Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 113035596
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: 113035596
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 271 characters in sequence are not A, C, G, or T
File 107 of 378
Found at i:29650963 original size:13 final size:13
Alignment explanation
Indices: 29650945--29650969 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
29650935 AATATCTTAG
29650945 AAAATAAATAATA
1 AAAATAAATAATA
29650958 AAAATAAATAAT
1 AAAATAAATAAT
29650970 TTTTCATTTA
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:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (13 bp):
AAAATAAATAATA
Found at i:29651998 original size:17 final size:17
Alignment explanation
Indices: 29651976--29652008 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
29651966 TTTATATAAA
29651976 TAAATAACTTTT-TCAAG
1 TAAATAA-TTTTCTCAAG
29651993 TAAATAATTTTCTCAA
1 TAAATAATTTTCTCAA
29652009 CCCAATTCTG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.42, C:0.12, G:0.03, T:0.42
Consensus pattern (17 bp):
TAAATAATTTTCTCAAG
Found at i:29653607 original size:12 final size:12
Alignment explanation
Indices: 29653590--29653620 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
29653580 TGCTAGACGA
*
29653590 CCGTGTGTTAGG
1 CCGTGTGGTAGG
29653602 CCGTGTGGTAGG
1 CCGTGTGGTAGG
29653614 CCGTGTG
1 CCGTGTG
29653621 CCATGACACA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.06, C:0.19, G:0.45, T:0.29
Consensus pattern (12 bp):
CCGTGTGGTAGG
Found at i:29660567 original size:41 final size:41
Alignment explanation
Indices: 29660510--29660659 Score: 221
Period size: 41 Copynumber: 3.7 Consensus size: 41
29660500 TTGGGGTTTA
29660510 AATCCGAGCTTGGTCTCGAAGGGCTTTTGAGCCAGTGTCAT
1 AATCCGAGCTTGGTCTCGAAGGGCTTTTGAGCCAGTGTCAT
29660551 AATCCGAGCTTGGTCTCGAAGGGCTTTTGAGCCAGTGTCAT
1 AATCCGAGCTTGGTCTCGAAGGGCTTTTGAGCCAGTGTCAT
* * * * * * *
29660592 AA-CCGAACCTAGTTTCGAAGGGCCTTTGGGCCAATGTCAT
1 AATCCGAGCTTGGTCTCGAAGGGCTTTTGAGCCAGTGTCAT
*
29660632 AATCCGAGCTTGGTCTTGAAGGGCTTTT
1 AATCCGAGCTTGGTCTCGAAGGGCTTTT
29660660 TGAGTCAGCG
Statistics
Matches: 95, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
40 33 0.35
41 62 0.65
ACGTcount: A:0.21, C:0.22, G:0.28, T:0.29
Consensus pattern (41 bp):
AATCCGAGCTTGGTCTCGAAGGGCTTTTGAGCCAGTGTCAT
Found at i:29667692 original size:28 final size:28
Alignment explanation
Indices: 29667647--29667715 Score: 113
Period size: 28 Copynumber: 2.5 Consensus size: 28
29667637 ATTAAAACCC
29667647 TAGGGGT-ATTTCGATAATTTTACTCTT
1 TAGGGGTAATTTCGATAATTTTACTCTT
* *
29667674 TAGGGGTAATTTCGGTAATTTTGCTCTT
1 TAGGGGTAATTTCGATAATTTTACTCTT
29667702 TAGGGGTAATTTCG
1 TAGGGGTAATTTCG
29667716 TGATCTACGC
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
27 7 0.18
28 32 0.82
ACGTcount: A:0.20, C:0.10, G:0.25, T:0.45
Consensus pattern (28 bp):
TAGGGGTAATTTCGATAATTTTACTCTT
Found at i:29669545 original size:19 final size:18
Alignment explanation
Indices: 29669508--29669551 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
29669498 ATACATACAG
29669508 TAAT-ATTTTTCTAATAA
1 TAATAATTTTTCTAATAA
*
29669525 TAATAATTTTATCTCATAA
1 TAATAATTTT-TCTAATAA
*
29669544 TACTAATT
1 TAATAATT
29669552 AAAATTTCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 4 0.17
18 5 0.22
19 14 0.61
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (18 bp):
TAATAATTTTTCTAATAA
Found at i:29669793 original size:16 final size:16
Alignment explanation
Indices: 29669772--29669803 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
29669762 GTTTTGTCCA
29669772 TATATCAAAGCACAAG
1 TATATCAAAGCACAAG
29669788 TATATCAAAGCACAAG
1 TATATCAAAGCACAAG
29669804 GCATAATTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.19, G:0.12, T:0.19
Consensus pattern (16 bp):
TATATCAAAGCACAAG
Found at i:29670134 original size:6 final size:6
Alignment explanation
Indices: 29670116--29670177 Score: 70
Period size: 6 Copynumber: 10.3 Consensus size: 6
29670106 ATATAAAGAC
* * * *
29670116 AAAATA AACATA AAAATA AAAATA AACATA AAAATA AACATA AACATA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA
* *
29670164 AAGATA AAGATA AA
1 AAAATA AAAATA AA
29670178 TGGACTCAAT
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 50 1.00
ACGTcount: A:0.74, C:0.06, G:0.03, T:0.16
Consensus pattern (6 bp):
AAAATA
Found at i:29670139 original size:18 final size:18
Alignment explanation
Indices: 29670116--29670177 Score: 97
Period size: 18 Copynumber: 3.4 Consensus size: 18
29670106 ATATAAAGAC
29670116 AAAATAAACATAAAAATA
1 AAAATAAACATAAAAATA
29670134 AAAATAAACATAAAAATA
1 AAAATAAACATAAAAATA
* *
29670152 AACATAAACATAAAGATA
1 AAAATAAACATAAAAATA
*
29670170 AAGATAAA
1 AAAATAAA
29670178 TGGACTCAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 41 1.00
ACGTcount: A:0.74, C:0.06, G:0.03, T:0.16
Consensus pattern (18 bp):
AAAATAAACATAAAAATA
Found at i:29671903 original size:14 final size:14
Alignment explanation
Indices: 29671884--29671910 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
29671874 AAACAAAGTA
29671884 AAATAATAATAAAG
1 AAATAATAATAAAG
29671898 AAATAATAATAAA
1 AAATAATAATAAA
29671911 AAGAGTAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.74, C:0.00, G:0.04, T:0.22
Consensus pattern (14 bp):
AAATAATAATAAAG
Found at i:29680547 original size:3 final size:3
Alignment explanation
Indices: 29680539--29680592 Score: 108
Period size: 3 Copynumber: 18.0 Consensus size: 3
29680529 GGATGTTTTA
29680539 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
29680587 ATT ATT
1 ATT ATT
29680593 TAGTATGTTT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:29681688 original size:16 final size:16
Alignment explanation
Indices: 29681648--29681690 Score: 68
Period size: 17 Copynumber: 2.6 Consensus size: 16
29681638 ATTTTTTACT
29681648 GAAACTAGAGAATTAAA
1 GAAAC-AGAGAATTAAA
29681665 GAAAACAGAGAATTAAA
1 G-AAACAGAGAATTAAA
29681682 GAAACAGAG
1 GAAACAGAG
29681691 TAAGCATTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.32
17 13 0.52
18 4 0.16
ACGTcount: A:0.60, C:0.07, G:0.21, T:0.12
Consensus pattern (16 bp):
GAAACAGAGAATTAAA
Found at i:29682080 original size:40 final size:40
Alignment explanation
Indices: 29682006--29682267 Score: 411
Period size: 40 Copynumber: 6.6 Consensus size: 40
29681996 AACCCAAGTA
* * *
29682006 CCTTCGGGAATTAG-CCGAATATAG-CAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATG
**
29682045 CCTTCGGGTTTTAGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
* *
29682085 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCATAATTG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
*
29682125 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAAGG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
*
29682165 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCATAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
*
29682205 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAAGG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
29682245 CCTTCGGGACTTAGCCCGGATAT
1 CCTTCGGGACTTAGCCCGGATAT
29682268 CATCCGAATA
Statistics
Matches: 206, Mismatches: 15, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
39 12 0.06
40 193 0.94
41 1 0.00
ACGTcount: A:0.27, C:0.26, G:0.23, T:0.24
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
Found at i:29684185 original size:29 final size:31
Alignment explanation
Indices: 29684153--29684210 Score: 93
Period size: 29 Copynumber: 1.9 Consensus size: 31
29684143 TGGAAATTTA
29684153 TATTTTTCTTTTT-TT-TTTTTCTCTTCTTC
1 TATTTTTCTTTTTCTTGTTTTTCTCTTCTTC
*
29684182 TATTTTTCTTTTTCTTGTTTTTCTTTTCT
1 TATTTTTCTTTTTCTTGTTTTTCTCTTCT
29684211 CCCCTATAGC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 13 0.50
30 2 0.08
31 11 0.42
ACGTcount: A:0.03, C:0.16, G:0.02, T:0.79
Consensus pattern (31 bp):
TATTTTTCTTTTTCTTGTTTTTCTCTTCTTC
Found at i:29684191 original size:14 final size:14
Alignment explanation
Indices: 29684153--29684208 Score: 60
Period size: 15 Copynumber: 3.9 Consensus size: 14
29684143 TGGAAATTTA
29684153 TATTTTTCTTTTT-
1 TATTTTTCTTTTTC
*
29684166 TTTTTTTCTCTTCTTC
1 TATTTTTCT-TT-TTC
29684182 TATTTTTCTTTTTC
1 TATTTTTCTTTTTC
*
29684196 TTGTTTTTCTTTT
1 -TATTTTTCTTTT
29684209 CTCCCCTATA
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
13 8 0.22
14 5 0.14
15 15 0.42
16 8 0.22
ACGTcount: A:0.04, C:0.14, G:0.02, T:0.80
Consensus pattern (14 bp):
TATTTTTCTTTTTC
Found at i:29684209 original size:14 final size:14
Alignment explanation
Indices: 29684153--29684210 Score: 55
Period size: 13 Copynumber: 4.0 Consensus size: 14
29684143 TGGAAATTTA
29684153 TATTTTTCTTTT-T
1 TATTTTTCTTTTCT
* *
29684166 TTTTTTTCTCTTCTT
1 TATTTTTCTTTTC-T
29684181 CTATTTTTCTTTTTCT
1 -TATTTTTC-TTTTCT
*
29684197 TGTTTTTCTTTTCT
1 TATTTTTCTTTTCT
29684211 CCCCTATAGC
Statistics
Matches: 36, Mismatches: 5, Indels: 7
0.75 0.10 0.15
Matches are distributed among these distances:
13 10 0.28
14 6 0.17
15 8 0.22
16 8 0.22
17 4 0.11
ACGTcount: A:0.03, C:0.16, G:0.02, T:0.79
Consensus pattern (14 bp):
TATTTTTCTTTTCT
Found at i:29685665 original size:20 final size:20
Alignment explanation
Indices: 29685622--29685669 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
29685612 GCTATTTTGT
29685622 TATGGGCCAACTGTATTGAA
1 TATGGGCCAACTGTATTGAA
*
29685642 -ATGGGCCCAACTGTGTT-AA
1 TATGGG-CCAACTGTATTGAA
29685661 TAT-GGCCAA
1 TATGGGCCAA
29685670 GGCCCAATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
18 4 0.16
19 9 0.36
20 12 0.48
ACGTcount: A:0.29, C:0.19, G:0.25, T:0.27
Consensus pattern (20 bp):
TATGGGCCAACTGTATTGAA
Found at i:29688523 original size:16 final size:16
Alignment explanation
Indices: 29688504--29688534 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
29688494 CTTCTTCACT
29688504 TACTCACTTACTTAAA
1 TACTCACTTACTTAAA
*
29688520 TACTTACTTACTTAA
1 TACTCACTTACTTAA
29688535 TCAAATTTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.23, G:0.00, T:0.42
Consensus pattern (16 bp):
TACTCACTTACTTAAA
Found at i:29688540 original size:20 final size:20
Alignment explanation
Indices: 29688501--29688540 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
29688491 AAACTTCTTC
* *
29688501 ACTTACTCACTTACTTAAAT
1 ACTTACTCACTTAATCAAAT
*
29688521 ACTTACTTACTTAATCAAAT
1 ACTTACTCACTTAATCAAAT
29688541 TTATTAATAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.23, G:0.00, T:0.40
Consensus pattern (20 bp):
ACTTACTCACTTAATCAAAT
Found at i:29688928 original size:55 final size:53
Alignment explanation
Indices: 29688726--29688980 Score: 204
Period size: 55 Copynumber: 4.8 Consensus size: 53
29688716 ACACGGGTAC
* * **
29688726 CTTACCATTGCCATGACTTTTCATGGTCTTACATGGTATCCTT---T-T-GAAA
1 CTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTATAG-AA
* * * *
29688775 CTTACCATTGCCATGTCC-CGACATGGTCATACATGGTATCCTTGCCT-TATGAT
1 CTTACCAATGCCATG-CCTTGACATGGTCTTACATGGTATCCTTGCCTATA-GAA
* * * *
29688828 CTCACCAATGCCATGCCTTGGCCTGGTCTTACATGGGA-CCTTTGCCTCATAGTAA
1 CTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCC-TTGCCT-ATAG-AA
* * *
29688883 CTTATCAATGTCATGTCTTGACATGGTCTTACATGGTATCCTTGCCT-TAGAAA
1 CTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTATAG-AA
* * *
29688936 CCTTACCAATTGCCATGCCTTGGCATGATCTCACATGGTATCCTT
1 -CTTACCAA-TGCCATGCCTTGACATGGTCTTACATGGTATCCTT
29688981 AAACCCTAAT
Statistics
Matches: 164, Mismatches: 28, Indels: 22
0.77 0.13 0.10
Matches are distributed among these distances:
49 36 0.22
50 1 0.01
52 6 0.04
53 40 0.24
54 9 0.05
55 70 0.43
56 2 0.01
ACGTcount: A:0.22, C:0.27, G:0.17, T:0.35
Consensus pattern (53 bp):
CTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTATAGAA
Found at i:29692279 original size:12 final size:13
Alignment explanation
Indices: 29692262--29692301 Score: 55
Period size: 14 Copynumber: 3.1 Consensus size: 13
29692252 TACTAAAAAT
29692262 ATTAAG-ACAAGA
1 ATTAAGAACAAGA
*
29692274 ATTAAGAACACATA
1 ATTAAGAACA-AGA
29692288 ATTAAGAACAAGA
1 ATTAAGAACAAGA
29692301 A
1 A
29692302 CAAGTATTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 6 0.25
13 6 0.25
14 12 0.50
ACGTcount: A:0.60, C:0.10, G:0.12, T:0.17
Consensus pattern (13 bp):
ATTAAGAACAAGA
Found at i:29693463 original size:26 final size:26
Alignment explanation
Indices: 29693434--29693483 Score: 84
Period size: 26 Copynumber: 1.9 Consensus size: 26
29693424 TCTCATTCCT
29693434 ATTTTACCCCT-AGTAAAATTTTGACG
1 ATTTTACCCCTGA-TAAAATTTTGACG
29693460 ATTTTACCCCTGATAAAATTTTGA
1 ATTTTACCCCTGATAAAATTTTGA
29693484 GAAAAAAGGT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
26 22 0.96
27 1 0.04
ACGTcount: A:0.32, C:0.18, G:0.10, T:0.40
Consensus pattern (26 bp):
ATTTTACCCCTGATAAAATTTTGACG
Found at i:29695759 original size:13 final size:13
Alignment explanation
Indices: 29695741--29695765 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
29695731 AAAGTAACAA
29695741 TTAGTAAATTAAG
1 TTAGTAAATTAAG
29695754 TTAGTAAATTAA
1 TTAGTAAATTAA
29695766 ATTAAAAAAA
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:0.48, C:0.00, G:0.12, T:0.40
Consensus pattern (13 bp):
TTAGTAAATTAAG
Found at i:29697624 original size:17 final size:18
Alignment explanation
Indices: 29697592--29697625 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
29697582 AACTTTGATT
29697592 TGAAGAAATAAGAAGAAG
1 TGAAGAAATAAGAAGAAG
*
29697610 TGAAGAAGT-AGAAGAA
1 TGAAGAAATAAGAAGAA
29697626 CAAAGGCGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.59, C:0.00, G:0.29, T:0.12
Consensus pattern (18 bp):
TGAAGAAATAAGAAGAAG
Found at i:29699795 original size:101 final size:101
Alignment explanation
Indices: 29699618--29699919 Score: 451
Period size: 103 Copynumber: 3.0 Consensus size: 101
29699608 TTGCATTCGC
** * * *
29699618 ACGTAAGACCATGGTTGGATGATGGCAGTGTTTATATGTAAGACCATAGCTGAGCTATGGAATTT
1 ACGTAAGACCATGGTTGGACCATGGCAGTGTTTATATGTAAGACCATAGCTGGGCTATGGCATTC
* *
29699683 TGATGACAAGACCAAAACTGAGTTATGGCACTATGG
66 TGATGATAAGACCAAAACTGGGTTATGGCACTATGG
29699719 ACGTAAGACCATGGTTGGACCATGGCAGTGTTTATATGTAAGACCATAGCTGGGCTATGGCATTC
1 ACGTAAGACCATGGTTGGACCATGGCAGTGTTTATATGTAAGACCATAGCTGGGCTATGGCATTC
* *
29699784 TGATGATAAGACCACATAATTGGGTTATGGTACTATGG
66 TGATGATAAGACCA-A-AACTGGGTTATGGCACTATGG
* * *
29699822 AGGTAAGATCATGGTTGGACCATGGCAGTGTTTATATGTAAGACCATAGATGGGCTATGGCATTC
1 ACGTAAGACCATGGTTGGACCATGGCAGTGTTTATATGTAAGACCATAGCTGGGCTATGGCATTC
* * *
29699887 TGATGATAAGACTATAACTGGGTTATAGCACTA
66 TGATGATAAGACCAAAACTGGGTTATGGCACTA
29699920 CGAATGTAAA
Statistics
Matches: 182, Mismatches: 17, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
101 88 0.48
102 1 0.01
103 93 0.51
ACGTcount: A:0.30, C:0.14, G:0.27, T:0.29
Consensus pattern (101 bp):
ACGTAAGACCATGGTTGGACCATGGCAGTGTTTATATGTAAGACCATAGCTGGGCTATGGCATTC
TGATGATAAGACCAAAACTGGGTTATGGCACTATGG
Found at i:29701087 original size:41 final size:41
Alignment explanation
Indices: 29701028--29701121 Score: 143
Period size: 41 Copynumber: 2.3 Consensus size: 41
29701018 AGATCCATAT
*
29701028 GGCTAGACACACTGGCGTGTGACTTGGCCGTATAAGACACAC
1 GGCTAG-CACACGGGCGTGTGACTTGGCCGTATAAGACACAC
* * *
29701070 GGCTAGTACACGGGCGTGTGACTTGGCCGTGTGAGACACAC
1 GGCTAGCACACGGGCGTGTGACTTGGCCGTATAAGACACAC
29701111 GGCTAGCACAC
1 GGCTAGCACAC
29701122 AGGCATGCGA
Statistics
Matches: 47, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
41 41 0.87
42 6 0.13
ACGTcount: A:0.23, C:0.27, G:0.32, T:0.18
Consensus pattern (41 bp):
GGCTAGCACACGGGCGTGTGACTTGGCCGTATAAGACACAC
Found at i:29701935 original size:13 final size:14
Alignment explanation
Indices: 29701917--29701954 Score: 60
Period size: 13 Copynumber: 2.8 Consensus size: 14
29701907 TATTAGTTAT
29701917 TAAATTAATTTAA-
1 TAAATTAATTTAAC
*
29701930 TAAATTAAATTAAC
1 TAAATTAATTTAAC
29701944 TAAATTAATTT
1 TAAATTAATTT
29701955 CTCACTTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 12 0.55
14 10 0.45
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (14 bp):
TAAATTAATTTAAC
Found at i:29701953 original size:18 final size:18
Alignment explanation
Indices: 29701915--29701953 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
29701905 AATATTAGTT
* *
29701915 ATTAAATTAATTTAATAA
1 ATTAAATTAACTAAATAA
*
29701933 ATTAAATTAACTAAATTA
1 ATTAAATTAACTAAATAA
29701951 ATT
1 ATT
29701954 TCTCACTTAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.44
Consensus pattern (18 bp):
ATTAAATTAACTAAATAA
Found at i:29711494 original size:26 final size:26
Alignment explanation
Indices: 29711461--29711512 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
29711451 GCTATATTGG
*
29711461 AATTTTTATCCATGAATAAAATTTAT
1 AATTTTTATCCATGAACAAAATTTAT
29711487 AATTTTTATCCATGAACAAAATTTAT
1 AATTTTTATCCATGAACAAAATTTAT
29711513 CTTTGTAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.42, C:0.10, G:0.04, T:0.44
Consensus pattern (26 bp):
AATTTTTATCCATGAACAAAATTTAT
Found at i:29713216 original size:13 final size:13
Alignment explanation
Indices: 29713198--29713225 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
29713188 TTAAATGTAC
29713198 AGGTTCTATCAAA
1 AGGTTCTATCAAA
29713211 AGGTTCTATCAAA
1 AGGTTCTATCAAA
29713224 AG
1 AG
29713226 ACTCTAGTAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.29
Consensus pattern (13 bp):
AGGTTCTATCAAA
Found at i:29714696 original size:22 final size:22
Alignment explanation
Indices: 29714671--29714729 Score: 52
Period size: 20 Copynumber: 2.8 Consensus size: 22
29714661 CAGTTTTCAA
*
29714671 TTATATAAATTAT-TACAATATC
1 TTAT-TAAATTATATAAAATATC
*
29714693 TTATTTAATTATATAAAATA--
1 TTATTAAATTATATAAAATATC
* *
29714713 TTATTCAATTACATAAA
1 TTATTAAATTATATAAA
29714730 TTATTACAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
20 15 0.47
21 7 0.22
22 10 0.31
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.46
Consensus pattern (22 bp):
TTATTAAATTATATAAAATATC
Found at i:29714722 original size:20 final size:20
Alignment explanation
Indices: 29714693--29714735 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
29714683 TTACAATATC
* *
29714693 TTATTTAATTATATAAAATA
1 TTATTCAATTACATAAAATA
*
29714713 TTATTCAATTACATAAATTA
1 TTATTCAATTACATAAAATA
29714733 TTA
1 TTA
29714736 CAAATTTACA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.49
Consensus pattern (20 bp):
TTATTCAATTACATAAAATA
Found at i:29717599 original size:23 final size:23
Alignment explanation
Indices: 29717567--29717613 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
29717557 TATAAAAAGG
*
29717567 ATAGCGTAAGTAATGCCATTTTT
1 ATAGCATAAGTAATGCCATTTTT
29717590 ATAGCATAAGTAATGCCATTTTT
1 ATAGCATAAGTAATGCCATTTTT
29717613 A
1 A
29717614 ATTTACTTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.34, C:0.13, G:0.15, T:0.38
Consensus pattern (23 bp):
ATAGCATAAGTAATGCCATTTTT
Found at i:29719634 original size:12 final size:12
Alignment explanation
Indices: 29719617--29719641 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
29719607 ATGTAGAGTT
29719617 AATTTATAACAG
1 AATTTATAACAG
29719629 AATTTATAACAG
1 AATTTATAACAG
29719641 A
1 A
29719642 TTTTGTAGGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.08, G:0.08, T:0.32
Consensus pattern (12 bp):
AATTTATAACAG
Found at i:29722112 original size:8 final size:8
Alignment explanation
Indices: 29722099--29722127 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
29722089 AAGGAACCAG
29722099 TTTTTTTC
1 TTTTTTTC
29722107 TTTTTTTC
1 TTTTTTTC
29722115 TTTTTTTC
1 TTTTTTTC
29722123 TTTTT
1 TTTTT
29722128 GTTGGCATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (8 bp):
TTTTTTTC
Found at i:29738662 original size:3 final size:3
Alignment explanation
Indices: 29738654--29738715 Score: 124
Period size: 3 Copynumber: 20.7 Consensus size: 3
29738644 CATACATACA
29738654 AAT AAT AAT 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
29738702 AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AA
29738716 ATTATAACCA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 59 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:29741679 original size:25 final size:25
Alignment explanation
Indices: 29741645--29741696 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
29741635 CATAAAGAAG
29741645 TCTCACAAATGGCCGATCACTACAT
1 TCTCACAAATGGCCGATCACTACAT
29741670 TCTCACAAATGGCCGATCACTACAT
1 TCTCACAAATGGCCGATCACTACAT
29741695 TC
1 TC
29741697 AGCCTAAGAA
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:0.31, C:0.33, G:0.12, T:0.25
Consensus pattern (25 bp):
TCTCACAAATGGCCGATCACTACAT
Found at i:29742966 original size:17 final size:14
Alignment explanation
Indices: 29742927--29742984 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
29742917 TAACTTCGCT
29742927 TAAATATATATATATA
1 TAAATATATA-ATA-A
* *
29742943 TATATATTTACATAA
1 TAAATATATA-ATAA
29742958 TAAATATATAATAA
1 TAAATATATAATAA
*
29742972 TAAATAAATAATA
1 TAAATATATAATA
29742985 TAATAATATG
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
14 16 0.44
15 9 0.25
16 11 0.31
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.40
Consensus pattern (14 bp):
TAAATATATAATAA
Found at i:29742973 original size:14 final size:15
Alignment explanation
Indices: 29742927--29742977 Score: 59
Period size: 16 Copynumber: 3.4 Consensus size: 15
29742917 TAACTTCGCT
*
29742927 TAAATATATATATATA
1 TAAATATATACATA-A
* *
29742943 TATATATTTACATAA
1 TAAATATATACATAA
29742958 TAAATATATA-ATAA
1 TAAATATATACATAA
29742972 TAAATA
1 TAAATA
29742978 AATAATATAA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
14 10 0.33
15 9 0.30
16 11 0.37
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (15 bp):
TAAATATATACATAA
Found at i:29742985 original size:19 final size:18
Alignment explanation
Indices: 29742956--29742992 Score: 65
Period size: 19 Copynumber: 2.0 Consensus size: 18
29742946 ATATTTACAT
29742956 AATAAATATATAATAATA
1 AATAAATATATAATAATA
29742974 AATAAATAATATAATAATA
1 AATAAAT-ATATAATAATA
29742993 TGAAACATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (18 bp):
AATAAATATATAATAATA
Found at i:29743428 original size:29 final size:29
Alignment explanation
Indices: 29743383--29743446 Score: 94
Period size: 29 Copynumber: 2.2 Consensus size: 29
29743373 TATAAAAAGA
29743383 AGGGTGATGGAGGTAGTGGAT-GGTTTAGT
1 AGGGTGATGGAGGTAGTGG-TCGGTTTAGT
*
29743412 AGGGTGATGGAGTTAGTGGTCGGTTTAGT
1 AGGGTGATGGAGGTAGTGGTCGGTTTAGT
*
29743441 GGGGTG
1 AGGGTG
29743447 TTTAATTTGG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
28 1 0.03
29 31 0.97
ACGTcount: A:0.17, C:0.02, G:0.50, T:0.31
Consensus pattern (29 bp):
AGGGTGATGGAGGTAGTGGTCGGTTTAGT
Found at i:29743899 original size:133 final size:133
Alignment explanation
Indices: 29743659--29744261 Score: 931
Period size: 133 Copynumber: 4.5 Consensus size: 133
29743649 GATCTGCTGT
** ** * *
29743659 AATTTGATCTGCTTTACTCCTGCTCAGTAAAGATAAGATCTGGTATGTTTATCCTGCTCCACTCC
1 AATTTGATCTGCTTCGCTCCTGCTCAGCGAAGATAAGATCTAGTA--TTTAGCCTGCTCCACTCC
* ** * * *
29743724 TGCTCAGTGAAGATAAGGCTGATGATTGGAATTTGCTCCATTGCCGATACATGAAGATAAGATTC
64 TGCTCAGTGAAGATAAGGCTGGTGGCTGAAATCTGCTCCATTGCCGATACATGGAGATAAGATTC
*
29743789 ATCAA
129 ACCAA
* *
29743794 AATTTGATCTGCTTTGCTCCTGCTCAGCGAAGATAAGATCTAGTATATAGCCTGCTCCACTCCTG
1 AATTTGATCTGCTTCGCTCCTGCTCAGCGAAGATAAGATCTAGTATTTAGCCTGCTCCACTCCTG
*
29743859 CTCAGTGAAGATAAGGCTGGTGGCTGAAATCTGCTCCATTGCCGATACATGGAGATAATATTCAC
66 CTCAGTGAAGATAAGGCTGGTGGCTGAAATCTGCTCCATTGCCGATACATGGAGATAAGATTCAC
29743924 CAA
131 CAA
*
29743927 AATTTGATCTGCTTCGCTCCTGCTCAGCGAAGATAAGATCTAGTATTTAGCCTGCTCCACTCTTG
1 AATTTGATCTGCTTCGCTCCTGCTCAGCGAAGATAAGATCTAGTATTTAGCCTGCTCCACTCCTG
*
29743992 CTCAGTGAAGATAAGGCTGGTGGCTGAAATCTGCTCCATTGCCGATACATGGAGA-AAGACTT-G
66 CTCAGTGAAGATAAGGCTGGTGGCTGAAATCTGCTCCATTGCCGATACATGGAGATAAGA-TTCA
29744055 CCAA
130 CCAA
* * *
29744059 AATTTGATCTGCTTCACTCCTGCTCAGTGAAGATAAGATCTGGTATGTTTAGCCTGCTCCACTCC
1 AATTTGATCTGCTTCGCTCCTGCTCAGCGAAGATAAGATCTAGTA--TTTAGCCTGCTCCACTCC
*
29744124 TGCTCAGTGAAGATAAGGCTAGTGGCTGAAATCTGCTCCATTGCCGATACATGGAGATAAGATTC
64 TGCTCAGTGAAGATAAGGCTGGTGGCTGAAATCTGCTCCATTGCCGATACATGGAGATAAGATTC
29744189 ACCAA
129 ACCAA
* *
29744194 AATTTGATCTGCTCCGCTCCTGCACAGCGAAGATAAGATCTAGTATTTAGCCTGCTCCACTCCTG
1 AATTTGATCTGCTTCGCTCCTGCTCAGCGAAGATAAGATCTAGTATTTAGCCTGCTCCACTCCTG
29744259 CTC
66 CTC
29744262 TGTAACGCCC
Statistics
Matches: 433, Mismatches: 30, Indels: 12
0.91 0.06 0.03
Matches are distributed among these distances:
132 49 0.11
133 220 0.51
134 75 0.17
135 89 0.21
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.30
Consensus pattern (133 bp):
AATTTGATCTGCTTCGCTCCTGCTCAGCGAAGATAAGATCTAGTATTTAGCCTGCTCCACTCCTG
CTCAGTGAAGATAAGGCTGGTGGCTGAAATCTGCTCCATTGCCGATACATGGAGATAAGATTCAC
CAA
Found at i:29744161 original size:267 final size:265
Alignment explanation
Indices: 29743659--29744261 Score: 931
Period size: 267 Copynumber: 2.3 Consensus size: 265
29743649 GATCTGCTGT
** ** * *
29743659 AATTTGATCTGCTTTACTCCTGCTCAGTAAAGATAAGATCTGGTATGTTTATCCTGCTCCACTCC
1 AATTTGATCTGCTTCGCTCCTGCTCAGCGAAGATAAGATCTAGTA--TTTAGCCTGCTCCACTCC
* * *
29743724 TGCTCAGTGAAGATAAGGCTGATGATTGGAATTTGCTCCATTGCCGATACATGAAGATAAGATTC
64 TGCTCAGTGAAGATAAGGCTGATGACTGAAATCTGCTCCATTGCCGATACATGAAGATAAGATTC
**
29743789 ATCAAAATTTGATCTGCTTTGCTCCTGCTCAGCGAAGATAAGATCTAGTATATAGCCTGCTCCAC
129 A-CAAAATTTGATCTGCTTCACTCCTGCTCAGCGAAGATAAGATCTAGTATATAGCCTGCTCCAC
* *
29743854 TCCTGCTCAGTGAAGATAAGGCTGGTGGCTGAAATCTGCTCCATTGCCGATACATGGAGATAATA
193 TCCTGCTCAGTGAAGATAAGGCTAGTGGCTGAAATCTGCTCCATTGCCGATACATGGAGATAAGA
29743919 TTCACCAA
258 TTCACCAA
*
29743927 AATTTGATCTGCTTCGCTCCTGCTCAGCGAAGATAAGATCTAGTATTTAGCCTGCTCCACTCTTG
1 AATTTGATCTGCTTCGCTCCTGCTCAGCGAAGATAAGATCTAGTATTTAGCCTGCTCCACTCCTG
* * *
29743992 CTCAGTGAAGATAAGGCTGGTGGCTGAAATCTGCTCCATTGCCGATACATGGAGA-AAGACTTGC
66 CTCAGTGAAGATAAGGCTGATGACTGAAATCTGCTCCATTGCCGATACATGAAGATAAGA-TT-C
* * *
29744056 -CAAAATTTGATCTGCTTCACTCCTGCTCAGTGAAGATAAGATCTGGTATGTTTAGCCTGCTCCA
129 ACAAAATTTGATCTGCTTCACTCCTGCTCAGCGAAGATAAGATCTAGTA--TATAGCCTGCTCCA
29744120 CTCCTGCTCAGTGAAGATAAGGCTAGTGGCTGAAATCTGCTCCATTGCCGATACATGGAGATAAG
192 CTCCTGCTCAGTGAAGATAAGGCTAGTGGCTGAAATCTGCTCCATTGCCGATACATGGAGATAAG
29744185 ATTCACCAA
257 ATTCACCAA
* *
29744194 AATTTGATCTGCTCCGCTCCTGCACAGCGAAGATAAGATCTAGTATTTAGCCTGCTCCACTCCTG
1 AATTTGATCTGCTTCGCTCCTGCTCAGCGAAGATAAGATCTAGTATTTAGCCTGCTCCACTCCTG
29744259 CTC
66 CTC
29744262 TGTAACGCCC
Statistics
Matches: 308, Mismatches: 23, Indels: 9
0.91 0.07 0.03
Matches are distributed among these distances:
265 48 0.16
266 69 0.22
267 151 0.49
268 40 0.13
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.30
Consensus pattern (265 bp):
AATTTGATCTGCTTCGCTCCTGCTCAGCGAAGATAAGATCTAGTATTTAGCCTGCTCCACTCCTG
CTCAGTGAAGATAAGGCTGATGACTGAAATCTGCTCCATTGCCGATACATGAAGATAAGATTCAC
AAAATTTGATCTGCTTCACTCCTGCTCAGCGAAGATAAGATCTAGTATATAGCCTGCTCCACTCC
TGCTCAGTGAAGATAAGGCTAGTGGCTGAAATCTGCTCCATTGCCGATACATGGAGATAAGATTC
ACCAA
Found at i:29744569 original size:26 final size:26
Alignment explanation
Indices: 29744533--29744616 Score: 150
Period size: 26 Copynumber: 3.2 Consensus size: 26
29744523 TGATACAAAT
29744533 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
29744559 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
29744585 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
29744611 TGATAA
1 TGATAA
29744617 GAATTTCATG
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 56 1.00
ACGTcount: A:0.35, C:0.06, G:0.24, T:0.36
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTCCA
Found at i:29748544 original size:5 final size:5
Alignment explanation
Indices: 29748531--29748616 Score: 63
Period size: 5 Copynumber: 17.0 Consensus size: 5
29748521 TTGGCCTCTC
* *
29748531 CTTTG CTTTT CTTTT C-TTT CTCTTT -TTTT GTTTT CTTTT CTTTTT CCTTTT
1 CTTTT CTTTT CTTTT CTTTT CT-TTT CTTTT CTTTT CTTTT C-TTTT -CTTTT
* *
29748582 CTTTT -TTTCT CTTTC CTTTTT CTCTT CTTTT -TTTT
1 CTTTT CTTT-T CTTTT C-TTTT CTTTT CTTTT CTTTT
29748617 TTGAAAGTGA
Statistics
Matches: 67, Mismatches: 6, Indels: 17
0.74 0.07 0.19
Matches are distributed among these distances:
4 14 0.21
5 34 0.51
6 18 0.27
7 1 0.01
ACGTcount: A:0.00, C:0.21, G:0.02, T:0.77
Consensus pattern (5 bp):
CTTTT
Found at i:29748553 original size:24 final size:24
Alignment explanation
Indices: 29748526--29748596 Score: 69
Period size: 24 Copynumber: 3.0 Consensus size: 24
29748516 TCGCCTTGGC
29748526 CTCTCCTTTGCTTTTCTTTTCTTT
1 CTCTCCTTTGCTTTTCTTTTCTTT
**
29748550 CTCTTTTTTTG-TTTTCTTTTCTTT
1 CTC-TCCTTTGCTTTTCTTTTCTTT
*
29748574 -T-TCCTTTTCTTTT-TTTCTCTTT
1 CTCTCCTTTGCTTTTCTTT-TCTTT
29748596 C
1 C
29748597 CTTTTTCTCT
Statistics
Matches: 38, Mismatches: 5, Indels: 9
0.73 0.10 0.17
Matches are distributed among these distances:
21 7 0.18
22 9 0.24
23 1 0.03
24 16 0.42
25 5 0.13
ACGTcount: A:0.00, C:0.24, G:0.03, T:0.73
Consensus pattern (24 bp):
CTCTCCTTTGCTTTTCTTTTCTTT
Found at i:29748564 original size:19 final size:18
Alignment explanation
Indices: 29748537--29748615 Score: 72
Period size: 17 Copynumber: 4.2 Consensus size: 18
29748527 TCTCCTTTGC
29748537 TTTTCTTTTCTTTCTCTTT
1 TTTTCTTTTCTTT-TCTTT
*
29748556 TTTTGTTTTCTTTTC-TT
1 TTTTCTTTTCTTTTCTTT
*
29748573 TTTCCTTTTCTTTT-TTT
1 TTTTCTTTTCTTTTCTTT
*
29748590 CTCTTTCCTTTTTCTCTTCTTT
1 -T-TTT-C-TTTTCTTTTCTTT
29748612 TTTT
1 TTTT
29748616 TTTGAAAGTG
Statistics
Matches: 49, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
17 16 0.33
18 3 0.06
19 14 0.29
20 4 0.08
21 9 0.18
22 3 0.06
ACGTcount: A:0.00, C:0.20, G:0.01, T:0.78
Consensus pattern (18 bp):
TTTTCTTTTCTTTTCTTT
Found at i:29748596 original size:26 final size:24
Alignment explanation
Indices: 29748537--29748615 Score: 97
Period size: 26 Copynumber: 3.2 Consensus size: 24
29748527 TCTCCTTTGC
*
29748537 TTTTCTTTTCTTTCTCTTTT-TTT
1 TTTTCTTTTCTTTTTCTTTTCTTT
29748560 GTTTTCTTTTCTTTTTCCTTTTCTTT
1 -TTTTCTTTTCTTTTT-CTTTTCTTT
*
29748586 TTTTCTCTTTCCTTTTTCTCTTCTTT
1 TTTTCT-TTT-CTTTTTCTTTTCTTT
29748612 TTTT
1 TTTT
29748616 TTTGAAAGTG
Statistics
Matches: 49, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
24 14 0.29
25 11 0.22
26 18 0.37
27 6 0.12
ACGTcount: A:0.00, C:0.20, G:0.01, T:0.78
Consensus pattern (24 bp):
TTTTCTTTTCTTTTTCTTTTCTTT
Found at i:29748614 original size:13 final size:12
Alignment explanation
Indices: 29748542--29748615 Score: 58
Period size: 13 Copynumber: 5.7 Consensus size: 12
29748532 TTTGCTTTTC
*
29748542 TTTTCTTTCTCT
1 TTTTTTTTCTCT
*
29748554 TTTTTTGTTTTCT
1 TTTTTT-TTCTCT
*
29748567 TTTCTTTTTCCTTT
1 TTT-TTTTT-CTCT
29748581 TCTTTTTTTCTCT
1 T-TTTTTTTCTCT
*
29748594 TTCCTTTTTCTCT
1 TT-TTTTTTCTCT
29748607 TCTTTTTTT
1 T-TTTTTTT
29748616 TTTGAAAGTG
Statistics
Matches: 49, Mismatches: 7, Indels: 11
0.73 0.10 0.16
Matches are distributed among these distances:
12 6 0.12
13 29 0.59
14 12 0.24
15 2 0.04
ACGTcount: A:0.00, C:0.20, G:0.01, T:0.78
Consensus pattern (12 bp):
TTTTTTTTCTCT
Found at i:29748616 original size:15 final size:15
Alignment explanation
Indices: 29748536--29748617 Score: 57
Period size: 14 Copynumber: 5.7 Consensus size: 15
29748526 CTCTCCTTTG
*
29748536 CTTTTCTTTTCT-TT
1 CTTTTTTTTTCTCTT
* * *
29748550 CTCTTTTTTTGTTTT
1 CTTTTTTTTTCTCTT
29748565 CTTTTCTTTTTC-CTT
1 CTTTT-TTTTTCTCTT
29748580 -TTCTTTTTTTCTC-T
1 CTT-TTTTTTTCTCTT
**
29748594 -TTCCTTTTTCTCTT
1 CTTTTTTTTTCTCTT
29748608 CTTTTTTTTT
1 CTTTTTTTTT
29748618 TGAAAGTGAA
Statistics
Matches: 52, Mismatches: 10, Indels: 11
0.71 0.14 0.15
Matches are distributed among these distances:
13 8 0.15
14 21 0.40
15 18 0.35
16 5 0.10
ACGTcount: A:0.00, C:0.21, G:0.01, T:0.78
Consensus pattern (15 bp):
CTTTTTTTTTCTCTT
Found at i:29748616 original size:27 final size:25
Alignment explanation
Indices: 29748547--29748617 Score: 81
Period size: 27 Copynumber: 2.7 Consensus size: 25
29748537 TTTTCTTTTC
*
29748547 TTTCTCTTTTTTTGTTTTCTTTTCTT
1 TTTCTCTTTTTTT-TTTTCTTTCCTT
29748573 TTTC-CTTTTCTTTTTTTCTCTTTCCTT
1 TTTCTC-TTT-TTTTTTT-TCTTTCCTT
29748600 TTTCTCTTCTTTTTTTTT
1 TTTCTCTT-TTTTTTTTT
29748618 TGAAAGTGAA
Statistics
Matches: 39, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
25 1 0.03
26 11 0.28
27 25 0.64
28 2 0.05
ACGTcount: A:0.00, C:0.20, G:0.01, T:0.79
Consensus pattern (25 bp):
TTTCTCTTTTTTTTTTTCTTTCCTT
Found at i:29751214 original size:21 final size:21
Alignment explanation
Indices: 29751189--29751233 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
29751179 GCTGACTTAT
*
29751189 CATGTTGT-TCTGGGATTCTAG
1 CATG-TGTCTCTGGGATTCCAG
29751210 CATGTGTCTCTGGGATTCCAG
1 CATGTGTCTCTGGGATTCCAG
29751231 CAT
1 CAT
29751234 CTGATCCCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 3 0.14
21 19 0.86
ACGTcount: A:0.16, C:0.20, G:0.27, T:0.38
Consensus pattern (21 bp):
CATGTGTCTCTGGGATTCCAG
Found at i:29753038 original size:13 final size:14
Alignment explanation
Indices: 29753017--29753067 Score: 54
Period size: 13 Copynumber: 3.9 Consensus size: 14
29753007 CTAACCATAT
*
29753017 ATAAATAATAAATA
1 ATAATTAATAAATA
29753031 ATAA-TAAT-AATA
1 ATAATTAATAAATA
* *
29753043 GTAATTAATAGA-A
1 ATAATTAATAAATA
29753056 ATAATTAATAAA
1 ATAATTAATAAA
29753068 ACAACAGTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
12 7 0.23
13 19 0.61
14 5 0.16
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (14 bp):
ATAATTAATAAATA
Found at i:29753402 original size:14 final size:14
Alignment explanation
Indices: 29753383--29753413 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
29753373 ATATATTTAC
*
29753383 ATAATAAATATATA
1 ATAATAAATAAATA
29753397 ATAATAAATAAATA
1 ATAATAAATAAATA
29753411 ATA
1 ATA
29753414 TAATAATATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (14 bp):
ATAATAAATAAATA
Found at i:29753414 original size:19 final size:18
Alignment explanation
Indices: 29753385--29753421 Score: 65
Period size: 19 Copynumber: 2.0 Consensus size: 18
29753375 ATATTTACAT
29753385 AATAAATATATAATAATA
1 AATAAATATATAATAATA
29753403 AATAAATAATATAATAATA
1 AATAAAT-ATATAATAATA
29753422 TGAAACATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (18 bp):
AATAAATATATAATAATA
Found at i:29753461 original size:60 final size:63
Alignment explanation
Indices: 29753396--29753529 Score: 161
Period size: 60 Copynumber: 2.2 Consensus size: 63
29753386 ATAAATATAT
* * *
29753396 AATAATAAATAAA-TAATATAATAAT-ATGAAACAT-AA-CTCAAATTAATTAAATTAATAG-AA
1 AATAATAAA-AAACAAATATAAAAATAATGAAA-ATAAAGCTCAAATTAATTAAATTAACAGTAA
* *
29753456 AATAATAAAAAACAAATATAAAAATAATGAGAATAAAGCTCAAATTAATTAATTTAACAGTAA
1 AATAATAAAAAACAAATATAAAAATAATGAAAATAAAGCTCAAATTAATTAAATTAACAGTAA
*
29753519 AATAACAAAAA
1 AATAATAAAAA
29753530 TAAAAAAAAG
Statistics
Matches: 63, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
59 3 0.05
60 21 0.33
61 7 0.11
62 20 0.32
63 12 0.19
ACGTcount: A:0.63, C:0.06, G:0.04, T:0.26
Consensus pattern (63 bp):
AATAATAAAAAACAAATATAAAAATAATGAAAATAAAGCTCAAATTAATTAAATTAACAGTAA
Found at i:29753462 original size:63 final size:64
Alignment explanation
Indices: 29753394--29753535 Score: 168
Period size: 62 Copynumber: 2.2 Consensus size: 64
29753384 TAATAAATAT
* *
29753394 ATAATAATAAATAAATAATATAATAAT-ATGAAACAT-AA-CTCAAATTAATTAAATTAATAG-A
1 ATAATAA-AAATAAA-AATATAAAAATAATGAAA-ATAAAGCTCAAATTAATTAAATTAACAGTA
29753455 AA
63 AA
* * *
29753457 ATAATAAAAA-ACAAATATAAAAATAATGAGAATAAAGCTCAAATTAATTAATTTAACAGTAAA
1 ATAATAAAAATAAAAATATAAAAATAATGAAAATAAAGCTCAAATTAATTAAATTAACAGTAAA
*
29753520 ATAACAAAAATAAAAA
1 ATAATAAAAATAAAAA
29753536 AAAGGGTTAA
Statistics
Matches: 67, Mismatches: 7, Indels: 9
0.81 0.08 0.11
Matches are distributed among these distances:
60 12 0.18
61 9 0.13
62 23 0.34
63 19 0.28
64 4 0.06
ACGTcount: A:0.64, C:0.06, G:0.04, T:0.26
Consensus pattern (64 bp):
ATAATAAAAATAAAAATATAAAAATAATGAAAATAAAGCTCAAATTAATTAAATTAACAGTAAA
Found at i:29753676 original size:22 final size:21
Alignment explanation
Indices: 29753637--29753677 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
29753627 TTGTTTGTGT
29753637 AAAGAAAAAAATGTGAATACC
1 AAAGAAAAAAATGTGAATACC
29753658 AAAGTAAACAAAAT-TGAATA
1 AAAG-AAA-AAAATGTGAATA
29753678 ATATAAAAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 4 0.22
22 9 0.50
23 5 0.28
ACGTcount: A:0.63, C:0.07, G:0.12, T:0.17
Consensus pattern (21 bp):
AAAGAAAAAAATGTGAATACC
Found at i:29753859 original size:37 final size:37
Alignment explanation
Indices: 29753809--29753879 Score: 142
Period size: 37 Copynumber: 1.9 Consensus size: 37
29753799 ATAACAAGTA
29753809 GGGTGATGGAGGTAGTGGATGGTTTAGTAGGGTGTGG
1 GGGTGATGGAGGTAGTGGATGGTTTAGTAGGGTGTGG
29753846 GGGTGATGGAGGTAGTGGATGGTTTAGTAGGGTG
1 GGGTGATGGAGGTAGTGGATGGTTTAGTAGGGTG
29753880 ATGGAGTTAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.17, C:0.00, G:0.54, T:0.30
Consensus pattern (37 bp):
GGGTGATGGAGGTAGTGGATGGTTTAGTAGGGTGTGG
Found at i:29753879 original size:29 final size:29
Alignment explanation
Indices: 29753846--29753908 Score: 92
Period size: 29 Copynumber: 2.2 Consensus size: 29
29753836 TAGGGTGTGG
29753846 GGGTGATGGAGGTAGTGGAT-GGTTTAGTA
1 GGGTGATGGAGGTAGTGG-TCGGTTTAGTA
* *
29753875 GGGTGATGGAGTTAGTGGTCGGTTTAGTG
1 GGGTGATGGAGGTAGTGGTCGGTTTAGTA
29753904 GGGTG
1 GGGTG
29753909 TTTAATTTGG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
28 1 0.03
29 30 0.97
ACGTcount: A:0.16, C:0.02, G:0.51, T:0.32
Consensus pattern (29 bp):
GGGTGATGGAGGTAGTGGTCGGTTTAGTA
Found at i:29754062 original size:18 final size:18
Alignment explanation
Indices: 29754035--29754071 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
29754025 TGTACTAATA
29754035 TTTTCACACATACACCCT
1 TTTTCACACATACACCCT
* *
29754053 TTTTCCCACATACCCCCT
1 TTTTCACACATACACCCT
29754071 T
1 T
29754072 CCTTATGCTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.22, C:0.43, G:0.00, T:0.35
Consensus pattern (18 bp):
TTTTCACACATACACCCT
Found at i:29761845 original size:43 final size:43
Alignment explanation
Indices: 29761781--29761897 Score: 110
Period size: 43 Copynumber: 2.7 Consensus size: 43
29761771 TAAATACAAT
* * * *
29761781 GCCAACGTCCCAGAC-GTGGTCTTACATGTAATCAAACATTGAT
1 GCCAATGTCCCACACAG-GGTCTTACATGTAATCAAACAATGAC
* * * * **
29761824 GCCATTGTCCCACACAGGGTCTTACACGAAATCGATTAATGAC
1 GCCAATGTCCCACACAGGGTCTTACATGTAATCAAACAATGAC
* *
29761867 GCCAATGTCCCAGACATGGTCTTACATGTAA
1 GCCAATGTCCCACACAGGGTCTTACATGTAA
29761898 AACAGAAGTT
Statistics
Matches: 58, Mismatches: 15, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
43 57 0.98
44 1 0.02
ACGTcount: A:0.30, C:0.26, G:0.19, T:0.25
Consensus pattern (43 bp):
GCCAATGTCCCACACAGGGTCTTACATGTAATCAAACAATGAC
Found at i:29763055 original size:13 final size:13
Alignment explanation
Indices: 29763037--29763070 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
29763027 ACGATTAAAT
29763037 TTTCATACGAAAC
1 TTTCATACGAAAC
*
29763050 TTTCATTCGAAAC
1 TTTCATACGAAAC
29763063 TTTCATAC
1 TTTCATAC
29763071 ATACTAACTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.32, C:0.24, G:0.06, T:0.38
Consensus pattern (13 bp):
TTTCATACGAAAC
Found at i:29763616 original size:18 final size:18
Alignment explanation
Indices: 29763593--29763637 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
29763583 AAGCTTAAGA
29763593 CTATTCTGAATCAGGCTC
1 CTATTCTGAATCAGGCTC
*
29763611 CTATTCTGACTCAGGCTC
1 CTATTCTGAATCAGGCTC
*
29763629 CTGTTCTGA
1 CTATTCTGA
29763638 TATAACCTGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.18, C:0.29, G:0.18, T:0.36
Consensus pattern (18 bp):
CTATTCTGAATCAGGCTC
Found at i:29778449 original size:18 final size:18
Alignment explanation
Indices: 29778428--29778466 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
29778418 TTTAAATTGT
29778428 TGTTATTATTATTATATG
1 TGTTATTATTATTATATG
*
29778446 TGTTTTTATTATTATATG
1 TGTTATTATTATTATATG
29778464 TGT
1 TGT
29778467 ATGGAAAGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.23, C:0.00, G:0.13, T:0.64
Consensus pattern (18 bp):
TGTTATTATTATTATATG
Found at i:29786047 original size:13 final size:13
Alignment explanation
Indices: 29786029--29786053 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
29786019 AACCTTGTTT
29786029 AAAAAAAGAAAAG
1 AAAAAAAGAAAAG
29786042 AAAAAAAGAAAA
1 AAAAAAAGAAAA
29786054 CATTGTTCAC
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:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (13 bp):
AAAAAAAGAAAAG
Found at i:29793956 original size:11 final size:11
Alignment explanation
Indices: 29793940--29793965 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
29793930 AGTTCGATTC
29793940 AAAATACTTTT
1 AAAATACTTTT
29793951 AAAATACTTTT
1 AAAATACTTTT
29793962 AAAA
1 AAAA
29793966 CCCTTTTAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (11 bp):
AAAATACTTTT
Found at i:29796764 original size:26 final size:26
Alignment explanation
Indices: 29796735--29796839 Score: 165
Period size: 26 Copynumber: 4.0 Consensus size: 26
29796725 TGGTACAAAT
29796735 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* * *
29796761 TGATAATGGATTAGGTAAATATTCTA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
29796787 TAATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
29796813 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
29796839 T
1 T
29796840 AATGGGCATT
Statistics
Matches: 70, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 70 1.00
ACGTcount: A:0.33, C:0.07, G:0.23, T:0.37
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:29796794 original size:52 final size:52
Alignment explanation
Indices: 29796737--29796842 Score: 185
Period size: 52 Copynumber: 2.0 Consensus size: 52
29796727 GTACAAATTG
*
29796737 ATAATGGGTTAGGTAAATGTTCCATGATAATGGATTAGGTAAATATTCTATA
1 ATAATGGGTTAGGTAAATGTTCCATGATAATGGATTAGGTAAATATTCCATA
* *
29796789 ATAATGGGTTAGGTAAATGTTCCATGATAATGGTTTAGGTAAATGTTCCATA
1 ATAATGGGTTAGGTAAATGTTCCATGATAATGGATTAGGTAAATATTCCATA
29796841 AT
1 AT
29796843 GGGCATTTCA
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.35, C:0.07, G:0.22, T:0.37
Consensus pattern (52 bp):
ATAATGGGTTAGGTAAATGTTCCATGATAATGGATTAGGTAAATATTCCATA
Found at i:29798496 original size:27 final size:27
Alignment explanation
Indices: 29798413--29798497 Score: 102
Period size: 27 Copynumber: 3.1 Consensus size: 27
29798403 AGGAAGCGTC
* *
29798413 CTGGTGGCTATGCCACAATTATTTG-AT
1 CTGGTGGCTCTGCCACAA-TATCTGTAT
*
29798440 CTGGTGGCTCTGCCACATATATCTAT-T
1 CTGGTGGCTCTGCCACA-ATATCTGTAT
*
29798467 CTGGCGGCTCTGCCACAATATCTGTAT
1 CTGGTGGCTCTGCCACAATATCTGTAT
29798494 CTGG
1 CTGG
29798498 AGACTTCGTC
Statistics
Matches: 50, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
26 7 0.14
27 42 0.84
28 1 0.02
ACGTcount: A:0.19, C:0.25, G:0.22, T:0.34
Consensus pattern (27 bp):
CTGGTGGCTCTGCCACAATATCTGTAT
Found at i:29799834 original size:40 final size:39
Alignment explanation
Indices: 29799778--29799854 Score: 102
Period size: 40 Copynumber: 1.9 Consensus size: 39
29799768 TAAGATATTC
*
29799778 ATAACAAATATAAAATTTTAAAA-AATAAAAATATATAAA
1 ATAACAAATATAAAA-TTAAAAATAATAAAAATATATAAA
* *
29799817 ATAACTAAATATCAAATTAAAAATAATATAAATATATA
1 ATAAC-AAATATAAAATTAAAAATAATAAAAATATATA
29799855 TTTTTAAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
39 11 0.33
40 22 0.67
ACGTcount: A:0.66, C:0.04, G:0.00, T:0.30
Consensus pattern (39 bp):
ATAACAAATATAAAATTAAAAATAATAAAAATATATAAA
Found at i:29803649 original size:48 final size:48
Alignment explanation
Indices: 29803591--29803688 Score: 187
Period size: 48 Copynumber: 2.0 Consensus size: 48
29803581 AATGTTTCCC
29803591 AACAAATTGAAAATAAATGAAAAAATATATGTATACTTAAATAACATT
1 AACAAATTGAAAATAAATGAAAAAATATATGTATACTTAAATAACATT
*
29803639 AACAAATTGAAAATAAATTAAAAAATATATGTATACTTAAATAACATT
1 AACAAATTGAAAATAAATGAAAAAATATATGTATACTTAAATAACATT
29803687 AA
1 AA
29803689 GATATGTGCA
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.59, C:0.06, G:0.05, T:0.30
Consensus pattern (48 bp):
AACAAATTGAAAATAAATGAAAAAATATATGTATACTTAAATAACATT
Found at i:29803785 original size:14 final size:14
Alignment explanation
Indices: 29803762--29803796 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
29803752 TACAATATCC
*
29803762 AAATAATAACAACA
1 AAATAGTAACAACA
29803776 AAATAGTAACAACA
1 AAATAGTAACAACA
*
29803790 TAATAGT
1 AAATAGT
29803797 GAAATATTAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.63, C:0.11, G:0.06, T:0.20
Consensus pattern (14 bp):
AAATAGTAACAACA
Found at i:29803835 original size:24 final size:24
Alignment explanation
Indices: 29803808--29803859 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
29803798 AAATATTAGC
** *
29803808 AAAATAGTGAAAAAAAATAACAAG
1 AAAATAGCAAAAAAAAAGAACAAG
*
29803832 AAAATAGCAAAAAAAAAGAAGAAG
1 AAAATAGCAAAAAAAAAGAACAAG
29803856 AAAA
1 AAAA
29803860 AACAACAGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.75, C:0.04, G:0.13, T:0.08
Consensus pattern (24 bp):
AAAATAGCAAAAAAAAAGAACAAG
Found at i:29804574 original size:22 final size:22
Alignment explanation
Indices: 29804549--29804590 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
29804539 TTAGAATTAT
29804549 AATTGTAATTATGTT-TAATTGA
1 AATTGTAATTAT-TTATAATTGA
*
29804571 AATTTTAATTATTTATAATT
1 AATTGTAATTATTTATAATT
29804591 CAGTACACAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 2 0.11
22 16 0.89
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (22 bp):
AATTGTAATTATTTATAATTGA
Found at i:29808615 original size:27 final size:27
Alignment explanation
Indices: 29808567--29808619 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
29808557 CATTCTATCA
* *
29808567 TACAGGGGTATTACGGTCATTTTACAC
1 TACAAGGGTATTACGATCATTTTACAC
* *
29808594 TACAAGGGTATTTCGATGATTTTACA
1 TACAAGGGTATTACGATCATTTTACA
29808620 AACCGGGGTC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.28, C:0.15, G:0.21, T:0.36
Consensus pattern (27 bp):
TACAAGGGTATTACGATCATTTTACAC
Found at i:29810961 original size:24 final size:24
Alignment explanation
Indices: 29810934--29810995 Score: 81
Period size: 24 Copynumber: 2.6 Consensus size: 24
29810924 AAAAACTAAG
*
29810934 TGGCACTATGTGTGCGA-GACTACA
1 TGGCACTATGTGTGCGAGGA-AACA
* *
29810958 TGGCACTCTGTGTGCGAGGAAACG
1 TGGCACTATGTGTGCGAGGAAACA
29810982 TGGCACTATGTGTG
1 TGGCACTATGTGTG
29810996 AGAATAAGTA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
24 31 0.94
25 2 0.06
ACGTcount: A:0.21, C:0.19, G:0.34, T:0.26
Consensus pattern (24 bp):
TGGCACTATGTGTGCGAGGAAACA
Found at i:29813773 original size:17 final size:16
Alignment explanation
Indices: 29813749--29813782 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
29813739 TTCTCAATTT
29813749 ATTATAT-TTTTTTGA
1 ATTATATATTTTTTGA
29813764 ATTATATATTTTTTGA
1 ATTATATATTTTTTGA
29813780 ATT
1 ATT
29813783 TTTGTATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 7 0.39
16 11 0.61
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (16 bp):
ATTATATATTTTTTGA
Found at i:29813790 original size:17 final size:17
Alignment explanation
Indices: 29813744--29813802 Score: 59
Period size: 17 Copynumber: 3.4 Consensus size: 17
29813734 ATGTATTCTC
29813744 AATTTATTATATTTTTTTG
1 AATTT-TTATA-TTTTTTG
*
29813763 AA-TTATATATTTTTTG
1 AATTTTTATATTTTTTG
*
29813779 AATTTTTGTATTTTCTT-
1 AATTTTTATATTTT-TTG
29813796 AATTTTT
1 AATTTTT
29813803 TTGAATTCTT
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
16 9 0.26
17 20 0.57
18 4 0.11
19 2 0.06
ACGTcount: A:0.25, C:0.02, G:0.05, T:0.68
Consensus pattern (17 bp):
AATTTTTATATTTTTTG
Found at i:29817642 original size:18 final size:18
Alignment explanation
Indices: 29817619--29817655 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
29817609 ATTGTTGGAG
29817619 AGGTGAGCTTTGGTCCAA
1 AGGTGAGCTTTGGTCCAA
29817637 AGGTGAGCTTTGGTCCAA
1 AGGTGAGCTTTGGTCCAA
29817655 A
1 A
29817656 ACCTTTGTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.24, C:0.16, G:0.32, T:0.27
Consensus pattern (18 bp):
AGGTGAGCTTTGGTCCAA
Found at i:29822804 original size:27 final size:27
Alignment explanation
Indices: 29822766--29822819 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
29822756 TTGACAACAT
29822766 AGCCAGTGGGTTGAACCATATAAATGG
1 AGCCAGTGGGTTGAACCATATAAATGG
29822793 AGCCAGTGGGTTGAACCATATAAATGG
1 AGCCAGTGGGTTGAACCATATAAATGG
29822820 TCTCATCAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.33, C:0.15, G:0.30, T:0.22
Consensus pattern (27 bp):
AGCCAGTGGGTTGAACCATATAAATGG
Found at i:29829843 original size:59 final size:61
Alignment explanation
Indices: 29829773--29829889 Score: 152
Period size: 62 Copynumber: 1.9 Consensus size: 61
29829763 ACCACTTTAA
* *
29829773 TATTAAATTAATATAATATTTA-T-CAAGATAAA-TATTAGATTAA-ATTTAATATTAAATGT
1 TATTAAATTAATAGAATATTTACTACAAGATAAACT-TTAAATTAATA-TTAATATTAAATGT
*
29829832 TATTAGATTAATAGAATATTTATCTACAAGATAAACTTTAAATTAATATTAATATTAA
1 TATTAAATTAATAGAATATTTA-CTACAAGATAAACTTTAAATTAATATTAATATTAA
29829890 GATAATTACT
Statistics
Matches: 50, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
59 20 0.40
61 1 0.02
62 27 0.54
63 2 0.04
ACGTcount: A:0.49, C:0.03, G:0.05, T:0.43
Consensus pattern (61 bp):
TATTAAATTAATAGAATATTTACTACAAGATAAACTTTAAATTAATATTAATATTAAATGT
Found at i:29829903 original size:31 final size:29
Alignment explanation
Indices: 29829859--29829916 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 29
29829849 ATTTATCTAC
29829859 AAGATAAACTTTAA-ATTAATATTAATATT
1 AAGATAAACTTTAATATTAA-ATTAATATT
29829888 AAGATAATTACTTTAATATTAAATTAATA
1 AAGATAA--ACTTTAATATTAAATTAATA
29829917 AAATACTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
29 7 0.27
31 14 0.54
32 5 0.19
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.41
Consensus pattern (29 bp):
AAGATAAACTTTAATATTAAATTAATATT
Found at i:29829914 original size:11 final size:11
Alignment explanation
Indices: 29829869--29829976 Score: 53
Period size: 11 Copynumber: 9.3 Consensus size: 11
29829859 AAGATAAACT
29829869 TTAAATTAATA
1 TTAAATTAATA
29829880 TTAATATTAAGATAA
1 TTAA-ATT-A-AT-A
**
29829895 TTACTTTAATA
1 TTAAATTAATA
29829906 TTAAATTAATA
1 TTAAATTAATA
*
29829917 --AAA-TACTA
1 TTAAATTAATA
29829925 TTAACA-TAACTA
1 TTAA-ATTAA-TA
*
29829937 TTAAATTAATT
1 TTAAATTAATA
29829948 TTAATATTAAATGTA
1 TTAA-ATT-AA--TA
*
29829963 TTAAAATAATA
1 TTAAATTAATA
29829974 TTA
1 TTA
29829977 TTTTTGGAAT
Statistics
Matches: 75, Mismatches: 9, Indels: 26
0.68 0.08 0.24
Matches are distributed among these distances:
8 4 0.05
9 3 0.04
10 2 0.03
11 28 0.37
12 17 0.23
13 6 0.08
14 6 0.08
15 9 0.12
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.44
Consensus pattern (11 bp):
TTAAATTAATA
Found at i:29829915 original size:20 final size:18
Alignment explanation
Indices: 29829869--29829959 Score: 56
Period size: 17 Copynumber: 5.3 Consensus size: 18
29829859 AAGATAAACT
29829869 TTAAATTAA-TATTAATA
1 TTAAATTAATTATTAATA
29829886 TTAAGA-TAATTACTTTAATA
1 TTAA-ATTAATTA--TTAATA
*
29829906 TTAAATTAA-TA-AAATA
1 TTAAATTAATTATTAATA
* *
29829922 CT--ATTAA-CA-TAACTA
1 TTAAATTAATTATTAA-TA
29829937 TTAAATTAATT-TTAATA
1 TTAAATTAATTATTAATA
29829954 TTAAAT
1 TTAAAT
29829960 GTATTAAAAT
Statistics
Matches: 58, Mismatches: 6, Indels: 20
0.69 0.07 0.24
Matches are distributed among these distances:
14 8 0.14
15 3 0.05
16 5 0.09
17 20 0.34
18 6 0.10
19 3 0.05
20 13 0.22
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.44
Consensus pattern (18 bp):
TTAAATTAATTATTAATA
Found at i:29834921 original size:2 final size:2
Alignment explanation
Indices: 29834914--29834950 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
29834904 ACATACATTA
29834914 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
29834951 AATAATTCAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:29840575 original size:20 final size:19
Alignment explanation
Indices: 29840542--29840579 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
29840532 ATTCCGAAAA
*
29840542 TAATATTATTTTAATAATT
1 TAATATTATCTTAATAATT
29840561 TAATACTTATCTTAATAAT
1 TAATA-TTATCTTAATAAT
29840580 ATTTTATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (19 bp):
TAATATTATCTTAATAATT
Found at i:29840686 original size:12 final size:12
Alignment explanation
Indices: 29840666--29840699 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
29840656 TATTATTTTA
*
29840666 ATAAGATTTAAT
1 ATAATATTTAAT
29840678 ATAATATTTAAT
1 ATAATATTTAAT
29840690 ATAATATTTA
1 ATAATATTTA
29840700 TTTTGATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (12 bp):
ATAATATTTAAT
Found at i:29840687 original size:62 final size:59
Alignment explanation
Indices: 29840611--29840727 Score: 146
Period size: 62 Copynumber: 1.9 Consensus size: 59
29840601 AATGATTATC
* *
29840611 TTAATATTAAATTTAATTTAACATTTATCTTGTAGATAAACACTATATTATTTTAATAAGAT
1 TTAATATTAAATTTAATATAACATTTAT-TT-T-GATAAACACTATATTAATTTAATAAGAT
* * *
29840673 TTAATA-TAATATTTAATATAATATTTATTTTGATAAATATTATATTAATTTAATA
1 TTAATATTAA-ATTTAATATAACATTTATTTTGATAAACACTATATTAATTTAATA
29840728 TTAAAGTGAT
Statistics
Matches: 49, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
59 21 0.43
60 1 0.02
61 5 0.10
62 22 0.45
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.50
Consensus pattern (59 bp):
TTAATATTAAATTTAATATAACATTTATTTTGATAAACACTATATTAATTTAATAAGAT
Found at i:29840727 original size:16 final size:16
Alignment explanation
Indices: 29840671--29840730 Score: 50
Period size: 16 Copynumber: 3.7 Consensus size: 16
29840661 TTTTAATAAG
*
29840671 ATTTAATATAATATTTA
1 ATTTAATATTATA-TTA
* * *
29840688 ATATAATATTTATTTTG
1 ATTTAATA-TTATATTA
*
29840705 A-TAAATATTATATTA
1 ATTTAATATTATATTA
29840720 ATTTAATATTA
1 ATTTAATATTA
29840731 AAGTGATTAA
Statistics
Matches: 32, Mismatches: 9, Indels: 5
0.70 0.20 0.11
Matches are distributed among these distances:
15 7 0.22
16 12 0.38
17 10 0.31
18 3 0.09
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (16 bp):
ATTTAATATTATATTA
Found at i:29847795 original size:2 final size:2
Alignment explanation
Indices: 29847788--29847814 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
29847778 ATGAAATGTG
29847788 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 T
29847815 CTTTTATTAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:29847937 original size:2 final size:2
Alignment explanation
Indices: 29847930--29847964 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
29847920 AAACTTACTC
*
29847930 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA AA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
29847965 TGAAATAGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:29857224 original size:31 final size:31
Alignment explanation
Indices: 29857189--29857264 Score: 93
Period size: 31 Copynumber: 2.5 Consensus size: 31
29857179 AAAAAAACTT
* *
29857189 AATAGCCTAGTGACTTAAAT-AAGAACTTTTG
1 AATAGCTTAGTGACTTAAATGAA-AACTTTCG
*
29857220 AATAG-TTCATTGACTTAAATGAAAACTTTCG
1 AATAGCTT-AGTGACTTAAATGAAAACTTTCG
29857251 AATAGCTTAGTGAC
1 AATAGCTTAGTGAC
29857265 CAAATTGTAA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
30 1 0.03
31 33 0.87
32 4 0.11
ACGTcount: A:0.38, C:0.13, G:0.16, T:0.33
Consensus pattern (31 bp):
AATAGCTTAGTGACTTAAATGAAAACTTTCG
Found at i:29858333 original size:48 final size:48
Alignment explanation
Indices: 29858281--29858372 Score: 184
Period size: 48 Copynumber: 1.9 Consensus size: 48
29858271 TTTTACTGGC
29858281 TGGTTAACTAAAAATAATAATATAAAAGAAATTAAAATAATTGGTGGA
1 TGGTTAACTAAAAATAATAATATAAAAGAAATTAAAATAATTGGTGGA
29858329 TGGTTAACTAAAAATAATAATATAAAAGAAATTAAAATAATTGG
1 TGGTTAACTAAAAATAATAATATAAAAGAAATTAAAATAATTGG
29858373 AGGAGTATTT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 44 1.00
ACGTcount: A:0.55, C:0.02, G:0.13, T:0.29
Consensus pattern (48 bp):
TGGTTAACTAAAAATAATAATATAAAAGAAATTAAAATAATTGGTGGA
Found at i:29860607 original size:21 final size:21
Alignment explanation
Indices: 29860582--29860629 Score: 96
Period size: 21 Copynumber: 2.3 Consensus size: 21
29860572 TTGATCCTTA
29860582 AACTTTCTAATCAAAACTTTT
1 AACTTTCTAATCAAAACTTTT
29860603 AACTTTCTAATCAAAACTTTT
1 AACTTTCTAATCAAAACTTTT
29860624 AACTTT
1 AACTTT
29860630 TAAAATAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.38, C:0.19, G:0.00, T:0.44
Consensus pattern (21 bp):
AACTTTCTAATCAAAACTTTT
Found at i:29861114 original size:30 final size:31
Alignment explanation
Indices: 29861071--29861130 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
29861061 AATAAAAGTA
* *
29861071 AAATTGTACTTTAA-CCTTTTTAAAATTATAG
1 AAATTGTAATTTAATCC-TTTAAAAATTATAG
29861102 AAATT-TAATTTAATCCTTTAAAAATTATA
1 AAATTGTAATTTAATCCTTTAAAAATTATA
29861131 AAGATATAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 19 0.73
31 7 0.27
ACGTcount: A:0.43, C:0.08, G:0.03, T:0.45
Consensus pattern (31 bp):
AAATTGTAATTTAATCCTTTAAAAATTATAG
Found at i:29861316 original size:2 final size:2
Alignment explanation
Indices: 29861309--29861349 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
29861299 AGTTAGTTAG
29861309 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
29861350 GCCTTTTACC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:29863568 original size:3 final size:3
Alignment explanation
Indices: 29863551--29863631 Score: 50
Period size: 3 Copynumber: 29.3 Consensus size: 3
29863541 TTATAGTAAC
* * * *
29863551 TAT TA- TAT T-T TAT TAT TAC TAT TA- CAT TAT TAG TA- CAT TAT T-T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * *
29863594 TAT TAT T-T TCT T-T TAT TGT AAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
29863632 TTAATATTCT
Statistics
Matches: 60, Mismatches: 11, Indels: 14
0.71 0.13 0.16
Matches are distributed among these distances:
2 12 0.20
3 48 0.80
ACGTcount: A:0.30, C:0.05, G:0.02, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:29888815 original size:87 final size:88
Alignment explanation
Indices: 29888719--29888886 Score: 207
Period size: 87 Copynumber: 1.9 Consensus size: 88
29888709 TCTTTGAAGC
* * * *
29888719 AAACATTAAAAACATAA-ATTGAAAATAGCTCAG-CGCGTGAGCCAAGGCGCAACTCATCTCTCG
1 AAACATTAAAAACA-AATATTGAAAATACCT-AGTCACGTGACCCAAGGCGCAACTCACCTCTCG
*
29888782 CAATATGAGTTGGTTTTTTTTTTTG
64 CAATATGAGTTGATTTTTTTTTTTG
* * * * *
29888807 AAAC-TTAAAAGCAAATTTTGAAAATACCTAGTCATGTGACCCGAGGCTCAACTCACCTCTCGCA
1 AAACATTAAAAACAAATATTGAAAATACCTAGTCACGTGACCCAAGGCGCAACTCACCTCTCGCA
29888871 ATATGAGTTGATTTTT
66 ATATGAGTTGATTTTT
29888887 GAAAAATAAA
Statistics
Matches: 68, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
86 4 0.06
87 60 0.88
88 4 0.06
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Consensus pattern (88 bp):
AAACATTAAAAACAAATATTGAAAATACCTAGTCACGTGACCCAAGGCGCAACTCACCTCTCGCA
ATATGAGTTGATTTTTTTTTTTG
Found at i:29889177 original size:54 final size:54
Alignment explanation
Indices: 29889098--29889322 Score: 405
Period size: 54 Copynumber: 4.1 Consensus size: 54
29889088 GAAAAGTAGA
*
29889098 TTTTGAAAAACAGACATTAAAAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
1 TTTTGAAAAACAGAAATTAAAAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
*
29889152 TTTTGAAAAACAGAAATTAAAAGGCTCAACTCACCTCTCACAATATGAGTTGAT
1 TTTTGAAAAACAGAAATTAAAAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
29889206 TTTTGAAAAACAGAAATTAAAAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
1 TTTTGAAAAACAGAAATTAAAAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
* *
29889260 TTTTGGAAAACAAAAATTAAAAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
1 TTTTGAAAAACAGAAATTAAAAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
29889314 TCTTTGAAA
1 T-TTTGAAA
29889323 CATACATTAA
Statistics
Matches: 164, Mismatches: 6, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
54 158 0.96
55 6 0.04
ACGTcount: A:0.39, C:0.19, G:0.14, T:0.28
Consensus pattern (54 bp):
TTTTGAAAAACAGAAATTAAAAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
Found at i:29889487 original size:173 final size:172
Alignment explanation
Indices: 29889281--29889595 Score: 465
Period size: 173 Copynumber: 1.8 Consensus size: 172
29889271 AAAAATTAAA
* *
29889281 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTCTTTG-AAACATACATTAAAAACAGAAATTG
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTCTTTGAAAACAGAAATTAAAAACAGAAATTG
* *
29889345 AAAATAGCTCAGTGCGTGAGC-GAAGGCGCAACTCACCTCTCGCAATATGAGTTG-GTTTTTGAA
66 AAAATACCTCA--GCGTGACCTG-AGGCGCAACTCACCTCTCGCAATATGAGTTGAGTTTTTGAA
*
29889408 AACATGAATTAAAATAGAATTTGAAAATACCTCGACATGTGACCCG
128 AACA-GAAATAAAATAGAATTTGAAAATACCTCGACATGTGACCCG
* *
29889454 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAACAGAAATTAAAAACAGGAATT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTCTTTG-AAAACAGAAATTAAAAACAGAAATT
* * *
29889519 GAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAA
65 GAAAATACCTCAGCGTGACCTGAGGCGCAACTCACCTCTCGCAATATGAGTTGA-GTTTTTGAAA
29889584 ACAGAAATAAAA
129 ACAGAAATAAAA
29889596 AGATCAAAAT
Statistics
Matches: 127, Mismatches: 10, Indels: 9
0.87 0.07 0.06
Matches are distributed among these distances:
173 74 0.58
174 9 0.07
175 44 0.35
ACGTcount: A:0.37, C:0.19, G:0.17, T:0.27
Consensus pattern (172 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTGATTCTTTGAAAACAGAAATTAAAAACAGAAATTG
AAAATACCTCAGCGTGACCTGAGGCGCAACTCACCTCTCGCAATATGAGTTGAGTTTTTGAAAAC
AGAAATAAAATAGAATTTGAAAATACCTCGACATGTGACCCG
Found at i:29889523 original size:14 final size:14
Alignment explanation
Indices: 29889490--29889523 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
29889480 AGTTGATTTT
29889490 TTGAAAAACAGAAA
1 TTGAAAAACAGAAA
*
29889504 TT-AAAAACAGGAA
1 TTGAAAAACAGAAA
29889517 TTGAAAA
1 TTGAAAA
29889524 TACCTCAGCG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.62, C:0.06, G:0.15, T:0.18
Consensus pattern (14 bp):
TTGAAAAACAGAAA
Found at i:29889560 original size:87 final size:85
Alignment explanation
Indices: 29889281--29889596 Score: 385
Period size: 87 Copynumber: 3.7 Consensus size: 85
29889271 AAAAATTAAA
* * * *
29889281 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTCTTTG-AAACATACATTAAAAACAGAAATTG
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAACAGAAATTAAAAACAGGAATTG
* *
29889345 AAAATAGCTCAGTGCGTGAGCG
66 AAAATACCTCA--GCGTGACCG
* * *
29889367 AAGGCGCAACTCACCTCTCGCAATATGAGTTG-GTTTTTGAAAACATG-AATT-AAAATA-GAAT
1 -AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAACA-GAAATTAAAAACAGGAA-
29889428 TTGAAAATACCTC-GACATGTGACCCG
63 TTGAAAATACCTCAG-C--GTGA-CCG
29889454 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAACAGAAATTAAAAACAGGAATT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTG-AAAACAGAAATTAAAAACAGGAATT
*
29889519 GAAAATACCTCAGCGTGTCCTG
65 GAAAATACCTCAGCGTGACC-G
29889541 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAACAGAAA-TAAAAA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTGAAAACAGAAATTAAAAA
29889597 GATCAAAATA
Statistics
Matches: 201, Mismatches: 13, Indels: 31
0.82 0.05 0.13
Matches are distributed among these distances:
83 1 0.00
84 1 0.00
85 2 0.01
86 64 0.32
87 93 0.46
88 17 0.08
89 19 0.09
90 4 0.02
ACGTcount: A:0.37, C:0.19, G:0.17, T:0.27
Consensus pattern (85 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAACAGAAATTAAAAACAGGAATTG
AAAATACCTCAGCGTGACCG
Found at i:29895809 original size:46 final size:46
Alignment explanation
Indices: 29895742--29895915 Score: 219
Period size: 46 Copynumber: 3.8 Consensus size: 46
29895732 ATGTAACCCG
*
29895742 ATAAGCGAACTCGGACTCAACTCAACGAGCTCGGACATTTGCATCC
1 ATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCC
* * * * *
29895788 ATAAGTGAACTCGGACTCAACTCAATGAGTTTGGATGCCTAGTTACAT-C
1 ATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-ATTTGCATCC
*
29895837 -TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCC
1 ATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCC
*
29895881 ATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 ATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
29895916 TGCTCAACCA
Statistics
Matches: 107, Mismatches: 14, Indels: 14
0.79 0.10 0.10
Matches are distributed among these distances:
43 6 0.06
44 2 0.02
45 2 0.02
46 60 0.56
47 27 0.25
48 2 0.02
49 2 0.02
50 6 0.06
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.23
Consensus pattern (46 bp):
ATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCC
Found at i:29895911 original size:93 final size:93
Alignment explanation
Indices: 29895747--29895918 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
29895737 ACCCGATAAG
29895747 CGAACTCGGACTCAACTCAACGAGCTCGGACATTTGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTTGCATCCATAAGTGAACTCGGACTCAACTCA
* *
29895812 ATGAGTTTGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
*
29895840 CGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTTGCATCCATAAGTGAACTCGGACTCAACTCA
29895905 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
29895919 TCAACCATCC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.29, C:0.27, G:0.20, T:0.23
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTTGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:29904939 original size:22 final size:24
Alignment explanation
Indices: 29904880--29904940 Score: 67
Period size: 22 Copynumber: 2.7 Consensus size: 24
29904870 GTATGTACAC
29904880 CAAATAAT-AATAATATATAAGTGA
1 CAAA-AATGAATAATATATAAGTGA
*
29904904 CAATAATGAA-AATA-ATAAGT-A
1 CAAAAATGAATAATATATAAGTGA
*
29904925 TAAAAATGAATAATAT
1 CAAAAATGAATAATAT
29904941 GATATACGGA
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
21 9 0.29
22 10 0.32
23 7 0.23
24 5 0.16
ACGTcount: A:0.61, C:0.03, G:0.08, T:0.28
Consensus pattern (24 bp):
CAAAAATGAATAATATATAAGTGA
Found at i:29905336 original size:26 final size:26
Alignment explanation
Indices: 29905289--29905389 Score: 82
Period size: 26 Copynumber: 3.9 Consensus size: 26
29905279 TATAAGTAAT
*
29905289 ATATAACTAGTAATATCAAAATATATAC
1 ATATAA-TA-TAATATAAAAATATATAC
**
29905317 ATGATAATAT-ATATAAAAATATATGT
1 AT-ATAATATAATATAAAAATATATAC
* *
29905343 ATATAATGTAATATGAAAATATAT--
1 ATATAATATAATATAAAAATATATAC
* * *
29905367 ATGTAGTATAATATTAAAATATA
1 ATATAATATAATATAAAAATATA
29905390 ATAATACAAC
Statistics
Matches: 62, Mismatches: 9, Indels: 8
0.78 0.11 0.10
Matches are distributed among these distances:
24 19 0.31
25 6 0.10
26 28 0.45
27 1 0.02
28 4 0.06
29 4 0.06
ACGTcount: A:0.53, C:0.03, G:0.07, T:0.37
Consensus pattern (26 bp):
ATATAATATAATATAAAAATATATAC
Found at i:29905427 original size:18 final size:17
Alignment explanation
Indices: 29905404--29905471 Score: 72
Period size: 18 Copynumber: 4.1 Consensus size: 17
29905394 TACAACATTA
29905404 AAAATATATGATATATAT
1 AAAATATAT-ATATATAT
*
29905422 AAAATACA-ATAT-TA-
1 AAAATATATATATATAT
*
29905436 AAAGTATATATAATATAT
1 AAAATATATAT-ATATAT
29905454 AAAATATATATA-ATAT
1 AAAATATATATATATAT
29905470 AA
1 AA
29905472 TACCTAAGTA
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
14 6 0.14
15 4 0.10
16 12 0.29
17 3 0.07
18 17 0.40
ACGTcount: A:0.60, C:0.01, G:0.03, T:0.35
Consensus pattern (17 bp):
AAAATATATATATATAT
Found at i:29905429 original size:32 final size:32
Alignment explanation
Indices: 29905377--29905459 Score: 107
Period size: 32 Copynumber: 2.6 Consensus size: 32
29905367 ATGTAGTATA
*
29905377 ATAT-TAAAATATAATAATACAACATTAAAAAT
1 ATATATAATATATAA-AATACAACATTAAAAAT
* *
29905409 ATATGAT-ATATATAAAATACAATATTAAAAGT
1 ATAT-ATAATATATAAAATACAACATTAAAAAT
29905441 ATATATAATATATAAAATA
1 ATATATAATATATAAAATA
29905460 TATATAATAT
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
31 2 0.04
32 35 0.78
33 7 0.16
34 1 0.02
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.34
Consensus pattern (32 bp):
ATATATAATATATAAAATACAACATTAAAAAT
Found at i:29906155 original size:11 final size:10
Alignment explanation
Indices: 29906131--29906170 Score: 53
Period size: 10 Copynumber: 3.9 Consensus size: 10
29906121 AATTAAAATT
*
29906131 TTTTTATATT
1 TTTTTATATG
29906141 TTTTTATTATG
1 TTTTTA-TATG
29906152 TTTTTATATG
1 TTTTTATATG
*
29906162 TTTTAATAT
1 TTTTTATAT
29906171 ATATAGGTGA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
10 18 0.67
11 9 0.33
ACGTcount: A:0.23, C:0.00, G:0.05, T:0.72
Consensus pattern (10 bp):
TTTTTATATG
Found at i:29907665 original size:12 final size:12
Alignment explanation
Indices: 29907649--29907694 Score: 51
Period size: 11 Copynumber: 3.9 Consensus size: 12
29907639 TATTATTATC
29907649 ATATTATATTTA
1 ATATTATATTTA
* *
29907661 GTATTA-CTTTA
1 ATATTATATTTA
29907672 ATATTATA-TTA
1 ATATTATATTTA
29907683 ACTATTATATTT
1 A-TATTATATTT
29907695 TATTATTACT
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
11 13 0.48
12 12 0.44
13 2 0.07
ACGTcount: A:0.37, C:0.04, G:0.02, T:0.57
Consensus pattern (12 bp):
ATATTATATTTA
Found at i:29907714 original size:17 final size:17
Alignment explanation
Indices: 29907631--29907735 Score: 81
Period size: 17 Copynumber: 5.9 Consensus size: 17
29907621 TTTGTACTGC
29907631 ATTATAATTATTATTATCAT
1 ATTAT-ATTATTATTA-C-T
*
29907651 ATTATATTTAGTATTACT
1 ATTATA-TTATTATTACT
29907669 -TTAATATTA-TATTAACT
1 ATT-ATATTATTATT-ACT
29907686 ATTATATTTTATTATTACT
1 ATTATA--TTATTATTACT
* *
29907705 ATTACATTATTAGTAC-
1 ATTATATTATTATTACT
*
29907721 ATTATTTTATTATTA
1 ATTATATTATTATTA
29907736 TTTTTATTGT
Statistics
Matches: 72, Mismatches: 6, Indels: 18
0.75 0.06 0.19
Matches are distributed among these distances:
16 16 0.22
17 20 0.28
18 6 0.08
19 13 0.18
20 17 0.24
ACGTcount: A:0.36, C:0.06, G:0.02, T:0.56
Consensus pattern (17 bp):
ATTATATTATTATTACT
Found at i:29907757 original size:15 final size:14
Alignment explanation
Indices: 29907747--29907779 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
29907737 TTTTATTGTA
29907747 AATATTATTATTCT
1 AATATTATTATTCT
*
29907761 AATATTA-TATTAT
1 AATATTATTATTCT
29907774 AATATT
1 AATATT
29907780 TTTCATTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 11 0.61
14 7 0.39
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (14 bp):
AATATTATTATTCT
Found at i:29907844 original size:12 final size:13
Alignment explanation
Indices: 29907816--29907848 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
29907806 TTATTTATTC
*
29907816 TTATATATGTCAT
1 TTATTTATGTCAT
29907829 TTATTTATGT-AT
1 TTATTTATGTCAT
29907841 TTATTTAT
1 TTATTTAT
29907849 TTTATTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 10 0.53
13 9 0.47
ACGTcount: A:0.27, C:0.03, G:0.06, T:0.64
Consensus pattern (13 bp):
TTATTTATGTCAT
Found at i:29916480 original size:19 final size:19
Alignment explanation
Indices: 29916456--29916493 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
29916446 GAAATGAATA
*
29916456 ATTTCAGGCAAATAGGTTG
1 ATTTCAAGCAAATAGGTTG
29916475 ATTTCAAGCAAATAGGTTG
1 ATTTCAAGCAAATAGGTTG
29916494 GCAATCTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.34, C:0.11, G:0.24, T:0.32
Consensus pattern (19 bp):
ATTTCAAGCAAATAGGTTG
Found at i:29918033 original size:44 final size:44
Alignment explanation
Indices: 29917984--29918560 Score: 899
Period size: 44 Copynumber: 13.4 Consensus size: 44
29917974 CCCCGTCTAA
* * * * *
29917984 TACAGAGATGCCAAATCCGTTATCTTCGATATGCTCTCTGTCGC
1 TACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
* *
29918028 TACAGAGACGCCAAATCTGTTATCTTTGATCTGCT-TCCGCC-T
1 TACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
29918070 TACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
1 TACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
* * *
29918114 TACAGAGATGCCAAATC----ATCTTCGATCTGCTCTTCACCGC
1 TACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
* *
29918154 TACAGAGACGCCAAATCTGTTATCTTCGATCTACTCTTCGCCGC
1 TACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
29918198 TACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
1 TACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
* *
29918242 TACAGAGACGCCAAATCTGTTATCTTTGATCTGCTCTCTGCCGC
1 TACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
29918286 TACAGAGACG-CAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
1 TACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
*
29918329 TACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCT-CTCCGC
1 TACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
*
29918372 TACAGAGACGCCAAATCTGTTATCTTCGATCTG-TCTCCGCCAC
1 TACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
29918415 TACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
1 TACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
*
29918459 TATAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
1 TACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
* *
29918503 TACAGAGACG---AATCTGTTATCTTCGATCTGCTCTCTGTCGC
1 TACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
29918544 TACAGAGACGCCAAATC
1 TACAGAGACGCCAAATC
29918561 ATCTTGGATT
Statistics
Matches: 492, Mismatches: 29, Indels: 24
0.90 0.05 0.04
Matches are distributed among these distances:
40 37 0.08
41 39 0.08
42 37 0.08
43 126 0.26
44 253 0.51
ACGTcount: A:0.22, C:0.31, G:0.18, T:0.29
Consensus pattern (44 bp):
TACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
Found at i:29918346 original size:87 final size:88
Alignment explanation
Indices: 29917984--29918560 Score: 910
Period size: 87 Copynumber: 6.7 Consensus size: 88
29917974 CCCCGTCTAA
* * * *
29917984 TACAGAGATGCCAAATCCGTTATCTTCGATATGCTCTCTGTCGCTACAGAGACGCCAAATCTGTT
1 TACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCTGCCGCTACAGAGACGCCAAATCTGTT
* *
29918049 ATCTTTGATCTGCT-TCCGCC-T
66 ATCTTCGATCTGCTCTCCGCCGC
* *
29918070 TACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGCTACAGAGATGCCAAATC----
1 TACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCTGCCGCTACAGAGACGCCAAATCTGTT
* *
29918131 ATCTTCGATCTGCTCTTCACCGC
66 ATCTTCGATCTGCTCTCCGCCGC
*
29918154 TACAGAGACGCCAAATCTGTTATCTTCGATCTACTCT-TCGCCGCTACAGAGACGCCAAATCTGT
1 TACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCT-GCCGCTACAGAGACGCCAAATCTGT
29918218 TATCTTCGATCTGCTCTCCGCCGC
65 TATCTTCGATCTGCTCTCCGCCGC
*
29918242 TACAGAGACGCCAAATCTGTTATCTTTGATCTGCTCTCTGCCGCTACAGAGACG-CAAATCTGTT
1 TACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCTGCCGCTACAGAGACGCCAAATCTGTT
29918306 ATCTTCGATCTGCTCTCCGCCGC
66 ATCTTCGATCTGCTCTCCGCCGC
29918329 TACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCT-CCGCTACAGAGACGCCAAATCTGTT
1 TACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCTGCCGCTACAGAGACGCCAAATCTGTT
*
29918393 ATCTTCGATCTG-TCTCCGCCAC
66 ATCTTCGATCTGCTCTCCGCCGC
* *
29918415 TACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGCTATAGAGACGCCAAATCTGTT
1 TACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCTGCCGCTACAGAGACGCCAAATCTGTT
29918480 ATCTTCGATCTGCTCTCCGCCGC
66 ATCTTCGATCTGCTCTCCGCCGC
*
29918503 TACAGAGACG---AATCTGTTATCTTCGATCTGCTCTCTGTCGCTACAGAGACGCCAAATC
1 TACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCTGCCGCTACAGAGACGCCAAATC
29918561 ATCTTGGATT
Statistics
Matches: 455, Mismatches: 25, Indels: 23
0.90 0.05 0.05
Matches are distributed among these distances:
82 13 0.03
83 4 0.01
84 57 0.13
85 45 0.10
86 116 0.25
87 129 0.28
88 90 0.20
89 1 0.00
ACGTcount: A:0.22, C:0.31, G:0.18, T:0.29
Consensus pattern (88 bp):
TACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCTGCCGCTACAGAGACGCCAAATCTGTT
ATCTTCGATCTGCTCTCCGCCGC
Found at i:29918447 original size:130 final size:132
Alignment explanation
Indices: 29917984--29918560 Score: 910
Period size: 130 Copynumber: 4.5 Consensus size: 132
29917974 CCCCGTCTAA
* * * *
29917984 TACAGAGATGCCAAATCCGTTATCTTCGATATGCTCTCTGTCGCTACAGAGACGCCAAATCTGTT
1 TACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCTGCCGCTACAGAGACGCCAAATCTGTT
* *
29918049 ATCTTTGATCTGCT-TCCGCC-TTACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCC
66 ATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCC
29918112 GC
131 GC
* *
29918114 TACAGAGATGCCAAATC----ATCTTCGATCTGCTCT-TCACCGCTACAGAGACGCCAAATCTGT
1 TACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCT-GCCGCTACAGAGACGCCAAATCTGT
* *
29918174 TATCTTCGATCTACTCTTCGCCGCTACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGC
65 TATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGC
29918239 CGC
130 CGC
*
29918242 TACAGAGACGCCAAATCTGTTATCTTTGATCTGCTCTCTGCCGCTACAGAGACG-CAAATCTGTT
1 TACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCTGCCGCTACAGAGACGCCAAATCTGTT
*
29918306 ATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCT-CTCC
66 ATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCC
29918370 GC
131 GC
* *
29918372 TACAGAGACGCCAAATCTGTTATCTTCGATCTG-TCTCCGCCACTACAGAGACGCCAAATCTGTT
1 TACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCTGCCGCTACAGAGACGCCAAATCTGTT
*
29918436 ATCTTCGATCTGCTCTCCGCCGCTATAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCC
66 ATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCC
29918501 GC
131 GC
*
29918503 TACAGAGACG---AATCTGTTATCTTCGATCTGCTCTCTGTCGCTACAGAGACGCCAAATC
1 TACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCTGCCGCTACAGAGACGCCAAATC
29918561 ATCTTGGATT
Statistics
Matches: 415, Mismatches: 21, Indels: 23
0.90 0.05 0.05
Matches are distributed among these distances:
125 1 0.00
126 51 0.12
127 5 0.01
128 80 0.19
129 42 0.10
130 123 0.30
131 83 0.20
132 29 0.07
133 1 0.00
ACGTcount: A:0.22, C:0.31, G:0.18, T:0.29
Consensus pattern (132 bp):
TACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCTGCCGCTACAGAGACGCCAAATCTGTT
ATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCC
GC
Found at i:29918866 original size:65 final size:65
Alignment explanation
Indices: 29918750--29918868 Score: 192
Period size: 61 Copynumber: 1.9 Consensus size: 65
29918740 GTATCCATGC
29918750 TTATGCCAAATAATTAGGATGCTATGATTGAAATGAATCAAATGTTCCTAAATAAATGTGACGCT
1 TTATGCCAAATAATTAGGATGCTATGATTGAAATGAATCAAATGTTCCTAAATAAATGTGACGCT
* *
29918815 TTATGTCAAATAATTAGGATG-T-T-A-TGAAATGAATCAAATGTTCCTAACTAAATG
1 TTATGCCAAATAATTAGGATGCTATGATTGAAATGAATCAAATGTTCCTAAATAAATG
29918869 AATGGTTATG
Statistics
Matches: 52, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
61 29 0.56
62 1 0.02
63 1 0.02
64 1 0.02
65 20 0.38
ACGTcount: A:0.39, C:0.11, G:0.16, T:0.34
Consensus pattern (65 bp):
TTATGCCAAATAATTAGGATGCTATGATTGAAATGAATCAAATGTTCCTAAATAAATGTGACGCT
Found at i:29923912 original size:19 final size:19
Alignment explanation
Indices: 29923888--29923925 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
29923878 GAAATGAATA
*
29923888 ATTTCAGGCAAATAGGTTG
1 ATTTCAAGCAAATAGGTTG
29923907 ATTTCAAGCAAATAGGTTG
1 ATTTCAAGCAAATAGGTTG
29923926 GCAATCTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.34, C:0.11, G:0.24, T:0.32
Consensus pattern (19 bp):
ATTTCAAGCAAATAGGTTG
Done.