Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 ID=Chr05-JGI_221_v2.0
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: 64140413
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 820884 characters in sequence are not A, C, G, or T
File 194 of 208
Found at i:59135140 original size:10 final size:10
Alignment explanation
Indices: 59135114--59135188 Score: 61
Period size: 10 Copynumber: 7.8 Consensus size: 10
59135104 AATAATTTTT
*
59135114 TTAAGAATTA
1 TTAAAAATTA
*
59135124 TTAAAAAATCA
1 TT-AAAAATTA
59135135 TTAAAAATTA
1 TTAAAAATTA
*
59135145 -TAAAACAAT-
1 TTAAAA-ATTA
*
59135154 TTAAAAA-GA
1 TTAAAAATTA
59135163 -TAAAAATTA
1 TTAAAAATTA
59135172 TTAAAAATTA
1 TTAAAAATTA
59135182 -TAAAAAT
1 TTAAAAAT
59135189 CTGTTTATAA
Statistics
Matches: 53, Mismatches: 6, Indels: 13
0.74 0.08 0.18
Matches are distributed among these distances:
8 6 0.11
9 14 0.26
10 25 0.47
11 8 0.15
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.32
Consensus pattern (10 bp):
TTAAAAATTA
Found at i:59135149 original size:18 final size:18
Alignment explanation
Indices: 59135123--59135186 Score: 60
Period size: 18 Copynumber: 3.5 Consensus size: 18
59135113 TTTAAGAATT
*
59135123 ATTAAAAAATCATTAAAA
1 ATTATAAAATCATTAAAA
59135141 ATTATAAAA-CAATTTAAAA
1 ATTATAAAATC-A-TTAAAA
* *
59135160 A-GATAAAAATTATTAAAA
1 ATTAT-AAAATCATTAAAA
59135178 ATTATAAAA
1 ATTATAAAA
59135187 ATCTGTTTAT
Statistics
Matches: 37, Mismatches: 4, Indels: 10
0.73 0.08 0.20
Matches are distributed among these distances:
17 1 0.03
18 22 0.59
19 14 0.38
ACGTcount: A:0.66, C:0.03, G:0.02, T:0.30
Consensus pattern (18 bp):
ATTATAAAATCATTAAAA
Found at i:59135170 original size:27 final size:27
Alignment explanation
Indices: 59135136--59135187 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
59135126 AAAAAATCAT
59135136 TAAAAATTATAAAACAATT-TAAAAAGA
1 TAAAAATTATAAAA-AATTATAAAAAGA
*
59135163 TAAAAATTATTAAAAATTATAAAAA
1 TAAAAATTATAAAAAATTATAAAAA
59135188 TCTGTTTATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 4 0.17
27 19 0.83
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (27 bp):
TAAAAATTATAAAAAATTATAAAAAGA
Found at i:59140251 original size:13 final size:13
Alignment explanation
Indices: 59140233--59140259 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
59140223 CCCGGCCCAT
59140233 TTTTTTAAATATA
1 TTTTTTAAATATA
59140246 TTTTTTAAATATA
1 TTTTTTAAATATA
59140259 T
1 T
59140260 ATATAATACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (13 bp):
TTTTTTAAATATA
Found at i:59141200 original size:13 final size:13
Alignment explanation
Indices: 59141182--59141219 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
59141172 AGTTCTTCAT
*
59141182 TGCTTTCGAAAAG
1 TGCTTTTGAAAAG
*
59141195 TGCTTTTGAGAAG
1 TGCTTTTGAAAAG
59141208 TGCTTTTGAAAA
1 TGCTTTTGAAAA
59141220 TTTTGAGTGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.29, C:0.11, G:0.24, T:0.37
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:59143358 original size:72 final size:72
Alignment explanation
Indices: 59143242--59143430 Score: 213
Period size: 72 Copynumber: 2.6 Consensus size: 72
59143232 TCACCTGTGA
** * * *
59143242 ATAAATTTTATATCC-AAAATCAAATATAAACAACTATTAATAAAACTA-ATTTAGTA-AAAAAA
1 ATAAATTCAATATCCAAAAACCAAACATAAACAACTATTAATAAAACTAGA-TTA-CACAAAAAA
*
59143304 AAGTGGAAC
64 AAGTAGAAC
* * * *
59143313 ATAAATTCAATATCTAAAGACCAAACATAAACAACTATTAATAAAACTAGATTACACATAAATAA
1 ATAAATTCAATATCCAAAAACCAAACATAAACAACTATTAATAAAACTAGATTACACAAAAAAAA
59143378 GTAGAAC
66 GTAGAAC
* * * *
59143385 ATAAATTCAGTATCCAAAAACTAAACATAAATAACTATTGATAAAA
1 ATAAATTCAATATCCAAAAACCAAACATAAACAACTATTAATAAAA
59143431 ACATACTTCG
Statistics
Matches: 99, Mismatches: 16, Indels: 5
0.82 0.13 0.04
Matches are distributed among these distances:
71 13 0.13
72 85 0.86
73 1 0.01
ACGTcount: A:0.56, C:0.13, G:0.05, T:0.26
Consensus pattern (72 bp):
ATAAATTCAATATCCAAAAACCAAACATAAACAACTATTAATAAAACTAGATTACACAAAAAAAA
GTAGAAC
Found at i:59144781 original size:15 final size:14
Alignment explanation
Indices: 59144761--59144792 Score: 55
Period size: 15 Copynumber: 2.2 Consensus size: 14
59144751 ATTTGTAATA
59144761 AAATAAGCAGACGAG
1 AAATAAGCAGAC-AG
59144776 AAATAAGCAGACAG
1 AAATAAGCAGACAG
59144790 AAA
1 AAA
59144793 ATTGTAAAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.59, C:0.12, G:0.22, T:0.06
Consensus pattern (14 bp):
AAATAAGCAGACAG
Found at i:59145343 original size:2 final size:2
Alignment explanation
Indices: 59145336--59145368 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
59145326 TCCATAAATC
59145336 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
59145369 CTGATTTTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:59147026 original size:7 final size:7
Alignment explanation
Indices: 59146994--59147025 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
59146984 AGAGGGAACC
59146994 AGCAAAG
1 AGCAAAG
59147001 AGCAAAG
1 AGCAAAG
59147008 AGCAAAG
1 AGCAAAG
*
59147015 AGCAGAG
1 AGCAAAG
59147022 AGCA
1 AGCA
59147026 GTGTAGCAGC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.53, C:0.16, G:0.31, T:0.00
Consensus pattern (7 bp):
AGCAAAG
Found at i:59149231 original size:2 final size:2
Alignment explanation
Indices: 59149224--59149273 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
59149214 TAATTTACCC
59149224 TA TA TA TA TA TA 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
59149266 TA TA TA TA
1 TA TA TA TA
59149274 AAACTTTTGA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:59149431 original size:17 final size:18
Alignment explanation
Indices: 59149399--59149433 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
59149389 AGAATTCATG
*
59149399 ATAATTATATATTTAATA
1 ATAATTATAGATTTAATA
59149417 ATAATTAT-GATTTAATA
1 ATAATTATAGATTTAATA
59149434 GAATTTGTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (18 bp):
ATAATTATAGATTTAATA
Found at i:59149486 original size:14 final size:14
Alignment explanation
Indices: 59149464--59149493 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
59149454 TTACATTTAC
59149464 ATTTATTAATTAAA
1 ATTTATTAATTAAA
*
59149478 ATTTTTTAATTAAA
1 ATTTATTAATTAAA
59149492 AT
1 AT
59149494 AATTATAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
ATTTATTAATTAAA
Found at i:59173510 original size:14 final size:14
Alignment explanation
Indices: 59173491--59173520 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
59173481 CATTAGGGAA
59173491 TATAAATTTATATT
1 TATAAATTTATATT
*
59173505 TATAAATTTATGTT
1 TATAAATTTATATT
59173519 TA
1 TA
59173521 ATTAAGTTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (14 bp):
TATAAATTTATATT
Found at i:59174803 original size:16 final size:15
Alignment explanation
Indices: 59174765--59174806 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
59174755 TCTAAAACAG
59174765 TAAAATTTTAATTTA
1 TAAAATTTTAATTTA
*
59174780 -AACCATTTATAATTTA
1 TAA-AATTT-TAATTTA
59174796 TAAAATTTTAA
1 TAAAATTTTAA
59174807 ATTAATAACG
Statistics
Matches: 22, Mismatches: 2, Indels: 6
0.73 0.07 0.20
Matches are distributed among these distances:
14 2 0.09
15 7 0.32
16 11 0.50
17 2 0.09
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (15 bp):
TAAAATTTTAATTTA
Found at i:59178863 original size:13 final size:13
Alignment explanation
Indices: 59178845--59178879 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 13
59178835 ATTAGCTAAA
59178845 ATCTTAAAAAAAT
1 ATCTTAAAAAAAT
59178858 ATCTT-AAAAAAT
1 ATCTTAAAAAAAT
*
59178870 ATATTAAAAA
1 ATCTTAAAAA
59178880 CAGTTATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
12 11 0.55
13 9 0.45
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (13 bp):
ATCTTAAAAAAAT
Found at i:59180738 original size:2 final size:2
Alignment explanation
Indices: 59180731--59180773 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
59180721 NNNNNNNNNN
59180731 TA TA TA TA TA TA 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
59180773 T
1 T
59180774 TACATGAAGC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:59184566 original size:38 final size:38
Alignment explanation
Indices: 59184514--59184604 Score: 146
Period size: 38 Copynumber: 2.3 Consensus size: 38
59184504 AAATTAAAAC
*
59184514 AAAAATTTTAAAAAGTATTTAAAAAATATTTTAAAATTA
1 AAAAAATTT-AAAAGTATTTAAAAAATATTTTAAAATTA
*
59184553 AAAAAATTTAAAAGTATTTTAAAAATATTTTAAAATTA
1 AAAAAATTTAAAAGTATTTAAAAAATATTTTAAAATTA
59184591 AAAAAAGTTTAAAA
1 AAAAAA-TTTAAAA
59184605 AAATATTTTA
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
38 34 0.69
39 15 0.31
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.36
Consensus pattern (38 bp):
AAAAAATTTAAAAGTATTTAAAAAATATTTTAAAATTA
Found at i:59184575 original size:11 final size:11
Alignment explanation
Indices: 59184550--59184587 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
59184540 TATTTTAAAA
*
59184550 TTAAAAA-AAT
1 TTAAAAATATT
*
59184560 TTAAAAGTATT
1 TTAAAAATATT
59184571 TTAAAAATATT
1 TTAAAAATATT
59184582 TTAAAA
1 TTAAAA
59184588 TTAAAAAAAG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
10 6 0.25
11 18 0.75
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (11 bp):
TTAAAAATATT
Found at i:59192687 original size:31 final size:31
Alignment explanation
Indices: 59192652--59192711 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
59192642 AAAAAAACTT
59192652 AATAGCCTAGTGACTTAAATAAAAACTTTCA
1 AATAGCCTAGTGACTTAAATAAAAACTTTCA
** * *
59192683 AATAGTTTAGTGATTTAAATGAAAACTTT
1 AATAGCCTAGTGACTTAAATAAAAACTTT
59192712 TGAATAATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.43, C:0.10, G:0.12, T:0.35
Consensus pattern (31 bp):
AATAGCCTAGTGACTTAAATAAAAACTTTCA
Found at i:59192723 original size:31 final size:31
Alignment explanation
Indices: 59192659--59192726 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 31
59192649 CTTAATAGCC
*
59192659 TAGTGACTTAAATAAAAACTTTCAAATAGTT
1 TAGTGACTTAAATAAAAACTTTCAAATAATT
* * **
59192690 TAGTGATTTAAATGAAAACTTTTGAATAATT
1 TAGTGACTTAAATAAAAACTTTCAAATAATT
59192721 TAGTGA
1 TAGTGA
59192727 ATATTTTGTA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.43, C:0.06, G:0.13, T:0.38
Consensus pattern (31 bp):
TAGTGACTTAAATAAAAACTTTCAAATAATT
Found at i:59194054 original size:20 final size:20
Alignment explanation
Indices: 59194008--59194059 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
59193998 GATTCAAAGG
* *
59194008 TTGTTTTCTTATTTTTATTT
1 TTGTTTTATTTTTTTTATTT
*
59194028 TTGTTTTGTTTTTTTTATTAT
1 TTGTTTTATTTTTTTTATT-T
59194049 TT-TTTTATTTT
1 TTGTTTTATTTT
59194060 CGAAATATTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 25 0.89
21 3 0.11
ACGTcount: A:0.10, C:0.02, G:0.06, T:0.83
Consensus pattern (20 bp):
TTGTTTTATTTTTTTTATTT
Found at i:59196046 original size:41 final size:41
Alignment explanation
Indices: 59195989--59196145 Score: 190
Period size: 41 Copynumber: 3.8 Consensus size: 41
59195979 TTTTTTAAGT
59195989 TCAGGCTTTATGCCTAGCAGGCTTTATGCCGGTGAATTATA
1 TCAGGCTTTATGCCTAGCAGGCTTTATGCCGGTGAATTATA
* * *
59196030 TCAGGCTTTATGCCTAGCAAGC-TCAGTGCCAGTGAATTATA
1 TCAGGCTTTATGCCTAGCAGGCTTTA-TGCCGGTGAATTATA
* * * * * *
59196071 TCAGACCTTATGTCTAGCAGGCTTTGTGCCGGTGAAATGTA
1 TCAGGCTTTATGCCTAGCAGGCTTTATGCCGGTGAATTATA
* * *
59196112 TCGGGCTTTGTGCCTAGTAGGCTTTATGCCGGTG
1 TCAGGCTTTATGCCTAGCAGGCTTTATGCCGGTG
59196146 TTTTATACAA
Statistics
Matches: 95, Mismatches: 19, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
40 2 0.02
41 92 0.97
42 1 0.01
ACGTcount: A:0.20, C:0.20, G:0.27, T:0.32
Consensus pattern (41 bp):
TCAGGCTTTATGCCTAGCAGGCTTTATGCCGGTGAATTATA
Found at i:59196982 original size:16 final size:16
Alignment explanation
Indices: 59196948--59196985 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 16
59196938 TTCGAAAATA
59196948 ATATGTGTATTAGATGT
1 ATATGTGTATTA-ATGT
59196965 ATATGATGTATT-ATGT
1 ATATG-TGTATTAATGT
59196981 ATATG
1 ATATG
59196986 CTGCCCATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 9 0.45
17 5 0.25
18 6 0.30
ACGTcount: A:0.32, C:0.00, G:0.21, T:0.47
Consensus pattern (16 bp):
ATATGTGTATTAATGT
Found at i:59197005 original size:2 final size:2
Alignment explanation
Indices: 59196998--59197039 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
59196988 GCCCATTTGT
59196998 TA TA TA TA TA TA 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
59197040 CTGTTCAATT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:59197105 original size:69 final size:69
Alignment explanation
Indices: 59197032--59197282 Score: 281
Period size: 70 Copynumber: 3.6 Consensus size: 69
59197022 TATATATATA
* ** * * *
59197032 TATATATACTGTTCAATTTTGGTGTAAAAATATTGCTCAATTTGGTATGTATATGCTGCCTAATT
1 TATATATACTGTTAAATTTTGGTGTAAAAATGGTGTTAAATTTGGTATGTATATGCTGCCTATTT
59197097 GTTG
66 GTTG
* * * *
59197101 TATATCTATGCTGTTAAATTTTGGTGT-AAAGTGGTGTTAAATTTGGTATATATATGTTGCCTAT
1 TATA--TATACTGTTAAATTTTGGTGTAAAAATGGTGTTAAATTTGGTATGTATATGCTGCCTAT
*
59197165 TTGCTG
64 TTGTTG
* * *
59197171 TATATATGCTGTTAAATTTTGGTGTAAAAGTGGTGTTAAATTTGGTATGTATATGCTGCCCATTT
1 TATATATACTGTTAAATTTTGGTGTAAAAATGGTGTTAAATTTGGTATGTATATGCTGCCTATTT
*
59197236 GTTA
66 GTTG
* * * *
59197240 TATATA-AGCTGTCCAAATTTTGGTGTATAAATGTTGTTTAATT
1 TATATATA-CTGT-TAAATTTTGGTGTAAAAATGGTGTTAAATT
59197283 AATTTGGTAT
Statistics
Matches: 155, Mismatches: 22, Indels: 9
0.83 0.12 0.05
Matches are distributed among these distances:
68 21 0.14
69 52 0.34
70 63 0.41
71 19 0.12
ACGTcount: A:0.27, C:0.08, G:0.20, T:0.46
Consensus pattern (69 bp):
TATATATACTGTTAAATTTTGGTGTAAAAATGGTGTTAAATTTGGTATGTATATGCTGCCTATTT
GTTG
Found at i:59197173 original size:70 final size:68
Alignment explanation
Indices: 59197070--59197266 Score: 272
Period size: 69 Copynumber: 2.8 Consensus size: 68
59197060 AATATTGCTC
*
59197070 AATTTGGTATGTATATGCTGCCTAATTGTTGTATATCTATGCTGTTAAATTTTGGTGTAAAGTGG
1 AATTTGGTATGTATATGCTGCCTATTTG-TGTATAT-TATGCTGTTAAATTTTGGTGTAAAGTGG
59197135 TGTTA
64 TGTTA
* *
59197140 AATTTGGTATATATATGTTGCCTATTTGCTGTATA-TATGCTGTTAAATTTTGGTGTAAAAGTGG
1 AATTTGGTATGTATATGCTGCCTATTTG-TGTATATTATGCTGTTAAATTTTGGTGT-AAAGTGG
59197204 TGTTA
64 TGTTA
* * *
59197209 AATTTGGTATGTATATGCTGCCCATTTGT-TATATATAAGCTGTCCAAATTTTGGTGTA
1 AATTTGGTATGTATATGCTGCCTATTTGTGTATAT-TATGCTGT-TAAATTTTGGTGTA
59197267 TAAATGTTGT
Statistics
Matches: 114, Mismatches: 9, Indels: 9
0.86 0.07 0.07
Matches are distributed among these distances:
67 4 0.04
68 22 0.19
69 45 0.39
70 43 0.38
ACGTcount: A:0.25, C:0.08, G:0.21, T:0.45
Consensus pattern (68 bp):
AATTTGGTATGTATATGCTGCCTATTTGTGTATATTATGCTGTTAAATTTTGGTGTAAAGTGGTG
TTA
Found at i:59197191 original size:24 final size:23
Alignment explanation
Indices: 59197107--59197213 Score: 71
Period size: 22 Copynumber: 4.7 Consensus size: 23
59197097 GTTGTATATC
59197107 TATGCTGTTAAATTTTGGTGTAA
1 TATGCTGTTAAATTTTGGTGTAA
* *
59197130 -AGTGGTGTTAAA-TTTGGTATATA
1 TA-TGCTGTTAAATTTTGGTGTA-A
* * *
59197153 TATGTTGCCT--A-TTTGCTGTATA
1 TATGCTG-TTAAATTTTGGTGTA-A
59197175 TATGCTGTTAAATTTTGGTGTAA
1 TATGCTGTTAAATTTTGGTGTAA
* *
59197198 AAGTGGTGTTAAATTT
1 TA-TGCTGTTAAATTT
59197214 GGTATGTATA
Statistics
Matches: 65, Mismatches: 11, Indels: 15
0.71 0.12 0.16
Matches are distributed among these distances:
21 1 0.02
22 25 0.38
23 17 0.26
24 22 0.34
ACGTcount: A:0.26, C:0.05, G:0.22, T:0.47
Consensus pattern (23 bp):
TATGCTGTTAAATTTTGGTGTAA
Found at i:59197294 original size:139 final size:139
Alignment explanation
Indices: 59197032--59197282 Score: 317
Period size: 139 Copynumber: 1.8 Consensus size: 139
59197022 TATATATATA
* * * *
59197032 TATATATACTGTTCAATTTTGGTGTAAAAATATTGCTCAATTTGGTATGTATATGCTGCCTAATT
1 TATATATACTGTTAAATTTTGGTGTAAAAATAGTGCTAAATTTGGTATGTATATGCTGCCCAATT
* * * * **
59197097 GTTGTATATCTATGCTGTTAAATTTTGGTGTAAAGTGGTGTTAAATTTGGTATATATATGTTGCC
66 GTTGTATATATAAGCTGTCAAATTTTGGTGTAAAATGGTGTTAAATTTAATATATATATGTTGCC
59197162 TATTTGCTG
131 TATTTGCTG
* * * * *
59197171 TATATATGCTGTTAAATTTTGGTGTAAAAGTGGTGTTAAATTTGGTATGTATATGCTGCCCATTT
1 TATATATACTGTTAAATTTTGGTGTAAAAATAGTGCTAAATTTGGTATGTATATGCTGCCCAATT
* *
59197236 G-T-TATATATAAGCTGTCCAAATTTTGGTGTATAAATGTTGTTTAATT
66 GTTGTATATATAAGCTGT-CAAATTTTGGTGTA-AAATGGTGTTAAATT
59197283 AATTTGGTAT
Statistics
Matches: 95, Mismatches: 15, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
137 12 0.13
138 14 0.15
139 69 0.73
ACGTcount: A:0.27, C:0.08, G:0.20, T:0.46
Consensus pattern (139 bp):
TATATATACTGTTAAATTTTGGTGTAAAAATAGTGCTAAATTTGGTATGTATATGCTGCCCAATT
GTTGTATATATAAGCTGTCAAATTTTGGTGTAAAATGGTGTTAAATTTAATATATATATGTTGCC
TATTTGCTG
Found at i:59197688 original size:3 final size:3
Alignment explanation
Indices: 59197680--59197728 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
59197670 TGTTACACTG
59197680 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
59197728 T
1 T
59197729 CAGGTACTTA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:59197946 original size:36 final size:35
Alignment explanation
Indices: 59197885--59197953 Score: 95
Period size: 36 Copynumber: 1.9 Consensus size: 35
59197875 ATACATAAGT
*
59197885 TTTTATAATATATATATACATATACATATATATATA
1 TTTTATAATATACATATACA-ATACATATATATATA
59197921 TTTTATAACTCATACATATAC-ATACATATATAT
1 TTTTATAA-T-ATACATATACAATACATATATAT
59197954 GTCCTTTATA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
36 20 0.67
37 1 0.03
38 9 0.30
ACGTcount: A:0.45, C:0.10, G:0.00, T:0.45
Consensus pattern (35 bp):
TTTTATAATATACATATACAATACATATATATATA
Found at i:59198159 original size:43 final size:46
Alignment explanation
Indices: 59198112--59198201 Score: 123
Period size: 43 Copynumber: 2.0 Consensus size: 46
59198102 CATATATATG
* ** *
59198112 TATATATACATACTTGTATATAT-TTTTTATA-TTTTAT-ATTTTA
1 TATATATACATACATACATATATCTTTTTACATTTTTATAATTTTA
59198155 TATATATACATACATACATATATCTTTTTACATTTTTATAATTTTA
1 TATATATACATACATACATATATCTTTTTACATTTTTATAATTTTA
59198201 T
1 T
59198202 TCATTTTCTA
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
43 20 0.50
44 7 0.17
45 6 0.15
46 7 0.17
ACGTcount: A:0.34, C:0.08, G:0.01, T:0.57
Consensus pattern (46 bp):
TATATATACATACATACATATATCTTTTTACATTTTTATAATTTTA
Found at i:59200554 original size:30 final size:30
Alignment explanation
Indices: 59200515--59200571 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
59200505 TTTTATAACT
59200515 AATTAATATTT-AT-TACTTAAAAATATTTAA
1 AATTAATATTTCATATA-TT-AAAATATTTAA
*
59200545 AATTTATATTTCATATATTAAAATATT
1 AATTAATATTTCATATATTAAAATATT
59200572 AACAACAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
30 18 0.75
31 4 0.17
32 2 0.08
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (30 bp):
AATTAATATTTCATATATTAAAATATTTAA
Found at i:59205648 original size:30 final size:30
Alignment explanation
Indices: 59205613--59205669 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
59205603 AAAAACTCTT
59205613 AAATTTCTCGC-TAAATTTCTCAAAGCTTTC
1 AAATTTCTC-CTTAAATTTCTCAAAGCTTTC
59205643 AAATTTCTCCTTAAATTTCTCAAAGCT
1 AAATTTCTCCTTAAATTTCTCAAAGCT
59205670 CTCATTAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 1 0.04
30 25 0.96
ACGTcount: A:0.32, C:0.23, G:0.05, T:0.40
Consensus pattern (30 bp):
AAATTTCTCCTTAAATTTCTCAAAGCTTTC
Found at i:59210940 original size:45 final size:45
Alignment explanation
Indices: 59210856--59210995 Score: 160
Period size: 45 Copynumber: 3.1 Consensus size: 45
59210846 TATTGCCGGC
* * * *
59210856 TTACTGA-TCAGGCAC-TTATGTGCCGACTACTGTTACTGTTACTG
1 TTACTGATTCA-GCACTTTGTGTGTCGAATACTATTACTGTTACTG
* *
59210900 TTACTGATTC-GATACTTTGTGTGTCGAATATTATTACTGTTACTG
1 TTACTGATTCAG-CACTTTGTGTGTCGAATACTATTACTGTTACTG
* * *
59210945 TTACAGATTCAGCACTTTGTGTGTTGAATACTGTTACTGTTACTG
1 TTACTGATTCAGCACTTTGTGTGTCGAATACTATTACTGTTACTG
59210990 TTACTG
1 TTACTG
59210996 CTACCGTTAC
Statistics
Matches: 80, Mismatches: 12, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
43 1 0.01
44 9 0.11
45 69 0.86
46 1 0.01
ACGTcount: A:0.21, C:0.17, G:0.19, T:0.42
Consensus pattern (45 bp):
TTACTGATTCAGCACTTTGTGTGTCGAATACTATTACTGTTACTG
Found at i:59210984 original size:6 final size:6
Alignment explanation
Indices: 59210973--59211014 Score: 57
Period size: 6 Copynumber: 6.8 Consensus size: 6
59210963 GTGTGTTGAA
* *
59210973 TACTGT TACTGT TACTGT TACTGC TACCGT TACTGTT TACTG
1 TACTGT TACTGT TACTGT TACTGT TACTGT TACTG-T TACTG
59211015 ATCAGGTACT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
6 25 0.81
7 6 0.19
ACGTcount: A:0.17, C:0.21, G:0.17, T:0.45
Consensus pattern (6 bp):
TACTGT
Found at i:59215103 original size:126 final size:126
Alignment explanation
Indices: 59214331--59215102 Score: 1221
Period size: 126 Copynumber: 6.1 Consensus size: 126
59214321 GGCGAAACAT
* * *
59214331 GAACTACTGTAGAAAAATAGCTTCAACGTAGGAGCTTTTTTCATCAATTTTGCTGATAGTGCATC
1 GAACTACTGTAGAAAAAGAGCGTCAACGTAGGAGCTTTTTTCATCAATTTTGCTGACAGTGCATC
*
59214396 CTGCTTGAAGCGTTTTTGACACTATTTGTTCATAACCGTCTTCTCAAAATTATTTTTTCAG
66 CTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAACCGTCTTCTCAAAATTATTTTTTCAG
* * *
59214457 GAACTACTGTAGAAAAATAGAGTCAACGTAGGAGCTTTTTTCATCAATTTTGCTGATAGTGCATC
1 GAACTACTGTAGAAAAAGAGCGTCAACGTAGGAGCTTTTTTCATCAATTTTGCTGACAGTGCATC
*
59214522 CTGCTTGAAGCGTTTTTGACACTATTTGTTCATAACCGTCTTCTCAAAATTATTTTTTCAG
66 CTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAACCGTCTTCTCAAAATTATTTTTTCAG
59214583 GAACTACTGTAGAAAAAGAGCGTCAACGTAGGAGCTTTTTTCATCAATTTTGCTGACAGTGCATC
1 GAACTACTGTAGAAAAAGAGCGTCAACGTAGGAGCTTTTTTCATCAATTTTGCTGACAGTGCATC
*
59214648 CTGCTTGAAGCGTTTTTGACACTATTTGTTCATAACCGTCTTCTCAAAATTATTTTTTCAG
66 CTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAACCGTCTTCTCAAAATTATTTTTTCAG
*
59214709 GAACTACTGTAGAAAAAGAGCGTCCACGT-GGAAGCTTTTTTCAGT-AATTTTGCTGACAGTGCA
1 GAACTACTGTAGAAAAAGAGCGTCAACGTAGG-AGCTTTTTTCA-TCAATTTTGCTGACAGTGCA
* * * * *
59214772 TCCTCCTTGAAGCTTTTTTGACACTATTTATTCAGAACTGTCTTCTCAAAATTATTTTTTCAA
64 TCCTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAACCGTCTTCTCAAAATTATTTTTTCAG
* * * *
59214835 GAACTACTGTAGAAAAAGAGCGTCCACATGGGAGCTTTTTTCAGT-AATTTTGCTGACAATGCAT
1 GAACTACTGTAGAAAAAGAGCGTCAACGTAGGAGCTTTTTTCA-TCAATTTTGCTGACAGTGCAT
* * *
59214899 CCTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAACGTCTTTTCAAAATTATTTTTTCAT
65 CCTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAACCGTCTTCTCAAAATTATTTTTTCAG
* * * *
59214961 GAACCACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTCCAGT-AATTTTGCTGACAGTGCAT
1 GAACTACTGTAGAAAAAGAGCGTCAACGTAGGAGCTTTTTTCA-TCAATTTTGCTGACAGTGCAT
* *
59215025 CCTACTTGAAGCGTTTTTGACACTATTTGTTCAGAACCGTATTCTCAAAATTATTTTTT-AG
65 CCTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAACCGTCTTCTCAAAATTATTTTTTCAG
59215086 GAACTACTGTAGAAAAA
1 GAACTACTGTAGAAAAA
59215103 AAAATAAAAT
Statistics
Matches: 612, Mismatches: 31, Indels: 7
0.94 0.05 0.01
Matches are distributed among these distances:
125 19 0.03
126 590 0.96
127 3 0.00
ACGTcount: A:0.28, C:0.18, G:0.17, T:0.37
Consensus pattern (126 bp):
GAACTACTGTAGAAAAAGAGCGTCAACGTAGGAGCTTTTTTCATCAATTTTGCTGACAGTGCATC
CTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAACCGTCTTCTCAAAATTATTTTTTCAG
Found at i:59215222 original size:34 final size:33
Alignment explanation
Indices: 59215184--59215273 Score: 108
Period size: 33 Copynumber: 2.7 Consensus size: 33
59215174 AACTATATCT
*
59215184 TAATTTAATTAAATTTCTTAAAAACACTAAACCC
1 TAATTTAATT-AATTTATTAAAAACACTAAACCC
* * * * *
59215218 TAATTAAATTTATTTATTTAAAACCCTTAACCC
1 TAATTTAATTAATTTATTAAAAACACTAAACCC
*
59215251 TAATTTAATTAATTTTTTAAAAA
1 TAATTTAATTAATTTATTAAAAA
59215274 GAATACTAAA
Statistics
Matches: 46, Mismatches: 10, Indels: 1
0.81 0.18 0.02
Matches are distributed among these distances:
33 37 0.80
34 9 0.20
ACGTcount: A:0.44, C:0.13, G:0.00, T:0.42
Consensus pattern (33 bp):
TAATTTAATTAATTTATTAAAAACACTAAACCC
Found at i:59215357 original size:15 final size:15
Alignment explanation
Indices: 59215337--59215375 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
59215327 TTATTTTAAC
* *
59215337 AAAACCCTAACCCTA
1 AAAACCCTAAACCAA
59215352 AAAACCCTAAACCAA
1 AAAACCCTAAACCAA
*
59215367 AAAATCCTA
1 AAAACCCTA
59215376 GGGACTAAAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.54, C:0.33, G:0.00, T:0.13
Consensus pattern (15 bp):
AAAACCCTAAACCAA
Found at i:59215484 original size:14 final size:14
Alignment explanation
Indices: 59215462--59215496 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
59215452 ACGTTAGTAA
*
59215462 AGCGCGTCCATGTC
1 AGCGCGTCCACGTC
*
59215476 AGTGCGTCCACGTC
1 AGCGCGTCCACGTC
59215490 AGCGCGT
1 AGCGCGT
59215497 TTTGTGCTGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.14, C:0.34, G:0.31, T:0.20
Consensus pattern (14 bp):
AGCGCGTCCACGTC
Found at i:59231621 original size:19 final size:19
Alignment explanation
Indices: 59231597--59231637 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
59231587 TTAAGCTCCT
*
59231597 CATGTGCTTTTTTGAAATC
1 CATGTGCTCTTTTGAAATC
59231616 CATGTGCTCTTTTGAAATC
1 CATGTGCTCTTTTGAAATC
59231635 CAT
1 CAT
59231638 AAAGTATGTC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.22, C:0.20, G:0.15, T:0.44
Consensus pattern (19 bp):
CATGTGCTCTTTTGAAATC
Found at i:59237254 original size:25 final size:25
Alignment explanation
Indices: 59237220--59237269 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
59237210 TCAATTGATA
** *
59237220 TATTAGTATGTCTCTTATGTATGTT
1 TATTAGTATGAATATTATGTATGTT
59237245 TATTAGTATGAATATTATGTATGTT
1 TATTAGTATGAATATTATGTATGTT
59237270 ATGTATATTA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.26, C:0.04, G:0.16, T:0.54
Consensus pattern (25 bp):
TATTAGTATGAATATTATGTATGTT
Found at i:59237290 original size:25 final size:25
Alignment explanation
Indices: 59237262--59237309 Score: 80
Period size: 25 Copynumber: 1.9 Consensus size: 25
59237252 ATGAATATTA
59237262 TGTATGTTATGTAT-ATTACTGTTCG
1 TGTATGTTATGT-TCATTACTGTTCG
59237287 TGTATGTTATGTTCATTACTGTT
1 TGTATGTTATGTTCATTACTGTT
59237310 TATAATATGT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 1 0.05
25 21 0.95
ACGTcount: A:0.19, C:0.08, G:0.19, T:0.54
Consensus pattern (25 bp):
TGTATGTTATGTTCATTACTGTTCG
Found at i:59237332 original size:13 final size:13
Alignment explanation
Indices: 59237316--59237340 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
59237306 TGTTTATAAT
59237316 ATGTATGTATATC
1 ATGTATGTATATC
59237329 ATGTATGTATAT
1 ATGTATGTATAT
59237341 TACTATTTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.04, G:0.16, T:0.48
Consensus pattern (13 bp):
ATGTATGTATATC
Found at i:59240786 original size:18 final size:17
Alignment explanation
Indices: 59240763--59240807 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
59240753 AAGTTAAAAT
59240763 ACTTTTTAAATGATTTTA
1 ACTTTTTAAATG-TTTTA
*
59240781 ACTTTTAAAATGTTTTA
1 ACTTTTTAAATGTTTTA
59240798 A-TTATTTAAA
1 ACTT-TTTAAA
59240808 ATTATATTGC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 2 0.08
17 11 0.46
18 11 0.46
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.53
Consensus pattern (17 bp):
ACTTTTTAAATGTTTTA
Found at i:59240808 original size:18 final size:18
Alignment explanation
Indices: 59240763--59240809 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
59240753 AAGTTAAAAT
*
59240763 ACTTTTTAAATGATTTTA
1 ACTTTTAAAATGATTTTA
59240781 ACTTTTAAAATG-TTTTA
1 ACTTTTAAAATGATTTTA
*
59240798 ATTATTTAAAAT
1 ACT-TTTAAAAT
59240810 TATATTGCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
17 7 0.27
18 19 0.73
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.53
Consensus pattern (18 bp):
ACTTTTAAAATGATTTTA
Found at i:59242187 original size:2 final size:2
Alignment explanation
Indices: 59242180--59242219 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
59242170 TTATAAAACT
59242180 TA TA TA TA TA 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
59242220 ATACATACTG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:59242460 original size:12 final size:12
Alignment explanation
Indices: 59242439--59242515 Score: 52
Period size: 12 Copynumber: 6.4 Consensus size: 12
59242429 ATATTATGAA
59242439 ATATAAATATGT
1 ATATAAATATGT
*
59242451 ATATATATATGT
1 ATATAAATATGT
* *
59242463 ATAAAAACTATGA
1 ATATAAA-TATGT
* **
59242476 AAATAAA-A-CA
1 ATATAAATATGT
59242486 ATAATAAAGTATGT
1 AT-ATAAA-TATGT
59242500 ATAT-AATATGT
1 ATATAAATATGT
59242511 ATATA
1 ATATA
59242516 TATTAAAACG
Statistics
Matches: 49, Mismatches: 10, Indels: 12
0.69 0.14 0.17
Matches are distributed among these distances:
10 2 0.04
11 15 0.31
12 18 0.37
13 12 0.24
14 2 0.04
ACGTcount: A:0.55, C:0.03, G:0.08, T:0.35
Consensus pattern (12 bp):
ATATAAATATGT
Found at i:59247699 original size:22 final size:22
Alignment explanation
Indices: 59247671--59247721 Score: 102
Period size: 22 Copynumber: 2.3 Consensus size: 22
59247661 CTCTCCAATC
59247671 CTCTCAATTTCCTTCCAAAATT
1 CTCTCAATTTCCTTCCAAAATT
59247693 CTCTCAATTTCCTTCCAAAATT
1 CTCTCAATTTCCTTCCAAAATT
59247715 CTCTCAA
1 CTCTCAA
59247722 ACCCATATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.27, C:0.33, G:0.00, T:0.39
Consensus pattern (22 bp):
CTCTCAATTTCCTTCCAAAATT
Found at i:59247824 original size:26 final size:27
Alignment explanation
Indices: 59247781--59247838 Score: 64
Period size: 26 Copynumber: 2.1 Consensus size: 27
59247771 AAATCTATTT
*
59247781 TTTTGAAATAAATATAAA-ATTTTATA
1 TTTTAAAATAAATATAAATATTTTATA
* * *
59247807 TTTTAAAATAATTTTAAATTTTTTTATA
1 TTTTAAAATAAATATAAA-TATTTTATA
59247835 TTTT
1 TTTT
59247839 CATCAATGGC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
26 15 0.58
28 11 0.42
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (27 bp):
TTTTAAAATAAATATAAATATTTTATA
Found at i:59247951 original size:15 final size:16
Alignment explanation
Indices: 59247931--59247961 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
59247921 TTTGTAATTA
59247931 TTATTTAAG-ATTTTT
1 TTATTTAAGTATTTTT
59247946 TTATTTAAGTATTTTT
1 TTATTTAAGTATTTTT
59247962 AGATAATTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (16 bp):
TTATTTAAGTATTTTT
Found at i:59249868 original size:133 final size:133
Alignment explanation
Indices: 59249630--59249873 Score: 398
Period size: 133 Copynumber: 1.8 Consensus size: 133
59249620 CTTACATGTA
* * ** *
59249630 TCCTTTTCCGAATACTATGGCAGGTTGGAGCCAAATGCCTGGTTTAGCTCCATTTCCTGTTATGC
1 TCCTTTTCCGAATACTATGCCAGGTTGGAACCAAATGCCCAGTTCAGCTCCATTTCCTGTTATGC
* * *
59249695 CGAGCGGGCCGTCGATATCTAGGCCAGTGGCGTAGGAGGGATCGCAAGGGGGGGCCGTCGGAGAG
66 CGAGCGGACCGTCGATATCTAGGCCAGCGGCGCAGGAGGGATCGCAAGGGGGGGCCGTCGGAGAG
59249760 CTC
131 CTC
* *
59249763 TCCTTTTCTGAATACTATGCCAGGTTGGAACCAAATGCCCAGTTCAGCTCCATTTCCTGTTATGT
1 TCCTTTTCCGAATACTATGCCAGGTTGGAACCAAATGCCCAGTTCAGCTCCATTTCCTGTTATGC
59249828 CGAGCGGACCGTCGATATCTAGGCCAGCGGCGCAGGAGGGATCGCA
66 CGAGCGGACCGTCGATATCTAGGCCAGCGGCGCAGGAGGGATCGCA
59249874 CATGCTTTCG
Statistics
Matches: 101, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
133 101 1.00
ACGTcount: A:0.20, C:0.25, G:0.30, T:0.25
Consensus pattern (133 bp):
TCCTTTTCCGAATACTATGCCAGGTTGGAACCAAATGCCCAGTTCAGCTCCATTTCCTGTTATGC
CGAGCGGACCGTCGATATCTAGGCCAGCGGCGCAGGAGGGATCGCAAGGGGGGGCCGTCGGAGAG
CTC
Found at i:59250301 original size:11 final size:11
Alignment explanation
Indices: 59250274--59250308 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
59250264 TTTAATTGAA
59250274 AACCCTAACCT
1 AACCCTAACCT
*
59250285 AA-CCTACCCT
1 AACCCTAACCT
59250295 AACCCTAACCT
1 AACCCTAACCT
59250306 AAC
1 AAC
59250309 TTAATTAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
10 9 0.43
11 12 0.57
ACGTcount: A:0.37, C:0.46, G:0.00, T:0.17
Consensus pattern (11 bp):
AACCCTAACCT
Found at i:59250303 original size:16 final size:15
Alignment explanation
Indices: 59250275--59250306 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
59250265 TTAATTGAAA
59250275 ACCCTAACCTAACCT
1 ACCCTAACCTAACCT
59250290 ACCCTAACCCTAACCT
1 ACCCTAA-CCTAACCT
59250306 A
1 A
59250307 ACTTAATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.34, C:0.47, G:0.00, T:0.19
Consensus pattern (15 bp):
ACCCTAACCTAACCT
Found at i:59250324 original size:29 final size:29
Alignment explanation
Indices: 59250290--59250595 Score: 455
Period size: 29 Copynumber: 10.8 Consensus size: 29
59250280 AACCTAACCT
*
59250290 ACCCTAACCCTAACCTAACTTAATTAAAA
1 ACCCTAACCCTAACCTAAATTAATTAAAA
*
59250319 ACCCTAACTCTAACCTAAATTAATTAAAA
1 ACCCTAACCCTAACCTAAATTAATTAAAA
59250348 ACCCTAACCCTAACCTAAATTAATTAAAA
1 ACCCTAACCCTAACCTAAATTAATTAAAA
* *
59250377 ACCCTAACCCTAACCTAACTTAACTAAAA
1 ACCCTAACCCTAACCTAAATTAATTAAAA
*
59250406 ACCCTAACCCTAACCTAAATTAACTAAAA
1 ACCCTAACCCTAACCTAAATTAATTAAAA
*
59250435 ACCCTAACCCTAACCTAAATTAACT--AA
1 ACCCTAACCCTAACCTAAATTAATTAAAA
59250462 A----AACCCTAACCTAAATTAATT-AAA
1 ACCCTAACCCTAACCTAAATTAATTAAAA
*
59250486 ACCTTAACCCTAACCTAAATTAATTAAAA
1 ACCCTAACCCTAACCTAAATTAATTAAAA
*
59250515 ACCCTAACCCTAATCTAAATTAATTAAAA
1 ACCCTAACCCTAACCTAAATTAATTAAAA
* * *
59250544 ACCCTAATCCTAACCTAAATTAACTGAAA
1 ACCCTAACCCTAACCTAAATTAATTAAAA
*
59250573 ACCCTAACCCTAACCTAACTTAA
1 ACCCTAACCCTAACCTAAATTAA
59250596 ACCCTAACCC
Statistics
Matches: 256, Mismatches: 15, Indels: 12
0.90 0.05 0.04
Matches are distributed among these distances:
23 19 0.07
24 3 0.01
27 3 0.01
28 20 0.08
29 211 0.82
ACGTcount: A:0.47, C:0.29, G:0.00, T:0.24
Consensus pattern (29 bp):
ACCCTAACCCTAACCTAAATTAATTAAAA
Found at i:59250610 original size:23 final size:24
Alignment explanation
Indices: 59250571--59250615 Score: 83
Period size: 23 Copynumber: 1.9 Consensus size: 24
59250561 AATTAACTGA
59250571 AAACCCTAACCCTAACC-TAACTT
1 AAACCCTAACCCTAACCGTAACTT
59250594 AAACCCTAACCCTAACCGTAAC
1 AAACCCTAACCCTAACCGTAAC
59250616 CATTAACAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
23 17 0.81
24 4 0.19
ACGTcount: A:0.40, C:0.40, G:0.02, T:0.18
Consensus pattern (24 bp):
AAACCCTAACCCTAACCGTAACTT
Found at i:59250710 original size:10 final size:10
Alignment explanation
Indices: 59250695--59250720 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
59250685 TTTTTGGCTT
59250695 CATAATTTTA
1 CATAATTTTA
59250705 CATAATTTTA
1 CATAATTTTA
59250715 CATAAT
1 CATAAT
59250721 GTTAGATTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.42, C:0.12, G:0.00, T:0.46
Consensus pattern (10 bp):
CATAATTTTA
Found at i:59253990 original size:126 final size:126
Alignment explanation
Indices: 59253757--59254111 Score: 579
Period size: 126 Copynumber: 2.8 Consensus size: 126
59253747 CCCAAGCTTG
*
59253757 CTACTGTAGCAAAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATTGCATCCTGG
1 CTACTGTAGCAAAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTGG
*
59253822 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAACAAAAAAATTATTTCTTACATGAC
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACATCAACAAAAAAATTATTTCTTACATGAC
* * * *
59253883 CTACTGTAGCAAAATCGCGTCCAGGAGCGCGCGATTTCACAATTTCTTCTCAAATAGCATTCTCG
1 CTACTGTAGCAAAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTGG
*
59253948 TAGAAACGATTTTATACTATTTGCTCAGAAACATCAGA-AAAAAAATTATTTCTTACATGAC
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACATCA-ACAAAAAAATTATTTCTTACATGAC
* * *
59254009 TTACTGTAGAAAAATTGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTGG
1 CTACTGTAGCAAAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTGG
*
59254074 TAGAAGCGATTTTATACTATTTGAC-CAGAAACGTCAAC
66 TAGAAGCGATTTTATACTATTTG-CTCAGAAACATCAAC
59254112 TCGAAATAAT
Statistics
Matches: 210, Mismatches: 16, Indels: 6
0.91 0.07 0.03
Matches are distributed among these distances:
125 1 0.00
126 207 0.99
127 2 0.01
ACGTcount: A:0.32, C:0.22, G:0.16, T:0.30
Consensus pattern (126 bp):
CTACTGTAGCAAAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTGG
TAGAAGCGATTTTATACTATTTGCTCAGAAACATCAACAAAAAAATTATTTCTTACATGAC
Found at i:59254886 original size:6 final size:6
Alignment explanation
Indices: 59254875--59254899 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
59254865 TTAGGTGTAA
59254875 TTTATT TTTATT TTTATT TTTATT T
1 TTTATT TTTATT TTTATT TTTATT T
59254900 ATACTTTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTATT
Found at i:59270820 original size:29 final size:29
Alignment explanation
Indices: 59270766--59270822 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 29
59270756 TGAATGAATA
*
59270766 TTTTTAATTAATAAATAGTATGAAATAATT
1 TTTTTAATTAATAAATA-TATAAAATAATT
59270796 TTTTTAATTTAATAAAT-TATAAAATAA
1 TTTTTAA-TTAATAAATATATAAAATAA
59270823 ATATTATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
29 9 0.36
30 7 0.28
31 9 0.36
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (29 bp):
TTTTTAATTAATAAATATATAAAATAATT
Found at i:59271229 original size:2 final size:2
Alignment explanation
Indices: 59271218--59271250 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
59271208 CCTTCTTTAT
59271218 TA TA -A 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
59271251 GTATTCTATA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:59273410 original size:3 final size:3
Alignment explanation
Indices: 59273395--59273475 Score: 110
Period size: 3 Copynumber: 26.7 Consensus size: 3
59273385 AGTAAATGAC
*
59273395 AAT AAT GAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* *
59273443 AAT AAT AACT AATT AGT TA- AAT AAT AAT AAT AA
1 AAT AAT AA-T AA-T AAT AAT AAT AAT AAT AAT AA
59273476 AAGGGACTAA
Statistics
Matches: 69, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
2 1 0.01
3 63 0.91
4 5 0.07
ACGTcount: A:0.63, C:0.01, G:0.02, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:59275842 original size:13 final size:13
Alignment explanation
Indices: 59275843--59275894 Score: 70
Period size: 13 Copynumber: 4.0 Consensus size: 13
59275833 GAGAATGAAA
59275843 AAAATGAAAAATG
1 AAAATGAAAAATG
**
59275856 GGAATGAAAAATG
1 AAAATGAAAAATG
59275869 AAAATG-AAAATG
1 AAAATGAAAAATG
59275881 AAAAATGAAAAATG
1 -AAAATGAAAAATG
59275895 GAGAGGCTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
12 6 0.18
13 21 0.64
14 6 0.18
ACGTcount: A:0.65, C:0.00, G:0.19, T:0.15
Consensus pattern (13 bp):
AAAATGAAAAATG
Found at i:59275845 original size:22 final size:22
Alignment explanation
Indices: 59275817--59275866 Score: 82
Period size: 22 Copynumber: 2.3 Consensus size: 22
59275807 TAAAAAAAAA
59275817 GAAAAAAAAGAAAAATGAGAAT
1 GAAAAAAAAGAAAAATGAGAAT
* *
59275839 GAAAAAAATGAAAAATGGGAAT
1 GAAAAAAAAGAAAAATGAGAAT
59275861 GAAAAA
1 GAAAAA
59275867 TGAAAATGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.70, C:0.00, G:0.20, T:0.10
Consensus pattern (22 bp):
GAAAAAAAAGAAAAATGAGAAT
Found at i:59275852 original size:6 final size:6
Alignment explanation
Indices: 59275843--59275891 Score: 53
Period size: 6 Copynumber: 7.7 Consensus size: 6
59275833 GAGAATGAAA
**
59275843 AAAATG AAAAATG GGAATG AAAAATG AAAATG AAAATG AAAAATG AAAA
1 AAAATG -AAAATG AAAATG -AAAATG AAAATG AAAATG -AAAATG AAAA
59275892 ATGGAGAGGC
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
6 20 0.56
7 16 0.44
ACGTcount: A:0.67, C:0.00, G:0.18, T:0.14
Consensus pattern (6 bp):
AAAATG
Found at i:59275854 original size:7 final size:7
Alignment explanation
Indices: 59275820--59275894 Score: 68
Period size: 7 Copynumber: 11.0 Consensus size: 7
59275810 AAAAAAAGAA
*
59275820 AAAAAAG
1 AAAAATG
59275827 AAAAATG
1 AAAAATG
*
59275834 -AGAATG
1 AAAAATG
59275840 AAAAAAATG
1 --AAAAATG
59275849 AAAAATG
1 AAAAATG
**
59275856 -GGAATG
1 AAAAATG
59275862 AAAAATG
1 AAAAATG
59275869 -AAAATG
1 AAAAATG
59275875 -AAAATG
1 AAAAATG
59275881 AAAAATG
1 AAAAATG
59275888 AAAAATG
1 AAAAATG
59275895 GAGAGGCTAA
Statistics
Matches: 56, Mismatches: 7, Indels: 10
0.77 0.10 0.14
Matches are distributed among these distances:
6 21 0.38
7 30 0.54
9 5 0.09
ACGTcount: A:0.68, C:0.00, G:0.19, T:0.13
Consensus pattern (7 bp):
AAAAATG
Found at i:59277280 original size:46 final size:46
Alignment explanation
Indices: 59277127--59277636 Score: 316
Period size: 46 Copynumber: 11.4 Consensus size: 46
59277117 ATCAGTGAAT
* * * *
59277127 ATTTCAGATCTTATCTCCCTG-AGATTACAGAGGAGCAGATCGAAGCC
1 ATTTCAGATCTTATCTCCCTGAAG-TTACAGTGGAGTAGACCGAAG-A
* * * **
59277174 A---CAAACCTTATCTCCCTGAAGTTACAGTGGAGCAG---GTTGA
1 ATTTCAGATCTTATCTCCCTGAAGTTACAGTGGAGTAGACCGAAGA
* * *
59277214 ATATGCA-AGTCTTATCTCCCTGAGGTTACAGTAGAGTAGACCGAAGA
1 AT-TTCAGA-TCTTATCTCCCTGAAGTTACAGTGGAGTAGACCGAAGA
* * **
59277261 ATTTCAGATCTTATCTCCCTGAAGTTACAATGGAGCAGA-TTAA-A
1 ATTTCAGATCTTATCTCCCTGAAGTTACAGTGGAGTAGACCGAAGA
** * * * * *
59277305 A-TAAAGGATCTCATCTCTCTGAAGTTACAGTAGAGTAGATC---GC
1 ATTTCA-GATCTTATCTCCCTGAAGTTACAGTGGAGTAGACCGAAGA
* *
59277348 A--TCAGGTCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGA
1 ATTTCAGATCTTATCTCCCTGAAGTTACAGTGGAGTAGACCGAAGA
* * * ** *
59277392 ATTTCAGATCTTGTCTCCCTGAGGTTACAGTGGAGCAGATTGGAG-
1 ATTTCAGATCTTATCTCCCTGAAGTTACAGTGGAGTAGACCGAAGA
* * * ** **
59277437 CTAGT-A-ATCCTATCTCCCTGAAGTTACAGTGGAGCGGA-TTAA-A
1 AT-TTCAGATCTTATCTCCCTGAAGTTACAGTGGAGTAGACCGAAGA
** ** *
59277480 A-TAAAGGAT-TTCATCTTTCTGAAGTTACAGTAGAGTAGACCGAAGA
1 ATTTCA-GATCTT-ATCTCCCTGAAGTTACAGTGGAGTAGACCGAAGA
*
59277526 ATTTCAGATCTTATCTCCCTGAAGTTAGAGTGGAGTAGACCGAAGA
1 ATTTCAGATCTTATCTCCCTGAAGTTACAGTGGAGTAGACCGAAGA
* **
59277572 ATTTCAGATCTTATCTCCCT-AAGGTTACAGTGGAGCAGGTCGAAG-
1 ATTTCAGATCTTATCTCCCTGAA-GTTACAGTGGAGTAGACCGAAGA
*
59277617 ATGGT-AGATCTTATCTCCCT
1 AT-TTCAGATCTTATCTCCCT
59277637 AAGCAGTAGT
Statistics
Matches: 360, Mismatches: 73, Indels: 62
0.73 0.15 0.13
Matches are distributed among these distances:
40 1 0.00
41 31 0.09
42 2 0.01
43 7 0.02
44 140 0.39
45 27 0.08
46 141 0.39
47 11 0.03
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (46 bp):
ATTTCAGATCTTATCTCCCTGAAGTTACAGTGGAGTAGACCGAAGA
Found at i:59277296 original size:90 final size:90
Alignment explanation
Indices: 59277180--59277560 Score: 329
Period size: 90 Copynumber: 4.3 Consensus size: 90
59277170 AGCCACAAAC
* * *
59277180 CTTATCTCCCTGAAGTTACAGTGGAGCAGGTTGAATATGCAA-G-TCTTATCTCCCTGAGGTTAC
1 CTTATCTCCCTGAAGTTACAGTGGAGCAGGTT-AAAAT-AAAGGATCTTATCTCCCTGAAGTTAC
59277243 AGTAGAGTAGACCGAAGAATTTCAGAT
64 AGTAGAGTAGACCGAAGAATTTCAGAT
* * * *
59277270 CTTATCTCCCTGAAGTTACAATGGAGCAGATTAAAATAAAGGATCTCATCTCTCTGAAGTTACAG
1 CTTATCTCCCTGAAGTTACAGTGGAGCAGGTTAAAATAAAGGATCTTATCTCCCTGAAGTTACAG
* * *
59277335 TAGAGTAGATC---GCA--TCAGGT
66 TAGAGTAGACCGAAGAATTTCAGAT
* * *** ** * *
59277355 CTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGAATTTCA-GATCTTGTCTCCCTGAGGTTA
1 CTTATCTCCCTGAAGTTACAGTGGAGCAG-GTTAA-AA-TAAAGGATCTTATCTCCCTGAAGTTA
* * ** * * *
59277419 CAGTGGAGCAGATTGGAG-CTAGT-A-AT
63 CAGTAGAGTAGACCGAAGAAT-TTCAGAT
* **
59277445 CCTATCTCCCTGAAGTTACAGTGGAGC-GGATTAAAATAAAGGAT-TTCATCTTTCTGAAGTTAC
1 CTTATCTCCCTGAAGTTACAGTGGAGCAGG-TTAAAATAAAGGATCTT-ATCTCCCTGAAGTTAC
59277508 AGTAGAGTAGACCGAAGAATTTCAGAT
64 AGTAGAGTAGACCGAAGAATTTCAGAT
*
59277535 CTTATCTCCCTGAAGTTAGAGTGGAG
1 CTTATCTCCCTGAAGTTACAGTGGAG
59277561 TAGACCGAAG
Statistics
Matches: 226, Mismatches: 48, Indels: 34
0.73 0.16 0.11
Matches are distributed among these distances:
85 31 0.14
86 2 0.01
87 36 0.16
88 34 0.15
89 10 0.04
90 111 0.49
91 1 0.00
92 1 0.00
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.29
Consensus pattern (90 bp):
CTTATCTCCCTGAAGTTACAGTGGAGCAGGTTAAAATAAAGGATCTTATCTCCCTGAAGTTACAG
TAGAGTAGACCGAAGAATTTCAGAT
Found at i:59277479 original size:175 final size:177
Alignment explanation
Indices: 59277272--59277609 Score: 536
Period size: 180 Copynumber: 1.9 Consensus size: 177
59277262 TTTCAGATCT
59277272 TATCTCCCTGAAGTTACAATGGAGCAGATTAAAATAAAGGATCTCATCTCTCTGAAGTTACAGTA
1 TATCTCCCTGAAGTTACAATGGAGCAGATTAAAATAAAGGATCTCATCTCTCTGAAGTTACAGTA
* * * *
59277337 GAGTAGATC-GCA-TCAGGTCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGAATTTCAGA
66 GAGTAGACCAGAATTCAGATCTTATCTCCCTGAAGTTACAGTGGAGTAGACCGAAGAATTTCAGA
* *
59277400 TCTTGTCTCCCTGAGGTTACAGTGGAGCAGATTGGAGCTAGTAATCC
131 TCTTATCTCCCTAAGGTTACAGTGGAGCAGATTGGAGCTAGTAATCC
* * * *
59277447 TATCTCCCTGAAGTTACAGTGGAGCGGATTAAAATAAAGGATTTCATCTTTCTGAAGTTACAGTA
1 TATCTCCCTGAAGTTACAATGGAGCAGATTAAAATAAAGGATCTCATCTCTCTGAAGTTACAGTA
*
59277512 GAGTAGACCGAAGAATTTCAGATCTTATCTCCCTGAAGTTAGAGTGGAGTAGACCGAAGAATTTC
66 GAGTAGACC--AGAA-TTCAGATCTTATCTCCCTGAAGTTACAGTGGAGTAGACCGAAGAATTTC
59277577 AGATCTTATCTCCCTAAGGTTACAGTGGAGCAG
128 AGATCTTATCTCCCTAAGGTTACAGTGGAGCAG
59277610 GTCGAAGATG
Statistics
Matches: 147, Mismatches: 11, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
175 69 0.47
178 2 0.01
180 76 0.52
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.28
Consensus pattern (177 bp):
TATCTCCCTGAAGTTACAATGGAGCAGATTAAAATAAAGGATCTCATCTCTCTGAAGTTACAGTA
GAGTAGACCAGAATTCAGATCTTATCTCCCTGAAGTTACAGTGGAGTAGACCGAAGAATTTCAGA
TCTTATCTCCCTAAGGTTACAGTGGAGCAGATTGGAGCTAGTAATCC
Found at i:59277544 original size:134 final size:131
Alignment explanation
Indices: 59277127--59277560 Score: 468
Period size: 134 Copynumber: 3.3 Consensus size: 131
59277117 ATCAGTGAAT
* * * * *
59277127 ATTTCAGATCTTATCTCCCTG-AGATTACAGAGGAGCAGATCGAAGCCACAAACCTTATCTCCCT
1 ATTTCAGATCTTATCTCCCTGAAG-TTACAGTGGAGCAGATTGAAGCTAGAATCC-TATCTCCCT
*
59277191 GAAGTTACAGTGGAGCAGG-TTGAATATGCAA-GTCTTATCTCCCTGAGGTTACAGTAGAGTAGA
64 GAAGTTACAGTGGAGC-GGATT-AAAAT--AAGGTCTTATCTCCCTGAGGTTACAGTAGAGTAGA
59277254 CCGAAGA
125 CCGAAGA
* ** * *
59277261 ATTTCAGATCTTATCTCCCTGAAGTTACAATGGAGCAGATT-AAAATAAAGGAT-CTCATCTCTC
1 ATTTCAGATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTGAAGCT--AGAATCCT-ATCTCCC
* ** *** * *
59277324 TGAAGTTACAGTAGAGTAGA-TCGCATCAGGTCTTATCTCCCTGAGGTTACAGTGGAGTAGACCG
63 TGAAGTTACAGTGGAGCGGATTAAAATAAGGTCTTATCTCCCTGAGGTTACAGTAGAGTAGACCG
59277388 AAGA
128 AAGA
* * *
59277392 ATTTCAGATCTTGTCTCCCTGAGGTTACAGTGGAGCAGATTGGAGCTAGTAATCCTATCTCCCTG
1 ATTTCAGATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTGAAGCTAG-AATCCTATCTCCCTG
** *
59277457 AAGTTACAGTGGAGCGGATTAAAATAAAGGAT-TTCATCTTTCTGAAGTTACAGTAGAGTAGACC
65 AAGTTACAGTGGAGCGGATTAAAAT-AAGG-TCTT-ATCTCCCTGAGGTTACAGTAGAGTAGACC
59277521 GAAGA
127 GAAGA
*
59277526 ATTTCAGATCTTATCTCCCTGAAGTTAGAGTGGAG
1 ATTTCAGATCTTATCTCCCTGAAGTTACAGTGGAG
59277561 TAGACCGAAG
Statistics
Matches: 247, Mismatches: 40, Indels: 26
0.79 0.13 0.08
Matches are distributed among these distances:
130 3 0.01
131 101 0.41
132 9 0.04
133 10 0.04
134 120 0.49
135 4 0.02
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (131 bp):
ATTTCAGATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTGAAGCTAGAATCCTATCTCCCTGA
AGTTACAGTGGAGCGGATTAAAATAAGGTCTTATCTCCCTGAGGTTACAGTAGAGTAGACCGAAG
A
Found at i:59277637 original size:45 final size:46
Alignment explanation
Indices: 59277130--59277639 Score: 232
Period size: 44 Copynumber: 11.4 Consensus size: 46
59277120 AGTGAATATT
* * * * *
59277130 TCAGATCTTATCTCCCTGAGATTACAGAGGAGCAGATCGAAGCCA--
1 TCAGATCTTATCTCCCTAAGGTTACAGTGGAGCAGACCGAAG-AATG
* * *** *
59277175 -CAAACCTTATCTCCCTGAA-GTTACAGTGGAGCAGGTTGAA-TATG
1 TCAGATCTTATCTCCCT-AAGGTTACAGTGGAGCAGACCGAAGAATG
* * * *
59277219 -CA-AGTCTTATCTCCCTGAGGTTACAGTAGAGTAGACCGAAGAATT
1 TCAGA-TCTTATCTCCCTAAGGTTACAGTGGAGCAGACCGAAGAATG
* **
59277264 TCAGATCTTATCTCCCTGAA-GTTACAATGGAGCAGA-TTAA-AAT-
1 TCAGATCTTATCTCCCT-AAGGTTACAGTGGAGCAGACCGAAGAATG
** * * * * * *
59277307 AAAGGATCTCATCTCTCTGAA-GTTACAGTAGAGTAGATC---GCA--
1 TCA-GATCTTATCTCCCT-AAGGTTACAGTGGAGCAGACCGAAGAATG
* * * *
59277349 TCAGGTCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGAATT
1 TCAGATCTTATCTCCCTAAGGTTACAGTGGAGCAGACCGAAGAATG
* * ** * *
59277395 TCAGATCTTGTCTCCCTGAGGTTACAGTGGAGCAGATTGGAG-CTAG
1 TCAGATCTTATCTCCCTAAGGTTACAGTGGAGCAGACCGAAGAAT-G
* * **
59277441 T-A-ATCCTATCTCCCTGAA-GTTACAGTGGAGCGGA-TTAA-AAT-
1 TCAGATCTTATCTCCCT-AAGGTTACAGTGGAGCAGACCGAAGAATG
** ** * * *
59277482 AAAGGAT-TTCATCTTTCTGAA-GTTACAGTAGAGTAGACCGAAGAATT
1 TCA-GATCTT-ATCTCCCT-AAGGTTACAGTGGAGCAGACCGAAGAATG
* * *
59277529 TCAGATCTTATCTCCCTGAA-GTTAGAGTGGAGTAGACCGAAGAATT
1 TCAGATCTTATCTCCCT-AAGGTTACAGTGGAGCAGACCGAAGAATG
**
59277575 TCAGATCTTATCTCCCTAAGGTTACAGTGGAGCAGGTCGAAG-ATGG
1 TCAGATCTTATCTCCCTAAGGTTACAGTGGAGCAGACCGAAGAAT-G
59277621 T-AGATCTTATCTCCCTAAG
1 TCAGATCTTATCTCCCTAAG
59277640 CAGTAGTGGA
Statistics
Matches: 358, Mismatches: 76, Indels: 62
0.72 0.15 0.12
Matches are distributed among these distances:
40 1 0.00
41 27 0.08
42 3 0.01
43 8 0.02
44 143 0.40
45 32 0.09
46 139 0.39
47 5 0.01
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (46 bp):
TCAGATCTTATCTCCCTAAGGTTACAGTGGAGCAGACCGAAGAATG
Found at i:59277651 original size:180 final size:175
Alignment explanation
Indices: 59277180--59277636 Score: 564
Period size: 175 Copynumber: 2.6 Consensus size: 175
59277170 AGCCACAAAC
* ** *
59277180 CTTATCTCCCTGAAGTTACAGTGGAGCAG---GTTGAATATGCA-AGTCTTATCTCCCTGAGGTT
1 CTTATCTCCCTGAAGTTACAGTGGAGTAGACCGAAGAAT-TTCAGA-TCTTATCTCCCTGAGGTT
* * * * *
59277241 ACAGTAGAGTAGACCGAAGAATTTCAGATCTTATCTCCCTGAAGTTACAATGGAGCAGATTAAAA
64 ACAGTGGAGCAGATCGAAG-ATGT-AGATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAA
* * *
59277306 TAAAGGATCTCATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAGGT
127 TAAAGGATCTCATCTCTCTGAAGTTACAGTAGAGTAGACCGAATCAGAT
* *
59277355 CTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGAATTTCAGATCTTGTCTCCCTGAGGTTAC
1 CTTATCTCCCTGAAGTTACAGTGGAGTAGACCGAAGAATTTCAGATCTTATCTCCCTGAGGTTAC
* * * * *
59277420 AGTGGAGCAGATTGGAGCTAGTA-ATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAATAA
66 AGTGGAGCAGATCGAAGAT-GTAGATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAATAA
* *
59277484 AGGATTTCATCTTTCTGAAGTTACAGTAGAGTAGACCGAAGAATTTCAGAT
130 AGGATCTCATCTCTCTGAAGTTACAGTAGAGTAGACC---GAA--TCAGAT
* *
59277535 CTTATCTCCCTGAAGTTAGAGTGGAGTAGACCGAAGAATTTCAGATCTTATCTCCCTAAGGTTAC
1 CTTATCTCCCTGAAGTTACAGTGGAGTAGACCGAAGAATTTCAGATCTTATCTCCCTGAGGTTAC
*
59277600 AGTGGAGCAGGTCGAAGATGGTAGATCTTATCTCCCT
66 AGTGGAGCAGATCGAAGAT-GTAGATCTTATCTCCCT
59277637 AAGCAGTAGT
Statistics
Matches: 240, Mismatches: 31, Indels: 16
0.84 0.11 0.06
Matches are distributed among these distances:
175 99 0.41
176 2 0.01
177 35 0.15
178 8 0.03
180 84 0.35
181 12 0.05
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.29
Consensus pattern (175 bp):
CTTATCTCCCTGAAGTTACAGTGGAGTAGACCGAAGAATTTCAGATCTTATCTCCCTGAGGTTAC
AGTGGAGCAGATCGAAGATGTAGATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAATAAA
GGATCTCATCTCTCTGAAGTTACAGTAGAGTAGACCGAATCAGAT
Found at i:59277682 original size:44 final size:44
Alignment explanation
Indices: 59277600--59278003 Score: 304
Period size: 44 Copynumber: 9.2 Consensus size: 44
59277590 CTAAGGTTAC
* * * *
59277600 AGTGGAGCAGGTCGAAGATGG-TAGATCTTATCTCCCTAAGCAGT
1 AGTGGAGCAGATCGAAGACGGCGA-ATCTCATCTCCCTAAGCAGT
*
59277644 AGTGGAGCAGATCGAAGACGGCGAATCTCATCTTCCTAAGCAGT
1 AGTGGAGCAGATCGAAGACGGCGAATCTCATCTCCCTAAGCAGT
* ** ** * *
59277688 AGTGAAGCAGATTTAAG-CCACCAGTC-CTATCTCCCTAAGCAGT
1 AGTGGAGCAGATCGAAGACGGCGAATCTC-ATCTCCCTAAGCAGT
* * * ** ** *
59277731 AGTGGAGCAGGTCAAAGATGTTAGACCCT-ATCTCCCTAAACAGT
1 AGTGGAGCAGATCGAAGACG-GCGAATCTCATCTCCCTAAGCAGT
*
59277775 AGTGGAGCAGATCGAAGACGGCGAATCTCATCTTCCTAAGCAGT
1 AGTGGAGCAGATCGAAGACGGCGAATCTCATCTCCCTAAGCAGT
* ** * ** *
59277819 AGTGAAGCAGATTTAAGCCATC-AGTC-CTATCTCCCTAAGCAGT
1 AGTGGAGCAGATCGAAGACGGCGAATCTC-ATCTCCCTAAGCAGT
* * * * *
59277862 AGTGGAGCAGGTCAAAGATGG-TAGATC-CTATCTCCCTAAGAAGT
1 AGTGGAGCAGATCGAAGACGGCGA-ATCTC-ATCTCCCTAAGCAGT
**
59277906 AGTGGAGCAGATCGAAGACGGCGAATCTCATCTTTCTAAGCAGT
1 AGTGGAGCAGATCGAAGACGGCGAATCTCATCTCCCTAAGCAGT
* ** ** * * *
59277950 AGTGAAGCAGATTTAAG-CCACCAGTCTTATCTCCCTAAGCAGT
1 AGTGGAGCAGATCGAAGACGGCGAATCTCATCTCCCTAAGCAGT
59277993 AGTGGAGCAGA
1 AGTGGAGCAGA
59278004 CTGAAAAAAA
Statistics
Matches: 279, Mismatches: 70, Indels: 23
0.75 0.19 0.06
Matches are distributed among these distances:
42 2 0.01
43 96 0.34
44 176 0.63
45 5 0.02
ACGTcount: A:0.30, C:0.22, G:0.25, T:0.23
Consensus pattern (44 bp):
AGTGGAGCAGATCGAAGACGGCGAATCTCATCTCCCTAAGCAGT
Found at i:59277727 original size:87 final size:87
Alignment explanation
Indices: 59277628--59278003 Score: 346
Period size: 87 Copynumber: 4.3 Consensus size: 87
59277618 TGGTAGATCT
*
59277628 TATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAATCTCATCTTCCTAAGCAGTAGTGA
1 TATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAATCTCATCTCCCTAAGCAGTAGTGA
*
59277693 AGCAGATTTAAGCCACCAGTCC
66 AGCAGATCTAAGCCACCAGTCC
* * * ** ** *
59277715 TATCTCCCTAAGCAGTAGTGGAGCAGGTCAAAGATGTTAGACCCT-ATCTCCCTAAACAGTAGTG
1 TATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACG-GCGAATCTCATCTCCCTAAGCAGTAGTG
* * ** * *
59277779 GAGCAGATCGAAGACGGCGAAT-C
65 AAGCAGATCTAAG-CCACCAGTCC
* * ** * ** *
59277802 TCATCTTCCTAAGCAGTAGTGAAGCAGATTTAAGCCATC-AGTC-CTATCTCCCTAAGCAGTAGT
1 T-ATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAATCTC-ATCTCCCTAAGCAGTAGT
* * * *****
59277865 GGAGCAGGTCAAAGATGGTAGATCC
64 GAAGCAGATCTAAGCCACCAG-TCC
* **
59277890 TATCTCCCTAAGAAGTAGTGGAGCAGATCGAAGACGGCGAATCTCATCTTTCTAAGCAGTAGTGA
1 TATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAATCTCATCTCCCTAAGCAGTAGTGA
* *
59277955 AGCAGATTTAAGCCACCAGTCT
66 AGCAGATCTAAGCCACCAGTCC
59277977 TATCTCCCTAAGCAGTAGTGGAGCAGA
1 TATCTCCCTAAGCAGTAGTGGAGCAGA
59278004 CTGAAAAAAA
Statistics
Matches: 223, Mismatches: 57, Indels: 18
0.75 0.19 0.06
Matches are distributed among these distances:
86 4 0.02
87 150 0.67
88 68 0.30
89 1 0.00
ACGTcount: A:0.30, C:0.23, G:0.24, T:0.23
Consensus pattern (87 bp):
TATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAATCTCATCTCCCTAAGCAGTAGTGA
AGCAGATCTAAGCCACCAGTCC
Found at i:59277749 original size:131 final size:131
Alignment explanation
Indices: 59277600--59278002 Score: 725
Period size: 131 Copynumber: 3.1 Consensus size: 131
59277590 CTAAGGTTAC
* *
59277600 AGTGGAGCAGGTCGAAGATGGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGG
1 AGTGGAGCAGGTCAAAGATGGTAGATCCTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGG
59277665 CGAATCTCATCTTCCTAAGCAGTAGTGAAGCAGATTTAAGCCACCAGTCCTATCTCCCTAAGCAG
66 CGAATCTCATCTTCCTAAGCAGTAGTGAAGCAGATTTAAGCCACCAGTCCTATCTCCCTAAGCAG
59277730 T
131 T
* * *
59277731 AGTGGAGCAGGTCAAAGATGTTAGACCCTATCTCCCTAAACAGTAGTGGAGCAGATCGAAGACGG
1 AGTGGAGCAGGTCAAAGATGGTAGATCCTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGG
*
59277796 CGAATCTCATCTTCCTAAGCAGTAGTGAAGCAGATTTAAGCCATCAGTCCTATCTCCCTAAGCAG
66 CGAATCTCATCTTCCTAAGCAGTAGTGAAGCAGATTTAAGCCACCAGTCCTATCTCCCTAAGCAG
59277861 T
131 T
*
59277862 AGTGGAGCAGGTCAAAGATGGTAGATCCTATCTCCCTAAGAAGTAGTGGAGCAGATCGAAGACGG
1 AGTGGAGCAGGTCAAAGATGGTAGATCCTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGG
* *
59277927 CGAATCTCATCTTTCTAAGCAGTAGTGAAGCAGATTTAAGCCACCAGTCTTATCTCCCTAAGCAG
66 CGAATCTCATCTTCCTAAGCAGTAGTGAAGCAGATTTAAGCCACCAGTCCTATCTCCCTAAGCAG
59277992 T
131 T
59277993 AGTGGAGCAG
1 AGTGGAGCAG
59278003 ACTGAAAAAA
Statistics
Matches: 259, Mismatches: 13, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
131 259 1.00
ACGTcount: A:0.30, C:0.22, G:0.25, T:0.23
Consensus pattern (131 bp):
AGTGGAGCAGGTCAAAGATGGTAGATCCTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGG
CGAATCTCATCTTCCTAAGCAGTAGTGAAGCAGATTTAAGCCACCAGTCCTATCTCCCTAAGCAG
T
Found at i:59279439 original size:3 final size:3
Alignment explanation
Indices: 59279431--59279502 Score: 92
Period size: 3 Copynumber: 23.7 Consensus size: 3
59279421 TTAGTCCCTT
* *
59279431 TTA TTA TTA TTA TT- TAA CTAA TTA GTTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA -TTA TTA -TTA TTA TTA TTA TTA TTA TTA
*
59279477 TTA TTA TTA TTA TTA TTA TCA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
59279503 GTCATTTACT
Statistics
Matches: 62, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
2 1 0.02
3 55 0.89
4 6 0.10
ACGTcount: A:0.33, C:0.03, G:0.01, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:59279507 original size:9 final size:9
Alignment explanation
Indices: 59279451--59279508 Score: 62
Period size: 9 Copynumber: 6.3 Consensus size: 9
59279441 TATTTAACTA
*
59279451 ATTAGTTATT
1 ATTA-TTATC
*
59279461 ATTATTATT
1 ATTATTATC
*
59279470 ATTATTATT
1 ATTATTATC
*
59279479 ATTATTATT
1 ATTATTATC
59279488 ATTATTATC
1 ATTATTATC
*
59279497 ATTATTGTC
1 ATTATTATC
59279506 ATT
1 ATT
59279509 TACTTATTTA
Statistics
Matches: 46, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
9 42 0.91
10 4 0.09
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.62
Consensus pattern (9 bp):
ATTATTATC
Found at i:59279701 original size:2 final size:2
Alignment explanation
Indices: 59279696--59279739 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
59279686 TTTTTTAGTT
59279696 TA TA TA TA TA TA 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
59279738 TA
1 TA
59279740 CCTACCTTTA
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:59279807 original size:12 final size:12
Alignment explanation
Indices: 59279792--59279825 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
59279782 CATTAGTATA
59279792 TACATACATATT
1 TACATACATATT
*
59279804 TACATATATATT
1 TACATACATATT
*
59279816 TACGTACATA
1 TACATACATA
59279826 GATTTTTCAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.41, C:0.15, G:0.03, T:0.41
Consensus pattern (12 bp):
TACATACATATT
Found at i:59279807 original size:24 final size:24
Alignment explanation
Indices: 59279775--59279825 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
59279765 ATAACTTTAT
59279775 ATATATACAT-TAGTATATACATAC
1 ATATATACATATA-TATATACATAC
* * *
59279799 ATATTTACATATATATTTACGTAC
1 ATATATACATATATATATACATAC
59279823 ATA
1 ATA
59279826 GATTTTTCAC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 21 0.91
25 2 0.09
ACGTcount: A:0.43, C:0.12, G:0.04, T:0.41
Consensus pattern (24 bp):
ATATATACATATATATATACATAC
Found at i:59282763 original size:48 final size:48
Alignment explanation
Indices: 59282708--59282802 Score: 181
Period size: 48 Copynumber: 2.0 Consensus size: 48
59282698 TTTCTATCTA
*
59282708 AACATCAAGTAAATTTAACATTTCATGCCATGAATCAAACTCAAACCT
1 AACATCAAGTAAATTTAACATTTCATGCAATGAATCAAACTCAAACCT
59282756 AACATCAAGTAAATTTAACATTTCATGCAATGAATCAAACTCAAACC
1 AACATCAAGTAAATTTAACATTTCATGCAATGAATCAAACTCAAACC
59282803 AAGTCATTTC
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.45, C:0.22, G:0.06, T:0.26
Consensus pattern (48 bp):
AACATCAAGTAAATTTAACATTTCATGCAATGAATCAAACTCAAACCT
Found at i:59284767 original size:17 final size:17
Alignment explanation
Indices: 59284743--59284992 Score: 302
Period size: 17 Copynumber: 14.7 Consensus size: 17
59284733 ATAAAGCCAG
59284743 CTCGCATATAAACATAA
1 CTCGCATATAAACATAA
* *
59284760 CTCACATATAAACATAG
1 CTCGCATATAAACATAA
* *
59284777 CTAGCATATAAACACAA
1 CTCGCATATAAACATAA
* *
59284794 CTTGCATATAAACATAG
1 CTCGCATATAAACATAA
*
59284811 CTCGCATATAAACACAA
1 CTCGCATATAAACATAA
*
59284828 CTCGCATATAAACATAG
1 CTCGCATATAAACATAA
*
59284845 CTAGCATATAAACATAA
1 CTCGCATATAAACATAA
*
59284862 CTCGCATATAAACATAG
1 CTCGCATATAAACATAA
*
59284879 CTCGCATATAAACACAA
1 CTCGCATATAAACATAA
* *
59284896 CTTGCATATAAACACAA
1 CTCGCATATAAACATAA
* *
59284913 CTCACATATAAACATAG
1 CTCGCATATAAACATAA
*
59284930 CTCGCATATAAACACAA
1 CTCGCATATAAACATAA
* * *
59284947 CTAGCATAGAAACATAG
1 CTCGCATATAAACATAA
* *
59284964 CTTGCTTATAAACATAA
1 CTCGCATATAAACATAA
*
59284981 CTCACATATAAA
1 CTCGCATATAAA
59284993 AATATATATA
Statistics
Matches: 194, Mismatches: 39, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 194 1.00
ACGTcount: A:0.46, C:0.23, G:0.08, T:0.23
Consensus pattern (17 bp):
CTCGCATATAAACATAA
Found at i:59296602 original size:59 final size:61
Alignment explanation
Indices: 59296541--59296868 Score: 324
Period size: 68 Copynumber: 5.2 Consensus size: 61
59296531 TTGACTAGTG
*
59296541 TTACAA-AA-TAATAATAATAAAACATCAAGTTTG-T-TTTACTAATCAAATGTTAGATTTTG
1 TTACAACAATTAATAATAATAAAA-AT-AAGTTTGATATTTACTAATCAAATGTTAGATTTTA
*
59296600 TTACAACAATTAAT-ATAAT--TAATAA-TTTGATAAATTTACTAATCAAATGTTAGATTTTA
1 TTACAACAATTAATAATAATAAAAATAAGTTTGAT--ATTTACTAATCAAATGTTAGATTTTA
59296659 TTACAACAATTAATACAATTAATACAATTAAT-AGTTTGATAAATTTACTAATCAAATGTTAGAT
1 TTACAACAATTAAT--AA-TAATA-AA--AATAAGTTTGAT--ATTTACTAATCAAATGTTAGAT
*
59296723 TTTG
58 TTTA
*
59296727 TTACAACAATTAAT-ATAAT--TAATAA-TTTGATAAATTTACTAATCAAATGTTAGATTTTA
1 TTACAACAATTAATAATAATAAAAATAAGTTTGAT--ATTTACTAATCAAATGTTAGATTTTA
59296786 TTACAACAATTAATACAATTAATATAATTAAT-AGTTTGATAAATTTACTAATCAAATGTTAGAT
1 TTACAACAATTAAT--AA-TAATA-AA--AATAAGTTTGAT--ATTTACTAATCAAATGTTAGAT
59296850 TTTA
58 TTTA
59296854 TTACAACAATTAATA
1 TTACAACAATTAATA
59296869 CAATTAATAC
Statistics
Matches: 235, Mismatches: 7, Indels: 47
0.81 0.02 0.16
Matches are distributed among these distances:
55 4 0.02
56 3 0.01
57 2 0.01
58 1 0.00
59 94 0.40
60 8 0.03
61 4 0.02
62 2 0.01
63 8 0.03
64 4 0.02
65 1 0.00
66 1 0.00
67 2 0.01
68 101 0.43
ACGTcount: A:0.45, C:0.08, G:0.06, T:0.41
Consensus pattern (61 bp):
TTACAACAATTAATAATAATAAAAATAAGTTTGATATTTACTAATCAAATGTTAGATTTTA
Found at i:59296676 original size:9 final size:9
Alignment explanation
Indices: 59296664--59296691 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
59296654 TTTTATTACA
59296664 ACAATTAAT
1 ACAATTAAT
59296673 ACAATTAAT
1 ACAATTAAT
59296682 ACAATTAAT
1 ACAATTAAT
59296691 A
1 A
59296692 GTTTGATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (9 bp):
ACAATTAAT
Found at i:59296679 original size:68 final size:68
Alignment explanation
Indices: 59296605--59296886 Score: 456
Period size: 68 Copynumber: 4.3 Consensus size: 68
59296595 TTTTGTTACA
59296605 ACAATTAATATAATTAATAATTTGATAAATTTACTAATCAAATGTTAGATTTTATTACAACAATT
1 ACAATTAATATAATTAATAATTTGATAAATTTACTAATCAAATGTTAGATTTTATTACAACAATT
59296670 AAT
66 AAT
* * *
59296673 ACAATTAATACAATTAATAGTTTGATAAATTTACTAATCAAATGTTAGATTTTGTT---AC----
1 ACAATTAATATAATTAATAATTTGATAAATTTACTAATCAAATGTTAGATTTTATTACAACAATT
59296731 -A-
66 AAT
59296732 ACAATTAATATAATTAATAATTTGATAAATTTACTAATCAAATGTTAGATTTTATTACAACAATT
1 ACAATTAATATAATTAATAATTTGATAAATTTACTAATCAAATGTTAGATTTTATTACAACAATT
59296797 AAT
66 AAT
*
59296800 ACAATTAATATAATTAATAGTTTGATAAATTTACTAATCAAATGTTAGATTTTATTACAACAATT
1 ACAATTAATATAATTAATAATTTGATAAATTTACTAATCAAATGTTAGATTTTATTACAACAATT
59296865 AAT
66 AAT
*
59296868 ACAATTAATACAATTAATA
1 ACAATTAATATAATTAATA
59296887 CAATTAATAC
Statistics
Matches: 197, Mismatches: 8, Indels: 18
0.88 0.04 0.08
Matches are distributed among these distances:
59 53 0.27
60 1 0.01
62 2 0.01
65 2 0.01
67 1 0.01
68 138 0.70
ACGTcount: A:0.46, C:0.08, G:0.05, T:0.40
Consensus pattern (68 bp):
ACAATTAATATAATTAATAATTTGATAAATTTACTAATCAAATGTTAGATTTTATTACAACAATT
AAT
Found at i:59296715 original size:127 final size:127
Alignment explanation
Indices: 59296575--59296877 Score: 579
Period size: 127 Copynumber: 2.4 Consensus size: 127
59296565 TCAAGTTTGT
59296575 TTTACTAATCAAATGTTAGATTTTGTTACAACAATTAATATAATTAATAATTTGATAAATTTACT
1 TTTACTAATCAAATGTTAGATTTTGTTACAACAATTAATATAATTAATAATTTGATAAATTTACT
59296640 AATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAGTTTGATAAA
66 AATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAGTTTGATAAA
59296702 TTTACTAATCAAATGTTAGATTTTGTTACAACAATTAATATAATTAATAATTTGATAAATTTACT
1 TTTACTAATCAAATGTTAGATTTTGTTACAACAATTAATATAATTAATAATTTGATAAATTTACT
*
59296767 AATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATATAATTAATAGTTTGATAAA
66 AATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAGTTTGATAAA
* *
59296829 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATA
1 TTTACTAATCAAATGTTAGATTTTGTTACAACAATTAATATAATTAATA
59296878 CAATTAATAC
Statistics
Matches: 173, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
127 173 1.00
ACGTcount: A:0.45, C:0.08, G:0.06, T:0.41
Consensus pattern (127 bp):
TTTACTAATCAAATGTTAGATTTTGTTACAACAATTAATATAATTAATAATTTGATAAATTTACT
AATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAGTTTGATAAA
Found at i:59296871 original size:9 final size:9
Alignment explanation
Indices: 59296859--59296904 Score: 92
Period size: 9 Copynumber: 5.1 Consensus size: 9
59296849 TTTTATTACA
59296859 ACAATTAAT
1 ACAATTAAT
59296868 ACAATTAAT
1 ACAATTAAT
59296877 ACAATTAAT
1 ACAATTAAT
59296886 ACAATTAAT
1 ACAATTAAT
59296895 ACAATTAAT
1 ACAATTAAT
59296904 A
1 A
59296905 GTTTGATAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 37 1.00
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.33
Consensus pattern (9 bp):
ACAATTAAT
Found at i:59296936 original size:86 final size:84
Alignment explanation
Indices: 59296790--59296970 Score: 326
Period size: 86 Copynumber: 2.1 Consensus size: 84
59296780 ATTTTATTAC
*
59296790 AACAATTAATACAATTAATATAATTAATAGTTTGATAAATTTACTAATCAAATGTTAGATTTTAT
1 AACAATTAATACAATTAATACAATTAATAGTTTGATAAATTTACTAATCAAATGTTAGATTTTAT
59296855 TACAACAATTAATACAATT
66 TACAACAATTAATACAATT
*
59296874 AATACAATTAATACAATTAATACAATTAATAGTTTGATAAATTTATTAATCAAATGTTAGATTTT
1 -A-ACAATTAATACAATTAATACAATTAATAGTTTGATAAATTTACTAATCAAATGTTAGATTTT
59296939 ATTACAACAATTAATACAATT
64 ATTACAACAATTAATACAATT
59296960 AACAATTAATA
1 AACAATTAATA
59296971 ATTTGATAAT
Statistics
Matches: 93, Mismatches: 2, Indels: 3
0.95 0.02 0.03
Matches are distributed among these distances:
84 10 0.11
85 2 0.02
86 81 0.87
ACGTcount: A:0.49, C:0.08, G:0.04, T:0.39
Consensus pattern (84 bp):
AACAATTAATACAATTAATACAATTAATAGTTTGATAAATTTACTAATCAAATGTTAGATTTTAT
TACAACAATTAATACAATT
Found at i:59296998 original size:16 final size:16
Alignment explanation
Indices: 59296977--59297018 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
59296967 AATAATTTGA
*
59296977 TAATTTTACTAACAAT
1 TAATTTTAATAACAAT
59296993 TAATTTTAATAACAAT
1 TAATTTTAATAACAAT
*
59297009 TAGTTTTAAT
1 TAATTTTAAT
59297019 TTTATTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (16 bp):
TAATTTTAATAACAAT
Found at i:59297002 original size:22 final size:23
Alignment explanation
Indices: 59296992--59297047 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 23
59296982 TTACTAACAA
* * *
59296992 TTAATTTTAAT-AACAATTAGTT
1 TTAATTTTAATAAAAAAATAATT
*
59297014 TTAATTTTATTAAAAAAATAATT
1 TTAATTTTAATAAAAAAATAATT
59297037 TTAATTTTAAT
1 TTAATTTTAAT
59297048 TTTAATTAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 10 0.36
23 18 0.64
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (23 bp):
TTAATTTTAATAAAAAAATAATT
Found at i:59302365 original size:18 final size:18
Alignment explanation
Indices: 59302338--59302380 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
59302328 GGCATAAAAA
* *
59302338 GAAAGCAAATAAATAAAC
1 GAAAGAAAATAAACAAAC
*
59302356 GAAAGAAAATAAACAAAT
1 GAAAGAAAATAAACAAAC
59302374 GAAAGAA
1 GAAAGAA
59302381 GGGGGAAAGA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.70, C:0.07, G:0.14, T:0.09
Consensus pattern (18 bp):
GAAAGAAAATAAACAAAC
Found at i:59306254 original size:23 final size:23
Alignment explanation
Indices: 59306206--59306272 Score: 84
Period size: 22 Copynumber: 3.0 Consensus size: 23
59306196 AATGCCATGA
*
59306206 ATTTATTTATATAAAATAAAAA-
1 ATTTATATATATAAAATAAAAAT
* *
59306228 ATTTATGTATATAAATTAAAAAT
1 ATTTATATATATAAAATAAAAAT
*
59306251 ATTTAAATAT-TAAAATAAAAAT
1 ATTTATATATATAAAATAAAAAT
59306273 TTAAAAATAT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
22 31 0.79
23 8 0.21
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.40
Consensus pattern (23 bp):
ATTTATATATATAAAATAAAAAT
Found at i:59306288 original size:22 final size:22
Alignment explanation
Indices: 59306213--59306288 Score: 59
Period size: 22 Copynumber: 3.4 Consensus size: 22
59306203 TGAATTTATT
* **
59306213 TATATAAAATAAAAA-ATTTATG
1 TATAT-AAATAAAAATATTAAAA
*
59306235 TATATAAATTAAAAATATTTAAA
1 TATATAAA-TAAAAATATTAAAA
59306258 TAT-TAAAATAAAAAT-TTAAAAA
1 TATAT-AAATAAAAATATT-AAAA
59306280 TATATAAAT
1 TATATAAAT
59306289 TAATTATATG
Statistics
Matches: 46, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
21 5 0.11
22 29 0.63
23 12 0.26
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.37
Consensus pattern (22 bp):
TATATAAATAAAAATATTAAAA
Found at i:59306827 original size:5 final size:6
Alignment explanation
Indices: 59306812--59306837 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
59306802 ATTAACTTTA
59306812 AAAAAT AAAAAT AAAAAT AAAAAT AA
1 AAAAAT AAAAAT AAAAAT AAAAAT AA
59306838 GAAGGTAGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAAAAT
Found at i:59307925 original size:11 final size:11
Alignment explanation
Indices: 59307911--59307997 Score: 51
Period size: 11 Copynumber: 8.3 Consensus size: 11
59307901 TCAATTATTT
59307911 TCTCAATTTCC
1 TCTCAATTTCC
* *
59307922 TCTCAAATTGC
1 TCTCAATTTCC
59307933 TCTCAATTTCC
1 TCTCAATTTCC
59307944 T-TCCAAATTT-C
1 TCT-C-AATTTCC
*
59307955 TCTCAA-ATCC
1 TCTCAATTTCC
* **
59307965 -AT--ATTTAA
1 TCTCAATTTCC
*
59307973 TCTCAATTTGC
1 TCTCAATTTCC
59307984 TCTCAATTTCC
1 TCTCAATTTCC
59307995 TCT
1 TCT
59307998 TAAATTTCTC
Statistics
Matches: 55, Mismatches: 13, Indels: 16
0.65 0.15 0.19
Matches are distributed among these distances:
7 1 0.02
8 1 0.02
9 3 0.05
10 4 0.07
11 40 0.73
12 6 0.11
ACGTcount: A:0.24, C:0.30, G:0.02, T:0.44
Consensus pattern (11 bp):
TCTCAATTTCC
Found at i:59307938 original size:22 final size:22
Alignment explanation
Indices: 59307911--59307960 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
59307901 TCAATTATTT
59307911 TCTCAATTTCC-TCTCAAATTGC
1 TCTCAATTTCCTTC-CAAATTGC
*
59307933 TCTCAATTTCCTTCCAAATTTC
1 TCTCAATTTCCTTCCAAATTGC
59307955 TCTCAA
1 TCTCAA
59307961 ATCCATATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 24 0.92
23 2 0.08
ACGTcount: A:0.24, C:0.32, G:0.02, T:0.42
Consensus pattern (22 bp):
TCTCAATTTCCTTCCAAATTGC
Found at i:59307984 original size:51 final size:51
Alignment explanation
Indices: 59307922--59308021 Score: 148
Period size: 51 Copynumber: 2.0 Consensus size: 51
59307912 CTCAATTTCC
59307922 TCTCAAATTGCTCTCAATTTCCT-TCCAAATTTCTCTCAAATCCATATTTAA
1 TCTCAAATTGCTCTCAATTTCCTCT-CAAATTTCTCTCAAATCCATATTTAA
* * * *
59307973 TCTCAATTTGCTCTCAATTTCCTCTTAAATTTCTCTTAAATCCCTATTT
1 TCTCAAATTGCTCTCAATTTCCTCTCAAATTTCTCTCAAATCCATATTT
59308022 TTAATTATTT
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
51 43 0.98
52 1 0.02
ACGTcount: A:0.26, C:0.27, G:0.02, T:0.45
Consensus pattern (51 bp):
TCTCAAATTGCTCTCAATTTCCTCTCAAATTTCTCTCAAATCCATATTTAA
Found at i:59310005 original size:21 final size:21
Alignment explanation
Indices: 59309981--59310025 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
59309971 AGACACCCTA
* * *
59309981 CCGGAGGAACCAGAATCCCCG
1 CCGGAGCAACCAAAACCCCCG
59310002 CCGGAGCAACCAAAACCCCCG
1 CCGGAGCAACCAAAACCCCCG
59310023 CCG
1 CCG
59310026 AAAGCTTAAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.29, C:0.44, G:0.24, T:0.02
Consensus pattern (21 bp):
CCGGAGCAACCAAAACCCCCG
Found at i:59310240 original size:7 final size:7
Alignment explanation
Indices: 59310220--59310259 Score: 57
Period size: 7 Copynumber: 5.9 Consensus size: 7
59310210 ATTTATTAAA
59310220 AATTTAT
1 AATTTAT
59310227 AAATTTAT
1 -AATTTAT
59310235 AATTTAT
1 AATTTAT
59310242 AA-TTA-
1 AATTTAT
59310247 AATTTAT
1 AATTTAT
59310254 AATTTA
1 AATTTA
59310260 ATTGACAAAC
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
5 2 0.07
6 6 0.20
7 15 0.50
8 7 0.23
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (7 bp):
AATTTAT
Found at i:59310290 original size:6 final size:6
Alignment explanation
Indices: 59310279--59310308 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
59310269 CCCTAACAAA
59310279 AACCCT AACCCT AACCCT AACCCT AACCCT
1 AACCCT AACCCT AACCCT AACCCT AACCCT
59310309 TAGCTTAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.33, C:0.50, G:0.00, T:0.17
Consensus pattern (6 bp):
AACCCT
Found at i:59310290 original size:18 final size:18
Alignment explanation
Indices: 59310267--59310352 Score: 64
Period size: 18 Copynumber: 4.5 Consensus size: 18
59310257 TTAATTGACA
59310267 AACCCTAACAAAAACCCT
1 AACCCTAACAAAAACCCT
***
59310285 AACCCTAACCCTAACCCT
1 AACCCTAACAAAAACCCT
* *
59310303 AACCCTTAGCTTAAAAACACCAA
1 AACCC-TAAC--AAAAAC-CC-T
*
59310326 AACCCTAATAAAAACCCT
1 AACCCTAACAAAAACCCT
*
59310344 AGCCCTAAC
1 AACCCTAAC
59310353 CCTAACCCTT
Statistics
Matches: 50, Mismatches: 13, Indels: 10
0.68 0.18 0.14
Matches are distributed among these distances:
18 27 0.54
19 5 0.10
20 6 0.12
21 3 0.06
22 4 0.08
23 5 0.10
ACGTcount: A:0.44, C:0.38, G:0.02, T:0.15
Consensus pattern (18 bp):
AACCCTAACAAAAACCCT
Found at i:59310372 original size:33 final size:32
Alignment explanation
Indices: 59310334--59310516 Score: 139
Period size: 33 Copynumber: 5.7 Consensus size: 32
59310324 AAAACCCTAA
59310334 TAAAAACCCTAGCCCTAACCCTAACCCTTAACT
1 TAAAAACCCTA-CCCTAACCCTAACCCTTAACT
59310367 T-AAAA----ACCCTAACCCTAACCCTTAACT
1 TAAAAACCCTACCCTAACCCTAACCCTTAACT
* **
59310394 TAAAAACCCTTAACCTAAAAACATCAAAACCC-TAAC-
1 TAAAAACCC-TACCCT---AAC--CCTAACCCTTAACT
* *
59310430 -AAAAACCCTAGCCTTTACCCTAACCCTTAACT
1 TAAAAACCCTA-CCCTAACCCTAACCCTTAACT
* *
59310462 TAAAAACCCTAACCATAACCTTAACCCTTAACT
1 TAAAAACCCT-ACCCTAACCCTAACCCTTAACT
**
59310495 TAAAAAAACTAACCCTAACCCT
1 TAAAAACCCT-ACCCTAACCCT
59310517 TAACTTGAAA
Statistics
Matches: 119, Mismatches: 15, Indels: 32
0.72 0.09 0.19
Matches are distributed among these distances:
27 22 0.18
28 5 0.04
30 6 0.05
31 4 0.03
32 6 0.05
33 50 0.42
34 3 0.03
35 10 0.08
36 3 0.03
37 4 0.03
38 6 0.05
ACGTcount: A:0.43, C:0.35, G:0.01, T:0.21
Consensus pattern (32 bp):
TAAAAACCCTACCCTAACCCTAACCCTTAACT
Found at i:59310376 original size:15 final size:15
Alignment explanation
Indices: 59310356--59310415 Score: 65
Period size: 15 Copynumber: 4.2 Consensus size: 15
59310346 CCCTAACCCT
*
59310356 AACCCTTAACTTAAA
1 AACCCTTAACCTAAA
59310371 AACCC-TAACCCT---
1 AACCCTTAA-CCTAAA
*
59310383 AACCCTTAACTTAAA
1 AACCCTTAACCTAAA
59310398 AACCCTTAACCTAAA
1 AACCCTTAACCTAAA
59310413 AAC
1 AAC
59310416 ATCAAAACCC
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
12 7 0.19
13 3 0.08
14 3 0.08
15 24 0.65
ACGTcount: A:0.45, C:0.33, G:0.00, T:0.22
Consensus pattern (15 bp):
AACCCTTAACCTAAA
Found at i:59310411 original size:27 final size:27
Alignment explanation
Indices: 59310346--59310408 Score: 117
Period size: 27 Copynumber: 2.3 Consensus size: 27
59310336 AAAACCCTAG
59310346 CCCTAACCCTAACCCTTAACTTAAAAA
1 CCCTAACCCTAACCCTTAACTTAAAAA
59310373 CCCTAACCCTAACCCTTAACTTAAAAA
1 CCCTAACCCTAACCCTTAACTTAAAAA
59310400 CCCTTAACC
1 CCC-TAACC
59310409 TAAAAACATC
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
27 30 0.86
28 5 0.14
ACGTcount: A:0.38, C:0.40, G:0.00, T:0.22
Consensus pattern (27 bp):
CCCTAACCCTAACCCTTAACTTAAAAA
Found at i:59310484 original size:21 final size:21
Alignment explanation
Indices: 59310446--59310485 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
59310436 CCTAGCCTTT
*
59310446 ACCCTAACCCTTAACTTAAAA
1 ACCCTAACCCATAACTTAAAA
59310467 ACCCTAA-CCATAACCTTAA
1 ACCCTAACCCATAA-CTTAA
59310486 CCCTTAACTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.42, C:0.35, G:0.00, T:0.23
Consensus pattern (21 bp):
ACCCTAACCCATAACTTAAAA
Found at i:59310489 original size:39 final size:39
Alignment explanation
Indices: 59310433--59310639 Score: 150
Period size: 39 Copynumber: 5.4 Consensus size: 39
59310423 CCCTAACAAA
* *
59310433 AACCCTAGCCTTTACCCTAACCCTTAACTTAAAAACCCT
1 AACCCTAACCTTAACCCTAACCCTTAACTTAAAAACCCT
* **
59310472 AACCATAACCTTAACCCTTAA--CTTAA-AAAAACTAACCCT
1 AACCCTAACCTTAACCC-TAACCCTTAACTTAAA--AACCCT
* *
59310511 AACCCTTAA-CTTGAAAACACCAAAACCTTAAC--AAAAACCCT
1 AACCC-TAACCTT---AAC-CCTAACCCTTAACTTAAAAACCCT
* * *
59310552 -A--GT--CC-TAACCCTAACCTTTAACTTAAAAACTCT
1 AACCCTAACCTTAACCCTAACCCTTAACTTAAAAACCCT
*
59310585 AACCCTAACCCTAACCCTAACCCTTAACTTAAAAACCCT
1 AACCCTAACCTTAACCCTAACCCTTAACTTAAAAACCCT
59310624 AACCCTAACCCTTAAC
1 AACCCTAA-CCTTAAC
59310640 TTAAAAACAC
Statistics
Matches: 131, Mismatches: 16, Indels: 41
0.70 0.09 0.22
Matches are distributed among these distances:
31 10 0.08
32 3 0.02
33 8 0.06
34 1 0.01
35 1 0.01
36 2 0.02
37 4 0.03
38 7 0.05
39 61 0.47
40 13 0.10
41 6 0.05
42 5 0.04
43 5 0.04
44 5 0.04
ACGTcount: A:0.41, C:0.35, G:0.01, T:0.23
Consensus pattern (39 bp):
AACCCTAACCTTAACCCTAACCCTTAACTTAAAAACCCT
Found at i:59310507 original size:27 final size:30
Alignment explanation
Indices: 59310446--59310648 Score: 103
Period size: 33 Copynumber: 6.8 Consensus size: 30
59310436 CCTAGCCTTT
59310446 ACCCTAACCCTTAACTTAAAAACCCTAACCATA
1 ACCCTAACCCTTAACTTAAAAA--C-AACCATA
*
59310479 ACCTTAACCCTTAACTTAAAAA-AA-C-TA
1 ACCCTAACCCTTAACTTAAAAACAACCATA
*
59310506 ACCCTAACCCTTAACTTGAAAAC-ACC--A
1 ACCCTAACCCTTAACTTAAAAACAACCATA
* * *
59310533 A----AA-CCTTAAC-AAAAACCCTAGTCC-TA
1 ACCCTAACCCTTAACTTAAAA-AC-A-ACCATA
* *
59310559 ACCCTAACCTTTAACTTAAAAACTCTAACCCTA
1 ACCCTAACCCTTAACTTAAAAA--C-AACCATA
*
59310592 ACCCTAACCC-TAACCCTTAACTTAAA-AACCCTA
1 ACCCTAACCCTTAA--CTTAA---AAACAACCATA
59310625 ACCCTAACCCTTAACTTAAAAACA
1 ACCCTAACCCTTAACTTAAAAACA
59310649 CCAAAACTCT
Statistics
Matches: 135, Mismatches: 12, Indels: 49
0.69 0.06 0.25
Matches are distributed among these distances:
21 3 0.02
22 8 0.06
23 2 0.01
25 2 0.01
26 2 0.01
27 25 0.19
28 2 0.01
29 5 0.04
30 3 0.02
31 6 0.04
32 14 0.10
33 52 0.39
34 8 0.06
37 3 0.02
ACGTcount: A:0.43, C:0.34, G:0.01, T:0.22
Consensus pattern (30 bp):
ACCCTAACCCTTAACTTAAAAACAACCATA
Found at i:59310529 original size:113 final size:115
Alignment explanation
Indices: 59310398--59310660 Score: 361
Period size: 119 Copynumber: 2.3 Consensus size: 115
59310388 TTAACTTAAA
* * *
59310398 AACCCTTAACCTAAAAACATCAAAACCCTAACAAAAACCCTAG-CCTTTACCCTAACCCTTAACT
1 AACCCTTAACTTAAAAACACCAAAACCCTAACAAAAACCCTAGTCC-TAACCCTAACCCTTAACT
*
59310462 T-AAA-AACCCTAACCATAACCTTAACCCTTAACTTAAAAAAACTAACCCT
65 TAAAACAACCCTAACCATAACCCTAACCCTTAACTTAAAAAAACTAACCCT
* * *
59310511 AACCCTTAACTTGAAAACACCAAAACCTTAACAAAAACCCTAGTCCTAACCCTAACCTTTAACTT
1 AACCCTTAACTTAAAAACACCAAAACCCTAACAAAAACCCTAGTCCTAACCCTAACCCTTAACTT
* **
59310576 AAAAACTCTAACCCTAACCCTAACCCTAACCCTTAACTTAAAAACCCTAACCCT
66 -AAAA--C-AACCCTAACCATAACCCTAACCCTTAACTTAAAAAAACTAACCCT
*
59310630 AACCCTTAACTTAAAAACACCAAAACTCTAA
1 AACCCTTAACTTAAAAACACCAAAACCCTAA
59310661 TGCTAACAAA
Statistics
Matches: 130, Mismatches: 13, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
113 56 0.43
114 2 0.02
115 3 0.02
119 69 0.53
ACGTcount: A:0.44, C:0.34, G:0.01, T:0.21
Consensus pattern (115 bp):
AACCCTTAACTTAAAAACACCAAAACCCTAACAAAAACCCTAGTCCTAACCCTAACCCTTAACTT
AAAACAACCCTAACCATAACCCTAACCCTTAACTTAAAAAAACTAACCCT
Found at i:59310594 original size:6 final size:6
Alignment explanation
Indices: 59310583--59310635 Score: 54
Period size: 6 Copynumber: 8.3 Consensus size: 6
59310573 CTTAAAAACT
*
59310583 CTAACC CTAACC CTAACC CTAACC CTTAA-C TTAAAAACC CTAACC CTAACC
1 CTAACC CTAACC CTAACC CTAACC C-TAACC CT---AACC CTAACC CTAACC
59310634 CT
1 CT
59310636 TAACTTAAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
5 1 0.03
6 32 0.80
7 3 0.08
8 2 0.05
9 2 0.05
ACGTcount: A:0.36, C:0.43, G:0.00, T:0.21
Consensus pattern (6 bp):
CTAACC
Found at i:59310675 original size:113 final size:115
Alignment explanation
Indices: 59310337--59310680 Score: 309
Period size: 119 Copynumber: 2.9 Consensus size: 115
59310327 ACCCTAATAA
*
59310337 AAACCCTAGCCCTAACCCTAACCCTTAACTTAAAAACCCTAACCCTAACCCTTAACTTAAAAACC
1 AAACCCTAACCCTAACCCTAACCCTTAACTTAAAAACCCTAACCCTAACCCTTAACTTAAAAA--
* * * * *
59310402 CTTAACCTAAAAACATCAAAACCCTAACAAAAACCCTAGCCTTTACCCTAACCCTTAACTT
64 C---ACC--AAAAC-TCATAACACTAACAAAAACCCTAACCTTTAACCTAA--C-AAACTT
* * ** *
59310463 AAAAACCCTAACCATAACCTTAACCCTTAACTTAAAAAAACTAACCCTAACCCTTAACTTGAAAA
1 --AAACCCTAACCCTAACCCTAACCCTTAACTTAAAAACCCTAACCCTAACCCTTAACTTAAAAA
* ** ** *
59310528 CACCAAAAC-CTTAACAAAAACCCTAGTCCTAACCCTAACCTTTAACTTAA-AAACTCT
64 CACCAAAACTCATAACACTAA--C-A---AAAACCCTAACCTTTAACCTAACAAACT-T
59310585 -AACCCTAACCCTAACCCTAACCCTTAACTTAAAAACCCTAACCCTAACCCTTAACTTAAAAACA
1 AAACCCTAACCCTAACCCTAACCCTTAACTTAAAAACCCTAACCCTAACCCTTAACTTAAAAACA
**
59310649 CCAAAACTC-TAATGCTAACAAAAACCCTAACC
66 CCAAAACTCATAACACTAACAAAAACCCTAACC
59310681 CTAACCCTAA
Statistics
Matches: 180, Mismatches: 28, Indels: 31
0.75 0.12 0.13
Matches are distributed among these distances:
113 10 0.06
116 1 0.01
117 1 0.01
119 77 0.43
120 1 0.01
121 10 0.06
122 2 0.01
123 3 0.02
125 17 0.09
126 1 0.01
128 57 0.32
ACGTcount: A:0.43, C:0.35, G:0.01, T:0.21
Consensus pattern (115 bp):
AAACCCTAACCCTAACCCTAACCCTTAACTTAAAAACCCTAACCCTAACCCTTAACTTAAAAACA
CCAAAACTCATAACACTAACAAAAACCCTAACCTTTAACCTAACAAACTT
Found at i:59310744 original size:35 final size:36
Alignment explanation
Indices: 59310705--59310867 Score: 107
Period size: 35 Copynumber: 4.4 Consensus size: 36
59310695 ATATAATTTG
59310705 ATAATTTTACTAACAATTAATACAATTA-ACAATTA
1 ATAATTTTACTAACAATTAATACAATTACACAATTA
* * ** * * * *
59310740 ATAATTTGACTAACAAAATGTTAGATTTTACAAAATGTT
1 ATAATTTTACTAAC-AATTAATACA-ATTACACAAT-TA
* * ** * * * *
59310779 TTGACTGGTACTAACAATTAATA-ATTTGATATAATTTG
1 AT-AATTTTACTAACAATTAATACAATT-ACACAA-TTA
59310817 ATAATTTTACTAACAATTAATACAATTA-ACAATTA
1 ATAATTTTACTAACAATTAATACAATTACACAATTA
59310852 ATAATTTTACTAACAA
1 ATAATTTTACTAACAA
59310868 AATGTTAGAT
Statistics
Matches: 94, Mismatches: 26, Indels: 16
0.69 0.19 0.12
Matches are distributed among these distances:
35 31 0.33
36 9 0.10
37 24 0.26
38 14 0.15
39 8 0.09
40 8 0.09
ACGTcount: A:0.46, C:0.10, G:0.06, T:0.39
Consensus pattern (36 bp):
ATAATTTTACTAACAATTAATACAATTACACAATTA
Found at i:59310890 original size:112 final size:112
Alignment explanation
Indices: 59310688--59310927 Score: 410
Period size: 112 Copynumber: 2.1 Consensus size: 112
59310678 ACCCTAACCC
*
59310688 TAATATGATATAATTTGATAATTTTACTAACAATTAATACAATTAACAATTAATAATTTGACTAA
1 TAATTTGATATAATTTGATAATTTTACTAACAATTAATACAATTAACAATTAATAATTTGACTAA
* * *
59310753 CAAAATGTTAGATTTTACAAAATGTTTTGACTGGTAC-TAACAATTAA
66 CAAAATGTTAGATTTTACAAAATGTTTTGACTGGTACAAAAAAAAT-A
*
59310800 TAATTTGATATAATTTGATAATTTTACTAACAATTAATACAATTAACAATTAATAATTTTACTAA
1 TAATTTGATATAATTTGATAATTTTACTAACAATTAATACAATTAACAATTAATAATTTGACTAA
*
59310865 CAAAATGTTAGATTTTACAAAATGTTTTGATTGGTACAAAAAAAATA
66 CAAAATGTTAGATTTTACAAAATGTTTTGACTGGTACAAAAAAAATA
59310912 TAATTTGATATAATTT
1 TAATTTGATATAATTT
59310928 TAATAATAAT
Statistics
Matches: 121, Mismatches: 6, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
112 116 0.96
113 5 0.04
ACGTcount: A:0.45, C:0.07, G:0.07, T:0.40
Consensus pattern (112 bp):
TAATTTGATATAATTTGATAATTTTACTAACAATTAATACAATTAACAATTAATAATTTGACTAA
CAAAATGTTAGATTTTACAAAATGTTTTGACTGGTACAAAAAAAATA
Found at i:59310938 original size:22 final size:22
Alignment explanation
Indices: 59310911--59310955 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
59310901 CAAAAAAAAT
*
59310911 ATAATTTGATATAATTTTAATA
1 ATAATTAGATATAATTTTAATA
* *
59310933 ATAATTAGTTTTAATTTTAATA
1 ATAATTAGATATAATTTTAATA
59310955 A
1 A
59310956 AAATATAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.51
Consensus pattern (22 bp):
ATAATTAGATATAATTTTAATA
Found at i:59311475 original size:27 final size:25
Alignment explanation
Indices: 59311424--59311477 Score: 63
Period size: 27 Copynumber: 2.1 Consensus size: 25
59311414 TTTAAAATAT
* * *
59311424 TTTTAAAATACTTTTTTTATTTTTA
1 TTTTAAAATAATTTTTCTATGTTTA
59311449 TTTTAAAATTAATTTTTCCTATGTTTA
1 TTTTAAAA-TAATTTTT-CTATGTTTA
59311476 TT
1 TT
59311478 AAAAAATGGG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 8 0.33
26 7 0.29
27 9 0.38
ACGTcount: A:0.28, C:0.06, G:0.02, T:0.65
Consensus pattern (25 bp):
TTTTAAAATAATTTTTCTATGTTTA
Found at i:59311674 original size:7 final size:7
Alignment explanation
Indices: 59311657--59311687 Score: 53
Period size: 7 Copynumber: 4.3 Consensus size: 7
59311647 TTTAATTCTT
59311657 AACCCTAA
1 AACCCT-A
59311665 AACCCTA
1 AACCCTA
59311672 AACCCTA
1 AACCCTA
59311679 AACCCTA
1 AACCCTA
59311686 AA
1 AA
59311688 AGTACAGGCA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 17 0.74
8 6 0.26
ACGTcount: A:0.48, C:0.39, G:0.00, T:0.13
Consensus pattern (7 bp):
AACCCTA
Found at i:59313976 original size:2 final size:2
Alignment explanation
Indices: 59313969--59313999 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
59313959 CCCAACTTAT
59313969 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
59314000 TACTCACTAA
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:59321621 original size:3 final size:3
Alignment explanation
Indices: 59321615--59321684 Score: 140
Period size: 3 Copynumber: 23.3 Consensus size: 3
59321605 TATTAGACTT
59321615 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
59321663 TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA T
59321685 GAAATGATCA
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 67 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:59346086 original size:107 final size:107
Alignment explanation
Indices: 59345900--59346114 Score: 421
Period size: 107 Copynumber: 2.0 Consensus size: 107
59345890 AGGCTTCAGT
59345900 ATATTATAAGCCCAAAACAACTATAAGCTTTAAACTCTTTTTTCTCTAATAATTCCCTTAATATA
1 ATATTATAAGCCCAAAACAACTATAAGCTTTAAACTCTTTTTTCTCTAATAATTCCCTTAATATA
59345965 TAATAAATATAAGTATAAATAATATAATTAAGAACATAAATA
66 TAATAAATATAAGTATAAATAATATAATTAAGAACATAAATA
*
59346007 ATATTATAAGCCGAAAACAACTATAAGCTTTAAACTCTTTTTTCTCTAATAATTCCCTTAATATA
1 ATATTATAAGCCCAAAACAACTATAAGCTTTAAACTCTTTTTTCTCTAATAATTCCCTTAATATA
59346072 TAATAAATATAAGTATAAATAATATAATTAAGAACATAAATA
66 TAATAAATATAAGTATAAATAATATAATTAAGAACATAAATA
59346114 A
1 A
59346115 AATTGAAGAA
Statistics
Matches: 107, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
107 107 1.00
ACGTcount: A:0.48, C:0.13, G:0.04, T:0.35
Consensus pattern (107 bp):
ATATTATAAGCCCAAAACAACTATAAGCTTTAAACTCTTTTTTCTCTAATAATTCCCTTAATATA
TAATAAATATAAGTATAAATAATATAATTAAGAACATAAATA
Found at i:59348659 original size:20 final size:20
Alignment explanation
Indices: 59348634--59348682 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
59348624 AATCCTTTGC
* **
59348634 TGTTTGAATCGATTGTTTAT
1 TGTTTGAATCGAGTCATTAT
59348654 TGTTTGAATCGAGTCATTAT
1 TGTTTGAATCGAGTCATTAT
59348674 TGTTTGAAT
1 TGTTTGAAT
59348683 TAATTCTTTG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.22, C:0.06, G:0.20, T:0.51
Consensus pattern (20 bp):
TGTTTGAATCGAGTCATTAT
Found at i:59352716 original size:20 final size:20
Alignment explanation
Indices: 59352689--59352830 Score: 113
Period size: 20 Copynumber: 7.0 Consensus size: 20
59352679 TTGTAGCCAC
*
59352689 TTTGAATCGATTGTTTGTTG
1 TTTGAATCGATTCTTTGTTG
* * * *
59352709 TTTAAATCAATTCTTTACTTC
1 TTTGAATCGATTCTTT-GTTG
* * *
59352730 TTTGAATCAATTGTTTCGTTA
1 TTTGAATCGATTCTTT-GTTG
* *
59352751 ATTGACTCGATTCTTTTGTTG
1 TTTGAATCGATTC-TTTGTTG
* *
59352772 TTTGAATCGATTGTTTATTG
1 TTTGAATCGATTCTTTGTTG
* * *
59352792 TTTGAATTGATTCATTATTG
1 TTTGAATCGATTCTTTGTTG
*
59352812 TTTGAATCAATTCTTTGTT
1 TTTGAATCGATTCTTTGTT
59352831 TTTTAACTTG
Statistics
Matches: 94, Mismatches: 26, Indels: 4
0.76 0.21 0.03
Matches are distributed among these distances:
20 51 0.54
21 40 0.43
22 3 0.03
ACGTcount: A:0.21, C:0.10, G:0.15, T:0.54
Consensus pattern (20 bp):
TTTGAATCGATTCTTTGTTG
Found at i:59352842 original size:40 final size:40
Alignment explanation
Indices: 59352769--59352845 Score: 102
Period size: 40 Copynumber: 1.9 Consensus size: 40
59352759 GATTCTTTTG
* *
59352769 TTGTTTGAATCGATTGTTTATTGTTTGAATTGATTCATTA
1 TTGTTTGAATCAATTCTTTATTGTTTGAATTGATTCATTA
* *
59352809 TTGTTTGAATCAATTCTTTGTT-TTTTAACTTGATTCA
1 TTGTTTGAATCAATTCTTTATTGTTTGAA-TTGATTCA
59352846 AACCCTAACA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
39 5 0.16
40 27 0.84
ACGTcount: A:0.22, C:0.08, G:0.14, T:0.56
Consensus pattern (40 bp):
TTGTTTGAATCAATTCTTTATTGTTTGAATTGATTCATTA
Done.