Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr8
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 78745976
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 2640508 characters in sequence are not A, C, G, or T
File 15 of 235
Found at i:4226671 original size:39 final size:35
Alignment explanation
Indices: 4226552--4226681 Score: 133
Period size: 39 Copynumber: 3.6 Consensus size: 35
4226542 CTCAGTTGTT
*
4226552 GGTTATGGCTTTTGCTAATACCACCTTGGATTTT----
1 GGTTATGGCTTTTGCTGATACCA---TGGATTTTGAAA
* *
4226586 GGTTATGGCTTTTGCTAATACCATGGATTTTGAAC
1 GGTTATGGCTTTTGCTGATACCATGGATTTTGAAA
*
4226621 GGTTATGGCTTTTGCTGATACCGGATGGATCGTTTTAAA
1 GGTTATGGCTTTTGCTGATACC--ATGGAT--TTTGAAA
4226660 GGTTATGGCTTTTGCTGATACC
1 GGTTATGGCTTTTGCTGATACC
4226682 TCGGATCCTT
Statistics
Matches: 85, Mismatches: 3, Indels: 11
0.86 0.03 0.11
Matches are distributed among these distances:
31 8 0.09
34 23 0.27
35 21 0.25
37 6 0.07
39 27 0.32
ACGTcount: A:0.19, C:0.15, G:0.25, T:0.41
Consensus pattern (35 bp):
GGTTATGGCTTTTGCTGATACCATGGATTTTGAAA
Found at i:4226814 original size:54 final size:54
Alignment explanation
Indices: 4226737--4226895 Score: 239
Period size: 54 Copynumber: 2.9 Consensus size: 54
4226727 CCAGTCAAAA
4226737 CTTTTGTTGTATGGCTTTTGCTGACACAACTAATGGCTGCACTGCATGCCTTTT
1 CTTTTGTTGTATGGCTTTTGCTGACACAACTAATGGCTGCACTGCATGCCTTTT
*
4226791 CTTTTGTTGTATGGCTTTTGCTGACACAACTATTGGCTGCACTGCATGCCTTTT
1 CTTTTGTTGTATGGCTTTTGCTGACACAACTAATGGCTGCACTGCATGCCTTTT
* * * * *
4226845 CTTCTATTGGTATGGCTTTTGCTGATC-CAATTACTGGCTGCATTGCATGCC
1 CTTTTGTT-GTATGGCTTTTGCTGA-CACAACTAATGGCTGCACTGCATGCC
4226896 ATATATTGCT
Statistics
Matches: 97, Mismatches: 6, Indels: 3
0.92 0.06 0.03
Matches are distributed among these distances:
54 59 0.61
55 37 0.38
56 1 0.01
ACGTcount: A:0.16, C:0.23, G:0.21, T:0.41
Consensus pattern (54 bp):
CTTTTGTTGTATGGCTTTTGCTGACACAACTAATGGCTGCACTGCATGCCTTTT
Found at i:4230889 original size:324 final size:323
Alignment explanation
Indices: 4230145--4230913 Score: 1405
Period size: 323 Copynumber: 2.4 Consensus size: 323
4230135 NNNNNNNNNN
*
4230145 TATCTTTCATTTTCTCTGAATATTCAGCGGCTTTACCAACAAATTTATTCAGGATTAGAGTAGCA
1 TATCTTTCATTTTCTCTGAATATTCAGCGGCTTTACCAACAAATTTATTCAGGATGAGAGTAGCA
4230210 TACTATGAAAGGCAATAATAAGGCGAATTTCTTATACTTAAAACAGGTAATATACACCATCTAAC
66 TACTATGAAAGGCAATAATAAGGCGAATTTCTTATACTTAAAACAGGTAATATACACCATCTAAC
4230275 CTTCTTTACGGAGTTGGTTGACACCATACACTCTAAAAAGAGTCGCTAACTTTACCGTAAAGTTT
131 CTTCTTTACGGAGTTGGTTGACACCATACACTCTAAAAAGAGTCGCTAACTTTACCGTAAAGTTT
*
4230340 TCATCAATGCTCGTTCTGATATAGCTTTTTTCGAACCAATACCTCACAATACAAATATTCTTCCC
196 TCATCAATGCTCGTTCTGATACAGCTTTTTTCGAACCAATACCTCACAATACAAATATTCTTCCC
* * *
4230405 GATTTGGGACGGCAGTAAACAATTCTTAAATAATTGGTTCAAAAAAATCGACGACACCAAATA
261 GATTTGGGACGGCAGTAAACAATCCTAAAATAATTGATTCAAAAAAATCGACGACACCAAATA
4230468 TATCTTTCATTTTCTCTGAATATTCAGCGGCTTTACCAACAAATTTATTCAGGATGAGAGTAGCA
1 TATCTTTCATTTTCTCTGAATATTCAGCGGCTTTACCAACAAATTTATTCAGGATGAGAGTAGCA
4230533 TACTATGAAAGGCAATAATAAGGCGAATTTCTTATACTTAAAACAGGTAATATACACCATCTAAC
66 TACTATGAAAGGCAATAATAAGGCGAATTTCTTATACTTAAAACAGGTAATATACACCATCTAAC
4230598 CTTCTTTACGGAGTTGGTTGACACCATACACTCTAAAAAGAGTCGCTAACTTTACCGTAAAGTTT
131 CTTCTTTACGGAGTTGGTTGACACCATACACTCTAAAAAGAGTCGCTAACTTTACCGTAAAGTTT
*
4230663 TCATCAATGCTCGTTCTGATACAGCTTTTTTCCGAACCAATACCTCACAATACAAATATTCTTGC
196 TCATCAATGCTCGTTCTGATACAGCTTTTTT-CGAACCAATACCTCACAATACAAATATTCTTCC
* *
4230728 CGATTTGGGACGGCAGTAAACAATCCTAAAATAATTGATTCATAAAAATCGTCGACA-CAAAGTA
260 CGATTTGGGACGGCAGTAAACAATCCTAAAATAATTGATTCAAAAAAATCGACGACACCAAA-TA
*
4230792 TATCTTTCATTTTCTCTGAATATTCAGCGGCTTTGCCAACAAATTTATTCAGGATGAGAGTAGCA
1 TATCTTTCATTTTCTCTGAATATTCAGCGGCTTTACCAACAAATTTATTCAGGATGAGAGTAGCA
* * *
4230857 GACTATGAAATGCAATAATAAGGCGAATTTCTTATGCTTAAAACAGGTAATATACAC
66 TACTATGAAAGGCAATAATAAGGCGAATTTCTTATACTTAAAACAGGTAATATACAC
4230914 TGTTGAAGCA
Statistics
Matches: 432, Mismatches: 12, Indels: 3
0.97 0.03 0.01
Matches are distributed among these distances:
323 228 0.53
324 204 0.47
ACGTcount: A:0.35, C:0.20, G:0.14, T:0.31
Consensus pattern (323 bp):
TATCTTTCATTTTCTCTGAATATTCAGCGGCTTTACCAACAAATTTATTCAGGATGAGAGTAGCA
TACTATGAAAGGCAATAATAAGGCGAATTTCTTATACTTAAAACAGGTAATATACACCATCTAAC
CTTCTTTACGGAGTTGGTTGACACCATACACTCTAAAAAGAGTCGCTAACTTTACCGTAAAGTTT
TCATCAATGCTCGTTCTGATACAGCTTTTTTCGAACCAATACCTCACAATACAAATATTCTTCCC
GATTTGGGACGGCAGTAAACAATCCTAAAATAATTGATTCAAAAAAATCGACGACACCAAATA
Found at i:4235840 original size:51 final size:51
Alignment explanation
Indices: 4235764--4236093 Score: 651
Period size: 51 Copynumber: 6.5 Consensus size: 51
4235754 NNNNNNNNNN
4235764 CTTCTCTCGTGGATCTTCATCTTCTTCTTCAGCATCATGGTTGCTCGTCTA
1 CTTCTCTCGTGGATCTTCATCTTCTTCTTCAGCATCATGGTTGCTCGTCTA
4235815 CTTCTCTCGTGGATCTTCATCTTCTTCTTCAGCATCATGGTTGCTCGTCTA
1 CTTCTCTCGTGGATCTTCATCTTCTTCTTCAGCATCATGGTTGCTCGTCTA
4235866 CTTCTCTCGTGGATCTTCATCTTCTTCTTCAGCATCATGGTTGCTCGTCTA
1 CTTCTCTCGTGGATCTTCATCTTCTTCTTCAGCATCATGGTTGCTCGTCTA
4235917 CTTCTCTCGTGGATCTTCATCTTCTTCTTCAGCATCATGGTTGCTCGTCTA
1 CTTCTCTCGTGGATCTTCATCTTCTTCTTCAGCATCATGGTTGCTCGTCTA
4235968 CTTCTCTCGTGGATCTTCATCTTCTTCTTCAGCATCATGGTTGCTCGTCTA
1 CTTCTCTCGTGGATCTTCATCTTCTTCTTCAGCATCATGGTTGCTCGTCTA
4236019 CTTCTCTCGTGGATCTTCATCTTCTTCTTCAGCATCATGGTTGCTCGTCTA
1 CTTCTCTCGTGGATCTTCATCTTCTTCTTCAGCATCATGGTTGCTCGTCTA
*
4236070 CTTCTCCCGTGGATCTTCATCTTC
1 CTTCTCTCGTGGATCTTCATCTTC
4236094 CTAGTGCAGG
Statistics
Matches: 278, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 278 1.00
ACGTcount: A:0.12, C:0.30, G:0.15, T:0.43
Consensus pattern (51 bp):
CTTCTCTCGTGGATCTTCATCTTCTTCTTCAGCATCATGGTTGCTCGTCTA
Found at i:4238937 original size:4 final size:4
Alignment explanation
Indices: 4238930--4239215 Score: 354
Period size: 4 Copynumber: 73.5 Consensus size: 4
4238920 CTCACACTCC
* *
4238930 CATA CATA CATA CATA CATG CATA CATA TATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * *
4238978 CATA C--A CACA CATA CACA CATA CATA CACA CATA CATA CATA C--A
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * * * * *
4239022 CACA CATA CACA CATA CATA TACA CATA CATA C--A CACA CATA CACA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* *
4239068 CATA C--A CATA CATA CATA CATA CATA CACA CATA CACA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * * *
4239114 CATA CATA CATA CACA CATA CATA TATA CATA TATA CATA TATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
*
4239162 CATA GATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
4239210 CATA CA
1 CATA CA
4239216 ACTCCTCAAA
Statistics
Matches: 241, Mismatches: 33, Indels: 16
0.83 0.11 0.06
Matches are distributed among these distances:
2 8 0.03
4 233 0.97
ACGTcount: A:0.50, C:0.28, G:0.01, T:0.22
Consensus pattern (4 bp):
CATA
Found at i:4241027 original size:42 final size:44
Alignment explanation
Indices: 4240913--4241040 Score: 124
Period size: 44 Copynumber: 3.0 Consensus size: 44
4240903 TATGTGTTAT
* * * *
4240913 CGTGTAAGACCACGTCT-AGGACGTTGGCATTGACT-TATGATTTA
1 CGTGTAAGACCATGTCTGA-GATGTTGGCATCGA-TATTTGATTTA
4240957 CGTGTAAGACCATGTCTGAGATGTTGGCATCG-TATTTGATTT-
1 CGTGTAAGACCATGTCTGAGATGTTGGCATCGATATTTGATTTA
* *
4240999 CGTGTAAGACCCTGTCTGGGGCA-G-TGGCATCGATATTTGATT
1 CGTGTAAGACCATGTCT-GAG-ATGTTGGCATCGATATTTGATT
4241041 ACAATTAGAC
Statistics
Matches: 73, Mismatches: 6, Indels: 11
0.81 0.07 0.12
Matches are distributed among these distances:
42 25 0.34
43 19 0.26
44 28 0.38
45 1 0.01
ACGTcount: A:0.22, C:0.17, G:0.27, T:0.34
Consensus pattern (44 bp):
CGTGTAAGACCATGTCTGAGATGTTGGCATCGATATTTGATTTA
Found at i:4241069 original size:42 final size:43
Alignment explanation
Indices: 4240913--4241070 Score: 148
Period size: 42 Copynumber: 3.7 Consensus size: 43
4240903 TATGTGTTAT
* * *
4240913 CGTGTAAGACCACGTCTAGGACGTTGGCATTGACT-TATGATTTA
1 CGTGTAAGACCACGTCTGGGACGTTGGCATCGA-TATTTGA-TTA
* * * *
4240957 CGTGTAAGACCATGTCTGAGATGTTGGCATCG-TATTTGATTT
1 CGTGTAAGACCACGTCTGGGACGTTGGCATCGATATTTGATTA
*
4240999 CGTGTAAGACC-CTGTCTGGGGCAG-TGGCATCGATATTTGATTA
1 CGTGTAAGACCAC-GTCTGGGAC-GTTGGCATCGATATTTGATTA
*
4241042 CAAT-T-AGACCACGTCTGGGACGTTGGCAT
1 C-GTGTAAGACCACGTCTGGGACGTTGGCAT
4241071 TGTATGAGGT
Statistics
Matches: 93, Mismatches: 14, Indels: 16
0.76 0.11 0.13
Matches are distributed among these distances:
41 1 0.01
42 47 0.51
43 17 0.18
44 28 0.30
ACGTcount: A:0.23, C:0.18, G:0.27, T:0.32
Consensus pattern (43 bp):
CGTGTAAGACCACGTCTGGGACGTTGGCATCGATATTTGATTA
Found at i:4242319 original size:1 final size:1
Alignment explanation
Indices: 4242313--4242340 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
4242303 TTGTATGAAT
4242313 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
4242341 CGAACATTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:4262007 original size:47 final size:48
Alignment explanation
Indices: 4261896--4262032 Score: 172
Period size: 47 Copynumber: 2.9 Consensus size: 48
4261886 ATGGGTAAAG
* *
4261896 TGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCACATCTCAA
1 TGCCGATGCTATGTCCCAGACATGGTCTTACACTGGCTCTCATCTCAA
** * *
4261944 -GTAGATG-TCATGTCCCAGACAT-GTCTTACACTAGCTCTCGTCTCAA
1 TGCCGATGCT-ATGTCCCAGACATGGTCTTACACTGGCTCTCATCTCAA
* *
4261990 TGCCGATGCTATATCCCAGACATGGTCTTACAATGGCTCTCAT
1 TGCCGATGCTATGTCCCAGACATGGTCTTACACTGGCTCTCAT
4262033 AATGTAGCCG
Statistics
Matches: 73, Mismatches: 12, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
46 21 0.29
47 35 0.48
48 17 0.23
ACGTcount: A:0.23, C:0.30, G:0.18, T:0.28
Consensus pattern (48 bp):
TGCCGATGCTATGTCCCAGACATGGTCTTACACTGGCTCTCATCTCAA
Found at i:4262057 original size:94 final size:94
Alignment explanation
Indices: 4261896--4262073 Score: 241
Period size: 94 Copynumber: 1.9 Consensus size: 94
4261886 ATGGGTAAAG
* * * *
4261896 TGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCACATCTCAAGTAGATGTCATGTCCCA
1 TGCCGATGCCATATCCCAGACATGGTCTTACAATGGCTCACATATCAAGCAGATGTCATGTCCCA
4261961 GACATGTCTTACACTAGCTCTCGTCTCAA
66 GACATGTCTTACACTAGCTCTCGTCTCAA
* * ** * *
4261990 TGCCGATGCTATATCCCAGACATGGTCTTACAATGGCTCTCATAATGTAGCCGAT-TCATGTCTC
1 TGCCGATGCCATATCCCAGACATGGTCTTACAATGGCTCACAT-ATCAAGCAGATGTCATGTCCC
*
4262054 AGACATGTCTTATACTAGCT
65 AGACATGTCTTACACTAGCT
4262074 TACACACAAA
Statistics
Matches: 72, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
94 66 0.92
95 6 0.08
ACGTcount: A:0.24, C:0.28, G:0.18, T:0.30
Consensus pattern (94 bp):
TGCCGATGCCATATCCCAGACATGGTCTTACAATGGCTCACATATCAAGCAGATGTCATGTCCCA
GACATGTCTTACACTAGCTCTCGTCTCAA
Found at i:4267316 original size:286 final size:286
Alignment explanation
Indices: 4266797--4267357 Score: 883
Period size: 286 Copynumber: 2.0 Consensus size: 286
4266787 ACACGGCCTA
* *
4266797 GACACATGGGCGTGTCTAAAGTCGTGTAAGGCACATGGCCTGTTCACACGAGCGTGTGACCTGTA
1 GACACACGGGCGTGTCTAAAGTCGTGTAAGGCACACGGCCTGTTCACACGAGCGTGTGACCTGTA
* * ** *
4266862 CAACTTTGAAAAATGTTTAAGTTTTGAAAAATTTTGTATGAGCTCAGATTAGTCCCGGCCCCTTT
66 CAACTTTGAAAAATGTTTAAGCTTTGAAAAATTTTGTATGAACTCAGATTAGTCCCAACCCATTT
* *
4266927 TTAATGCATGTTTAAGGTCTTAATGACCTATTTTACGGACTCTATGGTAGTGTTTGAATATGATT
131 TTAATACATGTTTAAGGTCTTAATGACCTATTTTACGGACTCTATGGTAATGTTTGAATATGATT
* * *
4266992 GTTGATGAAGTATATGAATTGTTCGTAAAATATTCTGATTTGTCTGGTAACGCCTTTAACCCTAG
196 GCTCATGAAGTATATGAATTGTTCGTAAAATATTCTGATTTGTCTGGTAACACCTTTAACCCTAG
4267057 TCCGATGACAGATACGGGTTTAGGGT
261 TCCGATGACAGATACGGGTTTAGGGT
* * *
4267083 GACACACGGGCGTGTCTAAAGTCGTGTGAGGCACACGGCCTGTTTACACGGGTC-TGTGACCTGT
1 GACACACGGGCGTGTCTAAAGTCGTGTAAGGCACACGGCCTGTTCACACGAG-CGTGTGACCTGT
* * * *
4267147 ACAACTTTGAAAAGTGTTTAAGCTTTGAAAAATTTTGTATGAACAT-GGTTTAGTCCTAACCCAT
65 ACAACTTTGAAAAATGTTTAAGCTTTGAAAAATTTTGTATGAAC-TCAGATTAGTCCCAACCCAT
*
4267211 TTTTAATACATGTTTAAGGTCTTAATGACCTATTTTAGGGACTCTATGGTAATGTTTGAATATGA
129 TTTTAATACATGTTTAAGGTCTTAATGACCTATTTTACGGACTCTATGGTAATGTTTGAATATGA
*
4267276 TTGCTCATGAAGTATATGAATTGTTCGTAAAATGTTCTGATTTGTCTGGTAACACCTTTAACCCT
194 TTGCTCATGAAGTATATGAATTGTTCGTAAAATATTCTGATTTGTCTGGTAACACCTTTAACCCT
* *
4267341 AGTCCGGTGATAGATAC
259 AGTCCGATGACAGATAC
4267358 TAGTTAGGGG
Statistics
Matches: 250, Mismatches: 23, Indels: 4
0.90 0.08 0.01
Matches are distributed among these distances:
286 248 0.99
287 2 0.01
ACGTcount: A:0.27, C:0.16, G:0.22, T:0.35
Consensus pattern (286 bp):
GACACACGGGCGTGTCTAAAGTCGTGTAAGGCACACGGCCTGTTCACACGAGCGTGTGACCTGTA
CAACTTTGAAAAATGTTTAAGCTTTGAAAAATTTTGTATGAACTCAGATTAGTCCCAACCCATTT
TTAATACATGTTTAAGGTCTTAATGACCTATTTTACGGACTCTATGGTAATGTTTGAATATGATT
GCTCATGAAGTATATGAATTGTTCGTAAAATATTCTGATTTGTCTGGTAACACCTTTAACCCTAG
TCCGATGACAGATACGGGTTTAGGGT
Found at i:4275353 original size:60 final size:60
Alignment explanation
Indices: 4275289--4275402 Score: 158
Period size: 60 Copynumber: 1.9 Consensus size: 60
4275279 ATTTAATACA
* *
4275289 TGAGTTTGGCTTCAATATTCAAATTGGTATTTAAGTTTTCTTTTA-TTCCAATTAGGCACC
1 TGAGTTTAGCTTCAATATTCAAATTGGTATTTAAGTTTT-TTCTAGTTCCAATTAGGCACC
** * *
4275349 TGAGTTTAGCTTTGATGTTCAATTTGGTATTTAAGTTTTTTCTAGTTCCAATTA
1 TGAGTTTAGCTTCAATATTCAAATTGGTATTTAAGTTTTTTCTAGTTCCAATTA
4275403 AAGTACTTAT
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
59 4 0.09
60 43 0.91
ACGTcount: A:0.24, C:0.12, G:0.16, T:0.48
Consensus pattern (60 bp):
TGAGTTTAGCTTCAATATTCAAATTGGTATTTAAGTTTTTTCTAGTTCCAATTAGGCACC
Found at i:4275624 original size:31 final size:32
Alignment explanation
Indices: 4275588--4275663 Score: 84
Period size: 31 Copynumber: 2.4 Consensus size: 32
4275578 ATTAAAAAAA
*
4275588 CTCAAATACTAAATTAAATATTGAAAC-AAAT
1 CTCAAATACTAAATTAAATATCGAAACTAAAT
** * * *
4275619 CTCAAATTTTAATTTGAGTATCGAAACTAAAT
1 CTCAAATACTAAATTAAATATCGAAACTAAAT
4275651 -TCAAATACTAAAT
1 CTCAAATACTAAAT
4275664 AGTATATTAA
Statistics
Matches: 35, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
31 31 0.89
32 4 0.11
ACGTcount: A:0.49, C:0.13, G:0.05, T:0.33
Consensus pattern (32 bp):
CTCAAATACTAAATTAAATATCGAAACTAAAT
Found at i:4277239 original size:22 final size:22
Alignment explanation
Indices: 4277214--4277256 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
4277204 TCTCCCTATT
4277214 TTGCTACCATTTTACTATTATG
1 TTGCTACCATTTTACTATTATG
* *
4277236 TTGCTACTATTTTATTATTAT
1 TTGCTACCATTTTACTATTAT
4277257 TGTTTGGATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.23, C:0.14, G:0.07, T:0.56
Consensus pattern (22 bp):
TTGCTACCATTTTACTATTATG
Found at i:4277489 original size:11 final size:11
Alignment explanation
Indices: 4277473--4277503 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
4277463 TATATATATT
4277473 TAAAAATTATA
1 TAAAAATTATA
*
4277484 TAAAAATAATA
1 TAAAAATTATA
4277495 TAAAAATTA
1 TAAAAATTA
4277504 ATACAGGCTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (11 bp):
TAAAAATTATA
Found at i:4288987 original size:17 final size:17
Alignment explanation
Indices: 4288965--4288998 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
4288955 ATCCACTAAT
*
4288965 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
4288982 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
4288999 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:4293627 original size:17 final size:17
Alignment explanation
Indices: 4293605--4293638 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
4293595 ATCCACTAAT
*
4293605 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
4293622 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
4293639 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:4298644 original size:50 final size:51
Alignment explanation
Indices: 4298578--4298704 Score: 193
Period size: 50 Copynumber: 2.5 Consensus size: 51
4298568 CCATGACAAC
4298578 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAAT-GA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGGA
** *
4298628 AAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGGACAAATGGC
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGGA
* * *
4298679 AAGTAAAAAGTGGTAGCTTCGGCTAC
1 AAGTGATAAGTGATAGCTTCGGCTAC
4298705 CTGATCAATG
Statistics
Matches: 68, Mismatches: 8, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
50 46 0.68
51 22 0.32
ACGTcount: A:0.35, C:0.16, G:0.23, T:0.26
Consensus pattern (51 bp):
AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGGA
Found at i:4298722 original size:31 final size:31
Alignment explanation
Indices: 4298684--4299486 Score: 1606
Period size: 31 Copynumber: 25.9 Consensus size: 31
4298674 ATGGCAAGTA
4298684 AAAAGTGGTAGCTTCGGCTACCTGATCAATG
1 AAAAGTGGTAGCTTCGGCTACCTGATCAATG
4298715 AAAAGTGGTAGCTTCGGCTACCTGATCAATG
1 AAAAGTGGTAGCTTCGGCTACCTGATCAATG
4298746 AAAAGTGGTAGCTTCGGCTACCTGATCAATG
1 AAAAGTGGTAGCTTCGGCTACCTGATCAATG
4298777 AAAAGTGGTAGCTTCGGCTACCTGATCAATG
1 AAAAGTGGTAGCTTCGGCTACCTGATCAATG
4298808 AAAAGTGGTAGCTTCGGCTACCTGATCAATG
1 AAAAGTGGTAGCTTCGGCTACCTGATCAATG
4298839 AAAAGTGGTAGCTTCGGCTACCTGATCAATG
1 AAAAGTGGTAGCTTCGGCTACCTGATCAATG
4298870 AAAAGTGGTAGCTTCGGCTACCTGATCAATG
1 AAAAGTGGTAGCTTCGGCTACCTGATCAATG
4298901 AAAAGTGGTAGCTTCGGCTACCTGATCAATG
1 AAAAGTGGTAGCTTCGGCTACCTGATCAATG
4298932 AAAAGTGGTAGCTTCGGCTACCTGATCAATG
1 AAAAGTGGTAGCTTCGGCTACCTGATCAATG
4298963 AAAAGTGGTAGCTTCGGCTACCTGATCAATG
1 AAAAGTGGTAGCTTCGGCTACCTGATCAATG
4298994 AAAAGTGGTAGCTTCGGCTACCTGATCAATG
1 AAAAGTGGTAGCTTCGGCTACCTGATCAATG
4299025 AAAAGTGGTAGCTTCGGCTACCTGATCAATG
1 AAAAGTGGTAGCTTCGGCTACCTGATCAATG
4299056 AAAAGTGGTAGCTTCGGCTACCTGATCAATG
1 AAAAGTGGTAGCTTCGGCTACCTGATCAATG
4299087 AAAAGTGGTAGCTTCGGCTACCTGATCAATG
1 AAAAGTGGTAGCTTCGGCTACCTGATCAATG
4299118 AAAAGTGGTAGCTTCGGCTACCTGATCAATG
1 AAAAGTGGTAGCTTCGGCTACCTGATCAATG
4299149 AAAAGTGGTAGCTTCGGCTACCTGATCAATG
1 AAAAGTGGTAGCTTCGGCTACCTGATCAATG
4299180 AAAAGTGGTAGCTTCGGCTACCTGATCAATG
1 AAAAGTGGTAGCTTCGGCTACCTGATCAATG
4299211 AAAAGTGGTAGCTTCGGCTACCTGATCAATG
1 AAAAGTGGTAGCTTCGGCTACCTGATCAATG
4299242 AAAAGTGGTAGCTTCGGCTACCTGATCAATG
1 AAAAGTGGTAGCTTCGGCTACCTGATCAATG
4299273 AAAAGTGGTAGCTTCGGCTACCTGATCAATG
1 AAAAGTGGTAGCTTCGGCTACCTGATCAATG
4299304 AAAAGTGGTAGCTTCGGCTACCTGATCAATG
1 AAAAGTGGTAGCTTCGGCTACCTGATCAATG
4299335 AAAAGTGGTAGCTTCGGCTACCTGATCAATG
1 AAAAGTGGTAGCTTCGGCTACCTGATCAATG
4299366 AAAAGTGGTAGCTTCGGCTACCTGATCAATG
1 AAAAGTGGTAGCTTCGGCTACCTGATCAATG
4299397 AAAAGTGGTAGCTTCGGCTACCTGATCAATG
1 AAAAGTGGTAGCTTCGGCTACCTGATCAATG
4299428 AAAAGTGGTAGCTTCGGCTACCTGATCAATG
1 AAAAGTGGTAGCTTCGGCTACCTGATCAATG
4299459 AAAAGTGGTAGCTTCGGCTACCTGATCA
1 AAAAGTGGTAGCTTCGGCTACCTGATCA
4299487 TCGGCTACTT
Statistics
Matches: 772, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 772 1.00
ACGTcount: A:0.29, C:0.19, G:0.26, T:0.26
Consensus pattern (31 bp):
AAAAGTGGTAGCTTCGGCTACCTGATCAATG
Found at i:4299508 original size:46 final size:46
Alignment explanation
Indices: 4299441--4299532 Score: 139
Period size: 46 Copynumber: 2.0 Consensus size: 46
4299431 AGTGGTAGCT
* *
4299441 TCGGCTACCTGATCAATGAAAAGTGGTAGCTTCGGCTACCTGATCA
1 TCGGCTACCTGATCAATGAAAAATGGTAGCTCCGGCTACCTGATCA
* * *
4299487 TCGGCTACTTGATTAGTGAAAAATGGTAGCTCCGGCTACCTGATCA
1 TCGGCTACCTGATCAATGAAAAATGGTAGCTCCGGCTACCTGATCA
4299533 GTGAATAGTG
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 41 1.00
ACGTcount: A:0.26, C:0.23, G:0.24, T:0.27
Consensus pattern (46 bp):
TCGGCTACCTGATCAATGAAAAATGGTAGCTCCGGCTACCTGATCA
Found at i:4299536 original size:31 final size:31
Alignment explanation
Indices: 4299488--4299556 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
4299478 ACCTGATCAT
* * *
4299488 CGGCTACTTGATTAGTGAAAAATGGTAGCTC
1 CGGCTACCTGATCAGTGAAAAATGATAGCTC
* * *
4299519 CGGCTACCTGATCAGTGAATAGTGATAGCTT
1 CGGCTACCTGATCAGTGAAAAATGATAGCTC
4299550 CGGCTAC
1 CGGCTAC
4299557 AAGTGACAAG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.26, C:0.20, G:0.26, T:0.28
Consensus pattern (31 bp):
CGGCTACCTGATCAGTGAAAAATGATAGCTC
Found at i:4299548 original size:77 final size:77
Alignment explanation
Indices: 4299410--4299556 Score: 222
Period size: 77 Copynumber: 1.9 Consensus size: 77
4299400 AGTGGTAGCT
* * *
4299410 TCGGCTACCTGATCAATGAAAAGTGGTAGCTTCGGCTACCTGATCAATGAAAAGTGGTAGCTTCG
1 TCGGCTACCTGATCAATGAAAAATGGTAGCTCCGGCTACCTGATCAATGAAAAGTGATAGCTTCG
4299475 GCTACCTGATCA
66 GCTACCTGATCA
* * * * *
4299487 TCGGCTACTTGATTAGTGAAAAATGGTAGCTCCGGCTACCTGATCAGTGAATAGTGATAGCTTCG
1 TCGGCTACCTGATCAATGAAAAATGGTAGCTCCGGCTACCTGATCAATGAAAAGTGATAGCTTCG
4299552 GCTAC
66 GCTAC
4299557 AAGTGACAAG
Statistics
Matches: 62, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
77 62 1.00
ACGTcount: A:0.27, C:0.21, G:0.25, T:0.27
Consensus pattern (77 bp):
TCGGCTACCTGATCAATGAAAAATGGTAGCTCCGGCTACCTGATCAATGAAAAGTGATAGCTTCG
GCTACCTGATCA
Found at i:4303218 original size:30 final size:30
Alignment explanation
Indices: 4303182--4303243 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 30
4303172 GTCTTCCAAA
*
4303182 TAAGTTCCGTGTTATATCAACTCGTGAATT
1 TAAGTTCCGTGCTATATCAACTCGTGAATT
* *
4303212 TAAGTTCTGTGCTATATCAACTGGTGAATT
1 TAAGTTCCGTGCTATATCAACTCGTGAATT
4303242 TA
1 TA
4303244 GATCATGATG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.27, C:0.15, G:0.18, T:0.40
Consensus pattern (30 bp):
TAAGTTCCGTGCTATATCAACTCGTGAATT
Found at i:4319285 original size:39 final size:39
Alignment explanation
Indices: 4319231--4319362 Score: 185
Period size: 39 Copynumber: 3.4 Consensus size: 39
4319221 TGCATGGTAT
* *
4319231 TGGAAAAATATCCGGACTTGAAGTCCGTAGGCTTTATGC
1 TGGAAAAATATCCGGACTTAAAGTCCGCAGGCTTTATGC
* *
4319270 TGGAAATATATCCGGACTTAAAGTCCACAGGCTTTATGC
1 TGGAAAAATATCCGGACTTAAAGTCCGCAGGCTTTATGC
* * *
4319309 TGGAAATATATCCGGACTTAAAGCCCGCAGGC-TAAGTGC
1 TGGAAAAATATCCGGACTTAAAGTCCGCAGGCTTTA-TGC
4319348 TGGAAAAATATCCGG
1 TGGAAAAATATCCGG
4319363 GCTAAGTCCT
Statistics
Matches: 84, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
38 2 0.02
39 82 0.98
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.25
Consensus pattern (39 bp):
TGGAAAAATATCCGGACTTAAAGTCCGCAGGCTTTATGC
Found at i:4319387 original size:39 final size:39
Alignment explanation
Indices: 4319355--4319560 Score: 342
Period size: 39 Copynumber: 5.3 Consensus size: 39
4319345 TGCTGGAAAA
4319355 ATATCCGGGCTAAGTCCTGAAGGCATTCGTGCTGGTATT
1 ATATCCGGGCTAAGTCCTGAAGGCATTCGTGCTGGTATT
4319394 ATATCCGGGCTAAGTCCTGAAGGCATTCGTGCTGGTATT
1 ATATCCGGGCTAAGTCCTGAAGGCATTCGTGCTGGTATT
**
4319433 ATATCCGGGCTAAGTTCC-GAAGGCATTCGTGCTGGTGCT
1 ATATCCGGGCTAAG-TCCTGAAGGCATTCGTGCTGGTATT
* **
4319472 ATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGCGTT
1 ATATCCGGGCTAAGTCCTGAAGGCATTCGTGCTGGTATT
4319511 ATATCCGGGCTAAGTCCTGAAGGCATTCGTGCTGGTATT
1 ATATCCGGGCTAAGTCCTGAAGGCATTCGTGCTGGTATT
*
4319550 ATATCTGGGCT
1 ATATCCGGGCT
4319561 TAAAGTCCCG
Statistics
Matches: 157, Mismatches: 8, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
38 3 0.02
39 151 0.96
40 3 0.02
ACGTcount: A:0.19, C:0.22, G:0.29, T:0.30
Consensus pattern (39 bp):
ATATCCGGGCTAAGTCCTGAAGGCATTCGTGCTGGTATT
Found at i:4319388 original size:78 final size:78
Alignment explanation
Indices: 4319238--4319570 Score: 313
Period size: 78 Copynumber: 4.3 Consensus size: 78
4319228 TATTGGAAAA
* * * *
4319238 ATATCCGGACTTGAAGT-CCGTAGGCTTTA-TGCTGGAAATATATCCGGACTTAAAGTCC-ACAG
1 ATATCCGGGCTT-AAGTCCCGAAGGCATTAGTGCTGGAAATATATCCGGGC-T-AAGTCCGA-AG
** *
4319300 GC-TTTATGCTGGAAAT
62 GCATTCGTGCTGGTAAT
* * * *
4319316 ATATCCGGACTTAAAG-CCCGCAGGC-TAAGTGCTGGAAAAATATCCGGGCTAAGTCCTGAAGGC
1 ATATCCGGGCTT-AAGTCCCGAAGGCATTAGTGCTGGAAATATATCCGGGCTAAGTCC-GAAGGC
*
4319379 ATTCGTGCTGGTATT
64 ATTCGTGCTGGTAAT
* * * *
4319394 ATATCCGGGC-TAAGTCCTGAAGGCATTCGTGCTGGTATTATATCCGGGCTAAGTTCCGAAGGCA
1 ATATCCGGGCTTAAGTCCCGAAGGCATTAGTGCTGGAAATATATCCGGGCTAAG-TCCGAAGGCA
**
4319458 TTCGTGCTGGTGCT
65 TTCGTGCTGGTAAT
* ***
4319472 ATATCCGGGC-TAAGTCCCGAAGGCATTCGTGCTGGCGTTATATCCGGGCTAAGTCCTGAAGGCA
1 ATATCCGGGCTTAAGTCCCGAAGGCATTAGTGCTGGAAATATATCCGGGCTAAGTCC-GAAGGCA
*
4319536 TTCGTGCTGGTATT
65 TTCGTGCTGGTAAT
*
4319550 ATATCTGGGCTTAAAGTCCCG
1 ATATCCGGGCTT-AAGTCCCG
4319571 CATGCTTTGT
Statistics
Matches: 219, Mismatches: 25, Indels: 20
0.83 0.09 0.08
Matches are distributed among these distances:
76 9 0.04
77 18 0.08
78 180 0.82
79 4 0.02
80 8 0.04
ACGTcount: A:0.23, C:0.22, G:0.27, T:0.28
Consensus pattern (78 bp):
ATATCCGGGCTTAAGTCCCGAAGGCATTAGTGCTGGAAATATATCCGGGCTAAGTCCGAAGGCAT
TCGTGCTGGTAAT
Found at i:4319437 original size:117 final size:119
Alignment explanation
Indices: 4319306--4319572 Score: 371
Period size: 117 Copynumber: 2.3 Consensus size: 119
4319296 ACAGGCTTTA
* * *
4319306 TGCTGGAAATATATCCGGACTTAAAG-CCCGCAGGC-TAAGTGCTGGAAAAATATCCGGGCTAAG
1 TGCTGGTATTATATCCGGGCTTAAAGTCCCGCAGGCATAAGTGCTGGAAAAATATCCGGGCTAAG
* *
4319369 TCCTGAAGGCATTCGTGCTGGTATTATATCCGGGCTAAGTCCTGAAGGCATTCG
66 TCCCGAAGGCATTCGTGCTGGCATTATATCCGGGCTAAGTCCTGAAGGCATTCG
* * ** ****
4319423 TGCTGGTATTATATCCGGGC-T-AAGTTCCGAAGGCATTCGTGCTGGTGCTATATCCGGGCTAAG
1 TGCTGGTATTATATCCGGGCTTAAAGTCCCGCAGGCATAAGTGCTGGAAAAATATCCGGGCTAAG
*
4319486 TCCCGAAGGCATTCGTGCTGGCGTTATATCCGGGCTAAGTCCTGAAGGCATTCG
66 TCCCGAAGGCATTCGTGCTGGCATTATATCCGGGCTAAGTCCTGAAGGCATTCG
*
4319540 TGCTGGTATTATATCTGGGCTTAAAGTCCCGCA
1 TGCTGGTATTATATCCGGGCTTAAAGTCCCGCA
4319573 TGCTTTGTGG
Statistics
Matches: 129, Mismatches: 17, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
115 3 0.02
116 8 0.06
117 109 0.84
118 1 0.01
119 8 0.06
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.27
Consensus pattern (119 bp):
TGCTGGTATTATATCCGGGCTTAAAGTCCCGCAGGCATAAGTGCTGGAAAAATATCCGGGCTAAG
TCCCGAAGGCATTCGTGCTGGCATTATATCCGGGCTAAGTCCTGAAGGCATTCG
Found at i:4328699 original size:31 final size:31
Alignment explanation
Indices: 4328661--4328724 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
4328651 CCCTATGTCA
4328661 ATTCAACCGATTAATTAAATCTAATAAGCAC
1 ATTCAACCGATTAATTAAATCTAATAAGCAC
4328692 ATTCAACCGATTAATTAAATCTAATAAGCAC
1 ATTCAACCGATTAATTAAATCTAATAAGCAC
4328723 AT
1 AT
4328725 AAAAGACTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.45, C:0.19, G:0.06, T:0.30
Consensus pattern (31 bp):
ATTCAACCGATTAATTAAATCTAATAAGCAC
Found at i:4332296 original size:40 final size:40
Alignment explanation
Indices: 4332227--4332303 Score: 109
Period size: 40 Copynumber: 1.9 Consensus size: 40
4332217 TAGTGCCTCA
** *
4332227 TATAGCCGAAGCTATTCCATTTCATACACTTAGTGCTATT
1 TATAGCCGAAGCTATTCCAAATCACACACTTAGTGCTATT
* *
4332267 TATAGCCGAAGCTATTTCAAATCGCACACTTAGTGCT
1 TATAGCCGAAGCTATTCCAAATCACACACTTAGTGCT
4332304 GAACATAGTC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 32 1.00
ACGTcount: A:0.29, C:0.23, G:0.14, T:0.34
Consensus pattern (40 bp):
TATAGCCGAAGCTATTCCAAATCACACACTTAGTGCTATT
Found at i:4360648 original size:40 final size:38
Alignment explanation
Indices: 4360595--4360733 Score: 125
Period size: 40 Copynumber: 3.5 Consensus size: 38
4360585 CATGATTGCT
* * *
4360595 CTTCGGGATTTAGCACGGATATATCACTAGCACGAATGC
1 CTTCGGAACTTAGCCCGGATATATCACTAGCAC-AATGC
* * *
4360634 TCTTCGGAACTTAGCCCGGATTTAGTAACTCGCACCAATGC
1 -CTTCGGAACTTAGCCCGGATATA-TCACTAGCA-CAATGC
* * * *
4360675 CTTCGGATCTTAGTCCGGATATGGTCACTTAGCACAAAGC
1 CTTCGGAACTTAGCCCGGATAT-ATCAC-TAGCACAATGC
*
4360715 CTTCGGGACTTAGCCCGGA
1 CTTCGGAACTTAGCCCGGA
4360734 CATCATTCGA
Statistics
Matches: 79, Mismatches: 16, Indels: 8
0.77 0.16 0.08
Matches are distributed among these distances:
40 62 0.78
41 16 0.20
42 1 0.01
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (38 bp):
CTTCGGAACTTAGCCCGGATATATCACTAGCACAATGC
Found at i:4361078 original size:29 final size:29
Alignment explanation
Indices: 4361039--4361117 Score: 106
Period size: 29 Copynumber: 2.7 Consensus size: 29
4361029 CTTAATAATC
*
4361039 AACCACGCACACTTAGTGCCATGTACTTT-A
1 AACC-CGCACACTTAGTGCCATGCA-TTTCA
*
4361069 AACTCGCACACTTAGTGCCATGCATTTCA
1 AACCCGCACACTTAGTGCCATGCATTTCA
*
4361098 AGCCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
4361118 ATCTCACAAC
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
28 3 0.07
29 38 0.86
30 3 0.07
ACGTcount: A:0.28, C:0.33, G:0.15, T:0.24
Consensus pattern (29 bp):
AACCCGCACACTTAGTGCCATGCATTTCA
Found at i:4363061 original size:37 final size:37
Alignment explanation
Indices: 4363011--4363089 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
4363001 TTATTACGAA
* * *
4363011 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
*
4363048 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
4363085 GTCTT
1 GTCTT
4363090 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
Found at i:4363311 original size:46 final size:47
Alignment explanation
Indices: 4363208--4363351 Score: 200
Period size: 47 Copynumber: 3.1 Consensus size: 47
4363198 CCCTTCGGGA
* * * * * * *
4363208 CTTATCACATTTATGCACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
4363255 CCTGTCACATATATACACTTTCACATTCA-CACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
4363301 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
4363348 CTTA
1 CTTA
4363352 CTATCATTTC
Statistics
Matches: 85, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
46 40 0.47
47 45 0.53
ACGTcount: A:0.26, C:0.32, G:0.10, T:0.31
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:4368116 original size:143 final size:143
Alignment explanation
Indices: 4367858--4368133 Score: 390
Period size: 143 Copynumber: 1.9 Consensus size: 143
4367848 AAAATGGTGG
* * * * *
4367858 ATCTTATCTTCCTGAAGTTGTAGTGGAGTAGATCGAAGCCACCAGTCTTATCTTCCTGAAGTTAC
1 ATCTTATCCTCCTGAAGTTGCAGTGGAGAAGATCGAAGCCACCAGCCTTATCTCCCTGAAGTTAC
* *
4367923 AACAGAGCAGACTGAAGACAACGAATCTTGTTTTCCTGATATTATAGTGGAATAGATTAAAGCTA
66 AACAGAGCAGACTGAAGACAACGAATCTTATTTCCCTGATATTATAGTGGAATAGATTAAAGCTA
4367988 CAAATTATGGCGA
131 CAAATTATGGCGA
* ** *
4368001 ATCTTATCCTCTTGAAGTTGCAGTGGAGAAGATTTAAGCCACCAGCCTTATCTCCCTGAAGTTGC
1 ATCTTATCCTCCTGAAGTTGCAGTGGAGAAGATCGAAGCCACCAGCCTTATCTCCCTGAAGTTAC
* * * * * * *
4368066 AGCGGAGCAGACTGAAGATAGCGAATCTTATTTCCCTGATGTTGTAGTGGAATAGATTGAAGCTA
66 AACAGAGCAGACTGAAGACAACGAATCTTATTTCCCTGATATTATAGTGGAATAGATTAAAGCTA
4368131 CAA
131 CAA
4368134 GTCGTAAACC
Statistics
Matches: 115, Mismatches: 18, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
143 115 1.00
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.29
Consensus pattern (143 bp):
ATCTTATCCTCCTGAAGTTGCAGTGGAGAAGATCGAAGCCACCAGCCTTATCTCCCTGAAGTTAC
AACAGAGCAGACTGAAGACAACGAATCTTATTTCCCTGATATTATAGTGGAATAGATTAAAGCTA
CAAATTATGGCGA
Found at i:4374404 original size:3 final size:3
Alignment explanation
Indices: 4374398--4374473 Score: 127
Period size: 3 Copynumber: 25.7 Consensus size: 3
4374388 TCCAGGTAAG
4374398 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
* *
4374446 TCT TAT TCT TCT TCT TCT T-T TAT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
4374474 AACTTTTTCC
Statistics
Matches: 69, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
2 2 0.03
3 67 0.97
ACGTcount: A:0.03, C:0.30, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:4376482 original size:448 final size:448
Alignment explanation
Indices: 4375647--4376992 Score: 2656
Period size: 448 Copynumber: 3.0 Consensus size: 448
4375637 TTTATTCCAC
4375647 TGCCCCCTCCTACCTTATGAAATCTACTAGGATAGAGAAGCTTTAGATTTGGTTTTAAGTTTGGA
1 TGCCCCCTCCTACCTTATGAAATCTACTAGGATAGAGAAGCTTTAGATTTGGTTTTAAGTTTGGA
4375712 ATCAAGTTTGAATACCTTTTTTAATTACTTCATTGTTAAAAAATTTTGGAGGCATGACCAATTGT
66 ATCAAGTTTGAATACCTTTTTTAATTACTTCATTGTTAAAAAATTTTGGAGGCATGACCAATTGT
4375777 GGTAAGTGATATTTGATGCAACAAGTCAAATTTGGATAGGATAAAGACCAAGGAATTCTATCAGC
131 GGTAAGTGATATTTGATGCAACAAGTCAAATTTGGATAGGATAAAGACCAAGGAATTCTATCAGC
4375842 ACTAGGGAATAAGTACATTGGTCTCAAGGTATCAGAAAAAGACCTAAAAGTAGTAGGTTTTTGGT
196 ACTAGGGAATAAGTACATTGGTCTCAAGGTATCAGAAAAAGACCTAAAAGTAGTAGGTTTTTGGT
4375907 GGAATGGAACCTGAATAAGCCGCTTATTTTGCCTAGAGTTTGACCATACTTTTTAAACCTTAGTA
261 GGAATGGAACCTGAATAAGCCGCTTATTTTGCCTAGAGTTTGACCATACTTTTTAAACCTTAGTA
*
4375972 ATACTTCATAACCTAGTTGTACTGCATTGTGCTAACTACGTTTAGAGAACCATTTGAAGGGGGAA
326 ATACTTCATAACCTAGTTGTACTGCATTGTGCTAACAACGTTTAGAGAACCATTTGAAGGGGGAA
4376037 AGAGATGTGAATGCCTATTGTTGTTGCCTTAATTATATTGTTCTCAATTATCTTTTGT
391 AGAGATGTGAATGCCTATTGTTGTTGCCTTAATTATATTGTTCTCAATTATCTTTTGT
4376095 TGCCCCCTCCTACCTTATGAAATCTACTAGGATAGAGAAGCTTTAGATTTGGTTTTAAGTTTGGA
1 TGCCCCCTCCTACCTTATGAAATCTACTAGGATAGAGAAGCTTTAGATTTGGTTTTAAGTTTGGA
4376160 ATCAAGTTTGAATACCTTTTTTAATTACTTCATTGTTAAAAAATTTTGGAGGCATGACCAATTGT
66 ATCAAGTTTGAATACCTTTTTTAATTACTTCATTGTTAAAAAATTTTGGAGGCATGACCAATTGT
4376225 GGTAAGTGATATTTGATGCAACAAGTCAAATTTGGATAGGATAAAGACCAAGGAATTCTATCAGC
131 GGTAAGTGATATTTGATGCAACAAGTCAAATTTGGATAGGATAAAGACCAAGGAATTCTATCAGC
4376290 ACTAGGGAATAAGTACATTGGTCTCAAGGTATCAGAAAAAGACCTAAAAGTAGTAGGTTTTTGGT
196 ACTAGGGAATAAGTACATTGGTCTCAAGGTATCAGAAAAAGACCTAAAAGTAGTAGGTTTTTGGT
4376355 GGAATGGAACCTGAATAAGCCGCTTATTTTGCCTAGAGTTTGACCATACTTTTTAAACCTTAGTA
261 GGAATGGAACCTGAATAAGCCGCTTATTTTGCCTAGAGTTTGACCATACTTTTTAAACCTTAGTA
4376420 ATACTTCATAACCTAGTTGTACTGCATTGTGCTAACAACGTTTAGAGAACCATTTGAAGGGGGAA
326 ATACTTCATAACCTAGTTGTACTGCATTGTGCTAACAACGTTTAGAGAACCATTTGAAGGGGGAA
4376485 AGAGATGTGAATGCCTATTGTTGTTGCCTTAATTATATTGTTCTCAATTATCTTTTGT
391 AGAGATGTGAATGCCTATTGTTGTTGCCTTAATTATATTGTTCTCAATTATCTTTTGT
4376543 TGCCCCCTCCTACCTTATGAAATCTACTAGGATAGAGAAGCTTTAGATTTGGTTTTAAGTTTGGA
1 TGCCCCCTCCTACCTTATGAAATCTACTAGGATAGAGAAGCTTTAGATTTGGTTTTAAGTTTGGA
4376608 ATCAAGTTTGAATACCTTTTTTAATTACTTCATTGTTAAAAAATTTTGGAGGCATGACCAATTGT
66 ATCAAGTTTGAATACCTTTTTTAATTACTTCATTGTTAAAAAATTTTGGAGGCATGACCAATTGT
*
4376673 GGTAAGTGATATTTGATGCAACAAGTCAAATTTGGATAGGATAAAGACCAAGGAATCCTATCAGC
131 GGTAAGTGATATTTGATGCAACAAGTCAAATTTGGATAGGATAAAGACCAAGGAATTCTATCAGC
* *
4376738 ACTAGGGAATAAGTACATTGGTCTCAAGGTATCAAAAAAAGACCTAAAAATAGTAGGTTTTTGGT
196 ACTAGGGAATAAGTACATTGGTCTCAAGGTATCAGAAAAAGACCTAAAAGTAGTAGGTTTTTGGT
4376803 GGAATGGAACCTGAATAAGCCGCTTATTTTGCCTAGAGTTTGACCATACTTTTTAAACCTTAGTA
261 GGAATGGAACCTGAATAAGCCGCTTATTTTGCCTAGAGTTTGACCATACTTTTTAAACCTTAGTA
4376868 ATACTTCATAACCTAGTTGTACTGCATTGTGCTAACAACGTTTAGAGAACCATTTGAAGGGGGAA
326 ATACTTCATAACCTAGTTGTACTGCATTGTGCTAACAACGTTTAGAGAACCATTTGAAGGGGGAA
4376933 AGAGATGTGAATGCCTATTGTTGTTGCCTTAATTATATTGTTCTCAATTATCTTTTGT
391 AGAGATGTGAATGCCTATTGTTGTTGCCTTAATTATATTGTTCTCAATTATCTTTTGT
4376991 TG
1 TG
4376993 GTTCCTATGC
Statistics
Matches: 894, Mismatches: 4, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
448 894 1.00
ACGTcount: A:0.31, C:0.15, G:0.20, T:0.34
Consensus pattern (448 bp):
TGCCCCCTCCTACCTTATGAAATCTACTAGGATAGAGAAGCTTTAGATTTGGTTTTAAGTTTGGA
ATCAAGTTTGAATACCTTTTTTAATTACTTCATTGTTAAAAAATTTTGGAGGCATGACCAATTGT
GGTAAGTGATATTTGATGCAACAAGTCAAATTTGGATAGGATAAAGACCAAGGAATTCTATCAGC
ACTAGGGAATAAGTACATTGGTCTCAAGGTATCAGAAAAAGACCTAAAAGTAGTAGGTTTTTGGT
GGAATGGAACCTGAATAAGCCGCTTATTTTGCCTAGAGTTTGACCATACTTTTTAAACCTTAGTA
ATACTTCATAACCTAGTTGTACTGCATTGTGCTAACAACGTTTAGAGAACCATTTGAAGGGGGAA
AGAGATGTGAATGCCTATTGTTGTTGCCTTAATTATATTGTTCTCAATTATCTTTTGT
Found at i:4379113 original size:15 final size:15
Alignment explanation
Indices: 4379093--4379124 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
4379083 CCCTTAAATG
4379093 ATGGTAACTTTAGTC
1 ATGGTAACTTTAGTC
4379108 ATGGTAACTTTAGTC
1 ATGGTAACTTTAGTC
4379123 AT
1 AT
4379125 TGCTTGAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.28, C:0.12, G:0.19, T:0.41
Consensus pattern (15 bp):
ATGGTAACTTTAGTC
Found at i:4380691 original size:32 final size:32
Alignment explanation
Indices: 4380643--4380718 Score: 116
Period size: 32 Copynumber: 2.3 Consensus size: 32
4380633 TTGAATTTGT
4380643 TTGATATTGATTATGTTTTAAGCTTGTTAGATA
1 TTGA-ATTGATTATGTTTTAAGCTTGTTAGATA
* *
4380676 TTGAATTTATTATGTTTTAAGCTTGTTCGATA
1 TTGAATTGATTATGTTTTAAGCTTGTTAGATA
*
4380708 TTGAAATGATT
1 TTGAATTGATT
4380719 GACAATGACA
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
32 35 0.90
33 4 0.10
ACGTcount: A:0.28, C:0.04, G:0.17, T:0.51
Consensus pattern (32 bp):
TTGAATTGATTATGTTTTAAGCTTGTTAGATA
Found at i:4382073 original size:14 final size:14
Alignment explanation
Indices: 4382036--4382062 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
4382026 CCAGAAAAGT
4382036 AAATCATTTTCCAA
1 AAATCATTTTCCAA
4382050 AAATCATTTTCCA
1 AAATCATTTTCCA
4382063 GAGAATATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.41, C:0.22, G:0.00, T:0.37
Consensus pattern (14 bp):
AAATCATTTTCCAA
Found at i:4382559 original size:21 final size:22
Alignment explanation
Indices: 4382519--4382559 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
4382509 TTAAGAAGGG
4382519 CACACGGGCGTGTCGCCCCTTC
1 CACACGGGCGTGTCGCCCCTTC
*
4382541 CACACTGGCGTGT-GCCCCT
1 CACACGGGCGTGTCGCCCCT
4382560 GTTTCAACAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.10, C:0.44, G:0.27, T:0.20
Consensus pattern (22 bp):
CACACGGGCGTGTCGCCCCTTC
Found at i:4384800 original size:41 final size:42
Alignment explanation
Indices: 4384675--4384820 Score: 113
Period size: 41 Copynumber: 3.4 Consensus size: 42
4384665 ATGTGTTCTT
* * *
4384675 GTGTAAGACCAC-GTTTGGGACGTTGGCATCGATATATGTGGTTAC
1 GTGTAAGACC-CTGTCTGGGAAG-TGGCATCG--ATATGTGATTAC
* * * *
4384720 GTATAAGAACATGTCTGGGACA-TCGGCATCG-TATTTGATT-C
1 GTGTAAGACCCTGTCTGGGA-AGT-GGCATCGATATGTGATTAC
4384761 GTGTAAGACCCTGTCTGGGAAGTGGCATCGATATGTGATTAC
1 GTGTAAGACCCTGTCTGGGAAGTGGCATCGATATGTGATTAC
* *
4384803 ATATAAGACCAC-GTCTGG
1 GTGTAAGACC-CTGTCTGG
4384821 AACATTGGCA
Statistics
Matches: 81, Mismatches: 13, Indels: 17
0.73 0.12 0.15
Matches are distributed among these distances:
40 8 0.10
41 27 0.33
42 22 0.27
43 1 0.01
44 1 0.01
45 22 0.27
ACGTcount: A:0.25, C:0.17, G:0.28, T:0.29
Consensus pattern (42 bp):
GTGTAAGACCCTGTCTGGGAAGTGGCATCGATATGTGATTAC
Found at i:4384819 original size:83 final size:85
Alignment explanation
Indices: 4384675--4384830 Score: 201
Period size: 83 Copynumber: 1.8 Consensus size: 85
4384665 ATGTGTTCTT
* * * * * *
4384675 GTGTAAGACCACGTTTGGGACGTTGGCATCGATATATGTGGTTACGTATAAGAACATGTCTGGGA
1 GTGTAAGACCACGTCTGGGAAGTTGGCATCGA-ATATGTGATTACATATAAGAACACGTCTGGAA
4384740 CATCGGCATCGTATTTGATTC
65 CATCGGCATCGTATTTGATTC
*
4384761 GTGTAAGACC-CTGTCTGGGAAG-TGGCATCG-ATATGTGATTACATATAAGACCACGTCTGGAA
1 GTGTAAGACCAC-GTCTGGGAAGTTGGCATCGAATATGTGATTACATATAAGAACACGTCTGGAA
*
4384823 CATTGGCA
65 CATCGGCA
4384831 CTATACGACA
Statistics
Matches: 61, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
83 34 0.56
85 9 0.15
86 18 0.30
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.29
Consensus pattern (85 bp):
GTGTAAGACCACGTCTGGGAAGTTGGCATCGAATATGTGATTACATATAAGAACACGTCTGGAAC
ATCGGCATCGTATTTGATTC
Found at i:4392085 original size:49 final size:49
Alignment explanation
Indices: 4392029--4392156 Score: 150
Period size: 49 Copynumber: 2.6 Consensus size: 49
4392019 TATGTGTGCT
* *
4392029 AGTGTAAGACCTGTCTGGGACACGGCATCGGCATCGATAGATG-AGAGCC
1 AGTGTAAGACCTGTCTGGGACACGGCATCGGCATCAAGAGATGCA-AGCC
* * * * *
4392078 AGTGTAAGACCTATCTAGGACACGGCATCGGCCTCAAGATATGCAAGCT
1 AGTGTAAGACCTGTCTGGGACACGGCATCGGCATCAAGAGATGCAAGCC
* * *
4392127 AGTGTAAGACCTGTCCGAGACATGGCATCG
1 AGTGTAAGACCTGTCTGGGACACGGCATCG
4392157 ACTTAAGGTG
Statistics
Matches: 66, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
49 65 0.98
50 1 0.02
ACGTcount: A:0.28, C:0.23, G:0.29, T:0.20
Consensus pattern (49 bp):
AGTGTAAGACCTGTCTGGGACACGGCATCGGCATCAAGAGATGCAAGCC
Found at i:4392245 original size:49 final size:46
Alignment explanation
Indices: 4392029--4392247 Score: 135
Period size: 49 Copynumber: 4.6 Consensus size: 46
4392019 TATGTGTGCT
* *
4392029 AGTGTAAGACCTGTCTGGGACACGGCATCGGCATCGATAGATGAGAGCC
1 AGTGTAAGACCTGTCTAGGACATGGCATC-GCA-CGATAG-TGAGAGCC
* * * *
4392078 AGTGTAAGACCTATCTAGGACACGGCATCGGCCTCAAGATA-TGCA-AGCT
1 AGTGTAAGACCTGTCTAGGACATGGCATC-G---CACGATAGTG-AGAGCC
* * * * *
4392127 AGTGTAAGACCTGTC-CGAGACATGGCATCG-AC-TTAAG-GTGTGTC
1 AGTGTAAGACCTGTCTAG-GACATGGCATCGCACGAT-AGTGAGAGCC
* * * *
4392171 AATGTAAGACCTATCTGGGATATGGCATCGACACAGATAAGTGAGAGCC
1 AGTGTAAGACCTGTCTAGGACATGGCATCG-CAC-GAT-AGTGAGAGCC
*
4392220 AGTGTAAGAGCTGTCTAGGACATGGCAT
1 AGTGTAAGACCTGTCTAGGACATGGCAT
4392248 AAGCCTCAAT
Statistics
Matches: 130, Mismatches: 26, Indels: 28
0.71 0.14 0.15
Matches are distributed among these distances:
43 1 0.01
44 28 0.22
45 1 0.01
46 2 0.02
48 6 0.05
49 85 0.65
50 1 0.01
51 4 0.03
52 2 0.02
ACGTcount: A:0.29, C:0.21, G:0.29, T:0.21
Consensus pattern (46 bp):
AGTGTAAGACCTGTCTAGGACATGGCATCGCACGATAGTGAGAGCC
Found at i:4392410 original size:16 final size:16
Alignment explanation
Indices: 4392387--4392442 Score: 85
Period size: 16 Copynumber: 3.5 Consensus size: 16
4392377 CGTTTGGTTG
*
4392387 GCTGTAATGGAATAGG
1 GCTGTAATGGAATAGA
* *
4392403 GTTGTAATTGAATAGA
1 GCTGTAATGGAATAGA
4392419 GCTGTAATGGAATAGA
1 GCTGTAATGGAATAGA
4392435 GCTGTAAT
1 GCTGTAAT
4392443 AAGTAATTCA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 35 1.00
ACGTcount: A:0.34, C:0.05, G:0.30, T:0.30
Consensus pattern (16 bp):
GCTGTAATGGAATAGA
Found at i:4392517 original size:44 final size:46
Alignment explanation
Indices: 4392424--4392517 Score: 138
Period size: 44 Copynumber: 2.1 Consensus size: 46
4392414 ATAGAGCTGT
*
4392424 AATGGAATAGAGCTGTAATAAGTAATTCAACTGTTTGGTTGAATGG
1 AATGGAATAGAACTGTAATAAGTAATTCAACTGTTTGGTTGAATGG
***
4392470 AATGGAATAGAACTGTAAT-AGT-ATTCTTGTGTTTGGTTGAATGG
1 AATGGAATAGAACTGTAATAAGTAATTCAACTGTTTGGTTGAATGG
4392514 AATG
1 AATG
4392518 ATGTTGTAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
44 23 0.52
45 3 0.07
46 18 0.41
ACGTcount: A:0.33, C:0.05, G:0.27, T:0.35
Consensus pattern (46 bp):
AATGGAATAGAACTGTAATAAGTAATTCAACTGTTTGGTTGAATGG
Found at i:4397062 original size:27 final size:27
Alignment explanation
Indices: 4396994--4397065 Score: 74
Period size: 27 Copynumber: 2.6 Consensus size: 27
4396984 AAATTCTAAT
*
4396994 AAAAATATTTAAAAATGAAAAAAATTACAA
1 AAAAATA-TTAAAAAT--ATAAAATTACAA
* *
4397024 TAATATATTAAAAATATAAAATTACAA
1 AAAAATATTAAAAATATAAAATTACAA
4397051 AAAAACTA-TAAAAAT
1 AAAAA-TATTAAAAAT
4397066 TTACTAAAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
27 21 0.58
28 2 0.06
29 8 0.22
30 5 0.14
ACGTcount: A:0.68, C:0.04, G:0.01, T:0.26
Consensus pattern (27 bp):
AAAAATATTAAAAATATAAAATTACAA
Found at i:4398618 original size:13 final size:14
Alignment explanation
Indices: 4398600--4398636 Score: 58
Period size: 13 Copynumber: 2.6 Consensus size: 14
4398590 GAATGAAGAA
4398600 GAAGGAAGATGA-T
1 GAAGGAAGATGAGT
4398613 GAAGGAAGATGATGT
1 GAAGGAAGATGA-GT
4398628 GAAGGAAGA
1 GAAGGAAGA
4398637 AGAAGCAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 12 0.55
15 10 0.45
ACGTcount: A:0.46, C:0.00, G:0.41, T:0.14
Consensus pattern (14 bp):
GAAGGAAGATGAGT
Found at i:4401549 original size:17 final size:17
Alignment explanation
Indices: 4401527--4401611 Score: 54
Period size: 17 Copynumber: 4.9 Consensus size: 17
4401517 AAAACAGAAT
4401527 AAATAATAATAAAAATA
1 AAATAATAATAAAAATA
*
4401544 AAATAA-AATAGCAAATAA
1 AAATAATAATA-AAAAT-A
*
4401562 TAAATAATAA-AGAAATA
1 -AAATAATAATAAAAATA
4401579 AAGA-AATAA-AATAAA-A
1 AA-ATAATAATAA-AAATA
4401595 AAATAAATAATATAAAA
1 AAAT-AATAATA-AAAA
4401612 GATAAGGGTA
Statistics
Matches: 55, Mismatches: 3, Indels: 19
0.71 0.04 0.25
Matches are distributed among these distances:
15 1 0.02
16 15 0.27
17 20 0.36
18 9 0.16
19 8 0.15
20 2 0.04
ACGTcount: A:0.75, C:0.01, G:0.04, T:0.20
Consensus pattern (17 bp):
AAATAATAATAAAAATA
Found at i:4401564 original size:36 final size:35
Alignment explanation
Indices: 4401524--4401616 Score: 102
Period size: 36 Copynumber: 2.6 Consensus size: 35
4401514 ACAAAAACAG
*
4401524 AATAAATAATAATAAAA-ATAAAATAAAATAGCAAAT
1 AATAAATAATAATAAAAGATAAAATAAAATA--AAAA
* *
4401560 AATAAATAATAA-AGAAATAAAGAAATAAAATAAAAA
1 AATAAATAATAATA-AAAGATA-AAATAAAATAAAAA
4401596 AATAAATAAT-ATAAAAGATAA
1 AATAAATAATAATAAAAGATAA
4401617 GGGTAAAAGG
Statistics
Matches: 49, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
34 1 0.02
35 7 0.14
36 29 0.59
37 2 0.04
38 10 0.20
ACGTcount: A:0.74, C:0.01, G:0.04, T:0.20
Consensus pattern (35 bp):
AATAAATAATAATAAAAGATAAAATAAAATAAAAA
Found at i:4401593 original size:21 final size:22
Alignment explanation
Indices: 4401541--4401611 Score: 65
Period size: 22 Copynumber: 3.3 Consensus size: 22
4401531 AATAATAAAA
* ** *
4401541 ATAAAATAAAATAGCAAATAAT
1 ATAAAATAAAAAAATAAAGAAT
*
4401563 A-AATAATAAAGAAATAAAGAA-
1 ATAA-AATAAAAAAATAAAGAAT
*
4401584 ATAAAATAAAAAAATAAATAAT
1 ATAAAATAAAAAAATAAAGAAT
4401606 ATAAAA
1 ATAAAA
4401612 GATAAGGGTA
Statistics
Matches: 39, Mismatches: 7, Indels: 6
0.75 0.13 0.12
Matches are distributed among these distances:
21 18 0.46
22 21 0.54
ACGTcount: A:0.75, C:0.01, G:0.04, T:0.20
Consensus pattern (22 bp):
ATAAAATAAAAAAATAAAGAAT
Found at i:4401604 original size:4 final size:4
Alignment explanation
Indices: 4401556--4401610 Score: 51
Period size: 4 Copynumber: 13.8 Consensus size: 4
4401546 ATAAAATAGC
* * *
4401556 AAAT -AAT AAAT -AAT AAAG AAAT AAAG AAAT AAAAT AAAA AAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT -AAAT AAAT AAAT AAAT
4401603 AATAT AAA
1 AA-AT AAA
4401611 AGATAAGGGT
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
3 6 0.15
4 27 0.66
5 8 0.20
ACGTcount: A:0.76, C:0.00, G:0.04, T:0.20
Consensus pattern (4 bp):
AAAT
Found at i:4405305 original size:23 final size:22
Alignment explanation
Indices: 4405279--4405337 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
4405269 GAAAAATTAG
4405279 AAAACAAAATTAAACTAAAAACA
1 AAAACAAAATTAAA-TAAAAACA
** *
4405302 AAAACAAAATGCAATAAAAATA
1 AAAACAAAATTAAATAAAAACA
* *
4405324 AAAATAAAAATAAA
1 AAAACAAAATTAAA
4405338 AATCTAGTGT
Statistics
Matches: 29, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
22 17 0.59
23 12 0.41
ACGTcount: A:0.76, C:0.08, G:0.02, T:0.14
Consensus pattern (22 bp):
AAAACAAAATTAAATAAAAACA
Found at i:4405326 original size:5 final size:6
Alignment explanation
Indices: 4405314--4405340 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
4405304 AACAAAATGC
4405314 AATAAA AATAAA AATAAA AATAAA AAT
1 AATAAA AATAAA AATAAA AATAAA AAT
4405341 CTAGTGTTCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (6 bp):
AATAAA
Found at i:4406423 original size:30 final size:30
Alignment explanation
Indices: 4406389--4406446 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 30
4406379 CATAGGCTGG
4406389 CACATGGGTC-TGTTGC-CAGCCTGTGTGGCT
1 CACATGGG-CATG-TGCTCAGCCTGTGTGGCT
4406419 CACATGGGCATGTGCTCAGCCTGTGTGG
1 CACATGGGCATGTGCTCAGCCTGTGTGG
4406447 GAATGCCCAG
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
29 4 0.15
30 22 0.85
ACGTcount: A:0.12, C:0.26, G:0.34, T:0.28
Consensus pattern (30 bp):
CACATGGGCATGTGCTCAGCCTGTGTGGCT
Found at i:4407254 original size:23 final size:23
Alignment explanation
Indices: 4407227--4407271 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
4407217 AAAAGATTAA
*
4407227 GGATTTCACGATTTGGGTCTAAG
1 GGATTTCAAGATTTGGGTCTAAG
*
4407250 GGATTTCAAGATTTGGTTCTAA
1 GGATTTCAAGATTTGGGTCTAA
4407272 AAGATTAAGG
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:0.24, C:0.11, G:0.27, T:0.38
Consensus pattern (23 bp):
GGATTTCAAGATTTGGGTCTAAG
Found at i:4407277 original size:23 final size:23
Alignment explanation
Indices: 4407228--4407277 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
4407218 AAAGATTAAG
* **
4407228 GATTTCACGATTTGGGTCTAAGG
1 GATTTCAAGATTTGGGTCTAAAA
*
4407251 GATTTCAAGATTTGGTTCTAAAA
1 GATTTCAAGATTTGGGTCTAAAA
4407274 GATT
1 GATT
4407278 AAGGATGTAG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.28, C:0.10, G:0.24, T:0.38
Consensus pattern (23 bp):
GATTTCAAGATTTGGGTCTAAAA
Found at i:4409824 original size:12 final size:12
Alignment explanation
Indices: 4409776--4409826 Score: 57
Period size: 12 Copynumber: 4.2 Consensus size: 12
4409766 AGGTCATGAT
*
4409776 CGTGGTCGTGGT
1 CGTGGTCGTGGA
4409788 CGTGGTCGTGGA
1 CGTGGTCGTGGA
* * *
4409800 CGTAGTAGGGGA
1 CGTGGTCGTGGA
*
4409812 CGTGGTCGAGGA
1 CGTGGTCGTGGA
4409824 CGT
1 CGT
4409827 ACTAGTAATC
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 32 1.00
ACGTcount: A:0.12, C:0.16, G:0.49, T:0.24
Consensus pattern (12 bp):
CGTGGTCGTGGA
Found at i:4418104 original size:15 final size:15
Alignment explanation
Indices: 4418084--4418115 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
4418074 GATACTGATC
4418084 CACCGTACCGATCAT
1 CACCGTACCGATCAT
4418099 CACCGTACCGATCAT
1 CACCGTACCGATCAT
4418114 CA
1 CA
4418116 AATCATCACT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.28, C:0.41, G:0.12, T:0.19
Consensus pattern (15 bp):
CACCGTACCGATCAT
Found at i:4420836 original size:16 final size:16
Alignment explanation
Indices: 4420815--4420871 Score: 87
Period size: 16 Copynumber: 3.6 Consensus size: 16
4420805 TTCGCTGTAT
4420815 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
4420831 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
* *
4420847 TGGAATAAAGGTGTAA
1 TGGAATAGAGGCGTAA
*
4420863 TGGATTAGA
1 TGGAATAGA
4420872 TGTGTAATAG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 37 1.00
ACGTcount: A:0.39, C:0.04, G:0.35, T:0.23
Consensus pattern (16 bp):
TGGAATAGAGGCGTAA
Found at i:4420876 original size:16 final size:16
Alignment explanation
Indices: 4420810--4420879 Score: 86
Period size: 16 Copynumber: 4.4 Consensus size: 16
4420800 TTTGGTTCGC
*
4420810 TGTATTGGAATAGAGG
1 TGTAATGGAATAGAGG
*
4420826 CGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
* *
4420842 CGTAATGGAATAAAGG
1 TGTAATGGAATAGAGG
* *
4420858 TGTAATGGATTAGATG
1 TGTAATGGAATAGAGG
4420874 TGTAAT
1 TGTAAT
4420880 AGCAAATCAA
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 47 1.00
ACGTcount: A:0.36, C:0.03, G:0.33, T:0.29
Consensus pattern (16 bp):
TGTAATGGAATAGAGG
Found at i:4421252 original size:16 final size:16
Alignment explanation
Indices: 4421212--4421257 Score: 60
Period size: 15 Copynumber: 3.0 Consensus size: 16
4421202 ATAAAATATA
*
4421212 AATTAACATA-ATTAT
1 AATTAAAATATATTAT
*
4421227 TATT-AAATATATTAT
1 AATTAAAATATATTAT
4421242 AATTAAAATATATTAT
1 AATTAAAATATATTAT
4421258 TTTTCATATT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
14 4 0.15
15 11 0.42
16 11 0.42
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (16 bp):
AATTAAAATATATTAT
Found at i:4421268 original size:12 final size:11
Alignment explanation
Indices: 4421250--4421289 Score: 62
Period size: 12 Copynumber: 3.5 Consensus size: 11
4421240 ATAATTAAAA
4421250 TATATTATTTT
1 TATATTATTTT
4421261 TCATATTATTTT
1 T-ATATTATTTT
4421273 TGATATTATTTT
1 T-ATATTATTTT
4421285 TATAT
1 TATAT
4421290 CATGTATTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
11 5 0.19
12 22 0.81
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.68
Consensus pattern (11 bp):
TATATTATTTT
Found at i:4428051 original size:29 final size:29
Alignment explanation
Indices: 4428008--4428071 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 29
4427998 TTAGCCTTGT
* * *
4428008 TTGATTCCTTTTAATAGTAGAGGGACTAAA
1 TTGA-TCCATTTAATAGCAGAAGGACTAAA
* *
4428038 TTGATCCATTTAATAGCAGAAGGATTAAT
1 TTGATCCATTTAATAGCAGAAGGACTAAA
4428067 TTGAT
1 TTGAT
4428072 TAGATACCTA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 25 0.86
30 4 0.14
ACGTcount: A:0.34, C:0.09, G:0.19, T:0.38
Consensus pattern (29 bp):
TTGATCCATTTAATAGCAGAAGGACTAAA
Found at i:4431498 original size:115 final size:115
Alignment explanation
Indices: 4431296--4432212 Score: 1834
Period size: 115 Copynumber: 8.0 Consensus size: 115
4431286 GGGGGGGGGG
4431296 GGTTAATTGAAAATACATGCTTGACCCTATGGGATTATCAGTTTTCTTTGGTATCTTAAATATAT
1 GGTTAATTGAAAATACATGCTTGACCCTATGGGATTATCAGTTTTCTTTGGTATCTTAAATATAT
4431361 TCCCGGGAAACAAGCAGAATTTTTACATAGTAATCAAAAGGGTAATAGGA
66 TCCCGGGAAACAAGCAGAATTTTTACATAGTAATCAAAAGGGTAATAGGA
4431411 GGTTAATTGAAAATACATGCTTGACCCTATGGGATTATCAGTTTTCTTTGGTATCTTAAATATAT
1 GGTTAATTGAAAATACATGCTTGACCCTATGGGATTATCAGTTTTCTTTGGTATCTTAAATATAT
4431476 TCCCGGGAAACAAGCAGAATTTTTACATAGTAATCAAAAGGGTAATAGGA
66 TCCCGGGAAACAAGCAGAATTTTTACATAGTAATCAAAAGGGTAATAGGA
4431526 GGTTAATTGAAAATACATGCTTGACCCTATGGGATTATCAGTTTTCTTTGGTATCTTAAATATAT
1 GGTTAATTGAAAATACATGCTTGACCCTATGGGATTATCAGTTTTCTTTGGTATCTTAAATATAT
4431591 TCCCGGGAAACAAGCAGAATTTTTACATAGTAATCAAAAGGGTAATAGGA
66 TCCCGGGAAACAAGCAGAATTTTTACATAGTAATCAAAAGGGTAATAGGA
4431641 GGTTAATTGAAAATACATGCTTGACCCTATGGGATTATCAGTTTTCTTTGGTATCTTAAATATAT
1 GGTTAATTGAAAATACATGCTTGACCCTATGGGATTATCAGTTTTCTTTGGTATCTTAAATATAT
4431706 TCCCGGGAAACAAGCAGAATTTTTACATAGTAATCAAAAGGGTAATAGGA
66 TCCCGGGAAACAAGCAGAATTTTTACATAGTAATCAAAAGGGTAATAGGA
4431756 GGTTAATTGAAAATACATGCTTGACCCTATGGGATTATCAGTTTTCTTTGGTATCTTAAATATAT
1 GGTTAATTGAAAATACATGCTTGACCCTATGGGATTATCAGTTTTCTTTGGTATCTTAAATATAT
4431821 TCCCGGGAAACAAGCAGAATTTTTACATAGTAATCAAAAGGGTAATAGGA
66 TCCCGGGAAACAAGCAGAATTTTTACATAGTAATCAAAAGGGTAATAGGA
4431871 GGTTAATTGAAAATACATGCTTGACCCTATGGGATTATCAGTTTTCTTTGGTATCTTAAATATAT
1 GGTTAATTGAAAATACATGCTTGACCCTATGGGATTATCAGTTTTCTTTGGTATCTTAAATATAT
4431936 TCCCGGGAAACAAGCAGAATTTTTACATAGTAATCAAAAGGGTAATAGGA
66 TCCCGGGAAACAAGCAGAATTTTTACATAGTAATCAAAAGGGTAATAGGA
4431986 GGTTAATTGAAAATACATGCTTGACCCTATGGGATTATCAGTTTTCTTTGGTATCTTAAATATAT
1 GGTTAATTGAAAATACATGCTTGACCCTATGGGATTATCAGTTTTCTTTGGTATCTTAAATATAT
4432051 TCCCGGGAAACAAGCAGAATTTTTACATAGTAATCAAAAGGGTAATAGGA
66 TCCCGGGAAACAAGCAGAATTTTTACATAGTAATCAAAAGGGTAATAGGA
4432101 GGTTAATTGAAAATACATGCTTGACCCTATGGGATTATCAGTTTTCTTTGGTATCTTAAATATAT
1 GGTTAATTGAAAATACATGCTTGACCCTATGGGATTATCAGTTTTCTTTGGTATCTTAAATATAT
4432166 TCCCGGGAAACAAGCAGAATTTTTACATAGTAATCAAAAGGGTAATA
66 TCCCGGGAAACAAGCAGAATTTTTACATAGTAATCAAAAGGGTAATA
4432213 TAACTTTATA
Statistics
Matches: 802, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
115 802 1.00
ACGTcount: A:0.35, C:0.13, G:0.19, T:0.33
Consensus pattern (115 bp):
GGTTAATTGAAAATACATGCTTGACCCTATGGGATTATCAGTTTTCTTTGGTATCTTAAATATAT
TCCCGGGAAACAAGCAGAATTTTTACATAGTAATCAAAAGGGTAATAGGA
Found at i:4438286 original size:14 final size:14
Alignment explanation
Indices: 4438267--4438298 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
4438257 TTTATATCAT
4438267 TAAAAAGTATCAAA
1 TAAAAAGTATCAAA
4438281 TAAAAAGTATCAAA
1 TAAAAAGTATCAAA
4438295 TAAA
1 TAAA
4438299 GTCGCTGATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.66, C:0.06, G:0.06, T:0.22
Consensus pattern (14 bp):
TAAAAAGTATCAAA
Found at i:4439839 original size:38 final size:38
Alignment explanation
Indices: 4439797--4439872 Score: 143
Period size: 38 Copynumber: 2.0 Consensus size: 38
4439787 AGTTGAAGAG
*
4439797 AGTATTAAACTGTTCGCAAGAAGTCAATTGAATTTTAA
1 AGTATTAAACTGTTCACAAGAAGTCAATTGAATTTTAA
4439835 AGTATTAAACTGTTCACAAGAAGTCAATTGAATTTTAA
1 AGTATTAAACTGTTCACAAGAAGTCAATTGAATTTTAA
4439873 CTTAATTGGC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.41, C:0.11, G:0.14, T:0.34
Consensus pattern (38 bp):
AGTATTAAACTGTTCACAAGAAGTCAATTGAATTTTAA
Found at i:4441010 original size:14 final size:15
Alignment explanation
Indices: 4440975--4441030 Score: 67
Period size: 15 Copynumber: 3.7 Consensus size: 15
4440965 AATTCAGTAT
* *
4440975 TTAAGTTTTCAATAC
1 TTAATTTTTCAACAC
4440990 TTAATTTTTCAACAC
1 TTAATTTTTCAACAC
* * *
4441005 TTATTTTTTCAGCAT
1 TTAATTTTTCAACAC
4441020 TTAATTTTTCA
1 TTAATTTTTCA
4441031 GTTTATCAAG
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 35 1.00
ACGTcount: A:0.29, C:0.14, G:0.04, T:0.54
Consensus pattern (15 bp):
TTAATTTTTCAACAC
Found at i:4446143 original size:64 final size:64
Alignment explanation
Indices: 4445933--4446187 Score: 194
Period size: 64 Copynumber: 4.0 Consensus size: 64
4445923 AGACAAGGAA
* * * * * * *
4445933 AAGCCACTCGAGTGAGTGGGATCTCACATGGGCCTGGGAGAAGCGAAAGA-AACCCTACACGGCC
1 AAGCCACACGAGTGTGTGGGATCTCACATGGGCATGGGAGAAGCGAAGGAGATCAC-ACACGACC
* * * * * *
4445997 AAGCCACACG-GTCGTGTGCGAT-TCCACACGGGCATAGGAGAAGCAAAGGGGATCATACACGGA
1 AAGCCACACGAGT-GTGTGGGATCT-CACATGGGCATGGGAGAAGCGAAGGAGATCACACAC-GA
*
4446060 -T
63 CC
* * * * * *
4446061 GAGCCACACGGGCGTGTGGGATCTCACATGGGCTTGGGAGAAGTGAAGGAGATTACACACGACC
1 AAGCCACACGAGTGTGTGGGATCTCACATGGGCATGGGAGAAGCGAAGGAGATCACACACGACC
* * * * * * * *
4446125 AAGCCACACGAGTGTGTGGAATCTTACATAGGCGTGGGAGAAGCAAAGAAAAACACACACGAC
1 AAGCCACACGAGTGTGTGGGATCTCACATGGGCATGGGAGAAGCGAAGGAGATCACACACGAC
4446188 TTGGCACACG
Statistics
Matches: 145, Mismatches: 39, Indels: 14
0.73 0.20 0.07
Matches are distributed among these distances:
63 5 0.03
64 135 0.93
65 5 0.03
ACGTcount: A:0.32, C:0.23, G:0.31, T:0.14
Consensus pattern (64 bp):
AAGCCACACGAGTGTGTGGGATCTCACATGGGCATGGGAGAAGCGAAGGAGATCACACACGACC
Found at i:4446185 original size:128 final size:128
Alignment explanation
Indices: 4445948--4446185 Score: 266
Period size: 128 Copynumber: 1.9 Consensus size: 128
4445938 ACTCGAGTGA
* *
4445948 GTGGGATCTCACATGGGCCTGGGAGAAGCGAAAGAAACCCTACACGGCCAAGCCACACGGTCGTG
1 GTGGGATCTCACATGGGCCTGGGAGAAGCGAAAGAAACACTACACGACCAAGCCACACGGTCGTG
* * *** * *
4446013 TGCGATTCCACACGGGCATAGGAGAAGCAAAGGGGATCATACACGGATGAGCCACACGGGCGT
66 TGCGAATCCACACAGGCATAGGAGAAGCAAAGAAAAACACACACGGATGAGCCACACGGGCGT
* * * **
4446076 GTGGGATCTCACATGGGCTTGGGAGAAGTGAAGGAGATTAC-ACACGACCAAGCCACACGAGT-G
1 GTGGGATCTCACATGGGCCTGGGAGAAGCGAAAGA-AACACTACACGACCAAGCCACACG-GTCG
* * * *
4446139 TGTG-GAATCTTACATAGGCGTGGGAGAAGCAAAGAAAAACACACACG
64 TGTGCGAATC-CACACAGGCATAGGAGAAGCAAAGAAAAACACACACG
4446186 ACTTGGCACA
Statistics
Matches: 89, Mismatches: 18, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
127 4 0.04
128 81 0.91
129 4 0.04
ACGTcount: A:0.32, C:0.23, G:0.32, T:0.14
Consensus pattern (128 bp):
GTGGGATCTCACATGGGCCTGGGAGAAGCGAAAGAAACACTACACGACCAAGCCACACGGTCGTG
TGCGAATCCACACAGGCATAGGAGAAGCAAAGAAAAACACACACGGATGAGCCACACGGGCGT
Found at i:4446839 original size:28 final size:27
Alignment explanation
Indices: 4446775--4446841 Score: 71
Period size: 28 Copynumber: 2.4 Consensus size: 27
4446765 ACATAAATTG
* * *
4446775 AAAATATAATAAAAAGTGATTATATTA
1 AAAATAAAATAAAAAGTAAATATATTA
* *
4446802 AAATTGAAAATAAAATGTAAATATGATTA
1 AAAAT-AAAATAAAAAGTAAATAT-ATTA
4446831 AAAATAAAATA
1 AAAATAAAATA
4446842 TATATATATT
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
27 4 0.12
28 20 0.62
29 8 0.25
ACGTcount: A:0.63, C:0.00, G:0.07, T:0.30
Consensus pattern (27 bp):
AAAATAAAATAAAAAGTAAATATATTA
Found at i:4447530 original size:20 final size:20
Alignment explanation
Indices: 4447505--4447551 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
4447495 GCTGGATTCT
4447505 CCTTCAAGACTGAAGACCTC
1 CCTTCAAGACTGAAGACCTC
* *
4447525 CCTTCAAGACTGAAGATCTT
1 CCTTCAAGACTGAAGACCTC
4447545 CCTTCAA
1 CCTTCAA
4447552 TTTCCTTCAG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.30, C:0.32, G:0.13, T:0.26
Consensus pattern (20 bp):
CCTTCAAGACTGAAGACCTC
Found at i:4448504 original size:25 final size:24
Alignment explanation
Indices: 4448441--4448506 Score: 68
Period size: 23 Copynumber: 2.8 Consensus size: 24
4448431 ATTTTCTTTC
4448441 TTTATTATTTGTTAT-AT-TATTTA
1 TTTATTATTT-TTATAATCTATTTA
*
4448464 TTT-TTA-TTTTACTAATCTATTTT
1 TTTATTATTTTTA-TAATCTATTTA
4448487 TTTATTATTTTTATTAATCT
1 TTTATTATTTTTA-TAATCT
4448507 TATACTTAGA
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
20 3 0.08
21 3 0.08
22 5 0.14
23 11 0.31
24 3 0.08
25 11 0.31
ACGTcount: A:0.24, C:0.05, G:0.02, T:0.70
Consensus pattern (24 bp):
TTTATTATTTTTATAATCTATTTA
Found at i:4448649 original size:24 final size:23
Alignment explanation
Indices: 4448614--4448663 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 23
4448604 ATTAAGTTTA
4448614 TTTCTTTTCTTTTTATATTTTGT
1 TTTCTTTTCTTTTTATATTTTGT
4448637 TTTCTTTTTCTTTTTATATTTTGT
1 TTTC-TTTTCTTTTTATATTTTGT
4448661 TTT
1 TTT
4448664 TAGTTGCTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 4 0.15
24 22 0.85
ACGTcount: A:0.08, C:0.08, G:0.04, T:0.80
Consensus pattern (23 bp):
TTTCTTTTCTTTTTATATTTTGT
Found at i:4448676 original size:25 final size:24
Alignment explanation
Indices: 4448614--4448675 Score: 74
Period size: 24 Copynumber: 2.6 Consensus size: 24
4448604 ATTAAGTTTA
*
4448614 TTTCT-TTTCTTTTTATATTTTGT
1 TTTCTGTTGCTTTTTATATTTTGT
* *
4448637 TTTCTTTTTCTTTTTATATTTTGT
1 TTTCTGTTGCTTTTTATATTTTGT
4448661 TTT-TAGTTGCTTTTT
1 TTTCT-GTTGCTTTTT
4448676 TTTATTTTCT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
23 6 0.17
24 29 0.83
ACGTcount: A:0.08, C:0.08, G:0.06, T:0.77
Consensus pattern (24 bp):
TTTCTGTTGCTTTTTATATTTTGT
Found at i:4453391 original size:44 final size:45
Alignment explanation
Indices: 4453276--4453428 Score: 177
Period size: 44 Copynumber: 3.4 Consensus size: 45
4453266 ACTCGGGAAA
* * * * *
4453276 CTCGCACACTTAGTGCCAAATA-A-ATAGCCGAAGCTGTATCAAT
1 CTCGCACACTAAGTGCCAAATATATATAGCTGAAGCTATCTCGAT
4453319 CTCGCACACTAAGTGCCAATATACATATATATAGCTGAAGCTATCTCGAT
1 CTCGCACACTAAGTGCC---A-A-ATATATATAGCTGAAGCTATCTCGAT
*
4453369 CTCGCACACTAAGTG-CAAATATATATAGCTGAAGCTATCTTGAT
1 CTCGCACACTAAGTGCCAAATATATATAGCTGAAGCTATCTCGAT
*
4453413 TTCGCACACTAAGTGC
1 CTCGCACACTAAGTGC
4453429 ACATAATTAG
Statistics
Matches: 95, Mismatches: 7, Indels: 14
0.82 0.06 0.12
Matches are distributed among these distances:
43 16 0.17
44 39 0.41
45 1 0.01
46 2 0.02
47 1 0.01
48 3 0.03
49 2 0.02
50 31 0.33
ACGTcount: A:0.33, C:0.24, G:0.16, T:0.27
Consensus pattern (45 bp):
CTCGCACACTAAGTGCCAAATATATATAGCTGAAGCTATCTCGAT
Found at i:4454905 original size:16 final size:16
Alignment explanation
Indices: 4454884--4454918 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
4454874 CCAATATCTA
* *
4454884 ATTATCATATTTGCAC
1 ATTATCACATTTACAC
4454900 ATTATCACATTTACAC
1 ATTATCACATTTACAC
4454916 ATT
1 ATT
4454919 TATTCATTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.34, C:0.20, G:0.03, T:0.43
Consensus pattern (16 bp):
ATTATCACATTTACAC
Found at i:4458399 original size:26 final size:26
Alignment explanation
Indices: 4458368--4458449 Score: 137
Period size: 26 Copynumber: 3.2 Consensus size: 26
4458358 TGAAATTCCC
*
4458368 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAATATTTACCTAAACCATT
*
4458394 ATCATGGAATATTTACCTAACCCATT
1 ATCATGGAATATTTACCTAAACCATT
*
4458420 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAATATTTACCTAAACCATT
4458446 ATCA
1 ATCA
4458450 GTTTGTATCA
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 53 1.00
ACGTcount: A:0.37, C:0.22, G:0.07, T:0.34
Consensus pattern (26 bp):
ATCATGGAATATTTACCTAAACCATT
Found at i:4465647 original size:6 final size:6
Alignment explanation
Indices: 4465636--4465667 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
4465626 GGATTCATCA
4465636 TCTTGC TCTTGC TCTTGC TCTTGC TCTTGC TC
1 TCTTGC TCTTGC TCTTGC TCTTGC TCTTGC TC
4465668 ATCATGTTGT
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:0.00, C:0.34, G:0.16, T:0.50
Consensus pattern (6 bp):
TCTTGC
Found at i:4476019 original size:39 final size:39
Alignment explanation
Indices: 4475975--4476172 Score: 333
Period size: 39 Copynumber: 5.1 Consensus size: 39
4475965 ATTATATTAT
* *
4475975 CAGCACAAAGCCTGCGGGACTTTAACCCGGATACATTTC
1 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
* * *
4476014 CAGCACGAAGCCTGCGGGACTTTGGCCCAGATATATTTC
1 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
* *
4476053 CAGCATGAAGCTTGCGGGACTTTAGCCCGGATACATTTC
1 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
4476092 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
1 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
4476131 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
1 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
4476170 CAG
1 CAG
4476173 TGTCTTGCAT
Statistics
Matches: 147, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 147 1.00
ACGTcount: A:0.24, C:0.29, G:0.25, T:0.22
Consensus pattern (39 bp):
CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
Found at i:4484117 original size:6 final size:6
Alignment explanation
Indices: 4484112--4484201 Score: 108
Period size: 6 Copynumber: 15.0 Consensus size: 6
4484102 TATACCTATA
* *
4484112 TATATA TATATG TATATG CATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
* * * * * *
4484160 TATATG TATATG TGTATG TGTTTG TGTATG TGTATG TGTATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG
4484202 CGTGTTATGG
Statistics
Matches: 78, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 78 1.00
ACGTcount: A:0.28, C:0.01, G:0.21, T:0.50
Consensus pattern (6 bp):
TATATG
Found at i:4484516 original size:22 final size:22
Alignment explanation
Indices: 4484491--4484556 Score: 72
Period size: 22 Copynumber: 3.3 Consensus size: 22
4484481 TAATTATACA
4484491 TAGTTTTAATTGGTATAATAAT
1 TAGTTTTAATTGGTATAATAAT
* *
4484513 TAG-TTTAGTT--T-T--TAAA
1 TAGTTTTAATTGGTATAATAAT
4484529 TAGTTTTAATTGGTATAATAAT
1 TAGTTTTAATTGGTATAATAAT
4484551 TAGTTT
1 TAGTTT
4484557 AGTTTTTAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 12
0.68 0.08 0.24
Matches are distributed among these distances:
16 6 0.18
17 6 0.18
18 1 0.03
19 2 0.06
20 1 0.03
21 6 0.18
22 12 0.35
ACGTcount: A:0.33, C:0.00, G:0.14, T:0.53
Consensus pattern (22 bp):
TAGTTTTAATTGGTATAATAAT
Found at i:4484532 original size:38 final size:38
Alignment explanation
Indices: 4484490--4484570 Score: 155
Period size: 38 Copynumber: 2.2 Consensus size: 38
4484480 TTAATTATAC
4484490 ATAGTTTTAATTGGTATAATAATTAGTTTAGTTTTTAA
1 ATAGTTTTAATTGGTATAATAATTAGTTTAGTTTTTAA
4484528 ATAGTTTTAATTGGTATAATAATTAGTTTAGTTTTTAA
1 ATAGTTTTAATTGGTATAATAATTAGTTTAGTTTTTAA
4484566 A-AGTT
1 ATAGTT
4484571 ACATATTTTG
Statistics
Matches: 43, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
37 4 0.09
38 39 0.91
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.52
Consensus pattern (38 bp):
ATAGTTTTAATTGGTATAATAATTAGTTTAGTTTTTAA
Found at i:4486616 original size:17 final size:16
Alignment explanation
Indices: 4486596--4486636 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
4486586 TTTTGTTGAC
*
4486596 TTTAGATTTCGGTTAAT
1 TTTAGATTT-GGATAAT
*
4486613 TTTAGATTTTGATAAT
1 TTTAGATTTGGATAAT
4486629 TTTAGATT
1 TTTAGATT
4486637 CTAGTTATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 13 0.59
17 9 0.41
ACGTcount: A:0.27, C:0.02, G:0.15, T:0.56
Consensus pattern (16 bp):
TTTAGATTTGGATAAT
Found at i:4492570 original size:19 final size:20
Alignment explanation
Indices: 4492548--4492600 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 20
4492538 TGAATCAAAA
4492548 TTTAAAA-TTTTAATAATTT
1 TTTAAAATTTTTAATAATTT
*
4492567 TTTAAAATTTTTATTAA--T
1 TTTAAAATTTTTAATAATTT
4492585 TTTAAGAATTTTTAAT
1 TTTAA-AATTTTTAAT
4492601 TGTTTATTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
18 6 0.20
19 16 0.53
20 8 0.27
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (20 bp):
TTTAAAATTTTTAATAATTT
Found at i:4492584 original size:20 final size:19
Alignment explanation
Indices: 4492548--4492587 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
4492538 TGAATCAAAA
4492548 TTTAAAATTTTAATAATTT
1 TTTAAAATTTTAATAATTT
*
4492567 TTTAAAATTTTTATTAATTT
1 TTTAAAA-TTTTAATAATTT
4492587 T
1 T
4492588 AAGAATTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 7 0.37
20 12 0.63
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
TTTAAAATTTTAATAATTT
Found at i:4492597 original size:10 final size:10
Alignment explanation
Indices: 4492555--4492600 Score: 51
Period size: 9 Copynumber: 4.7 Consensus size: 10
4492545 AAATTTAAAA
4492555 TTTTAATAATT
1 TTTTAATAA-T
4492566 TTTTAA-AAT
1 TTTTAATAAT
*
4492575 TTTTATTAA-
1 TTTTAATAAT
*
4492584 TTTTAAGAAT
1 TTTTAATAAT
4492594 TTTTAAT
1 TTTTAAT
4492601 TGTTTATTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
9 13 0.45
10 10 0.34
11 6 0.21
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (10 bp):
TTTTAATAAT
Found at i:4493942 original size:17 final size:17
Alignment explanation
Indices: 4493916--4493959 Score: 79
Period size: 17 Copynumber: 2.6 Consensus size: 17
4493906 CAAGACTTAT
4493916 GTAGTGTTTTTAATTAA
1 GTAGTGTTTTTAATTAA
*
4493933 GTAGTATTTTTAATTAA
1 GTAGTGTTTTTAATTAA
4493950 GTAGTGTTTT
1 GTAGTGTTTT
4493960 AAGACATAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.27, C:0.00, G:0.18, T:0.55
Consensus pattern (17 bp):
GTAGTGTTTTTAATTAA
Found at i:4508765 original size:37 final size:36
Alignment explanation
Indices: 4508669--4508778 Score: 102
Period size: 37 Copynumber: 3.0 Consensus size: 36
4508659 TACAAGATAA
* *
4508669 AAATTAAATTAA-ATTCAA-TATTAAGATAATCACTTT
1 AAATTAAATTAATATTAAACTATTAAGATAATTA--TT
* *
4508705 AATCTTAAATTAATA-AAATACTATTAAGATAATTATT
1 AA-ATTAAATTAATATTAA-ACTATTAAGATAATTATT
*
4508742 AAATTAAATTTAATATTAAACTATTAAAATAA-TATT
1 AAATTAAA-TTAATATTAAACTATTAAGATAATTATT
4508778 A
1 A
4508779 TTTTTGGAAT
Statistics
Matches: 61, Mismatches: 7, Indels: 12
0.76 0.09 0.15
Matches are distributed among these distances:
36 12 0.20
37 32 0.52
38 4 0.07
39 13 0.21
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.40
Consensus pattern (36 bp):
AAATTAAATTAATATTAAACTATTAAGATAATTATT
Found at i:4518252 original size:40 final size:40
Alignment explanation
Indices: 4518169--4518431 Score: 307
Period size: 40 Copynumber: 6.6 Consensus size: 40
4518159 GTGAATGCTG
* * * * * *
4518169 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAA
* * * * *
4518209 TCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTATTAAA
*
4518249 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
4518289 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
*
4518329 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
4518369 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * * *
4518408 ACCGGGCTATGTCCCAAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
4518432 TGAACGAGGA
Statistics
Matches: 198, Mismatches: 22, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
39 34 0.17
40 156 0.79
41 8 0.04
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
Found at i:4518451 original size:79 final size:80
Alignment explanation
Indices: 4518208--4518466 Score: 245
Period size: 80 Copynumber: 3.3 Consensus size: 80
4518198 AAGTGAATAT
* * * * * * *
4518208 ATCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCAT
1 ATCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCAAAGGCAT
** ** *
4518272 TCGTGCGAGTTGTTAA
65 TCGAACGAGGAGCTAA
* * * *
4518288 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATT
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCAAAGGCATT
** ** *
4518353 CGTGCGAGTTGTTAA
66 CGAACGAGGAGCTAA
* * *
4518368 ATCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCCAAAGGCATT
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCAAAGGCATT
* *
4518432 TGAACGAGGAGCTAT
66 CGAACGAGGAGCTAA
*
4518447 ATCC-GGTTAAATCCCGAAGG
1 ATCCGGGTTAAGTCCCGAAGG
4518467 TACGTGGTTT
Statistics
Matches: 157, Mismatches: 21, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
78 14 0.09
79 46 0.29
80 97 0.62
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.26
Consensus pattern (80 bp):
ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCAAAGGCATT
CGAACGAGGAGCTAA
Found at i:4519923 original size:56 final size:56
Alignment explanation
Indices: 4519856--4520087 Score: 455
Period size: 56 Copynumber: 4.1 Consensus size: 56
4519846 TATTAGTTTA
*
4519856 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
4519912 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
4519968 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
4520024 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
4520080 TTGCCCAT
1 TTGCCCAT
4520088 CATCCCTTGT
Statistics
Matches: 175, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
56 175 1.00
ACGTcount: A:0.23, C:0.22, G:0.09, T:0.46
Consensus pattern (56 bp):
TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
Found at i:4528981 original size:16 final size:17
Alignment explanation
Indices: 4528950--4528982 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
4528940 ATAAATTTCA
4528950 AAAATATTAATTTAATAT
1 AAAATATT-ATTTAATAT
4528968 AAAATATT-TTTAATA
1 AAAATATTATTTAATA
4528983 CTATAATTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
18 8 0.53
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
AAAATATTATTTAATAT
Found at i:4536173 original size:46 final size:46
Alignment explanation
Indices: 4536082--4536248 Score: 135
Period size: 46 Copynumber: 3.6 Consensus size: 46
4536072 ACATTATAAG
* * *
4536082 AGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGAGACG-A
1 AGCCAATGTAAGA-CATATCTGGGACAT-GCATCGGCATCGAGACGTA
* * * * *
4536129 GTGCTAATGTAAGACATTTCTGGGACATGCTTCGGCCTCGAGACGTA
1 -AGCCAATGTAAGACATATCTGGGACATGCATCGGCATCGAGACGTA
* * *
4536176 AGCCAGTGTAAGACATATCTGGGACATGCATTGGC-TACGAGATGT-
1 AGCCAATGTAAGACATATCTGGGACATGCATCGGCAT-CGAGACGTA
* * *
4536221 -GTCAGTGTAAGACCATGTCTGGGACATG
1 AGCCAATGTAAGA-CATATCTGGGACATG
4536249 GCATTAGCAC
Statistics
Matches: 100, Mismatches: 16, Indels: 9
0.80 0.13 0.07
Matches are distributed among these distances:
44 11 0.11
45 15 0.15
46 50 0.50
47 14 0.14
48 10 0.10
ACGTcount: A:0.26, C:0.20, G:0.30, T:0.24
Consensus pattern (46 bp):
AGCCAATGTAAGACATATCTGGGACATGCATCGGCATCGAGACGTA
Found at i:4546017 original size:46 final size:46
Alignment explanation
Indices: 4545926--4546092 Score: 135
Period size: 46 Copynumber: 3.6 Consensus size: 46
4545916 ACATTATAAG
* * *
4545926 AGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGAGACG-A
1 AGCCAATGTAAGA-CATATCTGGGACAT-GCATCGGCATCGAGACGTA
* * * * *
4545973 GTGCTAATGTAAGACATTTCTGGGACATGCTTCGGCCTCGAGACGTA
1 -AGCCAATGTAAGACATATCTGGGACATGCATCGGCATCGAGACGTA
* * *
4546020 AGCCAGTGTAAGACATATCTGGGACATGCATTGGC-TACGAGATGT-
1 AGCCAATGTAAGACATATCTGGGACATGCATCGGCAT-CGAGACGTA
* * *
4546065 -GTCAGTGTAAGACCATGTCTGGGACATG
1 AGCCAATGTAAGA-CATATCTGGGACATG
4546093 GCATGGGTAC
Statistics
Matches: 100, Mismatches: 16, Indels: 9
0.80 0.13 0.07
Matches are distributed among these distances:
44 11 0.11
45 15 0.15
46 50 0.50
47 14 0.14
48 10 0.10
ACGTcount: A:0.26, C:0.20, G:0.30, T:0.24
Consensus pattern (46 bp):
AGCCAATGTAAGACATATCTGGGACATGCATCGGCATCGAGACGTA
Found at i:4551179 original size:14 final size:15
Alignment explanation
Indices: 4551155--4551185 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
4551145 TTTCTTTGTT
4551155 TATTTTGGAACTTTA
1 TATTTTGGAACTTTA
4551170 TATTTT-GAACTTTA
1 TATTTTGGAACTTTA
4551184 TA
1 TA
4551186 CTTCATCATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.62
15 6 0.38
ACGTcount: A:0.29, C:0.06, G:0.10, T:0.55
Consensus pattern (15 bp):
TATTTTGGAACTTTA
Found at i:4553208 original size:26 final size:26
Alignment explanation
Indices: 4553179--4553234 Score: 94
Period size: 26 Copynumber: 2.2 Consensus size: 26
4553169 TGGTACAAAT
4553179 TGATAATGGGTTAGGCAAATGTTCCA
1 TGATAATGGGTTAGGCAAATGTTCCA
* *
4553205 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGCAAATGTTCCA
4553231 TGAT
1 TGAT
4553235 GGGCATTTCA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.30, C:0.09, G:0.25, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGCAAATGTTCCA
Found at i:4557873 original size:80 final size:80
Alignment explanation
Indices: 4557777--4557938 Score: 315
Period size: 80 Copynumber: 2.0 Consensus size: 80
4557767 GTCTAATTTC
*
4557777 AAATGAGATCAAATACAACACATTTTGAATTCTGTAAAATTAGAAATTTGATTCGTAGTGAAGAG
1 AAATGAGATCAAATACAACACATTTTGAATTCTGTAAAATGAGAAATTTGATTCGTAGTGAAGAG
4557842 TGGTCAGAATAGTCA
66 TGGTCAGAATAGTCA
4557857 AAATGAGATCAAATACAACACATTTTGAATTCTGTAAAATGAGAAATTTGATTCGTAGTGAAGAG
1 AAATGAGATCAAATACAACACATTTTGAATTCTGTAAAATGAGAAATTTGATTCGTAGTGAAGAG
4557922 TGGTCAGAATAGTCA
66 TGGTCAGAATAGTCA
4557937 AA
1 AA
4557939 CAGTGAAACA
Statistics
Matches: 81, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
80 81 1.00
ACGTcount: A:0.42, C:0.10, G:0.19, T:0.29
Consensus pattern (80 bp):
AAATGAGATCAAATACAACACATTTTGAATTCTGTAAAATGAGAAATTTGATTCGTAGTGAAGAG
TGGTCAGAATAGTCA
Found at i:4558655 original size:27 final size:27
Alignment explanation
Indices: 4558624--4558801 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
4558614 TAAATTGTAC
4558624 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
4558651 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
4558677 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
4558705 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
4558733 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
4558760 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
4558787 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
4558802 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:4558738 original size:82 final size:81
Alignment explanation
Indices: 4558625--4558780 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
4558615 AAATTGTACA
* *
4558625 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
4558689 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
4558706 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
4558771 TGCGAGTTGA
65 TGCGAATTGA
4558781 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:4558792 original size:82 final size:81
Alignment explanation
Indices: 4558621--4558801 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
4558611 GATTAAATTG
* *
4558621 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
4558686 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
4558702 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
4558766 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
4558784 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
4558802 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:4572345 original size:10 final size:10
Alignment explanation
Indices: 4572330--4572358 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
4572320 GTGTGGTGAT
4572330 GATCCTTGAC
1 GATCCTTGAC
4572340 GATCCTTGAC
1 GATCCTTGAC
4572350 GATCCTTGA
1 GATCCTTGA
4572359 GCTTGCAGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.21, C:0.28, G:0.21, T:0.31
Consensus pattern (10 bp):
GATCCTTGAC
Found at i:4575708 original size:80 final size:79
Alignment explanation
Indices: 4575559--4575781 Score: 223
Period size: 80 Copynumber: 2.8 Consensus size: 79
4575549 TTGAATGCTG
* * * ** * * * * *
4575559 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGCGAATATATCCGGACTAAGAT-CCGAAGGCCTT
1 TCCGGGTTAAGTCCCGAAGGCATTGTGC-GAGTTACTAAAACCGGGCTAAG-TCCCGAAGGCATT
*
4575623 TGTGCGAGATACTAAA
64 CGTGCGAGATACTAAA
* * * *
4575639 TCCGGGTTAAGTCCCGAGGGCATTCGTGCGAGTTATTAAAGCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGGCATT-GTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATTC
* **
4575704 GTGCGAGTTGTTAAA
65 GTGCGAGATACTAAA
* * *
4575719 TCCGGGTTACGTCCCGAAGGCATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATT
4575782 TGAACGAGGA
Statistics
Matches: 118, Mismatches: 23, Indels: 5
0.81 0.16 0.03
Matches are distributed among these distances:
79 35 0.30
80 79 0.67
81 4 0.03
ACGTcount: A:0.24, C:0.22, G:0.29, T:0.25
Consensus pattern (79 bp):
TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATTCG
TGCGAGATACTAAA
Found at i:4575763 original size:39 final size:40
Alignment explanation
Indices: 4575612--4575781 Score: 216
Period size: 40 Copynumber: 4.3 Consensus size: 40
4575602 GGACTAAGAT
* * *
4575612 CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGTTACTAAATCCGGGTTAAGTC
* * *
4575652 CCGAGGGCATTCGTGCGAGTTATTAAAGCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGTTACTAAATCCGGGTTAAGTC
** *
4575692 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTACGTC
1 CCGAAGGCATTCGTGCGAGTTACTAAATCCGGGTTAAGTC
* * * *
4575732 CCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTC
1 CCGAAGGCATTCGTGCGAGTTACTAAATCCGGGTTAAGTC
4575771 CCGAAGGCATT
1 CCGAAGGCATT
4575782 TGAACGAGGA
Statistics
Matches: 114, Mismatches: 16, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
39 33 0.29
40 81 0.71
ACGTcount: A:0.24, C:0.22, G:0.29, T:0.25
Consensus pattern (40 bp):
CCGAAGGCATTCGTGCGAGTTACTAAATCCGGGTTAAGTC
Found at i:4575801 original size:79 final size:80
Alignment explanation
Indices: 4575634--4575816 Score: 217
Period size: 79 Copynumber: 2.3 Consensus size: 80
4575624 GTGCGAGATA
* * * *
4575634 CTAAATCCGGGTTAAGTCCCGAGGGCATTCGTGCGAGTTATTAAAGCCGGGTTAAGTCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
** **
4575699 CATTCGTGCGAGTTG
66 CATTCGAACGAGGAG
* * * *
4575714 TTAAATCCGGGTTACGTCCCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
*
4575778 CATTTGAACGAGGAG
66 CATTCGAACGAGGAG
* *
4575793 CTATATCC-GGTTAAATCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGG
4575817 TACGTGAATT
Statistics
Matches: 86, Mismatches: 17, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
78 14 0.16
79 46 0.53
80 26 0.30
ACGTcount: A:0.25, C:0.21, G:0.29, T:0.25
Consensus pattern (80 bp):
CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
CATTCGAACGAGGAG
Found at i:4579295 original size:46 final size:46
Alignment explanation
Indices: 4579180--4579391 Score: 189
Period size: 46 Copynumber: 4.5 Consensus size: 46
4579170 TATGAGAGTT
* * * * *
4579180 AGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGAGACGAAAGCT
1 AGTGTAAGACCATGTCTGGGACAT-GCATCGGC-TCGAGATGTAGGCC
* * * * *
4579228 AGAGTAA-AACACGTCTAGGACATGCATCGGCCTCGAGACGTAGGCC
1 AGTGTAAGACCATGTCTGGGACATGCATCGG-CTCGAGATGTAGGCC
* * *
4579274 AGTGTAAGA-CATATTTGGGACATGCATCGGCTACGAGATGATA-GTC
1 AGTGTAAGACCATGTCTGGGACATGCATCGGCT-CGAGATG-TAGGCC
* * *
4579320 AGTGTAAGACCATGTCTAGGACATGGCATCGACTTGAGATGT-GAGCC
1 AGTGTAAGACCATGTCTGGGACAT-GCATCGGCTCGAGATGTAG-GCC
4579367 AGTGTAAGACCATGTCTGGGACATG
1 AGTGTAAGACCATGTCTGGGACATG
4579392 GCATTGGCAC
Statistics
Matches: 134, Mismatches: 22, Indels: 18
0.77 0.13 0.10
Matches are distributed among these distances:
45 2 0.01
46 59 0.44
47 59 0.44
48 14 0.10
ACGTcount: A:0.29, C:0.19, G:0.30, T:0.22
Consensus pattern (46 bp):
AGTGTAAGACCATGTCTGGGACATGCATCGGCTCGAGATGTAGGCC
Found at i:4579359 original size:47 final size:46
Alignment explanation
Indices: 4579134--4579391 Score: 195
Period size: 47 Copynumber: 5.5 Consensus size: 46
4579124 TGTGTGAGCT
* * * **
4579134 AGTGTAAGA-CATGTCTGGGACATGCATCGAC-CACATTATGAGAGTT
1 AGTGTAAGACCATGTCTGGGACATGCATCGACTC-GA-GATGATAGCC
* * * * *
4579180 AGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGAGACGAAAGCT
1 AGTGTAAGACCATGTCTGGGACAT-GCATCGAC-TCGAGATGATAGCC
* * * * * *
4579228 AGAGTAA-AACACGTCTAGGACATGCATCGGCCTCGAGACG-TAGGCC
1 AGTGTAAGACCATGTCTGGGACATGCATC-GACTCGAGATGATA-GCC
* * * *
4579274 AGTGTAAGA-CATATTTGGGACATGCATCGGCTACGAGATGATAGTC
1 AGTGTAAGACCATGTCTGGGACATGCATCGACT-CGAGATGATAGCC
* *
4579320 AGTGTAAGACCATGTCTAGGACATGGCATCGACTTGAGATG-TGAGCC
1 AGTGTAAGACCATGTCTGGGACAT-GCATCGACTCGAGATGAT-AGCC
4579367 AGTGTAAGACCATGTCTGGGACATG
1 AGTGTAAGACCATGTCTGGGACATG
4579392 GCATTGGCAC
Statistics
Matches: 170, Mismatches: 30, Indels: 24
0.76 0.13 0.11
Matches are distributed among these distances:
45 4 0.02
46 63 0.37
47 75 0.44
48 27 0.16
49 1 0.01
ACGTcount: A:0.29, C:0.19, G:0.29, T:0.22
Consensus pattern (46 bp):
AGTGTAAGACCATGTCTGGGACATGCATCGACTCGAGATGATAGCC
Found at i:4594935 original size:28 final size:28
Alignment explanation
Indices: 4594881--4594936 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
4594871 TATTAACAAT
**
4594881 ACAGTCTGGGCCTAAGCCCAATGCAGTA
1 ACAGTCTGGGCCTAAGCCCAAAACAGTA
* * *
4594909 ACAGTGTGGGCCTATGTCCAAAACAGTA
1 ACAGTCTGGGCCTAAGCCCAAAACAGTA
4594937 TAATCACAAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.30, C:0.25, G:0.25, T:0.20
Consensus pattern (28 bp):
ACAGTCTGGGCCTAAGCCCAAAACAGTA
Found at i:4595081 original size:23 final size:23
Alignment explanation
Indices: 4595055--4595109 Score: 83
Period size: 23 Copynumber: 2.4 Consensus size: 23
4595045 ATCGCAGCGT
*
4595055 AGCTGCTAATAGAAATGCATCAA
1 AGCTGCTAATAGAAATGCAGCAA
* *
4595078 AGCTACTAATAGTAATGCAGCAA
1 AGCTGCTAATAGAAATGCAGCAA
4595101 AGCTGCTAA
1 AGCTGCTAA
4595110 GAGCGGTAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.42, C:0.18, G:0.18, T:0.22
Consensus pattern (23 bp):
AGCTGCTAATAGAAATGCAGCAA
Found at i:4598658 original size:47 final size:47
Alignment explanation
Indices: 4598604--4598806 Score: 343
Period size: 47 Copynumber: 4.3 Consensus size: 47
4598594 TTAGGATTTT
** *
4598604 ATGTGATGAATGTGAATGTGTATATATGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
*
4598651 ATGTGATGAATGTGAACATGCATATATGTGATAAGACCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* *
4598698 ACGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCT
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
4598745 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
*
4598792 ATGTGATGAACGTGA
1 ATGTGATGAATGTGA
4598807 GTGTGACAGC
Statistics
Matches: 146, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 146 1.00
ACGTcount: A:0.33, C:0.12, G:0.28, T:0.27
Consensus pattern (47 bp):
ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
Found at i:4600399 original size:29 final size:29
Alignment explanation
Indices: 4600366--4600439 Score: 96
Period size: 29 Copynumber: 2.6 Consensus size: 29
4600356 GTTGTGAGAT
* *
4600366 TGGCACTAGGTGTGCGAACTTGAAA-TGCA
1 TGGCACTAAGTGTGCG-ACTTGAAAGTACA
* *
4600395 TGGCACTAAGTGTGCGAGTTTAAAGTACA
1 TGGCACTAAGTGTGCGACTTGAAAGTACA
4600424 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
4600440 CGGTTGATTA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
28 6 0.15
29 34 0.85
ACGTcount: A:0.27, C:0.16, G:0.31, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGACTTGAAAGTACA
Found at i:4607224 original size:229 final size:229
Alignment explanation
Indices: 4606823--4607242 Score: 840
Period size: 229 Copynumber: 1.8 Consensus size: 229
4606813 GGGGGAGAGT
4606823 TGTGACAGCCCTAATGTGACCCTAGTCGGAAAGTGGTTTCGGGACCACAAAACCGAGTCATAAAA
1 TGTGACAGCCCTAATGTGACCCTAGTCGGAAAGTGGTTTCGGGACCACAAAACCGAGTCATAAAA
4606888 ATAATTAATTGTTATATTCTATGCATATTATGTGTGTACATGCATATGTGGAAGTTTCATTCCCT
66 ATAATTAATTGTTATATTCTATGCATATTATGTGTGTACATGCATATGTGGAAGTTTCATTCCCT
4606953 AATTTTTCCAATTGCATGAGGAATTATTAAATAGGGATCAACATGAGACATGGTGAAATATATGT
131 AATTTTTCCAATTGCATGAGGAATTATTAAATAGGGATCAACATGAGACATGGTGAAATATATGT
4607018 GATAAGGCCGAATGGCCAATGTGATGAACGTGAG
196 GATAAGGCCGAATGGCCAATGTGATGAACGTGAG
4607052 TGTGACAGCCCTAATGTGACCCTAGTCGGAAAGTGGTTTCGGGACCACAAAACCGAGTCATAAAA
1 TGTGACAGCCCTAATGTGACCCTAGTCGGAAAGTGGTTTCGGGACCACAAAACCGAGTCATAAAA
4607117 ATAATTAATTGTTATATTCTATGCATATTATGTGTGTACATGCATATGTGGAAGTTTCATTCCCT
66 ATAATTAATTGTTATATTCTATGCATATTATGTGTGTACATGCATATGTGGAAGTTTCATTCCCT
4607182 AATTTTTCCAATTGCATGAGGAATTATTAAATAGGGATCAACATGAGACATGGTGAAATAT
131 AATTTTTCCAATTGCATGAGGAATTATTAAATAGGGATCAACATGAGACATGGTGAAATAT
4607243 GATAGGCTAA
Statistics
Matches: 191, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
229 191 1.00
ACGTcount: A:0.33, C:0.15, G:0.21, T:0.31
Consensus pattern (229 bp):
TGTGACAGCCCTAATGTGACCCTAGTCGGAAAGTGGTTTCGGGACCACAAAACCGAGTCATAAAA
ATAATTAATTGTTATATTCTATGCATATTATGTGTGTACATGCATATGTGGAAGTTTCATTCCCT
AATTTTTCCAATTGCATGAGGAATTATTAAATAGGGATCAACATGAGACATGGTGAAATATATGT
GATAAGGCCGAATGGCCAATGTGATGAACGTGAG
Found at i:4608796 original size:29 final size:29
Alignment explanation
Indices: 4608737--4608807 Score: 90
Period size: 29 Copynumber: 2.4 Consensus size: 29
4608727 GTTGTGAGAT
* *
4608737 TGGCACTAGGTGTGCGAACTTGAAATGCA
1 TGGCACTAAGTGTGCGAACTTGAAATACA
* *
4608766 TGGCACTAAGTGTGCG-AGTTTAAAGTACA
1 TGGCACTAAGTGTGCGAACTTGAAA-TACA
4608795 TGGCACTAAGTGT
1 TGGCACTAAGTGT
4608808 ACGTGGTTGA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
28 6 0.16
29 31 0.84
ACGTcount: A:0.28, C:0.15, G:0.30, T:0.27
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGAACTTGAAATACA
Found at i:4612028 original size:37 final size:37
Alignment explanation
Indices: 4611978--4612114 Score: 204
Period size: 37 Copynumber: 3.7 Consensus size: 37
4611968 ATTCCGGGTG
4611978 AGACCCGATGACTACGTGTGGAGATTATGTCCAGGTA
1 AGACCCGATGACTACGTGTGGAGATTATGTCCAGGTA
*
4612015 AGACCCGATGACTACGTGTGGAGATTATG-CCCGAGTA
1 AGACCCGATGACTACGTGTGGAGATTATGTCCAG-GTA
* *
4612052 AGACCCGATGACTACGTGTGGAGAGTATGTCCGGGTA
1 AGACCCGATGACTACGTGTGGAGATTATGTCCAGGTA
* * *
4612089 AGACCTGATAACTTCGTGTGGAGATT
1 AGACCCGATGACTACGTGTGGAGATT
4612115 TCGTCTGAGC
Statistics
Matches: 91, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
36 3 0.03
37 85 0.93
38 3 0.03
ACGTcount: A:0.26, C:0.19, G:0.31, T:0.24
Consensus pattern (37 bp):
AGACCCGATGACTACGTGTGGAGATTATGTCCAGGTA
Found at i:4613439 original size:40 final size:40
Alignment explanation
Indices: 4613384--4614175 Score: 1395
Period size: 40 Copynumber: 19.8 Consensus size: 40
4613374 GAGAATTGAG
4613384 AGTGATATATCCGGGCTAAATCCCGAAGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAATCCCGAAGAGCATTCGTGCT
* *
4613424 AGTGATATATTCGGGCTAAATCCTGAAGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAATCCCGAAGAGCATTCGTGCT
4613464 AGTGATATATCCGGGCTAAATCCCGAAGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAATCCCGAAGAGCATTCGTGCT
* *
4613504 AGTGATATATTCGGGCTAAATCCTGAAGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAATCCCGAAGAGCATTCGTGCT
4613544 AGTGATATATCCGGGCTAAATCCCGAAGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAATCCCGAAGAGCATTCGTGCT
* *
4613584 AGTGATATATTCGGGCTAAATCCTGAAGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAATCCCGAAGAGCATTCGTGCT
4613624 AGTGATATATCCGGGCTAAATCCCGAAGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAATCCCGAAGAGCATTCGTGCT
* *
4613664 AGTGATATATTCGGGCTAAATCCTGAAGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAATCCCGAAGAGCATTCGTGCT
4613704 AGTGATATATCCGGGCTAAATCCCGAAGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAATCCCGAAGAGCATTCGTGCT
* *
4613744 AGTGATATATTCGGGCTAAATCCTGAAGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAATCCCGAAGAGCATTCGTGCT
4613784 AGTGATATATCCGGGCTAAATCCCGAAGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAATCCCGAAGAGCATTCGTGCT
* *
4613824 AGTGATATATTCGGGCTAAATCCTGAAGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAATCCCGAAGAGCATTCGTGCT
4613864 AGTGATATATCCGGGCTAAATCCCGAAGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAATCCCGAAGAGCATTCGTGCT
* *
4613904 AGTGATATATTCGGGCTAAATCCTGAAGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAATCCCGAAGAGCATTCGTGCT
4613944 AGTGATATATCCGGGCTAAATCCCGAAGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAATCCCGAAGAGCATTCGTGCT
* *
4613984 AGTGATATATTCGGGCTAAATCCTGAAGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAATCCCGAAGAGCATTCGTGCT
4614024 AGTGATATATCCGGGCTAAATCCCGAAGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAATCCCGAAGAGCATTCGTGCT
* *
4614064 AGTGATATATTCGGGCTAAATCCTGAAGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAATCCCGAAGAGCATTCGTGCT
4614104 AGTGATATATCCGGGCTAAATCCCGAAGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAATCCCGAAGAGCATTCGTGCT
* **
4614144 AGTGATGTATCCGGGCTAGGTCCCGAAGAGCA
1 AGTGATATATCCGGGCTAAATCCCGAAGAGCA
4614176 ATCATGCTGG
Statistics
Matches: 713, Mismatches: 39, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 713 1.00
ACGTcount: A:0.27, C:0.20, G:0.25, T:0.27
Consensus pattern (40 bp):
AGTGATATATCCGGGCTAAATCCCGAAGAGCATTCGTGCT
Found at i:4613517 original size:80 final size:80
Alignment explanation
Indices: 4613384--4614175 Score: 1539
Period size: 80 Copynumber: 9.9 Consensus size: 80
4613374 GAGAATTGAG
4613384 AGTGATATATCCGGGCTAAATCCCGAAGAGCATTCGTGCTAGTGATATATTCGGGCTAAATCCTG
1 AGTGATATATCCGGGCTAAATCCCGAAGAGCATTCGTGCTAGTGATATATTCGGGCTAAATCCTG
4613449 AAGAGCATTCGTGCT
66 AAGAGCATTCGTGCT
4613464 AGTGATATATCCGGGCTAAATCCCGAAGAGCATTCGTGCTAGTGATATATTCGGGCTAAATCCTG
1 AGTGATATATCCGGGCTAAATCCCGAAGAGCATTCGTGCTAGTGATATATTCGGGCTAAATCCTG
4613529 AAGAGCATTCGTGCT
66 AAGAGCATTCGTGCT
4613544 AGTGATATATCCGGGCTAAATCCCGAAGAGCATTCGTGCTAGTGATATATTCGGGCTAAATCCTG
1 AGTGATATATCCGGGCTAAATCCCGAAGAGCATTCGTGCTAGTGATATATTCGGGCTAAATCCTG
4613609 AAGAGCATTCGTGCT
66 AAGAGCATTCGTGCT
4613624 AGTGATATATCCGGGCTAAATCCCGAAGAGCATTCGTGCTAGTGATATATTCGGGCTAAATCCTG
1 AGTGATATATCCGGGCTAAATCCCGAAGAGCATTCGTGCTAGTGATATATTCGGGCTAAATCCTG
4613689 AAGAGCATTCGTGCT
66 AAGAGCATTCGTGCT
4613704 AGTGATATATCCGGGCTAAATCCCGAAGAGCATTCGTGCTAGTGATATATTCGGGCTAAATCCTG
1 AGTGATATATCCGGGCTAAATCCCGAAGAGCATTCGTGCTAGTGATATATTCGGGCTAAATCCTG
4613769 AAGAGCATTCGTGCT
66 AAGAGCATTCGTGCT
4613784 AGTGATATATCCGGGCTAAATCCCGAAGAGCATTCGTGCTAGTGATATATTCGGGCTAAATCCTG
1 AGTGATATATCCGGGCTAAATCCCGAAGAGCATTCGTGCTAGTGATATATTCGGGCTAAATCCTG
4613849 AAGAGCATTCGTGCT
66 AAGAGCATTCGTGCT
4613864 AGTGATATATCCGGGCTAAATCCCGAAGAGCATTCGTGCTAGTGATATATTCGGGCTAAATCCTG
1 AGTGATATATCCGGGCTAAATCCCGAAGAGCATTCGTGCTAGTGATATATTCGGGCTAAATCCTG
4613929 AAGAGCATTCGTGCT
66 AAGAGCATTCGTGCT
4613944 AGTGATATATCCGGGCTAAATCCCGAAGAGCATTCGTGCTAGTGATATATTCGGGCTAAATCCTG
1 AGTGATATATCCGGGCTAAATCCCGAAGAGCATTCGTGCTAGTGATATATTCGGGCTAAATCCTG
4614009 AAGAGCATTCGTGCT
66 AAGAGCATTCGTGCT
4614024 AGTGATATATCCGGGCTAAATCCCGAAGAGCATTCGTGCTAGTGATATATTCGGGCTAAATCCTG
1 AGTGATATATCCGGGCTAAATCCCGAAGAGCATTCGTGCTAGTGATATATTCGGGCTAAATCCTG
4614089 AAGAGCATTCGTGCT
66 AAGAGCATTCGTGCT
* * ** *
4614104 AGTGATATATCCGGGCTAAATCCCGAAGAGCATTCGTGCTAGTGATGTATCCGGGCTAGGTCCCG
1 AGTGATATATCCGGGCTAAATCCCGAAGAGCATTCGTGCTAGTGATATATTCGGGCTAAATCCTG
4614169 AAGAGCA
66 AAGAGCA
4614176 ATCATGCTGG
Statistics
Matches: 707, Mismatches: 5, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
80 707 1.00
ACGTcount: A:0.27, C:0.20, G:0.25, T:0.27
Consensus pattern (80 bp):
AGTGATATATCCGGGCTAAATCCCGAAGAGCATTCGTGCTAGTGATATATTCGGGCTAAATCCTG
AAGAGCATTCGTGCT
Found at i:4617900 original size:47 final size:47
Alignment explanation
Indices: 4617846--4617963 Score: 173
Period size: 47 Copynumber: 2.5 Consensus size: 47
4617836 TTAGGATTTT
** * * * *
4617846 ATGTGATGAATGTGAATGTGTATATATGTGATAAGGCCGGATGGCCG
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGACCGAATGGCCA
4617893 ATGTGATGAATGTGAACATGCATATATGTGATAAGACCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGACCGAATGGCCA
*
4617940 ACGTGATGAATGTGAACATGCATA
1 ATGTGATGAATGTGAACATGCATA
4617964 GACCCGATGA
Statistics
Matches: 64, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
47 64 1.00
ACGTcount: A:0.33, C:0.11, G:0.29, T:0.27
Consensus pattern (47 bp):
ATGTGATGAATGTGAACATGCATATATGTGATAAGACCGAATGGCCA
Found at i:4628977 original size:31 final size:31
Alignment explanation
Indices: 4628937--4629019 Score: 152
Period size: 31 Copynumber: 2.7 Consensus size: 31
4628927 TCAGTCTCGA
4628937 CATAT-ACTGGGCCGAAGCCTTTTCATAAAT
1 CATATCACTGGGCCGAAGCCTTTTCATAAAT
4628967 CATATCACTGGGCCGAAGCCTTTTCATAAAT
1 CATATCACTGGGCCGAAGCCTTTTCATAAAT
4628998 CATATCACT-GGCCGAAGCCTTT
1 CATATCACTGGGCCGAAGCCTTT
4629020 ACTGTAAGCG
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
30 18 0.35
31 34 0.65
ACGTcount: A:0.28, C:0.27, G:0.17, T:0.29
Consensus pattern (31 bp):
CATATCACTGGGCCGAAGCCTTTTCATAAAT
Found at i:4630140 original size:27 final size:27
Alignment explanation
Indices: 4630099--4630172 Score: 89
Period size: 27 Copynumber: 2.7 Consensus size: 27
4630089 ATATTCGTCA
* *
4630099 TTTTACCATACAGGGGTATTACGGTCG
1 TTTTACCCTATAGGGGTATTACGGTCG
*
4630126 TTTTACCCTATAGGGGCT-TTACGGTCT
1 TTTTACCCTATAGGGG-TATTACGGTCG
4630153 TTTTA-CCTATTAGGGGTATT
1 TTTTACCCTA-TAGGGGTATT
4630173 TTAGTCATTT
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
26 5 0.12
27 35 0.85
28 1 0.02
ACGTcount: A:0.19, C:0.18, G:0.23, T:0.41
Consensus pattern (27 bp):
TTTTACCCTATAGGGGTATTACGGTCG
Found at i:4630300 original size:27 final size:26
Alignment explanation
Indices: 4630259--4630383 Score: 144
Period size: 27 Copynumber: 4.7 Consensus size: 26
4630249 GTATAAGTCA
**
4630259 AGGGTATTTCT-GTAATTTTGTAAATC
1 AGGGTATTT-TGGTAATTTTACAAATC
*
4630285 AGGAGTATTTTGGTAATTTTACAAATTG
1 AGG-GTATTTTGGTAATTTTACAAA-TC
*
4630313 AGGGTATTTTGGTAATTTCACAAATC
1 AGGGTATTTTGGTAATTTTACAAATC
* *
4630339 AGTGGTATTTTGGTAATTTTACGAACTA
1 AG-GGTATTTTGGTAATTTTAC-AAATC
4630367 AGGGTATTTTGGTAATT
1 AGGGTATTTTGGTAATT
4630384 CTACCCTATA
Statistics
Matches: 86, Mismatches: 8, Indels: 9
0.83 0.08 0.09
Matches are distributed among these distances:
26 7 0.08
27 70 0.81
28 9 0.10
ACGTcount: A:0.29, C:0.06, G:0.22, T:0.43
Consensus pattern (26 bp):
AGGGTATTTTGGTAATTTTACAAATC
Done.