Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006936.1 Hibiscus syriacus cultivar Beakdansim tig00017808_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2176229
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 9
Found at i:1871373 original size:114 final size:114
Alignment explanation
Indices: 1871169--1871397 Score: 368
Period size: 114 Copynumber: 2.0 Consensus size: 114
1871159 TAAAAATTGG
* * *
1871169 TGGCTAATTTTAACATTATACCTTTAATTTTAAATAATTTTGAAAATTTAAGGAAAATACGAGTT
1 TGGCTAATTTTAACATTATACATTTAATTGTAAATAATTTTAAAAATTTAAGGAAAATACGAGTT
*
1871234 TAAAAGGCATTGAACCTAAGCCTTAAGGGTAAACAACATTTAATTATTA
66 TAAAAGGCATTGAACCTAAGACTTAAGGGTAAACAACATTTAATTATTA
* * **
1871283 TGGCTAATTTTGATATTATACATTTAATTGTAAATAATTTTAAAAATTTAAGGAAAATGTGAGTT
1 TGGCTAATTTTAACATTATACATTTAATTGTAAATAATTTTAAAAATTTAAGGAAAATACGAGTT
* *
1871348 TAAAGGGCATTGAACCTAGGACTTAAGGGTAAACAACATTTAATTATTA
66 TAAAAGGCATTGAACCTAAGACTTAAGGGTAAACAACATTTAATTATTA
1871397 T
1 T
1871398 ATCAAATTAA
Statistics
Matches: 105, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
114 105 1.00
ACGTcount: A:0.41, C:0.09, G:0.14, T:0.37
Consensus pattern (114 bp):
TGGCTAATTTTAACATTATACATTTAATTGTAAATAATTTTAAAAATTTAAGGAAAATACGAGTT
TAAAAGGCATTGAACCTAAGACTTAAGGGTAAACAACATTTAATTATTA
Found at i:1872235 original size:14 final size:15
Alignment explanation
Indices: 1872218--1872250 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
1872208 AATGAATTAA
*
1872218 ATTTTTTGAAAAAC-
1 ATTTTCTGAAAAACG
1872232 ATTTTCTGAAAAACG
1 ATTTTCTGAAAAACG
1872247 ATTT
1 ATTT
1872251 ATGATGTTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.39, C:0.09, G:0.09, T:0.42
Consensus pattern (15 bp):
ATTTTCTGAAAAACG
Found at i:1872568 original size:11 final size:11
Alignment explanation
Indices: 1872552--1872607 Score: 50
Period size: 11 Copynumber: 5.5 Consensus size: 11
1872542 TTTAATATCT
1872552 TTATTAAAATA
1 TTATTAAAATA
1872563 TTATT---ATA
1 TTATTAAAATA
*
1872571 TTATTATAATA
1 TTATTAAAATA
1872582 TTATT-AAATA
1 TTATTAAAATA
*
1872592 -TATAAATAATA
1 TTATTAA-AATA
1872603 TTATT
1 TTATT
1872608 CATTATTAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 11
0.72 0.06 0.22
Matches are distributed among these distances:
8 8 0.22
9 3 0.08
10 5 0.14
11 17 0.47
12 3 0.08
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (11 bp):
TTATTAAAATA
Found at i:1872626 original size:27 final size:27
Alignment explanation
Indices: 1872581--1872661 Score: 135
Period size: 27 Copynumber: 3.0 Consensus size: 27
1872571 TTATTATAAT
* *
1872581 ATTATTAAATATATAAATAATATTATTC
1 ATTATT-AATATTTTAATAATATTATTC
1872609 ATTATTAATATTTTAATAATATTATTC
1 ATTATTAATATTTTAATAATATTATTC
1872636 ATTATTAATATTTTAATAATATTATT
1 ATTATTAATATTTTAATAATATTATT
1872662 TCTATGAAAT
Statistics
Matches: 51, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
27 45 0.88
28 6 0.12
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (27 bp):
ATTATTAATATTTTAATAATATTATTC
Found at i:1872791 original size:22 final size:23
Alignment explanation
Indices: 1872765--1872810 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 23
1872755 TGATTATTTA
1872765 ATTATAATATTAA-AAATA-TAAT
1 ATTATAATA-TAAGAAATATTAAT
*
1872787 ATTATATTATAAGAAATATTAAT
1 ATTATAATATAAGAAATATTAAT
1872810 A
1 A
1872811 AATATATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 3 0.14
22 13 0.62
23 5 0.24
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (23 bp):
ATTATAATATAAGAAATATTAAT
Found at i:1873583 original size:14 final size:14
Alignment explanation
Indices: 1873564--1873590 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1873554 TGCATTACCT
1873564 TTCAAAAAAAATTA
1 TTCAAAAAAAATTA
1873578 TTCAAAAAAAATT
1 TTCAAAAAAAATT
1873591 TGGTTATTCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.30
Consensus pattern (14 bp):
TTCAAAAAAAATTA
Found at i:1876944 original size:13 final size:13
Alignment explanation
Indices: 1876928--1876962 Score: 70
Period size: 13 Copynumber: 2.7 Consensus size: 13
1876918 GTTCATGCGC
1876928 TCTGCTACGTCGT
1 TCTGCTACGTCGT
1876941 TCTGCTACGTCGT
1 TCTGCTACGTCGT
1876954 TCTGCTACG
1 TCTGCTACG
1876963 GTGTCATGGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.09, C:0.31, G:0.23, T:0.37
Consensus pattern (13 bp):
TCTGCTACGTCGT
Found at i:1884907 original size:2 final size:2
Alignment explanation
Indices: 1884900--1884934 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1884890 TCATCATTAC
1884900 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1884935 TCGGTGAATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1887358 original size:17 final size:19
Alignment explanation
Indices: 1887316--1887358 Score: 54
Period size: 21 Copynumber: 2.3 Consensus size: 19
1887306 GGGAGAGTAG
1887316 GTGTATCGGTACACTATCAAA
1 GTGTATCGGTACAC-ATC-AA
1887337 GTGTATCGGTACAC-TC-A
1 GTGTATCGGTACACATCAA
1887354 GTGTA
1 GTGTA
1887359 AAATTCAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 6 0.27
19 2 0.09
21 14 0.64
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.30
Consensus pattern (19 bp):
GTGTATCGGTACACATCAA
Found at i:1889515 original size:20 final size:20
Alignment explanation
Indices: 1889479--1889516 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1889469 ATCCTATTCC
**
1889479 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
1889499 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
1889517 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:1890290 original size:13 final size:13
Alignment explanation
Indices: 1890259--1890292 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
1890249 AATGGGTAAA
*
1890259 ATTTGAAAACTAT
1 ATTTGAAAACAAT
1890272 -TTTGAAAACAAT
1 ATTTGAAAACAAT
1890284 ATTTGAAAA
1 ATTTGAAAA
1890293 AACATAACAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.50, C:0.06, G:0.09, T:0.35
Consensus pattern (13 bp):
ATTTGAAAACAAT
Found at i:1890813 original size:23 final size:22
Alignment explanation
Indices: 1890786--1890862 Score: 104
Period size: 21 Copynumber: 3.5 Consensus size: 22
1890776 ACTCGAGGGG
1890786 TGTATCGATACATATTCAAGGAA
1 TGTATCGATACATATTCAAGG-A
*
1890809 TGTATCGATACATATTCATGG-
1 TGTATCGATACATATTCAAGGA
*
1890830 TGTATCGATACATA-GCAAGGA
1 TGTATCGATACATATTCAAGGA
*
1890851 GGTATCGATACA
1 TGTATCGATACA
1890863 CTGTGCACAA
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
20 4 0.08
21 25 0.51
23 20 0.41
ACGTcount: A:0.35, C:0.14, G:0.21, T:0.30
Consensus pattern (22 bp):
TGTATCGATACATATTCAAGGA
Found at i:1892547 original size:18 final size:18
Alignment explanation
Indices: 1892516--1892561 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
1892506 CTAAATACCC
* *
1892516 ATTTAGTACCTACAATAA
1 ATTTATTACTTACAATAA
*
1892534 ATTTATTACTTACAGTAA
1 ATTTATTACTTACAATAA
1892552 ATTTATTACT
1 ATTTATTACT
1892562 AGGCCTTTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.39, C:0.13, G:0.04, T:0.43
Consensus pattern (18 bp):
ATTTATTACTTACAATAA
Found at i:1892894 original size:12 final size:12
Alignment explanation
Indices: 1892877--1892901 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1892867 ATGATGGTTC
1892877 TCCAATGTCATG
1 TCCAATGTCATG
1892889 TCCAATGTCATG
1 TCCAATGTCATG
1892901 T
1 T
1892902 GTATTTATAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.24, G:0.16, T:0.36
Consensus pattern (12 bp):
TCCAATGTCATG
Found at i:1896685 original size:19 final size:19
Alignment explanation
Indices: 1896661--1896711 Score: 93
Period size: 19 Copynumber: 2.7 Consensus size: 19
1896651 ATTTGACCAA
1896661 GTGTATCGGTACATCCCAG
1 GTGTATCGGTACATCCCAG
*
1896680 GTGTATCGTTACATCCCAG
1 GTGTATCGGTACATCCCAG
1896699 GTGTATCGGTACA
1 GTGTATCGGTACA
1896712 CTTTTTCCTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.22, C:0.24, G:0.25, T:0.29
Consensus pattern (19 bp):
GTGTATCGGTACATCCCAG
Found at i:1897963 original size:264 final size:264
Alignment explanation
Indices: 1897493--1898019 Score: 964
Period size: 264 Copynumber: 2.0 Consensus size: 264
1897483 GACTTTTTTT
**
1897493 ATGTTAATAATATATAAGTGTCAAAGAAATGTGTGGGAGTACATTATGGATATGTTTTATATTTC
1 ATGTTAATAATATATAAGTGTCAAAGAAATGTGAAGGAGTACATTATGGATATGTTTTATATTTC
**
1897558 AAAATTTAAGGCACTTAAGATCAAGTTTTTTCGAAGAATTACTTGTTATTTTGAATTTAATATTG
66 AAAATTTAAGGCACTTAAGATCAAGTTTTTTCGAAGAATTACTAATTATTTTGAATTTAATATTG
1897623 ATTTTTATAGAGTTTAATCAACTCAAAGGGAGAAATGAACTCTAAATGAACTCATTTTTCATTGT
131 ATTTTTATAGAGTTTAATCAACTCAAAGGGAGAAATGAACTCTAAATGAACTCATTTTTCATTGT
1897688 GTACAGGAGGAAGAAAGGTTGAAGCATAATAAGTCTAAAAGTACTCACTTGAAAAGTGCACATAA
196 GTACAGGAGGAAGAAAGGTTGAAGCATAATAAGTCTAAAAGTACTCACTTGAAAAGTGCACATAA
1897753 AGAA
261 AGAA
*
1897757 ATGTTAATAATATATTAGTGTCAAAGAAATGTGAAGGAGTACATTATGGATATGTTTTATATTTC
1 ATGTTAATAATATATAAGTGTCAAAGAAATGTGAAGGAGTACATTATGGATATGTTTTATATTTC
* *
1897822 AAAATTTAAGGCACTTAAGATCAAGTTTTTTCGAAGAATTTCTAATTATTTTGATTTTAATATTG
66 AAAATTTAAGGCACTTAAGATCAAGTTTTTTCGAAGAATTACTAATTATTTTGAATTTAATATTG
* *
1897887 ATTTTTATAGATTTTAATCAACTCAAAGGGAGAAATGAACTCTAAATTAACTCATTTTTCATTGT
131 ATTTTTATAGAGTTTAATCAACTCAAAGGGAGAAATGAACTCTAAATGAACTCATTTTTCATTGT
*
1897952 GTACAGGAGGAAGAAAGGTTGAAGCATAATATGTCTAAAAGTACTCACTTGAAAAGTGCACATAA
196 GTACAGGAGGAAGAAAGGTTGAAGCATAATAAGTCTAAAAGTACTCACTTGAAAAGTGCACATAA
1898017 AGA
261 AGA
1898020 TAAGGGAAAA
Statistics
Matches: 253, Mismatches: 10, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
264 253 1.00
ACGTcount: A:0.39, C:0.09, G:0.17, T:0.35
Consensus pattern (264 bp):
ATGTTAATAATATATAAGTGTCAAAGAAATGTGAAGGAGTACATTATGGATATGTTTTATATTTC
AAAATTTAAGGCACTTAAGATCAAGTTTTTTCGAAGAATTACTAATTATTTTGAATTTAATATTG
ATTTTTATAGAGTTTAATCAACTCAAAGGGAGAAATGAACTCTAAATGAACTCATTTTTCATTGT
GTACAGGAGGAAGAAAGGTTGAAGCATAATAAGTCTAAAAGTACTCACTTGAAAAGTGCACATAA
AGAA
Found at i:1901269 original size:26 final size:27
Alignment explanation
Indices: 1901240--1901290 Score: 86
Period size: 26 Copynumber: 1.9 Consensus size: 27
1901230 GTTAGTTACT
*
1901240 TACTAGTTTAGATTAAATT-TTTTGCC
1 TACTAGTTTAGAATAAATTATTTTGCC
1901266 TACTAGTTTAGAATAAATTATTTTG
1 TACTAGTTTAGAATAAATTATTTTG
1901291 TTAAATTAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 18 0.78
27 5 0.22
ACGTcount: A:0.31, C:0.08, G:0.12, T:0.49
Consensus pattern (27 bp):
TACTAGTTTAGAATAAATTATTTTGCC
Found at i:1904237 original size:69 final size:70
Alignment explanation
Indices: 1904103--1904263 Score: 204
Period size: 69 Copynumber: 2.3 Consensus size: 70
1904093 GTCATGCCAA
*
1904103 GATA-GGATTATACAAGGATATAGTTGTACCTAACTAGCAGAGTATGATTAGATCAACATTTAGT
1 GATATGGATTATACAAGGATATAGCTGTACCTAACTAGCAGAGTATGATTAGATCAACATTTAGT
1904167 GTCAG
66 GTCAG
* * * *
1904172 GATATGGATTATACATGGATATAGCTGTA-CTAATTAGCA-AGGTATGGTTGGATCAAC-TTGTA
1 GATATGGATTATACAAGGATATAGCTGTACCTAACTAGCAGA-GTATGATTAGATCAACATT-TA
1904234 GTGTCAG
64 GTGTCAG
* * *
1904241 GATATGAATTACACAAGAATATA
1 GATATGGATTATACAAGGATATA
1904264 ATTGTGCCTG
Statistics
Matches: 80, Mismatches: 9, Indels: 6
0.84 0.09 0.06
Matches are distributed among these distances:
68 3 0.04
69 55 0.69
70 22 0.28
ACGTcount: A:0.36, C:0.11, G:0.22, T:0.31
Consensus pattern (70 bp):
GATATGGATTATACAAGGATATAGCTGTACCTAACTAGCAGAGTATGATTAGATCAACATTTAGT
GTCAG
Found at i:1904361 original size:48 final size:49
Alignment explanation
Indices: 1904300--1904403 Score: 149
Period size: 50 Copynumber: 2.1 Consensus size: 49
1904290 TCGATTCATG
* * * *
1904300 ATTGAATGGGTG-AA-ATTCATTGAAAAAGCTTTGAAATTAAGGTGTAA
1 ATTGCATGGGTGAAATATTCATTAAAAAAGCTTTGAAATTAAGATGCAA
1904347 TATTGCATGGGTGAAATATTCATTAAAAAAGCTTTGAAATTAAGATGCAA
1 -ATTGCATGGGTGAAATATTCATTAAAAAAGCTTTGAAATTAAGATGCAA
1904397 ATTGCAT
1 ATTGCAT
1904404 CAAATTAAAG
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
48 11 0.22
49 9 0.18
50 30 0.60
ACGTcount: A:0.40, C:0.07, G:0.20, T:0.33
Consensus pattern (49 bp):
ATTGCATGGGTGAAATATTCATTAAAAAAGCTTTGAAATTAAGATGCAA
Found at i:1907018 original size:20 final size:23
Alignment explanation
Indices: 1906993--1907050 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 23
1906983 TTCCCCTTGA
1906993 AGTGCATCGATGCA-TC-AT-AC
1 AGTGCATCGATGCATTCTATAAC
*
1907013 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTCTATAAC
1907036 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
1907051 CTACTTATGC
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 14 0.42
21 2 0.06
22 1 0.03
23 3 0.09
24 13 0.39
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.29
Consensus pattern (23 bp):
AGTGCATCGATGCATTCTATAAC
Found at i:1925843 original size:24 final size:25
Alignment explanation
Indices: 1925816--1925916 Score: 72
Period size: 24 Copynumber: 4.3 Consensus size: 25
1925806 AACTTGCACC
*
1925816 GAAGTACCACATAGAATTTGT-CCT
1 GAAGGACCACATAGAATTTGTCCCT
* * * *
1925840 GAAGGACCGCGTATAATTTTTCCCT
1 GAAGGACCACATAGAATTTGTCCCT
* *
1925865 -AAGGACCACATAGAA-ATATCCC-
1 GAAGGACCACATAGAATTTGTCCCT
* *
1925887 GAAGGATCACATAG-A-TAGT-CCT
1 GAAGGACCACATAGAATTTGTCCCT
1925909 GAAGGACC
1 GAAGGACC
1925917 GCGTAGAACC
Statistics
Matches: 59, Mismatches: 15, Indels: 8
0.72 0.18 0.10
Matches are distributed among these distances:
21 2 0.03
22 9 0.15
23 17 0.29
24 28 0.47
25 3 0.05
ACGTcount: A:0.35, C:0.23, G:0.20, T:0.23
Consensus pattern (25 bp):
GAAGGACCACATAGAATTTGTCCCT
Found at i:1935642 original size:14 final size:14
Alignment explanation
Indices: 1935625--1935659 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
1935615 AAATTTTTTT
*
1935625 AAATTTCTTTTATA
1 AAATTTATTTTATA
1935639 AAATTGTATTTTATA
1 AAATT-TATTTTATA
1935654 AAATTT
1 AAATTT
1935660 TAAAATTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
14 6 0.32
15 13 0.68
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.54
Consensus pattern (14 bp):
AAATTTATTTTATA
Found at i:1936778 original size:3 final size:3
Alignment explanation
Indices: 1936772--1936824 Score: 79
Period size: 3 Copynumber: 17.0 Consensus size: 3
1936762 TTACCCATTT
1936772 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTAA TTA TTTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA -TTA TTA
*
1936819 ATA TTA
1 TTA TTA
1936825 CAAAGCCCAA
Statistics
Matches: 46, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
3 40 0.87
4 6 0.13
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:1949587 original size:10 final size:10
Alignment explanation
Indices: 1949568--1949624 Score: 52
Period size: 10 Copynumber: 6.2 Consensus size: 10
1949558 ATGCTTGAAG
*
1949568 AGAAAAAAAA
1 AGAAAGAAAA
1949578 AGAAAGAAAA
1 AGAAAGAAAA
*
1949588 AAAAAG-AAA
1 AGAAAGAAAA
1949597 AG--A-AAAA
1 AGAAAGAAAA
1949604 AGAAAGAAAA
1 AGAAAGAAAA
*
1949614 AGGAA-AAAA
1 AGAAAGAAAA
1949623 AG
1 AG
1949625 GTGGTCAAGG
Statistics
Matches: 39, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
7 6 0.15
9 11 0.28
10 22 0.56
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (10 bp):
AGAAAGAAAA
Found at i:1949587 original size:14 final size:14
Alignment explanation
Indices: 1949568--1949612 Score: 72
Period size: 15 Copynumber: 3.1 Consensus size: 14
1949558 ATGCTTGAAG
1949568 AGAAAAAAAAAGAA
1 AGAAAAAAAAAGAA
1949582 AGAAAAAAAAAGAAA
1 AGAAAAAAAAAG-AA
1949597 AGAAAAAAGAAAGAA
1 AGAAAAAA-AAAGAA
1949612 A
1 A
1949613 AAGGAAAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
14 12 0.41
15 13 0.45
16 4 0.14
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (14 bp):
AGAAAAAAAAAGAA
Found at i:1949589 original size:11 final size:10
Alignment explanation
Indices: 1949568--1949614 Score: 60
Period size: 10 Copynumber: 4.7 Consensus size: 10
1949558 ATGCTTGAAG
1949568 AGAAAAAAAA
1 AGAAAAAAAA
*
1949578 AGAAAGAAAA
1 AGAAAAAAAA
*
1949588 A-AAAAGAAA
1 AGAAAAAAAA
1949597 AGAAAAAAGAA
1 AGAAAAAA-AA
1949608 AGAAAAA
1 AGAAAAA
1949615 GGAAAAAAAG
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
9 7 0.23
10 15 0.48
11 9 0.29
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (10 bp):
AGAAAAAAAA
Found at i:1949589 original size:16 final size:15
Alignment explanation
Indices: 1949565--1949623 Score: 64
Period size: 15 Copynumber: 3.7 Consensus size: 15
1949555 ATTATGCTTG
*
1949565 AAGAGAAAAAAAAAGA
1 AAGA-AAAAAAAAAAA
*
1949581 AAGAAAAAAAAAGAA
1 AAGAAAAAAAAAAAA
1949596 AAGAAAAAAGAAAGAAA
1 AAGAAAAAA-AAA-AAA
1949613 AAGGAAAAAAA
1 AA-GAAAAAAA
1949624 GGTGGTCAAG
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
15 18 0.49
16 7 0.19
17 5 0.14
18 7 0.19
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (15 bp):
AAGAAAAAAAAAAAA
Found at i:1949590 original size:15 final size:15
Alignment explanation
Indices: 1949565--1949612 Score: 62
Period size: 16 Copynumber: 3.1 Consensus size: 15
1949555 ATTATGCTTG
1949565 AAGAGAAAAAAAAAGA
1 AAGA-AAAAAAAAAGA
1949581 AAG-AAAAAAAAAGAA
1 AAGAAAAAAAAAAG-A
*
1949596 AAGAAAAAAGAAAGA
1 AAGAAAAAAAAAAGA
1949611 AA
1 AA
1949613 AAGGAAAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
14 10 0.34
15 7 0.24
16 12 0.41
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (15 bp):
AAGAAAAAAAAAAGA
Found at i:1949624 original size:26 final size:26
Alignment explanation
Indices: 1949565--1949614 Score: 84
Period size: 26 Copynumber: 1.9 Consensus size: 26
1949555 ATTATGCTTG
1949565 AAGAGAAA-AAAAAAGAAAGAAAAAAA
1 AAGA-AAAGAAAAAAGAAAGAAAAAAA
1949591 AAGAAAAGAAAAAAGAAAGAAAAA
1 AAGAAAAGAAAAAAGAAAGAAAAA
1949615 GGAAAAAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
25 3 0.13
26 20 0.87
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (26 bp):
AAGAAAAGAAAAAAGAAAGAAAAAAA
Found at i:1951123 original size:83 final size:83
Alignment explanation
Indices: 1950984--1951187 Score: 390
Period size: 83 Copynumber: 2.5 Consensus size: 83
1950974 AACAAATGCC
*
1950984 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAATCAATC
1 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAATC
1951049 ATTGAATTTGGAAGAGTA
66 ATTGAATTTGGAAGAGTA
1951067 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAATC
1 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAATC
1951132 ATTGAATTTGGAAGAGTA
66 ATTGAATTTGGAAGAGTA
*
1951150 ATGTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTT
1 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTT
1951188 CTTTGAGTTC
Statistics
Matches: 119, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
83 119 1.00
ACGTcount: A:0.25, C:0.13, G:0.23, T:0.39
Consensus pattern (83 bp):
ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAATC
ATTGAATTTGGAAGAGTA
Found at i:1952279 original size:113 final size:113
Alignment explanation
Indices: 1951938--1952714 Score: 1180
Period size: 113 Copynumber: 6.8 Consensus size: 113
1951928 GCAAAGATTT
* *
1951938 AAATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAG
* * * *
1952003 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTTAACCTTTTGTTT
66 AAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTC
* * * * *** * *
1952051 GAATTCATCATTTGATGGATTAAAATTTCCAG-GTAGAGTTCATAATGAGAAGAACTCATTACTT
1 AAATCCATCACTTGATGGATCAGCTTTTCCAGAG-AAAGTTCATAATAAGAAGAACTCA-T-C-T
* * * *
1952115 GAAGGAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTATGCTC
62 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTC
* *
1952167 AAATTCATCACTTGATGGATCAGCTTTTACAGA-AGAAGTTCATAATAAGAAGAACTCATCTGAA
1 AAATCCATCACTTGATGGATCAGCTTTTCCAGAGA-AAGTTCATAATAAGAAGAACTCATCTGAA
*
1952231 GAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCTC
65 GAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTC
* *
1952280 AAATCGATCACTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAG
1 AAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAG
*
1952345 AAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCTC
66 AAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTC
*
1952393 AAATCCATCACTTGATGGATCAGCTTTTCTAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAG
1 AAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAG
*
1952458 AAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCTC
66 AAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTC
*
1952506 AAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATAAGAAGAACTCATTTGAAG
1 AAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAG
* * *
1952571 AAGGAAGAAGAAATTTATAATGAGAAGAATTTGTTCAACCTTTTGCTC
66 AAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTC
* * *
1952619 AAATCCATCACTTGATGGATCAGCTTTTCTAGAGAAAGTTCATAATGAGAAGAACTCATTTGAAG
1 AAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAG
*
1952684 AAGGAAGAAGAAGTTCATAATAAGAAGAACT
66 AAGGAAGAAGAAGTTCATAATGAGAAGAACT
1952715 CATCTCAAGA
Statistics
Matches: 611, Mismatches: 46, Indels: 14
0.91 0.07 0.02
Matches are distributed among these distances:
112 1 0.00
113 511 0.84
114 3 0.00
115 3 0.00
116 93 0.15
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.28
Consensus pattern (113 bp):
AAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAG
AAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTC
Found at i:1952734 original size:36 final size:36
Alignment explanation
Indices: 1952654--1952858 Score: 270
Period size: 36 Copynumber: 5.5 Consensus size: 36
1952644 TTTCTAGAGA
*
1952654 AAGTTCATAATGAGAAGAACTCATTTGAAGAAGGAAGAAG
1 AAGTTCATAATGAGAAGAACTCATCT---GAA-GAAGAAG
* *
1952694 AAGTTCATAATAAGAAGAACTCATCTCAAGAAGAAG
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAG
*
1952730 AAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAG
1 AAGTTCATAATGAGAAGAACTCATCT---GAA-GAAGAAG
1952770 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAG
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAG
*
1952806 AAGTTCATAATGAGAAGAACTCGTCTG-A-AAGAAG
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAG
*
1952840 AAATTCATAATGAGAAGAA
1 AAGTTCATAATGAGAAGAA
1952859 TTTGTTCAAC
Statistics
Matches: 154, Mismatches: 7, Indels: 14
0.88 0.04 0.08
Matches are distributed among these distances:
34 24 0.16
35 1 0.01
36 66 0.43
37 5 0.03
39 2 0.01
40 56 0.36
ACGTcount: A:0.49, C:0.10, G:0.21, T:0.20
Consensus pattern (36 bp):
AAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAG
Found at i:1952747 original size:76 final size:76
Alignment explanation
Indices: 1952654--1952839 Score: 318
Period size: 76 Copynumber: 2.4 Consensus size: 76
1952644 TTTCTAGAGA
*
1952654 AAGTTCATAATGAGAAGAACTCATTTGAAGAAGGAAGAAGAAGTTCATAATAAGAAGAACTCATC
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATAAGAAGAACTCATC
1952719 TCAAGAAGAAG
66 TCAAGAAGAAG
* *
1952730 AAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTCATC
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATAAGAAGAACTCATC
*
1952795 TGAAGAAGAAG
66 TCAAGAAGAAG
*
1952806 AAGTTCATAATGAGAAGAACTCGTCTGAAAGAAG
1 AAGTTCATAATGAGAAGAACTCATCTG-AAGAAG
1952840 AAATTCATAA
Statistics
Matches: 103, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
76 97 0.94
77 6 0.06
ACGTcount: A:0.48, C:0.11, G:0.22, T:0.19
Consensus pattern (76 bp):
AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATAAGAAGAACTCATC
TCAAGAAGAAG
Found at i:1952768 original size:43 final size:42
Alignment explanation
Indices: 1952654--1952808 Score: 204
Period size: 40 Copynumber: 3.9 Consensus size: 42
1952644 TTTCTAGAGA
* *
1952654 AAGTTCATAATGAGAAGAACTCATTTGAAGAAG--GAAGAAG
1 AAGTTCATAATAAGAAGAACTCATCTGAAGAAGAAGAAGAAG
*
1952694 AAGTTCATAATAAGAAGAACTCATCT------CAAGAAGAAG
1 AAGTTCATAATAAGAAGAACTCATCTGAAGAAGAAGAAGAAG
1952730 AAGTTCATAATAAGAAGAACTCATCTGAAGAAG--GAAGAAG
1 AAGTTCATAATAAGAAGAACTCATCTGAAGAAGAAGAAGAAG
*
1952770 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAG
1 AAGTTCATAATAAGAAGAACTCATCTGAAGAAGAAGAAG
1952809 TTCATAATGA
Statistics
Matches: 100, Mismatches: 5, Indels: 18
0.81 0.04 0.15
Matches are distributed among these distances:
36 33 0.33
40 63 0.63
42 4 0.04
ACGTcount: A:0.49, C:0.10, G:0.22, T:0.19
Consensus pattern (42 bp):
AAGTTCATAATAAGAAGAACTCATCTGAAGAAGAAGAAGAAG
Found at i:1953221 original size:3 final size:3
Alignment explanation
Indices: 1953215--1953258 Score: 61
Period size: 3 Copynumber: 14.0 Consensus size: 3
1953205 TTACCCATTT
*
1953215 TTA TTA TTA TTA TTA TTA TTA TTA TTAA TTA TTTA TTA ATA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA -TTA TTA TTA TTA
1953259 CAAAGCCCAA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
3 31 0.84
4 6 0.16
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:1953701 original size:18 final size:19
Alignment explanation
Indices: 1953660--1953695 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
1953650 GGAGAGACAG
1953660 AAACAGAGCAAAAACAACA
1 AAACAGAGCAAAAACAACA
*
1953679 AAACAGAG-AACAACAAC
1 AAACAGAGCAAAAACAAC
1953696 CCAACAAACC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.67, C:0.22, G:0.11, T:0.00
Consensus pattern (19 bp):
AAACAGAGCAAAAACAACA
Found at i:1957384 original size:21 final size:21
Alignment explanation
Indices: 1957355--1957407 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
1957345 ATTCTGACTA
1957355 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
* *
1957376 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTTCCAAAT
*
1957397 TCGCAATGCGA
1 TCGCATTGCGA
1957408 ATACGTAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.36
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:1957422 original size:20 final size:20
Alignment explanation
Indices: 1957397--1957505 Score: 191
Period size: 20 Copynumber: 5.5 Consensus size: 20
1957387 TTTTCCTAAT
*
1957397 TCGCAATGCGAATACGTAAA
1 TCGCAACGCGAATACGTAAA
*
1957417 TCGCAACGCGAATACATAAA
1 TCGCAACGCGAATACGTAAA
1957437 TCGCAACGCGAATACGTAAA
1 TCGCAACGCGAATACGTAAA
1957457 TCGCAACGCGAATACGTAAA
1 TCGCAACGCGAATACGTAAA
*
1957477 TCGCAACGCGAATACATAAA
1 TCGCAACGCGAATACGTAAA
1957497 TCGCAACGC
1 TCGCAACGC
1957506 AAATCTGACT
Statistics
Matches: 85, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 85 1.00
ACGTcount: A:0.40, C:0.26, G:0.18, T:0.16
Consensus pattern (20 bp):
TCGCAACGCGAATACGTAAA
Found at i:1957519 original size:20 final size:20
Alignment explanation
Indices: 1957496--1957582 Score: 140
Period size: 20 Copynumber: 4.3 Consensus size: 20
1957486 GAATACATAA
*
1957496 ATCGCAACGCA-AATCTGACT
1 ATCGCAACG-AGATTCTGACT
1957516 ATCGCAACGAGATTCTGACT
1 ATCGCAACGAGATTCTGACT
1957536 ATCGCAACGAGATTCTGACT
1 ATCGCAACGAGATTCTGACT
*
1957556 ATCGCAACGCGATTCTGACT
1 ATCGCAACGAGATTCTGACT
1957576 ATCGCAA
1 ATCGCAA
1957583 TACTGAATTT
Statistics
Matches: 64, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
19 1 0.02
20 63 0.98
ACGTcount: A:0.31, C:0.28, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAACGAGATTCTGACT
Found at i:1957520 original size:40 final size:40
Alignment explanation
Indices: 1957397--1957524 Score: 163
Period size: 40 Copynumber: 3.2 Consensus size: 40
1957387 TTTTCCTAAT
* *
1957397 TCGCAATGCGAATACGTAAATCGCAACGCGAATACAT-AAA
1 TCGCAACGCGAATACGTAAATCGCAACGCAAATAC-TGAAA
*
1957437 TCGCAACGCGAATACGTAAATCGCAACGCGAATAC-GTAAA
1 TCGCAACGCGAATACGTAAATCGCAACGCAAATACTG-AAA
* *
1957477 TCGCAACGCGAATACATAAATCGCAACGCAAAT-CTGACTA
1 TCGCAACGCGAATACGTAAATCGCAACGCAAATACTGA-AA
1957517 TCGCAACG
1 TCGCAACG
1957525 AGATTCTGAC
Statistics
Matches: 80, Mismatches: 4, Indels: 8
0.87 0.04 0.09
Matches are distributed among these distances:
39 2 0.03
40 78 0.98
ACGTcount: A:0.40, C:0.26, G:0.18, T:0.16
Consensus pattern (40 bp):
TCGCAACGCGAATACGTAAATCGCAACGCAAATACTGAAA
Found at i:1958450 original size:24 final size:24
Alignment explanation
Indices: 1958423--1958476 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
1958413 GTATTCAAAA
1958423 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
1958447 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
1958471 TTTGAT
1 TTTGAT
1958477 GATTTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:1961097 original size:20 final size:20
Alignment explanation
Indices: 1960965--1961140 Score: 101
Period size: 20 Copynumber: 9.5 Consensus size: 20
1960955 TGAAACTTAA
* *
1960965 AATCGCAACACGAAAATGAA
1 AATCGCAACGCGAAAATGAC
*
1960985 AATCGCAACACGAAAATGAC
1 AATCGCAACGCGAAAATGAC
* * ** *
1961005 TATCGCAACGTGAATTTGAT
1 AATCGCAACGCGAAAATGAC
*
1961025 TATCGCAACGC---AA-G--
1 AATCGCAACGCGAAAATGAC
* *
1961039 AATCACAACGCG-AAATGAA
1 AATCGCAACGCGAAAATGAC
*
1961058 AATCGCAACACGAAAATGAC
1 AATCGCAACGCGAAAATGAC
**
1961078 AATCGCAACGCGAATTTGAC
1 AATCGCAACGCGAAAATGAC
* *
1961098 TATCGTAACGC---AA-G--
1 AATCGCAACGCGAAAATGAC
*
1961112 AATCGCAACGCG-AAATGAA
1 AATCGCAACGCGAAAATGAC
1961131 AATCGCAACG
1 AATCGCAACG
1961141 ACAGAATCGC
Statistics
Matches: 121, Mismatches: 24, Indels: 23
0.72 0.14 0.14
Matches are distributed among these distances:
14 18 0.15
16 6 0.05
17 2 0.02
19 20 0.17
20 75 0.62
ACGTcount: A:0.44, C:0.23, G:0.18, T:0.15
Consensus pattern (20 bp):
AATCGCAACGCGAAAATGAC
Found at i:1961102 original size:73 final size:73
Alignment explanation
Indices: 1960978--1961139 Score: 279
Period size: 73 Copynumber: 2.2 Consensus size: 73
1960968 CGCAACACGA
* * *
1960978 AAATGAAAATCGCAACACGAAAATGACTATCGCAACGTGAATTTGATTATCGCAACGCAAGAATC
1 AAATGAAAATCGCAACACGAAAATGACAATCGCAACGCGAATTTGACTATCGCAACGCAAGAATC
1961043 ACAACGCG
66 ACAACGCG
*
1961051 AAATGAAAATCGCAACACGAAAATGACAATCGCAACGCGAATTTGACTATCGTAACGCAAGAATC
1 AAATGAAAATCGCAACACGAAAATGACAATCGCAACGCGAATTTGACTATCGCAACGCAAGAATC
*
1961116 GCAACGCG
66 ACAACGCG
1961124 AAATGAAAATCGCAAC
1 AAATGAAAATCGCAAC
1961140 GACAGAATCG
Statistics
Matches: 84, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
73 84 1.00
ACGTcount: A:0.44, C:0.22, G:0.18, T:0.16
Consensus pattern (73 bp):
AAATGAAAATCGCAACACGAAAATGACAATCGCAACGCGAATTTGACTATCGCAACGCAAGAATC
ACAACGCG
Found at i:1961121 original size:34 final size:34
Alignment explanation
Indices: 1961006--1961151 Score: 100
Period size: 33 Copynumber: 4.2 Consensus size: 34
1960996 GAAAATGACT
* * *
1961006 ATCGCAACGTGAATTTGATTATCGCAACGCAAGA
1 ATCGCAACGCGAATTTGAATATCGAAACGCAAGA
* * * *
1961040 ATCACAACGCGAA-ATGAAAATCGCAACACGAAAATGACA
1 ATCGCAACGCGAATTTGAATATCG-AA-ACG-CAA-G--A
* *
1961079 ATCGCAACGCGAATTTGACTATCGTAACGCAAGA
1 ATCGCAACGCGAATTTGAATATCGAAACGCAAGA
* * *
1961113 ATCGCAACGCGAA-ATGAAAATCGCAACG-ACAGA
1 ATCGCAACGCGAATTTGAATATCGAAACGCA-AGA
1961146 ATCGCA
1 ATCGCA
1961152 TTGCGATAGT
Statistics
Matches: 87, Mismatches: 17, Indels: 17
0.72 0.14 0.14
Matches are distributed among these distances:
32 1 0.01
33 27 0.31
34 26 0.30
35 3 0.03
36 3 0.03
37 3 0.03
38 3 0.03
39 14 0.16
40 7 0.08
ACGTcount: A:0.42, C:0.23, G:0.19, T:0.16
Consensus pattern (34 bp):
ATCGCAACGCGAATTTGAATATCGAAACGCAAGA
Found at i:1961540 original size:22 final size:22
Alignment explanation
Indices: 1961478--1961543 Score: 96
Period size: 22 Copynumber: 3.0 Consensus size: 22
1961468 TGTCCGTGAA
* *
1961478 TGATTTCGCCGGAGATGGAGAC
1 TGATTTCGTCGGAGATGGGGAC
*
1961500 TGATATCGTCGGAGATGGGGAC
1 TGATTTCGTCGGAGATGGGGAC
*
1961522 TGATTTCGTCAGAGATGGGGAC
1 TGATTTCGTCGGAGATGGGGAC
1961544 GGATGTCACC
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.23, C:0.15, G:0.38, T:0.24
Consensus pattern (22 bp):
TGATTTCGTCGGAGATGGGGAC
Found at i:1961744 original size:20 final size:20
Alignment explanation
Indices: 1961719--1961770 Score: 104
Period size: 20 Copynumber: 2.6 Consensus size: 20
1961709 GCTATGTAAA
1961719 TCGCATTGCGATAGTCAGAT
1 TCGCATTGCGATAGTCAGAT
1961739 TCGCATTGCGATAGTCAGAT
1 TCGCATTGCGATAGTCAGAT
1961759 TCGCATTGCGAT
1 TCGCATTGCGAT
1961771 TTACGTATTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.23, C:0.21, G:0.25, T:0.31
Consensus pattern (20 bp):
TCGCATTGCGATAGTCAGAT
Found at i:1961780 original size:20 final size:20
Alignment explanation
Indices: 1961757--1961806 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
1961747 CGATAGTCAG
1961757 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
*
1961777 ATTCGCATTGCGATTTACTT
1 ATTCGCATTGCGATTTACGT
*
1961797 ATTCGAATTG
1 ATTCGCATTG
1961807 TGAATTAGGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.22, C:0.18, G:0.18, T:0.42
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:1961838 original size:21 final size:21
Alignment explanation
Indices: 1961808--1961851 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
1961798 TTCGAATTGT
*
1961808 GAATTAGGAAAATTGCAACGC
1 GAATTAGGAAAATCGCAACGC
* *
1961829 GAATTTGGAAAATCGCAATGC
1 GAATTAGGAAAATCGCAACGC
1961850 GA
1 GA
1961852 TAGTCAGAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.41, C:0.14, G:0.25, T:0.20
Consensus pattern (21 bp):
GAATTAGGAAAATCGCAACGC
Found at i:1962303 original size:31 final size:31
Alignment explanation
Indices: 1962260--1962319 Score: 95
Period size: 31 Copynumber: 1.9 Consensus size: 31
1962250 AACTTAAAAG
*
1962260 AGTTTTGAAATACTGAGATTTAAATAATTTT
1 AGTTTTGAAATACTGAAATTTAAATAATTTT
1962291 AGTTTT-ACAATACTGAAATTTAAATAATT
1 AGTTTTGA-AATACTGAAATTTAAATAATT
1962320 CATACAACTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 1 0.04
31 26 0.96
ACGTcount: A:0.42, C:0.05, G:0.10, T:0.43
Consensus pattern (31 bp):
AGTTTTGAAATACTGAAATTTAAATAATTTT
Found at i:1962824 original size:20 final size:20
Alignment explanation
Indices: 1962776--1962837 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 20
1962766 AACTTAAATC
*
1962776 AAAATAATTAAAATAA-ATAT
1 AAAATAATT-TAATAATATAT
1962796 AAAAT--TTTAATAATATAT
1 AAAATAATTTAATAATATAT
1962814 AAAATAATTT-AT-ATGATAT
1 AAAATAATTTAATAAT-ATAT
1962833 AAAAT
1 AAAAT
1962838 TAAATATCTA
Statistics
Matches: 37, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
17 5 0.14
18 13 0.35
19 11 0.30
20 8 0.22
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (20 bp):
AAAATAATTTAATAATATAT
Found at i:1962931 original size:12 final size:12
Alignment explanation
Indices: 1962886--1962936 Score: 52
Period size: 12 Copynumber: 4.3 Consensus size: 12
1962876 ATTTATTTAA
* *
1962886 AAAATTAATTTT
1 AAAATTAAATAT
1962898 AAAATTAAA-AT
1 AAAATTAAATAT
*
1962909 CAAA-TATAATAT
1 AAAATTA-AATAT
1962921 AAAATTAAATAT
1 AAAATTAAATAT
1962933 AAAA
1 AAAA
1962937 CCTCTTTGAA
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
10 2 0.06
11 6 0.19
12 22 0.69
13 2 0.06
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (12 bp):
AAAATTAAATAT
Found at i:1963347 original size:23 final size:23
Alignment explanation
Indices: 1963314--1963376 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
1963304 AATGATTCAG
*
1963314 TGCTGACTGATTCAGCAAAACAA
1 TGCTGAATGATTCAGCAAAACAA
* * *
1963337 TGCTGATTGATTAAGCAAAACAG
1 TGCTGAATGATTCAGCAAAACAA
1963360 TGCTGAATGATTCAGCA
1 TGCTGAATGATTCAGCA
1963377 CAAAAGTACA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.37, C:0.17, G:0.21, T:0.25
Consensus pattern (23 bp):
TGCTGAATGATTCAGCAAAACAA
Found at i:1974746 original size:20 final size:20
Alignment explanation
Indices: 1974721--1974799 Score: 122
Period size: 20 Copynumber: 4.0 Consensus size: 20
1974711 AATGCGAGTA
*
1974721 TGACTATCGCAACGAGATTC
1 TGACTATCGCAACGCGATTC
1974741 TGACTATCGCAACGCGATTC
1 TGACTATCGCAACGCGATTC
* *
1974761 TGACTGTCGCAACGCGATGC
1 TGACTATCGCAACGCGATTC
*
1974781 TGACTATCGCAATGCGATT
1 TGACTATCGCAACGCGATT
1974800 TTCAAAGCGC
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 53 1.00
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (20 bp):
TGACTATCGCAACGCGATTC
Found at i:1975015 original size:22 final size:22
Alignment explanation
Indices: 1974975--1975016 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
1974965 GCGACATCCA
*
1974975 TCCCCATCTCCGACGAAATCAG
1 TCCCCATCTCCGACAAAATCAG
*
1974997 TCCCCATCTCCGGCAAAATC
1 TCCCCATCTCCGACAAAATC
1975017 CGTCTATCTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.26, C:0.43, G:0.12, T:0.19
Consensus pattern (22 bp):
TCCCCATCTCCGACAAAATCAG
Found at i:1975461 original size:20 final size:20
Alignment explanation
Indices: 1975436--1975484 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
1975426 TTTTATTTCA
1975436 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
**
1975456 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAAATTCG
*
1975476 TGTTGCGAT
1 CGTTGCGAT
1975485 TTTAAGTTTC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.18, C:0.18, G:0.27, T:0.37
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:1977238 original size:18 final size:18
Alignment explanation
Indices: 1977215--1977264 Score: 100
Period size: 18 Copynumber: 2.8 Consensus size: 18
1977205 TTTACTCGTA
1977215 ATTTCACTTAGATTAACC
1 ATTTCACTTAGATTAACC
1977233 ATTTCACTTAGATTAACC
1 ATTTCACTTAGATTAACC
1977251 ATTTCACTTAGATT
1 ATTTCACTTAGATT
1977265 GCTTAGTAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.32, C:0.20, G:0.06, T:0.42
Consensus pattern (18 bp):
ATTTCACTTAGATTAACC
Found at i:1977435 original size:20 final size:20
Alignment explanation
Indices: 1977410--1977450 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
1977400 AATAGTTTAC
1977410 TTTCGCGTTGCGATAGTCAT
1 TTTCGCGTTGCGATAGTCAT
*
1977430 TTTCGCGTTGCGTTAGTCAT
1 TTTCGCGTTGCGATAGTCAT
1977450 T
1 T
1977451 CGTGTTCGAT
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:0.12, C:0.20, G:0.24, T:0.44
Consensus pattern (20 bp):
TTTCGCGTTGCGATAGTCAT
Found at i:1979437 original size:14 final size:14
Alignment explanation
Indices: 1979403--1979464 Score: 52
Period size: 14 Copynumber: 4.3 Consensus size: 14
1979393 TTGCTTGTTT
*
1979403 AATTGATTTATAAA
1 AATTGATTTGTAAA
*
1979417 AACTGATTTGTAAA
1 AATTGATTTGTAAA
* *
1979431 AGTTGATTTGTTTAA
1 AATTGATTTG-TAAA
* *
1979446 TATTGATGTGTAAA
1 AATTGATTTGTAAA
1979460 TAATT
1 -AATT
1979465 CTTATTTGTG
Statistics
Matches: 36, Mismatches: 10, Indels: 3
0.73 0.20 0.06
Matches are distributed among these distances:
14 23 0.64
15 13 0.36
ACGTcount: A:0.39, C:0.02, G:0.15, T:0.45
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:1979608 original size:20 final size:19
Alignment explanation
Indices: 1979579--1979616 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
1979569 CGCTAAACTC
*
1979579 AAAATCGCAATGCGAAAGA
1 AAAATCGCAACGCGAAAGA
1979598 AAAATTCGCAACGCGAAAG
1 AAAA-TCGCAACGCGAAAG
1979617 TCAATTCGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.50, C:0.18, G:0.21, T:0.11
Consensus pattern (19 bp):
AAAATCGCAACGCGAAAGA
Found at i:1979688 original size:20 final size:20
Alignment explanation
Indices: 1979659--1979727 Score: 75
Period size: 20 Copynumber: 3.5 Consensus size: 20
1979649 GCGATTTTCT
* * * *
1979659 CGTTGGGATAGTCAAATACC
1 CGTTGCGATAATCAAATTCG
1979679 CGTTGCGATAATCAAATTCG
1 CGTTGCGATAATCAAATTCG
* * *
1979699 CGTTACGATACTTAAATTCG
1 CGTTGCGATAATCAAATTCG
1979719 CGTTGCGAT
1 CGTTGCGAT
1979728 TTTCTCGTTG
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.28, C:0.20, G:0.22, T:0.30
Consensus pattern (20 bp):
CGTTGCGATAATCAAATTCG
Found at i:1979827 original size:20 final size:20
Alignment explanation
Indices: 1979800--1979911 Score: 101
Period size: 20 Copynumber: 5.9 Consensus size: 20
1979790 TGCGATTTTT
*
1979800 GCGTTGCGATAGTCATATTC
1 GCGTTGCGATAGTCAAATTC
* *
1979820 GTGTTGCGATAGTCAAATAC
1 GCGTTGCGATAGTCAAATTC
* *
1979840 GCGTTGC-A-A-T---TTTT
1 GCGTTGCGATAGTCAAATTC
* *
1979854 GAGTTGCGATAATCAAATTC
1 GCGTTGCGATAGTCAAATTC
*
1979874 GTGTTGCGATAGTCAAATTC
1 GCGTTGCGATAGTCAAATTC
*
1979894 GCGTTGCGATATTCAAAT
1 GCGTTGCGATAGTCAAAT
1979912 GAATGTGTAA
Statistics
Matches: 72, Mismatches: 14, Indels: 12
0.73 0.14 0.12
Matches are distributed among these distances:
14 7 0.10
15 1 0.01
16 1 0.01
17 2 0.03
18 1 0.01
19 1 0.01
20 59 0.82
ACGTcount: A:0.26, C:0.16, G:0.23, T:0.35
Consensus pattern (20 bp):
GCGTTGCGATAGTCAAATTC
Found at i:1979829 original size:34 final size:33
Alignment explanation
Indices: 1979627--1979814 Score: 162
Period size: 34 Copynumber: 5.4 Consensus size: 33
1979617 TCAATTCGCA
* *
1979627 TTGCGATAGTCTAATATGCTTTGCGATTTTCTCG
1 TTGCGATAGTCAAATA-GCGTTGCGATTTTCTCG
* * *
1979661 TTGGGATAGTCAAATACCCGTTGCGATAATCAAATTCGCG
1 TTGCGATAGTCAAATA-GCGTTGCGAT--T----TTCTCG
* * * *
1979701 TTACGATACTTAAATTCGCGTTGCGATTTTCTCG
1 TTGCGATAGTCAAA-TAGCGTTGCGATTTTCTCG
*
1979735 TTGCAATAGTCAAATAGCCGTTGCGATTTTCTCG
1 TTGCGATAGTCAAATAG-CGTTGCGATTTTCTCG
*
1979769 TTGCGATAGTCAAATAGTCATTGCGATTTT-TGCG
1 TTGCGATAGTCAAATAG-CGTTGCGATTTTCT-CG
1979803 TTGCGATAGTCA
1 TTGCGATAGTCA
1979815 TATTCGTGTT
Statistics
Matches: 124, Mismatches: 21, Indels: 18
0.76 0.13 0.11
Matches are distributed among these distances:
33 3 0.02
34 94 0.76
36 1 0.01
38 1 0.01
40 24 0.19
41 1 0.01
ACGTcount: A:0.23, C:0.19, G:0.21, T:0.37
Consensus pattern (33 bp):
TTGCGATAGTCAAATAGCGTTGCGATTTTCTCG
Found at i:1979852 original size:54 final size:54
Alignment explanation
Indices: 1979768--1979900 Score: 196
Period size: 54 Copynumber: 2.5 Consensus size: 54
1979758 CGATTTTCTC
* * * * *
1979768 GTTGCGATAGTCAAATA-GTCATTGCGATTTTTGCGTTGCGATAGTCATATTCGT
1 GTTGCGATAGTCAAATACG-CGTTGCAATTTTTGAGTTGCGATAATCAAATTCGT
1979822 GTTGCGATAGTCAAATACGCGTTGCAATTTTTGAGTTGCGATAATCAAATTCGT
1 GTTGCGATAGTCAAATACGCGTTGCAATTTTTGAGTTGCGATAATCAAATTCGT
*
1979876 GTTGCGATAGTCAAATTCGCGTTGC
1 GTTGCGATAGTCAAATACGCGTTGC
1979901 GATATTCAAA
Statistics
Matches: 72, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
54 71 0.99
55 1 0.01
ACGTcount: A:0.24, C:0.16, G:0.24, T:0.36
Consensus pattern (54 bp):
GTTGCGATAGTCAAATACGCGTTGCAATTTTTGAGTTGCGATAATCAAATTCGT
Found at i:1980138 original size:140 final size:140
Alignment explanation
Indices: 1979884--1980151 Score: 473
Period size: 140 Copynumber: 1.9 Consensus size: 140
1979874 GTGTTGCGAT
* * *
1979884 AGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAATATATCATA
1 AGTCAAATTCGCGTTGCAATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCATA
1979949 GCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATATTAAAAGTTTACACATAAAA
66 GCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATATTAAAAGTTTACACATAAAA
1980014 TACACATAAC
131 TACACATAAC
*
1980024 AGTCAAATTCGCGTTGTAATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCATA
1 AGTCAAATTCGCGTTGCAATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCATA
** *
1980089 GTGATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
66 GCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATATTAAAAGTTTACACATAA
1980152 TACAACGTTT
Statistics
Matches: 121, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
140 121 1.00
ACGTcount: A:0.43, C:0.15, G:0.13, T:0.29
Consensus pattern (140 bp):
AGTCAAATTCGCGTTGCAATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCATA
GCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATATTAAAAGTTTACACATAAAA
TACACATAAC
Found at i:1982300 original size:14 final size:14
Alignment explanation
Indices: 1982281--1982317 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1982271 TCCCGTGGCA
1982281 TTTTCTTCGGGGAC
1 TTTTCTTCGGGGAC
*
1982295 TTTTCTTCGGGGAT
1 TTTTCTTCGGGGAC
1982309 TTCTTCTTC
1 TT-TTCTTC
1982318 TTCTTTTTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 15 0.71
15 6 0.29
ACGTcount: A:0.05, C:0.22, G:0.22, T:0.51
Consensus pattern (14 bp):
TTTTCTTCGGGGAC
Found at i:1983387 original size:20 final size:21
Alignment explanation
Indices: 1983362--1983429 Score: 97
Period size: 20 Copynumber: 3.4 Consensus size: 21
1983352 GAAATTCGGT
*
1983362 GTTGCGACAGTCAGAATCG-A
1 GTTGCGATAGTCAGAATCGCA
1983382 GTTGCGATAGTCAGAATCGCA
1 GTTGCGATAGTCAGAATCGCA
*
1983403 -TTGCGATAGTCATAATCGCA
1 GTTGCGATAGTCAGAATCGCA
1983423 -TTGCGAT
1 GTTGCGAT
1983430 TTACATATTC
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
20 44 0.98
21 1 0.02
ACGTcount: A:0.28, C:0.19, G:0.26, T:0.26
Consensus pattern (21 bp):
GTTGCGATAGTCAGAATCGCA
Found at i:1983436 original size:20 final size:20
Alignment explanation
Indices: 1983396--1983469 Score: 96
Period size: 20 Copynumber: 3.7 Consensus size: 20
1983386 CGATAGTCAG
*
1983396 AATCGCATTGCGATAGT-CAT
1 AATCGCATTGCGAT-TTACAT
1983416 AATCGCATTGCGATTTACAT
1 AATCGCATTGCGATTTACAT
* *
1983436 ATTCTCATTGCGATTTACAT
1 AATCGCATTGCGATTTACAT
*
1983456 ATTCGCATTGCGAT
1 AATCGCATTGCGAT
1983470 AGTCGGAAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
19 1 0.02
20 48 0.98
ACGTcount: A:0.27, C:0.20, G:0.16, T:0.36
Consensus pattern (20 bp):
AATCGCATTGCGATTTACAT
Found at i:1985391 original size:63 final size:62
Alignment explanation
Indices: 1985284--1985405 Score: 151
Period size: 63 Copynumber: 2.0 Consensus size: 62
1985274 TAATAATATC
* * *
1985284 TTTTAATTTAAAATATTTAAAAGATATAAACTCCTTTTACTATTCAAACTTAAATAGATATTA
1 TTTTAATTTAAAATATTCAAAAGATATAAACTCCTTTTAATATTCAAA-GTAAATAGATATTA
*
1985347 TTTTAATTTGAAATATTCAAAAGTATATAATTA-T-C-TTTAATATTCAAAGTAAATAGATA
1 TTTTAATTTAAAATATTCAAAAG-ATATAA--ACTCCTTTTAATATTCAAAGTAAATAGATA
1985406 ATAAATATAT
Statistics
Matches: 52, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
62 10 0.19
63 33 0.63
64 7 0.13
65 1 0.02
66 1 0.02
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.43
Consensus pattern (62 bp):
TTTTAATTTAAAATATTCAAAAGATATAAACTCCTTTTAATATTCAAAGTAAATAGATATTA
Found at i:1994666 original size:18 final size:18
Alignment explanation
Indices: 1994643--1994685 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
1994633 TCTTAAATTA
*
1994643 TTTATTTAATTATTTTCT
1 TTTATTTAATTATTATCT
*
1994661 TTTATTTAATTCTTATCT
1 TTTATTTAATTATTATCT
1994679 TTTATTT
1 TTTATTT
1994686 TAAAAATAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.21, C:0.07, G:0.00, T:0.72
Consensus pattern (18 bp):
TTTATTTAATTATTATCT
Found at i:1998969 original size:18 final size:18
Alignment explanation
Indices: 1998931--1998969 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
1998921 CTTTAAATTG
*
1998931 TTTATTTAATTATCATTT
1 TTTATTTAATTATCATCT
* *
1998949 TTTATTTAATTCTTATCT
1 TTTATTTAATTATCATCT
1998967 TTT
1 TTT
1998970 CTTTTAAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.23, C:0.08, G:0.00, T:0.69
Consensus pattern (18 bp):
TTTATTTAATTATCATCT
Found at i:1999204 original size:41 final size:41
Alignment explanation
Indices: 1999147--1999233 Score: 174
Period size: 41 Copynumber: 2.1 Consensus size: 41
1999137 TTTAAGAAGC
1999147 CAAAATTATTTTGACAGTAAAACGACACCTGTTAATGCTTT
1 CAAAATTATTTTGACAGTAAAACGACACCTGTTAATGCTTT
1999188 CAAAATTATTTTGACAGTAAAACGACACCTGTTAATGCTTT
1 CAAAATTATTTTGACAGTAAAACGACACCTGTTAATGCTTT
1999229 CAAAA
1 CAAAA
1999234 CATGAAAACT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 46 1.00
ACGTcount: A:0.39, C:0.17, G:0.11, T:0.32
Consensus pattern (41 bp):
CAAAATTATTTTGACAGTAAAACGACACCTGTTAATGCTTT
Found at i:2001119 original size:26 final size:26
Alignment explanation
Indices: 2001090--2001145 Score: 103
Period size: 26 Copynumber: 2.2 Consensus size: 26
2001080 ACCAATTCTT
2001090 TTAAAAGTTCTATCCAAAATTTTTCA
1 TTAAAAGTTCTATCCAAAATTTTTCA
*
2001116 TTAAAAGTTCTATCCAAATTTTTTCA
1 TTAAAAGTTCTATCCAAAATTTTTCA
2001142 TTAA
1 TTAA
2001146 GGTAATTTCA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.38, C:0.14, G:0.04, T:0.45
Consensus pattern (26 bp):
TTAAAAGTTCTATCCAAAATTTTTCA
Found at i:2003992 original size:32 final size:32
Alignment explanation
Indices: 2003956--2004019 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
2003946 CCATACTAAG
2003956 TGTAAACAAGCTGCAAGTAAATACTTGACGCC
1 TGTAAACAAGCTGCAAGTAAATACTTGACGCC
2003988 TGTAAACAAGCTGCAAGTAAATACTTGACGCC
1 TGTAAACAAGCTGCAAGTAAATACTTGACGCC
2004020 AGACAGAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.38, C:0.22, G:0.19, T:0.22
Consensus pattern (32 bp):
TGTAAACAAGCTGCAAGTAAATACTTGACGCC
Found at i:2011085 original size:42 final size:41
Alignment explanation
Indices: 2011007--2011294 Score: 186
Period size: 41 Copynumber: 7.0 Consensus size: 41
2010997 GCAATTGCGG
* * * *
2011007 TGTTTGGTATTAAATTTCCAATAAAGTAC-ACTTCTATAACGA
1 TGTTT-GTATTAAAATTCCACTAAAGTACGA-GTCTATAGCGA
* * *
2011049 TGTTTGTTATTAAAATTCCACTAAAGTATGAGTCTATATCGG
1 TGTTTG-TATTAAAATTCCACTAAAGTACGAGTCTATAGCGA
* ** ** *
2011091 CGTTTGTAACAAAACACCACTAAAGTACGAGTCTATAGCGG
1 TGTTTGTATTAAAATTCCACTAAAGTACGAGTCTATAGCGA
* * ** * *
2011132 TGTTTGTGTAAAAACACCACAAAAGTATGAGTCTATAGCGA
1 TGTTTGTATTAAAATTCCACTAAAGTACGAGTCTATAGCGA
* * *
2011173 CGTTTGT-GTAAAATTACCACTAAAGTACGAGTCTATAG-AA
1 TGTTTGTATTAAAATT-CCACTAAAGTACGAGTCTATAGCGA
* * ** * * *
2011213 GCGTTTGTATAAAAACACCACAAAAGTACGAGTATATAGTGA
1 -TGTTTGTATTAAAATTCCACTAAAGTACGAGTCTATAGCGA
** * ** * *
2011255 CATTTGTATAAAAACGCCACTAAAGTACTAGTTTATAGCG
1 TGTTTGTATTAAAATTCCACTAAAGTACGAGTCTATAGCG
2011295 GCGCTTATAT
Statistics
Matches: 199, Mismatches: 41, Indels: 13
0.79 0.16 0.05
Matches are distributed among these distances:
40 5 0.03
41 151 0.76
42 42 0.21
43 1 0.01
ACGTcount: A:0.37, C:0.16, G:0.17, T:0.30
Consensus pattern (41 bp):
TGTTTGTATTAAAATTCCACTAAAGTACGAGTCTATAGCGA
Found at i:2011261 original size:123 final size:122
Alignment explanation
Indices: 2011059--2011294 Score: 305
Period size: 123 Copynumber: 1.9 Consensus size: 122
2011049 TGTTTGTTAT
* *** * *
2011059 TAAAATTCCACTAAAGTATGAGTCTATATCGGCGTTTGTAACAAAACACCACTAAAGTACGAGTC
1 TAAAATTCCACTAAAGTACGAGTCTATAGAAGCGTTTGTAACAAAACACCACAAAAGTACGAGTA
*** *
2011124 TATAGCGGTGTTTGTGTAAAAACACCACAAAAGTA-TGAGTCTATAGCGACGTTTGTG
66 TATAGCGACATTTGTATAAAAACACCACAAAAGTACT-AGTCTATAGCGACGTTTGTG
2011181 TAAAATTACCACTAAAGTACGAGTCTATAGAAGCGTTTGTATA-AAAACACCACAAAAGTACGAG
1 TAAAATT-CCACTAAAGTACGAGTCTATAGAAGCGTTTGTA-ACAAAACACCACAAAAGTACGAG
* * * *
2011245 TATATAGTGACATTTGTATAAAAACGCCACTAAAGTACTAGTTTATAGCG
64 TATATAGCGACATTTGTATAAAAACACCACAAAAGTACTAGTCTATAGCG
2011295 GCGCTTATAT
Statistics
Matches: 97, Mismatches: 14, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
122 7 0.07
123 88 0.91
124 2 0.02
ACGTcount: A:0.39, C:0.17, G:0.18, T:0.27
Consensus pattern (122 bp):
TAAAATTCCACTAAAGTACGAGTCTATAGAAGCGTTTGTAACAAAACACCACAAAAGTACGAGTA
TATAGCGACATTTGTATAAAAACACCACAAAAGTACTAGTCTATAGCGACGTTTGTG
Found at i:2011317 original size:41 final size:41
Alignment explanation
Indices: 2011066--2011309 Score: 274
Period size: 41 Copynumber: 6.0 Consensus size: 41
2011056 TATTAAAATT
* *
2011066 CCACTAAAGTATGAGTCTATATCGGCGTTTGTA-ACAAAACA
1 CCACTAAAGTACGAGTCTATAGCGGCGTTTGTATA-AAAACA
* *
2011107 CCACTAAAGTACGAGTCTATAGCGGTGTTTGTGTAAAAACA
1 CCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAAAAACA
* * * * **
2011148 CCACAAAAGTATGAGTCTATAGCGACGTTTGTGTAAAATTA
1 CCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAAAAACA
**
2011189 CCACTAAAGTACGAGTCTATAGAAGCGTTTGTATAAAAACA
1 CCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAAAAACA
* * * * * *
2011230 CCACAAAAGTACGAGTATATAGTGACATTTGTATAAAAACG
1 CCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAAAAACA
* * * *
2011271 CCACTAAAGTACTAGTTTATAGCGGCGCTTATATAAAAA
1 CCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAAAAA
2011310 TGCCACTACA
Statistics
Matches: 169, Mismatches: 33, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
41 168 0.99
42 1 0.01
ACGTcount: A:0.39, C:0.17, G:0.18, T:0.27
Consensus pattern (41 bp):
CCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAAAAACA
Found at i:2012465 original size:17 final size:17
Alignment explanation
Indices: 2012443--2012475 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2012433 TCATTAAAGC
2012443 TAGTTCACTAATTAAAT
1 TAGTTCACTAATTAAAT
*
2012460 TAGTTCATTAATTAAA
1 TAGTTCACTAATTAAA
2012476 CTATCTCTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.42, C:0.09, G:0.06, T:0.42
Consensus pattern (17 bp):
TAGTTCACTAATTAAAT
Found at i:2020433 original size:22 final size:22
Alignment explanation
Indices: 2020408--2020458 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
2020398 TTAGTACTTA
2020408 AGAATAGACCCCAAGTATATCT
1 AGAATAGACCCCAAGTATATCT
*
2020430 AGAATAGACCCTAAGTATATCT
1 AGAATAGACCCCAAGTATATCT
2020452 AGAATAG
1 AGAATAG
2020459 TCATCTACCA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.43, C:0.18, G:0.16, T:0.24
Consensus pattern (22 bp):
AGAATAGACCCCAAGTATATCT
Found at i:2023617 original size:20 final size:20
Alignment explanation
Indices: 2023592--2023630 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
2023582 ATCTTTTACT
2023592 TGTTCATGAATTTACATGAG
1 TGTTCATGAATTTACATGAG
*
2023612 TGTTCATGAATTTGCATGA
1 TGTTCATGAATTTACATGA
2023631 TATTAAGCTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.21, T:0.41
Consensus pattern (20 bp):
TGTTCATGAATTTACATGAG
Found at i:2023766 original size:17 final size:17
Alignment explanation
Indices: 2023730--2023781 Score: 70
Period size: 17 Copynumber: 3.0 Consensus size: 17
2023720 AGTACCATCT
2023730 TTCATTCAA-TAAAGCTAG
1 TTCATT-AATTAAA-CTAG
*
2023748 TTCCTTAATTAAACTAG
1 TTCATTAATTAAACTAG
2023765 TTCATTAATTAAACTAG
1 TTCATTAATTAAACTAG
2023782 CTCTTTATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
17 22 0.71
18 9 0.29
ACGTcount: A:0.38, C:0.15, G:0.08, T:0.38
Consensus pattern (17 bp):
TTCATTAATTAAACTAG
Found at i:2026783 original size:17 final size:17
Alignment explanation
Indices: 2026747--2026815 Score: 68
Period size: 18 Copynumber: 3.9 Consensus size: 17
2026737 AGTATCCTCT
2026747 TTCATTCAA-TAAAGCTAG
1 TTCATT-AATTAAA-CTAG
*
2026765 TTCACTAATTAAACTAG
1 TTCATTAATTAAACTAG
* * *
2026782 TTCATTCATTTATACTGG
1 TTCATT-AATTAAACTAG
2026800 TTCATTAATTAAACTA
1 TTCATTAATTAAACTA
2026816 ACTCTTTATA
Statistics
Matches: 41, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
17 18 0.44
18 23 0.56
ACGTcount: A:0.36, C:0.16, G:0.07, T:0.41
Consensus pattern (17 bp):
TTCATTAATTAAACTAG
Found at i:2028089 original size:9 final size:9
Alignment explanation
Indices: 2028075--2028099 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
2028065 ATTACCACTA
2028075 CACTTTCTC
1 CACTTTCTC
2028084 CACTTTCTC
1 CACTTTCTC
2028093 CACTTTC
1 CACTTTC
2028100 CTTCATTTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.12, C:0.44, G:0.00, T:0.44
Consensus pattern (9 bp):
CACTTTCTC
Found at i:2030079 original size:17 final size:17
Alignment explanation
Indices: 2030052--2030094 Score: 77
Period size: 17 Copynumber: 2.5 Consensus size: 17
2030042 TTTCATTCAA
2030052 TAAAGCTAGTTCACTAAT
1 TAAA-CTAGTTCACTAAT
2030070 TAAACTAGTTCACTAAT
1 TAAACTAGTTCACTAAT
2030087 TAAACTAG
1 TAAACTAG
2030095 CTCTTTATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 21 0.84
18 4 0.16
ACGTcount: A:0.42, C:0.16, G:0.09, T:0.33
Consensus pattern (17 bp):
TAAACTAGTTCACTAAT
Found at i:2031494 original size:20 final size:20
Alignment explanation
Indices: 2031469--2031520 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
2031459 TGATGAAGGG
2031469 TGATGAAGATGGGATTGATT
1 TGATGAAGATGGGATTGATT
* *
2031489 TGATGAAG-TGAAGATTGGTT
1 TGATGAAGATG-GGATTGATT
*
2031509 TGATGATGATGG
1 TGATGAAGATGG
2031521 TCGTGGGTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
19 2 0.08
20 22 0.85
21 2 0.08
ACGTcount: A:0.29, C:0.00, G:0.37, T:0.35
Consensus pattern (20 bp):
TGATGAAGATGGGATTGATT
Found at i:2037908 original size:30 final size:30
Alignment explanation
Indices: 2037872--2037979 Score: 94
Period size: 30 Copynumber: 3.5 Consensus size: 30
2037862 ACCTATACTT
*
2037872 TTCACTTTATTCATTTCATAGCATGCTCCA
1 TTCACTTTATTCATTTCATAGCATGATCCA
* * * *
2037902 TTCACTTCATTTATTTCATAGCATTATTCA
1 TTCACTTTATTCATTTCATAGCATGATCCA
* *
2037932 TTCA-TTTAATTCATTTCGTAGCTTGTAT-CA
1 TTCACTTT-ATTCATTTCATAGCATG-ATCCA
*
2037962 TTCGCTTTCATATCATTT
1 TTCACTTT-AT-TCATTT
2037980 ACTATTGATT
Statistics
Matches: 62, Mismatches: 12, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
29 2 0.03
30 47 0.76
31 7 0.11
32 6 0.10
ACGTcount: A:0.23, C:0.21, G:0.06, T:0.49
Consensus pattern (30 bp):
TTCACTTTATTCATTTCATAGCATGATCCA
Found at i:2038126 original size:48 final size:48
Alignment explanation
Indices: 2038074--2038433 Score: 477
Period size: 48 Copynumber: 7.5 Consensus size: 48
2038064 CACCATTGTT
* *
2038074 ACACAGACGCCAAACGTGCTAATTATCATCAATAGTAGCACCACCGTC
1 ACACAGACGTCAAACATGCTAATTATCATCAATAGTAGCACCACCGTC
* **
2038122 ACACAGACGTCAGACATGCTAATTATCATCAATAGTAGCACCATTGTC
1 ACACAGACGTCAAACATGCTAATTATCATCAATAGTAGCACCACCGTC
*
2038170 ACACAGACGTCAAACTTGCTAATTATCATCAATAGTAGCACCACCGTC
1 ACACAGACGTCAAACATGCTAATTATCATCAATAGTAGCACCACCGTC
* * * **
2038218 ACACAAACGTCAGACGTGCTAATTATCATCAATAGTAGCACCATTGTC
1 ACACAGACGTCAAACATGCTAATTATCATCAATAGTAGCACCACCGTC
* * * *
2038266 ACACAGACGTCAGACGTGCTAATTATCATCAATAGTAGTACCACCATC
1 ACACAGACGTCAAACATGCTAATTATCATCAATAGTAGCACCACCGTC
* *
2038314 ACACAGACGTCAAACTTGCTAATTATCATCAATAGTAGCACCACCGTA
1 ACACAGACGTCAAACATGCTAATTATCATCAATAGTAGCACCACCGTC
** * ** * * *
2038362 ACATTGACGTCAGACATTATAACTATCATAAATAGTAGCACCACTGTC
1 ACACAGACGTCAAACATGCTAATTATCATCAATAGTAGCACCACCGTC
* *
2038410 AGAAAGACGTCAAACATGCTAATT
1 ACACAGACGTCAAACATGCTAATT
2038434 GATCCACCTT
Statistics
Matches: 271, Mismatches: 41, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
48 271 1.00
ACGTcount: A:0.37, C:0.26, G:0.14, T:0.23
Consensus pattern (48 bp):
ACACAGACGTCAAACATGCTAATTATCATCAATAGTAGCACCACCGTC
Found at i:2038633 original size:27 final size:26
Alignment explanation
Indices: 2038598--2038648 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 26
2038588 ACATATCATT
*
2038598 TATATAAAAGTAT-TTATAAATATGAA
1 TATATAAAA-TATAATATAAATATGAA
2038624 TATATCAAAATATAATATAAATATG
1 TATAT-AAAATATAATATAAATATG
2038649 CATTGGGCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 8 0.36
27 14 0.64
ACGTcount: A:0.55, C:0.02, G:0.06, T:0.37
Consensus pattern (26 bp):
TATATAAAATATAATATAAATATGAA
Found at i:2045694 original size:21 final size:21
Alignment explanation
Indices: 2045668--2045734 Score: 80
Period size: 21 Copynumber: 3.2 Consensus size: 21
2045658 GAAGTAGTGG
* *
2045668 AAGTAGATAAATTACCTTGGT
1 AAGTAGATGAAGTACCTTGGT
* *
2045689 AAGTAGATGAAGTACCCTAGT
1 AAGTAGATGAAGTACCTTGGT
* *
2045710 AAATAGGTGAAGTACCTTGGT
1 AAGTAGATGAAGTACCTTGGT
2045731 AAGT
1 AAGT
2045735 GTCTCTGAAA
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.37, C:0.10, G:0.24, T:0.28
Consensus pattern (21 bp):
AAGTAGATGAAGTACCTTGGT
Found at i:2049155 original size:17 final size:18
Alignment explanation
Indices: 2049133--2049166 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2049123 GAAAAATAAT
2049133 ATAAA-TAAACAATAAAA
1 ATAAATTAAACAATAAAA
*
2049150 ATAAATTAAACATTAAA
1 ATAAATTAAACAATAAA
2049167 TATTGTTGCC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.24
Consensus pattern (18 bp):
ATAAATTAAACAATAAAA
Found at i:2050126 original size:24 final size:24
Alignment explanation
Indices: 2050097--2050145 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
2050087 ATAAAAGTTC
* *
2050097 TCTCTTTTTTTAAGTTTTTATTTT
1 TCTCTTATTTTAACTTTTTATTTT
*
2050121 TCTCTTATTTTAACTTTTTGTTTT
1 TCTCTTATTTTAACTTTTTATTTT
2050145 T
1 T
2050146 TTAAAAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.12, C:0.10, G:0.04, T:0.73
Consensus pattern (24 bp):
TCTCTTATTTTAACTTTTTATTTT
Found at i:2051122 original size:12 final size:12
Alignment explanation
Indices: 2051098--2051132 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
2051088 ATGAGAAAAC
*
2051098 AATCAAATCCAT
1 AATCAAATTCAT
*
2051110 AATCGAATTCAT
1 AATCAAATTCAT
2051122 AATCAAATTCA
1 AATCAAATTCA
2051133 GGTGAATTTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.49, C:0.20, G:0.03, T:0.29
Consensus pattern (12 bp):
AATCAAATTCAT
Found at i:2056835 original size:20 final size:20
Alignment explanation
Indices: 2056806--2056847 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
2056796 ATTCCTCCAC
*
2056806 ATGCAACTATATGCTCCTAA
1 ATGCAACTATATGATCCTAA
*
2056826 ATGCATCTATATGATCCTAA
1 ATGCAACTATATGATCCTAA
2056846 AT
1 AT
2056848 CAGCTTTTAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.36, C:0.21, G:0.10, T:0.33
Consensus pattern (20 bp):
ATGCAACTATATGATCCTAA
Found at i:2062216 original size:18 final size:18
Alignment explanation
Indices: 2062195--2062231 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
2062185 TTTTCCCCCA
2062195 CTAAATCGCATTCCCATG
1 CTAAATCGCATTCCCATG
2062213 CTAAATCGCATTCCCATG
1 CTAAATCGCATTCCCATG
2062231 C
1 C
2062232 ATTTTCCCCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.27, C:0.35, G:0.11, T:0.27
Consensus pattern (18 bp):
CTAAATCGCATTCCCATG
Found at i:2072272 original size:14 final size:14
Alignment explanation
Indices: 2072253--2072292 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
2072243 AATTTGAAGT
2072253 AATCCCTGCA-AATA
1 AATCCCTGCATAA-A
2072267 AATCCCTGCATAAA
1 AATCCCTGCATAAA
*
2072281 AATCTCTGCATA
1 AATCCCTGCATA
2072293 TAGACAGAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 22 0.92
15 2 0.08
ACGTcount: A:0.40, C:0.28, G:0.07, T:0.25
Consensus pattern (14 bp):
AATCCCTGCATAAA
Found at i:2077442 original size:24 final size:23
Alignment explanation
Indices: 2077380--2077455 Score: 93
Period size: 24 Copynumber: 3.3 Consensus size: 23
2077370 CACCGAAGTT
* *
2077380 CCACATAA-TTT-TCCTGAAGAA
1 CCACATAAGTTTGTCCCGAAGGA
2077401 CCACATAAGTTTGTCCCGAAGGA
1 CCACATAAGTTTGTCCCGAAGGA
* *
2077424 CCACATAGGTTTTGTCCCGAATGA
1 CCACATAAG-TTTGTCCCGAAGGA
2077448 CCACATAA
1 CCACATAA
2077456 TTATTTGTCA
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
21 8 0.17
22 3 0.06
23 16 0.34
24 20 0.43
ACGTcount: A:0.33, C:0.26, G:0.16, T:0.25
Consensus pattern (23 bp):
CCACATAAGTTTGTCCCGAAGGA
Found at i:2078972 original size:58 final size:58
Alignment explanation
Indices: 2078900--2079368 Score: 584
Period size: 58 Copynumber: 8.3 Consensus size: 58
2078890 TACCAAATGT
* * * *
2078900 CACTAAGTGTGCAAAAAGTTAAGAAATTCATACTAAATGTATGAATTTCCGTATTGAG
1 CACTATGTGTGCAAAAAGCTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGG
* * * * *
2078958 CACTTTGTGCGCAAAAAGATAAGAAATTCATACTAAATGTATAAATTTCCGTATTGGG
1 CACTATGTGTGCAAAAAGCTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGG
*
2079016 CACTATGTGTACAAAAA--TAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGG
1 CACTATGTGTGCAAAAAGCTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGG
* * * * **
2079072 CACTTTGTGTGCAAAAAGTTAGGAAATTCATACTAAATGTATGAATTTATGTATTGGG
1 CACTATGTGTGCAAAAAGCTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGG
* * *
2079130 AACTATGTGTGC--AAACCTAAGAAATTCATACTAAGTTTATGAATTTCCGTATTGGG
1 CACTATGTGTGCAAAAAGCTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGG
* ** * *
2079186 CACTTTGTGTGCGGAAAGTTAAG-AATATCATACTAAGTGTATGAATTTTCGTATTGGG
1 CACTATGTGTGCAAAAAGCTAAGAAAT-TCATACTAAGTGTATGAATTTCCGTATTGGG
2079244 CACTATGTGTGC-AAAA-CTAAGAAATTCATACTAAGTGTATGAATTTCCGTA-TGGG
1 CACTATGTGTGCAAAAAGCTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGG
* *
2079299 CACTATGTGTGC-AGAA-CTAAGAAATCCATACTAAGTGTAT-AGATTTCCGTA-TGGG
1 CACTATGTGTGCAAAAAGCTAAGAAATTCATACTAAGTGTATGA-ATTTCCGTATTGGG
* *
2079354 CACTATATGTACAAA
1 CACTATGTGTGCAAA
2079369 TATAAGAAGT
Statistics
Matches: 362, Mismatches: 41, Indels: 18
0.86 0.10 0.04
Matches are distributed among these distances:
54 1 0.00
55 65 0.18
56 129 0.36
57 9 0.02
58 158 0.44
ACGTcount: A:0.35, C:0.13, G:0.19, T:0.32
Consensus pattern (58 bp):
CACTATGTGTGCAAAAAGCTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGG
Found at i:2079080 original size:114 final size:114
Alignment explanation
Indices: 2078900--2079383 Score: 636
Period size: 114 Copynumber: 4.3 Consensus size: 114
2078890 TACCAAATGT
* * *
2078900 CACTAAGTGTGCAAAAAGTTAAGAAATTCATACTAAATGTATGAATTTCCGTATTGAGCACTTTG
1 CACTATGTGTGCAAAAA--TAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTTG
* *
2078965 TGCGCAAAAAGATAAGAAATTCATACTAAATGTATAAATTTCCGTATTGGG
64 TGTGCAAAAAGTTAAGAAATTCATACTAAATGTATAAATTTCCGTATTGGG
*
2079016 CACTATGTGTACAAAAATAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTTGTG
1 CACTATGTGTGCAAAAATAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTTGTG
* * **
2079081 TGCAAAAAGTTAGGAAATTCATACTAAATGTATGAATTTATGTATTGGG
66 TGCAAAAAGTTAAGAAATTCATACTAAATGTATAAATTTCCGTATTGGG
* ** *
2079130 AACTATGTGTGCAAACCTAAGAAATTCATACTAAGTTTATGAATTTCCGTATTGGGCACTTTGTG
1 CACTATGTGTGCAAAAATAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTTGTG
** * * *
2079195 TGCGGAAAGTTAAG-AATATCATACTAAGTGTATGAATTTTCGTATTGGG
66 TGCAAAAAGTTAAGAAAT-TCATACTAAATGTATAAATTTCCGTATTGGG
* *
2079244 CACTATGTGTGCAAAACTAAGAAATTCATACTAAGTGTATGAATTTCCGTA-TGGGCACTATGTG
1 CACTATGTGTGCAAAAATAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTTGTG
* * * * *
2079308 TGC-AGAA-CTAAGAAATCCATACTAAGTGTATAGATTTCCGTA-TGGG
66 TGCAAAAAGTTAAGAAATTCATACTAAATGTATAAATTTCCGTATTGGG
* * * *
2079354 CACTATATGTACAAATATAAGAAGTTCATA
1 CACTATGTGTGCAAAAATAAGAAATTCATA
2079384 ATAATTAGGT
Statistics
Matches: 329, Mismatches: 37, Indels: 10
0.88 0.10 0.03
Matches are distributed among these distances:
110 29 0.09
111 26 0.08
112 5 0.02
113 18 0.05
114 236 0.72
116 15 0.05
ACGTcount: A:0.36, C:0.13, G:0.19, T:0.32
Consensus pattern (114 bp):
CACTATGTGTGCAAAAATAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTTGTG
TGCAAAAAGTTAAGAAATTCATACTAAATGTATAAATTTCCGTATTGGG
Found at i:2079684 original size:68 final size:68
Alignment explanation
Indices: 2079575--2079867 Score: 336
Period size: 68 Copynumber: 4.3 Consensus size: 68
2079565 TGGCCTAAAT
* * *
2079575 GTGTCAATCATGCTAGCTAGATGAAAGGTTAAGTGCCTTTGAGGCCTAAATGTGCAATTGATAGA
1 GTGTCAATCATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAGGCCTAAATGTGCAATTGATAGA
2079640 AAG
66 AAG
* * * * *
2079643 GTGTCATTCATGCCAGTTAGATTAAAGACTAAGTGTCTTTGAGGCCTAAATGTGCAATTGATATA
1 GTGTCAATCATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAGGCCTAAATGTGCAATTGATAGA
2079708 AAG
66 AAG
* * * * * * * *
2079711 G-GTTCAATCATGCTAGTTAGATGTAAGGCTAAGTGCCTTTGAGGCATAACTTTGCATTTGACAA
1 GTG-TCAATCATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAGGCCTAAATGTGCAATTGATAG
2079775 AAAG
65 AAAG
* * * * *** *
2079779 GTGTCAATCATACCAGTCAGATGAAAGGCTAAGTGACTTTGAGGCTTGGCTGTGCATTTGATAGA
1 GTGTCAATCATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAGGCCTAAATGTGCAATTGATAGA
2079844 AAG
66 AAG
* *
2079847 GTGTCAATTATGCCATTTAGA
1 GTGTCAATCATGCCAGTTAGA
2079868 CGAACGGTTA
Statistics
Matches: 188, Mismatches: 35, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
67 1 0.01
68 186 0.99
69 1 0.01
ACGTcount: A:0.31, C:0.14, G:0.25, T:0.30
Consensus pattern (68 bp):
GTGTCAATCATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAGGCCTAAATGTGCAATTGATAGA
AAG
Found at i:2079970 original size:81 final size:81
Alignment explanation
Indices: 2079829--2079977 Score: 199
Period size: 81 Copynumber: 1.8 Consensus size: 81
2079819 GAGGCTTGGC
* * * * * *
2079829 TGTGCATTTGATAGAAAGGTGTCAATTATGCCATTTAGACGAACGGTTAAATATCATTGAGTAAA
1 TGTGCACTTGACAGAAAGGTGTCAATCATGCCAGTTAGACGAAAGGTTAAATACCATTGAGTAAA
2079894 AGATTTAGGGCCTAAA
66 AGATTTAGGGCCTAAA
* * * * *
2079910 TGTGCACTTGACAGAAAGGTGTCAATCATGCTAGTTAGATGAAATGTTAAATGCCTTTGAGTAAA
1 TGTGCACTTGACAGAAAGGTGTCAATCATGCCAGTTAGACGAAAGGTTAAATACCATTGAGTAAA
2079975 AGA
66 AGA
2079978 CTAGATGTAA
Statistics
Matches: 57, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
81 57 1.00
ACGTcount: A:0.36, C:0.11, G:0.23, T:0.30
Consensus pattern (81 bp):
TGTGCACTTGACAGAAAGGTGTCAATCATGCCAGTTAGACGAAAGGTTAAATACCATTGAGTAAA
AGATTTAGGGCCTAAA
Found at i:2080076 original size:45 final size:45
Alignment explanation
Indices: 2080011--2080106 Score: 165
Period size: 45 Copynumber: 2.1 Consensus size: 45
2080001 ATTGTATAAA
* *
2080011 AGGCATGAAAGGATGCCATAATTGAAATTCATATGGGTGCATTAT
1 AGGCATGAAAGGATGACATAATTGAAATACATATGGGTGCATTAT
*
2080056 AGGCATGAAAGGATTACATAATTGAAATACATATGGGTGCATTAT
1 AGGCATGAAAGGATGACATAATTGAAATACATATGGGTGCATTAT
2080101 AGGCAT
1 AGGCAT
2080107 TGGCATAATT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
45 48 1.00
ACGTcount: A:0.38, C:0.10, G:0.24, T:0.28
Consensus pattern (45 bp):
AGGCATGAAAGGATGACATAATTGAAATACATATGGGTGCATTAT
Found at i:2084214 original size:45 final size:45
Alignment explanation
Indices: 2084163--2084352 Score: 276
Period size: 45 Copynumber: 4.2 Consensus size: 45
2084153 TATAAAAGGC
*
2084163 ATGAAAGGATGTCATAATTGAAATACATATGGGTGCATTATAGGT
1 ATGAAAGGATGCCATAATTGAAATACATATGGGTGCATTATAGGT
* * *
2084208 ATGAAAGGATGCTATAATTGAAATAAATATGGGTGCATTATAGGC
1 ATGAAAGGATGCCATAATTGAAATACATATGGGTGCATTATAGGT
* **
2084253 ATGAAAGGATGCCATAATTGAAATGCATATGGGTGCATTATACACT
1 ATGAAAGGATGCCATAATTGAAATACATATGGGTGCATTATA-GGT
*
2084299 -TGAAAGG-TGCCATAATTGAAATACATATGGGTGCATTATCGGT
1 ATGAAAGGATGCCATAATTGAAATACATATGGGTGCATTATAGGT
*
2084342 ATGAAAAGATG
1 ATGAAAGGATG
2084353 TTATAAATGA
Statistics
Matches: 127, Mismatches: 15, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
43 1 0.01
44 37 0.29
45 89 0.70
ACGTcount: A:0.38, C:0.09, G:0.24, T:0.29
Consensus pattern (45 bp):
ATGAAAGGATGCCATAATTGAAATACATATGGGTGCATTATAGGT
Found at i:2091031 original size:20 final size:20
Alignment explanation
Indices: 2091006--2091052 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
2090996 GGCTGGCAAT
*
2091006 GAACCGGCTGAAAACCGGTA
1 GAACCGGCTGAAAACCAGTA
*
2091026 GAACCGGTTGAAAACCAGTA
1 GAACCGGCTGAAAACCAGTA
*
2091046 AAACCGG
1 GAACCGG
2091053 GGTGAACCGG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.38, C:0.23, G:0.28, T:0.11
Consensus pattern (20 bp):
GAACCGGCTGAAAACCAGTA
Found at i:2091062 original size:30 final size:30
Alignment explanation
Indices: 2091026--2091091 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 30
2091016 AAAACCGGTA
* * *
2091026 GAACCGGTTGAAAACCAGTAAAACCGGGGT
1 GAACCGGCTAAAAACCAGCAAAACCGGGGT
**
2091056 GAACCGGCTAAAAACCAGCAAAACCGGTTT
1 GAACCGGCTAAAAACCAGCAAAACCGGGGT
2091086 GAACCG
1 GAACCG
2091092 CCGGTTCGCT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.38, C:0.24, G:0.26, T:0.12
Consensus pattern (30 bp):
GAACCGGCTAAAAACCAGCAAAACCGGGGT
Found at i:2104532 original size:21 final size:20
Alignment explanation
Indices: 2104494--2104532 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
2104484 TTTGTGTTTC
2104494 TGTTTAAATTTAATTATAAA
1 TGTTTAAATTTAATTATAAA
2104514 TGTTTATAATATT-ATTATA
1 TGTTTA-AAT-TTAATTATA
2104533 CTATTTTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 6 0.35
21 9 0.53
22 2 0.12
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (20 bp):
TGTTTAAATTTAATTATAAA
Found at i:2105935 original size:2 final size:2
Alignment explanation
Indices: 2105928--2105963 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
2105918 ATTAAAACAA
2105928 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2105964 GTAAGATGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 30 0.94
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:2106913 original size:20 final size:20
Alignment explanation
Indices: 2106890--2106935 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
2106880 ACTCACCTAT
2106890 TGGTATTGATATCAACACCA
1 TGGTATTGATATCAACACCA
*
2106910 TGGTCTTGATATCAACACCA
1 TGGTATTGATATCAACACCA
2106930 TGGTAT
1 TGGTAT
2106936 CGACACCAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.33
Consensus pattern (20 bp):
TGGTATTGATATCAACACCA
Found at i:2108278 original size:17 final size:17
Alignment explanation
Indices: 2108256--2108291 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
2108246 CTAGGAAGTT
2108256 AAGGTATCACATTTACA
1 AAGGTATCACATTTACA
2108273 AAGGTATCACATTTACA
1 AAGGTATCACATTTACA
2108290 AA
1 AA
2108292 TCTTTCATAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.44, C:0.17, G:0.11, T:0.28
Consensus pattern (17 bp):
AAGGTATCACATTTACA
Found at i:2119697 original size:31 final size:31
Alignment explanation
Indices: 2119662--2119725 Score: 110
Period size: 31 Copynumber: 2.1 Consensus size: 31
2119652 CTTTGTCTTC
2119662 TGGAAGATAATAAGGTTGAGGTGTCTTGGTT
1 TGGAAGATAATAAGGTTGAGGTGTCTTGGTT
* *
2119693 TGGAAGATGATAAGTTTGAGGTGTCTTGGTT
1 TGGAAGATAATAAGGTTGAGGTGTCTTGGTT
2119724 TG
1 TG
2119726 AAGGTACTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.23, C:0.03, G:0.36, T:0.38
Consensus pattern (31 bp):
TGGAAGATAATAAGGTTGAGGTGTCTTGGTT
Found at i:2121402 original size:26 final size:26
Alignment explanation
Indices: 2121347--2121402 Score: 76
Period size: 26 Copynumber: 2.2 Consensus size: 26
2121337 AGGCACAACC
* *
2121347 TTATGTGTATTATGATGGGGAGGACC
1 TTATGTGTATTATGATGGGCAGGACA
* *
2121373 TTATGTGTATTATGGTGGGCATGACA
1 TTATGTGTATTATGATGGGCAGGACA
2121399 TTAT
1 TTAT
2121403 TTATAAGAAC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.23, C:0.07, G:0.30, T:0.39
Consensus pattern (26 bp):
TTATGTGTATTATGATGGGCAGGACA
Found at i:2123169 original size:548 final size:549
Alignment explanation
Indices: 2122131--2123237 Score: 1982
Period size: 548 Copynumber: 2.0 Consensus size: 549
2122121 AGAACAATTT
* * * *
2122131 ACGAGTATGAATGTGAATTTCACAAGTTGAGTCGATTCACTTCAGAGTTTCTTCCGACTGAGAGA
1 ACGAGTATAAATGTGAATTTCACAAGTTGAGTCGACTCACTTCAGAGTTTCATCCGACTGAGAAA
2122196 TCTAGAATTGATAGATTTGTTTCTTGATTGGATTCTCATTATAAAAGAATTCTAGTTACACATCA
66 TCTAGAATTGATAGATTTGTTTCTTGATTGGATTCTCATTATAAAAGAATTCTAGTTACACATCA
* *
2122261 TTTTACTTCTTTTCAAGAAGCGGTAAATAAGGTTAGGGTTATGGAAAAAGTTAACCTTAAAGATA
131 TTTTACTACTTTTCAAGAAGCGGTAAACAAGGTTAGGGTTATGGAAAAAGTTAACCTTAAAGATA
2122326 TAGAGGTGAAGAAGGATCAGACACACAAAAGGTTTGGAAGCTCCTACTTTGCACCATTTTCCAAA
196 TAGAGGTGAAGAAGGATCAGACACACAAAAGGTTTGGAAGCTCCTACTTTGCACCATTTTCCAAA
* *
2122391 CGCAGCAAGGGCCAGTAGCAAAAAAGTTATGCTTCCTCATCATCCTCAGTATCTAAGGTTTGGGG
261 CGCAGCAAGGGCCAGTAGCAAAAAAGTTATGCTTCCTCAGCATCCTCAGTATCCAAGGTTTGGGG
*
2122456 TTCCATCTTGCTATAGAGTGTAAATTTATTGGAAAGAGACATTCTGGTCAATGTTGGTTTCCTGA
326 TTCCATCTTGCTATAGAGTGTAAATTTATTGGAAAGAGACATTCTAGTCAATGTTGGTTTCCTGA
2122521 GGGAAAATGTTACAACTGTGGGTAAACGGGGTCATTTTAAAAGGCATTGCCTAGAGCTATATCCA
391 GGGAAAATGTTACAACTGTGGGTAAACGGGGTCATTTTAAAAGGCATTGCCTAGAGCTATATCCA
* * *
2122586 GATCAGTTTATATCGGGACCCCAGAAGGGTAGATGTGGAAAAGCAGGTAAACCTGGTACATTTGA
456 GATCAGTTGATATCGGGACCCCAGAAGGATAGATGTGGAAAAACAGGTAAACCTGGTACATTTGA
2122651 -CATCTAATCGTGAAGGCATGACTATTGC
521 GCATCTAATCGTGAAGGCATGACTATTGC
*
2122679 ACGAGTATAAATGTGAATTTCACAAGTTGAGTCGACTCACTTCGGAGTTTCATCCGACTGAGAAA
1 ACGAGTATAAATGTGAATTTCACAAGTTGAGTCGACTCACTTCAGAGTTTCATCCGACTGAGAAA
2122744 TCTAGAATTGATAGATTTGTTTCTTGATTGGATTCTCATTATAAAAGAATTCTAGTTACACATCA
66 TCTAGAATTGATAGATTTGTTTCTTGATTGGATTCTCATTATAAAAGAATTCTAGTTACACATCA
2122809 TTTTACTACTTTTCAAGAAGCGGTAAACAAGGTTAGGGTTATGGAAAAAGTTAACCTTAAAGATA
131 TTTTACTACTTTTCAAGAAGCGGTAAACAAGGTTAGGGTTATGGAAAAAGTTAACCTTAAAGATA
*
2122874 TAGAGGTGAAGAAGGATCAGACACACAAAAGGTTTGTAAGCTCCTACTTTGCACCATTTTCCAAA
196 TAGAGGTGAAGAAGGATCAGACACACAAAAGGTTTGGAAGCTCCTACTTTGCACCATTTTCCAAA
2122939 CGCAGCAAGGGCCAGTAGCAAAAAAGTTATGCTTCCTCAGCATCCTCAGTATCCAAGGTTTGGGG
261 CGCAGCAAGGGCCAGTAGCAAAAAAGTTATGCTTCCTCAGCATCCTCAGTATCCAAGGTTTGGGG
* * * *
2123004 TTCTATCTTGCTATAGAGTGTAAGTTTATTGGAAAGATACATTCTAGTCAATGTTGGTTTGCTGA
326 TTCCATCTTGCTATAGAGTGTAAATTTATTGGAAAGAGACATTCTAGTCAATGTTGGTTTCCTGA
*
2123069 GGGAAAATGTTATAACTGTGGGTAAACGGGGTCATTTTAAAAGGCATTGCCTAGAGCTATATCCA
391 GGGAAAATGTTACAACTGTGGGTAAACGGGGTCATTTTAAAAGGCATTGCCTAGAGCTATATCCA
* *
2123134 GATTAGTTGATATCGGGACCCTAGAAGGATAGATGTGGAAAAACAGGTAAACCTGGTACATTTGA
456 GATCAGTTGATATCGGGACCCCAGAAGGATAGATGTGGAAAAACAGGTAAACCTGGTACATTTGA
2123199 GGTTGCATCTAATCGTGAAGGCATGACTATTGC
521 ----GCATCTAATCGTGAAGGCATGACTATTGC
2123232 ACGAGT
1 ACGAGT
2123238 TTATCACATC
Statistics
Matches: 533, Mismatches: 21, Indels: 5
0.95 0.04 0.01
Matches are distributed among these distances:
548 499 0.94
553 34 0.06
ACGTcount: A:0.32, C:0.16, G:0.22, T:0.30
Consensus pattern (549 bp):
ACGAGTATAAATGTGAATTTCACAAGTTGAGTCGACTCACTTCAGAGTTTCATCCGACTGAGAAA
TCTAGAATTGATAGATTTGTTTCTTGATTGGATTCTCATTATAAAAGAATTCTAGTTACACATCA
TTTTACTACTTTTCAAGAAGCGGTAAACAAGGTTAGGGTTATGGAAAAAGTTAACCTTAAAGATA
TAGAGGTGAAGAAGGATCAGACACACAAAAGGTTTGGAAGCTCCTACTTTGCACCATTTTCCAAA
CGCAGCAAGGGCCAGTAGCAAAAAAGTTATGCTTCCTCAGCATCCTCAGTATCCAAGGTTTGGGG
TTCCATCTTGCTATAGAGTGTAAATTTATTGGAAAGAGACATTCTAGTCAATGTTGGTTTCCTGA
GGGAAAATGTTACAACTGTGGGTAAACGGGGTCATTTTAAAAGGCATTGCCTAGAGCTATATCCA
GATCAGTTGATATCGGGACCCCAGAAGGATAGATGTGGAAAAACAGGTAAACCTGGTACATTTGA
GCATCTAATCGTGAAGGCATGACTATTGC
Found at i:2128505 original size:25 final size:26
Alignment explanation
Indices: 2128476--2128534 Score: 102
Period size: 26 Copynumber: 2.3 Consensus size: 26
2128466 GTAAGGGCAC
*
2128476 TATGTGTA-TATGGTGGGCACGACCT
1 TATGTGTATTATGGTGGGCACAACCT
2128501 TATGTGTATTATGGTGGGCACAACCT
1 TATGTGTATTATGGTGGGCACAACCT
2128527 TATGTGTA
1 TATGTGTA
2128535 AGCACTACGG
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
25 8 0.25
26 24 0.75
ACGTcount: A:0.22, C:0.14, G:0.29, T:0.36
Consensus pattern (26 bp):
TATGTGTATTATGGTGGGCACAACCT
Found at i:2135978 original size:12 final size:12
Alignment explanation
Indices: 2135961--2135991 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
2135951 CTTTGCCTCT
2135961 TCTCTTTTATTC
1 TCTCTTTTATTC
*
2135973 TCTCTTCTATTC
1 TCTCTTTTATTC
2135985 TCTCTTT
1 TCTCTTT
2135992 GCCTCTTCTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.06, C:0.29, G:0.00, T:0.65
Consensus pattern (12 bp):
TCTCTTTTATTC
Found at i:2140069 original size:81 final size:81
Alignment explanation
Indices: 2139815--2140634 Score: 1246
Period size: 81 Copynumber: 10.1 Consensus size: 81
2139805 TAAATTGTGT
* * * *
2139815 AGTAAAAGATTAATAGCCTAGATGTGCATTTGACAGAAAGATGTCAATTATTCCAGTTTGATGAA
1 AGTAAAAGATTAATAGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAA
* *
2139880 AAGTTAAATACCTCTG
66 AGGTTAAATACCTTTG
* *
2139896 AGTAAAAGATTAATAGCCTATTTGTGCATTTGATAGAAAGGTGTCAATTATG-CAGTTAGATGAA
1 AGTAAAAGATTAATAGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAA
*
2139960 AGGTTAAATAACTTTG
66 AGGTTAAATACCTTTG
* * *
2139976 AGTAAAAGATTAATTGCCTAGTTGTGCATTTGACAGAAAGGTGGCAATTATGACAGTTAGATGAA
1 AGTAAAAGATTAATAGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAA
2140041 AGGTTAAATACCTTTG
66 AGGTTAAATACCTTTG
* * *
2140057 AGTAAAAGATTAATAGCCTAGTTGTGCATTTGACAGAAATGTGTAAATTATGCCAATTAGATGAA
1 AGTAAAAGATTAATAGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAA
2140122 AGGTTAAATACCTTTG
66 AGGTTAAATACCTTTG
* *
2140138 AGTAAAAGATTAATAACCTAGTTGTGCATTTGATAGAAAGGTGTCAATTATGCCAGTTAGATGAA
1 AGTAAAAGATTAATAGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAA
2140203 AGGTTAAATACCTTTG
66 AGGTTAAATACCTTTG
* *
2140219 AGTAAAATATTAATAGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAA
1 AGTAAAAGATTAATAGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAA
*
2140284 AGATTAAATACCTTTG
66 AGGTTAAATACCTTTG
* * * *
2140300 AGTAAACGATTAATAGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGTCAATTATATGAA
1 AGTAAAAGATTAATAGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAA
*
2140365 AGGTTAAATACCTTTA
66 AGGTTAAATACCTTTG
* *
2140381 AGTAAAAGATTAATAGCCTAGCTGTGCATTTGACAGAAAGGTGCCAATTATGCCAGTTAGATGAA
1 AGTAAAAGATTAATAGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAA
2140446 AGGTTAAATACCTTTG
66 AGGTTAAATACCTTTG
* * * * *
2140462 AGTAAAATATTAATAGCCTAGCTATGCATTTGACAGAAATGTGTCAATTATTCCAGTTAGATGAA
1 AGTAAAAGATTAATAGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAA
2140527 AGGTTAAATACCTTTG
66 AGGTTAAATACCTTTG
* * * * * * *
2140543 AGTAAAATATTAATAGCCTAGCTATGCATTTGGCAGAAAGGTGTCAATCATTCAAGTTAGATGAA
1 AGTAAAAGATTAATAGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAA
* **
2140608 AGGCTAAATGTCTTTG
66 AGGTTAAATACCTTTG
*
2140624 GGTAAAAGATT
1 AGTAAAAGATT
2140635 TAAGGATTTG
Statistics
Matches: 679, Mismatches: 59, Indels: 2
0.92 0.08 0.00
Matches are distributed among these distances:
80 72 0.11
81 607 0.89
ACGTcount: A:0.37, C:0.11, G:0.20, T:0.32
Consensus pattern (81 bp):
AGTAAAAGATTAATAGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAA
AGGTTAAATACCTTTG
Found at i:2140726 original size:45 final size:45
Alignment explanation
Indices: 2140677--2140793 Score: 146
Period size: 45 Copynumber: 2.6 Consensus size: 45
2140667 TGCATTAACA
* * *
2140677 GTATGAAAGGATGCCATATAT-AAAATGTACAACAATGCATAATTG
1 GTATGAAAGGATGACATAAATGAAAATGTA-AACAATGCATAAGTG
*
2140722 GTATGAAAGGATGACATAAATGAAAATGTAAACAGTGCATAAGTG
1 GTATGAAAGGATGACATAAATGAAAATGTAAACAATGCATAAGTG
* * * *
2140767 GTATGAATGAATGTCACAAATGAAAAT
1 GTATGAAAGGATGACATAAATGAAAAT
2140794 ACAAAATGGT
Statistics
Matches: 63, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
45 55 0.87
46 8 0.13
ACGTcount: A:0.46, C:0.09, G:0.21, T:0.25
Consensus pattern (45 bp):
GTATGAAAGGATGACATAAATGAAAATGTAAACAATGCATAAGTG
Found at i:2146721 original size:81 final size:81
Alignment explanation
Indices: 2145500--2146709 Score: 1687
Period size: 81 Copynumber: 15.0 Consensus size: 81
2145490 TTATTTACAA
* *
2145500 TAAAAGATTAATAGCCTAGTTGTGCATTTGACAGAAAGGAGT-ATATTATGCCAGTTAGATGAAA
1 TAAAAGATTAATAGCCTAGCTGTGCATTTGACAGAAAGGTGTCA-ATTATGCCAGTTAGATGAAA
*
2145564 AGTT-AATACCTTTGAG
65 GGTTAAATACCTTTGAG
* * * * * * * * * *
2145580 TAAAAGATTAATTA-CCAATCAGTGCATTTGAAAAAAAGATGTTAATTATGTCACTTAAATGAAA
1 TAAAAGATTAA-TAGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAA
*
2145644 GGTTAAATACCTTCGAG
65 GGTTAAATACCTTTGAG
* * * **
2145661 TAAAAGATTAATAGCCTAGCTGTGCATTTGAGAAAAATGTGTC-ATTAATGGTAGTTAGATGAAA
1 TAAAAGATTAATAGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATT-ATGCCAGTTAGATGAAA
* *
2145725 TGTTAAATACCTTTGAT
65 GGTTAAATACCTTTGAG
* * *
2145742 TAAAAGATTAATAGTCTAGTTGTGCATTTGAAAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
1 TAAAAGATTAATAGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
2145807 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* * *
2145823 TAAAAGATTAATAGCCTAGTTGTGCATTTAACAGAAAGGTGTCAATTATG-CAGGTTAGACGAAA
1 TAAAAGATTAATAGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCA-GTTAGATGAAA
2145887 GGTTAAATACCTTTGAG
65 GGTTAAATACCTTTGAG
** * *
2145904 TAAATTATTAATAGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCTAGTTAGATGAAAG
1 TAAAAGATTAATAGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
2145969 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* * *
2145985 TAAAAGATTAATAGCCTAGCTGTGAATTTGGCAGAAAAGTGTCAATTATGCCAGTTAGATGAAAG
1 TAAAAGATTAATAGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
2146050 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* *
2146066 TAAAAGATTAATAGCCTA-CTTGTGAATTTGACAGAAAAGTGTCAATTATGCCAGTTAGATGAAA
1 TAAAAGATTAATAGCCTAGC-TGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAA
* *
2146130 GATTAAATACCTTTAAG
65 GGTTAAATACCTTTGAG
* * *
2146147 T-AAAGATTAATAGCCTAGTTGTGCATTTGATAGAAAAGTGTCAATTATGCCAGTTAGATGAAAG
1 TAAAAGATTAATAGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
2146211 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* * * * * * *
2146227 TAAAAGATTAATAGCTTAGCAGTGCAATTAACAGAAAGGTGTCAATTATACCAATTAGATGAAAT
1 TAAAAGATTAATAGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
2146292 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* *
2146308 TAAAAGATTAATAGCTTAGCTGTGCATTTGACAGAAAGGTGCCAATTATGCCAGTTAGATGAAAG
1 TAAAAGATTAATAGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
* *
2146373 ATTAAATACGTTTGAG
66 GTTAAATACCTTTGAG
* * * * * *
2146389 TAAACGATTAATAGCCTAGTTGTGCATTTGACAGAAATGTGTCAATTATGTCAATTATATGAAAG
1 TAAAAGATTAATAGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
*
2146454 GTTAAATACCTTTAAG
66 GTTAAATACCTTTGAG
* *
2146470 TAAAAGATTAATAGCCTAGCTATGCATTTGACAGAAAGGTGCCAATTATGCCAGTTAGATGAAAG
1 TAAAAGATTAATAGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
2146535 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* *
2146551 TAAAAGATTAATAGCCTAGCTATGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATGAAAG
1 TAAAAGATTAATAGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
2146616 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* * * * * *
2146632 TAAAATATTAATAGCCTAGCTATGCATTTGGCAGAAAGGTGTCAATCATGCAAGTTATATGAAAG
1 TAAAAGATTAATAGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
* *
2146697 GATAAATGCCTTT
66 GTTAAATACCTTT
2146710 CGGAAAAATA
Statistics
Matches: 1010, Mismatches: 109, Indels: 21
0.89 0.10 0.02
Matches are distributed among these distances:
80 133 0.13
81 873 0.86
82 4 0.00
ACGTcount: A:0.38, C:0.11, G:0.20, T:0.31
Consensus pattern (81 bp):
TAAAAGATTAATAGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
GTTAAATACCTTTGAG
Found at i:2146861 original size:45 final size:46
Alignment explanation
Indices: 2146763--2146880 Score: 132
Period size: 45 Copynumber: 2.6 Consensus size: 46
2146753 GCGCATTAAC
* *
2146763 AGTATGAAAGGATGCCATATAT-AAAATGTACAACAATGCATAATT
1 AGTATGAAAGGATGCCATAAATGAAAATGTACAACAATGCATAAGT
* *
2146808 AGTATGAAAGGATGCCATAAATGAAAATGTA-AACAGTTCATAAGT
1 AGTATGAAAGGATGCCATAAATGAAAATGTACAACAATGCATAAGT
* * ** * *
2146853 GGTTTGAAATAATGTCACAAATGAAAAT
1 AGTATGAAAGGATGCCATAAATGAAAAT
2146881 ACAAATCGGT
Statistics
Matches: 62, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
45 54 0.87
46 8 0.13
ACGTcount: A:0.47, C:0.09, G:0.18, T:0.26
Consensus pattern (46 bp):
AGTATGAAAGGATGCCATAAATGAAAATGTACAACAATGCATAAGT
Found at i:2151915 original size:81 final size:81
Alignment explanation
Indices: 2151725--2152784 Score: 1413
Period size: 81 Copynumber: 13.1 Consensus size: 81
2151715 TTGTTTAAAC
* * *
2151725 TAAAAGATTAATAGCCTAGTTGTGCATTTGATAGAAAAGTGTCAATTATGACAGTTAGATGAAAG
1 TAAAAGATTAATAGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
*
2151790 GTT-AATATCTTTGAG
66 GTTAAATACCTTTGAG
* * * * *
2151805 TAAAAGGTTAATAGCCTAGTTGTGCATTTGACATAGAGATGTCAATTACGCCAGTTAGATGAAAG
1 TAAAAGATTAATAGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
2151870 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* * *
2151886 TAAAAGATTAATAGCCTAGTTGTGCATTTGATAGAAAGGTGTAAATTATTCCAGTTAGATGAAAG
1 TAAAAGATTAATAGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
2151951 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* * * *
2151967 TAAAAGATTAATAGCCTAGTGGTGCATTTGAAAGAAATGTGTCAATTATGTCAGTTAGATGAAAG
1 TAAAAGATTAATAGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
2152032 G-----TACCTTTGAG
66 GTTAAATACCTTTGAG
* *
2152043 TAAAAGATTAATAGCCTA-TATGTGCATTTGACAGAAAGATGTCAATTATGTCAGTTAGATGAAA
1 TAAAAGATTAATAGCCTAGT-TGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAA
* *
2152107 TGTTAAATACATTTGAG
65 GGTTAAATACCTTTGAG
* * *
2152124 TAAAAGATTAATAGCCTAGTTGTGCATTTGACAGAAAGGTTTCAATTATGTCAGTTAGATGAGAG
1 TAAAAGATTAATAGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
2152189 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* * *
2152205 TAAAAGATTAATAGCTTAGTT-TCGCATTTAACAGAAAGGTGTCAAATATGCCAGTTAGATGAAA
1 TAAAAGATTAATAGCCTAGTTGT-GCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAA
2152269 GGTTAAATACCTTTGAG
65 GGTTAAATACCTTTGAG
* * **
2152286 TAAAATATTAATAGCCTAGTTGTGCAGTTGACAGAAATTTGTCAATTATGCCAGTTAGATGAAAG
1 TAAAAGATTAATAGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
*
2152351 GTTAAATATCTTTGAG
66 GTTAAATACCTTTGAG
* * *
2152367 TAAAAGATTAATAGCCTAGCTATGCACTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
1 TAAAAGATTAATAGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
*
2152432 ATTAAATTAAATACCTTTGAG
66 -----GTTAAATACCTTTGAG
* * *
2152453 TAAAAGATTAACAGCCTAGCTGTGAATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
1 TAAAAGATTAATAGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
* *
2152518 ATTAAATACCGTTGAG
66 GTTAAATACCTTTGAG
* * * * ** *
2152534 TAAAAGATTAAAAGCCTGGCTGTG-ATTTTGACATAAAGGTGTCAATTATATCAATTAGAT-AAT
1 TAAAAGATTAATAGCCTAGTTGTGCA-TTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAA-
*
2152597 AGGTTAAATACTTTTGAG
64 AGGTTAAATACCTTTGAG
* *
2152615 TAAAAGATTAATAGCCTAGTTGTGCATTTGACAGAAAGGTGACAATTATGCCAGTTAGACGAAAG
1 TAAAAGATTAATAGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
2152680 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* ** * * ** * *
2152696 TAAAAGATTAGTAGCCTAACTATGCATTTGATAGAAAGGTACCAATTATGCCA-ATAGATAAAAG
1 TAAAAGATTAATAGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
* *
2152760 GTTAAATTCCTTTGGG
66 GTTAAATACCTTTGAG
2152776 TAAAAGATT
1 TAAAAGATT
2152785 TAAGGATTTA
Statistics
Matches: 869, Mismatches: 92, Indels: 38
0.87 0.09 0.04
Matches are distributed among these distances:
75 1 0.00
76 69 0.08
80 95 0.11
81 624 0.72
82 5 0.01
86 75 0.09
ACGTcount: A:0.37, C:0.10, G:0.21, T:0.32
Consensus pattern (81 bp):
TAAAAGATTAATAGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
GTTAAATACCTTTGAG
Found at i:2152539 original size:329 final size:327
Alignment explanation
Indices: 2151725--2152748 Score: 1371
Period size: 329 Copynumber: 3.2 Consensus size: 327
2151715 TTGTTTAAAC
* * * * *
2151725 TAAAAGATTAATAGCCTAGTTGTGCATTTGATAGAAAAGTGTCAATTATGACAGTTAGATGAAAG
1 TAAAAGATTAATAGCCTAGCTATGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
* * * * *
2151790 GTTAA-T--AT--CTTTGAGTAAAAGGTTAATAGCCTAGTTGTGCATTTGACATAGAGATGTCAA
66 ATTAATTAAATACCTTTGAGTAAAAGATTAATAGCCTAGTTGTGCATTTGACAGAAAGGTGTCAA
*
2151850 TTACGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATAGCCTAGTTGTGCATTT
131 TTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATAGCCTAGTT-TGCATTT
* *
2151915 GATAGAAAGGTGT-AAATTATTCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAAT
195 GACAGAAAGGTGTCAAA-TATACCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAAT
* * *
2151979 AGCCTAGTGGTGCATTTGAAAGAAATGTGTCAATTATGTCAGTTAGATGAAAGG-----TACCTT
259 AGCCTAGTTGTGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTT
2152039 TGAG
324 TGAG
** * * *
2152043 TAAAAGATTAATAGCCTATATGTGCATTTGACAGAAAGATGTCAATTATGTCAGTTAGATG-AA-
1 TAAAAGATTAATAGCCTAGCTATGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
* * *
2152106 A-T-GTTAAATACATTTGAGTAAAAGATTAATAGCCTAGTTGTGCATTTGACAGAAAGGTTTCAA
66 ATTAATTAAATACCTTTGAGTAAAAGATTAATAGCCTAGTTGTGCATTTGACAGAAAGGTGTCAA
* * *
2152169 TTATGTCAGTTAGATGAGAGGTTAAATACCTTTGAGTAAAAGATTAATAGCTTAGTTTCGCATTT
131 TTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATAGCCTAGTTT-GCATTT
* * *
2152234 AACAGAAAGGTGTCAAATATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAATATTAATA
195 GACAGAAAGGTGTCAAATATACCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATA
* * *
2152299 GCCTAGTTGTGCAGTTGACAGAAATTTGTCAATTATGCCAGTTAGATGAAAGGTTAAATATCTTT
260 GCCTAGTTGTGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTT
2152364 GAG
325 GAG
*
2152367 TAAAAGATTAATAGCCTAGCTATGCACTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
1 TAAAAGATTAATAGCCTAGCTATGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
* * *
2152432 ATTAAATTAAATACCTTTGAGTAAAAGATTAACAGCCTAGCTGTGAATTTGACAGAAAGGTGTCA
66 ATT-AATTAAATACCTTTGAGTAAAAGATTAATAGCCTAGTTGTGCATTTGACAGAAAGGTGTCA
* * * * *
2152497 ATTATGCCAGTTAGATGAAAGATTAAATACCGTTGAGTAAAAGATTAAAAGCCTGGCTGTG-ATT
130 ATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATAGCCTAG-TTTGCA-T
* * * * *
2152561 TTGACATAAAGGTGTCAATTATATCAATTAGAT-AATAGGTTAAATACTTTTGAGTAAAAGATTA
193 TTGACAGAAAGGTGTCAAATATACCAGTTAGATGAA-AGGTTAAATACCTTTGAGTAAAAGATTA
* * *
2152625 ATAGCCTAGTTGTGCATTTGACAGAAAGGTGACAATTATGCCAGTTAGACGAAAGGTTAAATACC
257 ATAGCCTAGTTGTGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACC
2152690 TTTGAG
322 TTTGAG
* * * **
2152696 TAAAAGATTAGTAGCCTAACTATGCATTTGATAGAAAGGTACCAATTATGCCA
1 TAAAAGATTAATAGCCTAGCTATGCATTTGACAGAAAGGTGTCAATTATGCCA
2152749 ATAGATAAAA
Statistics
Matches: 618, Mismatches: 68, Indels: 29
0.86 0.10 0.04
Matches are distributed among these distances:
315 2 0.00
317 4 0.01
318 56 0.09
319 210 0.34
320 3 0.00
324 64 0.10
325 2 0.00
326 1 0.00
327 1 0.00
328 3 0.00
329 270 0.44
330 2 0.00
ACGTcount: A:0.37, C:0.11, G:0.21, T:0.32
Consensus pattern (327 bp):
TAAAAGATTAATAGCCTAGCTATGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
ATTAATTAAATACCTTTGAGTAAAAGATTAATAGCCTAGTTGTGCATTTGACAGAAAGGTGTCAA
TTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATAGCCTAGTTTGCATTTG
ACAGAAAGGTGTCAAATATACCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATAG
CCTAGTTGTGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTG
AG
Found at i:2152651 original size:410 final size:399
Alignment explanation
Indices: 2151725--2152784 Score: 1409
Period size: 410 Copynumber: 2.6 Consensus size: 399
2151715 TTGTTTAAAC
* *
2151725 TAAAAGATTAATAGCCTAGTTGTGCATTTGATAGAAAAGTGTCAATTATGA-CAGTTAGATGAAA
1 TAAAAGATTAATAGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTAT-ATCAGTTAGAT-AAA
* * * *
2151789 GGTT-AATA-TCTTTGAGTAAAAGGTTAATAGCCTAGTTGTGCATTTGACATAGAGATGTCAATT
64 GGTTAAATACT-TTTGAGTAAAAGATTAATAGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATT
*
2151852 ACGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATAGCCTAGTTGTGCATTTGA
128 ATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATAGCCTAGTTGTGCATTTGA
* * *
2151917 TAGAAAGGTGTAAATTATTCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATAGC
193 TAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATATCTTTGAGTAAAAGATTAATAGC
* * * * *
2151982 CTAGTGGTGCATTTGAAAGAAATGTGTCAATTATGTCAGTTAGATGAAAGGTACCTTTGAGTAAA
258 CTAGTGATGCACTTGAAAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGATACCTTTGAGTAAA
* * * *
2152047 AGATTAATAGCCTATATGTGCATTTGACAGAAAGATGTCAATTATGTCAGTTAGATGAAATGTTA
323 AGATTAACAGCCTAGATGTGAATTTGACAGAAAGATGTCAATTATGCCAGTTAGATGAAATGTTA
*
2152112 AATACATTTGAG
388 AATACAGTTGAG
* * *
2152124 TAAAAGATTAATAGCCTAGTTGTGCATTTGACAGAAAGGTTTCAATTATGTCAGTTAGATGAGAG
1 TAAAAGATTAATAGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATATCAGTTAGAT-AAAG
* * * *
2152189 GTTAAATACCTTTGAGTAAAAGATTAATAGCTTAGTT-TCGCATTTAACAGAAAGGTGTCAAATA
65 GTTAAATACTTTTGAGTAAAAGATTAATAGCCTAGTTGT-GCATTTGACAGAAAGGTGTCAATTA
* * *
2152253 TGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAATATTAATAGCCTAGTTGTGCAGTTGAC
129 TGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATAGCCTAGTTGTGCATTTGAT
**
2152318 AGAAATTTGTCAATTATGCCAGTTAGATGAAAGGTTAAATATCTTTGAGTAAAAGATTAATAGCC
194 AGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATATCTTTGAGTAAAAGATTAATAGCC
*
2152383 TAGCT-ATGCACTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGATTAAATTAAATACC
259 TAG-TGATGCACTTGAAAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG----------ATACC
* *
2152447 TTTGAGTAAAAGATTAACAGCCTAGCTGTGAATTTGACAGAAAGGTGTCAATTATGCCAGTTAGA
313 TTTGAGTAAAAGATTAACAGCCTAGATGTGAATTTGACAGAAAGATGTCAATTATGCCAGTTAGA
*
2152512 TGAAA-GATTAAATACCGTTGAG
378 TGAAATG-TTAAATACAGTTGAG
* * * * *
2152534 TAAAAGATTAAAAGCCTGGCTGTG-ATTTTGACATAAAGGTGTCAATTATATCAATTAGATAATA
1 TAAAAGATTAATAGCCTAGTTGTGCA-TTTGACAGAAAGGTGTCAATTATATCAGTTAGATAA-A
*
2152598 GGTTAAATACTTTTGAGTAAAAGATTAATAGCCTAGTTGTGCATTTGACAGAAAGGTGACAATTA
64 GGTTAAATACTTTTGAGTAAAAGATTAATAGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTA
* * ** *
2152663 TGCCAGTTAGACGAAAGGTTAAATACCTTTGAGTAAAAGATTAGTAGCCTAACTATGCATTTGAT
129 TGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATAGCCTAGTTGTGCATTTGAT
** * * *
2152728 AGAAAGGTACCAATTATGCCA-ATAGATAAAAGGTTAAAT-TCCTTTGGGTAAAAGATT
194 AGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATAT-CTTTGAGTAAAAGATT
2152785 TAAGGATTTA
Statistics
Matches: 577, Mismatches: 64, Indels: 30
0.86 0.10 0.04
Matches are distributed among these distances:
399 63 0.11
400 212 0.37
401 1 0.00
408 1 0.00
409 34 0.06
410 265 0.46
411 1 0.00
ACGTcount: A:0.37, C:0.10, G:0.21, T:0.32
Consensus pattern (399 bp):
TAAAAGATTAATAGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATATCAGTTAGATAAAGG
TTAAATACTTTTGAGTAAAAGATTAATAGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATG
CCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATAGCCTAGTTGTGCATTTGATAG
AAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATATCTTTGAGTAAAAGATTAATAGCCTA
GTGATGCACTTGAAAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGATACCTTTGAGTAAAAGA
TTAACAGCCTAGATGTGAATTTGACAGAAAGATGTCAATTATGCCAGTTAGATGAAATGTTAAAT
ACAGTTGAG
Found at i:2152877 original size:45 final size:45
Alignment explanation
Indices: 2152827--2152944 Score: 139
Period size: 45 Copynumber: 2.6 Consensus size: 45
2152817 CTCATTAACA
* *
2152827 GTATGAAAGGATGTCATATAT-AAAATGTACAACAATGAATAATTG
1 GTATGAAAGGATGTCATAAATGAAAATGTA-AACAATGAATAAGTG
* * *
2152872 GTATGAAAGGATGCCATAAATGAAAATGTAAACAGTGCATAAGTG
1 GTATGAAAGGATGTCATAAATGAAAATGTAAACAATGAATAAGTG
* * **
2152917 GTAAGAAAGAATGTCCCAAATGAAAATG
1 GTATGAAAGGATGTCATAAATGAAAATG
2152945 CAAAACGGTG
Statistics
Matches: 62, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
45 54 0.87
46 8 0.13
ACGTcount: A:0.47, C:0.08, G:0.21, T:0.24
Consensus pattern (45 bp):
GTATGAAAGGATGTCATAAATGAAAATGTAAACAATGAATAAGTG
Done.