Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D02
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: 67659327
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 461372 characters in sequence are not A, C, G, or T
File 5 of 216
Found at i:1600423 original size:13 final size:12
Alignment explanation
Indices: 1600390--1600430 Score: 64
Period size: 12 Copynumber: 3.3 Consensus size: 12
1600380 TTTGGGTTTG
*
1600390 TTTTGTTTTGTT
1 TTTTGTTTTGCT
1600402 TTTTGTTTTGCT
1 TTTTGTTTTGCT
1600414 TTTTGTTTTTGCT
1 TTTTG-TTTTGCT
1600427 TTTT
1 TTTT
1600431 TTTACCTCCA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
12 16 0.59
13 11 0.41
ACGTcount: A:0.00, C:0.05, G:0.15, T:0.80
Consensus pattern (12 bp):
TTTTGTTTTGCT
Found at i:1600429 original size:12 final size:11
Alignment explanation
Indices: 1600355--1600422 Score: 54
Period size: 10 Copynumber: 6.4 Consensus size: 11
1600345 GGTAGAGTTT
1600355 TTTTGTTTTT-
1 TTTTGTTTTTG
* *
1600365 TATT-TTCTTG
1 TTTTGTTTTTG
*
1600375 TTTT-TTTTGG
1 TTTTGTTTTTG
*
1600385 GTTTG-TTTTG
1 TTTTGTTTTTG
1600395 TTTTGTTTTTTG
1 TTTTG-TTTTTG
1600407 TTTTGCTTTTTG
1 TTTTG-TTTTTG
1600419 TTTT
1 TTTT
1600423 TGCTTTTTTT
Statistics
Matches: 45, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
9 4 0.09
10 21 0.47
12 20 0.44
ACGTcount: A:0.01, C:0.03, G:0.16, T:0.79
Consensus pattern (11 bp):
TTTTGTTTTTG
Found at i:1607540 original size:54 final size:54
Alignment explanation
Indices: 1607481--1607637 Score: 262
Period size: 54 Copynumber: 2.9 Consensus size: 54
1607471 GGTTGAGTGA
*
1607481 ATTAGACTAGAGATGTTCATTTGTTGGGCCGAGGGCCAATTCCAAAAAAATTAT
1 ATTAGACTAGAGATGTTCATTTGCTGGGCCGAGGGCCAATTCCAAAAAAATTAT
* *
1607535 ATTAGACTAGAGATGTTCATTTGCTCGGCTGAGGGCCAATTCCAAAAAAATTAT
1 ATTAGACTAGAGATGTTCATTTGCTGGGCCGAGGGCCAATTCCAAAAAAATTAT
* *
1607589 ATTAGACTAGAGATGTTCATTTGCTGGGCCGAGGGTC-AGTCCAAAAAAA
1 ATTAGACTAGAGATGTTCATTTGCTGGGCCGAGGGCCAATTCCAAAAAAA
1607638 GTTCTAGGCC
Statistics
Matches: 96, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
53 11 0.11
54 85 0.89
ACGTcount: A:0.33, C:0.16, G:0.23, T:0.28
Consensus pattern (54 bp):
ATTAGACTAGAGATGTTCATTTGCTGGGCCGAGGGCCAATTCCAAAAAAATTAT
Found at i:1608117 original size:28 final size:27
Alignment explanation
Indices: 1608078--1608147 Score: 81
Period size: 29 Copynumber: 2.6 Consensus size: 27
1608068 ATACATATCT
1608078 AATTATTT-ATATTTAGTTA-TATAATA
1 AATTATTTAATATTTA-TTATTATAATA
*
1608104 AATTATATTAATATTTTATTATTTTAATA
1 AATTAT-TTAATA-TTTATTATTATAATA
*
1608133 AATTATTTAGTATTT
1 AATTATTTAATATTT
1608148 CAATTTTATT
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
26 6 0.16
27 5 0.13
28 11 0.29
29 16 0.42
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (27 bp):
AATTATTTAATATTTATTATTATAATA
Found at i:1608188 original size:15 final size:17
Alignment explanation
Indices: 1608159--1608195 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 17
1608149 AATTTTATTT
1608159 TAATAATGAATTTTAAA
1 TAATAATGAATTTTAAA
1608176 -AATAATG-ATTTTAAA
1 TAATAATGAATTTTAAA
1608191 TAATA
1 TAATA
1608196 TTCTTCACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 8 0.42
16 11 0.58
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (17 bp):
TAATAATGAATTTTAAA
Found at i:1611706 original size:14 final size:14
Alignment explanation
Indices: 1611673--1611707 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
1611663 TATAATATTC
*
1611673 AAATAATAACAACA
1 AAATAGTAACAACA
1611687 AAATAGTAACAACA
1 AAATAGTAACAACA
*
1611701 TAATAGT
1 AAATAGT
1611708 GATATGATAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.63, C:0.11, G:0.06, T:0.20
Consensus pattern (14 bp):
AAATAGTAACAACA
Found at i:1621121 original size:7 final size:7
Alignment explanation
Indices: 1621109--1621134 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
1621099 AACGAATCCT
1621109 CACATTG
1 CACATTG
1621116 CACATTG
1 CACATTG
1621123 CACATTG
1 CACATTG
1621130 CACAT
1 CACAT
1621135 ATGAATAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.31, C:0.31, G:0.12, T:0.27
Consensus pattern (7 bp):
CACATTG
Found at i:1625062 original size:18 final size:19
Alignment explanation
Indices: 1625020--1625062 Score: 54
Period size: 17 Copynumber: 2.3 Consensus size: 19
1625010 CCCCCCCCCC
1625020 TTTATTCACATAAAAAATA
1 TTTATTCACATAAAAAATA
*
1625039 TATATT-AC-TAAAAAATAA
1 TTTATTCACATAAAAAAT-A
1625057 TTTATT
1 TTTATT
1625063 TTTTAACAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 8 0.38
18 8 0.38
19 5 0.24
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.42
Consensus pattern (19 bp):
TTTATTCACATAAAAAATA
Found at i:1628859 original size:48 final size:45
Alignment explanation
Indices: 1628807--1629340 Score: 282
Period size: 48 Copynumber: 11.7 Consensus size: 45
1628797 CTCCACCACC
* * * *
1628807 GCCTTATGTGTATAAATCTCCACCACCACCACCTAAACATGAGGAGAA
1 GCCTTATGAGTACAAGTCTCCACCACCACCACC--AACA-AAGGAGAA
* *
1628855 GCCTTATGAATACAAGTCTCCACCACCACCACCACCAAAGGAGAA
1 GCCTTATGAGTACAAGTCTCCACCACCACCACCAACAAAGGAGAA
* * * ******* *
1628900 GCCTTATGAGTACAAGTCTCCACCCCCACCATCACCTTCTCCTCCACC
1 GCCTTATGAGTACAAGTCTCCACCACCACCACCAAC--AAAGGAGA-A
* * * * * ***** * *
1628948 TCCTTATGAGTACAAATCTCCACCACCTCCATCACCTTCTCCACCACC
1 GCCTTATGAGTACAAGTCTCCACCACCACCACCAAC-AAAGGA-GA-A
* * * * *
1628996 TCCTTATGTGTATAAGTCTCCACCACCTCCACCAAAGCATGAGGAGAA
1 GCCTTATGAGTACAAGTCTCCACCACCACCACC-AA-CA-AAGGAGAA
* *
1629044 GCCTTATGAATACAAGTCTCCACCACCACCA-C--CGAAGGAGAA
1 GCCTTATGAGTACAAGTCTCCACCACCACCACCAACAAAGGAGAA
* *
1629086 GCCTTATGAATACAAGTCTCCACCACCACCA-C--CGAAGGAGAA
1 GCCTTATGAGTACAAGTCTCCACCACCACCACCAACAAAGGAGAA
* *
1629128 GCCTTATGAATACAAGTCTCCACCACCACCACC--GAAA-GAGAA
1 GCCTTATGAGTACAAGTCTCCACCACCACCACCAACAAAGGAGAA
* * * * ***** * *
1629170 GCCTTATGAATACAAGTCTCCACCACCTCCATCACCTTCTCCACCACC
1 GCCTTATGAGTACAAGTCTCCACCACCACCACCAAC-AAAGGA-GA-A
* * * * * *
1629218 TCCTTATGTGTATAAGTCTCCTCCACCTCCACCAAAGCATGAGGAGAA
1 GCCTTATGAGTACAAGTCTCCACCACCACCACC-AA-CA-AAGGAGAA
* *
1629266 GCCTTATGAATACAAGTCTCCACCACCACCA-C--CGAAGGAGAA
1 GCCTTATGAGTACAAGTCTCCACCACCACCACCAACAAAGGAGAA
*
1629308 GCCTTATGAATACAAGTCTCCACCACCACCACC
1 GCCTTATGAGTACAAGTCTCCACCACCACCACC
1629341 TCCATCTCCA
Statistics
Matches: 390, Mismatches: 78, Indels: 41
0.77 0.15 0.08
Matches are distributed among these distances:
42 154 0.39
43 6 0.02
45 40 0.10
46 4 0.01
47 6 0.02
48 172 0.44
49 4 0.01
50 4 0.01
ACGTcount: A:0.31, C:0.37, G:0.13, T:0.19
Consensus pattern (45 bp):
GCCTTATGAGTACAAGTCTCCACCACCACCACCAACAAAGGAGAA
Found at i:1628975 original size:27 final size:26
Alignment explanation
Indices: 1628937--1629025 Score: 71
Period size: 27 Copynumber: 3.5 Consensus size: 26
1628927 ACCATCACCT
*
1628937 TCTCCTCCACCTCCTTATGAGTACAAA
1 TCTCCACCACCTCCTTATG-GTACAAA
* **
1628964 TCTCCACCACCTCC--AT--CAC-CT
1 TCTCCACCACCTCCTTATGGTACAAA
* *
1628985 TCTCCACCACCTCCTTATGTGTATAAG
1 TCTCCACCACCTCCTTATG-GTACAAA
1629012 TCTCCACCACCTCC
1 TCTCCACCACCTCC
1629026 ACCAAAGCAT
Statistics
Matches: 48, Mismatches: 8, Indels: 12
0.71 0.12 0.18
Matches are distributed among these distances:
21 14 0.29
22 2 0.04
23 2 0.04
25 2 0.04
26 1 0.02
27 27 0.56
ACGTcount: A:0.21, C:0.45, G:0.06, T:0.28
Consensus pattern (26 bp):
TCTCCACCACCTCCTTATGGTACAAA
Found at i:1629069 original size:189 final size:186
Alignment explanation
Indices: 1628760--1629116 Score: 563
Period size: 189 Copynumber: 1.9 Consensus size: 186
1628750 ACCCCCTCCG
* * * *
1628760 CCTTATGAGTATAAGTCACCACCACCGCCTTCTCCTTCTCCACCACCGCCTTATGTGTATAAATC
1 CCTTATGAGTACAAATCACCACCACCGCCATCACCTTCTCCACCACCGCCTTATGTGTATAAATC
1628825 TCCACCACCACCACCTAAACATGAGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCACCAC
66 TCCACCACCACCACCTAAACATGAGGAGAAGCCTTATGAATACAAGTCT---CCACCACCACCAC
* *
1628890 CAAAGGAGAAGCCTTATGAGTACAAGTCTCCACCCCCACCATCACCTTCTCCTCCACCT
128 CAAAGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCATCACCTTCTCCTCCACCT
* * * *
1628949 CCTTATGAGTACAAATCTCCACCACCTCCATCACCTTCTCCACCACCTCCTTATGTGTATAAGTC
1 CCTTATGAGTACAAATCACCACCACCGCCATCACCTTCTCCACCACCGCCTTATGTGTATAAATC
* *
1629014 TCCACCACCTCCACC-AAAGCATGAGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCACCG
66 TCCACCACCACCACCTAAA-CATGAGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCACCA
1629078 AAGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCA
130 AAGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCA
1629117 CCGAAGGAGA
Statistics
Matches: 155, Mismatches: 12, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
186 51 0.33
188 3 0.02
189 101 0.65
ACGTcount: A:0.30, C:0.38, G:0.11, T:0.21
Consensus pattern (186 bp):
CCTTATGAGTACAAATCACCACCACCGCCATCACCTTCTCCACCACCGCCTTATGTGTATAAATC
TCCACCACCACCACCTAAACATGAGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCACCAA
AGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCATCACCTTCTCCTCCACCT
Found at i:1629083 original size:42 final size:42
Alignment explanation
Indices: 1629037--1629340 Score: 365
Period size: 42 Copynumber: 7.0 Consensus size: 42
1629027 CCAAAGCATG
1629037 AGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCACCGA
1 AGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCACCGA
1629079 AGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCACCGA
1 AGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCACCGA
1629121 AGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCACCGA
1 AGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCACCGA
* * **
1629163 AAGAGAAGCCTTATGAATACAAGTCTCCACCACCTCCATCACCTTC
1 AGGAGAAGCCTTATGAATACAAGTCTCCACCA---CCACCACC-GA
*** * ** ** * * *
1629209 TCCACCACCTCCTTATGTGTATAAGTCTCCTCCACCTCCACCAAAGCA
1 AGGA-GA-AGCCTTATGAATACAAGTCTCCACCACCACCACC---G-A
1629257 TGAGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCACCGA
1 --AGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCACCGA
1629301 AGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCACC
1 AGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCACC
1629341 TCCATCTCCA
Statistics
Matches: 221, Mismatches: 30, Indels: 22
0.81 0.11 0.08
Matches are distributed among these distances:
42 155 0.70
44 1 0.00
45 14 0.06
46 1 0.00
47 1 0.00
48 47 0.21
49 1 0.00
50 1 0.00
ACGTcount: A:0.33, C:0.35, G:0.14, T:0.17
Consensus pattern (42 bp):
AGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCACCGA
Found at i:1629214 original size:138 final size:135
Alignment explanation
Indices: 1628759--1629334 Score: 434
Period size: 138 Copynumber: 4.2 Consensus size: 135
1628749 CACCCCCTCC
* * * * * * ** ** * *
1628759 GCCTTATGAGTATAAGTCACCACCACCGCCTTCTCCTTCTCCACCACCGCCTTATGTGTATAAAT
1 GCCTTATGAATACAAGTCTCCACCACCTCCATCACCTTCTCCACCAAAGCCTTATGAATACAAGT
*
1628824 CTCCACCACCACCACCTAAACATGAGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCACCA
66 CTCCACCACCACCACC--AGCA-GAGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCA-C-
*
1628889 CCAAAGGAGAA
126 CGAAA-GAGAA
* * * * *** * *
1628900 GCCTTATGAGTACAAGTCTCCACCCCCACCATCACCTTCTCCTCCACCTCCTTATGAGTACAAAT
1 GCCTTATGAATACAAGTCTCCACCACCTCCATCACCTTCTCCACCAAAGCCTTATGAATACAAGT
* * * ***** * ** ** * *
1628965 CTCCACCACCTCCATCACCTTCTCCACCACCTCCTTATGTGTATAAGTCTCCACCACCTCCACCA
66 CTCCACCACCACCACCAGC-AGAGGA-GA-AGCCTTATGAATACAAGTCTCCACCACCACCACC-
*
1629030 AAGCATGAGGAGAA
127 --G-A--AAGAGAA
* ** **
1629044 GCCTTATGAATACAAGTCTCCACCA---CCACCA-C--C-GAAGGAGAAGCCTTATGAATACAAG
1 GCCTTATGAATACAAGTCTCCACCACCTCCATCACCTTCTCCACCA-AAGCCTTATGAATACAAG
1629102 TCTCCACCACCACCACC-G-A-AGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCACCGAA
65 TCTCCACCACCACCACCAGCAGAGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCACCGAA
1629164 AGAGAA
130 AGAGAA
*** ** *
1629170 GCCTTATGAATACAAGTCTCCACCACCTCCATCACCTTCTCCACCACCTCCTTATGTGTATAAGT
1 GCCTTATGAATACAAGTCTCCACCACCTCCATCACCTTCTCCACCAAAGCCTTATGAATACAAGT
* *
1629235 CTCCTCCACCTCCACCAAAGCATGAGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCACCG
66 CTCCACCACCACCACC--AGCA-GAGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCACCG
*
1629300 AAGGAGAA
128 AAAGAGAA
1629308 GCCTTATGAATACAAGTCTCCACCACC
1 GCCTTATGAATACAAGTCTCCACCACC
1629335 ACCACCTCCA
Statistics
Matches: 343, Mismatches: 69, Indels: 49
0.74 0.15 0.11
Matches are distributed among these distances:
126 31 0.09
128 1 0.00
129 6 0.02
130 1 0.00
132 56 0.16
133 3 0.01
134 1 0.00
135 1 0.00
136 1 0.00
137 1 0.00
138 104 0.30
139 4 0.01
140 3 0.01
141 100 0.29
143 1 0.00
144 28 0.08
145 1 0.00
ACGTcount: A:0.31, C:0.37, G:0.13, T:0.20
Consensus pattern (135 bp):
GCCTTATGAATACAAGTCTCCACCACCTCCATCACCTTCTCCACCAAAGCCTTATGAATACAAGT
CTCCACCACCACCACCAGCAGAGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCACCGAAA
GAGAA
Found at i:1629216 original size:222 final size:225
Alignment explanation
Indices: 1628848--1629340 Score: 776
Period size: 222 Copynumber: 2.2 Consensus size: 225
1628838 CCTAAACATG
*
1628848 AGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCACCACCAAAGGAGAAGCCTTATGAGTAC
1 AGGAGAAGCCTTATGAATACAAGTCT---CCACCACCACCACCAAAGGAGAAGCCTTATGAATAC
* ***** ** *
1628913 AAGTCTCCACCCCCACCATCACCTTCTCCTCCACCTCCTTATGAGTACAAATCTCCACCACCTCC
63 AAGTCTCCA--CCCACCACCACC-TCAAAGACACAGCCTTATGAATACAAATCTCCACCACCTCC
1628978 ATCACCTTCTCCACCACCTCCTTATGTGTATAAGTCTCCACCACCTCCACCAAAGCATGAGGAGA
125 ATCACCTTCTCCACCACCTCCTTATGTGTATAAGTCTCCACCACCTCCACCAAAGCATGAGGAGA
1629043 AGCCTTATGAATACAAGTCTCCACCACCACCACCGA
190 AGCCTTATGAATACAAGTCTCCACCACCACCACCGA
*
1629079 AGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCACCGAAGGAGAAGCCTTATGAATACAAG
1 AGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCACCAAAGGAGAAGCCTTATGAATACAAG
* * *
1629144 TCTCCA-CCACCACCACC-GAAAGAGA-AGCCTTATGAATACAAGTCTCCACCACCTCCATCACC
66 TCTCCACCCACCACCACCTCAAAGACACAGCCTTATGAATACAAATCTCCACCACCTCCATCACC
*
1629206 TTCTCCACCACCTCCTTATGTGTATAAGTCTCCTCCACCTCCACCAAAGCATGAGGAGAAGCCTT
131 TTCTCCACCACCTCCTTATGTGTATAAGTCTCCACCACCTCCACCAAAGCATGAGGAGAAGCCTT
1629271 ATGAATACAAGTCTCCACCACCACCACCGA
196 ATGAATACAAGTCTCCACCACCACCACCGA
1629301 AGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCACC
1 AGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCACC
1629341 TCCATCTCCA
Statistics
Matches: 247, Mismatches: 15, Indels: 9
0.91 0.06 0.03
Matches are distributed among these distances:
222 167 0.68
223 1 0.00
225 10 0.04
228 43 0.17
231 26 0.11
ACGTcount: A:0.31, C:0.37, G:0.13, T:0.19
Consensus pattern (225 bp):
AGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCACCAAAGGAGAAGCCTTATGAATACAAG
TCTCCACCCACCACCACCTCAAAGACACAGCCTTATGAATACAAATCTCCACCACCTCCATCACC
TTCTCCACCACCTCCTTATGTGTATAAGTCTCCACCACCTCCACCAAAGCATGAGGAGAAGCCTT
ATGAATACAAGTCTCCACCACCACCACCGA
Found at i:1629350 original size:21 final size:21
Alignment explanation
Indices: 1629324--1629366 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
1629314 TGAATACAAG
1629324 TCTCCACCACCACCACCTCCA
1 TCTCCACCACCACCACCTCCA
* *
1629345 TCTCCATCACCACCTCCTCCA
1 TCTCCACCACCACCACCTCCA
1629366 T
1 T
1629367 ACTACTATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.21, C:0.58, G:0.00, T:0.21
Consensus pattern (21 bp):
TCTCCACCACCACCACCTCCA
Found at i:1629385 original size:48 final size:48
Alignment explanation
Indices: 1629333--1629922 Score: 493
Period size: 48 Copynumber: 12.2 Consensus size: 48
1629323 GTCTCCACCA
* * * *
1629333 CCACCACCTCCATCTCCATCACCACCTCCTCCATACTACTATAAATCT
1 CCACCACCTCCATCACCATCACCACCACCTCCATACTACTACAAGTCT
*
1629381 CCACCACCTCCATCACCATCACCACCACCTCCATACTACTACAAGTCC
1 CCACCACCTCCATCACCATCACCACCACCTCCATACTACTACAAGTCT
* * * * ** * * * *
1629429 CCACCACCACCACCAAAGCATGAAGAACAACCACCATATTACTACAAGTCA
1 CCACCACCTCCATC--ACCAT-CACCACCACCTCCATACTACTACAAGTCT
* * * * *
1629480 CCTCCTCCTCCATCTCCATCACCACCTCCTCCATACTACTACAAGTCC
1 CCACCACCTCCATCACCATCACCACCACCTCCATACTACTACAAGTCT
*
1629528 CCACCACCTCCTTCACCATCACCACCACCTCCATACTACTACAAGTCT
1 CCACCACCTCCATCACCATCACCACCACCTCCATACTACTACAAGTCT
* ** * * * *
1629576 CCACCACCACCAAAACACGT-A-GAGCAACCCCCATACTACTACAAGTCT
1 CCACCACCTCCATCAC-CATCACCA-CCACCTCCATACTACTACAAGTCT
* * * * * *
1629624 CCTCCACCTCCATCACCCTCACCACCACCACCTTACTACTATAAATCT
1 CCACCACCTCCATCACCATCACCACCACCTCCATACTACTACAAGTCT
* * * * *
1629672 CCACCACCACCTTCACCATCTCCACCACCTCCTTACTACTACAAGTCC
1 CCACCACCTCCATCACCATCACCACCACCTCCATACTACTACAAGTCT
* * *
1629720 CCACCACCTCCATCTCCATCACCACCTCCTCCATACTACTACAAATCT
1 CCACCACCTCCATCACCATCACCACCACCTCCATACTACTACAAGTCT
* * * * ** * *
1629768 CCACCACCACCACCAAAGCATGAAGAACAACCCCCATACTACTACAAGTCT
1 CCACCACCTCCATC--ACCAT-CACCACCACCTCCATACTACTACAAGTCT
* * * * * * *
1629819 CCACCACCACCTTCACCATCTCCTCCACCACCTTACTACTACAAATCT
1 CCACCACCTCCATCACCATCACCACCACCTCCATACTACTACAAGTCT
* ** * ** * *
1629867 CCACCACCACCCCCA-CATTACGTCTCACCACCATACTACTACAAATCT
1 CCACCACCTCCATCACCATCACCAC-CACCTCCATACTACTACAAGTCT
1629915 CCACCACC
1 CCACCACC
1629923 ACCAGTGAAG
Statistics
Matches: 431, Mismatches: 100, Indels: 22
0.78 0.18 0.04
Matches are distributed among these distances:
47 9 0.02
48 339 0.79
49 10 0.02
50 7 0.02
51 66 0.15
ACGTcount: A:0.30, C:0.48, G:0.03, T:0.19
Consensus pattern (48 bp):
CCACCACCTCCATCACCATCACCACCACCTCCATACTACTACAAGTCT
Found at i:1629388 original size:138 final size:135
Alignment explanation
Indices: 1629121--1629385 Score: 354
Period size: 138 Copynumber: 1.9 Consensus size: 135
1629111 CCACCACCGA
1629121 AGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCACCGAAAGAGAAGCCTTATGAATACAAG
1 AGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCACCGAAAGAGAAGCCTTATGAATACAAG
* * * * * * *
1629186 TCTCCACCACCTCCATCACCTTCTCCACCACCTCCTTATGTGTATAAGTCTCCTCCACCTCCACC
66 TCTCCACCACCACCACCACCATCTCCACCACCTCCTCATCTCTATAAG-ATCCTCCA-C-CCACC
1629251 AAAGCATG
128 AAAGCATG
*
1629259 AGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCACCGAAGGAGAAGCCTTATGAATACAAG
1 AGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCACCGAAAGAGAAGCCTTATGAATACAAG
*
1629324 TCTCCACCACCACCACCTCCATCTCCATCACCACCTCCTCCATACTACTATAA-AT-CTCCACC
66 TCTCCACCACCACCACCACCATCT-C--CACCACCTCCT-CAT-CT-CTATAAGATCCTCCACC
1629386 ACCTCCATCA
Statistics
Matches: 112, Mismatches: 9, Indels: 11
0.85 0.07 0.08
Matches are distributed among these distances:
138 84 0.75
139 2 0.02
140 1 0.01
141 16 0.14
142 3 0.03
143 1 0.01
144 5 0.04
ACGTcount: A:0.31, C:0.37, G:0.11, T:0.20
Consensus pattern (135 bp):
AGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCACCGAAAGAGAAGCCTTATGAATACAAG
TCTCCACCACCACCACCACCATCTCCACCACCTCCTCATCTCTATAAGATCCTCCACCCACCAAA
GCATG
Found at i:1629407 original size:21 final size:21
Alignment explanation
Indices: 1629331--1629414 Score: 78
Period size: 21 Copynumber: 3.7 Consensus size: 21
1629321 AAGTCTCCAC
*
1629331 CACCACCACCTCCATCTCCAT
1 CACCACCACCTCCATCACCAT
* *
1629352 CACCACCTCCTCCATACTACTATAAAT
1 CACCACCACCTCCAT-C-AC----CAT
*
1629379 CTCCACCACCTCCATCACCAT
1 CACCACCACCTCCATCACCAT
1629400 CACCACCACCTCCAT
1 CACCACCACCTCCAT
1629415 ACTACTACAA
Statistics
Matches: 50, Mismatches: 7, Indels: 12
0.72 0.10 0.17
Matches are distributed among these distances:
21 30 0.60
22 1 0.02
23 1 0.02
25 2 0.04
26 1 0.02
27 15 0.30
ACGTcount: A:0.27, C:0.52, G:0.00, T:0.20
Consensus pattern (21 bp):
CACCACCACCTCCATCACCAT
Found at i:1629433 original size:144 final size:142
Alignment explanation
Indices: 1629276--1629727 Score: 454
Period size: 144 Copynumber: 3.1 Consensus size: 142
1629266 GCCTTATGAA
* * *
1629276 TACAAGTCTCCACCACCACCACCGAAGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCACC
1 TACAAGTCCCCACCACCACCACCGAAGGAGAAGCC-TAT-ACTACAAGTCTCCACCACCTCCACC
*
1629341 TCCATCTCCATCACCACCTCCTCCATACTACTATAAATCTCCACCACCTCCATCACCATCACCAC
64 TCCATCTCCATCACCACCTCCTCCATACTACTATAAATCTCCACCACCTCCTTCACCATCACCAC
1629406 CACCTCCATACTAC
129 CACCTCCATACTAC
* * * * * * *
1629420 TACAAGTCCCCACCACCACCACCAAAGCATGAAGAAC-A-ACCACCATATTACTACAAGTCACCT
1 TACAAGTCCCCACCACCACCACCGAAGGA-GAAG-CCTATACTA-CA-AGT-CT-CCA-CCACCT
* * * *
1629483 CCTCCTCCATCTCCATCACCACCTCCTCCATACTACTACAAGTCCCCACCACCTCCTTCACCATC
59 CCACCTCCATCTCCATCACCACCTCCTCCATACTACTATAAATCTCCACCACCTCCTTCACCATC
1629548 ACCACCACCTCCATACTAC
124 ACCACCACCTCCATACTAC
* * * *
1629567 TACAAGTCTCCACCACCACCAAAACACGTA-GAGCAACCCCCATACTACTACAAGTCTCCTCCAC
1 TACAAGTCCCCACCACCACC---AC-CGAAGGAG-AA--GCC-TA-TACTACAAGTCTCCACCAC
* * * *
1629631 CTCCA--T-CA-C-CC-TCACCACCACCACCTTACTACTATAAATCTCCACCACCACCTTCACCA
57 CTCCACCTCCATCTCCATCACCACCTCCTCCATACTACTATAAATCTCCACCACCTCCTTCACCA
* *
1629690 TCTCCACCACCTCCTTACTAC
122 TCACCACCACCTCCATACTAC
1629711 TACAAGTCCCCACCACC
1 TACAAGTCCCCACCACC
1629728 TCCATCTCCA
Statistics
Matches: 253, Mismatches: 37, Indels: 36
0.78 0.11 0.11
Matches are distributed among these distances:
142 2 0.01
143 2 0.01
144 105 0.42
145 8 0.03
146 4 0.02
147 104 0.41
148 1 0.00
149 1 0.00
150 12 0.05
151 4 0.02
152 2 0.01
153 3 0.01
154 2 0.01
155 3 0.01
ACGTcount: A:0.30, C:0.47, G:0.04, T:0.19
Consensus pattern (142 bp):
TACAAGTCCCCACCACCACCACCGAAGGAGAAGCCTATACTACAAGTCTCCACCACCTCCACCTC
CATCTCCATCACCACCTCCTCCATACTACTATAAATCTCCACCACCTCCTTCACCATCACCACCA
CCTCCATACTAC
Found at i:1629520 original size:147 final size:144
Alignment explanation
Indices: 1629331--1629727 Score: 578
Period size: 144 Copynumber: 2.7 Consensus size: 144
1629321 AAGTCTCCAC
* *
1629331 CACCACCACCTCCATCTCCATCACCACCTCCTCCATACTACTATAAATCTCCACCACCTCCATCA
1 CACCTCCACCTCCATCTCCATCACCACCTCCTCCATACTACTATAAATCTCCACCACCTCCTTCA
*
1629396 CCATCACCACCACCTCCATACTACTACAAGTCCCCACCACCACCACCAAAGCATGAAGAACAACC
66 CCATCACCACCACCTCCATACTACTACAAGTCCCCACCACCACCA--AAA-CACGAAGAACAACC
*
1629461 ACCATATTACTACAAGT
128 ACCATACTACTACAAGT
* * * *
1629478 CACCTCCTCCTCCATCTCCATCACCACCTCCTCCATACTACTACAAGTCCCCACCACCTCCTTCA
1 CACCTCCACCTCCATCTCCATCACCACCTCCTCCATACTACTATAAATCTCCACCACCTCCTTCA
* * * *
1629543 CCATCACCACCACCTCCATACTACTACAAGTCTCCACCACCACCAAAACACGTAGAGCAACCCCC
66 CCATCACCACCACCTCCATACTACTACAAGTCCCCACCACCACCAAAACACGAAGAACAACCACC
1629608 ATACTACTACAAGT
131 ATACTACTACAAGT
* * * * * * *
1629622 CTCCTCCACCTCCATCACCCTCACCACCACCACCTTACTACTATAAATCTCCACCACCACCTTCA
1 CACCTCCACCTCCATCTCCATCACCACCTCCTCCATACTACTATAAATCTCCACCACCTCCTTCA
* *
1629687 CCATCTCCACCACCTCCTTACTACTACAAGTCCCCACCACC
66 CCATCACCACCACCTCCATACTACTACAAGTCCCCACCACC
1629728 TCCATCTCCA
Statistics
Matches: 224, Mismatches: 26, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
144 118 0.53
145 3 0.01
147 103 0.46
ACGTcount: A:0.30, C:0.48, G:0.03, T:0.19
Consensus pattern (144 bp):
CACCTCCACCTCCATCTCCATCACCACCTCCTCCATACTACTATAAATCTCCACCACCTCCTTCA
CCATCACCACCACCTCCATACTACTACAAGTCCCCACCACCACCAAAACACGAAGAACAACCACC
ATACTACTACAAGT
Found at i:1629868 original size:24 final size:23
Alignment explanation
Indices: 1629841--1629922 Score: 69
Period size: 24 Copynumber: 3.4 Consensus size: 23
1629831 TCACCATCTC
1629841 CTCCACCACCTTACTACTACAAAT
1 CTCCACCACC-TACTACTACAAAT
** * *
1629865 CTCCACCACC-ACCCCCAC-ATT
1 CTCCACCACCTACTACTACAAAT
1629886 ACGTCTCACCACCATACTACTACAAAT
1 -C-TC-CACCACC-TACTACTACAAAT
1629913 CTCCACCACC
1 CTCCACCACC
1629923 ACCAGTGAAG
Statistics
Matches: 44, Mismatches: 8, Indels: 12
0.69 0.12 0.19
Matches are distributed among these distances:
21 2 0.05
22 6 0.14
23 2 0.05
24 24 0.55
25 2 0.05
26 6 0.14
27 2 0.05
ACGTcount: A:0.30, C:0.49, G:0.01, T:0.20
Consensus pattern (23 bp):
CTCCACCACCTACTACTACAAAT
Found at i:1629990 original size:6 final size:6
Alignment explanation
Indices: 1629979--1630012 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
1629969 ACTCCTTACT
*
1629979 ACCCCC ACCCCC ACCCTC ACCCCC ACCCCC ACCC
1 ACCCCC ACCCCC ACCCCC ACCCCC ACCCCC ACCC
1630013 ACATCCGCTC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.18, C:0.79, G:0.00, T:0.03
Consensus pattern (6 bp):
ACCCCC
Found at i:1631117 original size:36 final size:36
Alignment explanation
Indices: 1631070--1631158 Score: 97
Period size: 36 Copynumber: 2.5 Consensus size: 36
1631060 GTACTACTAT
* * * *
1631070 AAGTCTCCACCTCCTCCGGCTCCCACTTACGTTTAC
1 AAGTCACCACCTCCTCCAGCACCAACTTACGTTTAC
* * *
1631106 AAGTCACCACCTCCACCATCACCAACTTATGTTTAC
1 AAGTCACCACCTCCTCCAGCACCAACTTACGTTTAC
* *
1631142 AAGTCACCTCCACCTCC
1 AAGTCACCACCTCCTCC
1631159 TGTGTACTAC
Statistics
Matches: 43, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
36 43 1.00
ACGTcount: A:0.24, C:0.44, G:0.08, T:0.25
Consensus pattern (36 bp):
AAGTCACCACCTCCTCCAGCACCAACTTACGTTTAC
Found at i:1631256 original size:150 final size:150
Alignment explanation
Indices: 1631061--1631338 Score: 493
Period size: 150 Copynumber: 1.9 Consensus size: 150
1631051 GCCACCACCG
*
1631061 TACTACTATAAGTCTCCACCTCCTCCGGCTCCCACTTACGTTTACAAGTCACCACCTCCACCATC
1 TACTACTATAAGTCTCCACCTCCACCGGCTCCCACTTACGTTTACAAGTCACCACCTCCACCATC
* * *
1631126 ACCAACTTATGTTTACAAGTCACCTCCACCTCCTGTGTACTACTACAAGTCTCCACCACCACCAA
66 ACCAACTTATGTTTACAAGTCACCTCCACCACCTGTGTACTACTACAAATCACCACCACCACCAA
1631191 AGCATGTGGAACAACCTCCA
131 AGCATGTGGAACAACCTCCA
*
1631211 TACTACTATAAGTCTCCACCTCCACCGGCTCCCACTTATGTTTACAAGTCACCACCTCCACCATC
1 TACTACTATAAGTCTCCACCTCCACCGGCTCCCACTTACGTTTACAAGTCACCACCTCCACCATC
* *
1631276 GCCGACTTATGTTTACAAGTCACCTCCACCACCTGTGTACTACTACAAATCACCACCACCACC
66 ACCAACTTATGTTTACAAGTCACCTCCACCACCTGTGTACTACTACAAATCACCACCACCACC
1631339 CACTTATGTC
Statistics
Matches: 121, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
150 121 1.00
ACGTcount: A:0.27, C:0.40, G:0.09, T:0.24
Consensus pattern (150 bp):
TACTACTATAAGTCTCCACCTCCACCGGCTCCCACTTACGTTTACAAGTCACCACCTCCACCATC
ACCAACTTATGTTTACAAGTCACCTCCACCACCTGTGTACTACTACAAATCACCACCACCACCAA
AGCATGTGGAACAACCTCCA
Found at i:1631267 original size:36 final size:36
Alignment explanation
Indices: 1631220--1631308 Score: 115
Period size: 36 Copynumber: 2.5 Consensus size: 36
1631210 ATACTACTAT
* * *
1631220 AAGTCTCCACCTCCACCGGCTCCCACTTATGTTTAC
1 AAGTCACCACCTCCACCAGCGCCCACTTATGTTTAC
* *
1631256 AAGTCACCACCTCCACCATCGCCGACTTATGTTTAC
1 AAGTCACCACCTCCACCAGCGCCCACTTATGTTTAC
* *
1631292 AAGTCACCTCCACCACC
1 AAGTCACCACCTCCACC
1631309 TGTGTACTAC
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
36 46 1.00
ACGTcount: A:0.24, C:0.43, G:0.10, T:0.24
Consensus pattern (36 bp):
AAGTCACCACCTCCACCAGCGCCCACTTATGTTTAC
Found at i:1631500 original size:144 final size:143
Alignment explanation
Indices: 1631348--1632802 Score: 973
Period size: 144 Copynumber: 10.1 Consensus size: 143
1631338 CCACTTATGT
* * * *
1631348 CTACAAGTCTCCACCACCACCAAAGCATGTAGAGCAGCCCCCGTACTACTACAAATCTCCTCCAC
1 CTACAAGTCTCCACCACCACCAAAGCATGT-CAGCAGCCACCATACTACTACAAATCCCCTCCAC
* *
1631413 CACCATCGCCATCTCCTCCTCCACCATACTATTACAAGTCCCCACCACCACCAGTTCACTCTCCA
65 CACCATCGCCATCTCCTCCTCCACCATACTACTACAAATCCCCACCACCACCAGTTCACTCTCCA
1631478 CCACCACCATACTA
130 CCACCACCATACTA
* * * * * * *
1631492 CTACAAGTCCCCACCACCACCAAAACATGTGGAGCAACCTCCATACTACTACAAATCTCCTCCTC
1 CTACAAGTCTCCACCACCACCAAAGCATGT-CAGCAGCCACCATACTACTACAAATCCCCTCCAC
* *** * **
1631557 CACCATCGCCATCTCCTCCACCACCATACTACTACAAATCCCCACCACCACCAAAACA-TGTAGA
65 CACCATCGCCATCTCCTCCTCCACCATACTACTACAAATCCCCACCACCACCAGTTCACTCTCCA
** *
1631621 GGAGCCCCCATACTA
130 CCA-CCACCATACTA
* * * * * ** ** * *
1631636 CTACAAATCTCCTCCACCACCATCACCATCTCCTCCTCCACCATACTACTACAAGTCCCCACCAC
1 CTACAAGTCTCCACCACCACCA-AAGCATGTCAGCAGCCACCATACTACTACAAATCCCCTCCAC
*** * *** ** * *
1631701 CACCA-AAACATGTGGAGCAACCTCCATACTACTACAAATCACCC-CCACCACCA--TCGCCATC
65 CACCATCGCCATCT-CCTCCTCCACCATACTACTACAAATC-CCCACCACCACCAGTTC-AC-TC
* *
1631762 TCCTCCTCCACCATACTA
126 TCCACCACCACCATACTA
* * * * * *
1631780 CTACAAGTCCCCACCACCACCGAAGCATGTAGAGGAGCCCCCATACTACTACAAGTCTCCC-CCA
1 CTACAAGTCTCCACCACCACCAAAGCATGT-CAGCAGCCACCATACTACTACAAATC-CCCTCCA
* * *
1631844 CCACCATCGCCATCTCCTCCTCCACCATACTATTACAAATCTCCTCCACCACCA--TCACCATCT
64 CCACCATCGCCATCTCCTCCTCCACCATACTACTACAAATCCCCACCACCACCAGTTCA-C-TCT
* *
1631907 CCTCCTCCACCATACTA
127 CCACCACCACCATACTA
* * * * *
1631924 CTACAAGTCCCCACCACCACCGAAA-CATGTAGAGGAGCCCCCATAC-ATCTACAAATCTCCTCC
1 CTACAAGTCTCCACCACCACC-AAAGCATGT-CAGCAGCCACCATACTA-CTACAAATCCCCTCC
* * *
1631987 ACCACCATCGCCATCTCCTCCTCCACCATACTACTACAAGTCCCCACCACCCCCGAAG--CA-TG
63 ACCACCATCGCCATCTCCTCCTCCACCATACTACTACAAATCCCCACCACCACC--AGTTCACTC
** ** *
1632049 TAGAGGAGCCCCCATACTA
126 TCCACCA-CCACCATACTA
* ** * ** ** * *
1632068 CTACAAGTCTCCCCCACCACCATCGCCATCTCCTCCTCCACCATACTATTACAAATCTCCTCCAC
1 CTACAAGTCTCCACCACCACCAAAG-CATGTCAGCAGCCACCATACTACTACAAATCCCCTCCAC
* ** * **
1632133 CACCATCGCCATCTCCTCCTCCACCATACTACTACAAGTCCCCACCACCACC-G-AAACATGTAG
65 CACCATCGCCATCTCCTCCTCCACCATACTACTACAAATCCCCACCACCACCAGTTCAC-TCTCC
** *
1632196 AGGAGCCCCCATAC-A
129 ACCA-CCACCATACTA
* * ** * ** * * *
1632211 TCTACAAATCTCCTCCACCACCATCGCCATCTCCTCCA-CCACCATACTATTACAAGTCCCCACC
1 -CTACAAGTCTCCACCACCACCAAAG-CATGT-CAGCAGCCACCATACTACTACAAATCCCCTCC
* * * * * * * *
1632275 ACCACCAGC-CCATTCCCCACCACCACCATACTACTACAAGTCTCCACCACCACCAGTCCACTCC
63 ACCACCATCGCCA-TCTCCTCCTCCACCATACTACTACAAATCCCCACCACCACCAGTTCACTCT
*
1632339 CCACCCCCACCATACTA
127 CCACCACCACCATACTA
* **** * * * * * *
1632356 TTACAAGTCTCCACCACCACCTTCTCCT-TCACCACCTCCACCATACTATTACAAGTCCCCACCA
1 CTACAAGTCTCCACCACCACCAAAGCATGTCAGCA--GCCACCATACTACTACAAATCCCCTCCA
* * * * *
1632420 CCACCATCACCATCTCCTCCTCCACCATATTATTACAAGTCCCCACCACCACCAGTCCACTCTCC
64 CCACCATCGCCATCTCCTCCTCCACCATACTACTACAAATCCCCACCACCACCAGTTCACTCTCC
1632485 ACCACCACCATACTA
129 ACCACCACCATACTA
* * * * * ** * ** ** *
1632500 TTACAAATCCCCTCCTCCACCATCGCCATCTCCTCCTCCACCATACTACTACAAATCCCCACCAC
1 CTACAAGTCTCCACCACCACCAAAG-CATGTCAGCAGCCACCATACTACTACAAATCCCCTCCAC
* *
1632565 CACCA--GTCCACTCTCCACCCCCACCATACTACTACAAATCCCCACCACCACCA-TCTC-CTTC
65 CACCATCG-CCA-TCTCCTCCTCCACCATACTACTACAAATCCCCACCACCACCAGT-TCAC-TC
* *
1632626 ACCACCTCCACCATACTA
126 TCCACCACCACCATACTA
* * * * ** * * * * *
1632644 CTACAAATCACCCCCACCTCCAGTGAAGGCTCCAGCA-CCTACC-TACCATTACAACTCCCCTCC
1 CTACAAGTCTCCACCACCACCAAAGCATG-T-CAGCAGCC-ACCATACTACTACAAATCCCCTCC
* * * *
1632707 TCCACCATCACCATCTCCTCCTCCCCCATACTACTACAAATCTCCC-CCACCACCAGTCCACTCT
63 ACCACCATCGCCATCTCCTCCTCCACCATACTACTACAAATC-CCCACCACCACCAGTTCACTCT
*
1632771 CCCCCACCACCATACTA
127 CCACCACCACCATACTA
*
1632788 CTACAAATCTCCACC
1 CTACAAGTCTCCACC
1632803 TCCTCCATCT
Statistics
Matches: 1062, Mismatches: 200, Indels: 98
0.78 0.15 0.07
Matches are distributed among these distances:
141 5 0.00
142 3 0.00
143 33 0.03
144 965 0.91
145 48 0.05
146 8 0.01
ACGTcount: A:0.28, C:0.48, G:0.05, T:0.19
Consensus pattern (143 bp):
CTACAAGTCTCCACCACCACCAAAGCATGTCAGCAGCCACCATACTACTACAAATCCCCTCCACC
ACCATCGCCATCTCCTCCTCCACCATACTACTACAAATCCCCACCACCACCAGTTCACTCTCCAC
CACCACCATACTA
Found at i:1631509 original size:96 final size:94
Alignment explanation
Indices: 1631391--1632839 Score: 861
Period size: 96 Copynumber: 15.1 Consensus size: 94
1631381 GCAGCCCCCG
* * * * * *
1631391 TACTACTACAAATCTCCTCCACCACCATCGCCATCTCCTCCTCCACCATACTATTACAAGTCCCC
1 TACTACTACAAGTCCCCACCACCACCA-CGCCATCTCCGCCTCCACCATACTACTACAAATCCCC
* *
1631456 ACCACCACCAGTTCAC-TCTCCACCACCACCA
65 ACCACCACCA--TCACATCTCCTCCTCCACCA
*** * ** ** * *
1631487 TACTACTACAAGTCCCCACCACCACCAAAACATGTGGAGCAACCTCCATACTACTACAAATCTCC
1 TACTACTACAAGTCCCCACCACCACCACGCCATCT-CCGCCTCCACCATACTACTACAAATCCCC
* * * *
1631552 TCCTCCACCATCGCCATCTCCTCCACCACCA
65 ACCACCACCATC-ACATCTCCTCCTCCACCA
* *** * ** *** * *
1631583 TACTACTACAAATCCCCACCACCACCAAAACATGTAGAGGAGCCCCCATACTACTACAAATCTCC
1 TACTACTACAAGTCCCCACCACCACCACGCCATCT-CCGCCTCCACCATACTACTACAAATCCCC
*
1631648 TCCACCACCATCACCATCTCCTCCTCCACCA
65 ACCACCACCATCA-CATCTCCTCCTCCACCA
*** * ** ** *
1631679 TACTACTACAAGTCCCCACCACCACCAAAACATGTGGAGCAACCTCCATACTACTACAAATCACC
1 TACTACTACAAGTCCCCACCACCACCACGCCATCT-CCGCCTCCACCATACTACTACAAATC-CC
*
1631744 C-CCACCACCATCGCCATCTCCTCCTCCACCA
64 CACCACCACCATC-ACATCTCCTCCTCCACCA
* * ** *** * *
1631775 TACTACTACAAGTCCCCACCACCACCGAAG-CATGTAGAGGAGCCCCCATACTACTACAAGTCTC
1 TACTACTACAAGTCCCCACCACCACC-ACGCCATCT-CCGCCTCCACCATACTACTACAAATC-C
*
1631839 CC-CCACCACCATCGCCATCTCCTCCTCCACCA
63 CCACCACCACCATC-ACATCTCCTCCTCCACCA
* * * * * * *
1631871 TACTATTACAAATCTCCTCCACCACCATCACCATCTCCTCCTCCACCATACTACTACAAGTCCCC
1 TACTACTACAAGTCCCCACCACCACCA-CGCCATCTCCGCCTCCACCATACTACTACAAATCCCC
* * ****** *
1631936 ACCACCACCGA-AACATGTAGAGGAGCCCCCA
65 ACCACCACC-ATCACATCT-CCTCCTCCACCA
* * * * *
1631967 TAC-ATCTACAAATCTCCTCCACCACCATCGCCATCTCCTCCTCCACCATACTACTACAAGTCCC
1 TACTA-CTACAAGTCCCCACCACCACCA-CGCCATCTCCGCCTCCACCATACTACTACAAATCCC
* * ****** *
1632031 CACCACCCCCGA--AGCATGTAGAGGAGCCCCCA
64 CACCACCACC-ATCA-CATCT-CCTCCTCCACCA
* * *
1632063 TACTACTACAAGTCTCCC-CCACCACCATCGCCATCTCCTCCTCCACCATACTATTACAAATCTC
1 TACTACTACAAGTC-CCCACCACCACCA-CGCCATCTCCGCCTCCACCATACTACTACAAATCCC
* *
1632127 CTCCACCACCATCGCCATCTCCTCCTCCACCA
64 CACCACCACCATC-ACATCTCCTCCTCCACCA
** * ** *** * *
1632159 TACTACTACAAGTCCCCACCACCACCGA-AACATGTAGAGGAGCCCCCATAC-ATCTACAAATCT
1 TACTACTACAAGTCCCCACCACCACC-ACGCCATCT-CCGCCTCCACCATACTA-CTACAAATCC
* * *
1632222 CCTCCACCACCATCGCCATCTCCTCCACCACCA
63 CCACCACCACCATC-ACATCTCCTCCTCCACCA
* * * * * *
1632255 TACTATTACAAGTCCCCACCACCACCA-GCCCATTCCCCACCACCACCATACTACTACAAGTCTC
1 TACTACTACAAGTCCCCACCACCACCACG-CCA-TCTCCGCCTCCACCATACTACTACAAATCCC
* * *
1632319 CACCACCACCAGTC-CACTCCCCACCCCCACCA
64 CACCACCACCA-TCACA-TCTCCTCCTCCACCA
* * * * * * * * *
1632351 TACTATTACAAGTCTCCACCACCACCTTCTCCTTCACCACCTCCACCATACTATTACAAGTCCCC
1 TACTACTACAAGTCCCCACCACCACC-ACGCCATCTCCGCCTCCACCATACTACTACAAATCCCC
1632416 ACCACCACCATCACCATCTCCTCCTCCACCA
65 ACCACCACCATCA-CATCTCCTCCTCCACCA
* * * * *
1632447 TATTATTACAAGTCCCCACCACCACCA-GTCCACTCTCCACCACCACCATACTATTACAAATCCC
1 TACTACTACAAGTCCCCACCACCACCACG-CCA-TCTCCGCCTCCACCATACTACTACAAATCCC
* * *
1632511 CTCCTCCACCATCGCCATCTCCTCCTCCACCA
64 CACCACCACCATC-ACATCTCCTCCTCCACCA
* * *
1632543 TACTACTACAAATCCCCACCACCACCA-GTCCACTCTCCACCCCCACCATACTACTACAAATCCC
1 TACTACTACAAGTCCCCACCACCACCACG-CCA-TCTCCGCCTCCACCATACTACTACAAATCCC
* * * *
1632607 CACCACCACCATCTCCTTCACCACCTCCACCA
64 CACCACCACCATC-ACATCTCCTCCTCCACCA
* * ** * * * * *
1632639 TACTACTACAAATCACCC-CCACCTCCA-GTGAAGGCTCCAGCAC-CTACC-TACCATTACAACT
1 TACTACTACAAGTC-CCCACCACCACCACG-CCA-TCTCC-GC-CTCCACCATACTACTACAAAT
* * *
1632700 CCCCTCCTCCACCATCACCATCTCCTCCTCCCCCA
61 CCCCACCACCACCATCA-CATCTCCTCCTCCACCA
* * * *
1632735 TACTACTACAAATCTCCC-CCACCACCA-GTCCACTCTCCCCCACCACCATACTACTACAAATCT
1 TACTACTACAAGTC-CCCACCACCACCACG-CCA-TCTCCGCCTCCACCATACTACTACAAATCC
* * * * * * *
1632798 CCACCTCCTCCATCTCCCTCACCACCTCCTCCA
63 CCACCACCACCATC-ACATCTCCTCCTCCACCA
1632831 TACTACTAC
1 TACTACTAC
1632840 CACTCACCTC
Statistics
Matches: 1128, Mismatches: 183, Indels: 84
0.81 0.13 0.06
Matches are distributed among these distances:
94 3 0.00
95 36 0.03
96 1055 0.94
97 33 0.03
98 1 0.00
ACGTcount: A:0.28, C:0.48, G:0.05, T:0.19
Consensus pattern (94 bp):
TACTACTACAAGTCCCCACCACCACCACGCCATCTCCGCCTCCACCATACTACTACAAATCCCCA
CCACCACCATCACATCTCCTCCTCCACCA
Found at i:1631730 original size:240 final size:237
Alignment explanation
Indices: 1631348--1632802 Score: 1143
Period size: 240 Copynumber: 6.1 Consensus size: 237
1631338 CCACTTATGT
* * * * ** *
1631348 CTACAAGTCTCCACCACCACCAAAGCATGTAGAGCAGCCCCCGTACTACTACAAATCTCCTCCAC
1 CTACAAGTCCCCACCACCACCAAACCATCT-CA-CCCCCCCCATACTACTACAAATCTCCTCCAC
* * *** * **
1631413 CACCATCGCCATCTCCTCCTCCACCATACTATTACAAGTCCCCACCACCACCAGTTCACTCTCCA
64 CACCATCACCATCTCCTCCTCCACCATACTACTACAAGTCCCCACCACCACCAAAACA-TGTAGA
* * *** * *** * *
1631478 -CCACCACCATACTACTACAAGTCCCCACCACCACCA-AAACATGTGGAGCAACCTCCATACTAC
128 GCAACCACCATACTACTACAAATCCCCACCACCACCATCGCCATCT-CCTCCACCACCATACTAC
* * * * *
1631541 TACAAATCTCCTCCTCCACCATCGCCATCTCCTCCACCACCATACTA
192 TACAAGTCCCCACCACCACCA-CGCCATCTCCACCACCACCATACTA
* * * * ***
1631588 CTACAAATCCCCACCACCACCAAAACATGTAGAGGAGCCCCCATACTACTACAAATCTCCTCCAC
1 CTACAAGTCCCCACCACCACCAAACCATCT-CA-CCCCCCCCATACTACTACAAATCTCCTCCAC
*
1631653 CACCATCACCATCTCCTCCTCCACCATACTACTACAAGTCCCCACCACCACCAAAACATGTGGAG
64 CACCATCACCATCTCCTCCTCCACCATACTACTACAAGTCCCCACCACCACCAAAACATGTAGAG
* *
1631718 CAACCTCCATACTACTACAAATCACCC-CCACCACCATCGCCATCTCCTCCTCCACCATACTACT
129 CAACCACCATACTACTACAAATC-CCCACCACCACCATCGCCATCTCCTCCACCACCATACTACT
* * ** ** *
1631782 ACAAGTCCCCACCACCACCGAAG-CATGTAGAGGAGCCCCCATACTA
193 ACAAGTCCCCACCACCACC-ACGCCATCTCCACCA-CCACCATACTA
** * *
1631828 CTACAAGTCTCCC-CCACCACCATCGCCATCTC-CTCCTCCACCATACTATTACAAATCTCCTCC
1 CTACAAGTC-CCCACCACCACCA-AACCATCTCAC-CC-CCCCCATACTACTACAAATCTCCTCC
*
1631891 ACCACCATCACCATCTCCTCCTCCACCATACTACTACAAGTCCCCACCACCACCGAAACATGTAG
62 ACCACCATCACCATCTCCTCCTCCACCATACTACTACAAGTCCCCACCACCACCAAAACATGTAG
* * * * * *
1631956 AGGAGCCCCCATAC-ATCTACAAATCTCCTCCACCACCATCGCCATCTCCTCCTCCACCATACTA
127 AGCAACCACCATACTA-CTACAAATCCCCACCACCACCATCGCCATCTCCTCCACCACCATACTA
* * * ** ** *
1632020 CTACAAGTCCCCACCACCCCCGAAG-CATGTAGAGGAGCCCCCATACTA
191 CTACAAGTCCCCACCACCACC-ACGCCATCTCCACCA-CCACCATACTA
** * *
1632068 CTACAAGTCTCCC-CCACCACCATCGCCATCTC-CTCCTCCACCATACTATTACAAATCTCCTCC
1 CTACAAGTC-CCCACCACCACCA-AACCATCTCAC-CC-CCCCCATACTACTACAAATCTCCTCC
* *
1632131 ACCACCATCGCCATCTCCTCCTCCACCATACTACTACAAGTCCCCACCACCACCGAAACATGTAG
62 ACCACCATCACCATCTCCTCCTCCACCATACTACTACAAGTCCCCACCACCACCAAAACATGTAG
* * * * *
1632196 AGGAGCCCCCATAC-ATCTACAAATCTCCTCCACCACCATCGCCATCTCCTCCACCACCATACTA
127 AGCAACCACCATACTA-CTACAAATCCCCACCACCACCATCGCCATCTCCTCCACCACCATACTA
* *
1632260 TTACAAGTCCCCACCACCACCA-GCCCATTCCCCACCACCACCATACTA
191 CTACAAGTCCCCACCACCACCACG-CCA-TCTCCACCACCACCATACTA
* ** * * * * *
1632308 CTACAAGTCTCCACCACCACCAGTCCACTCCCCACCCCCACCATACTATTACAAGTCTCCACCAC
1 CTACAAGTCCCCACCACCACCAAACCA-T-CTCACCCCCCCCATACTACTACAAATCTCCTCCAC
* * * * * * * * * **
1632373 CACCTTCTCCTTCACCACCTCCACCATACTATTACAAGTCCCCACCACCACCATCACCATCT-CC
64 CACCATCACCATCTCCTCCTCCACCATACTACTACAAGTCCCCACCACCACCA-AAACATGTAGA
* ** * * * *
1632437 TCCTCCACCATATTATTACAAGTCCCCACCACCACCA--GTCCACTCTCCACCACCACCATACTA
128 GCAACCACCATACTACTACAAATCCCCACCACCACCATCG-CCA-TCTCCTCCACCACCATACTA
* * * * * *
1632500 TTACAAATCCCCTCCTCCACCATCGCCATCTCCTCCTCCACCATACTA
191 CTACAAGTCCCCACCACCACCA-CGCCATCTCCACCACCACCATACTA
* ** * * *
1632548 CTACAAATCCCCACCACCACCAGTCCACTCTCCACCCCCACCATACTACTACAAATCCCCACCAC
1 CTACAAGTCCCCACCACCACCAAACCA-TCT-CACCCCCCCCATACTACTACAAATCTCCTCCAC
* * * * * * ** * *
1632613 CACCATCTCCTTCACCACCTCCACCATACTACTACAAATCACCC-CCACCTCCAGTGA-AGGCTC
64 CACCATCACCATCTCCTCCTCCACCATACTACTACAAGTC-CCCACCACCACCA-AAACATG-TA
* * * * * * * * *
1632676 CAGC-ACCTACC-TACCATTACAACTCCCCTCCTCCACCATCACCATCTCCTCCTCCCCCATACT
126 GAGCAACC-ACCATACTACTACAAATCCCCACCACCACCATCGCCATCTCCTCCACCACCATACT
* *
1632739 ACTACAAATCTCCC-CCACCACCA-GTCCACTCTCCCCCACCACCATACTA
190 ACTACAAGTC-CCCACCACCACCACG-CCA-TCTCCACCACCACCATACTA
* *
1632788 CTACAAATCTCCACC
1 CTACAAGTCCCCACC
1632803 TCCTCCATCT
Statistics
Matches: 1046, Mismatches: 135, Indels: 68
0.84 0.11 0.05
Matches are distributed among these distances:
238 3 0.00
239 25 0.02
240 971 0.93
241 45 0.04
242 2 0.00
ACGTcount: A:0.28, C:0.48, G:0.05, T:0.19
Consensus pattern (237 bp):
CTACAAGTCCCCACCACCACCAAACCATCTCACCCCCCCCATACTACTACAAATCTCCTCCACCA
CCATCACCATCTCCTCCTCCACCATACTACTACAAGTCCCCACCACCACCAAAACATGTAGAGCA
ACCACCATACTACTACAAATCCCCACCACCACCATCGCCATCTCCTCCACCACCATACTACTACA
AGTCCCCACCACCACCACGCCATCTCCACCACCACCATACTA
Found at i:1631868 original size:24 final size:24
Alignment explanation
Indices: 1631836--1631918 Score: 80
Period size: 24 Copynumber: 3.5 Consensus size: 24
1631826 TACTACAAGT
* *
1631836 CTCCCCCACCACCATCGCCATCTC
1 CTCCTCCACCACCATCACCATCTC
* * **
1631860 CTCCTCCACCATACTATTA-CAAAT-
1 CTCCTCCACC--ACCATCACCATCTC
1631884 CTCCTCCACCACCATCACCATCTC
1 CTCCTCCACCACCATCACCATCTC
1631908 CTCCTCCACCA
1 CTCCTCCACCA
1631919 TACTACTACA
Statistics
Matches: 45, Mismatches: 10, Indels: 8
0.71 0.16 0.13
Matches are distributed among these distances:
22 5 0.11
23 3 0.07
24 30 0.67
25 3 0.07
26 4 0.09
ACGTcount: A:0.23, C:0.54, G:0.01, T:0.22
Consensus pattern (24 bp):
CTCCTCCACCACCATCACCATCTC
Found at i:1631906 original size:21 final size:21
Alignment explanation
Indices: 1631835--1631919 Score: 71
Period size: 21 Copynumber: 3.8 Consensus size: 21
1631825 CTACTACAAG
* *
1631835 TCTCCCCCACCACCATCGCCA
1 TCTCCTCCACCACCATCACCA
* *
1631856 TCTCCTCCTCCACCATACTATTACAAA
1 TCTCCTCCACCACCAT-C----AC-CA
1631883 TCTCCTCCACCACCATCACCA
1 TCTCCTCCACCACCATCACCA
*
1631904 TCTCCTCCTCCACCAT
1 TCTCCTCCACCACCAT
1631920 ACTACTACAA
Statistics
Matches: 51, Mismatches: 7, Indels: 12
0.73 0.10 0.17
Matches are distributed among these distances:
21 30 0.59
22 3 0.06
26 2 0.04
27 16 0.31
ACGTcount: A:0.22, C:0.53, G:0.01, T:0.24
Consensus pattern (21 bp):
TCTCCTCCACCACCATCACCA
Found at i:1632108 original size:24 final size:24
Alignment explanation
Indices: 1632076--1632158 Score: 80
Period size: 24 Copynumber: 3.5 Consensus size: 24
1632066 TACTACAAGT
*
1632076 CTCCCCCACCACCATCGCCATCTC
1 CTCCTCCACCACCATCGCCATCTC
* ** **
1632100 CTCCTCCACCATACTAT-TACAAAT-
1 CTCCTCCACC--ACCATCGCCATCTC
1632124 CTCCTCCACCACCATCGCCATCTC
1 CTCCTCCACCACCATCGCCATCTC
1632148 CTCCTCCACCA
1 CTCCTCCACCA
1632159 TACTACTACA
Statistics
Matches: 44, Mismatches: 11, Indels: 8
0.70 0.17 0.13
Matches are distributed among these distances:
22 4 0.09
23 3 0.07
24 30 0.68
25 3 0.07
26 4 0.09
ACGTcount: A:0.22, C:0.54, G:0.02, T:0.22
Consensus pattern (24 bp):
CTCCTCCACCACCATCGCCATCTC
Found at i:1632609 original size:27 final size:27
Alignment explanation
Indices: 1632246--1632661 Score: 117
Period size: 21 Copynumber: 17.2 Consensus size: 27
1632236 GCCATCTCCT
* *
1632246 CCACCACCATACTATTACAAGTCCCCA
1 CCACCACCATACTACTACAAATCCCCA
* *
1632273 CCACCACCA-GC--C--C-ATTCCCCA
1 CCACCACCATACTACTACAAATCCCCA
* *
1632294 CCACCACCATACTACTACAAGTCTCCA
1 CCACCACCATACTACTACAAATCCCCA
1632321 CCACCACCAGT-C--C-AC---TCCCCA
1 CCACCACCA-TACTACTACAAATCCCCA
* * * *
1632342 CCCCCACCATACTATTACAAGTCTCCA
1 CCACCACCATACTACTACAAATCCCCA
** *
1632369 CCACCACC-T--T-CT-C-CTTCACCA
1 CCACCACCATACTACTACAAATCCCCA
* * *
1632390 CCTCCACCATACTATTACAAGTCCCCA
1 CCACCACCATACTACTACAAATCCCCA
* *
1632417 CCACCACCAT-C-AC--C--ATCTCCT
1 CCACCACCATACTACTACAAATCCCCA
* * * *
1632438 CCTCCACCATATTATTACAAGTCCCCA
1 CCACCACCATACTACTACAAATCCCCA
*
1632465 CCACCACCAGT-C--C-AC---TCTCCA
1 CCACCACCA-TACTACTACAAATCCCCA
* *
1632486 CCACCACCATACTATTACAAATCCCCT
1 CCACCACCATACTACTACAAATCCCCA
* * * *
1632513 CCTCCACCAT-C-GC--C--ATCTCCT
1 CCACCACCATACTACTACAAATCCCCA
*
1632534 CCTCCACCATACTACTACAAATCCCCA
1 CCACCACCATACTACTACAAATCCCCA
*
1632561 CCACCACCAGT-C--C-AC---TCTCCA
1 CCACCACCA-TACTACTACAAATCCCCA
*
1632582 CCCCCACCATACTACTACAAATCCCCA
1 CCACCACCATACTACTACAAATCCCCA
* *
1632609 CCACCACCAT-CT-C--C--TTCACCA
1 CCACCACCATACTACTACAAATCCCCA
*
1632630 CCTCCACCATACTACTACAAATCACCC-
1 CCACCACCATACTACTACAAATC-CCCA
1632657 CCACC
1 CCACC
1632662 TCCAGTGAAG
Statistics
Matches: 278, Mismatches: 56, Indels: 110
0.63 0.13 0.25
Matches are distributed among these distances:
20 3 0.01
21 114 0.41
22 7 0.03
23 8 0.03
24 15 0.05
25 8 0.03
26 8 0.03
27 110 0.40
28 5 0.02
ACGTcount: A:0.28, C:0.51, G:0.02, T:0.19
Consensus pattern (27 bp):
CCACCACCATACTACTACAAATCCCCA
Found at i:1636218 original size:15 final size:15
Alignment explanation
Indices: 1636198--1636228 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
1636188 GATCTTAAGA
1636198 TACTAACATAAATCT
1 TACTAACATAAATCT
1636213 TACTAACATAAATCT
1 TACTAACATAAATCT
1636228 T
1 T
1636229 CAACCACTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.45, C:0.19, G:0.00, T:0.35
Consensus pattern (15 bp):
TACTAACATAAATCT
Found at i:1636536 original size:15 final size:15
Alignment explanation
Indices: 1636516--1636546 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1636506 CCATCTTTTC
*
1636516 TATGTTTGGTTTTAA
1 TATGTTTGGTTGTAA
1636531 TATGTTTGGTTGTAA
1 TATGTTTGGTTGTAA
1636546 T
1 T
1636547 GGTAACACTT
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:0.19, C:0.00, G:0.23, T:0.58
Consensus pattern (15 bp):
TATGTTTGGTTGTAA
Found at i:1639660 original size:15 final size:15
Alignment explanation
Indices: 1639640--1639669 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1639630 TAAAATTTTG
1639640 GGGTCATTGCAAGTT
1 GGGTCATTGCAAGTT
*
1639655 GGGTCATTTCAAGTT
1 GGGTCATTGCAAGTT
1639670 CCGATTCTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.13, G:0.30, T:0.37
Consensus pattern (15 bp):
GGGTCATTGCAAGTT
Found at i:1642362 original size:5 final size:5
Alignment explanation
Indices: 1642354--1642379 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
1642344 TATAATATGC
1642354 TTTAT TTTAT TTTAT TTTAT TTTAT T
1 TTTAT TTTAT TTTAT TTTAT TTTAT T
1642380 ATGCTTATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTAT
Found at i:1651440 original size:6 final size:6
Alignment explanation
Indices: 1651429--1651454 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
1651419 GCTGCCCCAA
1651429 CTCCTG CTCCTG CTCCTG CTCCTG CT
1 CTCCTG CTCCTG CTCCTG CTCCTG CT
1651455 GCTGTTCCCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.00, C:0.50, G:0.15, T:0.35
Consensus pattern (6 bp):
CTCCTG
Found at i:1652328 original size:33 final size:33
Alignment explanation
Indices: 1652273--1652348 Score: 82
Period size: 33 Copynumber: 2.3 Consensus size: 33
1652263 CAGGCACAAT
**
1652273 CAAGTGCTAATATGTACAGCCAACC-GACACAGC
1 CAAGTGCTAATACATACAGCCAACCTG-CACAGC
* *
1652306 CAAGTGCTAATCCATACGGCCAACCTGCACAGC
1 CAAGTGCTAATACATACAGCCAACCTGCACAGC
**
1652339 CTGGTGCTAA
1 CAAGTGCTAA
1652349 CGCATATGAC
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
33 35 0.97
34 1 0.03
ACGTcount: A:0.32, C:0.32, G:0.20, T:0.17
Consensus pattern (33 bp):
CAAGTGCTAATACATACAGCCAACCTGCACAGC
Found at i:1655265 original size:33 final size:33
Alignment explanation
Indices: 1655228--1655298 Score: 83
Period size: 33 Copynumber: 2.2 Consensus size: 33
1655218 AATATGTACA
1655228 GCCAACC-GACACAGCCAAGTGCTAATC-CATATG
1 GCCAACCTG-CACAGCCAAGTGCTAA-CGCATATG
**
1655261 GCCAACCTGCACAGCCTGGTGCTAACGCATATG
1 GCCAACCTGCACAGCCAAGTGCTAACGCATATG
*
1655294 ACCAA
1 GCCAA
1655299 GTTGGACAAC
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
32 1 0.03
33 31 0.94
34 1 0.03
ACGTcount: A:0.31, C:0.34, G:0.20, T:0.15
Consensus pattern (33 bp):
GCCAACCTGCACAGCCAAGTGCTAACGCATATG
Found at i:1661449 original size:27 final size:27
Alignment explanation
Indices: 1661411--1661466 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
1661401 CACTCTCTAA
1661411 CATCTTCAAGTTCTTCATCACCATTTT
1 CATCTTCAAGTTCTTCATCACCATTTT
*
1661438 CATCTTCAAGTTCTTCATGACCATTTT
1 CATCTTCAAGTTCTTCATCACCATTTT
1661465 CA
1 CA
1661467 GTGGAAATCA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.23, C:0.29, G:0.05, T:0.43
Consensus pattern (27 bp):
CATCTTCAAGTTCTTCATCACCATTTT
Found at i:1662871 original size:23 final size:24
Alignment explanation
Indices: 1662820--1662870 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 24
1662810 TGGATTGGTG
1662820 ATTTAATATAAATATAAATATAATT
1 ATTTAATAT-AATATAAATATAATT
*
1662845 ATTTAATATATATAATTAATATAATT
1 ATTTAATATA-AT-ATAAATATAATT
1662871 TTTTTAGGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 1 0.04
25 11 0.48
26 11 0.48
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (24 bp):
ATTTAATATAATATAAATATAATT
Found at i:1663425 original size:8 final size:8
Alignment explanation
Indices: 1663412--1663440 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
1663402 ATTTAAGTAA
1663412 ATATTATT
1 ATATTATT
1663420 ATATTATT
1 ATATTATT
1663428 ATATTATT
1 ATATTATT
1663436 ATATT
1 ATATT
1663441 GTATTGTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (8 bp):
ATATTATT
Found at i:1663535 original size:13 final size:12
Alignment explanation
Indices: 1663490--1663555 Score: 53
Period size: 12 Copynumber: 5.2 Consensus size: 12
1663480 AAAAGAATAG
* *
1663490 AAAGAAAAGAAC
1 AAAGAGAAGAAA
1663502 AAAGTAGAACG-AA
1 AAAG-AGAA-GAAA
*
1663515 ATAGAGAAGAAA
1 AAAGAGAAGAAA
1663527 AAGAGAGAAAGAAA
1 AA-AGAG-AAGAAA
*
1663541 AATGAGAAGAAA
1 AAAGAGAAGAAA
1663553 AAA
1 AAA
1663556 TTAGGGTTTT
Statistics
Matches: 43, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
11 1 0.02
12 19 0.44
13 14 0.33
14 9 0.21
ACGTcount: A:0.70, C:0.03, G:0.23, T:0.05
Consensus pattern (12 bp):
AAAGAGAAGAAA
Found at i:1666906 original size:12 final size:12
Alignment explanation
Indices: 1666889--1666916 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
1666879 ACAACCACCC
1666889 ATCACAACATTT
1 ATCACAACATTT
1666901 ATCACAACATTT
1 ATCACAACATTT
1666913 ATCA
1 ATCA
1666917 TCATACTCGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.43, C:0.25, G:0.00, T:0.32
Consensus pattern (12 bp):
ATCACAACATTT
Found at i:1674659 original size:90 final size:90
Alignment explanation
Indices: 1674543--1674724 Score: 355
Period size: 90 Copynumber: 2.0 Consensus size: 90
1674533 CCGCTTCACA
1674543 CTTGCTTTTGATGTTGGGTTGATTTGATATTCATGACTAAATTTATGAGATTTTTTTATCAATCC
1 CTTGCTTTTGATGTTGGGTTGATTTGATATTCATGACTAAATTTATGAGATTTTTTTATCAATCC
1674608 TTTTTTGTTTAATTTCGAAATTCCC
66 TTTTTTGTTTAATTTCGAAATTCCC
1674633 CTTGCTTTTGATGTTGGGTTGATTTGATATTCATGACTAAATTTATGAGATTTTTTTATCAATCC
1 CTTGCTTTTGATGTTGGGTTGATTTGATATTCATGACTAAATTTATGAGATTTTTTTATCAATCC
*
1674698 TTTTTTGTTTTATTTCGAAATTCCC
66 TTTTTTGTTTAATTTCGAAATTCCC
1674723 CT
1 CT
1674725 GTAATGATGT
Statistics
Matches: 91, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
90 91 1.00
ACGTcount: A:0.21, C:0.13, G:0.14, T:0.52
Consensus pattern (90 bp):
CTTGCTTTTGATGTTGGGTTGATTTGATATTCATGACTAAATTTATGAGATTTTTTTATCAATCC
TTTTTTGTTTAATTTCGAAATTCCC
Found at i:1703632 original size:18 final size:18
Alignment explanation
Indices: 1703605--1703697 Score: 123
Period size: 18 Copynumber: 5.2 Consensus size: 18
1703595 TACGACCGTT
1703605 TACGGTACTATTCACGTA
1 TACGGTACTATTCACGTA
* *
1703623 TACGGAACTATTCACATA
1 TACGGTACTATTCACGTA
*
1703641 TACGGTACTATTCATGTA
1 TACGGTACTATTCACGTA
** *
1703659 TATAGCACTATTCACGTA
1 TACGGTACTATTCACGTA
*
1703677 TACGGTACTGTTCACGTA
1 TACGGTACTATTCACGTA
1703695 TAC
1 TAC
1703698 AGTAGTTGGG
Statistics
Matches: 62, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 62 1.00
ACGTcount: A:0.30, C:0.22, G:0.15, T:0.33
Consensus pattern (18 bp):
TACGGTACTATTCACGTA
Found at i:1703652 original size:36 final size:36
Alignment explanation
Indices: 1703605--1703699 Score: 136
Period size: 36 Copynumber: 2.6 Consensus size: 36
1703595 TACGACCGTT
*
1703605 TACGGTACTATTCACGTATACGGAACTATTCACATA
1 TACGGTACTATTCACGTATACAGAACTATTCACATA
* * * *
1703641 TACGGTACTATTCATGTATATAGCACTATTCACGTA
1 TACGGTACTATTCACGTATACAGAACTATTCACATA
*
1703677 TACGGTACTGTTCACGTATACAG
1 TACGGTACTATTCACGTATACAG
1703700 TAGTTGGGAT
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 51 1.00
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.33
Consensus pattern (36 bp):
TACGGTACTATTCACGTATACAGAACTATTCACATA
Found at i:1713191 original size:18 final size:19
Alignment explanation
Indices: 1713158--1713195 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
1713148 AGACTCCAGG
*
1713158 TCTGATTCTTTTCAATCAT
1 TCTGATTCTCTTCAATCAT
1713177 TCTGATT-TCTTCAATCAT
1 TCTGATTCTCTTCAATCAT
1713195 T
1 T
1713196 GCTTGCTTCC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.21, C:0.21, G:0.05, T:0.53
Consensus pattern (19 bp):
TCTGATTCTCTTCAATCAT
Found at i:1721886 original size:20 final size:20
Alignment explanation
Indices: 1721861--1721901 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
1721851 TTCAATGTCG
1721861 CGACACCCACTTGATATTTT
1 CGACACCCACTTGATATTTT
*
1721881 CGACACCCACTTGATTTTTT
1 CGACACCCACTTGATATTTT
1721901 C
1 C
1721902 TTAAATTGAA
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:0.32, G:0.10, T:0.37
Consensus pattern (20 bp):
CGACACCCACTTGATATTTT
Found at i:1726625 original size:6 final size:6
Alignment explanation
Indices: 1726614--1726646 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
1726604 TGAACTCTCC
1726614 ATCTGA ATCTGA ATCTGA ATCTGA ATCTGA ATC
1 ATCTGA ATCTGA ATCTGA ATCTGA ATCTGA ATC
1726647 AGGTGGCTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.33
Consensus pattern (6 bp):
ATCTGA
Found at i:1727568 original size:22 final size:21
Alignment explanation
Indices: 1727541--1727590 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
1727531 TTTTATCTTT
*
1727541 TTAAAAAGTTATTGTAATTGAA
1 TTAAAAAGTTAGT-TAATTGAA
**
1727563 TTAAAATTTTAGTTAATTGAA
1 TTAAAAAGTTAGTTAATTGAA
*
1727584 TCAAAAA
1 TTAAAAA
1727591 ATAATTATCT
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
21 13 0.57
22 10 0.43
ACGTcount: A:0.48, C:0.02, G:0.10, T:0.40
Consensus pattern (21 bp):
TTAAAAAGTTAGTTAATTGAA
Found at i:1730525 original size:20 final size:21
Alignment explanation
Indices: 1730500--1730541 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
1730490 TAACAAAAAT
1730500 TATATATATATA-ATTTTTTA
1 TATATATATATAGATTTTTTA
* *
1730520 TATATATTTTTAGATTTTTTA
1 TATATATATATAGATTTTTTA
1730541 T
1 T
1730542 TTTTTATAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (21 bp):
TATATATATATAGATTTTTTA
Found at i:1731260 original size:20 final size:20
Alignment explanation
Indices: 1731228--1731267 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
1731218 ATAAAACACT
1731228 AAAAATTTATTTTAAAAATA
1 AAAAATTTATTTTAAAAATA
1731248 AAAAAGTTT-TTTTAAAAATA
1 AAAAA-TTTATTTTAAAAATA
1731268 TTTTAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 16 0.84
21 3 0.16
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (20 bp):
AAAAATTTATTTTAAAAATA
Found at i:1739781 original size:31 final size:32
Alignment explanation
Indices: 1739710--1739788 Score: 90
Period size: 32 Copynumber: 2.5 Consensus size: 32
1739700 AAATTAATAA
* * *
1739710 TAATAAAATTATATTTTTATTTTTCTTAAAAT
1 TAATAAAATTATAATTTAATTTTTCTAAAAAT
*
1739742 TAATAAAATTCTAATTTAATTTTT-TAAAAAT
1 TAATAAAATTATAATTTAATTTTTCTAAAAAT
*
1739773 T-ATAAAAATAATAATT
1 TAAT-AAAATTATAATT
1739789 AAAAATTTAA
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
30 2 0.05
31 17 0.43
32 21 0.52
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.49
Consensus pattern (32 bp):
TAATAAAATTATAATTTAATTTTTCTAAAAAT
Found at i:1741446 original size:3 final size:3
Alignment explanation
Indices: 1741435--1741485 Score: 59
Period size: 3 Copynumber: 17.0 Consensus size: 3
1741425 CAATAATACC
* * *
1741435 AAT ACT AAT AAT AGT AA- AGAT GAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT
1741480 AAT AAT
1 AAT AAT
1741486 GAAGTTAACA
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
2 1 0.03
3 39 0.98
ACGTcount: A:0.61, C:0.02, G:0.06, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1742983 original size:87 final size:87
Alignment explanation
Indices: 1742875--1743506 Score: 368
Period size: 87 Copynumber: 7.3 Consensus size: 87
1742865 ACCTACTCTG
* * * ** *
1742875 CTGTAACCTCAGAGAGATAAGATCCTTTATTTTAACCCACTCCACTGTAACTTCAGGGAGATAGG
1 CTGTAACCTCAGGGAGATAAGATCCTTTATTTCAATCTGCTCCACTGTAACTTCAGGGAGATAAG
* *
1742940 ATAGTGTCTTCGATCTGCTCCG
66 ATACTGTCTTCGATCTGCTCCA
* * *** *
1742962 CTGTAATCTCGGGGAGATAAGAT-CTCTGGCTTCAATCTGCTCCACTGTAACTTCAGGGGGATAA
1 CTGTAACCTCAGGGAGATAAGATCCT-TTATTTCAATCTGCTCCACTGTAACTTCAGGGAGATAA
* *
1743026 GAT-CTGCAATTCTTCGGTCTACTCCA
65 GATACTG----TCTTCGATCTGCTCCA
* * * * * * *
1743052 CTGTAACCTCAGAGAGATAAGA-CC-TGA-TGCGATCTACTCTACTGTAACTTCAGAGAGATAAG
1 CTGTAACCTCAGGGAGATAAGATCCTTTATTTCAATCTGCTCCACTGTAACTTCAGGGAGATAAG
* * * ** *
1743114 ATCCTTTATTTTAATCCGCTCCA
66 ATACTGT-CTTCGATCTGCTCCA
* * * * * * *
1743137 CTGTAACTTCAGGGAGATAGGAT--TATATCTTCGATCTGCTCCGCTGTAACCTCAGGGAGACAA
1 CTGTAACCTCAGGGAGATAAGATCCTTTAT-TTCAATCTGCTCCACTGTAACTTCAGGGAGATAA
* *
1743200 GAT-CTGTAATTCTTCGGTCTGTTCCA
65 GATACTG----TCTTCGATCTGCTCCA
* * * *
1743226 CTGTAATCTCAGGGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAACTTCAGGGAGATAGG
1 CTGTAACCTCAGGGAGATAAGATCCTTTATTTCAATCTGCTCCACTGTAACTTCAGGGAGATAAG
* *
1743291 ATTA-TATCTTCGATCTGCTCCG
66 A-TACTGTCTTCGATCTGCTCCA
* * * ** *
1743313 CTGTAACCTCAGGGAGACAAGATCTGCAATT-CTTCGGTCTGTTCCACTGTAA-TCTCAGGGAGA
1 CTGTAACCTCAGGGAGATAAGATC--C-TTTATTTCAATCTGCTCCACTGTAACT-TCAGGGAGA
* * * *
1743376 TAAGA-CCTGAT-GT-GATCTTCTCTA
62 TAAGATACTG-TCTTCGATCTGCTCCA
* * * * * * *
1743400 CTGTAACTTCAGAGAGATAAGATCC----TTT-AATCCGCTCTATTGTAA-TCTCAAGGAGATAG
1 CTGTAACCTCAGGGAGATAAGATCCTTTATTTCAATCTGCTCCACTGTAACT-TCAGGGAGATAA
* * *
1743459 GATTACTATCTTTGATCTGCTCCG
65 GA-TACTGTCTTCGATCTGCTCCA
*
1743483 CTGTAATCTCAGGGAGATAAGATC
1 CTGTAACCTCAGGGAGATAAGATC
1743507 TCTGGCTTCA
Statistics
Matches: 411, Mismatches: 104, Indels: 64
0.71 0.18 0.11
Matches are distributed among these distances:
80 25 0.06
81 3 0.01
82 3 0.01
83 29 0.07
84 1 0.00
85 30 0.07
86 6 0.01
87 177 0.43
88 7 0.02
89 59 0.14
90 65 0.16
91 6 0.01
ACGTcount: A:0.26, C:0.23, G:0.20, T:0.31
Consensus pattern (87 bp):
CTGTAACCTCAGGGAGATAAGATCCTTTATTTCAATCTGCTCCACTGTAACTTCAGGGAGATAAG
ATACTGTCTTCGATCTGCTCCA
Found at i:1743054 original size:46 final size:43
Alignment explanation
Indices: 1742914--1743526 Score: 347
Period size: 44 Copynumber: 14.1 Consensus size: 43
1742904 TTTTAACCCA
*
1742914 CTCCACTGTAACTTCAGGGAGATAGGA--TAGTGTCTTCGATCTG
1 CTCCACTGTAACTTCAGGGAGATAAGATCTA-T-TCTTCGATCTG
* * * * *
1742957 CTCCGCTGTAA-TCTCGGGGAGATAAGATCTCTGGCTTCAATCTG
1 CTCCACTGTAACT-TCAGGGAGATAAGATCTAT-TCTTCGATCTG
* * *
1743001 CTCCACTGTAACTTCAGGGGGATAAGATCTGCAATTCTTCGGTCTA
1 CTCCACTGTAACTTCAGGGAGATAAGATCT---ATTCTTCGATCTG
* * * * *
1743047 CTCCACTGTAACCTCAGAGAGATAAGACCTGA---TGCGATCTA
1 CTCCACTGTAACTTCAGGGAGATAAGATCT-ATTCTTCGATCTG
* * * *
1743088 CTCTACTGTAACTTCAGAGAGATAAGATCCTTTATT-TT-AATCCG
1 CTCCACTGTAACTTCAGGGAGATAAGAT-C--TATTCTTCGATCTG
*
1743132 CTCCACTGTAACTTCAGGGAGATAGGAT-TATATCTTCGATCTG
1 CTCCACTGTAACTTCAGGGAGATAAGATCTAT-TCTTCGATCTG
* * * *
1743175 CTCCGCTGTAACCTCAGGGAGACAAGATCTGTAATTCTTCGGTCTG
1 CTCCACTGTAACTTCAGGGAGATAAGATC--T-ATTCTTCGATCTG
* * *
1743221 TTCCACTGTAA-TCTCAGGGAGATAAGATCCTTTATT-TT-AATCCG
1 CTCCACTGTAACT-TCAGGGAGATAAGAT-C--TATTCTTCGATCTG
*
1743265 CTCCACTGTAACTTCAGGGAGATAGGAT-TATATCTTCGATCTG
1 CTCCACTGTAACTTCAGGGAGATAAGATCTAT-TCTTCGATCTG
* * * *
1743308 CTCCGCTGTAACCTCAGGGAGACAAGATCTGCAATTCTTCGGTCTG
1 CTCCACTGTAACTTCAGGGAGATAAGATCT---ATTCTTCGATCTG
* * * *
1743354 TTCCACTGTAA-TCTCAGGGAGATAAGACCTGA-T-GT-GATCTT
1 CTCCACTGTAACT-TCAGGGAGATAAGATCT-ATTCTTCGATCTG
* * ** *
1743395 CTCTACTGTAACTTCAGAGAGATAAGATC----CTTTAATCCG
1 CTCCACTGTAACTTCAGGGAGATAAGATCTATTCTTCGATCTG
* * * * *
1743434 CTCTATTGTAA-TCTCAAGGAGATAGGAT-TACTATCTTTGATCTG
1 CTCCACTGTAACT-TCAGGGAGATAAGATCTA-T-TCTTCGATCTG
* * * *
1743478 CTCCGCTGTAA-TCTCAGGGAGATAAGATCTCTGGCTTCAATCTG
1 CTCCACTGTAACT-TCAGGGAGATAAGATCTAT-TCTTCGATCTG
1743522 CTCCA
1 CTCCA
1743527 ATGCAACCGA
Statistics
Matches: 440, Mismatches: 89, Indels: 81
0.72 0.15 0.13
Matches are distributed among these distances:
38 2 0.00
39 25 0.06
40 6 0.01
41 61 0.14
42 8 0.02
43 80 0.18
44 139 0.32
45 7 0.02
46 104 0.24
47 8 0.02
ACGTcount: A:0.25, C:0.23, G:0.21, T:0.31
Consensus pattern (43 bp):
CTCCACTGTAACTTCAGGGAGATAAGATCTATTCTTCGATCTG
Found at i:1743251 original size:133 final size:132
Alignment explanation
Indices: 1742946--1743380 Score: 542
Period size: 133 Copynumber: 3.3 Consensus size: 132
1742936 TAGGATAGTG
* * *** * *
1742946 TCTTCGATCTGCTCCGCTGTAATCTCGGGGAGATAAGAT-CTCTGGCTTCAATCTGCTCCACTGT
1 TCTTCGATCTGCTCCACTGTAATCTCAGGGAGATAAGATCCT-TTATTTTAATCCGCTCCACTGT
* * * * * * *
1743010 AACTTCAGGGGGATAAGATCTGCA-ATTCTTCGGTCTACTCCACTGTAACCTCAGAGAGATAAGA
65 AACTTCAGGGAGATAGGAT-T--ATA-TCTTCGATCTGCTCCGCTGTAACCTCAGGGAGACAAGA
*
1743074 CCTG-A-
126 TCTGAAT
* * * *
1743079 --TGCGATCTACTCTACTGTAA-CTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGT
1 TCTTCGATCTGCTCCACTGTAATC-TCAGGGAGATAAGATCCTTTATTTTAATCCGCTCCACTGT
1743141 AACTTCAGGGAGATAGGATTATATCTTCGATCTGCTCCGCTGTAACCTCAGGGAGACAAGATCTG
65 AACTTCAGGGAGATAGGATTATATCTTCGATCTGCTCCGCTGTAACCTCAGGGAGACAAGATCTG
1743206 TAAT
130 -AAT
* *
1743210 TCTTCGGTCTGTTCCACTGTAATCTCAGGGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTA
1 TCTTCGATCTGCTCCACTGTAATCTCAGGGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTA
1743275 ACTTCAGGGAGATAGGATTATATCTTCGATCTGCTCCGCTGTAACCTCAGGGAGACAAGATCTGC
66 ACTTCAGGGAGATAGGATTATATCTTCGATCTGCTCCGCTGTAACCTCAGGGAGACAAGATCTG-
1743340 AAT
130 AAT
* *
1743343 TCTTCGGTCTGTTCCACTGTAATCTCAGGGAGATAAGA
1 TCTTCGATCTGCTCCACTGTAATCTCAGGGAGATAAGA
1743381 CCTGATGTGA
Statistics
Matches: 267, Mismatches: 26, Indels: 18
0.86 0.08 0.06
Matches are distributed among these distances:
128 37 0.14
129 1 0.00
130 3 0.01
131 63 0.24
132 2 0.01
133 160 0.60
134 1 0.00
ACGTcount: A:0.25, C:0.23, G:0.21, T:0.31
Consensus pattern (132 bp):
TCTTCGATCTGCTCCACTGTAATCTCAGGGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTA
ACTTCAGGGAGATAGGATTATATCTTCGATCTGCTCCGCTGTAACCTCAGGGAGACAAGATCTGA
AT
Found at i:1743271 original size:218 final size:218
Alignment explanation
Indices: 1742850--1743288 Score: 573
Period size: 218 Copynumber: 2.0 Consensus size: 218
1742840 CTTCAGGGAA
* *
1742850 ATAAGACTTGATGCGACCTACTCTGCTGTAACCTCAGAGAGATAAGATCCTTTATTTTAACCCAC
1 ATAAGACCTGATGCGACCTACTCTACTGTAACCTCAGAGAGATAAGATCCTTTATTTTAACCCAC
* * * *
1742915 TCCACTGTAACTTCAGGGAGATAGGATAGTGTCTTCGATCTGCTCCGCTGTAATCTCGGGGAGAT
66 TCCACTGTAACTTCAGGGAGATAGGATAGTATCTTCGATCTGCTCCGCTGTAACCTCAGGGAGAC
* **
1742980 AAGATCTCTGGCTTCAATCTGCTCCACTGTAACTTCAGGGGGATAAGATCTGCAATTCTTCGGTC
131 AAGATCTCTGGCTTCAATCTGCTCCACTGTAACTTCAGGGAGATAAGATCTGCAATTCTTCAATC
*
1743045 TACTCCACTGTAACCTCAGAGAG
196 CACTCCACTGTAACCTCAGAGAG
* * * *
1743068 ATAAGACCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGC
1 ATAAGACCTGATGCGACCTACTCTACTGTAACCTCAGAGAGATAAGATCCTTTATTTTAACCCAC
1743133 TCCACTGTAACTTCAGGGAGATAGGATTA-TATCTTCGATCTGCTCCGCTGTAACCTCAGGGAGA
66 TCCACTGTAACTTCAGGGAGATAGGA-TAGTATCTTCGATCTGCTCCGCTGTAACCTCAGGGAGA
* ** ** * **
1743197 CAAGATCTGTAATTCTTCGGTCTGTTCCACTGTAA-TCTCAGGGAGATAAGATCCT-TTATT-TT
130 CAAGATCTCT--GGCTTCAATCTGCTCCACTGTAACT-TCAGGGAGATAAGAT-CTGCAATTCTT
* * *
1743259 -AATCCGCTCCACTGTAACTTCAGGGAG
191 CAATCCACTCCACTGTAACCTCAGAGAG
1743286 ATA
1 ATA
1743289 GGATTATATC
Statistics
Matches: 191, Mismatches: 25, Indels: 10
0.85 0.11 0.04
Matches are distributed among these distances:
218 149 0.78
219 5 0.03
220 35 0.18
221 2 0.01
ACGTcount: A:0.26, C:0.23, G:0.20, T:0.30
Consensus pattern (218 bp):
ATAAGACCTGATGCGACCTACTCTACTGTAACCTCAGAGAGATAAGATCCTTTATTTTAACCCAC
TCCACTGTAACTTCAGGGAGATAGGATAGTATCTTCGATCTGCTCCGCTGTAACCTCAGGGAGAC
AAGATCTCTGGCTTCAATCTGCTCCACTGTAACTTCAGGGAGATAAGATCTGCAATTCTTCAATC
CACTCCACTGTAACCTCAGAGAG
Found at i:1743571 original size:86 final size:85
Alignment explanation
Indices: 1743467--1743766 Score: 275
Period size: 86 Copynumber: 3.5 Consensus size: 85
1743457 AGGATTACTA
* * * *
1743467 TCTTTGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCT-CTGGCTTCAATCT-GCTCCAATG
1 TCTTTGATCTGCTTCGCTGTAAT-GCAGGAAGACAAGATCTACT-GCTTCAA-CTAGCTCCAATG
1743530 CAACCGATGGAGGCAAGGCTTTG
63 CAACCGATGGAGGCAAGGCTTTG
* * * * *
1743553 TCTTTGATCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTACTTCTTTAACTAGCTCCACTGCG
1 TCTTTGATCTGCTTCGCTG-TAATGCAGGAAGACAAGATCTACTGCTTCAACTAGCTCCAATGCA
* *
1743618 ATCGATGGATGCAAGGCTTTG
65 ACCGATGGAGGCAAGGCTTTG
* * ** * *
1743639 T-TTTCGATCTGCTTCGCTGTTAATGTAGGAAGGCAAGATCTTTTGTCTTCAACCAGCT-CTATC
1 TCTTT-GATCTGCTTCGCTG-TAATGCAGGAAGACAAGATCTACTG-CTTCAACTAGCTCCAAT-
* ** *
1743702 ACAACCGAAAGAGGCAAGGTTTGTG
62 GCAACCGATGGAGGCAAGGCTT-TG
* *
1743727 TCTTCGATCTGCTTCGCTGCTAATGCAGGAAGGCAAGATC
1 TCTTTGATCTGCTTCGCTG-TAATGCAGGAAGACAAGATC
1743767 CTTTGTCTTC
Statistics
Matches: 177, Mismatches: 29, Indels: 14
0.80 0.13 0.06
Matches are distributed among these distances:
85 5 0.03
86 103 0.58
87 31 0.18
88 36 0.20
89 2 0.01
ACGTcount: A:0.23, C:0.23, G:0.24, T:0.31
Consensus pattern (85 bp):
TCTTTGATCTGCTTCGCTGTAATGCAGGAAGACAAGATCTACTGCTTCAACTAGCTCCAATGCAA
CCGATGGAGGCAAGGCTTTG
Found at i:1743751 original size:88 final size:88
Alignment explanation
Indices: 1743512--1743777 Score: 299
Period size: 86 Copynumber: 3.1 Consensus size: 88
1743502 AGATCTCTGG
* * * * * *
1743512 CTTCAATCTGCTCCAATGCAACCGATGGAGGCAAGGCTT-TGTCTTTGATCTGCTTCGCTGTTAA
1 CTTCAACCAGCTCCACTACAACCGATGGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTTAA
**
1743576 TGCAGGAAGGCAAGATCTACT-T
66 TGCAGGAAGGCAAGATCTTTTGT
* * * * * *
1743598 CTTTAACTAGCTCCACTGCGATCGATGGATGCAAGGCTTTGT-T-TTCGATCTGCTTCGCTGTTA
1 CTTCAACCAGCTCCACTACAACCGATGGAGGCAAGG-TTTGTGTCTTCGATCTGCTTCGCTGTTA
*
1743661 ATGTAGGAAGGCAAGATCTTTTGT
65 ATGCAGGAAGGCAAGATCTTTTGT
* ** *
1743685 CTTCAACCAGCTCTA-TCACAACCGAAAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGCTA
1 CTTCAACCAGCTCCACT-ACAACCGATGGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTTA
*
1743749 ATGCAGGAAGGCAAGATCCTTTGT
65 ATGCAGGAAGGCAAGATCTTTTGT
1743773 CTTCA
1 CTTCA
1743778 TTGATCTGTC
Statistics
Matches: 149, Mismatches: 25, Indels: 10
0.81 0.14 0.05
Matches are distributed among these distances:
86 72 0.48
87 30 0.20
88 47 0.32
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.31
Consensus pattern (88 bp):
CTTCAACCAGCTCCACTACAACCGATGGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTTAA
TGCAGGAAGGCAAGATCTTTTGT
Found at i:1745024 original size:1 final size:1
Alignment explanation
Indices: 1745018--1745048 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
1745008 CTCTCCAAAG
1745018 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1745049 AGGAAGCAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:1756522 original size:3 final size:3
Alignment explanation
Indices: 1756511--1756564 Score: 65
Period size: 3 Copynumber: 18.0 Consensus size: 3
1756501 CAATAATACC
* * *
1756511 AAT ACT AAT AAT AGT AA- AGAT GAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT
1756556 AAT AAT AAT
1 AAT AAT AAT
1756565 GAAGTTAACA
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
2 1 0.02
3 42 0.98
ACGTcount: A:0.61, C:0.02, G:0.06, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1757721 original size:19 final size:18
Alignment explanation
Indices: 1757685--1757728 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
1757675 GTTACCAAAA
1757685 TATAAATTTTAGAATTTT
1 TATAAATTTTAGAATTTT
*
1757703 TATAAATATTTAG-GTTTT
1 TATAAAT-TTTAGAATTTT
*
1757721 TAAAAATT
1 TATAAATT
1757729 ATTTTAATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 1 0.04
18 17 0.74
19 5 0.22
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (18 bp):
TATAAATTTTAGAATTTT
Found at i:1772626 original size:727 final size:728
Alignment explanation
Indices: 1771198--1772664 Score: 1973
Period size: 727 Copynumber: 2.0 Consensus size: 728
1771188 CTTGTCTCAA
* *
1771198 AAACAAAGTGAATGGATGTTCATGATTTGTATTCTTAATAACTTGTAATGATGATTGTGATGCAC
1 AAACAAAGTGAATGGATGTTCATGATTTGTACTCTTAATAACTCGTAATGATGATTGTGATGCAC
*
1771263 ATTCAATGTGAACAACAAACTTACAAGGAGAACAACCATAAACAAATCCTCTTCGCCTTGGTACT
66 ATTCAATGTGAACAACAAACTTACAAGGAGAACAACCATAAAAAAATCCTCTTCGCCTTGGTACT
* * *
1771328 TAGCATACATTGCAAGAGAGTCGTTTGCTATTAAATTGTAGAACAAGAGGATGCTTGCGATGGTC
131 GAGCATACATTGCAAGAGAGCCGTTGGCTATTAAATTGTAGAACAAGAGGATGCTTGCGATGGTC
* *
1771393 ACATGATTGAGTTTGAAAGGAAGCTCAGCGCATTTCTCATGTAAATTAAATCCACAATCAGGAGA
196 ACATGATTCAGTTTGAAAGGAAGCTCAGCGCATTTCTCATGTAAATTAAAACCACAATCAGGAGA
* *
1771458 AAAGTGTGTACACATTGCTAATGGTTCCCAACATCCAAAGCACTTACTAACATCTTTGAGTTTTT
261 AAAGTGTGTACACATTGCTAATGGTTCCCAACACCCAAAGCACTTACT-ACATC--T-A---TTC
*
1771523 TATCACCATTTTCAGTGGAAATCAATGGATCATGAAGGGCAACATGCTCAAGCTCTTTCAAATTA
319 TATCA-CATGTTCA-T----ATC-A---ATCATGAAGGGCAACATGCTCAAGCTCTTTCAAATTA
* * * *
1771588 TTCTCAGCAATATTAAGTGTAAACAAAGCACATTTAATATGAAAGTCCAATTCACAACTAGAGCA
374 TTCTCAGCAATATTAAATGTAAACAAAGCACATTAAATATGAAAGTCAAAATCACAAC-AGAGCA
* ** * * *
1771653 GTGATAAACAGACTTGTCACCAAATTCATGGCAGAAAGTGCAAAAGTACGCTCCAGATAAATGAG
438 GTGATAAACAAACTCATCACCAAATTCATCGCAAAAAGTGCAAAAGTACGCTCCAGATAAATAAG
* * * *
1771718 GTGACTTTTGCATAAGAAGAAGAGGATGGTTGAGATGAAAAGGGTGATTAAGTTCCAAAGGTGCC
503 GTGACTTTTGCAGAAGAAGAAGAGGATGGATGAGATGAAAAGGATGATTAAGCTCCAAAGGTGCC
* *
1771783 TCGGCACATACCTTGTGAAGATAAAACCCACAGTGCTCCGCACAGTAAAAACATGGAGCAGACAC
568 TCAGCACATACCTTGTGAAGATAAAACCCACAGTGCTCCGCACAGCAAAAACATGGAGCAGACAC
* *
1771848 TTTATCCCCACACCTGGAGCAATCAGTTACACCGCTTTGATTGTCGATCAGCTGCTCTTGATTCA
633 CTTATCCCCACACCTGGAGCAATCAGTTACACCACTTTGATTGTCGATCAGCTGCTCTTGATTCA
1771913 ACATAAGAAACAGGGGATGTTGGTGCTCATT
698 ACATAAGAAACAGGGGATGTTGGTGCTCATT
* *
1771944 AAACAAGGTGAATGGATGTTCATGATTTGTACTCTTAATAACTCGTAATGGTGATTGTGATGCAC
1 AAACAAAGTGAATGGATGTTCATGATTTGTACTCTTAATAACTCGTAATGATGATTGTGATGCAC
1772009 ATTCAATGTGAACAACAAACTTACAAGGAGAACAACCATAAAAAAATCCACTTTCTGTACTTCGC
66 ATTCAATGTGAACAACAAACTTACAAGGAGAACAACCATAAAAAAAT---C---C--T-CTTCGC
*
1772074 CTTGTTACTCGA-CATATC-TTGCAAGAGAGCCGTTGGCTATTAAATTGTAGAACAAGAGGATGC
122 CTTGGTACT-GAGCATA-CATTGCAAGAGAGCCGTTGGCTATTAAATTGTAGAACAAGAGGATGC
1772137 TTGCGATGG-CACCCATGATTCAGTTTGAAAAGGAAGCTCAGCGCATTTCTCATGTAAATTAAAA
185 TTGCGATGGTCA--CATGATTCAGTTTG-AAAGGAAGCTCAGCGCATTTCTCATGTAAATTAAAA
* * * *** *
1772201 CCACAGTCAGGAGAAAAGTGTGTATA-ATTTGTTAATGGTTCCTGGCACCCAAAGCACTTA-T-T
247 CCACAATCAGGAGAAAAGTGTGTACACA-TTGCTAATGGTTCCCAACACCCAAAGCACTTACTAC
*
1772263 ATC-A-TCT-TCA-A-GTTC-T-TC-ATCTTGAAGGGCAACATGCTCAAGCTCTTTCAAATTATT
311 ATCTATTCTATCACATGTTCATATCAATCATGAAGGGCAACATGCTCAAGCTCTTTCAAATTATT
**
1772320 CTCAGCAATATTAAATGTAAACAAAGCACATTAAATATGAAAGTCAAAATGGC-A-AGAGCAGTG
376 CTCAGCAATATTAAATGTAAACAAAGCACATTAAATATGAAAGTCAAAATCACAACAGAGCAGTG
* *** * * * *
1772383 ATAAACAAACTCATTACCGCCTTTATCGCAAAAATTGCAAATGTAC-CGTCCAGATGAATAAGGT
441 ATAAACAAACTCATCACCAAATTCATCGCAAAAAGTGCAAAAGTACGC-TCCAGATAAATAAGGT
1772447 G-CATTTTGCAGAAGAAGAAGAGGAT-GATGAGGATGAAAAGGATGATTAAGCTCCAAAGGTGCC
505 GAC-TTTTGCAGAAGAAGAAGAGGATGGATGA-GATGAAAAGGATGATTAAGCTCCAAAGGTGCC
1772510 TCAGCACATACCTTGTGAAGATAAAACCCACAGTGCTCCGCACAGCAAAAACATGGAGCAGACAC
568 TCAGCACATACCTTGTGAAGATAAAACCCACAGTGCTCCGCACAGCAAAAACATGGAGCAGACAC
* * * *
1772575 CTTCTCCCCACACCTGGAGCAATGAGTTACACCACTTTGATTGTGGATCAGCTGGTCTTGATTCA
633 CTTATCCCCACACCTGGAGCAATCAGTTACACCACTTTGATTGTCGATCAGCTGCTCTTGATTCA
* *
1772640 AGATAAGAAGCAGGGGATGTTGGTG
698 ACATAAGAAACAGGGGATGTTGGTG
1772665 GCCATAATTG
Statistics
Matches: 647, Mismatches: 56, Indels: 55
0.85 0.07 0.07
Matches are distributed among these distances:
726 6 0.01
727 254 0.39
729 1 0.00
730 85 0.13
735 2 0.00
740 1 0.00
742 3 0.00
743 1 0.00
745 3 0.00
746 109 0.17
749 1 0.00
750 1 0.00
752 1 0.00
754 6 0.01
755 70 0.11
756 17 0.03
757 86 0.13
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.26
Consensus pattern (728 bp):
AAACAAAGTGAATGGATGTTCATGATTTGTACTCTTAATAACTCGTAATGATGATTGTGATGCAC
ATTCAATGTGAACAACAAACTTACAAGGAGAACAACCATAAAAAAATCCTCTTCGCCTTGGTACT
GAGCATACATTGCAAGAGAGCCGTTGGCTATTAAATTGTAGAACAAGAGGATGCTTGCGATGGTC
ACATGATTCAGTTTGAAAGGAAGCTCAGCGCATTTCTCATGTAAATTAAAACCACAATCAGGAGA
AAAGTGTGTACACATTGCTAATGGTTCCCAACACCCAAAGCACTTACTACATCTATTCTATCACA
TGTTCATATCAATCATGAAGGGCAACATGCTCAAGCTCTTTCAAATTATTCTCAGCAATATTAAA
TGTAAACAAAGCACATTAAATATGAAAGTCAAAATCACAACAGAGCAGTGATAAACAAACTCATC
ACCAAATTCATCGCAAAAAGTGCAAAAGTACGCTCCAGATAAATAAGGTGACTTTTGCAGAAGAA
GAAGAGGATGGATGAGATGAAAAGGATGATTAAGCTCCAAAGGTGCCTCAGCACATACCTTGTGA
AGATAAAACCCACAGTGCTCCGCACAGCAAAAACATGGAGCAGACACCTTATCCCCACACCTGGA
GCAATCAGTTACACCACTTTGATTGTCGATCAGCTGCTCTTGATTCAACATAAGAAACAGGGGAT
GTTGGTGCTCATT
Found at i:1801246 original size:15 final size:14
Alignment explanation
Indices: 1801222--1801255 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1801212 AAACATAAAG
1801222 AAAAAACCAAAAATT
1 AAAAAACC-AAAATT
*
1801237 AAAAAGCCAAAATT
1 AAAAAACCAAAATT
1801251 AAAAA
1 AAAAA
1801256 TAAACCTCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 11 0.61
15 7 0.39
ACGTcount: A:0.74, C:0.12, G:0.03, T:0.12
Consensus pattern (14 bp):
AAAAAACCAAAATT
Found at i:1801994 original size:21 final size:20
Alignment explanation
Indices: 1801944--1801997 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 20
1801934 AAATCATGGT
1801944 TTAATAATATTAGTTTTTAA
1 TTAATAATATTAGTTTTTAA
*
1801964 TATATTTAAT-TTCAGTTTTTTAA
1 T-TA-ATAATATT-AG-TTTTTAA
1801987 TTAATAATATT
1 TTAATAATATT
1801998 TTATAAATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
20 1 0.04
21 8 0.30
22 10 0.37
23 8 0.30
ACGTcount: A:0.37, C:0.02, G:0.04, T:0.57
Consensus pattern (20 bp):
TTAATAATATTAGTTTTTAA
Found at i:1802083 original size:24 final size:24
Alignment explanation
Indices: 1802027--1802092 Score: 70
Period size: 22 Copynumber: 3.0 Consensus size: 24
1802017 AACTAATATA
* *
1802027 AAATTT-TAAAATTATA-TT-ATT
1 AAATTTATAAAAATATATTTAATC
*
1802048 AAATTTAAAAAAATATATTTAATC
1 AAATTTATAAAAATATATTTAATC
1802072 AAATTTATAAAAA-A-ATTTAAT
1 AAATTTATAAAAATATATTTAAT
1802093 ATAGTGATTA
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
21 6 0.16
22 15 0.39
23 3 0.08
24 14 0.37
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (24 bp):
AAATTTATAAAAATATATTTAATC
Found at i:1803084 original size:17 final size:17
Alignment explanation
Indices: 1803062--1803098 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
1803052 TACCCGACCC
1803062 TTAAACAAGTCTAAAAT
1 TTAAACAAGTCTAAAAT
1803079 TTAAACAAGTCTAAAAT
1 TTAAACAAGTCTAAAAT
1803096 TTA
1 TTA
1803099 CCAAAAATTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (17 bp):
TTAAACAAGTCTAAAAT
Found at i:1805722 original size:20 final size:19
Alignment explanation
Indices: 1805682--1805728 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
1805672 TTAATTTTTT
*
1805682 AAAAAATATATAATACATA
1 AAAAAATATAAAATACATA
1805701 AAAAAATACTAAAAGTAC-TA
1 AAAAAATA-TAAAA-TACATA
1805721 AAATAAAT
1 AAA-AAAT
1805729 GTTTCACAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
19 8 0.33
20 9 0.38
21 7 0.29
ACGTcount: A:0.68, C:0.06, G:0.02, T:0.23
Consensus pattern (19 bp):
AAAAAATATAAAATACATA
Found at i:1806079 original size:29 final size:29
Alignment explanation
Indices: 1806047--1806105 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
1806037 TGCCCAAACT
1806047 CATTTTTTGAGCATATTATTTTACCCAAA
1 CATTTTTTGAGCATATTATTTTACCCAAA
1806076 CATTTTTTGAGCATATTATTTTACCCAAA
1 CATTTTTTGAGCATATTATTTTACCCAAA
1806105 C
1 C
1806106 CCTCTCACTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.31, C:0.19, G:0.07, T:0.44
Consensus pattern (29 bp):
CATTTTTTGAGCATATTATTTTACCCAAA
Found at i:1807258 original size:216 final size:218
Alignment explanation
Indices: 1806842--1807280 Score: 470
Period size: 216 Copynumber: 2.0 Consensus size: 218
1806832 TTTAATATTC
* * * * *
1806842 TTTTTGAAGTTTTTGCTTATGCTGATGTAATTTAAATGTGATTTAATAAATGAATTTATTTTTTT
1 TTTTTGAAGTTTTTGCTAATGCTAATGTAATTTAAATGCGATTT-ATAAA-GAAATTAATTTTTT
** * ** * * *
1806907 TGTCATTTTCTTATACCGTGTTTAGAATTATTTATAATTTTTTCACAATTCTTAAATAGGAGAAT
64 TGTCATTTTCTTATACAATATTTAGAATTATCCATAATTTCTCCACAATCCTTAAATAGGAGAAT
* * *** * *
1806972 AAACGCGTTTTAGCATATTCAAATCTACGTCCTCTTACACTGGTAATAACGTCGGGGCCAAGAAA
129 AAACGCGTTTCAGCATATTCAAATCTACGTCATCTTACACTAACAATAACATCGAGGCCAAGAAA
1807037 ATTAAGATTTAGTCAACACTTATCA
194 ATTAAGATTTAGTCAACACTTATCA
*
1807062 TTTTTTAAGTTTTTGCTAATGCTAATGTAATTTAAATGCGATTT-TAAA-AAATTAATTTTTTTG
1 TTTTTGAAGTTTTTGCTAATGCTAATGTAATTTAAATGCGATTTATAAAGAAATTAATTTTTTTG
* * * * *
1807125 TCATTTTTTTATACAATATTTAGAATTATCCGTAATTTCTCCATAATCCTTAAATTGGAGGATAA
66 TCATTTTCTTATACAATATTTAGAATTATCCATAATTTCTCCACAATCCTTAAATAGGAGAATAA
* * * * * * * * * **
1807190 ATGTGTTTCAGCGTGTTTAAATTTATGTCATCTTACACTAACAATAATATCGATGCC-AGTCGAA
131 ACGCGTTTCAGCATATTCAAATCTACGTCATCTTACACTAACAATAACATCGAGGCCAAG-AAAA
* * *
1807254 TTAAGATTTAGTTAATAGTTATCA
195 TTAAGATTTAGTCAACACTTATCA
1807278 TTT
1 TTT
1807281 ATTCTGATGT
Statistics
Matches: 178, Mismatches: 40, Indels: 6
0.79 0.18 0.03
Matches are distributed among these distances:
215 2 0.01
216 132 0.74
218 4 0.02
220 40 0.22
ACGTcount: A:0.32, C:0.12, G:0.13, T:0.44
Consensus pattern (218 bp):
TTTTTGAAGTTTTTGCTAATGCTAATGTAATTTAAATGCGATTTATAAAGAAATTAATTTTTTTG
TCATTTTCTTATACAATATTTAGAATTATCCATAATTTCTCCACAATCCTTAAATAGGAGAATAA
ACGCGTTTCAGCATATTCAAATCTACGTCATCTTACACTAACAATAACATCGAGGCCAAGAAAAT
TAAGATTTAGTCAACACTTATCA
Found at i:1807531 original size:25 final size:25
Alignment explanation
Indices: 1807503--1807562 Score: 70
Period size: 24 Copynumber: 2.4 Consensus size: 25
1807493 TCATTAATGT
* *
1807503 TTATATTTTTGTTTTAAATTAGTCA
1 TTATATTTTTATTTAAAATTAGTCA
*
1807528 TTAT-TTTTTATTTAAAATTGGTCA
1 TTATATTTTTATTTAAAATTAGTCA
1807552 TT-TACTTTTTA
1 TTATA-TTTTTA
1807563 AAAAGAGTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
23 1 0.03
24 19 0.63
25 10 0.33
ACGTcount: A:0.27, C:0.05, G:0.07, T:0.62
Consensus pattern (25 bp):
TTATATTTTTATTTAAAATTAGTCA
Found at i:1812709 original size:233 final size:238
Alignment explanation
Indices: 1812354--1812790 Score: 614
Period size: 233 Copynumber: 1.8 Consensus size: 238
1812344 GGCGTTTTGT
* * *
1812354 TTAAAGCGCCGCAAAATATCTTTACTAAAACGCGTAGTTTTAATTTTGATGTATACTAATATTAG
1 TTAAAACGCCGCAAAATATCTTAACTAAAACGCATAGTTTTAATTTT-ATGTATA-TAATATTAG
* * * *
1812419 TGACGCTTACAAGAAAATGCCGTTAAAGAATATCTTTAGCGGCGATTTAGACGAAGCGCCGCAAC
64 TGACGCTTACAAGAAAACGCCGTTAAAGAATAGCATTAGCGGCGATTTAGACGAAGCGCCGCAAA
* * * * * * * *
1812484 TTATCTTAAGAAAATGCAGTGTTTGGTCTTAAGCCATGTTACATTTAGTGGCGCTTATGGGAAAA
129 GTACCTTAACAAAACGCAGTGTTTCGTCTGAAGCCATGTTACATTTAGTGGCGCTTATAGCAAAA
1812549 CGCCGCAAAAAATCTCGATGTATACTTCAATTAGTGGCGCTGACG
194 CGCCGCAAAAAATCTCGATGTATACTTCAATTAGTGGCGCTGACG
*
1812594 TTAAAACGCCGCAAAATATCTTAACTAAAATGCATAGTTTTAA-TTT-TG-AT-T-ATATTAGTG
1 TTAAAACGCCGCAAAATATCTTAACTAAAACGCATAGTTTTAATTTTATGTATATAATATTAGTG
* * * * *
1812654 GCGCTTACTAGAAAACGCCGTTATAGAATAGCATTAGCGGCGCTTTAGCCGAAGCGCCGCAAAGT
66 ACGCTTACAAGAAAACGCCGTTAAAGAATAGCATTAGCGGCGATTTAGACGAAGCGCCGCAAAGT
**
1812719 ACCTTAACAAAACGCAGTGTTTCGTCTGAAGTTATGTTACATTTAGTGGCGCTTATAGCAAAACG
131 ACCTTAACAAAACGCAGTGTTTCGTCTGAAGCCATGTTACATTTAGTGGCGCTTATAGCAAAACG
1812784 CCGCAAA
196 CCGCAAA
1812791 CTATCTGAAC
Statistics
Matches: 174, Mismatches: 23, Indels: 7
0.85 0.11 0.03
Matches are distributed among these distances:
233 127 0.73
234 1 0.01
236 2 0.01
237 2 0.01
239 3 0.02
240 39 0.22
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.29
Consensus pattern (238 bp):
TTAAAACGCCGCAAAATATCTTAACTAAAACGCATAGTTTTAATTTTATGTATATAATATTAGTG
ACGCTTACAAGAAAACGCCGTTAAAGAATAGCATTAGCGGCGATTTAGACGAAGCGCCGCAAAGT
ACCTTAACAAAACGCAGTGTTTCGTCTGAAGCCATGTTACATTTAGTGGCGCTTATAGCAAAACG
CCGCAAAAAATCTCGATGTATACTTCAATTAGTGGCGCTGACG
Found at i:1813051 original size:189 final size:189
Alignment explanation
Indices: 1812647--1813039 Score: 612
Period size: 189 Copynumber: 2.1 Consensus size: 189
1812637 TTTTGATTAT
* *
1812647 ATTAGTGGCGCTTACTAGAAAACGCCGTTATAGAATAGCATTAGCGGCGCTTTAGCCGAAGCGCC
1 ATTAGTGGCGCTTACTAGAAAACGCCGTTAAAGAATAGCATTAGCGGCGCTTTAGCCAAAGCGCC
*
1812712 GCAAAGTACCTTAACAAAACGCAGTGTTTCGTCTGAAGTTATGTTACATTTAGTGGCGCTTATAG
66 GCAAAGTACCTTAACAAAACGCAGTGTTTCGTCTGAAGCTATGTTACATTTAGTGGCGCTTATAG
*
1812777 CAAAACGCCGCAAACTATCTGAACCAAAACGCACCATTTTGGTCTCGATGTATACTTCA
131 CAAAACGCCGCAAAATATCTGAACCAAAACGCACCATTTTGGTCTCGATGTATACTTCA
* * **
1812836 ATTAGTGGCGCTTACTAGAAAACGCCGTTAAAGAATA-TATTTAGCGGCGCTTTGGGTAAAGCGC
1 ATTAGTGGCGCTTACTAGAAAACGCCGTTAAAGAATAGCA-TTAGCGGCGCTTTAGCCAAAGCGC
* * *
1812900 CGCAACGTATCTTAACAAAACGCAGTGGTTT-GTCTTAAGCTATGTTACATTTAGTGGCGCTTAT
65 CGCAAAGTACCTTAACAAAACGCAGT-GTTTCGTCTGAAGCTATGTTACATTTAGTGGCGCTTAT
* * *
1812964 ATG-AAAACGCCGCAAAATATCTGAACCAAAACGCACCGTTTTGTTCTCGATGTATACTTTA
129 A-GCAAAACGCCGCAAAATATCTGAACCAAAACGCACCATTTTGGTCTCGATGTATACTTCA
1813025 ATTAGTGGCGCTTAC
1 ATTAGTGGCGCTTAC
1813040 GTTCAAACGC
Statistics
Matches: 187, Mismatches: 14, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
188 1 0.01
189 181 0.97
190 5 0.03
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28
Consensus pattern (189 bp):
ATTAGTGGCGCTTACTAGAAAACGCCGTTAAAGAATAGCATTAGCGGCGCTTTAGCCAAAGCGCC
GCAAAGTACCTTAACAAAACGCAGTGTTTCGTCTGAAGCTATGTTACATTTAGTGGCGCTTATAG
CAAAACGCCGCAAAATATCTGAACCAAAACGCACCATTTTGGTCTCGATGTATACTTCA
Found at i:1813656 original size:21 final size:21
Alignment explanation
Indices: 1813638--1813692 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 21
1813628 TAAGGTTTGT
1813638 AGTTTAGGGTTTAAAGTTTAA
1 AGTTTAGGGTTTAAAGTTTAA
* *
1813659 AGGTTACGGGTTTAAAGTATAA
1 AGTTTA-GGGTTTAAAGTTTAA
*
1813681 AGGTTACGGGTT
1 AGTTTA-GGGTT
1813693 AAACTTAGGG
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
21 5 0.16
22 26 0.84
ACGTcount: A:0.31, C:0.04, G:0.29, T:0.36
Consensus pattern (21 bp):
AGTTTAGGGTTTAAAGTTTAA
Found at i:1813669 original size:22 final size:22
Alignment explanation
Indices: 1813644--1813692 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
1813634 TTGTAGTTTA
*
1813644 GGGTTTAAAGTTTAAAGGTTAC
1 GGGTTTAAAGTATAAAGGTTAC
1813666 GGGTTTAAAGTATAAAGGTTAC
1 GGGTTTAAAGTATAAAGGTTAC
1813688 GGGTT
1 GGGTT
1813693 AAACTTAGGG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.31, C:0.04, G:0.31, T:0.35
Consensus pattern (22 bp):
GGGTTTAAAGTATAAAGGTTAC
Found at i:1814264 original size:24 final size:24
Alignment explanation
Indices: 1814221--1814274 Score: 83
Period size: 24 Copynumber: 2.2 Consensus size: 24
1814211 TTCATTCCCT
*
1814221 AATTTCCCATTTCATATTCCCCCC
1 AATTCCCCATTTCATATTCCCCCC
1814245 AATTCCCCGATTTCAT-TTCCCCCC
1 AATTCCCC-ATTTCATATTCCCCCC
1814269 AATTCC
1 AATTCC
1814275 TATTCCCCCA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
24 21 0.75
25 7 0.25
ACGTcount: A:0.20, C:0.43, G:0.02, T:0.35
Consensus pattern (24 bp):
AATTCCCCATTTCATATTCCCCCC
Found at i:1815645 original size:42 final size:42
Alignment explanation
Indices: 1815598--1815862 Score: 161
Period size: 42 Copynumber: 6.2 Consensus size: 42
1815588 AATGATAACA
1815598 TTTCTAAATAATTATAAATATTGTTTTAATATCTATATAAGT
1 TTTCTAAATAATTATAAATATTGTTTTAATATCTATATAAGT
* * * * * *
1815640 TTTCT-AA-ACTTATAAGGT-TT-CTATATTA-CTAT-TAA-A
1 TTTCTAAATAATTATAA-ATATTGTTTTAATATCTATATAAGT
* * * *
1815676 TTTATAAAAAATTCTAAATATTGTTTTAATATCTATATTAGT
1 TTTCTAAATAATTATAAATATTGTTTTAATATCTATATAAGT
* * * * * *** * * *
1815718 ATTATAAATATTGTTTTAATATAACCTATAAAAT-T-TAAAAGT
1 TTTCTAAATAAT-TATAAATAT-TGTTTTAATATCTATATAAGT
1815760 TTTCTAAATAATTATAAATATTGTTTTAATATAACCTATAAAATTTAAAAGT
1 TTTCTAAATAATTATAAATATTGTTTTAATAT---CTAT---A--T--AAGT
1815812 TTTCTAAATAATTATAAATATTGTTTTAATATCTATATAAGT
1 TTTCTAAATAATTATAAATATTGTTTTAATATCTATATAAGT
1815854 TTTCTAAAT
1 TTTCTAAAT
1815863 TTATAAGGTT
Statistics
Matches: 163, Mismatches: 38, Indels: 44
0.67 0.16 0.18
Matches are distributed among these distances:
36 4 0.02
37 6 0.04
38 12 0.07
39 10 0.06
40 19 0.12
41 12 0.07
42 41 0.25
43 8 0.05
44 8 0.05
45 1 0.01
46 1 0.01
48 1 0.01
49 4 0.02
52 36 0.22
ACGTcount: A:0.42, C:0.06, G:0.05, T:0.48
Consensus pattern (42 bp):
TTTCTAAATAATTATAAATATTGTTTTAATATCTATATAAGT
Found at i:1815748 original size:24 final size:24
Alignment explanation
Indices: 1815720--1815801 Score: 71
Period size: 24 Copynumber: 3.2 Consensus size: 24
1815710 ATATTAGTAT
1815720 TATAAATATTGTTTTAATATAACC
1 TATAAATATTGTTTTAATATAACC
*
1815744 TATAAA-ATTTAAAAGTTTTCTAA-ATAA-T
1 TATAAATA-TT----G-TTT-TAATATAACC
1815772 TATAAATATTGTTTTAATATAACC
1 TATAAATATTGTTTTAATATAACC
1815796 TATAAA
1 TATAAA
1815802 ATTTAAAAGT
Statistics
Matches: 46, Mismatches: 2, Indels: 20
0.68 0.03 0.29
Matches are distributed among these distances:
22 3 0.07
23 8 0.17
24 15 0.33
28 9 0.20
29 8 0.17
30 3 0.07
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.44
Consensus pattern (24 bp):
TATAAATATTGTTTTAATATAACC
Found at i:1815774 original size:52 final size:52
Alignment explanation
Indices: 1815718--1815843 Score: 252
Period size: 52 Copynumber: 2.4 Consensus size: 52
1815708 CTATATTAGT
1815718 ATTATAAATATTGTTTTAATATAACCTATAAAATTTAAAAGTTTTCTAAATA
1 ATTATAAATATTGTTTTAATATAACCTATAAAATTTAAAAGTTTTCTAAATA
1815770 ATTATAAATATTGTTTTAATATAACCTATAAAATTTAAAAGTTTTCTAAATA
1 ATTATAAATATTGTTTTAATATAACCTATAAAATTTAAAAGTTTTCTAAATA
1815822 ATTATAAATATTGTTTTAATAT
1 ATTATAAATATTGTTTTAATAT
1815844 CTATATAAGT
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 74 1.00
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.46
Consensus pattern (52 bp):
ATTATAAATATTGTTTTAATATAACCTATAAAATTTAAAAGTTTTCTAAATA
Found at i:1815829 original size:21 final size:21
Alignment explanation
Indices: 1815801--1815862 Score: 51
Period size: 21 Copynumber: 3.0 Consensus size: 21
1815791 TAACCTATAA
1815801 AATT-TAAAAGTTTTCTAAAT
1 AATTATAAAAGTTTTCTAAAT
*
1815821 AATTATAAATA-TTGTT-TTAAT
1 AATTATAAA-AGTT-TTCTAAAT
*
1815842 -ATCTATATAAGTTTTCTAAAT
1 AAT-TATAAAAGTTTTCTAAAT
1815863 TTATAAGGTT
Statistics
Matches: 33, Mismatches: 3, Indels: 11
0.70 0.06 0.23
Matches are distributed among these distances:
20 9 0.27
21 21 0.64
22 3 0.09
ACGTcount: A:0.42, C:0.05, G:0.05, T:0.48
Consensus pattern (21 bp):
AATTATAAAAGTTTTCTAAAT
Found at i:1815901 original size:15 final size:15
Alignment explanation
Indices: 1815877--1815909 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
1815867 AAGGTTTCTA
*
1815877 TATTAGTATTAAATT
1 TATTACTATTAAATT
1815892 TATTACTATTAAATT
1 TATTACTATTAAATT
1815907 TAT
1 TAT
1815910 AAATAATTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.55
Consensus pattern (15 bp):
TATTACTATTAAATT
Found at i:1816056 original size:17 final size:17
Alignment explanation
Indices: 1816001--1816057 Score: 62
Period size: 17 Copynumber: 3.3 Consensus size: 17
1815991 TCTAAATAAT
1816001 TATAAATATTGTTTTAA
1 TATAAATATTGTTTTAA
* * *
1816018 TATTAAAT-TTATTAGTAT
1 TA-TAAATATTGTT-TTAA
1816036 TATAAATATTGTTTTAA
1 TATAAATATTGTTTTAA
1816053 TATAA
1 TATAA
1816058 CCTATAAAAT
Statistics
Matches: 31, Mismatches: 6, Indels: 6
0.72 0.14 0.14
Matches are distributed among these distances:
17 18 0.58
18 13 0.42
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (17 bp):
TATAAATATTGTTTTAA
Found at i:1816124 original size:87 final size:84
Alignment explanation
Indices: 1815770--1816107 Score: 412
Period size: 87 Copynumber: 3.9 Consensus size: 84
1815760 TTTCTAAATA
1815770 ATTATAAATATTGTTTTAATATAACCTATAAAATTTAAAAGTTTTCTAAATAATTATAAATATTG
1 ATTATAAATATTGTTTTAATATAACCTATAAAATTTAAAAGTTTTCTAAATAATTATAAATATTG
*
1815835 TTTTAATATCTATATAAGT
66 TTTTAATATCTATATTAGT
* * * * * * ** *
1815854 TTTCTAAATTTATAAGGTTTCT-ATATTA-GTATTAAATTTATTACTATTAAATTTATAAATAAT
1 ATTATAAA--TAT--TGTTT-TAATATAACCTATAAAATTTA--A--A--AGTTTTCTAAATAAT
*
1815917 TCTAAATATTGTTTTAATATCTATATTAGT
55 TATAAATATTGTTTTAATATCTATATTAGT
1815947 ATTATAAATATTGTTTTAATATAACCTATAAAATTTAAAAGTTTTCTAAATAATTATAAATATTG
1 ATTATAAATATTGTTTTAATATAACCTATAAAATTTAAAAGTTTTCTAAATAATTATAAATATTG
1816012 TTTTAATAT-TAAATTTATTAGT
66 TTTTAATATCT--A--TATTAGT
1816034 ATTATAAATATTGTTTTAATATAACCTATAAAATTTAAAAGTTTTCTAAATAATTATAAATATTG
1 ATTATAAATATTGTTTTAATATAACCTATAAAATTTAAAAGTTTTCTAAATAATTATAAATATTG
*
1816099 TTTAAATAT
66 TTTTAATAT
1816108 TAAATTTATT
Statistics
Matches: 215, Mismatches: 22, Indels: 31
0.80 0.08 0.12
Matches are distributed among these distances:
83 1 0.00
84 37 0.17
85 1 0.00
86 4 0.02
87 90 0.42
88 11 0.05
89 11 0.05
90 10 0.05
91 4 0.02
93 46 0.21
ACGTcount: A:0.43, C:0.04, G:0.05, T:0.48
Consensus pattern (84 bp):
ATTATAAATATTGTTTTAATATAACCTATAAAATTTAAAAGTTTTCTAAATAATTATAAATATTG
TTTTAATATCTATATTAGT
Found at i:1816346 original size:9 final size:9
Alignment explanation
Indices: 1816319--1816589 Score: 175
Period size: 9 Copynumber: 32.1 Consensus size: 9
1816309 AATAATACAC
1816319 ACTTACATA
1 ACTTACATA
* *
1816328 AATTAAATA
1 ACTTACATA
*
1816337 AGTTACATA
1 ACTTACATA
*
1816346 A--TACACA
1 ACTTACATA
*
1816353 AATTACATA
1 ACTTACATA
1816362 ACTTACATA
1 ACTTACATA
*
1816371 A--TATATA
1 ACTTACATA
*
1816378 ATTTACATA
1 ACTTACATA
*
1816387 A--TACACA
1 ACTTACATA
*
1816394 ACTGACATA
1 ACTTACATA
1816403 ACTTACATA
1 ACTTACATA
1816412 A--TACATA
1 ACTTACATA
** *
1816419 TTTTACATC
1 ACTTACATA
1816428 ACTTACATA
1 ACTTACATA
*
1816437 A--GACATA
1 ACTTACATA
1816444 ACTTACATA
1 ACTTACATA
* *
1816453 AGTTTCATA
1 ACTTACATA
*
1816462 A--TACACA
1 ACTTACATA
*
1816469 ACTAACATA
1 ACTTACATA
1816478 ACTTACATA
1 ACTTACATA
*
1816487 A--TACACA
1 ACTTACATA
1816494 ACTTACATA
1 ACTTACATA
*
1816503 AC-CATCATA
1 ACTTA-CATA
*
1816512 A--TACACA
1 ACTTACATA
1816519 ACTTACATA
1 ACTTACATA
* *
1816528 AGTTTCATA
1 ACTTACATA
*
1816537 A--TACACA
1 ACTTACATA
1816544 ACTTACATA
1 ACTTACATA
*
1816553 GCTTACATA
1 ACTTACATA
*
1816562 ACTTACACA
1 ACTTACATA
1816571 ACTTACATA
1 ACTTACATA
1816580 ACTTACATA
1 ACTTACATA
1816589 A
1 A
1816590 TAAACAAGTT
Statistics
Matches: 201, Mismatches: 42, Indels: 38
0.72 0.15 0.14
Matches are distributed among these distances:
7 50 0.25
8 2 0.01
9 149 0.74
ACGTcount: A:0.47, C:0.20, G:0.02, T:0.30
Consensus pattern (9 bp):
ACTTACATA
Found at i:1816383 original size:25 final size:25
Alignment explanation
Indices: 1816322--1816412 Score: 87
Period size: 25 Copynumber: 3.6 Consensus size: 25
1816312 AATACACACT
* *
1816322 TACATAAATTAAATAAGTTACATAA
1 TACATAAATTACATAACTTACATAA
*
1816347 TACACAAATTACATAACTTACATAA
1 TACATAAATTACATAACTTACATAA
* * *
1816372 TATATAATTTACATAA--TACACAA
1 TACATAAATTACATAACTTACATAA
*
1816395 CTGACATAACTTACATAA
1 -T-ACATAAATTACATAA
1816413 TACATATTTT
Statistics
Matches: 55, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
23 6 0.11
24 1 0.02
25 48 0.87
ACGTcount: A:0.52, C:0.15, G:0.02, T:0.31
Consensus pattern (25 bp):
TACATAAATTACATAACTTACATAA
Found at i:1816389 original size:41 final size:41
Alignment explanation
Indices: 1816319--1816453 Score: 148
Period size: 41 Copynumber: 3.2 Consensus size: 41
1816309 AATAATACAC
* *
1816319 ACTTACATAAATTAAATAAGTTACATAATACACAAATTACATA
1 ACTTACAT-AA-TAAATAATTTACATAATACACAAATGACATA
* *
1816362 ACTTACATAATATATAATTTACATAATACACAACTGACATA
1 ACTTACATAATAAATAATTTACATAATACACAAATGACATA
* * * *
1816403 ACTTACATAATACATATTTTACATCACTTACA-TAA-GACATA
1 ACTTACATAATAAATAATTTACAT-A-ATACACAAATGACATA
1816444 ACTTACATAA
1 ACTTACATAA
1816454 GTTTCATAAT
Statistics
Matches: 81, Mismatches: 9, Indels: 6
0.84 0.09 0.06
Matches are distributed among these distances:
41 65 0.80
42 4 0.05
43 12 0.15
ACGTcount: A:0.49, C:0.17, G:0.02, T:0.32
Consensus pattern (41 bp):
ACTTACATAATAAATAATTTACATAATACACAAATGACATA
Found at i:1816413 original size:25 final size:25
Alignment explanation
Indices: 1816375--1816596 Score: 266
Period size: 25 Copynumber: 8.8 Consensus size: 25
1816365 TACATAATAT
* *
1816375 ATAATTTACATAATACACAACTGAC
1 ATAACTTACATAATACACAACTTAC
* **
1816400 ATAACTTACATAATACATATTTTAC
1 ATAACTTACATAATACACAACTTAC
* * *
1816425 ATCACTTACATAAGACATAACTTAC
1 ATAACTTACATAATACACAACTTAC
* * *
1816450 ATAAGTTTCATAATACACAACTAAC
1 ATAACTTACATAATACACAACTTAC
1816475 ATAACTTACATAATACACAACTTAC
1 ATAACTTACATAATACACAACTTAC
*
1816500 ATAAC-CATCATAATACACAACTTAC
1 ATAACTTA-CATAATACACAACTTAC
* *
1816525 ATAAGTTTCATAATACACAACTTAC
1 ATAACTTACATAATACACAACTTAC
*
1816550 ATAGCTTACATAACTTACACAACTTAC
1 ATAACTTACATAA--TACACAACTTAC
*
1816577 ATAACTTACATAATAAACAA
1 ATAACTTACATAATACACAA
1816597 GTTATTCCTA
Statistics
Matches: 166, Mismatches: 27, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
24 1 0.01
25 141 0.85
27 24 0.14
ACGTcount: A:0.47, C:0.22, G:0.02, T:0.29
Consensus pattern (25 bp):
ATAACTTACATAATACACAACTTAC
Found at i:1816564 original size:18 final size:18
Alignment explanation
Indices: 1816319--1816589 Score: 175
Period size: 16 Copynumber: 16.1 Consensus size: 18
1816309 AATAATACAC
* *
1816319 ACTTACATAAATTAAATA
1 ACTTACATAACTTACATA
* *
1816337 AGTTACATAA--TACACA
1 ACTTACATAACTTACATA
*
1816353 AATTACATAACTTACATA
1 ACTTACATAACTTACATA
* *
1816371 A--TATATAATTTACATA
1 ACTTACATAACTTACATA
* *
1816387 A--TACACAACTGACATA
1 ACTTACATAACTTACATA
1816403 ACTTACATAA--TACATA
1 ACTTACATAACTTACATA
** *
1816419 TTTTACATCACTTACATA
1 ACTTACATAACTTACATA
*
1816437 A--GACATAACTTACATA
1 ACTTACATAACTTACATA
* * *
1816453 AGTTTCATAA--TACACA
1 ACTTACATAACTTACATA
*
1816469 ACTAACATAACTTACATA
1 ACTTACATAACTTACATA
*
1816487 A--TACACAACTTACATA
1 ACTTACATAACTTACATA
* *
1816503 AC-CATCATAA--TACACA
1 ACTTA-CATAACTTACATA
* *
1816519 ACTTACATAAGTTTCATA
1 ACTTACATAACTTACATA
*
1816537 A--TACACAACTTACATA
1 ACTTACATAACTTACATA
* *
1816553 GCTTACATAACTTACACA
1 ACTTACATAACTTACATA
1816571 ACTTACATAACTTACATA
1 ACTTACATAACTTACATA
1816589 A
1 A
1816590 TAAACAAGTT
Statistics
Matches: 194, Mismatches: 42, Indels: 34
0.72 0.16 0.13
Matches are distributed among these distances:
16 115 0.59
17 2 0.01
18 77 0.40
ACGTcount: A:0.47, C:0.20, G:0.02, T:0.30
Consensus pattern (18 bp):
ACTTACATAACTTACATA
Found at i:1822070 original size:21 final size:21
Alignment explanation
Indices: 1822045--1822113 Score: 84
Period size: 21 Copynumber: 3.3 Consensus size: 21
1822035 CAGCAACTTA
* * *
1822045 AAGCAGATGCGGCAGCGAGGG
1 AAGCAGAGGCTGCAGCGAGAG
* * *
1822066 AAGCAGCGGCTACAGTGAGAG
1 AAGCAGAGGCTGCAGCGAGAG
1822087 AAGCAGAGGCTGCAGCGAGAG
1 AAGCAGAGGCTGCAGCGAGAG
1822108 AAGCAG
1 AAGCAG
1822114 CGAGAGAAGC
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.33, C:0.19, G:0.42, T:0.06
Consensus pattern (21 bp):
AAGCAGAGGCTGCAGCGAGAG
Found at i:1822115 original size:12 final size:12
Alignment explanation
Indices: 1822098--1822124 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
1822088 AGCAGAGGCT
1822098 GCAGCGAGAGAA
1 GCAGCGAGAGAA
1822110 GCAGCGAGAGAA
1 GCAGCGAGAGAA
1822122 GCA
1 GCA
1822125 ACAATAGAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.41, C:0.19, G:0.41, T:0.00
Consensus pattern (12 bp):
GCAGCGAGAGAA
Found at i:1822742 original size:126 final size:127
Alignment explanation
Indices: 1822557--1822825 Score: 334
Period size: 126 Copynumber: 2.1 Consensus size: 127
1822547 ATTTGTGAAA
* * * *
1822557 TAAGCGCCGCTAAAGAACACTACTTTTAGCGGCGTTTTTGAACAAGCGCCGCTATAGAACATTA-
1 TAAGCGCCACTAAAGAACACTACTTTTAGCGGCGTTTTT-AACAACCGCCGCTAAAGAACATGAT
**
1822621 CTTTTAGAGGCGTTTATTTCTAAGCGCCGCTAAAGATTATAATCTTTAGCGGCG-TTTATT-TG
65 C-TTTAGAGGCGTTTATTTCTAAGCGCCGCTAAAGAACATAATCTTTAGCGGCGTTTTATTATG
*
1822683 TAAGCGCCACTAAAGAACA-TGA-TCTTTAGCGGCGCATTTTT-ATAACCGCCGCTAAAGAACAT
1 TAAGCGCCACTAAAGAACACT-ACT-TTTAGCGGCG--TTTTTAACAACCGCCGCTAAAGAACAT
* * * *
1822745 GATCTTTAGCGGCGTTTTTTTCTAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTAT
62 GATCTTTAGAGGCGTTTATTTCTAAGCGCCGCTAAAGAACATAATCTTTAGCGGCGTTTTATTAT
1822810 G
127 G
*
1822811 TAAGCGCCACAAAAG
1 TAAGCGCCACTAAAG
1822826 TTAGCGACGT
Statistics
Matches: 124, Mismatches: 12, Indels: 12
0.84 0.08 0.08
Matches are distributed among these distances:
125 2 0.02
126 95 0.77
127 6 0.05
128 21 0.17
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.31
Consensus pattern (127 bp):
TAAGCGCCACTAAAGAACACTACTTTTAGCGGCGTTTTTAACAACCGCCGCTAAAGAACATGATC
TTTAGAGGCGTTTATTTCTAAGCGCCGCTAAAGAACATAATCTTTAGCGGCGTTTTATTATG
Found at i:1822807 original size:42 final size:42
Alignment explanation
Indices: 1822557--1822807 Score: 294
Period size: 42 Copynumber: 6.0 Consensus size: 42
1822547 ATTTGTGAAA
**
1822557 TAAGCGCCGCTAAAGAACACT-A-CTTTTAGCGGCGTTTTTGAAC
1 TAAGCGCCGCTAAAGAACA-TGATC-TTTAGCGGCGTTTTT-TTC
* * * *
1822600 -AAGCGCCGCTATAGAACATTA-CTTTTAGAGGCGTTTATTTC
1 TAAGCGCCGCTAAAGAACATGATC-TTTAGCGGCGTTTTTTTC
** * * *
1822641 TAAGCGCCGCTAAAGATTATAATCTTTAGCGGCGTTTATTTG
1 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTC
* ** *
1822683 TAAGCGCCACTAAAGAACATGATCTTTAGCGGCGCATTTTTA
1 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTC
*
1822725 TAACCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTC
1 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTC
1822767 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTT
1 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTT
1822808 ATGTAAGCGC
Statistics
Matches: 180, Mismatches: 25, Indels: 7
0.85 0.12 0.03
Matches are distributed among these distances:
41 2 0.01
42 177 0.98
43 1 0.01
ACGTcount: A:0.27, C:0.21, G:0.20, T:0.32
Consensus pattern (42 bp):
TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTC
Found at i:1822928 original size:22 final size:22
Alignment explanation
Indices: 1822897--1822940 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
1822887 TAGTGGCGTT
* *
1822897 AAAAAGCGCCGCTAAAGACCTA
1 AAAAAACGCCGCTAAAAACCTA
1822919 AAAAAACGCCGCTAAAAACCTA
1 AAAAAACGCCGCTAAAAACCTA
1822941 TTCTGCTGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.50, C:0.27, G:0.14, T:0.09
Consensus pattern (22 bp):
AAAAAACGCCGCTAAAAACCTA
Found at i:1823639 original size:24 final size:24
Alignment explanation
Indices: 1823607--1823652 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
1823597 ATTGATGATG
*
1823607 TATTGATATTATATTCATCATACT
1 TATTCATATTATATTCATCATACT
1823631 TATTCATATTATATTCATCATA
1 TATTCATATTATATTCATCATA
1823653 TAGATTTAGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.35, C:0.13, G:0.02, T:0.50
Consensus pattern (24 bp):
TATTCATATTATATTCATCATACT
Found at i:1831528 original size:23 final size:23
Alignment explanation
Indices: 1831487--1831540 Score: 74
Period size: 23 Copynumber: 2.3 Consensus size: 23
1831477 TTACTATTCA
1831487 TTAATTATAGAAAATATATAAATT
1 TTAA-TATAGAAAATATATAAATT
*
1831511 TTAATATA-AAAATAATATAATTT
1 TTAATATAGAAAAT-ATATAAATT
1831534 TTAATAT
1 TTAATAT
1831541 GTGTTAGAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
22 5 0.18
23 19 0.68
24 4 0.14
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (23 bp):
TTAATATAGAAAATATATAAATT
Found at i:1841990 original size:138 final size:138
Alignment explanation
Indices: 1841818--1842132 Score: 467
Period size: 138 Copynumber: 2.3 Consensus size: 138
1841808 GAGAACACAT
1841818 ATATAATTAATATATAAATTTGATTCATACAAAATATTAATTGTAAATATTTTACCGAATTTATT
1 ATATAATTAATATATAAATTTGATTCATACAAAATATTAATTGTAAATATTTTACCGAATTTATT
* * *
1841883 AATATAAACTA-TTATATTAATTAATA-CTGCTCAGAATATAAAAGAAATGAAAATTAATATTAT
66 AATATAAAC-AGTTATATTAATTAATATC-GATCAAAATATAAAAGAAATGAAAAATAATATT-T
*
1841946 -TTT-AGAAATA
128 GTTTGA-AAAGA
* * * *
1841956 ATATAATTAATATATAAATTTGATTCAAACAAAATATTAATTGTATATGTTTTACTGAATTTATT
1 ATATAATTAATATATAAATTTGATTCATACAAAATATTAATTGTAAATATTTTACCGAATTTATT
* *
1842021 AATATAAACAGTTATATTAATTAATATCGATCAAAATATAAAAGATATGAAAAATATTATTTGTT
66 AATATAAACAGTTATATTAATTAATATCGATCAAAATATAAAAGAAATGAAAAATAATATTTGTT
1842086 TGAAAAGA
131 TGAAAAGA
*
1842094 ATATAATTAATATATGAATTTGATTCATACAAAATATTA
1 ATATAATTAATATATAAATTTGATTCATACAAAATATTA
1842133 CAAAATATTA
Statistics
Matches: 161, Mismatches: 12, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
137 2 0.01
138 157 0.98
139 2 0.01
ACGTcount: A:0.48, C:0.05, G:0.07, T:0.40
Consensus pattern (138 bp):
ATATAATTAATATATAAATTTGATTCATACAAAATATTAATTGTAAATATTTTACCGAATTTATT
AATATAAACAGTTATATTAATTAATATCGATCAAAATATAAAAGAAATGAAAAATAATATTTGTT
TGAAAAGA
Found at i:1846399 original size:138 final size:137
Alignment explanation
Indices: 1846250--1846565 Score: 528
Period size: 138 Copynumber: 2.3 Consensus size: 137
1846240 GAGAACATAG
1846250 ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTAAATATTTTACCGAATTTATT
1 ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTAAATATTTTACCGAATTTATT
1846315 AATATAAACAGTTATATTAATTAATATCGGTCAAAATATAAAAGACATGGAAATTAATATTA-TT
66 AATATAAACAGTTATATTAATTAATATCGGTCAAAATATAAAAGACAT-GAAA--AATATTATTT
*
1846379 -TTGGAAATA
128 CTTGGAAAGA
* * **
1846388 ATATAATTAATATATAAATTTGATTCATACAAAATATTAATTGTATATATTTTATTGAATTTATT
1 ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTAAATATTTTACCGAATTTATT
*
1846453 AATATAAACAGTTATATTAATTAATATCGGTCAAAATATAAAAGATATGAAAAATATTATTTGCT
66 AATATAAACAGTTATATTAATTAATATCGGTCAAAATATAAAAGACATGAAAAATATTATTT-CT
1846518 TGGAAAGA
130 TGGAAAGA
1846526 ATATAATTAATATATGAATTTGATTCATACAAAATATTAA
1 ATATAATTAATATATGAATTTGATTCATACAAAATATTAA
1846566 CTATTCATTA
Statistics
Matches: 168, Mismatches: 7, Indels: 6
0.93 0.04 0.03
Matches are distributed among these distances:
135 7 0.04
136 2 0.01
137 4 0.02
138 155 0.92
ACGTcount: A:0.47, C:0.05, G:0.08, T:0.40
Consensus pattern (137 bp):
ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTAAATATTTTACCGAATTTATT
AATATAAACAGTTATATTAATTAATATCGGTCAAAATATAAAAGACATGAAAAATATTATTTCTT
GGAAAGA
Found at i:1846488 original size:67 final size:67
Alignment explanation
Indices: 1846279--1846491 Score: 166
Period size: 67 Copynumber: 3.1 Consensus size: 67
1846269 TTGATTCATA
* **
1846279 CAAAATATTAATTGTAAATATTTTACCGAATTTATTAATATAAACAGTTATATTAATTAATATCG
1 CAAAATATTAATTGTATATATTTTATTGAATTTATTAATATAAACAGTTATATTAATTAATATCG
1846344 GT
66 GT
** * * * * * ** * *
1846346 CAAAATA-TAAAAGACATGGAAATTAATATT-ATTTTGGAAATAATATAATTA-ATATATAAATT
1 CAAAATATTAATTG-TAT--ATATT-TTATTGAATTT---ATTAATATAAACAGTTATATTAA-T
* *
1846408 TGAT-TC-AT
58 TAATATCGGT
1846416 ACAAAATATTAATTGTATATATTTTATTGAATTTATTAATATAAACAGTTATATTAATTAATATC
1 -CAAAATATTAATTGTATATATTTTATTGAATTTATTAATATAAACAGTTATATTAATTAATATC
1846481 GGT
65 GGT
1846484 CAAAATAT
1 CAAAATAT
1846492 AAAAGATATG
Statistics
Matches: 103, Mismatches: 29, Indels: 28
0.64 0.18 0.17
Matches are distributed among these distances:
66 18 0.17
67 25 0.24
68 5 0.05
69 16 0.16
70 3 0.03
71 18 0.17
72 18 0.17
ACGTcount: A:0.46, C:0.06, G:0.08, T:0.41
Consensus pattern (67 bp):
CAAAATATTAATTGTATATATTTTATTGAATTTATTAATATAAACAGTTATATTAATTAATATCG
GT
Found at i:1854488 original size:6 final size:6
Alignment explanation
Indices: 1854477--1854505 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
1854467 TTTTGATGTA
1854477 TATATC TATATC TATATC TATATC TATAT
1 TATATC TATATC TATATC TATATC TATAT
1854506 AATATATGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.34, C:0.14, G:0.00, T:0.52
Consensus pattern (6 bp):
TATATC
Found at i:1858084 original size:21 final size:21
Alignment explanation
Indices: 1858058--1858097 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
1858048 AGCGACGGAG
1858058 AAAATGATTTAGTGACGAATA
1 AAAATGATTTAGTGACGAATA
1858079 AAAATGATTTAGTGACGAA
1 AAAATGATTTAGTGACGAA
1858098 AGATATTACC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.47, C:0.05, G:0.20, T:0.28
Consensus pattern (21 bp):
AAAATGATTTAGTGACGAATA
Found at i:1861805 original size:29 final size:30
Alignment explanation
Indices: 1861759--1861815 Score: 98
Period size: 29 Copynumber: 1.9 Consensus size: 30
1861749 GTTTTGAGGA
1861759 ATCTAATTAAAATTTTTAAAAAAATTAAGG
1 ATCTAATTAAAATTTTTAAAAAAATTAAGG
*
1861789 ATCTAATTAAAA-TTTTAAGAAAATTAA
1 ATCTAATTAAAATTTTTAAAAAAATTAA
1861816 TGAGTATAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
29 14 0.54
30 12 0.46
ACGTcount: A:0.54, C:0.04, G:0.05, T:0.37
Consensus pattern (30 bp):
ATCTAATTAAAATTTTTAAAAAAATTAAGG
Found at i:1861826 original size:30 final size:30
Alignment explanation
Indices: 1861762--1861826 Score: 87
Period size: 29 Copynumber: 2.2 Consensus size: 30
1861752 TTGAGGAATC
*
1861762 TAATTAAAATTTTTAAAAAAATTAAGGATC
1 TAATTAAAATTTTTAAAAAAATTAAGGATA
* *
1861792 TAATTAAAA-TTTTAAGAAAATTAATGAGTA
1 TAATTAAAATTTTTAAAAAAATTAAGGA-TA
1861822 TAATT
1 TAATT
1861827 TTAGAGGGTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
29 16 0.52
30 15 0.48
ACGTcount: A:0.52, C:0.02, G:0.08, T:0.38
Consensus pattern (30 bp):
TAATTAAAATTTTTAAAAAAATTAAGGATA
Found at i:1864400 original size:40 final size:40
Alignment explanation
Indices: 1864363--1864586 Score: 258
Period size: 40 Copynumber: 5.6 Consensus size: 40
1864353 GCTACTCGTT
* *
1864363 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
1864403 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1864443 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* ** * *
1864483 CCAATGCCTTC-GGATCTTAGTCCAGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAACTCGCA
** * * * *
1864523 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
*
1864564 CAAA-GCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGGGACTTAACCCG
1864587 ACATCATTCG
Statistics
Matches: 165, Mismatches: 15, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
39 3 0.02
40 149 0.90
41 13 0.08
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:1865237 original size:37 final size:37
Alignment explanation
Indices: 1865187--1865274 Score: 176
Period size: 37 Copynumber: 2.4 Consensus size: 37
1865177 AAGCTACCTA
1865187 TGGCCGAACATACACATAACTTATGTACTTATTCATG
1 TGGCCGAACATACACATAACTTATGTACTTATTCATG
1865224 TGGCCGAACATACACATAACTTATGTACTTATTCATG
1 TGGCCGAACATACACATAACTTATGTACTTATTCATG
1865261 TGGCCGAACATACA
1 TGGCCGAACATACA
1865275 TGTCTATGTT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 51 1.00
ACGTcount: A:0.33, C:0.23, G:0.15, T:0.30
Consensus pattern (37 bp):
TGGCCGAACATACACATAACTTATGTACTTATTCATG
Found at i:1865820 original size:56 final size:56
Alignment explanation
Indices: 1865753--1865872 Score: 231
Period size: 56 Copynumber: 2.1 Consensus size: 56
1865743 TATTAGTTTA
1865753 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
*
1865809 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
1865865 TTGCCCAT
1 TTGCCCAT
1865873 CATCCCTTGT
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 63 1.00
ACGTcount: A:0.23, C:0.23, G:0.09, T:0.45
Consensus pattern (56 bp):
TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
Found at i:1866832 original size:41 final size:43
Alignment explanation
Indices: 1866787--1866880 Score: 102
Period size: 47 Copynumber: 2.1 Consensus size: 43
1866777 AAGGGGTAAA
* *
1866787 AATTATAAATGTT-AAC-TAAGGGCTAAAATTAACTTATATTG
1 AATTATAAATGTTGAACGAAAGGGCTAAAATAAACTTATATTG
* *
1866828 AATTATTAATTTTTGGACAACGAAAGGGCTAAAATAAACTTATATTG
1 AATTA-TAAATGTT-G--AACGAAAGGGCTAAAATAAACTTATATTG
1866875 AATTAT
1 AATTAT
1866881 TAATTTTTGA
Statistics
Matches: 43, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
41 5 0.12
42 6 0.14
46 4 0.09
47 28 0.65
ACGTcount: A:0.44, C:0.07, G:0.13, T:0.36
Consensus pattern (43 bp):
AATTATAAATGTTGAACGAAAGGGCTAAAATAAACTTATATTG
Found at i:1874909 original size:17 final size:17
Alignment explanation
Indices: 1874884--1874917 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1874874 TGGACAATTG
1874884 GATTCAAAATTGAAAGA
1 GATTCAAAATTGAAAGA
*
1874901 GATTGAAAATTGAAAGA
1 GATTCAAAATTGAAAGA
1874918 TACACTATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.53, C:0.03, G:0.21, T:0.24
Consensus pattern (17 bp):
GATTCAAAATTGAAAGA
Found at i:1880327 original size:20 final size:20
Alignment explanation
Indices: 1880302--1880341 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
1880292 ATTTATATAT
1880302 ATGATTTTATTGTTGAGTTG
1 ATGATTTTATTGTTGAGTTG
*
1880322 ATGATTTTGTTGTTGAGTTG
1 ATGATTTTATTGTTGAGTTG
1880342 CTTAAGGACC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.17, C:0.00, G:0.28, T:0.55
Consensus pattern (20 bp):
ATGATTTTATTGTTGAGTTG
Found at i:1886570 original size:30 final size:30
Alignment explanation
Indices: 1886538--1886593 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
1886528 ATATTACATA
*
1886538 AAAATAAAA-GATATAAGTATGTATATCGT
1 AAAATAAAACAATATAAGTATGTATATCGT
*
1886567 AAAATAAAACAATGTAAGTATGTATAT
1 AAAATAAAACAATATAAGTATGTATAT
1886594 GTATATATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 9 0.38
30 15 0.62
ACGTcount: A:0.54, C:0.04, G:0.12, T:0.30
Consensus pattern (30 bp):
AAAATAAAACAATATAAGTATGTATATCGT
Found at i:1886735 original size:18 final size:18
Alignment explanation
Indices: 1886714--1886773 Score: 75
Period size: 18 Copynumber: 3.2 Consensus size: 18
1886704 AAAATATGTT
*
1886714 TATAAAAAGATATATAGA
1 TATAAAAAGATATAAAGA
*
1886732 TATATAATAAGATATAAATA
1 TATA-AA-AAGATATAAAGA
*
1886752 TATAATAAGATATAAAGA
1 TATAAAAAGATATAAAGA
1886770 TATA
1 TATA
1886774 TATAAATAGT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
18 19 0.53
19 3 0.08
20 14 0.39
ACGTcount: A:0.60, C:0.00, G:0.08, T:0.32
Consensus pattern (18 bp):
TATAAAAAGATATAAAGA
Found at i:1888635 original size:44 final size:44
Alignment explanation
Indices: 1888585--1888899 Score: 183
Period size: 44 Copynumber: 7.2 Consensus size: 44
1888575 CAACCGAGAG
1888585 AGGCAAGGTTTGTGTCTTCGACCTGCTTCACTGTCAATGCAGGA
1 AGGCAAGGTTTGTGTCTTCGACCTGCTTCACTGTCAATGCAGGA
* * * * * ** * * *
1888629 AGGCAAGATCTTTTGTCTTCAACCAGCTCCA-TCACAACCGAAAG-
1 AGGCAAGGT-TTGTGTCTTCGACCTGCTTCACTGTCAA-TGCAGGA
* * *
1888673 AGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGAA
1 AGGCAAGGTTTGTGTCTTCGACCTGCTTCACTGTCAATGCAGGA
* * * * * ** * * *
1888717 AGGCAAGATCTTTTGTCTTCAACCAGCTCCA-TCACAACCGAAAG-
1 AGGCAAGGT-TTGTGTCTTCGACCTGCTTCACTGTCAA-TGCAGGA
* * *
1888761 AGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGAA
1 AGGCAAGGTTTGTGTCTTCGACCTGCTTCACTGTCAATGCAGGA
* * * * * ** * * *
1888805 AGGCAAGATCTTTTGTCTTCAACCAGCTCCA-TCACAACCGAAAG-
1 AGGCAAGGT-TTGTGTCTTCGACCTGCTTCACTGTCAA-TGCAGGA
* * *
1888849 AGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGAA
1 AGGCAAGGTTTGTGTCTTCGACCTGCTTCACTGTCAATGCAGGA
1888893 AGGCAAG
1 AGGCAAG
1888900 ATCTTTTGTC
Statistics
Matches: 184, Mismatches: 75, Indels: 24
0.65 0.27 0.08
Matches are distributed among these distances:
43 51 0.28
44 79 0.43
45 54 0.29
ACGTcount: A:0.26, C:0.24, G:0.23, T:0.27
Consensus pattern (44 bp):
AGGCAAGGTTTGTGTCTTCGACCTGCTTCACTGTCAATGCAGGA
Found at i:1888677 original size:88 final size:88
Alignment explanation
Indices: 1888389--1888992 Score: 816
Period size: 88 Copynumber: 6.9 Consensus size: 88
1888379 TGTAACCTTT
* ** * * *
1888389 AACCAGCTCCAAT-GCAACCGATGGAGGCAAGGCTTTGT-T-TTTGATCTGCTTTGCTGTTAATG
1 AACCAGCTCC-ATCACAACCGAAAGAGGCAAGG-TTTGTGTCTTCGATCTGCTTCGCTGTCAATG
* ** *
1888451 CAGGAAGGCAAGATCTGCT-TCTTT
64 CAGAAAGGCAAGATCTTTTGTCTTC
* * * ** * *
1888475 AACTAGCTCCA-CTGCAATCGATGGATGCAAGGCTTTGT-T-TTCGATCTGCTTCGCTGTTAATG
1 AACCAGCTCCATC-ACAACCGAAAGAGGCAAGG-TTTGTGTCTTCGATCTGCTTCGCTGTCAATG
* * * ** *
1888537 TAGGAAGGTAAGATCTGCT-TCTTT
64 CAGAAAGGCAAGATCTTTTGTCTTC
* * *
1888561 AACCAGCTCCA-CTACAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCACTGTCAATGC
1 AACCAGCTCCATC-ACAACCGAAAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGC
*
1888625 AGGAAGGCAAGATCTTTTGTCTTC
65 AGAAAGGCAAGATCTTTTGTCTTC
1888649 AACCAGCTCCATCACAACCGAAAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCA
1 AACCAGCTCCATCACAACCGAAAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCA
1888714 GAAAGGCAAGATCTTTTGTCTTC
66 GAAAGGCAAGATCTTTTGTCTTC
1888737 AACCAGCTCCATCACAACCGAAAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCA
1 AACCAGCTCCATCACAACCGAAAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCA
1888802 GAAAGGCAAGATCTTTTGTCTTC
66 GAAAGGCAAGATCTTTTGTCTTC
1888825 AACCAGCTCCATCACAACCGAAAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCA
1 AACCAGCTCCATCACAACCGAAAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCA
1888890 GAAAGGCAAGATCTTTTGTCTTC
66 GAAAGGCAAGATCTTTTGTCTTC
* **
1888913 AACCAGCTCCATCACAACCGAAAGAGGCAAGGTTTGTGTCTTCAATCTGCTTCGC-GAAAATGCA
1 AACCAGCTCCATCACAACCGAAAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCA
1888977 GAAAGGCAAGAT-TTTT
66 GAAAGGCAAGATCTTTT
1888993 AACTTCATTG
Statistics
Matches: 484, Mismatches: 28, Indels: 12
0.92 0.05 0.02
Matches are distributed among these distances:
85 6 0.01
86 107 0.22
87 54 0.11
88 316 0.65
89 1 0.00
ACGTcount: A:0.26, C:0.24, G:0.22, T:0.28
Consensus pattern (88 bp):
AACCAGCTCCATCACAACCGAAAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCA
GAAAGGCAAGATCTTTTGTCTTC
Found at i:1891150 original size:7 final size:8
Alignment explanation
Indices: 1891125--1891154 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
1891115 CTATTTTGAC
1891125 TTTGATTTT
1 TTTGA-TTT
1891134 TTTGATTT
1 TTTGATTT
1891142 TTTGATTT
1 TTTGATTT
1891150 TTTGA
1 TTTGA
1891155 ATTCATGAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 16 0.76
9 5 0.24
ACGTcount: A:0.13, C:0.00, G:0.13, T:0.73
Consensus pattern (8 bp):
TTTGATTT
Found at i:1895682 original size:30 final size:29
Alignment explanation
Indices: 1895648--1895719 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 29
1895638 ATATATTACA
1895648 TAAAAATAAAAGATATAAGTATGTATATCG
1 TAAAAATAAAAGATATAAGTATGTATAT-G
* *
1895678 T-AAAATAAAACAATGTAAGTATGTATATG
1 TAAAAATAAAA-GATATAAGTATGTATATG
* *
1895707 TATATATAAAAGA
1 TAAAAATAAAAGA
1895720 AAATAGACGT
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
29 12 0.34
30 23 0.66
ACGTcount: A:0.54, C:0.03, G:0.12, T:0.31
Consensus pattern (29 bp):
TAAAAATAAAAGATATAAGTATGTATATG
Found at i:1895848 original size:18 final size:18
Alignment explanation
Indices: 1895827--1895886 Score: 75
Period size: 18 Copynumber: 3.2 Consensus size: 18
1895817 AAAATATGTT
*
1895827 TATAAAAAGATATATAGA
1 TATAAAAAGATATAAAGA
*
1895845 TATATAATAAGATATAAATA
1 TATA-AA-AAGATATAAAGA
*
1895865 TATAATAAGATATAAAGA
1 TATAAAAAGATATAAAGA
1895883 TATA
1 TATA
1895887 TATAAATAGT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
18 19 0.53
19 3 0.08
20 14 0.39
ACGTcount: A:0.60, C:0.00, G:0.08, T:0.32
Consensus pattern (18 bp):
TATAAAAAGATATAAAGA
Found at i:1925443 original size:21 final size:21
Alignment explanation
Indices: 1925418--1925457 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1925408 ATGTGAATTA
* *
1925418 TAAAATATATATAATATATTT
1 TAAAATATAAAGAATATATTT
1925439 TAAAATATAAAGAATATAT
1 TAAAATATAAAGAATATAT
1925458 AAATATGTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (21 bp):
TAAAATATAAAGAATATATTT
Found at i:1925617 original size:12 final size:12
Alignment explanation
Indices: 1925600--1925641 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
1925590 AAAGCATATT
1925600 TATATATGTAAG
1 TATATATGTAAG
* **
1925612 TATATATATATT
1 TATATATGTAAG
1925624 TATATATGTAAG
1 TATATATGTAAG
1925636 TATATA
1 TATATA
1925642 ATAAAGGCGT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.43, C:0.00, G:0.10, T:0.48
Consensus pattern (12 bp):
TATATATGTAAG
Found at i:1925622 original size:24 final size:24
Alignment explanation
Indices: 1925595--1925641 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
1925585 GTATGAAAGC
1925595 ATATTTATATATGTAAGTATATAT
1 ATATTTATATATGTAAGTATATAT
1925619 ATATTTATATATGTAAGTATATA
1 ATATTTATATATGTAAGTATATA
1925642 ATAAAGGCGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.43, C:0.00, G:0.09, T:0.49
Consensus pattern (24 bp):
ATATTTATATATGTAAGTATATAT
Done.