Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007938.1 Hibiscus syriacus cultivar Beakdansim tig00110348_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: 2808856
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 14
Found at i:1810077 original size:21 final size:21
Alignment explanation
Indices: 1810051--1810102 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
1810041 AAATTAAGTT
*
1810051 AAATGAATTTTAAGATTTTCC
1 AAATGAATTTTAAGATTTTAC
1810072 AAATGAATTTTAAGATTTTAC
1 AAATGAATTTTAAGATTTTAC
1810093 AAATG-ATTTT
1 AAATGAATTTT
1810103 CTAAGTATAT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
20 5 0.17
21 25 0.83
ACGTcount: A:0.40, C:0.06, G:0.10, T:0.44
Consensus pattern (21 bp):
AAATGAATTTTAAGATTTTAC
Found at i:1810224 original size:22 final size:23
Alignment explanation
Indices: 1810199--1810242 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
1810189 AATTAAGTTT
1810199 TAATCTTA-AAA-TAATTTCAAAA
1 TAATCTTACAAAGT-ATTTCAAAA
*
1810221 TAATTTTACAAAGTATTTCAAA
1 TAATCTTACAAAGTATTTCAAA
1810243 CCATTTCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 7 0.37
23 11 0.58
24 1 0.05
ACGTcount: A:0.50, C:0.09, G:0.02, T:0.39
Consensus pattern (23 bp):
TAATCTTACAAAGTATTTCAAAA
Found at i:1823150 original size:41 final size:42
Alignment explanation
Indices: 1823093--1823177 Score: 163
Period size: 41 Copynumber: 2.0 Consensus size: 42
1823083 ATAAATGGGA
1823093 GAAGTGTTAGTGTTAAAGTAAGGG-GAGTAATTTCAAAACTT
1 GAAGTGTTAGTGTTAAAGTAAGGGCGAGTAATTTCAAAACTT
1823134 GAAGTGTTAGTGTTAAAGTAAGGGCGAGTAATTTCAAAACTT
1 GAAGTGTTAGTGTTAAAGTAAGGGCGAGTAATTTCAAAACTT
1823176 GA
1 GA
1823178 TTTCAAAATC
Statistics
Matches: 43, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
41 24 0.56
42 19 0.44
ACGTcount: A:0.36, C:0.06, G:0.27, T:0.31
Consensus pattern (42 bp):
GAAGTGTTAGTGTTAAAGTAAGGGCGAGTAATTTCAAAACTT
Found at i:1825487 original size:22 final size:22
Alignment explanation
Indices: 1825457--1825523 Score: 107
Period size: 22 Copynumber: 3.0 Consensus size: 22
1825447 AGTCGAGGGT
1825457 TACATAGGTCCTTCGGGACATA
1 TACATAGGTCCTTCGGGACATA
* *
1825479 TACACAGGTCCTTCGGGACACA
1 TACATAGGTCCTTCGGGACATA
*
1825501 TGCATAGGTCCTTCGGGACATA
1 TACATAGGTCCTTCGGGACATA
1825523 T
1 T
1825524 TTCACATACC
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 40 1.00
ACGTcount: A:0.25, C:0.25, G:0.24, T:0.25
Consensus pattern (22 bp):
TACATAGGTCCTTCGGGACATA
Found at i:1826210 original size:16 final size:17
Alignment explanation
Indices: 1826183--1826215 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1826173 TTTTTAGTCA
1826183 CTTTGTAAAAGTAAATG
1 CTTTGTAAAAGTAAATG
*
1826200 CTTTG-AAAAGTCAATG
1 CTTTGTAAAAGTAAATG
1826216 TGACACCTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.39, C:0.09, G:0.18, T:0.33
Consensus pattern (17 bp):
CTTTGTAAAAGTAAATG
Found at i:1836385 original size:3 final size:3
Alignment explanation
Indices: 1836314--1836367 Score: 72
Period size: 3 Copynumber: 17.7 Consensus size: 3
1836304 TTTGGTATTT
* * *
1836314 AAG AAG AAG GAG AAG AAG GAG AAG GAG AAG AAG AAG AAG AAAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG -AAG AAG
1836360 AAG AAG AA
1 AAG AAG AA
1836368 CGTGGGTGTA
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
3 41 0.93
4 3 0.07
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:1838072 original size:5 final size:5
Alignment explanation
Indices: 1838061--1838102 Score: 66
Period size: 5 Copynumber: 8.2 Consensus size: 5
1838051 TTAACCTTTG
*
1838061 TTTTCA TTTCA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA T
1 TTTT-A TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA T
1838103 GGGATGCGTT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
5 31 0.91
6 3 0.09
ACGTcount: A:0.19, C:0.05, G:0.00, T:0.76
Consensus pattern (5 bp):
TTTTA
Found at i:1840161 original size:24 final size:24
Alignment explanation
Indices: 1840129--1840185 Score: 114
Period size: 24 Copynumber: 2.4 Consensus size: 24
1840119 TTTTTTACTT
1840129 GTATCTTTTTTCCTGCATGTCTTA
1 GTATCTTTTTTCCTGCATGTCTTA
1840153 GTATCTTTTTTCCTGCATGTCTTA
1 GTATCTTTTTTCCTGCATGTCTTA
1840177 GTATCTTTT
1 GTATCTTTT
1840186 AAAAGTTACA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.12, C:0.19, G:0.12, T:0.56
Consensus pattern (24 bp):
GTATCTTTTTTCCTGCATGTCTTA
Found at i:1843838 original size:5 final size:5
Alignment explanation
Indices: 1843830--1843861 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
1843820 GGTTTGGTCT
1843830 GACCC GACCC GACCC GACCC GACCC GACCC GA
1 GACCC GACCC GACCC GACCC GACCC GACCC GA
1843862 TGTCCCAAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.22, C:0.56, G:0.22, T:0.00
Consensus pattern (5 bp):
GACCC
Found at i:1848304 original size:21 final size:22
Alignment explanation
Indices: 1848280--1848330 Score: 52
Period size: 21 Copynumber: 2.4 Consensus size: 22
1848270 GGTTCATGTA
1848280 TTGAGATATTTTCA-AATTCTT
1 TTGAGATATTTTCATAATTCTT
* * *
1848301 TTGA-ACATTTTGATGATTCTT
1 TTGAGATATTTTCATAATTCTT
*
1848322 TTGGGATAT
1 TTGAGATAT
1848331 GATATTTATT
Statistics
Matches: 23, Mismatches: 5, Indels: 3
0.74 0.16 0.10
Matches are distributed among these distances:
20 7 0.30
21 13 0.57
22 3 0.13
ACGTcount: A:0.25, C:0.08, G:0.16, T:0.51
Consensus pattern (22 bp):
TTGAGATATTTTCATAATTCTT
Found at i:1851488 original size:22 final size:22
Alignment explanation
Indices: 1851460--1851505 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
1851450 TATAAAAAAT
*
1851460 AAAAAT-ATTTTTATAAATTTTA
1 AAAAATAAATTTTAT-AATTTTA
*
1851482 AAAAATAAATTTTATATTTTTA
1 AAAAATAAATTTTATAATTTTA
1851504 AA
1 AA
1851506 TAATTGAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 14 0.67
23 7 0.33
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
AAAAATAAATTTTATAATTTTA
Found at i:1851585 original size:21 final size:22
Alignment explanation
Indices: 1851560--1851602 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1851550 TTCATACTTT
* *
1851560 TATTTTATA-AAAAATTAAAAA
1 TATTTAATACAAAAATAAAAAA
1851581 TATTTAATACAAAAATAAAAAA
1 TATTTAATACAAAAATAAAAAA
1851603 ATAATAATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (22 bp):
TATTTAATACAAAAATAAAAAA
Found at i:1851624 original size:29 final size:29
Alignment explanation
Indices: 1851566--1851623 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
1851556 CTTTTATTTT
*
1851566 ATAAAAAATTAAAAATATTTAATACAAAA
1 ATAAAAAAATAAAAATATTTAATACAAAA
* *
1851595 ATAAAAAAATAATAATTTTTAA-ACAAAA
1 ATAAAAAAATAAAAATATTTAATACAAAA
1851623 A
1 A
1851624 AAATGGAAGA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 7 0.27
29 19 0.73
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (29 bp):
ATAAAAAAATAAAAATATTTAATACAAAA
Found at i:1853233 original size:17 final size:17
Alignment explanation
Indices: 1853211--1853246 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
1853201 AGAGTAATGC
*
1853211 CCAGAGTTGTTCGAAAG
1 CCAGAGTTGTTCAAAAG
1853228 CCAGAGTTGTTCAAAAG
1 CCAGAGTTGTTCAAAAG
1853245 CC
1 CC
1853247 GGAGCTTTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.31, C:0.22, G:0.25, T:0.22
Consensus pattern (17 bp):
CCAGAGTTGTTCAAAAG
Found at i:1857285 original size:19 final size:19
Alignment explanation
Indices: 1857247--1857285 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
1857237 TCATCTATTT
* * *
1857247 AATTAAATTTAATTAGATA
1 AATTAAAATTAATAAAATA
1857266 AATTAAAATTAATAAAATA
1 AATTAAAATTAATAAAATA
1857285 A
1 A
1857286 GATTCCTCTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (19 bp):
AATTAAAATTAATAAAATA
Found at i:1857875 original size:31 final size:32
Alignment explanation
Indices: 1857825--1857891 Score: 91
Period size: 31 Copynumber: 2.1 Consensus size: 32
1857815 AAATAACTAT
**
1857825 AAATTATCGTTAAATTTTATTAAATTATTACA
1 AAATTATCAATAAATTTTATTAAATTATTACA
* *
1857857 AAATTATCAATAAA-TTTATTGAATTGTTACA
1 AAATTATCAATAAATTTTATTAAATTATTACA
1857888 AAAT
1 AAAT
1857892 AACAATTAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
31 19 0.61
32 12 0.39
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.43
Consensus pattern (32 bp):
AAATTATCAATAAATTTTATTAAATTATTACA
Found at i:1857907 original size:31 final size:31
Alignment explanation
Indices: 1857841--1857921 Score: 92
Period size: 31 Copynumber: 2.6 Consensus size: 31
1857831 TCGTTAAATT
* * *
1857841 TTATTAAATTATTACAAAATTATCAATAAAT
1 TTATTGAATTATTACAAAATTAACAATAAAC
*
1857872 TTATTGAATTGTTACAAAA-TAACAATTAAAC
1 TTATTGAATTATTACAAAATTAACAA-TAAAC
* *
1857903 TTATTGAGTTATTGCAAAA
1 TTATTGAATTATTACAAAA
1857922 ATGATCTTTA
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
30 5 0.12
31 37 0.88
ACGTcount: A:0.47, C:0.07, G:0.06, T:0.40
Consensus pattern (31 bp):
TTATTGAATTATTACAAAATTAACAATAAAC
Found at i:1859245 original size:22 final size:22
Alignment explanation
Indices: 1859220--1859266 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
1859210 CTCCCCCCTC
1859220 CACCCTATAAACCCTCCATCTA
1 CACCCTATAAACCCTCCATCTA
1859242 CACCCTATAAACCCTCCATCTA
1 CACCCTATAAACCCTCCATCTA
1859264 CAC
1 CAC
1859267 GATCGCTTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.32, C:0.47, G:0.00, T:0.21
Consensus pattern (22 bp):
CACCCTATAAACCCTCCATCTA
Found at i:1863006 original size:21 final size:21
Alignment explanation
Indices: 1862978--1863127 Score: 182
Period size: 21 Copynumber: 7.2 Consensus size: 21
1862968 GATTCGTAAC
1862978 GCGAACTTCGACTATCGCAAT
1 GCGAACTTCGACTATCGCAAT
* *
1862999 GAGAACTTGGACTATCGCAAT
1 GCGAACTTCGACTATCGCAAT
*
1863020 GCGAA-TAT-GTA-AATCGCAAT
1 GCGAACT-TCG-ACTATCGCAAT
*
1863040 GCGATA-GTCGACTATCGCAAT
1 GCGA-ACTTCGACTATCGCAAT
*
1863061 GCGAACTTCGACTATTGCAAT
1 GCGAACTTCGACTATCGCAAT
*
1863082 GCGAACTTCAACTATCGCAAT
1 GCGAACTTCGACTATCGCAAT
*
1863103 GCGAACTTGGACTATCGCAAT
1 GCGAACTTCGACTATCGCAAT
1863124 GCGA
1 GCGA
1863128 TAGTCGAAGT
Statistics
Matches: 111, Mismatches: 12, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
20 17 0.15
21 94 0.85
ACGTcount: A:0.31, C:0.23, G:0.21, T:0.24
Consensus pattern (21 bp):
GCGAACTTCGACTATCGCAAT
Found at i:1863141 original size:21 final size:21
Alignment explanation
Indices: 1863117--1863162 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
1863107 ACTTGGACTA
* *
1863117 TCGCAATGCGATAGTCGAAGT
1 TCGCAATGCGATAATCCAAGT
**
1863138 TCGCGTTGCGATAATCCAAGT
1 TCGCAATGCGATAATCCAAGT
1863159 TCGC
1 TCGC
1863163 GTTGCGATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.24, C:0.24, G:0.26, T:0.26
Consensus pattern (21 bp):
TCGCAATGCGATAATCCAAGT
Found at i:1863163 original size:21 final size:21
Alignment explanation
Indices: 1863123--1863170 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
1863113 ACTATCGCAA
* *
1863123 TGCGATAGTCGAAGTTCGCGT
1 TGCGATAATCCAAGTTCGCGT
1863144 TGCGATAATCCAAGTTCGCGT
1 TGCGATAATCCAAGTTCGCGT
1863165 TGCGAT
1 TGCGAT
1863171 TTATTCCAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (21 bp):
TGCGATAATCCAAGTTCGCGT
Found at i:1863184 original size:23 final size:22
Alignment explanation
Indices: 1863137--1863191 Score: 62
Period size: 21 Copynumber: 2.6 Consensus size: 22
1863127 ATAGTCGAAG
*
1863137 TTCGCGTTGCGA-TAATCCAAG
1 TTCGCGTTGCGATTAATCCAAA
*
1863158 TTCGCGTTGCGATTTATTCCAAA
1 TTCGCGTTGCGA-TTAATCCAAA
1863181 TT--CGTTGCGAT
1 TTCGCGTTGCGAT
1863192 AGTTCAAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
20 1 0.03
21 20 0.67
23 9 0.30
ACGTcount: A:0.20, C:0.22, G:0.22, T:0.36
Consensus pattern (22 bp):
TTCGCGTTGCGATTAATCCAAA
Found at i:1863966 original size:21 final size:20
Alignment explanation
Indices: 1863914--1864036 Score: 90
Period size: 21 Copynumber: 6.0 Consensus size: 20
1863904 CGTTGCGATT
1863914 TTGGACTATCGCAA--CGAA
1 TTGGACTATCGCAATGCGAA
* *
1863932 TTTGGAATAAATCGCAACGCGAA
1 -TTGGACT--ATCGCAATGCGAA
*
1863955 CTTGGACTATCGCAATACGAA
1 -TTGGACTATCGCAATGCGAA
* * *
1863976 TATGTA-AATCACAATGCGATA
1 T-TGGACTATCGCAATGCGA-A
* *
1863997 GTCGACTATCGCAATGCGAA
1 TTGGACTATCGCAATGCGAA
1864017 CTTGGACTATCGCAATGCGA
1 -TTGGACTATCGCAATGCGA
1864037 TGCTCCAAGT
Statistics
Matches: 80, Mismatches: 16, Indels: 14
0.73 0.15 0.13
Matches are distributed among these distances:
19 6 0.08
20 14 0.17
21 50 0.62
23 10 0.12
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.24
Consensus pattern (20 bp):
TTGGACTATCGCAATGCGAA
Found at i:1864050 original size:21 final size:21
Alignment explanation
Indices: 1864026--1864099 Score: 96
Period size: 21 Copynumber: 3.5 Consensus size: 21
1864016 ACTTGGACTA
*
1864026 TCGCAATGCGAT-GCTCCAAGT
1 TCGCATTGCGATAG-TCCAAGT
1864047 TCGCATTGCGATAGTCCAAGT
1 TCGCATTGCGATAGTCCAAGT
**
1864068 TCGCATTGCGATAGTAGAAGT
1 TCGCATTGCGATAGTCCAAGT
*
1864089 TCGCGTTGCGA
1 TCGCATTGCGA
1864100 ATCTGGAAAC
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
21 47 0.98
22 1 0.02
ACGTcount: A:0.23, C:0.23, G:0.27, T:0.27
Consensus pattern (21 bp):
TCGCATTGCGATAGTCCAAGT
Found at i:1872236 original size:116 final size:116
Alignment explanation
Indices: 1872022--1872323 Score: 268
Period size: 116 Copynumber: 2.6 Consensus size: 116
1872012 CAATGGAATG
* * * * * * *
1872022 GTTCATAATGAGAAGAACTCATCTGATGAGGGAGAATAAGTTCCTAGTGAGAAGAACTTGTTTAA
1 GTTCATAATGAGAAGAAATCATCCGATGAGGCAGAAAAAGTTCATAATGAGAAGAACTTGTTCAA
**
1872087 ACTTGTCTTGTCCATCACAAAAGAAGGAAGATCAACATTTTGAATGAAAGA
66 ACTTGTCTCATCCATCACAAAAGAAGGAAGATCAACATTTTGAATGAAAGA
*
1872138 GTTCATAATGAGAATAAATCATCCGATGATGGCA-AAAAAGTTCATAATGAGAAGAACTTGTTCA
1 GTTCATAATGAGAAGAAATCATCCGATGA-GGCAGAAAAAGTTCATAATGAGAAGAACTTGTTCA
* * * * ** * ** *
1872202 ACCTTAGT-TCATCCATCATAGAAGAATGTGGATCAACATCTCCACT-AGAAGA
65 AACTT-GTCTCATCCATCACAAAAGAAGGAAGATCAACATTTTGAATGA-AAGA
* * * * * * * * * * *
1872254 ATTCATAATGAGAAGAACTCGTCTGGTGGGGGAGAAGAAGTTCCTAATGAAAATAACTTGTTCAA
1 GTTCATAATGAGAAGAAATCATCCGATGAGGCAGAAAAAGTTCATAATGAGAAGAACTTGTTCAA
*
1872319 TCTTG
66 ACTTG
1872324 GTTCCTTCAT
Statistics
Matches: 149, Mismatches: 33, Indels: 9
0.78 0.17 0.05
Matches are distributed among these distances:
115 5 0.03
116 139 0.93
117 5 0.03
ACGTcount: A:0.38, C:0.15, G:0.21, T:0.27
Consensus pattern (116 bp):
GTTCATAATGAGAAGAAATCATCCGATGAGGCAGAAAAAGTTCATAATGAGAAGAACTTGTTCAA
ACTTGTCTCATCCATCACAAAAGAAGGAAGATCAACATTTTGAATGAAAGA
Found at i:1872500 original size:35 final size:35
Alignment explanation
Indices: 1872461--1872595 Score: 145
Period size: 35 Copynumber: 3.9 Consensus size: 35
1872451 AAATCATATC
*
1872461 TCACTTAAGATTG-TTTTCTTAAAACAAAGTTCGT
1 TCACTTAAGATTGTTTTTCTTAAAACAAATTTCGT
* **
1872495 ATCACTT--GATAT-TTTTTCCTAAAATGAATTTCGT
1 -TCACTTAAGAT-TGTTTTTCTTAAAACAAATTTCGT
*
1872529 TCACTTAAGATTGTTTTTCTTAAAAACTAATTTCGT
1 TCACTTAAGATTGTTTTTCTT-AAAACAAATTTCGT
*
1872565 CTCACTTGAGATTGTTTTTCTTAAAA-AAATT
1 -TCACTTAAGATTGTTTTTCTTAAAACAAATT
1872596 GTCTCGCATG
Statistics
Matches: 84, Mismatches: 9, Indels: 14
0.79 0.08 0.13
Matches are distributed among these distances:
33 9 0.11
34 19 0.23
35 20 0.24
36 16 0.19
37 20 0.24
ACGTcount: A:0.31, C:0.14, G:0.10, T:0.45
Consensus pattern (35 bp):
TCACTTAAGATTGTTTTTCTTAAAACAAATTTCGT
Found at i:1872591 original size:37 final size:36
Alignment explanation
Indices: 1872459--1872590 Score: 150
Period size: 37 Copynumber: 3.8 Consensus size: 36
1872449 ACAAATCATA
* *
1872459 TCTCACTTAAGATTG-TTTTCTTAAAACAAAGTTCG
1 TCTCACTTAAGATTGTTTTTCTTAAAACTAATTTCG
* *
1872494 TATCACTT--GATAT-TTTTTCCTAAAA-TGAATTTCG
1 TCTCACTTAAGAT-TGTTTTTCTTAAAACT-AATTTCG
1872528 T-TCACTTAAGATTGTTTTTCTTAAAAACTAATTTCG
1 TCTCACTTAAGATTGTTTTTCTT-AAAACTAATTTCG
*
1872564 TCTCACTTGAGATTGTTTTTCTTAAAA
1 TCTCACTTAAGATTGTTTTTCTTAAAA
1872591 AAATTGTCTC
Statistics
Matches: 82, Mismatches: 6, Indels: 17
0.78 0.06 0.16
Matches are distributed among these distances:
33 9 0.11
34 19 0.23
35 17 0.21
36 16 0.20
37 21 0.26
ACGTcount: A:0.30, C:0.15, G:0.10, T:0.45
Consensus pattern (36 bp):
TCTCACTTAAGATTGTTTTTCTTAAAACTAATTTCG
Found at i:1872797 original size:134 final size:127
Alignment explanation
Indices: 1872543--1872842 Score: 320
Period size: 134 Copynumber: 2.3 Consensus size: 127
1872533 TTAAGATTGT
*
1872543 TTTTCTTAAAAACTAATTTCGTCTCACTTGAGATTGTTTTTCTTAAAAAAATTGTCTCGCATGAG
1 TTTTCTT-AAAACTAATTCCGTCTCACTTGAGATTGTTTTTCTTAAAAAAATTGTCTCGCATGAG
*
1872608 ACAATTTCCTTTGAAACAAAAACTCATAAATCATTTAAAAAATCTAATATCACTTGAGATTAA
65 ACAATTTCCTTTGAAACAAAAACTCATAAATCATTTAAAAAATCTAATATAACTTGAGATTAA
* *
1872671 TTTTCTTGAAAA-TGAATTCCGTCTCACTTGAGTTTGTTTTTCTTAAAAAACAAAATTTGGTCTT
1 TTTTCTT-AAAACT-AATTCCGTCTCACTTGAGATTGTTTTTCTT---AAA-AAAA-TT-GTCTC
* * * * *
1872735 GCATGAGATC-GTTTCC-TT-CAACATACAAACTCCTAAATCATTTCAAAAATCTTATATAACTT
58 GCATGAGA-CAATTTCCTTTGAAACA-A-AAACTCATAAATCATTTAAAAAATCTAATATAACTT
**
1872797 GAGATTGT
120 GAGATTAA
* *** *
1872805 TTTTCTTAAAACAAATTTTATCTCACTTGAGATAGTTT
1 TTTTCTTAAAACTAATTCCGTCTCACTTGAGATTGTTT
1872843 CCTTTGAAAC
Statistics
Matches: 143, Mismatches: 18, Indels: 17
0.80 0.10 0.10
Matches are distributed among these distances:
127 1 0.01
128 39 0.27
131 3 0.02
132 8 0.06
133 29 0.20
134 62 0.43
135 1 0.01
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.40
Consensus pattern (127 bp):
TTTTCTTAAAACTAATTCCGTCTCACTTGAGATTGTTTTTCTTAAAAAAATTGTCTCGCATGAGA
CAATTTCCTTTGAAACAAAAACTCATAAATCATTTAAAAAATCTAATATAACTTGAGATTAA
Found at i:1873858 original size:37 final size:41
Alignment explanation
Indices: 1873767--1873858 Score: 113
Period size: 42 Copynumber: 2.3 Consensus size: 41
1873757 TCATATTCCC
*
1873767 ATAAAAAGAGACATTCTAATATGGGTAAATTATTGTGGACTTA
1 ATAAAAAGAGACATTATAATATGGGTAAATTATTGTGGA--TA
*
1873810 AT-AAAAGAGACATTATAATATGGGTAAGTTA-T-T-GA-A
1 ATAAAAAGAGACATTATAATATGGGTAAATTATTGTGGATA
1873846 ATAAAAAGAGACA
1 ATAAAAAGAGACA
1873859 AAGGGGATAT
Statistics
Matches: 46, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
36 3 0.07
37 10 0.22
39 2 0.04
40 1 0.02
41 1 0.02
42 27 0.59
43 2 0.04
ACGTcount: A:0.48, C:0.05, G:0.18, T:0.28
Consensus pattern (41 bp):
ATAAAAAGAGACATTATAATATGGGTAAATTATTGTGGATA
Found at i:1883023 original size:20 final size:20
Alignment explanation
Indices: 1882981--1883023 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1882971 TAGTCAGTAG
* *
1882981 GTATCGATACCTAGAGGTTA
1 GTATCGATACCCAGAGGTCA
*
1883001 GTATCGATACCCAGGGGTCA
1 GTATCGATACCCAGAGGTCA
1883021 GTA
1 GTA
1883024 CCAATACTGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.28, C:0.19, G:0.28, T:0.26
Consensus pattern (20 bp):
GTATCGATACCCAGAGGTCA
Found at i:1885125 original size:20 final size:20
Alignment explanation
Indices: 1885097--1885167 Score: 61
Period size: 20 Copynumber: 3.4 Consensus size: 20
1885087 GATTTGTTTT
* *
1885097 ATCTAAGATTATAAGATGTA
1 ATCTTAGATTATAAGATATA
* * *
1885117 ATCTTAGATTTTTTAATAGATTTG
1 ATCTTAGA--TTAT-A-AGATATA
1885141 ATCTTAGATTATAAGATATA
1 ATCTTAGATTATAAGATATA
1885161 ATCTTAG
1 ATCTTAG
1885168 GTTTCAGTAA
Statistics
Matches: 40, Mismatches: 7, Indels: 8
0.73 0.13 0.15
Matches are distributed among these distances:
20 19 0.47
21 1 0.03
22 6 0.15
23 1 0.03
24 13 0.32
ACGTcount: A:0.38, C:0.06, G:0.13, T:0.44
Consensus pattern (20 bp):
ATCTTAGATTATAAGATATA
Found at i:1892373 original size:19 final size:19
Alignment explanation
Indices: 1892349--1892400 Score: 77
Period size: 19 Copynumber: 2.7 Consensus size: 19
1892339 TTAATAAAAG
*
1892349 TTTTCTTCTTTTTATATTC
1 TTTTCTACTTTTTATATTC
*
1892368 TTTTCTAGTTTTTATATTC
1 TTTTCTACTTTTTATATTC
*
1892387 TTTTCTAGTTTTTA
1 TTTTCTACTTTTTA
1892401 CTTTCAAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.13, C:0.12, G:0.04, T:0.71
Consensus pattern (19 bp):
TTTTCTACTTTTTATATTC
Found at i:1898101 original size:42 final size:42
Alignment explanation
Indices: 1898034--1898243 Score: 339
Period size: 42 Copynumber: 5.0 Consensus size: 42
1898024 TCTAGAGCCC
* * *
1898034 TCTTCAGGAAATGAAGTATTATGTTGATTGTCATCTCCATTT
1 TCTTCAGCAAATAAAGTATTCTGTTGATTGTCATCTCCATTT
*
1898076 TCTTCAGCAAATAAAGCATTCTGTTGATTGTCATCTCCATTT
1 TCTTCAGCAAATAAAGTATTCTGTTGATTGTCATCTCCATTT
* *
1898118 TCTTCAGGAAATAAAGTATTATGTTGATTGTCATCTCCATTT
1 TCTTCAGCAAATAAAGTATTCTGTTGATTGTCATCTCCATTT
*
1898160 TCTTCAGCAAATAAAGCATTCTGTTGATTGTCATCTCCATTT
1 TCTTCAGCAAATAAAGTATTCTGTTGATTGTCATCTCCATTT
* *
1898202 TCTTCAGCAAATAATGTATTCTGTTGATTGTCATCTTCATTT
1 TCTTCAGCAAATAAAGTATTCTGTTGATTGTCATCTCCATTT
1898244 GAGTTGGTTG
Statistics
Matches: 155, Mismatches: 13, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 155 1.00
ACGTcount: A:0.26, C:0.18, G:0.13, T:0.43
Consensus pattern (42 bp):
TCTTCAGCAAATAAAGTATTCTGTTGATTGTCATCTCCATTT
Found at i:1898175 original size:84 final size:84
Alignment explanation
Indices: 1898034--1898243 Score: 375
Period size: 84 Copynumber: 2.5 Consensus size: 84
1898024 TCTAGAGCCC
*
1898034 TCTTCAGGAAATGAAGTATTATGTTGATTGTCATCTCCATTTTCTTCAGCAAATAAAGCATTCTG
1 TCTTCAGGAAATAAAGTATTATGTTGATTGTCATCTCCATTTTCTTCAGCAAATAAAGCATTCTG
1898099 TTGATTGTCATCTCCATTT
66 TTGATTGTCATCTCCATTT
1898118 TCTTCAGGAAATAAAGTATTATGTTGATTGTCATCTCCATTTTCTTCAGCAAATAAAGCATTCTG
1 TCTTCAGGAAATAAAGTATTATGTTGATTGTCATCTCCATTTTCTTCAGCAAATAAAGCATTCTG
1898183 TTGATTGTCATCTCCATTT
66 TTGATTGTCATCTCCATTT
* * * *
1898202 TCTTCAGCAAATAATGTATTCTGTTGATTGTCATCTTCATTT
1 TCTTCAGGAAATAAAGTATTATGTTGATTGTCATCTCCATTT
1898244 GAGTTGGTTG
Statistics
Matches: 121, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
84 121 1.00
ACGTcount: A:0.26, C:0.18, G:0.13, T:0.43
Consensus pattern (84 bp):
TCTTCAGGAAATAAAGTATTATGTTGATTGTCATCTCCATTTTCTTCAGCAAATAAAGCATTCTG
TTGATTGTCATCTCCATTT
Found at i:1900569 original size:229 final size:227
Alignment explanation
Indices: 1900164--1900612 Score: 808
Period size: 229 Copynumber: 2.0 Consensus size: 227
1900154 GTAAATTATC
* * *
1900164 TATCCTTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAATATATTTATTATTATCTTTAGT
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
**
1900229 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTT
66 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATTT
1900294 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAATAAATTG
131 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAATAAATTG
1900359 AAACATAAATTACATAACTTTCAAAAAAGTATA
196 AAACATAAATTACATAACTTT-AAAAAAGTATA
*
1900392 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTTGAAAACATATTTATTATTATATTTGG
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTG-TGAAAACATATTTATTATTATATTTAG
*
1900457 TTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATT
65 TTAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATT
*
1900522 TTGTGTAAATTAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAATAAATT
130 TTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAATAAATT
1900587 GAAACATAAATTACATAACTTTAAAA
195 GAAACATAAATTACATAACTTTAAAA
1900613 GCAGTTTAAA
Statistics
Matches: 212, Mismatches: 8, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
228 40 0.19
229 172 0.81
ACGTcount: A:0.45, C:0.08, G:0.07, T:0.40
Consensus pattern (227 bp):
TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATTT
TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAATAAATTG
AAACATAAATTACATAACTTTAAAAAAGTATA
Found at i:1900700 original size:20 final size:19
Alignment explanation
Indices: 1900677--1900722 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 19
1900667 CGATATACCA
1900677 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
1900697 GGTAACAAAATGATAAAACC
1 GGTAA-AAAATGATAAAACC
1900717 GGTAAA
1 GGTAAA
1900723 TTTAAAAGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.04
20 21 0.84
21 3 0.12
ACGTcount: A:0.54, C:0.11, G:0.17, T:0.17
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:1900867 original size:20 final size:19
Alignment explanation
Indices: 1900844--1900890 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
1900834 CGATATAACA
1900844 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
*
1900864 GGTATCAAAATGATAAAACC
1 GGTA-AAAAATGATAAAACC
1900884 GGTAAAA
1 GGTAAAA
1900891 TGATACCGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.53, C:0.11, G:0.17, T:0.19
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:1900892 original size:17 final size:19
Alignment explanation
Indices: 1900853--1900895 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
1900843 AGGTAAAAAT
1900853 ATGATAAAACCGGTATCAAA
1 ATGATAAAACCGG-ATCAAA
1900873 ATGATAAAACCGG-T-AAA
1 ATGATAAAACCGGATCAAA
1900890 ATGATA
1 ATGATA
1900896 CCGGATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.39
18 1 0.04
20 13 0.57
ACGTcount: A:0.51, C:0.12, G:0.16, T:0.21
Consensus pattern (19 bp):
ATGATAAAACCGGATCAAA
Found at i:1903164 original size:21 final size:21
Alignment explanation
Indices: 1903117--1903181 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
1903107 AAGACAATCA
* * *
1903117 AGAGTCGAAGAGAAACTTGATC
1 AGAGTCGAAGATAAACTCGA-G
*
1903139 A-AGTCGTAGATAAACTCGAG
1 AGAGTCGAAGATAAACTCGAG
*
1903159 AGAGTCGAAGATACACTCGAG
1 AGAGTCGAAGATAAACTCGAG
1903180 AG
1 AG
1903182 GCATAAGGGG
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
20 1 0.03
21 34 0.94
22 1 0.03
ACGTcount: A:0.40, C:0.15, G:0.28, T:0.17
Consensus pattern (21 bp):
AGAGTCGAAGATAAACTCGAG
Found at i:1903257 original size:33 final size:33
Alignment explanation
Indices: 1903215--1903280 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
1903205 AAATAGATGG
*
1903215 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
* *
1903248 AGTGGTGAAAGAAGTTGGGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
1903281 TATTAAGATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.29, C:0.00, G:0.48, T:0.23
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:1905098 original size:19 final size:19
Alignment explanation
Indices: 1905074--1905123 Score: 82
Period size: 19 Copynumber: 2.6 Consensus size: 19
1905064 AATGTAGGGT
1905074 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
1905093 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
*
1905112 TATTTTTGTATA
1 TAATTTTGTATA
1905124 TGAATATAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.32, C:0.02, G:0.10, T:0.56
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:1905639 original size:198 final size:198
Alignment explanation
Indices: 1905241--1906406 Score: 2255
Period size: 198 Copynumber: 5.9 Consensus size: 198
1905231 CAATATGGCC
1905241 AACAGGGTGCACCCATAAAGTGTCGATCCATATAT-AAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1905305 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
1905370 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTT-CCAGAATGAAT
1905435 GGAA
195 GGAA
1905439 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
* *
1905504 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACTGGTACATTTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
1905569 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATG
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATG
1905634 GAA
196 GAA
1905637 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1905702 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
1905767 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTTCCAGAATGAAT
1905832 GGAA
195 GGAA
1905836 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1905901 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
*
1905966 AATATGTATAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATG
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATG
1906031 GAA
196 GAA
1906034 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1906099 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
*
1906164 AATATGTATAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATG
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATG
1906229 GAA
196 GAA
*
1906232 AACAGGGTGCACCCATAAAGTGTCGATCCATATAT-AAAATTGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1906296 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
1906361 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA
1906407 CTAATTTAAA
Statistics
Matches: 959, Mismatches: 7, Indels: 5
0.99 0.01 0.01
Matches are distributed among these distances:
197 138 0.14
198 479 0.50
199 342 0.36
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.31
Consensus pattern (198 bp):
AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATG
GAA
Found at i:1906009 original size:397 final size:397
Alignment explanation
Indices: 1905241--1906406 Score: 2257
Period size: 397 Copynumber: 2.9 Consensus size: 397
1905231 CAATATGGCC
1905241 AACAGGGTGCACCCATAAAGTGTCGATCCATATAT-AAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1905305 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
*
1905370 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAAT
1905435 GGAAAACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG
196 GGAAAACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG
* *
1905500 AACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACTGGTACATTTATACCGGTTTTATG
261 AACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATG
1905565 AGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATG
326 AGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATG
1905630 AATGGAA
391 AATGGAA
1905637 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1905702 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
1905767 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAAT
1905832 GGAAAACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG
196 GGAAAACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG
1905897 AACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATG
261 AACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATG
*
1905962 AGAGAATATGTATAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATG
326 AGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATG
1906027 AATGGAA
391 AATGGAA
1906034 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1906099 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
*
1906164 AATATGTATAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTTCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAAT
*
1906228 GGAAAACAGGGTGCACCCATAAAGTGTCGATCCATATAT-AAAATTGTCGATCCCAAAATCATCG
196 GGAAAACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG
1906292 AACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATG
261 AACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATG
1906357 AGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA
326 AGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA
1906407 CTAATTTAAA
Statistics
Matches: 762, Mismatches: 7, Indels: 3
0.99 0.01 0.00
Matches are distributed among these distances:
395 138 0.18
396 92 0.12
397 532 0.70
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.31
Consensus pattern (397 bp):
AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAAT
GGAAAACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG
AACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATG
AGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATG
AATGGAA
Found at i:1907892 original size:6 final size:6
Alignment explanation
Indices: 1907867--1907928 Score: 54
Period size: 6 Copynumber: 10.3 Consensus size: 6
1907857 AGCGGTCGCA
* * * * *
1907867 GAAGAT GAAGCT GACA-AT GAAGAT GACGAT GATGAT GATGAT GATGAT
1 GAAGAT GAAGAT GA-AGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT
*
1907915 GATGAT GAAGAT GA
1 GAAGAT GAAGAT GA
1907929 TGATCCAAAC
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
5 1 0.02
6 47 0.96
7 1 0.02
ACGTcount: A:0.40, C:0.05, G:0.32, T:0.23
Consensus pattern (6 bp):
GAAGAT
Found at i:1907902 original size:3 final size:3
Alignment explanation
Indices: 1907883--1907932 Score: 73
Period size: 3 Copynumber: 16.7 Consensus size: 3
1907873 GAAGCTGACA
* * *
1907883 ATG AAG ATG ACG ATG ATG ATG ATG ATG ATG ATG ATG ATG AAG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
1907931 AT
1 AT
1907933 CCAAACAAGT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.38, C:0.02, G:0.32, T:0.28
Consensus pattern (3 bp):
ATG
Found at i:1909488 original size:76 final size:77
Alignment explanation
Indices: 1909397--1909552 Score: 287
Period size: 78 Copynumber: 2.0 Consensus size: 77
1909387 ACCGGTATAA
*
1909397 ATATACCGGTTTTAT-GCGAATAGGTCTACAACCTATATCGACACTTTTTAATATTGTGTTGGTA
1 ATATACCGGTTTTATCGCGAATAGGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTA
1909461 CTTTATGTCCAT
66 CTTTATGTCCAT
1909473 ATATACCGGTTTTATGCGCGAATAGGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGT
1 ATATACCGGTTTTAT-CGCGAATAGGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGT
1909538 ACTTTATGTCCAT
65 ACTTTATGTCCAT
1909551 AT
1 AT
1909553 TGGAAGAAAA
Statistics
Matches: 77, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
76 15 0.19
78 62 0.81
ACGTcount: A:0.26, C:0.18, G:0.16, T:0.40
Consensus pattern (77 bp):
ATATACCGGTTTTATCGCGAATAGGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTA
CTTTATGTCCAT
Found at i:1909781 original size:183 final size:183
Alignment explanation
Indices: 1909473--1910139 Score: 1237
Period size: 183 Copynumber: 3.7 Consensus size: 183
1909463 TTATGTCCAT
1909473 ATATACCGGTTTTATGCGCGAATAGGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGT
1 ATATACCGGTTTTATGCGCGAATAGGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGT
1909538 ACTTTATGTCCATATTGGAAGAAAAATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACA
66 ACTTTATGTCCATATTGGAAGAAAAATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACA
* *
1909603 TCAGAACCCATAATTATAATGTAATAGATAATTTTATAATATAACCGATATAA
131 TCGGAACCCATAATTATAATGTAATAGATAATTTTATAATATAACCGGTATAA
1909656 ATATACCGGTTTTATGCGCGAATAGGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGT
1 ATATACCGGTTTTATGCGCGAATAGGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGT
1909721 ACTTTATGTCCATATTGGAAGAAAAATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACA
66 ACTTTATGTCCATATTGGAAGAAAAATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACA
1909786 TCGGAACCCATAATTATAATGTAATAGATAATTTTATAATATAACCGGTATAA
131 TCGGAACCCATAATTATAATGTAATAGATAATTTTATAATATAACCGGTATAA
*
1909839 ATATACCGGTTTTATGCGCGAATAGGTCTACAACCTTTATCGACACTTTTTAATATTGTGTCGGT
1 ATATACCGGTTTTATGCGCGAATAGGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGT
*
1909904 ACTTTATGTCCATATTGGAAGAAAAATGTGTCGATACGATTTAAAAAAGTATCGACATTTACACA
66 ACTTTATGTCCATATTGGAAGAAAAATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACA
* * *
1909969 TCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAATATAACCGGTATAA
131 TCGGAACCCATAATTATAATGTAATAGATAATTTTATAATATAACCGGTATAA
* *
1910022 ATATATCGGTTTTATGCGCGAATAGGTCTACAACCTATATCGACACTTTATAATATTGTGTCGGT
1 ATATACCGGTTTTATGCGCGAATAGGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGT
*
1910087 ACTTTATGTCCA-ATTGGAAGAAAAATGTGTCGATACCATTTAAAAAAGTGTCG
66 ACTTTATGTCCATATTGGAAGAAAAATGTGTCGATACGATTTAAAAAAGTGTCG
1910140 GTAATTTTAA
Statistics
Matches: 472, Mismatches: 12, Indels: 1
0.97 0.02 0.00
Matches are distributed among these distances:
182 39 0.08
183 433 0.92
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Consensus pattern (183 bp):
ATATACCGGTTTTATGCGCGAATAGGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGT
ACTTTATGTCCATATTGGAAGAAAAATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACA
TCGGAACCCATAATTATAATGTAATAGATAATTTTATAATATAACCGGTATAA
Found at i:1912645 original size:25 final size:25
Alignment explanation
Indices: 1912611--1912675 Score: 85
Period size: 25 Copynumber: 2.6 Consensus size: 25
1912601 TTATCATTAA
1912611 ATTTAGGTATGTACAATAACTACAT
1 ATTTAGGTATGTACAATAACTACAT
****
1912636 ATTTAGGTATGTTTGTTAACTACAT
1 ATTTAGGTATGTACAATAACTACAT
*
1912661 ATTTAGGTATATACA
1 ATTTAGGTATGTACA
1912676 TCTTTTGAGT
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.35, C:0.09, G:0.14, T:0.42
Consensus pattern (25 bp):
ATTTAGGTATGTACAATAACTACAT
Found at i:1913053 original size:23 final size:23
Alignment explanation
Indices: 1913022--1913085 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
1913012 ATAGGTAAAC
*
1913022 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
1913045 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
1913068 ATATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
1913086 TGGTTATATT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.36, C:0.06, G:0.20, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:1913092 original size:23 final size:23
Alignment explanation
Indices: 1913022--1913094 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
1913012 ATAGGTAAAC
* **
1913022 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGTGCTT
*
1913045 ATATAATGTAATAGGTA-TCGTTT
1 ATATAATGTAATAGGTAGT-GCTT
*
1913068 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGTGCTT
1913091 ATAT
1 ATAT
1913095 TGTAAAGTGT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
23 42 0.98
24 1 0.02
ACGTcount: A:0.34, C:0.05, G:0.21, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGTGCTT
Found at i:1913397 original size:25 final size:25
Alignment explanation
Indices: 1913363--1913413 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
1913353 ACAACAAATC
*
1913363 AATTAAACATTGTTGTGGGTACATT
1 AATTAAACATTGTTATGGGTACATT
*
1913388 AATTGAACATTGTTATGGGTACATT
1 AATTAAACATTGTTATGGGTACATT
1913413 A
1 A
1913414 TTTGGAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.33, C:0.08, G:0.20, T:0.39
Consensus pattern (25 bp):
AATTAAACATTGTTATGGGTACATT
Found at i:1913823 original size:18 final size:18
Alignment explanation
Indices: 1913802--1913838 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1913792 GTAATTGGAG
1913802 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
1913820 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
1913838 T
1 T
1913839 ATATATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:1913846 original size:24 final size:24
Alignment explanation
Indices: 1913794--1913840 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
1913784 TTTCATATGT
* *
1913794 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATC
*
1913818 AATTTGAGTTTGAATTTCAATAT
1 AATTTGAGTTTGAATTTAAATAT
1913841 ATATTTCGGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.34, C:0.04, G:0.15, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATC
Found at i:1914139 original size:39 final size:39
Alignment explanation
Indices: 1914096--1914178 Score: 148
Period size: 39 Copynumber: 2.1 Consensus size: 39
1914086 TCCGATGCTC
*
1914096 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
*
1914135 ATCAAAATCCAAATCTCATATGATGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
1914174 ATCAA
1 ATCAA
1914179 TATCTACAAC
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 42 1.00
ACGTcount: A:0.48, C:0.20, G:0.14, T:0.17
Consensus pattern (39 bp):
ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
Found at i:1914617 original size:23 final size:23
Alignment explanation
Indices: 1914586--1914649 Score: 101
Period size: 23 Copynumber: 2.8 Consensus size: 23
1914576 ATAGGTAAAC
*
1914586 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* *
1914609 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
1914632 ATATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
1914650 TGGCTATATT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.36, C:0.05, G:0.22, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:1914657 original size:23 final size:23
Alignment explanation
Indices: 1914586--1914658 Score: 78
Period size: 23 Copynumber: 3.2 Consensus size: 23
1914576 ATAGGTAAAC
* *
1914586 ATATGATGTAATAGGTAG-CGCTT
1 ATATAATGTAATAGGTAGTGGC-T
**
1914609 ATATAATGTAATAGGTA-TCGTTT
1 ATATAATGTAATAGGTAGT-GGCT
1914632 ATATAATGTAATAGGTAGTGGCT
1 ATATAATGTAATAGGTAGTGGCT
1914655 ATAT
1 ATAT
1914659 TGTAAAGTGT
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
23 40 0.98
24 1 0.02
ACGTcount: A:0.34, C:0.05, G:0.22, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGTGGCT
Found at i:1915311 original size:335 final size:334
Alignment explanation
Indices: 1914701--1915370 Score: 1277
Period size: 335 Copynumber: 2.0 Consensus size: 334
1914691 CATACTTTTT
1914701 TCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAAT
1 TCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAAT
*
1914766 TATAGGCGTCTAATGATTTATTTTTTTCGTTACGATATATATTATTATTAAATTAAAAATTCTAA
66 TATAGGCGTCTAATGATTTATTTTTTACGTTACGATATATATTATTATTAAATTAAAAATTCTAA
* *
1914831 ATATTATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAAATGAAATTATTAAATTAA
131 ATAATATTTTATAAAATATCAAAACAATCAAATAAATTTTTGTGCAAATGAAATTATTAAATTAA
1914896 TATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAACATAAATTACATAACTTAAAAA
196 TATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAACATAAATTACATAACTTAAAAA
*
1914961 GAAGTATCGATCCTTTTTATAAAAAAGTATGGACACTTTCAATATAATATAATGTAATAGGTAAA
261 GAAATATCGATCCTTTTTAT-AAAAAGTATGGACACTTTCAATATAATATAATGTAATAGGTAAA
1915026 TTTGCAATGC
325 TTTGCAATGC
1915036 TCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAAT
1 TCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAAT
1915101 TATAGGCGTCTAATGATTTATTTTTTACGTTACGATATATATTATTATTAAATTAAAAATTCTAA
66 TATAGGCGTCTAATGATTTATTTTTTACGTTACGATATATATTATTATTAAATTAAAAATTCTAA
1915166 ATAATATTTTATAAAATATCAAAACAATCAAATAAATTTTTGTGCAAATGAAATTATTAAATTAA
131 ATAATATTTTATAAAATATCAAAACAATCAAATAAATTTTTGTGCAAATGAAATTATTAAATTAA
* *
1915231 TATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAACATAAATTACGTAACTTTAAAA
196 TATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAACATAAATTACATAACTTAAAAA
1915296 GAAATATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAATATAATGTAATAGGTAAAT
261 GAAATATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAATATAATGTAATAGGTAAAT
1915361 TTGCAATGC
326 TTGCAATGC
1915370 T
1 T
1915371 ATCGGTATAA
Statistics
Matches: 329, Mismatches: 6, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
334 55 0.17
335 274 0.83
ACGTcount: A:0.43, C:0.08, G:0.11, T:0.38
Consensus pattern (334 bp):
TCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAAT
TATAGGCGTCTAATGATTTATTTTTTACGTTACGATATATATTATTATTAAATTAAAAATTCTAA
ATAATATTTTATAAAATATCAAAACAATCAAATAAATTTTTGTGCAAATGAAATTATTAAATTAA
TATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAACATAAATTACATAACTTAAAAA
GAAATATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAATATAATGTAATAGGTAAAT
TTGCAATGC
Found at i:1915664 original size:24 final size:24
Alignment explanation
Indices: 1915632--1915705 Score: 112
Period size: 24 Copynumber: 3.0 Consensus size: 24
1915622 GTATTTGGAA
1915632 ACTGTTTCTGATCCTTCCTTTTCC
1 ACTGTTTCTGATCCTTCCTTTTCC
1915656 ACTGTTTCTGATCCTTCCTTTTCC
1 ACTGTTTCTGATCCTTCCTTTTCC
* **
1915680 ACTGTTTCAGCCCCTCTCCTTTTCC
1 ACTGTTTCTGATCCT-TCCTTTTCC
1915705 A
1 A
1915706 AGTTTGTTAT
Statistics
Matches: 46, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
24 36 0.78
25 10 0.22
ACGTcount: A:0.09, C:0.36, G:0.08, T:0.46
Consensus pattern (24 bp):
ACTGTTTCTGATCCTTCCTTTTCC
Found at i:1921576 original size:16 final size:16
Alignment explanation
Indices: 1921545--1921589 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
1921535 ATTTCAAAAT
1921545 ATATTA-TAATTA-TA
1 ATATTATTAATTATTA
1921559 ATATTATTAATTATTA
1 ATATTATTAATTATTA
*
1921575 AT-TATATTTATTATT
1 ATAT-TATTAATTATT
1921590 TTACACGTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
14 6 0.22
15 7 0.26
16 14 0.52
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
ATATTATTAATTATTA
Found at i:1921689 original size:16 final size:16
Alignment explanation
Indices: 1921665--1921755 Score: 67
Period size: 14 Copynumber: 6.3 Consensus size: 16
1921655 ATCTATTTTA
*
1921665 ATTACTATATTTATAT
1 ATTATTATATTTATAT
*
1921681 ATTATTATATTT-GA-
1 ATTATTATATTTATAT
1921695 ATTATT-TA-TTATAT
1 ATTATTATATTTATAT
* *
1921709 -TTAATA-ATTAATAT
1 ATTATTATATTTATAT
1921723 -TTATTA-A-TTAT-T
1 ATTATTATATTTATAT
*
1921735 ATTATTATATTTATTT
1 ATTATTATATTTATAT
1921751 ATTAT
1 ATTAT
1921756 ATTCATTTAA
Statistics
Matches: 60, Mismatches: 7, Indels: 16
0.72 0.08 0.19
Matches are distributed among these distances:
12 3 0.05
13 17 0.28
14 18 0.30
15 5 0.08
16 17 0.28
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.60
Consensus pattern (16 bp):
ATTATTATATTTATAT
Found at i:1921700 original size:14 final size:14
Alignment explanation
Indices: 1921658--1921736 Score: 59
Period size: 16 Copynumber: 5.1 Consensus size: 14
1921648 ATAAAATATC
*
1921658 TATTTTAATTACTA
1 TATTTTAATTATTA
1921672 TATTTATATATTATTA
1 TATTT-TA-ATTATTA
*
1921688 TATTTGAATTATTTA
1 TATTTTAATTA-TTA
*
1921703 TTATATTTAATAATTAA
1 -TAT-TTTAATTATT-A
1921720 TATTTATTAATTATTA
1 TA-TT-TTAATTATTA
1921736 T
1 T
1921737 TATTATATTT
Statistics
Matches: 52, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
14 9 0.17
15 6 0.12
16 21 0.40
17 16 0.31
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.59
Consensus pattern (14 bp):
TATTTTAATTATTA
Found at i:1921710 original size:48 final size:48
Alignment explanation
Indices: 1921658--1921758 Score: 120
Period size: 49 Copynumber: 2.1 Consensus size: 48
1921648 ATAAAATATC
1921658 TATTT-TAATTACTATATTTA-TATATTATTA-TATT-TGAATTATTTATTA
1 TATTTATAATTA--ATATTTATTA-ATTATTATTATTAT-AATTATTTATTA
*
1921706 TATTTAATAATTAATATTTATTAATTATTATTATTATATTTATTTATTA
1 TATTT-ATAATTAATATTTATTAATTATTATTATTATAATTATTTATTA
1921755 TATT
1 TATT
1921759 CATTTAATTT
Statistics
Matches: 47, Mismatches: 1, Indels: 9
0.82 0.02 0.16
Matches are distributed among these distances:
48 19 0.40
49 21 0.45
50 7 0.15
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.61
Consensus pattern (48 bp):
TATTTATAATTAATATTTATTAATTATTATTATTATAATTATTTATTA
Found at i:1921756 original size:13 final size:13
Alignment explanation
Indices: 1921696--1921764 Score: 65
Period size: 13 Copynumber: 5.5 Consensus size: 13
1921686 TATATTTGAA
1921696 TTATTTATTATAT
1 TTATTTATTATAT
* *
1921709 TTAATAATTAATAT
1 TTATTTATT-ATAT
*
1921723 TTA-TTAAT-TA-
1 TTATTTATTATAT
1921733 TTA-TTATTATAT
1 TTATTTATTATAT
1921745 TTATTTATTATAT
1 TTATTTATTATAT
*
1921758 TCATTTA
1 TTATTTA
1921765 ATTTATACGT
Statistics
Matches: 46, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
10 7 0.15
11 4 0.09
12 3 0.07
13 25 0.54
14 7 0.15
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.62
Consensus pattern (13 bp):
TTATTTATTATAT
Found at i:1921766 original size:36 final size:34
Alignment explanation
Indices: 1921665--1921767 Score: 95
Period size: 36 Copynumber: 2.9 Consensus size: 34
1921655 ATCTATTTTA
* *
1921665 ATTACTATATTTATATATTAT-TATATTTGAATTAT
1 ATTATTATATTTATTTATTATAT-TATTT-AATTAT
* *
1921700 -TTATTATATTTAATAATTAATATT-TATTAATTATT
1 ATTATTATATTTATTTATT-ATATTAT-TTAATTA-T
1921735 ATTATTATATTTATTTATTATATTCATTTAATT
1 ATTATTATATTTATTTATTATATT-ATTTAATT
1921768 TATACGTTTC
Statistics
Matches: 55, Mismatches: 6, Indels: 13
0.74 0.08 0.18
Matches are distributed among these distances:
34 20 0.36
35 11 0.20
36 23 0.42
37 1 0.02
ACGTcount: A:0.37, C:0.02, G:0.01, T:0.60
Consensus pattern (34 bp):
ATTATTATATTTATTTATTATATTATTTAATTAT
Found at i:1921770 original size:22 final size:22
Alignment explanation
Indices: 1921697--1921755 Score: 66
Period size: 22 Copynumber: 2.6 Consensus size: 22
1921687 ATATTTGAAT
* *
1921697 TATTTATTATATT-TAATAATTAA
1 TATTTATTA-ATTATTATTATT-A
1921720 TATTTATTAATTATTATTATTA
1 TATTTATTAATTATTATTATTA
*
1921742 TATTTATTTATTAT
1 TATTTATTAATTAT
1921756 ATTCATTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
22 17 0.53
23 15 0.47
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (22 bp):
TATTTATTAATTATTATTATTA
Found at i:1922779 original size:20 final size:21
Alignment explanation
Indices: 1922754--1922793 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
1922744 GAGGGCTGGA
1922754 AACCGGTT-TGACCGGTTTCC
1 AACCGGTTCTGACCGGTTTCC
1922774 AACCGGTTCTGACCGGTTTC
1 AACCGGTTCTGACCGGTTTC
1922794 GACTGGTTCG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.15, C:0.30, G:0.25, T:0.30
Consensus pattern (21 bp):
AACCGGTTCTGACCGGTTTCC
Found at i:1922790 original size:10 final size:9
Alignment explanation
Indices: 1922755--1922844 Score: 63
Period size: 9 Copynumber: 9.3 Consensus size: 9
1922745 AGGGCTGGAA
1922755 ACCGGTTTG
1 ACCGGTTTG
*
1922764 ACCGGTTTCCA
1 ACCGGTTT--G
1922775 ACCGGTTCTG
1 ACCGGTT-TG
1922785 ACCGGTTTCG
1 ACCGGTTT-G
* *
1922795 ACTGGTTCG
1 ACCGGTTTG
*
1922804 AATCGGTTTG
1 -ACCGGTTTG
*
1922814 ACCGGTATG
1 ACCGGTTTG
*
1922823 AACCAGTTTG
1 -ACCGGTTTG
*
1922833 ACCGGTCTG
1 ACCGGTTTG
1922842 ACC
1 ACC
1922845 CGACCCGACT
Statistics
Matches: 62, Mismatches: 13, Indels: 12
0.71 0.15 0.14
Matches are distributed among these distances:
9 27 0.44
10 27 0.44
11 7 0.11
12 1 0.02
ACGTcount: A:0.17, C:0.27, G:0.28, T:0.29
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:1922811 original size:30 final size:29
Alignment explanation
Indices: 1922755--1922819 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 29
1922745 AGGGCTGGAA
1922755 ACCGGTTTGACCGGTTTCCAACCGGTTCTG
1 ACCGGTTTGACCGGTTTCCAACCGGTT-TG
* * *
1922785 ACCGGTTTCGACTGG-TTCGAATCGGTTTG
1 ACCGGTTT-GACCGGTTTCCAACCGGTTTG
1922814 ACCGGT
1 ACCGGT
1922820 ATGAACCAGT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
29 8 0.26
30 18 0.58
31 5 0.16
ACGTcount: A:0.14, C:0.26, G:0.29, T:0.31
Consensus pattern (29 bp):
ACCGGTTTGACCGGTTTCCAACCGGTTTG
Found at i:1922868 original size:19 final size:19
Alignment explanation
Indices: 1922841--1922880 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
1922831 TGACCGGTCT
1922841 GACCCGACCCGACTGACCC
1 GACCCGACCCGACTGACCC
* *
1922860 GACCTGACCCGATTGACCC
1 GACCCGACCCGACTGACCC
1922879 GA
1 GA
1922881 TCGTTGACCG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.23, C:0.45, G:0.23, T:0.10
Consensus pattern (19 bp):
GACCCGACCCGACTGACCC
Found at i:1922881 original size:9 final size:9
Alignment explanation
Indices: 1922846--1922880 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
1922836 GGTCTGACCC
1922846 GACCCGACT
1 GACCCGACT
1922855 GACCCGACCT
1 GACCCGA-CT
*
1922865 GACCCGATT
1 GACCCGACT
1922874 GACCCGA
1 GACCCGA
1922881 TCGTTGACCG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
9 15 0.62
10 9 0.38
ACGTcount: A:0.23, C:0.43, G:0.23, T:0.11
Consensus pattern (9 bp):
GACCCGACT
Found at i:1929345 original size:20 final size:21
Alignment explanation
Indices: 1929320--1929358 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1929310 GAGGGCTGGA
1929320 AACCGGTT-TGACCGGTTTTC
1 AACCGGTTCTGACCGGTTTTC
1929340 AACCGGTTCTGACCGGTTT
1 AACCGGTTCTGACCGGTTT
1929359 CGACTGGTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.15, C:0.26, G:0.26, T:0.33
Consensus pattern (21 bp):
AACCGGTTCTGACCGGTTTTC
Found at i:1929356 original size:10 final size:9
Alignment explanation
Indices: 1929321--1929401 Score: 63
Period size: 10 Copynumber: 8.3 Consensus size: 9
1929311 AGGGCTGGAA
1929321 ACCGGTTTG
1 ACCGGTTTG
*
1929330 ACCGGTTTTCA
1 ACCGG-TTT-G
1929341 ACCGGTTCTG
1 ACCGGTT-TG
1929351 ACCGGTTTCG
1 ACCGGTTT-G
* *
1929361 ACTGGTTCG
1 ACCGGTTTG
1929370 AACCGGTTTG
1 -ACCGGTTTG
*
1929380 ACCGGTATG
1 ACCGGTTTG
*
1929389 AACCAGTTTG
1 -ACCGGTTTG
1929399 ACC
1 ACC
1929402 CGACTGACCC
Statistics
Matches: 57, Mismatches: 9, Indels: 12
0.73 0.12 0.15
Matches are distributed among these distances:
9 18 0.32
10 33 0.58
11 6 0.11
ACGTcount: A:0.17, C:0.26, G:0.27, T:0.30
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:1929411 original size:9 final size:9
Alignment explanation
Indices: 1929397--1929432 Score: 54
Period size: 9 Copynumber: 3.9 Consensus size: 9
1929387 TGAACCAGTT
1929397 TGACCCGAC
1 TGACCCGAC
1929406 TGACCCGACC
1 TGACCCGA-C
*
1929416 CGACCCGAC
1 TGACCCGAC
1929425 TGACCCGA
1 TGACCCGA
1929433 TCGTTGACTG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
9 16 0.67
10 8 0.33
ACGTcount: A:0.22, C:0.47, G:0.22, T:0.08
Consensus pattern (9 bp):
TGACCCGAC
Found at i:1933554 original size:20 final size:20
Alignment explanation
Indices: 1933529--1933566 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
1933519 CTTCACATAG
1933529 TAGTATCGATACCATAAGCT
1 TAGTATCGATACCATAAGCT
1933549 TAGTATCGATACCATAAG
1 TAGTATCGATACCATAAG
1933567 GCTCAACAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.37, C:0.18, G:0.16, T:0.29
Consensus pattern (20 bp):
TAGTATCGATACCATAAGCT
Found at i:1936090 original size:17 final size:17
Alignment explanation
Indices: 1936065--1936097 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1936055 CTTATTCTAA
1936065 CTTTACATGACATTTAT
1 CTTTACATGACATTTAT
*
1936082 CTTTCCATGACATTTA
1 CTTTACATGACATTTA
1936098 GATAAGCAAA
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:0.27, C:0.21, G:0.06, T:0.45
Consensus pattern (17 bp):
CTTTACATGACATTTAT
Found at i:1936944 original size:21 final size:21
Alignment explanation
Indices: 1936910--1936954 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1936900 AAGCTTATAC
*
1936910 TTTAGCATTTTTTTAATCATA
1 TTTAGCATTTTTTTAAGCATA
*
1936931 TTTAG-ATTTATTTTTAGCATA
1 TTTAGCATTT-TTTTAAGCATA
1936952 TTT
1 TTT
1936955 TACATCATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.27, C:0.07, G:0.07, T:0.60
Consensus pattern (21 bp):
TTTAGCATTTTTTTAAGCATA
Found at i:1941090 original size:20 final size:20
Alignment explanation
Indices: 1941067--1941111 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
1941057 TAAGTATCGG
* *
1941067 TACTGACCTATGGGTATCAA
1 TACTAACCTATAGGTATCAA
*
1941087 TACTAACCTCTAGGTATCAA
1 TACTAACCTATAGGTATCAA
1941107 TACTA
1 TACTA
1941112 CTGACTTATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.33, C:0.22, G:0.13, T:0.31
Consensus pattern (20 bp):
TACTAACCTATAGGTATCAA
Found at i:1942792 original size:27 final size:27
Alignment explanation
Indices: 1942762--1942834 Score: 78
Period size: 27 Copynumber: 2.7 Consensus size: 27
1942752 AGACCAAATG
1942762 AAATGACCAAAATACCCTTGAGCT-CTA
1 AAATGACCAAAATACCCTTGAG-TACTA
** * *
1942789 AAATGAATAAAATAACATTGAGTACTA
1 AAATGACCAAAATACCCTTGAGTACTA
1942816 AAATGACTC-AAATACCCTT
1 AAATGAC-CAAAATACCCTT
1942835 ATGATTTGGA
Statistics
Matches: 36, Mismatches: 8, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
26 1 0.03
27 35 0.97
ACGTcount: A:0.47, C:0.19, G:0.10, T:0.25
Consensus pattern (27 bp):
AAATGACCAAAATACCCTTGAGTACTA
Found at i:1943582 original size:25 final size:25
Alignment explanation
Indices: 1943554--1943601 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
1943544 GTTTTATATG
1943554 TTTTAAAATATGAATGAATTATCCA
1 TTTTAAAATATGAATGAATTATCCA
* **
1943579 TTTTGATTTATGAATGAATTATC
1 TTTTAAAATATGAATGAATTATC
1943602 ATATTGAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.38, C:0.06, G:0.10, T:0.46
Consensus pattern (25 bp):
TTTTAAAATATGAATGAATTATCCA
Found at i:1947180 original size:17 final size:17
Alignment explanation
Indices: 1947158--1947205 Score: 50
Period size: 15 Copynumber: 3.1 Consensus size: 17
1947148 AGAACGATCT
1947158 TATATAGAATTTGAAAA
1 TATATAGAATTTGAAAA
*
1947175 TATATA-AAATT-AAAA
1 TATATAGAATTTGAAAA
*
1947190 GA-A-AGAATTTGAAAA
1 TATATAGAATTTGAAAA
1947205 T
1 T
1947206 GGGGTCTACC
Statistics
Matches: 25, Mismatches: 4, Indels: 6
0.71 0.11 0.17
Matches are distributed among these distances:
13 1 0.04
14 5 0.20
15 9 0.36
16 4 0.16
17 6 0.24
ACGTcount: A:0.58, C:0.00, G:0.10, T:0.31
Consensus pattern (17 bp):
TATATAGAATTTGAAAA
Found at i:1947820 original size:20 final size:20
Alignment explanation
Indices: 1947795--1947834 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
1947785 GACTGGCAAT
*
1947795 GAACCGGCTGAAAACCGGTA
1 GAACCGGCTAAAAACCGGTA
*
1947815 GAACCGGCTAAAAATCGGTA
1 GAACCGGCTAAAAACCGGTA
1947835 AAATCGGGGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.38, C:0.23, G:0.28, T:0.12
Consensus pattern (20 bp):
GAACCGGCTAAAAACCGGTA
Found at i:1947878 original size:30 final size:29
Alignment explanation
Indices: 1947805--1947880 Score: 89
Period size: 30 Copynumber: 2.6 Consensus size: 29
1947795 GAACCGGCTG
* *
1947805 AAAACCGGTAGAACCGGCTAAAAATCGGT
1 AAAACCGGTTGAACCGGCTAAAAATCGGC
* * *
1947834 AAAATCGGGGTGAACCGGCTGAAAATCGGC
1 AAAA-CCGGTTGAACCGGCTAAAAATCGGC
1947864 AAAACCGGTTTGAACCG
1 AAAACCGG-TTGAACCG
1947881 CCGGTTCACT
Statistics
Matches: 38, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
29 7 0.18
30 31 0.82
ACGTcount: A:0.37, C:0.21, G:0.28, T:0.14
Consensus pattern (29 bp):
AAAACCGGTTGAACCGGCTAAAAATCGGC
Found at i:1948355 original size:17 final size:17
Alignment explanation
Indices: 1948321--1948353 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1948311 ATGTTGTATA
1948321 ATTATGTAATTATATTT
1 ATTATGTAATTATATTT
*
1948338 ATTATTTAA-TATATTT
1 ATTATGTAATTATATTT
1948354 TACCTTAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (17 bp):
ATTATGTAATTATATTT
Found at i:1950239 original size:2 final size:2
Alignment explanation
Indices: 1950227--1950269 Score: 63
Period size: 2 Copynumber: 22.0 Consensus size: 2
1950217 ATATTTTAGA
1950227 AT AT A- AT AT AT AT -T GAT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT
1950268 AT
1 AT
1950270 TATGATTAGA
Statistics
Matches: 38, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
1 2 0.05
2 35 0.92
3 1 0.03
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1952776 original size:13 final size:13
Alignment explanation
Indices: 1952758--1952782 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1952748 CATTGCGATT
1952758 TTCCAAATTCGCG
1 TTCCAAATTCGCG
1952771 TTCCAAATTCGC
1 TTCCAAATTCGC
1952783 AACGCGATAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.32, G:0.12, T:0.32
Consensus pattern (13 bp):
TTCCAAATTCGCG
Found at i:1952837 original size:19 final size:20
Alignment explanation
Indices: 1952682--1952863 Score: 111
Period size: 20 Copynumber: 9.6 Consensus size: 20
1952672 AATGACCAAT
* *
1952682 AAATTCGTAACGCG-ATCTC
1 AAATTCGCAACGCGAATTTC
*
1952701 AAATTCGCAAAGCGAATTTC
1 AAATTCGCAACGCGAATTTC
*
1952721 AATTTCGCAACGCGAATATGT-
1 AAATTCGCAACGCGAAT-T-TC
** *
1952742 AAA-TCGCATTGCGATTTTCC
1 AAATTCGCAACGCGAATTT-C
*
1952762 AAATT-----CGCG--TTCC
1 AAATTCGCAACGCGAATTTC
*
1952775 AAATTCGCAACGCG-ATAGTC
1 AAATTCGCAACGCGAAT-TTC
* **
1952795 AAATTCTCAACGCGAAAGTC
1 AAATTCGCAACGCGAATTTC
*
1952815 AAATTCGCAAC-TGAATTTC
1 AAATTCGCAACGCGAATTTC
1952834 AAATTCGCAACGCGAATTT-
1 AAATTCGCAACGCGAATTTC
*
1952853 AATTTCGCAAC
1 AAATTCGCAAC
1952864 AGGTTTTAGT
Statistics
Matches: 127, Mismatches: 21, Indels: 30
0.71 0.12 0.17
Matches are distributed among these distances:
13 6 0.05
14 2 0.02
16 3 0.02
18 5 0.04
19 40 0.31
20 65 0.51
21 5 0.04
22 1 0.01
ACGTcount: A:0.34, C:0.24, G:0.15, T:0.27
Consensus pattern (20 bp):
AAATTCGCAACGCGAATTTC
Found at i:1952940 original size:8 final size:8
Alignment explanation
Indices: 1952927--1952951 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
1952917 CAACTCATAA
1952927 CCCTAAAT
1 CCCTAAAT
1952935 CCCTAAAT
1 CCCTAAAT
1952943 CCCTAAAT
1 CCCTAAAT
1952951 C
1 C
1952952 GCAACTCATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.36, C:0.40, G:0.00, T:0.24
Consensus pattern (8 bp):
CCCTAAAT
Found at i:1953640 original size:12 final size:12
Alignment explanation
Indices: 1953619--1953652 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1953609 ACCACATTTC
*
1953619 CAATACCAAACA
1 CAATATCAAACA
1953631 CAATATCAAACA
1 CAATATCAAACA
*
1953643 CAATCTCAAA
1 CAATATCAAA
1953653 ACCCACAACT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:1953829 original size:24 final size:24
Alignment explanation
Indices: 1953778--1953831 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1953768 GTATTCGAAA
*
1953778 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCAGAC
* *
1953802 TTTGATCTTGGTCAATACTCAGAT
1 TTTGATCTTGGTCAATACCCAGAC
1953826 TTTGAT
1 TTTGAT
1953832 GATGTGATGG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCAGAC
Found at i:1962076 original size:23 final size:21
Alignment explanation
Indices: 1962025--1962085 Score: 79
Period size: 23 Copynumber: 2.9 Consensus size: 21
1962015 TTTGGTGCAG
*
1962025 AGGGAATCGA-TCCCCCCTTA
1 AGGGAACCGATTCCCCCCTTA
*
1962045 AGGGAACCGATTCCCCCTTTGA
1 AGGGAACCGATTCCCCCCTT-A
1962067 AGGGGAACCGATTCCCCCC
1 A-GGGAACCGATTCCCCCC
1962086 ACAGGGGAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
20 9 0.26
21 8 0.23
22 2 0.06
23 16 0.46
ACGTcount: A:0.23, C:0.36, G:0.23, T:0.18
Consensus pattern (21 bp):
AGGGAACCGATTCCCCCCTTA
Found at i:1962093 original size:21 final size:21
Alignment explanation
Indices: 1962067--1962106 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1962057 CCCCCTTTGA
*
1962067 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
1962088 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
1962107 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:1964440 original size:13 final size:14
Alignment explanation
Indices: 1964422--1964451 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
1964412 TAAGGGGGAG
1964422 TAATTTCAAAA-CT
1 TAATTTCAAAATCT
1964435 TAATTTCAAAATCT
1 TAATTTCAAAATCT
1964449 TAA
1 TAA
1964452 AATTACTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.69
14 5 0.31
ACGTcount: A:0.47, C:0.13, G:0.00, T:0.40
Consensus pattern (14 bp):
TAATTTCAAAATCT
Found at i:1966001 original size:34 final size:34
Alignment explanation
Indices: 1965958--1966022 Score: 94
Period size: 34 Copynumber: 1.9 Consensus size: 34
1965948 TCAACGCAAA
* * *
1965958 AGTCAAATTCGCAATGCGAAATAAGCGTTGCGAT
1 AGTCAAATTCGAAACGCAAAATAAGCGTTGCGAT
*
1965992 AGTCAAATTCGAAACGCAAAATAATCGTTGC
1 AGTCAAATTCGAAACGCAAAATAAGCGTTGC
1966023 AAATTTGACT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
34 27 1.00
ACGTcount: A:0.38, C:0.18, G:0.20, T:0.23
Consensus pattern (34 bp):
AGTCAAATTCGAAACGCAAAATAAGCGTTGCGAT
Found at i:1966049 original size:20 final size:20
Alignment explanation
Indices: 1966024--1966077 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
1966014 AATCGTTGCA
1966024 AATTTGACTATCGCGTAGCG
1 AATTTGACTATCGCGTAGCG
* *
1966044 AATTTGACTTTCGCGTTGCG
1 AATTTGACTATCGCGTAGCG
1966064 AATTTGACTATCGC
1 AATTTGACTATCGC
1966078 AACGCTTATT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.35
Consensus pattern (20 bp):
AATTTGACTATCGCGTAGCG
Found at i:1966196 original size:25 final size:25
Alignment explanation
Indices: 1966168--1966217 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
1966158 AAATTAATTA
* *
1966168 AACATTGTTGTGGGTACATTATTTG
1 AACATTGTTATGAGTACATTATTTG
*
1966193 AACATTGTTATGATTACATTATTTG
1 AACATTGTTATGAGTACATTATTTG
1966218 GAAAAATAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.28, C:0.08, G:0.18, T:0.46
Consensus pattern (25 bp):
AACATTGTTATGAGTACATTATTTG
Found at i:1966625 original size:18 final size:18
Alignment explanation
Indices: 1966604--1966640 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1966594 GTAATTGGAG
1966604 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
1966622 TTTGATTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
1966640 T
1 T
1966641 ATAAATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.08, T:0.54
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:1966987 original size:39 final size:39
Alignment explanation
Indices: 1966944--1967030 Score: 165
Period size: 39 Copynumber: 2.2 Consensus size: 39
1966934 TCTGATGCTC
1966944 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
*
1966983 ATCAAAATCCAAATCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
1967022 ATCAAAATC
1 ATCAAAATC
1967031 TACAACTTTA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 47 1.00
ACGTcount: A:0.47, C:0.21, G:0.15, T:0.17
Consensus pattern (39 bp):
ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
Found at i:1967528 original size:61 final size:63
Alignment explanation
Indices: 1967397--1967537 Score: 171
Period size: 61 Copynumber: 2.2 Consensus size: 63
1967387 TTTTAGAAAC
*
1967397 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAAATAATTCTTATTTACAAATCAAATT
1 AACAAATCAACTTTTACAAATCAATT--A-AAGCAAAAAAATAAATCTTATTTACAAATCAAATT
1967462 A
63 A
* * ** *
1967463 AACAAATCAACTTTTACAAATCAATT-AATC-AAAAAATAAATCTTATTTCCTCATC-AATTGG
1 AACAAATCAACTTTTACAAATCAATTAAAGCAAAAAAATAAATCTTATTTACAAATCAAATT-A
1967524 AACAAATCAACTTT
1 AACAAATCAACTTT
1967538 CAATGTAAAA
Statistics
Matches: 68, Mismatches: 6, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
60 4 0.06
61 35 0.51
62 3 0.04
66 26 0.38
ACGTcount: A:0.50, C:0.17, G:0.02, T:0.30
Consensus pattern (63 bp):
AACAAATCAACTTTTACAAATCAATTAAAGCAAAAAAATAAATCTTATTTACAAATCAAATTA
Found at i:1968939 original size:21 final size:21
Alignment explanation
Indices: 1968915--1969016 Score: 109
Period size: 21 Copynumber: 4.9 Consensus size: 21
1968905 AAACGATGAC
* * *
1968915 AGGGGCCTCTTGAACGGTGGG
1 AGGGGCCTCTTGAATGATAGG
* *
1968936 AGGGGCTTCTTCG-ATGAT-GAT
1 AGGGGCCTCTT-GAATGATAG-G
1968957 AGGGGCCTCTTGAATGATAGG
1 AGGGGCCTCTTGAATGATAGG
*
1968978 AGGTGCCTCTTGAATGATAGG
1 AGGGGCCTCTTGAATGATAGG
*
1968999 AGGCGCCTCTTGAATGAT
1 AGGGGCCTCTTGAATGAT
1969017 GATAGGTGCA
Statistics
Matches: 69, Mismatches: 8, Indels: 8
0.81 0.09 0.09
Matches are distributed among these distances:
20 2 0.03
21 65 0.94
22 2 0.03
ACGTcount: A:0.21, C:0.17, G:0.36, T:0.26
Consensus pattern (21 bp):
AGGGGCCTCTTGAATGATAGG
Found at i:1970076 original size:31 final size:31
Alignment explanation
Indices: 1970054--1970162 Score: 191
Period size: 31 Copynumber: 3.5 Consensus size: 31
1970044 ATAGATTCCT
* *
1970054 AAGAACCTAGGTAATCAGTCCATATGTCCCG
1 AAGAACATAGGTAAACAGTCCATATGTCCCG
1970085 AAGAACATAGGTAAACAGTCCATATGTCCCG
1 AAGAACATAGGTAAACAGTCCATATGTCCCG
*
1970116 AAGAACATAGGTAAACAGTCCATATATCCCG
1 AAGAACATAGGTAAACAGTCCATATGTCCCG
1970147 AAGAACATAGGTAAAC
1 AAGAACATAGGTAAAC
1970163 CCTCGACCCT
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 75 1.00
ACGTcount: A:0.40, C:0.22, G:0.18, T:0.19
Consensus pattern (31 bp):
AAGAACATAGGTAAACAGTCCATATGTCCCG
Found at i:1971084 original size:20 final size:21
Alignment explanation
Indices: 1971043--1971096 Score: 83
Period size: 20 Copynumber: 2.6 Consensus size: 21
1971033 TTCGCTTGAG
*
1971043 GGGTATCGATTCCCCATTGAAT
1 GGGTACCGATT-CCCATTGAAT
1971065 GGGTACCGATTCCC-TTGAAT
1 GGGTACCGATTCCCATTGAAT
1971085 GGGTACCGATTC
1 GGGTACCGATTC
1971097 TTCTTGCCCA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 18 0.58
21 3 0.10
22 10 0.32
ACGTcount: A:0.20, C:0.24, G:0.26, T:0.30
Consensus pattern (21 bp):
GGGTACCGATTCCCATTGAAT
Found at i:1972028 original size:16 final size:16
Alignment explanation
Indices: 1971989--1972031 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
1971979 AGCATCAGTT
*
1971989 ATTATCACTCAAAATC
1 ATTATCAATCAAAATC
*
1972005 ATTAATCAATCAAATTC
1 ATT-ATCAATCAAAATC
*
1972022 CTTATCAATC
1 ATTATCAATC
1972032 TTTAATTACC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
16 10 0.43
17 13 0.57
ACGTcount: A:0.42, C:0.23, G:0.00, T:0.35
Consensus pattern (16 bp):
ATTATCAATCAAAATC
Found at i:1974866 original size:31 final size:31
Alignment explanation
Indices: 1974818--1974942 Score: 153
Period size: 31 Copynumber: 4.0 Consensus size: 31
1974808 CCCGAAGGAC
* * * *
1974818 CAGTCCATA-GATTCCGAAAAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
1974849 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
* * *
1974880 CACTACATATGTCCTGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
* *
1974911 CAGTCCATATATCCCGAAGAACATACGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1974942 C
1 C
1974943 CCTCGACCCT
Statistics
Matches: 81, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
31 80 0.99
32 1 0.01
ACGTcount: A:0.40, C:0.23, G:0.16, T:0.21
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:1975851 original size:22 final size:21
Alignment explanation
Indices: 1975826--1975885 Score: 95
Period size: 20 Copynumber: 2.9 Consensus size: 21
1975816 TTCGCTTGAG
*
1975826 GGGTATCGATTCCCCATTGAAT
1 GGGTACCGATTCCCC-TTGAAT
1975848 GGGTACCGATT-CCCTTGAAT
1 GGGTACCGATTCCCCTTGAAT
1975868 GGGTACCGATTCCCCTTG
1 GGGTACCGATTCCCCTTG
1975886 CCCAGAAATC
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
20 17 0.47
21 9 0.25
22 10 0.28
ACGTcount: A:0.18, C:0.27, G:0.25, T:0.30
Consensus pattern (21 bp):
GGGTACCGATTCCCCTTGAAT
Found at i:1978713 original size:22 final size:22
Alignment explanation
Indices: 1978685--1978727 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
1978675 GAGATAGACG
*
1978685 GATTTCGTCGGAAATGGGGACA
1 GATTTCGTCAGAAATGGGGACA
*
1978707 GATTTCGTCAGAGATGGGGAC
1 GATTTCGTCAGAAATGGGGAC
1978728 GGATGTCTCC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.26, C:0.14, G:0.37, T:0.23
Consensus pattern (22 bp):
GATTTCGTCAGAAATGGGGACA
Found at i:1978884 original size:20 final size:20
Alignment explanation
Indices: 1978859--1978990 Score: 122
Period size: 20 Copynumber: 6.2 Consensus size: 20
1978849 GCGTAAAAAC
*
1978859 ATTTGACTTTTGCGTTGCGA
1 ATTTGACTTTCGCGTTGCGA
*
1978879 ATTTGACTATCGCGTTGCGA
1 ATTTGACTTTCGCGTTGCGA
* *
1978899 ATTTGAC-TTCTGTGTTGTGATTTACAA
1 ATTTGACTTTC-GCG-T-TG-----CGA
*
1978926 ATTTGACTTTCGCGTTGTGA
1 ATTTGACTTTCGCGTTGCGA
*
1978946 ATTTTACTTTCGCGTTGCGA
1 ATTTGACTTTCGCGTTGCGA
*
1978966 ATTTGACTTTCGTGTTGCGA
1 ATTTGACTTTCGCGTTGCGA
1978986 ATTTG
1 ATTTG
1978991 GAAAATCGCA
Statistics
Matches: 91, Mismatches: 12, Indels: 18
0.75 0.10 0.15
Matches are distributed among these distances:
19 2 0.02
20 69 0.76
21 1 0.01
22 2 0.02
25 2 0.02
26 1 0.01
27 11 0.12
28 3 0.03
ACGTcount: A:0.17, C:0.15, G:0.23, T:0.45
Consensus pattern (20 bp):
ATTTGACTTTCGCGTTGCGA
Found at i:1979043 original size:20 final size:20
Alignment explanation
Indices: 1979020--1979067 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
1979010 ACATATTCGT
1979020 GTTGCGAAATTGGAAACT-GG
1 GTTGCGAAATTGG-AACTCGG
* *
1979040 GTTGTGAAATTGGAATTCGG
1 GTTGCGAAATTGGAACTCGG
1979060 GTTGCGAA
1 GTTGCGAA
1979068 TTTTGTTGGT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 3 0.12
20 21 0.88
ACGTcount: A:0.27, C:0.08, G:0.35, T:0.29
Consensus pattern (20 bp):
GTTGCGAAATTGGAACTCGG
Found at i:1979371 original size:3 final size:3
Alignment explanation
Indices: 1979363--1979464 Score: 87
Period size: 3 Copynumber: 33.7 Consensus size: 3
1979353 TCATTTAAAT
** * * *
1979363 TTA TTA TTA TTA TTA AAA TTA TTA TTA TTA GTA TTA TTA TTA TAA TAA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * * * *
1979411 TAA TAA TAA TTA TTA TTA TTA TTA TTTA ATA TTA ATA TTA ATA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA
*
1979457 ATA TTA TT
1 TTA TTA TT
1979465 TAATAAATAA
Statistics
Matches: 82, Mismatches: 16, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
3 79 0.96
4 3 0.04
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (3 bp):
TTA
Found at i:1980136 original size:11 final size:11
Alignment explanation
Indices: 1980122--1980146 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1980112 AATAGCTGCC
1980122 GAACCACCGTG
1 GAACCACCGTG
1980133 GAACCACCGTG
1 GAACCACCGTG
1980144 GAA
1 GAA
1980147 TCAAAAGTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.32, C:0.32, G:0.28, T:0.08
Consensus pattern (11 bp):
GAACCACCGTG
Found at i:1983198 original size:3 final size:3
Alignment explanation
Indices: 1983190--1983292 Score: 98
Period size: 3 Copynumber: 33.7 Consensus size: 3
1983180 TCATTTAAGT
** * * *
1983190 TTA TTA TTA TTA TTA AAA TTA TTA TTA TTA GTA TTA TTA TTA TAA TAA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * * *
1983238 TAA TAA TTA TTA TTA TTA TTTA TTA TTTA ATA TTA ATA TTA ATA TTA
1 TTA TTA TTA TTA TTA TTA -TTA TTA -TTA TTA TTA TTA TTA TTA TTA
1983285 TTA TTA TT
1 TTA TTA TT
1983293 TAATAAATAA
Statistics
Matches: 84, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
3 78 0.93
4 6 0.07
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (3 bp):
TTA
Found at i:1983967 original size:11 final size:11
Alignment explanation
Indices: 1983953--1983977 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1983943 AATAGCTGCC
1983953 GAACCACCGTG
1 GAACCACCGTG
1983964 GAACCACCGTG
1 GAACCACCGTG
1983975 GAA
1 GAA
1983978 TCAAAAGTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.32, C:0.32, G:0.28, T:0.08
Consensus pattern (11 bp):
GAACCACCGTG
Found at i:1985565 original size:18 final size:20
Alignment explanation
Indices: 1985542--1985589 Score: 55
Period size: 18 Copynumber: 2.5 Consensus size: 20
1985532 TTCTTTTCAA
1985542 ATTTTTTATA-TACTTAT-T
1 ATTTTTTATAGTACTTATAT
* *
1985560 ATTTTTCATAGTATTTATAT
1 ATTTTTTATAGTACTTATAT
1985580 ATTTTCTTAT
1 ATTTT-TTAT
1985590 TAATATTTCA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
18 9 0.38
19 6 0.25
20 6 0.25
21 3 0.12
ACGTcount: A:0.27, C:0.06, G:0.02, T:0.65
Consensus pattern (20 bp):
ATTTTTTATAGTACTTATAT
Found at i:1992956 original size:76 final size:76
Alignment explanation
Indices: 1992830--1993005 Score: 221
Period size: 76 Copynumber: 2.3 Consensus size: 76
1992820 AACAAGAAAC
* * *
1992830 AAATGTTAGGGCATGCTGAAA-ACCCTTGTCAATCAGAATCATGAATGTTGATGTATCATGAATG
1 AAATGTTAGGGCATGCTGAAAGCCCCTTGTCAATCAGAATCAAGAATGTTGATGTATCATGAACG
* * *
1992894 TTTATATCAGCA
66 CTCATATCA-AA
* * **
1992906 AAATGGTAGGGCATGCTGAAAGCCCCTT-TCAATCAGAATGAAGAATGTTGATGTATTTTGAACG
1 AAATGTTAGGGCATGCTGAAAGCCCCTTGTCAATCAGAATCAAGAATGTTGATGTATCATGAACG
1992970 CTCATATCAAA
66 CTCATATCAAA
* *
1992981 AAATATTAGGGCATGCTGAAGGCCC
1 AAATGTTAGGGCATGCTGAAAGCCC
1993006 ACAACATCCT
Statistics
Matches: 86, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
75 23 0.27
76 58 0.67
77 5 0.06
ACGTcount: A:0.34, C:0.16, G:0.22, T:0.28
Consensus pattern (76 bp):
AAATGTTAGGGCATGCTGAAAGCCCCTTGTCAATCAGAATCAAGAATGTTGATGTATCATGAACG
CTCATATCAAA
Found at i:1993948 original size:54 final size:54
Alignment explanation
Indices: 1993866--1994140 Score: 478
Period size: 54 Copynumber: 5.1 Consensus size: 54
1993856 CAATGATTGA
* *
1993866 GAACATCTGAGCAGAAGCCACACAAAAAGATGAATGTGTTGTCAAATATTTTAC
1 GAACATCTGAGCAGAAGCCACAAAAAAAGATGAATGTGTTGTCAAATGTTTTAC
1993920 GAACATCTGAGCAGAAGCCACAAAAAAAGGATGAATGTGTTGTCAAATGTTTTAC
1 GAACATCTGAGCAGAAGCCACAAAAAAA-GATGAATGTGTTGTCAAATGTTTTAC
* *
1993975 GAACATCTGAGAAGAAGCCACAAAAAAGGATGAATGTGTTGTCAAATGTTTTAC
1 GAACATCTGAGCAGAAGCCACAAAAAAAGATGAATGTGTTGTCAAATGTTTTAC
*
1994029 GAACATCTGAGCAGAAGCCACAAAAAATGATGAATGTGTTGTCAAATGTTTTAC
1 GAACATCTGAGCAGAAGCCACAAAAAAAGATGAATGTGTTGTCAAATGTTTTAC
* *
1994083 GAACATCTGAGCAGAAGCCACAAAAAAGGATGAATGTGTTGTCAAATATTTTAC
1 GAACATCTGAGCAGAAGCCACAAAAAAAGATGAATGTGTTGTCAAATGTTTTAC
1994137 GAAC
1 GAAC
1994141 CTGCTATTCT
Statistics
Matches: 212, Mismatches: 8, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
54 161 0.76
55 51 0.24
ACGTcount: A:0.40, C:0.15, G:0.21, T:0.24
Consensus pattern (54 bp):
GAACATCTGAGCAGAAGCCACAAAAAAAGATGAATGTGTTGTCAAATGTTTTAC
Found at i:1994520 original size:22 final size:22
Alignment explanation
Indices: 1994491--1994545 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
1994481 ATCTACACTC
1994491 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
*
1994513 TTTAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
1994535 TTCAAAGATGA
1 TTCAAAGATGA
1994546 AAGTTTTATG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.35, C:0.11, G:0.15, T:0.40
Consensus pattern (22 bp):
TTCAAAGATGATAGATTCTCTT
Found at i:1995572 original size:76 final size:76
Alignment explanation
Indices: 1995393--1996254 Score: 1473
Period size: 76 Copynumber: 11.4 Consensus size: 76
1995383 CTATTTCCCA
1995393 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATG-TTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1995457 AGCCTTAGGGT
66 AGCCTTAGGGT
* * **
1995468 CATCTATAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTTAGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1995533 AGCCTTAGGGT
66 AGCCTTAGGGT
*
1995544 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGATTTTTGATG-TTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1995608 AGCCTTAGGGT
66 AGCCTTAGGGT
* *
1995619 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTTGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
1995684 AACCTTAGGGT
66 AGCCTTAGGGT
*
1995695 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTTGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
1995760 AACCTTAGGGT
66 AGCCTTAGGGT
*
1995771 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGTTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
1995836 A-CCTTAGGTT
66 AGCCTTAGGGT
*
1995846 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGATTTTTGATGTTTT-AA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1995910 AGCCTTAGGGT
66 AGCCTTAGGGT
* *
1995921 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTTGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
1995986 AACCTTAGGGT
66 AGCCTTAGGGT
1995997 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1996062 AGCCTTAGGGT
66 AGCCTTAGGGT
1996073 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
* *
1996138 A-ACTTCGGGT
66 AGCCTTAGGGT
* *
1996148 CATCTGTATGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTC-A
* *
1996213 AAACCTTCGGGT
65 AAGCCTTAGGGT
*
1996225 CATCTGTAAGCCCTTCAGTGCATGATGTTT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTT
1996255 TCAACATTTC
Statistics
Matches: 747, Mismatches: 34, Indels: 10
0.94 0.04 0.01
Matches are distributed among these distances:
74 3 0.00
75 330 0.44
76 379 0.51
77 35 0.05
ACGTcount: A:0.23, C:0.19, G:0.22, T:0.36
Consensus pattern (76 bp):
CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTAGGGT
Found at i:1995640 original size:151 final size:151
Alignment explanation
Indices: 1995393--1996254 Score: 1487
Period size: 151 Copynumber: 5.7 Consensus size: 151
1995383 CTATTTCCCA
1995393 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATG-TTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
* *
1995457 AGCCTTAGGGTCATCTATAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTTAGGAGCTTTTT
66 AGCCTTAGGGTCATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTTGGGAGCTTTTT
1995522 GATGTTTTCAAAGCCTTAGGGT
131 GATGTTTTCAAA-CCTTAGGGT
*
1995544 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGATTTTTGATG-TTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1995608 AGCCTTAGGGTCATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTTGGGAGCTTTTT
66 AGCCTTAGGGTCATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTTGGGAGCTTTTT
1995673 GATGTTTTCAAAACCTTAGGGT
131 GATGTTTTC-AAACCTTAGGGT
*
1995695 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTTGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
* * * *
1995760 AACCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGTTTTTT
66 AGCCTTAGGGTCATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTTGGGAGCTTTTT
*
1995825 GATGTTTTCAAACCTTAGGTT
131 GATGTTTTCAAACCTTAGGGT
*
1995846 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGATTTTTGATGTTTT-AA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1995910 AGCCTTAGGGTCATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTTGGGAGCTTTTT
66 AGCCTTAGGGTCATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTTGGGAGCTTTTT
1995975 GATGTTTTCAAAACCTTAGGGT
131 GATGTTTTC-AAACCTTAGGGT
1995997 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
* *
1996062 AGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
66 AGCCTTAGGGTCATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTTGGGAGCTTTTT
* *
1996127 GATGTTTTCAAAACTTCGGGT
131 GATGTTTTCAAACCTTAGGGT
* *
1996148 CATCTGTATGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTC-A
* * * *
1996213 AAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTT
65 AAGCCTTAGGGTCATCTGTAAGTCCTGCAGTGCATGATGTTT
1996255 TCAACATTTC
Statistics
Matches: 679, Mismatches: 27, Indels: 9
0.95 0.04 0.01
Matches are distributed among these distances:
150 72 0.11
151 414 0.61
152 193 0.28
ACGTcount: A:0.23, C:0.19, G:0.22, T:0.36
Consensus pattern (151 bp):
CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTAGGGTCATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTTGGGAGCTTTTT
GATGTTTTCAAACCTTAGGGT
Found at i:1996392 original size:3 final size:3
Alignment explanation
Indices: 1996384--1996485 Score: 123
Period size: 3 Copynumber: 33.7 Consensus size: 3
1996374 TCATTTAAAT
** * *
1996384 TTA TTA TTA TTA TTA AAA TTA TTA TTA TTA GTA TTA TTA TTA TAA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * *
1996432 TTA TAA TTA TTA TTA TTA TTA TTA TTA ATG TTA ATA TTA TATA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA
1996478 TTA TTA TT
1 TTA TTA TT
1996486 TAATAAATAA
Statistics
Matches: 82, Mismatches: 16, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
3 79 0.96
4 3 0.04
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:1997162 original size:11 final size:11
Alignment explanation
Indices: 1997146--1997170 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1997136 AAGAGTTGCT
1997146 GAACCACCGTG
1 GAACCACCGTG
1997157 GAACCACCGTG
1 GAACCACCGTG
1997168 GAA
1 GAA
1997171 TCAAAAGTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.32, C:0.32, G:0.28, T:0.08
Consensus pattern (11 bp):
GAACCACCGTG
Found at i:1999366 original size:39 final size:39
Alignment explanation
Indices: 1999312--1999390 Score: 149
Period size: 39 Copynumber: 2.0 Consensus size: 39
1999302 AGATGCACTT
*
1999312 CCACTGAAAAGGGTAAGTTACCTTGTGACGTATGAGTAG
1 CCACTGAAAAGGGTAAGTTACCTTGTGACATATGAGTAG
1999351 CCACTGAAAAGGGTAAGTTACCTTGTGACATATGAGTAG
1 CCACTGAAAAGGGTAAGTTACCTTGTGACATATGAGTAG
1999390 C
1 C
1999391 TAATCAGGAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.32, C:0.16, G:0.27, T:0.25
Consensus pattern (39 bp):
CCACTGAAAAGGGTAAGTTACCTTGTGACATATGAGTAG
Done.