Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002341.1 Hibiscus syriacus cultivar Beakdansim tig00004779_pilon, whole genome shotgun sequence
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: 1266629
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 5
Found at i:905298 original size:52 final size:47
Alignment explanation
Indices: 905183--905301 Score: 130
Period size: 52 Copynumber: 2.3 Consensus size: 47
905173 TATAATATAT
905183 ATATTTTTAAAAACTAATTTTAAAACTATATAATATATATATTAAAA
1 ATATTTTTAAAAACTAATTTTAAAACTATATAATATATATATTAAAA
* * *
905230 ACTAATTTTCAAAAAAACTAATTTTCAAAATTATATAATATATATGTTTTTCAAAA
1 A-T-ATTTT--TAAAAACTAATTTT-AAAACTATATAATATATA---TATT-AAAA
905286 ATATTTTTAAAAACTA
1 ATATTTTTAAAAACTA
905302 TATATTATAT
Statistics
Matches: 59, Mismatches: 4, Indels: 13
0.78 0.05 0.17
Matches are distributed among these distances:
47 1 0.02
48 1 0.02
49 5 0.08
51 13 0.22
52 25 0.42
54 5 0.08
55 4 0.07
56 5 0.08
ACGTcount: A:0.50, C:0.07, G:0.01, T:0.42
Consensus pattern (47 bp):
ATATTTTTAAAAACTAATTTTAAAACTATATAATATATATATTAAAA
Found at i:905303 original size:129 final size:125
Alignment explanation
Indices: 905115--905372 Score: 324
Period size: 129 Copynumber: 2.0 Consensus size: 125
905105 TATATGTTTT
* *
905115 AAAAAATAATTTTAAAAACCATATCATATATATTTTTAAAAAATAATTTTCAAAACTATATAATA
1 AAAAAATAATTTTAAAAACCATATAATATATATTTTTAAAAAATAATTTTAAAAACTATATAATA
* *
905180 TATATAT-TTTTAAAAACTAATTTT-AAAACTATATAATATATATATT-AAAAACTAATTTTCA
66 TATATATATATTAAAAA--AATTTTCAAAACAATATAATATATATATTCAAAAA-T-ATTTTCA
* ** * *
905241 AAAAAACTAATTTTCAAAATTATATAATATATATGTTTTTCAAAAATATTTTTAAAAACTATATA
1 AAAAAA-TAATTTTAAAAACCATATAATATATA--TTTTTAAAAAATAATTTTAAAAACTATATA
* * *
905306 TTATATATATATATTAAAAAAGTTTTCAAAACAATATAATATATATTTTCAAAAATATTTTCA
63 ATATATATATATATTAAAAAAATTTTCAAAACAATATAATATATATATTCAAAAATATTTTCA
905369 AAAA
1 AAAA
905373 CTATATATTA
Statistics
Matches: 114, Mismatches: 12, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
126 6 0.05
127 22 0.19
128 16 0.14
129 57 0.50
130 13 0.11
ACGTcount: A:0.52, C:0.07, G:0.01, T:0.41
Consensus pattern (125 bp):
AAAAAATAATTTTAAAAACCATATAATATATATTTTTAAAAAATAATTTTAAAAACTATATAATA
TATATATATATTAAAAAAATTTTCAAAACAATATAATATATATATTCAAAAATATTTTCA
Found at i:905337 original size:90 final size:86
Alignment explanation
Indices: 905148--905337 Score: 222
Period size: 90 Copynumber: 2.1 Consensus size: 86
905138 TCATATATAT
* *
905148 TTTTAAAAAATAATTTTCAAAACTATATAATATATATATTTTTAAAAACTAATTTTAAAACTATA
1 TTTTCAAAACTAATTTTCAAAACTATATAATATATATATTTTTAAAAACTAATTTTAAAACTATA
905213 TAATATATATATTAAAAACTAA
66 TAATATATATATTAAAAAC-AA
* * *
905235 TTTTCAAAAAAACTAATTTTCAAAATTATATAATATATATGTTTTTCAAAAA-TATTTTTAAAAA
1 TTTTC---AAAACTAATTTTCAAAACTATATAATATATATATTTTT-AAAAACTAATTTT-AAAA
*
905299 CTATATATTATATATATATATTAAAAA-AG
61 C--TATA-TA-ATATATATATTAAAAACAA
905328 TTTTCAAAAC
1 TTTTCAAAAC
905338 AATATAATAT
Statistics
Matches: 88, Mismatches: 6, Indels: 15
0.81 0.06 0.14
Matches are distributed among these distances:
87 4 0.05
90 46 0.52
91 10 0.11
93 10 0.11
94 2 0.02
95 16 0.18
ACGTcount: A:0.51, C:0.06, G:0.01, T:0.42
Consensus pattern (86 bp):
TTTTCAAAACTAATTTTCAAAACTATATAATATATATATTTTTAAAAACTAATTTTAAAACTATA
TAATATATATATTAAAAACAA
Found at i:905365 original size:12 final size:12
Alignment explanation
Indices: 905348--905372 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
905338 AATATAATAT
905348 ATATTTTCAAAA
1 ATATTTTCAAAA
905360 ATATTTTCAAAA
1 ATATTTTCAAAA
905372 A
1 A
905373 CTATATATTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (12 bp):
ATATTTTCAAAA
Found at i:905373 original size:36 final size:36
Alignment explanation
Indices: 905262--905400 Score: 133
Period size: 36 Copynumber: 3.8 Consensus size: 36
905252 TTTCAAAATT
*
905262 ATATAATATATATGTTTTTCAAAAATATTTTTAAAAACTA
1 ATATAATATATA---TTTTCAAAAATATTTTCAAAAAC-A
*
905302 TATATTATATATATATATT-AAAAA-AGTTTTC-AAAACA
1 -ATA-TA-ATATATATTTTCAAAAATA-TTTTCAAAAACA
*
905339 ATATAATATATATTTTCAAAAATATTTTCAAAAACT
1 ATATAATATATATTTTCAAAAATATTTTCAAAAACA
* *
905375 ATATATTATTTATTTTC-AAAATATTT
1 ATATAATATATATTTTCAAAAATATTT
905401 AAAAACCTCA
Statistics
Matches: 86, Mismatches: 6, Indels: 18
0.78 0.05 0.16
Matches are distributed among these distances:
34 10 0.12
35 21 0.24
36 24 0.28
37 1 0.01
38 6 0.07
39 9 0.10
40 3 0.03
41 3 0.03
42 2 0.02
43 7 0.08
ACGTcount: A:0.47, C:0.06, G:0.01, T:0.45
Consensus pattern (36 bp):
ATATAATATATATTTTCAAAAATATTTTCAAAAACA
Found at i:905426 original size:36 final size:34
Alignment explanation
Indices: 905329--905439 Score: 118
Period size: 36 Copynumber: 3.1 Consensus size: 34
905319 TTAAAAAAGT
* *
905329 TTTC-AAAACAATATAATATATATTTTCAAAAATA
1 TTTCAAAAACTATATATTATATATTTTC-AAAATA
*
905363 TTTTCAAAAACTATATATTATTTATTTTCAAAATA
1 -TTTCAAAAACTATATATTATATATTTTCAAAATA
*
905398 TTT-AAAAACCTCATATATTATATAATTTTTAAAATGA
1 TTTCAAAAA-CT-ATATATTATAT-ATTTTCAAAAT-A
905435 TTTCA
1 TTTCA
905440 TATTATAATA
Statistics
Matches: 65, Mismatches: 5, Indels: 9
0.82 0.06 0.11
Matches are distributed among these distances:
33 5 0.08
34 5 0.08
35 20 0.31
36 30 0.46
37 4 0.06
38 1 0.02
ACGTcount: A:0.46, C:0.09, G:0.01, T:0.44
Consensus pattern (34 bp):
TTTCAAAAACTATATATTATATATTTTCAAAATA
Found at i:907373 original size:2 final size:2
Alignment explanation
Indices: 907366--907399 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
907356 ATTCCTTCGA
907366 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
907400 AGATGGTGAC
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:915247 original size:25 final size:24
Alignment explanation
Indices: 915201--915248 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
915191 GACTCAAACT
*
915201 CGAAATAAAAATTAAGGCTCGACA
1 CGAAATAAAAATTAAGGATCGACA
915225 CGAAATAAACAATTCAA-GATCGAC
1 CGAAATAAA-AATT-AAGGATCGAC
915249 TCGAGCACAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 9 0.43
25 10 0.48
26 2 0.10
ACGTcount: A:0.50, C:0.19, G:0.15, T:0.17
Consensus pattern (24 bp):
CGAAATAAAAATTAAGGATCGACA
Found at i:915486 original size:30 final size:30
Alignment explanation
Indices: 915452--915512 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
915442 AATTCCGGCT
915452 CGAGTTGAGTCTATTCAATTTAAGAATTAA
1 CGAGTTGAGTCTATTCAATTTAAGAATTAA
*
915482 CGAGTTGAGTCTATTCGATTTAAGAATTAA
1 CGAGTTGAGTCTATTCAATTTAAGAATTAA
915512 C
1 C
915513 CGAACTTTGA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.34, C:0.11, G:0.18, T:0.36
Consensus pattern (30 bp):
CGAGTTGAGTCTATTCAATTTAAGAATTAA
Found at i:915665 original size:14 final size:14
Alignment explanation
Indices: 915646--915672 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
915636 TTTTCATTTC
915646 ATTGGGTCGTCTTA
1 ATTGGGTCGTCTTA
915660 ATTGGGTCGTCTT
1 ATTGGGTCGTCTT
915673 GAACATATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.11, C:0.15, G:0.30, T:0.44
Consensus pattern (14 bp):
ATTGGGTCGTCTTA
Found at i:921917 original size:12 final size:13
Alignment explanation
Indices: 921881--921924 Score: 63
Period size: 13 Copynumber: 3.5 Consensus size: 13
921871 TAATACTCGC
921881 CCCGATTACCCGG
1 CCCGATTACCCGG
921894 CCCGATTACCCGG
1 CCCGATTACCCGG
* *
921907 CCCTA-TACCCGA
1 CCCGATTACCCGG
921919 CCCGAT
1 CCCGAT
921925 AAATATTAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
12 10 0.37
13 17 0.63
ACGTcount: A:0.18, C:0.48, G:0.18, T:0.16
Consensus pattern (13 bp):
CCCGATTACCCGG
Found at i:924138 original size:50 final size:50
Alignment explanation
Indices: 924079--924180 Score: 204
Period size: 50 Copynumber: 2.0 Consensus size: 50
924069 CTCGATAGAT
924079 CTGCAGGTGAGTTGTAATTAGAGAAGGACATTAGAGTGATGGGTTTCGAC
1 CTGCAGGTGAGTTGTAATTAGAGAAGGACATTAGAGTGATGGGTTTCGAC
924129 CTGCAGGTGAGTTGTAATTAGAGAAGGACATTAGAGTGATGGGTTTCGAC
1 CTGCAGGTGAGTTGTAATTAGAGAAGGACATTAGAGTGATGGGTTTCGAC
924179 CT
1 CT
924181 AATCTTATAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 52 1.00
ACGTcount: A:0.27, C:0.11, G:0.33, T:0.28
Consensus pattern (50 bp):
CTGCAGGTGAGTTGTAATTAGAGAAGGACATTAGAGTGATGGGTTTCGAC
Found at i:924340 original size:22 final size:20
Alignment explanation
Indices: 924311--924353 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
924301 CTTCTATTTA
924311 TATATTTTTTCAATTAAGTC
1 TATATTTTTTCAATTAAGTC
924331 TATATTTTTTCAATTAAGTC
1 TATATTTTTTCAATTAAGTC
924351 TAT
1 TAT
924354 TTTATCTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.09, G:0.05, T:0.56
Consensus pattern (20 bp):
TATATTTTTTCAATTAAGTC
Found at i:925971 original size:19 final size:19
Alignment explanation
Indices: 925947--926003 Score: 105
Period size: 19 Copynumber: 3.0 Consensus size: 19
925937 AAAAACCCAA
*
925947 ATCTCCTTTCATTTTTCAT
1 ATCTCCGTTCATTTTTCAT
925966 ATCTCCGTTCATTTTTCAT
1 ATCTCCGTTCATTTTTCAT
925985 ATCTCCGTTCATTTTTCAT
1 ATCTCCGTTCATTTTTCAT
926004 GTCCGTGGCA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 37 1.00
ACGTcount: A:0.16, C:0.26, G:0.04, T:0.54
Consensus pattern (19 bp):
ATCTCCGTTCATTTTTCAT
Found at i:930131 original size:82 final size:82
Alignment explanation
Indices: 930026--930200 Score: 287
Period size: 82 Copynumber: 2.1 Consensus size: 82
930016 TATCTTAAAT
* * *
930026 TAATTCTTAATTTCTTTAATATTTTAAATTCATCTCTAAATTGCTATCTTTATTTTATATTAGTC
1 TAATT-TT-ATTTCTTGAATATTTTAAATTAATCTCTAAATTACTATCTTTATTTTATATTAGTC
930091 CTCAAAATTGTAGATATTC
64 CTCAAAATTGTAGATATTC
930110 TAATTTTATTTCTTGAATATTTTAAATTAATCTCTAAATTACTATCTTTATTTTATATTAGTCCT
1 TAATTTTATTTCTTGAATATTTTAAATTAATCTCTAAATTACTATCTTTATTTTATATTAGTCCT
*
930175 CAAAATTTTAGATATTC
66 CAAAATTGTAGATATTC
*
930192 TGATTTTAT
1 TAATTTTAT
930201 CTCCAGTTTT
Statistics
Matches: 86, Mismatches: 5, Indels: 2
0.92 0.05 0.02
Matches are distributed among these distances:
82 79 0.92
83 2 0.02
84 5 0.06
ACGTcount: A:0.31, C:0.11, G:0.05, T:0.53
Consensus pattern (82 bp):
TAATTTTATTTCTTGAATATTTTAAATTAATCTCTAAATTACTATCTTTATTTTATATTAGTCCT
CAAAATTGTAGATATTC
Found at i:930277 original size:13 final size:13
Alignment explanation
Indices: 930259--930288 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
930249 TTTAAGGATT
930259 AATTTAAAATAAA
1 AATTTAAAATAAA
*
930272 AATTTAAAATAAG
1 AATTTAAAATAAA
930285 AATT
1 AATT
930289 ATATTTTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.33
Consensus pattern (13 bp):
AATTTAAAATAAA
Found at i:930416 original size:20 final size:17
Alignment explanation
Indices: 930378--930413 Score: 54
Period size: 19 Copynumber: 2.0 Consensus size: 17
930368 TTTAAAACTT
930378 TAAAAATAAATTTAAAA
1 TAAAAATAAATTTAAAA
930395 TAAAAATTATAATTTAAAA
1 TAAAAA-TA-AATTTAAAA
930414 ATATGTGATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.35
18 2 0.12
19 9 0.53
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
TAAAAATAAATTTAAAA
Found at i:933635 original size:245 final size:247
Alignment explanation
Indices: 933169--933777 Score: 723
Period size: 245 Copynumber: 2.5 Consensus size: 247
933159 AATCTGTTTT
* * *
933169 GTGAAGTTGAGCTTTAGAATTGGATATCCTTCGTCATGAAGTTGAAATCCAATGTAAGTTGTGTT
1 GTGAAGTTGAGCCTT-GAATTGGATATCATTCGTCATGAAGTTGAAATCCAA-GT-AGTTGTATT
* * *
933234 TTTTCGATGCCAATATCCTTCGCCGTGAA-TTGAAATTGACTCTGAAACTGGAAAGTTTATTGAC
63 GTTTCGAGGCCAATATCCTTCGCCGTGAAGTTGAAATTGACTTTGAAACTGGAAAGTTTATTGAC
* * * *
933298 TACTCATTCTTTAAGTTGAATATCCTTCGTCGTGAAGTTGAAATCCAATCTAGAGATGGGTGCTG
128 TACTCATTCTCTAAGTTGAATATCCTTCGCCGTGAAGTTGAAATCCAATATAGAGATGGATGCTG
* * * *
933363 TTGTGTGCACGATTCCCTTCGTCGTGAAGTTGAAACCGCGGGTGGCCCCTAATTC
193 CTGTGTGCACGATTCCCTTCATCGTGAAGTTGAAACCGCGGATGGCCCCTAAGTC
* * ** *
933418 GTGAAGTTGAGCCTTGACTTGAATATCATTCGTTGTGAAGTTGAAATCCAA-T-CTTGTATTGTT
1 GTGAAGTTGAGCCTTGAATTGGATATCATTCGTCATGAAGTTGAAATCCAAGTAGTTGTATTGTT
** * * *
933481 T-GAGGCCAATATCCTTCGATGTGAAGTTGAAGTTGACTTTGAAACTGGATAGTTTGTTGAAAGA
66 TCGAGGCCAATATCCTTCGCCGTGAAGTTGAAATTGACTTTGAAACTGGAAAGTTTATT----GA
* * * *
933545 CT-CTCCTTCTCTGAGTTGGATATCC-TCTGCCGTGAAGTT-AAATCCAATATGGAGATGGATGC
127 CTACTCATTCTCTAAGTTGAATATCCTTC-GCCGTGAAGTTGAAATCCAATATAGAGATGGATGC
* * **
933607 TGCT-TGTGCATGATTCCCTTCATCGTGAAGTTGAAACCGTGGATGGCCCCTCCGTC
191 TGCTGTGTGCACGATTCCCTTCATCGTGAAGTTGAAACCGCGGATGGCCCCTAAGTC
* * *
933663 GTGAAGTTGAGCCTTGAATTGGATATCATTCATCACGAAGTTAAAATCCAAGTAAGTTGTATTGT
1 GTGAAGTTGAGCCTTGAATTGGATATCATTCGTCATGAAGTTGAAATCCAAGT-AGTTGTATTGT
* * *
933728 TTCGAGTCCAATATCCTCCGCCGTGAAGTTGAAATTGGCTCTT-AAACTGG
65 TTCGAGGCCAATATCCTTCGCCGTGAAGTTGAAATTGACT-TTGAAACTGG
933778 GAAACCCCTT
Statistics
Matches: 303, Mismatches: 46, Indels: 22
0.82 0.12 0.06
Matches are distributed among these distances:
243 21 0.07
244 37 0.12
245 89 0.29
246 27 0.09
247 29 0.10
248 46 0.15
249 52 0.17
250 2 0.01
ACGTcount: A:0.25, C:0.18, G:0.23, T:0.34
Consensus pattern (247 bp):
GTGAAGTTGAGCCTTGAATTGGATATCATTCGTCATGAAGTTGAAATCCAAGTAGTTGTATTGTT
TCGAGGCCAATATCCTTCGCCGTGAAGTTGAAATTGACTTTGAAACTGGAAAGTTTATTGACTAC
TCATTCTCTAAGTTGAATATCCTTCGCCGTGAAGTTGAAATCCAATATAGAGATGGATGCTGCTG
TGTGCACGATTCCCTTCATCGTGAAGTTGAAACCGCGGATGGCCCCTAAGTC
Found at i:934228 original size:104 final size:106
Alignment explanation
Indices: 933970--934272 Score: 392
Period size: 108 Copynumber: 2.9 Consensus size: 106
933960 TATTGTTTCA
* *
933970 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTAAATGAAACTGAAAAGTTTTTTGTTGA
1 AGTCCAATATCCTTCGC-GTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGTTGA
*
934035 CA-TACAGTCGCCCCTTCG-GTGAAGTTGAGCTTGTGTTGTCTTG
65 CAGT-CAGTCG-CCCTTCGTGTG-AGTTGAGCTTGTGTTGTCTCG
* *
934078 AGTCTAATATCCTTCGCCGTGAAGTTGAAATTGACTCTGAACGAAACTGAAAAGTTGTTTGTTGA
1 AGTCCAATATCCTTCG-CGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGTTGA
934143 CAGTCAGTCGCCCTTCGCTGTGAGTT-A-CTTGTGTTGTCTCG
65 CAGTCAGTCGCCCTTCG-TGTGAGTTGAGCTTGTGTTGTCTCG
* * *
934184 AGTCCATTATCCTTCG-ATGAAGTTGAAATTGACTCTGAATGAAACT-AAAAATTGTTT-TTGAC
1 AGTCCAATATCCTTCGCGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGTTGAC
934246 AGTC-G-C-CCCTTCGTTGTGAAGTTGAGC
66 AGTCAGTCGCCCTTCG-TGTG-AGTTGAGC
934273 AACCACCATC
Statistics
Matches: 177, Mismatches: 11, Indels: 20
0.85 0.05 0.10
Matches are distributed among these distances:
99 11 0.06
100 5 0.03
101 2 0.01
102 10 0.06
103 10 0.06
104 28 0.16
106 27 0.15
107 8 0.05
108 71 0.40
109 5 0.03
ACGTcount: A:0.25, C:0.18, G:0.22, T:0.34
Consensus pattern (106 bp):
AGTCCAATATCCTTCGCGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGTTGAC
AGTCAGTCGCCCTTCGTGTGAGTTGAGCTTGTGTTGTCTCG
Found at i:939540 original size:36 final size:36
Alignment explanation
Indices: 939498--939573 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
939488 TTATAGCTAA
*
939498 AAAAATCGTCTTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
939534 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
939570 AAAA
1 AAAA
939574 TCCCGAAAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (36 bp):
AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
Found at i:940128 original size:23 final size:23
Alignment explanation
Indices: 940102--940165 Score: 85
Period size: 23 Copynumber: 2.8 Consensus size: 23
940092 CATCTCATAT
940102 AATTACACCGAAGTGCCACGTAG
1 AATTACACCGAAGTGCCACGTAG
*
940125 AATTACACC-AGAGTGCCGCGTAG
1 AATTACACCGA-AGTGCCACGTAG
* *
940148 AATTGCACCGTAGTGCCA
1 AATTACACCGAAGTGCCA
940166 TATAATAATG
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
22 1 0.03
23 34 0.97
ACGTcount: A:0.31, C:0.27, G:0.23, T:0.19
Consensus pattern (23 bp):
AATTACACCGAAGTGCCACGTAG
Found at i:940962 original size:64 final size:62
Alignment explanation
Indices: 940848--940988 Score: 169
Period size: 64 Copynumber: 2.2 Consensus size: 62
940838 TTAATGGAGG
* * *
940848 TATGCATCGATGCATAAATCTTATTCGATGTTTGTATTTAATGGGGATGCATCGATGCACTCC
1 TATGCATCGATGCATAAATCCTATTCGATGTTTCTATTTAAT-GGAATGCATCGATGCACTCC
* * *
940911 TTATGCATCGATGCATAAATCCTATTCGATGTTTTCTTTTTAAAT-TAATGCATCGATGCACTGC
1 -TATGCATCGATGCATAAATCCTATTCGATG-TTTCTATTT-AATGGAATGCATCGATGCACTCC
940975 -AGTGCATCGATGCA
1 TA-TGCATCGATGCA
940989 CCTTAAACAA
Statistics
Matches: 68, Mismatches: 6, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
62 1 0.01
63 12 0.18
64 45 0.66
65 7 0.10
66 3 0.04
ACGTcount: A:0.26, C:0.18, G:0.18, T:0.37
Consensus pattern (62 bp):
TATGCATCGATGCATAAATCCTATTCGATGTTTCTATTTAATGGAATGCATCGATGCACTCC
Found at i:947892 original size:64 final size:60
Alignment explanation
Indices: 947763--947901 Score: 163
Period size: 64 Copynumber: 2.2 Consensus size: 60
947753 TTAAGGAGGT
* *
947763 ATGCATCGATGCACACCATGCATCGATGCATAAATCTATTCGATGTTTTTATTTAATGGGG
1 ATGCATCGATGCACACCATGCATCGATACATAAATCTATTCGATGTTTTTATTTAAT-GGA
* * * *
947824 ATGCATTGATGCACTCCTTATGCATCGATACATAAATCCTATTCGATGTTTTCTTTTTAAAT-TA
1 ATGCATCGATGCACACC--ATGCATCGATACATAAAT-CTATTCGATGTTTT-TATTT-AATGGA
947888 ATGCATCGATGCAC
1 ATGCATCGATGCAC
947902 CTTAAACAAT
Statistics
Matches: 66, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
61 15 0.23
63 17 0.26
64 27 0.41
65 4 0.06
66 3 0.05
ACGTcount: A:0.28, C:0.19, G:0.16, T:0.37
Consensus pattern (60 bp):
ATGCATCGATGCACACCATGCATCGATACATAAATCTATTCGATGTTTTTATTTAATGGA
Found at i:951079 original size:18 final size:18
Alignment explanation
Indices: 951038--951079 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
951028 TAAGTTAATT
*
951038 AAAAAATGTTTTACTTTA
1 AAAAAATGTTTTACTTCA
*
951056 AGAAAATGTTTTTA-TTCA
1 AAAAAATG-TTTTACTTCA
951074 AAAAAA
1 AAAAAA
951080 AAAAAATATT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
18 15 0.75
19 5 0.25
ACGTcount: A:0.50, C:0.05, G:0.07, T:0.38
Consensus pattern (18 bp):
AAAAAATGTTTTACTTCA
Found at i:957202 original size:3 final size:3
Alignment explanation
Indices: 957196--957236 Score: 73
Period size: 3 Copynumber: 13.3 Consensus size: 3
957186 TTGTTGTTGC
957196 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT CTCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT -TCT T
957237 ACAGCTCGGT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 34 0.92
4 3 0.08
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:961133 original size:18 final size:18
Alignment explanation
Indices: 961110--961159 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 18
961100 AACCCATTCT
*
961110 GGAGTAATCACTAGGTCG
1 GGAGTAATCACTAGGCCG
* *
961128 GGAGTAGTCGCTAGGCCG
1 GGAGTAATCACTAGGCCG
*
961146 GGAGAAATCACTAG
1 GGAGTAATCACTAG
961160 ACCTATTACC
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.28, C:0.18, G:0.36, T:0.18
Consensus pattern (18 bp):
GGAGTAATCACTAGGCCG
Found at i:971132 original size:34 final size:34
Alignment explanation
Indices: 971088--971156 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
971078 GATTTGTAAT
971088 TAGTTAGCTGTATTTTGGTTTCAAATATTAATCA
1 TAGTTAGCTGTATTTTGGTTTCAAATATTAATCA
*
971122 TAGTTGGCTGTATTTTGGTTTCAAATATTAATCA
1 TAGTTAGCTGTATTTTGGTTTCAAATATTAATCA
971156 T
1 T
971157 GTGGCATATG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.28, C:0.09, G:0.16, T:0.48
Consensus pattern (34 bp):
TAGTTAGCTGTATTTTGGTTTCAAATATTAATCA
Found at i:971679 original size:305 final size:305
Alignment explanation
Indices: 971122--971688 Score: 1107
Period size: 305 Copynumber: 1.9 Consensus size: 305
971112 ATATTAATCA
*
971122 TAGTTGGCTGTATTTTGGTTTCAAATATTAATCATGTGGCATATGTAAATAAAGCATATTTGTTT
1 TAGTTAGCTGTATTTTGGTTTCAAATATTAATCATGTGGCATATGTAAATAAAGCATATTTGTTT
*
971187 ATCTTCGTTGAAGCTTATTGGCATATGTAACTGTAAGATGATAGGTTTTGTTCTCAATTTCTATT
66 ATCTTCGTTGAAACTTATTGGCATATGTAACTGTAAGATGATAGGTTTTGTTCTCAATTTCTATT
971252 AATCTAGAAATTATAAAAAAGGGGCTTTTGATTCTTTGGCATTTTCTTCCTCTCGTCCCCCCAAT
131 AATCTAGAAATTATAAAAAAGGGGCTTTTGATTCTTTGGCATTTTCTTCCTCTCGTCCCCCCAAT
971317 TCCCATTCACTGAATTTCCATATATAATTTCTGTATATCATTTGTAAACTTATTTTTTTGTTTAT
196 TCCCATTCACTGAATTTCCATATATAATTTCTGTATATCATTTGTAAACTTATTTTTTTGTTTAT
971382 CTTTATAAAACCTGAATGTCTAGGTTTTTAAATTTGATTTGTAAT
261 CTTTATAAAACCTGAATGTCTAGGTTTTTAAATTTGATTTGTAAT
971427 TAGTTAGCTGTATTTTGGTTTCAAATATTAATCATGTGGCATATGTAAATAAAGCATATTTGTTT
1 TAGTTAGCTGTATTTTGGTTTCAAATATTAATCATGTGGCATATGTAAATAAAGCATATTTGTTT
*
971492 ATCTTCTTTGAAACTTATTGGCATATGTAACTGTAAGATGATAGGTTTTGTTCTCAATTTCTATT
66 ATCTTCGTTGAAACTTATTGGCATATGTAACTGTAAGATGATAGGTTTTGTTCTCAATTTCTATT
971557 AATCTAGAAATTATAAAAAAGGGGCTTTTGATTCTTTGGCATTTTCTTCCTCTCGTCCCCCCAAT
131 AATCTAGAAATTATAAAAAAGGGGCTTTTGATTCTTTGGCATTTTCTTCCTCTCGTCCCCCCAAT
971622 TCCCATTCACTGAATTTCCATATATAATTTCTGTATATCATTTGTAAACTTATTTTTTTGTTTAT
196 TCCCATTCACTGAATTTCCATATATAATTTCTGTATATCATTTGTAAACTTATTTTTTTGTTTAT
971687 CT
261 CT
971689 CAGCCGTCCT
Statistics
Matches: 259, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
305 259 1.00
ACGTcount: A:0.27, C:0.14, G:0.14, T:0.45
Consensus pattern (305 bp):
TAGTTAGCTGTATTTTGGTTTCAAATATTAATCATGTGGCATATGTAAATAAAGCATATTTGTTT
ATCTTCGTTGAAACTTATTGGCATATGTAACTGTAAGATGATAGGTTTTGTTCTCAATTTCTATT
AATCTAGAAATTATAAAAAAGGGGCTTTTGATTCTTTGGCATTTTCTTCCTCTCGTCCCCCCAAT
TCCCATTCACTGAATTTCCATATATAATTTCTGTATATCATTTGTAAACTTATTTTTTTGTTTAT
CTTTATAAAACCTGAATGTCTAGGTTTTTAAATTTGATTTGTAAT
Found at i:979463 original size:22 final size:21
Alignment explanation
Indices: 979428--979478 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 21
979418 ATTAATATAA
*
979428 AATAATA-TTATAATTATTAT
1 AATAATATTTATAATAATTAT
**
979448 TTTAATATTTATTAATAATTAT
1 AATAATATTTA-TAATAATTAT
979470 AATAATATT
1 AATAATATT
979479 CTTTTCTTTA
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
20 5 0.21
21 3 0.12
22 16 0.67
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
AATAATATTTATAATAATTAT
Found at i:981526 original size:17 final size:17
Alignment explanation
Indices: 981499--981553 Score: 83
Period size: 17 Copynumber: 3.2 Consensus size: 17
981489 AATCCTCAAT
981499 CCGAGATCCGATCTAAC
1 CCGAGATCCGATCTAAC
* * *
981516 CTGATATCCGATTTAAC
1 CCGAGATCCGATCTAAC
981533 CCGAGATCCGATCTAAC
1 CCGAGATCCGATCTAAC
981550 CCGA
1 CCGA
981554 CCAAAACAAG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 32 1.00
ACGTcount: A:0.29, C:0.33, G:0.16, T:0.22
Consensus pattern (17 bp):
CCGAGATCCGATCTAAC
Found at i:996415 original size:20 final size:21
Alignment explanation
Indices: 996390--996439 Score: 57
Period size: 24 Copynumber: 2.3 Consensus size: 21
996380 TTATATTTGA
*
996390 TTTTAAT-TTTAATATTAGTT
1 TTTTAATATTAAATATTAGTT
996410 TTTTAAATAAATTAAATATTAGTT
1 TTTT-AAT--ATTAAATATTAGTT
996434 TTTTAA
1 TTTTAA
996440 ATAATTTGAT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 4 0.16
21 3 0.12
23 2 0.08
24 16 0.64
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (21 bp):
TTTTAATATTAAATATTAGTT
Found at i:1003429 original size:18 final size:20
Alignment explanation
Indices: 1003408--1003453 Score: 60
Period size: 18 Copynumber: 2.4 Consensus size: 20
1003398 ATTTAAATAA
1003408 TAAAATTAAT-TTTTAA-GT
1 TAAAATTAATATTTTAAGGT
*
1003426 TAAAAATAATATTTTAAGGT
1 TAAAATTAATATTTTAAGGT
1003446 TATAAATT
1 TA-AAATT
1003454 TACTATTGTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 9 0.39
19 6 0.26
20 4 0.17
21 4 0.17
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.46
Consensus pattern (20 bp):
TAAAATTAATATTTTAAGGT
Found at i:1004267 original size:49 final size:49
Alignment explanation
Indices: 1004213--1004311 Score: 146
Period size: 49 Copynumber: 2.0 Consensus size: 49
1004203 TATTGATGTT
* * **
1004213 AAAAACTTAAAGGAATTGTTGCGTGACATTTTTAT-GAGTAAATTACATC
1 AAAAACCTAAAGGAACTACTGCGTGACATTTTTATAG-GTAAATTACATC
1004262 AAAAACCTAAAGGAACTACTGCGTGACATTTTTATAGGTAAATTACATC
1 AAAAACCTAAAGGAACTACTGCGTGACATTTTTATAGGTAAATTACATC
1004311 A
1 A
1004312 TTTAACTATC
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
49 44 0.98
50 1 0.02
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.31
Consensus pattern (49 bp):
AAAAACCTAAAGGAACTACTGCGTGACATTTTTATAGGTAAATTACATC
Found at i:1006400 original size:37 final size:37
Alignment explanation
Indices: 1006359--1006430 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
1006349 ATGACCTATG
* *
1006359 TAACTGTTCATATGTTCC-AAAGAACATAGGCAAACTA
1 TAACTGTCCATATGTCCCAAAAG-ACATAGGCAAACTA
*
1006396 TAACTGTCCATATGTCCCAAAAGACATAGGTAAAC
1 TAACTGTCCATATGTCCCAAAAGACATAGGCAAAC
1006431 CCTCGACTCT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
37 27 0.87
38 4 0.13
ACGTcount: A:0.40, C:0.21, G:0.14, T:0.25
Consensus pattern (37 bp):
TAACTGTCCATATGTCCCAAAAGACATAGGCAAACTA
Found at i:1006777 original size:2 final size:2
Alignment explanation
Indices: 1006770--1006796 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1006760 TTTATATCAT
1006770 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1006797 CATCTATGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1012855 original size:7 final size:7
Alignment explanation
Indices: 1012809--1012855 Score: 53
Period size: 7 Copynumber: 6.9 Consensus size: 7
1012799 TATTTATATA
1012809 AAATTTT
1 AAATTTT
1012816 -AATTTT
1 AAATTTT
1012822 -AATTTT
1 AAATTTT
*
1012828 AAATCTT
1 AAATTTT
1012835 AAATTTT
1 AAATTTT
1012842 AATATTTT
1 AA-ATTTT
*
1012850 GAATTT
1 AAATTT
1012856 GTACAATCTC
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
6 12 0.34
7 17 0.49
8 6 0.17
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.57
Consensus pattern (7 bp):
AAATTTT
Found at i:1013048 original size:7 final size:7
Alignment explanation
Indices: 1013036--1013075 Score: 62
Period size: 7 Copynumber: 5.7 Consensus size: 7
1013026 TTTACAAAAC
1013036 TTTATAT
1 TTTATAT
1013043 TTTATAT
1 TTTATAT
1013050 TTTATAT
1 TTTATAT
1013057 TTTATAT
1 TTTATAT
* *
1013064 TCTAAAT
1 TTTATAT
1013071 TTTAT
1 TTTAT
1013076 TTTATATAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.68
Consensus pattern (7 bp):
TTTATAT
Found at i:1013062 original size:21 final size:20
Alignment explanation
Indices: 1013036--1013082 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 20
1013026 TTTACAAAAC
* *
1013036 TTTATATTTTATATTTTATAT
1 TTTATATTCTAAATTTTAT-T
1013057 TTTATATTCTAAATTTTA-T
1 TTTATATTCTAAATTTTATT
1013076 TTTATAT
1 TTTATAT
1013083 AATGGTTCAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 8 0.33
21 16 0.67
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (20 bp):
TTTATATTCTAAATTTTATT
Found at i:1013220 original size:16 final size:16
Alignment explanation
Indices: 1013199--1013232 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
1013189 CGAACCAAAC
1013199 TTGGTCGCACACCTGA
1 TTGGTCGCACACCTGA
1013215 TTGGTCGCACACCTGA
1 TTGGTCGCACACCTGA
1013231 TT
1 TT
1013233 TTAATTGTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.18, C:0.29, G:0.24, T:0.29
Consensus pattern (16 bp):
TTGGTCGCACACCTGA
Found at i:1013586 original size:2 final size:2
Alignment explanation
Indices: 1013577--1013618 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
1013567 TAAAAAACAA
1013577 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1013618 A
1 A
1013619 ATAAAGCAAG
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1016216 original size:43 final size:43
Alignment explanation
Indices: 1016166--1016251 Score: 145
Period size: 43 Copynumber: 2.0 Consensus size: 43
1016156 CTTACGGAAG
**
1016166 CTGCTCTCAACTGGTGTTGGAGTAGTCTACTATCTTACCTCCC
1 CTGCTCTCAACTGGTGTTGGAGTAACCTACTATCTTACCTCCC
*
1016209 CTGCTCTCAACTGGTGTTGGGGTAACCTACTATCTTACCTCCC
1 CTGCTCTCAACTGGTGTTGGAGTAACCTACTATCTTACCTCCC
1016252 ACTTACTCCA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.16, C:0.31, G:0.19, T:0.34
Consensus pattern (43 bp):
CTGCTCTCAACTGGTGTTGGAGTAACCTACTATCTTACCTCCC
Found at i:1020823 original size:59 final size:59
Alignment explanation
Indices: 1020728--1020902 Score: 174
Period size: 60 Copynumber: 2.9 Consensus size: 59
1020718 GTATATACAT
* * * * *
1020728 ATAGCTTG-TGATGAAACTGTAATATCCAAAAAGTTTGGGGACCAA-TTAAAATGAAGGTG
1 ATAGCTTGAGGATGAAATTGAAATATTC-AAAAGTTTGGGGACCAATTTAAAATGAA-ATG
** * *
1020787 ATAGCTTGAGGATGAAATTGAAATATTCAAAAGTTTGAAGACTAATTTAAAATGATAATT
1 ATAGCTTGAGGATGAAATTGAAATATTCAAAAGTTTGGGGACCAATTTAAAATGA-AATG
* * * * * *
1020847 ATAGTTTAAGGATGAAATTAAAATATTTAAAAATTTAGGGACCAATTTAAAATGAA
1 ATAGCTTGAGGATGAAATTGAAATATTCAAAAGTTTGGGGACCAATTTAAAATGAA
1020903 TATCATACTT
Statistics
Matches: 95, Mismatches: 18, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
59 23 0.24
60 71 0.75
61 1 0.01
ACGTcount: A:0.45, C:0.06, G:0.18, T:0.31
Consensus pattern (59 bp):
ATAGCTTGAGGATGAAATTGAAATATTCAAAAGTTTGGGGACCAATTTAAAATGAAATG
Found at i:1022006 original size:16 final size:15
Alignment explanation
Indices: 1021987--1022025 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
1021977 TTTGATATTC
1021987 TAATAATATAATATA
1 TAATAATATAATATA
1022002 T--TAATCATAATATA
1 TAATAAT-ATAATATA
1022016 TAATAATATA
1 TAATAATATA
1022026 TCTCTTTAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 6
0.78 0.00 0.22
Matches are distributed among these distances:
13 4 0.19
14 9 0.43
15 4 0.19
16 4 0.19
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (15 bp):
TAATAATATAATATA
Found at i:1022290 original size:15 final size:15
Alignment explanation
Indices: 1022256--1022295 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
1022246 CCCCTCTAAG
*
1022256 CTTCCTCTTC-CATT
1 CTTCTTCTTCTCATT
1022270 -TTCTTCTTCTCATT
1 CTTCTTCTTCTCATT
1022284 CTTCTTCTTCTC
1 CTTCTTCTTCTC
1022296 TCTCTCTCTC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
13 8 0.35
14 4 0.17
15 11 0.48
ACGTcount: A:0.05, C:0.38, G:0.00, T:0.57
Consensus pattern (15 bp):
CTTCTTCTTCTCATT
Found at i:1024726 original size:26 final size:26
Alignment explanation
Indices: 1024697--1024748 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
1024687 TTTTTTCCAT
1024697 GCACGCCATTCTGATGCCATGCTAGA
1 GCACGCCATTCTGATGCCATGCTAGA
1024723 GCACGCCATTCTGATGCCATGCTAGA
1 GCACGCCATTCTGATGCCATGCTAGA
1024749 CTGTTGGCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.23, C:0.31, G:0.23, T:0.23
Consensus pattern (26 bp):
GCACGCCATTCTGATGCCATGCTAGA
Found at i:1030983 original size:18 final size:19
Alignment explanation
Indices: 1030948--1030990 Score: 70
Period size: 18 Copynumber: 2.3 Consensus size: 19
1030938 ATATATATAA
*
1030948 TATAAAATTATGTATAAAC
1 TATATAATTATGTATAAAC
1030967 TATATAATTAT-TATAAAC
1 TATATAATTATGTATAAAC
1030985 TATATA
1 TATATA
1030991 TAAATTATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 13 0.57
19 10 0.43
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.42
Consensus pattern (19 bp):
TATATAATTATGTATAAAC
Found at i:1030997 original size:18 final size:18
Alignment explanation
Indices: 1030960--1031090 Score: 88
Period size: 18 Copynumber: 6.9 Consensus size: 18
1030950 TAAAATTATG
1030960 TATAAACTATATA-ATTAT
1 TATAAACTATATATA-TAT
*
1030978 TATAAACTATATATAAAT
1 TATAAACTATATATATAT
** * *
1030996 TAT-ATTTATGTGCACTCTAT
1 TATAAACTATAT--A-TATAT
*
1031016 ATATAAACTATGTATATAAAAT
1 -TATAAACTA--TATAT-ATAT
*
1031038 TATAAACTATATTTATAT
1 TATAAACTATATATATAT
1031056 TATAAACTATAT-TATTAT
1 TATAAACTATATATA-TAT
*
1031074 TATAAGCTATATATATA
1 TATAAACTATATATATA
1031091 AATTATGTTT
Statistics
Matches: 88, Mismatches: 14, Indels: 22
0.71 0.11 0.18
Matches are distributed among these distances:
17 7 0.08
18 49 0.56
19 8 0.09
20 3 0.03
21 13 0.15
22 6 0.07
24 2 0.02
ACGTcount: A:0.46, C:0.07, G:0.03, T:0.44
Consensus pattern (18 bp):
TATAAACTATATATATAT
Found at i:1031033 original size:96 final size:97
Alignment explanation
Indices: 1030933--1031142 Score: 255
Period size: 98 Copynumber: 2.2 Consensus size: 97
1030923 AATTGAAAAA
*
1030933 ATATAATATATATAATA-TAAAATTAT-GTATAAACTATATAATTATTATAAAC-TATATATAAA
1 ATATAAAAT-TATAA-ACTAAAATTATAGTATAAACTATATAATTATTATAAACATATATATAAA
* *
1030995 TTATATTTATGTGCACTCTATATATAAACTATGT
64 TTATATTTATGTGAACTATATATATAAACTATGT
* * * * *
1031029 ATATAAAATTATAAACTATATTTATATTATAAACTATATTATTATTATAAGCTATATATATAAAT
1 ATATAAAATTATAAACTAAAATTATAGTATAAACTATATAATTATTATAAAC-ATATATATAAAT
* *
1031094 TATGTTTATGTGAACTATATATATAAACTATAT
65 TATATTTATGTGAACTATATATATAAACTATGT
* *
1031127 ATGTATAAACTATAAA
1 ATATA-AAATTATAAA
1031143 AAGTATATAG
Statistics
Matches: 97, Mismatches: 12, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
94 1 0.01
95 12 0.12
96 31 0.32
98 44 0.45
99 9 0.09
ACGTcount: A:0.47, C:0.06, G:0.04, T:0.43
Consensus pattern (97 bp):
ATATAAAATTATAAACTAAAATTATAGTATAAACTATATAATTATTATAAACATATATATAAATT
ATATTTATGTGAACTATATATATAAACTATGT
Found at i:1031073 original size:15 final size:14
Alignment explanation
Indices: 1031051--1031140 Score: 69
Period size: 15 Copynumber: 6.1 Consensus size: 14
1031041 AAACTATATT
1031051 TATATTATAAACTA
1 TATATTATAAACTA
1031065 TATTATTATTATAAGCTA
1 TA-TATTA-TA-AA-CTA
*
1031083 TATA-TATAAATTA
1 TATATTATAAACTA
* *
1031096 TGT-TTATGTGAACTA
1 TATATTA--TAAACTA
1031111 TATA-TATAAACTA
1 TATATTATAAACTA
1031124 TATATGTATAAACTA
1 TATAT-TATAAACTA
1031139 TA
1 TA
1031141 AAAAGTATAT
Statistics
Matches: 60, Mismatches: 6, Indels: 19
0.71 0.07 0.22
Matches are distributed among these distances:
13 16 0.27
14 4 0.07
15 27 0.45
16 4 0.07
17 4 0.07
18 5 0.08
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.44
Consensus pattern (14 bp):
TATATTATAAACTA
Found at i:1031189 original size:2 final size:2
Alignment explanation
Indices: 1031176--1031304 Score: 76
Period size: 2 Copynumber: 65.5 Consensus size: 2
1031166 ATTTATATTA
* *
1031176 AT AT AGT AT AT AT AT AT AT A- ACT AT AT AT GT AT AA ACT AT AT
1 AT AT A-T AT AT AT AT AT AT AT A-T AT AT AT AT AT AT A-T AT AT
* * * *
1031218 AA ACT AT AT A- AT TT AT AT GT -T AT A- AT TT AT AT -T A- AT AT
1 AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
1031256 AGT AT AT AT AT GT AT GT AT A- ACT A- AT AT AT AT AT AT AT AT AT
1 A-T AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT
1031298 AT AT AT A
1 AT AT AT A
1031305 ATAAAAATAT
Statistics
Matches: 98, Mismatches: 15, Indels: 28
0.70 0.11 0.20
Matches are distributed among these distances:
1 8 0.08
2 82 0.84
3 8 0.08
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.46
Consensus pattern (2 bp):
AT
Found at i:1031212 original size:76 final size:75
Alignment explanation
Indices: 1031109--1031266 Score: 244
Period size: 76 Copynumber: 2.1 Consensus size: 75
1031099 TTATGTGAAC
* * *
1031109 TATATATATAAACTATATATGTATAAACTATAAAAAGTATATAGTTTATAAACTATTATTTATAT
1 TATATATATAAACTATATATGTATAAACTATAAAAACTATATAATTTATAAACTATAATTTATAT
1031174 TAATATAGTA
66 TAATATAGTA
* ***
1031184 TATATATATATAACTATATATGTATAAACTATATAAACTATATAATTTATATGTTATAATTTATA
1 TATATATATA-AACTATATATGTATAAACTATAAAAACTATATAATTTATAAACTATAATTTATA
1031249 TTAATATAGTA
65 TTAATATAGTA
1031260 TATATAT
1 TATATAT
1031267 GTATGTATAA
Statistics
Matches: 75, Mismatches: 7, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
75 10 0.13
76 65 0.87
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (75 bp):
TATATATATAAACTATATATGTATAAACTATAAAAACTATATAATTTATAAACTATAATTTATAT
TAATATAGTA
Found at i:1031518 original size:42 final size:42
Alignment explanation
Indices: 1031472--1031581 Score: 193
Period size: 42 Copynumber: 2.6 Consensus size: 42
1031462 ACAATAGTTA
*
1031472 ATATATGTAACTTATAGTATGTGTATACATGCAATGTAAACT
1 ATATATGTAACTTATAGTATATGTATACATGCAATGTAAACT
*
1031514 ATATATGTAACTTATAGTATATGTATACATGTAATGTAAACT
1 ATATATGTAACTTATAGTATATGTATACATGCAATGTAAACT
*
1031556 ATATATGTAACTTATAGTACATGTAT
1 ATATATGTAACTTATAGTATATGTAT
1031582 GTATAAACTA
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 65 1.00
ACGTcount: A:0.39, C:0.08, G:0.13, T:0.40
Consensus pattern (42 bp):
ATATATGTAACTTATAGTATATGTATACATGCAATGTAAACT
Found at i:1031540 original size:24 final size:22
Alignment explanation
Indices: 1031513--1031605 Score: 54
Period size: 24 Copynumber: 4.3 Consensus size: 22
1031503 CAATGTAAAC
1031513 TATATATGTAACTTATAGTATATG
1 TATATATGTAAC-TAT-GTATATG
* **
1031537 TATACATGT-A--ATGTA-AAC
1 TATATATGTAACTATGTATATG
*
1031555 TATATATGTAACTTATAGTACATG
1 TATATATGTAAC-TAT-GTATATG
* *
1031579 TATGTAT-AAACTATGTATA-G
1 TATATATGTAACTATGTATATG
1031599 TATATAT
1 TATATAT
1031606 CTATATATCA
Statistics
Matches: 53, Mismatches: 10, Indels: 16
0.67 0.13 0.20
Matches are distributed among these distances:
18 9 0.17
19 4 0.08
20 9 0.17
21 4 0.08
22 5 0.09
23 7 0.13
24 15 0.28
ACGTcount: A:0.40, C:0.06, G:0.12, T:0.42
Consensus pattern (22 bp):
TATATATGTAACTATGTATATG
Found at i:1031726 original size:14 final size:14
Alignment explanation
Indices: 1031709--1031743 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
1031699 AACCTATTAC
1031709 CCTAAACTCTAAAT
1 CCTAAACTCTAAAT
*
1031723 CCTAAACTTTAAAT
1 CCTAAACTCTAAAT
*
1031737 CTTAAAC
1 CCTAAAC
1031744 CTTAACCCTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.43, C:0.26, G:0.00, T:0.31
Consensus pattern (14 bp):
CCTAAACTCTAAAT
Found at i:1031787 original size:18 final size:18
Alignment explanation
Indices: 1031764--1031798 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1031754 ACCTATGTAA
1031764 TTTACATATGAACTATAG
1 TTTACATATGAACTATAG
*
1031782 TTTACATATTAACTATA
1 TTTACATATGAACTATA
1031799 TATATAGTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.40, C:0.11, G:0.06, T:0.43
Consensus pattern (18 bp):
TTTACATATGAACTATAG
Found at i:1031883 original size:2 final size:2
Alignment explanation
Indices: 1031872--1032140 Score: 87
Period size: 2 Copynumber: 139.0 Consensus size: 2
1031862 AAAACAAAAT
1031872 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
1031912 TA TA -A GTT TA TA TA TA AA CTA TA TA TA TA AA CTA TG TA TA TA
1 TA TA TA -TA TA TA TA TA TA -TA TA TA TA TA TA -TA TA TA TA TA
* * * * * * *
1031954 AA CTA TA TA TG TA TA AA CTA TA AA AA GTA TA TA GTT TA TA -A AA
1 TA -TA TA TA TA TA TA TA -TA TA TA TA -TA TA TA -TA TA TA TA TA
1031997 TA TA -A CT- TA TA T- TA -A TA T- TA -A TA TA TA TA TA TGA -A T-
1 TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA
* * * * *
1032033 TA TA TA TG TA TA -A AA TA TA TA GTT TA TA AA T- TA TA -A TT TA
1 TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA
* *
1032073 TA T- TA -A TA TA GTA TA TA TA TG TA TG TA TA -A CTA -A TA TA -A
1 TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA
* *
1032112 GTA -A TC TA TA GA -A TA TA TA TA TA TA TA TA
1 -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1032141 GTTTATAGAA
Statistics
Matches: 197, Mismatches: 35, Indels: 70
0.65 0.12 0.23
Matches are distributed among these distances:
1 22 0.11
2 163 0.83
3 12 0.06
ACGTcount: A:0.49, C:0.03, G:0.05, T:0.43
Consensus pattern (2 bp):
TA
Found at i:1032209 original size:7 final size:7
Alignment explanation
Indices: 1032197--1032253 Score: 50
Period size: 7 Copynumber: 8.6 Consensus size: 7
1032187 TAGTTGATAA
1032197 AAACCCT
1 AAACCCT
1032204 AAACCCT
1 AAACCCT
1032211 -AA--CT
1 AAACCCT
1032215 AAACACC-
1 AAAC-CCT
* *
1032222 GAACCTT
1 AAACCCT
1032229 AAACCCT
1 AAACCCT
*
1032236 AAACCTT
1 AAACCCT
1032243 AAACCCT
1 AAACCCT
1032250 AAAC
1 AAAC
1032254 ATTGTACATA
Statistics
Matches: 39, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
4 2 0.05
5 2 0.05
6 3 0.08
7 31 0.79
8 1 0.03
ACGTcount: A:0.46, C:0.37, G:0.02, T:0.16
Consensus pattern (7 bp):
AAACCCT
Found at i:1032240 original size:14 final size:14
Alignment explanation
Indices: 1032223--1032253 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
1032213 CTAAACACCG
1032223 AACCTTAAACCCTA
1 AACCTTAAACCCTA
1032237 AACCTTAAACCCTA
1 AACCTTAAACCCTA
1032251 AAC
1 AAC
1032254 ATTGTACATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.45, C:0.35, G:0.00, T:0.19
Consensus pattern (14 bp):
AACCTTAAACCCTA
Found at i:1032365 original size:55 final size:57
Alignment explanation
Indices: 1032306--1032441 Score: 152
Period size: 57 Copynumber: 2.4 Consensus size: 57
1032296 TGTATACATG
* * *
1032306 TAAACTATATATGTAACTTATAGTATATGTATGCATA-AA-CTATGTAT-AGCATATA
1 TAAACTATATATGTAACCTATAGTATATGTATACAAACAATCTATGTATAAG-ATATA
* * * * * *
1032361 TAAACTATATATATAACCTATAATATATTTATATAAACAATCTATTTATAAGTTATA
1 TAAACTATATATGTAACCTATAGTATATGTATACAAACAATCTATGTATAAGATATA
*
1032418 TAAATTATATATGTAACCTATAGT
1 TAAACTATATATGTAACCTATAGT
1032442 TTATAAGCAA
Statistics
Matches: 66, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
55 30 0.45
56 2 0.03
57 32 0.48
58 2 0.03
ACGTcount: A:0.44, C:0.09, G:0.07, T:0.40
Consensus pattern (57 bp):
TAAACTATATATGTAACCTATAGTATATGTATACAAACAATCTATGTATAAGATATA
Found at i:1032524 original size:21 final size:21
Alignment explanation
Indices: 1032472--1032524 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
1032462 TAGTGTACTA
* *
1032472 TATAGTTTATACTTTATAACC
1 TATAGTTTATAATTTATAAAC
* *
1032493 TATTGTATATAATTTATAAAC
1 TATAGTTTATAATTTATAAAC
1032514 TATAGTTTATA
1 TATAGTTTATA
1032525 TTAATGTTAA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.38, C:0.08, G:0.06, T:0.49
Consensus pattern (21 bp):
TATAGTTTATAATTTATAAAC
Found at i:1032576 original size:88 final size:88
Alignment explanation
Indices: 1032471--1032650 Score: 240
Period size: 88 Copynumber: 2.0 Consensus size: 88
1032461 TTAGTGTACT
* * *** *
1032471 ATATAGTTTATACTTTATAACCTATTGTATATAATTTATAA-ACTATAGTTTATATTAATGTTAA
1 ATATAGTATATACTTTATAAACTATACAATATAATTTATAACA-TATAGTTTATATTAATATTAA
1032535 TTATCT-TA-ACTATAATTTATATTA
65 TT-T-TATAGACTATAATTTATATTA
*
1032559 ATATAGTATATAGTTTATAAACTATACAATATAATTTATAACATATAGTTTATATTAATATTAAT
1 ATATAGTATATACTTTATAAACTATACAATATAATTTATAACATATAGTTTATATTAATATTAAT
*
1032624 TTTATAGACTATATTTTATATTA
66 TTTATAGACTATAATTTATATTA
1032647 ATAT
1 ATAT
1032651 TAATTACAAA
Statistics
Matches: 81, Mismatches: 8, Indels: 6
0.85 0.08 0.06
Matches are distributed among these distances:
86 1 0.01
87 3 0.04
88 76 0.94
89 1 0.01
ACGTcount: A:0.41, C:0.06, G:0.04, T:0.49
Consensus pattern (88 bp):
ATATAGTATATACTTTATAAACTATACAATATAATTTATAACATATAGTTTATATTAATATTAAT
TTTATAGACTATAATTTATATTA
Found at i:1032612 original size:21 final size:21
Alignment explanation
Indices: 1032471--1032612 Score: 60
Period size: 21 Copynumber: 6.6 Consensus size: 21
1032461 TTAGTGTACT
* *
1032471 ATATAGTTTATACTTTATAAC
1 ATATAGTATATAATTTATAAC
* *
1032492 CTATTGTATATAATTTATAA-
1 ATATAGTATATAATTTATAAC
*
1032512 ACTATAGTTTATATTAATGT-TAA-
1 A-TATAG--TATA-TAATTTATAAC
* **
1032535 TTATCTTAACTATAATTTATATTA-
1 ATATAGT-A-TATAATTTATA--AC
*
1032559 ATATAGTATATAGTTTATAA-
1 ATATAGTATATAATTTATAAC
**
1032579 ACTATACAATATAATTTATAAC
1 A-TATAGTATATAATTTATAAC
*
1032601 ATATAGTTTATA
1 ATATAGTATATA
1032613 TTAATATTAA
Statistics
Matches: 89, Mismatches: 21, Indels: 22
0.67 0.16 0.17
Matches are distributed among these distances:
20 3 0.03
21 50 0.56
22 18 0.20
23 8 0.09
24 10 0.11
ACGTcount: A:0.42, C:0.06, G:0.05, T:0.47
Consensus pattern (21 bp):
ATATAGTATATAATTTATAAC
Found at i:1032665 original size:88 final size:88
Alignment explanation
Indices: 1032499--1032672 Score: 230
Period size: 88 Copynumber: 2.0 Consensus size: 88
1032489 AACCTATTGT
*
1032499 ATATAATTTATAAACTATAGTTTATATTAATGTTAATTATCTTAACTATAATTTATATTAATATA
1 ATATAATTTATAAACTATAGTTTATATTAATATTAATTATCTTAACTATAATTTATATTAATATA
* * **
1032564 GTATATAGTTTATAAACTATACA
66 ATATACAAATTATAAACTATACA
*
1032587 ATATAATTTAT-AACATATAGTTTATATTAATATTAATT-T-TATAGACTATATTTTATATTAAT
1 ATATAATTTATAAAC-TATAGTTTATATTAATATTAATTATCT-TA-ACTATAATTTATATTAAT
1032649 ATTAAT-TACAAATTATAAACTATA
63 A-TAATATACAAATTATAAACTATA
1032673 TTATATTAAT
Statistics
Matches: 76, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
86 1 0.01
87 6 0.08
88 66 0.87
89 3 0.04
ACGTcount: A:0.44, C:0.05, G:0.03, T:0.47
Consensus pattern (88 bp):
ATATAATTTATAAACTATAGTTTATATTAATATTAATTATCTTAACTATAATTTATATTAATATA
ATATACAAATTATAAACTATACA
Found at i:1032706 original size:12 final size:12
Alignment explanation
Indices: 1032689--1032731 Score: 50
Period size: 12 Copynumber: 3.2 Consensus size: 12
1032679 TAATATAAGT
1032689 TAATATTAATTA
1 TAATATTAATTA
1032701 TAATATATAATTA
1 TAATAT-TAATTA
1032714 TTTTAATATTAATTA
1 ---TAATATTAATTA
1032729 TAA
1 TAA
1032732 ATATCATTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
12 9 0.33
13 6 0.22
15 6 0.22
16 6 0.22
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (12 bp):
TAATATTAATTA
Found at i:1032706 original size:28 final size:28
Alignment explanation
Indices: 1032669--1032735 Score: 82
Period size: 28 Copynumber: 2.4 Consensus size: 28
1032659 AATTATAAAC
*
1032669 TATATTATATTAATATAAGTTAATATTAAT
1 TATAATATA-TAAT-TAAGTTAATATTAAT
**
1032699 TATAATATATAATTATTTTAATATTAAT
1 TATAATATATAATTAAGTTAATATTAAT
1032727 TATAA-ATAT
1 TATAATATAT
1032736 CATTTTCTCC
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
27 4 0.12
28 18 0.53
29 4 0.12
30 8 0.24
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (28 bp):
TATAATATATAATTAAGTTAATATTAAT
Found at i:1032726 original size:22 final size:23
Alignment explanation
Indices: 1032670--1032731 Score: 62
Period size: 22 Copynumber: 2.9 Consensus size: 23
1032660 ATTATAAACT
*
1032670 ATATT-ATATTAATATA-AGTTA
1 ATATTAATATTAATATATAATTA
1032691 ATATTAAT-TATAATATATAATT-
1 ATATTAATAT-TAATATATAATTA
*
1032713 ATTTTAATATTAAT-TATAA
1 ATATTAATATTAATATATAA
1032732 ATATCATTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
21 11 0.31
22 20 0.57
23 4 0.11
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (23 bp):
ATATTAATATTAATATATAATTA
Found at i:1034116 original size:13 final size:13
Alignment explanation
Indices: 1034098--1034123 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1034088 CCAATGGGGA
1034098 GAGGTCGCCATGC
1 GAGGTCGCCATGC
1034111 GAGGTCGCCATGC
1 GAGGTCGCCATGC
1034124 AGTCCTGGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.31, G:0.38, T:0.15
Consensus pattern (13 bp):
GAGGTCGCCATGC
Found at i:1034189 original size:29 final size:29
Alignment explanation
Indices: 1034139--1034247 Score: 184
Period size: 29 Copynumber: 3.8 Consensus size: 29
1034129 TGGAATAGAG
* *
1034139 AGGTCGCCATGCAG-CCTAGGCGACCTTGT
1 AGGTCGCCATGTAGTCC-CGGCGACCTTGT
1034168 AGGTCGCCATGTAGTCCCGGCGACCTTGT
1 AGGTCGCCATGTAGTCCCGGCGACCTTGT
1034197 AGGTCGCCATGTAGTCCCGGCGACCTTGT
1 AGGTCGCCATGTAGTCCCGGCGACCTTGT
1034226 AGGTCGCCATGTAGTCCCGGCG
1 AGGTCGCCATGTAGTCCCGGCG
1034248 CCATTCCCAT
Statistics
Matches: 77, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
29 75 0.97
30 2 0.03
ACGTcount: A:0.15, C:0.31, G:0.32, T:0.22
Consensus pattern (29 bp):
AGGTCGCCATGTAGTCCCGGCGACCTTGT
Found at i:1034452 original size:102 final size:102
Alignment explanation
Indices: 1034276--1034479 Score: 399
Period size: 102 Copynumber: 2.0 Consensus size: 102
1034266 CACAGCCACA
1034276 TAGATTCCTTCACGTGCTCCCCGCTGCATGCTGCATGCCTACAGCTCCCAATGAAACCATGTGAA
1 TAGATTCCTTCACGTGCTCCCCGCTGCATGCTGCATGCCTACAGCTCCCAATGAAACCATGTGAA
*
1034341 CCATTTGAGCCAATGCATGTGAAATAATTGGTTCAAT
66 CCATTTGAGCCAATGCATGTGAAATAATTGGTACAAT
1034378 TAGATTCCTTCACGTGCTCCCCGCTGCATGCTGCATGCCTACAGCTCCCAATGAAACCATGTGAA
1 TAGATTCCTTCACGTGCTCCCCGCTGCATGCTGCATGCCTACAGCTCCCAATGAAACCATGTGAA
1034443 CCATTTGAGCCAATGCATGTGAAATAATTGGTACAAT
66 CCATTTGAGCCAATGCATGTGAAATAATTGGTACAAT
1034480 AATTGAACCA
Statistics
Matches: 101, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
102 101 1.00
ACGTcount: A:0.27, C:0.27, G:0.19, T:0.27
Consensus pattern (102 bp):
TAGATTCCTTCACGTGCTCCCCGCTGCATGCTGCATGCCTACAGCTCCCAATGAAACCATGTGAA
CCATTTGAGCCAATGCATGTGAAATAATTGGTACAAT
Found at i:1034557 original size:25 final size:25
Alignment explanation
Indices: 1034528--1034579 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
1034518 TGTACAATTA
1034528 TTGGTGAAATAATTGAGGCAGCCGG
1 TTGGTGAAATAATTGAGGCAGCCGG
1034553 TTGGTGAAATAATTGAGGCAGCCGG
1 TTGGTGAAATAATTGAGGCAGCCGG
1034578 TT
1 TT
1034580 ATAAAAGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.27, C:0.12, G:0.35, T:0.27
Consensus pattern (25 bp):
TTGGTGAAATAATTGAGGCAGCCGG
Found at i:1034620 original size:23 final size:23
Alignment explanation
Indices: 1034592--1034637 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
1034582 AAAAGAAAGA
1034592 AAGAAAGGGAGAAGAGATTGCAG
1 AAGAAAGGGAGAAGAGATTGCAG
**
1034615 AAGAAAGTTAGAAGAGATTGCAG
1 AAGAAAGGGAGAAGAGATTGCAG
1034638 CCGAGAAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.48, C:0.04, G:0.35, T:0.13
Consensus pattern (23 bp):
AAGAAAGGGAGAAGAGATTGCAG
Found at i:1034652 original size:25 final size:23
Alignment explanation
Indices: 1034592--1034652 Score: 59
Period size: 23 Copynumber: 2.6 Consensus size: 23
1034582 AAAAGAAAGA
**
1034592 AAGAAAGGGAGAAGAGATTGCAG
1 AAGAAAGAAAGAAGAGATTGCAG
**
1034615 AAGAAAGTTAGAAGAGATTGCAG
1 AAGAAAGAAAGAAGAGATTGCAG
*
1034638 CCGAGAAAGAAAGAA
1 --AAGAAAGAAAGAA
1034653 AGGGAGAAAG
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
23 21 0.68
25 10 0.32
ACGTcount: A:0.51, C:0.07, G:0.33, T:0.10
Consensus pattern (23 bp):
AAGAAAGAAAGAAGAGATTGCAG
Found at i:1034666 original size:21 final size:21
Alignment explanation
Indices: 1034642--1034694 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
1034632 TTGCAGCCGA
1034642 GAAAGAAAGAAAGGGAGAAAG
1 GAAAGAAAGAAAGGGAGAAAG
1034663 GAAAGAAAGAAAGGGAGAAAG
1 GAAAGAAAGAAAGGGAGAAAG
*
1034684 GAAAGTAAGAA
1 GAAAGAAAGAA
1034695 GAAGAAAGGG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.62, C:0.00, G:0.36, T:0.02
Consensus pattern (21 bp):
GAAAGAAAGAAAGGGAGAAAG
Found at i:1034688 original size:17 final size:16
Alignment explanation
Indices: 1034640--1034671 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
1034630 GATTGCAGCC
1034640 GAGAAAGAAAGAAAGG
1 GAGAAAGAAAGAAAGG
1034656 GAGAAAGGAAAGAAAG
1 GAGAAA-GAAAGAAAG
1034672 AAAGGGAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (16 bp):
GAGAAAGAAAGAAAGG
Found at i:1034951 original size:45 final size:48
Alignment explanation
Indices: 1034902--1034992 Score: 134
Period size: 45 Copynumber: 2.0 Consensus size: 48
1034892 TTATATAGTT
*
1034902 AAAAAATAATTAATTAGTTTGT-TTTGTT-AATAGTT-AGTTATATAA
1 AAAAAATAATTAATTAGTTTGTGTTAGTTAAATAGTTAAGTTATATAA
* *
1034947 AAAAATTATTTAATTAGTTTGTGTTAGTTAAATAGTTAAGTTATAT
1 AAAAAATAATTAATTAGTTTGTGTTAGTTAAATAGTTAAGTTATAT
1034993 TTTGTTTGTT
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
45 20 0.50
46 5 0.12
47 7 0.17
48 8 0.20
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.47
Consensus pattern (48 bp):
AAAAAATAATTAATTAGTTTGTGTTAGTTAAATAGTTAAGTTATATAA
Found at i:1035188 original size:16 final size:16
Alignment explanation
Indices: 1035156--1035202 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
1035146 TTTAAAAAGT
*
1035156 TTAGTTTGTTAGT-TTA
1 TTAGTTTATTA-TATTA
1035172 TTAGTTTATTATATTA
1 TTAGTTTATTATATTA
*
1035188 TAAG-TTATTATATTA
1 TTAGTTTATTATATTA
1035203 AAGTTTAGTG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 12 0.43
16 16 0.57
ACGTcount: A:0.30, C:0.00, G:0.11, T:0.60
Consensus pattern (16 bp):
TTAGTTTATTATATTA
Found at i:1035197 original size:15 final size:14
Alignment explanation
Indices: 1035177--1035207 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
1035167 GTTTATTAGT
1035177 TTATTATATTATAAG
1 TTATTATATTA-AAG
1035192 TTATTATATTAAAG
1 TTATTATATTAAAG
1035206 TT
1 TT
1035208 TAGTGTTGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (14 bp):
TTATTATATTAAAG
Found at i:1037380 original size:17 final size:17
Alignment explanation
Indices: 1037358--1037390 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1037348 CAATGATGTT
*
1037358 TAGTATCAAATCATTAC
1 TAGTATCAAATAATTAC
1037375 TAGTATCAAATAATTA
1 TAGTATCAAATAATTA
1037391 AATATTTAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.45, C:0.12, G:0.06, T:0.36
Consensus pattern (17 bp):
TAGTATCAAATAATTAC
Found at i:1037407 original size:24 final size:22
Alignment explanation
Indices: 1037375--1037443 Score: 77
Period size: 22 Copynumber: 3.0 Consensus size: 22
1037365 AAATCATTAC
1037375 TAGTATCAAATAATTAAATATT
1 TAGTATCAAATAATTAAATATT
* *
1037397 TAGTAAATCAACTATTTTAAATCA-T
1 TAGT--ATCAAATA-ATTAAAT-ATT
1037422 TAGTATCAAATAATTAAATATT
1 TAGTATCAAATAATTAAATATT
1037444 AACAATAAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
21 1 0.03
22 11 0.29
23 7 0.18
24 7 0.18
25 11 0.29
26 1 0.03
ACGTcount: A:0.48, C:0.07, G:0.04, T:0.41
Consensus pattern (22 bp):
TAGTATCAAATAATTAAATATT
Found at i:1037663 original size:35 final size:37
Alignment explanation
Indices: 1037582--1037668 Score: 99
Period size: 38 Copynumber: 2.4 Consensus size: 37
1037572 TTAGTATTCT
* * *
1037582 ATAATTATTAGT-AATAATTATTAAATCATTAGTATTAA
1 ATAATTATTA-TAAATAATTACTAAATCAATAG-ACTAA
*
1037620 ATCATTATTATAAATAATTACTAAAT-AATA-ACTAA
1 ATAATTATTATAAATAATTACTAAATCAATAGACTAA
1037655 ATAATTATTATAAA
1 ATAATTATTATAAA
1037669 ATCATTATTA
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
35 17 0.40
37 4 0.09
38 22 0.51
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.41
Consensus pattern (37 bp):
ATAATTATTATAAATAATTACTAAATCAATAGACTAA
Found at i:1037689 original size:12 final size:13
Alignment explanation
Indices: 1037598--1037825 Score: 111
Period size: 14 Copynumber: 17.1 Consensus size: 13
1037588 ATTAGTAATA
1037598 ATTATTAAATCATT
1 ATTA-TAAATCATT
*
1037612 AGTATTAAATCATT
1 ATTA-TAAATCATT
1037626 ATTATAAAT-A--
1 ATTATAAATCATT
1037636 ATTACTAAAT-A--
1 ATTA-TAAATCATT
* *
1037647 ATAACTAAATAATT
1 ATTA-TAAATCATT
1037661 ATTATAAAATCATT
1 ATTAT-AAATCATT
*
1037675 ATTAT-AATGATT
1 ATTATAAATCATT
1037687 ATTATCAAATCATT
1 ATTAT-AAATCATT
1037701 ACTAAATCATCAAATCATT
1 A-T---T-AT-AAATCATT
*
1037720 AAATATTTAAATCATT
1 --AT-TATAAATCATT
1037736 A-T-TAAATCATT
1 ATTATAAATCATT
* *
1037747 TTTAT-AATGATT
1 ATTATAAATCATT
1037759 ATTACTAAATCATT
1 ATTA-TAAATCATT
*
1037773 ATTAT-AATGATT
1 ATTATAAATCATT
*
1037785 ATTATCAAATCAAT
1 ATTAT-AAATCATT
* *
1037799 ACTAT-AATGATT
1 ATTATAAATCATT
1037811 ATTATCAAATCATT
1 ATTAT-AAATCATT
1037825 A
1 A
1037826 CTAAATCATC
Statistics
Matches: 172, Mismatches: 20, Indels: 44
0.73 0.08 0.19
Matches are distributed among these distances:
10 4 0.02
11 24 0.14
12 44 0.26
13 9 0.05
14 65 0.38
15 1 0.01
16 8 0.05
17 1 0.01
18 3 0.02
19 11 0.06
20 1 0.01
21 1 0.01
ACGTcount: A:0.46, C:0.09, G:0.02, T:0.43
Consensus pattern (13 bp):
ATTATAAATCATT
Found at i:1037696 original size:26 final size:26
Alignment explanation
Indices: 1037598--1037825 Score: 165
Period size: 26 Copynumber: 9.2 Consensus size: 26
1037588 ATTAGTAATA
* * *
1037598 ATTATTA-AATCATTAGTATTAAATC
1 ATTATTATAATGATTATTATCAAATC
* *
1037623 ATTATTATAA--ATAATTA-CTAAATA
1 ATTATTATAATGATTATTATC-AAATC
* * * *
1037647 ATAACTA-AATAATTATTATAAAATC
1 ATTATTATAATGATTATTATCAAATC
1037672 ATTATTATAATGATTATTATCAAATC
1 ATTATTATAATGATTATTATCAAATC
* * * * * *
1037698 ATTACTA-AATCATCA-AATC-ATTA
1 ATTATTATAATGATTATTATCAAATC
* * *
1037721 AATATT-TAA--ATCATTATTAAATC
1 ATTATTATAATGATTATTATCAAATC
*
1037744 ATTTTTATAATGATTATTA-CTAAATC
1 ATTATTATAATGATTATTATC-AAATC
1037770 ATTATTATAATGATTATTATCAAATC
1 ATTATTATAATGATTATTATCAAATC
* *
1037796 AATACTATAATGATTATTATCAAATC
1 ATTATTATAATGATTATTATCAAATC
1037822 ATTA
1 ATTA
1037826 CTAAATCATC
Statistics
Matches: 156, Mismatches: 33, Indels: 27
0.72 0.15 0.12
Matches are distributed among these distances:
21 4 0.03
22 2 0.01
23 16 0.10
24 20 0.13
25 28 0.18
26 85 0.54
27 1 0.01
ACGTcount: A:0.46, C:0.09, G:0.02, T:0.43
Consensus pattern (26 bp):
ATTATTATAATGATTATTATCAAATC
Found at i:1037822 original size:124 final size:123
Alignment explanation
Indices: 1037614--1037883 Score: 436
Period size: 124 Copynumber: 2.2 Consensus size: 123
1037604 AAATCATTAG
* * * *
1037614 TATTAAATCATTATTATAA--ATAATTACTAAATAATAACTAAATAATTATTATAAAATCATTAT
1 TATTAAATCATTTTTATAATGATTATTACTAAATAATAACTAAATAATTATTATAAAATCAATAC
1037677 TATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCAT
66 TATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCAT
* * * * *
1037735 TATTAAATCATTTTTATAATGATTATTACTAAATCATTATTATAATGATTATTATCAAATCAATA
1 TATTAAATCATTTTTATAATGATTATTACTAAATAATAACTA-AATAATTATTATAAAATCAATA
1037800 CTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCAT
65 CTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCAT
1037859 TATTAAATCATTTTTATAATGATTA
1 TATTAAATCATTTTTATAATGATTA
1037884 ATAAATACAT
Statistics
Matches: 137, Mismatches: 9, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
121 18 0.13
123 17 0.12
124 102 0.74
ACGTcount: A:0.46, C:0.09, G:0.02, T:0.43
Consensus pattern (123 bp):
TATTAAATCATTTTTATAATGATTATTACTAAATAATAACTAAATAATTATTATAAAATCAATAC
TATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCAT
Found at i:1041043 original size:19 final size:19
Alignment explanation
Indices: 1041019--1041081 Score: 60
Period size: 19 Copynumber: 3.4 Consensus size: 19
1041009 CAATATAAAA
1041019 AAACAAATATATTTTTTTT
1 AAACAAATATATTTTTTTT
* *
1041038 AAACAACACTA-A-ATATTTT
1 AAACAA-A-TATATTTTTTTT
*
1041057 AAACACA-ATATTTTTTTT
1 AAACAAATATATTTTTTTT
1041075 AAACAAA
1 AAACAAA
1041082 AATTATCTCG
Statistics
Matches: 34, Mismatches: 6, Indels: 9
0.69 0.12 0.18
Matches are distributed among these distances:
16 1 0.03
17 1 0.03
18 12 0.35
19 16 0.47
20 2 0.06
21 2 0.06
ACGTcount: A:0.49, C:0.11, G:0.00, T:0.40
Consensus pattern (19 bp):
AAACAAATATATTTTTTTT
Found at i:1041171 original size:14 final size:14
Alignment explanation
Indices: 1041152--1041178 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1041142 CACATACACA
1041152 ACAACAAAAAATAG
1 ACAACAAAAAATAG
1041166 ACAACAAAAAATA
1 ACAACAAAAAATA
1041179 ATAAATTACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.74, C:0.15, G:0.04, T:0.07
Consensus pattern (14 bp):
ACAACAAAAAATAG
Found at i:1041171 original size:17 final size:17
Alignment explanation
Indices: 1041149--1041181 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1041139 TTACACATAC
1041149 ACAACAACAAAA-AATAG
1 ACAACAA-AAAATAATAG
1041166 ACAACAAAAAATAATA
1 ACAACAAAAAATAATA
1041182 AATTACTCAC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.73, C:0.15, G:0.03, T:0.09
Consensus pattern (17 bp):
ACAACAAAAAATAATAG
Found at i:1041580 original size:47 final size:46
Alignment explanation
Indices: 1041492--1041594 Score: 136
Period size: 47 Copynumber: 2.2 Consensus size: 46
1041482 GTTTAAAGAC
* * *
1041492 ACTAACAAATTAATTAATATTTTTTTATATTTAATAACTTAAACTA
1 ACTAACTAATTAACTAATATTTTTTTATATATAATAACTTAAACTA
*
1041538 ATTAACTAATTAACTAAT-TTTTTTTATATAATATATAACTTAAACTA
1 ACTAACTAATTAACTAATATTTTTTTATAT-ATA-ATAACTTAAACTA
*
1041585 ACCAACTAAT
1 ACTAACTAAT
1041595 AATTTATACT
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
45 11 0.22
46 17 0.35
47 21 0.43
ACGTcount: A:0.46, C:0.11, G:0.00, T:0.44
Consensus pattern (46 bp):
ACTAACTAATTAACTAATATTTTTTTATATATAATAACTTAAACTA
Found at i:1041605 original size:21 final size:21
Alignment explanation
Indices: 1041572--1041620 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
1041562 TATATAATAT
*
1041572 ATAACTTAAACTAACCAACTA
1 ATAACTTAAACTAACAAACTA
* *
1041593 ATAATTTATACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
1041614 ATTAACT
1 A-TAACT
1041621 AGATTTTAGT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.51, C:0.18, G:0.00, T:0.31
Consensus pattern (21 bp):
ATAACTTAAACTAACAAACTA
Found at i:1042092 original size:35 final size:35
Alignment explanation
Indices: 1042052--1042119 Score: 127
Period size: 35 Copynumber: 1.9 Consensus size: 35
1042042 TGGATGCAAC
1042052 GCATGCATGAGTGATACAGTTAAAGCTTGGTCGTT
1 GCATGCATGAGTGATACAGTTAAAGCTTGGTCGTT
*
1042087 GCATGCATGAGTGCTACAGTTAAAGCTTGGTCG
1 GCATGCATGAGTGATACAGTTAAAGCTTGGTCG
1042120 CGATGCAGGA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.25, C:0.16, G:0.29, T:0.29
Consensus pattern (35 bp):
GCATGCATGAGTGATACAGTTAAAGCTTGGTCGTT
Found at i:1042176 original size:12 final size:12
Alignment explanation
Indices: 1042159--1042183 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1042149 TCCATGGCGA
1042159 CCTACCACCTAC
1 CCTACCACCTAC
1042171 CCTACCACCTAC
1 CCTACCACCTAC
1042183 C
1 C
1042184 ATGTCGTAGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.60, G:0.00, T:0.16
Consensus pattern (12 bp):
CCTACCACCTAC
Found at i:1042210 original size:29 final size:29
Alignment explanation
Indices: 1042177--1042276 Score: 191
Period size: 29 Copynumber: 3.4 Consensus size: 29
1042167 CTACCCTACC
*
1042177 ACCTACCATGTCGTAGGGACTCCATGGCG
1 ACCTACCATGTCGTCGGGACTCCATGGCG
1042206 ACCTACCATGTCGTCGGGACTCCATGGCG
1 ACCTACCATGTCGTCGGGACTCCATGGCG
1042235 ACCTACCATGTCGTCGGGACTCCATGGCG
1 ACCTACCATGTCGTCGGGACTCCATGGCG
1042264 ACCTACCATGTCG
1 ACCTACCATGTCG
1042277 CCGGCAACCT
Statistics
Matches: 70, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
29 70 1.00
ACGTcount: A:0.19, C:0.34, G:0.26, T:0.21
Consensus pattern (29 bp):
ACCTACCATGTCGTCGGGACTCCATGGCG
Found at i:1042473 original size:31 final size:31
Alignment explanation
Indices: 1042438--1042502 Score: 130
Period size: 31 Copynumber: 2.1 Consensus size: 31
1042428 CCCATGCATA
1042438 GCACCAAAGCAGCATCAGCGAGCAACAGCGG
1 GCACCAAAGCAGCATCAGCGAGCAACAGCGG
1042469 GCACCAAAGCAGCATCAGCGAGCAACAGCGG
1 GCACCAAAGCAGCATCAGCGAGCAACAGCGG
1042500 GCA
1 GCA
1042503 AAGAACCAGG
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:0.35, C:0.32, G:0.29, T:0.03
Consensus pattern (31 bp):
GCACCAAAGCAGCATCAGCGAGCAACAGCGG
Found at i:1042567 original size:29 final size:29
Alignment explanation
Indices: 1042525--1042609 Score: 170
Period size: 29 Copynumber: 2.9 Consensus size: 29
1042515 AAATAATGAT
1042525 GGACGCCGGGCGTGCATGGCGACCTATAA
1 GGACGCCGGGCGTGCATGGCGACCTATAA
1042554 GGACGCCGGGCGTGCATGGCGACCTATAA
1 GGACGCCGGGCGTGCATGGCGACCTATAA
1042583 GGACGCCGGGCGTGCATGGCGACCTAT
1 GGACGCCGGGCGTGCATGGCGACCTAT
1042610 GTTGCCACTG
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 56 1.00
ACGTcount: A:0.19, C:0.28, G:0.39, T:0.14
Consensus pattern (29 bp):
GGACGCCGGGCGTGCATGGCGACCTATAA
Found at i:1046005 original size:20 final size:20
Alignment explanation
Indices: 1045982--1046030 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
1045972 ATTCACGTTT
1045982 GCAACGCGAAATGGAAAATC
1 GCAACGCGAAATGGAAAATC
*
1046002 GCAACACGAAATGGAAAATC
1 GCAACGCGAAATGGAAAATC
1046022 GCAACGCGA
1 GCAACGCGA
1046031 TTTTCAACTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.45, C:0.22, G:0.24, T:0.08
Consensus pattern (20 bp):
GCAACGCGAAATGGAAAATC
Found at i:1046059 original size:21 final size:20
Alignment explanation
Indices: 1045982--1046058 Score: 82
Period size: 20 Copynumber: 3.8 Consensus size: 20
1045972 ATTCACGTTT
*
1045982 GCAACGCGAAATGGAAAATC
1 GCAACGCGAAATGCAAAATC
* *
1046002 GCAACACGAAATGGAAAATC
1 GCAACGCGAAATGCAAAATC
** * *
1046022 GCAACGCGATTTTCAACTATC
1 GCAACGCGAAATGCAA-AATC
1046043 GCAACGCGAAATGCAA
1 GCAACGCGAAATGCAA
1046059 CGCGAATTTG
Statistics
Matches: 46, Mismatches: 10, Indels: 1
0.81 0.18 0.02
Matches are distributed among these distances:
20 30 0.65
21 16 0.35
ACGTcount: A:0.42, C:0.23, G:0.21, T:0.14
Consensus pattern (20 bp):
GCAACGCGAAATGCAAAATC
Found at i:1047264 original size:18 final size:19
Alignment explanation
Indices: 1047229--1047271 Score: 70
Period size: 18 Copynumber: 2.3 Consensus size: 19
1047219 ATATATATAA
*
1047229 TATAAAATTATGTATAAAC
1 TATATAATTATGTATAAAC
1047248 TATATAATTAT-TATAAAC
1 TATATAATTATGTATAAAC
1047266 TATATA
1 TATATA
1047272 TAAATTATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 13 0.57
19 10 0.43
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.42
Consensus pattern (19 bp):
TATATAATTATGTATAAAC
Found at i:1047278 original size:18 final size:18
Alignment explanation
Indices: 1047241--1047371 Score: 88
Period size: 18 Copynumber: 6.9 Consensus size: 18
1047231 TAAAATTATG
1047241 TATAAACTATATA-ATTAT
1 TATAAACTATATATA-TAT
*
1047259 TATAAACTATATATAAAT
1 TATAAACTATATATATAT
** * *
1047277 TAT-ATTTATGTGCACTCTAT
1 TATAAACTATAT--A-TATAT
*
1047297 ATATAAACTATGTATATAAAAT
1 -TATAAACTA--TATAT-ATAT
*
1047319 TATAAACTATATTTATAT
1 TATAAACTATATATATAT
1047337 TATAAACTATAT-TATTAT
1 TATAAACTATATATA-TAT
*
1047355 TATAAGCTATATATATA
1 TATAAACTATATATATA
1047372 AATTATGTTT
Statistics
Matches: 88, Mismatches: 14, Indels: 22
0.71 0.11 0.18
Matches are distributed among these distances:
17 7 0.08
18 49 0.56
19 8 0.09
20 3 0.03
21 13 0.15
22 6 0.07
24 2 0.02
ACGTcount: A:0.46, C:0.07, G:0.03, T:0.44
Consensus pattern (18 bp):
TATAAACTATATATATAT
Found at i:1047314 original size:96 final size:97
Alignment explanation
Indices: 1047214--1047423 Score: 255
Period size: 98 Copynumber: 2.2 Consensus size: 97
1047204 AATTGAAAAA
*
1047214 ATATAATATATATAATA-TAAAATTAT-GTATAAACTATATAATTATTATAAAC-TATATATAAA
1 ATATAAAAT-TATAA-ACTAAAATTATAGTATAAACTATATAATTATTATAAACATATATATAAA
* *
1047276 TTATATTTATGTGCACTCTATATATAAACTATGT
64 TTATATTTATGTGAACTATATATATAAACTATGT
* * * * *
1047310 ATATAAAATTATAAACTATATTTATATTATAAACTATATTATTATTATAAGCTATATATATAAAT
1 ATATAAAATTATAAACTAAAATTATAGTATAAACTATATAATTATTATAAAC-ATATATATAAAT
* *
1047375 TATGTTTATGTGAACTATATATATAAACTATAT
65 TATATTTATGTGAACTATATATATAAACTATGT
* *
1047408 ATGTATAAACTATAAA
1 ATATA-AAATTATAAA
1047424 AAGTATATAG
Statistics
Matches: 97, Mismatches: 12, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
94 1 0.01
95 12 0.12
96 31 0.32
98 44 0.45
99 9 0.09
ACGTcount: A:0.47, C:0.06, G:0.04, T:0.43
Consensus pattern (97 bp):
ATATAAAATTATAAACTAAAATTATAGTATAAACTATATAATTATTATAAACATATATATAAATT
ATATTTATGTGAACTATATATATAAACTATGT
Found at i:1047354 original size:15 final size:14
Alignment explanation
Indices: 1047332--1047421 Score: 69
Period size: 15 Copynumber: 6.1 Consensus size: 14
1047322 AAACTATATT
1047332 TATATTATAAACTA
1 TATATTATAAACTA
1047346 TATTATTATTATAAGCTA
1 TA-TATTA-TA-AA-CTA
*
1047364 TATA-TATAAATTA
1 TATATTATAAACTA
* *
1047377 TGT-TTATGTGAACTA
1 TATATTA--TAAACTA
1047392 TATA-TATAAACTA
1 TATATTATAAACTA
1047405 TATATGTATAAACTA
1 TATAT-TATAAACTA
1047420 TA
1 TA
1047422 AAAAGTATAT
Statistics
Matches: 60, Mismatches: 6, Indels: 19
0.71 0.07 0.22
Matches are distributed among these distances:
13 16 0.27
14 4 0.07
15 27 0.45
16 4 0.07
17 4 0.07
18 5 0.08
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.44
Consensus pattern (14 bp):
TATATTATAAACTA
Found at i:1047470 original size:2 final size:2
Alignment explanation
Indices: 1047457--1047591 Score: 63
Period size: 2 Copynumber: 69.0 Consensus size: 2
1047447 ATTTATATTA
* * *
1047457 AT AT AGT AT AT AT AT AT A- AA ACT AT AT AT GT AT AA ACT AT AT
1 AT AT A-T AT AT AT AT AT AT AT A-T AT AT AT AT AT AT A-T AT AT
* * * *
1047499 AA ACT AT AT A- AT TT AT AT GT -T AT A- AT TT AT AT -T A- AT AT
1 AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
1047537 AGT AT AT AT GT AT GT AT A- ACT A- AT AT AT AG A- AT AT AT AT AT
1 A-T AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT
1047578 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
1047592 TAAAAACACT
Statistics
Matches: 101, Mismatches: 17, Indels: 30
0.68 0.11 0.20
Matches are distributed among these distances:
1 9 0.09
2 84 0.83
3 8 0.08
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.44
Consensus pattern (2 bp):
AT
Found at i:1047484 original size:16 final size:15
Alignment explanation
Indices: 1047463--1047499 Score: 56
Period size: 15 Copynumber: 2.4 Consensus size: 15
1047453 ATTAATATAG
1047463 TATATATATATAAAAC
1 TATATATATAT-AAAC
*
1047479 TATATATGTATAAAC
1 TATATATATATAAAC
1047494 TATATA
1 TATATA
1047500 AACTATATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 10 0.50
16 10 0.50
ACGTcount: A:0.51, C:0.05, G:0.03, T:0.41
Consensus pattern (15 bp):
TATATATATATAAAC
Found at i:1047490 original size:76 final size:75
Alignment explanation
Indices: 1047390--1047545 Score: 240
Period size: 76 Copynumber: 2.1 Consensus size: 75
1047380 TTATGTGAAC
* * *
1047390 TATATATATAAACTATATATGTATAAACTATAAAAAGTATATAGTTTATAAACTATTATTTATAT
1 TATATATATAAACTATATATGTATAAACTATAAAAACTATATAATTTATAAACTATAATTTATAT
1047455 TAATATAGTA
66 TAATATAGTA
* ***
1047465 TATATATATAAAACTATATATGTATAAACTATATAAACTATATAATTTATATGTTATAATTTATA
1 TATATATAT-AAACTATATATGTATAAACTATAAAAACTATATAATTTATAAACTATAATTTATA
1047530 TTAATATAGTA
65 TTAATATAGTA
1047541 TATAT
1 TATAT
1047546 GTATGTATAA
Statistics
Matches: 73, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
75 9 0.12
76 64 0.88
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.44
Consensus pattern (75 bp):
TATATATATAAACTATATATGTATAAACTATAAAAACTATATAATTTATAAACTATAATTTATAT
TAATATAGTA
Found at i:1047849 original size:42 final size:42
Alignment explanation
Indices: 1047803--1047912 Score: 193
Period size: 42 Copynumber: 2.6 Consensus size: 42
1047793 ACAATAGTTA
*
1047803 ATATATGTAACTTATAGTATGTGTATACATGCAATGTAAACT
1 ATATATGTAACTTATAGTATATGTATACATGCAATGTAAACT
*
1047845 ATATATGTAACTTATAGTATATGTATACATGTAATGTAAACT
1 ATATATGTAACTTATAGTATATGTATACATGCAATGTAAACT
*
1047887 ATATATGTAACTTATAGTACATGTAT
1 ATATATGTAACTTATAGTATATGTAT
1047913 GTATAAACTA
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 65 1.00
ACGTcount: A:0.39, C:0.08, G:0.13, T:0.40
Consensus pattern (42 bp):
ATATATGTAACTTATAGTATATGTATACATGCAATGTAAACT
Found at i:1047871 original size:24 final size:22
Alignment explanation
Indices: 1047844--1047936 Score: 54
Period size: 24 Copynumber: 4.3 Consensus size: 22
1047834 CAATGTAAAC
1047844 TATATATGTAACTTATAGTATATG
1 TATATATGTAAC-TAT-GTATATG
* **
1047868 TATACATGT-A--ATGTA-AAC
1 TATATATGTAACTATGTATATG
*
1047886 TATATATGTAACTTATAGTACATG
1 TATATATGTAAC-TAT-GTATATG
* *
1047910 TATGTAT-AAACTATGTATA-G
1 TATATATGTAACTATGTATATG
1047930 TATATAT
1 TATATAT
1047937 ATATATCATA
Statistics
Matches: 53, Mismatches: 10, Indels: 16
0.67 0.13 0.20
Matches are distributed among these distances:
18 9 0.17
19 4 0.08
20 9 0.17
21 4 0.08
22 5 0.09
23 7 0.13
24 15 0.28
ACGTcount: A:0.40, C:0.06, G:0.12, T:0.42
Consensus pattern (22 bp):
TATATATGTAACTATGTATATG
Found at i:1048055 original size:14 final size:14
Alignment explanation
Indices: 1048038--1048072 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
1048028 AACCTATTAC
1048038 CCTAAACTCTAAAT
1 CCTAAACTCTAAAT
*
1048052 CCTAAACTTTAAAT
1 CCTAAACTCTAAAT
*
1048066 CTTAAAC
1 CCTAAAC
1048073 CTTAACCCTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.43, C:0.26, G:0.00, T:0.31
Consensus pattern (14 bp):
CCTAAACTCTAAAT
Found at i:1048116 original size:18 final size:18
Alignment explanation
Indices: 1048093--1048127 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1048083 ACCTATGTAA
1048093 TTTACATATGAACTATAG
1 TTTACATATGAACTATAG
*
1048111 TTTACATATTAACTATA
1 TTTACATATGAACTATA
1048128 TATATAGTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.40, C:0.11, G:0.06, T:0.43
Consensus pattern (18 bp):
TTTACATATGAACTATAG
Found at i:1048212 original size:2 final size:2
Alignment explanation
Indices: 1048201--1048465 Score: 70
Period size: 2 Copynumber: 137.0 Consensus size: 2
1048191 AAAACAAAAT
*
1048201 TA TA -A TA TA TA TA TA TA TA TA TA -A TA TA -A GTT TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA
* * * * * *
1048241 AA CTA TA TA TA AA CTA TG TA TA TA AA CTA TA TA TG TA TA AA CTA
1 TA -TA TA TA TA TA -TA TA TA TA TA TA -TA TA TA TA TA TA TA -TA
* * * * *
1048285 TA AA AA GTA TA TA GTT TA -A AA AA TA TA -A CT- TA TA T- TA -A
1 TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA -TA TA TA TA TA TA
* *
1048323 TA T- TA -A TA TA TA TA TA TGA -A T- TA TA TA TG TA TA -A AA TA
1 TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA
* * *
1048361 TA TA GTT TA TA AA T- TA TA -A TT TA TA T- TA -A TA TA GTA TA TA
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA
* * * *
1048401 TA TG TA TG TA TA -A CTA -A TA TA -A GTA -A TC TA TA GA -A TA TA
1 TA TA TA TA TA TA TA -TA TA TA TA TA -TA TA TA TA TA TA TA TA TA
1048440 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
1048466 GTTTATAGAA
Statistics
Matches: 193, Mismatches: 35, Indels: 70
0.65 0.12 0.23
Matches are distributed among these distances:
1 22 0.11
2 159 0.82
3 12 0.06
ACGTcount: A:0.49, C:0.03, G:0.05, T:0.43
Consensus pattern (2 bp):
TA
Found at i:1048534 original size:7 final size:7
Alignment explanation
Indices: 1048522--1048578 Score: 50
Period size: 7 Copynumber: 8.6 Consensus size: 7
1048512 TAGTTGATAA
1048522 AAACCCT
1 AAACCCT
1048529 AAACCCT
1 AAACCCT
1048536 -AA--CT
1 AAACCCT
1048540 AAACACC-
1 AAAC-CCT
* *
1048547 GAACCTT
1 AAACCCT
1048554 AAACCCT
1 AAACCCT
*
1048561 AAACCTT
1 AAACCCT
1048568 AAACCCT
1 AAACCCT
1048575 AAAC
1 AAAC
1048579 ATTGTACATA
Statistics
Matches: 39, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
4 2 0.05
5 2 0.05
6 3 0.08
7 31 0.79
8 1 0.03
ACGTcount: A:0.46, C:0.37, G:0.02, T:0.16
Consensus pattern (7 bp):
AAACCCT
Found at i:1048565 original size:14 final size:14
Alignment explanation
Indices: 1048548--1048578 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
1048538 CTAAACACCG
1048548 AACCTTAAACCCTA
1 AACCTTAAACCCTA
1048562 AACCTTAAACCCTA
1 AACCTTAAACCCTA
1048576 AAC
1 AAC
1048579 ATTGTACATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.45, C:0.35, G:0.00, T:0.19
Consensus pattern (14 bp):
AACCTTAAACCCTA
Found at i:1048847 original size:21 final size:21
Alignment explanation
Indices: 1048795--1048847 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
1048785 TAGTGTACTA
* *
1048795 TATAGTTTATACTTTATAACC
1 TATAGTTTATAATTTATAAAC
* *
1048816 TATTGTATATAATTTATAAAC
1 TATAGTTTATAATTTATAAAC
1048837 TATAGTTTATA
1 TATAGTTTATA
1048848 TTAATGTTAA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.38, C:0.08, G:0.06, T:0.49
Consensus pattern (21 bp):
TATAGTTTATAATTTATAAAC
Found at i:1048899 original size:88 final size:88
Alignment explanation
Indices: 1048794--1048973 Score: 240
Period size: 88 Copynumber: 2.0 Consensus size: 88
1048784 TTAGTGTACT
* * *** *
1048794 ATATAGTTTATACTTTATAACCTATTGTATATAATTTATAA-ACTATAGTTTATATTAATGTTAA
1 ATATAGTATATACTTTATAAACTATACAATATAATTTATAACA-TATAGTTTATATTAATATTAA
1048858 TTATCT-TA-ACTATAATTTATATTA
65 TT-T-TATAGACTATAATTTATATTA
*
1048882 ATATAGTATATAGTTTATAAACTATACAATATAATTTATAACATATAGTTTATATTAATATTAAT
1 ATATAGTATATACTTTATAAACTATACAATATAATTTATAACATATAGTTTATATTAATATTAAT
*
1048947 TTTATAGACTATATTTTATATTA
66 TTTATAGACTATAATTTATATTA
1048970 ATAT
1 ATAT
1048974 TAATTACAAA
Statistics
Matches: 81, Mismatches: 8, Indels: 6
0.85 0.08 0.06
Matches are distributed among these distances:
86 1 0.01
87 3 0.04
88 76 0.94
89 1 0.01
ACGTcount: A:0.41, C:0.06, G:0.04, T:0.49
Consensus pattern (88 bp):
ATATAGTATATACTTTATAAACTATACAATATAATTTATAACATATAGTTTATATTAATATTAAT
TTTATAGACTATAATTTATATTA
Found at i:1048935 original size:21 final size:21
Alignment explanation
Indices: 1048794--1048935 Score: 60
Period size: 21 Copynumber: 6.6 Consensus size: 21
1048784 TTAGTGTACT
* *
1048794 ATATAGTTTATACTTTATAAC
1 ATATAGTATATAATTTATAAC
* *
1048815 CTATTGTATATAATTTATAA-
1 ATATAGTATATAATTTATAAC
*
1048835 ACTATAGTTTATATTAATGT-TAA-
1 A-TATAG--TATA-TAATTTATAAC
* **
1048858 TTATCTTAACTATAATTTATATTA-
1 ATATAGT-A-TATAATTTATA--AC
*
1048882 ATATAGTATATAGTTTATAA-
1 ATATAGTATATAATTTATAAC
**
1048902 ACTATACAATATAATTTATAAC
1 A-TATAGTATATAATTTATAAC
*
1048924 ATATAGTTTATA
1 ATATAGTATATA
1048936 TTAATATTAA
Statistics
Matches: 89, Mismatches: 21, Indels: 22
0.67 0.16 0.17
Matches are distributed among these distances:
20 3 0.03
21 50 0.56
22 18 0.20
23 8 0.09
24 10 0.11
ACGTcount: A:0.42, C:0.06, G:0.05, T:0.47
Consensus pattern (21 bp):
ATATAGTATATAATTTATAAC
Found at i:1048988 original size:88 final size:88
Alignment explanation
Indices: 1048822--1048995 Score: 230
Period size: 88 Copynumber: 2.0 Consensus size: 88
1048812 AACCTATTGT
*
1048822 ATATAATTTATAAACTATAGTTTATATTAATGTTAATTATCTTAACTATAATTTATATTAATATA
1 ATATAATTTATAAACTATAGTTTATATTAATATTAATTATCTTAACTATAATTTATATTAATATA
* * **
1048887 GTATATAGTTTATAAACTATACA
66 ATATACAAATTATAAACTATACA
*
1048910 ATATAATTTAT-AACATATAGTTTATATTAATATTAATT-T-TATAGACTATATTTTATATTAAT
1 ATATAATTTATAAAC-TATAGTTTATATTAATATTAATTATCT-TA-ACTATAATTTATATTAAT
1048972 ATTAAT-TACAAATTATAAACTATA
63 A-TAATATACAAATTATAAACTATA
1048996 TTATATTAAT
Statistics
Matches: 76, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
86 1 0.01
87 6 0.08
88 66 0.87
89 3 0.04
ACGTcount: A:0.44, C:0.05, G:0.03, T:0.47
Consensus pattern (88 bp):
ATATAATTTATAAACTATAGTTTATATTAATATTAATTATCTTAACTATAATTTATATTAATATA
ATATACAAATTATAAACTATACA
Found at i:1049019 original size:21 final size:19
Alignment explanation
Indices: 1048992--1049051 Score: 59
Period size: 21 Copynumber: 2.9 Consensus size: 19
1048982 AATTATAAAC
1048992 TATATTATATTAATATAAGT
1 TATATTATATTAATATAA-T
1049012 TAATATTA-ATTATATATAAT
1 T-ATATTATATTA-ATATAAT
*
1049032 TATTTTAATATTAATTATAA
1 TATATT-ATATTAA-TATAA
1049052 ATATCATTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
19 4 0.12
20 9 0.26
21 21 0.62
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (19 bp):
TATATTATATTAATATAAT
Found at i:1050590 original size:20 final size:20
Alignment explanation
Indices: 1050567--1050611 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
1050557 ATTCTATTTT
**
1050567 ATATTGTTTGCTTCTGTTTG
1 ATATTGTTTGCTTCTACTTG
*
1050587 ATATTGTTTGTTTCTACTTG
1 ATATTGTTTGCTTCTACTTG
1050607 ATATT
1 ATATT
1050612 TGTAAGGGTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.16, C:0.09, G:0.16, T:0.60
Consensus pattern (20 bp):
ATATTGTTTGCTTCTACTTG
Found at i:1050754 original size:23 final size:23
Alignment explanation
Indices: 1050704--1050757 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
1050694 CTTAATGCAG
* *
1050704 GATGCTTGTTGAATTGATGCAAT
1 GATGCTTGATGAATTGATACAAT
* * *
1050727 AATGCTTGATGAATTGGTACATT
1 GATGCTTGATGAATTGATACAAT
1050750 GATGCTTG
1 GATGCTTG
1050758 CCGGTTGCTG
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.26, C:0.09, G:0.26, T:0.39
Consensus pattern (23 bp):
GATGCTTGATGAATTGATACAAT
Found at i:1051549 original size:23 final size:24
Alignment explanation
Indices: 1051523--1051572 Score: 84
Period size: 23 Copynumber: 2.1 Consensus size: 24
1051513 TTATTTTTTC
1051523 TTTATATAAATTAAAATATA-TAA
1 TTTATATAAATTAAAATATATTAA
*
1051546 TTTATATAAATTAAACTATATTAA
1 TTTATATAAATTAAAATATATTAA
1051570 TTT
1 TTT
1051573 TCCTTTTGCA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
23 19 0.76
24 6 0.24
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (24 bp):
TTTATATAAATTAAAATATATTAA
Found at i:1051828 original size:16 final size:16
Alignment explanation
Indices: 1051807--1051893 Score: 120
Period size: 16 Copynumber: 5.4 Consensus size: 16
1051797 CGGATCATTT
1051807 ACAGGTCAGGTTAAAA
1 ACAGGTCAGGTTAAAA
*
1051823 ACAGGTTAGGTTAAAA
1 ACAGGTCAGGTTAAAA
1051839 ACAGGTCAGGTTAAAA
1 ACAGGTCAGGTTAAAA
* * *
1051855 ACATGTCAAGTTGAAA
1 ACAGGTCAGGTTAAAA
* *
1051871 ACAAGTCAGGTTGAAA
1 ACAGGTCAGGTTAAAA
1051887 ACAGGTC
1 ACAGGTC
1051894 GGGTAATACC
Statistics
Matches: 63, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 63 1.00
ACGTcount: A:0.43, C:0.13, G:0.24, T:0.21
Consensus pattern (16 bp):
ACAGGTCAGGTTAAAA
Found at i:1055205 original size:21 final size:21
Alignment explanation
Indices: 1055179--1055264 Score: 154
Period size: 21 Copynumber: 4.1 Consensus size: 21
1055169 GACCGAAATT
*
1055179 ACTGTAGCAGTGTATCGGTAC
1 ACTGTAGCAGTGCATCGGTAC
1055200 ACTGTAGCAGTGCATCGGTAC
1 ACTGTAGCAGTGCATCGGTAC
1055221 ACTGTAGCAGTGCATCGGTAC
1 ACTGTAGCAGTGCATCGGTAC
*
1055242 ACTGTAGCAGTGCATCGATAC
1 ACTGTAGCAGTGCATCGGTAC
1055263 AC
1 AC
1055265 ATTTTAAATT
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 63 1.00
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.24
Consensus pattern (21 bp):
ACTGTAGCAGTGCATCGGTAC
Found at i:1055310 original size:20 final size:21
Alignment explanation
Indices: 1055285--1055325 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
1055275 CGATGATTTT
*
1055285 GTGCATC-TACACTTTAGCAA
1 GTGCATCGTACACTATAGCAA
1055305 GTGCATCGGTACACTATAGCA
1 GTGCATC-GTACACTATAGCA
1055326 TTGGTCATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 7 0.39
22 11 0.61
ACGTcount: A:0.29, C:0.24, G:0.20, T:0.27
Consensus pattern (21 bp):
GTGCATCGTACACTATAGCAA
Done.