Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr4
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: 31929104
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 1434590 characters in sequence are not A, C, G, or T
File 6 of 82
Found at i:1895283 original size:22 final size:22
Alignment explanation
Indices: 1895258--1895397 Score: 97
Period size: 22 Copynumber: 6.2 Consensus size: 22
1895248 CATGGCATGC
1895258 AACAATTTTTGAACTTGCGTGT
1 AACAATTTTTGAACTTGCGTGT
1895280 AAC-ATTTTTGAA-TATGGCGTGT
1 AACAATTTTTGAACT-T-GCGTGT
* *
1895302 AACATTTTTTGAACTTGCATGT
1 AACAATTTTTGAACTTGCGTGT
* * *
1895324 AAC-ATATTTGAACATAGCATGT
1 AACAATTTTTGAAC-TTGCGTGT
* * * *
1895346 AACATTTTTTAAACATGATGTGT
1 AACAATTTTTGAACTTG-CGTGT
* * *
1895369 AACATTTTTTTGAAAATGGCGTGT
1 AACA-ATTTTTG-AACTTGCGTGT
1895393 AACAA
1 AACAA
1895398 CATAACTAAC
Statistics
Matches: 91, Mismatches: 18, Indels: 17
0.72 0.14 0.13
Matches are distributed among these distances:
20 1 0.01
21 18 0.20
22 31 0.34
23 23 0.25
24 15 0.16
25 3 0.03
ACGTcount: A:0.33, C:0.11, G:0.16, T:0.39
Consensus pattern (22 bp):
AACAATTTTTGAACTTGCGTGT
Found at i:1895312 original size:44 final size:44
Alignment explanation
Indices: 1895199--1895396 Score: 189
Period size: 44 Copynumber: 4.3 Consensus size: 44
1895189 ATGTGTTAGC
* * * *
1895199 ACATGGCGTGTAAGATTTTTATTGAACATGGCGTGTAACATGTTGTAA
1 ACATGGCGTGTAACA-TTTT-TTGAAC-TTGCGTGTAACAT-TTTTGA
* * *
1895247 ACATGGCATGCAACAATTTTTGAACTTGCGTGTAACATTTTTGA
1 ACATGGCGTGTAACATTTTTTGAACTTGCGTGTAACATTTTTGA
* * *
1895291 ATATGGCGTGTAACATTTTTTGAACTTGCATGTAACATATTTGA
1 ACATGGCGTGTAACATTTTTTGAACTTGCGTGTAACATTTTTGA
* * * * *
1895335 ACATAGCATGTAACATTTTTTAAACATGATGTGTAACATTTTTTTGA
1 ACATGGCGTGTAACATTTTTTGAACTTG-CGTGTAACA--TTTTTGA
*
1895382 AAATGGCGTGTAACA
1 ACATGGCGTGTAACA
1895397 ACATAACTAA
Statistics
Matches: 123, Mismatches: 24, Indels: 7
0.80 0.16 0.05
Matches are distributed among these distances:
44 65 0.53
45 19 0.15
46 6 0.05
47 21 0.17
48 12 0.10
ACGTcount: A:0.31, C:0.12, G:0.19, T:0.37
Consensus pattern (44 bp):
ACATGGCGTGTAACATTTTTTGAACTTGCGTGTAACATTTTTGA
Found at i:1895355 original size:67 final size:68
Alignment explanation
Indices: 1895215--1895378 Score: 181
Period size: 67 Copynumber: 2.4 Consensus size: 68
1895205 CGTGTAAGAT
* * * * *
1895215 TTTTATTGAACATGGCGTGTAACATGTTGTAAACATGGCATGCAACAATTTTTGAACTTGCGTGT
1 TTTT-TTGAACATGGCGTGTAACATTTTTTAAACATGGCATGCAACAATATTTGAACTAGCATGT
1895280 AACA
65 AACA
* * * *
1895284 -TTTTTGAATATGGCGTGTAACATTTTTTGAAC-TTGCATGTAAC-ATATTTGAACATAGCATGT
1 TTTTTTGAACATGGCGTGTAACATTTTTTAAACATGGCATGCAACAATATTTGAAC-TAGCATGT
1895346 AACA
65 AACA
* **
1895350 TTTTTTAAACATGATGTGTAACATTTTTT
1 TTTTTTGAACATGGCGTGTAACATTTTTT
1895379 TGAAAATGGC
Statistics
Matches: 80, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
65 9 0.11
66 19 0.24
67 49 0.61
68 3 0.04
ACGTcount: A:0.30, C:0.12, G:0.17, T:0.40
Consensus pattern (68 bp):
TTTTTTGAACATGGCGTGTAACATTTTTTAAACATGGCATGCAACAATATTTGAACTAGCATGTA
ACA
Found at i:1899198 original size:19 final size:19
Alignment explanation
Indices: 1899174--1899231 Score: 55
Period size: 18 Copynumber: 3.0 Consensus size: 19
1899164 CTTTCAATTA
1899174 TTTATTTATTTTTTATGTT
1 TTTATTTATTTTTTATGTT
* * *
1899193 TTTATTT-TGTTTAATATT
1 TTTATTTATTTTTTATGTT
*
1899211 TTAAGTTATATTTTTTATGTT
1 TTTA-TT-TATTTTTTATGTT
1899232 GAAATTTCCT
Statistics
Matches: 29, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
18 11 0.38
19 9 0.31
20 1 0.03
21 8 0.28
ACGTcount: A:0.21, C:0.00, G:0.07, T:0.72
Consensus pattern (19 bp):
TTTATTTATTTTTTATGTT
Found at i:1900241 original size:30 final size:30
Alignment explanation
Indices: 1900207--1900269 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
1900197 AGAGAACAAA
* *
1900207 AAACCCAGACTGAAACCTAGCCTAAACACT
1 AAACCCAGACTGAAACCTAGCCAAAAAACT
* * *
1900237 AAACCGAGATTGAAACTTAGCCAAAAAACT
1 AAACCCAGACTGAAACCTAGCCAAAAAACT
1900267 AAA
1 AAA
1900270 GCTAAACCCT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.49, C:0.25, G:0.11, T:0.14
Consensus pattern (30 bp):
AAACCCAGACTGAAACCTAGCCAAAAAACT
Found at i:1900677 original size:81 final size:80
Alignment explanation
Indices: 1900578--1900733 Score: 208
Period size: 81 Copynumber: 1.9 Consensus size: 80
1900568 TTGCTTATAA
* * * **
1900578 ATAGTATTAGGTTTTGTTTTTAATGT-TGACTGAGATTGGGTTTTGG-TGTTTCATTTTTTATTG
1 ATAGTATTAGGTTGTGTTTTTAATGTATG-CT--GATTGGGCTTTGGTTGTTTAATTTGCTATTG
1900641 TTGCTGATGTATTTGTTT
63 TTGCTGATGTATTTGTTT
* *
1900659 ATAGTATTAGGTTGTGTTTTTAATGTATGCTGATTTGGCTTTGGTTTTTTAATTTGCTATTGTTG
1 ATAGTATTAGGTTGTGTTTTTAATGTATGCTGATTGGGCTTTGGTTGTTTAATTTGCTATTGTTG
1900724 CTGATGTATT
66 CTGATGTATT
1900734 AGATAAGACA
Statistics
Matches: 66, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
79 11 0.17
80 26 0.39
81 27 0.41
82 2 0.03
ACGTcount: A:0.17, C:0.04, G:0.23, T:0.56
Consensus pattern (80 bp):
ATAGTATTAGGTTGTGTTTTTAATGTATGCTGATTGGGCTTTGGTTGTTTAATTTGCTATTGTTG
CTGATGTATTTGTTT
Found at i:1901851 original size:21 final size:21
Alignment explanation
Indices: 1901825--1901870 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
1901815 ATGAACTTGG
*
1901825 AGATGAGGAACGTTTAAATGA
1 AGATGAAGAACGTTTAAATGA
*
1901846 AGATGAAGAAGGTTTAAATGA
1 AGATGAAGAACGTTTAAATGA
1901867 AGAT
1 AGAT
1901871 TATTTTGATA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.46, C:0.02, G:0.28, T:0.24
Consensus pattern (21 bp):
AGATGAAGAACGTTTAAATGA
Found at i:1902126 original size:21 final size:21
Alignment explanation
Indices: 1902102--1902152 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
1902092 TTTAAATCTA
* *
1902102 CTGGAGGCCCATCTAGAGTTG
1 CTGGAGGCCAATCTAAAGTTG
* *
1902123 CTGGAGGTCAATTTAAAGTTG
1 CTGGAGGCCAATCTAAAGTTG
*
1902144 CTGGTGGCC
1 CTGGAGGCC
1902153 TTTTTGAAGC
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.20, C:0.20, G:0.33, T:0.27
Consensus pattern (21 bp):
CTGGAGGCCAATCTAAAGTTG
Found at i:1904585 original size:24 final size:24
Alignment explanation
Indices: 1904558--1904617 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 24
1904548 TAGTAGAGCG
*
1904558 AGTGAAACTGTTACTAGTGCACCA
1 AGTGAAGCTGTTACTAGTGCACCA
* ** *
1904582 AGTGAAGCTGCTGTTGGTGCACCA
1 AGTGAAGCTGTTACTAGTGCACCA
1904606 AGTGAAGCTGTT
1 AGTGAAGCTGTT
1904618 GTTGGTGCAA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.27, C:0.18, G:0.28, T:0.27
Consensus pattern (24 bp):
AGTGAAGCTGTTACTAGTGCACCA
Found at i:1904620 original size:24 final size:24
Alignment explanation
Indices: 1904574--1904626 Score: 97
Period size: 24 Copynumber: 2.2 Consensus size: 24
1904564 ACTGTTACTA
1904574 GTGCACCAAGTGAAGCTGCTGTTG
1 GTGCACCAAGTGAAGCTGCTGTTG
*
1904598 GTGCACCAAGTGAAGCTGTTGTTG
1 GTGCACCAAGTGAAGCTGCTGTTG
1904622 GTGCA
1 GTGCA
1904627 AGTGAACTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.21, C:0.19, G:0.34, T:0.26
Consensus pattern (24 bp):
GTGCACCAAGTGAAGCTGCTGTTG
Found at i:1904628 original size:21 final size:22
Alignment explanation
Indices: 1904579--1904632 Score: 74
Period size: 24 Copynumber: 2.4 Consensus size: 22
1904569 TACTAGTGCA
1904579 CCAAGTGAAGCTGCTGTTGGTG
1 CCAAGTGAAGCTGCTGTTGGTG
*
1904601 CACCAAGTGAAGCTGTTGTTGGTG
1 --CCAAGTGAAGCTGCTGTTGGTG
1904625 -CAAGTGAA
1 CCAAGTGAA
1904633 CTTCTTTCTA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
21 8 0.28
24 21 0.72
ACGTcount: A:0.24, C:0.17, G:0.33, T:0.26
Consensus pattern (22 bp):
CCAAGTGAAGCTGCTGTTGGTG
Found at i:1905558 original size:108 final size:108
Alignment explanation
Indices: 1905398--1905592 Score: 318
Period size: 108 Copynumber: 1.8 Consensus size: 108
1905388 AGTAGAATTA
** *
1905398 TGGGGTGACACGCCACGGCTAAATTCCTAGATGTTGATGACATCTTGGGGTGACGCGTTAAGTGG
1 TGGGGTGACACGCCACACCTAAATTCCTAGATGTTGATGACATCTTGGGGTGACACGTTAAGTGG
1905463 TAGCGGATTTATGGGGTGACACGTTGAGTTATTGCAGTATTTG
66 TAGCGGATTTATGGGGTGACACGTTGAGTTATTGCAGTATTTG
* * * * *
1905506 TGGGGTGACACGCCACACCTTAATTCTTAGATGTTGATGACATCTTGTGGTGACATGTTGAGTGG
1 TGGGGTGACACGCCACACCTAAATTCCTAGATGTTGATGACATCTTGGGGTGACACGTTAAGTGG
1905571 TAGCGGATTTATGGGGTGACAC
66 TAGCGGATTTATGGGGTGACAC
1905593 ACTGAGTGGT
Statistics
Matches: 79, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
108 79 1.00
ACGTcount: A:0.22, C:0.15, G:0.32, T:0.31
Consensus pattern (108 bp):
TGGGGTGACACGCCACACCTAAATTCCTAGATGTTGATGACATCTTGGGGTGACACGTTAAGTGG
TAGCGGATTTATGGGGTGACACGTTGAGTTATTGCAGTATTTG
Found at i:1905599 original size:31 final size:31
Alignment explanation
Indices: 1905564--1905630 Score: 89
Period size: 31 Copynumber: 2.2 Consensus size: 31
1905554 GGTGACATGT
* * *
1905564 TGAGTGGTAGCGGATTTATGGGGTGACACAC
1 TGAGTGGTAGCAGAATTATGAGGTGACACAC
* *
1905595 TGAGTGGTAGCAGAATTATGAGGTGGCACGC
1 TGAGTGGTAGCAGAATTATGAGGTGACACAC
1905626 TGAGT
1 TGAGT
1905631 TGTTGCAGTA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.24, C:0.12, G:0.39, T:0.25
Consensus pattern (31 bp):
TGAGTGGTAGCAGAATTATGAGGTGACACAC
Found at i:1905698 original size:138 final size:138
Alignment explanation
Indices: 1905458--1906038 Score: 745
Period size: 138 Copynumber: 4.2 Consensus size: 138
1905448 TGACGCGTTA
* * * * *
1905458 AGTGGTAGCGGATTTATGGGGTGACACGTTGAGTTATTGCAGTATTTGTGGGGTGACACGCCACA
1 AGTGGTAGCAGAATTATGGGGTGACACGCTGAGTTGTTGCAGTA-TTGTGGGGTGACACGCCACG
** * * * * *
1905523 CCTTAATTCTTAGATGTTGATGACATCTTGTGGTGACATGTTGAGTGGTAGCGGATTTATGGGGT
65 CCCCAATTCTTAGATGTCGATGACATCTTGTGGTGACATGCTGAATGATAGCAGATTTATGGGGT
1905588 GACACACTG
130 GACACACTG
* * * * *
1905597 AGTGGTAGCAGAATTATGAGGTGGCACGCTGAGTTGTTGCAGTATTGTGGGGTGAGACGTCATGC
1 AGTGGTAGCAGAATTATGGGGTGACACGCTGAGTTGTTGCAGTATTGTGGGGTGACACGCCACGC
* * *
1905662 CCCAATTGTTAGATGTCGATGACATCTTGTGGTGACATGCCGAGTGATAGCAGATTTATGGGGTG
66 CCCAATTCTTAGATGTCGATGACATCTTGTGGTGACATGCTGAATGATAGCAGATTTATGGGGTG
*
1905727 ACACGCTG
131 ACACACTG
* * * *
1905735 AGTGGTGGCAGAATT-TTGGGTGACACGCTGAGTTGTTGTAGTGTTGTGGGGTGACACGCCACGC
1 AGTGGTAGCAGAATTATGGGGTGACACGCTGAGTTGTTGCAGTATTGTGGGGTGACACGCCACGC
* * * *
1905799 CCCAATTCTTAGATGTCGATGACATCTTGTGGTGACACT-CTGAATGGTCGCAAATTTATGAGGT
66 CCCAATTCTTAGATGTCGATGACATCTTGTGGTGACA-TGCTGAATGATAGCAGATTTATGGGGT
*
1905863 GACACGCTG
130 GACACACTG
* * * *
1905872 AGTGGTAGCAGAATTATGTGGTCACACGTTGAGTTGTTGCAGTATTGTGGGGTGACATGCCACGC
1 AGTGGTAGCAGAATTATGGGGTGACACGCTGAGTTGTTGCAGTATTGTGGGGTGACACGCCACGC
* * * * *
1905937 CCCAATTGTTAGATGTCGATGACATCTTGTCGTGTCACGCTGAATGATAGTAGATTTATGGGGTG
66 CCCAATTCTTAGATGTCGATGACATCTTGTGGTGACATGCTGAATGATAGCAGATTTATGGGGTG
*
1906002 ACA-AGTTG
131 ACACA-CTG
*
1906010 AGTGGTAGCATAATTATGGGGTGACACGC
1 AGTGGTAGCAGAATTATGGGGTGACACGC
1906039 CATGCCCCTA
Statistics
Matches: 380, Mismatches: 58, Indels: 9
0.85 0.13 0.02
Matches are distributed among these distances:
137 119 0.31
138 223 0.59
139 38 0.10
ACGTcount: A:0.22, C:0.15, G:0.32, T:0.30
Consensus pattern (138 bp):
AGTGGTAGCAGAATTATGGGGTGACACGCTGAGTTGTTGCAGTATTGTGGGGTGACACGCCACGC
CCCAATTCTTAGATGTCGATGACATCTTGTGGTGACATGCTGAATGATAGCAGATTTATGGGGTG
ACACACTG
Found at i:1905738 original size:31 final size:30
Alignment explanation
Indices: 1905692--1905767 Score: 91
Period size: 31 Copynumber: 2.5 Consensus size: 30
1905682 GACATCTTGT
* *
1905692 GGTGACATGCCGAGTGATAGCAG-ATTTATGG
1 GGTGACACGCTGAGTGATAGCAGAATTT-T-G
* *
1905723 GGTGACACGCTGAGTGGTGGCAGAATTTTG
1 GGTGACACGCTGAGTGATAGCAGAATTTTG
1905753 GGTGACACGCTGAGT
1 GGTGACACGCTGAGT
1905768 TGTTGTAGTG
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
30 16 0.40
31 20 0.50
32 4 0.10
ACGTcount: A:0.22, C:0.14, G:0.38, T:0.25
Consensus pattern (30 bp):
GGTGACACGCTGAGTGATAGCAGAATTTTG
Found at i:1905889 original size:31 final size:31
Alignment explanation
Indices: 1905829--1905928 Score: 85
Period size: 31 Copynumber: 3.2 Consensus size: 31
1905819 GACATCTTGT
* * *
1905829 GGTGACACTCTGAATGGTCGCA-AATTTATGA
1 GGTGACACGCTGAGTGGTAGCAGAA-TTATGA
*
1905860 GGTGACACGCTGAGTGGTAGCAGAATTATGT
1 GGTGACACGCTGAGTGGTAGCAGAATTATGA
* * * * * * *
1905891 GGTCACACGTTGAGTTGTTGCAGTATTGTGG
1 GGTGACACGCTGAGTGGTAGCAGAATTATGA
1905922 GGTGACA
1 GGTGACA
1905929 TGCCACGCCC
Statistics
Matches: 56, Mismatches: 12, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
31 54 0.96
32 2 0.04
ACGTcount: A:0.24, C:0.14, G:0.33, T:0.29
Consensus pattern (31 bp):
GGTGACACGCTGAGTGGTAGCAGAATTATGA
Found at i:1905994 original size:275 final size:277
Alignment explanation
Indices: 1905458--1906038 Score: 808
Period size: 275 Copynumber: 2.1 Consensus size: 277
1905448 TGACGCGTTA
* * * *
1905458 AGTGGTAGCGGATTTATGGGGTGACACGTTGAGTTATTGCAGTATTTGTGGGGTGACACGCCACA
1 AGTGGTAGCAGAATTATGGGGTGACACGCTGAGTTATTGCAGTAGTTGTGGGGTGACACGCCACA
** * * * ** *
1905523 CCTTAATTCTTAGATGTTGATGACATCTTGTGGTGACATGTTGAGTGGTAGCGGATTTATGGGGT
66 CCCCAATTCTTAGATGTCGATGACATCTTGTGGTGACATGCTGAATGGTAGCAAATTTATGAGGT
** *
1905588 GACACACTGAGTGGTAGCAGAATTATGAGGTGGCACGCTGAGTTGTTGCAGTATTGTGGGGTGAG
131 GACACACTGAGTGGTAGCAGAATTATGAGGTCACACGCTGAGTTGTTGCAGTATTGTGGGGTGAC
* * * * *
1905653 ACGTCATGCCCCAATTGTTAGATGTCGATGACATCTTGTGGTGACATGCCGAGTGATAGCAGATT
196 ACGCCACGCCCCAATTGTTAGATGTCGATGACATCTTGTCGTGACACGCCGAATGATAGCAGATT
*
1905718 TATGGGGTGACACGCTG
261 TATGGGGTGACAAGCTG
* * * * *
1905735 AGTGGTGGCAGAATT-TTGGGTGACACGCTGAGTTGTTGTAGT-GTTGTGGGGTGACACGCCACG
1 AGTGGTAGCAGAATTATGGGGTGACACGCTGAGTTATTGCAGTAGTTGTGGGGTGACACGCCACA
*
1905798 CCCCAATTCTTAGATGTCGATGACATCTTGTGGTGACACT-CTGAATGGTCGCAAATTTATGAGG
66 CCCCAATTCTTAGATGTCGATGACATCTTGTGGTGACA-TGCTGAATGGTAGCAAATTTATGAGG
* * *
1905862 TGACACGCTGAGTGGTAGCAGAATTATGTGGTCACACGTTGAGTTGTTGCAGTATTGTGGGGTGA
130 TGACACACTGAGTGGTAGCAGAATTATGAGGTCACACGCTGAGTTGTTGCAGTATTGTGGGGTGA
* * * *
1905927 CATGCCACGCCCCAATTGTTAGATGTCGATGACATCTTGTCGTGTCACGCTGAATGATAGTAGAT
195 CACGCCACGCCCCAATTGTTAGATGTCGATGACATCTTGTCGTGACACGCCGAATGATAGCAGAT
*
1905992 TTATGGGGTGACAAGTTG
260 TTATGGGGTGACAAGCTG
*
1906010 AGTGGTAGCATAATTATGGGGTGACACGC
1 AGTGGTAGCAGAATTATGGGGTGACACGC
1906039 CATGCCCCTA
Statistics
Matches: 264, Mismatches: 38, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
275 216 0.82
276 36 0.14
277 12 0.05
ACGTcount: A:0.22, C:0.15, G:0.32, T:0.30
Consensus pattern (277 bp):
AGTGGTAGCAGAATTATGGGGTGACACGCTGAGTTATTGCAGTAGTTGTGGGGTGACACGCCACA
CCCCAATTCTTAGATGTCGATGACATCTTGTGGTGACATGCTGAATGGTAGCAAATTTATGAGGT
GACACACTGAGTGGTAGCAGAATTATGAGGTCACACGCTGAGTTGTTGCAGTATTGTGGGGTGAC
ACGCCACGCCCCAATTGTTAGATGTCGATGACATCTTGTCGTGACACGCCGAATGATAGCAGATT
TATGGGGTGACAAGCTG
Found at i:1909957 original size:31 final size:31
Alignment explanation
Indices: 1909819--1909960 Score: 203
Period size: 31 Copynumber: 4.6 Consensus size: 31
1909809 AGAAAGAAAT
* * *
1909819 AAATGTTGTTACACACTATGCATACCAAGTA
1 AAATGTTGTTACACGCCATGCATATCAAGTA
*
1909850 AAATGTTGTTACATGCCATGCATATCAAGTA
1 AAATGTTGTTACACGCCATGCATATCAAGTA
* * *
1909881 AGATGTTGTTACACGACATGTATATCAAGTA
1 AAATGTTGTTACACGCCATGCATATCAAGTA
* *
1909912 AAATATTGTTACACGCCATGCATATCAAGTC
1 AAATGTTGTTACACGCCATGCATATCAAGTA
1909943 AAATGTTGTTACACGCCA
1 AAATGTTGTTACACGCCA
1909961 CCCCTGAGCG
Statistics
Matches: 97, Mismatches: 14, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 97 1.00
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.30
Consensus pattern (31 bp):
AAATGTTGTTACACGCCATGCATATCAAGTA
Found at i:1910767 original size:58 final size:58
Alignment explanation
Indices: 1910677--1910803 Score: 166
Period size: 58 Copynumber: 2.2 Consensus size: 58
1910667 AAGCCATGGC
1910677 GTGTCACATATTCAAGCCATGGCGTGTAACAAACTCTAAACCTT-ACTGTGTCACAGTT
1 GTGTCACATATTCAAGCCATGGCGTGTAACAAACTCTAAACCTTGACT-TGTCACAGTT
*** * * * * *
1910735 GTGTCACATATTCCTTCTATGGCGTGTCACAAACTCTGATCCTTGTCTTGTCACAGTT
1 GTGTCACATATTCAAGCCATGGCGTGTAACAAACTCTAAACCTTGACTTGTCACAGTT
1910793 GTGTCACATAT
1 GTGTCACATAT
1910804 GCTTACCATG
Statistics
Matches: 60, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
58 58 0.97
59 2 0.03
ACGTcount: A:0.24, C:0.24, G:0.17, T:0.34
Consensus pattern (58 bp):
GTGTCACATATTCAAGCCATGGCGTGTAACAAACTCTAAACCTTGACTTGTCACAGTT
Found at i:1910845 original size:23 final size:23
Alignment explanation
Indices: 1910794--1910903 Score: 85
Period size: 23 Copynumber: 4.7 Consensus size: 23
1910784 GTCACAGTTG
* * *
1910794 TGTCACATATGCTTACCATGCCG
1 TGTCACATATTCTCACCATGCCA
* *
1910817 TCTCACATATTCTCACCATGGCA
1 TGTCACATATTCTCACCATGCCA
* * * *
1910840 TGTCACAAACTCTAAACCCTGCCA
1 TGTCACATATTCT-CACCATGCCA
* *
1910864 TGTCACATATTTTCACCGTGCCA
1 TGTCACATATTCTCACCATGCCA
* * *
1910887 TCTCACACATTATCACC
1 TGTCACATATTCTCACC
1910904 TTGTCGTATC
Statistics
Matches: 67, Mismatches: 19, Indels: 2
0.76 0.22 0.02
Matches are distributed among these distances:
23 50 0.75
24 17 0.25
ACGTcount: A:0.26, C:0.35, G:0.10, T:0.29
Consensus pattern (23 bp):
TGTCACATATTCTCACCATGCCA
Found at i:1911085 original size:23 final size:23
Alignment explanation
Indices: 1910969--1911119 Score: 96
Period size: 23 Copynumber: 6.7 Consensus size: 23
1910959 CATAGCTGTG
* *
1910969 TCACATATGCTCACCATGTCGTC
1 TCACATATTCTCACCATGTCATC
* * * *
1910992 TCACATATTCTCATCATGGCGTG
1 TCACATATTCTCACCATGTCATC
* * * *
1911015 TCACATATTCACAACATGGCGTGC
1 TCACATATTCTCACCATGTCAT-C
*
1911039 -CACAT-TT-TCACGC-TAG-CATG
1 TCACATATTCTCAC-CAT-GTCATC
1911059 TCACATATTCTCACCATGTCATC
1 TCACATATTCTCACCATGTCATC
** * *
1911082 TCACATATTCTTTCCAAGTCATG
1 TCACATATTCTCACCATGTCATC
*
1911105 TCATATATTCTCACC
1 TCACATATTCTCACC
1911120 CTGACGTGTT
Statistics
Matches: 101, Mismatches: 19, Indels: 16
0.74 0.14 0.12
Matches are distributed among these distances:
21 10 0.10
22 8 0.08
23 83 0.82
ACGTcount: A:0.25, C:0.30, G:0.11, T:0.33
Consensus pattern (23 bp):
TCACATATTCTCACCATGTCATC
Found at i:1911087 original size:44 final size:46
Alignment explanation
Indices: 1910958--1911119 Score: 138
Period size: 46 Copynumber: 3.5 Consensus size: 46
1910948 CCCTGTGGTG
* *
1910958 TCATAGCTGTGTCACATATGCTCACCATGTCGTCTCACATATTCTCA
1 TCATAGC-ATGTCACATATTCTCACCATGTCGTCTCACATATTCTCA
* * * * *
1911005 TCATGGCGTGTCACATATTCACAACATGGCGTGC-CACAT-TT-TCA
1 TCATAGCATGTCACATATTCTCACCATGTCGT-CTCACATATTCTCA
* * *
1911049 -CGCTAGCATGTCACATATTCTCACCATGTCATCTCACATATTCT-T
1 TC-ATAGCATGTCACATATTCTCACCATGTCGTCTCACATATTCTCA
*
1911094 TCCA-AGTCATGTCATATATTCTCACC
1 T-CATAG-CATGTCACATATTCTCACC
1911120 CTGACGTGTT
Statistics
Matches: 92, Mismatches: 15, Indels: 17
0.74 0.12 0.14
Matches are distributed among these distances:
43 2 0.02
44 31 0.34
45 6 0.07
46 45 0.49
47 8 0.09
ACGTcount: A:0.25, C:0.30, G:0.12, T:0.33
Consensus pattern (46 bp):
TCATAGCATGTCACATATTCTCACCATGTCGTCTCACATATTCTCA
Found at i:1911197 original size:23 final size:23
Alignment explanation
Indices: 1911171--1911248 Score: 93
Period size: 23 Copynumber: 3.4 Consensus size: 23
1911161 TAAACCCTAC
**
1911171 CGTGTCACTTATTCTCACCATGA
1 CGTGTCACACATTCTCACCATGA
* * *
1911194 CGTGTTACACATTCCCACCATGT
1 CGTGTCACACATTCTCACCATGA
*
1911217 CGTGTCACACATTCTCACCATGC
1 CGTGTCACACATTCTCACCATGA
*
1911240 CGTTTCACA
1 CGTGTCACA
1911249 AACTCCAAAC
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.22, C:0.35, G:0.13, T:0.31
Consensus pattern (23 bp):
CGTGTCACACATTCTCACCATGA
Found at i:1914560 original size:36 final size:36
Alignment explanation
Indices: 1914503--1914573 Score: 115
Period size: 36 Copynumber: 2.0 Consensus size: 36
1914493 ATAATCATCT
* *
1914503 GGAATACAAAAACCACCCCCAAGCTAACAACCTTCG
1 GGAACACAAAAACCACCCCCAACCTAACAACCTTCG
*
1914539 GGAACACAAAAACCACTCCCAACCTAACAACCTTC
1 GGAACACAAAAACCACCCCCAACCTAACAACCTTC
1914574 AAATGAACTT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.42, C:0.38, G:0.08, T:0.11
Consensus pattern (36 bp):
GGAACACAAAAACCACCCCCAACCTAACAACCTTCG
Found at i:1920866 original size:43 final size:43
Alignment explanation
Indices: 1920818--1921030 Score: 327
Period size: 43 Copynumber: 5.0 Consensus size: 43
1920808 TGTGATAATT
**
1920818 ATGACCCAGCTATGTGCGGTGTATGAGTGCACATGAGCTGATG
1 ATGACCCAGCTATGTGCGGTGTGGGAGTGCACATGAGCTGATG
*
1920861 ATGACCCAGCTATGTGCGGTGTGGTAGTGCACATGAGCTGATG
1 ATGACCCAGCTATGTGCGGTGTGGGAGTGCACATGAGCTGATG
** * * *
1920904 ATGACTTAACTATGTGCGGTGTGGGAGTACACATGAACTGATG
1 ATGACCCAGCTATGTGCGGTGTGGGAGTGCACATGAGCTGATG
*
1920947 ATGACTCAGCTATGTGCGGTGTGGGAGTGCACATGAGCTGATG
1 ATGACCCAGCTATGTGCGGTGTGGGAGTGCACATGAGCTGATG
* *
1920990 ATGACCTAGTTATGTGCGGTGTGGGAGTGCACATGAGCTGA
1 ATGACCCAGCTATGTGCGGTGTGGGAGTGCACATGAGCTGA
1921031 GGGAGAGTTG
Statistics
Matches: 154, Mismatches: 16, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 154 1.00
ACGTcount: A:0.23, C:0.16, G:0.34, T:0.26
Consensus pattern (43 bp):
ATGACCCAGCTATGTGCGGTGTGGGAGTGCACATGAGCTGATG
Found at i:1922600 original size:78 final size:78
Alignment explanation
Indices: 1922471--1922703 Score: 448
Period size: 78 Copynumber: 3.0 Consensus size: 78
1922461 TACCATTATT
1922471 TGCAAATAGAAGATAAGTAATATTTGTCCATCTATGACATAACTTTATACCCAAGATACTCTTTG
1 TGCAAATAGAAGATAAGTAATATTTGTCCATCTATGACATAACTTTATACCCAAGATACTCTTTG
1922536 CTTCATTAGCCTC
66 CTTCATTAGCCTC
1922549 TGCAAATAGAAGATAAGTAATATTTGTCCATCTATGACATAACTTTATACCCAAGATACTCTTTG
1 TGCAAATAGAAGATAAGTAATATTTGTCCATCTATGACATAACTTTATACCCAAGATACTCTTTG
1922614 CTTCATTAGCCTC
66 CTTCATTAGCCTC
*
1922627 TGCAAATAGAAGATAAGTAATATTTGTCCATCTATGACATAACTTTATACCCAAGATACTTTTTG
1 TGCAAATAGAAGATAAGTAATATTTGTCCATCTATGACATAACTTTATACCCAAGATACTCTTTG
*
1922692 CCTCATTAGCCT
66 CTTCATTAGCCT
1922704 TATTTAGTAG
Statistics
Matches: 153, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
78 153 1.00
ACGTcount: A:0.33, C:0.20, G:0.12, T:0.35
Consensus pattern (78 bp):
TGCAAATAGAAGATAAGTAATATTTGTCCATCTATGACATAACTTTATACCCAAGATACTCTTTG
CTTCATTAGCCTC
Found at i:1925398 original size:18 final size:18
Alignment explanation
Indices: 1925375--1925409 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1925365 ATCAGGCAGC
*
1925375 GACTTAGTAGCAATTTTT
1 GACTTAATAGCAATTTTT
1925393 GACTTAATAGCAATTTT
1 GACTTAATAGCAATTTT
1925410 CAAAAAACTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.11, G:0.14, T:0.43
Consensus pattern (18 bp):
GACTTAATAGCAATTTTT
Found at i:1927356 original size:51 final size:51
Alignment explanation
Indices: 1927296--1927400 Score: 192
Period size: 51 Copynumber: 2.1 Consensus size: 51
1927286 ACAGAAGCAC
* *
1927296 TAGTAATTTATTCAAAGTCTTAATAGTTTAGATATTGTGTTGTATAAGGAT
1 TAGTAATTTATTCAAAGTCTTAATAGTTTAGATATTATGTTGTACAAGGAT
1927347 TAGTAATTTATTCAAAGTCTTAATAGTTTAGATATTATGTTGTACAAGGAT
1 TAGTAATTTATTCAAAGTCTTAATAGTTTAGATATTATGTTGTACAAGGAT
1927398 TAG
1 TAG
1927401 GAAAGTTAAG
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.34, C:0.05, G:0.17, T:0.44
Consensus pattern (51 bp):
TAGTAATTTATTCAAAGTCTTAATAGTTTAGATATTATGTTGTACAAGGAT
Found at i:1932792 original size:42 final size:42
Alignment explanation
Indices: 1932675--1932799 Score: 196
Period size: 42 Copynumber: 3.0 Consensus size: 42
1932665 CATCTCATAT
* * * *
1932675 GCAATGGATTATGTGCACTCCCACTCGCACATAACCGAGTCA
1 GCAATGGCTTATGTGCACTCCTACTCGCACATAGCCGGGTCA
**
1932717 GCAACAGCTTATGTGCACTCCTACTCGCACATAGCCGGGTCA
1 GCAATGGCTTATGTGCACTCCTACTCGCACATAGCCGGGTCA
1932759 GCAATGGCTTATGTGCACTCCTACTCGCACATAGCCGGGTC
1 GCAATGGCTTATGTGCACTCCTACTCGCACATAGCCGGGTC
1932800 CACATCAACA
Statistics
Matches: 75, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 75 1.00
ACGTcount: A:0.24, C:0.32, G:0.22, T:0.22
Consensus pattern (42 bp):
GCAATGGCTTATGTGCACTCCTACTCGCACATAGCCGGGTCA
Found at i:1939478 original size:24 final size:23
Alignment explanation
Indices: 1939417--1939462 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
1939407 ATAAAATAAC
*
1939417 CTTATCCTAATGTAATTAGGAAT
1 CTTATCCTAATATAATTAGGAAT
1939440 CTTATCCTAATATAATTAGGAAT
1 CTTATCCTAATATAATTAGGAAT
1939463 TGTTATTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.37, C:0.13, G:0.11, T:0.39
Consensus pattern (23 bp):
CTTATCCTAATATAATTAGGAAT
Found at i:1942938 original size:23 final size:23
Alignment explanation
Indices: 1942912--1942973 Score: 88
Period size: 23 Copynumber: 2.7 Consensus size: 23
1942902 ATACAATAAC
*
1942912 CTTATCCTAATGTAATTAGGAAT
1 CTTATCCTAATATAATTAGGAAT
1942935 CTTATCCTAATATAATTAGGAATT
1 CTTATCCTAATATAATTAGGAA-T
* *
1942959 GTTATTCTAATATAA
1 CTTATCCTAATATAA
1942974 CTAGATTTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
23 21 0.60
24 14 0.40
ACGTcount: A:0.37, C:0.11, G:0.10, T:0.42
Consensus pattern (23 bp):
CTTATCCTAATATAATTAGGAAT
Found at i:1944431 original size:2 final size:2
Alignment explanation
Indices: 1944426--1944455 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1944416 GATATATGTT
1944426 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1944456 AGTATTTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1948359 original size:21 final size:22
Alignment explanation
Indices: 1948335--1948415 Score: 57
Period size: 21 Copynumber: 3.9 Consensus size: 22
1948325 ACCTAAAAAA
*
1948335 ATAAATAAATAAATTTAAAT-T
1 ATAAATAAATAAATTAAAATAT
* *
1948356 AT-AATAAAACAAAATAAAATAT
1 ATAAAT-AAATAAATTAAAATAT
* *
1948378 ATAAAAAAATAAA-TAAAGA-AA
1 ATAAATAAATAAATTAAA-ATAT
1948399 AT-AATAAA-AAATTAAAA
1 ATAAATAAATAAATTAAAA
1948416 AAAAAAAGAA
Statistics
Matches: 48, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
19 4 0.08
20 12 0.25
21 20 0.42
22 10 0.21
23 2 0.04
ACGTcount: A:0.73, C:0.01, G:0.01, T:0.25
Consensus pattern (22 bp):
ATAAATAAATAAATTAAAATAT
Found at i:1948404 original size:12 final size:11
Alignment explanation
Indices: 1948371--1948420 Score: 57
Period size: 12 Copynumber: 4.4 Consensus size: 11
1948361 AAAACAAAAT
1948371 AAAATATATAAA
1 AAAATA-ATAAA
1948383 AAAATAAATAAA
1 AAAAT-AATAAA
1948395 GAAAATAATAAA
1 -AAAATAATAAA
*
1948407 AAATTAA-AAA
1 AAAATAATAAA
1948417 AAAA
1 AAAA
1948421 AAGAAGAGAG
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
10 6 0.18
11 6 0.18
12 16 0.47
13 6 0.18
ACGTcount: A:0.80, C:0.00, G:0.02, T:0.18
Consensus pattern (11 bp):
AAAATAATAAA
Found at i:1948414 original size:24 final size:24
Alignment explanation
Indices: 1948366--1948422 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
1948356 ATAATAAAAC
*
1948366 AAAATAAAATATATAAAAAAATAA
1 AAAAAAAAATATATAAAAAAATAA
* *
1948390 ATAAAGAAAATA-ATAAAAAATTAA
1 A-AAAAAAAATATATAAAAAAATAA
1948414 AAAAAAAAA
1 AAAAAAAAA
1948423 GAAGAGAGGT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
23 7 0.24
24 13 0.45
25 9 0.31
ACGTcount: A:0.81, C:0.00, G:0.02, T:0.18
Consensus pattern (24 bp):
AAAAAAAAATATATAAAAAAATAA
Found at i:1951765 original size:18 final size:18
Alignment explanation
Indices: 1951739--1951773 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1951729 CAAGAGTTAT
*
1951739 GTTTGTTCAAACAATTAA
1 GTTTATTCAAACAATTAA
*
1951757 GTTTATTCAAATAATTA
1 GTTTATTCAAACAATTA
1951774 TGGTGAAAAA
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:0.40, C:0.09, G:0.09, T:0.43
Consensus pattern (18 bp):
GTTTATTCAAACAATTAA
Found at i:1952355 original size:15 final size:16
Alignment explanation
Indices: 1952330--1952369 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 16
1952320 TATAATTTTT
1952330 TATTTAAT-AT-TTAA
1 TATTTAATAATATTAA
1952344 T-TTTAA-AATATTAA
1 TATTTAATAATATTAA
1952358 TATTTAATAATA
1 TATTTAATAATA
1952370 AATTTATTCC
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
13 7 0.32
14 6 0.27
15 5 0.23
16 4 0.18
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TATTTAATAATATTAA
Found at i:1953464 original size:46 final size:46
Alignment explanation
Indices: 1953408--1953518 Score: 213
Period size: 46 Copynumber: 2.4 Consensus size: 46
1953398 AAGATTTCTT
1953408 CTTTTTTCTCAAATATTTCTAACAATTATGAGGTATTCTCTCCAAA
1 CTTTTTTCTCAAATATTTCTAACAATTATGAGGTATTCTCTCCAAA
1953454 CTTTTTTCTCAAATATTTCTAACAATTATGAGGTATTCTCTCCAAA
1 CTTTTTTCTCAAATATTTCTAACAATTATGAGGTATTCTCTCCAAA
*
1953500 CTTTTTTCTCAATTATTTC
1 CTTTTTTCTCAAATATTTC
1953519 ATAATGGAGA
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 64 1.00
ACGTcount: A:0.28, C:0.20, G:0.05, T:0.47
Consensus pattern (46 bp):
CTTTTTTCTCAAATATTTCTAACAATTATGAGGTATTCTCTCCAAA
Found at i:1962468 original size:9 final size:9
Alignment explanation
Indices: 1962454--1962479 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
1962444 CAAACAAGCA
1962454 CAAAGTAAC
1 CAAAGTAAC
1962463 CAAAGTAAC
1 CAAAGTAAC
1962472 CAAAGTAA
1 CAAAGTAA
1962480 TCTGAAACAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.58, C:0.19, G:0.12, T:0.12
Consensus pattern (9 bp):
CAAAGTAAC
Found at i:1964339 original size:6 final size:6
Alignment explanation
Indices: 1964328--1964353 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
1964318 AAATTAGTCA
1964328 AAATAT AAATAT AAATAT AAATAT AA
1 AAATAT AAATAT AAATAT AAATAT AA
1964354 TAAACATAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (6 bp):
AAATAT
Found at i:1970396 original size:49 final size:49
Alignment explanation
Indices: 1970324--1970422 Score: 198
Period size: 49 Copynumber: 2.0 Consensus size: 49
1970314 CGACTTATCC
1970324 TTAGTACCCAAAAGGCTGCTTTTAGTCACAAGCTTAGGAACAACTCAAT
1 TTAGTACCCAAAAGGCTGCTTTTAGTCACAAGCTTAGGAACAACTCAAT
1970373 TTAGTACCCAAAAGGCTGCTTTTAGTCACAAGCTTAGGAACAACTCAAT
1 TTAGTACCCAAAAGGCTGCTTTTAGTCACAAGCTTAGGAACAACTCAAT
1970422 T
1 T
1970423 AGCCGATGTT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.34, C:0.22, G:0.16, T:0.27
Consensus pattern (49 bp):
TTAGTACCCAAAAGGCTGCTTTTAGTCACAAGCTTAGGAACAACTCAAT
Found at i:1983605 original size:24 final size:23
Alignment explanation
Indices: 1983577--1983630 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 23
1983567 GATGGTGAAA
*
1983577 ATTAATTAATTAATTAA-AATATT
1 ATTAATTAATAAATTAATAA-ATT
*
1983600 ATTTAACTAATAAATTAATAAATT
1 A-TTAATTAATAAATTAATAAATT
1983624 ATTAATT
1 ATTAATT
1983631 TATATATCAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
23 6 0.23
24 18 0.69
25 2 0.08
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (23 bp):
ATTAATTAATAAATTAATAAATT
Found at i:1985964 original size:27 final size:27
Alignment explanation
Indices: 1985923--1985989 Score: 82
Period size: 26 Copynumber: 2.4 Consensus size: 27
1985913 CTTTTGATTA
1985923 TTATTTTTAACAAAATCATAAAATTATAAAT
1 TTATTTTT-A-AAAAT--TAAAATTATAAAT
*
1985954 TT-TTTTTAAAAATTAAAATTTTAAAT
1 TTATTTTTAAAAATTAAAATTATAAAT
1985980 TTATTTTTAA
1 TTATTTTTAA
1985990 CTTTTTTGAA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
26 14 0.41
27 7 0.21
28 5 0.15
29 1 0.03
30 5 0.15
31 2 0.06
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (27 bp):
TTATTTTTAAAAATTAAAATTATAAAT
Found at i:1993057 original size:17 final size:17
Alignment explanation
Indices: 1993037--1993079 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
1993027 ACAATTATAA
*
1993037 TTGTTCAAGAC-TTATGT
1 TTGTTCAA-ACATTAAGT
1993054 TTGTTCAAACAATTAAGT
1 TTGTTCAAAC-ATTAAGT
1993072 TTGTTCAA
1 TTGTTCAA
1993080 TTAATTATGG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 2 0.09
17 8 0.35
18 13 0.57
ACGTcount: A:0.30, C:0.12, G:0.14, T:0.44
Consensus pattern (17 bp):
TTGTTCAAACATTAAGT
Found at i:1993136 original size:24 final size:24
Alignment explanation
Indices: 1993109--1993162 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 24
1993099 AACAATTAGA
* *
1993109 TTTGTTGGAAAATAGACAATTGTG
1 TTTGTTGGAAAACAAACAATTGTG
**
1993133 TTTGTT-GAAAACAAACCTTTGTG
1 TTTGTTGGAAAACAAACAATTGTG
1993156 TTTGTTG
1 TTTGTTG
1993163 AGAAGAGGCA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
23 19 0.76
24 6 0.24
ACGTcount: A:0.28, C:0.07, G:0.22, T:0.43
Consensus pattern (24 bp):
TTTGTTGGAAAACAAACAATTGTG
Found at i:1994084 original size:53 final size:54
Alignment explanation
Indices: 1993984--1994089 Score: 178
Period size: 53 Copynumber: 2.0 Consensus size: 54
1993974 TTCATCTCTT
1993984 AACTTTCTCTAGATTTTATTCCAGATCCTTAGTCTCTTTCTCAATAATCAACAA
1 AACTTTCTCTAGATTTTATTCCAGATCCTTAGTCTCTTTCTCAATAATCAACAA
* * *
1994038 AACTTTCTCTAGATTTT-TTCTAGATTCTTTGTCTCTTTCTCAATAATCAACA
1 AACTTTCTCTAGATTTTATTCCAGATCCTTAGTCTCTTTCTCAATAATCAACA
1994090 TGGTATCAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
53 32 0.65
54 17 0.35
ACGTcount: A:0.27, C:0.23, G:0.06, T:0.44
Consensus pattern (54 bp):
AACTTTCTCTAGATTTTATTCCAGATCCTTAGTCTCTTTCTCAATAATCAACAA
Found at i:1999122 original size:54 final size:53
Alignment explanation
Indices: 1999021--1999126 Score: 140
Period size: 54 Copynumber: 2.0 Consensus size: 53
1999011 TTTATCTCTT
* * * *
1999021 AACTTTCTCTAGATTTTTTCTAGATTCTTCGTCTCTTTCTTAGTAATCAACAA
1 AACTTTCTCTAGATTTTTTCCAGATTCTTCATCTCTTTCTCAATAATCAACAA
* * *
1999074 AACTTTCTTTAGATTTTTTTCCAGATTTTTCATCTTTTTCTCAATAATCAACA
1 AACTTTCTCTAGA-TTTTTTCCAGATTCTTCATCTCTTTCTCAATAATCAACA
1999127 GGAACATTGC
Statistics
Matches: 45, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
53 12 0.27
54 33 0.73
ACGTcount: A:0.25, C:0.20, G:0.06, T:0.49
Consensus pattern (53 bp):
AACTTTCTCTAGATTTTTTCCAGATTCTTCATCTCTTTCTCAATAATCAACAA
Found at i:2003113 original size:2 final size:2
Alignment explanation
Indices: 2003108--2003144 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2003098 GAAAATATTT
2003108 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
2003145 TTGCTTTCGG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2014160 original size:5 final size:5
Alignment explanation
Indices: 2014156--2014186 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
2014146 CTATTCAACC
*
2014156 TAACC TAACT TAACT TAACT TAACT TAACT T
1 TAACT TAACT TAACT TAACT TAACT TAACT T
2014187 GGGCCACACT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.39, C:0.23, G:0.00, T:0.39
Consensus pattern (5 bp):
TAACT
Found at i:2022792 original size:2 final size:2
Alignment explanation
Indices: 2022785--2022830 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
2022775 GCAAGAACAG
2022785 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
2022827 AT AT
1 AT AT
2022831 GTACTTATGG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2023099 original size:2 final size:2
Alignment explanation
Indices: 2023092--2023168 Score: 136
Period size: 2 Copynumber: 37.5 Consensus size: 2
2023082 ATTAATCATG
2023092 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA NTA TA TA TA GTA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA -TA TA
2023136 TA 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 TA T
2023169 TGCATAACTT
Statistics
Matches: 73, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
2 69 0.95
3 4 0.05
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.49
Consensus pattern (2 bp):
TA
Found at i:2025252 original size:326 final size:317
Alignment explanation
Indices: 2024683--2025283 Score: 790
Period size: 326 Copynumber: 1.9 Consensus size: 317
2024673 TGGTAGACAA
* * *
2024683 AAAACATATAAAGAAATTAATATTCAAAATGGAGTAACTTAAATGAAACAATTTTCAAGGAAGGC
1 AAAACATATAAAGAAATAAATACTCAAAATGGAGCAACTTAAATGAAACAATTTTCAAGGAAGGC
* * *
2024748 AGGTGAAGAGACATTTAGTGTTTATATAGTAATCACAATAATGAGAACCAAGACTATCGATTTAA
66 AAGTGAAAAGACATTTAGTGTTTATACAGTAATCACAATAATGAGAACCAAGACTATCGATTTAA
* * * *
2024813 TGTCTCAAAACTCTGCATTTGAATTTAAAGTTGCTGGGTGAATACAAGTGTTTCTTGGTATGATG
131 TGTCTCAAAACTCTGCATCTAAATTTAAAGTTGCTGGATGAATACAAGTGCTTCTTGGTATGATG
* ** * * *
2024878 CTTTCAAACAAACACATAAACATGTAGGTTATCTGTCATTTGTTACGCATGG-TGCATAAGAACT
196 CTTTCAAACAAACACATAAACATGCAGGGCATCTGTCAGTTATTACGCATGGCTG--TAACAACT
*
2024942 TTATTTGTTGGCATGGCATGTAGAAACATTTGGTAATTTGAAAGGGTTTAGCTTGATAG
259 CTATTTGTTGGCATGGCATGTAGAAACATTTGGTAATTTGAAAGGGTTTAGCTTGATAG
* * * * *
2025001 AAAACATATAAATAAGTAAATACTCAAAATGGAGCAACTTCATAATGTAATAGTTTTCAAGGAAG
1 AAAACATATAAAGAAATAAATACTCAAAATGGAGCAACTT-A-AATGAAACAATTTTCAAGGAAG
* * * * * *
2025066 GCAAGTGAAAAGACATTTAGTTTAGTTTCTATACATTTAATCAGAGTAATGAGAATCAAGATTGT
64 GCAAGTGAAAAGACATTTAG--T-G-TT-TATACA-GTAATCACAATAATGAGAACCAAGACTAT
* * *
2025131 TGATTTAATGTCTCAAAACTTTGCATCTAAATTTAAAGTTGTTGGATGAATACAAGTGCTTCTTG
123 CGATTTAATGTCTCAAAACTCTGCATCTAAATTTAAAGTTGCTGGATGAATACAAGTGCTTCTTG
* * *
2025196 GTATGATGCTTTCAATCAAACACATGAACATGCAGGGCATCTGTTAGTTATTACGCATGGCCTGT
188 GTATGATGCTTTCAAACAAACACATAAACATGCAGGGCATCTGTCAGTTATTACGCATGG-CTGT
2025261 AACAACTCTATTTGTTGGCATGG
252 AACAACTCTATTTGTTGGCATGG
2025284 TGTGTAGCCA
Statistics
Matches: 239, Mismatches: 34, Indels: 12
0.84 0.12 0.04
Matches are distributed among these distances:
318 35 0.15
319 1 0.00
320 37 0.15
322 1 0.00
323 1 0.00
324 2 0.01
325 5 0.02
326 155 0.65
328 2 0.01
ACGTcount: A:0.36, C:0.12, G:0.19, T:0.33
Consensus pattern (317 bp):
AAAACATATAAAGAAATAAATACTCAAAATGGAGCAACTTAAATGAAACAATTTTCAAGGAAGGC
AAGTGAAAAGACATTTAGTGTTTATACAGTAATCACAATAATGAGAACCAAGACTATCGATTTAA
TGTCTCAAAACTCTGCATCTAAATTTAAAGTTGCTGGATGAATACAAGTGCTTCTTGGTATGATG
CTTTCAAACAAACACATAAACATGCAGGGCATCTGTCAGTTATTACGCATGGCTGTAACAACTCT
ATTTGTTGGCATGGCATGTAGAAACATTTGGTAATTTGAAAGGGTTTAGCTTGATAG
Found at i:2039498 original size:25 final size:25
Alignment explanation
Indices: 2039470--2039517 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
2039460 GTTAAGTTCT
2039470 AAAATATTGCTACACGCCATGTTGA
1 AAAATATTGCTACACGCCATGTTGA
* * * *
2039495 AAAATGTTGTTACATGCCTTGTT
1 AAAATATTGCTACACGCCATGTT
2039518 CAAAGAAAAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Consensus pattern (25 bp):
AAAATATTGCTACACGCCATGTTGA
Found at i:2040322 original size:14 final size:14
Alignment explanation
Indices: 2040303--2040330 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2040293 ATTCTATTTA
2040303 CATTAATGCAATAC
1 CATTAATGCAATAC
2040317 CATTAATGCAATAC
1 CATTAATGCAATAC
2040331 TTAATTCTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.21, G:0.07, T:0.29
Consensus pattern (14 bp):
CATTAATGCAATAC
Found at i:2043564 original size:20 final size:18
Alignment explanation
Indices: 2043524--2043566 Score: 59
Period size: 20 Copynumber: 2.3 Consensus size: 18
2043514 TCAGTTCGAG
2043524 AAATTATTTTATTAATAA
1 AAATTATTTTATTAATAA
*
2043542 AAATTATTTATATTTAATTA
1 AAATTATTT-TA-TTAATAA
2043562 AAATT
1 AAATT
2043567 TTAATTATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 9 0.41
19 2 0.09
20 11 0.50
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
AAATTATTTTATTAATAA
Found at i:2044345 original size:26 final size:27
Alignment explanation
Indices: 2044299--2044367 Score: 86
Period size: 26 Copynumber: 2.6 Consensus size: 27
2044289 ATTTATTTAA
* *
2044299 AATATTAATAATTGATAATTTAAATATT
1 AATA-TAATTATTTATAATTTAAATATT
*
2044327 AATAT-TTTATTTATAATTTAAATATT
1 AATATAATTATTTATAATTTAAATATT
*
2044353 ATTATAATTATTTAT
1 AATATAATTATTTAT
2044368 TTTTATTTTT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
26 22 0.63
27 9 0.26
28 4 0.11
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (27 bp):
AATATAATTATTTATAATTTAAATATT
Found at i:2044357 original size:112 final size:111
Alignment explanation
Indices: 2044241--2044470 Score: 261
Period size: 111 Copynumber: 2.1 Consensus size: 111
2044231 AATATATATA
* * * *
2044241 ATTATT-TATT-TTAATGTTATATTATTTTTT-GAACATTAGTAATTCAAAATTTATTTAAAATA
1 ATTATTATATTATTTAT-TTATATT-TTTTTTAAAACATTAATAATTCAAAATTTATTTAAAACA
*
2044303 TTAATAATTGATAATTT-AAATATTAATATTTTATTTATAATTTAAAT
64 ATAATAATTGATAATTTAAAATATTAATATTTTATTTATAATTTAAAT
* * * ***
2044350 ATTATTATAATTATTTATTTTTATTTTTTTTAAAATATTAATATTTTGTAATTTATTTAAAACAA
1 ATTATTAT-ATTATTTATTTATATTTTTTTTAAAACATTAATAATTCAAAATTTATTTAAAACAA
* * * *
2044415 TCATAGTTTATAATTTAAAATGTTAATATTTTATTTATAATTTAAAT
65 TAATAATTGATAATTTAAAATATTAATATTTTATTTATAATTTAAAT
*
2044462 GTTATTATA
1 ATTATTATA
2044471 ATTNNNNNNN
Statistics
Matches: 100, Mismatches: 16, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
109 6 0.06
110 7 0.07
111 47 0.47
112 40 0.40
ACGTcount: A:0.40, C:0.02, G:0.03, T:0.55
Consensus pattern (111 bp):
ATTATTATATTATTTATTTATATTTTTTTTAAAACATTAATAATTCAAAATTTATTTAAAACAAT
AATAATTGATAATTTAAAATATTAATATTTTATTTATAATTTAAAT
Found at i:2044368 original size:118 final size:112
Alignment explanation
Indices: 2044272--2044473 Score: 280
Period size: 112 Copynumber: 1.8 Consensus size: 112
2044262 TTATTTTTTG
* * *
2044272 AACATTAGTAATTCAAAATTTATTTAAAATATTAATAATTGATAATTT-AAATATTAATATTTTA
1 AACATTAATAATTCAAAATTTATTTAAAACAATAATAATTGATAATTTAAAATATTAATATTTTA
2044336 TTTATAATTTAAATATTATTATAATTATTTATTTTTATTTTTTTTAA
66 TTTATAATTTAAATATTATTATAATTATTTATTTTTATTTTTTTTAA
* * *** * * * *
2044383 AATATTAATATTTTGTAATTTATTTAAAACAATCATAGTTTATAATTTAAAATGTTAATATTTTA
1 AACATTAATAATTCAAAATTTATTTAAAACAATAATAATTGATAATTTAAAATATTAATATTTTA
*
2044448 TTTATAATTTAAATGTTATTATAATT
66 TTTATAATTTAAATATTATTATAATT
2044474 NNNNNNNNNN
Statistics
Matches: 77, Mismatches: 13, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
111 37 0.48
112 40 0.52
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.53
Consensus pattern (112 bp):
AACATTAATAATTCAAAATTTATTTAAAACAATAATAATTGATAATTTAAAATATTAATATTTTA
TTTATAATTTAAATATTATTATAATTATTTATTTTTATTTTTTTTAA
Found at i:2044406 original size:42 final size:42
Alignment explanation
Indices: 2044290--2044408 Score: 118
Period size: 42 Copynumber: 2.8 Consensus size: 42
2044280 TAATTCAAAA
* **
2044290 TTTATTTAAAATATTAATA-ATTGATAATTTAAATATTAATAT
1 TTTATTTAAAATATTAATATTTTG-TAATTTATTTATTAATAT
* * **
2044332 TTTATTTATAAT-TTAAATATTATTATAA-TTATTTATTTTTAT
1 TTTATTTAAAATATT-AATATT-TTGTAATTTATTTATTAATAT
*
2044374 TTTTTTTAAAATATTAATATTTTGTAATTTATTTA
1 TTTATTTAAAATATTAATATTTTGTAATTTATTTA
2044409 AAACAATCAT
Statistics
Matches: 62, Mismatches: 10, Indels: 10
0.76 0.12 0.12
Matches are distributed among these distances:
41 7 0.11
42 48 0.77
43 5 0.08
44 2 0.03
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (42 bp):
TTTATTTAAAATATTAATATTTTGTAATTTATTTATTAATAT
Found at i:2044903 original size:23 final size:23
Alignment explanation
Indices: 2044872--2044921 Score: 66
Period size: 26 Copynumber: 2.1 Consensus size: 23
2044862 AAATTCTAAC
2044872 TTTTTTAT-AATAATATTAATAA
1 TTTTTTATAAATAATATTAATAA
2044894 TTTTTATATAAAAATAATATTAATAA
1 TTTTT-TAT--AAATAATATTAATAA
2044920 TT
1 TT
2044922 GATTATTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
22 5 0.21
23 3 0.12
26 16 0.67
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
TTTTTTATAAATAATATTAATAA
Found at i:2044911 original size:20 final size:21
Alignment explanation
Indices: 2044873--2044912 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
2044863 AATTCTAACT
* *
2044873 TTTTTATAATAATATTAATAA
1 TTTTTATAATAAAAATAATAA
2044894 TTTTTAT-ATAAAAATAATA
1 TTTTTATAATAAAAATAATA
2044913 TTAATAATTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
TTTTTATAATAAAAATAATAA
Found at i:2045074 original size:21 final size:21
Alignment explanation
Indices: 2045032--2045084 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
2045022 AATAATTTTA
*
2045032 ATTAATTTTTAAATTTAAAAT
1 ATTAATTTTTAAATATAAAAT
* * *
2045053 ATTATTTTTTGAATATATAAT
1 ATTAATTTTTAAATATAAAAT
2045074 ATATAATTTTT
1 AT-TAATTTTT
2045085 CAAACTTATA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
21 19 0.73
22 7 0.27
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.57
Consensus pattern (21 bp):
ATTAATTTTTAAATATAAAAT
Found at i:2056288 original size:141 final size:141
Alignment explanation
Indices: 2056051--2056323 Score: 395
Period size: 141 Copynumber: 1.9 Consensus size: 141
2056041 ACATCATGTT
* * *
2056051 GGGAATGTGTGACACGGCACCGCTCAGAGTTGATGAGACGTCATGGAGGGAATCTGTGAGACACC
1 GGGAATCTGTGACACGGCACCGCTCAGAGTTGATGAGACGCCATGGAGGGAATCTGTGACACACC
* * * *
2056116 AAAGTTAAGAGTTGGTGACACGGCATAGAGGGAATCTGTGACACGCCAGAGTTAAGAGTTGGTGA
66 AAAGTTAAGAGTTAGTGACACGCCATAGAGGGAAACTGTGACACGCCAAAGTTAAGAGTTGGTGA
2056181 CATGGCATGGA
131 CATGGCATGGA
* ** *
2056192 GGGAATCTGTGACACGTCAGTGTTCAGAGTTTG-TGAGACGCCATGGAGGGAATCTGTGACACAC
1 GGGAATCTGTGACACGGCACCGCTCAGAG-TTGATGAGACGCCATGGAGGGAATCTGTGACACAC
* * * *
2056256 CAAAGTTCAGAGTTAGTGACACGCCATGGAGGGAAACTGTGACACTCCAAAGTTCAGAGTTGGTG
65 CAAAGTTAAGAGTTAGTGACACGCCATAGAGGGAAACTGTGACACGCCAAAGTTAAGAGTTGGTG
2056321 ACA
130 ACA
2056324 CACCATGGTC
Statistics
Matches: 116, Mismatches: 15, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
141 113 0.97
142 3 0.03
ACGTcount: A:0.29, C:0.18, G:0.33, T:0.21
Consensus pattern (141 bp):
GGGAATCTGTGACACGGCACCGCTCAGAGTTGATGAGACGCCATGGAGGGAATCTGTGACACACC
AAAGTTAAGAGTTAGTGACACGCCATAGAGGGAAACTGTGACACGCCAAAGTTAAGAGTTGGTGA
CATGGCATGGA
Found at i:2056330 original size:47 final size:47
Alignment explanation
Indices: 2056074--2056331 Score: 318
Period size: 47 Copynumber: 5.5 Consensus size: 47
2056064 ACGGCACCGC
* * * *
2056074 TCAGAGTTGATGAGACGTCATGGAGGGAATCTGTGAGACACCAAAGT
1 TCAGAGTTGGTGACACGCCATGGAGGGAATCTGTGACACACCAAAGT
* * * * *
2056121 TAAGAGTTGGTGACACGGCATAGAGGGAATCTGTGACACGCCAGAGT
1 TCAGAGTTGGTGACACGCCATGGAGGGAATCTGTGACACACCAAAGT
* * * ** **
2056168 TAAGAGTTGGTGACATGGCATGGAGGGAATCTGTGACACGTCAGTGT
1 TCAGAGTTGGTGACACGCCATGGAGGGAATCTGTGACACACCAAAGT
* *
2056215 TCAGAGTTTGTGAGACGCCATGGAGGGAATCTGTGACACACCAAAGT
1 TCAGAGTTGGTGACACGCCATGGAGGGAATCTGTGACACACCAAAGT
* * *
2056262 TCAGAGTTAGTGACACGCCATGGAGGGAAACTGTGACACTCCAAAGT
1 TCAGAGTTGGTGACACGCCATGGAGGGAATCTGTGACACACCAAAGT
*
2056309 TCAGAGTTGGTGACACACCATGG
1 TCAGAGTTGGTGACACGCCATGG
2056332 TCATGGTTTA
Statistics
Matches: 184, Mismatches: 27, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
47 184 1.00
ACGTcount: A:0.29, C:0.17, G:0.32, T:0.21
Consensus pattern (47 bp):
TCAGAGTTGGTGACACGCCATGGAGGGAATCTGTGACACACCAAAGT
Found at i:2056417 original size:53 final size:53
Alignment explanation
Indices: 2056321--2056438 Score: 164
Period size: 53 Copynumber: 2.2 Consensus size: 53
2056311 AGAGTTGGTG
* * *
2056321 ACACACCATGGTCATGGTTTAGAGTGTGTGACACAGCATTGCTTGAAAAGCTA
1 ACACGCCATGGTCATGGTTTAGAGTGTGTGACACAGAAGTGCTTGAAAAGCTA
* ** *
2056374 ACACGCCATGGTCATGGTTTAGAGTGTGTGACACGGAAGTGCTTGAGCAGCTG
1 ACACGCCATGGTCATGGTTTAGAGTGTGTGACACAGAAGTGCTTGAAAAGCTA
*
2056427 ACACGTCATGGT
1 ACACGCCATGGT
2056439 TTGAAATAAA
Statistics
Matches: 57, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
53 57 1.00
ACGTcount: A:0.26, C:0.19, G:0.29, T:0.25
Consensus pattern (53 bp):
ACACGCCATGGTCATGGTTTAGAGTGTGTGACACAGAAGTGCTTGAAAAGCTA
Found at i:2056947 original size:31 final size:31
Alignment explanation
Indices: 2056909--2057139 Score: 302
Period size: 31 Copynumber: 7.5 Consensus size: 31
2056899 AGTTATTGGT
* * *
2056909 GTGTGACAGCATTTTACTTGATATGCATGGC
1 GTGTCACAACATTTTACTTGTTATGCATGGC
* * *
2056940 GTGTGACAGCATTTTACTTGATATGCATGGC
1 GTGTCACAACATTTTACTTGTTATGCATGGC
*
2056971 GTGTCACAACATTTTACTTGTTATGCATGGT
1 GTGTCACAACATTTTACTTGTTATGCATGGC
** *
2057002 GTGTCACAATGTTTAACTTGTTATGCATGGC
1 GTGTCACAACATTTTACTTGTTATGCATGGC
*
2057033 GTGTCACAA-AGTTTAACTTGTTATGCATGGC
1 GTGTCACAACA-TTTTACTTGTTATGCATGGC
* *
2057064 GTGCCACAAAATTTTACTTGTTATGCATGGC
1 GTGTCACAACATTTTACTTGTTATGCATGGC
* *
2057095 GTGTCACAACATTTTGCTTGCTATGCATGGC
1 GTGTCACAACATTTTACTTGTTATGCATGGC
*
2057126 ATGTCACAACATTT
1 GTGTCACAACATTT
2057140 ATTCCTTATT
Statistics
Matches: 182, Mismatches: 16, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
31 181 0.99
32 1 0.01
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.37
Consensus pattern (31 bp):
GTGTCACAACATTTTACTTGTTATGCATGGC
Found at i:2059806 original size:31 final size:31
Alignment explanation
Indices: 2059480--2059809 Score: 356
Period size: 31 Copynumber: 10.6 Consensus size: 31
2059470 GTCAACTTTA
* * *
2059480 GCGTGTGACAACATTTGACTTGATATGCATG
1 GCGTGTCACAACATTTTACTTGTTATGCATG
* * *
2059511 GTGTGTCACAACGTTTTACTTGTTATTCATG
1 GCGTGTCACAACATTTTACTTGTTATGCATG
* * * *
2059542 GAGTGTCACAACGTTTGA-TGTGATATGCATG
1 GCGTGTCACAACATTTTACT-TGTTATGCATG
* * * *
2059573 GCGTGTCAGAACATTTTGCTTGTTATCCTTG
1 GCGTGTCACAACATTTTACTTGTTATGCATG
* * *
2059604 GCGTGTCACAACAATTTGCTTGTTATGGATG
1 GCGTGTCACAACATTTTACTTGTTATGCATG
* * *
2059635 GCGTGTCACAACGTTTAACTTCTTATGCATG
1 GCGTGTCACAACATTTTACTTGTTATGCATG
*
2059666 GCATGTCACAACATTTTACTTGTTATGCATG
1 GCGTGTCACAACATTTTACTTGTTATGCATG
* * * * *
2059697 GCATGTCACAACGTTTAACTTCTTATGCATT
1 GCGTGTCACAACATTTTACTTGTTATGCATG
* *
2059728 GCGCGTCACAACATTTTACTTGTTTTGCATG
1 GCGTGTCACAACATTTTACTTGTTATGCATG
* * * *
2059759 GCATGTGACAACATTTTACTTGATATGCACG
1 GCGTGTCACAACATTTTACTTGTTATGCATG
2059790 GCGTGTCACAACATTTTACT
1 GCGTGTCACAACATTTTACT
2059810 GTTTATGGTT
Statistics
Matches: 245, Mismatches: 52, Indels: 4
0.81 0.17 0.01
Matches are distributed among these distances:
30 1 0.00
31 243 0.99
32 1 0.00
ACGTcount: A:0.23, C:0.19, G:0.21, T:0.37
Consensus pattern (31 bp):
GCGTGTCACAACATTTTACTTGTTATGCATG
Found at i:2061303 original size:18 final size:17
Alignment explanation
Indices: 2061263--2061362 Score: 54
Period size: 17 Copynumber: 6.4 Consensus size: 17
2061253 CCTTGTCTGT
2061263 ATAATTTTTTTGTATAC
1 ATAATTTTTTTGTATAC
*
2061280 AGAATTTTTTT-TATAC
1 ATAATTTTTTTGTATAC
** *
2061296 --AATTAATTT-TATGC
1 ATAATTTTTTTGTATAC
* *
2061310 ATAAATTTTTTGTGTAC
1 ATAATTTTTTTGTATAC
* *
2061327 ACAATTTATTT-TAT--
1 ATAATTTTTTTGTATAC
**
2061341 ATAA-TTCATTGTATAC
1 ATAATTTTTTTGTATAC
2061357 ATAATT
1 ATAATT
2061363 AATTCTTTCT
Statistics
Matches: 60, Mismatches: 16, Indels: 14
0.67 0.18 0.16
Matches are distributed among these distances:
13 4 0.07
14 17 0.28
16 17 0.28
17 22 0.37
ACGTcount: A:0.34, C:0.07, G:0.06, T:0.53
Consensus pattern (17 bp):
ATAATTTTTTTGTATAC
Found at i:2061339 original size:47 final size:46
Alignment explanation
Indices: 2061263--2061408 Score: 139
Period size: 47 Copynumber: 3.0 Consensus size: 46
2061253 CCTTGTCTGT
* * * *
2061263 ATAATTTTTTTGTATACAGAATTTTTTTTATACAATTAATTTTATGC
1 ATAAATTTTTTGTATACACAATTTATTTTATACAATT-ATTTTATAC
* * *
2061310 ATAAATTTTTTGTGTACACAATTTATTTTATATAATTCATTGTATAC
1 ATAAATTTTTTGTATACACAATTTATTTTATACAATT-ATTTTATAC
* * *
2061357 ATAATTAATTCTTTCTGTATACATAATATACTTTATACAATTATTTTATAC
1 AT-A--AATT-TTT-TGTATACACAATTTATTTTATACAATTATTTTATAC
2061408 A
1 A
2061409 CAATTAATTT
Statistics
Matches: 80, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
47 41 0.51
48 1 0.01
50 4 0.05
51 12 0.15
52 22 0.28
ACGTcount: A:0.35, C:0.09, G:0.05, T:0.51
Consensus pattern (46 bp):
ATAAATTTTTTGTATACACAATTTATTTTATACAATTATTTTATAC
Found at i:2061367 original size:20 final size:22
Alignment explanation
Indices: 2061342--2061383 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
2061332 TTATTTTATA
2061342 TAATTC-AT-TGTATACATAAT
1 TAATTCTATCTGTATACATAAT
*
2061362 TAATTCTTTCTGTATACATAAT
1 TAATTCTATCTGTATACATAAT
2061384 ATACTTTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 6 0.32
21 1 0.05
22 12 0.63
ACGTcount: A:0.36, C:0.12, G:0.05, T:0.48
Consensus pattern (22 bp):
TAATTCTATCTGTATACATAAT
Found at i:2061592 original size:31 final size:31
Alignment explanation
Indices: 2061557--2061697 Score: 95
Period size: 31 Copynumber: 4.5 Consensus size: 31
2061547 CTCAACTTAC
*
2061557 ATCTGCTTGCACTCAGTGTGTCACCCCATAA
1 ATCTGCTTGCACTCAGCGTGTCACCCCATAA
** * * * * *
2061588 ATCTGCAAGAAGTCAACGTGTCACACCGTAA
1 ATCTGCTTGCACTCAGCGTGTCACCCCATAA
** ** * ** *
2061619 ATCCACTAACACTCAGTGTGTCAATCTATAA
1 ATCTGCTTGCACTCAGCGTGTCACCCCATAA
* * *
2061650 ATCTGCTTCCATTCAGCGTGTCAGCCCATAA
1 ATCTGCTTGCACTCAGCGTGTCACCCCATAA
2061681 ATCTGCTT-CTACTCAGC
1 ATCTGCTTGC-ACTCAGC
2061698 CCAGGTTGGC
Statistics
Matches: 79, Mismatches: 30, Indels: 2
0.71 0.27 0.02
Matches are distributed among these distances:
30 1 0.01
31 78 0.99
ACGTcount: A:0.28, C:0.30, G:0.15, T:0.28
Consensus pattern (31 bp):
ATCTGCTTGCACTCAGCGTGTCACCCCATAA
Found at i:2062095 original size:31 final size:32
Alignment explanation
Indices: 2061998--2062469 Score: 546
Period size: 31 Copynumber: 15.2 Consensus size: 32
2061988 GTGTGACAAC
* * *
2061998 ATTTTACTTGTTATGCATGGCGGGTTAGAACA
1 ATTTAACTTGTTATGCATGGCGTGTCAGAACA
*
2062030 ATTTAA-TTGTTA-GCATGGCGTGTCACAAC-
1 ATTTAACTTGTTATGCATGGCGTGTCAGAACA
*
2062059 TTTTAACTTGTTATGCATGG-GTGTCAGAACA
1 ATTTAACTTGTTATGCATGGCGTGTCAGAACA
* * *
2062090 ATTTAA-TTGTTATGCATGGCATGCCACAAC-
1 ATTTAACTTGTTATGCATGGCGTGTCAGAACA
*
2062120 -GTTAACTTGTTATGCATGGCGTGTCAGAACA
1 ATTTAACTTGTTATGCATGGCGTGTCAGAACA
* *
2062151 ATTTTAA-TTGTTATGCATGGCGTGTCACAACG
1 A-TTTAACTTGTTATGCATGGCGTGTCAGAACA
*
2062183 A-TTAACTTGTTATGCATGGCGTGTCAGAACT
1 ATTTAACTTGTTATGCATGGCGTGTCAGAACA
*
2062214 ATTT-ACTTGTTATACATGGCGTGTCAGAACA
1 ATTTAACTTGTTATGCATGGCGTGTCAGAACA
*
2062245 ATTTAA-TTGTTATGCATGGCGTGTCAAAAC-
1 ATTTAACTTGTTATGCATGGCGTGTCAGAACA
* * * *
2062275 GTTTTACTTGTTATGCATGGCATGTCAGATCA
1 ATTTAACTTGTTATGCATGGCGTGTCAGAACA
* *
2062307 TTTNTTTAA-TTGTTATGCATGGCGTGTCACAAC-
1 ---ATTTAACTTGTTATGCATGGCGTGTCAGAACA
* * *
2062340 GTTTAATTTGTTATGCATGGCGTGTCAGAACT
1 ATTTAACTTGTTATGCATGGCGTGTCAGAACA
*
2062372 ATTT-ACTTGTTATACATGGCGTGTCAGAACA
1 ATTTAACTTGTTATGCATGGCGTGTCAGAACA
*
2062403 ATTTAA-TTGTTATGCATGGCGTGTCACAAC-
1 ATTTAACTTGTTATGCATGGCGTGTCAGAACA
* *
2062433 GTTTAACTTGTTATGCATGGCATGTCAGAACA
1 ATTTAACTTGTTATGCATGGCGTGTCAGAACA
2062465 ATTTA
1 ATTTA
2062470 CTCATGAAAT
Statistics
Matches: 374, Mismatches: 45, Indels: 42
0.81 0.10 0.09
Matches are distributed among these distances:
29 9 0.02
30 81 0.22
31 215 0.57
32 40 0.11
33 4 0.01
34 21 0.06
35 4 0.01
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.37
Consensus pattern (32 bp):
ATTTAACTTGTTATGCATGGCGTGTCAGAACA
Found at i:2062353 original size:158 final size:155
Alignment explanation
Indices: 2061998--2062468 Score: 725
Period size: 158 Copynumber: 3.0 Consensus size: 155
2061988 GTGTGACAAC
* * * * * *
2061998 ATTTTACTTGTTATGCATGGCGGGTTAGAACAATTTAATTGTTA-GCATGGCGTGTCACAACT-T
1 ATTTTAATTGTTATGCATGGCGTGTCACAAC-GTTTAATTGTTATGCATGGCGTGTCAGAACTAT
* * *
2062061 TTAACTTGTTATGCATGG-GTGTCAGAACAATTTAATTGTTATGCATGGCATGCCACAACG-TTA
65 TT-ACTTGTTATACATGGCGTGTCAGAACAATTTAATTGTTATGCATGGCGTGTCACAACGTTTA
*
2062124 ACTTGTTATGCATGGCGTGTCAGAACA
129 ACTTGTTATGCATGGCATGTCAGAACA
*
2062151 ATTTTAATTGTTATGCATGGCGTGTCACAACGATTAACTTGTTATGCATGGCGTGTCAGAACTAT
1 ATTTTAATTGTTATGCATGGCGTGTCACAACGTTTAA-TTGTTATGCATGGCGTGTCAGAACTAT
* *
2062216 TTACTTGTTATACATGGCGTGTCAGAACAATTTAATTGTTATGCATGGCGTGTCAAAACGTTTTA
65 TTACTTGTTATACATGGCGTGTCAGAACAATTTAATTGTTATGCATGGCGTGTCACAACGTTTAA
*
2062281 CTTGTTATGCATGGCATGTCAGATCA
130 CTTGTTATGCATGGCATGTCAGAACA
*
2062307 TTTNTTTAATTGTTATGCATGGCGTGTCACAACGTTTAATTTGTTATGCATGGCGTGTCAGAACT
1 -AT-TTTAATTGTTATGCATGGCGTGTCACAACGTTTAA-TTGTTATGCATGGCGTGTCAGAACT
2062372 ATTTACTTGTTATACATGGCGTGTCAGAACAATTTAATTGTTATGCATGGCGTGTCACAACGTTT
63 ATTTACTTGTTATACATGGCGTGTCAGAACAATTTAATTGTTATGCATGGCGTGTCACAACGTTT
2062437 AACTTGTTATGCATGGCATGTCAGAACA
128 AACTTGTTATGCATGGCATGTCAGAACA
2062465 ATTT
1 ATTT
2062469 ACTCATGAAA
Statistics
Matches: 290, Mismatches: 21, Indels: 11
0.90 0.07 0.03
Matches are distributed among these distances:
152 4 0.01
153 33 0.11
154 31 0.11
155 42 0.14
156 29 0.10
157 2 0.01
158 149 0.51
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.37
Consensus pattern (155 bp):
ATTTTAATTGTTATGCATGGCGTGTCACAACGTTTAATTGTTATGCATGGCGTGTCAGAACTATT
TACTTGTTATACATGGCGTGTCAGAACAATTTAATTGTTATGCATGGCGTGTCACAACGTTTAAC
TTGTTATGCATGGCATGTCAGAACA
Found at i:2066119 original size:31 final size:31
Alignment explanation
Indices: 2066084--2066156 Score: 94
Period size: 31 Copynumber: 2.4 Consensus size: 31
2066074 GTGTTGTTAA
*
2066084 ACGCCATGCATAT-AACGTAAAATGTTATAAC
1 ACGCCATGCATATCAA-GTAAAATGTCATAAC
* * *
2066115 ACGCCATGCATATCAAGTCAAATGTCGTGAC
1 ACGCCATGCATATCAAGTAAAATGTCATAAC
2066146 ACGCCATGCAT
1 ACGCCATGCAT
2066157 CAGTATCGTG
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
31 35 0.95
32 2 0.05
ACGTcount: A:0.36, C:0.25, G:0.16, T:0.23
Consensus pattern (31 bp):
ACGCCATGCATATCAAGTAAAATGTCATAAC
Found at i:2066296 original size:55 final size:54
Alignment explanation
Indices: 2066210--2066381 Score: 182
Period size: 55 Copynumber: 3.1 Consensus size: 54
2066200 CACCAATAAC
* *
2066210 CGTGACACGCCAAAAACCCATAAATTCAGTTAACCCACAACACGCCAAGAACAG
1 CGTGACAAGCCAAAAACCCATAAATTTAGTTAACCCACAACACGCCAAGAACAG
* * * * *
2066264 TCGTGACATGCCAAAAACCCATAAATTTAGTTAATCCACGACACACCAGGAACAG
1 -CGTGACAAGCCAAAAACCCATAAATTTAGTTAACCCACAACACGCCAAGAACAG
* * * * ** * *
2066319 CCATGACAAGCTAACAACCCAAAAAACTAGGTAACCCACAACACGCCAAAAACAG
1 -CGTGACAAGCCAAAAACCCATAAATTTAGTTAACCCACAACACGCCAAGAACAG
2066374 CTGTGACA
1 C-GTGACA
2066382 CTTTAAAATA
Statistics
Matches: 95, Mismatches: 21, Indels: 2
0.81 0.18 0.02
Matches are distributed among these distances:
54 1 0.01
55 94 0.99
ACGTcount: A:0.43, C:0.31, G:0.13, T:0.13
Consensus pattern (54 bp):
CGTGACAAGCCAAAAACCCATAAATTTAGTTAACCCACAACACGCCAAGAACAG
Found at i:2070063 original size:73 final size:73
Alignment explanation
Indices: 2069928--2070088 Score: 173
Period size: 73 Copynumber: 2.2 Consensus size: 73
2069918 AGATAGAGAC
* * *
2069928 GACTTAATCAACTAAGAGAAATTGTTAGTCGACTAAGTGTTTACTGCCAGAAACCAAGTTCAGA-
1 GACTTAATCGACTAAGAGAAATTGTTAGTCGACTAAGTGCTCACTGCCAGAAACCAAGTTCAGAG
*
2069992 ACCATAATT
66 ACCA-AAAT
*** * * * **
2070001 GACTTAATCGACTAAGAGGTTTTGTTAGTTGACTAAGTGCTCACTGCTAGAGA-CTGGATTCAGA
1 GACTTAATCGACTAAGAGAAATTGTTAGTCGACTAAGTGCTCACTGCCAGAAACCAAG-TTCAGA
*
2070065 GACGAAAAT
65 GACCAAAAT
2070074 GACTTAATCGACTAA
1 GACTTAATCGACTAA
2070089 AAAGCTATGT
Statistics
Matches: 73, Mismatches: 13, Indels: 4
0.81 0.14 0.04
Matches are distributed among these distances:
72 2 0.03
73 68 0.93
74 3 0.04
ACGTcount: A:0.35, C:0.17, G:0.20, T:0.28
Consensus pattern (73 bp):
GACTTAATCGACTAAGAGAAATTGTTAGTCGACTAAGTGCTCACTGCCAGAAACCAAGTTCAGAG
ACCAAAAT
Found at i:2082824 original size:11 final size:14
Alignment explanation
Indices: 2082792--2082827 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
2082782 TTTGATCGTA
2082792 TGGTGATGACATTG
1 TGGTGATGACATTG
2082806 TGGTGATGACATTG
1 TGGTGATGACATTG
*
2082820 TGATGATG
1 TGGTGATG
2082828 TAGAAAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.22, C:0.06, G:0.36, T:0.36
Consensus pattern (14 bp):
TGGTGATGACATTG
Found at i:2083053 original size:40 final size:40
Alignment explanation
Indices: 2082995--2083073 Score: 122
Period size: 40 Copynumber: 2.0 Consensus size: 40
2082985 TTGTGAAAGA
*
2082995 CACCAATCGTGGCGAGGTTGAAAACCCCACTAAGGTGAAT
1 CACCAATCGTGGCAAGGTTGAAAACCCCACTAAGGTGAAT
* * *
2083035 CACCAATCTTGGTAAGGTTGAAAACTCCACTAAGGTGAA
1 CACCAATCGTGGCAAGGTTGAAAACCCCACTAAGGTGAA
2083074 AAATAGTCAA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.34, C:0.23, G:0.23, T:0.20
Consensus pattern (40 bp):
CACCAATCGTGGCAAGGTTGAAAACCCCACTAAGGTGAAT
Found at i:2084113 original size:40 final size:40
Alignment explanation
Indices: 2084047--2084177 Score: 190
Period size: 40 Copynumber: 3.2 Consensus size: 40
2084037 TGATCTCAAA
* * **
2084047 TTTGCTTCAAGGGTCTTGCGACTTGATCTTGAACTTCATAT
1 TTTGATTCAAGGGT-TTACGACTTGATCTTGAACTTTGTAT
2084088 TTTGATTCAAGGGTTTACGACTTGATCTTGAACTTTGTAT
1 TTTGATTCAAGGGTTTACGACTTGATCTTGAACTTTGTAT
* * *
2084128 TTTGATTCAAAGGTCTACAACTTGATCTTGAACTTTGTAT
1 TTTGATTCAAGGGTTTACGACTTGATCTTGAACTTTGTAT
2084168 TTTGATTCAA
1 TTTGATTCAA
2084178 ACTTCTTGTG
Statistics
Matches: 83, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
40 70 0.84
41 13 0.16
ACGTcount: A:0.24, C:0.15, G:0.18, T:0.44
Consensus pattern (40 bp):
TTTGATTCAAGGGTTTACGACTTGATCTTGAACTTTGTAT
Found at i:2084283 original size:23 final size:23
Alignment explanation
Indices: 2084257--2084331 Score: 60
Period size: 23 Copynumber: 3.1 Consensus size: 23
2084247 AACGAACGAT
2084257 TTGGAGACTTCACTTCAAAGGTC
1 TTGGAGACTTCACTTCAAAGGTC
* * * *
2084280 TTGGCGACTTGATCTTGAACGAGTGAC
1 TTGGAGACTTCA-CTTCAA--AG-GTC
* *
2084307 TTGGAAACTTCACTTCAAGGGTC
1 TTGGAGACTTCACTTCAAAGGTC
2084330 TT
1 TT
2084332 TACCACTTGA
Statistics
Matches: 38, Mismatches: 10, Indels: 8
0.68 0.18 0.14
Matches are distributed among these distances:
23 14 0.37
24 6 0.16
26 7 0.18
27 11 0.29
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.32
Consensus pattern (23 bp):
TTGGAGACTTCACTTCAAAGGTC
Found at i:2084361 original size:50 final size:50
Alignment explanation
Indices: 2084194--2084366 Score: 181
Period size: 50 Copynumber: 3.5 Consensus size: 50
2084184 TGTGATTTGG
* *** *
2084194 TCTTGAACGAATGATATGGAGACTTTGTTTC-AAGAGTCTTG-CAACTTGA
1 TCTTGAACGAATGATTTGGAGACTTCACTTCAAAG-GTCTTGACCACTTGA
* * *
2084243 TCTT-AACGAACGATTTGGAGACTTCACTTCAAAGGTCTTGGCGACTTGA
1 TCTTGAACGAATGATTTGGAGACTTCACTTCAAAGGTCTTGACCACTTGA
* * * * *
2084292 TCTTGAACGAGTGACTTGGAAACTTCACTTCAAGGGTCTTTACCACTTGA
1 TCTTGAACGAATGATTTGGAGACTTCACTTCAAAGGTCTTGACCACTTGA
* *
2084342 CCTTGAACGAATAATTTGGAGACTT
1 TCTTGAACGAATGATTTGGAGACTT
2084367 AGACTTGTAG
Statistics
Matches: 102, Mismatches: 19, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
48 27 0.26
49 18 0.18
50 57 0.56
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.32
Consensus pattern (50 bp):
TCTTGAACGAATGATTTGGAGACTTCACTTCAAAGGTCTTGACCACTTGA
Found at i:2084478 original size:30 final size:30
Alignment explanation
Indices: 2084442--2084579 Score: 104
Period size: 28 Copynumber: 4.5 Consensus size: 30
2084432 GAAACCTAAA
*
2084442 AAGGCTTTGATCTTCAGAATCTTCCTTCTT
1 AAGGCTTTGATCTTCAAAATCTTCCTTCTT
*
2084472 AAGGCTTTTATCTTCAAAATCTTCCTTC--
1 AAGGCTTTGATCTTCAAAATCTTCCTTCTT
* * * *
2084500 GAGGCTTTAATCATCAAAATCTTTCTTTGAGGCTT
1 AAGGCTTTGATCTTCAAAATC-TTCCTT----CTT
* * * *
2084535 CGAGGCTTTAATCATCAAAATCTTTCTTC-T
1 -AAGGCTTTGATCTTCAAAATCTTCCTTCTT
2084565 -AGGCTTTGATCTTCA
1 AAGGCTTTGATCTTCA
2084580 TAATTTTTGT
Statistics
Matches: 90, Mismatches: 10, Indels: 18
0.76 0.08 0.15
Matches are distributed among these distances:
28 31 0.34
29 5 0.06
30 27 0.30
31 1 0.01
33 1 0.01
35 4 0.04
36 21 0.23
ACGTcount: A:0.24, C:0.22, G:0.13, T:0.41
Consensus pattern (30 bp):
AAGGCTTTGATCTTCAAAATCTTCCTTCTT
Found at i:2084536 original size:36 final size:36
Alignment explanation
Indices: 2084496--2084570 Score: 134
Period size: 36 Copynumber: 2.1 Consensus size: 36
2084486 CAAAATCTTC
2084496 CTTCGAGGCTTTAATCATCAAAATCTTTCTT-TGAGG
1 CTTCGAGGCTTTAATCATCAAAATCTTTCTTCT-AGG
2084532 CTTCGAGGCTTTAATCATCAAAATCTTTCTTCTAGG
1 CTTCGAGGCTTTAATCATCAAAATCTTTCTTCTAGG
2084568 CTT
1 CTT
2084571 TGATCTTCAT
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
36 37 0.97
37 1 0.03
ACGTcount: A:0.24, C:0.21, G:0.15, T:0.40
Consensus pattern (36 bp):
CTTCGAGGCTTTAATCATCAAAATCTTTCTTCTAGG
Found at i:2090201 original size:15 final size:15
Alignment explanation
Indices: 2090181--2090210 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2090171 TATTTGTGGA
2090181 TAATTAATAAATATT
1 TAATTAATAAATATT
*
2090196 TAATTAATTAATATT
1 TAATTAATAAATATT
2090211 AGATATTATT
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TAATTAATAAATATT
Found at i:2090343 original size:21 final size:21
Alignment explanation
Indices: 2090319--2090388 Score: 77
Period size: 21 Copynumber: 3.3 Consensus size: 21
2090309 TATTCATTAT
*
2090319 ATTTAAATTTAATTTGTTTAA
1 ATTTAAATTTAATTTATTTAA
** ** * *
2090340 ATTTAAATAAAAACTAATTAC
1 ATTTAAATTTAATTTATTTAA
2090361 ATTTAAATTTAATTTATTTAA
1 ATTTAAATTTAATTTATTTAA
2090382 ATTTAAA
1 ATTTAAA
2090389 AGTAATATCC
Statistics
Matches: 36, Mismatches: 13, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.47, C:0.03, G:0.01, T:0.49
Consensus pattern (21 bp):
ATTTAAATTTAATTTATTTAA
Found at i:2091528 original size:29 final size:29
Alignment explanation
Indices: 2091487--2091545 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
2091477 ACATAGCAAA
*
2091487 TTTTTTTTACTCTATTATTTTACATATGT
1 TTTTTTTTACTCTACTATTTTACATATGT
* *
2091516 TTTTTTTTCCTCTGCTATTTTACATATGT
1 TTTTTTTTACTCTACTATTTTACATATGT
2091545 T
1 T
2091546 GTAAAATTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.17, C:0.14, G:0.05, T:0.64
Consensus pattern (29 bp):
TTTTTTTTACTCTACTATTTTACATATGT
Found at i:2097535 original size:21 final size:21
Alignment explanation
Indices: 2097509--2097627 Score: 71
Period size: 21 Copynumber: 5.3 Consensus size: 21
2097499 TAGGATATAG
2097509 ATTTAAATTTAATTTATTTAA
1 ATTTAAATTTAATTTATTTAA
** *
2097530 ATTTAAATAAAAATTATACATCCATTAT
1 ATTTAAAT-TTAATT-T--AT---TTAA
*
2097558 ATTTAAATTTAATTTGTTTAA
1 ATTTAAATTTAATTTATTTAA
* * * *
2097579 ATTTAAA-TAAGAATTAATTAC
1 ATTTAAATTTA-ATTTATTTAA
2097600 ATTTAAATTTAATTT-TTTAAA
1 ATTTAAATTTAATTTATTT-AA
2097621 ATTTAAA
1 ATTTAAA
2097628 AGTAATATCC
Statistics
Matches: 72, Mismatches: 16, Indels: 20
0.67 0.15 0.19
Matches are distributed among these distances:
20 4 0.06
21 42 0.58
22 6 0.08
23 1 0.01
24 1 0.01
25 2 0.03
26 1 0.01
27 4 0.06
28 11 0.15
ACGTcount: A:0.46, C:0.03, G:0.02, T:0.49
Consensus pattern (21 bp):
ATTTAAATTTAATTTATTTAA
Found at i:2100192 original size:20 final size:21
Alignment explanation
Indices: 2100142--2100232 Score: 71
Period size: 16 Copynumber: 4.9 Consensus size: 21
2100132 ATTGAATAAT
2100142 TTAAATATTAATA-TTTTAAG
1 TTAAATATTAATATTTTTAAG
2100162 TT-AA-A--AA-ATTTTTAA-
1 TTAAATATTAATATTTTTAAG
2100177 TTAAATATTAATATTTTTTAAG
1 TTAAATATTAATA-TTTTTAAG
*
2100199 TT---T-TTAGTA-TTTTAAG
1 TTAAATATTAATATTTTTAAG
*
2100215 TTAAATAATAATATTTTT
1 TTAAATATTAATATTTTT
2100233 TAATATTTTA
Statistics
Matches: 55, Mismatches: 3, Indels: 25
0.66 0.04 0.30
Matches are distributed among these distances:
15 3 0.05
16 19 0.35
17 1 0.02
18 6 0.11
19 6 0.11
20 7 0.13
21 11 0.20
22 2 0.04
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (21 bp):
TTAAATATTAATATTTTTAAG
Found at i:2100234 original size:30 final size:30
Alignment explanation
Indices: 2100199--2100259 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
2100189 ATTTTTTAAG
*
2100199 TTTTTAGTATTTTAAGTTAAATAATAATAT
1 TTTTTAATATTTTAAGTTAAATAATAATAT
*
2100229 TTTTTAATATTTTAAGTTAAATATTAATAT
1 TTTTTAATATTTTAAGTTAAATAATAATAT
2100259 T
1 T
2100260 CAGCAAACCT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.56
Consensus pattern (30 bp):
TTTTTAATATTTTAAGTTAAATAATAATAT
Found at i:2101322 original size:2 final size:2
Alignment explanation
Indices: 2101317--2101354 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
2101307 CCTCTCTAAC
2101317 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
2101355 TCAATTTTCA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2117176 original size:2 final size:2
Alignment explanation
Indices: 2117169--2117195 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2117159 CAAGGCCAAA
2117169 CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT C
2117196 AAGGAGGCTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:2117227 original size:2 final size:2
Alignment explanation
Indices: 2117220--2117244 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2117210 CTANAAACTA
2117220 CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT C
2117245 AAAGGAGGCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:2123931 original size:18 final size:18
Alignment explanation
Indices: 2123918--2124030 Score: 131
Period size: 18 Copynumber: 6.3 Consensus size: 18
2123908 CAAACATAAT
*
2123918 TAATTATTTGAACAAACA
1 TAATTATTTGAACAAATA
* *
2123936 TAACTATTTGGACAAACT-
1 TAATTATTTGAACAAA-TA
* *
2123954 TAACTCTTT-AAGCAAATA
1 TAATTATTTGAA-CAAATA
* *
2123972 TAATTATTTGAATAATTA
1 TAATTATTTGAACAAATA
2123990 TAATTATTTGAACAAATA
1 TAATTATTTGAACAAATA
2124008 TAATTATTTGAACAAATA
1 TAATTATTTGAACAAATA
2124026 TAATT
1 TAATT
2124031 GTTTAAAAGA
Statistics
Matches: 80, Mismatches: 11, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
17 2 0.03
18 76 0.95
19 2 0.03
ACGTcount: A:0.46, C:0.09, G:0.06, T:0.39
Consensus pattern (18 bp):
TAATTATTTGAACAAATA
Found at i:2131270 original size:26 final size:23
Alignment explanation
Indices: 2131213--2131273 Score: 70
Period size: 22 Copynumber: 2.6 Consensus size: 23
2131203 ATTCAAAAAA
*
2131213 ATTTTAAATAAATTTTTTATTAT
1 ATTTTAATTAAATTTTTTATTAT
*
2131236 A-TTTAATTAAATTTTTATATTTCT
1 ATTTTAATTAAATTTTT-TA-TTAT
2131260 ATTTTAGATTAAAT
1 ATTTTA-ATTAAAT
2131274 AAATTTTTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
22 14 0.44
23 3 0.09
24 4 0.12
25 4 0.12
26 7 0.22
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.59
Consensus pattern (23 bp):
ATTTTAATTAAATTTTTTATTAT
Found at i:2140062 original size:92 final size:92
Alignment explanation
Indices: 2139902--2140175 Score: 303
Period size: 92 Copynumber: 3.0 Consensus size: 92
2139892 CTTATGGTAG
* * * * *
2139902 AATATGTAATAACTCAATCTCTCTT-AAAAT-TCTATCTTTAGCTA-ATTGGTTTGCACCTCTTT
1 AATATGTAGTAACTCAATTTCT-TTCAAAATCTCTATCTTTAACTAGA-TGATATGCACC-CTTT
2139964 -TCATTAGTTACATTTAACATTGAAAAATAA
63 AT-ATTAGTTACATTTAACATTGAAAAATAA
*
2139994 AATATGTAGTAACTCAATTTCTTTCAAAATCT-TATGTTTAACTAGATGATATGCACCACTTTAT
1 AATATGTAGTAACTCAATTTCTTTCAAAATCTCTATCTTTAACTAGATGATATGCACC-CTTTAT
*
2140058 ATTAGTTACATTTAACACTTGAAAAATAG
65 ATTAGTTACATTTAACA-TTGAAAAATAA
* ** * *
2140087 AGTATAAAGTAACTCAATTTCTCTCAAAA-CTCTATCTTTAACTAG-TCGATATGTACTCC-TTA
1 AATATGTAGTAACTCAATTTCTTTCAAAATCTCTATCTTTAACTAGAT-GATATGCAC-CCTTTA
*
2140149 CATTAGTTACATTTAACATTGAAAAAT
64 TATTAGTTACATTTAACATTGAAAAAT
2140176 GATATAAGAG
Statistics
Matches: 159, Mismatches: 15, Indels: 17
0.83 0.08 0.09
Matches are distributed among these distances:
91 11 0.07
92 88 0.55
93 59 0.37
94 1 0.01
ACGTcount: A:0.36, C:0.16, G:0.08, T:0.39
Consensus pattern (92 bp):
AATATGTAGTAACTCAATTTCTTTCAAAATCTCTATCTTTAACTAGATGATATGCACCCTTTATA
TTAGTTACATTTAACATTGAAAAATAA
Found at i:2142182 original size:21 final size:19
Alignment explanation
Indices: 2142158--2142208 Score: 50
Period size: 20 Copynumber: 2.5 Consensus size: 19
2142148 ATTTATTATA
2142158 TCCTTTATTTCTCTTTTTCTT
1 TCCTTTATTTCT-TTTTT-TT
2142179 TCC-TTATTATCTTTTTTTT
1 TCCTTTATT-TCTTTTTTTT
*
2142198 CCCTTTCATTT
1 TCCTTT-ATTT
2142209 TTGGAAACTT
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
19 4 0.15
20 13 0.50
21 9 0.35
ACGTcount: A:0.08, C:0.24, G:0.00, T:0.69
Consensus pattern (19 bp):
TCCTTTATTTCTTTTTTTT
Found at i:2143056 original size:35 final size:35
Alignment explanation
Indices: 2143008--2143093 Score: 154
Period size: 35 Copynumber: 2.5 Consensus size: 35
2142998 CTGGCAGGGT
* *
2143008 AGTGGAACATGCCCCCCAGTGCCCAGGGACAAGGC
1 AGTGGAGCGTGCCCCCCAGTGCCCAGGGACAAGGC
2143043 AGTGGAGCGTGCCCCCCAGTGCCCAGGGACAAGGC
1 AGTGGAGCGTGCCCCCCAGTGCCCAGGGACAAGGC
2143078 AGTGGAGCGTGCCCCC
1 AGTGGAGCGTGCCCCC
2143094 TCCAGAGCCT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
35 49 1.00
ACGTcount: A:0.21, C:0.35, G:0.35, T:0.09
Consensus pattern (35 bp):
AGTGGAGCGTGCCCCCCAGTGCCCAGGGACAAGGC
Found at i:2143588 original size:104 final size:104
Alignment explanation
Indices: 2143371--2143589 Score: 359
Period size: 104 Copynumber: 2.1 Consensus size: 104
2143361 TCGTTGGTTG
* *
2143371 GGGAAAGCCAACTTGAGCGACGTCGATTGGAGAGAGAGCCGACCGATTGGGGAGCAGCAACCACC
1 GGGAAAGCCGACTTGAGCAACGTCGATTGGAGAGAGAGCCGACCGATTGGGGAGCAGCAACCACC
* *
2143436 GTTTGAAAAGTCGACTATTAGGGAGCAGCAGCCACCGGT
66 GGTTGAAAAGTCGACTATTAGGGAGCAACAGCCACCGGT
* *
2143475 TGAAAAGCCGACTTGAGCAACGTCGATTGGAGAGAGAGCCGACCGATTGGGGAGCAGCAACCACC
1 GGGAAAGCCGACTTGAGCAACGTCGATTGGAGAGAGAGCCGACCGATTGGGGAGCAGCAACCACC
2143540 GGTTGAAAAGTCGACTGA-TAGGGAGCAACAGCCACCGGT
66 GGTTGAAAAGTCGACT-ATTAGGGAGCAACAGCCACCGGT
*
2143579 GGGAGAGCCGA
1 GGGAAAGCCGA
2143590 TCGTTGGAGG
Statistics
Matches: 105, Mismatches: 9, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
104 104 0.99
105 1 0.01
ACGTcount: A:0.30, C:0.23, G:0.34, T:0.13
Consensus pattern (104 bp):
GGGAAAGCCGACTTGAGCAACGTCGATTGGAGAGAGAGCCGACCGATTGGGGAGCAGCAACCACC
GGTTGAAAAGTCGACTATTAGGGAGCAACAGCCACCGGT
Found at i:2143817 original size:43 final size:43
Alignment explanation
Indices: 2143727--2143818 Score: 107
Period size: 43 Copynumber: 2.1 Consensus size: 43
2143717 TAAGGGAACC
* *
2143727 CGTGAGGCCACCTATAGATCGACTGCAAGGAGGAGTTCGCCGG
1 CGTGAGGCCACCTACAGATCGACTGCAAGGAGGAGTTCGCCGA
* * *
2143770 CGTGAGGCCTCCTGCAGATCGAC-GACCAAGG-GGAGTTCGCCTA
1 CGTGAGGCCACCTACAGATCGACTG--CAAGGAGGAGTTCGCCGA
2143813 CGTGAG
1 CGTGAG
2143819 AAGGAGAAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
42 1 0.02
43 36 0.86
44 5 0.12
ACGTcount: A:0.22, C:0.27, G:0.35, T:0.16
Consensus pattern (43 bp):
CGTGAGGCCACCTACAGATCGACTGCAAGGAGGAGTTCGCCGA
Found at i:2145086 original size:14 final size:13
Alignment explanation
Indices: 2145000--2145086 Score: 59
Period size: 13 Copynumber: 6.3 Consensus size: 13
2144990 NNNNNNTAAT
*
2145000 AATAATAATAAGA
1 AATAATAATAAAA
* *
2145013 AATAAGAATAGAA
1 AATAATAATAAAA
2145026 AATAGGATAATGAAAA
1 AATA--ATAAT-AAAA
*
2145042 TATAATAA-ATAAA
1 AATAATAATA-AAA
**
2145055 AATAATAATTAATT
1 AATAATAA-TAAAA
2145069 AATAATAACTAAAA
1 AATAATAA-TAAAA
2145083 AATA
1 AATA
2145087 TAGATAATTG
Statistics
Matches: 56, Mismatches: 12, Indels: 11
0.71 0.15 0.14
Matches are distributed among these distances:
12 1 0.02
13 24 0.43
14 20 0.36
15 5 0.09
16 6 0.11
ACGTcount: A:0.67, C:0.01, G:0.07, T:0.25
Consensus pattern (13 bp):
AATAATAATAAAA
Found at i:2151531 original size:2 final size:2
Alignment explanation
Indices: 2151524--2151599 Score: 81
Period size: 2 Copynumber: 39.5 Consensus size: 2
2151514 AAGAATGACA
**
2151524 AT AT AT AT A- AT AT A- AT A- AT AT AT AT AT AT AT AT GC AT NAT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT
2151564 AT AT AT AT AT A- ACT AT AT AT A- AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT A
2151600 AATGAACAAA
Statistics
Matches: 63, Mismatches: 4, Indels: 14
0.78 0.05 0.17
Matches are distributed among these distances:
1 5 0.08
2 55 0.87
3 3 0.05
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.43
Consensus pattern (2 bp):
AT
Found at i:2151550 original size:21 final size:21
Alignment explanation
Indices: 2151524--2151597 Score: 96
Period size: 21 Copynumber: 3.4 Consensus size: 21
2151514 AAGAATGACA
2151524 ATATATATAATATAATAATAT
1 ATATATATAATATAATAATAT
* *
2151545 ATATATAT-ATATGCATNATAT
1 ATATATATAATAT-AATAATAT
2151566 ATATATATAACTATATATAATAT
1 ATATATATAA-TATA-ATAATAT
2151589 ATATATATA
1 ATATATATA
2151598 TAAATGAACA
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
20 4 0.09
21 22 0.49
22 1 0.02
23 18 0.40
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.43
Consensus pattern (21 bp):
ATATATATAATATAATAATAT
Found at i:2151554 original size:23 final size:23
Alignment explanation
Indices: 2151524--2151600 Score: 88
Period size: 23 Copynumber: 3.4 Consensus size: 23
2151514 AAGAATGACA
2151524 ATATATATAATATAATAATATAT
1 ATATATATAATATAATAATATAT
** *
2151547 ATATATAT-AT-GCATNATATAT
1 ATATATATAATATAATAATATAT
*
2151568 ATATATA-ACTATATATAATATAT
1 ATATATATAATATA-ATAATATAT
2151591 ATATATATAA
1 ATATATATAA
2151601 ATGAACAAAA
Statistics
Matches: 42, Mismatches: 8, Indels: 7
0.74 0.14 0.12
Matches are distributed among these distances:
21 16 0.38
22 2 0.05
23 23 0.55
24 1 0.02
ACGTcount: A:0.52, C:0.03, G:0.01, T:0.43
Consensus pattern (23 bp):
ATATATATAATATAATAATATAT
Found at i:2157514 original size:2 final size:2
Alignment explanation
Indices: 2157507--2157549 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
2157497 GTGTTAAGAA
2157507 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
2157549 A
1 A
2157550 AATTCTTACT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2169375 original size:19 final size:19
Alignment explanation
Indices: 2169351--2169391 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
2169341 AATCCAACAA
2169351 ATTATAATATGTT-TATATT
1 ATTAT-ATATGTTGTATATT
*
2169370 ATTATATATGTTGTATGTT
1 ATTATATATGTTGTATATT
2169389 ATT
1 ATT
2169392 TTTTGTGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 7 0.35
19 13 0.65
ACGTcount: A:0.32, C:0.00, G:0.10, T:0.59
Consensus pattern (19 bp):
ATTATATATGTTGTATATT
Found at i:2169889 original size:297 final size:296
Alignment explanation
Indices: 2169347--2169940 Score: 1170
Period size: 297 Copynumber: 2.0 Consensus size: 296
2169337 AAATAATCCA
2169347 ACAAATTATAATATGTTTATATTATTATATATGTTGTATGTTATTTTTTGTGAAAAAAATGGAAA
1 ACAAATTATAATATGTTTATATTATTATATATGTTGTATGTTATTTTTTGTGAAAAAAATGGAAA
2169412 TTTCATTCGATAATAAAGTACCATAGAAAATTACAATATGTATCATAATAATAATTGTACCCTCA
66 TTTCATTCGATAATAAAGTACCATAGAAAATTACAATATGTATCATAATAATAATTGTACCCTCA
2169477 ACCCCACACATTATAAAATTCCTACGACATCAAGAAGGTCTCATTAATTGTCTATTTGGCCCTGC
131 ACCCCACACATTATAAAATTCCTACGACATCAAGAAGGTCTCATTAATTGTCTATTTGGCCCTGC
2169542 TTATTTTTAGCTTATCTACTTTTTAAAAGCAAAAATTGGACTAAATAGTATTTTGTGAGAAACTC
196 TTATTTTTAGCTTATCTACTTTTTAAAAGCAAAAATTGGACTAAATAGTATTTTGTGAGAAACTC
2169607 TAAAAAAAAAACTTTTTTTTAAAAGAACAAAATTTT
261 TAAAAAAAAAACTTTTTTTTAAAAGAACAAAATTTT
*
2169643 ANCAAATTTTAATATGTTTATATTATTATATATGTTGTATGTTATTTTTTGTGAAAAAAATGGAA
1 A-CAAATTATAATATGTTTATATTATTATATATGTTGTATGTTATTTTTTGTGAAAAAAATGGAA
2169708 ATTTCATTCGATAATAAAGTACCATAGAAAATTACAATATGTATCATAATAATAATTGTACCCTC
65 ATTTCATTCGATAATAAAGTACCATAGAAAATTACAATATGTATCATAATAATAATTGTACCCTC
2169773 AACCCCACACATTATAAAATTCCTACGACATCAAGAAGGTCTCATTAATTGTCTATTTGGCCCTG
130 AACCCCACACATTATAAAATTCCTACGACATCAAGAAGGTCTCATTAATTGTCTATTTGGCCCTG
2169838 CTTATTTTTAGCTTATCTACTTTTTAAAAGCAAAAATTGGACTAAATAGTATTTTGTGAGAAACT
195 CTTATTTTTAGCTTATCTACTTTTTAAAAGCAAAAATTGGACTAAATAGTATTTTGTGAGAAACT
2169903 CTAAAAAAAAAACTTTTTTTTAAAAGAACAAAATTTT
260 CTAAAAAAAAAACTTTTTTTTAAAAGAACAAAATTTT
2169940 A
1 A
2169941 TAAAAAAAGA
Statistics
Matches: 296, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
296 1 0.00
297 295 1.00
ACGTcount: A:0.39, C:0.13, G:0.10, T:0.38
Consensus pattern (296 bp):
ACAAATTATAATATGTTTATATTATTATATATGTTGTATGTTATTTTTTGTGAAAAAAATGGAAA
TTTCATTCGATAATAAAGTACCATAGAAAATTACAATATGTATCATAATAATAATTGTACCCTCA
ACCCCACACATTATAAAATTCCTACGACATCAAGAAGGTCTCATTAATTGTCTATTTGGCCCTGC
TTATTTTTAGCTTATCTACTTTTTAAAAGCAAAAATTGGACTAAATAGTATTTTGTGAGAAACTC
TAAAAAAAAAACTTTTTTTTAAAAGAACAAAATTTT
Found at i:2182156 original size:13 final size:12
Alignment explanation
Indices: 2182129--2182165 Score: 58
Period size: 12 Copynumber: 3.1 Consensus size: 12
2182119 CAAGGTGGAA
2182129 TCTTTTCTTCTT
1 TCTTTTCTTCTT
2182141 TCTTTTCTTCCTT
1 TCTTTTCTT-CTT
2182154 TCTTTTC-TCTT
1 TCTTTTCTTCTT
2182165 T
1 T
2182166 TAAATTTTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
11 4 0.17
12 10 0.42
13 10 0.42
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (12 bp):
TCTTTTCTTCTT
Found at i:2193216 original size:21 final size:21
Alignment explanation
Indices: 2193192--2193231 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2193182 TCATATTAAG
2193192 ATTTAGAGTTAAGAGTTTATA
1 ATTTAGAGTTAAGAGTTTATA
* *
2193213 ATTTAGAGTTTAGGGTTTA
1 ATTTAGAGTTAAGAGTTTA
2193232 AGATTCGAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.33, C:0.00, G:0.23, T:0.45
Consensus pattern (21 bp):
ATTTAGAGTTAAGAGTTTATA
Found at i:2193259 original size:15 final size:16
Alignment explanation
Indices: 2193228--2193262 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
2193218 GAGTTTAGGG
*
2193228 TTTAAGATTCGAAATT
1 TTTAAGATTCAAAATT
2193244 TTTAAGATT-AAAATT
1 TTTAAGATTCAAAATT
2193259 TTTA
1 TTTA
2193263 GTTAATAGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.40, C:0.03, G:0.09, T:0.49
Consensus pattern (16 bp):
TTTAAGATTCAAAATT
Found at i:2208520 original size:15 final size:15
Alignment explanation
Indices: 2208500--2208530 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
2208490 GATATAAATA
2208500 AATAAATATTAACAT
1 AATAAATATTAACAT
2208515 AATAAATATTAACAT
1 AATAAATATTAACAT
2208530 A
1 A
2208531 TTGTATTATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.32
Consensus pattern (15 bp):
AATAAATATTAACAT
Found at i:2209018 original size:30 final size:30
Alignment explanation
Indices: 2208965--2209050 Score: 77
Period size: 30 Copynumber: 2.9 Consensus size: 30
2208955 TGTAAATAAT
**
2208965 TTTCATGGGCTTGATT-TACAAAAAGAAAAA
1 TTTCATGGGCCAGATTAT-CAAAAAGAAAAA
* * * *
2208995 TTTGATGGGCTAGATTATTAAAAATG-GAAA
1 TTTCATGGGCCAGATTATCAAAAA-GAAAAA
*
2209025 TTTCATGGGCCGGATTATCAAAAAGA
1 TTTCATGGGCCAGATTATCAAAAAGA
2209051 TTGGATCTGA
Statistics
Matches: 45, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
29 1 0.02
30 42 0.93
31 2 0.04
ACGTcount: A:0.40, C:0.09, G:0.21, T:0.30
Consensus pattern (30 bp):
TTTCATGGGCCAGATTATCAAAAAGAAAAA
Found at i:2211308 original size:17 final size:17
Alignment explanation
Indices: 2211286--2211320 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
2211276 AGTTGCAGTT
2211286 GCTCTTGTTGAATCTTG
1 GCTCTTGTTGAATCTTG
2211303 GCTCTTGTTGAATCTTG
1 GCTCTTGTTGAATCTTG
2211320 G
1 G
2211321 ATCATGTACC
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:0.11, C:0.17, G:0.26, T:0.46
Consensus pattern (17 bp):
GCTCTTGTTGAATCTTG
Found at i:2212602 original size:30 final size:31
Alignment explanation
Indices: 2212545--2212603 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
2212535 TTGATTAAAA
*
2212545 TTTTATATTTTTATTTTTGAATCAAATAAGT
1 TTTTATATTTTTAGTTTTGAATCAAATAAGT
* *
2212576 TTTTATATTTTT-GTTTTGAGTTAAATAA
1 TTTTATATTTTTAGTTTTGAATCAAATAA
2212604 ATCTTTATGA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 13 0.52
31 12 0.48
ACGTcount: A:0.31, C:0.02, G:0.08, T:0.59
Consensus pattern (31 bp):
TTTTATATTTTTAGTTTTGAATCAAATAAGT
Found at i:2212611 original size:30 final size:30
Alignment explanation
Indices: 2212542--2212611 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 30
2212532 TAATTGATTA
*
2212542 AAATTTTATATTTTTATTTTTGAATCAAAT
1 AAATTTTATATTTTTAGTTTTGAATCAAAT
* * *
2212572 AAGTTTTTATATTTTT-GTTTTGAGTTAAAT
1 AA-ATTTTATATTTTTAGTTTTGAATCAAAT
2212602 AAATCTTTAT
1 AAAT-TTTAT
2212612 GATTAATGGG
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
29 1 0.03
30 20 0.61
31 12 0.36
ACGTcount: A:0.33, C:0.03, G:0.07, T:0.57
Consensus pattern (30 bp):
AAATTTTATATTTTTAGTTTTGAATCAAAT
Found at i:2226583 original size:34 final size:34
Alignment explanation
Indices: 2226540--2226608 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
2226530 AATAATTTAC
*
2226540 AGATAAGACTAGACTATTCTAAGCAAAATCTAGT
1 AGATAAGACTAGACTAATCTAAGCAAAATCTAGT
2226574 AGATAAGACTAGACTAATCTAAGCAAAATCTAGT
1 AGATAAGACTAGACTAATCTAAGCAAAATCTAGT
2226608 A
1 A
2226609 AACACCTGAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.46, C:0.14, G:0.14, T:0.25
Consensus pattern (34 bp):
AGATAAGACTAGACTAATCTAAGCAAAATCTAGT
Found at i:2239604 original size:2 final size:2
Alignment explanation
Indices: 2239599--2239640 Score: 68
Period size: 2 Copynumber: 21.0 Consensus size: 2
2239589 AATATATCTC
2239599 AT AT AT AT AT A- AT ACT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT
2239641 TCAGTTATAA
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 1 0.03
2 35 0.92
3 2 0.05
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2240179 original size:21 final size:18
Alignment explanation
Indices: 2240155--2240198 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 18
2240145 AATATCTAAT
2240155 TTTTAAAAAATAATTAATAAA
1 TTTTAAAAAA-AATT--TAAA
*
2240176 TTTTATAAAAAATTTAAA
1 TTTTAAAAAAAATTTAAA
2240194 TTTTA
1 TTTTA
2240199 TAATTGGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 9 0.41
20 4 0.18
21 9 0.41
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
TTTTAAAAAAAATTTAAA
Found at i:2244759 original size:18 final size:18
Alignment explanation
Indices: 2244736--2244774 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
2244726 CTACAGCTAA
2244736 TGTGATTT-CAATGATGTC
1 TGTGATTTGC-ATGATGTC
*
2244754 TGTGATTTGCATGATTTC
1 TGTGATTTGCATGATGTC
2244772 TGT
1 TGT
2244775 CTATTATAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 18 0.95
19 1 0.05
ACGTcount: A:0.18, C:0.10, G:0.23, T:0.49
Consensus pattern (18 bp):
TGTGATTTGCATGATGTC
Found at i:2263856 original size:18 final size:18
Alignment explanation
Indices: 2263833--2263868 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
2263823 ATGTCATCAC
2263833 GTTATATGTGATATGAAT
1 GTTATATGTGATATGAAT
2263851 GTTATATGTGATATGAAT
1 GTTATATGTGATATGAAT
2263869 AGAAAATGTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (18 bp):
GTTATATGTGATATGAAT
Found at i:2263877 original size:18 final size:18
Alignment explanation
Indices: 2263838--2263888 Score: 50
Period size: 18 Copynumber: 2.7 Consensus size: 18
2263828 ATCACGTTAT
* *
2263838 ATGTGATATGAATGTTAT
1 ATGTGATATGAATGTAAA
2263856 ATGTGATATGAATAG-AAA
1 ATGTGATATGAAT-GTAAA
2263874 ATGTCGATATTGAAT
1 ATGT-GATA-TGAAT
2263889 TTCATTAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 18 0.64
19 5 0.18
20 5 0.18
ACGTcount: A:0.39, C:0.02, G:0.22, T:0.37
Consensus pattern (18 bp):
ATGTGATATGAATGTAAA
Done.