Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 ID=Chr04-JGI_221_v2.0
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: 62178258
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 912357 characters in sequence are not A, C, G, or T
File 186 of 198
Found at i:57905990 original size:53 final size:53
Alignment explanation
Indices: 57905932--57906049 Score: 182
Period size: 53 Copynumber: 2.2 Consensus size: 53
57905922 GCCTGAGAAC
*
57905932 ATTTATTTTTACCTCATTTCATTTTATATTTAAATTTTATATTTCCAATGGAA
1 ATTTATTTTTACCTCATTTCATTTTATATTTAAATTTTATATTTCCAATGCAA
** * *
57905985 ATTTATTTTTTTCTCATTTCATTTTATATTTAAATTTTCTATTTTCAATGCAA
1 ATTTATTTTTACCTCATTTCATTTTATATTTAAATTTTATATTTCCAATGCAA
*
57906038 ATTTGTTTTTAC
1 ATTTATTTTTAC
57906050 AAGAATATGC
Statistics
Matches: 57, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
53 57 1.00
ACGTcount: A:0.27, C:0.11, G:0.03, T:0.58
Consensus pattern (53 bp):
ATTTATTTTTACCTCATTTCATTTTATATTTAAATTTTATATTTCCAATGCAA
Found at i:57906041 original size:26 final size:26
Alignment explanation
Indices: 57905959--57906041 Score: 60
Period size: 26 Copynumber: 3.2 Consensus size: 26
57905949 TTCATTTTAT
* * *
57905959 ATTTAAATTTTATATTTCCAATGGAA
1 ATTTAAATTTTCTATTTTCAATGCAA
** * ** *
57905985 ATTTATTTTTTTCTCA-TTTCATTTTAT
1 ATTTA-AATTTTCT-ATTTTCAATGCAA
57906012 ATTTAAATTTTCTATTTTCAATGCAA
1 ATTTAAATTTTCTATTTTCAATGCAA
57906038 ATTT
1 ATTT
57906042 GTTTTTACAA
Statistics
Matches: 40, Mismatches: 14, Indels: 6
0.67 0.23 0.10
Matches are distributed among these distances:
25 1 0.03
26 22 0.55
27 16 0.40
28 1 0.03
ACGTcount: A:0.30, C:0.10, G:0.04, T:0.57
Consensus pattern (26 bp):
ATTTAAATTTTCTATTTTCAATGCAA
Found at i:57913785 original size:41 final size:42
Alignment explanation
Indices: 57913740--57913832 Score: 109
Period size: 41 Copynumber: 2.2 Consensus size: 42
57913730 AATATTTTTT
*
57913740 TAAAAGTCATGTTT-TTAGTGGCGTTCGTT-AAAAAGCGCCGC
1 TAAAAGTCATCTTTATT-GTGGCGTTCGTTGAAAAAGCGCCGC
* * * *
57913781 TAAAAGTCATCTTTATTGTGGCGTTTGTTGTAGAAGCGTCGC
1 TAAAAGTCATCTTTATTGTGGCGTTCGTTGAAAAAGCGCCGC
*
57913823 TAAAGGTCAT
1 TAAAAGTCAT
57913833 AGCCTTTAGC
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
41 24 0.55
42 20 0.45
ACGTcount: A:0.26, C:0.15, G:0.25, T:0.34
Consensus pattern (42 bp):
TAAAAGTCATCTTTATTGTGGCGTTCGTTGAAAAAGCGCCGC
Found at i:57913869 original size:43 final size:43
Alignment explanation
Indices: 57913822--57914020 Score: 229
Period size: 43 Copynumber: 4.7 Consensus size: 43
57913812 AGAAGCGTCG
* * *
57913822 CTAAAGGTCATAGCCTTTAGCAGCGTTTTTGGGAAAAGCGCCA
1 CTAAAGGTCATGGCCTTTAGCGGCGTTTGTGGGAAAAGCGCCA
*
57913865 CTAAAGGTCATGGCCTTTAGCGGCATTTGTGGGAAAAGCGCCA
1 CTAAAGGTCATGGCCTTTAGCGGCGTTTGTGGGAAAAGCGCCA
* * *
57913908 ATAAAGGTCATGGCCTATAGCGGCGTTTGTGGGAAAAGCGCCG
1 CTAAAGGTCATGGCCTTTAGCGGCGTTTGTGGGAAAAGCGCCA
* * * * ** *
57913951 CTAAAGGTCATGGTCTATAGTGGCGTTTTTCTG-AAAGCGCCG
1 CTAAAGGTCATGGCCTTTAGCGGCGTTTGTGGGAAAAGCGCCA
* * * *
57913993 CTAAAAGCCATGACCTTTGGCGGCGTTT
1 CTAAAGGTCATGGCCTTTAGCGGCGTTT
57914021 ATTTTAAAAA
Statistics
Matches: 135, Mismatches: 21, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
42 30 0.22
43 105 0.78
ACGTcount: A:0.25, C:0.21, G:0.29, T:0.26
Consensus pattern (43 bp):
CTAAAGGTCATGGCCTTTAGCGGCGTTTGTGGGAAAAGCGCCA
Found at i:57915247 original size:109 final size:110
Alignment explanation
Indices: 57914826--57915587 Score: 680
Period size: 111 Copynumber: 6.8 Consensus size: 110
57914816 TTGATAAATT
* * ** *
57914826 TGGTGTCGGCCATTGGCAGGCTACCACCAAAAGT-TTTTTTTTTTGAATTTTTTTTGTATACTGG
1 TGGTGCCGGCCATTGGCAGGCCACCACCAAAA-TAAATTTTTTTTGAA-TTTTTTCGTATACTGG
** * ******
57914890 TGCCGGTCAATGACAACCCAAAATGT-AAATTTTTTTTACATAAAGG
64 TGCCGACCAATGACAGCCCAAAATGTAAAAAAAAAATTACATAAAGG
* *
57914936 TGGTGCCGGCCATTGGCAGGCCACCACCAAAAAACTAAATTTTTTTTGAATTTTTTCTTGTACTG
1 TGGTGCCGGCCATTGGCAGGCCACCACC--AAAA-TAAATTTTTTTTGAATTTTTTCGTATACTG
* *
57915001 GTGCCAACCAATGACAGCCCAAAATGTAAAAAAAAAAATTTACATACAGG
63 GTGCCGACCAATGACAGCCCAAAATGT-AAAAAAAAAA-TTACATAAAGG
* * *
57915051 TGGTGCCGGTCATTGGTAGGCCACCACCAAAA-AAATATATTTTTTTAATTTTTTCGTATACTGG
1 TGGTGCCGGCCATTGGCAGGCCACCACCAAAATAAAT-T-TTTTTTGAATTTTTTCGTATACTGG
*
57915115 TGCC-AGCCAATGACAACCCAAAATGTAAAAAAAAAATTACATAAAGG
64 TGCCGA-CCAATGACAGCCCAAAATGTAAAAAAAAAATTACATAAAGG
* * *
57915162 TGGTGCCGGCAATAT-GCAGGCCACCACTAAAATAAATTTTTTTTGAA-TTTTTCGTATACTGAT
1 TGGTGCCGGCCAT-TGGCAGGCCACCACCAAAATAAATTTTTTTTGAATTTTTTCGTATACTGGT
* * ** *****
57915225 ACCGACTAATGACAGCCCAAAATGTAATTTATTTTTTTACATAAAGG
65 GCCGACCAATGACAGCCCAAAATGTAA-AAAAAAAATTACATAAAGG
* * * * * * * * *
57915272 TAGTGCCGGCCATTAGCAGGCCACTACCAAAAAAAAATTTCTCTGAATTTTTTTGTATATTGGTG
1 TGGTGCCGGCCATTGGCAGGCCACCACCAAAATAAATTTTTTTTGAATTTTTTCGTATACTGGTG
* *
57915337 CCGGCCAATAACAGCCCAAAATGTAAAAAAAAAAAATTACATAAAGG
66 CCGACCAATGACAGCCCAAAATGT--AAAAAAAAAATTACATAAAGG
* * * * *
57915384 TGGTGCCGGCCATTGGCAGGCCACCATC-AACT--TTTTTTTTTGAATTTTTTCGTATACCGGTA
1 TGGTGCCGGCCATTGGCAGGCCACCACCAAAATAAATTTTTTTTGAATTTTTTCGTATACTGGTG
* ******** *
57915446 CCGGCCAATGACAGCCCAAAATGTAATTCTTTTTTTTTTTACATAAAGA
66 CCGACCAATGACAGCCCAAAATGTAA----AAAAAAAATTACATAAAGG
* * * *
57915495 TGATGCCGGCCATTGACAGGCCACCACCAACAAAAAATTTTTTTTTTGAATCTTTT-GTATACTG
1 TGGTGCCGGCCATTGGCAGGCCACCACCAA-AATAAA--TTTTTTTTGAATTTTTTCGTATACTG
*
57915559 GTGCCGGCCAATGACAGCCCAAAATGTAA
63 GTGCCGACCAATGACAGCCCAAAATGTAA
57915588 TTTTTTTTTT
Statistics
Matches: 528, Mismatches: 97, Indels: 48
0.78 0.14 0.07
Matches are distributed among these distances:
107 2 0.00
109 83 0.16
110 84 0.16
111 112 0.21
112 94 0.18
113 63 0.12
114 3 0.01
115 36 0.07
116 35 0.07
117 16 0.03
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Consensus pattern (110 bp):
TGGTGCCGGCCATTGGCAGGCCACCACCAAAATAAATTTTTTTTGAATTTTTTCGTATACTGGTG
CCGACCAATGACAGCCCAAAATGTAAAAAAAAAATTACATAAAGG
Found at i:57915466 original size:220 final size:219
Alignment explanation
Indices: 57914832--57915587 Score: 776
Period size: 225 Copynumber: 3.4 Consensus size: 219
57914822 AATTTGGTGT
* **** * *
57914832 CGGCCATTGGCAGGCTACCACCAAAAGTTTTTTTTTTTGAATTTTTTTTGTATACTGGTGCCGGT
1 CGGCCATT-GCAGGCCACCACCAAAAAAAATATTTTTTGAA-TTTTTTTGTATACTGGTGCCGGC
* ******
57914897 CAATGACAACCCAAAATGT---AAATTTTTTTTACATAAAGGTGGTGCCGGCCATTGGCAGGCCA
64 CAATGACAGCCCAAAATGTAAAAAAAAAAAATTACATAAAGGTGGTGCCGGCCATTGGCAGGCCA
* * * * *
57914959 CCACCAAAAAACTAAATTTTTTTTGAATTTTTTCTTGTACTGGTGCCAACCAATGACAGCCCAAA
129 CCATC----AACT-AATTTTTTTTGAATTTTTTCGTATACTGGTACCGACCAATGACAGCCCAAA
*** **** *
57915024 ATGTAAAAAAAAAAATTTACATACAGGTGGTGC
189 ATGT-AATTTATTTTTTTACATAAAGGT-GTGC
* * * * *
57915057 CGGTCATTGGTAGGCCACCACCAAAAAAATATATTTTTTTAATTTTTTCGTATACTGGTGCCAGC
1 CGGCCATT-GCAGGCCACCACCAAAAAAA-ATATTTTTTGAATTTTTTTGTATACTGGTGCCGGC
* *
57915122 CAATGACAACCCAAAATGT--AAAAAAAAAATTACATAAAGGTGGTGCCGGCAATAT-GCAGGCC
64 CAATGACAGCCCAAAATGTAAAAAAAAAAAATTACATAAAGGTGGTGCCGGCCAT-TGGCAGGCC
* * * *
57915184 ACCACTAAAATAAATTTTTTTTGAA-TTTTTCGTATACTGATACCGACTAATGACAGCCCAAAAT
128 ACCA-TCAACT-AATTTTTTTTGAATTTTTTCGTATACTGGTACCGACCAATGACAGCCCAAAAT
57915248 GTAATTTATTTTTTTACATAAAGGTAGTGC
191 GTAATTTATTTTTTTACATAAAGGT-GTGC
* * *
57915278 CGGCCATTAGCAGGCCACTACCAAAAAAAA-ATTTCTCTGAATTTTTTTGTATATTGGTGCCGGC
1 CGGCCATT-GCAGGCCACCACCAAAAAAAATATTT-TTTGAATTTTTTTGTATACTGGTGCCGGC
*
57915342 CAATAACAGCCCAAAATGTAAAAAAAAAAAATTACATAAAGGTGGTGCCGGCCATTGGCAGGCCA
64 CAATGACAGCCCAAAATGTAAAAAAAAAAAATTACATAAAGGTGGTGCCGGCCATTGGCAGGCCA
* * *
57915407 CCATCAACT-TTTTTTTTTGAATTTTTTCGTATACCGGTACCGGCCAATGACAGCCCAAAATGTA
129 CCATCAACTAATTTTTTTTGAATTTTTTCGTATACTGGTACCGACCAATGACAGCCCAAAATGTA
* *
57915471 ATTCTTTTTTTTTTTACATAAAGATGATGC
194 A---TTTATTTTTTTACATAAAGGTG-TGC
* *
57915501 CGGCCATTGACAGGCCACCACCAACAAAAAATTTTTTTTTTGAA-TCTTTTGTATACTGGTGCCG
1 CGGCCATTG-CAGGCCACCACCAA-AAAAAA--TATTTTTTGAATTTTTTTGTATACTGGTGCCG
57915565 GCCAATGACAGCCCAAAATGTAA
62 GCCAATGACAGCCCAAAATGTAA
57915588 TTTTTTTTTT
Statistics
Matches: 449, Mismatches: 64, Indels: 36
0.82 0.12 0.07
Matches are distributed among these distances:
219 15 0.03
220 81 0.18
221 49 0.11
222 81 0.18
223 60 0.13
224 6 0.01
225 102 0.23
226 51 0.11
227 4 0.01
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.31
Consensus pattern (219 bp):
CGGCCATTGCAGGCCACCACCAAAAAAAATATTTTTTGAATTTTTTTGTATACTGGTGCCGGCCA
ATGACAGCCCAAAATGTAAAAAAAAAAAATTACATAAAGGTGGTGCCGGCCATTGGCAGGCCACC
ATCAACTAATTTTTTTTGAATTTTTTCGTATACTGGTACCGACCAATGACAGCCCAAAATGTAAT
TTATTTTTTTACATAAAGGTGTGC
Found at i:57915490 original size:333 final size:331
Alignment explanation
Indices: 57914861--57915597 Score: 862
Period size: 333 Copynumber: 2.2 Consensus size: 331
57914851 ACCAAAAGTT
* * *
57914861 TTTTTTTTTGAATTTTTTTTGTATACTGGTGCCGGTCAATGACAACCCAAAATGTAA-ATTTTTT
1 TTTTTTTTTGAA---TTTTTGTATACTGGTGCCGCT-AATGACAGCCCAAAATGTAATTTTTTTT
* * * *
57914925 TTACATAAAGGTGGTGCCGGCCATTGGCAGGCCACCACCAAAAAACTAAATTTTTTTTGAATTTT
62 TTACATAAAGGTAGTGCCGGCCATTAGCAGGCCACCACCAAAAAAC-AAATTTTCTCTGAATTTT
* * * *
57914990 TTCTTGTACTGGTGCCAACCAATGACAGCCCAAAATGTAAAAAAAAAAATTTACATACAGGTGGT
126 TTCTTATACTGGTGCCAACCAATAACAGCCCAAAATGTAAAAAAAAAAAATTACATAAAGGTGGT
* * * *
57915055 GCCGGTCATTGGTAGGCCACCACCAAAAAAATATATTTTTTTAATTTTTTCGTATACTGGTGCCA
191 GCCGGCCATTGGCAGGCCACCACC---AAAATATATTTTTTTAATTTTTTCGTATACCGGTACCA
* *
57915120 GCCAATGACAACCCAAAATGTAAAAAAAAAATTACATAAAGGTGGTGCCGGCAATATG-CAGGCC
253 GCCAATGACAACCCAAAATGTAAAAAAAAAATTACATAAAGATGATGCCGGCAAT-TGACAGGCC
* *
57915184 ACCACTAA-AATAAA
317 ACCACCAACAAAAAA
* *
57915198 -TTTTTTTTGAATTTTTCGTATACTGATACCGACTAATGACAGCCCAAAATGTAATTTATTTTTT
1 TTTTTTTTTGAATTTTT-GTATACTGGTGCCG-CTAATGACAGCCCAAAATGTAATTT-TTTTTT
*
57915262 TACATAAAGGTAGTGCCGGCCATTAGCAGGCCACTACCAAAAAA-AAA-TTTCTCTGAATTTTTT
63 TACATAAAGGTAGTGCCGGCCATTAGCAGGCCACCACCAAAAAACAAATTTTCTCTGAATTTTTT
* **
57915325 -TGTATATTGGTGCCGGCCAATAACAGCCCAAAATGTAAAAAAAAAAAATTACATAAAGGTGGTG
128 CT-TATACTGGTGCCAACCAATAACAGCCCAAAATGTAAAAAAAAAAAATTACATAAAGGTGGTG
* * * *
57915389 CCGGCCATTGGCAGGCCACCATC-AACT-TTTTTTTTTGAATTTTTTCGTATACCGGTACCGGCC
192 CCGGCCATTGGCAGGCCACCACCAAAATATATTTTTTT-AATTTTTTCGTATACCGGTACCAGCC
* ******** *
57915452 AATGACAGCCCAAAATGTAATTCTTTTTTTTTTTACATAAAGATGATGCCGGCCATTGACAGGCC
256 AATGACAACCCAAAATGTAA----AAAAAAAATTACATAAAGATGATGCCGGCAATTGACAGGCC
57915517 ACCACCAACAAAAAA
317 ACCACCAACAAAAAA
*
57915532 TTTTTTTTTTGAATCTTTTGTATACTGGTGCCGGCCAATGACAGCCCAAAATGTAATTTTTTTTT
1 -TTTTTTTTTGAAT-TTTTGTATACTGGTGCC-GCTAATGACAGCCCAAAATGTAATTTTTTTTT
57915597 T
63 T
57915598 TTTACAGAAT
Statistics
Matches: 342, Mismatches: 42, Indels: 34
0.82 0.10 0.08
Matches are distributed among these distances:
328 8 0.02
329 45 0.13
332 3 0.01
333 128 0.37
334 39 0.11
335 9 0.03
336 105 0.31
337 5 0.01
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Consensus pattern (331 bp):
TTTTTTTTTGAATTTTTGTATACTGGTGCCGCTAATGACAGCCCAAAATGTAATTTTTTTTTTAC
ATAAAGGTAGTGCCGGCCATTAGCAGGCCACCACCAAAAAACAAATTTTCTCTGAATTTTTTCTT
ATACTGGTGCCAACCAATAACAGCCCAAAATGTAAAAAAAAAAAATTACATAAAGGTGGTGCCGG
CCATTGGCAGGCCACCACCAAAATATATTTTTTTAATTTTTTCGTATACCGGTACCAGCCAATGA
CAACCCAAAATGTAAAAAAAAAATTACATAAAGATGATGCCGGCAATTGACAGGCCACCACCAAC
AAAAAA
Found at i:57916088 original size:10 final size:11
Alignment explanation
Indices: 57916071--57916155 Score: 80
Period size: 11 Copynumber: 8.5 Consensus size: 11
57916061 AGCCCATTTT
57916071 TATTTTAAAAA
1 TATTTTAAAAA
57916082 T-TTTT-AAAA
1 TATTTTAAAAA
*
57916091 -ATTTAAAAAA
1 TATTTTAAAAA
57916101 TATTTTAAAAA
1 TATTTTAAAAA
57916112 TATTTT--AAA
1 TATTTTAAAAA
57916121 -A--TTAAAAA
1 TATTTTAAAAA
*
57916129 -ATTTAAAAAA
1 TATTTTAAAAA
57916139 GTATTTTAAAAA
1 -TATTTTAAAAA
57916151 TATTT
1 TATTT
57916156 CCCGGGCCGA
Statistics
Matches: 61, Mismatches: 4, Indels: 18
0.73 0.05 0.22
Matches are distributed among these distances:
6 2 0.03
8 5 0.08
9 10 0.16
10 14 0.23
11 21 0.34
12 9 0.15
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (11 bp):
TATTTTAAAAA
Found at i:57916105 original size:11 final size:10
Alignment explanation
Indices: 57916074--57916155 Score: 66
Period size: 10 Copynumber: 8.3 Consensus size: 10
57916064 CCATTTTTAT
*
57916074 TTTAAAAATT
1 TTTAAAAATA
57916084 TTTAAAAAT-
1 TTTAAAAATA
*
57916093 TTAAAAAATA
1 TTTAAAAATA
57916103 TTTTAAAAATA
1 -TTTAAAAATA
*
57916114 TTT-TAAA-A
1 TTTAAAAATA
57916122 -TTAAAAA-A
1 TTTAAAAATA
57916130 TTTAAAAAAGTA
1 TTT-AAAAA-TA
57916142 TTTTAAAAATA
1 -TTTAAAAATA
57916153 TTT
1 TTT
57916156 CCCGGGCCGA
Statistics
Matches: 60, Mismatches: 4, Indels: 16
0.75 0.05 0.20
Matches are distributed among these distances:
7 2 0.03
8 5 0.08
9 13 0.22
10 20 0.33
11 11 0.18
12 6 0.10
13 3 0.05
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (10 bp):
TTTAAAAATA
Found at i:57916107 original size:30 final size:30
Alignment explanation
Indices: 57916071--57916151 Score: 107
Period size: 30 Copynumber: 2.8 Consensus size: 30
57916061 AGCCCATTTT
57916071 TATTTTAAAAAT-TTTTAAAAATTTAAAAAA
1 TATTTTAAAAATATTTTAAAAATTT-AAAAA
57916101 TATTTTAAAAATATTTT-AAAA-TTAAAAA
1 TATTTTAAAAATATTTTAAAAATTTAAAAA
*
57916129 -ATTTAAAAAAGTATTTTAAAAAT
1 TATTTTAAAAA-TATTTTAAAAAT
57916152 ATTTCCCGGG
Statistics
Matches: 46, Mismatches: 1, Indels: 8
0.84 0.02 0.15
Matches are distributed among these distances:
27 9 0.20
28 11 0.24
29 6 0.13
30 16 0.35
31 4 0.09
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (30 bp):
TATTTTAAAAATATTTTAAAAATTTAAAAA
Found at i:57916138 original size:17 final size:17
Alignment explanation
Indices: 57916105--57916137 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
57916095 AAAAAATATT
*
57916105 TTAAAAATATTTTAAAA
1 TTAAAAATATTTAAAAA
57916122 TTAAAAA-ATTTAAAAA
1 TTAAAAATATTTAAAAA
57916138 AGTATTTTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
TTAAAAATATTTAAAAA
Found at i:57917457 original size:18 final size:18
Alignment explanation
Indices: 57917434--57917468 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
57917424 TTTAAAATAA
57917434 AAAATAAA-AAAGTATTTT
1 AAAATAAATAAA-TATTTT
57917452 AAAATAAATAAATATTT
1 AAAATAAATAAATATTT
57917469 ATTATATTCG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 13 0.81
19 3 0.19
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (18 bp):
AAAATAAATAAATATTTT
Found at i:57919103 original size:14 final size:13
Alignment explanation
Indices: 57919015--57919117 Score: 62
Period size: 14 Copynumber: 7.3 Consensus size: 13
57919005 TCCTTTTCGT
*
57919015 TATTATTATTTTC
1 TATTATTATTTTA
57919028 TAGTTATTATATTTA
1 TA-TTATTAT-TTTA
*
57919043 TACTTATATATTTACA
1 TA-TTAT-TATTT-TA
* *
57919059 TTACTATTATATTA
1 -TATTATTATTTTA
* * *
57919073 TATCATTGGTTTCA
1 TATTATT-ATTTTA
57919087 TATTATTATTGTTA
1 TATTATTATT-TTA
*
57919101 TATTTTTATTTTA
1 TATTATTATTTTA
57919114 TATT
1 TATT
57919118 TACTTATTTA
Statistics
Matches: 68, Mismatches: 15, Indels: 14
0.70 0.15 0.14
Matches are distributed among these distances:
13 16 0.24
14 28 0.41
15 15 0.22
16 7 0.10
17 2 0.03
ACGTcount: A:0.29, C:0.06, G:0.04, T:0.61
Consensus pattern (13 bp):
TATTATTATTTTA
Found at i:57919186 original size:22 final size:24
Alignment explanation
Indices: 57919161--57919204 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
57919151 ATTATTACTA
57919161 TTATAAC-TATT-TATATATATCT
1 TTATAACTTATTATATATATATCT
*
57919183 TTATATCTTATTATATATATAT
1 TTATAACTTATTATATATATAT
57919205 ATATATCTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 6 0.32
23 4 0.21
24 9 0.47
ACGTcount: A:0.36, C:0.07, G:0.00, T:0.57
Consensus pattern (24 bp):
TTATAACTTATTATATATATATCT
Found at i:57919195 original size:32 final size:32
Alignment explanation
Indices: 57919159--57919219 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
57919149 TTATTATTAC
*
57919159 TATTATA-ACTATTTATATATATCTTTATATCT
1 TATTATATA-TATATATATATATCTTTATATCT
*
57919191 TATTATATATATATATATATCTCTTTATA
1 TATTATATATATATATATATATCTTTATA
57919220 AACATTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
32 25 0.96
33 1 0.04
ACGTcount: A:0.36, C:0.08, G:0.00, T:0.56
Consensus pattern (32 bp):
TATTATATATATATATATATATCTTTATATCT
Found at i:57919209 original size:22 final size:22
Alignment explanation
Indices: 57919171--57919212 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
57919161 TTATAACTAT
* *
57919171 TTATATATATCTTTATATCTTA
1 TTATATATATATATATATCTTA
57919193 TTATATATATATATATATCT
1 TTATATATATATATATATCT
57919213 CTTTATAAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.36, C:0.07, G:0.00, T:0.57
Consensus pattern (22 bp):
TTATATATATATATATATCTTA
Found at i:57919218 original size:22 final size:21
Alignment explanation
Indices: 57919170--57919219 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 21
57919160 ATTATAACTA
* *
57919170 TTTATATATATCTTTATATCT
1 TTTATATATATATATATATCT
57919191 TATTATATATATATATATATCT
1 T-TTATATATATATATATATCT
57919213 CTTTATA
1 -TTTATA
57919220 AACATTTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 1 0.04
22 23 0.92
23 1 0.04
ACGTcount: A:0.34, C:0.08, G:0.00, T:0.58
Consensus pattern (21 bp):
TTTATATATATATATATATCT
Found at i:57919409 original size:16 final size:16
Alignment explanation
Indices: 57919388--57919422 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
57919378 TTTTTATATG
*
57919388 TATTTTATTATTTTCA
1 TATTTTATGATTTTCA
*
57919404 TATTTTATGATTTTTA
1 TATTTTATGATTTTCA
57919420 TAT
1 TAT
57919423 ACCTACATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.69
Consensus pattern (16 bp):
TATTTTATGATTTTCA
Found at i:57921849 original size:26 final size:26
Alignment explanation
Indices: 57921819--57921881 Score: 72
Period size: 26 Copynumber: 2.4 Consensus size: 26
57921809 AAAATATAAC
**
57921819 AAATATATATGTATATATAAATTATA
1 AAATATATATACATATATAAATTATA
* **
57921845 AAATATATGTACATATATGCATTATA
1 AAATATATATACATATATAAATTATA
*
57921871 AAATGTATATA
1 AAATATATATA
57921882 AGTATACGTA
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.51, C:0.03, G:0.06, T:0.40
Consensus pattern (26 bp):
AAATATATATACATATATAAATTATA
Found at i:57921998 original size:2 final size:2
Alignment explanation
Indices: 57921991--57922033 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
57921981 AGAATGCATG
*
57921991 TA TA TA TA TG TA TA TA 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 TA TA TA TA TA TA TA TA
57922033 T
1 T
57922034 TTTAAAGTTA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:57922410 original size:27 final size:28
Alignment explanation
Indices: 57922365--57922436 Score: 71
Period size: 27 Copynumber: 2.7 Consensus size: 28
57922355 ATAATAAATA
* ** *
57922365 ATAATGATACAATGCTAATAGTAT-AAT
1 ATAATGATAAAATAATAATAGCATGAAT
57922392 ATAATGATAAAATAATAAT-GCATGAAT
1 ATAATGATAAAATAATAATAGCATGAAT
*
57922419 A-AAT-ATAAAATAAAAATA
1 ATAATGATAAAATAATAATA
57922437 TAAGTATGAT
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
25 12 0.32
26 6 0.16
27 20 0.53
ACGTcount: A:0.58, C:0.04, G:0.08, T:0.29
Consensus pattern (28 bp):
ATAATGATAAAATAATAATAGCATGAAT
Found at i:57927786 original size:16 final size:16
Alignment explanation
Indices: 57927765--57927816 Score: 95
Period size: 16 Copynumber: 3.2 Consensus size: 16
57927755 TTTGGTTCGC
*
57927765 TGTATTGGATTAGAGT
1 TGTATTGGATTAGAGG
57927781 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
57927797 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
57927813 TGTA
1 TGTA
57927817 ATAGCTAATC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 35 1.00
ACGTcount: A:0.25, C:0.00, G:0.35, T:0.40
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:57927881 original size:44 final size:45
Alignment explanation
Indices: 57927797--57927887 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
57927787 GGATTAGAGG
* * *
57927797 TGTATTGGATTAGAGGTGTAATAGCTAATCCACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
***
57927842 TGTAATGGAATAGAGGCGTAATAG-TAATCTTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
57927886 TG
1 TG
57927888 GAATAGAGGT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 19 0.47
45 21 0.52
ACGTcount: A:0.27, C:0.07, G:0.29, T:0.37
Consensus pattern (45 bp):
TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
Found at i:57928361 original size:122 final size:121
Alignment explanation
Indices: 57928034--57928617 Score: 1010
Period size: 121 Copynumber: 4.8 Consensus size: 121
57928024 ATCATATTTA
* * *
57928034 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTAAAAAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATAAATTTTAATTAAACTATATAATTTAAAAAAATTCTTAATAATTAA
*
57928099 TATTCTTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
*
57928155 AACATAATTATTATTAAATAAATTTTAATTAAACTATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATAAATTTTAATTAAACTATATAATTTAAAAAAATTCTTAATAATTAA
57928220 TATTCTTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
57928276 AACATAATTTATTATTAAATAAATTTTAATTAAACTATATAATTTAAAAAAATTCTTAATAATTA
1 AACATAA-TTATTATTAAATAAATTTTAATTAAACTATATAATTTAAAAAAATTCTTAATAATTA
*
57928341 ATATTCTTTATATTAATTTACTCACATCATAATATATGATACTGTAAAATATAAATT
65 ATATTCTTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
*
57928398 AACATAATTATTATTAAATAAATTTTAATTAAACTATATATTTTAAAAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATAAATTTTAATTAAACTATATAATTTAAAAAAATTCTTAATAATTAA
*
57928463 TATTCTTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
* * * * *
57928519 AACATAATATATGATTAAATATATTTTAATTGAACAATATAATTTAATAAAATTCTTAATAATTA
1 AACATAAT-TATTATTAAATAAATTTTAATTAAACTATATAATTTAAAAAAATTCTTAATAATTA
57928584 ATATTC-TTATATTAATTTAAC-CAAATCATAATAT
65 ATATTCTTTATATTAATTT-ACTCAAATCATAATAT
57928618 TCTTAATAAT
Statistics
Matches: 443, Mismatches: 17, Indels: 6
0.95 0.04 0.01
Matches are distributed among these distances:
121 266 0.60
122 177 0.40
ACGTcount: A:0.48, C:0.06, G:0.02, T:0.43
Consensus pattern (121 bp):
AACATAATTATTATTAAATAAATTTTAATTAAACTATATAATTTAAAAAAATTCTTAATAATTAA
TATTCTTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
Found at i:57928469 original size:243 final size:243
Alignment explanation
Indices: 57928034--57928617 Score: 1021
Period size: 243 Copynumber: 2.4 Consensus size: 243
57928024 ATCATATTTA
* *
57928034 AACATAA-TTATTATTAAATATATTTTAATTAAAATATATAATTAAAAAAAATTCTTAATAATTA
1 AACATAATTTATTATTAAATATATTTTAATTAAACTATATAATTTAAAAAAATTCTTAATAATTA
*
57928098 ATATTCTTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATTAACATAAT
66 ATATTCTTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATTAACATAAT
*
57928163 TATTATTAAATAAATTTTAATTAAACTATATAATTTAATAAAATTCTTAATAATTAATATTCTTT
131 TATTATTAAATAAATTTTAATTAAACTATATAATTTAAAAAAATTCTTAATAATTAATATTCTTT
57928228 ATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
196 ATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
*
57928276 AACATAATTTATTATTAAATAAATTTTAATTAAACTATATAATTTAAAAAAATTCTTAATAATTA
1 AACATAATTTATTATTAAATATATTTTAATTAAACTATATAATTTAAAAAAATTCTTAATAATTA
*
57928341 ATATTCTTTATATTAATTTACTCACATCATAATATATGATACTGTAAAATATAAATTAACATAAT
66 ATATTCTTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATTAACATAAT
*
57928406 TATTATTAAATAAATTTTAATTAAACTATATATTTTAAAAAAATTCTTAATAATTAATATTCTTT
131 TATTATTAAATAAATTTTAATTAAACTATATAATTTAAAAAAATTCTTAATAATTAATATTCTTT
*
57928471 ATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
196 ATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
* * * * *
57928519 AACATAATATATGATTAAATATATTTTAATTGAACAATATAATTTAATAAAATTCTTAATAATTA
1 AACATAATTTATTATTAAATATATTTTAATTAAACTATATAATTTAAAAAAATTCTTAATAATTA
57928584 ATATTC-TTATATTAATTTAAC-CAAATCATAATAT
66 ATATTCTTTATATTAATTT-ACTCAAATCATAATAT
57928618 TCTTAATAAT
Statistics
Matches: 325, Mismatches: 15, Indels: 4
0.94 0.04 0.01
Matches are distributed among these distances:
242 31 0.10
243 294 0.90
ACGTcount: A:0.48, C:0.06, G:0.02, T:0.43
Consensus pattern (243 bp):
AACATAATTTATTATTAAATATATTTTAATTAAACTATATAATTTAAAAAAATTCTTAATAATTA
ATATTCTTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATTAACATAAT
TATTATTAAATAAATTTTAATTAAACTATATAATTTAAAAAAATTCTTAATAATTAATATTCTTT
ATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
Found at i:57928599 original size:14 final size:16
Alignment explanation
Indices: 57928570--57928638 Score: 65
Period size: 16 Copynumber: 4.4 Consensus size: 16
57928560 ATTTAATAAA
57928570 ATTCTTAATAATTAAT
1 ATTCTTAATAATTAAT
57928586 ATTCTT-AT-ATTAAT
1 ATTCTTAATAATTAAT
** *
57928600 -TTAACCAAATCA-TAAT
1 ATT--CTTAATAATTAAT
57928616 ATTCTTAATAATTAAT
1 ATTCTTAATAATTAAT
57928632 ATTCTTA
1 ATTCTTA
57928639 TATTAACTTA
Statistics
Matches: 42, Mismatches: 5, Indels: 12
0.71 0.08 0.20
Matches are distributed among these distances:
13 2 0.05
14 6 0.14
15 8 0.19
16 23 0.55
17 3 0.07
ACGTcount: A:0.42, C:0.10, G:0.00, T:0.48
Consensus pattern (16 bp):
ATTCTTAATAATTAAT
Found at i:57932989 original size:21 final size:21
Alignment explanation
Indices: 57932946--57933001 Score: 76
Period size: 21 Copynumber: 2.6 Consensus size: 21
57932936 AAGCAGATGG
* *
57932946 AGCCGCTGCAAATTAATTATAT
1 AGCCACTGCAAA-CAATTATAT
*
57932968 AGCCACTGCAAACAATTGTAT
1 AGCCACTGCAAACAATTATAT
57932989 AGCCACTGCAAAC
1 AGCCACTGCAAAC
57933002 GGGGGAAACT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
21 20 0.65
22 11 0.35
ACGTcount: A:0.38, C:0.25, G:0.14, T:0.23
Consensus pattern (21 bp):
AGCCACTGCAAACAATTATAT
Found at i:57938078 original size:30 final size:29
Alignment explanation
Indices: 57938042--57938128 Score: 75
Period size: 31 Copynumber: 2.9 Consensus size: 29
57938032 AATATTTTAT
57938042 ATTTTTATAAATTTTAAAGAATTAAATCAA
1 ATTTTTATAAATTTTAAA-AATTAAATCAA
* * * * *
57938072 ATTTTTATTATTTTTATAATCATTAATTTAA
1 ATTTTTATAAATTTTA-AA-AATTAAATCAA
* * *
57938103 AATTTTATAAATTATAAAAAATAAAT
1 ATTTTTATAAATTTTAAAAATTAAAT
57938129 AAAAAAATTT
Statistics
Matches: 43, Mismatches: 13, Indels: 3
0.73 0.22 0.05
Matches are distributed among these distances:
29 5 0.12
30 16 0.37
31 22 0.51
ACGTcount: A:0.48, C:0.02, G:0.01, T:0.48
Consensus pattern (29 bp):
ATTTTTATAAATTTTAAAAATTAAATCAA
Found at i:57938315 original size:16 final size:16
Alignment explanation
Indices: 57938294--57938324 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
57938284 CTTTTTTACT
57938294 GGCCCAACAAGTAAAG
1 GGCCCAACAAGTAAAG
*
57938310 GGCCCAACAATTAAA
1 GGCCCAACAAGTAAA
57938325 AGGCTAAGCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.45, C:0.26, G:0.19, T:0.10
Consensus pattern (16 bp):
GGCCCAACAAGTAAAG
Found at i:57946532 original size:132 final size:132
Alignment explanation
Indices: 57945900--57946517 Score: 952
Period size: 132 Copynumber: 4.7 Consensus size: 132
57945890 GTGATGATAA
* **
57945900 CAGATCTTGCCTCCCTAAGCAGTAGTGGGGCAGATCAAAGATGGCGGATTTTACCTCCCTGAAAT
1 CAGATCTTGCCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCGGATTTTACCTCCCTGAGGT
*
57945965 TGCAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGCAGCAGCGGAATAAATTGAAGAT
66 TGCAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGCAGCAGCGGAATAGATTGAAGAT
*
57946030 TA
131 TT
*
57946032 CAGATCTTGCCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAGATTTTACCTCCCTGAGGT
1 CAGATCTTGCCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCGGATTTTACCTCCCTGAGGT
*
57946097 TGCAGTGGAGTACATTGAAGCCAG-AATTTCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAGA
66 TGCAGTGGAGTACATTGAAGCCAGTAA-TTCTACTTCCCTGGGCAGCAGCGGAATAGATTGAAGA
57946161 TTT
130 TTT
* * * *
57946164 TAGATCTTGTCTCCCTAAGCAATAGTGGAGCAGATCAAAGATGGCGGATTTTACCTCCCTGAAGT
1 CAGATCTTGCCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCGGATTTTACCTCCCTGAGGT
* *
57946229 TGCAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTAGGCAGCAGCGAAATAGATTGAAGAT
66 TGCAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGCAGCAGCGGAATAGATTGAAGAT
57946294 TT
131 TT
*
57946296 CAGATCTTGCCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCGGATTTTACCTCCCTGTGGT
1 CAGATCTTGCCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCGGATTTTACCTCCCTGAGGT
* * * * *
57946361 TACAGTGGAGTACATTGAAACCAGTAATTTTA-TCTCCCTGGGCAGCAGTGGAATAGATTGAGGA
66 TGCAGTGGAGTACATTGAAGCCAGTAATTCTACT-TCCCTGGGCAGCAGCGGAATAGATTGAAGA
57946425 TTT
130 TTT
** * * * * * *
57946428 CAGATCTTGTTTCTCTAAGCAGTGGTGGAGCAGATCAAAGATAGTGGATTTTACCTCCCTGTGTT
1 CAGATCTTGCCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCGGATTTTACCTCCCTGAGGT
*
57946493 TACAGTGGAGTACATTGAAGCCAGT
66 TGCAGTGGAGTACATTGAAGCCAGT
57946518 TACCCTATTT
Statistics
Matches: 448, Mismatches: 35, Indels: 6
0.92 0.07 0.01
Matches are distributed among these distances:
131 3 0.01
132 443 0.99
133 2 0.00
ACGTcount: A:0.28, C:0.20, G:0.25, T:0.27
Consensus pattern (132 bp):
CAGATCTTGCCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCGGATTTTACCTCCCTGAGGT
TGCAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGCAGCAGCGGAATAGATTGAAGAT
TT
Found at i:57947011 original size:16 final size:16
Alignment explanation
Indices: 57946990--57947020 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
57946980 CTTTTTTACT
57946990 GGCCCAACAAGTAAAG
1 GGCCCAACAAGTAAAG
*
57947006 GGCCCAACAATTAAA
1 GGCCCAACAAGTAAA
57947021 AGGCTAAGCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.45, C:0.26, G:0.19, T:0.10
Consensus pattern (16 bp):
GGCCCAACAAGTAAAG
Found at i:57948045 original size:3 final size:3
Alignment explanation
Indices: 57948037--57948086 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
57948027 ATACTATGAC
57948037 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
57948085 TT
1 TT
57948087 CCTACTATAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:57950227 original size:20 final size:21
Alignment explanation
Indices: 57950171--57950230 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 21
57950161 ACACCTTATT
57950171 ATTATCATTATAGAATAATTG
1 ATTATCATTATAGAATAATTG
* *
57950192 ATTAT--TTAAATTAATAATT-
1 ATTATCATTATA-GAATAATTG
*
57950211 TTTATCATTATAGAATAATT
1 ATTATCATTATAGAATAATT
57950231 CTTAATTTTT
Statistics
Matches: 31, Mismatches: 5, Indels: 7
0.72 0.12 0.16
Matches are distributed among these distances:
19 8 0.26
20 14 0.45
21 9 0.29
ACGTcount: A:0.43, C:0.03, G:0.05, T:0.48
Consensus pattern (21 bp):
ATTATCATTATAGAATAATTG
Found at i:57952745 original size:2 final size:2
Alignment explanation
Indices: 57952738--57952764 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
57952728 TATAATACTA
57952738 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 A
57952765 ATTCAACACA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:57953131 original size:15 final size:15
Alignment explanation
Indices: 57953106--57953141 Score: 63
Period size: 15 Copynumber: 2.3 Consensus size: 15
57953096 TAAAACCCAA
57953106 TAAACTTTAACTAAAT
1 TAAA-TTTAACTAAAT
57953122 TAAATTTAACTAAAT
1 TAAATTTAACTAAAT
57953137 TAAAT
1 TAAAT
57953142 ATTTTAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 16 0.80
16 4 0.20
ACGTcount: A:0.53, C:0.08, G:0.00, T:0.39
Consensus pattern (15 bp):
TAAATTTAACTAAAT
Found at i:57953825 original size:10 final size:10
Alignment explanation
Indices: 57953809--57953848 Score: 50
Period size: 10 Copynumber: 4.2 Consensus size: 10
57953799 TACTTAAATT
57953809 TTTTAA-ATA
1 TTTTAATATA
57953818 TGTTTAA-A-A
1 T-TTTAATATA
57953827 TTTTAATATA
1 TTTTAATATA
57953837 TTTTAATATA
1 TTTTAATATA
57953847 TT
1 TT
57953849 AAGTATATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
8 5 0.18
9 4 0.14
10 19 0.68
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (10 bp):
TTTTAATATA
Found at i:57953830 original size:19 final size:18
Alignment explanation
Indices: 57953809--57953857 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
57953799 TACTTAAATT
57953809 TTTTAA-ATATGTTTAAAA
1 TTTTAATATAT-TTTAAAA
*
57953827 TTTTAATATATTTTAATA
1 TTTTAATATATTTTAAAA
*
57953845 TATTAAGTATATT
1 TTTTAA-TATATT
57953858 AAAAACTTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
18 17 0.63
19 10 0.37
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (18 bp):
TTTTAATATATTTTAAAA
Found at i:57953917 original size:17 final size:17
Alignment explanation
Indices: 57953891--57953981 Score: 80
Period size: 17 Copynumber: 5.3 Consensus size: 17
57953881 CAACCTTTTC
*
57953891 TTTAACATATTTAAAAT
1 TTTAATATATTTAAAAT
**
57953908 TTTAATATATTTAAGTTT
1 TTTAATATATTTAA-AAT
*
57953926 TTTAA-AAATTTTAAAAT
1 TTTAATATA-TTTAAAAT
*
57953943 ATTGAATATA-TTAAAAT
1 -TTTAATATATTTAAAAT
57953960 TTGTAATATA-TTAAAAT
1 TT-TAATATATTTAAAAT
57953977 TTTAA
1 TTTAA
57953982 AATTGGTTAT
Statistics
Matches: 60, Mismatches: 9, Indels: 11
0.75 0.11 0.14
Matches are distributed among these distances:
16 5 0.08
17 38 0.63
18 15 0.25
19 2 0.03
ACGTcount: A:0.46, C:0.01, G:0.03, T:0.49
Consensus pattern (17 bp):
TTTAATATATTTAAAAT
Found at i:57953920 original size:9 final size:9
Alignment explanation
Indices: 57953891--57953984 Score: 56
Period size: 9 Copynumber: 10.9 Consensus size: 9
57953881 CAACCTTTTC
*
57953891 TTTAACATA
1 TTTAAAATA
57953900 TTTAAAAT-
1 TTTAAAATA
*
57953908 TTTAATATA
1 TTTAAAATA
** *
57953917 TTTAAGTTT
1 TTTAAAATA
57953926 TTTAAAA-A
1 TTTAAAATA
57953934 TTTTAAAATA
1 -TTTAAAATA
* *
57953944 TTGAATATA
1 TTTAAAATA
57953953 -TTAAAAT-
1 TTTAAAATA
*
57953960 TTGTAATATA
1 TT-TAAAATA
57953970 -TTAAAAT-
1 TTTAAAATA
57953977 TTTAAAAT
1 TTTAAAAT
57953985 TGGTTATACT
Statistics
Matches: 64, Mismatches: 14, Indels: 15
0.69 0.15 0.16
Matches are distributed among these distances:
8 25 0.39
9 38 0.59
10 1 0.02
ACGTcount: A:0.47, C:0.01, G:0.03, T:0.49
Consensus pattern (9 bp):
TTTAAAATA
Found at i:57953920 original size:26 final size:26
Alignment explanation
Indices: 57953891--57953985 Score: 88
Period size: 25 Copynumber: 3.7 Consensus size: 26
57953881 CAACCTTTTC
*
57953891 TTTAACATATTTAAAATTTTAATATA
1 TTTAAAATATTTAAAATTTTAATATA
** * *
57953917 TTTAAGTTTTTTAAAAATTTTAAAATA
1 TTTAAAATATTT-AAAATTTTAATATA
* *
57953944 TTGAATATA-TTAAAATTTGTAATATA
1 TTTAAAATATTTAAAATTT-TAATATA
57953970 -TTAAAAT-TTTAAAATT
1 TTTAAAATATTTAAAATT
57953986 GGTTATACTT
Statistics
Matches: 55, Mismatches: 11, Indels: 7
0.75 0.15 0.10
Matches are distributed among these distances:
25 20 0.36
26 17 0.31
27 18 0.33
ACGTcount: A:0.46, C:0.01, G:0.03, T:0.49
Consensus pattern (26 bp):
TTTAAAATATTTAAAATTTTAATATA
Found at i:57953940 original size:80 final size:78
Alignment explanation
Indices: 57953786--57953941 Score: 179
Period size: 80 Copynumber: 2.0 Consensus size: 78
57953776 AAAAAATATT
* * *
57953786 TTAAAATTAGTTATACTTAAATTTTTTAAATATGTTTAAAATTTTAATATATTTTAATATATTAA
1 TTAAAATTAGTTATACTCAAATTTTTTAAACATATTTAAAATTTTAATATATTTTAATATATTAA
**
57953851 GTATATTAAAAAC
66 AAATATTAAAAAC
* * * * *
57953864 TTAAAATTGGTTATACTCAACCTTTTCTTTAACATATTTAAAATTTTAATATA-TTTAAGTTTTT
1 TTAAAATTAGTTATACTCAA-ATTTT-TTAAACATATTTAAAATTTTAATATATTTTAA-TATAT
*
57953928 TAAAAATTTTAAAA
63 TAAAAATATTAAAA
57953942 TATTGAATAT
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
78 18 0.28
79 9 0.14
80 37 0.58
ACGTcount: A:0.42, C:0.05, G:0.04, T:0.49
Consensus pattern (78 bp):
TTAAAATTAGTTATACTCAAATTTTTTAAACATATTTAAAATTTTAATATATTTTAATATATTAA
AAATATTAAAAAC
Found at i:57953983 original size:8 final size:8
Alignment explanation
Indices: 57953900--57953985 Score: 55
Period size: 8 Copynumber: 10.1 Consensus size: 8
57953890 CTTTAACATA
57953900 TTTAAAAT
1 TTTAAAAT
*
57953908 TTTAATAT
1 TTTAAAAT
**
57953916 ATTTAAGTTT
1 -TTTAA-AAT
57953926 TTTAAAAAT
1 TTT-AAAAT
57953935 TTTAAAAT
1 TTTAAAAT
* *
57953943 ATTGAATAT
1 -TTTAAAAT
*
57953952 ATTAAAAT
1 TTTAAAAT
*
57953960 TTGTAATAT
1 TT-TAAAAT
*
57953969 ATTAAAAT
1 TTTAAAAT
57953977 TTTAAAAT
1 TTTAAAAT
57953985 T
1 T
57953986 GGTTATACTT
Statistics
Matches: 59, Mismatches: 14, Indels: 10
0.71 0.17 0.12
Matches are distributed among these distances:
8 31 0.53
9 24 0.41
10 4 0.07
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (8 bp):
TTTAAAAT
Found at i:57954034 original size:59 final size:61
Alignment explanation
Indices: 57953968--57954103 Score: 222
Period size: 59 Copynumber: 2.2 Consensus size: 61
57953958 ATTTGTAATA
57953968 TATTAAAATTTTAAAATTGGTTATACTTAACA-TTTTTAATATATTT-ATTTTTTTAAAAT
1 TATTAAAATTTTAAAATTGGTTATACTTAACATTTTTTAATATATTTAATTTTTTTAAAAT
**
57954027 TATTAAAATTTTAAAATTGGTTATACTTAACATTTTTTAATATATTTAAATTTTTTTAAGTT
1 TATTAAAATTTTAAAATTGGTTATACTTAACATTTTTTAATATATTT-AATTTTTTTAAAAT
*
57954089 TTTTAAAATTTTAAA
1 TATTAAAATTTTAAA
57954104 TATATAGATA
Statistics
Matches: 71, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
59 32 0.45
60 14 0.20
62 25 0.35
ACGTcount: A:0.39, C:0.03, G:0.04, T:0.54
Consensus pattern (61 bp):
TATTAAAATTTTAAAATTGGTTATACTTAACATTTTTTAATATATTTAATTTTTTTAAAAT
Found at i:57954199 original size:15 final size:15
Alignment explanation
Indices: 57954183--57954214 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
57954173 AAATTAGTTA
57954183 AAAT-AATAATAAAT
1 AAATAAATAATAAAT
57954197 AAATAAATAATAAA-
1 AAATAAATAATAAAT
57954211 AAAT
1 AAAT
57954215 GATAGATTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (15 bp):
AAATAAATAATAAAT
Found at i:57954607 original size:31 final size:31
Alignment explanation
Indices: 57954514--57954609 Score: 165
Period size: 31 Copynumber: 3.1 Consensus size: 31
57954504 AGCAAATTAC
*
57954514 AAGAGTAATTGAATCCTAATAAAACTCTTTC
1 AAGAGTAATTGAATCCTAATAAAACTCTTTA
57954545 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
1 AAGAGTAATTGAATCCTAAT-AAAACTCTTTA
*
57954577 AAGAGTAATTGACTCCTAATAAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAACTCTTTA
57954608 AA
1 AA
57954610 ATTATCTAAG
Statistics
Matches: 62, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
31 33 0.53
32 29 0.47
ACGTcount: A:0.45, C:0.15, G:0.09, T:0.31
Consensus pattern (31 bp):
AAGAGTAATTGAATCCTAATAAAACTCTTTA
Found at i:57955006 original size:21 final size:20
Alignment explanation
Indices: 57954975--57955045 Score: 67
Period size: 21 Copynumber: 3.5 Consensus size: 20
57954965 TGTCTTTACC
57954975 TATTAAAAATTTATATTAAGTA
1 TATT-AAAATTTATATTAA-TA
57954997 TATTAAAATTT-TA--AATA
1 TATTAAAATTTATATTAATA
* **
57955014 TGTTAAAAAATATATTAAATA
1 TATTAAAATTTATATT-AATA
57955035 TATTAAAATTT
1 TATTAAAATTT
57955046 TAAAATTAAT
Statistics
Matches: 39, Mismatches: 6, Indels: 9
0.72 0.11 0.17
Matches are distributed among these distances:
17 10 0.26
18 4 0.10
20 2 0.05
21 19 0.49
22 4 0.10
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (20 bp):
TATTAAAATTTATATTAATA
Found at i:57955033 original size:9 final size:9
Alignment explanation
Indices: 57954986--57955041 Score: 51
Period size: 9 Copynumber: 6.0 Consensus size: 9
57954976 ATTAAAAATT
*
57954986 TATATTAAG
1 TATATTAAA
57954995 TATATTAAA
1 TATATTAAA
*
57955004 -ATTTTAAA
1 TATATTAAA
*
57955012 TATGTTAAAAAA
1 TATATT---AAA
57955024 TATATTAAA
1 TATATTAAA
57955033 TATATTAAA
1 TATATTAAA
57955042 ATTTTAAAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
8 7 0.18
9 24 0.62
12 8 0.21
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.43
Consensus pattern (9 bp):
TATATTAAA
Found at i:57955322 original size:99 final size:97
Alignment explanation
Indices: 57955140--57955330 Score: 292
Period size: 99 Copynumber: 1.9 Consensus size: 97
57955130 GGTGGCGCCG
57955140 ATTTATTTAGCTCCAACAGAAAATGGAAATTTTTTGTAAAGTCTCCCCTTTTTTCAAAAATTATA
1 ATTTATTTAGCTCCAACAGAAAATGGAAATTTTTTGTAAAGTCTCCCCTTTTTTCAAAAATTATA
* *
57955205 GTATTTCCTTGATATTTATATAGGTGGTGTCA
66 GTATTTCCTTAATATTTATACAGGTGGTGTCA
* * * * *
57955237 ATTTATTTCGCTCCACCAGAAAATGGAAAATTTTTTTTTAAGTCTCCCCATTTTTTCAGAAATTA
1 ATTTATTTAGCTCCAACAGAAAATGG-AAATTTTTTGTAAAGTCTCCCC-TTTTTTCAAAAATTA
*
57955302 TAGTATTTCTTTAATATTTATACAGGTGG
64 TAGTATTTCCTTAATATTTATACAGGTGG
57955331 CGCCATTCTA
Statistics
Matches: 84, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
97 24 0.29
98 20 0.24
99 40 0.48
ACGTcount: A:0.30, C:0.14, G:0.13, T:0.43
Consensus pattern (97 bp):
ATTTATTTAGCTCCAACAGAAAATGGAAATTTTTTGTAAAGTCTCCCCTTTTTTCAAAAATTATA
GTATTTCCTTAATATTTATACAGGTGGTGTCA
Found at i:57955350 original size:99 final size:97
Alignment explanation
Indices: 57955130--57955359 Score: 284
Period size: 99 Copynumber: 2.4 Consensus size: 97
57955120 GTTGGAAACT
* * * * *
57955130 GGTGGCGCCGATTTATTTAGCTCCAACAGAAAATGGAAATTTTTTGTAAAGTCTCCCCTTTTTTC
1 GGTGGCGTCAATTTATATCGCTCCACCAGAAAATGGAAATTTTTTGTAAAGTCTCCCCTTTTTTC
* *
57955195 AAAAATTATAGTATTTCCTTGATATTTATATA
66 AAAAATTATAGTATTTCCTTAATATTTATACA
* * * *
57955227 GGTGGTGTCAATTTATTTCGCTCCACCAGAAAATGGAAAATTTTTTTTTAAGTCTCCCCATTTTT
1 GGTGGCGTCAATTTATATCGCTCCACCAGAAAATGG-AAATTTTTTGTAAAGTCTCCCC-TTTTT
* *
57955292 TCAGAAATTATAGTATTTCTTTAATATTTATACA
64 TCAAAAATTATAGTATTTCCTTAATATTTATACA
*
57955326 GGTGGCG-CCATTCTATAT-GACTCCACCAGAAAAT
1 GGTGGCGTCAATT-TATATCG-CTCCACCAGAAAAT
57955360 CGATTTTTTT
Statistics
Matches: 115, Mismatches: 14, Indels: 6
0.85 0.10 0.04
Matches are distributed among these distances:
97 31 0.27
98 25 0.22
99 59 0.51
ACGTcount: A:0.30, C:0.17, G:0.14, T:0.39
Consensus pattern (97 bp):
GGTGGCGTCAATTTATATCGCTCCACCAGAAAATGGAAATTTTTTGTAAAGTCTCCCCTTTTTTC
AAAAATTATAGTATTTCCTTAATATTTATACA
Found at i:57959168 original size:4 final size:4
Alignment explanation
Indices: 57959159--57959199 Score: 82
Period size: 4 Copynumber: 10.2 Consensus size: 4
57959149 ACATATTAAA
57959159 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC A
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC A
57959200 ATAGGACTAC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 37 1.00
ACGTcount: A:0.51, C:0.24, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAC
Found at i:57965080 original size:7 final size:7
Alignment explanation
Indices: 57965062--57965091 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
57965052 ATTATGAGAG
57965062 TATTTT-
1 TATTTTA
57965068 TATTTTA
1 TATTTTA
57965075 TATTTTA
1 TATTTTA
57965082 TATTTTA
1 TATTTTA
57965089 TAT
1 TAT
57965092 AAAAGTAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 6 0.26
7 17 0.74
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (7 bp):
TATTTTA
Found at i:57967832 original size:10 final size:10
Alignment explanation
Indices: 57967819--57967852 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
57967809 TATTTAAGTA
57967819 TAATTTTTTT
1 TAATTTTTTT
57967829 TAA--TTTTT
1 TAATTTTTTT
57967837 TAATTTTTTT
1 TAATTTTTTT
57967847 TAATTT
1 TAATTT
57967853 GTTTATAAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
8 8 0.36
10 14 0.64
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (10 bp):
TAATTTTTTT
Found at i:57967842 original size:18 final size:19
Alignment explanation
Indices: 57967819--57967857 Score: 71
Period size: 18 Copynumber: 2.1 Consensus size: 19
57967809 TATTTAAGTA
57967819 TAATTTTTTTTAATTT-TT
1 TAATTTTTTTTAATTTGTT
57967837 TAATTTTTTTTAATTTGTT
1 TAATTTTTTTTAATTTGTT
57967856 TA
1 TA
57967858 TAAACATTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 16 0.80
19 4 0.20
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.74
Consensus pattern (19 bp):
TAATTTTTTTTAATTTGTT
Found at i:57968279 original size:31 final size:31
Alignment explanation
Indices: 57968228--57968286 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
57968218 TAAAATGGTT
57968228 AAATTTTAATTTAATATTTATA-TTTCACTC
1 AAATTTTAATTTAATATTTATACTTTCACTC
*
57968258 AAATTTTAATTTTAATCTTTATACTTTCA
1 AAATTTTAA-TTTAATATTTATACTTTCA
57968287 TTTTAACATA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 9 0.35
31 12 0.46
32 5 0.19
ACGTcount: A:0.36, C:0.10, G:0.00, T:0.54
Consensus pattern (31 bp):
AAATTTTAATTTAATATTTATACTTTCACTC
Found at i:57973804 original size:34 final size:35
Alignment explanation
Indices: 57973744--57973810 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
57973734 CAAACACCAG
* *
57973744 AAAATATTTTCCAGTAAATTATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
57973779 AAAACATTTTCCCG-AAATCATTTTACAGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
57973811 TATTTTACTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.46, C:0.13, G:0.07, T:0.33
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:57975372 original size:25 final size:24
Alignment explanation
Indices: 57975326--57975372 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 24
57975316 CAGGGTAACA
*
57975326 ATTTCTCACATTTCATTTATAAAC
1 ATTTCTCACATTTCATTCATAAAC
57975350 ATTTCTC-CATTTCAAATTCATAA
1 ATTTCTCACATTTC--ATTCATAA
57975373 TCACAATCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 6 0.30
24 7 0.35
25 7 0.35
ACGTcount: A:0.34, C:0.21, G:0.00, T:0.45
Consensus pattern (24 bp):
ATTTCTCACATTTCATTCATAAAC
Found at i:57977754 original size:25 final size:25
Alignment explanation
Indices: 57977720--57977773 Score: 99
Period size: 25 Copynumber: 2.2 Consensus size: 25
57977710 CTACTCGATC
57977720 AAAGCGTTCATCTTAGACGAATAAA
1 AAAGCGTTCATCTTAGACGAATAAA
*
57977745 AAAGTGTTCATCTTAGACGAATAAA
1 AAAGCGTTCATCTTAGACGAATAAA
57977770 AAAG
1 AAAG
57977774 GTACAATTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.46, C:0.13, G:0.17, T:0.24
Consensus pattern (25 bp):
AAAGCGTTCATCTTAGACGAATAAA
Found at i:57978089 original size:17 final size:18
Alignment explanation
Indices: 57978059--57978093 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
57978049 AACTTTTTTA
*
57978059 AAAAATATATATAAAAAT
1 AAAAATATACATAAAAAT
57978077 AAAAA-ATACATAAAAAT
1 AAAAATATACATAAAAAT
57978094 TCAAAAAAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.23
Consensus pattern (18 bp):
AAAAATATACATAAAAAT
Found at i:57978101 original size:19 final size:19
Alignment explanation
Indices: 57978057--57978092 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
57978047 CTAACTTTTT
*
57978057 TAAAAAATATATATAAAAA
1 TAAAAAATACATATAAAAA
57978076 TAAAAAATACATA-AAAA
1 TAAAAAATACATATAAAA
57978093 TTCAAAAAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.75, C:0.03, G:0.00, T:0.22
Consensus pattern (19 bp):
TAAAAAATACATATAAAAA
Found at i:57985649 original size:21 final size:19
Alignment explanation
Indices: 57985625--57985669 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
57985615 ATGTGATTAG
57985625 TAAAACAACATATAAATATCT
1 TAAAACAA-A-ATAAATATCT
* *
57985646 TAAAATAAAATATATATCT
1 TAAAACAAAATAAATATCT
57985665 TAAAA
1 TAAAA
57985670 TTAAAATACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 14 0.64
20 1 0.05
21 7 0.32
ACGTcount: A:0.60, C:0.09, G:0.00, T:0.31
Consensus pattern (19 bp):
TAAAACAAAATAAATATCT
Found at i:57985664 original size:19 final size:20
Alignment explanation
Indices: 57985640--57985677 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
57985630 CAACATATAA
57985640 ATATCTTAAAA-TAAAATAT
1 ATATCTTAAAATTAAAATAT
57985659 ATATCTTAAAATTAAAATA
1 ATATCTTAAAATTAAAATA
57985678 CAATTATTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (20 bp):
ATATCTTAAAATTAAAATAT
Found at i:57988054 original size:116 final size:119
Alignment explanation
Indices: 57987854--57988082 Score: 333
Period size: 116 Copynumber: 1.9 Consensus size: 119
57987844 GGCAACTTTT
57987854 CTTGGTGGCCATATATTTTTCTTTTTCATACACCATTTGTATATGACGTAAGATCCCAAATTCCC
1 CTTGGTGGCCATATATTTTTCTTTTTCATACACCATTTGTATATGACGTAAGATCCCAAATTCCC
* *
57987919 AAAAGAATGAAAGGGATTT-CC-TAA-TTCTAATCTTTAGATTAATTATAACCTC
66 AAAAGAATAAAAGCGATTTCCCATAAGTT-TAATCTTTAGATTAATTATAACCTC
** *
57987971 CTTGGTGGCCATAT-TCTTTTCTTTTTCATACACCATTT-TATATGATTTAAGATCCCACATTCC
1 CTTGGTGGCCATATAT-TTTTCTTTTTCATACACCATTTGTATATGACGTAAGATCCCAAATTCC
* *
57988034 TAAAAGAATAAAAGCGATTTCCCAATAAGTTTAATCTTTATATTAATTA
65 CAAAAGAATAAAAGCGATTTCCC-ATAAGTTTAATCTTTAGATTAATTA
57988083 GAGTTTCCTT
Statistics
Matches: 100, Mismatches: 7, Indels: 8
0.87 0.06 0.07
Matches are distributed among these distances:
116 40 0.40
117 38 0.38
119 20 0.20
120 2 0.02
ACGTcount: A:0.32, C:0.18, G:0.10, T:0.39
Consensus pattern (119 bp):
CTTGGTGGCCATATATTTTTCTTTTTCATACACCATTTGTATATGACGTAAGATCCCAAATTCCC
AAAAGAATAAAAGCGATTTCCCATAAGTTTAATCTTTAGATTAATTATAACCTC
Found at i:57995057 original size:22 final size:19
Alignment explanation
Indices: 57994998--57995048 Score: 59
Period size: 18 Copynumber: 2.7 Consensus size: 19
57994988 TTAAAAAAAC
* * *
57994998 AATATTTTTTTATTTTT-T
1 AATAATTTTTAATTTTTAA
57995016 AATAATTTTTAATTTTTAA
1 AATAATTTTTAATTTTTAA
57995035 AATAATTTTATAAT
1 AATAATTTT-TAAT
57995049 GCTTTTAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
18 15 0.54
19 9 0.32
20 4 0.14
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (19 bp):
AATAATTTTTAATTTTTAA
Found at i:58001015 original size:20 final size:22
Alignment explanation
Indices: 58000985--58001029 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
58000975 TTGAATCAAT
58000985 ATAATATATATAATACTAAAAA
1 ATAATATATATAATACTAAAAA
58001007 ATAATATATATAATACTAAAAA
1 ATAATATATATAATACTAAAAA
58001029 A
1 A
58001030 GAACACATGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.31
Consensus pattern (22 bp):
ATAATATATATAATACTAAAAA
Found at i:58015261 original size:32 final size:32
Alignment explanation
Indices: 58015225--58015286 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
58015215 ATATTTTGGT
58015225 TTATACAATTTTT-GATAATTTAATAATTTCTA
1 TTATACAATTTTTAGATAATTT-ATAATTTCTA
* * *
58015257 TTATATAATTTTTAGATTATTTGTAATTTC
1 TTATACAATTTTTAGATAATTTATAATTTC
58015287 AGATCTTATG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
32 19 0.73
33 7 0.27
ACGTcount: A:0.34, C:0.05, G:0.05, T:0.56
Consensus pattern (32 bp):
TTATACAATTTTTAGATAATTTATAATTTCTA
Found at i:58018957 original size:32 final size:32
Alignment explanation
Indices: 58018921--58018982 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
58018911 ATATTTTGAT
58018921 TTATACAATTTTT-GATAATTTAATAATTTCTA
1 TTATACAATTTTTAGATAATTT-ATAATTTCTA
* * *
58018953 TTATATAATTTTTAGATTATTTGTAATTTC
1 TTATACAATTTTTAGATAATTTATAATTTC
58018983 AGATCTTATG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
32 19 0.73
33 7 0.27
ACGTcount: A:0.34, C:0.05, G:0.05, T:0.56
Consensus pattern (32 bp):
TTATACAATTTTTAGATAATTTATAATTTCTA
Found at i:58023816 original size:21 final size:21
Alignment explanation
Indices: 58023792--58023842 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
58023782 CCATATTGTA
58023792 ACCCATCTGACCACCCATTTG
1 ACCCATCTGACCACCCATTTG
58023813 ACCCATCTGACCACCCATTTG
1 ACCCATCTGACCACCCATTTG
*
58023834 GCCCATCTG
1 ACCCATCTG
58023843 CCCCATATTC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.22, C:0.43, G:0.12, T:0.24
Consensus pattern (21 bp):
ACCCATCTGACCACCCATTTG
Found at i:58024476 original size:12 final size:11
Alignment explanation
Indices: 58024459--58024524 Score: 60
Period size: 12 Copynumber: 5.5 Consensus size: 11
58024449 AAATTCCCCT
*
58024459 TCATCATCATC
1 TCATCATCAAC
58024470 ATCATCATCGAAC
1 -TCATCATC-AAC
*
58024483 TCATCATCAAAT
1 TCATCATC-AAC
58024495 TCATCATCGAAC
1 TCATCATC-AAC
*
58024507 TCATCACCAAAC
1 TCATCATC-AAC
58024519 TCATCA
1 TCATCA
58024525 AAATCACAAT
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
12 44 0.96
13 2 0.04
ACGTcount: A:0.36, C:0.33, G:0.03, T:0.27
Consensus pattern (11 bp):
TCATCATCAAC
Found at i:58024491 original size:24 final size:24
Alignment explanation
Indices: 58024471--58024524 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
58024461 ATCATCATCA
58024471 TCATCATCGAACTCATCATCAAAT
1 TCATCATCGAACTCATCATCAAAT
* *
58024495 TCATCATCGAACTCATCACCAAAC
1 TCATCATCGAACTCATCATCAAAT
58024519 TCATCA
1 TCATCA
58024525 AAATCACAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.37, C:0.33, G:0.04, T:0.26
Consensus pattern (24 bp):
TCATCATCGAACTCATCATCAAAT
Found at i:58025322 original size:16 final size:16
Alignment explanation
Indices: 58025301--58025343 Score: 61
Period size: 16 Copynumber: 2.7 Consensus size: 16
58025291 GAAAGACAAC
58025301 ACAGAGAAAGAGACAG
1 ACAGAGAAAGAGACAG
*
58025317 ACAGAGAGAGAGACAG
1 ACAGAGAAAGAGACAG
58025333 A-AGATGAAAGA
1 ACAGA-GAAAGA
58025344 TTTGTTTTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 3 0.12
16 21 0.88
ACGTcount: A:0.56, C:0.09, G:0.33, T:0.02
Consensus pattern (16 bp):
ACAGAGAAAGAGACAG
Found at i:58026036 original size:2 final size:2
Alignment explanation
Indices: 58026029--58026055 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
58026019 TTGCAAGGAA
58026029 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 A
58026056 AAAGAATCAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:58028827 original size:31 final size:30
Alignment explanation
Indices: 58028771--58028828 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 30
58028761 TAGCAAAGTT
**
58028771 AACAATAAAACAAAAGTTATACAATATCCA
1 AACAATAAAACAAAAGGAATACAATATCCA
58028801 AACAATAATAACAAAAGAGAAT-CAATAT
1 AACAATAA-AACAAAAG-GAATACAATAT
58028829 AATAACGAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 8 0.33
31 14 0.58
32 2 0.08
ACGTcount: A:0.62, C:0.14, G:0.05, T:0.19
Consensus pattern (30 bp):
AACAATAAAACAAAAGGAATACAATATCCA
Found at i:58052887 original size:19 final size:20
Alignment explanation
Indices: 58052850--58052888 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
58052840 AATTTCAAGT
*
58052850 TTTTTATTTTTAATTAATAAC
1 TTTTTATTTATAA-TAATAAC
58052871 TTTTTATTTATAA-AATAA
1 TTTTTATTTATAATAATAA
58052889 AATAATAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
21 12 0.71
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (20 bp):
TTTTTATTTATAATAATAAC
Found at i:58055781 original size:21 final size:21
Alignment explanation
Indices: 58055757--58055797 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
58055747 ACGAGCGTTT
58055757 TTTTAAAAAAAAAATTTATAA
1 TTTTAAAAAAAAAATTTATAA
***
58055778 TTTTTTTAAAAAAATTTATA
1 TTTTAAAAAAAAAATTTATA
58055798 TAAAAAAGAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (21 bp):
TTTTAAAAAAAAAATTTATAA
Found at i:58056261 original size:3 final size:3
Alignment explanation
Indices: 58056253--58056281 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
58056243 ACTAATTAGC
58056253 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
58056282 CTTTTCCTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:58058718 original size:11 final size:11
Alignment explanation
Indices: 58058702--58058735 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
58058692 CTCAACTTGC
58058702 AAAAAAAAAGA
1 AAAAAAAAAGA
58058713 AAAAAAAAAGA
1 AAAAAAAAAGA
* *
58058724 AAGAAAGAAGA
1 AAAAAAAAAGA
58058735 A
1 A
58058736 GATAGTTTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAGA
Found at i:58059593 original size:21 final size:21
Alignment explanation
Indices: 58059568--58059609 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
58059558 TGCTTCATAT
58059568 AAGTTTAATTCTTGCTCTTTC
1 AAGTTTAATTCTTGCTCTTTC
58059589 AAGTTTAATTCTTGCTCTTTC
1 AAGTTTAATTCTTGCTCTTTC
58059610 CTTTAATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.10, T:0.52
Consensus pattern (21 bp):
AAGTTTAATTCTTGCTCTTTC
Found at i:58060641 original size:24 final size:24
Alignment explanation
Indices: 58060575--58060641 Score: 91
Period size: 24 Copynumber: 2.8 Consensus size: 24
58060565 TATCCGGTGT
*
58060575 TACCCGTTAATTGCTCTTAAGAGC
1 TACCCGTTAATTGCTCTTTAGAGC
* *
58060599 TACCTGTTAATTACTCTTTAGAGC
1 TACCCGTTAATTGCTCTTTAGAGC
58060623 TACCCGTT-ATATGCTCTTT
1 TACCCGTTAAT-TGCTCTTT
58060642 GTGAGCTTCT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
23 2 0.05
24 35 0.95
ACGTcount: A:0.22, C:0.24, G:0.13, T:0.40
Consensus pattern (24 bp):
TACCCGTTAATTGCTCTTTAGAGC
Found at i:58072579 original size:21 final size:22
Alignment explanation
Indices: 58072553--58072597 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
58072543 AATTTTAAGT
*
58072553 TAAATATAAATATAATAT-ATA
1 TAAATATAAATATAAAATAATA
*
58072574 TAAATATTAATATAAAATAATA
1 TAAATATAAATATAAAATAATA
58072596 TA
1 TA
58072598 TTTTTAATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (22 bp):
TAAATATAAATATAAAATAATA
Found at i:58076699 original size:25 final size:26
Alignment explanation
Indices: 58076653--58076714 Score: 72
Period size: 25 Copynumber: 2.3 Consensus size: 26
58076643 TAAACATATG
58076653 AATTATAAAACATGAAAATATA-AAT
1 AATTATAAAACATGAAAATATATAAT
* **
58076678 AATTATAAAATATGAATGTATATAAT
1 AATTATAAAACATGAAAATATATAAT
58076704 ATATATATAAA
1 A-AT-TATAAA
58076715 CTATATACAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
25 19 0.61
26 4 0.13
27 2 0.06
28 6 0.19
ACGTcount: A:0.60, C:0.02, G:0.05, T:0.34
Consensus pattern (26 bp):
AATTATAAAACATGAAAATATATAAT
Found at i:58077425 original size:16 final size:16
Alignment explanation
Indices: 58077400--58077434 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
58077390 ATTATTTTTT
58077400 CAAAAACAAAGGAAAA
1 CAAAAACAAAGGAAAA
* *
58077416 CAAAATCAAATGAAAA
1 CAAAAACAAAGGAAAA
58077432 CAA
1 CAA
58077435 TAAAAGAACA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.71, C:0.14, G:0.09, T:0.06
Consensus pattern (16 bp):
CAAAAACAAAGGAAAA
Found at i:58078328 original size:44 final size:44
Alignment explanation
Indices: 58078269--58078481 Score: 164
Period size: 44 Copynumber: 4.8 Consensus size: 44
58078259 CTGTAACCTC
* * * * *
58078269 AGGGAGGTAAAATCTGCCATCTTCGATCTACTCCACTAATGTCT
1 AGGGAGATAAGATCTGCAATCTTCAATCTACTCCACTAATGCCT
* * ** *
58078313 AGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTGCCC
1 AGGGAGATAAGATCTGCAATCTTCAATCTACTCCACTAATGCCT
* *** *
58078357 AGGGAGAT-AGAAT-TACTGGCTTCAATGTACTCCACTGTAA--CCT
1 AGGGAGATAAG-ATCTGCAATCTTCAATCTACTCCAC--TAATGCCT
* * ** *
58078400 CAGGGAGGTAAAATCTGCCCTCTTCGATCTACTCCACTAATGCCT
1 -AGGGAGATAAGATCTGCAATCTTCAATCTACTCCACTAATGCCT
* *
58078445 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACT
1 AGGGAGATAAGATCTGCAATCTTCAATCTACTCCACT
58078482 GCCAACTAGG
Statistics
Matches: 126, Mismatches: 35, Indels: 16
0.71 0.20 0.09
Matches are distributed among these distances:
43 22 0.17
44 83 0.66
45 21 0.17
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (44 bp):
AGGGAGATAAGATCTGCAATCTTCAATCTACTCCACTAATGCCT
Found at i:58078482 original size:132 final size:133
Alignment explanation
Indices: 58078198--58078505 Score: 485
Period size: 132 Copynumber: 2.3 Consensus size: 133
58078188 GCCGTCATGA
* * *
58078198 CTTCAATCTATTCCACTACACTACCAGAGA-AGTAAGAATTACTGGCTTTCAATGTACTCCACTG
1 CTTCAATCTATTCCACTGC-CAACCAGGGAGA-T-AGAATTACTGGCTTTCAATGTACTCCACTG
*
58078262 TAACCTCAGGGAGGTAAAATCTGCCATCTTCGATCTACTCCACTAATGTCTAGGGAGATAAGATC
63 TAACCTCAGGGAGGTAAAATCTGCCATCTTCGATCTACTCCACTAATGCCTAGGGAGATAAGATC
*
58078327 TGTAAT
128 TGAAAT
***
58078333 CTTCAATCTATTCCACTGCTGCCCAGGGAGATAGAATTACTGGC-TTCAATGTACTCCACTGTAA
1 CTTCAATCTATTCCACTGCCAACCAGGGAGATAGAATTACTGGCTTTCAATGTACTCCACTGTAA
*
58078397 CCTCAGGGAGGTAAAATCTGCCCTCTTCGATCTACTCCACTAATGCCTAGGGAGATAAGATCTGA
66 CCTCAGGGAGGTAAAATCTGCCATCTTCGATCTACTCCACTAATGCCTAGGGAGATAAGATCTGA
58078462 AAT
131 AAT
*
58078465 CTTCAATCTATTCCACTGCCAACTAGGGAGATAGAATTACT
1 CTTCAATCTATTCCACTGCCAACCAGGGAGATAGAATTACT
58078506 ATCTTCGATC
Statistics
Matches: 160, Mismatches: 12, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
132 122 0.76
133 12 0.08
134 7 0.04
135 19 0.12
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.28
Consensus pattern (133 bp):
CTTCAATCTATTCCACTGCCAACCAGGGAGATAGAATTACTGGCTTTCAATGTACTCCACTGTAA
CCTCAGGGAGGTAAAATCTGCCATCTTCGATCTACTCCACTAATGCCTAGGGAGATAAGATCTGA
AAT
Found at i:58078548 original size:132 final size:131
Alignment explanation
Indices: 58078198--58078549 Score: 384
Period size: 132 Copynumber: 2.6 Consensus size: 131
58078188 GCCGTCATGA
* * * * *
58078198 CTTCAATCTATTCCACTACACTACCAGAGA-AGTAAGAATTACTGGCTTTCAATGTACTCCACTG
1 CTTCAATCTATTCCACTGC-CAACCAGGGAGA-T-AGAATTACTAGC-TTCAATCTACTCCACTG
* * * *
58078262 TAACCTCAGGGAGGTAAAATCTGCCATCTTCGATCTACTCCACTAATGTCTAGGGAGATAAGATC
62 T-ACATCAGGAAGGCAAAATCTGCCATCTTCGATCTACTCCACTAATGCCTAGGGAGATAAGATC
*
58078327 TGTAAT
126 TGAAAT
*** * *
58078333 CTTCAATCTATTCCACTGCTGCCCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAAC
1 CTTCAATCTATTCCACTGCCAACCAGGGAGATAGAATTACTAGCTTCAATCTACTCCACTGT-AC
* * * *
58078398 CTCAGGGAGGTAAAATCTGCCCTCTTCGATCTACTCCACTAATGCCTAGGGAGATAAGATCTGAA
65 ATCAGGAAGGCAAAATCTGCCATCTTCGATCTACTCCACTAATGCCTAGGGAGATAAGATCTGAA
58078463 AT
130 AT
* * * * * *
58078465 CTTCAATCTATTCCACTGCCAACTAGGGAGATAGAATTACTATCTTCGATCTCCTTCGCTGT-CG
1 CTTCAATCTATTCCACTGCCAACCAGGGAGATAGAATTACTAGCTTCAATCTACTCCACTGTAC-
*
58078529 ATGCAGGAAGGCAAGATCTGC
65 AT-CAGGAAGGCAAAATCTGC
58078550 TACTTTCACT
Statistics
Matches: 191, Mismatches: 23, Indels: 9
0.86 0.10 0.04
Matches are distributed among these distances:
130 1 0.01
131 1 0.01
132 151 0.79
133 12 0.06
134 7 0.04
135 19 0.10
ACGTcount: A:0.29, C:0.25, G:0.18, T:0.28
Consensus pattern (131 bp):
CTTCAATCTATTCCACTGCCAACCAGGGAGATAGAATTACTAGCTTCAATCTACTCCACTGTACA
TCAGGAAGGCAAAATCTGCCATCTTCGATCTACTCCACTAATGCCTAGGGAGATAAGATCTGAAA
T
Found at i:58079828 original size:23 final size:23
Alignment explanation
Indices: 58079791--58079840 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
58079781 AGCCTTTCCA
*
58079791 TTTTACTTTTCCATTTTTCAT-T
1 TTTTACTTTTCCATTTCTCATCT
*
58079813 TTTTCACTTTTTCATTTCTCATCT
1 TTTT-ACTTTTCCATTTCTCATCT
58079837 TTTT
1 TTTT
58079841 TTTTTACGAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 4 0.17
23 15 0.62
24 5 0.21
ACGTcount: A:0.12, C:0.20, G:0.00, T:0.68
Consensus pattern (23 bp):
TTTTACTTTTCCATTTCTCATCT
Found at i:58080275 original size:1 final size:1
Alignment explanation
Indices: 58080269--58080374 Score: 77
Period size: 1 Copynumber: 106.0 Consensus size: 1
58080259 CCGGTAGAGG
* * * * * * * * * * * *
58080269 TTTTTTTTGTTTCTTTTTGTTTTTTATTTTTTGTTCTTTTTTGTTCTTTTTTTTATTTTTGTCTA
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * *
58080334 TTTTTTTTGTTTTTTTTTTGTTTTTTTTTCTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
58080375 GAACTGAATC
Statistics
Matches: 75, Mismatches: 30, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
1 75 1.00
ACGTcount: A:0.03, C:0.05, G:0.07, T:0.86
Consensus pattern (1 bp):
T
Found at i:58080351 original size:52 final size:52
Alignment explanation
Indices: 58080272--58080374 Score: 136
Period size: 52 Copynumber: 2.0 Consensus size: 52
58080262 GTAGAGGTTT
* * *
58080272 TTTTTGTTTCTTTTTGTTTTTTATTTTTTGTTCTTTTTTGTTCTTTTTTTTA
1 TTTTTGTCTATTTTTGTTTTTTATTTTTTGTTCTTTTTTCTTCTTTTTTTTA
* * *
58080324 TTTTTGTCTATTTTT-TTTGTTTTTTTTTTGTTTTTTTTTCTTTTTTTTTTT
1 TTTTTGTCTATTTTTGTTT-TTTATTTTTTGTTCTTTTTTCTTCTTTTTTTT
58080375 GAACTGAATC
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
51 3 0.07
52 41 0.93
ACGTcount: A:0.03, C:0.05, G:0.07, T:0.85
Consensus pattern (52 bp):
TTTTTGTCTATTTTTGTTTTTTATTTTTTGTTCTTTTTTCTTCTTTTTTTTA
Found at i:58086961 original size:25 final size:26
Alignment explanation
Indices: 58086915--58086974 Score: 70
Period size: 25 Copynumber: 2.3 Consensus size: 26
58086905 TAAACATATG
58086915 AATTATAAAACATGAAAATATA-AAT
1 AATTATAAAACATGAAAATATATAAT
* **
58086940 AATTATAAAATATGAATGTATATAAT
1 AATTATAAAACATGAAAATATATAAT
58086966 -ATATATAAA
1 AAT-TATAAA
58086975 CTATATACAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
25 21 0.70
26 9 0.30
ACGTcount: A:0.60, C:0.02, G:0.05, T:0.33
Consensus pattern (26 bp):
AATTATAAAACATGAAAATATATAAT
Found at i:58087608 original size:16 final size:16
Alignment explanation
Indices: 58087583--58087617 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
58087573 ATTATTTTTT
58087583 CAAAAACAAAGGAAAA
1 CAAAAACAAAGGAAAA
* *
58087599 CAAAATCAAATGAAAA
1 CAAAAACAAAGGAAAA
58087615 CAA
1 CAA
58087618 TAAAAGAACA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.71, C:0.14, G:0.09, T:0.06
Consensus pattern (16 bp):
CAAAAACAAAGGAAAA
Found at i:58091853 original size:19 final size:21
Alignment explanation
Indices: 58091807--58091854 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
58091797 ATGTGTATCA
*
58091807 GTCACACGGTCGTGTACCCTT
1 GTCACACGGTCGTGGACCCTT
58091828 GTCACACGGTC-TGGACCCTT
1 GTCACACGGTCGTGGACCCTT
58091848 -TCACACG
1 GTCACACG
58091855 ACTTGGGCAC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 7 0.27
20 8 0.31
21 11 0.42
ACGTcount: A:0.17, C:0.35, G:0.23, T:0.25
Consensus pattern (21 bp):
GTCACACGGTCGTGGACCCTT
Found at i:58092185 original size:41 final size:41
Alignment explanation
Indices: 58092128--58092222 Score: 156
Period size: 41 Copynumber: 2.3 Consensus size: 41
58092118 TTTTTGGGGA
58092128 TTTAGCGGCGTTTTTGAATAAGCGCCGCTAATGCTCT-TATC
1 TTTAGCGGCGTTTTTGAATAAGCGCCGCTAATGCTCTGT-TC
* *
58092169 TTTAGTGGCGTTTTTGAATAGGCGCCGCTAATGCTCTGTTC
1 TTTAGCGGCGTTTTTGAATAAGCGCCGCTAATGCTCTGTTC
58092210 TTTAGCGGCGTTT
1 TTTAGCGGCGTTT
58092223 GTGCGAAAAA
Statistics
Matches: 50, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
41 49 0.98
42 1 0.02
ACGTcount: A:0.16, C:0.20, G:0.25, T:0.39
Consensus pattern (41 bp):
TTTAGCGGCGTTTTTGAATAAGCGCCGCTAATGCTCTGTTC
Found at i:58092276 original size:43 final size:43
Alignment explanation
Indices: 58092190--58092464 Score: 329
Period size: 43 Copynumber: 6.4 Consensus size: 43
58092180 TTTTGAATAG
* * * *
58092190 GCGCCGCTAATGCTC-TGTTCTTTAGCGGCGTTTGTGCGAAAAA
1 GCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTG-GGAAAA
* *
58092233 GTGCCGCTAAAGGTCATGGTCTTTGGCGGCGTTTGTGGGAAAA
1 GCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTGGGAAAA
* * ** *
58092276 GCGCCACCAAAACTCATGGTCTTTAGCGGCATTTGTGGGAAAA
1 GCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTGGGAAAA
* ** *
58092319 GCGCCGCTAACGGTCAT-AACTTTTAGCGGCGTTTGTGGAAAAA
1 GCGCCGCTAAAGGTCATGGTC-TTTAGCGGCGTTTGTGGGAAAA
* *
58092362 ACGCCACTAAAGGTCATGGTCTTTAGCGGCGTTTGTGGGAAAA
1 GCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTGGGAAAA
* * *
58092405 GCGCCGCTAAAGGTCATGGTCTATAGCGGAGTTTGTGGGGAAA
1 GCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTGGGAAAA
*
58092448 GCGTCGCTAAAGGTCAT
1 GCGCCGCTAAAGGTCAT
58092465 TACTTTTAGC
Statistics
Matches: 195, Mismatches: 34, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
42 1 0.01
43 174 0.89
44 20 0.10
ACGTcount: A:0.23, C:0.20, G:0.31, T:0.26
Consensus pattern (43 bp):
GCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTGGGAAAA
Found at i:58092361 original size:129 final size:130
Alignment explanation
Indices: 58092210--58092477 Score: 396
Period size: 129 Copynumber: 2.1 Consensus size: 130
58092200 TGCTCTGTTC
** * *
58092210 TTTAGCGGCGTTTGTGCGAAAAAGTGCCGCTAAAGGTCATGGTCTTTGGCGGCGTTTGTGGGAAA
1 TTTAGCGGCGTTTGTGCGAAAAAACGCCACTAAAGGTCATGGTCTTTAGCGGCGTTTGTGGGAAA
* *
58092275 AGCGCCACCAAAACTCATGGTCTTTAGCGGCA-TTTGTGGGAAAAGCGCCGCTAACGGTCATAAC
66 AGCGCCACCAAAACTCATGGTCTATAGCGG-AGTTTGTGGGAAAAGCGCCGCTAAAGGTCATAAC
58092339 T
130 T
58092340 TTTAGCGGCGTTTGTG-GAAAAAACGCCACTAAAGGTCATGGTCTTTAGCGGCGTTTGTGGGAAA
1 TTTAGCGGCGTTTGTGCGAAAAAACGCCACTAAAGGTCATGGTCTTTAGCGGCGTTTGTGGGAAA
* * ** * * *
58092404 AGCGCCGCTAAAGGTCATGGTCTATAGCGGAGTTTGTGGGGAAAGCGTCGCTAAAGGTCATTACT
66 AGCGCCACCAAAACTCATGGTCTATAGCGGAGTTTGTGGGAAAAGCGCCGCTAAAGGTCATAACT
58092469 TTTAGCGGC
1 TTTAGCGGC
58092478 ATTTATTTCC
Statistics
Matches: 124, Mismatches: 13, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
128 1 0.01
129 107 0.86
130 16 0.13
ACGTcount: A:0.24, C:0.19, G:0.31, T:0.26
Consensus pattern (130 bp):
TTTAGCGGCGTTTGTGCGAAAAAACGCCACTAAAGGTCATGGTCTTTAGCGGCGTTTGTGGGAAA
AGCGCCACCAAAACTCATGGTCTATAGCGGAGTTTGTGGGAAAAGCGCCGCTAAAGGTCATAACT
Found at i:58092589 original size:22 final size:22
Alignment explanation
Indices: 58092561--58092603 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
58092551 TAGCGACGCT
*
58092561 AAAAAGCACCGCTAAAGGCCTA
1 AAAAAGCACCGCTAAAAGCCTA
*
58092583 AAAAAGCGCCGCTAAAAGCCT
1 AAAAAGCACCGCTAAAAGCCT
58092604 GTTTTGGTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.44, C:0.28, G:0.19, T:0.09
Consensus pattern (22 bp):
AAAAAGCACCGCTAAAAGCCTA
Found at i:58093199 original size:40 final size:41
Alignment explanation
Indices: 58093060--58093254 Score: 257
Period size: 41 Copynumber: 4.8 Consensus size: 41
58093050 CCTTTCGAGT
* ** * *
58093060 CTTTAGCGGCATTTTCAAAAAAGCACCGCTAATGCTCGGGG
1 CTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTGGGGG
* *
58093101 TTTTAGCAGCGTTTTTGAAAAAGCGCCGCTAATGCTGGGGG
1 CTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTGGGGG
58093142 CTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTGGGGG
1 CTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTGGGGG
* * * *
58093183 C-TTAGCGGCGTTTTTGAGAAAGTGCCGCTAATGTTGGTGG
1 CTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTGGGGG
* * *
58093223 CTTTAGCGCCGTTTTTGAGAAAGCGCCACTAA
1 CTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAA
58093255 AAACATTTTA
Statistics
Matches: 137, Mismatches: 16, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
40 36 0.26
41 101 0.74
ACGTcount: A:0.22, C:0.20, G:0.30, T:0.28
Consensus pattern (41 bp):
CTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTGGGGG
Found at i:58093225 original size:81 final size:82
Alignment explanation
Indices: 58093060--58093254 Score: 257
Period size: 81 Copynumber: 2.4 Consensus size: 82
58093050 CCTTTCGAGT
* ** * **
58093060 CTTTAGCGGCATTTTCAAAAAAGCACCGCTAATGCTCGGGGTTTTAGCAGCGTTTTTGAAAAAGC
1 CTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCGGGGGCTTAGCAGCGTTTTTGAAAAAGC
58093125 GCCGCTAATGCTGGGGG
66 GCCGCTAATGCTGGGGG
* * *
58093142 CTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCT-GGGGGCTTAGCGGCGTTTTTGAGAAAGT
1 CTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCGGGGGCTTAGCAGCGTTTTTGAAAAAGC
* *
58093206 GCCGCTAATGTTGGTGG
66 GCCGCTAATGCTGGGGG
* * *
58093223 CTTTAGCGCCGTTTTTGAGAAAGCGCCACTAA
1 CTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAA
58093255 AAACATTTTA
Statistics
Matches: 99, Mismatches: 14, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
81 67 0.68
82 32 0.32
ACGTcount: A:0.22, C:0.20, G:0.30, T:0.28
Consensus pattern (82 bp):
CTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCGGGGGCTTAGCAGCGTTTTTGAAAAAGC
GCCGCTAATGCTGGGGG
Found at i:58093623 original size:14 final size:14
Alignment explanation
Indices: 58093606--58093665 Score: 68
Period size: 14 Copynumber: 4.2 Consensus size: 14
58093596 GGGCTGAGAT
58093606 TTAAGGTTTAGGGG
1 TTAAGGTTTAGGGG
* *
58093620 TTAAGGGTTAAGGG
1 TTAAGGTTTAGGGG
58093634 TTAAGGGTTTAGGGG
1 TTAA-GGTTTAGGGG
*
58093649 TTAGACG-TTAGGGG
1 TTA-AGGTTTAGGGG
58093663 TTA
1 TTA
58093666 GAGTTAGGAA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
14 26 0.67
15 12 0.31
16 1 0.03
ACGTcount: A:0.23, C:0.02, G:0.42, T:0.33
Consensus pattern (14 bp):
TTAAGGTTTAGGGG
Found at i:58093627 original size:7 final size:7
Alignment explanation
Indices: 58093606--58093647 Score: 57
Period size: 7 Copynumber: 6.0 Consensus size: 7
58093596 GGGCTGAGAT
*
58093606 TTAAGGT
1 TTAAGGG
*
58093613 TTAGGGG
1 TTAAGGG
58093620 TTAAGGG
1 TTAAGGG
58093627 TTAAGGG
1 TTAAGGG
58093634 TTAAGGG
1 TTAAGGG
*
58093641 TTTAGGG
1 TTAAGGG
58093648 GTTAGACGTT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.24, C:0.00, G:0.43, T:0.33
Consensus pattern (7 bp):
TTAAGGG
Found at i:58093652 original size:7 final size:7
Alignment explanation
Indices: 58093613--58093666 Score: 54
Period size: 7 Copynumber: 7.6 Consensus size: 7
58093603 GATTTAAGGT
58093613 TTAGGGG
1 TTAGGGG
*
58093620 TTAAGGG
1 TTAGGGG
*
58093627 TTAAGGG
1 TTAGGGG
*
58093634 TTAAGGGT
1 TT-AGGGG
58093642 TTAGGGG
1 TTAGGGG
**
58093649 TTAGACG
1 TTAGGGG
58093656 TTAGGGG
1 TTAGGGG
58093663 TTAG
1 TTAG
58093667 AGTTAGGAAT
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
7 33 0.87
8 5 0.13
ACGTcount: A:0.22, C:0.02, G:0.44, T:0.31
Consensus pattern (7 bp):
TTAGGGG
Found at i:58093658 original size:29 final size:28
Alignment explanation
Indices: 58093606--58093665 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 28
58093596 GGGCTGAGAT
*
58093606 TTAAGGTTTAGGGGTTAAGGGTTAAGGG
1 TTAAGGTTTAGGGGTTAAGCGTTAAGGG
*
58093634 TTAAGGGTTTAGGGGTT-AGACGTTAGGGG
1 TTAA-GGTTTAGGGGTTAAG-CGTTAAGGG
58093663 TTA
1 TTA
58093666 GAGTTAGGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 6 0.21
29 22 0.79
ACGTcount: A:0.23, C:0.02, G:0.42, T:0.33
Consensus pattern (28 bp):
TTAAGGTTTAGGGGTTAAGCGTTAAGGG
Found at i:58093666 original size:14 final size:13
Alignment explanation
Indices: 58093613--58093673 Score: 59
Period size: 14 Copynumber: 4.4 Consensus size: 13
58093603 GATTTAAGGT
*
58093613 TTAGGGGTTAAGGG
1 TTAGGGGTT-AGAG
* *
58093627 TTAAGGGTTAAGGG
1 TTAGGGGTT-AGAG
58093641 TTTAGGGGTTAGACG
1 -TTAGGGGTTAGA-G
58093656 TTAGGGGTTAGAG
1 TTAGGGGTTAGAG
58093669 TTAGG
1 TTAGG
58093674 AATTTAGGGT
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
13 6 0.14
14 27 0.64
15 9 0.21
ACGTcount: A:0.23, C:0.02, G:0.44, T:0.31
Consensus pattern (13 bp):
TTAGGGGTTAGAG
Found at i:58103576 original size:31 final size:31
Alignment explanation
Indices: 58103534--58103600 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 31
58103524 AACAGGTTGG
*
58103534 AGCGGAGAAGGCGACAGAGGAGATCACTAGA
1 AGCGGAAAAGGCGACAGAGGAGATCACTAGA
* * *
58103565 AGCGGAAAAGGCGATAGTGGAGATCACTGGA
1 AGCGGAAAAGGCGACAGAGGAGATCACTAGA
58103596 A-CGGA
1 AGCGGA
58103601 CGCTGATGGG
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
30 4 0.12
31 28 0.88
ACGTcount: A:0.37, C:0.15, G:0.39, T:0.09
Consensus pattern (31 bp):
AGCGGAAAAGGCGACAGAGGAGATCACTAGA
Found at i:58113635 original size:22 final size:22
Alignment explanation
Indices: 58113609--58113650 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
58113599 AAAGAATAGT
58113609 AACCATTACATGCATAATTGAA
1 AACCATTACATGCATAATTGAA
**
58113631 AACCATTTTATGCATAATTG
1 AACCATTACATGCATAATTG
58113651 TGAAGTTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.40, C:0.17, G:0.10, T:0.33
Consensus pattern (22 bp):
AACCATTACATGCATAATTGAA
Found at i:58114926 original size:16 final size:17
Alignment explanation
Indices: 58114902--58114935 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
58114892 TTTCATTTTT
58114902 TAATATATATT-TTAAA
1 TAATATATATTATTAAA
*
58114918 TAATTTATATTATTAAA
1 TAATATATATTATTAAA
58114935 T
1 T
58114936 TACATTATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TAATATATATTATTAAA
Found at i:58125070 original size:19 final size:19
Alignment explanation
Indices: 58125042--58125081 Score: 64
Period size: 19 Copynumber: 2.1 Consensus size: 19
58125032 ATAGGGAAAG
58125042 AAAAAAAAATTAAA-AGAA
1 AAAAAAAAATTAAAGAGAA
58125060 AAAACAAAAATTAAAGAGAA
1 AAAA-AAAAATTAAAGAGAA
58125080 AA
1 AA
58125082 TATGGTGAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 4 0.20
19 10 0.50
20 6 0.30
ACGTcount: A:0.80, C:0.03, G:0.07, T:0.10
Consensus pattern (19 bp):
AAAAAAAAATTAAAGAGAA
Found at i:58133846 original size:105 final size:105
Alignment explanation
Indices: 58133611--58133924 Score: 344
Period size: 105 Copynumber: 3.0 Consensus size: 105
58133601 TGTGATATTG
* * * * * *
58133611 TCACATATAATATATTGATCGATGCACATTGTAAGGAGGGGATGATTTATAAAGCTGTAGATATC
1 TCACGTATAATATATTTATTGATGCATATTGTAAGGAGGGGATGGTTTCTAAAGCTGTAGATATC
* * * * *
58133676 GTTGATACAATG-GTGAAGCAAGGCATTGAACCTAATATTG
66 GTTGACACAATGAG-AAAGCAAGGCATTGAGCCTAATGTTA
* * *
58133716 TCACGTATAATATATTTATTGATGCATATTGCAAGGAGGGGATGGTTTCTAAAGCTGTAGAAACC
1 TCACGTATAATATATTTATTGATGCATATTGTAAGGAGGGGATGGTTTCTAAAGCTGTAGATATC
*
58133781 ATTGACACAATGAGAAAGCAAGGCATTGAGCCTAATGTTA
66 GTTGACACAATGAGAAAGCAAGGCATTGAGCCTAATGTTA
* * ** ** * *
58133821 TCACGTATAATATA-TTAGTTTATGCATATTTTAACAAGGCAATGGTTTCTGAAGCTGAAGATAT
1 TCACGTATAATATATTTA-TTGATGCATATTGTAAGGAGGGGATGGTTTCTAAAGCTGTAGATAT
* * * * *
58133885 TGTTGACACAATGATAAAGCAGGGTATTGAGCCTGATGTT
65 CGTTGACACAATGAGAAAGCAAGGCATTGAGCCTAATGTT
58133925 GTTACCTATA
Statistics
Matches: 175, Mismatches: 32, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
104 3 0.02
105 171 0.98
106 1 0.01
ACGTcount: A:0.34, C:0.12, G:0.22, T:0.31
Consensus pattern (105 bp):
TCACGTATAATATATTTATTGATGCATATTGTAAGGAGGGGATGGTTTCTAAAGCTGTAGATATC
GTTGACACAATGAGAAAGCAAGGCATTGAGCCTAATGTTA
Found at i:58147530 original size:14 final size:14
Alignment explanation
Indices: 58147511--58147544 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
58147501 TCATCATTTG
58147511 CCTATAACCAAAAC
1 CCTATAACCAAAAC
*
58147525 CCTATAACTAAAAC
1 CCTATAACCAAAAC
58147539 CC-ATAA
1 CCTATAA
58147545 ACCCATACCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 4 0.21
14 15 0.79
ACGTcount: A:0.50, C:0.32, G:0.00, T:0.18
Consensus pattern (14 bp):
CCTATAACCAAAAC
Found at i:58147979 original size:22 final size:22
Alignment explanation
Indices: 58147956--58148031 Score: 107
Period size: 22 Copynumber: 3.5 Consensus size: 22
58147946 TTTTATTAGC
**
58147956 CATGAGAGCTTAGTACGTTAGC
1 CATGAGAGCTTAGTACGTTAAA
* * *
58147978 CATGAGGGTTTAGTTCGTTAAA
1 CATGAGAGCTTAGTACGTTAAA
58148000 CATGAGAGCTTAGTACGTTAAA
1 CATGAGAGCTTAGTACGTTAAA
58148022 CATGAGAGCT
1 CATGAGAGCT
58148032 GTTAAATTCT
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 46 1.00
ACGTcount: A:0.30, C:0.14, G:0.26, T:0.29
Consensus pattern (22 bp):
CATGAGAGCTTAGTACGTTAAA
Found at i:58152002 original size:22 final size:22
Alignment explanation
Indices: 58151972--58152025 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
58151962 TTATGTTATG
*
58151972 TATAT-TATTTTATTATATAA-
1 TATATATATTATATTATATAAT
*
58151992 TATAATATATTATATTATATTAT
1 TAT-ATATATTATATTATATAAT
58152015 TATATATATTA
1 TATATATATTA
58152026 AATAAAGTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 3 0.10
21 2 0.07
22 21 0.72
23 3 0.10
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
TATATATATTATATTATATAAT
Found at i:58152022 original size:17 final size:17
Alignment explanation
Indices: 58151967--58152025 Score: 63
Period size: 17 Copynumber: 3.7 Consensus size: 17
58151957 GATTTTTATG
* *
58151967 TTATGTATATTATTTTA
1 TTATATATATTATATTA
*
58151984 TTATATA-A-TATAATA
1 TTATATATATTATATTA
58151999 -TAT-TATATTATATTA
1 TTATATATATTATATTA
58152014 TTATATATATTA
1 TTATATATATTA
58152026 AATAAAGTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
13 2 0.06
14 4 0.12
15 11 0.32
16 4 0.12
17 13 0.38
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.58
Consensus pattern (17 bp):
TTATATATATTATATTA
Found at i:58154081 original size:2 final size:2
Alignment explanation
Indices: 58154074--58154111 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
58154064 ATAAATATGA
58154074 AT 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
58154112 GCAAGAGGAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:58156346 original size:37 final size:37
Alignment explanation
Indices: 58156297--58156425 Score: 231
Period size: 37 Copynumber: 3.5 Consensus size: 37
58156287 CACTTGTCCC
*
58156297 TGATCAGATAAGTGTAGCCACCTATCACTTTGTTTCT
1 TGATCAGATAAGTGTAGCCACTTATCACTTTGTTTCT
*
58156334 TGATTAGATAAGTGTAGCCACTTATCACTTTGTTTCT
1 TGATCAGATAAGTGTAGCCACTTATCACTTTGTTTCT
*
58156371 TGATCAGATAAGTGTAGCCACTTATCACTTTGTCTCT
1 TGATCAGATAAGTGTAGCCACTTATCACTTTGTTTCT
58156408 TGATCAGATAAGTGTAGC
1 TGATCAGATAAGTGTAGC
58156426 TAAAGCTATC
Statistics
Matches: 88, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 88 1.00
ACGTcount: A:0.26, C:0.19, G:0.18, T:0.38
Consensus pattern (37 bp):
TGATCAGATAAGTGTAGCCACTTATCACTTTGTTTCT
Found at i:58156442 original size:46 final size:46
Alignment explanation
Indices: 58156389--58156596 Score: 254
Period size: 52 Copynumber: 4.3 Consensus size: 46
58156379 TAAGTGTAGC
* **
58156389 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
* *
58156435 CACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
58156481 CACTTATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
1 CACTTATCAC---T---TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
*
58156533 CACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTAT
1 CACTTATCAC--T----TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
58156585 CACTTATCACTT
1 CACTTATCACTT
58156597 NNNNNNNNNN
Statistics
Matches: 149, Mismatches: 6, Indels: 14
0.88 0.04 0.08
Matches are distributed among these distances:
46 54 0.36
49 1 0.01
50 1 0.01
51 3 0.02
52 90 0.60
ACGTcount: A:0.27, C:0.23, G:0.14, T:0.36
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
Found at i:58156508 original size:52 final size:52
Alignment explanation
Indices: 58156432--58156596 Score: 276
Period size: 52 Copynumber: 3.2 Consensus size: 52
58156422 TAGCTAAAGC
* * *
58156432 TATCACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTATCACT
1 TATCACTTTTCAC-TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACT
58156485 TATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACT
* *
58156537 TATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTATCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACT
58156589 TATCACTT
1 TATCACTT
58156597 NNNNNNNNNN
Statistics
Matches: 107, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
52 95 0.89
53 12 0.11
ACGTcount: A:0.27, C:0.23, G:0.14, T:0.36
Consensus pattern (52 bp):
TATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACT
Found at i:58159938 original size:25 final size:24
Alignment explanation
Indices: 58159910--58159965 Score: 62
Period size: 24 Copynumber: 2.3 Consensus size: 24
58159900 TATTTGGGCT
58159910 ATATAACGGAAAGCTCATAAGAGCC
1 ATATAACGG-AAGCTCATAAGAGCC
* *
58159935 ATAT-TCAGGAAGCTCATACGAGCC
1 ATATAAC-GGAAGCTCATAAGAGCC
58159959 A-ATAACG
1 ATATAACG
58159966 AGTAACTCTG
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
23 3 0.12
24 17 0.65
25 6 0.23
ACGTcount: A:0.41, C:0.21, G:0.20, T:0.18
Consensus pattern (24 bp):
ATATAACGGAAGCTCATAAGAGCC
Found at i:58161626 original size:31 final size:29
Alignment explanation
Indices: 58161591--58161661 Score: 88
Period size: 31 Copynumber: 2.4 Consensus size: 29
58161581 ACAATATCAT
58161591 ATTTAATACTTATATTTTGATGAAATATTTA
1 ATTTAATACTTATATTTTGA--AAATATTTA
* *
58161622 ATTTAATATTTTTATTTTGAAAATATTTA
1 ATTTAATACTTATATTTTGAAAATATTTA
* *
58161651 ATGTGATACTT
1 ATTTAATACTT
58161662 GAACTACCGA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
29 17 0.49
31 18 0.51
ACGTcount: A:0.37, C:0.03, G:0.07, T:0.54
Consensus pattern (29 bp):
ATTTAATACTTATATTTTGAAAATATTTA
Found at i:58161875 original size:12 final size:12
Alignment explanation
Indices: 58161858--58161882 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
58161848 AAGGCACATT
58161858 GTATTCTCAAAG
1 GTATTCTCAAAG
58161870 GTATTCTCAAAG
1 GTATTCTCAAAG
58161882 G
1 G
58161883 GAGATACAGA
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:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (12 bp):
GTATTCTCAAAG
Found at i:58170447 original size:25 final size:24
Alignment explanation
Indices: 58170414--58170462 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 24
58170404 AGGGTGGGGT
58170414 TTATTTTATTTAATATTAATATAA
1 TTATTTTATTTAATATTAATATAA
58170438 TTATATTTATTTAATATTAATATAA
1 TTAT-TTTATTTAATATTAATATAA
58170463 AGTTTAAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 4 0.17
25 20 0.83
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (24 bp):
TTATTTTATTTAATATTAATATAA
Found at i:58173236 original size:2 final size:2
Alignment explanation
Indices: 58173229--58173253 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
58173219 AATTATAAAT
58173229 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 T
58173254 TTACTATTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:58177204 original size:12 final size:12
Alignment explanation
Indices: 58177189--58177244 Score: 51
Period size: 12 Copynumber: 4.7 Consensus size: 12
58177179 CACGAAATCC
58177189 ACCACCTCCACG
1 ACCACCTCCACG
* *
58177201 ACCACCTCCTCT
1 ACCACCTCCACG
* *
58177213 ACCACCACCTCTG
1 ACCACCTCCAC-G
*
58177226 -CCTCCTCCACG
1 ACCACCTCCACG
58177237 ACCACCTC
1 ACCACCTC
58177245 TTCCACCACC
Statistics
Matches: 34, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
11 1 0.03
12 33 0.97
ACGTcount: A:0.20, C:0.59, G:0.05, T:0.16
Consensus pattern (12 bp):
ACCACCTCCACG
Done.