Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A05
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: 102776486
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2328156 characters in sequence are not A, C, G, or T
File 125 of 325
Found at i:38933645 original size:22 final size:23
Alignment explanation
Indices: 38933617--38933666 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
38933607 TTATTTAATA
38933617 ATAATAAT-TTTA-ATATAAAAT
1 ATAATAATATTTATATATAAAAT
*
38933638 CATAATAATATTTATATATAATAT
1 -ATAATAATATTTATATATAAAAT
38933662 ATAAT
1 ATAAT
38933667 CGAAGAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
22 8 0.32
23 9 0.36
24 8 0.32
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (23 bp):
ATAATAATATTTATATATAAAAT
Found at i:38933842 original size:20 final size:19
Alignment explanation
Indices: 38933796--38933842 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 19
38933786 AGTCTTTTTT
*
38933796 CCTAATTTCTCCTAATTAAG
1 CCTAA-TTCACCTAATTAAG
38933816 -CTAAATTCACCTAATTAAAG
1 CCT-AATTCACCTAATT-AAG
38933836 CCTAATT
1 CCTAATT
38933843 AAATATACTA
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
19 12 0.52
20 9 0.39
21 2 0.09
ACGTcount: A:0.36, C:0.23, G:0.04, T:0.36
Consensus pattern (19 bp):
CCTAATTCACCTAATTAAG
Found at i:38935049 original size:18 final size:18
Alignment explanation
Indices: 38935026--38935069 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
38935016 CTATTTTAAT
38935026 TTTA-TTTATTTATTATTA
1 TTTATTTTA-TTATTATTA
38935044 TTTATTTTATTATTATTA
1 TTTATTTTATTATTATTA
*
38935062 TTCATTTT
1 TTTATTTT
38935070 CTGATCTTCG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 20 0.83
19 4 0.17
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (18 bp):
TTTATTTTATTATTATTA
Found at i:38935052 original size:15 final size:15
Alignment explanation
Indices: 38935017--38935060 Score: 65
Period size: 15 Copynumber: 3.0 Consensus size: 15
38935007 GTACTTACAC
38935017 TATTTTAATT-TTATT
1 TATTTT-ATTATTATT
38935032 TA-TTTATTATTATT
1 TATTTTATTATTATT
38935046 TATTTTATTATTATT
1 TATTTTATTATTATT
38935061 ATTCATTTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
13 3 0.11
14 10 0.37
15 14 0.52
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (15 bp):
TATTTTATTATTATT
Found at i:38935210 original size:3 final size:3
Alignment explanation
Indices: 38935197--38935246 Score: 82
Period size: 3 Copynumber: 16.3 Consensus size: 3
38935187 CTCTAGCTCT
*
38935197 TTA TCA TTA TTA TTA TTA TTA TTTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA
38935243 TTA T
1 TTA T
38935247 ATACATGTAC
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
3 41 0.93
4 3 0.07
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:38935222 original size:22 final size:22
Alignment explanation
Indices: 38935196--38935241 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
38935186 ACTCTAGCTC
38935196 TTTATCATTATTATTATTATTA
1 TTTATCATTATTATTATTATTA
*
38935218 TTTATTATTATTATTATTATTA
1 TTTATCATTATTATTATTATTA
38935240 TT
1 TT
38935242 ATTATATACA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (22 bp):
TTTATCATTATTATTATTATTA
Found at i:38937344 original size:6 final size:6
Alignment explanation
Indices: 38937333--38937374 Score: 50
Period size: 6 Copynumber: 7.0 Consensus size: 6
38937323 AAATCATTTC
* *
38937333 TCAATT TCAATT TCAATT TCACTT TCAATGT ACAA-T TCAATT
1 TCAATT TCAATT TCAATT TCAATT TCAAT-T TCAATT TCAATT
38937375 CAGTACAATT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
5 4 0.13
6 22 0.73
7 4 0.13
ACGTcount: A:0.33, C:0.19, G:0.02, T:0.45
Consensus pattern (6 bp):
TCAATT
Found at i:38938242 original size:7 final size:7
Alignment explanation
Indices: 38938199--38938252 Score: 63
Period size: 7 Copynumber: 7.4 Consensus size: 7
38938189 ACTTTACTAT
38938199 ATATATA
1 ATATATA
38938206 ATATAATA
1 ATAT-ATA
38938214 ATAATATA
1 AT-ATATA
* *
38938222 GTATCTA
1 ATATATA
38938229 ATATATA
1 ATATATA
*
38938236 ATTTATA
1 ATATATA
38938243 ATATATA
1 ATATATA
38938250 ATA
1 ATA
38938253 AAACATAATA
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
7 28 0.72
8 9 0.23
9 2 0.05
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (7 bp):
ATATATA
Found at i:38939470 original size:14 final size:15
Alignment explanation
Indices: 38939442--38939471 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
38939432 ACATTAAGCA
38939442 AACAAATGTGTTTTT
1 AACAAATGTGTTTTT
38939457 AACAAATG-GTTTTT
1 AACAAATGTGTTTTT
38939471 A
1 A
38939472 GAAAACGAGC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.37, C:0.07, G:0.13, T:0.43
Consensus pattern (15 bp):
AACAAATGTGTTTTT
Found at i:38952935 original size:32 final size:33
Alignment explanation
Indices: 38952898--38952971 Score: 89
Period size: 33 Copynumber: 2.3 Consensus size: 33
38952888 TGGCATATTG
* * *
38952898 ATGATAAGACTGTAGC-TGACTATAG-CATTCTA
1 ATGATAAGACTATAGCGGGACTAT-GTCATACTA
*
38952930 ATGATAAGACTATAGCGGGGCTATGTCATACTA
1 ATGATAAGACTATAGCGGGACTATGTCATACTA
38952963 ATGATAAGA
1 ATGATAAGA
38952972 ACATAGCTGG
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
32 16 0.44
33 20 0.56
ACGTcount: A:0.36, C:0.14, G:0.22, T:0.28
Consensus pattern (33 bp):
ATGATAAGACTATAGCGGGACTATGTCATACTA
Found at i:38952969 original size:33 final size:33
Alignment explanation
Indices: 38952917--38953003 Score: 95
Period size: 33 Copynumber: 2.6 Consensus size: 33
38952907 CTGTAGCTGA
* *
38952917 CTATAGCATTCTAATGATAAG-ACTATAGCGGGG
1 CTATGGCATACTAATGATAAGAAC-ATAGCGGGG
* *
38952950 CTATGTCATACTAATGATAAGAACATAGCTGGG
1 CTATGGCATACTAATGATAAGAACATAGCGGGG
* * *
38952983 CTCTGGCATTCTGATGATAAG
1 CTATGGCATACTAATGATAAG
38953004 GTCATAACCG
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
33 43 0.96
34 2 0.04
ACGTcount: A:0.32, C:0.16, G:0.23, T:0.29
Consensus pattern (33 bp):
CTATGGCATACTAATGATAAGAACATAGCGGGG
Found at i:38956926 original size:31 final size:31
Alignment explanation
Indices: 38956890--38956952 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
38956880 CCAAAAAGAA
38956890 AAAAGAGAGAAAGTCTTTTGGTATGTTATAG
1 AAAAGAGAGAAAGTCTTTTGGTATGTTATAG
38956921 AAAAGAGAGAAAGTCTTTTGGTATGTTATAG
1 AAAAGAGAGAAAGTCTTTTGGTATGTTATAG
38956952 A
1 A
38956953 CAAAATAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.40, C:0.03, G:0.25, T:0.32
Consensus pattern (31 bp):
AAAAGAGAGAAAGTCTTTTGGTATGTTATAG
Found at i:38961762 original size:24 final size:24
Alignment explanation
Indices: 38961735--38961784 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
38961725 GTTGATGAAC
*
38961735 CTCTTTGGGTTCGTGTTCTCAGAT
1 CTCTTTAGGTTCGTGTTCTCAGAT
38961759 CTCTTTAGGTTCGTGTTCTCAGAT
1 CTCTTTAGGTTCGTGTTCTCAGAT
38961783 CT
1 CT
38961785 AAGTATGAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.10, C:0.22, G:0.22, T:0.46
Consensus pattern (24 bp):
CTCTTTAGGTTCGTGTTCTCAGAT
Found at i:38969186 original size:5 final size:5
Alignment explanation
Indices: 38969178--38969208 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
38969168 AAAGCAAAAG
*
38969178 GAGAG GAGAA GAGAA GAGAA GAGAA GAGAA G
1 GAGAA GAGAA GAGAA GAGAA GAGAA GAGAA G
38969209 GGACGAATTC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.55, C:0.00, G:0.45, T:0.00
Consensus pattern (5 bp):
GAGAA
Found at i:38969626 original size:18 final size:17
Alignment explanation
Indices: 38969608--38969640 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
38969598 TATGATGATT
38969608 TTTTA-ATATAAAAATA
1 TTTTATATATAAAAATA
*
38969624 TTTTATATATTAAAATA
1 TTTTATATATAAAAATA
38969641 ATAAAATTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
TTTTATATATAAAAATA
Found at i:38971838 original size:45 final size:45
Alignment explanation
Indices: 38971782--38971873 Score: 175
Period size: 45 Copynumber: 2.0 Consensus size: 45
38971772 AACAAATCAC
38971782 TATATTCATCGTCCATATATGTCACCTAAAAGCACACCAAATTTT
1 TATATTCATCGTCCATATATGTCACCTAAAAGCACACCAAATTTT
*
38971827 TATATTCATCGTCCATGTATGTCACCTAAAAGCACACCAAATTTT
1 TATATTCATCGTCCATATATGTCACCTAAAAGCACACCAAATTTT
38971872 TA
1 TA
38971874 CATTGAGAAA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.35, C:0.24, G:0.08, T:0.34
Consensus pattern (45 bp):
TATATTCATCGTCCATATATGTCACCTAAAAGCACACCAAATTTT
Found at i:38973331 original size:21 final size:21
Alignment explanation
Indices: 38973306--38973350 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
38973296 CCAATCAATT
* * *
38973306 AACCTATTCAAAATATGATAA
1 AACCTACTAAAAACATGATAA
*
38973327 AACCTACTAAAAACATGCTAA
1 AACCTACTAAAAACATGATAA
38973348 AAC
1 AAC
38973351 AATCATCTTA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.53, C:0.20, G:0.04, T:0.22
Consensus pattern (21 bp):
AACCTACTAAAAACATGATAA
Found at i:38975304 original size:13 final size:14
Alignment explanation
Indices: 38975281--38975309 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
38975271 ATGTCCACTC
38975281 TTCTCTTCTTTCTT
1 TTCTCTTCTTTCTT
38975295 TTCT-TTCTTTCTT
1 TTCTCTTCTTTCTT
38975308 TT
1 TT
38975310 ATTTTGCATG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (14 bp):
TTCTCTTCTTTCTT
Found at i:38981975 original size:19 final size:21
Alignment explanation
Indices: 38981934--38981981 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 21
38981924 TTAAAATTTT
38981934 AACTAAAAATATTAAAATAAA
1 AACTAAAAATATTAAAATAAA
* *
38981955 AA-TAAAAAT-TTAGAATCAA
1 AACTAAAAATATTAAAATAAA
38981974 AACTAAAA
1 AACTAAAA
38981982 TAAATAATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 10 0.42
20 12 0.50
21 2 0.08
ACGTcount: A:0.69, C:0.06, G:0.02, T:0.23
Consensus pattern (21 bp):
AACTAAAAATATTAAAATAAA
Found at i:38985774 original size:8 final size:7
Alignment explanation
Indices: 38985706--38985786 Score: 74
Period size: 7 Copynumber: 11.3 Consensus size: 7
38985696 TCACTATTGA
38985706 TTAATTT
1 TTAATTT
*
38985713 TAAATTT
1 TTAATTT
38985720 TTAAGTTTT
1 TTAA--TTT
*
38985729 TTAGTTT
1 TTAATTT
*
38985736 TTAAATT
1 TTAATTT
38985743 TTAATTT
1 TTAATTT
*
38985750 TTTATTT
1 TTAATTT
*
38985757 TTTATTT
1 TTAATTT
38985764 TTAATATT
1 TTAAT-TT
*
38985772 TTAA-TA
1 TTAATTT
38985778 TTAATTT
1 TTAATTT
38985785 TT
1 TT
38985787 TGAGTTTATT
Statistics
Matches: 60, Mismatches: 10, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
6 5 0.08
7 43 0.72
8 6 0.10
9 6 0.10
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.69
Consensus pattern (7 bp):
TTAATTT
Found at i:38986405 original size:15 final size:15
Alignment explanation
Indices: 38986382--38986432 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 15
38986372 ATACCCATGG
*
38986382 CCATTAAACCTTAAA
1 CCATAAAACCTTAAA
*
38986397 CCATAAAACCCTAAA
1 CCATAAAACCTTAAA
* *
38986412 CTAT-AGACCTTAAA
1 CCATAAAACCTTAAA
*
38986426 CCTTAAA
1 CCATAAA
38986433 TATTAAACCG
Statistics
Matches: 27, Mismatches: 8, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
14 10 0.37
15 17 0.63
ACGTcount: A:0.47, C:0.27, G:0.02, T:0.24
Consensus pattern (15 bp):
CCATAAAACCTTAAA
Found at i:38986739 original size:40 final size:40
Alignment explanation
Indices: 38986676--38986836 Score: 189
Period size: 40 Copynumber: 4.0 Consensus size: 40
38986666 GGGATTATAT
* * *
38986676 GACTTTTAGCGGCATTTACCAAAAGCACCACTATTGCTCC
1 GACTTTTAGCGGCTTTTAGCAAAAGCGCCACTATTGCTCC
* *
38986716 GACTTTTAGCGGTTTTTAGCAAAAGCGCCGCTATTGCTCC
1 GACTTTTAGCGGCTTTTAGCAAAAGCGCCACTATTGCTCC
**
38986756 GACTTTTAGCGGCGTTTTAGCAAAA-CGCCACTATTGCTTT
1 GACTTTTAGCGGC-TTTTAGCAAAAGCGCCACTATTGCTCC
* * * *
38986796 GACTTTTAGCAGCGTTTTAACAAAAAACGCCGCTATTGCTC
1 GACTTTTAGCGGC-TTTTAGC-AAAAGCGCCACTATTGCTC
38986837 TGTTTTTAGC
Statistics
Matches: 105, Mismatches: 13, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
40 78 0.74
41 15 0.14
42 12 0.11
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.31
Consensus pattern (40 bp):
GACTTTTAGCGGCTTTTAGCAAAAGCGCCACTATTGCTCC
Found at i:38986848 original size:81 final size:81
Alignment explanation
Indices: 38986676--38986854 Score: 213
Period size: 80 Copynumber: 2.2 Consensus size: 81
38986666 GGGATTATAT
* *
38986676 GACTTTTAGCGGC-ATTTACCAAAAGCACCACTATTGCTCCGACTTTTAGCGGTTTTTAGCAAAA
1 GACTTTTAGCGGCGTTTTACCAAAAGCACCACTATTGCTCCGACTTTTAGCGGTTTTTAACAAAA
*
38986740 GCGCCGCTATTGCTCC
66 ACGCCGCTATTGCTCC
* * **
38986756 GACTTTTAGCGGCGTTTTAGCAAAA-CGCCACTATTGCTTTGACTTTTAGCAGCG-TTTTAACAA
1 GACTTTTAGCGGCGTTTTACCAAAAGCACCACTATTGCTCCGACTTTTAGC-G-GTTTTTAAC-A
*
38986819 AAAACGCCGCTATTGCTCT
63 AAAACGCCGCTATTGCTCC
* *
38986838 G-TTTTTAGCGGTGTTTT
1 GACTTTTAGCGGCGTTTT
38986855 TGGTAGAACA
Statistics
Matches: 85, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
80 35 0.41
81 30 0.35
82 20 0.24
ACGTcount: A:0.23, C:0.23, G:0.20, T:0.34
Consensus pattern (81 bp):
GACTTTTAGCGGCGTTTTACCAAAAGCACCACTATTGCTCCGACTTTTAGCGGTTTTTAACAAAA
ACGCCGCTATTGCTCC
Found at i:38989886 original size:25 final size:25
Alignment explanation
Indices: 38989858--38989909 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
38989848 AGATAATCAT
38989858 TTTCAAATTGTATGAGAGATGTAAG
1 TTTCAAATTGTATGAGAGATGTAAG
38989883 TTTCAAATTGTATGAGAGATGTAAG
1 TTTCAAATTGTATGAGAGATGTAAG
38989908 TT
1 TT
38989910 AAGTGTTCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.35, C:0.04, G:0.23, T:0.38
Consensus pattern (25 bp):
TTTCAAATTGTATGAGAGATGTAAG
Found at i:38997341 original size:46 final size:48
Alignment explanation
Indices: 38997109--38997378 Score: 211
Period size: 46 Copynumber: 5.7 Consensus size: 48
38997099 GGGTAAGTTA
* * * *
38997109 CCGATGCCATGTGCCAGACATGGTCTTACACT-GGATATCATCATCGAGG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTAGCA-CTCGTC-TCGAGG
* * *
38997158 CCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCGCATATCTG-TG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTAGCACTCG--TCTC-GAGG
* * * * *
38997208 CCGATGCCACGTCCTAGACATGGTCTTACACT-G-ACACATCTC-ATAG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTAGCACTCGTCTCGA-GG
* * *
38997254 CCGATG-CATGTCCCAAACAT-GTCTTACATTGGCTTA-T-GTCTCGAGG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTAGC--ACTCGTCTCGAGG
* * *
38997300 CCGATG-CATTTCCCAGACAT-GTCTTACACTAGCACTCGTCTCAATG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTAGCACTCGTCTCGAGG
* *
38997346 CCGATGCCATGTCCTAGACATGGCCTTACACTA
1 CCGATGCCATGTCCCAGACATGGTCTTACACTA
38997379 ACTTTCATAA
Statistics
Matches: 176, Mismatches: 30, Indels: 31
0.74 0.13 0.13
Matches are distributed among these distances:
44 10 0.06
45 13 0.07
46 57 0.32
47 13 0.07
48 13 0.07
49 34 0.19
50 34 0.19
51 2 0.01
ACGTcount: A:0.23, C:0.30, G:0.20, T:0.27
Consensus pattern (48 bp):
CCGATGCCATGTCCCAGACATGGTCTTACACTAGCACTCGTCTCGAGG
Found at i:38997415 original size:140 final size:141
Alignment explanation
Indices: 38997152--38997421 Score: 363
Period size: 140 Copynumber: 1.9 Consensus size: 141
38997142 GATATCATCA
* **
38997152 TCGAGGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCGCATATCTGTGCCGATGCCA
1 TCGAGGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCACTCG-ATATCAATGCCGATGCCA
* *
38997217 CGTCCTAGACATGGTCTTACACTGACACATCTCATAGCCGATGCATGTCCCAAACATGTCTTACA
65 CGTCCTAGACATGGCCTTACACTGACACATCTCATAGCCAATGCATGTCCCAAACATGTCTTACA
38997282 TTGGCTTATGTC
130 TTGGCTTATGTC
* * *
38997294 TCGAGGCCGATG-CATTTCCCAGACAT-GTCTTACACTAGCACTCG-TCTCAATGCCGATGCCAT
1 TCGAGGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCACTCGATATCAATGCCGATGCCAC
*
38997356 GTCCTAGACATGGCCTTACACT-A-AC-TTTCATAATGTGGCCAATGCATGTCCCAAACATGTCT
66 GTCCTAGACATGGCCTTACACTGACACATCTCAT-A----GCCAATGCATGTCCCAAACATGTCT
38997418 TACA
126 TACA
38997422 CTAGCCCACA
Statistics
Matches: 114, Mismatches: 9, Indels: 12
0.84 0.07 0.09
Matches are distributed among these distances:
135 5 0.04
136 3 0.03
137 1 0.01
138 35 0.31
140 45 0.39
141 13 0.11
142 12 0.11
ACGTcount: A:0.24, C:0.30, G:0.19, T:0.27
Consensus pattern (141 bp):
TCGAGGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCACTCGATATCAATGCCGATGCCAC
GTCCTAGACATGGCCTTACACTGACACATCTCATAGCCAATGCATGTCCCAAACATGTCTTACAT
TGGCTTATGTC
Found at i:38998247 original size:11 final size:11
Alignment explanation
Indices: 38998231--38998258 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
38998221 TGGCTAAGAA
38998231 GAAGAGAGGAT
1 GAAGAGAGGAT
38998242 GAAGAGAGGAT
1 GAAGAGAGGAT
38998253 GAAGAG
1 GAAGAG
38998259 GTGAAACCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.46, C:0.00, G:0.46, T:0.07
Consensus pattern (11 bp):
GAAGAGAGGAT
Found at i:39002768 original size:16 final size:16
Alignment explanation
Indices: 39002713--39002769 Score: 51
Period size: 16 Copynumber: 3.4 Consensus size: 16
39002703 TGTCATGTTG
*
39002713 CCATGGTATCTTTCAA
1 CCATGGTATTTTTCAA
* * * *
39002729 CCATGGTCTTGTGCATTG
1 CCATGGTATTTTTCA--A
39002747 CCATGGTATTTTTCAA
1 CCATGGTATTTTTCAA
39002763 CCATGGT
1 CCATGGT
39002770 CTTATTCATT
Statistics
Matches: 30, Mismatches: 9, Indels: 4
0.70 0.21 0.09
Matches are distributed among these distances:
16 18 0.60
18 12 0.40
ACGTcount: A:0.19, C:0.23, G:0.19, T:0.39
Consensus pattern (16 bp):
CCATGGTATTTTTCAA
Found at i:39002957 original size:46 final size:46
Alignment explanation
Indices: 39002744--39002966 Score: 333
Period size: 46 Copynumber: 4.9 Consensus size: 46
39002734 GTCTTGTGCA
*
39002744 TTGCCATGGTATTTTTCAACCATGGTCTTATTCA-TTC-TCGTCATG
1 TTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCAT-GTCATG
* *
39002789 TTGCCATGGTATCTTTCAACCATGGTCTTATTCTTTTCATGTCACG
1 TTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGTCATG
* *
39002835 TTGCCATGATATCTTTCAACCATGGTCTTATTCTTTTCATGTCATG
1 TTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGTCATG
** *
39002881 TTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCATG
1 TTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGTCATG
**
39002927 TTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCAT
1 TTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCAT
39002967 TTCAGAAAGC
Statistics
Matches: 166, Mismatches: 10, Indels: 3
0.93 0.06 0.02
Matches are distributed among these distances:
45 32 0.19
46 133 0.80
47 1 0.01
ACGTcount: A:0.20, C:0.23, G:0.14, T:0.43
Consensus pattern (46 bp):
TTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGTCATG
Found at i:39003838 original size:51 final size:51
Alignment explanation
Indices: 39003774--39003889 Score: 196
Period size: 51 Copynumber: 2.3 Consensus size: 51
39003764 CTCAAACTTA
* *
39003774 CTTCATACTTCATCTGAAATTATTACTTTGTTGCTCTAGCTTCAACAAGAG
1 CTTCATATTTCATCTGAAATTATTACTTTATTGCTCTAGCTTCAACAAGAG
*
39003825 CTTCATATTTCATCTGGAATTATTACTTTATTGCTCTAGCTTCAACAAGAG
1 CTTCATATTTCATCTGAAATTATTACTTTATTGCTCTAGCTTCAACAAGAG
*
39003876 TTTCATATTTCATC
1 CTTCATATTTCATC
39003890 CAGATAACTT
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 61 1.00
ACGTcount: A:0.27, C:0.21, G:0.10, T:0.42
Consensus pattern (51 bp):
CTTCATATTTCATCTGAAATTATTACTTTATTGCTCTAGCTTCAACAAGAG
Found at i:39006056 original size:20 final size:20
Alignment explanation
Indices: 39006031--39006073 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
39006021 GGTTCTAGAA
*
39006031 GTTGCGTTCTGTCTGTTCTT
1 GTTGCGTTCTGTCGGTTCTT
39006051 GTTGCGTTCTGTCGGTTCTT
1 GTTGCGTTCTGTCGGTTCTT
39006071 GTT
1 GTT
39006074 CTATTTGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.00, C:0.19, G:0.28, T:0.53
Consensus pattern (20 bp):
GTTGCGTTCTGTCGGTTCTT
Found at i:39008628 original size:46 final size:47
Alignment explanation
Indices: 39008491--39008755 Score: 237
Period size: 46 Copynumber: 5.7 Consensus size: 47
39008481 GGGTAAGTTA
*
39008491 CCGATGCCATGTGCCAGACATGGTCTTACACTGGCTATCATCATCGAGG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTGGCTA-CATC-TCGAGG
*
39008540 CCGATGCCATGTCCCAGACATGGTCTTACACTGAC-ACATCTCGTA-G
1 CCGATGCCATGTCCCAGACATGGTCTTACACTGGCTACATCTCG-AGG
* **
39008586 CTGATG-CATGTCCCAGACAT-GAATTACACTGGCTTACATCTCGAGG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTGGC-TACATCTCGAGG
* * * * * *
39008632 CCGATG-CATGTCCCAGACAT-GTCTTGCATTAGC-ACTCCTCTCAATG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTGGCTA--CATCTCGAGG
* * * *
39008678 TCGATGCCATTTCCCAGACATGGTCTTACACTGGCTCTCATAAT-GCA-G
1 CCGATGCCATGTCCCAGACATGGTCTTACACTGGCT-ACAT-CTCG-AGG
39008726 CCGATG-CATGTCCCAGACAT-GTCTTACACT
1 CCGATGCCATGTCCCAGACATGGTCTTACACT
39008756 AGCCCAAAAT
Statistics
Matches: 178, Mismatches: 26, Indels: 27
0.77 0.11 0.12
Matches are distributed among these distances:
44 11 0.06
45 15 0.08
46 67 0.38
47 31 0.17
48 19 0.11
49 35 0.20
ACGTcount: A:0.23, C:0.30, G:0.20, T:0.26
Consensus pattern (47 bp):
CCGATGCCATGTCCCAGACATGGTCTTACACTGGCTACATCTCGAGG
Found at i:39008730 original size:94 final size:90
Alignment explanation
Indices: 39008492--39008755 Score: 286
Period size: 94 Copynumber: 2.8 Consensus size: 90
39008482 GGTAAGTTAC
*
39008492 CGATGCCATGTGCCAGACATGGTCTTACACTGGCTATCATCATCGAGGCCGATGCCATGTCCCAG
1 CGATGCCATGTCCCAGACATGGTCTTACACTGGCT-TCAT-ATCGAGGCCGATG-CATGTCCCAG
*
39008557 ACATGGTCTTACACTGACACATCTCGTAG
63 ACAT-GTCTTACACTGACACATCTCATAG
** *
39008586 CTGATG-CATGTCCCAGACAT-GAATTACACTGGCTTACATCTCGAGGCCGATGCATGTCCCAGA
1 C-GATGCCATGTCCCAGACATGGTCTTACACTGGCTT-CATATCGAGGCCGATGCATGTCCCAGA
* * * *
39008649 CATGTCTTGCATTAGCACTCCTCTCA-ATG
64 CATGTCTTACACT-G-ACACATCTCATA-G
*
39008678 TCGATGCCATTTCCCAGACATGGTCTTACACTGGCTCTCATAAT-GCA-GCCGATGCATGTCCCA
1 -CGATGCCATGTCCCAGACATGGTCTTACACTGGCT-TCAT-ATCG-AGGCCGATGCATGTCCCA
39008741 GACATGTCTTACACT
62 GACATGTCTTACACT
39008756 AGCCCAAAAT
Statistics
Matches: 144, Mismatches: 15, Indels: 22
0.80 0.08 0.12
Matches are distributed among these distances:
90 8 0.06
91 16 0.11
92 25 0.17
93 29 0.20
94 59 0.41
95 7 0.05
ACGTcount: A:0.23, C:0.30, G:0.20, T:0.27
Consensus pattern (90 bp):
CGATGCCATGTCCCAGACATGGTCTTACACTGGCTTCATATCGAGGCCGATGCATGTCCCAGACA
TGTCTTACACTGACACATCTCATAG
Found at i:39011111 original size:10 final size:9
Alignment explanation
Indices: 39011096--39011172 Score: 52
Period size: 10 Copynumber: 8.4 Consensus size: 9
39011086 GAGAACTACC
39011096 AAAATAAAA
1 AAAATAAAA
39011105 TAAAATAAAA
1 -AAAATAAAA
*
39011115 ACAAATAAAC
1 A-AAATAAAA
39011125 AAAATAATAA
1 AAAATAA-AA
*
39011135 AAGAT-AAA
1 AAAATAAAA
*
39011143 GAAAT-AAA
1 AAAATAAAA
*
39011151 TAAAT-AAA
1 AAAATAAAA
*
39011159 TAAATAAAGA
1 AAAATAAA-A
39011169 AAAA
1 AAAA
39011173 GAAATGATAA
Statistics
Matches: 56, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
8 20 0.36
9 10 0.18
10 26 0.46
ACGTcount: A:0.78, C:0.03, G:0.04, T:0.16
Consensus pattern (9 bp):
AAAATAAAA
Found at i:39011133 original size:27 final size:26
Alignment explanation
Indices: 39011103--39011166 Score: 67
Period size: 27 Copynumber: 2.4 Consensus size: 26
39011093 ACCAAAATAA
39011103 AATAAAATAAAAACAAATAAACAAAAT
1 AATAAAATAAAAACAAATAAA-AAAAT
* * * *
39011130 AATAAAAGATAAAGAAATAAATAAAT
1 AATAAAATAAAAACAAATAAAAAAAT
39011156 AA-ATAAATAAA
1 AATA-AAATAAA
39011167 GAAAAAGAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
25 1 0.03
26 11 0.37
27 18 0.60
ACGTcount: A:0.77, C:0.03, G:0.03, T:0.17
Consensus pattern (26 bp):
AATAAAATAAAAACAAATAAAAAAAT
Found at i:39011153 original size:4 final size:4
Alignment explanation
Indices: 39011117--39011166 Score: 50
Period size: 4 Copynumber: 12.8 Consensus size: 4
39011107 AAATAAAAAC
* * *
39011117 AAAT AAAC AAA- ATAAT AAA- AGAT AAAG AAAT AAAT AAAT AAAT AAAT
1 AAAT AAAT AAAT A-AAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
39011164 AAA
1 AAA
39011167 GAAAAAGAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
3 3 0.08
4 34 0.89
5 1 0.03
ACGTcount: A:0.76, C:0.02, G:0.04, T:0.18
Consensus pattern (4 bp):
AAAT
Found at i:39011153 original size:12 final size:12
Alignment explanation
Indices: 39011138--39011170 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
39011128 ATAATAAAAG
39011138 ATAAAGAAATAA
1 ATAAAGAAATAA
*
39011150 ATAAATAAATAA
1 ATAAAGAAATAA
39011162 ATAAAGAAA
1 ATAAAGAAA
39011171 AAGAAATGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.76, C:0.00, G:0.06, T:0.18
Consensus pattern (12 bp):
ATAAAGAAATAA
Found at i:39012966 original size:13 final size:13
Alignment explanation
Indices: 39012948--39012973 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
39012938 ATCCCATCCC
39012948 AAAACAGATACAG
1 AAAACAGATACAG
39012961 AAAACAGATACAG
1 AAAACAGATACAG
39012974 TAATAATAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.15, G:0.15, T:0.08
Consensus pattern (13 bp):
AAAACAGATACAG
Found at i:39030887 original size:21 final size:21
Alignment explanation
Indices: 39030863--39030905 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
39030853 GAATATGCTA
*
39030863 AAAATTAAAAATT-TATGATAG
1 AAAATGAAAAATTGT-TGATAG
*
39030884 AAAATGAAATATTGTTGATAG
1 AAAATGAAAAATTGTTGATAG
39030905 A
1 A
39030906 TAAACAACTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 18 0.95
22 1 0.05
ACGTcount: A:0.53, C:0.00, G:0.14, T:0.33
Consensus pattern (21 bp):
AAAATGAAAAATTGTTGATAG
Found at i:39036515 original size:23 final size:22
Alignment explanation
Indices: 39036488--39036539 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 22
39036478 ATATCCATTA
39036488 GTTTATTCGATCTATCTTCTATTT
1 GTTTATTCGATC-AT-TTCTATTT
* *
39036512 -TTTATTCTATCATTTTTATTT
1 GTTTATTCGATCATTTCTATTT
39036533 GTTTATT
1 GTTTATT
39036540 ATGTTGAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
21 7 0.28
22 8 0.32
23 10 0.40
ACGTcount: A:0.17, C:0.12, G:0.06, T:0.65
Consensus pattern (22 bp):
GTTTATTCGATCATTTCTATTT
Found at i:39036764 original size:18 final size:19
Alignment explanation
Indices: 39036743--39036786 Score: 65
Period size: 18 Copynumber: 2.4 Consensus size: 19
39036733 GAAAACAAGA
39036743 AAAATAAAGAAA-TTAAGT
1 AAAATAAAGAAATTTAAGT
39036761 AAAAT-AAGAAATTTAAGT
1 AAAATAAAGAAATTTAAGT
39036779 ATAAATAA
1 A-AAATAA
39036787 TAAATATTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 6 0.26
18 12 0.52
19 4 0.17
20 1 0.04
ACGTcount: A:0.66, C:0.00, G:0.09, T:0.25
Consensus pattern (19 bp):
AAAATAAAGAAATTTAAGT
Found at i:39044612 original size:27 final size:27
Alignment explanation
Indices: 39044581--39044836 Score: 293
Period size: 27 Copynumber: 9.6 Consensus size: 27
39044571 ACATAGCGGT
*
39044581 AAAACAGTCATCTTACCACATAAGGG-
1 AAAACAGTCATTTTACCACATAAGGGC
* *
39044607 ATAAACAATCATTTTATCAC--AAGGGC
1 A-AAACAGTCATTTTACCACATAAGGGC
* * **
39044633 AAAATAGTTATTTTACCTTATAAGGGC
1 AAAACAGTCATTTTACCACATAAGGGC
* ** *
39044660 AAAATAGTCATTTTACCATGTAAGAGC
1 AAAACAGTCATTTTACCACATAAGGGC
* * *
39044687 AAAATAATCATTTTACCACGTAAGGGC
1 AAAACAGTCATTTTACCACATAAGGGC
* *
39044714 AAAACAATCATTTTACCACGTAAGGGC
1 AAAACAGTCATTTTACCACATAAGGGC
* * *
39044741 AAAATAGTCATTTTACCATATAAGCGC
1 AAAACAGTCATTTTACCACATAAGGGC
*
39044768 AAAACAGTCATTTTACCACAAAAGGGC
1 AAAACAGTCATTTTACCACATAAGGGC
*
39044795 AAAATAGTCATTTTACCACATAAGGGC
1 AAAACAGTCATTTTACCACATAAGGGC
39044822 AAAACAGTCATTTTA
1 AAAACAGTCATTTTA
39044837 TCAATTAGGG
Statistics
Matches: 197, Mismatches: 29, Indels: 7
0.85 0.12 0.03
Matches are distributed among these distances:
25 17 0.09
26 2 0.01
27 178 0.90
ACGTcount: A:0.41, C:0.18, G:0.14, T:0.27
Consensus pattern (27 bp):
AAAACAGTCATTTTACCACATAAGGGC
Found at i:39044702 original size:54 final size:54
Alignment explanation
Indices: 39044581--39044836 Score: 329
Period size: 54 Copynumber: 4.8 Consensus size: 54
39044571 ACATAGCGGT
* * * *
39044581 AAAACAGTCATCTTACCACATAAGGG-ATAAACAATCATTTTATCAC--AAGGGC
1 AAAATAGTCATTTTACCACATAAGGGCA-AAACAGTCATTTTACCACGTAAGGGC
* ** * * *
39044633 AAAATAGTTATTTTACCTTATAAGGGCAAAATAGTCATTTTACCATGTAAGAGC
1 AAAATAGTCATTTTACCACATAAGGGCAAAACAGTCATTTTACCACGTAAGGGC
* * *
39044687 AAAATAATCATTTTACCACGTAAGGGCAAAACAATCATTTTACCACGTAAGGGC
1 AAAATAGTCATTTTACCACATAAGGGCAAAACAGTCATTTTACCACGTAAGGGC
* * **
39044741 AAAATAGTCATTTTACCATATAAGCGCAAAACAGTCATTTTACCACAAAAGGGC
1 AAAATAGTCATTTTACCACATAAGGGCAAAACAGTCATTTTACCACGTAAGGGC
39044795 AAAATAGTCATTTTACCACATAAGGGCAAAACAGTCATTTTA
1 AAAATAGTCATTTTACCACATAAGGGCAAAACAGTCATTTTA
39044837 TCAATTAGGG
Statistics
Matches: 173, Mismatches: 28, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
52 35 0.20
53 1 0.01
54 137 0.79
ACGTcount: A:0.41, C:0.18, G:0.14, T:0.27
Consensus pattern (54 bp):
AAAATAGTCATTTTACCACATAAGGGCAAAACAGTCATTTTACCACGTAAGGGC
Found at i:39046667 original size:16 final size:16
Alignment explanation
Indices: 39046646--39046679 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
39046636 CTTCTCAGAC
39046646 ACTCCTAGAACAAATA
1 ACTCCTAGAACAAATA
39046662 ACTCCTAGAACAAATA
1 ACTCCTAGAACAAATA
39046678 AC
1 AC
39046680 CACTGAAGCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.50, C:0.26, G:0.06, T:0.18
Consensus pattern (16 bp):
ACTCCTAGAACAAATA
Found at i:39047943 original size:17 final size:17
Alignment explanation
Indices: 39047921--39047970 Score: 55
Period size: 20 Copynumber: 2.8 Consensus size: 17
39047911 TATCAAGATA
39047921 AATATTAGATTAAATTT
1 AATATTAGATTAAATTT
*
39047938 AATATTAAGATAATAACTTT
1 AATATT-AGAT--TAAATTT
*
39047958 AATATTAAATTAA
1 AATATTAGATTAA
39047971 TAAAATACTA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
17 9 0.32
18 4 0.14
19 3 0.11
20 12 0.43
ACGTcount: A:0.52, C:0.02, G:0.04, T:0.42
Consensus pattern (17 bp):
AATATTAGATTAAATTT
Found at i:39048030 original size:36 final size:35
Alignment explanation
Indices: 39047961--39048031 Score: 83
Period size: 36 Copynumber: 2.0 Consensus size: 35
39047951 TAACTTTAAT
*
39047961 ATTAAATTAATAAAATACTATTAAGAAAGTATTAC
1 ATTAAATTAATAAAATACTATTAAGAAAATATTAC
*
39047996 ATTAAATTTAATATTAA-ACTATTAA-AATAATATTAC
1 ATTAAA-TTAATA-AAATACTATTAAGAA-AATATTAC
39048032 TTTTGAAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
35 8 0.26
36 21 0.68
37 2 0.06
ACGTcount: A:0.54, C:0.06, G:0.03, T:0.38
Consensus pattern (35 bp):
ATTAAATTAATAAAATACTATTAAGAAAATATTAC
Found at i:39054599 original size:33 final size:36
Alignment explanation
Indices: 39054562--39054640 Score: 101
Period size: 34 Copynumber: 2.2 Consensus size: 36
39054552 TAAGGTAATA
39054562 TAATATTAT-ACCTGTTTTTTATTTT-TTTC-AATT
1 TAATATTATAACCTGTTTTTTATTTTATTTCAAATT
* *
39054595 TAATATTATAACTTTTTTTTTATTTTAGTTTCAAATT
1 TAATATTATAACCTGTTTTTTATTTTA-TTTCAAATT
39054632 TATATATTA
1 TA-ATATTA
39054641 AATGTAATAG
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
33 9 0.23
34 14 0.36
36 4 0.10
37 6 0.15
38 6 0.15
ACGTcount: A:0.29, C:0.06, G:0.03, T:0.62
Consensus pattern (36 bp):
TAATATTATAACCTGTTTTTTATTTTATTTCAAATT
Found at i:39056358 original size:20 final size:21
Alignment explanation
Indices: 39056315--39056367 Score: 60
Period size: 20 Copynumber: 2.7 Consensus size: 21
39056305 TAGATATTAA
39056315 TAAAAAA-ATAAA--AATCTT
1 TAAAAAATATAAATTAATCTT
*
39056333 TTAAAAATATAAATTAAT-TT
1 TAAAAAATATAAATTAATCTT
*
39056353 TAAAAAGTATAAATT
1 TAAAAAATATAAATT
39056368 TTTGGACAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
18 6 0.21
19 5 0.17
20 15 0.52
21 3 0.10
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (21 bp):
TAAAAAATATAAATTAATCTT
Found at i:39058029 original size:17 final size:17
Alignment explanation
Indices: 39058009--39058043 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
39057999 AAGATGTATT
39058009 AAAAATAAATTTTATAA
1 AAAAATAAATTTTATAA
*
39058026 AAAAATGAATTTTATAA
1 AAAAATAAATTTTATAA
39058043 A
1 A
39058044 TTGTCATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (17 bp):
AAAAATAAATTTTATAA
Found at i:39059859 original size:5 final size:5
Alignment explanation
Indices: 39059849--39059879 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
39059839 TTATGTTTTA
39059849 ATTAT ATTAT ATTAT ATTAT ATTAT A-TAT AT
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT AT
39059880 AAACTAAAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.16
5 21 0.84
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (5 bp):
ATTAT
Found at i:39061368 original size:18 final size:19
Alignment explanation
Indices: 39061342--39061389 Score: 64
Period size: 18 Copynumber: 2.6 Consensus size: 19
39061332 AATTGATTGA
39061342 TACTGAATAACTT-ATTAT
1 TACTGAATAACTTGATTAT
* *
39061360 TATTGAATAA-TTGATTGT
1 TACTGAATAACTTGATTAT
39061378 TACTGAATAACT
1 TACTGAATAACT
39061390 GACTGATACT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
17 2 0.08
18 22 0.88
19 1 0.04
ACGTcount: A:0.38, C:0.08, G:0.10, T:0.44
Consensus pattern (19 bp):
TACTGAATAACTTGATTAT
Found at i:39061399 original size:18 final size:17
Alignment explanation
Indices: 39061339--39061405 Score: 53
Period size: 18 Copynumber: 3.8 Consensus size: 17
39061329 ATCAATTGAT
*
39061339 TGATACTGAATAACTTA
1 TGATACTGAATAACTGA
* * *
39061356 TTATTATTGAATAATTGA
1 TGA-TACTGAATAACTGA
*
39061374 TTGTTACTGAATAACTGA
1 -TGATACTGAATAACTGA
*
39061392 CTGATACTAAATAA
1 -TGATACTGAATAA
39061406 ATAATTGTTC
Statistics
Matches: 37, Mismatches: 11, Indels: 3
0.73 0.22 0.06
Matches are distributed among these distances:
17 2 0.05
18 34 0.92
19 1 0.03
ACGTcount: A:0.40, C:0.09, G:0.12, T:0.39
Consensus pattern (17 bp):
TGATACTGAATAACTGA
Found at i:39061405 original size:36 final size:36
Alignment explanation
Indices: 39061332--39061427 Score: 88
Period size: 36 Copynumber: 2.7 Consensus size: 36
39061322 ATAACCAATC
* * * * *
39061332 AATTGATTGATACTGAATAACTTATTATTATTGAAT
1 AATTGATTGTTACTGAATAACTGATGATTACTAAAT
39061368 AATTGATTGTTACTGAATAACTGACTGA-TACTAAAT
1 AATTGATTGTTACTGAATAACTGA-TGATTACTAAAT
* * * *
39061404 AAATAATTGTT-CTGATTGACTGAT
1 AATTGATTGTTACTGAATAACTGAT
39061428 TGTTAATGAA
Statistics
Matches: 50, Mismatches: 9, Indels: 4
0.79 0.14 0.06
Matches are distributed among these distances:
34 1 0.02
35 10 0.20
36 37 0.74
37 2 0.04
ACGTcount: A:0.38, C:0.08, G:0.14, T:0.41
Consensus pattern (36 bp):
AATTGATTGTTACTGAATAACTGATGATTACTAAAT
Found at i:39065788 original size:5 final size:5
Alignment explanation
Indices: 39065778--39065808 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
39065768 TTATGTTTTA
39065778 ATTAT ATTAT ATTAT ATTAT ATTAT A-TAT AT
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT AT
39065809 AAACTAAAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.16
5 21 0.84
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (5 bp):
ATTAT
Found at i:39067032 original size:47 final size:47
Alignment explanation
Indices: 39066954--39067060 Score: 117
Period size: 47 Copynumber: 2.3 Consensus size: 47
39066944 CTGTTACCGT
* * * * * * *
39066954 TACTGTTACTATTTCAGATTCGTTCCGATGAGTTACTGTGTGTATCG
1 TACTGTTACTGTTCCAGATTCGTTCCCATGAGGTACTCTGTGTACCA
*
39067001 TACTGTTACTGTTCCGGATTTC-TTCCCATGAGGTACTCTGTGTACCA
1 TACTGTTACTGTTCCAGA-TTCGTTCCCATGAGGTACTCTGTGTACCA
*
39067048 TACTGCTACTGTT
1 TACTGTTACTGTT
39067061 ACTGTTACTG
Statistics
Matches: 50, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
47 47 0.94
48 3 0.06
ACGTcount: A:0.18, C:0.21, G:0.20, T:0.41
Consensus pattern (47 bp):
TACTGTTACTGTTCCAGATTCGTTCCCATGAGGTACTCTGTGTACCA
Found at i:39067344 original size:18 final size:18
Alignment explanation
Indices: 39067265--39067379 Score: 106
Period size: 18 Copynumber: 6.3 Consensus size: 18
39067255 ACTGATCAGT
*
39067265 TGATTGATACTGAATAAC
1 TGATTGTTACTGAATAAC
* * * *
39067283 TTATTATTATTGAATAAT
1 TGATTGTTACTGAATAAC
39067301 TGATTGTTACTGAATAAC
1 TGATTGTTACTGAATAAC
* *
39067319 TGACTGTTACTGAATAAA
1 TGATTGTTACTGAATAAC
* * *
39067337 TAATTGTT-CTGATTGAC
1 TGATTGTTACTGAATAAC
*
39067354 TGATTGTTAATGAATATTAC
1 TGATTGTTACTGAATA--AC
39067374 TGATTG
1 TGATTG
39067380 ATTAATTGCT
Statistics
Matches: 74, Mismatches: 20, Indels: 4
0.76 0.20 0.04
Matches are distributed among these distances:
17 13 0.18
18 53 0.72
20 8 0.11
ACGTcount: A:0.34, C:0.08, G:0.16, T:0.43
Consensus pattern (18 bp):
TGATTGTTACTGAATAAC
Found at i:39074071 original size:21 final size:21
Alignment explanation
Indices: 39074045--39074089 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
39074035 CGAGATGTGA
39074045 AACATATCATGGATACGATCT
1 AACATATCATGGATACGATCT
39074066 AACATATCATGGATACGATCT
1 AACATATCATGGATACGATCT
39074087 AAC
1 AAC
39074090 TCTGGAGGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.40, C:0.20, G:0.13, T:0.27
Consensus pattern (21 bp):
AACATATCATGGATACGATCT
Found at i:39079087 original size:27 final size:27
Alignment explanation
Indices: 39079054--39079247 Score: 108
Period size: 27 Copynumber: 7.2 Consensus size: 27
39079044 TTTACCCTAT
*
39079054 AAGGGTATTTCAGTAATTTTAC-ACTAC
1 AAGGGTATTTCAGTAATTTTACAAAT-C
* *
39079081 AATGGTATTTC-GATAATTTTACAAATT
1 AAGGGTATTTCAG-TAATTTTACAAATC
* *
39079108 AGGGGTATTTCAGTAATTTTACAAGTC
1 AAGGGTATTTCAGTAATTTTACAAATC
* ** * * *
39079135 -GGGGTATTTTGGTAGTTTCACAAATT
1 AAGGGTATTTCAGTAATTTTACAAATC
* * * * *
39079161 GAGGATATTT-TGATAATTTCACAAATT
1 AAGGGTATTTCAG-TAATTTTACAAATC
* * **
39079188 AGGGGTATTTCGGTAATTTTACAACCC
1 AAGGGTATTTCAGTAATTTTACAAATC
* * * *
39079215 GAGGGTATTTTAATAATTTTACAAGTC
1 AAGGGTATTTCAGTAATTTTACAAATC
*
39079242 AGGGGT
1 AAGGGT
39079248 CTTAACAACC
Statistics
Matches: 127, Mismatches: 34, Indels: 12
0.73 0.20 0.07
Matches are distributed among these distances:
26 22 0.17
27 101 0.80
28 4 0.03
ACGTcount: A:0.31, C:0.10, G:0.20, T:0.39
Consensus pattern (27 bp):
AAGGGTATTTCAGTAATTTTACAAATC
Found at i:39099314 original size:15 final size:16
Alignment explanation
Indices: 39099280--39099319 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
39099270 TATATATTCT
39099280 TTTTATTTTAAATTAG
1 TTTTATTTTAAATTAG
*
39099296 TTTTATTTTAATTTA-
1 TTTTATTTTAAATTAG
*
39099311 TTTTCTTTT
1 TTTTATTTT
39099320 CCCAAATCCC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 8 0.36
16 14 0.64
ACGTcount: A:0.23, C:0.03, G:0.03, T:0.72
Consensus pattern (16 bp):
TTTTATTTTAAATTAG
Found at i:39114665 original size:23 final size:22
Alignment explanation
Indices: 39114633--39114687 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 22
39114623 ACCAATCCAA
*
39114633 TTCAACATATTT-TCAAGATAGA-
1 TTCATCATATTTAT-AAGATA-AC
39114655 TTCATGCATATTTATAAGATAAC
1 TTCAT-CATATTTATAAGATAAC
39114678 TTCATCATAT
1 TTCATCATAT
39114688 ACCAAAATTA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
22 10 0.34
23 18 0.62
24 1 0.03
ACGTcount: A:0.38, C:0.15, G:0.07, T:0.40
Consensus pattern (22 bp):
TTCATCATATTTATAAGATAAC
Found at i:39117946 original size:3 final size:3
Alignment explanation
Indices: 39117940--39117965 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
39117930 AGGCCAAAAA
39117940 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
39117966 AGGAGAGTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:39118321 original size:30 final size:31
Alignment explanation
Indices: 39118285--39118342 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
39118275 CAAACGAACT
39118285 ATTTTTT-TAAAATTATAAAAAATAATTTTA
1 ATTTTTTATAAAATTATAAAAAATAATTTTA
* *
39118315 ATTTTTTATAAATTTATAAAATATAATT
1 ATTTTTTATAAAATTATAAAAAATAATT
39118343 AAAATTAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
30 7 0.28
31 18 0.72
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (31 bp):
ATTTTTTATAAAATTATAAAAAATAATTTTA
Found at i:39132846 original size:25 final size:25
Alignment explanation
Indices: 39132816--39132868 Score: 90
Period size: 25 Copynumber: 2.1 Consensus size: 25
39132806 TTAAAAAAAG
39132816 TATGAATTTATCATAAGT-ATTTTCT
1 TATGAATTTATCATAA-TCATTTTCT
39132841 TATGAATTTATCATAATCATTTTCT
1 TATGAATTTATCATAATCATTTTCT
39132866 TAT
1 TAT
39132869 AGCACTAGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
24 1 0.04
25 26 0.96
ACGTcount: A:0.32, C:0.09, G:0.06, T:0.53
Consensus pattern (25 bp):
TATGAATTTATCATAATCATTTTCT
Found at i:39146865 original size:69 final size:70
Alignment explanation
Indices: 39146733--39146865 Score: 214
Period size: 69 Copynumber: 1.9 Consensus size: 70
39146723 TAGTTTATTA
* * * * *
39146733 CTAATTAATTTGCTGCTGTAATGCTGTAAATTATTGGCTGTCCAAATTAGGACAAATTTATGGTA
1 CTAATTAATATGCTGCTGTAATACTGTAAATTATTGGCTCTCCAAATTAGGACAAAATCATGGTA
39146798 CTTAG
66 CTTAG
39146803 CTAATTAATATGCTGCTGTAATACT-TAAATTATTGGCTCTCCAAATTAGGACAAAATCATGGT
1 CTAATTAATATGCTGCTGTAATACTGTAAATTATTGGCTCTCCAAATTAGGACAAAATCATGGT
39146866 GTTATGTGCT
Statistics
Matches: 58, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
69 35 0.60
70 23 0.40
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.37
Consensus pattern (70 bp):
CTAATTAATATGCTGCTGTAATACTGTAAATTATTGGCTCTCCAAATTAGGACAAAATCATGGTA
CTTAG
Found at i:39148300 original size:47 final size:47
Alignment explanation
Indices: 39148246--39148507 Score: 418
Period size: 47 Copynumber: 5.6 Consensus size: 47
39148236 TATTTGAATA
*
39148246 AATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
39148293 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
*
39148340 AATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
39148387 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* * * * *
39148434 AATGTGAAAGTGTATATATGTGA-CAGGGCTGAGTGGCCAACGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCT-AATGGCCGATGTGATG
* * *
39148481 GATGTCAAAGTGTATAAATGTGATAAG
1 AATGTGAAAGTGTATATATGTGATAAG
39148508 TCCCGAATGG
Statistics
Matches: 201, Mismatches: 12, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
46 5 0.02
47 194 0.97
48 2 0.01
ACGTcount: A:0.33, C:0.08, G:0.29, T:0.29
Consensus pattern (47 bp):
AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
Found at i:39148801 original size:37 final size:37
Alignment explanation
Indices: 39148626--39148800 Score: 305
Period size: 37 Copynumber: 4.7 Consensus size: 37
39148616 CCGAGCTCTA
*
39148626 AAGACTCGATGACTACGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATGACTACGTGTGGAGATTATGTCCGGGT
39148663 AAGACCCGATGACTACGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATGACTACGTGTGGAGATTATGTCCGGGT
39148700 AAGACCCGATGACTACGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATGACTACGTGTGGAGATTATGTCCGGGT
*
39148737 AAGACCCGATGACTACGTGTGGAGATTTTGTCCGGGT
1 AAGACCCGATGACTACGTGTGGAGATTATGTCCGGGT
* * *
39148774 AAGACCCGATAACTTCATGTGGAGATT
1 AAGACCCGATGACTACGTGTGGAGATT
39148801 TCGTCTGAGC
Statistics
Matches: 133, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 133 1.00
ACGTcount: A:0.25, C:0.18, G:0.31, T:0.26
Consensus pattern (37 bp):
AAGACCCGATGACTACGTGTGGAGATTATGTCCGGGT
Found at i:39150789 original size:51 final size:47
Alignment explanation
Indices: 39150735--39150829 Score: 190
Period size: 47 Copynumber: 2.0 Consensus size: 47
39150725 TCGAAAACGT
39150735 TAATTAATTGTTTTCTTTGCCAAAACTTATTTACAGTGGAAGTATAA
1 TAATTAATTGTTTTCTTTGCCAAAACTTATTTACAGTGGAAGTATAA
39150782 TAATTAATTGTTTTCTTTGCCAAAACTTATTTACAGTGGAAGTATAA
1 TAATTAATTGTTTTCTTTGCCAAAACTTATTTACAGTGGAAGTATAA
39150829 T
1 T
39150830 CAAAACCAAT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 48 1.00
ACGTcount: A:0.34, C:0.11, G:0.13, T:0.43
Consensus pattern (47 bp):
TAATTAATTGTTTTCTTTGCCAAAACTTATTTACAGTGGAAGTATAA
Found at i:39156932 original size:3 final size:3
Alignment explanation
Indices: 39156926--39156994 Score: 53
Period size: 3 Copynumber: 24.7 Consensus size: 3
39156916 TTATTAATCG
*
39156926 TAT TAT TAC TAT TAT T-T CT-T TAT T-T TAT T-T TA- TAT TA- TAT
1 TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
39156966 TA- CAT TAT TAGT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TA-T TAT TAT TAT TAT TAT TA
39156995 GTTTTAGCTT
Statistics
Matches: 54, Mismatches: 4, Indels: 16
0.73 0.05 0.22
Matches are distributed among these distances:
2 11 0.20
3 40 0.74
4 3 0.06
ACGTcount: A:0.30, C:0.04, G:0.01, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:39157414 original size:12 final size:12
Alignment explanation
Indices: 39157397--39157459 Score: 69
Period size: 12 Copynumber: 5.2 Consensus size: 12
39157387 CTCTCTGTAT
39157397 TTACTTATATTA
1 TTACTTATATTA
39157409 TTACTTATATTA
1 TTACTTATATTA
39157421 TTA-TTACTATTA
1 TTACTTA-TATTA
*
39157433 TCA-TTATGATTTA
1 TTACTTAT-A-TTA
39157446 TTACTT-TATTA
1 TTACTTATATTA
39157457 TTA
1 TTA
39157460 TCATTATTAC
Statistics
Matches: 45, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
11 10 0.22
12 27 0.60
13 6 0.13
14 2 0.04
ACGTcount: A:0.32, C:0.08, G:0.02, T:0.59
Consensus pattern (12 bp):
TTACTTATATTA
Found at i:39157438 original size:15 final size:14
Alignment explanation
Indices: 39157397--39157470 Score: 50
Period size: 15 Copynumber: 5.4 Consensus size: 14
39157387 CTCTCTGTAT
39157397 TTAC-TTAT-ATTA
1 TTACTTTATCATTA
*
39157409 TTACTTATATTATTA
1 TTACTT-TATCATTA
39157424 TTACTATTATCATTA
1 TTACT-TTATCATTA
* *
39157439 TGA-TTTATTACTTTA
1 TTACTTTA-T-CATTA
39157454 TTA--TTATCATTA
1 TTACTTTATCATTA
39157466 TTACT
1 TTACT
39157471 GCCATTGTAT
Statistics
Matches: 49, Mismatches: 5, Indels: 14
0.72 0.07 0.21
Matches are distributed among these distances:
12 11 0.22
13 5 0.10
14 8 0.16
15 24 0.49
16 1 0.02
ACGTcount: A:0.31, C:0.09, G:0.01, T:0.58
Consensus pattern (14 bp):
TTACTTTATCATTA
Found at i:39157466 original size:27 final size:25
Alignment explanation
Indices: 39157397--39157466 Score: 76
Period size: 27 Copynumber: 2.8 Consensus size: 25
39157387 CTCTCTGTAT
39157397 TTACTTATATTATTA-C-TTATATTA
1 TTACTT-TATTATTATCATTATATTA
*
39157421 TTA--TTACTATTATCATTATGATTTA
1 TTACTTTATTATTATCATTAT-A-TTA
39157446 TTACTTTATTATTATCATTAT
1 TTACTTTATTATTATCATTAT
39157467 TACTGCCATT
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
21 7 0.18
22 2 0.05
23 4 0.11
24 4 0.11
25 6 0.16
27 15 0.39
ACGTcount: A:0.31, C:0.09, G:0.01, T:0.59
Consensus pattern (25 bp):
TTACTTTATTATTATCATTATATTA
Found at i:39157484 original size:3 final size:3
Alignment explanation
Indices: 39157404--39157468 Score: 53
Period size: 3 Copynumber: 21.7 Consensus size: 3
39157394 TATTTACTTA
* * * *
39157404 TAT TAT TACT TA- TAT TAT TAT TAC TAT TAT CAT TAT GATT TAT TAC
1 TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT
*
39157450 T-T TAT TAT TAT CAT TAT TA
1 TAT TAT TAT TAT TAT TAT TA
39157469 CTGCCATTGT
Statistics
Matches: 48, Mismatches: 10, Indels: 8
0.73 0.15 0.12
Matches are distributed among these distances:
2 3 0.06
3 40 0.83
4 5 0.10
ACGTcount: A:0.32, C:0.08, G:0.02, T:0.58
Consensus pattern (3 bp):
TAT
Found at i:39163927 original size:30 final size:30
Alignment explanation
Indices: 39163891--39163951 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
39163881 TTTAACCTCT
39163891 ATACATAGATTGTATTCTACACAATCTACC
1 ATACATAGATTGTATTCTACACAATCTACC
39163921 ATACATAGATTGTATTCTACACAATCTACC
1 ATACATAGATTGTATTCTACACAATCTACC
39163951 A
1 A
39163952 CAAAATCATG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.38, C:0.23, G:0.07, T:0.33
Consensus pattern (30 bp):
ATACATAGATTGTATTCTACACAATCTACC
Found at i:39169719 original size:14 final size:14
Alignment explanation
Indices: 39169700--39169733 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
39169690 ATGACGTTAA
39169700 GGTGTGGCAATGGC
1 GGTGTGGCAATGGC
39169714 GGTGTGGCAATGGC
1 GGTGTGGCAATGGC
39169728 GGTGTG
1 GGTGTG
39169734 CATGTCTAGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.12, C:0.12, G:0.53, T:0.24
Consensus pattern (14 bp):
GGTGTGGCAATGGC
Found at i:39171071 original size:36 final size:36
Alignment explanation
Indices: 39171024--39171120 Score: 124
Period size: 36 Copynumber: 2.7 Consensus size: 36
39171014 TCCAAAAAAC
39171024 ACACACCAGATGCTCATAAGAGCTAATACATCCAAA
1 ACACACCAGATGCTCATAAGAGCTAATACATCCAAA
* * * **
39171060 ACACACTAGATGCTTATAAGAGCTAATCCATCTGAA
1 ACACACCAGATGCTCATAAGAGCTAATACATCCAAA
*
39171096 ACACACCA-ATAGCTCAGAAGAGCTA
1 ACACACCAGAT-GCTCATAAGAGCTA
39171121 GTCCAATCGA
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
35 2 0.04
36 50 0.96
ACGTcount: A:0.42, C:0.26, G:0.13, T:0.19
Consensus pattern (36 bp):
ACACACCAGATGCTCATAAGAGCTAATACATCCAAA
Found at i:39177994 original size:42 final size:43
Alignment explanation
Indices: 39177947--39178028 Score: 114
Period size: 43 Copynumber: 1.9 Consensus size: 43
39177937 TCAAACTATG
* *
39177947 TCTGGGACA-TCAGCATC-ATATTTGATTTCGTGTAAGACCCTA
1 TCTGGGACAGT-AGCATCGATATTTGATTACATGTAAGACCCTA
*
39177989 TCTGGGACAGTGGCATCGATATTTGATTACATGTAAGACC
1 TCTGGGACAGTAGCATCGATATTTGATTACATGTAAGACC
39178029 ACGTCTGGGA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
42 14 0.40
43 21 0.60
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.32
Consensus pattern (43 bp):
TCTGGGACAGTAGCATCGATATTTGATTACATGTAAGACCCTA
Found at i:39178036 original size:43 final size:42
Alignment explanation
Indices: 39177945--39178047 Score: 113
Period size: 43 Copynumber: 2.4 Consensus size: 42
39177935 TGTCAAACTA
* * *
39177945 TGTCTGGGACA-TCAGCATCATATTTGATTTCGTGTAAGACCC
1 TGTCTGGGACAGT-GGCATCATATTTGATTACATGTAAGACCC
*
39177987 TATCTGGGACAGTGGCATCGATATTTGATTACATGTAAGACCAC
1 TGTCTGGGACAGTGGCATC-ATATTTGATTACATGTAAGACC-C
39178031 -GTCTGGGAC-GTTGGCAT
1 TGTCTGGGACAG-TGGCAT
39178048 TGTACGATCT
Statistics
Matches: 52, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
42 16 0.31
43 35 0.67
44 1 0.02
ACGTcount: A:0.24, C:0.19, G:0.25, T:0.31
Consensus pattern (42 bp):
TGTCTGGGACAGTGGCATCATATTTGATTACATGTAAGACCC
Found at i:39182597 original size:23 final size:25
Alignment explanation
Indices: 39182555--39182602 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
39182545 ATATAATGCC
*
39182555 TTATATGTTGGCTTATTTTTTATTA
1 TTATATGTTGGCTTATTTTTGATTA
*
39182580 TTATGTGTTGG-TTA-TTTTGATTA
1 TTATATGTTGGCTTATTTTTGATTA
39182603 GTTGTTAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 8 0.38
24 3 0.14
25 10 0.48
ACGTcount: A:0.19, C:0.02, G:0.17, T:0.62
Consensus pattern (25 bp):
TTATATGTTGGCTTATTTTTGATTA
Found at i:39186237 original size:43 final size:41
Alignment explanation
Indices: 39186141--39186288 Score: 136
Period size: 43 Copynumber: 3.5 Consensus size: 41
39186131 TATGGATATG
* * *
39186141 TGATTTCATGTAAAACCATGTCTGGGAAATTGGCATTGTAT
1 TGATTTCATGTAAGACCATGTCTGGGACATTGGCATCGTAT
* *
39186182 TGAGATTACATGTAAGACCATGTCGGGGACATTGGCATCGTTAAT
1 T--GATTTCATGTAAGACCATGTCTGGGACATTGGCATCG-T-AT
***
39186227 TGATTTCATGTAAGACTC-TGTCTGGGACAGCAGCATCGATAT
1 TGATTTCATGTAAGAC-CATGTCTGGGACATTGGCATCG-TAT
**
39186269 GTGATAACATGTAAGACCAT
1 -TGATTTCATGTAAGACCAT
39186289 ATCTAGGATA
Statistics
Matches: 87, Mismatches: 13, Indels: 12
0.78 0.12 0.11
Matches are distributed among these distances:
41 1 0.01
42 3 0.03
43 78 0.90
44 2 0.02
45 3 0.03
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.31
Consensus pattern (41 bp):
TGATTTCATGTAAGACCATGTCTGGGACATTGGCATCGTAT
Found at i:39189960 original size:35 final size:35
Alignment explanation
Indices: 39189921--39189988 Score: 127
Period size: 35 Copynumber: 1.9 Consensus size: 35
39189911 ATTTTCACAG
*
39189921 AATCATGCAATCATATCATATACCTCAAAATAAAC
1 AATCATGCAATCATATCATAGACCTCAAAATAAAC
39189956 AATCATGCAATCATATCATAGACCTCAAAATAA
1 AATCATGCAATCATATCATAGACCTCAAAATAA
39189989 TCATAAAATA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.49, C:0.22, G:0.04, T:0.25
Consensus pattern (35 bp):
AATCATGCAATCATATCATAGACCTCAAAATAAAC
Found at i:39193713 original size:27 final size:27
Alignment explanation
Indices: 39193683--39193807 Score: 110
Period size: 27 Copynumber: 4.6 Consensus size: 27
39193673 CATAGGGGTC
*
39193683 AAACAATCATCTTACCATAAAAGGGCA
1 AAACAATCATTTTACCATAAAAGGGCA
* * * *
39193710 AAACAAACATTTTACCACATAAGGGAA
1 AAACAATCATTTTACCATAAAAGGGCA
*
39193737 AAACAGTCATTTTACCCCAT-AAAGGGCA
1 AAACAATCATTTTA--CCATAAAAGGGCA
* *
39193765 AAATAATCATTTTACC-TCATAAGGGCA
1 AAACAATCATTTTACCAT-AAAAGGGCA
* * *
39193792 GAATAGTCATTTTACC
1 AAACAATCATTTTACC
39193808 CCATAAGGGA
Statistics
Matches: 79, Mismatches: 15, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
25 1 0.01
26 2 0.03
27 55 0.70
28 18 0.23
29 3 0.04
ACGTcount: A:0.43, C:0.21, G:0.12, T:0.24
Consensus pattern (27 bp):
AAACAATCATTTTACCATAAAAGGGCA
Found at i:39193776 original size:55 final size:55
Alignment explanation
Indices: 39193697--39193832 Score: 184
Period size: 55 Copynumber: 2.5 Consensus size: 55
39193687 AATCATCTTA
* *
39193697 CCATAAAAGGGCAAAACAAACATTTTACCACATAAGGGAAAAACAGTCATTTTACC
1 CCAT-AAAGGGCAAAATAATCATTTTACCACATAAGGGAAAAACAGTCATTTTACC
* * * *
39193753 CCATAAAGGGCAAAATAATCATTTTACCTCATAAGGGCAGAATAGTCATTTTACC
1 CCATAAAGGGCAAAATAATCATTTTACCACATAAGGGAAAAACAGTCATTTTACC
* *
39193808 CCAT-AAGGGAAAAATAGTCATTTTA
1 CCATAAAGGGCAAAATAATCATTTTA
39193833 TCGATTATGG
Statistics
Matches: 72, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
54 19 0.26
55 49 0.68
56 4 0.06
ACGTcount: A:0.43, C:0.19, G:0.14, T:0.24
Consensus pattern (55 bp):
CCATAAAGGGCAAAATAATCATTTTACCACATAAGGGAAAAACAGTCATTTTACC
Found at i:39193812 original size:27 final size:27
Alignment explanation
Indices: 39193717--39193832 Score: 160
Period size: 27 Copynumber: 4.3 Consensus size: 27
39193707 GCAAAACAAA
* *
39193717 CATTTTACCACATAAGGGAAAAACAGT
1 CATTTTACCCCATAAGGGAAAAATAGT
* *
39193744 CATTTTACCCCATAAAGGGCAAAATAAT
1 CATTTTACCCCAT-AAGGGAAAAATAGT
* * *
39193772 CATTTTACCTCATAAGGGCAGAATAGT
1 CATTTTACCCCATAAGGGAAAAATAGT
39193799 CATTTTACCCCATAAGGGAAAAATAGT
1 CATTTTACCCCATAAGGGAAAAATAGT
39193826 CATTTTA
1 CATTTTA
39193833 TCGATTATGG
Statistics
Matches: 78, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
27 55 0.71
28 23 0.29
ACGTcount: A:0.40, C:0.19, G:0.14, T:0.28
Consensus pattern (27 bp):
CATTTTACCCCATAAGGGAAAAATAGT
Found at i:39200572 original size:39 final size:39
Alignment explanation
Indices: 39200529--39200695 Score: 253
Period size: 39 Copynumber: 4.3 Consensus size: 39
39200519 CTTTAACCCA
** *
39200529 GATATTTTTCCAGCACGTAGCCTGCGGACCTCAAGTCCG
1 GATATTTTTCCAGCATATAGCCTGCGGACCTCATGTCCG
* * *
39200568 GATATATTTCTAGCATATAGCCTGCGGATCTCATGTCCG
1 GATATTTTTCCAGCATATAGCCTGCGGACCTCATGTCCG
* *
39200607 GATAATTTTCCAGCATATAGCCTGCGGACCTTATGTCCG
1 GATATTTTTCCAGCATATAGCCTGCGGACCTCATGTCCG
39200646 GATATTTTTCCAGCATATAGCCTGCGGACCTCATGTCCG
1 GATATTTTTCCAGCATATAGCCTGCGGACCTCATGTCCG
39200685 GATATATTTTC
1 GATAT-TTTTC
39200696 AATCTCATAC
Statistics
Matches: 114, Mismatches: 13, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
39 109 0.96
40 5 0.04
ACGTcount: A:0.22, C:0.26, G:0.20, T:0.32
Consensus pattern (39 bp):
GATATTTTTCCAGCATATAGCCTGCGGACCTCATGTCCG
Found at i:39208499 original size:39 final size:39
Alignment explanation
Indices: 39208456--39208625 Score: 259
Period size: 39 Copynumber: 4.3 Consensus size: 39
39208446 GGACTTTAAC
** *
39208456 CCGGATATTTTTCCAGCACGTAGCCTGCGGACCTCAAGT
1 CCGGATATTTTTCCAGCATATAGCCTGCGGACCTCATGT
* * *
39208495 CCGGATATATTTCTAGCATATAGCCTGCGGATCTCATGT
1 CCGGATATTTTTCCAGCATATAGCCTGCGGACCTCATGT
*
39208534 TCGGATATTTTTCCAGCATATAGCCTGCGGACCTCATGT
1 CCGGATATTTTTCCAGCATATAGCCTGCGGACCTCATGT
39208573 CCGGATATTTTTCCAGCATATAGCCTGCGGACCTCATGT
1 CCGGATATTTTTCCAGCATATAGCCTGCGGACCTCATGT
*
39208612 CGGGATATATTTTC
1 CCGGATAT-TTTTC
39208626 AATCTCATAC
Statistics
Matches: 118, Mismatches: 12, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
39 113 0.96
40 5 0.04
ACGTcount: A:0.21, C:0.26, G:0.21, T:0.32
Consensus pattern (39 bp):
CCGGATATTTTTCCAGCATATAGCCTGCGGACCTCATGT
Found at i:39239668 original size:68 final size:68
Alignment explanation
Indices: 39239559--39239695 Score: 240
Period size: 68 Copynumber: 2.0 Consensus size: 68
39239549 CATTGGTGTA
*
39239559 CACGGCCATGTTGCACAGCCGTGTCAATCTTCATTCACCTCTCCCATGCCCGTGTATGTAGGCAC
1 CACGGCCATGTTGCACAGCCGTGTCAATCTTCATTCACCTCTCCCACGCCCGTGTATGTAGGCAC
39239624 ACG
66 ACG
*
39239627 CACGGCCATGTTGCA-TGACCGTGTCAATCTTCATTCACCTCTCCCACGCCCGTGTATGTAGGCA
1 CACGGCCATGTTGCACAG-CCGTGTCAATCTTCATTCACCTCTCCCACGCCCGTGTATGTAGGCA
39239691 CACG
65 CACG
39239695 C
1 C
39239696 CCGTGTTATT
Statistics
Matches: 66, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
67 1 0.02
68 65 0.98
ACGTcount: A:0.19, C:0.36, G:0.20, T:0.25
Consensus pattern (68 bp):
CACGGCCATGTTGCACAGCCGTGTCAATCTTCATTCACCTCTCCCACGCCCGTGTATGTAGGCAC
ACG
Found at i:39244858 original size:29 final size:30
Alignment explanation
Indices: 39244814--39244878 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 30
39244804 CGAGGCTATC
*
39244814 CCTTTTCATAATTTGACAGTTGTCACCA-T
1 CCTTTTCATAATTTGACAGTCGTCACCATT
**
39244843 CCTTTTCTATAA-TTGATGGTCGTCACCATT
1 CCTTTTC-ATAATTTGACAGTCGTCACCATT
39244873 CCTTTT
1 CCTTTT
39244879 TGTAATCAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
29 20 0.65
30 11 0.35
ACGTcount: A:0.20, C:0.25, G:0.11, T:0.45
Consensus pattern (30 bp):
CCTTTTCATAATTTGACAGTCGTCACCATT
Found at i:39248578 original size:28 final size:28
Alignment explanation
Indices: 39248545--39248609 Score: 96
Period size: 28 Copynumber: 2.3 Consensus size: 28
39248535 ATTTACTAGA
*
39248545 ATACCCCTATGTATGCAAAATTACCATTT
1 ATACCCCTATGTATGCAAAATGACC-TTT
*
39248574 -TACCCCTATGTATGCTAAATGACCTTT
1 ATACCCCTATGTATGCAAAATGACCTTT
39248601 ATACCCCTA
1 ATACCCCTA
39248610 GGGTTAATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
27 3 0.09
28 30 0.91
ACGTcount: A:0.31, C:0.28, G:0.08, T:0.34
Consensus pattern (28 bp):
ATACCCCTATGTATGCAAAATGACCTTT
Found at i:39248760 original size:28 final size:29
Alignment explanation
Indices: 39248715--39248777 Score: 85
Period size: 28 Copynumber: 2.2 Consensus size: 29
39248705 AGGAAGCGTC
* *
39248715 CTGGTGGCTATGCTACAAATTATCTGT-T
1 CTGGTGGCTATGCCACAAAATATCTGTAT
39248743 CTGGTGGC-ACTGCCACAAAATATCTGTAT
1 CTGGTGGCTA-TGCCACAAAATATCTGTAT
39248772 CTGGTG
1 CTGGTG
39248778 ACTCTGTCAC
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
27 1 0.03
28 23 0.74
29 7 0.23
ACGTcount: A:0.22, C:0.21, G:0.24, T:0.33
Consensus pattern (29 bp):
CTGGTGGCTATGCCACAAAATATCTGTAT
Found at i:39248788 original size:29 final size:28
Alignment explanation
Indices: 39248729--39248788 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 28
39248719 TGGCTATGCT
* *
39248729 ACAAATTATCTGTTCTGGTGGCACTGCC
1 ACAAAATATCTGTTCTGGTGACACTGCC
* *
39248757 ACAAAATATCTGTATCTGGTGACTCTGTC
1 ACAAAATATCTGT-TCTGGTGACACTGCC
39248786 ACA
1 ACA
39248789 TTTTCTGTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
28 12 0.44
29 15 0.56
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.32
Consensus pattern (28 bp):
ACAAAATATCTGTTCTGGTGACACTGCC
Found at i:39249266 original size:19 final size:19
Alignment explanation
Indices: 39249242--39249280 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
39249232 TTTTAATTAT
* *
39249242 TTTTATGGTTTTGTTTTAC
1 TTTTATGATTTTATTTTAC
*
39249261 TTTTATTATTTTATTTTAC
1 TTTTATGATTTTATTTTAC
39249280 T
1 T
39249281 ATGATGAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.15, C:0.05, G:0.08, T:0.72
Consensus pattern (19 bp):
TTTTATGATTTTATTTTAC
Found at i:39255653 original size:22 final size:22
Alignment explanation
Indices: 39255628--39255696 Score: 60
Period size: 22 Copynumber: 3.3 Consensus size: 22
39255618 TGATATCCGG
39255628 GCTAAGTCCCGAAGGCTTTTGT
1 GCTAAGTCCCGAAGGCTTTTGT
*
39255650 GCTAAG---CG-A--CTATATTCGG
1 GCTAAGTCCCGAAGGCT-T-TT-GT
39255669 GCTAAGTCCCGAAGGCTTTTGT
1 GCTAAGTCCCGAAGGCTTTTGT
39255691 GCTAAG
1 GCTAAG
39255697 CGACTACATC
Statistics
Matches: 36, Mismatches: 2, Indels: 18
0.64 0.04 0.32
Matches are distributed among these distances:
16 2 0.06
17 1 0.03
18 3 0.08
19 9 0.25
22 15 0.42
23 3 0.08
24 1 0.03
25 2 0.06
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.29
Consensus pattern (22 bp):
GCTAAGTCCCGAAGGCTTTTGT
Found at i:39255755 original size:40 final size:41
Alignment explanation
Indices: 39255620--39255802 Score: 237
Period size: 41 Copynumber: 4.5 Consensus size: 41
39255610 TACTCGAATG
*
39255620 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGCGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGCGACT
* *
39255661 ATATTCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGCGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGCGACT
* * *
39255702 ACATCCAGACTAAGAT-CCGAAGGCATTTGTGCT-AGCGACT
1 ATATCCGGGCTAAG-TCCCGAAGGCATTTGTGCTAAGCGACT
* * *
39255742 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCT-AGTGACC
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGCGACT
* *
39255782 ATATCCGGGTTAAGACCCGAA
1 ATATCCGGGCTAAGTCCCGAA
39255803 AGCCTTGTGC
Statistics
Matches: 126, Mismatches: 14, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
39 1 0.01
40 58 0.46
41 66 0.52
42 1 0.01
ACGTcount: A:0.26, C:0.24, G:0.25, T:0.25
Consensus pattern (41 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGCGACT
Found at i:39262043 original size:29 final size:32
Alignment explanation
Indices: 39262005--39262064 Score: 90
Period size: 29 Copynumber: 2.0 Consensus size: 32
39261995 TAACAAAGCA
*
39262005 AACGTGAGTAACGTGA-AG-G-GGATAGGGAG
1 AACGTAAGTAACGTGAGAGAGAGGATAGGGAG
39262034 AACGTAAGTAACGTGAGAGAGAGGATAGGGA
1 AACGTAAGTAACGTGAGAGAGAGGATAGGGA
39262065 TTTTTTAGGG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 15 0.56
30 2 0.07
31 1 0.04
32 9 0.33
ACGTcount: A:0.38, C:0.07, G:0.42, T:0.13
Consensus pattern (32 bp):
AACGTAAGTAACGTGAGAGAGAGGATAGGGAG
Found at i:39280568 original size:28 final size:28
Alignment explanation
Indices: 39280536--39280599 Score: 101
Period size: 28 Copynumber: 2.3 Consensus size: 28
39280526 ATTTACTAGA
*
39280536 ATACCCCTATGTATGCAAAATTACCATT
1 ATACCCCTATGTATGCAAAATGACCATT
* *
39280564 ATACCCCTATGTATGCTAAATGACCTTT
1 ATACCCCTATGTATGCAAAATGACCATT
39280592 ATACCCCT
1 ATACCCCT
39280600 TGGGTTAATT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.31, C:0.28, G:0.08, T:0.33
Consensus pattern (28 bp):
ATACCCCTATGTATGCAAAATGACCATT
Found at i:39281246 original size:19 final size:19
Alignment explanation
Indices: 39281222--39281260 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
39281212 TTTTAATTAT
* *
39281222 TTTTATGGTTTTGTTTTAC
1 TTTTATGATTTTATTTTAC
*
39281241 TTTTATTATTTTATTTTAC
1 TTTTATGATTTTATTTTAC
39281260 T
1 T
39281261 CTGATGAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.15, C:0.05, G:0.08, T:0.72
Consensus pattern (19 bp):
TTTTATGATTTTATTTTAC
Found at i:39288393 original size:28 final size:28
Alignment explanation
Indices: 39288357--39288421 Score: 94
Period size: 28 Copynumber: 2.3 Consensus size: 28
39288347 ATTTACTAGA
*
39288357 ATACCCCTATGTATGCAAAATTACCATT
1 ATACCCCTATGTATGCAAAATGACCATT
* * *
39288385 ATAGCCCTATGTATGCTAAATGACCTTT
1 ATACCCCTATGTATGCAAAATGACCATT
39288413 ATACCCCTA
1 ATACCCCTA
39288422 GGGTTAATTT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.32, C:0.26, G:0.09, T:0.32
Consensus pattern (28 bp):
ATACCCCTATGTATGCAAAATGACCATT
Found at i:39288568 original size:28 final size:28
Alignment explanation
Indices: 39288527--39288581 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
39288517 AGGAAGCGTC
*
39288527 CTGGTGGCTATGCCACAAATTATCTGTT
1 CTGGTGGCTATGCCACAAAATATCTGTT
*
39288555 CTGGTGGC-ACTGCCATAAAATATCTGT
1 CTGGTGGCTA-TGCCACAAAATATCTGT
39288582 ATCTAGTGAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 1 0.04
28 23 0.96
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.33
Consensus pattern (28 bp):
CTGGTGGCTATGCCACAAAATATCTGTT
Found at i:39289077 original size:19 final size:19
Alignment explanation
Indices: 39289053--39289091 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
39289043 TTTTAATTAT
* *
39289053 TTTTATGGTTTTGTTTTAC
1 TTTTATGATTTTATTTTAC
*
39289072 TTTTATTATTTTATTTTAC
1 TTTTATGATTTTATTTTAC
39289091 T
1 T
39289092 ATGATGAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.15, C:0.05, G:0.08, T:0.72
Consensus pattern (19 bp):
TTTTATGATTTTATTTTAC
Found at i:39290309 original size:30 final size:30
Alignment explanation
Indices: 39290275--39290335 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
39290265 TCCTTAACTC
39290275 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
39290305 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
39290335 A
1 A
39290336 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACAATTTTGCCCCT
Found at i:39291423 original size:35 final size:35
Alignment explanation
Indices: 39291365--39291552 Score: 304
Period size: 35 Copynumber: 5.3 Consensus size: 35
39291355 AATCATATCT
39291365 TCTAAGATTGTATATCATATCTAAGATTGCAATCATA
1 TCTAAGATTG--TATCATATCTAAGATTGCAATCATA
39291402 TCTAAGATTGTATCATATCTAAGATTGCAATCATA
1 TCTAAGATTGTATCATATCTAAGATTGCAATCATA
*
39291437 TCTAAGATTGTATCATATCTAAGATTGCAATGATA
1 TCTAAGATTGTATCATATCTAAGATTGCAATCATA
39291472 TCTAAGATTGTATCATATCTAAGATTGCAATCATA
1 TCTAAGATTGTATCATATCTAAGATTGCAATCATA
* * * *
39291507 TCTAAGATTGTATTATATCTAGGATTGCATCTCACA
1 TCTAAGATTGTATCATATCTAAGATTGCA-ATCATA
39291543 TCTAAGATTG
1 TCTAAGATTG
39291553 CATATCATTG
Statistics
Matches: 144, Mismatches: 6, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
35 120 0.83
36 14 0.10
37 10 0.07
ACGTcount: A:0.36, C:0.14, G:0.13, T:0.38
Consensus pattern (35 bp):
TCTAAGATTGTATCATATCTAAGATTGCAATCATA
Found at i:39292301 original size:205 final size:205
Alignment explanation
Indices: 39291918--39292621 Score: 1122
Period size: 205 Copynumber: 3.4 Consensus size: 205
39291908 AAATTAACTT
* * * *
39291918 CTTCGATTTGTTCCCTGACAATACAGATATG-CAAATCATCTTAGATTTGCTTTAACGTAAGCAC
1 CTTCGATTTGTTCTCTGACAATACAGAGATGACAAATCATCTTAGATTTGCTTCAACGTAAACAC
* * * *
39291982 ATGAAATCCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAGCACAAGGATGCCAAACCATCTT
66 GTGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATACCAAACCATCTT
* * *
39292047 GGATCTGCTTTAGCATAAACATCTGAAGGTGAGATCTGCCATGTATCTGCTCTCCATTGAAGTGG
131 GGATCTGCTTTAGCATAAACATCTGAAGGTGAGATCTGCTATGTATCTGCTCTCTATTGAAGTAG
39292112 AGATGCCAGA
196 AGATGCCAGA
* * * * *
39292122 CTTCGATTTTTTCTCTGACACTACAGAGATGACAAATCATCTTAGATTTGCTTCATCATAAATAC
1 CTTCGATTTGTTCTCTGACAATACAGAGATGACAAATCATCTTAGATTTGCTTCAACGTAAACAC
*
39292187 GTGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATACAAAACCATCTT
66 GTGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATACCAAACCATCTT
*
39292252 GGATCTGCTTCAGCATAAACATCTGAAGGTGAGATCTGCTATGTATCTGCTCTCTATTGAAGTAG
131 GGATCTGCTTTAGCATAAACATCTGAAGGTGAGATCTGCTATGTATCTGCTCTCTATTGAAGTAG
39292317 AGATGCCAGA
196 AGATGCCAGA
* * * * *
39292327 CTTCGATTTGTTCTCTGACACTACAGAGACGACAAATCATCTTATATTTGCTTTAACGTAAGCAC
1 CTTCGATTTGTTCTCTGACAATACAGAGATGACAAATCATCTTAGATTTGCTTCAACGTAAACAC
* * *
39292392 GTGAAAGCCAAATCAGCTATGTCTTCGATTTTTTCATTGTAAGCACAATGATACCAAACCATCTT
66 GTGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATACCAAACCATCTT
39292457 GGATCTGCTTTAGCATAAACATCTGAAGGTGAGATCTGCTATGTATCTGCTCTCTATTGAAGTAG
131 GGATCTGCTTTAGCATAAACATCTGAAGGTGAGATCTGCTATGTATCTGCTCTCTATTGAAGTAG
39292522 AGATGCCAGA
196 AGATGCCAGA
* * **
39292532 CTTCTATTTGTTCTCTGACAATACAGAGATGAAAAATCATCTTAGATTTGCTTCATTGTAAACAC
1 CTTCGATTTGTTCTCTGACAATACAGAGATGACAAATCATCTTAGATTTGCTTCAACGTAAACAC
*
39292597 GTGAAAGCTAAATCAGCTATGTCTT
66 GTGAAAGCCAAATCAGCTATGTCTT
39292622 TGATCTACTC
Statistics
Matches: 458, Mismatches: 41, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
204 27 0.06
205 431 0.94
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.32
Consensus pattern (205 bp):
CTTCGATTTGTTCTCTGACAATACAGAGATGACAAATCATCTTAGATTTGCTTCAACGTAAACAC
GTGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATACCAAACCATCTT
GGATCTGCTTTAGCATAAACATCTGAAGGTGAGATCTGCTATGTATCTGCTCTCTATTGAAGTAG
AGATGCCAGA
Found at i:39292710 original size:44 final size:44
Alignment explanation
Indices: 39292616--39292710 Score: 136
Period size: 44 Copynumber: 2.2 Consensus size: 44
39292606 AAATCAGCTA
* * *
39292616 TGTCTTTGATCTACTCTCTGCCAATACAGAGATGCCAAATCTGG
1 TGTCTTCGATCTACTCTCTGACAATACAGAGATGCCAAATCTGC
* * *
39292660 TATCTTCGATCTGCTCTCTGACAATACAGAGATGCCGAATCTGC
1 TGTCTTCGATCTACTCTCTGACAATACAGAGATGCCAAATCTGC
39292704 TGTCTTC
1 TGTCTTC
39292711 AACTTGTTCC
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.23, C:0.26, G:0.18, T:0.33
Consensus pattern (44 bp):
TGTCTTCGATCTACTCTCTGACAATACAGAGATGCCAAATCTGC
Found at i:39292840 original size:44 final size:44
Alignment explanation
Indices: 39292641--39293229 Score: 409
Period size: 44 Copynumber: 13.4 Consensus size: 44
39292631 CTCTGCCAAT
* * * * * *
39292641 ACAGAGATGCCAAATCTGGTATCTTCGATCTGCTCTCTGA-CAAT
1 ACAGGGATGCCAAATCTGCTATCTTCGATCTGTTCCCT-ATAAAC
* * * *
39292685 ACAGAGATGCCGAATCTGCTGTCTTC-AACTTGTTCCCTATAAAC
1 ACAGGGATGCCAAATCTGCTATCTTCGATC-TGTTCCCTATAAAC
* ** * * *
39292729 ACAGGGATACC--ATGCTGAAATCTTCGATCTGCTTCGCTGTAAGC
1 ACAGGGATGCCAAAT-CTGCTATCTTCGATCTG-TTCCCTATAAAC
* * ** * *
39292773 ACA-GGAGTGTCAGATCTATTATCTTTGATCTGTTCCATATAAAC
1 ACAGGGA-TGCCAAATCTGCTATCTTCGATCTGTTCCCTATAAAC
*
39292817 ACAGGGATGCCAAATCTGCTATCTTC-AACTTGTTCCCTATAAAC
1 ACAGGGATGCCAAATCTGCTATCTTCGATC-TGTTCCCTATAAAC
** * * * *
39292861 ACAGGGATGCC--ATGCTGAAATCCTCGATCTGTTTCGCTGTAAGC
1 ACAGGGATGCCAAAT-CTGCTATCTTCGATCTG-TTCCCTATAAAC
* * * * *
39292905 ACA-GGAGTGTCAGATCTGTTATCGTCGATCTGTTCCCTATAAAT
1 ACAGGGA-TGCCAAATCTGCTATCTTCGATCTGTTCCCTATAAAC
*
39292949 ACAGGGATGCCAAATCTGCTATCTTC-AACTTGTTCCCTATAAAC
1 ACAGGGATGCCAAATCTGCTATCTTCGATC-TGTTCCCTATAAAC
* ** * * * *
39292993 ATAGGGATGCC--ATGCTGAAATCCTCGATCTGCTTCACTGTAAGC
1 ACAGGGATGCCAAAT-CTGCTATCTTCGATCTG-TTCCCTATAAAC
* * * *
39293037 ACA-GGAGTGTCAGATCTGTTATCTTCGATCTATTCCCTATAAAC
1 ACAGGGA-TGCCAAATCTGCTATCTTCGATCTGTTCCCTATAAAC
* * *
39293081 ACAAGGATGCCAAATCCGCTATCTTC-AACTTGTTCCCTATAAAC
1 ACAGGGATGCCAAATCTGCTATCTTCGATC-TGTTCCCTATAAAC
** * * *
39293125 ACAGGGATGCC--ATGCTGAAATCTTCGATCTGCTTCGCTGTAAGC
1 ACAGGGATGCCAAAT-CTGCTATCTTCGATCTG-TTCCCTATAAAC
* * *
39293169 ACAGGAATGTCAGATCTGCTATCTTCGATCTGTTCCCTATAAAC
1 ACAGGGATGCCAAATCTGCTATCTTCGATCTGTTCCCTATAAAC
39293213 ACAGGGATGCCAAATCT
1 ACAGGGATGCCAAATCT
39293230 TGTTTCTTTG
Statistics
Matches: 418, Mismatches: 96, Indels: 62
0.73 0.17 0.11
Matches are distributed among these distances:
42 8 0.02
43 58 0.14
44 280 0.67
45 64 0.15
46 8 0.02
ACGTcount: A:0.27, C:0.25, G:0.18, T:0.30
Consensus pattern (44 bp):
ACAGGGATGCCAAATCTGCTATCTTCGATCTGTTCCCTATAAAC
Found at i:39292897 original size:132 final size:132
Alignment explanation
Indices: 39292654--39293229 Score: 920
Period size: 132 Copynumber: 4.4 Consensus size: 132
39292644 GAGATGCCAA
* * * * * * * *
39292654 ATCTGGTATCTTCGATCTGCTCTCTGA-CAATACAGAGATGCCGAATCTGCTGTCTTCAACTTGT
1 ATCTGTTATCTTCGATCTGTTCCCT-ATAAACACAGGGATGCCAAATCTGCTATCTTCAACTTGT
* *
39292718 TCCCTATAAACACAGGGATACCATGCTGAAATCTTCGATCTGCTTCGCTGTAAGCACAGGAGTGT
65 TCCCTATAAACACAGGGATGCCATGCTGAAATCCTCGATCTGCTTCGCTGTAAGCACAGGAGTGT
39292783 CAG
130 CAG
* * *
39292786 ATCTATTATCTTTGATCTGTTCCATATAAACACAGGGATGCCAAATCTGCTATCTTCAACTTGTT
1 ATCTGTTATCTTCGATCTGTTCCCTATAAACACAGGGATGCCAAATCTGCTATCTTCAACTTGTT
*
39292851 CCCTATAAACACAGGGATGCCATGCTGAAATCCTCGATCTGTTTCGCTGTAAGCACAGGAGTGTC
66 CCCTATAAACACAGGGATGCCATGCTGAAATCCTCGATCTGCTTCGCTGTAAGCACAGGAGTGTC
39292916 AG
131 AG
* *
39292918 ATCTGTTATCGTCGATCTGTTCCCTATAAATACAGGGATGCCAAATCTGCTATCTTCAACTTGTT
1 ATCTGTTATCTTCGATCTGTTCCCTATAAACACAGGGATGCCAAATCTGCTATCTTCAACTTGTT
* *
39292983 CCCTATAAACATAGGGATGCCATGCTGAAATCCTCGATCTGCTTCACTGTAAGCACAGGAGTGTC
66 CCCTATAAACACAGGGATGCCATGCTGAAATCCTCGATCTGCTTCGCTGTAAGCACAGGAGTGTC
39293048 AG
131 AG
* * *
39293050 ATCTGTTATCTTCGATCTATTCCCTATAAACACAAGGATGCCAAATCCGCTATCTTCAACTTGTT
1 ATCTGTTATCTTCGATCTGTTCCCTATAAACACAGGGATGCCAAATCTGCTATCTTCAACTTGTT
* *
39293115 CCCTATAAACACAGGGATGCCATGCTGAAATCTTCGATCTGCTTCGCTGTAAGCACAGGAATGTC
66 CCCTATAAACACAGGGATGCCATGCTGAAATCCTCGATCTGCTTCGCTGTAAGCACAGGAGTGTC
39293180 AG
131 AG
*
39293182 ATCTGCTATCTTCGATCTGTTCCCTATAAACACAGGGATGCCAAATCT
1 ATCTGTTATCTTCGATCTGTTCCCTATAAACACAGGGATGCCAAATCT
39293230 TGTTTCTTTG
Statistics
Matches: 408, Mismatches: 35, Indels: 2
0.92 0.08 0.00
Matches are distributed among these distances:
131 1 0.00
132 407 1.00
ACGTcount: A:0.27, C:0.25, G:0.18, T:0.30
Consensus pattern (132 bp):
ATCTGTTATCTTCGATCTGTTCCCTATAAACACAGGGATGCCAAATCTGCTATCTTCAACTTGTT
CCCTATAAACACAGGGATGCCATGCTGAAATCCTCGATCTGCTTCGCTGTAAGCACAGGAGTGTC
AG
Found at i:39294133 original size:7 final size:7
Alignment explanation
Indices: 39294121--39294186 Score: 52
Period size: 7 Copynumber: 9.7 Consensus size: 7
39294111 GGCCTCTCCA
39294121 TTTTTCT
1 TTTTTCT
39294128 TTTTTCT
1 TTTTTCT
39294135 CTTTTT-T
1 -TTTTTCT
39294142 ATTTTTCT
1 -TTTTTCT
39294150 TTTTAT-T
1 TTTT-TCT
*
39294157 TTTTT-A
1 TTTTTCT
*
39294163 TTTAT-T
1 TTTTTCT
39294169 TTTTTC-
1 TTTTTCT
39294175 TTTTTCT
1 TTTTTCT
39294182 TTTTT
1 TTTTT
39294187 TTTGAAATAG
Statistics
Matches: 49, Mismatches: 5, Indels: 10
0.77 0.08 0.16
Matches are distributed among these distances:
6 15 0.31
7 27 0.55
8 7 0.14
ACGTcount: A:0.06, C:0.09, G:0.00, T:0.85
Consensus pattern (7 bp):
TTTTTCT
Found at i:39294139 original size:9 final size:8
Alignment explanation
Indices: 39294121--39294189 Score: 54
Period size: 8 Copynumber: 8.6 Consensus size: 8
39294111 GGCCTCTCCA
39294121 TTTTTC-T
1 TTTTTCTT
*
39294128 TTTTTCTC
1 TTTTTCTT
*
39294136 TTTTT-TA
1 TTTTTCTT
39294143 TTTTTCTT
1 TTTTTCTT
*
39294151 TTTATTTTT
1 TTT-TTCTT
*
39294160 TTATTTATT
1 TT-TTTCTT
39294169 TTTTTCTT
1 TTTTTCTT
39294177 TTTCTT-TT
1 TTT-TTCTT
39294185 TTTTT
1 TTTTT
39294190 GAAATAGAAG
Statistics
Matches: 51, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
7 14 0.27
8 22 0.43
9 14 0.27
10 1 0.02
ACGTcount: A:0.06, C:0.09, G:0.00, T:0.86
Consensus pattern (8 bp):
TTTTTCTT
Found at i:39294154 original size:12 final size:11
Alignment explanation
Indices: 39294136--39294188 Score: 63
Period size: 12 Copynumber: 4.5 Consensus size: 11
39294126 CTTTTTTCTC
39294136 TTTTTTATTTT
1 TTTTTTATTTT
39294147 TCTTTTTATTTT
1 T-TTTTTATTTT
39294159 TTTATTTATTTT
1 TTT-TTTATTTT
39294171 TTTCTTT-TTCTT
1 TTT-TTTATT-TT
39294183 TTTTTT
1 TTTTTT
39294189 TGAAATAGAA
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
11 8 0.21
12 30 0.79
ACGTcount: A:0.08, C:0.06, G:0.00, T:0.87
Consensus pattern (11 bp):
TTTTTTATTTT
Found at i:39299895 original size:23 final size:22
Alignment explanation
Indices: 39299867--39299918 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 22
39299857 TTTGGGTATG
*
39299867 TGATGACGTTATCTT-ATAAATA
1 TGATGAAGTTATCTTGA-AAATA
*
39299889 TGCATGAATTTATCTTGAAAATA
1 TG-ATGAAGTTATCTTGAAAATA
39299912 TGATGAA
1 TGATGAA
39299919 TTGGTTTGGT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
22 7 0.27
23 18 0.69
24 1 0.04
ACGTcount: A:0.38, C:0.08, G:0.15, T:0.38
Consensus pattern (22 bp):
TGATGAAGTTATCTTGAAAATA
Found at i:39299920 original size:22 final size:23
Alignment explanation
Indices: 39299875--39299920 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
39299865 TGTGATGACG
39299875 TTATCTTATAAATATGCATGAAT
1 TTATCTTATAAATATGCATGAAT
39299898 TTATCTTGA-AAATATG-ATGAAT
1 TTATCTT-ATAAATATGCATGAAT
39299920 T
1 T
39299921 GGTTTGGTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 7 0.32
23 14 0.64
24 1 0.05
ACGTcount: A:0.39, C:0.07, G:0.11, T:0.43
Consensus pattern (23 bp):
TTATCTTATAAATATGCATGAAT
Found at i:39308990 original size:48 final size:48
Alignment explanation
Indices: 39308930--39309061 Score: 169
Period size: 48 Copynumber: 2.8 Consensus size: 48
39308920 TCAATCAATA
* *
39308930 AGTAGCTATACCATGGC-CTGAAGCCAAATCAAGGTAACTTATCCCCAG-
1 AGTACCTATACCATGGCTC-GAAGCCAAATCAAGGTAACTCAT-CCCAGT
* * *
39308978 AGTACCTATACCATGGCTCGTAGCCAAATCAAGGTAACTCATCTCTGT
1 AGTACCTATACCATGGCTCGAAGCCAAATCAAGGTAACTCATCCCAGT
* *
39309026 AATACCTATACCATGGCTCGAAGCGAAATCAAGGTA
1 AGTACCTATACCATGGCTCGAAGCCAAATCAAGGTA
39309062 TAATTCGCAC
Statistics
Matches: 74, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
47 3 0.04
48 70 0.95
49 1 0.01
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.23
Consensus pattern (48 bp):
AGTACCTATACCATGGCTCGAAGCCAAATCAAGGTAACTCATCCCAGT
Found at i:39315063 original size:26 final size:26
Alignment explanation
Indices: 39315033--39315084 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
39315023 GCTAAGGGAA
39315033 AGAAAAAAAGTCGACTAAGTCTTCGG
1 AGAAAAAAAGTCGACTAAGTCTTCGG
39315059 AGAAAAAAAGTCGACTAAGTCTTCGG
1 AGAAAAAAAGTCGACTAAGTCTTCGG
39315085 TTCCACCTCG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.42, C:0.15, G:0.23, T:0.19
Consensus pattern (26 bp):
AGAAAAAAAGTCGACTAAGTCTTCGG
Found at i:39323283 original size:25 final size:25
Alignment explanation
Indices: 39323255--39323303 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
39323245 AAAAATCATG
* *
39323255 ATTAAAGAACTAGTGAATTTACCTA
1 ATTAAAGAAATAGTAAATTTACCTA
39323280 ATTAAAGAAATAGTAAATTTACCT
1 ATTAAAGAAATAGTAAATTTACCT
39323304 GAGAGATAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.47, C:0.10, G:0.10, T:0.33
Consensus pattern (25 bp):
ATTAAAGAAATAGTAAATTTACCTA
Found at i:39323889 original size:43 final size:42
Alignment explanation
Indices: 39323842--39323967 Score: 180
Period size: 43 Copynumber: 3.0 Consensus size: 42
39323832 CAGCGTCAAG
39323842 ACCAGGACCTTTAGCGGCGCTTTTATAAAAAACGCCGCTAAAC
1 ACCAGGACCTTTAGCGGCGCTTTT-TAAAAAACGCCGCTAAAC
* * *
39323885 ACCAGGACCTTTAGCGGCGCTTTTTAAAAAACGCCACGAAAG
1 ACCAGGACCTTTAGCGGCGCTTTTTAAAAAACGCCGCTAAAC
* * *
39323927 ACCTGTACTTTTAGCGGCGCTTTTTTAAAAAACGCCGCTAA
1 ACCAGGACCTTTAGCGGCGC-TTTTTAAAAAACGCCGCTAA
39323968 TTTGCCCAAT
Statistics
Matches: 74, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
42 32 0.43
43 42 0.57
ACGTcount: A:0.31, C:0.26, G:0.19, T:0.24
Consensus pattern (42 bp):
ACCAGGACCTTTAGCGGCGCTTTTTAAAAAACGCCGCTAAAC
Found at i:39324290 original size:21 final size:21
Alignment explanation
Indices: 39324266--39324329 Score: 110
Period size: 21 Copynumber: 3.0 Consensus size: 21
39324256 TTCTGCTTTA
*
39324266 CCTCCCTCGCTGCTGCCTCTG
1 CCTCCCTCGCTGCTGCCTCCG
39324287 CCTCCCTCGCTGCTGCCTCCG
1 CCTCCCTCGCTGCTGCCTCCG
*
39324308 CCTCCCTCGCTGCTGACTCCG
1 CCTCCCTCGCTGCTGCCTCCG
39324329 C
1 C
39324330 TCTAAGTTGA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.02, C:0.55, G:0.19, T:0.25
Consensus pattern (21 bp):
CCTCCCTCGCTGCTGCCTCCG
Found at i:39324910 original size:18 final size:18
Alignment explanation
Indices: 39324878--39324915 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
39324868 TACAATATAG
39324878 TAGTAAAAATATTATTTAA
1 TAGTAAAAATATTA-TTAA
*
39324897 TAGTAAAAA-GTTATTAA
1 TAGTAAAAATATTATTAA
39324914 TA
1 TA
39324916 CTTGATAGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 6 0.33
18 3 0.17
19 9 0.50
ACGTcount: A:0.53, C:0.00, G:0.08, T:0.39
Consensus pattern (18 bp):
TAGTAAAAATATTATTAA
Found at i:39329681 original size:15 final size:15
Alignment explanation
Indices: 39329661--39329689 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
39329651 ACAATTTTGA
39329661 AATAAAACGTACCTT
1 AATAAAACGTACCTT
39329676 AATAAAACGTACCT
1 AATAAAACGTACCT
39329690 GGTCTACTCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.21, G:0.07, T:0.24
Consensus pattern (15 bp):
AATAAAACGTACCTT
Found at i:39331141 original size:20 final size:19
Alignment explanation
Indices: 39331112--39331173 Score: 56
Period size: 20 Copynumber: 3.2 Consensus size: 19
39331102 ATAAGCTTAA
39331112 AAATTTAGGAATGTAATTT
1 AAATTTAGGAATGTAATTT
** *
39331131 AAATGTTAGGAA-AAACATTAA
1 AAAT-TTAGGAATGTA-ATT-T
39331152 AAATTTAGGAATGTAA-TT
1 AAATTTAGGAATGTAATTT
39331170 AAAT
1 AAAT
39331174 GTTAATTAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 9
0.69 0.12 0.19
Matches are distributed among these distances:
18 4 0.12
19 6 0.18
20 18 0.55
21 5 0.15
ACGTcount: A:0.50, C:0.02, G:0.15, T:0.34
Consensus pattern (19 bp):
AAATTTAGGAATGTAATTT
Found at i:39340289 original size:25 final size:25
Alignment explanation
Indices: 39340252--39340305 Score: 90
Period size: 25 Copynumber: 2.2 Consensus size: 25
39340242 AGGGTCACAC
* *
39340252 GGCCGTGTTACACGCTCGTGTTCTA
1 GGCCGTGTCACACGCCCGTGTTCTA
39340277 GGCCGTGTCACACGCCCGTGTTCTA
1 GGCCGTGTCACACGCCCGTGTTCTA
39340302 GGCC
1 GGCC
39340306 ATGTAACTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.11, C:0.33, G:0.30, T:0.26
Consensus pattern (25 bp):
GGCCGTGTCACACGCCCGTGTTCTA
Found at i:39341773 original size:20 final size:20
Alignment explanation
Indices: 39341750--39341803 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
39341740 TGAATAACAA
* * *
39341750 CACCAAAGTGTATACAAGGG
1 CACCAAAGTGCAAACAAAGG
*
39341770 CACCGAAGTGCAAACAAAGG
1 CACCAAAGTGCAAACAAAGG
39341790 CACCAAAGTGCAAA
1 CACCAAAGTGCAAA
39341804 TCCTGTACAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.44, C:0.24, G:0.22, T:0.09
Consensus pattern (20 bp):
CACCAAAGTGCAAACAAAGG
Done.