Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr12 103066607
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: 103066607
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 238 characters in sequence are not A, C, G, or T
File 152 of 345
Found at i:41590354 original size:79 final size:79
Alignment explanation
Indices: 41590204--41590357 Score: 186
Period size: 79 Copynumber: 1.9 Consensus size: 79
41590194 CTAGGATCCG
* * *
41590204 AAGGCATTCGTGCGAGTTAATAAATCCGGGCTAAGCCCGAAGGCATTTGTGCAAGTTATTAAACC
1 AAGGCATTCGTGCGAGTCAATAAATCCGGGCTAAGCCCGAAGGCATTTGAGCAAGTCATTAAACC
41590269 CGGGTTAAGTCCAA
66 CGGGTTAAGTCCAA
* * * * * *
41590283 AAGGCATTCGTGCGAGTCACTATAA-CCGGGCTTCATCCCGAAGGCATTTGAGCGAGTCGTTATA
1 AAGGCATTCGTGCGAGTCAATA-AATCCGGGC-TAAGCCCGAAGGCATTTGAGCAAGTCATTAAA
*
41590347 TCC-GGTTAAGT
64 CCCGGGTTAAGT
41590358 TCCGAAGGTA
Statistics
Matches: 63, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
79 34 0.54
80 29 0.46
ACGTcount: A:0.27, C:0.21, G:0.26, T:0.25
Consensus pattern (79 bp):
AAGGCATTCGTGCGAGTCAATAAATCCGGGCTAAGCCCGAAGGCATTTGAGCAAGTCATTAAACC
CGGGTTAAGTCCAA
Found at i:41611729 original size:47 final size:47
Alignment explanation
Indices: 41611661--41611832 Score: 244
Period size: 47 Copynumber: 3.7 Consensus size: 47
41611651 ATCCATAAGT
41611661 GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATCTCAC
1 GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATCTCAC
* * * *
41611708 GAACTCGGACTCAACTCAACGAGTTCGGACG-CTCG---CATCCATAAGT
1 GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT-C-TCA-C
41611754 GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATCTCAC
1 GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATCTCAC
*
41611801 GAACTCGGACTCAACTCAATGAGTTCGGATGC
1 GAACTCGGACTCAACTCAACGAGTTCGGATGC
41611833 TCAACCATCC
Statistics
Matches: 109, Mismatches: 9, Indels: 14
0.83 0.07 0.11
Matches are distributed among these distances:
43 3 0.03
44 1 0.01
45 2 0.02
46 33 0.30
47 64 0.59
48 2 0.02
49 1 0.01
50 3 0.03
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.22
Consensus pattern (47 bp):
GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:41611782 original size:46 final size:46
Alignment explanation
Indices: 41611607--41611782 Score: 232
Period size: 46 Copynumber: 3.8 Consensus size: 46
41611597 TGTAACCCGC
* * *
41611607 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
* *
41611653 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACG-CTCG---CAT
* *
41611703 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
41611746 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
41611783 TGCCTAGTTA
Statistics
Matches: 112, Mismatches: 11, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
43 3 0.03
44 1 0.01
45 2 0.02
46 68 0.61
47 32 0.29
48 2 0.02
49 1 0.01
50 3 0.03
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.20
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
Found at i:41611848 original size:93 final size:93
Alignment explanation
Indices: 41611615--41611834 Score: 395
Period size: 93 Copynumber: 2.4 Consensus size: 93
41611605 GCCCATAAGT
* * *
41611615 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
41611680 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
41611708 GAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
41611773 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
* *
41611801 GAACTCGGACTCAACTCAATGAGTTCGGATGCTC
1 GAACTCGGACTCAACTCAACGAGTTCGGACGCTC
41611835 AACCATCCTA
Statistics
Matches: 122, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 122 1.00
ACGTcount: A:0.27, C:0.30, G:0.21, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:41614540 original size:39 final size:39
Alignment explanation
Indices: 41614353--41614529 Score: 291
Period size: 39 Copynumber: 4.5 Consensus size: 39
41614343 ACAAAGCATG
*
41614353 CGGGACTTTAAGCCCGGATATAATACCAGCACGAATGCCTT
1 CGGGAC-TT-AGCCCGGATATAACACCAGCACGAATGCCTT
*
41614394 CGGGACTTAGCCCGGATATAACGCCAGCACGAATGCCTT
1 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
*
41614433 CGGGACTTAGCCCGGATATAACGCCAGCACGAATGCCTT
1 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
* *
41614472 CGGGACTTAGCCCAGATATAGCACCAGCACGAATGCCTT
1 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
41614511 CGGGACTTAGCCCGGATAT
1 CGGGACTTAGCCCGGATAT
41614530 TTTTCCAGCA
Statistics
Matches: 130, Mismatches: 6, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
39 122 0.94
40 2 0.02
41 6 0.05
ACGTcount: A:0.27, C:0.29, G:0.25, T:0.19
Consensus pattern (39 bp):
CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
Found at i:41614569 original size:78 final size:78
Alignment explanation
Indices: 41614353--41614646 Score: 217
Period size: 78 Copynumber: 3.7 Consensus size: 78
41614343 ACAAAGCATG
* * * * * * *
41614353 CGGGACTTTAAGCCCGGATATAATACCAGCACGAATGCCTTCGGGAC-TT-AGCCCGGATATAAC
1 CGGGAC-TT-AGCCCGGATATATTTCCAGCACTAA-GCCTGC-GGACTTTAAGTCCGAATATAGC
*
41614416 GCCAGCACGAATGCCTT
62 ACCAGCACGAATGCCTT
*** * * *
41614433 CGGGACTTAGCCCGGATATAACGCCAGCACGAATGCCTTCGGGAC-TT-AG-CCCAGATATAGCA
1 CGGGACTTAGCCCGGATATATTTCCAGCACTAA-GCCTGC-GGACTTTAAGTCCGA-ATATAGCA
41614495 CCAGCACGAATGCCTT
63 CCAGCACGAATGCCTT
* * ***
41614511 CGGGACTTAGCCCGGATATTTTTCCAGCACTTAGCCTGCGGACTTTAAGTCCGAATATATTTCCA
1 CGGGACTTAGCCCGGATATATTTCCAGCACTAAGCCTGCGGACTTTAAGTCCGAATATAGCACCA
* * *
41614576 GCA-TAAAGCCTG
66 GCACGAATGCCTT
* * *
41614588 C-GGACTTCAAGTCCGGATATATTTCCAGCA-TAAAGCCTGCGGACTTCAAGTCCGGATAT
1 CGGGACTT--AGCCCGGATATATTTCCAGCACT-AAGCCTGCGGACTTTAAGTCCGAATAT
41614647 TTTTCCAATA
Statistics
Matches: 182, Mismatches: 25, Indels: 16
0.82 0.11 0.07
Matches are distributed among these distances:
76 10 0.05
77 17 0.09
78 144 0.79
79 5 0.03
80 6 0.03
ACGTcount: A:0.27, C:0.28, G:0.23, T:0.23
Consensus pattern (78 bp):
CGGGACTTAGCCCGGATATATTTCCAGCACTAAGCCTGCGGACTTTAAGTCCGAATATAGCACCA
GCACGAATGCCTT
Found at i:41614574 original size:39 final size:39
Alignment explanation
Indices: 41614522--41614653 Score: 203
Period size: 39 Copynumber: 3.4 Consensus size: 39
41614512 GGGACTTAGC
* * *
41614522 CCGGATATTTTTCCAGCACT-TAGCCTGCGGACTTTAAGT
1 CCGGATATATTTCCAGCA-TAAAGCCTGCGGACTTCAAGT
*
41614561 CCGAATATATTTCCAGCATAAAGCCTGCGGACTTCAAGT
1 CCGGATATATTTCCAGCATAAAGCCTGCGGACTTCAAGT
41614600 CCGGATATATTTCCAGCATAAAGCCTGCGGACTTCAAGT
1 CCGGATATATTTCCAGCATAAAGCCTGCGGACTTCAAGT
*
41614639 CCGGATATTTTTCCA
1 CCGGATATATTTCCA
41614654 ATACCATGCA
Statistics
Matches: 86, Mismatches: 6, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
38 1 0.01
39 85 0.99
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.30
Consensus pattern (39 bp):
CCGGATATATTTCCAGCATAAAGCCTGCGGACTTCAAGT
Found at i:41614616 original size:117 final size:118
Alignment explanation
Indices: 41614345--41614653 Score: 281
Period size: 117 Copynumber: 2.6 Consensus size: 118
41614335 TCACCACCAC
*
41614345 AAAGCATGCGGGACTTTAAGCCCGGATATAATACCAGCACGAATGCCTTCGGGACTTAGCCCGGA
1 AAAGCCTGCGGGAC-TTAAGCCCGGATATAATACCAGCACGAATGCCTTCGGGACTTAGCCCGGA
**** * *
41614410 TATAACGCCAGCACGAATGCCTTCGGGACTTAGCCCGGATATAACGCCAGCACG
65 TATTTTTCCAGCACGAATGCCTGCGGGACTTAGCCCGAATATAACGCCAGCACG
* * * **
41614464 AATGCCTTCGGGACTT-AGCCCAGATATAGCACCAGCACGAATGCCTTCGGGACTTAGCCCGGAT
1 AAAGCCTGCGGGACTTAAGCCCGGATATAATACCAGCACGAATGCCTTCGGGACTTAGCCCGGAT
** * *** *
41614528 ATTTTTCCAGCACTTA-GCCTGC-GGACTTTAAGTCCGAATATATTTCCAGCA-T
66 ATTTTTCCAGCACGAATGCCTGCGGGAC-TT-AGCCCGAATATAACGCCAGCACG
* * * * * * *
41614580 AAAGCCTGC-GGACTTCAAGTCCGGATATATTTCCAGCA-TAAAGCCTGC-GGACTTCAAGTCCG
1 AAAGCCTGCGGGACTT-AAGCCCGGATATAATACCAGCACGAATGCCTTCGGGACTT--AGCCCG
41614642 GATATTTTTCCA
63 GATATTTTTCCA
41614654 ATACCATGCA
Statistics
Matches: 154, Mismatches: 30, Indels: 14
0.78 0.15 0.07
Matches are distributed among these distances:
115 16 0.10
116 21 0.14
117 104 0.68
118 2 0.01
119 11 0.07
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (118 bp):
AAAGCCTGCGGGACTTAAGCCCGGATATAATACCAGCACGAATGCCTTCGGGACTTAGCCCGGAT
ATTTTTCCAGCACGAATGCCTGCGGGACTTAGCCCGAATATAACGCCAGCACG
Found at i:41636890 original size:19 final size:19
Alignment explanation
Indices: 41636853--41636897 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 19
41636843 TAAACAACCT
41636853 ACAAATTAAAAAGAAATTAA
1 ACAAA-TAAAAAGAAATTAA
41636873 ACAAATAACAAA-AAATTAA
1 ACAAATAA-AAAGAAATTAA
*
41636892 AAAAAT
1 ACAAAT
41636898 TTAAAATAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 15 0.65
20 8 0.35
ACGTcount: A:0.73, C:0.07, G:0.02, T:0.18
Consensus pattern (19 bp):
ACAAATAAAAAGAAATTAA
Found at i:41637261 original size:15 final size:15
Alignment explanation
Indices: 41637243--41637295 Score: 63
Period size: 16 Copynumber: 3.4 Consensus size: 15
41637233 AATTCTATAT
*
41637243 AATAAAAAATCATAA
1 AATAAAAAATAATAA
41637258 AATAAAAAAATAATTAA
1 AAT-AAAAAATAA-TAA
41637275 AATAAATAAA-AATAA
1 AATAAA-AAATAATAA
41637290 AATAAA
1 AATAAA
41637296 CAAACAACTA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
15 12 0.35
16 13 0.38
17 9 0.26
ACGTcount: A:0.77, C:0.02, G:0.00, T:0.21
Consensus pattern (15 bp):
AATAAAAAATAATAA
Found at i:41637267 original size:16 final size:15
Alignment explanation
Indices: 41637246--41637295 Score: 57
Period size: 15 Copynumber: 3.1 Consensus size: 15
41637236 TCTATATAAT
41637246 AAAAAATCATAAAATA
1 AAAAAAT-ATAAAATA
41637262 AAAAAATAATTAAAATA
1 AAAAAAT-A-TAAAATA
41637279 AATAAAA-ATAAAATA
1 AA-AAAATATAAAATA
41637294 AA
1 AA
41637296 CAAACAACTA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
15 9 0.29
16 9 0.29
17 9 0.29
18 4 0.13
ACGTcount: A:0.78, C:0.02, G:0.00, T:0.20
Consensus pattern (15 bp):
AAAAAATATAAAATA
Found at i:41638977 original size:68 final size:69
Alignment explanation
Indices: 41638886--41639055 Score: 256
Period size: 69 Copynumber: 2.5 Consensus size: 69
41638876 AAGTGACAAT
* * * * * *
41638886 TTCTTTATTGTTTTCCTTTAAAAGTTAATTTTATCC-CACATTGACTAGAGAATACTCTCATAGC
1 TTCTTTACTATTTTCATTAAAAAGTTAATTTTAACCTCACATTCACTAGAGAATACTCTCATAGC
41638950 TCAC
66 TCAC
41638954 TT-TTTCACTATTTTCATTAAAAAGTTAATTTTAACCTCACATTCACTAGAGAATACTCTCATAG
1 TTCTTT-ACTATTTTCATTAAAAAGTTAATTTTAACCTCACATTCACTAGAGAATACTCTCATAG
41639018 CTCAC
65 CTCAC
41639023 TTCTTTACTATTTTCATTAAAAA-TTAATTTTAA
1 TTCTTTACTATTTTCATTAAAAAGTTAATTTTAA
41639056 TCACTTAAAA
Statistics
Matches: 93, Mismatches: 6, Indels: 6
0.89 0.06 0.06
Matches are distributed among these distances:
67 3 0.03
68 37 0.40
69 50 0.54
70 3 0.03
ACGTcount: A:0.32, C:0.19, G:0.06, T:0.44
Consensus pattern (69 bp):
TTCTTTACTATTTTCATTAAAAAGTTAATTTTAACCTCACATTCACTAGAGAATACTCTCATAGC
TCAC
Found at i:41640381 original size:18 final size:17
Alignment explanation
Indices: 41640358--41640391 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
41640348 TAGCTGTGCC
41640358 GTTTTCTCTTCTGTATTA
1 GTTTTCTCTTCT-TATTA
41640376 GTTTTCTCTTCTTATT
1 GTTTTCTCTTCTTATT
41640392 TTCTTCCCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.09, C:0.18, G:0.09, T:0.65
Consensus pattern (17 bp):
GTTTTCTCTTCTTATTA
Found at i:41641627 original size:20 final size:20
Alignment explanation
Indices: 41641598--41641644 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
41641588 ATTTTGATAA
* * *
41641598 ACATGGTATGTATGATATGC
1 ACATGATATGAATGACATGC
41641618 ACATGATATGAATGACATGC
1 ACATGATATGAATGACATGC
41641638 ACATGAT
1 ACATGAT
41641645 GTATTTATGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.36, C:0.13, G:0.21, T:0.30
Consensus pattern (20 bp):
ACATGATATGAATGACATGC
Found at i:41641725 original size:24 final size:24
Alignment explanation
Indices: 41641693--41641846 Score: 240
Period size: 24 Copynumber: 6.4 Consensus size: 24
41641683 GAGGAAGTGC
41641693 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
41641717 AAAAGGGCTGATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
41641741 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
41641765 AAAAGGGCTTATACCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
41641789 -AAAGGGCTTATGCCCTAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
41641812 AAAAAAGGGCTT-TGCCCCAGTTATT
1 --AAAAGGGCTTATGCCCCAGTTATT
41641837 AAAAGAGGCT
1 AAAAG-GGCT
41641847 AGGCGTCCAG
Statistics
Matches: 120, Mismatches: 6, Indels: 8
0.90 0.04 0.06
Matches are distributed among these distances:
23 26 0.22
24 73 0.61
25 12 0.10
26 9 0.08
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.28
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATT
Found at i:41642088 original size:31 final size:31
Alignment explanation
Indices: 41642053--41642116 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
41642043 TGTTTATAGT
41642053 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
** *
41642084 AAAGGCTTCGGCCCAGTGTTATGAATTATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
41642115 AA
1 AA
41642117 TATGAAAAGG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.36, C:0.16, G:0.23, T:0.25
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:41643979 original size:47 final size:47
Alignment explanation
Indices: 41643907--41644345 Score: 702
Period size: 47 Copynumber: 9.4 Consensus size: 47
41643897 CCCTTCGGGA
* *
41643907 CTTATCACATTTATACA-TTTCACATCCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* * * * *
41643953 CTTATCACATATATACACCTTCACATCCATCACATCGGCCATTAGGT
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
41644000 CTTATCTCATATATACACTTTCACATTCATCATATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
41644047 CTTATCACATATATACACTTTCACATTCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
41644094 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
41644141 CTTATCACATATATACAC-TTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* * *
41644187 CTTATCACATATATACACTTTCACATTCATCACGTTGGCCACTCGAC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
*
41644234 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGAC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
41644281 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
*
41644328 CTTATCACATATACACAC
1 CTTATCACATATATACAC
41644346 CTTGTACATC
Statistics
Matches: 364, Mismatches: 27, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
46 62 0.17
47 302 0.83
ACGTcount: A:0.28, C:0.31, G:0.08, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
Found at i:41644150 original size:22 final size:22
Alignment explanation
Indices: 41644122--41644196 Score: 71
Period size: 22 Copynumber: 3.3 Consensus size: 22
41644112 TTTCACATTC
41644122 ATCACATTGGCCATTCGGCCTT
1 ATCACATTGGCCATTCGGCCTT
*** * *
41644144 ATCACATATATACACTTC-ACATT
1 ATCACAT-TGGCCA-TTCGGCCTT
41644167 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
41644190 ATCACAT
1 ATCACAT
41644197 ATATACACTT
Statistics
Matches: 39, Mismatches: 10, Indels: 8
0.68 0.18 0.14
Matches are distributed among these distances:
22 17 0.44
23 12 0.31
24 10 0.26
ACGTcount: A:0.27, C:0.31, G:0.11, T:0.32
Consensus pattern (22 bp):
ATCACATTGGCCATTCGGCCTT
Found at i:41644227 original size:187 final size:187
Alignment explanation
Indices: 41643907--41644345 Score: 709
Period size: 187 Copynumber: 2.3 Consensus size: 187
41643897 CCCTTCGGGA
* *
41643907 CTTATCACATTTATACA-TTTCACATCCATCACATTGGCCATTCGGCCTTATCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACA-
* * *
41643971 CTTCACATCCATCACATCGGCCATTAGGTCTTATCTCATATATACACTTTCACATTCATCATATT
65 CTTCACATCCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATT
* * * *
41644036 GGCCATTCGGCCTTATCACATATATACACTTTCACATTCATCACGTTGGCCACTCGGC
130 GGCCACTCGACCTTATCACATATATACACTTTCACATTCATCACATTGGCCACTCGAC
41644094 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACAC
* * * *
41644159 TTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACACTTTCACATTCATCACGTTG
66 TTCACATCCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATTG
*
41644224 GCCACTCGACCTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGAC
131 GCCACTCGACCTTATCACATATATACACTTTCACATTCATCACATTGGCCACTCGAC
* * *
41644281 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATACACAC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACAC
41644346 CTTGTACATC
Statistics
Matches: 234, Mismatches: 17, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
187 189 0.81
188 45 0.19
ACGTcount: A:0.28, C:0.31, G:0.08, T:0.33
Consensus pattern (187 bp):
CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACAC
TTCACATCCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATTG
GCCACTCGACCTTATCACATATATACACTTTCACATTCATCACATTGGCCACTCGAC
Found at i:41648857 original size:16 final size:17
Alignment explanation
Indices: 41648827--41648859 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
41648817 ACTCATCAAG
41648827 ATTCGATTATATAATTT
1 ATTCGATTATATAATTT
*
41648844 ATTC-ATTATTTAATTT
1 ATTCGATTATATAATTT
41648860 CATTTCTACT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.33, C:0.06, G:0.03, T:0.58
Consensus pattern (17 bp):
ATTCGATTATATAATTT
Found at i:41649857 original size:40 final size:41
Alignment explanation
Indices: 41649749--41649955 Score: 192
Period size: 40 Copynumber: 5.2 Consensus size: 41
41649739 AAATTTGGCT
* * * * *
41649749 CGGATGTAACAACCAGCACGAACGCCTTCGGGA-CTTAACC
1 CGGATATAATAACTAGCACAAATGCCTTCGGGATCTTAACC
* * *
41649789 CGGTTATAATAACCT-GCACGAATACCTTCGGGA-CTTAACC
1 CGGATATAATAA-CTAGCACAAATGCCTTCGGGATCTTAACC
* * * **
41649829 CGGTTATAATAACTAGTACAATTGCCTTC-GGATCTTAGTC
1 CGGATATAATAACTAGCACAAATGCCTTCGGGATCTTAACC
* **
41649869 CGGATATAGTAACTAGCACAAATGCCTTC-GGATCTTAGTC
1 CGGATATAATAACTAGCACAAATGCCTTCGGGATCTTAACC
* **
41649909 CGGATATAGTAACTAGCACAAATGCCTTC-GGATCTTAGTC
1 CGGATATAATAACTAGCACAAATGCCTTCGGGATCTTAACC
41649949 CGGATAT
1 CGGATAT
41649956 CCTCCGAATA
Statistics
Matches: 148, Mismatches: 16, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
39 5 0.03
40 142 0.96
41 1 0.01
ACGTcount: A:0.29, C:0.25, G:0.20, T:0.26
Consensus pattern (41 bp):
CGGATATAATAACTAGCACAAATGCCTTCGGGATCTTAACC
Found at i:41655643 original size:18 final size:17
Alignment explanation
Indices: 41655620--41655668 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 17
41655610 TAAAATGACA
41655620 CAAATTAATAATATTTAT
1 CAAATTAATAATATTT-T
*
41655638 CAAATTAATTTTATATTTT
1 CAAATTAA--TAATATTTT
41655657 CAAATATAATAA
1 CAAAT-TAATAA
41655669 GAGTTAAGTA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
18 10 0.38
19 6 0.23
20 10 0.38
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.45
Consensus pattern (17 bp):
CAAATTAATAATATTTT
Found at i:41655867 original size:16 final size:16
Alignment explanation
Indices: 41655846--41655876 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
41655836 ATTTTTATTA
*
41655846 TTTTAATATTAAATAT
1 TTTTAAAATTAAATAT
41655862 TTTTAAAATTAAATA
1 TTTTAAAATTAAATA
41655877 ATGTTAATAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TTTTAAAATTAAATAT
Found at i:41659140 original size:21 final size:21
Alignment explanation
Indices: 41659116--41659155 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
41659106 CTAATAACCT
*
41659116 ACCTTTACCACCTAATTCTTC
1 ACCTATACCACCTAATTCTTC
* *
41659137 ACCTATCCCACCTGATTCT
1 ACCTATACCACCTAATTCT
41659156 CCATCACCTC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.23, C:0.40, G:0.03, T:0.35
Consensus pattern (21 bp):
ACCTATACCACCTAATTCTTC
Found at i:41666468 original size:47 final size:47
Alignment explanation
Indices: 41666414--41667095 Score: 942
Period size: 47 Copynumber: 14.2 Consensus size: 47
41666404 AAGATATGTA
41666414 ATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTATAT
1 ATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTATAT
*
41666461 ATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATAT
1 ATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTATAT
*
41666508 ATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATAT
1 ATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTATAT
* *
41666555 ATGTGACAAGGCCTAA-GGCCGATGTGATGAATGTGAAAGTGTATAT
1 ATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTATAT
41666601 ATGTGATAAGGCC-AATGGCCAATGTGATGAATGTGAAAGTGTATAT
1 ATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTATAT
* *
41666647 ATGTGACAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
1 ATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTATAT
*
41666694 ATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATAT
1 ATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTATAT
* *
41666741 ATGTGAAGGTGTATATATGTG-ATAA-GGCCGAATG-GCCAATGTGATGAATGTGAAAGTGTATA
1 A--T----GTG-ATA-A-G-GCCTAATGGCC-AATGTG---ATG-A----ATGTGAAAGTGTATA
41666803 T
47 T
*
41666804 ATGTGAGAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTATAT
1 ATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTATAT
* *
41666851 ATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGAGTATAT
1 ATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTATAT
* *
41666898 ATGTGACAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
1 ATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTATAT
*
41666945 ATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATAT
1 ATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTATAT
* * * * *
41666992 ATGAGATAAGACCTAATGGCCGATGTGATGGATGTGAAGGTGTATAT
1 ATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTATAT
* * * *
41667039 ATGTGATAAGACCGAATGGCCAATGTGATGGATGTGAAAGTGTATAA
1 ATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTATAT
41667086 ATGTGATAAG
1 ATGTGATAAG
41667096 TCCCGAAGGG
Statistics
Matches: 573, Mismatches: 38, Indels: 48
0.87 0.06 0.07
Matches are distributed among these distances:
45 2 0.00
46 82 0.14
47 424 0.74
49 1 0.00
52 3 0.01
53 4 0.01
54 11 0.02
55 12 0.02
56 9 0.02
57 4 0.01
58 3 0.01
61 1 0.00
63 17 0.03
ACGTcount: A:0.34, C:0.09, G:0.30, T:0.28
Consensus pattern (47 bp):
ATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTATAT
Found at i:41666489 original size:22 final size:22
Alignment explanation
Indices: 41666461--41666536 Score: 64
Period size: 22 Copynumber: 3.3 Consensus size: 22
41666451 AAGTGTATAT
41666461 ATGTGATAAGGCCGAATGGCCA
1 ATGTGATAAGGCCGAATGGCCA
* * ***
41666483 ATGTGATGAATG-TGAAAGTGTATA
1 ATGTGAT-AAGGCCG-AA-TGGCCA
41666507 TATGTGATAAGGCCGAATGGCCA
1 -ATGTGATAAGGCCGAATGGCCA
41666530 ATGTGAT
1 ATGTGAT
41666537 GAATGTGAAA
Statistics
Matches: 39, Mismatches: 10, Indels: 10
0.66 0.17 0.17
Matches are distributed among these distances:
22 15 0.38
23 8 0.21
24 8 0.21
25 8 0.21
ACGTcount: A:0.33, C:0.11, G:0.30, T:0.26
Consensus pattern (22 bp):
ATGTGATAAGGCCGAATGGCCA
Found at i:41666744 original size:16 final size:16
Alignment explanation
Indices: 41666725--41666762 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
41666715 AATGTGATGA
41666725 ATGTGAAAGTGTATAT
1 ATGTGAAAGTGTATAT
*
41666741 ATGTGAAGGTGTATAT
1 ATGTGAAAGTGTATAT
41666757 ATGTGA
1 ATGTGA
41666763 TAAGGCCGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.34, C:0.00, G:0.29, T:0.37
Consensus pattern (16 bp):
ATGTGAAAGTGTATAT
Found at i:41666756 original size:63 final size:63
Alignment explanation
Indices: 41666678--41666809 Score: 255
Period size: 63 Copynumber: 2.1 Consensus size: 63
41666668 GATGTGATGA
41666678 ATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATAT
1 ATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATAT
*
41666741 ATGTGAAGGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATAT
1 ATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATAT
41666804 ATGTGA
1 ATGTGA
41666810 GAAGGCCTAA
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
63 68 1.00
ACGTcount: A:0.34, C:0.06, G:0.30, T:0.30
Consensus pattern (63 bp):
ATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATAT
Found at i:41666756 original size:110 final size:110
Alignment explanation
Indices: 41666631--41666856 Score: 398
Period size: 110 Copynumber: 2.1 Consensus size: 110
41666621 AATGTGATGA
* *
41666631 ATGTGAAAGTGTATATATGTGACAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATAT
1 ATGTGAAAGTGTATATATGTGACAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATAT
*
41666696 GTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATAT
66 GTGAGAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATAT
* *
41666741 ATGTGAAGGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATAT
1 ATGTGAAAGTGTATATATGTGACAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATAT
*
41666806 GTGAGAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTATAT
66 GTGAGAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATAT
41666851 ATGTGA
1 ATGTGA
41666857 TAAGGCCGAA
Statistics
Matches: 110, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
110 110 1.00
ACGTcount: A:0.34, C:0.08, G:0.30, T:0.29
Consensus pattern (110 bp):
ATGTGAAAGTGTATATATGTGACAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATAT
GTGAGAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATAT
Found at i:41666767 original size:18 final size:17
Alignment explanation
Indices: 41666725--41666767 Score: 63
Period size: 16 Copynumber: 2.6 Consensus size: 17
41666715 AATGTGATGA
41666725 ATGTGAAA-GTGTATAT
1 ATGTGAAAGGTGTATAT
41666741 ATGTG-AAGGTGTATAT
1 ATGTGAAAGGTGTATAT
41666757 ATGTGATAAGG
1 ATGTGA-AAGG
41666768 CCGAATGGCC
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
15 2 0.08
16 18 0.75
18 4 0.17
ACGTcount: A:0.35, C:0.00, G:0.30, T:0.35
Consensus pattern (17 bp):
ATGTGAAAGGTGTATAT
Found at i:41666798 original size:157 final size:156
Alignment explanation
Indices: 41666585--41666903 Score: 593
Period size: 157 Copynumber: 2.0 Consensus size: 156
41666575 GATGTGATGA
41666585 ATGTGAAAGTGTATATATGTGATAAGGCCAATGGCCAATGTGATGAATGTGAAAGTGTATATATG
1 ATGTGAAAGTGTATATATGTGATAAGGCCAATGGCCAATGTGATGAATGTGAAAGTGTATATATG
*
41666650 TGACAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCC
66 TGACAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCC
*
41666715 AATGTGATGAATGTGAAAGTGTATAT
131 AATGTGATGAATGTGAAAGAGTATAT
*
41666741 ATGTGAAGGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATAT
1 ATGTGAAAGTGTATATATGTGATAAGGCC-AATGGCCAATGTGATGAATGTGAAAGTGTATATAT
*
41666806 GTGAGAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCGAATGGC
65 GTGACAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCGAATGGC
41666871 CAATGTGATGAATGTGAAAGAGTATAT
130 CAATGTGATGAATGTGAAAGAGTATAT
41666898 ATGTGA
1 ATGTGA
41666904 CAAGGCCTAA
Statistics
Matches: 158, Mismatches: 4, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
156 28 0.18
157 130 0.82
ACGTcount: A:0.34, C:0.08, G:0.29, T:0.29
Consensus pattern (156 bp):
ATGTGAAAGTGTATATATGTGATAAGGCCAATGGCCAATGTGATGAATGTGAAAGTGTATATATG
TGACAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCC
AATGTGATGAATGTGAAAGAGTATAT
Found at i:41669088 original size:38 final size:38
Alignment explanation
Indices: 41669043--41669155 Score: 147
Period size: 38 Copynumber: 3.0 Consensus size: 38
41669033 AATCCGGGCT
* *
41669043 TAAAGACCCGATGACTATAAGTAGAGATTGTGTCCGGG
1 TAAAGACCCGATGACTATATGTAGAGATTATGTCCGGG
*
41669081 TAAAGACCCGATGACTATATGTGGAGATTATG-CCTGGG
1 TAAAGACCCGATGACTATATGTAGAGATTATGTCC-GGG
* * * *
41669119 TAAAGATCCGATGGCTATGTGCAGAGATTATGTCCGG
1 TAAAGACCCGATGACTATATGTAGAGATTATGTCCGG
41669156 ATTAAAATTC
Statistics
Matches: 65, Mismatches: 8, Indels: 4
0.84 0.10 0.05
Matches are distributed among these distances:
37 2 0.03
38 61 0.94
39 2 0.03
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.26
Consensus pattern (38 bp):
TAAAGACCCGATGACTATATGTAGAGATTATGTCCGGG
Found at i:41669276 original size:40 final size:40
Alignment explanation
Indices: 41669213--41669403 Score: 301
Period size: 40 Copynumber: 4.8 Consensus size: 40
41669203 CTCAACAATG
*
41669213 ATCCGGGTTAAGTCCCGAAGAGCATTCGTGCTGGTGTTAC
1 ATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGTTAC
*
41669253 ATCTGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGTTAC
1 ATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGTTAC
* * *
41669293 ATCCAGACTAAGTCCCGAAGAGCATTCGTGCTGGTATTAC
1 ATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGTTAC
*
41669333 ATCTGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGTTAC
1 ATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGTTAC
** *
41669373 ATCCGGGCTAAGTCTTGAAGGGCATTCGTGC
1 ATCCGGGCTAAGTCCCGAAGAGCATTCGTGC
41669404 CGATGATGTG
Statistics
Matches: 137, Mismatches: 14, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
40 137 1.00
ACGTcount: A:0.21, C:0.23, G:0.29, T:0.27
Consensus pattern (40 bp):
ATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGTTAC
Found at i:41669614 original size:25 final size:25
Alignment explanation
Indices: 41669572--41669626 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 25
41669562 TGTGTAATAA
*
41669572 CGAATGAATATAGGCACTATGTGTG
1 CGAATGAATATAGACACTATGTGTG
*
41669597 CGAATGAAT-TGAGACACTGTGTGTG
1 CGAATGAATAT-AGACACTATGTGTG
41669622 CGAAT
1 CGAAT
41669627 TCTTTAACCG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
24 1 0.04
25 26 0.96
ACGTcount: A:0.31, C:0.13, G:0.29, T:0.27
Consensus pattern (25 bp):
CGAATGAATATAGACACTATGTGTG
Found at i:41669650 original size:28 final size:28
Alignment explanation
Indices: 41669611--41669764 Score: 118
Period size: 28 Copynumber: 5.5 Consensus size: 28
41669601 TGAATTGAGA
*
41669611 CACTGTGTGTGCGAATTCTTTAACCGAG
1 CACTATGTGTGCGAATTCTTTAACCGAG
** * **
41669639 CACTATGTGTGCGAGA-TCGGTCAGTG-G
1 CACTATGTGTGCGA-ATTCTTTAACCGAG
*
41669666 ACACTGTGTGTGCGAATTCTTTAACCGAG
1 -CACTATGTGTGCGAATTCTTTAACCGAG
* ** * **
41669695 CACTATGTGTGC-AAGATCGGTCAGTG-G
1 CACTATGTGTGCGAA-TTCTTTAACCGAG
*
41669722 ACACTGTGTGTGCGAATTCTTTAACCGAG
1 -CACTATGTGTGCGAATTCTTTAACCGAG
41669751 CACTATGTGTGCGA
1 CACTATGTGTGCGA
41669765 GATCGGTCAG
Statistics
Matches: 91, Mismatches: 27, Indels: 16
0.68 0.20 0.12
Matches are distributed among these distances:
27 5 0.05
28 81 0.89
29 5 0.05
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.29
Consensus pattern (28 bp):
CACTATGTGTGCGAATTCTTTAACCGAG
Found at i:41669679 original size:56 final size:56
Alignment explanation
Indices: 41669609--41669795 Score: 356
Period size: 56 Copynumber: 3.3 Consensus size: 56
41669599 AATGAATTGA
41669609 GACACTGTGTGTGCGAATTCTTTAACCGAGCACTATGTGTGCGAGATCGGTCAGTG
1 GACACTGTGTGTGCGAATTCTTTAACCGAGCACTATGTGTGCGAGATCGGTCAGTG
*
41669665 GACACTGTGTGTGCGAATTCTTTAACCGAGCACTATGTGTGCAAGATCGGTCAGTG
1 GACACTGTGTGTGCGAATTCTTTAACCGAGCACTATGTGTGCGAGATCGGTCAGTG
41669721 GACACTGTGTGTGCGAATTCTTTAACCGAGCACTATGTGTGCGAGATCGGTCAGTG
1 GACACTGTGTGTGCGAATTCTTTAACCGAGCACTATGTGTGCGAGATCGGTCAGTG
*
41669777 GGCACTGTGTGTGCGAATT
1 GACACTGTGTGTGCGAATT
41669796 TCGTTTCATG
Statistics
Matches: 128, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 128 1.00
ACGTcount: A:0.21, C:0.19, G:0.30, T:0.29
Consensus pattern (56 bp):
GACACTGTGTGTGCGAATTCTTTAACCGAGCACTATGTGTGCGAGATCGGTCAGTG
Found at i:41669781 original size:28 final size:28
Alignment explanation
Indices: 41669638--41669792 Score: 116
Period size: 28 Copynumber: 5.5 Consensus size: 28
41669628 CTTTAACCGA
41669638 GCACTATGTGTGCGAGATCGGTCAGTGG
1 GCACTATGTGTGCGAGATCGGTCAGTGG
* * ** * ** *
41669666 ACACTGTGTGTGCGA-ATTCTTTAACCGA
1 GCACTATGTGTGCGAGA-TCGGTCAGTGG
*
41669694 GCACTATGTGTGCAAGATCGGTCAGTGG
1 GCACTATGTGTGCGAGATCGGTCAGTGG
* * ** * ** *
41669722 ACACTGTGTGTGCGA-ATTCTTTAACCGA
1 GCACTATGTGTGCGAGA-TCGGTCAGTGG
41669750 GCACTATGTGTGCGAGATCGGTCAGTGG
1 GCACTATGTGTGCGAGATCGGTCAGTGG
*
41669778 GCACTGTGTGTGCGA
1 GCACTATGTGTGCGA
41669793 ATTTCGTTTC
Statistics
Matches: 88, Mismatches: 35, Indels: 8
0.67 0.27 0.06
Matches are distributed among these distances:
27 2 0.02
28 84 0.95
29 2 0.02
ACGTcount: A:0.21, C:0.19, G:0.32, T:0.28
Consensus pattern (28 bp):
GCACTATGTGTGCGAGATCGGTCAGTGG
Found at i:41672772 original size:25 final size:25
Alignment explanation
Indices: 41672744--41672868 Score: 77
Period size: 25 Copynumber: 5.2 Consensus size: 25
41672734 CTAATGGCCA
41672744 ATGTGATGAATGTGAAAGTGTATAT
1 ATGTGATGAATGTGAAAGTGTATAT
* * ***
41672769 ATGTGAT-AAGGCCG-AA-TGGCCA-
1 ATGTGATGAATG-TGAAAGTGTATAT
41672791 ATGTGATGAATGTGAAAGTGTATAT
1 ATGTGATGAATGTGAAAGTGTATAT
* * ***
41672816 ATGTGAT-AAGGCCG-AA-TGGCCA-
1 ATGTGATGAATG-TGAAAGTGTATAT
*
41672838 ATGTGATGAATATGAAAGTGTATAT
1 ATGTGATGAATGTGAAAGTGTATAT
41672863 ATGTGA
1 ATGTGA
41672869 CAAGGCCTAA
Statistics
Matches: 69, Mismatches: 21, Indels: 20
0.63 0.19 0.18
Matches are distributed among these distances:
22 16 0.23
23 15 0.22
24 16 0.23
25 22 0.32
ACGTcount: A:0.35, C:0.06, G:0.29, T:0.30
Consensus pattern (25 bp):
ATGTGATGAATGTGAAAGTGTATAT
Found at i:41672772 original size:47 final size:47
Alignment explanation
Indices: 41672719--41673341 Score: 1032
Period size: 47 Copynumber: 13.3 Consensus size: 47
41672709 ACAAGATATG
*
41672719 TATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTA
1 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTA
41672766 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTA
1 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTA
*
41672813 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATATGAAAGTGTA
1 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTA
* * *
41672860 TATATGTGACAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTA
1 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTA
41672907 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTA
1 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTA
* * * * * *
41672954 TATATGAGATAAGACCTAATGGCCGATGTGATGGATGTGAAGGTGTA
1 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTA
41673001 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTA
1 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTA
*
41673048 TATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTA
1 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTA
*
41673095 TATATGTGATAAGGCCGAATGGCCAATCTGATGAATGTGAAAGTGTA
1 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTA
* *
41673142 TATATGTGACAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTA
1 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTA
41673189 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTA
1 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTA
* * * * * *
41673236 TATATGAGATAAGACCTAATGGCCGATGTGATGGATGTGAAGGTGTA
1 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTA
*
41673283 TA-ATGTGATAAGGCCGAATGGCCAATGTGATGGATGTGAAAGTGTA
1 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTA
*
41673329 TAAATGTGATAAG
1 TATATGTGATAAG
41673342 TCCCGAAGGG
Statistics
Matches: 535, Mismatches: 40, Indels: 2
0.93 0.07 0.00
Matches are distributed among these distances:
46 41 0.08
47 494 0.92
ACGTcount: A:0.34, C:0.09, G:0.29, T:0.28
Consensus pattern (47 bp):
TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTA
Found at i:41672797 original size:22 final size:22
Alignment explanation
Indices: 41672769--41672844 Score: 64
Period size: 22 Copynumber: 3.3 Consensus size: 22
41672759 AAGTGTATAT
41672769 ATGTGATAAGGCCGAATGGCCA
1 ATGTGATAAGGCCGAATGGCCA
* * ***
41672791 ATGTGATGAATG-TGAAAGTGTATA
1 ATGTGAT-AAGGCCG-AA-TGGCCA
41672815 TATGTGATAAGGCCGAATGGCCA
1 -ATGTGATAAGGCCGAATGGCCA
41672838 ATGTGAT
1 ATGTGAT
41672845 GAATATGAAA
Statistics
Matches: 39, Mismatches: 10, Indels: 10
0.66 0.17 0.17
Matches are distributed among these distances:
22 15 0.38
23 8 0.21
24 8 0.21
25 8 0.21
ACGTcount: A:0.33, C:0.11, G:0.30, T:0.26
Consensus pattern (22 bp):
ATGTGATAAGGCCGAATGGCCA
Found at i:41675373 original size:27 final size:27
Alignment explanation
Indices: 41675289--41675442 Score: 173
Period size: 27 Copynumber: 5.5 Consensus size: 27
41675279 GACGAGAATG
* * *
41675289 GCACTAAGTGTGCAAGCTGGAAATATATG
1 GCACTAAGTGTGCGAGCT-G-ATTATATA
*
41675318 GCACTAAGTGTGCGAGCTCAAATTATATA
1 GCACTAAGTGTGCGAGCT--GATTATATA
* *
41675347 GCACTATGTGTGCGAGCTGATTTTATA
1 GCACTAAGTGTGCGAGCTGATTATATA
**
41675374 GCACTAAGTGTGCGAATTTGATTATATA
1 GCACTAAGTGTGCG-AGCTGATTATATA
* *
41675402 GCACTATGTGTGCGAGCTGATTTTATA
1 GCACTAAGTGTGCGAGCTGATTATATA
41675429 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
41675443 GATTCACTAT
Statistics
Matches: 106, Mismatches: 17, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
27 43 0.41
28 23 0.22
29 40 0.38
ACGTcount: A:0.29, C:0.15, G:0.25, T:0.31
Consensus pattern (27 bp):
GCACTAAGTGTGCGAGCTGATTATATA
Found at i:41675410 original size:55 final size:55
Alignment explanation
Indices: 41675339--41675442 Score: 208
Period size: 55 Copynumber: 1.9 Consensus size: 55
41675329 GCGAGCTCAA
41675339 ATTATATAGCACTATGTGTGCGAGCTGATTTTATAGCACTAAGTGTGCGAATTTG
1 ATTATATAGCACTATGTGTGCGAGCTGATTTTATAGCACTAAGTGTGCGAATTTG
41675394 ATTATATAGCACTATGTGTGCGAGCTGATTTTATAGCACTAAGTGTGCG
1 ATTATATAGCACTATGTGTGCGAGCTGATTTTATAGCACTAAGTGTGCG
41675443 GATTCACTAT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 49 1.00
ACGTcount: A:0.27, C:0.13, G:0.24, T:0.36
Consensus pattern (55 bp):
ATTATATAGCACTATGTGTGCGAGCTGATTTTATAGCACTAAGTGTGCGAATTTG
Found at i:41683229 original size:27 final size:27
Alignment explanation
Indices: 41683145--41683298 Score: 173
Period size: 27 Copynumber: 5.5 Consensus size: 27
41683135 GACGAGAATG
* * *
41683145 GCACTAAGTGTGCAAGCTGGAAATATATG
1 GCACTAAGTGTGCGAGCT-G-ATTATATA
*
41683174 GCACTAAGTGTGCGAGCTCAAATTATATA
1 GCACTAAGTGTGCGAGCT--GATTATATA
* *
41683203 GCACTATGTGTGCGAGCTGATTTTATA
1 GCACTAAGTGTGCGAGCTGATTATATA
**
41683230 GCACTAAGTGTGCGAATTTGATTATATA
1 GCACTAAGTGTGCG-AGCTGATTATATA
* *
41683258 GCACTATGTGTGCGAGCTGATTTTATA
1 GCACTAAGTGTGCGAGCTGATTATATA
41683285 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
41683299 GATTCACTAT
Statistics
Matches: 106, Mismatches: 17, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
27 43 0.41
28 23 0.22
29 40 0.38
ACGTcount: A:0.29, C:0.15, G:0.25, T:0.31
Consensus pattern (27 bp):
GCACTAAGTGTGCGAGCTGATTATATA
Found at i:41683266 original size:55 final size:55
Alignment explanation
Indices: 41683195--41683298 Score: 208
Period size: 55 Copynumber: 1.9 Consensus size: 55
41683185 GCGAGCTCAA
41683195 ATTATATAGCACTATGTGTGCGAGCTGATTTTATAGCACTAAGTGTGCGAATTTG
1 ATTATATAGCACTATGTGTGCGAGCTGATTTTATAGCACTAAGTGTGCGAATTTG
41683250 ATTATATAGCACTATGTGTGCGAGCTGATTTTATAGCACTAAGTGTGCG
1 ATTATATAGCACTATGTGTGCGAGCTGATTTTATAGCACTAAGTGTGCG
41683299 GATTCACTAT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 49 1.00
ACGTcount: A:0.27, C:0.13, G:0.24, T:0.36
Consensus pattern (55 bp):
ATTATATAGCACTATGTGTGCGAGCTGATTTTATAGCACTAAGTGTGCGAATTTG
Found at i:41686262 original size:29 final size:28
Alignment explanation
Indices: 41686230--41686332 Score: 116
Period size: 29 Copynumber: 3.6 Consensus size: 28
41686220 GGGACGAGAT
* *
41686230 TGGCACTGAGTGTGCGAGCTTGTAATGTA
1 TGGCACTAAGTGTGCGAGCTTG-AATATA
* *
41686259 TGGCACTAAGTGTGCGAGTTTGGACTATA
1 TGGCACTAAGTGTGCGAGCTT-GAATATA
* * *
41686288 TGGCACTATGTGTGCGGGCTTGAATCACA
1 TGGCACTAAGTGTGCGAGCTTGAAT-ATA
41686317 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
41686333 TGATTGAGTA
Statistics
Matches: 62, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
28 3 0.05
29 58 0.94
30 1 0.02
ACGTcount: A:0.21, C:0.17, G:0.33, T:0.29
Consensus pattern (28 bp):
TGGCACTAAGTGTGCGAGCTTGAATATA
Found at i:41691229 original size:33 final size:33
Alignment explanation
Indices: 41691188--41691250 Score: 126
Period size: 33 Copynumber: 1.9 Consensus size: 33
41691178 TTTTTGTTCA
41691188 TCATTTCCTTTGGGCTGAAAATTCTAAGGATTT
1 TCATTTCCTTTGGGCTGAAAATTCTAAGGATTT
41691221 TCATTTCCTTTGGGCTGAAAATTCTAAGGA
1 TCATTTCCTTTGGGCTGAAAATTCTAAGGA
41691251 AGAAGGAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.16, G:0.19, T:0.40
Consensus pattern (33 bp):
TCATTTCCTTTGGGCTGAAAATTCTAAGGATTT
Found at i:41692478 original size:28 final size:28
Alignment explanation
Indices: 41692409--41692509 Score: 114
Period size: 28 Copynumber: 3.5 Consensus size: 28
41692399 GACAAGATTG
* * * *
41692409 GCACTAAGTGTGCGGGTTTAAAATTGTACA
1 GCACTAAGTGTGCGAGTTT--GATTATATA
41692439 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
41692467 GCACTAAGTGTGCGAG-TTGAATACATATA
1 GCACTAAGTGTGCGAGTTTG-AT-TATATA
41692496 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
41692510 GATCCACTAT
Statistics
Matches: 64, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
27 3 0.05
28 24 0.38
29 19 0.30
30 18 0.28
ACGTcount: A:0.30, C:0.14, G:0.27, T:0.30
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:41694272 original size:44 final size:42
Alignment explanation
Indices: 41694191--41694272 Score: 110
Period size: 44 Copynumber: 1.9 Consensus size: 42
41694181 GGATTTCAAG
* * *
41694191 TTGTGATTTGTGTAAGACCACGTCTGGGTCGTTGGCATCGAT
1 TTGTGATTTGTGTAAGACCACGTCTGGGACATCGGCATCGAT
*
41694233 TTGTGATTTACGTGTAAGACCATGTCTGGGACATCGGCAT
1 TTGTGATTT--GTGTAAGACCACGTCTGGGACATCGGCAT
41694273 TGTATATGAG
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
42 9 0.26
44 25 0.74
ACGTcount: A:0.20, C:0.17, G:0.29, T:0.34
Consensus pattern (42 bp):
TTGTGATTTGTGTAAGACCACGTCTGGGACATCGGCATCGAT
Found at i:41697394 original size:22 final size:22
Alignment explanation
Indices: 41697360--41697422 Score: 58
Period size: 21 Copynumber: 2.9 Consensus size: 22
41697350 AAGAAATATA
* **
41697360 TAAAAATA-CATAAATATTTTT
1 TAAAAATATAATAAATAAATTT
41697381 TAAAAATATAAT-AATAAATTT
1 TAAAAATATAATAAATAAATTT
*
41697402 TAAAATATATATAAAAATAAA
1 TAAAA-ATATA-ATAAATAAA
41697423 AAAATATTCT
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
21 20 0.59
22 7 0.21
23 1 0.03
24 6 0.18
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.37
Consensus pattern (22 bp):
TAAAAATATAATAAATAAATTT
Found at i:41697396 original size:21 final size:22
Alignment explanation
Indices: 41697378--41697419 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
41697368 CATAAATATT
41697378 TTTTAAAA-ATATAATAATAAA
1 TTTTAAAATATATAATAATAAA
41697399 TTTTAAAATATAT-ATAA-AAA
1 TTTTAAAATATATAATAATAAA
41697419 T
1 T
41697420 AAAAAAATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 4 0.20
21 12 0.60
22 4 0.20
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
TTTTAAAATATATAATAATAAA
Found at i:41697408 original size:20 final size:21
Alignment explanation
Indices: 41697378--41697419 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 21
41697368 CATAAATATT
41697378 TTTTAAAAATATA-ATAATAAA
1 TTTTAAAAATATATATAA-AAA
41697399 TTTT-AAAATATATATAAAAA
1 TTTTAAAAATATATATAAAAA
41697419 T
1 T
41697420 AAAAAAATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
TTTTAAAAATATATATAAAAA
Found at i:41697450 original size:12 final size:12
Alignment explanation
Indices: 41697384--41697493 Score: 55
Period size: 11 Copynumber: 10.1 Consensus size: 12
41697374 TATTTTTTAA
41697384 AAATATAATAAT
1 AAATATAATAAT
*
41697396 AAAT-T--TTA-
1 AAATATAATAAT
41697404 AAATAT-AT-AT
1 AAATATAATAAT
*
41697414 AAAAATAA-AA-
1 AAATATAATAAT
**
41697424 AAATATTCTAA-
1 AAATATAATAAT
41697435 AAATATAATAAT
1 AAATATAATAAT
*
41697447 AAATTTAAT-AT
1 AAATATAATAAT
* *
41697458 TAATATTAATATT
1 AAATA-TAATAAT
41697471 AAATA-AAT-AT
1 AAATATAATAAT
*
41697481 AAATATATTAAT
1 AAATATAATAAT
41697493 A
1 A
41697494 TTAAATAAAC
Statistics
Matches: 73, Mismatches: 14, Indels: 22
0.67 0.13 0.20
Matches are distributed among these distances:
8 4 0.05
9 4 0.05
10 17 0.23
11 24 0.33
12 19 0.26
13 5 0.07
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (12 bp):
AAATATAATAAT
Found at i:41697460 original size:6 final size:6
Alignment explanation
Indices: 41697451--41697497 Score: 51
Period size: 6 Copynumber: 7.7 Consensus size: 6
41697441 AATAATAAAT
* *
41697451 TTAATA TTAATA TTAATA TTAA-A TAAATA TAAATATA TTAATA TTAA
1 TTAATA TTAATA TTAATA TTAATA TTAATA T-TA-ATA TTAATA TTAA
41697498 ATAAACTAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
5 4 0.11
6 25 0.69
7 3 0.08
8 4 0.11
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (6 bp):
TTAATA
Found at i:41697462 original size:23 final size:22
Alignment explanation
Indices: 41697435--41697493 Score: 64
Period size: 23 Copynumber: 2.6 Consensus size: 22
41697425 AATATTCTAA
*
41697435 AAATATAATAATAAATTTAATAT
1 AAATATAATAATAAA-TAAATAT
* *
41697458 TAATATTAATATTAAATAAATAT
1 AAATA-TAATAATAAATAAATAT
*
41697481 AAATATATTAATA
1 AAATATAATAATA
41697494 TTAAATAAAC
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
22 6 0.21
23 14 0.48
24 9 0.31
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (22 bp):
AAATATAATAATAAATAAATAT
Found at i:41697485 original size:17 final size:17
Alignment explanation
Indices: 41697435--41697486 Score: 52
Period size: 17 Copynumber: 2.9 Consensus size: 17
41697425 AATATTCTAA
41697435 AAATATAATAATAAAT-TT
1 AAATA-AAT-ATAAATATT
* *
41697453 AATATTAATATTAATATT
1 AA-ATAAATATAAATATT
41697471 AAATAAATATAAATAT
1 AAATAAATATAAATAT
41697487 ATTAATATTA
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
17 17 0.61
18 9 0.32
19 2 0.07
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
AAATAAATATAAATATT
Found at i:41699541 original size:23 final size:24
Alignment explanation
Indices: 41699499--41699546 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
41699489 ACATTTAAGA
41699499 AATTAAGTAAATTACCCAAGATTT
1 AATTAAGTAAATTACCCAAGATTT
* *
41699523 AATTAAGTAATTTA-GCAAGATTT
1 AATTAAGTAAATTACCCAAGATTT
41699546 A
1 A
41699547 GGAATTTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 9 0.41
24 13 0.59
ACGTcount: A:0.46, C:0.08, G:0.10, T:0.35
Consensus pattern (24 bp):
AATTAAGTAAATTACCCAAGATTT
Found at i:41699644 original size:69 final size:69
Alignment explanation
Indices: 41699564--41699702 Score: 210
Period size: 69 Copynumber: 2.0 Consensus size: 69
41699554 TTAATATTTT
* * *
41699564 AAGTAACATTTAAGAAATTAAGT-AATTTTGTCATTATTTTAAGTTACTTAATTT-TTTAAAAGT
1 AAGTAACATTTAAGAAATTAAGTAAAATTT-TCATTATTATAAGTTACTTAATTTCTTTAAAA-C
41699627 CCTTTA
64 CCTTTA
*
41699633 AAGTAACATTTAAGAAATTAAGTAAAATTTTCATTATTATGAGTTACTTAATTTCTTTAAAACCC
1 AAGTAACATTTAAGAAATTAAGTAAAATTTTCATTATTATAAGTTACTTAATTTCTTTAAAACCC
41699698 TTTA
66 TTTA
41699702 A
1 A
41699703 TGGTTTAAGT
Statistics
Matches: 64, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
69 52 0.81
70 12 0.19
ACGTcount: A:0.40, C:0.09, G:0.08, T:0.44
Consensus pattern (69 bp):
AAGTAACATTTAAGAAATTAAGTAAAATTTTCATTATTATAAGTTACTTAATTTCTTTAAAACCC
TTTA
Found at i:41701724 original size:20 final size:21
Alignment explanation
Indices: 41701688--41701727 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
41701678 AATAGGAGAG
41701688 TAAAAAGAGCGAGAAATGGGC
1 TAAAAAGAGCGAGAAATGGGC
41701709 TAAAAA-AG-GAGAAAATGGG
1 TAAAAAGAGCGAG-AAATGGG
41701728 TCAACGTGGG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 3 0.17
20 9 0.50
21 6 0.33
ACGTcount: A:0.53, C:0.05, G:0.33, T:0.10
Consensus pattern (21 bp):
TAAAAAGAGCGAGAAATGGGC
Found at i:41714855 original size:19 final size:18
Alignment explanation
Indices: 41714805--41714855 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 18
41714795 TTTTGTCATC
41714805 TTTGTTCTTTATTACTAT
1 TTTGTTCTTTATTACTAT
41714823 TTTGATT-TTCTATTATCTAT
1 TTTG-TTCTT-TATTA-CTAT
*
41714843 TTTGTTCGTTATT
1 TTTGTTCTTTATT
41714856 CTTTATGTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
18 6 0.21
19 13 0.46
20 9 0.32
ACGTcount: A:0.16, C:0.10, G:0.08, T:0.67
Consensus pattern (18 bp):
TTTGTTCTTTATTACTAT
Found at i:41723536 original size:32 final size:32
Alignment explanation
Indices: 41723477--41723538 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
41723467 ATTTTTTACA
** *
41723477 TAATTAAATATTTTGATTTTGATTTTTTTTGT
1 TAATTAAATATTTAAATTTTGAATTTTTTTGT
41723509 TAATTAAATATTTAAAATTTT-AATTTTTTT
1 TAATTAAATATTT-AAATTTTGAATTTTTTT
41723539 ATTTGCCTTG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
32 21 0.81
33 5 0.19
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.63
Consensus pattern (32 bp):
TAATTAAATATTTAAATTTTGAATTTTTTTGT
Found at i:41730502 original size:44 final size:44
Alignment explanation
Indices: 41730439--41730602 Score: 211
Period size: 44 Copynumber: 3.6 Consensus size: 44
41730429 TCACATTTAT
* * *
41730439 CACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTGTCACTGATCAGATAAGTGTAGCTGAGGCTAC
* *
41730483 CACTTATCACTTGTCACTGATTAGATAAGTGTAGTTGAGGCTAC
1 CACTTATCACTTGTCACTGATCAGATAAGTGTAGCTGAGGCTAC
41730527 CACTTATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTGAGGCTAC
1 CAC-T-T-A----TCACTTGTCACTGATCAGATAAGTGTAGCTGAGGCTAC
*
41730578 CAGTTATCACTTGTCACTGATCAGA
1 CACTTATCACTTGTCACTGATCAGA
41730603 AGTACTCAAA
Statistics
Matches: 105, Mismatches: 8, Indels: 14
0.83 0.06 0.11
Matches are distributed among these distances:
44 61 0.58
45 1 0.01
46 1 0.01
47 1 0.01
48 1 0.01
49 1 0.01
50 1 0.01
51 38 0.36
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.32
Consensus pattern (44 bp):
CACTTATCACTTGTCACTGATCAGATAAGTGTAGCTGAGGCTAC
Found at i:41730538 original size:51 final size:51
Alignment explanation
Indices: 41730435--41730595 Score: 237
Period size: 51 Copynumber: 3.3 Consensus size: 51
41730425 CAGATCACAT
* *
41730435 TTATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCAC
1 TTATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTGAGGCTACCAC
*
41730486 TTATCACTTGTCAC-TG--A-T--T-AGATAAGTGTAGTTGAGGCTACCAC
1 TTATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTGAGGCTACCAC
*
41730530 TTATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTGAGGCTACCAG
1 TTATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTGAGGCTACCAC
41730581 TTATCACTTGTCACT
1 TTATCACTTGTCACT
41730596 GATCAGAAGT
Statistics
Matches: 98, Mismatches: 5, Indels: 14
0.84 0.04 0.12
Matches are distributed among these distances:
44 36 0.37
45 3 0.03
47 2 0.02
48 2 0.02
50 3 0.03
51 52 0.53
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.34
Consensus pattern (51 bp):
TTATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTGAGGCTACCAC
Found at i:41737001 original size:37 final size:37
Alignment explanation
Indices: 41736951--41737035 Score: 134
Period size: 37 Copynumber: 2.3 Consensus size: 37
41736941 TATCACTTGT
* *
41736951 CACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTGATAAGATAAGTGTAGCTAAAGCTAC
* *
41736988 CACTTATCACTGATAAGATAAGTGTAGCTGAGGCTAC
1 CACTTATCACTGATAAGATAAGTGTAGCTAAAGCTAC
41737025 CACTTATCACT
1 CACTTATCACT
41737036 TGTCATTGAT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 44 1.00
ACGTcount: A:0.32, C:0.22, G:0.18, T:0.28
Consensus pattern (37 bp):
CACTTATCACTGATAAGATAAGTGTAGCTAAAGCTAC
Found at i:41743481 original size:20 final size:20
Alignment explanation
Indices: 41743456--41743507 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
41743446 AAGTTTAAGC
41743456 TAAGTAAATGAAATAGAAAG
1 TAAGTAAATGAAATAGAAAG
* *
41743476 TAAGTAAATGGAATGGAAAG
1 TAAGTAAATGAAATAGAAAG
41743496 TAAGTAAATGAA
1 TAAGTAAATGAA
41743508 GTGGCTCTAG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.56, C:0.00, G:0.23, T:0.21
Consensus pattern (20 bp):
TAAGTAAATGAAATAGAAAG
Found at i:41747307 original size:18 final size:17
Alignment explanation
Indices: 41747284--41747322 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
41747274 GAAAGTAAGT
*
41747284 TAAAAAGATAAATAAAGA
1 TAAAAAGAGAAATAAA-A
*
41747302 TAAAAATAGAAATAAAA
1 TAAAAAGAGAAATAAAA
41747319 TAAA
1 TAAA
41747323 TAAAAGATGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.74, C:0.00, G:0.08, T:0.18
Consensus pattern (17 bp):
TAAAAAGAGAAATAAAA
Found at i:41755513 original size:40 final size:40
Alignment explanation
Indices: 41755430--41755582 Score: 168
Period size: 40 Copynumber: 3.8 Consensus size: 40
41755420 TCGAATGATG
* * * *
41755430 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTAC-GAGTTACTAAA
*
41755470 TCCGGACTAAGAT-CCGAAGGCATTTGTACGAGTTACTAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTACGAGTTACTAAA
* * *
41755510 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACGATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTACGAGTTACTA-AA
* *
41755551 -CCGGGCTATGTCCCGAAGGCATTTGAACGAGT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTACGAGT
41755583 AGCTATATCC
Statistics
Matches: 96, Mismatches: 13, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
39 1 0.01
40 86 0.90
41 9 0.09
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTACGAGTTACTAAA
Found at i:41755567 original size:80 final size:80
Alignment explanation
Indices: 41755430--41755598 Score: 202
Period size: 80 Copynumber: 2.1 Consensus size: 80
41755420 TCGAATGATG
* * *
41755430 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACTATATCCGGACTAAGATCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCTTTGTGCTAAGTGACGATAACCGGACTAAGATCCGAAGGCATTT
*
41755495 GTACGAGTTA-CTAAA
66 GAACGAG-TAGCTAAA
* * * *
41755510 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTACGATAACCGGGCTATG-TCCCGAAGGCAT
1 TCCGGGTTAAGTCCCGAAGGC-TTTGTGCTAAGTGACGATAACCGGACTAAGAT-CCGAAGGCAT
*
41755573 TTGAACGAGTAGCTATA
64 TTGAACGAGTAGCTAAA
41755590 TCC-GGTTAA
1 TCCGGGTTAA
41755599 ACTCCGAAGG
Statistics
Matches: 77, Mismatches: 9, Indels: 7
0.83 0.10 0.08
Matches are distributed among these distances:
79 9 0.12
80 61 0.79
81 7 0.09
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (80 bp):
TCCGGGTTAAGTCCCGAAGGCTTTGTGCTAAGTGACGATAACCGGACTAAGATCCGAAGGCATTT
GAACGAGTAGCTAAA
Found at i:41759115 original size:27 final size:27
Alignment explanation
Indices: 41759097--41759166 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
41759087 ATAGTGAGTC
41759097 CGCACACTTAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTATATAATCAACT
*
41759124 CGCACACTTAGTGCTATATGATCAAACT
1 CGCACACTTAGTGCTATATAATC-AACT
*
41759152 CACACACTTAGTGCT
1 CGCACACTTAGTGCT
41759167 GTACAAGTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
27 22 0.55
28 18 0.45
ACGTcount: A:0.31, C:0.27, G:0.13, T:0.29
Consensus pattern (27 bp):
CGCACACTTAGTGCTATATAATCAACT
Found at i:41765516 original size:49 final size:48
Alignment explanation
Indices: 41765463--41765555 Score: 134
Period size: 48 Copynumber: 1.9 Consensus size: 48
41765453 AGAGGGTTTA
* *
41765463 AAATAAATAATATATAAAATAGTTT-AACTACATAATGTATATAAATTTG
1 AAATAAATAATATAT-AAA-AGTTTAAAATAAATAATGTATATAAATTTG
*
41765512 AAATAAATAATATGTAAAAGTTTAAAATAAATAATGTATATAAA
1 AAATAAATAATATATAAAAGTTTAAAATAAATAATGTATATAAA
41765556 AGAAAATCAT
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
47 5 0.12
48 21 0.52
49 14 0.35
ACGTcount: A:0.57, C:0.02, G:0.06, T:0.34
Consensus pattern (48 bp):
AAATAAATAATATATAAAAGTTTAAAATAAATAATGTATATAAATTTG
Found at i:41765539 original size:24 final size:24
Alignment explanation
Indices: 41765458--41765557 Score: 96
Period size: 24 Copynumber: 4.0 Consensus size: 24
41765448 AATAAAGAGG
41765458 GTTTAAAATAAATAATATATAAAATA
1 GTTTAAAATAAATAATATAT-AAA-A
* * *
41765484 GTTT-AACTACATAATGTATATAAA
1 GTTTAAAATAAATAATATATA-AAA
* *
41765508 -TTTGAAATAAATAATATGTAAAA
1 GTTTAAAATAAATAATATATAAAA
41765531 GTTTAAAATAAATAATGTATATAAAA
1 GTTTAAAATAAATAA--TATATAAAA
41765557 G
1 G
41765558 AAAATCATAA
Statistics
Matches: 60, Mismatches: 9, Indels: 10
0.76 0.11 0.13
Matches are distributed among these distances:
23 6 0.10
24 27 0.45
25 14 0.23
26 13 0.22
ACGTcount: A:0.55, C:0.02, G:0.08, T:0.35
Consensus pattern (24 bp):
GTTTAAAATAAATAATATATAAAA
Found at i:41765738 original size:2 final size:2
Alignment explanation
Indices: 41765731--41765759 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
41765721 AAGAGAATTA
41765731 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
41765760 AAGATCTAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:41767447 original size:16 final size:15
Alignment explanation
Indices: 41767426--41767459 Score: 59
Period size: 16 Copynumber: 2.2 Consensus size: 15
41767416 AAAAAGAAGG
41767426 AAAAAGAATAATAGAT
1 AAAAAGAATAATA-AT
41767442 AAAAAGAATAATAAT
1 AAAAAGAATAATAAT
41767457 AAA
1 AAA
41767460 TAATTAGCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.74, C:0.00, G:0.09, T:0.18
Consensus pattern (15 bp):
AAAAAGAATAATAAT
Found at i:41767545 original size:16 final size:16
Alignment explanation
Indices: 41767523--41767566 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 16
41767513 GGAGTTTGTT
*
41767523 ATTATTTATTTACCAA
1 ATTATTTATTTACAAA
*
41767539 TTTATTTATTTACAAA
1 ATTATTTATTTACAAA
*
41767555 ATTATTTTTTTA
1 ATTATTTATTTA
41767567 ACGACTAATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.34, C:0.07, G:0.00, T:0.59
Consensus pattern (16 bp):
ATTATTTATTTACAAA
Found at i:41768474 original size:30 final size:30
Alignment explanation
Indices: 41768440--41768500 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
41768430 ATTTGGATAC
41768440 ATAGTCAACGACTACAAAGATGTACCTATT
1 ATAGTCAACGACTACAAAGATGTACCTATT
* *
41768470 ATAGTCAATGACTACCAAGATGTACCTATT
1 ATAGTCAACGACTACAAAGATGTACCTATT
41768500 A
1 A
41768501 CCATAAGAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.39, C:0.20, G:0.13, T:0.28
Consensus pattern (30 bp):
ATAGTCAACGACTACAAAGATGTACCTATT
Found at i:41770668 original size:24 final size:25
Alignment explanation
Indices: 41770600--41770692 Score: 84
Period size: 24 Copynumber: 3.8 Consensus size: 25
41770590 AGTTGATGAA
41770600 TAGTAAGCTC-TATCGAGCTG-GAAC
1 TAGTAAGCTCTTA-CGAGCTGAGAAC
* * *
41770624 CAGTAAGCTCTAACTAGCTGAG-AC
1 TAGTAAGCTCTTACGAGCTGAGAAC
* *
41770648 TAGTAAGCTCTTACGAGCTGATATAT
1 TAGTAAGCTCTTACGAGCTGAGA-AC
* *
41770674 TGGTAAGCTCATACGAGCT
1 TAGTAAGCTCTTACGAGCT
41770693 ACTGTGAGTC
Statistics
Matches: 55, Mismatches: 10, Indels: 6
0.77 0.14 0.08
Matches are distributed among these distances:
24 35 0.64
25 2 0.04
26 18 0.33
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (25 bp):
TAGTAAGCTCTTACGAGCTGAGAAC
Found at i:41774155 original size:8 final size:8
Alignment explanation
Indices: 41774131--41774180 Score: 55
Period size: 8 Copynumber: 6.2 Consensus size: 8
41774121 ATGTATCGAC
*
41774131 AAAGCTGA
1 AAAGCCGA
*
41774139 AATGCCGA
1 AAAGCCGA
*
41774147 AAAGTCGA
1 AAAGCCGA
41774155 AAAGCCGA
1 AAAGCCGA
*
41774163 AATGCCGA
1 AAAGCCGA
*
41774171 AAAGCTGA
1 AAAGCCGA
41774179 AA
1 AA
41774181 GTTTGGCTAC
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
8 34 1.00
ACGTcount: A:0.48, C:0.18, G:0.24, T:0.10
Consensus pattern (8 bp):
AAAGCCGA
Found at i:41774159 original size:24 final size:25
Alignment explanation
Indices: 41774126--41774174 Score: 82
Period size: 24 Copynumber: 2.0 Consensus size: 25
41774116 ACATTATGTA
*
41774126 TCGACAAAGCTGAAATGCCGAAAAG
1 TCGACAAAGCCGAAATGCCGAAAAG
41774151 TCGA-AAAGCCGAAATGCCGAAAAG
1 TCGACAAAGCCGAAATGCCGAAAAG
41774175 CTGAAAGTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.45, C:0.20, G:0.24, T:0.10
Consensus pattern (25 bp):
TCGACAAAGCCGAAATGCCGAAAAG
Found at i:41774443 original size:29 final size:28
Alignment explanation
Indices: 41774391--41774503 Score: 127
Period size: 29 Copynumber: 4.0 Consensus size: 28
41774381 GTGAGCATGA
* *
41774391 ATATGAATGTGACTGGGCCTAATGGGCC
1 ATATAAATGTGATTGGGCCTAATGGGCC
41774419 ATATAAATGTGATTTGGGCCTAATGGGCC
1 ATATAAATGTGA-TTGGGCCTAATGGGCC
* * *
41774448 ATATACAGGTGATTTAGGCCTAATGGGCC
1 ATATAAATGTGA-TTGGGCCTAATGGGCC
* * * *
41774477 ATATGAATATGATTGGGCTTAGTGGGC
1 ATATAAATGTGATTGGGCCTAATGGGC
41774504 TAGATACAGG
Statistics
Matches: 72, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
28 23 0.32
29 49 0.68
ACGTcount: A:0.27, C:0.14, G:0.30, T:0.29
Consensus pattern (28 bp):
ATATAAATGTGATTGGGCCTAATGGGCC
Found at i:41774474 original size:58 final size:57
Alignment explanation
Indices: 41774406--41774514 Score: 155
Period size: 58 Copynumber: 1.9 Consensus size: 57
41774396 AATGTGACTG
* *
41774406 GGCCTAATGGGCCATATAAATGTGATTTGGGCCTAATGGGCCATATACAGGTGATTTA
1 GGCCTAATGGGCCATATAAATATGA-TTGGGCCTAATGGGCCAGATACAGGTGATTTA
* * * *
41774464 GGCCTAATGGGCCATATGAATATGATTGGGCTTAGTGGGCTAGATACAGGT
1 GGCCTAATGGGCCATATAAATATGATTGGGCCTAATGGGCCAGATACAGGT
41774515 ATGTGAAATT
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
57 22 0.49
58 23 0.51
ACGTcount: A:0.27, C:0.15, G:0.30, T:0.28
Consensus pattern (57 bp):
GGCCTAATGGGCCATATAAATATGATTGGGCCTAATGGGCCAGATACAGGTGATTTA
Found at i:41777024 original size:28 final size:28
Alignment explanation
Indices: 41776955--41777055 Score: 114
Period size: 28 Copynumber: 3.5 Consensus size: 28
41776945 GACAAGATTG
* * * *
41776955 GCACTAAGTGTGCGGGTTTAAAATTGTACA
1 GCACTAAGTGTGCGAGTTT--GATTATATA
41776985 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
41777013 GCACTAAGTGTGCGAG-TTGAATACATATA
1 GCACTAAGTGTGCGAGTTTG-AT-TATATA
41777042 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
41777056 GATTCACTAT
Statistics
Matches: 64, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
27 3 0.05
28 24 0.38
29 19 0.30
30 18 0.28
ACGTcount: A:0.30, C:0.14, G:0.27, T:0.30
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:41784948 original size:28 final size:28
Alignment explanation
Indices: 41784879--41784979 Score: 114
Period size: 28 Copynumber: 3.5 Consensus size: 28
41784869 GACAAGATTG
* * * *
41784879 GCACTAAGTGTGCGGGTTTAAAATTGTACA
1 GCACTAAGTGTGCGAGTTT--GATTATATA
41784909 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
41784937 GCACTAAGTGTGCGAG-TTGAATACATATA
1 GCACTAAGTGTGCGAGTTTG-AT-TATATA
41784966 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
41784980 GATTCACTAT
Statistics
Matches: 64, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
27 3 0.05
28 24 0.38
29 19 0.30
30 18 0.28
ACGTcount: A:0.30, C:0.14, G:0.27, T:0.30
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:41793960 original size:40 final size:40
Alignment explanation
Indices: 41793916--41794073 Score: 262
Period size: 40 Copynumber: 4.0 Consensus size: 40
41793906 TGGATGTAAC
41793916 AACCAGCACAAATGCCTTCGGGACTTAACCCGGTTATAAT
1 AACCAGCACAAATGCCTTCGGGACTTAACCCGGTTATAAT
* *
41793956 AACCAGCACGAATGCCTTCAGGACTTAACCCGGTTATAAT
1 AACCAGCACAAATGCCTTCGGGACTTAACCCGGTTATAAT
* * * *
41793996 AACCCGCACGAGTGCCTTCGGGACTTAACCCGGTTATAGT
1 AACCAGCACAAATGCCTTCGGGACTTAACCCGGTTATAAT
41794036 AACCAGCACAAATGCCTTCGGGACTTAACCCGGTTATA
1 AACCAGCACAAATGCCTTCGGGACTTAACCCGGTTATA
41794074 TTTTTTTTCA
Statistics
Matches: 109, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 109 1.00
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.22
Consensus pattern (40 bp):
AACCAGCACAAATGCCTTCGGGACTTAACCCGGTTATAAT
Found at i:41796981 original size:42 final size:42
Alignment explanation
Indices: 41796863--41796991 Score: 150
Period size: 42 Copynumber: 3.0 Consensus size: 42
41796853 CACACAGTAC
** **
41796863 CATACCAATGCCATATCTTAGATATGGTCTTACTTGTAATCT
1 CATACCAATGCCATATCCCAGATATGGTCTTACACGTAATCT
* * * * * *
41796905 CGTACCGATACCAATAGCCCAGCTATGGTCTTACACGAAATCT
1 CATACCAATGCC-ATATCCCAGATATGGTCTTACACGTAATCT
*
41796948 CATATCAATGCCATATCCCAGATATGGTCTTACACGTAATCT
1 CATACCAATGCCATATCCCAGATATGGTCTTACACGTAATCT
41796990 CA
1 CA
41796992 GTAACCCTAA
Statistics
Matches: 69, Mismatches: 17, Indels: 2
0.78 0.19 0.02
Matches are distributed among these distances:
42 38 0.55
43 31 0.45
ACGTcount: A:0.30, C:0.26, G:0.13, T:0.30
Consensus pattern (42 bp):
CATACCAATGCCATATCCCAGATATGGTCTTACACGTAATCT
Found at i:41798622 original size:30 final size:30
Alignment explanation
Indices: 41798588--41798647 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
41798578 GATTCCCTTC
41798588 AGTTCGAGTTCCAATTCAACCATATTTCTT
1 AGTTCGAGTTCCAATTCAACCATATTTCTT
41798618 AGTTCGAGTTCCAATTCAACCATATTTCTT
1 AGTTCGAGTTCCAATTCAACCATATTTCTT
41798648 TCATCTTCAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.27, C:0.23, G:0.10, T:0.40
Consensus pattern (30 bp):
AGTTCGAGTTCCAATTCAACCATATTTCTT
Found at i:41803602 original size:42 final size:42
Alignment explanation
Indices: 41803555--41803652 Score: 196
Period size: 42 Copynumber: 2.3 Consensus size: 42
41803545 TTGGTCTCGA
41803555 CACTAAGTGTGCGGGTATAAATGGACACGGTGACAAGATTGG
1 CACTAAGTGTGCGGGTATAAATGGACACGGTGACAAGATTGG
41803597 CACTAAGTGTGCGGGTATAAATGGACACGGTGACAAGATTGG
1 CACTAAGTGTGCGGGTATAAATGGACACGGTGACAAGATTGG
41803639 CACTAAGTGTGCGG
1 CACTAAGTGTGCGG
41803653 TTTAAAATTG
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 56 1.00
ACGTcount: A:0.30, C:0.15, G:0.34, T:0.21
Consensus pattern (42 bp):
CACTAAGTGTGCGGGTATAAATGGACACGGTGACAAGATTGG
Found at i:41803671 original size:29 final size:30
Alignment explanation
Indices: 41803638--41803796 Score: 213
Period size: 29 Copynumber: 5.5 Consensus size: 30
41803628 GACAAGATTG
* * * *
41803638 GCACTAAGTGTGCG-GTTTAAAATTGTACA
1 GCACTAAGTGTGCGAGCTGAAAATTATATA
* *
41803667 GCACTAAGTGTGCGAGTTTG---ATTATACA
1 GCACTAAGTGTGCGAG-CTGAAAATTATATA
41803695 GCACTAAGTGTGCGAGCTGAAAA-TATATA
1 GCACTAAGTGTGCGAGCTGAAAATTATATA
41803724 GCACTAAGTGTGCGAGCTGAAAATTATATA
1 GCACTAAGTGTGCGAGCTGAAAATTATATA
41803754 GCACTAAGTGTGCGAGCTGAAAA-TATATA
1 GCACTAAGTGTGCGAGCTGAAAATTATATA
41803783 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
41803797 GATTCACTAT
Statistics
Matches: 120, Mismatches: 4, Indels: 12
0.88 0.03 0.09
Matches are distributed among these distances:
27 2 0.02
28 23 0.19
29 62 0.52
30 31 0.26
31 2 0.02
ACGTcount: A:0.33, C:0.14, G:0.25, T:0.27
Consensus pattern (30 bp):
GCACTAAGTGTGCGAGCTGAAAATTATATA
Found at i:41803765 original size:59 final size:57
Alignment explanation
Indices: 41803638--41803796 Score: 214
Period size: 59 Copynumber: 2.8 Consensus size: 57
41803628 GACAAGATTG
* * * * *
41803638 GCACTAAGTGTGCG-GTTTAAAATTGTACAGCACTAAGTGTGCGAGTTTGATTATACA
1 GCACTAAGTGTGCGAGCTGAAAA-TATATAGCACTAAGTGTGCGAGTCTGATTATACA
*
41803695 GCACTAAGTGTGCGAGCTGAAAATATATAGCACTAAGTGTGCGAG-CTGAAAATTATATA
1 GCACTAAGTGTGCGAGCTGAAAATATATAGCACTAAGTGTGCGAGTCTG---ATTATACA
41803754 GCACTAAGTGTGCGAGCTGAAAATATATAGCACTAAGTGTGCG
1 GCACTAAGTGTGCGAGCTGAAAATATATAGCACTAAGTGTGCG
41803797 GATTCACTAT
Statistics
Matches: 92, Mismatches: 6, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
56 2 0.02
57 34 0.37
58 6 0.07
59 50 0.54
ACGTcount: A:0.33, C:0.14, G:0.25, T:0.27
Consensus pattern (57 bp):
GCACTAAGTGTGCGAGCTGAAAATATATAGCACTAAGTGTGCGAGTCTGATTATACA
Found at i:41813403 original size:39 final size:39
Alignment explanation
Indices: 41813359--41813554 Score: 313
Period size: 39 Copynumber: 5.0 Consensus size: 39
41813349 GATGTGTATG
41813359 AATGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCA
1 AATGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCA
41813398 AATGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCA
1 AATGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCA
41813437 AATGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCA
1 AATGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCA
* * *
41813476 ATTGTGCGAGA-TATGATATCCGGGCTAAGCCCGAAGGCG
1 AATGTGCGA-ATTGTGATATCCGGGCTAAGCCCGAAGGCA
* * *
41813515 ATTGTGCGAGTTGTGATATCCGGGTTAAGTCCCGAAGGCA
1 AATGTGCGAATTGTGATATCCGGGCTAAG-CCCGAAGGCA
41813555 TTTGTGCGGG
Statistics
Matches: 147, Mismatches: 7, Indels: 5
0.92 0.04 0.03
Matches are distributed among these distances:
39 137 0.93
40 10 0.07
ACGTcount: A:0.27, C:0.20, G:0.32, T:0.22
Consensus pattern (39 bp):
AATGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCA
Found at i:41813452 original size:78 final size:78
Alignment explanation
Indices: 41813359--41813594 Score: 314
Period size: 78 Copynumber: 3.0 Consensus size: 78
41813349 GATGTGTATG
*
41813359 AATGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAAATGTGCGA-ATTGTGATATCCGGGC
1 AATGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAAATGTGCGAGA-TATGATATCCGGGC
41813423 TAAGCCCGAAGGCA
65 TAAGCCCGAAGGCA
*
41813437 AATGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGATATGATATCCGGGCT
1 AATGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAAATGTGCGAGATATGATATCCGGGCT
*
41813502 AAGCCCGAAGGCG
66 AAGCCCGAAGGCA
* * * ** * * *
41813515 ATTGTGCGAGTTGTGATATCCGGGTTAAGTCCCGAAGGCATTTGTGCGGGTTATCATAAT-CGGG
1 AATGTGCGAATTGTGATATCCGGGCTAAG-CCCGAAGGCAAATGTGCGAGATATGAT-ATCCGGG
*
41813579 CTATGTCCCGAAGGCA
64 CTAAG-CCCGAAGGCA
41813595 TTTGAACGAG
Statistics
Matches: 142, Mismatches: 12, Indels: 6
0.89 0.08 0.04
Matches are distributed among these distances:
78 99 0.70
79 32 0.23
80 11 0.08
ACGTcount: A:0.25, C:0.20, G:0.31, T:0.23
Consensus pattern (78 bp):
AATGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAAATGTGCGAGATATGATATCCGGGCT
AAGCCCGAAGGCA
Found at i:41813620 original size:79 final size:78
Alignment explanation
Indices: 41813361--41813631 Score: 266
Period size: 78 Copynumber: 3.4 Consensus size: 78
41813351 TGTGTATGAA
* * * * * *
41813361 TGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAAATGTGCGA-ATTGTGATATCCGGGCTA
1 TGTGCGAGTAGTGATATCCGGGTTAAGCCCGAAGGCAATTGTGCGAGA-TATCATATCCGGGCTA
* *
41813425 AGCCCGAAGGCAAA
65 AGCCCGAAGGCGAT
* * * *
41813439 TGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGATATGATATCCGGGCTAA
1 TGTGCGAGTAGTGATATCCGGGTTAAGCCCGAAGGCAATTGTGCGAGATATCATATCCGGGCTAA
41813504 GCCCGAAGGCGAT
66 GCCCGAAGGCGAT
* * * *
41813517 TGTGCGAGTTGTGATATCCGGGTTAAGTCCCGAAGGCATTTGTGCGGGTTATCATAAT-CGGGCT
1 TGTGCGAGTAGTGATATCCGGGTTAAG-CCCGAAGGCAATTGTGCGAGATATCAT-ATCCGGGCT
*
41813581 ATGTCCCGAAGGC-AT
64 AAG-CCCGAAGGCGAT
*
41813596 T-TGAACGAGTAGCT-ATATCC-GGTTAAACTCCGAAGG
1 TGTG--CGAGTAG-TGATATCCGGGTTAAGC-CCGAAGG
41813632 TATGTGATTT
Statistics
Matches: 172, Mismatches: 13, Indels: 15
0.86 0.06 0.08
Matches are distributed among these distances:
78 100 0.58
79 48 0.28
80 23 0.13
81 1 0.01
ACGTcount: A:0.25, C:0.20, G:0.31, T:0.24
Consensus pattern (78 bp):
TGTGCGAGTAGTGATATCCGGGTTAAGCCCGAAGGCAATTGTGCGAGATATCATATCCGGGCTAA
GCCCGAAGGCGAT
Found at i:41830698 original size:12 final size:12
Alignment explanation
Indices: 41830674--41830726 Score: 60
Period size: 10 Copynumber: 4.7 Consensus size: 12
41830664 CTCTATCACT
41830674 TCATATACATATA
1 TCATAT-CATATA
*
41830687 TCTTATCATATA
1 TCATATCATATA
41830699 -CATAT-ATATA
1 TCATATCATATA
41830709 T-ATAT-ATATA
1 TCATATCATATA
41830719 TCATATCA
1 TCATATCA
41830727 ATCCATCTCA
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
10 15 0.43
11 8 0.23
12 7 0.20
13 5 0.14
ACGTcount: A:0.43, C:0.13, G:0.00, T:0.43
Consensus pattern (12 bp):
TCATATCATATA
Found at i:41830715 original size:18 final size:18
Alignment explanation
Indices: 41830674--41830716 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
41830664 CTCTATCACT
*
41830674 TCATATACATATATCTTA
1 TCATATACATATATATTA
41830692 TCATATACATATATATATA
1 TCATATACATATATAT-TA
41830711 T-ATATA
1 TCATATA
41830717 TATCATATCA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 20 0.87
19 3 0.13
ACGTcount: A:0.44, C:0.12, G:0.00, T:0.44
Consensus pattern (18 bp):
TCATATACATATATATTA
Found at i:41833527 original size:48 final size:48
Alignment explanation
Indices: 41833451--41833575 Score: 148
Period size: 48 Copynumber: 2.6 Consensus size: 48
41833441 GTCATTAGGG
*
41833451 GATA-CATTGATTTGGCTTCGGTCTATGATAACAACACTTCGGGTATGA
1 GATATCATTGATTTGGCTTCGG-CCATGATAACAACACTTCGGGTATGA
* ** *
41833499 GCT-TCATTGATTTGGCTTCAGGCCATGATATTAGCACTTCGGGTATGA
1 GATATCATTGATTTGGCTTC-GGCCATGATAACAACACTTCGGGTATGA
*
41833547 GATAT-ATTGAGTTGGCTTCGGGCCATGAT
1 GATATCATTGATTTGGCTTC-GGCCATGAT
41833576 TTGAGCACTT
Statistics
Matches: 66, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
48 63 0.95
49 3 0.05
ACGTcount: A:0.23, C:0.17, G:0.26, T:0.34
Consensus pattern (48 bp):
GATATCATTGATTTGGCTTCGGCCATGATAACAACACTTCGGGTATGA
Found at i:41841486 original size:27 final size:27
Alignment explanation
Indices: 41841387--41841519 Score: 131
Period size: 27 Copynumber: 4.9 Consensus size: 27
41841377 CCAAATTGAC
* * *
41841387 AAAATGATTATTTTGCCTTTATGGGGT
1 AAAATGACTATTTTGCCCTTATGTGGT
* *
41841414 AAAATGACTGTTTTGCCCTTATGAGGT
1 AAAATGACTATTTTGCCCTTATGTGGT
*
41841441 AAAATGACTGTTTTGCCCTTATGTGGT
1 AAAATGACTATTTTGCCCTTATGTGGT
* * * * *
41841468 AAAATGATTCTTTTACCCTTTTATGGT
1 AAAATGACTATTTTGCCCTTATGTGGT
** * *
41841495 ATGATGACTATTTTACCCCTATGTG
1 AAAATGACTATTTTGCCCTTATGTG
41841520 ATGTATGTTT
Statistics
Matches: 89, Mismatches: 17, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 89 1.00
ACGTcount: A:0.25, C:0.14, G:0.19, T:0.42
Consensus pattern (27 bp):
AAAATGACTATTTTGCCCTTATGTGGT
Found at i:41844102 original size:18 final size:17
Alignment explanation
Indices: 41844079--41844112 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
41844069 TAGTTGTGCC
41844079 GTTTTCTCTTCTGTATTA
1 GTTTTCTCTTCT-TATTA
41844097 GTTTTCTCTTCTTATT
1 GTTTTCTCTTCTTATT
41844113 TTCTTCCCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.09, C:0.18, G:0.09, T:0.65
Consensus pattern (17 bp):
GTTTTCTCTTCTTATTA
Found at i:41846353 original size:49 final size:49
Alignment explanation
Indices: 41846224--41846622 Score: 612
Period size: 49 Copynumber: 8.3 Consensus size: 49
41846214 CCCTTCAGGA
* * *
41846224 CTTATCACAT-T-TATACACTTTCACATTCATCACATTGGTCATTCGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
41846271 CCTATCAC--ATATATACACCTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
41846318 CTTATCACATATATATACACGTTCACATTCTTCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
41846367 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
41846416 CCTATCAC--ATATATACACCTTCACATTCGTCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
41846463 CTTATCACATATATATACACTTTCACATTCGTCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
41846512 CTTATCACATATATATACACTTTCACATTCTTCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
41846561 CTTATCACATATATATATACTTTCACATTCTTCACATAGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
41846610 CCTATCACATATA
1 CTTATCACATATA
41846623 AATATCTCAT
Statistics
Matches: 327, Mismatches: 19, Indels: 10
0.92 0.05 0.03
Matches are distributed among these distances:
46 1 0.00
47 90 0.28
49 236 0.72
ACGTcount: A:0.29, C:0.29, G:0.09, T:0.33
Consensus pattern (49 bp):
CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:41846488 original size:145 final size:145
Alignment explanation
Indices: 41846224--41846622 Score: 649
Period size: 145 Copynumber: 2.8 Consensus size: 145
41846214 CCCTTCAGGA
* * *
41846224 CTTATCACAT-T-TATACACTTTCACATTCATCACATTGGTCATTCGGCCCTATCACATATATAC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACATATATAC
*
41846287 ACCTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACGTTCACATTCTTCA
66 ACCTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACGTTCACATTCGTCA
41846352 CATCGGCCATTAGGC
131 CATCGGCCATTAGGC
41846367 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACATATATAC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACATATATAC
* *
41846432 ACCTTCACATTCGTCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCGTCA
66 ACCTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACGTTCACATTCGTCA
41846497 CATCGGCCATTAGGC
131 CATCGGCCATTAGGC
* *
41846512 CTTATCACATATATATACACTTTCACATTCTTCACATCGGCCATTAGGCCTTATCACATATATAT
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCCTATCAC--ATATAT
* * * * *
41846577 ATACTTTCACATTCTTCACATAGGCCATTAGGCCCTATCACATATA
64 ACACCTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATA
41846623 AATATCTCAT
Statistics
Matches: 239, Mismatches: 13, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
143 10 0.04
144 1 0.00
145 181 0.76
147 47 0.20
ACGTcount: A:0.29, C:0.29, G:0.09, T:0.33
Consensus pattern (145 bp):
CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACATATATAC
ACCTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACGTTCACATTCGTCA
CATCGGCCATTAGGC
Found at i:41849506 original size:25 final size:25
Alignment explanation
Indices: 41849477--41849524 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
41849467 TTATAATATG
* * *
41849477 AAAATGACCGTTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
41849502 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
41849525 GTTTATACAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:41849597 original size:20 final size:20
Alignment explanation
Indices: 41849566--41849623 Score: 80
Period size: 20 Copynumber: 2.9 Consensus size: 20
41849556 GATAAACAGG
41849566 GTATGTATATGCACATGACAT
1 GTATG-ATATGCACATGACAT
*
41849587 GTATGATATGCACATGATAT
1 GTATGATATGCACATGACAT
* *
41849607 GAATGACATGCACATGA
1 GTATGATATGCACATGA
41849624 TGTATTTATG
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
20 29 0.85
21 5 0.15
ACGTcount: A:0.36, C:0.14, G:0.21, T:0.29
Consensus pattern (20 bp):
GTATGATATGCACATGACAT
Found at i:41849605 original size:11 final size:11
Alignment explanation
Indices: 41849572--41849624 Score: 51
Period size: 11 Copynumber: 5.2 Consensus size: 11
41849562 CAGGGTATGT
41849572 ATATGCACATG
1 ATATGCACATG
* *
41849583 ACATG--TATG
1 ATATGCACATG
41849592 ATATGCACATG
1 ATATGCACATG
41849603 ATATG-A-ATG
1 ATATGCACATG
*
41849612 ACATGCACATG
1 ATATGCACATG
41849623 AT
1 AT
41849625 GTATTTATGA
Statistics
Matches: 32, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
9 14 0.44
10 2 0.06
11 16 0.50
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.28
Consensus pattern (11 bp):
ATATGCACATG
Found at i:41849702 original size:26 final size:25
Alignment explanation
Indices: 41849673--41849725 Score: 97
Period size: 25 Copynumber: 2.1 Consensus size: 25
41849663 GAGGAAGTGC
41849673 AAAAGGGCTTATGCCCCAGTTATTAA
1 AAAAGGGCTT-TGCCCCAGTTATTAA
41849699 AAAAGGGCTTTGCCCCAGTTATTAA
1 AAAAGGGCTTTGCCCCAGTTATTAA
41849724 AA
1 AA
41849726 GAGGCTAGGC
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 17 0.63
26 10 0.37
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.26
Consensus pattern (25 bp):
AAAAGGGCTTTGCCCCAGTTATTAA
Found at i:41849741 original size:25 final size:25
Alignment explanation
Indices: 41849673--41849742 Score: 79
Period size: 25 Copynumber: 2.8 Consensus size: 25
41849663 GAGGAAGTGC
*
41849673 AAAAGGGCTTATGCCCCAGTTATTAA
1 AAAAGGGC-TAGGCCCCAGTTATTAA
**
41849699 AAAAGGGCTTTGCCCCAGTTATTAA
1 AAAAGGGCTAGGCCCCAGTTATTAA
*
41849724 AAGA-GGCTAGGCCTCCAGT
1 AAAAGGGCTAGGCC-CCAGT
41849743 AATATGATAA
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
24 7 0.18
25 24 0.62
26 8 0.21
ACGTcount: A:0.31, C:0.21, G:0.23, T:0.24
Consensus pattern (25 bp):
AAAAGGGCTAGGCCCCAGTTATTAA
Found at i:41849972 original size:31 final size:31
Alignment explanation
Indices: 41849937--41850000 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
41849927 CATTTACAGT
41849937 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
** *
41849968 AAAGGCTTCGGCCCAGTGTTATGAATTATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
41849999 AA
1 AA
41850001 TATGAAAAGG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.36, C:0.16, G:0.23, T:0.25
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:41856388 original size:18 final size:17
Alignment explanation
Indices: 41856365--41856398 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
41856355 TAGTTGTGCC
41856365 GTTTTCTCTTCTGTATTA
1 GTTTTCTCTTCT-TATTA
41856383 GTTTTCTCTTCTTATT
1 GTTTTCTCTTCTTATT
41856399 TTCTTCCCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.09, C:0.18, G:0.09, T:0.65
Consensus pattern (17 bp):
GTTTTCTCTTCTTATTA
Found at i:41857548 original size:25 final size:25
Alignment explanation
Indices: 41857519--41857566 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
41857509 TTATAATATG
* * *
41857519 AAAATGACCGTTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
41857544 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
41857567 GTTTATACAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:41857650 original size:11 final size:11
Alignment explanation
Indices: 41857614--41857669 Score: 57
Period size: 11 Copynumber: 5.5 Consensus size: 11
41857604 CATGGTATGT
41857614 ATGATATGCAC
1 ATGATATGCAC
* *
41857625 ATGACATG--T
1 ATGATATGCAC
41857634 ATGATATGCAC
1 ATGATATGCAC
41857645 ATGATATG-A-
1 ATGATATGCAC
*
41857654 ATGACATGCAC
1 ATGATATGCAC
41857665 ATGAT
1 ATGAT
41857670 GTATTTATGA
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
9 14 0.40
10 2 0.06
11 19 0.54
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.29
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:41857669 original size:20 final size:20
Alignment explanation
Indices: 41857603--41857669 Score: 98
Period size: 20 Copynumber: 3.4 Consensus size: 20
41857593 ATTTTGATAA
*
41857603 ACATGGTATGTATGATATGC
1 ACATGATATGTATGATATGC
*
41857623 ACATGACATGTATGATATGC
1 ACATGATATGTATGATATGC
* *
41857643 ACATGATATGAATGACATGC
1 ACATGATATGTATGATATGC
41857663 ACATGAT
1 ACATGAT
41857670 GTATTTATGA
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.36, C:0.13, G:0.21, T:0.30
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:41857881 original size:25 final size:24
Alignment explanation
Indices: 41857718--41857885 Score: 234
Period size: 24 Copynumber: 7.0 Consensus size: 24
41857708 GAGGAAGTGC
* *
41857718 AAAAGGGCTTATGCCTCGGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
41857742 AAAAGGGCTTATGCCTCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
41857766 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
41857790 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
41857814 -AAAGGGCTTATACCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
41857837 AAAAAAGGGCTT-TGCCCCAGTTATT
1 --AAAAGGGCTTATGCCCCAGTTATT
*
41857862 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
41857886 ATGATAAAGC
Statistics
Matches: 133, Mismatches: 5, Indels: 11
0.89 0.03 0.07
Matches are distributed among these distances:
23 28 0.21
24 76 0.57
25 20 0.15
26 9 0.07
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.29
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATT
Found at i:41858131 original size:31 final size:31
Alignment explanation
Indices: 41858077--41858140 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
41858067 CGTTTACAGT
41858077 AAAGGCTTCGGCCCAGTAATATGAAATT-TGA
1 AAAGGCTTCGGCCCAGTAATATG-AATTATGA
**
41858108 AAAGGCTTCGGCCCAGTGTTATGAATTATGA
1 AAAGGCTTCGGCCCAGTAATATGAATTATGA
41858139 AA
1 AA
41858141 TATGAAAAGG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 4 0.13
31 26 0.87
ACGTcount: A:0.34, C:0.16, G:0.23, T:0.27
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAATTATGA
Found at i:41861817 original size:17 final size:18
Alignment explanation
Indices: 41861795--41861842 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 18
41861785 GGGATTCTCC
41861795 ATTTGGAAAACTCTA-GG
1 ATTTGGAAAACTCTACGG
**
41861812 ATTTGGTGAACTCTACGG
1 ATTTGGAAAACTCTACGG
*
41861830 -TTTGGCAAACTCT
1 ATTTGGAAAACTCT
41861843 TCTGTTAAGC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
17 24 0.92
18 2 0.08
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.33
Consensus pattern (18 bp):
ATTTGGAAAACTCTACGG
Found at i:41872667 original size:53 final size:54
Alignment explanation
Indices: 41872567--41872774 Score: 235
Period size: 53 Copynumber: 3.9 Consensus size: 54
41872557 CCATGGCAAC
* ** **
41872567 ATGTGAT-ATGTGATTTTCGCATAAGACCATAGTTACGCTATGGCATCGATGTG
1 ATGTGATCATGTGATTTTCGTATAAGACCATAACTGGGCTATGGCATCGATGTG
*
41872620 ATGTGATCATGCGATTTTCGTATAAGACCATAACTGGGC-ATGGCATCGATGTG
1 ATGTGATCATGTGATTTTCGTATAAGACCATAACTGGGCTATGGCATCGATGTG
* * * *
41872673 ACGTGATCATGTGATTTTCGTATAAGACCATAGCTTGGCTATGGCATCAGA-GAG
1 ATGTGATCATGTGATTTTCGTATAAGACCATAACTGGGCTATGGCATC-GATGTG
* * * ** *
41872727 ATGTGATTATGTG-CTTCCGTATAAGACCATATTTGGGATATGGCATCG
1 ATGTGATCATGTGATTTTCGTATAAGACCATAACTGGGCTATGGCATCG
41872775 GCGTGATATG
Statistics
Matches: 133, Mismatches: 19, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
52 1 0.01
53 84 0.63
54 46 0.35
55 2 0.02
ACGTcount: A:0.26, C:0.16, G:0.25, T:0.32
Consensus pattern (54 bp):
ATGTGATCATGTGATTTTCGTATAAGACCATAACTGGGCTATGGCATCGATGTG
Found at i:41877362 original size:54 final size:54
Alignment explanation
Indices: 41877200--41877403 Score: 212
Period size: 54 Copynumber: 3.9 Consensus size: 54
41877190 CCATGGCAAC
* *
41877200 ATGTGAT-ATGTGATTTTTGTATAAGACCATA-----GCTATGGCATC-AATGTG
1 ATGTGATCATCTGATTTTCGTATAAGACCATAGCTGGGCTATGGCATCGAA-GTG
*
41877248 ATGTGATCATGC-GATTTTCGTATAAGACCATAGCTGGGCTATGGCATCGATGTG
1 ATGTGATCAT-CTGATTTTCGTATAAGACCATAGCTGGGCTATGGCATCGAAGTG
* * *
41877302 ACGTGATCATCTGATTTTCGTATAAGACCATAGCTGGGCTATGGTATCGAAGAG
1 ATGTGATCATCTGATTTTCGTATAAGACCATAGCTGGGCTATGGCATCGAAGTG
* * * * *
41877356 ATGTGATTATGTGCTTCT-GTATAAGACCAT-GTCTGGGATATGGCATCG
1 ATGTGATCATCTGATTTTCGTATAAGACCATAG-CTGGGCTATGGCATCG
41877404 GCGTGATATG
Statistics
Matches: 132, Mismatches: 14, Indels: 15
0.82 0.09 0.09
Matches are distributed among these distances:
48 7 0.05
49 21 0.16
52 1 0.01
53 27 0.20
54 75 0.57
55 1 0.01
ACGTcount: A:0.26, C:0.15, G:0.26, T:0.33
Consensus pattern (54 bp):
ATGTGATCATCTGATTTTCGTATAAGACCATAGCTGGGCTATGGCATCGAAGTG
Found at i:41877428 original size:47 final size:47
Alignment explanation
Indices: 41877358--41877462 Score: 138
Period size: 47 Copynumber: 2.2 Consensus size: 47
41877348 TCGAAGAGAT
* * * ** *
41877358 GTGATTATGTGCTTCTGTATAAGACCATGTCTGGGATATGGCATCGGC
1 GTGA-TATGTGCTACTATATAAGACCATATCTGGGATATAACATCAGC
*
41877406 GTGATATGTGCTACTATATAAGACCATATCTGGGATATAACATCAGT
1 GTGATATGTGCTACTATATAAGACCATATCTGGGATATAACATCAGC
41877453 GTGATATGTG
1 GTGATATGTG
41877463 ATCCGTGTAA
Statistics
Matches: 50, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
47 46 0.92
48 4 0.08
ACGTcount: A:0.27, C:0.14, G:0.26, T:0.33
Consensus pattern (47 bp):
GTGATATGTGCTACTATATAAGACCATATCTGGGATATAACATCAGC
Found at i:41882939 original size:6 final size:6
Alignment explanation
Indices: 41882928--41882979 Score: 81
Period size: 6 Copynumber: 9.0 Consensus size: 6
41882918 AGACAACCCA
*
41882928 ATTTTT A-TTTT -TCTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT
1 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT
41882974 ATTTTT
1 ATTTTT
41882980 TATTATATCT
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
5 7 0.17
6 35 0.83
ACGTcount: A:0.15, C:0.02, G:0.00, T:0.83
Consensus pattern (6 bp):
ATTTTT
Found at i:41882954 original size:5 final size:5
Alignment explanation
Indices: 41882930--41883042 Score: 65
Period size: 5 Copynumber: 21.8 Consensus size: 5
41882920 ACAACCCAAT
*
41882930 TTTTA TTTT- TCTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTT- TATT-
1 TTTTA TTTTA T-TTTA -TTTTA -TTTTA -TTTTA -TTTTA TTTTA TTTTA
* * *
41882977 TTTTA TTATA TCTTA TTAATTA -ATTA TTTTA TTTTA TTAGTTA -TTTA
1 TTTTA TTTTA TTTTA TT--TTA TTTTA TTTTA TTTTA TT--TTA TTTTA
*
41883024 CTTTA TTTTA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTT
41883043 TTGGGTAATA
Statistics
Matches: 89, Mismatches: 9, Indels: 20
0.75 0.08 0.17
Matches are distributed among these distances:
4 13 0.15
5 46 0.52
6 23 0.26
7 7 0.08
ACGTcount: A:0.21, C:0.03, G:0.01, T:0.75
Consensus pattern (5 bp):
TTTTA
Found at i:41887830 original size:24 final size:23
Alignment explanation
Indices: 41887802--41887855 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
41887792 ATGAAATTCT
*
41887802 ATATT-TATGTTTTAGATTGATTTA
1 ATATTATATGATTTAGA-TGA-TTA
*
41887826 ATATTATATGATTTATATGATTA
1 ATATTATATGATTTAGATGATTA
41887849 ATATTAT
1 ATATTAT
41887856 GAGCAAGTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
23 10 0.37
24 8 0.30
25 9 0.33
ACGTcount: A:0.35, C:0.00, G:0.09, T:0.56
Consensus pattern (23 bp):
ATATTATATGATTTAGATGATTA
Found at i:41888023 original size:36 final size:36
Alignment explanation
Indices: 41887976--41888044 Score: 102
Period size: 36 Copynumber: 1.9 Consensus size: 36
41887966 TATCTGGGAT
* ** *
41887976 ATGGCATCGATATGTGATTTCATGTAAGACCATGAC
1 ATGGCATCGATATGAGACATCATGTAAAACCATGAC
41888012 ATGGCATCGATATGAGACATCATGTAAAACCAT
1 ATGGCATCGATATGAGACATCATGTAAAACCAT
41888045 AGCTGGGCTA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 29 1.00
ACGTcount: A:0.35, C:0.17, G:0.20, T:0.28
Consensus pattern (36 bp):
ATGGCATCGATATGAGACATCATGTAAAACCATGAC
Found at i:41893252 original size:40 final size:40
Alignment explanation
Indices: 41893151--41893406 Score: 335
Period size: 40 Copynumber: 6.5 Consensus size: 40
41893141 TGGATGATAA
* * *
41893151 CCGGGCTAAGTCCCGAAGGCATTTGCGCTAGTGACTAGT-T
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-TAT
*
41893191 TCGGGC-AAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
41893230 CTGGGCTAAGTCCCGAAGGCATTGGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
41893270 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAAG-TACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCG-AGTTACTATAT
*
41893310 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* * *
41893350 CTGGGCTAAGTCCCAAAGGCATTTGAGC-AG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
**
41893389 CC-GGCTAAACCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
41893407 TACTTGGTTG
Statistics
Matches: 193, Mismatches: 18, Indels: 12
0.87 0.08 0.05
Matches are distributed among these distances:
38 16 0.08
39 42 0.22
40 133 0.69
41 2 0.01
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:41896918 original size:40 final size:40
Alignment explanation
Indices: 41896830--41896941 Score: 125
Period size: 40 Copynumber: 2.8 Consensus size: 40
41896820 TCTTCCACGT
* * * *
41896830 GCACAAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTA
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATATAACCACCA
* ***
41896870 GCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTCCA
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATATAACCACCA
* * *
41896910 GCATAATTGTCTTCGGGGCTTAGCCCGGATAT
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATAT
41896942 CATTCAATTT
Statistics
Matches: 60, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 60 1.00
ACGTcount: A:0.22, C:0.27, G:0.23, T:0.28
Consensus pattern (40 bp):
GCACAATTGCCTTCGGGTCTTAGCCCGGATATAACCACCA
Found at i:41904574 original size:18 final size:19
Alignment explanation
Indices: 41904551--41904600 Score: 52
Period size: 18 Copynumber: 2.7 Consensus size: 19
41904541 GCCAAATGCA
41904551 TCATTCATTAATACACA-T
1 TCATTCATTAATACACACT
* *
41904569 TCATTC-TTACTTCACACT
1 TCATTCATTAATACACACT
41904587 TCA-TCATTATATAC
1 TCATTCATTA-ATAC
41904601 TTTCACAAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 5
0.74 0.12 0.15
Matches are distributed among these distances:
17 10 0.40
18 13 0.52
19 2 0.08
ACGTcount: A:0.32, C:0.26, G:0.00, T:0.42
Consensus pattern (19 bp):
TCATTCATTAATACACACT
Done.