Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008164.1 Hibiscus syriacus cultivar Beakdansim tig00110744_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: 2577652
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 11
Found at i:1894487 original size:15 final size:15
Alignment explanation
Indices: 1894469--1894498 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1894459 AATTTAATTT
1894469 TTATTTTTATTTTTA
1 TTATTTTTATTTTTA
1894484 TTATTTTTATTTTTA
1 TTATTTTTATTTTTA
1894499 GAATAATATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (15 bp):
TTATTTTTATTTTTA
Found at i:1894633 original size:81 final size:82
Alignment explanation
Indices: 1894506--1894670 Score: 244
Period size: 82 Copynumber: 2.0 Consensus size: 82
1894496 TTAGAATAAT
* *
1894506 ATTTTAAGTTTAAAAATATTTTATATTTTTCTAAAAAATTAAATAGATACTTGAAC-TTTTAAAA
1 ATTTTAAATTTAAAAATATTTTATATTTTTATAAAAAATTAAATAGATACTTGAACTTTTTAAAA
1894570 AAACAATTTAGCTGTAAC
66 AAA-AATTTAGCTGTAAC
* * **
1894588 ATTTTAAATTTAAAAATATTTT-TATTTTTATAAAAAATTACATAGATCCTTGAACTTTTTTTTA
1 ATTTTAAATTTAAAAATATTTTATATTTTTATAAAAAATTAAATAGATACTTGAAC-TTTTTAAA
1894652 AAAAAATTTAGCTGTAAC
65 AAAAAATTTAGCTGTAAC
1894670 A
1 A
1894671 CCCTTAACCA
Statistics
Matches: 75, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
81 30 0.40
82 36 0.48
83 9 0.12
ACGTcount: A:0.44, C:0.07, G:0.05, T:0.44
Consensus pattern (82 bp):
ATTTTAAATTTAAAAATATTTTATATTTTTATAAAAAATTAAATAGATACTTGAACTTTTTAAAA
AAAAATTTAGCTGTAAC
Found at i:1895670 original size:34 final size:35
Alignment explanation
Indices: 1895608--1895674 Score: 102
Period size: 34 Copynumber: 1.9 Consensus size: 35
1895598 ATCAAACAAG
1895608 TACTATTTATTTCTTCCTATATTGTTCCTTTTTTA
1 TACTATTTATTTCTTCCTATATTGTTCCTTTTTTA
*
1895643 TACTATTT-TTCTCTT-CTGTATTGTTCCTTTTT
1 TACTATTTATT-TCTTCCTATATTGTTCCTTTTT
1895675 CTTATATTGT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
34 18 0.60
35 12 0.40
ACGTcount: A:0.13, C:0.18, G:0.04, T:0.64
Consensus pattern (35 bp):
TACTATTTATTTCTTCCTATATTGTTCCTTTTTTA
Found at i:1895714 original size:17 final size:17
Alignment explanation
Indices: 1895672--1895714 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
1895662 ATTGTTCCTT
*
1895672 TTTCTTATATTGTTCTA
1 TTTCTTATATTGTACTA
*
1895689 TATCTTATATTGTACTA
1 TTTCTTATATTGTACTA
*
1895706 TTTCATATA
1 TTTCTTATA
1895715 CTATACCACT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.26, C:0.12, G:0.05, T:0.58
Consensus pattern (17 bp):
TTTCTTATATTGTACTA
Found at i:1895995 original size:65 final size:65
Alignment explanation
Indices: 1895916--1896138 Score: 255
Period size: 65 Copynumber: 3.6 Consensus size: 65
1895906 CAAATCTCAT
* * *
1895916 TGAGTGATCAGTACAATATTCAATTATCATTATACCTCATGCACAATAAAAGTACATGAGTCACG
1 TGAGTGATCTGTACAATATTCAATTATCACTACACCTCATGCACAATAAAAGTACATGAGTCACG
* * * *
1895981 TGAGTGATCTGTACAATATTCAATTATCACTCCACCTCATGCACCATAAAGGTACATGAGTCATG
1 TGAGTGATCTGTACAATATTCAATTATCACTACACCTCATGCACAATAAAAGTACATGAGTCACG
* * * *
1896046 TGAGTGATCTGTACAGTATTCAATTATTACTTCACCCCATGCAC--------TACATGAGTCACG
1 TGAGTGATCTGTACAATATTCAATTATCACTACACCTCATGCACAATAAAAGTACATGAGTCACG
* * * *
1896103 TGAGTCATCTATACAGTATTCAATTATCACTCCACC
1 TGAGTGATCTGTACAATATTCAATTATCACTACACC
1896139 GTCACATGAG
Statistics
Matches: 142, Mismatches: 16, Indels: 8
0.86 0.10 0.05
Matches are distributed among these distances:
57 44 0.31
65 98 0.69
ACGTcount: A:0.33, C:0.23, G:0.14, T:0.30
Consensus pattern (65 bp):
TGAGTGATCTGTACAATATTCAATTATCACTACACCTCATGCACAATAAAAGTACATGAGTCACG
Found at i:1896251 original size:65 final size:65
Alignment explanation
Indices: 1896139--1896432 Score: 401
Period size: 65 Copynumber: 4.5 Consensus size: 65
1896129 TCACTCCACC
* * * *
1896139 GTCACATGAGTGATCTGTACAATATTCAATTATCTCTCTACCCCATGCACCACAAAGGTACTTGA
1 GTCACATGAGTGATCTGTACAATATTCAATTATCACTCCACCTCATGCACCACAAAGGTACATGA
* * *
1896204 GTAACATGAATGATCTGTACAGTATTCAATTATCACTCCACCTCATGCACCACAAAGGTACATGA
1 GTCACATGAGTGATCTGTACAATATTCAATTATCACTCCACCTCATGCACCACAAAGGTACATGA
* * * * *
1896269 GTCATATGAGTGATCTGTAC-ATATTCAATTATCACTCCACCTCATGCGCCATAAAGATACACGA
1 GTCACATGAGTGATCTGTACAATATTCAATTATCACTCCACCTCATGCACCACAAAGGTACATGA
* * * ** *
1896333 GTCATATGAGTGATTTGTACAATATTTAATTATCACTCCATGTCATGCACCACTAAGGTACATGA
1 GTCACATGAGTGATCTGTACAATATTCAATTATCACTCCACCTCATGCACCACAAAGGTACATGA
* *
1896398 GTCGCATGAGTGATCTGTACAGTATTCAATTATCA
1 GTCACATGAGTGATCTGTACAATATTCAATTATCA
1896433 ACTTTATATA
Statistics
Matches: 199, Mismatches: 29, Indels: 2
0.87 0.13 0.01
Matches are distributed among these distances:
64 58 0.29
65 141 0.71
ACGTcount: A:0.32, C:0.23, G:0.15, T:0.30
Consensus pattern (65 bp):
GTCACATGAGTGATCTGTACAATATTCAATTATCACTCCACCTCATGCACCACAAAGGTACATGA
Found at i:1896379 original size:129 final size:129
Alignment explanation
Indices: 1896139--1896432 Score: 399
Period size: 129 Copynumber: 2.3 Consensus size: 129
1896129 TCACTCCACC
* * * **
1896139 GTCACATGAGTGATCTGTACAATATTCAATTATCTCTCTACCCCATGCACCACAAAGGTACTTGA
1 GTCACATGAGTGATCTGTAC-ATATTCAATTATCACTCCACCCCATGCACCACAAAGATACACGA
*
1896204 GTAACATGAATGATCTGTACAGTATTCAATTATCACTCCACCTCATGCACCACAAAGGTACATGA
65 GTAACATGAATGATCTGTACAATATTCAATTATCACTCCACCTCATGCACCACAAAGGTACATGA
* * * *
1896269 GTCATATGAGTGATCTGTACATATTCAATTATCACTCCACCTCATGCGCCATAAAGATACACGAG
1 GTCACATGAGTGATCTGTACATATTCAATTATCACTCCACCCCATGCACCACAAAGATACACGAG
* * * * * ** *
1896334 TCATATGAGTGATTTGTACAATATTTAATTATCACTCCATGTCATGCACCACTAAGGTACATGA
66 TAACATGAATGATCTGTACAATATTCAATTATCACTCCACCTCATGCACCACAAAGGTACATGA
*
1896398 GTCGCATGAGTGATCTGTACAGTATTCAATTATCA
1 GTCACATGAGTGATCTGTACA-TATTCAATTATCA
1896433 ACTTTATATA
Statistics
Matches: 143, Mismatches: 20, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
129 111 0.78
130 32 0.22
ACGTcount: A:0.32, C:0.23, G:0.15, T:0.30
Consensus pattern (129 bp):
GTCACATGAGTGATCTGTACATATTCAATTATCACTCCACCCCATGCACCACAAAGATACACGAG
TAACATGAATGATCTGTACAATATTCAATTATCACTCCACCTCATGCACCACAAAGGTACATGA
Found at i:1896602 original size:3 final size:3
Alignment explanation
Indices: 1896594--1896630 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
1896584 AAGCCACTTA
1896594 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1896631 TTATTATTAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1897307 original size:30 final size:31
Alignment explanation
Indices: 1897256--1897316 Score: 72
Period size: 30 Copynumber: 2.0 Consensus size: 31
1897246 TTTCACAACA
* *
1897256 ATCCCTATATTTTTCATAATTTGC-AATTGG
1 ATCCCTATATCTTTCAAAATTTGCAAATTGG
*
1897286 ATCCCTATA-CTTTCACAAATTTTCAAATTGG
1 ATCCCTATATCTTTCA-AAATTTGCAAATTGG
1897317 TTCAAAACAC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
29 5 0.19
30 15 0.58
31 6 0.23
ACGTcount: A:0.30, C:0.20, G:0.08, T:0.43
Consensus pattern (31 bp):
ATCCCTATATCTTTCAAAATTTGCAAATTGG
Found at i:1904706 original size:46 final size:44
Alignment explanation
Indices: 1904574--1904699 Score: 191
Period size: 46 Copynumber: 2.8 Consensus size: 44
1904564 GATAAGCTGG
* *
1904574 AAAATAAGCTTATGAGCTTATGGA-ATAATGGCAAGTATATTGGT
1 AAAATAAGCTTATGAGCTTATGGATA-AATGGTAAGTATTTTGGT
1904618 AAAATAAGCTTATGAGCTTATGGGATTAAATGGTAAGTATTTTGGT
1 AAAATAAGCTTATGAGCTTAT-GGA-TAAATGGTAAGTATTTTGGT
1904664 AAAATAAGCTTATGAGCTTATAGGATAAATGGTAAG
1 AAAATAAGCTTATGAGCTTAT-GGATAAATGGTAAG
1904700 AGATTTTATC
Statistics
Matches: 76, Mismatches: 3, Indels: 5
0.90 0.04 0.06
Matches are distributed among these distances:
44 21 0.28
45 14 0.18
46 40 0.53
47 1 0.01
ACGTcount: A:0.39, C:0.06, G:0.23, T:0.33
Consensus pattern (44 bp):
AAAATAAGCTTATGAGCTTATGGATAAATGGTAAGTATTTTGGT
Found at i:1906070 original size:3 final size:3
Alignment explanation
Indices: 1906064--1906135 Score: 80
Period size: 3 Copynumber: 25.0 Consensus size: 3
1906054 TGTATTATTT
* * *
1906064 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT- ATA CTA ATA A-C ATT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1906110 ATA AT- ATA TATA ATA AT- ATA ATA ATA
1 ATA ATA ATA -ATA ATA ATA ATA ATA ATA
1906136 TATTATTATA
Statistics
Matches: 59, Mismatches: 5, Indels: 10
0.80 0.07 0.14
Matches are distributed among these distances:
2 7 0.12
3 49 0.83
4 3 0.05
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (3 bp):
ATA
Found at i:1906417 original size:42 final size:41
Alignment explanation
Indices: 1906327--1906433 Score: 133
Period size: 42 Copynumber: 2.6 Consensus size: 41
1906317 GCCCAAAGGT
* * * * *
1906327 CTGACGGATGGCCCTAAGGACTTATCATCTTGCTCGAAAGA
1 CTGACAGATGACCCGAAGGATTTATCATCATGCTCGAAAGA
*
1906368 CTGACAGATGACCCGAAGGATTTATACATCATGCTCGAAGGA
1 CTGACAGATGACCCGAAGGATTTAT-CATCATGCTCGAAAGA
* *
1906410 CTTACAGATGACCCGAATGATTTA
1 CTGACAGATGACCCGAAGGATTTA
1906434 AAAATTCATG
Statistics
Matches: 57, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
41 21 0.37
42 36 0.63
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.24
Consensus pattern (41 bp):
CTGACAGATGACCCGAAGGATTTATCATCATGCTCGAAAGA
Found at i:1906426 original size:20 final size:20
Alignment explanation
Indices: 1906361--1906426 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
1906351 TCATCTTGCT
* *
1906361 CGAAAGACTGACAGATGACC
1 CGAAGGACTTACAGATGACC
* * *
1906381 CGAAGGATTTATACATCATG-CT
1 CGAAGGA-CT-TACA-GATGACC
1906403 CGAAGGACTTACAGATGACC
1 CGAAGGACTTACAGATGACC
1906423 CGAA
1 CGAA
1906427 TGATTTAAAA
Statistics
Matches: 34, Mismatches: 8, Indels: 8
0.68 0.16 0.16
Matches are distributed among these distances:
19 3 0.09
20 15 0.44
21 2 0.06
22 11 0.32
23 3 0.09
ACGTcount: A:0.36, C:0.23, G:0.23, T:0.18
Consensus pattern (20 bp):
CGAAGGACTTACAGATGACC
Found at i:1906683 original size:20 final size:20
Alignment explanation
Indices: 1906620--1906684 Score: 60
Period size: 20 Copynumber: 3.1 Consensus size: 20
1906610 CGAGAGACTA
*
1906620 ACAGATGACCCGAAGGATTT
1 ACAGATGACTCGAAGGATTT
* * *
1906640 A-AGTATCATGCTCGAAAGACTT
1 ACAG-ATGA--CTCGAAGGATTT
1906662 ACAGATGACTCGAAGGATTT
1 ACAGATGACTCGAAGGATTT
1906682 ACA
1 ACA
1906685 AATTCATGGG
Statistics
Matches: 34, Mismatches: 7, Indels: 8
0.69 0.14 0.16
Matches are distributed among these distances:
19 2 0.06
20 17 0.50
22 13 0.38
23 2 0.06
ACGTcount: A:0.37, C:0.18, G:0.22, T:0.23
Consensus pattern (20 bp):
ACAGATGACTCGAAGGATTT
Found at i:1914607 original size:23 final size:22
Alignment explanation
Indices: 1914555--1914607 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 22
1914545 AGTCTCTTTC
1914555 TTGCTCTCTGTTTTGTGTTTGT
1 TTGCTCTCTGTTTTGTGTTTGT
*
1914577 TATTCTCTCTCGTTGTTGTGTTT-T
1 T-TGCTCTCT-GTT-TTGTGTTTGT
1914601 TTGCTCT
1 TTGCTCT
1914608 TTGGTTGCCC
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
22 1 0.04
23 12 0.46
24 5 0.19
25 8 0.31
ACGTcount: A:0.02, C:0.17, G:0.19, T:0.62
Consensus pattern (22 bp):
TTGCTCTCTGTTTTGTGTTTGT
Found at i:1915136 original size:3 final size:3
Alignment explanation
Indices: 1915130--1915212 Score: 100
Period size: 3 Copynumber: 28.0 Consensus size: 3
1915120 TGTATTATTT
1915130 ATA ATAA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * *
1915176 ATA AT- ATA CTA ATA A-C ATT ATA AT- ATA TATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA
1915213 TATTATTATA
Statistics
Matches: 70, Mismatches: 5, Indels: 10
0.82 0.06 0.12
Matches are distributed among these distances:
2 5 0.07
3 59 0.84
4 6 0.09
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:1916843 original size:26 final size:29
Alignment explanation
Indices: 1916781--1916846 Score: 75
Period size: 31 Copynumber: 2.3 Consensus size: 29
1916771 AAGTTTAATT
*
1916781 TTTTAATTTAATTACTTAACTTTCAAATTA
1 TTTTAATTTAATCACTTAACTTTCAAA-TA
*
1916811 TTCTTAATTTAATCAC-TCACTTTC-AA-A
1 TT-TTAATTTAATCACTTAACTTTCAAATA
1916838 TTTTAATTT
1 TTTTAATTT
1916847 TTTTAATTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
26 7 0.21
27 3 0.09
29 2 0.06
30 9 0.27
31 12 0.36
ACGTcount: A:0.33, C:0.14, G:0.00, T:0.53
Consensus pattern (29 bp):
TTTTAATTTAATCACTTAACTTTCAAATA
Found at i:1918049 original size:75 final size:75
Alignment explanation
Indices: 1917906--1918049 Score: 182
Period size: 75 Copynumber: 1.9 Consensus size: 75
1917896 GAGGAAGAAT
* * * * * * * * * *
1917906 AAGACGAAAGATAAGTATGAATACTTACCAATCTGATGTAGTAAACAACTTATAGATAGGGGTGA
1 AAGACAAAAGACAAATATGAAGACTTACCAATCCGATGTAGCAAACAACTTATAGAGAAGGCTAA
1917971 AAAATATAAA
66 AAAATATAAA
1917981 AAGACAAAAGACAAATATGAAGACTTACCAATCCGATGTAGCAAACGAA-TTATAGAGAAGGCTA
1 AAGACAAAAGACAAATATGAAGACTTACCAATCCGATGTAGCAAAC-AACTTATAGAGAAGGCTA
1918045 AAAAA
65 AAAAA
1918050 AATCAAAATA
Statistics
Matches: 58, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
75 56 0.97
76 2 0.03
ACGTcount: A:0.50, C:0.12, G:0.18, T:0.20
Consensus pattern (75 bp):
AAGACAAAAGACAAATATGAAGACTTACCAATCCGATGTAGCAAACAACTTATAGAGAAGGCTAA
AAAATATAAA
Found at i:1922209 original size:22 final size:21
Alignment explanation
Indices: 1922133--1922202 Score: 72
Period size: 22 Copynumber: 3.3 Consensus size: 21
1922123 ATATCTAGAG
**
1922133 TTAATTAAATATATGTTTTAA
1 TTAATTAAATATATAATTTAA
*
1922154 -TAATCTCAAATATTTAATTTCAA
1 TTAAT-T-AAATATATAATTT-AA
1922177 TTAATTAAATATAT-ATTTAA
1 TTAATTAAATATATAATTTAA
1922197 TTAATT
1 TTAATT
1922203 TGAAATAATA
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
20 12 0.29
21 5 0.12
22 17 0.41
23 3 0.07
24 4 0.10
ACGTcount: A:0.44, C:0.04, G:0.01, T:0.50
Consensus pattern (21 bp):
TTAATTAAATATATAATTTAA
Found at i:1922285 original size:90 final size:88
Alignment explanation
Indices: 1922167--1922340 Score: 285
Period size: 90 Copynumber: 2.0 Consensus size: 88
1922157 TCTCAAATAT
* * *
1922167 TTAATTTCAATTAATTAAATATATATTTAATTAATTTGAAATAATAAAATCCCTAATATGATTAG
1 TTAAATTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAA-CCCTAATATGATTAA
*
1922232 GGTAACTTGTATATAAAAGGATTA
65 GGTAACTTGGATATAAAAGGATTA
1922256 TTAAATTCTAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCCTAATATGATTAA
1 TTAAATTC-AATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCCTAATATGATTAA
*
1922321 GGTAACTTGGCTATAAAAGG
65 GGTAACTTGGATATAAAAGG
1922341 GTGTGTTAGA
Statistics
Matches: 79, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
89 39 0.49
90 40 0.51
ACGTcount: A:0.45, C:0.06, G:0.10, T:0.39
Consensus pattern (88 bp):
TTAAATTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCCTAATATGATTAAG
GTAACTTGGATATAAAAGGATTA
Found at i:1926012 original size:17 final size:17
Alignment explanation
Indices: 1925976--1926017 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
1925966 GTGTTTGTTG
* * *
1925976 CTCGAAAAAGAGTTTTT
1 CTCGAAAGAGAATTTCT
1925993 CTCGAAAGAGAATTTCT
1 CTCGAAAGAGAATTTCT
1926010 CTC-AAAGA
1 CTCGAAAGA
1926018 AAGGGAAGGG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.29
Consensus pattern (17 bp):
CTCGAAAGAGAATTTCT
Found at i:1928876 original size:22 final size:22
Alignment explanation
Indices: 1928807--1928876 Score: 58
Period size: 20 Copynumber: 3.2 Consensus size: 22
1928797 AGAGTTAATT
*
1928807 AAATATATGTTTTAA-TAATCTTG
1 AAATATA-GATTTAATTAAT-TTG
*
1928830 AATATTTA-ATTTCAATTAA-TT-
1 AA-ATATAGATTT-AATTAATTTG
1928851 AAATATAGATTTAATTAATTTG
1 AAATATAGATTTAATTAATTTG
1928873 AAAT
1 AAAT
1928877 GATAAAATTC
Statistics
Matches: 38, Mismatches: 3, Indels: 13
0.70 0.06 0.24
Matches are distributed among these distances:
20 10 0.26
21 8 0.21
22 9 0.24
23 4 0.11
24 7 0.18
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.47
Consensus pattern (22 bp):
AAATATAGATTTAATTAATTTG
Found at i:1935910 original size:218 final size:218
Alignment explanation
Indices: 1935532--1935944 Score: 817
Period size: 218 Copynumber: 1.9 Consensus size: 218
1935522 AATATAATCA
1935532 TCGAAAATTTCTTTATGAATCTTCGATAGTAACCAACAAATCCCAAGAAACTTTGAAATTTGAAA
1 TCGAAAATTTCTTTATGAATCTTCGATAGTAACCAACAAATCCCAAGAAACTTTGAAATTTGAAA
1935597 ACATTCTTTAGAATTTATCATTTGACTATATCTTGTGCTTTCTTGATATTTATTCTTATTAACTT
66 ACATTCTTTAGAATTTATCATTTGACTATATCTTGTGCTTTCTTGATATTTATTCTTATTAACTT
1935662 AATTGAGTCCAAATGACCAAGGAATACAACCTTAGACAACCAACATTTACACTTGGTCAACATAG
131 AATTGAGTCCAAATGACCAAGGAATACAACCTTAGACAACCAACATTTACACTTGGTCAACATAG
1935727 CATGCTATTTTTCTCCCGAATAG
196 CATGCTATTTTTCTCCCGAATAG
1935750 TCGAAAATTTCTTTATGAATCTTCGATAGTAACCAACAAATCCCAAGAAACTTTGAAATTTGAAA
1 TCGAAAATTTCTTTATGAATCTTCGATAGTAACCAACAAATCCCAAGAAACTTTGAAATTTGAAA
1935815 ACATTCTTTAGAATTTATCATTTGACTATATCTTGTGCTTTCTTGATATTTATTCTTATTAACTT
66 ACATTCTTTAGAATTTATCATTTGACTATATCTTGTGCTTTCTTGATATTTATTCTTATTAACTT
*
1935880 AGTTGAGTCCAAATGACCAAGGAATACAACCTTAGACAACCAACATTTACACTTGGTCAACATAG
131 AATTGAGTCCAAATGACCAAGGAATACAACCTTAGACAACCAACATTTACACTTGGTCAACATAG
1935945 GTCTTACAAA
Statistics
Matches: 194, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
218 194 1.00
ACGTcount: A:0.35, C:0.18, G:0.11, T:0.36
Consensus pattern (218 bp):
TCGAAAATTTCTTTATGAATCTTCGATAGTAACCAACAAATCCCAAGAAACTTTGAAATTTGAAA
ACATTCTTTAGAATTTATCATTTGACTATATCTTGTGCTTTCTTGATATTTATTCTTATTAACTT
AATTGAGTCCAAATGACCAAGGAATACAACCTTAGACAACCAACATTTACACTTGGTCAACATAG
CATGCTATTTTTCTCCCGAATAG
Found at i:1937996 original size:61 final size:64
Alignment explanation
Indices: 1937920--1938064 Score: 165
Period size: 61 Copynumber: 2.3 Consensus size: 64
1937910 CTGCACTAAG
* * * * **
1937920 CTTACGCTCTAGTGCTAATCCGA-ATATGATAT-GTAGGGTCGTGCCCATGACCTACAC-TAG-G
1 CTTACACTCTAGTGCTAATCC-ATATATGACATAG-AAGGTCATGCCCACCACCTACACTTAGTG
1937981 T
64 T
1937982 -TTACACTCTAGTGCTAATCCATATATGACATAGAAGGTCATGCCCACCACCTACACTTAGTGT
1 CTTACACTCTAGTGCTAATCCATATATGACATAGAAGGTCATGCCCACCACCTACACTTAGTGT
*
1938045 CCTTACACACTAGTGCTAAT
1 -CTTACACTCTAGTGCTAAT
1938065 ATAAACCTAC
Statistics
Matches: 70, Mismatches: 7, Indels: 9
0.81 0.08 0.10
Matches are distributed among these distances:
60 1 0.01
61 46 0.66
62 4 0.06
63 2 0.03
65 17 0.24
ACGTcount: A:0.28, C:0.26, G:0.17, T:0.29
Consensus pattern (64 bp):
CTTACACTCTAGTGCTAATCCATATATGACATAGAAGGTCATGCCCACCACCTACACTTAGTGT
Found at i:1939594 original size:30 final size:31
Alignment explanation
Indices: 1939535--1939594 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
1939525 AACAATCCAC
* *
1939535 AACTTTTCCAAAATTTTGAATTAGATCCCCT
1 AACTTTTCAAAAATTTAGAATTAGATCCCCT
1939566 AACTTTTCAAAAATTATAGAA-TAG-TCCCC
1 AACTTTTCAAAAATT-TAGAATTAGATCCCC
1939595 AAATTATTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 5 0.19
31 17 0.65
32 4 0.15
ACGTcount: A:0.37, C:0.22, G:0.07, T:0.35
Consensus pattern (31 bp):
AACTTTTCAAAAATTTAGAATTAGATCCCCT
Found at i:1943451 original size:17 final size:17
Alignment explanation
Indices: 1943429--1943461 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1943419 ATACACAGTA
*
1943429 GTATCGATACCCTTTTG
1 GTATCGATACCATTTTG
1943446 GTATCGATACCATTTT
1 GTATCGATACCATTTT
1943462 TTCATTATGG
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:0.21, C:0.21, G:0.15, T:0.42
Consensus pattern (17 bp):
GTATCGATACCATTTTG
Found at i:1956594 original size:18 final size:18
Alignment explanation
Indices: 1956571--1956606 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1956561 ATACACAGAA
* *
1956571 GTATCGGTACCCTTTTTG
1 GTATCGATACCATTTTTG
1956589 GTATCGATACCATTTTTG
1 GTATCGATACCATTTTTG
1956607 CATTCTGGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.19, G:0.19, T:0.44
Consensus pattern (18 bp):
GTATCGATACCATTTTTG
Found at i:1962141 original size:17 final size:17
Alignment explanation
Indices: 1962119--1962151 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1962109 ATACAGAGTA
*
1962119 GTATCGATACCCTTTTG
1 GTATCGATACCATTTTG
1962136 GTATCGATACCATTTT
1 GTATCGATACCATTTT
1962152 TGCATTCTGA
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:0.21, C:0.21, G:0.15, T:0.42
Consensus pattern (17 bp):
GTATCGATACCATTTTG
Found at i:1968587 original size:13 final size:14
Alignment explanation
Indices: 1968559--1968591 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
1968549 ATGATGATTG
1968559 TATT-ATCATATAT
1 TATTGATCATATAT
1968572 TATTGATCATAT-T
1 TATTGATCATATAT
1968585 TATTGAT
1 TATTGAT
1968592 TAAAGGAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 12 0.63
14 7 0.37
ACGTcount: A:0.33, C:0.06, G:0.06, T:0.55
Consensus pattern (14 bp):
TATTGATCATATAT
Found at i:1984901 original size:12 final size:13
Alignment explanation
Indices: 1984875--1984903 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1984865 GATAAACACG
1984875 TTTTAAAATTATT
1 TTTTAAAATTATT
1984888 TTTTAAAATT-TT
1 TTTTAAAATTATT
1984900 TTTT
1 TTTT
1984904 GTTCAACATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.38
13 10 0.62
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
TTTTAAAATTATT
Found at i:1986711 original size:18 final size:16
Alignment explanation
Indices: 1986688--1986736 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
1986678 AATCAAACTT
*
1986688 TATTGTTCTTTATTCCTG
1 TATTGTTCTTT-TT-CTC
1986706 TATTGTTTCTTTTTCTC
1 TATTG-TTCTTTTTCTC
*
1986723 TATTGTTCCTTTTC
1 TATTGTTCTTTTTC
1986737 CTTTACTACC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
16 8 0.29
17 7 0.25
18 7 0.25
19 6 0.21
ACGTcount: A:0.08, C:0.18, G:0.08, T:0.65
Consensus pattern (16 bp):
TATTGTTCTTTTTCTC
Found at i:1986728 original size:17 final size:18
Alignment explanation
Indices: 1986688--1986735 Score: 55
Period size: 17 Copynumber: 2.7 Consensus size: 18
1986678 AATCAAACTT
*
1986688 TATTG-TTCTTTATTCCTG
1 TATTGTTTCTTT-TTCCTC
1986706 TATTGTTTCTTTTT-CTC
1 TATTGTTTCTTTTTCCTC
*
1986723 TATTGTTCCTTTT
1 TATTGTTTCTTTT
1986736 CCTTTACTAC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 14 0.52
18 7 0.26
19 6 0.22
ACGTcount: A:0.08, C:0.17, G:0.08, T:0.67
Consensus pattern (18 bp):
TATTGTTTCTTTTTCCTC
Found at i:1988524 original size:20 final size:20
Alignment explanation
Indices: 1988488--1988532 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
1988478 GATAAAAAGT
*
1988488 AAAAGTTAAAAATGAAATAG
1 AAAAGTTAAAAATGAAAGAG
*
1988508 AAAAGTTAAGGAA-GAAAGAG
1 AAAAGTTAA-AAATGAAAGAG
1988528 AAAAG
1 AAAAG
1988533 AAAAAGTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 20 0.91
21 2 0.09
ACGTcount: A:0.64, C:0.00, G:0.22, T:0.13
Consensus pattern (20 bp):
AAAAGTTAAAAATGAAAGAG
Found at i:1995422 original size:23 final size:23
Alignment explanation
Indices: 1995396--1995441 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
1995386 AAGAACCAAG
1995396 ATAAACT-TAAATATACCATTAAA
1 ATAAACTCTAAATAT-CCATTAAA
*
1995419 ATAAAGTCTAAATATCCATTAAA
1 ATAAACTCTAAATATCCATTAAA
1995442 CCAACCACCA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 14 0.67
24 7 0.33
ACGTcount: A:0.54, C:0.13, G:0.02, T:0.30
Consensus pattern (23 bp):
ATAAACTCTAAATATCCATTAAA
Found at i:2008909 original size:25 final size:25
Alignment explanation
Indices: 2008880--2008928 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
2008870 AGTCTATTAA
* *
2008880 AAAAT-AATTTTTGAAATTATAAAAT
1 AAAATAAAATTTT-AAATTAAAAAAT
2008905 AAAATAAAATTTTAAATTAAAAAA
1 AAAATAAAATTTTAAATTAAAAAA
2008929 AAGATGGAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 15 0.71
26 6 0.29
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (25 bp):
AAAATAAAATTTTAAATTAAAAAAT
Found at i:2027098 original size:12 final size:12
Alignment explanation
Indices: 2027081--2027106 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2027071 TTAATAATTA
2027081 TAGCCTCTATTT
1 TAGCCTCTATTT
2027093 TAGCCTCTATTT
1 TAGCCTCTATTT
2027105 TA
1 TA
2027107 AATGTTGTCA
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:0.19, C:0.23, G:0.08, T:0.50
Consensus pattern (12 bp):
TAGCCTCTATTT
Found at i:2032754 original size:61 final size:61
Alignment explanation
Indices: 2032654--2032777 Score: 203
Period size: 61 Copynumber: 2.0 Consensus size: 61
2032644 ATGCACTGAT
* * *
2032654 GTACTAATACACATAAGGTCATGTCCACCATATGCACTAAGTGTCCTTTATATACACTATA
1 GTACCAATACACATAAGGTCATGCCCACCATATACACTAAGTGTCCTTTATATACACTATA
**
2032715 GTACCAATACACATAAGGTTGTGCCCACCATATACACTAAGTGTCCTTTATATACACTATA
1 GTACCAATACACATAAGGTCATGCCCACCATATACACTAAGTGTCCTTTATATACACTATA
2032776 GT
1 GT
2032778 GTTATACCAG
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
61 58 1.00
ACGTcount: A:0.34, C:0.23, G:0.12, T:0.31
Consensus pattern (61 bp):
GTACCAATACACATAAGGTCATGCCCACCATATACACTAAGTGTCCTTTATATACACTATA
Found at i:2035190 original size:28 final size:31
Alignment explanation
Indices: 2035133--2035201 Score: 81
Period size: 28 Copynumber: 2.3 Consensus size: 31
2035123 TGAAAATCAC
* *
2035133 ACTTTGGCCCTTAAACTATTCCAAACTTTAT
1 ACTTTGGCCATTAAACTATTCCAAAATTTAT
2035164 ACTTT-GCCATTAAACT-TT-CAAAATTTAT
1 ACTTTGGCCATTAAACTATTCCAAAATTTAT
**
2035192 GTTTTGGCCA
1 ACTTTGGCCA
2035202 CTAACCAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
28 12 0.36
29 6 0.18
30 10 0.30
31 5 0.15
ACGTcount: A:0.29, C:0.22, G:0.09, T:0.41
Consensus pattern (31 bp):
ACTTTGGCCATTAAACTATTCCAAAATTTAT
Found at i:2039732 original size:20 final size:21
Alignment explanation
Indices: 2039707--2039747 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
2039697 AATTTTCACC
2039707 TTATAACATCAAATT-CAACA
1 TTATAACATCAAATTCCAACA
*
2039727 TTATAACATTAAATTCCAACA
1 TTATAACATCAAATTCCAACA
2039748 AGTTATATCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.49, C:0.20, G:0.00, T:0.32
Consensus pattern (21 bp):
TTATAACATCAAATTCCAACA
Found at i:2043826 original size:17 final size:18
Alignment explanation
Indices: 2043799--2043835 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
2043789 TACGTTGTCT
2043799 TATAGGAAATGGTTAGGG
1 TATAGGAAATGGTTAGGG
*
2043817 TATA-GAAATGGTTATGG
1 TATAGGAAATGGTTAGGG
2043834 TA
1 TA
2043836 GAGGTAGGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 14 0.78
18 4 0.22
ACGTcount: A:0.35, C:0.00, G:0.32, T:0.32
Consensus pattern (18 bp):
TATAGGAAATGGTTAGGG
Found at i:2043908 original size:16 final size:16
Alignment explanation
Indices: 2043859--2043923 Score: 53
Period size: 16 Copynumber: 4.1 Consensus size: 16
2043849 AAAGGTTAAA
*
2043859 AAAGGATAAGGAAATG
1 AAAGAATAAGGAAATG
* *
2043875 AAATAAGAA--AAGATG
1 AAAGAATAAGGAA-ATG
2043890 AAAGAATAAGGAAATG
1 AAAGAATAAGGAAATG
* * *
2043906 AAATAGTAAGAAAATG
1 AAAGAATAAGGAAATG
2043922 AA
1 AA
2043924 GATAACTTAC
Statistics
Matches: 38, Mismatches: 8, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
14 2 0.05
15 10 0.26
16 24 0.63
17 2 0.05
ACGTcount: A:0.63, C:0.00, G:0.23, T:0.14
Consensus pattern (16 bp):
AAAGAATAAGGAAATG
Found at i:2047666 original size:29 final size:29
Alignment explanation
Indices: 2047633--2047713 Score: 83
Period size: 31 Copynumber: 2.7 Consensus size: 29
2047623 CTAGTGACAA
* *
2047633 AAAATGTAAGTTTTGAAAGTTTAGTGG-CG
1 AAAATGTAACTTTTAAAAGTTTAG-GGACG
* *
2047662 AAAATATAAACTTTGTAAAAGTTTAGGGACT
1 AAAATGT-AACTTT-TAAAAGTTTAGGGACG
*
2047693 AAAATGTAATTTTTAAAAGTT
1 AAAATGTAACTTTTAAAAGTT
2047714 ATATATTTTG
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
29 14 0.33
30 12 0.28
31 17 0.40
ACGTcount: A:0.42, C:0.04, G:0.19, T:0.36
Consensus pattern (29 bp):
AAAATGTAACTTTTAAAAGTTTAGGGACG
Found at i:2049028 original size:21 final size:21
Alignment explanation
Indices: 2048986--2049029 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
2048976 GCCCAAAAAT
* * * *
2048986 ATTGGAAGTTTTGAAGATTGA
1 ATTGCAAGTTTTCAAAAGTGA
2049007 ATTGCAAGTTTTCAAAAGTGA
1 ATTGCAAGTTTTCAAAAGTGA
2049028 AT
1 AT
2049030 GTACTTGATT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.36, C:0.05, G:0.23, T:0.36
Consensus pattern (21 bp):
ATTGCAAGTTTTCAAAAGTGA
Found at i:2053849 original size:26 final size:26
Alignment explanation
Indices: 2053809--2053859 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
2053799 GATGTTAGAT
* * *
2053809 TTTCATGTTCTATGGTTGGTTTATGA
1 TTTCATGGTCGATGGTCGGTTTATGA
2053835 TTTCATGGTCGATGGTCGGTTTATG
1 TTTCATGGTCGATGGTCGGTTTATG
2053860 TTGAAGTTGA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.14, C:0.10, G:0.27, T:0.49
Consensus pattern (26 bp):
TTTCATGGTCGATGGTCGGTTTATGA
Found at i:2059733 original size:54 final size:54
Alignment explanation
Indices: 2059672--2059901 Score: 318
Period size: 54 Copynumber: 4.3 Consensus size: 54
2059662 TTCCGTGATT
** * * * * *
2059672 TTGCACACATAGTGTCGGTATGGTAATTCACAAACTCATTGTGATTTACATGGG
1 TTGCACACATAGTGTCAATACGGTAATTCACAAACTCATTATGAATTACTTAGG
* *
2059726 TTGCACACATAGTGCCAATACGGTAATTTACAAACTCATTATGAATTACTTAGG
1 TTGCACACATAGTGTCAATACGGTAATTCACAAACTCATTATGAATTACTTAGG
* * *
2059780 TTGCACACATAGTG-CAAATACGGTAAATCAAAAACTCATTATGAATTTCTTAGG
1 TTGCACACATAGTGTC-AATACGGTAATTCACAAACTCATTATGAATTACTTAGG
*
2059834 TTGCACACATAGTGTCAATACGGTAATTCACAAACTTATTATGAATTACTTAGG
1 TTGCACACATAGTGTCAATACGGTAATTCACAAACTCATTATGAATTACTTAGG
*
2059888 TTGCATACATAGTG
1 TTGCACACATAGTG
2059902 CCTGTCGACA
Statistics
Matches: 156, Mismatches: 18, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
53 1 0.01
54 154 0.99
55 1 0.01
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (54 bp):
TTGCACACATAGTGTCAATACGGTAATTCACAAACTCATTATGAATTACTTAGG
Found at i:2066860 original size:20 final size:19
Alignment explanation
Indices: 2066834--2066913 Score: 63
Period size: 20 Copynumber: 4.1 Consensus size: 19
2066824 TTCCACGAAT
2066834 TTGTAAAACCTTCGGGTCA
1 TTGTAAAACCTTCGGGTCA
* *
2066853 TCTGTAAAGCCTTAGGGT-A
1 T-TGTAAAACCTTCGGGTCA
* ** *
2066872 GGATGTAAAACCTTTTGGTAA
1 --TTGTAAAACCTTCGGGTCA
*
2066893 TTGTAAATCCTTCGGGTCA
1 TTGTAAAACCTTCGGGTCA
2066912 TT
1 TT
2066914 TGTTACTCTT
Statistics
Matches: 46, Mismatches: 11, Indels: 8
0.71 0.17 0.12
Matches are distributed among these distances:
19 18 0.39
20 27 0.59
21 1 0.02
ACGTcount: A:0.26, C:0.16, G:0.23, T:0.35
Consensus pattern (19 bp):
TTGTAAAACCTTCGGGTCA
Found at i:2067126 original size:92 final size:92
Alignment explanation
Indices: 2066973--2067178 Score: 313
Period size: 92 Copynumber: 2.2 Consensus size: 92
2066963 ACCTCCATGG
* ** * *
2066973 AAGAGTAGTGAAGTATTCCAACATGAATTTGATCTTCACGGAAGAGTAGTGAAATAAATTATGTT
1 AAGAGTAGTGAAGTATTCAAACATGAAACTGATCTTCACAGAAGAGTAATGAAATAAATTATGTT
*
2067038 CAAATCATTCAAATTCAACCTTCACGA
66 CAAATCATTCAAATTCAAACTTCACGA
* * *
2067065 AAGAGTAGTGAAGTATTCAAACTTGAAACTGATCTTCACAGAAGAGTAATGGAATAGATTATGTT
1 AAGAGTAGTGAAGTATTCAAACATGAAACTGATCTTCACAGAAGAGTAATGAAATAAATTATGTT
*
2067130 CAAATCATTCAAATTCAAATTTCACGA
66 CAAATCATTCAAATTCAAACTTCACGA
2067157 AAGAGTAGTGAAGTCATTCAAA
1 AAGAGTAGTGAAGT-ATTCAAA
2067179 TTCAACCTTC
Statistics
Matches: 103, Mismatches: 10, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
92 96 0.93
93 7 0.07
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.29
Consensus pattern (92 bp):
AAGAGTAGTGAAGTATTCAAACATGAAACTGATCTTCACAGAAGAGTAATGAAATAAATTATGTT
CAAATCATTCAAATTCAAACTTCACGA
Found at i:2067181 original size:36 final size:36
Alignment explanation
Indices: 2067134--2067210 Score: 104
Period size: 36 Copynumber: 2.2 Consensus size: 36
2067124 TATGTTCAAA
*
2067134 TCATTCAAATTCAAATTTCAC-GAAAGAGTAGTGAAG
1 TCATTCAAATTCAAACTTCACAG-AAGAGTAGTGAAG
* *
2067170 TCATTCAAATTCAACCTTCACAGAAGAGTATTGAAG
1 TCATTCAAATTCAAACTTCACAGAAGAGTAGTGAAG
2067206 T-ATTC
1 TCATTC
2067211 CAACCTTGAA
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
35 4 0.11
36 32 0.86
37 1 0.03
ACGTcount: A:0.39, C:0.17, G:0.14, T:0.30
Consensus pattern (36 bp):
TCATTCAAATTCAAACTTCACAGAAGAGTAGTGAAG
Found at i:2069406 original size:54 final size:54
Alignment explanation
Indices: 2069318--2069546 Score: 282
Period size: 54 Copynumber: 4.3 Consensus size: 54
2069308 GTCTTGAGAG
** * *
2069318 TGCCAATAAAGTAATTCACAAACGT-ATTACGAATTACTTGGGTTGTACACATAA
1 TGCCAATACGGTAATTCACAAAC-TCATTATGAATTACTTGGGTTGCACACATAA
* * * *
2069372 TACCAATACGGTAATTCACAAACTTATTATGAATTACTT-AGTTGCACACATAG
1 TGCCAATACGGTAATTCACAAACTCATTATGAATTACTTGGGTTGCACACATAA
* * * *
2069425 TGCCAATATGGTAATTTATAAACTCATTATGAATTACTTAGGTTGCACACATAA
1 TGCCAATACGGTAATTCACAAACTCATTATGAATTACTTGGGTTGCACACATAA
** * * *
2069479 TGCCAATATAGTAATTCACAAACTCATTGTGAATTACGTGGGTTGCACACATAG
1 TGCCAATACGGTAATTCACAAACTCATTATGAATTACTTGGGTTGCACACATAA
2069533 TGCCAATACGGTAA
1 TGCCAATACGGTAA
2069547 ATGCAACATA
Statistics
Matches: 150, Mismatches: 23, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
53 46 0.31
54 104 0.69
ACGTcount: A:0.37, C:0.17, G:0.15, T:0.31
Consensus pattern (54 bp):
TGCCAATACGGTAATTCACAAACTCATTATGAATTACTTGGGTTGCACACATAA
Found at i:2069502 original size:107 final size:108
Alignment explanation
Indices: 2069316--2069546 Score: 304
Period size: 107 Copynumber: 2.1 Consensus size: 108
2069306 ACGTCTTGAG
* * *
2069316 AGTGCCAATAAAGTAATTCACAAACGTATTACGAATTACTTGGGTTGTACACATAATACCAATAC
1 AGTGCCAATAAGGTAATTCACAAACGTATTACGAATTACTTAGGTTGCACACATAATACCAATAC
* * *
2069381 GGTAATTCACAAACTTATTATGAATTAC-TTAGTTGCACACAT
66 AGTAATTCACAAACTCATTATGAATTACGTGAGTTGCACACAT
* * * * *
2069423 AGTGCCAATATGGTAATTTATAAAC-TCATTATGAATTACTTAGGTTGCACACATAATGCCAATA
1 AGTGCCAATAAGGTAATTCACAAACGT-ATTACGAATTACTTAGGTTGCACACATAATACCAATA
* * *
2069487 TAGTAATTCACAAACTCATTGTGAATTACGTGGGTTGCACACAT
65 CAGTAATTCACAAACTCATTATGAATTACGTGAGTTGCACACAT
*
2069531 AGTGCCAATACGGTAA
1 AGTGCCAATAAGGTAA
2069547 ATGCAACATA
Statistics
Matches: 107, Mismatches: 15, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
106 1 0.01
107 79 0.74
108 27 0.25
ACGTcount: A:0.37, C:0.17, G:0.15, T:0.31
Consensus pattern (108 bp):
AGTGCCAATAAGGTAATTCACAAACGTATTACGAATTACTTAGGTTGCACACATAATACCAATAC
AGTAATTCACAAACTCATTATGAATTACGTGAGTTGCACACAT
Found at i:2073685 original size:54 final size:54
Alignment explanation
Indices: 2073621--2074069 Score: 557
Period size: 54 Copynumber: 8.4 Consensus size: 54
2073611 TTCTGTGATT
* * ** * * *
2073621 TTGCAGACATAGTGACGGTACGGTAATTCACAAACTCATTGTGAATTACGTGGG
1 TTGCACACATAGTGCCAATACGGTAATTCACAAACTCATTATGAATTACTTAGG
* *
2073675 TTGCACACATAGTGCCAATATGGTAATTCAAAAACTCATTATGAATTACTTAGG
1 TTGCACACATAGTGCCAATACGGTAATTCACAAACTCATTATGAATTACTTAGG
** * * *
2073729 TTGCACACATAGTGCCAATATTGTAATTCAAAAACTTATTATGAATTACTTAAG
1 TTGCACACATAGTGCCAATACGGTAATTCACAAACTCATTATGAATTACTTAGG
* *
2073783 TTGTACACATAGTGCCAATACGGTAATT----AAC-AATTATGAATTACTTAGG
1 TTGCACACATAGTGCCAATACGGTAATTCACAAACTCATTATGAATTACTTAGG
* * * *
2073832 TTGCACACATAGTACCAATACGGAAATTCACAAACTTATTATGAATTACATAGG
1 TTGCACACATAGTGCCAATACGGTAATTCACAAACTCATTATGAATTACTTAGG
* * *
2073886 TTGCACACATAGTGCCAATATGGTAATTCACAAACTTATAATGAATTACTTAGG
1 TTGCACACATAGTGCCAATACGGTAATTCACAAACTCATTATGAATTACTTAGG
* * * *
2073940 TTGCACACATAGTGACAATACAGTAATTAACAAACTCATTATGAATTACTTAGA
1 TTGCACACATAGTGCCAATACGGTAATTCACAAACTCATTATGAATTACTTAGG
* * * * * *
2073994 TTGCACACATAATGTCAATACGGTAATTCACAAACTCATTGTAAATTACGTGGG
1 TTGCACACATAGTGCCAATACGGTAATTCACAAACTCATTATGAATTACTTAGG
*
2074048 TTGCACACATGGTGCCAATACG
1 TTGCACACATAGTGCCAATACG
2074070 ATAAATGTAA
Statistics
Matches: 344, Mismatches: 46, Indels: 10
0.86 0.12 0.03
Matches are distributed among these distances:
49 41 0.12
50 3 0.01
53 3 0.01
54 297 0.86
ACGTcount: A:0.37, C:0.17, G:0.16, T:0.30
Consensus pattern (54 bp):
TTGCACACATAGTGCCAATACGGTAATTCACAAACTCATTATGAATTACTTAGG
Found at i:2073948 original size:157 final size:159
Alignment explanation
Indices: 2073621--2074067 Score: 565
Period size: 157 Copynumber: 2.8 Consensus size: 159
2073611 TTCTGTGATT
* ** * * * * *
2073621 TTGCAGACATAGTGACGGTACGGTAATTCACAAACTCATTGTGAATTACGTGGGTTGCACACATA
1 TTGCACACATAGTGACAATACAGTAATTAAC-AA--CATTATGAATTACTTAGGTTGCACACATA
* * * *
2073686 GTGCCAATATGGTAATTCAAAAACTCATTATGAATTACTTAGGTTGCACACATAGTGCCAATATT
63 GTGCCAATACGGTAATTCACAAACTCATTATGAATTACATAGGTTGCACACATAGTGCCAATATG
*
2073751 GTAATTCAAAAACTTATTATGAATTACTTAAG
128 GTAATTCAAAAACTTATAATGAATTACTTAAG
* * * *
2073783 TTGTACACATAGTGCCAATACGGTAATTAAC-A-ATTATGAATTACTTAGGTTGCACACATAGTA
1 TTGCACACATAGTGACAATACAGTAATTAACAACATTATGAATTACTTAGGTTGCACACATAGTG
* *
2073846 CCAATACGGAAATTCACAAACTTATTATGAATTACATAGGTTGCACACATAGTGCCAATATGGTA
66 CCAATACGGTAATTCACAAACTCATTATGAATTACATAGGTTGCACACATAGTGCCAATATGGTA
* *
2073911 ATTCACAAACTTATAATGAATTACTTAGG
131 ATTCAAAAACTTATAATGAATTACTTAAG
*
2073940 TTGCACACATAGTGACAATACAGTAATTAACAAACTCATTATGAATTACTTAGATTGCACACATA
1 TTGCACACATAGTGACAATACAGTAATTAAC-AA--CATTATGAATTACTTAGGTTGCACACATA
* * * * * * *
2074005 ATGTCAATACGGTAATTCACAAACTCATTGTAAATTACGTGGGTTGCACACATGGTGCCAATA
63 GTGCCAATACGGTAATTCACAAACTCATTATGAATTACATAGGTTGCACACATAGTGCCAATA
2074068 CGATAAATGT
Statistics
Matches: 247, Mismatches: 33, Indels: 10
0.85 0.11 0.03
Matches are distributed among these distances:
157 140 0.57
159 1 0.00
160 1 0.00
162 105 0.43
ACGTcount: A:0.37, C:0.17, G:0.16, T:0.30
Consensus pattern (159 bp):
TTGCACACATAGTGACAATACAGTAATTAACAACATTATGAATTACTTAGGTTGCACACATAGTG
CCAATACGGTAATTCACAAACTCATTATGAATTACATAGGTTGCACACATAGTGCCAATATGGTA
ATTCAAAAACTTATAATGAATTACTTAAG
Found at i:2073991 original size:211 final size:211
Alignment explanation
Indices: 2073639--2074026 Score: 600
Period size: 211 Copynumber: 1.8 Consensus size: 211
2073629 ATAGTGACGG
* * * *
2073639 TACGGTAATTCACAAACTCATTGTGAATTACGTGGGTTGCACACATAGTGCCAATATGGTAATTC
1 TACGGAAATTCACAAACTCATTATGAATTACATAGGTTGCACACATAGTGCCAATATGGTAATTC
* * ** *
2073704 AAAAACTCATTATGAATTACTTAGGTTGCACACATAGTGCCAATATTGTAATTCAAAAACTTATT
66 AAAAACTCATAATGAATTACTTAGGTTGCACACATAGTGACAATACAGTAATTCAAAAACTCATT
* *
2073769 ATGAATTACTTA-AGTTGTACACATAGTGCCAATACGGTAATTAACAATTATGAATTACTTAGGT
131 ATGAATTACTTAGA-TTGCACACATAATGCCAATACGGTAATTAACAATTATGAATTACTTAGGT
2073833 TGCACACATAGTACCAA
195 TGCACACATAGTACCAA
*
2073850 TACGGAAATTCACAAACTTATTATGAATTACATAGGTTGCACACATAGTGCCAATATGGTAATTC
1 TACGGAAATTCACAAACTCATTATGAATTACATAGGTTGCACACATAGTGCCAATATGGTAATTC
* *
2073915 ACAAACTTATAATGAATTACTTAGGTTGCACACATAGTGACAATACAGTAATT-AACAAACTCAT
66 AAAAACTCATAATGAATTACTTAGGTTGCACACATAGTGACAATACAGTAATTCAA-AAACTCAT
* *
2073979 TATGAATTACTTAGATTGCACACATAATGTCAATACGGTAATTCACAA
130 TATGAATTACTTAGATTGCACACATAATGCCAATACGGTAATTAACAA
2074027 ACTCATTGTA
Statistics
Matches: 159, Mismatches: 16, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
210 2 0.01
211 156 0.98
212 1 0.01
ACGTcount: A:0.38, C:0.17, G:0.14, T:0.31
Consensus pattern (211 bp):
TACGGAAATTCACAAACTCATTATGAATTACATAGGTTGCACACATAGTGCCAATATGGTAATTC
AAAAACTCATAATGAATTACTTAGGTTGCACACATAGTGACAATACAGTAATTCAAAAACTCATT
ATGAATTACTTAGATTGCACACATAATGCCAATACGGTAATTAACAATTATGAATTACTTAGGTT
GCACACATAGTACCAA
Found at i:2080297 original size:30 final size:30
Alignment explanation
Indices: 2080261--2080318 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
2080251 CAATATTGGA
*
2080261 ACTTGAATTATTAAGAAATATTTGCAAGTT
1 ACTTGAATTATTAAGAAAGATTTGCAAGTT
*
2080291 ACTTGAATTGTTAAGAAAGATTTGCAAG
1 ACTTGAATTATTAAGAAAGATTTGCAAG
2080319 CTAATTATAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.40, C:0.07, G:0.17, T:0.36
Consensus pattern (30 bp):
ACTTGAATTATTAAGAAAGATTTGCAAGTT
Found at i:2083049 original size:21 final size:21
Alignment explanation
Indices: 2083025--2083064 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2083015 CAATGGGATT
*
2083025 AGGATTAGGAATTGGATTTTG
1 AGGATTAGGAAGTGGATTTTG
*
2083046 AGGATTTGGAAGTGGATTT
1 AGGATTAGGAAGTGGATTT
2083065 GGTTGACGGT
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:0.28, C:0.00, G:0.35, T:0.38
Consensus pattern (21 bp):
AGGATTAGGAAGTGGATTTTG
Found at i:2083795 original size:23 final size:23
Alignment explanation
Indices: 2083766--2083826 Score: 122
Period size: 23 Copynumber: 2.7 Consensus size: 23
2083756 ACCCCTGTGG
2083766 GGGGAATCGGTTCCCCTTCAAAT
1 GGGGAATCGGTTCCCCTTCAAAT
2083789 GGGGAATCGGTTCCCCTTCAAAT
1 GGGGAATCGGTTCCCCTTCAAAT
2083812 GGGGAATCGGTTCCC
1 GGGGAATCGGTTCCC
2083827 TCATGAGGGG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.20, C:0.26, G:0.30, T:0.25
Consensus pattern (23 bp):
GGGGAATCGGTTCCCCTTCAAAT
Found at i:2087697 original size:22 final size:21
Alignment explanation
Indices: 2087655--2087694 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
2087645 GAGCTTATTT
*
2087655 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
2087676 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
2087695 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:2094308 original size:19 final size:18
Alignment explanation
Indices: 2094275--2094310 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
2094265 AAAATGATTA
*
2094275 TAAAAATGAATATGAAAG
1 TAAAAATGAAAATGAAAG
2094293 TAAAAGATGAAAATGAAA
1 TAAAA-ATGAAAATGAAA
2094311 AATAAAAGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.64, C:0.00, G:0.17, T:0.19
Consensus pattern (18 bp):
TAAAAATGAAAATGAAAG
Found at i:2099834 original size:25 final size:25
Alignment explanation
Indices: 2099803--2099852 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
2099793 CGAGTACATT
* *
2099803 ATGAAAGGCACCGTTGGTGCAAATG
1 ATGAAAGACACCATTGGTGCAAATG
2099828 ATGAAAGACACCATTGGTGCAAATG
1 ATGAAAGACACCATTGGTGCAAATG
2099853 TTATCAATGC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.36, C:0.16, G:0.28, T:0.20
Consensus pattern (25 bp):
ATGAAAGACACCATTGGTGCAAATG
Found at i:2100002 original size:38 final size:38
Alignment explanation
Indices: 2099960--2100049 Score: 121
Period size: 38 Copynumber: 2.4 Consensus size: 38
2099950 TAAATTGGGC
*
2099960 TATGAATAT-GAAATTAAGTTGTAAATCTGAAAATAAAT
1 TATGAATATGGAAA-TAAGTTCTAAATCTGAAAATAAAT
*
2099998 TATGAATATGGAAATAAGTTCTAAATCTGAAAATGAAT
1 TATGAATATGGAAATAAGTTCTAAATCTGAAAATAAAT
*
2100036 TCTGAA-ATGTGAAA
1 TATGAATATG-GAAA
2100050 GTATTTGTTA
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
37 3 0.06
38 40 0.85
39 4 0.09
ACGTcount: A:0.48, C:0.04, G:0.16, T:0.32
Consensus pattern (38 bp):
TATGAATATGGAAATAAGTTCTAAATCTGAAAATAAAT
Found at i:2100031 original size:19 final size:19
Alignment explanation
Indices: 2099968--2100049 Score: 67
Period size: 19 Copynumber: 4.3 Consensus size: 19
2099958 GCTATGAATA
* *
2099968 TGAAATTAAGTTGTAAATC
1 TGAAAATAAGTTCTAAATC
* * * *
2099987 TGAAAATAAATTATGAATA
1 TGAAAATAAGTTCTAAATC
*
2100006 TGGAAATAAGTTCTAAATC
1 TGAAAATAAGTTCTAAATC
*
2100025 TGAAAATGAA-TTCTGAAATG
1 TGAAAAT-AAGTTCT-AAATC
2100045 TGAAA
1 TGAAA
2100050 GTATTTGTTA
Statistics
Matches: 49, Mismatches: 12, Indels: 3
0.77 0.19 0.05
Matches are distributed among these distances:
19 38 0.78
20 11 0.22
ACGTcount: A:0.48, C:0.05, G:0.16, T:0.32
Consensus pattern (19 bp):
TGAAAATAAGTTCTAAATC
Found at i:2100078 original size:13 final size:13
Alignment explanation
Indices: 2100060--2100115 Score: 55
Period size: 13 Copynumber: 4.4 Consensus size: 13
2100050 GTATTTGTTA
2100060 TGAAAATGAAATG
1 TGAAAATGAAATG
2100073 TGAAAATGAATATG
1 TGAAAATGAA-ATG
* *
2100087 -G-AAGT-AAAAG
1 TGAAAATGAAATG
2100097 TTGAAAATGAAATG
1 -TGAAAATGAAATG
2100111 TGAAA
1 TGAAA
2100116 TTTCTAAAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
10 2 0.06
11 2 0.06
12 4 0.12
13 19 0.56
14 7 0.21
ACGTcount: A:0.54, C:0.00, G:0.23, T:0.23
Consensus pattern (13 bp):
TGAAAATGAAATG
Found at i:2105536 original size:18 final size:18
Alignment explanation
Indices: 2105513--2105582 Score: 59
Period size: 18 Copynumber: 3.7 Consensus size: 18
2105503 GTAAAAATGA
2105513 TATCGATACCCAGGGGAG
1 TATCGATACCCAGGGGAG
* *
2105531 TATCGATACCAAAGAGGATGTG
1 TATCGATACC-CAG-GG--GAG
* *
2105553 TATCAATACCCAGGTGAG
1 TATCGATACCCAGGGGAG
*
2105571 TATCGATGCCCA
1 TATCGATACCCA
2105583 CGTTAAAACA
Statistics
Matches: 40, Mismatches: 8, Indels: 8
0.71 0.14 0.14
Matches are distributed among these distances:
18 22 0.55
19 2 0.05
20 3 0.08
21 2 0.05
22 11 0.28
ACGTcount: A:0.31, C:0.21, G:0.26, T:0.21
Consensus pattern (18 bp):
TATCGATACCCAGGGGAG
Found at i:2119843 original size:2 final size:2
Alignment explanation
Indices: 2119836--2119878 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
2119826 CCAAATAAAC
2119836 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
2119878 A
1 A
2119879 CATAAAACAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2121562 original size:50 final size:50
Alignment explanation
Indices: 2121503--2121602 Score: 200
Period size: 50 Copynumber: 2.0 Consensus size: 50
2121493 TGACATGGAC
2121503 AAAAATTCTCAAATCAAATGAACCATATTATTTTTCCATCGTTTTAAAAT
1 AAAAATTCTCAAATCAAATGAACCATATTATTTTTCCATCGTTTTAAAAT
2121553 AAAAATTCTCAAATCAAATGAACCATATTATTTTTCCATCGTTTTAAAAT
1 AAAAATTCTCAAATCAAATGAACCATATTATTTTTCCATCGTTTTAAAAT
2121603 GTGGAAATAA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.42, C:0.16, G:0.04, T:0.38
Consensus pattern (50 bp):
AAAAATTCTCAAATCAAATGAACCATATTATTTTTCCATCGTTTTAAAAT
Found at i:2124451 original size:23 final size:23
Alignment explanation
Indices: 2124421--2124474 Score: 99
Period size: 23 Copynumber: 2.3 Consensus size: 23
2124411 CTCGAGGCTA
2124421 CGGGGCCTACCCAAGAAAGATCT
1 CGGGGCCTACCCAAGAAAGATCT
2124444 CGGGGCCTACCCAAGAAAGATCT
1 CGGGGCCTACCCAAGAAAGATCT
*
2124467 CGGAGCCT
1 CGGGGCCT
2124475 CGGAGCCTAC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.28, C:0.31, G:0.28, T:0.13
Consensus pattern (23 bp):
CGGGGCCTACCCAAGAAAGATCT
Found at i:2126903 original size:13 final size:13
Alignment explanation
Indices: 2126885--2126911 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2126875 TAACTTTGAG
2126885 GTCAAAGTCAACT
1 GTCAAAGTCAACT
2126898 GTCAAAGTCAACT
1 GTCAAAGTCAACT
2126911 G
1 G
2126912 GTTGACTCGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.22, G:0.19, T:0.22
Consensus pattern (13 bp):
GTCAAAGTCAACT
Found at i:2129053 original size:31 final size:31
Alignment explanation
Indices: 2128980--2129055 Score: 84
Period size: 31 Copynumber: 2.4 Consensus size: 31
2128970 TTGGGGCCCG
*
2128980 AGAGCCTACCCAAGAAAGTTACTCGAGGCCA
1 AGAGCCTACCCAAGAAAGATACTCGAGGCCA
* *
2129011 AGGGGCCTACCCAAGAAAGAT-CTC-AGGGCCTT
1 A-GAGCCTACCCAAGAAAGATACTCGA-GGCC-A
2129043 AGAGCCTACCCAA
1 AGAGCCTACCCAA
2129056 TGATCACCTT
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
30 1 0.03
31 19 0.50
32 18 0.47
ACGTcount: A:0.33, C:0.30, G:0.24, T:0.13
Consensus pattern (31 bp):
AGAGCCTACCCAAGAAAGATACTCGAGGCCA
Found at i:2136045 original size:137 final size:133
Alignment explanation
Indices: 2135809--2136177 Score: 316
Period size: 137 Copynumber: 2.7 Consensus size: 133
2135799 AAATTTTTTT
** * * ** * * ** *
2135809 ACTGGAAAATAGCTCCTCACTATTGAGTTAAGCTAGATTGTATACAACTCCTCCACCATGATTTA
1 ACTGGAAAATAGCTCCTCGTTGTTGAGTTGAGCTAGATTACAAACGACTCCTCCATTATGAGTTA
* * * * * *
2135874 AGTTGACTTTGGAATTGCTTTTGGATCCAATATCCTTCGTT-GTGAAGTTGAGA-TCGCTCTTCA
66 AGTCGA-TTTTGAATTG-TTTTCGATCCAATATCCTT-GTTCATGAAGATGAAACTCG-TC-TCA
**
2135937 TAAACTTTA
126 -AAAAATTA
* * *
2135946 ATTGGAAAATAGCTCCTCGTTGTTGAGTTGAGCTAGATCACAGACGACTCCTCCATTATGAGTTA
1 ACTGGAAAATAGCTCCTCGTTGTTGAGTTGAGCTAGATTACAAACGACTCCTCCATTATGAGTTA
* *
2136011 AGTCGATTTTGAATGTGTTTTCGAGT-CAAGTATCCTTTTTCATGAAGATGAAACTTGTCTCAAA
66 AGTCGATTTTGAAT-TGTTTTCGA-TCCAA-TATCCTTGTTCATGAAGATGAAACTCGTCTCAAA
2136075 AAATTA
128 AAATTA
** * * *
2136081 ACTGGAAGCTAGCTCCTCGTTGTTGAGCTGAGCTAGATTACAAATGACTCCCCCAATTCAT--GT
1 ACTGGAAAATAGCTCCTCGTTGTTGAGTTGAGCTAGATTACAAACGACTCCTCC-ATT-ATGAGT
* *
2136144 TAAGTCAATTTTGAATTGCTTTCGAATCCAATAT
64 TAAGTCGATTTTGAATTGTTTTCG-ATCCAATAT
2136178 TCTCCATTGT
Statistics
Matches: 190, Mismatches: 33, Indels: 21
0.78 0.14 0.09
Matches are distributed among these distances:
134 11 0.06
135 73 0.38
136 24 0.13
137 80 0.42
138 2 0.01
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.35
Consensus pattern (133 bp):
ACTGGAAAATAGCTCCTCGTTGTTGAGTTGAGCTAGATTACAAACGACTCCTCCATTATGAGTTA
AGTCGATTTTGAATTGTTTTCGATCCAATATCCTTGTTCATGAAGATGAAACTCGTCTCAAAAAA
TTA
Found at i:2147256 original size:12 final size:12
Alignment explanation
Indices: 2147214--2147255 Score: 52
Period size: 12 Copynumber: 3.5 Consensus size: 12
2147204 ATTTAATTTA
2147214 TTTTATGTTGTT
1 TTTTATGTTGTT
2147226 TTTTACTGTT-TT
1 TTTTA-TGTTGTT
2147238 TTTTAT-TTGTT
1 TTTTATGTTGTT
2147249 ATTTTAT
1 -TTTTAT
2147256 TCTTTTTAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
10 2 0.07
11 3 0.11
12 18 0.67
13 4 0.15
ACGTcount: A:0.12, C:0.02, G:0.10, T:0.76
Consensus pattern (12 bp):
TTTTATGTTGTT
Found at i:2147261 original size:24 final size:24
Alignment explanation
Indices: 2147214--2147262 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
2147204 ATTTAATTTA
*
2147214 TTTTATGTTGTTTTTTACTGTTTT
1 TTTTATGTTGTTTTTTACTCTTTT
*
2147238 TTTTAT-TTGTTATTTTATTCTTTT
1 TTTTATGTTGTT-TTTTACTCTTTT
2147262 T
1 T
2147263 AATTAGGTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 5 0.23
24 17 0.77
ACGTcount: A:0.10, C:0.04, G:0.08, T:0.78
Consensus pattern (24 bp):
TTTTATGTTGTTTTTTACTCTTTT
Found at i:2149165 original size:28 final size:31
Alignment explanation
Indices: 2149129--2149185 Score: 84
Period size: 28 Copynumber: 1.9 Consensus size: 31
2149119 TGACTAATCA
2149129 TTTCAACTAAC-TTGA-TTC-TTTTGTCTTC
1 TTTCAACTAACATTGATTTCATTTTGTCTTC
*
2149157 TTTCTACTAACATTGATTTCATTTTGTCT
1 TTTCAACTAACATTGATTTCATTTTGTCT
2149186 GGTCTTGTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 10 0.40
29 4 0.16
30 3 0.12
31 8 0.32
ACGTcount: A:0.19, C:0.19, G:0.07, T:0.54
Consensus pattern (31 bp):
TTTCAACTAACATTGATTTCATTTTGTCTTC
Found at i:2152073 original size:36 final size:36
Alignment explanation
Indices: 2152033--2152148 Score: 117
Period size: 36 Copynumber: 3.1 Consensus size: 36
2152023 ACTACAAACT
2152033 GTTTTTCTTAAAACAAGATTCATCTCGCTTGAGATA
1 GTTTTTCTTAAAACAAGATTCATCTCGCTTGAGATA
** * * **
2152069 GTTTTTACTCGAAACAAGACATTTCATTTCACTACAGATTA
1 GTTTTT-CTTAAAACAAG--A-TTCATCTCGCTTGAGA-TA
*
2152110 -TTTTTCTTAAAACAAGATTCATCTCGCCTGAGATA
1 GTTTTTCTTAAAACAAGATTCATCTCGCTTGAGATA
2152145 GTTT
1 GTTT
2152149 CACTCGAAAC
Statistics
Matches: 61, Mismatches: 13, Indels: 12
0.71 0.15 0.14
Matches are distributed among these distances:
35 2 0.03
36 20 0.33
37 10 0.16
39 10 0.16
40 17 0.28
41 2 0.03
ACGTcount: A:0.31, C:0.18, G:0.12, T:0.39
Consensus pattern (36 bp):
GTTTTTCTTAAAACAAGATTCATCTCGCTTGAGATA
Found at i:2152135 original size:76 final size:76
Alignment explanation
Indices: 2151952--2152159 Score: 294
Period size: 76 Copynumber: 2.8 Consensus size: 76
2151942 ATCTCACTTT
** * * * *
2151952 AGATTATTTTTCTTAAAACAA-ACTTTGTCTCACTTGAGACAATTTTTACTCAAAACAAGACATT
1 AGATTATTTTTCTTAAAACAAGA-TTCATCTCGCTTGAGATAGTTTTTACTCGAAACAAGACATT
2152016 TCATTTCACTAC
65 TCATTTCACTAC
* * *
2152028 AAACTGTTTTTCTTAAAACAAGATTCATCTCGCTTGAGATAGTTTTTACTCGAAACAAGACATTT
1 AGATTATTTTTCTTAAAACAAGATTCATCTCGCTTGAGATAGTTTTTACTCGAAACAAGACATTT
2152093 CATTTCACTAC
66 CATTTCACTAC
* *
2152104 AGATTATTTTTCTTAAAACAAGATTCATCTCGCCTGAGATAG-TTTCACTCGAAACA
1 AGATTATTTTTCTTAAAACAAGATTCATCTCGCTTGAGATAGTTTTTACTCGAAACA
2152160 GAAGATTTAT
Statistics
Matches: 117, Mismatches: 14, Indels: 3
0.87 0.10 0.02
Matches are distributed among these distances:
75 13 0.11
76 103 0.88
77 1 0.01
ACGTcount: A:0.34, C:0.20, G:0.10, T:0.37
Consensus pattern (76 bp):
AGATTATTTTTCTTAAAACAAGATTCATCTCGCTTGAGATAGTTTTTACTCGAAACAAGACATTT
CATTTCACTAC
Found at i:2152219 original size:39 final size:39
Alignment explanation
Indices: 2152130--2152493 Score: 511
Period size: 39 Copynumber: 9.4 Consensus size: 39
2152120 AACAAGATTC
*
2152130 ATCTCGCCTGAGATAGTTTCACTCGAAACAGAAGA-TTT
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTT
* * *
2152168 ATATCACTTGAGAGT-GTTTCACTCGAAACAAAAGATTTT
1 ATCTCGCTTGAGA-TAGTTTCACTCGAAACAGAAGATTTT
*
2152207 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAATATTTT
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTT
* * *
2152246 ATCTCACTTGAGATATTTTCACTCGAAACAAAAGATTTT
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTT
* *
2152285 ATCTCGCTTGAGATAGTTTCACTCAAAATAGAAGATTTT
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTT
*
2152324 ATCTCACTTGAGATAGTTTCACTCGAAACAGAAGATTTT
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTT
* *
2152363 ATTTTGCTTGAGATAGTTTCACTCGAAACAGAAGATTTT
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTT
*
2152402 ATCTTGCTTGAGATAGATTT-ACTCGAAACAGAAGATTTTT
1 ATCTCGCTTGAGATAG-TTTCACTCGAAACAGAAGA-TTTT
* *
2152442 ATCTCTCTTGAGATAGTTTCACTCGAAATAGAAGA-TTT
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTT
* *
2152480 ATTTCACTTGAGAT
1 ATCTCGCTTGAGAT
2152494 TTTTTTCTTA
Statistics
Matches: 291, Mismatches: 29, Indels: 12
0.88 0.09 0.04
Matches are distributed among these distances:
38 45 0.15
39 211 0.73
40 35 0.12
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (39 bp):
ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTT
Found at i:2152278 original size:78 final size:78
Alignment explanation
Indices: 2152054--2152498 Score: 521
Period size: 78 Copynumber: 5.7 Consensus size: 78
2152044 AACAAGATTC
* * * * ** *
2152054 ATCTCGCTTGAGATAGTTTTTACTCGAAACA-AGACATTTCATTTCACTACAGATTATTTT-TCT
1 ATCTCGCTTGAGATAG-TTTCACTCGAAACAGA-AGATTTTATCTCACTTGAGA-TATTTTCACT
* * *
2152117 -TAAA-ACAAGA-TTC
63 CGAAACAAAAGATTTT
* * *
2152130 ATCTCGCCTGAGATAGTTTCACTCGAAACAGAAGA-TTTATATCACTTGAGAGT-GTTTCACTCG
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTTATCTCACTTGAGA-TATTTTCACTCG
2152193 AAACAAAAGATTTT
65 AAACAAAAGATTTT
*
2152207 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAATATTTTATCTCACTTGAGATATTTTCACTCGA
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTTATCTCACTTGAGATATTTTCACTCGA
2152272 AACAAAAGATTTT
66 AACAAAAGATTTT
* * *
2152285 ATCTCGCTTGAGATAGTTTCACTCAAAATAGAAGATTTTATCTCACTTGAGATAGTTTCACTCGA
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTTATCTCACTTGAGATATTTTCACTCGA
*
2152350 AACAGAAGATTTT
66 AACAAAAGATTTT
* * ** *
2152363 ATTTTGCTTGAGATAGTTTCACTCGAAACAGAAGATTTTATCTTGCTTGAGATAGATTT-ACTCG
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTTATCTCACTTGAGATA-TTTTCACTCG
*
2152427 AAACAGAAGATTTTT
65 AAACAAAAGA-TTTT
* * * *
2152442 ATCTCTCTTGAGATAGTTTCACTCGAAATAGAAGA-TTTATTTCACTTGAGATTTTTT
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTTATCTCACTTGAGATATTTT
2152499 TCTTAAAACA
Statistics
Matches: 322, Mismatches: 38, Indels: 17
0.85 0.10 0.05
Matches are distributed among these distances:
73 3 0.01
74 15 0.05
75 18 0.06
76 21 0.07
77 39 0.12
78 188 0.58
79 38 0.12
ACGTcount: A:0.32, C:0.16, G:0.15, T:0.37
Consensus pattern (78 bp):
ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTTATCTCACTTGAGATATTTTCACTCGA
AACAAAAGATTTT
Found at i:2152696 original size:42 final size:41
Alignment explanation
Indices: 2152650--2152730 Score: 117
Period size: 42 Copynumber: 2.0 Consensus size: 41
2152640 TGGGCCATCA
* *
2152650 ATAAGTCTTTCAAGCATGATGCTTAAATCCTTCAGGTCATTT
1 ATAAGTCTTTCAAGCAAGATG-ATAAATCCTTCAGGTCATTT
* *
2152692 ATAAGTCTTTCAAGCAAGATGATAAGTCTTTCAGGTCAT
1 ATAAGTCTTTCAAGCAAGATGATAAATCCTTCAGGTCAT
2152731 CCATAAGACC
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
41 15 0.43
42 20 0.57
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.36
Consensus pattern (41 bp):
ATAAGTCTTTCAAGCAAGATGATAAATCCTTCAGGTCATTT
Found at i:2152737 original size:41 final size:42
Alignment explanation
Indices: 2152645--2152737 Score: 116
Period size: 42 Copynumber: 2.2 Consensus size: 42
2152635 TCCTTTGGGC
* *
2152645 CATCAATAAGTCTTTCAAGCATGATGCTTAAATCCTTCAGGT
1 CATCAATAAGTCTTTCAAGCAAGATGCATAAATCCTTCAGGT
** * *
2152687 CATTTATAAGTCTTTCAAGCAAGATG-ATAAGTCTTTCAGGT
1 CATCAATAAGTCTTTCAAGCAAGATGCATAAATCCTTCAGGT
*
2152728 CATCCATAAG
1 CATCAATAAG
2152738 ACCTTCGGGT
Statistics
Matches: 43, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
41 20 0.47
42 23 0.53
ACGTcount: A:0.32, C:0.19, G:0.15, T:0.33
Consensus pattern (42 bp):
CATCAATAAGTCTTTCAAGCAAGATGCATAAATCCTTCAGGT
Found at i:2157447 original size:19 final size:19
Alignment explanation
Indices: 2157404--2157483 Score: 79
Period size: 19 Copynumber: 4.2 Consensus size: 19
2157394 GTCTGACTCA
* * *
2157404 TGAATATGAAATTAAGTTG
1 TGAATATGAAAATAAATTC
* * *
2157423 TAAATATCAAAATAAATTA
1 TGAATATGAAAATAAATTC
* *
2157442 TGAATATGGAAATAAGTTC
1 TGAATATGAAAATAAATTC
*
2157461 TGAATCTGAAAATAAATTC
1 TGAATATGAAAATAAATTC
2157480 TGAA
1 TGAA
2157484 ATGTGAAAGT
Statistics
Matches: 48, Mismatches: 13, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
19 48 1.00
ACGTcount: A:0.49, C:0.05, G:0.14, T:0.33
Consensus pattern (19 bp):
TGAATATGAAAATAAATTC
Found at i:2157458 original size:38 final size:39
Alignment explanation
Indices: 2157403--2157491 Score: 103
Period size: 38 Copynumber: 2.3 Consensus size: 39
2157393 TGTCTGACTC
*
2157403 ATGAATAT-GAAATTAAGTTGTAAATATCAAAATAAATT
1 ATGAATATGGAAATTAAGTTCTAAATATCAAAATAAATT
* * *
2157441 ATGAATATGGAAA-TAAGTTCTGAATCTGAAAATAAATT
1 ATGAATATGGAAATTAAGTTCTAAATATCAAAATAAATT
*
2157479 CTGAA-ATGTGAAA
1 ATGAATATG-GAAA
2157492 GTACTAGTTA
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
37 3 0.07
38 37 0.84
39 4 0.09
ACGTcount: A:0.49, C:0.04, G:0.15, T:0.31
Consensus pattern (39 bp):
ATGAATATGGAAATTAAGTTCTAAATATCAAAATAAATT
Found at i:2157520 original size:13 final size:13
Alignment explanation
Indices: 2157500--2157569 Score: 72
Period size: 13 Copynumber: 5.5 Consensus size: 13
2157490 AAGTACTAGT
2157500 TATGAAAATGAAA
1 TATGAAAATGAAA
* *
2157513 TGTGAAAAT-AAT
1 TATGAAAATGAAA
*
2157525 TATAAAAATG-AA
1 TATGAAAATGAAA
* *
2157537 TATGAAAGTAAAA
1 TATGAAAATGAAA
*
2157550 GATGAAAATGAAA
1 TATGAAAATGAAA
2157563 TATGAAA
1 TATGAAA
2157570 GTTCTAGAAT
Statistics
Matches: 43, Mismatches: 12, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
12 17 0.40
13 26 0.60
ACGTcount: A:0.60, C:0.00, G:0.16, T:0.24
Consensus pattern (13 bp):
TATGAAAATGAAA
Found at i:2157533 original size:25 final size:27
Alignment explanation
Indices: 2157480--2157544 Score: 73
Period size: 25 Copynumber: 2.5 Consensus size: 27
2157470 AAATAAATTC
* *
2157480 TGAAATGTGAAAGTACTAGTTATGAAAA
1 TGAAATGTGAAAG-ACTAATTATAAAAA
2157508 TGAAATGTGAAA-A-TAATTATAAAAA
1 TGAAATGTGAAAGACTAATTATAAAAA
*
2157533 TG-AATATGAAAG
1 TGAAATGTGAAAG
2157545 TAAAAGATGA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
24 8 0.24
25 12 0.36
26 1 0.03
28 12 0.36
ACGTcount: A:0.52, C:0.02, G:0.18, T:0.28
Consensus pattern (27 bp):
TGAAATGTGAAAGACTAATTATAAAAA
Found at i:2157560 original size:19 final size:18
Alignment explanation
Indices: 2157527--2157562 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
2157517 AAAATAATTA
*
2157527 TAAAAATGAATATGAAAG
1 TAAAAATGAAAATGAAAG
2157545 TAAAAGATGAAAATGAAA
1 TAAAA-ATGAAAATGAAA
2157563 TATGAAAGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.64, C:0.00, G:0.17, T:0.19
Consensus pattern (18 bp):
TAAAAATGAAAATGAAAG
Found at i:2158385 original size:19 final size:19
Alignment explanation
Indices: 2158341--2158388 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
2158331 ATTGGTTATG
* *
2158341 AAAATGAAATGTGAAAATG
1 AAAATGAAATGTAAAAATA
*
2158360 AATATGAAA-GTAAAAGATA
1 AAAATGAAATGTAAAA-ATA
2158379 AAAATGAAAT
1 AAAATGAAAT
2158389 TTGAAATTTC
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
18 5 0.22
19 18 0.78
ACGTcount: A:0.62, C:0.00, G:0.17, T:0.21
Consensus pattern (19 bp):
AAAATGAAATGTAAAAATA
Found at i:2160050 original size:18 final size:19
Alignment explanation
Indices: 2160015--2160051 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
2160005 ATAAAAAATT
2160015 AGTATCGATACTCCCATGTG
1 AGTATCGATAC-CCCATGTG
2160035 AGTATCGATA-CCCATGT
1 AGTATCGATACCCCATGT
2160052 TAAATCTTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.30
Consensus pattern (19 bp):
AGTATCGATACCCCATGTG
Found at i:2161320 original size:19 final size:19
Alignment explanation
Indices: 2161296--2161333 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
2161286 CTTAAGCTAT
2161296 TTGTTATCCTCAAGAAATG
1 TTGTTATCCTCAAGAAATG
2161315 TTGTTATCCTCAAGAAATG
1 TTGTTATCCTCAAGAAATG
2161334 GATTGTGATC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.37
Consensus pattern (19 bp):
TTGTTATCCTCAAGAAATG
Found at i:2162346 original size:44 final size:44
Alignment explanation
Indices: 2162274--2162423 Score: 230
Period size: 44 Copynumber: 3.4 Consensus size: 44
2162264 TATAAAATCT
*
2162274 TTACCATTTATCCAACAAGCTCGTAAGCTTATTTTACCAATATAC
1 TTACCATTTATCC-ATAAGCTCGTAAGCTTATTTTACCAATATAC
*
2162319 TTACCATTTATCCGTAAGCTCGTAAGCTTATTTTACCAATATAC
1 TTACCATTTATCCATAAGCTCGTAAGCTTATTTTACCAATATAC
* *
2162363 TTACCATTTATCCATAAGCTTGTAAGCTTATTTTACCAATACAC
1 TTACCATTTATCCATAAGCTCGTAAGCTTATTTTACCAATATAC
*
2162407 TTGCCA-TTATTCCATAA
1 TTACCATTTA-TCCATAA
2162424 CCATATACCA
Statistics
Matches: 98, Mismatches: 6, Indels: 3
0.92 0.06 0.03
Matches are distributed among these distances:
43 3 0.03
44 82 0.84
45 13 0.13
ACGTcount: A:0.31, C:0.23, G:0.07, T:0.38
Consensus pattern (44 bp):
TTACCATTTATCCATAAGCTCGTAAGCTTATTTTACCAATATAC
Found at i:2168789 original size:81 final size:81
Alignment explanation
Indices: 2168293--2168773 Score: 694
Period size: 81 Copynumber: 5.9 Consensus size: 81
2168283 TTTTAAAATG
* * * * *
2168293 AAAGATTAAA-AGACTAATTGTGCATTTGGCAGAAAAGTGTCAATCATACAAGTTAGATGAAAGG
1 AAAGATTAAACA-CCTAACTGTGCATTTGGCAGAAAGGTGCCAATCATGCAAGTTAGATGAAAGG
2168357 TTAAATGCCTTTGGGTA
65 TTAAATGCCTTTGGGTA
* * * * * * *
2168374 AAATATTAAACGCCTAACTTTGCATTTGGTAGAAAGGTGCCAATCTTGCTAGTTAGATGAAATGT
1 AAAGATTAAACACCTAACTGTGCATTTGGCAGAAAGGTGCCAATCATGCAAGTTAGATGAAAGGT
2168439 TAAATGCCTTTGGGTA
66 TAAATGCCTTTGGGTA
* * *
2168455 AAAGATTAAACACCTAACTGTGCATTTGGCAGAAAGGTGCCAATCTTGCAAGTTAGTTGAAACGT
1 AAAGATTAAACACCTAACTGTGCATTTGGCAGAAAGGTGCCAATCATGCAAGTTAGATGAAAGGT
2168520 TAAATGCCTTTGGGTA
66 TAAATGCCTTTGGGTA
* *
2168536 AAAGATTAAACACCTAACTGTGCATTTGGTAGAAATGTGCCAATCATGCAAGTTAGATGAAAGGT
1 AAAGATTAAACACCTAACTGTGCATTTGGCAGAAAGGTGCCAATCATGCAAGTTAGATGAAAGGT
*
2168601 TAAATGTCTTTGGGTA
66 TAAATGCCTTTGGGTA
* * * *
2168617 AAAGATTAAACGCCTAACTGTGCATTTGGCAGAAAGGTACCAATCTTGAAAGTTAGATGAAAGGT
1 AAAGATTAAACACCTAACTGTGCATTTGGCAGAAAGGTGCCAATCATGCAAGTTAGATGAAAGGT
2168682 TAAATGCCTTTGGGTA
66 TAAATGCCTTTGGGTA
* * * * * *
2168698 AAAGGTTAAATATCTAACTGTGCATTTGGCAAAAAGGTTCCAATAATGCAAGTTAGATGAAAGGT
1 AAAGATTAAACACCTAACTGTGCATTTGGCAGAAAGGTGCCAATCATGCAAGTTAGATGAAAGGT
2168763 TAAATGCCTTT
66 TAAATGCCTTT
2168774 AGAGAAAAGA
Statistics
Matches: 358, Mismatches: 41, Indels: 2
0.89 0.10 0.00
Matches are distributed among these distances:
81 358 1.00
ACGTcount: A:0.36, C:0.13, G:0.22, T:0.30
Consensus pattern (81 bp):
AAAGATTAAACACCTAACTGTGCATTTGGCAGAAAGGTGCCAATCATGCAAGTTAGATGAAAGGT
TAAATGCCTTTGGGTA
Found at i:2178670 original size:13 final size:13
Alignment explanation
Indices: 2178652--2178677 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2178642 ATTATCAAAG
2178652 ATATCAATATATC
1 ATATCAATATATC
2178665 ATATCAATATATC
1 ATATCAATATATC
2178678 CAACTTTTCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.15, G:0.00, T:0.38
Consensus pattern (13 bp):
ATATCAATATATC
Found at i:2179369 original size:2 final size:2
Alignment explanation
Indices: 2179362--2179389 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2179352 TACGAAATAA
2179362 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
2179390 TCATAAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2188533 original size:35 final size:36
Alignment explanation
Indices: 2188492--2188592 Score: 100
Period size: 35 Copynumber: 2.9 Consensus size: 36
2188482 TTGTTAAATT
2188492 TGTTTTTGAATTATCTATGAGATGTCTGAACCATA-A
1 TGTTTTTGAATTATCTATGAGATGTCTGAACCA-ACA
* * * *
2188528 T-TTTTTTAATTATCTATAAGATTTCGGAA-CAACA
1 TGTTTTTGAATTATCTATGAGATGTCTGAACCAACA
* * * *
2188562 TGTTTCTGAAATAACTGTGAGATGTCTGAAC
1 TGTTTTTGAATTATCTATGAGATGTCTGAAC
2188593 TATGATCGTT
Statistics
Matches: 50, Mismatches: 12, Indels: 6
0.74 0.18 0.09
Matches are distributed among these distances:
33 1 0.02
34 4 0.08
35 44 0.88
36 1 0.02
ACGTcount: A:0.32, C:0.12, G:0.16, T:0.41
Consensus pattern (36 bp):
TGTTTTTGAATTATCTATGAGATGTCTGAACCAACA
Found at i:2190895 original size:30 final size:30
Alignment explanation
Indices: 2190826--2190884 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
2190816 AATTTAAGGC
2190826 AAAATGTTTTTGGACTTGAATTGAATTTAA
1 AAAATGTTTTTGGACTTGAATTGAATTTAA
*
2190856 AAAATGTTTTTGGATTTGAATTGAATTTA
1 AAAATGTTTTTGGACTTGAATTGAATTTA
2190885 TTCAAAGTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.36, C:0.02, G:0.17, T:0.46
Consensus pattern (30 bp):
AAAATGTTTTTGGACTTGAATTGAATTTAA
Found at i:2191032 original size:20 final size:19
Alignment explanation
Indices: 2191007--2191096 Score: 66
Period size: 20 Copynumber: 4.8 Consensus size: 19
2190997 CATCTGCACT
2191007 AATGCATCGATGCATCAGGC
1 AATGCATCGATGCATCA-GC
*
2191027 AATGCATCCATGCATC--C
1 AATGCATCGATGCATCAGC
* *
2191044 AA-ACATCGAATGCAATTAG-
1 AATGCATCG-ATGC-ATCAGC
2191063 --TGCATCGATGCATCAGGC
1 AATGCATCGATGCATCA-GC
*
2191081 AATGCATCCATGCATC
1 AATGCATCGATGCATC
2191097 CAAACATCGA
Statistics
Matches: 54, Mismatches: 7, Indels: 18
0.68 0.09 0.23
Matches are distributed among these distances:
16 7 0.13
17 12 0.22
18 7 0.13
20 28 0.52
ACGTcount: A:0.32, C:0.27, G:0.19, T:0.22
Consensus pattern (19 bp):
AATGCATCGATGCATCAGC
Found at i:2191070 original size:54 final size:54
Alignment explanation
Indices: 2191009--2191152 Score: 243
Period size: 54 Copynumber: 2.6 Consensus size: 54
2190999 TCTGCACTAA
2191009 TGCATCGATGCATCAGGCAATGCATCCATGCATCCAAACATCGAATGCAATTAG
1 TGCATCGATGCATCAGGCAATGCATCCATGCATCCAAACATCGAATGCAATTAG
2191063 TGCATCGATGCATCAGGCAATGCATCCATGCATCCAAACATCGAATGCAATTAG
1 TGCATCGATGCATCAGGCAATGCATCCATGCATCCAAACATCGAATGCAATTAG
* ** *
2191117 TGCATCGATGCCTCCTTGCCATGCATCCATGCATCC
1 TGCATCGATGCAT-CAGGCAATGCATCCATGCATCC
2191153 TTGCCATGCA
Statistics
Matches: 85, Mismatches: 4, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
54 66 0.78
55 19 0.22
ACGTcount: A:0.29, C:0.29, G:0.18, T:0.24
Consensus pattern (54 bp):
TGCATCGATGCATCAGGCAATGCATCCATGCATCCAAACATCGAATGCAATTAG
Found at i:2191143 original size:21 final size:21
Alignment explanation
Indices: 2191117--2191192 Score: 118
Period size: 21 Copynumber: 3.7 Consensus size: 21
2191107 ATGCAATTAG
* *
2191117 TGCATCGATGCCTCCTTGCCA
1 TGCATCCATGCATCCTTGCCA
2191138 TGCATCCATGCATCCTTGCCA
1 TGCATCCATGCATCCTTGCCA
*
2191159 TGCATCGATGCATCCTT-CCA
1 TGCATCCATGCATCCTTGCCA
2191179 TGCATCCATGCATC
1 TGCATCCATGCATC
2191193 AAGGCTGCAA
Statistics
Matches: 51, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
20 16 0.31
21 35 0.69
ACGTcount: A:0.18, C:0.37, G:0.16, T:0.29
Consensus pattern (21 bp):
TGCATCCATGCATCCTTGCCA
Found at i:2191585 original size:34 final size:32
Alignment explanation
Indices: 2191546--2191615 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 32
2191536 TTTTGTAAAG
*
2191546 GGGAAAGGTTCTAGCTTAGCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
*
2191580 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
2191612 GGGA
1 GGGA
2191616 GTTGTAAGGT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 11 0.32
33 1 0.03
34 22 0.65
ACGTcount: A:0.31, C:0.16, G:0.31, T:0.21
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:2192499 original size:19 final size:20
Alignment explanation
Indices: 2192475--2192522 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
2192465 AATGATTTTC
*
2192475 TTTTGAAAACAAAAAT-AGA
1 TTTTGAAAACAAAAATGAAA
* *
2192494 TTTTGAAAGCCAAAATGAAA
1 TTTTGAAAACAAAAATGAAA
2192514 TTTTGAAAA
1 TTTTGAAAA
2192523 AGGATTTAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.52, C:0.06, G:0.12, T:0.29
Consensus pattern (20 bp):
TTTTGAAAACAAAAATGAAA
Found at i:2193686 original size:21 final size:21
Alignment explanation
Indices: 2193660--2193699 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
2193650 CAACAATTGG
2193660 TAACAATTGATATCATTTTGT
1 TAACAATTGATATCATTTTGT
*
2193681 TAACAATTGATATCTTTTT
1 TAACAATTGATATCATTTT
2193700 CATTAAACAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.10, G:0.07, T:0.50
Consensus pattern (21 bp):
TAACAATTGATATCATTTTGT
Found at i:2193880 original size:30 final size:30
Alignment explanation
Indices: 2193809--2193868 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
2193799 ACAATTTATG
2193809 GCAAAATGTTTTTGGACTTGAATTGAATTT
1 GCAAAATGTTTTTGGACTTGAATTGAATTT
*
2193839 GCAAAATGTTTTTGGATTTGAATTGAATTT
1 GCAAAATGTTTTTGGACTTGAATTGAATTT
2193869 ATTCAAAGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.30, C:0.05, G:0.20, T:0.45
Consensus pattern (30 bp):
GCAAAATGTTTTTGGACTTGAATTGAATTT
Found at i:2197006 original size:25 final size:26
Alignment explanation
Indices: 2196978--2197028 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
2196968 CAAAACACAA
2196978 TAATTT-GAAAA-TTAACATTTTTTTT
1 TAATTTCGAAAATTTAA-ATTTTTTTT
2197003 TAATTTCGAAAATTTAAATTTTTTTT
1 TAATTTCGAAAATTTAAATTTTTTTT
2197029 GGAAAATTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
25 6 0.25
26 14 0.58
27 4 0.17
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.57
Consensus pattern (26 bp):
TAATTTCGAAAATTTAAATTTTTTTT
Found at i:2197238 original size:20 final size:20
Alignment explanation
Indices: 2197201--2197239 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2197191 AGATTGAGTG
* * *
2197201 GATTTTGATGTTGTTTGCAC
1 GATTTTAATGATGATTGCAC
2197221 GATTTTAATGATGATTGCA
1 GATTTTAATGATGATTGCA
2197240 TGTTTAGGAG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.23, C:0.08, G:0.23, T:0.46
Consensus pattern (20 bp):
GATTTTAATGATGATTGCAC
Found at i:2205149 original size:2 final size:2
Alignment explanation
Indices: 2205142--2205168 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2205132 ATTGTTAATG
2205142 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
2205169 GTTCACAGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2210792 original size:46 final size:46
Alignment explanation
Indices: 2210725--2210812 Score: 158
Period size: 46 Copynumber: 1.9 Consensus size: 46
2210715 ACCTCTAAGT
*
2210725 ATTTTCATTTGTGGCATCCTTTCATGCCAATTATGCACTGTTATAC
1 ATTTTCATTTATGGCATCCTTTCATGCCAATTATGCACTGTTATAC
*
2210771 ATTTTCATTTATGGCATCCTTTCATGCCAATTATGCATTGTT
1 ATTTTCATTTATGGCATCCTTTCATGCCAATTATGCACTGTT
2210813 CTTCATCTAA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 40 1.00
ACGTcount: A:0.22, C:0.20, G:0.12, T:0.45
Consensus pattern (46 bp):
ATTTTCATTTATGGCATCCTTTCATGCCAATTATGCACTGTTATAC
Found at i:2211169 original size:55 final size:55
Alignment explanation
Indices: 2211110--2211536 Score: 665
Period size: 56 Copynumber: 7.7 Consensus size: 55
2211100 ACCAATAGGA
*
2211110 AAATTCATAAACTGATTATGAATTTCTTAGTTTTGCACACAAAGTGCCCATACGG
1 AAATTCATAAACTCATTATGAATTTCTTAGTTTTGCACACAAAGTGCCCATACGG
* * * ** **
2211165 AAATTCATAAACTGATTATGAATTTCTTAACTTTTACACACAAAGTGCTTATACAA
1 AAATTCATAAACTCATTATGAATTTCTT-AGTTTTGCACACAAAGTGCCCATACGG
*
2211221 AAATTCATAAACTCATTATGAATTTCTTAGTTTTGCACACAAAGTGCCCATACGA
1 AAATTCATAAACTCATTATGAATTTCTTAGTTTTGCACACAAAGTGCCCATACGG
*
2211276 AAATTCATAAACTCAATATGAATTTCTTAGTTTTGCACACAAAGTGCCCATACGG
1 AAATTCATAAACTCATTATGAATTTCTTAGTTTTGCACACAAAGTGCCCATACGG
2211331 AAATTCATAAACTCATTATGAATTTCTTAGTTTTTGCACACAAAGTGCCCATACGG
1 AAATTCATAAACTCATTATGAATTTCTTAG-TTTTGCACACAAAGTGCCCATACGG
* * *
2211387 AAATTCATAAAATCATTATGAATTTCTTAGTTTTTGCACACAAAGTGCCTATACTG
1 AAATTCATAAACTCATTATGAATTTCTTAG-TTTTGCACACAAAGTGCCCATACGG
**
2211443 AAATTCATAAACTCATTATGAATTTCTTAGGTTTTGCACACAAAGTGCCCATACAA
1 AAATTCATAAACTCATTATGAATTTCTTA-GTTTTGCACACAAAGTGCCCATACGG
*
2211499 AAATTCATAAACTCATCATGAATTTCTTAGCTTTTGCA
1 AAATTCATAAACTCATTATGAATTTCTTAG-TTTTGCA
2211537 AATATTGTTC
Statistics
Matches: 345, Mismatches: 23, Indels: 7
0.92 0.06 0.02
Matches are distributed among these distances:
55 133 0.39
56 211 0.61
57 1 0.00
ACGTcount: A:0.36, C:0.19, G:0.11, T:0.34
Consensus pattern (55 bp):
AAATTCATAAACTCATTATGAATTTCTTAGTTTTGCACACAAAGTGCCCATACGG
Found at i:2211257 original size:111 final size:111
Alignment explanation
Indices: 2211109--2211536 Score: 660
Period size: 111 Copynumber: 3.8 Consensus size: 111
2211099 TACCAATAGG
* *
2211109 AAAATTCATAAACTGATTATGAATTTCTTAGTTTTGCACACAAAGTGCCCATACGGAAATTCATA
1 AAAATTCATAAACTCATTATGAATTTCTTAGTTTTGCACACAAAGTGCCCATACGAAAATTCATA
* * *
2211174 AACTGATTATGAATTTCTTAACTTTTACACACAAAGTGCTTATACA
66 AACTCATTATGAATTTCTTAACTTTTGCACACAAAGTGCCTATACA
2211220 AAAATTCATAAACTCATTATGAATTTCTTAGTTTTGCACACAAAGTGCCCATACGAAAATTCATA
1 AAAATTCATAAACTCATTATGAATTTCTTAGTTTTGCACACAAAGTGCCCATACGAAAATTCATA
* * * *
2211285 AACTCAATATGAATTTCTT-AGTTTTGCACACAAAGTGCCCATACG
66 AACTCATTATGAATTTCTTAACTTTTGCACACAAAGTGCCTATACA
* *
2211330 GAAATTCATAAACTCATTATGAATTTCTTAGTTTTTGCACACAAAGTGCCCATACGGAAATTCAT
1 AAAATTCATAAACTCATTATGAATTTCTTAG-TTTTGCACACAAAGTGCCCATACGAAAATTCAT
* ** *
2211395 AAAATCATTATGAATTTCTTAGTTTTTGCACACAAAGTGCCTATACT
65 AAACTCATTATGAATTTCTTAACTTTTGCACACAAAGTGCCTATACA
* *
2211442 GAAATTCATAAACTCATTATGAATTTCTTAGGTTTTGCACACAAAGTGCCCATACAAAAATTCAT
1 AAAATTCATAAACTCATTATGAATTTCTTA-GTTTTGCACACAAAGTGCCCATACGAAAATTCAT
* *
2211507 AAACTCATCATGAATTTCTTAGCTTTTGCA
65 AAACTCATTATGAATTTCTTAACTTTTGCA
2211537 AATATTGTTC
Statistics
Matches: 292, Mismatches: 22, Indels: 5
0.92 0.07 0.02
Matches are distributed among these distances:
110 51 0.17
111 130 0.45
112 110 0.38
113 1 0.00
ACGTcount: A:0.36, C:0.18, G:0.11, T:0.34
Consensus pattern (111 bp):
AAAATTCATAAACTCATTATGAATTTCTTAGTTTTGCACACAAAGTGCCCATACGAAAATTCATA
AACTCATTATGAATTTCTTAACTTTTGCACACAAAGTGCCTATACA
Found at i:2216476 original size:46 final size:46
Alignment explanation
Indices: 2216426--2216513 Score: 122
Period size: 46 Copynumber: 1.9 Consensus size: 46
2216416 ACCCGTATGT
* * *
2216426 ATTTTCATTTGTGGCATCCTTTTATACCAATTATGCACTGTTATAC
1 ATTTTCATTTATCGCATCCTTTCATACCAATTATGCACTGTTATAC
** *
2216472 ATTTTCATTTATCGCATCCTTTCATGTCAATTATGCATTGTT
1 ATTTTCATTTATCGCATCCTTTCATACCAATTATGCACTGTT
2216514 CTTTATCTAA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
46 36 1.00
ACGTcount: A:0.23, C:0.19, G:0.10, T:0.48
Consensus pattern (46 bp):
ATTTTCATTTATCGCATCCTTTCATACCAATTATGCACTGTTATAC
Found at i:2216913 original size:22 final size:22
Alignment explanation
Indices: 2216881--2216959 Score: 122
Period size: 22 Copynumber: 3.6 Consensus size: 22
2216871 CATAAAATCA
* * *
2216881 TGGTATTGATACTTCTATACTA
1 TGGTATCGATACTTCTATATTG
*
2216903 TGGAATCGATACTTCTATATTG
1 TGGTATCGATACTTCTATATTG
2216925 TGGTATCGATACTTCTATATTG
1 TGGTATCGATACTTCTATATTG
2216947 TGGTATCGATACT
1 TGGTATCGATACT
2216960 CCCTTACAGT
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 52 1.00
ACGTcount: A:0.25, C:0.14, G:0.18, T:0.43
Consensus pattern (22 bp):
TGGTATCGATACTTCTATATTG
Found at i:2219306 original size:23 final size:21
Alignment explanation
Indices: 2219240--2219400 Score: 119
Period size: 21 Copynumber: 7.5 Consensus size: 21
2219230 TAATTTTCAT
**
2219240 GAAGGACCACATATATGTCTT
1 GAAGGACCACATATATGTCCC
* * *
2219261 GAAGGACCACGAGGAAATATCCC
1 GAAGGACCAC-A-TATATGTCCC
2219284 GAAGGACCACATATAATTGTCCC
1 GAAGGACCACATAT-A-TGTCCC
* ** *
2219307 TAAGGATTACATATATGTTCC
1 GAAGGACCACATATATGTCCC
*
2219328 AAAGGACCA-ACTATATGTCCC
1 GAAGGACCACA-TATATGTCCC
* * *
2219349 GAAGGACCTCATATATATTCC
1 GAAGGACCACATATATGTCCC
* *
2219370 AAAGGATCACATATATGTCCC
1 GAAGGACCACATATATGTCCC
2219391 -AATGGACCAC
1 GAA-GGACCAC
2219401 GTAGAACCCT
Statistics
Matches: 107, Mismatches: 26, Indels: 14
0.73 0.18 0.10
Matches are distributed among these distances:
20 3 0.03
21 68 0.64
22 5 0.05
23 31 0.29
ACGTcount: A:0.36, C:0.24, G:0.17, T:0.23
Consensus pattern (21 bp):
GAAGGACCACATATATGTCCC
Found at i:2219354 original size:42 final size:42
Alignment explanation
Indices: 2219241--2219398 Score: 133
Period size: 42 Copynumber: 3.7 Consensus size: 42
2219231 AATTTTCATG
** * * * * *
2219241 AAGGACCACATATATGTCTTGAAGGACCACGAGGAAATATCCCG
1 AAGGACCACATATATGTCCCGAAGGACCTC-A-TATATATTCCA
* * *
2219285 AAGGACCACATATAATTGTCCCTAAGGA-TTACATATATGTTCCA
1 AAGGACCACATAT-A-TGTCCCGAAGGACCT-CATATATATTCCA
2219329 AAGGACCA-ACTATATGTCCCGAAGGACCTCATATATATTCCA
1 AAGGACCACA-TATATGTCCCGAAGGACCTCATATATATTCCA
*
2219371 AAGGATCACATATATGTCCC-AATGGACC
1 AAGGACCACATATATGTCCCGAA-GGACC
2219399 ACGTAGAACC
Statistics
Matches: 93, Mismatches: 14, Indels: 16
0.76 0.11 0.13
Matches are distributed among these distances:
41 2 0.02
42 45 0.48
43 4 0.04
44 30 0.32
45 2 0.02
46 10 0.11
ACGTcount: A:0.36, C:0.23, G:0.17, T:0.23
Consensus pattern (42 bp):
AAGGACCACATATATGTCCCGAAGGACCTCATATATATTCCA
Found at i:2223733 original size:25 final size:24
Alignment explanation
Indices: 2223705--2223758 Score: 65
Period size: 23 Copynumber: 2.2 Consensus size: 24
2223695 CACTGAGTGC
*
2223705 CATATAAAATTGTCCCGAAGAACCT
1 CATAT-AAATTGTCCCGAAGAACCA
* *
2223730 CATAT-AATTGTCCTGAAGGACCA
1 CATATAAATTGTCCCGAAGAACCA
2223753 CATATA
1 CATATA
2223759 TGTCCCAAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
23 20 0.80
25 5 0.20
ACGTcount: A:0.39, C:0.22, G:0.13, T:0.26
Consensus pattern (24 bp):
CATATAAATTGTCCCGAAGAACCA
Found at i:2223741 original size:23 final size:23
Alignment explanation
Indices: 2223712--2223825 Score: 72
Period size: 23 Copynumber: 5.0 Consensus size: 23
2223702 TGCCATATAA
*
2223712 AATTGTCCCGAAGAACCTCATAT
1 AATTGTCCCGAAGAACCACATAT
* *
2223735 AATTGTCCTGAAGGACCACATAT
1 AATTGTCCCGAAGAACCACATAT
* * * **
2223758 -A-TGTCCCAAAGGACCACGTGG
1 AATTGTCCCGAAGAACCACATAT
* * * *
2223779 AAATATCCCGAAGGACCACATAG
1 AATTGTCCCGAAGAACCACATAT
* *
2223802 AATTATCCC-AAAAGACCACATAT
1 AATTGTCCCGAAGA-ACCACATAT
2223825 A
1 A
2223826 TGTTCCAAAT
Statistics
Matches: 72, Mismatches: 16, Indels: 6
0.77 0.17 0.06
Matches are distributed among these distances:
21 15 0.21
22 4 0.06
23 53 0.74
ACGTcount: A:0.39, C:0.25, G:0.16, T:0.20
Consensus pattern (23 bp):
AATTGTCCCGAAGAACCACATAT
Found at i:2223769 original size:21 final size:21
Alignment explanation
Indices: 2223745--2223904 Score: 122
Period size: 21 Copynumber: 7.4 Consensus size: 21
2223735 AATTGTCCTG
2223745 AAGGACCACATATATGTCCCA
1 AAGGACCACATATATGTCCCA
* * * *
2223766 AAGGACCACGTGGAAATATCCCG
1 AAGGACCACAT--ATATGTCCCA
* *
2223789 AAGGACCACATAGAATTATCCCA
1 AAGGACCACATA-TA-TGTCCCA
* *
2223812 AAAGACCACATATATGTTCCA
1 AAGGACCACATATATGTCCCA
** * *
2223833 AATTACCAAATATATGTCCCG
1 AAGGACCACATATATGTCCCA
* *
2223854 AAGGACCTCATATATGTTCCA
1 AAGGACCACATATATGTCCCA
* * * *
2223875 AATGATCACATATATGTCTCG
1 AAGGACCACATATATGTCCCA
2223896 AAGGACCAC
1 AAGGACCAC
2223905 GTAGAACCCT
Statistics
Matches: 106, Mismatches: 29, Indels: 8
0.74 0.20 0.06
Matches are distributed among these distances:
21 69 0.65
22 3 0.03
23 34 0.32
ACGTcount: A:0.38, C:0.25, G:0.15, T:0.22
Consensus pattern (21 bp):
AAGGACCACATATATGTCCCA
Found at i:2223888 original size:42 final size:42
Alignment explanation
Indices: 2223815--2223904 Score: 135
Period size: 42 Copynumber: 2.1 Consensus size: 42
2223805 TATCCCAAAA
*
2223815 GACCACATATATGTTCCAAATTACCAAATATATGTCCCGAAG
1 GACCACATATATGTTCCAAATGACCAAATATATGTCCCGAAG
* * * *
2223857 GACCTCATATATGTTCCAAATGATCACATATATGTCTCGAAG
1 GACCACATATATGTTCCAAATGACCAAATATATGTCCCGAAG
2223899 GACCAC
1 GACCAC
2223905 GTAGAACCCT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.36, C:0.24, G:0.13, T:0.27
Consensus pattern (42 bp):
GACCACATATATGTTCCAAATGACCAAATATATGTCCCGAAG
Found at i:2224092 original size:23 final size:23
Alignment explanation
Indices: 2224066--2224109 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
2224056 ATCAGGTAGA
*
2224066 TCATATAACATTCTCATATATTC
1 TCATAGAACATTCTCATATATTC
**
2224089 TCATAGCTCATTCTCATATAT
1 TCATAGAACATTCTCATATAT
2224110 AGCATATCAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.32, C:0.23, G:0.02, T:0.43
Consensus pattern (23 bp):
TCATAGAACATTCTCATATATTC
Found at i:2229447 original size:40 final size:40
Alignment explanation
Indices: 2229403--2229483 Score: 101
Period size: 40 Copynumber: 2.0 Consensus size: 40
2229393 CTATGTGTAC
* *
2229403 TAGGTGGGTAAAT-CCCGACCTCAGCACTACGGTGCATTAT
1 TAGGTGAG-AAATGCCCGACCTCAGCACTACGGTGCAATAT
* * *
2229443 TAGGTGAGCAATGCTCGACCTCAGCACTTCGGTGCAATAT
1 TAGGTGAGAAATGCCCGACCTCAGCACTACGGTGCAATAT
2229483 T
1 T
2229484 TGACTCCTAT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
39 3 0.09
40 32 0.91
ACGTcount: A:0.25, C:0.25, G:0.25, T:0.26
Consensus pattern (40 bp):
TAGGTGAGAAATGCCCGACCTCAGCACTACGGTGCAATAT
Found at i:2229655 original size:45 final size:45
Alignment explanation
Indices: 2229564--2229765 Score: 334
Period size: 45 Copynumber: 4.5 Consensus size: 45
2229554 GGTAAGTATG
*
2229564 AAAATAAGCTTACGAGCTTATGGAAT-AATGGCAAGTATGTTGGT
1 AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATGTTGGT
*
2229608 AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATGTTTGT
1 AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATGTTGGT
*
2229653 AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGT
1 AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATGTTGGT
* *
2229698 AAAATAAGCTTATGGGCTTATGGAATAAATGGTAAGTATGTTGGT
1 AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATGTTGGT
* *
2229743 AAAATAAGTTTACAAGCTTATGG
1 AAAATAAGCTTACGAGCTTATGG
2229766 GATTAAATTG
Statistics
Matches: 146, Mismatches: 11, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
44 26 0.18
45 120 0.82
ACGTcount: A:0.38, C:0.07, G:0.23, T:0.32
Consensus pattern (45 bp):
AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATGTTGGT
Found at i:2231776 original size:14 final size:15
Alignment explanation
Indices: 2231757--2231796 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
2231747 TTATATATTT
2231757 TTTTCATTTTCTTC-
1 TTTTCATTTTCTTCA
*
2231771 TTTTCACTTTCTTCA
1 TTTTCATTTTCTTCA
*
2231786 TTCTCATTTTC
1 TTTTCATTTTC
2231797 CTCCTCCCAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
14 13 0.59
15 9 0.41
ACGTcount: A:0.10, C:0.25, G:0.00, T:0.65
Consensus pattern (15 bp):
TTTTCATTTTCTTCA
Found at i:2233139 original size:22 final size:21
Alignment explanation
Indices: 2233110--2233154 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
2233100 AAAAATGAGC
2233110 AATATAACAACTAGAAACAGT
1 AATATAACAACTAGAAACAGT
* *
2233131 AATAGTAACAGCTAGAATCAGT
1 AATA-TAACAACTAGAAACAGT
2233153 AA
1 AA
2233155 CATCAAGAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 4 0.19
22 17 0.81
ACGTcount: A:0.53, C:0.13, G:0.13, T:0.20
Consensus pattern (21 bp):
AATATAACAACTAGAAACAGT
Found at i:2233155 original size:16 final size:16
Alignment explanation
Indices: 2233134--2233177 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 16
2233124 AAACAGTAAT
*
2233134 AGTAACAGCTAGAATC
1 AGTAACAGCTAGAAAC
* *
2233150 AGTAACATCAAGAAAC
1 AGTAACAGCTAGAAAC
2233166 AGTAACAGCTAG
1 AGTAACAGCTAG
2233178 GATGTCATAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.48, C:0.18, G:0.18, T:0.16
Consensus pattern (16 bp):
AGTAACAGCTAGAAAC
Found at i:2237014 original size:16 final size:17
Alignment explanation
Indices: 2236993--2237033 Score: 68
Period size: 16 Copynumber: 2.5 Consensus size: 17
2236983 GAAATAGTAA
2236993 CAGTAACAGCTAG-AAT
1 CAGTAACAGCTAGAAAT
2237009 CAGTAACAGCTAGAAAT
1 CAGTAACAGCTAGAAAT
2237026 -AGTAACAG
1 CAGTAACAG
2237034 TTAGGGTGTC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 21 0.88
17 3 0.12
ACGTcount: A:0.46, C:0.17, G:0.20, T:0.17
Consensus pattern (17 bp):
CAGTAACAGCTAGAAAT
Done.