Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold471
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 1282308
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.29
Warning! 143812 characters in sequence are not A, C, G, or T
File 4 of 4
Found at i:693769 original size:17 final size:16
Alignment explanation
Indices: 693747--693780 Score: 59
Period size: 17 Copynumber: 2.1 Consensus size: 16
693737 TTTCTTTTAA
693747 TTTGTTTAGTTGTGTTG
1 TTTGTTTAGTTG-GTTG
693764 TTTGTTTAGTTGGTTG
1 TTTGTTTAGTTGGTTG
693780 T
1 T
693781 GTGGTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.06, C:0.00, G:0.29, T:0.65
Consensus pattern (16 bp):
TTTGTTTAGTTGGTTG
Found at i:693787 original size:17 final size:17
Alignment explanation
Indices: 693750--693787 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
693740 CTTTTAATTT
*
693750 GTTTAGTTGTGTTGTTT
1 GTTTAGTTGTGTTGTTG
693767 GTTTAGTTG-GTTGTGTG
1 GTTTAGTTGTGTTGT-TG
693784 GTTT
1 GTTT
693788 TTTTTTCTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 5 0.26
17 14 0.74
ACGTcount: A:0.05, C:0.00, G:0.34, T:0.61
Consensus pattern (17 bp):
GTTTAGTTGTGTTGTTG
Found at i:698173 original size:169 final size:168
Alignment explanation
Indices: 697865--698523 Score: 969
Period size: 168 Copynumber: 3.9 Consensus size: 168
697855 ACCATGCTTT
* * * * *
697865 AATATATACGGGAGTAGAGAAGAAGATTTTTTAAGATTTAATACATTTTTACTATAAGGCCATAT
1 AATATATACGAGAGTAGAGAAGAAGATTTTCTAAGATTAAATACATTTTTAATATATGGCCATAT
697930 TGGCCCCACCCTAGAGCCTGAACCCCTGACCCAGGGGTCATGAATTTCACAATTTAGATAGAGGG
66 TGGCCCCACCCTAGAGCCTGAACCCCTGACCCAGGGGTCATGAATTTCACAATTTAGATAGAGGG
*
697995 CCTCATGGACATCATAATCATGCATTTAGTTTTTAACA
131 CCTCATGGACATCATAACCATGCATTTAGTTTTTAACA
* * * * *
698033 AATATATATGAGAGTAAAGAAGAATATTTGTTTAAGATTAAATACTTTTTTAATATATGGCCATA
1 AATATATACGAGAGTAGAGAAGAAGATTT-TCTAAGATTAAATACATTTTTAATATATGGCCATA
* * * * * *
698098 TTGTCCCCACCCTAGAGCCTGAACCCCTGAGCCAGGGGTTATGAATTTCACAATTTAGGTTGAAG
65 TTGGCCCCACCCTAGAGCCTGAACCCCTGACCCAGGGGTCATGAATTTCACAATTTAGATAGAGG
* * *
698163 GCTTCATGGACAACATAACCATGCATTTACTTTTTAACA
130 GCCTCATGGACATCATAACCATGCATTTAGTTTTTAACA
*
698202 AATATATACGGGAGTAGAGAAGAAGATTTTCTAAGATTAAATACATTTTTAATATATGGCCATAT
1 AATATATACGAGAGTAGAGAAGAAGATTTTCTAAGATTAAATACATTTTTAATATATGGCCATAT
* * *
698267 TGGCCCCAGCCTAGACCCTGAACCCCTGACCCAGGGGTCATGAATTTCACAATTTTGATAGAGGG
66 TGGCCCCACCCTAGAGCCTGAACCCCTGACCCAGGGGTCATGAATTTCACAATTTAGATAGAGGG
*
698332 CCTCATGGACATCATAATCATGCATTTAGTTTTTAACA
131 CCTCATGGACATCATAACCATGCATTTAGTTTTTAACA
* * * *
698370 AATATATATGAGAGTAGAGAAGCAGATTTTCTAAGATTTAATACATTTTTACTATATGGCCATAT
1 AATATATACGAGAGTAGAGAAGAAGATTTTCTAAGATTAAATACATTTTTAATATATGGCCATAT
** * * * *
698435 TGGCCCCACCCTAGAGCCAAAATCCCTGACCCAGGGGCCATAAATTTCACAAGTTT-GGTAGAGG
66 TGGCCCCACCCTAGAGCCTGAACCCCTGACCCAGGGGTCATGAATTTCACAA-TTTAGATAGAGG
*
698499 GCCTCATGGAAATCATAACCATGCA
130 GCCTCATGGACATCATAACCATGCA
698524 ACCAGTTTTC
Statistics
Matches: 437, Mismatches: 52, Indels: 4
0.89 0.11 0.01
Matches are distributed among these distances:
168 284 0.65
169 153 0.35
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Consensus pattern (168 bp):
AATATATACGAGAGTAGAGAAGAAGATTTTCTAAGATTAAATACATTTTTAATATATGGCCATAT
TGGCCCCACCCTAGAGCCTGAACCCCTGACCCAGGGGTCATGAATTTCACAATTTAGATAGAGGG
CCTCATGGACATCATAACCATGCATTTAGTTTTTAACA
Found at i:698343 original size:337 final size:336
Alignment explanation
Indices: 697865--698523 Score: 1052
Period size: 337 Copynumber: 2.0 Consensus size: 336
697855 ACCATGCTTT
* * *
697865 AATATATACGGGAGTAGAGAAGAAGATTTTTTAAGATTTAATACATTTTTACTATAAGGCCATAT
1 AATATATACGGGAGTAGAGAAGAAGATTTTCTAAGATTAAATACATTTTTAATATAAGGCCATAT
*
697930 TGGCCCCACCCTAGAGCCTGAACCCCTGACCCAGGGGTCATGAATTTCACAATTTAGATAGAGGG
66 TGGCCCCACCCTAGACCCTGAACCCCTGACCCAGGGGTCATGAATTTCACAATTTAGATAGAGGG
*
697995 CCTCATGGACATCATAATCATGCATTTAGTTTTTAACAAATATATATGAGAGTAAAGAAGAATAT
131 CCTCATGGACATCATAATCATGCATTTAGTTTTTAACAAATATATATGAGAGTAAAGAAGAAGAT
* * * **
698060 TTGTTTAAGATTAAATACTTTTTTAATATATGGCCATATTGTCCCCACCCTAGAGCCTGAACCCC
196 TT-TCTAAGATTAAATACATTTTTAATATATGGCCATATTGGCCCCACCCTAGAGCCAAAACCCC
* ** * * *
698125 TGAGCCAGGGGTTATGAATTTCACAA-TTTAGGTTGAAGGCTTCATGGACAA-CATAACCATGCA
260 TGACCCAGGGGCCATAAATTTCACAAGTTT-GGTAGAAGGCCTCATGGA-AATCATAACCATGCA
698188 TTTACTTTTTAACA
323 TTTACTTTTTAACA
*
698202 AATATATACGGGAGTAGAGAAGAAGATTTTCTAAGATTAAATACATTTTTAATATATGGCCATAT
1 AATATATACGGGAGTAGAGAAGAAGATTTTCTAAGATTAAATACATTTTTAATATAAGGCCATAT
* *
698267 TGGCCCCAGCCTAGACCCTGAACCCCTGACCCAGGGGTCATGAATTTCACAATTTTGATAGAGGG
66 TGGCCCCACCCTAGACCCTGAACCCCTGACCCAGGGGTCATGAATTTCACAATTTAGATAGAGGG
* *
698332 CCTCATGGACATCATAATCATGCATTTAGTTTTTAACAAATATATATGAGAGTAGAGAAGCAGAT
131 CCTCATGGACATCATAATCATGCATTTAGTTTTTAACAAATATATATGAGAGTAAAGAAGAAGAT
* * *
698397 TTTCTAAGATTTAATACATTTTTACTATATGGCCATATTGGCCCCACCCTAGAGCCAAAATCCCT
196 TTTCTAAGATTAAATACATTTTTAATATATGGCCATATTGGCCCCACCCTAGAGCCAAAACCCCT
*
698462 GACCCAGGGGCCATAAATTTCACAAGTTTGGTAGAGGGCCTCATGGAAATCATAACCATGCA
261 GACCCAGGGGCCATAAATTTCACAAGTTTGGTAGAAGGCCTCATGGAAATCATAACCATGCA
698524 ACCAGTTTTC
Statistics
Matches: 295, Mismatches: 25, Indels: 5
0.91 0.08 0.02
Matches are distributed among these distances:
335 2 0.01
336 103 0.35
337 190 0.64
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Consensus pattern (336 bp):
AATATATACGGGAGTAGAGAAGAAGATTTTCTAAGATTAAATACATTTTTAATATAAGGCCATAT
TGGCCCCACCCTAGACCCTGAACCCCTGACCCAGGGGTCATGAATTTCACAATTTAGATAGAGGG
CCTCATGGACATCATAATCATGCATTTAGTTTTTAACAAATATATATGAGAGTAAAGAAGAAGAT
TTTCTAAGATTAAATACATTTTTAATATATGGCCATATTGGCCCCACCCTAGAGCCAAAACCCCT
GACCCAGGGGCCATAAATTTCACAAGTTTGGTAGAAGGCCTCATGGAAATCATAACCATGCATTT
ACTTTTTAACA
Found at i:701808 original size:49 final size:49
Alignment explanation
Indices: 701745--701842 Score: 196
Period size: 49 Copynumber: 2.0 Consensus size: 49
701735 TCAAACTTTA
701745 ATTTTATGTTTATCATCTACACAAAGTAAATTACAGTGCTCTTTAAAAC
1 ATTTTATGTTTATCATCTACACAAAGTAAATTACAGTGCTCTTTAAAAC
701794 ATTTTATGTTTATCATCTACACAAAGTAAATTACAGTGCTCTTTAAAAC
1 ATTTTATGTTTATCATCTACACAAAGTAAATTACAGTGCTCTTTAAAAC
701843 GTAAACAGAA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 49 1.00
ACGTcount: A:0.37, C:0.16, G:0.08, T:0.39
Consensus pattern (49 bp):
ATTTTATGTTTATCATCTACACAAAGTAAATTACAGTGCTCTTTAAAAC
Found at i:704227 original size:2 final size:2
Alignment explanation
Indices: 704220--704271 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
704210 CCTTATCCTG
704220 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
704262 CA CA CA CA CA
1 CA CA CA CA CA
704272 NNNNNNNNNN
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:709893 original size:34 final size:34
Alignment explanation
Indices: 709846--710587 Score: 684
Period size: 34 Copynumber: 21.5 Consensus size: 34
709836 TGCATCTGTC
* * * * *
709846 GTCCATTGCCTGCATTGGCTTTAAACCATCAGTT
1 GTCCAATGCCTGCATTGACTCTAGATCATCAGTT
* * * *
709880 GTCCAATGTCTGCATTGACGCTAGACCATCAGTC
1 GTCCAATGCCTGCATTGACTCTAGATCATCAGTT
* *
709914 GTCCAATGCCTGCATTGACTCTAGACCATCAGAT
1 GTCCAATGCCTGCATTGACTCTAGATCATCAGTT
* *
709948 GTCCAATGTCTGCATT-AGCTCTAGATCATCAGTC
1 GTCCAATGCCTGCATTGA-CTCTAGATCATCAGTT
* * *
709982 GTCCAATGCCTGCATTGACGCTAGACCATCAGTC
1 GTCCAATGCCTGCATTGACTCTAGATCATCAGTT
* *
710016 GTCCAATGCCTGCGTTGACTCTAGACCATCAGTT
1 GTCCAATGCCTGCATTGACTCTAGATCATCAGTT
* *
710050 GTCCAATGTCTGCATTGGCTCTAGATCATCAGTT
1 GTCCAATGCCTGCATTGACTCTAGATCATCAGTT
* * *
710084 GTCCAATGCCTGCATTGACGCTACATCATCAGTC
1 GTCCAATGCCTGCATTGACTCTAGATCATCAGTT
* * * *
710118 GCCCAATGTCTGCATTGGCTCTAAATCATCAGTT
1 GTCCAATGCCTGCATTGACTCTAGATCATCAGTT
* * * *
710152 GTCCAATGTCTGCATTGACCCAAGATCATCAGTC
1 GTCCAATGCCTGCATTGACTCTAGATCATCAGTT
*
710186 GTCTAATGCCTGCATTGACTCTAGATCATCAGTT
1 GTCCAATGCCTGCATTGACTCTAGATCATCAGTT
* *** * * *
710220 GGCTGGTGTCTGCATTGGCTCTAGACCATCAGTT
1 GTCCAATGCCTGCATTGACTCTAGATCATCAGTT
* *
710254 GTCCAATGTCTGTC-TTGACTCTAGATCATCAGTC
1 GTCCAATGCCTG-CATTGACTCTAGATCATCAGTT
710288 GTCCAATGCCTG-ATT-AGCTCTAGATCATCAGTT
1 GTCCAATGCCTGCATTGA-CTCTAGATCATCAGTT
* *
710321 GTCCAATGCCTGCATTGACTCTAGATCAACAGTC
1 GTCCAATGCCTGCATTGACTCTAGATCATCAGTT
* * * *
710355 GTCCATTGCCTGCATTGGCTTAGTAGACCATCAGTT
1 GTCCAATGCCTGCATTGAC-T-CTAGATCATCAGTT
** * *
710391 GTCCAATGCCTGCATTGCCATTGACTCTTTACCATCAGTC
1 GTCCAATG-C--C--TG-CATTGACTCTAGATCATCAGTT
* * * * *
710431 GTCTAATGCCTGCATCGACCCTTGATCATCAGTC
1 GTCCAATGCCTGCATTGACTCTAGATCATCAGTT
* * * *
710465 GTCCAATGCATGCACTGGCT-TAGTTGACCATCAGTT
1 GTCCAATGCCTGCATTGACTCTA---GATCATCAGTT
* * *
710501 GTTCAATGCCTGCATTGACTCTTGATCATCAGTC
1 GTCCAATGCCTGCATTGACTCTAGATCATCAGTT
* * * *
710535 GTCCAATGCCTGCATTGGCTGTGTAGACCATCAGTC
1 GTCCAATGCCTGCATTGAC--TCTAGATCATCAGTT
* *
710571 GTCAAATGCCTGAATTG
1 GTCCAATGCCTGCATTG
710588 GCCTATAGAT
Statistics
Matches: 583, Mismatches: 104, Indels: 40
0.80 0.14 0.06
Matches are distributed among these distances:
32 1 0.00
33 31 0.05
34 445 0.76
35 6 0.01
36 69 0.12
37 3 0.01
39 2 0.00
40 17 0.03
41 3 0.01
42 6 0.01
ACGTcount: A:0.22, C:0.27, G:0.20, T:0.31
Consensus pattern (34 bp):
GTCCAATGCCTGCATTGACTCTAGATCATCAGTT
Found at i:710466 original size:110 final size:110
Alignment explanation
Indices: 710313--710549 Score: 315
Period size: 110 Copynumber: 2.2 Consensus size: 110
710303 AGCTCTAGAT
* * * * * *
710313 CATCAGTTGTCCAATGCCTGCATTGACTCTAGATCAACAGTCGTCCATTGCCTGCATTGGCTTAG
1 CATCAGTCGTCCAATGCCTGCATCGACCCTAGATCAACAGTCGTCCAATGCATGCACTGGCTTAG
710378 TAGACCATCAGTTGTCCAATGCCTGCATTGCCATTGACTCTTTAC
66 TAGACCATCAGTTGTCCAATGCCTGCATTGCCATTGACTCTTTAC
* * *
710423 CATCAGTCGTCTAATGCCTGCATCGACCCTTGATCATCAGTCGTCCAATGCATGCACTGGCTTAG
1 CATCAGTCGTCCAATGCCTGCATCGACCCTAGATCAACAGTCGTCCAATGCATGCACTGGCTTAG
* * * *
710488 TTGACCATCAGTTGTTCAATG-C--C--TG-CATTGACTCTTGAT
66 TAGACCATCAGTTGTCCAATGCCTGCATTGCCATTGACTCTTTAC
710527 CATCAGTCGTCCAATGCCTGCAT
1 CATCAGTCGTCCAATGCCTGCAT
710550 TGGCTGTGTA
Statistics
Matches: 113, Mismatches: 14, Indels: 6
0.85 0.11 0.05
Matches are distributed among these distances:
104 34 0.30
105 2 0.02
107 1 0.01
109 1 0.01
110 75 0.66
ACGTcount: A:0.22, C:0.29, G:0.19, T:0.31
Consensus pattern (110 bp):
CATCAGTCGTCCAATGCCTGCATCGACCCTAGATCAACAGTCGTCCAATGCATGCACTGGCTTAG
TAGACCATCAGTTGTCCAATGCCTGCATTGCCATTGACTCTTTAC
Found at i:712585 original size:21 final size:22
Alignment explanation
Indices: 712559--712600 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
712549 CTGTACACAG
*
712559 ATTTGATAAATA-TGAATCAAT
1 ATTTGAAAAATAGTGAATCAAT
712580 ATTTGAAAAATAGTTGAATCA
1 ATTTGAAAAATAG-TGAATCA
712601 TTTTTTTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 11 0.61
23 7 0.39
ACGTcount: A:0.48, C:0.05, G:0.12, T:0.36
Consensus pattern (22 bp):
ATTTGAAAAATAGTGAATCAAT
Found at i:716068 original size:7 final size:8
Alignment explanation
Indices: 716049--716078 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
716039 AGAACTGACG
716049 ATTTTACA
1 ATTTTACA
716057 ATTTTA-A
1 ATTTTACA
716064 ATTTTACA
1 ATTTTACA
716072 ATTTTAC
1 ATTTTAC
716079 GTTTTTTGTC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.33
8 14 0.67
ACGTcount: A:0.37, C:0.10, G:0.00, T:0.53
Consensus pattern (8 bp):
ATTTTACA
Found at i:716083 original size:15 final size:15
Alignment explanation
Indices: 716049--716077 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
716039 AGAACTGACG
716049 ATTTTACAATTTTAA
1 ATTTTACAATTTTAA
716064 ATTTTACAATTTTA
1 ATTTTACAATTTTA
716078 CGTTTTTTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.55
Consensus pattern (15 bp):
ATTTTACAATTTTAA
Found at i:723441 original size:239 final size:239
Alignment explanation
Indices: 723021--723503 Score: 957
Period size: 239 Copynumber: 2.0 Consensus size: 239
723011 AGAATATAAA
723021 ATTTTCACACTGGTAAAATATCATTTTAATGAAAACGTACCTAACCTTTTTTTCCATGGGTATTT
1 ATTTTCACACTGGTAAAATATCATTTTAATGAAAACGTACCTAACCTTTTTTTCCATGGGTATTT
723086 CTTTAACTTGTTAATATCTGTATTATAGACGCGATACATCATCAGAATTGTTTATAGGTTGGTCT
66 CTTTAACTTGTTAATATCTGTATTATAGACGCGATACATCATCAGAATTGTTTATAGGTTGGTCT
723151 TTTTTATGACATAAAATTTATGAGATATTTTAGAAGTTAGTAAGTCAAGCGTTACAGTGCAAAAT
131 TTTTTATGACATAAAATTTATGAGATATTTTAGAAGTTAGTAAGTCAAGCGTTACAGTGCAAAAT
723216 CTGAATTATCAAAGAATTTTAAGTCGATGCATACTAAAAAATGT
196 CTGAATTATCAAAGAATTTTAAGTCGATGCATACTAAAAAATGT
*
723260 NTTTTCACACTGGTAAAATATCATTTTAATGAAAACGTACCTAACCTTTTTTTCCATGGGTATTT
1 ATTTTCACACTGGTAAAATATCATTTTAATGAAAACGTACCTAACCTTTTTTTCCATGGGTATTT
723325 CTTTAACTTGTTAATATCTGTATTATAGACGCGATACATCATCAGAATTGTTTATAGGTTGGTCT
66 CTTTAACTTGTTAATATCTGTATTATAGACGCGATACATCATCAGAATTGTTTATAGGTTGGTCT
723390 TTTTTATGACATAAAATTTATGAGATATTTTAGAAGTTAGTAAGTCAAGCGTTACAGTGCAAAAT
131 TTTTTATGACATAAAATTTATGAGATATTTTAGAAGTTAGTAAGTCAAGCGTTACAGTGCAAAAT
723455 CTGAATTATCAAAGAATTTTAAGTCGATGCATACTAAAAAATGT
196 CTGAATTATCAAAGAATTTTAAGTCGATGCATACTAAAAAATGT
723499 ATTTT
1 ATTTT
723504 ATCAAATATT
Statistics
Matches: 242, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
239 242 1.00
ACGTcount: A:0.34, C:0.12, G:0.14, T:0.39
Consensus pattern (239 bp):
ATTTTCACACTGGTAAAATATCATTTTAATGAAAACGTACCTAACCTTTTTTTCCATGGGTATTT
CTTTAACTTGTTAATATCTGTATTATAGACGCGATACATCATCAGAATTGTTTATAGGTTGGTCT
TTTTTATGACATAAAATTTATGAGATATTTTAGAAGTTAGTAAGTCAAGCGTTACAGTGCAAAAT
CTGAATTATCAAAGAATTTTAAGTCGATGCATACTAAAAAATGT
Found at i:725301 original size:21 final size:21
Alignment explanation
Indices: 725277--725319 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
725267 GCAGTTTTTA
*
725277 ATTTGTATTGTATAATTATCC
1 ATTTGTATTCTATAATTATCC
*
725298 ATTTGTATTCTATAATTTTCC
1 ATTTGTATTCTATAATTATCC
725319 A
1 A
725320 AAATTATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.28, C:0.12, G:0.07, T:0.53
Consensus pattern (21 bp):
ATTTGTATTCTATAATTATCC
Found at i:725345 original size:21 final size:21
Alignment explanation
Indices: 725319--725482 Score: 166
Period size: 21 Copynumber: 8.2 Consensus size: 21
725309 ATAATTTTCC
*
725319 AAAATTATAAAATACAAATGG
1 AAAATTATACAATACAAATGG
*
725340 AAAATTATA-GA-AC-----G
1 AAAATTATACAATACAAATGG
725354 AAAATTATACAATACAAATGG
1 AAAATTATACAATACAAATGG
725375 AAAATTATACAATACAAATGG
1 AAAATTATACAATACAAATGG
* * * *
725396 AAAACTATAGAATAGAAAAGG
1 AAAATTATACAATACAAATGG
*
725417 AAAATTATACAATACAAATAG
1 AAAATTATACAATACAAATGG
725438 AAAATTATACAATACAAA--G
1 AAAATTATACAATACAAATGG
* * *
725457 ATTATTTATACAATTCAAATGG
1 A-AAATTATACAATACAAATGG
725479 AAAA
1 AAAA
725483 GATCGAATAT
Statistics
Matches: 117, Mismatches: 16, Indels: 20
0.76 0.10 0.13
Matches are distributed among these distances:
14 10 0.09
15 1 0.01
16 2 0.02
19 4 0.03
20 15 0.13
21 83 0.71
22 2 0.02
ACGTcount: A:0.59, C:0.08, G:0.10, T:0.24
Consensus pattern (21 bp):
AAAATTATACAATACAAATGG
Found at i:726689 original size:14 final size:14
Alignment explanation
Indices: 726670--726697 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
726660 CCATATTTGC
726670 CTCCCCAACCCCCA
1 CTCCCCAACCCCCA
726684 CTCCCCAACCCCCA
1 CTCCCCAACCCCCA
726698 AAGAAGACCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.71, G:0.00, T:0.07
Consensus pattern (14 bp):
CTCCCCAACCCCCA
Found at i:741965 original size:38 final size:35
Alignment explanation
Indices: 741908--741985 Score: 93
Period size: 38 Copynumber: 2.1 Consensus size: 35
741898 TTTCTTCAAA
**
741908 TGTTTTGTTTTTGAAACGTGTATAATTGAATGTGCGG
1 TGTTTTGTTTTACAAACGTGTATAATT--ATGTGCGG
**
741945 TGTTTTGATTTTACAAACGTGTATCGTTATGTGCGG
1 TGTTTTG-TTTTACAAACGTGTATAATTATGTGCGG
741981 TGTTT
1 TGTTT
741986 ACTCACATCC
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
36 13 0.36
37 7 0.19
38 16 0.44
ACGTcount: A:0.19, C:0.08, G:0.26, T:0.47
Consensus pattern (35 bp):
TGTTTTGTTTTACAAACGTGTATAATTATGTGCGG
Found at i:744166 original size:84 final size:84
Alignment explanation
Indices: 744025--744207 Score: 330
Period size: 84 Copynumber: 2.2 Consensus size: 84
744015 CCAAGATTGA
744025 AATATATTTCTCTGTATTTATATTACCATTGACAAGGCAACGTGTTACAACTTCGTTATATCTAA
1 AATATATTTCTCTGTATTTATATTACCATTGACAAGGCAACGTGTTACAACTTCGTTATATCTAA
744090 TGCAACTCCACATCACACT
66 TGCAACTCCACATCACACT
*
744109 AATATATTTCTCTGTATTTATATTACCATTGACAAGGCAACGTGTTACAACTTCGTTATATGTAA
1 AATATATTTCTCTGTATTTATATTACCATTGACAAGGCAACGTGTTACAACTTCGTTATATCTAA
744174 TGCAACTCCACATCACACT
66 TGCAACTCCACATCACACT
**
744193 AGATATCCTTCTCTG
1 A-ATATATTTCTCTG
744208 ACGAGGGGAC
Statistics
Matches: 95, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
84 84 0.88
85 11 0.12
ACGTcount: A:0.31, C:0.22, G:0.10, T:0.36
Consensus pattern (84 bp):
AATATATTTCTCTGTATTTATATTACCATTGACAAGGCAACGTGTTACAACTTCGTTATATCTAA
TGCAACTCCACATCACACT
Found at i:767461 original size:5 final size:5
Alignment explanation
Indices: 767451--767476 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
767441 AGCGAATAAA
767451 GAATT GAATT GAATT GAATT GAATT G
1 GAATT GAATT GAATT GAATT GAATT G
767477 TTTTGAAAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.23, T:0.38
Consensus pattern (5 bp):
GAATT
Found at i:772658 original size:16 final size:16
Alignment explanation
Indices: 772637--772670 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
772627 GAATAATACA
*
772637 AATGTATGTTTAATCG
1 AATGTATGTATAATCG
772653 AATGTATGTATAATCG
1 AATGTATGTATAATCG
772669 AA
1 AA
772671 AATTGGCAGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.38, C:0.06, G:0.18, T:0.38
Consensus pattern (16 bp):
AATGTATGTATAATCG
Found at i:773483 original size:22 final size:21
Alignment explanation
Indices: 773443--773508 Score: 60
Period size: 22 Copynumber: 3.0 Consensus size: 21
773433 CGGCCGCAAC
* * *
773443 TTATCTAGCAGCCGTCACATA
1 TTATCTCGCGGCCGCCACATA
* *
773464 TTATTCTGGCGGTCGCCACATCA
1 TTA-TCTCGCGGCCGCCACAT-A
*
773487 TTATCTCGCGGCCGCCAGATA
1 TTATCTCGCGGCCGCCACATA
773508 T
1 T
773509 ACAACCTGGC
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
21 5 0.14
22 27 0.75
23 4 0.11
ACGTcount: A:0.21, C:0.30, G:0.20, T:0.29
Consensus pattern (21 bp):
TTATCTCGCGGCCGCCACATA
Found at i:804383 original size:60 final size:59
Alignment explanation
Indices: 804228--804406 Score: 249
Period size: 56 Copynumber: 3.1 Consensus size: 59
804218 AAATAATAGG
*
804228 GAAAAAGAAACCGAAGAATAACAATAAGGTCTTCCGTTGGAAACGGAAGACCTTAAT--
1 GAAAAAGAAACCGTAGAATAACAATAAGGTCTTCCGTTGGAAACGGAAGACCTTAATAA
* * *
804285 -AATAAGAAATCGTACGAA-AACTATAAGGTCTTCCGTTGGAAACGGAAGACCTTAATAAA
1 GAAAAAGAAACCGTA-GAATAACAATAAGGTCTTCCGTTGGAAACGGAAGACCTTAAT-AA
* * *
804344 GAAAAAGAAACCGTAGAATAACAAGAGGGTCTTCCGTTGGAAACGGAAGACCCTAATAA
1 GAAAAAGAAACCGTAGAATAACAATAAGGTCTTCCGTTGGAAACGGAAGACCTTAATAA
804403 GAAA
1 GAAA
804407 GTCGACAAAA
Statistics
Matches: 106, Mismatches: 10, Indels: 10
0.84 0.08 0.08
Matches are distributed among these distances:
56 48 0.45
57 3 0.03
59 9 0.08
60 46 0.43
ACGTcount: A:0.45, C:0.16, G:0.21, T:0.18
Consensus pattern (59 bp):
GAAAAAGAAACCGTAGAATAACAATAAGGTCTTCCGTTGGAAACGGAAGACCTTAATAA
Found at i:805695 original size:18 final size:18
Alignment explanation
Indices: 805640--805696 Score: 62
Period size: 18 Copynumber: 3.1 Consensus size: 18
805630 TTTTTATCAC
*
805640 ATAATACAATATCATAAAAT
1 ATAATACAATATCAT--ATT
805660 ATAATACAATAT-AGTATT
1 ATAATACAATATCA-TATT
*
805678 ATATTACAATATCATATT
1 ATAATACAATATCATATT
805696 A
1 A
805697 CATAATACAT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
18 18 0.55
19 2 0.06
20 13 0.39
ACGTcount: A:0.53, C:0.09, G:0.02, T:0.37
Consensus pattern (18 bp):
ATAATACAATATCATATT
Found at i:805935 original size:15 final size:15
Alignment explanation
Indices: 805906--806047 Score: 83
Period size: 15 Copynumber: 8.9 Consensus size: 15
805896 ATACATATTG
* *
805906 TATCATATGACACAA
1 TATCATATAATACAA
*
805921 TAAT-ATATATTACAA
1 T-ATCATATAATACAA
805936 TATCATATAATACAA
1 TATCATATAATACAA
*
805951 TTTCATGTCATAAGATA-ATA
1 TATCA--T-AT-A-ATACA-A
805971 TATCATATAA-ACCAA
1 TATCATATAATA-CAA
*
805986 TATCATATCATACAA
1 TATCATATAATACAA
** *
806001 TATTGTATGATACAA
1 TATCATATAATACAA
*
806016 TATTATATAATATTACAA
1 TATCATAT-A-A-TACAA
806034 TATCATATAATACA
1 TATCATATAATACA
806048 TTTTCATGTG
Statistics
Matches: 100, Mismatches: 13, Indels: 28
0.71 0.09 0.20
Matches are distributed among these distances:
14 3 0.03
15 61 0.61
16 6 0.06
17 5 0.05
18 15 0.15
19 2 0.02
20 8 0.08
ACGTcount: A:0.48, C:0.13, G:0.04, T:0.36
Consensus pattern (15 bp):
TATCATATAATACAA
Found at i:805962 original size:50 final size:48
Alignment explanation
Indices: 805908--806062 Score: 131
Period size: 50 Copynumber: 3.1 Consensus size: 48
805898 ACATATTGTA
805908 TCATATGACACAATA-ATATATATTACAATATCATATAATACAATTTCATG
1 TCATAT-ACA-AATATATA-ATATTACAATATCATATAATACAATTTCATG
* * * * *
805958 TCATA-AGATAATATATCATATAAACCAATATCATATCATACAATAT--TG
1 TCATATACA-AATATATAATAT-TA-CAATATCATATAATACAATTTCATG
*
806006 T-ATGATACAATATTATATAATATTACAATATCATATAATACATTTTCATG
1 TCAT-ATACAA-A-TATATAATATTACAATATCATATAATACAATTTCATG
*
806056 TGATATA
1 TCATATA
806063 ATTCTATATT
Statistics
Matches: 83, Mismatches: 12, Indels: 20
0.72 0.10 0.17
Matches are distributed among these distances:
47 2 0.02
48 33 0.40
49 7 0.08
50 39 0.47
51 2 0.02
ACGTcount: A:0.46, C:0.12, G:0.05, T:0.37
Consensus pattern (48 bp):
TCATATACAAATATATAATATTACAATATCATATAATACAATTTCATG
Found at i:806034 original size:18 final size:18
Alignment explanation
Indices: 806011--806045 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
806001 TATTGTATGA
*
806011 TACAATATTATATAATAT
1 TACAATATCATATAATAT
806029 TACAATATCATATAATA
1 TACAATATCATATAATA
806046 CATTTTCATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.40
Consensus pattern (18 bp):
TACAATATCATATAATAT
Found at i:806041 original size:98 final size:98
Alignment explanation
Indices: 805906--806133 Score: 295
Period size: 98 Copynumber: 2.4 Consensus size: 98
805896 ATACATATTG
* *
805906 TATCATATGACACAATA--ATAT-ATATTACAATATCATATAATACAATTTCATGTCATA-AGAT
1 TATCGTATGATACAATATTATATAATATTACAATATCATATAATACAATTTCATGTCATATA-AT
* *
805967 AATATATCATATAAACCAATATCATATCATACAA
65 AATATATCACAGAAACCAATATCATATCATACAA
* * * *
806001 TATTGTATGATACAATATTATATAATATTACAATATCATATAATACATTTTCATGTGATATAATT
1 TATCGTATGATACAATATTATATAATATTACAATATCATATAATACAATTTCATGTCATATAATA
* * ** *
806066 CTATATTACAGAAACTGATATCATATTATACAA
66 ATATATCACAGAAACCAATATCATATCATACAA
806099 TATCGTATGATACAATATTATATAATA-TACAATAT
1 TATCGTATGATACAATATTATATAATATTACAATAT
806134 TGTATCATAG
Statistics
Matches: 115, Mismatches: 14, Indels: 6
0.85 0.10 0.04
Matches are distributed among these distances:
95 14 0.12
97 12 0.10
98 88 0.77
99 1 0.01
ACGTcount: A:0.46, C:0.12, G:0.05, T:0.38
Consensus pattern (98 bp):
TATCGTATGATACAATATTATATAATATTACAATATCATATAATACAATTTCATGTCATATAATA
ATATATCACAGAAACCAATATCATATCATACAA
Found at i:806101 original size:15 final size:15
Alignment explanation
Indices: 806083--806133 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
806073 ACAGAAACTG
806083 ATATCATATTATACA
1 ATATCATATTATACA
* *
806098 ATATCGTATGATACA
1 ATATCATATTATACA
*
806113 ATATTATATAATATACA
1 ATATCATAT--TATACA
806130 ATAT
1 ATAT
806134 TGTATCATAG
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
15 20 0.69
17 9 0.31
ACGTcount: A:0.47, C:0.10, G:0.04, T:0.39
Consensus pattern (15 bp):
ATATCATATTATACA
Found at i:806382 original size:20 final size:20
Alignment explanation
Indices: 806359--806411 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
806349 ATATGATATC
806359 ATATTGTATCATATCAAACA
1 ATATTGTATCATATCAAACA
* *
806379 ATATTGTTTCATATCATACA
1 ATATTGTATCATATCAAACA
* *
806399 ATACTATATCATA
1 ATATTGTATCATA
806412 GGAATCATGT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.42, C:0.15, G:0.04, T:0.40
Consensus pattern (20 bp):
ATATTGTATCATATCAAACA
Found at i:807361 original size:177 final size:176
Alignment explanation
Indices: 807060--807581 Score: 712
Period size: 177 Copynumber: 2.9 Consensus size: 176
807050 CATCCGAAAC
* * *
807060 CAGACTCAGCATTCAAGCCTGTCAGGTGCATCAGTATCATAAGACACACCATCCATGGAAGTCTG
1 CAGATTCAGCATTCAAGCCTGTCAGGTGCATCAGTATCATAAGACACACCATCCATGCAAGTTTG
* * *
807125 GTGAAGTAAGGACAAGTAATAACTAAGATA-T-CATCATCAGAGGGCACCTGCAACAAAAACTTT
66 GTGAAGTTAGGACCAGTAGTAACTAAGATATTGC-T-ATCA-AGGGCACCTGCAACAAAAACTTT
* * * *
807188 AACCAGCTCTAAAAACCTTAACCTCTTCCAGCATCCGAAACCTATTGCT
128 AACCTGCTCCAAAAACCTTAACCTCCTCCAGCATCCGAAACCTATAGCT
* * * *
807237 CAGATTCAGCATTCAAGCTTGTCAGGTGCATCAGTATCATAAGACGCATCATCCATACAAGTTTG
1 CAGATTCAGCATTCAAGCCTGTCAGGTGCATCAGTATCATAAGACACACCATCCATGCAAGTTTG
**
807302 GTGAAGTTAGGACCAGTAGTAACTTAA-ATATTGCTATCAATGGGCACCCACAACAAAAACTTTA
66 GTGAAGTTAGGACCAGTAGTAAC-TAAGATATTGCTATCAA-GGGCACCTGCAACAAAAACTTTA
807366 ACCTGCTCCAAAAACCTTAACCTCCTCCAGCATCCGAAACCTATAGCT
129 ACCTGCTCCAAAAACCTTAACCTCCTCCAGCATCCGAAACCTATAGCT
* * *
807414 CAGATTCAGCACTCAAGCCTGTCTGGTGCATCAGTATCATAAGGCACACCATCCATGCAAGTTTG
1 CAGATTCAGCATTCAAGCCTGTCAGGTGCATCAGTATCATAAGACACACCATCCATGCAAGTTTG
* * *
807479 GTGATG-TACGGACCA-TCAGTAACTAAGATATTGCTATCAAAGGGGACCTGCAACAAAAACTTC
66 GTGAAGTTA-GGACCAGT-AGTAACTAAGATATTGCTATC-AAGGGCACCTGCAACAAAAACTTT
* * *
807542 AACCTGGTCCAACAACCTTAACCTCCTCCAGCATCTGAAA
128 AACCTGCTCCAAAAACCTTAACCTCCTCCAGCATCCGAAA
807582 TTTAGGACCC
Statistics
Matches: 306, Mismatches: 31, Indels: 16
0.87 0.09 0.05
Matches are distributed among these distances:
176 7 0.02
177 291 0.95
178 7 0.02
179 1 0.00
ACGTcount: A:0.34, C:0.26, G:0.16, T:0.23
Consensus pattern (176 bp):
CAGATTCAGCATTCAAGCCTGTCAGGTGCATCAGTATCATAAGACACACCATCCATGCAAGTTTG
GTGAAGTTAGGACCAGTAGTAACTAAGATATTGCTATCAAGGGCACCTGCAACAAAAACTTTAAC
CTGCTCCAAAAACCTTAACCTCCTCCAGCATCCGAAACCTATAGCT
Found at i:807379 original size:19 final size:19
Alignment explanation
Indices: 807355--807394 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
807345 GCACCCACAA
* *
807355 CAAAAACTTTAACCTGCTC
1 CAAAAACCTTAACCTCCTC
807374 CAAAAACCTTAACCTCCTC
1 CAAAAACCTTAACCTCCTC
807393 CA
1 CA
807395 GCATCCGAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.38, C:0.38, G:0.03, T:0.23
Consensus pattern (19 bp):
CAAAAACCTTAACCTCCTC
Found at i:807730 original size:6 final size:6
Alignment explanation
Indices: 807719--807750 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
807709 ACCAGGTCCG
*
807719 GACGCC GACGCC GACGCC GCCGCC GACGCC GA
1 GACGCC GACGCC GACGCC GACGCC GACGCC GA
807751 GGGTATAGCA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.16, C:0.50, G:0.34, T:0.00
Consensus pattern (6 bp):
GACGCC
Found at i:815901 original size:48 final size:49
Alignment explanation
Indices: 815799--815903 Score: 140
Period size: 48 Copynumber: 2.1 Consensus size: 49
815789 AGTGTAATTC
** *
815799 TTAATATTACATTAACAGAGCTGACTAATGATATTACATGCCGATCTTTACT
1 TTAA-ATTACATTAACAGAGCTGAC--ACCATATTACATGCCGATCATTACT
*
815851 TTAAATTACATTAACAGAGCTGAC-CCATATTACATGCCGATCATTCCT
1 TTAAATTACATTAACAGAGCTGACACCATATTACATGCCGATCATTACT
815899 TTAAA
1 TTAAA
815904 AGGAAAACTT
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
48 25 0.51
51 20 0.41
52 4 0.08
ACGTcount: A:0.35, C:0.20, G:0.10, T:0.34
Consensus pattern (49 bp):
TTAAATTACATTAACAGAGCTGACACCATATTACATGCCGATCATTACT
Found at i:818817 original size:11 final size:11
Alignment explanation
Indices: 818803--818854 Score: 95
Period size: 11 Copynumber: 4.7 Consensus size: 11
818793 TTTTTTAATT
818803 GCTTAAAGGTG
1 GCTTAAAGGTG
*
818814 GCTTAAAGGTA
1 GCTTAAAGGTG
818825 GCTTAAAGGTG
1 GCTTAAAGGTG
818836 GCTTAAAGGTG
1 GCTTAAAGGTG
818847 GCTTAAAG
1 GCTTAAAG
818855 AAGTTTGGAC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 39 1.00
ACGTcount: A:0.31, C:0.10, G:0.33, T:0.27
Consensus pattern (11 bp):
GCTTAAAGGTG
Found at i:818902 original size:11 final size:11
Alignment explanation
Indices: 818886--818914 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
818876 ATAAGTTGTC
818886 CTTAAAGGTGG
1 CTTAAAGGTGG
818897 CTTAAAGGTGG
1 CTTAAAGGTGG
818908 CTTAAAG
1 CTTAAAG
818915 ATAGTCTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.31, C:0.10, G:0.31, T:0.28
Consensus pattern (11 bp):
CTTAAAGGTGG
Found at i:818996 original size:11 final size:11
Alignment explanation
Indices: 818980--819011 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
818970 GCAATACATA
818980 TAGCTTAAAGG
1 TAGCTTAAAGG
818991 TAGCTTAAAGG
1 TAGCTTAAAGG
*
819002 TGGCTTAAAG
1 TAGCTTAAAG
819012 ATCGTCTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.34, C:0.09, G:0.28, T:0.28
Consensus pattern (11 bp):
TAGCTTAAAGG
Found at i:819033 original size:11 final size:11
Alignment explanation
Indices: 819017--819055 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
819007 TAAAGATCGT
819017 CTTTAAGCTAC
1 CTTTAAGCTAC
*
819028 CTTTAAAC-AC
1 CTTTAAGCTAC
*
819038 CTTTAAGCTAT
1 CTTTAAGCTAC
819049 CTTTAAG
1 CTTTAAG
819056 GAGGACTTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
10 9 0.38
11 15 0.62
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (11 bp):
CTTTAAGCTAC
Found at i:819503 original size:19 final size:19
Alignment explanation
Indices: 819481--819549 Score: 75
Period size: 19 Copynumber: 3.6 Consensus size: 19
819471 TAATATATTG
* *
819481 TCATTATGGTAACCTACGA
1 TCATCATGGTAACCTACAA
819500 TCATCATGGTAACCTACAA
1 TCATCATGGTAACCTACAA
* * *
819519 TTATCATGGTAAACTCCAA
1 TCATCATGGTAACCTACAA
* *
819538 CCTTCATGGTAA
1 TCATCATGGTAA
819550 TGTGTGCTTA
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 42 1.00
ACGTcount: A:0.33, C:0.23, G:0.13, T:0.30
Consensus pattern (19 bp):
TCATCATGGTAACCTACAA
Found at i:819592 original size:97 final size:97
Alignment explanation
Indices: 819426--819615 Score: 362
Period size: 97 Copynumber: 2.0 Consensus size: 97
819416 ATACAGTCTA
*
819426 CATGGTAACCTCCAACCTTCATGGTAATGTGTGCTTATCATATAGTAATATATTGTCATTATGGT
1 CATGGTAAACTCCAACCTTCATGGTAATGTGTGCTTATCATATAGTAATATATTGTCATTATGGT
819491 AACCTACGATCATCATGGTAACCTACAATTAT
66 AACCTACGATCATCATGGTAACCTACAATTAT
*
819523 CATGGTAAACTCCAACCTTCATGGTAATGTGTGCTTATCATATAGTAATGTATTGTCATTATGGT
1 CATGGTAAACTCCAACCTTCATGGTAATGTGTGCTTATCATATAGTAATATATTGTCATTATGGT
819588 AACCTACGATCATCATGGTAACCTACAA
66 AACCTACGATCATCATGGTAACCTACAA
819616 CTAGAAAACT
Statistics
Matches: 91, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
97 91 1.00
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.34
Consensus pattern (97 bp):
CATGGTAAACTCCAACCTTCATGGTAATGTGTGCTTATCATATAGTAATATATTGTCATTATGGT
AACCTACGATCATCATGGTAACCTACAATTAT
Found at i:820245 original size:21 final size:22
Alignment explanation
Indices: 820219--820303 Score: 149
Period size: 21 Copynumber: 4.0 Consensus size: 22
820209 TGCGTCTTTT
820219 TACCCCAATGA-ACCCCAATGA
1 TACCCCAATGATACCCCAATGA
820240 TACCCCAATGA-ACCCCAATGA
1 TACCCCAATGATACCCCAATGA
820261 TACCCCAATGATACCCCAATGA
1 TACCCCAATGATACCCCAATGA
820283 -ACCCCAATGATACCCCAATGA
1 TACCCCAATGATACCCCAATGA
820304 ACTTTGAAAT
Statistics
Matches: 63, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
21 53 0.84
22 10 0.16
ACGTcount: A:0.38, C:0.38, G:0.09, T:0.15
Consensus pattern (22 bp):
TACCCCAATGATACCCCAATGA
Found at i:820246 original size:11 final size:11
Alignment explanation
Indices: 820219--820303 Score: 149
Period size: 11 Copynumber: 8.0 Consensus size: 11
820209 TGCGTCTTTT
820219 TACCCCAATGA
1 TACCCCAATGA
820230 -ACCCCAATGA
1 TACCCCAATGA
820240 TACCCCAATGA
1 TACCCCAATGA
820251 -ACCCCAATGA
1 TACCCCAATGA
820261 TACCCCAATGA
1 TACCCCAATGA
820272 TACCCCAATGA
1 TACCCCAATGA
820283 -ACCCCAATGA
1 TACCCCAATGA
820293 TACCCCAATGA
1 TACCCCAATGA
820304 ACTTTGAAAT
Statistics
Matches: 71, Mismatches: 0, Indels: 6
0.92 0.00 0.08
Matches are distributed among these distances:
10 30 0.42
11 41 0.58
ACGTcount: A:0.38, C:0.38, G:0.09, T:0.15
Consensus pattern (11 bp):
TACCCCAATGA
Found at i:820271 original size:32 final size:32
Alignment explanation
Indices: 820219--820305 Score: 135
Period size: 32 Copynumber: 2.8 Consensus size: 32
820209 TGCGTCTTTT
820219 TACCCCAATGA-ACCCCAATGATACCCCAATGA
1 TACCCCAATGATACCCCAATGA-ACCCCAATGA
820251 -ACCCCAATGATACCCCAATGATACCCCAATGA
1 TACCCCAATGATACCCCAATGA-ACCCCAATGA
820283 -ACCCCAATGATACCCCAATGAAC
1 TACCCCAATGATACCCCAATGAAC
820306 TTTGAAATAC
Statistics
Matches: 54, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
31 12 0.22
32 42 0.78
ACGTcount: A:0.38, C:0.38, G:0.09, T:0.15
Consensus pattern (32 bp):
TACCCCAATGATACCCCAATGAACCCCAATGA
Found at i:821041 original size:11 final size:11
Alignment explanation
Indices: 821018--821154 Score: 162
Period size: 11 Copynumber: 13.0 Consensus size: 11
821008 ATTTCAAAGT
*
821018 TCATTAGGGTA
1 TCATTGGGGTA
*
821029 TCATTGGGATA
1 TCATTGGGGTA
*
821040 TCATT-TGGTA
1 TCATTGGGGTA
*
821050 TCATAGGGGTA
1 TCATTGGGGTA
*
821061 TCATTAGGTGTA
1 TCATT-GGGGTA
821073 T--TT-GGGTA
1 TCATTGGGGTA
821081 TCATTGGGGTA
1 TCATTGGGGTA
*
821092 ACATTGGGGT-
1 TCATTGGGGTA
821102 TCATTGGGGTA
1 TCATTGGGGTA
821113 TCATTGGGGT-
1 TCATTGGGGTA
821123 TCATTGGGGTA
1 TCATTGGGGTA
821134 TCATTGGGGT-
1 TCATTGGGGTA
821144 TCATTGGGGTA
1 TCATTGGGGTA
821155 AAAAGACGCA
Statistics
Matches: 107, Mismatches: 11, Indels: 16
0.80 0.08 0.12
Matches are distributed among these distances:
8 5 0.05
10 40 0.37
11 56 0.52
12 6 0.06
ACGTcount: A:0.20, C:0.09, G:0.34, T:0.38
Consensus pattern (11 bp):
TCATTGGGGTA
Found at i:821050 original size:21 final size:22
Alignment explanation
Indices: 821018--821154 Score: 162
Period size: 21 Copynumber: 6.5 Consensus size: 22
821008 ATTTCAAAGT
* *
821018 TCATTAGGGTATCATTGGGATA
1 TCATTGGGGTATCATTGGGGTA
* *
821040 TCATT-TGGTATCATAGGGGTA
1 TCATTGGGGTATCATTGGGGTA
*
821061 TCATTAGGTGTAT--TT-GGGTA
1 TCATT-GGGGTATCATTGGGGTA
*
821081 TCATTGGGGTAACATTGGGGT-
1 TCATTGGGGTATCATTGGGGTA
821102 TCATTGGGGTATCATTGGGGT-
1 TCATTGGGGTATCATTGGGGTA
821123 TCATTGGGGTATCATTGGGGT-
1 TCATTGGGGTATCATTGGGGTA
821144 TCATTGGGGTA
1 TCATTGGGGTA
821155 AAAAGACGCA
Statistics
Matches: 101, Mismatches: 9, Indels: 11
0.83 0.07 0.09
Matches are distributed among these distances:
19 5 0.05
20 10 0.10
21 73 0.72
22 9 0.09
23 4 0.04
ACGTcount: A:0.20, C:0.09, G:0.34, T:0.38
Consensus pattern (22 bp):
TCATTGGGGTATCATTGGGGTA
Found at i:821081 original size:31 final size:32
Alignment explanation
Indices: 821018--821154 Score: 149
Period size: 32 Copynumber: 4.3 Consensus size: 32
821008 ATTTCAAAGT
* *
821018 TCATTAGGGTATCATTGGGATATCATTT-GGTA
1 TCATTGGGGTATCATTGGGGT-TCATTTGGGTA
* *
821050 TCATAGGGGTATCATT-AGGTGT-ATTTGGGTA
1 TCATTGGGGTATCATTGGGGT-TCATTTGGGTA
* *
821081 TCATTGGGGTAACATTGGGGTTCATTGGGGTA
1 TCATTGGGGTATCATTGGGGTTCATTTGGGTA
*
821113 TCATTGGGGT-TCATTGGGGTATCATTGGGGT-
1 TCATTGGGGTATCATTGGGGT-TCATTTGGGTA
821144 TCATTGGGGTA
1 TCATTGGGGTA
821155 AAAAGACGCA
Statistics
Matches: 90, Mismatches: 10, Indels: 10
0.82 0.09 0.09
Matches are distributed among these distances:
30 4 0.04
31 41 0.46
32 45 0.50
ACGTcount: A:0.20, C:0.09, G:0.34, T:0.38
Consensus pattern (32 bp):
TCATTGGGGTATCATTGGGGTTCATTTGGGTA
Found at i:821081 original size:52 final size:53
Alignment explanation
Indices: 821016--821141 Score: 150
Period size: 52 Copynumber: 2.4 Consensus size: 53
821006 ATATTTCAAA
* * * *
821016 GTTCATTAGGGTATCATTGGGATATCATT-TGGTATCATAGGGGTATCATT-AG
1 GTTCATTGGGGTATCATTGGGATAACATTGGGGT-TCATAGGGGTATCATTGGG
* * *
821068 GTGT-ATTTGGGTATCATTGGGGTAACATTGGGGTTCATTGGGGTATCATTGGG
1 GT-TCATTGGGGTATCATTGGGATAACATTGGGGTTCATAGGGGTATCATTGGG
821121 GTTCATTGGGGTATCATTGGG
1 GTTCATTGGGGTATCATTGGG
821142 GTTCATTGGG
Statistics
Matches: 63, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
52 40 0.63
53 23 0.37
ACGTcount: A:0.20, C:0.09, G:0.33, T:0.38
Consensus pattern (53 bp):
GTTCATTGGGGTATCATTGGGATAACATTGGGGTTCATAGGGGTATCATTGGG
Found at i:822128 original size:4 final size:4
Alignment explanation
Indices: 822119--822216 Score: 196
Period size: 4 Copynumber: 24.5 Consensus size: 4
822109 TTGTGGACGN
822119 TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA
1 TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA
822167 TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA
1 TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA
822215 TA
1 TA
822217 CAGGAAACAA
Statistics
Matches: 94, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 94 1.00
ACGTcount: A:0.50, C:0.00, G:0.24, T:0.26
Consensus pattern (4 bp):
TAGA
Found at i:838662 original size:12 final size:12
Alignment explanation
Indices: 838631--838665 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
838621 TGTTATTGGG
*
838631 GTTTTTTTTTTT
1 GTTTTTTGTTTT
*
838643 TTTTTTTGTTTT
1 GTTTTTTGTTTT
838655 GTTTTTTGTTT
1 GTTTTTTGTTT
838666 CAGGGTCTGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (12 bp):
GTTTTTTGTTTT
Found at i:840021 original size:5 final size:5
Alignment explanation
Indices: 840011--840104 Score: 72
Period size: 5 Copynumber: 18.8 Consensus size: 5
840001 TTATAGGTTT
*
840011 TTTTG TTTTG TTTTTG TTCTTT TATTTG TTTTG TTTTG ATTTTG TTTTG
1 TTTTG TTTTG -TTTTG TT-TTG T-TTTG TTTTG TTTTG -TTTTG TTTTG
* * *
840060 -TTTG GTTTG -GTTG TTTT- TTTTT TTTTG TTTT- TTTGTG TTTT- TTTT
1 TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG TTT-TG TTTTG TTTT
840105 TTGGGGGGGG
Statistics
Matches: 75, Mismatches: 5, Indels: 19
0.76 0.05 0.19
Matches are distributed among these distances:
4 18 0.24
5 37 0.49
6 19 0.25
7 1 0.01
ACGTcount: A:0.02, C:0.01, G:0.17, T:0.80
Consensus pattern (5 bp):
TTTTG
Found at i:840042 original size:9 final size:8
Alignment explanation
Indices: 840016--840106 Score: 55
Period size: 8 Copynumber: 11.2 Consensus size: 8
840006 GGTTTTTTTG
840016 TTTTGTTT
1 TTTTGTTT
*
840024 TTGTTCTTT
1 TT-TTGTTT
840033 TATTTGTTT
1 T-TTTGTTT
**
840042 TGTTT-TGA
1 T-TTTGTTT
840050 TTTTGTTT
1 TTTTGTTT
840058 TGTTTGGTTT
1 T-TTT-GTTT
**
840068 GGTTG-TT
1 TTTTGTTT
840075 TTTT-TTT
1 TTTTGTTT
840082 TTTTGTTT
1 TTTTGTTT
*
840090 TTTTGTGT
1 TTTTGTTT
840098 TTTT-TTT
1 TTTTGTTT
840105 TT
1 TT
840107 GGGGGGGGGG
Statistics
Matches: 63, Mismatches: 13, Indels: 15
0.69 0.14 0.16
Matches are distributed among these distances:
7 17 0.27
8 21 0.33
9 20 0.32
10 5 0.08
ACGTcount: A:0.02, C:0.01, G:0.16, T:0.80
Consensus pattern (8 bp):
TTTTGTTT
Found at i:840088 original size:27 final size:24
Alignment explanation
Indices: 840050--840106 Score: 69
Period size: 24 Copynumber: 2.2 Consensus size: 24
840040 TTTGTTTTGA
*
840050 TTTTGTTTTGTTTGGTTTGGTTGTTTT
1 TTTTTTTTTGTTT--TTTGG-TGTTTT
*
840077 TTTTTTTTTGTTTTTTTGTGTTTT
1 TTTTTTTTTGTTTTTTGGTGTTTT
840101 TTTTTT
1 TTTTTT
840107 GGGGGGGGGG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
24 12 0.43
25 4 0.14
27 12 0.43
ACGTcount: A:0.00, C:0.00, G:0.18, T:0.82
Consensus pattern (24 bp):
TTTTTTTTTGTTTTTTGGTGTTTT
Found at i:842374 original size:89 final size:89
Alignment explanation
Indices: 842223--842404 Score: 346
Period size: 89 Copynumber: 2.0 Consensus size: 89
842213 CAGTAATATA
*
842223 TCGGGTTAATCAATCTCATGGATGCAAGGTCTCGCAATATATACTTAAATAGTATATAAAGAATC
1 TCGGGTTAATCAATCTCATGGAGGCAAGGTCTCGCAATATATACTTAAATAGTATATAAAGAATC
842288 AAGAGTCTTTACCCGTGTCACAAG
66 AAGAGTCTTTACCCGTGTCACAAG
*
842312 TCGGGTTAATCAATCTCATGGAGGCAAGGTCTCGCAATATATACTTAAATAGTATATCAAGAATC
1 TCGGGTTAATCAATCTCATGGAGGCAAGGTCTCGCAATATATACTTAAATAGTATATAAAGAATC
842377 AAGAGTCTTTACCCGTGTCACAAG
66 AAGAGTCTTTACCCGTGTCACAAG
842401 TCGG
1 TCGG
842405 TTCTCTGTAT
Statistics
Matches: 91, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
89 91 1.00
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.29
Consensus pattern (89 bp):
TCGGGTTAATCAATCTCATGGAGGCAAGGTCTCGCAATATATACTTAAATAGTATATAAAGAATC
AAGAGTCTTTACCCGTGTCACAAG
Found at i:847656 original size:12 final size:12
Alignment explanation
Indices: 847641--847686 Score: 58
Period size: 12 Copynumber: 3.9 Consensus size: 12
847631 TAGGTTTTAG
847641 TTAGGGTTAGGA
1 TTAGGGTTAGGA
**
847653 TTAGGGTTA-CT
1 TTAGGGTTAGGA
847664 TTAGGGTTAGGA
1 TTAGGGTTAGGA
*
847676 TTAGTGTTAGG
1 TTAGGGTTAGG
847687 GTAACCATTG
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
11 9 0.32
12 19 0.68
ACGTcount: A:0.22, C:0.02, G:0.37, T:0.39
Consensus pattern (12 bp):
TTAGGGTTAGGA
Found at i:847656 original size:23 final size:23
Alignment explanation
Indices: 847640--847684 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
847630 TTAGGTTTTA
847640 GTTAGGGTTAGGATTAGGGTTAC
1 GTTAGGGTTAGGATTAGGGTTAC
* *
847663 TTTAGGGTTAGGATTAGTGTTA
1 GTTAGGGTTAGGATTAGGGTTA
847685 GGGTAACCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.22, C:0.02, G:0.36, T:0.40
Consensus pattern (23 bp):
GTTAGGGTTAGGATTAGGGTTAC
Found at i:848756 original size:13 final size:13
Alignment explanation
Indices: 848738--848762 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
848728 ATAAACAATG
848738 TTTTTTATTTTAT
1 TTTTTTATTTTAT
848751 TTTTTTATTTTA
1 TTTTTTATTTTA
848763 CATGTATATC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (13 bp):
TTTTTTATTTTAT
Found at i:852486 original size:23 final size:23
Alignment explanation
Indices: 852455--852500 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
852445 GTATGTAAGC
852455 CCCCCTACATTAAATTCACAATA
1 CCCCCTACATTAAATTCACAATA
* *
852478 CCCCGTACATTATATTCACAATA
1 CCCCCTACATTAAATTCACAATA
852501 GCCCATGCAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.37, C:0.33, G:0.02, T:0.28
Consensus pattern (23 bp):
CCCCCTACATTAAATTCACAATA
Found at i:853042 original size:2 final size:2
Alignment explanation
Indices: 853037--853066 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
853027 TGTACATATT
*
853037 TC TC TC TC TC TC TC TC CC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
853067 ATAAAATTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (2 bp):
TC
Found at i:874597 original size:33 final size:33
Alignment explanation
Indices: 874560--874624 Score: 130
Period size: 33 Copynumber: 2.0 Consensus size: 33
874550 ACAAGTACAT
874560 AAATTATTACAAAATGTTTTCTTTATTAAAGTG
1 AAATTATTACAAAATGTTTTCTTTATTAAAGTG
874593 AAATTATTACAAAATGTTTTCTTTATTAAAGT
1 AAATTATTACAAAATGTTTTCTTTATTAAAGT
874625 AATGTTTAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.40, C:0.06, G:0.08, T:0.46
Consensus pattern (33 bp):
AAATTATTACAAAATGTTTTCTTTATTAAAGTG
Found at i:875519 original size:202 final size:202
Alignment explanation
Indices: 875173--875579 Score: 796
Period size: 202 Copynumber: 2.0 Consensus size: 202
875163 TATTTTTGTC
875173 AGCATGATTCAGCTGTTCCAATGGCTTTTCCGTTAATTGCACATTGCTCGTTGAATAAGGAAGAG
1 AGCATGATTCAGCTGTTCCAATGGCTTTTCCGTTAATTGCACATTGCTCGTTGAATAAGGAAGAG
875238 ATTTTAAAAAATAAATCATGTTTTTAGAAAGAGAATAAATGTTAAAAAACGTAAATATAAGCATT
66 ATTTTAAAAAATAAATCATGTTTTTAGAAAGAGAATAAATGTTAAAAAACGTAAATATAAGCATT
*
875303 GAATCATTATTTTTTTAAAGATGTGGTATCATTACTGCAACGGGGTGTGGAAACAAATTTTCATA
131 GAATCATTATTTTTTTAAAGATGTGGTATCATTACTGCAACAGGGTGTGGAAACAAATTTTCATA
875368 ACGCGGT
196 ACGCGGT
875375 AGCATGATTCAGCTGTTCCAATGGCTTTTCCGTTAATTGCACATTGCTCGTTGAATAAGGAAGAG
1 AGCATGATTCAGCTGTTCCAATGGCTTTTCCGTTAATTGCACATTGCTCGTTGAATAAGGAAGAG
*
875440 ATTTTTAAAAATAAATCATGTTTTTAGAAAGAGAATAAATGTTAAAAAACGTAAATATAAGCATT
66 ATTTTAAAAAATAAATCATGTTTTTAGAAAGAGAATAAATGTTAAAAAACGTAAATATAAGCATT
875505 GAATCATTATTTTTTTAAAGATGTGGTATCATTACTGCAACAGGGTGTGGAAACAAATTTTCATA
131 GAATCATTATTTTTTTAAAGATGTGGTATCATTACTGCAACAGGGTGTGGAAACAAATTTTCATA
875570 ACGCGGT
196 ACGCGGT
875577 AGC
1 AGC
875580 GTGCGTTATT
Statistics
Matches: 203, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
202 203 1.00
ACGTcount: A:0.36, C:0.12, G:0.19, T:0.33
Consensus pattern (202 bp):
AGCATGATTCAGCTGTTCCAATGGCTTTTCCGTTAATTGCACATTGCTCGTTGAATAAGGAAGAG
ATTTTAAAAAATAAATCATGTTTTTAGAAAGAGAATAAATGTTAAAAAACGTAAATATAAGCATT
GAATCATTATTTTTTTAAAGATGTGGTATCATTACTGCAACAGGGTGTGGAAACAAATTTTCATA
ACGCGGT
Found at i:877481 original size:17 final size:18
Alignment explanation
Indices: 877459--877498 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
877449 GGTAGGTAGG
*
877459 AAAAAA-ATTTTATTTTT
1 AAAAAATATTTTAATTTT
877476 AAAAAATATTTTAATTTT
1 AAAAAATATTTTAATTTT
877494 AAAAA
1 AAAAA
877499 CTAAGAATGT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 6 0.29
18 15 0.71
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
AAAAAATATTTTAATTTT
Found at i:891751 original size:160 final size:158
Alignment explanation
Indices: 891285--891755 Score: 538
Period size: 159 Copynumber: 3.0 Consensus size: 158
891275 TTTTGACAGC
** * *
891285 TTCATTTTCTTTGCAAAGGGTGCACATATTGAAATAAAATTTGATATACAGGTTTATCATAATAA
1 TTCATTTTCTACGCAAAGGATGCACATATTGAAATGAAATTTGATATACAGGTTTATCATAATAA
* * *
891350 TATCTAGGTCAAGTTCGATTTTGGGTACGATTGAGCAATTTTTGACAGAGTTGTGCCCCTTGGAC
66 TATCTAGGTCAAGTTCGA-TTTGAGTACGATCGAGCAATTTTTGACAGAGTTATGCCCCTTGGAC
* *
891415 ATAGAAAAATTCCAATTATTTGCAGTTTG
130 TTAGAAAAATTTCAATTATTTGCAGTTTG
* * * * *
891444 TTCATTTTCTTCGCAAAGGATGCACATATTGAAACGAAATTTAATATAC-GTGTTTATTATAATG
1 TTCATTTTCTACGCAAAGGATGCACATATTGAAATGAAATTTGATATACAG-GTTTATCATAATA
* * * * * *
891508 TTATCTAGATCAAGTTCGATTTTAGGTACGATCGAGCAATTTTCGATA-ATGTTATGCCCCTTTG
65 ATATCTAGGTCAAGTTCGATTTGA-GTACGATCGAGCAATTTTTGACAGA-GTTATGCCCCTTGG
891572 ACTTAGAAAAATTTCAATTATTTGCAGTTTCTG
128 ACTTAGAAAAATTTCAATTATTTGCAG-TT-TG
** * * *
891605 TTCATTTTCTACGCTTAGGATGCGCATATTGAAATGAAA-TTGGTATACAGGCTTATCATAATAA
1 TTCATTTTCTACGCAAAGGATGCACATATTGAAATGAAATTTGATATACAGGTTTATCATAATAA
* * * * ** *
891669 TATCTAGGTCGAGTGT-TACTTTGAGTACGATCAAGCATTTTTTTGACAGAGTTATGTGCCTCGG
66 TATCTAGGTCAAGT-TCGA-TTTGAGTACGATCGAGCA-ATTTTTGACAGAGTTATGCCCCTTGG
891733 ACTTA-AAAAATTTCAATTATTTG
128 ACTTAGAAAAATTTCAATTATTTG
891756 TACCGGTAGT
Statistics
Matches: 261, Mismatches: 41, Indels: 19
0.81 0.13 0.06
Matches are distributed among these distances:
158 5 0.02
159 129 0.49
160 62 0.24
161 64 0.25
162 1 0.00
ACGTcount: A:0.30, C:0.14, G:0.18, T:0.38
Consensus pattern (158 bp):
TTCATTTTCTACGCAAAGGATGCACATATTGAAATGAAATTTGATATACAGGTTTATCATAATAA
TATCTAGGTCAAGTTCGATTTGAGTACGATCGAGCAATTTTTGACAGAGTTATGCCCCTTGGACT
TAGAAAAATTTCAATTATTTGCAGTTTG
Found at i:893062 original size:21 final size:21
Alignment explanation
Indices: 893038--893108 Score: 117
Period size: 21 Copynumber: 3.4 Consensus size: 21
893028 TAAGTTGCAA
893038 GTCTCTTTTCCAGATCTTGTT
1 GTCTCTTTTCCAGATCTTGTT
893059 GTCTCTTTTCCAGATCTTGTT
1 GTCTCTTTTCCAGATCTTGTT
*
893080 TTCTCTTTTCCAGATCTTGTT
1 GTCTCTTTTCCAGATCTTGTT
*
893101 -TTTCTTTT
1 GTCTCTTTT
893109 GTAAGTTCCT
Statistics
Matches: 48, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
20 7 0.15
21 41 0.85
ACGTcount: A:0.08, C:0.23, G:0.11, T:0.58
Consensus pattern (21 bp):
GTCTCTTTTCCAGATCTTGTT
Found at i:894528 original size:2 final size:2
Alignment explanation
Indices: 894471--894519 Score: 80
Period size: 2 Copynumber: 24.5 Consensus size: 2
894461 ACTGAATAAT
* *
894471 TC TC TC TC TC TC TC TG TC TC TC TC TG TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
894513 TC TC TC T
1 TC TC TC T
894520 TTTTCTCTCA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.00, C:0.45, G:0.04, T:0.51
Consensus pattern (2 bp):
TC
Found at i:895602 original size:13 final size:13
Alignment explanation
Indices: 895584--895608 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
895574 TGTATTAGTT
895584 TTGAATTTGAATC
1 TTGAATTTGAATC
895597 TTGAATTTGAAT
1 TTGAATTTGAAT
895609 GCTGTATATT
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:0.04, G:0.16, T:0.48
Consensus pattern (13 bp):
TTGAATTTGAATC
Found at i:903341 original size:21 final size:21
Alignment explanation
Indices: 903317--903356 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
903307 TGTCCCTTGG
903317 CTGGCTCAGCTTGGTTTTTCA
1 CTGGCTCAGCTTGGTTTTTCA
* * *
903338 CTGGGTCAGTTTGTTTTTT
1 CTGGCTCAGCTTGGTTTTT
903357 TGCTACCTCA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.07, C:0.17, G:0.25, T:0.50
Consensus pattern (21 bp):
CTGGCTCAGCTTGGTTTTTCA
Found at i:906058 original size:25 final size:25
Alignment explanation
Indices: 906027--906075 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
906017 ACTTGCACAT
906027 GTAATAACATTATTACATAGAGCAC
1 GTAATAACATTATTACATAGAGCAC
906052 GTAATAACATTATTACATAGAGCA
1 GTAATAACATTATTACATAGAGCA
906076 AGGACTAGCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.45, C:0.14, G:0.12, T:0.29
Consensus pattern (25 bp):
GTAATAACATTATTACATAGAGCAC
Found at i:913313 original size:166 final size:165
Alignment explanation
Indices: 913119--913465 Score: 622
Period size: 166 Copynumber: 2.1 Consensus size: 165
913109 ATATTTTTAA
*
913119 AAAAATCTTCTTTTCAAAAATCATTTGGCCAGAAAAGCTGAAACTTGTGTGGAAGCATCCTCAGA
1 AAAAATCTTCTTCTCAAAAATCATTTGGCCAGAAAAGCTGAAACTTGTGTGGAAGCATCCTCAGA
*
913184 TAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCTGGGGGTAAAGTGGGGCCTCAATGTGGGGT
66 TAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCTGGGGATAAAGTGGGGCCTCAATG-GGGGT
*
913249 CGAATTTTTACATAGGAATATATAAAGTTAATCTTT
130 CAAATTTTTACATAGGAATATATAAAGTTAATCTTT
913285 AAAAATCTTCTTCTCAAAAATCATTTGGCCAGAAAAGCTGAAACTTGTGTGGAAGCATCCTCAGA
1 AAAAATCTTCTTCTCAAAAATCATTTGGCCAGAAAAGCTGAAACTTGTGTGGAAGCATCCTCAGA
*
913350 TAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCTGGGGATAAGGTGGGGCCTCAATGGGGGTC
66 TAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCTGGGGATAAAGTGGGGCCTCAATGGGGGTC
* *
913415 AAATTTTTACATAGGAGTATATAGAGTTAATCTTT
131 AAATTTTTACATAGGAATATATAAAGTTAATCTTT
*
913450 AAAAATCTTTTTCTCA
1 AAAAATCTTCTTCTCA
913466 TAAACTTTCA
Statistics
Matches: 174, Mismatches: 7, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
165 53 0.30
166 121 0.70
ACGTcount: A:0.31, C:0.15, G:0.22, T:0.32
Consensus pattern (165 bp):
AAAAATCTTCTTCTCAAAAATCATTTGGCCAGAAAAGCTGAAACTTGTGTGGAAGCATCCTCAGA
TAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCTGGGGATAAAGTGGGGCCTCAATGGGGGTC
AAATTTTTACATAGGAATATATAAAGTTAATCTTT
Found at i:914310 original size:4 final size:4
Alignment explanation
Indices: 914301--914365 Score: 55
Period size: 4 Copynumber: 16.0 Consensus size: 4
914291 GGTATATTGA
914301 TGTT TGTT TG-T TG-T TGTTT TGTTT TGTTT TGTTT TGTT TGTT TGTT
1 TGTT TGTT TGTT TGTT TG-TT TG-TT TG-TT TG-TT TGTT TGTT TGTT
* *
914347 TGTT T-TT TCTT TTTT TGTT
1 TGTT TGTT TGTT TGTT TGTT
914366 AAAGCAATAT
Statistics
Matches: 56, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
3 9 0.16
4 29 0.52
5 18 0.32
ACGTcount: A:0.00, C:0.02, G:0.20, T:0.78
Consensus pattern (4 bp):
TGTT
Found at i:914324 original size:5 final size:5
Alignment explanation
Indices: 914303--914365 Score: 64
Period size: 5 Copynumber: 13.2 Consensus size: 5
914293 TATATTGATG
914303 TTTG- TTTGT TGTTGT TTTGT TTTGT TTTGT TTTG- TTTG- TTTG- TTTGT
1 TTTGT TTTGT T-TTGT TTTGT TTTGT TTTGT TTTGT TTTGT TTTGT TTTGT
*
914350 TTT-T TCTTTT TTTGT T
1 TTTGT T-TTGT TTTGT T
914366 AAAGCAATAT
Statistics
Matches: 53, Mismatches: 1, Indels: 9
0.84 0.02 0.14
Matches are distributed among these distances:
4 18 0.34
5 28 0.53
6 7 0.13
ACGTcount: A:0.00, C:0.02, G:0.19, T:0.79
Consensus pattern (5 bp):
TTTGT
Found at i:916301 original size:31 final size:32
Alignment explanation
Indices: 916259--916318 Score: 104
Period size: 31 Copynumber: 1.9 Consensus size: 32
916249 CATAATTATG
916259 TGTTAGCAGATCTTTGG-AAAAGAAACTACTT
1 TGTTAGCAGATCTTTGGAAAAAGAAACTACTT
*
916290 TGTTAGTAGATCTTTGGAAAAAGAAACTA
1 TGTTAGCAGATCTTTGGAAAAAGAAACTA
916319 TTATGCCAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
31 16 0.59
32 11 0.41
ACGTcount: A:0.38, C:0.10, G:0.20, T:0.32
Consensus pattern (32 bp):
TGTTAGCAGATCTTTGGAAAAAGAAACTACTT
Found at i:917333 original size:2 final size:2
Alignment explanation
Indices: 917326--917358 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
917316 AAGTAAGTTT
917326 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
917359 NCATAATGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:919315 original size:168 final size:168
Alignment explanation
Indices: 919030--919615 Score: 838
Period size: 168 Copynumber: 3.5 Consensus size: 168
919020 ACATGTGAGG
* * * * * * *
919030 AAAAACTGAATGCATGGTTATGATGCCCATGAGGCCCTCTACCAAAATTGTGAAATTTATGGCCC
1 AAAAACTAAATGCATGGTTATGATGTCCATGAAGCCCTCAACCTAAATTGTGAAATTCATGACCC
919095 CTGGGTCAGGGGTTCAGGCTCTAGGGTGGGGCCAATATGGCCATAA-AGTAAAAATTTATTAAAT
66 CTGGGTCAGGGGTTCAGGCTCTAGGGTGGGGCCAATATGGCCA-AATAGTAAAAATTTATTAAAT
919159 CTTAGAAAATCTTCTTCTCTACTACCATATATATTTGTT
130 CTTAGAAAATCTTCTTCTCTACTACCATATATATTTGTT
*
919198 AAAAACTAAATGCATGATTATGATGTCCATGAAGCCCTCAACCTAAATTGTGAAATTCATGACCC
1 AAAAACTAAATGCATGGTTATGATGTCCATGAAGCCCTCAACCTAAATTGTGAAATTCATGACCC
*
919263 CTGGGTCAGGGGTTCAGGCTCTAGGGTGGGGCCAATATGGCCAAATAGTAAAAATGTATTAAATC
66 CTGGGTCAGGGGTTCAGGCTCTAGGGTGGGGCCAATATGGCCAAATAGTAAAAATTTATTAAATC
*
919328 TTAGAAAATCTTCTTCTCTACTATCATATATATTTGTT
131 TTAGAAAATCTTCTTCTCTACTACCATATATATTTGTT
919366 AAAAACTAAATGCATGGTTATGATGTCCATGAAGCCCTCAACCTAAATTGTGAAATTCATGACCC
1 AAAAACTAAATGCATGGTTATGATGTCCATGAAGCCCTCAACCTAAATTGTGAAATTCATGACCC
** * *
919431 CTCTGTCAGGGGTTCAGGCTCTAGGGTGGGGCCGATATGGCCAAATAGT-AAAA-TGATTTAAAT
66 CTGGGTCAGGGGTTCAGGCTCTAGGGTGGGGCCAATATGGCCAAATAGTAAAAATTTA-TTAAAT
* * * * * ** **
919494 CTTAAAAAATCTTCTTCTCTACTCCCACACATGTGGGCA
130 CTTAGAAAATCTTCTTCTCTACTACCATATATATTTGTT
* * * * * ** *
919533 AAAAACTGAATACATGGTTATGATATCCA-CAATCTCCTTTACCTAAATTGTGAAATTCATGGCC
1 AAAAACTAAATGCATGGTTATGATGTCCATGAAGC-CCTCAACCTAAATTGTGAAATTCATGACC
919597 CCTGGGTCAGGGGTTCAGG
65 CCTGGGTCAGGGGTTCAGG
919616 ACATGAGGGG
Statistics
Matches: 379, Mismatches: 36, Indels: 7
0.90 0.09 0.02
Matches are distributed among these distances:
166 4 0.01
167 110 0.29
168 265 0.70
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30
Consensus pattern (168 bp):
AAAAACTAAATGCATGGTTATGATGTCCATGAAGCCCTCAACCTAAATTGTGAAATTCATGACCC
CTGGGTCAGGGGTTCAGGCTCTAGGGTGGGGCCAATATGGCCAAATAGTAAAAATTTATTAAATC
TTAGAAAATCTTCTTCTCTACTACCATATATATTTGTT
Found at i:926926 original size:2 final size:2
Alignment explanation
Indices: 926919--926948 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
926909 ACGTTGGAAA
*
926919 TC TC TC TC TC TC TC TC TT TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
926949 AAAAAGATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
TC
Found at i:942441 original size:31 final size:31
Alignment explanation
Indices: 942406--942596 Score: 213
Period size: 31 Copynumber: 6.2 Consensus size: 31
942396 TATAATCAGT
* * * *
942406 ATGTTAAGAATTCATCGTTGTTGTGAAGATG
1 ATGTTAAGAATTTACCGGTGTTGTGAATATG
* *
942437 ATGTTACGTATTTACCGGTGTTGTGAATATG
1 ATGTTAAGAATTTACCGGTGTTGTGAATATG
*
942468 ATGTTAAGAATTTACCGGTGTTGCGAATATG
1 ATGTTAAGAATTTACCGGTGTTGTGAATATG
* *
942499 ATGTTCAGAATTTACCGGTGTTGCGAATAAT-
1 ATGTTAAGAATTTACCGGTGTTGTGAAT-ATG
* * * *
942530 ATGTTAAGTATTTATCGGTGCTGTTAATATG
1 ATGTTAAGAATTTACCGGTGTTGTGAATATG
* ** *
942561 ATGTCAACTATTTACTGGTGTTGTGAATATG
1 ATGTTAAGAATTTACCGGTGTTGTGAATATG
942592 ATGTT
1 ATGTT
942597 GACTTGCTGG
Statistics
Matches: 135, Mismatches: 23, Indels: 4
0.83 0.14 0.02
Matches are distributed among these distances:
30 2 0.01
31 131 0.97
32 2 0.01
ACGTcount: A:0.27, C:0.09, G:0.24, T:0.40
Consensus pattern (31 bp):
ATGTTAAGAATTTACCGGTGTTGTGAATATG
Found at i:944398 original size:18 final size:18
Alignment explanation
Indices: 944375--944418 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
944365 ATGTGTTTTA
944375 AAAAATCAAAATAC-ATCT
1 AAAAATCAAAAT-CGATCT
* *
944393 AAAAATAAAAATCGATGT
1 AAAAATCAAAATCGATCT
944411 AAAAATCA
1 AAAAATCA
944419 GCTATATGTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 1 0.05
18 21 0.95
ACGTcount: A:0.64, C:0.11, G:0.05, T:0.20
Consensus pattern (18 bp):
AAAAATCAAAATCGATCT
Found at i:944592 original size:66 final size:66
Alignment explanation
Indices: 944509--945496 Score: 1057
Period size: 64 Copynumber: 15.3 Consensus size: 66
944499 AACAAAACTT
** * * *
944509 AACGGATGTCTGCATCATCTAAAAACAAAACTGGACGGGTGTCTAAATCATCTATAAAAACAAAA
1 AACGGATGTCTAAATCATCTAAAAACCAAACTGGACGGATGTCTAAATCATCT-T-AAAACCAAA
*
944574 CTG
64 GTG
* * * *
944577 -ACGG-TGTCTGAATCATCTAAAAACAAAACTGGACGGGTGTCTAAATAATC-TATAAACCAAAG
1 AACGGATGTCTAAATCATCTAAAAACCAAACTGGACGGATGTCTAAATCATCTTA-AAACCAAAG
944639 TG
65 TG
* * *
944641 AACGGATGTCTAAATCATCTAAAAACCAAAGTGAACGGATGTCTAAATCATCTAAAAACCAAAGT
1 AACGGATGTCTAAATCATCTAAAAACCAAACTGGACGGATGTCTAAATCATCTTAAAACCAAAGT
944706 G
66 G
*
944707 AACGGATGTCTAAATCATCT-AAAACCAAA-GGGAACGGATGTCTAAATCA--TTAAAACCAAAG
1 AACGGATGTCTAAATCATCTAAAAACCAAACTGG-ACGGATGTCTAAATCATCTTAAAACCAAAG
*
944768 GG
65 TG
* * *
944770 AACGGATGTCTAAATCATCTAAAAACCAAAGTGAACGGATGTCTAAATCATC-TAAAACTAAAGT
1 AACGGATGTCTAAATCATCTAAAAACCAAACTGGACGGATGTCTAAATCATCTTAAAACCAAAGT
944834 G
66 G
* * ** * * **
944835 AACGGATGTCTAAATCATCT-AAAACTAAA-GGGAACGGATGTCTACCT-ATGGCTCAGATTCAG
1 AACGGATGTCTAAATCATCTAAAAACCAAACTGG-ACGGATGTCTAAATCAT--CTTAAAACCA-
*
944897 CA-T-
62 AAGTG
** * * * *
944900 TCCGGATGTCTAAATCATCTAAAACCCAAAGTGAACGGATGTCTAAATCA--TTAAAACCAAAGG
1 AACGGATGTCTAAATCATCTAAAAACCAAACTGGACGGATGTCTAAATCATCTTAAAACCAAAGT
944963 G
66 G
* *
944964 AACGGATGTCTAAATCAT-T-AAAACCAAAGTGAACGGATGTCTAAATCATC-TAAAACCCAAAG
1 AACGGATGTCTAAATCATCTAAAAACCAAACTGGACGGATGTCTAAATCATCTTAAAA-CCAAAG
945026 TG
65 TG
*
945028 AACGGATGTCTAAATCAT-T-AAAACCAAA-GGGAACGGATGTCTAAATCA--TTAAAACCAAAG
1 AACGGATGTCTAAATCATCTAAAAACCAAACTGG-ACGGATGTCTAAATCATCTTAAAACCAAAG
*
945088 GG
65 TG
* *
945090 AACGGATGTCTAAATCAT-T-AAATCCAAA-GGGAACGGATGTCTAAATCA--TTAAAACCAAAG
1 AACGGATGTCTAAATCATCTAAAAACCAAACTGG-ACGGATGTCTAAATCATCTTAAAACCAAAG
*
945150 GG
65 TG
* * *
945152 AACGGATGTCTAAATCATCTAAAAACCAAA-GGGAACGGATGTCTGAATCATCTAAAAACCAAAC
1 AACGGATGTCTAAATCATCTAAAAACCAAACTGG-ACGGATGTCTAAATCATCTTAAAACCAAA-
945216 G-G
64 GTG
* * * *
945218 AACGGATGTCTAAATCAT-T-AAAACCAAAGTGAACGGATGTCTAAATCATATAAAAACCAAAGT
1 AACGGATGTCTAAATCATCTAAAAACCAAACTGGACGGATGTCTAAATCATCTTAAAACCAAAGT
945281 G
66 G
* * *
945282 AACGGATGTCTAAATCATCTAAAAACCAAAGTGAACGGATGTCTAAATCA--TTAAAACCAAAGG
1 AACGGATGTCTAAATCATCTAAAAACCAAACTGGACGGATGTCTAAATCATCTTAAAACCAAAGT
945345 G
66 G
* *
945346 AACGGATGTCTAAATCAT-T-AAAACCAAA-GGGAACGGATGTCTAAATCATCTAAAAACCAAAG
1 AACGGATGTCTAAATCATCTAAAAACCAAACTGG-ACGGATGTCTAAATCATCTTAAAACCAAAG
945408 TG
65 TG
* *
945410 AACGGATGTCTTAATCATCTAAAAACCAAA-GGGAACGGATGTCTAAATCA--TTAAAACCAAAG
1 AACGGATGTCTAAATCATCTAAAAACCAAACTGG-ACGGATGTCTAAATCATCTTAAAACCAAAG
*
945472 GG
65 TG
*
945474 AACGGATGTCTAAATCATTTAAA
1 AACGGATGTCTAAATCATCTAAA
945497 GCAATATGAG
Statistics
Matches: 812, Mismatches: 70, Indels: 80
0.84 0.07 0.08
Matches are distributed among these distances:
61 1 0.00
62 140 0.17
63 56 0.07
64 297 0.37
65 84 0.10
66 225 0.28
67 9 0.01
ACGTcount: A:0.43, C:0.18, G:0.17, T:0.21
Consensus pattern (66 bp):
AACGGATGTCTAAATCATCTAAAAACCAAACTGGACGGATGTCTAAATCATCTTAAAACCAAAGT
G
Found at i:944601 original size:31 final size:33
Alignment explanation
Indices: 944492--945496 Score: 1298
Period size: 33 Copynumber: 31.2 Consensus size: 33
944482 TTCAAGATAT
* * * **
944492 ATCTAAAAACAAAACTTAACGGATGTCTGCATC
1 ATCTAAAAACCAAAGTGAACGGATGTCTAAATC
* * * *
944525 ATCTAAAAACAAAACTGGACGGGTGTCTAAATC
1 ATCTAAAAACCAAAGTGAACGGATGTCTAAATC
* * *
944558 ATCTATAAAAACAAAACTG-ACGG-TGTCTGAATC
1 ATC--TAAAAACCAAAGTGAACGGATGTCTAAATC
* * * * *
944591 ATCTAAAAACAAAACTGGACGGGTGTCTAAATA
1 ATCTAAAAACCAAAGTGAACGGATGTCTAAATC
*
944624 ATCTATAAACCAAAGTGAACGGATGTCTAAATC
1 ATCTAAAAACCAAAGTGAACGGATGTCTAAATC
944657 ATCTAAAAACCAAAGTGAACGGATGTCTAAATC
1 ATCTAAAAACCAAAGTGAACGGATGTCTAAATC
944690 ATCTAAAAACCAAAGTGAACGGATGTCTAAATC
1 ATCTAAAAACCAAAGTGAACGGATGTCTAAATC
*
944723 ATCT-AAAACCAAAGGGAACGGATGTCTAAATC
1 ATCTAAAAACCAAAGTGAACGGATGTCTAAATC
*
944755 AT-T-AAAACCAAAGGGAACGGATGTCTAAATC
1 ATCTAAAAACCAAAGTGAACGGATGTCTAAATC
944786 ATCTAAAAACCAAAGTGAACGGATGTCTAAATC
1 ATCTAAAAACCAAAGTGAACGGATGTCTAAATC
*
944819 ATCT-AAAACTAAAGTGAACGGATGTCTAAATC
1 ATCTAAAAACCAAAGTGAACGGATGTCTAAATC
* * **
944851 ATCT-AAAACTAAAGGGAACGGATGTCTACCT-
1 ATCTAAAAACCAAAGTGAACGGATGTCTAAATC
* * ** * **
944882 ATGGCTCAGATTCAGCA-T-TCCGGATGTCTAAATC
1 AT--CTAAAAACCA-AAGTGAACGGATGTCTAAATC
*
944916 ATCTAAAACCCAAAGTGAACGGATGTCTAAATC
1 ATCTAAAAACCAAAGTGAACGGATGTCTAAATC
*
944949 AT-T-AAAACCAAAGGGAACGGATGTCTAAATC
1 ATCTAAAAACCAAAGTGAACGGATGTCTAAATC
944980 AT-T-AAAACCAAAGTGAACGGATGTCTAAATC
1 ATCTAAAAACCAAAGTGAACGGATGTCTAAATC
*
945011 ATCTAAAACCCAAAGTGAACGGATGTCTAAATC
1 ATCTAAAAACCAAAGTGAACGGATGTCTAAATC
*
945044 AT-T-AAAACCAAAGGGAACGGATGTCTAAATC
1 ATCTAAAAACCAAAGTGAACGGATGTCTAAATC
*
945075 AT-T-AAAACCAAAGGGAACGGATGTCTAAATC
1 ATCTAAAAACCAAAGTGAACGGATGTCTAAATC
* *
945106 AT-T-AAATCCAAAGGGAACGGATGTCTAAATC
1 ATCTAAAAACCAAAGTGAACGGATGTCTAAATC
*
945137 AT-T-AAAACCAAAGGGAACGGATGTCTAAATC
1 ATCTAAAAACCAAAGTGAACGGATGTCTAAATC
* *
945168 ATCTAAAAACCAAAGGGAACGGATGTCTGAATC
1 ATCTAAAAACCAAAGTGAACGGATGTCTAAATC
945201 ATCTAAAAACCAAACG-GAACGGATGTCTAAATC
1 ATCTAAAAACCAAA-GTGAACGGATGTCTAAATC
945234 AT-T-AAAACCAAAGTGAACGGATGTCTAAATC
1 ATCTAAAAACCAAAGTGAACGGATGTCTAAATC
*
945265 ATATAAAAACCAAAGTGAACGGATGTCTAAATC
1 ATCTAAAAACCAAAGTGAACGGATGTCTAAATC
945298 ATCTAAAAACCAAAGTGAACGGATGTCTAAATC
1 ATCTAAAAACCAAAGTGAACGGATGTCTAAATC
*
945331 AT-T-AAAACCAAAGGGAACGGATGTCTAAATC
1 ATCTAAAAACCAAAGTGAACGGATGTCTAAATC
*
945362 AT-T-AAAACCAAAGGGAACGGATGTCTAAATC
1 ATCTAAAAACCAAAGTGAACGGATGTCTAAATC
*
945393 ATCTAAAAACCAAAGTGAACGGATGTCTTAATC
1 ATCTAAAAACCAAAGTGAACGGATGTCTAAATC
*
945426 ATCTAAAAACCAAAGGGAACGGATGTCTAAATC
1 ATCTAAAAACCAAAGTGAACGGATGTCTAAATC
*
945459 AT-T-AAAACCAAAGGGAACGGATGTCTAAATC
1 ATCTAAAAACCAAAGTGAACGGATGTCTAAATC
*
945490 ATTTAAA
1 ATCTAAA
945497 GCAATATGAG
Statistics
Matches: 893, Mismatches: 54, Indels: 50
0.90 0.05 0.05
Matches are distributed among these distances:
30 1 0.00
31 343 0.38
32 106 0.12
33 418 0.47
34 10 0.01
35 15 0.02
ACGTcount: A:0.44, C:0.18, G:0.17, T:0.21
Consensus pattern (33 bp):
ATCTAAAAACCAAAGTGAACGGATGTCTAAATC
Found at i:944986 original size:128 final size:128
Alignment explanation
Indices: 944492--945492 Score: 1360
Period size: 128 Copynumber: 7.8 Consensus size: 128
944482 TTCAAGATAT
* * * ** * * * *
944492 ATCTAAAAACAAAACTTAACGGATGTCTGCATCATCTAAAAACAAAACTGGACGGGTGTCTAAAT
1 ATCTAAAAACCAAAGTGAACGGATGTCTAAATCATCTAAAAACCAAAGTGAACGGATGTCTAAAT
* ** * * * *
944557 CATCTATAAAAACAAAACTG-ACGG-TGTCTGAATCATCTAAAAACAAAACTGG-ACGGGTGTCT
66 CA--T-T-AAAACCAAAGGGAACGGATGTCTAAATCAT-T-AAAACCAAA-GGGAACGGATGTCT
*
944619 AAATA
124 AAATC
*
944624 ATCTATAAACCAAAGTGAACGGATGTCTAAATCATCTAAAAACCAAAGTGAACGGATGTCTAAAT
1 ATCTAAAAACCAAAGTGAACGGATGTCTAAATCATCTAAAAACCAAAGTGAACGGATGTCTAAAT
*
944689 CATCTAAAAACCAAAGTGAACGGATGTCTAAATCATCTAAAACCAAAGGGAACGGATGTCTAAAT
66 CAT-T-AAAACCAAAGGGAACGGATGTCTAAATCAT-TAAAACCAAAGGGAACGGATGTCTAAAT
944754 C
128 C
*
944755 AT-T-AAAACCAAAGGGAACGGATGTCTAAATCATCTAAAAACCAAAGTGAACGGATGTCTAAAT
1 ATCTAAAAACCAAAGTGAACGGATGTCTAAATCATCTAAAAACCAAAGTGAACGGATGTCTAAAT
* * * **
944818 CATCTAAAACTAAAGTGAACGGATGTCTAAATCATCTAAAACTAAAGGGAACGGATGTCTACCT-
66 CAT-TAAAACCAAAGGGAACGGATGTCTAAATCAT-TAAAACCAAAGGGAACGGATGTCTAAATC
* * ** * ** *
944882 ATGGCTCAGATTCAGCA-T-TCCGGATGTCTAAATCATCTAAAACCCAAAGTGAACGGATGTCTA
1 AT--CTAAAAACCA-AAGTGAACGGATGTCTAAATCATCTAAAAACCAAAGTGAACGGATGTCTA
*
944945 AATCATTAAAACCAAAGGGAACGGATGTCTAAATCATTAAAACCAAAGTGAACGGATGTCTAAAT
63 AATCATTAAAACCAAAGGGAACGGATGTCTAAATCATTAAAACCAAAGGGAACGGATGTCTAAAT
945010 C
128 C
* *
945011 ATCTAAAACCCAAAGTGAACGGATGTCTAAATCAT-T-AAAACCAAAGGGAACGGATGTCTAAAT
1 ATCTAAAAACCAAAGTGAACGGATGTCTAAATCATCTAAAAACCAAAGTGAACGGATGTCTAAAT
*
945074 CATTAAAACCAAAGGGAACGGATGTCTAAATCATTAAATCCAAAGGGAACGGATGTCTAAATC
66 CATTAAAACCAAAGGGAACGGATGTCTAAATCATTAAAACCAAAGGGAACGGATGTCTAAATC
* * *
945137 AT-T-AAAACCAAAGGGAACGGATGTCTAAATCATCTAAAAACCAAAGGGAACGGATGTCTGAAT
1 ATCTAAAAACCAAAGTGAACGGATGTCTAAATCATCTAAAAACCAAAGTGAACGGATGTCTAAAT
* *
945200 CATCTAAAAACCAAACGGAACGGATGTCTAAATCATTAAAACCAAAGTGAACGGATGTCTAAATC
66 CAT-T-AAAACCAAAGGGAACGGATGTCTAAATCATTAAAACCAAAGGGAACGGATGTCTAAATC
*
945265 ATATAAAAACCAAAGTGAACGGATGTCTAAATCATCTAAAAACCAAAGTGAACGGATGTCTAAAT
1 ATCTAAAAACCAAAGTGAACGGATGTCTAAATCATCTAAAAACCAAAGTGAACGGATGTCTAAAT
945330 CATTAAAACCAAAGGGAACGGATGTCTAAATCATTAAAACCAAAGGGAACGGATGTCTAAATC
66 CATTAAAACCAAAGGGAACGGATGTCTAAATCATTAAAACCAAAGGGAACGGATGTCTAAATC
* *
945393 ATCTAAAAACCAAAGTGAACGGATGTCTTAATCATCTAAAAACCAAAGGGAACGGATGTCTAAAT
1 ATCTAAAAACCAAAGTGAACGGATGTCTAAATCATCTAAAAACCAAAGTGAACGGATGTCTAAAT
945458 CATTAAAACCAAAGGGAACGGATGTCTAAATCATT
66 CATTAAAACCAAAGGGAACGGATGTCTAAATCATT
945493 TAAAGCAATA
Statistics
Matches: 789, Mismatches: 63, Indels: 38
0.89 0.07 0.04
Matches are distributed among these distances:
124 28 0.04
125 2 0.00
126 118 0.15
127 11 0.01
128 307 0.39
129 96 0.12
130 125 0.16
131 31 0.04
132 71 0.09
ACGTcount: A:0.44, C:0.18, G:0.17, T:0.21
Consensus pattern (128 bp):
ATCTAAAAACCAAAGTGAACGGATGTCTAAATCATCTAAAAACCAAAGTGAACGGATGTCTAAAT
CATTAAAACCAAAGGGAACGGATGTCTAAATCATTAAAACCAAAGGGAACGGATGTCTAAATC
Found at i:945032 original size:225 final size:221
Alignment explanation
Indices: 944509--945492 Score: 1276
Period size: 225 Copynumber: 4.4 Consensus size: 221
944499 AACAAAACTT
** * * * *
944509 AACGGATGTCTGCATCATCTAAAAACAAAACTGG-ACGGGTGTCTAAATCATCTATAAAAACAAA
1 AACGGATGTCTAAATCATCTAAAAACCAAA-GGGAACGGATGTCTAAATCA--T-T-AAAACCAA
* * * * * * *
944573 ACTG-ACGG-TGTCTGAATCATCTAAAAACAAAACTGGACGGGTGTCTAAATAATCTATAAACCA
61 AGTGAACGGATGTCTAAATCAT-T-AAAACCAAAGTGAACGGATGTCTAAATCATCTA-AAACCA
* * *
944636 AAGTGAACGGATGTCTAAATCATCTAAAAACCAAAGTGAACGGATGTCTAAATCATCTAAAAACC
123 AAGGGAACGGATGTCTAAATCAT-T-AAATCC-AAGGGAACGGATGTCTAAATCAT-T-AAAACC
*
944701 AAAGTGAACGGATGTCTAAATCATCT-AAAACCAAAGGG
183 AAAGGGAACGGATGTCTAAATCATCTAAAAACCAAAGGG
944739 AACGGATGTCTAAATCAT-T-AAAACCAAAGGGAACGGATGTCTAAATCATCTAAAAACCAAAGT
1 AACGGATGTCTAAATCATCTAAAAACCAAAGGGAACGGATGTCTAAATCAT-T-AAAACCAAAGT
* *
944802 GAACGGATGTCTAAATCATCTAAAACTAAAGTGAACGGATGTCTAAATCATCTAAAACTAAAGGG
64 GAACGGATGTCTAAATCAT-TAAAACCAAAGTGAACGGATGTCTAAATCATCTAAAACCAAAGGG
* * * * * *
944867 AACGGATGTCTACCTATGGC-TCAGATTC-A-GCATTCCGGATGTCTAAATCATCTAAAACCCAA
128 AACGGATGTCTA--AAT--CATTAAATCCAAGGGA--ACGGATGTCTAAATCAT-TAAAA-CCAA
*
944929 AGTGAACGGATGTCTAAATCAT-T-AAAACCAAAGGG
185 AGGGAACGGATGTCTAAATCATCTAAAAACCAAAGGG
*
944964 AACGGATGTCTAAATCAT-T-AAAACCAAAGTGAACGGATGTCTAAATCATCTAAAACCCAAAGT
1 AACGGATGTCTAAATCATCTAAAAACCAAAGGGAACGGATGTCTAAATCAT-TAAAA-CCAAAGT
*
945027 GAACGGATGTCTAAATCATTAAAACCAAAGGGAACGGATGTCTAAATCAT-TAAAACCAAAGGGA
64 GAACGGATGTCTAAATCATTAAAACCAAAGTGAACGGATGTCTAAATCATCTAAAACCAAAGGGA
945091 ACGGATGTCTAAATCATTAAATCCAAAGGGAACGGATGTCTAAATCATTAAAACCAAAGGGAACG
129 ACGGATGTCTAAATCATTAAATCC-AAGGGAACGGATGTCTAAATCATTAAAACCAAAGGGAACG
945156 GATGTCTAAATCATCTAAAAACCAAAGGG
193 GATGTCTAAATCATCTAAAAACCAAAGGG
* *
945185 AACGGATGTCTGAATCATCTAAAAACCAAACGGAACGGATGTCTAAATCATTAAAACCAAAGTGA
1 AACGGATGTCTAAATCATCTAAAAACCAAAGGGAACGGATGTCTAAATCATTAAAACCAAAGTGA
*
945250 ACGGATGTCTAAATCATATAAAAACCAAAGTGAACGGATGTCTAAATCATCTAAAAACCAAAGTG
66 ACGGATGTCTAAATCAT-T-AAAACCAAAGTGAACGGATGTCTAAATCATCT-AAAACCAAAGGG
*
945315 AACGGATGTCTAAATCATTAAAACCAAAGGGAACGGATGTCTAAATCATTAAAACCAAAGGGAAC
128 AACGGATGTCTAAATCATTAAATCC-AAGGGAACGGATGTCTAAATCATTAAAACCAAAGGGAAC
*
945380 GGATGTCTAAATCATCTAAAAACCAAAGTG
192 GGATGTCTAAATCATCTAAAAACCAAAGGG
* *
945410 AACGGATGTCTTAATCATCTAAAAACCAAAGGGAACGGATGTCTAAATCATTAAAACCAAAGGGA
1 AACGGATGTCTAAATCATCTAAAAACCAAAGGGAACGGATGTCTAAATCATTAAAACCAAAGTGA
945475 ACGGATGTCTAAATCATT
66 ACGGATGTCTAAATCATT
945493 TAAAGCAATA
Statistics
Matches: 686, Mismatches: 45, Indels: 52
0.88 0.06 0.07
Matches are distributed among these distances:
219 26 0.04
220 11 0.02
221 73 0.11
222 8 0.01
223 83 0.12
224 36 0.05
225 277 0.40
226 78 0.11
227 37 0.05
228 38 0.06
229 2 0.00
230 17 0.02
ACGTcount: A:0.43, C:0.18, G:0.17, T:0.21
Consensus pattern (221 bp):
AACGGATGTCTAAATCATCTAAAAACCAAAGGGAACGGATGTCTAAATCATTAAAACCAAAGTGA
ACGGATGTCTAAATCATTAAAACCAAAGTGAACGGATGTCTAAATCATCTAAAACCAAAGGGAAC
GGATGTCTAAATCATTAAATCCAAGGGAACGGATGTCTAAATCATTAAAACCAAAGGGAACGGAT
GTCTAAATCATCTAAAAACCAAAGGG
Found at i:953281 original size:167 final size:165
Alignment explanation
Indices: 952985--953447 Score: 621
Period size: 167 Copynumber: 2.8 Consensus size: 165
952975 GTCGCATTTA
* * *
952985 TCTCGGCAACTATTTATCGCAGATGCTTGAAATTTTTACACAGTGTTTGT-TAAGGCATGCCATA
1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTTACACAATATTTGTAT-AGGCATGCCATA
* * *
953049 TCGTAGGATATATTTTTGTACCAATCGGACTTCAACTTCCTGTTAAATGACGACTTTGCTTATTT
65 TCGTGGGATATATTTTTGTACCAATCAGACGTCAACTTCCTGTTAAATGACGACTTTGCTTA--T
953114 TTTAACCAAAATTTTCAAACAAATTTTCATCAAAGATT
128 TTTAACCAAAATTTTCAAACAAATTTTCATCAAAGATT
* *
953152 TCTCAGCAACTATTTATAGCAGATCCTTGAAATTTTTACACAATATTTGTATAGGCATGCCATAT
1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTTACACAATATTTGTATAGGCATGCCATAT
*
953217 CGTGGGATATATTTTTGTACCAATCAGACGTCAACTTCCTGTTAAATGA-GTACTTTGTTTATTT
66 CGTGGGATATATTTTTGTACCAATCAGACGTCAACTTCCTGTTAAATGACG-ACTTTGCTTATTT
* *
953281 TAGCCAAAATTTTCAAACAAATTTTCCTCAAAGATT
130 TAACCAAAATTTTCAAACAAATTTTCATCAAAGATT
* * *
953317 TCTCAG-AAGCTATTTATCGCAGATGCTTAAAAATTTTGACACACTATTTG-ATTAGGCATGCCA
1 TCTCAGCAA-CTATTTATCGCAGATGCTT-GAAATTTTTACACAATATTTGTA-TAGGCATGCCA
* * * * * * **
953380 TATTGTGGGATATATTTCTGTACCAATC-GAATGCCAGCTTTCTGTTAAATGTTGACTTTGCTTA
63 TATCGTGGGATATATTTTTGTACCAATCAG-ACGTCAACTTCCTGTTAAATGACGACTTTGCTTA
953444 TTTT
127 TTTT
953448 GCATATTCAC
Statistics
Matches: 265, Mismatches: 24, Indels: 15
0.87 0.08 0.05
Matches are distributed among these distances:
164 2 0.01
165 62 0.23
166 86 0.32
167 114 0.43
168 1 0.00
ACGTcount: A:0.30, C:0.17, G:0.14, T:0.39
Consensus pattern (165 bp):
TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTTACACAATATTTGTATAGGCATGCCATAT
CGTGGGATATATTTTTGTACCAATCAGACGTCAACTTCCTGTTAAATGACGACTTTGCTTATTTT
AACCAAAATTTTCAAACAAATTTTCATCAAAGATT
Found at i:960854 original size:215 final size:214
Alignment explanation
Indices: 960483--960879 Score: 767
Period size: 215 Copynumber: 1.9 Consensus size: 214
960473 TTTTATAGAA
960483 TTCTGTAAGGATAAAGATGGGGTTTTCAATCGGGTAAGCTTATAAGCTTGTTAATGAGCTCATCT
1 TTCTGTAAGGATAAAGATGGGGTTTTCAATCGGGTAAGCTTATAAGCTTGTTAATGAGCTCATCT
960548 CAACCAGAACAATTCTTAATCAAGTGTACAGAAATATTGTAGATAATTAGTGCTAAATCTACAGT
66 CAACCAGAACAATTCTTAATCAAGTGTACAGAAATATTGTAGATAATTAGTGCTAAATCTACAGT
960613 TGATTAAATTTTCTTCTAATTATGATTATTTTAGCTGTTTCACCTACCAAGANTCCACATTATTT
131 TGATTAAATTTTCTTCTAATTATGATTATTTTAGCTGTTTCACCTACCAAGA-TCCACATTATTT
960678 TATAGAATTACATTCGCTGG
195 TATAGAATTACATTCGCTGG
960698 TTCTGTAAGGATAAAGATGGGGTTTTCAATCGGGTAAGCTTATAAGCTTGTTAATGAGCTCATCT
1 TTCTGTAAGGATAAAGATGGGGTTTTCAATCGGGTAAGCTTATAAGCTTGTTAATGAGCTCATCT
* *
960763 TAACCAGAACAATTCTTGATCAAGTGTACAGAAATATTGTAGATAATTAGTGCTAAATCTACAGT
66 CAACCAGAACAATTCTTAATCAAGTGTACAGAAATATTGTAGATAATTAGTGCTAAATCTACAGT
960828 TGATTAAATTTTCTTCTAATTATGATTATTTTAGCTGTTTCACCTACCAAGA
131 TGATTAAATTTTCTTCTAATTATGATTATTTTAGCTGTTTCACCTACCAAGA
960880 GATCGCAGTT
Statistics
Matches: 180, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
215 180 1.00
ACGTcount: A:0.32, C:0.14, G:0.16, T:0.37
Consensus pattern (214 bp):
TTCTGTAAGGATAAAGATGGGGTTTTCAATCGGGTAAGCTTATAAGCTTGTTAATGAGCTCATCT
CAACCAGAACAATTCTTAATCAAGTGTACAGAAATATTGTAGATAATTAGTGCTAAATCTACAGT
TGATTAAATTTTCTTCTAATTATGATTATTTTAGCTGTTTCACCTACCAAGATCCACATTATTTT
ATAGAATTACATTCGCTGG
Found at i:963991 original size:12 final size:12
Alignment explanation
Indices: 963974--963998 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
963964 AACAATCATG
963974 GAGATTTATACA
1 GAGATTTATACA
963986 GAGATTTATACA
1 GAGATTTATACA
963998 G
1 G
963999 CGATATAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.08, G:0.20, T:0.32
Consensus pattern (12 bp):
GAGATTTATACA
Found at i:966899 original size:24 final size:24
Alignment explanation
Indices: 966867--966917 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
966857 CTTAGTGTGA
966867 ATTAACACCCATTTTTGAAGGTTG
1 ATTAACACCCATTTTTGAAGGTTG
966891 ATTAACACCCATTTTTGAAGGTTG
1 ATTAACACCCATTTTTGAAGGTTG
966915 ATT
1 ATT
966918 TTTTAATCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.39
Consensus pattern (24 bp):
ATTAACACCCATTTTTGAAGGTTG
Found at i:972204 original size:2 final size:2
Alignment explanation
Indices: 972197--972240 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
972187 AGAAACAGTG
972197 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
972239 CT
1 CT
972241 AAAAACAACA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:973753 original size:2 final size:2
Alignment explanation
Indices: 973746--973805 Score: 86
Period size: 2 Copynumber: 30.0 Consensus size: 2
973736 TAATAACAAT
* *
973746 TC TC TC TC TC TA TA TC TC TC -C ATC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC -TC TC TC TC TC TC TC TC TC TC
973788 TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC
973806 ACAAGCCTTG
Statistics
Matches: 54, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
1 1 0.02
2 52 0.96
3 1 0.02
ACGTcount: A:0.05, C:0.47, G:0.00, T:0.48
Consensus pattern (2 bp):
TC
Found at i:975560 original size:2 final size:2
Alignment explanation
Indices: 975553--975614 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
975543 AGCTGTTCAT
975553 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
975595 TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC
975615 ATATTTCATC
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:981318 original size:2 final size:2
Alignment explanation
Indices: 981311--981344 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
981301 ATAGGCCGGC
981311 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
981345 ACCAGTCCCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:982986 original size:4 final size:4
Alignment explanation
Indices: 982977--983001 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
982967 TGTAGGAGAG
982977 GTCT GTCT GTCT GTCT GTCT GTCT G
1 GTCT GTCT GTCT GTCT GTCT GTCT G
983002 AGGGTAACAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.00, C:0.24, G:0.28, T:0.48
Consensus pattern (4 bp):
GTCT
Found at i:985278 original size:16 final size:18
Alignment explanation
Indices: 985247--985280 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
985237 TCTGCTTTTC
985247 TAAAACATTACAACATTT
1 TAAAACATTACAACATTT
985265 TAAAACA-T-CAACATTT
1 TAAAACATTACAACATTT
985281 GAACACTTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.50
17 1 0.06
18 7 0.44
ACGTcount: A:0.50, C:0.18, G:0.00, T:0.32
Consensus pattern (18 bp):
TAAAACATTACAACATTT
Found at i:990114 original size:180 final size:180
Alignment explanation
Indices: 989811--990531 Score: 1244
Period size: 180 Copynumber: 4.0 Consensus size: 180
989801 GGCTGCCAAA
* * **
989811 AGGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTTTCAAGATAGGAAGTTGTTCTTCTGTT
1 AGGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTCTCAAGATAGGAAGTTGTTCTTTTGCA
*
989876 GATCAATTGTACATATATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCCGATAATTTATCGA
66 GATCAATTGTACATATATCAGAGGTGTGCATATTGCTAGGATTTGGATTTCCGATAATTTATCGA
*
989941 AAAAATACCAGCTTTTGAACTTAGTCATTTTTTGGCAAAATGTTGCATAT
131 AAAAATACCAGCTTTTGAACTTAGTCATTTTTTGGCAAAATATTGCATAT
*
989991 AGGGTACCCTCATTATACGGATAACTCCTCCTACAGTTCTCAAGATAGGAAGTTGTTCTTTTGCA
1 AGGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTCTCAAGATAGGAAGTTGTTCTTTTGCA
* * * *
990056 GATCAATTGTACATATATCAGAGGTGTGCACATTGCTAGGATTTTGTTTTCTGATAATTTATCGA
66 GATCAATTGTACATATATCAGAGGTGTGCATATTGCTAGGATTTGGATTTCCGATAATTTATCGA
* *
990121 AAAAATACTAGCTTTTGAACTTAGTCATATTTTGGCAAAATATTGCATAT
131 AAAAATACCAGCTTTTGAACTTAGTCATTTTTTGGCAAAATATTGCATAT
990171 AGGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTCTCAAGATAGGAAGTTGTTCTTTTGCA
1 AGGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTCTCAAGATAGGAAGTTGTTCTTTTGCA
*
990236 GATCAATTGTACATATATTAGAGGTGTGCATATTGCTAGGATTTGGATTTCCGATAATTTATCGA
66 GATCAATTGTACATATATCAGAGGTGTGCATATTGCTAGGATTTGGATTTCCGATAATTTATCGA
*
990301 AAAAATACCAGCTTTTGAACTTAGTCATTTTTTTGCAAAATATTGCATAT
131 AAAAATACCAGCTTTTGAACTTAGTCATTTTTTGGCAAAATATTGCATAT
990351 AGGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTCTCAAGATAGGAAGTTGTTCTTTTGCA
1 AGGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTCTCAAGATAGGAAGTTGTTCTTTTGCA
**
990416 GATCAATTGTACATATATCAGAGGTGTGCATATTGCTAGGATTTGGATTTCCGATAATTTATTAA
66 GATCAATTGTACATATATCAGAGGTGTGCATATTGCTAGGATTTGGATTTCCGATAATTTATCGA
* * * * *
990481 AAAAATACTAGCTTTTGAACTTACTTATTTTTTGGCAAAATGTTGTATAT
131 AAAAATACCAGCTTTTGAACTTAGTCATTTTTTGGCAAAATATTGCATAT
990531 A
1 A
990532 CATGTAGGGT
Statistics
Matches: 512, Mismatches: 29, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
180 512 1.00
ACGTcount: A:0.29, C:0.16, G:0.18, T:0.37
Consensus pattern (180 bp):
AGGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTCTCAAGATAGGAAGTTGTTCTTTTGCA
GATCAATTGTACATATATCAGAGGTGTGCATATTGCTAGGATTTGGATTTCCGATAATTTATCGA
AAAAATACCAGCTTTTGAACTTAGTCATTTTTTGGCAAAATATTGCATAT
Found at i:996738 original size:433 final size:438
Alignment explanation
Indices: 995932--997068 Score: 1625
Period size: 433 Copynumber: 2.6 Consensus size: 438
995922 NNNNNNNNNN
995932 TGATACTGATGCACCTGACAGGCTTGAATGCTGAATCTGAGACATAGGTTTCGGATGCTGGAGGA
1 TGATACTGATGCACCTGACAGGCTTGAATGCTGAATCTGAGACATAGGTTTCGGATGCTGGAGGA
* *
995997 GGTTAAGGTTTTAAGAGCTGGTTTAAGTTTTTGAAATAGGTGCCCTCTTATGATGATATCTTTGT
66 GGTTAAGGTTTTAAGAGCTGGTTTAAGTTTTTGAAACAGGTGCCCTCTTATGATGATATCTTAGT
* * *
996062 TATTACTTGTCCTAACTTTACTAGACTTCCATGGATGGTGCGTTTTACGTTACTGATGCACCTGA
131 TATTACTTGTCCTAACTTCACTAGACTTCCATGGATGGTGCGTTTTATGATACTGATGCACCTGA
* *
996127 CAGGCTTGAATGCTGAGTCTGAGCCATAAGTTTCGGATGCTGGAAAAGGTTAAGTTTTTTTTAAC
196 CAGGCTTGAATGCTGAGTCTGAGCCATAGGTTTCGGATGCTGGATAAGGTTAAGTTTTTTTTAAC
996192 AAGTCACATGTTACGTAGATAGTAGTACTATTTCAAACATTTTCAAATTGATTAAACTGTAATAT
261 AAGTCACATGTTACGTAGATAGTAGTACTATTTCAAACATTTTCAAATTGATTAAACTGTAATAT
996257 GAATGAATCTCAGAGGAAGCTTCAGATGCAGAGCTTGATCTCCATTATCAAGGATGCT-AAAAA-
326 GAATGAATCTCAGAGGAAGCTTCAGATGCAGAGCTTGATCTCCATTATCAAGGATGCTAAAAAAT
* * * *
996320 ATA-C-T-GGTCCTTACTTCACCAAACTTGTATGGTTGGTGCGTCTTT
391 ATATCTTAGGTCCTAACTTCACCAAACTTGAATGGATGGTGCGTCTTA
996365 TGATACTGATGCACCTGACAGGCTTGAATGCTGAATCTGAGACATAGGTTTCGGATGCTGGAGGA
1 TGATACTGATGCACCTGACAGGCTTGAATGCTGAATCTGAGACATAGGTTTCGGATGCTGGAGGA
*
996430 GGTAAAGGTTTTAAGAGCTGGTTTAAGTTTTTGAAACAGGTGCCCTCTTATGATGATATCTTAGT
66 GGTTAAGGTTTTAAGAGCTGGTTTAAGTTTTTGAAACAGGTGCCCTCTTATGATGATATCTTAGT
996495 TATTACTTGTCCTAACTTCACTAGACTTCCATGGATGGTGCGTTTTATGATACTGATGCACCTGA
131 TATTACTTGTCCTAACTTCACTAGACTTCCATGGATGGTGCGTTTTATGATACTGATGCACCTGA
996560 CAGGCTTGAATGCTGAGTCTGAGCCATAGGTTTCGGATGCTGGATAAGGTTAAGTTTTTTTTAAC
196 CAGGCTTGAATGCTGAGTCTGAGCCATAGGTTTCGGATGCTGGATAAGGTTAAGTTTTTTTTAAC
996625 AAGTCACATGTTACGTAGATAGTAGTACTATTTCAAACATTTTCAAATTGATTAAACTGTAATAT
261 AAGTCACATGTTACGTAGATAGTAGTACTATTTCAAACATTTTCAAATTGATTAAACTGTAATAT
996690 GAATGAATCTCAGAGGAAGCTTCAGATGCAGAGCTTGATCTCCATTATCAAGGATGCTAAAAAAT
326 GAATGAATCTCAGAGGAAGCTTCAGATGCAGAGCTTGATCTCCATTATCAAGGATGCTAAAAAAT
* *
996755 ATATCTTAGTTATTACAGGTCCTAACTTCACCAAATTTGAATGGATGGTGTGTCTTA
391 ATATC-------TT--AGGTCCTAACTTCACCAAACTTGAATGGATGGTGCGTCTTA
* * * * * * *
996812 TAATACAGATGCACATGATAGGCATGGATGCTGAATCTGAGCCATAGGTTGT-GGATGCTGGAGG
1 TGATACTGATGCACCTGACAGGCTTGAATGCTGAATCTGAGACATAGGTT-TCGGATGCTGGAGG
** ** *
996876 AGGTTAAGGTTTTAATTGCTGG--T--GCCCTCTG---CA--TG-------ATGATGATATCTTA
65 AGGTTAAGGTTTTAAGAGCTGGTTTAAG-TTTTTGAAACAGGTGCCCTCTTATGATGATATCTTA
* * * * * * * *
996925 GTTATTTCTGGTCCTAACTTCACCAAACTTGCATGGGTGATGCGTCTTATGATACTGATGCACCT
129 GTTATTACTTGTCCTAACTTCACTAGACTTCCATGGATGGTGCGTTTTATGATACTGATGCACCT
* ** * * * * **
996990 GACAGGCTTGAATGCTGAATCTGAGCCATAGGTTAAGGATGCTAGATGAGGTTTAGTTTGTTGGA
194 GACAGGCTTGAATGCTGAGTCTGAGCCATAGGTTTCGGATGCTGGATAAGGTTAAGTTTTTTTTA
*
997055 ACAGGTCACATGTT
259 ACAAGTCACATGTT
997069 TAATAGATGA
Statistics
Matches: 643, Mismatches: 45, Indels: 33
0.89 0.06 0.05
Matches are distributed among these distances:
432 140 0.22
433 375 0.58
434 5 0.01
435 3 0.00
436 1 0.00
439 2 0.00
441 2 0.00
443 1 0.00
444 4 0.01
445 1 0.00
447 108 0.17
448 1 0.00
ACGTcount: A:0.27, C:0.16, G:0.23, T:0.34
Consensus pattern (438 bp):
TGATACTGATGCACCTGACAGGCTTGAATGCTGAATCTGAGACATAGGTTTCGGATGCTGGAGGA
GGTTAAGGTTTTAAGAGCTGGTTTAAGTTTTTGAAACAGGTGCCCTCTTATGATGATATCTTAGT
TATTACTTGTCCTAACTTCACTAGACTTCCATGGATGGTGCGTTTTATGATACTGATGCACCTGA
CAGGCTTGAATGCTGAGTCTGAGCCATAGGTTTCGGATGCTGGATAAGGTTAAGTTTTTTTTAAC
AAGTCACATGTTACGTAGATAGTAGTACTATTTCAAACATTTTCAAATTGATTAAACTGTAATAT
GAATGAATCTCAGAGGAAGCTTCAGATGCAGAGCTTGATCTCCATTATCAAGGATGCTAAAAAAT
ATATCTTAGGTCCTAACTTCACCAAACTTGAATGGATGGTGCGTCTTA
Found at i:999724 original size:14 final size:15
Alignment explanation
Indices: 999686--999725 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
999676 CATATTTCAG
*
999686 CTTCACTTTTTTTTC
1 CTTCACTTTTTTTCC
*
999701 CTTCAATTTTTTTCC
1 CTTCACTTTTTTTCC
999716 CTTC-CTTTTT
1 CTTCACTTTTT
999726 CTTTATTAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
14 5 0.23
15 17 0.77
ACGTcount: A:0.07, C:0.28, G:0.00, T:0.65
Consensus pattern (15 bp):
CTTCACTTTTTTTCC
Found at i:1001883 original size:2 final size:2
Alignment explanation
Indices: 1001876--1001964 Score: 144
Period size: 2 Copynumber: 45.0 Consensus size: 2
1001866 AACAACAAAA
* *
1001876 TC TC TC TC AC TC TC TC TC TC -C TC TC TC TC TC TC TC TT TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
*
1001917 TC TT TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1001959 TC TC TC
1 TC TC TC
1001965 ATAATTATTA
Statistics
Matches: 80, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
1 1 0.01
2 79 0.99
ACGTcount: A:0.01, C:0.48, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:1011660 original size:12 final size:12
Alignment explanation
Indices: 1011643--1011668 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1011633 TACATAAATG
1011643 TCTGCATTTCCT
1 TCTGCATTTCCT
1011655 TCTGCATTTCCT
1 TCTGCATTTCCT
1011667 TC
1 TC
1011669 AGACAATTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.35, G:0.08, T:0.50
Consensus pattern (12 bp):
TCTGCATTTCCT
Found at i:1011903 original size:2 final size:2
Alignment explanation
Indices: 1011898--1011943 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
1011888 AGTAAAAAAA
1011898 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1011940 TC TC
1 TC TC
1011944 CAAGTTTTAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1012729 original size:22 final size:22
Alignment explanation
Indices: 1012665--1012742 Score: 86
Period size: 24 Copynumber: 3.5 Consensus size: 22
1012655 TGTAACCAAT
*
1012665 ATCATACCACACATACACTTGG
1 ATCATACCTCACATACACTTGG
*
1012687 ATCAATTACCTCACATTCACTTGG
1 ATC-A-TACCTCACATACACTTGG
* *
1012711 ATCATACCTTACACACACTT-G
1 ATCATACCTCACATACACTTGG
*
1012732 TTCATACCTCA
1 ATCATACCTCA
1012743 TACCATACCA
Statistics
Matches: 47, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
21 10 0.21
22 16 0.34
23 2 0.04
24 19 0.40
ACGTcount: A:0.32, C:0.32, G:0.06, T:0.29
Consensus pattern (22 bp):
ATCATACCTCACATACACTTGG
Found at i:1012886 original size:21 final size:21
Alignment explanation
Indices: 1012860--1012954 Score: 118
Period size: 21 Copynumber: 4.4 Consensus size: 21
1012850 CTTGGATCAC
*
1012860 ACCTCACAGACACATGTTCAT
1 ACCTCACATACACATGTTCAT
*
1012881 ACCTCACGTATACACTTGTTCAT
1 ACCTCAC--ATACACATGTTCAT
1012904 ACCTCACATACACATGTTCAT
1 ACCTCACATACACATGTTCAT
* * *
1012925 ACCTCACTTACACTTGAATCAT
1 ACCTCACATACACATG-TTCAT
1012947 ACCTCACA
1 ACCTCACA
1012955 CAGCTTGAAA
Statistics
Matches: 64, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
21 34 0.53
22 11 0.17
23 19 0.30
ACGTcount: A:0.32, C:0.34, G:0.06, T:0.28
Consensus pattern (21 bp):
ACCTCACATACACATGTTCAT
Found at i:1012909 original size:44 final size:43
Alignment explanation
Indices: 1012849--1012954 Score: 151
Period size: 44 Copynumber: 2.4 Consensus size: 43
1012839 CCTCATATTT
* *
1012849 ACTTGGATCACACCTCACAGACACATGTTCATACCTCACGTATAC
1 ACTTGAATCATACCTCACAGACACATGTTCATACCTCAC-T-TAC
* *
1012894 ACTTG-TTCATACCTCACATACACATGTTCATACCTCACTTAC
1 ACTTGAATCATACCTCACAGACACATGTTCATACCTCACTTAC
1012936 ACTTGAATCATACCTCACA
1 ACTTGAATCATACCTCACA
1012955 CAGCTTGAAA
Statistics
Matches: 56, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
42 8 0.14
43 13 0.23
44 30 0.54
45 5 0.09
ACGTcount: A:0.31, C:0.33, G:0.08, T:0.28
Consensus pattern (43 bp):
ACTTGAATCATACCTCACAGACACATGTTCATACCTCACTTAC
Found at i:1012963 original size:21 final size:21
Alignment explanation
Indices: 1012877--1012968 Score: 73
Period size: 21 Copynumber: 4.2 Consensus size: 21
1012867 AGACACATGT
*
1012877 TCATACCTCACGTATACACTTG-T
1 TCATACCTCAC---TACACTTGAA
* *
1012900 TCATACCTCACATACACATG-T
1 TCATACCTCAC-TACACTTGAA
1012921 TCATACCTCACTTACACTTGAA
1 TCATACCTCAC-TACACTTGAA
1012943 TCATACCTCAC-ACAGCTTGAA
1 TCATACCTCACTACA-CTTGAA
*
1012964 ACATA
1 TCATA
1012969 TTCTAACATA
Statistics
Matches: 62, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
20 3 0.05
21 37 0.60
22 11 0.18
23 11 0.18
ACGTcount: A:0.33, C:0.32, G:0.07, T:0.29
Consensus pattern (21 bp):
TCATACCTCACTACACTTGAA
Found at i:1015285 original size:2 final size:2
Alignment explanation
Indices: 1015278--1015348 Score: 142
Period size: 2 Copynumber: 35.5 Consensus size: 2
1015268 AACTTCAGGG
1015278 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1015320 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1015349 AGGAATATAG
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 69 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:1016486 original size:2 final size:2
Alignment explanation
Indices: 1016479--1016507 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1016469 TCAGGTAGAA
1016479 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1016508 AGACACACAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:1016951 original size:13 final size:14
Alignment explanation
Indices: 1016933--1016961 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
1016923 CAAATAGTTC
1016933 AAATGAGGTC-AGA
1 AAATGAGGTCAAGA
1016946 AAATGAGGTCAAGA
1 AAATGAGGTCAAGA
1016960 AA
1 AA
1016962 TAACGAGGAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.52, C:0.07, G:0.28, T:0.14
Consensus pattern (14 bp):
AAATGAGGTCAAGA
Found at i:1024063 original size:2 final size:2
Alignment explanation
Indices: 1024056--1024116 Score: 59
Period size: 2 Copynumber: 28.5 Consensus size: 2
1024046 TCAGAAACTG
* *
1024056 CT CT CT CT CT CT CT CT CT CT CT CT ACT GCT ACT GCT CT TT CT AT
1 CT CT CT CT CT CT CT CT CT CT CT CT -CT -CT -CT -CT CT CT CT CT
*
1024100 CT CC CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT C
1024117 ATTCATGCTT
Statistics
Matches: 49, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
2 41 0.84
3 8 0.16
ACGTcount: A:0.05, C:0.46, G:0.03, T:0.46
Consensus pattern (2 bp):
CT
Found at i:1027673 original size:13 final size:13
Alignment explanation
Indices: 1027655--1027679 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1027645 GACCATCCAT
1027655 CCATTTTTTTTTC
1 CCATTTTTTTTTC
1027668 CCATTTTTTTTT
1 CCATTTTTTTTT
1027680 TGGGGGGGGG
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:0.08, C:0.20, G:0.00, T:0.72
Consensus pattern (13 bp):
CCATTTTTTTTTC
Found at i:1033625 original size:21 final size:21
Alignment explanation
Indices: 1033565--1033667 Score: 86
Period size: 21 Copynumber: 4.8 Consensus size: 21
1033555 GTGTCTGTCG
*
1033565 GTCTAATTATGGGTGTTCAAAT
1 GTCTAA-TATGGGTGTCCAAAT
*
1033587 GTCTTAA-ATGTGTCTGTCCAAAT
1 GTC-TAATATG-G-GTGTCCAAAT
1033610 GTCTAATGA-GGGTGTCCAAAT
1 GTCTAAT-ATGGGTGTCCAAAT
**
1033631 GTCTAATATGGGTGTTTAAAT
1 GTCTAATATGGGTGTCCAAAT
*
1033652 GTC-ATATATGTGTGTC
1 GTCTA-ATATGGGTGTC
1033668 TGATTTGTTT
Statistics
Matches: 67, Mismatches: 7, Indels: 15
0.75 0.08 0.17
Matches are distributed among these distances:
20 2 0.03
21 41 0.61
22 8 0.12
23 15 0.22
24 1 0.01
ACGTcount: A:0.26, C:0.12, G:0.23, T:0.39
Consensus pattern (21 bp):
GTCTAATATGGGTGTCCAAAT
Found at i:1040093 original size:18 final size:18
Alignment explanation
Indices: 1040038--1040094 Score: 62
Period size: 18 Copynumber: 3.1 Consensus size: 18
1040028 ATTTGATCAC
*
1040038 ATAATACAATATCATAAAAT
1 ATAATACAATATCAT--ATT
1040058 ATAATACAATAT-AGTATT
1 ATAATACAATATCA-TATT
*
1040076 ATATTACAATATCATATT
1 ATAATACAATATCATATT
1040094 A
1 A
1040095 CATAATACAN
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
18 18 0.55
19 2 0.06
20 13 0.39
ACGTcount: A:0.53, C:0.09, G:0.02, T:0.37
Consensus pattern (18 bp):
ATAATACAATATCATATT
Found at i:1041855 original size:6 final size:6
Alignment explanation
Indices: 1041844--1041875 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
1041834 ACCAGGTCCG
1041844 GACGCC GACGCC GACGCC GACGCC GACGCC GA
1 GACGCC GACGCC GACGCC GACGCC GACGCC GA
1041876 GGGTATAGCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.19, C:0.47, G:0.34, T:0.00
Consensus pattern (6 bp):
GACGCC
Found at i:1046216 original size:48 final size:48
Alignment explanation
Indices: 1046160--1046257 Score: 196
Period size: 48 Copynumber: 2.0 Consensus size: 48
1046150 TTCTAATTTC
1046160 TGATAGAGTTCACCCTTTCTCAAAATACTCACTTTCTTTTAAGTTAAA
1 TGATAGAGTTCACCCTTTCTCAAAATACTCACTTTCTTTTAAGTTAAA
1046208 TGATAGAGTTCACCCTTTCTCAAAATACTCACTTTCTTTTAAGTTAAA
1 TGATAGAGTTCACCCTTTCTCAAAATACTCACTTTCTTTTAAGTTAAA
1046256 TG
1 TG
1046258 CCAATACATT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 50 1.00
ACGTcount: A:0.31, C:0.20, G:0.09, T:0.40
Consensus pattern (48 bp):
TGATAGAGTTCACCCTTTCTCAAAATACTCACTTTCTTTTAAGTTAAA
Found at i:1057696 original size:55 final size:55
Alignment explanation
Indices: 1057611--1057723 Score: 208
Period size: 55 Copynumber: 2.1 Consensus size: 55
1057601 AAAGATTTCT
* *
1057611 ATTGGATGGGACAACTACCTGATAATGATTGACCAATGCTGATTAGAATCATATG
1 ATTGGATGGGACAACTACCTGATAACGATTGACCAATACTGATTAGAATCATATG
1057666 ATTGGATGGGACAACTACCTGATAACGATTGACCAATACTGATTAGAATCATATG
1 ATTGGATGGGACAACTACCTGATAACGATTGACCAATACTGATTAGAATCATATG
1057721 ATT
1 ATT
1057724 CTCAGGGTTA
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
55 56 1.00
ACGTcount: A:0.35, C:0.15, G:0.20, T:0.29
Consensus pattern (55 bp):
ATTGGATGGGACAACTACCTGATAACGATTGACCAATACTGATTAGAATCATATG
Found at i:1070319 original size:12 final size:12
Alignment explanation
Indices: 1070302--1070336 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
1070292 CGATTGCACA
1070302 GACAGACGGACG
1 GACAGACGGACG
1070314 GACAGACGGACG
1 GACAGACGGACG
*
1070326 GACGGACGGAC
1 GACAGACGGAC
1070337 AAGGTGATTC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.31, C:0.26, G:0.43, T:0.00
Consensus pattern (12 bp):
GACAGACGGACG
Found at i:1070325 original size:4 final size:4
Alignment explanation
Indices: 1070306--1070336 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
1070296 TGCACAGACA
*
1070306 GACG GACG GACA GACG GACG GACG GACG GAC
1 GACG GACG GACG GACG GACG GACG GACG GAC
1070337 AAGGTGATTC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.29, C:0.26, G:0.45, T:0.00
Consensus pattern (4 bp):
GACG
Found at i:1073627 original size:4 final size:4
Alignment explanation
Indices: 1073618--1073655 Score: 60
Period size: 4 Copynumber: 9.8 Consensus size: 4
1073608 AAAGTTTACA
*
1073618 GACG GACG GACA GACG GACG GACG GACG GAC- GACG GAC
1 GACG GACG GACG GACG GACG GACG GACG GACG GACG GAC
1073656 AACGGGTGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
3 3 0.10
4 28 0.90
ACGTcount: A:0.29, C:0.26, G:0.45, T:0.00
Consensus pattern (4 bp):
GACG
Found at i:1078400 original size:167 final size:166
Alignment explanation
Indices: 1077704--1078661 Score: 1363
Period size: 167 Copynumber: 5.8 Consensus size: 166
1077694 GTGAATATGC
* * * * * * * *
1077704 AAAATAAGCAAAGTCGACATTTAACAGAAAGCTGGCATCCGATTGGTACAGAAATATATCCCACA
1 AAAATAAACAAAGTCGTCATTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCACG
* * * * *
1077769 ATATGGCATGCCTAAACAAAAAGTGTGTTAAAATTTCAAGCATCTGCGATAAATAGCTGCTGAGA
66 ATATGGCATGCCTATACAAATACTGTGTAAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAGA
*
1077834 AATCTTTGACGAAAATTTGTTTGAAAATTTTGGCT-
131 AATCTTTGACGAAAATTTGTTTGAAAATTTTTGCTA
*
1077869 AAAATAAACAAAGTCGTCATTTAACAGGAAGTTGACGTCTGATTGGTA-AAAAATATATCCCACG
1 AAAATAAACAAAGTCGTCATTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCACG
*
1077933 ATATGGCATGCCT-TAACAAACACTGTGTAAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAG
66 ATATGGCATGCCTAT-ACAAATACTGTGTAAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAG
*
1077997 AAATCTTTGACGGAAATTTGTTTGAAAATTTTTGCTA
130 AAATCTTTGACGAAAATTTGTTTGAAAATTTTTGCTA
* * * *
1078034 AAAATAAACAAAGTAC-TCATTAAACAGGATGTTGACATCCGATTGGTACAAAAATACATCCCAC
1 AAAATAAACAAAGT-CGTCATTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCAC
* * * * *
1078098 GATATAGCATGCCTATACAAATAATGTGTAAAAATTTCAAGCATCTG-AAAAAACAGTTGCTGAG
65 GATATGGCATGCCTATACAAATACTGTGTAAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAG
* *
1078162 AATTCTTTGACGGAAATTTGTTTGAAAATTTTTGCTA
130 AAATCTTTGACGAAAATTTGTTTGAAAATTTTTGCTA
* * * *
1078199 AAAATAAGCAAAGTCGACATTTAACAGGAAGTTGACGTCTGATTGGTACAAAAATATATCCCACC
1 AAAATAAACAAAGTCGTCATTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCACG
* * *
1078264 ATATGGCATGCCTATACAAATACTGTGTCAAAATTTCAAGCATCTGCGTTAAACAGTTGCTGAGA
66 ATATGGCATGCCTATACAAATACTGTGTAAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAGA
* *
1078329 ATTCTTTGACAAAAAATTTGTTTGAAAATTTTTGCTA
131 AATCTTTGAC-GAAAATTTGTTTGAAAATTTTTGCTA
* * * *
1078366 AAAATAAACAAAGTCGTCATTTAACAGGAAGTTGATGTCTGATTGGTACAAAAATCTATCCCACA
1 AAAATAAACAAAGTCGTCATTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCACG
* * *
1078431 ATATGGCATGCCTAAACAAATATTGTGTAAAAATTTCAAGCATCTGCGATAAATAGCTGCTGAGA
66 ATATGGCATGCCTATACAAATACTGTGTAAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAGA
* *
1078496 AATCTTTGACGAAAATTTGTTTGAAAATTTTGGTTAA
131 AATCTTTGACGAAAATTTGTTTGAAAATTTTTGCT-A
** *
1078533 AAAATAAGTAAAGTCGTCATTTAACAGGAAGTTGACGTCCGATTGGTTCAAAAATATATCCCACG
1 AAAATAAACAAAGTCGTCATTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCACG
* *
1078598 ATATGGCATGCCT-TAACAAACACTATGTAAAAATTTCAAGCATCTGCGAT-AATAGTTGCTGAG
66 ATATGGCATGCCTAT-ACAAATACTGTGTAAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAG
1078661 A
130 A
1078662 TAAATGCACC
Statistics
Matches: 712, Mismatches: 71, Indels: 19
0.89 0.09 0.02
Matches are distributed among these distances:
164 107 0.15
165 231 0.32
166 117 0.16
167 257 0.36
ACGTcount: A:0.39, C:0.15, G:0.17, T:0.29
Consensus pattern (166 bp):
AAAATAAACAAAGTCGTCATTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCACG
ATATGGCATGCCTATACAAATACTGTGTAAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAGA
AATCTTTGACGAAAATTTGTTTGAAAATTTTTGCTA
Found at i:1085713 original size:21 final size:20
Alignment explanation
Indices: 1085684--1085737 Score: 54
Period size: 20 Copynumber: 2.5 Consensus size: 20
1085674 ATCATGTCGA
1085684 TTTTCTTGTTTCTTGTTTTGTG
1 TTTT-TTGTTTCTT-TTTTGTG
* * *
1085706 TTTTTTGTTTGTTTTTTTTT
1 TTTTTTGTTTCTTTTTTGTG
1085726 TTTTTTGCTTTC
1 TTTTTTG-TTTC
1085738 GAAGTTTTCG
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 12 0.44
21 11 0.41
22 4 0.15
ACGTcount: A:0.00, C:0.07, G:0.13, T:0.80
Consensus pattern (20 bp):
TTTTTTGTTTCTTTTTTGTG
Found at i:1086965 original size:20 final size:19
Alignment explanation
Indices: 1086935--1086976 Score: 66
Period size: 20 Copynumber: 2.2 Consensus size: 19
1086925 TCATATTTAT
1086935 AAATTAAATAAATAAAATA
1 AAATTAAATAAATAAAATA
*
1086954 AAATTAAAATAAATAAATTA
1 AAATT-AAATAAATAAAATA
1086974 AAA
1 AAA
1086977 AGGAAGATGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (19 bp):
AAATTAAATAAATAAAATA
Found at i:1086967 original size:15 final size:15
Alignment explanation
Indices: 1086944--1086976 Score: 50
Period size: 14 Copynumber: 2.2 Consensus size: 15
1086934 TAAATTAAAT
1086944 AAATAAAATAAAATTA
1 AAATAAAAT-AAATTA
1086960 AAAT-AAATAAATTA
1 AAATAAAATAAATTA
1086974 AAA
1 AAA
1086977 AGGAAGATGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 9 0.53
15 4 0.24
16 4 0.24
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (15 bp):
AAATAAAATAAATTA
Found at i:1087221 original size:4 final size:4
Alignment explanation
Indices: 1087205--1087242 Score: 51
Period size: 4 Copynumber: 9.8 Consensus size: 4
1087195 TTAATGATTT
* *
1087205 TTTG TTTG CTTG TTTG TTTG TTTG TTT- TTTT TTTG TTT
1 TTTG TTTG TTTG TTTG TTTG TTTG TTTG TTTG TTTG TTT
1087243 TTTTTTTTGG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
3 3 0.10
4 27 0.90
ACGTcount: A:0.00, C:0.03, G:0.18, T:0.79
Consensus pattern (4 bp):
TTTG
Found at i:1087241 original size:11 final size:11
Alignment explanation
Indices: 1087214--1087249 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
1087204 TTTTGTTTGC
*
1087214 TTGTTTGTTTGT
1 TTGTTT-TTTTT
1087226 TTGTTTTTTTT
1 TTGTTTTTTTT
1087237 TTGTTTTTTTT
1 TTGTTTTTTTT
1087248 TT
1 TT
1087250 TGGGGGGGGG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 17 0.74
12 6 0.26
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (11 bp):
TTGTTTTTTTT
Found at i:1087244 original size:12 final size:12
Alignment explanation
Indices: 1087214--1087251 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
1087204 TTTTGTTTGC
* *
1087214 TTGTTTGTTTGT
1 TTGTTTTTTTTT
1087226 TTG-TTTTTTTT
1 TTGTTTTTTTTT
1087237 TTGTTTTTTTTT
1 TTGTTTTTTTTT
1087249 TTG
1 TTG
1087252 GGGGGGGGTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
11 9 0.39
12 14 0.61
ACGTcount: A:0.00, C:0.00, G:0.16, T:0.84
Consensus pattern (12 bp):
TTGTTTTTTTTT
Found at i:1102349 original size:42 final size:42
Alignment explanation
Indices: 1102272--1102367 Score: 97
Period size: 42 Copynumber: 2.3 Consensus size: 42
1102262 AAAAATGTCT
*
1102272 TTTTCGCGAATAAACACGAAACTTTCCCGAAATAACG-CATAAC
1 TTTT-GCGAATAAACACGAAACTTTCCAGAAATAACGTCAT-AC
* * * *
1102315 TTTTGCGAATAAACGCTAAACTTTCGCAG-TATAACGTGATAC
1 TTTTGCGAATAAACACGAAACTTTC-CAGAAATAACGTCATAC
*
1102357 TTTCGCGAATA
1 TTTTGCGAATA
1102368 TTTTGGAGAA
Statistics
Matches: 45, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
42 37 0.82
43 8 0.18
ACGTcount: A:0.35, C:0.22, G:0.15, T:0.28
Consensus pattern (42 bp):
TTTTGCGAATAAACACGAAACTTTCCAGAAATAACGTCATAC
Found at i:1109557 original size:11 final size:11
Alignment explanation
Indices: 1109541--1109566 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1109531 TCTCTTCAAA
1109541 CATTCAGATAG
1 CATTCAGATAG
1109552 CATTCAGATAG
1 CATTCAGATAG
1109563 CATT
1 CATT
1109567 TCAGGTGTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.35, C:0.19, G:0.15, T:0.31
Consensus pattern (11 bp):
CATTCAGATAG
Done.