Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009067.1 Hibiscus syriacus cultivar Beakdansim tig00112491_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: 2329927
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 10
Found at i:1839142 original size:21 final size:19
Alignment explanation
Indices: 1838999--1839136 Score: 114
Period size: 21 Copynumber: 6.7 Consensus size: 19
1838989 CGTTGCGATT
*
1838999 TTGGACTATCGCAACGAAT
1 TTGGACTATCGCAACGAAC
*
1839018 TTGGAATAAATCGCAACGAAC
1 TTGGACT--ATCGCAACGAAC
* *
1839039 TTGGACTATCGAAACGAAT
1 TTGGACTATCGCAACGAAC
* *
1839058 TTGGAATAAATTGCAACGCGAAC
1 TTGGACT--ATCGCAA--CGAAC
*
1839081 TTCGACTATCGCAACGAAC
1 TTGGACTATCGCAACGAAC
*
1839100 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAA--CGAAC
1839123 TTGGACTATCGCAA
1 TTGGACTATCGCAA
1839137 TGCGAATATG
Statistics
Matches: 94, Mismatches: 15, Indels: 18
0.74 0.12 0.14
Matches are distributed among these distances:
19 32 0.34
21 42 0.45
23 20 0.21
ACGTcount: A:0.36, C:0.21, G:0.20, T:0.22
Consensus pattern (19 bp):
TTGGACTATCGCAACGAAC
Found at i:1846947 original size:65 final size:65
Alignment explanation
Indices: 1846787--1846947 Score: 204
Period size: 64 Copynumber: 2.5 Consensus size: 65
1846777 TTGTTTAAGG
* * * **
1846787 TGCATCGATGCACATGCAGTGCATCGATGCAT--GAAGTTAAATAGAAAACATCGAATAGGATTT
1 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCA-TTAAATAGAAAACATCGAATAGGATTT
1846850 A
65 A
*
1846851 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATA-CAAACATCGAATAGGATTTA
1 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATAGAAAACATCGAATAGGATTTA
*
1846915 TGCATCGATGCAT-GGTGTAGTGCATCGATGCAT
1 TGCATCGATGCATAAG-G-AGTGCATCGATGCAT
1846948 ACCTTCATTA
Statistics
Matches: 86, Mismatches: 7, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
63 1 0.01
64 62 0.72
65 22 0.26
66 1 0.01
ACGTcount: A:0.34, C:0.18, G:0.22, T:0.26
Consensus pattern (65 bp):
TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATAGAAAACATCGAATAGGATTTA
Found at i:1847461 original size:18 final size:18
Alignment explanation
Indices: 1847438--1847472 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
1847428 CTAGGAGATT
1847438 TGAACATA-AATGATAAGA
1 TGAACATATAA-GATAAGA
1847456 TGAACATATAAGATAAG
1 TGAACATATAAGATAAG
1847473 CTAGATGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.54, C:0.06, G:0.17, T:0.23
Consensus pattern (18 bp):
TGAACATATAAGATAAGA
Found at i:1847809 original size:2 final size:2
Alignment explanation
Indices: 1847802--1847865 Score: 128
Period size: 2 Copynumber: 32.0 Consensus size: 2
1847792 GAACATGTGA
1847802 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
1847844 AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
1847866 GTCTAAGAGA
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1848583 original size:149 final size:149
Alignment explanation
Indices: 1848410--1848724 Score: 560
Period size: 149 Copynumber: 2.1 Consensus size: 149
1848400 GAGTCGAGGG
* **
1848410 TCTACGCGGTCCTTCGGGACATATATATATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACAT
1 TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCTGGAAAGACACAT
1848475 ATATGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
66 ATATGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
1848540 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
* *
1848559 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCTGGAAAGACACAT
*
1848624 ATATGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATTATTA
66 ATATGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
1848689 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
1848708 TCTACGCGG-CACTTCGG
1 TCTACGCGGTC-CTTCGG
1848725 TGCAATTATA
Statistics
Matches: 159, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
148 1 0.01
149 158 0.99
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.34
Consensus pattern (149 bp):
TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCTGGAAAGACACAT
ATATGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
TATGGCACTACGGTGCAAT
Found at i:1848725 original size:23 final size:23
Alignment explanation
Indices: 1848692--1848736 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
1848682 ATTATTATAT
*
1848692 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
*
1848715 GGCACTTCGGTGCAATTATACG
1 GGCACTACGGTGCAATTATACG
1848737 AGCTGTGGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.22, C:0.27, G:0.27, T:0.24
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:1852262 original size:65 final size:65
Alignment explanation
Indices: 1852102--1852262 Score: 204
Period size: 64 Copynumber: 2.5 Consensus size: 65
1852092 TTGTTTAAGG
* * * **
1852102 TGCATCGATGCACATGCAGTGCATCGATGCAT--GAAGTTAAATAGAAAACATCGAATAGGATTT
1 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCA-TTAAATAGAAAACATCGAATAGGATTT
1852165 A
65 A
*
1852166 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATA-CAAACATCGAATAGGATTTA
1 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATAGAAAACATCGAATAGGATTTA
*
1852230 TGCATCGATGCAT-GGTGTAGTGCATCGATGCAT
1 TGCATCGATGCATAAG-G-AGTGCATCGATGCAT
1852263 ACCTTCATTA
Statistics
Matches: 86, Mismatches: 7, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
63 1 0.01
64 62 0.72
65 22 0.26
66 1 0.01
ACGTcount: A:0.34, C:0.18, G:0.22, T:0.26
Consensus pattern (65 bp):
TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATAGAAAACATCGAATAGGATTTA
Found at i:1852777 original size:18 final size:18
Alignment explanation
Indices: 1852754--1852788 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
1852744 CTAGGAGATT
1852754 TGAACATA-AATGATAAGA
1 TGAACATATAA-GATAAGA
1852772 TGAACATATAAGATAAG
1 TGAACATATAAGATAAG
1852789 CTAGATGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.54, C:0.06, G:0.17, T:0.23
Consensus pattern (18 bp):
TGAACATATAAGATAAGA
Found at i:1853129 original size:2 final size:2
Alignment explanation
Indices: 1853122--1853183 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
1853112 GAACATGTGA
1853122 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
1853164 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
1853184 GTCTAAGAGA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1853900 original size:143 final size:146
Alignment explanation
Indices: 1853730--1854036 Score: 514
Period size: 147 Copynumber: 2.1 Consensus size: 146
1853720 GAGTCGAGGG
* ** *
1853730 TCTACGCGGTCCTTCGGGACATATATATTCTTTGGAACATGTGTGAAGTC-TG-GTGAGAC-ATA
1 TCTACGCGGTCCTTCGGGACATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACAATA
1853792 TGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTATAT
66 TGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTATAT
1853857 GGCACTACGGTGCAAT
131 GGCACTACGGTGCAAT
*
1853873 TCTACGCGGTCCTTCGGGATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACATAT
1 TCTACGCGGTCCTTCGGGACATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACA-AT
*
1853938 ATGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATTATTATA
65 ATGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTATA
1854003 TGGCACTACGGTGCAAT
130 TGGCACTACGGTGCAAT
1854020 TCTACGCGG-CACTTCGG
1 TCTACGCGGTC-CTTCGG
1854037 TGCAATTATA
Statistics
Matches: 153, Mismatches: 6, Indels: 6
0.93 0.04 0.04
Matches are distributed among these distances:
143 48 0.31
144 2 0.01
145 4 0.03
146 1 0.01
147 98 0.64
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.34
Consensus pattern (146 bp):
TCTACGCGGTCCTTCGGGACATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACAATA
TGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTATAT
GGCACTACGGTGCAAT
Found at i:1854037 original size:23 final size:23
Alignment explanation
Indices: 1854004--1854048 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
1853994 ATTATTATAT
*
1854004 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
*
1854027 GGCACTTCGGTGCAATTATACG
1 GGCACTACGGTGCAATTATACG
1854049 AGCTGTGGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.22, C:0.27, G:0.27, T:0.24
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:1858692 original size:19 final size:20
Alignment explanation
Indices: 1858655--1858695 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
1858645 TTTTGTTAAA
*
1858655 GTCAAAGGTCAACGGGTCGG
1 GTCAAAGGTCAACAGGTCGG
*
1858675 GTCAAA-GTCAACATGTCGG
1 GTCAAAGGTCAACAGGTCGG
1858694 GT
1 GT
1858696 TGGTTGACTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.27, C:0.20, G:0.34, T:0.20
Consensus pattern (20 bp):
GTCAAAGGTCAACAGGTCGG
Found at i:1864050 original size:17 final size:18
Alignment explanation
Indices: 1864017--1864053 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
1864007 ACTCTATTAA
1864017 AAACGTTATATTTTCTTT
1 AAACGTTATATTTTCTTT
*
1864035 AAACGTTGTA-TTTCTTT
1 AAACGTTATATTTTCTTT
1864052 AA
1 AA
1864054 CAATTTACGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.30, C:0.11, G:0.08, T:0.51
Consensus pattern (18 bp):
AAACGTTATATTTTCTTT
Found at i:1865288 original size:25 final size:24
Alignment explanation
Indices: 1865249--1865312 Score: 71
Period size: 24 Copynumber: 2.7 Consensus size: 24
1865239 TGTTTAACAA
*
1865249 TTTA-ATTTTTATTTTTG-ATA-T
1 TTTATATTTTAATTTTTGAATATT
*
1865270 TTTATTATATTTACTTTTTGAATATT
1 TTTA-TAT-TTTAATTTTTGAATATT
1865296 TTTATATTTTAATTTTT
1 TTTATATTTTAATTTTT
1865313 TTAAAATCAA
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
21 4 0.11
23 2 0.06
24 18 0.51
25 6 0.17
26 5 0.14
ACGTcount: A:0.25, C:0.02, G:0.03, T:0.70
Consensus pattern (24 bp):
TTTATATTTTAATTTTTGAATATT
Found at i:1865313 original size:25 final size:24
Alignment explanation
Indices: 1865256--1865304 Score: 68
Period size: 23 Copynumber: 2.1 Consensus size: 24
1865246 CAATTTAATT
1865256 TTTA-TTTTTGATATTTTATTATA
1 TTTACTTTTTGATATTTTATTATA
1865279 TTTACTTTTTGA-ATATTT-TTATA
1 TTTACTTTTTGATAT-TTTATTATA
1865302 TTT
1 TTT
1865305 TAATTTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
23 14 0.58
24 10 0.42
ACGTcount: A:0.24, C:0.02, G:0.04, T:0.69
Consensus pattern (24 bp):
TTTACTTTTTGATATTTTATTATA
Found at i:1868466 original size:18 final size:17
Alignment explanation
Indices: 1868425--1868469 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
1868415 ATAATGTTAT
1868425 GTTTGAATTCTAAAATA
1 GTTTGAATTCTAAAATA
*
1868442 GTTTGAATAT-TAAAATT
1 GTTTGAAT-TCTAAAATA
1868459 GATTTGAATTC
1 G-TTTGAATTC
1868470 CGACTTAACA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
17 16 0.67
18 8 0.33
ACGTcount: A:0.38, C:0.04, G:0.13, T:0.44
Consensus pattern (17 bp):
GTTTGAATTCTAAAATA
Found at i:1879553 original size:18 final size:18
Alignment explanation
Indices: 1879525--1879592 Score: 86
Period size: 18 Copynumber: 3.8 Consensus size: 18
1879515 ATTCTAAATG
1879525 TTTACAGTTATCAGATGAT
1 TTTACAGTTATCAGAT-AT
1879544 TTTA-AGTTATCAGATA-
1 TTTACAGTTATCAGATAT
* *
1879560 TTTACAGATATCAAATAT
1 TTTACAGTTATCAGATAT
*
1879578 TTTATAGTTATCAGA
1 TTTACAGTTATCAGA
1879593 GACATATTAA
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
16 4 0.10
17 11 0.26
18 23 0.55
19 4 0.10
ACGTcount: A:0.37, C:0.09, G:0.12, T:0.43
Consensus pattern (18 bp):
TTTACAGTTATCAGATAT
Found at i:1879565 original size:35 final size:35
Alignment explanation
Indices: 1879525--1879592 Score: 102
Period size: 35 Copynumber: 1.9 Consensus size: 35
1879515 ATTCTAAATG
* *
1879525 TTTACAGTTATCAGATGATTTTA-AGTTATCAGATA
1 TTTACAGATATCAAAT-ATTTTATAGTTATCAGATA
1879560 TTTACAGATATCAAATATTTTATAGTTATCAGA
1 TTTACAGATATCAAATATTTTATAGTTATCAGA
1879593 GACATATTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
34 6 0.20
35 24 0.80
ACGTcount: A:0.37, C:0.09, G:0.12, T:0.43
Consensus pattern (35 bp):
TTTACAGATATCAAATATTTTATAGTTATCAGATA
Found at i:1880586 original size:18 final size:17
Alignment explanation
Indices: 1880563--1880623 Score: 70
Period size: 17 Copynumber: 3.5 Consensus size: 17
1880553 ATGTTTACAG
1880563 TTATCAGATGATTTTCAA
1 TTATCAGAT-ATTTTCAA
*
1880581 TTATCAGATATTTACAGA
1 TTATCAGATATTTTCA-A
*
1880599 -TATCAAATATTTTACAA
1 TTATCAGATATTTT-CAA
1880616 TTATCAGA
1 TTATCAGA
1880624 CACATATTAA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
17 18 0.50
18 18 0.50
ACGTcount: A:0.39, C:0.11, G:0.08, T:0.41
Consensus pattern (17 bp):
TTATCAGATATTTTCAA
Found at i:1880596 original size:35 final size:35
Alignment explanation
Indices: 1880556--1880623 Score: 102
Period size: 35 Copynumber: 1.9 Consensus size: 35
1880546 ATTCTAAATG
* *
1880556 TTTACAGTTATCAGATGATTTT-CAATTATCAGATA
1 TTTACAGATATCAAAT-ATTTTACAATTATCAGATA
1880591 TTTACAGATATCAAATATTTTACAATTATCAGA
1 TTTACAGATATCAAATATTTTACAATTATCAGA
1880624 CACATATTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
34 5 0.17
35 25 0.83
ACGTcount: A:0.38, C:0.12, G:0.09, T:0.41
Consensus pattern (35 bp):
TTTACAGATATCAAATATTTTACAATTATCAGATA
Found at i:1890194 original size:70 final size:70
Alignment explanation
Indices: 1889946--1890186 Score: 428
Period size: 70 Copynumber: 3.4 Consensus size: 70
1889936 TTTTTTTTAA
* * *
1889946 AAAACAATCTCACATGGCTAAGAAACATAAAAGAGCATCCCAAAAGTCTAAAGAGTACAAATATG
1 AAAACAATCTCACATTGCTAAGAAACATAGAAGAGCATCCCAAAAGTCTAAAGAGTAAAAATATG
1890011 AGAAC
66 AGAAC
*
1890016 AAAACAATCTCACATTGCTAAGAAACATAGAAGAGCATCCCAAAAATCTAAAGAGTAAAAATATG
1 AAAACAATCTCACATTGCTAAGAAACATAGAAGAGCATCCCAAAAGTCTAAAGAGTAAAAATATG
1890081 AGAAC
66 AGAAC
*
1890086 AAAACAATCTTACATTGCTAAGAAACATAGAAGAGCATCCCAAAAGTCTAAAGAGTAAAAATATG
1 AAAACAATCTCACATTGCTAAGAAACATAGAAGAGCATCCCAAAAGTCTAAAGAGTAAAAATATG
1890151 AGAAC
66 AGAAC
*
1890156 AAAACAATCTCATATTGCTAAGAAACATAGA
1 AAAACAATCTCACATTGCTAAGAAACATAGA
1890187 TGCGCATCAC
Statistics
Matches: 163, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
70 163 1.00
ACGTcount: A:0.52, C:0.17, G:0.13, T:0.18
Consensus pattern (70 bp):
AAAACAATCTCACATTGCTAAGAAACATAGAAGAGCATCCCAAAAGTCTAAAGAGTAAAAATATG
AGAAC
Found at i:1894604 original size:182 final size:180
Alignment explanation
Indices: 1894312--1894783 Score: 692
Period size: 180 Copynumber: 2.6 Consensus size: 180
1894302 GATCCAAATT
* * * * **
1894312 AAAAATGTGTCGATCCAAAACGATATAACAGGTAAAACTATGACAAAATCGGTATTGAAATGATA
1 AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
* * * * * * *
1894377 AAACCGGTAAAGCGCTACCAGATACATTTAAAGTGTTGGTACTTTAATATAAGGATCGACACTTC
66 AAACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTT-ATATAAGGATCGACACTTC
*
1894442 GTGAATTTAAAAGAGAAGCAGTTATAAATCCTATAAAGTGTCGATACTTTTA
130 GTGAATTTAAAAGAGAAGCAGTTATAAAGCCTATAAAGTGTCGATAC-TTTA
* *
1894494 AAAAATGTATCGATCCAAAACGATATACCATGTAAAAATATGATAAAACCGGTATCAAAATGATA
1 AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
* *
1894559 AAACCGGTAAAACGTTACCGGATATATTGAAAGTGTCGATACTTTATATAAGGATCGACACTTTG
66 AAACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTTATATAAGGATCGACACTTCG
* * ** *
1894624 TGAATTTAAAAGAGAATCAGTTTTAGCGCCTATAATGTGTCGATACTTTA
131 TGAATTTAAAAGAGAAGCAGTTATAAAGCCTATAAAGTGTCGATACTTTA
** *
1894674 AAAAAAATATCGATCCACAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
1 AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
1894739 AAACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTT
66 AAACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTT
1894784 CGTAAGTACG
Statistics
Matches: 262, Mismatches: 28, Indels: 2
0.90 0.10 0.01
Matches are distributed among these distances:
180 108 0.41
181 59 0.23
182 95 0.36
ACGTcount: A:0.42, C:0.14, G:0.17, T:0.27
Consensus pattern (180 bp):
AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
AAACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTTATATAAGGATCGACACTTCG
TGAATTTAAAAGAGAAGCAGTTATAAAGCCTATAAAGTGTCGATACTTTA
Found at i:1894727 original size:20 final size:19
Alignment explanation
Indices: 1894704--1894750 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
1894694 CGATATAACA
1894704 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
*
1894724 GGTATCAAAATGATAAAACC
1 GGTA-AAAAATGATAAAACC
1894744 GGTAAAA
1 GGTAAAA
1894751 CGATACCGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.53, C:0.11, G:0.17, T:0.19
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:1894755 original size:17 final size:19
Alignment explanation
Indices: 1894715--1894755 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
1894705 GTAAAAATAT
*
1894715 GATAAAACCGGTATCAAAAT
1 GATAAAACCGG-ATCAAAAC
1894735 GATAAAACCGG-T-AAAAC
1 GATAAAACCGGATCAAAAC
1894752 GATA
1 GATA
1894756 CCGGATATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
17 8 0.40
18 1 0.05
20 11 0.55
ACGTcount: A:0.51, C:0.15, G:0.17, T:0.17
Consensus pattern (19 bp):
GATAAAACCGGATCAAAAC
Found at i:1896999 original size:21 final size:21
Alignment explanation
Indices: 1896971--1897035 Score: 94
Period size: 21 Copynumber: 3.1 Consensus size: 21
1896961 AAGACAATCA
* *
1896971 AGAGTCGAAGAGAAACTTGAT
1 AGAGTCGAAGATAAACTTGAG
*
1896992 ATAGTCGAAGATAAACTTGAG
1 AGAGTCGAAGATAAACTTGAG
*
1897013 AGAGTCGAAGATACACTTGAG
1 AGAGTCGAAGATAAACTTGAG
1897034 AG
1 AG
1897036 GTATAAGGGG
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.42, C:0.11, G:0.28, T:0.20
Consensus pattern (21 bp):
AGAGTCGAAGATAAACTTGAG
Found at i:1898940 original size:19 final size:19
Alignment explanation
Indices: 1898916--1898964 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
1898906 AATGTAGGGT
1898916 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
1898935 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
1898954 TAATTTTGTAT
1 TAATTTTGTAT
1898965 GTGAATATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.33, C:0.02, G:0.10, T:0.55
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:1899546 original size:200 final size:200
Alignment explanation
Indices: 1899198--1899993 Score: 1394
Period size: 200 Copynumber: 4.0 Consensus size: 200
1899188 AATTTACAAT
* *
1899198 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAGAGTGTCGATCCCATAAACAT
1 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
* *
1899263 CGAAACCCAAAAGTATAATGTAATAGGTAATTTTTCAATCTAATCGGTACAAGTATACCGGTTTT
66 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
*
1899328 ATGAGAGAATATGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
131 ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
1899393 AATGA
196 AATGA
* *
1899398 ATGGCAAACAGGATGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCGATAAACAT
1 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
* *
1899463 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCAAACCGGTACAAGTATATCGGTTTT
66 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
1899528 ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
131 ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
*
1899593 AATAA
196 AATGA
* *
1899598 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATGTATAAAAAGTGTCGATCCGATAAACAT
1 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
**
1899663 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATATTGGTTTT
66 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
* * *
1899728 ATGAGAGAATAGGTCTAAATAATGTTTCGACACTTTTTTAGTCTGTGTCGATATTTTTGGTCCAG
131 ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
1899793 AATGA
196 AATGA
* * *
1899798 ATGGCAAATAGGGTGCAACAATAAAGTATCGATCCATATATAAAAAGTGTTGATCCCATAAACAT
1 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
*
1899863 CGAAACCCATAAGTATAATGTAATAGGTACTTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
66 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
*
1899928 ATGAGAGAATAGGTCTAAATAATGTGTCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
131 ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
1899993 A
196 A
1899994 TTTAAATATC
Statistics
Matches: 567, Mismatches: 29, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
200 567 1.00
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.31
Consensus pattern (200 bp):
ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
AATGA
Found at i:1901479 original size:12 final size:12
Alignment explanation
Indices: 1901457--1901493 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
1901447 CAAGCAGTCA
*
1901457 ATGAAGATGAAG
1 ATGACGATGAAG
*
1901469 CTGACGATGAAG
1 ATGACGATGAAG
1901481 ATGACGATGAAG
1 ATGACGATGAAG
1901493 A
1 A
1901494 AGATGATGAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.43, C:0.08, G:0.32, T:0.16
Consensus pattern (12 bp):
ATGACGATGAAG
Found at i:1901501 original size:3 final size:3
Alignment explanation
Indices: 1901474--1901524 Score: 57
Period size: 3 Copynumber: 17.0 Consensus size: 3
1901464 TGAAGCTGAC
* * * * *
1901474 GAT GAA GAT GAC GAT GAA GAA GAT GAT GAT GAT AAT GAT GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
1901522 GAT
1 GAT
1901525 CCAAACAAGT
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.41, C:0.02, G:0.31, T:0.25
Consensus pattern (3 bp):
GAT
Found at i:1903030 original size:120 final size:120
Alignment explanation
Indices: 1902817--1903059 Score: 405
Period size: 120 Copynumber: 2.0 Consensus size: 120
1902807 CGGAACCCAT
* *
1902817 AATTATAATGTAATAGATAATTTTGTAATGTAACCGGTATAAATATACCGGTTTTATGAGCGAAT
1 AATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGATTTTATGAGCGAAT
* *
1902882 AGGTCTACAACCTATATCGACACTTTTTAATTTTGTGTCGGTACTTTATGTACAG
66 AAGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTACAG
* * *
1902937 AATTATAATGTACTAGATAATTTTGTAATATAACCGGTATAAGTATACCGATTTTATTAGCGAAT
1 AATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGATTTTATGAGCGAAT
* *
1903002 AAGTCTACAACCTATGTCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCAG
66 AAGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTACAG
1903057 AAT
1 AAT
1903060 GGAAGAAAAA
Statistics
Matches: 114, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
120 114 1.00
ACGTcount: A:0.33, C:0.13, G:0.16, T:0.38
Consensus pattern (120 bp):
AATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGATTTTATGAGCGAAT
AAGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTACAG
Found at i:1903273 original size:118 final size:117
Alignment explanation
Indices: 1903116--1903353 Score: 365
Period size: 118 Copynumber: 2.0 Consensus size: 117
1903106 ACATCGGAAC
1903116 CCAGATTAAATGTAATAGATAATTTTGTAATATAACGGTATAAGTATACCGGTTTTATGAGCGAA
1 CCAGATTAAATGTAATAGATAATTTTGTAATATAACGGTATAAGTATACCGGTTTTATGAGCGAA
*
1903181 TAGGTCTACAACCTATATTAACAC-TTTTAAT-TTTGTGTCGGTACTTTATAT
66 TAGGTCTACAACCTATATCAACACTTTTTAATATTT-TGTCGGTACTTTATAT
* *
1903232 CCAGAATTATAATGTACTAGATAA-TTTGTAATATAACCGGTATAAGTATACCGGTTTTATTAGC
1 CCAG-ATTA-AATGTAATAGATAATTTTGTAATATAA-CGGTATAAGTATACCGGTTTTATGAGC
* * *
1903296 GAATAGGTCTACAACCTATGTCGACACTTTTTAATATTTTGTCGGTACTTTATGT
63 GAATAGGTCTACAACCTATATCAACACTTTTTAATATTTTGTCGGTACTTTATAT
1903351 CCA
1 CCA
1903354 AATGGAAGAA
Statistics
Matches: 111, Mismatches: 6, Indels: 7
0.90 0.05 0.06
Matches are distributed among these distances:
116 4 0.04
117 16 0.14
118 63 0.57
119 25 0.23
120 3 0.03
ACGTcount: A:0.32, C:0.14, G:0.16, T:0.38
Consensus pattern (117 bp):
CCAGATTAAATGTAATAGATAATTTTGTAATATAACGGTATAAGTATACCGGTTTTATGAGCGAA
TAGGTCTACAACCTATATCAACACTTTTTAATATTTTGTCGGTACTTTATAT
Found at i:1903627 original size:120 final size:120
Alignment explanation
Indices: 1903413--1903659 Score: 433
Period size: 120 Copynumber: 2.1 Consensus size: 120
1903403 ACATCGGAAC
1903413 CCAGAATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAGTATACCGATTTTATGAGC
1 CCAGAATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAGTATACCGATTTTATGAGC
*
1903478 GAATAGGTCTACAACCTATATCGACACTTTTTAATTTTGTGTCGGTACTTTATGT
66 GAATAGGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGT
* *
1903533 CCAGAATTATAATGTACTAGATAATTTTGTAATATAACCGGTATAAGTATACC-AGTTTTATTAG
1 CCAGAATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAGTATACCGA-TTTTATGAG
* *
1903597 CGAATAGGTCTACAACCTATGTCGATACTTTTTAATATTGTGTCGGTACTTTATGT
65 CGAATAGGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGT
1903653 CCAGAAT
1 CCAGAAT
1903660 GGAAGAAAAA
Statistics
Matches: 121, Mismatches: 5, Indels: 2
0.95 0.04 0.02
Matches are distributed among these distances:
119 1 0.01
120 120 0.99
ACGTcount: A:0.32, C:0.14, G:0.16, T:0.38
Consensus pattern (120 bp):
CCAGAATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAGTATACCGATTTTATGAGC
GAATAGGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGT
Found at i:1906593 original size:23 final size:23
Alignment explanation
Indices: 1906538--1906607 Score: 92
Period size: 21 Copynumber: 3.2 Consensus size: 23
1906528 ATAGGTAAAA
*
1906538 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
*
1906561 ATATAA--TAATAGGTAGCGTTT
1 ATATAATGTAATAGGTAGCGCTT
*
1906582 ATATAATGTAATA-GTAGTGCTT
1 ATATAATGTAATAGGTAGCGCTT
1906604 ATAT
1 ATAT
1906608 TGTAAAATAT
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
21 20 0.49
22 11 0.27
23 10 0.24
ACGTcount: A:0.36, C:0.06, G:0.20, T:0.39
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:1919608 original size:16 final size:17
Alignment explanation
Indices: 1919576--1919609 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
1919566 AAAAAAAGTG
1919576 TTTAAATTATGTTTTAT
1 TTTAAATTATGTTTTAT
*
1919593 TTTAAA-TATTTTTTAT
1 TTTAAATTATGTTTTAT
1919609 T
1 T
1919610 AAAATATACG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (17 bp):
TTTAAATTATGTTTTAT
Found at i:1919697 original size:21 final size:20
Alignment explanation
Indices: 1919646--1919698 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 20
1919636 TTTAAGATTC
*
1919646 ATTTAATTATTTGTTAAAAAT
1 ATTT-ATTATTCGTTAAAAAT
*
1919667 ATTATTTTATTCGTTAAAAATT
1 ATT-TATTATTCGTTAAAAA-T
1919689 ATTTATTATT
1 ATTTATTATT
1919699 GATAAGTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
21 22 0.81
22 5 0.19
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.57
Consensus pattern (20 bp):
ATTTATTATTCGTTAAAAAT
Found at i:1921250 original size:2 final size:2
Alignment explanation
Indices: 1921243--1921277 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
1921233 CTCATATCCC
*
1921243 TA TA TA TA TA TA TA TA TC TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1921278 GCGGACGCTC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1921535 original size:19 final size:20
Alignment explanation
Indices: 1921446--1921536 Score: 96
Period size: 19 Copynumber: 4.4 Consensus size: 20
1921436 AACGCGATTT
1921446 TGAAAAATGTGTTGCGATAG
1 TGAAAAATGTGTTGCGATAG
* * *
1921466 T-TAAAATGTGTTACGAGAG
1 TGAAAAATGTGTTGCGATAG
1921485 TTTGAAAAACGTGTTGTTGCGATAG
1 --TGAAAAA--TG-TGTTGCGATAG
1921510 TGAAAAA-GTGTTGCGATAG
1 TGAAAAATGTGTTGCGATAG
1921529 TGAAAAAT
1 TGAAAAAT
1921537 CCAAAATAAG
Statistics
Matches: 58, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
19 33 0.57
20 2 0.03
21 1 0.02
22 4 0.07
23 7 0.12
24 2 0.03
25 9 0.16
ACGTcount: A:0.36, C:0.05, G:0.27, T:0.31
Consensus pattern (20 bp):
TGAAAAATGTGTTGCGATAG
Found at i:1927906 original size:5 final size:5
Alignment explanation
Indices: 1927896--1927921 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
1927886 TATTTATTAT
1927896 TTTTC TTTTC TTTTC TTTTC TTTTC T
1 TTTTC TTTTC TTTTC TTTTC TTTTC T
1927922 GGACATTAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTC
Found at i:1929170 original size:25 final size:25
Alignment explanation
Indices: 1929119--1929197 Score: 81
Period size: 26 Copynumber: 3.2 Consensus size: 25
1929109 AGGCGTTGTT
* * *
1929119 TAAA-ATTTTAAATTTATACTTTT-
1 TAAATATTTTATATTTAAAATTTTA
*
1929142 TAAATATTTTATATTTTAAATTTTA
1 TAAATATTTTATATTTAAAATTTTA
* *
1929167 TAAATTCTTTTTTATTTAAAATTTTA
1 TAAA-TATTTTATATTTAAAATTTTA
1929193 TAAAT
1 TAAAT
1929198 TTACCCATAA
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
23 4 0.09
24 15 0.33
25 5 0.11
26 22 0.48
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (25 bp):
TAAATATTTTATATTTAAAATTTTA
Found at i:1929183 original size:26 final size:26
Alignment explanation
Indices: 1929148--1929198 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
1929138 TTTTTAAATA
*
1929148 TTTTATATTTTAAATTTTATAAATTC
1 TTTTATATTTAAAATTTTATAAATTC
*
1929174 TTTTTTATTTAAAATTTTATAAATT
1 TTTTATATTTAAAATTTTATAAATT
1929199 TACCCATAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (26 bp):
TTTTATATTTAAAATTTTATAAATTC
Found at i:1929829 original size:18 final size:19
Alignment explanation
Indices: 1929794--1929830 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
1929784 CACGGAATGT
1929794 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
1929814 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
1929831 GGATTACTGA
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:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:1930899 original size:31 final size:29
Alignment explanation
Indices: 1930848--1930905 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 29
1930838 ATCGCATTGG
1930848 ATACTTTTTCAAAGCACAAGTACCACATA
1 ATACTTTTTCAAAGCACAAGTACCACATA
*
1930877 ATACATTTTTACAAAGTC-CAAGTATCACA
1 ATAC-TTTTT-CAAAG-CACAAGTACCACA
1930906 GATATTTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
29 4 0.16
30 5 0.20
31 15 0.60
32 1 0.04
ACGTcount: A:0.41, C:0.22, G:0.07, T:0.29
Consensus pattern (29 bp):
ATACTTTTTCAAAGCACAAGTACCACATA
Found at i:1934667 original size:20 final size:20
Alignment explanation
Indices: 1934619--1934685 Score: 71
Period size: 20 Copynumber: 3.2 Consensus size: 20
1934609 ACTTTTAGTA
*
1934619 TTTTTTTAAAAAATTTTAACT
1 TTTTTTTAAAAAACTTTAA-T
**
1934640 CTAATTTTAAAAAACTTTAAT
1 -TTTTTTTAAAAAACTTTAAT
**
1934661 TTTTTTTGTAAAACTTTAAT
1 TTTTTTTAAAAAACTTTAAT
1934681 TTTTT
1 TTTTT
1934686 AAAGTTCAAA
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 21 0.55
21 1 0.03
22 16 0.42
ACGTcount: A:0.36, C:0.06, G:0.01, T:0.57
Consensus pattern (20 bp):
TTTTTTTAAAAAACTTTAAT
Found at i:1935099 original size:2 final size:2
Alignment explanation
Indices: 1935088--1935129 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
1935078 CTTTTACACA
1935088 AT AT -T 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
1935129 A
1 A
1935130 CTTTTTTATA
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1935828 original size:2 final size:2
Alignment explanation
Indices: 1935823--1935853 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1935813 TCTCTCTCTC
1935823 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1935854 TTATCAAGCG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1940349 original size:21 final size:21
Alignment explanation
Indices: 1940323--1940362 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
1940313 GGCCGTTTCT
1940323 AGCCGTTGGGGAATATTTTGG
1 AGCCGTTGGGGAATATTTTGG
1940344 AGCCGTTGGGGAATATTTT
1 AGCCGTTGGGGAATATTTT
1940363 TCTACAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.20, C:0.10, G:0.35, T:0.35
Consensus pattern (21 bp):
AGCCGTTGGGGAATATTTTGG
Found at i:1940835 original size:11 final size:11
Alignment explanation
Indices: 1940819--1940848 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
1940809 AAATATGGTT
1940819 CAACAAATATG
1 CAACAAATATG
1940830 CAACAAATATG
1 CAACAAATATG
1940841 CAACAAAT
1 CAACAAAT
1940849 TTGTTTATGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.57, C:0.20, G:0.07, T:0.17
Consensus pattern (11 bp):
CAACAAATATG
Found at i:1942766 original size:72 final size:73
Alignment explanation
Indices: 1942672--1942858 Score: 268
Period size: 73 Copynumber: 2.6 Consensus size: 73
1942662 AGTGTTAACT
*
1942672 AAATTATGAAAAAAAATACATTAATACGTTTGATTCACTAAATA-TAAAAAAACGAATATAATGC
1 AAATTAT-ATAAAAAATACATTAATACGTTTGATTCACTAAATATTAAAAAAACGAATATAATGC
*
1942736 CATTTCTTC
65 CATTACTTC
* * ***
1942745 AAATTATATAAAAAATACATTAATACGTTTGATTAACTAAATATTTAAAAAACGAATATAATTTT
1 AAATTATATAAAAAATACATTAATACGTTTGATTCACTAAATATTAAAAAAACGAATATAATGCC
*
1942810 ATTACTTG
66 ATTACTTC
* *
1942818 AAATTACATAAAAAATTCATTAATACGTTTGATTCACTAAA
1 AAATTATATAAAAAATACATTAATACGTTTGATTCACTAAA
1942859 CTTTATCGGC
Statistics
Matches: 102, Mismatches: 11, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
72 34 0.33
73 68 0.67
ACGTcount: A:0.49, C:0.10, G:0.06, T:0.35
Consensus pattern (73 bp):
AAATTATATAAAAAATACATTAATACGTTTGATTCACTAAATATTAAAAAAACGAATATAATGCC
ATTACTTC
Found at i:1942794 original size:37 final size:35
Alignment explanation
Indices: 1942682--1942858 Score: 91
Period size: 37 Copynumber: 4.9 Consensus size: 35
1942672 AAATTATGAA
1942682 AAAAAATACATTAATACGTTTGATTCACTAAATA-T
1 AAAAAATACATTAATACGTTTGATT-ACTAAATATT
* * *
1942717 AAAAAA-ACGAATATAATGCCATTT-CTT-C-AAATTATAT
1 AAAAAATAC--AT-TAAT-ACGTTTGATTACTAAA-TAT-T
1942754 AAAAAATACATTAATACGTTTGATTAACTAAATATT
1 AAAAAATACATTAATACGTTTGATT-ACTAAATATT
* * * * *
1942790 TAAAAA-ACGAAT-ATA-ATTTTATTACTTGAAATTACAT
1 AAAAAATAC-ATTAATACGTTTGATTAC-T-AAA-TA-TT
*
1942827 AAAAAATTCATTAATACGTTTGATTCACTAAA
1 AAAAAATACATTAATACGTTTGATT-ACTAAA
1942859 CTTTATCGGC
Statistics
Matches: 105, Mismatches: 16, Indels: 39
0.66 0.10 0.24
Matches are distributed among these distances:
33 2 0.02
34 16 0.15
35 23 0.22
36 14 0.13
37 25 0.24
38 16 0.15
39 7 0.07
40 2 0.02
ACGTcount: A:0.49, C:0.11, G:0.06, T:0.35
Consensus pattern (35 bp):
AAAAAATACATTAATACGTTTGATTACTAAATATT
Found at i:1942796 original size:38 final size:37
Alignment explanation
Indices: 1942666--1942796 Score: 87
Period size: 36 Copynumber: 3.5 Consensus size: 37
1942656 TGTACAAGTG
*
1942666 TTAACTAAATTATGAAAAAAAATACATTAATACGTTTGA
1 TTAACTAAA-TAT-TAAAAAAATACATTAATACGTTTGA
* * * * *
1942705 TTCACTAAATA-TAAAAAAACGA-ATATAATGCCATTT-C
1 TTAACTAAATATTAAAAAAA-TACAT-TAAT-ACGTTTGA
1942742 TT--C-AAAT-TATATAAAAAATACATTAATACGTTTGA
1 TTAACTAAATAT-TA-AAAAAATACATTAATACGTTTGA
*
1942777 TTAACTAAATATTTAAAAAA
1 TTAACTAAATATTAAAAAAA
1942797 CGAATATAAT
Statistics
Matches: 69, Mismatches: 11, Indels: 26
0.65 0.10 0.25
Matches are distributed among these distances:
34 8 0.12
35 10 0.14
36 17 0.25
37 14 0.20
38 11 0.16
39 9 0.13
ACGTcount: A:0.51, C:0.10, G:0.05, T:0.34
Consensus pattern (37 bp):
TTAACTAAATATTAAAAAAATACATTAATACGTTTGA
Found at i:1950542 original size:5 final size:5
Alignment explanation
Indices: 1950528--1950576 Score: 62
Period size: 5 Copynumber: 9.8 Consensus size: 5
1950518 GTCCGTCCGT
* * * *
1950528 CTCGT CTCGG CTCGG CACGG CACGG CACGG CTCGG CTCGG CTCGG CTCG
1 CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCG
1950577 TGGTCGTGGT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 41 1.00
ACGTcount: A:0.06, C:0.41, G:0.37, T:0.16
Consensus pattern (5 bp):
CTCGG
Found at i:1950585 original size:6 final size:6
Alignment explanation
Indices: 1950574--1950640 Score: 98
Period size: 6 Copynumber: 11.2 Consensus size: 6
1950564 TCGGCTCGGC
* * * *
1950574 TCGTGG TCGTGG TCGTGG TCGAGG TCGAGG TCGAGG TCGAGG TCGTGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
1950622 TCGTGG TCGTGG TCGTGG T
1 TCGTGG TCGTGG TCGTGG T
1950641 AATACGTGTC
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 59 1.00
ACGTcount: A:0.06, C:0.16, G:0.49, T:0.28
Consensus pattern (6 bp):
TCGTGG
Found at i:1950937 original size:22 final size:22
Alignment explanation
Indices: 1950912--1950966 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
1950902 TCAGGAGTTA
* *
1950912 CAGGAGTTATTTGATTTAATTC
1 CAGGAGTTATATGATATAATTC
* * *
1950934 CAGGGGTTACATGATATAATTT
1 CAGGAGTTATATGATATAATTC
*
1950956 CGGGAGTTATA
1 CAGGAGTTATA
1950967 ACAGCTGAAT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.29, C:0.09, G:0.24, T:0.38
Consensus pattern (22 bp):
CAGGAGTTATATGATATAATTC
Found at i:1956505 original size:5 final size:5
Alignment explanation
Indices: 1956491--1956539 Score: 62
Period size: 5 Copynumber: 9.8 Consensus size: 5
1956481 GTCCGTCCGT
* * * *
1956491 CTCGT CTCGG CTCGG CACGG CACGG CACGG CTCGG CTCGG CTCGG CTCG
1 CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCG
1956540 TGGTCGTGGT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 41 1.00
ACGTcount: A:0.06, C:0.41, G:0.37, T:0.16
Consensus pattern (5 bp):
CTCGG
Found at i:1956548 original size:6 final size:6
Alignment explanation
Indices: 1956537--1956597 Score: 95
Period size: 6 Copynumber: 10.2 Consensus size: 6
1956527 TCGGCTCGGC
* * *
1956537 TCGTGG TCGTGG TCGTGG TCGAGG TCGAGG TCGAGG TCGTGG TCGTGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
1956585 TCGTGG TCGTGG T
1 TCGTGG TCGTGG T
1956598 AATACGTGTC
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 53 1.00
ACGTcount: A:0.05, C:0.16, G:0.49, T:0.30
Consensus pattern (6 bp):
TCGTGG
Found at i:1956895 original size:21 final size:22
Alignment explanation
Indices: 1956871--1956924 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
1956861 TCAGGAGTTA
*
1956871 CAGGAGTTATTTGAT-TAATTC
1 CAGGAGTTATATGATATAATTC
* * *
1956892 CAGGGGTTACATGATATAATTT
1 CAGGAGTTATATGATATAATTC
*
1956914 CGGGAGTTATA
1 CAGGAGTTATA
1956925 ACAGCTGAAT
Statistics
Matches: 25, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
21 12 0.48
22 13 0.52
ACGTcount: A:0.30, C:0.09, G:0.24, T:0.37
Consensus pattern (22 bp):
CAGGAGTTATATGATATAATTC
Found at i:1958864 original size:32 final size:34
Alignment explanation
Indices: 1958801--1958867 Score: 86
Period size: 32 Copynumber: 2.0 Consensus size: 34
1958791 TATCCATCAC
*
1958801 ATTTGATTTTATATAATTATGTAATTTAAATTTT
1 ATTTGATTTTATATAATTATATAATTTAAATTTT
*
1958835 ATTT-ATTTT-TATAATTATAT-GTTTGAAATTTT
1 ATTTGATTTTATATAATTATATAATTT-AAATTTT
1958867 A
1 A
1958868 ATTTTAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
31 3 0.10
32 18 0.60
33 5 0.17
34 4 0.13
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.60
Consensus pattern (34 bp):
ATTTGATTTTATATAATTATATAATTTAAATTTT
Found at i:1959181 original size:69 final size:69
Alignment explanation
Indices: 1959070--1959214 Score: 263
Period size: 69 Copynumber: 2.1 Consensus size: 69
1959060 GAACAAATTT
*
1959070 TCATGAAACTTGTAAGGAATGTTAGAAACACTTTTACTGTTTTACCGCAACATATTGAGTTAATA
1 TCATGTAACTTGTAAGGAATGTTAGAAACACTTTTACTGTTTTACCGCAACATATTGAGTTAATA
1959135 TGTA
66 TGTA
* *
1959139 TCATGTAACTTGTAAGGAATGTTAGAAATACTTTTACTGTTTTACTGCAACATATTGAGTTAATA
1 TCATGTAACTTGTAAGGAATGTTAGAAACACTTTTACTGTTTTACCGCAACATATTGAGTTAATA
1959204 TGTA
66 TGTA
1959208 TCATGTA
1 TCATGTA
1959215 GCTGGTGTAT
Statistics
Matches: 73, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
69 73 1.00
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.39
Consensus pattern (69 bp):
TCATGTAACTTGTAAGGAATGTTAGAAACACTTTTACTGTTTTACCGCAACATATTGAGTTAATA
TGTA
Found at i:1967732 original size:15 final size:15
Alignment explanation
Indices: 1967712--1967746 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
1967702 TGCTCACCAT
1967712 TCGAACAAACTTCAC
1 TCGAACAAACTTCAC
*
1967727 TCGAACAAGCTTCAC
1 TCGAACAAACTTCAC
1967742 TCGAA
1 TCGAA
1967747 GAGCCTTGCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.37, C:0.31, G:0.11, T:0.20
Consensus pattern (15 bp):
TCGAACAAACTTCAC
Found at i:1972735 original size:35 final size:35
Alignment explanation
Indices: 1972696--1972766 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
1972686 CTTTAACCAC
*
1972696 TGAAATAGTTTGATTCGTACTGATTCAATAACCTT
1 TGAAATAGCTTGATTCGTACTGATTCAATAACCTT
1972731 TGAAATAGCTTGATTCGTACTGATTCAATAACCTT
1 TGAAATAGCTTGATTCGTACTGATTCAATAACCTT
1972766 T
1 T
1972767 TACTTGTGCA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.31, C:0.15, G:0.14, T:0.39
Consensus pattern (35 bp):
TGAAATAGCTTGATTCGTACTGATTCAATAACCTT
Found at i:1978727 original size:49 final size:51
Alignment explanation
Indices: 1978670--1978860 Score: 208
Period size: 55 Copynumber: 3.6 Consensus size: 51
1978660 GGCGGGTCTA
*
1978670 CTCCCTATTCTTTCATGGAGTATAAGACTCGAACAATCTTCAGTAAA-C-G
1 CTCCCTATTCTTTCAGGGAGTATAAGACTCGAACAATCTTCAGTAAAGCTG
* *
1978719 CTCCCTATTCATTCAGGGAGTATAAGACTCGAATAATCTTCAGTAAACGTGTCTG
1 CTCCCTATTCTTTCAGGGAGTATAAGACTCGAACAATCTTCAGTAAA---G-CTG
** *
1978774 CTCCCTATT-TGTTCAGGGAGTATAAGACTCGAACAATCTTCAAAAAACGGGTCCG
1 CTCCCTATTCT-TTCAGGGAGTATAAGACTCGAACAATCTTCAGTAAA---G-CTG
* *
1978829 CTCCCTATTCCTTCAGAGAGTATAAGACTCGA
1 CTCCCTATTCTTTCAGGGAGTATAAGACTCGA
1978861 TCTTCAATAA
Statistics
Matches: 123, Mismatches: 11, Indels: 10
0.85 0.08 0.07
Matches are distributed among these distances:
49 44 0.36
54 1 0.01
55 78 0.63
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.29
Consensus pattern (51 bp):
CTCCCTATTCTTTCAGGGAGTATAAGACTCGAACAATCTTCAGTAAAGCTG
Found at i:1978802 original size:55 final size:55
Alignment explanation
Indices: 1978670--1979011 Score: 342
Period size: 51 Copynumber: 6.5 Consensus size: 55
1978660 GGCGGGTCTA
* * *
1978670 CTCCCTATTCTTTCATGGAGTATAAGACTCGAACAATCTTCAGTAAA------CG
1 CTCCCTATTCCTTCAGGGAGTATAAGACTCGAACAATCTTCAATAAACGTGTCCG
* * * *
1978719 CTCCCTATTCATTCAGGGAGTATAAGACTCGAATAATCTTCAGTAAACGTGTCTG
1 CTCCCTATTCCTTCAGGGAGTATAAGACTCGAACAATCTTCAATAAACGTGTCCG
** * *
1978774 CTCCCTATTTGTTCAGGGAGTATAAGACTCGAACAATCTTCAAAAAACGGGTCCG
1 CTCCCTATTCCTTCAGGGAGTATAAGACTCGAACAATCTTCAATAAACGTGTCCG
*
1978829 CTCCCTATTCCTTCAGAGAGTATAAGACTCG----ATCTTCAATAAACGTGTCCG
1 CTCCCTATTCCTTCAGGGAGTATAAGACTCGAACAATCTTCAATAAACGTGTCCG
* * ** *
1978880 CTCCCTATTCCTTCAGAGAGTATAGGACT----CAATCTTCAACGAACTTGTCCG
1 CTCCCTATTCCTTCAGGGAGTATAAGACTCGAACAATCTTCAATAAACGTGTCCG
* * ** *
1978931 CTCCCTATTCCTTCAGAGAGTATAGGACT----CAATCTTCAACGAACTTGTCCG
1 CTCCCTATTCCTTCAGGGAGTATAAGACTCGAACAATCTTCAATAAACGTGTCCG
* *
1978982 CTCCCTATTCCTTCAGAGAGTATAGGACTC
1 CTCCCTATTCCTTCAGGGAGTATAAGACTC
1979012 AATCTTCAAC
Statistics
Matches: 264, Mismatches: 20, Indels: 15
0.88 0.07 0.05
Matches are distributed among these distances:
49 44 0.17
51 143 0.54
55 77 0.29
ACGTcount: A:0.28, C:0.26, G:0.17, T:0.29
Consensus pattern (55 bp):
CTCCCTATTCCTTCAGGGAGTATAAGACTCGAACAATCTTCAATAAACGTGTCCG
Found at i:1978885 original size:51 final size:51
Alignment explanation
Indices: 1978717--1979026 Score: 377
Period size: 51 Copynumber: 5.9 Consensus size: 51
1978707 CTTCAGTAAA
* * **
1978717 CGCTCCCTATTCATTCAGGGAGTATAAGACTCGAATAATCTTCAGTAAACGTGTC
1 CGCTCCCTATTCCTTCAGAGAGTATAAGACTC----AATCTTCAACAAACGTGTC
* ** * * *
1978772 TGCTCCCTATTTGTTCAGGGAGTATAAGACTCGAACAATCTTCAAAAAACGGGTC
1 CGCTCCCTATTCCTTCAGAGAGTATAAGACT----CAATCTTCAACAAACGTGTC
* *
1978827 CGCTCCCTATTCCTTCAGAGAGTATAAGACTCGATCTTCAATAAACGTGTC
1 CGCTCCCTATTCCTTCAGAGAGTATAAGACTCAATCTTCAACAAACGTGTC
* * *
1978878 CGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTC
1 CGCTCCCTATTCCTTCAGAGAGTATAAGACTCAATCTTCAACAAACGTGTC
* * *
1978929 CGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTC
1 CGCTCCCTATTCCTTCAGAGAGTATAAGACTCAATCTTCAACAAACGTGTC
*
1978980 CGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACAAACG
1 CGCTCCCTATTCCTTCAGAGAGTATAAGACTCAATCTTCAACAAACG
1979027 AGTTTGCTTC
Statistics
Matches: 231, Mismatches: 20, Indels: 12
0.88 0.08 0.05
Matches are distributed among these distances:
51 159 0.69
55 71 0.31
59 1 0.00
ACGTcount: A:0.28, C:0.27, G:0.17, T:0.28
Consensus pattern (51 bp):
CGCTCCCTATTCCTTCAGAGAGTATAAGACTCAATCTTCAACAAACGTGTC
Found at i:1979239 original size:17 final size:17
Alignment explanation
Indices: 1979217--1979251 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
1979207 ATTTGAATCT
1979217 GCTTTGACTCAATTTTC
1 GCTTTGACTCAATTTTC
1979234 GCTTTGACTCAATTTTC
1 GCTTTGACTCAATTTTC
1979251 G
1 G
1979252 TCTGAACAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.17, C:0.23, G:0.14, T:0.46
Consensus pattern (17 bp):
GCTTTGACTCAATTTTC
Found at i:1980379 original size:8 final size:8
Alignment explanation
Indices: 1980368--1980405 Score: 53
Period size: 8 Copynumber: 4.9 Consensus size: 8
1980358 TTTCTTTTTT
1980368 TTTTTTCA
1 TTTTTTCA
1980376 TTTTTCTC-
1 TTTTT-TCA
1980384 TTTTTTCA
1 TTTTTTCA
1980392 -TTTTTCA
1 TTTTTTCA
1980399 TTTTTTC
1 TTTTTTC
1980406 TTCCCTTTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
7 9 0.33
8 16 0.59
9 2 0.07
ACGTcount: A:0.08, C:0.16, G:0.00, T:0.76
Consensus pattern (8 bp):
TTTTTTCA
Found at i:1980386 original size:22 final size:22
Alignment explanation
Indices: 1980358--1980407 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
1980348 CCTCCTTTTA
*
1980358 TTTCTTTTTT-TTTTTTCATTT
1 TTTCTTTTTTCATTTTTCATTT
1980379 TTCTCTTTTTTCATTTTTCATTT
1 TT-TCTTTTTTCATTTTTCATTT
1980402 TTTCTT
1 TTTCTT
1980408 CCCTTTTCCC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 2 0.08
22 12 0.46
23 12 0.46
ACGTcount: A:0.06, C:0.14, G:0.00, T:0.80
Consensus pattern (22 bp):
TTTCTTTTTTCATTTTTCATTT
Found at i:1980403 original size:16 final size:15
Alignment explanation
Indices: 1980352--1980405 Score: 67
Period size: 16 Copynumber: 3.6 Consensus size: 15
1980342 TTGAACCCTC
1980352 CTTTTATTTC-TTTTT
1 CTTTT-TTTCATTTTT
1980367 -TTTTTTTCATTTTT
1 CTTTTTTTCATTTTT
1980381 CTCTTTTTTCATTTTT
1 CT-TTTTTTCATTTTT
*
1980397 CATTTTTTC
1 CTTTTTTTC
1980406 TTCCCTTTTC
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
13 4 0.11
14 9 0.26
15 8 0.23
16 14 0.40
ACGTcount: A:0.07, C:0.15, G:0.00, T:0.78
Consensus pattern (15 bp):
CTTTTTTTCATTTTT
Found at i:1980448 original size:17 final size:18
Alignment explanation
Indices: 1980428--1980469 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
1980418 TTTTTTCTTC
*
1980428 TTTTTCTTTC-TTTTTGT
1 TTTTTCTATCATTTTTGT
*
1980445 TTTTTCCATCATTTTTGT
1 TTTTTCTATCATTTTTGT
1980463 TTTTTCT
1 TTTTTCT
1980470 CATTTTTTCT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.05, C:0.14, G:0.05, T:0.76
Consensus pattern (18 bp):
TTTTTCTATCATTTTTGT
Found at i:1980477 original size:18 final size:18
Alignment explanation
Indices: 1980438--1980476 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
1980428 TTTTTCTTTC
1980438 TTTTTGTTTTTTCCATCA
1 TTTTTGTTTTTTCCATCA
1980456 TTTTTGTTTTTT-C-TCA
1 TTTTTGTTTTTTCCATCA
1980472 TTTTT
1 TTTTT
1980477 TCTCTTTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 8 0.38
17 1 0.05
18 12 0.57
ACGTcount: A:0.08, C:0.13, G:0.05, T:0.74
Consensus pattern (18 bp):
TTTTTGTTTTTTCCATCA
Found at i:1996264 original size:35 final size:34
Alignment explanation
Indices: 1996213--1996306 Score: 125
Period size: 35 Copynumber: 2.7 Consensus size: 34
1996203 AACAGAACCA
*
1996213 TCAATTACATTATAAACCCAAAAATCTAAAATACT
1 TCAATTACATTCTAAACCC-AAAATCTAAAATACT
*
1996248 TCAATTACATTCTAAACCTCAAATTCTAAAATACT
1 TCAATTACATTCTAAACC-CAAAATCTAAAATACT
* * *
1996283 TCAATTACATGCCAAACCCCAAAT
1 TCAATTACATTCTAAACCCAAAAT
1996307 TCATAATCCA
Statistics
Matches: 52, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
34 4 0.08
35 47 0.90
36 1 0.02
ACGTcount: A:0.46, C:0.24, G:0.01, T:0.29
Consensus pattern (34 bp):
TCAATTACATTCTAAACCCAAAATCTAAAATACT
Found at i:1996640 original size:143 final size:144
Alignment explanation
Indices: 1996472--1996749 Score: 459
Period size: 148 Copynumber: 1.9 Consensus size: 144
1996462 ATTCAGTTTA
* *
1996472 TAAAATAGTTGACTCGAAATTTTTTCGATTTGAGTTTATAAAATTTAAATCAAGTC-GAATTGAA
1 TAAAATAATTGACTCGAAATTTTTTCAATTTGAGTTTATAAAATTTAAATCAAGTCAGAATTGAA
* * *
1996536 TTTTCGAGTTTCTGTTTAAATTTAATTATAAATATTTATCATATTATAATATTATTTTATTATAA
66 TTTTCGAGTTTCTGTTTAAATTTAATTATAAATATTTATAATACTATAATATTATTTGATTATAA
1996601 TCCAGGTCAATTTG
131 TCCAGGTCAATTTG
1996615 TAAAATAATTGACTCGAAATTTTTTCAATTTGAGTTTATAAAATTTAAATCAAGTCGAATTGAAT
1 TAAAATAATTGACTCGAAATTTTTTCAATTTGAGTTTATAAAATTTAAATCAAGTC--A--GAAT
1996680 TGAATTTTCGAGTTTCTGTTTAAATTTAATTATAAATATTTATAATACTATAATATTATTTGATT
62 TGAATTTTCGAGTTTCTGTTTAAATTTAATTATAAATATTTATAATACTATAATATTATTTGATT
*
1996745 CTAAT
127 ATAAT
1996750 TTAAATAGTT
Statistics
Matches: 124, Mismatches: 6, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
143 54 0.44
148 70 0.56
ACGTcount: A:0.37, C:0.07, G:0.10, T:0.46
Consensus pattern (144 bp):
TAAAATAATTGACTCGAAATTTTTTCAATTTGAGTTTATAAAATTTAAATCAAGTCAGAATTGAA
TTTTCGAGTTTCTGTTTAAATTTAATTATAAATATTTATAATACTATAATATTATTTGATTATAA
TCCAGGTCAATTTG
Found at i:2000810 original size:18 final size:18
Alignment explanation
Indices: 2000787--2000821 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2000777 CTACCGGTTC
*
2000787 ACTGGTTCAACCGGTCGA
1 ACTGGTCCAACCGGTCGA
*
2000805 ACTGGTCCGACCGGTCG
1 ACTGGTCCAACCGGTCG
2000822 GAAGAATCGG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.17, C:0.31, G:0.31, T:0.20
Consensus pattern (18 bp):
ACTGGTCCAACCGGTCGA
Found at i:2000884 original size:22 final size:21
Alignment explanation
Indices: 2000850--2000890 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
2000840 ATAATTATTT
2000850 AAAAAATTAAATAAAAATACC
1 AAAAAATTAAATAAAAATACC
*
2000871 AAAAATATTTAATAAAAATA
1 AAAAA-ATTAAATAAAAATA
2000891 TTTTTTTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.24
Consensus pattern (21 bp):
AAAAAATTAAATAAAAATACC
Found at i:2003428 original size:33 final size:33
Alignment explanation
Indices: 2003391--2003460 Score: 131
Period size: 33 Copynumber: 2.1 Consensus size: 33
2003381 TGCTTAAACA
*
2003391 ATATTAGAATATAAAGCATTACCATATATGTTT
1 ATATTAGAATATAAAGCATTACCATATATATTT
2003424 ATATTAGAATATAAAGCATTACCATATATATTT
1 ATATTAGAATATAAAGCATTACCATATATATTT
2003457 ATAT
1 ATAT
2003461 CTACAGTCAT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.44, C:0.09, G:0.07, T:0.40
Consensus pattern (33 bp):
ATATTAGAATATAAAGCATTACCATATATATTT
Found at i:2005918 original size:2 final size:2
Alignment explanation
Indices: 2005911--2005941 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2005901 AGCAGGCATT
2005911 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
2005942 GAGTGTCTAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:2008796 original size:35 final size:35
Alignment explanation
Indices: 2008750--2008825 Score: 118
Period size: 35 Copynumber: 2.2 Consensus size: 35
2008740 AAAATAGTCC
*
2008750 TCAATTTCATTCTAAACCCCAATTTCC-AAAGTAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAAG-AAT
*
2008785 TCAATTTCATTCTAAACCCTAAATTCCAAAAGAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAAGAAT
2008820 TCAATT
1 TCAATT
2008826 AAATTCAATT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
35 34 0.89
36 4 0.11
ACGTcount: A:0.39, C:0.24, G:0.03, T:0.34
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCCAAATTCCAAAAGAAT
Found at i:2009362 original size:129 final size:130
Alignment explanation
Indices: 2009222--2009468 Score: 399
Period size: 129 Copynumber: 1.9 Consensus size: 130
2009212 TATTTATATA
* * *
2009222 ATCAATTTGGTCCTAAATTAAATAGAATTTAATAAATTAATTATTTAAATAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAAACAGGATCTGACATGTG
* *
2009287 TTAGA-ACATGATCATGACACGTG-TCATTGTGACACATGTCACCACCTAATTATTTATATATGC
66 TTA-ACACATGATCATGACACGTGTTAATGGTGACACATGTCACCACCTAATTATTTATATATGC
2009350 T
130 T
*
2009351 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAAACAGGATCTGACATGTG
* *
2009416 TTAACACATGATCATGATATGTGTTAATGGTGACACATGTCACCACCTAATTA
66 TTAACACATGATCATGACACGTGTTAATGGTGACACATGTCACCACCTAATTA
2009469 GAAGAAAATT
Statistics
Matches: 108, Mismatches: 8, Indels: 3
0.91 0.07 0.03
Matches are distributed among these distances:
128 1 0.01
129 80 0.74
130 27 0.25
ACGTcount: A:0.37, C:0.15, G:0.13, T:0.35
Consensus pattern (130 bp):
ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAAACAGGATCTGACATGTG
TTAACACATGATCATGACACGTGTTAATGGTGACACATGTCACCACCTAATTATTTATATATGCT
Found at i:2009438 original size:23 final size:21
Alignment explanation
Indices: 2009395--2009442 Score: 60
Period size: 23 Copynumber: 2.2 Consensus size: 21
2009385 AATTAATCAT
2009395 TTAACCAGGATCTGACATGTG
1 TTAACCAGGATCTGACATGTG
* *
2009416 TTAACACATGATCATGATATGTG
1 TTAAC-CAGGATC-TGACATGTG
2009439 TTAA
1 TTAA
2009443 TGGTGACACA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 5 0.22
22 6 0.26
23 12 0.52
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.33
Consensus pattern (21 bp):
TTAACCAGGATCTGACATGTG
Found at i:2009828 original size:28 final size:27
Alignment explanation
Indices: 2009797--2009859 Score: 63
Period size: 28 Copynumber: 2.3 Consensus size: 27
2009787 AGTTGATACA
*
2009797 ATATTTTAAAAGAATAAATTTAAGATTT
1 ATATTTTAAAA-AATAAATTTAAGAATT
** * *
2009825 ATATATTTTTAAACTAAATTTAATAATT
1 ATAT-TTTAAAAAATAAATTTAAGAATT
2009853 ATATTTT
1 ATATTTT
2009860 TCATATTTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
27 3 0.10
28 21 0.72
29 5 0.17
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (27 bp):
ATATTTTAAAAAATAAATTTAAGAATT
Found at i:2009960 original size:16 final size:18
Alignment explanation
Indices: 2009939--2009972 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
2009929 ATTTCTTATT
2009939 AAAAATA-AAAT-ATTCA
1 AAAAATATAAATGATTCA
2009955 AAAAATATAAATGATTCA
1 AAAAATATAAATGATTCA
2009973 TACATTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.65, C:0.06, G:0.03, T:0.26
Consensus pattern (18 bp):
AAAAATATAAATGATTCA
Found at i:2013321 original size:15 final size:15
Alignment explanation
Indices: 2013303--2013332 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2013293 GATATTTAGT
*
2013303 GGGCGGATGTGGGGC
1 GGGCGGATGCGGGGC
2013318 GGGCGGATGCGGGGC
1 GGGCGGATGCGGGGC
2013333 AGGTAAGGTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.07, C:0.17, G:0.67, T:0.10
Consensus pattern (15 bp):
GGGCGGATGCGGGGC
Found at i:2017394 original size:21 final size:21
Alignment explanation
Indices: 2017365--2017412 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
2017355 TTATCTTTGT
* *
2017365 AGAATATAAACTACAAATAAA
1 AGAAGATAAACTACAAAGAAA
2017386 AGAAGATAAACTACAAAGAAA
1 AGAAGATAAACTACAAAGAAA
2017407 AGAAGA
1 AGAAGA
2017413 AGATAGTAGC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.67, C:0.08, G:0.12, T:0.12
Consensus pattern (21 bp):
AGAAGATAAACTACAAAGAAA
Found at i:2022569 original size:20 final size:21
Alignment explanation
Indices: 2022544--2022585 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
2022534 TTTTTACAAA
2022544 TTATAATA-TTTTCTTTAAAT
1 TTATAATATTTTTCTTTAAAT
2022564 TTATAATATTTTTCTTTAAAT
1 TTATAATATTTTTCTTTAAAT
2022585 T
1 T
2022586 ATTAACATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (21 bp):
TTATAATATTTTTCTTTAAAT
Found at i:2022587 original size:20 final size:19
Alignment explanation
Indices: 2022541--2022587 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 19
2022531 TTGTTTTTAC
2022541 AAATTATAATATTTTCTTT
1 AAATTATAATATTTTCTTT
2022560 AAATTTATAATATTTTTCTTT
1 AAA-TTATAATA-TTTTCTTT
2022581 AAATTAT
1 AAATTAT
2022588 TAACATTAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 3 0.12
20 12 0.46
21 11 0.42
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.57
Consensus pattern (19 bp):
AAATTATAATATTTTCTTT
Found at i:2023009 original size:2 final size:2
Alignment explanation
Indices: 2023002--2023049 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
2022992 ATGAACTCCA
2023002 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
2023044 AT AT AT
1 AT AT AT
2023050 TTGAACAATC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2029598 original size:90 final size:91
Alignment explanation
Indices: 2029444--2029616 Score: 244
Period size: 90 Copynumber: 1.9 Consensus size: 91
2029434 TTTTTCAAAG
* *
2029444 TGATGCACCGATGCACCAATCCATGCATCAATGCACCATGGATTAAATTAAACATCGAATGCATT
1 TGATGCACCGATGCACCAAACCATGCATCAATGCACCATGGACTAAATTAAACATCGAATGCATT
2029509 TTATGCATCGATGCACTCAGTGCGTT
66 TTATGCATCGATGCACTCAGTGCGTT
* * **
2029535 TGATGCATCGATGCA-CAAACCATGCATCGATGCACTC-TGG-CTATTTTGAAACATCGAATGCA
1 TGATGCACCGATGCACCAAACCATGCATCAATGCAC-CATGGACTAAATT-AAACATCGAATGCA
*
2029597 TTTTATGCATCGTTGCACTC
64 TTTTATGCATCGATGCACTC
2029617 TTAGTGCATC
Statistics
Matches: 73, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
89 4 0.05
90 54 0.74
91 15 0.21
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (91 bp):
TGATGCACCGATGCACCAAACCATGCATCAATGCACCATGGACTAAATTAAACATCGAATGCATT
TTATGCATCGATGCACTCAGTGCGTT
Found at i:2029605 original size:45 final size:44
Alignment explanation
Indices: 2029493--2029617 Score: 119
Period size: 45 Copynumber: 2.8 Consensus size: 44
2029483 GGATTAAATT
*
2029493 AAACATCGAATGCATTTTATGCATCGATGCACTCAGTGCGTTTG
1 AAACATCGAATGCATTTTATGCATCGATGCACTCTGTGCGTTTG
** **** *
2029537 ATGCATCG-ATGCACAAACCATGCATCGATGCACTCTG-GCTATTTTG
1 AAACATCGAATG--CATTTTATGCATCGATGCACTCTGTGC--GTTTG
*
2029583 AAACATCGAATGCATTTTATGCATCGTTGCACTCT
1 AAACATCGAATGCATTTTATGCATCGATGCACTCT
2029618 TAGTGCATCG
Statistics
Matches: 61, Mismatches: 15, Indels: 9
0.72 0.18 0.11
Matches are distributed among these distances:
43 3 0.05
44 8 0.13
45 37 0.61
46 10 0.16
47 3 0.05
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.31
Consensus pattern (44 bp):
AAACATCGAATGCATTTTATGCATCGATGCACTCTGTGCGTTTG
Found at i:2035516 original size:23 final size:23
Alignment explanation
Indices: 2035447--2035527 Score: 96
Period size: 23 Copynumber: 3.7 Consensus size: 23
2035437 GCACCTAACC
*
2035447 GTGCATCGATGCA-TCCTTGAAT
1 GTGCATCGATGCACACCTTGAAT
* *
2035469 GTGCATCGAT--ACACCATGAAG
1 GTGCATCGATGCACACCTTGAAT
* *
2035490 GTGCACCGATGCACGCCTTGAAT
1 GTGCATCGATGCACACCTTGAAT
2035513 GTGCATCGATGCACA
1 GTGCATCGATGCACA
2035528 AGGTCATGCA
Statistics
Matches: 47, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
20 1 0.02
21 15 0.32
22 10 0.21
23 21 0.45
ACGTcount: A:0.26, C:0.26, G:0.25, T:0.23
Consensus pattern (23 bp):
GTGCATCGATGCACACCTTGAAT
Found at i:2035543 original size:43 final size:42
Alignment explanation
Indices: 2035447--2035545 Score: 110
Period size: 43 Copynumber: 2.3 Consensus size: 42
2035437 GCACCTAACC
* * *
2035447 GTGCATCGATGCATCCTTGAATGTGCATCGATACACCATGAA
1 GTGCATCGATGCAGCCTTGAATGTGCATCGATACACAAGGAA
* * *
2035489 GGTGCACCGATGCACGCCTTGAATGTGCATCGATGCACAAGGTCA
1 -GTGCATCGATGCA-GCCTTGAATGTGCATCGATACACAAGG-AA
2035534 -TGCATCGATGCA
1 GTGCATCGATGCA
2035546 TCCGTCGGGT
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
43 23 0.49
44 23 0.49
45 1 0.02
ACGTcount: A:0.26, C:0.25, G:0.25, T:0.23
Consensus pattern (42 bp):
GTGCATCGATGCAGCCTTGAATGTGCATCGATACACAAGGAA
Found at i:2038154 original size:19 final size:19
Alignment explanation
Indices: 2038130--2038181 Score: 95
Period size: 19 Copynumber: 2.7 Consensus size: 19
2038120 AATGTATTTT
*
2038130 ATGCATCGATGCACATACC
1 ATGCATCGATGCACAAACC
2038149 ATGCATCGATGCACAAACC
1 ATGCATCGATGCACAAACC
2038168 ATGCATCGATGCAC
1 ATGCATCGATGCAC
2038182 TTTGGCTATT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.33, C:0.31, G:0.17, T:0.19
Consensus pattern (19 bp):
ATGCATCGATGCACAAACC
Found at i:2038205 original size:83 final size:84
Alignment explanation
Indices: 2038065--2038226 Score: 220
Period size: 83 Copynumber: 1.9 Consensus size: 84
2038055 TTTTAAAGTA
* * *
2038065 ATGCACCGATGCACCAATCCATGCATCGATGCACCATGGATTAAATTGAACATCGAATGTATTTT
1 ATGCACCGATGCACCAAACCATGCATCGATGCACCATGGACTAAATTGAACATCGAATGCATTTT
2038130 ATGCATCGATGCACATACC
66 ATGCATCGATGCACATACC
* ** **
2038149 ATGCATCGATGCA-CAAACCATGCATCGATGCACTTTGG-CTATTTTGAAACATCGAATGCATTT
1 ATGCACCGATGCACCAAACCATGCATCGATGCACCATGGACTAAATTG-AACATCGAATGCATTT
*
2038212 TATGCATCGTTGCAC
65 TATGCATCGATGCAC
2038227 TCTTAGTGCA
Statistics
Matches: 68, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
82 5 0.07
83 51 0.75
84 12 0.18
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.28
Consensus pattern (84 bp):
ATGCACCGATGCACCAAACCATGCATCGATGCACCATGGACTAAATTGAACATCGAATGCATTTT
ATGCATCGATGCACATACC
Found at i:2053098 original size:14 final size:14
Alignment explanation
Indices: 2053079--2053105 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2053069 CCAGCATTAT
2053079 CCTGTCCACTATAC
1 CCTGTCCACTATAC
2053093 CCTGTCCACTATA
1 CCTGTCCACTATA
2053106 GTACATCGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.41, G:0.07, T:0.30
Consensus pattern (14 bp):
CCTGTCCACTATAC
Found at i:2058770 original size:27 final size:29
Alignment explanation
Indices: 2058719--2058773 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
2058709 ACGACTAGAG
2058719 GTGCACAAAAAATCCGAATATCCGATTTT
1 GTGCACAAAAAATCCGAATATCCGATTTT
2058748 GTGCA-AAAAATATCCGAA-A-CCGATTT
1 GTGCACAAAAA-ATCCGAATATCCGATTT
2058774 GGGAAAAATC
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
27 7 0.28
28 6 0.24
29 12 0.48
ACGTcount: A:0.40, C:0.20, G:0.15, T:0.25
Consensus pattern (29 bp):
GTGCACAAAAAATCCGAATATCCGATTTT
Found at i:2058781 original size:26 final size:28
Alignment explanation
Indices: 2058725--2058781 Score: 66
Period size: 29 Copynumber: 2.1 Consensus size: 28
2058715 AGAGGTGCAC
*
2058725 AAAAAATCCGAATATCCGATTTTGTGCAA
1 AAAAAATCCGAATATCCGATTTTG-GGAA
*
2058754 AAAATATCCGAA-A-CCGA-TTTGGGAA
1 AAAAAATCCGAATATCCGATTTTGGGAA
2058779 AAA
1 AAA
2058782 TCGATTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
25 6 0.23
26 4 0.15
27 4 0.15
28 1 0.04
29 11 0.42
ACGTcount: A:0.46, C:0.16, G:0.16, T:0.23
Consensus pattern (28 bp):
AAAAAATCCGAATATCCGATTTTGGGAA
Found at i:2061183 original size:21 final size:21
Alignment explanation
Indices: 2061159--2061199 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
2061149 AGTTTATTTT
2061159 TAAACTTTATTTCAATTATCA
1 TAAACTTTATTTCAATTATCA
*
2061180 TAAACTTTGTTTCAATTATC
1 TAAACTTTATTTCAATTATC
2061200 GAACTTGGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.34, C:0.15, G:0.02, T:0.49
Consensus pattern (21 bp):
TAAACTTTATTTCAATTATCA
Found at i:2061247 original size:33 final size:33
Alignment explanation
Indices: 2061195--2061298 Score: 165
Period size: 33 Copynumber: 3.2 Consensus size: 33
2061185 TTTGTTTCAA
2061195 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
* *
2061228 TTATTGAACTTGGAGGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
* *
2061261 TTATCGAACTTGGAAGTATTTAAGTATTTCAA-
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
2061293 TTATCG
1 TTATCG
2061299 TAAACTTTAT
Statistics
Matches: 65, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
32 6 0.09
33 59 0.91
ACGTcount: A:0.30, C:0.07, G:0.18, T:0.45
Consensus pattern (33 bp):
TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
Found at i:2065105 original size:102 final size:101
Alignment explanation
Indices: 2064935--2065139 Score: 311
Period size: 102 Copynumber: 2.0 Consensus size: 101
2064925 ACTGACTACA
* * *
2064935 ATCTCTTAACATGTCCATATAATTTAACAGTCCATATCTATTATCTAACAATCAGATCTATTCAA
1 ATCTCTTAACATGTCCATATAATCTAACAGTCCAAATCTACTATCTAACAATCAGATCTATTCAA
*
2065000 CTTATCAACGTATAAATAATTATGACTCTAAACCTG
66 CTTATCAACCTATAAATAATTATGACTCTAAACCTG
* * ** *
2065036 ATCTCTTAACATGTTCATATAATCTAACAGATTCAAATCTACTATCTAAGTATCAGATCTATTCC
1 ATCTCTTAACATGTCCATATAATCTAACAG-TCCAAATCTACTATCTAACAATCAGATCTATTCA
*
2065101 ACTTATTAACCTATAAATAATTATGACTCTAAACCTG
65 ACTTATCAACCTATAAATAATTATGACTCTAAACCTG
2065138 AT
1 AT
2065140 ATCAACACTA
Statistics
Matches: 93, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
101 28 0.30
102 65 0.70
ACGTcount: A:0.38, C:0.20, G:0.06, T:0.36
Consensus pattern (101 bp):
ATCTCTTAACATGTCCATATAATCTAACAGTCCAAATCTACTATCTAACAATCAGATCTATTCAA
CTTATCAACCTATAAATAATTATGACTCTAAACCTG
Found at i:2072252 original size:31 final size:31
Alignment explanation
Indices: 2072215--2072282 Score: 127
Period size: 31 Copynumber: 2.2 Consensus size: 31
2072205 TTATGTTTTG
2072215 TTGGTTTAGCAGGAATGTAAGATTACCGTGC
1 TTGGTTTAGCAGGAATGTAAGATTACCGTGC
*
2072246 TTGGTTTAGCAGGAATGTAAGATTACTGTGC
1 TTGGTTTAGCAGGAATGTAAGATTACCGTGC
2072277 TTGGTT
1 TTGGTT
2072283 AAATGAATAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.24, C:0.10, G:0.29, T:0.37
Consensus pattern (31 bp):
TTGGTTTAGCAGGAATGTAAGATTACCGTGC
Found at i:2073308 original size:36 final size:36
Alignment explanation
Indices: 2073237--2073309 Score: 96
Period size: 36 Copynumber: 2.0 Consensus size: 36
2073227 GTTAGAAAAT
* *
2073237 ATTTATATATTTTATTTAAAAATTTAAATTCATAAA
1 ATTTATATATTTTATTTAAAAATTGAAAATCATAAA
2073273 ATTTATATAATTTT-TTTACAAAATTGAAAAT-ATAAA
1 ATTTATAT-ATTTTATTTA-AAAATTGAAAATCATAAA
2073309 A
1 A
2073310 ATGTTTAATG
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
36 18 0.55
37 15 0.45
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.47
Consensus pattern (36 bp):
ATTTATATATTTTATTTAAAAATTGAAAATCATAAA
Found at i:2073311 original size:37 final size:37
Alignment explanation
Indices: 2073232--2073311 Score: 94
Period size: 37 Copynumber: 2.2 Consensus size: 37
2073222 AACAAGTTAG
* *
2073232 AAAATATTTATATATTTTATTTAAAAATTTAAATTCAT
1 AAAA-ATTTATATATTTTATTTAAAAATTGAAAATCAT
2073270 -AAAATTTATATAATTTT-TTTACAAAATTGAAAAT-AT
1 AAAAATTTATAT-ATTTTATTTA-AAAATTGAAAATCAT
2073306 AAAAAT
1 AAAAAT
2073312 GTTTAATGAA
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
36 14 0.38
37 23 0.62
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.45
Consensus pattern (37 bp):
AAAAATTTATATATTTTATTTAAAAATTGAAAATCAT
Found at i:2079566 original size:58 final size:57
Alignment explanation
Indices: 2079472--2079591 Score: 213
Period size: 58 Copynumber: 2.1 Consensus size: 57
2079462 AGCTATACTT
2079472 AAAATTGGAAATAAATATGGTAAATTTCAAGGTAAGATTATTAAAGGTTTAATAAAA
1 AAAATTGGAAATAAATATGGTAAATTTCAAGGTAAGATTATTAAAGGTTTAATAAAA
* *
2079529 AAAAGTTGGAAATAAATATGGTAAATTTCATGGTAAGATTATTAAAGGTTTAATATAA
1 AAAA-TTGGAAATAAATATGGTAAATTTCAAGGTAAGATTATTAAAGGTTTAATAAAA
2079587 AAAAT
1 AAAAT
2079592 ATTTAAATTA
Statistics
Matches: 60, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
57 5 0.08
58 55 0.92
ACGTcount: A:0.50, C:0.02, G:0.16, T:0.33
Consensus pattern (57 bp):
AAAATTGGAAATAAATATGGTAAATTTCAAGGTAAGATTATTAAAGGTTTAATAAAA
Found at i:2080035 original size:76 final size:76
Alignment explanation
Indices: 2079897--2080040 Score: 218
Period size: 76 Copynumber: 1.9 Consensus size: 76
2079887 TTACATTATT
* ** *
2079897 ATTATTATTATACCTTTAAACAAACCGGTAGACAGTTTAACGTAATAGGTAGTGTCTCTTTTATT
1 ATTATTATTATACCTTTAAACAAACAGGTAGACAGTTTAACGTAATAGGTAGTCACTATTTTATT
2079962 TTACCCTTTAC
66 TTACCCTTTAC
* *
2079973 ATTATTATTATACCTTTAAACAAACAGGTAGATAGTTTAACGTAATATGTAG-CACATATTTTAT
1 ATTATTATTATACCTTTAAACAAACAGGTAGACAGTTTAACGTAATAGGTAGTCAC-TATTTTAT
2080037 TTTA
65 TTTA
2080041 ACTTGTTAAG
Statistics
Matches: 61, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
75 1 0.02
76 60 0.98
ACGTcount: A:0.34, C:0.14, G:0.11, T:0.41
Consensus pattern (76 bp):
ATTATTATTATACCTTTAAACAAACAGGTAGACAGTTTAACGTAATAGGTAGTCACTATTTTATT
TTACCCTTTAC
Found at i:2080073 original size:100 final size:100
Alignment explanation
Indices: 2079958--2080141 Score: 271
Period size: 100 Copynumber: 1.8 Consensus size: 100
2079948 GTGTCTCTTT
* * *
2079958 TATTTTACCCTTTACATTATTATTATACCTTTAAACAAA-CAGGTAGATAGTTTAACGTAATATG
1 TATTTTACCCTTTACATTAATATTATACCTTTAAACAAATC-GATAGATAGTTTAACGTAATAGG
2080022 TAGCACATATTTTATTTTAACTTGTTAAGTTGTAAA
65 TAGCACATATTTTATTTTAACTTGTTAAGTTGTAAA
** * *
2080058 TATTTTACTGTTTACATTAATATTATACCTTTAGACAAATCGATAGGTAGTTTAACGTAATAGGT
1 TATTTTACCCTTTACATTAATATTATACCTTTAAACAAATCGATAGATAGTTTAACGTAATAGGT
* *
2080123 AGCGCCTATTTTATTTTAA
66 AGCACATATTTTATTTTAA
2080142 TCAGTTACAT
Statistics
Matches: 74, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
100 73 0.99
101 1 0.01
ACGTcount: A:0.34, C:0.12, G:0.11, T:0.43
Consensus pattern (100 bp):
TATTTTACCCTTTACATTAATATTATACCTTTAAACAAATCGATAGATAGTTTAACGTAATAGGT
AGCACATATTTTATTTTAACTTGTTAAGTTGTAAA
Found at i:2080159 original size:77 final size:76
Alignment explanation
Indices: 2080069--2080301 Score: 247
Period size: 77 Copynumber: 3.0 Consensus size: 76
2080059 ATTTTACTGT
* *
2080069 TTACATTAATATTATACCTTTAGACAAATCGATAGGTAGTTTAACGTAATAGGTAGCGCCTATTT
1 TTACATTAATATTATACCTTTAAACAAATCGATAGATAGTTTAACGTAATAGGTAGCG-CTATTT
*
2080134 TATTTTAATCAG
65 TATTTTAACCAG
* * * * * *
2080146 TTACATTAGTATTATACCTTTAAACATATCGATAGCTAGTTTAATGTAATAAGTTGCATGC-ATT
1 TTACATTAATATTATACCTTTAAACAAATCGATAGATAGTTTAACGTAATAGGTAGC--GCTATT
*
2080210 TTATTTT-ACCAT
64 TTATTTTAACCAG
* * * * *
2080222 TTACATTATTATTATACCTTTAAACAAAACGGTATATTGTTTAACGTAATAGGTTA-CGTCTATT
1 TTACATTAATATTATACCTTTAAACAAATCGATAGATAGTTTAACGTAATAGG-TAGCG-CTATT
* *
2080286 TGATTTTAACCGG
64 TTATTTTAACCAG
2080299 TTA
1 TTA
2080302 AGTTATAAAT
Statistics
Matches: 128, Mismatches: 22, Indels: 12
0.79 0.14 0.07
Matches are distributed among these distances:
74 1 0.01
75 1 0.01
76 57 0.45
77 67 0.52
78 1 0.01
79 1 0.01
ACGTcount: A:0.33, C:0.13, G:0.12, T:0.42
Consensus pattern (76 bp):
TTACATTAATATTATACCTTTAAACAAATCGATAGATAGTTTAACGTAATAGGTAGCGCTATTTT
ATTTTAACCAG
Found at i:2080243 original size:19 final size:19
Alignment explanation
Indices: 2080206--2080243 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
2080196 AAGTTGCATG
*
2080206 CATTTTATTTTACCATTTA
1 CATTTTATTATACCATTTA
2080225 CATTATTATTATACC-TTTA
1 CATT-TTATTATACCATTTA
2080244 AACAAAACGG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.29, C:0.16, G:0.00, T:0.55
Consensus pattern (19 bp):
CATTTTATTATACCATTTA
Found at i:2080292 original size:76 final size:76
Alignment explanation
Indices: 2080058--2080293 Score: 251
Period size: 76 Copynumber: 3.1 Consensus size: 76
2080048 AAGTTGTAAA
** * *
2080058 TATTTTACTGTTTACATTAATATTATACCTTTAGACAAATCGATAGGTAGTTTAACGTAATAGG-
1 TATTTTACCATTTACATTAATATTATACCTTTAAACAAATCGATAGATAGTTTAACGTAATAGGT
*
2080122 TAGCGCCTATTT
66 TA-CGTCTATTT
* * * * * * *
2080134 TATTTTAATCAGTTACATTAGTATTATACCTTTAAACATATCGATAGCTAGTTTAATGTAATAAG
1 TATTTT-ACCATTTACATTAATATTATACCTTTAAACAAATCGATAGATAGTTTAACGTAATAGG
* *
2080199 TTGCATGC-ATTT
65 TTACGT-CTATTT
* * * * *
2080211 TATTTTACCATTTACATTATTATTATACCTTTAAACAAAACGGTATATTGTTTAACGTAATAGGT
1 TATTTTACCATTTACATTAATATTATACCTTTAAACAAATCGATAGATAGTTTAACGTAATAGGT
2080276 TACGTCTATTT
66 TACGTCTATTT
*
2080287 GATTTTA
1 TATTTTA
2080294 ACCGGTTAAG
Statistics
Matches: 129, Mismatches: 27, Indels: 8
0.79 0.16 0.05
Matches are distributed among these distances:
75 1 0.01
76 67 0.52
77 59 0.46
78 2 0.02
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.43
Consensus pattern (76 bp):
TATTTTACCATTTACATTAATATTATACCTTTAAACAAATCGATAGATAGTTTAACGTAATAGGT
TACGTCTATTT
Found at i:2080313 original size:253 final size:252
Alignment explanation
Indices: 2079897--2080469 Score: 687
Period size: 253 Copynumber: 2.3 Consensus size: 252
2079887 TTACATTATT
* * * * * * * ** *
2079897 ATTATTATTATACCTTTAAACAAACCGGTAGAC-AGTTTAACGTAATAGGTAGTGTCTCTTTTAT
1 ATTAGTATTATACCTTTAAACGAACTGATAG-CTAATTTAACGTAATAAGTTGCATCTATTTTAT
* *
2079961 TTTACCCTTTACATTATTATTATACCTTTAAACAAACAGGTAGATAGTTTAACGTAATATGTAGC
65 TTTACCATTTACATTATTATTATACCTTTAAACAAACAGGTAGATAGTTTAACGTAATAGGTAGC
* ** * * *
2080026 ACATATTTTATTTTAACTTGTTAAGTTGTAAATATTTTACTGTTTACATTAATATTATACCTTTA
130 ACATATTTGATTTTAACCGGTTAAGTTATAAATATTTTACCGTTTACATTAATATTATACATTTA
* * * *
2080091 GACAAATC-GATAGGTAGTTTAACGTAATAGGTAGCGCCTATTTTATTTTAATCAG-TTAC
195 AACAAATCAG-TAGCTAGTTTAACATAATAGGCAGCGCCTATTTTATTTT-A-CAGTTTAC
* *
2080150 ATTAGTATTATACCTTTAAAC-ATA-TCGATAGCTAGTTTAATGTAATAAGTTGCATGC-ATTTT
1 ATTAGTATTATACCTTTAAACGA-ACT-GATAGCTAATTTAACGTAATAAGTTGCAT-CTATTTT
* *
2080212 ATTTTACCATTTACATTATTATTATACCTTTAAACAAA-ACGGTATATTGTTTAACGTAATAGGT
63 ATTTTACCATTTACATTATTATTATACCTTTAAACAAACA-GGTAGATAGTTTAACGTAATAGG-
* * *
2080276 TA-CGTC-TATTTGATTTTAACCGGTTAAGTTATAAATATTTTACCGTTTACGTTACTATTATAC
126 TAGC-ACATATTTGATTTTAACCGGTTAAGTTATAAATATTTTACCGTTTACATTAATATTATAC
*
2080339 ATTTAAACAAATCAGTAGCTAGTTTAACATAATAGGCAGCGCCTATTTTATTTTACCGTTTAC
190 ATTTAAACAAATCAGTAGCTAGTTTAACATAATAGGCAGCGCCTATTTTATTTTACAGTTTAC
* * * *
2080402 ATTATTATTATACCTTTAAACGAACTGGTAGCTAATTTAACGTAATAGGTTGCGTCTATTTTATT
1 ATTAGTATTATACCTTTAAACGAACTGATAGCTAATTTAACGTAATAAGTTGCATCTATTTTATT
2080467 TTA
66 TTA
2080470 ATTGGCTAAA
Statistics
Matches: 275, Mismatches: 33, Indels: 25
0.83 0.10 0.08
Matches are distributed among these distances:
251 3 0.01
252 64 0.23
253 203 0.74
254 5 0.02
ACGTcount: A:0.33, C:0.13, G:0.12, T:0.42
Consensus pattern (252 bp):
ATTAGTATTATACCTTTAAACGAACTGATAGCTAATTTAACGTAATAAGTTGCATCTATTTTATT
TTACCATTTACATTATTATTATACCTTTAAACAAACAGGTAGATAGTTTAACGTAATAGGTAGCA
CATATTTGATTTTAACCGGTTAAGTTATAAATATTTTACCGTTTACATTAATATTATACATTTAA
ACAAATCAGTAGCTAGTTTAACATAATAGGCAGCGCCTATTTTATTTTACAGTTTAC
Found at i:2080363 original size:176 final size:179
Alignment explanation
Indices: 2080146--2080566 Score: 510
Period size: 176 Copynumber: 2.4 Consensus size: 179
2080136 TTTTAATCAG
* * * *
2080146 TTACATTAGTATTATACCTTTAAACATATCGATAGCTAGTTTAATGTAATAAGTTGCA-TG-C-A
1 TTACATTACTATTATACCTTTAAACAAATCGATAGCTAGTTTAACGTAATAAGTTGCAGCGCCTA
* **
2080208 TTTTATTTTACCATTTACATTATTATTATACCTTTAAACAAAAC-GGTATATTGTTTAACGTAAT
66 TTTTATTTTACCATTTACATTATTATTATACCTTTAAAC-AAACTGGTAGATAATTTAACGTAAT
* *
2080272 AGGTTACGTCTATTTGATTTTAACCGGTTAAGTTATAAATATTTTACCGT
130 AGGTTACGTCTATTTGATTTTAACCGGCTAAATTATAAATATTTTACCGT
* * *
2080322 TTACGTTACTATTATACATTTAAACAAATC-AGTAGCTAGTTTAACATAAT-AG--GCAGCGCCT
1 TTACATTACTATTATACCTTTAAACAAATCGA-TAGCTAGTTTAACGTAATAAGTTGCAGCGCCT
* * *
2080383 ATTTTATTTTACCGTTTACATTATTATTATACCTTTAAACGAACTGGTAGCTAATTTAACGTAAT
65 ATTTTATTTTACCATTTACATTATTATTATACCTTTAAACAAACTGGTAGATAATTTAACGTAAT
* * ** * *
2080448 AGGTTGCGTCTATTTTATTTTAATTGGCTAAATTGTAAATATTTTATCGT
130 AGGTTACGTCTATTTGATTTTAACCGGCTAAATTATAAATATTTTACCGT
* * *
2080498 TTACATTAC---TATACCTTTAAATAAATCGATAGTTAATTTAACGTAATAAGTT---GCGCCTA
1 TTACATTACTATTATACCTTTAAACAAATCGATAGCTAGTTTAACGTAATAAGTTGCAGCGCCTA
2080557 TTTTATTTTA
66 TTTTATTTTA
2080567 ACCGGTTACT
Statistics
Matches: 209, Mismatches: 27, Indels: 21
0.81 0.11 0.08
Matches are distributed among these distances:
173 51 0.24
174 4 0.02
175 7 0.03
176 147 0.70
ACGTcount: A:0.33, C:0.13, G:0.11, T:0.43
Consensus pattern (179 bp):
TTACATTACTATTATACCTTTAAACAAATCGATAGCTAGTTTAACGTAATAAGTTGCAGCGCCTA
TTTTATTTTACCATTTACATTATTATTATACCTTTAAACAAACTGGTAGATAATTTAACGTAATA
GGTTACGTCTATTTGATTTTAACCGGCTAAATTATAAATATTTTACCGT
Found at i:2080385 original size:100 final size:100
Alignment explanation
Indices: 2080211--2080393 Score: 233
Period size: 100 Copynumber: 1.8 Consensus size: 100
2080201 GCATGCATTT
* * * * * *
2080211 TATTTTACCATTTACATTATTATTATACCTTTAAACAAAACGGTATATTGTTTAACGTAATAGGT
1 TATTTTACCATTTACATTACTATTATACATTTAAACAAAACAGTAGATAGTTTAACATAATAGGT
* *
2080276 TACGTCTATTTGATTTTAACCGGTTAAGTTATAAA
66 CACGCCTATTTGATTTTAACCGGTTAAGTTATAAA
* * * *
2080311 TATTTTACCGTTTACGTTACTATTATACATTTAAACAAATCAGTAGCTAGTTTAACATAATAGG-
1 TATTTTACCATTTACATTACTATTATACATTTAAACAAAACAGTAGATAGTTTAACATAATAGGT
*
2080375 CAGCGCCTATTTTATTTTA
66 CA-CGCCTATTTGATTTTA
2080394 CCGTTTACAT
Statistics
Matches: 69, Mismatches: 13, Indels: 2
0.82 0.15 0.02
Matches are distributed among these distances:
99 1 0.01
100 68 0.99
ACGTcount: A:0.33, C:0.14, G:0.11, T:0.42
Consensus pattern (100 bp):
TATTTTACCATTTACATTACTATTATACATTTAAACAAAACAGTAGATAGTTTAACATAATAGGT
CACGCCTATTTGATTTTAACCGGTTAAGTTATAAA
Found at i:2080411 original size:76 final size:76
Alignment explanation
Indices: 2080311--2080469 Score: 212
Period size: 76 Copynumber: 2.1 Consensus size: 76
2080301 AAGTTATAAA
* *
2080311 TATTTTACCGTTTACGTTACTATTATACATTTAAACAAA-TCAGTAGCTAGTTTAACATAATAGG
1 TATTTTACCGTTTACATTACTATTATACATTTAAACAAACT-AGTAGCTAATTTAACATAATAGG
2080375 CAGCGCCTATTT
65 CAGCGCCTATTT
* * * * * *
2080387 TATTTTACCGTTTACATTATTATTATACCTTTAAACGAACTGGTAGCTAATTTAACGTAATAGGT
1 TATTTTACCGTTTACATTACTATTATACATTTAAACAAACTAGTAGCTAATTTAACATAATAGGC
* *
2080452 TGCGTCTATTT
66 AGCGCCTATTT
2080463 TATTTTA
1 TATTTTA
2080470 ATTGGCTAAA
Statistics
Matches: 72, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
76 71 0.99
77 1 0.01
ACGTcount: A:0.31, C:0.15, G:0.12, T:0.42
Consensus pattern (76 bp):
TATTTTACCGTTTACATTACTATTATACATTTAAACAAACTAGTAGCTAATTTAACATAATAGGC
AGCGCCTATTT
Found at i:2082174 original size:29 final size:26
Alignment explanation
Indices: 2082097--2082174 Score: 71
Period size: 23 Copynumber: 3.2 Consensus size: 26
2082087 TATATAAATA
2082097 TTATA-TTTTAATTAA---AATATAT
1 TTATATTTTTAATTAATTTAATATAT
*
2082119 TTAGATTTTTAATTAATTT-ATA-A-
1 TTATATTTTTAATTAATTTAATATAT
2082142 TTATATTTTATAAATTAATTTAATAGTAT
1 TTATATTTT-T-AATTAATTTAATA-TAT
2082171 TTAT
1 TTAT
2082175 CATTAACGAT
Statistics
Matches: 44, Mismatches: 2, Indels: 13
0.75 0.03 0.22
Matches are distributed among these distances:
22 4 0.09
23 18 0.41
24 2 0.05
25 12 0.27
26 3 0.07
28 1 0.02
29 4 0.09
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (26 bp):
TTATATTTTTAATTAATTTAATATAT
Found at i:2095584 original size:29 final size:30
Alignment explanation
Indices: 2095541--2095608 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 30
2095531 AAAAAGTACA
*
2095541 AAAATAGCA-ACATTTTCAAAACAATTACC
1 AAAATAGCACACATTTCCAAAACAATTACC
* * * *
2095570 AGAATAGCACA-ATTTCCCAAATAATTACT
1 AAAATAGCACACATTTCCAAAACAATTACC
2095599 AAAATAGCAC
1 AAAATAGCAC
2095609 CCGTCAACGG
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
29 31 0.97
30 1 0.03
ACGTcount: A:0.50, C:0.21, G:0.06, T:0.24
Consensus pattern (30 bp):
AAAATAGCACACATTTCCAAAACAATTACC
Found at i:2095632 original size:13 final size:13
Alignment explanation
Indices: 2095614--2095638 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2095604 AGCACCCGTC
2095614 AACGGGTCGGGTA
1 AACGGGTCGGGTA
2095627 AACGGGTCGGGT
1 AACGGGTCGGGT
2095639 CGGGTTGCAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.16, G:0.48, T:0.16
Consensus pattern (13 bp):
AACGGGTCGGGTA
Found at i:2102671 original size:29 final size:28
Alignment explanation
Indices: 2102588--2102672 Score: 102
Period size: 29 Copynumber: 3.0 Consensus size: 28
2102578 ATTAACATTT
* *
2102588 TTTTTAAAA-AATTACGAAAATAGCAACC
1 TTTTCAAAATAATTACCAAAATAGC-ACC
*
2102616 TTTTCAAAATAATTACCAGAATAGCACC
1 TTTTCAAAATAATTACCAAAATAGCACC
2102644 ATTTCTC-AAATAATTACCAAAATAGCACC
1 -TTT-TCAAAATAATTACCAAAATAGCACC
2102673 CGATCAACGG
Statistics
Matches: 50, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
28 11 0.22
29 37 0.74
30 2 0.04
ACGTcount: A:0.46, C:0.20, G:0.06, T:0.28
Consensus pattern (28 bp):
TTTTCAAAATAATTACCAAAATAGCACC
Found at i:2107669 original size:42 final size:42
Alignment explanation
Indices: 2107610--2107690 Score: 117
Period size: 42 Copynumber: 1.9 Consensus size: 42
2107600 ATGGTAACTG
** *
2107610 ATTTAAGGCTAAAGAAAGACGTAACCGAAAATGTTAAATCTA
1 ATTTAAGGCTAAAGAAAGACACAACCGAAAATATTAAATCTA
* *
2107652 ATTTAAGGCTAAGGAAAGACACAACTGAAAATATTAAAT
1 ATTTAAGGCTAAAGAAAGACACAACCGAAAATATTAAAT
2107691 ATTTTTAATA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 34 1.00
ACGTcount: A:0.49, C:0.11, G:0.16, T:0.23
Consensus pattern (42 bp):
ATTTAAGGCTAAAGAAAGACACAACCGAAAATATTAAATCTA
Found at i:2107751 original size:32 final size:32
Alignment explanation
Indices: 2107715--2107778 Score: 110
Period size: 32 Copynumber: 2.0 Consensus size: 32
2107705 CGGCTAAGCC
*
2107715 CAACCTAAAATGTTAATCTTTTAACATTTCCG
1 CAACCTAAAATGTTAATATTTTAACATTTCCG
*
2107747 CAACCTAGAATGTTAATATTTTAACATTTCCG
1 CAACCTAAAATGTTAATATTTTAACATTTCCG
2107779 ATTGCAACCG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.34, C:0.20, G:0.08, T:0.38
Consensus pattern (32 bp):
CAACCTAAAATGTTAATATTTTAACATTTCCG
Found at i:2120054 original size:34 final size:34
Alignment explanation
Indices: 2120011--2120079 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
2120001 AGTTTAGTGG
2120011 CTTGAATTTTAACGGCACTCTATCATGGAATGAA
1 CTTGAATTTTAACGGCACTCTATCATGGAATGAA
2120045 CTTGAATTTTAACGGCACTCTATCATGGAATGAA
1 CTTGAATTTTAACGGCACTCTATCATGGAATGAA
2120079 C
1 C
2120080 AGCAATGTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Consensus pattern (34 bp):
CTTGAATTTTAACGGCACTCTATCATGGAATGAA
Found at i:2138936 original size:21 final size:21
Alignment explanation
Indices: 2138924--2138965 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
2138914 ATAAAAGAGA
2138924 AAAAATGAAAAATGAAAAAAG
1 AAAAATGAAAAATGAAAAAAG
*
2138945 AAAAATGAAAAAAGAGAAAAA
1 AAAAATGAAAAATGA-AAAAA
2138966 AGGAGGGTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.79, C:0.00, G:0.14, T:0.07
Consensus pattern (21 bp):
AAAAATGAAAAATGAAAAAAG
Found at i:2138958 original size:14 final size:14
Alignment explanation
Indices: 2138922--2138964 Score: 68
Period size: 14 Copynumber: 2.9 Consensus size: 14
2138912 AAATAAAAGA
2138922 GAAAAAATGAAAAAT
1 GAAAAAA-GAAAAAT
2138937 GAAAAAAGAAAAAT
1 GAAAAAAGAAAAAT
2138951 GAAAAAAGAGAAAA
1 GAAAAAAGA-AAAA
2138965 AAGGAGGGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
14 16 0.59
15 11 0.41
ACGTcount: A:0.77, C:0.00, G:0.16, T:0.07
Consensus pattern (14 bp):
GAAAAAAGAAAAAT
Found at i:2138964 original size:8 final size:7
Alignment explanation
Indices: 2138906--2138965 Score: 57
Period size: 7 Copynumber: 8.3 Consensus size: 7
2138896 ATTTTGCTTG
*
2138906 AAGAAGA
1 AAGAAAA
*
2138913 AATAAAA
1 AAGAAAA
*
2138920 GAGAAAA
1 AAGAAAA
2138927 AATGAAAA
1 AA-GAAAA
*
2138935 ATGAAAA
1 AAGAAAA
2138942 AAGAAAA
1 AAGAAAA
*
2138949 ATGAAAA
1 AAGAAAA
2138956 AAGAGAAA
1 AAGA-AAA
2138964 AA
1 AA
2138966 AGGAGGGTTC
Statistics
Matches: 42, Mismatches: 9, Indels: 3
0.78 0.17 0.06
Matches are distributed among these distances:
7 31 0.74
8 11 0.26
ACGTcount: A:0.77, C:0.00, G:0.17, T:0.07
Consensus pattern (7 bp):
AAGAAAA
Done.