Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr1
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: 37323695
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.32
Warning! 1370832 characters in sequence are not A, C, G, or T
File 80 of 93
Found at i:30777577 original size:26 final size:26
Alignment explanation
Indices: 30777524--30777589 Score: 89
Period size: 27 Copynumber: 2.5 Consensus size: 26
30777514 TATTTTAAAA
* *
30777524 ATTTTAAATAAATTTTTATTTTTATT
1 ATTTTAATTAAATTTTTATATTTATT
30777550 ATATTTAATTAAATTTTTATATTT-TT
1 AT-TTTAATTAAATTTTTATATTTATT
30777576 ATTTTAAATTAAAT
1 ATTTT-AATTAAAT
30777590 AAATTTTTAT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
25 3 0.08
26 14 0.39
27 19 0.53
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (26 bp):
ATTTTAATTAAATTTTTATATTTATT
Found at i:30777595 original size:30 final size:29
Alignment explanation
Indices: 30777527--30777600 Score: 98
Period size: 30 Copynumber: 2.6 Consensus size: 29
30777517 TTTAAAAATT
*
30777527 TTAAATAAA-TTTT-TATTTTTATTATAT
1 TTAAATAAATTTTTATATTTTTATTATAA
* *
30777554 TTAATTAAATTTTTATATTTTTATTTTAAA
1 TTAAATAAATTTTTATATTTTTATTAT-AA
30777584 TTAAATAAATTTTTATA
1 TTAAATAAATTTTTATA
30777601 ATTAACTATC
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
27 8 0.20
28 4 0.10
29 11 0.28
30 17 0.43
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (29 bp):
TTAAATAAATTTTTATATTTTTATTATAA
Found at i:30793371 original size:12 final size:12
Alignment explanation
Indices: 30793339--30793373 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
30793329 ATAAACTAAT
*
30793339 TTATTATTATTA
1 TTATTATTGTTA
30793351 TTATTATTGTTA
1 TTATTATTGTTA
*
30793363 TTGTTATTGTT
1 TTATTATTGTT
30793374 GTGATTCGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.23, C:0.00, G:0.09, T:0.69
Consensus pattern (12 bp):
TTATTATTGTTA
Found at i:30795590 original size:2 final size:2
Alignment explanation
Indices: 30795583--30795617 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
30795573 CTGGACGTGT
30795583 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 A
30795618 TTTCCTTTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:30797796 original size:44 final size:44
Alignment explanation
Indices: 30797733--30797820 Score: 176
Period size: 44 Copynumber: 2.0 Consensus size: 44
30797723 TCTCTAAACT
30797733 CTCTTCCACGCATCTCTTTAACCCTTTCTTTCAAAAATCTTTAG
1 CTCTTCCACGCATCTCTTTAACCCTTTCTTTCAAAAATCTTTAG
30797777 CTCTTCCACGCATCTCTTTAACCCTTTCTTTCAAAAATCTTTAG
1 CTCTTCCACGCATCTCTTTAACCCTTTCTTTCAAAAATCTTTAG
30797821 AATCTCGCAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.23, C:0.32, G:0.05, T:0.41
Consensus pattern (44 bp):
CTCTTCCACGCATCTCTTTAACCCTTTCTTTCAAAAATCTTTAG
Found at i:30798816 original size:17 final size:17
Alignment explanation
Indices: 30798796--30798828 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
30798786 ACATTGCTAA
30798796 TATATCA-AATATAAATC
1 TATATCATAAT-TAAATC
30798813 TATATCATAATTAAAT
1 TATATCATAATTAAAT
30798829 AAAATAGTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.80
18 3 0.20
ACGTcount: A:0.52, C:0.09, G:0.00, T:0.39
Consensus pattern (17 bp):
TATATCATAATTAAATC
Found at i:30801381 original size:13 final size:15
Alignment explanation
Indices: 30801352--30801391 Score: 57
Period size: 14 Copynumber: 2.8 Consensus size: 15
30801342 TTTCTTTTCT
30801352 TTTCTCTCTCTTCAC
1 TTTCTCTCTCTTCAC
30801367 TTTC-CTCTC-TCAC
1 TTTCTCTCTCTTCAC
*
30801380 TTTCTCTTTCTT
1 TTTCTCTCTCTT
30801392 GCTGCCACTC
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
13 8 0.36
14 9 0.41
15 5 0.23
ACGTcount: A:0.05, C:0.38, G:0.00, T:0.57
Consensus pattern (15 bp):
TTTCTCTCTCTTCAC
Found at i:30801873 original size:15 final size:15
Alignment explanation
Indices: 30801855--30801897 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 15
30801845 TTTTTAATTT
30801855 TTTATTATTTTATTA
1 TTTATTATTTTATTA
30801870 TTTATT-TTATTATTA
1 TTTATTATT-TTATTA
*
30801885 TATATATATTTTA
1 TTTAT-TATTTTA
30801898 GAGGTGTCTA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
14 2 0.08
15 16 0.67
16 4 0.17
17 2 0.08
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (15 bp):
TTTATTATTTTATTA
Found at i:30801876 original size:12 final size:12
Alignment explanation
Indices: 30801851--30801883 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
30801841 TTAATTTTTA
30801851 ATTTT-TTA-TT
1 ATTTTATTATTT
30801861 ATTTTATTATTT
1 ATTTTATTATTT
30801873 ATTTTATTATT
1 ATTTTATTATT
30801884 ATATATATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 5 0.24
11 3 0.14
12 13 0.62
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (12 bp):
ATTTTATTATTT
Found at i:30801879 original size:20 final size:19
Alignment explanation
Indices: 30801854--30801897 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 19
30801844 ATTTTTAATT
* *
30801854 TTTTATTATTTTATTATTTA
1 TTTTATTATTATA-TATATA
30801874 TTTTATTATTATATATATA
1 TTTTATTATTATATATATA
30801893 TTTTA
1 TTTTA
30801898 GAGGTGTCTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 10 0.45
20 12 0.55
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (19 bp):
TTTTATTATTATATATATA
Found at i:30803282 original size:23 final size:23
Alignment explanation
Indices: 30803255--30803305 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
30803245 GTTTAGAGTT
30803255 TGTGAAACGGAATAGTGCGAATG
1 TGTGAAACGGAATAGTGCGAATG
* ** * *
30803278 TGTGATACGTCATGGTGGGAATG
1 TGTGAAACGGAATAGTGCGAATG
30803301 TGTGA
1 TGTGA
30803306 CACGTCATGG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.27, C:0.08, G:0.37, T:0.27
Consensus pattern (23 bp):
TGTGAAACGGAATAGTGCGAATG
Found at i:30803310 original size:23 final size:23
Alignment explanation
Indices: 30803273--30803328 Score: 85
Period size: 23 Copynumber: 2.4 Consensus size: 23
30803263 GGAATAGTGC
* *
30803273 GAATGTGTGATACGTCATGGTGG
1 GAATGTGTGACACGTCATGGTGA
30803296 GAATGTGTGACACGTCATGGTGA
1 GAATGTGTGACACGTCATGGTGA
*
30803319 GAATATGTGA
1 GAATGTGTGA
30803329 GATGGGTGTG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.27, C:0.09, G:0.36, T:0.29
Consensus pattern (23 bp):
GAATGTGTGACACGTCATGGTGA
Found at i:30803389 original size:23 final size:23
Alignment explanation
Indices: 30803359--30803435 Score: 100
Period size: 23 Copynumber: 3.3 Consensus size: 23
30803349 GTATAGAGTT
*
30803359 TGTGACACGGCTTGGTGGCAATG
1 TGTGACACGGCATGGTGGCAATG
30803382 TGTGACACGGCATGGTGGCAATG
1 TGTGACACGGCATGGTGGCAATG
* * * **
30803405 TGTGAAACGACATAGTGATAATG
1 TGTGACACGGCATGGTGGCAATG
30803428 TGTGACAC
1 TGTGACAC
30803436 TGGTGTGACG
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 47 1.00
ACGTcount: A:0.26, C:0.16, G:0.34, T:0.25
Consensus pattern (23 bp):
TGTGACACGGCATGGTGGCAATG
Found at i:30803432 original size:104 final size:103
Alignment explanation
Indices: 30803237--30803810 Score: 458
Period size: 104 Copynumber: 5.5 Consensus size: 103
30803227 GGTCTGTGTG
* ** * * **
30803237 ACGGCAGGGTTTAGAGTTTGTGAAACGGAATAGTGCGAATGTGTGATACGTCATGGTGGGAATGT
1 ACGGCAGGGTTTAGAGTTTGTGACACGCCATAGTG-GAATGTGTGACACGGCATGGTGATAATGT
* * * * *
30803302 GTGACACGTCATGGTGAGAATATGTGAGATGGGTGTGAC
65 GTGAAACGACATAGTGAGAATATGTGACACGGGTGTGAC
* * * * **
30803341 ACGGCAGGGTATAGAGTTTGTGACACGGCTTGGTGGCAATGTGTGACACGGCATGGTGGCAATGT
1 ACGGCAGGGTTTAGAGTTTGTGACACGCCATAGTGG-AATGTGTGACACGGCATGGTGATAATGT
* * *
30803406 GTGAAACGACATAGTGATAATGTGTGACACTGGTGTGAC
65 GTGAAACGACATAGTGAGAATATGTGACACGGGTGTGAC
* * * * * * *
30803445 GCGGTAGGGTTTAGAGTGTGTGACACGCCATAGAGAGAATCTGTGACACGACAGGGTGATAATGT
1 ACGGCAGGGTTTAGAGTTTGTGACACGCCATAGTG-GAATGTGTGACACGGCATGGTGATAATGT
* * * *
30803510 GTGAGACGGCA-CGTTGAGAATATGTGACACGGGTGTGAG
65 GTGAAACGACATAG-TGAGAATATGTGACACGGGTGTGAC
* ** * * * * * *
30803549 ACGACAGCTTTTAGAGTTTGTGACATGCCATGGTCAGAACGTGTGACACGGAATGGTCATAATGT
1 ACGGCAGGGTTTAGAGTTTGTGACACGCCATAGT-GGAATGTGTGACACGGCATGGTGATAATGT
* *
30803614 GTGAAACGACACAGTGATAATATGTGACACGGGTGTGAC
65 GTGAAACGACATAGTGAGAATATGTGACACGGGTGTGAC
** * * **
30803653 ACGATAGGGTTTAGAGTGTGTGACACGCC-TGGAG-GGAAT-TGGTGACACGTCGGGGTGATAAT
1 ACGGCAGGGTTTAGAGTTTGTGACACGCCAT--AGTGGAATGT-GTGACACGGCATGGTGATAAT
* ** *
30803715 GTGTGAGAC-AGCACGGTGAGAATATGTGAAACGGGTGTGAC
63 GTGTGAAACGA-CATAGTGAGAATATGTGACACGGGTGTGAC
** ** * * * * *
30803756 ACGATAGCATTTAGAGTGTGGGACACGCCATGGT-CAGATGTGTGACACGACATGG
1 ACGGCAGGGTTTAGAGTTTGTGACACGCCATAGTGGA-ATGTGTGACACGGCATGG
30803811 CTTGAATGTG
Statistics
Matches: 375, Mismatches: 82, Indels: 27
0.77 0.17 0.06
Matches are distributed among these distances:
102 4 0.01
103 96 0.26
104 272 0.73
105 3 0.01
ACGTcount: A:0.27, C:0.14, G:0.35, T:0.24
Consensus pattern (103 bp):
ACGGCAGGGTTTAGAGTTTGTGACACGCCATAGTGGAATGTGTGACACGGCATGGTGATAATGTG
TGAAACGACATAGTGAGAATATGTGACACGGGTGTGAC
Found at i:30803541 original size:23 final size:23
Alignment explanation
Indices: 30803479--30803541 Score: 63
Period size: 23 Copynumber: 2.7 Consensus size: 23
30803469 ACGCCATAGA
* * *
30803479 GAGAATCTGTGACACGACAGGGT
1 GAGAATATGTGACACGGCACGGT
* * * *
30803502 GATAATGTGTGAGACGGCACGTT
1 GAGAATATGTGACACGGCACGGT
30803525 GAGAATATGTGACACGG
1 GAGAATATGTGACACGG
30803542 GTGTGAGACG
Statistics
Matches: 31, Mismatches: 9, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.30, C:0.14, G:0.35, T:0.21
Consensus pattern (23 bp):
GAGAATATGTGACACGGCACGGT
Found at i:30803615 original size:208 final size:207
Alignment explanation
Indices: 30803242--30803804 Score: 664
Period size: 208 Copynumber: 2.7 Consensus size: 207
30803232 GTGTGACGGC
* * ** * * * * ** *
30803242 AGGGTTTAGAGTTTGTGAAACGGAATAGTGCGAATGTGTGATACGTCATGGTGGGAATGTGTGAC
1 AGGGTTTAGAGTGTGTGACACGCCATAGAGAGAAT-TGTGACACGTCAGGGTGATAATGTGTGAG
* * * * * ** * * *
30803307 ACGTCATGGTGAGAATATGTGAGATGGGTGTGACACGGCAGGGTATAGAGTTTGTGACACGGCTT
65 ACGGCACGGTGAGAATATGTGAAACGGGTGTGACACGACAGCATTTAGAGTTTGTGACACGCCAT
* * ** * *
30803372 GGT-GGCAATGTGTGACACGGCATGGTGGCAATGTGTGAAACGACATAGTGATAATGTGTGACAC
130 GGTCAG-AATGTGTGACACGGAATGGTCACAATGTGTGAAACGACACAGTGATAATATGTGACAC
* * *
30803436 TGGTGTGACGCGGT
194 GGGTGTGACACGAT
*
30803450 AGGGTTTAGAGTGTGTGACACGCCATAGAGAGAATCTGTGACACGACAGGGTGATAATGTGTGAG
1 AGGGTTTAGAGTGTGTGACACGCCATAGAGAGAAT-TGTGACACGTCAGGGTGATAATGTGTGAG
* * * * *
30803515 ACGGCACGTTGAGAATATGTGACACGGGTGTGAGACGACAGCTTTTAGAGTTTGTGACATGCCAT
65 ACGGCACGGTGAGAATATGTGAAACGGGTGTGACACGACAGCATTTAGAGTTTGTGACACGCCAT
* *
30803580 GGTCAGAACGTGTGACACGGAATGGTCATAATGTGTGAAACGACACAGTGATAATATGTGACACG
130 GGTCAGAATGTGTGACACGGAATGGTCACAATGTGTGAAACGACACAGTGATAATATGTGACACG
30803645 GGTGTGACACGAT
195 GGTGTGACACGAT
* * *
30803658 AGGGTTTAGAGTGTGTGACACGCC-TGGAGGGAATTGGTGACACGTCGGGGTGATAATGTGTGAG
1 AGGGTTTAGAGTGTGTGACACGCCATAGAGAGAATT-GTGACACGTCAGGGTGATAATGTGTGAG
* * * *
30803722 ACAGCACGGTGAGAATATGTGAAACGGGTGTGACACGATAGCATTTAGAGTGTGGGACACGCCAT
65 ACGGCACGGTGAGAATATGTGAAACGGGTGTGACACGACAGCATTTAGAGTTTGTGACACGCCAT
30803787 GGTCAG-ATGTGTGACACG
130 GGTCAGAATGTGTGACACG
30803805 ACATGGCTTG
Statistics
Matches: 302, Mismatches: 51, Indels: 6
0.84 0.14 0.02
Matches are distributed among these distances:
206 12 0.04
207 96 0.32
208 193 0.64
209 1 0.00
ACGTcount: A:0.27, C:0.13, G:0.35, T:0.24
Consensus pattern (207 bp):
AGGGTTTAGAGTGTGTGACACGCCATAGAGAGAATTGTGACACGTCAGGGTGATAATGTGTGAGA
CGGCACGGTGAGAATATGTGAAACGGGTGTGACACGACAGCATTTAGAGTTTGTGACACGCCATG
GTCAGAATGTGTGACACGGAATGGTCACAATGTGTGAAACGACACAGTGATAATATGTGACACGG
GTGTGACACGAT
Found at i:30803802 original size:22 final size:24
Alignment explanation
Indices: 30803767--30803834 Score: 79
Period size: 23 Copynumber: 3.0 Consensus size: 24
30803757 CGATAGCATT
* *
30803767 TAGAGTGTGGGACACGCCATGGTC
1 TAGAATGTGTGACACGCCATGGTC
*
30803791 -AG-ATGTGTGACACGACATGG-C
1 TAGAATGTGTGACACGCCATGGTC
*
30803812 TTGAATGTGTGACACGCCATGGT
1 TAGAATGTGTGACACGCCATGGT
30803835 GTGAAAGAAG
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
21 1 0.03
22 16 0.44
23 19 0.53
ACGTcount: A:0.24, C:0.19, G:0.34, T:0.24
Consensus pattern (24 bp):
TAGAATGTGTGACACGCCATGGTC
Found at i:30804580 original size:168 final size:167
Alignment explanation
Indices: 30804364--30804665 Score: 450
Period size: 168 Copynumber: 1.8 Consensus size: 167
30804354 TATTCTTAAC
* *
30804364 GTGTTGTGGGTTTACTGGATTTTTGGATTTTTGGCGTATCACGGCTGTTCCTAGCGTGTTGTGGG
1 GTGTTGTGGGTTAACTGGATTTTTGGATTTTTAGCGTATCACGGCTGTTCCTAGCGTGTTGTGGG
* *
30804429 TTAACT-G-GTTTTTTGGGTTTTTAGCGTGTCACGGCTGTTCTTGGCGTGTAGTGGGTTAACTAG
66 TTAACTAGAG-TTTTT-GGTTTTTAGCGTGTCACGGCTGTTCCTGACGTGTAGTGGGTTAACTAG
30804492 ATTTTTTTTTTGTTTTTGGCATGTCATGGTTGTTCCTAGT
129 -TTTTTTTTTTGTTTTTGGCATGTCATGGTTGTTCCTAGT
* *
30804532 GTGTTGTGGGTTAATTGG-TTATTT-GAGTTTTTAGCGTATCATGGCTGTTCCTAGCGTGTTGTG
1 GTGTTGTGGGTTAACTGGATT-TTTGGA-TTTTTAGCGTATCACGGCTGTTCCTAGCGTGTTGTG
* * *
30804595 GGTTAACTAGAGTTTTTGGTTTTTGGCGTGTCACGGCTGTTCCTGACGTGTTGTGGGTTAATTAG
64 GGTTAACTAGAGTTTTTGGTTTTTAGCGTGTCACGGCTGTTCCTGACGTGTAGTGGGTTAACTAG
30804660 TTTTTT
129 TTTTTT
30804666 GTATTTTTAG
Statistics
Matches: 121, Mismatches: 9, Indels: 9
0.87 0.06 0.06
Matches are distributed among these distances:
167 10 0.08
168 104 0.86
169 6 0.05
170 1 0.01
ACGTcount: A:0.12, C:0.11, G:0.30, T:0.47
Consensus pattern (167 bp):
GTGTTGTGGGTTAACTGGATTTTTGGATTTTTAGCGTATCACGGCTGTTCCTAGCGTGTTGTGGG
TTAACTAGAGTTTTTGGTTTTTAGCGTGTCACGGCTGTTCCTGACGTGTAGTGGGTTAACTAGTT
TTTTTTTTGTTTTTGGCATGTCATGGTTGTTCCTAGT
Found at i:30804673 original size:110 final size:109
Alignment explanation
Indices: 30804307--30804690 Score: 448
Period size: 110 Copynumber: 3.5 Consensus size: 109
30804297 TCTACATATG
* * *
30804307 GCGTGTTGTGGGTTAACTGGTTTTTTGGATTTTTAGCGTGTCACGATTATTCTTAACGTGTTGTG
1 GCGTGTTGTGGGTTAACTGGTTTTTTGGATTTTTAGCGTGTCACGACTGTTCTTAGCGTGTTGTG
* * *
30804372 GGTTTACTGGATTTTTGGATTTTTGGCGTATCACGGCTGTTCCTA
66 GGTTAACTAGATTTTTGG-TTTTTGGCGTGTCACGGCTGTTCCTA
* * * *
30804417 GCGTGTTGTGGGTTAACTGGTTTTTTGGGTTTTTAGCGTGTCACGGCTGTTCTTGGCGTGTAGTG
1 GCGTGTTGTGGGTTAACTGGTTTTTTGGATTTTTAGCGTGTCACGACTGTTCTTAGCGTGTTGTG
* * * *
30804482 GGTTAACTAGATTTTTTTTTTGTTTTTGGCATGTCATGGTTGTTCCTA
66 GGTTAACTAGA----TTTTTGGTTTTTGGCGTGTCACGGCTGTTCCTA
* * * * * * *
30804530 GTGTGTTGTGGGTTAATTGGTTATTT-GAGTTTTTAGCGTATCATGGCTGTTCCTAGCGTGTTGT
1 GCGTGTTGTGGGTTAACTGGTTTTTTGGA-TTTTTAGCGTGTCACGACTGTTCTTAGCGTGTTGT
30804594 GGGTTAACTAGAGTTTTTGGTTTTTGGCGTGTCACGGCTGTTCCT-
65 GGGTTAACTAGA-TTTTTGGTTTTTGGCGTGTCACGGCTGTTCCTA
* * * * *
30804639 GACGTGTTGTGGGTTAATTAGTTTTTTGTATTTTTAGCATGTCATGACTGTT
1 G-CGTGTTGTGGGTTAACTGGTTTTTTGGATTTTTAGCGTGTCACGACTGTT
30804691 GGTGTAATGA
Statistics
Matches: 232, Mismatches: 35, Indels: 14
0.83 0.12 0.05
Matches are distributed among these distances:
109 1 0.00
110 136 0.59
111 1 0.00
112 1 0.00
113 87 0.38
114 6 0.03
ACGTcount: A:0.13, C:0.11, G:0.29, T:0.47
Consensus pattern (109 bp):
GCGTGTTGTGGGTTAACTGGTTTTTTGGATTTTTAGCGTGTCACGACTGTTCTTAGCGTGTTGTG
GGTTAACTAGATTTTTGGTTTTTGGCGTGTCACGGCTGTTCCTA
Found at i:30804690 original size:55 final size:55
Alignment explanation
Indices: 30804307--30804682 Score: 384
Period size: 55 Copynumber: 6.8 Consensus size: 55
30804297 TCTACATATG
** * *
30804307 GCGTGTTGTGGGTTAACTGGTTTTTTGGATTTTTAGCGTGTCACGATTATTCTTA
1 GCGTGTTGTGGGTTAACTGGTTTTTTGGATTTTTAGCGTGTCACGGCTGTTCCTA
* * * * *
30804362 ACGTGTTGTGGGTTTACTGGATTTTTGGATTTTTGGCGTATCACGGCTGTTCCTA
1 GCGTGTTGTGGGTTAACTGGTTTTTTGGATTTTTAGCGTGTCACGGCTGTTCCTA
* * *
30804417 GCGTGTTGTGGGTTAACTGGTTTTTTGGGTTTTTAGCGTGTCACGGCTGTTCTTG
1 GCGTGTTGTGGGTTAACTGGTTTTTTGGATTTTTAGCGTGTCACGGCTGTTCCTA
* * * * * * *
30804472 GCGTGTAGTGGGTTAACTAGATTTTTTTTTTG-TTTTTGGCATGTCATGGTTGTTCCTA
1 GCGTGTTGTGGGTTAACT-G---GTTTTTTGGATTTTTAGCGTGTCACGGCTGTTCCTA
* * * * *
30804530 GTGTGTTGTGGGTTAATTGGTTATTT-GAGTTTTTAGCGTATCATGGCTGTTCCTA
1 GCGTGTTGTGGGTTAACTGGTTTTTTGGA-TTTTTAGCGTGTCACGGCTGTTCCTA
*
30804585 GCGTGTTGTGGGTTAACTAGAG-TTTTTGG-TTTTTGGCGTGTCACGGCTGTTCCT-
1 GCGTGTTGTGGGTTAACT-G-GTTTTTTGGATTTTTAGCGTGTCACGGCTGTTCCTA
* * * *
30804639 GACGTGTTGTGGGTTAATTAGTTTTTTGTATTTTTAGCATGTCA
1 G-CGTGTTGTGGGTTAACTGGTTTTTTGGATTTTTAGCGTGTCA
30804683 TGACTGTTGG
Statistics
Matches: 263, Mismatches: 46, Indels: 24
0.79 0.14 0.07
Matches are distributed among these distances:
53 2 0.01
54 12 0.05
55 198 0.75
56 6 0.02
57 3 0.01
58 35 0.13
59 7 0.03
ACGTcount: A:0.13, C:0.11, G:0.29, T:0.47
Consensus pattern (55 bp):
GCGTGTTGTGGGTTAACTGGTTTTTTGGATTTTTAGCGTGTCACGGCTGTTCCTA
Found at i:30807121 original size:41 final size:41
Alignment explanation
Indices: 30807073--30807172 Score: 200
Period size: 41 Copynumber: 2.4 Consensus size: 41
30807063 AATAAAATAT
30807073 CCTAACCCTATTAACTACTCGAATAATTTAAAAATTACTAC
1 CCTAACCCTATTAACTACTCGAATAATTTAAAAATTACTAC
30807114 CCTAACCCTATTAACTACTCGAATAATTTAAAAATTACTAC
1 CCTAACCCTATTAACTACTCGAATAATTTAAAAATTACTAC
30807155 CCTAACCCTATTAACTAC
1 CCTAACCCTATTAACTAC
30807173 CCTAACCTTA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 59 1.00
ACGTcount: A:0.40, C:0.27, G:0.02, T:0.31
Consensus pattern (41 bp):
CCTAACCCTATTAACTACTCGAATAATTTAAAAATTACTAC
Found at i:30808307 original size:81 final size:81
Alignment explanation
Indices: 30808190--30808440 Score: 367
Period size: 81 Copynumber: 3.1 Consensus size: 81
30808180 CAGATGATGC
* * **
30808190 TGAAGGAGTCCATGTTCCTTAGGCTGATTCAGTTATCGATGCATCTGCGGGAGGTAAGGGGGACC
1 TGAAGGAGTCCATGTTCCTGAGGCTGATTCGGTTATCGATGCATCTGCGGGAGGGGAGGGGGACC
30808255 TTCACTTGCTCGTGGT
66 TTCACTTGCTCGTGGT
* * **
30808271 TGAAGGAGTCCATGTTCCTGAGGCTGATTCGGTTATCAATGCATATGCAAGAGGGGAGGGGGACC
1 TGAAGGAGTCCATGTTCCTGAGGCTGATTCGGTTATCGATGCATCTGCGGGAGGGGAGGGGGACC
*
30808336 TTCACTCGCTCGTGGT
66 TTCACTTGCTCGTGGT
* * * *
30808352 TGAAGGAGTCCATATTCTTGAGGCTAATTCGGTTATCGATGCATCTGCGGGAGGGGATGGGGACC
1 TGAAGGAGTCCATGTTCCTGAGGCTGATTCGGTTATCGATGCATCTGCGGGAGGGGAGGGGGACC
* *
30808417 TTCACTTGCTTGTGGC
66 TTCACTTGCTCGTGGT
30808433 TGAAGGAG
1 TGAAGGAG
30808441 AGCATCTTCC
Statistics
Matches: 150, Mismatches: 20, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
81 150 1.00
ACGTcount: A:0.20, C:0.19, G:0.33, T:0.28
Consensus pattern (81 bp):
TGAAGGAGTCCATGTTCCTGAGGCTGATTCGGTTATCGATGCATCTGCGGGAGGGGAGGGGGACC
TTCACTTGCTCGTGGT
Found at i:30810024 original size:86 final size:86
Alignment explanation
Indices: 30809861--30810107 Score: 311
Period size: 86 Copynumber: 2.9 Consensus size: 86
30809851 TGGGGCATGG
* * * *
30809861 CGTGTCACCCTACAAGATTGCAACAAGTCAGCGTGTCACGCCAGAAGTCTGC-TTGCACTTAGCG
1 CGTGTCACCCCACAAGATTGCAACAAGTTAGCGTGTCACGCCAGAAGTCTGCATT-CACTCAACG
* *
30809925 TGC-CATCATAATTGGCCCGTGC
65 T-CTCACCACAATTGGCCCGTGC
* * *
30809947 CGTGTCACCCCACAAGACTGCAATAAGTTAGCGTGTCACGCCAGAAGTCTGCATTCACTCAATGT
1 CGTGTCACCCCACAAGATTGCAACAAGTTAGCGTGTCACGCCAGAAGTCTGCATTCACTCAACGT
30810012 CTCACCACAATTGGCCCGTGC
66 CTCACCACAATTGGCCCGTGC
* * ** *
30810033 CGTGCCACCCCACAAGATTGCAACAAGTTAGCATGTCACTTC-GTAAGTCTGCATGCACTCAACG
1 CGTGTCACCCCACAAGATTGCAACAAGTTAGCGTGTCACGCCAG-AAGTCTGCATTCACTCAACG
*
30810097 TGTCACCACAA
65 TCTCACCACAA
30810108 GCATCTGCTC
Statistics
Matches: 140, Mismatches: 18, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
85 2 0.01
86 136 0.97
87 2 0.01
ACGTcount: A:0.26, C:0.32, G:0.20, T:0.22
Consensus pattern (86 bp):
CGTGTCACCCCACAAGATTGCAACAAGTTAGCGTGTCACGCCAGAAGTCTGCATTCACTCAACGT
CTCACCACAATTGGCCCGTGC
Found at i:30810880 original size:31 final size:31
Alignment explanation
Indices: 30810842--30810973 Score: 201
Period size: 31 Copynumber: 4.3 Consensus size: 31
30810832 TCATGTTGTT
**
30810842 ACACGCCATGCATATAATATAAAATGTGGTA
1 ACACGCCATGCATATAACGTAAAATGTGGTA
30810873 ACACGCCATGCATATAACGTAAAATGTGGTA
1 ACACGCCATGCATATAACGTAAAATGTGGTA
* * * *
30810904 ATACGTCACGCATATAACGTAAAATGTTGTA
1 ACACGCCATGCATATAACGTAAAATGTGGTA
*
30810935 ACACGCCATACATATAACGTAAAATGTGGTA
1 ACACGCCATGCATATAACGTAAAATGTGGTA
30810966 ACACGCCA
1 ACACGCCA
30810974 ATGCTGACAT
Statistics
Matches: 90, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 90 1.00
ACGTcount: A:0.40, C:0.20, G:0.17, T:0.23
Consensus pattern (31 bp):
ACACGCCATGCATATAACGTAAAATGTGGTA
Found at i:30811328 original size:63 final size:63
Alignment explanation
Indices: 30811226--30811345 Score: 161
Period size: 63 Copynumber: 1.9 Consensus size: 63
30811216 CAGCCCGATG
* * *
30811226 ACGATGGTGCTTTACAAAGAGTTGACAGAGCTCATATAGTTTAGAGA-TCTGAGAGAGCTGACA
1 ACGATGGTGCTTAACAAAGAGTTGACAGAGCTCAGATAGTTCAGAGAGT-TGAGAGAGCTGACA
** * *
30811289 ACGATGGTGCTTAACAAAGAGTTGGTAGAGTTGAGATAGTTCAGAGAGTTGAGAGAG
1 ACGATGGTGCTTAACAAAGAGTTGACAGAGCTCAGATAGTTCAGAGAGTTGAGAGAG
30811346 AAAGATGACC
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
63 48 0.98
64 1 0.02
ACGTcount: A:0.33, C:0.11, G:0.31, T:0.25
Consensus pattern (63 bp):
ACGATGGTGCTTAACAAAGAGTTGACAGAGCTCAGATAGTTCAGAGAGTTGAGAGAGCTGACA
Found at i:30821605 original size:24 final size:25
Alignment explanation
Indices: 30821573--30821639 Score: 77
Period size: 24 Copynumber: 2.8 Consensus size: 25
30821563 TTTAGATATT
*
30821573 AATAATATTTAAATATTTTTAAA-A
1 AATAATATTTAAATATTTATAAACA
*
30821597 AATAATATTTAATTA-TTATAAACA
1 AATAATATTTAAATATTTATAAACA
*
30821621 AATTATATATT-AATATTTA
1 AATAATAT-TTAAATATTTA
30821640 AATTCTACAT
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
23 6 0.17
24 25 0.69
25 5 0.14
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.46
Consensus pattern (25 bp):
AATAATATTTAAATATTTATAAACA
Found at i:30842418 original size:97 final size:96
Alignment explanation
Indices: 30842252--30842440 Score: 324
Period size: 97 Copynumber: 2.0 Consensus size: 96
30842242 GGAAACAAAA
** *
30842252 GCATAGGAAAGGTAGAAATCAAGCTAAAGTCGAAAAATCTTACCGTTAGACGTGTAAACGGACGA
1 GCATAGGAAAGGTAGAAATCAAGCTAAAGTCGAAAAATCTTACCGTTAGACACGTAAACGAACGA
30842317 AAAACGCGAATTCCCCTTTGAATTTTNCAGAG
66 AAAACGCGAATTCCCCTTTGAATTTT-CAGAG
30842349 GCATAGGAAAGGTAGAAATCAAGCTAAAGTCGAAAAATCTTACCGTTAGACACGTAAACGAACGA
1 GCATAGGAAAGGTAGAAATCAAGCTAAAGTCGAAAAATCTTACCGTTAGACACGTAAACGAACGA
* *
30842414 AAAACGCGAATTCTCTTTTGAATTTTC
66 AAAACGCGAATTCCCCTTTGAATTTTC
30842441 TAGTTTTCCT
Statistics
Matches: 87, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
96 1 0.01
97 86 0.99
ACGTcount: A:0.39, C:0.17, G:0.20, T:0.23
Consensus pattern (96 bp):
GCATAGGAAAGGTAGAAATCAAGCTAAAGTCGAAAAATCTTACCGTTAGACACGTAAACGAACGA
AAAACGCGAATTCCCCTTTGAATTTTCAGAG
Found at i:30846982 original size:38 final size:38
Alignment explanation
Indices: 30846931--30847032 Score: 150
Period size: 38 Copynumber: 2.7 Consensus size: 38
30846921 AAAGGTAGAG
*
30846931 AGGTTGTGCTTGATCTTTAAAAGGTATTTTGATTGTAA
1 AGGTTGTGCTTGATCTTTAAAAGGCATTTTGATTGTAA
** *
30846969 AGGTTGTGCTTGATCCCTAACAGGCATTTTGATTGTAA
1 AGGTTGTGCTTGATCTTTAAAAGGCATTTTGATTGTAA
* *
30847007 AGGTTGTACTTGATCTTAAAAAGGCA
1 AGGTTGTGCTTGATCTTTAAAAGGCA
30847033 GTGACTTTGG
Statistics
Matches: 55, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
38 55 1.00
ACGTcount: A:0.27, C:0.11, G:0.24, T:0.38
Consensus pattern (38 bp):
AGGTTGTGCTTGATCTTTAAAAGGCATTTTGATTGTAA
Found at i:30847258 original size:14 final size:14
Alignment explanation
Indices: 30847234--30847268 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
30847224 CTTGCTTAGC
30847234 TTATACTCTGTT-T
1 TTATACTCTGTTCT
30847247 TTATAGCTCTGTTCT
1 TTATA-CTCTGTTCT
30847262 TTATACT
1 TTATACT
30847269 TGAGCTACAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
13 5 0.25
14 9 0.45
15 6 0.30
ACGTcount: A:0.17, C:0.17, G:0.09, T:0.57
Consensus pattern (14 bp):
TTATACTCTGTTCT
Found at i:30852067 original size:9 final size:10
Alignment explanation
Indices: 30852054--30852091 Score: 53
Period size: 10 Copynumber: 3.9 Consensus size: 10
30852044 TATAATTAAT
30852054 TATATTAAAAA
1 TATA-TAAAAA
30852065 TATATAAAAA
1 TATATAAAAA
30852075 T-TA-AAAAA
1 TATATAAAAA
30852083 TATATAAAA
1 TATATAAAA
30852092 GTAAAAAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
8 6 0.24
9 4 0.16
10 11 0.44
11 4 0.16
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (10 bp):
TATATAAAAA
Found at i:30852079 original size:17 final size:17
Alignment explanation
Indices: 30852057--30852101 Score: 63
Period size: 18 Copynumber: 2.6 Consensus size: 17
30852047 AATTAATTAT
30852057 ATTAAAAATATATAAAA
1 ATTAAAAATATATAAAA
30852074 ATTAAAAAATATATAAAA
1 ATT-AAAAATATATAAAA
* *
30852092 GTAAAAAATA
1 ATTAAAAATA
30852102 ATTAATAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 10 0.40
18 15 0.60
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (17 bp):
ATTAAAAATATATAAAA
Found at i:30852083 original size:18 final size:17
Alignment explanation
Indices: 30852060--30852101 Score: 66
Period size: 17 Copynumber: 2.4 Consensus size: 17
30852050 TAATTATATT
*
30852060 AAAAATATATAAAAATTA
1 AAAAATATAT-AAAAGTA
30852078 AAAAATATATAAAAGTA
1 AAAAATATATAAAAGTA
30852095 AAAAATA
1 AAAAATA
30852102 ATTAATAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 13 0.57
18 10 0.43
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.24
Consensus pattern (17 bp):
AAAAATATATAAAAGTA
Found at i:30858371 original size:2 final size:2
Alignment explanation
Indices: 30858364--30858392 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
30858354 TGTATGTATA
30858364 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
30858393 CTATGTATGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:30859472 original size:2 final size:2
Alignment explanation
Indices: 30859465--30859498 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
30859455 ACGACGCACC
30859465 AG AG AG AG AG AG AG AG AG AG AG AG AG AG -G AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
30859499 AGATTGACCA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:30866156 original size:27 final size:27
Alignment explanation
Indices: 30866126--30866182 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
30866116 CCAAATGCTA
*
30866126 AAGCACTCAAGAATGTTCCAAGCGGAG
1 AAGCACTCAAGAATGTTCCAAACGGAG
** *
30866153 AAGCACTCAAGGGTGTTCCAAACGTAG
1 AAGCACTCAAGAATGTTCCAAACGGAG
30866180 AAG
1 AAG
30866183 TGCCTAAGGT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.37, C:0.21, G:0.26, T:0.16
Consensus pattern (27 bp):
AAGCACTCAAGAATGTTCCAAACGGAG
Found at i:30866172 original size:54 final size:53
Alignment explanation
Indices: 30866056--30866174 Score: 123
Period size: 54 Copynumber: 2.2 Consensus size: 53
30866046 ATTACATTAG
* * * * *
30866056 GGGTGTTCGAAGTGCGAAAGTACTAAGAGTGTTCCAAGCGCAAAAGCGTCCAA
1 GGGTGTTCCAAATGCGAAAGCACTAAGAATGTTCCAAGCGCAAAAGCCTCCAA
* * * * *
30866109 AGGTATTCCAAATGCTAAAGCACTCAAGAATGTTCCAAGCGGAGAAGCACT-CAA
1 GGGTGTTCCAAATGCGAAAGCACT-AAGAATGTTCCAAGCGCAAAAGC-CTCCAA
30866163 GGGTGTTCCAAA
1 GGGTGTTCCAAA
30866175 CGTAGAAGTG
Statistics
Matches: 52, Mismatches: 12, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
53 18 0.35
54 33 0.63
55 1 0.02
ACGTcount: A:0.34, C:0.20, G:0.26, T:0.19
Consensus pattern (53 bp):
GGGTGTTCCAAATGCGAAAGCACTAAGAATGTTCCAAGCGCAAAAGCCTCCAA
Found at i:30866490 original size:20 final size:20
Alignment explanation
Indices: 30866465--30866504 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
30866455 TTCTTTCTTT
*
30866465 CTTAAGAATACACGTGACGC
1 CTTAAGAATACACATGACGC
30866485 CTTAAGAATACACATGACGC
1 CTTAAGAATACACATGACGC
30866505 ACTATCAAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.38, C:0.25, G:0.17, T:0.20
Consensus pattern (20 bp):
CTTAAGAATACACATGACGC
Found at i:30867726 original size:27 final size:26
Alignment explanation
Indices: 30867696--30867788 Score: 123
Period size: 27 Copynumber: 3.5 Consensus size: 26
30867686 AAACGCCCAA
*
30867696 GGGTGTTCCAAATGTGGAAGCACTCAT
1 GGGTGTTCCAAGTG-GGAAGCACTCAT
30867723 GGGTGTTCCAAGTGGAGAAGCACTCAT
1 GGGTGTTCCAAGTGG-GAAGCACTCAT
* * *
30867750 GGGTGTTCCAAGTGAAGAAGCACTAAG
1 GGGTGTTCCAAGTG-GGAAGCACTCAT
30867777 GGGTGTTCCAAG
1 GGGTGTTCCAAG
30867789 CAAGGAAGCG
Statistics
Matches: 60, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
26 1 0.02
27 59 0.98
ACGTcount: A:0.27, C:0.17, G:0.33, T:0.23
Consensus pattern (26 bp):
GGGTGTTCCAAGTGGGAAGCACTCAT
Found at i:30867796 original size:27 final size:27
Alignment explanation
Indices: 30867711--30867824 Score: 108
Period size: 27 Copynumber: 4.2 Consensus size: 27
30867701 TTCCAAATGT
**
30867711 GGAAGCACTCATGGGTGTTCCAAG-TG
1 GGAAGCACTCATGGGTGTTCCAAGCAA
*
30867737 GAGAAGCACTCATGGGTGTTCCAAGTGAA
1 G-GAAGCACTCATGGGTGTTCCAAG-CAA
* *
30867766 -GAAGCACTAAGGGGTGTTCCAAGCAA
1 GGAAGCACTCATGGGTGTTCCAAGCAA
* * *
30867792 GGAAGCGC-CCTAGGGTGTTCCAAGCAG
1 GGAAGCACTCAT-GGGTGTTCCAAGCAA
30867819 GGAAGC
1 GGAAGC
30867825 TAGCGTGGAA
Statistics
Matches: 73, Mismatches: 10, Indels: 9
0.79 0.11 0.10
Matches are distributed among these distances:
26 3 0.04
27 70 0.96
ACGTcount: A:0.28, C:0.20, G:0.34, T:0.18
Consensus pattern (27 bp):
GGAAGCACTCATGGGTGTTCCAAGCAA
Found at i:30867797 original size:54 final size:54
Alignment explanation
Indices: 30867695--30867815 Score: 129
Period size: 54 Copynumber: 2.2 Consensus size: 54
30867685 AAAACGCCCA
* ** * * **
30867695 AGGGTGTTCCAAATGTGGAAGCACTCATGGGTGTTCCAAGTGGAGAAGCACTCAT
1 AGGGTGTTCCAAGTGAAGAAGCACTAAGGGGTGTTCCAAGAAGAGAAGCAC-CAT
* *
30867750 -GGGTGTTCCAAGTGAAGAAGCACTAAGGGGTGTTCCAAGCAAG-GAAGCGCCCT
1 AGGGTGTTCCAAGTGAAGAAGCACTAAGGGGTGTTCCAAG-AAGAGAAGCACCAT
30867803 AGGGTGTTCCAAG
1 AGGGTGTTCCAAG
30867816 CAGGGAAGCT
Statistics
Matches: 55, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
53 2 0.04
54 52 0.95
55 1 0.02
ACGTcount: A:0.27, C:0.19, G:0.33, T:0.21
Consensus pattern (54 bp):
AGGGTGTTCCAAGTGAAGAAGCACTAAGGGGTGTTCCAAGAAGAGAAGCACCAT
Found at i:30869288 original size:31 final size:31
Alignment explanation
Indices: 30869250--30869314 Score: 121
Period size: 31 Copynumber: 2.1 Consensus size: 31
30869240 TTAGGTGGGT
*
30869250 TAATTTTCTGGAGTTATATAATAAATGTATA
1 TAATTTTCTAGAGTTATATAATAAATGTATA
30869281 TAATTTTCTAGAGTTATATAATAAATGTATA
1 TAATTTTCTAGAGTTATATAATAAATGTATA
30869312 TAA
1 TAA
30869315 ATATTTTTAT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.42, C:0.03, G:0.11, T:0.45
Consensus pattern (31 bp):
TAATTTTCTAGAGTTATATAATAAATGTATA
Found at i:30870041 original size:28 final size:26
Alignment explanation
Indices: 30869994--30870049 Score: 67
Period size: 28 Copynumber: 2.1 Consensus size: 26
30869984 AAATTATCAT
** *
30869994 ATAAAATTTTTTTATTATAAATATAA
1 ATAAAATTTTTCAATTATAAATAAAA
30870020 ATAAAATTTCTTCAATTCATAAATAAAA
1 ATAAAATTT-TTCAATT-ATAAATAAAA
30870048 AT
1 AT
30870050 TCTAATTCCA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 9 0.36
27 5 0.20
28 11 0.44
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (26 bp):
ATAAAATTTTTCAATTATAAATAAAA
Found at i:30870099 original size:83 final size:81
Alignment explanation
Indices: 30869985--30870136 Score: 216
Period size: 83 Copynumber: 1.9 Consensus size: 81
30869975 TGTATTTCTA
*
30869985 AATTATCATATAAAATTTTTTTATTATAAATATAAATAAAATTTCTTCAATTCATAAATAAAAAT
1 AATTATCATATAAAATTTTTTTATTATAAATATAAATAAAATTTATTCAATTCATAAATAAAAAT
30870050 TCTAATTCCATCCAAT
66 TCTAATTCCATCCAAT
* * ** *
30870066 AATTATCAT-TAAAATTATCTTTTCATTATAAATATTAATAAGATTTATTCAATTTGTAAATAAT
1 AATTATCATATAAAATT-T-TTTT-ATTATAAATATAAATAAAATTTATTCAATTCATAAATAAA
30870130 AATTCTA
63 AATTCTA
30870137 GTTGTATTAA
Statistics
Matches: 62, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
80 7 0.11
81 10 0.16
82 4 0.06
83 41 0.66
ACGTcount: A:0.45, C:0.09, G:0.01, T:0.44
Consensus pattern (81 bp):
AATTATCATATAAAATTTTTTTATTATAAATATAAATAAAATTTATTCAATTCATAAATAAAAAT
TCTAATTCCATCCAAT
Found at i:30870236 original size:42 final size:43
Alignment explanation
Indices: 30870190--30870272 Score: 98
Period size: 42 Copynumber: 2.0 Consensus size: 43
30870180 TAATAATTGA
* *
30870190 ATAATTTATAAATTA-ATTTTACAAA-ATTTTAATTATATATTT
1 ATAATTCA-AAATTACATTTTACAAATATTTAAATTATATATTT
* **
30870232 ATAATTCAAATTTACATTTTGGAAATATTTAAATTATATAT
1 ATAATTCAAAATTACATTTTACAAATATTTAAATTATATAT
30870273 ATAATTATTA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
41 5 0.15
42 15 0.44
43 14 0.41
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.49
Consensus pattern (43 bp):
ATAATTCAAAATTACATTTTACAAATATTTAAATTATATATTT
Found at i:30877245 original size:24 final size:23
Alignment explanation
Indices: 30877218--30877268 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
30877208 TTTATGTTAG
30877218 CTTCTCGCA-TTACCTTTTTCTTTT
1 CTTCTC-CATTTACC-TTTTCTTTT
*
30877242 CTTCTCNATTTACCTTTTCTTTT
1 CTTCTCCATTTACCTTTTCTTTT
30877265 CTTC
1 CTTC
30877269 CTCCCCCACC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
23 14 0.56
24 11 0.44
ACGTcount: A:0.08, C:0.29, G:0.02, T:0.59
Consensus pattern (23 bp):
CTTCTCCATTTACCTTTTCTTTT
Found at i:30887698 original size:166 final size:168
Alignment explanation
Indices: 30887420--30887805 Score: 578
Period size: 166 Copynumber: 2.3 Consensus size: 168
30887410 GTTTCTGTCT
* *
30887420 GGTTAAGATAGAGTAGCAGTGTCCTACAATGTAATTTCATTTTGCAAAATCAAAATTAGTGACAT
1 GGTTAAGATAGAGTAGCAGTGTCCTACAATATAATTTCTTTTTGCAAAATCAAAATTAGTGACAT
*
30887485 TTCCAGTAAAATTTATGTACATGCTACAGGCATATTAATCAAAGGACAAAACTGAGATAAATTTA
66 TTCCAGTAAAATTTATGTACATGCTACAGGCATATTAATCAAAGGACAAAACTGAAATAAATTTA
*
30887550 TGTATTGTCCAGGAAATAC-A-AATTAAGCTTATGTAA
131 TGGATTGTCCAGGAAATACAATAATTAAGCTTATGTAA
* * * * * *
30887586 GGTTAAGATAGAGTAGCAGAGTCGTACGATATAACTTCTTTTTGCAAAATCAAAGTTAGTGGCAT
1 GGTTAAGATAGAGTAGCAGTGTCCTACAATATAATTTCTTTTTGCAAAATCAAAATTAGTGACAT
* * * * *
30887651 TTCTAGTAAAATTTATGTACATGCTACATGCATATTAATCTAAGGACAAACCTTAAATAAATTTA
66 TTCCAGTAAAATTTATGTACATGCTACAGGCATATTAATCAAAGGACAAAACTGAAATAAATTTA
30887716 TGGATTGTCCAGGAAATACAAATTAATTAAGCTTATGTAA
131 TGGATTGTCCAGGAAATAC-AA-TAATTAAGCTTATGTAA
* * *
30887756 GGTTAAGATAGAGTACCAGTGTCCTACAATATAATTTGTTTTTGTAAAAT
1 GGTTAAGATAGAGTAGCAGTGTCCTACAATATAATTTCTTTTTGCAAAAT
30887806 GGAAATTAAT
Statistics
Matches: 194, Mismatches: 22, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
166 134 0.69
168 1 0.01
170 59 0.30
ACGTcount: A:0.38, C:0.12, G:0.17, T:0.33
Consensus pattern (168 bp):
GGTTAAGATAGAGTAGCAGTGTCCTACAATATAATTTCTTTTTGCAAAATCAAAATTAGTGACAT
TTCCAGTAAAATTTATGTACATGCTACAGGCATATTAATCAAAGGACAAAACTGAAATAAATTTA
TGGATTGTCCAGGAAATACAATAATTAAGCTTATGTAA
Found at i:30893095 original size:10 final size:10
Alignment explanation
Indices: 30893082--30893106 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
30893072 AATTTTATAA
30893082 TTATTTAAAT
1 TTATTTAAAT
30893092 TTATTTAAAT
1 TTATTTAAAT
30893102 TTATT
1 TTATT
30893107 ATTTGAACTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (10 bp):
TTATTTAAAT
Found at i:30893524 original size:15 final size:15
Alignment explanation
Indices: 30893500--30893575 Score: 57
Period size: 15 Copynumber: 5.1 Consensus size: 15
30893490 AACTTCTCTT
*
30893500 TAAGTATATATTTTA
1 TAAGTTTATATTTTA
**
30893515 TAAGTTTATATAATA
1 TAAGTTTATATTTTA
* * *
30893530 AAAGTATATATATTA
1 TAAGTTTATATTTTA
*
30893545 TAA-TTAATAATTTTA
1 TAAGTTTAT-ATTTTA
*
30893560 TAAG-TTATAATTTA
1 TAAGTTTATATTTTA
30893574 TA
1 TA
30893576 TAACGTTAAT
Statistics
Matches: 47, Mismatches: 12, Indels: 5
0.73 0.19 0.08
Matches are distributed among these distances:
14 10 0.21
15 37 0.79
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (15 bp):
TAAGTTTATATTTTA
Found at i:30893942 original size:53 final size:53
Alignment explanation
Indices: 30893861--30893978 Score: 159
Period size: 53 Copynumber: 2.2 Consensus size: 53
30893851 ACTCAATTAT
* * * *
30893861 AAGATACATTAATATTATATAATCGGATTGTATACTCGCGAGTATCC-TGTAAC
1 AAGATATATTAATATTATATAATCGGATTGAATACTCGCGAATA-CCTTATAAC
30893914 AAGATATATTAATATTATATAA-CTGGATTGAATACTCGCGAATACCTTATAAC
1 AAGATATATTAATATTATATAATC-GGATTGAATACTCGCGAATACCTTATAAC
30893967 AAGATACTATTA
1 AAGATA-TATTA
30893979 CCATCTTTAT
Statistics
Matches: 58, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
52 3 0.05
53 50 0.86
54 5 0.09
ACGTcount: A:0.40, C:0.14, G:0.13, T:0.34
Consensus pattern (53 bp):
AAGATATATTAATATTATATAATCGGATTGAATACTCGCGAATACCTTATAAC
Found at i:30905053 original size:18 final size:19
Alignment explanation
Indices: 30905022--30905060 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
30905012 CACACCTCCA
*
30905022 TTTAATTATACTTCCCAAT
1 TTTAATTATACTTCACAAT
*
30905041 TTTAA-TATGCTTCACAAT
1 TTTAATTATACTTCACAAT
30905059 TT
1 TT
30905061 ACTACCTTGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.31, C:0.18, G:0.03, T:0.49
Consensus pattern (19 bp):
TTTAATTATACTTCACAAT
Found at i:30912078 original size:41 final size:42
Alignment explanation
Indices: 30912014--30912094 Score: 119
Period size: 42 Copynumber: 2.0 Consensus size: 42
30912004 TTCATTTAGC
* *
30912014 CAGCCTTTCTTTGTTTTA-TTTAAACGGTGCGCTTTGCTCCT
1 CAGCCTTTCTTTGTTTTACTTAAAACAGTGCGCTTTGCTCCT
* *
30912055 CAGCCTTTCTTTTTTTTGCTTAAAACAGTGCGCTTTGCTC
1 CAGCCTTTCTTTGTTTTACTTAAAACAGTGCGCTTTGCTC
30912095 ATTCTTTATT
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
41 16 0.46
42 19 0.54
ACGTcount: A:0.14, C:0.25, G:0.16, T:0.46
Consensus pattern (42 bp):
CAGCCTTTCTTTGTTTTACTTAAAACAGTGCGCTTTGCTCCT
Found at i:30921146 original size:22 final size:23
Alignment explanation
Indices: 30921111--30921157 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
30921101 ATTTCTATAC
*
30921111 ATTATTACAAAAATTTAGC-CAA
1 ATTATTACAAAAATTAAGCTCAA
30921133 ATTATTATC-AAAATTAAGCTCAA
1 ATTATTA-CAAAAATTAAGCTCAA
30921156 AT
1 AT
30921158 AACTCTATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 16 0.73
23 6 0.27
ACGTcount: A:0.49, C:0.13, G:0.04, T:0.34
Consensus pattern (23 bp):
ATTATTACAAAAATTAAGCTCAA
Found at i:30928584 original size:28 final size:28
Alignment explanation
Indices: 30928553--30928607 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
30928543 TAACTGTACA
* *
30928553 TGAATAGGTACAAGAGAAGAAGCTGTAT
1 TGAATAGATACAAGAAAAGAAGCTGTAT
*
30928581 TGAATAGATACAAGAAAAGAAGTTGTA
1 TGAATAGATACAAGAAAAGAAGCTGTA
30928608 CGTGTGAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.47, C:0.05, G:0.25, T:0.22
Consensus pattern (28 bp):
TGAATAGATACAAGAAAAGAAGCTGTAT
Found at i:30929467 original size:2 final size:2
Alignment explanation
Indices: 30929462--30929492 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
30929452 TTTCTATACT
30929462 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
30929493 GAATAAATGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:30930051 original size:26 final size:26
Alignment explanation
Indices: 30930011--30930084 Score: 107
Period size: 26 Copynumber: 2.9 Consensus size: 26
30930001 TTAACAATCT
30930011 ATAGTA-ATATATTAATACACTATAC
1 ATAGTATATATATTAATACACTATAC
* *
30930036 ATAGTATATATCTTAATACACTATAT
1 ATAGTATATATATTAATACACTATAC
30930062 ATAGTATACT-TATTAATACACTA
1 ATAGTATA-TATATTAATACACTA
30930085 ATTAATAAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
25 6 0.14
26 37 0.84
27 1 0.02
ACGTcount: A:0.45, C:0.12, G:0.04, T:0.39
Consensus pattern (26 bp):
ATAGTATATATATTAATACACTATAC
Found at i:30931604 original size:23 final size:23
Alignment explanation
Indices: 30931560--30931604 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
30931550 TGGTTAATAA
* *
30931560 GTGAAATTGTGGTTGTTGTTTGT
1 GTGAAATTGTGGTTATTATTTGT
*
30931583 GTGAAATTGTTGTTATTATTTG
1 GTGAAATTGTGGTTATTATTTG
30931605 AATTTTTTTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.18, C:0.00, G:0.29, T:0.53
Consensus pattern (23 bp):
GTGAAATTGTGGTTATTATTTGT
Found at i:30932014 original size:48 final size:45
Alignment explanation
Indices: 30931960--30932051 Score: 123
Period size: 48 Copynumber: 2.0 Consensus size: 45
30931950 ATTTAAATAT
*
30931960 AAGTTTTAAA-CCCTAAGAAAATAAAATAAGAAAAAAGAAAAGGAAAAC
1 AAGTTTTAAATCCC-AAGAAAA-AAAAGAA-AAAAAA-AAAAGGAAAAC
*
30932008 AAGTTTTAAATCCCAAGAAAAAAAAGAAAAAGAAAAAAGGAAAA
1 AAGTTTTAAATCCCAAGAAAAAAAAGAAAAAAAAAAAAGGAAAA
30932052 AAATAATTGT
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
45 10 0.24
46 5 0.12
47 6 0.15
48 17 0.41
49 3 0.07
ACGTcount: A:0.66, C:0.08, G:0.13, T:0.13
Consensus pattern (45 bp):
AAGTTTTAAATCCCAAGAAAAAAAAGAAAAAAAAAAAAGGAAAAC
Found at i:30932052 original size:22 final size:22
Alignment explanation
Indices: 30932026--30932077 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
30932016 AATCCCAAGA
30932026 AAAAAAAGAAAAAG-AAAAAAGG
1 AAAAAAA-AAAAAGTAAAAAAGG
* **
30932048 AAAAAAATAATTGTAAAAAAGG
1 AAAAAAAAAAAAGTAAAAAAGG
30932070 AAAAAAAA
1 AAAAAAAA
30932078 TAATTCTAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
21 3 0.12
22 22 0.88
ACGTcount: A:0.79, C:0.00, G:0.13, T:0.08
Consensus pattern (22 bp):
AAAAAAAAAAAAGTAAAAAAGG
Found at i:30932066 original size:23 final size:23
Alignment explanation
Indices: 30932040--30932088 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
30932030 AAAGAAAAAG
*
30932040 AAAAAAGG-AAAAAAATAATTGT
1 AAAAAAGGAAAAAAAATAATTCT
30932062 AAAAAAGGAAAAAAAATAATTCT
1 AAAAAAGGAAAAAAAATAATTCT
30932085 AAAA
1 AAAA
30932089 TTTGAGCTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
22 8 0.32
23 17 0.68
ACGTcount: A:0.71, C:0.02, G:0.10, T:0.16
Consensus pattern (23 bp):
AAAAAAGGAAAAAAAATAATTCT
Found at i:30943509 original size:3 final size:3
Alignment explanation
Indices: 30943491--30943550 Score: 57
Period size: 3 Copynumber: 18.0 Consensus size: 3
30943481 TTCCAATTAC
*
30943491 ATT ATTT ATT ATTT ATT ATT ATTT ATGT ATT TTT CACTT ATT ATT ATT
1 ATT A-TT ATT A-TT ATT ATT A-TT AT-T ATT ATT -A-TT ATT ATT ATT
30943539 ATT ATT ATT ATT
1 ATT ATT ATT ATT
30943551 TTTTTATTTA
Statistics
Matches: 49, Mismatches: 2, Indels: 12
0.78 0.03 0.19
Matches are distributed among these distances:
3 34 0.69
4 13 0.27
5 2 0.04
ACGTcount: A:0.28, C:0.03, G:0.02, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:30948339 original size:18 final size:18
Alignment explanation
Indices: 30948296--30948341 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 18
30948286 TTTTAAAATT
30948296 ATAATA-AAACAAACTAAA
1 ATAATATAAA-AAACTAAA
30948314 AT-ATATAAAAAA-TAATA
1 ATAATATAAAAAACTAA-A
30948331 ATAATATAAAA
1 ATAATATAAAA
30948342 TTAAAAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
16 3 0.12
17 9 0.36
18 13 0.52
ACGTcount: A:0.72, C:0.04, G:0.00, T:0.24
Consensus pattern (18 bp):
ATAATATAAAAAACTAAA
Found at i:30948601 original size:20 final size:20
Alignment explanation
Indices: 30948578--30948618 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
30948568 GAGCCTAGCC
30948578 ACAAAAAAAAAAAAAACAAA
1 ACAAAAAAAAAAAAAACAAA
** *
30948598 ACAAAAAGCAAAAAAAGAAA
1 ACAAAAAAAAAAAAAACAAA
30948618 A
1 A
30948619 TGGGGTTAGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.85, C:0.10, G:0.05, T:0.00
Consensus pattern (20 bp):
ACAAAAAAAAAAAAAACAAA
Found at i:30948868 original size:29 final size:29
Alignment explanation
Indices: 30948831--30948895 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 29
30948821 AGAGGGAAAG
*
30948831 AGAGGGATCAACCGGCGAGTAGAGAGAAC
1 AGAGAGATCAACCGGCGAGTAGAGAGAAC
*** *
30948860 AGAGAGATCTGTCGGCGAGTAGAGAGAAG
1 AGAGAGATCAACCGGCGAGTAGAGAGAAC
30948889 AGAGAGA
1 AGAGAGA
30948896 GAGGCCGACG
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.38, C:0.12, G:0.40, T:0.09
Consensus pattern (29 bp):
AGAGAGATCAACCGGCGAGTAGAGAGAAC
Found at i:30948907 original size:29 final size:29
Alignment explanation
Indices: 30948846--30948914 Score: 75
Period size: 29 Copynumber: 2.4 Consensus size: 29
30948836 GATCAACCGG
*** * *
30948846 CGAGTAGAGAGAACAGAGAGATCTGTCGG
1 CGAGTAGAGAGAACAGAGAGAGAGGCCGA
*
30948875 CGAGTAGAGAGAAGAGAGAGAGAGGCCGA
1 CGAGTAGAGAGAACAGAGAGAGAGGCCGA
*
30948904 CGAGAAGAGAG
1 CGAGTAGAGAG
30948915 GGGAGGACGC
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.39, C:0.12, G:0.42, T:0.07
Consensus pattern (29 bp):
CGAGTAGAGAGAACAGAGAGAGAGGCCGA
Found at i:30949473 original size:13 final size:14
Alignment explanation
Indices: 30949455--30949484 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
30949445 ATATTTTTTT
30949455 TAAAAAAAATA-AA
1 TAAAAAAAATATAA
30949468 TAAAAAAAATATAA
1 TAAAAAAAATATAA
30949482 TAA
1 TAA
30949485 TAATTAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.69
14 5 0.31
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (14 bp):
TAAAAAAAATATAA
Found at i:30965977 original size:23 final size:25
Alignment explanation
Indices: 30965908--30965979 Score: 78
Period size: 26 Copynumber: 2.9 Consensus size: 25
30965898 AACAATATAT
*
30965908 TTTTTTCAA-CATAGCGTGTAACAATA
1 TTTTTT-AATCATGGCGTGTAAC-ATA
*
30965934 TTTTTTAATCATGGCGGGTAACATA
1 TTTTTTAATCATGGCGTGTAACATA
*
30965959 TTTTTT-A-GATGGCGTGTAACA
1 TTTTTTAATCATGGCGTGTAACA
30965980 ACAGTATTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
23 12 0.29
24 1 0.02
25 11 0.27
26 17 0.41
ACGTcount: A:0.29, C:0.12, G:0.18, T:0.40
Consensus pattern (25 bp):
TTTTTTAATCATGGCGTGTAACATA
Found at i:30966053 original size:45 final size:45
Alignment explanation
Indices: 30965998--30966086 Score: 126
Period size: 45 Copynumber: 2.0 Consensus size: 45
30965988 TTTTTTTAAC
* * * *
30965998 ATGGCGTGTAACAA-CTTAATCATAGCTTGTCACAGGTTTTTGTAT
1 ATGGCGTGTAACAAGC-TAACCATAACTTCTCACAAGTTTTTGTAT
30966043 ATGGCGTGTAACAAGCTAACCATAACTTCTCACAAGTTTTTGTA
1 ATGGCGTGTAACAAGCTAACCATAACTTCTCACAAGTTTTTGTA
30966087 CTTGGCTTGT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
45 38 0.97
46 1 0.03
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (45 bp):
ATGGCGTGTAACAAGCTAACCATAACTTCTCACAAGTTTTTGTAT
Found at i:30966107 original size:69 final size:69
Alignment explanation
Indices: 30966022--30966228 Score: 218
Period size: 69 Copynumber: 3.0 Consensus size: 69
30966012 CTTAATCATA
** * * * *
30966022 GCTTGTCACAGGTTTTTGTATATGGCGTGTAACA-AGCTAACCATAACTTCTCACAAGTTTTTGT
1 GCTTGTCACATATTTTTGTACATAGCGTGTAACACA-CTAACCATAACTTATCACAAGTTTTTAT
*
30966086 ACTTG
65 ACATG
* *
30966091 GCTTGTCACATATTTTTGTACATAGCGTGTAACACACTAACCATAGCTTATCACAGGTTTTTATA
1 GCTTGTCACATATTTTTGTACATAGCGTGTAACACACTAACCATAACTTATCACAAGTTTTTATA
30966156 CATG
66 CATG
* * * * * * * * * * *
30966160 ACGTGTCACATATTTTTATACATAACGTATAATACGCTAACAATGATTTATCACAAGTTTTTGTA
1 GCTTGTCACATATTTTTGTACATAGCGTGTAACACACTAACCATAACTTATCACAAGTTTTTATA
30966225 CATG
66 CATG
30966229 ACGTGTAACA
Statistics
Matches: 115, Mismatches: 22, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
69 114 0.99
70 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.15, T:0.37
Consensus pattern (69 bp):
GCTTGTCACATATTTTTGTACATAGCGTGTAACACACTAACCATAACTTATCACAAGTTTTTATA
CATG
Found at i:30966288 original size:23 final size:24
Alignment explanation
Indices: 30966250--30966298 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
30966240 GCTAACCATA
*
30966250 GCTTGTCACAG-GTTTTGTACATG
1 GCTTGTCACAGATTTTTGTACATG
* *
30966273 GCTTGTCACATATTTTTGTATATG
1 GCTTGTCACAGATTTTTGTACATG
30966297 GC
1 GC
30966299 ATGTAACAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 10 0.45
24 12 0.55
ACGTcount: A:0.18, C:0.16, G:0.22, T:0.43
Consensus pattern (24 bp):
GCTTGTCACAGATTTTTGTACATG
Found at i:30966337 original size:45 final size:45
Alignment explanation
Indices: 30966273--30966388 Score: 151
Period size: 45 Copynumber: 2.6 Consensus size: 45
30966263 TTTGTACATG
*
30966273 GCTTGTCACATATTTTTGTATATGGCATGTAACAAGCTAACCATT
1 GCTTGTCACATATTTTTGTATATAGCATGTAACAAGCTAACCATT
* * * *
30966318 GCTTGTTACATATTTTTGTATATAGCATGTAACACGTTAACCATG
1 GCTTGTCACATATTTTTGTATATAGCATGTAACAAGCTAACCATT
* ** *
30966363 GTTTGTCACAGGTTTTTGTAAATAGC
1 GCTTGTCACATATTTTTGTATATAGC
30966389 GTGTCACATA
Statistics
Matches: 61, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 61 1.00
ACGTcount: A:0.28, C:0.16, G:0.17, T:0.40
Consensus pattern (45 bp):
GCTTGTCACATATTTTTGTATATAGCATGTAACAAGCTAACCATT
Found at i:30966402 original size:24 final size:24
Alignment explanation
Indices: 30966366--30966416 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
30966356 AACCATGGTT
*
30966366 TGTCACAGGTTTTTGTAAATAGCG
1 TGTCACAGATTTTTGTAAATAGCG
* *
30966390 TGTCACATATTTTTGTACATAGCG
1 TGTCACAGATTTTTGTAAATAGCG
30966414 TGT
1 TGT
30966417 AACACGCTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.24, C:0.14, G:0.22, T:0.41
Consensus pattern (24 bp):
TGTCACAGATTTTTGTAAATAGCG
Found at i:30966465 original size:114 final size:113
Alignment explanation
Indices: 30966103--30966454 Score: 406
Period size: 114 Copynumber: 3.1 Consensus size: 113
30966093 TTGTCACATA
* * *
30966103 TTTTTGTACATAGCGTGTAACACACTAACCATAGCTTATCACAGGTTTTTATACATGACGTGTCA
1 TTTTTGTACATAGCGTGTAACACGCTAACCATAGCTTGTCACAGGTTTTTGTACATG-CGTGTCA
* * * * * * * *
30966168 CATATTTTTATACATAACGTATAATACGCTAACAATGATTTATCACAAG
65 CATATTTTTGTACATAGCGTGTAACACGCTAACCATGACTTGTTACAAG
* *
30966217 TTTTTGTACAT-GACGTGTAACAAGCTAACCATAGCTTGTCACAGG-TTTTGTACATGGCTTGTC
1 TTTTTGTACATAG-CGTGTAACACGCTAACCATAGCTTGTCACAGGTTTTTGTACAT-GCGTGTC
* * * *
30966280 ACATATTTTTGTATATGGCATGTAACAAGCTAACCATTG-CTTGTTACATA-
64 ACATATTTTTGTACATAGCGTGTAACACGCTAACCA-TGACTTGTTACA-AG
* * * * * *
30966330 TTTTTGTATATAGCATGTAACACGTTAACCATGGTTTGTCACAGGTTTTTGTAAATAGCGTGTCA
1 TTTTTGTACATAGCGTGTAACACGCTAACCATAGCTTGTCACAGGTTTTTGTACAT-GCGTGTCA
*
30966395 CATATTTTTGTACATAGCGTGTAACACGCTAACCATGACTTGTTACAGG
65 CATATTTTTGTACATAGCGTGTAACACGCTAACCATGACTTGTTACAAG
30966444 TTTTTGTACAT
1 TTTTTGTACAT
30966455 GGTGTATAAC
Statistics
Matches: 198, Mismatches: 32, Indels: 16
0.80 0.13 0.07
Matches are distributed among these distances:
113 87 0.44
114 111 0.56
ACGTcount: A:0.29, C:0.17, G:0.16, T:0.37
Consensus pattern (113 bp):
TTTTTGTACATAGCGTGTAACACGCTAACCATAGCTTGTCACAGGTTTTTGTACATGCGTGTCAC
ATATTTTTGTACATAGCGTGTAACACGCTAACCATGACTTGTTACAAG
Found at i:30967090 original size:14 final size:15
Alignment explanation
Indices: 30967071--30967103 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
30967061 TTACTTAAAG
30967071 TTTAAATTAAC-GAC
1 TTTAAATTAACTGAC
30967085 TTTAAATTAACTGAC
1 TTTAAATTAACTGAC
30967100 TTTA
1 TTTA
30967104 GTCGGTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 11 0.61
15 7 0.39
ACGTcount: A:0.39, C:0.12, G:0.06, T:0.42
Consensus pattern (15 bp):
TTTAAATTAACTGAC
Found at i:30967285 original size:15 final size:15
Alignment explanation
Indices: 30967265--30967303 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
30967255 CTAATTAATA
* *
30967265 TATTAATAAGTATCC
1 TATTAATAACTATAC
30967280 TATTAATAACTATAC
1 TATTAATAACTATAC
30967295 TATATAATA
1 TAT-TAATA
30967304 TTTATAATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 16 0.76
16 5 0.24
ACGTcount: A:0.46, C:0.10, G:0.03, T:0.41
Consensus pattern (15 bp):
TATTAATAACTATAC
Found at i:30967454 original size:73 final size:74
Alignment explanation
Indices: 30967358--30967515 Score: 194
Period size: 73 Copynumber: 2.1 Consensus size: 74
30967348 ATTAAGTCAT
* * * * * * *
30967358 TAATATTAATATGTAACTCATATTAATAAGTTATTATATTTAGTTGCTAATATAAGTTATATTGC
1 TAATATTAATATATAACTCATATTAATAAGTTACTATATTAAATTACTAATATAAGTCA-ATTAC
*
30967423 TGTAGTATAC
65 TATAGTATAC
* *
30967433 TAATATTAATATAT-AGT-ATATTAATAAGTTACTATATTAAATTATTAATATAAGTCAATTACT
1 TAATATTAATATATAACTCATATTAATAAGTTACTATATTAAATTACTAATATAAGTCAATTACT
*
30967496 ATGGTATAC
66 ATAGTATAC
30967505 TAATATTAATA
1 TAATATTAATA
30967516 ATTTAATATA
Statistics
Matches: 72, Mismatches: 11, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
72 23 0.32
73 34 0.47
74 2 0.03
75 13 0.18
ACGTcount: A:0.42, C:0.06, G:0.08, T:0.44
Consensus pattern (74 bp):
TAATATTAATATATAACTCATATTAATAAGTTACTATATTAAATTACTAATATAAGTCAATTACT
ATAGTATAC
Found at i:30967690 original size:16 final size:15
Alignment explanation
Indices: 30967645--30967702 Score: 53
Period size: 16 Copynumber: 3.6 Consensus size: 15
30967635 TAGATCAATA
*
30967645 AATATACTATATAGTAT
1 AATATAATATA-AGT-T
* *
30967662 AATATATTAATAATTT
1 AATATAAT-ATAAGTT
30967678 AATAGTAATATAAGTT
1 AATA-TAATATAAGTT
30967694 AATATAATA
1 AATATAATA
30967703 AGTTAGATTA
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
15 5 0.14
16 15 0.43
17 12 0.34
18 3 0.09
ACGTcount: A:0.52, C:0.02, G:0.05, T:0.41
Consensus pattern (15 bp):
AATATAATATAAGTT
Found at i:30967730 original size:26 final size:23
Alignment explanation
Indices: 30967661--30967732 Score: 58
Period size: 26 Copynumber: 2.9 Consensus size: 23
30967651 CTATATAGTA
30967661 TAATATATTAATAATTTAA--TAG
1 TAATATATTAATAA-TTAAGTTAG
*
30967683 TAATATAAGTTAATATAATAAGTTAG
1 TAATAT-A-TTAATA-ATTAAGTTAG
30967709 ATTAATATATTAATAACTTAAGTT
1 --TAATATATTAATAA-TTAAGTT
30967733 TAAGGTATAA
Statistics
Matches: 40, Mismatches: 2, Indels: 12
0.74 0.04 0.22
Matches are distributed among these distances:
22 6 0.15
23 1 0.03
24 9 0.22
25 2 0.05
26 15 0.38
27 1 0.03
28 6 0.15
ACGTcount: A:0.49, C:0.01, G:0.07, T:0.43
Consensus pattern (23 bp):
TAATATATTAATAATTAAGTTAG
Found at i:30973981 original size:17 final size:16
Alignment explanation
Indices: 30973954--30973992 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
30973944 TAACATGTTG
30973954 ATAATAAATATAAATT
1 ATAATAAATATAAATT
*
30973970 ATAATCAAATATTAATT
1 ATAAT-AAATATAAATT
30973987 -TAATAA
1 ATAATAA
30973993 TTGATTTATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 2 0.10
16 9 0.43
17 10 0.48
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (16 bp):
ATAATAAATATAAATT
Found at i:30975077 original size:3 final size:3
Alignment explanation
Indices: 30975069--30975117 Score: 70
Period size: 3 Copynumber: 17.7 Consensus size: 3
30975059 GTTTATATAT
30975069 TTA TTA TTA TTA TT- TTA TT- TT- TTA -TA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
30975113 TTA TT
1 TTA TT
30975118 TACTANGCTA
Statistics
Matches: 43, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
2 8 0.19
3 35 0.81
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (3 bp):
TTA
Found at i:30975080 original size:26 final size:26
Alignment explanation
Indices: 30975050--30975106 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 26
30975040 TAGGGTGATC
*
30975050 TATTACCTT-GTTTATATATTTATTAT
1 TATTACCTTATTTTATATA-TTATTAT
** *
30975076 TATTATTTTATTTTTTATATTATTAT
1 TATTACCTTATTTTATATATTATTAT
30975102 TATTA
1 TATTA
30975107 TTATTATTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
26 19 0.73
27 7 0.27
ACGTcount: A:0.28, C:0.04, G:0.02, T:0.67
Consensus pattern (26 bp):
TATTACCTTATTTTATATATTATTAT
Found at i:30975082 original size:29 final size:29
Alignment explanation
Indices: 30975050--30975112 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 29
30975040 TAGGGTGATC
*
30975050 TATTACCTTGTTTATA-TATTTATTATTAT
1 TATTACATTGTTTATATTA-TTATTATTAT
** *
30975079 TATTTTATTTTTTATATTATTATTATTAT
1 TATTACATTGTTTATATTATTATTATTAT
30975108 TATTA
1 TATTA
30975113 TTATTTACTA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
29 26 0.93
30 2 0.07
ACGTcount: A:0.29, C:0.03, G:0.02, T:0.67
Consensus pattern (29 bp):
TATTACATTGTTTATATTATTATTATTAT
Found at i:30975227 original size:16 final size:16
Alignment explanation
Indices: 30975196--30975238 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 16
30975186 AATATATATT
*
30975196 ATTATTTTAG-TAATG
1 ATTATTTGAGTTAATG
30975211 ATTATTTGAGTTAATG
1 ATTATTTGAGTTAATG
* *
30975227 AGTATTGGAGTT
1 ATTATTTGAGTT
30975239 TAGAGTTCGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
15 9 0.38
16 15 0.62
ACGTcount: A:0.30, C:0.00, G:0.21, T:0.49
Consensus pattern (16 bp):
ATTATTTGAGTTAATG
Found at i:30975410 original size:1 final size:1
Alignment explanation
Indices: 30975404--30975476 Score: 146
Period size: 1 Copynumber: 73.0 Consensus size: 1
30975394 TTTGTATAAT
30975404 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
30975469 AAAAAAAA
1 AAAAAAAA
30975477 TTTTATATAT
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 72 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:30976139 original size:2 final size:2
Alignment explanation
Indices: 30976134--30976177 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
30976124 CCCTCACCAA
30976134 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
30976176 CT
1 CT
30976178 ATGGCCTCAG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:30978922 original size:34 final size:34
Alignment explanation
Indices: 30978879--30978944 Score: 96
Period size: 34 Copynumber: 1.9 Consensus size: 34
30978869 ACCAAAAAAA
* *
30978879 AGGGAGCTTGCTATCGGTTTTTGAGAGAGAAATG
1 AGGGAGCTTGCTACCGGTTTGTGAGAGAGAAATG
* *
30978913 AGGGAGCTTGCTGCCTGTTTGTGAGAGAGAAA
1 AGGGAGCTTGCTACCGGTTTGTGAGAGAGAAA
30978945 GGAAAAAGTC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.26, C:0.11, G:0.36, T:0.27
Consensus pattern (34 bp):
AGGGAGCTTGCTACCGGTTTGTGAGAGAGAAATG
Found at i:30979070 original size:38 final size:37
Alignment explanation
Indices: 30979011--30979112 Score: 159
Period size: 38 Copynumber: 2.7 Consensus size: 37
30979001 AAAGTTGGCC
*
30979011 TTTGTGGTGACCGGTAGAAAAGAGAGAAAGAGTTGGGT
1 TTTGTGGTGACCGGCA-AAAAGAGAGAAAGAGTTGGGT
*
30979049 TTTGTGGTGATCGGCGAAAAAGAGAGAAAGAGTTGGGT
1 TTTGTGGTGACCGGC-AAAAAGAGAGAAAGAGTTGGGT
*
30979087 ATTGTGGTGACCGGCAAAAAGAGAGA
1 TTTGTGGTGACCGGCAAAAAGAGAGA
30979113 TCTAGTCGGT
Statistics
Matches: 59, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
37 11 0.19
38 47 0.80
39 1 0.02
ACGTcount: A:0.33, C:0.07, G:0.38, T:0.22
Consensus pattern (37 bp):
TTTGTGGTGACCGGCAAAAAGAGAGAAAGAGTTGGGT
Found at i:30979726 original size:2 final size:2
Alignment explanation
Indices: 30979719--30979760 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
30979709 TGTGTTTTGA
*
30979719 AT AT AT AT AT A- AT AT AT AT AT AT AA 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
30979760 A
1 A
30979761 AATTATACGT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:30994604 original size:30 final size:31
Alignment explanation
Indices: 30994568--30994633 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 31
30994558 GTTATCTCCA
* *
30994568 ATTTTGTT-GTTTCTTCA-AATGAAAATCTTG
1 ATTTTGTTGGTCT-TTCACAATCAAAATCTTG
*
30994598 ATTTTGTTGGTCTTTCACAATCAAAATTTTG
1 ATTTTGTTGGTCTTTCACAATCAAAATCTTG
30994629 ATTTT
1 ATTTT
30994634 AACTTTACTG
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
30 12 0.39
31 19 0.61
ACGTcount: A:0.26, C:0.11, G:0.12, T:0.52
Consensus pattern (31 bp):
ATTTTGTTGGTCTTTCACAATCAAAATCTTG
Found at i:30995244 original size:51 final size:50
Alignment explanation
Indices: 30995105--30995237 Score: 133
Period size: 51 Copynumber: 2.6 Consensus size: 50
30995095 GAGATCCATG
*
30995105 TTTATTTTTTTTTCTTTTTTTCCTTAGCTCAAATTTTGAAATTATTTTTCT
1 TTTA-TTTTTTTTCTTTTTTTCCTTAGCTCAAATTTTGGAATTATTTTTCT
* * * * * * * *
30995156 TTTCTTTCTATT-TTTATCTCATCTTGGCCCAAGTTTTGGAATTATTTTTCT
1 TTTATTTTTTTTCTTTTTTTC--CTTAGCTCAAATTTTGGAATTATTTTTCT
*
30995207 TTTATTTTTTTCTCTTTTTTTCCTTAACTCA
1 TTTATTTTTTT-TCTTTTTTTCCTTAGCTCA
30995238 TCTTTTGAAT
Statistics
Matches: 61, Mismatches: 17, Indels: 8
0.71 0.20 0.09
Matches are distributed among these distances:
49 6 0.10
50 6 0.10
51 42 0.69
52 1 0.02
53 6 0.10
ACGTcount: A:0.16, C:0.16, G:0.05, T:0.63
Consensus pattern (50 bp):
TTTATTTTTTTTCTTTTTTTCCTTAGCTCAAATTTTGGAATTATTTTTCT
Found at i:30995340 original size:201 final size:208
Alignment explanation
Indices: 30995016--30995513 Score: 644
Period size: 213 Copynumber: 2.4 Consensus size: 208
30995006 TTTATTTTAT
* * *
30995016 TTTTTTTCCTTAACTCAT-TTTTTAATCCTAAAGATGGATGTAATTATTCAAGATTGATGACATT
1 TTTTTTTCCTTAACTCATCTTTTGAAT-CTAAAGATGGATTTAATTATTCATGATTGATGACATT
* *
30995080 G-ACTTTATATTATGCGAGATCCATGTTTATTTTTTTTTCTTTTTTTCCTTAGCTCAAATTTTGA
65 GAACTTGATATTATGCGAGATCCATG--T-TTTTTTTTTCTTTTTTTCCTAAGCTCAAATTTTGA
* * * *
30995144 AATTATTTTTCTTTTCTTTCTA-TTTTTAT-C-TCA-TC-TT-GGCCCAAGTTTTGGAATTATTT
127 AATTATTTTTCTTTTCTTCCTATTTTTTATCCTTAACTCATTAAGCCCAAATTTTGGAATTATTT
*
30995203 TTCTTTTATT-TTTTTCTC
192 TTCTTTT-TTATTTTGC-C
* *
30995221 TTTTTTTCCTTAACTCATCTTTTGAAT-TAAAAATGGATTTAATTAGTCATGATTGATGACATTG
1 TTTTTTTCCTTAACTCATCTTTTGAATCTAAAGATGGATTTAATTATTCATGATTGATGACATTG
*
30995285 AACTTGATATTATGCGAGATTCATG-TTTTTTTTTCTTTTTTTCCTAAGCTCAAATTTTGAAATT
66 AACTTGATATTATGCGAGATCCATGTTTTTTTTTTCTTTTTTTCCTAAGCTCAAATTTTGAAATT
*
30995349 ATTTTTCTTTTCTTCCTATTTTCCTTTTTTTCCTTAACTCATTTAAGCCCAAATTTTGGAATTAT
131 ATTTTTCTTTTCTTCCTA---T--TTTTTATCCTTAACTCA-TTAAGCCCAAATTTTGGAATTAT
30995414 TTTTCTTTTTTATTTTGCC
190 TTTTCTTTTTTATTTTGCC
30995433 TTTTTTTCCTTAACTCATCTTTTG-ATCCTAAAGATGGATTTAATTATTCAAT-ATTGATGACAT
1 TTTTTTTCCTTAACTCATCTTTTGAAT-CTAAAGATGGATTTAATTATTC-ATGATTGATGACAT
*
30995496 CGAACTTGATATTATGCG
64 TGAACTTGATATTATGCG
30995514 TGACCTATGT
Statistics
Matches: 258, Mismatches: 17, Indels: 28
0.85 0.06 0.09
Matches are distributed among these distances:
201 55 0.21
204 33 0.13
205 40 0.16
206 7 0.03
207 6 0.02
208 1 0.00
209 2 0.01
210 2 0.01
211 2 0.01
212 29 0.11
213 79 0.31
214 2 0.01
ACGTcount: A:0.23, C:0.14, G:0.10, T:0.53
Consensus pattern (208 bp):
TTTTTTTCCTTAACTCATCTTTTGAATCTAAAGATGGATTTAATTATTCATGATTGATGACATTG
AACTTGATATTATGCGAGATCCATGTTTTTTTTTTCTTTTTTTCCTAAGCTCAAATTTTGAAATT
ATTTTTCTTTTCTTCCTATTTTTTATCCTTAACTCATTAAGCCCAAATTTTGGAATTATTTTTCT
TTTTTATTTTGCC
Found at i:30995368 original size:17 final size:17
Alignment explanation
Indices: 30995348--30995382 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
30995338 ATTTTGAAAT
*
30995348 TATTTTTCTTTTCTTCC
1 TATTTTCCTTTTCTTCC
*
30995365 TATTTTCCTTTTTTTCC
1 TATTTTCCTTTTCTTCC
30995382 T
1 T
30995383 TAACTCATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.06, C:0.23, G:0.00, T:0.71
Consensus pattern (17 bp):
TATTTTCCTTTTCTTCC
Found at i:30995396 original size:63 final size:60
Alignment explanation
Indices: 30995329--30995450 Score: 183
Period size: 63 Copynumber: 2.0 Consensus size: 60
30995319 CTTTTTTTCC
*
30995329 TAAGCTCAAATTTTGAAATTATTTTTCTTTTCTTCCTATTTT-CCTTTTTTTCCTTAACTCATT
1 TAAGCCCAAATTTTGAAATTATTTTTC-TTT-TT--TATTTTGCCTTTTTTTCCTTAACTCATT
*
30995392 TAAGCCCAAATTTTGGAATTATTTTTCTTTTTTATTTTGCCTTTTTTTCCTTAACTCAT
1 TAAGCCCAAATTTTGAAATTATTTTTCTTTTTTATTTTGCCTTTTTTTCCTTAACTCAT
30995451 CTTTTGATCC
Statistics
Matches: 56, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
59 6 0.11
60 20 0.36
61 2 0.04
62 3 0.05
63 25 0.45
ACGTcount: A:0.20, C:0.18, G:0.05, T:0.57
Consensus pattern (60 bp):
TAAGCCCAAATTTTGAAATTATTTTTCTTTTTTATTTTGCCTTTTTTTCCTTAACTCATT
Found at i:31010905 original size:24 final size:24
Alignment explanation
Indices: 31010873--31010931 Score: 93
Period size: 24 Copynumber: 2.5 Consensus size: 24
31010863 CACATGTTTC
31010873 TGTTGATAATTCTATTAG-TCTTAT
1 TGTTGATAATTCTATTAGTTC-TAT
31010897 TGTTGATAATTCTATTAGTTCTAT
1 TGTTGATAATTCTATTAGTTCTAT
*
31010921 TGATGATAATT
1 TGTTGATAATT
31010932 ATGCTAGTCC
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
24 31 0.94
25 2 0.06
ACGTcount: A:0.27, C:0.07, G:0.14, T:0.53
Consensus pattern (24 bp):
TGTTGATAATTCTATTAGTTCTAT
Found at i:31010939 original size:24 final size:24
Alignment explanation
Indices: 31010876--31010939 Score: 58
Period size: 24 Copynumber: 2.7 Consensus size: 24
31010866 ATGTTTCTGT
* * *
31010876 TGATAATTCTATTAG-TCTTATTGT
1 TGATAATTATACTAGTTC-TATTGA
* *
31010900 TGATAATTCTATTAGTTCTATTGA
1 TGATAATTATACTAGTTCTATTGA
*
31010924 TGATAATTATGCTAGT
1 TGATAATTATACTAGT
31010940 CCAGATTCTT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
24 33 0.94
25 2 0.06
ACGTcount: A:0.28, C:0.08, G:0.14, T:0.50
Consensus pattern (24 bp):
TGATAATTATACTAGTTCTATTGA
Found at i:31013148 original size:13 final size:13
Alignment explanation
Indices: 31013130--31013155 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
31013120 CGGAAATACT
31013130 TTTCGTTGGAAAA
1 TTTCGTTGGAAAA
31013143 TTTCGTTGGAAAA
1 TTTCGTTGGAAAA
31013156 AAAAATAATC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.08, G:0.23, T:0.38
Consensus pattern (13 bp):
TTTCGTTGGAAAA
Found at i:31017573 original size:13 final size:13
Alignment explanation
Indices: 31017555--31017587 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
31017545 AAAGTTTAGC
31017555 CTTTATTGATAGT
1 CTTTATTGATAGT
31017568 CTTTATTGATAGT
1 CTTTATTGATAGT
31017581 CTTTATT
1 CTTTATT
31017588 CTTAAATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.21, C:0.09, G:0.12, T:0.58
Consensus pattern (13 bp):
CTTTATTGATAGT
Found at i:31018676 original size:20 final size:20
Alignment explanation
Indices: 31018639--31018677 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
31018629 AACATTTTAT
*
31018639 ATTTTAAAACTAAGTTAAAG
1 ATTTTAAAACTAAATTAAAG
31018659 ATTTTAAATA-TAAATTAAA
1 ATTTTAAA-ACTAAATTAAA
31018678 AAAATAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 16 0.94
21 1 0.06
ACGTcount: A:0.54, C:0.03, G:0.05, T:0.38
Consensus pattern (20 bp):
ATTTTAAAACTAAATTAAAG
Found at i:31022555 original size:215 final size:217
Alignment explanation
Indices: 31022181--31022608 Score: 702
Period size: 215 Copynumber: 2.0 Consensus size: 217
31022171 CTTTTACTTT
*
31022181 GCTCTGTGATATGGTGAGACAGATACTTCTGCTGTCCAATTTAAATGGCCTGTAACGCTTTGGCT
1 GCTCTGTGATATGGTGAGACAGATACTTCTGCTGTCCAATTTAAATGGCCTGT-ACGCTTTAGCT
*
31022246 TCTCAGTGTTCGTGGAATCCACTACTTACCTAATTGTCAACTCCATCTTAAACTTTTATAAGGGT
65 TCTCAGTGTTCGTGGAATCCACTACTTACCTAAGTGTCAACTCCATCTTAAACTTTTATAAGGGT
* *
31022311 CACGAAGCACAAATCCAAACTGATAGACAGACTCCTATTCGACTGAGTTGTGTAAAGGGAGTTCT
130 CACGAAGCACAAATCCAAACTGATAGACAGACTCCTATTCGACTGAGTTGTGTAAAGGGAATCCT
31022376 TGTAATAAGGAGAGAAAGCGTTC
195 TGTAATAAGGAGAGAAAGCGTTC
31022399 GCTCTGTGATATGGTGAGACAGATACTTCTGCTGTCCAATTTAAATGGCCT-T-CGCTTTAGCTT
1 GCTCTGTGATATGGTGAGACAGATACTTCTGCTGTCCAATTTAAATGGCCTGTACGCTTTAGCTT
*
31022462 CTCAGTGTTCGTGGAATCCACTACTTACCTAAGTGTCAATTCCATCTTAAACTTTTATGAA-GGT
66 CTCAGTGTTCGTGGAATCCACTACTTACCTAAGTGTCAACTCCATCTTAAACTTTTAT-AAGGGT
* * * * *
31022526 CA-TAAGGCACAAATCCAAACTGATAGACAGACTCTTCTTTGATTGAGTTGTGTAAAGGGAATCC
130 CACGAA-GCACAAATCCAAACTGATAGACAGACTCCTATTCGACTGAGTTGTGTAAAGGGAATCC
*
31022590 TTGTAATAGGGAGAGAAAG
194 TTGTAATAAGGAGAGAAAG
31022609 TATTGCAAAC
Statistics
Matches: 197, Mismatches: 11, Indels: 7
0.92 0.05 0.03
Matches are distributed among these distances:
214 2 0.01
215 141 0.72
216 2 0.01
217 1 0.01
218 51 0.26
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.31
Consensus pattern (217 bp):
GCTCTGTGATATGGTGAGACAGATACTTCTGCTGTCCAATTTAAATGGCCTGTACGCTTTAGCTT
CTCAGTGTTCGTGGAATCCACTACTTACCTAAGTGTCAACTCCATCTTAAACTTTTATAAGGGTC
ACGAAGCACAAATCCAAACTGATAGACAGACTCCTATTCGACTGAGTTGTGTAAAGGGAATCCTT
GTAATAAGGAGAGAAAGCGTTC
Found at i:31023080 original size:4 final size:4
Alignment explanation
Indices: 31023071--31023096 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
31023061 CACAAAAGAA
31023071 AATT AATT AATT AATT AATT AATT AA
1 AATT AATT AATT AATT AATT AATT AA
31023097 AAAAAAAAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (4 bp):
AATT
Found at i:31025155 original size:16 final size:15
Alignment explanation
Indices: 31025134--31025165 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
31025124 CTTTTGAGCA
31025134 TTATTGTTTTGTGTAT
1 TTATTGTTTTGT-TAT
31025150 TTATTGTTTTGTTAT
1 TTATTGTTTTGTTAT
31025165 T
1 T
31025166 GTTATTTAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.12, C:0.00, G:0.16, T:0.72
Consensus pattern (15 bp):
TTATTGTTTTGTTAT
Found at i:31032125 original size:55 final size:55
Alignment explanation
Indices: 31032050--31032164 Score: 169
Period size: 55 Copynumber: 2.1 Consensus size: 55
31032040 ATACTTAGAT
* * *
31032050 AAGC-TACTAGACAAATCAATAATCAACACTTGGAAGACAACATGTCGATTTTGG
1 AAGCTTACTAGACAAATCAATAATCAACACTTGGAAGACAACATGTCAATTCTGA
* * *
31032104 AAGCTTACTGGACAGATCAATAATCGACACTTGGAAGACAACATGTCAATTCTGA
1 AAGCTTACTAGACAAATCAATAATCAACACTTGGAAGACAACATGTCAATTCTGA
31032159 AAGCTT
1 AAGCTT
31032165 CAAAGAAAAA
Statistics
Matches: 54, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
54 4 0.07
55 50 0.93
ACGTcount: A:0.39, C:0.19, G:0.17, T:0.24
Consensus pattern (55 bp):
AAGCTTACTAGACAAATCAATAATCAACACTTGGAAGACAACATGTCAATTCTGA
Found at i:31032950 original size:29 final size:29
Alignment explanation
Indices: 31032915--31033013 Score: 110
Period size: 30 Copynumber: 3.4 Consensus size: 29
31032905 AAAGGCTGAA
* *
31032915 GTTATGCTTAATCTTTAAAAGGCAAAAAG
1 GTTATGCTTAATCTTTAAAAAGTAAAAAG
* **
31032944 GTTATGCTTAAGCCTTTAAAAAGTAGTAAG
1 GTTATGCTTAA-TCTTTAAAAAGTAAAAAG
* *
31032974 GTTATGCTTGATCCTTTAAAAAATAAAAA-
1 GTTATGCTTAAT-CTTTAAAAAGTAAAAAG
31033003 GTTATGCTTAA
1 GTTATGCTTAA
31033014 CCCTTGAAAG
Statistics
Matches: 57, Mismatches: 11, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
29 21 0.37
30 36 0.63
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.34
Consensus pattern (29 bp):
GTTATGCTTAATCTTTAAAAAGTAAAAAG
Found at i:31033034 original size:88 final size:88
Alignment explanation
Indices: 31032913--31033083 Score: 209
Period size: 88 Copynumber: 1.9 Consensus size: 88
31032903 GAAAAGGCTG
* * * *
31032913 AAGTTATGCTTAATCTTTAAAAGGCAAAAAGGTTAT-GCTTAAGCCTTTAAAAAGTAGTAAGGTT
1 AAGTTATGCTTAACCCTTAAAAGGCAAAAAGGTTATAG-TCAAGCCTTTAAAAAGTAGTAACGTT
* * *
31032977 ATGCTTGATCCTTTAAAAAATAAA
65 ATCCTTGACCCTTCAAAAAATAAA
* * * * * *
31033001 AAGTTATGCTTAACCCTTGAAAGGTAGAGAGGTTATAGTCAAGCCTTTAAAATGTAGTGACGTTA
1 AAGTTATGCTTAACCCTTAAAAGGCAAAAAGGTTATAGTCAAGCCTTTAAAAAGTAGTAACGTTA
31033066 TCCTTGACCCTTCAAAAA
66 TCCTTGACCCTTCAAAAA
31033084 GTAATGGGTT
Statistics
Matches: 69, Mismatches: 13, Indels: 2
0.82 0.15 0.02
Matches are distributed among these distances:
88 68 0.99
89 1 0.01
ACGTcount: A:0.37, C:0.13, G:0.18, T:0.32
Consensus pattern (88 bp):
AAGTTATGCTTAACCCTTAAAAGGCAAAAAGGTTATAGTCAAGCCTTTAAAAAGTAGTAACGTTA
TCCTTGACCCTTCAAAAAATAAA
Found at i:31034276 original size:60 final size:60
Alignment explanation
Indices: 31034201--31034602 Score: 351
Period size: 60 Copynumber: 6.7 Consensus size: 60
31034191 AATCGAATTC
* *
31034201 ATTTTGAGATGGGTTGAGCCTAGATTAAGT-TTAGAAATTTCAAATTTTTAAATCAAACCT
1 ATTTTGAGATAGGTTGAGCCTAGATTAAGTCTAAG-AATTTCAAATTTTTAAATCAAACCT
** * * **
31034261 GGTTTAAGATAGGTTGAGCCTAGATTAAATCTAAGAATTTCAAATTTTTAAATTGAACCT
1 ATTTTGAGATAGGTTGAGCCTAGATTAAGTCTAAGAATTTCAAATTTTTAAATCAAACCT
* ** * * * * * *
31034321 ATTTTGAGGTAGGTCAAGTCTAGATTACGTCTAAGAATTTTAATTTTTTTAAGTTAAACCT
1 ATTTTGAGATAGGTTGAGCCTAGATTAAGTCTAAGAATTTCAA-ATTTTTAAATCAAACCT
* * * * * *
31034382 ATTTTGAGATATGTTGAGCTTATATTAAGTCTAAGAATTCCAATTTTTTTAATCAAACCT
1 ATTTTGAGATAGGTTGAGCCTAGATTAAGTCTAAGAATTTCAAATTTTTAAATCAAACCT
* * * *
31034442 ATTTTGAGATAGGTTAAGCTTAGGTTAAGTCTAAGAATTTCAAGAATTTATAAATCAAACCT
1 ATTTTGAGATAGGTTGAGCCTAGATTAAGTCTAAGAATTTC-A-AATTTTTAAATCAAACCT
* *** * * * * * **
31034504 GTTTTGAGATAGGCCAAACCTAGATCAAGT-TTAGAAACTT-AAGAATCATAAATCAAACCT
1 ATTTTGAGATAGGTTGAGCCTAGATTAAGTCTAAG-AATTTCAA-ATTTTTAAATCAAACCT
* * * *
31034564 ATTTTGAGATAAGTTGAGCCTAAATTAAATATAAGAATT
1 ATTTTGAGATAGGTTGAGCCTAGATTAAGTCTAAGAATT
31034603 ATTAAAGTTG
Statistics
Matches: 271, Mismatches: 64, Indels: 14
0.78 0.18 0.04
Matches are distributed among these distances:
59 1 0.00
60 171 0.63
61 57 0.21
62 42 0.15
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.37
Consensus pattern (60 bp):
ATTTTGAGATAGGTTGAGCCTAGATTAAGTCTAAGAATTTCAAATTTTTAAATCAAACCT
Found at i:31040954 original size:34 final size:35
Alignment explanation
Indices: 31040876--31040957 Score: 128
Period size: 35 Copynumber: 2.3 Consensus size: 35
31040866 CCCATGTTGC
* * *
31040876 AATAAAAGAAAAAGTTATGTCTATTGAAAATTAGAA
1 AATAAAA-AAAAAGTCATGTCTATTGAAAATAAAAA
31040912 AATAAAAAAAAAGTCATGTCTATTGAAAATAAAAA
1 AATAAAAAAAAAGTCATGTCTATTGAAAATAAAAA
31040947 AATAAAAAAAA
1 AATAAAAAAAA
31040958 TCACATCTGT
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
35 36 0.84
36 7 0.16
ACGTcount: A:0.63, C:0.04, G:0.10, T:0.23
Consensus pattern (35 bp):
AATAAAAAAAAAGTCATGTCTATTGAAAATAAAAA
Found at i:31040971 original size:33 final size:35
Alignment explanation
Indices: 31040876--31040973 Score: 101
Period size: 35 Copynumber: 2.8 Consensus size: 35
31040866 CCCATGTTGC
* ** * *
31040876 AATAAAAGAAAAAGTTATGTCTATTGAAAATTAGAA
1 AATAAAA-AAAAAGTCACATCTATTGAAAATAAAAA
**
31040912 AATAAAAAAAAAGTCATGTCTATTGAAAATAAAAA
1 AATAAAAAAAAAGTCACATCTATTGAAAATAAAAA
*
31040947 AAT-AAAAAAAA-TCACATCTGTTGAAAA
1 AATAAAAAAAAAGTCACATCTATTGAAAA
31040974 AGATCAATAG
Statistics
Matches: 56, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
33 13 0.23
34 8 0.14
35 28 0.50
36 7 0.12
ACGTcount: A:0.59, C:0.06, G:0.10, T:0.24
Consensus pattern (35 bp):
AATAAAAAAAAAGTCACATCTATTGAAAATAAAAA
Found at i:31054391 original size:2 final size:2
Alignment explanation
Indices: 31054384--31054432 Score: 91
Period size: 2 Copynumber: 25.0 Consensus size: 2
31054374 AATAAACAAT
31054384 TA TA TA TA TA -A 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 TA TA TA TA TA TA
31054425 TA TA TA TA
1 TA TA TA TA
31054433 AAAAAAGAGT
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 45 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:31062567 original size:25 final size:25
Alignment explanation
Indices: 31062538--31062601 Score: 78
Period size: 25 Copynumber: 2.6 Consensus size: 25
31062528 CTTATTGAAG
*
31062538 TGAGTTCCTTATCTCTTA-AAGAAAT
1 TGAGTTGCTTATCTCTTATAA-AAAT
31062563 TGAGTTGCTT-TCATCTTATAAAAAT
1 TGAGTTGCTTATC-TCTTATAAAAAT
*
31062588 TGAGCTGCTTATCT
1 TGAGTTGCTTATCT
31062602 TTTTTAGTTG
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
24 2 0.06
25 28 0.82
26 4 0.12
ACGTcount: A:0.28, C:0.16, G:0.14, T:0.42
Consensus pattern (25 bp):
TGAGTTGCTTATCTCTTATAAAAAT
Found at i:31062689 original size:13 final size:14
Alignment explanation
Indices: 31062673--31062701 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
31062663 AAAAACCAAA
31062673 AAAT-AAAAAAATG
1 AAATAAAAAAAATG
31062686 AAATAAAAAAAATG
1 AAATAAAAAAAATG
31062700 AA
1 AA
31062702 TGATGATGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.27
14 11 0.73
ACGTcount: A:0.79, C:0.00, G:0.07, T:0.14
Consensus pattern (14 bp):
AAATAAAAAAAATG
Found at i:31076723 original size:60 final size:60
Alignment explanation
Indices: 31076642--31077144 Score: 398
Period size: 60 Copynumber: 8.4 Consensus size: 60
31076632 TCGGTGAATT
* * *
31076642 AAATTGAACCTGTTTTGAGATAGGTCGAGCCTAGATCAAGTTTAAGAACTTTAATTTTTC
1 AAATCGAACCTGTTTTAAGATAGGTCGAGCCTAGATCAAGTTTAAGAAATTTAATTTTTC
* * * * * * *
31076702 AAATCGAACCTATTTTAAGATAGGTCTAGCCTATATCAAGTTGAGGAACTTCAATTTTTC
1 AAATCGAACCTGTTTTAAGATAGGTCGAGCCTAGATCAAGTTTAAGAAATTTAATTTTTC
* * * * * **
31076762 AAATTGAACCTATTTTAAGATAGGTCGAGCCTATATCAAGTTTAGGAAATTCAACCTTT-
1 AAATCGAACCTGTTTTAAGATAGGTCGAGCCTAGATCAAGTTTAAGAAATTTAATTTTTC
* * *
31076821 AGAATCAAACTTGTTTTGAAGATAGGTCGAGCCTAAATCAAGTTT-AGAAATTTCAA----TC
1 A-AATCGAACCTGTTTT-AAGATAGGTCGAGCCTAGATCAAGTTTAAGAAATTT-AATTTTTC
* * * * * * * * * *
31076879 AAATCAAACCTATTGTGAGATAGGTCGAACCTAAATTAAGTTTAGGAATTTTAATTTTTA
1 AAATCGAACCTGTTTTAAGATAGGTCGAGCCTAGATCAAGTTTAAGAAATTTAATTTTTC
* * * * * * * *
31076939 AAATTGAACTTGTTGTGAGATAGGTCGGGCCTAGATTAAGTCTAA-AAATTTCAATTTTTA
1 AAATCGAACCTGTTTTAAGATAGGTCGAGCCTAGATCAAGTTTAAGAAATTT-AATTTTTC
* * *
31076999 AAATCAAACCTGTTTTAAGATAGGTCGAACCTAGATCAAGTTT-AGGAATATTAA-TTTTC
1 AAATCGAACCTGTTTTAAGATAGGTCGAGCCTAGATCAAGTTTAAGAAAT-TTAATTTTTC
* * * * * ** *
31077058 AAAATCGAACTTGTTCTAAGATAAGTCGAGCCTAGATCGAGTCTAA-AAATTTTCGTTTTTA
1 -AAATCGAACCTGTTTTAAGATAGGTCGAGCCTAGATCAAGTTTAAGAAA-TTTAATTTTTC
* * *
31077119 AAAT-GAACCTATTTTGAGATGGGTCG
1 AAATCGAACCTGTTTTAAGATAGGTCG
31077145 TGCTTGAATC
Statistics
Matches: 359, Mismatches: 68, Indels: 33
0.78 0.15 0.07
Matches are distributed among these distances:
56 26 0.07
57 19 0.05
58 1 0.00
59 27 0.08
60 250 0.70
61 36 0.10
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.35
Consensus pattern (60 bp):
AAATCGAACCTGTTTTAAGATAGGTCGAGCCTAGATCAAGTTTAAGAAATTTAATTTTTC
Found at i:31076962 original size:177 final size:177
Alignment explanation
Indices: 31076648--31077054 Score: 471
Period size: 177 Copynumber: 2.3 Consensus size: 177
31076638 AATTAAATTG
* *
31076648 AACCTGTTTTG-AGATAGGTCGAGCCTAGATCAAGTTTAAGAACTTTAATTTTTCAAATCGAACC
1 AACCTGTTTTGAAGATAGGTCGAGCCTAGATCAAGTTT-AGAAATTTAA---TTCAAATCAAACC
* * * * * *
31076712 TATTTTAAGATAGGTCTAGCCTATATCAAGTTGAGGAACTTCAATTTTTCAAATTGAACCTATTT
62 TATTGTAAGATAGGTCGAACCTAAATCAAGTTGAGGAACTTCAATTTTTAAAATTGAACCTATTG
* * * *
31076777 TAAGATAGGTCGAGCCTATATCAAGTTTAGGAAA-TTCAACCTTTAGAATCA
127 TAAGATAGGTCGAGCCTAGATCAAGTCTA-AAAATTTCAACCTTTAAAATCA
* *
31076828 AACTTGTTTTGAAGATAGGTCGAGCCTAAATCAAGTTTAGAAATTTCAA-TCAAATCAAACCTAT
1 AACCTGTTTTGAAGATAGGTCGAGCCTAGATCAAGTTTAGAAATTT-AATTCAAATCAAACCTAT
* * * * * * * *
31076892 TGTGAGATAGGTCGAACCTAAATTAAGTTTAGGAATTTTAATTTTTAAAATTGAACTTGTTGTGA
65 TGTAAGATAGGTCGAACCTAAATCAAGTTGAGGAACTTCAATTTTTAAAATTGAACCTATTGTAA
* * **
31076957 GATAGGTCGGGCCTAGATTAAGTCTAAAAATTTCAATTTTTAAAATCA
130 GATAGGTCGAGCCTAGATCAAGTCTAAAAATTTCAACCTTTAAAATCA
* *
31077005 AACCTGTTTT-AAGATAGGTCGAACCTAGATCAAGTTTAGGAATATTAATT
1 AACCTGTTTTGAAGATAGGTCGAGCCTAGATCAAGTTTAGAAAT-TTAATT
31077055 TTCAAAATCG
Statistics
Matches: 192, Mismatches: 30, Indels: 13
0.82 0.13 0.06
Matches are distributed among these distances:
176 35 0.18
177 113 0.59
180 17 0.09
181 27 0.14
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.35
Consensus pattern (177 bp):
AACCTGTTTTGAAGATAGGTCGAGCCTAGATCAAGTTTAGAAATTTAATTCAAATCAAACCTATT
GTAAGATAGGTCGAACCTAAATCAAGTTGAGGAACTTCAATTTTTAAAATTGAACCTATTGTAAG
ATAGGTCGAGCCTAGATCAAGTCTAAAAATTTCAACCTTTAAAATCA
Found at i:31077029 original size:120 final size:120
Alignment explanation
Indices: 31076648--31077144 Score: 504
Period size: 120 Copynumber: 4.2 Consensus size: 120
31076638 AATTAAATTG
* * * * * *
31076648 AACCTGTTTTGAGATAGGTCGAGCCTAGATCAAGTTTAAGAACTTTAATTTTTCAAATCGAACCT
1 AACCTATTTTGAGATAGGTCGAACCTAGATCAAGTTTAGGAATTTTAATTTTTAAAATCGAACTT
* * * ** * * **
31076713 ATTTTAAGATAGGTCTAGCCTATATCAAGT-TGAGGAACTTCAATTTTTCAAATTG
66 GTTTTAAGATAGGTCGAGCCTAGATCAAGTCT-AAAAATTTCAATTTTTAAAATCA
* * * * * ** * *
31076768 AACCTATTTTAAGATAGGTCGAGCCTATATCAAGTTTAGGAAATTCAACCTTTAGAATCAAACTT
1 AACCTATTTTGAGATAGGTCGAACCTAGATCAAGTTTAGGAATTTTAATTTTTAAAATCGAACTT
* * * *
31076833 GTTTTGAAGATAGGTCGAGCCTAAATCAAGTTTAGAAATTTCAA----TCAAATCA
66 GTTTT-AAGATAGGTCGAGCCTAGATCAAGTCTAAAAATTTCAATTTTTAAAATCA
* * * *
31076885 AACCTATTGTGAGATAGGTCGAACCTAAATTAAGTTTAGGAATTTTAATTTTTAAAATTGAACTT
1 AACCTATTTTGAGATAGGTCGAACCTAGATCAAGTTTAGGAATTTTAATTTTTAAAATCGAACTT
* * * *
31076950 GTTGTGAGATAGGTCGGGCCTAGATTAAGTCTAAAAATTTCAATTTTTAAAATCA
66 GTTTTAAGATAGGTCGAGCCTAGATCAAGTCTAAAAATTTCAATTTTTAAAATCA
* * * *
31077005 AACCTGTTTTAAGATAGGTCGAACCTAGATCAAGTTTAGGAATATTAATTTTCAAAATCGAACTT
1 AACCTATTTTGAGATAGGTCGAACCTAGATCAAGTTTAGGAATTTTAATTTTTAAAATCGAACTT
* * * * *
31077070 GTTCTAAGATAAGTCGAGCCTAGATCGAGTCTAAAAATTTTC-GTTTTTAAAAT-G
66 GTTTTAAGATAGGTCGAGCCTAGATCAAGTCTAAAAA-TTTCAATTTTTAAAATCA
*
31077124 AACCTATTTTGAGATGGGTCG
1 AACCTATTTTGAGATAGGTCG
31077145 TGCTTGAATC
Statistics
Matches: 312, Mismatches: 58, Indels: 15
0.81 0.15 0.04
Matches are distributed among these distances:
116 32 0.10
117 63 0.20
119 18 0.06
120 162 0.52
121 36 0.12
122 1 0.00
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.35
Consensus pattern (120 bp):
AACCTATTTTGAGATAGGTCGAACCTAGATCAAGTTTAGGAATTTTAATTTTTAAAATCGAACTT
GTTTTAAGATAGGTCGAGCCTAGATCAAGTCTAAAAATTTCAATTTTTAAAATCA
Found at i:31077072 original size:237 final size:236
Alignment explanation
Indices: 31076648--31077109 Score: 552
Period size: 237 Copynumber: 2.0 Consensus size: 236
31076638 AATTAAATTG
* * * * *
31076648 AACCTGTTTTGAGATAGGTCGAGCCTAGATCAAGTTTAAGAACTTTAATTTTTCAAATCGAACCT
1 AACCTATTGTGAGATAGGTCGAACCTAAATCAAGTTTAAGAACTTTAATTTTTAAAATCGAACCT
* * * ** * **
31076713 ATTTTAAGATAGGTCTAGCCTATATCAAGTTGAGGAACTTCAATTTTTCAAATTGAACCTATTTT
66 ATTGTAAGATAGGTCGAGCCTAGATCAAGTTGAAAAACTTCAATTTTTAAAATCAAACCTATTTT
* * * *
31076778 AAGATAGGTCGAGCCTATATCAAGTTTAGGAAATTCAACCTTTAGAATCAAACTTGTTTTGAAGA
131 AAGATAGGTCGAACCTAGATCAAGTTTAGGAAATTCAACCTTTAAAATCAAACTTGTTCT-AAGA
* * *
31076843 TAGGTCGAGCCTAAATCAAGTTTAGAAATTTCAATCAAATCA
195 TAAGTCGAGCCTAAATCAAGTCTAAAAATTTCAATCAAATCA
* * * * *
31076885 AACCTATTGTGAGATAGGTCGAACCTAAATTAAGTTTAGGAATTTTAATTTTTAAAATTGAACTT
1 AACCTATTGTGAGATAGGTCGAACCTAAATCAAGTTTAAGAACTTTAATTTTTAAAATCGAACCT
* * * * * *
31076950 GTTGTGAGATAGGTCGGGCCTAGATTAAGTCT-AAAAATTTCAATTTTTAAAATCAAACCTGTTT
66 ATTGTAAGATAGGTCGAGCCTAGATCAAGT-TGAAAAACTTCAATTTTTAAAATCAAACCTATTT
* *
31077014 TAAGATAGGTCGAACCTAGATCAAGTTTAGGAATATT-AA-TTTTCAAAATCGAACTTGTTCTAA
130 TAAGATAGGTCGAACCTAGATCAAGTTTAGGAA-ATTCAACCTTT-AAAATCAAACTTGTTCTAA
* *
31077077 GATAAGTCGAGCCTAGATCGAGTCTAAAAATTT
193 GATAAGTCGAGCCTAAATCAAGTCTAAAAATTT
31077110 TCGTTTTTAA
Statistics
Matches: 187, Mismatches: 35, Indels: 7
0.82 0.15 0.03
Matches are distributed among these distances:
236 33 0.18
237 150 0.80
238 4 0.02
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.34
Consensus pattern (236 bp):
AACCTATTGTGAGATAGGTCGAACCTAAATCAAGTTTAAGAACTTTAATTTTTAAAATCGAACCT
ATTGTAAGATAGGTCGAGCCTAGATCAAGTTGAAAAACTTCAATTTTTAAAATCAAACCTATTTT
AAGATAGGTCGAACCTAGATCAAGTTTAGGAAATTCAACCTTTAAAATCAAACTTGTTCTAAGAT
AAGTCGAGCCTAAATCAAGTCTAAAAATTTCAATCAAATCA
Found at i:31078756 original size:16 final size:16
Alignment explanation
Indices: 31078718--31078759 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
31078708 AATAATCAAT
31078718 AAAT-AAATAAAAATA
1 AAATAAAATAAAAATA
31078733 AAATAAAATAGAAAATA
1 AAATAAAATA-AAAATA
*
31078750 GAA-AAAATAA
1 AAATAAAATAA
31078760 TAAGACTTAG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
15 5 0.21
16 11 0.46
17 8 0.33
ACGTcount: A:0.79, C:0.00, G:0.05, T:0.17
Consensus pattern (16 bp):
AAATAAAATAAAAATA
Found at i:31081198 original size:68 final size:70
Alignment explanation
Indices: 31081120--31081258 Score: 239
Period size: 68 Copynumber: 2.0 Consensus size: 70
31081110 ATAAAAATCT
*
31081120 TATATAAAGTATGTATATATATATATATATATATATATATATATGATCTAATTATATA-G-CATA
1 TATATAAAGTATATATATATATATATATATATATATATATATATGATCTAATTATATAGGCCATA
31081183 TAGTA
66 TAGTA
31081188 TNATAT-AAGTATATATATATATATATATATATATATATATATATGATCTAATTATATAGGCCAT
1 T-ATATAAAGTATATATATATATATATATATATATATATATATATGATCTAATTATATAGGCCAT
31081252 ATAGTA
65 ATAGTA
31081258 T
1 T
31081259 GATAAGTGTT
Statistics
Matches: 67, Mismatches: 1, Indels: 4
0.93 0.01 0.06
Matches are distributed among these distances:
68 52 0.78
69 5 0.07
70 10 0.15
ACGTcount: A:0.45, C:0.04, G:0.07, T:0.44
Consensus pattern (70 bp):
TATATAAAGTATATATATATATATATATATATATATATATATATGATCTAATTATATAGGCCATA
TAGTA
Found at i:31081245 original size:2 final size:2
Alignment explanation
Indices: 31081133--31081231 Score: 114
Period size: 2 Copynumber: 48.5 Consensus size: 2
31081123 ATAAAGTATG
*
31081133 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TGA TC TA -A T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA
*
31081174 TA TA GCA TA TA GTA TNA TA TA -A GTA TA TA TA TA TA TA TA TA TA
1 TA TA -TA TA TA -TA T-A TA TA TA -TA TA TA TA TA TA TA TA TA TA
31081217 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
31081232 GATCTAATTA
Statistics
Matches: 85, Mismatches: 4, Indels: 16
0.81 0.04 0.15
Matches are distributed among these distances:
1 3 0.04
2 74 0.87
3 8 0.09
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.46
Consensus pattern (2 bp):
TA
Found at i:31082446 original size:35 final size:34
Alignment explanation
Indices: 31082364--31082450 Score: 102
Period size: 35 Copynumber: 2.5 Consensus size: 34
31082354 TTCTAAGTAA
* * * *
31082364 AATAGTGCTTCAATTTTTTTAGTTGTTTTGCGTG
1 AATAGTGCTTCACTTATTTTAGTTGTTCTACGTG
*
31082398 AAGTAGTACTTCACTTATTTTAGTTGTTCTACGTG
1 AA-TAGTGCTTCACTTATTTTAGTTGTTCTACGTG
*
31082433 CAATAGTGTTTCACTTAT
1 -AATAGTGCTTCACTTAT
31082451 AATGGTTGTT
Statistics
Matches: 44, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
34 2 0.05
35 40 0.91
36 2 0.05
ACGTcount: A:0.22, C:0.13, G:0.17, T:0.48
Consensus pattern (34 bp):
AATAGTGCTTCACTTATTTTAGTTGTTCTACGTG
Found at i:31083941 original size:23 final size:22
Alignment explanation
Indices: 31083899--31083943 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
31083889 TGGAGTACCA
*
31083899 CATTTTTTAAGAATGTAGATGT
1 CATTTTTTAAGAATGGAGATGT
31083921 CATTTGTTTAATG-ATGGAGATGT
1 CATTT-TTTAA-GAATGGAGATGT
31083944 TGGGTAAAGC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 5 0.25
23 14 0.70
24 1 0.05
ACGTcount: A:0.29, C:0.04, G:0.22, T:0.44
Consensus pattern (22 bp):
CATTTTTTAAGAATGGAGATGT
Found at i:31085571 original size:29 final size:29
Alignment explanation
Indices: 31085527--31085601 Score: 89
Period size: 29 Copynumber: 2.6 Consensus size: 29
31085517 GAAGAGGTAT
* **
31085527 ACGTGAA-AGATACAAGAGAAAAAGTTGC
1 ACGTGAATAGGTACAAGAGAAAAAGCAGC
* * *
31085555 ATGTGAATAGGTACAAGAGAAGAAGCAGT
1 ACGTGAATAGGTACAAGAGAAAAAGCAGC
31085584 ACGTGAATAGGTACAAGA
1 ACGTGAATAGGTACAAGA
31085602 AAAGAAGGGG
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
28 6 0.15
29 33 0.85
ACGTcount: A:0.47, C:0.09, G:0.28, T:0.16
Consensus pattern (29 bp):
ACGTGAATAGGTACAAGAGAAAAAGCAGC
Found at i:31085625 original size:29 final size:29
Alignment explanation
Indices: 31085555--31085619 Score: 94
Period size: 29 Copynumber: 2.2 Consensus size: 29
31085545 AAAAAGTTGC
*
31085555 ATGTGAATAGGTACAAGAGAAGAAGCAGT
1 ATGTGAATAGGTACAAGAAAAGAAGCAGT
* **
31085584 ACGTGAATAGGTACAAGAAAAGAAGGGGT
1 ATGTGAATAGGTACAAGAAAAGAAGCAGT
31085613 ATGTGAA
1 ATGTGAA
31085620 CTGGTAGACA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.45, C:0.06, G:0.32, T:0.17
Consensus pattern (29 bp):
ATGTGAATAGGTACAAGAAAAGAAGCAGT
Done.