACATG-ACCA-AA
1 TGTATCGATACATGCA-AAGAA
*
504812 TGTATCGATACTTGCAAAGAA
1 TGTATCGATACATGCAAAGAA
504833 TGTATCGATACA
1 TGTATCGATACA
504845 GGTGATTGGC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 14 0.50
21 14 0.50
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.28
Consensus pattern (21 bp):
TGTATCGATACATGCAAAGAA
Found at i:504930 original size:20 final size:21
Alignment explanation
Indices: 504885--504937 Score: 76
Period size: 20 Copynumber: 2.7 Consensus size: 21
504875 CCTTAACTGT
504885 TTGTATCGATACA-CACAAGA
1 TTGTATCGATACATCACAAGA
*
504905 -TGTATCGATACATCCCAA-A
1 TTGTATCGATACATCACAAGA
504924 TTGTATCGATACAT
1 TTGTATCGATACAT
504938 TGGCTTGTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
19 13 0.43
20 17 0.57
ACGTcount: A:0.36, C:0.21, G:0.13, T:0.30
Consensus pattern (21 bp):
TTGTATCGATACATCACAAGA
Found at i:507857 original size:22 final size:22
Alignment explanation
Indices: 507832--507899 Score: 54
Period size: 22 Copynumber: 3.1 Consensus size: 22
507822 ATGCTGATTC
507832 AAGGCTAGCTATATTGGACTTA
1 AAGGCTAGCTATATTGGACTTA
* *
507854 AAGG-T-GCCA-ATGTGCTGA-TTC
1 AAGGCTAGCTATAT-TG--GACTTA
*
507875 AAGGCCAGCTATATTGGACTTA
1 AAGGCTAGCTATATTGGACTTA
507897 AAG
1 AAG
507900 ATGAGAAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 14
0.64 0.09 0.26
Matches are distributed among these distances:
19 2 0.06
20 5 0.15
21 9 0.26
22 11 0.32
23 5 0.15
24 2 0.06
ACGTcount: A:0.31, C:0.16, G:0.25, T:0.28
Consensus pattern (22 bp):
AAGGCTAGCTATATTGGACTTA
Found at i:507878 original size:21 final size:20
Alignment explanation
Indices: 507811--507878 Score: 50
Period size: 21 Copynumber: 3.2 Consensus size: 20
507801 CTTAAAGATA
507811 AAGGTGCCAATATGCTGATTC
1 AAGGTGCCAAT-TGCTGATTC
* *
507832 AAGGCTAGCTATATTG--GACTTA
1 AAGG-T-GCCA-ATTGCTGA-TTC
507854 AAGGTGCCAATGTGCTGATTC
1 AAGGTGCCAAT-TGCTGATTC
507875 AAGG
1 AAGG
507879 CCAGCTATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 14
0.67 0.07 0.26
Matches are distributed among these distances:
19 2 0.06
20 5 0.14
21 13 0.36
22 9 0.25
23 5 0.14
24 2 0.06
ACGTcount: A:0.29, C:0.16, G:0.26, T:0.28
Consensus pattern (20 bp):
AAGGTGCCAATTGCTGATTC
Found at i:508026 original size:92 final size:92
Alignment explanation
Indices: 507916--508857 Score: 970
Period size: 92 Copynumber: 9.9 Consensus size: 92
507906 AAAATGATGT
* * *
507916 CAATGTGCTGATTCAAGGCCAGCTACATTGAACTTGAAGATAAAGGTGCTAATATGCTGATTCAA
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCTGATTCAA
*
507981 TGCCAGCTATATTGGACTTAAAGGTGC
66 GGCCAGCTATATTGGACTTAAAGGTGC
*
508008 CAATGTGCTGATTCAAGGCTAGCTACATTGGACTTAAAGA-AGAAGGTGCCAATATGCTGATTCA
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATA-AAGGTGCCAATATGCTGATTCA
*
508072 AGGCCAGCTATATTGGACTTAAAGATAAAGGCGC
65 AGGCCAGCTATATTGGAC-T-----TAAAGGTGC
* * * * *
508106 CAATATGCTGATTCAAAGCCAGCTATATTGGAC-T-----TAAAGGTGCTAATGTGCTGATTCAA
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCTGATTCAA
*
508165 GGCCAGCTATATTGAACTTAAAGATAAAGGTGC
66 GGCCAGCTATATTGGAC-T-----TAAAGGTGC
* * * *
508198 CAATATGCTGATTTAAGGCCAGCTATATTGGAC-T-----TAAAGGTGCCAATGTGCTGATTCAA
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCTGATTCAA
* *
508257 GGCCAGCTACATTGGACTTAAAGATGAGAAAAAGGATGT
66 GGCCAGCTATATTGGAC-T-----T-----AAAGG-TGC
*
508296 CAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATAAAGGTGCCAATATGCTGATTCAA
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCTGATTCAA
*
508361 GGCCAGCTATATTAGACTTAAAGGTGC
66 GGCCAGCTATATTGGACTTAAAGGTGC
* * *
508388 CAATGTGCTGATTCAAGGCTAACTACATTGGACTTAAAGA-AGAAGGTGCCAATATACTGATTCA
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATA-AAGGTGCCAATATGCTGATTCA
508452 AGGCCAGCTATATTGGACTTAAAGGTGC
65 AGGCCAGCTATATTGGACTTAAAGGTGC
* * *
508480 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAGAAAAAAGATGTCAATGTGCTG
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT------AAAGGTGCCAATATGCTG
* *
508545 ATTCAAGGCCAGCTACATTGAACTTAAAGATAAAAGTGC
60 ATTCAAGGCCAGCTATATTGGACTTAAAG------GTGC
* * * * *
508584 CAATATGCTGATTCAAGGCCAGCTATATTGGAC-T-----TCAAGGTGCCAATGTGTTGATTCAA
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCTGATTCAA
* *
508643 GGCTAGCTACATTGGACTTAAAGAAGAAGGTGC
66 GGCCAGCTATATTGGACTT-----A-AAGGTGC
* *
508676 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATAAAGGTGCCAATATGCTGATTCAA
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCTGATTCAA
508741 GGCCAGCTATATTGGACTTAAAGGTGC
66 GGCCAGCTATATTGGACTTAAAGGTGC
*
508768 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAAATGGAAAAGGTGCCAATATGCTGATT
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT---AAAGGTGCCAATATGCTGATT
*
508833 CAAGGCCAGCGATATTGGACTTAAA
63 CAAGGCCAGCTATATTGGACTTAAA
508858 AGAAGATGCC
Statistics
Matches: 743, Mismatches: 58, Indels: 95
0.83 0.06 0.11
Matches are distributed among these distances:
91 2 0.00
92 450 0.61
93 9 0.01
95 45 0.06
97 7 0.01
98 152 0.20
99 2 0.00
103 2 0.00
104 74 0.10
ACGTcount: A:0.34, C:0.17, G:0.23, T:0.26
Consensus pattern (92 bp):
CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCTGATTCAA
GGCCAGCTATATTGGACTTAAAGGTGC
Found at i:508316 original size:55 final size:49
Alignment explanation
Indices: 507769--508857 Score: 1119
Period size: 49 Copynumber: 22.8 Consensus size: 49
507759 AAAAATATGT
* *
507769 CAATGTGCTGATTCAAGGCCAGCTATATTGAACTTAAAGATAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGC
* * *
507818 CAATATGCTGATTCAAGGCTAGCTATATTGGAC-T-----TAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGC
* * *
507861 CAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAGAAAAATGATGT
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-----AAA-GGTGC
* *
507916 CAATGTGCTGATTCAAGGCCAGCTACATTGAACTTGAAGATAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGC
* * * *
507965 TAATATGCTGATTCAATGCCAGCTATATTGGAC-T-----TAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGC
*
508008 CAATGTGCTGATTCAAGGCTAGCTACATTGGACTTAAAGA-AGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATA-AAGGTGC
* * *
508057 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATAAAGGCGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGC
* * *
508106 CAATATGCTGATTCAAAGCCAGCTATATTGGAC-T-----TAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGC
* * *
508149 TAATGTGCTGATTCAAGGCCAGCTATATTGAACTTAAAGATAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGC
* * *
508198 CAATATGCTGATTTAAGGCCAGCTATATTGGAC-T-----TAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGC
*
508241 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAGAAAAAGGATGT
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-----AAAGG-TGC
*
508296 CAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGC
* * *
508345 CAATATGCTGATTCAAGGCCAGCTATATTAGAC-T-----TAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGC
* *
508388 CAATGTGCTGATTCAAGGCTAACTACATTGGACTTAAAGA-AGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATA-AAGGTGC
* * *
508437 CAATATACTGATTCAAGGCCAGCTATATTGGAC-T-----TAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGC
* *
508480 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAGAAAAAAGATGT
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT------AAAGGTGC
* *
508535 CAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATAAAAGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGC
* * *
508584 CAATATGCTGATTCAAGGCCAGCTATATTGGAC-T-----TCAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGC
* *
508627 CAATGTGTTGATTCAAGGCTAGCTACATTGGACTTAAAGA-AGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATA-AAGGTGC
* *
508676 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGC
* *
508725 CAATATGCTGATTCAAGGCCAGCTATATTGGAC-T-----TAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGC
*
508768 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAAATGGAAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT---AAAGGTGC
* * *
508820 CAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAA
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAA
508858 AGAAGATGCC
Statistics
Matches: 881, Mismatches: 84, Indels: 147
0.79 0.08 0.13
Matches are distributed among these distances:
43 303 0.34
44 9 0.01
48 10 0.01
49 369 0.42
50 10 0.01
52 43 0.05
54 8 0.01
55 129 0.15
ACGTcount: A:0.34, C:0.17, G:0.23, T:0.26
Consensus pattern (49 bp):
CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGC
Found at i:508425 original size:239 final size:235
Alignment explanation
Indices: 507916--508857 Score: 1359
Period size: 239 Copynumber: 4.0 Consensus size: 235
507906 AAAATGATGT
* *
507916 CAATGTGCTGATTCAAGGCCAGCTACATTGAACTTGAAGATA-AAGGTGCTAATATGCTGATTCA
1 CAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGA-AGAAGGTGCCAATATGCTGATTCA
* *
507980 ATGCCAGCTATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCTAGCTACATTGGACTTAA
65 AGGCCAGCTATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAA
* * * *
508045 AGA-AG-AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATAAAGGCGCCA
130 AGATAGAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATAAAGGTGCCA
*
508108 ATATGCTGATTCAAAGCCAGCTATATTGGACTTAAAGGTGC
195 ATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGC
* * *
508149 TAATGTGCTGATTCAAGGCCAGCTATATTGAACTTAAAGATA-AAGGTGCCAATATGCTGATTTA
1 CAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGA-AGAAGGTGCCAATATGCTGATTCA
508213 AGGCCAGCTATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAA
65 AGGCCAGCTATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAA
*
508278 AGATGAGAAAAAGGATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATAAAGGT
130 AGAT-AG--AAAGG-TGCCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATAAAGGT
*
508343 GCCAATATGCTGATTCAAGGCCAGCTATATTAGACTTAAAGGTGC
191 GCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGC
* * * *
508388 CAATGTGCTGATTCAAGGCTAACTACATTGGACTTAAAGAAGAAGGTGCCAATATACTGATTCAA
1 CAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGAAGAAGGTGCCAATATGCTGATTCAA
508453 GGCCAGCTATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAA
66 GGCCAGCTATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAA
* * *
508518 GATGAGAAAAAAGATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATAAAAGTG
131 GAT-AG---AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATAAAGGTG
*
508583 CCAATATGCTGATTCAAGGCCAGCTATATTGGACTTCAAGGTGC
192 CCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGC
* * *
508627 CAATGTGTTGATTCAAGGCTAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGCTGATTCAA
1 CAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGAAGAAGGTGCCAATATGCTGATTCAA
* *
508692 GGCCAGCTATATTGGACTTAAAGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGA
66 GGCCAGCTATATTGGAC-T-----TAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGA
* *
508757 C-T-----T--AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAAATGGAAA
125 CTTAAAGATAGAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGAT---AA
*
508814 AGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAA
187 AGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAA
508858 AGAAGATGCC
Statistics
Matches: 655, Mismatches: 37, Indels: 31
0.91 0.05 0.04
Matches are distributed among these distances:
233 170 0.26
235 2 0.00
236 43 0.07
238 5 0.01
239 387 0.59
240 7 0.01
244 1 0.00
245 40 0.06
ACGTcount: A:0.34, C:0.17, G:0.23, T:0.26
Consensus pattern (235 bp):
CAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGAAGAAGGTGCCAATATGCTGATTCAA
GGCCAGCTATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAA
GATAGAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATAAAGGTGCCAA
TATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGC
Found at i:508471 original size:380 final size:383
Alignment explanation
Indices: 507765--508857 Score: 1716
Period size: 380 Copynumber: 2.9 Consensus size: 383
507755 GAGAAAAAAT
507765 ATGTCAATGTGCTGATTCAAGGCCAGCTATATTGAACTTAAAGATAAAGGTGCCAATATGCTGAT
1 ATGTCAATGTGCTGATTCAAGGCCAGCTATATTGAACTTAAAGATAAAGGTGCCAATATGCTGAT
* *
507830 TCAAGGCTAGCTATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTATATTGGACT
66 TCAAGGCCAGCTATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACT
* *
507895 TAAAGATGAGAAAAATGATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTGAAGATAAA
131 TAAAGATGAGAAAAAGGATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATAAA
* *
507960 GGTGCTAATATGCTGATTCAATGCCAGCTATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAG
196 GGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAG
508025 GCTAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC
261 GCTAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC
*
508090 TTAAAGATAAAGGCGCCAATATGCTGATTCAAAGCCAGCTATATTGGACTT-A-A-AG-G
326 TT-AA-ATAAAGGCGCCAATATGCTGATTCAAAGCCAGCTACATTGGACTTAAGAGAGAG
508146 -TG-CTAATGTGCTGATTCAAGGCCAGCTATATTGAACTTAAAGATAAAGGTGCCAATATGCTGA
1 ATGTC-AATGTGCTGATTCAAGGCCAGCTATATTGAACTTAAAGATAAAGGTGCCAATATGCTGA
*
508209 TTTAAGGCCAGCTATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGAC
65 TTCAAGGCCAGCTATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGAC
508274 TTAAAGATGAGAAAAAGGATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATAA
130 TTAAAGATGAGAAAAAGGATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATAA
*
508339 AGGTGCCAATATGCTGATTCAAGGCCAGCTATATTAGACTTAAAGGTGCCAATGTGCTGATTCAA
195 AGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGCCAATGTGCTGATTCAA
* *
508404 GGCTAACTACATTGGACTTAAAGAAGAAGGTGCCAATATACTGATTCAAGGCCAGCTATATTGGA
260 GGCTAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGA
* * *
508469 C-T---TAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAGAAAAAA
325 CTTAAATAAAGGCGCCAATATGCTGATTCAAAGCCAGCTACATTGGACTT-AAGA-GAG-----A
508530 G
383 G
* *
508531 ATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATAAAAGTGCCAATATGCTGAT
1 ATGTCAATGTGCTGATTCAAGGCCAGCTATATTGAACTTAAAGATAAAGGTGCCAATATGCTGAT
* * *
508596 TCAAGGCCAGCTATATTGGACTTCAAGGTGCCAATGTGTTGATTCAAGGCTAGCTACATTGGACT
66 TCAAGGCCAGCTATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACT
* * * *
508661 TAAAGA--AG---AAGG-TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATAAA
131 TAAAGATGAGAAAAAGGATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATAAA
508720 GGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAG
196 GGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAG
* *
508785 GCCAGCTACATTGGACTTAAA-AATGGAAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATT
261 GCTAGCTACATTGGACTTAAAGAA--G--AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATT
508849 GGACTTAAA
322 GGACTTAAA
508858 AGAAGATGCC
Statistics
Matches: 661, Mismatches: 29, Indels: 38
0.91 0.04 0.05
Matches are distributed among these distances:
374 40 0.06
376 1 0.00
377 1 0.00
379 6 0.01
380 438 0.66
381 5 0.01
383 38 0.06
384 3 0.00
385 1 0.00
386 127 0.19
387 1 0.00
ACGTcount: A:0.34, C:0.17, G:0.23, T:0.27
Consensus pattern (383 bp):
ATGTCAATGTGCTGATTCAAGGCCAGCTATATTGAACTTAAAGATAAAGGTGCCAATATGCTGAT
TCAAGGCCAGCTATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACT
TAAAGATGAGAAAAAGGATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATAAA
GGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAG
GCTAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC
TTAAATAAAGGCGCCAATATGCTGATTCAAAGCCAGCTACATTGGACTTAAGAGAGAG
Found at i:508838 original size:52 final size:52
Alignment explanation
Indices: 508760--508858 Score: 171
Period size: 52 Copynumber: 1.9 Consensus size: 52
508750 TATTGGACTT
* *
508760 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAAATGGA
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAAATGGA
*
508812 AAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAA
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAA
508859 GAAGATGCCA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 44 1.00
ACGTcount: A:0.35, C:0.17, G:0.24, T:0.23
Consensus pattern (52 bp):
AAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAAATGGA
Found at i:509071 original size:33 final size:33
Alignment explanation
Indices: 508889--509218 Score: 322
Period size: 33 Copynumber: 9.8 Consensus size: 33
508879 TGGGCTTTTG
* * *
508889 AAGGTTGCCACTGACTTGTGGGCTTTTGAAAAGGAGA
1 AAGG-TGCCACGGAGTTGTGGGC-TTT-AAAAAGA-A
* * *
508926 AAGATGCCACGGAGTTGTGGAC-TTAAAAGGAA
1 AAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAA
** * *
508958 CAAGGGTGCCATAGAGTTGTGGAC-TTAAAAGGAA
1 -AA-GGTGCCACGGAGTTGTGGGCTTTAAAAAGAA
* ** *
508992 CAAGGATGCCACGAAGTTGTGGATTTTGAAAAGGAA
1 -AAGG-TGCCACGGAGTTGTGGGCTTT-AAAAAGAA
509028 AAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAA
1 AAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAA
* * *
509061 AAGGTACCACGGAGTGGTGGACTTTAAAAAGAA
1 AAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAA
* *
509094 AAGGTGCCACAGAGTGGTGGGCTTTAAAAAGAA
1 AAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAA
* * *
509127 AAGGTGCAACGGAGTGGTGGGCTTTGAAAAGAA
1 AAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAA
* * *
509160 AAGGTGCCACAGAGTGGTGGGCTTTGAAAAGAAA
1 AAGGTGCCACGGAGTTGTGGGCTTTAAAAAG-AA
*
509194 AAGGTGCCACAGAGTTGTGGGCTTT
1 AAGGTGCCACGGAGTTGTGGGCTTT
509219 GAAGAAAATA
Statistics
Matches: 260, Mismatches: 27, Indels: 15
0.86 0.09 0.05
Matches are distributed among these distances:
32 1 0.00
33 137 0.53
34 90 0.35
35 6 0.02
36 23 0.09
37 3 0.01
ACGTcount: A:0.34, C:0.12, G:0.33, T:0.21
Consensus pattern (33 bp):
AAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAA
Found at i:509262 original size:30 final size:30
Alignment explanation
Indices: 509215--509666 Score: 235
Period size: 30 Copynumber: 14.8 Consensus size: 30
509205 GAGTTGTGGG
*
509215 CTTTGAAGAAAATATGCC-CTTGAGTCATGCA
1 CTTTG-AGAAAAGATGCCAC-TGAGTCATGCA
* *
509246 CTTTG-GAAAGAGATGCCACTGAGTCGTGGA
1 CTTTGAGAAA-AGATGCCACTGAGTCATGCA
** *
509276 CTTTGAAGAAAAGATGCCACTGAGTTGTGGA
1 CTTTG-AGAAAAGATGCCACTGAGTCATGCA
* * **
509307 CTTTGGGACAAA-ATGCCACTGAGTTATGGG
1 CTTTGAGA-AAAGATGCCACTGAGTCATGCA
* *
509337 CTTTGAGAAAAGATTGCCACTGAGTCGTGGA
1 CTTTGAGAAAAGA-TGCCACTGAGTCATGCA
**
509368 CTTT-AGGACAAA-ATGCCACTGAGTCATGGG
1 CTTTGA-GA-AAAGATGCCACTGAGTCATGCA
* * *
509398 CTTTGAGAAGAGATTGCCACTGAGTCGTGGA
1 CTTTGAGAAAAGA-TGCCACTGAGTCATGCA
* * **
509429 CTTTGGGACAAA-ATGCCACTGAGTCGTGGG
1 CTTTGAGA-AAAGATGCCACTGAGTCATGCA
* * *
509459 CTTTGAGAAGAGATTGCCACTGAGTCGTGGA
1 CTTTGAGAAAAGA-TGCCACTGAGTCATGCA
* * **
509490 CTTT-AGGACAAA-ATGCCACTAAGTCGTGGG
1 CTTTGA-GA-AAAGATGCCACTGAGTCATGCA
** * * *
509520 CTTTGAGAAGGGATTGCCACTAAGTCGTGGA
1 CTTTGAGAAAAGA-TGCCACTGAGTCATGCA
* *
509551 CTTT-AGGACAAA-ATGCCACTGAGTCGTGGA
1 CTTTGA-GA-AAAGATGCCACTGAGTCATGCA
* * * * * **
509581 CTTTGGGAAAAAATGTCACTAAGTCGTGGG
1 CTTTGAGAAAAGATGCCACTGAGTCATGCA
* * *
509611 CTTTGAGAAGAGATTGCCACTGAGTCGTGGA
1 CTTTGAGAAAAGA-TGCCACTGAGTCATGCA
*
509642 CTTT-AGGACAAA-ATGTCACTGAGTC
1 CTTTGA-GA-AAAGATGCCACTGAGTC
509667 GTGGGCTTTG
Statistics
Matches: 351, Mismatches: 43, Indels: 55
0.78 0.10 0.12
Matches are distributed among these distances:
29 15 0.04
30 176 0.50
31 146 0.42
32 14 0.04
ACGTcount: A:0.28, C:0.17, G:0.29, T:0.25
Consensus pattern (30 bp):
CTTTGAGAAAAGATGCCACTGAGTCATGCA
Found at i:509286 original size:61 final size:60
Alignment explanation
Indices: 509198--509675 Score: 504
Period size: 61 Copynumber: 7.8 Consensus size: 60
509188 AAGAAAAAGG
* * * *
509198 TGCCACAGAGTTGTGGGCTTTGAAGAAAATATGCC-CTTGAGTCATGCACTTT-GGA-AAGAGA
1 TGCCACTGAGTCGTGGGCTTTG-AGAAAATATGCCAC-TGAGTCGTGGACTTTAGGACAA-A-A
* * * *
509259 TGCCACTGAGTCGTGGACTTTGAAGAAAAGATGCCACTGAGTTGTGGACTTTGGGACAAAA
1 TGCCACTGAGTCGTGGGCTTTG-AGAAAATATGCCACTGAGTCGTGGACTTTAGGACAAAA
** *
509320 TGCCACTGAGTTATGGGCTTTGAGAAAAGATTGCCACTGAGTCGTGGACTTTAGGACAAAA
1 TGCCACTGAGTCGTGGGCTTTGAGAAAATA-TGCCACTGAGTCGTGGACTTTAGGACAAAA
* *
509381 TGCCACTGAGTCATGGGCTTTGAGAAGAGAT-TGCCACTGAGTCGTGGACTTTGGGACAAAA
1 TGCCACTGAGTCGTGGGCTTTGAGAA-A-ATATGCCACTGAGTCGTGGACTTTAGGACAAAA
509442 TGCCACTGAGTCGTGGGCTTTGAGAAGAGAT-TGCCACTGAGTCGTGGACTTTAGGACAAAA
1 TGCCACTGAGTCGTGGGCTTTGAGAA-A-ATATGCCACTGAGTCGTGGACTTTAGGACAAAA
* * *
509503 TGCCACTAAGTCGTGGGCTTTGAGAAGGGAT-TGCCACTAAGTCGTGGACTTTAGGACAAAA
1 TGCCACTGAGTCGTGGGCTTTGAGAA--AATATGCCACTGAGTCGTGGACTTTAGGACAAAA
* * * * * * * * * *
509564 TGCCACTGAGTCGTGGACTTTGGGAAAAAATGTCACTAAGTCGTGGGCTTTGAGAAGAGAT
1 TGCCACTGAGTCGTGGGCTTTGAGAAAATATGCCACTGAGTCGTGGACTTT-AGGACAAAA
* * *
509625 TGCCACTGAGTCGTGGACTTT-AGGACAAA-ATGTCACTGAGTCGTGGGCTTT
1 TGCCACTGAGTCGTGGGCTTTGA-GA-AAATATGCCACTGAGTCGTGGACTTT
509676 GAAAAGGTAT
Statistics
Matches: 373, Mismatches: 33, Indels: 22
0.87 0.08 0.05
Matches are distributed among these distances:
59 1 0.00
60 27 0.07
61 332 0.89
62 10 0.03
63 3 0.01
ACGTcount: A:0.27, C:0.17, G:0.30, T:0.26
Consensus pattern (60 bp):
TGCCACTGAGTCGTGGGCTTTGAGAAAATATGCCACTGAGTCGTGGACTTTAGGACAAAA
Found at i:509402 original size:91 final size:91
Alignment explanation
Indices: 509246--509676 Score: 523
Period size: 91 Copynumber: 4.7 Consensus size: 91
509236 GAGTCATGCA
* *
509246 CTTTG-GAAAGAGA-TGCCACTGAGTCGTGGACTTTGAAGA-AAAGATGCCACTGAGTTGTGGAC
1 CTTTGAGAAA-AGATTGCCACTGAGTCGTGGACTTT-AGGACAAA-ATGCCACTGAGTCGTGGAC
* **
509308 TTTGGGACAAAATGCCACTGAGTTATGGG
63 TTTGGGACAAAATGCCACTAAGTCGTGGG
* *
509337 CTTTGAGAAAAGATTGCCACTGAGTCGTGGACTTTAGGACAAAATGCCACTGAGTCATGGGCTTT
1 CTTTGAGAAAAGATTGCCACTGAGTCGTGGACTTTAGGACAAAATGCCACTGAGTCGTGGACTTT
* * * *
509402 GAGA-AGAGATTGCCACTGAGTCGTGGA
66 GGGACA-A-AATGCCACTAAGTCGTGGG
* * * * * *
509429 CTTTGGGACAAA-A-TGCCACTGAGTCGTGGGCTTTGAGAAGAGATTGCCACTGAGTCGTGGACT
1 CTTTGAGA-AAAGATTGCCACTGAGTCGTGGACTTT-AGGACAAAATGCCACTGAGTCGTGGACT
*
509492 TTAGGACAAAATGCCACTAAGTCGTGGG
64 TTGGGACAAAATGCCACTAAGTCGTGGG
** *
509520 CTTTGAGAAGGGATTGCCACTAAGTCGTGGACTTTAGGACAAAATGCCACTGAGTCGTGGACTTT
1 CTTTGAGAAAAGATTGCCACTGAGTCGTGGACTTTAGGACAAAATGCCACTGAGTCGTGGACTTT
* *
509585 GGGAAAAAATGTCACTAAGTCGTGGG
66 GGGACAAAATGCCACTAAGTCGTGGG
* * *
509611 CTTTGAGAAGAGATTGCCACTGAGTCGTGGACTTTAGGACAAAATGTCACTGAGTCGTGGGCTTT
1 CTTTGAGAAAAGATTGCCACTGAGTCGTGGACTTTAGGACAAAATGCCACTGAGTCGTGGACTTT
509676 G
66 G
509677 AAAAGGTATT
Statistics
Matches: 292, Mismatches: 38, Indels: 20
0.83 0.11 0.06
Matches are distributed among these distances:
90 2 0.01
91 189 0.65
92 97 0.33
93 4 0.01
ACGTcount: A:0.27, C:0.17, G:0.30, T:0.26
Consensus pattern (91 bp):
CTTTGAGAAAAGATTGCCACTGAGTCGTGGACTTTAGGACAAAATGCCACTGAGTCGTGGACTTT
GGGACAAAATGCCACTAAGTCGTGGG
Found at i:509676 original size:61 final size:62
Alignment explanation
Indices: 509138--509677 Score: 442
Period size: 61 Copynumber: 8.8 Consensus size: 62
509128 AGGTGCAACG
* ** * * * * *
509138 GAGTGGTGGGCTTTGAAAAGAAAAGGTGCCACAGAGTGGTGGGCTTTGAAAAGAAAAAGGTGCCA
1 GAGTCGTGGGCTTTGAGGAGAAAA--TGCCACTGAGTCGTGGACTTTGAGAA-CAAAA--TGCCA
*
509203 CA
61 CT
* * * * *
509205 GAGTTGTGGGCTTTGAAGA-AAATATGCC-CTTGAGTCATGCACTTTG-GAA-AGAGATGCCACT
1 GAGTCGTGGGCTTTGAGGAGAAA-ATGCCAC-TGAGTCGTGGACTTTGAGAACA-AAATGCCACT
* * * *
509266 GAGTCGTGGACTTTGAAGA-AAAGATGCCACTGAGTTGTGGACTTTG-GGACAAAATGCCACT
1 GAGTCGTGGGCTTTGAGGAGAAA-ATGCCACTGAGTCGTGGACTTTGAGAACAAAATGCCACT
** *
509327 GAGTTATGGGCTTTGA-GA-AAAGATTGCCACTGAGTCGTGGACTTT-AGGACAAAATGCCACT
1 GAGTCGTGGGCTTTGAGGAGAAA-A-TGCCACTGAGTCGTGGACTTTGAGAACAAAATGCCACT
* * * * *
509388 GAGTCATGGGCTTTGAGAAGAGATTGCCACTGAGTCGTGGACTTTG-GGACAAAATGCCACT
1 GAGTCGTGGGCTTTGAGGAGAAAATGCCACTGAGTCGTGGACTTTGAGAACAAAATGCCACT
* * * *
509449 GAGTCGTGGGCTTTGAGAAGAGATTGCCACTGAGTCGTGGACTTT-AGGACAAAATGCCACT
1 GAGTCGTGGGCTTTGAGGAGAAAATGCCACTGAGTCGTGGACTTTGAGAACAAAATGCCACT
* * ** * * *
509510 AAGTCGTGGGCTTTGAGAAGGGATTGCCACTAAGTCGTGGACTTT-AGGACAAAATGCCACT
1 GAGTCGTGGGCTTTGAGGAGAAAATGCCACTGAGTCGTGGACTTTGAGAACAAAATGCCACT
* * * * * * * *
509571 GAGTCGTGGACTTTG-GGAAAAAATGTCACTAAGTCGTGGGCTTTGAGAAGAGATTGCCACT
1 GAGTCGTGGGCTTTGAGGAGAAAATGCCACTGAGTCGTGGACTTTGAGAACAAAATGCCACT
* * * *
509632 GAGTCGTGGACTTT-AGGACAAAATGTCACTGAGTCGTGGGCTTTGA
1 GAGTCGTGGGCTTTGAGGAGAAAATGCCACTGAGTCGTGGACTTTGA
509678 AAAGGTATTT
Statistics
Matches: 415, Mismatches: 45, Indels: 32
0.84 0.09 0.07
Matches are distributed among these distances:
60 29 0.07
61 339 0.82
62 4 0.01
63 4 0.01
64 3 0.01
65 15 0.04
66 3 0.01
67 18 0.04
ACGTcount: A:0.28, C:0.16, G:0.31, T:0.25
Consensus pattern (62 bp):
GAGTCGTGGGCTTTGAGGAGAAAATGCCACTGAGTCGTGGACTTTGAGAACAAAATGCCACT
Found at i:510885 original size:13 final size:12
Alignment explanation
Indices: 510867--510912 Score: 58
Period size: 12 Copynumber: 3.8 Consensus size: 12
510857 GCCTTTACAC
510867 TTTTTTTTGTGT
1 TTTTTTTTGTGT
510879 GTTTTTTTTGT-T
1 -TTTTTTTTGTGT
510891 TTGTTTTTTGTGT
1 TT-TTTTTTGTGT
*
510904 TTTGTTTTG
1 TTTTTTTTG
510913 ATTTTTATCA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
11 2 0.07
12 15 0.50
13 13 0.43
ACGTcount: A:0.00, C:0.00, G:0.20, T:0.80
Consensus pattern (12 bp):
TTTTTTTTGTGT
Found at i:510897 original size:25 final size:25
Alignment explanation
Indices: 510869--510917 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
510859 CTTTACACTT
*
510869 TTTTTTGTGTGTTTTTTTTG-TTTTG
1 TTTTTTGTGT-TTTGTTTTGATTTTG
510894 TTTTTTGTGTTTTGTTTTGATTTT
1 TTTTTTGTGTTTTGTTTTGATTTT
510918 TATCATTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 8 0.36
25 14 0.64
ACGTcount: A:0.02, C:0.00, G:0.18, T:0.80
Consensus pattern (25 bp):
TTTTTTGTGTTTTGTTTTGATTTTG
Found at i:517518 original size:173 final size:174
Alignment explanation
Indices: 517097--517542 Score: 527
Period size: 173 Copynumber: 2.6 Consensus size: 174
517087 CTGGAGTAGT
* * *** * * * *
517097 AACAACAAATTTCTATTAGGACTAGTGTAAATGTAGTTTAAATTAGACTACTTCGATAAGTAATG
1 AACAACAAATTTCAATTAGAACTAGTGTAAATGTACAGTAAATTGGACTATTTAGACAAGTAATG
* * * * *
517162 ATCAATTTCAATTAGAATTAGTGTTATTATATATACAAATTTATCAACTAAACTACTAATCACTA
66 ATCAATTTCAATTAGAATTAATGTAACTATATATACAAATTCATCAACTAAACTACTAATCACAA
* * * *
517227 ATTTAAAGTAGAATTAGTGTAACCATATATGTAATTAGAGTAGC
131 ATTTAAAATAGAATTAGTGTAACCATATATGAAATTAAAATAGC
* * * * *
517271 AACAACCAATTTCAATTAGAAATAGTGCAAATGTATAGTAAA-TGGACTATTTGGACAAGTAATG
1 AACAACAAATTTCAATTAGAACTAGTGTAAATGTACAGTAAATTGGACTATTTAGACAAGTAATG
* * * * * * ** * * *
517335 ACCGATTTCAATTAGAATCAATGTAACTATATGTACATATTCATCAATTGGATTATTAATTACAA
66 ATCAATTTCAATTAGAATTAATGTAACTATATATACAAATTCATCAACTAAACTACTAATCACAA
*
517400 ATTTAAAATAGAATTAGTGTAACTATATA-GAAATTAAAATAGC
131 ATTTAAAATAGAATTAGTGTAACCATATATGAAATTAAAATAGC
* * * *
517443 AACAACTAATTTCAATTAGAACTAGTGTAAGTGTACAGTAAATTGGATTATTTAGACAATTAATG
1 AACAACAAATTTCAATTAGAACTAGTGTAAATGTACAGTAAATTGGACTATTTAGACAAGTAATG
517508 ATCAATTTCAATTAGAATTAATGTAACTATATATA
66 ATCAATTTCAATTAGAATTAATGTAACTATATATA
517543 TATTTATAAA
Statistics
Matches: 226, Mismatches: 45, Indels: 3
0.82 0.16 0.01
Matches are distributed among these distances:
172 48 0.21
173 144 0.64
174 34 0.15
ACGTcount: A:0.43, C:0.10, G:0.12, T:0.35
Consensus pattern (174 bp):
AACAACAAATTTCAATTAGAACTAGTGTAAATGTACAGTAAATTGGACTATTTAGACAAGTAATG
ATCAATTTCAATTAGAATTAATGTAACTATATATACAAATTCATCAACTAAACTACTAATCACAA
ATTTAAAATAGAATTAGTGTAACCATATATGAAATTAAAATAGC
Found at i:517920 original size:16 final size:16
Alignment explanation
Indices: 517891--517931 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
517881 TGAATATACG
517891 AATTTA-TT-TTTTTT
1 AATTTATTTATTTTTT
*
517905 GATTTATTTATTTTTT
1 AATTTATTTATTTTTT
*
517921 AATTTTTTTAT
1 AATTTATTTAT
517932 CTACTAAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
14 5 0.23
15 2 0.09
16 15 0.68
ACGTcount: A:0.22, C:0.00, G:0.02, T:0.76
Consensus pattern (16 bp):
AATTTATTTATTTTTT
Found at i:518550 original size:22 final size:23
Alignment explanation
Indices: 518511--518553 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
518501 TAATAATTTA
518511 AAAAAATTAAATTGATTCAAATT
1 AAAAAATTAAATTGATTCAAATT
* *
518534 AAAAAA-TAATTTTATTCAAA
1 AAAAAATTAAATTGATTCAAA
518554 CATAACTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.58, C:0.05, G:0.02, T:0.35
Consensus pattern (23 bp):
AAAAAATTAAATTGATTCAAATT
Found at i:519380 original size:17 final size:16
Alignment explanation
Indices: 519347--519400 Score: 60
Period size: 16 Copynumber: 3.4 Consensus size: 16
519337 TATTTAAAGT
519347 ATTTTATATTTATATAA
1 ATTTTATA-TTATATAA
519364 ATTTTGATA-TATA-ATA
1 ATTTT-ATATTATATA-A
519380 A-TTTATATTATATAA
1 ATTTTATATTATATAA
519395 ATTTTA
1 ATTTTA
519401 AAATATATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 11
0.74 0.00 0.26
Matches are distributed among these distances:
14 3 0.09
15 10 0.31
16 11 0.34
17 5 0.16
18 3 0.09
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56
Consensus pattern (16 bp):
ATTTTATATTATATAA
Found at i:527506 original size:12 final size:12
Alignment explanation
Indices: 527489--527513 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
527479 CTTATATCAC
527489 ATTATTACATAA
1 ATTATTACATAA
527501 ATTATTACATAA
1 ATTATTACATAA
527513 A
1 A
527514 GATAATGTTT
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:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (12 bp):
ATTATTACATAA
Found at i:528078 original size:31 final size:31
Alignment explanation
Indices: 528037--528096 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
528027 TCGGAAAAAA
* *
528037 AAAAAAGCCAAGCA-GTCAATGAAGTAAATCC
1 AAAAAAGCCAAACACGT-AATGAAGCAAATCC
*
528068 AAAAATGCCAAACACGTAATGAAGCAAAT
1 AAAAAAGCCAAACACGTAATGAAGCAAAT
528097 TATATTGGTG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 23 0.92
32 2 0.08
ACGTcount: A:0.53, C:0.18, G:0.15, T:0.13
Consensus pattern (31 bp):
AAAAAAGCCAAACACGTAATGAAGCAAATCC
Found at i:528766 original size:22 final size:23
Alignment explanation
Indices: 528712--528770 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
528702 TTTTAAATTT
*
528712 AAGCTCATCTAAACCTAAACTAA
1 AAGCCCATCTAAACCTAAACTAA
* * *
528735 AAGCCTATCTAAACTTAAACT-C
1 AAGCCCATCTAAACCTAAACTAA
528757 AAGCCCATCTAAAC
1 AAGCCCATCTAAAC
528771 AAAACAAAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
22 13 0.42
23 18 0.58
ACGTcount: A:0.44, C:0.29, G:0.05, T:0.22
Consensus pattern (23 bp):
AAGCCCATCTAAACCTAAACTAA
Found at i:530066 original size:254 final size:254
Alignment explanation
Indices: 529617--530125 Score: 1000
Period size: 254 Copynumber: 2.0 Consensus size: 254
529607 TACTTCAACT
529617 TAATTATAACTCTATAGAGATAAAGTGATAGAGTTTAAAATTATCTAGGGGTCTAGATTTTGTAA
1 TAATTATAACTCTATAGAGATAAAGTGATAGAGTTTAAAATTATCTAGGGGTCTAGATTTTGTAA
529682 ATAAGTATTAATCCTAGCCGTCCATTAGATTTAATTTGAGCCATTGATCTATGGGGGATTCAACT
66 ATAAGTATTAATCCTAGCCGTCCATTAGATTTAATTTGAGCCATTGATCTATGGGGGATTCAACT
*
529747 ATAAATAGAGGGCTCCCTAACCTCATTTGTATCATCAAATACTTAAGAAATATAAGTAGCATTCC
131 ATAAATAGAGGGCTCCCTAACCTCATTTGTATAATCAAATACTTAAGAAATATAAGTAGCATTCC
529812 TCTCTATTTTTCTTTGTCTTTAGTTTTCTGCTTAGCTTCAAAGCTTTTTAGCTTTAGTG
196 TCTCTATTTTTCTTTGTCTTTAGTTTTCTGCTTAGCTTCAAAGCTTTTTAGCTTTAGTG
529871 TAATTATAACTCTATAGAGATAAAGTGATAGAGTTTAAAATTATCTAGGGGTCTAGATTTTGTAA
1 TAATTATAACTCTATAGAGATAAAGTGATAGAGTTTAAAATTATCTAGGGGTCTAGATTTTGTAA
*
529936 ATAAGTATTAATCCTAGCCGTCCATTAGATTTAATTTGAGCTATTGATCTATGGGGGATTCAACT
66 ATAAGTATTAATCCTAGCCGTCCATTAGATTTAATTTGAGCCATTGATCTATGGGGGATTCAACT
530001 ATAAATAGAGGGCTCCCTAACCTCATTTGTATAATCAAATACTTAAGAAATATAAGTAGCATTCC
131 ATAAATAGAGGGCTCCCTAACCTCATTTGTATAATCAAATACTTAAGAAATATAAGTAGCATTCC
530066 TCTCTATTTTTCTTTGTCTTTAGTTTTCTGCTTAGCTTCAAAGCTTTTTAGCTTTAGTG
196 TCTCTATTTTTCTTTGTCTTTAGTTTTCTGCTTAGCTTCAAAGCTTTTTAGCTTTAGTG
530125 T
1 T
530126 CTTAGGGAAT
Statistics
Matches: 253, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
254 253 1.00
ACGTcount: A:0.30, C:0.15, G:0.16, T:0.39
Consensus pattern (254 bp):
TAATTATAACTCTATAGAGATAAAGTGATAGAGTTTAAAATTATCTAGGGGTCTAGATTTTGTAA
ATAAGTATTAATCCTAGCCGTCCATTAGATTTAATTTGAGCCATTGATCTATGGGGGATTCAACT
ATAAATAGAGGGCTCCCTAACCTCATTTGTATAATCAAATACTTAAGAAATATAAGTAGCATTCC
TCTCTATTTTTCTTTGTCTTTAGTTTTCTGCTTAGCTTCAAAGCTTTTTAGCTTTAGTG
Found at i:530853 original size:33 final size:33
Alignment explanation
Indices: 530809--530877 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
530799 CTACCACTGT
*
530809 TTGTATCGATACATGGT-ACAATGTATCGATACA
1 TTGTATCGATACATGATGA-AATGTATCGATACA
* *
530842 TTGTATGGATACATGATGAATTGTATCGATACA
1 TTGTATCGATACATGATGAAATGTATCGATACA
530875 TTG
1 TTG
530878 CTTGTAACGG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
33 31 0.97
34 1 0.03
ACGTcount: A:0.32, C:0.12, G:0.20, T:0.36
Consensus pattern (33 bp):
TTGTATCGATACATGATGAAATGTATCGATACA
Found at i:537262 original size:22 final size:22
Alignment explanation
Indices: 537237--537286 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
537227 AAGTAAACAC
*
537237 AAAAAACAAAGCAAAAAAAAAA
1 AAAAAACAAAACAAAAAAAAAA
* * *
537259 AAAAAACAAAACAACACACAAA
1 AAAAAACAAAACAAAAAAAAAA
537281 AAAAAA
1 AAAAAA
537287 GTGCAAAGGC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.84, C:0.14, G:0.02, T:0.00
Consensus pattern (22 bp):
AAAAAACAAAACAAAAAAAAAA
Found at i:538635 original size:31 final size:31
Alignment explanation
Indices: 538578--538788 Score: 211
Period size: 30 Copynumber: 6.9 Consensus size: 31
538568 CCTCAAATAC
* *
538578 CTTCTTAAAGTCCACGACTCAGTGGCAATCT
1 CTTCTCAAAGTCCATGACTCAGTGGCAATCT
* *
538609 CTTCTCAAAG-CTCATGATTCAATGGC-AT-T
1 CTTCTCAAAGTC-CATGACTCAGTGGCAATCT
* * *
538638 TTGTCTCAAAGTCCACGACTGAGTGGCAATCT
1 CT-TCTCAAAGTCCATGACTCAGTGGCAATCT
*
538670 CTTCTCAAAGCCCATGACTCAGT-GCAAT-T
1 CTTCTCAAAGTCCATGACTCAGTGGCAATCT
* *
538699 TTGTCTCAAAGTCCATGACTCAGTGGCATTCT
1 CT-TCTCAAAGTCCATGACTCAGTGGCAATCT
*
538731 TTTCTTCAAAGTCCATGACTCAGTGGC-ATCT
1 CTTC-TCAAAGTCCATGACTCAGTGGCAATCT
* *
538762 CTT-TCCAAGGTCCACGACTCAGTGGCA
1 CTTCT-CAAAGTCCATGACTCAGTGGCA
538789 CCTTCCTTTT
Statistics
Matches: 149, Mismatches: 20, Indels: 22
0.78 0.10 0.12
Matches are distributed among these distances:
29 5 0.03
30 65 0.44
31 52 0.35
32 27 0.18
ACGTcount: A:0.25, C:0.27, G:0.18, T:0.30
Consensus pattern (31 bp):
CTTCTCAAAGTCCATGACTCAGTGGCAATCT
Found at i:538654 original size:61 final size:61
Alignment explanation
Indices: 538584--538788 Score: 265
Period size: 61 Copynumber: 3.3 Consensus size: 61
538574 ATACCTTCTT
* *
538584 AAAGTCCACGACTCAGTGGCAATCTCTTCTCAAAGCTCATGATTCAATGGCATTTTGTCTC
1 AAAGTCCACGACTCAGTGGCAATCTCTTCTCAAAGCTCATGACTCAGTGGCATTTTGTCTC
* *
538645 AAAGTCCACGACTGAGTGGCAATCTCTTCTCAAAGCCCATGACTCAGT-GCAATTTTGTCTC
1 AAAGTCCACGACTCAGTGGCAATCTCTTCTCAAAGCTCATGACTCAGTGGC-ATTTTGTCTC
* * *
538706 AAAGTCCATGACTCAGTGGCATTCTTTTCTTCAAAG-TCCATGACTCAGTGGCATCTCTT-TC-C
1 AAAGTCCACGACTCAGTGGCAATCTCTTC-TCAAAGCT-CATGACTCAGTGGCAT-T-TTGTCTC
*
538768 AAGGTCCACGACTCAGTGGCA
1 AAAGTCCACGACTCAGTGGCA
538789 CCTTCCTTTT
Statistics
Matches: 127, Mismatches: 11, Indels: 11
0.85 0.07 0.07
Matches are distributed among these distances:
60 2 0.02
61 79 0.62
62 39 0.31
63 5 0.04
64 2 0.02
ACGTcount: A:0.25, C:0.27, G:0.18, T:0.29
Consensus pattern (61 bp):
AAAGTCCACGACTCAGTGGCAATCTCTTCTCAAAGCTCATGACTCAGTGGCATTTTGTCTC
Found at i:538938 original size:33 final size:33
Alignment explanation
Indices: 538897--538988 Score: 157
Period size: 33 Copynumber: 2.8 Consensus size: 33
538887 TCTTTTCTTC
*
538897 AAAGCCCACACAAGTCGGTGGCAACCATTCTCT
1 AAAGCCCACACAAGTCGGTGGCAACCACTCTCT
*
538930 AAAGCCCACACAAGTCAGTGGCAACCACTCTCT
1 AAAGCCCACACAAGTCGGTGGCAACCACTCTCT
*
538963 AAAGCCCACACAAGTTGGTGGCAACC
1 AAAGCCCACACAAGTCGGTGGCAACC
538989 CCTTTAAGTC
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 55 1.00
ACGTcount: A:0.33, C:0.34, G:0.18, T:0.15
Consensus pattern (33 bp):
AAAGCCCACACAAGTCGGTGGCAACCACTCTCT
Found at i:539047 original size:49 final size:49
Alignment explanation
Indices: 538990--540100 Score: 1508
Period size: 49 Copynumber: 22.7 Consensus size: 49
538980 GTGGCAACCC
* *
538990 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCAT
1 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
* *
539039 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCATATTGGCACTTTCAT
1 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
539088 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACC-TCAT
1 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
* *
539136 CTTTAAGTCCAATGTAGTTGGCCTTGAATCAGCACATTGGCACC-TCAC
1 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
* *
539184 CTTCTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCAT
1 CTT-TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
*
539234 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACC-TCAC
1 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
* *
539282 CTTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCAT
1 C-TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
*
539332 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCATATTGGCACCTTCAT
1 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
*
539381 CTTTAAGTCCAATGTAGCTGGCCTTGAATTAGCACATTGGCACC-TCAT
1 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
* ** *
539429 CTTTAAGTCCAATGTAGTTGGCCTTGAATCAGCACATTTTCACC-TCAC
1 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
* * *
539477 CTTCTAAGTCCAATATAGCTGGCCTTGAATCAACATATTGGCACCTTCAT
1 CTT-TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
*
539527 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACC-TCAC
1 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
** *
539575 CTTTTAAGTCCAACATAGCTGGCCTTGAATCAGCATATTGGCACCTTCAT
1 C-TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
*
539625 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACC-TCAC
1 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
* *
539673 CTTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCAT
1 C-TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
* *
539723 CTTTAAGTCCAATGTAGCTGGCCTTAAATCAGCACATTGGCACC-TCAC
1 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
* * *
539771 CTTTTAAGTCTAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCAT
1 C-TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
* *
539821 CTTTAAGTCCAATGTAGCTGGCCTTGACTTAGCACATTGGCACC-TCAT
1 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
* * * * *
539869 CTTTTAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTT-GT
1 C-TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
* * * *
539918 CTTTAAGACCAATGTAGCTGGCCTTGACTCAACACATTGTCACCTTCAT
1 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
* * * * *
539967 CTTTAAGTCCAATATCGCTGGCCTTGACTCAGCATATTGGCGCCTTCAT
1 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
* * * * * *
540016 C-ATAA-CCCAATGTCGTTGGCCTTGAATCAGAACATTGGCATTCTTTTCAT
1 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA--C-CTTCAT
* * * * *
540066 CTTCAAGTCTAACTGTTGCTGACCGTGAATCAGCA
1 CTTTAAGTCCAA-TGTAGCTGGCCTTGAATCAGCA
540101 TATTAACATC
Statistics
Matches: 941, Mismatches: 100, Indels: 38
0.87 0.09 0.04
Matches are distributed among these distances:
47 28 0.03
48 165 0.18
49 691 0.73
50 35 0.04
51 2 0.00
52 3 0.00
53 17 0.02
ACGTcount: A:0.25, C:0.26, G:0.17, T:0.31
Consensus pattern (49 bp):
CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
Found at i:539275 original size:98 final size:98
Alignment explanation
Indices: 538991--540055 Score: 1696
Period size: 98 Copynumber: 10.9 Consensus size: 98
538981 TGGCAACCCC
538991 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAG
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAG
* * *
539056 CTGGCCTTGAATCAGCATATTGGCACTTTCATC-
66 CTGGCCTTGAATCAGCACATTGGCAC-CTCACCT
* *
539089 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACC-TCATCTTTAAGTCCAATGTAG
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAG
*
539153 TTGGCCTTGAATCAGCACATTGGCACCTCACCT
66 CTGGCCTTGAATCAGCACATTGGCACCTCACCT
*
539186 TCTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAG
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAG
539251 CTGGCCTTGAATCAGCACATTGGCACCTCACCT
66 CTGGCCTTGAATCAGCACATTGGCACCTCACCT
539284 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAG
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAG
* *
539349 CTGGCCTTGAATCAGCATATTGGCACCTTCATC-
66 CTGGCCTTGAATCAGCACATTGGCACC-TCACCT
* * *
539382 TTTAAGTCCAATGTAGCTGGCCTTGAATTAGCACATTGGCACC-TCATCTTTAAGTCCAATGTAG
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAG
* **
539446 TTGGCCTTGAATCAGCACATTTTCACCTCACCT
66 CTGGCCTTGAATCAGCACATTGGCACCTCACCT
* *
539479 TCTAAGTCCAATATAGCTGGCCTTGAATCAACATATTGGCACCTTCATCTTTAAGTCCAATGTAG
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAG
539544 CTGGCCTTGAATCAGCACATTGGCACCTCACCT
66 CTGGCCTTGAATCAGCACATTGGCACCTCACCT
*
539577 TTTAAGTCCAACATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAG
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAG
539642 CTGGCCTTGAATCAGCACATTGGCACCTCACCT
66 CTGGCCTTGAATCAGCACATTGGCACCTCACCT
539675 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAG
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAG
*
539740 CTGGCCTTAAATCAGCACATTGGCACCTCACCT
66 CTGGCCTTGAATCAGCACATTGGCACCTCACCT
*
539773 TTTAAGTCTAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAG
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAG
* * *
539838 CTGGCCTTGACTTAGCACATTGGCACCTCATCT
66 CTGGCCTTGAATCAGCACATTGGCACCTCACCT
* * * *
539871 TTTAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTT-GTCTTTAAGACCAATGTAG
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAG
* * * *
539935 CTGGCCTTGACTCAACACATTGTCACCTTCATC-
66 CTGGCCTTGAATCAGCACATTGGCACC-TCACCT
* * * * * *
539968 TTTAAGTCCAATATCGCTGGCCTTGACTCAGCATATTGGCGCCTTCATC-ATAA-CCCAATGTCG
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAG
* *
540031 TTGGCCTTGAATCAGAACATTGGCA
66 CTGGCCTTGAATCAGCACATTGGCA
540056 TTCTTTTCAT
Statistics
Matches: 901, Mismatches: 59, Indels: 16
0.92 0.06 0.02
Matches are distributed among these distances:
96 36 0.04
97 253 0.28
98 608 0.67
99 4 0.00
ACGTcount: A:0.25, C:0.26, G:0.17, T:0.31
Consensus pattern (98 bp):
TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAG
CTGGCCTTGAATCAGCACATTGGCACCTCACCT
Found at i:539518 original size:293 final size:294
Alignment explanation
Indices: 538991--540055 Score: 1773
Period size: 293 Copynumber: 3.6 Consensus size: 294
538981 TGGCAACCCC
538991 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAG
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAG
* * *
539056 CTGGCCTTGAATCAGCATATTGGCACTTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGC
66 CTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGC
539121 ACATTGGCACC-TCATCTTTAAGTCCAATGTAGTTGGCCTTGAATCAGCACATTGGCACCTCACC
131 ACATTGGCACCTTCATCTTTAAGTCCAATGTAGTTGGCCTTGAATCAGCACATTGGCACCTCACC
539185 TTCTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTA
196 TTCTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTA
539250 GCTGGCCTTGAATCAGCACATTGGCACCTCACCT
261 GCTGGCCTTGAATCAGCACATTGGCACCTCACCT
539284 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAG
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAG
* * *
539349 CTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATTAGC
66 CTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGC
**
539414 ACATTGGCACC-TCATCTTTAAGTCCAATGTAGTTGGCCTTGAATCAGCACATTTTCACCTCACC
131 ACATTGGCACCTTCATCTTTAAGTCCAATGTAGTTGGCCTTGAATCAGCACATTGGCACCTCACC
*
539478 TTCTAAGTCCAATATAGCTGGCCTTGAATCAACATATTGGCACCTTCATCTTTAAGTCCAATGTA
196 TTCTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTA
539543 GCTGGCCTTGAATCAGCACATTGGCACCTCACCT
261 GCTGGCCTTGAATCAGCACATTGGCACCTCACCT
*
539577 TTTAAGTCCAACATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAG
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAG
*
539642 CTGGCCTTGAATCAGCACATTGGCACC-TCACCTTTTAAGTCCAATATAGCTGGCCTTGAATCAG
66 CTGGCCTTGAATCAGCACATTGGCACCTTCATC-TTTAAGTCCAATATAGCTGGCCTTGAATCAG
* * *
539706 CATATTGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTAAATCAGCACATTGGCACCTCAC
130 CACATTGGCACCTTCATCTTTAAGTCCAATGTAGTTGGCCTTGAATCAGCACATTGGCACCTCAC
* *
539771 CTTTTAAGTCTAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGT
195 CTTCTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGT
* * *
539836 AGCTGGCCTTGACTTAGCACATTGGCACCTCATCT
260 AGCTGGCCTTGAATCAGCACATTGGCACCTCACCT
* * * *
539871 TTTAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTT-GTCTTTAAGACCAATGTAG
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAG
* * * * *
539935 CTGGCCTTGACTCAACACATTGTCACCTTCATCTTTAAGTCCAATATCGCTGGCCTTGACTCAGC
66 CTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGC
* * * * * *
540000 ATATTGGCGCCTTCATC-ATAA-CCCAATGTCGTTGGCCTTGAATCAGAACATTGGCA
131 ACATTGGCACCTTCATCTTTAAGTCCAATGTAGTTGGCCTTGAATCAGCACATTGGCA
540056 TTCTTTTCAT
Statistics
Matches: 730, Mismatches: 39, Indels: 8
0.94 0.05 0.01
Matches are distributed among these distances:
291 30 0.04
292 7 0.01
293 505 0.69
294 188 0.26
ACGTcount: A:0.25, C:0.26, G:0.17, T:0.31
Consensus pattern (294 bp):
TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAG
CTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGC
ACATTGGCACCTTCATCTTTAAGTCCAATGTAGTTGGCCTTGAATCAGCACATTGGCACCTCACC
TTCTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTA
GCTGGCCTTGAATCAGCACATTGGCACCTCACCT
Found at i:541500 original size:19 final size:19
Alignment explanation
Indices: 541474--541532 Score: 82
Period size: 19 Copynumber: 3.1 Consensus size: 19
541464 TTTATATCGA
541474 TACATTGTATCGATACATG
1 TACATTGTATCGATACATG
*
541493 TTCATTGTATCGATACATG
1 TACATTGTATCGATACATG
* *
541512 GACAATTGTATCGATAAATG
1 TAC-ATTGTATCGATACATG
541532 T
1 T
541533 GATTGGCAGT
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 19 0.56
20 15 0.44
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.37
Consensus pattern (19 bp):
TACATTGTATCGATACATG
Found at i:541586 original size:20 final size:20
Alignment explanation
Indices: 541561--541609 Score: 98
Period size: 20 Copynumber: 2.5 Consensus size: 20
541551 TACCACTGTT
541561 TGTATCGATACATGGTACAA
1 TGTATCGATACATGGTACAA
541581 TGTATCGATACATGGTACAA
1 TGTATCGATACATGGTACAA
541601 TGTATCGAT
1 TGTATCGAT
541610 TCATTGTATC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.33, C:0.14, G:0.20, T:0.33
Consensus pattern (20 bp):
TGTATCGATACATGGTACAA
Found at i:541924 original size:19 final size:18
Alignment explanation
Indices: 541899--541966 Score: 74
Period size: 19 Copynumber: 3.9 Consensus size: 18
541889 AATTCAACGA
541899 TTTGTATCGATACATAAG
1 TTTGTATCGATACATAAG
541917 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
*
541933 --TGTATTGATACATAAG
1 TTTGTATCGATACATAAG
541949 TTTTGTATCGATACATAA
1 -TTTGTATCGATACATAA
541967 TTAGCTACTG
Statistics
Matches: 41, Mismatches: 2, Indels: 13
0.73 0.04 0.23
Matches are distributed among these distances:
13 10 0.24
15 2 0.05
17 2 0.05
18 1 0.02
19 26 0.63
ACGTcount: A:0.34, C:0.10, G:0.16, T:0.40
Consensus pattern (18 bp):
TTTGTATCGATACATAAG
Found at i:541937 original size:32 final size:32
Alignment explanation
Indices: 541901--541963 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
541891 TTCAACGATT
541901 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
* *
541933 TGTATTGATACATAAGTTTTGTATCGATACA
1 TGTATCGATACATAAGTGTTGTATCGATACA
541964 TAATTAGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.33, C:0.11, G:0.17, T:0.38
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:542025 original size:13 final size:13
Alignment explanation
Indices: 542007--542031 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
541997 ATTACTCAAG
542007 TGTATCGATACAT
1 TGTATCGATACAT
542020 TGTATCGATACA
1 TGTATCGATACA
542032 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:542084 original size:52 final size:52
Alignment explanation
Indices: 542040--542165 Score: 216
Period size: 52 Copynumber: 2.4 Consensus size: 52
542030 CACTGATCTT
*
542040 TGTATCGATACATGCAGGCAAATATGCCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATATGCCCAAATGTATCGATACACTATGAAA
* *
542092 TGTATTGATACATGCAGGCAAATTTGCCCAAATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATATGCCCAAATGTATCGATACACTATGAAA
*
542144 TGTATCAATACATGCAGGCAAA
1 TGTATCGATACATGCAGGCAAA
542166 ATTTCATATT
Statistics
Matches: 69, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
52 69 1.00
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.26
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATATGCCCAAATGTATCGATACACTATGAAA
Found at i:551407 original size:13 final size:13
Alignment explanation
Indices: 551389--551426 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
551379 ACAACATTCT
551389 TTGTATCGATACA
1 TTGTATCGATACA
*
551402 TTGTATGGATACA
1 TTGTATCGATACA
551415 TTGTATCGATAC
1 TTGTATCGATAC
551427 CTGGGTTACT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.29, C:0.13, G:0.18, T:0.39
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:553374 original size:22 final size:22
Alignment explanation
Indices: 553317--553380 Score: 101
Period size: 22 Copynumber: 2.9 Consensus size: 22
553307 TGATTTGACA
**
553317 AAGGGGGAGAAATGCTTTGATT
1 AAGGGGGAGAAATTTTTTGATT
*
553339 AAGGGGAAGAAATTTTTTGATT
1 AAGGGGGAGAAATTTTTTGATT
553361 AAGGGGGAGAAATTTTTTGA
1 AAGGGGGAGAAATTTTTTGA
553381 GAAATTTTTA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 38 1.00
ACGTcount: A:0.34, C:0.02, G:0.33, T:0.31
Consensus pattern (22 bp):
AAGGGGGAGAAATTTTTTGATT
Found at i:554092 original size:33 final size:33
Alignment explanation
Indices: 554050--554114 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
554040 CTACTGTTTG
*
554050 TATCGATACATGGT-ACAATGTATCGATACATTA
1 TATCGATACATGATGA-AATGTATCGATACATTA
*
554083 TATCGATACATGATGAATTGTATCGATACATT
1 TATCGATACATGATGAAATGTATCGATACATT
554115 GCTTGTAACG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 28 0.97
34 1 0.03
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.35
Consensus pattern (33 bp):
TATCGATACATGATGAAATGTATCGATACATTA
Found at i:555012 original size:12 final size:12
Alignment explanation
Indices: 554995--555023 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
554985 GGAGATAGAA
554995 GAGCTCAAGGGT
1 GAGCTCAAGGGT
555007 GAGCTCAAGGGT
1 GAGCTCAAGGGT
555019 GAGCT
1 GAGCT
555024 ATTGTCATGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.24, C:0.17, G:0.41, T:0.17
Consensus pattern (12 bp):
GAGCTCAAGGGT
Found at i:561924 original size:20 final size:19
Alignment explanation
Indices: 561878--561934 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
561868 TTTTATCGAT
*
561878 ACATTGTATCGATACATGT
1 ACATTGTATCGATACATGC
* *
561897 TCATTGTATCTATACATGC
1 ACATTGTATCGATACATGC
561916 ACAATTGTATCGATACATG
1 AC-ATTGTATCGATACATG
561935 AAACTGGCAG
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
19 17 0.53
20 15 0.47
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.37
Consensus pattern (19 bp):
ACATTGTATCGATACATGC
Found at i:566984 original size:13 final size:13
Alignment explanation
Indices: 566966--566991 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
566956 ACATAAGTGT
566966 TGTATCGATACAA
1 TGTATCGATACAA
566979 TGTATCGATACAA
1 TGTATCGATACAA
566992 AGTTACCTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Done.