Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold31
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: 2401195
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 123915 characters in sequence are not A, C, G, or T
File 15 of 16
Found at i:2133309 original size:26 final size:26
Alignment explanation
Indices: 2133273--2133331 Score: 84
Period size: 26 Copynumber: 2.3 Consensus size: 26
2133263 CACTCTTTTT
* *
2133273 CCTTTTAAGTCCATAACT-ATGTGGCA
1 CCTTTTTAGTCCACAACTCA-GTGGCA
2133299 CCTTTTTAGTCCACAACTCAGTGGCA
1 CCTTTTTAGTCCACAACTCAGTGGCA
2133325 CCTTTTT
1 CCTTTTT
2133332 CTTTTCAAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 29 0.97
27 1 0.03
ACGTcount: A:0.22, C:0.27, G:0.14, T:0.37
Consensus pattern (26 bp):
CCTTTTTAGTCCACAACTCAGTGGCA
Found at i:2133347 original size:60 final size:59
Alignment explanation
Indices: 2133249--2133390 Score: 173
Period size: 60 Copynumber: 2.4 Consensus size: 59
2133239 TTTTCAAAGC
* * * * *
2133249 CCACAACTCCGTGACACTCTTTTTCCTTTTAAGTCCATAACTATGTGGCACCTTTTTAGT
1 CCACAACTCAGTGGCACTCTTTTTCCTTTTAAGCCCATAACTACGTGGCACC-TTTAAGT
*
2133309 CCACAACTCAGTGGCAC-CTTTTT-CTTTTCAAAGCCCATAACTCCGTGGCACCTTTAAGT
1 CCACAACTCAGTGGCACTCTTTTTCCTTTT--AAGCCCATAACTACGTGGCACCTTTAAGT
2133368 CCACAACTCCA-TGGCACTCTTTT
1 CCACAACT-CAGTGGCACTCTTTT
2133391 AAGTCCACAA
Statistics
Matches: 72, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
58 5 0.07
59 26 0.36
60 41 0.57
ACGTcount: A:0.23, C:0.32, G:0.12, T:0.34
Consensus pattern (59 bp):
CCACAACTCAGTGGCACTCTTTTTCCTTTTAAGCCCATAACTACGTGGCACCTTTAAGT
Found at i:2133375 original size:25 final size:27
Alignment explanation
Indices: 2133347--2133402 Score: 89
Period size: 27 Copynumber: 2.1 Consensus size: 27
2133337 CAAAGCCCAT
*
2133347 AACTCCGTGGCAC-C-TTTAAGTCCAC
1 AACTCCATGGCACTCTTTTAAGTCCAC
2133372 AACTCCATGGCACTCTTTTAAGTCCAC
1 AACTCCATGGCACTCTTTTAAGTCCAC
2133399 AACT
1 AACT
2133403 TAGTGACACA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
25 12 0.43
26 1 0.04
27 15 0.54
ACGTcount: A:0.27, C:0.34, G:0.12, T:0.27
Consensus pattern (27 bp):
AACTCCATGGCACTCTTTTAAGTCCAC
Found at i:2133418 original size:86 final size:84
Alignment explanation
Indices: 2133276--2133514 Score: 292
Period size: 86 Copynumber: 2.9 Consensus size: 84
2133266 TCTTTTTCCT
* * * * *
2133276 TTTAAGTCCATAACTATGTGGCAC-CTTTTTAGTCCACAACTCAGTGGCACCTTTTTCTTTTCAA
1 TTTAAGTCCACAACTCTGTGGCACTCTTTTAAGTCCACAACTTAGTGGCACATTTTTCTTTTCAA
*
2133340 AGCCCATAACTCCGTGGCA
66 AGCCCACAACTCCGTGGCA
** *
2133359 CCTTTAAGTCCACAACTCCATGGCACTCTTTTAAGTCCACAACTTAGTGACACATTTTTCTTTTC
1 --TTTAAGTCCACAACTCTGTGGCACTCTTTTAAGTCCACAACTTAGTGGCACATTTTTCTTTTC
*
2133424 AAAGCCCACAACTTCGTGGCA
64 AAAGCCCACAACTCCGTGGCA
* *
2133445 --TAAGTCCACAACTCTGTGGCA-TCCTTTTAAGTCCACAACTTTA-TGGCACATTTTCCTTCT-
1 TTTAAGTCCACAACTCTGTGGCACT-CTTTTAAGTCCACAAC-TTAGTGGCACATTTTTCTTTTC
2133505 AAAGCCCACA
64 AAAGCCCACA
2133515 GAAGCTGGTG
Statistics
Matches: 136, Mismatches: 15, Indels: 10
0.84 0.09 0.06
Matches are distributed among these distances:
81 11 0.08
82 49 0.36
83 3 0.02
85 20 0.15
86 53 0.39
ACGTcount: A:0.26, C:0.29, G:0.13, T:0.32
Consensus pattern (84 bp):
TTTAAGTCCACAACTCTGTGGCACTCTTTTAAGTCCACAACTTAGTGGCACATTTTTCTTTTCAA
AGCCCACAACTCCGTGGCA
Found at i:2133542 original size:32 final size:31
Alignment explanation
Indices: 2133499--2133664 Score: 199
Period size: 32 Copynumber: 5.3 Consensus size: 31
2133489 GGCACATTTT
*
2133499 CCTTCTAAAGCCCACAGAAG-CTGGTGGCAAC
1 CCTTCTAAAGCCCACACAAGTC-GGTGGCAAC
*
2133530 CCTTCTCAAAGCCCACACAAGTCGGTGGTAAC
1 CCTTCT-AAAGCCCACACAAGTCGGTGGCAAC
* * *
2133562 CTTTCTCAAAGCCAACACAAGTCTGTGGCAACC
1 CCTTCT-AAAGCCCACACAAGTCGGTGGCAA-C
* *
2133595 CCTTTTAAAGCCCACACAAGTCGGTGACAAC
1 CCTTCTAAAGCCCACACAAGTCGGTGGCAAC
* **
2133626 CTTTCTAAAGCCCACACAAGTCAATGGCAAC
1 CCTTCTAAAGCCCACACAAGTCGGTGGCAAC
2133657 CCTTCTAA
1 CCTTCTAA
2133665 GCTTAATGTC
Statistics
Matches: 115, Mismatches: 17, Indels: 6
0.83 0.12 0.04
Matches are distributed among these distances:
31 40 0.35
32 69 0.60
33 6 0.05
ACGTcount: A:0.31, C:0.33, G:0.16, T:0.20
Consensus pattern (31 bp):
CCTTCTAAAGCCCACACAAGTCGGTGGCAAC
Found at i:2133789 original size:52 final size:51
Alignment explanation
Indices: 2133669--2134268 Score: 301
Period size: 52 Copynumber: 11.8 Consensus size: 51
2133659 TTCTAAGCTT
* * * *
2133669 AATGTCGCTGGCCTTGAATTAGCACATTGGCACTTTTT--TTTTCCTAAGTCC
1 AATGTCACTGGCCTTGAATCAGCATATTGGCACTTTTTCATCTT--TAAGTCC
* * * * *
2133720 AATATCGCTAGCATTGAATCAGCATATTGGCAGCTTTATCATCTTTAAGTCC
1 AATGTCACTGGCCTTGAATCAGCATATTGGCA-CTTTTTCATCTTTAAGTCC
*** * * * *
2133772 AATGTTGTTGGCCTTGAATCAGCACATTAGCACATTTTTC-TTTGTTAAGTCT
1 AATGTCACTGGCCTTGAATCAGCATATTGGCAC-TTTTTCATCT-TTAAGTCC
* ** * * *
2133824 AATATCGTTGGCCTTGAATTAGTATATTGGCGCCTTTTTCATCTTTAAGTCC
1 AATGTCACTGGCCTTGAATCAGCATATTGGC-ACTTTTTCATCTTTAAGTCC
* ** * * * *
2133876 AATGTCGCAAGCCTTGAATCAGCACATTGGCATTTTTTTCTTCCTTAAGTCC
1 AATGTCACTGGCCTTGAATCAGCATATTGGCA-CTTTTTCATCTTTAAGTCC
* * * *
2133928 AATAT-ACTGGCCTTGAATAAGCATATTGGCACCTTTATCATCTTTAAGTCT
1 AATGTCACTGGCCTTGAATCAGCATATTGGCA-CTTTTTCATCTTTAAGTCC
* * *
2133979 AACGTCACTAGCCTTGAATCAGCACATTGGCACATTTTTC-T-TTCTCAAGTCC
1 AATGTCACTGGCCTTGAATCAGCATATTGGCAC-TTTTTCATCTT-T-AAGTCC
* * * * * *
2134031 AATATCATTGGCCTTGAATTAGCATATTGGTACCCTTGTCATCTTT--G--C
1 AATGTCACTGGCCTTGAATCAGCATATTGGCA-CTTTTTCATCTTTAAGTCC
* * *
2134079 --TG--A----CCTTGAATCAACATATTGGCATCTTTATCAT-TCCTAAG-CC
1 AATGTCACTGGCCTTGAATCAGCATATTGGCA-CTTTTTCATCT-TTAAGTCC
* * * *
2134122 TAGTGTCACTGGCCTTAAATCAGCACATTGGCA-TTCTTCTCAT-TTTCAAGTCT
1 -AATGTCACTGGCCTTGAATCAGCATATTGGCACTT-TT-TCATCTTT-AAGTCC
** * * * * *
2134175 AATGTCGTTGGCCGTGAATCAGCACATTAGCA-TTCTTCGCATCTTTAAGCCC
1 AATGTCACTGGCCTTGAATCAGCATATTGGCACTT-TT-TCATCTTTAAGTCC
* * * * *
2134227 AATATCACTAGCCTTGAATCAACGTATTGGCACATTTATCAT
1 AATGTCACTGGCCTTGAATCAGCATATTGGCAC-TTTTTCAT
2134269 TTTTTCTCAT
Statistics
Matches: 415, Mismatches: 99, Indels: 69
0.71 0.17 0.12
Matches are distributed among these distances:
39 1 0.00
40 26 0.06
42 1 0.00
43 1 0.00
44 1 0.00
46 3 0.01
48 2 0.00
50 5 0.01
51 73 0.18
52 284 0.68
53 11 0.03
54 7 0.02
ACGTcount: A:0.25, C:0.23, G:0.15, T:0.37
Consensus pattern (51 bp):
AATGTCACTGGCCTTGAATCAGCATATTGGCACTTTTTCATCTTTAAGTCC
Found at i:2133851 original size:104 final size:104
Alignment explanation
Indices: 2133669--2134060 Score: 495
Period size: 104 Copynumber: 3.8 Consensus size: 104
2133659 TTCTAAGCTT
* * * * * * *
2133669 AATGTCGCTGGCCTTGAATTAGCACATTGGCAC-TTTTTTTTTCCTAAGTCCAATATCGCTAGCA
1 AATGTCGCTAGCCTTGAATCAGCACATTGGCACATTTTTCTTTCTTAAGTCCAATATCGTTGGCC
*
2133733 TTGAATCAGCATATTGGCAGCTTTATCATCTTTAAGTCC
66 TTGAATTAGCATATTGGCAGCTTTATCATCTTTAAGTCC
* * * * * *
2133772 AATGTTGTTGGCCTTGAATCAGCACATTAGCACATTTTTCTTTGTTAAGTCTAATATCGTTGGCC
1 AATGTCGCTAGCCTTGAATCAGCACATTGGCACATTTTTCTTTCTTAAGTCCAATATCGTTGGCC
* *
2133837 TTGAATTAGTATATTGGC-GCCTTTTTCATCTTTAAGTCC
66 TTGAATTAGCATATTGGCAG-CTTTATCATCTTTAAGTCC
* ** *
2133876 AATGTCGCAAGCCTTGAATCAGCACATTGGCATTTTTTTCTTCCTTAAGTCCAATATAC--TGGC
1 AATGTCGCTAGCCTTGAATCAGCACATTGGCACATTTTTCTTTCTTAAGTCCAATAT-CGTTGGC
* * *
2133939 CTTGAATAAGCATATTGGCACCTTTATCATCTTTAAGTCT
65 CTTGAATTAGCATATTGGCAGCTTTATCATCTTTAAGTCC
* * * *
2133979 AACGTCACTAGCCTTGAATCAGCACATTGGCACATTTTTCTTTCTCAAGTCCAATATCATTGGCC
1 AATGTCGCTAGCCTTGAATCAGCACATTGGCACATTTTTCTTTCTTAAGTCCAATATCGTTGGCC
2134044 TTGAATTAGCATATTGG
66 TTGAATTAGCATATTGG
2134061 TACCCTTGTC
Statistics
Matches: 246, Mismatches: 37, Indels: 11
0.84 0.13 0.04
Matches are distributed among these distances:
102 1 0.00
103 118 0.48
104 126 0.51
105 1 0.00
ACGTcount: A:0.25, C:0.21, G:0.16, T:0.38
Consensus pattern (104 bp):
AATGTCGCTAGCCTTGAATCAGCACATTGGCACATTTTTCTTTCTTAAGTCCAATATCGTTGGCC
TTGAATTAGCATATTGGCAGCTTTATCATCTTTAAGTCC
Found at i:2134044 original size:207 final size:207
Alignment explanation
Indices: 2133669--2134060 Score: 572
Period size: 207 Copynumber: 1.9 Consensus size: 207
2133659 TTCTAAGCTT
** * *
2133669 AATGTCGCTGGCCTTGAATTAGCACATTGGCACTTTTTTTTTCCTAAGTCCAATATCGCTAGCAT
1 AATGTCGCAAGCCTTGAATCAGCACATTGGCACTTTTTTTTTCCTAAGTCCAATATCACTAGCAT
* * * *** *
2133734 TGAATCAGCATATTGGCAGCTTTATCATCTTTAAGTCCAATGTTGTTGGCCTTGAATCAGCACAT
66 TGAATAAGCATATTGGCACCTTTATCATCTTTAAGTCCAACGTCACTAGCCTTGAATCAGCACAT
* * * * *
2133799 TAGCACATTTTTCTTTGTTAAGTCTAATATCGTTGGCCTTGAATTAGTATATTGGCGCCTTTTTC
131 TAGCACATTTTTCTTTCTCAAGTCCAATATCATTGGCCTTGAATTAGCATATTGGCGCCTTTTTC
2133864 ATCTTTAAGTCC
196 ATCTTTAAGTCC
*
2133876 AATGTCGCAAGCCTTGAATCAGCACATTGGCA-TTTTTTTCTTCCTTAAGTCCAATAT-ACTGGC
1 AATGTCGCAAGCCTTGAATCAGCACATTGGCACTTTTTTT-TTCC-TAAGTCCAATATCACTAGC
* *
2133939 CTTGAATAAGCATATTGGCACCTTTATCATCTTTAAGTCTAACGTCACTAGCCTTGAATCAGCAC
64 ATTGAATAAGCATATTGGCACCTTTATCATCTTTAAGTCCAACGTCACTAGCCTTGAATCAGCAC
*
2134004 ATTGGCACATTTTTCTTTCTCAAGTCCAATATCATTGGCCTTGAATTAGCATATTGG
129 ATTAGCACATTTTTCTTTCTCAAGTCCAATATCATTGGCCTTGAATTAGCATATTGG
2134061 TACCCTTGTC
Statistics
Matches: 163, Mismatches: 20, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
206 7 0.04
207 144 0.88
208 12 0.07
ACGTcount: A:0.25, C:0.21, G:0.16, T:0.38
Consensus pattern (207 bp):
AATGTCGCAAGCCTTGAATCAGCACATTGGCACTTTTTTTTTCCTAAGTCCAATATCACTAGCAT
TGAATAAGCATATTGGCACCTTTATCATCTTTAAGTCCAACGTCACTAGCCTTGAATCAGCACAT
TAGCACATTTTTCTTTCTCAAGTCCAATATCATTGGCCTTGAATTAGCATATTGGCGCCTTTTTC
ATCTTTAAGTCC
Found at i:2134220 original size:144 final size:143
Alignment explanation
Indices: 2133938--2134206 Score: 321
Period size: 144 Copynumber: 1.9 Consensus size: 143
2133928 AATATACTGG
* * *
2133938 CCTTGAATAAGCATATTGGCACCTTTATCATCTTTAAGTCTAACGTCACTAGCCTTGAATCAGCA
1 CCTTGAATAAGCATATTGGCACCTTTATCATCTCTAAGCCTAACGTCACTAGCCTTAAATCAGCA
* * * * *
2134003 CATTGGCACATTTTTCTTTCTCAAGTCCAATATCATTGGCCTTGAATTAGCATATTGGTACCCTT
66 CATTGG-ACATTTTTCTTTCTCAAGTCCAATATCATTGGCCGTGAATCAGCACATTAGCACCCTT
2134068 GTCATCTTTGCTGA
130 GTCATCTTTGCTGA
* ** *
2134082 CCTTGAATCAA-CATATTGGCATCTTTATCAT-TCCTAAGCCTAGTGTCACTGGCCTTAAATCAG
1 CCTTGAAT-AAGCATATTGGCACCTTTATCATCT-CTAAGCCTAACGTCACTAGCCTTAAATCAG
* * *
2134145 CACATTGG-CATTCTTCTCATTT-TCAAGTCTAATGTCGTTGGCCGTGAATCAGCACATTAGCA
64 CACATTGGACATT-TT-TC-TTTCTCAAGTCCAATATCATTGGCCGTGAATCAGCACATTAGCA
2134207 TTCTTCGCAT
Statistics
Matches: 105, Mismatches: 15, Indels: 10
0.81 0.12 0.08
Matches are distributed among these distances:
142 4 0.04
143 3 0.03
144 93 0.89
145 5 0.05
ACGTcount: A:0.25, C:0.24, G:0.15, T:0.35
Consensus pattern (143 bp):
CCTTGAATAAGCATATTGGCACCTTTATCATCTCTAAGCCTAACGTCACTAGCCTTAAATCAGCA
CATTGGACATTTTTCTTTCTCAAGTCCAATATCATTGGCCGTGAATCAGCACATTAGCACCCTTG
TCATCTTTGCTGA
Found at i:2134294 original size:62 final size:62
Alignment explanation
Indices: 2134214--2134332 Score: 148
Period size: 62 Copynumber: 1.9 Consensus size: 62
2134204 GCATTCTTCG
* * *
2134214 CATCTTTAAGCCCAATATCACTAGCCTTGAATCAACGTATTGGCACATTTATCATTTTTTCT
1 CATCTTCAAGCCCAATATCACTAGCCATGAATCAACATATTGGCACATTTATCATTTTTTCT
** * * * * *
2134276 CATCTTCAAGCCTGATATCGCTGGCCATGACTCAACATATTGGCACCTTTGTCATTT
1 CATCTTCAAGCCCAATATCACTAGCCATGAATCAACATATTGGCACATTTATCATTT
2134333 CTTTGCATCC
Statistics
Matches: 47, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
62 47 1.00
ACGTcount: A:0.25, C:0.26, G:0.13, T:0.36
Consensus pattern (62 bp):
CATCTTCAAGCCCAATATCACTAGCCATGAATCAACATATTGGCACATTTATCATTTTTTCT
Found at i:2135172 original size:23 final size:20
Alignment explanation
Indices: 2135138--2135193 Score: 67
Period size: 20 Copynumber: 2.6 Consensus size: 20
2135128 CAAAGAAATA
2135138 TATCGATACATTACTTACAATTG
1 TATCGATACATTAC-T-C-ATTG
* *
2135161 TATTGATACATTTCTCATTG
1 TATCGATACATTACTCATTG
2135181 TATCGATACATTA
1 TATCGATACATTA
2135194 TGGGTTTTTG
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
20 15 0.52
21 1 0.03
22 1 0.03
23 12 0.41
ACGTcount: A:0.32, C:0.16, G:0.09, T:0.43
Consensus pattern (20 bp):
TATCGATACATTACTCATTG
Found at i:2142400 original size:17 final size:16
Alignment explanation
Indices: 2142363--2142401 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
2142353 CATTACTATT
*
2142363 AAAAAAGTTTAATTTA
1 AAAAAAGTTTAATTGA
*
2142379 GAAAAAGTTTGAATTGA
1 AAAAAAGTTT-AATTGA
2142396 AAAAAA
1 AAAAAA
2142402 TATGTTCAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
16 9 0.47
17 10 0.53
ACGTcount: A:0.59, C:0.00, G:0.13, T:0.28
Consensus pattern (16 bp):
AAAAAAGTTTAATTGA
Found at i:2144613 original size:13 final size:12
Alignment explanation
Indices: 2144585--2144618 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
2144575 ATTTATCAAA
2144585 TCAAA-TTAAAT
1 TCAAATTTAAAT
2144596 TCAAATTTAAACT
1 TCAAATTTAAA-T
2144609 TCAAATTTAA
1 TCAAATTTAA
2144619 TTTTTTTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 5 0.24
12 5 0.24
13 11 0.52
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (12 bp):
TCAAATTTAAAT
Found at i:2145234 original size:13 final size:13
Alignment explanation
Indices: 2145216--2145279 Score: 60
Period size: 13 Copynumber: 4.9 Consensus size: 13
2145206 ATTTAAATAA
*
2145216 AATTAATTGATTT
1 AATTAATTAATTT
2145229 AATTAATTAATTT
1 AATTAATTAATTT
*
2145242 AGTTAATTTAATTT
1 AATTAA-TTAATTT
* *
2145256 GATTTATGTAATTT
1 AATTAAT-TAATTT
2145270 AA--AATTAATT
1 AATTAATTAATT
2145280 GTTTTTAAAA
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
11 5 0.12
12 2 0.05
13 18 0.43
14 17 0.40
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (13 bp):
AATTAATTAATTT
Found at i:2145414 original size:16 final size:16
Alignment explanation
Indices: 2145393--2145423 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2145383 TGATTTATGT
*
2145393 GATTTTAAAATTAATC
1 GATTTTAAAAATAATC
2145409 GATTTTAAAAATAAT
1 GATTTTAAAAATAAT
2145424 TAGTTTAATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.03, G:0.06, T:0.42
Consensus pattern (16 bp):
GATTTTAAAAATAATC
Found at i:2145561 original size:5 final size:5
Alignment explanation
Indices: 2145551--2145585 Score: 70
Period size: 5 Copynumber: 7.0 Consensus size: 5
2145541 AATATACTAT
2145551 TTATA TTATA TTATA TTATA TTATA TTATA TTATA
1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA
2145586 AAACTTTGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TTATA
Found at i:2148225 original size:26 final size:26
Alignment explanation
Indices: 2148185--2148242 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 26
2148175 GCTCATTTTA
* *
2148185 TTTTATAATTATATA-ATATATATTAT
1 TTTTATAATTATATATAT-TAAATAAT
* *
2148211 TTTTATATTTTTATATATTAAATAAT
1 TTTTATAATTATATATATTAAATAAT
2148237 TTTTAT
1 TTTTAT
2148243 CATATAAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 25 0.93
27 2 0.07
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (26 bp):
TTTTATAATTATATATATTAAATAAT
Found at i:2148352 original size:16 final size:16
Alignment explanation
Indices: 2148331--2148383 Score: 60
Period size: 16 Copynumber: 3.6 Consensus size: 16
2148321 TAAAAAATAT
2148331 ATTAAATTATTTAAAA
1 ATTAAATTATTTAAAA
* *
2148347 ATTAAATTTTTTAAAC
1 ATTAAATTATTTAAAA
2148363 ATT--ATT-TTTAAAA
1 ATTAAATTATTTAAAA
2148376 A-TAAATTA
1 ATTAAATTA
2148384 AAAATAATAT
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
12 1 0.03
13 7 0.23
14 6 0.19
16 17 0.55
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (16 bp):
ATTAAATTATTTAAAA
Found at i:2148352 original size:36 final size:37
Alignment explanation
Indices: 2148278--2148357 Score: 101
Period size: 36 Copynumber: 2.2 Consensus size: 37
2148268 ATTATTATAT
* * *
2148278 AAATATTAATAAAAATATTAAGTTATTTTAAAATTTA
1 AAATTTTAATAAAAATATTAAATTATTTTAAAAATTA
2148315 AAATTTTAA-AAAATATATTAAATTA-TTTAAAAATTA
1 AAATTTTAATAAAA-ATATTAAATTATTTTAAAAATTA
*
2148351 AATTTTT
1 AAATTTT
2148358 TAAACATTAT
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
36 20 0.53
37 18 0.47
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (37 bp):
AAATTTTAATAAAAATATTAAATTATTTTAAAAATTA
Found at i:2148833 original size:9 final size:9
Alignment explanation
Indices: 2148821--2148863 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
2148811 TTTTATAATT
2148821 TTTATATAA
1 TTTATATAA
*
2148830 TTTATATTA
1 TTTATATAA
*
2148839 TTTAATTTAA
1 TTT-ATATAA
*
2148849 TTTATATAT
1 TTTATATAA
2148858 TTTATA
1 TTTATA
2148864 CTTTATTAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
9 21 0.75
10 7 0.25
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (9 bp):
TTTATATAA
Found at i:2148861 original size:19 final size:19
Alignment explanation
Indices: 2148812--2148861 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
2148802 TTTACATATT
*
2148812 TTTATA-ATTTTTATATAA
1 TTTATATATTTTAATATAA
*
2148830 TTTATAT-TATTTAATTTAA
1 TTTATATAT-TTTAATATAA
2148849 TTTATATATTTTA
1 TTTATATATTTTA
2148862 TACTTTATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
18 7 0.26
19 19 0.70
20 1 0.04
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (19 bp):
TTTATATATTTTAATATAA
Found at i:2149040 original size:19 final size:18
Alignment explanation
Indices: 2149006--2149060 Score: 65
Period size: 19 Copynumber: 2.9 Consensus size: 18
2148996 AATTAAAAAT
* *
2149006 TTAAAAATTATTAATTTC
1 TTAAAAACTATCAATTTC
*
2149024 TTAAAAAACTATCAATTAC
1 TT-AAAAACTATCAATTTC
2149043 TTAAAAACTACTCAATTT
1 TTAAAAACTA-TCAATTT
2149061 TTTTTAAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
18 10 0.32
19 21 0.68
ACGTcount: A:0.47, C:0.13, G:0.00, T:0.40
Consensus pattern (18 bp):
TTAAAAACTATCAATTTC
Found at i:2149365 original size:18 final size:19
Alignment explanation
Indices: 2149342--2149383 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
2149332 AATTAAAAAA
*
2149342 TTAAAAAT-TATCCATTTC
1 TTAAAAATCTATCAATTTC
2149360 TT-AAAATCCTATCAATTTC
1 TTAAAAAT-CTATCAATTTC
2149379 TTAAA
1 TTAAA
2149384 GTTATTCAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
17 5 0.25
18 2 0.10
19 11 0.55
20 2 0.10
ACGTcount: A:0.40, C:0.17, G:0.00, T:0.43
Consensus pattern (19 bp):
TTAAAAATCTATCAATTTC
Found at i:2149509 original size:19 final size:19
Alignment explanation
Indices: 2149476--2149513 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
2149466 CTACCTATTA
2149476 ATTTCACTTTAAAAATAATT
1 ATTTCACTTTAAAAA-AATT
*
2149496 ATTT-ACTTTTAAAAAATT
1 ATTTCACTTTAAAAAAATT
2149514 TAACTATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 4 0.24
19 9 0.53
20 4 0.24
ACGTcount: A:0.45, C:0.08, G:0.00, T:0.47
Consensus pattern (19 bp):
ATTTCACTTTAAAAAAATT
Found at i:2149831 original size:2 final size:2
Alignment explanation
Indices: 2149826--2149867 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
2149816 ATCGTGTGTG
2149826 TA TA TA TA TA 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
2149868 GAGAGAGAGA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2149872 original size:2 final size:2
Alignment explanation
Indices: 2149867--2149923 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
2149857 ATATATATAT
2149867 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
2149909 AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG A
2149924 AACCAAAATT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2150602 original size:3 final size:3
Alignment explanation
Indices: 2150591--2150621 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
2150581 AATTGAAAAA
2150591 AAT AA- AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
2150622 ATAAGCTTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:2150948 original size:15 final size:14
Alignment explanation
Indices: 2150902--2150963 Score: 51
Period size: 15 Copynumber: 4.6 Consensus size: 14
2150892 TCTTTTCTTT
*
2150902 TTTTTCTTTCATTTA
1 TTTTTCTTTC-TCTA
*
2150917 CTTTT-TTTCTCTA
1 TTTTTCTTTCTCTA
*
2150930 ---TTCTTTCTCTT
1 TTTTTCTTTCTCTA
2150941 TTATTTCTTTCTCTA
1 TT-TTTCTTTCTCTA
2150956 TTTTTCTT
1 TTTTTCTT
2150964 AAAAAAATTT
Statistics
Matches: 38, Mismatches: 4, Indels: 11
0.72 0.08 0.21
Matches are distributed among these distances:
10 2 0.05
11 7 0.18
13 3 0.08
14 10 0.26
15 16 0.42
ACGTcount: A:0.08, C:0.19, G:0.00, T:0.73
Consensus pattern (14 bp):
TTTTTCTTTCTCTA
Found at i:2150952 original size:19 final size:18
Alignment explanation
Indices: 2150884--2150952 Score: 63
Period size: 19 Copynumber: 3.7 Consensus size: 18
2150874 TATTATTAAT
*
2150884 TTTTTTTCTCT-TTTCT-
1 TTTTTTTCTTTCTTTCTC
2150900 TTTTTTTCTTTCATTTACT-
1 TTTTTTTCTTTC-TTT-CTC
2150919 TTTTTTCTCTATTCTTTCTC
1 TTTTTT-TCT-TTCTTTCTC
2150939 TTTTATTTCTTTCT
1 TTTT-TTTCTTTCT
2150953 CTATTTTTCT
Statistics
Matches: 45, Mismatches: 1, Indels: 11
0.79 0.02 0.19
Matches are distributed among these distances:
16 10 0.22
18 3 0.07
19 14 0.31
20 13 0.29
21 5 0.11
ACGTcount: A:0.06, C:0.19, G:0.00, T:0.75
Consensus pattern (18 bp):
TTTTTTTCTTTCTTTCTC
Found at i:2150954 original size:26 final size:26
Alignment explanation
Indices: 2150913--2150962 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
2150903 TTTTCTTTCA
*
2150913 TTTACTTTTTTTCTCTATTCTTTCTCT
1 TTTACTTTCTTTCTCTATT-TTTCTCT
2150940 TTTA-TTTCTTTCTCTATTTTTCT
1 TTTACTTTCTTTCTCTATTTTTCT
2150963 TAAAAAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 5 0.23
26 13 0.59
27 4 0.18
ACGTcount: A:0.08, C:0.20, G:0.00, T:0.72
Consensus pattern (26 bp):
TTTACTTTCTTTCTCTATTTTTCTCT
Found at i:2151214 original size:22 final size:22
Alignment explanation
Indices: 2151189--2151230 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
2151179 TTTTTATTTA
2151189 AAAT-TTAATTATAAAAATATAT
1 AAATATTAA-TATAAAAATATAT
2151211 AAATATTAATATAAAAATAT
1 AAATATTAATATAAAAATAT
2151231 TTTTTTAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (22 bp):
AAATATTAATATAAAAATATAT
Found at i:2151493 original size:20 final size:20
Alignment explanation
Indices: 2151449--2151539 Score: 69
Period size: 21 Copynumber: 4.5 Consensus size: 20
2151439 TTCTATAATT
* * *
2151449 TGTATCGATATAACAAGTTAA
1 TGTATCGATA-AATAAATGAA
*
2151470 TGTATTGATAAATAAATGAA
1 TGTATCGATAAATAAATGAA
* *
2151490 TGTATCGATACATAAGTG-A
1 TGTATCGATAAATAAATGAA
* *
2151509 TGTATATCGATACATAAGTG-A
1 TG--TATCGATAAATAAATGAA
2151530 TGTATCGATA
1 TGTATCGATA
2151540 TTGGACCTTG
Statistics
Matches: 61, Mismatches: 7, Indels: 6
0.82 0.09 0.08
Matches are distributed among these distances:
19 11 0.18
20 22 0.36
21 28 0.46
ACGTcount: A:0.41, C:0.08, G:0.18, T:0.34
Consensus pattern (20 bp):
TGTATCGATAAATAAATGAA
Found at i:2151518 original size:21 final size:21
Alignment explanation
Indices: 2151492--2151534 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
2151482 TAAATGAATG
2151492 TATCGATACATAAGTGATGTA
1 TATCGATACATAAGTGATGTA
2151513 TATCGATACATAAGTGATGTA
1 TATCGATACATAAGTGATGTA
2151534 T
1 T
2151535 CGATATTGGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.37, C:0.09, G:0.19, T:0.35
Consensus pattern (21 bp):
TATCGATACATAAGTGATGTA
Found at i:2151675 original size:52 final size:52
Alignment explanation
Indices: 2151591--2151720 Score: 163
Period size: 52 Copynumber: 2.5 Consensus size: 52
2151581 GTATCGGTAT
* *
2151591 ATTTTTTATTGTATCGATACATTCTCGATTTTTGACCCAAATATATTGATAC
1 ATTTTTCATTGTATCGATACATTCTAGATTTTTGACCCAAATATATTGATAC
* * * * * *
2151643 GTTTTTCATTGTATTGATATATTTTAGGTTTTTGACCCAAATGTATTGATAC
1 ATTTTTCATTGTATCGATACATTCTAGATTTTTGACCCAAATATATTGATAC
* *
2151695 ATTTTTCAATGTATCGTTACA-TCTAG
1 ATTTTTCATTGTATCGATACATTCTAG
2151721 TTAAATTTGA
Statistics
Matches: 64, Mismatches: 14, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
51 4 0.06
52 60 0.94
ACGTcount: A:0.27, C:0.13, G:0.12, T:0.48
Consensus pattern (52 bp):
ATTTTTCATTGTATCGATACATTCTAGATTTTTGACCCAAATATATTGATAC
Found at i:2153087 original size:104 final size:105
Alignment explanation
Indices: 2152906--2153116 Score: 379
Period size: 104 Copynumber: 2.0 Consensus size: 105
2152896 TGATTTTTCA
*
2152906 AAACCTCCCCAAGTTAAGCATAGTTAGCTTCAATCAATGGGGATTAACATGAGCTTAAAGTTTTT
1 AAACCTCCCCAAGTTAAACATAGTTAGCTTCAATCAATGGGGATTAACATGAGCTTAAAGTTTTT
*
2152971 ACTAAGCAAGCATTACAAACTTGGGGTAAATAAGGTTACC
66 ACTAAGCAAGCATTACAAACTTGGGGTAAATAAAGTTACC
*
2153011 AAACCTCCCTAAGTTAAACAT-GTTAGCTTCAATCAATGGGGATTAACATGAGCTTAAAGTTTTT
1 AAACCTCCCCAAGTTAAACATAGTTAGCTTCAATCAATGGGGATTAACATGAGCTTAAAGTTTTT
*
2153075 ACTAAGCAAGCATTACAAACTTGGGTTAAATAAAGTTACC
66 ACTAAGCAAGCATTACAAACTTGGGGTAAATAAAGTTACC
2153115 AA
1 AA
2153117 GTCTAGATTC
Statistics
Matches: 102, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
104 83 0.81
105 19 0.19
ACGTcount: A:0.37, C:0.18, G:0.17, T:0.28
Consensus pattern (105 bp):
AAACCTCCCCAAGTTAAACATAGTTAGCTTCAATCAATGGGGATTAACATGAGCTTAAAGTTTTT
ACTAAGCAAGCATTACAAACTTGGGGTAAATAAAGTTACC
Found at i:2154621 original size:50 final size:50
Alignment explanation
Indices: 2154541--2154645 Score: 165
Period size: 50 Copynumber: 2.1 Consensus size: 50
2154531 TTTCACAATT
* * * *
2154541 TGTATCGATACATTCTTTATTGTATCGATACATTCTGGGTTTTACCTAGG
1 TGTATCAATACATTATTCATTGTATCGATACATTCTGGGTTTTACCTAGA
*
2154591 TGTATCAATACATTATTCATTGTATTGATACATTCTGGGTTTTACCTAGA
1 TGTATCAATACATTATTCATTGTATCGATACATTCTGGGTTTTACCTAGA
2154641 TGTAT
1 TGTAT
2154646 TGATATATTT
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.25, C:0.14, G:0.16, T:0.45
Consensus pattern (50 bp):
TGTATCAATACATTATTCATTGTATCGATACATTCTGGGTTTTACCTAGA
Found at i:2154671 original size:50 final size:50
Alignment explanation
Indices: 2154541--2154675 Score: 146
Period size: 50 Copynumber: 2.7 Consensus size: 50
2154531 TTTCACAATT
* * * * * *
2154541 TGTATCGATACATTCTTTATTGTATCGATACATTCTGGGTTTTACCTAGG
1 TGTATCAATACATTATTCAATGCATCGATACATTCTGGGTTTTACCTAGA
* * *
2154591 TGTATCAATACATTATTCATTGTATTGATACATTCTGGGTTTTACCTAGA
1 TGTATCAATACATTATTCAATGCATCGATACATTCTGGGTTTTACCTAGA
** *
2154641 TGTATTGATATATT-TCTCAATGCATCGATACATTC
1 TGTATCAATACATTAT-TCAATGCATCGATACATTC
2154676 AGGCATTTTT
Statistics
Matches: 73, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
49 1 0.01
50 72 0.99
ACGTcount: A:0.26, C:0.16, G:0.15, T:0.44
Consensus pattern (50 bp):
TGTATCAATACATTATTCAATGCATCGATACATTCTGGGTTTTACCTAGA
Found at i:2157199 original size:79 final size:78
Alignment explanation
Indices: 2157035--2157314 Score: 264
Period size: 79 Copynumber: 3.6 Consensus size: 78
2157025 TCCACCATCG
* *** * * *
2157035 GGGATACTCCAACCCCGTTATTTCCAATGGGG-TACTTTAACTCC-GATTTTTATTTCTAAAATA
1 GGGATACTCCAACCTCGTTATTTTTGA-GGGGATACTTCAAC-CCAGATTTAT-TTTCTAAAACA
*
2157098 TCAATTTTTCATAAATG
63 TCAATTTTTCAT-AATC
* * * *
2157115 GGGATACTCCAACCTCGGTAGTTTTGAGGGGATACTTTAACCCTAGCTTTATTTTC-AAAACATC
1 GGGATACTCCAACCTCGTTATTTTTGAGGGGATACTTCAACCC-AGATTTATTTTCTAAAACATC
*
2157179 GATTTTTCATAATC
65 AATTTTTCATAATC
* * * *
2157193 AGGGATATTCCAACCTTGTTATTTTTGAGGGGATACTTCAACCCCGATTT-TATTTCTAAAACAC
1 -GGGATACTCCAACCTCGTTATTTTTGAGGGGATACTTCAACCCAGATTTAT-TTTCTAAAACAT
*
2157257 CAA-TTTTCACAATC
64 CAATTTTTCATAATC
* * *
2157271 GGATATACTTCAACCTCGTTATTTTTGAGGGGATACTCCAACCC
1 GG-GATACTCCAACCTCGTTATTTTTGAGGGGATACTTCAACCC
2157315 CATTTTTATC
Statistics
Matches: 167, Mismatches: 26, Indels: 16
0.80 0.12 0.08
Matches are distributed among these distances:
77 3 0.02
78 57 0.34
79 68 0.41
80 34 0.20
81 5 0.03
ACGTcount: A:0.28, C:0.21, G:0.15, T:0.36
Consensus pattern (78 bp):
GGGATACTCCAACCTCGTTATTTTTGAGGGGATACTTCAACCCAGATTTATTTTCTAAAACATCA
ATTTTTCATAATC
Found at i:2163215 original size:20 final size:20
Alignment explanation
Indices: 2163190--2163236 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
2163180 GTTATAAACA
2163190 ATGTATCAATACAATTCATC
1 ATGTATCAATACAATTCATC
*
2163210 ATGTATCGATACAATTCATC
1 ATGTATCAATACAATTCATC
2163230 ATGTATC
1 ATGTATC
2163237 TATATGTATC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.36, C:0.19, G:0.09, T:0.36
Consensus pattern (20 bp):
ATGTATCAATACAATTCATC
Found at i:2163259 original size:13 final size:13
Alignment explanation
Indices: 2163241--2163270 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
2163231 TGTATCTATA
2163241 TGTATCGATACAT
1 TGTATCGATACAT
2163254 TGTATCGATACAT
1 TGTATCGATACAT
2163267 TGTA
1 TGTA
2163271 CTATGTATCG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.30, C:0.13, G:0.17, T:0.40
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2163948 original size:20 final size:21
Alignment explanation
Indices: 2163923--2163972 Score: 75
Period size: 20 Copynumber: 2.4 Consensus size: 21
2163913 AGTTTTCGTT
2163923 TTTCTCCCCCTTAATCAAA-A
1 TTTCTCCCCCTTAATCAAACA
*
2163943 TTTCTCACCCTTAATCAAAGCA
1 TTTCTCCCCCTTAATCAAA-CA
2163965 TTTCTCCC
1 TTTCTCCC
2163973 TCTTTGTCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
20 18 0.69
22 8 0.31
ACGTcount: A:0.26, C:0.36, G:0.02, T:0.36
Consensus pattern (21 bp):
TTTCTCCCCCTTAATCAAACA
Found at i:2165741 original size:20 final size:19
Alignment explanation
Indices: 2165700--2165739 Score: 53
Period size: 22 Copynumber: 1.9 Consensus size: 19
2165690 TTTTGTTGAT
2165700 GATTTTGATGAAAAATGAAA
1 GATTTTGATGAAAAAT-AAA
2165720 GATTTTGAAGTGAAAAATAA
1 GATTTTG-A-TGAAAAATAA
2165740 GAAATTTGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.39
21 3 0.17
22 8 0.44
ACGTcount: A:0.50, C:0.00, G:0.20, T:0.30
Consensus pattern (19 bp):
GATTTTGATGAAAAATAAA
Found at i:2165905 original size:13 final size:13
Alignment explanation
Indices: 2165871--2165907 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
2165861 GTACCCTATA
2165871 TATCAATACAATG
1 TATCAATACAATG
**
2165884 TATTGATACAATG
1 TATCAATACAATG
2165897 TATCAATACAA
1 TATCAATACAA
2165908 GGAATATTGT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.46, C:0.14, G:0.08, T:0.32
Consensus pattern (13 bp):
TATCAATACAATG
Found at i:2166687 original size:33 final size:32
Alignment explanation
Indices: 2166626--2166693 Score: 91
Period size: 33 Copynumber: 2.1 Consensus size: 32
2166616 ATAGCCAAAC
** *
2166626 TTGTATCGATACACACAGTATGTATCGATCCA
1 TTGTATCGATACACACAAAATGTATCGATACA
*
2166658 TTGTATCGATACACCATAAAATGTATCGATACA
1 TTGTATCGATACA-CACAAAATGTATCGATACA
2166691 TTG
1 TTG
2166694 GCTTGTAACG
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
32 13 0.42
33 18 0.58
ACGTcount: A:0.34, C:0.19, G:0.15, T:0.32
Consensus pattern (32 bp):
TTGTATCGATACACACAAAATGTATCGATACA
Found at i:2171628 original size:20 final size:20
Alignment explanation
Indices: 2171603--2171670 Score: 78
Period size: 20 Copynumber: 3.8 Consensus size: 20
2171593 GTTACAAACA
2171603 ATGTATCGATACAATTCATC
1 ATGTATCGATACAATTCATC
2171623 ATGTATCGAT---A--CA--
1 ATGTATCGATACAATTCATC
*
2171636 ATGTATCGATACAATTTATC
1 ATGTATCGATACAATTCATC
2171656 ATGTATCGATACAAT
1 ATGTATCGATACAAT
2171671 GTATCGATAC
Statistics
Matches: 40, Mismatches: 1, Indels: 14
0.73 0.02 0.25
Matches are distributed among these distances:
13 10 0.25
15 2 0.05
16 1 0.03
17 1 0.03
18 1 0.03
20 25 0.62
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.35
Consensus pattern (20 bp):
ATGTATCGATACAATTCATC
Found at i:2171641 original size:13 final size:13
Alignment explanation
Indices: 2171600--2171686 Score: 81
Period size: 13 Copynumber: 7.6 Consensus size: 13
2171590 GCCGTTACAA
2171600 ACAATGTATCGAT
1 ACAATGTATCGAT
2171613 ACAA--T-TC-AT
1 ACAATGTATCGAT
2171622 -C-ATGTATCGAT
1 ACAATGTATCGAT
2171633 ACAATGTATCGAT
1 ACAATGTATCGAT
2171646 ACAAT-T-T--AT
1 ACAATGTATCGAT
2171655 -C-ATGTATCGAT
1 ACAATGTATCGAT
2171666 ACAATGTATCGAT
1 ACAATGTATCGAT
*
2171679 ACATTGTA
1 ACAATGTA
2171687 CCATGTATCG
Statistics
Matches: 61, Mismatches: 1, Indels: 24
0.71 0.01 0.28
Matches are distributed among these distances:
7 3 0.05
8 3 0.05
9 6 0.10
10 4 0.07
11 6 0.10
12 3 0.05
13 36 0.59
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.34
Consensus pattern (13 bp):
ACAATGTATCGAT
Found at i:2171641 original size:33 final size:33
Alignment explanation
Indices: 2171600--2171702 Score: 172
Period size: 33 Copynumber: 3.1 Consensus size: 33
2171590 GCCGTTACAA
*
2171600 ACAATGTATCGATACAATTCATCATGTATCGAT
1 ACAATGTATCGATACAATTTATCATGTATCGAT
2171633 ACAATGTATCGATACAATTTATCATGTATCGAT
1 ACAATGTATCGATACAATTTATCATGTATCGAT
*
2171666 ACAATGTATCGATAC-ATTGTACCATGTATCGAT
1 ACAATGTATCGATACAATT-TATCATGTATCGAT
2171699 ACAA
1 ACAA
2171703 ATAGTGATAG
Statistics
Matches: 67, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
32 3 0.04
33 64 0.96
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (33 bp):
ACAATGTATCGATACAATTTATCATGTATCGAT
Found at i:2179202 original size:7 final size:7
Alignment explanation
Indices: 2179190--2179238 Score: 57
Period size: 7 Copynumber: 6.9 Consensus size: 7
2179180 TCTTTCTAAA
2179190 AAAAAAG
1 AAAAAAG
2179197 AAAAAA-
1 AAAAAAG
2179203 ACAAAATA-
1 A-AAAA-AG
2179211 AAAAAAG
1 AAAAAAG
2179218 AAAAAAG
1 AAAAAAG
2179225 AAAAAAG
1 AAAAAAG
2179232 AGAAAAA
1 A-AAAAA
2179239 AAGAATATGC
Statistics
Matches: 38, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
6 2 0.05
7 29 0.76
8 7 0.18
ACGTcount: A:0.86, C:0.02, G:0.10, T:0.02
Consensus pattern (7 bp):
AAAAAAG
Found at i:2179202 original size:8 final size:8
Alignment explanation
Indices: 2179187--2179243 Score: 57
Period size: 8 Copynumber: 7.2 Consensus size: 8
2179177 TTCTCTTTCT
2179187 AAAAAAA-
1 AAAAAAAG
2179194 AAGAAAAA-
1 AA-AAAAAG
* *
2179202 AACAAAAT
1 AAAAAAAG
2179210 AAAAAAAG
1 AAAAAAAG
2179218 -AAAAAAG
1 AAAAAAAG
2179225 AAAAAAGAG
1 AAAAAA-AG
2179234 AAAAAAAG
1 AAAAAAAG
2179242 AA
1 AA
2179244 TATGCTTAAG
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
7 13 0.30
8 22 0.51
9 8 0.19
ACGTcount: A:0.86, C:0.02, G:0.11, T:0.02
Consensus pattern (8 bp):
AAAAAAAG
Found at i:2179235 original size:16 final size:15
Alignment explanation
Indices: 2179190--2179239 Score: 59
Period size: 15 Copynumber: 3.4 Consensus size: 15
2179180 TCTTTCTAAA
2179190 AAAAAAG-AAAAAA-
1 AAAAAAGAAAAAAAG
* *
2179203 ACAAAATAAAAAAAG
1 AAAAAAGAAAAAAAG
2179218 AAAAAAGAAAAAAGAG
1 AAAAAAGAAAAAA-AG
2179234 AAAAAA
1 AAAAAA
2179240 AGAATATGCT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
13 5 0.17
14 6 0.20
15 11 0.37
16 8 0.27
ACGTcount: A:0.86, C:0.02, G:0.10, T:0.02
Consensus pattern (15 bp):
AAAAAAGAAAAAAAG
Found at i:2180299 original size:61 final size:61
Alignment explanation
Indices: 2180204--2180709 Score: 533
Period size: 61 Copynumber: 8.3 Consensus size: 61
2180194 AACCTTTTAT
2180204 CCTTTCAGTCCTCAAAGTA-CAAGATGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
1 CCTTTCAGTCCTCAAAG-AGCAAGATGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
* * * * *
2180265 CCTTTCAATCCTCGAAGAGCAAGATGCCTTTTCCTTTTAAAACCCATATAAGTTGGTGGCA
1 CCTTTCAGTCCTCAAAGAGCAAGATGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
* * * * * *
2180326 CCTTTTAGTCCTCAAAGAGCAGGACGTCTTTTCCTTTTAAAGCCCATACAAGTTAGTGGCA
1 CCTTTCAGTCCTCAAAGAGCAAGATGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
* * *
2180387 CCTTTCAATCCTCAAAGAGTAGGATGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
1 CCTTTCAGTCCTCAAAGAGCAAGATGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
* * * *
2180448 CCTTTCAGTCCTCAAAGAGCAGGAT-CTTTTTCCTTTTAAAACCCACACAAGTTAGTGGCA
1 CCTTTCAGTCCTCAAAGAGCAAGATGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
* * * *
2180508 CCTTCCAATCCTCAAAGAGCAAGA--CGTTTT-CTTTTCAAAGCCCACACAAGTTGGTGGTA
1 CCTTTCAGTCCTCAAAGAGCAAGATGCCTTTTCCTTTT-AAAGCCCACACAAGTTGGTGGCA
* * ** ** * **
2180567 CTTTTCAGTCCTTAAAGAGCAAGACACCTTCTT-CTTGCAAAGCCCACAAAAGTTGGTACCA
1 CCTTTCAGTCCTCAAAGAGCAAGATGCCTT-TTCCTTTTAAAGCCCACACAAGTTGGTGGCA
* * * *
2180628 CC-TTCTAGT-CTCCAAAGAGCAGGACATTTTCCTTTTTCCTTTTAAAGCCTACATAAGTTGGTG
1 CCTTTC-AGTCCT-CAAAGAGCA--AGA--TGCC-TTTTCCTTTTAAAGCCCACACAAGTTGGTG
2180691 GCA
59 GCA
* *
2180694 CTTTTTAGTCCTCAAA
1 CCTTTCAGTCCTCAAA
2180710 AAGTAGGACA
Statistics
Matches: 373, Mismatches: 57, Indels: 25
0.82 0.13 0.05
Matches are distributed among these distances:
58 5 0.01
59 45 0.12
60 59 0.16
61 217 0.58
62 5 0.01
63 2 0.01
65 4 0.01
66 32 0.09
67 4 0.01
ACGTcount: A:0.27, C:0.26, G:0.16, T:0.30
Consensus pattern (61 bp):
CCTTTCAGTCCTCAAAGAGCAAGATGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
Found at i:2180647 original size:180 final size:181
Alignment explanation
Indices: 2180204--2180663 Score: 493
Period size: 180 Copynumber: 2.5 Consensus size: 181
2180194 AACCTTTTAT
* ** ** * **
2180204 CCTTTCAGTCCTCAAAGTA-CAAGATGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCT
1 CCTTTCAATCCTCAAAG-AGCAAGACACCTTTTCCTTGCAAAGCCCACAAAAGTTGGTACCACCT
* * * * * * * **
2180268 TTCAATCCTCGAAGAGCAAGATGCCTTTTCCTTTTAAAACCCATATAAGTTGGTGGCACCTTTTA
65 TTCAGTCCTCAAAGAGCAGGAT-CATTTTCCTTTTAAAACCCACACAAGTTAGTGGCACCTTCCA
* * *
2180333 GTCCTCAAAGAGCAGGACGTCTTTTCCTTTTAAAGCCCATACAAGTTAGTGGCA
129 ATCCTCAAAGAGCAAGACG-CTTTTCCTTTTAAAGCCCACACAAGTTAGTGGCA
* * ** ** * **
2180387 CCTTTCAATCCTCAAAGAGTAGGATGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTT
1 CCTTTCAATCCTCAAAGAGCAAGACACCTTTTCCTTGCAAAGCCCACAAAAGTTGGTACCACCTT
*
2180452 TCAGTCCTCAAAGAGCAGGATCTTTTTCCTTTTAAAACCCACACAAGTTAGTGGCACCTTCCAAT
66 TCAGTCCTCAAAGAGCAGGATCATTTTCCTTTTAAAACCCACACAAGTTAGTGGCACCTTCCAAT
* *
2180517 CCTCAAAGAGCAAGACG-TTTT-CTTTTCAAAGCCCACACAAGTTGGTGGTA
131 CCTCAAAGAGCAAGACGCTTTTCCTTTT-AAAGCCCACACAAGTTAGTGGCA
* * *
2180567 CTTTTCAGTCCTTAAAGAGCAAGACACCTTCTT-CTTGCAAAGCCCACAAAAGTTGGTACCACC-
1 CCTTTCAATCCTCAAAGAGCAAGACACCTT-TTCCTTGCAAAGCCCACAAAAGTTGGTACCACCT
2180630 TTCTAGT-CTCCAAAGAGCAGGA-CATTTTCCTTTT
65 TTC-AGTCCT-CAAAGAGCAGGATCATTTTCCTTTT
2180664 TCCTTTTAAA
Statistics
Matches: 242, Mismatches: 30, Indels: 14
0.85 0.10 0.05
Matches are distributed among these distances:
179 21 0.09
180 87 0.36
181 2 0.01
182 54 0.22
183 78 0.32
ACGTcount: A:0.27, C:0.27, G:0.16, T:0.30
Consensus pattern (181 bp):
CCTTTCAATCCTCAAAGAGCAAGACACCTTTTCCTTGCAAAGCCCACAAAAGTTGGTACCACCTT
TCAGTCCTCAAAGAGCAGGATCATTTTCCTTTTAAAACCCACACAAGTTAGTGGCACCTTCCAAT
CCTCAAAGAGCAAGACGCTTTTCCTTTTAAAGCCCACACAAGTTAGTGGCA
Found at i:2180821 original size:42 final size:42
Alignment explanation
Indices: 2180701--2180968 Score: 297
Period size: 42 Copynumber: 6.3 Consensus size: 42
2180691 GCACTTTTTA
* * *
2180701 GTCCTCAAAAAGTAGGACACACTTCATTTCCTTCTTTTCCCTTTT
1 GTCCTCAAAGAGCAGGACACACTTTATTTCC-T-TTTTCCC-TTT
* *
2180746 GTCCTCAAAGAGCATGACGCACTTTATTT-CTTTTTCCCTTT
1 GTCCTCAAAGAGCAGGACACACTTTATTTCCTTTTTCCCTTT
* * **
2180787 GTCCTCAAAGAGTAGGCCACACTTTATTTCC-TTTTCTGTTT
1 GTCCTCAAAGAGCAGGACACACTTTATTTCCTTTTTCCCTTT
* *
2180828 GTCCTCAAAGAGCAGCACACACTTTATTTCCTTTTTTCCTTT
1 GTCCTCAAAGAGCAGGACACACTTTATTTCCTTTTTCCCTTT
* * * *
2180870 GTCCTCAAAAAGCAGGACACGCTTAATTTCCTTCTTTTCCTTT
1 GTCCTCAAAGAGCAGGACACACTTTATTTCCTT-TTTCCCTTT
* * * * * *
2180913 TTCCTTAAAGAGCAAGACGCATTTTATTTCCTTTTTTCCTTT
1 GTCCTCAAAGAGCAGGACACACTTTATTTCCTTTTTCCCTTT
2180955 GTCCTCAAAGAGCA
1 GTCCTCAAAGAGCA
2180969 AGATGTATTC
Statistics
Matches: 189, Mismatches: 31, Indels: 9
0.83 0.14 0.04
Matches are distributed among these distances:
41 64 0.34
42 65 0.34
43 35 0.19
44 1 0.01
45 24 0.13
ACGTcount: A:0.22, C:0.26, G:0.12, T:0.40
Consensus pattern (42 bp):
GTCCTCAAAGAGCAGGACACACTTTATTTCCTTTTTCCCTTT
Found at i:2180908 original size:127 final size:127
Alignment explanation
Indices: 2180701--2180968 Score: 310
Period size: 127 Copynumber: 2.1 Consensus size: 127
2180691 GCACTTTTTA
* * * * * *
2180701 GTCCTCAAAAAGTAGGACACACTTCATTTCCTTCTTTTCCCTTTTGTCCTCAAAGAGCATGACGC
1 GTCCTCAAAGAGCAGCACACACTTCATTTCCTTCTTTTCCCTTTTGTCCTCAAAAAGCAGGACAC
* * * * *
2180766 ACTTTATTTCTTTTTCCCTTTGTCCTCAAAGAGTAGGCCACACTTTATTTCCTTTTCT-GTTT
66 ACTTAATTTCTTTTT-CCTTTGTCCTCAAAGAGCAAGACACACTTTATTTCCTTTTCTCCTTT
*
2180828 GTCCTCAAAGAGCAGCACACACTTTATTTCCTT-TTTT-CC-TTTGTCCTCAAAAAGCAGGACAC
1 GTCCTCAAAGAGCAGCACACACTTCATTTCCTTCTTTTCCCTTTTGTCCTCAAAAAGCAGGACAC
* * * * * *
2180890 GCTTAATTTCCTTCTTTTCCTTTTTCCTTAAAGAGCAAGACGCATTTTATTTCCTTTTTTCCTTT
66 ACTTAATTT-C-T-TTTTCCTTTGTCCTCAAAGAGCAAGACACACTTTATTTCCTTTTCTCCTTT
2180955 GTCCTCAAAGAGCA
1 GTCCTCAAAGAGCA
2180969 AGATGTATTC
Statistics
Matches: 119, Mismatches: 18, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
124 27 0.23
125 3 0.03
126 39 0.33
127 50 0.42
ACGTcount: A:0.22, C:0.26, G:0.12, T:0.40
Consensus pattern (127 bp):
GTCCTCAAAGAGCAGCACACACTTCATTTCCTTCTTTTCCCTTTTGTCCTCAAAAAGCAGGACAC
ACTTAATTTCTTTTTCCTTTGTCCTCAAAGAGCAAGACACACTTTATTTCCTTTTCTCCTTT
Found at i:2180969 original size:42 final size:42
Alignment explanation
Indices: 2180701--2180971 Score: 296
Period size: 41 Copynumber: 6.4 Consensus size: 42
2180691 GCACTTTTTA
* * * *
2180701 GTCCTCAAAAAGTAGGACACACTTCATTTCCTTCTTTTCCCTTTT
1 GTCCTCAAAGAGCAAGACACACTTTATTTCCTT-TTTT-CC-TTT
* * *
2180746 GTCCTCAAAGAGCATGACGCACTTTATTT-CTTTTTCCCTTT
1 GTCCTCAAAGAGCAAGACACACTTTATTTCCTTTTTTCCTTT
* * * * *
2180787 GTCCTCAAAGAGTAGGCCACACTTTATTTCCTTTTCT-GTTT
1 GTCCTCAAAGAGCAAGACACACTTTATTTCCTTTTTTCCTTT
2180828 GTCCTCAAAGAGC-AGCACACACTTTATTTCCTTTTTTCCTTT
1 GTCCTCAAAGAGCAAG-ACACACTTTATTTCCTTTTTTCCTTT
* * * *
2180870 GTCCTCAAAAAGCAGGACACGCTTAATTTCCTTCTTTTCCTTT
1 GTCCTCAAAGAGCAAGACACACTTTATTTCCTT-TTTTCCTTT
* * * *
2180913 TTCCTTAAAGAGCAAGACGCATTTTATTTCCTTTTTTCCTTT
1 GTCCTCAAAGAGCAAGACACACTTTATTTCCTTTTTTCCTTT
2180955 GTCCTCAAAGAGCAAGA
1 GTCCTCAAAGAGCAAGA
2180972 TGTATTCCTT
Statistics
Matches: 189, Mismatches: 32, Indels: 13
0.81 0.14 0.06
Matches are distributed among these distances:
40 1 0.01
41 62 0.33
42 61 0.32
43 38 0.20
44 3 0.02
45 24 0.13
ACGTcount: A:0.23, C:0.26, G:0.12, T:0.39
Consensus pattern (42 bp):
GTCCTCAAAGAGCAAGACACACTTTATTTCCTTTTTTCCTTT
Found at i:2181013 original size:35 final size:35
Alignment explanation
Indices: 2180940--2181072 Score: 126
Period size: 35 Copynumber: 3.7 Consensus size: 35
2180930 CGCATTTTAT
* * * **
2180940 TTCCTTTTTTCCTTTGTCCTCAAAGAGCAAGATGTA
1 TTCC-TTTTTCCTTTATCCTCAAAGAGTAGGACATA
* * *
2180976 TTCCTTTTTCCTTTGTCCTCAAGGAGTAGGACCTA
1 TTCCTTTTTCCTTTATCCTCAAAGAGTAGGACATA
*
2181011 TTCTTCTCTTTTCTTTTATCCTCAAAGAGTAGGACATA
1 TTC--CT-TTTTCCTTTATCCTCAAAGAGTAGGACATA
2181049 CTT--TTTTTCCTTTATCCTCAAAGA
1 -TTCCTTTTTCCTTTATCCTCAAAGA
2181073 ACAGGACTCC
Statistics
Matches: 83, Mismatches: 10, Indels: 10
0.81 0.10 0.10
Matches are distributed among these distances:
34 19 0.23
35 30 0.36
36 4 0.05
37 2 0.02
38 26 0.31
39 2 0.02
ACGTcount: A:0.21, C:0.23, G:0.12, T:0.44
Consensus pattern (35 bp):
TTCCTTTTTCCTTTATCCTCAAAGAGTAGGACATA
Found at i:2184250 original size:79 final size:78
Alignment explanation
Indices: 2183984--2184391 Score: 338
Period size: 79 Copynumber: 5.2 Consensus size: 78
2183974 TCATTCATGT
* * * * * * * *
2183984 TTTTATTT-CTAAACTACTAATTTTCCACCATCGAGGATACTGCAATCTCGTTA-TTTCTGAGGG
1 TTTTATTTCCAAAAC-ACTGATTTTTCACAATCG-GGATACTCCAACCCCGTTATTTTC-AAGGG
2184047 GATACTCCAACCCTGA
63 GATACTCCAACCCTGA
* * * * * * **
2184063 TTTTTATTACTAAAATATTGATTTTTCACAATTTGGGATACTCCAATCCTATTA-TTTCAAAGGG
1 -TTTTATTTCCAAAACACTGATTTTTCACAA-TCGGGATACTCCAACCCCGTTATTTTC-AAGGG
* *
2184127 GATACT-TAACCCCGA
63 GATACTCCAACCCTGA
* * * * * * *
2184142 TTTTATTTTCAAAATACTAATTTTTCACAATCGGAGATTCTCTAACCCCGGTATTTTCGAGGGGA
1 TTTTATTTCCAAAACACTGATTTTTCACAATCGG-GATACTCCAACCCCGTTATTTTCAAGGGGA
* *
2184207 TACTCCAACCTTGG
65 TACTCCAACCCTGA
* * * ** * *
2184221 TTTTATTTCCAAAACATTGATTTTTCACAATCGGGGATACTTCAATCCCGTTATTTTTTAGAGAA
1 TTTTATTTCCAAAACACTGATTTTTCACAATC-GGGATACTCCAACCCCGTTATTTTCAAGGGGA
*
2184286 TACTCCAATCCTGA
65 TACTCCAACCCTGA
* * * *
2184300 TTTTATTTCTAAAACACTGATTTTTCACAATCAGGATACTCCAACCCCGTTATTTCCAAAGGGAT
1 TTTTATTTCCAAAACACTGATTTTTCACAATCGGGATACTCCAACCCCGTTATTTTCAAGGGGAT
* *
2184365 ACTCCAACCCCGT
66 ACTCCAACCCTGA
*
2184378 TTTTATCTCCAAAA
1 TTTTATTTCCAAAA
2184392 TATTAAAATT
Statistics
Matches: 256, Mismatches: 66, Indels: 14
0.76 0.20 0.04
Matches are distributed among these distances:
77 3 0.01
78 93 0.36
79 106 0.41
80 49 0.19
81 5 0.02
ACGTcount: A:0.29, C:0.22, G:0.12, T:0.37
Consensus pattern (78 bp):
TTTTATTTCCAAAACACTGATTTTTCACAATCGGGATACTCCAACCCCGTTATTTTCAAGGGGAT
ACTCCAACCCTGA
Found at i:2184275 original size:157 final size:157
Alignment explanation
Indices: 2183984--2184391 Score: 419
Period size: 157 Copynumber: 2.6 Consensus size: 157
2183974 TCATTCATGT
* * * * * *
2183984 TTTTATTTCT-AAACTACTAATTTTCCACCATCGAGGATACTGCAATCTCGTTA-TTTCTGAGGG
1 TTTTATTTCTAAAAC-ACTAATTTTTCACAATC-AGGATACTCCAACCCCGGTATTTTC-GAGGG
* * * **
2184047 GATACTCCAACCCTGATTTTTATTACTAAAATATTGATTTTTCACAATTTGGGATACTCCAATCC
63 GATACTCCAACCCTG-TTTTTATTTCCAAAACATTGATTTTTCACAATCGGGGATACTCCAATCC
* * * *
2184112 TATTATTTCAAAGGGGATACT-TAACCCCGA
127 CATTATTTCAAAGAGAATACTCCAACCCCGA
* * * *
2184142 TTTTATTT-TCAAAATACTAATTTTTCACAATCGGAGATTCTCTAACCCCGGTATTTTCGAGGGG
1 TTTTATTTCT-AAAACACTAATTTTTCACAATCAG-GATACTCCAACCCCGGTATTTTCGAGGGG
* * * *
2184206 ATACTCCAACCTTGGTTTTATTTCCAAAACATTGATTTTTCACAATCGGGGATACTTCAATCCCG
64 ATACTCCAACCCTGTTTTTATTTCCAAAACATTGATTTTTCACAATCGGGGATACTCCAATCCCA
*** * *
2184271 TTATTTTTTAGAGAATACTCCAATCCTGA
129 TTATTTCAAAGAGAATACTCCAACCCCGA
* * * * *
2184300 TTTTATTTCTAAAACACTGATTTTTCACAATCAGGATACTCCAACCCCGTTATTTCCAAAGGGAT
1 TTTTATTTCTAAAACACTAATTTTTCACAATCAGGATACTCCAACCCCGGTATTTTCGAGGGGAT
* *
2184365 ACTCCAACCCCGTTTTTATCTCCAAAA
66 ACTCCAACCCTGTTTTTATTTCCAAAA
2184392 TATTAAAATT
Statistics
Matches: 203, Mismatches: 41, Indels: 13
0.79 0.16 0.05
Matches are distributed among these distances:
157 106 0.52
158 89 0.44
159 8 0.04
ACGTcount: A:0.29, C:0.22, G:0.12, T:0.37
Consensus pattern (157 bp):
TTTTATTTCTAAAACACTAATTTTTCACAATCAGGATACTCCAACCCCGGTATTTTCGAGGGGAT
ACTCCAACCCTGTTTTTATTTCCAAAACATTGATTTTTCACAATCGGGGATACTCCAATCCCATT
ATTTCAAAGAGAATACTCCAACCCCGA
Found at i:2186442 original size:3 final size:3
Alignment explanation
Indices: 2186434--2186490 Score: 114
Period size: 3 Copynumber: 19.0 Consensus size: 3
2186424 TCATAAGTAG
2186434 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
2186482 ATT ATT ATT
1 ATT ATT ATT
2186491 TTAATGGCGC
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:2187684 original size:13 final size:13
Alignment explanation
Indices: 2187641--2187715 Score: 54
Period size: 13 Copynumber: 6.2 Consensus size: 13
2187631 TTTTCACAAT
2187641 TTGTATCGATACA
1 TTGTATCGATACA
* ** *
2187654 TTGTTTAAAATTCA
1 TTGTAT-CGATACA
2187668 TTGTATCGATACA
1 TTGTATCGATACA
2187681 TTG--T---T-CA
1 TTGTATCGATACA
*
2187688 TTGTATCGATGCA
1 TTGTATCGATACA
2187701 TTGTATCGATACA
1 TTGTATCGATACA
2187714 TT
1 TT
2187716 CTGGGTTTAC
Statistics
Matches: 46, Mismatches: 9, Indels: 14
0.67 0.13 0.20
Matches are distributed among these distances:
7 5 0.11
8 1 0.02
9 1 0.02
11 1 0.02
12 1 0.02
13 28 0.61
14 9 0.20
ACGTcount: A:0.28, C:0.13, G:0.15, T:0.44
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:2187689 original size:20 final size:20
Alignment explanation
Indices: 2187664--2187704 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
2187654 TTGTTTAAAA
2187664 TTCATTGTATCGATACATTG
1 TTCATTGTATCGATACATTG
*
2187684 TTCATTGTATCGATGCATTG
1 TTCATTGTATCGATACATTG
2187704 T
1 T
2187705 ATCGATACAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.22, C:0.15, G:0.17, T:0.46
Consensus pattern (20 bp):
TTCATTGTATCGATACATTG
Found at i:2190322 original size:130 final size:130
Alignment explanation
Indices: 2190070--2190357 Score: 294
Period size: 130 Copynumber: 2.2 Consensus size: 130
2190060 CCAACCCCGG
* * *
2190070 TTTTATTTCCAAAATATCAATTTTTCATAATCAGGGATACTCCAATCCTGTTATTTCCGAAGTGA
1 TTTTATTTCCAAAACACCAATTTTTCACAATCAGGGATACTCCAATCCTGTTATTTCCGAAGTGA
* ** * * * *
2190135 TACTCTAACCCTGACTTCATTTTTAAAATTTTGATTTCTCACAATTGGGGATGCTCCAATCCTAA
66 TACTCTAACCCTGACTTCATTTTCAAAACATCGATTTCTCACAATCGAGGATACTCCAATCCTAA
* * * ** *
2190200 TTTTATTTCTAAAACACCAATTTTTCACAATCAGGGATACTTCAATTCTGTTATTTTTGAGGTGA
1 TTTTATTTCCAAAACACCAATTTTTCACAATCAGGGATACTCCAATCCTGTTATTTCCGAAGTGA
* * * * *
2190265 TACTCTAA-CCTCGATTTTATTTTCAGAACATCGATTT-TCCATAATCGAGGATACTCC-AGCCT
66 TACTCTAACCCT-GACTTCATTTTCAAAACATCGATTTCT-CACAATCGAGGATACTCCAATCCT
*
2190327 TA
129 AA
* * *
2190329 TTGTTATCTCCAAAATATCAAATTTTTCA
1 TT-TTATTTCCAAAACA-CCAATTTTTCA
2190358 TCGAGAGATT
Statistics
Matches: 128, Mismatches: 26, Indels: 7
0.80 0.16 0.04
Matches are distributed among these distances:
129 11 0.09
130 107 0.84
131 10 0.08
ACGTcount: A:0.30, C:0.20, G:0.10, T:0.40
Consensus pattern (130 bp):
TTTTATTTCCAAAACACCAATTTTTCACAATCAGGGATACTCCAATCCTGTTATTTCCGAAGTGA
TACTCTAACCCTGACTTCATTTTCAAAACATCGATTTCTCACAATCGAGGATACTCCAATCCTAA
Found at i:2202613 original size:8 final size:8
Alignment explanation
Indices: 2202600--2202652 Score: 54
Period size: 8 Copynumber: 6.5 Consensus size: 8
2202590 TTCTTTTTTT
2202600 AAAAAAAC
1 AAAAAAAC
2202608 -AAAAAAC
1 AAAAAAAC
2202615 AAAAAAAC
1 AAAAAAAC
*
2202623 AAAACAAAG
1 AAAA-AAAC
*
2202632 AAAAAAAG
1 AAAAAAAC
*
2202640 ATAAAAAAG
1 A-AAAAAAC
2202649 AAAA
1 AAAA
2202653 GAATCTGCTT
Statistics
Matches: 41, Mismatches: 1, Indels: 6
0.85 0.02 0.12
Matches are distributed among these distances:
7 7 0.17
8 19 0.46
9 15 0.37
ACGTcount: A:0.85, C:0.08, G:0.06, T:0.02
Consensus pattern (8 bp):
AAAAAAAC
Found at i:2202635 original size:17 final size:16
Alignment explanation
Indices: 2202600--2202652 Score: 63
Period size: 17 Copynumber: 3.2 Consensus size: 16
2202590 TTCTTTTTTT
*
2202600 AAAAAAAC-AAAAAAC
1 AAAAAAACAAAAAAAG
2202615 AAAAAAACAAAACAAAG
1 AAAAAAACAAAA-AAAG
*
2202632 AAAAAAAGATAAAAAAG
1 AAAAAAACA-AAAAAAG
2202649 AAAA
1 AAAA
2202653 GAATCTGCTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
15 8 0.24
16 3 0.09
17 19 0.58
18 3 0.09
ACGTcount: A:0.85, C:0.08, G:0.06, T:0.02
Consensus pattern (16 bp):
AAAAAAACAAAAAAAG
Found at i:2203950 original size:100 final size:101
Alignment explanation
Indices: 2203626--2203949 Score: 476
Period size: 100 Copynumber: 3.2 Consensus size: 101
2203616 TTTACTTTTC
*
2203626 AGTCCTCAAAGAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCA-TTTCCTAGT
1 AGTCCTCAAAGAGCAGGACGCCTTCTCCTTTTAAAGCCCACATAAGTTGGTGGCACTTTCCTAGT
* *
2203690 CCTTAAAAAGTA-AGACGCTCTCTCCTTTCACCCTTT
66 CCTCAAAAAGTAGA-ATGCTCTCTCCTTTCACCCTTT
* * *
2203726 AGTCCTCAACGAGTAGGAAGCCTTCTCCTTTTAAAGCCCACATAAGTTGGTGGCAC-TTCCTAGT
1 AGTCCTCAAAGAGCAGGACGCCTTCTCCTTTTAAAGCCCACATAAGTTGGTGGCACTTTCCTAGT
* * *
2203790 CCTCAAAGAGTAGGATACTCTCTCCTTTCACCCTTT
66 CCTCAAAAAGTAGAATGCTCTCTCCTTTCACCCTTT
* * * *
2203826 AGTCCTCAAAGAGCAGGATGCCTTTTCCTTTTAAAGCCCACATAAGTTGGTGGCACTTTTC-AAT
1 AGTCCTCAAAGAGCAGGACGCCTTCTCCTTTTAAAGCCCACATAAGTTGGTGGCACTTTCCTAGT
*
2203890 CCTCAAAAAGTAGAATGCTCTCTCCTTTTACCCTTT
66 CCTCAAAAAGTAGAATGCTCTCTCCTTTCACCCTTT
*
2203926 AGTCCTCAAAGAGTAGGACGCCTT
1 AGTCCTCAAAGAGCAGGACGCCTT
2203950 TCAAAGCCCA
Statistics
Matches: 200, Mismatches: 21, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
100 197 0.99
101 3 0.01
ACGTcount: A:0.25, C:0.28, G:0.17, T:0.30
Consensus pattern (101 bp):
AGTCCTCAAAGAGCAGGACGCCTTCTCCTTTTAAAGCCCACATAAGTTGGTGGCACTTTCCTAGT
CCTCAAAAAGTAGAATGCTCTCTCCTTTCACCCTTT
Found at i:2204089 original size:62 final size:61
Alignment explanation
Indices: 2203946--2204443 Score: 605
Period size: 62 Copynumber: 8.1 Consensus size: 61
2203936 GAGTAGGACG
* * * *
2203946 CCTTTCAAAGCCCACACAAGCTGGTGGCACCTT-TAGTCCTCAAAGAGCAGGACAT-CTTTTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTTCTAGTCCTCAAAGAGCAGG--ATGCCTTTT
*
2204007 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTTGCTAGTCCTCAAAGAGCAGGACGCCTTTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTT-CTAGTCCTCAAAGAGCAGGATGCCTTTT
*
2204069 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAAGATGCCTTTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCAC-TTTCTAGTCCTCAAAGAGCAGGATGCCTTTT
* * * * *
2204131 CCTTTTAAAGCCTACACAAGTTAGCGGCACCTTCCAGTCCTCAAAGAGCAGGATG-CTTTCT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTTCTAGTCCTCAAAGAGCAGGATGCCTTT-T
* * * *
2204192 CCTTTTAAAGCTCACACAAGTTGGTGGCACTTTTCCAGTCCTCAAAGAGCAAGATGCCTTTC
1 CCTTTTAAAGCCCACACAAGTTGGTGGCAC-TTTCTAGTCCTCAAAGAGCAGGATGCCTTTT
* * * * *
2204254 CCTTTCAAAGCCCACACATGTTGGTAGCACCCTT-TAGTCCTCAAAAAGCAGGATGCCTTCTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCA-CTTTCTAGTCCTCAAAGAGCAGGATGCCTT-TT
* **
2204316 -CTTTTCAAAGCCCACACGAGTTGGTGGCACCTTT-TAGTCCTCAAAGAGCAGGACACCTTTT
1 CCTTTT-AAAGCCCACACAAGTTGGTGGCA-CTTTCTAGTCCTCAAAGAGCAGGATGCCTTTT
* * * *
2204377 -CTTTTCGAAGCCCACACGAGTTGGTGGCACTTTTTAGTCCTCAAAGAGCAGGATGCCTTAT
1 CCTTTT-AAAGCCCACACAAGTTGGTGGCACTTTCTAGTCCTCAAAGAGCAGGATGCCTTTT
2204438 CCTTTT
1 CCTTTT
2204444 CTCCTTTGTC
Statistics
Matches: 384, Mismatches: 41, Indels: 23
0.86 0.09 0.05
Matches are distributed among these distances:
60 8 0.02
61 160 0.42
62 190 0.49
63 26 0.07
ACGTcount: A:0.25, C:0.28, G:0.19, T:0.29
Consensus pattern (61 bp):
CCTTTTAAAGCCCACACAAGTTGGTGGCACTTTCTAGTCCTCAAAGAGCAGGATGCCTTTT
Found at i:2204271 original size:185 final size:182
Alignment explanation
Indices: 2203946--2204444 Score: 637
Period size: 185 Copynumber: 2.7 Consensus size: 182
2203936 GAGTAGGACG
* *
2203946 CCTTTCAAAGCCCACACAAGCTGGTGGCACCTTTAGTCCTCAAAGAGCAGGACATCTTTTTCCTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTAGTCCTCAAAGAGCAGG--ATC-TTTTCCTT
* * * *
2204011 TTAAAGCCCACACAAGTTGGTGGCACTTTGCTAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTA
63 TTAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGATGCCTTTCCCTTTCA
* ** *
2204076 AAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAAGATGCCTT-TT
128 AAGCCCACACAAGTTGGTAGCACCCTT-TAGTCCTCAAAAAGCAAGATGCCTTCTT
* * * *
2204131 CCTTTTAAAGCCTACACAAGTTAGCGGCACCTTCCAGTCCTCAAAGAGCAGGATGCTTTCTCCTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACCTT-TAGTCCTCAAAGAGCAGGAT-CTTT-TCCTT
* * *
2204196 TTAAAGCTCACACAAGTTGGTGGCACTTTTCCAGTCCTCAAAGAGCAAGATGCCTTTCCCTTTCA
63 TTAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGATGCCTTTCCCTTTCA
* *
2204261 AAGCCCACACATGTTGGTAGCACCCTTTAGTCCTCAAAAAGCAGGATGCCTTCTT
128 AAGCCCACACAAGTTGGTAGCACCCTTTAGTCCTCAAAAAGCAAGATGCCTTCTT
* *
2204316 -CTTTTCAAAGCCCACACGAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAGGACACCTTTT-CT
1 CCTTTT-AAAGCCCACACAAGTTGGTGGCACC-TTTAGTCCTCAAAGAGCAGG--ATCTTTTCCT
* * *
2204379 TTTCGAAGCCCACACGAGTTGGTGGCACTTTT-TAGTCCTCAAAGAGCAGGATGCCTTATCCTTT
62 TTT-AAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGATGCCTT-TCCCTT
2204443 TC
125 TC
2204445 TCCTTTGTCC
Statistics
Matches: 273, Mismatches: 31, Indels: 20
0.84 0.10 0.06
Matches are distributed among these distances:
184 61 0.22
185 188 0.69
186 23 0.08
187 1 0.00
ACGTcount: A:0.25, C:0.28, G:0.19, T:0.28
Consensus pattern (182 bp):
CCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTAGTCCTCAAAGAGCAGGATCTTTTCCTTTTA
AAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGATGCCTTTCCCTTTCAAAG
CCCACACAAGTTGGTAGCACCCTTTAGTCCTCAAAAAGCAAGATGCCTTCTT
Found at i:2204444 original size:123 final size:123
Alignment explanation
Indices: 2203948--2204444 Score: 619
Period size: 123 Copynumber: 4.0 Consensus size: 123
2203938 GTAGGACGCC
* * *
2203948 TTTCAAAGCCCACACAAGCTGGTGGCACC-TTTAGTCCTCAAAGAGCAGGACATCTTTTTCCTTT
1 TTTCAAAGCCCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAAGACA-CCTTTTCCTTT
* * *
2204012 TAAAGCCCACACAAGTTGGTGGCACTTTGCTAGTCCTCAAAGAGCAGGACGCCTTTTCCT
65 TAAAGCCCACACAAGTTGGTGGCACCTT-CTAGTCCTCAAAGAGCAGGATGCCTTCTCCT
* **
2204072 TTT-AAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAAGATGCCTTTTCCTTT
1 TTTCAAAGCCCACACAAGTTGGTGGCACCTTT-TAGTCCTCAAAGAGCAAGACACCTTTTCCTTT
* * * * *
2204136 TAAAGCCTACACAAGTTAGCGGCACCTTCCAGTCCTCAAAGAGCAGGATGCTTTCTCCT
65 TAAAGCCCACACAAGTTGGTGGCACCTTCTAGTCCTCAAAGAGCAGGATGCCTTCTCCT
* ** *
2204195 TTT-AAAGCTCACACAAGTTGGTGGCA-CTTTTCCAGTCCTCAAAGAGCAAGATGCCTTTCCCTT
1 TTTCAAAGCCCACACAAGTTGGTGGCACCTTTT--AGTCCTCAAAGAGCAAGACACCTTTTCCTT
* * * * *
2204258 TCAAAGCCCACACATGTTGGTAGCACCCTT-TAGTCCTCAAAAAGCAGGATGCCTTCTTCT
64 TTAAAGCCCACACAAGTTGGTGGCA-CCTTCTAGTCCTCAAAGAGCAGGATGCCTTCTCCT
* *
2204318 TTTCAAAGCCCACACGAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAGGACACCTTTT-CTTTT
1 TTTCAAAGCCCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAAGACACCTTTTCCTTTT
* * * * *
2204382 CGAAGCCCACACGAGTTGGTGGCACTTTTTAGTCCTCAAAGAGCAGGATGCCTTATCCT
66 -AAAGCCCACACAAGTTGGTGGCACCTTCTAGTCCTCAAAGAGCAGGATGCCTTCTCCT
2204441 TTTC
1 TTTC
2204445 TCCTTTGTCC
Statistics
Matches: 322, Mismatches: 42, Indels: 19
0.84 0.11 0.05
Matches are distributed among these distances:
121 1 0.00
122 10 0.03
123 224 0.70
124 64 0.20
125 23 0.07
ACGTcount: A:0.25, C:0.28, G:0.19, T:0.29
Consensus pattern (123 bp):
TTTCAAAGCCCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAAGACACCTTTTCCTTTT
AAAGCCCACACAAGTTGGTGGCACCTTCTAGTCCTCAAAGAGCAGGATGCCTTCTCCT
Found at i:2204498 original size:45 final size:44
Alignment explanation
Indices: 2204440--2204621 Score: 145
Period size: 45 Copynumber: 4.1 Consensus size: 44
2204430 TGCCTTATCC
*
2204440 TTTTCTCCTTTGTCCTCAAAGAGCAGGACACATTTCATTTCCTTT
1 TTTTC-CCTTTGTCCTCAAAGAGCAGGACGCATTTCATTTCCTTT
* * * ** *
2204485 TTTTCCCTTTTGTCCTTAAAGAGCAGGATGCTTTTTTTTTTC-TT
1 TTTTCCC-TTTGTCCTCAAAGAGCAGGACGCATTTCATTTCCTTT
* * * * *
2204529 TTTT-CCTTTATCCCCAAAGAGTAGGACGCACTTCATTTCCTTC
1 TTTTCCCTTTGTCCTCAAAGAGCAGGACGCATTTCATTTCCTTT
* * * * *
2204572 TTTTCCCTTCTAGTTCTCAAAAAGCAAGATGCACTT-ATTCTCCTTT
1 TTTTCCCTT-T-GTCCTCAAAGAGCAGGACGCATTTCATT-TCCTTT
2204618 TTTT
1 TTTT
2204622 TATCCTCAAA
Statistics
Matches: 105, Mismatches: 26, Indels: 11
0.74 0.18 0.08
Matches are distributed among these distances:
42 24 0.23
43 7 0.07
44 12 0.11
45 36 0.34
46 26 0.25
ACGTcount: A:0.19, C:0.25, G:0.11, T:0.45
Consensus pattern (44 bp):
TTTTCCCTTTGTCCTCAAAGAGCAGGACGCATTTCATTTCCTTT
Found at i:2204619 original size:87 final size:87
Alignment explanation
Indices: 2204409--2204655 Score: 213
Period size: 87 Copynumber: 2.9 Consensus size: 87
2204399 GGTGGCACTT
* * * *
2204409 TTTAGTCCTCAAAGAGCAGGATGC--CTTA---TCCTTTTCTCCTTTGTCCTCAAAGAGCAGGAC
1 TTTAGTCCTCAAAAAGCAAGATGCTACTTATTCTCCTTTT-TCCTTTATCCTCAAAGAGAAGGAC
* *
2204469 ACATTTCATTTCCTTTTTTTCCC
65 ACACTTCATTTCCTTCTTTTCCC
* * * * ** * * * * * *
2204492 TTTTGTCCTTAAAGAGCAGGATGCTTTTTTTTTTCTTTTTTCCTTTATCCCCAAAGAGTAGGACG
1 TTTAGTCCTCAAAAAGCAAGATGCTACTTATTCTCCTTTTTCCTTTATCCTCAAAGAGAAGGACA
2204557 CACTTCATTTCCTTCTTTTCCC
66 CACTTCATTTCCTTCTTTTCCC
* *
2204579 TTCTAGTTCTCAAAAAGCAAGATGC-ACTTATTCTCCTTTTT--TTTATCCTCAAAAAGAAGGAC
1 TT-TAGTCCTCAAAAAGCAAGATGCTACTTATTCTCCTTTTTCCTTTATCCTCAAAGAGAAGGAC
* * *
2204641 ATATTTAATTTCCTT
65 ACACTTCATTTCCTT
2204656 TTTCCTTCAT
Statistics
Matches: 130, Mismatches: 28, Indels: 10
0.77 0.17 0.06
Matches are distributed among these distances:
83 22 0.17
85 31 0.24
87 54 0.42
88 23 0.18
ACGTcount: A:0.23, C:0.24, G:0.12, T:0.42
Consensus pattern (87 bp):
TTTAGTCCTCAAAAAGCAAGATGCTACTTATTCTCCTTTTTCCTTTATCCTCAAAGAGAAGGACA
CACTTCATTTCCTTCTTTTCCC
Found at i:2204760 original size:41 final size:40
Alignment explanation
Indices: 2204445--2204763 Score: 140
Period size: 41 Copynumber: 7.6 Consensus size: 40
2204435 TATCCTTTTC
* *
2204445 TCCTTTGTCCTCAAAGAGCAGGACACATTTCATTTCCTTTTTT
1 TCCTTTATCCTCAAAGAGCAGGACACATTTTATTTCC---TTT
* * ** * * *
2204488 TCCCTTTTGTCCTTAAAGAGCAGGATGCTTTTTTTTTTCTTTTT
1 T-CC-TTTATCCTCAAAGAGCAGGACAC-ATTTTATTTC-CTTT
* * * * *
2204532 TCCTTTATCCCCAAAGAGTAGGACGCACTTCATTTCCTTCTTT
1 TCCTTTATCCTCAAAGAGCAGGACACATTTTATTT-C--CTTT
* * * ** *
2204575 TCCCTTCTAGTTCTCAAAAAGCAAGATGCA-CTTATTCTCCTTT
1 T-CCTT-TA-TCCTCAAAGAGCAGGACACATTTTATT-TCCTTT
* * * * *
2204618 T-TTTTATCCTCAAAAAGAAGGACATATTTAATTTCCTTTT
1 TCCTTTATCCTCAAAGAGCAGGACACATTTTATTTCC-TTT
* * * **
2204658 TCCTTCATCTTCAAA-AGGTAGGATGCATTTTATTTCCTTT
1 TCCTTTATCCTCAAAGA-GCAGGACACATTTTATTTCCTTT
* * *
2204698 TCTCTTTTGTCCTCAAGGAGCAGGACCCATTTTATTCTCCTTT
1 TC-C-TTTATCCTCAAAGAGCAGGACACATTTTATT-TCCTTT
*
2204741 TCCTTAATCCTCAAAGAGCAGGA
1 TCCTTTATCCTCAAAGAGCAGGA
2204764 TGGCCCTTTC
Statistics
Matches: 206, Mismatches: 52, Indels: 38
0.70 0.18 0.13
Matches are distributed among these distances:
39 17 0.08
40 16 0.08
41 50 0.24
42 42 0.20
43 22 0.11
44 10 0.05
45 27 0.13
46 22 0.11
ACGTcount: A:0.23, C:0.24, G:0.12, T:0.42
Consensus pattern (40 bp):
TCCTTTATCCTCAAAGAGCAGGACACATTTTATTTCCTTT
Found at i:2204764 original size:83 final size:84
Alignment explanation
Indices: 2204409--2204765 Score: 261
Period size: 83 Copynumber: 4.3 Consensus size: 84
2204399 GGTGGCACTT
* *
2204409 TTTAGTCCTCAAAGAGCAGGATGC-CTTA--TCCTTTTCTCCTTTGTCCTCAAAGAGCAGGACAC
1 TTTAATCCTCAAAGAGCAGGATGCACTTATTTCCTTTTCTCCTTTATCCTCAAAGAGCAGGACAC
2204471 ATTTCATTTCCTTTTTTTCCC
66 ATTTCATTTCC--TTTTTCCC
** * ** * * * * * *
2204492 TTTTGTCCTTAAAGAGCAGGATGCTTTTTTTTTTCTTTTTTCCTTTATCCCCAAAGAGTAGGACG
1 TTTAATCCTCAAAGAGCAGGATGC-ACTTATTTCCTTTTCTCCTTTATCCTCAAAGAGCAGGACA
*
2204557 CACTTCATTTCCTTCTTTTCCC
65 CATTTCATTTCC-T-TTTTCCC
* * * * * *
2204579 TTCTAGTTCTCAAAAAGCAAGATGCACTTATTCTCCTTTT-T--TTTATCCTCAAAAAGAAGGAC
1 TT-TAATCCTCAAAGAGCAGGATGCACTTATT-TCCTTTTCTCCTTTATCCTCAAAGAGCAGGAC
* *
2204641 ATATTTAATTTCCTTTTT-CC
64 ACATTTCATTTCCTTTTTCCC
* * * * * * *
2204661 -TTCATCTTCAAA-AGGTAGGATGCATTTTATTTCCTTTTCTCTTTTGTCCTCAAGGAGCAGGAC
1 TTTAATCCTCAAAGA-GCAGGATGCA-CTTATTTCCTTTTCTCCTTTATCCTCAAAGAGCAGGAC
* *
2204724 CCATTTTATTCTCC-TTTT-CC
64 ACATTTCATT-TCCTTTTTCCC
2204744 -TTAATCCTCAAAGAGCAGGATG
1 TTTAATCCTCAAAGAGCAGGATG
2204766 GCCCTTTCTT
Statistics
Matches: 216, Mismatches: 44, Indels: 28
0.75 0.15 0.10
Matches are distributed among these distances:
79 1 0.00
80 22 0.10
81 7 0.03
82 2 0.01
83 73 0.34
84 5 0.02
85 29 0.13
86 2 0.01
87 52 0.24
88 23 0.11
ACGTcount: A:0.22, C:0.24, G:0.13, T:0.41
Consensus pattern (84 bp):
TTTAATCCTCAAAGAGCAGGATGCACTTATTTCCTTTTCTCCTTTATCCTCAAAGAGCAGGACAC
ATTTCATTTCCTTTTTCCC
Found at i:2205393 original size:20 final size:20
Alignment explanation
Indices: 2205368--2205406 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
2205358 TTGTTCAAAA
2205368 TTCATTGTATCAATACATTG
1 TTCATTGTATCAATACATTG
*
2205388 TTCATTGTATCGATACATT
1 TTCATTGTATCAATACATT
2205407 CTGGGTTTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.15, G:0.10, T:0.46
Consensus pattern (20 bp):
TTCATTGTATCAATACATTG
Found at i:2209994 original size:13 final size:12
Alignment explanation
Indices: 2209969--2210011 Score: 54
Period size: 13 Copynumber: 3.6 Consensus size: 12
2209959 GTATATATAT
2209969 ATATATATAAAA
1 ATATATATAAAA
2209981 ATATATACTAAAA
1 ATATATA-TAAAA
2209994 ATATA-A-AAAGA
1 ATATATATAAA-A
2210005 ATATATA
1 ATATATA
2210012 AAATATTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
10 3 0.11
11 6 0.21
12 9 0.32
13 10 0.36
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.30
Consensus pattern (12 bp):
ATATATATAAAA
Found at i:2210013 original size:21 final size:20
Alignment explanation
Indices: 2209963--2210014 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
2209953 ATCAAGGTAT
* * *
2209963 ATATATATATATATAAAAAT
1 ATATATAAAAATATAAAAAA
2209983 ATATACTAAAAATATAAAAAGA
1 ATATA-TAAAAATATAAAAA-A
2210005 ATATATAAAA
1 ATATATAAAA
2210015 TATTTTAAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 5 0.19
21 17 0.63
22 5 0.19
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (20 bp):
ATATATAAAAATATAAAAAA
Found at i:2210014 original size:20 final size:19
Alignment explanation
Indices: 2209963--2210017 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 19
2209953 ATCAAGGTAT
* *
2209963 ATATATATATATATAAAAAT
1 ATATATA-AAATATAAAAAA
2209983 ATATACTAAAAATATAAAAAGA
1 ATATA-T-AAAATATAAAAA-A
2210005 ATATATAAAATAT
1 ATATATAAAATAT
2210018 TTTAAAGAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
20 12 0.40
21 12 0.40
22 6 0.20
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.33
Consensus pattern (19 bp):
ATATATAAAATATAAAAAA
Found at i:2215875 original size:13 final size:13
Alignment explanation
Indices: 2215857--2215887 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
2215847 ACAATTCATC
2215857 ATGTATCGATACA
1 ATGTATCGATACA
2215870 ATGTATCGATACA
1 ATGTATCGATACA
*
2215883 TTGTA
1 ATGTA
2215888 CCATGTATCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.35
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2215882 original size:33 final size:33
Alignment explanation
Indices: 2215835--2215903 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
2215825 CTGTTACAAG
* *
2215835 CAATATATCTATACAATT-CATCATGTATCGATA
1 CAATATATCGATAC-ATTGCACCATGTATCGATA
* *
2215868 CAATGTATCGATACATTGTACCATGTATCGATA
1 CAATATATCGATACATTGCACCATGTATCGATA
2215901 CAA
1 CAA
2215904 ACAGTGGTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 3 0.10
33 28 0.90
ACGTcount: A:0.38, C:0.19, G:0.10, T:0.33
Consensus pattern (33 bp):
CAATATATCGATACATTGCACCATGTATCGATA
Found at i:2216561 original size:22 final size:22
Alignment explanation
Indices: 2216533--2216584 Score: 86
Period size: 22 Copynumber: 2.4 Consensus size: 22
2216523 AGTTTTCGTT
*
2216533 TTTCTCCCCCTTAATTAAAGAA
1 TTTCTCCCCCTTAATCAAAGAA
*
2216555 TTTCTCCCCCTTAATCAAAGCA
1 TTTCTCCCCCTTAATCAAAGAA
2216577 TTTCTCCC
1 TTTCTCCC
2216585 TTTTTGTCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.25, C:0.35, G:0.04, T:0.37
Consensus pattern (22 bp):
TTTCTCCCCCTTAATCAAAGAA
Found at i:2225117 original size:51 final size:51
Alignment explanation
Indices: 2225052--2225218 Score: 194
Period size: 51 Copynumber: 3.3 Consensus size: 51
2225042 GAAAATAACG
* * * * * *
2225052 GGGTTGGAGTATCCTCGATTATGGAAAATCGATGCTTTAGAAATAAAACCA
1 GGGTTAGAGTATCCTCGATTGTGGAAAATTGGTGATTTAGAAATAAAATCA
* *
2225103 GGGTTAGAGTATCCTCGATTGT-GAGAAATTGGTGTTTTGGAAATAAAATCA
1 GGGTTAGAGTATCCTCGATTGTGGA-AAATTGGTGATTTAGAAATAAAATCA
* ** *
2225154 GAGTCGGAGTATCCCCGATTGTGGAAAATTGGT-ATATTAGAAATAAAATCA
1 GGGTTAGAGTATCCTCGATTGTGGAAAATTGGTGAT-TTAGAAATAAAATCA
2225205 GGGTTAGAGTATCC
1 GGGTTAGAGTATCC
2225219 CATCGAAAAT
Statistics
Matches: 97, Mismatches: 16, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
50 3 0.03
51 92 0.95
52 2 0.02
ACGTcount: A:0.34, C:0.11, G:0.26, T:0.29
Consensus pattern (51 bp):
GGGTTAGAGTATCCTCGATTGTGGAAAATTGGTGATTTAGAAATAAAATCA
Found at i:2225279 original size:28 final size:29
Alignment explanation
Indices: 2225203--2225279 Score: 90
Period size: 28 Copynumber: 2.7 Consensus size: 29
2225193 GAAATAAAAT
*
2225203 CAGGGTTAGAGTATCCC-ATCGAAAATAA
1 CAGGGTTGGAGTATCCCGATCGAAAATAA
2225231 C-GGGATTGGAGTATCCCCGAT-G-AAATAA
1 CAGGG-TTGGAGTAT-CCCGATCGAAAATAA
2225259 CAGGGTTGGAGTATCCTCGAT
1 CAGGGTTGGAGTATCC-CGAT
2225280 TATGAAAAAA
Statistics
Matches: 43, Mismatches: 1, Indels: 10
0.80 0.02 0.19
Matches are distributed among these distances:
27 5 0.12
28 29 0.67
29 7 0.16
30 2 0.05
ACGTcount: A:0.31, C:0.18, G:0.27, T:0.23
Consensus pattern (29 bp):
CAGGGTTGGAGTATCCCGATCGAAAATAA
Found at i:2225354 original size:28 final size:28
Alignment explanation
Indices: 2225314--2225386 Score: 128
Period size: 28 Copynumber: 2.6 Consensus size: 28
2225304 GATATAAAGC
2225314 TGGGGTTGGAGTATCCCCTCGGAAATAA
1 TGGGGTTGGAGTATCCCCTCGGAAATAA
*
2225342 TGGGGTTTGAGTATCCCCTCGGAAATAA
1 TGGGGTTGGAGTATCCCCTCGGAAATAA
*
2225370 CGGGGTTGGAGTATCCC
1 TGGGGTTGGAGTATCCC
2225387 TAATTAAGAA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 42 1.00
ACGTcount: A:0.22, C:0.19, G:0.33, T:0.26
Consensus pattern (28 bp):
TGGGGTTGGAGTATCCCCTCGGAAATAA
Found at i:2227739 original size:13 final size:13
Alignment explanation
Indices: 2227721--2227750 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
2227711 TACAATGAGC
2227721 AATGTATCGATAA
1 AATGTATCGATAA
*
2227734 AATGTATCGATAC
1 AATGTATCGATAA
2227747 AATG
1 AATG
2227751 AGCAGTGTAT
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:0.43, C:0.10, G:0.17, T:0.30
Consensus pattern (13 bp):
AATGTATCGATAA
Found at i:2227743 original size:33 final size:33
Alignment explanation
Indices: 2227698--2227772 Score: 114
Period size: 33 Copynumber: 2.3 Consensus size: 33
2227688 CGATACATTG
*
2227698 TAAAATGCATCGATACAATGAGCAATGTATCGA
1 TAAAATGCATCGATACAATGAGCAATGTATCAA
* *
2227731 TAAAATGTATCGATACAATGAGCAGTGTATCAA
1 TAAAATGCATCGATACAATGAGCAATGTATCAA
*
2227764 TATAATGCA
1 TAAAATGCA
2227773 AAATGTATCA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.43, C:0.13, G:0.17, T:0.27
Consensus pattern (33 bp):
TAAAATGCATCGATACAATGAGCAATGTATCAA
Found at i:2227761 original size:20 final size:19
Alignment explanation
Indices: 2227682--2227761 Score: 55
Period size: 20 Copynumber: 4.4 Consensus size: 19
2227672 AAATGCCTGA
* **
2227682 ATGTATCGATACATTGTAAA
1 ATGTATCGATACAATG-AGC
*
2227702 ATGCATCGATACAATGAGC
1 ATGTATCGATACAATGAGC
2227721 AATGTATCGAT--AA--A--
1 -ATGTATCGATACAATGAGC
2227735 ATGTATCGATACAATGAGC
1 ATGTATCGATACAATGAGC
2227754 AGTGTATC
1 A-TGTATC
2227762 AATATAATGC
Statistics
Matches: 47, Mismatches: 5, Indels: 16
0.69 0.07 0.24
Matches are distributed among these distances:
13 10 0.21
15 2 0.04
16 1 0.02
17 1 0.02
18 2 0.04
19 2 0.04
20 29 0.62
ACGTcount: A:0.39, C:0.14, G:0.19, T:0.29
Consensus pattern (19 bp):
ATGTATCGATACAATGAGC
Found at i:2227863 original size:13 final size:13
Alignment explanation
Indices: 2227803--2227845 Score: 77
Period size: 13 Copynumber: 3.3 Consensus size: 13
2227793 GTAAACCCAG
2227803 AATGTATCGATAC
1 AATGTATCGATAC
2227816 AATGTATCGATAC
1 AATGTATCGATAC
*
2227829 AATGTATTGATAC
1 AATGTATCGATAC
2227842 AATG
1 AATG
2227846 AACAATGTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
13 29 1.00
ACGTcount: A:0.40, C:0.12, G:0.16, T:0.33
Consensus pattern (13 bp):
AATGTATCGATAC
Found at i:2228711 original size:45 final size:42
Alignment explanation
Indices: 2228558--2228745 Score: 149
Period size: 42 Copynumber: 4.5 Consensus size: 42
2228548 TAGTATGTCT
* * * *
2228558 TGCTTTTTGAGGAC-AAAGGAAAAAAGGAAACGAAATACGTCC
1 TGCTCTTTGAGGACAAAAAGAAAAAAGGAAA-TAAATGCGTCC
* * *
2228600 TACTCTTCGAGGA-AAAAAG-AAAGAGGAAAATAAAATGCGTCC
1 TGCTCTTTGAGGACAAAAAGAAAAAAGG-AAAT-AAATGCGTCC
* * * *
2228642 TGCTCTTTGAAGATAAAAGGGAAAATAAGGAAATAAAGTGTGTCC
1 TGCTCTTTGAGGACAAAA-AGAAAA-AAGGAAATAAA-TGCGTCC
2228687 TGCTCTTTGAGGAC--AAAGAAGAAAAGG--A-AAATGCGTCC
1 TGCTCTTTGAGGACAAAAAGAA-AAAAGGAAATAAATGCGTCC
2228725 TGCTCTTTGAGGACTAAAAAG
1 TGCTCTTTGAGGAC-AAAAAG
2228746 TGCCACCAAC
Statistics
Matches: 117, Mismatches: 17, Indels: 25
0.74 0.11 0.16
Matches are distributed among these distances:
38 20 0.17
39 3 0.03
40 1 0.01
41 10 0.09
42 43 0.37
43 8 0.07
44 4 0.03
45 25 0.21
46 3 0.03
ACGTcount: A:0.42, C:0.13, G:0.24, T:0.21
Consensus pattern (42 bp):
TGCTCTTTGAGGACAAAAAGAAAAAAGGAAATAAATGCGTCC
Found at i:2228784 original size:61 final size:59
Alignment explanation
Indices: 2228708--2228974 Score: 295
Period size: 61 Copynumber: 4.6 Consensus size: 59
2228698 GACAAAGAAG
*
2228708 AAAAGGAAAATGCGTCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTTGTGTGGGCTTT
1 AAAA-GAAAAGGCGTCCTGCTCTTTGAGGACTAAAAA-TGCCACCAACTTGTGTGGGCTTT
** * * *
2228769 GAAAAGAAAAGGCGTCCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTCGAGTGGTCTTT
1 -AAAAGAAAAGGCGTCCTGCTCTTTGAGGACTA-AAAATGCCACCAACTTGTGTGGGCTTT
*
2228830 AAAAGGAGAAA-GCATCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTT
1 AAAA-GA-AAAGGCGTCCTGCTCTTTGAGGACT-AAAAATGCCACCAACTTGTGTGGGCTTT
* *
2228891 ----G-AAAGGTGTCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTT
1 AAAAGAAAAGGCGTCCTGCTCTTTGAGGACT-AAAAATGCCACCAACTTGTGTGGGCTTT
*
2228946 -----AAAAGGCATCCTGCTCTTTGAGGACTAAA
1 AAAAGAAAAGGCGTCCTGCTCTTTGAGGACTAAA
2228975 GGGTGAAAGG
Statistics
Matches: 181, Mismatches: 18, Indels: 20
0.83 0.08 0.09
Matches are distributed among these distances:
54 5 0.03
55 70 0.39
56 1 0.01
60 4 0.02
61 91 0.50
62 10 0.06
ACGTcount: A:0.28, C:0.20, G:0.26, T:0.25
Consensus pattern (59 bp):
AAAAGAAAAGGCGTCCTGCTCTTTGAGGACTAAAAATGCCACCAACTTGTGTGGGCTTT
Found at i:2228874 original size:122 final size:116
Alignment explanation
Indices: 2228708--2228974 Score: 334
Period size: 116 Copynumber: 2.3 Consensus size: 116
2228698 GACAAAGAAG
*
2228708 AAAAGGAAAATGCGTCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTTGTGTGGGCTTTGAAA
1 AAAAGGAAAATGCATCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTTGTGTGGGCTTT----
** *
2228773 AGAAAAGGCGTCCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTCGAGTGGTCTTT
62 -G-AAAGGCGTCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTCGAGTGGGCTTT
2228830 AAAAGGAGAAA-GCATCCTGCTCTTTGAGGACTGAAAAA-TGCCACCAACTTGTGTGGGCTTTGA
1 AAAAGGA-AAATGCATCCTGCTCTTTGAGGACT-AAAAAGTGCCACCAACTTGTGTGGGCTTTGA
* * * *
2228893 AAGGTGTCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTT
64 AAGGCGTCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTCGAGTGGGCTTT
2228946 AAAA-G-----GCATCCTGCTCTTTGAGGACTAAA
1 AAAAGGAAAATGCATCCTGCTCTTTGAGGACTAAA
2228975 GGGTGAAAGG
Statistics
Matches: 135, Mismatches: 8, Indels: 17
0.84 0.05 0.11
Matches are distributed among these distances:
109 3 0.02
110 21 0.16
115 1 0.01
116 51 0.38
117 1 0.01
122 50 0.37
123 8 0.06
ACGTcount: A:0.28, C:0.20, G:0.26, T:0.25
Consensus pattern (116 bp):
AAAAGGAAAATGCATCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTTGTGTGGGCTTTGAAA
GGCGTCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTCGAGTGGGCTTT
Found at i:2229059 original size:94 final size:94
Alignment explanation
Indices: 2228898--2229157 Score: 430
Period size: 94 Copynumber: 2.8 Consensus size: 94
2228888 TTTGAAAGGT
*
2228898 GTCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGCATCCTGCTCT
1 GTCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTATGGGCTTTAAAAGGCATCCTGCTCT
**
2228963 TTGAGGACTAAAGGGTGAAAGGAGAGAGC
66 TTGAGGACTAAAGGCCGAAAGGAGAGAGC
* *
2228992 GTCCTGCTCTTTGAGGACTGGGAAGTGCCACCAACTTGTATGGGCTTTAAAAGGCATCCTGCTCT
1 GTCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTATGGGCTTTAAAAGGCATCCTGCTCT
2229057 TTGAGGACTAAAGGCCGAAAGGAGAGAGC
66 TTGAGGACTAAAGGCCGAAAGGAGAGAGC
* * * **
2229086 GTCCTGTTCTTTGAGGACTAGAAAATGCCACCAACTTGTATGGGCTTTGAAAGGTGTCCTGCTCT
1 GTCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTATGGGCTTTAAAAGGCATCCTGCTCT
2229151 TTGAGGA
66 TTGAGGA
2229158 TTAGAAAATG
Statistics
Matches: 154, Mismatches: 12, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
94 154 1.00
ACGTcount: A:0.25, C:0.20, G:0.29, T:0.26
Consensus pattern (94 bp):
GTCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTATGGGCTTTAAAAGGCATCCTGCTCT
TTGAGGACTAAAGGCCGAAAGGAGAGAGC
Found at i:2229140 original size:243 final size:243
Alignment explanation
Indices: 2228831--2229288 Score: 792
Period size: 243 Copynumber: 1.9 Consensus size: 243
2228821 GTGGTCTTTA
*
2228831 AAAGGAGAAAGCATCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTGAAAG
1 AAAGGAGAAAGCATCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTATGGGCTTTGAAAG
*
2228896 GTGTCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGCATCCTGCT
66 GTGTCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGCATCCTGCT
* *
2228961 CTTTGAGGACTAAAGGGTGAAAGGAGAGAGCGTCCTGCTCTTTGAGGACTGGGAAGTGCCACCAA
131 CTTTGAGGACTAAAGGGCGAAAGGAGAGAGCGTCCTGCTCTTTGAAGACTGGGAAGTGCCACCAA
*
2229026 CTTGTATGGGCTTTAAAAGGCATCCTGCTCTTTGAGGACTAAAGGCCG
196 CTTATATGGGCTTTAAAAGGCATCCTGCTCTTTGAGGACTAAAGGCCG
* * *
2229074 AAAGGAGAGAGCGTCCTGTTCTTTGAGGACT-AGAAAATGCCACCAACTTGTATGGGCTTTGAAA
1 AAAGGAGAAAGCATCCTGCTCTTTGAGGACTGA-AAAATGCCACCAACTTGTATGGGCTTTGAAA
* *
2229138 GGTGTCCTGCTCTTTGAGGATTAGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGCGTCCTGC
65 GGTGTCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGCATCCTGC
*
2229203 TCTTTGAGGACTAAAGGGCGAAAGGAGAGAGTGTCCTGCTCTTTGAAGACTGGGAAGTGCCACCA
130 TCTTTGAGGACTAAAGGGCGAAAGGAGAGAGCGTCCTGCTCTTTGAAGACTGGGAAGTGCCACCA
*
2229268 ACTTATGTGGGCTTTAAAAGG
195 ACTTATATGGGCTTTAAAAGG
2229289 AGAAGGCGTC
Statistics
Matches: 202, Mismatches: 12, Indels: 2
0.94 0.06 0.01
Matches are distributed among these distances:
242 1 0.00
243 201 1.00
ACGTcount: A:0.27, C:0.19, G:0.29, T:0.26
Consensus pattern (243 bp):
AAAGGAGAAAGCATCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTATGGGCTTTGAAAG
GTGTCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGCATCCTGCT
CTTTGAGGACTAAAGGGCGAAAGGAGAGAGCGTCCTGCTCTTTGAAGACTGGGAAGTGCCACCAA
CTTATATGGGCTTTAAAAGGCATCCTGCTCTTTGAGGACTAAAGGCCG
Found at i:2229145 original size:149 final size:149
Alignment explanation
Indices: 2228992--2229288 Score: 450
Period size: 149 Copynumber: 2.0 Consensus size: 149
2228982 AGGAGAGAGC
* * *
2228992 GTCCTGCTCTTTGAGGACTGGGAAGTGCCACCAACTTGTATGGGCTTTAAAAGGCATCCTGCTCT
1 GTCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTATGGGCTTTAAAAGGCATCCTGCTCT
* *
2229057 TTGAGGACTAAAGGCCGAAAGGAGAGAGCGTCCTGTTCTTTGAGGACTAGAAAATGCCACCAACT
66 TTGAGGACTAAAGGCCGAAAGGAGAGAGCGTCCTGCTCTTTGAAGACTAGAAAATGCCACCAACT
* *
2229122 TGTATGGGCTTTGAAAGGT
131 TATATGGGCTTTAAAAGGT
* * *
2229141 GTCCTGCTCTTTGAGGATTAGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGCGTCCTGCTCT
1 GTCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTATGGGCTTTAAAAGGCATCCTGCTCT
* * * * *
2229206 TTGAGGACTAAAGGGCGAAAGGAGAGAGTGTCCTGCTCTTTGAAGACTGGGAAGTGCCACCAACT
66 TTGAGGACTAAAGGCCGAAAGGAGAGAGCGTCCTGCTCTTTGAAGACTAGAAAATGCCACCAACT
*
2229271 TATGTGGGCTTTAAAAGG
131 TATATGGGCTTTAAAAGG
2229289 AGAAGGCGTC
Statistics
Matches: 132, Mismatches: 16, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
149 132 1.00
ACGTcount: A:0.26, C:0.20, G:0.29, T:0.26
Consensus pattern (149 bp):
GTCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTATGGGCTTTAAAAGGCATCCTGCTCT
TTGAGGACTAAAGGCCGAAAGGAGAGAGCGTCCTGCTCTTTGAAGACTAGAAAATGCCACCAACT
TATATGGGCTTTAAAAGGT
Found at i:2229170 original size:55 final size:55
Alignment explanation
Indices: 2229084--2229215 Score: 219
Period size: 55 Copynumber: 2.4 Consensus size: 55
2229074 AAAGGAGAGA
* *
2229084 GCGTCCTGTTCTTTGAGGACTAGAAAATGCCACCAACTTGTATGGGCTTTGAAAG
1 GCGTCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTATGGGCTTTAAAAG
* * *
2229139 GTGTCCTGCTCTTTGAGGATTAGAAAATGCCACCAACTTGTGTGGGCTTTAAAAG
1 GCGTCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTATGGGCTTTAAAAG
2229194 GCGTCCTGCTCTTTGAGGACTA
1 GCGTCCTGCTCTTTGAGGACTA
2229216 AAGGGCGAAA
Statistics
Matches: 70, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
55 70 1.00
ACGTcount: A:0.23, C:0.20, G:0.26, T:0.30
Consensus pattern (55 bp):
GCGTCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTATGGGCTTTAAAAG
Found at i:2240637 original size:4 final size:4
Alignment explanation
Indices: 2240630--2240664 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
2240620 CAAAACAAAC
2240630 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
2240665 CACCTCAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:2242864 original size:51 final size:50
Alignment explanation
Indices: 2242771--2242939 Score: 160
Period size: 51 Copynumber: 3.3 Consensus size: 50
2242761 AAAATAACGA
* ** **
2242771 GGTTGGAGTATCCCCGATTGTGAAAAATTAATTCTTTAGAAATAAGGCCGG
1 GGTTGGAGTATCCCCGATTGTGAGAAATTGGTT-TTTAGAAATAAAACCGG
* *
2242822 GGTTGGAGTATCCCCGATTGTGAGAAATTGGTGTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTGTGAGAAATTGGT-TTTTAGAAATAAAACCGG
* * * * *
2242873 AGTTGGAGTATTCCCAATTGTG-GAAAATTGGTATTTTAGAAAAAAAAAATCGG
1 GGTTGGAGTATCCCCGATTGTGAG-AAATTGGT-TTTTAG--AAATAAAACCGG
*
2242926 GGTTTGAGTATCCC
1 GGTTGGAGTATCCC
2242940 TTCGGAAATA
Statistics
Matches: 98, Mismatches: 16, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
50 1 0.01
51 74 0.76
52 1 0.01
53 22 0.22
ACGTcount: A:0.31, C:0.11, G:0.27, T:0.31
Consensus pattern (50 bp):
GGTTGGAGTATCCCCGATTGTGAGAAATTGGTTTTTAGAAATAAAACCGG
Found at i:2243078 original size:28 final size:30
Alignment explanation
Indices: 2243038--2243108 Score: 87
Period size: 28 Copynumber: 2.5 Consensus size: 30
2243028 GTAAAGGCGA
2243038 GGTTGGAGTATCCCCTC-A-AAAATAACAG
1 GGTTGGAGTATCCCCTCGATAAAATAACAG
* *
2243066 GGTTGGAGTAT--CCTCGATGAAATAACGG
1 GGTTGGAGTATCCCCTCGATAAAATAACAG
*
2243094 GGTTAGAGTATCCCC
1 GGTTGGAGTATCCCC
2243109 GATTAAGAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
26 4 0.11
27 1 0.03
28 29 0.81
30 2 0.06
ACGTcount: A:0.30, C:0.20, G:0.27, T:0.24
Consensus pattern (30 bp):
GGTTGGAGTATCCCCTCGATAAAATAACAG
Found at i:2245102 original size:20 final size:20
Alignment explanation
Indices: 2245059--2245135 Score: 102
Period size: 20 Copynumber: 3.9 Consensus size: 20
2245049 AAAATGCCTT
* *
2245059 AATGTATCGATACATTGTA-A
1 AATGTATCGATACAATG-AGC
2245079 AATGTATCGATACAATGAGC
1 AATGTATCGATACAATGAGC
*
2245099 AATGTATTGATACAATGAGC
1 AATGTATCGATACAATGAGC
*
2245119 AATGTATCAATACAATG
1 AATGTATCGATACAATG
2245136 CAAATGTATT
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
19 1 0.02
20 50 0.98
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.30
Consensus pattern (20 bp):
AATGTATCGATACAATGAGC
Found at i:2245213 original size:13 final size:13
Alignment explanation
Indices: 2245166--2245195 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
2245156 GGTAACCTAG
2245166 AATGTATCGATAC
1 AATGTATCGATAC
2245179 AATGTATCGATAC
1 AATGTATCGATAC
2245192 AATG
1 AATG
2245196 AACAATGTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.30
Consensus pattern (13 bp):
AATGTATCGATAC
Found at i:2246116 original size:19 final size:19
Alignment explanation
Indices: 2246071--2246163 Score: 141
Period size: 19 Copynumber: 4.8 Consensus size: 19
2246061 CTACCAATTT
**
2246071 CATGTATCGATACAATTGTT
1 CATGTATCGATACAA-TGAA
* *
2246091 TATGTATCGATATAATGAA
1 CATGTATCGATACAATGAA
2246110 CATGTATCGATACAATGAA
1 CATGTATCGATACAATGAA
2246129 CATGTATCGATACAATGAA
1 CATGTATCGATACAATGAA
2246148 CATGTATCGATACAAT
1 CATGTATCGATACAAT
2246164 ATATCGATAC
Statistics
Matches: 67, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
19 54 0.81
20 13 0.19
ACGTcount: A:0.39, C:0.14, G:0.15, T:0.32
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:2246191 original size:33 final size:32
Alignment explanation
Indices: 2246095--2246194 Score: 94
Period size: 38 Copynumber: 2.9 Consensus size: 32
2246085 ATTGTTTATG
* *
2246095 TATCGATATAATGAACATGTATCGATACAATGAACA
1 TATCGATACAAAGAACATGTATCGATACAAT----A
*
2246131 TGTATCGATACAATGAACATGTATCGATACAATA
1 --TATCGATACAAAGAACATGTATCGATACAATA
2246165 TATCGATACAAAGCATA-ATGTATCGATACA
1 TATCGATACAAAG-A-ACATGTATCGATACA
2246195 TCTGGGTGAG
Statistics
Matches: 58, Mismatches: 2, Indels: 9
0.84 0.03 0.13
Matches are distributed among these distances:
32 12 0.21
33 14 0.24
34 2 0.03
38 30 0.52
ACGTcount: A:0.43, C:0.15, G:0.14, T:0.28
Consensus pattern (32 bp):
TATCGATACAAAGAACATGTATCGATACAATA
Found at i:2248988 original size:13 final size:13
Alignment explanation
Indices: 2248970--2248995 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2248960 TACAGCAAGT
2248970 ATGTATCGATACA
1 ATGTATCGATACA
2248983 ATGTATCGATACA
1 ATGTATCGATACA
2248996 CAAAAAATTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2253079 original size:15 final size:15
Alignment explanation
Indices: 2253059--2253089 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2253049 TAAAAATGTC
*
2253059 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
2253074 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
2253089 C
1 C
2253090 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:2255186 original size:13 final size:13
Alignment explanation
Indices: 2255168--2255193 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2255158 ACATTTTTCT
2255168 TTGTATCGATACA
1 TTGTATCGATACA
2255181 TTGTATCGATACA
1 TTGTATCGATACA
2255194 GGGTGATTAT
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:2255357 original size:20 final size:20
Alignment explanation
Indices: 2255314--2255359 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
2255304 AAATCTTTTG
2255314 CAAAATACTTGTTTTTCAGTT
1 CAAAATACTTGTTTTTCAG-T
*
2255335 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCAGT
2255355 CAAAA
1 CAAAA
2255360 CCAGCATAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.17, G:0.07, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCAGT
Found at i:2257679 original size:20 final size:19
Alignment explanation
Indices: 2257624--2257679 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 19
2257614 AAAACCCTTA
*
2257624 AAAGTATCGATACATAATTC
1 AAAGTATCGATACAT-GTTC
2257644 AAAGTATCGATACATGTTGC
1 AAAGTATCGATACATGTT-C
*
2257664 AATGTATCGATACATG
1 AAAGTATCGATACATG
2257680 AAAAAGATGT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 2 0.06
20 31 0.94
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.30
Consensus pattern (19 bp):
AAAGTATCGATACATGTTC
Found at i:2257756 original size:13 final size:13
Alignment explanation
Indices: 2257738--2257763 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2257728 TACAGCAAGT
2257738 ATGTATCGATACA
1 ATGTATCGATACA
2257751 ATGTATCGATACA
1 ATGTATCGATACA
2257764 CAAAAAATTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2259147 original size:14 final size:14
Alignment explanation
Indices: 2259128--2259154 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2259118 GCTTTTCCTT
2259128 TTTTGCTCTTTTTC
1 TTTTGCTCTTTTTC
2259142 TTTTGCTCTTTTT
1 TTTTGCTCTTTTT
2259155 ACTTGTGGCT
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:0.00, C:0.19, G:0.07, T:0.74
Consensus pattern (14 bp):
TTTTGCTCTTTTTC
Found at i:2261430 original size:2 final size:2
Alignment explanation
Indices: 2261423--2261459 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2261413 ACTTAACTTC
2261423 TA TA TA TA TA 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 TA TA TA TA TA T
2261460 GTTATATTCC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2262333 original size:17 final size:17
Alignment explanation
Indices: 2262311--2262374 Score: 77
Period size: 17 Copynumber: 4.1 Consensus size: 17
2262301 TTAATTAAAA
*
2262311 ATTAATTGTTATAATAT
1 ATTAATTGTTATAACAT
2262328 ATTAATTGTTATAACAT
1 ATTAATTGTTATAACAT
2262345 ATTAA---TTA-AA-A-
1 ATTAATTGTTATAACAT
2262356 ATTAATTGTTATAACAT
1 ATTAATTGTTATAACAT
2262373 AT
1 AT
2262375 GCGTAATTAC
Statistics
Matches: 40, Mismatches: 1, Indels: 12
0.75 0.02 0.23
Matches are distributed among these distances:
11 5 0.12
12 1 0.03
13 2 0.05
14 6 0.15
15 2 0.05
16 1 0.03
17 23 0.57
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (17 bp):
ATTAATTGTTATAACAT
Found at i:2264419 original size:21 final size:22
Alignment explanation
Indices: 2264386--2264429 Score: 81
Period size: 21 Copynumber: 2.0 Consensus size: 22
2264376 TAACACATAA
2264386 AAATATCATAACATGAAACATG
1 AAATATCATAACATGAAACATG
2264408 AAATAT-ATAACATGAAACATG
1 AAATATCATAACATGAAACATG
2264429 A
1 A
2264430 GTGACATTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 16 0.73
22 6 0.27
ACGTcount: A:0.57, C:0.11, G:0.09, T:0.23
Consensus pattern (22 bp):
AAATATCATAACATGAAACATG
Found at i:2264809 original size:20 final size:20
Alignment explanation
Indices: 2264780--2264839 Score: 67
Period size: 17 Copynumber: 3.1 Consensus size: 20
2264770 TGAAGAAACC
2264780 TTCT-TTTTTCTTTTGTTTT
1 TTCTCTTTTTCTTTTGTTTT
2264799 TTCTCTTTTTC--TT-TTTT
1 TTCTCTTTTTCTTTTGTTTT
2264816 TTCTCTTTTT-TTTCTGATTTT
1 TTCTCTTTTTCTTT-TG-TTTT
2264837 TTC
1 TTC
2264840 CTACTAGAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
17 14 0.40
18 3 0.09
19 5 0.14
20 6 0.17
21 7 0.20
ACGTcount: A:0.02, C:0.15, G:0.03, T:0.80
Consensus pattern (20 bp):
TTCTCTTTTTCTTTTGTTTT
Found at i:2266207 original size:32 final size:32
Alignment explanation
Indices: 2266146--2266208 Score: 81
Period size: 32 Copynumber: 2.0 Consensus size: 32
2266136 ATATTGATCT
* * *
2266146 TAAATTTGATGAATGCTATATGTAATTACTTG
1 TAAATTTGATGAATACTAGATATAATTACTTG
* *
2266178 TAAATTTGATGAATATTAGATATAGTTACTT
1 TAAATTTGATGAATACTAGATATAATTACTT
2266209 ACAATTTTGA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.37, C:0.05, G:0.14, T:0.44
Consensus pattern (32 bp):
TAAATTTGATGAATACTAGATATAATTACTTG
Found at i:2266506 original size:32 final size:32
Alignment explanation
Indices: 2266460--2266533 Score: 112
Period size: 32 Copynumber: 2.3 Consensus size: 32
2266450 ATATTGATCT
2266460 TAAATTTGACGAATATAAGACATAATTACTCA
1 TAAATTTGACGAATATAAGACATAATTACTCA
* * * *
2266492 TAAATTTGATGAATATTAGATATAATTACTTA
1 TAAATTTGACGAATATAAGACATAATTACTCA
2266524 TAAATTTGAC
1 TAAATTTGAC
2266534 TGTTATTAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.45, C:0.08, G:0.09, T:0.38
Consensus pattern (32 bp):
TAAATTTGACGAATATAAGACATAATTACTCA
Found at i:2266960 original size:24 final size:24
Alignment explanation
Indices: 2266933--2267005 Score: 73
Period size: 24 Copynumber: 3.2 Consensus size: 24
2266923 TTTAAAATAT
2266933 TATATATAATTGATGAGTATTTGA
1 TATATATAATTGATGAGTATTTGA
* * * **
2266957 TATATAAAATTTATTA--ACAT--
1 TATATATAATTGATGAGTATTTGA
2266977 TATATATAATTGATGAGTATTTGA
1 TATATATAATTGATGAGTATTTGA
2267001 TATAT
1 TATAT
2267006 GAAATATATT
Statistics
Matches: 35, Mismatches: 10, Indels: 8
0.66 0.19 0.15
Matches are distributed among these distances:
20 13 0.37
22 4 0.11
24 18 0.51
ACGTcount: A:0.41, C:0.01, G:0.11, T:0.47
Consensus pattern (24 bp):
TATATATAATTGATGAGTATTTGA
Found at i:2266992 original size:44 final size:44
Alignment explanation
Indices: 2266908--2267015 Score: 157
Period size: 44 Copynumber: 2.5 Consensus size: 44
2266898 GATCTTTTTA
* * *
2266908 TATTTGATA-AAAAAATTTA-AAATATTATATATAATTGATGAG
1 TATTTGATATATAAAATTTATTAACATTATATATAATTGATGAG
2266950 TATTTGATATATAAAATTTATTAACATTATATATAATTGATGAG
1 TATTTGATATATAAAATTTATTAACATTATATATAATTGATGAG
* *
2266994 TATTTGATATATGAAATATATT
1 TATTTGATATATAAAATTTATT
2267016 TAATCTCATT
Statistics
Matches: 59, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
42 9 0.15
43 9 0.15
44 41 0.69
ACGTcount: A:0.45, C:0.01, G:0.09, T:0.44
Consensus pattern (44 bp):
TATTTGATATATAAAATTTATTAACATTATATATAATTGATGAG
Found at i:2269493 original size:16 final size:16
Alignment explanation
Indices: 2269472--2269505 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
2269462 TGACCTGAAT
2269472 CCGAAATGATCCAAAC
1 CCGAAATGATCCAAAC
*
2269488 CCGAAATGATCCGAAC
1 CCGAAATGATCCAAAC
2269504 CC
1 CC
2269506 AATAATAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.38, C:0.35, G:0.15, T:0.12
Consensus pattern (16 bp):
CCGAAATGATCCAAAC
Found at i:2269813 original size:15 final size:16
Alignment explanation
Indices: 2269794--2269832 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
2269784 ATTATTTATA
2269794 ATAAAATAAAAAATTT
1 ATAAAATAAAAAATTT
*
2269810 -TAAAA-ATAAAATTT
1 ATAAAATAAAAAATTT
2269824 ATAAAATAA
1 ATAAAATAA
2269833 TATCTATTCT
Statistics
Matches: 19, Mismatches: 2, Indels: 4
0.76 0.08 0.16
Matches are distributed among these distances:
14 8 0.42
15 10 0.53
16 1 0.05
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (16 bp):
ATAAAATAAAAAATTT
Found at i:2269868 original size:18 final size:18
Alignment explanation
Indices: 2269845--2269906 Score: 52
Period size: 18 Copynumber: 3.3 Consensus size: 18
2269835 TCTATTCTAT
2269845 TTTTTATTTTTAAATATA
1 TTTTTATTTTTAAATATA
* *** * *
2269863 TTTTTAATAAGATATTTA
1 TTTTTATTTTTAAATATA
2269881 TTTTTTATTTTTTAAATATA
1 -TTTTTA-TTTTTAAATATA
2269901 TTTTTA
1 TTTTTA
2269907 ATAAAATACG
Statistics
Matches: 30, Mismatches: 12, Indels: 3
0.67 0.27 0.07
Matches are distributed among these distances:
18 12 0.40
19 12 0.40
20 6 0.20
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (18 bp):
TTTTTATTTTTAAATATA
Found at i:2269895 original size:38 final size:38
Alignment explanation
Indices: 2269837--2269910 Score: 132
Period size: 38 Copynumber: 1.9 Consensus size: 38
2269827 AAATAATATC
2269837 TATTCTATTTTTTATTTTTAAATATATTTTTAATAAGA
1 TATTCTATTTTTTATTTTTAAATATATTTTTAATAAGA
2269875 TATT-TATTTTTTATTTTTTAAATATATTTTTAATAA
1 TATTCTATTTTTTA-TTTTTAAATATATTTTTAATAA
2269911 AATACGTATG
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
37 9 0.26
38 26 0.74
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.64
Consensus pattern (38 bp):
TATTCTATTTTTTATTTTTAAATATATTTTTAATAAGA
Found at i:2270527 original size:3 final size:3
Alignment explanation
Indices: 2270519--2270549 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
2270509 TTTTCTGATG
*
2270519 CTT CTT CTT CTT CTT CTT TTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
2270550 GGCTGAGAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
CTT
Done.