Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 113035596
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: 113035596
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 271 characters in sequence are not A, C, G, or T
File 224 of 378
Found at i:66333219 original size:28 final size:28
Alignment explanation
Indices: 66333154--66333254 Score: 114
Period size: 28 Copynumber: 3.5 Consensus size: 28
66333144 ATAGTGAATC
*
66333154 CGCACACTTAGTGCTATATGTATTC-AACT
1 CGCACACTTAGTGCTATA--TAATCAAACT
66333183 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
66333211 CGCACACTTAGTGCTGTACAATTTTAAACC
1 CGCACACTTAGTGCTATATAA--TCAAACT
66333241 CGCACACTTAGTGC
1 CGCACACTTAGTGC
66333255 CAATCTTGTC
Statistics
Matches: 64, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
27 4 0.06
28 23 0.36
29 18 0.28
30 19 0.30
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.30
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:66348041 original size:21 final size:22
Alignment explanation
Indices: 66348017--66348071 Score: 94
Period size: 23 Copynumber: 2.5 Consensus size: 22
66348007 TGAGTTTTAT
66348017 GAAGTTTGATG-ATAGTACATG
1 GAAGTTTGATGAATAGTACATG
66348038 GAAGTTTGATGATATAGTACATG
1 GAAGTTTGATGA-ATAGTACATG
66348061 GAAGTTTGATG
1 GAAGTTTGATG
66348072 TTGGTTTAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
21 11 0.34
23 21 0.66
ACGTcount: A:0.33, C:0.04, G:0.29, T:0.35
Consensus pattern (22 bp):
GAAGTTTGATGAATAGTACATG
Found at i:66358379 original size:40 final size:40
Alignment explanation
Indices: 66358177--66358384 Score: 233
Period size: 40 Copynumber: 5.2 Consensus size: 40
66358167 TGAATGATAC
* * *
66358177 CCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGAATATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATTATAT
* *
66358217 CCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATTATAT
* * *
66358257 CCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG-TCATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAG-TGATTATAT
* ** *
66358297 CCGGGCTAAGACCCGAAGGCATTTGTGCAAGAT-ACCAAAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAG-TGATTATAT
* * * *
66358337 CCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATTATAT
66358377 CC-GGCTAA
1 CCGGGCTAA
66358385 ATTCCGAAGA
Statistics
Matches: 145, Mismatches: 20, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
39 6 0.04
40 137 0.94
41 2 0.01
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATTATAT
Found at i:66366477 original size:40 final size:40
Alignment explanation
Indices: 66366275--66366482 Score: 233
Period size: 40 Copynumber: 5.2 Consensus size: 40
66366265 TGAATGATAC
* * *
66366275 CCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGAATATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATTATAT
* *
66366315 CCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATTATAT
* * *
66366355 CCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG-TCATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAG-TGATTATAT
* ** *
66366395 CCGGGCTAAGACCCGAAGGCATTTGTGCAAGAT-ACCAAAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAG-TGATTATAT
* * * *
66366435 CCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATTATAT
66366475 CC-GGCTAA
1 CCGGGCTAA
66366483 ATTCCGAAGA
Statistics
Matches: 145, Mismatches: 20, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
39 6 0.04
40 137 0.94
41 2 0.01
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATTATAT
Found at i:66369137 original size:40 final size:40
Alignment explanation
Indices: 66369010--66369139 Score: 163
Period size: 40 Copynumber: 3.2 Consensus size: 40
66369000 ATGCTGGAAA
* * *
66369010 TTATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGG
* * * **
66369050 CTACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCA
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGG
*
66369090 TTCTATCCGGGCTAAGACCCGAAGGCATTTGTGC-ACGTGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGA-GTGG
66369130 TTATATCCGG
1 TTATATCCGG
66369140 TTATATTCCG
Statistics
Matches: 74, Mismatches: 15, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
39 1 0.01
40 73 0.99
ACGTcount: A:0.23, C:0.24, G:0.28, T:0.25
Consensus pattern (40 bp):
TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGG
Found at i:66376979 original size:28 final size:28
Alignment explanation
Indices: 66376910--66377008 Score: 110
Period size: 28 Copynumber: 3.4 Consensus size: 28
66376900 GACAAGATTG
* * * *
66376910 GCACTAAGTGTGCGGGTTTAAAATTGTACA
1 GCACTAAGTGTGCGAGTTT--GATTATATA
66376940 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
66376968 GCACTAAGTGTGCGAG-TTGAATACATATA
1 GCACTAAGTGTGCGAGTTTG-AT-TATATA
66376997 GCACTAAGTGTG
1 GCACTAAGTGTG
66377009 TGATTCACTA
Statistics
Matches: 62, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
27 3 0.05
28 24 0.39
29 17 0.27
30 18 0.29
ACGTcount: A:0.30, C:0.13, G:0.26, T:0.30
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:66380306 original size:40 final size:40
Alignment explanation
Indices: 66380179--66380308 Score: 163
Period size: 40 Copynumber: 3.2 Consensus size: 40
66380169 ATGCTGGAAA
* * *
66380179 TTATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGG
* * * **
66380219 CTACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCA
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGG
*
66380259 TTCTATCCGGGCTAAGACCCGAAGGCATTTGTGC-ACGTGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGA-GTGG
66380299 TTATATCCGG
1 TTATATCCGG
66380309 TTATATTCCG
Statistics
Matches: 74, Mismatches: 15, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
39 1 0.01
40 73 0.99
ACGTcount: A:0.23, C:0.24, G:0.28, T:0.25
Consensus pattern (40 bp):
TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGG
Found at i:66385556 original size:20 final size:20
Alignment explanation
Indices: 66385527--66385567 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
66385517 TACCCGGGTT
*
66385527 AGTTCTGATATATTGAGTAA
1 AGTTCGGATATATTGAGTAA
66385547 AGTTCGGATATATTGAGTAA
1 AGTTCGGATATATTGAGTAA
66385567 A
1 A
66385568 CCAATCATTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.37, C:0.05, G:0.22, T:0.37
Consensus pattern (20 bp):
AGTTCGGATATATTGAGTAA
Found at i:66391535 original size:17 final size:18
Alignment explanation
Indices: 66391513--66391547 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
66391503 TCACATTAAA
66391513 GTGTTTT-AGTGAAAACC
1 GTGTTTTCAGTGAAAACC
*
66391530 GTGTTTTCATTGAAAACC
1 GTGTTTTCAGTGAAAACC
66391548 CTTCTTAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.29, C:0.14, G:0.20, T:0.37
Consensus pattern (18 bp):
GTGTTTTCAGTGAAAACC
Found at i:66392642 original size:29 final size:29
Alignment explanation
Indices: 66392602--66392678 Score: 109
Period size: 29 Copynumber: 2.7 Consensus size: 29
66392592 ATTCATATTC
* *
66392602 ATATGGCTCATTAGGCCCAAATCACCTGT
1 ATATGGCCCATTAGGCCCAAATCACATGT
* *
66392631 ATATGGCCCATTAGGCTCAAATCACATTT
1 ATATGGCCCATTAGGCCCAAATCACATGT
*
66392660 ATATGGCCCGTTAGGCCCA
1 ATATGGCCCATTAGGCCCA
66392679 GTCACATTCA
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 42 1.00
ACGTcount: A:0.27, C:0.27, G:0.18, T:0.27
Consensus pattern (29 bp):
ATATGGCCCATTAGGCCCAAATCACATGT
Found at i:66393870 original size:38 final size:38
Alignment explanation
Indices: 66393827--66394270 Score: 229
Period size: 38 Copynumber: 10.9 Consensus size: 38
66393817 TTTCAAATTA
*
66393827 ACATGTATAACCGTGGCATATCCACTTAGTACCACGTT
1 ACATGTATAACCGTGGCATATCCACTTAGCACCACGTT
* * *
66393865 ACATGTTTAACCGTGGTATATCCACTTAGCACCACATTAAT
1 ACATGTATAACCGTGGCATATCCACTTAGCACCAC-GT--T
* * *
66393906 GAATCAATATATGTAACCGTGGAATATCCATTTAGCACCACGTT
1 --A-C-ATGTA--TAACCGTGGCATATCCACTTAGCACCACGTT
* *
66393950 ACATGTTTAACCGTGGTATATCCACTTAGCACCACGTT
1 ACATGTATAACCGTGGCATATCCACTTAGCACCACGTT
* *
66393988 A-ATGAATCAA---T----TATCCACTTAGCACCACATTAAT
1 ACATGTAT-AACCGTGGCATATCCACTTAGCACCAC-GT--T
*
66394022 GAATCAATATATGTAACCGTGGCATATCCACTTAGCACCACGTT
1 --A-C-ATGTA--TAACCGTGGCATATCCACTTAGCACCACGTT
* * ** * *
66394066 ATATGTTTAACTATGGCAAATCCACTTAGTACCACGTT
1 ACATGTATAACCGTGGCATATCCACTTAGCACCACGTT
* * * *
66394104 ACATGTTTAACCATGGTATATCCCCTTAGCACCACGTTAAT
1 ACATGTATAACCGTGGCATATCCACTTAGCACCACG-T--T
*
66394145 GAATCAATATATGTAACCGTGGCATATCCACTTAGCACCACGTT
1 --A-C-ATGTA--TAACCGTGGCATATCCACTTAGCACCACGTT
* * *
66394189 ACATGTATCAATATGTGTAATCGTGGTATATCCATTTAGCACCACGTT
1 ACATG------TA----TAACCGTGGCATATCCACTTAGCACCACGTT
* * *
66394237 ACACGTATAACTGTGGTATATCCACTTAGCACCA
1 ACATGTATAACCGTGGCATATCCACTTAGCACCA
66394271 TATTTTTTTC
Statistics
Matches: 317, Mismatches: 45, Indels: 88
0.70 0.10 0.20
Matches are distributed among these distances:
31 17 0.05
32 1 0.00
34 1 0.00
35 1 0.00
36 1 0.00
37 4 0.01
38 145 0.46
39 5 0.02
40 10 0.03
41 5 0.02
42 5 0.02
43 3 0.01
44 5 0.02
45 6 0.02
46 5 0.02
47 69 0.22
48 34 0.11
ACGTcount: A:0.32, C:0.24, G:0.14, T:0.30
Consensus pattern (38 bp):
ACATGTATAACCGTGGCATATCCACTTAGCACCACGTT
Found at i:66393926 original size:85 final size:84
Alignment explanation
Indices: 66393834--66394194 Score: 378
Period size: 85 Copynumber: 4.4 Consensus size: 84
66393824 TTAACATGTA
66393834 TAACCGTGGCATATCCACTTAGTACCACGTTACATGTTTAACCGTGGTATATCCACTTAGCACCA
1 TAACCGTGGCATATCCACTTAGTACCACGTTACATGTTTAACCGTGGTATATCCACTTAGCACCA
*
66393899 CATTAATGAATCAATATAT
66 CGTTAATGAATCAATATAT
* * *
66393918 GTAACCGTGGAATATCCATTTAGCACCACGTTACATGTTTAACCGTGGTATATCCACTTAGCACC
1 -TAACCGTGGCATATCCACTTAGTACCACGTTACATGTTTAACCGTGGTATATCCACTTAGCACC
66393983 ACGTTAATGAATCAAT-TAT
65 ACGTTAATGAATCAATATAT
** * * * ** * *
66394002 CCA-CTTAGC--A-CCACATTAATGA--ATCAATATATG--TAACCGTGGCATATCCACTTAGCA
1 TAACCGTGGCATATCCAC-TTAGT-ACCA-CGTTACATGTTTAACCGTGGTATATCCACTTAGCA
*
66394059 CCACG-T--T--AT--ATGT-T
63 CCACGTTAATGAATCAATATAT
** * * *
66394073 TAACTATGGCAAATCCACTTAGTACCACGTTACATGTTTAACCATGGTATATCCCCTTAGCACCA
1 TAACCGTGGCATATCCACTTAGTACCACGTTACATGTTTAACCGTGGTATATCCACTTAGCACCA
66394138 CGTTAATGAATCAATATAT
66 CGTTAATGAATCAATATAT
*
66394157 GTAACCGTGGCATATCCACTTAGCACCACGTTACATGT
1 -TAACCGTGGCATATCCACTTAGTACCACGTTACATGT
66394195 ATCAATATGT
Statistics
Matches: 222, Mismatches: 33, Indels: 42
0.75 0.11 0.14
Matches are distributed among these distances:
71 4 0.02
72 4 0.02
73 3 0.01
74 11 0.05
75 6 0.03
76 26 0.12
77 2 0.01
78 28 0.13
79 5 0.02
80 10 0.05
81 3 0.01
82 3 0.01
83 4 0.02
84 4 0.02
85 109 0.49
ACGTcount: A:0.32, C:0.24, G:0.14, T:0.30
Consensus pattern (84 bp):
TAACCGTGGCATATCCACTTAGTACCACGTTACATGTTTAACCGTGGTATATCCACTTAGCACCA
CGTTAATGAATCAATATAT
Found at i:66394006 original size:31 final size:31
Alignment explanation
Indices: 66393968--66394029 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
66393958 AACCGTGGTA
*
66393968 TATCCACTTAGCACCACGTTAATGAATCAAT
1 TATCCACTTAGCACCACATTAATGAATCAAT
66393999 TATCCACTTAGCACCACATTAATGAATCAAT
1 TATCCACTTAGCACCACATTAATGAATCAAT
66394030 ATATGTAACC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.37, C:0.26, G:0.08, T:0.29
Consensus pattern (31 bp):
TATCCACTTAGCACCACATTAATGAATCAAT
Found at i:66394029 original size:116 final size:120
Alignment explanation
Indices: 66393827--66394194 Score: 492
Period size: 123 Copynumber: 3.0 Consensus size: 120
66393817 TTTCAAATTA
* * * * * *
66393827 ACATGTATAACCGTGGCATATCCACTTAGTACCACGTTACATGTTTAACCGTGGTATATCCACTT
1 ACATGTTTAACCATGGCAAATCCACTTAGCACCACGTTACATG--TAACC-AGATATATCCACTT
* *
66393892 AGCACCACATTAATGAATCAATATATGTAACCGTGGAATATCCATTTAGCACCACGTT
63 AGCACCACATTAATGAATCAATATATGTAACCGTGGCATATCCACTTAGCACCACGTT
* * * *
66393950 ACATGTTTAACCGTGGTATATCCACTTAGCACCACGTTA-ATG-AATCA-AT-TATCCACTTAGC
1 ACATGTTTAACCATGGCAAATCCACTTAGCACCACGTTACATGTAACCAGATATATCCACTTAGC
66394011 ACCACATTAATGAATCAATATATGTAACCGTGGCATATCCACTTAGCACCACGTT
66 ACCACATTAATGAATCAATATATGTAACCGTGGCATATCCACTTAGCACCACGTT
* * * * *
66394066 ATATGTTTAACTATGGCAAATCCACTTAGTACCACGTTACATGTTTAACCATGGTATATCCCCTT
1 ACATGTTTAACCATGGCAAATCCACTTAGCACCACGTTACATG--TAACCA-GATATATCCACTT
*
66394131 AGCACCACGTTAATGAATCAATATATGTAACCGTGGCATATCCACTTAGCACCACGTT
63 AGCACCACATTAATGAATCAATATATGTAACCGTGGCATATCCACTTAGCACCACGTT
66394189 ACATGT
1 ACATGT
66394195 ATCAATATGT
Statistics
Matches: 219, Mismatches: 19, Indels: 14
0.87 0.08 0.06
Matches are distributed among these distances:
116 98 0.45
117 4 0.02
119 3 0.01
120 4 0.02
122 4 0.02
123 106 0.48
ACGTcount: A:0.32, C:0.24, G:0.14, T:0.30
Consensus pattern (120 bp):
ACATGTTTAACCATGGCAAATCCACTTAGCACCACGTTACATGTAACCAGATATATCCACTTAGC
ACCACATTAATGAATCAATATATGTAACCGTGGCATATCCACTTAGCACCACGTT
Found at i:66394220 original size:48 final size:48
Alignment explanation
Indices: 66394111--66394244 Score: 189
Period size: 48 Copynumber: 2.8 Consensus size: 48
66394101 GTTACATGTT
* * *
66394111 TAACCATGGTATATCCCCTTAGCACCACGTTA-ATGAATCAATATATG
1 TAACCGTGGTATATCCACTTAGCACCACGTTACATGTATCAATATATG
* *
66394158 TAACCGTGGCATATCCACTTAGCACCACGTTACATGTATCAATATGTG
1 TAACCGTGGTATATCCACTTAGCACCACGTTACATGTATCAATATATG
* * *
66394206 TAATCGTGGTATATCCATTTAGCACCACGTTACACGTAT
1 TAACCGTGGTATATCCACTTAGCACCACGTTACATGTAT
66394245 AACTGTGGTA
Statistics
Matches: 77, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
47 29 0.38
48 48 0.62
ACGTcount: A:0.31, C:0.24, G:0.15, T:0.31
Consensus pattern (48 bp):
TAACCGTGGTATATCCACTTAGCACCACGTTACATGTATCAATATATG
Found at i:66400609 original size:40 final size:40
Alignment explanation
Indices: 66400537--66400720 Score: 205
Period size: 40 Copynumber: 4.6 Consensus size: 40
66400527 GCTACTCGTT
* *
66400537 CAAATGCCTTCGGGACATAGCTCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
* *
66400577 CAGATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
**
66400617 CAAATGCCTTC-GGATCTTAGTTCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAACTCGCA
* * * * *
66400657 CAAATGCCTTC-GAATCTTAGTCCGGATATAGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
66400698 CAAA-GCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGGGACTTAGCCCG
66400721 AACATCATTC
Statistics
Matches: 125, Mismatches: 15, Indels: 8
0.84 0.10 0.05
Matches are distributed among these distances:
39 3 0.02
40 110 0.88
41 12 0.10
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.27
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:66403512 original size:38 final size:38
Alignment explanation
Indices: 66403470--66403546 Score: 109
Period size: 38 Copynumber: 2.0 Consensus size: 38
66403460 TTTCAAATTA
66403470 ACATGTATAACCGTGGCATATCCACTTAGAACCACGTT
1 ACATGTATAACCGTGGCATATCCACTTAGAACCACGTT
* * ** *
66403508 ACATGTTTAACCGTGGTATATCGGCTTAGCACCACGTT
1 ACATGTATAACCGTGGCATATCCACTTAGAACCACGTT
66403546 A
1 A
66403547 ATGAATTAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.29, C:0.25, G:0.18, T:0.29
Consensus pattern (38 bp):
ACATGTATAACCGTGGCATATCCACTTAGAACCACGTT
Found at i:66403624 original size:48 final size:48
Alignment explanation
Indices: 66403510--66403643 Score: 171
Period size: 48 Copynumber: 2.8 Consensus size: 48
66403500 ACCACGTTAC
* ** *
66403510 ATGTTTAACCGTGGTATATCGGCTTAGCACCACGTTA-ATGAATTAAT
1 ATGTGTAACCGTGGTATATCCACTTAGCACCACGTTACATGAATCAAT
* * * *
66403557 ATATGTAACCATGGCATATCCACTTAGCACCACGTTACATGTATCAAT
1 ATGTGTAACCGTGGTATATCCACTTAGCACCACGTTACATGAATCAAT
* *
66403605 ATGTGTAATCGTGGTATATCCACTTAGCATCACGTTACA
1 ATGTGTAACCGTGGTATATCCACTTAGCACCACGTTACA
66403644 CATTATAACC
Statistics
Matches: 73, Mismatches: 13, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
47 31 0.42
48 42 0.58
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.32
Consensus pattern (48 bp):
ATGTGTAACCGTGGTATATCCACTTAGCACCACGTTACATGAATCAAT
Found at i:66405931 original size:22 final size:22
Alignment explanation
Indices: 66405903--66405950 Score: 96
Period size: 22 Copynumber: 2.2 Consensus size: 22
66405893 TCGTTGCTTC
66405903 GAATACTCTAAGACCCATGTAA
1 GAATACTCTAAGACCCATGTAA
66405925 GAATACTCTAAGACCCATGTAA
1 GAATACTCTAAGACCCATGTAA
66405947 GAAT
1 GAAT
66405951 TTTTTTAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.42, C:0.21, G:0.15, T:0.23
Consensus pattern (22 bp):
GAATACTCTAAGACCCATGTAA
Found at i:66407607 original size:93 final size:93
Alignment explanation
Indices: 66407479--66407649 Score: 290
Period size: 93 Copynumber: 1.8 Consensus size: 93
66407469 GCCCATAAGT
* *
66407479 GAACTCGGACTCAACTCAATGAGCTCGAGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGAGCATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
66407544 TGAGTTCGGATGCCTAGTTACATTTCAC
66 CGAGTTCGGATGCCTAGTTACATTTCAC
*
66407572 GAACTCGGACTCAACTCAACGAGTTCG-GACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 GAACTCGGACTCAACTCAACGAGCTCGAG-CATTCGCATCCATAAGTGAACTCGGACTCAACTCA
66407636 ACGAGTTCGGATGC
65 ACGAGTTCGGATGC
66407650 TCAACCATCC
Statistics
Matches: 73, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
92 1 0.01
93 72 0.99
ACGTcount: A:0.29, C:0.27, G:0.21, T:0.23
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGAGCATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATTTCAC
Found at i:66407645 original size:46 final size:47
Alignment explanation
Indices: 66407471--66407646 Score: 202
Period size: 46 Copynumber: 3.8 Consensus size: 47
66407461 TGTAACCCGC
* * *
66407471 CCATAAGTGAACTCGGACTCAACTCAATGAGCTC-GAGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGAGCATTCGCAT
* *
66407517 CCATAAGTGAACTCGGACTCAACTCAATGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA-G-C-A-TTCGCAT
* * *
66407567 --TTCA-CGAACTCGGACTCAACTCAACGAGTTCGGA-CATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGAGCATTCGCAT
66407610 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
66407647 TGCTCAACCA
Statistics
Matches: 110, Mismatches: 11, Indels: 18
0.79 0.08 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 1 0.01
45 2 0.02
46 62 0.56
47 30 0.27
48 3 0.03
49 1 0.01
50 3 0.03
51 2 0.02
ACGTcount: A:0.30, C:0.27, G:0.20, T:0.23
Consensus pattern (47 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGAGCATTCGCAT
Found at i:66408103 original size:30 final size:30
Alignment explanation
Indices: 66408069--66408128 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
66408059 ATTTAATACG
66408069 AACTTTGGAAAAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
* * *
66408099 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
66408129 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.30, C:0.25, G:0.08, T:0.37
Consensus pattern (30 bp):
AACTTTGGAAAAATTACACTTTTGCCCCTA
Found at i:66412591 original size:16 final size:16
Alignment explanation
Indices: 66412570--66412601 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
66412560 TGATGCAGTG
66412570 GTGAATTATAAAAGAA
1 GTGAATTATAAAAGAA
66412586 GTGAATTATAAAAGAA
1 GTGAATTATAAAAGAA
66412602 AAACTATTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.19, T:0.25
Consensus pattern (16 bp):
GTGAATTATAAAAGAA
Found at i:66419597 original size:16 final size:16
Alignment explanation
Indices: 66419578--66419609 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
66419568 AATTGTTTTA
66419578 TTACAAAATTTCACTT
1 TTACAAAATTTCACTT
*
66419594 TTACATAATTTCACTT
1 TTACAAAATTTCACTT
66419610 ACTCCATTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.19, G:0.00, T:0.47
Consensus pattern (16 bp):
TTACAAAATTTCACTT
Found at i:66419874 original size:50 final size:50
Alignment explanation
Indices: 66419809--66420046 Score: 275
Period size: 50 Copynumber: 4.7 Consensus size: 50
66419799 ACCAAAGCTC
* *
66419809 TCTGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAA
1 TCTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAA
* * * * * *
66419859 TTTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACTTAACCA
1 TCTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAA
* * **
66419909 TCTGATACACGTAGTAGCCTACACTTAGTACTACACACATGATCGAAGT-T-AA
1 TCTGGTACACGTAGTAGCCTGCACTTAGTACT--ACACATG--CGACCTATCAA
* * *
66419961 -CGGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAA
1 TCTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAA
*
66420010 TCTGGTACACGTTGTAGCCTGCACTTAGTACTACACA
1 TCTGGTACACGTAGTAGCCTGCACTTAGTACTACACA
66420047 CATGACTCAC
Statistics
Matches: 153, Mismatches: 28, Indels: 14
0.78 0.14 0.07
Matches are distributed among these distances:
47 4 0.03
48 1 0.01
49 9 0.06
50 103 0.67
51 26 0.17
52 7 0.05
54 3 0.02
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.26
Consensus pattern (50 bp):
TCTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAA
Found at i:66419994 original size:101 final size:101
Alignment explanation
Indices: 66419870--66420051 Score: 292
Period size: 101 Copynumber: 1.8 Consensus size: 101
66419860 TTGGTACACG
* * *
66419870 TAGTAGCCTGCACTTAGTACTACACACGTGACTTAACCATCTGATACACGTAGTAGCCTACACTT
1 TAGTAGCCTGCACTTAGTACTACACACGCGACCTAACAATCTGATACACGTAGTAGCCTACACTT
66419935 AGTACTACACACATGATCGAAGTTAACGGGTACGCA
66 AGTACTACACACATGATCGAAGTTAACGGGTACGCA
* * * * *
66419971 TAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAATCTGGTACACGTTGTAGCCTGCACTT
1 TAGTAGCCTGCACTTAGTACTACACACGCGACCTAACAATCTGATACACGTAGTAGCCTACACTT
66420036 AGTACTACACACATGA
66 AGTACTACACACATGA
66420052 CTCACAATGA
Statistics
Matches: 73, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
101 73 1.00
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.26
Consensus pattern (101 bp):
TAGTAGCCTGCACTTAGTACTACACACGCGACCTAACAATCTGATACACGTAGTAGCCTACACTT
AGTACTACACACATGATCGAAGTTAACGGGTACGCA
Found at i:66423035 original size:15 final size:16
Alignment explanation
Indices: 66423011--66423053 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
66423001 ATAGATAACA
*
66423011 AGAAAACCAAGATTA-
1 AGAAATCCAAGATTAG
*
66423026 AGAAGTCCAAGA-TAG
1 AGAAATCCAAGATTAG
66423041 AGAAATCCAAGAT
1 AGAAATCCAAGAT
66423054 ACAATATCAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
14 2 0.09
15 21 0.91
ACGTcount: A:0.53, C:0.14, G:0.19, T:0.14
Consensus pattern (16 bp):
AGAAATCCAAGATTAG
Found at i:66426327 original size:16 final size:16
Alignment explanation
Indices: 66426308--66426339 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
66426298 AATTGTTTTA
66426308 TTACAAAATTTCACTT
1 TTACAAAATTTCACTT
*
66426324 TTACATAATTTCACTT
1 TTACAAAATTTCACTT
66426340 ACTCCATTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.19, G:0.00, T:0.47
Consensus pattern (16 bp):
TTACAAAATTTCACTT
Found at i:66426625 original size:50 final size:50
Alignment explanation
Indices: 66426539--66426934 Score: 368
Period size: 50 Copynumber: 7.9 Consensus size: 50
66426529 ACTGAAGCTC
*
66426539 TCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAA
1 TCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGTGACCTATCAA
* * * * ** * * *
66426589 TTTGGCACACGTAGTAGCCTGCACTTATTACTACACACATGACTTAACCA
1 TCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGTGACCTATCAA
* * ** *
66426639 TCTGATACACATAGTAGCCTGCACTTAGTACTACACACGTGATCAAAGTTAA
1 TCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGTGA-CCTA-TCAA
* * *
66426691 -CGGGTACGCATAGTAGCCTGCACTTAGTACTACACATATGACCTATCAA
1 TCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGTGACCTATCAA
* * * * * *
66426740 TCTGGTACACGTAGTAGCCTGCACTTAGTATTACATATGTGACTTAACCA
1 TCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGTGACCTATCAA
* * * ** *
66426790 TCTGATACACATAGTAGACTACACTTAGTACTACACAAT-TGATCGGAGTTAA
1 TCTGGTACACATAGTAGCCTGCACTTAGTACTACAC-ATGTGA-CCTA-TCAA
** *
66426842 -C-GTGTATGCATAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAA
1 TCTG-GTACACATAGTAGCCTGCACTTAGTACTACACATGTGACCTATCAA
* * * * *
66426891 TCTGGTAAACGTAGTAGCCTGTACTTAGTACTACGCACGTGACC
1 TCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGTGACC
66426935 CACAATAAAT
Statistics
Matches: 271, Mismatches: 65, Indels: 20
0.76 0.18 0.06
Matches are distributed among these distances:
49 6 0.02
50 190 0.70
51 73 0.27
52 2 0.01
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.28
Consensus pattern (50 bp):
TCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGTGACCTATCAA
Found at i:66426743 original size:101 final size:100
Alignment explanation
Indices: 66426539--66426934 Score: 298
Period size: 101 Copynumber: 3.9 Consensus size: 100
66426529 ACTGAAGCTC
* ** ** *
66426539 TCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAATTTGGCACACGTAGT
1 TCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGCGACAAATCAATCGGGCACACATAGT
* * *
66426604 AGCCTGCACTTATTACTACACACATGACTTAACCA
66 AGCCTGCACTTAGTACTACACACATGACCTAACAA
* * * * *
66426639 TCTGATACACATAGTAGCCTGCACTTAGTACTACACACGTGATCAAAGTTAA-CGGGTACGCATA
1 TCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGCGA-CAAA-TCAATCGGGCACACATA
* *
66426703 GTAGCCTGCACTTAGTACTACACATATGACCTATCAA
64 GTAGCCTGCACTTAGTACTACACACATGACCTAACAA
* * * * * * * * **
66426740 TCTGGTACACGTAGTAGCCTGCACTTAGTATTACATATGTGACTTAA-CCATCTGATACACATAG
1 TCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGCGAC-AAATCAATCGGGCACACATAG
* * ** **
66426804 TAGACTACACTTAGTACTACACA-ATTGATCGGAGTTAA
65 TAGCCTGCACTTAGTACTACACACA-TGA-CCTA-ACAA
** * ** * * * *
66426842 -C-GTGTATGCATAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAATCTGGTAAACGTAG
1 TCTG-GTACACATAGTAGCCTGCACTTAGTACTACACACGCGACAAATCAATCGGGCACACATAG
* * *
66426905 TAGCCTGTACTTAGTACTACGCACGTGACC
65 TAGCCTGCACTTAGTACTACACACATGACC
66426935 CACAATAAAT
Statistics
Matches: 236, Mismatches: 50, Indels: 20
0.77 0.16 0.07
Matches are distributed among these distances:
99 2 0.01
100 77 0.33
101 151 0.64
102 6 0.03
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.28
Consensus pattern (100 bp):
TCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGCGACAAATCAATCGGGCACACATAGT
AGCCTGCACTTAGTACTACACACATGACCTAACAA
Found at i:66426816 original size:151 final size:151
Alignment explanation
Indices: 66426542--66426933 Score: 586
Period size: 151 Copynumber: 2.6 Consensus size: 151
66426532 GAAGCTCTCT
* * *
66426542 GGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAATTTGGCACACGTAGTAGC
1 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAATCTGGTACACGTAGTAGC
* * *
66426607 CTGCACTTATTACTACACACATGACTTAACCATCTGATACACATAGTAGCCTGCACTTAGTACTA
66 CTGCACTTAGTACTACACACATGACTTAACCATCTGATACACATAGTAGACTACACTTAGTACTA
*
66426672 CACACGTGATCAAAGTTAACG
131 CACAAGTGATCAAAGTTAACG
**
66426693 GGTACGCATAGTAGCCTGCACTTAGTACTACACATATGACCTATCAATCTGGTACACGTAGTAGC
1 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAATCTGGTACACGTAGTAGC
* * **
66426758 CTGCACTTAGTATTACATATGTGACTTAACCATCTGATACACATAGTAGACTACACTTAGTACTA
66 CTGCACTTAGTACTACACACATGACTTAACCATCTGATACACATAGTAGACTACACTTAGTACTA
* **
66426823 CACAATTGATCGGAGTTAACG
131 CACAAGTGATCAAAGTTAACG
* * *
66426844 TGTATGCATAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAATCTGGTAAACGTAGTAGC
1 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAATCTGGTACACGTAGTAGC
* * *
66426909 CTGTACTTAGTACTACGCACGTGAC
66 CTGCACTTAGTACTACACACATGAC
66426934 CCACAATAAA
Statistics
Matches: 215, Mismatches: 26, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
151 215 1.00
ACGTcount: A:0.31, C:0.24, G:0.17, T:0.27
Consensus pattern (151 bp):
GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAATCTGGTACACGTAGTAGC
CTGCACTTAGTACTACACACATGACTTAACCATCTGATACACATAGTAGACTACACTTAGTACTA
CACAAGTGATCAAAGTTAACG
Found at i:66428042 original size:26 final size:26
Alignment explanation
Indices: 66427987--66428148 Score: 224
Period size: 26 Copynumber: 6.3 Consensus size: 26
66427977 CTGGAGGCGT
66427987 AGCCTCTTTT-AATAAA-TGGGGCA-A
1 AGCC-CTTTTCAATAAACTGGGGCATA
**
66428011 AGCCCTTTTCGGTAAACTGGGGCATA
1 AGCCCTTTTCAATAAACTGGGGCATA
*
66428037 AGCCCTTTTTAATAAACTGGGGCATA
1 AGCCCTTTTCAATAAACTGGGGCATA
*
66428063 AGCTCTTTTCAATAAACTGGGGCATA
1 AGCCCTTTTCAATAAACTGGGGCATA
* **
66428089 AGCCCTTTTCGATAAACTAAGGCATA
1 AGCCCTTTTCAATAAACTGGGGCATA
66428115 AGCCCTTTTCAATAAACTGGGGCAT-
1 AGCCCTTTTCAATAAACTGGGGCATA
66428140 AGCCCTTTT
1 AGCCCTTTT
66428149 GCACTTCCTC
Statistics
Matches: 121, Mismatches: 14, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
23 5 0.04
24 8 0.07
25 16 0.13
26 92 0.76
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.30
Consensus pattern (26 bp):
AGCCCTTTTCAATAAACTGGGGCATA
Found at i:66437743 original size:27 final size:28
Alignment explanation
Indices: 66437686--66437755 Score: 115
Period size: 27 Copynumber: 2.5 Consensus size: 28
66437676 AAACTTGTAC
*
66437686 AGCACTAAGTGTGCGAGTTTGATCATGT
1 AGCACTAAGTGTGCGAGTTTGATCATAT
*
66437714 AGCACTAAGTGTGCGAG-TTGATTATAT
1 AGCACTAAGTGTGCGAGTTTGATCATAT
66437741 AGCACTAAGTGTGCG
1 AGCACTAAGTGTGCG
66437756 GACTCACTAT
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
27 23 0.57
28 17 0.43
ACGTcount: A:0.27, C:0.14, G:0.29, T:0.30
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGTTTGATCATAT
Found at i:66437766 original size:27 final size:27
Alignment explanation
Indices: 66437686--66437767 Score: 69
Period size: 27 Copynumber: 3.0 Consensus size: 27
66437676 AAACTTGTAC
* * *
66437686 AGCACTAAGTGTGCGAGTTTGA-TCATGT
1 AGCACTAAGTGTGCGAG-CTCACT-ATAT
* * *
66437714 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAGCTCACTATAT
66437741 AGCACTAAGTGTGCG-GACTCACTATAT
1 AGCACTAAGTGTGCGAG-CTCACTATAT
66437768 GCTTTTGAAT
Statistics
Matches: 48, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
26 1 0.02
27 29 0.60
28 18 0.38
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAGCTCACTATAT
Found at i:66439264 original size:26 final size:26
Alignment explanation
Indices: 66439206--66439367 Score: 242
Period size: 26 Copynumber: 6.3 Consensus size: 26
66439196 CTGGAGGCCT
66439206 AGCCTCTTTT-AAT-AACTGGGGCA-A
1 AGCC-CTTTTCAATAAACTGGGGCATA
**
66439230 AGCCCTTTTCGGTAAACTGGGGCATA
1 AGCCCTTTTCAATAAACTGGGGCATA
66439256 AGCCCTTTTCAATAAACTGGGGCATA
1 AGCCCTTTTCAATAAACTGGGGCATA
*
66439282 AGCCCTTTTCAATAAACTAGGGCATA
1 AGCCCTTTTCAATAAACTGGGGCATA
**
66439308 AGCCCTTTTCGGTAAACTGGGGCATA
1 AGCCCTTTTCAATAAACTGGGGCATA
66439334 AGCCCTTTTCAATAAACTGGGGCAT-
1 AGCCCTTTTCAATAAACTGGGGCATA
66439359 AGCCCTTTT
1 AGCCCTTTT
66439368 ACACTTCCTC
Statistics
Matches: 125, Mismatches: 10, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
23 5 0.04
24 5 0.04
25 19 0.15
26 96 0.77
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.28
Consensus pattern (26 bp):
AGCCCTTTTCAATAAACTGGGGCATA
Found at i:66439311 original size:78 final size:74
Alignment explanation
Indices: 66439196--66439368 Score: 274
Period size: 78 Copynumber: 2.3 Consensus size: 74
66439186 TATCATATAT
* *
66439196 CTGGAGGCCTAGCCTCTTTTAATAACTGGGGCAAAGCCCTTTTCGGTAAACTGGGGCATAAGCCC
1 CTGG-GGCATAGCC-CTTTTAATAACTAGGGCAAAGCCCTTTTCGGTAAACTGGGGCATAAGCCC
66439261 TTTTCAATAAA
64 TTTTCAATAAA
66439272 CTGGGGCATAAGCCCTTTTCAATAAACTAGGGCATAAGCCCTTTTCGGTAAACTGGGGCATAAGC
1 CTGGGGCAT-AGCCCTTTT-AAT-AACTAGGGCA-AAGCCCTTTTCGGTAAACTGGGGCATAAGC
66439337 CCTTTTCAATAAA
62 CCTTTTCAATAAA
66439350 CTGGGGCATAGCCCTTTTA
1 CTGGGGCATAGCCCTTTTA
66439369 CACTTCCTCC
Statistics
Matches: 91, Mismatches: 2, Indels: 8
0.90 0.02 0.08
Matches are distributed among these distances:
75 9 0.10
76 12 0.13
77 18 0.20
78 52 0.57
ACGTcount: A:0.27, C:0.24, G:0.22, T:0.28
Consensus pattern (74 bp):
CTGGGGCATAGCCCTTTTAATAACTAGGGCAAAGCCCTTTTCGGTAAACTGGGGCATAAGCCCTT
TTCAATAAA
Found at i:66439445 original size:20 final size:20
Alignment explanation
Indices: 66439420--66439491 Score: 105
Period size: 20 Copynumber: 3.7 Consensus size: 20
66439410 TGATTACATT
*
66439420 ATGTGCATTTCATACATATC
1 ATGTGCATATCATACATATC
66439440 ATGTGCATATCATACATATC
1 ATGTGCATATCATACATATC
66439460 ATGTGCATATCATATCAT-TC
1 ATGTGCATATCATA-CATATC
66439480 ATGT--ATATCATA
1 ATGTGCATATCATA
66439492 TCCCACGTAT
Statistics
Matches: 50, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
18 8 0.16
20 39 0.78
21 3 0.06
ACGTcount: A:0.33, C:0.18, G:0.10, T:0.39
Consensus pattern (20 bp):
ATGTGCATATCATACATATC
Found at i:66439450 original size:11 final size:11
Alignment explanation
Indices: 66439434--66439472 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
66439424 GCATTTCATA
66439434 CATATCATGTG
1 CATATCATGTG
*
66439445 CATATCA--TA
1 CATATCATGTG
66439454 CATATCATGTG
1 CATATCATGTG
66439465 CATATCAT
1 CATATCAT
66439473 ATCATTCATG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
9 8 0.33
11 16 0.67
ACGTcount: A:0.33, C:0.21, G:0.10, T:0.36
Consensus pattern (11 bp):
CATATCATGTG
Found at i:66439490 original size:9 final size:10
Alignment explanation
Indices: 66439434--66439490 Score: 57
Period size: 9 Copynumber: 5.8 Consensus size: 10
66439424 GCATTTCATA
66439434 CATATCATGT
1 CATATCATGT
*
66439444 GCATATCAT-A
1 -CATATCATGT
66439454 CATATCATGT
1 CATATCATGT
*
66439464 GCATATCATAT
1 -CATATCATGT
66439475 CAT-TCATGT
1 CATATCATGT
66439484 -ATATCAT
1 CATATCAT
66439491 ATCCCACGTA
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
8 2 0.05
9 17 0.44
10 3 0.08
11 17 0.44
ACGTcount: A:0.33, C:0.19, G:0.09, T:0.39
Consensus pattern (10 bp):
CATATCATGT
Found at i:66439547 original size:25 final size:25
Alignment explanation
Indices: 66439519--66439566 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
66439509 ATAATTAAAT
* * *
66439519 CCTAGGGGTATAATGGTCATTTTTA
1 CCTAGGGGCAAAATAGTCATTTTTA
66439544 CCTAGGGGCAAAATAGTCATTTT
1 CCTAGGGGCAAAATAGTCATTTT
66439567 CATATTATAG
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:0.27, C:0.15, G:0.23, T:0.35
Consensus pattern (25 bp):
CCTAGGGGCAAAATAGTCATTTTTA
Found at i:66441540 original size:18 final size:20
Alignment explanation
Indices: 66441515--66441555 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
66441505 AGGTTATACC
*
66441515 ATCAAAATAATCACATA-AT
1 ATCAAATTAATCACATATAT
*
66441534 ATCAAATTATTCACATATAT
1 ATCAAATTAATCACATATAT
66441554 AT
1 AT
66441556 ACTTATAACT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.51, C:0.15, G:0.00, T:0.34
Consensus pattern (20 bp):
ATCAAATTAATCACATATAT
Found at i:66444552 original size:42 final size:42
Alignment explanation
Indices: 66444462--66444573 Score: 129
Period size: 42 Copynumber: 2.7 Consensus size: 42
66444452 TTAGGGTTAC
* ** *
66444462 TAAGACTAT-GTGTAAGACCAAATCTGGGATATGGCATCTATA
1 TAAGACT-TCGTGTAAGACCATATCTGGGATATGAAATCGATA
*
66444504 TAAGACTTCGTGTAAGGCCATATCTGGGATATGAAATCGATA
1 TAAGACTTCGTGTAAGACCATATCTGGGATATGAAATCGATA
* *
66444546 -AGAGACTTCATGTAAGACCATAGCTGGG
1 TA-AGACTTCGTGTAAGACCATATCTGGG
66444574 TTATTGGCAT
Statistics
Matches: 60, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
41 2 0.03
42 58 0.97
ACGTcount: A:0.34, C:0.15, G:0.24, T:0.27
Consensus pattern (42 bp):
TAAGACTTCGTGTAAGACCATATCTGGGATATGAAATCGATA
Found at i:66454014 original size:29 final size:29
Alignment explanation
Indices: 66453982--66454168 Score: 272
Period size: 29 Copynumber: 6.5 Consensus size: 29
66453972 ATAGTGAATC
66453982 CGCACACTTAGTGCTATATATTTTCAGCT
1 CGCACACTTAGTGCTATATATTTTCAGCT
66454011 CGCACACTTAGTGCTATATAATTTTCAGCT
1 CGCACACTTAGTGCTATAT-ATTTTCAGCT
66454041 CGCACACTTAGTGCTATATATTTTCAGCT
1 CGCACACTTAGTGCTATATATTTTCAGCT
66454070 CGCACACTTAGTGCTATATA-TTTCAGCT
1 CGCACACTTAGTGCTATATATTTTCAGCT
* *
66454098 CGCACACTTAGTGCTATATA--ATCAAACT
1 CGCACACTTAGTGCTATATATTTTC-AGCT
* * * * *
66454126 CGCACACTTAGTGCTATACAATTTAAACC
1 CGCACACTTAGTGCTATATATTTTCAGCT
66454155 CGCACACTTAGTGC
1 CGCACACTTAGTGC
66454169 CAATCTTGTC
Statistics
Matches: 148, Mismatches: 6, Indels: 8
0.91 0.04 0.05
Matches are distributed among these distances:
27 2 0.01
28 50 0.34
29 66 0.45
30 30 0.20
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (29 bp):
CGCACACTTAGTGCTATATATTTTCAGCT
Found at i:66454074 original size:59 final size:58
Alignment explanation
Indices: 66453982--66454168 Score: 281
Period size: 57 Copynumber: 3.2 Consensus size: 58
66453972 ATAGTGAATC
66453982 CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAATTTTCAGCT
1 CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAA-TTTCAGCT
66454041 CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATAT-ATTTCAGCT
1 CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAATTTCAGCT
* * * * * *
66454098 CGCACACTTAGTGCTATATA--ATCAAACTCGCACACTTAGTGCTATACAATTTAAACC
1 CGCACACTTAGTGCTATATATTTTC-AGCTCGCACACTTAGTGCTATATAATTTCAGCT
66454155 CGCACACTTAGTGC
1 CGCACACTTAGTGC
66454169 CAATCTTGTC
Statistics
Matches: 120, Mismatches: 6, Indels: 6
0.91 0.05 0.05
Matches are distributed among these distances:
55 2 0.02
56 21 0.17
57 48 0.40
58 1 0.01
59 48 0.40
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (58 bp):
CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAATTTCAGCT
Found at i:66458202 original size:80 final size:79
Alignment explanation
Indices: 66458063--66458285 Score: 216
Period size: 80 Copynumber: 2.8 Consensus size: 79
66458053 TTTGGTTTAC
* * * **
66458063 AAAATTACCAAAATACCCTGCTTTGTAAAATTACTAAAATACCCTTGGTTTATAAAATTACCAAA
1 AAAATTATCAAAATACCCTGATTTGTAAAATTACCAAAATACCC-TAATTTATAAAATTACCAAA
**
66458128 ATACCCCTAG-TTTGT
65 ATA-CCCTAGACCTGT
* * **
66458143 AAAATTATCAAAATACCCCT-AGTTTGTAAAATTACCAAAATACCCTAATTTGTGAAATTACTGA
1 AAAATTATCAAAATA-CCCTGA-TTTGTAAAATTACCAAAATACCCTAATTTATAAAATTACCAA
*
66458207 AATACCCTCGACCTGT
64 AATACCCTAGACCTGT
** * * * *
66458223 AAAATTATTGAAATACCCTCGACTTGTAAAATTACCAAAGTACCCTCGATTTATAGAATTACC
1 AAAATTATCAAAATACCCT-GATTTGTAAAATTACCAAAATACCCT-AATTTATAAAATTACC
66458286 GTTTTACCCT
Statistics
Matches: 116, Mismatches: 21, Indels: 11
0.78 0.14 0.07
Matches are distributed among these distances:
79 9 0.08
80 69 0.59
81 38 0.33
ACGTcount: A:0.40, C:0.21, G:0.09, T:0.31
Consensus pattern (79 bp):
AAAATTATCAAAATACCCTGATTTGTAAAATTACCAAAATACCCTAATTTATAAAATTACCAAAA
TACCCTAGACCTGT
Found at i:66458250 original size:107 final size:107
Alignment explanation
Indices: 66458063--66458267 Score: 250
Period size: 107 Copynumber: 1.9 Consensus size: 107
66458053 TTTGGTTTAC
** * ***
66458063 AAAATTACCAAAATACCCTGCTTTGTAAAATTACTAAAATACCCTTGGTTTATAAAATTACCAAA
1 AAAATTACCAAAATACCCTAATTTGTAAAATTACTAAAATACCCTCGACCTATAAAATTACCAAA
* * *
66458128 ATACCCCTAGTTTGTAAAATTATCAAAATACCCCTAGTTTGT
66 ATACCCCGAGCTTGTAAAATTACCAAAATACCCCTAGTTTGT
* * * ***
66458170 AAAATTACCAAAATACCCTAATTTGTGAAATTACTGAAATACCCTCGACCTGTAAAATTATTGAA
1 AAAATTACCAAAATACCCTAATTTGTAAAATTACTAAAATACCCTCGACCTATAAAATTACCAAA
*
66458235 ATACCCTCGA-CTTGTAAAATTACCAAAGTACCC
66 ATACCC-CGAGCTTGTAAAATTACCAAAATACCC
66458268 TCGATTTATA
Statistics
Matches: 81, Mismatches: 16, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
107 79 0.98
108 2 0.02
ACGTcount: A:0.40, C:0.21, G:0.08, T:0.30
Consensus pattern (107 bp):
AAAATTACCAAAATACCCTAATTTGTAAAATTACTAAAATACCCTCGACCTATAAAATTACCAAA
ATACCCCGAGCTTGTAAAATTACCAAAATACCCCTAGTTTGT
Found at i:66458269 original size:27 final size:27
Alignment explanation
Indices: 66458063--66458312 Score: 229
Period size: 27 Copynumber: 9.3 Consensus size: 27
66458053 TTTGGTTTAC
*
66458063 AAAATTACCAAAATACCCT-GCTTTGT
1 AAAATTACCAAAATACCCTCGATTTGT
* * * *
66458089 AAAATTACTAAAATACCCTTGGTTTAT
1 AAAATTACCAAAATACCCTCGATTTGT
*
66458116 AAAATTACCAAAATACCC-CTAGTTTGT
1 AAAATTACCAAAATACCCTCGA-TTTGT
* *
66458143 AAAATTATCAAAATACCC-CTAGTTTGT
1 AAAATTACCAAAATACCCTCGA-TTTGT
*
66458170 AAAATTACCAAAATACCCT-AATTTGT
1 AAAATTACCAAAATACCCTCGATTTGT
* ** **
66458196 GAAATTACTGAAATACCCTCGACCTGT
1 AAAATTACCAAAATACCCTCGATTTGT
*** *
66458223 AAAATTATTGAAATACCCTCGACTTGT
1 AAAATTACCAAAATACCCTCGATTTGT
* *
66458250 AAAATTACCAAAGTACCCTCGATTTAT
1 AAAATTACCAAAATACCCTCGATTTGT
* ****
66458277 AGAATTACCGTTTTACCCTCGATTTGT
1 AAAATTACCAAAATACCCTCGATTTGT
66458304 AAAATTACC
1 AAAATTACC
66458313 GTTTTACCCT
Statistics
Matches: 187, Mismatches: 33, Indels: 7
0.82 0.15 0.03
Matches are distributed among these distances:
26 39 0.21
27 148 0.79
ACGTcount: A:0.38, C:0.21, G:0.09, T:0.32
Consensus pattern (27 bp):
AAAATTACCAAAATACCCTCGATTTGT
Found at i:66458283 original size:54 final size:54
Alignment explanation
Indices: 66458058--66458338 Score: 148
Period size: 54 Copynumber: 5.2 Consensus size: 54
66458048 AATACTTTGG
* * * * * *
66458058 TTTACAAAATTACCAAAATACCCT-G-CTTTGTAAAATTACTAAAATACCCTTGG
1 TTTACAGAATTACCGAAATACCCTCGAC-TTGTAAAATTACCAAAGTACCCTCGA
* * * * * * * * *
66458111 TTTATAAAATTACCAAAATACCC-CTAGTTTGTAAAATTATCAAAATACCCCTAGT
1 TTTACAGAATTACCGAAATACCCTCGA-CTTGTAAAATTACCAAAGTA-CCCTCGA
* * * * *
66458166 TTGTA-A-AATTACCAAAATACCCT-AATTTGTGAAATTACTGAAA-TACCCTCGA
1 TT-TACAGAATTACCGAAATACCCTCGACTTGTAAAATTAC-CAAAGTACCCTCGA
* **
66458218 CCTGTA-A-AATTATTGAAATACCCTCGACTTGTAAAATTACCAAAGTACCCTCGA
1 --TTTACAGAATTACCGAAATACCCTCGACTTGTAAAATTACCAAAGTACCCTCGA
* *** * ****
66458272 TTTATAGAATTACCGTTTTACCCTCGATTTGTAAAATTACCGTTTTACCCTCGA
1 TTTACAGAATTACCGAAATACCCTCGACTTGTAAAATTACCAAAGTACCCTCGA
66458326 TTTACAGAATTAC
1 TTTACAGAATTAC
66458339 GTTTTACCCT
Statistics
Matches: 182, Mismatches: 33, Indels: 25
0.76 0.14 0.10
Matches are distributed among these distances:
52 8 0.04
53 56 0.31
54 108 0.59
55 8 0.04
56 2 0.01
ACGTcount: A:0.37, C:0.21, G:0.09, T:0.33
Consensus pattern (54 bp):
TTTACAGAATTACCGAAATACCCTCGACTTGTAAAATTACCAAAGTACCCTCGA
Found at i:66458283 original size:107 final size:107
Alignment explanation
Indices: 66458057--66458285 Score: 246
Period size: 107 Copynumber: 2.1 Consensus size: 107
66458047 AAATACTTTG
* ** * ***
66458057 GTTTACAAAATTACCAAAATACCCTGCTTTGTAAAATTACTAAAATACCCTTGGTTTATAAAATT
1 GTTTATAAAATTACCAAAATACCCTAATTTGTAAAATTACTAAAATACCCTCGACCTATAAAATT
* * * *
66458122 ACCAAAATACCCCTAGTTTGTAAAATTATCAAAATACCCCTA
66 ACCAAAATACCCCGAGCTTGTAAAATTACCAAAATACCCCGA
* * * *
66458164 GTTTGTAAAATTACCAAAATACCCTAATTTGTGAAATTACTGAAATACCCTCGACCTGTAAAATT
1 GTTTATAAAATTACCAAAATACCCTAATTTGTAAAATTACTAAAATACCCTCGACCTATAAAATT
*** *
66458229 ATTGAAATACCCTCGA-CTTGTAAAATTACCAAAGTACCCTCGA
66 ACCAAAATACCC-CGAGCTTGTAAAATTACCAAAATACCC-CGA
*
66458272 -TTTATAGAATTACC
1 GTTTATAAAATTACC
66458286 GTTTTACCCT
Statistics
Matches: 99, Mismatches: 21, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
107 95 0.96
108 4 0.04
ACGTcount: A:0.39, C:0.21, G:0.09, T:0.31
Consensus pattern (107 bp):
GTTTATAAAATTACCAAAATACCCTAATTTGTAAAATTACTAAAATACCCTCGACCTATAAAATT
ACCAAAATACCCCGAGCTTGTAAAATTACCAAAATACCCCGA
Found at i:66458313 original size:27 final size:27
Alignment explanation
Indices: 66458263--66458658 Score: 462
Period size: 27 Copynumber: 14.8 Consensus size: 27
66458253 ATTACCAAAG
66458263 TACCCTCGATTTATAGAATTACCGTTT
1 TACCCTCGATTTATAGAATTACCGTTT
* *
66458290 TACCCTCGATTTGTAAAATTACCGTTT
1 TACCCTCGATTTATAGAATTACCGTTT
*
66458317 TACCCTCGATTTACAGAATTA-CGTTT
1 TACCCTCGATTTATAGAATTACCGTTT
* * **
66458343 TACCCT-TAGTTTACAGAATTACTATTT
1 TACCCTCGA-TTTATAGAATTACCGTTT
66458370 TACCCTCGATTTATAGAATTACCGTTT
1 TACCCTCGATTTATAGAATTACCGTTT
* * *
66458397 TACCC-CTAATTTACATAATTACCGTTT
1 TACCCTC-GATTTATAGAATTACCGTTT
* * *
66458424 TACCC-CGATTTACATAATTATCGTTT
1 TACCCTCGATTTATAGAATTACCGTTT
66458450 TACCCTCGATTTATAGAATTACCGTTT
1 TACCCTCGATTTATAGAATTACCGTTT
* * *
66458477 CACCCTCGATTTACAGAATTACCATTT
1 TACCCTCGATTTATAGAATTACCGTTT
* * *
66458504 TACCC-CGATTTACATAATTATCGTTT
1 TACCCTCGATTTATAGAATTACCGTTT
*
66458530 TACCCTCGATTTACAGAATTACCGTTT
1 TACCCTCGATTTATAGAATTACCGTTT
* * *
66458557 CACCCTCGATTTACAGAATTACCATTT
1 TACCCTCGATTTATAGAATTACCGTTT
*
66458584 TACCCTCGATTTATAGAATTACTGTTT
1 TACCCTCGATTTATAGAATTACCGTTT
* * * **
66458611 TACCCTTGATTTACAAAATTACTATTT
1 TACCCTCGATTTATAGAATTACCGTTT
*
66458638 TACCCTCGATTTA-AAAATTAC
1 TACCCTCGATTTATAGAATTAC
66458659 TAAAATACCC
Statistics
Matches: 323, Mismatches: 40, Indels: 13
0.86 0.11 0.03
Matches are distributed among these distances:
25 1 0.00
26 78 0.24
27 243 0.75
28 1 0.00
ACGTcount: A:0.28, C:0.23, G:0.09, T:0.40
Consensus pattern (27 bp):
TACCCTCGATTTATAGAATTACCGTTT
Found at i:66458379 original size:80 final size:80
Alignment explanation
Indices: 66458263--66458658 Score: 496
Period size: 80 Copynumber: 4.9 Consensus size: 80
66458253 ATTACCAAAG
* * * *
66458263 TACCCTCGATTTATAGAATTACCGTTTTACCCTCGATTTGTAAAATTACCGTTTTACCCTCGATT
1 TACCC-CGATTTACAGAATTACTGTTTTACCCTCGATTTATAGAATTACCGTTTTACCCTCGATT
*
66458328 TACAGAATTA-CGTTT
65 TACAGAATTACCATTT
** * *
66458343 TACCCTTAGTTTACAGAATTACTATTTTACCCTCGATTTATAGAATTACCGTTTTACCC-CTAAT
1 TACCCCGA-TTTACAGAATTACTGTTTTACCCTCGATTTATAGAATTACCGTTTTACCCTC-GAT
* *
66458407 TTACATAATTACCGTTT
64 TTACAGAATTACCATTT
* *
66458424 TACCCCGATTTACATAATTA-TCGTTTTACCCTCGATTTATAGAATTACCGTTTCACCCTCGATT
1 TACCCCGATTTACAGAATTACT-GTTTTACCCTCGATTTATAGAATTACCGTTTTACCCTCGATT
66458488 TACAGAATTACCATTT
65 TACAGAATTACCATTT
* * *
66458504 TACCCCGATTTACATAATTA-TCGTTTTACCCTCGATTTACAGAATTACCGTTTCACCCTCGATT
1 TACCCCGATTTACAGAATTACT-GTTTTACCCTCGATTTATAGAATTACCGTTTTACCCTCGATT
66458568 TACAGAATTACCATTT
65 TACAGAATTACCATTT
* * * * **
66458584 TACCCTCGATTTATAGAATTACTGTTTTACCCTTGATTTACAAAATTACTATTTTACCCTCGATT
1 TACCC-CGATTTACAGAATTACTGTTTTACCCTCGATTTATAGAATTACCGTTTTACCCTCGATT
*
66458649 TA-AAAATTAC
65 TACAGAATTAC
66458659 TAAAATACCC
Statistics
Matches: 283, Mismatches: 26, Indels: 14
0.88 0.08 0.04
Matches are distributed among these distances:
79 3 0.01
80 215 0.76
81 64 0.23
82 1 0.00
ACGTcount: A:0.28, C:0.23, G:0.09, T:0.40
Consensus pattern (80 bp):
TACCCCGATTTACAGAATTACTGTTTTACCCTCGATTTATAGAATTACCGTTTTACCCTCGATTT
ACAGAATTACCATTT
Found at i:66458685 original size:53 final size:54
Alignment explanation
Indices: 66458222--66458671 Score: 180
Period size: 54 Copynumber: 8.4 Consensus size: 54
66458212 CCTCGACCTG
* * * * ** ***
66458222 TAAAATTATTGAAATACCCTCGACTTGTAAAATTACCAAAGTACCCTCGATTTA
1 TAAAATTACTAAAATACCCTTGATTTACAAAATTACCATTTTACCCTCGATTTA
* ***** * ** *
66458276 TAGAATTACCGTTTTACCCTCGATTTGTAAAATTACCGTTTTACCCTCGATTTA
1 TAAAATTACTAAAATACCCTTGATTTACAAAATTACCATTTTACCCTCGATTTA
* * ** * *
66458330 CAGAATTACGT--TTTACCCTT-AGTTTACAGAATTACTATTTTACCCTCGATTTA
1 TAAAATTAC-TAAAATACCCTTGA-TTTACAAAATTACCATTTTACCCTCGATTTA
* ***** * * * *
66458383 TAGAATTACCGTTTTACCCCTAATTTACATAATTACCGTTTTACCC-CGATTTA
1 TAAAATTACTAAAATACCCTTGATTTACAAAATTACCATTTTACCCTCGATTTA
* * ** * * * * *
66458436 CATAATTATCGT--TTTACCCTCGATTTATAGAATTACCGTTTCACCCTCGATTTA
1 TAAAATTA-C-TAAAATACCCTTGATTTACAAAATTACCATTTTACCCTCGATTTA
* * * *** * * * *
66458490 CAGAATTACCATTTTACCC-CGATTTACATAATTATCGTTTTACCCTCGATTTA
1 TAAAATTACTAAAATACCCTTGATTTACAAAATTACCATTTTACCCTCGATTTA
* * **** * *
66458543 CAGAATTAC-CGTTTCACCCTCGATTTACAGAATTACCATTTTACCCTCGATTTA
1 TAAAATTACTAAAAT-ACCCTTGATTTACAAAATTACCATTTTACCCTCGATTTA
* **** *
66458597 TAGAATTACTGTTTTACCCTTGATTTACAAAATTACTATTTTACCCTCGATTTA
1 TAAAATTACTAAAATACCCTTGATTTACAAAATTACCATTTTACCCTCGATTTA
66458651 -AAAATTACTAAAATACCCTTG
1 TAAAATTACTAAAATACCCTTG
66458672 GTTTGTGAAA
Statistics
Matches: 327, Mismatches: 56, Indels: 27
0.80 0.14 0.07
Matches are distributed among these distances:
52 4 0.01
53 143 0.44
54 176 0.54
55 4 0.01
ACGTcount: A:0.30, C:0.23, G:0.09, T:0.39
Consensus pattern (54 bp):
TAAAATTACTAAAATACCCTTGATTTACAAAATTACCATTTTACCCTCGATTTA
Found at i:66458685 original size:107 final size:107
Alignment explanation
Indices: 66458263--66458658 Score: 541
Period size: 107 Copynumber: 3.7 Consensus size: 107
66458253 ATTACCAAAG
**
66458263 TACCCTCGATTTATAGAATTACCGTTTTACCCTCGATTTGTAAAATTACCGTTTTACCCTCGATT
1 TACCCTCGATTTATAGAATTACCGTTTTACCCTCGATTTACAAAATTACCGTTTTACCCTCGATT
* *
66458328 TACAGAATTACGTTTTACCCT-TAGTTTACAGAATTACTATTT
66 TACAGAATTACGTTTTACCCTCGA-TTTACAGAATTACCATTT
* *
66458370 TACCCTCGATTTATAGAATTACCGTTTTACCC-CTAATTTACATAATTACCGTTTTACCC-CGAT
1 TACCCTCGATTTATAGAATTACCGTTTTACCCTC-GATTTACAAAATTACCGTTTTACCCTCGAT
* * *
66458433 TTACATAATTATCGTTTTACCCTCGATTTATAGAATTACCGTTT
65 TTACAGAATTA-CGTTTTACCCTCGATTTACAGAATTACCATTT
* * * * *
66458477 CACCCTCGATTTACAGAATTACCATTTTACCC-CGATTTACATAATTATCGTTTTACCCTCGATT
1 TACCCTCGATTTATAGAATTACCGTTTTACCCTCGATTTACAAAATTACCGTTTTACCCTCGATT
*
66458541 TACAGAATTACCGTTTCACCCTCGATTTACAGAATTACCATTT
66 TACAGAATTA-CGTTTTACCCTCGATTTACAGAATTACCATTT
* * **
66458584 TACCCTCGATTTATAGAATTACTGTTTTACCCTTGATTTACAAAATTACTATTTTACCCTCGATT
1 TACCCTCGATTTATAGAATTACCGTTTTACCCTCGATTTACAAAATTACCGTTTTACCCTCGATT
*
66458649 TA-AAAATTAC
66 TACAGAATTAC
66458659 TAAAATACCC
Statistics
Matches: 255, Mismatches: 29, Indels: 11
0.86 0.10 0.04
Matches are distributed among these distances:
106 39 0.15
107 186 0.73
108 30 0.12
ACGTcount: A:0.28, C:0.23, G:0.09, T:0.40
Consensus pattern (107 bp):
TACCCTCGATTTATAGAATTACCGTTTTACCCTCGATTTACAAAATTACCGTTTTACCCTCGATT
TACAGAATTACGTTTTACCCTCGATTTACAGAATTACCATTT
Found at i:66459918 original size:25 final size:25
Alignment explanation
Indices: 66459890--66459937 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
66459880 TTATACCATG
* * *
66459890 AAAATGACCGTTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
66459915 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
66459938 GTTTATGTAT
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:66460040 original size:20 final size:20
Alignment explanation
Indices: 66459980--66460040 Score: 104
Period size: 20 Copynumber: 3.0 Consensus size: 20
66459970 ATAAATATGG
*
66459980 TATGTATGAGATGCACATGA
1 TATGTATGATATGCACATGA
*
66460000 CATGTATGATATGCACATGA
1 TATGTATGATATGCACATGA
66460020 TATGTATGATATGCACATGA
1 TATGTATGATATGCACATGA
66460040 T
1 T
66460041 GTAATCATAA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.34, C:0.11, G:0.21, T:0.33
Consensus pattern (20 bp):
TATGTATGATATGCACATGA
Found at i:66460117 original size:24 final size:24
Alignment explanation
Indices: 66460090--66460208 Score: 170
Period size: 24 Copynumber: 5.0 Consensus size: 24
66460080 GAGGAAGTGA
*
66460090 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATT
66460114 AAAAGGGCTTATGCCCCAGTTA-T
1 AAAAGGGCTTATGCCCCAGTTATT
66460137 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
* *
66460161 GAAAGGGCTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
66460185 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
66460209 ATGATAAAGC
Statistics
Matches: 86, Mismatches: 6, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
23 22 0.26
24 53 0.62
25 11 0.13
ACGTcount: A:0.29, C:0.22, G:0.23, T:0.27
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATT
Found at i:66460159 original size:47 final size:48
Alignment explanation
Indices: 66460090--66460208 Score: 170
Period size: 47 Copynumber: 2.5 Consensus size: 48
66460080 GAGGAAGTGA
66460090 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTA-T
1 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATT
** *
66460137 AAAAGGGCTTATGCCCCAGTTATTGAAAGGGCTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATT
*
66460185 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
66460209 ATGATAAAGC
Statistics
Matches: 65, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
47 43 0.66
48 11 0.17
49 11 0.17
ACGTcount: A:0.29, C:0.22, G:0.23, T:0.27
Consensus pattern (48 bp):
AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATT
Found at i:66460460 original size:30 final size:31
Alignment explanation
Indices: 66460400--66460462 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
66460390 CGTTTACAGT
66460400 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
**
66460431 AAAGGCTTCGGCCCAGTGTTATG-AATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
66460461 AA
1 AA
66460463 TGATATGAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 9 0.30
31 21 0.70
ACGTcount: A:0.37, C:0.16, G:0.24, T:0.24
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:66463272 original size:26 final size:26
Alignment explanation
Indices: 66463243--66463382 Score: 145
Period size: 26 Copynumber: 5.3 Consensus size: 26
66463233 ATCCCTATTT
* *
66463243 AAAATACTTTGGTTTACAAAATTACC
1 AAAATACCTTGGTTTATAAAATTACC
* * * *
66463269 AAAATACCCTGCTTTGTAAAATTACT
1 AAAATACCTTGGTTTATAAAATTACC
66463295 AAAATACCCTTGGTTTATAAAATTACC
1 AAAATA-CCTTGGTTTATAAAATTACC
* * * *
66463322 AAAATACCCCTAGTTTGTAAAATTATC
1 AAAATA-CCTTGGTTTATAAAATTACC
* * *
66463349 AAAATACCCTAGTTTGTAAAATTACC
1 AAAATACCTTGGTTTATAAAATTACC
66463375 AAAATACC
1 AAAATACC
66463383 CCTAATTTGT
Statistics
Matches: 98, Mismatches: 15, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
26 53 0.54
27 45 0.46
ACGTcount: A:0.42, C:0.19, G:0.07, T:0.32
Consensus pattern (26 bp):
AAAATACCTTGGTTTATAAAATTACC
Found at i:66463398 original size:80 final size:80
Alignment explanation
Indices: 66463260--66463482 Score: 218
Period size: 80 Copynumber: 2.8 Consensus size: 80
66463250 TTTGGTTTAC
* * * * **
66463260 AAAATTACCAAAATACCCTGCTTTGTAAAATTACTAAAATACCCTTGGTTTATAAAATTACCAAA
1 AAAATTATCAAAATACCCTGATTTGTAAAATTACCAAAATACCCCTAATTTATAAAATTACCAAA
**
66463325 ATACCCCTAG-TTTGT
66 ATA-CCCTAGACCTGT
* * **
66463340 AAAATTATCAAAATACCCT-AGTTTGTAAAATTACCAAAATACCCCTAATTTGTGAAATTACTGA
1 AAAATTATCAAAATACCCTGA-TTTGTAAAATTACCAAAATACCCCTAATTTATAAAATTACCAA
*
66463404 AATACCCTCGACCTGT
65 AATACCCTAGACCTGT
** * * * *
66463420 AAAATTATTGAAATACCCTCGACTTGTAAAATTACCAAAGTA-CCCTCGATTTATAGAATTACC
1 AAAATTATCAAAATACCCT-GATTTGTAAAATTACCAAAATACCCCT-AATTTATAAAATTACC
66463483 GTTTTACCCT
Statistics
Matches: 116, Mismatches: 22, Indels: 9
0.79 0.15 0.06
Matches are distributed among these distances:
79 5 0.04
80 81 0.70
81 29 0.25
82 1 0.01
ACGTcount: A:0.40, C:0.21, G:0.09, T:0.31
Consensus pattern (80 bp):
AAAATTATCAAAATACCCTGATTTGTAAAATTACCAAAATACCCCTAATTTATAAAATTACCAAA
ATACCCTAGACCTGT
Found at i:66463466 original size:27 final size:27
Alignment explanation
Indices: 66463260--66463508 Score: 227
Period size: 27 Copynumber: 9.3 Consensus size: 27
66463250 TTTGGTTTAC
*
66463260 AAAATTACCAAAATACCCT-GCTTTGT
1 AAAATTACCAAAATACCCTCGATTTGT
* * * *
66463286 AAAATTACTAAAATACCCTTGGTTTAT
1 AAAATTACCAAAATACCCTCGATTTGT
*
66463313 AAAATTACCAAAATACCC-CTAGTTTGT
1 AAAATTACCAAAATACCCTCGA-TTTGT
* *
66463340 AAAATTATCAAAATACCCTAG-TTTGT
1 AAAATTACCAAAATACCCTCGATTTGT
*
66463366 AAAATTACCAAAATACCC-CTAATTTGT
1 AAAATTACCAAAATACCCTC-GATTTGT
* ** **
66463393 GAAATTACTGAAATACCCTCGACCTGT
1 AAAATTACCAAAATACCCTCGATTTGT
*** *
66463420 AAAATTATTGAAATACCCTCGACTTGT
1 AAAATTACCAAAATACCCTCGATTTGT
* *
66463447 AAAATTACCAAAGTACCCTCGATTTAT
1 AAAATTACCAAAATACCCTCGATTTGT
* ****
66463474 AGAATTACCGTTTTACCCTCGATTTGT
1 AAAATTACCAAAATACCCTCGATTTGT
66463501 AAAATTAC
1 AAAATTAC
66463509 TGTTTTACCC
Statistics
Matches: 181, Mismatches: 36, Indels: 11
0.79 0.16 0.05
Matches are distributed among these distances:
26 40 0.22
27 140 0.77
28 1 0.01
ACGTcount: A:0.39, C:0.20, G:0.09, T:0.32
Consensus pattern (27 bp):
AAAATTACCAAAATACCCTCGATTTGT
Found at i:66463491 original size:81 final size:80
Alignment explanation
Indices: 66463260--66463507 Score: 216
Period size: 80 Copynumber: 3.1 Consensus size: 80
66463250 TTTGGTTTAC
* * * ** * *
66463260 AAAATTACCAAAATACCCT-GCTTTGTAAAATTACTAAAATACCCTTGGTTTATAAAATTACCAA
1 AAAATTATCAAAATACCCTAGC-TTGTAAAATTACCAAAATACCCCTAATTTATGAAATTACCGA
* **
66463324 AATACCC-CTAGTTTGT
65 AATACCCTCGA-CCTGT
* * *
66463340 AAAATTATCAAAATACCCTAGTTTGTAAAATTACCAAAATACCCCTAATTTGTGAAATTACTGAA
1 AAAATTATCAAAATACCCTAGCTTGTAAAATTACCAAAATACCCCTAATTTATGAAATTACCGAA
66463405 ATACCCTCGACCTGT
66 ATACCCTCGACCTGT
** * * *
66463420 AAAATTATTGAAATACCCTCGACTTGTAAAATTACCAAAGTA-CCCTCGATTTAT-AGAATTACC
1 AAAATTATCAAAATACCCTAG-CTTGTAAAATTACCAAAATACCCCT-AATTTATGA-AATTACC
*** **
66463483 GTTTTACCCTCGATTTGT
63 GAAATACCCTCGACCTGT
66463501 AAAATTA
1 AAAATTA
66463508 CTGTTTTACC
Statistics
Matches: 137, Mismatches: 26, Indels: 9
0.80 0.15 0.05
Matches are distributed among these distances:
80 85 0.62
81 52 0.38
ACGTcount: A:0.39, C:0.20, G:0.09, T:0.32
Consensus pattern (80 bp):
AAAATTATCAAAATACCCTAGCTTGTAAAATTACCAAAATACCCCTAATTTATGAAATTACCGAA
ATACCCTCGACCTGT
Found at i:66463518 original size:81 final size:81
Alignment explanation
Indices: 66463460--66463857 Score: 507
Period size: 80 Copynumber: 4.9 Consensus size: 81
66463450 ATTACCAAAG
* * *
66463460 TACCCTCGATTTATAGAATTACCGTTTTACCCTCGATTTGTAAAATTACTGTTTTACCCTCGATT
1 TACCCTCGATTTACAGAATTACCGTTTTACCCTCGATTTATAAAATTACCGTTTTACCCTCGATT
66463525 TACAGAATTACCATTT
66 TACAGAATTACCATTT
* ** * *
66463541 TACCCT-TAGTTTACAGAATTACTATTTTACCCTCGATTTATAGAATTACCGTTTTACCC-CTAA
1 TACCCTCGA-TTTACAGAATTACCGTTTTACCCTCGATTTATAAAATTACCGTTTTACCCTC-GA
* *
66463604 TTTACATAATTACCGTTT
64 TTTACAGAATTACCATTT
* * * *
66463622 TACCC-CGATTTACATAATTATCGTTTTACCCTCGATTTATAGAATTACCGTTTCACCCTCGATT
1 TACCCTCGATTTACAGAATTACCGTTTTACCCTCGATTTATAAAATTACCGTTTTACCCTCGATT
*
66463686 TATAGAATTACCATTT
66 TACAGAATTACCATTT
* * * * *
66463702 TACCC-CGATTTACATAATTATCGTTTTACCCTCGATTTACAGAATTACCGTTTCACCCTCGATT
1 TACCCTCGATTTACAGAATTACCGTTTTACCCTCGATTTATAAAATTACCGTTTTACCCTCGATT
66463766 TACAGAATTACCATTT
66 TACAGAATTACCATTT
* * * * **
66463782 TACCCTCGATTTATAGAATTACTGTTTTACCCTTGATTTACAAAATTACTATTTTACCCTCGATT
1 TACCCTCGATTTACAGAATTACCGTTTTACCCTCGATTTATAAAATTACCGTTTTACCCTCGATT
*
66463847 TACAAAATTAC
66 TACAGAATTAC
66463858 TAAAATACCC
Statistics
Matches: 280, Mismatches: 32, Indels: 10
0.87 0.10 0.03
Matches are distributed among these distances:
80 146 0.52
81 134 0.48
ACGTcount: A:0.28, C:0.23, G:0.08, T:0.40
Consensus pattern (81 bp):
TACCCTCGATTTACAGAATTACCGTTTTACCCTCGATTTATAAAATTACCGTTTTACCCTCGATT
TACAGAATTACCATTT
Found at i:66463859 original size:27 final size:27
Alignment explanation
Indices: 66463460--66463857 Score: 489
Period size: 27 Copynumber: 14.8 Consensus size: 27
66463450 ATTACCAAAG
*
66463460 TACCCTCGATTTATAGAATTACCGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
** * *
66463487 TACCCTCGATTTGTAAAATTACTGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
*
66463514 TACCCTCGATTTACAGAATTACCATTT
1 TACCCTCGATTTACAGAATTACCGTTT
* **
66463541 TACCCT-TAGTTTACAGAATTACTATTT
1 TACCCTCGA-TTTACAGAATTACCGTTT
*
66463568 TACCCTCGATTTATAGAATTACCGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
* *
66463595 TACCC-CTAATTTACATAATTACCGTTT
1 TACCCTC-GATTTACAGAATTACCGTTT
* *
66463622 TACCC-CGATTTACATAATTATCGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
*
66463648 TACCCTCGATTTATAGAATTACCGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
* * *
66463675 CACCCTCGATTTATAGAATTACCATTT
1 TACCCTCGATTTACAGAATTACCGTTT
* *
66463702 TACCC-CGATTTACATAATTATCGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
66463728 TACCCTCGATTTACAGAATTACCGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
* *
66463755 CACCCTCGATTTACAGAATTACCATTT
1 TACCCTCGATTTACAGAATTACCGTTT
* *
66463782 TACCCTCGATTTATAGAATTACTGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
* * **
66463809 TACCCTTGATTTACAAAATTACTATTT
1 TACCCTCGATTTACAGAATTACCGTTT
*
66463836 TACCCTCGATTTACAAAATTAC
1 TACCCTCGATTTACAGAATTAC
66463858 TAAAATACCC
Statistics
Matches: 324, Mismatches: 42, Indels: 10
0.86 0.11 0.03
Matches are distributed among these distances:
26 47 0.15
27 276 0.85
28 1 0.00
ACGTcount: A:0.28, C:0.23, G:0.08, T:0.40
Consensus pattern (27 bp):
TACCCTCGATTTACAGAATTACCGTTT
Found at i:66465121 original size:25 final size:25
Alignment explanation
Indices: 66465093--66465140 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
66465083 TTATACCATG
* * *
66465093 AAAATGACCGTTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
66465118 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
66465141 GTTTATGTAT
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:66465242 original size:20 final size:20
Alignment explanation
Indices: 66465183--66465242 Score: 95
Period size: 19 Copynumber: 3.0 Consensus size: 20
66465173 ATAAATATGG
*
66465183 TATGTATGAGATGCACATGA
1 TATGTATGATATGCACATGA
*
66465203 CATGTATGATA-GCACATGA
1 TATGTATGATATGCACATGA
66465222 TATGTATGATATGCACATGA
1 TATGTATGATATGCACATGA
66465242 T
1 T
66465243 GTAATCATAA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
19 18 0.50
20 18 0.50
ACGTcount: A:0.35, C:0.12, G:0.22, T:0.32
Consensus pattern (20 bp):
TATGTATGATATGCACATGA
Found at i:66465360 original size:47 final size:49
Alignment explanation
Indices: 66465293--66465386 Score: 140
Period size: 47 Copynumber: 2.0 Consensus size: 49
66465283 AGGAAGTGAA
*
66465293 AAAGGGCTTATGCCCCAGTTA-TAAAAG-GGCTTATGCC-CCAGTTATTG
1 AAAGGGCTTATGCCCCAGTTATTAAAAGAGGC-TAGGCCTCCAGTTATTG
*
66465340 AAAGGGCTTTTGCCCCAGTTATTAAAAGAGGCTAGGCCTCCAGTTAT
1 AAAGGGCTTATGCCCCAGTTATTAAAAGAGGCTAGGCCTCCAGTTAT
66465387 ATGATAAAGC
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
47 20 0.48
48 11 0.26
49 11 0.26
ACGTcount: A:0.28, C:0.21, G:0.23, T:0.28
Consensus pattern (49 bp):
AAAGGGCTTATGCCCCAGTTATTAAAAGAGGCTAGGCCTCCAGTTATTG
Found at i:66465382 original size:25 final size:24
Alignment explanation
Indices: 66465292--66465386 Score: 131
Period size: 24 Copynumber: 4.0 Consensus size: 24
66465282 GAGGAAGTGA
66465292 AAAAGGGCTTATGCCCCAGTTA-T
1 AAAAGGGCTTATGCCCCAGTTATT
66465315 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
* *
66465339 GAAAGGGCTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
66465363 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
66465387 ATGATAAAGC
Statistics
Matches: 64, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
23 22 0.34
24 31 0.48
25 11 0.17
ACGTcount: A:0.28, C:0.21, G:0.23, T:0.27
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATT
Found at i:66465613 original size:31 final size:31
Alignment explanation
Indices: 66465578--66465641 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
66465568 CGTTTACAGT
66465578 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
** *
66465609 AAAGGCTTCGGCCCAGTGTTATGGAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
66465640 AA
1 AA
66465642 TGATATGAAA
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:0.25, T:0.23
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:66467225 original size:43 final size:42
Alignment explanation
Indices: 66467094--66467254 Score: 175
Period size: 42 Copynumber: 3.8 Consensus size: 42
66467084 TAAGACTATG
* *
66467094 TGTAAGACCATATCTAGGATATGACATCT-ATATGAGACTTCA
1 TGTAAGACCATATCTGGGATATGGCAT-TGATATGAGACTTCA
* * **
66467136 TGTAAGACCATCA-CTGGGATATGGCATCGATAAGAGACTTTT
1 TGTAAGACCAT-ATCTGGGATATGGCATTGATATGAGACTTCA
* *
66467178 TGTAAGACCATAGCTGGGATATTGGCATTGATATGAGA-TCCCA
1 TGTAAGACCATATCTGGGATA-TGGCATTGATATGAGACT-TCA
* *
66467221 TGTAAGACCATATTTGGGATATGGCATTGGTATG
1 TGTAAGACCATATCTGGGATATGGCATTGATATG
66467255 GTACCATGTG
Statistics
Matches: 100, Mismatches: 14, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
41 1 0.01
42 65 0.65
43 34 0.34
ACGTcount: A:0.31, C:0.15, G:0.24, T:0.30
Consensus pattern (42 bp):
TGTAAGACCATATCTGGGATATGGCATTGATATGAGACTTCA
Found at i:66467446 original size:15 final size:16
Alignment explanation
Indices: 66467420--66467449 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
66467410 TGAACCCTCG
66467420 GTAAGATTATGATTGA
1 GTAAGATTATGATTGA
66467436 GTAAG-TTATGATTG
1 GTAAGATTATGATTG
66467450 TAAAATATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.33, C:0.00, G:0.27, T:0.40
Consensus pattern (16 bp):
GTAAGATTATGATTGA
Found at i:66470116 original size:6 final size:6
Alignment explanation
Indices: 66470105--66470183 Score: 81
Period size: 6 Copynumber: 12.8 Consensus size: 6
66470095 TATCAAAACT
*
66470105 AGAATC AGAATC AGAATC AGAATC A-AGTGAC AGAATC AGAATC AGAATC
1 AGAATC AGAATC AGAATC AGAATC AGAAT--C AGAATC AGAATC AGAATC
* *
66470154 AGTATC AGGTAA-C AGAATC AAAATC AGAAT
1 AGAATC A-G-AATC AGAATC AGAATC AGAAT
66470184 GTGAATGCAA
Statistics
Matches: 61, Mismatches: 6, Indels: 12
0.77 0.08 0.15
Matches are distributed among these distances:
5 4 0.07
6 49 0.80
7 5 0.08
8 3 0.05
ACGTcount: A:0.49, C:0.15, G:0.18, T:0.18
Consensus pattern (6 bp):
AGAATC
Found at i:66470143 original size:31 final size:31
Alignment explanation
Indices: 66470105--66470183 Score: 122
Period size: 31 Copynumber: 2.5 Consensus size: 31
66470095 TATCAAAACT
*
66470105 AGAATCAGAATCAGAATCAGAATCAAGTGAC
1 AGAATCAGAATCAGAATCAGAATCAAGTAAC
* *
66470136 AGAATCAGAATCAGAATCAGTATCAGGTAAC
1 AGAATCAGAATCAGAATCAGAATCAAGTAAC
*
66470167 AGAATCAAAATCAGAAT
1 AGAATCAGAATCAGAAT
66470184 GTGAATGCAA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.49, C:0.15, G:0.18, T:0.18
Consensus pattern (31 bp):
AGAATCAGAATCAGAATCAGAATCAAGTAAC
Found at i:66470173 original size:25 final size:24
Alignment explanation
Indices: 66470110--66470156 Score: 85
Period size: 25 Copynumber: 1.9 Consensus size: 24
66470100 AAACTAGAAT
66470110 CAGAATCAGAATCAGAATCAAGTGA
1 CAGAATCAGAATCAGAATC-AGTGA
66470135 CAGAATCAGAATCAGAATCAGT
1 CAGAATCAGAATCAGAATCAGT
66470157 ATCAGGTAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 3 0.14
25 19 0.86
ACGTcount: A:0.47, C:0.17, G:0.19, T:0.17
Consensus pattern (24 bp):
CAGAATCAGAATCAGAATCAGTGA
Found at i:66470350 original size:27 final size:28
Alignment explanation
Indices: 66470302--66470359 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 28
66470292 GCGAGGCTGC
*
66470302 CAGATATTGTGACGAAGTCACCAGA-TA
1 CAGATATTGTGACGAAGCCACCAGATTA
* * *
66470329 CAGATATTGTGGCTAGGCCACCAGATTA
1 CAGATATTGTGACGAAGCCACCAGATTA
66470357 CAG
1 CAG
66470360 CGAGGCTGGC
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
27 21 0.81
28 5 0.19
ACGTcount: A:0.33, C:0.21, G:0.24, T:0.22
Consensus pattern (28 bp):
CAGATATTGTGACGAAGCCACCAGATTA
Found at i:66470407 original size:67 final size:67
Alignment explanation
Indices: 66470290--66470439 Score: 239
Period size: 67 Copynumber: 2.2 Consensus size: 67
66470280 ACAGAAATTG
*
66470290 CAGCGAGGCTGCCAGATATTGTGACGAAGTCACCAGATACAGATATTGTGGCTAGGCCACCAGAT
1 CAGCGAGGCTGCCAGATATTGTGACGAAGTCACCAGATACAGATATTGTGGCGAGGCCACCAGAT
66470355 TA
66 TA
* * *
66470357 CAGCGAGGCTGGCAGATATTGTGACGAAGTCACTAGA-ACAGATATATGTGGCGAGGCCACCATA
1 CAGCGAGGCTGCCAGATATTGTGACGAAGTCACCAGATACAGATAT-TGTGGCGAGGCCACCAGA
*
66470421 TTG
65 TTA
66470424 CAGCGAGGCTGCCAGA
1 CAGCGAGGCTGCCAGA
66470440 ACGCTTCCTC
Statistics
Matches: 76, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
66 8 0.11
67 68 0.89
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.19
Consensus pattern (67 bp):
CAGCGAGGCTGCCAGATATTGTGACGAAGTCACCAGATACAGATATTGTGGCGAGGCCACCAGAT
TA
Found at i:66470695 original size:27 final size:27
Alignment explanation
Indices: 66470665--66470862 Score: 190
Period size: 27 Copynumber: 7.3 Consensus size: 27
66470655 GGGGTAAAAT
* *
66470665 GGTAATTTTACCCCACAAGGGTATCTC
1 GGTAATTTTACCCTACAAGGGTATTTC
* *
66470692 GGTAATTCTACCTTAC-AGGAGTATTTC
1 GGTAATTTTACCCTACAAGG-GTATTTC
* * *
66470719 AGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTTTACCCTACAAGGGTATTTC
*
66470746 GAT-ATTTCTACCCTACAAGGGTATTTC
1 GGTAATTT-TACCCTACAAGGGTATTTC
* *
66470773 GGTAATTCTACCCTA-TAGCGGTATTTC
1 GGTAATTTTACCCTACAAG-GGTATTTC
* * *
66470800 GATATTTTTA-CTTGACAAGGGTATTTC
1 GGTAATTTTACCCT-ACAAGGGTATTTC
66470827 GGT-ATTTCTACCCTACAAGGGTATTTC
1 GGTAATTT-TACCCTACAAGGGTATTTC
*
66470854 AGTAATTTT
1 GGTAATTTT
66470863 GTAAATCGAG
Statistics
Matches: 138, Mismatches: 23, Indels: 20
0.76 0.13 0.11
Matches are distributed among these distances:
26 13 0.09
27 112 0.81
28 13 0.09
ACGTcount: A:0.25, C:0.20, G:0.18, T:0.37
Consensus pattern (27 bp):
GGTAATTTTACCCTACAAGGGTATTTC
Found at i:66470731 original size:54 final size:54
Alignment explanation
Indices: 66470665--66470853 Score: 222
Period size: 54 Copynumber: 3.5 Consensus size: 54
66470655 GGGGTAAAAT
* * * *
66470665 GGTAATTTTACCCCACAAGGGTATCTCGGTAATTCTACCTTAC-AGGAGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTCGATAATTCTACCTTACAAGG-GTATTTC
* * * *
66470719 AGTAATTCTACCCTACAGGGGTATTTCGATATTTCTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTCGATAATTCTACCTTACAAGGGTATTTC
* * *
66470773 GGTAATTCTACCCTA-TAGCGGTATTTCGATATTTTTA-CTTGACAAGGGTATTTC
1 GGTAATTCTACCCTACAAG-GGTATTTCGATAATTCTACCTT-ACAAGGGTATTTC
*
66470827 GGTATTTCTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
66470854 AGTAATTTTG
Statistics
Matches: 116, Mismatches: 15, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
53 3 0.03
54 108 0.93
55 5 0.04
ACGTcount: A:0.25, C:0.21, G:0.18, T:0.37
Consensus pattern (54 bp):
GGTAATTCTACCCTACAAGGGTATTTCGATAATTCTACCTTACAAGGGTATTTC
Found at i:66470797 original size:81 final size:81
Alignment explanation
Indices: 66470669--66470860 Score: 239
Period size: 81 Copynumber: 2.4 Consensus size: 81
66470659 TAAAATGGTA
* * *
66470669 ATTT-TACCCCACAAGGGTATCTCGGTAATTCTACCTTACAGGAGTATTTC-AGTAATTCTACCC
1 ATTTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTACAGGAGTATTTCGA-TAATTCTA-CC
*
66470732 T-ACAGGGGTATTTCGAT
64 TGACAAGGGTATTTCGAT
* * * *
66470749 ATTTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTATAGCG-GTATTTCGATATTTTTACTT
1 ATTTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTACAG-GAGTATTTCGATAATTCTACCT
*
66470813 GACAAGGGTATTTCGGT
65 GACAAGGGTATTTCGAT
*
66470830 ATTTCTACCCTACAAGGGTATTTCAGTAATT
1 ATTTCTACCCTACAAGGGTATTTCGGTAATT
66470861 TTGTAAATCG
Statistics
Matches: 98, Mismatches: 10, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
80 6 0.06
81 90 0.92
82 2 0.02
ACGTcount: A:0.26, C:0.20, G:0.17, T:0.37
Consensus pattern (81 bp):
ATTTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTACAGGAGTATTTCGATAATTCTACCTG
ACAAGGGTATTTCGAT
Found at i:66470874 original size:27 final size:27
Alignment explanation
Indices: 66470844--66471158 Score: 160
Period size: 27 Copynumber: 11.7 Consensus size: 27
66470834 CTACCCTACA
**
66470844 AGGGTATTTCAGTAATTTTGTAAATCG
1 AGGGTATTTCAGTAATTTTACAAATCG
*** * **
66470871 AGGGTAAAACGGTAATTTTGTAAATC-
1 AGGGTATTTCAGTAATTTTACAAATCG
*
66470897 AGGGGTACTTT-AGTAATTTTACAAGTCG
1 A-GGGTA-TTTCAGTAATTTTACAAATCG
* **
66470925 AGGGTATTTCAATAATTTTACAGGTCG
1 AGGGTATTTCAGTAATTTTACAAATCG
* *
66470952 AGGGTATTTCAGTAATTTCACCAATC-
1 AGGGTATTTCAGTAATTTTACAAATCG
** *
66470978 AGGGGTATTTTGGTAATTTTACAAA-CT
1 A-GGGTATTTCAGTAATTTTACAAATCG
** *
66471005 AGGGGTATTTTGGTAATTTTACAAA-CC
1 A-GGGTATTTCAGTAATTTTACAAATCG
** *
66471032 AGGGGTATTTTGGTAATTTTATAAA-CTG
1 A-GGGTATTTCAGTAATTTTACAAATC-G
** *
66471060 AGGGTATTTTGGTAATTTTACAAA-CC
1 AGGGTATTTCAGTAATTTTACAAATCG
** * * * *
66471086 AGGGGTATTTTGGTGATTTTATAAACCA
1 A-GGGTATTTCAGTAATTTTACAAATCG
* * * *
66471114 AAGGTATTTGAGCAATTTTAC-AATCCA
1 AGGGTATTTCAGTAATTTTACAAAT-CG
**
66471141 AGGGTATTTTGGTAATTT
1 AGGGTATTTCAGTAATTT
66471159 GGTAAAATAA
Statistics
Matches: 237, Mismatches: 41, Indels: 20
0.80 0.14 0.07
Matches are distributed among these distances:
26 9 0.04
27 224 0.95
28 4 0.02
ACGTcount: A:0.30, C:0.10, G:0.22, T:0.38
Consensus pattern (27 bp):
AGGGTATTTCAGTAATTTTACAAATCG
Found at i:66470995 original size:54 final size:53
Alignment explanation
Indices: 66470950--66471158 Score: 249
Period size: 54 Copynumber: 3.9 Consensus size: 53
66470940 TTTTACAGGT
** * * *
66470950 CGAGGGTATTTCAGTAATTTCACCAATCAGGGGTATTTTGGTAATTTTACAAA
1 CGAGGGTATTTTGGTAATTTTACAAACCAGGGGTATTTTGGTAATTTTACAAA
* *
66471003 CTAGGGGTATTTTGGTAATTTTACAAACCAGGGGTATTTTGGTAATTTTATAAA
1 CGA-GGGTATTTTGGTAATTTTACAAACCAGGGGTATTTTGGTAATTTTACAAA
* *
66471057 CTGAGGGTATTTTGGTAATTTTACAAACCAGGGGTATTTTGGTGATTTTATAAA
1 C-GAGGGTATTTTGGTAATTTTACAAACCAGGGGTATTTTGGTAATTTTACAAA
* * * * *
66471111 CCAAAGGTA-TTTGAGCAATTTTACAATCCAAGGGTATTTTGGTAATTT
1 -CGAGGGTATTTTG-GTAATTTTACAAACCAGGGGTATTTTGGTAATTT
66471159 GGTAAAATAA
Statistics
Matches: 137, Mismatches: 15, Indels: 7
0.86 0.09 0.04
Matches are distributed among these distances:
53 6 0.04
54 129 0.94
55 2 0.01
ACGTcount: A:0.30, C:0.10, G:0.22, T:0.39
Consensus pattern (53 bp):
CGAGGGTATTTTGGTAATTTTACAAACCAGGGGTATTTTGGTAATTTTACAAA
Found at i:66471011 original size:81 final size:80
Alignment explanation
Indices: 66470893--66471158 Score: 221
Period size: 81 Copynumber: 3.3 Consensus size: 80
66470883 TAATTTTGTA
* * * * ***
66470893 AATCAGGGGTACTTTAGTAATTTTAC-AAGTCGAGGGTATTTCAATAATTTTACAGGTC-GAGGG
1 AATCAGGGGTATTTTGGTAATTTTACAAACTAG-GGGTATTTCAATAATTTTACAAACCAG-GGG
66470956 TATTTCAGTAATTTCACC
64 TATTTCAGTAATTTCA-C
***
66470974 AATCAGGGGTATTTTGGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTACAAACCAGGGGTA
1 AATCAGGGGTATTTTGGTAATTTTACAAACTAGGGGTATTTCAATAATTTTACAAACCAGGGGTA
** * *
66471039 TTTTGGTAATTTTAT
66 TTTCAGTAATTTCAC
* * * *** * * **
66471054 AAACTGAGGGTATTTTGGTAATTTTACAAACCAGGGGTATTTTGGTGATTTTATAAACCAAAGGT
1 AATCAG-GGGTATTTTGGTAATTTTACAAACTAGGGGTATTTCAATAATTTTACAAACCAGGGGT
* * *
66471119 ATTTGAGCAATTTTAC
65 ATTTCAGTAATTTCAC
*
66471135 AATCCAAGGGTATTTTGGTAATTT
1 AAT-CAGGGGTATTTTGGTAATTT
66471159 GGTAAAATAA
Statistics
Matches: 153, Mismatches: 28, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
80 4 0.03
81 143 0.93
82 6 0.04
ACGTcount: A:0.30, C:0.10, G:0.21, T:0.38
Consensus pattern (80 bp):
AATCAGGGGTATTTTGGTAATTTTACAAACTAGGGGTATTTCAATAATTTTACAAACCAGGGGTA
TTTCAGTAATTTCAC
Found at i:66473382 original size:40 final size:40
Alignment explanation
Indices: 66473332--66473520 Score: 186
Period size: 40 Copynumber: 4.7 Consensus size: 40
66473322 TTGACGATGA
*
66473332 TTCGGATATATATGGCACTTAGTGTGCGATTCAAGATAGC
1 TTCGGCTATATATGGCACTTAGTGTGCGATTCAAGATAGC
* * *
66473372 TTCGACTATATATGGCACTTAGTGTGTGATTC-GGAATAGC
1 TTCGGCTATATATGGCACTTAGTGTGCGATTCAAG-ATAGC
* * ** * *
66473412 TTCGGCTATATATAGCACTTAGTGTGTGAGACTGAGATAGT
1 TTCGGCTATATATGGCACTTAGTGTGCGATTC-AAGATAGC
* *
66473453 TTCGGCTATGTAAGGCACTTAGTGTGCGAAATT-ATA-ATAGC
1 TTCGGCTATATATGGCACTTAGTGTGCG--ATTCA-AGATAGC
*
66473494 TTCGGCTATGTATTGGCACTTAGTGTG
1 TTCGGCTATATA-TGGCACTTAGTGTG
66473521 AGAGATATCG
Statistics
Matches: 123, Mismatches: 19, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
39 1 0.01
40 62 0.50
41 44 0.36
42 15 0.12
43 1 0.01
ACGTcount: A:0.25, C:0.14, G:0.26, T:0.34
Consensus pattern (40 bp):
TTCGGCTATATATGGCACTTAGTGTGCGATTCAAGATAGC
Found at i:66473520 original size:81 final size:80
Alignment explanation
Indices: 66473332--66473523 Score: 208
Period size: 81 Copynumber: 2.4 Consensus size: 80
66473322 TTGACGATGA
* * * *
66473332 TTCGGATATATATGGCACTTAGTGTGCGATTCAAGATAGCTTCGACTATATATGGCACTTAGTGT
1 TTCGGCTATATATGGCACTTAGTGTGAGACTCAAGATAGCTTCGACTATATAAGGCACTTAGTGT
* *
66473397 GTGATTCGGAATAGC
66 GCGATTCAGAATAGC
* * * * *
66473412 TTCGGCTATATATAGCACTTAGTGTGTGAGACT-GAGATAGTTTCGGCTATGTAAGGCACTTAGT
1 TTCGGCTATATATGGCACTTA--GTGTGAGACTCAAGATAGCTTCGACTATATAAGGCACTTAGT
*
66473476 GTGCGAAATT-ATAATAGC
64 GTGCG--ATTCAGAATAGC
*
66473494 TTCGGCTATGTATTGGCACTTAGTGTGAGA
1 TTCGGCTATATA-TGGCACTTAGTGTGAGA
66473524 GATATCGAGT
Statistics
Matches: 93, Mismatches: 14, Indels: 9
0.80 0.12 0.08
Matches are distributed among these distances:
80 19 0.20
81 38 0.41
82 25 0.27
83 11 0.12
ACGTcount: A:0.26, C:0.14, G:0.26, T:0.34
Consensus pattern (80 bp):
TTCGGCTATATATGGCACTTAGTGTGAGACTCAAGATAGCTTCGACTATATAAGGCACTTAGTGT
GCGATTCAGAATAGC
Found at i:66485301 original size:13 final size:13
Alignment explanation
Indices: 66485276--66485301 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
66485266 TAATTTGATA
66485276 AAAGGATTTAATC
1 AAAGGATTTAATC
66485289 AAAGGATTTAATC
1 AAAGGATTTAATC
66485302 GCATAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.08, G:0.15, T:0.31
Consensus pattern (13 bp):
AAAGGATTTAATC
Found at i:66492081 original size:42 final size:42
Alignment explanation
Indices: 66491968--66492136 Score: 171
Period size: 43 Copynumber: 4.0 Consensus size: 42
66491958 TTTCGATATG
** *
66491968 TGATTTCATGTAAGACCACATATGGGACATTGGCATTG-ATT
1 TGATTTCATGTAAGACCATGTCTGGGACATTGGCATTGTATT
66492009 TGAGATTT-ATGTGTAAGACCATGTCTGGGACATTGGCATTGTATT
1 T--GATTTCA--TGTAAGACCATGTCTGGGACATTGGCATTGTATT
* * * ** *
66492054 TGATTTCATATAAGACCTTGTCGGGGACAGAGGCATCGATATT
1 TGATTTCATGTAAGACCATGTCTGGGACATTGGCATTG-TATT
* * *
66492097 TGATTACATGTAAGACCACGTCTGGGACATTAGCATTGTA
1 TGATTTCATGTAAGACCATGTCTGGGACATTGGCATTGTA
66492137 CAATCTTCCC
Statistics
Matches: 103, Mismatches: 18, Indels: 13
0.77 0.13 0.10
Matches are distributed among these distances:
41 1 0.01
42 27 0.26
43 43 0.42
44 28 0.27
45 4 0.04
ACGTcount: A:0.28, C:0.15, G:0.24, T:0.33
Consensus pattern (42 bp):
TGATTTCATGTAAGACCATGTCTGGGACATTGGCATTGTATT
Found at i:66499675 original size:43 final size:43
Alignment explanation
Indices: 66499628--66499792 Score: 170
Period size: 43 Copynumber: 3.8 Consensus size: 43
66499618 ACATAGGATT
* *
66499628 TCGATATGTGATTTCGTGTAAGACCACATCTGGGACATTGGCA
1 TCGATATGTGATTTCGTGTAAGACCACGTCTGGGACATAGGCA
* * * *
66499671 TCGATTTGAGATTTACGTGTAAGACCATGTCTGGGACATCGGCA
1 TCGATATGTGATTT-CGTGTAAGACCACGTCTGGGACATAGGCA
* * * ** * *
66499715 TC-ATATTTGATTTCGTATATGACCTTGTCGGGGACAGAGGCA
1 TCGATATGTGATTTCGTGTAAGACCACGTCTGGGACATAGGCA
* * *
66499757 TCGATATTTGATTACATGTAAGACCACGTCTGGGAC
1 TCGATATGTGATTTCGTGTAAGACCACGTCTGGGAC
66499793 GTTAGCATTG
Statistics
Matches: 99, Mismatches: 21, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
42 25 0.25
43 46 0.46
44 28 0.28
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.31
Consensus pattern (43 bp):
TCGATATGTGATTTCGTGTAAGACCACGTCTGGGACATAGGCA
Found at i:66509576 original size:40 final size:39
Alignment explanation
Indices: 66509527--66509636 Score: 139
Period size: 40 Copynumber: 2.7 Consensus size: 39
66509517 ATAATCACGT
* *
66509527 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATAACTC
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGATAGAACAACTA
* * *
66509567 GCACGAATGCCTTCGGGTCTTAGCCCGGATATAGCCACTA
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGATAGAACAACTA
*
66509607 GCACAATTGCCTTCGGGTCTTAACCCGGAT
1 GCACAA-TGCCTTCGGGTCTTAGCCCGGAT
66509637 GTAATTTCCA
Statistics
Matches: 62, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
39 2 0.03
40 60 0.97
ACGTcount: A:0.24, C:0.29, G:0.24, T:0.24
Consensus pattern (39 bp):
GCACAATGCCTTCGGGTCTTAGCCCGGATAGAACAACTA
Found at i:66509655 original size:40 final size:40
Alignment explanation
Indices: 66509511--66509678 Score: 124
Period size: 40 Copynumber: 4.2 Consensus size: 40
66509501 CAGAATATAA
* ** * *
66509511 CCGGATATAATCACGTGCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCACCAGCACAATTGCCTTCGGGTCTTAAC
* ** *
66509551 CCGGATAGAATAACTC-GCACGAA-TGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-CAGCAC-AATTGCCTTCGGGTCTTAAC
* *
66509591 CCGGATATAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAACCACCAGCACAATTGCCTTCGGGTCTTAAC
* *** * * * *
66509631 CCGGATGTAATTTCCAGCATAATTGTCTTCGGGGCTTAGC
1 CCGGATATAACCACCAGCACAATTGCCTTCGGGTCTTAAC
*
66509671 CTGGATAT
1 CCGGATAT
66509679 CATTCAATTT
Statistics
Matches: 103, Mismatches: 21, Indels: 8
0.78 0.16 0.06
Matches are distributed among these distances:
39 2 0.02
40 99 0.96
41 2 0.02
ACGTcount: A:0.24, C:0.26, G:0.23, T:0.27
Consensus pattern (40 bp):
CCGGATATAACCACCAGCACAATTGCCTTCGGGTCTTAAC
Found at i:66512019 original size:80 final size:80
Alignment explanation
Indices: 66511935--66512083 Score: 183
Period size: 80 Copynumber: 1.9 Consensus size: 80
66511925 TATGGTAACC
* * * *
66511935 CGCACCAAGGCCTACGGGACTTAACCCGGATATCA-CGATTTGCACAAATGCCTTCGGGTCTTAG
1 CGCACCAAGGCCTACGGGACTTAACCCGGATAT-AGCCACTAGCACAAATGCCTTCGGGTCTTAA
66511999 CCCGGATAGAATGACT
65 CCCGGATAGAATGACT
* * * * * * *
66512015 CGCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
66512080 CCGG
66 CCGG
66512084 TTATAATTTC
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
79 1 0.02
80 56 0.98
ACGTcount: A:0.23, C:0.30, G:0.25, T:0.22
Consensus pattern (80 bp):
CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
CCGGATAGAATGACT
Found at i:66512025 original size:40 final size:38
Alignment explanation
Indices: 66511976--66512083 Score: 128
Period size: 40 Copynumber: 2.7 Consensus size: 38
66511966 ATCACGATTT
*
66511976 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATG-ACTC
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGAT-GAA-GCACTA
*
66512016 GCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTA
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGATGAAG-CACTA
*
66512056 GCACAATTGCCTTCGGGTCTTAACCCGG
1 GCACAA-TGCCTTCGGGTCTTAGCCCGG
66512084 TTATAATTTC
Statistics
Matches: 61, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
38 1 0.02
39 4 0.07
40 56 0.92
ACGTcount: A:0.21, C:0.30, G:0.26, T:0.23
Consensus pattern (38 bp):
GCACAATGCCTTCGGGTCTTAGCCCGGATGAAGCACTA
Found at i:66520843 original size:40 final size:40
Alignment explanation
Indices: 66520798--66520965 Score: 185
Period size: 40 Copynumber: 4.2 Consensus size: 40
66520788 CGGAATATAA
66520798 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * * *
66520838 CCGGATAGAATAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * *
66520878 CCGGATATAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * * *
66520918 CCGGATATAATTTCCAGCATAATTGTCTTCGGGGCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
66520958 CCGGATAT
1 CCGGATAT
66520966 CATTCAATTT
Statistics
Matches: 107, Mismatches: 20, Indels: 2
0.83 0.16 0.02
Matches are distributed among these distances:
39 1 0.01
40 106 0.99
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:66527184 original size:27 final size:27
Alignment explanation
Indices: 66527154--66527223 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
66527144 TTCATTAGGC
66527154 CAAAACAGTCATTTTACCACATAAGGG
1 CAAAACAGTCATTTTACCACATAAGGG
* *
66527181 CAAAAAAGTCATTTTACCATATAAGGG
1 CAAAACAGTCATTTTACCACATAAGGG
*
66527208 CAAAACAATCATTTTA
1 CAAAACAGTCATTTTA
66527224 TCAATTAGAA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.44, C:0.19, G:0.11, T:0.26
Consensus pattern (27 bp):
CAAAACAGTCATTTTACCACATAAGGG
Found at i:66527363 original size:18 final size:17
Alignment explanation
Indices: 66527340--66527373 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
66527330 TAAAATACGT
66527340 GCCCATCTGGGCCCACAC
1 GCCCATCT-GGCCCACAC
*
66527358 GCCCATGTGGCCCACA
1 GCCCATCTGGCCCACA
66527374 TAGCCCAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.18, C:0.47, G:0.24, T:0.12
Consensus pattern (17 bp):
GCCCATCTGGCCCACAC
Found at i:66530232 original size:40 final size:40
Alignment explanation
Indices: 66530122--66530234 Score: 183
Period size: 40 Copynumber: 2.8 Consensus size: 40
66530112 AAGTGACTAT
*
66530122 ATCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTCCCAA
1 ATCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTCCAAA
66530162 ATCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTCCAAA
1 ATCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTCCAAA
**
66530202 ATCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAG
1 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAG
66530235 CTATTATAAT
Statistics
Matches: 69, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
39 1 0.01
40 68 0.99
ACGTcount: A:0.27, C:0.23, G:0.27, T:0.23
Consensus pattern (40 bp):
ATCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTCCAAA
Found at i:66530257 original size:40 final size:40
Alignment explanation
Indices: 66530083--66530275 Score: 180
Period size: 40 Copynumber: 4.8 Consensus size: 40
66530073 TCGAATGATG
* ** * *
66530083 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTCCAAAA
* *
66530123 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTCCCAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTCCAAAA
*
66530163 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTCCAAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTCCAAAA
* * *
66530203 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGCTAT-TATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAG-T-TCCAAAA
* * *
66530244 T-CGGGCTATGTCCCGAAGGCTTTTGAGCGAGT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGT
66530276 CGCTATATCC
Statistics
Matches: 133, Mismatches: 15, Indels: 11
0.84 0.09 0.07
Matches are distributed among these distances:
39 2 0.02
40 117 0.88
41 13 0.10
42 1 0.01
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTCCAAAA
Found at i:66530286 original size:80 final size:79
Alignment explanation
Indices: 66530083--66530301 Score: 216
Period size: 80 Copynumber: 2.7 Consensus size: 79
66530073 TCGAATGATG
*
66530083 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGT-GACTATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCTTTGTGC-GAGTCG-CTATATCCGGACTAAGATCCGAAGGCATT
* *
66530147 TGTGCGAGTTCCCAAA
64 TGTGCGAGCTACCAAA
* * * **
66530163 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTC-CAAAATCCGGGTTAAG-TCCCGAAGGCA
1 TCCGGGCTAAG-TCCCGAAGGC-TTTGTGCGAG-TCGCTATATCCGGACTAAGAT-CCGAAGGCA
**
66530225 TTTGTGCGAGCTATTATAA
62 TTTGTGCGAGCTACCA-AA
* *
66530244 T-CGGGCTATGTCCCGAAGGCTTTTGAGCGAGTCGCTATATCCGGA-TAAGATCCGAAGG
1 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCGAGTCGCTATATCCGGACTAAGATCCGAAGG
66530302 TATGTGATTC
Statistics
Matches: 113, Mismatches: 17, Indels: 19
0.76 0.11 0.13
Matches are distributed among these distances:
79 15 0.13
80 86 0.76
81 12 0.11
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.25
Consensus pattern (79 bp):
TCCGGGCTAAGTCCCGAAGGCTTTGTGCGAGTCGCTATATCCGGACTAAGATCCGAAGGCATTTG
TGCGAGCTACCAAA
Found at i:66538268 original size:40 final size:40
Alignment explanation
Indices: 66538174--66538353 Score: 197
Period size: 40 Copynumber: 4.5 Consensus size: 40
66538164 TCGAATGATG
* * * * *
66538174 TCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGTGACTATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACCAAA
66538215 TCCGGGCTAAGAT-CCGAAGGCATTTGTGCGAGTTACCAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACCAAA
66538255 TCCGGGCTAAGAT-CCGAAGGCATTTGTGCGAGTT-CCAAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACC-AAA
* * **
66538295 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGCTATTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACCA-AA
*
66538336 -CCGGGCTATGTCCCGAAG
1 TCCGGGCTAAGTCCCGAAG
66538354 ACTTTTGATC
Statistics
Matches: 123, Mismatches: 11, Indels: 11
0.85 0.08 0.08
Matches are distributed among these distances:
39 3 0.02
40 91 0.74
41 28 0.23
42 1 0.01
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACCAAA
Found at i:66538378 original size:80 final size:80
Alignment explanation
Indices: 66538174--66538393 Score: 238
Period size: 80 Copynumber: 2.8 Consensus size: 80
66538164 TCGAATGATG
* *
66538174 TCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGT-GACTATATCCGGGCTAAGATCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCTTTTGTGC-GAGTCG-CTATATCCGGGTTAAGATCCGAAGGCAT
*
66538238 TTGTGCGAGTTACCAAA
64 TTGTGCGAGCTACCAAA
* * *
66538255 TCCGGGCTAAGAT-CCGAAGGCATTTGTGCGAGTTC-CAAAATCCGGGTTAAG-TCCCGAAGGCA
1 TCCGGGCTAAG-TCCCGAAGGCTTTTGTGCGAG-TCGCTATATCCGGGTTAAGAT-CCGAAGGCA
**
66538317 TTTGTGCGAGCTATTATAA
63 TTTGTGCGAGCTACCA-AA
* *
66538336 -CCGGGCTATGTCCCGAAGACTTTTGAT-CGAGTCGCTATATCC-GGTTAAGATCCGAAGG
1 TCCGGGCTAAGTCCCGAAGGCTTTTG-TGCGAGTCGCTATATCCGGGTTAAGATCCGAAGG
66538394 TACGTGATTC
Statistics
Matches: 117, Mismatches: 13, Indels: 20
0.78 0.09 0.13
Matches are distributed among these distances:
79 18 0.15
80 68 0.58
81 30 0.26
82 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCGAAGGCTTTTGTGCGAGTCGCTATATCCGGGTTAAGATCCGAAGGCATTT
GTGCGAGCTACCAAA
Found at i:66539805 original size:27 final size:26
Alignment explanation
Indices: 66539760--66539822 Score: 90
Period size: 27 Copynumber: 2.3 Consensus size: 26
66539750 CGGGGTGTTA
66539760 CACCAGATACAGATATTGTGGCAGAGC
1 CACCAGA-ACAGATATTGTGGCAGAGC
* *
66539787 CACCAGAATAGATATTTGTGGCATAGC
1 CACCAGAACAGATA-TTGTGGCAGAGC
66539814 CACCAGAAC
1 CACCAGAAC
66539823 GCTTCCTCCA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
26 6 0.19
27 26 0.81
ACGTcount: A:0.35, C:0.24, G:0.22, T:0.19
Consensus pattern (26 bp):
CACCAGAACAGATATTGTGGCAGAGC
Found at i:66540609 original size:21 final size:22
Alignment explanation
Indices: 66540585--66540627 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
66540575 CCTTAATCTA
66540585 AACGC-AGCCACCCTTAAGGGG
1 AACGCTAGCCACCCTTAAGGGG
66540606 AACGCTAGCCACCCTTAAGGGG
1 AACGCTAGCCACCCTTAAGGGG
66540628 TTTCGGCTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 5 0.24
22 16 0.76
ACGTcount: A:0.28, C:0.33, G:0.28, T:0.12
Consensus pattern (22 bp):
AACGCTAGCCACCCTTAAGGGG
Found at i:66547658 original size:27 final size:26
Alignment explanation
Indices: 66547621--66547715 Score: 82
Period size: 27 Copynumber: 3.5 Consensus size: 26
66547611 AGTATGGCTG
* *
66547621 CCAGAACAGATGTTGTGACAGAGTCA
1 CCAGAACAGATATTGTGACAGAGCCA
**
66547647 CCAGATACAGATATTGTGGTAGAGCCA
1 CCAGA-ACAGATATTGTGACAGAGCCA
* * * *
66547674 CCAGAACAAATATTGGTGGCATAACCA
1 CCAGAACAGATATT-GTGACAGAGCCA
*
66547701 CCAGAAACAAATATT
1 CCAG-AACAGATATT
66547716 TGTGGCATAT
Statistics
Matches: 58, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
26 13 0.22
27 35 0.60
28 10 0.17
ACGTcount: A:0.39, C:0.20, G:0.21, T:0.20
Consensus pattern (26 bp):
CCAGAACAGATATTGTGACAGAGCCA
Found at i:66547720 original size:28 final size:28
Alignment explanation
Indices: 66547645--66547735 Score: 98
Period size: 27 Copynumber: 3.4 Consensus size: 28
66547635 GTGACAGAGT
* * * * *
66547645 CACCAGATACAGATA-TTGTGGTAGAGC
1 CACCAGAAACAAATATTTGTGGCATAAC
*
66547672 CACCAG-AACAAATATTGGTGGCATAAC
1 CACCAGAAACAAATATTTGTGGCATAAC
*
66547699 CACCAGAAACAAATATTTGTGGCATATC
1 CACCAGAAACAAATATTTGTGGCATAAC
66547727 CACCA-AAAC
1 CACCAGAAAC
66547736 GCTTCCTCCA
Statistics
Matches: 54, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
26 6 0.11
27 24 0.44
28 24 0.44
ACGTcount: A:0.40, C:0.23, G:0.18, T:0.20
Consensus pattern (28 bp):
CACCAGAAACAAATATTTGTGGCATAAC
Found at i:66552609 original size:64 final size:64
Alignment explanation
Indices: 66552528--66552712 Score: 178
Period size: 67 Copynumber: 2.9 Consensus size: 64
66552518 AGACATTATG
* * * *
66552528 ATGTAGCTAGGTTGCATGGGTGATATTATGTGTACACCATGTAGACAAGAGAGCTATGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGATATTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
* * * *
66552592 ATGTAGCTAGGTCGCATGCGTGAT-TCCAGGTGAAGGACACCATGTAGACAAGAGAGCTACGAGA
1 ATGTAGCTAGGTCGCATGGGTGATAT-TA--TG-TGTACACCATGTAGACAAGAGAGCTACGAGA
66552656 TAA
62 TAA
* * * * * *
66552659 AT-TGGCTAGGTCACATGGGTGGTACTAAGTGTTCACCATGT-GTACAAGAGAGCT
1 ATGTAGCTAGGTCGCATGGGTGATATTATGTGTACACCATGTAG-ACAAGAGAGCT
66552713 GAACTATATG
Statistics
Matches: 97, Mismatches: 18, Indels: 13
0.76 0.14 0.10
Matches are distributed among these distances:
62 1 0.01
63 21 0.22
64 24 0.25
66 20 0.21
67 31 0.32
ACGTcount: A:0.30, C:0.15, G:0.30, T:0.25
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGATATTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:66556281 original size:18 final size:18
Alignment explanation
Indices: 66556255--66556290 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
66556245 CTTGGCCCAT
*
66556255 TGCAATAACAGTTAACAG
1 TGCAATAACAGTAAACAG
*
66556273 TGCAGTAACAGTAAACAG
1 TGCAATAACAGTAAACAG
66556291 CATGCAAGTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.44, C:0.17, G:0.19, T:0.19
Consensus pattern (18 bp):
TGCAATAACAGTAAACAG
Found at i:66556642 original size:27 final size:27
Alignment explanation
Indices: 66556612--66556691 Score: 124
Period size: 27 Copynumber: 3.0 Consensus size: 27
66556602 AAACATATAT
* *
66556612 CACATAGGGGCAAAACAGTTATTTTAC
1 CACATAAGGGCAAAACAGTCATTTTAC
*
66556639 CACAAAAGGGCAAAACAGTCATTTTAC
1 CACATAAGGGCAAAACAGTCATTTTAC
*
66556666 TACATAAGGGCAAAACAGTCATTTTA
1 CACATAAGGGCAAAACAGTCATTTTA
66556692 TCAATTAGGG
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 48 1.00
ACGTcount: A:0.41, C:0.19, G:0.16, T:0.24
Consensus pattern (27 bp):
CACATAAGGGCAAAACAGTCATTTTAC
Found at i:66557394 original size:32 final size:32
Alignment explanation
Indices: 66557351--66557413 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
66557341 TCCTTCGACA
*
66557351 AGCTCTTGAGCACCAACTAAGCATAGGTAAAT
1 AGCTCTAGAGCACCAACTAAGCATAGGTAAAT
66557383 AGCTCTAGAGCACCAACTAAGCATAGGTAAA
1 AGCTCTAGAGCACCAACTAAGCATAGGTAAA
66557414 CACTTAATAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.40, C:0.22, G:0.19, T:0.19
Consensus pattern (32 bp):
AGCTCTAGAGCACCAACTAAGCATAGGTAAAT
Found at i:66559604 original size:13 final size:13
Alignment explanation
Indices: 66559588--66559612 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
66559578 GACTCGTGGT
66559588 AAAGATACGTCGC
1 AAAGATACGTCGC
66559601 AAAGATACGTCG
1 AAAGATACGTCG
66559613 ATACTGAAGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.20, G:0.24, T:0.16
Consensus pattern (13 bp):
AAAGATACGTCGC
Found at i:66563594 original size:49 final size:49
Alignment explanation
Indices: 66563449--66563660 Score: 279
Period size: 47 Copynumber: 4.4 Consensus size: 49
66563439 TTATCACCTT
* * * * * *
66563449 TATACACTTTCACATCCATCACGTTGGCCACTCGGCCCTAT--CATATA
1 TATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATA
* * *
66563496 TATACACTTTCACATTCATCACATTGGCCATTCGGCCTTGTCAC--ATA
1 TATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATA
*
66563543 TATACACCTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATA
1 TATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATA
* *
66563592 TATACACTTTCACATTCATCACTTCGGCCATTAGGCCTTATCTCATATA
1 TATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATA
*
66563641 TATACACATTCACATTCATC
1 TATACACTTTCACATTCATC
66563661 GCGTAAAATC
Statistics
Matches: 148, Mismatches: 13, Indels: 6
0.89 0.08 0.04
Matches are distributed among these distances:
47 79 0.53
49 69 0.47
ACGTcount: A:0.28, C:0.31, G:0.08, T:0.33
Consensus pattern (49 bp):
TATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATA
Found at i:66563629 original size:96 final size:96
Alignment explanation
Indices: 66563449--66563660 Score: 277
Period size: 96 Copynumber: 2.2 Consensus size: 96
66563439 TTATCACCTT
* * * * *
66563449 TATACACTTTCACATCCATCACGTTGGCCACTCGGCCCTATCATATATATACACTTTCACATTCA
1 TATACACATTCACATTCATCACATCGGCCACTAGGCCCTATCATATATATACACTTTCACATTCA
* *
66563514 TCACATTGGCCATTCGGCC-T-TGTCACATA
66 TCACATTGGCCATTAGGCCTTATCTCACATA
* * *
66563543 TATACACCTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATT
1 TATACACATTCACATTCATCACATCGGCCACTAGGCCCTAT--CATATATATACACTTTCACATT
*
66563608 CATCAC-TTCGGCCATTAGGCCTTATCTCATATA
64 CATCACATT-GGCCATTAGGCCTTATCTCACATA
66563641 TATACACATTCACATTCATC
1 TATACACATTCACATTCATC
66563661 GCGTAAAATC
Statistics
Matches: 102, Mismatches: 11, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
94 34 0.33
95 2 0.02
96 39 0.38
97 1 0.01
98 26 0.25
ACGTcount: A:0.28, C:0.31, G:0.08, T:0.33
Consensus pattern (96 bp):
TATACACATTCACATTCATCACATCGGCCACTAGGCCCTATCATATATATACACTTTCACATTCA
TCACATTGGCCATTAGGCCTTATCTCACATA
Found at i:66578449 original size:18 final size:17
Alignment explanation
Indices: 66578423--66578456 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
66578413 CATGATGCGG
66578423 GCTTATGTGGGCCCACAC
1 GCTTATGT-GGCCCACAC
*
66578441 GCTTGTGTGGCCCACA
1 GCTTATGTGGCCCACA
66578457 AGGCTAAATC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.15, C:0.32, G:0.29, T:0.24
Consensus pattern (17 bp):
GCTTATGTGGCCCACAC
Found at i:66585101 original size:29 final size:29
Alignment explanation
Indices: 66585068--66585171 Score: 163
Period size: 29 Copynumber: 3.6 Consensus size: 29
66585058 TTTATACCTA
* * *
66585068 TTTGGTTTCGGGCCATGTATATCGGATGC
1 TTTGGCTTCAGGCCATGCATATCGGATGC
66585097 TTTGGCTTCAGGCCATGCATATCGGATGC
1 TTTGGCTTCAGGCCATGCATATCGGATGC
* *
66585126 TTTGGCTTCAGGCCATGCATATCGAATGA
1 TTTGGCTTCAGGCCATGCATATCGGATGC
66585155 TTTGGCTTCAGGCCATG
1 TTTGGCTTCAGGCCATG
66585172 ATAATTGTTT
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 70 1.00
ACGTcount: A:0.17, C:0.21, G:0.28, T:0.34
Consensus pattern (29 bp):
TTTGGCTTCAGGCCATGCATATCGGATGC
Found at i:66596523 original size:40 final size:40
Alignment explanation
Indices: 66596419--66596635 Score: 341
Period size: 40 Copynumber: 5.5 Consensus size: 40
66596409 AAACCAAGTA
* * *
66596419 CCTTCGGGATTTA-ACCGGATATAGCT-ACTCGCTCAAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
* *
66596458 TCTTCGGGAC-TAGCCCGGTTATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
66596497 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
66596537 CCTTCGAGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
66596577 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
66596617 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
66596636 TTATCATCCG
Statistics
Matches: 166, Mismatches: 9, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
38 3 0.02
39 38 0.23
40 125 0.75
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:66605891 original size:27 final size:26
Alignment explanation
Indices: 66605819--66605934 Score: 142
Period size: 27 Copynumber: 4.3 Consensus size: 26
66605809 ATAGAGGAAG
66605819 TGTTCTGGTGGCTATGCCACAATTATC
1 TGTTCTGGTGGCTATGCCACAA-TATC
*
66605846 TGTTTCTGGTGGCTATGCCACAGATATT
1 TG-TTCTGGTGGCTATGCCACA-ATATC
* *
66605874 TGTTCTAGTGGCTCTGCCACAATATC
1 TGTTCTGGTGGCTATGCCACAATATC
* * *
66605900 TGTATCTGGTGACTCTGTCACAATATC
1 TGT-TCTGGTGGCTATGCCACAATATC
66605927 TGTTCTGG
1 TGTTCTGG
66605935 CAGCCATGCT
Statistics
Matches: 79, Mismatches: 7, Indels: 7
0.85 0.08 0.08
Matches are distributed among these distances:
26 12 0.15
27 42 0.53
28 24 0.30
29 1 0.01
ACGTcount: A:0.18, C:0.22, G:0.22, T:0.38
Consensus pattern (26 bp):
TGTTCTGGTGGCTATGCCACAATATC
Found at i:66608553 original size:25 final size:24
Alignment explanation
Indices: 66608470--66608579 Score: 82
Period size: 24 Copynumber: 4.5 Consensus size: 24
66608460 TGAAAGTCCA
* *
66608470 CACACATAGTG-CTCTTACTTATTCG
1 CACACATAGTGCCACTTA-TT-TTTG
*
66608495 CACACATAGTGCCACTT-TTTCT-
1 CACACATAGTGCCACTTATTTTTG
66608517 CACACATATAGTGCCACTTAGTTTTTG
1 CACAC--ATAGTGCCACTTA-TTTTTG
* * ***
66608544 CACACATAGTGCCGCATAACCTTG
1 CACACATAGTGCCACTTATTTTTG
66608568 CACACATAGTGC
1 CACACATAGTGC
66608580 TGAAATTTCT
Statistics
Matches: 70, Mismatches: 9, Indels: 13
0.76 0.10 0.14
Matches are distributed among these distances:
22 5 0.07
23 1 0.01
24 29 0.41
25 22 0.31
26 8 0.11
27 5 0.07
ACGTcount: A:0.26, C:0.29, G:0.14, T:0.31
Consensus pattern (24 bp):
CACACATAGTGCCACTTATTTTTG
Found at i:66610474 original size:2 final size:2
Alignment explanation
Indices: 66610467--66610495 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
66610457 ATGATTTGTG
66610467 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
66610496 AGTTAAAATG
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:66619984 original size:31 final size:31
Alignment explanation
Indices: 66619946--66620010 Score: 130
Period size: 31 Copynumber: 2.1 Consensus size: 31
66619936 GGCCATAAGC
66619946 AAGTCATTTCAATCTCAATCAAAGAGGTCCA
1 AAGTCATTTCAATCTCAATCAAAGAGGTCCA
66619977 AAGTCATTTCAATCTCAATCAAAGAGGTCCA
1 AAGTCATTTCAATCTCAATCAAAGAGGTCCA
66620008 AAG
1 AAG
66620011 AGACAACCCT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.40, C:0.22, G:0.14, T:0.25
Consensus pattern (31 bp):
AAGTCATTTCAATCTCAATCAAAGAGGTCCA
Found at i:66623406 original size:40 final size:39
Alignment explanation
Indices: 66623241--66623424 Score: 138
Period size: 40 Copynumber: 4.6 Consensus size: 39
66623231 AAATTGAATG
* * *
66623241 ATATCCGGGCTAAGCCCCGAAGACAATTATGCTGGAAAT--T
1 ATATCCGGGCTAAGACCCGAAGGC-ATT-TG-TGCAAATCGT
* * * * * *
66623281 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-T
* * * * *
66623321 ACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATC-GT
*
66623361 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
* * *
66623400 GATATCCGGGTTAAGTCCCGTAGGC
1 -ATATCCGGGCTAAGACCCGAAGGC
66623425 CTTGGTGCGG
Statistics
Matches: 113, Mismatches: 26, Indels: 10
0.76 0.17 0.07
Matches are distributed among these distances:
37 4 0.04
38 2 0.02
39 3 0.03
40 104 0.92
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.22
Consensus pattern (39 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
Found at i:66623449 original size:80 final size:81
Alignment explanation
Indices: 66623281--66623469 Score: 186
Period size: 80 Copynumber: 2.4 Consensus size: 81
66623271 GCTGGAAATT
* * * *
66623281 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCTACATCCGGGCTAAGACCCGAAGGCA
1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCA
*
66623346 TTCGTGCGAGTCATTC
66 TTCGTGCGAGTCATCC
* * * * * *
66623362 -TATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-TGATATCCGGGTTAAGTCCCGTAGGC
1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCT-ACATCCGGGCTAAGACCCGAAGGC
* * * *
66623425 CTTGGTGCGGGTTA-CC
65 ATTCGTGCGAGTCATCC
* * *
66623441 ATAACCGGGCTATGTCCCGAAGGCGATTG
1 ATAACCGGGCTAAGACCCGAAGGCAATTG
66623470 ATCGAGTAGC
Statistics
Matches: 86, Mismatches: 20, Indels: 5
0.77 0.18 0.05
Matches are distributed among these distances:
79 2 0.02
80 84 0.98
ACGTcount: A:0.23, C:0.24, G:0.30, T:0.23
Consensus pattern (81 bp):
ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCA
TTCGTGCGAGTCATCC
Found at i:66631506 original size:40 final size:39
Alignment explanation
Indices: 66631341--66631524 Score: 138
Period size: 40 Copynumber: 4.6 Consensus size: 39
66631331 AAATTGAATG
* * *
66631341 ATATCCGGGCTAAGCCCCGAAGACAATTATGCTGGAAAT--T
1 ATATCCGGGCTAAGACCCGAAGGC-ATT-TG-TGCAAATCGT
* * * * * *
66631381 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-T
* * * * *
66631421 ACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATC-GT
*
66631461 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
* * *
66631500 GATATCCGGGTTAAGTCCCGTAGGC
1 -ATATCCGGGCTAAGACCCGAAGGC
66631525 CTTGGTGCGG
Statistics
Matches: 113, Mismatches: 26, Indels: 10
0.76 0.17 0.07
Matches are distributed among these distances:
37 4 0.04
38 2 0.02
39 3 0.03
40 104 0.92
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.22
Consensus pattern (39 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
Done.