Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D06
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: 68668488
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1920000 characters in sequence are not A, C, G, or T
File 101 of 230
Found at i:28776518 original size:18 final size:18
Alignment explanation
Indices: 28776495--28776530 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
28776485 ATCATGCATG
28776495 AGTTAAAGCTATGGATGT
1 AGTTAAAGCTATGGATGT
28776513 AGTTAAAGCTATGGATGT
1 AGTTAAAGCTATGGATGT
28776531 CTAAGTAACC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.06, G:0.28, T:0.33
Consensus pattern (18 bp):
AGTTAAAGCTATGGATGT
Found at i:28778452 original size:47 final size:47
Alignment explanation
Indices: 28778384--28778506 Score: 228
Period size: 47 Copynumber: 2.6 Consensus size: 47
28778374 ATCCATAAGT
28778384 GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATTTCAC
1 GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATTTCAC
28778431 GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATTTCAC
1 GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATTTCAC
* *
28778478 GAACTAGGACTCAACTCAATGAGTTCGGA
1 GAACTCGGACTCAACTCAACGAGTTCGGA
28778507 CATTCGCACC
Statistics
Matches: 74, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
47 74 1.00
ACGTcount: A:0.29, C:0.26, G:0.20, T:0.24
Consensus pattern (47 bp):
GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATTTCAC
Found at i:28785028 original size:48 final size:48
Alignment explanation
Indices: 28784967--28785242 Score: 426
Period size: 48 Copynumber: 5.8 Consensus size: 48
28784957 ATCGTGGTAA
*
28784967 ATGTGCCTGTGTAAGACCATGTCTGGGACATGGCATCGGTGATGATAT
1 ATGTGCCTGTGTAAGACCATGTCTGGGACATGGCATCGGCGATGATAT
*
28785015 ATGTTCCTGTGTAAGACCATGTCTGGGACATGGCATCGGCGATGATAT
1 ATGTGCCTGTGTAAGACCATGTCTGGGACATGGCATCGGCGATGATAT
* * **
28785063 TTGTGCATGTGTAAGACCATGTCTGGGACATGGCATCGATGATGATAT
1 ATGTGCCTGTGTAAGACCATGTCTGGGACATGGCATCGGCGATGATAT
**
28785111 ATGTGCCTGTGTAAGACCATGTCTGGGACATGGCATTAGCGATGATAT
1 ATGTGCCTGTGTAAGACCATGTCTGGGACATGGCATCGGCGATGATAT
* * *
28785159 ATGTGCTTGTGTAAGACCTTGTCTGGGACATGGAATCGGCGATGATAT
1 ATGTGCCTGTGTAAGACCATGTCTGGGACATGGCATCGGCGATGATAT
* * *
28785207 GTGTGCCAGTGTAAGACCCTGTCTGGGACATGGCAT
1 ATGTGCCTGTGTAAGACCATGTCTGGGACATGGCAT
28785243 TGGTACTTTA
Statistics
Matches: 205, Mismatches: 23, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
48 205 1.00
ACGTcount: A:0.23, C:0.17, G:0.30, T:0.29
Consensus pattern (48 bp):
ATGTGCCTGTGTAAGACCATGTCTGGGACATGGCATCGGCGATGATAT
Found at i:28786066 original size:18 final size:18
Alignment explanation
Indices: 28786043--28786078 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
28786033 ATCATGCATG
28786043 AGTTAAAGCTATGGATGT
1 AGTTAAAGCTATGGATGT
*
28786061 AGTTAAAGTTATGGATGT
1 AGTTAAAGCTATGGATGT
28786079 CTAAGTAATC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.33, C:0.03, G:0.28, T:0.36
Consensus pattern (18 bp):
AGTTAAAGCTATGGATGT
Found at i:28787114 original size:46 final size:45
Alignment explanation
Indices: 28787047--28787246 Score: 249
Period size: 46 Copynumber: 4.3 Consensus size: 45
28787037 ATATGGTCTT
* *
28787047 ACATGTTTTACACTGGCTTACATCTCGAGGCTGATGCATGTCCCAG
1 ACATGTCTTACACTGGCTT-CATCTCGAGGCCGATGCATGTCCCAG
28787093 ACATGTCTTACACTGGCTTACATCTCGAGGCCGATGCATGTCCCAG
1 ACATGTCTTACACTGGCTT-CATCTCGAGGCCGATGCATGTCCCAG
* * * * *
28787139 ACATGTCTTACACTAGCACTCGTCTCAATGCCGATGCCATGTCCCAG
1 ACATGTCTTACACTGGC-TTCATCTCGAGGCCGATG-CATGTCCCAG
* *
28787186 ACATGGTCTTACACTGGCTCTCATAAT-GTGGCCGATGCATGTCCCAG
1 ACAT-GTCTTACACTGGCT-TCAT-CTCGAGGCCGATGCATGTCCCAG
28787233 ACATGTCTTACACT
1 ACATGTCTTACACT
28787247 AGCTCACAGA
Statistics
Matches: 135, Mismatches: 14, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
46 83 0.61
47 29 0.21
48 22 0.16
49 1 0.01
ACGTcount: A:0.23, C:0.29, G:0.20, T:0.28
Consensus pattern (45 bp):
ACATGTCTTACACTGGCTTCATCTCGAGGCCGATGCATGTCCCAG
Found at i:28787219 original size:94 final size:92
Alignment explanation
Indices: 28787079--28787249 Score: 274
Period size: 94 Copynumber: 1.8 Consensus size: 92
28787069 TCTCGAGGCT
*
28787079 GATGCATGTCCCAGACATGTCTTACACTGGCTTACATCTCGAGGCCGATGCATGTCCCAGACATG
1 GATGCATGTCCCAGACATGTCTTACACTGGCTTACATATCGAGGCCGATGCATGTCCCAGACATG
28787144 TCTTACACTAGCACTCGTCTCAATGCC
66 TCTTACACTAGCACTCGTCTCAATGCC
*
28787171 GATGCCATGTCCCAGACATGGTCTTACACTGGCTCT-CATAAT-GTGGCCGATGCATGTCCCAGA
1 GATG-CATGTCCCAGACAT-GTCTTACACTGGCT-TACAT-ATCGAGGCCGATGCATGTCCCAGA
28787234 CATGTCTTACACTAGC
62 CATGTCTTACACTAGC
28787250 TCACAGAAGT
Statistics
Matches: 73, Mismatches: 2, Indels: 6
0.90 0.02 0.07
Matches are distributed among these distances:
92 4 0.05
93 14 0.19
94 53 0.73
95 2 0.03
ACGTcount: A:0.23, C:0.30, G:0.20, T:0.26
Consensus pattern (92 bp):
GATGCATGTCCCAGACATGTCTTACACTGGCTTACATATCGAGGCCGATGCATGTCCCAGACATG
TCTTACACTAGCACTCGTCTCAATGCC
Found at i:28790712 original size:18 final size:20
Alignment explanation
Indices: 28790689--28790730 Score: 61
Period size: 18 Copynumber: 2.2 Consensus size: 20
28790679 TTTATTACAA
*
28790689 TTTTATTAAT-TTTTATG-T
1 TTTTATAAATATTTTATGAT
28790707 TTTTATAAATATTTTATGAT
1 TTTTATAAATATTTTATGAT
28790727 TTTT
1 TTTT
28790731 TTTATAATCA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 9 0.43
19 7 0.33
20 5 0.24
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.69
Consensus pattern (20 bp):
TTTTATAAATATTTTATGAT
Found at i:28791764 original size:17 final size:17
Alignment explanation
Indices: 28791744--28791777 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
28791734 AATATATTCG
28791744 TTTAAAAAAATAATGAC
1 TTTAAAAAAATAATGAC
*
28791761 TTTAAAAAATTAATGAC
1 TTTAAAAAAATAATGAC
28791778 AAAATTTAAT
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:0.56, C:0.06, G:0.06, T:0.32
Consensus pattern (17 bp):
TTTAAAAAAATAATGAC
Found at i:28794364 original size:17 final size:17
Alignment explanation
Indices: 28794341--28794374 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
28794331 TGGTTTGACA
*
28794341 AAAAAAATTAAATATTAG
1 AAAAAAA-TAAAAATTAG
28794359 AAAAAAATAAAAATTA
1 AAAAAAATAAAAATTA
28794375 AATGTAAGAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.24
Consensus pattern (17 bp):
AAAAAAATAAAAATTAG
Found at i:28796754 original size:13 final size:13
Alignment explanation
Indices: 28796736--28796781 Score: 65
Period size: 13 Copynumber: 3.5 Consensus size: 13
28796726 CTTAAATTTT
28796736 TCAAAAGCACTTC
1 TCAAAAGCACTTC
*
28796749 TCAAAAGCACTTT
1 TCAAAAGCACTTC
* *
28796762 TCCACAGCACTTC
1 TCAAAAGCACTTC
28796775 TCAAAAG
1 TCAAAAG
28796782 TATTGCCAAA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.37, C:0.30, G:0.09, T:0.24
Consensus pattern (13 bp):
TCAAAAGCACTTC
Found at i:28798521 original size:234 final size:233
Alignment explanation
Indices: 28798112--28798581 Score: 886
Period size: 234 Copynumber: 2.0 Consensus size: 233
28798102 CCGCACTTAG
*
28798112 AAAAGTGATATGTTCGGTTAACAAGGAAAGGATAGACGCCACAAGCAAAGCTTGATAAGTCAGAT
1 AAAAGTGATAAGTTCGGTTAACAAGGAAAGGATAGACGCCACAAGCAAAGCTTGATAAGTCAGAT
* *
28798177 CAGTTTCGAAAGAACAAAGAGAATTGGATAACTCATGAAACTCAAATATAGCATAAATTCAGCAA
66 CAGTTCCGAAAGAACAAAGAGAATTGGATAACTCACGAAACTCAAATATAGCATAAATTCAGCAA
28798242 AAAGGTTCTCTACAAAAGGCTGATTACACATATTTATAGTACCAAAGAGGTCTAGCCGAATAGTC
131 AAAGGTTCTCTACAAAAGGCTGATTACACATATTTATAGTACCAAAGAGGTCTAGCCGAATAGTC
28798307 ACATATGATCATCTTAATGAGCTAATAATGAGCTCAAAT
196 ACA-ATGATCATCTTAATGAGCTAATAATGAGCTCAAAT
28798346 AAAAGTGATAAGTTCGGTTAACAAGGAAAGGATAGACGCCACAAGCAAAGCTTGATAAGTCAGAT
1 AAAAGTGATAAGTTCGGTTAACAAGGAAAGGATAGACGCCACAAGCAAAGCTTGATAAGTCAGAT
28798411 CAGTTCCGAAAGAACAAAGAGAATTGGATAACTCACGAAACTCAAATATAGCATAAATTCAGCAA
66 CAGTTCCGAAAGAACAAAGAGAATTGGATAACTCACGAAACTCAAATATAGCATAAATTCAGCAA
*
28798476 AAAGGTTCTCTACAAAAGGTTGATTACACATATTTATAGTACCAAAGAGGTCTAGCCGAATAGTC
131 AAAGGTTCTCTACAAAAGGCTGATTACACATATTTATAGTACCAAAGAGGTCTAGCCGAATAGTC
*
28798541 ACAATGATCATCTTAATGAGCTAATAATGAGCTGAAAT
196 ACAATGATCATCTTAATGAGCTAATAATGAGCTCAAAT
28798579 AAA
1 AAA
28798582 GCTAAAAAAC
Statistics
Matches: 231, Mismatches: 5, Indels: 1
0.97 0.02 0.00
Matches are distributed among these distances:
233 37 0.16
234 194 0.84
ACGTcount: A:0.43, C:0.16, G:0.19, T:0.23
Consensus pattern (233 bp):
AAAAGTGATAAGTTCGGTTAACAAGGAAAGGATAGACGCCACAAGCAAAGCTTGATAAGTCAGAT
CAGTTCCGAAAGAACAAAGAGAATTGGATAACTCACGAAACTCAAATATAGCATAAATTCAGCAA
AAAGGTTCTCTACAAAAGGCTGATTACACATATTTATAGTACCAAAGAGGTCTAGCCGAATAGTC
ACAATGATCATCTTAATGAGCTAATAATGAGCTCAAAT
Found at i:28798981 original size:23 final size:21
Alignment explanation
Indices: 28798955--28799012 Score: 82
Period size: 23 Copynumber: 2.7 Consensus size: 21
28798945 GACACCTGAA
28798955 ATTAAACACATTAAAACAGACAT
1 ATTAAACACATTAAAAC--ACAT
*
28798978 ATTAAACACATTTAAACACAT
1 ATTAAACACATTAAAACACAT
28798999 -TTAAACACATTAAA
1 ATTAAACACATTAAA
28799013 CACTTAAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
20 13 0.39
21 4 0.12
23 16 0.48
ACGTcount: A:0.55, C:0.17, G:0.02, T:0.26
Consensus pattern (21 bp):
ATTAAACACATTAAAACACAT
Found at i:28798994 original size:10 final size:10
Alignment explanation
Indices: 28798956--28799015 Score: 77
Period size: 10 Copynumber: 5.8 Consensus size: 10
28798946 ACACCTGAAA
28798956 TTAAACACAT
1 TTAAACACAT
*
28798966 TAAAACAGACAT
1 TTAAAC--ACAT
28798978 ATTAAACACAT
1 -TTAAACACAT
28798989 TTAAACACAT
1 TTAAACACAT
28798999 TTAAACACA-
1 TTAAACACAT
28799008 TTAAACAC
1 TTAAACAC
28799016 TTAAATAAAT
Statistics
Matches: 45, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
9 8 0.18
10 24 0.53
11 4 0.09
12 4 0.09
13 5 0.11
ACGTcount: A:0.53, C:0.20, G:0.02, T:0.25
Consensus pattern (10 bp):
TTAAACACAT
Found at i:28799100 original size:19 final size:19
Alignment explanation
Indices: 28799073--28799165 Score: 77
Period size: 19 Copynumber: 5.1 Consensus size: 19
28799063 TTATTCCAGC
*
28799073 AACTAAATTAACTAAGATG
1 AACTTAATTAACTAAGATG
*
28799092 AACTTAATTAACTAACATG
1 AACTTAATTAACTAAGATG
* * * *
28799111 AA--TAATTTATTCCAG--C
1 AACTTAATTAACT-AAGATG
*
28799127 AACTTAATTAATTAAGATG
1 AACTTAATTAACTAAGATG
*
28799146 AACTCAATTAACTAAGATG
1 AACTTAATTAACTAAGATG
28799165 A
1 A
28799166 GTAATTTATT
Statistics
Matches: 57, Mismatches: 12, Indels: 10
0.72 0.15 0.13
Matches are distributed among these distances:
16 2 0.04
17 9 0.16
18 9 0.16
19 37 0.65
ACGTcount: A:0.47, C:0.13, G:0.09, T:0.31
Consensus pattern (19 bp):
AACTTAATTAACTAAGATG
Found at i:28799188 original size:54 final size:54
Alignment explanation
Indices: 28799063--28799195 Score: 203
Period size: 54 Copynumber: 2.5 Consensus size: 54
28799053 ATCATTAAAA
* * *
28799063 TTATTCCAGCAACTAAATTAACTAAGATGAACTTAATTAACTAACATGAATAAT
1 TTATTCCAGCAACTTAATTAATTAAGATGAACTCAATTAACTAACATGAATAAT
* *
28799117 TTATTCCAGCAACTTAATTAATTAAGATGAACTCAATTAACTAAGATGAGTAAT
1 TTATTCCAGCAACTTAATTAATTAAGATGAACTCAATTAACTAACATGAATAAT
* *
28799171 TTATTCCATCAATTTAATTAATTAA
1 TTATTCCAGCAACTTAATTAATTAA
28799196 ACTAAGTATT
Statistics
Matches: 72, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 72 1.00
ACGTcount: A:0.44, C:0.14, G:0.08, T:0.35
Consensus pattern (54 bp):
TTATTCCAGCAACTTAATTAATTAAGATGAACTCAATTAACTAACATGAATAAT
Found at i:28801871 original size:39 final size:39
Alignment explanation
Indices: 28801776--28802037 Score: 320
Period size: 39 Copynumber: 6.6 Consensus size: 39
28801766 TTGAATGCTG
*
28801776 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTA-AGTGAC-AAT
1 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGA-T-ACTAAT
* * *
28801814 ATCCGGACTAAGATCCGAAGGCATTTGTACGAGATACTAAT
1 -TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
28801855 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGATACTAAT
28801894 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGATACTAAT
* *
28801933 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGATACTAAT
*
28801972 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGA-ATTACT-AT
1 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGA-TACTAAT
* *
28802011 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAG-CCCGAAGGCATTTG
28802038 AACGAGGAGC
Statistics
Matches: 200, Mismatches: 16, Indels: 13
0.87 0.07 0.06
Matches are distributed among these distances:
39 131 0.65
40 58 0.29
41 10 0.05
42 1 0.00
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.24
Consensus pattern (39 bp):
TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:28802070 original size:79 final size:79
Alignment explanation
Indices: 28801828--28802062 Score: 257
Period size: 78 Copynumber: 3.0 Consensus size: 79
28801818 GGACTAAGAT
* * **
28801828 CCGAAGGCATTTGTACGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGAT-ACTA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAG-TGACTA
* * *
28801892 ATTCCGGGCT-AAGC
65 AATCCGGGTTAAATC
* ** *
28801906 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTGACTAA
*
28801971 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
*
28801985 CCGAAGGCATTTGTGCGA-ATTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-GAG
1 CCGAAGGCATTTGTGCGAGA-TACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTGA-
*
28802047 CTATATCC-GGTTAAAT
62 CTAAATCCGGGTTAAAT
28802063 TCTGAAGGTA
Statistics
Matches: 139, Mismatches: 12, Indels: 11
0.86 0.07 0.07
Matches are distributed among these distances:
77 1 0.01
78 72 0.52
79 41 0.29
80 25 0.18
ACGTcount: A:0.27, C:0.22, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTGACTAA
ATCCGGGTTAAATC
Found at i:28809891 original size:39 final size:40
Alignment explanation
Indices: 28809796--28810056 Score: 328
Period size: 39 Copynumber: 6.7 Consensus size: 40
28809786 TTGAATGCTG
*
28809796 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTA-AGTGAC-AAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAT
*
28809834 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAT
28809875 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
28809914 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* *
28809953 TCCGGGCTAAG--CCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
*
28809991 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGA-ATTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-TACTAAT
* *
28810030 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
28810057 AACGAGGAGC
Statistics
Matches: 201, Mismatches: 11, Indels: 19
0.87 0.05 0.08
Matches are distributed among these distances:
38 35 0.17
39 96 0.48
40 58 0.29
41 11 0.05
42 1 0.00
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:28812150 original size:39 final size:40
Alignment explanation
Indices: 28812049--28812311 Score: 337
Period size: 39 Copynumber: 6.7 Consensus size: 40
28812039 TTGAATGATG
* *
28812049 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTA-AGTGAC-CAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAT
*
28812088 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAT
28812129 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
28812168 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* *
28812207 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
*
28812246 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGA-ATTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-TACTAAT
* *
28812285 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
28812312 AACGAGGAGC
Statistics
Matches: 203, Mismatches: 12, Indels: 16
0.88 0.05 0.07
Matches are distributed among these distances:
39 114 0.56
40 76 0.37
41 12 0.06
42 1 0.00
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:28814813 original size:53 final size:52
Alignment explanation
Indices: 28814627--28814830 Score: 174
Period size: 53 Copynumber: 3.8 Consensus size: 52
28814617 CATTAGGTTT
* * * * * * *
28814627 AAGGATACCAAGTAAGACCATGCCAAGGCATGACATTGGTAAGTTTTACAAGAC
1 AAGGATACCATGTAAGACCATGTCAAGACATGGCAATGGTAAG--TTATAAGGC
* * * * **
28814681 AAGGATATCATGTAAGACCATGTGAAGACATGGCATTGATAAACTACTAGATGGC
1 AAGGATACCATGTAAGACCATGTCAAGACATGGCAATGGTAAGTTA-TA-A-GGC
* * * *
28814736 AAAGATCCCATGTAAGACCATGTCAAGGCATGGCAATGGTGAGTTCATAAGGC
1 AAGGATACCATGTAAGACCATGTCAAGACATGGCAATGGTAAGTT-ATAAGGC
* * *
28814789 AAGGATACCACGTAAGACCATGTCAAAACATGGAAATGGTAA
1 AAGGATACCATGTAAGACCATGTCAAGACATGGCAATGGTAA
28814831 CTTTAAAAAG
Statistics
Matches: 118, Mismatches: 28, Indels: 9
0.76 0.18 0.06
Matches are distributed among these distances:
52 2 0.02
53 39 0.33
54 37 0.31
55 39 0.33
56 1 0.01
ACGTcount: A:0.39, C:0.17, G:0.24, T:0.21
Consensus pattern (52 bp):
AAGGATACCATGTAAGACCATGTCAAGACATGGCAATGGTAAGTTATAAGGC
Found at i:28816417 original size:28 final size:28
Alignment explanation
Indices: 28816373--28816429 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
28816363 ATTCATGACA
*
28816373 TAGTTCATTTGGTCACTTACTGTTCCTT
1 TAGTTCATTTGGACACTTACTGTTCCTT
28816401 TAGTTCATTTGGACACTTACTGTTCCTT
1 TAGTTCATTTGGACACTTACTGTTCCTT
28816429 T
1 T
28816430 CCTTTTCATG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.16, C:0.21, G:0.14, T:0.49
Consensus pattern (28 bp):
TAGTTCATTTGGACACTTACTGTTCCTT
Found at i:28821119 original size:27 final size:27
Alignment explanation
Indices: 28821081--28821515 Score: 171
Period size: 27 Copynumber: 16.1 Consensus size: 27
28821071 CAAAACAGTC
* * *
28821081 ATTTTACCCTACAGGGGTATGTCGGTC
1 ATTTTACACTACAGGGGTATTTCGGTA
* * *
28821108 ATTTTACACTACAGGGGTATATCAGTT
1 ATTTTACACTACAGGGGTATTTCGGTA
** * *
28821135 ATTTTACACCGCAAGGGTATTTTGGTA
1 ATTTTACACTACAGGGGTATTTCGGTA
* * *
28821162 ATTTTATACTACAAAGGGTATTTCAGTA
1 ATTTTACACTAC-AGGGGTATTTCGGTA
*
28821190 ATTTTACAAATA-AGGGGTATTTCGGTA
1 ATTTTAC-ACTACAGGGGTATTTCGGTA
* * *
28821217 ATTTTACA-AATCAAGGATATTTCGGTA
1 ATTTTACACTA-CAGGGGTATTTCGGTA
* * *
28821244 ATTTTACA-AATC-GAAGGTATTTTGGTA
1 ATTTTACACTA-CAG-GGGTATTTCGGTA
* * *
28821271 ATTTTACA-AATCAAGGGTGTTTCGGTA
1 ATTTTACACTA-CAGGGGTATTTCGGTA
* ** **
28821298 ATTTTACA-AATTGAGGGTATTTTAGTA
1 ATTTTACACTACAG-GGGTATTTCGGTA
* *
28821325 ATTTTACA-AATC-GAGGGTATTTCAGTA
1 ATTTTACACTA-CAG-GGGTATTTCGGTA
* * ** *
28821352 ATTTCACAATTGA-GGGTATTTTGGTA
1 ATTTTACACTACAGGGGTATTTCGGTA
* * * ***
28821378 ATTTTACA-AATCAAGGGTTTTTTAATA
1 ATTTTACACTA-CAGGGGTATTTCGGTA
* *
28821405 ATTTCACAAT-C-GAGGGTATTTCGGTA
1 ATTTTACACTACAG-GGGTATTTCGGTA
* *
28821431 ATTTTACA-AATCAGGGGTATTTTGGTA
1 ATTTTACACTA-CAGGGGTATTTCGGTA
* * * *
28821458 ATTTTACA-AATCGGGGGTACTTCGATA
1 ATTTTACACTA-CAGGGGTATTTCGGTA
* * *
28821485 ATTTTACA-AACTGGGGGTATTTCAGTA
1 ATTTTACACTAC-AGGGGTATTTCGGTA
28821512 ATTT
1 ATTT
28821516 CTCTTTGTTA
Statistics
Matches: 321, Mismatches: 69, Indels: 36
0.75 0.16 0.08
Matches are distributed among these distances:
25 1 0.00
26 38 0.12
27 259 0.81
28 20 0.06
29 3 0.01
ACGTcount: A:0.31, C:0.11, G:0.20, T:0.39
Consensus pattern (27 bp):
ATTTTACACTACAGGGGTATTTCGGTA
Found at i:28821181 original size:28 final size:27
Alignment explanation
Indices: 28821147--28821515 Score: 252
Period size: 27 Copynumber: 13.7 Consensus size: 27
28821137 TTTACACCGC
* * *
28821147 AAGGGTATTTTGGTAATTTTATACTACA
1 AAGGGTATTTCGGTAATTTTACA-AACA
* *
28821175 AAGGGTATTTCAGTAATTTTACAAATA
1 AAGGGTATTTCGGTAATTTTACAAACA
*
28821202 AGGGGTATTTCGGTAATTTTACAAATC-
1 AAGGGTATTTCGGTAATTTTACAAA-CA
* *
28821229 AAGGATATTTCGGTAATTTTACAAATCG
1 AAGGGTATTTCGGTAATTTTACAAA-CA
*
28821257 AA-GGTATTTTGGTAATTTTACAAATC-
1 AAGGGTATTTCGGTAATTTTACAAA-CA
* **
28821283 AAGGGTGTTTCGGTAATTTTACAAATT
1 AAGGGTATTTCGGTAATTTTACAAACA
* **
28821310 GAGGGTATTTTAGTAATTTTACAAATC-
1 AAGGGTATTTCGGTAATTTTACAAA-CA
* * * **
28821337 GAGGGTATTTCAGTAATTTCAC-AATT
1 AAGGGTATTTCGGTAATTTTACAAACA
* *
28821363 GAGGGTATTTTGGTAATTTTACAAATC-
1 AAGGGTATTTCGGTAATTTTACAAA-CA
* *** * *
28821390 AAGGGTTTTTTAATAATTTCACAATC-
1 AAGGGTATTTCGGTAATTTTACAAACA
*
28821416 GAGGGTATTTCGGTAATTTTACAAATC-
1 AAGGGTATTTCGGTAATTTTACAAA-CA
* *
28821443 AGGGGTATTTTGGTAATTTTACAAATC-
1 AAGGGTATTTCGGTAATTTTACAAA-CA
** * * *
28821470 GGGGGTACTTCGATAATTTTACAAACT
1 AAGGGTATTTCGGTAATTTTACAAACA
** *
28821497 GGGGGTATTTCAGTAATTT
1 AAGGGTATTTCGGTAATTT
28821516 CTCTTTGTTA
Statistics
Matches: 281, Mismatches: 50, Indels: 21
0.80 0.14 0.06
Matches are distributed among these distances:
26 43 0.15
27 216 0.77
28 22 0.08
ACGTcount: A:0.32, C:0.09, G:0.20, T:0.39
Consensus pattern (27 bp):
AAGGGTATTTCGGTAATTTTACAAACA
Found at i:28821386 original size:53 final size:54
Alignment explanation
Indices: 28821148--28821515 Score: 413
Period size: 54 Copynumber: 6.8 Consensus size: 54
28821138 TTACACCGCA
* * *
28821148 AGGGTATTTTGGTAATTTTA-TACTACAAAGGGTATTTCAGTAATTTTACAAAT-A
1 AGGGTATTTTGGTAATTTTACAAAT-C-AAGGGTATTTCAGTAATTTTACAAATCG
* * *
28821202 AGGGGTATTTCGGTAATTTTACAAATCAAGGATATTTCGGTAATTTTACAAATCG
1 A-GGGTATTTTGGTAATTTTACAAATCAAGGGTATTTCAGTAATTTTACAAATCG
* * * *
28821257 AAGGTATTTTGGTAATTTTACAAATCAAGGGTGTTTCGGTAATTTTACAAATTG
1 AGGGTATTTTGGTAATTTTACAAATCAAGGGTATTTCAGTAATTTTACAAATCG
* * * *
28821311 AGGGTATTTTAGTAATTTTACAAATCGAGGGTATTTCAGTAATTTCAC-AATTG
1 AGGGTATTTTGGTAATTTTACAAATCAAGGGTATTTCAGTAATTTTACAAATCG
* * * *
28821364 AGGGTATTTTGGTAATTTTACAAATCAAGGGTTTTTTAATAATTTCAC-AATCG
1 AGGGTATTTTGGTAATTTTACAAATCAAGGGTATTTCAGTAATTTTACAAATCG
* * **
28821417 AGGGTATTTCGGTAATTTTACAAATCAGGGGTATTTTGGTAATTTTACAAATCG
1 AGGGTATTTTGGTAATTTTACAAATCAAGGGTATTTCAGTAATTTTACAAATCG
* * * * **
28821471 GGGGTACTTCGATAATTTTACAAA-CTGGGGGTATTTCAGTAATTT
1 AGGGTATTTTGGTAATTTTACAAATC-AAGGGTATTTCAGTAATTT
28821516 CTCTTTGTTA
Statistics
Matches: 274, Mismatches: 35, Indels: 10
0.86 0.11 0.03
Matches are distributed among these distances:
53 95 0.35
54 157 0.57
55 20 0.07
56 2 0.01
ACGTcount: A:0.32, C:0.09, G:0.20, T:0.39
Consensus pattern (54 bp):
AGGGTATTTTGGTAATTTTACAAATCAAGGGTATTTCAGTAATTTTACAAATCG
Found at i:28821869 original size:28 final size:28
Alignment explanation
Indices: 28821832--28821895 Score: 101
Period size: 28 Copynumber: 2.3 Consensus size: 28
28821822 TGGCCCCTTT
* *
28821832 AGGCCCAATCTCGTTCACATGGCCCATC
1 AGGCCCAATCACATTCACATGGCCCATC
*
28821860 AGGCCCAATCACATTCATATGGCCCATC
1 AGGCCCAATCACATTCACATGGCCCATC
28821888 AGGCCCAA
1 AGGCCCAA
28821896 CTACTTCCCA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.27, C:0.38, G:0.17, T:0.19
Consensus pattern (28 bp):
AGGCCCAATCACATTCACATGGCCCATC
Found at i:28824456 original size:50 final size:52
Alignment explanation
Indices: 28824397--28824535 Score: 185
Period size: 51 Copynumber: 2.7 Consensus size: 52
28824387 AAAAATGTGG
* * *
28824397 TACACGTAGTAGCCTACACTTAGTACAACACACGTGACTT-AA-CCATCGGA
1 TACACGTAGTAGCTTGCACTTAGTACTACACACGTGACTTGAAGCCATCGGA
* * * *
28824447 TCCATGTAGTAGCTTGCACTTAGTACTACACACGTGA-TTGAAGCTATCGGG
1 TACACGTAGTAGCTTGCACTTAGTACTACACACGTGACTTGAAGCCATCGGA
*
28824498 TACACGTAGTAGCTTGCACTTAGTACTACACATGTGAC
1 TACACGTAGTAGCTTGCACTTAGTACTACACACGTGAC
28824536 CTAAAACCAT
Statistics
Matches: 76, Mismatches: 10, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
49 2 0.03
50 34 0.45
51 40 0.53
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.27
Consensus pattern (52 bp):
TACACGTAGTAGCTTGCACTTAGTACTACACACGTGACTTGAAGCCATCGGA
Found at i:28824517 original size:51 final size:50
Alignment explanation
Indices: 28824353--28824535 Score: 190
Period size: 50 Copynumber: 3.6 Consensus size: 50
28824343 CTGGTACGCA
* * * * * **
28824353 TAGTAGCCTGCACTTAGTACTTCACATGCGACCTAAAAAT-GTGGTACACG
1 TAGTAGCTTGCACTTAGTACTACACACGTGACTTAACCATCG-GGTACACG
* * * * * *
28824403 TAGTAGCCTACACTTAGTACAACACACGTGACTTAACCATCGGATCCATG
1 TAGTAGCTTGCACTTAGTACTACACACGTGACTTAACCATCGGGTACACG
*
28824453 TAGTAGCTTGCACTTAGTACTACACACGTGA-TTGAAGCTATCGGGTACACG
1 TAGTAGCTTGCACTTAGTACTACACACGTGACTT-AA-CCATCGGGTACACG
*
28824504 TAGTAGCTTGCACTTAGTACTACACATGTGAC
1 TAGTAGCTTGCACTTAGTACTACACACGTGAC
28824536 CTAAAACCAT
Statistics
Matches: 110, Mismatches: 19, Indels: 6
0.81 0.14 0.04
Matches are distributed among these distances:
49 2 0.02
50 67 0.61
51 41 0.37
ACGTcount: A:0.30, C:0.24, G:0.20, T:0.27
Consensus pattern (50 bp):
TAGTAGCTTGCACTTAGTACTACACACGTGACTTAACCATCGGGTACACG
Found at i:28830360 original size:7 final size:7
Alignment explanation
Indices: 28830348--28830373 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
28830338 CCCTTATTCA
28830348 TCATCCC
1 TCATCCC
28830355 TCATCCC
1 TCATCCC
28830362 TCATCCC
1 TCATCCC
28830369 TCATC
1 TCATC
28830374 ATTCTCTTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.15, C:0.54, G:0.00, T:0.31
Consensus pattern (7 bp):
TCATCCC
Found at i:28835095 original size:40 final size:40
Alignment explanation
Indices: 28835012--28835274 Score: 325
Period size: 40 Copynumber: 6.6 Consensus size: 40
28835002 TTGAATGCTG
* * * * * *
28835012 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAA
* * * * *
28835052 TCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTATTAAA
28835092 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
28835132 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
*
28835172 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
28835212 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
28835251 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
28835275 TGAACGAGGA
Statistics
Matches: 201, Mismatches: 19, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
39 35 0.17
40 158 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:28835294 original size:79 final size:80
Alignment explanation
Indices: 28835051--28835309 Score: 256
Period size: 80 Copynumber: 3.3 Consensus size: 80
28835041 AAGTGAATAT
* * * * * *
28835051 ATCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCAT
1 ATCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCAT
** * *
28835115 TCGTGCGAGTTA-TTAA
65 TCGAACGAG-GAGCTAA
* * *
28835131 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATT
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATT
** ** *
28835196 CGTGCGAGTTGTTAA
66 CGAACGAGGAGCTAA
* * *
28835211 ATCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATT
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATT
* *
28835275 TGAACGAGGAGCTAT
66 CGAACGAGGAGCTAA
*
28835290 ATCC-GGTTAAATCCCGAAGG
1 ATCCGGGTTAAGTCCCGAAGG
28835310 TACGTGATTT
Statistics
Matches: 156, Mismatches: 21, Indels: 6
0.85 0.11 0.03
Matches are distributed among these distances:
78 14 0.09
79 48 0.31
80 94 0.60
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.26
Consensus pattern (80 bp):
ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATT
CGAACGAGGAGCTAA
Found at i:28841755 original size:44 final size:44
Alignment explanation
Indices: 28841705--28841863 Score: 175
Period size: 43 Copynumber: 3.7 Consensus size: 44
28841695 TATGTGTTCT
*
28841705 CGTGTAAGACCACGTTTGGGACATTGGCATCGAT-TTATGATTTA
1 CGTGTAAGACCACGTCTGGGACATTGGCATCGATATT-TGATTTA
* **
28841749 CGTGTAAGACCATGTCTGGGACATCAGCATCG-TATTTGATTT-
1 CGTGTAAGACCACGTCTGGGACATTGGCATCGATATTTGATTTA
* *
28841791 CGTGTAAGACC-CTGTCTGGGACAATGGGATCGATATTTGA-TTA
1 CGTGTAAGACCAC-GTCTGGGACATTGGCATCGATATTTGATTTA
* * * *
28841834 CATGTAAGACCACGCCTGGAACGTTGGCAT
1 CGTGTAAGACCACGTCTGGGACATTGGCAT
28841864 TGTATGAGCT
Statistics
Matches: 95, Mismatches: 15, Indels: 11
0.79 0.12 0.09
Matches are distributed among these distances:
42 28 0.29
43 36 0.38
44 31 0.33
ACGTcount: A:0.25, C:0.19, G:0.26, T:0.30
Consensus pattern (44 bp):
CGTGTAAGACCACGTCTGGGACATTGGCATCGATATTTGATTTA
Found at i:28848727 original size:21 final size:23
Alignment explanation
Indices: 28848703--28848757 Score: 87
Period size: 23 Copynumber: 2.5 Consensus size: 23
28848693 TGAGTTTTAT
28848703 GAAGTTTGATGAT-T-GTACATG
1 GAAGTTTGATGATATAGTACATG
*
28848724 GAAGTTTGAAGATATAGTACATG
1 GAAGTTTGATGATATAGTACATG
28848747 GAAGTTTGATG
1 GAAGTTTGATG
28848758 TTGGTTTAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 12 0.40
22 1 0.03
23 17 0.57
ACGTcount: A:0.33, C:0.04, G:0.29, T:0.35
Consensus pattern (23 bp):
GAAGTTTGATGATATAGTACATG
Found at i:28849367 original size:43 final size:42
Alignment explanation
Indices: 28849222--28849368 Score: 102
Period size: 43 Copynumber: 3.4 Consensus size: 42
28849212 TGTGTTCTCG
* *
28849222 TGTAAGACCACATCTGGGACATTGGCATCGACT-TATGATTTACA
1 TGTAAGACCACATCTGGGACA-TGGCATC-AATATTTGA-TTACA
* * ** ** * * *
28849266 CGTAAGATCATGTCCAGGACATCGGTATC-GTATTTGATTTCA
1 TGTAAGACCACATCTGGGACAT-GGCATCAATATTTGATTACA
*
28849308 TGTAAGGCC-CTATCTGGGACAGTGGCATCAATATTTGATTACA
1 TGTAAGACCAC-ATCTGGGACA-TGGCATCAATATTTGATTACA
*
28849351 TGTAAGACCACGTCTGGG
1 TGTAAGACCACATCTGGG
28849369 TTGTTGGCAT
Statistics
Matches: 75, Mismatches: 22, Indels: 13
0.68 0.20 0.12
Matches are distributed among these distances:
42 23 0.31
43 31 0.41
44 21 0.28
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.30
Consensus pattern (42 bp):
TGTAAGACCACATCTGGGACATGGCATCAATATTTGATTACA
Found at i:28852283 original size:27 final size:23
Alignment explanation
Indices: 28852244--28852300 Score: 114
Period size: 23 Copynumber: 2.5 Consensus size: 23
28852234 CCGTACCTAG
28852244 TGTTCAGTTTTCATTCATTACTT
1 TGTTCAGTTTTCATTCATTACTT
28852267 TGTTCAGTTTTCATTCATTACTT
1 TGTTCAGTTTTCATTCATTACTT
28852290 TGTTCAGTTTT
1 TGTTCAGTTTT
28852301 AAAGGGGGTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.16, C:0.16, G:0.11, T:0.58
Consensus pattern (23 bp):
TGTTCAGTTTTCATTCATTACTT
Found at i:28860082 original size:20 final size:20
Alignment explanation
Indices: 28860053--28860093 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
28860043 TACCCGGGTT
*
28860053 AGTTCTGATATATTGAGTAA
1 AGTTCGGATATATTGAGTAA
28860073 AGTTCGGATATATTGAGTAA
1 AGTTCGGATATATTGAGTAA
28860093 A
1 A
28860094 CCAATCATTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.37, C:0.05, G:0.22, T:0.37
Consensus pattern (20 bp):
AGTTCGGATATATTGAGTAA
Found at i:28864131 original size:20 final size:20
Alignment explanation
Indices: 28864106--28864143 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
28864096 TGAGAAATCC
28864106 AAGACAAAGCTAAAGGTTCG
1 AAGACAAAGCTAAAGGTTCG
28864126 AAGACAAAGCTAAAGGTT
1 AAGACAAAGCTAAAGGTT
28864144 AAGATTTTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.47, C:0.13, G:0.24, T:0.16
Consensus pattern (20 bp):
AAGACAAAGCTAAAGGTTCG
Found at i:28867193 original size:28 final size:29
Alignment explanation
Indices: 28867151--28867265 Score: 128
Period size: 29 Copynumber: 4.0 Consensus size: 29
28867141 TACCTGTGTT
* * *
28867151 TGGCCCATTAAGCCC-ATTCATATTCATA
1 TGGCCCATTAGGCCCAAATCACATTCATA
* *
28867179 TGGCTCATTAGGCCCAAATCACCTGT-ATA
1 TGGCCCATTAGGCCCAAATCACAT-TCATA
*
28867208 TGGCCCATTAGGCCCAAATCACATTTATA
1 TGGCCCATTAGGCCCAAATCACATTCATA
* *
28867237 TGGCCCGTTAGGCCC-AGTCACATTCATA
1 TGGCCCATTAGGCCCAAATCACATTCATA
28867265 T
1 T
28867266 TCATGCTAAC
Statistics
Matches: 74, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
28 26 0.35
29 47 0.64
30 1 0.01
ACGTcount: A:0.27, C:0.29, G:0.16, T:0.29
Consensus pattern (29 bp):
TGGCCCATTAGGCCCAAATCACATTCATA
Found at i:28868499 original size:47 final size:44
Alignment explanation
Indices: 28868443--28868843 Score: 188
Period size: 38 Copynumber: 9.7 Consensus size: 44
28868433 CCGTTACATG
28868443 TTTAACCGTGGTATATCCACTTAGCACCACGTTAATGAATCAATA
1 TTTAACCGTGGTATATCCACTTAGCACCACGTTAATGAATC-ATA
* * *
28868488 TATGTAACCGTGGAATATCCATTTAGCACCACG-T--T--A-CATG
1 T-T-TAACCGTGGTATATCCACTTAGCACCACGTTAATGAATCATA
* *
28868528 TTTAACCGTGGTATATCCACTTAGCACAACGTTAATGAATGA-A
1 TTTAACCGTGGTATATCCACTTAGCACCACGTTAATGAATCATA
* ** * * ** * ** *
28868571 -TTATCC--ACT-TA-GCAC-CA-CATTA-ATGGATCAAT-ATA
1 TTTAACCGTGGTATATCCACTTAGCACCACGTTAATGAATCATA
* * * *
28868606 TGTAACCATGGCATATCCACTTAGCACCACG-T--T--AT-ATG
1 TTTAACCGTGGTATATCCACTTAGCACCACGTTAATGAATCATA
* * *
28868644 TTTAATCGTGGCATATCCACTTAGCACCACG-T--T--A-CATG
1 TTTAACCGTGGTATATCCACTTAGCACCACGTTAATGAATCATA
28868682 TTTAACCGTGGTATATCCACTTAGCACCACGTTAATGAATCAATA
1 TTTAACCGTGGTATATCCACTTAGCACCACGTTAATGAATC-ATA
* *
28868727 TATGTAACCGTGGCATATCCACTTAGCACCACGTTACATGTATCAATA
1 T-T-TAACCGTGGTATATCCACTTAGCACCACGTTA-ATGAATC-ATA
* * * * *
28868775 TGTGTAATCC-TAGTATATCCATTTAGCACCACGCT-A--CA-CGTA
1 T-T-TAA-CCGTGGTATATCCACTTAGCACCACGTTAATGAATCATA
28868817 --TAACCGTGGTATATCCACTTAGCACCA
1 TTTAACCGTGGTATATCCACTTAGCACCA
28868844 TGTTTTTTTT
Statistics
Matches: 278, Mismatches: 48, Indels: 67
0.71 0.12 0.17
Matches are distributed among these distances:
34 1 0.00
35 7 0.03
36 7 0.03
37 3 0.01
38 118 0.42
39 7 0.03
40 8 0.03
41 4 0.01
42 11 0.04
43 3 0.01
44 4 0.01
45 4 0.01
46 4 0.01
47 58 0.21
48 37 0.13
49 2 0.01
ACGTcount: A:0.31, C:0.24, G:0.14, T:0.30
Consensus pattern (44 bp):
TTTAACCGTGGTATATCCACTTAGCACCACGTTAATGAATCATA
Found at i:28868534 original size:85 final size:84
Alignment explanation
Indices: 28868408--28868767 Score: 333
Period size: 85 Copynumber: 4.4 Consensus size: 84
28868398 TTAACATGTA
* * *
28868408 TAACCGTGGCATATCCACTTAGTACCCGTTACATGTTTAACCGTGGTATATCCACTTAGCACCAC
1 TAACCGTGGAATATCCACTTAGCACCCGTTACATGTTTAACCGTGGTATATCCACTTAGCACAAC
28868473 GTTAATGAATCAATATATG
66 GTTAATGAATCAATATATG
*
28868492 TAACCGTGGAATATCCATTTAGCACCACGTTACATGTTTAACCGTGGTATATCCACTTAGCACAA
1 TAACCGTGGAATATCCACTTAGCACC-CGTTACATGTTTAACCGTGGTATATCCACTTAGCACAA
*
28868557 CGTTAATGAATGAAT-TAT-
65 CGTTAATGAATCAATATATG
** * ** * * ** * * *
28868575 CCA-C-T-TAGCA-CCACATTAATGGA-TCAATATATG--TAACCATGGCATATCCACTTAGCAC
1 TAACCGTGGAATATCCAC-TT-A-GCACCCGTTACATGTTTAACCGTGGTATATCCACTTAGCAC
* *
28868633 CACG-T--T--AT--ATGT-T-
63 AACGTTAATGAATCAATATATG
* * *
28868646 TAATCGTGGCATATCCACTTAGCACCACGTTACATGTTTAACCGTGGTATATCCACTTAGCACCA
1 TAACCGTGGAATATCCACTTAGCACC-CGTTACATGTTTAACCGTGGTATATCCACTTAGCACAA
28868711 CGTTAATGAATCAATATATG
65 CGTTAATGAATCAATATATG
*
28868731 TAACCGTGGCATATCCACTTAGCACCACGTTACATGT
1 TAACCGTGGAATATCCACTTAGCACC-CGTTACATGT
28868768 ATCAATATGT
Statistics
Matches: 220, Mismatches: 34, Indels: 43
0.74 0.11 0.14
Matches are distributed among these distances:
71 4 0.02
72 4 0.02
73 4 0.02
74 9 0.04
75 5 0.02
76 27 0.12
77 2 0.01
78 26 0.12
79 4 0.02
80 10 0.05
81 4 0.02
82 3 0.01
83 4 0.02
84 27 0.12
85 87 0.40
ACGTcount: A:0.31, C:0.24, G:0.15, T:0.30
Consensus pattern (84 bp):
TAACCGTGGAATATCCACTTAGCACCCGTTACATGTTTAACCGTGGTATATCCACTTAGCACAAC
GTTAATGAATCAATATATG
Found at i:28868544 original size:38 final size:38
Alignment explanation
Indices: 28868492--28868767 Score: 208
Period size: 38 Copynumber: 7.0 Consensus size: 38
28868482 TCAATATATG
*
28868492 TAACCGTGGAATATCCATTTAGCACCACGTTACATGTT
1 TAACCGTGGAATATCCACTTAGCACCACGTTACATGTT
* *
28868530 TAACCGTGGTATATCCACTTAGCACAACGTTA-ATG--
1 TAACCGTGGAATATCCACTTAGCACCACGTTACATGTT
* *
28868565 -AA---T-GAATTATCCACTTAGCACCACATTAATGGATCAATATAT
1 TAACCGTGGAA-TATCCACTTAGCACCAC-GT--T--A-C-ATGT-T
* * *
28868607 GTAACCATGGCATATCCACTTAGCACCACGTTATATGTT
1 -TAACCGTGGAATATCCACTTAGCACCACGTTACATGTT
* *
28868646 TAATCGTGGCATATCCACTTAGCACCACGTTACATGTT
1 TAACCGTGGAATATCCACTTAGCACCACGTTACATGTT
* *
28868684 TAACCGTGGTATATCCACTTAGCACCACGTTAATGAATCAATATAT
1 TAACCGTGGAATATCCACTTAGCACCACG-T--T--A-C-ATGT-T
*
28868730 GTAACCGTGGCATATCCACTTAGCACCACGTTACATGT
1 -TAACCGTGGAATATCCACTTAGCACCACGTTACATGT
28868768 ATCAATATGT
Statistics
Matches: 192, Mismatches: 19, Indels: 52
0.73 0.07 0.20
Matches are distributed among these distances:
30 2 0.01
31 17 0.09
32 1 0.01
34 3 0.02
36 1 0.01
37 3 0.02
38 91 0.47
39 4 0.02
40 6 0.03
41 2 0.01
42 2 0.01
43 1 0.01
44 5 0.03
45 3 0.02
46 3 0.02
47 46 0.24
48 2 0.01
ACGTcount: A:0.31, C:0.24, G:0.15, T:0.30
Consensus pattern (38 bp):
TAACCGTGGAATATCCACTTAGCACCACGTTACATGTT
Found at i:28868611 original size:116 final size:119
Alignment explanation
Indices: 28868401--28868767 Score: 492
Period size: 116 Copynumber: 3.1 Consensus size: 119
28868391 TTTCAAATTA
* * * *
28868401 ACATGTATAACCGTGGCATATCCACTTAGTAC-CCGTTACATGTTTAACCGTGGTATATCCACTT
1 ACATGTTTAACCGTGGCATATCCACTTAGCACAACGTTACATG--TAA-C-TGATATATCCACTT
* *
28868465 AGCACCACGTTAATGAATCAATATATGTAACCGTGGAATATCCATTTAGCACCACGTT
62 AGCACCACGTTAATGAATCAATATATGTAACCGTGGCATATCCACTTAGCACCACGTT
*
28868523 ACATGTTTAACCGTGGTATATCCACTTAGCACAACGTTA-ATG-AA-TGA-ATTATCCACTTAGC
1 ACATGTTTAACCGTGGCATATCCACTTAGCACAACGTTACATGTAACTGATA-TATCCACTTAGC
* * *
28868584 ACCACATTAATGGATCAATATATGTAACCATGGCATATCCACTTAGCACCACGTT
65 ACCACGTTAATGAATCAATATATGTAACCGTGGCATATCCACTTAGCACCACGTT
* * * *
28868639 ATATGTTTAATCGTGGCATATCCACTTAGCACCACGTTACATGTTTAACCGTGGTATATCCACTT
1 ACATGTTTAACCGTGGCATATCCACTTAGCACAACGTTACATG--TAA-C-TGATATATCCACTT
28868704 AGCACCACGTTAATGAATCAATATATGTAACCGTGGCATATCCACTTAGCACCACGTT
62 AGCACCACGTTAATGAATCAATATATGTAACCGTGGCATATCCACTTAGCACCACGTT
28868762 ACATGT
1 ACATGT
28868768 ATCAATATGT
Statistics
Matches: 216, Mismatches: 19, Indels: 19
0.85 0.07 0.07
Matches are distributed among these distances:
115 1 0.00
116 99 0.46
117 3 0.01
119 2 0.01
120 2 0.01
122 32 0.15
123 76 0.35
124 1 0.00
ACGTcount: A:0.31, C:0.24, G:0.15, T:0.30
Consensus pattern (119 bp):
ACATGTTTAACCGTGGCATATCCACTTAGCACAACGTTACATGTAACTGATATATCCACTTAGCA
CCACGTTAATGAATCAATATATGTAACCGTGGCATATCCACTTAGCACCACGTT
Found at i:28868793 original size:48 final size:48
Alignment explanation
Indices: 28868684--28868817 Score: 173
Period size: 48 Copynumber: 2.8 Consensus size: 48
28868674 GTTACATGTT
* *
28868684 TAACCGTGGTATATCCACTTAGCACCACGTTA-ATGAATCAATATATG
1 TAACCGTAGTATATCCACTTAGCACCACGTTACATGTATCAATATATG
* * *
28868731 TAACCGTGGCATATCCACTTAGCACCACGTTACATGTATCAATATGTG
1 TAACCGTAGTATATCCACTTAGCACCACGTTACATGTATCAATATATG
* * *
28868779 TAATCC-TAGTATATCCATTTAGCACCACGCTACACGTAT
1 TAA-CCGTAGTATATCCACTTAGCACCACGTTACATGTAT
28868818 AACCGTGGTA
Statistics
Matches: 77, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
47 31 0.40
48 44 0.57
49 2 0.03
ACGTcount: A:0.31, C:0.25, G:0.14, T:0.30
Consensus pattern (48 bp):
TAACCGTAGTATATCCACTTAGCACCACGTTACATGTATCAATATATG
Found at i:28871591 original size:15 final size:15
Alignment explanation
Indices: 28871568--28871609 Score: 66
Period size: 15 Copynumber: 2.8 Consensus size: 15
28871558 GAAGCCCAGA
28871568 ATAAGGAAATCCAAG
1 ATAAGGAAATCCAAG
* *
28871583 ATAAAGAAATCCATG
1 ATAAGGAAATCCAAG
28871598 ATAAGGAAATCC
1 ATAAGGAAATCC
28871610 CATTTATAGC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.52, C:0.14, G:0.17, T:0.17
Consensus pattern (15 bp):
ATAAGGAAATCCAAG
Found at i:28874897 original size:38 final size:38
Alignment explanation
Indices: 28874855--28874931 Score: 109
Period size: 38 Copynumber: 2.0 Consensus size: 38
28874845 TTTCAAATTA
28874855 ACATGTATAACCGTGGCATATCCACTTAGAACCACGTT
1 ACATGTATAACCGTGGCATATCCACTTAGAACCACGTT
* * ** *
28874893 ACATGTTTAACCGTGGTATATCGGCTTAGCACCACGTT
1 ACATGTATAACCGTGGCATATCCACTTAGAACCACGTT
28874931 A
1 A
28874932 ATGAATTAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.29, C:0.25, G:0.18, T:0.29
Consensus pattern (38 bp):
ACATGTATAACCGTGGCATATCCACTTAGAACCACGTT
Found at i:28875009 original size:48 final size:48
Alignment explanation
Indices: 28874900--28875033 Score: 171
Period size: 48 Copynumber: 2.8 Consensus size: 48
28874890 GTTACATGTT
** * *
28874900 TAACCGTGGTATATCGGCTTAGCACCACGTTA-ATGAATTAATATATG
1 TAACCGTGGTATATCCACTTAGCACCACGTTACATGTATCAATATATG
* * *
28874947 TAACCATGGCATATCCACTTAGCACCACGTTACATGTATCAATATGTG
1 TAACCGTGGTATATCCACTTAGCACCACGTTACATGTATCAATATATG
** *
28874995 TAATTGTGGTATATCCACTTAGCACCACGTTACACGTAT
1 TAACCGTGGTATATCCACTTAGCACCACGTTACATGTAT
28875034 AACCGTGGTA
Statistics
Matches: 74, Mismatches: 12, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
47 28 0.38
48 46 0.62
ACGTcount: A:0.31, C:0.22, G:0.16, T:0.31
Consensus pattern (48 bp):
TAACCGTGGTATATCCACTTAGCACCACGTTACATGTATCAATATATG
Found at i:28880750 original size:50 final size:50
Alignment explanation
Indices: 28880687--28880924 Score: 253
Period size: 50 Copynumber: 4.7 Consensus size: 50
28880677 CAAAGCTTTC
* * *
28880687 TGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAATT
1 TGGTACACGTAGTAGCCTGCACTTAGTACTACACACGCGACCTATCAATT
* * * * *
28880737 TGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACTTAACCATA
1 TGGTACACGTAGTAGCCTGCACTTAGTACTACACACGCGACCTATCAATT
* ** * * ** *
28880787 TGATACACGTAGTAGCCTAAACTTATTACTACACACGTGATCGAAGTTAA-T
1 TGGTACACGTAGTAGCCTGCACTTAGTACTACACACGCGA-CCTA-TCAATT
* * * * *
28880838 GGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAATC
1 TGGTACACGTAGTAGCCTGCACTTAGTACTACACACGCGACCTATCAATT
*
28880888 TGGTACACGTTGTAGCCTGCACTTAGTACTACACACG
1 TGGTACACGTAGTAGCCTGCACTTAGTACTACACACG
28880925 TGACTCACAA
Statistics
Matches: 149, Mismatches: 36, Indels: 6
0.78 0.19 0.03
Matches are distributed among these distances:
49 3 0.02
50 112 0.75
51 33 0.22
52 1 0.01
ACGTcount: A:0.29, C:0.25, G:0.18, T:0.27
Consensus pattern (50 bp):
TGGTACACGTAGTAGCCTGCACTTAGTACTACACACGCGACCTATCAATT
Found at i:28880870 original size:101 final size:101
Alignment explanation
Indices: 28880746--28880927 Score: 265
Period size: 101 Copynumber: 1.8 Consensus size: 101
28880736 TTGGTACACG
* * *
28880746 TAGTAGCCTGCACTTAGTACTACACACGTGACTTAACCATATGATACACGTAGTAGCCTAAACTT
1 TAGTAGCCTGCACTTAGTACTACACACGCGACCTAACAATATGATACACGTAGTAGCCTAAACTT
*
28880811 ATTACTACACACGTGATCGAAGTTAATGGGTACGCA
66 AGTACTACACACGTGATCGAAGTTAATGGGTACGCA
* * * * * **
28880847 TAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAATCTGGTACACGTTGTAGCCTGCACTT
1 TAGTAGCCTGCACTTAGTACTACACACGCGACCTAACAATATGATACACGTAGTAGCCTAAACTT
28880912 AGTACTACACACGTGA
66 AGTACTACACACGTGA
28880928 CTCACAATGA
Statistics
Matches: 70, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
101 70 1.00
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.27
Consensus pattern (101 bp):
TAGTAGCCTGCACTTAGTACTACACACGCGACCTAACAATATGATACACGTAGTAGCCTAAACTT
AGTACTACACACGTGATCGAAGTTAATGGGTACGCA
Found at i:28883913 original size:15 final size:16
Alignment explanation
Indices: 28883889--28883931 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
28883879 ATAGATAACA
*
28883889 AGAAAACCAAGATTA-
1 AGAAATCCAAGATTAG
*
28883904 AGAAGTCCAAGA-TAG
1 AGAAATCCAAGATTAG
28883919 AGAAATCCAAGAT
1 AGAAATCCAAGAT
28883932 ACAATATCAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
14 2 0.09
15 21 0.91
ACGTcount: A:0.53, C:0.14, G:0.19, T:0.14
Consensus pattern (16 bp):
AGAAATCCAAGATTAG
Found at i:28887535 original size:50 final size:50
Alignment explanation
Indices: 28887449--28887844 Score: 355
Period size: 50 Copynumber: 7.9 Consensus size: 50
28887439 ACTGAAGCTC
*
28887449 TCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAA
1 TCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGTGACCTATCAA
* * * * ** * * *
28887499 TTTGGCACACGTAGTAGCCTGCACTTATTACTACACACATGACTTAACCA
1 TCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGTGACCTATCAA
* * ** ** *
28887549 TCTGATACACATAGTAGCCTACACTTAGTACTACACACATGATCGAAGTTAA
1 TCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGTGA-CCTA-TCAA
* * *
28887601 -CGGGTACGCATAGTAGCCTGCACTTAGTACTACACATATGACCTATCAA
1 TCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGTGACCTATCAA
* * * * * * *
28887650 TCTGGTACACGTAGTACCCTGCACTTAGTATTACATATGTGACTTAACCA
1 TCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGTGACCTATCAA
* * * * ** *
28887700 TCTGATACACATAGTAGACTACACTTAGTACTACACAAGTGATCGGAGTTAA
1 TCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGTGA-CCTA-TCAA
* ** * *
28887752 -CGGGTATGCATAATAGCCTGCACTTAGTACTACACATGCGACCTATCAA
1 TCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGTGACCTATCAA
* * * *
28887801 TCTGGTACACGTAGTAGCCTGTACTTAGTACTACGCACGTGACC
1 TCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGTGACC
28887845 CACAATGAAT
Statistics
Matches: 267, Mismatches: 73, Indels: 12
0.76 0.21 0.03
Matches are distributed among these distances:
49 6 0.02
50 187 0.70
51 72 0.27
52 2 0.01
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.27
Consensus pattern (50 bp):
TCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGTGACCTATCAA
Found at i:28887726 original size:151 final size:151
Alignment explanation
Indices: 28887452--28887843 Score: 606
Period size: 151 Copynumber: 2.6 Consensus size: 151
28887442 GAAGCTCTCT
* * *
28887452 GGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAATTTGGCACACGTAGTAGC
1 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAATCTGGTACACGTAGTAGC
* *
28887517 CTGCACTTATTACTACACACATGACTTAACCATCTGATACACATAGTAGCCTACACTTAGTACTA
66 CTGCACTTAGTACTACACACATGACTTAACCATCTGATACACATAGTAGACTACACTTAGTACTA
28887582 CACACA-TGATCGAAGTTAACG
131 CACA-AGTGATCGAAGTTAACG
** *
28887603 GGTACGCATAGTAGCCTGCACTTAGTACTACACATATGACCTATCAATCTGGTACACGTAGTACC
1 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAATCTGGTACACGTAGTAGC
* * **
28887668 CTGCACTTAGTATTACATATGTGACTTAACCATCTGATACACATAGTAGACTACACTTAGTACTA
66 CTGCACTTAGTACTACACACATGACTTAACCATCTGATACACATAGTAGACTACACTTAGTACTA
*
28887733 CACAAGTGATCGGAGTTAACG
131 CACAAGTGATCGAAGTTAACG
* *
28887754 GGTATGCATAATAGCCTGCACTTAGTACTACACATGCGACCTATCAATCTGGTACACGTAGTAGC
1 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAATCTGGTACACGTAGTAGC
* * *
28887819 CTGTACTTAGTACTACGCACGTGAC
66 CTGCACTTAGTACTACACACATGAC
28887844 CCACAATGAA
Statistics
Matches: 217, Mismatches: 23, Indels: 2
0.90 0.10 0.01
Matches are distributed among these distances:
150 1 0.00
151 216 1.00
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.27
Consensus pattern (151 bp):
GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAATCTGGTACACGTAGTAGC
CTGCACTTAGTACTACACACATGACTTAACCATCTGATACACATAGTAGACTACACTTAGTACTA
CACAAGTGATCGAAGTTAACG
Found at i:28888961 original size:26 final size:26
Alignment explanation
Indices: 28888910--28889058 Score: 203
Period size: 26 Copynumber: 5.8 Consensus size: 26
28888900 CTCTTTTAAT
* *
28888910 AACTGGGGCA-AAGCCCTTGTCGGTA
1 AACTGGGGCATAAGCCCTTTTCAGTA
*
28888935 AACTGGGGCATAAGCCCCTTTCAGTA
1 AACTGGGGCATAAGCCCTTTTCAGTA
* * *
28888961 AACTGGGGCATAAGTCCTTTTCAATG
1 AACTGGGGCATAAGCCCTTTTCAGTA
* *
28888987 AACTAGGGCATAAGCCCTTTTCGGTA
1 AACTGGGGCATAAGCCCTTTTCAGTA
*
28889013 AACTGGGGCATAAGCCCTTTTCAATA
1 AACTGGGGCATAAGCCCTTTTCAGTA
28889039 AACTGGGGCAT-AGCCCTTTT
1 AACTGGGGCATAAGCCCTTTT
28889059 GCACTTCCTC
Statistics
Matches: 108, Mismatches: 15, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
25 19 0.18
26 89 0.82
ACGTcount: A:0.26, C:0.23, G:0.24, T:0.26
Consensus pattern (26 bp):
AACTGGGGCATAAGCCCTTTTCAGTA
Found at i:28889005 original size:78 final size:74
Alignment explanation
Indices: 28888887--28889058 Score: 236
Period size: 78 Copynumber: 2.2 Consensus size: 74
28888877 TATCATATAT
* *
28888887 CTGGAGGCCTAGCCTCTTTTAATAACTGGGGCAAAGCCCTTGTCGGTAAACTGGGGCATAAGCCC
1 CTGG-GGCATAGCC-CTTTTAATAACTAGGGCAAAGCCCTTGTCGGTAAACTGGGGCATAAGCCC
*
28888952 CTTTCAGTAAA
64 CTTTCAATAAA
* *
28888963 CTGGGGCATAAGTCCTTTTCAATGAACTAGGGCATAAGCCCTTTTCGGTAAACTGGGGCATAAGC
1 CTGGGGCAT-AGCCCTTTT-AAT-AACTAGGGCA-AAGCCCTTGTCGGTAAACTGGGGCATAAGC
*
28889028 CCTTTTCAATAAA
62 CCCTTTCAATAAA
28889041 CTGGGGCATAGCCCTTTT
1 CTGGGGCATAGCCCTTTT
28889059 GCACTTCCTC
Statistics
Matches: 85, Mismatches: 7, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
75 9 0.11
76 10 0.12
77 17 0.20
78 49 0.58
ACGTcount: A:0.25, C:0.24, G:0.24, T:0.27
Consensus pattern (74 bp):
CTGGGGCATAGCCCTTTTAATAACTAGGGCAAAGCCCTTGTCGGTAAACTGGGGCATAAGCCCCT
TTCAATAAA
Found at i:28889141 original size:11 final size:11
Alignment explanation
Indices: 28889108--28889165 Score: 52
Period size: 11 Copynumber: 5.6 Consensus size: 11
28889098 TAATGATTAC
*
28889108 ATCATGTGCAT
1 ATCATATGCAT
*
28889119 TTCATA--CAT
1 ATCATATGCAT
*
28889128 ATCATATGCGT
1 ATCATATGCAT
28889139 ATCATA--CAT
1 ATCATATGCAT
*
28889148 ATCATGTGCAT
1 ATCATATGCAT
28889159 ATCATAT
1 ATCATAT
28889166 CATTCATGTA
Statistics
Matches: 36, Mismatches: 7, Indels: 8
0.71 0.14 0.16
Matches are distributed among these distances:
9 15 0.42
11 21 0.58
ACGTcount: A:0.33, C:0.19, G:0.10, T:0.38
Consensus pattern (11 bp):
ATCATATGCAT
Found at i:28889172 original size:20 final size:20
Alignment explanation
Indices: 28889108--28889174 Score: 91
Period size: 20 Copynumber: 3.4 Consensus size: 20
28889098 TAATGATTAC
*
28889108 ATCATGTGCATTTCATACAT
1 ATCATGTGCATATCATACAT
* *
28889128 ATCATATGCGTATCATACAT
1 ATCATGTGCATATCATACAT
28889148 ATCATGTGCATATCATATCAT
1 ATCATGTGCATATCATA-CAT
28889169 -TCATGT
1 ATCATGT
28889175 ACATCATATC
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
20 38 0.93
21 3 0.07
ACGTcount: A:0.31, C:0.19, G:0.10, T:0.39
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Found at i:28896150 original size:40 final size:39
Alignment explanation
Indices: 28896066--28896250 Score: 203
Period size: 40 Copynumber: 4.6 Consensus size: 39
28896056 TTGAATGATG
* * * *
28896066 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
28896106 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCGAAGGCATTTGTGCGAGTTACTAAA
*
28896146 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
* *
28896185 TCCGGGTTAAGTCTCGAAGGCAATTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTC-CGAAGGCATTTGTGCGAGTTACTA-AA
*
28896226 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGT-CCGAAGGCATTTG
28896251 AACGAGTAGC
Statistics
Matches: 123, Mismatches: 17, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
39 36 0.29
40 76 0.62
41 11 0.09
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (39 bp):
TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:28896203 original size:79 final size:81
Alignment explanation
Indices: 28896066--28896250 Score: 227
Period size: 79 Copynumber: 2.3 Consensus size: 81
28896056 TTGAATGATG
* *
28896066 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAAT
28896130 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * * **
28896145 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCTCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATC-CGAAGGCA
*
28896207 ATTGTGCGAGTTACTATA
64 ATTGTGCGAGATACTATA
* *
28896225 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
28896251 AACGAGTAGC
Statistics
Matches: 91, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 2 0.02
79 56 0.62
80 33 0.36
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAAT
TGTGCGAGATACTATA
Found at i:28896272 original size:79 final size:78
Alignment explanation
Indices: 28896067--28896273 Score: 197
Period size: 79 Copynumber: 2.6 Consensus size: 78
28896057 TGAATGATGT
** * * * * *
28896067 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTT
1 CCGGGCTAAG-CCCGAAGGCATTTGAAC-GAGTTACTATATCCGG-TTAAGATCCGAAGGCAATT
*
28896131 GTGCGAGATACTAATT
63 GTGCGAGATACTAATA
** *
28896147 CCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAG-TCTCGAAGGCAATTG
1 CCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTATATCC-GGTTAAGATC-CGAAGGCAATTG
*
28896211 TGCGAGTTACT-ATAA
64 TGCGAGATACTAAT-A
*
28896226 CCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGCTATATCCGGTTAA
1 CCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-CTATATCCGGTTAA
28896274 ATTCTGAAGG
Statistics
Matches: 109, Mismatches: 12, Indels: 13
0.81 0.09 0.10
Matches are distributed among these distances:
78 4 0.04
79 61 0.56
80 44 0.40
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (78 bp):
CCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTATATCCGGTTAAGATCCGAAGGCAATTGTG
CGAGATACTAATA
Found at i:28913996 original size:43 final size:42
Alignment explanation
Indices: 28913933--28914055 Score: 140
Period size: 43 Copynumber: 2.9 Consensus size: 42
28913923 AGCTTGTACA
* * * *
28913933 ATGCCATATCCCAGATATGGTCTTACATGTCAAT-ACATTTCG
1 ATGCCATGTCCCAGACATGGTCTTACACGT-AATCACACTTCG
* *
28913975 ATGCCACTGTCCCAGACATGGTCTTACACGTTATCTCACTTCG
1 ATGCCA-TGTCCCAGACATGGTCTTACACGTAATCACACTTCG
* *
28914018 ATGCCAATGTCTCAGACATGGTCTTACACGAAATCACA
1 ATGCC-ATGTCCCAGACATGGTCTTACACGTAATCACA
28914056 TCTCAGAAAT
Statistics
Matches: 68, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
42 8 0.12
43 59 0.87
44 1 0.01
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.29
Consensus pattern (42 bp):
ATGCCATGTCCCAGACATGGTCTTACACGTAATCACACTTCG
Found at i:28926338 original size:22 final size:22
Alignment explanation
Indices: 28926281--28926345 Score: 76
Period size: 22 Copynumber: 3.0 Consensus size: 22
28926271 CTCCGATTAT
* *
28926281 TAGCACATTAGTGCTCTCCGTT
1 TAGCACATTAGTGCTCTCTGTA
* **
28926303 TAACACATCCGTGCTCTCTGTA
1 TAGCACATTAGTGCTCTCTGTA
*
28926325 TAGCACTTTAGTGCTCTCTGT
1 TAGCACATTAGTGCTCTCTGT
28926346 TCAATAGGGC
Statistics
Matches: 34, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.18, C:0.28, G:0.17, T:0.37
Consensus pattern (22 bp):
TAGCACATTAGTGCTCTCTGTA
Found at i:28928769 original size:80 final size:80
Alignment explanation
Indices: 28928627--28928872 Score: 298
Period size: 80 Copynumber: 3.1 Consensus size: 80
28928617 AATTATTGTA
* *
28928627 TGAATGCACATACGTGCCCC-AGTTTGTACTTCGGTACCCCTGA-TGTCACATACGTGCTCCTAT
1 TGAATGCACATACGTGCCCCTA-TTTGTACTTCGGTACCCCTGATTG-CACATATGTGCCCCTAT
*
28928690 TTGTACTTTGATACCCC
64 TTGTACTTCGATACCCC
* * * * **
28928707 TAAATGCACATTCGTGCCCCTATTTGTATTTTGGTACTGCTGATTGCACATATGTGCCCCTATTT
1 TGAATGCACATACGTGCCCCTATTTGTACTTCGGTACCCCTGATTGCACATATGTGCCCCTATTT
*
28928772 GTACTTCAATACCCC
66 GTACTTCGATACCCC
* * * * * ** *
28928787 TGAATTCACATACGTGCCCCTTTTTGTACTTCAGTACCCCTGATTGTACATTTGTGCCTATGTTT
1 TGAATGCACATACGTGCCCCTATTTGTACTTCGGTACCCCTGATTGCACATATGTGCCCCTATTT
28928852 GTACTTCGATACCCC
66 GTACTTCGATACCCC
28928867 TGAATG
1 TGAATG
28928873 TACTCAATAC
Statistics
Matches: 138, Mismatches: 26, Indels: 4
0.82 0.15 0.02
Matches are distributed among these distances:
80 135 0.98
81 3 0.02
ACGTcount: A:0.20, C:0.27, G:0.16, T:0.36
Consensus pattern (80 bp):
TGAATGCACATACGTGCCCCTATTTGTACTTCGGTACCCCTGATTGCACATATGTGCCCCTATTT
GTACTTCGATACCCC
Found at i:28928833 original size:20 final size:20
Alignment explanation
Indices: 28928810--28928888 Score: 56
Period size: 20 Copynumber: 4.0 Consensus size: 20
28928800 GTGCCCCTTT
28928810 TTGTACTTCAGTACCCCTGA
1 TTGTACTTCAGTACCCCTGA
* * ** *
28928830 TTGTACATT-TGTGCCTATGT
1 TTGTAC-TTCAGTACCCCTGA
28928850 TTGTACTTC-GATACCCCTGA
1 TTGTACTTCAG-TACCCCTGA
* *
28928870 ATGTAC-TCAATACCCCTGA
1 TTGTACTTCAGTACCCCTGA
28928889 ATGCACTTAC
Statistics
Matches: 44, Mismatches: 11, Indels: 9
0.69 0.17 0.14
Matches are distributed among these distances:
19 14 0.32
20 28 0.64
21 2 0.05
ACGTcount: A:0.22, C:0.27, G:0.15, T:0.37
Consensus pattern (20 bp):
TTGTACTTCAGTACCCCTGA
Found at i:28928853 original size:120 final size:120
Alignment explanation
Indices: 28928631--28928854 Score: 283
Period size: 120 Copynumber: 1.9 Consensus size: 120
28928621 ATTGTATGAA
** *
28928631 TGCACATACGTGCCCCAGTTTGTACTTCGGTACCCCTGATGTCACATACGTGCTCCTATTTGTAC
1 TGCACATACGTGCCCCAGTTTGTACTTCAATACCCCTGATGTCACATACGTGCCCCTATTTGTAC
* *
28928696 TTTGATACCCCTAAATGCACATTCGTGCCCCTATTTGTATTTTGGTACTGCTGAT
66 TTAGATACCCCTAAATGCACATTCGTGCCCATATTTGTATTTTGGTACTGCTGAT
* *
28928751 TGCACATATGTGCCCCTA-TTTGTACTTCAATACCCCTGAAT-TCACATACGTGCCCCTTTTTGT
1 TGCACATACGTGCCCC-AGTTTGTACTTCAATACCCCTG-ATGTCACATACGTGCCCCTATTTGT
* * * * * *
28928814 ACTTCAG-TACCCCTGATTGTACATTTGTGCCTATGTTTGTA
64 ACTT-AGATACCCCTAAATGCACATTCGTGCCCATATTTGTA
28928855 CTTCGATACC
Statistics
Matches: 88, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
120 84 0.95
121 4 0.05
ACGTcount: A:0.20, C:0.27, G:0.16, T:0.37
Consensus pattern (120 bp):
TGCACATACGTGCCCCAGTTTGTACTTCAATACCCCTGATGTCACATACGTGCCCCTATTTGTAC
TTAGATACCCCTAAATGCACATTCGTGCCCATATTTGTATTTTGGTACTGCTGAT
Found at i:28928875 original size:40 final size:40
Alignment explanation
Indices: 28928627--28928875 Score: 227
Period size: 40 Copynumber: 6.2 Consensus size: 40
28928617 AATTATTGTA
* *
28928627 TGAATGCACATACGTGCCCC-AGTTTGTACTTCGGTACCCC
1 TGAATGTACATACGTGCCCCTA-TTTGTACTTCGATACCCC
* *
28928667 TG-ATGTCACATACGTGCTCCTATTTGTACTTTGATACCCC
1 TGAATGT-ACATACGTGCCCCTATTTGTACTTCGATACCCC
* * * * * * **
28928707 TAAATGCACATTCGTGCCCCTATTTGTATTTTGGTACTGC
1 TGAATGTACATACGTGCCCCTATTTGTACTTCGATACCCC
* * * *
28928747 TGATTGCACATATGTGCCCCTATTTGTACTTCAATACCCC
1 TGAATGTACATACGTGCCCCTATTTGTACTTCGATACCCC
*
28928787 TGAAT-TCACATACGTGCCCCTTTTTGTACTTC-AGTACCCC
1 TGAATGT-ACATACGTGCCCCTATTTGTACTTCGA-TACCCC
* ** ** *
28928827 TGATTGTACATTTGTGCCTATGTTTGTACTTCGATACCCC
1 TGAATGTACATACGTGCCCCTATTTGTACTTCGATACCCC
28928867 TGAATGTAC
1 TGAATGTAC
28928876 TCAATACCCC
Statistics
Matches: 169, Mismatches: 33, Indels: 14
0.78 0.15 0.06
Matches are distributed among these distances:
39 4 0.02
40 159 0.94
41 6 0.04
ACGTcount: A:0.20, C:0.27, G:0.16, T:0.36
Consensus pattern (40 bp):
TGAATGTACATACGTGCCCCTATTTGTACTTCGATACCCC
Found at i:28936300 original size:16 final size:16
Alignment explanation
Indices: 28936279--28936347 Score: 129
Period size: 16 Copynumber: 4.2 Consensus size: 16
28936269 TTTGGTTCGC
28936279 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
28936295 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
28936311 TGTATTGGGATTAGAGG
1 TGTATT-GGATTAGAGG
28936328 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
28936344 TGTA
1 TGTA
28936348 ATAGCTAATC
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
16 36 0.69
17 16 0.31
ACGTcount: A:0.25, C:0.00, G:0.38, T:0.38
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:28936325 original size:33 final size:32
Alignment explanation
Indices: 28936279--28936347 Score: 129
Period size: 33 Copynumber: 2.1 Consensus size: 32
28936269 TTTGGTTCGC
28936279 TGTATTGGATTAGAGGTGTATTGGATTAGAGG
1 TGTATTGGATTAGAGGTGTATTGGATTAGAGG
28936311 TGTATTGGGATTAGAGGTGTATTGGATTAGAGG
1 TGTATT-GGATTAGAGGTGTATTGGATTAGAGG
28936344 TGTA
1 TGTA
28936348 ATAGCTAATC
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 6 0.17
33 30 0.83
ACGTcount: A:0.25, C:0.00, G:0.38, T:0.38
Consensus pattern (32 bp):
TGTATTGGATTAGAGGTGTATTGGATTAGAGG
Found at i:28936412 original size:44 final size:45
Alignment explanation
Indices: 28936328--28936418 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
28936318 GGATTAGAGG
* * *
28936328 TGTATTGGATTAGAGGTGTAATAGCTAATCCACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
***
28936373 TGTAATGGAATAGAGGCGTAATAG-TAATCTTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
28936417 TG
1 TG
28936419 GAATAGAGGT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 19 0.47
45 21 0.52
ACGTcount: A:0.27, C:0.07, G:0.29, T:0.37
Consensus pattern (45 bp):
TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
Found at i:28936604 original size:18 final size:17
Alignment explanation
Indices: 28936583--28936617 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
28936573 TTATTATTAA
*
28936583 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
28936601 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
28936618 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:28936703 original size:120 final size:120
Alignment explanation
Indices: 28936566--28937668 Score: 2071
Period size: 120 Copynumber: 9.2 Consensus size: 120
28936556 ATCATATTTA
28936566 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
28936631 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
*
28936686 AACATAATTATTATTAAATATATTTTAATTAAACTATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
28936751 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
*
28936806 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATGAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
28936871 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
*
28936926 AACATAATTATTATTAAATATATTTTAATTAAACTATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
* *
28936991 TATTCTTATATTAATTTATTGAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
* *
28937046 AACATAATTATTATTAAATATATTTTATTTAAAATATATAATTTAATGAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
*
28937111 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
*
28937166 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATGAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
28937231 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
*
28937286 AACATAATTATTATTAAATATATTTTAATTAAACTATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
28937351 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
* * *
28937406 AACATATTTATTATTAAATATATTTTAATTAAAATATATAATTTAATGAAATTCTTAATCATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
28937471 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
*
28937526 AACATAATTATTATTAAATATATTTTAATTAAACTATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
28937591 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
*
28937646 AACATATTTATTATTAAATATAT
1 AACATAATTATTATTAAATATAT
28937669 AACTTGAAAA
Statistics
Matches: 959, Mismatches: 24, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
120 959 1.00
ACGTcount: A:0.47, C:0.06, G:0.02, T:0.45
Consensus pattern (120 bp):
AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
Found at i:28940986 original size:8 final size:9
Alignment explanation
Indices: 28940966--28941000 Score: 63
Period size: 9 Copynumber: 4.0 Consensus size: 9
28940956 ATATTACAAC
28940966 AAAAATTTA
1 AAAAATTTA
28940975 AAAAATTTA
1 AAAAATTTA
28940984 AAAAATTT-
1 AAAAATTTA
28940992 AAAAATTTA
1 AAAAATTTA
28941001 GAAGAGTGGA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
8 8 0.32
9 17 0.68
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (9 bp):
AAAAATTTA
Found at i:28940989 original size:18 final size:17
Alignment explanation
Indices: 28940966--28941000 Score: 61
Period size: 17 Copynumber: 2.0 Consensus size: 17
28940956 ATATTACAAC
28940966 AAAAATTTAAAAAATTTA
1 AAAAATTT-AAAAATTTA
28940984 AAAAATTTAAAAATTTA
1 AAAAATTTAAAAATTTA
28941001 GAAGAGTGGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
AAAAATTTAAAAATTTA
Found at i:28947212 original size:20 final size:20
Alignment explanation
Indices: 28947189--28947231 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
28947179 AAAAATTAAA
28947189 AAAAAATCAAAATAATTTTT
1 AAAAAATCAAAATAATTTTT
** *
28947209 AAAATTTTAAAATAATTTTT
1 AAAAAATCAAAATAATTTTT
28947229 AAA
1 AAA
28947232 GTTCAAAATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (20 bp):
AAAAAATCAAAATAATTTTT
Found at i:28947258 original size:20 final size:19
Alignment explanation
Indices: 28947195--28947311 Score: 70
Period size: 19 Copynumber: 6.4 Consensus size: 19
28947185 TAAAAAAAAA
28947195 TCAAAATAATTTTTAAAATT
1 TCAAAATAA-TTTTAAAATT
* * *
28947215 TTAAAATAATTTTTAAAGT
1 TCAAAATAATTTTAAAATT
28947234 TCAAAAT-ATTTATAAGAATT
1 TCAAAATAATTT-TAA-AATT
28947254 TC---A-AATTTT-AAATT
1 TCAAAATAATTTTAAAATT
* *
28947268 T-AAAA-AATTATAAAAAT
1 TCAAAATAATTTTAAAATT
* *
28947285 TCTAAAATAAATATAAAATT
1 TC-AAAATAATTTTAAAATT
*
28947305 TTAAAAT
1 TCAAAAT
28947312 TTTTCTAAAA
Statistics
Matches: 76, Mismatches: 11, Indels: 21
0.70 0.10 0.19
Matches are distributed among these distances:
14 5 0.07
15 1 0.01
16 7 0.09
17 10 0.13
18 4 0.05
19 25 0.33
20 24 0.32
ACGTcount: A:0.54, C:0.03, G:0.02, T:0.41
Consensus pattern (19 bp):
TCAAAATAATTTTAAAATT
Found at i:28948398 original size:15 final size:15
Alignment explanation
Indices: 28948378--28948407 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
28948368 ATCAATTTAA
*
28948378 TTATTTTTAAATTTT
1 TTATTTTAAAATTTT
28948393 TTATTTTAAAATTTT
1 TTATTTTAAAATTTT
28948408 AATCTAATAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (15 bp):
TTATTTTAAAATTTT
Found at i:28950226 original size:28 final size:28
Alignment explanation
Indices: 28950186--28950239 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
28950176 TTTAGTAAAT
*
28950186 GTTTCACCTGTCAACATATGAAGAGCAA
1 GTTTCAACTGTCAACATATGAAGAGCAA
28950214 GTTTCAACTGTCAACATATGAAGAGC
1 GTTTCAACTGTCAACATATGAAGAGC
28950240 TTAGGGCCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.26
Consensus pattern (28 bp):
GTTTCAACTGTCAACATATGAAGAGCAA
Found at i:28950794 original size:31 final size:31
Alignment explanation
Indices: 28950759--28950817 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
28950749 AGGCATAAGC
* *
28950759 TAAATGTTGAGAGCTTATTTGGGTACAATTT
1 TAAATGTTGAGAACTTATTTGAGTACAATTT
28950790 TAAATGTTGAGAACTTATTTGAGTACAA
1 TAAATGTTGAGAACTTATTTGAGTACAA
28950818 GATAAAAGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.34, C:0.07, G:0.20, T:0.39
Consensus pattern (31 bp):
TAAATGTTGAGAACTTATTTGAGTACAATTT
Found at i:28956417 original size:116 final size:121
Alignment explanation
Indices: 28956274--28956508 Score: 329
Period size: 126 Copynumber: 1.9 Consensus size: 121
28956264 TAAATATAAA
*
28956274 ATATTTTATATTAAATTAATTTAATATTTTATAATAA-ATTAT-A-TTAAAATATTTTA-TTTTA
1 ATATTTTATATCAAATTAATTTAATATTTTATAATAATATTATAATTTAAAATATTTTATTTTTA
*
28956335 TATTATT-TGAAATTTGGAAATAATATTTTATATTAAATTATATTAAAATATTTAAC
66 TATT-TTCTAAAATTTGGAAATAATATTTTATATTAAATTATATTAAAATATTTAAC
* *
28956391 ATATTTTATA-CAAATTAATTTTATATTTTATATTAAGTTATTATAAAAGATTTAAAATATTTTA
1 ATATTTTATATCAAATTAATTTAATATTTTATAATAA--TATTAT---A-ATTTAAAATATTTTA
28956455 TTTTTATATTTTCTAAAATTTGGAAATAATATTTTATATTAAATTATATTAAAA
60 TTTTTATATTTTCTAAAATTTGGAAATAATATTTTATATTAAATTATATTAAAA
28956509 GTTTTTTTTA
Statistics
Matches: 103, Mismatches: 4, Indels: 13
0.86 0.03 0.11
Matches are distributed among these distances:
116 23 0.22
117 10 0.10
119 5 0.05
124 1 0.01
125 15 0.15
126 49 0.48
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.52
Consensus pattern (121 bp):
ATATTTTATATCAAATTAATTTAATATTTTATAATAATATTATAATTTAAAATATTTTATTTTTA
TATTTTCTAAAATTTGGAAATAATATTTTATATTAAATTATATTAAAATATTTAAC
Found at i:28966546 original size:19 final size:18
Alignment explanation
Indices: 28966510--28966549 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
28966500 TTTCCACTCG
*
28966510 TTTCTTTTTCAACTTCTC
1 TTTCTTTTTCAACATCTC
*
28966528 TTTCTTTTTCCACAATCTC
1 TTTCTTTTTCAAC-ATCTC
28966547 TTT
1 TTT
28966550 GTTTGTTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.12, C:0.28, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTCTTTTTCAACATCTC
Found at i:28967626 original size:13 final size:14
Alignment explanation
Indices: 28967608--28967642 Score: 63
Period size: 13 Copynumber: 2.6 Consensus size: 14
28967598 AAAACTAGCT
28967608 TTTTTTTTCACG-A
1 TTTTTTTTCACGAA
28967621 TTTTTTTTCACGAA
1 TTTTTTTTCACGAA
28967635 TTTTTTTT
1 TTTTTTTT
28967643 TCAACTTGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 12 0.57
14 9 0.43
ACGTcount: A:0.14, C:0.11, G:0.06, T:0.69
Consensus pattern (14 bp):
TTTTTTTTCACGAA
Found at i:28967627 original size:15 final size:14
Alignment explanation
Indices: 28967607--28967645 Score: 62
Period size: 13 Copynumber: 2.8 Consensus size: 14
28967597 CAAAACTAGC
28967607 TTTTTTTTTCACGA
1 TTTTTTTTTCACGA
28967621 -TTTTTTTTCACGAA
1 TTTTTTTTTCACG-A
28967635 TTTTTTTTTCA
1 TTTTTTTTTCA
28967646 ACTTGATATC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 12 0.52
14 1 0.04
15 10 0.43
ACGTcount: A:0.15, C:0.13, G:0.05, T:0.67
Consensus pattern (14 bp):
TTTTTTTTTCACGA
Found at i:28988494 original size:37 final size:38
Alignment explanation
Indices: 28988437--28988520 Score: 116
Period size: 37 Copynumber: 2.2 Consensus size: 38
28988427 CACAGAGCAT
* * **
28988437 GAATATCACTGGCACAAAGCCTGCTAGACACGGAGCCC
1 GAATATCACTGACACAAAGCCTGCTAAACACAAAGCCC
28988475 GAATATCAC-GACACAAAGCCTGCTAAACACAAAGCCC
1 GAATATCACTGACACAAAGCCTGCTAAACACAAAGCCC
*
28988512 AAATATCAC
1 GAATATCAC
28988521 CACGTTTCTA
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
37 32 0.78
38 9 0.22
ACGTcount: A:0.39, C:0.31, G:0.17, T:0.13
Consensus pattern (38 bp):
GAATATCACTGACACAAAGCCTGCTAAACACAAAGCCC
Found at i:28989989 original size:13 final size:13
Alignment explanation
Indices: 28989971--28989996 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
28989961 AGGTATAGGG
28989971 TTTTTGCATGATT
1 TTTTTGCATGATT
28989984 TTTTTGCATGATT
1 TTTTTGCATGATT
28989997 CTTGATTTTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.08, G:0.15, T:0.62
Consensus pattern (13 bp):
TTTTTGCATGATT
Found at i:28990524 original size:40 final size:41
Alignment explanation
Indices: 28990463--28990578 Score: 155
Period size: 40 Copynumber: 2.9 Consensus size: 41
28990453 AGAAAAATGA
* *
28990463 TGAATTGCACATATGTTCCCCTATTTGTACTTCGATACCC-
1 TGAATTGCACATACGTGCCCCTATTTGTACTTCGATACCCT
*
28990503 TGAATTGCACATACGTGCCCCTGTTTGTACTTCGATACCCT
1 TGAATTGCACATACGTGCCCCTATTTGTACTTCGATACCCT
* * *
28990544 TGAATTACACACACGTGCCCCTGATTAG-ACTTCGA
1 TGAATTGCACATACGTGCCCCT-ATTTGTACTTCGA
28990579 AAATTCTGAA
Statistics
Matches: 67, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
40 37 0.55
41 27 0.40
42 3 0.04
ACGTcount: A:0.23, C:0.28, G:0.16, T:0.33
Consensus pattern (41 bp):
TGAATTGCACATACGTGCCCCTATTTGTACTTCGATACCCT
Found at i:28990576 original size:41 final size:40
Alignment explanation
Indices: 28990480--28990578 Score: 128
Period size: 41 Copynumber: 2.5 Consensus size: 40
28990470 CACATATGTT
* * * *
28990480 CCCCTATTTGTACTTCGATACCCTGAATTGCACATACGTG
1 CCCCTGTTAGTACTTCGATACCCTGAATTACACACACGTG
*
28990520 CCCCTGTTTGTACTTCGATACCCTTGAATTACACACACGTG
1 CCCCTGTTAGTACTTCGATACCC-TGAATTACACACACGTG
28990561 CCCCTGATTAG-ACTTCGA
1 CCCCTG-TTAGTACTTCGA
28990579 AAATTCTGAA
Statistics
Matches: 53, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
40 22 0.42
41 28 0.53
42 3 0.06
ACGTcount: A:0.22, C:0.31, G:0.15, T:0.31
Consensus pattern (40 bp):
CCCCTGTTAGTACTTCGATACCCTGAATTACACACACGTG
Found at i:28996812 original size:49 final size:49
Alignment explanation
Indices: 28996752--28997257 Score: 772
Period size: 47 Copynumber: 10.6 Consensus size: 49
28996742 GATAATTGTG
*
28996752 ATGTG-AA-TGTATATATATGTGATAAGGCCTAATGGCCGGTGTGATGA
1 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
*
28996799 ATGTGAAAGTG--TATATATGTGATAAGGCCGAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
28996846 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGTGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATATGTGATAAGGCCTAA--TGGCCGATGTGATGA
28996897 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
28996946 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
*
28996995 ATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGCTGTGATGA
1 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
28997042 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
* *
28997091 ATGTGAAAGTG--TATATATGTGATGAGGCCTAATAGCCGATGTGATGA
1 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
*
28997138 ATGTGAAAGTG--TATATATGTGATGAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
* * * * * *
28997185 ATGTGAAAGTG--TATATATGTGA-CAGAGCCGAGTGGCCAACGTGATGG
1 ATGTGAAAGTGTATATATATGTGATAAG-GCCTAATGGCCGATGTGATGA
28997232 ATGTGAAAGTGTATA-A-ATGTGATAAG
1 ATGTGAAAGTGTATATATATGTGATAAG
28997258 TCCCGAAGGG
Statistics
Matches: 432, Mismatches: 15, Indels: 23
0.92 0.03 0.05
Matches are distributed among these distances:
46 2 0.00
47 231 0.53
48 5 0.01
49 145 0.34
51 49 0.11
ACGTcount: A:0.32, C:0.08, G:0.30, T:0.30
Consensus pattern (49 bp):
ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
Found at i:28996859 original size:96 final size:96
Alignment explanation
Indices: 28996752--28997257 Score: 810
Period size: 96 Copynumber: 5.3 Consensus size: 96
28996742 GATAATTGTG
*
28996752 ATGTG-AA-TGTATATATATGTGATAAGGCCTAATGGCCGGTGTGATGAATGTGAAAGTGTATAT
1 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
*
28996815 ATGTGATAAGGCCGAATGGCCGATGTGATGA
66 ATGTGATAAGGCCTAATGGCCGATGTGATGA
28996846 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGTGGCCGATGTGATGAATGTGAAAGTGTAT
1 ATGTGAAAGTGTATATATATGTGATAAGGCCTAA--TGGCCGATGTGATGAATGTGAAAGTG--T
28996911 ATATATGTGATAAGGCCTAATGGCCGATGTGATGA
62 ATATATGTGATAAGGCCTAATGGCCGATGTGATGA
28996946 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
1 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
*
28997011 ATGTGATAAGGCCTAATGGCCGCTGTGATGA
66 ATGTGATAAGGCCTAATGGCCGATGTGATGA
28997042 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
1 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
* *
28997107 ATGTGATGAGGCCTAATAGCCGATGTGATGA
66 ATGTGATAAGGCCTAATGGCCGATGTGATGA
*
28997138 ATGTGAAAGTG--TATATATGTGATGAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
1 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
* * * * * *
28997201 ATGTGA-CAGAGCCGAGTGGCCAACGTGATGG
66 ATGTGATAAG-GCCTAATGGCCGATGTGATGA
28997232 ATGTGAAAGTGTATA-A-ATGTGATAAG
1 ATGTGAAAGTGTATATATATGTGATAAG
28997258 TCCCGAAGGG
Statistics
Matches: 388, Mismatches: 15, Indels: 18
0.92 0.04 0.04
Matches are distributed among these distances:
93 2 0.01
94 97 0.25
95 3 0.01
96 166 0.43
98 51 0.13
100 69 0.18
ACGTcount: A:0.32, C:0.08, G:0.30, T:0.30
Consensus pattern (96 bp):
ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
ATGTGATAAGGCCTAATGGCCGATGTGATGA
Found at i:29003953 original size:27 final size:27
Alignment explanation
Indices: 29003917--29004075 Score: 161
Period size: 27 Copynumber: 6.1 Consensus size: 27
29003907 AAAGGTCAAT
*
29003917 AAATGACCAAAATACCCCTATAGGGTA
1 AAATGACCAAAATACCCCCATAGGGTA
*
29003944 AAATGACCAAAAT-------TAAGGTA
1 AAATGACCAAAATACCCCCATAGGGTA
* * *
29003964 AAATGATCGAGATACCCCCATAGGGTA
1 AAATGACCAAAATACCCCCATAGGGTA
** *
29003991 AGCTGACCAAGATACCCCCATAGGGTA
1 AAATGACCAAAATACCCCCATAGGGTA
* *
29004018 AAATGACCGAAATATCCCCATAGGGTA
1 AAATGACCAAAATACCCCCATAGGGTA
* *
29004045 AGATGACCGAAATACCCCCATAGGGTA
1 AAATGACCAAAATACCCCCATAGGGTA
29004072 AAAT
1 AAAT
29004076 AACTATTATA
Statistics
Matches: 108, Mismatches: 17, Indels: 14
0.78 0.12 0.10
Matches are distributed among these distances:
20 16 0.15
27 92 0.85
ACGTcount: A:0.42, C:0.22, G:0.19, T:0.18
Consensus pattern (27 bp):
AAATGACCAAAATACCCCCATAGGGTA
Found at i:29004042 original size:54 final size:54
Alignment explanation
Indices: 29003960--29004075 Score: 180
Period size: 54 Copynumber: 2.1 Consensus size: 54
29003950 CCAAAATTAA
* * *
29003960 GGTAAAATGATCGAGATACCCCCATAGGGTAAGCTGACC-AAGATACCCCCATAG
1 GGTAAAATGACCGAAATACCCCCATAGGGTAAGATGACCGAA-ATACCCCCATAG
*
29004014 GGTAAAATGACCGAAATATCCCCATAGGGTAAGATGACCGAAATACCCCCATAG
1 GGTAAAATGACCGAAATACCCCCATAGGGTAAGATGACCGAAATACCCCCATAG
29004068 GGTAAAAT
1 GGTAAAAT
29004076 AACTATTATA
Statistics
Matches: 57, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
54 55 0.96
55 2 0.04
ACGTcount: A:0.38, C:0.23, G:0.22, T:0.17
Consensus pattern (54 bp):
GGTAAAATGACCGAAATACCCCCATAGGGTAAGATGACCGAAATACCCCCATAG
Found at i:29004405 original size:28 final size:28
Alignment explanation
Indices: 29004361--29004419 Score: 100
Period size: 28 Copynumber: 2.1 Consensus size: 28
29004351 ATTACACTGT
*
29004361 ACTATTATTGTACTGGGCTAAGGCCCAC
1 ACTATTACTGTACTGGGCTAAGGCCCAC
*
29004389 ACTATTACTGTATTGGGCTAAGGCCCAC
1 ACTATTACTGTACTGGGCTAAGGCCCAC
29004417 ACT
1 ACT
29004420 GTATAATTAC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.25, C:0.25, G:0.20, T:0.29
Consensus pattern (28 bp):
ACTATTACTGTACTGGGCTAAGGCCCAC
Found at i:29004429 original size:33 final size:32
Alignment explanation
Indices: 29004354--29004448 Score: 92
Period size: 28 Copynumber: 3.0 Consensus size: 32
29004344 TTGCATTATT
* *
29004354 ACACTGTACTATTATTGTACTGGGCTAAGGCCC
1 ACACTGTA-TATTACTGTATTGGGCTAAGGCCC
29004387 ACAC----TATTACTGTATTGGGCTAAGGCCC
1 ACACTGTATATTACTGTATTGGGCTAAGGCCC
* *
29004415 ACACTGTATAATTACTGAATAT-GGCTCAGGCCC
1 ACACTGTAT-ATTACTGTAT-TGGGCTAAGGCCC
29004448 A
1 A
29004449 GACCATTACT
Statistics
Matches: 52, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
28 26 0.50
32 1 0.02
33 24 0.46
34 1 0.02
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.28
Consensus pattern (32 bp):
ACACTGTATATTACTGTATTGGGCTAAGGCCC
Found at i:29011417 original size:50 final size:50
Alignment explanation
Indices: 29011363--29011487 Score: 169
Period size: 50 Copynumber: 2.5 Consensus size: 50
29011353 TATCCCAAAT
** * *
29011363 ATGGTCTTACATGGGAGTTCTCATATCGATGCCTATGCCATGTCCAAGAC
1 ATGGTCTTACATGGGACCTCTCATATCGATGCCAACGCCATGTCCAAGAC
** * * *
29011413 ATGGTCTTACGGGGGACCTCTCATCTCGGTGCCAACGCCATGTCCCAGAC
1 ATGGTCTTACATGGGACCTCTCATATCGATGCCAACGCCATGTCCAAGAC
29011463 ATGGTCTTACATGGGACCTCTCATA
1 ATGGTCTTACATGGGACCTCTCATA
29011488 ATCTCAATGA
Statistics
Matches: 63, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
50 63 1.00
ACGTcount: A:0.22, C:0.28, G:0.23, T:0.27
Consensus pattern (50 bp):
ATGGTCTTACATGGGACCTCTCATATCGATGCCAACGCCATGTCCAAGAC
Found at i:29013301 original size:26 final size:26
Alignment explanation
Indices: 29013272--29013353 Score: 130
Period size: 26 Copynumber: 3.2 Consensus size: 26
29013262 TCATGCGAAT
* *
29013272 TGTGAAATGAG-TATGCTCACACGAGC
1 TGTGAAATGGGCT-TGCTCACATGAGC
29013298 TGTGAAATGGGCTTGCTCACATGAGC
1 TGTGAAATGGGCTTGCTCACATGAGC
29013324 TGTGAAATGGGCTTGCTCACATGAGC
1 TGTGAAATGGGCTTGCTCACATGAGC
29013350 TGTG
1 TGTG
29013354 GGTCAGAACG
Statistics
Matches: 53, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
26 52 0.98
27 1 0.02
ACGTcount: A:0.24, C:0.18, G:0.30, T:0.27
Consensus pattern (26 bp):
TGTGAAATGGGCTTGCTCACATGAGC
Found at i:29018969 original size:21 final size:22
Alignment explanation
Indices: 29018945--29018989 Score: 58
Period size: 20 Copynumber: 2.1 Consensus size: 22
29018935 AAAAATATTT
*
29018945 AAAAATA-AATAAATT-TTTAA
1 AAAAATATAAAAAATTGTTTAA
*
29018965 AAAAATATAAAAAATTGTTTTA
1 AAAAATATAAAAAATTGTTTAA
29018987 AAA
1 AAA
29018990 TTATTTTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 7 0.33
21 7 0.33
22 7 0.33
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (22 bp):
AAAAATATAAAAAATTGTTTAA
Found at i:29018974 original size:22 final size:21
Alignment explanation
Indices: 29018945--29018989 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
29018935 AAAAATATTT
29018945 AAAAATAAATAAATT-TTTAAA
1 AAAAATAAA-AAATTGTTTAAA
*
29018966 AAAATATAAAAAATTGTTTTAA
1 AAAA-ATAAAAAATTGTTTAAA
29018988 AA
1 AA
29018990 TTATTTTAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 9 0.43
22 12 0.57
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (21 bp):
AAAAATAAAAAATTGTTTAAA
Found at i:29025106 original size:28 final size:26
Alignment explanation
Indices: 29025075--29025131 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 26
29025065 TTTAAAATTT
29025075 AATTA-ATAACTCTATTTTACATAAATAA
1 AATTACATAACTCT-TTTTA-A-AAATAA
29025103 AATTAGCATAACTCTTTTTAAAAATAA
1 AATTA-CATAACTCTTTTTAAAAATAA
29025130 AA
1 AA
29025132 AGTCATTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
27 8 0.30
28 6 0.22
29 5 0.19
30 8 0.30
ACGTcount: A:0.51, C:0.11, G:0.02, T:0.37
Consensus pattern (26 bp):
AATTACATAACTCTTTTTAAAAATAA
Found at i:29026093 original size:11 final size:11
Alignment explanation
Indices: 29026077--29026101 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
29026067 TACAAAGTTT
29026077 ATTATAATAAA
1 ATTATAATAAA
29026088 ATTATAATAAA
1 ATTATAATAAA
29026099 ATT
1 ATT
29026102 CATTGTGTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (11 bp):
ATTATAATAAA
Found at i:29026205 original size:15 final size:15
Alignment explanation
Indices: 29026185--29026214 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
29026175 TTCACTGATA
*
29026185 TGTCTTTTATATTTT
1 TGTCTTTCATATTTT
29026200 TGTCTTTCATATTTT
1 TGTCTTTCATATTTT
29026215 GCATGCATAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.13, C:0.10, G:0.07, T:0.70
Consensus pattern (15 bp):
TGTCTTTCATATTTT
Found at i:29027879 original size:20 final size:19
Alignment explanation
Indices: 29027854--29027903 Score: 61
Period size: 20 Copynumber: 2.7 Consensus size: 19
29027844 TACTAGTATT
29027854 TGATTAATTTAATATTAAA
1 TGATTAATTTAATATTAAA
29027873 GTGATT-ATCTTAATATTAAA
1 -TGATTAAT-TTAATATTAAA
29027893 T--TTAATTTAAT
1 TGATTAATTTAAT
29027904 GTTTATCTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
17 7 0.25
18 2 0.07
19 3 0.11
20 16 0.57
ACGTcount: A:0.42, C:0.02, G:0.06, T:0.50
Consensus pattern (19 bp):
TGATTAATTTAATATTAAA
Found at i:29030499 original size:30 final size:29
Alignment explanation
Indices: 29030398--29030591 Score: 217
Period size: 29 Copynumber: 6.6 Consensus size: 29
29030388 AGCTTCAACT
* * ** * *
29030398 ATCGATCATGAAAAGGGATAGTTTCGGCT
1 ATCGATTATGAAAAGGGATGGTGACGACC
29030427 ATCGATTATGAAAAGGGATGGTGACGACC
1 ATCGATTATGAAAAGGGATGGTGACGACC
* *
29030456 ATCAAGTATGAAAAGGGATGGTGACGACC
1 ATCGATTATGAAAAGGGATGGTGACGACC
**
29030485 ATCGATTAATGAAAAGGGATGGTTTCGACC
1 ATCGATT-ATGAAAAGGGATGGTGACGACC
* *
29030515 ATCAAGTATGAAAAGGGATGGTGACGACC
1 ATCGATTATGAAAAGGGATGGTGACGACC
** *
29030544 ATCGATTAATGAAAAGGGATGGTTTCAACC
1 ATCGATT-ATGAAAAGGGATGGTGACGACC
* *
29030574 ATGGAATATGAAAAGGGA
1 ATCGATTATGAAAAGGGA
29030592 CGGTTACAAC
Statistics
Matches: 140, Mismatches: 23, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
29 91 0.65
30 49 0.35
ACGTcount: A:0.37, C:0.12, G:0.29, T:0.22
Consensus pattern (29 bp):
ATCGATTATGAAAAGGGATGGTGACGACC
Found at i:29030585 original size:88 final size:88
Alignment explanation
Indices: 29030368--29030596 Score: 275
Period size: 88 Copynumber: 2.6 Consensus size: 88
29030358 TATAGGCGAT
* * * * * * * *
29030368 CATCGAATATGAAAAGGGATAGCTTCAACTATCG-ATCATGAAAAGGGATAGTTTCGGCTATCGA
1 CATCGAATATGAAAAGGGATGGTTTCAACCATCGAATAATGAAAAGGGATGGTTTCGACCATCAA
*
29030432 TTATGAAAAGGGATGGTGACGAC
66 GTATGAAAAGGGATGGTGACGAC
** * *
29030455 CATC-AAGTATGAAAAGGGATGGTGACGACCATCGATTAATGAAAAGGGATGGTTTCGACCATCA
1 CATCGAA-TATGAAAAGGGATGGTTTCAACCATCGAATAATGAAAAGGGATGGTTTCGACCATCA
29030519 AGTATGAAAAGGGATGGTGACGAC
65 AGTATGAAAAGGGATGGTGACGAC
* * *
29030543 CATCGATTAATGAAAAGGGATGGTTTCAACCATGGAAT-ATGAAAAGGGACGGTT
1 CATCGAAT-ATGAAAAGGGATGGTTTCAACCATCGAATAATGAAAAGGGATGGTT
29030597 ACAACCATTG
Statistics
Matches: 118, Mismatches: 20, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
86 2 0.02
87 25 0.21
88 66 0.56
89 25 0.21
ACGTcount: A:0.36, C:0.13, G:0.28, T:0.23
Consensus pattern (88 bp):
CATCGAATATGAAAAGGGATGGTTTCAACCATCGAATAATGAAAAGGGATGGTTTCGACCATCAA
GTATGAAAAGGGATGGTGACGAC
Found at i:29030596 original size:29 final size:28
Alignment explanation
Indices: 29030372--29030604 Score: 155
Period size: 29 Copynumber: 8.0 Consensus size: 28
29030362 GGCGATCATC
* *
29030372 GAATATGAAAAGGGATAGCTT-CAACTAT
1 GAATATGAAAAGGGAT-GGTTACAACCAT
* * ** *
29030400 CG-ATCATGAAAAGGGATAGTTTCGGCTAT
1 -GAAT-ATGAAAAGGGATGGTTACAACCAT
* * *
29030429 CGATTATGAAAAGGGATGGTGACGACCAT
1 -GAATATGAAAAGGGATGGTTACAACCAT
* * *
29030458 CAAGTATGAAAAGGGATGGTGACGACCAT
1 GAA-TATGAAAAGGGATGGTTACAACCAT
* * *
29030487 CGATTAATGAAAAGGGATGGTTTCGACCAT
1 -GAAT-ATGAAAAGGGATGGTTACAACCAT
* * *
29030517 CAAGTATGAAAAGGGATGGTGACGACCAT
1 GAA-TATGAAAAGGGATGGTTACAACCAT
* *
29030546 CGATTAATGAAAAGGGATGGTTTCAACCAT
1 -GAAT-ATGAAAAGGGATGGTTACAACCAT
*
29030576 GGAATATGAAAAGGGACGGTTACAACCAT
1 -GAATATGAAAAGGGATGGTTACAACCAT
29030605 TGTTTAGCAC
Statistics
Matches: 166, Mismatches: 29, Indels: 18
0.78 0.14 0.08
Matches are distributed among these distances:
28 5 0.03
29 111 0.67
30 50 0.30
ACGTcount: A:0.37, C:0.13, G:0.27, T:0.22
Consensus pattern (28 bp):
GAATATGAAAAGGGATGGTTACAACCAT
Found at i:29030604 original size:59 final size:59
Alignment explanation
Indices: 29030427--29030591 Score: 271
Period size: 59 Copynumber: 2.8 Consensus size: 59
29030417 AGTTTCGGCT
**
29030427 ATCGATT-ATGAAAAGGGATGGTGACGACCATCAAGTATGAAAAGGGATGGTGACGACC
1 ATCGATTAATGAAAAGGGATGGTTTCGACCATCAAGTATGAAAAGGGATGGTGACGACC
29030485 ATCGATTAATGAAAAGGGATGGTTTCGACCATCAAGTATGAAAAGGGATGGTGACGACC
1 ATCGATTAATGAAAAGGGATGGTTTCGACCATCAAGTATGAAAAGGGATGGTGACGACC
* *
29030544 ATCGATTAATGAAAAGGGATGGTTTCAACCATGGAA-TATGAAAAGGGA
1 ATCGATTAATGAAAAGGGATGGTTTCGACCAT-CAAGTATGAAAAGGGA
29030592 CGGTTACAAC
Statistics
Matches: 101, Mismatches: 4, Indels: 3
0.94 0.04 0.03
Matches are distributed among these distances:
58 7 0.07
59 92 0.91
60 2 0.02
ACGTcount: A:0.38, C:0.12, G:0.29, T:0.21
Consensus pattern (59 bp):
ATCGATTAATGAAAAGGGATGGTTTCGACCATCAAGTATGAAAAGGGATGGTGACGACC
Found at i:29033468 original size:20 final size:19
Alignment explanation
Indices: 29033439--29033489 Score: 75
Period size: 20 Copynumber: 2.6 Consensus size: 19
29033429 CAGAAAATGA
*
29033439 TTTCTGGAAAATTACTTAC
1 TTTCTGGAAAATGACTTAC
29033458 TTTCTTGGAAAATGACTTAC
1 TTTC-TGGAAAATGACTTAC
29033478 TTTCCTGGAAAA
1 TTT-CTGGAAAA
29033490 GTTAATATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 4 0.14
20 24 0.83
21 1 0.03
ACGTcount: A:0.31, C:0.16, G:0.14, T:0.39
Consensus pattern (19 bp):
TTTCTGGAAAATGACTTAC
Found at i:29033926 original size:14 final size:15
Alignment explanation
Indices: 29033903--29033952 Score: 59
Period size: 14 Copynumber: 3.3 Consensus size: 15
29033893 GACTTATGAC
*
29033903 ATATTTTAATAT-TT
1 ATATTATAATATATT
29033917 ATATTATAATATATT
1 ATATTATAATATATT
29033932 -TATTATTAATATATTT
1 ATATTA-TAATATA-TT
29033948 ATATT
1 ATATT
29033953 TGTAATAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
14 16 0.52
15 9 0.29
16 2 0.06
17 4 0.13
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
ATATTATAATATATT
Found at i:29033945 original size:17 final size:17
Alignment explanation
Indices: 29033911--29033979 Score: 65
Period size: 17 Copynumber: 4.1 Consensus size: 17
29033901 ACATATTTTA
29033911 ATATTTA-TATT-ATAAT
1 ATATTTATTATTAAT-AT
29033927 ATATTTATTATTAATAT
1 ATATTTATTATTAATAT
*
29033944 AT-TTATATT-TGTAATAA
1 ATATT-TATTAT-TAATAT
*
29033961 ATATTTATTATTAAAAT
1 ATATTTATTATTAATAT
29033978 AT
1 AT
29033980 TAATATTGAA
Statistics
Matches: 44, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
16 10 0.23
17 29 0.66
18 5 0.11
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.55
Consensus pattern (17 bp):
ATATTTATTATTAATAT
Found at i:29033970 original size:34 final size:32
Alignment explanation
Indices: 29033910--29033986 Score: 102
Period size: 34 Copynumber: 2.4 Consensus size: 32
29033900 GACATATTTT
29033910 AATATTTATA-TTATAATATATTTATTATTAA
1 AATATTTATATTTATAATATATTTATTATTAA
* *
29033941 TATATTTATATTTGTAATAAATATTTATTATTAA
1 AATATTTATATTTATAAT--ATATTTATTATTAA
*
29033975 AATATTAATATT
1 AATATTTATATT
29033987 GAATATTTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
31 9 0.23
32 6 0.15
34 24 0.62
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (32 bp):
AATATTTATATTTATAATATATTTATTATTAA
Found at i:29033986 original size:14 final size:15
Alignment explanation
Indices: 29033910--29034000 Score: 51
Period size: 15 Copynumber: 5.7 Consensus size: 15
29033900 GACATATTTT
29033910 AATATTT-ATATTATA
1 AATATTTAATATTA-A
*
29033925 ATATATTTATTATTAA
1 A-ATATTTAATATTAA
* *
29033941 TATATTTATATTTGTAATA
1 AATATTTA-ATAT-T-A-A
*
29033960 AATATTTATTATTAA
1 AATATTTAATATTAA
29033975 AATA-TTAATATTGAA
1 AATATTTAATATT-AA
* *
29033990 TATTTTTAATA
1 AATATTTAATA
29034001 ATATGTGAAG
Statistics
Matches: 58, Mismatches: 10, Indels: 15
0.70 0.12 0.18
Matches are distributed among these distances:
14 7 0.12
15 17 0.29
16 16 0.28
17 7 0.12
18 3 0.05
19 8 0.14
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
AATATTTAATATTAA
Found at i:29033986 original size:17 final size:16
Alignment explanation
Indices: 29033910--29033986 Score: 54
Period size: 15 Copynumber: 4.7 Consensus size: 16
29033900 GACATATTTT
29033910 AATATTTATATTA-TAA
1 AATA-TTATATTATTAA
*
29033926 TATATT-TATTATTAA
1 AATATTATATTATTAA
*
29033941 TATATTTATATT-TGTAATA
1 AATA-TTATATTAT-T-A-A
29033960 AATATT-TATTATTAA
1 AATATTATATTATTAA
29033975 AATATTAATATT
1 AATATT-ATATT
29033987 GAATATTTTT
Statistics
Matches: 50, Mismatches: 2, Indels: 17
0.72 0.03 0.25
Matches are distributed among these distances:
14 5 0.10
15 16 0.32
16 7 0.14
17 14 0.28
18 4 0.08
19 4 0.08
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (16 bp):
AATATTATATTATTAA
Found at i:29034118 original size:25 final size:23
Alignment explanation
Indices: 29034059--29034118 Score: 57
Period size: 25 Copynumber: 2.4 Consensus size: 23
29034049 AAAATAAAAT
*
29034059 TAAAATATTAAATAATTTATTAA
1 TAAATTATTAAATAATTTATTAA
* *
29034082 AATAATAAATTAAATTAATTGTATTAA
1 TA-AAT-TATTAAA-TAATT-TATTAA
29034109 TAAATTATTA
1 TAAATTATTA
29034119 TGTGACTAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 6
0.72 0.13 0.15
Matches are distributed among these distances:
23 1 0.04
24 2 0.07
25 10 0.36
26 8 0.29
27 7 0.25
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (23 bp):
TAAATTATTAAATAATTTATTAA
Found at i:29039888 original size:43 final size:40
Alignment explanation
Indices: 29039822--29039933 Score: 109
Period size: 41 Copynumber: 2.7 Consensus size: 40
29039812 AGCTCGTACA
* * *
29039822 ATGCCATATCCCGGATATGGTCTTACATGTTAACGCATAT-CG
1 ATGCCATGTCCCAGATATGGTCTTACACG--AA-GCATATACG
* * *
29039864 ATGCCACTGTCCCAGATAGGGTCTTATACGAATCATATACG
1 ATGCCA-TGTCCCAGATATGGTCTTACACGAAGCATATACG
*
29039905 ATGCCAATGTCCCAGACATGGTCTTACAC
1 ATGCC-ATGTCCCAGATATGGTCTTACAC
29039934 ATTTTCTGAC
Statistics
Matches: 58, Mismatches: 9, Indels: 7
0.78 0.12 0.09
Matches are distributed among these distances:
40 5 0.09
41 28 0.48
42 7 0.12
43 18 0.31
ACGTcount: A:0.28, C:0.26, G:0.19, T:0.28
Consensus pattern (40 bp):
ATGCCATGTCCCAGATATGGTCTTACACGAAGCATATACG
Found at i:29041715 original size:24 final size:25
Alignment explanation
Indices: 29041670--29041720 Score: 77
Period size: 24 Copynumber: 2.1 Consensus size: 25
29041660 ATTTTTGGGA
*
29041670 AAATTAATTTTGATTAAGTAAAATT
1 AAATTAATTTAGATTAAGTAAAATT
*
29041695 AAATTAA-TTAGATTAATTAAAATT
1 AAATTAATTTAGATTAAGTAAAATT
29041719 AA
1 AA
29041721 TATGATAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 17 0.71
25 7 0.29
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (25 bp):
AAATTAATTTAGATTAAGTAAAATT
Found at i:29042229 original size:13 final size:13
Alignment explanation
Indices: 29042194--29042231 Score: 67
Period size: 14 Copynumber: 2.8 Consensus size: 13
29042184 GAGATATTTG
29042194 TAATTTGAAAACT
1 TAATTTGAAAACT
29042207 TAAGTTTGAAAACT
1 TAA-TTTGAAAACT
29042221 TAATTTGAAAA
1 TAATTTGAAAA
29042232 TTTGGAAACT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 11 0.46
14 13 0.54
ACGTcount: A:0.47, C:0.05, G:0.11, T:0.37
Consensus pattern (13 bp):
TAATTTGAAAACT
Found at i:29042513 original size:35 final size:35
Alignment explanation
Indices: 29042469--29042644 Score: 185
Period size: 35 Copynumber: 5.1 Consensus size: 35
29042459 TTCACTTGTC
* * *
29042469 TTTTCTTGCAGGGAATATTTCCTGTTCACGCATTA
1 TTTTCTTGCAGGGAATATCTCCTGTTCACACATCA
* * * *
29042504 TTTTGTTGCAAGGAATCTCTCCTGTTCACAAATCA
1 TTTTCTTGCAGGGAATATCTCCTGTTCACACATCA
* * * * *
29042539 -TTTCTTGCAGGGAATATTTCCTCTTTACGCATTA
1 TTTTCTTGCAGGGAATATCTCCTGTTCACACATCA
* *
29042573 TTTTGTTGCAGGGAATCTCTCCTGTTCACACATCA
1 TTTTCTTGCAGGGAATATCTCCTGTTCACACATCA
* * *
29042608 -TTTCTTGCAGGGAATCTCTCCTATTCATACATCA
1 TTTTCTTGCAGGGAATATCTCCTGTTCACACATCA
29042642 TTT
1 TTT
29042645 CTGGTATTAT
Statistics
Matches: 113, Mismatches: 26, Indels: 4
0.79 0.18 0.03
Matches are distributed among these distances:
34 56 0.50
35 57 0.50
ACGTcount: A:0.22, C:0.23, G:0.15, T:0.41
Consensus pattern (35 bp):
TTTTCTTGCAGGGAATATCTCCTGTTCACACATCA
Found at i:29042553 original size:34 final size:34
Alignment explanation
Indices: 29042470--29042646 Score: 192
Period size: 34 Copynumber: 5.1 Consensus size: 34
29042460 TCACTTGTCT
* * * *
29042470 TTTCTTGCAGGGAATATTTCCTGTTCACGCATTA
1 TTTCTTGCAGGGAATCTCTCCTGTTCACACATCA
* * *
29042504 TTTTGTTGCAAGGAATCTCTCCTGTTCACAAATCA
1 -TTTCTTGCAGGGAATCTCTCCTGTTCACACATCA
* * * * * *
29042539 TTTCTTGCAGGGAATATTTCCTCTTTACGCATTA
1 TTTCTTGCAGGGAATCTCTCCTGTTCACACATCA
*
29042573 TTTTGTTGCAGGGAATCTCTCCTGTTCACACATCA
1 -TTTCTTGCAGGGAATCTCTCCTGTTCACACATCA
* *
29042608 TTTCTTGCAGGGAATCTCTCCTATTCATACATCA
1 TTTCTTGCAGGGAATCTCTCCTGTTCACACATCA
29042642 TTTCT
1 TTTCT
29042647 GGTATTATTT
Statistics
Matches: 115, Mismatches: 26, Indels: 3
0.80 0.18 0.02
Matches are distributed among these distances:
34 61 0.53
35 54 0.47
ACGTcount: A:0.21, C:0.23, G:0.15, T:0.41
Consensus pattern (34 bp):
TTTCTTGCAGGGAATCTCTCCTGTTCACACATCA
Found at i:29042570 original size:69 final size:69
Alignment explanation
Indices: 29042470--29042622 Score: 270
Period size: 69 Copynumber: 2.2 Consensus size: 69
29042460 TCACTTGTCT
*
29042470 TTTCTTGCAGGGAATATTTCCTGTTCACGCATTATTTTGTTGCAAGGAATCTCTCCTGTTCACAA
1 TTTCTTGCAGGGAATATTTCCTCTTCACGCATTATTTTGTTGCAAGGAATCTCTCCTGTTCACAA
29042535 ATCA
66 ATCA
* * *
29042539 TTTCTTGCAGGGAATATTTCCTCTTTACGCATTATTTTGTTGCAGGGAATCTCTCCTGTTCACAC
1 TTTCTTGCAGGGAATATTTCCTCTTCACGCATTATTTTGTTGCAAGGAATCTCTCCTGTTCACAA
29042604 ATCA
66 ATCA
29042608 TTTCTTGCAGGGAAT
1 TTTCTTGCAGGGAAT
29042623 CTCTCCTATT
Statistics
Matches: 80, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
69 80 1.00
ACGTcount: A:0.22, C:0.22, G:0.17, T:0.40
Consensus pattern (69 bp):
TTTCTTGCAGGGAATATTTCCTCTTCACGCATTATTTTGTTGCAAGGAATCTCTCCTGTTCACAA
ATCA
Found at i:29045499 original size:20 final size:20
Alignment explanation
Indices: 29045469--29045506 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
29045459 GAACAAATTG
29045469 TTGATTCTATTTCTTTTTTAT
1 TTGATTCTA-TTCTTTTTTAT
29045490 TTGA-TCTATTCTTTTTT
1 TTGATTCTATTCTTTTTT
29045507 GTATTTCTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 9 0.53
20 4 0.24
21 4 0.24
ACGTcount: A:0.13, C:0.11, G:0.05, T:0.71
Consensus pattern (20 bp):
TTGATTCTATTCTTTTTTAT
Found at i:29045506 original size:21 final size:21
Alignment explanation
Indices: 29045469--29045512 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
29045459 GAACAAATTG
*
29045469 TTGATTCTATTTCTTTTTTAT
1 TTGATTCTATTTCTTTTGTAT
*
29045490 TTGA-TCTATTCTTTTTTGTAT
1 TTGATTCTATT-TCTTTTGTAT
29045511 TT
1 TT
29045513 CTCTTTTTCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.14, C:0.09, G:0.07, T:0.70
Consensus pattern (21 bp):
TTGATTCTATTTCTTTTGTAT
Found at i:29046503 original size:15 final size:15
Alignment explanation
Indices: 29046483--29046513 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
29046473 AGATGTTGTA
29046483 TGTAATTCATCTATT
1 TGTAATTCATCTATT
29046498 TGTAATTCATCTATT
1 TGTAATTCATCTATT
29046513 T
1 T
29046514 CAGTAGATGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.26, C:0.13, G:0.06, T:0.55
Consensus pattern (15 bp):
TGTAATTCATCTATT
Found at i:29050870 original size:12 final size:12
Alignment explanation
Indices: 29050825--29050937 Score: 53
Period size: 12 Copynumber: 9.8 Consensus size: 12
29050815 ATTCTAAAAA
*
29050825 TAATA-TTATTT
1 TAATATTTAATT
29050836 TAATAATTTAATAT
1 TAAT-ATTTAAT-T
29050850 TAA-ATTTAATT
1 TAATATTTAATT
* *
29050861 TAATACTTAACT
1 TAATATTTAATT
*
29050873 TAATA-GT-ATT
1 TAATATTTAATT
29050883 T--TA-TTAATT
1 TAATATTTAATT
* *
29050892 TAATATTAAAGT
1 TAATATTTAATT
* *
29050904 GATTATCTTAATAT
1 TAATAT-TTAAT-T
29050918 TAA-ATTTAATT
1 TAATATTTAATT
*
29050929 TAATGTTTA
1 TAATATTTA
29050938 TCTTGTATAT
Statistics
Matches: 76, Mismatches: 15, Indels: 21
0.68 0.13 0.19
Matches are distributed among these distances:
8 3 0.04
9 4 0.05
10 3 0.04
11 15 0.20
12 36 0.47
13 9 0.12
14 6 0.08
ACGTcount: A:0.42, C:0.03, G:0.04, T:0.52
Consensus pattern (12 bp):
TAATATTTAATT
Found at i:29060853 original size:19 final size:19
Alignment explanation
Indices: 29060817--29060853 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
29060807 TAATTGGGAC
* *
29060817 ATTAATTTAATTTTTTTAA
1 ATTAATTTAATATGTTTAA
29060836 ATTAATTTAATATGTTTA
1 ATTAATTTAATATGTTTA
29060854 TTTTTGGAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (19 bp):
ATTAATTTAATATGTTTAA
Found at i:29063662 original size:16 final size:14
Alignment explanation
Indices: 29063641--29063680 Score: 55
Period size: 13 Copynumber: 2.8 Consensus size: 14
29063631 TGTGAGTGAA
29063641 TATAAATATTATATAT
1 TATAAA-ATTATA-AT
29063657 TATAAAA-TATAAT
1 TATAAAATTATAAT
29063670 TATAAAATTAT
1 TATAAAATTAT
29063681 TTCAATTAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 9 0.39
14 7 0.30
15 1 0.04
16 6 0.26
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
TATAAAATTATAAT
Done.