Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr9
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: 91122320
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2661692 characters in sequence are not A, C, G, or T
File 36 of 279
Found at i:12222748 original size:26 final size:26
Alignment explanation
Indices: 12222683--12222799 Score: 166
Period size: 26 Copynumber: 4.6 Consensus size: 26
12222673 TAATAACTGC
** *
12222683 GGCA-AAGCCCTTTTCGGTAAACTGG
1 GGCATAAGCCCTTTTCAATAAACTAG
12222708 GGCA-AAGCCCTTTTCAATAAACTAG
1 GGCATAAGCCCTTTTCAATAAACTAG
**
12222733 GGCATAAGCCCTTTTCGGTAAACTAG
1 GGCATAAGCCCTTTTCAATAAACTAG
*
12222759 GGCATAAGCCCTTTTCAATAAACTGG
1 GGCATAAGCCCTTTTCAATAAACTAG
12222785 GGCATAAGCCCTTTT
1 GGCATAAGCCCTTTT
12222800 GCACTTCCTC
Statistics
Matches: 83, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
25 26 0.31
26 57 0.69
ACGTcount: A:0.28, C:0.24, G:0.21, T:0.26
Consensus pattern (26 bp):
GGCATAAGCCCTTTTCAATAAACTAG
Found at i:12222788 original size:52 final size:51
Alignment explanation
Indices: 12222677--12222799 Score: 203
Period size: 52 Copynumber: 2.4 Consensus size: 51
12222667 CCTCTTTAAT
* *
12222677 AACTGCGGCA-AAGCCCTTTTCGGTAAACTGGGGCAAAGCCCTTTTCAATA
1 AACTGGGGCATAAGCCCTTTTCGGTAAACTAGGGCAAAGCCCTTTTCAATA
*
12222727 AACTAGGGCATAAGCCCTTTTCGGTAAACTAGGGCATAAGCCCTTTTCAATA
1 AACTGGGGCATAAGCCCTTTTCGGTAAACTAGGGCA-AAGCCCTTTTCAATA
12222779 AACTGGGGCATAAGCCCTTTT
1 AACTGGGGCATAAGCCCTTTT
12222800 GCACTTCCTC
Statistics
Matches: 67, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
50 8 0.12
51 24 0.36
52 35 0.52
ACGTcount: A:0.28, C:0.24, G:0.21, T:0.26
Consensus pattern (51 bp):
AACTGGGGCATAAGCCCTTTTCGGTAAACTAGGGCAAAGCCCTTTTCAATA
Found at i:12222879 original size:26 final size:26
Alignment explanation
Indices: 12222846--12222913 Score: 118
Period size: 26 Copynumber: 2.6 Consensus size: 26
12222836 CAACATGTCT
**
12222846 GGGCATAAGCCCTTTTCGGTAAACTG
1 GGGCATAAGCCCTTTTCAATAAACTG
12222872 GGGCATAAGCCCTTTTCAATAAACTG
1 GGGCATAAGCCCTTTTCAATAAACTG
12222898 GGGCATAAGCCCTTTT
1 GGGCATAAGCCCTTTT
12222914 GCACTTCCTC
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 40 1.00
ACGTcount: A:0.25, C:0.24, G:0.24, T:0.28
Consensus pattern (26 bp):
GGGCATAAGCCCTTTTCAATAAACTG
Found at i:12222932 original size:114 final size:114
Alignment explanation
Indices: 12222732--12222958 Score: 445
Period size: 114 Copynumber: 2.0 Consensus size: 114
12222722 CAATAAACTA
12222732 GGGCATAAGCCCTTTTCGGTAAACTAGGGCATAAGCCCTTTTCAATAAACTGGGGCATAAGCCCT
1 GGGCATAAGCCCTTTTCGGTAAACTAGGGCATAAGCCCTTTTCAATAAACTGGGGCATAAGCCCT
12222797 TTTGCACTTCCTCCATCCATACAAAAACCCAACCCAATGCAACATGTCT
66 TTTGCACTTCCTCCATCCATACAAAAACCCAACCCAATGCAACATGTCT
*
12222846 GGGCATAAGCCCTTTTCGGTAAACTGGGGCATAAGCCCTTTTCAATAAACTGGGGCATAAGCCCT
1 GGGCATAAGCCCTTTTCGGTAAACTAGGGCATAAGCCCTTTTCAATAAACTGGGGCATAAGCCCT
12222911 TTTGCACTTCCTCCATCCATACAAAAACCCAACCCAATGCAACATGTC
66 TTTGCACTTCCTCCATCCATACAAAAACCCAACCCAATGCAACATGTC
12222959 ATGTATGCAG
Statistics
Matches: 112, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
114 112 1.00
ACGTcount: A:0.30, C:0.30, G:0.16, T:0.24
Consensus pattern (114 bp):
GGGCATAAGCCCTTTTCGGTAAACTAGGGCATAAGCCCTTTTCAATAAACTGGGGCATAAGCCCT
TTTGCACTTCCTCCATCCATACAAAAACCCAACCCAATGCAACATGTCT
Found at i:12223778 original size:27 final size:27
Alignment explanation
Indices: 12223714--12223770 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
12223704 GGGCATATTC
*
12223714 GTCATTTTACCATACAGGGGTATTACG
1 GTCACTTTACCATACAGGGGTATTACG
*
12223741 GTCACTTTACCCTACAGGGGCT-TTACG
1 GTCACTTTACCATACAGGGG-TATTACG
12223768 GTC
1 GTC
12223771 TGTTTACCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
27 26 0.96
28 1 0.04
ACGTcount: A:0.21, C:0.25, G:0.23, T:0.32
Consensus pattern (27 bp):
GTCACTTTACCATACAGGGGTATTACG
Found at i:12223862 original size:27 final size:27
Alignment explanation
Indices: 12223810--12224344 Score: 272
Period size: 27 Copynumber: 19.8 Consensus size: 27
12223800 TTCATCCTAT
* * * * *
12223810 AAGGGTGTTTTGGTAAATCTACAAACC
1 AAGGGTATTTTGGTAATTTTATAAATC
** * *
12223837 AAGGGTATTTCAGTAATTTTGTAAACC
1 AAGGGTATTTTGGTAATTTTATAAATC
* * *
12223864 AATGGTATTTCT-ATAATTTTTAGAAAGTC
1 AAGGGTATTT-TGGTAA-TTTTATAAA-TC
* * *
12223893 AAGGGTATTTTTGTAACTTTGTAAATC
1 AAGGGTATTTTGGTAATTTTATAAATC
* * *
12223920 AGGGGTATTTTGGTAATTTTACAAATT
1 AAGGGTATTTTGGTAATTTTATAAATC
* * * *
12223947 GAGGGTATTTCGGTAATTTCACAAA-C
1 AAGGGTATTTTGGTAATTTTATAAATC
* * *
12223973 CAGTGGTATTTTGGTAATTTTACAAATT
1 AAG-GGTATTTTGGTAATTTTATAAATC
* * *
12224001 GAGGGTATTTCGGTAATTTCATAAA-C
1 AAGGGTATTTTGGTAATTTTATAAATC
* *
12224027 CAGTGGTATTTTGGTAATTTTACAAA-C
1 AAG-GGTATTTTGGTAATTTTATAAATC
* *
12224054 TAGGGGTATTTTGGTAATTTTATAAATT
1 -AAGGGTATTTTGGTAATTTTATAAATC
* * *
12224082 GAGGGTATTTTGGTAATTTTACAAACC
1 AAGGGTATTTTGGTAATTTTATAAATC
* * * *
12224109 AGGGGTATTTTAGAAATTTTACAAA-C
1 AAGGGTATTTTGGTAATTTTATAAATC
* * *
12224135 TAGGGTATTTTGGTAATTTTACT-GATT
1 AAGGGTATTTTGGTAATTTTA-TAAATC
* * * *
12224162 GAGGGTATTTTGTTAATTTTGTAAACC
1 AAGGGTATTTTGGTAATTTTATAAATC
* * *
12224189 AAGGGTATTTTAGTAATTTTGTACATC
1 AAGGGTATTTTGGTAATTTTATAAATC
* ***** * *
12224216 GAGGGTAAAACAGTAATTCTGTAAATC
1 AAGGGTATTTTGGTAATTTTATAAATC
*** * *
12224243 AAGGGTAAAATAGTAATTCTATAAATC
1 AAGGGTATTTTGGTAATTTTATAAATC
* **** *
12224270 GAGGGTAAAACGGTAATTCTATAAATC
1 AAGGGTATTTTGGTAATTTTATAAATC
* ***** *
12224297 GAGGGTAAAACAGTAATTCTATAAATC
1 AAGGGTATTTTGGTAATTTTATAAATC
* *
12224324 GAGGGTACTTTGGTAATTTTA
1 AAGGGTATTTTGGTAATTTTA
12224345 CAATTTGAGG
Statistics
Matches: 403, Mismatches: 93, Indels: 24
0.77 0.18 0.05
Matches are distributed among these distances:
26 24 0.06
27 349 0.87
28 17 0.04
29 13 0.03
ACGTcount: A:0.33, C:0.09, G:0.20, T:0.38
Consensus pattern (27 bp):
AAGGGTATTTTGGTAATTTTATAAATC
Found at i:12223981 original size:54 final size:53
Alignment explanation
Indices: 12223894--12224208 Score: 346
Period size: 54 Copynumber: 5.8 Consensus size: 53
12223884 TAGAAAGTCA
* * * *
12223894 AGGGTATTTTTGTAACTTTGTAAATCAGGGGTATTTTGGTAATTTTACAAATTG
1 AGGGTATTTTGGTAATTTTATAAACCA-GGGTATTTTGGTAATTTTACAAATTG
* * *
12223948 AGGGTATTTCGGTAATTTCACAAACCAGTGGTATTTTGGTAATTTTACAAATTG
1 AGGGTATTTTGGTAATTTTATAAACCAG-GGTATTTTGGTAATTTTACAAATTG
* * *
12224002 AGGGTATTTCGGTAATTTCATAAACCAGTGGTATTTTGGTAATTTTACAAACT-
1 AGGGTATTTTGGTAATTTTATAAACCAG-GGTATTTTGGTAATTTTACAAATTG
** **
12224055 AGGGGTATTTTGGTAATTTTATAAATTGAGGGTATTTTGGTAATTTTACAAA-CC
1 A-GGGTATTTTGGTAATTTTATAAA-CCAGGGTATTTTGGTAATTTTACAAATTG
* * * * **
12224109 AGGGGTATTTTAGAAATTTTACAAACTAGGGTATTTTGGTAATTTTACTGATTG
1 A-GGGTATTTTGGTAATTTTATAAACCAGGGTATTTTGGTAATTTTACAAATTG
* * *
12224163 AGGGTATTTTGTTAATTTTGTAAACCAAGGGTATTTTAGTAATTTT
1 AGGGTATTTTGGTAATTTTATAAACC-AGGGTATTTTGGTAATTTT
12224209 GTACATCGAG
Statistics
Matches: 225, Mismatches: 30, Indels: 12
0.84 0.11 0.04
Matches are distributed among these distances:
53 43 0.19
54 180 0.80
55 2 0.01
ACGTcount: A:0.29, C:0.07, G:0.21, T:0.43
Consensus pattern (53 bp):
AGGGTATTTTGGTAATTTTATAAACCAGGGTATTTTGGTAATTTTACAAATTG
Found at i:12224017 original size:81 final size:79
Alignment explanation
Indices: 12223922--12224208 Score: 367
Period size: 81 Copynumber: 3.6 Consensus size: 79
12223912 TGTAAATCAG
** * * *
12223922 GGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCGGTAATTTCACAAACCAGTGGTATTTTGG
1 GGGTATTTTGGTAATTTTACAAA-CCAGGGTATTTTGGTAATTTTACAAACTAG-GGTATTTTGG
12223987 TAATTTTACAAATTGA
64 TAATTTTACAAATTGA
* * *
12224003 GGGTATTTCGGTAATTTCATAAACCAGTGGTATTTTGGTAATTTTACAAACTAGGGGTATTTTGG
1 GGGTATTTTGGTAATTTTACAAACCAG-GGTATTTTGGTAATTTTACAAACTA-GGGTATTTTGG
*
12224068 TAATTTTATAAATTGA
64 TAATTTTACAAATTGA
* *
12224084 GGGTATTTTGGTAATTTTACAAACCAGGGGTATTTTAGAAATTTTACAAACTAGGGTATTTTGGT
1 GGGTATTTTGGTAATTTTACAAACCA-GGGTATTTTGGTAATTTTACAAACTAGGGTATTTTGGT
**
12224149 AATTTTACTGATTGA
65 AATTTTACAAATTGA
* ** *
12224164 GGGTATTTTGTTAATTTTGTAAACCAAGGGTATTTTAGTAATTTT
1 GGGTATTTTGGTAATTTTACAAACC-AGGGTATTTTGGTAATTTT
12224209 GTACATCGAG
Statistics
Matches: 181, Mismatches: 21, Indels: 9
0.86 0.10 0.04
Matches are distributed among these distances:
80 65 0.36
81 114 0.63
82 2 0.01
ACGTcount: A:0.29, C:0.07, G:0.21, T:0.43
Consensus pattern (79 bp):
GGGTATTTTGGTAATTTTACAAACCAGGGTATTTTGGTAATTTTACAAACTAGGGTATTTTGGTA
ATTTTACAAATTGA
Found at i:12224367 original size:81 final size:81
Alignment explanation
Indices: 12224190--12224368 Score: 187
Period size: 81 Copynumber: 2.2 Consensus size: 81
12224180 TTGTAAACCA
* * * * *
12224190 AGGGTATTTTAGTAATTTTGTACATCGAGGGTAAAACAGTAATTCTGTAAATCAAGGGTAAAATA
1 AGGGTATTTCAGTAATTCTATAAATCGAGGGTAAAACAGTAATTCTATAAATCAAGGGTAAAATA
*
12224255 GTAATTCTATAAATCG
66 GTAATTCTACAAATCG
*** * * *** *
12224271 AGGGTAAAACGGTAATTCTATAAATCGAGGGTAAAACAGTAATTCTATAAATCGAGGGTACTTTG
1 AGGGTATTTCAGTAATTCTATAAATCGAGGGTAAAACAGTAATTCTATAAATCAAGGGTAAAATA
* * *
12224336 GTAATTTTACAATTTG
66 GTAATTCTACAAATCG
*
12224352 AGGGCATTTCAGTAATT
1 AGGGTATTTCAGTAATT
12224369 TGGTAAACTA
Statistics
Matches: 75, Mismatches: 23, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
81 75 1.00
ACGTcount: A:0.37, C:0.09, G:0.21, T:0.33
Consensus pattern (81 bp):
AGGGTATTTCAGTAATTCTATAAATCGAGGGTAAAACAGTAATTCTATAAATCAAGGGTAAAATA
GTAATTCTACAAATCG
Found at i:12227813 original size:27 final size:27
Alignment explanation
Indices: 12227782--12227835 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
12227772 AAGGCTTATT
12227782 TATGATCTTCATATGTTGAACTTAGTA
1 TATGATCTTCATATGTTGAACTTAGTA
12227809 TATGATCTTCATATGTTGAACTTAGTA
1 TATGATCTTCATATGTTGAACTTAGTA
12227836 CTTCCTCTCT
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:0.30, C:0.11, G:0.15, T:0.44
Consensus pattern (27 bp):
TATGATCTTCATATGTTGAACTTAGTA
Found at i:12229563 original size:21 final size:20
Alignment explanation
Indices: 12229531--12229571 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 20
12229521 ATATGTATGA
12229531 ATTTTGATGATTGATGATAG
1 ATTTTGATGATTGATGATAG
12229551 ATTTTGAATGATTGATGATAG
1 ATTTTG-ATGATTGATGATAG
12229572 TTAGACAAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.32, C:0.00, G:0.24, T:0.44
Consensus pattern (20 bp):
ATTTTGATGATTGATGATAG
Found at i:12236820 original size:83 final size:83
Alignment explanation
Indices: 12236672--12236838 Score: 255
Period size: 83 Copynumber: 2.0 Consensus size: 83
12236662 GAGAGAAAGA
* * * * *
12236672 CCATTCCATAATGTTGGAAATGTGAGTGGTAGTAGAGGTGCAACACGAGATACTGCTGTAGGATC
1 CCATTCCATAATGTTGGAAACGTAAGTGGTAGTAGAGATGCAACACGAGATACTACTGTAAGATC
12236737 TGAAG-CTAGAGCACCTGC
66 TGAAGTC-AGAGCACCTGC
* *
12236755 CCATTTCATAATGTTGGAAACGTAAGTGGTAGTAGAGATGCAACACGAGATACTATTGTAAGATC
1 CCATTCCATAATGTTGGAAACGTAAGTGGTAGTAGAGATGCAACACGAGATACTACTGTAAGATC
12236820 TGAAGTCAGAGCACCTGC
66 TGAAGTCAGAGCACCTGC
12236838 C
1 C
12236839 AGAAGTTATG
Statistics
Matches: 76, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
83 75 0.99
84 1 0.01
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.25
Consensus pattern (83 bp):
CCATTCCATAATGTTGGAAACGTAAGTGGTAGTAGAGATGCAACACGAGATACTACTGTAAGATC
TGAAGTCAGAGCACCTGC
Found at i:12247857 original size:42 final size:41
Alignment explanation
Indices: 12247781--12247912 Score: 138
Period size: 42 Copynumber: 3.1 Consensus size: 41
12247771 TTAGGGTTAT
* * *
12247781 TGAGATTCTGTATAAGACCATATTTGGAATATGGCATCGACA
1 TGAGATTTTGTATAAGACCATATCTGG-ATATGGCATCGAAA
* * * * *
12247823 TGTGATTTTGTATAAGACCACATCTGAGACATGGCTTTGAAAA
1 TGAGATTTTGTATAAGACCATATCTG-GATATGGCATCG-AAA
* *
12247866 TGAGATTTCGTATAAGACCATATCTGGGATATGGCATCGATA
1 TGAGATTTTGTATAAGACCATATCT-GGATATGGCATCGAAA
12247908 TGAGA
1 TGAGA
12247913 CATCGTGTAA
Statistics
Matches: 72, Mismatches: 15, Indels: 6
0.77 0.16 0.06
Matches are distributed among these distances:
42 37 0.51
43 34 0.47
44 1 0.01
ACGTcount: A:0.33, C:0.14, G:0.23, T:0.31
Consensus pattern (41 bp):
TGAGATTTTGTATAAGACCATATCTGGATATGGCATCGAAA
Found at i:12247924 original size:42 final size:42
Alignment explanation
Indices: 12247781--12247987 Score: 166
Period size: 43 Copynumber: 4.9 Consensus size: 42
12247771 TTAGGGTTAT
* * *
12247781 TGAGA-TTCTGTATAAGACCATATTTGGAATATGGCATCGACA
1 TGAGACTTC-GTATAAGACCATATCTGGGATATGGCATCGATA
* * * * * * * * *
12247823 TGTGATTTTGTATAAGACCACATCTGAGACATGGCTTTGAAAA
1 TGAGACTTCGTATAAGACCATATCTGGGATATGGCATCG-ATA
*
12247866 TGAGATTTCGTATAAGACCATATCTGGGATATGGCATCGATA
1 TGAGACTTCGTATAAGACCATATCTGGGATATGGCATCGATA
* * * * *
12247908 TGAGACATCGTGTAAGACCATAACTGGGCTATTGGCATCAATA
1 TGAGACTTCGTATAAGACCATATCTGGGATA-TGGCATCGATA
* * * *
12247951 TGTGA-TCCCATGTAAGACCATATCTGGGATATGGCAT
1 TGAGACT-TCGTATAAGACCATATCTGGGATATGGCAT
12247988 TGGCATCTTA
Statistics
Matches: 131, Mismatches: 30, Indels: 8
0.78 0.18 0.05
Matches are distributed among these distances:
42 61 0.47
43 70 0.53
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.30
Consensus pattern (42 bp):
TGAGACTTCGTATAAGACCATATCTGGGATATGGCATCGATA
Found at i:12252351 original size:27 final size:27
Alignment explanation
Indices: 12252297--12252407 Score: 154
Period size: 27 Copynumber: 4.1 Consensus size: 27
12252287 AGCATGGCTG
* *
12252297 CCAGAACAGATAA-TGTGACAGAGTCA
1 CCAGAACAGATAATTGTGGCAGAGCCA
12252323 CCAGAACAGATAATTGTGGCAGAGCCA
1 CCAGAACAGATAATTGTGGCAGAGCCA
12252350 CCAGAACAGAT-ATATGTGGCAGAGCCA
1 CCAGAACAGATAAT-TGTGGCAGAGCCA
* * *
12252377 CCAGATCAGATAAATGTGGCATAGCCA
1 CCAGAACAGATAATTGTGGCAGAGCCA
12252404 CCAG
1 CCAG
12252408 GACGCTTCCT
Statistics
Matches: 77, Mismatches: 5, Indels: 5
0.89 0.06 0.06
Matches are distributed among these distances:
26 15 0.19
27 61 0.79
28 1 0.01
ACGTcount: A:0.38, C:0.23, G:0.24, T:0.15
Consensus pattern (27 bp):
CCAGAACAGATAATTGTGGCAGAGCCA
Found at i:12253860 original size:24 final size:24
Alignment explanation
Indices: 12253832--12253884 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
12253822 CCAACACCGT
*
12253832 TCTCCCTAATCAGCTCCTAAATCC
1 TCTCCCTAATCAGCTCCCAAATCC
* *
12253856 TCTCCCTTATCAGCTCCCAAATCT
1 TCTCCCTAATCAGCTCCCAAATCC
12253880 TCTCC
1 TCTCC
12253885 TGATAGCCTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.21, C:0.43, G:0.04, T:0.32
Consensus pattern (24 bp):
TCTCCCTAATCAGCTCCCAAATCC
Found at i:12256103 original size:38 final size:38
Alignment explanation
Indices: 12256049--12256121 Score: 110
Period size: 38 Copynumber: 1.9 Consensus size: 38
12256039 CATCAGGCTG
* *
12256049 TGATGGTTCCCGAGTGGAAATGGGATAAAATTACTTTT
1 TGATGGTTCCCGAGTGGAAATGGGAAAAAAATACTTTT
**
12256087 TGATGGTTCCTTAGTGGAAATGGGAAAAAAATACT
1 TGATGGTTCCCGAGTGGAAATGGGAAAAAAATACT
12256122 ATGGACTTTG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 31 1.00
ACGTcount: A:0.33, C:0.10, G:0.26, T:0.32
Consensus pattern (38 bp):
TGATGGTTCCCGAGTGGAAATGGGAAAAAAATACTTTT
Found at i:12271442 original size:47 final size:48
Alignment explanation
Indices: 12271366--12271496 Score: 140
Period size: 47 Copynumber: 2.8 Consensus size: 48
12271356 CTCAATCGAT
* * * ***
12271366 AGTACCTATACCATAGCCCA-TAACCAAATCAAGGTAACTTATCT-TGG
1 AGTACCTATACCAT-GGCCAGTAGCCAAATCAAGGTAACTCATCTCCAA
* *
12271413 AGTACCTATACCATGGCCAGTAGCTAAATCAAGGTAACTCCTCTCCAA
1 AGTACCTATACCATGGCCAGTAGCCAAATCAAGGTAACTCATCTCCAA
* * *
12271461 AATACCTATACCATGGCCTGTAGCCAACTCAAGGTA
1 AGTACCTATACCATGGCCAGTAGCCAAATCAAGGTA
12271497 TCACTCGCAT
Statistics
Matches: 70, Mismatches: 12, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
46 4 0.06
47 34 0.49
48 32 0.46
ACGTcount: A:0.34, C:0.27, G:0.15, T:0.24
Consensus pattern (48 bp):
AGTACCTATACCATGGCCAGTAGCCAAATCAAGGTAACTCATCTCCAA
Found at i:12273489 original size:44 final size:44
Alignment explanation
Indices: 12273426--12273513 Score: 167
Period size: 44 Copynumber: 2.0 Consensus size: 44
12273416 CTAGCCATTT
12273426 GTCATACATAGCACTAAAATGATCGTGATTAACCATTCCAATGG
1 GTCATACATAGCACTAAAATGATCGTGATTAACCATTCCAATGG
*
12273470 GTCATACATAGCACTAAAATGTTCGTGATTAACCATTCCAATGG
1 GTCATACATAGCACTAAAATGATCGTGATTAACCATTCCAATGG
12273514 CTAATCATTA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.35, C:0.20, G:0.16, T:0.28
Consensus pattern (44 bp):
GTCATACATAGCACTAAAATGATCGTGATTAACCATTCCAATGG
Found at i:12274183 original size:40 final size:40
Alignment explanation
Indices: 12274114--12274319 Score: 326
Period size: 40 Copynumber: 5.2 Consensus size: 40
12274104 AACCCAAGTA
* **
12274114 CCTTCGGGATTTAG-CCGGATATAACAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
12274153 CCTTCGGGACTTAGCCCGGATATAGTAACTCACACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
12274193 CCTTCGGGACTTAGCCCGGATATAGTAACTCTG-ACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTC-GCACAAATG
*
12274233 CCTTCGAGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
12274273 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
12274313 CCTTCGG
1 CCTTCGG
12274320 ATCTTAGTCC
Statistics
Matches: 155, Mismatches: 9, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
39 14 0.09
40 141 0.91
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:12278916 original size:27 final size:27
Alignment explanation
Indices: 12278878--12278932 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
12278868 CGAATGCCAT
*
12278878 TTACCACAATACTGGTACTCTATTCTA
1 TTACCACAATACTGGCACTCTATTCTA
*
12278905 TTACCACAATACTGGCACTCTGTTCTA
1 TTACCACAATACTGGCACTCTATTCTA
12278932 T
1 T
12278933 CTCGACGATC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.27, C:0.27, G:0.09, T:0.36
Consensus pattern (27 bp):
TTACCACAATACTGGCACTCTATTCTA
Found at i:12285941 original size:40 final size:40
Alignment explanation
Indices: 12285769--12285934 Score: 262
Period size: 40 Copynumber: 4.2 Consensus size: 40
12285759 AACCCAAGTA
* **
12285769 CCTTCGGGATTTAG-CCGGATATAACAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
12285808 CCTTCGGGACTTAGCCCAGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
12285848 CCTTCGGGACTTAGCCCGAATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
12285888 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
12285928 CCTTCGG
1 CCTTCGG
12285935 ATCTTAGTCC
Statistics
Matches: 117, Mismatches: 9, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
39 13 0.11
40 104 0.89
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:12289281 original size:44 final size:43
Alignment explanation
Indices: 12289228--12289310 Score: 114
Period size: 44 Copynumber: 1.9 Consensus size: 43
12289218 TGTAAGACTG
* *
12289228 TGTCTGGGACACAGGCTTCGAT-TTGAGATTTACATGTAAGCCCC
1 TGTCTGGGACACAGGCATCGATATTGA-A-TTACAAGTAAGCCCC
*
12289272 TGTCTGGGACAGAGGCATCGATATTGAATTACAAGTAAG
1 TGTCTGGGACACAGGCATCGATATTGAATTACAAGTAAG
12289311 ACCACATCTG
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
43 10 0.29
44 21 0.60
45 4 0.11
ACGTcount: A:0.28, C:0.18, G:0.27, T:0.28
Consensus pattern (43 bp):
TGTCTGGGACACAGGCATCGATATTGAATTACAAGTAAGCCCC
Found at i:12289321 original size:43 final size:44
Alignment explanation
Indices: 12289230--12289324 Score: 106
Period size: 44 Copynumber: 2.2 Consensus size: 44
12289220 TAAGACTGTG
* * * *
12289230 TCTGGGACACAGGCTTCGATTTGAGATTTACATGTAAGCCCCTG
1 TCTGGGACACAGGCATCGATTTGAGATTTACAAGTAAGCCACTA
*
12289274 TCTGGGACAGAGGCATCGATATTGA-A-TTACAAGTAAGACCAC-A
1 TCTGGGACACAGGCATCGAT-TTGAGATTTACAAGTAAG-CCACTA
12289317 TCTGGGAC
1 TCTGGGAC
12289325 TTTGGCATTG
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
43 18 0.41
44 22 0.50
45 4 0.09
ACGTcount: A:0.28, C:0.21, G:0.25, T:0.25
Consensus pattern (44 bp):
TCTGGGACACAGGCATCGATTTGAGATTTACAAGTAAGCCACTA
Found at i:12298294 original size:16 final size:15
Alignment explanation
Indices: 12298268--12298297 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
12298258 ACTAGATTGG
12298268 CAAAAGCCGAAAAGC
1 CAAAAGCCGAAAAGC
12298283 CAAAATGCCGAAAAG
1 CAAAA-GCCGAAAAG
12298298 TCGGTATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.53, C:0.23, G:0.20, T:0.03
Consensus pattern (15 bp):
CAAAAGCCGAAAAGC
Found at i:12298752 original size:27 final size:27
Alignment explanation
Indices: 12298712--12298823 Score: 104
Period size: 27 Copynumber: 4.1 Consensus size: 27
12298702 AGGAAGCGTC
*
12298712 CTGGTGGCTATGCCACAATTATCTGAT
1 CTGGTGGCTCTGCCACAATTATCTGAT
*
12298739 CTGGTGGCTCTGCCATATATT-TCT-ATT
1 CTGGTGGCTCTGCCACA-ATTATCTGA-T
* *
12298766 CTGATGGCTCTGCCACGATTATCTGTAT
1 CTGGTGGCTCTGCCACAATTATCTG-AT
* * * *
12298794 CTGGTGACTCTGTCAC-ATTATATGTT
1 CTGGTGGCTCTGCCACAATTATCTGAT
12298820 CTGG
1 CTGG
12298824 CAGCCATGCT
Statistics
Matches: 70, Mismatches: 10, Indels: 11
0.77 0.11 0.12
Matches are distributed among these distances:
26 9 0.13
27 43 0.61
28 17 0.24
29 1 0.01
ACGTcount: A:0.18, C:0.22, G:0.21, T:0.38
Consensus pattern (27 bp):
CTGGTGGCTCTGCCACAATTATCTGAT
Found at i:12298822 original size:54 final size:54
Alignment explanation
Indices: 12298716--12298822 Score: 126
Period size: 54 Copynumber: 2.0 Consensus size: 54
12298706 AGCGTCCTGG
* * * *
12298716 TGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCATATATTTCTATTCTGA
1 TGGCTATGCCACAATTATCTGATCTGGTGACTCTGCCACATATATATATTCTGA
* * * *
12298770 TGGCTCTGCCACGATTATCTGTATCTGGTGACTCTGTCACAT-TATATGTTCTG
1 TGGCTATGCCACAATTATCTG-ATCTGGTGACTCTGCCACATATATATATTCTG
12298823 GCAGCCATGC
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
54 27 0.61
55 17 0.39
ACGTcount: A:0.19, C:0.22, G:0.20, T:0.39
Consensus pattern (54 bp):
TGGCTATGCCACAATTATCTGATCTGGTGACTCTGCCACATATATATATTCTGA
Found at i:12299899 original size:51 final size:49
Alignment explanation
Indices: 12299736--12299959 Score: 277
Period size: 49 Copynumber: 4.5 Consensus size: 49
12299726 GGGCTGTTAC
* *
12299736 AGCCTGCACTTAGTACTACACATGCGACCAATTATCTGGTACACGTAGT
1 AGCCTGCACTTAGTACTACACACGTGACCAATTATCTGGTACACGTAGT
* * ** *
12299785 AGCCTACACTTAGTACTACACACATGACCTAACCATCTGATACACGTAGT
1 AGCCTGCACTTAGTACTACACACGTGACC-AATTATCTGGTACACGTAGT
* * * * *
12299835 AGCCCGCACTTAGTACTACACACGTGATCAAAGTTATCAGGTACGCATAGT
1 AGCCTGCACTTAGTACTACACACGTGA-CCAA-TTATCTGGTACACGTAGT
* * *
12299886 AGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACACGTAGT
1 AGCCTGCACTTAGTACTACACACGTGACCAATTATCTGGTACACGTAGT
*
12299935 AGCCTGCACTTAATACTACACACGT
1 AGCCTGCACTTAGTACTACACACGT
12299960 CACCTCACAA
Statistics
Matches: 145, Mismatches: 27, Indels: 6
0.81 0.15 0.03
Matches are distributed among these distances:
49 62 0.43
50 46 0.32
51 37 0.26
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.25
Consensus pattern (49 bp):
AGCCTGCACTTAGTACTACACACGTGACCAATTATCTGGTACACGTAGT
Found at i:12300229 original size:27 final size:27
Alignment explanation
Indices: 12300189--12300242 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
12300179 AGGTACAACC
* *
12300189 CATGTAATAGTAATTTAACATTCAATT
1 CATGTAACAATAATTTAACATTCAATT
**
12300216 CATGTAACAATAATTTTCCATTCAATT
1 CATGTAACAATAATTTAACATTCAATT
12300243 TCACATGACA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.39, C:0.15, G:0.06, T:0.41
Consensus pattern (27 bp):
CATGTAACAATAATTTAACATTCAATT
Found at i:12304070 original size:27 final size:27
Alignment explanation
Indices: 12303956--12304089 Score: 137
Period size: 27 Copynumber: 5.0 Consensus size: 27
12303946 ACAGAGTTAT
*
12303956 TGAAATA-CCCTGTAGGGTAGAATTAT
1 TGAAATACCCCTGTAGGGTAGAATTAC
*
12303982 TGAAATACACCTGTAGGGTAGAATTAC
1 TGAAATACCCCTGTAGGGTAGAATTAC
** * * *
12304009 CAAAATACCCTTGTAAGGTAGAAATA-
1 TGAAATACCCCTGTAGGGTAGAATTAC
*
12304035 TCGAAATACCCCTGTAGGGTAGAATCAC
1 T-GAAATACCCCTGTAGGGTAGAATTAC
* * * *
12304063 TGAGATACCCTTGTGGGGTAAAATTAC
1 TGAAATACCCCTGTAGGGTAGAATTAC
12304090 CATTTTGCCC
Statistics
Matches: 86, Mismatches: 19, Indels: 5
0.78 0.17 0.05
Matches are distributed among these distances:
26 7 0.08
27 78 0.91
28 1 0.01
ACGTcount: A:0.36, C:0.16, G:0.22, T:0.26
Consensus pattern (27 bp):
TGAAATACCCCTGTAGGGTAGAATTAC
Found at i:12304071 original size:54 final size:54
Alignment explanation
Indices: 12303958--12304076 Score: 159
Period size: 54 Copynumber: 2.2 Consensus size: 54
12303948 AGAGTTATTG
* * * *
12303958 AAATACCC-TGTAGGGTAGAATTATTGAAATACACCTGTAGGGTAGAATTACCA
1 AAATACCCTTGTAAGGTAGAAATATCGAAATACACCTGTAGGGTAGAATCACCA
* **
12304011 AAATACCCTTGTAAGGTAGAAATATCGAAATACCCCTGTAGGGTAGAATCACTG
1 AAATACCCTTGTAAGGTAGAAATATCGAAATACACCTGTAGGGTAGAATCACCA
*
12304065 AGATACCCTTGT
1 AAATACCCTTGT
12304077 GGGGTAAAAT
Statistics
Matches: 57, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
53 8 0.14
54 49 0.86
ACGTcount: A:0.36, C:0.18, G:0.20, T:0.26
Consensus pattern (54 bp):
AAATACCCTTGTAAGGTAGAAATATCGAAATACACCTGTAGGGTAGAATCACCA
Found at i:12304330 original size:28 final size:27
Alignment explanation
Indices: 12304291--12304406 Score: 128
Period size: 27 Copynumber: 4.3 Consensus size: 27
12304281 ATGGAGGATG
*
12304291 TGTTCTGGTGGCTATGCCACAAATTTC
1 TGTTCTGGTGGCTATGCCACAAATATC
12304318 TGTTACTGGTGGCTATGCCACAAATATC
1 TGTT-CTGGTGGCTATGCCACAAATATC
* * **
12304346 TTTTCTGGTGGCTCTGCCAC-TGTATC
1 TGTTCTGGTGGCTATGCCACAAATATC
* * *
12304372 TGTATCTGGTGACTCTGTCAC-AATATC
1 TGT-TCTGGTGGCTATGCCACAAATATC
12304399 TGTTCTGG
1 TGTTCTGG
12304407 CAGCCATGCT
Statistics
Matches: 77, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
26 11 0.14
27 41 0.53
28 25 0.32
ACGTcount: A:0.17, C:0.22, G:0.22, T:0.38
Consensus pattern (27 bp):
TGTTCTGGTGGCTATGCCACAAATATC
Found at i:12304564 original size:12 final size:12
Alignment explanation
Indices: 12304547--12304578 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
12304537 TTCTGTCACA
12304547 TGATTCTAATTT
1 TGATTCTAATTT
*
12304559 TGATTCTTATTT
1 TGATTCTAATTT
12304571 TGATTCTA
1 TGATTCTA
12304579 GTTCTGATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.22, C:0.09, G:0.09, T:0.59
Consensus pattern (12 bp):
TGATTCTAATTT
Found at i:12306648 original size:27 final size:27
Alignment explanation
Indices: 12306575--12306649 Score: 71
Period size: 27 Copynumber: 2.8 Consensus size: 27
12306565 ATTACTGTAA
* **
12306575 TACCCTCGACTTGTAAAATTACCAATG
1 TACCCTCGATTTAAAAAATTACCAATG
* * * *
12306602 TACCC-CTGATTTACAGAATTACCATTT
1 TACCCTC-GATTTAAAAAATTACCAATG
12306629 TACCCTCGATTTAAAAAATTA
1 TACCCTCGATTTAAAAAATTA
12306650 TTAAAATACC
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
26 1 0.03
27 36 0.95
28 1 0.03
ACGTcount: A:0.35, C:0.24, G:0.08, T:0.33
Consensus pattern (27 bp):
TACCCTCGATTTAAAAAATTACCAATG
Found at i:12306718 original size:40 final size:39
Alignment explanation
Indices: 12306653--12306728 Score: 125
Period size: 40 Copynumber: 1.9 Consensus size: 39
12306643 AAAATTATTA
*
12306653 AAATACCCTGTAAGGTAGAATTACTGAAATACCCCTTCG
1 AAATACCCTGTAAGGTAGAAATACTGAAATACCCCTTCG
*
12306692 AAATACCCTTGTAGGGTAGAAATACTGAAATACCCCT
1 AAATACCC-TGTAAGGTAGAAATACTGAAATACCCCT
12306729 GTAGGGTAGA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
39 8 0.24
40 26 0.76
ACGTcount: A:0.37, C:0.22, G:0.16, T:0.25
Consensus pattern (39 bp):
AAATACCCTGTAAGGTAGAAATACTGAAATACCCCTTCG
Found at i:12306731 original size:27 final size:27
Alignment explanation
Indices: 12306690--12306767 Score: 104
Period size: 27 Copynumber: 2.9 Consensus size: 27
12306680 AATACCCCTT
12306690 CGAAATACCCTTGTAGGGTAGAAATAC
1 CGAAATACCCTTGTAGGGTAGAAATAC
* * *
12306717 TGAAATACCCCTGTAGGGTAGAATTAC
1 CGAAATACCCTTGTAGGGTAGAAATAC
* *
12306744 CGAGATACCCTTGTGGGGTA-AAAT
1 CGAAATACCCTTGTAGGGTAGAAAT
12306768 TACCATTTTG
Statistics
Matches: 43, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
26 3 0.07
27 40 0.93
ACGTcount: A:0.33, C:0.18, G:0.24, T:0.24
Consensus pattern (27 bp):
CGAAATACCCTTGTAGGGTAGAAATAC
Found at i:12307006 original size:28 final size:28
Alignment explanation
Indices: 12306974--12307060 Score: 124
Period size: 28 Copynumber: 3.2 Consensus size: 28
12306964 GGAGGAAGTG
*
12306974 TTCTGGTGGTTATGCCACAAATATCTGT
1 TTCTGGTGGCTATGCCACAAATATCTGT
12307002 TTCTGGTGGCTATGCCACAAATATCTGT
1 TTCTGGTGGCTATGCCACAAATATCTGT
**
12307030 TT-TGGTGGCTCCGCCAC-AATATCTGT
1 TTCTGGTGGCTATGCCACAAATATCTGT
*
12307056 ATCTG
1 TTCTG
12307061 ATGACTCTAT
Statistics
Matches: 54, Mismatches: 4, Indels: 3
0.89 0.07 0.05
Matches are distributed among these distances:
26 10 0.19
27 15 0.28
28 29 0.54
ACGTcount: A:0.20, C:0.22, G:0.22, T:0.37
Consensus pattern (28 bp):
TTCTGGTGGCTATGCCACAAATATCTGT
Found at i:12315448 original size:48 final size:48
Alignment explanation
Indices: 12315393--12315726 Score: 318
Period size: 48 Copynumber: 7.0 Consensus size: 48
12315383 AGGGTGGATT
* * *
12315393 GCCGATGCCATGTTCTAAACATGGTCTTACACTAGCTCACATGTCGA-G
1 GCCGATGCCATGTCCCAAACATGGTCTTACACTAGCTCACATATC-ATG
* * * **
12315441 GCCGATGCCATGTCCCAAACATGATCTTACACT-GC-CTCTTAGAAGGTG
1 GCCGATGCCATGTCCCAAACATGGTCTTACACTAGCTCACATATCA--TG
** *
12315489 GCCGATGCCATGTCCCGGACATGGTCTTACACTAGCGCACATATCAAT-
1 GCCGATGCCATGTCCCAAACATGGTCTTACACTAGCTCACATATC-ATG
*
12315537 GCCGATGCCATGTCCCAAACATGGTCTTACACTAGCGCACATATCAATG
1 GCCGATGCCATGTCCCAAACATGGTCTTACACTAGCTCACATATC-ATG
* * * * * * *
12315586 G-CAATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCACAACATC
1 GCCGATGCCATGTCCCAAACATGGTCTTACACTAGCTCACATATCATG
* * * * *
12315633 GCTGATGCCATGTTCTAAACATGGTCTTACACTGGCTCTCATATCATG
1 GCCGATGCCATGTCCCAAACATGGTCTTACACTAGCTCACATATCATG
* * * * * *
12315681 GCTGAAGCCATGTCCCAGACATGGTCTTACATTGGCACACATATCA
1 GCCGATGCCATGTCCCAAACATGGTCTTACACTAGCTCACATATCA
12315727 CTCAAATGTC
Statistics
Matches: 238, Mismatches: 40, Indels: 16
0.81 0.14 0.05
Matches are distributed among these distances:
45 1 0.00
46 3 0.01
47 5 0.02
48 220 0.92
49 4 0.02
50 4 0.02
51 1 0.00
ACGTcount: A:0.26, C:0.29, G:0.19, T:0.25
Consensus pattern (48 bp):
GCCGATGCCATGTCCCAAACATGGTCTTACACTAGCTCACATATCATG
Found at i:12315655 original size:144 final size:143
Alignment explanation
Indices: 12315392--12315726 Score: 384
Period size: 144 Copynumber: 2.3 Consensus size: 143
12315382 GAGGGTGGAT
* * * * * *
12315392 TGCCGATGCCATGTTCTAAACATGGTCTTACACTAGCTCACATGTCGAGGCCGATGCCATGTCCC
1 TGCCGATGCCATGTCCCAAACATGGTCTTACACTAGCACACATATCAAGGCCAATGCCATGTCCC
* * ** * **
12315457 AAACATGATCTTACACTGCCTCTTAGAAGGTGGCCGATGCCATGTCCCGGACATGGTCTTACACT
66 AAACATGATCTTACACTGCCTCTCACAACATCGCCGATGCCATGTCCCAAACATGGTCTTACACT
12315522 AGCGCACATATCAA
131 AGCGCACATATC-A
*
12315536 TGCCGATGCCATGTCCCAAACATGGTCTTACACTAGCGCACATATCAATGG-CAATGCCATGTCC
1 TGCCGATGCCATGTCCCAAACATGGTCTTACACTAGCACACATATCAA-GGCCAATGCCATGTCC
* * * * * *
12315600 CAGACATGGTCTTACACTGGCTCTCACAACATCGCTGATGCCATGTTCTAAACATGGTCTTACAC
65 CAAACATGATCTTACACTGCCTCTCACAACATCGCCGATGCCATGTCCCAAACATGGTCTTACAC
* * *
12315665 TGGCTCTCATATCA
130 TAGCGCACATATCA
* * * * *
12315679 TGGCTGAAGCCATGTCCCAGACATGGTCTTACATTGGCACACATATCA
1 T-GCCGATGCCATGTCCCAAACATGGTCTTACACTAGCACACATATCA
12315727 CTCAAATGTC
Statistics
Matches: 161, Mismatches: 28, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
143 2 0.01
144 157 0.98
145 2 0.01
ACGTcount: A:0.26, C:0.29, G:0.19, T:0.26
Consensus pattern (143 bp):
TGCCGATGCCATGTCCCAAACATGGTCTTACACTAGCACACATATCAAGGCCAATGCCATGTCCC
AAACATGATCTTACACTGCCTCTCACAACATCGCCGATGCCATGTCCCAAACATGGTCTTACACT
AGCGCACATATCA
Found at i:12323301 original size:48 final size:48
Alignment explanation
Indices: 12323049--12323512 Score: 294
Period size: 48 Copynumber: 9.7 Consensus size: 48
12323039 GGTGGATTGC
* * * * * ** * *
12323049 CGATGCCATGTTCCAAACATGGTCTTATAGTGGCTCACATGTCGAGGC
1 CGATGCCATGTCCCAGACATGGTCTTACATTGGCTCTCATAACGTGGT
* * * * ** * *
12323097 CGATGCCATGTCCCATACATGGCCTTACACTAGCTCT-AGTCTCTTTG-
1 CGATGCCATGTCCCAGACATGGTCTTACATTGGCTCTCA-TAACGTGGT
* * * * * *
12323144 CTGATGCCATGTCCCAGACATGGTCTTACACTAGCTTTCAAAAGGT-GC
1 C-GATGCCATGTCCCAGACATGGTCTTACATTGGCTCTCATAACGTGGT
* * * ** * * * * *
12323192 CTATGCCATGTCCTAG-CATGGTCTTACACTAACGCACATATCAAT-GC
1 CGATGCCATGTCCCAGACATGGTCTTACATTGGCTCTCATAAC-GTGGT
* * * *
12323239 CGGTGCTATTTCCCAGACATGGTCTTACATTGGCTCTCATAAGGTGG-
1 CGATGCCATGTCCCAGACATGGTCTTACATTGGCTCTCATAACGTGGT
* * *
12323286 CTGATGCCACGTCCCAAACATGGTCTTACACTGGCTCTCATAACGTGGT
1 C-GATGCCATGTCCCAGACATGGTCTTACATTGGCTCTCATAACGTGGT
* * * * ***
12323335 CGATGCCATGTCCCAGACATGGTCTTACATTAGCGCACATATCAAAGT
1 CGATGCCATGTCCCAGACATGGTCTTACATTGGCTCTCATAACGTGGT
* * * *
12323383 CGATGCCATGTCCCAGACACGGTCTTACATTGGCTCTCACAACATCGT
1 CGATGCCATGTCCCAGACATGGTCTTACATTGGCTCTCATAACGTGGT
* * * *
12323431 CGATGCCATGTTCCAAACATGGTCTTACATTGGCTCTCATATCGTGGC
1 CGATGCCATGTCCCAGACATGGTCTTACATTGGCTCTCATAACGTGGT
* * * * *
12323479 CAACT-CTATGTCTCAGAAATGGTCTTACACTGGC
1 CGA-TGCCATGTCCCAGACATGGTCTTACATTGGC
12323513 ACACATATCA
Statistics
Matches: 324, Mismatches: 82, Indels: 20
0.76 0.19 0.05
Matches are distributed among these distances:
46 19 0.06
47 32 0.10
48 270 0.83
49 3 0.01
ACGTcount: A:0.23, C:0.28, G:0.20, T:0.28
Consensus pattern (48 bp):
CGATGCCATGTCCCAGACATGGTCTTACATTGGCTCTCATAACGTGGT
Found at i:12323409 original size:144 final size:144
Alignment explanation
Indices: 12323143--12323522 Score: 444
Period size: 144 Copynumber: 2.7 Consensus size: 144
12323133 TAGTCTCTTT
* * * * * * *
12323143 GCTGATGCCATGTCCCAGACATGGTCTTACACTAGCTTTCAAAAGGT-GCCTATGCCATGTCCTA
1 GCTGATGCCATGTCCCAAACATGGTCTTACACTGGCTCTCATAACGTGGCCAATGCCATGTCCCA
* * * * * *
12323207 G-CATGGTCTTACACTAACGCACATATCAATGCCGGTGCTATTTCCCAGACATGGTCTTACATTG
66 GACATGGTCTTACACTAGCGCACATATCAAAGCCGATGCCATGTCCCAGACACGGTCTTACATTG
* ** *
12323271 GCTCTCATAAGGTG
131 GCTCTCACAACATC
* * *
12323285 GCTGATGCCACGTCCCAAACATGGTCTTACACTGGCTCTCATAACGTGGTCGATGCCATGTCCCA
1 GCTGATGCCATGTCCCAAACATGGTCTTACACTGGCTCTCATAACGTGGCCAATGCCATGTCCCA
* *
12323350 GACATGGTCTTACATTAGCGCACATATCAAAGTCGATGCCATGTCCCAGACACGGTCTTACATTG
66 GACATGGTCTTACACTAGCGCACATATCAAAGCCGATGCCATGTCCCAGACACGGTCTTACATTG
12323415 GCTCTCACAACATC
131 GCTCTCACAACATC
* * * * *
12323429 G-TCGATGCCATGTTCCAAACATGGTCTTACATTGGCTCTCATATCGTGGCCAACT-CTATGTCT
1 GCT-GATGCCATGTCCCAAACATGGTCTTACACTGGCTCTCATAACGTGGCCAA-TGCCATGTCC
* * *
12323492 CAGAAATGGTCTTACACTGGCACACATATCA
64 CAGACATGGTCTTACACTAGCGCACATATCA
12323523 CCCAAATGTC
Statistics
Matches: 201, Mismatches: 33, Indels: 6
0.84 0.14 0.03
Matches are distributed among these distances:
142 41 0.20
143 16 0.08
144 143 0.71
145 1 0.00
ACGTcount: A:0.25, C:0.28, G:0.19, T:0.28
Consensus pattern (144 bp):
GCTGATGCCATGTCCCAAACATGGTCTTACACTGGCTCTCATAACGTGGCCAATGCCATGTCCCA
GACATGGTCTTACACTAGCGCACATATCAAAGCCGATGCCATGTCCCAGACACGGTCTTACATTG
GCTCTCACAACATC
Found at i:12323490 original size:96 final size:96
Alignment explanation
Indices: 12323049--12323512 Score: 339
Period size: 96 Copynumber: 4.9 Consensus size: 96
12323039 GGTGGATTGC
* * * * * * *
12323049 CGATGCCATGTTCCAAACATGGTCTTATAGTGGCTCACATGTCGAGGCCGATGCCATGTCCCATA
1 CGATGCCATGTCCCAAACATGGTCTTACATTGGCTCTCATATCGTGGCCGATGCCATGTCCCAGA
* * ** *
12323114 CATGGCCTTACACTAGCTCT-A-GTC-TCTTT
66 CATGGTCTTACACTGGCTCTCACAACATC-GT
* * * * * ** * *
12323143 GCTGATGCCATGTCCCAGACATGGTCTTACACTAGCTTTCAAAAGGT-GCCTATGCCATGTCCTA
1 -C-GATGCCATGTCCCAAACATGGTCTTACATTGGCTCTCATATCGTGGCCGATGCCATGTCCCA
** * * * * *
12323207 G-CATGGTCTTACACTAACGCACATATCAAT-GC
64 GACATGGTCTTACACTGGCTCTCACAAC-ATCGT
* * * * ** * * *
12323239 CGGTGCTATTTCCCAGACATGGTCTTACATTGGCTCTCATAAGGTGGCTGATGCCACGTCCCAAA
1 CGATGCCATGTCCCAAACATGGTCTTACATTGGCTCTCATATCGTGGCCGATGCCATGTCCCAGA
* * *
12323304 CATGGTCTTACACTGGCTCTCATAACGTGGT
66 CATGGTCTTACACTGGCTCTCACAACATCGT
* * * * *** *
12323335 CGATGCCATGTCCCAGACATGGTCTTACATTAGCGCACATATCAAAGTCGATGCCATGTCCCAGA
1 CGATGCCATGTCCCAAACATGGTCTTACATTGGCTCTCATATCGTGGCCGATGCCATGTCCCAGA
* *
12323400 CACGGTCTTACATTGGCTCTCACAACATCGT
66 CATGGTCTTACACTGGCTCTCACAACATCGT
* * * *
12323431 CGATGCCATGTTCCAAACATGGTCTTACATTGGCTCTCATATCGTGGCCAACT-CTATGTCTCAG
1 CGATGCCATGTCCCAAACATGGTCTTACATTGGCTCTCATATCGTGGCCGA-TGCCATGTCCCAG
*
12323495 AAATGGTCTTACACTGGC
65 ACATGGTCTTACACTGGC
12323513 ACACATATCA
Statistics
Matches: 284, Mismatches: 76, Indels: 17
0.75 0.20 0.05
Matches are distributed among these distances:
94 53 0.19
95 32 0.11
96 197 0.69
97 1 0.00
98 1 0.00
ACGTcount: A:0.23, C:0.28, G:0.20, T:0.28
Consensus pattern (96 bp):
CGATGCCATGTCCCAAACATGGTCTTACATTGGCTCTCATATCGTGGCCGATGCCATGTCCCAGA
CATGGTCTTACACTGGCTCTCACAACATCGT
Found at i:12333125 original size:28 final size:28
Alignment explanation
Indices: 12333019--12333119 Score: 150
Period size: 28 Copynumber: 3.6 Consensus size: 28
12333009 TGGGAAACAG
* *
12333019 TTGGGCCTGATAGGCCATATGAATGTGA
1 TTGGGCTTGATGGGCCATATGAATGTGA
*
12333047 CTGGG-TCTGATGGGCCATATGAATGTGA
1 TTGGGCT-TGATGGGCCATATGAATGTGA
*
12333075 TTGGGCTTGATGGGCCATATGAATGTAA
1 TTGGGCTTGATGGGCCATATGAATGTGA
12333103 TTGGGCTTGATGGGCCA
1 TTGGGCTTGATGGGCCA
12333120 AGTGAACGAG
Statistics
Matches: 66, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
28 65 0.98
29 1 0.02
ACGTcount: A:0.22, C:0.14, G:0.35, T:0.30
Consensus pattern (28 bp):
TTGGGCTTGATGGGCCATATGAATGTGA
Found at i:12333485 original size:27 final size:27
Alignment explanation
Indices: 12333455--12334119 Score: 591
Period size: 27 Copynumber: 24.7 Consensus size: 27
12333445 TAATAAAGAG
*
12333455 AAATTACTAAAATACCCTCGATTTGTA
1 AAATTACTGAAATACCCTCGATTTGTA
*
12333482 AAATTAC-GAAAATACCCTTGATTTGTA
1 AAATTACTG-AAATACCCTCGATTTGTA
*
12333509 AAATTA-TCGAAATACCCTCGA-TTGTG
1 AAATTACT-GAAATACCCTCGATTTGTA
*
12333535 AAATTATTGAAATACCCTCGATTTGTA
1 AAATTACTGAAATACCCTCGATTTGTA
* *
12333562 CAATTA-TCAAAATA-CCTCCGATTTGTA
1 AAATTACT-GAAATACCCT-CGATTTGTA
* *
12333589 AAATTA-TCGAAACACCCTCAATTTGTA
1 AAATTACT-GAAATACCCTCGATTTGTA
* * * *
12333616 AAATTACCGAAACACTCTCAATTTGTA
1 AAATTACTGAAATACCCTCGATTTGTA
* *
12333643 AAATTACTGAAACACCCTCGATTTGTG
1 AAATTACTGAAATACCCTCGATTTGTA
* *
12333670 AAATTATTAAAATACCCTCGATTTGTA
1 AAATTACTGAAATACCCTCGATTTGTA
* * *
12333697 AAATTA-TCAAAACACCCTTGATTTGTA
1 AAATTACT-GAAATACCCTCGATTTGTA
* * *
12333724 AAATTATTGAAACACGCTCGATTTGTA
1 AAATTACTGAAATACCCTCGATTTGTA
* * *
12333751 AAATTA-TCAAAATACCATCAATTTGTA
1 AAATTACT-GAAATACCCTCGATTTGTA
* **
12333778 AAATTACCGAAATACCCTTTATTTGTA
1 AAATTACTGAAATACCCTCGATTTGTA
* * *
12333805 AAATTACCGAAATACCATTGATTTGTA
1 AAATTACTGAAATACCCTCGATTTGTA
*
12333832 AAATTA-TCGAAATACCCCCGATTTGTA
1 AAATTACT-GAAATACCCTCGATTTGTA
* * *
12333859 AAATTACCGAAATACCATCAATTTGTA
1 AAATTACTGAAATACCCTCGATTTGTA
* * * *
12333886 AAATTATTGAAACACCCCCAATTTGTA
1 AAATTACTGAAATACCCTCGATTTGTA
* ** *
12333913 AAATTA-TCAAAATACTGTCAATTTGTA
1 AAATTACT-GAAATACCCTCGATTTGTA
**
12333940 AAATTACTGAAATACCCTTTATTTGTA
1 AAATTACTGAAATACCCTCGATTTGTA
* * *
12333967 AAATTACCGAAATACCATTGATTTGTA
1 AAATTACTGAAATACCCTCGATTTGTA
*
12333994 AAATTA-TCGAAATACCCCCGATTTGTA
1 AAATTACT-GAAATACCCTCGATTTGTA
* *
12334021 AAATTACTGAAATACCATCAATTTGTA
1 AAATTACTGAAATACCCTCGATTTGTA
* * * *
12334048 AAATTATTGAAACACCCCCAATTTGTA
1 AAATTACTGAAATACCCTCGATTTGTA
* * *
12334075 ATATTA-TCGAAATACCCTTG-TAGTGTA
1 AAATTACT-GAAATACCCTCGAT-TTGTA
* *
12334102 AAATGACTGACATACCCT
1 AAATTACTGAAATACCCT
12334120 TGTAGGGTTT
Statistics
Matches: 532, Mismatches: 84, Indels: 44
0.81 0.13 0.07
Matches are distributed among these distances:
26 32 0.06
27 492 0.92
28 8 0.02
ACGTcount: A:0.40, C:0.18, G:0.09, T:0.33
Consensus pattern (27 bp):
AAATTACTGAAATACCCTCGATTTGTA
Found at i:12333614 original size:54 final size:54
Alignment explanation
Indices: 12333464--12334092 Score: 676
Period size: 54 Copynumber: 11.7 Consensus size: 54
12333454 GAAATTACTA
*
12333464 AAATACCCTCGATTTGTAAAATTA-CGAAAATACCCTTGATTTGTAAAATTATCG
1 AAATACCCTCGATTTGTAAAATTATCG-AAATACCCTCGATTTGTAAAATTATCG
* * * *
12333518 AAATACCCTCGA-TTGTGAAATTATTGAAATACCCTCGATTTGTACAATTATCA
1 AAATACCCTCGATTTGTAAAATTATCGAAATACCCTCGATTTGTAAAATTATCG
* * *
12333571 AAATA-CCTCCGATTTGTAAAATTATCGAAACACCCTCAATTTGTAAAATTACCG
1 AAATACCCT-CGATTTGTAAAATTATCGAAATACCCTCGATTTGTAAAATTATCG
* * * * * **
12333625 AAACACTCTCAATTTGTAAAATTA-CTGAAACACCCTCGATTTGTGAAATTATTA
1 AAATACCCTCGATTTGTAAAATTATC-GAAATACCCTCGATTTGTAAAATTATCG
* * * *
12333679 AAATACCCTCGATTTGTAAAATTATCAAAACACCCTTGATTTGTAAAATTATTG
1 AAATACCCTCGATTTGTAAAATTATCGAAATACCCTCGATTTGTAAAATTATCG
* * * * * *
12333733 AAACACGCTCGATTTGTAAAATTATCAAAATACCATCAATTTGTAAAATTACCG
1 AAATACCCTCGATTTGTAAAATTATCGAAATACCCTCGATTTGTAAAATTATCG
** * * *
12333787 AAATACCCTTTATTTGTAAAATTACCGAAATACCATTGATTTGTAAAATTATCG
1 AAATACCCTCGATTTGTAAAATTATCGAAATACCCTCGATTTGTAAAATTATCG
* * * * *
12333841 AAATACCCCCGATTTGTAAAATTACCGAAATACCATCAATTTGTAAAATTATTG
1 AAATACCCTCGATTTGTAAAATTATCGAAATACCCTCGATTTGTAAAATTATCG
* * * * ** *
12333895 AAACACCCCCAATTTGTAAAATTATCAAAATACTGTCAATTTGTAAAATTA-CTG
1 AAATACCCTCGATTTGTAAAATTATCGAAATACCCTCGATTTGTAAAATTATC-G
** * * *
12333949 AAATACCCTTTATTTGTAAAATTACCGAAATACCATTGATTTGTAAAATTATCG
1 AAATACCCTCGATTTGTAAAATTATCGAAATACCCTCGATTTGTAAAATTATCG
* * * *
12334003 AAATACCCCCGATTTGTAAAATTA-CTGAAATACCATCAATTTGTAAAATTATTG
1 AAATACCCTCGATTTGTAAAATTATC-GAAATACCCTCGATTTGTAAAATTATCG
* * * *
12334057 AAACACCCCCAATTTGTAATATTATCGAAATACCCT
1 AAATACCCTCGATTTGTAAAATTATCGAAATACCCT
12334093 TGTAGTGTAA
Statistics
Matches: 488, Mismatches: 77, Indels: 20
0.83 0.13 0.03
Matches are distributed among these distances:
52 3 0.01
53 44 0.09
54 436 0.89
55 5 0.01
ACGTcount: A:0.40, C:0.18, G:0.09, T:0.33
Consensus pattern (54 bp):
AAATACCCTCGATTTGTAAAATTATCGAAATACCCTCGATTTGTAAAATTATCG
Found at i:12334102 original size:81 final size:81
Alignment explanation
Indices: 12333455--12334119 Score: 703
Period size: 81 Copynumber: 8.2 Consensus size: 81
12333445 TAATAAAGAG
* * * *
12333455 AAATTACTAAAATACCCTCGATTTGTAAAATTA-CGAAAATACCCTTGATTTGTAAAATTATCGA
1 AAATTACTGAAATACCCTCAATTTGTAAAATTATCG-AAACACCCTCGATTTGTAAAATTATCGA
*
12333519 AATACCCTCGA-TTGTG
65 AATACCCTCGATTTGTA
* * * * *
12333535 AAATTATTGAAATACCCTCGATTTGTACAATTATCAAAATA-CCTCCGATTTGTAAAATTATCGA
1 AAATTACTGAAATACCCTCAATTTGTAAAATTATCGAAACACCCT-CGATTTGTAAAATTATCGA
* *
12333599 AACACCCTCAATTTGTA
65 AATACCCTCGATTTGTA
* * * * **
12333616 AAATTACCGAAACACTCTCAATTTGTAAAATTA-CTGAAACACCCTCGATTTGTGAAATTATTAA
1 AAATTACTGAAATACCCTCAATTTGTAAAATTATC-GAAACACCCTCGATTTGTAAAATTATCGA
12333680 AATACCCTCGATTTGTA
65 AATACCCTCGATTTGTA
* * ** * * *
12333697 AAATTA-TCAAAACACCCTTGATTTGTAAAATTATTGAAACACGCTCGATTTGTAAAATTATCAA
1 AAATTACT-GAAATACCCTCAATTTGTAAAATTATCGAAACACCCTCGATTTGTAAAATTATCGA
* *
12333761 AATACCATCAATTTGTA
65 AATACCCTCGATTTGTA
* ** * * * *
12333778 AAATTACCGAAATACCCTTTATTTGTAAAATTACCGAAATACCATTGATTTGTAAAATTATCGAA
1 AAATTACTGAAATACCCTCAATTTGTAAAATTATCGAAACACCCTCGATTTGTAAAATTATCGAA
*
12333843 ATACCCCCGATTTGTA
66 ATACCCTCGATTTGTA
* * * * * *
12333859 AAATTACCGAAATACCATCAATTTGTAAAATTATTGAAACACCCCCAATTTGTAAAATTATCAAA
1 AAATTACTGAAATACCCTCAATTTGTAAAATTATCGAAACACCCTCGATTTGTAAAATTATCGAA
** *
12333924 ATACTGTCAATTTGTA
66 ATACCCTCGATTTGTA
** * * * *
12333940 AAATTACTGAAATACCCTTTATTTGTAAAATTACCGAAATACCATTGATTTGTAAAATTATCGAA
1 AAATTACTGAAATACCCTCAATTTGTAAAATTATCGAAACACCCTCGATTTGTAAAATTATCGAA
*
12334005 ATACCCCCGATTTGTA
66 ATACCCTCGATTTGTA
* * * * *
12334021 AAATTACTGAAATACCATCAATTTGTAAAATTATTGAAACACCCCCAATTTGTAATATTATCGAA
1 AAATTACTGAAATACCCTCAATTTGTAAAATTATCGAAACACCCTCGATTTGTAAAATTATCGAA
* *
12334086 ATACCCTTG-TAGTGTA
66 ATACCCTCGAT-TTGTA
* *
12334102 AAATGACTGACATACCCT
1 AAATTACTGAAATACCCT
12334120 TGTAGGGTTT
Statistics
Matches: 482, Mismatches: 94, Indels: 17
0.81 0.16 0.03
Matches are distributed among these distances:
79 3 0.01
80 64 0.13
81 412 0.85
82 3 0.01
ACGTcount: A:0.40, C:0.18, G:0.09, T:0.33
Consensus pattern (81 bp):
AAATTACTGAAATACCCTCAATTTGTAAAATTATCGAAACACCCTCGATTTGTAAAATTATCGAA
ATACCCTCGATTTGTA
Found at i:12336338 original size:16 final size:16
Alignment explanation
Indices: 12336319--12336349 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
12336309 ACGACAAAGG
*
12336319 CTGAAAAGTTGAAAAA
1 CTGAAAAGGTGAAAAA
12336335 CTGAAAAGGTGAAAA
1 CTGAAAAGGTGAAAA
12336350 GCTAAAATGT
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:0.55, C:0.06, G:0.23, T:0.16
Consensus pattern (16 bp):
CTGAAAAGGTGAAAAA
Found at i:12353152 original size:33 final size:33
Alignment explanation
Indices: 12353114--12353182 Score: 129
Period size: 33 Copynumber: 2.1 Consensus size: 33
12353104 GCTAGCTTTG
*
12353114 AAGTCACTAAAATCATGGAAAAATAAACAAAGT
1 AAGTCACTAAAATCATGGAAAAACAAACAAAGT
12353147 AAGTCACTAAAATCATGGAAAAACAAACAAAGT
1 AAGTCACTAAAATCATGGAAAAACAAACAAAGT
12353180 AAG
1 AAG
12353183 CTTTATAGGA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.58, C:0.13, G:0.13, T:0.16
Consensus pattern (33 bp):
AAGTCACTAAAATCATGGAAAAACAAACAAAGT
Found at i:12362779 original size:22 final size:23
Alignment explanation
Indices: 12362731--12362793 Score: 85
Period size: 22 Copynumber: 2.8 Consensus size: 23
12362721 GACTCACCAC
*
12362731 AGCTCGTATGAGCTTACCATTTT
1 AGCTCTTATGAGCTTACCATTTT
*
12362754 AGCTCTTATGAGCTTATCA-TTT
1 AGCTCTTATGAGCTTACCATTTT
12362776 AGCTCTTCA-GAGCTTACC
1 AGCTCTT-ATGAGCTTACC
12362794 GTTTCAGTCC
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
22 18 0.50
23 18 0.50
ACGTcount: A:0.22, C:0.24, G:0.16, T:0.38
Consensus pattern (23 bp):
AGCTCTTATGAGCTTACCATTTT
Found at i:12366335 original size:46 final size:45
Alignment explanation
Indices: 12366285--12366460 Score: 212
Period size: 46 Copynumber: 3.8 Consensus size: 45
12366275 TGTTTGGGCA
12366285 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
*** * *
12366331 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAG-GCA-
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GCGAAG
*
12366378 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
* *
12366424 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
12366461 GCGGGTTACA
Statistics
Matches: 111, Mismatches: 12, Indels: 14
0.81 0.09 0.10
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 1 0.01
46 69 0.62
47 32 0.29
48 1 0.01
49 3 0.03
50 1 0.01
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.28
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAG
Found at i:12366440 original size:93 final size:93
Alignment explanation
Indices: 12366281--12366452 Score: 308
Period size: 93 Copynumber: 1.8 Consensus size: 93
12366271 AGGATGTTTG
* *
12366281 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
12366346 TTGAGTCCGAGTTCGAGAGATGTAACTA
66 TTGAGTCCGAGTTCGAGAGATGTAACTA
* *
12366374 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
12366439 TTGAGTCCGAGTTC
66 TTGAGTCCGAGTTC
12366453 ACTTATGGGC
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.27
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
TTGAGTCCGAGTTCGAGAGATGTAACTA
Found at i:12374754 original size:43 final size:42
Alignment explanation
Indices: 12374633--12374765 Score: 124
Period size: 43 Copynumber: 3.1 Consensus size: 42
12374623 AAACACATAT
* * * * *
12374633 ATCACATA-CAATGCCATATCCCAGATATGGTCTTACATGTT
1 ATCACATATCGATGCCATGTCCCAGACATGGTCTTACACGTA
* * *
12374674 ATCACATATCGATGCCTCTGTCCCAGACAGGGCCTTACACGTA
1 ATCACATATCGATGCC-ATGTCCCAGACATGGTCTTACACGTA
* * * * *
12374717 ATCTCATATCGATGCCAATGTCCCAGAGATAGTCTTACATGAA
1 ATCACATATCGATGCC-ATGTCCCAGACATGGTCTTACACGTA
12374760 ATCACA
1 ATCACA
12374766 CCTCAGAAGT
Statistics
Matches: 72, Mismatches: 18, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
41 8 0.11
42 6 0.08
43 58 0.81
ACGTcount: A:0.31, C:0.27, G:0.15, T:0.27
Consensus pattern (42 bp):
ATCACATATCGATGCCATGTCCCAGACATGGTCTTACACGTA
Found at i:12376370 original size:21 final size:20
Alignment explanation
Indices: 12376340--12376378 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
12376330 ACATACTTGT
12376340 ATAACTATCATCAAACATTC
1 ATAACTATCATCAAACATTC
*
12376360 ATAATCTATCATTAAACAT
1 ATAA-CTATCATCAAACAT
12376379 CAAAATACTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.46, C:0.21, G:0.00, T:0.33
Consensus pattern (20 bp):
ATAACTATCATCAAACATTC
Found at i:12377508 original size:126 final size:126
Alignment explanation
Indices: 12377283--12377536 Score: 463
Period size: 126 Copynumber: 2.0 Consensus size: 126
12377273 ATGAAATACA
*
12377283 TTATGGTTATTTTCTAATTCTGATGGTAAAGCTAGCCGATATGCCACTGGCCCTATTCTTTCGAT
1 TTATGGATATTTTCTAATTCTGATGGTAAAGCTAGCCGATATGCCACTGGCCCTATTCTTTCGAT
12377348 GATCTTATACGGCCCGATGAAACGCAGACTCAATTTGCCTTTGCGACCAAAACGAAAAATT
66 GATCTTATACGGCCCGATGAAACGCAGACTCAATTTGCCTTTGCGACCAAAACGAAAAATT
12377409 TTATGGATATTTTCTAATTCTGATGGTAAAGCTAGCCGATATGCCACTGGCCCTATTCTTTCGAT
1 TTATGGATATTTTCTAATTCTGATGGTAAAGCTAGCCGATATGCCACTGGCCCTATTCTTTCGAT
* * * *
12377474 GATTTTATATGGCCCGATGAAACGCGGACTCAATTTGCCTTTGCGACCAAAACGAAGAATT
66 GATCTTATACGGCCCGATGAAACGCAGACTCAATTTGCCTTTGCGACCAAAACGAAAAATT
12377535 TT
1 TT
12377537 CTTCCACGGA
Statistics
Matches: 123, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
126 123 1.00
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.33
Consensus pattern (126 bp):
TTATGGATATTTTCTAATTCTGATGGTAAAGCTAGCCGATATGCCACTGGCCCTATTCTTTCGAT
GATCTTATACGGCCCGATGAAACGCAGACTCAATTTGCCTTTGCGACCAAAACGAAAAATT
Found at i:12379644 original size:49 final size:49
Alignment explanation
Indices: 12379588--12379813 Score: 245
Period size: 49 Copynumber: 4.6 Consensus size: 49
12379578 CTGGTATGCA
*
12379588 TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACACGCGACCAATTATCCGGTACACG
* ** * * ** * *
12379637 TAGTAGCCTACTTTTAGTACTACATACGTGACCTAACCATCTGATACACG
1 TAGTAGCCTGCACTTAGTACTACACACGCGACC-AATTATCCGGTACACG
* ** * * * *
12379687 TAGTAGCATGCACTTAGTACTACACACGTTATCGAAGTTATCGGGTACGCA
1 TAGTAGCCTGCACTTAGTACTACACACGCGA-CCAA-TTATCCGGTACACG
* **
12379738 TAGTAGCCTGCACTTACTACTACACATACGACCAATTATCCGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACACGCGACCAATTATCCGGTACACG
12379787 TAGTAGCCTGCACTTAGTACTACACAC
1 TAGTAGCCTGCACTTAGTACTACACAC
12379814 ATGACCTCAC
Statistics
Matches: 139, Mismatches: 35, Indels: 6
0.77 0.19 0.03
Matches are distributed among these distances:
49 63 0.45
50 42 0.30
51 34 0.24
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.27
Consensus pattern (49 bp):
TAGTAGCCTGCACTTAGTACTACACACGCGACCAATTATCCGGTACACG
Found at i:12380468 original size:13 final size:13
Alignment explanation
Indices: 12380452--12380476 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12380442 CAAACGAAAT
12380452 TTTCATGAAATCA
1 TTTCATGAAATCA
12380465 TTTCATGAAATC
1 TTTCATGAAATC
12380477 GTAGACTATA
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:0.36, C:0.16, G:0.08, T:0.40
Consensus pattern (13 bp):
TTTCATGAAATCA
Found at i:12384973 original size:20 final size:20
Alignment explanation
Indices: 12384937--12384980 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
12384927 AGGGACTAAA
*
12384937 ATGAAAAGTTGTAAAATTTG
1 ATGAAAAATTGTAAAATTTG
*
12384957 ATGAAAAATTG-AGAAATTTT
1 ATGAAAAATTGTA-AAATTTG
12384977 ATGA
1 ATGA
12384981 GTACATGTGC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 1 0.05
20 20 0.95
ACGTcount: A:0.48, C:0.00, G:0.18, T:0.34
Consensus pattern (20 bp):
ATGAAAAATTGTAAAATTTG
Found at i:12390478 original size:93 final size:93
Alignment explanation
Indices: 12390366--12390538 Score: 310
Period size: 93 Copynumber: 1.9 Consensus size: 93
12390356 CGCCCATAAG
* *
12390366 TGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 TGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
12390431 ACGAGCTCGGATGCCTAGTTACATCTCT
66 ACGAGCTCGGATGCCTAGTTACATCTCT
*
12390459 TGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 TGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
*
12390524 ACGAGTTCGGATGCC
66 ACGAGCTCGGATGCC
12390539 CAAATATCCT
Statistics
Matches: 76, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.27, C:0.29, G:0.21, T:0.22
Consensus pattern (93 bp):
TGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGCTCGGATGCCTAGTTACATCTCT
Found at i:12390534 original size:46 final size:46
Alignment explanation
Indices: 12390359--12390534 Score: 218
Period size: 46 Copynumber: 3.8 Consensus size: 46
12390349 TGTAACCCGC
* *
12390359 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
*
12390405 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA---C-A-TTCGCAT
*
12390455 CTC-T---TGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 C-CATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
*
12390498 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA
12390535 TGCCCAAATA
Statistics
Matches: 114, Mismatches: 5, Indels: 22
0.81 0.04 0.16
Matches are distributed among these distances:
42 3 0.03
43 6 0.05
44 1 0.01
46 66 0.58
47 29 0.25
49 1 0.01
50 5 0.04
51 3 0.03
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.22
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
Found at i:12396298 original size:33 final size:33
Alignment explanation
Indices: 12396256--12396322 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
12396246 ATATACAAAA
* *
12396256 TAGTCTGGGCTGTAGCCTTATTCAGTACTAGAG
1 TAGTCTGGGCTGTAGCCCTATACAGTACTAGAG
* *
12396289 TAGTCTGGGCTTTAGCCCTATACAGTAGTAGAG
1 TAGTCTGGGCTGTAGCCCTATACAGTACTAGAG
12396322 T
1 T
12396323 GGGCCCAAGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.22, C:0.18, G:0.27, T:0.33
Consensus pattern (33 bp):
TAGTCTGGGCTGTAGCCCTATACAGTACTAGAG
Found at i:12396698 original size:27 final size:27
Alignment explanation
Indices: 12396667--12396756 Score: 110
Period size: 27 Copynumber: 3.3 Consensus size: 27
12396657 GGCATAATCG
* * *
12396667 TCATTTTACCATATAGGGGTGTTACGA
1 TCATTTTACCCTACAGGGGTATTACGA
* * *
12396694 TCATTTTACCCTACATGGGTATTATGG
1 TCATTTTACCCTACAGGGGTATTACGA
12396721 TCATTTTACCCTACAGGGGTATTAC-A
1 TCATTTTACCCTACAGGGGTATTACGA
12396747 GTCATTTTAC
1 -TCATTTTAC
12396757 TTACTTTAGG
Statistics
Matches: 53, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
27 53 1.00
ACGTcount: A:0.24, C:0.19, G:0.18, T:0.39
Consensus pattern (27 bp):
TCATTTTACCCTACAGGGGTATTACGA
Found at i:12398341 original size:20 final size:20
Alignment explanation
Indices: 12398316--12398365 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
12398306 TCTCCCAGTT
* **
12398316 ACCAAGTCACGCCACTTGCC
1 ACCAAGCCACGCCACTCACC
12398336 ACCAAGCCACGCCACTCACC
1 ACCAAGCCACGCCACTCACC
12398356 ACCAAGCCAC
1 ACCAAGCCAC
12398366 AAGGCTTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.30, C:0.50, G:0.12, T:0.08
Consensus pattern (20 bp):
ACCAAGCCACGCCACTCACC
Found at i:12402989 original size:56 final size:56
Alignment explanation
Indices: 12402928--12403232 Score: 477
Period size: 56 Copynumber: 5.4 Consensus size: 56
12402918 GACCATGGCC
* * *
12402928 TCGATATATGTGTGCGAGTAAGACAATGTTTTATACGTTGGCATAGATATGTGACT
1 TCGATATATGTGTGCGAGTAAGACCACGTTTTATACGTTGGCATCGATATGTGACT
* * *
12402984 TCGATATATGTGTGTGAGTAAGACCACCTTTTATACGTTGGCATCGATATCTGACT
1 TCGATATATGTGTGCGAGTAAGACCACGTTTTATACGTTGGCATCGATATGTGACT
12403040 TCGATATATGTGTGCGAGTAAGACCACGTTTTATACGTTGGCATCGATATGTGACT
1 TCGATATATGTGTGCGAGTAAGACCACGTTTTATACGTTGGCATCGATATGTGACT
* * *
12403096 TCAATATATGTGTGCGAGTAAGACCACGTTTTATCCGTTGGCATCGATATGTCACT
1 TCGATATATGTGTGCGAGTAAGACCACGTTTTATACGTTGGCATCGATATGTGACT
* * * *
12403152 TCGATATATTTGTGCAAGTAAGACCACGTTTTATATGTTGGCATCGATATATGAC-
1 TCGATATATGTGTGCGAGTAAGACCACGTTTTATACGTTGGCATCGATATGTGACT
12403207 TCTGATATATGTGTGCGAGTAAGACC
1 TC-GATATATGTGTGCGAGTAAGACC
12403233 TTGTCTGGGA
Statistics
Matches: 227, Mismatches: 21, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
55 2 0.01
56 225 0.99
ACGTcount: A:0.27, C:0.16, G:0.23, T:0.35
Consensus pattern (56 bp):
TCGATATATGTGTGCGAGTAAGACCACGTTTTATACGTTGGCATCGATATGTGACT
Found at i:12405324 original size:27 final size:27
Alignment explanation
Indices: 12405264--12405344 Score: 101
Period size: 27 Copynumber: 3.0 Consensus size: 27
12405254 TGGCTGCCAA
* * *
12405264 AACAGATA-ATGTGACATAGTCACCAG
1 AACAGATATTTGTGGCATAGCCACCAG
*
12405290 ATAAAGATATTTGTGGCATAGCCACCAG
1 A-ACAGATATTTGTGGCATAGCCACCAG
*
12405318 AACAGATATTTGTGGCAGAGCCACCAG
1 AACAGATATTTGTGGCATAGCCACCAG
12405345 GACACTTCCT
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
26 1 0.02
27 30 0.64
28 16 0.34
ACGTcount: A:0.37, C:0.20, G:0.22, T:0.21
Consensus pattern (27 bp):
AACAGATATTTGTGGCATAGCCACCAG
Found at i:12409617 original size:50 final size:50
Alignment explanation
Indices: 12409485--12409685 Score: 224
Period size: 50 Copynumber: 4.0 Consensus size: 50
12409475 ATGATCTATT
* * * * * *
12409485 GTGAGGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGAAAA
1 GTGAGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAG-ATA
* * * * *
12409536 CTGTGATCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATG
1 GTGAGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATA
*
12409586 GTGAGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATA
1 GTGAGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATA
* * * * * *
12409636 AT-TGGTCGCGTGTGTAGTACTATGTGCAGGCTACTATGCGTACCAGATA
1 GTGAGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATA
12409685 G
1 G
12409686 CTTTGGCTAC
Statistics
Matches: 125, Mismatches: 25, Indels: 2
0.82 0.16 0.01
Matches are distributed among these distances:
49 41 0.33
50 46 0.37
51 38 0.30
ACGTcount: A:0.24, C:0.18, G:0.30, T:0.27
Consensus pattern (50 bp):
GTGAGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATA
Found at i:12412706 original size:15 final size:15
Alignment explanation
Indices: 12412686--12412750 Score: 73
Period size: 15 Copynumber: 4.4 Consensus size: 15
12412676 GTATCTTGGG
12412686 TTTCTTTATTCTGGA
1 TTTCTTTATTCTGGA
*
12412701 TTTCTTTATTCTGGG
1 TTTCTTTATTCTGGA
12412716 TTT-TTCTA-TCTTGGA
1 TTTCTT-TATTC-TGGA
*
12412731 TTTCTTTATTC-GGT
1 TTTCTTTATTCTGGA
12412745 TTTCTT
1 TTTCTT
12412751 GTTATCTTTA
Statistics
Matches: 43, Mismatches: 3, Indels: 9
0.78 0.05 0.16
Matches are distributed among these distances:
14 12 0.28
15 27 0.63
16 4 0.09
ACGTcount: A:0.09, C:0.14, G:0.14, T:0.63
Consensus pattern (15 bp):
TTTCTTTATTCTGGA
Found at i:12412718 original size:30 final size:31
Alignment explanation
Indices: 12412682--12412750 Score: 92
Period size: 30 Copynumber: 2.3 Consensus size: 31
12412672 TATCGTATCT
12412682 TGGGTTTCTT-TAT-TCTGGATTTCTTTATTC
1 TGGGTTTCTTCTATCT-TGGATTTCTTTATTC
12412712 TGGGTTT-TTCTATCTTGGATTTCTTTATTC
1 TGGGTTTCTTCTATCTTGGATTTCTTTATTC
*
12412742 -GGTTTTCTT
1 TGGGTTTCTT
12412751 GTTATCTTTA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
29 7 0.20
30 27 0.77
31 1 0.03
ACGTcount: A:0.09, C:0.13, G:0.17, T:0.61
Consensus pattern (31 bp):
TGGGTTTCTTCTATCTTGGATTTCTTTATTC
Found at i:12419410 original size:49 final size:50
Alignment explanation
Indices: 12419280--12419420 Score: 160
Period size: 51 Copynumber: 2.8 Consensus size: 50
12419270 TCTATTGTGA
*
12419280 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGAAAACTGT
1 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTACGCGTACCC-AAAACTGT
* * * * * *
12419331 GATCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGT-GCC-AGACTGCT
1 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTACGCGTACCCAAAACTG-T
* * *
12419380 GGTCGCATGTGTAATACTAAGTGCAAGCTACTATGCGTACC
1 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTACGCGTACC
12419421 AGATAGCTTC
Statistics
Matches: 73, Mismatches: 15, Indels: 5
0.78 0.16 0.05
Matches are distributed among these distances:
48 5 0.07
49 32 0.44
50 3 0.04
51 33 0.45
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (50 bp):
GGTCGCATGTGTAGTACTAAGTGCAGGCTACTACGCGTACCCAAAACTGT
Found at i:12419423 original size:49 final size:48
Alignment explanation
Indices: 12419280--12419423 Score: 171
Period size: 49 Copynumber: 2.9 Consensus size: 48
12419270 TCTATTGTGA
*
12419280 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGAAAACTGT
1 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTA-CC--AGACTGT
* * * * * *
12419331 GATCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTGCCAGACTGCT
1 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGACTG-T
* *
12419380 GGTCGCATGTGTAATACTAAGTGCAAGCTACTATGCGTACCAGA
1 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGA
12419424 TAGCTTCGGC
Statistics
Matches: 77, Mismatches: 15, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
48 5 0.06
49 37 0.48
50 2 0.03
51 33 0.43
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.26
Consensus pattern (48 bp):
GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGACTGT
Found at i:12422445 original size:15 final size:15
Alignment explanation
Indices: 12422422--12422487 Score: 59
Period size: 15 Copynumber: 4.5 Consensus size: 15
12422412 GTATCGTATC
*
12422422 TTGGGTTTCTTTATT
1 TTGGATTTCTTTATT
12422437 TTGGATTTCTTTATT
1 TTGGATTTCTTTATT
* *
12422452 CTAGG-TTT-TTCTATC
1 -TTGGATTTCTT-TATT
12422467 TTGGATTTCTTT-TT
1 TTGGATTTCTTTATT
12422481 TT-GATTT
1 TTGGATTT
12422488 TCTTGTTATC
Statistics
Matches: 42, Mismatches: 5, Indels: 10
0.74 0.09 0.18
Matches are distributed among these distances:
13 5 0.12
14 8 0.19
15 24 0.57
16 5 0.12
ACGTcount: A:0.11, C:0.09, G:0.15, T:0.65
Consensus pattern (15 bp):
TTGGATTTCTTTATT
Found at i:12430850 original size:28 final size:27
Alignment explanation
Indices: 12430795--12430878 Score: 89
Period size: 27 Copynumber: 3.1 Consensus size: 27
12430785 AGCATGGCTG
* * * *
12430795 CCAGAACAGATAA-TGTGACATAGTCA
1 CCAGAAAAGATAATTGTGGCAGAGCCA
*
12430821 CCAGATAAAGATATTTGTGGCAGAGCCA
1 CCAGA-AAAGATAATTGTGGCAGAGCCA
* *
12430849 CCAGAACAGATAATTGTGGCATAGCCA
1 CCAGAAAAGATAATTGTGGCAGAGCCA
12430876 CCA
1 CCA
12430879 AGACGCATCC
Statistics
Matches: 48, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
26 5 0.10
27 28 0.58
28 15 0.31
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.19
Consensus pattern (27 bp):
CCAGAAAAGATAATTGTGGCAGAGCCA
Found at i:12435574 original size:32 final size:33
Alignment explanation
Indices: 12435548--12435627 Score: 126
Period size: 32 Copynumber: 2.4 Consensus size: 33
12435538 TTAATGCTTA
12435548 ATTAATGTATGAATTTCTATGTTTAATTGTTAC
1 ATTAATGTATGAATTTCTATGTTTAATTGTTAC
* *
12435581 AATGA-GTATGAATTTCTATGTTTAATTGTTAC
1 ATTAATGTATGAATTTCTATGTTTAATTGTTAC
12435613 ATTAAGTGTATGAAT
1 ATTAA-TGTATGAAT
12435628 GATACTATGG
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
32 30 0.73
33 3 0.07
34 8 0.20
ACGTcount: A:0.33, C:0.05, G:0.15, T:0.47
Consensus pattern (33 bp):
ATTAATGTATGAATTTCTATGTTTAATTGTTAC
Found at i:12441665 original size:18 final size:18
Alignment explanation
Indices: 12441642--12441678 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
12441632 TAATTAATAA
12441642 AAATAAGCATTTTGATTC
1 AAATAAGCATTTTGATTC
12441660 AAATAAGCATTTTGATTC
1 AAATAAGCATTTTGATTC
12441678 A
1 A
12441679 TACTTCATTC
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:0.41, C:0.11, G:0.11, T:0.38
Consensus pattern (18 bp):
AAATAAGCATTTTGATTC
Found at i:12442465 original size:29 final size:29
Alignment explanation
Indices: 12442426--12442483 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
12442416 CAGCTAACCA
12442426 AATACATAATTACATAGACAATCCATAAT
1 AATACATAATTACATAGACAATCCATAAT
12442455 AATACATAATTACATAGACAATCCATAAT
1 AATACATAATTACATAGACAATCCATAAT
12442484 TTAAACACAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.52, C:0.17, G:0.03, T:0.28
Consensus pattern (29 bp):
AATACATAATTACATAGACAATCCATAAT
Found at i:12450811 original size:27 final size:27
Alignment explanation
Indices: 12450751--12450813 Score: 81
Period size: 27 Copynumber: 2.3 Consensus size: 27
12450741 CCCTAATTTA
* *
12450751 TAAAATGACCGTAATACCCCTGTAGGG
1 TAAAATGACCATAATACCCCTGTAGAG
* *
12450778 TAAAATGACCATAATATCCCTGTATAG
1 TAAAATGACCATAATACCCCTGTAGAG
*
12450805 TAGAATGAC
1 TAAAATGAC
12450814 GATTATGGCC
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.38, C:0.19, G:0.17, T:0.25
Consensus pattern (27 bp):
TAAAATGACCATAATACCCCTGTAGAG
Found at i:12457489 original size:5 final size:5
Alignment explanation
Indices: 12457479--12457522 Score: 56
Period size: 5 Copynumber: 9.0 Consensus size: 5
12457469 AGAGAAAGAA
*
12457479 AAATT AAATT -AA-T AAATA ATAATT AAATT AAATT AAATT AAATT
1 AAATT AAATT AAATT AAATT A-AATT AAATT AAATT AAATT AAATT
12457523 TCAAGAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
3 1 0.03
4 4 0.12
5 25 0.74
6 4 0.12
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (5 bp):
AAATT
Found at i:12457818 original size:13 final size:13
Alignment explanation
Indices: 12457800--12457832 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
12457790 GGTTGTGTAT
12457800 TAAACTAATTAAC
1 TAAACTAATTAAC
12457813 TAAACTAATTAAC
1 TAAACTAATTAAC
12457826 T-AACTAA
1 TAAACTAA
12457833 ACTAAAGTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 6 0.30
13 14 0.70
ACGTcount: A:0.55, C:0.15, G:0.00, T:0.30
Consensus pattern (13 bp):
TAAACTAATTAAC
Found at i:12470760 original size:44 final size:43
Alignment explanation
Indices: 12470610--12470760 Score: 152
Period size: 44 Copynumber: 3.6 Consensus size: 43
12470600 CATACAATGA
* *
12470610 CAACGTCCCAGATGTGGTCTTACATGT-AATCAAATATCGATGC
1 CAACGTCCCAGACGTGGTCTTACACGTAAATCAAA-ATCGATGC
*
12470653 C-ACTGTCCCAGA--TGGTCTTACACG-AAATC-ATATACGATGC
1 CAAC-GTCCCAGACGTGGTCTTACACGTAAATCAAAAT-CGATGC
* * * *
12470693 CAATGTCCCAGGCATGGTCTTACACGTAAATCACAAATCGATTC
1 CAACGTCCCAGACGTGGTCTTACACGTAAATCA-AAATCGATGC
*
12470737 CAACGTCCTAGACGTGGTCTTACA
1 CAACGTCCCAGACGTGGTCTTACA
12470761 TGATAACAGA
Statistics
Matches: 89, Mismatches: 10, Indels: 17
0.77 0.09 0.15
Matches are distributed among these distances:
39 2 0.02
40 15 0.17
41 16 0.18
42 14 0.16
43 14 0.16
44 25 0.28
45 3 0.03
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.26
Consensus pattern (43 bp):
CAACGTCCCAGACGTGGTCTTACACGTAAATCAAAATCGATGC
Found at i:12475983 original size:46 final size:46
Alignment explanation
Indices: 12475933--12476108 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
12475923 TGGTTGAGCA
12475933 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
12475979 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
12476024 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
12476072 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
12476109 GCGGGTTACA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 63 0.57
47 29 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:12476089 original size:93 final size:93
Alignment explanation
Indices: 12475930--12476101 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
12475920 GGATGGTTGA
* *
12475930 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
12475995 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
12476023 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
12476088 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
12476102 CTTATGGGCG
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:0.21, C:0.22, G:0.30, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:12499606 original size:56 final size:56
Alignment explanation
Indices: 12499534--12499723 Score: 272
Period size: 56 Copynumber: 3.4 Consensus size: 56
12499524 CGCCAGACAG
* ** *
12499534 GGTCTTACTCGAACACATATATTGGAGTCATTTATCGATGCCAACGTATTAAACGT
1 GGTCTTACTCGCACACATATATTGGAGTCAAATATCGATGCCAACATATTAAACGT
* ** *
12499590 GGTCTTACTTGCACACATATATCAGAGTCACATATCGATGCCAACATATTAAACGT
1 GGTCTTACTCGCACACATATATTGGAGTCAAATATCGATGCCAACATATTAAACGT
*
12499646 GGTCTTACTCGCATACATATATTGGAGTCAAATATCGATGCCAACATATTAAACGT
1 GGTCTTACTCGCACACATATATTGGAGTCAAATATCGATGCCAACATATTAAACGT
* * *
12499702 GGACTTACTCGTACACTTATAT
1 GGTCTTACTCGCACACATATAT
12499724 CAGTGTCACA
Statistics
Matches: 118, Mismatches: 16, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
56 118 1.00
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.31
Consensus pattern (56 bp):
GGTCTTACTCGCACACATATATTGGAGTCAAATATCGATGCCAACATATTAAACGT
Found at i:12499702 original size:112 final size:112
Alignment explanation
Indices: 12499534--12499736 Score: 316
Period size: 112 Copynumber: 1.8 Consensus size: 112
12499524 CGCCAGACAG
** * *
12499534 GGTCTTACTCGAACACATATATTGGAGTCATTTATCGATGCCAACGTATTAAACGTGGTCTTACT
1 GGTCTTACTCGAACACATATATTGGAGTCAAATATCGATGCCAACATATTAAACGTGGACTTACT
*
12499599 TGCACACATATATCAGAGTCACATATCGATGCCAACATATTAAACGT
66 CGCACACATATATCAGAGTCACATATCGATGCCAACATATTAAACGT
* *
12499646 GGTCTTACTCGCATACATATATTGGAGTCAAATATCGATGCCAACATATTAAACGTGGACTTACT
1 GGTCTTACTCGAACACATATATTGGAGTCAAATATCGATGCCAACATATTAAACGTGGACTTACT
* * *
12499711 CGTACACTTATATCAGTGTCACATAT
66 CGCACACATATATCAGAGTCACATAT
12499737 TGATATATCA
Statistics
Matches: 81, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
112 81 1.00
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.31
Consensus pattern (112 bp):
GGTCTTACTCGAACACATATATTGGAGTCAAATATCGATGCCAACATATTAAACGTGGACTTACT
CGCACACATATATCAGAGTCACATATCGATGCCAACATATTAAACGT
Found at i:12501353 original size:42 final size:43
Alignment explanation
Indices: 12501248--12501357 Score: 127
Period size: 44 Copynumber: 2.6 Consensus size: 43
12501238 TGATATGTGT
* * * *
12501248 TTTCGTGTGAGACCTCGTCTGGGACGTTGGCATCGACTTATGA
1 TTTCGTGTAAGACCTTGTCTGGGACATAGGCATCGACTTATGA
*
12501291 TTTACGTGTAAGACCATGTCTGGGACATCAGG-ATCGTA-TT-TGA
1 TTT-CGTGTAAGACCTTGTCTGGGACAT-AGGCATCG-ACTTATGA
12501334 TTTCGTGTAAGACCTTGTCTGGGA
1 TTTCGTGTAAGACCTTGTCTGGGA
12501358 TAGTGGCATT
Statistics
Matches: 58, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
42 20 0.34
43 9 0.16
44 26 0.45
45 3 0.05
ACGTcount: A:0.20, C:0.18, G:0.28, T:0.34
Consensus pattern (43 bp):
TTTCGTGTAAGACCTTGTCTGGGACATAGGCATCGACTTATGA
Found at i:12504477 original size:29 final size:29
Alignment explanation
Indices: 12504403--12504483 Score: 103
Period size: 29 Copynumber: 2.8 Consensus size: 29
12504393 ACATACATGT
* *
12504403 ATATGGCCCA-CTAGGCCAAATCTCATTC
1 ATATGGCCCATCTAGCCCAAATCACATTC
*
12504431 ATATGGCCCAT-TCGGCCCAAATCACATTC
1 ATATGGCCCATCT-AGCCCAAATCACATTC
*
12504460 ATATGGCCCATCTAGCCCGAATCA
1 ATATGGCCCATCTAGCCCAAATCA
12504484 AATCCAAGCC
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
28 11 0.24
29 33 0.73
30 1 0.02
ACGTcount: A:0.28, C:0.33, G:0.15, T:0.23
Consensus pattern (29 bp):
ATATGGCCCATCTAGCCCAAATCACATTC
Found at i:12510276 original size:47 final size:47
Alignment explanation
Indices: 12510198--12510581 Score: 642
Period size: 47 Copynumber: 8.1 Consensus size: 47
12510188 CCCTTCGTGA
* * * * * *
12510198 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
12510245 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
12510292 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
12510339 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
12510386 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
12510433 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
12510480 CTTATCACGTATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC----ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
12510531 CTTATCACATATATACACTTTCACATTCATCCCATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
12510578 CTTA
1 CTTA
12510582 CTATCATTTC
Statistics
Matches: 320, Mismatches: 13, Indels: 8
0.94 0.04 0.02
Matches are distributed among these distances:
47 273 0.85
51 47 0.15
ACGTcount: A:0.28, C:0.30, G:0.09, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:12528795 original size:80 final size:81
Alignment explanation
Indices: 12528659--12528817 Score: 198
Period size: 80 Copynumber: 2.0 Consensus size: 81
12528649 CCTTGTCTCA
* * *
12528659 ATGTCTATTTCAATTCAAAAAGTATAGCCACATTCGGCTCAATTTATTTATTCAAACACACATGC
1 ATGTCTATTTCAATTCAAAAAGTATAGCCACATTCGGCTCAATTCATTTATCCAAACACACATCC
12528724 AGCACATTATATTTCT
66 AGCACATTATATTTCT
* * * * *
12528740 ATGTCTATTTCAGATT-AATAA-TTTAGCCACATTCGGCTCTAA-TCATTTCTCCAAACATATAT
1 ATGTCTATTTCA-ATTCAAAAAGTATAGCCACATTCGGCTC-AATTCATTTATCCAAACACACAT
*
12528802 CCATCACATTATATTT
64 CCAGCACATTATATTT
12528818 ATACATCTAT
Statistics
Matches: 67, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
80 46 0.69
81 18 0.27
82 3 0.04
ACGTcount: A:0.33, C:0.21, G:0.08, T:0.38
Consensus pattern (81 bp):
ATGTCTATTTCAATTCAAAAAGTATAGCCACATTCGGCTCAATTCATTTATCCAAACACACATCC
AGCACATTATATTTCT
Found at i:12529963 original size:12 final size:13
Alignment explanation
Indices: 12529946--12529977 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
12529936 ATAAAAAATA
12529946 TATTTTTA-TTTT
1 TATTTTTATTTTT
12529958 TATTTTTATTTTT
1 TATTTTTATTTTT
12529971 TATTTTT
1 TATTTTT
12529978 TTACTCGGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 8 0.42
13 11 0.58
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (13 bp):
TATTTTTATTTTT
Found at i:12529978 original size:7 final size:6
Alignment explanation
Indices: 12529946--12529977 Score: 55
Period size: 6 Copynumber: 5.2 Consensus size: 6
12529936 ATAAAAAATA
12529946 TATTTT TATTTT TATTTT TATTTTT TATTTT T
1 TATTTT TATTTT TATTTT TA-TTTT TATTTT T
12529978 TTACTCGGAT
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:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TATTTT
Found at i:12530844 original size:29 final size:29
Alignment explanation
Indices: 12530809--12530882 Score: 112
Period size: 29 Copynumber: 2.6 Consensus size: 29
12530799 TTATACCAAA
12530809 TTGGCTTCGGGCCATGCATATCAAATGAT
1 TTGGCTTCGGGCCATGCATATCAAATGAT
* **
12530838 TTGGCTTCGGGACATGCATATCGGATGAT
1 TTGGCTTCGGGCCATGCATATCAAATGAT
*
12530867 TTGGCTTCAGGCCATG
1 TTGGCTTCGGGCCATG
12530883 ATAATTGATC
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.20, C:0.20, G:0.28, T:0.31
Consensus pattern (29 bp):
TTGGCTTCGGGCCATGCATATCAAATGAT
Found at i:12531452 original size:25 final size:25
Alignment explanation
Indices: 12531422--12531472 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
12531412 AATAGGAATG
12531422 GCTTATTTTGGCATGTTTAGTATGA
1 GCTTATTTTGGCATGTTTAGTATGA
12531447 GCTTATTTTGGCATGTTTAGTATGA
1 GCTTATTTTGGCATGTTTAGTATGA
12531472 G
1 G
12531473 TTTGGTTAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.20, C:0.08, G:0.25, T:0.47
Consensus pattern (25 bp):
GCTTATTTTGGCATGTTTAGTATGA
Found at i:12536023 original size:50 final size:49
Alignment explanation
Indices: 12535910--12536035 Score: 162
Period size: 50 Copynumber: 2.6 Consensus size: 49
12535900 CTGGTACGCA
** * *
12535910 TAGTAGCCTGCACTTAGTACTACACATGCGACCAAATATCCGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACACACGACCAAACATCCGATACACG
* * * **
12535959 TAGTAGCCTACACTTAGTACTACACACATGACCTAACCATTTGATACACG
1 TAGTAGCCTGCACTTAGTACTACACACACGACC-AAACATCCGATACACG
12536009 TAGTAGCCTGCACTTAGTACTACACAC
1 TAGTAGCCTGCACTTAGTACTACACAC
12536036 GTGATCGAAG
Statistics
Matches: 66, Mismatches: 10, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
49 29 0.44
50 37 0.56
ACGTcount: A:0.32, C:0.29, G:0.15, T:0.25
Consensus pattern (49 bp):
TAGTAGCCTGCACTTAGTACTACACACACGACCAAACATCCGATACACG
Found at i:12538558 original size:15 final size:15
Alignment explanation
Indices: 12538529--12538567 Score: 60
Period size: 15 Copynumber: 2.5 Consensus size: 15
12538519 AACAGAGAAG
12538529 CCAAGAATAAAGAAAT
1 CCAAG-ATAAAGAAAT
12538545 CCAAGATAAAGAAAT
1 CCAAGATAAAGAAAT
*
12538560 CCATGATA
1 CCAAGATA
12538568 CGAGAATCCA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 17 0.77
16 5 0.23
ACGTcount: A:0.56, C:0.15, G:0.13, T:0.15
Consensus pattern (15 bp):
CCAAGATAAAGAAAT
Found at i:12553055 original size:150 final size:150
Alignment explanation
Indices: 12552784--12553083 Score: 600
Period size: 150 Copynumber: 2.0 Consensus size: 150
12552774 TTCCTAATAA
12552784 CTGTTGTTGTATGCAAACTTTGCCACCGGTAAGTAATCCTCCCAACTGCCTCGAAAGTCGATAAC
1 CTGTTGTTGTATGCAAACTTTGCCACCGGTAAGTAATCCTCCCAACTGCCTCGAAAGTCGATAAC
12552849 GCATCCCCTCAACATGTCTTTCAGAATCTGAATAACCCTTTCCAACTAACCATCAGTCTGAGGAT
66 GCATCCCCTCAACATGTCTTTCAGAATCTGAATAACCCTTTCCAACTAACCATCAGTCTGAGGAT
12552914 GAAAGGCTGTACTAAGGTTC
131 GAAAGGCTGTACTAAGGTTC
12552934 CTGTTGTTGTATGCAAACTTTGCCACCGGTAAGTAATCCTCCCAACTGCCTCGAAAGTCGATAAC
1 CTGTTGTTGTATGCAAACTTTGCCACCGGTAAGTAATCCTCCCAACTGCCTCGAAAGTCGATAAC
12552999 GCATCCCCTCAACATGTCTTTCAGAATCTGAATAACCCTTTCCAACTAACCATCAGTCTGAGGAT
66 GCATCCCCTCAACATGTCTTTCAGAATCTGAATAACCCTTTCCAACTAACCATCAGTCTGAGGAT
12553064 GAAAGGCTGTACTAAGGTTC
131 GAAAGGCTGTACTAAGGTTC
12553084 AACCGCGTAC
Statistics
Matches: 150, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
150 150 1.00
ACGTcount: A:0.28, C:0.27, G:0.17, T:0.27
Consensus pattern (150 bp):
CTGTTGTTGTATGCAAACTTTGCCACCGGTAAGTAATCCTCCCAACTGCCTCGAAAGTCGATAAC
GCATCCCCTCAACATGTCTTTCAGAATCTGAATAACCCTTTCCAACTAACCATCAGTCTGAGGAT
GAAAGGCTGTACTAAGGTTC
Found at i:12558204 original size:27 final size:26
Alignment explanation
Indices: 12558156--12558207 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
12558146 GCAAGGCTGC
*
12558156 CAGATATTGTGACAAAGTCACCAGAA
1 CAGATATTGTGACAAAGCCACCAGAA
* *
12558182 CAGATATATGTGGCAAGGCCACCAGA
1 CAGATAT-TGTGACAAAGCCACCAGA
12558208 TTGCAGTGAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.38, C:0.21, G:0.23, T:0.17
Consensus pattern (26 bp):
CAGATATTGTGACAAAGCCACCAGAA
Found at i:12558495 original size:19 final size:19
Alignment explanation
Indices: 12558471--12558522 Score: 86
Period size: 19 Copynumber: 2.7 Consensus size: 19
12558461 TGGGCCCGTT
*
12558471 GGCCCATTGGCCCGTTTTC
1 GGCCCATTAGCCCGTTTTC
12558490 GGCCCATTAGCCCGTTTTC
1 GGCCCATTAGCCCGTTTTC
12558509 GGCCCATTAAGCCC
1 GGCCCATT-AGCCC
12558523 AAAAATACCG
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 26 0.84
20 5 0.16
ACGTcount: A:0.12, C:0.38, G:0.23, T:0.27
Consensus pattern (19 bp):
GGCCCATTAGCCCGTTTTC
Found at i:12563918 original size:32 final size:33
Alignment explanation
Indices: 12563845--12563941 Score: 142
Period size: 32 Copynumber: 3.0 Consensus size: 33
12563835 TTCTTTCTGA
*
12563845 GTGGTACACACAAAGTATACCTTTCCTTTTCAT
1 GTGGTATACACAAAGTATACCTTTCCTTTTCAT
* *
12563878 ATGCTATACACAAAGTATACCTTTCC-TTTCAT
1 GTGGTATACACAAAGTATACCTTTCCTTTTCAT
**
12563910 GTGGTATACACAAAGTATACCTCACCTTTTCA
1 GTGGTATACACAAAGTATACCTTTCCTTTTCA
12563942 CATTTGATAG
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
32 28 0.50
33 28 0.50
ACGTcount: A:0.30, C:0.25, G:0.10, T:0.35
Consensus pattern (33 bp):
GTGGTATACACAAAGTATACCTTTCCTTTTCAT
Found at i:12563967 original size:29 final size:29
Alignment explanation
Indices: 12563934--12564000 Score: 98
Period size: 29 Copynumber: 2.3 Consensus size: 29
12563924 GTATACCTCA
*
12563934 CCTTTTCACATTTGATAGCCAAAGCTATC
1 CCTTTTCACATTCGATAGCCAAAGCTATC
*
12563963 CCTTTTCACATTCGATAGCCGAAGCTATC
1 CCTTTTCACATTCGATAGCCAAAGCTATC
* *
12563992 ACTATTCAC
1 CCTTTTCAC
12564001 TGATCAGGTA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.27, C:0.30, G:0.10, T:0.33
Consensus pattern (29 bp):
CCTTTTCACATTCGATAGCCAAAGCTATC
Found at i:12564020 original size:31 final size:31
Alignment explanation
Indices: 12563978--12564248 Score: 355
Period size: 31 Copynumber: 8.7 Consensus size: 31
12563968 TCACATTCGA
* *
12563978 TAGCCGAAGCTATCACTATTCACTGATCAGG
1 TAGCCGAAGCTACCACTTTTCACTGATCAGG
* * *
12564009 TAG-CTAGAGCTACAACTTTTCACTAATCAGG
1 TAGCCGA-AGCTACCACTTTTCACTGATCAGG
* * *
12564040 TAGCCGAAGCTACTACTTTACACTGATAAGG
1 TAGCCGAAGCTACCACTTTTCACTGATCAGG
* * *
12564071 TAGCCGAAGCCATCACTTTTCACTGATTAGG
1 TAGCCGAAGCTACCACTTTTCACTGATCAGG
*
12564102 TAGCCGAAGCCACCACTTTTCACTGATCAGG
1 TAGCCGAAGCTACCACTTTTCACTGATCAGG
* *
12564133 TAGTCGAAGCTACCACTTTTCCCTGATCAGG
1 TAGCCGAAGCTACCACTTTTCACTGATCAGG
*
12564164 TAGCCGAAGCTACCACTTTTCATTGATCAGG
1 TAGCCGAAGCTACCACTTTTCACTGATCAGG
* * *
12564195 TAGCTGAAACTACCACTTTTCACTGATTAGG
1 TAGCCGAAGCTACCACTTTTCACTGATCAGG
*
12564226 TAGCCAAAGCTACCACTTTTCAC
1 TAGCCGAAGCTACCACTTTTCAC
12564249 ATTGTACACA
Statistics
Matches: 208, Mismatches: 30, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
30 2 0.01
31 204 0.98
32 2 0.01
ACGTcount: A:0.28, C:0.27, G:0.18, T:0.28
Consensus pattern (31 bp):
TAGCCGAAGCTACCACTTTTCACTGATCAGG
Found at i:12567724 original size:12 final size:12
Alignment explanation
Indices: 12567707--12567732 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
12567697 CATTCCGAAG
12567707 TATATATATACA
1 TATATATATACA
12567719 TATATATATACA
1 TATATATATACA
12567731 TA
1 TA
12567733 AGTATGCCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.08, G:0.00, T:0.42
Consensus pattern (12 bp):
TATATATATACA
Found at i:12568243 original size:27 final size:27
Alignment explanation
Indices: 12568212--12568389 Score: 214
Period size: 27 Copynumber: 6.6 Consensus size: 27
12568202 TAAATTGTAC
12568212 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
12568239 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* *
12568265 ATGCACTAAGTGTGCGAATTGACCATGT
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
12568293 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
12568321 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
12568348 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
12568375 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
12568390 GACTCGATAT
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:12568326 original size:82 final size:81
Alignment explanation
Indices: 12568213--12568368 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
12568203 AAATTGTACA
* *
12568213 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
12568277 TGCGAATTGACCATGTG
65 TGCGAATTGACCATGTG
** *
12568294 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
12568359 TGCGAGTTGA
65 TGCGAATTGA
12568369 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGTG
Found at i:12568380 original size:82 final size:81
Alignment explanation
Indices: 12568212--12568389 Score: 232
Period size: 82 Copynumber: 2.2 Consensus size: 81
12568202 TAAATTGTAC
* *
12568212 AGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAAGTG
1 AGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAAGTG
*
12568277 TGCGAATTGACCATGT
66 TGCGAATTGACCATAT
* ** *
12568293 GGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACTAAG
1 AGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACTAAG
* **
12568357 TGTGCGAGTTGATTATAT
64 TGTGCGAATTGACCATAT
*
12568375 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
12568390 GACTCGATAT
Statistics
Matches: 83, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
81 16 0.19
82 67 0.81
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
AGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAAGTG
TGCGAATTGACCATAT
Found at i:12573426 original size:48 final size:48
Alignment explanation
Indices: 12573359--12573683 Score: 452
Period size: 48 Copynumber: 6.8 Consensus size: 48
12573349 TACAAGATAA
* *
12573359 ATATATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATATGAG
* *
12573407 ATATGTATATGTGGTAAAGCCGAATGGCTAACGTAAAATATATATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATATGAG
* * * * *
12573455 ATACGAATATGTGGTAAAGCTGAATGGCTAGTGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATATGAG
* *
12573503 ATATGTATATGTGGTAAAGCCGAATGGCTAACGTAAAATATATATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATATGAG
* * * * *
12573551 ATACGAATATGTGGTAAAGCTGAATGGCTAGTGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATATGAG
* *
12573599 ATATGTATATGTGGTAAAGCCGAATGGCTAACGTAAAATATATATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATATGAG
* * * *
12573647 ATACGAATATGTGGTAAAGCTGAATGGCTAGTGTGAA
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAA
12573684 GGAGATGTGT
Statistics
Matches: 239, Mismatches: 38, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
48 239 1.00
ACGTcount: A:0.38, C:0.07, G:0.26, T:0.29
Consensus pattern (48 bp):
ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATATGAG
Found at i:12573529 original size:96 final size:96
Alignment explanation
Indices: 12573365--12573683 Score: 620
Period size: 96 Copynumber: 3.3 Consensus size: 96
12573355 ATAAATATAT
* *
12573365 ATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCGA
1 ATATGTGGTAAAGCTGAATGGCTAGTGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCGA
12573430 ATGGCTAACGTAAAATATATATGAGATACGA
66 ATGGCTAACGTAAAATATATATGAGATACGA
12573461 ATATGTGGTAAAGCTGAATGGCTAGTGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCGA
1 ATATGTGGTAAAGCTGAATGGCTAGTGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCGA
12573526 ATGGCTAACGTAAAATATATATGAGATACGA
66 ATGGCTAACGTAAAATATATATGAGATACGA
12573557 ATATGTGGTAAAGCTGAATGGCTAGTGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCGA
1 ATATGTGGTAAAGCTGAATGGCTAGTGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCGA
12573622 ATGGCTAACGTAAAATATATATGAGATACGA
66 ATGGCTAACGTAAAATATATATGAGATACGA
12573653 ATATGTGGTAAAGCTGAATGGCTAGTGTGAA
1 ATATGTGGTAAAGCTGAATGGCTAGTGTGAA
12573684 GGAGATGTGT
Statistics
Matches: 221, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
96 221 1.00
ACGTcount: A:0.37, C:0.08, G:0.26, T:0.29
Consensus pattern (96 bp):
ATATGTGGTAAAGCTGAATGGCTAGTGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCGA
ATGGCTAACGTAAAATATATATGAGATACGA
Found at i:12573885 original size:37 final size:37
Alignment explanation
Indices: 12573833--12573932 Score: 173
Period size: 37 Copynumber: 2.7 Consensus size: 37
12573823 AATATATTCC
12573833 GGGTAAGACCCGATGACTACGTGTGGAGATTATGTCT
1 GGGTAAGACCCGATGACTACGTGTGGAGATTATGTCT
* *
12573870 GGGTAAGACCTGATGACTACGTGTGGAGATTTTGTCT
1 GGGTAAGACCCGATGACTACGTGTGGAGATTATGTCT
*
12573907 GGGTAAGACCCGATAACTACGTGTGG
1 GGGTAAGACCCGATGACTACGTGTGG
12573933 GGACTATTCG
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 59 1.00
ACGTcount: A:0.24, C:0.16, G:0.33, T:0.27
Consensus pattern (37 bp):
GGGTAAGACCCGATGACTACGTGTGGAGATTATGTCT
Found at i:12582608 original size:40 final size:40
Alignment explanation
Indices: 12582557--12582793 Score: 227
Period size: 40 Copynumber: 6.0 Consensus size: 40
12582547 GGATATAGCT
* *
12582557 ACTCGCTCAAATGCCTTCGGGACATAGCCCGGTTATAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTA
* *
12582597 ACTCACACAAATGCCTTCGGGACTTAACCCGGATT-TAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGG-TTATAGTA
* ** *
12582637 ACTCGCACCAATGCCTTCAAG-CTTAGCCCGG-AATTAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTA-TAGTA
* * *
12582676 ACTCGCACAAATGCCTTCGGAACTTAACCCGAATT-TAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCG-GTTATAGTA
* ** *
12582716 ACTCGCACCAATGCCTTCAAG-CTTAGCCCGG-AATTAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTA-TAGTA
* *
12582755 ACTCGCACAAATGCCTTC-GGATCTTAGTCCGGATATAGT
1 ACTCGCACAAATGCCTTCGGGA-CTTAGCCCGGTTATAGT
12582794 CACTTAGCAC
Statistics
Matches: 158, Mismatches: 28, Indels: 22
0.76 0.13 0.11
Matches are distributed among these distances:
38 1 0.01
39 61 0.39
40 93 0.59
41 3 0.02
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.25
Consensus pattern (40 bp):
ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTA
Found at i:12582667 original size:79 final size:79
Alignment explanation
Indices: 12582592--12582780 Score: 342
Period size: 79 Copynumber: 2.4 Consensus size: 79
12582582 AGCCCGGTTA
* * *
12582592 TAGTAACTCACACAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACCAATGCCTTCAA
1 TAGTAACTCGCACAAATGCCTTCGGAACTTAACCCGAATTTAGTAACTCGCACCAATGCCTTCAA
12582657 GCTTAGCCCGGAAT
66 GCTTAGCCCGGAAT
12582671 TAGTAACTCGCACAAATGCCTTCGGAACTTAACCCGAATTTAGTAACTCGCACCAATGCCTTCAA
1 TAGTAACTCGCACAAATGCCTTCGGAACTTAACCCGAATTTAGTAACTCGCACCAATGCCTTCAA
12582736 GCTTAGCCCGGAAT
66 GCTTAGCCCGGAAT
*
12582750 TAGTAACTCGCACAAATGCCTTCGGATCTTA
1 TAGTAACTCGCACAAATGCCTTCGGAACTTA
12582781 GTCCGGATAT
Statistics
Matches: 106, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
79 106 1.00
ACGTcount: A:0.30, C:0.29, G:0.17, T:0.25
Consensus pattern (79 bp):
TAGTAACTCGCACAAATGCCTTCGGAACTTAACCCGAATTTAGTAACTCGCACCAATGCCTTCAA
GCTTAGCCCGGAAT
Found at i:12582678 original size:39 final size:39
Alignment explanation
Indices: 12582592--12582772 Score: 240
Period size: 39 Copynumber: 4.6 Consensus size: 39
12582582 AGCCCGGTTA
* ** *
12582592 TAGTAACTCACACAAATGCCTTCGGGACTTAACCCGGATT
1 TAGTAACTCGCACAAATGCCTTCAAG-CTTAACCCGGAAT
* *
12582632 TAGTAACTCGCACCAATGCCTTCAAGCTTAGCCCGGAAT
1 TAGTAACTCGCACAAATGCCTTCAAGCTTAACCCGGAAT
12582671 TAGTAACTCGCACAAATGCCTTCGGAA-CTTAACCC-GAATT
1 TAGTAACTCGCACAAATGCCTTC--AAGCTTAACCCGGAA-T
* *
12582711 TAGTAACTCGCACCAATGCCTTCAAGCTTAGCCCGGAAT
1 TAGTAACTCGCACAAATGCCTTCAAGCTTAACCCGGAAT
12582750 TAGTAACTCGCACAAATGCCTTC
1 TAGTAACTCGCACAAATGCCTTC
12582773 GGATCTTAGT
Statistics
Matches: 125, Mismatches: 11, Indels: 11
0.85 0.07 0.07
Matches are distributed among these distances:
38 2 0.02
39 66 0.53
40 55 0.44
41 2 0.02
ACGTcount: A:0.30, C:0.29, G:0.17, T:0.24
Consensus pattern (39 bp):
TAGTAACTCGCACAAATGCCTTCAAGCTTAACCCGGAAT
Found at i:12584974 original size:12 final size:12
Alignment explanation
Indices: 12584957--12584981 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
12584947 TAAAAATGTA
12584957 AAAATCATCAAG
1 AAAATCATCAAG
12584969 AAAATCATCAAG
1 AAAATCATCAAG
12584981 A
1 A
12584982 TCACTTACAT
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:0.60, C:0.16, G:0.08, T:0.16
Consensus pattern (12 bp):
AAAATCATCAAG
Found at i:12589605 original size:6 final size:6
Alignment explanation
Indices: 12589587--12589618 Score: 55
Period size: 6 Copynumber: 5.2 Consensus size: 6
12589577 CATCATCTAT
12589587 TCAGAA TTCAGAA TCAGAA TCAGAA TCAGAA T
1 TCAGAA -TCAGAA TCAGAA TCAGAA TCAGAA T
12589619 TACACGAAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 19 0.76
7 6 0.24
ACGTcount: A:0.47, C:0.16, G:0.16, T:0.22
Consensus pattern (6 bp):
TCAGAA
Found at i:12607768 original size:13 final size:13
Alignment explanation
Indices: 12607742--12607776 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
12607732 CTTAAAATAG
12607742 AATAAAAGTAACA
1 AATAAAAGTAACA
12607755 ACATAAAA-TAACA
1 A-ATAAAAGTAACA
12607768 AATAAAAGT
1 AATAAAAGT
12607777 TTTTAAACAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
12 6 0.30
13 8 0.40
14 6 0.30
ACGTcount: A:0.69, C:0.09, G:0.06, T:0.17
Consensus pattern (13 bp):
AATAAAAGTAACA
Found at i:12614097 original size:27 final size:27
Alignment explanation
Indices: 12614085--12614384 Score: 372
Period size: 27 Copynumber: 11.1 Consensus size: 27
12614075 AAGTACTCCT
12614085 GATTTACAGAATTACCGTTTTACCCTC
1 GATTTACAGAATTACCGTTTTACCCTC
12614112 GATTTACAGAATTACCGTTTTACCCTC
1 GATTTACAGAATTACCGTTTTACCCTC
12614139 GATTTACAGAATTACCGTTTTACCCTC
1 GATTTACAGAATTACCGTTTTACCCTC
*
12614166 GATTTGCAGAATTACCGTTTTACCCTC
1 GATTTACAGAATTACCGTTTTACCCTC
* * *
12614193 -AGTTTATAAAATTACTGTTTTACCCTC
1 GA-TTTACAGAATTACCGTTTTACCCTC
*
12614220 GATTTATAGAATTACCGTTTTACCCTC
1 GATTTACAGAATTACCGTTTTACCCTC
** * * *
12614247 GATTTGTAAAATTATCATTTTACCCTC
1 GATTTACAGAATTACCGTTTTACCCTC
** * *
12614274 GATTTGTAAAATTACCGTTTTACCCTT
1 GATTTACAGAATTACCGTTTTACCCTC
* *
12614301 GATTTACAGAATTACTGGTTTACCCTC
1 GATTTACAGAATTACCGTTTTACCCTC
* * *
12614328 -AGTTTACAAAATTATCATTTTACCCTC
1 GA-TTTACAGAATTACCGTTTTACCCTC
* *
12614355 GATTTACAGAATTACC-TTTTAACCTT
1 GATTTACAGAATTACCGTTTTACCCTC
12614381 GATT
1 GATT
12614385 GTGAAATTAC
Statistics
Matches: 240, Mismatches: 29, Indels: 9
0.86 0.10 0.03
Matches are distributed among these distances:
26 14 0.06
27 224 0.93
28 2 0.01
ACGTcount: A:0.27, C:0.22, G:0.10, T:0.40
Consensus pattern (27 bp):
GATTTACAGAATTACCGTTTTACCCTC
Found at i:12614453 original size:54 final size:54
Alignment explanation
Indices: 12614389--12614584 Score: 243
Period size: 54 Copynumber: 3.6 Consensus size: 54
12614379 TTGATTGTGA
* * * * *
12614389 AATTACTGAAATACCCCTGTAGGGTAGAATTTCTGAAATACCCCTATAAGGTAG
1 AATTACTGAAATACCCTTGTAGGGTAGAATTACCGAAATACCCCTGTAGGGTAG
* * *
12614443 AATTACTGAAATACCCTTATAGGATAGAATTACCAAAATACCCCTGTAGGGTAG
1 AATTACTGAAATACCCTTGTAGGGTAGAATTACCGAAATACCCCTGTAGGGTAG
* *
12614497 AATTA-TCGAAATACCCTTGTAGGGTAGAAATACCGAAATACCCCTGGAGGGTAG
1 AATTACT-GAAATACCCTTGTAGGGTAGAATTACCGAAATACCCCTGTAGGGTAG
* * *
12614551 AATTACCGAGATACCCTTGT-GAGGTAAAATTACC
1 AATTACTGAAATACCCTTGTAG-GGTAGAATTACC
12614585 ATTTTGCCCC
Statistics
Matches: 122, Mismatches: 17, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
53 2 0.02
54 120 0.98
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.26
Consensus pattern (54 bp):
AATTACTGAAATACCCTTGTAGGGTAGAATTACCGAAATACCCCTGTAGGGTAG
Found at i:12614584 original size:27 final size:27
Alignment explanation
Indices: 12614389--12614584 Score: 214
Period size: 27 Copynumber: 7.3 Consensus size: 27
12614379 TTGATTGTGA
* *
12614389 AATTACTGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCTTGTAGGGTAG
* * * * *
12614416 AATTTCTGAAATACCCCTATAAGGTAG
1 AATTACCGAAATACCCTTGTAGGGTAG
* * *
12614443 AATTACTGAAATACCCTTATAGGATAG
1 AATTACCGAAATACCCTTGTAGGGTAG
* *
12614470 AATTACCAAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCTTGTAGGGTAG
*
12614497 AATTATCGAAATACCCTTGTAGGGTAG
1 AATTACCGAAATACCCTTGTAGGGTAG
* * *
12614524 AAATACCGAAATACCCCTGGAGGGTAG
1 AATTACCGAAATACCCTTGTAGGGTAG
* *
12614551 AATTACCGAGATACCCTTGT-GAGGTAA
1 AATTACCGAAATACCCTTGTAG-GGTAG
12614578 AATTACC
1 AATTACC
12614585 ATTTTGCCCC
Statistics
Matches: 144, Mismatches: 24, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
26 1 0.01
27 143 0.99
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.26
Consensus pattern (27 bp):
AATTACCGAAATACCCTTGTAGGGTAG
Found at i:12614821 original size:27 final size:26
Alignment explanation
Indices: 12614783--12614865 Score: 112
Period size: 27 Copynumber: 3.1 Consensus size: 26
12614773 CGGAGGAAGC
*
12614783 GTTCTGGTGGCTATGCCACAAATATCT
1 GTTCTGGTGGCTCTGCCAC-AATATCT
12614810 GTTCTGGTGGCTCTGCCACAATATCT
1 GTTCTGGTGGCTCTGCCACAATATCT
* * *
12614836 GTATTTGGTGACTCTGTCACAATATCT
1 GT-TCTGGTGGCTCTGCCACAATATCT
12614863 GTT
1 GTT
12614866 GACCGATCGA
Statistics
Matches: 51, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
26 10 0.20
27 41 0.80
ACGTcount: A:0.19, C:0.22, G:0.22, T:0.37
Consensus pattern (26 bp):
GTTCTGGTGGCTCTGCCACAATATCT
Found at i:12614985 original size:22 final size:22
Alignment explanation
Indices: 12614953--12615011 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 22
12614943 CCCGTTATTA
*
12614953 ATGGCTCTGTGCCAACCTAAAT
1 ATGGCTTTGTGCCAACCTAAAT
* * * *
12614975 ATGGCTTTGTGCCATCTTGACT
1 ATGGCTTTGTGCCAACCTAAAT
*
12614997 ATGGCTTCGTGCCAA
1 ATGGCTTTGTGCCAA
12615012 ACGTATTTAC
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.20, C:0.25, G:0.22, T:0.32
Consensus pattern (22 bp):
ATGGCTTTGTGCCAACCTAAAT
Found at i:12615230 original size:27 final size:27
Alignment explanation
Indices: 12615176--12615249 Score: 80
Period size: 27 Copynumber: 2.8 Consensus size: 27
12615166 TAGGTGGGTT
* * *
12615176 TGCCACATTATCTG-ATTCTAGTGGCTC
1 TGCCACAATATCTGTA-TCTGGTGACTC
12615203 TGCCACAATATCTGTATCTGGTGACTC
1 TGCCACAATATCTGTATCTGGTGACTC
* *
12615230 TGTCACGATATCTGT-TCTGG
1 TGCCACAATATCTGTATCTGG
12615250 CAGCCATGCT
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
26 5 0.12
27 35 0.85
28 1 0.02
ACGTcount: A:0.19, C:0.24, G:0.20, T:0.36
Consensus pattern (27 bp):
TGCCACAATATCTGTATCTGGTGACTC
Found at i:12615376 original size:6 final size:6
Alignment explanation
Indices: 12615367--12615485 Score: 140
Period size: 6 Copynumber: 19.8 Consensus size: 6
12615357 TTGCATTCAC
*
12615367 ATTCTG ATTCTG ATTCTG ATTCTG ATTCTG ATTCTG -TTACTA ATAT-TG
1 ATTCTG ATTCTG ATTCTG ATTCTG ATTCTG ATTCTG ATT-CTG AT-TCTG
*
12615415 ATTCTG ATTCTG ATTCTG -TTACTA ATAT-TG ATTCTG ATTCTG ATTCTG
1 ATTCTG ATTCTG ATTCTG ATT-CTG AT-TCTG ATTCTG ATTCTG ATTCTG
12615463 -TTACTG ATTCTG ATTCTG ATTCT
1 ATT-CTG ATTCTG ATTCTG ATTCT
12615486 CATTTTGGTT
Statistics
Matches: 99, Mismatches: 4, Indels: 20
0.80 0.03 0.16
Matches are distributed among these distances:
5 8 0.08
6 85 0.86
7 4 0.04
8 2 0.02
ACGTcount: A:0.20, C:0.15, G:0.14, T:0.50
Consensus pattern (6 bp):
ATTCTG
Found at i:12615401 original size:30 final size:30
Alignment explanation
Indices: 12615383--12615485 Score: 181
Period size: 30 Copynumber: 3.4 Consensus size: 30
12615373 ATTCTGATTC
12615383 TGATTCTGATTCTGATTCTGTTACTAATAT
1 TGATTCTGATTCTGATTCTGTTACTAATAT
12615413 TGATTCTGATTCTGATTCTGTTACTAATAT
1 TGATTCTGATTCTGATTCTGTTACTAATAT
*
12615443 TGATTCTGATTCTGATTCTGTTACTGAT-T
1 TGATTCTGATTCTGATTCTGTTACTAATAT
12615472 CTGATTCTGATTCT
1 -TGATTCTGATTCT
12615486 CATTTTGGTT
Statistics
Matches: 71, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
29 1 0.01
30 70 0.99
ACGTcount: A:0.20, C:0.15, G:0.15, T:0.50
Consensus pattern (30 bp):
TGATTCTGATTCTGATTCTGTTACTAATAT
Found at i:12620010 original size:40 final size:39
Alignment explanation
Indices: 12619966--12620070 Score: 122
Period size: 39 Copynumber: 2.6 Consensus size: 39
12619956 AGTGACCATA
*
12619966 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGACTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
* *
12620006 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACT-AT
1 TCCGGACTAAGCCCGAAGGCATTTGTGCGAGATACTAAT
* * *
12620044 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGACTAAG-CCCGAAGGCATTTG
12620071 AACGAGTAGC
Statistics
Matches: 58, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
38 2 0.03
39 32 0.55
40 24 0.41
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.25
Consensus pattern (39 bp):
TCCGGACTAAGCCCGAAGGCATTTGTGCGAGATACTAAT
Done.