Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D01
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: 62811768
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 736185 characters in sequence are not A, C, G, or T
File 6 of 211
Found at i:1831611 original size:10 final size:10
Alignment explanation
Indices: 1831598--1831638 Score: 55
Period size: 10 Copynumber: 4.1 Consensus size: 10
1831588 TACCTTACAT
*
1831598 ACATACATAT
1 ACATACATAC
1831608 ACATACATAC
1 ACATACATAC
**
1831618 ACACGCATAC
1 ACATACATAC
1831628 ACATACATAC
1 ACATACATAC
1831638 A
1 A
1831639 TGCTAATCAC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
10 26 1.00
ACGTcount: A:0.49, C:0.29, G:0.02, T:0.20
Consensus pattern (10 bp):
ACATACATAC
Found at i:1841693 original size:25 final size:26
Alignment explanation
Indices: 1841647--1841698 Score: 63
Period size: 25 Copynumber: 2.0 Consensus size: 26
1841637 AAATAACTTT
*
1841647 TAAATAGAAAGAAACAAGAAAAAAAA
1 TAAATAGAAAGAAACAACAAAAAAAA
*
1841673 TAAAT-GAAA-AAACAAACAAAATAAA
1 TAAATAGAAAGAAAC-AACAAAAAAAA
1841698 T
1 T
1841699 GGACATGGCC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
24 4 0.17
25 14 0.61
26 5 0.22
ACGTcount: A:0.75, C:0.06, G:0.08, T:0.12
Consensus pattern (26 bp):
TAAATAGAAAGAAACAACAAAAAAAA
Found at i:1845536 original size:32 final size:30
Alignment explanation
Indices: 1845463--1845537 Score: 78
Period size: 32 Copynumber: 2.4 Consensus size: 30
1845453 AAAAGTTTAA
* *
1845463 GTACTAACTTAAGAAAAAGTGTCAAGTTTGG
1 GTACTAA-TTAGGAAAAAATGTCAAGTTTGG
* *
1845494 ATACCAAATTAGGAAAAAAATGTCAAGTTTGGG
1 GTA-CTAATTAGG-AAAAAATGTCAAGTTT-GG
1845527 GTACTAATTAG
1 GTACTAATTAG
1845538 ACTAAAAAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
31 6 0.17
32 25 0.71
33 4 0.11
ACGTcount: A:0.41, C:0.09, G:0.21, T:0.28
Consensus pattern (30 bp):
GTACTAATTAGGAAAAAATGTCAAGTTTGG
Found at i:1846640 original size:312 final size:310
Alignment explanation
Indices: 1845923--1846680 Score: 913
Period size: 314 Copynumber: 2.4 Consensus size: 310
1845913 AAATTCAGGT
* * * * *
1845923 CCATACAAATATTAGTCATACCGATATCAATTAGGT-TCAATTATTAACACCATTAAAACGTACA
1 CCATACAAGTATTAATCACACCAATATCAATCAGGTCT-AATTATTAACACCATTAAAACGTACA
1845987 AAGAGCACAGGGATTTGGGTATATTTTAATCTTTAAACAGGTTTTGTTTTTCTTCCTCAACTCCA
65 AAGAGCACAGGGATTTGGGTATATTTTAA-CTTTAAACAGG--TTGTTTTTCTTCCTCAACTCCA
* * *
1846052 TTTCTCAAACCTAATACTTTCATCCAAACCATCCCAAAAAATGAATAAAACTTTGAACTTGAACA
127 TTTCTCAAACCAAATACTTTCATCCAAACCACCCCAAAAAA-GAATAAAACTTCGAACTTGAACA
* *
1846117 GGTGTGTCGACCCTCAAAAAAGCCTTAAAGGGGGCAACTTGGATCACCAAGATTGGGTCATCTAA
191 GGTGTGTCGACCCTCAAAAAAGCCCTAAAGGGGGCAACTTGGATCACCAAGATTGAGTCATCTAA
*
1846182 AAATTTGGTTAAACACTACCACAAAATTTATGAAATAAGAACAAGATACATGAAC
256 AAATTTGGTTAAACACTACCACAAAATTCATGAAATAAGAACAAGATACATGAAC
* * * * * *
1846237 CCATACAAGTATTAATCACATCAATATCAATCAAGTCCAATTGTTAACATCGTTAAAACGTACAA
1 CCATACAAGTATTAATCACACCAATATCAATCAGGTCTAATTATTAACACCATTAAAACGTACAA
* * * * **
1846302 AGAGCACAGGGACTT-CGAACTATTTTAACCTTTAAACAGGTTGTTTTTGCTTCCTTAACTTTAT
66 AGAGCACAGGGATTTGGGTA-TATTTTAA-CTTTAAACAGGTTGTTTTT-CTTCCTCAACTCCAT
* * * ** *
1846366 TTCTCAGACCAAATACTTTCATCCAAATCACCCCAAAGATCAA-AATGAGTCTTCGAGCTTGAAC
128 TTCTCAAACCAAATACTTTCATCCAAACCACCCCAAA-A--AAGAATAAAACTTCGAACTTGAAC
* * * * * **
1846430 AGGTCGT-TCGACCCTCGAACAAGCCCT-AAGGGGGTAGCTTGGATCACCATGATTGAGTGGTCT
190 AGGT-GTGTCGACCCTCAAAAAAGCCCTAAAGGGGGCAACTTGGATCACCAAGATTGAGTCATCT
* * *
1846493 AAAAATATT-GTTAAACCCTACCCCAGAATTCATGAACA-AA-AACAAGATACATGAAC
254 AAAAAT-TTGGTTAAACACTACCACAAAATTCATGAA-ATAAGAACAAGATACATGAAC
*
1846549 CCATACAAGTATTAATCACACCAATAACAATCAGGTCTAATTATTAACACCATTAAAACGTACAA
1 CCATACAAGTATTAATCACACCAATATCAATCAGGTCTAATTATTAACACCATTAAAACGTACAA
* * * *
1846614 AAAGCACAGAGG-TTTGGGTATATTTTAACTTCTAAACAGGTTTTTTTTCTTCTTCAACTCAATT
66 AGAGCACAG-GGATTTGGGTATATTTTAACTT-TAAACAGGTTGTTTTTCTTCCTCAACTCCATT
1846678 TCT
129 TCT
1846681 TGAGCCTATT
Statistics
Matches: 376, Mismatches: 56, Indels: 27
0.82 0.12 0.06
Matches are distributed among these distances:
311 18 0.05
312 115 0.31
313 112 0.30
314 127 0.34
315 2 0.01
316 2 0.01
ACGTcount: A:0.37, C:0.21, G:0.13, T:0.29
Consensus pattern (310 bp):
CCATACAAGTATTAATCACACCAATATCAATCAGGTCTAATTATTAACACCATTAAAACGTACAA
AGAGCACAGGGATTTGGGTATATTTTAACTTTAAACAGGTTGTTTTTCTTCCTCAACTCCATTTC
TCAAACCAAATACTTTCATCCAAACCACCCCAAAAAAGAATAAAACTTCGAACTTGAACAGGTGT
GTCGACCCTCAAAAAAGCCCTAAAGGGGGCAACTTGGATCACCAAGATTGAGTCATCTAAAAATT
TGGTTAAACACTACCACAAAATTCATGAAATAAGAACAAGATACATGAAC
Found at i:1857526 original size:3 final size:3
Alignment explanation
Indices: 1857520--1857544 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1857510 AGAAGAACAA
1857520 ACC ACC ACC ACC ACC ACC ACC ACC A
1 ACC ACC ACC ACC ACC ACC ACC ACC A
1857545 TTTCTGTCCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.64, G:0.00, T:0.00
Consensus pattern (3 bp):
ACC
Found at i:1857677 original size:3 final size:3
Alignment explanation
Indices: 1857669--1857694 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1857659 CAATTGAAGT
1857669 TGA TGA TGA TGA TGA TGA TGA TGA TG
1 TGA TGA TGA TGA TGA TGA TGA TGA TG
1857695 GTAGCAGCAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.35, T:0.35
Consensus pattern (3 bp):
TGA
Found at i:1863912 original size:20 final size:21
Alignment explanation
Indices: 1863870--1863912 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 21
1863860 GTTTAATAAA
*
1863870 AAATATTTGAAAGTAAAAGAG
1 AAATATTTGAAAGCAAAAGAG
* *
1863891 AAATTTTTG-AAGCAAAATAG
1 AAATATTTGAAAGCAAAAGAG
1863911 AA
1 AA
1863913 GAAGAAGAAG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.56, C:0.02, G:0.16, T:0.26
Consensus pattern (21 bp):
AAATATTTGAAAGCAAAAGAG
Found at i:1870864 original size:31 final size:31
Alignment explanation
Indices: 1870829--1870889 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
1870819 TTTCAATTTA
* *
1870829 ATCACTAAAATTTTAGATTATTTTTATTTTG
1 ATCACTAAAATTGTAGATCATTTTTATTTTG
* *
1870860 ATCACTCACATTGTAGATCATTTTTATTTT
1 ATCACTAAAATTGTAGATCATTTTTATTTT
1870890 AATTACTCTC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.07, T:0.52
Consensus pattern (31 bp):
ATCACTAAAATTGTAGATCATTTTTATTTTG
Found at i:1871384 original size:9 final size:9
Alignment explanation
Indices: 1871366--1871405 Score: 53
Period size: 9 Copynumber: 4.3 Consensus size: 9
1871356 CTAACTTGAA
1871366 TTTTAGATTT
1 TTTTA-ATTT
*
1871376 TTTTTATTT
1 TTTTAATTT
*
1871385 TTTTAATAT
1 TTTTAATTT
1871394 TTTTAATTT
1 TTTTAATTT
1871403 TTT
1 TTT
1871406 AGATACATAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
9 22 0.85
10 4 0.15
ACGTcount: A:0.20, C:0.00, G:0.03, T:0.78
Consensus pattern (9 bp):
TTTTAATTT
Found at i:1871501 original size:23 final size:24
Alignment explanation
Indices: 1871455--1871502 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
1871445 ATTTATACAA
***
1871455 TTTTTATATATTTTTATTTTAAAT
1 TTTTTATATATTTTTATAAAAAAT
1871479 TTTTTAT-TATTTTTATAAAAAAT
1 TTTTTATATATTTTTATAAAAAAT
1871502 T
1 T
1871503 AGATTATGAC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 14 0.67
24 7 0.33
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (24 bp):
TTTTTATATATTTTTATAAAAAAT
Found at i:1871855 original size:31 final size:31
Alignment explanation
Indices: 1871814--1871882 Score: 102
Period size: 31 Copynumber: 2.2 Consensus size: 31
1871804 ATTTAAGAGA
* *
1871814 GAGTGCCCAAAATATAAATCATCTAAAACGT
1 GAGTGACCAAAATAGAAATCATCTAAAACGT
*
1871845 GAGTGACCAAAATAGAAATGATCTAAAACGT
1 GAGTGACCAAAATAGAAATCATCTAAAACGT
*
1871876 TAGTGAC
1 GAGTGAC
1871883 TAAATTAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.45, C:0.16, G:0.17, T:0.22
Consensus pattern (31 bp):
GAGTGACCAAAATAGAAATCATCTAAAACGT
Found at i:1873430 original size:18 final size:19
Alignment explanation
Indices: 1873404--1873443 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
1873394 ATTTTTCATG
*
1873404 TCAACAAAAATTTAAAA-T
1 TCAAAAAAAATTTAAAAGT
1873422 TCAAAAAAAATTTAAAAGT
1 TCAAAAAAAATTTAAAAGT
1873441 TCA
1 TCA
1873444 CAAACTTTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 16 0.80
19 4 0.20
ACGTcount: A:0.60, C:0.10, G:0.03, T:0.28
Consensus pattern (19 bp):
TCAAAAAAAATTTAAAAGT
Found at i:1876645 original size:5 final size:5
Alignment explanation
Indices: 1876629--1876664 Score: 54
Period size: 5 Copynumber: 6.8 Consensus size: 5
1876619 TATTTCTGAT
1876629 TTATA TTTATA TTATA TTATA TTATA TTATAA TTAT
1 TTATA -TTATA TTATA TTATA TTATA TTAT-A TTAT
1876665 TCGGACATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 19 0.66
6 10 0.34
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (5 bp):
TTATA
Found at i:1877141 original size:24 final size:22
Alignment explanation
Indices: 1877114--1877160 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 22
1877104 ATAAAAAGCA
1877114 AAAATTTTATAAAATA-AAAATATT
1 AAAA-TTTA-AAAATACAAAA-ATT
1877138 AAAATTTAAAAATACAAAAATT
1 AAAATTTAAAAATACAAAAATT
1877160 A
1 A
1877161 TAAAGTTGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 10 0.45
23 8 0.36
24 4 0.18
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (22 bp):
AAAATTTAAAAATACAAAAATT
Found at i:1877157 original size:16 final size:17
Alignment explanation
Indices: 1877127--1877164 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
1877117 ATTTTATAAA
**
1877127 ATAAAAATATTAAAATT
1 ATAAAAATACAAAAATT
1877144 -TAAAAATACAAAAATT
1 ATAAAAATACAAAAATT
1877160 ATAAA
1 ATAAA
1877165 GTTGTTGGAG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (17 bp):
ATAAAAATACAAAAATT
Found at i:1877985 original size:18 final size:18
Alignment explanation
Indices: 1877934--1877985 Score: 52
Period size: 18 Copynumber: 2.8 Consensus size: 18
1877924 GTCCACATAT
*
1877934 AATTCATACAAATTTTAAA
1 AATTCA-ACAAAATTTAAA
* *
1877953 AATTTTAA-AATATTTAAA
1 AA-TTCAACAAAATTTAAA
1877971 AATTCAACAAAATTT
1 AATTCAACAAAATTT
1877986 TTAAAAAGTT
Statistics
Matches: 26, Mismatches: 5, Indels: 5
0.72 0.14 0.14
Matches are distributed among these distances:
17 4 0.15
18 16 0.62
19 3 0.12
20 3 0.12
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (18 bp):
AATTCAACAAAATTTAAA
Found at i:1878024 original size:21 final size:22
Alignment explanation
Indices: 1877983--1878025 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1877973 TTCAACAAAA
*
1877983 TTTTTAAAAAGTTCTTAAATTT
1 TTTTTAAAAAGTTATTAAATTT
*
1878005 TTTTTAAAAA-TTATTCAATTT
1 TTTTTAAAAAGTTATTAAATTT
1878026 AGTAATGAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.37, C:0.05, G:0.02, T:0.56
Consensus pattern (22 bp):
TTTTTAAAAAGTTATTAAATTT
Found at i:1884665 original size:61 final size:60
Alignment explanation
Indices: 1884549--1884665 Score: 130
Period size: 61 Copynumber: 1.9 Consensus size: 60
1884539 AAATTGATAC
* ** * *
1884549 TAAATATAAAAAATCCAATAAATTTAGCCCTCAATGGTTACAAAATTTATCATTTTAATT
1 TAAATATAAAAAATCCAATAAATTTAACCCTCAATCATTACAAAATTGATAATTTTAATT
* *
1884609 TAAATTATAAAAAATTCAATAATTTTAACCCTCAA-CATT-CACAAATTGATAAATTTT
1 TAAA-TATAAAAAATCCAATAAATTTAACCCTCAATCATTACA-AAATTGAT-AATTTT
1884666 GATTATTTTA
Statistics
Matches: 47, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
59 2 0.04
60 13 0.28
61 32 0.68
ACGTcount: A:0.46, C:0.14, G:0.03, T:0.37
Consensus pattern (60 bp):
TAAATATAAAAAATCCAATAAATTTAACCCTCAATCATTACAAAATTGATAATTTTAATT
Found at i:1894228 original size:22 final size:22
Alignment explanation
Indices: 1894200--1894256 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 22
1894190 GTATTCAAAC
* *
1894200 AATAACAACAAAATAGTAGTAA
1 AATAACAACAAAATAGCAGCAA
** *
1894222 AATAACAATGAAATGGCAGCAA
1 AATAACAACAAAATAGCAGCAA
*
1894244 AATAATAACAAAA
1 AATAACAACAAAA
1894257 AATGAAATTT
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.63, C:0.11, G:0.11, T:0.16
Consensus pattern (22 bp):
AATAACAACAAAATAGCAGCAA
Found at i:1895326 original size:18 final size:20
Alignment explanation
Indices: 1895295--1895340 Score: 69
Period size: 19 Copynumber: 2.4 Consensus size: 20
1895285 GGCATAGTTT
1895295 AAAATGAAAAA-TTTAAAGA
1 AAAATGAAAAATTTTAAAGA
*
1895314 AAAAT-AAAGATTTTAAAGA
1 AAAATGAAAAATTTTAAAGA
1895333 AAAATGAA
1 AAAATGAA
1895341 TATTGTAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 4 0.17
19 18 0.75
20 2 0.08
ACGTcount: A:0.67, C:0.00, G:0.11, T:0.22
Consensus pattern (20 bp):
AAAATGAAAAATTTTAAAGA
Found at i:1895962 original size:14 final size:13
Alignment explanation
Indices: 1895941--1895976 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 13
1895931 TTTTTTCATA
1895941 TTATAAATATATT
1 TTATAAATATATT
1895954 TTATGAAATATATT
1 TTAT-AAATATATT
1895968 TTCATAAAT
1 TT-ATAAAT
1895977 TTTGATAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 4 0.19
14 15 0.71
15 2 0.10
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.50
Consensus pattern (13 bp):
TTATAAATATATT
Found at i:1902379 original size:30 final size:31
Alignment explanation
Indices: 1902344--1902404 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
1902334 CAACCTTATT
* *
1902344 ACTTAAATAAAAA-ATTTAAATAGTTTAATA
1 ACTTAAATAAAAACATTTAAACAATTTAATA
*
1902374 ACTTAAATAAAAACTTTTAAACAATTTAATA
1 ACTTAAATAAAAACATTTAAACAATTTAATA
1902405 TTGTACACTT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 13 0.48
31 14 0.52
ACGTcount: A:0.56, C:0.07, G:0.02, T:0.36
Consensus pattern (31 bp):
ACTTAAATAAAAACATTTAAACAATTTAATA
Found at i:1905939 original size:24 final size:24
Alignment explanation
Indices: 1905910--1905958 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
1905900 CTTTGCTCAT
1905910 ATAAGAAAAACAACCAAATCAGCA
1 ATAAGAAAAACAACCAAATCAGCA
1905934 ATAAGAAAAACAACCAAATCAGCA
1 ATAAGAAAAACAACCAAATCAGCA
1905958 A
1 A
1905959 GTTAAGGCCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.63, C:0.20, G:0.08, T:0.08
Consensus pattern (24 bp):
ATAAGAAAAACAACCAAATCAGCA
Found at i:1908364 original size:9 final size:9
Alignment explanation
Indices: 1908346--1908385 Score: 62
Period size: 9 Copynumber: 4.4 Consensus size: 9
1908336 TTTGGTTAAA
*
1908346 AATTACCCG
1 AATTAACCG
1908355 AATTAACCG
1 AATTAACCG
*
1908364 AATTACCCG
1 AATTAACCG
1908373 AATTAACCG
1 AATTAACCG
1908382 AATT
1 AATT
1908386 GAATCACTAC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 28 1.00
ACGTcount: A:0.40, C:0.25, G:0.10, T:0.25
Consensus pattern (9 bp):
AATTAACCG
Found at i:1908369 original size:18 final size:18
Alignment explanation
Indices: 1908346--1908385 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
1908336 TTTGGTTAAA
1908346 AATTACCCGAATTAACCG
1 AATTACCCGAATTAACCG
1908364 AATTACCCGAATTAACCG
1 AATTACCCGAATTAACCG
1908382 AATT
1 AATT
1908386 GAATCACTAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.40, C:0.25, G:0.10, T:0.25
Consensus pattern (18 bp):
AATTACCCGAATTAACCG
Found at i:1909634 original size:27 final size:26
Alignment explanation
Indices: 1909573--1909658 Score: 109
Period size: 26 Copynumber: 3.2 Consensus size: 26
1909563 GGCTCGGCCC
* * * **
1909573 ATTTTTAAAATAAACATTAAAAATTT
1 ATTTTAAAAATAAAAAATAAAAAAAT
1909599 ATTTTAAAAATAAAAAATAAAAAAAT
1 ATTTTAAAAATAAAAAATAAAAAAAT
1909625 ATTTTAAAAATAAAAAATAAAAAAAAT
1 ATTTTAAAAATAAAAAAT-AAAAAAAT
1909652 ATATTTA
1 AT-TTTA
1909659 TTATATTTGG
Statistics
Matches: 53, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
26 39 0.74
27 10 0.19
28 4 0.08
ACGTcount: A:0.65, C:0.01, G:0.00, T:0.34
Consensus pattern (26 bp):
ATTTTAAAAATAAAAAATAAAAAAAT
Found at i:1914642 original size:15 final size:16
Alignment explanation
Indices: 1914612--1914650 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
1914602 TGGTAAAAAT
1914612 ATAATTTTATTATTTTA
1 ATAA-TTTATTATTTTA
*
1914629 ATAATTTA-TATTTTT
1 ATAATTTATTATTTTA
1914644 ATAATTT
1 ATAATTT
1914651 TTAAAAGATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 13 0.62
16 4 0.19
17 4 0.19
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
ATAATTTATTATTTTA
Found at i:1917859 original size:93 final size:93
Alignment explanation
Indices: 1917677--1917871 Score: 257
Period size: 93 Copynumber: 2.1 Consensus size: 93
1917667 AACTGAAGAA
* **
1917677 GAAGAAGAAGAAGAAGAAAAAGGGTTGTTCGAAGTGAAAGAAGTGATAACATCGGAAGCCGAGTC
1 GAAGAAGAAGAAGAAGAAAAAGGGTCGTTCGAAGTGAAAGAAGTGATAACATCGGAAGCCGACCC
* *
1917742 CGGGGAGGAAGAACAAACACGTGAAGTT
66 CGGGGAAGAAGAACAAACACGTGAAATT
* *
1917770 GAAGAAGAAGAAGAAGAAAAAGGGTCGTTCGAAGTGAAAGACGTGATAACATC-GAAGGTCGACC
1 GAAGAAGAAGAAGAAGAAAAAGGGTCGTTCGAAGTGAAAGAAGTGATAACATCGGAA-GCCGACC
** * * *
1917834 CCTTGGAAGAGGAACGAACATGTGAAATT
65 CCGGGGAAGAAGAACAAACACGTGAAATT
*
1917863 AAAGAAGAA
1 GAAGAAGAA
1917872 AAAGGGTTGA
Statistics
Matches: 88, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
92 3 0.03
93 85 0.97
ACGTcount: A:0.44, C:0.11, G:0.31, T:0.13
Consensus pattern (93 bp):
GAAGAAGAAGAAGAAGAAAAAGGGTCGTTCGAAGTGAAAGAAGTGATAACATCGGAAGCCGACCC
CGGGGAAGAAGAACAAACACGTGAAATT
Found at i:1917918 original size:14 final size:14
Alignment explanation
Indices: 1917901--1917929 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1917891 AAGAAACGAA
1917901 AACATGGAAGGTCG
1 AACATGGAAGGTCG
1917915 AACATGGAAGGTCG
1 AACATGGAAGGTCG
1917929 A
1 A
1917930 TTGTTGAAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.38, C:0.14, G:0.34, T:0.14
Consensus pattern (14 bp):
AACATGGAAGGTCG
Found at i:1918787 original size:15 final size:15
Alignment explanation
Indices: 1918767--1918810 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 15
1918757 ATGATTACCT
*
1918767 ATAAAATTTAATAAA
1 ATAAAATATAATAAA
*
1918782 ATAAAATATATTAAA
1 ATAAAATATAATAAA
*
1918797 TTAAAATAT-ATAAA
1 ATAAAATATAATAAA
1918811 TATTTTTTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
14 4 0.16
15 21 0.84
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (15 bp):
ATAAAATATAATAAA
Found at i:1924360 original size:12 final size:12
Alignment explanation
Indices: 1924345--1924369 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1924335 ATATTTTGGA
1924345 TAATAAAATATT
1 TAATAAAATATT
1924357 TAATAAAATATT
1 TAATAAAATATT
1924369 T
1 T
1924370 CATGCTTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
TAATAAAATATT
Found at i:1926816 original size:26 final size:26
Alignment explanation
Indices: 1926776--1926827 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
1926766 TAAGGATACC
*
1926776 TTAATTATAGTTTCTTATTCTACAAG
1 TTAATTATAGATTCTTATTCTACAAG
*
1926802 TTAATTTTAGATTCTTATTCTACAAG
1 TTAATTATAGATTCTTATTCTACAAG
1926828 ACTAAAACCC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.31, C:0.12, G:0.08, T:0.50
Consensus pattern (26 bp):
TTAATTATAGATTCTTATTCTACAAG
Found at i:1934975 original size:18 final size:17
Alignment explanation
Indices: 1934946--1934979 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
1934936 TTTTAATTTG
1934946 TTTATATGTATTATATT
1 TTTATATGTATTATATT
1934963 TTTATATTGTATTATAT
1 TTTATA-TGTATTATAT
1934980 GGACCATATG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (17 bp):
TTTATATGTATTATATT
Found at i:1934988 original size:27 final size:26
Alignment explanation
Indices: 1934932--1934988 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 26
1934922 AAACCAAAAT
* **
1934932 ATATTTTTAATTTGTTTATATGTATT
1 ATATTTTTAATTTGTTTATATGGACC
1934958 ATATTTTT-ATATTGTATTATATGGACC
1 ATATTTTTAAT-TTGT-TTATATGGACC
1934985 ATAT
1 ATAT
1934989 GTCAATGGGT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
25 2 0.08
26 12 0.46
27 12 0.46
ACGTcount: A:0.30, C:0.04, G:0.09, T:0.58
Consensus pattern (26 bp):
ATATTTTTAATTTGTTTATATGGACC
Found at i:1937694 original size:20 final size:20
Alignment explanation
Indices: 1937648--1937696 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 20
1937638 TTGAACGGAT
1937648 AATTAGTGTAGCTGAAATCGA
1 AATTAGT-TAGCTGAAATCGA
* *
1937669 ACTTAGTTAGTTGAAAT-GA
1 AATTAGTTAGCTGAAATCGA
1937688 GAATTAGTT
1 -AATTAGTT
1937697 GATATACCAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
19 2 0.08
20 16 0.67
21 6 0.25
ACGTcount: A:0.37, C:0.06, G:0.22, T:0.35
Consensus pattern (20 bp):
AATTAGTTAGCTGAAATCGA
Found at i:1944541 original size:26 final size:26
Alignment explanation
Indices: 1944505--1944558 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
1944495 TTGTCAATGA
1944505 CAATGAGTAAAACATTCCTCCTTTTT
1 CAATGAGTAAAACATTCCTCCTTTTT
1944531 CAATGAGTAAAACATTCCTCCTTTTT
1 CAATGAGTAAAACATTCCTCCTTTTT
1944557 CA
1 CA
1944559 TTCGCACAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.31, C:0.24, G:0.07, T:0.37
Consensus pattern (26 bp):
CAATGAGTAAAACATTCCTCCTTTTT
Found at i:1951740 original size:20 final size:19
Alignment explanation
Indices: 1951688--1951740 Score: 52
Period size: 20 Copynumber: 2.6 Consensus size: 19
1951678 GTGAGTGTTC
*
1951688 ACCAGTCAAAAACTGGATTG
1 ACCAGT-AAAAAATGGATTG
* *
1951708 ACCGGTATGAAAATGGATTG
1 ACCAGTA-AAAAATGGATTG
1951728 AACCAGTAAAAAA
1 -ACCAGTAAAAAA
1951741 CGGTTTTTTA
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
19 1 0.04
20 19 0.73
21 6 0.23
ACGTcount: A:0.45, C:0.15, G:0.21, T:0.19
Consensus pattern (19 bp):
ACCAGTAAAAAATGGATTG
Found at i:1956881 original size:6 final size:6
Alignment explanation
Indices: 1956870--1956906 Score: 65
Period size: 6 Copynumber: 6.2 Consensus size: 6
1956860 AATTAATAGT
*
1956870 ATAAAA ATAAAA ATGAAA ATAAAA ATAAAA ATAAAA A
1 ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA A
1956907 GTTTATTTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.81, C:0.00, G:0.03, T:0.16
Consensus pattern (6 bp):
ATAAAA
Found at i:1965593 original size:12 final size:11
Alignment explanation
Indices: 1965578--1965684 Score: 63
Period size: 11 Copynumber: 10.4 Consensus size: 11
1965568 AAAAATTAAA
1965578 AAAAAGTATTTT
1 AAAAA-TATTTT
1965590 AAAAATATTTT
1 AAAAATATTTT
1965601 --AAA-A--TT
1 AAAAATATTTT
* * *
1965607 AAAAAAAATTA
1 AAAAATATTTT
1965618 AAAAAGTATTTT
1 AAAAA-TATTTT
*
1965630 AAAAAAATTTT
1 AAAAATATTTT
1965641 --AAA-A-TTT
1 AAAAATATTTT
*
1965648 AAAAAT-TTTA
1 AAAAATATTTT
1965658 AAAAAGTATTTT
1 AAAAA-TATTTT
*
1965670 AAAAGTATTTT
1 AAAAATATTTT
1965681 AAAA
1 AAAA
1965685 TTAAAAAAAA
Statistics
Matches: 75, Mismatches: 8, Indels: 25
0.69 0.07 0.23
Matches are distributed among these distances:
6 2 0.03
7 3 0.04
8 5 0.07
9 10 0.13
10 7 0.09
11 28 0.37
12 20 0.27
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:1965623 original size:40 final size:40
Alignment explanation
Indices: 1965550--1965701 Score: 214
Period size: 40 Copynumber: 3.7 Consensus size: 40
1965540 AACAAAAATT
1965550 TATTTTAAAAATTAAAACAAAAATTAAAAAAAAGTATTTTAAAAA
1 TATTTT-AAAATT-AAA-AAAAATT--AAAAAAGTATTTTAAAAA
1965595 TATTTTAAAATTAAAAAAAATTAAAAAAGTATTTTAAAAA
1 TATTTTAAAATTAAAAAAAATTAAAAAAGTATTTTAAAAA
* * ** *
1965635 AATTTTAAAATTTAAAAATTTTAAAAAAGTATTTTAAAAG
1 TATTTTAAAATTAAAAAAAATTAAAAAAGTATTTTAAAAA
1965675 TATTTTAAAATTAAAAAAAATTAAAAA
1 TATTTTAAAATTAAAAAAAATTAAAAA
1965702 TAAAAAAATT
Statistics
Matches: 98, Mismatches: 9, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
40 76 0.78
42 7 0.07
43 3 0.03
44 6 0.06
45 6 0.06
ACGTcount: A:0.62, C:0.01, G:0.03, T:0.35
Consensus pattern (40 bp):
TATTTTAAAATTAAAAAAAATTAAAAAAGTATTTTAAAAA
Found at i:1965700 original size:16 final size:16
Alignment explanation
Indices: 1965679--1965709 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1965669 TAAAAGTATT
*
1965679 TTAAAATTAAAAAAAA
1 TTAAAAATAAAAAAAA
1965695 TTAAAAATAAAAAAA
1 TTAAAAATAAAAAAA
1965710 TTATTATATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (16 bp):
TTAAAAATAAAAAAAA
Found at i:1977787 original size:13 final size:14
Alignment explanation
Indices: 1977769--1977798 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
1977759 CTTTGTTGGG
1977769 TTTGTATT-AGTTT
1 TTTGTATTAAGTTT
1977782 TTTGTATTAAGTTT
1 TTTGTATTAAGTTT
1977796 TTT
1 TTT
1977799 TTTTTTTGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.50
14 8 0.50
ACGTcount: A:0.17, C:0.00, G:0.13, T:0.70
Consensus pattern (14 bp):
TTTGTATTAAGTTT
Found at i:1988154 original size:4 final size:4
Alignment explanation
Indices: 1988147--1988197 Score: 70
Period size: 4 Copynumber: 13.2 Consensus size: 4
1988137 TCTATCTATA
* *
1988147 TATG TATG TATG TATG TATG TATG TATG TATG --TG TATT TATA TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1988193 TATG T
1 TATG T
1988198 GGTTGTGGCA
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
2 2 0.05
4 40 0.95
ACGTcount: A:0.25, C:0.00, G:0.22, T:0.53
Consensus pattern (4 bp):
TATG
Found at i:1989830 original size:19 final size:18
Alignment explanation
Indices: 1989798--1989842 Score: 54
Period size: 18 Copynumber: 2.3 Consensus size: 18
1989788 ACTTCATAAA
1989798 ATTTATATATTTTTTAACATT
1 ATTTATA-A-TTTTTAA-ATT
*
1989819 TTTTATAATTTTTAAATT
1 ATTTATAATTTTTAAATT
1989837 ATTTAT
1 ATTTAT
1989843 TAATATGGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 8 0.36
19 7 0.32
20 1 0.05
21 6 0.27
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (18 bp):
ATTTATAATTTTTAAATT
Found at i:1989846 original size:19 final size:20
Alignment explanation
Indices: 1989798--1989846 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
1989788 ACTTCATAAA
*
1989798 ATTTATATATTTTTTAACATT
1 ATTTAT-TAATTTTTAACATT
*
1989819 TTTTA-TAATTTTTAA-ATT
1 ATTTATTAATTTTTAACATT
1989837 ATTTATTAAT
1 ATTTATTAAT
1989847 ATGGTATATA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
18 7 0.29
19 13 0.54
21 4 0.17
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (20 bp):
ATTTATTAATTTTTAACATT
Found at i:1989878 original size:27 final size:24
Alignment explanation
Indices: 1989848--1989898 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 24
1989838 TTTATTAATA
1989848 TGGTATATAAAAAATATATAATAAATT
1 TGGTAT-TAAAAAAT-TATAA-AAATT
*
1989875 TGGTATTATAAAATTATAAAAATT
1 TGGTATTAAAAAATTATAAAAATT
1989899 ATAATTTAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 5 0.22
25 5 0.22
26 7 0.30
27 6 0.26
ACGTcount: A:0.53, C:0.00, G:0.08, T:0.39
Consensus pattern (24 bp):
TGGTATTAAAAAATTATAAAAATT
Found at i:1992012 original size:15 final size:15
Alignment explanation
Indices: 1991994--1992023 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1991984 CTTAAATAAA
1991994 AGTAGTAGTAATAGT
1 AGTAGTAGTAATAGT
1992009 AGTAGTAGTAATAGT
1 AGTAGTAGTAATAGT
1992024 TTGTTTTTTA
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:0.40, C:0.00, G:0.27, T:0.33
Consensus pattern (15 bp):
AGTAGTAGTAATAGT
Found at i:1995704 original size:220 final size:220
Alignment explanation
Indices: 1995322--1995762 Score: 882
Period size: 220 Copynumber: 2.0 Consensus size: 220
1995312 TCAAGTGTGA
1995322 CACCTATAAAGTTATCACAACAAATGAAGTCAGCCAAAGATTCAATTCAGGCTCGCCATTGATCA
1 CACCTATAAAGTTATCACAACAAATGAAGTCAGCCAAAGATTCAATTCAGGCTCGCCATTGATCA
1995387 AGCACGCCTTCTAGTAGGCAACAGATTGCTAAGATTCCCCATAGAAACTGCACCCAAGTTCCTAA
66 AGCACGCCTTCTAGTAGGCAACAGATTGCTAAGATTCCCCATAGAAACTGCACCCAAGTTCCTAA
1995452 CAATCTGGAACCTAACCTAACCTTATCATTTCTTTATAAAAGCCTGTAACCTCAGTTTCCAATCA
131 CAATCTGGAACCTAACCTAACCTTATCATTTCTTTATAAAAGCCTGTAACCTCAGTTTCCAATCA
1995517 ATTCCCCATACAAATTACATCTGAG
196 ATTCCCCATACAAATTACATCTGAG
1995542 CACCTATAAAGTTATCACAACAAATGAAGTCAGCCAAAGATTCAATTCAGGCTCGCCATTGATCA
1 CACCTATAAAGTTATCACAACAAATGAAGTCAGCCAAAGATTCAATTCAGGCTCGCCATTGATCA
1995607 AGCACGCCTTCTAGTAGGCAACAGATTGCTAAGATTCCCCATAGAAACTGCACCCAAGTTCCTAA
66 AGCACGCCTTCTAGTAGGCAACAGATTGCTAAGATTCCCCATAGAAACTGCACCCAAGTTCCTAA
1995672 CAATCTGGAACCTAACCTAACCTTATCATTTCTTTATAAAAGCCTGTAACCTCAGTTTCCAATCA
131 CAATCTGGAACCTAACCTAACCTTATCATTTCTTTATAAAAGCCTGTAACCTCAGTTTCCAATCA
1995737 ATTCCCCATACAAATTACATCTGAG
196 ATTCCCCATACAAATTACATCTGAG
1995762 C
1 C
1995763 TCCTTACATT
Statistics
Matches: 221, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
220 221 1.00
ACGTcount: A:0.34, C:0.27, G:0.12, T:0.26
Consensus pattern (220 bp):
CACCTATAAAGTTATCACAACAAATGAAGTCAGCCAAAGATTCAATTCAGGCTCGCCATTGATCA
AGCACGCCTTCTAGTAGGCAACAGATTGCTAAGATTCCCCATAGAAACTGCACCCAAGTTCCTAA
CAATCTGGAACCTAACCTAACCTTATCATTTCTTTATAAAAGCCTGTAACCTCAGTTTCCAATCA
ATTCCCCATACAAATTACATCTGAG
Found at i:1998264 original size:19 final size:19
Alignment explanation
Indices: 1998240--1998277 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
1998230 CCTCTTTCCC
1998240 TTTAAAATCTCATTCTACG
1 TTTAAAATCTCATTCTACG
1998259 TTTAAAATCTCATTCTACG
1 TTTAAAATCTCATTCTACG
1998278 AAGAAAATAT
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:0.21, G:0.05, T:0.42
Consensus pattern (19 bp):
TTTAAAATCTCATTCTACG
Found at i:1998284 original size:19 final size:19
Alignment explanation
Indices: 1998243--1998285 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
1998233 CTTTCCCTTT
***
1998243 AAAATCTCATTCTACGTTT
1 AAAATCTCATTCTACGAAG
1998262 AAAATCTCATTCTACGAAG
1 AAAATCTCATTCTACGAAG
1998281 AAAAT
1 AAAAT
1998286 ATCTCATTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.42, C:0.19, G:0.07, T:0.33
Consensus pattern (19 bp):
AAAATCTCATTCTACGAAG
Found at i:2006542 original size:28 final size:27
Alignment explanation
Indices: 2006498--2006550 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
2006488 ACCAAAAATT
*
2006498 TATTTTAAAAGTAAAAAATATAAAAGG
1 TATTTTAAAAGTAAAAAATAAAAAAGG
*
2006525 TATTTTAAAATTAAAAAAATAAAAAA
1 TATTTTAAAAGT-AAAAAATAAAAAA
2006551 TAAAAATATT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 11 0.48
28 12 0.52
ACGTcount: A:0.64, C:0.00, G:0.06, T:0.30
Consensus pattern (27 bp):
TATTTTAAAAGTAAAAAATAAAAAAGG
Found at i:2006549 original size:27 final size:27
Alignment explanation
Indices: 2006498--2006548 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
2006488 ACCAAAAATT
2006498 TATTTTAAAAGTAAAAAATATAAAAGG
1 TATTTTAAAAGTAAAAAATATAAAAGG
*
2006525 TATTTTAAAATTAAAAAA-ATAAAA
1 TATTTTAAAAGTAAAAAATATAAAA
2006549 AATAAAAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 6 0.26
27 17 0.74
ACGTcount: A:0.63, C:0.00, G:0.06, T:0.31
Consensus pattern (27 bp):
TATTTTAAAAGTAAAAAATATAAAAGG
Found at i:2018524 original size:15 final size:15
Alignment explanation
Indices: 2018503--2018538 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
2018493 ATTTTGAGAA
2018503 AAAAATAAATATTGT
1 AAAAATAAATATTGT
* *
2018518 TAAAATAAATGTTGT
1 AAAAATAAATATTGT
2018533 AAAAAT
1 AAAAAT
2018539 CTTGATTTTG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.58, C:0.00, G:0.08, T:0.33
Consensus pattern (15 bp):
AAAAATAAATATTGT
Found at i:2023141 original size:22 final size:20
Alignment explanation
Indices: 2023105--2023163 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 20
2023095 GGCCCGGCCC
2023105 ATTT-TTTTAATAAATACCAAAA
1 ATTTATTTTAA-AAATA--AAAA
2023127 ATTTATTTTAAAAATTAAAAA
1 ATTTATTTTAAAAA-TAAAAA
**
2023148 AAGTATTTTAAAAATA
1 ATTTATTTTAAAAATA
2023164 TTTTAAAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
20 2 0.06
21 16 0.48
22 7 0.21
23 8 0.24
ACGTcount: A:0.54, C:0.03, G:0.02, T:0.41
Consensus pattern (20 bp):
ATTTATTTTAAAAATAAAAA
Found at i:2023228 original size:42 final size:41
Alignment explanation
Indices: 2023145--2023263 Score: 204
Period size: 40 Copynumber: 2.9 Consensus size: 41
2023135 TAAAAATTAA
2023145 AAAAAGTATTTTAAAAATATTTTAAAATTAAAAAA-AAAAT
1 AAAAAGTATTTTAAAAATATTTTAAAATTAAAAAATAAAAT
*
2023185 AAAAAGTGTTTTAAAAATATTTTAAAATTAAAAAATAATAAT
1 AAAAAGTATTTTAAAAATATTTTAAAATTAAAAAATAA-AAT
2023227 AAAAAGTATTTTAAAAATATTTTAAAATTTAAAAAAT
1 AAAAAGTATTTTAAAAATATTTTAAAA-TTAAAAAAT
2023264 TTAAAAAATA
Statistics
Matches: 74, Mismatches: 2, Indels: 3
0.94 0.03 0.04
Matches are distributed among these distances:
40 34 0.46
41 2 0.03
42 29 0.39
43 9 0.12
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.35
Consensus pattern (41 bp):
AAAAAGTATTTTAAAAATATTTTAAAATTAAAAAATAAAAT
Found at i:2023271 original size:18 final size:18
Alignment explanation
Indices: 2023194--2023283 Score: 58
Period size: 18 Copynumber: 4.8 Consensus size: 18
2023184 TAAAAAGTGT
*
2023194 TTTAAAAATATTTTAAAA
1 TTTAAAAATATTTAAAAA
* *
2023212 TTAAAAAATAATAATAAAAAGTA
1 TTTAAAAAT-AT--TTAAAA--A
*
2023235 TTTTAAAAATATTTTAAAA
1 -TTTAAAAATATTTAAAAA
2023254 TTTAAAAA-ATTTAAAAA
1 TTTAAAAATATTTAAAAA
* *
2023271 -ATAAATATATTTA
1 TTTAAAAATATTTA
2023284 TTATATCGGG
Statistics
Matches: 56, Mismatches: 9, Indels: 15
0.70 0.11 0.19
Matches are distributed among these distances:
16 5 0.09
17 13 0.23
18 16 0.29
19 3 0.05
21 8 0.14
23 3 0.05
24 8 0.14
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (18 bp):
TTTAAAAATATTTAAAAA
Found at i:2031496 original size:105 final size:105
Alignment explanation
Indices: 2031293--2031535 Score: 373
Period size: 105 Copynumber: 2.3 Consensus size: 105
2031283 CCTTCATAAA
* *
2031293 CGGTGATCACAGGATTATTTCTGGCCAATTTATGGAAATGTTAAAATAATTGTCTTTACGCTTGT
1 CGGTGATCACAGTATTATTTCTGGCCAATTTATGGAAATGTTAAAACAATTGTCTTTACGCTTGT
* * *
2031358 TGCTTCGTTGCAAGCAACTCAATCATTTTCACCAATCCAT
66 TGCTTCATTACAAGCAACTCAACCATTTTCACCAATCCAT
* *
2031398 TGGTGATCACAGTATTACTTCTGG-CAATTTATGGAAATGTTAAAACAATTGTCTTTACGCTTGT
1 CGGTGATCACAGTATTATTTCTGGCCAATTTATGGAAATGTTAAAACAATTGTCTTTACGCTTGT
2031462 TGCTTCCATTACAAGCAACTCAACCATTTTCACCAATCCAT
66 TGCTT-CATTACAAGCAACTCAACCATTTTCACCAATCCAT
**
2031503 CATTGATCACA-TAATTATTTCTGGCCAATTTAT
1 CGGTGATCACAGT-ATTATTTCTGGCCAATTTAT
2031536 CTTAACGCTT
Statistics
Matches: 124, Mismatches: 11, Indels: 5
0.89 0.08 0.04
Matches are distributed among these distances:
104 45 0.36
105 71 0.57
106 8 0.06
ACGTcount: A:0.29, C:0.21, G:0.14, T:0.37
Consensus pattern (105 bp):
CGGTGATCACAGTATTATTTCTGGCCAATTTATGGAAATGTTAAAACAATTGTCTTTACGCTTGT
TGCTTCATTACAAGCAACTCAACCATTTTCACCAATCCAT
Found at i:2034480 original size:29 final size:30
Alignment explanation
Indices: 2034421--2034492 Score: 83
Period size: 29 Copynumber: 2.4 Consensus size: 30
2034411 ACATTTACAG
* **
2034421 TCACTAAACTATTAATAACTTTACATTTTGA
1 TCACTAAACT-TTAAAAACTTTACAAATTGA
*
2034452 TCACTCAACTTTAAAAAC-TTACAAATTGA
1 TCACTAAACTTTAAAAACTTTACAAATTGA
*
2034481 TCACTGAACTTT
1 TCACTAAACTTT
2034493 TCGAATGTTT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
29 20 0.56
30 7 0.19
31 9 0.25
ACGTcount: A:0.39, C:0.19, G:0.04, T:0.38
Consensus pattern (30 bp):
TCACTAAACTTTAAAAACTTTACAAATTGA
Found at i:2040000 original size:17 final size:17
Alignment explanation
Indices: 2039965--2039997 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
2039955 AACAAAATTT
2039965 TATTTTAAAAATAAAAA
1 TATTTTAAAAATAAAAA
2039982 TATTTT-AAAATAAAAA
1 TATTTTAAAAATAAAAA
2039998 ATAAAAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
TATTTTAAAAATAAAAA
Found at i:2040818 original size:49 final size:48
Alignment explanation
Indices: 2040714--2040816 Score: 156
Period size: 46 Copynumber: 2.2 Consensus size: 48
2040704 TTCATCCTTG
* *
2040714 TATTATTAATGTTATGTGGTGAAAGAACTTAGCGAGTCTCTAGTCTTAT
1 TATTATTAATGTTATGTGGTG-AAGAACCTAGCAAGTCTCTAGTCTTAT
*
2040763 TATTATTGATGTTATGTGGTG-A-AACCTAGCAAGTCTCTAGTCTTAT
1 TATTATTAATGTTATGTGGTGAAGAACCTAGCAAGTCTCTAGTCTTAT
2040809 TATTATTA
1 TATTATTA
2040817 TTAGGATAAT
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
46 29 0.58
47 1 0.02
49 20 0.40
ACGTcount: A:0.28, C:0.11, G:0.18, T:0.43
Consensus pattern (48 bp):
TATTATTAATGTTATGTGGTGAAGAACCTAGCAAGTCTCTAGTCTTAT
Found at i:2041130 original size:33 final size:32
Alignment explanation
Indices: 2041071--2041132 Score: 81
Period size: 33 Copynumber: 1.9 Consensus size: 32
2041061 TGTTTGGACA
*
2041071 ACATTTTGTAATTGATTGAGAGTGTAATTACT
1 ACATTTTGTAATTGAATGAGAGTGTAATTACT
*
2041103 ACATTCTTGTAATTGTAATGA-ATTGTAATT
1 ACATT-TTGTAATTG-AATGAGAGTGTAATT
2041133 CTCTAGACGC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
32 5 0.19
33 17 0.65
34 4 0.15
ACGTcount: A:0.32, C:0.06, G:0.16, T:0.45
Consensus pattern (32 bp):
ACATTTTGTAATTGAATGAGAGTGTAATTACT
Found at i:2042719 original size:21 final size:18
Alignment explanation
Indices: 2042680--2042724 Score: 54
Period size: 18 Copynumber: 2.3 Consensus size: 18
2042670 CAAATAATTT
2042680 AAAAATTATAAAATATTC
1 AAAAATTATAAAATATTC
2042698 AAAAATATATATAAATAGTTC
1 AAAAAT-TATA-AAATA-TTC
2042719 ATAAAA
1 A-AAAA
2042725 AGAATGAAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 6 0.26
19 4 0.17
20 5 0.22
21 4 0.17
22 4 0.17
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.31
Consensus pattern (18 bp):
AAAAATTATAAAATATTC
Found at i:2044314 original size:196 final size:197
Alignment explanation
Indices: 2043980--2044369 Score: 586
Period size: 196 Copynumber: 2.0 Consensus size: 197
2043970 GATTATGATA
* * *
2043980 GTGGTATGCTTTTGGATCACTATCTTCTTTGGTTGAATGCCCTTTATTCTTTTGAGCATATATCT
1 GTGGTATGCTTTTAGATCACTATCATCTTTGGTTGAATGCCCTTTATGCTTTTGAGCATATATCT
* * *
2044045 GTATATCTGTGTATTCTCAATGGTTATAATGTCTATCGAGGCTTTAGGTTGAATCCTTTATATAT
66 CTATATCAGTGTATTCTCAATGGTTATAAAGTCTATCGAGGCTTTAGGTTGAATCCTTTATATAT
* * * *
2044110 TAAATCCAACATTGTCTCC-AAAACAATGAGTGATTAAATTGAATGG-CATGGTAAGAAGATTGG
131 TAAATCCAACATTATCTCCAAAAACAATGAGTGACTAAATGGAATGGTC-TGATAAGAAGATTGG
2044173 GTT
195 GTT
* * * * *
2044176 GTGGTATGCTTTTAGATCATTTTCATCTTTGGTTGAATGCTCTTTATGCTTTTGAGCATATGTTT
1 GTGGTATGCTTTTAGATCACTATCATCTTTGGTTGAATGCCCTTTATGCTTTTGAGCATATATCT
* * *
2044241 CTATGTCAGTGTATTCTCAATTGTTATAAAGTCTATCGAGGCTTTAGGTTGAATCCTTTATATGT
66 CTATATCAGTGTATTCTCAATGGTTATAAAGTCTATCGAGGCTTTAGGTTGAATCCTTTATATAT
*
2044306 TAAATCCAACATTATCTCCAAAAACAATGTGTGACTAAATGGAATGGTCTGATAAGAAGATTGG
131 TAAATCCAACATTATCTCCAAAAACAATGAGTGACTAAATGGAATGGTCTGATAAGAAGATTGG
2044370 ATTGCATTCA
Statistics
Matches: 173, Mismatches: 19, Indels: 3
0.89 0.10 0.02
Matches are distributed among these distances:
196 134 0.77
197 38 0.22
198 1 0.01
ACGTcount: A:0.27, C:0.14, G:0.19, T:0.40
Consensus pattern (197 bp):
GTGGTATGCTTTTAGATCACTATCATCTTTGGTTGAATGCCCTTTATGCTTTTGAGCATATATCT
CTATATCAGTGTATTCTCAATGGTTATAAAGTCTATCGAGGCTTTAGGTTGAATCCTTTATATAT
TAAATCCAACATTATCTCCAAAAACAATGAGTGACTAAATGGAATGGTCTGATAAGAAGATTGGG
TT
Found at i:2054913 original size:24 final size:25
Alignment explanation
Indices: 2054886--2054944 Score: 70
Period size: 24 Copynumber: 2.4 Consensus size: 25
2054876 AGATGACTAT
2054886 ATATAAAATGTAATAAA-TAAAA-AA
1 ATATAAAAT-TAATAAATTAAAATAA
* *
2054910 ATATTAAA-TATTAAATTAAAATAA
1 ATATAAAATTAATAAATTAAAATAA
2054934 ATATAAAATTA
1 ATATAAAATTA
2054945 TATTTTTTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
22 6 0.21
23 5 0.17
24 16 0.55
25 2 0.07
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (25 bp):
ATATAAAATTAATAAATTAAAATAA
Found at i:2056954 original size:26 final size:26
Alignment explanation
Indices: 2056925--2056990 Score: 64
Period size: 28 Copynumber: 2.4 Consensus size: 26
2056915 TTAATAATAG
2056925 TAAAATTATATTTTAATT-TTTAAAA-A
1 TAAAATTA-A-TTTAATTCTTTAAAAGA
2056951 TAAAAAATTAATTTAATTCTTTAAAAGA
1 T--AAAATTAATTTAATTCTTTAAAAGA
2056979 TATAAATATAAT
1 TA-AAAT-TAAT
2056991 AAATAATTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
26 9 0.26
27 12 0.35
28 13 0.38
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (26 bp):
TAAAATTAATTTAATTCTTTAAAAGA
Found at i:2056956 original size:27 final size:28
Alignment explanation
Indices: 2056926--2056980 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
2056916 TAATAATAGT
2056926 AAAATTATATTTTAATT-TTTAAAA-ATAA
1 AAAATTA-A-TTTAATTCTTTAAAAGATAA
2056954 AAAATTAATTTAATTCTTTAAAAGATA
1 AAAATTAATTTAATTCTTTAAAAGATA
2056981 TAAATATAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
26 7 0.28
27 8 0.32
28 10 0.40
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (28 bp):
AAAATTAATTTAATTCTTTAAAAGATAA
Found at i:2065241 original size:27 final size:28
Alignment explanation
Indices: 2065203--2065269 Score: 93
Period size: 27 Copynumber: 2.5 Consensus size: 28
2065193 GACAGCACTG
2065203 ATAGGCGGCACCAAAT-GTGCCATTCCC
1 ATAGGCGGCACCAAATGGTGCCATTCCC
*
2065230 ATAGGCGGCACC-GATGGTGCCATTCCC
1 ATAGGCGGCACCAAATGGTGCCATTCCC
* *
2065257 ATGGGTGGCACCA
1 ATAGGCGGCACCA
2065270 CTCGTGTTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
26 2 0.06
27 33 0.94
ACGTcount: A:0.22, C:0.31, G:0.28, T:0.18
Consensus pattern (28 bp):
ATAGGCGGCACCAAATGGTGCCATTCCC
Found at i:2065331 original size:11 final size:12
Alignment explanation
Indices: 2065306--2065334 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
2065296 CAGCTGAAGG
2065306 AGAAAAATAAGA
1 AGAAAAATAAGA
2065318 AGAAAAATAA-A
1 AGAAAAATAAGA
2065329 AGAAAA
1 AGAAAA
2065335 GAAGAGGTGC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 7 0.41
12 10 0.59
ACGTcount: A:0.79, C:0.00, G:0.14, T:0.07
Consensus pattern (12 bp):
AGAAAAATAAGA
Found at i:2066764 original size:17 final size:17
Alignment explanation
Indices: 2066742--2066802 Score: 59
Period size: 17 Copynumber: 3.4 Consensus size: 17
2066732 TATATTTATT
2066742 TTTTTAATTTTAAAATA
1 TTTTTAATTTTAAAATA
** *
2066759 TTTTTACATACTTTTTAATT
1 TTTTTA-AT--TTTAAAATA
*
2066779 TTTTTAATTTCAAAATA
1 TTTTTAATTTTAAAATA
2066796 TTTTTAA
1 TTTTTAA
2066803 AATACTTTTT
Statistics
Matches: 34, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
17 18 0.53
18 2 0.06
19 2 0.06
20 12 0.35
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (17 bp):
TTTTTAATTTTAAAATA
Found at i:2066780 original size:37 final size:39
Alignment explanation
Indices: 2066739--2066835 Score: 153
Period size: 37 Copynumber: 2.5 Consensus size: 39
2066729 AAATATATTT
*
2066739 ATTTTTTTAATTTTAAAATATTTTT-ACATAC-TTTTTA
1 ATTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTA
*
2066776 ATTTTTTTAATTTCAAAATATTTTTAAAATACTTTTTTA
1 ATTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTA
2066815 ATTTTTTTAATTTTTAAAATA
1 ATTTTTTTAA-TTTTAAAATA
2066836 AAAATGGGCC
Statistics
Matches: 54, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
37 24 0.44
38 5 0.09
39 16 0.30
40 9 0.17
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (39 bp):
ATTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTA
Found at i:2068831 original size:11 final size:11
Alignment explanation
Indices: 2068815--2068841 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
2068805 GTTTATGCTT
2068815 AAATTGTATCC
1 AAATTGTATCC
2068826 AAATTGTATCC
1 AAATTGTATCC
2068837 AAATT
1 AAATT
2068842 AAGTTATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.41, C:0.15, G:0.07, T:0.37
Consensus pattern (11 bp):
AAATTGTATCC
Found at i:2071675 original size:284 final size:283
Alignment explanation
Indices: 2071063--2071687 Score: 1076
Period size: 282 Copynumber: 2.2 Consensus size: 283
2071053 GCATGTTGAA
*
2071063 AAAAAAGTTAGTAAAACACTCTTACTTCGGCCATTTCTTCATATTTTTTTCTCCGCATTTTATTA
1 AAAAAAGTTAGTAAAACACTCTTACTTCGGCCATTTCTTCGTATTTTTTTCTCCGCATTTTATTA
* *
2071128 CTTTAAAAAATATTATAATTTCTAATTTTATAAATTTATTAATTTAGTGTGTTTTTTAAATTAAT
66 CTTTAAAAAATATCATAATTTCTAATTTTATAAATTTATTAATTTAGTGTGTTTTTTAAAATAAT
* * *
2071193 TTAGTGTAAAAAAACGCTTATTCTTGCCCTTTGCTCATATTATTTTCCCGAATTTTATTACTTTC
131 TTAGTGTAAAAAAACCCTTATTCCTGCCATTTGCTCATATTATTTTCCCGAATTTTATTACTTTC
*
2071258 AATAAAAAATTATTTTCGTATTTTATTATTTTATATTATTTCAGTACATTTTGTTTGAAATATTT
196 AATAAAAAATTATTTTCGTATTTTATTATTTTATATTATTTCAGTACATTTTGTTTCAAATATTT
2071323 GTATTAATTATTTCTGAATTTTT
261 GTATTAATTATTTCTGAATTTTT
2071346 -AAAAAGTTAGTAAAACACTCTTACTTCGGCCATTTCTTCGTATTTTTTTCTCCGCATTTTATTA
1 AAAAAAGTTAGTAAAACACTCTTACTTCGGCCATTTCTTCGTATTTTTTTCTCCGCATTTTATTA
2071410 CTTTAAAAAATATCATAATTTCTAATTTTATAAATTTATTAATTTAGTGTG-TTTTTAAAATAAT
66 CTTTAAAAAATATCATAATTTCTAATTTTATAAATTTATTAATTTAGTGTGTTTTTTAAAATAAT
* *
2071474 TTAGTGTAAAAAAACCCTTATTCCTGCCATTTGCTCGTATTATTTTTCCGAATTTTATTACTTTC
131 TTAGTGTAAAAAAACCCTTATTCCTGCCATTTGCTCATATTATTTTCCCGAATTTTATTACTTTC
*
2071539 AATAAAATAATTTTATTTTCGTATTTTATTATTTTATATTATTTCAGTACATTTT-TTTCAAGTA
196 AATAAAA-AA--TTATTTTCGTATTTTATTATTTTATATTATTTCAGTACATTTTGTTTCAAATA
*
2071603 TTTGTATTAATTATTTTTGAATTTTT
258 TTTGTATTAATTATTTCTGAATTTTT
* * *
2071629 AAAAAATTTTGTAAAACACTCTTACCTCGGCCATTTCTTCGTATTTTTTTCTCCGCATT
1 AAAAAAGTTAGTAAAACACTCTTACTTCGGCCATTTCTTCGTATTTTTTTCTCCGCATT
2071688 CTTTTCTCCA
Statistics
Matches: 324, Mismatches: 14, Indels: 7
0.94 0.04 0.02
Matches are distributed among these distances:
281 79 0.24
282 115 0.35
283 32 0.10
284 98 0.30
ACGTcount: A:0.30, C:0.13, G:0.07, T:0.50
Consensus pattern (283 bp):
AAAAAAGTTAGTAAAACACTCTTACTTCGGCCATTTCTTCGTATTTTTTTCTCCGCATTTTATTA
CTTTAAAAAATATCATAATTTCTAATTTTATAAATTTATTAATTTAGTGTGTTTTTTAAAATAAT
TTAGTGTAAAAAAACCCTTATTCCTGCCATTTGCTCATATTATTTTCCCGAATTTTATTACTTTC
AATAAAAAATTATTTTCGTATTTTATTATTTTATATTATTTCAGTACATTTTGTTTCAAATATTT
GTATTAATTATTTCTGAATTTTT
Found at i:2072176 original size:43 final size:44
Alignment explanation
Indices: 2072129--2072259 Score: 149
Period size: 44 Copynumber: 3.0 Consensus size: 44
2072119 TTTTTTTTTT
*
2072129 CTTTCCTCCCCTCTT-CTTCTTCTTCTTTTTTTTTTC-TCTTCTC
1 CTTTCCTCCCCT-TTCCTTCTTCTTCTTTCTTTTTTCTTCTTCTC
*** *
2072172 CTTTCCTTTTCTTTCCTTCTTTTTCTTTCTTTTTTCTTCTTCTC
1 CTTTCCTCCCCTTTCCTTCTTCTTCTTTCTTTTTTCTTCTTCTC
*** *
2072216 CTTTCCTTTTCTTTCCTTCTTTTTCTTTCTTTCTTTCTTCTTCT
1 CTTTCCTCCCCTTTCCTTCTTCTTCTTTCTTT-TTTCTTCTTCT
2072260 TCCCCTCTCC
Statistics
Matches: 80, Mismatches: 5, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
42 2 0.03
43 28 0.35
44 39 0.49
45 11 0.14
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (44 bp):
CTTTCCTCCCCTTTCCTTCTTCTTCTTTCTTTTTTCTTCTTCTC
Found at i:2072181 original size:20 final size:21
Alignment explanation
Indices: 2072142--2072259 Score: 91
Period size: 24 Copynumber: 5.5 Consensus size: 21
2072132 TCCTCCCCTC
* *
2072142 TTCTTCTTCTTCTTT-TTTTT
1 TTCTTCTTCTCCTTTCCTTTT
2072162 TTC-TCTTCTCCTTTCCTTTTCT
1 TTCTTCTTCTCCTTTCC-TTT-T
* *
2072184 TTCCTTCTTTTTCTTT-CTTTT
1 TT-CTTCTTCTCCTTTCCTTTT
2072205 TTCTTCTTCTCCTTTCCTTTTCT
1 TTCTTCTTCTCCTTTCC-TTT-T
* *
2072228 TTCCTTCTTTTTCTTT-CTTTCT
1 TT-CTTCTTCTCCTTTCCTTT-T
2072250 TTCTTCTTCT
1 TTCTTCTTCT
2072260 TCCCCTCTCC
Statistics
Matches: 80, Mismatches: 9, Indels: 17
0.75 0.08 0.16
Matches are distributed among these distances:
19 10 0.12
20 14 0.17
21 14 0.17
22 16 0.20
23 6 0.08
24 20 0.25
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (21 bp):
TTCTTCTTCTCCTTTCCTTTT
Found at i:2072187 original size:10 final size:11
Alignment explanation
Indices: 2072161--2072260 Score: 84
Period size: 10 Copynumber: 9.2 Consensus size: 11
2072151 TTCTTTTTTT
*
2072161 TTTCTCTTCTCC
1 TTTC-CTTCTTC
2072173 TTTCCTT-TTC
1 TTTCCTTCTTC
2072183 TTTCCTTCTT-
1 TTTCCTTCTTC
* *
2072193 TTTCTTTCTTT
1 TTTCCTTCTTC
*
2072204 TTTCTTCTTCTCC
1 TTTC--CTTCTTC
2072217 TTTCCTT-TTC
1 TTTCCTTCTTC
2072227 TTTCCTTCTT-
1 TTTCCTTCTTC
*
2072237 TTTCTTTCTTTC
1 TTTCCTTC-TTC
2072249 TTT-CTTCTTC
1 TTTCCTTCTTC
2072259 TT
1 TT
2072261 CCCCTCTCCT
Statistics
Matches: 73, Mismatches: 8, Indels: 16
0.75 0.08 0.16
Matches are distributed among these distances:
10 39 0.53
11 19 0.26
12 7 0.10
13 8 0.11
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (11 bp):
TTTCCTTCTTC
Found at i:2072197 original size:14 final size:14
Alignment explanation
Indices: 2072178--2072257 Score: 90
Period size: 14 Copynumber: 5.5 Consensus size: 14
2072168 TCTCCTTTCC
2072178 TTTTCTTTCCTTCT
1 TTTTCTTTCCTTCT
*
2072192 TTTTCTTT-CTTTT
1 TTTTCTTTCCTTCT
*
2072205 TTCTTCTTCTCCTTTCC
1 TT-TTCTT-TCC-TTCT
2072222 TTTTCTTTCCTTCT
1 TTTTCTTTCCTTCT
*
2072236 TTTTCTTTCTTTCT
1 TTTTCTTTCCTTCT
2072250 TTCTTCTT
1 TT-TTCTT
2072258 CTTCCCCTCT
Statistics
Matches: 56, Mismatches: 5, Indels: 9
0.80 0.07 0.13
Matches are distributed among these distances:
13 6 0.11
14 31 0.55
15 9 0.16
16 6 0.11
17 4 0.07
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (14 bp):
TTTTCTTTCCTTCT
Found at i:2072200 original size:4 final size:4
Alignment explanation
Indices: 2072179--2072254 Score: 56
Period size: 4 Copynumber: 19.5 Consensus size: 4
2072169 CTCCTTTCCT
*
2072179 TTTC TTTC CTTC -TT- TTTC TTTC TTT- TTTC -TTC TTCTCC TTTCC TTTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TT-T-C TTT-C -TTTC
*
2072227 TTTC CTTC -TT- TTTC TTTC TTTC TTTC TT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TT
2072255 CTTCTTCCCC
Statistics
Matches: 61, Mismatches: 2, Indels: 18
0.75 0.02 0.22
Matches are distributed among these distances:
3 14 0.23
4 36 0.59
5 5 0.08
6 6 0.10
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (4 bp):
TTTC
Found at i:2072220 original size:44 final size:44
Alignment explanation
Indices: 2072144--2072259 Score: 198
Period size: 44 Copynumber: 2.6 Consensus size: 44
2072134 CTCCCCTCTT
* *
2072144 CTTCTTCTTCTTTTTTTTTTC-TCTTCTCCTTTCCTTTTCTTTC
1 CTTCTTTTTCTTTCTTTTTTCTTCTTCTCCTTTCCTTTTCTTTC
2072187 CTTCTTTTTCTTTCTTTTTTCTTCTTCTCCTTTCCTTTTCTTTC
1 CTTCTTTTTCTTTCTTTTTTCTTCTTCTCCTTTCCTTTTCTTTC
2072231 CTTCTTTTTCTTTCTTTCTTTCTTCTTCT
1 CTTCTTTTTCTTTCTTT-TTTCTTCTTCT
2072260 TCCCCTCTCC
Statistics
Matches: 69, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
43 19 0.28
44 39 0.57
45 11 0.16
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (44 bp):
CTTCTTTTTCTTTCTTTTTTCTTCTTCTCCTTTCCTTTTCTTTC
Found at i:2072246 original size:34 final size:34
Alignment explanation
Indices: 2072182--2072262 Score: 91
Period size: 34 Copynumber: 2.5 Consensus size: 34
2072172 CTTTCCTTTT
*
2072182 CTTTCCTTCTTTTTCTTTCTTTTTTCTTCTTCTC
1 CTTTCCTTCTTTTTCCTTCTTTTTTCTTCTTCTC
2072216 CTTTCCTT-TTCTTTCCTTC-TTTTTCTTTCTT-T-
1 CTTTCCTTCTT-TTTCCTTCTTTTTTC-TTCTTCTC
*
2072248 CTTT-CTTCTTCTTCC
1 CTTTCCTTCTTTTTCC
2072263 CCTCTCCTTC
Statistics
Matches: 42, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
31 7 0.17
32 6 0.14
33 9 0.21
34 20 0.48
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (34 bp):
CTTTCCTTCTTTTTCCTTCTTTTTTCTTCTTCTC
Found at i:2072249 original size:48 final size:47
Alignment explanation
Indices: 2072141--2072276 Score: 174
Period size: 48 Copynumber: 3.0 Consensus size: 47
2072131 TTCCTCCCCT
*
2072141 CTTCTTCTTC-TTCTTTTTTTTTTC-TCTTCTCCTTTCCTTTTCTTTC
1 CTTCTT-TTCTTTCTTTCTTTTTTCTTCTTCTCCTTTCCTTTTCTTTC
2072187 CTTC--TT-TTTCTTTCTTTTTTCTTCTTCTCCTTTCCTTTTCTTTC
1 CTTCTTTTCTTTCTTTCTTTTTTCTTCTTCTCCTTTCCTTTTCTTTC
* * * *
2072231 CTTCTTTTTCTTTCTTTCTTTCTTCTTCTTCCCCTCTCCTTCTCTT
1 CTTC-TTTTCTTTCTTTCTTTTTTCTTCTTCTCCTTTCCTTTTCTT
2072277 CTCCCCACCC
Statistics
Matches: 79, Mismatches: 5, Indels: 10
0.84 0.05 0.11
Matches are distributed among these distances:
43 15 0.19
44 26 0.33
46 4 0.05
47 2 0.03
48 32 0.41
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (47 bp):
CTTCTTTTCTTTCTTTCTTTTTTCTTCTTCTCCTTTCCTTTTCTTTC
Found at i:2072260 original size:14 final size:14
Alignment explanation
Indices: 2072145--2072257 Score: 79
Period size: 14 Copynumber: 7.8 Consensus size: 14
2072135 TCCCCTCTTC
*
2072145 TTCTTCTTCTTTTT
1 TTCTTCTTCTTTCT
*
2072159 TTTTTC-TCTTCTCCT
1 TTCTTCTTCTT-T-CT
*
2072174 TTCCTT-TTCTTTCC
1 TT-CTTCTTCTTTCT
*
2072188 TTCTTTTTCTTTCT
1 TTCTTCTTCTTTCT
*
2072202 TTTTTCTTCTTCTCCT
1 TTCTTCTTCTT-T-CT
*
2072218 TTCCTT-TTCTTTCC
1 TT-CTTCTTCTTTCT
*
2072232 TTCTTTTTCTTTCT
1 TTCTTCTTCTTTCT
2072246 TTCTTTCTTCTT
1 TTC-TTCTTCTT
2072258 CTTCCCCTCT
Statistics
Matches: 78, Mismatches: 11, Indels: 19
0.72 0.10 0.18
Matches are distributed among these distances:
13 10 0.13
14 38 0.49
15 13 0.17
16 15 0.19
17 2 0.03
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (14 bp):
TTCTTCTTCTTTCT
Found at i:2072842 original size:19 final size:20
Alignment explanation
Indices: 2072813--2072873 Score: 65
Period size: 19 Copynumber: 3.1 Consensus size: 20
2072803 ATTTAATAAA
2072813 ATAAAATATTTATTATATTT
1 ATAAAATATTTATTATATTT
** *
2072833 AT-TTATATTT-TTA-ATATA
1 ATAAAATATTTATTATAT-TT
2072851 ATAAAATATTTATTATATTT
1 ATAAAATATTTATTATATTT
2072871 ATA
1 ATA
2072874 GTAGCATTTT
Statistics
Matches: 31, Mismatches: 6, Indels: 8
0.69 0.13 0.18
Matches are distributed among these distances:
17 2 0.06
18 6 0.19
19 12 0.39
20 9 0.29
21 2 0.06
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
ATAAAATATTTATTATATTT
Found at i:2072893 original size:38 final size:38
Alignment explanation
Indices: 2072804--2072892 Score: 124
Period size: 38 Copynumber: 2.3 Consensus size: 38
2072794 TAAAATTATA
* * *
2072804 TTTAATAAAATAAAATATTTATTATATTTATTTATATT
1 TTTAATATAATAAAATATTTATTATATTTATGTACATT
2072842 TTTAATATAATAAAATATTTATTATATTTATAGTAGCATTT
1 TTTAATATAATAAAATATTTATTATATTTAT-GTA-CA-TT
2072883 TTTAATATAA
1 TTTAATATAA
2072893 ATATTTTTAA
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
38 30 0.67
39 2 0.04
40 1 0.02
41 12 0.27
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.53
Consensus pattern (38 bp):
TTTAATATAATAAAATATTTATTATATTTATGTACATT
Found at i:2073910 original size:25 final size:24
Alignment explanation
Indices: 2073856--2073913 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 24
2073846 AATTAGTGTT
* * *
2073856 AATTGAATTAATTAAATTTTTTAAT
1 AATT-AATTAATTAAAATTTTAAAA
*
2073881 TATTAATTAAATTAAAATTTTAAAA
1 AATTAATT-AATTAAAATTTTAAAA
2073906 AATTAATT
1 AATTAATT
2073914 GAATCGAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
24 4 0.15
25 23 0.85
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (24 bp):
AATTAATTAATTAAAATTTTAAAA
Found at i:2074798 original size:20 final size:21
Alignment explanation
Indices: 2074761--2074804 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 21
2074751 TAATAATATC
*
2074761 AGTAATTATTATTTTTAA-TT
1 AGTAATTATTATTCTTAACTT
2074781 AGTAATTCATTA-TCTTAACTT
1 AGTAATT-ATTATTCTTAACTT
2074802 AGT
1 AGT
2074805 TACTAGGGCA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 12 0.57
21 9 0.43
ACGTcount: A:0.34, C:0.07, G:0.07, T:0.52
Consensus pattern (21 bp):
AGTAATTATTATTCTTAACTT
Found at i:2075449 original size:25 final size:22
Alignment explanation
Indices: 2075404--2075458 Score: 74
Period size: 25 Copynumber: 2.4 Consensus size: 22
2075394 AAAAATCCAG
2075404 TTTAATTTTTATTTTAATTAAT
1 TTTAATTTTTATTTTAATTAAT
*
2075426 TTTGATTTTTATAATTTAATTTAAT
1 TTTAATTTTTAT--TTTAA-TTAAT
2075451 TTTAATTT
1 TTTAATTT
2075459 AAAAATGTCA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
22 11 0.39
24 5 0.18
25 12 0.43
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (22 bp):
TTTAATTTTTATTTTAATTAAT
Found at i:2075580 original size:31 final size:31
Alignment explanation
Indices: 2075522--2075580 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 31
2075512 GCTAATTTGG
* * * *
2075522 GTAACGGAATATAGTTTAGGTATCACTTAGC
1 GTAACAGAATATAATTTAAGTACCACTTAGC
*
2075553 GTAACAGAGTATAATTTAAGTACCACTT
1 GTAACAGAATATAATTTAAGTACCACTT
2075581 GTGACAAAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 23 1.00
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (31 bp):
GTAACAGAATATAATTTAAGTACCACTTAGC
Found at i:2081945 original size:6 final size:6
Alignment explanation
Indices: 2081934--2081971 Score: 58
Period size: 6 Copynumber: 6.3 Consensus size: 6
2081924 CCCTTTTTCG
* *
2081934 AACCTT AACCTT AACCCT AACCCT AACCCT AACCCT AA
1 AACCCT AACCCT AACCCT AACCCT AACCCT AACCCT AA
2081972 TTTTTCCCCT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.37, C:0.42, G:0.00, T:0.21
Consensus pattern (6 bp):
AACCCT
Found at i:2084936 original size:14 final size:15
Alignment explanation
Indices: 2084917--2084950 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
2084907 TGTTTTTAAA
2084917 TTTTAA-AATACGGG
1 TTTTAAGAATACGGG
*
2084931 TTTTAAGAATATGGG
1 TTTTAAGAATACGGG
2084946 TTTTA
1 TTTTA
2084951 TTTGATAACT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 6 0.33
15 12 0.67
ACGTcount: A:0.32, C:0.03, G:0.21, T:0.44
Consensus pattern (15 bp):
TTTTAAGAATACGGG
Found at i:2085882 original size:37 final size:37
Alignment explanation
Indices: 2085834--2085926 Score: 159
Period size: 37 Copynumber: 2.5 Consensus size: 37
2085824 CACTTGTCCC
2085834 TGATCAGATAAGTATAGCCACCTATCACTTTGTTTCT
1 TGATCAGATAAGTATAGCCACCTATCACTTTGTTTCT
* * *
2085871 TGATCACATAAGTGTAGCCACTTATCACTTTGTTTCT
1 TGATCAGATAAGTATAGCCACCTATCACTTTGTTTCT
2085908 TGATCAGATAAGTATAGCC
1 TGATCAGATAAGTATAGCC
2085927 GAAGCTATCA
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 51 1.00
ACGTcount: A:0.28, C:0.20, G:0.15, T:0.37
Consensus pattern (37 bp):
TGATCAGATAAGTATAGCCACCTATCACTTTGTTTCT
Found at i:2085968 original size:52 final size:52
Alignment explanation
Indices: 2085906--2086203 Score: 413
Period size: 52 Copynumber: 5.9 Consensus size: 52
2085896 CACTTTGTTT
2085906 CTTGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTTCACTTGTCA
1 CTTGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTTCACTTGTCA
* *
2085958 CTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTCCACTTGTCA
1 CTTGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTTCACTTGTCA
* *
2086010 CTTGATCAGATAAGTGTAGCTGAAGCTATCACTTATCAC--TT--C--GTCA
1 CTTGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTTCACTTGTCA
2086056 CTTGATCAGATAAGTATAGCCGAAGCTATCACTTATCAC-TTT-A----TCA
1 CTTGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTTCACTTGTCA
* *
2086102 CTTGATCAGATAAGTATAGCCGAAGCTATTACTTATCACTTTCCACTTGTCA
1 CTTGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTTCACTTGTCA
* ** *
2086154 CTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTATCACTTG
1 CTTGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTT-TCACTTG
2086204 ATCAGAAGTA
Statistics
Matches: 223, Mismatches: 14, Indels: 17
0.88 0.06 0.07
Matches are distributed among these distances:
46 82 0.37
47 4 0.02
48 2 0.01
50 1 0.00
52 128 0.57
53 6 0.03
ACGTcount: A:0.29, C:0.23, G:0.14, T:0.34
Consensus pattern (52 bp):
CTTGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTTCACTTGTCA
Found at i:2086064 original size:46 final size:46
Alignment explanation
Indices: 2085991--2086209 Score: 262
Period size: 46 Copynumber: 4.7 Consensus size: 46
2085981 AGCTATCACT
*
2085991 TATCACTT-TCCACTT-GTCACTTGATCAGATAAGTGTAGCTGAAGC
1 TATCACTTAT-CACTTCGTCACTTGATCAGATAAGTGTAGCCGAAGC
*
2086036 TATCACTTATCACTTCGTCACTTGATCAGATAAGTATAGCCGAAGC
1 TATCACTTATCACTTCGTCACTTGATCAGATAAGTGTAGCCGAAGC
** *
2086082 TATCACTTATCACTTTATCACTTGATCAGATAAGTATAGCCGAAGC
1 TATCACTTATCACTTCGTCACTTGATCAGATAAGTGTAGCCGAAGC
* **
2086128 TATTACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGC
1 TATCACTTATCAC-TT---C--GTCACTTGATCAGATAAGTGTAGCCGAAGC
* **
2086180 TACCACTTATCACTTTATCACTTGATCAGA
1 TATCACTTATCACTTCGTCACTTGATCAGA
2086210 AGTACTCAAA
Statistics
Matches: 152, Mismatches: 14, Indels: 15
0.84 0.08 0.08
Matches are distributed among these distances:
45 13 0.09
46 98 0.64
47 2 0.01
51 2 0.01
52 37 0.24
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.34
Consensus pattern (46 bp):
TATCACTTATCACTTCGTCACTTGATCAGATAAGTGTAGCCGAAGC
Found at i:2086199 original size:98 final size:97
Alignment explanation
Indices: 2085888--2086209 Score: 438
Period size: 98 Copynumber: 3.3 Consensus size: 97
2085878 ATAAGTGTAG
* **
2085888 CCACTTATCACTTTGTTTCTTGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTTCACT
1 CCACTTATCACTTTATCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTATCAC-TTTCACT
2085953 TGTCACTTGATCAGATAAGTGTAGCCGAAGCTA
65 TGTCACTTGATCAGATAAGTGTAGCCGAAGCTA
* * *
2085986 TCACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTATCACTTATCAC-T
1 CCACTTATCACTTT--A----TCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTT
*
2086050 T--C--GTCACTTGATCAGATAAGTATAGCCGAAGCTA
60 TCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTA
* *
2086084 TCACTTATCACTTTATCACTTGATCAGATAAGTATAGCCGAAGCTATTACTTATCACTTTCCACT
1 CCACTTATCACTTTATCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTT-CACT
**
2086149 TGTCACTTGATCAGATAAGTGTAGCTAAAGCTA
65 TGTCACTTGATCAGATAAGTGTAGCCGAAGCTA
2086182 CCACTTATCACTTTATCACTTGATCAGA
1 CCACTTATCACTTTATCACTTGATCAGA
2086210 AGTACTCAAA
Statistics
Matches: 198, Mismatches: 14, Indels: 24
0.84 0.06 0.10
Matches are distributed among these distances:
92 39 0.20
93 2 0.01
96 2 0.01
98 114 0.58
100 1 0.01
102 2 0.01
104 38 0.19
ACGTcount: A:0.29, C:0.23, G:0.14, T:0.34
Consensus pattern (97 bp):
CCACTTATCACTTTATCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTCACTT
GTCACTTGATCAGATAAGTGTAGCCGAAGCTA
Found at i:2089526 original size:45 final size:45
Alignment explanation
Indices: 2089460--2089549 Score: 162
Period size: 45 Copynumber: 2.0 Consensus size: 45
2089450 CTTATCTTTC
2089460 CATTAGTAATTTAATGATTGGTGACCAAAAAAGAAAAATTCGAAT
1 CATTAGTAATTTAATGATTGGTGACCAAAAAAGAAAAATTCGAAT
* *
2089505 CATTAGTAATTTAATGGTTGGTGATCAAAAAAGAAAAATTCGAAT
1 CATTAGTAATTTAATGATTGGTGACCAAAAAAGAAAAATTCGAAT
2089550 GGTTGAGTGA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.46, C:0.08, G:0.17, T:0.30
Consensus pattern (45 bp):
CATTAGTAATTTAATGATTGGTGACCAAAAAAGAAAAATTCGAAT
Found at i:2089604 original size:5 final size:6
Alignment explanation
Indices: 2089586--2089613 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
2089576 AATTTTCTTT
2089586 AATAAA AATAAA AATAAA AATAAA AATA
1 AATAAA AATAAA AATAAA AATAAA AATA
2089614 TCAAAATGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (6 bp):
AATAAA
Found at i:2097026 original size:23 final size:23
Alignment explanation
Indices: 2096996--2097581 Score: 535
Period size: 23 Copynumber: 23.2 Consensus size: 23
2096986 TAAAATTATC
* *
2096996 AAATTAGGTTAGAGTTTTTAACT
1 AAATTAGGTTAGGGTTTTTAATT
* *
2097019 AATTTAGGTTAGGGTTTTTAACT
1 AAATTAGGTTAGGGTTTTTAATT
2097042 AAATTAGGTTAGGGTTTTTAATTAAATT
1 AAATTAGGTTAGGG--TTT--TT-AATT
*
2097070 AAATTAGGTTAGGGTTTTTAAAT
1 AAATTAGGTTAGGGTTTTTAATT
*
2097093 AAATTATGGTTAGAGTTTTTAATT
1 AAATTA-GGTTAGGGTTTTTAATT
*
2097117 AAATTAGGTTAGGATTTTTAATTAAATT
1 AAATTAGGTTAGG--GTTT--TT-AATT
2097145 AAATTAGGGTTAGGGTTTTTAATT
1 AAATTA-GGTTAGGGTTTTTAATT
*
2097169 AAATTGGGTTAGGGTTTTTAATTAAATT
1 AAATTAGGTTAGGG--TTT--TT-AATT
*
2097197 AAATTAGGTTAGGGTTTTTAAAT
1 AAATTAGGTTAGGGTTTTTAATT
2097220 AAATTATGGTTAGGG-TTTTAATT
1 AAATTA-GGTTAGGGTTTTTAATT
2097243 AAATTAGGTTAGGGTTTTTAATTAAATT
1 AAATTAGGTTAGGG--TTT--TT-AATT
2097271 AAATTAGGGTTAGGGTTTTTAATT
1 AAATTA-GGTTAGGGTTTTTAATT
*
2097295 AAATTGGGTTAGGGTTTTTAATTAAATT
1 AAATTAGGTTAGGG--TTT--TT-AATT
*
2097323 AAATTAGGTTAGGGTTTTTAAAT
1 AAATTAGGTTAGGGTTTTTAATT
2097346 AAATTATGGTTAGGGTTTTTAATT
1 AAATTA-GGTTAGGGTTTTTAATT
2097370 AAATTAGGTTAGGGTTTTTAATTAAATT
1 AAATTAGGTTAGGG--TTT--TT-AATT
2097398 AAATTAGAGTTAGGGTTTTTAATTAAATT
1 AAATTAG-GTTAGGG-T-TT--TT-AATT
2097427 AAATTAGGTTAGGGTTTTTAATT
1 AAATTAGGTTAGGGTTTTTAATT
*
2097450 AAATTAGGTTAGGGTTTAGGATTTTTAAAT
1 AAATTAGGTTA--G----GG-TTTTTAATT
2097480 AAATTAGGTTAGGGTTTTTAATTAAATT
1 AAATTAGGTTAGGG--TTT--TT-AATT
*
2097508 AAATTAGGTTAGAGTTTTTAATT
1 AAATTAGGTTAGGGTTTTTAATT
*
2097531 AAATTATGGTTACGGTTTTTAATT
1 AAATTA-GGTTAGGGTTTTTAATT
* *
2097555 AAATTAGGTTAGGATTTTTAATC
1 AAATTAGGTTAGGGTTTTTAATT
2097578 AAAT
1 AAAT
2097582 AATATCAAAA
Statistics
Matches: 486, Mismatches: 27, Indels: 100
0.79 0.04 0.16
Matches are distributed among these distances:
22 8 0.02
23 147 0.30
24 102 0.21
25 25 0.05
26 14 0.03
27 21 0.04
28 108 0.22
29 42 0.09
30 19 0.04
ACGTcount: A:0.34, C:0.01, G:0.20, T:0.46
Consensus pattern (23 bp):
AAATTAGGTTAGGGTTTTTAATT
Found at i:2097121 original size:75 final size:75
Alignment explanation
Indices: 2096996--2097581 Score: 543
Period size: 75 Copynumber: 7.7 Consensus size: 75
2096986 TAAAATTATC
* * * *
2096996 AAATTAGGTTAGAGTTTTTAACTAATTTAGGTTAGGG-TTTTTAACTAAATTAGGTTAGGGTTTT
1 AAATTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTTAATTAAATTAGGTTAGGGTTTT
2097060 TAATTAAATT
66 TAATTAAATT
* * *
2097070 AAATTAGGTTAGGGTTTTTAAATAAATTATGGTTAGAG-TTTTTAATTAAATTAGGTTAGGATTT
1 AAATTAGGTTAGGGTTTTTAATTAAATTA-GGTTAGGGTTTTTTAATTAAATTAGGTTAGGGTTT
2097134 TTAATTAAATT
65 TTAATTAAATT
*
2097145 AAATTAGGGTTAGGGTTTTTAATTAAATTGGGTTAGGGTTTTTAATTAAATTAAATTAGGTTAGG
1 AAATTA-GGTTAGGGTTTTTAATTAAATTAGGTTAGGG-TTTT--TT-AATTAAATTAGGTTAGG
*
2097210 GTTTTTAAATAAATT
61 GTTTTTAATTAAATT
2097225 --A-T-GGTTAGGG-TTTTAATTAAATTAGGTTAGGGTTTTTAATTAAATTAAATTAGGGTTAGG
1 AAATTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGG-TTTT--TT-AATTAAATTA-GGTTAGG
2097285 G--TTT--TT-AATT
61 GTTTTTAATTAAATT
* *
2097295 AAATTGGGTTAGGGTTTTTAATTAAATTAAATTAGGTTAGGG-TTTTTAAATAAATTATGGTTAG
1 AAATTAGGTTAGGG--TTT--TT-AATTAAATTAGGTTAGGGTTTTTTAATTAAATTA-GGTTAG
2097359 GG--TTT--TT-AATT
60 GGTTTTTAATTAAATT
2097370 AAATTAGGTTAGGGTTTTTAATTAAATTAAATTAGAGTTAGGGTTTTTAATTAAATTAAATTAGG
1 AAATTAGGTTAGGG--TTT--TT-AATTAAATTAG-GTTAGGG-TTTT--TT-AATTAAATTAGG
2097435 TTAGGGTTTTTAATTAAATT
56 TTAGGGTTTTTAATTAAATT
** * *
2097455 AGGTTAGGGTTTAGGATTTTTAAATAAATTAGGTTAGGGTTTTTAATTAAATTAAATTAGGTTAG
1 AAATTA-GG-TTAGGGTTTTTAATTAAATTAGGTTAGGG-TTTT--TT-AATTAAATTAGGTTAG
*
2097520 AGTTTTTAATTAAATT
60 GGTTTTTAATTAAATT
* * *
2097536 --A-T-GGTTACGGTTTTTAATTAAATTAGGTTA-GGATTTTTAATCAAAT
1 AAATTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTTAATTAAAT
2097582 AATATCAAAA
Statistics
Matches: 453, Mismatches: 28, Indels: 66
0.83 0.05 0.12
Matches are distributed among these distances:
70 11 0.02
71 3 0.01
72 1 0.00
73 7 0.02
74 77 0.17
75 154 0.34
76 32 0.07
77 6 0.01
78 8 0.02
79 4 0.01
80 58 0.13
81 57 0.13
82 13 0.03
83 2 0.00
84 2 0.00
85 11 0.02
86 2 0.00
87 5 0.01
ACGTcount: A:0.34, C:0.01, G:0.20, T:0.46
Consensus pattern (75 bp):
AAATTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTTAATTAAATTAGGTTAGGGTTTT
TAATTAAATT
Found at i:2097129 original size:52 final size:51
Alignment explanation
Indices: 2097022--2097581 Score: 574
Period size: 52 Copynumber: 10.9 Consensus size: 51
2097012 TTTAACTAAT
*
2097022 TTAGGTTAGGGTTTTTAACTAAATTAGGTTAGGGTTTTTAATTAAATTAAA
1 TTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAATTAAA
* *
2097073 TTAGGTTAGGGTTTTTAAATAAATTATGGTTAGAG--TTT--TT-AATTAAA
1 TTAGGTTAGGGTTTTTAATTAAATTA-GGTTAGGGTTTTTAATTAAATTAAA
* **
2097120 TTAGGTTAGGATTTTTAATTAAATTAAATTAGGGTTAGGGTTT--TT-AATTAAA
1 TTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTT----TTTAATTAAATTAAA
* *
2097172 TTGGGTTAGGGTTTTTAATTAAATTAAATTAGGTTAGGGTTTTTAAATAAATT--A
1 TTAGGTTAGGG--TTT--TT-AATTAAATTAGGTTAGGGTTTTTAATTAAATTAAA
2097226 -T-GGTTAGGG-TTTTAATTAAATTAGGTTAGGGTTTTTAATTAAATTAAA
1 TTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAATTAAA
*
2097274 TTAGGGTTAGGGTTTTTAATTAAATTGGGTTAGGGTTTTTAATTAAATTAAA
1 TTA-GGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAATTAAA
*
2097326 TTAGGTTAGGGTTTTTAAATAAATTATGGTTAGGG--TTT--TT-AATTAAA
1 TTAGGTTAGGGTTTTTAATTAAATTA-GGTTAGGGTTTTTAATTAAATTAAA
2097373 TTAGGTTAGGGTTTTTAATTAAATTAAATTAGAGTTAGGGTTTTTAATTAAATTAAA
1 TTAGGTTAGGG--TTT--TT-AATTAAATTAG-GTTAGGGTTTTTAATTAAATTAAA
*
2097430 TTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTAGGATT-TTTAAA-TAAA
1 TTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTT----TTAATTAAATTAAA
*
2097483 TTAGGTTAGGGTTTTTAATTAAATTAAATTAGGTTAGAGTTTTTAATTAAATT--A
1 TTAGGTTAGGG--TTT--TT-AATTAAATTAGGTTAGGGTTTTTAATTAAATTAAA
* * *
2097537 -T-GGTTACGGTTTTTAATTAAATTAGGTTAGGATTTTTAATCAAAT
1 TTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAAT
2097582 AATATCAAAA
Statistics
Matches: 441, Mismatches: 24, Indels: 92
0.79 0.04 0.17
Matches are distributed among these distances:
46 36 0.08
47 79 0.18
48 7 0.02
49 6 0.01
50 9 0.02
51 67 0.15
52 119 0.27
53 22 0.05
54 15 0.03
55 14 0.03
56 9 0.02
57 38 0.09
58 20 0.05
ACGTcount: A:0.33, C:0.01, G:0.20, T:0.46
Consensus pattern (51 bp):
TTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAATTAAA
Found at i:2097411 original size:34 final size:31
Alignment explanation
Indices: 2097045--2097536 Score: 188
Period size: 28 Copynumber: 18.8 Consensus size: 31
2097035 TTTAACTAAA
2097045 TTAGGTTAGGGTTTTTAATTAAATTAAA---
1 TTAGGTTAGGGTTTTTAATTAAATTAAATTG
2097073 TTAGGTTAGGG--TTT--TTAAA-TAAATT-
1 TTAGGTTAGGGTTTTTAATTAAATTAAATTG
* *
2097098 AT-GGTTAGAGTTTTTAA-T---T-AAA---
1 TTAGGTTAGGGTTTTTAATTAAATTAAATTG
*
2097120 TTAGGTTAGGATTTTTAATTAAATTAAA---
1 TTAGGTTAGGGTTTTTAATTAAATTAAATTG
2097148 TTAGGGTTAGGG--TTT--TT-AATTAAATTG
1 TTA-GGTTAGGGTTTTTAATTAAATTAAATTG
2097175 ---GGTTAGGGTTTTTAATTAAATTAAA---
1 TTAGGTTAGGGTTTTTAATTAAATTAAATTG
2097200 TTAGGTTAGGG--TTT--TTAAA-TAAATT-
1 TTAGGTTAGGGTTTTTAATTAAATTAAATTG
*
2097225 AT-GGTTAGGG-TTTTAATT--A--A-A---
1 TTAGGTTAGGGTTTTTAATTAAATTAAATTG
2097246 TTAGGTTAGGGTTTTTAATTAAATTAAA---
1 TTAGGTTAGGGTTTTTAATTAAATTAAATTG
2097274 TTAGGGTTAGGG--TTT--TT-AATTAAATTG
1 TTA-GGTTAGGGTTTTTAATTAAATTAAATTG
2097301 ---GGTTAGGGTTTTTAATTAAATTAAA---
1 TTAGGTTAGGGTTTTTAATTAAATTAAATTG
2097326 TTAGGTTAGGG--TTT--TTAAA-TAAATT-
1 TTAGGTTAGGGTTTTTAATTAAATTAAATTG
*
2097351 AT-GGTTAGGG--TTT--TT-AATTAAA---
1 TTAGGTTAGGGTTTTTAATTAAATTAAATTG
2097373 TTAGGTTAGGGTTTTTAATTAAATTAAA---
1 TTAGGTTAGGGTTTTTAATTAAATTAAATTG
2097401 TTAGAGTTAGGGTTTTTAATTAAATTAAA---
1 TTAG-GTTAGGGTTTTTAATTAAATTAAATTG
*
2097430 TTAGGTTAGGGTTTTTAATTAAATT--A-GG
1 TTAGGTTAGGGTTTTTAATTAAATTAAATTG
*
2097458 TTAGGGTTTA-GG-ATTT--TTAAA-TAAA---
1 TTA-GG-TTAGGGTTTTTAATTAAATTAAATTG
2097483 TTAGGTTAGGGTTTTTAATTAAATTAAA---
1 TTAGGTTAGGGTTTTTAATTAAATTAAATTG
*
2097511 TTAGGTTAGAGTTTTTAATTAAATTA
1 TTAGGTTAGGGTTTTTAATTAAATTA
2097537 TGGTTACGGT
Statistics
Matches: 381, Mismatches: 13, Indels: 140
0.71 0.02 0.26
Matches are distributed among these distances:
21 1 0.00
22 10 0.03
23 63 0.17
24 70 0.18
25 28 0.07
26 18 0.05
27 23 0.06
28 118 0.31
29 47 0.12
30 3 0.01
ACGTcount: A:0.34, C:0.00, G:0.20, T:0.46
Consensus pattern (31 bp):
TTAGGTTAGGGTTTTTAATTAAATTAAATTG
Found at i:2098757 original size:7 final size:7
Alignment explanation
Indices: 2098747--2098771 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
2098737 ATATATACAT
2098747 AATACTA
1 AATACTA
2098754 AATACTA
1 AATACTA
2098761 AATACTA
1 AATACTA
2098768 AATA
1 AATA
2098772 TCAATCCATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:2099872 original size:28 final size:29
Alignment explanation
Indices: 2099839--2099896 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 29
2099829 TTGAAAATAT
2099839 TAAAAAT-TTTAAAATTATT-TTAAAAAAA
1 TAAAAATATTTAAAATT-TTCTTAAAAAAA
2099867 TAAAAATATTTAAAATTTTCTTAAAAAAA
1 TAAAAATATTTAAAATTTTCTTAAAAAAA
2099896 T
1 T
2099897 GAAATTGAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
28 9 0.32
29 19 0.68
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.40
Consensus pattern (29 bp):
TAAAAATATTTAAAATTTTCTTAAAAAAA
Found at i:2099955 original size:22 final size:21
Alignment explanation
Indices: 2099930--2099980 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 21
2099920 TAATATGGAT
*
2099930 TTGAGAGATTTTTTGAAGGAAA
1 TTGAGAGA-TTTTGGAAGGAAA
*
2099952 TTGAGAGGATTTTGGAAGGAAT
1 TTGAGA-GATTTTGGAAGGAAA
2099974 TTGAGAG
1 TTGAGAG
2099981 TTTAAGAGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
21 1 0.04
22 23 0.88
23 2 0.08
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (21 bp):
TTGAGAGATTTTGGAAGGAAA
Found at i:2100006 original size:22 final size:22
Alignment explanation
Indices: 2099981--2100024 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
2099971 AATTTGAGAG
2099981 TTTAAGAGAATTTTGGAAGGAA
1 TTTAAGAGAATTTTGGAAGGAA
*
2100003 TTTAAGAGAATTTTTGAAGGAA
1 TTTAAGAGAATTTTGGAAGGAA
2100025 ATTGAGATAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.41, C:0.00, G:0.25, T:0.34
Consensus pattern (22 bp):
TTTAAGAGAATTTTGGAAGGAA
Found at i:2100016 original size:52 final size:52
Alignment explanation
Indices: 2099933--2100031 Score: 135
Period size: 52 Copynumber: 1.9 Consensus size: 52
2099923 TATGGATTTG
* * * * *
2099933 AGAGATTTTTTGAAGGAAATTGAGAGGATTTTGGAAGGAATTTGAGAGTTTA
1 AGAGAATTTTGGAAGGAAATTAAGAGAATTTTGGAAGGAAATTGAGAGTTTA
* *
2099985 AGAGAATTTTGGAAGGAATTTAAGAGAATTTTTGAAGGAAATTGAGA
1 AGAGAATTTTGGAAGGAAATTAAGAGAATTTTGGAAGGAAATTGAGA
2100032 TAGGATTTGT
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
52 40 1.00
ACGTcount: A:0.38, C:0.00, G:0.29, T:0.32
Consensus pattern (52 bp):
AGAGAATTTTGGAAGGAAATTAAGAGAATTTTGGAAGGAAATTGAGAGTTTA
Found at i:2118131 original size:24 final size:24
Alignment explanation
Indices: 2118098--2118144 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
2118088 TGTTTCCATG
2118098 AAAGAGGGTGACATA-TTCTTTGGT
1 AAAGAGGGTGACA-AGTTCTTTGGT
*
2118122 AAAGATGGTGACAAGTTCTTTGG
1 AAAGAGGGTGACAAGTTCTTTGG
2118145 ACTGTGCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.30, C:0.09, G:0.30, T:0.32
Consensus pattern (24 bp):
AAAGAGGGTGACAAGTTCTTTGGT
Found at i:2120795 original size:29 final size:29
Alignment explanation
Indices: 2120740--2120796 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
2120730 TATTGAATTA
* *
2120740 TTTTATAAATTTTAAATATGTTCTTTAAT
1 TTTTATAAATTTTAAATATATTATTTAAT
*
2120769 TTTTATGAAATTTTAATTA-ATTATTTAA
1 TTTTAT-AAATTTTAAATATATTATTTAA
2120797 AATTTTAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 13 0.54
30 11 0.46
ACGTcount: A:0.37, C:0.02, G:0.04, T:0.58
Consensus pattern (29 bp):
TTTTATAAATTTTAAATATATTATTTAAT
Found at i:2120803 original size:30 final size:29
Alignment explanation
Indices: 2120739--2120803 Score: 69
Period size: 30 Copynumber: 2.2 Consensus size: 29
2120729 ATATTGAATT
* *
2120739 ATTTTATAAATTTTAAATATGTTCTTTAA
1 ATTTTATAAATTTTAAATATATTATTTAA
* *
2120768 TTTTTATGAAATTTTAATTA-ATTATTTAAA
1 ATTTTAT-AAATTTTAAATATATTATTT-AA
2120798 ATTTTA
1 ATTTTA
2120804 AATAATTATA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
29 11 0.38
30 18 0.62
ACGTcount: A:0.38, C:0.02, G:0.03, T:0.57
Consensus pattern (29 bp):
ATTTTATAAATTTTAAATATATTATTTAA
Found at i:2126303 original size:17 final size:18
Alignment explanation
Indices: 2126281--2126314 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
2126271 TTAATTGAGT
2126281 TCATCTTAG-TTAATAAC
1 TCATCTTAGATTAATAAC
2126298 TCATCTTAGATTAATAA
1 TCATCTTAGATTAATAA
2126315 ATGAGTTGCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.38, C:0.15, G:0.06, T:0.41
Consensus pattern (18 bp):
TCATCTTAGATTAATAAC
Found at i:2128877 original size:17 final size:17
Alignment explanation
Indices: 2128855--2128889 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
2128845 GGAAATATGC
2128855 TTGTGATCATGAAAGGG
1 TTGTGATCATGAAAGGG
2128872 TTGTGATCATGAAAGGG
1 TTGTGATCATGAAAGGG
2128889 T
1 T
2128890 GGTAAGGTTT
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:0.29, C:0.06, G:0.34, T:0.31
Consensus pattern (17 bp):
TTGTGATCATGAAAGGG
Found at i:2132400 original size:46 final size:46
Alignment explanation
Indices: 2132332--2132516 Score: 300
Period size: 46 Copynumber: 4.0 Consensus size: 46
2132322 ACATTGCTAT
* *
2132332 AACTCAGTATG-GTTTCTTCATTGAAATACCATACCTACTTTTCAC
1 AACTCAGTATGATTTTCTTCATTGAAACACCATACCTACTTTTCAC
2132377 AACTCAGTATGATTTTCTTCATTGAAACACCATACCTACTTTTCAC
1 AACTCAGTATGATTTTCTTCATTGAAACACCATACCTACTTTTCAC
* * * *
2132423 AACTCAGTATGGTTTTCTTCATTAAAACTCCATACTTACTTTTCAC
1 AACTCAGTATGATTTTCTTCATTGAAACACCATACCTACTTTTCAC
*
2132469 AACTCAGTATGATTTTCTTCACTGAAACACCATACCTACTTTTCAC
1 AACTCAGTATGATTTTCTTCATTGAAACACCATACCTACTTTTCAC
2132515 AA
1 AA
2132517 TTTGCCATGG
Statistics
Matches: 128, Mismatches: 11, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
45 11 0.09
46 117 0.91
ACGTcount: A:0.30, C:0.25, G:0.07, T:0.37
Consensus pattern (46 bp):
AACTCAGTATGATTTTCTTCATTGAAACACCATACCTACTTTTCAC
Found at i:2133786 original size:16 final size:17
Alignment explanation
Indices: 2133740--2133784 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
2133730 AAATTCTTTT
*
2133740 TAAATCACAAAATTCAA
1 TAAATCAAAAAATTCAA
*
2133757 TAAATCAAAAAATTCAC
1 TAAATCAAAAAATTCAA
*
2133774 TAATTCAAAAA
1 TAAATCAAAAA
2133785 TTATTCTAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.60, C:0.16, G:0.00, T:0.24
Consensus pattern (17 bp):
TAAATCAAAAAATTCAA
Found at i:2135431 original size:23 final size:23
Alignment explanation
Indices: 2135405--2135594 Score: 283
Period size: 23 Copynumber: 8.3 Consensus size: 23
2135395 ATAAGTGCCA
2135405 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* * * *
2135428 CACTGATACGTAGACGAAGTTAT
1 CACTGATATGTAGCCGAAGCTAC
* * *
2135451 CACTAAAATATAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
2135474 CACTGAAATGTAGCCG-AGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
2135496 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
2135519 CACTGATATGTAGCCGTAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
2135542 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
2135565 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
2135588 CACTGAT
1 CACTGAT
2135595 CAATAACACT
Statistics
Matches: 150, Mismatches: 16, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
22 22 0.15
23 128 0.85
ACGTcount: A:0.33, C:0.25, G:0.21, T:0.22
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:2135560 original size:91 final size:92
Alignment explanation
Indices: 2135405--2135593 Score: 281
Period size: 91 Copynumber: 2.1 Consensus size: 92
2135395 ATAAGTGCCA
* * *
2135405 CACTGATATGTAGCCGAAGCTACCACTGATACGTAGACGAAGTTATCACTAAAATATAGCCGAAG
1 CACTGAAATGTAGCCGAAGCTACCACTGATACGTAGACGAAGCTACCACTAAAATATAGCCGAAG
2135470 CTACCACTGAAATGTAGCCG-AGCTAC
66 CTACCACTGAAATGTAGCCGAAGCTAC
* * * * * *
2135496 CACTGAAATGTAGCCGAAGCTACCACTGATATGTAGCCGTAGCTACCACTGATATGTAGCCGAAG
1 CACTGAAATGTAGCCGAAGCTACCACTGATACGTAGACGAAGCTACCACTAAAATATAGCCGAAG
*
2135561 CTACCACTGATATGTAGCCGAAGCTAC
66 CTACCACTGAAATGTAGCCGAAGCTAC
2135588 CACTGA
1 CACTGA
2135594 TCAATAACAC
Statistics
Matches: 87, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
91 75 0.86
92 12 0.14
ACGTcount: A:0.33, C:0.25, G:0.21, T:0.21
Consensus pattern (92 bp):
CACTGAAATGTAGCCGAAGCTACCACTGATACGTAGACGAAGCTACCACTAAAATATAGCCGAAG
CTACCACTGAAATGTAGCCGAAGCTAC
Found at i:2138242 original size:21 final size:23
Alignment explanation
Indices: 2138210--2138252 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
2138200 GAGCGATTAT
*
2138210 GGTGCTTAAAAA-TGGTAGCAAG
1 GGTGCTTAAAAATTGGCAGCAAG
2138232 GGTGC-TAAAAATTGGCAGCAA
1 GGTGCTTAAAAATTGGCAGCAA
2138253 AAAGGGGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.37, C:0.12, G:0.30, T:0.21
Consensus pattern (23 bp):
GGTGCTTAAAAATTGGCAGCAAG
Found at i:2155482 original size:96 final size:98
Alignment explanation
Indices: 2155342--2155558 Score: 257
Period size: 96 Copynumber: 2.2 Consensus size: 98
2155332 GGGGTCTTGA
* * * * *
2155342 CCTC-AAAGTTTTTAAAAAATTTAATTAGA-CTCCAAAATTTTTGAAAATTC-ACATTAAATCT-
1 CCTCAAAATTTTTTAAAAATTTTTATTAAATCTCCAAAATTTTTGAAAATTCTA-ATTAAACCTA
* *
2155403 TTAAATTTTTTTTTAAAAAAAATCA-ATT-AAAC
65 TCAAATTTTTTTTAAAAAAAAATCAGATTAAAAC
** * *
2155435 CCTTCAAAATTTTTTGTAAATTTTTATTAAATCTCCAAAATTTTTGAAAGTTCTAATTAGACCTA
1 CC-TCAAAATTTTTTAAAAATTTTTATTAAATCTCCAAAATTTTTGAAAATTCTAATTAAACCTA
2155500 TCAAATTTTTTTTAAAAAAAAATCATGATTAAAAAC
65 TCAAATTTTTTTTAAAAAAAAATCA-GATT-AAAAC
2155536 CCTCAAAATTTTTTAAAAATTTT
1 CCTCAAAATTTTTTAAAAATTTT
2155559 AGTTACCCAG
Statistics
Matches: 102, Mismatches: 13, Indels: 11
0.81 0.10 0.09
Matches are distributed among these distances:
93 2 0.02
94 2 0.02
95 19 0.19
96 27 0.26
97 24 0.24
99 3 0.03
100 19 0.19
101 6 0.06
ACGTcount: A:0.43, C:0.12, G:0.04, T:0.41
Consensus pattern (98 bp):
CCTCAAAATTTTTTAAAAATTTTTATTAAATCTCCAAAATTTTTGAAAATTCTAATTAAACCTAT
CAAATTTTTTTTAAAAAAAAATCAGATTAAAAC
Found at i:2167061 original size:22 final size:22
Alignment explanation
Indices: 2167036--2167081 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
2167026 AAAATACTGA
* *
2167036 TTAAAACGTGTTGAATTGTTAT
1 TTAAAAAGTGTTAAATTGTTAT
2167058 TTAAAAAGTGTTAAATTGTTAT
1 TTAAAAAGTGTTAAATTGTTAT
2167080 TT
1 TT
2167082 TTTAACGAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.35, C:0.02, G:0.15, T:0.48
Consensus pattern (22 bp):
TTAAAAAGTGTTAAATTGTTAT
Found at i:2176529 original size:26 final size:27
Alignment explanation
Indices: 2176482--2176532 Score: 70
Period size: 26 Copynumber: 1.9 Consensus size: 27
2176472 AAAGTTGGTA
*
2176482 AAAAAAAATTTTGGACCGTTAAAAGCT
1 AAAAAAAATTTTGGACCCTTAAAAGCT
2176509 AAAAAAAA-TTT-GAGCCCTTAAAAG
1 AAAAAAAATTTTGGA-CCCTTAAAAG
2176533 TTGGTTTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 2 0.09
26 12 0.55
27 8 0.36
ACGTcount: A:0.51, C:0.12, G:0.14, T:0.24
Consensus pattern (27 bp):
AAAAAAAATTTTGGACCCTTAAAAGCT
Found at i:2177041 original size:28 final size:25
Alignment explanation
Indices: 2177020--2177068 Score: 59
Period size: 25 Copynumber: 2.0 Consensus size: 25
2177010 ATTAATTTAA
2177020 TTTT-TTTTAAAGAGTAAA-ATT-ATT
1 TTTTCTTTTAAA-AG-AAATATTAATT
2177044 TTTTCTTTTAAAAGAAATATTAATT
1 TTTTCTTTTAAAAGAAATATTAATT
2177069 AAAATATTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
23 3 0.14
24 9 0.41
25 10 0.45
ACGTcount: A:0.39, C:0.02, G:0.06, T:0.53
Consensus pattern (25 bp):
TTTTCTTTTAAAAGAAATATTAATT
Found at i:2178994 original size:33 final size:32
Alignment explanation
Indices: 2178856--2179002 Score: 96
Period size: 33 Copynumber: 4.4 Consensus size: 32
2178846 ATAACTCAGT
* * *
2178856 TATGGTCTTATCATCAGAATGCCATAGCCTAGC
1 TATGGTCTTA-CATTAGAATGCCATAGCCCAAC
* * * *
2178889 TATGGTCTTACATATAAACACTACCATGGTCCAAC
1 TATGGTCTTACAT-TAGA-A-TGCCATAGCCCAAC
* * * * * * * **
2178924 CATAGTCTTACGTTTATAGTGCCATAACCTAGT
1 TATGGTCTTAC-ATTAGAATGCCATAGCCCAAC
2178957 TATGGTCTTATCATTAGAATGCCATAGCCCAAC
1 TATGGTCTTA-CATTAGAATGCCATAGCCCAAC
2178990 TATGGTCTTACAT
1 TATGGTCTTACAT
2179003 ATAAACACGG
Statistics
Matches: 81, Mismatches: 28, Indels: 11
0.68 0.23 0.09
Matches are distributed among these distances:
32 6 0.07
33 51 0.63
34 2 0.02
35 21 0.26
36 1 0.01
ACGTcount: A:0.29, C:0.23, G:0.15, T:0.33
Consensus pattern (32 bp):
TATGGTCTTACATTAGAATGCCATAGCCCAAC
Found at i:2179017 original size:101 final size:101
Alignment explanation
Indices: 2178830--2179069 Score: 374
Period size: 101 Copynumber: 2.4 Consensus size: 101
2178820 AATTCATCAT
* * * *
2178830 TTACATTCGTAGTGCCATAA-CTCAGTTATGGTCTTATCATCAGAATGCCATAGCCTAGCTATGG
1 TTACGTTCATAGTGCCATAACCT-AGTTATGGTCTTATCATCAGAATGCCATAGCCCAACTATGG
*
2178894 TCTTACATATAAACACTACCATGGTCCAACCATAGTC
65 TCTTACATATAAACACGACCATGGTCCAACCATAGTC
* *
2178931 TTACGTTTATAGTGCCATAACCTAGTTATGGTCTTATCATTAGAATGCCATAGCCCAACTATGGT
1 TTACGTTCATAGTGCCATAACCTAGTTATGGTCTTATCATCAGAATGCCATAGCCCAACTATGGT
* *
2178996 CTTACATATAAACACGGCCATGGTCCAACCATGGTC
66 CTTACATATAAACACGACCATGGTCCAACCATAGTC
*
2179032 TTACGTTCATAGTGCCATAACCCAGTTATGGTCTTATC
1 TTACGTTCATAGTGCCATAACCTAGTTATGGTCTTATC
2179070 CGTCAATTCA
Statistics
Matches: 127, Mismatches: 11, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
101 125 0.98
102 2 0.02
ACGTcount: A:0.28, C:0.24, G:0.16, T:0.32
Consensus pattern (101 bp):
TTACGTTCATAGTGCCATAACCTAGTTATGGTCTTATCATCAGAATGCCATAGCCCAACTATGGT
CTTACATATAAACACGACCATGGTCCAACCATAGTC
Done.