Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A12
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: 102106374
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 3186644 characters in sequence are not A, C, G, or T
File 56 of 311
Found at i:16268767 original size:51 final size:51
Alignment explanation
Indices: 16268686--16268790 Score: 201
Period size: 51 Copynumber: 2.1 Consensus size: 51
16268676 GGGAACCCGA
16268686 GGATGCTATGAGAAAACAATATTCAAACCTATTCACTGGTAAGATTTTCGG
1 GGATGCTATGAGAAAACAATATTCAAACCTATTCACTGGTAAGATTTTCGG
*
16268737 GGATTCTATGAGAAAACAATATTCAAACCTATTCACTGGTAAGATTTTCGG
1 GGATGCTATGAGAAAACAATATTCAAACCTATTCACTGGTAAGATTTTCGG
16268788 GGA
1 GGA
16268791 CGAAAATCCC
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 53 1.00
ACGTcount: A:0.35, C:0.15, G:0.20, T:0.30
Consensus pattern (51 bp):
GGATGCTATGAGAAAACAATATTCAAACCTATTCACTGGTAAGATTTTCGG
Found at i:16271936 original size:23 final size:22
Alignment explanation
Indices: 16271908--16272033 Score: 101
Period size: 23 Copynumber: 5.5 Consensus size: 22
16271898 AGCTGATGGA
*
16271908 CAGTAAGCTCTATTAAGCTGAAT
1 CAGTAAGCTCTATT-AGCTAAAT
* *
16271931 CGGTAAGCTCTAATTAGCTAAAA
1 CAGTAAGCTCT-ATTAGCTAAAT
*
16271954 CAGTAAGCTCTATCGAGCTAAAT
1 CAGTAAGCTCTAT-TAGCTAAAT
* *
16271977 CAGTAAGCTCCAATGAGCTGAAA-
1 CAGTAAGCT-CTATTAGCT-AAAT
* * * *
16272000 CAGTAAGCACCAATGAGCTAAAA
1 CAGTAAGC-TCTATTAGCTAAAT
16272023 CAGTAAGCTCT
1 CAGTAAGCTCT
16272034 TACGAGCTGA
Statistics
Matches: 87, Mismatches: 10, Indels: 13
0.79 0.09 0.12
Matches are distributed among these distances:
22 6 0.07
23 72 0.83
24 9 0.10
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.23
Consensus pattern (22 bp):
CAGTAAGCTCTATTAGCTAAAT
Found at i:16271959 original size:46 final size:46
Alignment explanation
Indices: 16271907--16272007 Score: 139
Period size: 46 Copynumber: 2.2 Consensus size: 46
16271897 GAGCTGATGG
* * * * *
16271907 ACAGTAAGCTCTATTAAGCTGAATCGGTAAGCTCTAATTAGCTAAA
1 ACAGTAAGCTCTATCAAGCTAAATCAGTAAGCTCCAATGAGCTAAA
* *
16271953 ACAGTAAGCTCTATCGAGCTAAATCAGTAAGCTCCAATGAGCTGAA
1 ACAGTAAGCTCTATCAAGCTAAATCAGTAAGCTCCAATGAGCTAAA
16271999 ACAGTAAGC
1 ACAGTAAGC
16272008 ACCAATGAGC
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
46 48 1.00
ACGTcount: A:0.38, C:0.20, G:0.19, T:0.24
Consensus pattern (46 bp):
ACAGTAAGCTCTATCAAGCTAAATCAGTAAGCTCCAATGAGCTAAA
Found at i:16271983 original size:69 final size:69
Alignment explanation
Indices: 16271908--16272055 Score: 190
Period size: 69 Copynumber: 2.1 Consensus size: 69
16271898 AGCTGATGGA
* * * * * * *
16271908 CAGTAAGCTCTATTAAGCTGAATCGGTAAGCTCTAATTAGCTAAAACAGTAAGCTC-TATCGAGC
1 CAGTAAGCTCCAATAAGCTGAAACAGTAAGCACCAATGAGCTAAAACAGTAAGCTCTTA-CGAGC
16271972 TAAAT
65 TAAAT
*
16271977 CAGTAAGCTCCAATGAGCTGAAACAGTAAGCACCAATGAGCTAAAACAGTAAGCTCTTACGAGCT
1 CAGTAAGCTCCAATAAGCTGAAACAGTAAGCACCAATGAGCTAAAACAGTAAGCTCTTACGAGCT
*
16272042 GAAT
66 AAAT
*
16272046 CGGTAAGCTC
1 CAGTAAGCTC
16272056 ATACAAGCTA
Statistics
Matches: 68, Mismatches: 10, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
69 66 0.97
70 2 0.03
ACGTcount: A:0.36, C:0.21, G:0.20, T:0.23
Consensus pattern (69 bp):
CAGTAAGCTCCAATAAGCTGAAACAGTAAGCACCAATGAGCTAAAACAGTAAGCTCTTACGAGCT
AAAT
Found at i:16272018 original size:46 final size:46
Alignment explanation
Indices: 16271923--16272032 Score: 132
Period size: 46 Copynumber: 2.4 Consensus size: 46
16271913 AGCTCTATTA
* * * * * *
16271923 AGCTGAATCGGTAAGCTCTAATTAGCTAAAACAGTAAGCTCTATCG
1 AGCTAAATCAGTAAGCTCCAATGAGCTAAAACAGTAAGCCCAATCG
*
16271969 AGCTAAATCAGTAAGCTCCAATGAGCTGAAACAGTAAGCACCAAT-G
1 AGCTAAATCAGTAAGCTCCAATGAGCTAAAACAGTAAGC-CCAATCG
*
16272015 AGCTAAAACAGTAAGCTC
1 AGCTAAATCAGTAAGCTC
16272033 TTACGAGCTG
Statistics
Matches: 55, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
46 52 0.95
47 3 0.05
ACGTcount: A:0.39, C:0.21, G:0.19, T:0.21
Consensus pattern (46 bp):
AGCTAAATCAGTAAGCTCCAATGAGCTAAAACAGTAAGCCCAATCG
Found at i:16272040 original size:23 final size:23
Alignment explanation
Indices: 16271946--16272065 Score: 107
Period size: 23 Copynumber: 5.2 Consensus size: 23
16271936 AGCTCTAATT
16271946 AGCTAAAACAGTAAGCT-CTATCG
1 AGCTAAAACAGTAAGCTCCTA-CG
* * *
16271969 AGCTAAATCAGTAAGCTCCAATG
1 AGCTAAAACAGTAAGCTCCTACG
* * * *
16271992 AGCTGAAACAGTAAGCACCAATG
1 AGCTAAAACAGTAAGCTCCTACG
*
16272015 AGCTAAAACAGTAAGCTCTTACG
1 AGCTAAAACAGTAAGCTCCTACG
* * * * *
16272038 AGCTGAATCGGTAAGCTCATACA
1 AGCTAAAACAGTAAGCTCCTACG
16272061 AGCTA
1 AGCTA
16272066 TGGTGAGTCC
Statistics
Matches: 79, Mismatches: 17, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
23 77 0.97
24 2 0.03
ACGTcount: A:0.39, C:0.22, G:0.19, T:0.20
Consensus pattern (23 bp):
AGCTAAAACAGTAAGCTCCTACG
Found at i:16272041 original size:46 final size:46
Alignment explanation
Indices: 16271946--16272053 Score: 119
Period size: 46 Copynumber: 2.3 Consensus size: 46
16271936 AGCTCTAATT
* * * * *
16271946 AGCTAAAACAGTAAGCTCTATCGAGCTAAATCAGTAAGCTCCAATG
1 AGCTGAAACAGTAAGCCCAATCGAGCTAAAACAGTAAGCTCCAACG
**
16271992 AGCTGAAACAGTAAGCACCAAT-GAGCTAAAACAGTAAGCTCTTACG
1 AGCTGAAACAGTAAGC-CCAATCGAGCTAAAACAGTAAGCTCCAACG
* *
16272038 AGCTGAATCGGTAAGC
1 AGCTGAAACAGTAAGC
16272054 TCATACAAGC
Statistics
Matches: 52, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
46 49 0.94
47 3 0.06
ACGTcount: A:0.39, C:0.21, G:0.20, T:0.19
Consensus pattern (46 bp):
AGCTGAAACAGTAAGCCCAATCGAGCTAAAACAGTAAGCTCCAACG
Found at i:16272969 original size:26 final size:24
Alignment explanation
Indices: 16272927--16272976 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 24
16272917 GATTTTTGTT
16272927 TTATTATTAATAACTTAATACATAAA
1 TTATTATTAATAACTT-ATA-ATAAA
16272953 TTATTATT-ATAACCTTATAATAAA
1 TTATTATTAATAA-CTTATAATAAA
16272977 ACTTAATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 5 0.22
25 7 0.30
26 11 0.48
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (24 bp):
TTATTATTAATAACTTATAATAAA
Found at i:16275481 original size:42 final size:44
Alignment explanation
Indices: 16275404--16275543 Score: 162
Period size: 42 Copynumber: 3.2 Consensus size: 44
16275394 TCCTGGACGT
* * * *
16275404 GGTCTTACATGTAATTCAG-TATCGATGCCTCTGTCCCAGACAG
1 GGTCTTACACGTAAATCAGATATCGATGCCTATGTCCCAGACAC
*
16275447 GGTCTTACACG-AAATCAGATAT-GATGCCTATGTCCCAGACAT
1 GGTCTTACACGTAAATCAGATATCGATGCCTATGTCCCAGACAC
* * *
16275489 GGTCTTACACGTAAATCTA-AAATCGAGGCCTGTGTCCCAGACAC
1 GGTCTTACACGTAAATC-AGATATCGATGCCTATGTCCCAGACAC
*
16275533 AGTCTTACACG
1 GGTCTTACACG
16275544 ATATCTCAGA
Statistics
Matches: 84, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
42 35 0.42
43 21 0.25
44 28 0.33
ACGTcount: A:0.28, C:0.26, G:0.20, T:0.26
Consensus pattern (44 bp):
GGTCTTACACGTAAATCAGATATCGATGCCTATGTCCCAGACAC
Found at i:16285639 original size:21 final size:22
Alignment explanation
Indices: 16285597--16285639 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
16285587 TAAACAAAGT
*
16285597 ACAATATTATTTAACTACATAA
1 ACAATATTATTTAACTAAATAA
16285619 ACAATA-TACTTT-ACTAAATAA
1 ACAATATTA-TTTAACTAAATAA
16285640 TTACATGTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
ACAATATTATTTAACTAAATAA
Found at i:16286762 original size:20 final size:21
Alignment explanation
Indices: 16286725--16286764 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
16286715 ATGACTAAGC
16286725 CTATCTTCAGTTTTACTTGAT
1 CTATCTTCAGTTTTACTTGAT
16286746 CTAT-TTCA-TTTTCACTTGA
1 CTATCTTCAGTTTT-ACTTGA
16286765 ACTTGGAGCT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.22
20 10 0.56
21 4 0.22
ACGTcount: A:0.20, C:0.20, G:0.07, T:0.53
Consensus pattern (21 bp):
CTATCTTCAGTTTTACTTGAT
Found at i:16289192 original size:36 final size:36
Alignment explanation
Indices: 16289152--16289224 Score: 110
Period size: 36 Copynumber: 2.0 Consensus size: 36
16289142 TGCGCATGAC
* * *
16289152 TTAAATGAAGGAAAACATTATATATATGCATTAATA
1 TTAAATGAAGCAAAACAGTATACATATGCATTAATA
*
16289188 TTAAATGAAGCTAAACAGTATACATATGCATTAATA
1 TTAAATGAAGCAAAACAGTATACATATGCATTAATA
16289224 T
1 T
16289225 ATATATGATT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.48, C:0.08, G:0.11, T:0.33
Consensus pattern (36 bp):
TTAAATGAAGCAAAACAGTATACATATGCATTAATA
Found at i:16289272 original size:45 final size:45
Alignment explanation
Indices: 16289222--16289312 Score: 130
Period size: 45 Copynumber: 2.0 Consensus size: 45
16289212 TATGCATTAA
* **
16289222 TATATATATG-ATTGACTTAAATGAAGCTAAACCTGCTAATAATGG
1 TATATATATGCA-TGACTTAAATGAAACTAAAAATGCTAATAATGG
*
16289267 TATATATATGCATGACTTAAATGAAACTAAAAATGTTAATAATGG
1 TATATATATGCATGACTTAAATGAAACTAAAAATGCTAATAATGG
16289312 T
1 T
16289313 TAATTTAATT
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
45 40 0.98
46 1 0.02
ACGTcount: A:0.43, C:0.09, G:0.14, T:0.34
Consensus pattern (45 bp):
TATATATATGCATGACTTAAATGAAACTAAAAATGCTAATAATGG
Found at i:16293444 original size:23 final size:23
Alignment explanation
Indices: 16293412--16293578 Score: 156
Period size: 23 Copynumber: 7.3 Consensus size: 23
16293402 AGCTGATGGA
16293412 CAGTAAGCTCTATTGAGCTGAAT
1 CAGTAAGCTCTATTGAGCTGAAT
* * * *
16293435 CGGTAAGCTCCAATGAGCTGAAA
1 CAGTAAGCTCTATTGAGCTGAAT
* *
16293458 CAATAAGCTCTATCGAGCTGAAT
1 CAGTAAGCTCTATTGAGCTGAAT
** * *
16293481 TGGTAAGCTCTAATGAGCTGAAA
1 CAGTAAGCTCTATTGAGCTGAAT
* * *
16293504 CAGAAAACTCTATCGAGCTGAAT
1 CAGTAAGCTCTATTGAGCTGAAT
* * *
16293527 CAGTAAGCTCCAATGAGCTGAAA
1 CAGTAAGCTCTATTGAGCTGAAT
*
16293550 CAGTAAGCTC-ATACGAGCTGAAT
1 CAGTAAGCTCTAT-TGAGCTGAAT
*
16293573 CGGTAA
1 CAGTAA
16293579 ACTCATACGA
Statistics
Matches: 110, Mismatches: 33, Indels: 2
0.76 0.23 0.01
Matches are distributed among these distances:
22 1 0.01
23 109 0.99
ACGTcount: A:0.35, C:0.20, G:0.22, T:0.23
Consensus pattern (23 bp):
CAGTAAGCTCTATTGAGCTGAAT
Found at i:16293592 original size:46 final size:46
Alignment explanation
Indices: 16293411--16293578 Score: 257
Period size: 46 Copynumber: 3.7 Consensus size: 46
16293401 GAGCTGATGG
*
16293411 ACAGTAAGCTCTATTGAGCTGAATCGGTAAGCTCCAATGAGCTGAA
1 ACAGTAAGCTCTATCGAGCTGAATCGGTAAGCTCCAATGAGCTGAA
* * *
16293457 ACAATAAGCTCTATCGAGCTGAATTGGTAAGCTCTAATGAGCTGAA
1 ACAGTAAGCTCTATCGAGCTGAATCGGTAAGCTCCAATGAGCTGAA
* * *
16293503 ACAGAAAACTCTATCGAGCTGAATCAGTAAGCTCCAATGAGCTGAA
1 ACAGTAAGCTCTATCGAGCTGAATCGGTAAGCTCCAATGAGCTGAA
16293549 ACAGTAAGCTC-ATACGAGCTGAATCGGTAA
1 ACAGTAAGCTCTAT-CGAGCTGAATCGGTAA
16293579 ACTCATACGA
Statistics
Matches: 108, Mismatches: 13, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
45 2 0.02
46 106 0.98
ACGTcount: A:0.36, C:0.20, G:0.22, T:0.23
Consensus pattern (46 bp):
ACAGTAAGCTCTATCGAGCTGAATCGGTAAGCTCCAATGAGCTGAA
Found at i:16299644 original size:15 final size:15
Alignment explanation
Indices: 16299624--16299655 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
16299614 TATGTGATGA
*
16299624 ATTTATTGAATTTAT
1 ATTTATTGAATTGAT
16299639 ATTTATTGAATTGAT
1 ATTTATTGAATTGAT
16299654 AT
1 AT
16299656 ATATACATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.34, C:0.00, G:0.09, T:0.56
Consensus pattern (15 bp):
ATTTATTGAATTGAT
Found at i:16300816 original size:13 final size:13
Alignment explanation
Indices: 16300800--16300832 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
16300790 TTTAATTAAA
*
16300800 TTAGTTAATTAGT
1 TTAGATAATTAGT
16300813 TTAGATAATTAGT
1 TTAGATAATTAGT
16300826 TTA-ATAA
1 TTAGATAA
16300833 ACAAACCCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.48
Consensus pattern (13 bp):
TTAGATAATTAGT
Found at i:16301277 original size:37 final size:38
Alignment explanation
Indices: 16301182--16301279 Score: 101
Period size: 37 Copynumber: 2.5 Consensus size: 38
16301172 CGAGTCGATA
*
16301182 AGACACTGGGTGTCAATCTATTACTTCGGATTAATTCGATG
1 AGACACTGGGTGTCAA--T-TTACTTCGGATTAATTCAATG
* * * *
16301223 AGGCACTAGGTGCCAATTTACTTC-GATTTAGTT-AATG
1 AGACACTGGGTGTCAATTTACTTCGGA-TTAATTCAATG
16301260 AGACACTGGGTGTCAATTTA
1 AGACACTGGGTGTCAATTTA
16301280 TTACTTCGAA
Statistics
Matches: 48, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
37 22 0.46
38 12 0.25
39 1 0.02
41 13 0.27
ACGTcount: A:0.28, C:0.16, G:0.22, T:0.34
Consensus pattern (38 bp):
AGACACTGGGTGTCAATTTACTTCGGATTAATTCAATG
Found at i:16301301 original size:40 final size:38
Alignment explanation
Indices: 16301182--16301311 Score: 129
Period size: 40 Copynumber: 3.3 Consensus size: 38
16301172 CGAGTCGATA
*
16301182 AGACACTGGGTGTCAATCTATTACTTCGGATTAATTCGATG
1 AGACACTGGGTGTCAAT-TATTACTTCGAATT-ATT-GATG
* * * * *
16301223 AGGCACTAGGTGCCAA-T-TTACTTCGATTTAGTTAATG
1 AGACACTGGGTGTCAATTATTACTTCGAATTA-TTGATG
16301260 AGACACTGGGTGTCAATTTATTACTTCGAATTATCTGATG
1 AGACACTGGGTGTCAA-TTATTACTTCGAATTAT-TGATG
*
16301300 AGGCACTGGGTG
1 AGACACTGGGTG
16301312 CCAAACTGGT
Statistics
Matches: 72, Mismatches: 12, Indels: 11
0.76 0.13 0.12
Matches are distributed among these distances:
37 17 0.24
38 12 0.17
39 3 0.04
40 27 0.38
41 13 0.18
ACGTcount: A:0.26, C:0.16, G:0.24, T:0.34
Consensus pattern (38 bp):
AGACACTGGGTGTCAATTATTACTTCGAATTATTGATG
Found at i:16320611 original size:26 final size:25
Alignment explanation
Indices: 16320534--16320611 Score: 66
Period size: 26 Copynumber: 2.9 Consensus size: 25
16320524 CCTCTTAAAA
*
16320534 AATTCAAAATAATATTAAAAAAATATTT
1 AATTCAAAA-AAT-TT-AAAAAATATAT
** * *
16320562 TTTTCAAAAAAATTATAAATATATAT
1 AATTCAAAAAATTTA-AAAAATATAT
16320588 AATTCAAAAAATTTAAGAAAATAT
1 AATTCAAAAAATTTAA-AAAATAT
16320612 TATTTGTGTA
Statistics
Matches: 39, Mismatches: 9, Indels: 6
0.72 0.17 0.11
Matches are distributed among these distances:
25 2 0.05
26 28 0.72
27 2 0.05
28 7 0.18
ACGTcount: A:0.59, C:0.04, G:0.01, T:0.36
Consensus pattern (25 bp):
AATTCAAAAAATTTAAAAAATATAT
Found at i:16322712 original size:32 final size:32
Alignment explanation
Indices: 16322672--16322740 Score: 131
Period size: 32 Copynumber: 2.2 Consensus size: 32
16322662 AGGAGCTATT
16322672 AAAG-TATATGGACAAAATCATGAAAGGGCTA
1 AAAGTTATATGGACAAAATCATGAAAGGGCTA
16322703 AAAGTTATATGGACAAAATCATGAAAGGGCTA
1 AAAGTTATATGGACAAAATCATGAAAGGGCTA
16322735 AAAGTT
1 AAAGTT
16322741 GAATTATAGA
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 4 0.11
32 33 0.89
ACGTcount: A:0.48, C:0.09, G:0.22, T:0.22
Consensus pattern (32 bp):
AAAGTTATATGGACAAAATCATGAAAGGGCTA
Found at i:16324108 original size:18 final size:19
Alignment explanation
Indices: 16324081--16324137 Score: 62
Period size: 20 Copynumber: 3.0 Consensus size: 19
16324071 GGGATGACAA
16324081 GGATGAGAAAT-GGATATG
1 GGATGAGAAATGGGATATG
*
16324099 GGATGGGAAATGGGATATG
1 GGATGAGAAATGGGATATG
** *
16324118 AAATGACGAAACGGGATATG
1 GGATGA-GAAATGGGATATG
16324138 AATATTAAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
18 10 0.31
19 10 0.31
20 12 0.38
ACGTcount: A:0.39, C:0.04, G:0.39, T:0.19
Consensus pattern (19 bp):
GGATGAGAAATGGGATATG
Found at i:16328348 original size:46 final size:48
Alignment explanation
Indices: 16328229--16328348 Score: 133
Period size: 46 Copynumber: 2.6 Consensus size: 48
16328219 TGAGAGCCAA
* *
16328229 TGTAAGACCATGTCTGGGACATGGCATCAGCATTGAGACGAGTGCTAG
1 TGTAAGACCATGTTTGGGACATGGCATCAGCATCGAGACGAGTGCTAG
* * * *
16328277 TGTAAGA-CATTTTTGGTACAT-GCATCAGC-TACGAGATGTGT-C-AG
1 TGTAAGACCATGTTTGGGACATGGCATCAGCAT-CGAGACGAGTGCTAG
*
16328321 TGTAAAACCATGTTTGGGACATGGCATC
1 TGTAAGACCATGTTTGGGACATGGCATC
16328349 GGCACAGATA
Statistics
Matches: 60, Mismatches: 9, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
44 8 0.13
45 14 0.23
46 20 0.33
47 11 0.18
48 7 0.12
ACGTcount: A:0.28, C:0.17, G:0.28, T:0.28
Consensus pattern (48 bp):
TGTAAGACCATGTTTGGGACATGGCATCAGCATCGAGACGAGTGCTAG
Found at i:16329576 original size:21 final size:21
Alignment explanation
Indices: 16329550--16329605 Score: 112
Period size: 21 Copynumber: 2.7 Consensus size: 21
16329540 GTCAAAATGG
16329550 CCACACGGGCGTGTTGCCCTT
1 CCACACGGGCGTGTTGCCCTT
16329571 CCACACGGGCGTGTTGCCCTT
1 CCACACGGGCGTGTTGCCCTT
16329592 CCACACGGGCGTGT
1 CCACACGGGCGTGT
16329606 GCCTTATTTC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.11, C:0.38, G:0.30, T:0.21
Consensus pattern (21 bp):
CCACACGGGCGTGTTGCCCTT
Found at i:16333715 original size:30 final size:30
Alignment explanation
Indices: 16333671--16333739 Score: 95
Period size: 30 Copynumber: 2.3 Consensus size: 30
16333661 CAAAGATAAC
*
16333671 AAGAAAACC-GAATAAAGAAATCCAAGATA
1 AAGAAACCCAGAATAAAGAAATCCAAGATA
* * *
16333700 GAGAAACCCAGAATAAAGAGATCCAGGATA
1 AAGAAACCCAGAATAAAGAAATCCAAGATA
16333730 AAGAAACCCA
1 AAGAAACCCA
16333740 AGATACGATA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 7 0.21
30 27 0.79
ACGTcount: A:0.57, C:0.17, G:0.17, T:0.09
Consensus pattern (30 bp):
AAGAAACCCAGAATAAAGAAATCCAAGATA
Found at i:16333744 original size:15 final size:15
Alignment explanation
Indices: 16333682--16333744 Score: 65
Period size: 15 Copynumber: 4.2 Consensus size: 15
16333672 AGAAAACCGA
*
16333682 ATAAAGAAATCCAAG
1 ATAAAGAAACCCAAG
*
16333697 ATAGAGAAACCC-AG
1 ATAAAGAAACCCAAG
* * *
16333711 AATAAAGAGATCCAGG
1 -ATAAAGAAACCCAAG
16333727 ATAAAGAAACCCAAG
1 ATAAAGAAACCCAAG
16333742 ATA
1 ATA
16333745 CGATACTATG
Statistics
Matches: 37, Mismatches: 9, Indels: 4
0.74 0.18 0.08
Matches are distributed among these distances:
14 2 0.05
15 34 0.92
16 1 0.03
ACGTcount: A:0.56, C:0.16, G:0.17, T:0.11
Consensus pattern (15 bp):
ATAAAGAAACCCAAG
Found at i:16338219 original size:19 final size:19
Alignment explanation
Indices: 16338183--16338238 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 19
16338173 GGGCACAAAT
*
16338183 GTGCACACAAGAGCACCGAA
1 GTGCAAACAAG-GCACCGAA
16338203 GTGCAAACAAGGCACCGAA
1 GTGCAAACAAGGCACCGAA
*
16338222 GTGCATAACAGGGCACC
1 GTGCA-AACAAGGCACC
16338239 AATATGTAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 13 0.39
20 20 0.61
ACGTcount: A:0.38, C:0.29, G:0.27, T:0.07
Consensus pattern (19 bp):
GTGCAAACAAGGCACCGAA
Found at i:16348694 original size:48 final size:48
Alignment explanation
Indices: 16348637--16348753 Score: 164
Period size: 48 Copynumber: 2.4 Consensus size: 48
16348627 TGATCACTTT
* * *
16348637 AATATTAAATTAATATAAA-CTTATCAAGATAAATATTAGATTAAACTA
1 AATATTAAATTAATA-AAATATTATCAAAATAAATATTAAATTAAACTA
*
16348685 AATATTAAATTAATAAAATATTATCAAAATAAATATTAAATTAAATTA
1 AATATTAAATTAATAAAATATTATCAAAATAAATATTAAATTAAACTA
*
16348733 AATATTAAATTTATTAAAATA
1 AATATTAAA-TTAATAAAATA
16348754 ATTTTATTTT
Statistics
Matches: 62, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
47 3 0.05
48 49 0.79
49 10 0.16
ACGTcount: A:0.57, C:0.03, G:0.02, T:0.38
Consensus pattern (48 bp):
AATATTAAATTAATAAAATATTATCAAAATAAATATTAAATTAAACTA
Found at i:16348705 original size:16 final size:16
Alignment explanation
Indices: 16348684--16348753 Score: 65
Period size: 17 Copynumber: 4.3 Consensus size: 16
16348674 AGATTAAACT
16348684 AAATATTAAATTAATA
1 AAATATTAAATTAATA
16348700 AAATATTATCAA--AAT-
1 AAATATTA--AATTAATA
*
16348715 AAATATTAAATTAAATT
1 AAATATTAAATT-AATA
*
16348732 AAATATTAAATTTATTA
1 AAATATTAAA-TTAATA
16348749 AAATA
1 AAATA
16348754 ATTTTATTTT
Statistics
Matches: 45, Mismatches: 2, Indels: 13
0.75 0.03 0.22
Matches are distributed among these distances:
13 2 0.04
15 8 0.18
16 14 0.31
17 17 0.38
18 4 0.09
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (16 bp):
AAATATTAAATTAATA
Found at i:16348753 original size:17 final size:17
Alignment explanation
Indices: 16348666--16348743 Score: 90
Period size: 17 Copynumber: 4.8 Consensus size: 17
16348656 CTTATCAAGA
* *
16348666 TAAATATTAGATTAAAC
1 TAAATATTAAATTAAAT
16348683 TAAATATTAAATT-AAT
1 TAAATATTAAATTAAAT
* * *
16348699 AAAATATT--ATCAAAA
1 TAAATATTAAATTAAAT
16348714 TAAATATTAAATTAAAT
1 TAAATATTAAATTAAAT
16348731 TAAATATTAAATT
1 TAAATATTAAATT
16348744 TATTAAAATA
Statistics
Matches: 50, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
14 2 0.04
15 9 0.18
16 9 0.18
17 30 0.60
ACGTcount: A:0.58, C:0.03, G:0.01, T:0.38
Consensus pattern (17 bp):
TAAATATTAAATTAAAT
Found at i:16351364 original size:24 final size:25
Alignment explanation
Indices: 16351336--16351406 Score: 67
Period size: 25 Copynumber: 2.9 Consensus size: 25
16351326 ATATTGTTTG
16351336 GAAAGCCTTTGTGGCAAGTTATCTA
1 GAAAGCCTTTGTGGCAAGTTATCTA
* *
16351361 -AAAGACCTATGTGGCATA-TTGTCTA
1 GAAAG-CCTTTGTGGCA-AGTTATCTA
* *
16351386 GAAAG-CATTGTGGCGAGTTAT
1 GAAAGCCTTTGTGGCAAGTTAT
16351407 TTGAAAGGCC
Statistics
Matches: 36, Mismatches: 6, Indels: 9
0.71 0.12 0.18
Matches are distributed among these distances:
23 1 0.03
24 14 0.39
25 16 0.44
26 5 0.14
ACGTcount: A:0.30, C:0.14, G:0.25, T:0.31
Consensus pattern (25 bp):
GAAAGCCTTTGTGGCAAGTTATCTA
Found at i:16351405 original size:49 final size:50
Alignment explanation
Indices: 16351298--16351429 Score: 160
Period size: 49 Copynumber: 2.7 Consensus size: 50
16351288 AAAGCTTTTT
* * * * *
16351298 TGGCGAGTTATTTCAAAGGCCT-TGTAGCATATTGTTTGGAAAGCCTTTG
1 TGGCGAGTTATTTAAAAGGCCTATGTGGCATATTGTCTAGAAAGCCATTG
* * *
16351347 TGGCAAGTTATCTAAAAGACCTATGTGGCATATTGTCTAGAAAG-CATTG
1 TGGCGAGTTATTTAAAAGGCCTATGTGGCATATTGTCTAGAAAGCCATTG
* *
16351396 TGGCGAGTTATTTGAAAGGCCTATGTGACATATT
1 TGGCGAGTTATTTAAAAGGCCTATGTGGCATATT
16351430 ATTTGGGTAG
Statistics
Matches: 69, Mismatches: 13, Indels: 2
0.82 0.15 0.02
Matches are distributed among these distances:
49 51 0.74
50 18 0.26
ACGTcount: A:0.27, C:0.14, G:0.25, T:0.34
Consensus pattern (50 bp):
TGGCGAGTTATTTAAAAGGCCTATGTGGCATATTGTCTAGAAAGCCATTG
Found at i:16355199 original size:52 final size:52
Alignment explanation
Indices: 16355129--16355232 Score: 163
Period size: 52 Copynumber: 2.0 Consensus size: 52
16355119 TAAAATAAGG
* *
16355129 TACATAAAACACGCCCTTTAAAATAATCTTCCTAAAATTATCAAAATGTAAA
1 TACATAAAACACACCCTTTAAAACAATCTTCCTAAAATTATCAAAATGTAAA
* * *
16355181 TACATAAAAGACATCCTTTAAAACAATCTTTCTAAAATTATCAAAATGTAAA
1 TACATAAAACACACCCTTTAAAACAATCTTCCTAAAATTATCAAAATGTAAA
16355233 ATAACTTCTC
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
52 47 1.00
ACGTcount: A:0.49, C:0.17, G:0.04, T:0.30
Consensus pattern (52 bp):
TACATAAAACACACCCTTTAAAACAATCTTCCTAAAATTATCAAAATGTAAA
Found at i:16358072 original size:12 final size:12
Alignment explanation
Indices: 16358012--16358075 Score: 55
Period size: 12 Copynumber: 5.2 Consensus size: 12
16358002 AAACTTAATT
16358012 AATTTAATATTA
1 AATTTAATATTA
16358024 AA-TTAATA-TA
1 AATTTAATATTA
16358034 ATATTT-ATCAATGTA
1 A-ATTTAAT--AT-TA
16358049 AATATTAA-ATTA
1 AAT-TTAATATTA
16358061 AATTTAATATTA
1 AATTTAATATTA
16358073 AAT
1 AAT
16358076 CTATTAAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 18
0.70 0.00 0.30
Matches are distributed among these distances:
10 3 0.07
11 13 0.30
12 16 0.37
13 3 0.07
14 2 0.05
15 5 0.12
16 1 0.02
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (12 bp):
AATTTAATATTA
Found at i:16358081 original size:58 final size:61
Alignment explanation
Indices: 16358019--16358158 Score: 173
Period size: 63 Copynumber: 2.3 Consensus size: 61
16358009 ATTAATTTAA
* * *
16358019 TATTAAATTAATATAATATTTATC-A-ATG-TAAATATTAAATTAAATTTAATATTAAATC
1 TATTAAATTAATATAATATTTATCTACAAGATAAAAATTAAATTAAATTAAATATTAAATC
* *
16358077 TATTAAATTAATAGAATATAATTATCTACAAGATAAAAATTAAATTAAATTAAATATTAAATT
1 TATTAAATTAATATAATAT--TTATCTACAAGATAAAAATTAAATTAAATTAAATATTAAATC
*
16358140 TATTAAA--ATTATAATATTT
1 TATTAAATTAATATAATATTT
16358159 TTGAAATAGT
Statistics
Matches: 70, Mismatches: 7, Indels: 9
0.81 0.08 0.10
Matches are distributed among these distances:
58 18 0.26
59 2 0.03
60 5 0.07
61 9 0.13
62 2 0.03
63 34 0.49
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.43
Consensus pattern (61 bp):
TATTAAATTAATATAATATTTATCTACAAGATAAAAATTAAATTAAATTAAATATTAAATC
Found at i:16360917 original size:20 final size:21
Alignment explanation
Indices: 16360882--16360929 Score: 57
Period size: 19 Copynumber: 2.4 Consensus size: 21
16360872 TCTTTTTCAA
16360882 CAAAAATTACAAAATAATTT-T
1 CAAAAATTACAAAAT-ATTTAT
*
16360903 CAAAAATT-CATAATATTTAT
1 CAAAAATTACAAAATATTTAT
16360923 -AAAAATT
1 CAAAAATT
16360930 TTAAAATTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
19 11 0.44
20 6 0.24
21 8 0.32
ACGTcount: A:0.56, C:0.08, G:0.00, T:0.35
Consensus pattern (21 bp):
CAAAAATTACAAAATATTTAT
Found at i:16360938 original size:18 final size:18
Alignment explanation
Indices: 16360917--16360993 Score: 59
Period size: 17 Copynumber: 4.2 Consensus size: 18
16360907 AATTCATAAT
16360917 ATTTATAAAAATTTTAAA
1 ATTTATAAAAATTTTAAA
*** *
16360935 ATTTAT-ATTTTTTTTAA
1 ATTTATAAAAATTTTAAA
*
16360952 A-TTATAAAAATTCTAAAAA
1 ATTTATAAAAATT-T-TAAA
*
16360971 ATATATAAAGAATTTTAAA
1 ATTTATAAA-AATTTTAAA
16360990 ATTT
1 ATTT
16360994 TAATTTTTTT
Statistics
Matches: 42, Mismatches: 12, Indels: 9
0.67 0.19 0.14
Matches are distributed among these distances:
16 4 0.10
17 11 0.26
18 7 0.17
19 9 0.21
20 7 0.17
21 4 0.10
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (18 bp):
ATTTATAAAAATTTTAAA
Found at i:16360989 original size:21 final size:19
Alignment explanation
Indices: 16360950--16360990 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
16360940 TATTTTTTTT
16360950 AAATTATAAAAATTCTAAA
1 AAATTATAAAAATTCTAAA
*
16360969 AAATATATAAAGAATTTTAAA
1 AAAT-TATAAA-AATTCTAAA
16360990 A
1 A
16360991 TTTTAATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 4 0.21
20 6 0.32
21 9 0.47
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.32
Consensus pattern (19 bp):
AAATTATAAAAATTCTAAA
Found at i:16361517 original size:25 final size:23
Alignment explanation
Indices: 16361475--16361524 Score: 73
Period size: 25 Copynumber: 2.1 Consensus size: 23
16361465 GGAGGGAGAA
16361475 ATTTTTTTTAATATTTTATATTT
1 ATTTTTTTTAATATTTTATATTT
*
16361498 ATTTTTGTTCTAATTTTTTATATTT
1 ATTTTT-TT-TAATATTTTATATTT
16361523 AT
1 AT
16361525 AGTATTGCAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 6 0.25
24 2 0.08
25 16 0.67
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.72
Consensus pattern (23 bp):
ATTTTTTTTAATATTTTATATTT
Found at i:16363061 original size:28 final size:28
Alignment explanation
Indices: 16363021--16363076 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
16363011 AAAGCAGCAG
16363021 CCAGTCGCCCACCAAATGTATATCCCAA
1 CCAGTCGCCCACCAAATGTATATCCCAA
16363049 CCAGTCGCCCACCAAATGTATATCCCAA
1 CCAGTCGCCCACCAAATGTATATCCCAA
16363077 GCTCAGTCTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.32, C:0.39, G:0.11, T:0.18
Consensus pattern (28 bp):
CCAGTCGCCCACCAAATGTATATCCCAA
Found at i:16365791 original size:77 final size:77
Alignment explanation
Indices: 16365705--16365860 Score: 312
Period size: 77 Copynumber: 2.0 Consensus size: 77
16365695 CACTTTCATT
16365705 TGGTTTTTAAATGGGTTGGTAATGTTAGCCTCTTTTAGTTTCAAACATGTTGAATTTGGTTTTGT
1 TGGTTTTTAAATGGGTTGGTAATGTTAGCCTCTTTTAGTTTCAAACATGTTGAATTTGGTTTTGT
16365770 AAACAAGTAATA
66 AAACAAGTAATA
16365782 TGGTTTTTAAATGGGTTGGTAATGTTAGCCTCTTTTAGTTTCAAACATGTTGAATTTGGTTTTGT
1 TGGTTTTTAAATGGGTTGGTAATGTTAGCCTCTTTTAGTTTCAAACATGTTGAATTTGGTTTTGT
16365847 AAACAAGTAATA
66 AAACAAGTAATA
16365859 TG
1 TG
16365861 AGTTATTTCC
Statistics
Matches: 79, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
77 79 1.00
ACGTcount: A:0.27, C:0.08, G:0.21, T:0.44
Consensus pattern (77 bp):
TGGTTTTTAAATGGGTTGGTAATGTTAGCCTCTTTTAGTTTCAAACATGTTGAATTTGGTTTTGT
AAACAAGTAATA
Found at i:16384381 original size:13 final size:14
Alignment explanation
Indices: 16384363--16384396 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
16384353 TTTAAAATCC
16384363 AAAACCCTA-CTTT
1 AAAACCCTAGCTTT
16384376 AAAACCCTAGCTTT
1 AAAACCCTAGCTTT
16384390 -AAACCCT
1 AAAACCCT
16384397 TAAACACTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 16 0.80
14 4 0.20
ACGTcount: A:0.38, C:0.32, G:0.03, T:0.26
Consensus pattern (14 bp):
AAAACCCTAGCTTT
Found at i:16386706 original size:24 final size:24
Alignment explanation
Indices: 16386668--16386716 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
16386658 AGTATGTAGC
16386668 ATCATTCACAATAGTGGAATTCAT
1 ATCATTCACAATAGTGGAATTCAT
* *
16386692 ATCATTCATAGTAGTGGAATTCAT
1 ATCATTCACAATAGTGGAATTCAT
16386716 A
1 A
16386717 GCCTGACCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.35
Consensus pattern (24 bp):
ATCATTCACAATAGTGGAATTCAT
Found at i:16398784 original size:15 final size:15
Alignment explanation
Indices: 16398764--16398794 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
16398754 TCTGGGTGGA
*
16398764 AAAAAAGGAAAAAAG
1 AAAAAAGAAAAAAAG
16398779 AAAAAAGAAAAAAAG
1 AAAAAAGAAAAAAAG
16398794 A
1 A
16398795 GTGAAGAATG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (15 bp):
AAAAAAGAAAAAAAG
Found at i:16398794 original size:8 final size:8
Alignment explanation
Indices: 16398762--16398794 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
16398752 ATTCTGGGTG
16398762 GAAAAAAA
1 GAAAAAAA
*
16398770 GGAAAAAA
1 GAAAAAAA
16398778 G-AAAAAA
1 GAAAAAAA
16398785 GAAAAAAA
1 GAAAAAAA
16398793 GA
1 GA
16398795 GTGAAGAATG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
7 7 0.30
8 16 0.70
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (8 bp):
GAAAAAAA
Found at i:16399300 original size:44 final size:44
Alignment explanation
Indices: 16399251--16399342 Score: 175
Period size: 44 Copynumber: 2.1 Consensus size: 44
16399241 GACATAATTT
*
16399251 TTAGAACTAAATAAGTGTTAAATTTATATTATAAAATTGTTATG
1 TTAGAACTAAATAAATGTTAAATTTATATTATAAAATTGTTATG
16399295 TTAGAACTAAATAAATGTTAAATTTATATTATAAAATTGTTATG
1 TTAGAACTAAATAAATGTTAAATTTATATTATAAAATTGTTATG
16399339 TTAG
1 TTAG
16399343 TAAAATTTAA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 47 1.00
ACGTcount: A:0.43, C:0.02, G:0.11, T:0.43
Consensus pattern (44 bp):
TTAGAACTAAATAAATGTTAAATTTATATTATAAAATTGTTATG
Found at i:16399335 original size:22 final size:22
Alignment explanation
Indices: 16399266--16399336 Score: 67
Period size: 22 Copynumber: 3.2 Consensus size: 22
16399256 ACTAAATAAG
16399266 TGTTAAATTTATATTATAAAAT
1 TGTTAAATTTATATTATAAAAT
* * *
16399288 TGTT--ATGTTAGAACTA-AATAAA
1 TGTTAAAT-TTA-TATTATAA-AAT
16399310 TGTTAAATTTATATTATAAAAT
1 TGTTAAATTTATATTATAAAAT
16399332 TGTTA
1 TGTTA
16399337 TGTTAGTAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 12
0.67 0.11 0.22
Matches are distributed among these distances:
20 2 0.05
21 5 0.14
22 23 0.62
23 5 0.14
24 2 0.05
ACGTcount: A:0.44, C:0.01, G:0.08, T:0.46
Consensus pattern (22 bp):
TGTTAAATTTATATTATAAAAT
Found at i:16400268 original size:22 final size:24
Alignment explanation
Indices: 16400242--16400287 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 24
16400232 TACTTATTTC
16400242 ATAATTT-TA-ATTTTTTAATATA
1 ATAATTTATATATTTTTTAATATA
16400264 ATAATTTATATTATTTTTTAATAT
1 ATAATTTATA-TATTTTTTAATAT
16400288 TTTGAGATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 7 0.33
23 2 0.10
25 12 0.57
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (24 bp):
ATAATTTATATATTTTTTAATATA
Found at i:16401293 original size:13 final size:13
Alignment explanation
Indices: 16401275--16401304 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
16401265 TAGGTGGTTT
*
16401275 GCATATTGAGCTC
1 GCATATCGAGCTC
16401288 GCATATCGAGCTC
1 GCATATCGAGCTC
16401301 GCAT
1 GCAT
16401305 GATATTGAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.23, C:0.27, G:0.23, T:0.27
Consensus pattern (13 bp):
GCATATCGAGCTC
Found at i:16401712 original size:13 final size:13
Alignment explanation
Indices: 16401694--16401757 Score: 74
Period size: 13 Copynumber: 4.8 Consensus size: 13
16401684 TGTTTGGCAA
16401694 TGCTTTTAAAAAG
1 TGCTTTTAAAAAG
16401707 TGCTTTTAAAAAG
1 TGCTTTTAAAAAG
* **
16401720 TGCTGTGGAAAAG
1 TGCTTTTAAAAAG
* *
16401733 TGCTTTTGAGAAG
1 TGCTTTTAAAAAG
16401746 TGCTTTTGAAAA
1 TGCTTTT-AAAA
16401758 TTTTAGGTGT
Statistics
Matches: 42, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
13 40 0.95
14 2 0.05
ACGTcount: A:0.33, C:0.08, G:0.23, T:0.36
Consensus pattern (13 bp):
TGCTTTTAAAAAG
Found at i:16401756 original size:26 final size:26
Alignment explanation
Indices: 16401694--16401757 Score: 83
Period size: 26 Copynumber: 2.5 Consensus size: 26
16401684 TGTTTGGCAA
*
16401694 TGCTTTTAAAAAGTGCTTTTAAAAAG
1 TGCTTTTGAAAAGTGCTTTTAAAAAG
* * * *
16401720 TGCTGTGGAAAAGTGCTTTTGAGAAG
1 TGCTTTTGAAAAGTGCTTTTAAAAAG
16401746 TGCTTTTGAAAA
1 TGCTTTTGAAAA
16401758 TTTTAGGTGT
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.33, C:0.08, G:0.23, T:0.36
Consensus pattern (26 bp):
TGCTTTTGAAAAGTGCTTTTAAAAAG
Found at i:16403917 original size:73 final size:72
Alignment explanation
Indices: 16403808--16404041 Score: 337
Period size: 72 Copynumber: 3.2 Consensus size: 72
16403798 ATATATTAAT
** * *
16403808 AACTATTGATAAAACTA-ATTTA-GTATAAATAAGTAGAGCATAAATTCAATATCCCAAAGACCA
1 AACTATTGATAAAACTAGA-TTACACATAAATAAGTAGAACATAAATTCAATAT-CCAAAAACCA
16403871 AACATAAAC
64 AACATAAAC
* * * *
16403880 AACTATTAATAAAAGTAGATTACACATAAATAAGTAGAACATAAATTCAATATTCAAAAACTAAA
1 AACTATTGATAAAACTAGATTACACATAAATAAGTAGAACATAAATTCAATATCCAAAAACCAAA
16403945 CATAAAC
66 CATAAAC
* *
16403952 AACCATTGATAAAACTAGATTACACATAAATAAGTAGAACATAAGTTCAATATCCAAAAACCAAA
1 AACTATTGATAAAACTAGATTACACATAAATAAGTAGAACATAAATTCAATATCCAAAAACCAAA
*
16404017 CATAAAT
66 CATAAAC
16404024 AACTATTGATAAAACTAG
1 AACTATTGATAAAACTAG
16404042 TTTAGCATTT
Statistics
Matches: 144, Mismatches: 16, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
72 116 0.81
73 28 0.19
ACGTcount: A:0.54, C:0.15, G:0.07, T:0.24
Consensus pattern (72 bp):
AACTATTGATAAAACTAGATTACACATAAATAAGTAGAACATAAATTCAATATCCAAAAACCAAA
CATAAAC
Found at i:16404491 original size:18 final size:18
Alignment explanation
Indices: 16404470--16404517 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
16404460 TCCATCAATT
*
16404470 TGAACATCATTTGAAATG
1 TGAACATCATTTAAAATG
16404488 TGAACATCATTTAAAATG
1 TGAACATCATTTAAAATG
16404506 TGAACATCATTT
1 TGAACATCATTT
16404518 CTCACATTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.35
Consensus pattern (18 bp):
TGAACATCATTTAAAATG
Found at i:16405674 original size:19 final size:19
Alignment explanation
Indices: 16405650--16405686 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
16405640 GCTATTAATA
*
16405650 TAAAAGGTGCTATATCTAT
1 TAAAAGGTCCTATATCTAT
*
16405669 TAAAAGGTCCTGTATCTA
1 TAAAAGGTCCTATATCTA
16405687 AAACATAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Consensus pattern (19 bp):
TAAAAGGTCCTATATCTAT
Found at i:16410678 original size:13 final size:14
Alignment explanation
Indices: 16410662--16410697 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
16410652 CAATCTCATA
16410662 TCTCAATTTCAA-T
1 TCTCAATTTCAATT
16410675 TCTCAA-TTCAATT
1 TCTCAATTTCAATT
16410688 TCTC-ATTTCA
1 TCTCAATTTCA
16410698 TTCCAATAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 6 0.29
13 15 0.71
ACGTcount: A:0.28, C:0.25, G:0.00, T:0.47
Consensus pattern (14 bp):
TCTCAATTTCAATT
Found at i:16410687 original size:18 final size:19
Alignment explanation
Indices: 16410649--16410689 Score: 59
Period size: 18 Copynumber: 2.2 Consensus size: 19
16410639 TGGTTCATGT
16410649 TTTCAATCTCATATCTCAA
1 TTTCAATCTCATATCTCAA
16410668 TTTCAATTCTCA-AT-TCAA
1 TTTCAA-TCTCATATCTCAA
16410686 TTTC
1 TTTC
16410690 TCATTTCATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 8 0.38
20 5 0.24
ACGTcount: A:0.29, C:0.24, G:0.00, T:0.46
Consensus pattern (19 bp):
TTTCAATCTCATATCTCAA
Found at i:16410879 original size:39 final size:38
Alignment explanation
Indices: 16410812--16410946 Score: 101
Period size: 39 Copynumber: 3.4 Consensus size: 38
16410802 ACCAATATGG
* * *
16410812 CACCCAGTGCCTCATCGGATAGTTCGAAGCAATATTTGA
1 CACCCAGTGCCTCATCGGCTAG-CCGAAGAAATATTTGA
* * * *
16410851 CACCCAGTGTCTCATCGGCCTAGCCGAAGTAA-AGTTGG
1 CACCCAGTGCCTCATCGG-CTAGCCGAAGAAATATTTGA
* * * * *
16410889 TACCCAGTACCTCATCGAATCTATCCGAAGAAATATAGTGA
1 CACCCAGTGCCTCATCG--GCTAGCCGAAGAAATAT-TTGA
*
16410930 CACCCAGTGTCTCATCG
1 CACCCAGTGCCTCATCG
16410947 ACTCGAGGTC
Statistics
Matches: 73, Mismatches: 18, Indels: 8
0.74 0.18 0.08
Matches are distributed among these distances:
38 18 0.25
39 35 0.48
40 4 0.05
41 16 0.22
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.24
Consensus pattern (38 bp):
CACCCAGTGCCTCATCGGCTAGCCGAAGAAATATTTGA
Found at i:16411212 original size:18 final size:19
Alignment explanation
Indices: 16411186--16411224 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
16411176 TTTCAATTCA
16411186 ATTCAAATAATCAATATAT
1 ATTCAAATAATCAATATAT
*
16411205 ATTC-AATATTCAATATAT
1 ATTCAAATAATCAATATAT
16411223 AT
1 AT
16411225 ATCTATATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.41
Consensus pattern (19 bp):
ATTCAAATAATCAATATAT
Found at i:16411262 original size:15 final size:15
Alignment explanation
Indices: 16411242--16411279 Score: 76
Period size: 15 Copynumber: 2.5 Consensus size: 15
16411232 TATATACGCC
16411242 AATTCAATCAATATA
1 AATTCAATCAATATA
16411257 AATTCAATCAATATA
1 AATTCAATCAATATA
16411272 AATTCAAT
1 AATTCAAT
16411280 AATTTCATCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.34
Consensus pattern (15 bp):
AATTCAATCAATATA
Found at i:16412566 original size:5 final size:5
Alignment explanation
Indices: 16412556--16412612 Score: 62
Period size: 5 Copynumber: 11.0 Consensus size: 5
16412546 TTACTTATTT
* *
16412556 ATATA ATATAA TATATA ATATA ATATA CTATA ATATA ATAATA ATTTA
1 ATATA ATAT-A -ATATA ATATA ATATA ATATA ATATA AT-ATA ATATA
16412604 ATAT- ATATA
1 ATATA ATATA
16412613 TTTTAACACA
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
4 4 0.09
5 29 0.66
6 7 0.16
7 4 0.09
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (5 bp):
ATATA
Found at i:16412572 original size:12 final size:12
Alignment explanation
Indices: 16412555--16412610 Score: 69
Period size: 12 Copynumber: 4.5 Consensus size: 12
16412545 TTTACTTATT
16412555 TATATAATATAA
1 TATATAATATAA
16412567 TATATAATATAATA
1 TATATAATAT-A-A
16412581 TACTATAATATAA
1 TA-TATAATATAA
*
16412594 TA-ATAATTTAA
1 TATATAATATAA
16412605 TATATA
1 TATATA
16412611 TATTTTAACA
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
11 10 0.26
12 13 0.33
13 4 0.10
14 4 0.10
15 8 0.21
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (12 bp):
TATATAATATAA
Found at i:16412625 original size:26 final size:26
Alignment explanation
Indices: 16412557--16412612 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
16412547 TACTTATTTA
*
16412557 TATAATATAATATATAATATAATATAC
1 TATAATATAACA-ATAATATAATATAC
* *
16412584 TATAATATAATAATAATTTAATATA-
1 TATAATATAACAATAATATAATATAC
16412609 TATA
1 TATA
16412613 TTTTAACACA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
25 4 0.14
26 12 0.43
27 12 0.43
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (26 bp):
TATAATATAACAATAATATAATATAC
Found at i:16420330 original size:15 final size:14
Alignment explanation
Indices: 16420292--16420321 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
16420282 GGGCCCATAC
*
16420292 AAAAACTAAAACCA
1 AAAAAATAAAACCA
16420306 AAAAAATAAAACCA
1 AAAAAATAAAACCA
16420320 AA
1 AA
16420322 TTAATTAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.77, C:0.17, G:0.00, T:0.07
Consensus pattern (14 bp):
AAAAAATAAAACCA
Found at i:16421177 original size:19 final size:20
Alignment explanation
Indices: 16421140--16421177 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
16421130 TGTTTTTTTT
*
16421140 AAGTTTTTCAAACAGAAATG
1 AAGTTTTTCAAACAAAAATG
16421160 AAGTTTTTCAAA-AAAAAT
1 AAGTTTTTCAAACAAAAAT
16421178 TTGGTTTTTA
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:0.50, C:0.08, G:0.11, T:0.32
Consensus pattern (20 bp):
AAGTTTTTCAAACAAAAATG
Found at i:16425801 original size:27 final size:27
Alignment explanation
Indices: 16425577--16425799 Score: 295
Period size: 27 Copynumber: 8.3 Consensus size: 27
16425567 GGGGAAAAAT
* * * *
16425577 GGTAATTTTACCCCACAAGGGTATCTC
1 GGTAATTCTACCCTACAGGGGTATTTC
16425604 GGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
16425631 GGT-ATTCCTACCCTACAAGGGTATTTC
1 GGTAATT-CTACCCTACAGGGGTATTTC
* *
16425658 GGTAATTCTATCCTATAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
16425685 GGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
** * *
16425712 AATAATTCTATCCTATAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
16425739 GGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* * *
16425766 GGTAATTTTACCCTATAGGGGTGTTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
16425793 GATAATT
1 GGTAATT
16425800 TTGTAAATCG
Statistics
Matches: 172, Mismatches: 22, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
26 3 0.02
27 166 0.97
28 3 0.02
ACGTcount: A:0.24, C:0.20, G:0.21, T:0.36
Consensus pattern (27 bp):
GGTAATTCTACCCTACAGGGGTATTTC
Found at i:16425823 original size:81 final size:81
Alignment explanation
Indices: 16425565--16425826 Score: 222
Period size: 81 Copynumber: 3.2 Consensus size: 81
16425555 TTTAACACCC
* * * * * *
16425565 TAGGGGAAAAATGGTAATTTTACCCCACAAGGGTATCTCGGTAATTCTACCCTACAGGGGTATTT
1 TAGGGGTAAAACGGTAATTCTACCCTACAGGGGTATTTCGGTAATTCTACCCTACAGGGGTATTT
** * **
16425630 CGGT-ATTCCTACCCTA
66 CAATAATT-CTATCAAA
* * *** * *
16425646 CAAGGGTATTTCGGTAATTCTATCCTATAGGGGTATTTCGGTAATTCTACCCTACAGGGGTATTT
1 TAGGGGTAAAACGGTAATTCTACCCTACAGGGGTATTTCGGTAATTCTACCCTACAGGGGTATTT
**
16425711 CAATAATTCTATCCTA
66 CAATAATTCTATCAAA
*** * * *
16425727 TAGGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCGGTAATTTTACCCTATAGGGGTGTTT
1 TAGGGGTAAAACGGTAATTCTACCCTACAGGGGTATTTCGGTAATTCTACCCTACAGGGGTATTT
* * *
16425792 CGATAATTTTGT-AAA
66 CAATAATTCTATCAAA
*
16425807 TCGAGGGTAAAACGGTAATT
1 TAG-GGGTAAAACGGTAATT
16425827 TTGTAAATCG
Statistics
Matches: 147, Mismatches: 32, Indels: 4
0.80 0.17 0.02
Matches are distributed among these distances:
80 3 0.02
81 141 0.96
82 3 0.02
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.34
Consensus pattern (81 bp):
TAGGGGTAAAACGGTAATTCTACCCTACAGGGGTATTTCGGTAATTCTACCCTACAGGGGTATTT
CAATAATTCTATCAAA
Found at i:16425850 original size:27 final size:27
Alignment explanation
Indices: 16425820--16426069 Score: 240
Period size: 27 Copynumber: 9.3 Consensus size: 27
16425810 AGGGTAAAAC
** *
16425820 GGTAATTTTGTAAATCGGAGGTACTTT
1 GGTAATTTTACAAATCGGAGGTATTTT
* * *
16425847 GGTAATTTTACAAGTTGAAGGTATTTT
1 GGTAATTTTACAAATCGGAGGTATTTT
* *
16425874 AGTAATTTTACAAATCGG-GGTATTTC
1 GGTAATTTTACAAATCGGAGGTATTTT
* * *
16425900 AGTAATTTTTCAAATCGGAGGTATTTC
1 GGTAATTTTACAAATCGGAGGTATTTT
* *
16425927 GGTAATTTTACAAATCGGGGGTATTTC
1 GGTAATTTTACAAATCGGAGGTATTTT
* *
16425954 GATAATTTTACAAATCAGG-GGTAATTT
1 GGTAATTTTACAAATC-GGAGGTATTTT
*
16425981 GGTAATTTTACAAACCAGG-GGTATTTT
1 GGTAATTTTACAAATC-GGAGGTATTTT
* **
16426008 GGTAATTTTATAAA-CCAAGGGTATTTT
1 GGTAATTTTACAAATCGGA-GGTATTTT
* *
16426035 GGTAATTTTGCTAATC-GAGGGTATTTT
1 GGTAATTTTACAAATCGGA-GGTATTTT
16426062 GGTAATTT
1 GGTAATTT
16426070 GGTAAACTAA
Statistics
Matches: 190, Mismatches: 28, Indels: 10
0.83 0.12 0.04
Matches are distributed among these distances:
26 25 0.13
27 162 0.85
28 3 0.02
ACGTcount: A:0.29, C:0.08, G:0.22, T:0.40
Consensus pattern (27 bp):
GGTAATTTTACAAATCGGAGGTATTTT
Found at i:16425985 original size:54 final size:53
Alignment explanation
Indices: 16425783--16426069 Score: 213
Period size: 54 Copynumber: 5.3 Consensus size: 53
16425773 TTACCCTATA
* ** *** **
16425783 GGGGTGTTTCGATAATTTTGTAAATCGAGGGTAAAACGGTAATTTTGTAAATCG
1 GGGGTATTTCGATAATTTTACAAATCG-GGGTAATTTGGTAATTTTACAAATCG
* * * * * * *
16425837 GAGGTACTTT-GGTAATTTTACAAGTTGAAGGTATTTTAGTAATTTTACAAATC-
1 GGGGTA-TTTCGATAATTTTACAAATCG-GGGTAATTTGGTAATTTTACAAATCG
*
16425890 GGGGTATTTC-AGTAATTTTTCAAATCGGAGGT-ATTTCGGTAATTTTACAAATCG
1 GGGGTATTTCGA-TAATTTTACAAATCGG-GGTAATTT-GGTAATTTTACAAATCG
* *
16425944 GGGGTATTTCGATAATTTTACAAATCAGGGGTAATTTGGTAATTTTACAAACCA
1 GGGGTATTTCGATAATTTTACAAATC-GGGGTAATTTGGTAATTTTACAAATCG
* * * * * * * *
16425998 GGGGTATTTTGGTAATTTTATAAACCAAGGGTATTTTGGTAATTTTGCTAATCG
1 GGGGTATTTCGATAATTTTACAAATC-GGGGTAATTTGGTAATTTTACAAATCG
* * *
16426052 AGGGTATTTTGGTAATTT
1 GGGGTATTTCGATAATTT
16426070 GGTAAACTAA
Statistics
Matches: 187, Mismatches: 37, Indels: 18
0.77 0.15 0.07
Matches are distributed among these distances:
52 6 0.03
53 35 0.19
54 136 0.73
55 10 0.05
ACGTcount: A:0.29, C:0.08, G:0.23, T:0.39
Consensus pattern (53 bp):
GGGGTATTTCGATAATTTTACAAATCGGGGTAATTTGGTAATTTTACAAATCG
Found at i:16426030 original size:81 final size:80
Alignment explanation
Indices: 16425758--16426069 Score: 235
Period size: 81 Copynumber: 3.9 Consensus size: 80
16425748 ACCCTACAGG
* ** ***
16425758 GGTATTTCGGTAATTTTAC---CCTATAGGGGTGTTTCGATAATTTTGTAAATCGAGGGTAAAAC
1 GGTATTTCGGTAATTTTACAAACC-A-A-GGGTATTTCGATAATTTTACAAATCG-GGGTAATTT
** *
16425820 GGTAATTTTGTAAATCGGA
62 GGTAATTTTACAAACCGGA
*** *
16425839 GGTACTTT-GGTAATTTTACAAGTTGAA-GGTATTT-TAGTAATTTTACAAATCGGGGT-ATTTC
1 GGTA-TTTCGGTAATTTTACAA-ACCAAGGGTATTTCGA-TAATTTTACAAATCGGGGTAATTT-
* * *
16425900 AGTAATTTTTCAAATCGGA
62 GGTAATTTTACAAACCGGA
* **
16425919 GGTATTTCGGTAATTTTACAAATCGGGGGTATTTCGATAATTTTACAAATCAGGGGTAATTTGGT
1 GGTATTTCGGTAATTTTACAAACCAAGGGTATTTCGATAATTTTACAAATC-GGGGTAATTTGGT
16425984 AATTTTACAAACCAGG-
65 AATTTTACAAACC-GGA
* * * * * * *
16426000 GGTATTTTGGTAATTTTATAAACCAAGGGTATTTTGGTAATTTTGCTAATCGAGGGTATTTTGGT
1 GGTATTTCGGTAATTTTACAAACCAAGGGTATTTCGATAATTTTACAAATCG-GGGTAATTTGGT
16426065 AATTT
65 AATTT
16426070 GGTAAACTAA
Statistics
Matches: 187, Mismatches: 30, Indels: 28
0.76 0.12 0.11
Matches are distributed among these distances:
79 5 0.03
80 60 0.32
81 111 0.59
82 9 0.05
83 1 0.01
84 1 0.01
ACGTcount: A:0.29, C:0.09, G:0.22, T:0.40
Consensus pattern (80 bp):
GGTATTTCGGTAATTTTACAAACCAAGGGTATTTCGATAATTTTACAAATCGGGGTAATTTGGTA
ATTTTACAAACCGGA
Found at i:16430881 original size:27 final size:26
Alignment explanation
Indices: 16430833--16430892 Score: 75
Period size: 27 Copynumber: 2.3 Consensus size: 26
16430823 GCGAGGCTGC
*
16430833 CAGATATTGTGACAAAGTCACCAGATA
1 CAGATATTGTGACAAAGCCACCAGA-A
* * *
16430860 CAGATATTGTGGCTAGGCCACCAGAA
1 CAGATATTGTGACAAAGCCACCAGAA
16430886 CAGATAT
1 CAGATAT
16430893 ATATATAATT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 8 0.28
27 21 0.72
ACGTcount: A:0.37, C:0.20, G:0.22, T:0.22
Consensus pattern (26 bp):
CAGATATTGTGACAAAGCCACCAGAA
Found at i:16431606 original size:27 final size:27
Alignment explanation
Indices: 16431576--16431825 Score: 331
Period size: 27 Copynumber: 9.3 Consensus size: 27
16431566 GGGGAAAAAT
* * * *
16431576 GGTAATTTTACCCCACAAGGGTATCTC
1 GGTAATTCTACCCTACAGGGGTATTTC
16431603 GGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
16431630 GGT-ATTCCTACCCTACAAGGGTATTTC
1 GGTAATT-CTACCCTACAGGGGTATTTC
*
16431657 GGTAATTCTATCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
16431684 GGTAATTCTACCCTATAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
** *
16431711 AATAATTCTACCCTACAGGGGTATTTT
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
16431738 GGTAATTTTACCCTATAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
16431765 GGTAATTCTACCCTACAGGGATATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
** * *
16431792 AATAATTCTACCCTATAGGGGTGTTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
16431819 GGTAATT
1 GGTAATT
16431826 TTGTAAATCG
Statistics
Matches: 193, Mismatches: 28, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
26 3 0.02
27 187 0.97
28 3 0.02
ACGTcount: A:0.24, C:0.20, G:0.20, T:0.36
Consensus pattern (27 bp):
GGTAATTCTACCCTACAGGGGTATTTC
Found at i:16431840 original size:27 final size:26
Alignment explanation
Indices: 16431809--16432154 Score: 160
Period size: 27 Copynumber: 12.9 Consensus size: 26
16431799 CTACCCTATA
*
16431809 GGGGTGTTTCGGTAATTTTGTAAATC
1 GGGGTATTTCGGTAATTTTGTAAATC
*** *
16431835 GAGGGTAAAACTGTAATTTTGTAAATC
1 G-GGGTATTTCGGTAATTTTGTAAATC
** *
16431862 GGGGTACTTT-GGTAATTTTACAAGTC
1 GGGGTA-TTTCGGTAATTTTGTAAATC
** ** **
16431888 GAAAGTATTTTAGTAATTTTACAAATC
1 G-GGGTATTTCGGTAATTTTGTAAATC
* **
16431915 GGGGTATTTCAGTAATTTTACAAATC
1 GGGGTATTTCGGTAATTTTGTAAATC
** * **
16431941 AGATGTATTTCGATAATTTTACAAATC
1 -GGGGTATTTCGGTAATTTTGTAAATC
**
16431968 AGGGGTATTTCGGTAATTTTACAAATC
1 -GGGGTATTTCGGTAATTTTGTAAATC
* ** *
16431995 AGGGGTAATTT-GATAATTTTACAAACC
1 -GGGGT-ATTTCGGTAATTTTGTAAATC
* ** *
16432022 AGGGGTATTTTGGTAATTTTACAAACTA
1 -GGGGTATTTCGGTAATTTTGTAAA-TC
**
16432050 GGGGTATTTTTGTAATTTTGCT-AATC
1 GGGGTATTTCGGTAATTTTG-TAAATC
* * *
16432076 GAGGGTATTTTGGTAATTTTTTTAATC
1 G-GGGTATTTCGGTAATTTTGTAAATC
* *
16432103 AAGGGTATTTTGGTAATTTTGCT-AATC
1 -GGGGTATTTCGGTAATTTTG-TAAATC
* * *
16432130 GAGGGTATTTTGATAATTTGGTAAA
1 G-GGGTATTTCGGTAATTTTGTAAA
16432155 CTAAAGTATT
Statistics
Matches: 263, Mismatches: 42, Indels: 29
0.79 0.13 0.09
Matches are distributed among these distances:
26 52 0.20
27 206 0.78
28 5 0.02
ACGTcount: A:0.30, C:0.08, G:0.21, T:0.41
Consensus pattern (26 bp):
GGGGTATTTCGGTAATTTTGTAAATC
Found at i:16431990 original size:54 final size:52
Alignment explanation
Indices: 16431848--16432095 Score: 234
Period size: 54 Copynumber: 4.6 Consensus size: 52
16431838 GGTAAAACTG
** * *
16431848 TAATTTTGTAAATCGGGGTACTTT-GGTAATTTTACAAGTC-GAAAGTATTTTA
1 TAATTTTACAAATCGGGGTA-TTTCGGTAATTTTACAAATCAG-AAGTATTTGA
* *
16431900 GTAATTTTACAAATCGGGGTATTTCAGTAATTTTACAAATCAGATGTATTTCGA
1 -TAATTTTACAAATCGGGGTATTTCGGTAATTTTACAAATCAGAAGTATTT-GA
**
16431954 TAATTTTACAAATCAGGGGTATTTCGGTAATTTTACAAATCAGGGGTAATTTGA
1 TAATTTTACAAATC-GGGGTATTTCGGTAATTTTACAAATCAGAAGT-ATTTGA
* * **
16432008 TAATTTTACAAACCAGGGGTATTTTGGTAATTTTACAAA-CTAGGGGTATTTTTG-
1 TAATTTTACAAATC-GGGGTATTTCGGTAATTTTACAAATC-AGAAGTA--TTTGA
* * *
16432062 TAATTTTGCTAATCGAGGGTATTTTGGTAATTTT
1 TAATTTTACAAATCG-GGGTATTTCGGTAATTTT
16432096 TTTAATCAAG
Statistics
Matches: 172, Mismatches: 14, Indels: 17
0.85 0.07 0.08
Matches are distributed among these distances:
52 3 0.02
53 56 0.33
54 105 0.61
55 8 0.05
ACGTcount: A:0.31, C:0.09, G:0.19, T:0.41
Consensus pattern (52 bp):
TAATTTTACAAATCGGGGTATTTCGGTAATTTTACAAATCAGAAGTATTTGA
Found at i:16432042 original size:81 final size:80
Alignment explanation
Indices: 16431848--16432148 Score: 286
Period size: 81 Copynumber: 3.8 Consensus size: 80
16431838 GGTAAAACTG
** * * ** *
16431848 TAATTTTGTAAATC-GGGGTACTTTGGTAATTTTACAAGTCGAAAGTATTTTAGTAATTTTACAA
1 TAATTTTACAAATCAGGGGTATTTTGGTAATTTTACAAATCGAGGGTATTTTGGTAATTTTACAA
*
16431912 ATCGGGGT-ATTTCA
66 ATCGGGGTAATTTGA
** * * *
16431926 GTAATTTTACAAATCAGATGTATTTCGATAATTTTACAAATC-AGGGGTATTTCGGTAATTTTAC
1 -TAATTTTACAAATCAGGGGTATTTTGGTAATTTTACAAATCGA-GGGTATTTTGGTAATTTTAC
16431990 AAATCAGGGGTAATTTGA
64 AAATC-GGGGTAATTTGA
* * * * *
16432008 TAATTTTACAAACCAGGGGTATTTTGGTAATTTTACAAA-CTAGGGGTATTTTTGTAATTTTGCT
1 TAATTTTACAAATCAGGGGTATTTTGGTAATTTTACAAATCGA-GGGTATTTTGGTAATTTTACA
* *
16432072 AATCGAGGGTATTTTGG
65 AATCG-GGGTAATTTGA
*** * * * *
16432089 TAATTTTTTTAATCAAGGGTATTTTGGTAATTTTGCTAATCGAGGGTATTTTGATAATTT
1 TAATTTTACAAATCAGGGGTATTTTGGTAATTTTACAAATCGAGGGTATTTTGGTAATTT
16432149 GGTAAACTAA
Statistics
Matches: 181, Mismatches: 34, Indels: 12
0.80 0.15 0.05
Matches are distributed among these distances:
79 13 0.07
80 43 0.24
81 118 0.65
82 7 0.04
ACGTcount: A:0.30, C:0.08, G:0.20, T:0.42
Consensus pattern (80 bp):
TAATTTTACAAATCAGGGGTATTTTGGTAATTTTACAAATCGAGGGTATTTTGGTAATTTTACAA
ATCGGGGTAATTTGA
Found at i:16432109 original size:54 final size:55
Alignment explanation
Indices: 16431847--16432148 Score: 207
Period size: 54 Copynumber: 5.6 Consensus size: 55
16431837 GGGTAAAACT
* * * * *
16431847 GTAATTTTG-TAAATCG-GGGTACTTTGGTAA-TTTTACAAGTCGAA-AGTATTTTA
1 GTAATTTTGCT-AATCGAGGGTATTTTGGTAATTTTTACAA-ACTAAGGGTATTTTG
* * ** * * *
16431900 GTAATTTTACAAATCG-GGGTATTTCAGTAA-TTTTACAAA-TCAGATGTATTTCG
1 GTAATTTTGCTAATCGAGGGTATTTTGGTAATTTTTACAAACTAAG-GGTATTTTG
* * * * * *
16431953 ATAATTTTACAAATC-AGGGGTATTTCGGTAA-TTTTACAAA-TCAGGGGTAATTTG
1 GTAATTTTGCTAATCGA-GGGTATTTTGGTAATTTTTACAAACT-AAGGGTATTTTG
* * * * * *
16432007 ATAATTTTAC-AAACCAGGGGTATTTTGGTAA-TTTTACAAACTAGGGGTATTTTT
1 GTAATTTTGCTAATCGA-GGGTATTTTGGTAATTTTTACAAACTAAGGGTATTTTG
** *
16432061 GTAATTTTGCTAATCGAGGGTATTTTGGTAATTTTTTTAATC-AAGGGTATTTTG
1 GTAATTTTGCTAATCGAGGGTATTTTGGTAATTTTTACAAACTAAGGGTATTTTG
*
16432115 GTAATTTTGCTAATCGAGGGTATTTTGATAATTT
1 GTAATTTTGCTAATCGAGGGTATTTTGGTAATTT
16432149 GGTAAACTAA
Statistics
Matches: 207, Mismatches: 32, Indels: 19
0.80 0.12 0.07
Matches are distributed among these distances:
51 1 0.00
53 55 0.27
54 138 0.67
55 13 0.06
ACGTcount: A:0.30, C:0.08, G:0.20, T:0.42
Consensus pattern (55 bp):
GTAATTTTGCTAATCGAGGGTATTTTGGTAATTTTTACAAACTAAGGGTATTTTG
Found at i:16443157 original size:16 final size:16
Alignment explanation
Indices: 16443136--16443171 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
16443126 CTAATTTAAT
*
16443136 ATAAAATCAAAAGAAA
1 ATAAAATAAAAAGAAA
*
16443152 ATAAAATAAAAATAAA
1 ATAAAATAAAAAGAAA
16443168 ATAA
1 ATAA
16443172 GATTTTTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.78, C:0.03, G:0.03, T:0.17
Consensus pattern (16 bp):
ATAAAATAAAAAGAAA
Found at i:16443955 original size:19 final size:19
Alignment explanation
Indices: 16443931--16443968 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
16443921 TTTATTTTAT
*
16443931 TTATTTATGTACAAGCAAA
1 TTATTTATATACAAGCAAA
16443950 TTATTTATATACAAGCAAA
1 TTATTTATATACAAGCAAA
16443969 CATTTTTTCA
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:0.45, C:0.11, G:0.08, T:0.37
Consensus pattern (19 bp):
TTATTTATATACAAGCAAA
Found at i:16457319 original size:46 final size:46
Alignment explanation
Indices: 16457269--16457383 Score: 135
Period size: 46 Copynumber: 2.5 Consensus size: 46
16457259 CAAGTGCTAG
* *
16457269 TGTAAGACATGTCTGCGACATGCAGCGGC-ATCGAGATG-TAAGCCAA
1 TGTAAGACATGTCTGGGACATGCAGCGACTA-CGAGATGAT-AGCCAA
* * * *
16457315 TGTAAGACATGTTTGGGACATGCATCGACTACGAGATGATAGTCAG
1 TGTAAGACATGTCTGGGACATGCAGCGACTACGAGATGATAGCCAA
16457361 TGTAAGACCATGTCTGGGACATG
1 TGTAAGA-CATGTCTGGGACATG
16457384 GCATCGAAAC
Statistics
Matches: 59, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
46 43 0.73
47 16 0.27
ACGTcount: A:0.30, C:0.18, G:0.29, T:0.23
Consensus pattern (46 bp):
TGTAAGACATGTCTGGGACATGCAGCGACTACGAGATGATAGCCAA
Found at i:16458577 original size:21 final size:21
Alignment explanation
Indices: 16458538--16458577 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
16458528 TCGAAATGGT
* **
16458538 CACACGGGCGTGTTGCCCTTC
1 CACACGGGCGTCTACCCCTTC
16458559 CACACGGGCGTCTACCCCT
1 CACACGGGCGTCTACCCCT
16458578 GTATCAAGTG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.12, C:0.42, G:0.25, T:0.20
Consensus pattern (21 bp):
CACACGGGCGTCTACCCCTTC
Found at i:16468737 original size:33 final size:33
Alignment explanation
Indices: 16468700--16468767 Score: 127
Period size: 33 Copynumber: 2.1 Consensus size: 33
16468690 AATTGGACAC
*
16468700 AATGCTATAGAATGTTAATGCCAAATTGAAAGG
1 AATGCTATAGAATGTTAATGCAAAATTGAAAGG
16468733 AATGCTATAGAATGTTAATGCAAAATTGAAAGG
1 AATGCTATAGAATGTTAATGCAAAATTGAAAGG
16468766 AA
1 AA
16468768 AAAATGAAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.46, C:0.07, G:0.21, T:0.26
Consensus pattern (33 bp):
AATGCTATAGAATGTTAATGCAAAATTGAAAGG
Found at i:16468905 original size:5 final size:5
Alignment explanation
Indices: 16468889--16468918 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
16468879 CTAATTTAAT
16468889 ATAAA ATCAAA ATAAA ATAAA ATAAA ATAA
1 ATAAA AT-AAA ATAAA ATAAA ATAAA ATAA
16468919 GACTTTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 19 0.79
6 5 0.21
ACGTcount: A:0.77, C:0.03, G:0.00, T:0.20
Consensus pattern (5 bp):
ATAAA
Found at i:16470896 original size:27 final size:27
Alignment explanation
Indices: 16470839--16470932 Score: 91
Period size: 27 Copynumber: 3.5 Consensus size: 27
16470829 AAGGGATTTT
** * * *
16470839 CCTTCAGAGTTCGTTATACCTACCATT
1 CCTTCAGAGTTCGCCATACATACTATC
16470866 CCTTCAGAGTTCGCCATACATACTATC
1 CCTTCAGAGTTCGCCATACATACTATC
* *
16470893 CCTTTA-ATGTTCGCCACACATACTATC
1 CCTTCAGA-GTTCGCCATACATACTATC
* *
16470920 TCTTGAGAGTTCG
1 CCTTCAGAGTTCG
16470933 TCGGGAATAC
Statistics
Matches: 56, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
26 1 0.02
27 54 0.96
28 1 0.02
ACGTcount: A:0.23, C:0.30, G:0.13, T:0.34
Consensus pattern (27 bp):
CCTTCAGAGTTCGCCATACATACTATC
Found at i:16471134 original size:27 final size:27
Alignment explanation
Indices: 16471074--16471160 Score: 95
Period size: 27 Copynumber: 3.3 Consensus size: 27
16471064 CCTTAGATCA
* * *
16471074 CCAC-AAGTCTTCCATTTCATAGGTTA
1 CCACAAAGACTTCCATTTCATAGATTG
* *
16471100 CCACAAAGGCTTTCATTTCATAGATTG
1 CCACAAAGACTTCCATTTCATAGATTG
* * *
16471127 TCATAAAGACTTCCATTTCGTAGATTG
1 CCACAAAGACTTCCATTTCATAGATTG
16471154 CCACAAA
1 CCACAAA
16471161 AGCTTCTATT
Statistics
Matches: 49, Mismatches: 11, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
26 4 0.08
27 45 0.92
ACGTcount: A:0.31, C:0.24, G:0.13, T:0.32
Consensus pattern (27 bp):
CCACAAAGACTTCCATTTCATAGATTG
Found at i:16471166 original size:27 final size:27
Alignment explanation
Indices: 16471082--16471171 Score: 92
Period size: 27 Copynumber: 3.3 Consensus size: 27
16471072 CACCACAAGT
* * *
16471082 CTTCCATTTCATAGGTTACCACAAAGG
1 CTTCCATTTCATAGATTGCCACAAAAG
* * *
16471109 CTTTCATTTCATAGATTGTCA-TAAAG
1 CTTCCATTTCATAGATTGCCACAAAAG
*
16471135 ACTTCCATTTCGTAGATTGCCACAAAAG
1 -CTTCCATTTCATAGATTGCCACAAAAG
*
16471163 CTTCTATTT
1 CTTCCATTT
16471172 TTTGGTGTGT
Statistics
Matches: 50, Mismatches: 11, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
26 3 0.06
27 43 0.86
28 4 0.08
ACGTcount: A:0.29, C:0.22, G:0.12, T:0.37
Consensus pattern (27 bp):
CTTCCATTTCATAGATTGCCACAAAAG
Found at i:16473758 original size:21 final size:20
Alignment explanation
Indices: 16473720--16473759 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
16473710 ATTTTTTTAA
*
16473720 TTTAAAAAATAGATTAAAGG
1 TTTAAAAAATAAATTAAAGG
*
16473740 TTTACAAAATAAATATAAAG
1 TTTAAAAAATAAAT-TAAAG
16473760 CTTATCTAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.57, C:0.03, G:0.10, T:0.30
Consensus pattern (20 bp):
TTTAAAAAATAAATTAAAGG
Found at i:16474245 original size:18 final size:18
Alignment explanation
Indices: 16474216--16474279 Score: 50
Period size: 16 Copynumber: 3.7 Consensus size: 18
16474206 TAATTTTTTA
16474216 AAAATA-TA-AAATTATT
1 AAAATATTATAAATTATT
*
16474232 AAAAT-TTAGTAAATATAATA
1 AAAATATTA-TAAAT-T-ATT
16474252 AAAATATTATAAATT-TT
1 AAAATATTATAAATTATT
16474269 -AAATA-TATAAA
1 AAAATATTATAAA
16474280 AACAAAAAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 13
0.73 0.04 0.24
Matches are distributed among these distances:
15 6 0.15
16 12 0.30
17 1 0.03
18 4 0.10
19 2 0.05
20 12 0.30
21 3 0.08
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.38
Consensus pattern (18 bp):
AAAATATTATAAATTATT
Found at i:16474259 original size:28 final size:26
Alignment explanation
Indices: 16474211--16474281 Score: 90
Period size: 27 Copynumber: 2.7 Consensus size: 26
16474201 AACTTTAATT
* *
16474211 TTTTAAAAATATAAAATTATTA-AAA
1 TTTTAAATATATAAAAATATTATAAA
16474236 TTTAGTAAATATAATAAAAATATTATAAA
1 TTT--TAAATAT-ATAAAAATATTATAAA
16474265 TTTTAAATATATAAAAA
1 TTTTAAATATATAAAAA
16474282 CAAAAAAAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
25 3 0.08
26 7 0.17
27 13 0.32
28 11 0.28
29 6 0.15
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.39
Consensus pattern (26 bp):
TTTTAAATATATAAAAATATTATAAA
Found at i:16474495 original size:15 final size:14
Alignment explanation
Indices: 16474465--16474506 Score: 50
Period size: 15 Copynumber: 3.0 Consensus size: 14
16474455 GAAGAAAAAG
16474465 AAAATATATAT-AT
1 AAAATATATATAAT
*
16474478 AAAGTATATATAAGT
1 AAAATATATATAA-T
*
16474493 AAAATATTTATAAT
1 AAAATATATATAAT
16474507 TTATAATTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
13 10 0.42
14 2 0.08
15 12 0.50
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (14 bp):
AAAATATATATAAT
Found at i:16476196 original size:31 final size:32
Alignment explanation
Indices: 16476158--16476218 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
16476148 AATATAGTAA
* *
16476158 TTATAAT-AAAATCTAATTAGTATAAAAATCC
1 TTATAATAAAAATCTAATAAGCATAAAAATCC
*
16476189 TTATAATAAAAATCTTATAAGCATAAAAAT
1 TTATAATAAAAATCTAATAAGCATAAAAAT
16476219 TTAAATTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 7 0.27
32 19 0.73
ACGTcount: A:0.54, C:0.08, G:0.03, T:0.34
Consensus pattern (32 bp):
TTATAATAAAAATCTAATAAGCATAAAAATCC
Found at i:16476205 original size:14 final size:15
Alignment explanation
Indices: 16476179--16476208 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
16476169 TCTAATTAGT
16476179 ATAAAAATCCTTATA
1 ATAAAAATCCTTATA
16476194 ATAAAAAT-CTTATA
1 ATAAAAATCCTTATA
16476208 A
1 A
16476209 GCATAAAAAT
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:0.57, C:0.10, G:0.00, T:0.33
Consensus pattern (15 bp):
ATAAAAATCCTTATA
Found at i:16479817 original size:29 final size:29
Alignment explanation
Indices: 16479773--16479832 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 29
16479763 CCACTTTGTT
16479773 TCTCAAATGAACAAGTAATCTCATTAAAA
1 TCTCAAATGAACAAGTAATCTCATTAAAA
*
16479802 TCTCAAATGAATAAGTAATCTCATTAAAA
1 TCTCAAATGAACAAGTAATCTCATTAAAA
16479831 TC
1 TC
16479833 ACCCACAACA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.47, C:0.17, G:0.07, T:0.30
Consensus pattern (29 bp):
TCTCAAATGAACAAGTAATCTCATTAAAA
Found at i:16480750 original size:31 final size:31
Alignment explanation
Indices: 16480707--16480765 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
16480697 TTTTAGTTAA
16480707 CCAATTAAAAAACACCTAGTTTATTTAAATT
1 CCAATTAAAAAACACCTAGTTTATTTAAATT
*
16480738 CCAATTAGAAAACACCTAGTTTATTTAA
1 CCAATTAAAAAACACCTAGTTTATTTAA
16480766 GTTACATAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.44, C:0.17, G:0.05, T:0.34
Consensus pattern (31 bp):
CCAATTAAAAAACACCTAGTTTATTTAAATT
Found at i:16481542 original size:328 final size:326
Alignment explanation
Indices: 16480938--16481908 Score: 1492
Period size: 328 Copynumber: 3.0 Consensus size: 326
16480928 AGTTACAAAA
* * * *
16480938 AAACGTGATGATTTTAAGACCTCTGACTTGCCGAATCCAGTTGCAAAAAAGAAAAGTGTACCTAA
1 AAACGCGATGATTTTAAGACCTCTGACTTG-CGAGTCTAGTTGCAGAAAAGAAAAGTGTACCTAA
* * *
16481003 AAAGGAAACACTAAGATGGGGTGAGCCATACGAGCTCAGTGTGAGTCCAAATCAAGATGAAAACA
65 AAAGGAAACACTAAGAGGGGGTGAGCCATACGAGCTCAGTGTGAGTTCGAATCAAGATGAAAACA
16481068 GAAATACAGTACACAATTCAATATCGAACAACTACAGATACATATTCAGAAGCAGAAGGTAATAC
130 GAAATACAGTACACAATTCAATATCGAACAACTACAGATA-ATATTCAGAAGCA-AAGGTAATAC
* * *
16481133 CGTAATCAACATCCCAATAGAACGTAACATCTCAAACACAAACACTCGGTCATATATATATTTAC
193 CGAAATCAACATCCCAATGGAACGTAACATCTCAAACACAAACACTCAGTCATATATATATTTAC
* * *
16481198 AGTTAGACAAAGAACAGTTAGACGATCTAGCATCCAGAATGCTCAAAAAGATACGTATGAAAAGT
258 AGTTAGACAAAGAACAGTCAGACGGTCTAGCATCCAGAATGCTCAAAAAGATACGTATGAAAAGC
16481263 AGTC
323 AGTC
* *
16481267 AAACGCGATGATTTTTAGACCTCCGACTTGTCGAGTCTAGTTGCAGAAAAGAAAAGTGTACCTAA
1 AAACGCGATGATTTTAAGACCTCTGACTTG-CGAGTCTAGTTGCAGAAAAGAAAAGTGTACCTAA
* *
16481332 AAAAGAAACACTAAGA-GGGGTGAGCCATACGAGTTCAGTGTGAGTTCGAATCAAGATGAAAACA
65 AAAGGAAACACTAAGAGGGGGTGAGCCATACGAGCTCAGTGTGAGTTCGAATCAAGATGAAAACA
16481396 GAAATACAGTACACAATTCAATATCGAACAACTACAGATATATATTCAGAAGCAAAAGGTAATAC
130 GAAATACAGTACACAATTCAATATCGAACAACTACAGATA-ATATTCAGAAGC-AAAGGTAATAC
* * *
16481461 CGGAATCAACATCCCAACGGAACGTAACATCTCAAACACAAACACTCAATCATATATATATTTAC
193 CGAAATCAACATCCCAATGGAACGTAACATCTCAAACACAAACACTCAGTCATATATATATTTAC
*
16481526 AGCTAGACAAAGAACAGTCAGACGGTCTAGCATCCAGAATGCTCAAAAAGATACGTATGAAAAGC
258 AGTTAGACAAAGAACAGTCAGACGGTCTAGCATCCAGAATGCTCAAAAAGATACGTATGAAAAGC
16481591 AGTC
323 AGTC
* * *
16481595 AAACGCGACGATTTTGAGACCTCTGACTTGCGGAGTCTAATTGCAGAAAAGAAAAGTGTACCTAA
1 AAACGCGATGATTTTAAGACCTCTGACTTGC-GAGTCTAGTTGCAGAAAAGAAAAGTGTACCTAA
*
16481660 AAAGGAAACACTAAGAGGGGGTGAGCCATATGAGCTCAGTGTGAGTTCGAATCAAGATGAAAACA
65 AAAGGAAACACTAAGAGGGGGTGAGCCATACGAGCTCAGTGTGAGTTCGAATCAAGATGAAAACA
*
16481725 GAAATATAGTACACAATTCAATATCGAAC-A--AC------TA--C---AG---AGGTAATACCG
130 GAAATACAGTACACAATTCAATATCGAACAACTACAGATAATATTCAGAAGCAAAGGTAATACCG
*
16481773 AAATCAACATCCTAATGGAACGTAACATCTCAAACACAAACACTCAGTCATATATATATTTACAG
195 AAATCAACATCCCAATGGAACGTAACATCTCAAACACAAACACTCAGTCATATATATATTTACAG
* *
16481838 TTAGACAAAGAACAGTCAAACGGTCTAGCATCTAGAATGCTCAAAAAGATACGTATGAAAAGCAG
260 TTAGACAAAGAACAGTCAGACGGTCTAGCATCCAGAATGCTCAAAAAGATACGTATGAAAAGCAG
16481903 TC
325 TC
16481905 AAAC
1 AAAC
16481909 AATGAAACCC
Statistics
Matches: 603, Mismatches: 36, Indels: 25
0.91 0.05 0.04
Matches are distributed among these distances:
310 140 0.23
314 2 0.00
317 1 0.00
319 2 0.00
326 2 0.00
327 1 0.00
328 307 0.51
329 148 0.25
ACGTcount: A:0.42, C:0.19, G:0.18, T:0.21
Consensus pattern (326 bp):
AAACGCGATGATTTTAAGACCTCTGACTTGCGAGTCTAGTTGCAGAAAAGAAAAGTGTACCTAAA
AAGGAAACACTAAGAGGGGGTGAGCCATACGAGCTCAGTGTGAGTTCGAATCAAGATGAAAACAG
AAATACAGTACACAATTCAATATCGAACAACTACAGATAATATTCAGAAGCAAAGGTAATACCGA
AATCAACATCCCAATGGAACGTAACATCTCAAACACAAACACTCAGTCATATATATATTTACAGT
TAGACAAAGAACAGTCAGACGGTCTAGCATCCAGAATGCTCAAAAAGATACGTATGAAAAGCAGT
C
Found at i:16482636 original size:22 final size:22
Alignment explanation
Indices: 16482610--16482651 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
16482600 ACCGTGTGGC
*
16482610 AGAGGTACAC-GCCAGTATGAAG
1 AGAGGCACACAGCCA-TATGAAG
16482632 AGAGGCACACAGCCATATGA
1 AGAGGCACACAGCCATATGA
16482652 CTAAGGCATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.38, C:0.21, G:0.29, T:0.12
Consensus pattern (22 bp):
AGAGGCACACAGCCATATGAAG
Found at i:16483445 original size:15 final size:15
Alignment explanation
Indices: 16483425--16483462 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 15
16483415 CCAAGAAGAC
16483425 AAAAATAATAAAAAT
1 AAAAATAATAAAAAT
16483440 AAAAATAAT-AAAAT
1 AAAAATAATAAAAAT
16483454 -AAAATAATA
1 AAAAATAATA
16483463 GAAAGTAACT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 8 0.36
14 5 0.23
15 9 0.41
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (15 bp):
AAAAATAATAAAAAT
Found at i:16484140 original size:21 final size:19
Alignment explanation
Indices: 16484113--16484161 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 19
16484103 CTCAAAATAA
*
16484113 AAATTAATTAAAAATAAATT
1 AAATTAAAT-AAAATAAATT
16484133 AAAGTTAAATAAAATACAATT
1 AAA-TTAAATAAAATA-AATT
16484154 AAATTAAA
1 AAATTAAA
16484162 CTTTATGAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
20 14 0.54
21 12 0.46
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (19 bp):
AAATTAAATAAAATAAATT
Found at i:16485092 original size:6 final size:6
Alignment explanation
Indices: 16485081--16485112 Score: 55
Period size: 6 Copynumber: 5.2 Consensus size: 6
16485071 AAGTTATAAA
16485081 ATAATT ATAATT ATAATT ATAATT AATAATT A
1 ATAATT ATAATT ATAATT ATAATT -ATAATT A
16485113 ATTAACAATG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 19 0.76
7 6 0.24
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (6 bp):
ATAATT
Found at i:16485096 original size:12 final size:13
Alignment explanation
Indices: 16485068--16485112 Score: 60
Period size: 12 Copynumber: 3.6 Consensus size: 13
16485058 ATTTATATGC
16485068 AATAAGTTATAA--
1 AATAA-TTATAATT
16485080 AATAATTATAATT
1 AATAATTATAATT
16485093 -ATAATTATAATT
1 AATAATTATAATT
16485105 AATAATTA
1 AATAATTA
16485113 ATTAACAATG
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
11 6 0.20
12 17 0.57
13 7 0.23
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (13 bp):
AATAATTATAATT
Found at i:16485191 original size:25 final size:25
Alignment explanation
Indices: 16485163--16485217 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 25
16485153 TTTTTCTATT
*
16485163 TTTTTATATGTTA-CTTGAAATTTAA
1 TTTTTATAT-TCACCTTGAAATTTAA
*
16485188 TTTTTTTATTCACTCTTGAAATTTAA
1 TTTTTATATTCAC-CTTGAAATTTAA
16485214 TTTT
1 TTTT
16485218 ATTTAGTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
24 2 0.08
25 8 0.31
26 16 0.62
ACGTcount: A:0.27, C:0.07, G:0.05, T:0.60
Consensus pattern (25 bp):
TTTTTATATTCACCTTGAAATTTAA
Found at i:16485661 original size:24 final size:24
Alignment explanation
Indices: 16485624--16485679 Score: 60
Period size: 24 Copynumber: 2.4 Consensus size: 24
16485614 AGAGAAATTG
* * * *
16485624 AGAAGAGAGGAAAACAAAGGGAGA
1 AGAAGAGAAGAAAAAAAAAGAAGA
*
16485648 AGAAGAGAATAAAAAAAAAGAAGA
1 AGAAGAGAAGAAAAAAAAAGAAGA
16485672 AGAA-AGAA
1 AGAAGAGAA
16485680 AGTTAAAAGA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
23 4 0.15
24 23 0.85
ACGTcount: A:0.68, C:0.02, G:0.29, T:0.02
Consensus pattern (24 bp):
AGAAGAGAAGAAAAAAAAAGAAGA
Found at i:16486283 original size:23 final size:24
Alignment explanation
Indices: 16486257--16486307 Score: 63
Period size: 22 Copynumber: 2.2 Consensus size: 24
16486247 TTTGAAATTT
16486257 AATTTTTA-TATTTTTATTTTAAA
1 AATTTTTAGTATTTTTATTTTAAA
* *
16486280 AA--TTTAGTTTTTTTATTTTTAA
1 AATTTTTAGTATTTTTATTTTAAA
16486302 AATTTT
1 AATTTT
16486308 AAAATTTAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
21 4 0.17
22 15 0.65
23 2 0.09
24 2 0.09
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (24 bp):
AATTTTTAGTATTTTTATTTTAAA
Found at i:16487378 original size:27 final size:27
Alignment explanation
Indices: 16487317--16487378 Score: 83
Period size: 27 Copynumber: 2.3 Consensus size: 27
16487307 AGTTTGTCAA
16487317 TTTTG-AAAAATACTTTTGAAAAGTGC
1 TTTTGAAAAAATACTTTTGAAAAGTGC
* *
16487343 -TGTGAAAAAAATACTTTTGAGAAGTGC
1 TTTTG-AAAAAATACTTTTGAAAAGTGC
16487370 TTTTGAAAA
1 TTTTGAAAA
16487379 GTTTAAAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
25 3 0.10
27 24 0.80
28 3 0.10
ACGTcount: A:0.40, C:0.06, G:0.18, T:0.35
Consensus pattern (27 bp):
TTTTGAAAAAATACTTTTGAAAAGTGC
Found at i:16492928 original size:49 final size:49
Alignment explanation
Indices: 16492871--16493001 Score: 154
Period size: 49 Copynumber: 2.7 Consensus size: 49
16492861 TGTTGTGTGT
* *
16492871 CAGTGTAAGACCTGTCTGGGACATGGCATCGACACCGATAGATGAGAGC
1 CAGTGTAAGACCTGTCTAGGACATGGCATCGACACCGATAGATGAAAGC
* * * * *
16492920 CAGTGTAAGACCTGTCTAGGATATGGCATCGACTCTGATATATGAAAGT
1 CAGTGTAAGACCTGTCTAGGACATGGCATCGACACCGATAGATGAAAGC
* * * * *
16492969 CAGTGTAAAACTTGTTTAGGAAACGGCATCGAC
1 CAGTGTAAGACCTGTCTAGGACATGGCATCGAC
16493002 TTTAATGTAC
Statistics
Matches: 70, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
49 70 1.00
ACGTcount: A:0.31, C:0.19, G:0.27, T:0.24
Consensus pattern (49 bp):
CAGTGTAAGACCTGTCTAGGACATGGCATCGACACCGATAGATGAAAGC
Found at i:16493696 original size:14 final size:17
Alignment explanation
Indices: 16493659--16493700 Score: 68
Period size: 17 Copynumber: 2.5 Consensus size: 17
16493649 CTGTTTTTAC
16493659 ATATATTAATAAATTAT
1 ATATATTAATAAATTAT
16493676 ATATATTAATAAATT-T
1 ATATATTAATAAATTAT
*
16493692 ATATTTTAA
1 ATATATTAA
16493701 ACTGTTTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 9 0.38
17 15 0.62
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
ATATATTAATAAATTAT
Found at i:16496666 original size:29 final size:29
Alignment explanation
Indices: 16496624--16496685 Score: 106
Period size: 29 Copynumber: 2.1 Consensus size: 29
16496614 CTGATTATTG
16496624 GCTAATCATAATAGCTGCGAAATTCGTAT
1 GCTAATCATAATAGCTGCGAAATTCGTAT
* *
16496653 GCTAATTATAATAGTTGCGAAATTCGTAT
1 GCTAATCATAATAGCTGCGAAATTCGTAT
16496682 GCTA
1 GCTA
16496686 TAAATTGTCA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.34
Consensus pattern (29 bp):
GCTAATCATAATAGCTGCGAAATTCGTAT
Found at i:16502481 original size:25 final size:24
Alignment explanation
Indices: 16502452--16502511 Score: 84
Period size: 24 Copynumber: 2.4 Consensus size: 24
16502442 GCCATACCTT
16502452 AGAAAGAGAGATTTGCCTTTGCCTA
1 AGAAA-AGAGATTTGCCTTTGCCTA
* *
16502477 AGAAATGAGATTTGCCTTTGCCTG
1 AGAAAAGAGATTTGCCTTTGCCTA
16502501 AGAAAAAGAGA
1 AG-AAAAGAGA
16502512 AAAAGAGGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
24 19 0.61
25 12 0.39
ACGTcount: A:0.37, C:0.13, G:0.25, T:0.25
Consensus pattern (24 bp):
AGAAAAGAGATTTGCCTTTGCCTA
Found at i:16502486 original size:24 final size:24
Alignment explanation
Indices: 16502459--16502505 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
16502449 CTTAGAAAGA
16502459 GAGATTTGCCTTTGCCTAAGAAAT
1 GAGATTTGCCTTTGCCTAAGAAAT
*
16502483 GAGATTTGCCTTTGCCTGAGAAA
1 GAGATTTGCCTTTGCCTAAGAAA
16502506 AAGAGAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.28, C:0.17, G:0.23, T:0.32
Consensus pattern (24 bp):
GAGATTTGCCTTTGCCTAAGAAAT
Found at i:16502818 original size:22 final size:22
Alignment explanation
Indices: 16502793--16502838 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
16502783 TGTCACATTG
*
16502793 TTTTGGGGCCAAATGTGTTGGC
1 TTTTAGGGCCAAATGTGTTGGC
16502815 TTTTAGGGCCAAATGTGTTGGC
1 TTTTAGGGCCAAATGTGTTGGC
16502837 TT
1 TT
16502839 ACTTTAGTAT
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:0.15, C:0.13, G:0.33, T:0.39
Consensus pattern (22 bp):
TTTTAGGGCCAAATGTGTTGGC
Found at i:16503618 original size:20 final size:21
Alignment explanation
Indices: 16503579--16503618 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
16503569 GTCAACAGGG
16503579 CCACACGGGCGTGTTGCCCTT
1 CCACACGGGCGTGTTGCCCTT
*
16503600 CCACACGGGTGTG-TGCCCT
1 CCACACGGGCGTGTTGCCCT
16503619 GTTTCAAGTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.10, C:0.38, G:0.30, T:0.23
Consensus pattern (21 bp):
CCACACGGGCGTGTTGCCCTT
Found at i:16504194 original size:8 final size:9
Alignment explanation
Indices: 16504167--16504196 Score: 60
Period size: 9 Copynumber: 3.3 Consensus size: 9
16504157 ACCAAATACT
16504167 CCACCTCCC
1 CCACCTCCC
16504176 CCACCTCCC
1 CCACCTCCC
16504185 CCACCTCCC
1 CCACCTCCC
16504194 CCA
1 CCA
16504197 GTTCCTCAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.13, C:0.77, G:0.00, T:0.10
Consensus pattern (9 bp):
CCACCTCCC
Found at i:16510565 original size:21 final size:21
Alignment explanation
Indices: 16510491--16510585 Score: 63
Period size: 21 Copynumber: 4.6 Consensus size: 21
16510481 ATGTCTTTCA
* *
16510491 AAATAAAATAATAATAAAATT
1 AAATAAAATAAAAATAAAAAT
* *
16510512 GAAGTGAAAATAAAAAT-CAAA-
1 -AAAT-AAAATAAAAATAAAAAT
* * *
16510533 AGA-AAAAGAAAAA-GAAAAT
1 AAATAAAATAAAAATAAAAAT
*
16510552 AAATAAAATAAAAATAAGAAT
1 AAATAAAATAAAAATAAAAAT
*
16510573 AAATGAAATAAAA
1 AAATAAAATAAAA
16510586 TAGGAGGATT
Statistics
Matches: 55, Mismatches: 13, Indels: 11
0.70 0.16 0.14
Matches are distributed among these distances:
18 12 0.22
19 2 0.04
20 10 0.18
21 16 0.29
22 5 0.09
23 10 0.18
ACGTcount: A:0.74, C:0.01, G:0.08, T:0.17
Consensus pattern (21 bp):
AAATAAAATAAAAATAAAAAT
Found at i:16520823 original size:16 final size:16
Alignment explanation
Indices: 16520802--16520840 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
16520792 ATGTATCGGC
*
16520802 AAAAGCCAAAATGTAG
1 AAAAGCCAAAATGCAG
*
16520818 AAAAGCCAAAATGCCG
1 AAAAGCCAAAATGCAG
16520834 AAAAGCC
1 AAAAGCC
16520841 GAAAGTTTGG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.54, C:0.21, G:0.18, T:0.08
Consensus pattern (16 bp):
AAAAGCCAAAATGCAG
Found at i:16521104 original size:29 final size:29
Alignment explanation
Indices: 16521068--16521167 Score: 130
Period size: 29 Copynumber: 3.5 Consensus size: 29
16521058 TGAATGGGAC
*
16521068 TGGGCCTAACGGGCCATATAAATGTGATT
1 TGGGCCTAATGGGCCATATAAATGTGATT
* *
16521097 TGGGCCTAATGGGCCATATACAGGTGATT
1 TGGGCCTAATGGGCCATATAAATGTGATT
* * *
16521126 TGAGCCTAATGGGCCATATGAATATGA-T
1 TGGGCCTAATGGGCCATATAAATGTGATT
*
16521154 TGGGCTTAATGGGC
1 TGGGCCTAATGGGC
16521168 TAGATACAGG
Statistics
Matches: 61, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
28 13 0.21
29 48 0.79
ACGTcount: A:0.26, C:0.16, G:0.30, T:0.28
Consensus pattern (29 bp):
TGGGCCTAATGGGCCATATAAATGTGATT
Found at i:16522858 original size:126 final size:126
Alignment explanation
Indices: 16522638--16523176 Score: 783
Period size: 126 Copynumber: 4.3 Consensus size: 126
16522628 AAAAGCTTCT
* *
16522638 ACGTGGACGCTCTTTTGGTACAGTAGTCTCTGAAAAAATAAATTTGAGAAGACGTGTCTGCACAA
1 ACGTGGACGCTCTTTTGCTACAGTAGTCTCTGAAAAAATAATTTTGAGAAGACGTGTCTGCACAA
16522703 ATAGTGTCAAAAACGCTTCAAGCAGGATGCATTGTCAGCAAAAGTACTGAAAGAAGCTCCC
66 ATAGTGTCAAAAACGCTTCAAGCAGGATGCATTGTCAGCAAAAGTACTGAAAGAAGCTCCC
* * **
16522764 ACGTGGACGCTCTTTTGCTACAGTAGTATCTGAAAAAATAATTTTTAGAAGACGTGTCTGTGCAA
1 ACGTGGACGCTCTTTTGCTACAGTAGTCTCTGAAAAAATAATTTTGAGAAGACGTGTCTGCACAA
* * * * *
16522829 ATAGTGTAAAAAATGCTTCAAGCAAGATGCATTGTCAGCAAAAGTACGGAAAGAAGCTTCC
66 ATAGTGTCAAAAACGCTTCAAGCAGGATGCATTGTCAGCAAAAGTACTGAAAGAAGCTCCC
* * * *
16522890 ACGTGGACGCTTTTTTGCTACAGTAGTCTCTGAAAAAATAATTTTGAAAAGACGTGTTTGCGCAA
1 ACGTGGACGCTCTTTTGCTACAGTAGTCTCTGAAAAAATAATTTTGAGAAGACGTGTCTGCACAA
* * * * *
16522955 ATAGTGGTC-AAAGCGCTTCAAGCAGGATGCATTTTCAGCAAAATTACAGGAAGAAGCTCCC
66 ATAGT-GTCAAAAACGCTTCAAGCAGGATGCATTGTCAGCAAAAGTACTGAAAGAAGCTCCC
* * * * * * *
16523016 ACGTAGATGCTCTTTTGCTACAGTGGTCTCTGAAAAAATAATTTTAAGAAGACATGTCCGCATAA
1 ACGTGGACGCTCTTTTGCTACAGTAGTCTCTGAAAAAATAATTTTGAGAAGACGTGTCTGCACAA
* *
16523081 ATAGTGTCAAAAACGCTTCAAGTAGGATGCATTTTCAGCAAAAGTACTGAAAGAAGCTCCC
66 ATAGTGTCAAAAACGCTTCAAGCAGGATGCATTGTCAGCAAAAGTACTGAAAGAAGCTCCC
* *
16523142 ACGTGGACGCTCTTTTGCTACAGTGGTTTCTGAAA
1 ACGTGGACGCTCTTTTGCTACAGTAGTCTCTGAAA
16523177 TAACTTGGGC
Statistics
Matches: 366, Mismatches: 45, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
125 3 0.01
126 361 0.99
127 2 0.01
ACGTcount: A:0.34, C:0.18, G:0.22, T:0.27
Consensus pattern (126 bp):
ACGTGGACGCTCTTTTGCTACAGTAGTCTCTGAAAAAATAATTTTGAGAAGACGTGTCTGCACAA
ATAGTGTCAAAAACGCTTCAAGCAGGATGCATTGTCAGCAAAAGTACTGAAAGAAGCTCCC
Found at i:16526308 original size:116 final size:116
Alignment explanation
Indices: 16526131--16526486 Score: 595
Period size: 116 Copynumber: 3.1 Consensus size: 116
16526121 TATTTATATT
* * *
16526131 TTATTACATGAAATAATATAAAAATATTCAAAATATTGCTTTATTTAAAATAATTTTCATTTTAT
1 TTATTACATGAAATAATATAAAAATATTCAAAATGTTGCCTTATTTAAAATAATTTCCATTTTAT
*
16526196 TAAAAATATAAAAGTAAATTATAATTACTTTATTTAAAACAACCTTTTATA
66 TAAAAATATAAAAGTAAATTACAATTACTTTATTTAAAACAACCTTTTATA
* *
16526247 TTATCACAAGAAATAATATAAAAATATTCAAAATGTTGCCTTATTTAAAATAATTTCCATTTTAT
1 TTATTACATGAAATAATATAAAAATATTCAAAATGTTGCCTTATTTAAAATAATTTCCATTTTAT
* * *
16526312 TAAAAATATAAAAGTAAATTACAATTACTTTATTCAAAATAACCTTTTATC
66 TAAAAATATAAAAGTAAATTACAATTACTTTATTTAAAACAACCTTTTATA
* *
16526363 TAATTACATGAAATAGTATAAAAATATTCAAAATGTTGCCTTATTTAAAATAATTTCCATTTTAT
1 TTATTACATGAAATAATATAAAAATATTCAAAATGTTGCCTTATTTAAAATAATTTCCATTTTAT
*
16526428 TAAAAATATAAAAGTAAATTACAATTACTTTATTTAAAACAACCTTTTATC
66 TAAAAATATAAAAGTAAATTACAATTACTTTATTTAAAACAACCTTTTATA
*
16526479 TAATTACA
1 TTATTACA
16526487 ATTGTGTGGG
Statistics
Matches: 225, Mismatches: 15, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
116 225 1.00
ACGTcount: A:0.47, C:0.10, G:0.03, T:0.40
Consensus pattern (116 bp):
TTATTACATGAAATAATATAAAAATATTCAAAATGTTGCCTTATTTAAAATAATTTCCATTTTAT
TAAAAATATAAAAGTAAATTACAATTACTTTATTTAAAACAACCTTTTATA
Found at i:16528150 original size:15 final size:15
Alignment explanation
Indices: 16528130--16528160 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
16528120 TTTTTATTTT
*
16528130 AAAAAATAAATTTAG
1 AAAAAATAAAATTAG
16528145 AAAAAATAAAATTAG
1 AAAAAATAAAATTAG
16528160 A
1 A
16528161 GCTTTTTTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.71, C:0.00, G:0.06, T:0.23
Consensus pattern (15 bp):
AAAAAATAAAATTAG
Found at i:16528199 original size:22 final size:22
Alignment explanation
Indices: 16528187--16528236 Score: 77
Period size: 20 Copynumber: 2.4 Consensus size: 22
16528177 TAACGAGAGT
16528187 TTTGAGAGGAATTTAAGAGAAA
1 TTTGAGAGGAATTTAAGAGAAA
*
16528209 TTTGAGA-G-ATTTGAGAGAAA
1 TTTGAGAGGAATTTAAGAGAAA
16528229 TTTGAGAG
1 TTTGAGAG
16528237 AATATTGAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 18 0.69
21 1 0.04
22 7 0.27
ACGTcount: A:0.40, C:0.00, G:0.30, T:0.30
Consensus pattern (22 bp):
TTTGAGAGGAATTTAAGAGAAA
Found at i:16528210 original size:11 final size:11
Alignment explanation
Indices: 16528187--16528238 Score: 72
Period size: 11 Copynumber: 4.9 Consensus size: 11
16528177 TAACGAGAGT
*
16528187 TTTGAGAGGAA
1 TTTGAGAGAAA
*
16528198 TTTAAGAGAAA
1 TTTGAGAGAAA
16528209 TTTGAGAG--A
1 TTTGAGAGAAA
16528218 TTTGAGAGAAA
1 TTTGAGAGAAA
16528229 TTTGAGAGAA
1 TTTGAGAGAA
16528239 TATTGAAAGA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
9 9 0.25
11 27 0.75
ACGTcount: A:0.42, C:0.00, G:0.29, T:0.29
Consensus pattern (11 bp):
TTTGAGAGAAA
Found at i:16528250 original size:31 final size:31
Alignment explanation
Indices: 16528187--16528250 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
16528177 TAACGAGAGT
* *
16528187 TTTGAGAGGAATTTAAGAGAAATTTGAGAGA
1 TTTGAGAGAAATTTAAGAGAAATTTGAAAGA
*
16528218 TTTGAGAGAAATTTGAGAG-AATATTGAAAGA
1 TTTGAGAGAAATTTAAGAGAAAT-TTGAAAGA
16528249 TT
1 TT
16528251 GAAGATTGAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 3 0.10
31 26 0.90
ACGTcount: A:0.42, C:0.00, G:0.27, T:0.31
Consensus pattern (31 bp):
TTTGAGAGAAATTTAAGAGAAATTTGAAAGA
Found at i:16531203 original size:27 final size:27
Alignment explanation
Indices: 16531166--16531221 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
16531156 TCAGGTCACC
16531166 CCCTATAACTTATGGAAGGGTAGAAAA
1 CCCTATAACTTATGGAAGGGTAGAAAA
16531193 CCCTATAACTTATGGAAGGGTAGAAAA
1 CCCTATAACTTATGGAAGGGTAGAAAA
16531220 CC
1 CC
16531222 AAGTGTGAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.39, C:0.18, G:0.21, T:0.21
Consensus pattern (27 bp):
CCCTATAACTTATGGAAGGGTAGAAAA
Done.