Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009643.1 Hibiscus syriacus cultivar Beakdansim tig00117056_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: 8859806
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 41
Found at i:1806261 original size:31 final size:29
Alignment explanation
Indices: 1806188--1806276 Score: 97
Period size: 30 Copynumber: 2.9 Consensus size: 29
1806178 ATTTTATCCA
*
1806188 TAAACTTAGATAGAATATTAATTTGACCTC
1 TAAACTTAGATA-AATATTAATTTGACCAC
1806218 TAAACTTAGATAAAGTATTAATTTGACCAC
1 TAAACTTAGATAAA-TATTAATTTGACCAC
** * *
1806248 TGAATTTTAGATAAAATATCAAATTGACC
1 T-AAACTTAGAT-AAATATTAATTTGACC
1806277 CTTGAATCTA
Statistics
Matches: 51, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
29 2 0.04
30 27 0.53
31 19 0.37
32 3 0.06
ACGTcount: A:0.43, C:0.12, G:0.10, T:0.35
Consensus pattern (29 bp):
TAAACTTAGATAAATATTAATTTGACCAC
Found at i:1807866 original size:14 final size:14
Alignment explanation
Indices: 1807847--1807874 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1807837 CAGACATTTC
1807847 AATGTCTACTGGTA
1 AATGTCTACTGGTA
1807861 AATGTCTACTGGTA
1 AATGTCTACTGGTA
1807875 GTAGAGCGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.14, G:0.21, T:0.36
Consensus pattern (14 bp):
AATGTCTACTGGTA
Found at i:1820549 original size:17 final size:16
Alignment explanation
Indices: 1820504--1820553 Score: 64
Period size: 17 Copynumber: 3.0 Consensus size: 16
1820494 ATTTTATTAT
1820504 ATAAGTATTAATATAA
1 ATAAGTATTAATATAA
* *
1820520 AAAAGTTAGTAATATAA
1 ATAAG-TATTAATATAA
1820537 CATAAGTATTAATATAA
1 -ATAAGTATTAATATAA
1820554 GTTTGCTTCA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
16 4 0.14
17 20 0.71
18 4 0.14
ACGTcount: A:0.56, C:0.02, G:0.08, T:0.34
Consensus pattern (16 bp):
ATAAGTATTAATATAA
Found at i:1821210 original size:38 final size:38
Alignment explanation
Indices: 1821155--1821232 Score: 111
Period size: 38 Copynumber: 2.1 Consensus size: 38
1821145 GCAAACAAAT
* * * *
1821155 ATGTTATCAAAATCGTAACTTTTTAGGTTGAATCGAAA
1 ATGTTATCAAAAGCGTAACCTTTTAGGCTGAACCGAAA
*
1821193 ATGTTATCAAGAGCGTAACCTTTTAGGCTGAACCGAAA
1 ATGTTATCAAAAGCGTAACCTTTTAGGCTGAACCGAAA
1821231 AT
1 AT
1821233 ATTACCATCT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.32
Consensus pattern (38 bp):
ATGTTATCAAAAGCGTAACCTTTTAGGCTGAACCGAAA
Found at i:1822891 original size:12 final size:13
Alignment explanation
Indices: 1822867--1822896 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
1822857 GGTTTCCATC
1822867 CTCATCGCTTTCT
1 CTCATCGCTTTCT
1822880 CTCATC-CTTTCT
1 CTCATCGCTTTCT
1822892 CTCAT
1 CTCAT
1822897 TACGATCGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.65
13 6 0.35
ACGTcount: A:0.10, C:0.40, G:0.03, T:0.47
Consensus pattern (13 bp):
CTCATCGCTTTCT
Found at i:1827852 original size:12 final size:11
Alignment explanation
Indices: 1827827--1827858 Score: 55
Period size: 12 Copynumber: 2.8 Consensus size: 11
1827817 ATCAGAACAA
1827827 AAAGAAAAAAT
1 AAAGAAAAAAT
1827838 AAAGAAAATAAT
1 AAAGAAAA-AAT
1827850 AAAGAAAAA
1 AAAGAAAAA
1827859 GGAAAAAGTG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 9 0.45
12 11 0.55
ACGTcount: A:0.81, C:0.00, G:0.09, T:0.09
Consensus pattern (11 bp):
AAAGAAAAAAT
Found at i:1829846 original size:116 final size:116
Alignment explanation
Indices: 1829687--1830035 Score: 524
Period size: 116 Copynumber: 3.0 Consensus size: 116
1829677 CAATGCAAGC
* * * *
1829687 TTGGATTTCAACTTTACGGCGAAGGATATTCAAGTT-AAGGCTCAACTTCACAACGAATGGGCCA
1 TTGGATTTCAACTTCACGACGAAGGATATCCAA-TTCAAGGCTCAACTTCACGACGAATGGGCCA
* *
1829751 TCCACGGTTTCAACTTTACGACGAAA-AGAATCATGCTCACCAGCAACATTCA
65 TCCACGGTTTCAACTTCACGAC-AAAGGGAATCATGCTCACCAGCAACATTCA
* * *
1829803 TTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAATTTCACGACGAATAGGCCAG
1 TTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACGACGAATGGGCCAT
1829868 CCACGGTTTCAACTTCACGACAAAGGGAATCATGCTCACCAGCAACATTCA
66 CCACGGTTTCAACTTCACGACAAAGGGAATCATGCTCACCAGCAACATTCA
* * *
1829919 TTGGATTTCAACTTCACGACGAATGATATCCAATTCAAGGCTCAACTTCACGACGAAGGGGTCAT
1 TTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACGACGAATGGGCCAT
* *
1829984 CCACGGTTTCAACTTCACGACAAAGGGAATCGTAC-CACCTAGCAACATTCA
66 CCACGGTTTCAACTTCACGACAAAGGGAATCATGCTCACC-AGCAACATTCA
1830035 T
1 T
1830036 CTTCAGGAAC
Statistics
Matches: 213, Mismatches: 17, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
115 9 0.04
116 204 0.96
ACGTcount: A:0.32, C:0.26, G:0.18, T:0.24
Consensus pattern (116 bp):
TTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACGACGAATGGGCCAT
CCACGGTTTCAACTTCACGACAAAGGGAATCATGCTCACCAGCAACATTCA
Found at i:1830178 original size:36 final size:37
Alignment explanation
Indices: 1830134--1830218 Score: 138
Period size: 37 Copynumber: 2.3 Consensus size: 37
1830124 CAAAGTTGTC
*
1830134 TCTCTTGAAGCAAA-TTTTGTCTCTCTTGAGACAGTT
1 TCTCTTGAAACAAAGTTTTGTCTCTCTTGAGACAGTT
1830170 T-TCATTGAAACAAAGTTTTGTCTCTCTTGAGACAGTT
1 TCTC-TTGAAACAAAGTTTTGTCTCTCTTGAGACAGTT
1830207 TCTCTTGAAACA
1 TCTCTTGAAACA
1830219 CCAATTTTTT
Statistics
Matches: 45, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
35 2 0.04
36 10 0.22
37 31 0.69
38 2 0.04
ACGTcount: A:0.26, C:0.19, G:0.15, T:0.40
Consensus pattern (37 bp):
TCTCTTGAAACAAAGTTTTGTCTCTCTTGAGACAGTT
Found at i:1830476 original size:84 final size:84
Alignment explanation
Indices: 1830332--1830507 Score: 280
Period size: 84 Copynumber: 2.1 Consensus size: 84
1830322 CACCAAACCA
* * ***
1830332 TCGAGTTCAATTATATTCAGCTCCAAGGCACATCATTTGCAACATAGCTCAAGTTGAGAAGGGTT
1 TCGAGTTCAACTATACTCAGCTCCAAGGCACATCATTTGCAACATAGCTCAAGGCAAGAAGGGTT
1830397 ATTTGCCAACAAAAGACCT
66 ATTTGCCAACAAAAGACCT
*
1830416 TCGAGTTCAACTATGCTCAGCTCCAAGGCACATCATTTGCAACATAGCTCAAGGCAAGAAGGGTT
1 TCGAGTTCAACTATACTCAGCTCCAAGGCACATCATTTGCAACATAGCTCAAGGCAAGAAGGGTT
* *
1830481 ATTTGCCAACCAAATACCT
66 ATTTGCCAACAAAAGACCT
1830500 TCGAGTTC
1 TCGAGTTC
1830508 GATTACATTC
Statistics
Matches: 84, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
84 84 1.00
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.26
Consensus pattern (84 bp):
TCGAGTTCAACTATACTCAGCTCCAAGGCACATCATTTGCAACATAGCTCAAGGCAAGAAGGGTT
ATTTGCCAACAAAAGACCT
Found at i:1831329 original size:12 final size:13
Alignment explanation
Indices: 1831305--1831334 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
1831295 GGTTTCCATC
1831305 CTCATCGCTTTCT
1 CTCATCGCTTTCT
1831318 CTCATC-CTTTCT
1 CTCATCGCTTTCT
1831330 CTCAT
1 CTCAT
1831335 TACGATCGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.65
13 6 0.35
ACGTcount: A:0.10, C:0.40, G:0.03, T:0.47
Consensus pattern (13 bp):
CTCATCGCTTTCT
Found at i:1835605 original size:24 final size:25
Alignment explanation
Indices: 1835572--1835622 Score: 70
Period size: 24 Copynumber: 2.1 Consensus size: 25
1835562 TCTCCTAATC
1835572 AGGGCATGCCACCCG-ACAACATGGG
1 AGGGCATGCC-CCCGAACAACATGGG
*
1835597 AGGG-ATGCCGCCGAACAACATGGG
1 AGGGCATGCCCCCGAACAACATGGG
1835621 AG
1 AG
1835623 ATATGCCGCC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 3 0.12
24 17 0.71
25 4 0.17
ACGTcount: A:0.29, C:0.27, G:0.35, T:0.08
Consensus pattern (25 bp):
AGGGCATGCCCCCGAACAACATGGG
Found at i:1835628 original size:24 final size:24
Alignment explanation
Indices: 1835587--1835636 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
1835577 ATGCCACCCG
*
1835587 ACAACATGGGAGGGATGCCGCCGA
1 ACAACATGGGAGAGATGCCGCCGA
*
1835611 ACAACATGGGAGATATGCCGCCGA
1 ACAACATGGGAGAGATGCCGCCGA
1835635 AC
1 AC
1835637 CAAGGGTACT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.32, C:0.26, G:0.32, T:0.10
Consensus pattern (24 bp):
ACAACATGGGAGAGATGCCGCCGA
Found at i:1836561 original size:30 final size:30
Alignment explanation
Indices: 1836525--1836582 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
1836515 TTGTTTATAC
*
1836525 CTCTGGCAAAGCAAAAGTGAGCACAGATGT
1 CTCTGGCAAAACAAAAGTGAGCACAGATGT
1836555 CTCTGGCAAAACAAAAGTGAGCACAGAT
1 CTCTGGCAAAACAAAAGTGAGCACAGAT
1836583 AAAATTTAGT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.40, C:0.21, G:0.24, T:0.16
Consensus pattern (30 bp):
CTCTGGCAAAACAAAAGTGAGCACAGATGT
Found at i:1845828 original size:18 final size:18
Alignment explanation
Indices: 1845791--1845828 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
1845781 TCCTTTCAAA
*
1845791 TTCTCTCTCTCTACGTTT
1 TTCTCTCTCTCTACATTT
1845809 TTCTCTCTCTC-ACATCTT
1 TTCTCTCTCTCTACAT-TT
1845827 TT
1 TT
1845829 AAAAGTTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 3 0.17
18 15 0.83
ACGTcount: A:0.08, C:0.34, G:0.03, T:0.55
Consensus pattern (18 bp):
TTCTCTCTCTCTACATTT
Found at i:1856710 original size:6 final size:6
Alignment explanation
Indices: 1856699--1856732 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
1856689 CATTATATAC
* *
1856699 TATATG TATATG TATATG CATATG CATATG TATA
1 TATATG TATATG TATATG TATATG TATATG TATA
1856733 CCTAGGTAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.35, C:0.06, G:0.15, T:0.44
Consensus pattern (6 bp):
TATATG
Found at i:1870173 original size:10 final size:9
Alignment explanation
Indices: 1870148--1870234 Score: 57
Period size: 9 Copynumber: 10.2 Consensus size: 9
1870138 ATATTTGCTT
1870148 AAAGAAGAA
1 AAAGAAGAA
*
1870157 TAA-AAGAGA
1 AAAGAAGA-A
1870166 AAAGAAG-A
1 AAAGAAGAA
1870174 AAA-AAGAA
1 AAAGAAGAA
1870182 AAA-AA-AA
1 AAAGAAGAA
1870189 AAA-AA-AA
1 AAAGAAGAA
1870196 AAATGAA-AA
1 AAA-GAAGAA
*
1870205 AAACGAAAAA
1 AAA-GAAGAA
1870215 AAACGAA-AA
1 AAA-GAAGAA
1870224 AAAGAAGAA
1 AAAGAAGAA
1870233 AA
1 AA
1870235 TGGAAAAAGA
Statistics
Matches: 68, Mismatches: 3, Indels: 14
0.80 0.04 0.16
Matches are distributed among these distances:
7 15 0.22
8 17 0.25
9 24 0.35
10 12 0.18
ACGTcount: A:0.82, C:0.02, G:0.14, T:0.02
Consensus pattern (9 bp):
AAAGAAGAA
Found at i:1870174 original size:8 final size:8
Alignment explanation
Indices: 1870152--1870292 Score: 89
Period size: 7 Copynumber: 17.4 Consensus size: 8
1870142 TTGCTTAAAG
1870152 AAGAATAAA
1 AAGAA-AAA
*
1870161 AGAGAAAAG
1 A-AGAAAAA
1870170 AAG-AAAA
1 AAGAAAAA
1870177 AAG-AAAA
1 AAGAAAAA
1870184 AA-AAAAA
1 AAGAAAAA
1870191 AA-AAAAA
1 AAGAAAAA
*
1870198 ATGAAAAA
1 AAGAAAAA
1870206 AACGAAAAAA
1 AA-G-AAAAA
1870216 AACGAAAAA
1 AA-GAAAAA
1870225 AAGAAGAAA
1 AAGAA-AAA
* *
1870234 ATG-GAAA
1 AAGAAAAA
1870241 AAGAAAAA
1 AAGAAAAA
*
1870249 ATG-AAAA
1 AAGAAAAA
*
1870256 ATGAAAAA
1 AAGAAAAA
1870264 AGAGAAAAA
1 A-AGAAAAA
1870273 TAA-AAAAA
1 -AAGAAAAA
*
1870281 GAGAAATAA
1 AAGAAA-AA
1870290 AAG
1 AAG
1870293 GAGGGTTCAA
Statistics
Matches: 108, Mismatches: 12, Indels: 24
0.75 0.08 0.17
Matches are distributed among these distances:
7 37 0.34
8 29 0.27
9 28 0.26
10 14 0.13
ACGTcount: A:0.79, C:0.01, G:0.15, T:0.05
Consensus pattern (8 bp):
AAGAAAAA
Found at i:1870340 original size:45 final size:46
Alignment explanation
Indices: 1870289--1870377 Score: 128
Period size: 46 Copynumber: 2.0 Consensus size: 46
1870279 AAGAGAAATA
*
1870289 AAAGGAGGGT-TCAAGATG-AAAACCCGAAAAGGGCGTCTTGGAACC
1 AAAGGA-GGTCTCAAGATGAAAAACCCGAAAAGGGCGACTTGGAACC
* *
1870334 AAAGGAGGTCTCAAGTTGAAAAACCCGCAAAGGGCGACTTGGAA
1 AAAGGAGGTCTCAAGATGAAAAACCCGAAAAGGGCGACTTGGAA
1870378 TTTGAAATTC
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
44 3 0.08
45 13 0.33
46 23 0.59
ACGTcount: A:0.38, C:0.18, G:0.30, T:0.13
Consensus pattern (46 bp):
AAAGGAGGTCTCAAGATGAAAAACCCGAAAAGGGCGACTTGGAACC
Found at i:1871471 original size:51 final size:51
Alignment explanation
Indices: 1871405--1871785 Score: 338
Period size: 51 Copynumber: 7.3 Consensus size: 51
1871395 GAAGCAAATT
* * *
1871405 CGTTTGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACA
1 CGTTTATTGAAGATTGAGTCCTATACTCTCTGAAAGAATAGGGAGCGGACC
* **
1871456 AGTTCGTTGAAGATTGAGTCCTATACTCTCTGAAAGAATAGGGAGCGGACC
1 CGTTTATTGAAGATTGAGTCCTATACTCTCTGAAAGAATAGGGAGCGGACC
* * * * * *
1871507 TGTTTATCGAAGATTTTTCGAGTTCTATACTCTATGAAGGAATAGAGAGCGGACC
1 CGTTTATTGAAGA---TT-GAGTCCTATACTCTCTGAAAGAATAGGGAGCGGACC
** * * * * * *
1871562 CGTTTTATTGAAGAGCGAGTTCTATACTCCCTGAACGGATAGGGAGCGAACA
1 CG-TTTATTGAAGATTGAGTCCTATACTCTCTGAAAGAATAGGGAGCGGACC
* *
1871614 CGTTTGTTAAAGATTGAGTCCTATACTCTCTGAAAGAATAGGGAGCGGACC
1 CGTTTATTGAAGATTGAGTCCTATACTCTCTGAAAGAATAGGGAGCGGACC
* * * *
1871665 TGTTTATTG-AGATTTTCGAGTTCTATACTCTCTG-AAGGATAGAGAGCGGACC
1 CGTTTATTGAAGA--TT-GAGTCCTATACTCTCTGAAAGAATAGGGAGCGGACC
* * * * *
1871717 CGTTTATT-AAGATTGTTCAAGTCTTATACTCTCTGAATGAATAGAGAGCAGACA
1 CGTTTATTGAAGATTG----AGTCCTATACTCTCTGAAAGAATAGGGAGCGGACC
*
1871771 CATTTA-TGAAGATTG
1 CGTTTATTGAAGATTG
1871786 CTCGAGTCTA
Statistics
Matches: 268, Mismatches: 47, Indels: 27
0.78 0.14 0.08
Matches are distributed among these distances:
49 1 0.00
50 5 0.02
51 101 0.38
52 59 0.22
53 31 0.12
54 28 0.10
55 33 0.12
56 10 0.04
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.30
Consensus pattern (51 bp):
CGTTTATTGAAGATTGAGTCCTATACTCTCTGAAAGAATAGGGAGCGGACC
Found at i:1871607 original size:158 final size:154
Alignment explanation
Indices: 1871405--1871728 Score: 488
Period size: 158 Copynumber: 2.1 Consensus size: 154
1871395 GAAGCAAATT
* ** * * * *
1871405 CGTTTGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTCGTTGAAGAT
1 CGTTTATTGAAGAGCGAGTCCTATACTCCCTGAACGAATAGGGAGCGAACAAGTTCGTTAAAGAT
1871470 TGAGTCCTATACTCTCTGAAAGAATAGGGAGCGGACCTGTTTATCGAAGATTTTTCGAGTTCTAT
66 TGAGTCCTATACTCTCTGAAAGAATAGGGAGCGGACCTGTTTATCG-AGA-TTTTCGAGTTCTAT
1871535 ACTCTATGAAGGAATAGAGAGCGGACC
129 ACTCTATGAAGG-ATAGAGAGCGGACC
* * * *
1871562 CGTTTTATTGAAGAGCGAGTTCTATACTCCCTGAACGGATAGGGAGCGAACACGTTTGTTAAAGA
1 CG-TTTATTGAAGAGCGAGTCCTATACTCCCTGAACGAATAGGGAGCGAACAAGTTCGTTAAAGA
*
1871627 TTGAGTCCTATACTCTCTGAAAGAATAGGGAGCGGACCTGTTTATTGAGATTTTCGAGTTCTATA
65 TTGAGTCCTATACTCTCTGAAAGAATAGGGAGCGGACCTGTTTATCGAGATTTTCGAGTTCTATA
*
1871692 CTCTCTGAAGGATAGAGAGCGGACC
130 CTCTATGAAGGATAGAGAGCGGACC
1871717 CGTTTATT-AAGA
1 CGTTTATTGAAGA
1871729 TTGTTCAAGT
Statistics
Matches: 153, Mismatches: 13, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
153 4 0.03
154 6 0.04
155 16 0.10
156 25 0.16
157 5 0.03
158 97 0.63
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (154 bp):
CGTTTATTGAAGAGCGAGTCCTATACTCCCTGAACGAATAGGGAGCGAACAAGTTCGTTAAAGAT
TGAGTCCTATACTCTCTGAAAGAATAGGGAGCGGACCTGTTTATCGAGATTTTCGAGTTCTATAC
TCTATGAAGGATAGAGAGCGGACC
Found at i:1871765 original size:209 final size:207
Alignment explanation
Indices: 1871405--1871817 Score: 523
Period size: 209 Copynumber: 2.0 Consensus size: 207
1871395 GAAGCAAATT
* * *
1871405 CGTTTGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTCGTTGAAGAT
1 CGTTTGTTAAAGATTGAGTCCTATACTCTCTGAAAGAATAGGGAGCGGACAAGTTCATTGAAGAT
* * * *
1871470 TGAGTCCTATACTCTCTGAAAGAATAGGGAGCGGACCTGTTTATCGAAGATTTTTCGAGTTCTAT
66 TGAGTCCTATACTCTCTGAAAGAATAGAGAGCGGACCCGTTTATCGAAGATTGTTCAAGTTCTAT
* * *
1871535 ACTCTATGAAGGAATAGAGAGCGGACCCGTTTTATTGAAGA-G-CGAGTTCTATACTCCCTGAAC
131 ACTCTATGAAGGAATAGAGAGCAGACAC-ATTTA-TGAAGATGCCGAG-TCTATACTCCCTGAA-
1871598 GGATAGGGAGCGAACA
192 GGATAGGGAGCGAACA
** *
1871614 CGTTTGTTAAAGATTGAGTCCTATACTCTCTGAAAGAATAGGGAGCGGACCTGTTTATTG-AGAT
1 CGTTTGTTAAAGATTGAGTCCTATACTCTCTGAAAGAATAGGGAGCGGACAAGTTCATTGAAGA-
* * *
1871678 TTTCGAGTTCTATACTCTCTG-AAGGATAGAGAGCGGACCCGTTTAT-TAAGATTGTTCAAG-TC
65 -TT-GAGTCCTATACTCTCTGAAAGAATAGAGAGCGGACCCGTTTATCGAAGATTGTTCAAGTTC
* * *
1871740 TTATACTCTCTGAATGAATAGAGAGCAGACACATTTATGAAGATTGCTCGAGTCTATACTTCCTG
128 -TATACTCTATGAAGGAATAGAGAGCAGACACATTTATGAAGA-TGC-CGAGTCTATACTCCCTG
1871805 AAGGATAGGGAGC
190 AAGGATAGGGAGC
1871818 AGGCTCGTCA
Statistics
Matches: 177, Mismatches: 19, Indels: 16
0.83 0.09 0.08
Matches are distributed among these distances:
207 6 0.03
208 9 0.05
209 104 0.59
210 38 0.21
211 20 0.11
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.30
Consensus pattern (207 bp):
CGTTTGTTAAAGATTGAGTCCTATACTCTCTGAAAGAATAGGGAGCGGACAAGTTCATTGAAGAT
TGAGTCCTATACTCTCTGAAAGAATAGAGAGCGGACCCGTTTATCGAAGATTGTTCAAGTTCTAT
ACTCTATGAAGGAATAGAGAGCAGACACATTTATGAAGATGCCGAGTCTATACTCCCTGAAGGAT
AGGGAGCGAACA
Found at i:1871817 original size:158 final size:155
Alignment explanation
Indices: 1871421--1871785 Score: 465
Period size: 158 Copynumber: 2.3 Consensus size: 155
1871411 TTGAAGATTG
*
1871421 AGTCCTATACTCTCTGAATGAATAGGGAGCGGACA-AGTTCGTTGAAGATTGAGTCCTATACTCT
1 AGTCTTATACTCTCTGAATGAATAGGGAGC-GACACA-TT--TTGAAGATTGAGTCCTATACTCT
1871485 CTGAAAGAATAGGGAGCGGACCTGTTTATCGAAGATTTTTCGAGTTCTATACTCTATGAAGGAAT
62 CTGAAAGAATAGGGAGCGGACCTGTTTATCGAAGATTTTTCGAGTTCTATACTCTATGAAGGAAT
*
1871550 AGAGAGCGGACCCGTTTTATTGAAGAGCG
127 AGAGAGCGGACCCGTTTTATTGAAGAGCA
* * * * *
1871579 AGT-TCTATACTCCCTGAACGGATAGGGAGCGAACACGTTTGTTAAAGATTGAGTCCTATACTCT
1 AGTCT-TATACTCTCTGAATGAATAGGGAGCG-ACAC-ATT-TTGAAGATTGAGTCCTATACTCT
* *
1871643 CTGAAAGAATAGGGAGCGGACCTGTTTATTG-AGA-TTTTCGAGTTCTATACTCTCTGAAGG-AT
62 CTGAAAGAATAGGGAGCGGACCTGTTTATCGAAGATTTTTCGAGTTCTATACTCTATGAAGGAAT
1871705 AGAGAGCGGACCCG-TTTATT-AAGATTGTTCA
127 AGAGAGCGGACCCGTTTTATTGAAGA--G--CA
*
1871736 AGTCTTATACTCTCTGAATGAATAGAGAGCAGACACATTTATGAAGATTG
1 AGTCTTATACTCTCTGAATGAATAGGGAGC-GACACATTT-TGAAGATTG
1871786 CTCGAGTCTA
Statistics
Matches: 181, Mismatches: 15, Indels: 24
0.82 0.07 0.11
Matches are distributed among these distances:
153 4 0.02
154 6 0.03
155 18 0.10
156 35 0.19
157 33 0.18
158 83 0.46
159 2 0.01
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.30
Consensus pattern (155 bp):
AGTCTTATACTCTCTGAATGAATAGGGAGCGACACATTTTGAAGATTGAGTCCTATACTCTCTGA
AAGAATAGGGAGCGGACCTGTTTATCGAAGATTTTTCGAGTTCTATACTCTATGAAGGAATAGAG
AGCGGACCCGTTTTATTGAAGAGCA
Found at i:1871844 original size:106 final size:106
Alignment explanation
Indices: 1871471--1871817 Score: 279
Period size: 106 Copynumber: 3.3 Consensus size: 106
1871461 GTTGAAGATT
* * * * * *
1871471 GAGTCCTATACTCTCTGAAAGAATAGGGAGCGGACCTGTTTATCGAAGATTTTTCGAGT-TCTAT
1 GAGTTCTATACTCTCTG-AAGGATAGAGAGCGGACCCGTTTAT-GAAGATTGTTCAAGTCT-TAT
* * * *
1871535 ACTCTATGAAGGAATAGAGAGCGGACCCGT-TTTATTGAAGA---GC
63 ACTCTCTGAAAGAATAGAGAGCAGA-CC-TATTTATTG-AGATTCTC
* * * * * * *
1871578 GAGTTCTATACTCCCTGAACGGATAGGGAGCGAACACGTTTGTTAAAGATTG----AGTCCTATA
1 GAGTTCTATACTCTCTGAA-GGATAGAGAGCGGACCCGTTT-ATGAAGATTGTTCAAGTCTTATA
* * * *
1871639 CTCTCTGAAAGAATAGGGAGCGGACCTGTTTATTGAGATTTTC
64 CTCTCTGAAAGAATAGAGAGCAGACCTATTTATTGAGATTCTC
*
1871682 GAGTTCTATACTCTCTGAAGGATAGAGAGCGGACCCGTTTATTAAGATTGTTCAAGTCTTATACT
1 GAGTTCTATACTCTCTGAAGGATAGAGAGCGGACCCGTTTATGAAGATTGTTCAAGTCTTATACT
*
1871747 CTCTGAATGAATAGAGAGCAGACAC-ATTTA-TGAAGATTGCTC
66 CTCTGAAAGAATAGAGAGCAGAC-CTATTTATTG-AGATT-CTC
*
1871789 GAG-TCTATACT-TCCTGAAGGATAGGGAGC
1 GAGTTCTATACTCT-CTGAAGGATAGAGAGC
1871818 AGGCTCGTCA
Statistics
Matches: 198, Mismatches: 27, Indels: 31
0.77 0.11 0.12
Matches are distributed among these distances:
101 4 0.02
102 17 0.09
103 46 0.23
104 19 0.10
105 3 0.02
106 64 0.32
107 44 0.22
108 1 0.01
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.29
Consensus pattern (106 bp):
GAGTTCTATACTCTCTGAAGGATAGAGAGCGGACCCGTTTATGAAGATTGTTCAAGTCTTATACT
CTCTGAAAGAATAGAGAGCAGACCTATTTATTGAGATTCTC
Found at i:1875540 original size:99 final size:101
Alignment explanation
Indices: 1875414--1875627 Score: 369
Period size: 103 Copynumber: 2.1 Consensus size: 101
1875404 AGTCGAGGTT
1875414 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACA-TGTGAAGTCTGGTGAG-ACATACTT
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACAGTGTGAAGTCTGGTGAGAACATACTT
* *
1875477 GATCCTTTGCATATGTATATGATTCTTAAGGAATGA
66 GATCCCTAGCATATGTATATGATTCTTAAGGAATGA
1875513 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACA-GTGTGAAGTCTGGTGAGA-ACATAC
*
1875578 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
64 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
1875616 TATGTGGTCCTT
1 TATGTGGTCCTT
1875628 ATGGACATTA
Statistics
Matches: 108, Mismatches: 3, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
99 39 0.36
101 16 0.15
103 53 0.49
ACGTcount: A:0.26, C:0.14, G:0.23, T:0.37
Consensus pattern (101 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACAGTGTGAAGTCTGGTGAGAACATACTT
GATCCCTAGCATATGTATATGATTCTTAAGGAATGA
Found at i:1875681 original size:23 final size:23
Alignment explanation
Indices: 1875651--1875709 Score: 73
Period size: 23 Copynumber: 2.6 Consensus size: 23
1875641 TATGGAACTA
*
1875651 CGGTGCAATTCTACGCAGCACTC
1 CGGTGCAATTATACGCAGCACTC
* ** *
1875674 CGGTGCAATTATATGTGGCACTT
1 CGGTGCAATTATACGCAGCACTC
1875697 CGGTGCAATTATA
1 CGGTGCAATTATA
1875710 TTGTGGTGAC
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.29
Consensus pattern (23 bp):
CGGTGCAATTATACGCAGCACTC
Found at i:1875710 original size:23 final size:24
Alignment explanation
Indices: 1875668--1875715 Score: 80
Period size: 23 Copynumber: 2.0 Consensus size: 24
1875658 ATTCTACGCA
1875668 GCACTCCGGTGCAATTATA-TGTG
1 GCACTCCGGTGCAATTATATTGTG
*
1875691 GCACTTCGGTGCAATTATATTGTG
1 GCACTCCGGTGCAATTATATTGTG
1875715 G
1 G
1875716 TGACAGCATT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 18 0.78
24 5 0.22
ACGTcount: A:0.21, C:0.19, G:0.27, T:0.33
Consensus pattern (24 bp):
GCACTCCGGTGCAATTATATTGTG
Found at i:1879403 original size:64 final size:65
Alignment explanation
Indices: 1879330--1879491 Score: 161
Period size: 64 Copynumber: 2.5 Consensus size: 65
1879320 ATTGTTTGAA
* * ** *
1879330 GGTGTATCGATGCACAGGTAGTGCATCGATGCACTCT-TTTAATCAAA-AAACATCGAATGCAAT
1 GGTGCATCGATGCACAAGTAGTGCATCGATGCACTCTCAGTAAT-AAACAAACATCAAATGCAAT
1879393 T
65 T
* * * *
1879394 GGTGCATCGATGCATAAG-ACATGCATCGATGCA-TCTCAGTAATAAACAAACATCAAATGTATT
1 GGTGCATCGATGCACAAGTA-GTGCATCGATGCACTCTCAGTAATAAACAAACATCAAATGCAAT
1879457 T
65 T
** * *
1879458 TATTCACCGATGCACAAGTAGTGCATCGATGCAC
1 GGTGCATCGATGCACAAGTAGTGCATCGATGCAC
1879492 CGATAGGGAA
Statistics
Matches: 78, Mismatches: 15, Indels: 9
0.76 0.15 0.09
Matches are distributed among these distances:
63 7 0.09
64 70 0.90
65 1 0.01
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.27
Consensus pattern (65 bp):
GGTGCATCGATGCACAAGTAGTGCATCGATGCACTCTCAGTAATAAACAAACATCAAATGCAATT
Found at i:1880462 original size:103 final size:104
Alignment explanation
Indices: 1880277--1880495 Score: 359
Period size: 103 Copynumber: 2.1 Consensus size: 104
1880267 GTCGAGGGTC
* * * *
1880277 TATGTGGTCCTTCGGGGACATATATGTATTCTTTGGAATATGTGTGAAGTCTGGTGAGATACATA
1 TATGTGGTCCTTCGGAGACATATATGTATTCTTTAGAACATGTGTGAAGTCTGGTGAGACACATA
* *
1880342 CTTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 CTTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
1880381 TATGTGGTCCTTC-GAGACATATATGTATTCTTTAGAACATGTGTGAAGTCTGGTGAGACACATA
1 TATGTGGTCCTTCGGAGACATATATGTATTCTTTAGAACATGTGTGAAGTCTGGTGAGACACATA
* *
1880445 CTTGATCCCTAGTATATGTATATGATTTTTAAGGAATGA
66 CTTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
1880484 TATGTGGTCCTT
1 TATGTGGTCCTT
1880496 ATGGACATTA
Statistics
Matches: 107, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
103 94 0.88
104 13 0.12
ACGTcount: A:0.26, C:0.12, G:0.23, T:0.38
Consensus pattern (104 bp):
TATGTGGTCCTTCGGAGACATATATGTATTCTTTAGAACATGTGTGAAGTCTGGTGAGACACATA
CTTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
Found at i:1880578 original size:23 final size:23
Alignment explanation
Indices: 1880502--1880579 Score: 93
Period size: 23 Copynumber: 3.3 Consensus size: 23
1880492 CCTTATGGAC
*
1880502 ATTATTATATGGCACTACGGTGCA
1 ATTA-TATGTGGCACTACGGTGCA
* * * *
1880526 ATTCTACGCGGCACTCCGGTGCA
1 ATTATATGTGGCACTACGGTGCA
*
1880549 ATTATATGTGGCACTTCGGTGCA
1 ATTATATGTGGCACTACGGTGCA
1880572 ATTATATG
1 ATTATATG
1880580 AGCTGTGGTG
Statistics
Matches: 45, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
23 42 0.93
24 3 0.07
ACGTcount: A:0.24, C:0.21, G:0.23, T:0.32
Consensus pattern (23 bp):
ATTATATGTGGCACTACGGTGCA
Found at i:1882257 original size:27 final size:29
Alignment explanation
Indices: 1882202--1882257 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 29
1882192 TGAAATATTC
**
1882202 TTTTATATATTTTTTACTTCTTATTATTT
1 TTTTATATATTTTTTACTTCTTAGAATTT
1882231 TTTTATAT-TTTTTTACTT-TTAGAATTT
1 TTTTATATATTTTTTACTTCTTAGAATTT
1882258 AACATTTTCC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 7 0.28
28 10 0.40
29 8 0.32
ACGTcount: A:0.21, C:0.05, G:0.02, T:0.71
Consensus pattern (29 bp):
TTTTATATATTTTTTACTTCTTAGAATTT
Found at i:1887300 original size:117 final size:122
Alignment explanation
Indices: 1887167--1887384 Score: 290
Period size: 123 Copynumber: 1.8 Consensus size: 122
1887157 AACAAAAATA
*
1887167 ATTTACATTTTATTATTATTATGAATATCTAT-G-AAGAAT-TT-T-TACAATGT-AA-ACATTT
1 ATTTACATTTTATTATTATTATGAATAT-TATAGTAA-AATGTTATGTAAAATGTAAATACATTT
*
1887225 TTACATAAATTATGTAAAATTTAATATTAATTAAAATATCTTAAATTATAAACATTTTT
64 TTACACAAATTATGTAAAATTTAATATTAATTAAAATATCTTAAATTATAAACATTTTT
* * * *
1887284 ATTTACATCTTT-TTATTATTATGAATATTTTAGTTAAATGTTGATGTAAAATTTAAATATATTT
1 ATTTACAT-TTTATTATTATTATGAATATTATAGTAAAATGTT-ATGTAAAATGTAAATACATTT
1887348 TTACACAAATTATGTAAAATTTAATATTAATTAAAAT
64 TTACACAAATTATGTAAAATTTAATATTAATTAAAAT
1887385 TAAAATAATA
Statistics
Matches: 86, Mismatches: 6, Indels: 12
0.83 0.06 0.12
Matches are distributed among these distances:
116 2 0.02
117 28 0.33
118 6 0.07
120 1 0.01
121 6 0.07
122 2 0.02
123 41 0.48
ACGTcount: A:0.42, C:0.05, G:0.05, T:0.48
Consensus pattern (122 bp):
ATTTACATTTTATTATTATTATGAATATTATAGTAAAATGTTATGTAAAATGTAAATACATTTTT
ACACAAATTATGTAAAATTTAATATTAATTAAAATATCTTAAATTATAAACATTTTT
Found at i:1887459 original size:15 final size:15
Alignment explanation
Indices: 1887439--1887469 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1887429 CAACAAATAG
1887439 AATTTTTATATAAAT
1 AATTTTTATATAAAT
*
1887454 AATTTTTATTTAAAT
1 AATTTTTATATAAAT
1887469 A
1 A
1887470 TTTAGAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
AATTTTTATATAAAT
Found at i:1888431 original size:77 final size:77
Alignment explanation
Indices: 1888341--1888501 Score: 223
Period size: 77 Copynumber: 2.1 Consensus size: 77
1888331 AGTTTTCAAA
* * *** *
1888341 ATCGCGATGCGATTCTCAAATTCGCAACTCAATTTTCGTTTTCGCAACGCTAATTACCGATATAG
1 ATCGCAATGCGATTCTCAAATTCGCAACGCAATTTTCAAATTCGCAACGCTAATTACCGACATAG
*
1888406 GTAAACAGTACT
66 GTAAACAATACT
* * * *
1888418 ATCGCAATGCGATTTTCAAATTCGCAACGCGATTTTCAAATTCGCAACGTTAATTACCGACATTG
1 ATCGCAATGCGATTCTCAAATTCGCAACGCAATTTTCAAATTCGCAACGCTAATTACCGACATAG
1888483 GTAAACAATACT
66 GTAAACAATACT
1888495 ATCGCAA
1 ATCGCAA
1888502 CACGGTAGAA
Statistics
Matches: 73, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
77 73 1.00
ACGTcount: A:0.32, C:0.23, G:0.15, T:0.30
Consensus pattern (77 bp):
ATCGCAATGCGATTCTCAAATTCGCAACGCAATTTTCAAATTCGCAACGCTAATTACCGACATAG
GTAAACAATACT
Found at i:1888444 original size:20 final size:20
Alignment explanation
Indices: 1888419--1888466 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
1888409 AACAGTACTA
*
1888419 TCGCAATGCGATTTTCAAAT
1 TCGCAACGCGATTTTCAAAT
1888439 TCGCAACGCGATTTTCAAAT
1 TCGCAACGCGATTTTCAAAT
1888459 TCGCAACG
1 TCGCAACG
1888467 TTAATTACCG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.29
Consensus pattern (20 bp):
TCGCAACGCGATTTTCAAAT
Found at i:1888614 original size:20 final size:19
Alignment explanation
Indices: 1888516--1888625 Score: 80
Period size: 20 Copynumber: 5.5 Consensus size: 19
1888506 GTAGAAATTC
1888516 GAGTTGCGAATTTGAAAAT
1 GAGTTGCGAATTTGAAAAT
*
1888535 CGCA-TTACGAATTTGAAAAT
1 -G-AGTTGCGAATTTGAAAAT
* *
1888555 CGTGTAGCGAATTTGGAAAAT
1 -GAGTTGCGAATTT-GAAAAT
* * *
1888576 CACG-TGCGATTTTCGAAACT
1 GA-GTTGCGAATTT-GAAAAT
1888596 GAGTTGCGAATTTGAAAACT
1 GAGTTGCGAATTTGAAAA-T
*
1888616 GTGTTGCGAA
1 GAGTTGCGAA
1888626 ATTGGAGTTT
Statistics
Matches: 70, Mismatches: 14, Indels: 12
0.73 0.15 0.12
Matches are distributed among these distances:
19 5 0.07
20 57 0.81
21 8 0.11
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.30
Consensus pattern (19 bp):
GAGTTGCGAATTTGAAAAT
Found at i:1888658 original size:19 final size:19
Alignment explanation
Indices: 1888598--1888668 Score: 70
Period size: 19 Copynumber: 3.6 Consensus size: 19
1888588 TCGAAACTGA
* * *
1888598 GTTGCGAATTTGAAAACTGT
1 GTTGCGAATTTGAGATC-GC
* * *
1888618 GTTGCGAAATTGGAGTTTGC
1 GTTGCG-AATTTGAGATCGC
1888638 GTTGCGAATTTGAGATCGC
1 GTTGCGAATTTGAGATCGC
1888657 GTTGCGAATTTG
1 GTTGCGAATTTG
1888669 TTGGTTATTT
Statistics
Matches: 41, Mismatches: 9, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
19 22 0.54
20 13 0.32
21 6 0.15
ACGTcount: A:0.23, C:0.11, G:0.31, T:0.35
Consensus pattern (19 bp):
GTTGCGAATTTGAGATCGC
Found at i:1889366 original size:21 final size:21
Alignment explanation
Indices: 1889340--1889392 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
1889330 GTTTCCAGAT
1889340 TCGCAACGCGAACATCGACTA
1 TCGCAACGCGAACATCGACTA
*
1889361 TCGCAACGCGAACTTCGACTA
1 TCGCAACGCGAACATCGACTA
*
1889382 TCGCAATGCGA
1 TCGCAACGCGA
1889393 TTTTCCAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.30, C:0.32, G:0.21, T:0.17
Consensus pattern (21 bp):
TCGCAACGCGAACATCGACTA
Found at i:1889449 original size:21 final size:21
Alignment explanation
Indices: 1889424--1889537 Score: 74
Period size: 21 Copynumber: 5.4 Consensus size: 21
1889414 GTCCAAGTTT
*
1889424 CGTTGCAATTTATTCCAAATC
1 CGTTGCGATTTATTCCAAATC
* *
1889445 CGTTGCGA--TAGTCCAAGTTC
1 CGTTGCGATTTATTCCAA-ATC
*
1889465 ACGTTGCGATTTATTCCAAATT
1 -CGTTGCGATTTATTCCAAATC
* * * *
1889487 TGTTGC-A-ATAGTCCAAGTTC
1 CGTTGCGATTTATTCCAA-ATC
* *
1889507 GCGTTGCGATTTATTACAAATT
1 -CGTTGCGATTTATTCCAAATC
1889529 CGTTGCGAT
1 CGTTGCGAT
1889538 AGTCCAAGTT
Statistics
Matches: 68, Mismatches: 17, Indels: 16
0.67 0.17 0.16
Matches are distributed among these distances:
19 14 0.21
20 4 0.06
21 34 0.50
22 3 0.04
23 13 0.19
ACGTcount: A:0.25, C:0.20, G:0.18, T:0.37
Consensus pattern (21 bp):
CGTTGCGATTTATTCCAAATC
Found at i:1889549 original size:42 final size:42
Alignment explanation
Indices: 1889388--1889549 Score: 240
Period size: 42 Copynumber: 3.9 Consensus size: 42
1889378 ACTATCGCAA
*
1889388 TGCGA-TT-TTCCAAATTCGTTGCGATAGTCCAAGTT-TCGT
1 TGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCGT
* * *
1889427 TGCAATTTATTCCAAATCCGTTGCGATAGTCCAAGTTCACGT
1 TGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCGT
* *
1889469 TGCGATTTATTCCAAATTTGTTGCAATAGTCCAAGTTCGCGT
1 TGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCGT
*
1889511 TGCGATTTATTACAAATTCGTTGCGATAGTCCAAGTTCG
1 TGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCG
1889550 TTGCAATAGT
Statistics
Matches: 109, Mismatches: 11, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
39 4 0.04
40 2 0.02
41 27 0.25
42 76 0.70
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.36
Consensus pattern (42 bp):
TGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCGT
Found at i:1889558 original size:19 final size:19
Alignment explanation
Indices: 1889396--1889568 Score: 103
Period size: 19 Copynumber: 8.5 Consensus size: 19
1889386 AATGCGATTT
* *
1889396 TCCAAATTCGTTGCGATAG
1 TCCAAGTTCGTTGCAATAG
*
1889415 TCCAAGTTTCGTTGCAATTTAT
1 TCCAAG-TTCGTTGCAA--TAG
* * *
1889437 TCCAAATCCGTTGCGATAG
1 TCCAAGTTCGTTGCAATAG
* *
1889456 TCCAAGTTCACGTTGCGATTTAT
1 TCCAAGTT--CGTTGC-A-ATAG
* *
1889479 TCCAAATTTGTTGCAATAG
1 TCCAAGTTCGTTGCAATAG
* *
1889498 TCCAAGTTCGCGTTGCGATTTAT
1 TCCAAGTT--CGTTGC-A-ATAG
* * *
1889521 TACAAATTCGTTGCGATAG
1 TCCAAGTTCGTTGCAATAG
1889540 TCCAAGTTCGTTGCAATAG
1 TCCAAGTTCGTTGCAATAG
*
1889559 TCGAAGTTCG
1 TCCAAGTTCG
1889569 CGTTACGATT
Statistics
Matches: 114, Mismatches: 29, Indels: 22
0.69 0.18 0.13
Matches are distributed among these distances:
19 49 0.43
20 10 0.09
21 30 0.26
22 8 0.07
23 17 0.15
ACGTcount: A:0.25, C:0.20, G:0.20, T:0.35
Consensus pattern (19 bp):
TCCAAGTTCGTTGCAATAG
Found at i:1889558 original size:61 final size:61
Alignment explanation
Indices: 1889388--1889605 Score: 241
Period size: 61 Copynumber: 3.6 Consensus size: 61
1889378 ACTATCGCAA
* *
1889388 TGCGA-TT-TTCCAAATTCGTTGCGATAGTCCAAGTTTCGTTGCAATTTATTCCAA-ATC-CGT
1 TGCGATTTATTCCAAATTCGTTGCGATAGTCCAAG-TTCGTTGCAA--TAGTCCAAGTTCGCGT
* * * * *
1889448 TGCGA--TAGTCCAAGTTCACGTTGCGATTTATTCCAAATTTGTTGCAATAGTCCAAGTTCGCGT
1 TGCGATTTATTCCAAATT--CGTTGCGA--TAGTCCAAGTTCGTTGCAATAGTCCAAGTTCGCGT
* *
1889511 TGCGATTTATTACAAATTCGTTGCGATAGTCCAAGTTCGTTGCAATAGTCGAAGTTCGCGT
1 TGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGTTGCAATAGTCCAAGTTCGCGT
*
1889572 TACGATTTATTCCAAATTCGTTGCGATAGTCCAA
1 TGCGATTTATTCCAAATTCGTTGCGATAGTCCAA
1889606 AATCACAACG
Statistics
Matches: 133, Mismatches: 16, Indels: 17
0.80 0.10 0.10
Matches are distributed among these distances:
59 1 0.01
60 12 0.09
61 70 0.53
62 10 0.08
63 25 0.19
64 7 0.05
65 8 0.06
ACGTcount: A:0.25, C:0.20, G:0.19, T:0.36
Consensus pattern (61 bp):
TGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGTTGCAATAGTCCAAGTTCGCGT
Found at i:1890456 original size:21 final size:20
Alignment explanation
Indices: 1890423--1890601 Score: 123
Period size: 21 Copynumber: 8.7 Consensus size: 20
1890413 CGTTGCGATT
* *
1890423 TTGGACTATCGCAA-CGAAT
1 TTGGAATATCGCAAGCGAAC
1890442 TTGGAATAAATCGCAACGCGAAC
1 TTGGAAT--ATCGCAA-GCGAAC
* *
1890465 TTCGACTATCGCAACGCGAAC
1 TTGGAATATCGCAA-GCGAAC
* *
1890486 TTGGACTATCGCAA-CGAAT
1 TTGGAATATCGCAAGCGAAC
1890505 TTGGAATAAATCGCAAAGCGAAC
1 TTGGAAT--ATCGC-AAGCGAAC
* * *
1890528 TTGGACTATCGCAA-CGGAT
1 TTGGAATATCGCAAGCGAAC
*
1890547 TTGGAATAAATTGCAAAGCGAAC
1 TTGGAAT--ATCGC-AAGCGAAC
* *
1890570 TTGGACTATCGCAA-CGAAT
1 TTGGAATATCGCAAGCGAAC
*
1890589 TTGGAAAATCGCA
1 TTGGAATATCGCA
1890602 TTGCGATAGT
Statistics
Matches: 128, Mismatches: 20, Indels: 24
0.74 0.12 0.14
Matches are distributed among these distances:
19 40 0.31
20 4 0.03
21 52 0.41
22 4 0.03
23 28 0.22
ACGTcount: A:0.35, C:0.21, G:0.22, T:0.22
Consensus pattern (20 bp):
TTGGAATATCGCAAGCGAAC
Found at i:1890497 original size:42 final size:43
Alignment explanation
Indices: 1890451--1890601 Score: 183
Period size: 42 Copynumber: 3.7 Consensus size: 43
1890441 TTTGGAATAA
* * * *
1890451 ATCGCAACGCGAACTTCGACT-ATCGCAACGCGAACTTGGACT
1 ATCGCAACGCGAATTTGGAATAATCGCAAAGCGAACTTGGACT
1890493 ATCGCAA--CGAATTTGGAATAAATCGCAAAGCGAACTTGGACT
1 ATCGCAACGCGAATTTGGAAT-AATCGCAAAGCGAACTTGGACT
*
1890535 ATCGCAACG-G-ATTTGGAATAAATTGCAAAGCGAACTTGGACT
1 ATCGCAACGCGAATTTGGAAT-AATCGCAAAGCGAACTTGGACT
1890577 ATCGCAA--CGAATTTGGAA-AATCGCA
1 ATCGCAACGCGAATTTGGAATAATCGCA
1890602 TTGCGATAGT
Statistics
Matches: 97, Mismatches: 6, Indels: 14
0.83 0.05 0.12
Matches are distributed among these distances:
40 15 0.15
41 1 0.01
42 80 0.82
43 1 0.01
ACGTcount: A:0.35, C:0.22, G:0.22, T:0.21
Consensus pattern (43 bp):
ATCGCAACGCGAATTTGGAATAATCGCAAAGCGAACTTGGACT
Found at i:1890526 original size:63 final size:63
Alignment explanation
Indices: 1890423--1890543 Score: 224
Period size: 63 Copynumber: 1.9 Consensus size: 63
1890413 CGTTGCGATT
*
1890423 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGCGAAC
1 TTGGACTATCGCAACGAATTTGGAATAAATCGCAAAGCGAACTTCGACTATCGCAACGCGAAC
*
1890486 TTGGACTATCGCAACGAATTTGGAATAAATCGCAAAGCGAACTTGGACTATCGCAACG
1 TTGGACTATCGCAACGAATTTGGAATAAATCGCAAAGCGAACTTCGACTATCGCAACG
1890544 GATTTGGAAT
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
63 56 1.00
ACGTcount: A:0.34, C:0.23, G:0.21, T:0.21
Consensus pattern (63 bp):
TTGGACTATCGCAACGAATTTGGAATAAATCGCAAAGCGAACTTCGACTATCGCAACGCGAAC
Found at i:1890626 original size:21 final size:21
Alignment explanation
Indices: 1890597--1890646 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
1890587 ATTTGGAAAA
*
1890597 TCGCATTGCGATAGTCGAAGT
1 TCGCGTTGCGATAGTCGAAGT
* *
1890618 TCGCGTTGCGATAGTTGATGT
1 TCGCGTTGCGATAGTCGAAGT
1890639 TCGCGTTG
1 TCGCGTTG
1890647 AAAATCTGGA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.16, C:0.18, G:0.32, T:0.34
Consensus pattern (21 bp):
TCGCGTTGCGATAGTCGAAGT
Found at i:1898994 original size:24 final size:24
Alignment explanation
Indices: 1898958--1899015 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
1898948 ATTAAAATGA
**
1898958 TAAACGAACACAAGTGAACGAACG
1 TAAACGAACACAAACGAACGAACG
* *
1898982 TAAATGAATACAAACGAACGAACG
1 TAAACGAACACAAACGAACGAACG
*
1899006 TAAACAAACA
1 TAAACGAACA
1899016 TAAAATTAAC
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.55, C:0.19, G:0.16, T:0.10
Consensus pattern (24 bp):
TAAACGAACACAAACGAACGAACG
Found at i:1899220 original size:14 final size:14
Alignment explanation
Indices: 1899197--1899235 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
1899187 TGGGCTAAAT
*
1899197 ATAAACGAACGAAC
1 ATAAACGAACAAAC
*
1899211 ATAAATGAACAAAC
1 ATAAACGAACAAAC
1899225 ATAAACGAACA
1 ATAAACGAACA
1899236 GATTACTGAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.62, C:0.18, G:0.10, T:0.10
Consensus pattern (14 bp):
ATAAACGAACAAAC
Found at i:1905582 original size:21 final size:21
Alignment explanation
Indices: 1905558--1905600 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1905548 ACGAACTCAG
*
1905558 TGGATCTCCCAGTCGAAGGCC
1 TGGATCTCCCAGTCAAAGGCC
* *
1905579 TGGATCTCTCTGTCAAAGGCC
1 TGGATCTCCCAGTCAAAGGCC
1905600 T
1 T
1905601 CTTTGAGGTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.19, C:0.30, G:0.26, T:0.26
Consensus pattern (21 bp):
TGGATCTCCCAGTCAAAGGCC
Found at i:1906226 original size:23 final size:23
Alignment explanation
Indices: 1906191--1906238 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
1906181 ATCAAGTACA
* * *
1906191 ATAATATATTAGGTAGTGTTTAT
1 ATAATATAATAGGTAGCGCTTAT
*
1906214 ATAATGTAATAGGTAGCGCTTAT
1 ATAATATAATAGGTAGCGCTTAT
1906237 AT
1 AT
1906239 TGACATTTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.35, C:0.04, G:0.19, T:0.42
Consensus pattern (23 bp):
ATAATATAATAGGTAGCGCTTAT
Found at i:1906274 original size:14 final size:14
Alignment explanation
Indices: 1906255--1906292 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
1906245 TTTTTCTAAC
1906255 TAAACAGGTATATT
1 TAAACAGGTATATT
*
1906269 TAAACATGTATATT
1 TAAACAGGTATATT
*
1906283 TAAACCGGTA
1 TAAACAGGTA
1906293 ACATTGTAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.42, C:0.11, G:0.13, T:0.34
Consensus pattern (14 bp):
TAAACAGGTATATT
Found at i:1906917 original size:116 final size:116
Alignment explanation
Indices: 1906701--1906939 Score: 388
Period size: 116 Copynumber: 2.1 Consensus size: 116
1906691 TTTTGTCATT
* * * * *
1906701 TCGAGACCGATTTTGTTATATTTTTACCTGTTATATTGTTGTTGATCGATACATTTTTATAAAGT
1 TCGATACCGATTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACAATTTTATAAAGT
* *
1906766 ATCGACACTTTATTGGCACTATAACTTCTTTTCTTTTAAATTCCAAAAGTG
66 ATCGACACTTTATTAGCACTATAACTTCTTCTCTTTTAAATTCCAAAAGTG
*
1906817 TCGATACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACAATTTTATAAAGT
1 TCGATACCGATTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACAATTTTATAAAGT
* *
1906882 ATCGACACTTTATTAGCGCTATAATTTCTTCTCTTTTAAATTCCAAAAGTG
66 ATCGACACTTTATTAGCACTATAACTTCTTCTCTTTTAAATTCCAAAAGTG
1906933 TCGATAC
1 TCGATAC
1906940 TTATAATAAA
Statistics
Matches: 113, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
116 113 1.00
ACGTcount: A:0.27, C:0.15, G:0.13, T:0.44
Consensus pattern (116 bp):
TCGATACCGATTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACAATTTTATAAAGT
ATCGACACTTTATTAGCACTATAACTTCTTCTCTTTTAAATTCCAAAAGTG
Found at i:1907305 original size:112 final size:112
Alignment explanation
Indices: 1906945--1907401 Score: 792
Period size: 112 Copynumber: 4.1 Consensus size: 112
1906935 GATACTTATA
* * * *
1906945 ATAAAGTATCGACACTATCAACATATCCGGTAGCGTTTTACCTGTTTTGTCATTTATAGACCGGT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGAT
1907010 TTTGTCA-TTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
* *
1907056 ATAAAGTATCAACACTTTCAATATATCCGGTAGCGTTTTACCTGTTTTGTCATTTATAGACCGAT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGAT
1907121 TTTGTCATTTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
66 TTTGTCA-TTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
*
1907169 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTTTCATTTATAGACC-AG
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGA-
*
1907233 TTTTGTCATTTTTTTATCTGTTATATTGTTATGGATCGATACATTTTT
65 TTTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
1907281 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGAT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGAT
* *
1907346 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCAATATATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
1907393 ATAAAGTAT
1 ATAAAGTAT
1907402 TTACACAAAC
Statistics
Matches: 330, Mismatches: 12, Indels: 7
0.95 0.03 0.02
Matches are distributed among these distances:
111 68 0.21
112 155 0.47
113 107 0.32
ACGTcount: A:0.25, C:0.15, G:0.14, T:0.46
Consensus pattern (112 bp):
ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGAT
TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
Found at i:1909317 original size:175 final size:175
Alignment explanation
Indices: 1909026--1909377 Score: 587
Period size: 175 Copynumber: 2.0 Consensus size: 175
1909016 TGGCCTGTGT
* *
1909026 TCTCAGGCATGCTGATATCTTTTCTTTTTCATTCGGGGAATCGTGCCTTGTTGAGCTTGAAACCT
1 TCTCAGGCATGCTGATATCTTTTCTTTGTCATTCGGGAAATCGTGCCTTGTTGAGCTTGAAACCT
* *
1909091 TTGAATGTGTGTTTCTTTGCCTCTTTATGCCTTCTTATTTTTCCATAGGGGATTCTTCTTCTTCG
66 TTGAATGAGTGTTTCTTTGCCTCTTTATGCCTTCTTATTTTTCCATAGGGGATTCTTCTTCTGCG
* *
1909156 CCGATCATGATTACATCAGAGGATAAGTTTAGTCCTATCTTTATA
131 CCGATCATGATTACATCAGAGGATAAGTTCAATCCTATCTTTATA
* * *
1909201 TCTCAGGCCTGCTGATATCTTTTCTTTGTCATTCGGGAAATCGTGCCTTGTTGATCTTGAGACCT
1 TCTCAGGCATGCTGATATCTTTTCTTTGTCATTCGGGAAATCGTGCCTTGTTGAGCTTGAAACCT
* *
1909266 TTGAATGAGTGTTTCTTTTCCTCTTTATGCCTTCTTCTTTTTCCATAGGGGATTCTTCTTCTGCG
66 TTGAATGAGTGTTTCTTTGCCTCTTTATGCCTTCTTATTTTTCCATAGGGGATTCTTCTTCTGCG
* *
1909331 CCGATCATTATTACATCAGAGGATAAGTTCAATCCTGTCTTTATA
131 CCGATCATGATTACATCAGAGGATAAGTTCAATCCTATCTTTATA
1909376 TC
1 TC
1909378 ATTTCTTATA
Statistics
Matches: 164, Mismatches: 13, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
175 164 1.00
ACGTcount: A:0.18, C:0.21, G:0.18, T:0.43
Consensus pattern (175 bp):
TCTCAGGCATGCTGATATCTTTTCTTTGTCATTCGGGAAATCGTGCCTTGTTGAGCTTGAAACCT
TTGAATGAGTGTTTCTTTGCCTCTTTATGCCTTCTTATTTTTCCATAGGGGATTCTTCTTCTGCG
CCGATCATGATTACATCAGAGGATAAGTTCAATCCTATCTTTATA
Found at i:1913387 original size:29 final size:29
Alignment explanation
Indices: 1913345--1913423 Score: 122
Period size: 29 Copynumber: 2.7 Consensus size: 29
1913335 CGGTGATCGA
* *
1913345 TATATTTATCGATCTAATACCAGTCAGAC
1 TATATTTTTCGATCTAACACCAGTCAGAC
* *
1913374 TATATTTTTTGATCTAACACTAGTCAGAC
1 TATATTTTTCGATCTAACACCAGTCAGAC
1913403 TATATTTTTCGATCTAACACC
1 TATATTTTTCGATCTAACACC
1913424 CTTAGCAGTA
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 44 1.00
ACGTcount: A:0.32, C:0.20, G:0.09, T:0.39
Consensus pattern (29 bp):
TATATTTTTCGATCTAACACCAGTCAGAC
Found at i:1913795 original size:9 final size:9
Alignment explanation
Indices: 1913783--1913834 Score: 56
Period size: 9 Copynumber: 6.1 Consensus size: 9
1913773 TAATATTTTG
1913783 TATTTAATT
1 TATTTAATT
*
1913792 TATTTAA-G
1 TATTTAATT
1913800 TATTTAATT
1 TATTTAATT
1913809 TATTTAA--
1 TATTTAATT
* *
1913816 TATTTTACT
1 TATTTAATT
1913825 TATTTAATT
1 TATTTAATT
1913834 T
1 T
1913835 TTTTGCAGAT
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
7 6 0.17
8 7 0.20
9 22 0.63
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (9 bp):
TATTTAATT
Found at i:1913804 original size:17 final size:17
Alignment explanation
Indices: 1913782--1913831 Score: 75
Period size: 17 Copynumber: 3.0 Consensus size: 17
1913772 TTAATATTTT
1913782 GTATTTAATTTATTTAA
1 GTATTTAATTTATTTAA
1913799 GTATTTAATTTATTTAA
1 GTATTTAATTTATTTAA
* *
1913816 -TATTTTACTTATTTAA
1 GTATTTAATTTATTTAA
1913832 TTTTTTTGCA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
16 14 0.45
17 17 0.55
ACGTcount: A:0.34, C:0.02, G:0.04, T:0.60
Consensus pattern (17 bp):
GTATTTAATTTATTTAA
Found at i:1913827 original size:16 final size:16
Alignment explanation
Indices: 1913791--1913836 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
1913781 TGTATTTAAT
* *
1913791 TTATTTAAGTATTTAAT
1 TTATTTAA-TATTTTAC
1913808 TTATTTAATATTTTAC
1 TTATTTAATATTTTAC
1913824 TTATTTAAT-TTTT
1 TTATTTAATATTTT
1913837 TTGCAGATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
15 4 0.15
16 15 0.56
17 8 0.30
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.65
Consensus pattern (16 bp):
TTATTTAATATTTTAC
Found at i:1915712 original size:9 final size:9
Alignment explanation
Indices: 1915700--1915756 Score: 57
Period size: 9 Copynumber: 6.7 Consensus size: 9
1915690 TAATATTTTG
1915700 TATTTAATT
1 TATTTAATT
*
1915709 TATTTAA-G
1 TATTTAATT
1915717 TATTTAATT
1 TATTTAATT
1915726 TATTTAA--
1 TATTTAATT
*
1915733 TATTTTATT
1 TATTTAATT
*
1915742 TAATTAATT
1 TATTTAATT
*
1915751 TTTTTA
1 TATTTA
1915757 CAGATATAAA
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
7 6 0.16
8 7 0.18
9 25 0.66
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (9 bp):
TATTTAATT
Found at i:1915721 original size:17 final size:17
Alignment explanation
Indices: 1915699--1915748 Score: 75
Period size: 17 Copynumber: 3.0 Consensus size: 17
1915689 TTAATATTTT
1915699 GTATTTAATTTATTTAA
1 GTATTTAATTTATTTAA
1915716 GTATTTAATTTATTTAA
1 GTATTTAATTTATTTAA
* *
1915733 -TATTTTATTTAATTAA
1 GTATTTAATTTATTTAA
1915749 TTTTTTTACA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
16 14 0.45
17 17 0.55
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (17 bp):
GTATTTAATTTATTTAA
Found at i:1919178 original size:14 final size:14
Alignment explanation
Indices: 1919159--1919186 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1919149 CGCGCGCGCG
1919159 CGCGCACACACACA
1 CGCGCACACACACA
1919173 CGCGCACACACACA
1 CGCGCACACACACA
1919187 TATATATATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.50, G:0.14, T:0.00
Consensus pattern (14 bp):
CGCGCACACACACA
Found at i:1919191 original size:2 final size:2
Alignment explanation
Indices: 1919186--1919236 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
1919176 GCACACACAC
1919186 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1919228 AT AT AT AT A
1 AT AT AT AT A
1919237 CTTAGTCTTC
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1921757 original size:36 final size:36
Alignment explanation
Indices: 1921650--1921758 Score: 182
Period size: 36 Copynumber: 3.0 Consensus size: 36
1921640 ACATCTGTTT
*
1921650 ATCTTGAACCTCACCTATATCCTTCACTTGAAGACA
1 ATCTTGAACCTCACCTATATCCTTCACTTGAAGACG
*
1921686 ATCTTAAACCTCACCTATATCCTTCACTTGAAGACG
1 ATCTTGAACCTCACCTATATCCTTCACTTGAAGACG
* *
1921722 ATCTTGAACCTCACCCATATCCATCACTTGAAGACG
1 ATCTTGAACCTCACCTATATCCTTCACTTGAAGACG
1921758 A
1 A
1921759 CTAGTGAGGT
Statistics
Matches: 68, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 68 1.00
ACGTcount: A:0.31, C:0.31, G:0.09, T:0.28
Consensus pattern (36 bp):
ATCTTGAACCTCACCTATATCCTTCACTTGAAGACG
Found at i:1926587 original size:24 final size:24
Alignment explanation
Indices: 1926560--1926610 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
1926550 TTCATGTACT
1926560 TGAGAGTTCGAAAAACATTAACGG
1 TGAGAGTTCGAAAAACATTAACGG
1926584 TGAGAGTTCGAAAAACATTAACGG
1 TGAGAGTTCGAAAAACATTAACGG
1926608 TGA
1 TGA
1926611 CACATTGGTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.41, C:0.12, G:0.25, T:0.22
Consensus pattern (24 bp):
TGAGAGTTCGAAAAACATTAACGG
Found at i:1928160 original size:12 final size:12
Alignment explanation
Indices: 1928143--1928168 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1928133 ATAAAGTTGA
1928143 TAAGTTGAATTT
1 TAAGTTGAATTT
1928155 TAAGTTGAATTT
1 TAAGTTGAATTT
1928167 TA
1 TA
1928169 CTTGTCAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.00, G:0.15, T:0.50
Consensus pattern (12 bp):
TAAGTTGAATTT
Found at i:1928524 original size:23 final size:22
Alignment explanation
Indices: 1928480--1928524 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
1928470 AATCTCATAG
*
1928480 GGGAACCGATTCCCCCACAGGA
1 GGGAACCGATTCCCCCAAAGGA
*
1928502 GGGAATCGATTCCCCCTAAAGGA
1 GGGAACCGATTCCCCC-AAAGGA
1928525 AAAATGTGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.29, C:0.31, G:0.27, T:0.13
Consensus pattern (22 bp):
GGGAACCGATTCCCCCAAAGGA
Found at i:1929754 original size:16 final size:16
Alignment explanation
Indices: 1929735--1929765 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1929725 TGTGAATGCA
1929735 TGTTAACATAAATATG
1 TGTTAACATAAATATG
1929751 TGTTAACATAAATAT
1 TGTTAACATAAATAT
1929766 TAATGCCCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.45, C:0.06, G:0.10, T:0.39
Consensus pattern (16 bp):
TGTTAACATAAATATG
Found at i:1930013 original size:103 final size:103
Alignment explanation
Indices: 1929834--1930054 Score: 381
Period size: 103 Copynumber: 2.1 Consensus size: 103
1929824 GGGTCTACGC
* *
1929834 GGTCCTTCGGAACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
1 GGTCCTTTGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
* *
1929899 CCTTGGCATATGTATATGATTCTTAAGGAATGATATGT
66 CCCTAGCATATGTATATGATTCTTAAGGAATGATATGT
1929937 GGTCCTTTGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
1 GGTCCTTTGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
*
1930002 CCCTAGTATATGTATATGATTCTTAAGGAATGATATGT
66 CCCTAGCATATGTATATGATTCTTAAGGAATGATATGT
1930040 GGTCCTTAT-GGACAT
1 GGTCCTT-TGGGACAT
1930055 TATTATATGG
Statistics
Matches: 112, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
103 111 0.99
104 1 0.01
ACGTcount: A:0.27, C:0.14, G:0.24, T:0.36
Consensus pattern (103 bp):
GGTCCTTTGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
CCCTAGCATATGTATATGATTCTTAAGGAATGATATGT
Found at i:1930153 original size:23 final size:23
Alignment explanation
Indices: 1930062--1930153 Score: 103
Period size: 23 Copynumber: 4.0 Consensus size: 23
1930052 CATTATTATA
* **
1930062 TGGCACTACGGTGCAATTCTACA
1 TGGCACTCCGGTGCAATTCTATG
* * *
1930085 CGGCACTCCAGTGCAATTCTACG
1 TGGCACTCCGGTGCAATTCTATG
*
1930108 TAGCACTCCGGTGCAATTCTATG
1 TGGCACTCCGGTGCAATTCTATG
* *
1930131 TGGCACTTCGGTGCAATTATATG
1 TGGCACTCCGGTGCAATTCTATG
1930154 AGCTGTGGTG
Statistics
Matches: 58, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 58 1.00
ACGTcount: A:0.23, C:0.26, G:0.23, T:0.28
Consensus pattern (23 bp):
TGGCACTCCGGTGCAATTCTATG
Found at i:1942337 original size:16 final size:16
Alignment explanation
Indices: 1942316--1942349 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1942306 TCAAAGCAAA
1942316 AAAAAAAAAAAAGAAG
1 AAAAAAAAAAAAGAAG
* *
1942332 AAAAAAGAAGAAGAAG
1 AAAAAAAAAAAAGAAG
1942348 AA
1 AA
1942350 GAAGAAGCTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (16 bp):
AAAAAAAAAAAAGAAG
Found at i:1942337 original size:19 final size:19
Alignment explanation
Indices: 1942313--1942352 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
1942303 CGTTCAAAGC
1942313 AAAAAAAAAAAAAAAGAAG
1 AAAAAAAAAAAAAAAGAAG
* * *
1942332 AAAAAAGAAGAAGAAGAAG
1 AAAAAAAAAAAAAAAGAAG
1942351 AA
1 AA
1942353 GAAGCTGTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.82, C:0.00, G:0.17, T:0.00
Consensus pattern (19 bp):
AAAAAAAAAAAAAAAGAAG
Found at i:1946186 original size:2 final size:2
Alignment explanation
Indices: 1946179--1946212 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1946169 AGATAAGAAC
1946179 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1946213 TAATTTTTTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1947422 original size:31 final size:30
Alignment explanation
Indices: 1947384--1947461 Score: 120
Period size: 31 Copynumber: 2.5 Consensus size: 30
1947374 CTTTTAAAAC
*
1947384 TTGCAATATAATCCCTCAATATTTAGTCCGT
1 TTGCAATATGATCCC-CAATATTTAGTCCGT
*
1947415 TTGCAATATGGTCTCCCAATATTTAGTCCGT
1 TTGCAATATGATC-CCCAATATTTAGTCCGT
1947446 TTGCAATATGATCCCC
1 TTGCAATATGATCCCC
1947462 GACGTAACTG
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
30 3 0.07
31 38 0.88
32 2 0.05
ACGTcount: A:0.26, C:0.24, G:0.13, T:0.37
Consensus pattern (30 bp):
TTGCAATATGATCCCCAATATTTAGTCCGT
Found at i:1952005 original size:23 final size:23
Alignment explanation
Indices: 1951979--1952023 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1951969 CACCACAGCT
*
1951979 CGTATAAATGCACCGAAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCG
* *
1952002 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
1952024 ATGTAATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCG
Found at i:1952191 original size:152 final size:149
Alignment explanation
Indices: 1951991--1952308 Score: 530
Period size: 152 Copynumber: 2.1 Consensus size: 149
1951981 TATAAATGCA
* *
1951991 CCGAAGTG-CCGCGTAGAATTGCACCGTAGTGCCATGTAATGATGTCCATAAGGACCACATATAA
1 CCGAAG-GACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAA
*
1952055 TTCCTTAAGAATCATATACATATACTAAGGATCAAGTATGTGTCTTTCCAAGACTTCACACATGT
65 TTCCTTAAGAATCATATACATATACTAAGGATCAAGCATGTGTCTTT-CAAGACTTCACACATGT
* * *
1952120 TTCACAGAATATATATATATATC
129 TCCAAAG-A-ATATACATATATC
1952143 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAAT
1 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAAT
1952208 TCCTTAAGAATCATATACATATACTAAGGATCAAGCATGTGTCTTTCAAGACTTCACACATGTTC
66 TCCTTAAGAATCATATACATATACTAAGGATCAAGCATGTGTCTTTCAAGACTTCACACATGTTC
*
1952273 CAAAGAATATACATATGTC
131 CAAAGAATATACATATATC
1952292 CCGAAGGACCGCGTAGA
1 CCGAAGGACCGCGTAGA
1952309 CCCTCTACCC
Statistics
Matches: 158, Mismatches: 7, Indels: 5
0.93 0.04 0.03
Matches are distributed among these distances:
149 28 0.18
150 1 0.01
151 23 0.15
152 106 0.67
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.27
Consensus pattern (149 bp):
CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAAT
TCCTTAAGAATCATATACATATACTAAGGATCAAGCATGTGTCTTTCAAGACTTCACACATGTTC
CAAAGAATATACATATATC
Found at i:1957247 original size:21 final size:21
Alignment explanation
Indices: 1957217--1957268 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
1957207 CGCATCGAAA
*
1957217 ACAAGTCCCAGCAGCCATACG
1 ACAAGCCCCAGCAGCCATACG
1957238 ACAAGCCCCAGCAGCCATACG
1 ACAAGCCCCAGCAGCCATACG
1957259 ACAAGCCCCA
1 ACAAGCCCCA
1957269 TAATGGTTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.35, C:0.42, G:0.17, T:0.06
Consensus pattern (21 bp):
ACAAGCCCCAGCAGCCATACG
Found at i:1958987 original size:23 final size:23
Alignment explanation
Indices: 1958961--1959005 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1958951 CACCACATCT
*
1958961 CGTATAAATGCACCGAAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCG
* *
1958984 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
1959006 ATGTAATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCG
Found at i:1963047 original size:69 final size:69
Alignment explanation
Indices: 1962936--1963073 Score: 276
Period size: 69 Copynumber: 2.0 Consensus size: 69
1962926 CATGAAACAG
1962936 ACCTGTATTACAAAATCAGTGGCAGACTGCCCAGGTCCATGAAGTTTAGGTCGAATCCCCGAGTA
1 ACCTGTATTACAAAATCAGTGGCAGACTGCCCAGGTCCATGAAGTTTAGGTCGAATCCCCGAGTA
1963001 ACCT
66 ACCT
1963005 ACCTGTATTACAAAATCAGTGGCAGACTGCCCAGGTCCATGAAGTTTAGGTCGAATCCCCGAGTA
1 ACCTGTATTACAAAATCAGTGGCAGACTGCCCAGGTCCATGAAGTTTAGGTCGAATCCCCGAGTA
1963070 ACCT
66 ACCT
1963074 GTCAGTAGAG
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
69 69 1.00
ACGTcount: A:0.29, C:0.26, G:0.22, T:0.23
Consensus pattern (69 bp):
ACCTGTATTACAAAATCAGTGGCAGACTGCCCAGGTCCATGAAGTTTAGGTCGAATCCCCGAGTA
ACCT
Found at i:1963590 original size:37 final size:37
Alignment explanation
Indices: 1963540--1963618 Score: 149
Period size: 37 Copynumber: 2.1 Consensus size: 37
1963530 GCAAGTAAAT
1963540 CAATAAAATCCATGTGATAACCTCTCATGCCAACACC
1 CAATAAAATCCATGTGATAACCTCTCATGCCAACACC
*
1963577 CAATAAAATCCATGTGATACCCTCTCATGCCAACACC
1 CAATAAAATCCATGTGATAACCTCTCATGCCAACACC
1963614 CAATA
1 CAATA
1963619 TAGGTGTTCT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 41 1.00
ACGTcount: A:0.38, C:0.33, G:0.08, T:0.22
Consensus pattern (37 bp):
CAATAAAATCCATGTGATAACCTCTCATGCCAACACC
Found at i:1968577 original size:3 final size:3
Alignment explanation
Indices: 1968569--1968593 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1968559 AGTTACTTTG
1968569 ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
1968594 AGGTAAAGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:1968800 original size:12 final size:12
Alignment explanation
Indices: 1968783--1968807 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1968773 TTCTTCTTCT
1968783 TCTCTCTTCACA
1 TCTCTCTTCACA
1968795 TCTCTCTTCACA
1 TCTCTCTTCACA
1968807 T
1 T
1968808 TCTTTGATTT
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:0.16, C:0.40, G:0.00, T:0.44
Consensus pattern (12 bp):
TCTCTCTTCACA
Found at i:1973104 original size:23 final size:23
Alignment explanation
Indices: 1973078--1973125 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
1973068 ATAAAGTACA
*
1973078 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
**
1973101 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
1973124 AT
1 AT
1973126 TTACCTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:1973532 original size:21 final size:22
Alignment explanation
Indices: 1973507--1973558 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 22
1973497 ACACTTTACA
*
1973507 ATATAACCACTACCTATTACATT
1 ATATAAACA-TACCTATTACATT
1973530 ATATAAACGATACCTATTACATT
1 ATATAAAC-ATACCTATTACATT
1973553 ATATAA
1 ATATAA
1973559 GGGCTACCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 26 0.96
24 1 0.04
ACGTcount: A:0.44, C:0.19, G:0.02, T:0.35
Consensus pattern (22 bp):
ATATAAACATACCTATTACATT
Found at i:1973543 original size:23 final size:23
Alignment explanation
Indices: 1973517--1973579 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
1973507 ATATAACCAC
1973517 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
1973540 TACCTATTACATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
1973563 TACCTATTACATCATAT
1 TACCTATTACATTATAT
1973580 GTTTACCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:1974037 original size:39 final size:39
Alignment explanation
Indices: 1973983--1974069 Score: 156
Period size: 39 Copynumber: 2.2 Consensus size: 39
1973973 TCAAGTTGTA
*
1973983 GATTTTGATTTCCTTTTGCTTGGCATCATATGAGATTTG
1 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
*
1974022 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGCTTTG
1 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
1974061 GATTTTGAT
1 GATTTTGAT
1974070 GAGCATCGGA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.17, C:0.14, G:0.21, T:0.48
Consensus pattern (39 bp):
GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
Found at i:1974351 original size:18 final size:18
Alignment explanation
Indices: 1974328--1974364 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1974318 CGAAATATAT
1974328 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
1974346 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
1974364 A
1 A
1974365 CTCCAATTAC
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:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:1974693 original size:25 final size:25
Alignment explanation
Indices: 1974659--1974709 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
1974649 TTTTTCCAAA
*
1974659 TAATGTACCCATAACAATGTTCAAT
1 TAATGTACCCACAACAATGTTCAAT
*
1974684 TAATGTACCCACAACAATGTTTAAT
1 TAATGTACCCACAACAATGTTCAAT
1974709 T
1 T
1974710 GATTTGTTGT
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:0.39, C:0.20, G:0.08, T:0.33
Consensus pattern (25 bp):
TAATGTACCCACAACAATGTTCAAT
Found at i:1975003 original size:21 final size:22
Alignment explanation
Indices: 1974978--1975029 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 22
1974968 ACACTTTACA
*
1974978 ATATAACCACTACCTATTACATT
1 ATATAAACA-TACCTATTACATT
1975001 ATATAAACGATACCTATTACATT
1 ATATAAAC-ATACCTATTACATT
1975024 ATATAA
1 ATATAA
1975030 GGGCTACCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 26 0.96
24 1 0.04
ACGTcount: A:0.44, C:0.19, G:0.02, T:0.35
Consensus pattern (22 bp):
ATATAAACATACCTATTACATT
Found at i:1975014 original size:23 final size:23
Alignment explanation
Indices: 1974988--1975050 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
1974978 ATATAACCAC
1974988 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
1975011 TACCTATTACATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
1975034 TACCTATTACATCATAT
1 TACCTATTACATTATAT
1975051 GTTTACCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:1975394 original size:25 final size:25
Alignment explanation
Indices: 1975337--1975402 Score: 87
Period size: 25 Copynumber: 2.6 Consensus size: 25
1975327 CACTCAAAAG
*
1975337 ATGTATATACCTAAATATGTAGTTA
1 ATGTACATACCTAAATATGTAGTTA
***
1975362 ACAAACATACCTAAATATGTAGTTA
1 ATGTACATACCTAAATATGTAGTTA
*
1975387 TTGTACATACCTAAAT
1 ATGTACATACCTAAAT
1975403 TTAATGATAA
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.42, C:0.14, G:0.09, T:0.35
Consensus pattern (25 bp):
ATGTACATACCTAAATATGTAGTTA
Found at i:1977256 original size:184 final size:184
Alignment explanation
Indices: 1976947--1977290 Score: 589
Period size: 184 Copynumber: 1.9 Consensus size: 184
1976937 TTCAAATTAC
* *
1976947 CGACACTTTTTTAAATGGTATCGACACATTTTTATTCCAATCTGGACATAAAGTACCGACACAAT
1 CGACACTTTTTTAAATCGTATCGACACATTTTTATTCCAATATGGACATAAAGTACCGACACAAT
* *
1977012 ATTATAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTATACCGGTT
66 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
*
1977077 ATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAAATGT
131 ATATTACAAAATTACCTATTACATTATAATTATGGGTTCCGATGTGTAAAATGT
*
1977131 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
1 CGACACTTTTTTAAATCGTATCGACACATTTTTATTCCAATATGGACATAAAGTACCGACACAAT
*
1977196 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAGACCGGTATATTTATACCGGTT
66 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
* * **
1977261 ATATTGCAAATTTACCTATTTTATTATAAT
131 ATATTACAAAATTACCTATTACATTATAAT
1977291 ATGTTGAAAG
Statistics
Matches: 149, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
184 149 1.00
ACGTcount: A:0.33, C:0.17, G:0.14, T:0.36
Consensus pattern (184 bp):
CGACACTTTTTTAAATCGTATCGACACATTTTTATTCCAATATGGACATAAAGTACCGACACAAT
ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
ATATTACAAAATTACCTATTACATTATAATTATGGGTTCCGATGTGTAAAATGT
Found at i:1978764 original size:3 final size:3
Alignment explanation
Indices: 1978756--1978833 Score: 66
Period size: 3 Copynumber: 26.0 Consensus size: 3
1978746 ACTTGTTTGG
* * * ** * *
1978756 ATC ATC ATC TTC ATC ATC ATC GTC ATC ATC TTC ATC GCC AGC TTC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
* * *
1978804 GTC ATC ATC ATC ATC ATC GTC ATC TTC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
1978834 GTCAGCTTCA
Statistics
Matches: 56, Mismatches: 19, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.23, C:0.35, G:0.06, T:0.36
Consensus pattern (3 bp):
ATC
Found at i:1978816 original size:42 final size:42
Alignment explanation
Indices: 1978757--1978845 Score: 133
Period size: 42 Copynumber: 2.1 Consensus size: 42
1978747 CTTGTTTGGA
* *
1978757 TCATCATCTTCATCATCATCGTCATCATCTTCATCGCCAGCT
1 TCATCATCATCATCATCATCATCATCATCTTCATCGCCAGCT
* * *
1978799 TCATCGTCATCATCATCATCATCGTCATCTTCATCGTCAGCT
1 TCATCATCATCATCATCATCATCATCATCTTCATCGCCAGCT
1978841 TCATC
1 TCATC
1978846 TTCTGCGACC
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.21, C:0.35, G:0.08, T:0.36
Consensus pattern (42 bp):
TCATCATCATCATCATCATCATCATCATCTTCATCGCCAGCT
Found at i:1978832 original size:18 final size:18
Alignment explanation
Indices: 1978756--1978833 Score: 75
Period size: 18 Copynumber: 4.3 Consensus size: 18
1978746 ACTTGTTTGG
* *
1978756 ATCATCATCTTCATCATC
1 ATCATCATCATCGTCATC
* *
1978774 ATCGTCATCATCTTCATC
1 ATCATCATCATCGTCATC
** * *
1978792 GCCAGCTTCATCGTCATC
1 ATCATCATCATCGTCATC
1978810 ATCATCATCATCGTCATC
1 ATCATCATCATCGTCATC
*
1978828 TTCATC
1 ATCATC
1978834 GTCAGCTTCA
Statistics
Matches: 46, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 46 1.00
ACGTcount: A:0.23, C:0.35, G:0.06, T:0.36
Consensus pattern (18 bp):
ATCATCATCATCGTCATC
Found at i:1978844 original size:18 final size:18
Alignment explanation
Indices: 1978764--1978848 Score: 59
Period size: 21 Copynumber: 4.6 Consensus size: 18
1978754 GGATCATCAT
*
1978764 CTTCATCATCATCGTCA-
1 CTTCATCTTCATCGTCAG
*
1978781 --TCATCTTCATCGCCAG
1 CTTCATCTTCATCGTCAG
* *
1978797 CTTCATCGTCATCATCATCAT
1 CTTCATC-T--TCATCGTCAG
1978818 CATCGTCATCTTCATCGTCAG
1 C-T--TCATCTTCATCGTCAG
1978839 CTTCATCTTC
1 CTTCATCTTC
1978849 TGCGACCGCT
Statistics
Matches: 52, Mismatches: 7, Indels: 17
0.68 0.09 0.22
Matches are distributed among these distances:
15 13 0.25
18 13 0.25
19 1 0.02
20 1 0.02
21 17 0.33
22 1 0.02
23 1 0.02
24 5 0.10
ACGTcount: A:0.20, C:0.35, G:0.08, T:0.36
Consensus pattern (18 bp):
CTTCATCTTCATCGTCAG
Found at i:1978848 original size:6 final size:6
Alignment explanation
Indices: 1978760--1978848 Score: 61
Period size: 6 Copynumber: 14.3 Consensus size: 6
1978750 GTTTGGATCA
* * * * * *
1978760 TCATCT TCATCA TCATCGT CATCATCT TCATCG CCAGCT TCATCG TCATCA
1 TCATCT TCATCT TCATC-T --TCATCT TCATCT TCATCT TCATCT TCATCT
* * * *
1978811 TCATCA TCATCG TCATCT TCATCG TCAGCT TCATCT TC
1 TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TC
1978849 TGCGACCGCT
Statistics
Matches: 64, Mismatches: 16, Indels: 6
0.74 0.19 0.07
Matches are distributed among these distances:
6 58 0.91
8 1 0.02
9 5 0.08
ACGTcount: A:0.20, C:0.35, G:0.08, T:0.37
Consensus pattern (6 bp):
TCATCT
Found at i:1980168 original size:199 final size:199
Alignment explanation
Indices: 1979497--1980407 Score: 1749
Period size: 198 Copynumber: 4.6 Consensus size: 199
1979487 CCCACTAGGT
1979497 CGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATT
1 CGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATT
1979562 TTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTC
66 TTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTC
1979627 TGG-AAAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATA
131 TGGAAAAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATA
1979691 AAAC
196 AAAC
1979695 CGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATT
1 CGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATT
1979760 TTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTC
66 TTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTC
1979825 TGGAAAAAAAATATCGACACAAACTA-ATTAGTGTCGACACATTATTTAGACATATTCTCTCATA
131 TGGAAAAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATA
1979889 AAAC
196 AAAC
1979893 CGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATT
1 CGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATT
1979958 TTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTC
66 TTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTC
1980023 TGGAAAAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATA
131 TGGAAAAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATA
1980088 AAAC
196 AAAC
*
1980092 CGGTATAATTGTACCGGTTAGATTGAAAAATTACTTATTACATTATACTTTTGGGTTCGATGATT
1 CGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATT
1980157 TTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTC
66 TTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTC
1980222 TGGAAAAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATA
131 TGGAAAAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATA
1980287 AAAC
196 AAAC
*
1980291 CGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATG-T
1 CGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGG-GTTCGATGAT
* *
1980355 TTTGGGATTGACACTTTTT-TATATGGATCGACACTTTATGGGTGCACCCTGTT
65 TTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTT
1980408 GGCCATATTG
Statistics
Matches: 705, Mismatches: 5, Indels: 6
0.98 0.01 0.01
Matches are distributed among these distances:
198 364 0.52
199 334 0.47
200 7 0.01
ACGTcount: A:0.31, C:0.15, G:0.16, T:0.38
Consensus pattern (199 bp):
CGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATT
TTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTC
TGGAAAAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATA
AAAC
Found at i:1980229 original size:397 final size:397
Alignment explanation
Indices: 1979497--1980407 Score: 1747
Period size: 397 Copynumber: 2.3 Consensus size: 397
1979487 CCCACTAGGT
1979497 CGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATT
1 CGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATT
1979562 TTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTC
66 TTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTC
1979627 TGGAAAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAA
131 TGGAAAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAA
1979692 AACCGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATG
196 AACCGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATG
1979757 ATTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCA
261 ATTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCA
1979822 TTCTGGAAAAAAAATATCGACACAAACTA-ATTAGTGTCGACACATTATTTAGACATATTCTCTC
326 TTCTGGAAAAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTC
1979886 ATAAAAC
391 ATAAAAC
1979893 CGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATT
1 CGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATT
1979958 TTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTC
66 TTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTC
1980023 TGGAAAAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATA
131 TGG-AAAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATA
*
1980088 AAACCGGTATAATTGTACCGGTTAGATTGAAAAATTACTTATTACATTATACTTTTGGGTTCGAT
195 AAACCGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGAT
1980153 GATTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTC
260 GATTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTC
1980218 ATTCTGGAAAAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCT
325 ATTCTGGAAAAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCT
1980283 CATAAAAC
390 CATAAAAC
*
1980291 CGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATG-T
1 CGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGG-GTTCGATGAT
* *
1980355 TTTGGGATTGACACTTTTT-TATATGGATCGACACTTTATGGGTGCACCCTGTT
65 TTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTT
1980408 GGCCATATTG
Statistics
Matches: 508, Mismatches: 4, Indels: 5
0.98 0.01 0.01
Matches are distributed among these distances:
396 133 0.26
397 253 0.50
398 115 0.23
399 7 0.01
ACGTcount: A:0.31, C:0.15, G:0.16, T:0.38
Consensus pattern (397 bp):
CGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATT
TTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTC
TGGAAAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAA
AACCGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATG
ATTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCA
TTCTGGAAAAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTC
ATAAAAC
Found at i:1980572 original size:19 final size:19
Alignment explanation
Indices: 1980526--1980574 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
1980516 TTATATTCAC
*
1980526 ATACAAAAATATAAATCGT
1 ATACAAAATTATAAATCGT
*
1980545 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
1980564 ATACAAAATTA
1 ATACAAAATTA
1980575 ACTCGACATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.57, C:0.10, G:0.02, T:0.31
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:1982403 original size:33 final size:33
Alignment explanation
Indices: 1982366--1982431 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
1982356 CATCTTAATA
*
1982366 TCACCCCTTAACACCCCAACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
* *
1982399 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
1982432 CCATCTATTT
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:0.23, C:0.48, G:0.00, T:0.29
Consensus pattern (33 bp):
TCACCCCTCAACACCCCAACTTCTTTCACCACT
Found at i:1982505 original size:21 final size:21
Alignment explanation
Indices: 1982465--1982529 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
1982455 CCCCTTATGC
* *
1982465 CTCTCGAGTGTATCTTCGACT
1 CTCTCGAGTTTCTCTTCGACT
*
1982486 CTCTCGAGTTTCTCTACGACT
1 CTCTCGAGTTTCTCTTCGACT
* *
1982507 -TGATCAAGTTTCTCTTCGACT
1 CT-CTCGAGTTTCTCTTCGACT
1982528 CT
1 CT
1982530 TGATTGTCTT
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:0.15, C:0.29, G:0.15, T:0.40
Consensus pattern (21 bp):
CTCTCGAGTTTCTCTTCGACT
Found at i:1984779 original size:17 final size:18
Alignment explanation
Indices: 1984757--1984799 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 18
1984747 ATATATCCGG
1984757 TATCATT-TTACCGGTTT
1 TATCATTGTTACCGGTTT
1984774 TATCATTTTGTTACCGGTTT
1 TATCA--TTGTTACCGGTTT
1984794 TATCAT
1 TATCAT
1984800 ATTTTTACCT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
17 5 0.22
18 1 0.04
19 2 0.09
20 15 0.65
ACGTcount: A:0.19, C:0.16, G:0.12, T:0.53
Consensus pattern (18 bp):
TATCATTGTTACCGGTTT
Found at i:1984789 original size:20 final size:20
Alignment explanation
Indices: 1984762--1984808 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
1984752 TCCGGTATCA
1984762 TTTTACCGGTTTTATCAT-T
1 TTTTACCGGTTTTATCATAT
1984781 TTGTTACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCATAT
1984802 TTTTACC
1 TTTTACC
1984809 TGTTATATCG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.08
20 21 0.81
21 3 0.12
ACGTcount: A:0.17, C:0.17, G:0.11, T:0.55
Consensus pattern (20 bp):
TTTTACCGGTTTTATCATAT
Found at i:1984955 original size:20 final size:20
Alignment explanation
Indices: 1984929--1984974 Score: 76
Period size: 20 Copynumber: 2.3 Consensus size: 20
1984919 CACTTTTAAA
1984929 TTTACCGGTTTTATCAT-TT
1 TTTACCGGTTTTATCATATT
1984948 TGTTACCGGTTTTATCATATT
1 T-TTACCGGTTTTATCATATT
1984969 TTTACC
1 TTTACC
1984975 TGGTATATCG
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:0.17, C:0.17, G:0.11, T:0.54
Consensus pattern (20 bp):
TTTACCGGTTTTATCATATT
Found at i:1985455 original size:228 final size:226
Alignment explanation
Indices: 1985039--1985486 Score: 765
Period size: 228 Copynumber: 2.0 Consensus size: 226
1985029 TTAAAACTGC
*
1985039 TTTTAAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTTCATGTTTTCTACCTACAATA
1 TTTTAAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTTCATGTTTTCCACCTACAATA
**
1985104 TTAATTTAATAATTTAATTTACACAAAATTTTATTTGATTGTTTGATATTTTATAAAATATTATT
66 TTAATTTAATAATTTAATTTACACAAAAAATTATTTGATTGTTTGATATTTTATAAAATATTATT
* *
1985169 TAGAATTTAAATTTAACAATATTAACCAAATAATTTAATAAATATGTTTTCAACAGTGAAATAAG
131 TAGAATTTAAATTTAACAATATTAACAAAATAA-TTAATAAATATATTTTCAACAGTGAAATAAG
*
1985234 TATGGACACTTTTATAAAAATGATATATACTT
195 TATGGACACTTTTATAAAAAGGATATATACTT
*
1985266 TTTTGAAAGTTATGTAATTTATGTTTCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAAT
1 TTTT-AAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTTCATGTTTTCCACCTACAAT
1985331 ATTAATTTAATAATTTAATTTACACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTA
65 ATTAATTTAATAATTTAATTTACACAAAAAATTATTTGATTG-TTTGATATTTTATAAAATATTA
*
1985396 TTTAGATTTTAAATTTAACAATATTAACTAAAGATAA-TAATAAATATATTTTC-ACAGTGAAAT
129 TTTAGAATTTAAATTTAACAATATTAAC-AAA-ATAATTAATAAATATATTTTCAACAGTGAAAT
1985459 AAGTATGGACACTTTTATAAAAAGGATA
192 AAGTATGGACACTTTTATAAAAAGGATA
1985487 GATAATTTAC
Statistics
Matches: 209, Mismatches: 8, Indels: 7
0.93 0.04 0.03
Matches are distributed among these distances:
227 4 0.02
228 135 0.65
229 64 0.31
230 2 0.01
231 4 0.02
ACGTcount: A:0.40, C:0.07, G:0.08, T:0.46
Consensus pattern (226 bp):
TTTTAAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTTCATGTTTTCCACCTACAATA
TTAATTTAATAATTTAATTTACACAAAAAATTATTTGATTGTTTGATATTTTATAAAATATTATT
TAGAATTTAAATTTAACAATATTAACAAAATAATTAATAAATATATTTTCAACAGTGAAATAAGT
ATGGACACTTTTATAAAAAGGATATATACTT
Found at i:1987056 original size:184 final size:184
Alignment explanation
Indices: 1986740--1987110 Score: 697
Period size: 184 Copynumber: 2.0 Consensus size: 184
1986730 ATCAAATTAT
1986740 TTTAAAAGCTTCGATGTTTGAATAATTTTATATTTATGTTGCACATATTGAGAAATTTTAATATA
1 TTTAAAAGCTTCGATGTTTGAATAATTTTATATTTATGTTGCACATATTGAGAAATTTTAATATA
* *
1986805 AATTTGGACGTTACAGAATGATACTTTAGAAATACAATATTTTATTTAGTTTTTATATTTCCTCT
66 AATTTGGACGTTACAGAATGATACTTTAGAAATACAATATTTTATTTAATTTTTATATTTACTCT
* * *
1986870 TCAAAATATAAAATCTATTAGTTAGTTTGAAATAATGATTTATCTATATGAATA
131 TCAAAATATAAAATATATTAGTTAGTTTAAAATAATGATTTATATATATGAATA
1986924 TTTAAAAGCTTCGATGTTTGAATAATTTTATATTTATGTTGCACATATTGAGAAATTTTAATATA
1 TTTAAAAGCTTCGATGTTTGAATAATTTTATATTTATGTTGCACATATTGAGAAATTTTAATATA
1986989 AATTTGGACGTTACAGAATGATACTTTAGAAATACAATATTTTATTTAATTTTTATATTTACTCT
66 AATTTGGACGTTACAGAATGATACTTTAGAAATACAATATTTTATTTAATTTTTATATTTACTCT
1987054 TCAAAATATAAAATATATTAGTTAGTTTAAAATAATGATTTATATATATGAATA
131 TCAAAATATAAAATATATTAGTTAGTTTAAAATAATGATTTATATATATGAATA
1987108 TTT
1 TTT
1987111 TAAATATTTA
Statistics
Matches: 182, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
184 182 1.00
ACGTcount: A:0.38, C:0.07, G:0.10, T:0.45
Consensus pattern (184 bp):
TTTAAAAGCTTCGATGTTTGAATAATTTTATATTTATGTTGCACATATTGAGAAATTTTAATATA
AATTTGGACGTTACAGAATGATACTTTAGAAATACAATATTTTATTTAATTTTTATATTTACTCT
TCAAAATATAAAATATATTAGTTAGTTTAAAATAATGATTTATATATATGAATA
Found at i:1994496 original size:16 final size:16
Alignment explanation
Indices: 1994475--1994511 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
1994465 AATTATTTTT
1994475 TATTTTGAATAATTTA
1 TATTTTGAATAATTTA
1994491 TATTTTGAATAATTTA
1 TATTTTGAATAATTTA
1994507 TATTT
1 TATTT
1994512 GAGGGAGAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.59
Consensus pattern (16 bp):
TATTTTGAATAATTTA
Found at i:1994878 original size:19 final size:19
Alignment explanation
Indices: 1994847--1994894 Score: 87
Period size: 19 Copynumber: 2.5 Consensus size: 19
1994837 TTTAGTCGAG
1994847 CTTTCTCCTCCTCTTCGTCT
1 CTTTCT-CTCCTCTTCGTCT
1994867 CTTTCTCTCCTCTTCGTCT
1 CTTTCTCTCCTCTTCGTCT
1994886 CTTTCTCTC
1 CTTTCTCTC
1994895 TTGGTTTCAG
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
19 22 0.79
20 6 0.21
ACGTcount: A:0.00, C:0.44, G:0.04, T:0.52
Consensus pattern (19 bp):
CTTTCTCTCCTCTTCGTCT
Found at i:1995670 original size:41 final size:40
Alignment explanation
Indices: 1995619--1995741 Score: 113
Period size: 41 Copynumber: 3.2 Consensus size: 40
1995609 AAAAATTTTG
1995619 TTGCTCGACTCGATTTGTTGCTCGTTAAGCTCATTAAAATT
1 TTGCTCGACTCGA-TTGTTGCTCGTTAAGCTCATTAAAATT
* *
1995660 TTGCTTGACTC----G-TGCTCGTTAA----A-AAAAATT
1 TTGCTCGACTCGATTGTTGCTCGTTAAGCTCATTAAAATT
* *
1995690 GTTGTTCGACTCGATGTGTTACTCGTTAAGCTCATTAAAATT
1 -TTGCTCGACTCGAT-TGTTGCTCGTTAAGCTCATTAAAATT
1995732 TTGCTCGACT
1 TTGCTCGACT
1995742 TGTGCTCGTT
Statistics
Matches: 63, Mismatches: 7, Indels: 24
0.67 0.07 0.26
Matches are distributed among these distances:
30 6 0.10
31 10 0.16
35 10 0.16
36 2 0.03
37 9 0.14
41 20 0.32
42 6 0.10
ACGTcount: A:0.24, C:0.19, G:0.18, T:0.40
Consensus pattern (40 bp):
TTGCTCGACTCGATTGTTGCTCGTTAAGCTCATTAAAATT
Found at i:1995674 original size:72 final size:72
Alignment explanation
Indices: 1995589--1995774 Score: 291
Period size: 72 Copynumber: 2.6 Consensus size: 72
1995579 AGTTGGGTGG
** * *
1995589 TGCTTGACTCGTGCTCGTTAAAAAATTTTGTTGCTCGACTCGATTTGTTGCTCGTTAAGCTCATT
1 TGCTTGACTCGTGCTCGTTAAAAAAAATTGTTGCTCGACTCGATGTGTTACTCGTTAAGCTCATT
1995654 AAAATTT
66 AAAATTT
*
1995661 TGCTTGACTCGTGCTCGTTAAAAAAAATTGTTGTTCGACTCGATGTGTTACTCGTTAAGCTCATT
1 TGCTTGACTCGTGCTCGTTAAAAAAAATTGTTGCTCGACTCGATGTGTTACTCGTTAAGCTCATT
1995726 AAAATTT
66 AAAATTT
* * * *
1995733 TGCTCGACTTGTGCTCGTTAAAAAAACTTGTTGCTTGACTCG
1 TGCTTGACTCGTGCTCGTTAAAAAAAATTGTTGCTCGACTCG
1995775 TCGCTCATTA
Statistics
Matches: 104, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
72 104 1.00
ACGTcount: A:0.24, C:0.18, G:0.19, T:0.39
Consensus pattern (72 bp):
TGCTTGACTCGTGCTCGTTAAAAAAAATTGTTGCTCGACTCGATGTGTTACTCGTTAAGCTCATT
AAAATTT
Found at i:1995681 original size:35 final size:35
Alignment explanation
Indices: 1995637--1995753 Score: 93
Period size: 35 Copynumber: 3.3 Consensus size: 35
1995627 CTCGATTTGT
1995637 TGCTCGTTAAGCTCATTAAAATTTTGCTTGACTCG
1 TGCTCGTTAAGCTCATTAAAATTTTGCTTGACTCG
*
1995672 TGCTCGTTAA----A-AAAAATTGTTG-TTCGACTCGATG
1 TGCTCGTTAAGCTCATTAAAATT-TTGCTT-GACTC---G
* *
1995706 TGTTACTCGTTAAGCTCATTAAAATTTTGCTCGACTTG
1 TG---CTCGTTAAGCTCATTAAAATTTTGCTTGACTCG
1995744 TGCTCGTTAA
1 TGCTCGTTAA
1995754 AAAAACTTGT
Statistics
Matches: 64, Mismatches: 4, Indels: 28
0.67 0.04 0.29
Matches are distributed among these distances:
30 8 0.12
31 9 0.14
34 3 0.05
35 18 0.28
37 8 0.12
38 3 0.05
41 8 0.12
42 7 0.11
ACGTcount: A:0.25, C:0.18, G:0.18, T:0.39
Consensus pattern (35 bp):
TGCTCGTTAAGCTCATTAAAATTTTGCTTGACTCG
Found at i:2006976 original size:23 final size:21
Alignment explanation
Indices: 2006927--2006989 Score: 81
Period size: 21 Copynumber: 2.9 Consensus size: 21
2006917 TTTTGGTGCA
* *
2006927 GAGGGAATCGATCCCCCCCTT
1 GAGGGAACCGATTCCCCCCTT
*
2006948 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATTCCCCCCTT
2006969 GAAGGGGAACCGATTCCCCCC
1 G-A-GGGAACCGATTCCCCCC
2006990 ACAGGGGGAA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
21 19 0.53
22 1 0.03
23 16 0.44
ACGTcount: A:0.21, C:0.37, G:0.25, T:0.17
Consensus pattern (21 bp):
GAGGGAACCGATTCCCCCCTT
Found at i:2014097 original size:22 final size:21
Alignment explanation
Indices: 2014070--2014152 Score: 67
Period size: 23 Copynumber: 3.8 Consensus size: 21
2014060 TATAGGGCAG
*
2014070 AGGGAATCGATACCCCCTTGA
1 AGGGAACCGATACCCCCTTGA
*
2014091 AGGGGAACCGATTCCCCCTTTGA
1 A-GGGAACCGATACCCCC-TTGA
* * * **
2014114 ATGGGAACCAATTCCCTCTTTT
1 A-GGGAACCGATACCCCCTTGA
*
2014136 AGGGAATCGATACCCCC
1 AGGGAACCGATACCCCC
2014153 ATGAGTTCTG
Statistics
Matches: 49, Mismatches: 11, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
21 13 0.27
22 17 0.35
23 19 0.39
ACGTcount: A:0.25, C:0.30, G:0.22, T:0.23
Consensus pattern (21 bp):
AGGGAACCGATACCCCCTTGA
Found at i:2014113 original size:23 final size:23
Alignment explanation
Indices: 2014071--2014134 Score: 76
Period size: 23 Copynumber: 2.8 Consensus size: 23
2014061 ATAGGGCAGA
* *
2014071 GGGAATCGATACCCCC-TTGAAG
1 GGGAACCGATTCCCCCTTTGAAG
*
2014093 GGGAACCGATTCCCCCTTTGAAT
1 GGGAACCGATTCCCCCTTTGAAG
* *
2014116 GGGAACCAATTCCCTCTTT
1 GGGAACCGATTCCCCCTTT
2014135 TAGGGAATCG
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
22 14 0.39
23 22 0.61
ACGTcount: A:0.23, C:0.30, G:0.22, T:0.25
Consensus pattern (23 bp):
GGGAACCGATTCCCCCTTTGAAG
Found at i:2016427 original size:19 final size:19
Alignment explanation
Indices: 2016403--2016451 Score: 98
Period size: 19 Copynumber: 2.6 Consensus size: 19
2016393 CGGAGGGAAC
2016403 CGATTCCCCCCAGGGGTAT
1 CGATTCCCCCCAGGGGTAT
2016422 CGATTCCCCCCAGGGGTAT
1 CGATTCCCCCCAGGGGTAT
2016441 CGATTCCCCCC
1 CGATTCCCCCC
2016452 TGTTTAATGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.14, C:0.43, G:0.22, T:0.20
Consensus pattern (19 bp):
CGATTCCCCCCAGGGGTAT
Found at i:2023878 original size:2 final size:2
Alignment explanation
Indices: 2023871--2023902 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2023861 ACTGTAAATA
2023871 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2023903 TAAAATAGTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2028287 original size:6 final size:6
Alignment explanation
Indices: 2028278--2028360 Score: 67
Period size: 6 Copynumber: 13.8 Consensus size: 6
2028268 TCAATACAAT
* * * * * * *
2028278 CACCAC CACCAC CATCAC AACCAT CATCAT CACCAC CATCAC CATCAC
1 CACCAC CACCAC CACCAC CACCAC CACCAC CACCAC CACCAC CACCAC
* * * *
2028326 CACCAC CACCAT CACCAT CACCAT CACCAC GACCA
1 CACCAC CACCAC CACCAC CACCAC CACCAC CACCA
2028361 TAGTGCTAAT
Statistics
Matches: 64, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
6 64 1.00
ACGTcount: A:0.35, C:0.53, G:0.01, T:0.11
Consensus pattern (6 bp):
CACCAC
Found at i:2028300 original size:15 final size:15
Alignment explanation
Indices: 2028276--2028348 Score: 101
Period size: 15 Copynumber: 4.9 Consensus size: 15
2028266 CCTCAATACA
2028276 ATCACCACCACCACC
1 ATCACCACCACCACC
* * *
2028291 ATCACAACCATCATC
1 ATCACCACCACCACC
*
2028306 ATCACCACCATCACC
1 ATCACCACCACCACC
2028321 ATCACCACCACCACC
1 ATCACCACCACCACC
*
2028336 ATCACCATCACCA
1 ATCACCACCACCA
2028349 TCACCACGAC
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 51 1.00
ACGTcount: A:0.36, C:0.52, G:0.00, T:0.12
Consensus pattern (15 bp):
ATCACCACCACCACC
Found at i:2028311 original size:21 final size:21
Alignment explanation
Indices: 2028297--2028355 Score: 100
Period size: 21 Copynumber: 2.8 Consensus size: 21
2028287 CACCATCACA
*
2028297 ACCATCATCATCACCACCATC
1 ACCATCACCATCACCACCATC
*
2028318 ACCATCACCACCACCACCATC
1 ACCATCACCATCACCACCATC
2028339 ACCATCACCATCACCAC
1 ACCATCACCATCACCAC
2028356 GACCATAGTG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.34, C:0.53, G:0.00, T:0.14
Consensus pattern (21 bp):
ACCATCACCATCACCACCATC
Found at i:2028353 original size:12 final size:12
Alignment explanation
Indices: 2028281--2028361 Score: 87
Period size: 12 Copynumber: 7.0 Consensus size: 12
2028271 ATACAATCAC
2028281 CACCACCACCAT
1 CACCACCACCAT
* *
2028293 CACAACCATCAT
1 CACCACCACCAT
*
2028305 CATCACCACCAT
1 CACCACCACCAT
*
2028317 CACCATCA-C--
1 CACCACCACCAT
2028326 CACCACCACCAT
1 CACCACCACCAT
*
2028338 CACCATCACCAT
1 CACCACCACCAT
*
2028350 CACCACGACCAT
1 CACCACCACCAT
2028362 AGTGCTAATC
Statistics
Matches: 55, Mismatches: 11, Indels: 6
0.76 0.15 0.08
Matches are distributed among these distances:
9 7 0.13
10 1 0.02
11 1 0.02
12 46 0.84
ACGTcount: A:0.35, C:0.52, G:0.01, T:0.12
Consensus pattern (12 bp):
CACCACCACCAT
Found at i:2031555 original size:36 final size:36
Alignment explanation
Indices: 2031515--2031586 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
2031505 GTAGTGACTG
*
2031515 TTTAGCTAATGATATTTTAACAACAATACAATAGCA
1 TTTAGCTAATGATATTTTAACAACAATACAACAGCA
2031551 TTTAGCTAATGATATTTTAACAACAATACAACAGCA
1 TTTAGCTAATGATATTTTAACAACAATACAACAGCA
2031587 AAACCATTAG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.44, C:0.15, G:0.08, T:0.32
Consensus pattern (36 bp):
TTTAGCTAATGATATTTTAACAACAATACAACAGCA
Done.