Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A01
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: 104050246
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 4660000 characters in sequence are not A, C, G, or T
File 109 of 316
Found at i:34326630 original size:21 final size:22
Alignment explanation
Indices: 34326588--34326633 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 22
34326578 AAAATTATAA
*
34326588 AAAATATTAATAATTACTAAAT
1 AAAATATTAATAATAACTAAAT
34326610 AAAATATT-ATAA-AACTAAAAT
1 AAAATATTAATAATAACT-AAAT
34326631 AAA
1 AAA
34326634 GAAAAAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 3 0.14
21 11 0.50
22 8 0.36
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.30
Consensus pattern (22 bp):
AAAATATTAATAATAACTAAAT
Found at i:34329772 original size:24 final size:24
Alignment explanation
Indices: 34329727--34329773 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
34329717 TCTCATGAAA
* *
34329727 ATATAATAAAATATTAAGAAAAAC
1 ATATAATAAAATATAAAAAAAAAC
**
34329751 ATATAATAACTTATAAAAAAAAA
1 ATATAATAAAATATAAAAAAAAA
34329774 TGATCAATAC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.68, C:0.04, G:0.02, T:0.26
Consensus pattern (24 bp):
ATATAATAAAATATAAAAAAAAAC
Found at i:34349072 original size:46 final size:45
Alignment explanation
Indices: 34349008--34349174 Score: 169
Period size: 46 Copynumber: 3.6 Consensus size: 45
34348998 ACAACTCGTA
* *
34349008 GCCGATGCATGTCCCAGACATGTTTTACACTGGCTTACGTCTCAAG
1 GCCGATGCATGTCACAGACATGTCTTACACTGGCTT-CGTCTCAAG
* * * *
34349054 GCCGATGCATGTCTCAGACATGTCTTACACTAGCATTCGTCTTAAT
1 GCCGATGCATGTCACAGACATGTCTTACACTGGC-TTCGTCTCAAG
34349100 GCCGATGCCATGTCACAGACATGGTCTTACACTGGC-TC-TCAT-AATGTG
1 GCCGATG-CATGTCACAGACAT-GTCTTACACTGGCTTCGTC-TCAA---G
* *
34349148 GCTGATGCATGTCCCAGACATGTCTTA
1 GCCGATGCATGTCACAGACATGTCTTA
34349175 TATTAGCTCA
Statistics
Matches: 104, Mismatches: 10, Indels: 14
0.81 0.08 0.11
Matches are distributed among these distances:
45 4 0.04
46 54 0.52
47 28 0.27
48 18 0.17
ACGTcount: A:0.23, C:0.27, G:0.21, T:0.29
Consensus pattern (45 bp):
GCCGATGCATGTCACAGACATGTCTTACACTGGCTTCGTCTCAAG
Found at i:34357388 original size:47 final size:47
Alignment explanation
Indices: 34357336--34357589 Score: 207
Period size: 46 Copynumber: 5.4 Consensus size: 47
34357326 CGATGTCATA
* * *
34357336 TCCCAGATATGGTCTTACACTGGCTCACATCTC-AAGTCGATGCCATG
1 TCCCAGACATGGTCTTACACTGGCTCACATCTCGAAGCCAATG-CATG
* * * * *
34357383 GCCCAGACATGGTCTTACACTGACT-ATCATATCGTAGCCGATGCATG
1 TCCCAGACATGGTCTTACACTGGCTCA-CATCTCGAAGCCAATGCATG
* * *
34357430 TCCCAGACAT-GTCTTACACTGGCTTACGTCTCGAGGCCAATGCATG
1 TCCCAGACATGGTCTTACACTGGCTCACATCTCGAAGCCAATGCATG
* * * * * *
34357476 TCCCATACAT-GTTTTACACTAGTTCTCGTCTC-AATGCCAATGCCATG
1 TCCCAGACATGGTCTTACACTGGCTCACATCTCGAA-GCCAATG-CATG
* * ** **
34357523 TCCCAGACATGGTCTTACACTGGCTCTCATAAT-GTGGCTGATGCATG
1 TCCCAGACATGGTCTTACACTGGCTCACAT-CTCGAAGCCAATGCATG
34357570 TCCCAGACAT-GTCTTACACT
1 TCCCAGACATGGTCTTACACT
34357590 AGTCAACAGT
Statistics
Matches: 169, Mismatches: 30, Indels: 17
0.78 0.14 0.08
Matches are distributed among these distances:
45 1 0.01
46 72 0.43
47 68 0.40
48 27 0.16
49 1 0.01
ACGTcount: A:0.23, C:0.29, G:0.19, T:0.29
Consensus pattern (47 bp):
TCCCAGACATGGTCTTACACTGGCTCACATCTCGAAGCCAATGCATG
Found at i:34357473 original size:46 final size:47
Alignment explanation
Indices: 34357324--34357589 Score: 208
Period size: 47 Copynumber: 5.7 Consensus size: 47
34357314 TGGGTAAAGT
* * * *
34357324 GCCGATGTCATATCCCAGATATGGTCTTACACTGGCTCACATCTC-AA
1 GCCGATG-CATGTCCCAGACATGGTCTTACACTGGCTTACATCTCGAG
* * * *
34357371 GTCGATGCCATGGCCCAGACATGGTCTTACACTGAC-TATCATATCGTA-
1 GCCGATG-CATGTCCCAGACATGGTCTTACACTGGCTTA-CATCTCG-AG
*
34357419 GCCGATGCATGTCCCAGACAT-GTCTTACACTGGCTTACGTCTCGAG
1 GCCGATGCATGTCCCAGACATGGTCTTACACTGGCTTACATCTCGAG
* * * * * * * *
34357465 GCCAATGCATGTCCCATACAT-GTTTTACACTAG-TTCTCGTCTCAAT
1 GCCGATGCATGTCCCAGACATGGTCTTACACTGGCTT-ACATCTCGAG
* * *
34357511 GCCAATGCCATGTCCCAGACATGGTCTTACACTGGCTCT-CATAAT-GTG
1 GCCGATG-CATGTCCCAGACATGGTCTTACACTGGCT-TACAT-CTCGAG
*
34357559 GCTGATGCATGTCCCAGACAT-GTCTTACACT
1 GCCGATGCATGTCCCAGACATGGTCTTACACT
34357590 AGTCAACAGT
Statistics
Matches: 178, Mismatches: 30, Indels: 23
0.77 0.13 0.10
Matches are distributed among these distances:
45 3 0.02
46 71 0.40
47 77 0.43
48 23 0.13
49 3 0.02
50 1 0.01
ACGTcount: A:0.23, C:0.29, G:0.19, T:0.29
Consensus pattern (47 bp):
GCCGATGCATGTCCCAGACATGGTCTTACACTGGCTTACATCTCGAG
Found at i:34357486 original size:93 final size:94
Alignment explanation
Indices: 34357323--34357548 Score: 228
Period size: 93 Copynumber: 2.4 Consensus size: 94
34357313 GTGGGTAAAG
* * * * *
34357323 TGCCGATGTCATATCCCAGATATGGTCTTACACTGGCTCACATCTCAAGTCGATGCCATGGCCCA
1 TGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCACATCTCAAGCCAATGCCATGGCCCA
*
34357388 GACATGGTCTTACACT-GACTATCATATC-G
66 GACAT-GTCTTACACTAG-CTATCATATCAA
* * * *
34357417 TAGCCGATG-CATGTCCCAGACAT-GTCTTACACTGGCTTACGTCTCGAGGCCAATG-CATGTCC
1 T-GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCACATCTC-AAGCCAATGCCATGGCC
* * * * * *
34357479 CATACATGTTTTACACTAGTTCTCGTCTCAA
64 CAGACATGTCTTACACTAGCTATCATATCAA
*
34357510 TGCCAATGCCATGTCCCAGACATGGTCTTACACTGGCTC
1 TGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTC
34357549 TCATAATGTG
Statistics
Matches: 109, Mismatches: 17, Indels: 12
0.79 0.12 0.09
Matches are distributed among these distances:
92 21 0.19
93 48 0.44
94 33 0.30
95 7 0.06
ACGTcount: A:0.23, C:0.30, G:0.19, T:0.28
Consensus pattern (94 bp):
TGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCACATCTCAAGCCAATGCCATGGCCCA
GACATGTCTTACACTAGCTATCATATCAA
Found at i:34359651 original size:95 final size:94
Alignment explanation
Indices: 34359528--34359702 Score: 255
Period size: 95 Copynumber: 1.9 Consensus size: 94
34359518 CATATCTGTG
* * *
34359528 CCGATGCCATGTCCCAGACATGTCTTACACTGGCT-TACGT-CTCGAGGCCGATGCATGTCCCAT
1 CCGATGCCATGTCCCAGACATGTCTTACACTGGCTCT-CATAAT-GAGGCCGATGCATGTCCCAA
34359591 ACATGTCTTACACTAGCACTTGTCTTAAATA
64 ACATGTCTTACACTAGCACTTGTCTTAAATA
* * *
34359622 CCGATGCCATGTCCCAGGCATGGTCTTACACTGGCTCTCATAATGTGGCTGATGCATGTCCCAAA
1 CCGATGCCATGTCCCAGACAT-GTCTTACACTGGCTCTCATAATGAGGCCGATGCATGTCCCAAA
34359687 CATGTCTTACACTAGC
65 CATGTCTTACACTAGC
34359703 TCACAATAAC
Statistics
Matches: 72, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
94 20 0.28
95 50 0.69
96 2 0.03
ACGTcount: A:0.23, C:0.30, G:0.19, T:0.28
Consensus pattern (94 bp):
CCGATGCCATGTCCCAGACATGTCTTACACTGGCTCTCATAATGAGGCCGATGCATGTCCCAAAC
ATGTCTTACACTAGCACTTGTCTTAAATA
Found at i:34361593 original size:27 final size:28
Alignment explanation
Indices: 34361555--34361609 Score: 103
Period size: 27 Copynumber: 2.0 Consensus size: 28
34361545 TCCTTTTGTA
34361555 AATTATGGATGTTAATT-TTAGTACTTT
1 AATTATGGATGTTAATTCTTAGTACTTT
34361582 AATTATGGATGTTAATTCTTAGTACTTT
1 AATTATGGATGTTAATTCTTAGTACTTT
34361610 TGATCTTAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
27 17 0.63
28 10 0.37
ACGTcount: A:0.29, C:0.05, G:0.15, T:0.51
Consensus pattern (28 bp):
AATTATGGATGTTAATTCTTAGTACTTT
Found at i:34362187 original size:40 final size:40
Alignment explanation
Indices: 34362142--34362242 Score: 114
Period size: 40 Copynumber: 2.5 Consensus size: 40
34362132 TTAACAATTG
*
34362142 CCAAAATTTCTATGACTTTACCAA-ATAATCCAATGATTTA
1 CCAAAATTTCTATGACTTTACCAAGAT-ATCCAACGATTTA
* ** *
34362182 CCAAAATATCTAAAACTTTACCAAGATATCTAACGATTTA
1 CCAAAATTTCTATGACTTTACCAAGATATCCAACGATTTA
* *
34362222 CCAGAATTTCTAATGAATTTA
1 CCAAAATTTCT-ATGACTTTA
34362243 TCAATATTTA
Statistics
Matches: 49, Mismatches: 10, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
40 41 0.84
41 8 0.16
ACGTcount: A:0.42, C:0.19, G:0.06, T:0.34
Consensus pattern (40 bp):
CCAAAATTTCTATGACTTTACCAAGATATCCAACGATTTA
Found at i:34362221 original size:20 final size:18
Alignment explanation
Indices: 34362158--34362403 Score: 93
Period size: 20 Copynumber: 12.4 Consensus size: 18
34362148 TTTCTATGAC
*
34362158 TTTACCAAATAATCCAATGA
1 TTTACCAAAT-ATCTAA-GA
*
34362178 TTTACCAAAATATCTAAAA
1 TTTACC-AAATATCTAAGA
34362197 CTTTACCAAGATATCTAACGA
1 -TTTACCAA-ATATCTAA-GA
*
34362218 TTTACCAGAATTTCTAATGAA
1 TTTACCA-AATATCTAA-G-A
* * * *
34362239 TTTATCAATATTTATAAGC
1 TTTACCAA-ATATCTAAGA
34362258 TTATACCAAA-AGTCTTATAGA
1 TT-TACCAAATA-TC-TA-AGA
* **
34362279 -TTACCACAATTTCTATTA
1 TTTACCA-AATATCTAAGA
*
34362297 CTTTACCAAAAATCTAAAGGA
1 -TTTACCAAATATCT-AA-GA
34362318 -TTACCAAATTATCTAAGA
1 TTTACCAAA-TATCTAAGA
*
34362336 TTTTACCAATATTTCTAAGGA
1 -TTTACCAA-ATATCTAA-GA
* *
34362357 TTTACCAAATTATATAAAA
1 TTTACCAAA-TATCTAAGA
* *
34362376 CTTTACCTGAATTTCTAACGA
1 -TTTACC-AAATATCTAA-GA
34362397 TTTACCA
1 TTTACCA
34362404 TTACTTTTAA
Statistics
Matches: 171, Mismatches: 29, Indels: 53
0.68 0.11 0.21
Matches are distributed among these distances:
18 3 0.02
19 31 0.18
20 108 0.63
21 29 0.17
ACGTcount: A:0.41, C:0.17, G:0.06, T:0.36
Consensus pattern (18 bp):
TTTACCAAATATCTAAGA
Found at i:34362364 original size:40 final size:40
Alignment explanation
Indices: 34362296--34362403 Score: 114
Period size: 40 Copynumber: 2.7 Consensus size: 40
34362286 AATTTCTATT
** * *
34362296 ACTTTACC-AAAAATCTAAAGGA-TTACCAAATTATCTAAG
1 ACTTTACCTAAATTTCT-AAGGATTTACCAAATTATATAAA
*
34362335 ATTTTACC-AATATTTCTAAGGATTTACCAAATTATATAAA
1 ACTTTACCTAA-ATTTCTAAGGATTTACCAAATTATATAAA
* *
34362375 ACTTTACCTGAATTTCTAACGATTTACCA
1 ACTTTACCTAAATTTCTAAGGATTTACCA
34362404 TTACTTTTAA
Statistics
Matches: 58, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
39 14 0.24
40 43 0.74
41 1 0.02
ACGTcount: A:0.41, C:0.18, G:0.06, T:0.35
Consensus pattern (40 bp):
ACTTTACCTAAATTTCTAAGGATTTACCAAATTATATAAA
Found at i:34362615 original size:20 final size:20
Alignment explanation
Indices: 34362553--34362705 Score: 79
Period size: 20 Copynumber: 7.7 Consensus size: 20
34362543 GTCTTACCAA
*
34362553 TTACCAAAATTT-TTATAACT
1 TTACCAAAATTTCTTA-GACT
* *
34362573 TTATCAAAATAT-TTA-ACGAT
1 TTACCAAAATTTCTTAGAC--T
34362593 TTACCAAAATTTCTTAGACT
1 TTACCAAAATTTCTTAGACT
* *
34362613 TTACTC-AAATATCTAAG-CT
1 TTAC-CAAAATTTCTTAGACT
*
34362632 TTACCAAATTTTCTTAGGA-T
1 TTACCAAAATTTCTTA-GACT
* *
34362652 TTACCAAAATATCTAATGA-T
1 TTACCAAAATTTCTTA-GACT
* * *
34362672 TTA-CAAGAATTTCTAACAAT
1 TTACCAA-AATTTCTTAGACT
*
34362692 TTACCAATATTTCT
1 TTACCAAAATTTCT
34362706 AGGCATATAT
Statistics
Matches: 106, Mismatches: 16, Indels: 22
0.74 0.11 0.15
Matches are distributed among these distances:
18 3 0.03
19 17 0.16
20 77 0.73
21 7 0.07
22 2 0.02
ACGTcount: A:0.39, C:0.16, G:0.05, T:0.41
Consensus pattern (20 bp):
TTACCAAAATTTCTTAGACT
Found at i:34362645 original size:39 final size:41
Alignment explanation
Indices: 34362553--34362675 Score: 134
Period size: 39 Copynumber: 3.1 Consensus size: 41
34362543 GTCTTACCAA
*
34362553 TTACCAAAATTTT-TATA-ACTTTA-TCAAAATATTTAACGAT
1 TTACC-AAATTTTCT-TAGACTTTACTCAAAATATCTAACGAT
* *
34362593 TTACCAAAATTTCTTAGACTTTACTC-AAATATCTAA-GCT
1 TTACCAAATTTTCTTAGACTTTACTCAAAATATCTAACGAT
*
34362632 TTACCAAATTTTCTTAGGA-TTTAC-CAAAATATCTAATGAT
1 TTACCAAATTTTCTTA-GACTTTACTCAAAATATCTAACGAT
34362672 TTAC
1 TTAC
34362676 AAGAATTTCT
Statistics
Matches: 72, Mismatches: 5, Indels: 12
0.81 0.06 0.13
Matches are distributed among these distances:
38 1 0.01
39 40 0.56
40 29 0.40
41 2 0.03
ACGTcount: A:0.38, C:0.16, G:0.05, T:0.41
Consensus pattern (41 bp):
TTACCAAATTTTCTTAGACTTTACTCAAAATATCTAACGAT
Found at i:34362723 original size:20 final size:20
Alignment explanation
Indices: 34362679--34362747 Score: 70
Period size: 20 Copynumber: 3.5 Consensus size: 20
34362669 GATTTACAAG
*
34362679 AATTTCTAA-CAATTTACC-A
1 AATTTCTAAGC-ATATACCGA
* *
34362698 ATATTTCTAGGCATATATCGA
1 A-ATTTCTAAGCATATACCGA
*
34362719 AATTTCTAAGCCTATACCGA
1 AATTTCTAAGCATATACCGA
34362739 AATTTCTAA
1 AATTTCTAA
34362748 AATTTCTCTG
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
19 1 0.02
20 37 0.90
21 3 0.07
ACGTcount: A:0.38, C:0.19, G:0.07, T:0.36
Consensus pattern (20 bp):
AATTTCTAAGCATATACCGA
Found at i:34362877 original size:29 final size:29
Alignment explanation
Indices: 34362833--34362903 Score: 124
Period size: 29 Copynumber: 2.4 Consensus size: 29
34362823 AACACTTTAC
*
34362833 CAAAATATCTAGGAGTTTACTAATATTTT
1 CAAAATATCTAAGAGTTTACTAATATTTT
34362862 CAAAATATCTAAGAGTTTACTAATATTTT
1 CAAAATATCTAAGAGTTTACTAATATTTT
*
34362891 CAAAATTTCTAAG
1 CAAAATATCTAAG
34362904 CACATACCAA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.41, C:0.11, G:0.08, T:0.39
Consensus pattern (29 bp):
CAAAATATCTAAGAGTTTACTAATATTTT
Found at i:34363381 original size:20 final size:20
Alignment explanation
Indices: 34363350--34363438 Score: 81
Period size: 20 Copynumber: 4.5 Consensus size: 20
34363340 TACCATGTCT
*
34363350 TAACAA-TTATCAAAATATC
1 TAACAATTTATCAAAATTTC
**
34363369 TAACAATTTATCACTATTTC
1 TAACAATTTATCAAAATTTC
** * * *
34363389 TAGTACTTTATCAATATTTT
1 TAACAATTTATCAAAATTTC
*
34363409 TAACAATTTATCAAAATTTG
1 TAACAATTTATCAAAATTTC
*
34363429 TAATAATTTA
1 TAACAATTTA
34363439 CTGTTATTTA
Statistics
Matches: 55, Mismatches: 14, Indels: 1
0.79 0.20 0.01
Matches are distributed among these distances:
19 6 0.11
20 49 0.89
ACGTcount: A:0.42, C:0.12, G:0.02, T:0.44
Consensus pattern (20 bp):
TAACAATTTATCAAAATTTC
Found at i:34365555 original size:15 final size:16
Alignment explanation
Indices: 34365523--34365560 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
34365513 AAAAAGGTTT
34365523 TTTTATATTTTTAATAA
1 TTTTA-ATTTTTAATAA
*
34365540 TTTTAATTTTT-TTAA
1 TTTTAATTTTTAATAA
34365555 TTTTAA
1 TTTTAA
34365561 AAATAATTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 9 0.45
16 6 0.30
17 5 0.25
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
TTTTAATTTTTAATAA
Found at i:34365830 original size:25 final size:25
Alignment explanation
Indices: 34365800--34365910 Score: 84
Period size: 26 Copynumber: 4.2 Consensus size: 25
34365790 TGTATTATAA
*
34365800 ATTT-AATATTTATTAAAGATATTTT
1 ATTTAAATATTTAATAAA-ATATTTT
34365825 ATTTAAATATTTAATAAAATATTTT
1 ATTTAAATATTTAATAAAATATTTT
* *
34365850 ATTTTGAAACAAATT--TAAAATATTTGT
1 A-TTT-AAA-TATTTAATAAAATATTT-T
34365877 ATTTAATAATATTTAAAATAAAATATTTGT
1 ATTT-A-AATATTT--AATAAAATATTT-T
34365907 ATTT
1 ATTT
34365911 TATTAAATTT
Statistics
Matches: 70, Mismatches: 6, Indels: 15
0.77 0.07 0.16
Matches are distributed among these distances:
25 12 0.17
26 32 0.46
27 7 0.10
28 3 0.04
30 16 0.23
ACGTcount: A:0.45, C:0.01, G:0.04, T:0.50
Consensus pattern (25 bp):
ATTTAAATATTTAATAAAATATTTT
Found at i:34365835 original size:26 final size:24
Alignment explanation
Indices: 34365800--34365853 Score: 81
Period size: 25 Copynumber: 2.2 Consensus size: 24
34365790 TGTATTATAA
*
34365800 ATTTAATATTTATTAAAGATATTTT
1 ATTTAATATTTAATAAA-ATATTTT
34365825 ATTTAAATATTTAATAAAATATTTT
1 ATTT-AATATTTAATAAAATATTTT
34365850 ATTT
1 ATTT
34365854 TGAAACAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 15 0.56
26 12 0.44
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56
Consensus pattern (24 bp):
ATTTAATATTTAATAAAATATTTT
Found at i:34365850 original size:13 final size:12
Alignment explanation
Indices: 34365804--34365848 Score: 54
Period size: 12 Copynumber: 3.6 Consensus size: 12
34365794 TTATAAATTT
34365804 AATATTTATTAA
1 AATATTTATTAA
*
34365816 AGATATTTTATTTA
1 A-ATA-TTTATTAA
*
34365830 AATATTTAATAA
1 AATATTTATTAA
34365842 AATATTT
1 AATATTT
34365849 TATTTTGAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
12 14 0.50
13 6 0.21
14 8 0.29
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (12 bp):
AATATTTATTAA
Found at i:34370785 original size:31 final size:31
Alignment explanation
Indices: 34370750--34370816 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 31
34370740 CTTTTTGCAT
* *
34370750 TAAAATCCAACCAAATACAACAAATATAGTA
1 TAAAATCCAACCAAAAACAACAAATATAGCA
* * * *
34370781 TAAAATGCAGCCAAAAACATCAAATTTAGCA
1 TAAAATCCAACCAAAAACAACAAATATAGCA
34370812 TAAAA
1 TAAAA
34370817 AATACAACAA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.57, C:0.18, G:0.06, T:0.19
Consensus pattern (31 bp):
TAAAATCCAACCAAAAACAACAAATATAGCA
Found at i:34371077 original size:21 final size:21
Alignment explanation
Indices: 34371064--34371139 Score: 109
Period size: 21 Copynumber: 3.6 Consensus size: 21
34371054 TCTGCTGCCA
34371064 TCGCTGCTGCCTCTGCCTCCC
1 TCGCTGCTGCCTCTGCCTCCC
*
34371085 TCACT-CGTGCCTCTGCCTCCC
1 TCGCTGC-TGCCTCTGCCTCCC
*
34371106 TCGCTGCTGCCGCTGCCTCCC
1 TCGCTGCTGCCTCTGCCTCCC
*
34371127 TCTCTGCTGCCTC
1 TCGCTGCTGCCTC
34371140 CGCTCTAAGT
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
20 1 0.02
21 46 0.96
22 1 0.02
ACGTcount: A:0.01, C:0.51, G:0.18, T:0.29
Consensus pattern (21 bp):
TCGCTGCTGCCTCTGCCTCCC
Found at i:34371578 original size:13 final size:14
Alignment explanation
Indices: 34371553--34371581 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
34371543 TGATGAATTG
34371553 AATTAAACAATTAT
1 AATTAAACAATTAT
34371567 AATTAAAC-ATTAT
1 AATTAAACAATTAT
34371580 AA
1 AA
34371582 ATATTTTGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.34
Consensus pattern (14 bp):
AATTAAACAATTAT
Found at i:34374121 original size:39 final size:39
Alignment explanation
Indices: 34374000--34374104 Score: 183
Period size: 39 Copynumber: 2.7 Consensus size: 39
34373990 GAGATTGGAA
34374000 ATATCCGGACATGAGATCCGCAGGCTATATGCTAGAAAT
1 ATATCCGGACATGAGATCCGCAGGCTATATGCTAGAAAT
34374039 ATATCCGGACATGAGATCCGCAGGCTATATGCTAGAAAT
1 ATATCCGGACATGAGATCCGCAGGCTATATGCTAGAAAT
* * *
34374078 ATATCTGGACTTGAGGTCCGCAGGCTA
1 ATATCCGGACATGAGATCCGCAGGCTA
34374105 CGTGCTGGGA
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 63 1.00
ACGTcount: A:0.30, C:0.21, G:0.25, T:0.24
Consensus pattern (39 bp):
ATATCCGGACATGAGATCCGCAGGCTATATGCTAGAAAT
Found at i:34374352 original size:2 final size:2
Alignment explanation
Indices: 34374347--34374376 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
34374337 TATATATATA
*
34374347 TG TG TG TG TG TA TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
34374377 CGAATGAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.03, C:0.00, G:0.47, T:0.50
Consensus pattern (2 bp):
TG
Found at i:34380200 original size:9 final size:9
Alignment explanation
Indices: 34380186--34380421 Score: 212
Period size: 9 Copynumber: 26.7 Consensus size: 9
34380176 TATTTAAGTA
34380186 TTATGTAAG
1 TTATGTAAG
34380195 TTATGTAAG
1 TTATGTAAG
*
34380204 TTATGATATG
1 TTATG-TAAG
* * *
34380214 ATATAT-AT
1 TTATGTAAG
34380222 TTATGTAAG
1 TTATGTAAG
* *
34380231 TTATAT-AT
1 TTATGTAAG
*
34380239 TTATCTAAG
1 TTATGTAAG
*
34380248 TTATATAAG
1 TTATGTAAG
34380257 TTATGTAAG
1 TTATGTAAG
34380266 TTATGTAAG
1 TTATGTAAG
*
34380275 TTATAT-AG
1 TTATGTAAG
**
34380283 TTATCAAAG
1 TTATGTAAG
* *
34380292 TTATATCAG
1 TTATGTAAG
*
34380301 TTATATAAG
1 TTATGTAAG
34380310 TTATGTAAG
1 TTATGTAAG
*
34380319 TTATATAAG
1 TTATGTAAG
* *
34380328 TTATAT-AT
1 TTATGTAAG
*
34380336 TTATCTAAG
1 TTATGTAAG
*
34380345 TTATATAAG
1 TTATGTAAG
34380354 TTATGTAAG
1 TTATGTAAG
34380363 TTATGTAAG
1 TTATGTAAG
* *
34380372 TTATAT-AT
1 TTATGTAAG
*
34380380 TTATCTAAG
1 TTATGTAAG
*
34380389 TTATATAAG
1 TTATGTAAG
34380398 TTATGTAAG
1 TTATGTAAG
*
34380407 TTTTGTAAG
1 TTATGTAAG
34380416 TTATGT
1 TTATGT
34380422 TAAATATTTA
Statistics
Matches: 185, Mismatches: 36, Indels: 12
0.79 0.15 0.05
Matches are distributed among these distances:
8 28 0.15
9 151 0.82
10 6 0.03
ACGTcount: A:0.36, C:0.02, G:0.14, T:0.47
Consensus pattern (9 bp):
TTATGTAAG
Found at i:34380257 original size:53 final size:51
Alignment explanation
Indices: 34380186--34380401 Score: 217
Period size: 44 Copynumber: 4.4 Consensus size: 51
34380176 TATTTAAGTA
* * *
34380186 TTATGTAAGTTATGTAAGTTATGATATGATATATATTTATGTAAGTTATATAT
1 TTATCTAAGTTATATAAGTTAT-ATATG-TATATAGTTATGTAAGTTATATAT
*
34380239 TTATCTAAGTTATATAAG---T-TATG--TA-AGTTATGTAAGTTATATAG
1 TTATCTAAGTTATATAAGTTATATATGTATATAGTTATGTAAGTTATATAT
* * * * *
34380283 TTATCAAAGTTATATCAGTTATATAAGTTATGTAAGTTATATAAGTTATATAT
1 TTATCTAAGTTATATAAGTTATATATG-TATAT-AGTTATGTAAGTTATATAT
34380336 TTATCTAAGTTATATAAG---T-TATG--TA-AGTTATGTAAGTTATATAT
1 TTATCTAAGTTATATAAGTTATATATGTATATAGTTATGTAAGTTATATAT
34380380 TTATCTAAGTTATATAAGTTAT
1 TTATCTAAGTTATATAAGTTAT
34380402 GTAAGTTTTG
Statistics
Matches: 136, Mismatches: 15, Indels: 30
0.75 0.08 0.17
Matches are distributed among these distances:
44 69 0.51
45 2 0.01
46 1 0.01
47 2 0.01
48 7 0.05
49 3 0.02
50 2 0.01
51 1 0.01
53 49 0.36
ACGTcount: A:0.37, C:0.02, G:0.13, T:0.47
Consensus pattern (51 bp):
TTATCTAAGTTATATAAGTTATATATGTATATAGTTATGTAAGTTATATAT
Found at i:34380270 original size:44 final size:44
Alignment explanation
Indices: 34380222--34380419 Score: 288
Period size: 44 Copynumber: 4.3 Consensus size: 44
34380212 TGATATATAT
34380222 TTATGTAAGTTATATATTTATCTAAGTTATATAAGTTATGTAAG
1 TTATGTAAGTTATATATTTATCTAAGTTATATAAGTTATGTAAG
*
34380266 TTATGTAAGTTATATAGTTATCAAAGTTATATCAGTTATATAAGTTATGTAAG
1 TTATGTAAGTTATATA-TT-T---A--TCTA--AGTTATATAAGTTATGTAAG
*
34380319 TTATATAAGTTATATATTTATCTAAGTTATATAAGTTATGTAAG
1 TTATGTAAGTTATATATTTATCTAAGTTATATAAGTTATGTAAG
34380363 TTATGTAAGTTATATATTTATCTAAGTTATATAAGTTATGTAAG
1 TTATGTAAGTTATATATTTATCTAAGTTATATAAGTTATGTAAG
*
34380407 TTTTGTAAGTTAT
1 TTATGTAAGTTAT
34380420 GTTAAATATT
Statistics
Matches: 140, Mismatches: 5, Indels: 18
0.86 0.03 0.11
Matches are distributed among these distances:
44 91 0.65
45 2 0.01
46 4 0.03
48 1 0.01
49 1 0.01
51 4 0.03
52 2 0.01
53 35 0.25
ACGTcount: A:0.36, C:0.03, G:0.14, T:0.47
Consensus pattern (44 bp):
TTATGTAAGTTATATATTTATCTAAGTTATATAAGTTATGTAAG
Found at i:34380407 original size:53 final size:53
Alignment explanation
Indices: 34380186--34380421 Score: 255
Period size: 53 Copynumber: 4.5 Consensus size: 53
34380176 TATTTAAGTA
* * * * * *
34380186 TTATGTAAGTTATGTAAGTTATGATATGATATAT-ATTTATGTAAGTTATAT-AT
1 TTATATAAGTTATGTAAGTTATG-TAAGTTATATAAGTTATAT-AGTTATATAAG
* * *
34380239 TTATCTAAGTTATATAAGTTATGTAAGTTATGTAAGTTATATAGTTATCA-AAG
1 TTATATAAGTTATGTAAGTTATGTAAGTTATATAAGTTATATAGTTAT-ATAAG
* * * *
34380292 TTATATCAGTTATATAAGTTATGTAAGTTATATAAGTTATATATTTATCTAAG
1 TTATATAAGTTATGTAAGTTATGTAAGTTATATAAGTTATATAGTTATATAAG
* *
34380345 TTATATAAGTTATGTAAGTTATGTAAGTTATAT-ATTTATCTAAGTTATATAAG
1 TTATATAAGTTATGTAAGTTATGTAAGTTATATAAGTTATAT-AGTTATATAAG
* *
34380398 TTATGTAAGTTTTGTAAGTTATGT
1 TTATATAAGTTATGTAAGTTATGT
34380422 TAAATATTTA
Statistics
Matches: 157, Mismatches: 21, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
52 19 0.12
53 138 0.88
ACGTcount: A:0.36, C:0.02, G:0.14, T:0.47
Consensus pattern (53 bp):
TTATATAAGTTATGTAAGTTATGTAAGTTATATAAGTTATATAGTTATATAAG
Found at i:34380551 original size:15 final size:15
Alignment explanation
Indices: 34380531--34380615 Score: 95
Period size: 14 Copynumber: 5.9 Consensus size: 15
34380521 GTAAGTTGCG
34380531 AATTAAATAATATTT
1 AATTAAATAATATTT
34380546 AATTAAATAATATTT
1 AATTAAATAATATTT
* *
34380561 -ATAAAATTAT-TTT
1 AATTAAATAATATTT
*
34380574 AATTAAATAATATTG
1 AATTAAATAATATTT
** *
34380589 AAAAAAATTAT-TTT
1 AATTAAATAATATTT
34380603 AATTAAATAATAT
1 AATTAAATAATAT
34380616 AATGTCGTTC
Statistics
Matches: 55, Mismatches: 12, Indels: 6
0.75 0.16 0.08
Matches are distributed among these distances:
13 3 0.05
14 26 0.47
15 26 0.47
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (15 bp):
AATTAAATAATATTT
Found at i:34380574 original size:28 final size:29
Alignment explanation
Indices: 34380543--34380615 Score: 121
Period size: 29 Copynumber: 2.6 Consensus size: 29
34380533 TTAAATAATA
* *
34380543 TTTAATTAAATAATATT-TATAAAATTAT
1 TTTAATTAAATAATATTGAAAAAAATTAT
34380571 TTTAATTAAATAATATTGAAAAAAATTAT
1 TTTAATTAAATAATATTGAAAAAAATTAT
34380600 TTTAATTAAATAATAT
1 TTTAATTAAATAATAT
34380616 AATGTCGTTC
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
28 17 0.40
29 25 0.60
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (29 bp):
TTTAATTAAATAATATTGAAAAAAATTAT
Found at i:34380820 original size:24 final size:24
Alignment explanation
Indices: 34380788--34380834 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
34380778 TTAACTTAAA
* *
34380788 TGATAAAACGGACGATAATATTTG
1 TGATAAAACAGACGAGAATATTTG
34380812 TGATAAAACAGACGAGAATATTT
1 TGATAAAACAGACGAGAATATTT
34380835 TAATAATAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.45, C:0.09, G:0.19, T:0.28
Consensus pattern (24 bp):
TGATAAAACAGACGAGAATATTTG
Found at i:34381089 original size:64 final size:64
Alignment explanation
Indices: 34380882--34381079 Score: 342
Period size: 64 Copynumber: 3.1 Consensus size: 64
34380872 ATATTTTATT
* * *
34380882 AAATATTTGTATATTAGATGGGATATATAATATTAATAAATAAATTTATTAAAAATTGTGATAG
1 AAATATTTGTATATTAGATGGGACATATTATATTAATAAATAAATTTATTAAAAATCGTGATAG
* *
34380946 AAATATTTGTATATTAGATGTGACATATTATATTAATGAATAAATTTATTAAAAATCGTGATAG
1 AAATATTTGTATATTAGATGGGACATATTATATTAATAAATAAATTTATTAAAAATCGTGATAG
*
34381010 AAATATTTGTATATTAGATGGGACATATTATATCAATAAATAAATTTATTAAAAATCGTGATAG
1 AAATATTTGTATATTAGATGGGACATATTATATTAATAAATAAATTTATTAAAAATCGTGATAG
34381074 AAATAT
1 AAATAT
34381080 AGAAATATTA
Statistics
Matches: 126, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
64 126 1.00
ACGTcount: A:0.46, C:0.03, G:0.12, T:0.39
Consensus pattern (64 bp):
AAATATTTGTATATTAGATGGGACATATTATATTAATAAATAAATTTATTAAAAATCGTGATAG
Found at i:34381879 original size:40 final size:40
Alignment explanation
Indices: 34381835--34381931 Score: 176
Period size: 40 Copynumber: 2.4 Consensus size: 40
34381825 AAACAGATTA
*
34381835 AAAAAGCAAAAAGCAAAAAGCAATTGTTACTTATAAACGC
1 AAAAAGCAAAAAGCAAAAAGCAACTGTTACTTATAAACGC
*
34381875 AAAAAGAAAAAAGCAAAAAGCAACTGTTACTTATAAACGC
1 AAAAAGCAAAAAGCAAAAAGCAACTGTTACTTATAAACGC
34381915 AAAAAGCAAAAAGCAAA
1 AAAAAGCAAAAAGCAAA
34381932 TCTATAAACC
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 54 1.00
ACGTcount: A:0.60, C:0.14, G:0.12, T:0.13
Consensus pattern (40 bp):
AAAAAGCAAAAAGCAAAAAGCAACTGTTACTTATAAACGC
Found at i:34382282 original size:21 final size:21
Alignment explanation
Indices: 34382241--34382283 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
34382231 GAAATAAGTC
* *
34382241 AAATATTTATAAACTCTTAAA
1 AAATAATTAAAAACTCTTAAA
34382262 AAATAATTAAAAA-TCTCTAAA
1 AAATAATTAAAAACTCT-TAAA
34382283 A
1 A
34382284 TAAAGATAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 3 0.16
21 16 0.84
ACGTcount: A:0.58, C:0.09, G:0.00, T:0.33
Consensus pattern (21 bp):
AAATAATTAAAAACTCTTAAA
Found at i:34385307 original size:13 final size:13
Alignment explanation
Indices: 34385289--34385322 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
34385279 ACCCAAATAC
34385289 CCTAAACTTTAAA
1 CCTAAACTTTAAA
*
34385302 CCTAAATTTTAAA
1 CCTAAACTTTAAA
34385315 CTCTAAAC
1 C-CTAAAC
34385323 CCTAATTCTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 13 0.72
14 5 0.28
ACGTcount: A:0.44, C:0.24, G:0.00, T:0.32
Consensus pattern (13 bp):
CCTAAACTTTAAA
Found at i:34385460 original size:19 final size:19
Alignment explanation
Indices: 34385436--34385478 Score: 86
Period size: 19 Copynumber: 2.3 Consensus size: 19
34385426 CCTTACCTTA
34385436 AAACCATATATAATACTCT
1 AAACCATATATAATACTCT
34385455 AAACCATATATAATACTCT
1 AAACCATATATAATACTCT
34385474 AAACC
1 AAACC
34385479 TGTACTAAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.49, C:0.23, G:0.00, T:0.28
Consensus pattern (19 bp):
AAACCATATATAATACTCT
Found at i:34386284 original size:40 final size:41
Alignment explanation
Indices: 34386199--34386333 Score: 179
Period size: 40 Copynumber: 3.3 Consensus size: 41
34386189 TGTTTGCTAA
*
34386199 AAAAACGCCGCTACTT-CTCAGTTTTTAGCGGCGTTTGGA-C
1 AAAAACGCCGCTA-TTACTCAGTTTTTAGCGGCGTTTTGAGC
*
34386239 TAAAAACGCCGCTATTACTCAG-TTTTAGCGGCATTTTGAGC
1 -AAAAACGCCGCTATTACTCAGTTTTTAGCGGCGTTTTGAGC
* *
34386280 AAAAACGCCGCTATTACTTAGTTTTTTAGCGGCGTTTTTAG-
1 AAAAACGCCGCTATTACTCAG-TTTTTAGCGGCGTTTTGAGC
34386321 AAAAACGCCGCTA
1 AAAAACGCCGCTA
34386334 ATGCATAATC
Statistics
Matches: 85, Mismatches: 5, Indels: 8
0.87 0.05 0.08
Matches are distributed among these distances:
40 37 0.44
41 32 0.38
42 16 0.19
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.31
Consensus pattern (41 bp):
AAAAACGCCGCTATTACTCAGTTTTTAGCGGCGTTTTGAGC
Found at i:34391987 original size:51 final size:51
Alignment explanation
Indices: 34391917--34392025 Score: 157
Period size: 51 Copynumber: 2.1 Consensus size: 51
34391907 AGCTATAGCA
* *
34391917 TCCATAAACACACCTAGGCACTGAGCG-TCAAGCCCGTAGGCTTCACATCCC
1 TCCAGAAACAAACCTAGGCACTGAGCGCT-AAGCCCGTAGGCTTCACATCCC
* * *
34391968 TCTAGAAACAAACCTAGGCACTGAGTGCTAAGCCTGTAGGCTTCACATCCC
1 TCCAGAAACAAACCTAGGCACTGAGCGCTAAGCCCGTAGGCTTCACATCCC
34392019 TCCAGAA
1 TCCAGAA
34392026 CACACTTGAA
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
51 50 0.98
52 1 0.02
ACGTcount: A:0.29, C:0.33, G:0.18, T:0.19
Consensus pattern (51 bp):
TCCAGAAACAAACCTAGGCACTGAGCGCTAAGCCCGTAGGCTTCACATCCC
Found at i:34395989 original size:2 final size:2
Alignment explanation
Indices: 34395982--34396014 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
34395972 CCTTTCTTCT
*
34395982 TA TA TA TA TA TA TG TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
34396015 AAACAATTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:34399632 original size:7 final size:7
Alignment explanation
Indices: 34399620--34399664 Score: 90
Period size: 7 Copynumber: 6.4 Consensus size: 7
34399610 CGAATCAAAA
34399620 GCAGCAG
1 GCAGCAG
34399627 GCAGCAG
1 GCAGCAG
34399634 GCAGCAG
1 GCAGCAG
34399641 GCAGCAG
1 GCAGCAG
34399648 GCAGCAG
1 GCAGCAG
34399655 GCAGCAG
1 GCAGCAG
34399662 GCA
1 GCA
34399665 AATAGAGAGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 38 1.00
ACGTcount: A:0.29, C:0.29, G:0.42, T:0.00
Consensus pattern (7 bp):
GCAGCAG
Found at i:34404304 original size:49 final size:49
Alignment explanation
Indices: 34404227--34404323 Score: 158
Period size: 49 Copynumber: 2.0 Consensus size: 49
34404217 TCCTCTAAAT
* * *
34404227 ATATTTGAAAAAACTTAGAGATGATTAAGCATACTTGTAGTGGACACAG
1 ATATGTGAAAAAACTTAGAGATAATTAAGCATACTTGTAATGGACACAG
*
34404276 ATATGTGAAAAAACTTGGAGATAATTAAGCATACTTGTAATGGACACA
1 ATATGTGAAAAAACTTAGAGATAATTAAGCATACTTGTAATGGACACA
34404324 TACCCAGTAT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
49 44 1.00
ACGTcount: A:0.42, C:0.10, G:0.20, T:0.28
Consensus pattern (49 bp):
ATATGTGAAAAAACTTAGAGATAATTAAGCATACTTGTAATGGACACAG
Found at i:34409367 original size:12 final size:12
Alignment explanation
Indices: 34409350--34409374 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
34409340 GCCGACTACT
34409350 GTTACTGTTATC
1 GTTACTGTTATC
34409362 GTTACTGTTATC
1 GTTACTGTTATC
34409374 G
1 G
34409375 ATTCGGCATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.16, G:0.20, T:0.48
Consensus pattern (12 bp):
GTTACTGTTATC
Found at i:34409402 original size:45 final size:45
Alignment explanation
Indices: 34409352--34409461 Score: 150
Period size: 45 Copynumber: 2.4 Consensus size: 45
34409342 CGACTACTGT
* *
34409352 TACTGTTA-TCGTTACTGTTATCGATTCGGCATTTTGTGTGTCGAA
1 TACTGTTACT-GTTACTGTTATCGATTCAGCACTTTGTGTGTCGAA
* * * *
34409397 TACTGTTACTGTTACCGTTTTCGATTCAGTACTTTGTGTGTTGAA
1 TACTGTTACTGTTACTGTTATCGATTCAGCACTTTGTGTGTCGAA
34409442 TACTGTTACTGTTACTGTTA
1 TACTGTTACTGTTACTGTTA
34409462 CTGTTACTGT
Statistics
Matches: 56, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
45 55 0.98
46 1 0.02
ACGTcount: A:0.18, C:0.15, G:0.20, T:0.46
Consensus pattern (45 bp):
TACTGTTACTGTTACTGTTATCGATTCAGCACTTTGTGTGTCGAA
Found at i:34409453 original size:6 final size:6
Alignment explanation
Indices: 34409442--34409472 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
34409432 GTGTGTTGAA
34409442 TACTGT TACTGT TACTGT TACTGT TACTGT T
1 TACTGT TACTGT TACTGT TACTGT TACTGT T
34409473 TCAGATTTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.16, C:0.16, G:0.16, T:0.52
Consensus pattern (6 bp):
TACTGT
Found at i:34409851 original size:18 final size:18
Alignment explanation
Indices: 34409648--34409850 Score: 162
Period size: 18 Copynumber: 11.3 Consensus size: 18
34409638 TAACTGATTA
34409648 TTACTGAATAATTGACTG
1 TTACTGAATAATTGACTG
*
34409666 TTACCGAATAATTGACTG
1 TTACTGAATAATTGACTG
* * * *
34409684 TTACTGGACAATAGACTA
1 TTACTGAATAATTGACTG
* * *
34409702 TTACTGAATAACTGAATA
1 TTACTGAATAATTGACTG
*
34409720 TTACTGAATAATTGA-TCA
1 TTACTGAATAATTGACT-G
*
34409738 TTACTGAATAATTGA-TCA
1 TTACTGAATAATTGACT-G
* *
34409756 TTACTGAATAACTGATTG
1 TTACTGAATAATTGACTG
* *
34409774 TCACTGAATAAATGACTG
1 TTACTGAATAATTGACTG
* * *
34409792 TTATTGAATAACTTAATTG
1 TTACTGAATAA-TTGACTG
* *
34409811 CTACTGAAT-ATCTGA-TT
1 TTACTGAATAAT-TGACTG
*
34409828 TTACTAAATAATTGACTG
1 TTACTGAATAATTGACTG
34409846 TTACT
1 TTACT
34409851 AGATAACTGA
Statistics
Matches: 150, Mismatches: 29, Indels: 12
0.79 0.15 0.06
Matches are distributed among these distances:
17 13 0.09
18 125 0.83
19 12 0.08
ACGTcount: A:0.36, C:0.13, G:0.13, T:0.37
Consensus pattern (18 bp):
TTACTGAATAATTGACTG
Found at i:34409925 original size:18 final size:18
Alignment explanation
Indices: 34409902--34409936 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
34409892 ATTGAACAAT
34409902 TGATTGTTACCGAATAAG
1 TGATTGTTACCGAATAAG
*
34409920 TGATTGTTACTGAATAA
1 TGATTGTTACCGAATAA
34409937 ATAATTGTTC
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:0.34, C:0.09, G:0.20, T:0.37
Consensus pattern (18 bp):
TGATTGTTACCGAATAAG
Found at i:34409943 original size:18 final size:18
Alignment explanation
Indices: 34409904--34409949 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
34409894 TGAACAATTG
* * *
34409904 ATTGTTACCGAATAAGTG
1 ATTGTTACTGAATAAATA
34409922 ATTGTTACTGAATAAATA
1 ATTGTTACTGAATAAATA
34409940 ATTGTT-CTGA
1 ATTGTTACTGA
34409950 TTGTTAATGA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
17 4 0.16
18 21 0.84
ACGTcount: A:0.35, C:0.09, G:0.17, T:0.39
Consensus pattern (18 bp):
ATTGTTACTGAATAAATA
Found at i:34411408 original size:57 final size:57
Alignment explanation
Indices: 34411334--34411465 Score: 160
Period size: 57 Copynumber: 2.3 Consensus size: 57
34411324 TCTTTCAGGT
* * *
34411334 TATTTCCATTTTCATTTTGGA-GAAAACCATATTTATTTTCAAATGATT-CAATTTCTC
1 TATTTTCATTTTCATTTT-GATGAAAACCATAATCATTTTCAAATGATTCCAATTT-TC
* * * *
34411391 TGTTTTCATTTTTATTTTGATGAAAATCATAATCATTTTCAAATGATTCCAGTTTTC
1 TATTTTCATTTTCATTTTGATGAAAACCATAATCATTTTCAAATGATTCCAATTTTC
*
34411448 TATTTTTATTTTCATTTT
1 TATTTTCATTTTCATTTT
34411466 CAAAAAAAAA
Statistics
Matches: 63, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
56 2 0.03
57 56 0.89
58 5 0.08
ACGTcount: A:0.27, C:0.13, G:0.07, T:0.53
Consensus pattern (57 bp):
TATTTTCATTTTCATTTTGATGAAAACCATAATCATTTTCAAATGATTCCAATTTTC
Found at i:34411482 original size:57 final size:57
Alignment explanation
Indices: 34411368--34411495 Score: 141
Period size: 57 Copynumber: 2.2 Consensus size: 57
34411358 AACCATATTT
* * * ** ** *
34411368 ATTTTCAAATGATTCAATTTCTCTGTTTTCATTTTTATTTTGATGAAAATCATAATC
1 ATTTTCAAATGATTCAATTTCTCTATTTTCATTTTCATTTTCAAAAAAAAAAAAATC
* *
34411425 ATTTTCAAATGATTCCAGTTT-TCTATTTTTATTTTCATTTTCAAAAAAAAAAAAATC
1 ATTTTCAAATGATT-CAATTTCTCTATTTTCATTTTCATTTTCAAAAAAAAAAAAATC
*
34411482 ATTTCCAAATGATT
1 ATTTTCAAATGATT
34411496 TCTCATTTCT
Statistics
Matches: 59, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
57 54 0.92
58 5 0.08
ACGTcount: A:0.34, C:0.12, G:0.05, T:0.48
Consensus pattern (57 bp):
ATTTTCAAATGATTCAATTTCTCTATTTTCATTTTCATTTTCAAAAAAAAAAAAATC
Found at i:34414247 original size:43 final size:43
Alignment explanation
Indices: 34414186--34414273 Score: 167
Period size: 43 Copynumber: 2.0 Consensus size: 43
34414176 TCAATTTTGG
34414186 ACTCCTAGTGTCATTAGGTTTGCTTTGCTAGATTGATTCTTAC
1 ACTCCTAGTGTCATTAGGTTTGCTTTGCTAGATTGATTCTTAC
*
34414229 ACTCCTAGTGTCATTAGGTTTGCTTTGTTAGATTGATTCTTAC
1 ACTCCTAGTGTCATTAGGTTTGCTTTGCTAGATTGATTCTTAC
34414272 AC
1 AC
34414274 ATTTTGATTT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.19, C:0.18, G:0.18, T:0.44
Consensus pattern (43 bp):
ACTCCTAGTGTCATTAGGTTTGCTTTGCTAGATTGATTCTTAC
Found at i:34416917 original size:27 final size:27
Alignment explanation
Indices: 34416879--34416936 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 27
34416869 GAGTTAATAA
34416879 AATTCTCTTTGAGTTTTTCTTTT-AAAG
1 AATTCTCTTTGAG-TTTTCTTTTGAAAG
*
34416906 AATTC-CTCTTGAGTTTTCTTTTGGAAG
1 AATTCTCT-TTGAGTTTTCTTTTGAAAG
34416933 AATT
1 AATT
34416937 TTAATAATCT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
26 11 0.39
27 17 0.61
ACGTcount: A:0.22, C:0.12, G:0.14, T:0.52
Consensus pattern (27 bp):
AATTCTCTTTGAGTTTTCTTTTGAAAG
Found at i:34417881 original size:47 final size:47
Alignment explanation
Indices: 34417812--34417906 Score: 154
Period size: 47 Copynumber: 2.0 Consensus size: 47
34417802 ATTTATAGAG
* *
34417812 ATAAAATTTAGAATTCTAATTCTAATAGACACCAAAATGCTAAAACT
1 ATAAAATATAGAATTCTAATTCTAATAGACACCAAAATACTAAAACT
* *
34417859 ATAAAATATAGAATTCTAATTCTAATAGGCATCAAAATACTAAAACT
1 ATAAAATATAGAATTCTAATTCTAATAGACACCAAAATACTAAAACT
34417906 A
1 A
34417907 AAATTTTATT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
47 44 1.00
ACGTcount: A:0.51, C:0.14, G:0.06, T:0.29
Consensus pattern (47 bp):
ATAAAATATAGAATTCTAATTCTAATAGACACCAAAATACTAAAACT
Found at i:34419142 original size:19 final size:19
Alignment explanation
Indices: 34419105--34419168 Score: 67
Period size: 21 Copynumber: 3.3 Consensus size: 19
34419095 TTTTTCGATA
* **
34419105 AAAATACATAAGATTTTAT
1 AAAATACATAAAAAATTAT
*
34419124 AAAATACATATAAAATTAT
1 AAAATACATAAAAAATTAT
34419143 AAAAAATACATAAAAAATTA-
1 --AAAATACATAAAAAATTAT
34419163 AAAATA
1 AAAATA
34419169 AATGAATATT
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
18 6 0.16
19 15 0.39
21 17 0.45
ACGTcount: A:0.66, C:0.05, G:0.02, T:0.28
Consensus pattern (19 bp):
AAAATACATAAAAAATTAT
Found at i:34419148 original size:21 final size:20
Alignment explanation
Indices: 34419124--34419166 Score: 68
Period size: 21 Copynumber: 2.1 Consensus size: 20
34419114 AAGATTTTAT
*
34419124 AAAATACATATAAAATTATAA
1 AAAATACATAAAAAATTA-AA
34419145 AAAATACATAAAAAATTAAA
1 AAAATACATAAAAAATTAAA
34419165 AA
1 AA
34419167 TAAATGAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.72, C:0.05, G:0.00, T:0.23
Consensus pattern (20 bp):
AAAATACATAAAAAATTAAA
Found at i:34424478 original size:27 final size:25
Alignment explanation
Indices: 34424419--34424564 Score: 127
Period size: 27 Copynumber: 5.6 Consensus size: 25
34424409 ATATTGAGTC
* * *
34424419 CGCACACTCAGTGCTATATAATCAAT
1 CGCACACTTAGTGCTA-CTAGTCAAT
34424445 CGCACACTTAGTGCTACTAGTCAAACT
1 CGCACACTTAGTGCTACTAGTC-AA-T
*
34424472 CGCACACTTAGTGC-GC-ATGTCAAT
1 CGCACACTTAGTGCTACTA-GTCAAT
* *
34424496 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-C-TAGTCA-AT
*
34424523 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTAC-TAGTC-AAT
34424550 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
34424565 GTACAATTTA
Statistics
Matches: 101, Mismatches: 10, Indels: 17
0.79 0.08 0.13
Matches are distributed among these distances:
24 15 0.15
25 8 0.08
26 24 0.24
27 52 0.51
28 2 0.02
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (25 bp):
CGCACACTTAGTGCTACTAGTCAAT
Found at i:34424503 original size:51 final size:54
Alignment explanation
Indices: 34424419--34424564 Score: 167
Period size: 51 Copynumber: 2.8 Consensus size: 54
34424409 ATATTGAGTC
* * * *
34424419 CGCACACTCAGTGCTATATAATCAATCGCACACTTAGTGCTA-C-TAGTCAAACT
1 CGCACACTTAGTGCAACATAGTCAATCGCACACTTAGTGCTATCATAGTC-AACT
* * **
34424472 CGCACACTTAGTGC-GCAT-GTCAATCGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCAACATAGTCAATCGCACACTTAGTGCTATCATAGTCAACT
34424523 CGCACACTTAGTGCAACATAGTCAAATCGCACACTTAGTGCT
1 CGCACACTTAGTGCAACATAGTC-AATCGCACACTTAGTGCT
34424565 GTACAATTTA
Statistics
Matches: 79, Mismatches: 8, Indels: 10
0.81 0.08 0.10
Matches are distributed among these distances:
50 1 0.01
51 36 0.46
52 9 0.11
53 16 0.20
54 17 0.22
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (54 bp):
CGCACACTTAGTGCAACATAGTCAATCGCACACTTAGTGCTATCATAGTCAACT
Found at i:34424553 original size:78 final size:77
Alignment explanation
Indices: 34424419--34424563 Score: 213
Period size: 78 Copynumber: 1.9 Consensus size: 77
34424409 ATATTGAGTC
*
34424419 CGCACACTCAGTGCTATATAATCAATCGCACACTTAGTGCTACTAGTCAAACTCGCACACTTAGT
1 CGCACACTCAGTGCTATATAATCAATCGCACACTTAGTGCAACTAGTCAAACTCGCACACTTAGT
34424484 GCGCATGTCAAT
66 GCGCATGTCAAT
* * *
34424496 CGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAA-TCGCACACTT
1 CGCACACTCAGTGCTAT-ATAATCA-ATCGCACACTTAGTGCAAC-TAGTCAAACTCGCACACTT
34424559 AGTGC
63 AGTGC
34424564 TGTACAATTT
Statistics
Matches: 61, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
76 2 0.03
77 19 0.31
78 32 0.52
79 8 0.13
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (77 bp):
CGCACACTCAGTGCTATATAATCAATCGCACACTTAGTGCAACTAGTCAAACTCGCACACTTAGT
GCGCATGTCAAT
Found at i:34432498 original size:27 final size:27
Alignment explanation
Indices: 34432468--34432618 Score: 160
Period size: 27 Copynumber: 5.6 Consensus size: 27
34432458 ATATTGAGTC
* * *
34432468 CGCACACTCAGTGCTATATAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
34432495 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
* ** * *
34432523 CGCACCCTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
34432550 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
* *
34432577 CGTACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
34432604 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
34432619 GTACAATTTA
Statistics
Matches: 102, Mismatches: 19, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
27 79 0.77
28 23 0.23
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.28
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:34436591 original size:18 final size:19
Alignment explanation
Indices: 34436563--34436600 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
34436553 TCTCTTTCAA
34436563 TTTCTTTTTCAATCTCTTT
1 TTTCTTTTTCAATCTCTTT
*
34436582 TTTC-TTTTCACTCTCTTT
1 TTTCTTTTTCAATCTCTTT
34436600 T
1 T
34436601 GTTTTTGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.08, C:0.24, G:0.00, T:0.68
Consensus pattern (19 bp):
TTTCTTTTTCAATCTCTTT
Found at i:34437281 original size:18 final size:18
Alignment explanation
Indices: 34437253--34437287 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
34437243 CAACAAAATG
34437253 TTAGAAAACAAAAGATAAA
1 TTAGAAAACAAAA-ATAAA
34437272 TTAG-AAACAAAAATAA
1 TTAGAAAACAAAAATAA
34437288 TCCTCACCAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 8 0.50
19 4 0.25
ACGTcount: A:0.69, C:0.06, G:0.09, T:0.17
Consensus pattern (18 bp):
TTAGAAAACAAAAATAAA
Found at i:34449763 original size:22 final size:22
Alignment explanation
Indices: 34449705--34449851 Score: 70
Period size: 22 Copynumber: 6.6 Consensus size: 22
34449695 TTTGCAGGTT
* *
34449705 TTTGGTGCTA-TTTTGGTGTTG
1 TTTGGTGCTATTTTTTGTGCTG
* *
34449726 TTGGTGATGCTGTTTTTTGTGCTG
1 TT--TGGTGCTATTTTTTGTGCTG
**
34449750 TTTGGTGCTATTTTTTGTATTG
1 TTTGGTGCTATTTTTTGTGCTG
* * *
34449772 TTTGGTGTTGTTTTAT-TGCTG
1 TTTGGTGCTATTTTTTGTGCTG
* * *
34449793 TGTTAGTG-T-TGTTTTGTTGTTG
1 T-TTGGTGCTATTTTTTG-TGCTG
* *
34449815 TTTTGGTGCTA-TGTTGGTGCTG
1 -TTTGGTGCTATTTTTTGTGCTG
*
34449837 TTTTGTTGCTATTTT
1 -TTTGGTGCTATTTT
34449852 GGTACTATTT
Statistics
Matches: 92, Mismatches: 24, Indels: 18
0.69 0.18 0.13
Matches are distributed among these distances:
20 4 0.04
21 7 0.08
22 57 0.62
23 13 0.14
24 11 0.12
ACGTcount: A:0.05, C:0.05, G:0.29, T:0.60
Consensus pattern (22 bp):
TTTGGTGCTATTTTTTGTGCTG
Found at i:34449816 original size:33 final size:33
Alignment explanation
Indices: 34449772--34449844 Score: 92
Period size: 33 Copynumber: 2.2 Consensus size: 33
34449762 TTTTGTATTG
* * * *
34449772 TTTGGTGTTGTTTTATTGCTGTGTTAGTGTTGT
1 TTTGTTGTTGTTTTAGTGCTATGTTAGTGCTGT
* *
34449805 TTTGTTGTTGTTTTGGTGCTATGTTGGTGCTGT
1 TTTGTTGTTGTTTTAGTGCTATGTTAGTGCTGT
34449838 TTTGTTG
1 TTTGTTG
34449845 CTATTTTGGT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.04, C:0.04, G:0.32, T:0.60
Consensus pattern (33 bp):
TTTGTTGTTGTTTTAGTGCTATGTTAGTGCTGT
Found at i:34449831 original size:11 final size:11
Alignment explanation
Indices: 34449815--34449873 Score: 64
Period size: 11 Copynumber: 5.4 Consensus size: 11
34449805 TTTGTTGTTG
34449815 TTTTGGTGCTA
1 TTTTGGTGCTA
* *
34449826 TGTTGGTGCTG
1 TTTTGGTGCTA
*
34449837 TTTTGTTGCTA
1 TTTTGGTGCTA
*
34449848 TTTTGGTACTA
1 TTTTGGTGCTA
* *
34449859 TTTTGTTACTA
1 TTTTGGTGCTA
34449870 TTTT
1 TTTT
34449874 TATATTTAGG
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 40 1.00
ACGTcount: A:0.10, C:0.08, G:0.22, T:0.59
Consensus pattern (11 bp):
TTTTGGTGCTA
Found at i:34449852 original size:33 final size:33
Alignment explanation
Indices: 34449788--34449859 Score: 90
Period size: 33 Copynumber: 2.2 Consensus size: 33
34449778 GTTGTTTTAT
* * * *
34449788 TGCTGTGTTAGTGTTGTTTTGTTGTTGTTTTGG
1 TGCTATGTTAGTGCTGTTTTGTTGCTATTTTGG
*
34449821 TGCTATGTTGGTGCTGTTTTGTTGCTATTTTGG
1 TGCTATGTTAGTGCTGTTTTGTTGCTATTTTGG
*
34449854 TACTAT
1 TGCTAT
34449860 TTTGTTACTA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.07, C:0.07, G:0.29, T:0.57
Consensus pattern (33 bp):
TGCTATGTTAGTGCTGTTTTGTTGCTATTTTGG
Found at i:34449853 original size:22 final size:22
Alignment explanation
Indices: 34449804--34449873 Score: 77
Period size: 22 Copynumber: 3.2 Consensus size: 22
34449794 GTTAGTGTTG
* * *
34449804 TTTTGTTGTTGTTTTGGTGCTA
1 TTTTGGTGCTGTTTTGTTGCTA
*
34449826 TGTTGGTGCTGTTTTGTTGCTA
1 TTTTGGTGCTGTTTTGTTGCTA
* * *
34449848 TTTTGGTACTATTTTGTTACTA
1 TTTTGGTGCTGTTTTGTTGCTA
34449870 TTTT
1 TTTT
34449874 TATATTTAGG
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 40 1.00
ACGTcount: A:0.09, C:0.07, G:0.23, T:0.61
Consensus pattern (22 bp):
TTTTGGTGCTGTTTTGTTGCTA
Found at i:34450919 original size:12 final size:11
Alignment explanation
Indices: 34450902--34450934 Score: 50
Period size: 12 Copynumber: 3.0 Consensus size: 11
34450892 TTATTTGTTT
34450902 TTTGTTTTAATA
1 TTTGTTTTAA-A
34450914 TTTGTTTTAAA
1 TTTGTTTTAAA
34450925 TTT-TTTTAAA
1 TTTGTTTTAAA
34450935 ATGAAATAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 7 0.33
11 4 0.19
12 10 0.48
ACGTcount: A:0.27, C:0.00, G:0.06, T:0.67
Consensus pattern (11 bp):
TTTGTTTTAAA
Found at i:34458913 original size:124 final size:124
Alignment explanation
Indices: 34458677--34458994 Score: 361
Period size: 124 Copynumber: 2.6 Consensus size: 124
34458667 GGGCTTAACC
* * * *
34458677 CTGCAAGCTCTTAGAATA-TCGATTGGGAGCGTAGGTCCGCTAACTGTTTTTGGAGGTTGCGATC
1 CTGCAAGCTCTTAGAATATTAG-CTGGGAGCATAGGTCCGCTAACTGTTTTTGGAGGTTGCGACC
** *
34458741 ATGTACCGACAAACCTTTATAACATCAGCTGGAAACGTAAGTCCGCTAGCTA-TGTTGGAG
65 ATAAACCGACAAACCTTTATAACATCAGCTGGAAACATAAGTCCGCTAG-TAGTGTTGGAG
* * ** * *
34458801 CTGCGAGCTCTTAGAATATTAGCTGTGAGCATAGGTCCGCTATTTGTTTTTTGAGGTTGTGACCA
1 CTGCAAGCTCTTAGAATATTAGCTGGGAGCATAGGTCCGCTAACTGTTTTTGGAGGTTGCGACCA
* * * * *
34458866 TAAACCGGCAAACCTTTATAACATCAGCTGGGAACATAGGTCTGCTAGTAGTGTTTGAG
66 TAAACCGACAAACCTTTATAACATCAGCTGGAAACATAAGTCCGCTAGTAGTGTTGGAG
* ** * * * * * *
34458925 CTGTAAGCTCTTAGAATATTAGCTGGGAGTGTAGGTCTGCTAGCTATTTTTGAAGGTTACGATCA
1 CTGCAAGCTCTTAGAATATTAGCTGGGAGCATAGGTCCGCTAACTGTTTTTGGAGGTTGCGACCA
34458990 TAAAC
66 TAAAC
34458995 TAGCAAATGT
Statistics
Matches: 160, Mismatches: 32, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
123 2 0.01
124 156 0.98
125 2 0.01
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.31
Consensus pattern (124 bp):
CTGCAAGCTCTTAGAATATTAGCTGGGAGCATAGGTCCGCTAACTGTTTTTGGAGGTTGCGACCA
TAAACCGACAAACCTTTATAACATCAGCTGGAAACATAAGTCCGCTAGTAGTGTTGGAG
Found at i:34459657 original size:22 final size:22
Alignment explanation
Indices: 34459632--34459673 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
34459622 AATAAGGCGG
34459632 CATAAGTGTAAGAAAAATCTTA
1 CATAAGTGTAAGAAAAATCTTA
34459654 CATAAGTGTAAGAAAAATCT
1 CATAAGTGTAAGAAAAATCT
34459674 AAGATTTTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.50, C:0.10, G:0.14, T:0.26
Consensus pattern (22 bp):
CATAAGTGTAAGAAAAATCTTA
Found at i:34459714 original size:16 final size:16
Alignment explanation
Indices: 34459693--34459737 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
34459683 CTTAATTTCT
34459693 TAATTATTATATTATA
1 TAATTATTATATTATA
* *
34459709 TAATTATTATTTTATT
1 TAATTATTATATTATA
*
34459725 TAAATTATAATAT
1 T-AATTATTATAT
34459738 GAATTATAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
16 15 0.62
17 9 0.38
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
TAATTATTATATTATA
Found at i:34459883 original size:3 final size:3
Alignment explanation
Indices: 34459875--34459921 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
34459865 TAAGTAAAAG
34459875 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
34459922 TATTATTATT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:34473752 original size:3 final size:3
Alignment explanation
Indices: 34473744--34473801 Score: 116
Period size: 3 Copynumber: 19.3 Consensus size: 3
34473734 TAAAAAGTTG
34473744 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
34473792 ATA ATA ATA A
1 ATA ATA ATA A
34473802 AGTAAGGACA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:34476072 original size:17 final size:18
Alignment explanation
Indices: 34476050--34476085 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
34476040 ATTTTTATTT
*
34476050 AAAAAAATTAAT-AATGA
1 AAAAAAATGAATGAATGA
34476067 AAAAAAATGAATGAATGA
1 AAAAAAATGAATGAATGA
34476085 A
1 A
34476086 GTCAATTAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.69, C:0.00, G:0.11, T:0.19
Consensus pattern (18 bp):
AAAAAAATGAATGAATGA
Found at i:34482681 original size:25 final size:25
Alignment explanation
Indices: 34482643--34482710 Score: 95
Period size: 25 Copynumber: 2.7 Consensus size: 25
34482633 AGACATACCA
34482643 CAGCTCGTATGAGCTTACCGATTTG
1 CAGCTCGTATGAGCTTACCGATTTG
34482668 CAGCTCGTGA-GAGCTTACCGATTCT-
1 CAGCTCGT-ATGAGCTTACCGATT-TG
*
34482693 CAGTTCGTATGAGCTTAC
1 CAGCTCGTATGAGCTTAC
34482711 TTGTAATAGC
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
24 1 0.03
25 36 0.92
26 2 0.05
ACGTcount: A:0.21, C:0.25, G:0.24, T:0.31
Consensus pattern (25 bp):
CAGCTCGTATGAGCTTACCGATTTG
Found at i:34484042 original size:43 final size:42
Alignment explanation
Indices: 34483914--34484073 Score: 223
Period size: 44 Copynumber: 3.7 Consensus size: 42
34483904 TTTGCGTGTA
34483914 AAGACCATATCTGGGATATGGCATTGATATGAGACTTCATGTT
1 AAGACCATATCTGGGATATGGCATTGATATGAGACTTCATG-T
34483957 GAAGACCATATCTGGGATATGGCATTGATATGAGACTTCATGT
1 -AAGACCATATCTGGGATATGGCATTGATATGAGACTTCATGT
* * * * *
34484000 AAGACCATAGCTGGGCTATTGGCATTGATATAAG-GTCCCATGT
1 AAGACCATATCTGGGATA-TGGCATTGATATGAGACT-TCATGT
*
34484043 AAGACCATATCTGGGATATGGCATTGGTATG
1 AAGACCATATCTGGGATATGGCATTGATATG
34484074 GTACTATGTA
Statistics
Matches: 105, Mismatches: 9, Indels: 6
0.88 0.08 0.05
Matches are distributed among these distances:
42 28 0.27
43 36 0.34
44 41 0.39
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.30
Consensus pattern (42 bp):
AAGACCATATCTGGGATATGGCATTGATATGAGACTTCATGT
Found at i:34484064 original size:85 final size:86
Alignment explanation
Indices: 34483914--34484073 Score: 227
Period size: 85 Copynumber: 1.9 Consensus size: 86
34483904 TTTGCGTGTA
* * *
34483914 AAGACCATATCTGGGATATGGCATTGATATGAGACTTCATGTTGAAGACCATATCTGGGATATGG
1 AAGACCATAGCTGGGATATGGCATTGATATAAGACTCCATGTTGAAGACCATATCTGGGATATGG
34483979 CATTGATATGAGACTTCATGT
66 CATTGATATGAGACTTCATGT
* *
34484000 AAGACCATAGCTGGGCTATTGGCATTGATATAAG-GTCCCATG-T-AAGACCATATCTGGGATAT
1 AAGACCATAGCTGGGATA-TGGCATTGATATAAGACT-CCATGTTGAAGACCATATCTGGGATAT
*
34484062 GGCATTGGTATG
64 GGCATTGATATG
34484074 GTACTATGTA
Statistics
Matches: 66, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
85 30 0.45
86 18 0.27
87 18 0.27
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.30
Consensus pattern (86 bp):
AAGACCATAGCTGGGATATGGCATTGATATAAGACTCCATGTTGAAGACCATATCTGGGATATGG
CATTGATATGAGACTTCATGT
Found at i:34491779 original size:43 final size:43
Alignment explanation
Indices: 34491731--34491818 Score: 131
Period size: 43 Copynumber: 2.0 Consensus size: 43
34491721 CCTAAGACAC
*
34491731 GGGTGTGTCTCTTGGACGTGTAAGTCACACAGCCTGGTCACAT
1 GGGTGTGTCTCTTGGACATGTAAGTCACACAGCCTGGTCACAT
* * * *
34491774 GGGTGTGTCTTTTGGACATGTGAGTCAGACGGCCTGGTCACAT
1 GGGTGTGTCTCTTGGACATGTAAGTCACACAGCCTGGTCACAT
34491817 GG
1 GG
34491819 TCGTGTGACC
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.17, C:0.20, G:0.34, T:0.28
Consensus pattern (43 bp):
GGGTGTGTCTCTTGGACATGTAAGTCACACAGCCTGGTCACAT
Found at i:34494410 original size:40 final size:40
Alignment explanation
Indices: 34494365--34494445 Score: 99
Period size: 40 Copynumber: 2.0 Consensus size: 40
34494355 TTTTATCTGA
* *
34494365 ATTTTTATAAATATTTTGTAGTGTTAATTATAAGTTTTAT
1 ATTTTTATAAATATTTTGTAGTATTAATTATAAGTCTTAT
* * * * *
34494405 ATTTTTGTGAATCTTTTGTATTATTAATTATAGGTCTTAT
1 ATTTTTATAAATATTTTGTAGTATTAATTATAAGTCTTAT
34494445 A
1 A
34494446 AATTTTTTTT
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.30, C:0.02, G:0.11, T:0.57
Consensus pattern (40 bp):
ATTTTTATAAATATTTTGTAGTATTAATTATAAGTCTTAT
Found at i:34494534 original size:34 final size:33
Alignment explanation
Indices: 34494487--34494587 Score: 123
Period size: 34 Copynumber: 3.0 Consensus size: 33
34494477 CTACTATTAG
*
34494487 AGTTTTAAGTCTTATTACTTTTGTTTCATTTTGT
1 AGTTTTAACTCTTATTA-TTTTGTTTCATTTTGT
*
34494521 AGTTTTAACTCTTATTATATTTGTTTCATTTTTT
1 AGTTTTAACTCTTATTAT-TTTGTTTCATTTTGT
* *
34494555 AGTTTTAAGC-CTTATCATTTTTGTTCCATTTTG
1 AGTTTTAA-CTCTTATTA-TTTTGTTTCATTTTG
34494588 GTGAATATTT
Statistics
Matches: 59, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
33 1 0.02
34 56 0.95
35 2 0.03
ACGTcount: A:0.19, C:0.11, G:0.10, T:0.60
Consensus pattern (33 bp):
AGTTTTAACTCTTATTATTTTGTTTCATTTTGT
Found at i:34498166 original size:22 final size:23
Alignment explanation
Indices: 34498141--34498183 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
34498131 ATTGAAGAAA
34498141 AATTCAAATT-TT-GAGTTAAACG
1 AATT-AAATTATTCGAGTTAAACG
34498163 AATTAAATTATTCGAGTTAAA
1 AATTAAATTATTCGAGTTAAA
34498184 TAAGTTATTC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 5 0.26
22 6 0.32
23 8 0.42
ACGTcount: A:0.44, C:0.07, G:0.12, T:0.37
Consensus pattern (23 bp):
AATTAAATTATTCGAGTTAAACG
Found at i:34499181 original size:6 final size:6
Alignment explanation
Indices: 34499167--34499200 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
34499157 ATTCGATTCG
* *
34499167 ATTCGA ATTCAA ATTCAA ATTCGA ATTCAA ATTC
1 ATTCAA ATTCAA ATTCAA ATTCAA ATTCAA ATTC
34499201 CATCTCACTC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.41, C:0.18, G:0.06, T:0.35
Consensus pattern (6 bp):
ATTCAA
Found at i:34503488 original size:52 final size:52
Alignment explanation
Indices: 34503425--34503565 Score: 187
Period size: 52 Copynumber: 2.7 Consensus size: 52
34503415 AGGGAGGGAA
34503425 GCCAAAGTGAAAACCCGCAAAGGGCGCTTTGAGACTTTCAAA-AAAAATGG-GG
1 GCCAAAGTGAAAACCCGCAAAGGGCGCTTTGAGAC--TCAAATAAAAATGGAGG
* * *
34503477 GGCAAAGTGAAAACCCGCAAAGGGCACTTTGATACTCAAATAAAAATGGAAAGG
1 GCCAAAGTGAAAACCCGCAAAGGGCGCTTTGAGACTCAAATAAAAATGG--AGG
* *
34503531 GCCAAAGTGAAAACTCGCAAAGGACGCTTTGAGAC
1 GCCAAAGTGAAAACCCGCAAAGGGCGCTTTGAGAC
34503566 CCAATAATAA
Statistics
Matches: 77, Mismatches: 8, Indels: 6
0.85 0.09 0.07
Matches are distributed among these distances:
50 5 0.06
51 8 0.10
52 32 0.42
54 32 0.42
ACGTcount: A:0.40, C:0.19, G:0.26, T:0.15
Consensus pattern (52 bp):
GCCAAAGTGAAAACCCGCAAAGGGCGCTTTGAGACTCAAATAAAAATGGAGG
Found at i:34504995 original size:178 final size:178
Alignment explanation
Indices: 34504685--34505384 Score: 1121
Period size: 178 Copynumber: 3.9 Consensus size: 178
34504675 GTAAAGATTT
* * * ** *
34504685 AAGATCTTATTTCCCTGAAGTTGCAGTGGAATAGATCTTCGCAGATGGAATCTTATCTTCATGTA
1 AAGATTTTATCTCCCTGAAGTTGCAGCGGAGCAGATCTTCGCAGATGGAATCTTATCTCCATGTA
* * *
34504750 TCGACAATGGAGAAGATTTCACCAGCAAGCCCTATCTCTCTGAGGTAGCAAGAGAGCAGGTTGAA
66 TCGACAATGGAGCAGATTTCACCACCAAGCCTTATCTCTCTGAGGTAGCAAGAGAGCAGGTTGAA
* * * *
34504815 GAATGAGTCTTATCTTCCTGAGGAAGCAAGGAAGTAGATTGAGAATTG
131 GAATGAATTTTATCTTCCTGAGGTAGCAAGGAAGCAGATTGAGAATTG
34504863 AAGATTTTATCTCCCTGAAGTTGCAGCGGAGCAGATCTTCGCAGATGGAATCTTATCTCCATGTA
1 AAGATTTTATCTCCCTGAAGTTGCAGCGGAGCAGATCTTCGCAGATGGAATCTTATCTCCATGTA
* *
34504928 TCGGCAAAGGAGCAGATTTCACCACCAAGCCTTATCTCTCTGAGGTAGCAAGAGAGCAGGTTGAA
66 TCGACAATGGAGCAGATTTCACCACCAAGCCTTATCTCTCTGAGGTAGCAAGAGAGCAGGTTGAA
*
34504993 GAATGAATTTTATCTTCCCGAGGTAGCAAGGAAGCAGATTGAGAATTG
131 GAATGAATTTTATCTTCCTGAGGTAGCAAGGAAGCAGATTGAGAATTG
*
34505041 AAGATTTTATCTCCCTGAAGTTGCAGCGGAGCAGATCTTCGTAGATGGAATCTTATCTCCATGTA
1 AAGATTTTATCTCCCTGAAGTTGCAGCGGAGCAGATCTTCGCAGATGGAATCTTATCTCCATGTA
* * * *
34505106 TCGGCAAGGGAGCAGATTTCACCACCAAGCCTTATCTCTCCGAGGTAGCAAGAGAACAGGTTGAA
66 TCGACAATGGAGCAGATTTCACCACCAAGCCTTATCTCTCTGAGGTAGCAAGAGAGCAGGTTGAA
*
34505171 GAATGAATTTCATCTTCCTGAGGTAGCAAGGAAGCAGATTGAGAATTG
131 GAATGAATTTTATCTTCCTGAGGTAGCAAGGAAGCAGATTGAGAATTG
* * *
34505219 AAGATTTTATCTCCCTGAAGATACAGCGGAGCAGATCTTCGCAGATGAAATCTTATCTCCATGTA
1 AAGATTTTATCTCCCTGAAGTTGCAGCGGAGCAGATCTTCGCAGATGGAATCTTATCTCCATGTA
* * *
34505284 TCGACAATGGAGCATATTTCACCACCAAGCCTTATCTCTCTAAGGTAGCAAGAGAGCAAGTTGAA
66 TCGACAATGGAGCAGATTTCACCACCAAGCCTTATCTCTCTGAGGTAGCAAGAGAGCAGGTTGAA
* * *
34505349 GAATGAGTTTTATTTTCCTGAGGTAGCAGGGAAGCA
131 GAATGAATTTTATCTTCCTGAGGTAGCAAGGAAGCA
34505385 AACTGAAGGT
Statistics
Matches: 485, Mismatches: 37, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
178 485 1.00
ACGTcount: A:0.30, C:0.19, G:0.24, T:0.27
Consensus pattern (178 bp):
AAGATTTTATCTCCCTGAAGTTGCAGCGGAGCAGATCTTCGCAGATGGAATCTTATCTCCATGTA
TCGACAATGGAGCAGATTTCACCACCAAGCCTTATCTCTCTGAGGTAGCAAGAGAGCAGGTTGAA
GAATGAATTTTATCTTCCTGAGGTAGCAAGGAAGCAGATTGAGAATTG
Found at i:34505016 original size:43 final size:45
Alignment explanation
Indices: 34504969--34505052 Score: 113
Period size: 43 Copynumber: 1.9 Consensus size: 45
34504959 TTATCTCTCT
*
34504969 GAGGTAGCAA-GAGAGCAGGTTGAAGAA-TG-A-ATTTTATCTTCCC
1 GAGGTAGCAAGGA-AGCAGATTG-AGAATTGAAGATTTTATCTTCCC
34505012 GAGGTAGCAAGGAAGCAGATTGAGAATTGAAGATTTTATCT
1 GAGGTAGCAAGGAAGCAGATTGAGAATTGAAGATTTTATCT
34505053 CCCTGAAGTT
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
42 4 0.11
43 20 0.56
44 3 0.08
45 9 0.25
ACGTcount: A:0.35, C:0.11, G:0.29, T:0.26
Consensus pattern (45 bp):
GAGGTAGCAAGGAAGCAGATTGAGAATTGAAGATTTTATCTTCCC
Found at i:34516428 original size:199 final size:193
Alignment explanation
Indices: 34516094--34516485 Score: 507
Period size: 199 Copynumber: 2.0 Consensus size: 193
34516084 TGTATTTAAT
* * *
34516094 TTTTTTGGGACTTAACTAGTACCTAAACTTAAAAATTGTAAGTTGATACTTTTTTAAGTACCTAA
1 TTTTTTGGGACATAACTAGTACCTAAACTTAAAAATTGTAACTTGATACTTTTTTAAGTACATAA
* * ** * *
34516159 CTAACACTATTAAAATATGTTGATATGGAACTGACGACCAATTAACATGGTTACACATGTTAAGT
66 CTAACACAATTAAAAAACATTGATATGGAACTGACGACCAATTAACATGGTGACACATATTAAGT
* * * *
34516224 TTGTAATG-CCTTCAACCCGATCCAATTCGCTAGATCCGAATCTTAGGTGTTACAACTCGATTA
131 TTGTAACGCCCTT-AACCCGATCCAATTCGCCAAATCCGAATCTTAGGTGTTACAACTCAATTA
*
34516287 TTTTTTGGGACATAACTAGTACTTAAACTTAAAAATCGTAAGTTAACTTGATACTTTTTTTAAGT
1 TTTTTTGGGACATAACTAGTACCTAAACTTAAAAAT--T--G-TAACTTGATAC-TTTTTTAAGT
* * * *
34516352 ACATGACTAACACAATTAAAAAACATTGATATGGAGCTGATGACCAATTAGCATGGTGACACATA
60 ACATAACTAACACAATTAAAAAACATTGATATGGAACTGACGACCAATTAACATGGTGACACATA
* * * * *
34516417 TTAATTTTGTAACGCCCTTAACCCGATCCTATTTGCCAAATCTGAATCTTGGGTGTTACAACTCA
125 TTAAGTTTGTAACGCCCTTAACCCGATCCAATTCGCCAAATCCGAATCTTAGGTGTTACAACTCA
34516482 ATTA
190 ATTA
34516486 CATACTTACT
Statistics
Matches: 169, Mismatches: 23, Indels: 8
0.85 0.12 0.04
Matches are distributed among these distances:
193 34 0.20
195 1 0.01
197 1 0.01
198 10 0.06
199 119 0.70
200 4 0.02
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.34
Consensus pattern (193 bp):
TTTTTTGGGACATAACTAGTACCTAAACTTAAAAATTGTAACTTGATACTTTTTTAAGTACATAA
CTAACACAATTAAAAAACATTGATATGGAACTGACGACCAATTAACATGGTGACACATATTAAGT
TTGTAACGCCCTTAACCCGATCCAATTCGCCAAATCCGAATCTTAGGTGTTACAACTCAATTA
Found at i:34517165 original size:211 final size:211
Alignment explanation
Indices: 34516801--34517220 Score: 759
Period size: 211 Copynumber: 2.0 Consensus size: 211
34516791 CTGTAGCACA
34516801 ATACACAAAGGTAAGTTCATGAGAGCTTCGTGAGTTAGACTCAATTTACTTGTATTGTCTCCATA
1 ATACACAAAGGTAAGTTCATGAGAGCTTCGTGAGTTAGACTCAATTTACTTGTATTGTCTCCATA
*
34516866 CAACGTATCTAGGAATTTCATTATCATGTGATTGTTCTTCGTTCTTCAACTTGACTTTGGCGAGT
66 CAACGTATCTAGGAATTTCATTATCATGTCATTGTTCTTCGTTCTTCAACTTGACTTTGGCGAGT
* *
34516931 ATCTTTCTTCTTTATACCATAGACATCACACCTAACCTTGAAATCATGTTTTATCCTTCTCTTCA
131 ATCTTTCTTCTTCATACCATAGACATCACACCTAACCTTGAAATCATGTTTTACCCTTCTCTTCA
*
34516996 CTGATTCATTACTTGT
196 CTAATTCATTACTTGT
*
34517012 ATACACAAAGGTAAGTTCATGAGAGCTTCGTGAGTTAGATTCAATTTACTTGTATTGTCTCCATA
1 ATACACAAAGGTAAGTTCATGAGAGCTTCGTGAGTTAGACTCAATTTACTTGTATTGTCTCCATA
* * *
34517077 CAACGTATCTAGGAATTTTATTGTCATGTCATTGTTCTTCGTTCTTCATCTTGACTTTGGCGAGT
66 CAACGTATCTAGGAATTTCATTATCATGTCATTGTTCTTCGTTCTTCAACTTGACTTTGGCGAGT
*
34517142 ATTTTTCTTCTTCATACCATAGACATCACACCTAACCTTGAAATCATGTTTTACCCTTCTCTTCA
131 ATCTTTCTTCTTCATACCATAGACATCACACCTAACCTTGAAATCATGTTTTACCCTTCTCTTCA
34517207 CTAATTCATTACTT
196 CTAATTCATTACTT
34517221 ACATTATTTA
Statistics
Matches: 200, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
211 200 1.00
ACGTcount: A:0.25, C:0.21, G:0.13, T:0.40
Consensus pattern (211 bp):
ATACACAAAGGTAAGTTCATGAGAGCTTCGTGAGTTAGACTCAATTTACTTGTATTGTCTCCATA
CAACGTATCTAGGAATTTCATTATCATGTCATTGTTCTTCGTTCTTCAACTTGACTTTGGCGAGT
ATCTTTCTTCTTCATACCATAGACATCACACCTAACCTTGAAATCATGTTTTACCCTTCTCTTCA
CTAATTCATTACTTGT
Found at i:34517515 original size:27 final size:27
Alignment explanation
Indices: 34517428--34517517 Score: 126
Period size: 27 Copynumber: 3.3 Consensus size: 27
34517418 ATTTTTTCTC
*
34517428 TCAGTGTTCGCCATATGTTCTATTCCT
1 TCAGTGTTCGCCATATGTACTATTCCT
** *
34517455 TCAAAGTTCGTCATATGTACTATTCCT
1 TCAGTGTTCGCCATATGTACTATTCCT
*
34517482 TCAGTGTTTGCCATATGTACTATTCCT
1 TCAGTGTTCGCCATATGTACTATTCCT
*
34517509 TCTGTGTTC
1 TCAGTGTTC
34517518 ACGATACTTA
Statistics
Matches: 53, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 53 1.00
ACGTcount: A:0.18, C:0.23, G:0.14, T:0.44
Consensus pattern (27 bp):
TCAGTGTTCGCCATATGTACTATTCCT
Found at i:34517699 original size:27 final size:27
Alignment explanation
Indices: 34517632--34517703 Score: 99
Period size: 27 Copynumber: 2.7 Consensus size: 27
34517622 TCCATGATCA
* *
34517632 CCACAAAGGCTCCCATTTCACAGATTG
1 CCACAAAAGCTTCCATTTCACAGATTG
* *
34517659 CCACAAAGGCTTCCATTTCATAGATTG
1 CCACAAAAGCTTCCATTTCACAGATTG
*
34517686 CCACAAAAGTTTCCATTT
1 CCACAAAAGCTTCCATTT
34517704 TTTAACGTGT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.31, C:0.29, G:0.12, T:0.28
Consensus pattern (27 bp):
CCACAAAAGCTTCCATTTCACAGATTG
Found at i:34520313 original size:134 final size:133
Alignment explanation
Indices: 34520073--34520760 Score: 710
Period size: 134 Copynumber: 5.2 Consensus size: 133
34520063 GGATAAGTTA
** * *
34520073 TAGAGTTCATTGATTTACGATTGCAACTACATTCAAACAGTTCACTGATTTATGATCACAATTGA
1 TAGAGTTCACCGATTTACGATTGCAACT-CATTCAAACAGTTCACTAATTTACGATCACAATTGA
* * * *
34520138 TATTATCAAAGCTCAG-TGATTTA-TATTCATAGCTTACGTTCATTGATTTACGATCATGAACTA
65 TATTATTAAAGCTC-GTTGATTTACGA-TCACAGCTTAAGTTCATTGATTTACGATCATGAACTA
34520201 TTCACT
128 TTCACT
* *
34520207 TAGAGTTCACCAATTTACGATTGCAACTCTATTCAAACATTTCACTAATTTACGATCACAATTGA
1 TAGAGTTCACCGATTTACGATTGCAACTC-ATTCAAACAGTTCACTAATTTACGATCACAATTGA
* * *
34520272 TATTGTTAAAGCTCGTTGATTTACGTTCACATG-TTAGGTTCATTGATTTACGATCATGAA-TAG
65 TATTATTAAAGCTCGTTGATTTACGATCACA-GCTTAAGTTCATTGATTTACGATCATGAACTA-
34520335 TTCACT
128 TTCACT
* ** *
34520341 TAGAGGTT-ACTGATTTACGATTGCAACTCCATTTGAATAGTTCGACT-ATTTACGATCACAATT
1 TAGA-GTTCACCGATTTACGATTGCAACT-CATTCAAACAGTTC-ACTAATTTACGATCACAATT
* * **
34520404 GATAATATTAAAGCTTGTTGATTTACGATCACAGCTTAAGTTCATTGATTTACGATCATGAACGG
63 GATATTATTAAAGCTCGTTGATTTACGATCACAGCTTAAGTTCATTGATTTACGATCATGAACTA
34520469 TTCACT
128 TTCACT
* * * * *
34520475 TAGAGTTCACTGATTTACG-TTCACAACTCCATTCAAATAGTTCATTAATTTACGATCACAACTG
1 TAGAGTTCACCGATTTACGATT-GCAACT-CATTCAAACAGTTCACTAATTTACGATCACAATTG
* * * * * * ** *
34520539 ATATTGTTAAAACTCGTTGATTTACGATCATAGATTAAGTTTATTAATTTATAATCATAAACT-T
64 ATATTATTAAAGCTCGTTGATTTACGATCACAGCTTAAGTTCATTGATTTACGATCATGAACTAT
34520603 TCACT
129 TCACT
* * ** * * * *
34520608 TAAAGTTCATCGATTTATAATCGCAACTACATTCAAACATTTCACTAATTTATGATCACAACTGA
1 TAGAGTTCACCGATTTACGATTGCAACT-CATTCAAACAGTTCACTAATTTACGATCACAATTGA
* * * * * * * *
34520673 TATTCTTAAAACTCGTTGATTTATGATCACAACTT-AGTTCATTGATTTATGATTATGAACAACT
65 TATTATTAAAGCTCGTTGATTTACGATCACAGCTTAAGTTCATTGATTTACGATCATGAACTATT
*
34520737 CATT
130 CACT
* * *
34520741 TTGAGTTAACTGATTTACGA
1 TAGAGTTCACCGATTTACGA
34520761 GTTAACTGAT
Statistics
Matches: 465, Mismatches: 74, Indels: 31
0.82 0.13 0.05
Matches are distributed among these distances:
132 20 0.04
133 116 0.25
134 321 0.69
135 8 0.02
ACGTcount: A:0.33, C:0.17, G:0.12, T:0.38
Consensus pattern (133 bp):
TAGAGTTCACCGATTTACGATTGCAACTCATTCAAACAGTTCACTAATTTACGATCACAATTGAT
ATTATTAAAGCTCGTTGATTTACGATCACAGCTTAAGTTCATTGATTTACGATCATGAACTATTC
ACT
Found at i:34520764 original size:16 final size:16
Alignment explanation
Indices: 34520743--34520774 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
34520733 AACTCATTTT
34520743 GAGTTAACTGATTTAC
1 GAGTTAACTGATTTAC
34520759 GAGTTAACTGATTTAC
1 GAGTTAACTGATTTAC
34520775 AATCACAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.12, G:0.19, T:0.38
Consensus pattern (16 bp):
GAGTTAACTGATTTAC
Found at i:34522290 original size:13 final size:13
Alignment explanation
Indices: 34522272--34522309 Score: 76
Period size: 13 Copynumber: 2.9 Consensus size: 13
34522262 GTTTCGGGAC
34522272 CACTTAATTTGGG
1 CACTTAATTTGGG
34522285 CACTTAATTTGGG
1 CACTTAATTTGGG
34522298 CACTTAATTTGG
1 CACTTAATTTGG
34522310 TCAAAAGGAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.24, C:0.16, G:0.21, T:0.39
Consensus pattern (13 bp):
CACTTAATTTGGG
Found at i:34523415 original size:42 final size:42
Alignment explanation
Indices: 34523350--34523460 Score: 134
Period size: 42 Copynumber: 2.6 Consensus size: 42
34523340 ATTAAGATTC
* *
34523350 CATATAAGACCATATCTGAGATATGGCCTCGATATG-TGATTT
1 CATATAAGACCATATCGGGGATATGGCCTCGATATGAT-ATTT
* * * *
34523392 CGTATAAGACTATGTCGGGGATATGGCGTCGATATGATATTT
1 CATATAAGACCATATCGGGGATATGGCCTCGATATGATATTT
* *
34523434 CATGTAAGACCATATCGGGAATATGGC
1 CATATAAGACCATATCGGGGATATGGC
34523461 ATTGAAACAA
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
42 56 0.98
43 1 0.02
ACGTcount: A:0.30, C:0.15, G:0.24, T:0.31
Consensus pattern (42 bp):
CATATAAGACCATATCGGGGATATGGCCTCGATATGATATTT
Found at i:34524920 original size:18 final size:19
Alignment explanation
Indices: 34524888--34524925 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
34524878 AAATAGTTCG
34524888 AGTTATTTGAGTTAA-TCA
1 AGTTATTTGAGTTAACTCA
34524906 AGTTATTTG-GATTAACTCA
1 AGTTATTTGAG-TTAACTCA
34524925 A
1 A
34524926 ATAAAAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 1 0.06
18 13 0.72
19 4 0.22
ACGTcount: A:0.34, C:0.08, G:0.16, T:0.42
Consensus pattern (19 bp):
AGTTATTTGAGTTAACTCA
Found at i:34539177 original size:130 final size:129
Alignment explanation
Indices: 34538943--34539312 Score: 417
Period size: 130 Copynumber: 2.9 Consensus size: 129
34538933 AAAATTCTTC
* **
34538943 AAAACGAAGACGAAATTTGATGTTCGGTGATTCGCGGAATCGTGCCCTAACGTGTT-GGTTGCAA
1 AAAACGAAGACGAAATTTGATGTTTGGCAATTCGCGGAATCGTGCCCTAACGTGTTGGGTTGCAA
* * *
34539007 TTTCGCATTTGCTCAAAATAATCGAATTTTCCTTTGAAATTTCA-TTCATATCTTTTAAAATCAC
66 TTTCGCATTTGTTCAAAATAATCGAA-TATCCTTTAAAATTTCACTT-ATATCTTTTAAAATCAC
34539071 T
129 T
* * * * *
34539072 TAAATGAAGATGAGATTTGATGTTTGGCAATTCGCGGAATCATGCCCTAACGTGTTGGGTTGCAA
1 AAAACGAAGACGAAATTTGATGTTTGGCAATTCGCGGAATCGTGCCCTAACGTGTTGGGTTGCAA
* * * *
34539137 TTTCGCATTTGTTCAAAATAATCGAATATCACTTTAAAATTTTACTTGTGTCTTTTAAAATCTCT
66 TTTCGCATTTGTTCAAAATAATCGAATATC-CTTTAAAATTTCACTTATATCTTTTAAAATCACT
* * * * * * *
34539202 AAAACGAAGGCGATATGTGATATTTGGCAATTCGCAGG-ATCGTGCGCTAACGTGTTGGGTAGAA
1 AAAACGAAGACGAAATTTGATGTTTGGCAATTCGC-GGAATCGTGCCCTAACGTGTTGGGTTGCA
* * *
34539266 ATTTC-C-TGATTGTTTAAAATAATCAAATATCCCTTCAAAATTTCACT
65 ATTTCGCAT--TTGTTCAAAATAATCGAATAT-CCTTTAAAATTTCACT
34539313 CGGCTCTTCT
Statistics
Matches: 204, Mismatches: 30, Indels: 13
0.83 0.12 0.05
Matches are distributed among these distances:
128 1 0.00
129 52 0.25
130 146 0.72
131 5 0.02
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.35
Consensus pattern (129 bp):
AAAACGAAGACGAAATTTGATGTTTGGCAATTCGCGGAATCGTGCCCTAACGTGTTGGGTTGCAA
TTTCGCATTTGTTCAAAATAATCGAATATCCTTTAAAATTTCACTTATATCTTTTAAAATCACT
Found at i:34551035 original size:44 final size:44
Alignment explanation
Indices: 34550986--34551277 Score: 433
Period size: 44 Copynumber: 6.6 Consensus size: 44
34550976 CCCGCAGATC
* *
34550986 GCGGAGAGCAGATCGAGGATAGTAGATTTGGCATCTCTGTATTG
1 GCGGAGAGCAGATCGAAGATAGCAGATTTGGCATCTCTGTATTG
*
34551030 GCGGAGAGCAGATCGAGGATAGCAGATTTGGCATCTCTGTATTG
1 GCGGAGAGCAGATCGAAGATAGCAGATTTGGCATCTCTGTATTG
* *
34551074 ACGGAGAGTAGATCGAAGATAGCAGATTTGGCATCTCTGTATTG
1 GCGGAGAGCAGATCGAAGATAGCAGATTTGGCATCTCTGTATTG
34551118 GCGGAGAGCAGATCGAAGATAGCAGATTTGGCATCTCTGTATTG
1 GCGGAGAGCAGATCGAAGATAGCAGATTTGGCATCTCTGTATTG
* * *
34551162 GCAGAGAGCAGATCGAAAATAACAGATTTGGCATCTCTGTATTG
1 GCGGAGAGCAGATCGAAGATAGCAGATTTGGCATCTCTGTATTG
* *
34551206 GCGGAGAGCAGATCGAAGA-CGACAGATTTGACATCTCTGTATTG
1 GCGGAGAGCAGATCGAAGATAG-CAGATTTGGCATCTCTGTATTG
* * * * *
34551250 ACAGAGAGCAGATTGAAAATAACAGATT
1 GCGGAGAGCAGATCGAAGATAGCAGATT
34551278 GGTGTTCCCG
Statistics
Matches: 226, Mismatches: 20, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
44 226 1.00
ACGTcount: A:0.30, C:0.15, G:0.30, T:0.25
Consensus pattern (44 bp):
GCGGAGAGCAGATCGAAGATAGCAGATTTGGCATCTCTGTATTG
Found at i:34554346 original size:130 final size:131
Alignment explanation
Indices: 34554097--34554463 Score: 397
Period size: 130 Copynumber: 2.8 Consensus size: 131
34554087 AAAATTCTTC
* * *
34554097 AAAACGAAGACGAAATTTGATGTTCGGCGATTCACGGAATCGT-GCCCTAACGTGTTGGGTTACA
1 AAAACGAAGACGAAATTTGATGTTTGGCAATTCACGGAATCGTAGCCCTAACGTGTTGGGTTGCA
* * **
34554161 ATTTCGCATTTGCTCAAAATAATCGAATTTTCCTTCGAAA-TTTCATTCATATCTTTTAAAATCC
66 ATTTCGCATTTGTTCAAAATAATCGAA-TATCCTTTAAAATTTTCATTCATATCTTTTAAAATCC
34554225 CT
130 CT
* * * * *
34554227 TAAATGAAGATGAGATTTGATGTTTGGCAATTCGCGGAATC-TAGCCCTAACGTGTTGGGTTGCA
1 AAAACGAAGACGAAATTTGATGTTTGGCAATTCACGGAATCGTAGCCCTAACGTGTTGGGTTGCA
* *
34554291 ATTTCGCATTTGTTCAAAATAATCGAATATCACTTTAAAATTTTGC-TT-GTGTCTTTTAAAATC
66 ATTTCGCATTTGTTCAAAATAATCGAATATC-CTTTAAAATTTT-CATTCATATCTTTTAAAATC
*
34554354 TCT
129 CCT
* * * * * * * * *
34554357 AAAACAAAGGCGATATGTGATATTTGGCAATTCTCGGGATCGTA-CCTTAACGTGTTGGGTAGCA
1 AAAACGAAGACGAAATTTGATGTTTGGCAATTCACGGAATCGTAGCCCTAACGTGTTGGGTTGCA
* * *
34554421 ATTTCCCGA-TTGTTTAAAATAATCAAATATCCTTTCAAAATTT
66 ATTTCGC-ATTTGTTCAAAATAATCGAATATCCTTT-AAAATTT
34554464 CACTCGACTC
Statistics
Matches: 200, Mismatches: 30, Indels: 14
0.82 0.12 0.06
Matches are distributed among these distances:
129 8 0.04
130 183 0.92
131 8 0.04
132 1 0.00
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.35
Consensus pattern (131 bp):
AAAACGAAGACGAAATTTGATGTTTGGCAATTCACGGAATCGTAGCCCTAACGTGTTGGGTTGCA
ATTTCGCATTTGTTCAAAATAATCGAATATCCTTTAAAATTTTCATTCATATCTTTTAAAATCCC
T
Found at i:34554481 original size:130 final size:132
Alignment explanation
Indices: 34554244--34554499 Score: 306
Period size: 130 Copynumber: 2.0 Consensus size: 132
34554234 AGATGAGATT
* * *
34554244 TGATGTTTGGCAATTCGCGGAATCTAGCCCTAACGTGTTGGGTTGCAATTTCGCATTTGTTCAAA
1 TGATATTTGGCAATTCGCGGAATCTAGCCCTAACGTGTTGGGTAGCAATTTCCCATTTGTTCAAA
* ** * ** *
34554309 ATAATCGAATATCACTTTAAAATTTTGCTTGTGTCTT-TTAAAATC-TCTAAAACAAAGGCGATA
66 ATAATCAAATATCACTTTAAAATTTCACTCGACTCTTCTAAAAATCTTCTAAAACAAAGGCGATA
34554372 TG
131 TG
* * * *
34554374 TGATATTTGGCAATTCTCGGGATCGTA-CCTTAACGTGTTGGGTAGCAATTTCCCGA-TTGTTTA
1 TGATATTTGGCAATTCGCGGAATC-TAGCCCTAACGTGTTGGGTAGCAATTTCCC-ATTTGTTCA
* *
34554437 AAATAATCAAATATC-CTTTCAAAATTTCACTCGACTCTTCTAAAAATCTTTTAAAACGAAGGC
64 AAATAATCAAATATCACTTT-AAAATTTCACTCGACTCTTCTAAAAATCTTCTAAAACAAAGGC
34554500 AATACTCGGT
Statistics
Matches: 105, Mismatches: 16, Indels: 8
0.81 0.12 0.06
Matches are distributed among these distances:
129 4 0.04
130 79 0.75
131 10 0.10
132 12 0.11
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.36
Consensus pattern (132 bp):
TGATATTTGGCAATTCGCGGAATCTAGCCCTAACGTGTTGGGTAGCAATTTCCCATTTGTTCAAA
ATAATCAAATATCACTTTAAAATTTCACTCGACTCTTCTAAAAATCTTCTAAAACAAAGGCGATA
TG
Found at i:34562113 original size:8 final size:8
Alignment explanation
Indices: 34562100--34562125 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
34562090 TAATTAATCG
34562100 AATTAACC
1 AATTAACC
34562108 AATTAACC
1 AATTAACC
34562116 AATTAACC
1 AATTAACC
34562124 AA
1 AA
34562126 AATATTTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.54, C:0.23, G:0.00, T:0.23
Consensus pattern (8 bp):
AATTAACC
Found at i:34562930 original size:10 final size:9
Alignment explanation
Indices: 34562866--34562949 Score: 69
Period size: 9 Copynumber: 8.7 Consensus size: 9
34562856 CTTACACGGT
34562866 ATTATAAAA
1 ATTATAAAA
*
34562875 ATTTTAGAAA
1 ATTATA-AAA
*
34562885 ACTATAGTAAA
1 ATTATA--AAA
*
34562896 ATTATATAA
1 ATTATAAAA
34562905 ATTACTAAAA
1 ATTA-TAAAA
*
34562915 TTTTATAAAGA
1 -ATTATAAA-A
34562926 ATTATAAAA
1 ATTATAAAA
*
34562935 ATAATAAAA
1 ATTATAAAA
34562944 ATTATA
1 ATTATA
34562950 GATAAAATTT
Statistics
Matches: 59, Mismatches: 11, Indels: 10
0.74 0.14 0.12
Matches are distributed among these distances:
9 25 0.42
10 22 0.37
11 12 0.20
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.36
Consensus pattern (9 bp):
ATTATAAAA
Found at i:34573177 original size:19 final size:19
Alignment explanation
Indices: 34573150--34573186 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
34573140 GATTCAACTT
*
34573150 TCTTTTCTGACATTCTTGA
1 TCTTCTCTGACATTCTTGA
34573169 TCTTCTCTGACATTCTTG
1 TCTTCTCTGACATTCTTG
34573187 CAACTGAGAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.14, C:0.24, G:0.11, T:0.51
Consensus pattern (19 bp):
TCTTCTCTGACATTCTTGA
Found at i:34573339 original size:216 final size:216
Alignment explanation
Indices: 34572964--34573384 Score: 743
Period size: 216 Copynumber: 1.9 Consensus size: 216
34572954 CTATCGGTCA
* *
34572964 ATTCTTGCAACTAAGACTTCAGTTTTTTAAGTTTGGTCGGATCCATTCTATATGGAGCTATCAAA
1 ATTCTTGCAACTAAGACTTCAGTTTTTTAAGTTTGGTCGGAGCCATTCTATACGGAGCTATCAAA
* * *
34573029 ATCGGAGTAGTACCAGGTACCAATTCAATGCCAAATTCAACTTCTCTAACCGAAGGTAATCCCGG
66 ATCGGAGTAGTACCAAGTACCAATTCAATGCCAAATTCAACATCTCTAACCGAAGGTAATCCCAG
*
34573094 AAGTTCTTCAAGAAACACATCAGGGAACTCACAGACAACAGGCACAGATTCAACTTTCTTTTCTG
131 AAGTTCTTCAAGAAACACATCAAGGAACTCACAGACAACAGGCACAGATTCAACTTTCTTTTCTG
34573159 ACATTCTTGATCTTCTCTGAC
196 ACATTCTTGATCTTCTCTGAC
*
34573180 ATTCTTGCAACTGAGACTTCAGTTTTTTAAGTTTGGTCGGAGCCATTCTATACGGAGCTATCAAA
1 ATTCTTGCAACTAAGACTTCAGTTTTTTAAGTTTGGTCGGAGCCATTCTATACGGAGCTATCAAA
* * * *
34573245 ATCGGAGTAGTACCAAGTACCAATTCAATGCCAAATTTAACATCTCTAGCTGGAGGTAATCCCAG
66 ATCGGAGTAGTACCAAGTACCAATTCAATGCCAAATTCAACATCTCTAACCGAAGGTAATCCCAG
34573310 AAGTTCTTCAAGAAACACATCAAGGAACTCACAGACAACAGGCACAGATTCAACTTTCTTTTCTG
131 AAGTTCTTCAAGAAACACATCAAGGAACTCACAGACAACAGGCACAGATTCAACTTTCTTTTCTG
34573375 ACATTCTTGA
196 ACATTCTTGA
34573385 ATCAATCACA
Statistics
Matches: 194, Mismatches: 11, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
216 194 1.00
ACGTcount: A:0.31, C:0.23, G:0.17, T:0.29
Consensus pattern (216 bp):
ATTCTTGCAACTAAGACTTCAGTTTTTTAAGTTTGGTCGGAGCCATTCTATACGGAGCTATCAAA
ATCGGAGTAGTACCAAGTACCAATTCAATGCCAAATTCAACATCTCTAACCGAAGGTAATCCCAG
AAGTTCTTCAAGAAACACATCAAGGAACTCACAGACAACAGGCACAGATTCAACTTTCTTTTCTG
ACATTCTTGATCTTCTCTGAC
Found at i:34579067 original size:16 final size:16
Alignment explanation
Indices: 34579046--34579080 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
34579036 AGTATCACAG
*
34579046 TAAATAAAAAAATTAT
1 TAAATAAAAAAATAAT
*
34579062 TAAATAACAAAATAAT
1 TAAATAAAAAAATAAT
34579078 TAA
1 TAA
34579081 TAACTTGAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.29
Consensus pattern (16 bp):
TAAATAAAAAAATAAT
Found at i:34585524 original size:26 final size:26
Alignment explanation
Indices: 34585495--34585554 Score: 66
Period size: 27 Copynumber: 2.3 Consensus size: 26
34585485 TTTGGAGGAA
* **
34585495 GTTCTATACTAGTGGTTTTGCCACGT
1 GTTCTATACTAGTGGCTCCGCCACGT
*
34585521 GTTCTGATTCTAGTGGCTCCGCCACGT
1 GTTCT-ATACTAGTGGCTCCGCCACGT
*
34585548 TTTCTAT
1 GTTCTAT
34585555 TATTAGCAGT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
26 7 0.25
27 21 0.75
ACGTcount: A:0.13, C:0.23, G:0.22, T:0.42
Consensus pattern (26 bp):
GTTCTATACTAGTGGCTCCGCCACGT
Found at i:34585722 original size:33 final size:33
Alignment explanation
Indices: 34585670--34585733 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
34585660 TTGAGGCCAC
* *
34585670 TCTGCTACTGTATAGGGCTAAAGCCCAGACTGA
1 TCTGCTACTGAATAAGGCTAAAGCCCAGACTGA
* *
34585703 TCTGTTACTGAATAAGGCTAAGGCCCAGACT
1 TCTGCTACTGAATAAGGCTAAAGCCCAGACT
34585734 ATTTTGCATA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.28, C:0.23, G:0.23, T:0.25
Consensus pattern (33 bp):
TCTGCTACTGAATAAGGCTAAAGCCCAGACTGA
Found at i:34589488 original size:18 final size:18
Alignment explanation
Indices: 34589429--34589489 Score: 52
Period size: 18 Copynumber: 3.2 Consensus size: 18
34589419 TTAAAAAATG
34589429 AAATTTTAACATAAAAA-
1 AAATTTTAACATAAAAAC
* *
34589446 AAATTGTCTACTAACACAAACAC
1 AAA-T-T-T--TAACATAAAAAC
34589469 AAATTTTAACATAAAAAC
1 AAATTTTAACATAAAAAC
34589487 AAA
1 AAA
34589490 GCTTATGTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 11
0.69 0.08 0.22
Matches are distributed among these distances:
17 3 0.09
18 14 0.41
19 1 0.03
20 2 0.06
21 1 0.03
22 10 0.29
23 3 0.09
ACGTcount: A:0.59, C:0.15, G:0.02, T:0.25
Consensus pattern (18 bp):
AAATTTTAACATAAAAAC
Found at i:34600717 original size:40 final size:40
Alignment explanation
Indices: 34600641--34600715 Score: 125
Period size: 40 Copynumber: 1.9 Consensus size: 40
34600631 TGAAATTTCA
*
34600641 ATCAAAACTTTTAGTTCTATTTTTATTTTATTTTTTCTAG
1 ATCAAAACTTTTAATTCTATTTTTATTTTATTTTTTCTAG
*
34600681 ATCAAAACTTTTAATTTTATTTTT-TTTTATTTTTT
1 ATCAAAACTTTTAATTCTATTTTTATTTTATTTTTT
34600716 TCCAAGTAAG
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
39 11 0.33
40 22 0.67
ACGTcount: A:0.25, C:0.08, G:0.03, T:0.64
Consensus pattern (40 bp):
ATCAAAACTTTTAATTCTATTTTTATTTTATTTTTTCTAG
Found at i:34606218 original size:20 final size:22
Alignment explanation
Indices: 34606181--34606220 Score: 57
Period size: 20 Copynumber: 1.9 Consensus size: 22
34606171 ATTATTAGAA
*
34606181 TTTATAAAAATGTTAAATAAAT
1 TTTATAAAAATGTAAAATAAAT
34606203 TTTA-AAAAAT-TAAAATAA
1 TTTATAAAAATGTAAAATAA
34606221 TAAAAATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 7 0.41
21 6 0.35
22 4 0.24
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.38
Consensus pattern (22 bp):
TTTATAAAAATGTAAAATAAAT
Found at i:34606655 original size:51 final size:54
Alignment explanation
Indices: 34606595--34606702 Score: 186
Period size: 55 Copynumber: 2.0 Consensus size: 54
34606585 AAACTTTACA
34606595 AGTATGATTAATAAAATT-AAA-A-TTATTTATTTATTTTTTAATTTTTTATAT
1 AGTATGATTAATAAAATTAAAATATTTATTTATTTATTTTTTAATTTTTTATAT
34606646 AGTATGATTAATAAAATTAAAATTATTTATTTATTTATTTTTTAATTTTTTATAT
1 AGTATGATTAATAAAATTAAAA-TATTTATTTATTTATTTTTTAATTTTTTATAT
34606701 AG
1 AG
34606703 CCTAAAAGGT
Statistics
Matches: 53, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
51 18 0.34
52 3 0.06
54 1 0.02
55 31 0.58
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.56
Consensus pattern (54 bp):
AGTATGATTAATAAAATTAAAATATTTATTTATTTATTTTTTAATTTTTTATAT
Found at i:34607600 original size:10 final size:10
Alignment explanation
Indices: 34607585--34607614 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
34607575 TTAGTGGTCA
34607585 GATTTAGTGG
1 GATTTAGTGG
34607595 GATTTAGTGG
1 GATTTAGTGG
*
34607605 GATTTGGTGG
1 GATTTAGTGG
34607615 TTAGTGGGGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.17, C:0.00, G:0.43, T:0.40
Consensus pattern (10 bp):
GATTTAGTGG
Found at i:34610767 original size:13 final size:13
Alignment explanation
Indices: 34610749--34610774 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
34610739 TAATTTTGTA
34610749 TATCTGTATCTGT
1 TATCTGTATCTGT
34610762 TATCTGTATCTGT
1 TATCTGTATCTGT
34610775 ACATGGGGTG
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:0.15, C:0.15, G:0.15, T:0.54
Consensus pattern (13 bp):
TATCTGTATCTGT
Found at i:34612632 original size:18 final size:19
Alignment explanation
Indices: 34612602--34612638 Score: 51
Period size: 18 Copynumber: 2.0 Consensus size: 19
34612592 GTAACTACTC
34612602 ATTTTCCCTATTAT-AAAT
1 ATTTTCCCTATTATGAAAT
34612620 ATTTT-CCTCATTATGAAAT
1 ATTTTCCCT-ATTATGAAAT
34612639 TCTTTTTTCC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
17 3 0.18
18 10 0.59
19 4 0.24
ACGTcount: A:0.32, C:0.16, G:0.03, T:0.49
Consensus pattern (19 bp):
ATTTTCCCTATTATGAAAT
Found at i:34616099 original size:84 final size:84
Alignment explanation
Indices: 34616006--34616166 Score: 304
Period size: 84 Copynumber: 1.9 Consensus size: 84
34615996 GCAGACGAGG
34616006 TTGAAGATAACAAGAAGCAAGAAAGTGAAAGTTGGGATTAAGTTGGCAAGAGCAAAAGTAAGGGT
1 TTGAAGATAACAAGAAGCAAGAAAGTGAAAGTTGGGATTAAGTTGGCAAGAGCAAAAGTAAGGGT
34616071 TGGAGAGCTGTAGACGAAC
66 TGGAGAGCTGTAGACGAAC
34616090 TTGAAGATAACAAGAAGCAAGAAAGTGAAAGTTGGGATTAAGTTGGCAAGAGCAAAAGTAAGGGT
1 TTGAAGATAACAAGAAGCAAGAAAGTGAAAGTTGGGATTAAGTTGGCAAGAGCAAAAGTAAGGGT
* *
34616155 TGGGGAGTTGTA
66 TGGAGAGCTGTA
34616167 TCTTGCACCA
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
84 75 1.00
ACGTcount: A:0.41, C:0.07, G:0.33, T:0.19
Consensus pattern (84 bp):
TTGAAGATAACAAGAAGCAAGAAAGTGAAAGTTGGGATTAAGTTGGCAAGAGCAAAAGTAAGGGT
TGGAGAGCTGTAGACGAAC
Found at i:34619864 original size:31 final size:31
Alignment explanation
Indices: 34619829--34619890 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
34619819 ATATTGTAGA
34619829 CCTTAAAGAAATAATAAAAAATAAATATTTT
1 CCTTAAAGAAATAATAAAAAATAAATATTTT
34619860 CCTTAAAGAAATAATAAAAAATAAATATTTT
1 CCTTAAAGAAATAATAAAAAATAAATATTTT
34619891 TACTTCGGAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.58, C:0.06, G:0.03, T:0.32
Consensus pattern (31 bp):
CCTTAAAGAAATAATAAAAAATAAATATTTT
Found at i:34623813 original size:35 final size:35
Alignment explanation
Indices: 34623767--34623878 Score: 174
Period size: 35 Copynumber: 3.2 Consensus size: 35
34623757 TGAAGATCTT
*
34623767 GAAGAAAATGGAAGGAAAATAAAAAAGAATAGAGA
1 GAAGAAGATGGAAGGAAAATAAAAAAGAATAGAGA
**
34623802 GAAGAAGATGGAAGGAAAATAAAAAAG-ATCCAGA
1 GAAGAAGATGGAAGGAAAATAAAAAAGAATAGAGA
34623836 G-AGAAGATGGAAGGAAAATAAAAAAGAACTAGAGA
1 GAAGAAGATGGAAGGAAAATAAAAAAGAA-TAGAGA
34623871 GAAGAAGA
1 GAAGAAGA
34623879 AATGAAGAAG
Statistics
Matches: 69, Mismatches: 5, Indels: 5
0.87 0.06 0.06
Matches are distributed among these distances:
33 25 0.36
34 7 0.10
35 31 0.45
36 6 0.09
ACGTcount: A:0.62, C:0.03, G:0.28, T:0.08
Consensus pattern (35 bp):
GAAGAAGATGGAAGGAAAATAAAAAAGAATAGAGA
Found at i:34623846 original size:33 final size:33
Alignment explanation
Indices: 34623769--34623875 Score: 151
Period size: 33 Copynumber: 3.2 Consensus size: 33
34623759 AAGATCTTGA
* **
34623769 AGAAAATGGAAGGAAAATAAAAAAGAATAGAGAG
1 AGAAGATGGAAGGAAAATAAAAAAG-ATCCAGAG
34623803 AAGAAGATGGAAGGAAAATAAAAAAGATCCAGAG
1 -AGAAGATGGAAGGAAAATAAAAAAGATCCAGAG
* *
34623837 AGAAGATGGAAGGAAAATAAAAAAGAACTAGAG
1 AGAAGATGGAAGGAAAATAAAAAAGATCCAGAG
34623870 AGAAGA
1 AGAAGA
34623876 AGAAATGAAG
Statistics
Matches: 67, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
33 37 0.55
34 6 0.09
35 24 0.36
ACGTcount: A:0.62, C:0.03, G:0.27, T:0.08
Consensus pattern (33 bp):
AGAAGATGGAAGGAAAATAAAAAAGATCCAGAG
Found at i:34628014 original size:46 final size:46
Alignment explanation
Indices: 34627947--34628116 Score: 295
Period size: 46 Copynumber: 3.7 Consensus size: 46
34627937 TAACCCGCCA
* * * * *
34627947 ATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATAC
1 ATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCC
34627993 ATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCC
1 ATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCC
34628039 ATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCC
1 ATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCC
34628085 ATAAGTGAACTCGGACTCAACTCAACGAGTTC
1 ATAAGTGAACTCGGACTCAACTCAACGAGTTC
34628117 AGATGCCCAA
Statistics
Matches: 119, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 119 1.00
ACGTcount: A:0.31, C:0.28, G:0.21, T:0.21
Consensus pattern (46 bp):
ATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCC
Found at i:34633572 original size:46 final size:46
Alignment explanation
Indices: 34633505--34633674 Score: 304
Period size: 46 Copynumber: 3.7 Consensus size: 46
34633495 TAACCCGCCA
* * * *
34633505 ATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCC
1 ATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCC
34633551 ATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCC
1 ATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCC
34633597 ATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCC
1 ATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCC
34633643 ATAAGTGAACTCGGACTCAACTCAACGAGTTC
1 ATAAGTGAACTCGGACTCAACTCAACGAGTTC
34633675 AGATGCCCAA
Statistics
Matches: 120, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
46 120 1.00
ACGTcount: A:0.30, C:0.29, G:0.21, T:0.21
Consensus pattern (46 bp):
ATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCC
Found at i:34635792 original size:50 final size:53
Alignment explanation
Indices: 34635724--34635822 Score: 159
Period size: 50 Copynumber: 1.9 Consensus size: 53
34635714 AGAACACACT
*
34635724 TGGGCACTGAGTGCCAAGCCCGAAGGCTA-ACATCC-CT-CCAGAAACATGTC
1 TGGGCACTAAGTGCCAAGCCCGAAGGCTACACATCCTCTCCCAGAAACATGTC
*
34635774 TGGGCACTAAGTGTCAAGCCCGAAGGCTACACATCCTCTCCCAGAAACA
1 TGGGCACTAAGTGCCAAGCCCGAAGGCTACACATCCTCTCCCAGAAACA
34635823 CGCCTGAATC
Statistics
Matches: 44, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
50 27 0.61
51 6 0.14
52 2 0.05
53 9 0.20
ACGTcount: A:0.29, C:0.32, G:0.22, T:0.16
Consensus pattern (53 bp):
TGGGCACTAAGTGCCAAGCCCGAAGGCTACACATCCTCTCCCAGAAACATGTC
Found at i:34638411 original size:14 final size:14
Alignment explanation
Indices: 34638392--34638418 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
34638382 ACTTCTGTGA
34638392 AAATAAAATAAAAT
1 AAATAAAATAAAAT
34638406 AAATAAAATAAAA
1 AAATAAAATAAAA
34638419 AACACACAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (14 bp):
AAATAAAATAAAAT
Found at i:34638539 original size:28 final size:28
Alignment explanation
Indices: 34638495--34638548 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
34638485 TGTCAAATTC
*
34638495 GAATAATTAGAAGAGGAATAGACTATGA
1 GAATAATTAGAAAAGGAATAGACTATGA
*
34638523 GAATAATTATAAAAGGAATAGACTAT
1 GAATAATTAGAAAAGGAATAGACTAT
34638549 ATCTATATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.52, C:0.04, G:0.20, T:0.24
Consensus pattern (28 bp):
GAATAATTAGAAAAGGAATAGACTATGA
Done.