Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001993.1 Hibiscus syriacus cultivar Beakdansim tig00004075_pilon, whole genome shotgun sequence
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: 637348
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:424839 original size:17 final size:17
Alignment explanation
Indices: 424817--424849 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
424807 TAAGATTTGA
424817 TTTAATAAATGAACTAG
1 TTTAATAAATGAACTAG
*
424834 TTTAATTAATGAACTA
1 TTTAATAAATGAACTA
424850 CTTCCCTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.45, C:0.06, G:0.09, T:0.39
Consensus pattern (17 bp):
TTTAATAAATGAACTAG
Found at i:429352 original size:15 final size:15
Alignment explanation
Indices: 429320--429348 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
429310 ATTAGCAATA
429320 AAAAAATAACCTCAC
1 AAAAAATAACCTCAC
429335 AAAAAA-AACCTCAC
1 AAAAAATAACCTCAC
429349 CAAACACTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.62, C:0.28, G:0.00, T:0.10
Consensus pattern (15 bp):
AAAAAATAACCTCAC
Found at i:445334 original size:21 final size:21
Alignment explanation
Indices: 445304--445356 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
445294 GGCTTATGCT
* *
445304 GGAGTTGGTTGCTCAGCAGCG
1 GGAGTCGGTTGCTCAGCAACG
445325 GGAGTCGGTTGCTCAGCAACG
1 GGAGTCGGTTGCTCAGCAACG
*
445346 AGAGTCGGTTG
1 GGAGTCGGTTG
445357 TGCAGGAACT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.17, C:0.19, G:0.42, T:0.23
Consensus pattern (21 bp):
GGAGTCGGTTGCTCAGCAACG
Found at i:448060 original size:11 final size:11
Alignment explanation
Indices: 448044--448069 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
448034 TGGGAAAGGG
448044 TCCATGAAATC
1 TCCATGAAATC
448055 TCCATGAAATC
1 TCCATGAAATC
448066 TCCA
1 TCCA
448070 AAGGATGTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.35, C:0.31, G:0.08, T:0.27
Consensus pattern (11 bp):
TCCATGAAATC
Found at i:449207 original size:12 final size:12
Alignment explanation
Indices: 449190--449215 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
449180 GGAGAAGTCA
449190 TCCATAAATTTT
1 TCCATAAATTTT
449202 TCCATAAATTTT
1 TCCATAAATTTT
449214 TC
1 TC
449216 TACCATATCT
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:0.31, C:0.19, G:0.00, T:0.50
Consensus pattern (12 bp):
TCCATAAATTTT
Found at i:456479 original size:51 final size:51
Alignment explanation
Indices: 456369--456533 Score: 242
Period size: 51 Copynumber: 3.2 Consensus size: 51
456359 AGGATTAGAT
* * * * *
456369 TTATTATTTTATTAGGAATTA-AGATAGATTTAAAAACATTTTCTTTAGTTTA
1 TTATTATTTTATTAGGAATTACA-ATAGA-ATCACAACATTATCCTTAGTTTA
*
456421 TTATTATTTTATTAAGAATTACAATAGAATCACAACATTATCCTTAGTTTA
1 TTATTATTTTATTAGGAATTACAATAGAATCACAACATTATCCTTAGTTTA
456472 TTATTATTTTATTAGGAATTACAATAGAATCACAACATTATCCTTAGTTTA
1 TTATTATTTTATTAGGAATTACAATAGAATCACAACATTATCCTTAGTTTA
456523 TTATTAATTTT
1 TTATT-ATTTT
456534 TATTTAGTAG
Statistics
Matches: 104, Mismatches: 7, Indels: 4
0.90 0.06 0.03
Matches are distributed among these distances:
51 73 0.70
52 30 0.29
53 1 0.01
ACGTcount: A:0.37, C:0.08, G:0.07, T:0.47
Consensus pattern (51 bp):
TTATTATTTTATTAGGAATTACAATAGAATCACAACATTATCCTTAGTTTA
Found at i:461674 original size:133 final size:134
Alignment explanation
Indices: 461360--461783 Score: 530
Period size: 133 Copynumber: 3.2 Consensus size: 134
461350 AATTTTTCGT
*** * *
461360 TGCTCTTCAGGAAGACCAAATCTGAAAGAAGAAGAATATGCTCCACTTCTCTTTAGAGGAGATCA
1 TGCTCTTCAGGAAGACCAAATCTGAAAGAAGAAGAATATGCTATGCTACTCTTTAGGGGAGATCA
* * * * *
461425 GACTCGAGAAATCTTTGATCCTCTTCTCTGCTCTTCAAGAAAGATTTAATTGAACTTGATTTGCT
66 GACTCGAGAAATATTTGATCCACTTCACTGCTCTTCAGGAAAGATTGAATTGAACTTGATTTGCT
*
461490 TCAT
131 TCAC
* * * *
461494 TGCTCTTTAGGAATACGAAATCTGAAAGAAGAAGAATATGCTTTGCTACTCTTTAGGGGAGATCA
1 TGCTCTTCAGGAAGACCAAATCTGAAAGAAGAAGAATATGCTATGCTACTCTTTAGGGGAGATCA
* * * ** *
461559 GGCTCGAG-AATATTTGATCCACTTCACTGCTCTTCAGGGAACATTGAATCAAACTTTATTTGCT
66 GACTCGAGAAATATTTGATCCACTTCACTGCTCTTCAGGAAAGATTGAATTGAACTTGATTTGCT
461623 TCAC
131 TCAC
* * * * * * * *
461627 TGATCTTCAAGAAGGCCAAATCTGAAAGAAGAATAATCTACTATGCTACTCTTTAGGGAATATCA
1 TGCTCTTCAGGAAGACCAAATCTGAAAGAAGAAGAATATGCTATGCTACTCTTTAGGGGAGATCA
*
461692 GACTCGAGAAATATTTTGATCCACTTCGCTGCTCTT-AGGAAAGATTGAATTGAACTTGATTTGC
66 GACTCGAGAAATA-TTTGATCCACTTCACTGCTCTTCAGGAAAGATTGAATTGAACTTGATTTGC
*
461756 TTCGC
130 TTCAC
*
461761 TGCTCTTCAGGAAGA-AAAATCTG
1 TGCTCTTCAGGAAGACCAAATCTG
461784 GGGGTTTTAG
Statistics
Matches: 244, Mismatches: 44, Indels: 5
0.83 0.15 0.02
Matches are distributed among these distances:
133 116 0.48
134 107 0.44
135 21 0.09
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (134 bp):
TGCTCTTCAGGAAGACCAAATCTGAAAGAAGAAGAATATGCTATGCTACTCTTTAGGGGAGATCA
GACTCGAGAAATATTTGATCCACTTCACTGCTCTTCAGGAAAGATTGAATTGAACTTGATTTGCT
TCAC
Found at i:462704 original size:25 final size:25
Alignment explanation
Indices: 462670--462722 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
462660 TTATAAAATC
462670 TTAAAATTCAATAACACTTAATTTG
1 TTAAAATTCAATAACACTTAATTTG
462695 TTAAAATTCAATAACACTTAATTTG
1 TTAAAATTCAATAACACTTAATTTG
462720 TTA
1 TTA
462723 TATCGAAACA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.43, C:0.11, G:0.04, T:0.42
Consensus pattern (25 bp):
TTAAAATTCAATAACACTTAATTTG
Found at i:462816 original size:13 final size:14
Alignment explanation
Indices: 462798--462833 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
462788 TTTAAGATTT
462798 TCTTTGAAAATC-A
1 TCTTTGAAAATCAA
462811 TCTTTG-AAATCAA
1 TCTTTGAAAATCAA
462824 T-TTTGAAAAT
1 TCTTTGAAAAT
462834 TACTCCCCCT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 9 0.43
13 12 0.57
ACGTcount: A:0.39, C:0.11, G:0.08, T:0.42
Consensus pattern (14 bp):
TCTTTGAAAATCAA
Found at i:466178 original size:18 final size:18
Alignment explanation
Indices: 466155--466189 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
466145 TTCCATCTGG
*
466155 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
466173 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
466190 GTCCTTTCGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:469333 original size:18 final size:19
Alignment explanation
Indices: 469300--469340 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
469290 AGTTTTCATG
469300 AAAACAACATAATTAAATCA
1 AAAACAACA-AATTAAATCA
*
469320 AAAACAAC-AATTAAATTA
1 AAAACAACAAATTAAATCA
469338 AAA
1 AAA
469341 CAATTTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 12 0.60
20 8 0.40
ACGTcount: A:0.68, C:0.12, G:0.00, T:0.20
Consensus pattern (19 bp):
AAAACAACAAATTAAATCA
Found at i:469824 original size:44 final size:44
Alignment explanation
Indices: 469765--469953 Score: 315
Period size: 44 Copynumber: 4.3 Consensus size: 44
469755 CAATGCACTA
* * * *
469765 CATAGTGTATTGATGCACATTCAAGGAATGCATCGGTGTACATT
1 CATAGTGTATCGATGCATATTCAAGGAATGCATCGGTGCACCTT
469809 CATAGTGTATCGATGCATATTCAAGGAATGCATCGGTGCACCTT
1 CATAGTGTATCGATGCATATTCAAGGAATGCATCGGTGCACCTT
469853 CATAGTGTATCGATGCATATTCAAGGAATGCATCGGTGCACCTT
1 CATAGTGTATCGATGCATATTCAAGGAATGCATCGGTGCACCTT
* * *
469897 CATAGTGTATCGATGCATATTCAAGGGATGCATCGGTACACTTT
1 CATAGTGTATCGATGCATATTCAAGGAATGCATCGGTGCACCTT
469941 CATAGTGTATCGA
1 CATAGTGTATCGA
469954 AGCACAAAGC
Statistics
Matches: 138, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 138 1.00
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.31
Consensus pattern (44 bp):
CATAGTGTATCGATGCATATTCAAGGAATGCATCGGTGCACCTT
Found at i:469830 original size:21 final size:21
Alignment explanation
Indices: 469806--469919 Score: 88
Period size: 21 Copynumber: 5.2 Consensus size: 21
469796 ATCGGTGTAC
469806 ATTCATAGTGTATCGATGCAT
1 ATTCATAGTGTATCGATGCAT
* * *
469827 ATTCA-AGGAATGCATCGGTGCAC
1 ATTCATA-G--TGTATCGATGCAT
*
469850 CTTCATAGTGTATCGATGCAT
1 ATTCATAGTGTATCGATGCAT
* * *
469871 ATTCA-AGGAATGCATCGGTGCAC
1 ATTCATA-G--TGTATCGATGCAT
*
469894 CTTCATAGTGTATCGATGCAT
1 ATTCATAGTGTATCGATGCAT
469915 ATTCA
1 ATTCA
469920 AGGGATGCAT
Statistics
Matches: 69, Mismatches: 16, Indels: 16
0.68 0.16 0.16
Matches are distributed among these distances:
20 2 0.03
21 35 0.51
23 30 0.43
24 2 0.03
ACGTcount: A:0.28, C:0.19, G:0.21, T:0.32
Consensus pattern (21 bp):
ATTCATAGTGTATCGATGCAT
Found at i:469848 original size:23 final size:22
Alignment explanation
Indices: 469778--469942 Score: 99
Period size: 23 Copynumber: 7.5 Consensus size: 22
469768 AGTGTATTGA
469778 TGCACATTCAAGGAATGCATCGG
1 TGCACATTCAAGG-ATGCATCGG
* * *
469801 TGTACATTCATA-G-TGTATCGA
1 TGCACATTCA-AGGATGCATCGG
*
469822 TGCATATTCAAGGAATGCATCGG
1 TGCACATTCAAGG-ATGCATCGG
* * *
469845 TGCACCTTCATA-G-TGTATCGA
1 TGCACATTCA-AGGATGCATCGG
*
469866 TGCATATTCAAGGAATGCATCGG
1 TGCACATTCAAGG-ATGCATCGG
* * *
469889 TGCACCTTCATA-G-TGTATCGA
1 TGCACATTCA-AGGATGCATCGG
*
469910 TGCATATTCAAGGGATGCATCGG
1 TGCACATTCAA-GGATGCATCGG
* *
469933 TACACTTTCA
1 TGCACATTCA
469943 TAGTGTATCG
Statistics
Matches: 104, Mismatches: 26, Indels: 24
0.68 0.17 0.16
Matches are distributed among these distances:
20 3 0.03
21 44 0.42
22 1 0.01
23 53 0.51
24 3 0.03
ACGTcount: A:0.28, C:0.20, G:0.22, T:0.30
Consensus pattern (22 bp):
TGCACATTCAAGGATGCATCGG
Found at i:477580 original size:90 final size:90
Alignment explanation
Indices: 477408--477580 Score: 276
Period size: 90 Copynumber: 1.9 Consensus size: 90
477398 TACCGTGTAT
*
477408 CCAATACCAAAGTGTTGGTCCTACAAGGGGAAACGAATGCTCAAACTAGATTAAATTAAATAAAT
1 CCAATACCAAAGTGTTGGTCCTACAAGGGGAAAC-AATGCTCAAACTAAATTAAATTAAATAAAT
**
477473 TGTATCTCGTTAAAAACCTTGAATAC
65 TGTATCTCGGGAAAAACCTTGAATAC
*
477499 CCAATACCAAAGTGTTGGTCTTACAAGGGGAAA-AAGTGCTCAAACTAAATTAAATTAAATAAAT
1 CCAATACCAAAGTGTTGGTCCTACAAGGGGAAACAA-TGCTCAAACTAAATTAAATTAAATAAAT
*
477563 TGTATCTCGGGACAAACC
65 TGTATCTCGGGAAAAACC
477581 GAGTAAAATT
Statistics
Matches: 76, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
89 2 0.03
90 42 0.55
91 32 0.42
ACGTcount: A:0.41, C:0.17, G:0.16, T:0.25
Consensus pattern (90 bp):
CCAATACCAAAGTGTTGGTCCTACAAGGGGAAACAATGCTCAAACTAAATTAAATTAAATAAATT
GTATCTCGGGAAAAACCTTGAATAC
Found at i:477974 original size:35 final size:34
Alignment explanation
Indices: 477891--477978 Score: 106
Period size: 34 Copynumber: 2.6 Consensus size: 34
477881 AATTCACGTT
***
477891 TAACCCAATTCACGTTTTATGTGCATTTTAGCCA
1 TAACCCAATTCACGTTTTATGTGCATGAAAGCCA
* *
477925 TAACCCAATTCACGTTTTATGTGCACTGAAATCTA
1 TAACCCAATTCACGTTTTATGTGCA-TGAAAGCCA
477960 -AAGCCCAATTCACGTTTTA
1 TAA-CCCAATTCACGTTTTA
477979 ATTTGATGAT
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
34 27 0.57
35 20 0.43
ACGTcount: A:0.30, C:0.24, G:0.11, T:0.35
Consensus pattern (34 bp):
TAACCCAATTCACGTTTTATGTGCATGAAAGCCA
Found at i:481995 original size:94 final size:95
Alignment explanation
Indices: 481826--482024 Score: 251
Period size: 94 Copynumber: 2.1 Consensus size: 95
481816 ACTGAGGTGG
* * * * *
481826 GTATCGATACTATGAAGAAGGTATTGATACCATTGATTCCAGAATGCAGAAATGGTATTGATACT
1 GTATCGATACTAAGAAGAAGGTATCGATACCATGGATTCCAGAATGCAGAAATGATATCGATACT
* *
481891 ATAATAGAGTATCAGTACCATAGTATAGAA
66 ATAAGAGAGTATCAGTACCACAGTATAGAA
* *
481921 GTATCGGTACTAAG-AGAAAGGTATCGATACCATGGA-TCCAGAATGTAGAAATGATATCGATAC
1 GTATCGATACTAAGAAG-AAGGTATCGATACCATGGATTCCAGAATGCAGAAATGATATCGATAC
* * *
481984 TGA-AAGGGAGTATCGGTACCACGGTATAGAA
65 T-ATAAGAGAGTATCAGTACCACAGTATAGAA
482015 GTATCGATAC
1 GTATCGATAC
482025 CATGGTAAGG
Statistics
Matches: 89, Mismatches: 13, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
94 59 0.66
95 30 0.34
ACGTcount: A:0.38, C:0.13, G:0.23, T:0.26
Consensus pattern (95 bp):
GTATCGATACTAAGAAGAAGGTATCGATACCATGGATTCCAGAATGCAGAAATGATATCGATACT
ATAAGAGAGTATCAGTACCACAGTATAGAA
Found at i:482043 original size:94 final size:95
Alignment explanation
Indices: 481851--482044 Score: 223
Period size: 94 Copynumber: 2.1 Consensus size: 95
481841 AGAAGGTATT
* * * * *
481851 GATACCATTGATTCCAGAATGCAGAAATGGTATTGATACTATAATAGAGTATCAGTACCATAGTA
1 GATACCATGGATTCCAGAATGCAGAAATGATATCGATACTATAAGAGAGTATCAGTACCACAGTA
* * *
481916 TAGAAGTATCGGTACTAAGAGAAAGGTATC
66 TAGAAGTATCGATACCAAGAGAAAGGTACC
* * * *
481946 GATACCATGGA-TCCAGAATGTAGAAATGATATCGATACTGA-AAGGGAGTATCGGTACCACGGT
1 GATACCATGGATTCCAGAATGCAGAAATGATATCGATACT-ATAAGAGAGTATCAGTACCACAGT
* *
482009 ATAGAAGTATCGATACCATG-GTAAGGATACC
65 ATAGAAGTATCGATACCAAGAGAAAGG-TACC
482040 GATAC
1 GATAC
482045 TATTGAGCCA
Statistics
Matches: 83, Mismatches: 14, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
93 5 0.06
94 67 0.81
95 11 0.13
ACGTcount: A:0.38, C:0.14, G:0.23, T:0.25
Consensus pattern (95 bp):
GATACCATGGATTCCAGAATGCAGAAATGATATCGATACTATAAGAGAGTATCAGTACCACAGTA
TAGAAGTATCGATACCAAGAGAAAGGTACC
Found at i:482634 original size:161 final size:162
Alignment explanation
Indices: 482366--482758 Score: 617
Period size: 161 Copynumber: 2.4 Consensus size: 162
482356 ATCGAATAGG
*
482366 CACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTTCATATTGGCACTATGTGTG
1 CACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTTCGTATTGGCACTATGTGTG
* * * * *
482431 CAACCTAAGAAATTCATAATAAGTTTATGAATTTCTGTATTGGCATTATGTGTGCAACCTAAGAA
66 CAACCTAAGAAATTCATAATAAGTTTATAAATTTCCGTATTGGAACTATATGTGCAACCTAAGAA
* *
482496 ATT-ATAATAAGTTTATGAATTTCCATATTGG
131 ATTCATAATAAGTTTATGAATTCCCATATTGA
* * * *
482527 TACTATGTGTGCAATCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGGCACTATGTGTT
1 CACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTTCGTATTGGCACTATGTGTG
* *
482592 CAACCTAAGAAATTCATAATAAGTTTCTAAATTTCCGTATTGGAACTATATGTTCAACCTAAGAA
66 CAACCTAAGAAATTCATAATAAGTTTATAAATTTCCGTATTGGAACTATATGTGCAACCTAAGAA
482657 ATTCATAATAAGTTTATGAATTCCCATATTGA
131 ATTCATAATAAGTTTATGAATTCCCATATTGA
* * **
482689 CACTATGTATGCAACCTAAGGAATTCATAATAAGTTTATGAATTTTCGTATTGGCACTGGGTGTG
1 CACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTTCGTATTGGCACTATGTGTG
482754 CAACC
66 CAACC
482759 CACGTAATTT
Statistics
Matches: 209, Mismatches: 22, Indels: 1
0.90 0.09 0.00
Matches are distributed among these distances:
161 121 0.58
162 88 0.42
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.36
Consensus pattern (162 bp):
CACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTTCGTATTGGCACTATGTGTG
CAACCTAAGAAATTCATAATAAGTTTATAAATTTCCGTATTGGAACTATATGTGCAACCTAAGAA
ATTCATAATAAGTTTATGAATTCCCATATTGA
Found at i:482778 original size:54 final size:54
Alignment explanation
Indices: 482364--482758 Score: 594
Period size: 54 Copynumber: 7.3 Consensus size: 54
482354 TTATCGAATA
* *
482364 GGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTTCATATT
1 GGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATT
*
482418 GGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCTGTATT
1 GGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATT
* *
482472 GGCATTATGTGTGCAACCTAAGAAATT-ATAATAAGTTTATGAATTTCCATATT
1 GGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATT
* *
482525 GGTACTATGTGTGCAATCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATT
1 GGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATT
* * *
482579 GGCACTATGTGTTCAACCTAAGAAATTCATAATAAGTTTCTAAATTTCCGTATT
1 GGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATT
* * * * *
482633 GGAACTATATGTTCAACCTAAGAAATTCATAATAAGTTTATGAATTCCCATATT
1 GGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATT
* * * *
482687 GACACTATGTATGCAACCTAAGGAATTCATAATAAGTTTATGAATTTTCGTATT
1 GGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATT
**
482741 GGCACTGGGTGTGCAACC
1 GGCACTATGTGTGCAACC
482759 CACGTAATTT
Statistics
Matches: 306, Mismatches: 34, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
53 48 0.16
54 258 0.84
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Consensus pattern (54 bp):
GGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATT
Found at i:485483 original size:24 final size:26
Alignment explanation
Indices: 485456--485507 Score: 72
Period size: 24 Copynumber: 2.1 Consensus size: 26
485446 TTGACTAATC
*
485456 GTTTCAACTGAC-TTGA-TTCTTTTT
1 GTTTCAACTAACATTGATTTCTTTTT
*
485480 GTTTCTACTAACATTGATTTCTTTTT
1 GTTTCAACTAACATTGATTTCTTTTT
485506 GT
1 GT
485508 CTAGTCTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 10 0.42
25 4 0.17
26 10 0.42
ACGTcount: A:0.17, C:0.15, G:0.12, T:0.56
Consensus pattern (26 bp):
GTTTCAACTAACATTGATTTCTTTTT
Found at i:487449 original size:13 final size:14
Alignment explanation
Indices: 487426--487476 Score: 77
Period size: 13 Copynumber: 3.6 Consensus size: 14
487416 AGATTCATCG
487426 AAAGAAAAAAAGAA
1 AAAGAAAAAAAGAA
487440 AAAGAAAAAAA-AA
1 AAAGAAAAAAAGAA
487453 AAAGAAAAAAAGAGA
1 AAAGAAAAAAAGA-A
*
487468 GAAGAAAAA
1 AAAGAAAAA
487477 GAAATAAAGG
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
13 13 0.38
14 12 0.35
15 9 0.26
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (14 bp):
AAAGAAAAAAAGAA
Found at i:487462 original size:21 final size:21
Alignment explanation
Indices: 487430--487485 Score: 53
Period size: 20 Copynumber: 2.8 Consensus size: 21
487420 TCATCGAAAG
*
487430 AAAAAAAGAAAAAGA-AAAAA
1 AAAAAAAGAAAAAAAGAAAAA
* *
487450 AAAAAA-GAAAAAAAGAGAGA
1 AAAAAAAGAAAAAAAGAAAAA
* *
487470 AGAAAAAGAAATAAAG
1 AAAAAAAGAAAAAAAG
487486 GACAAGAAGC
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
19 7 0.24
20 14 0.48
21 8 0.28
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.02
Consensus pattern (21 bp):
AAAAAAAGAAAAAAAGAAAAA
Found at i:487477 original size:13 final size:11
Alignment explanation
Indices: 487438--487479 Score: 50
Period size: 11 Copynumber: 3.7 Consensus size: 11
487428 AGAAAAAAAG
487438 AAAAAGAA-AA
1 AAAAAGAAGAA
*
487448 AAAAAAAAGAA
1 AAAAAGAAGAA
487459 AAAAAGAGAGAA
1 AAAAAGA-AGAA
487471 GAAAAAGAA
1 -AAAAAGAA
487480 ATAAAGGACA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
10 7 0.26
11 8 0.30
12 5 0.19
13 7 0.26
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (11 bp):
AAAAAGAAGAA
Found at i:487492 original size:20 final size:21
Alignment explanation
Indices: 487427--487493 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 21
487417 GATTCATCGA
* *
487427 AAGAAAAA-AAGAAAAAGAAAA
1 AAGAAAAAGAA-AAAAAGAGAC
* *
487448 AAAAAAAAGAAAAAAAGAGAG
1 AAGAAAAAGAAAAAAAGAGAC
*
487469 AAGAAAAAGAAATAAAG-GAC
1 AAGAAAAAGAAAAAAAGAGAC
487489 AAGAA
1 AAGAA
487494 GCAAATATAA
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
20 7 0.18
21 30 0.77
22 2 0.05
ACGTcount: A:0.79, C:0.01, G:0.18, T:0.01
Consensus pattern (21 bp):
AAGAAAAAGAAAAAAAGAGAC
Found at i:489235 original size:75 final size:73
Alignment explanation
Indices: 489035--489268 Score: 258
Period size: 75 Copynumber: 3.2 Consensus size: 73
489025 ATATCATAAA
* * * ** * * * *
489035 TTTATCTCACTTGAGAGTGTTTTTTCTCAAAACGAGTTTTGTCTCACTTGAGATAATTTTCCCTT
1 TTTATCTCACTTGAGA-TGGTTTTTCTTAAAACAAGTTTCATCTCACTAGAGA-CAGTTTCCCAT
489100 GAAACA-AAA-
64 GAAA-AGAAAT
* * * *
489109 TTTATCTCAATTGAGATTGTTTTT-TTAAAACAAGTTTCATCTCACTGGAGACAGTTTCCCCTGA
1 TTTATCTCACTTGAGATGGTTTTTCTTAAAACAAGTTTCATCTCACTAGAGACAGTTTCCCATGA
489173 ATTAAGAAAT
66 A--AAGAAAT
*
489183 TTTATCTCACTTGAGATGGTTTTTCTTAAAACCAGTTTCATCTCACTAGAGACAGTTTCCCATGA
1 TTTATCTCACTTGAGATGGTTTTTCTTAAAACAAGTTTCATCTCACTAGAGACAGTTTCCCATG-
489248 AACAAGAAAT
65 AA-AAGAAAT
489258 TTTATCTCACT
1 TTTATCTCACT
489269 CGTCTTTGAG
Statistics
Matches: 137, Mismatches: 17, Indels: 11
0.83 0.10 0.07
Matches are distributed among these distances:
71 11 0.08
72 23 0.17
73 10 0.07
74 37 0.27
75 54 0.39
76 2 0.01
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (73 bp):
TTTATCTCACTTGAGATGGTTTTTCTTAAAACAAGTTTCATCTCACTAGAGACAGTTTCCCATGA
AAAGAAAT
Found at i:492732 original size:17 final size:17
Alignment explanation
Indices: 492710--492743 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
492700 TACTTGAATC
492710 TATTTTTATTAAACGTG
1 TATTTTTATTAAACGTG
492727 TATTTTTATTAAACGTG
1 TATTTTTATTAAACGTG
492744 AAGAATAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.06, G:0.12, T:0.53
Consensus pattern (17 bp):
TATTTTTATTAAACGTG
Found at i:495879 original size:73 final size:73
Alignment explanation
Indices: 495782--496027 Score: 260
Period size: 73 Copynumber: 3.4 Consensus size: 73
495772 GAGTCCCAAC
* * * *
495782 AACTCGAGATGGTTTTTCTTAAAACCAAATTCGTA-TTGTTTGAGATAGTTTTCGCTTGAAACAA
1 AACTCGAGATGGTTTTTCTTAAAACCAAATTCG-ACTCGCTTGAGATAATTTTCCCTTGAAACAA
495846 AATGTATCT
65 AATGTATCT
* * * * *
495855 CAGTTGAGATGATTTTTCTTAAAACCAACTTCGACTCGCTTGAGATAATTTTCCCTTGAAACAAA
1 AACTCGAGATGGTTTTTCTTAAAACCAAATTCGACTCGCTTGAGATAATTTTCCCTTGAAACAAA
* *
495920 ATTTTTCT
66 ATGTATCT
* * * * * * ** *
495928 AACTCGAGATGGTTTTTCTTAAAACTAACTTTGTCTCGCTTGATACAGCTTTCCCTCGAAACAAA
1 AACTCGAGATGGTTTTTCTTAAAACCAAATTCGACTCGCTTGAGATAATTTTCCCTTGAAACAAA
*
495993 ATCTATCT
66 ATGTATCT
* **
496001 CACTCGAGATGGTTTTTCCCAAAACCA
1 AACTCGAGATGGTTTTTCTTAAAACCA
496028 GCTTCGTGTC
Statistics
Matches: 143, Mismatches: 29, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
72 1 0.01
73 142 0.99
ACGTcount: A:0.30, C:0.20, G:0.14, T:0.36
Consensus pattern (73 bp):
AACTCGAGATGGTTTTTCTTAAAACCAAATTCGACTCGCTTGAGATAATTTTCCCTTGAAACAAA
ATGTATCT
Found at i:496062 original size:146 final size:146
Alignment explanation
Indices: 495782--496069 Score: 317
Period size: 146 Copynumber: 2.0 Consensus size: 146
495772 GAGTCCCAAC
* * * * * *
495782 AACTCGAGATGGTTTTTCTTAAAACCAAATTCGTATTGTTTGAGATAGTTTTCGCTTGAAACAAA
1 AACTCGAGATGGTTTTTCTTAAAACCAAATTCGTATCGCTTGAGACAGCTTTCCCTCGAAACAAA
* * * ** * ** * *
495847 ATGTATCTCAGTTGAGATGATTTTTCTTAAAACCAACTTCGACTCGCTTGAGATAATTTTCCCTT
66 ATCTATCTCACTCGAGATGATTTTTCCCAAAACCAACTTCGACTCACTAAAGACAATTTTCCATT
495912 GAAACAAAATTTTTCT
131 GAAACAAAATTTTTCT
* * * * *
495928 AACTCGAGATGGTTTTTCTTAAAACTAACTTTGTCTCGCTTGATACAGCTTTCCCTCGAAACAAA
1 AACTCGAGATGGTTTTTCTTAAAACCAAATTCGTATCGCTTGAGACAGCTTTCCCTCGAAACAAA
* * ** * *
495993 ATCTATCTCACTCGAGATGGTTTTTCCCAAAACCAGCTTCGTGTCACTAAAGACAGTTTT-GATT
66 ATCTATCTCACTCGAGATGATTTTTCCCAAAACCAACTTCGACTCACTAAAGACAATTTTCCATT
496057 CGAAACAAAATTT
131 -GAAACAAAATTT
496070 ATCTCACCCG
Statistics
Matches: 114, Mismatches: 27, Indels: 2
0.80 0.19 0.01
Matches are distributed among these distances:
145 2 0.02
146 112 0.98
ACGTcount: A:0.31, C:0.19, G:0.14, T:0.36
Consensus pattern (146 bp):
AACTCGAGATGGTTTTTCTTAAAACCAAATTCGTATCGCTTGAGACAGCTTTCCCTCGAAACAAA
ATCTATCTCACTCGAGATGATTTTTCCCAAAACCAACTTCGACTCACTAAAGACAATTTTCCATT
GAAACAAAATTTTTCT
Found at i:496610 original size:136 final size:135
Alignment explanation
Indices: 496362--496618 Score: 361
Period size: 136 Copynumber: 1.9 Consensus size: 135
496352 TAAACCGATC
* * *
496362 AACATTTCAAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGAGAGAAGAGTTCATAAT
1 AACATTTCAAATGGAGAGTTCATAATGAGAAGAAATCATCCAACAGAGAGAGAAAAGTTCATAAT
* **
496427 GAGAAGATCTTGTTTAACCTATCACTCGATTCACAACATTTTGAATCAGTGACGCCTCGCTTGAG
66 GAGAAGATCTTGTTCAACCTATCACTCGATTCACAACATTTCAAATCAGTGACGCCTCGCTTGAG
496492 GGATT
131 GGATT
* * * * *
496497 AACATTTCATATGGAGAGTTTATAATGAGAATAAATCATCCAATAGAGATAGAATAAGTTCATAA
1 AACATTTCAAATGGAGAGTTCATAATGAGAAGAAATCATCCAACAGAGAGAGAA-AAGTTCATAA
* * ***
496562 TGAGAAGATCTTGTTCGACCTATCACTCGATTTATGGCATTTCAAATCAGTGACGCC
65 TGAGAAGATCTTGTTCAACCTATCACTCGATTCACAACATTTCAAATCAGTGACGCC
496619 CCACCAGAGG
Statistics
Matches: 105, Mismatches: 16, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
135 47 0.45
136 58 0.55
ACGTcount: A:0.36, C:0.17, G:0.19, T:0.28
Consensus pattern (135 bp):
AACATTTCAAATGGAGAGTTCATAATGAGAAGAAATCATCCAACAGAGAGAGAAAAGTTCATAAT
GAGAAGATCTTGTTCAACCTATCACTCGATTCACAACATTTCAAATCAGTGACGCCTCGCTTGAG
GGATT
Found at i:496676 original size:59 final size:59
Alignment explanation
Indices: 496584--496729 Score: 177
Period size: 59 Copynumber: 2.5 Consensus size: 59
496574 GTTCGACCTA
* * * * *
496584 TCACTCGATTTATGGCATTTCAAATCAGTGACGCCCCACCAGAGGGGTTAA-TATTTCCT
1 TCACTCGATTCACGACATTTCGAATCAATGACGCCCCACCAGAGGGGTTAACT-TTTCCT
* *
496643 TCACTTGGTTCACGACATTTCGAATCAATGACGCCCCACCAGAGGGGTTAACTTTTCCT
1 TCACTCGATTCACGACATTTCGAATCAATGACGCCCCACCAGAGGGGTTAACTTTTCCT
** * *
496702 TTGCTCGATTCATGACATTTTGAATCAA
1 TCACTCGATTCACGACATTTCGAATCAA
496730 AAATGCCTCG
Statistics
Matches: 73, Mismatches: 13, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
59 72 0.99
60 1 0.01
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.32
Consensus pattern (59 bp):
TCACTCGATTCACGACATTTCGAATCAATGACGCCCCACCAGAGGGGTTAACTTTTCCT
Found at i:500076 original size:28 final size:28
Alignment explanation
Indices: 500045--500107 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
500035 CGATCCATTG
* * *
500045 CTTGAAACATTATGTCGTCGAGATAGTA
1 CTTGAAACATTATGTCATCAAGACAGTA
* *
500073 CTTGAAATATTATGTCATCAAGACAGTG
1 CTTGAAACATTATGTCATCAAGACAGTA
500101 CTTGAAA
1 CTTGAAA
500108 GCAATAACGA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.32
Consensus pattern (28 bp):
CTTGAAACATTATGTCATCAAGACAGTA
Found at i:508660 original size:13 final size:13
Alignment explanation
Indices: 508642--508674 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
508632 AGCTGAATAG
508642 ATCACCATCACAA
1 ATCACCATCACAA
508655 ATCACCATCACAA
1 ATCACCATCACAA
508668 ATCACCA
1 ATCACCA
508675 GTGAACGAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.45, C:0.39, G:0.00, T:0.15
Consensus pattern (13 bp):
ATCACCATCACAA
Found at i:511774 original size:16 final size:16
Alignment explanation
Indices: 511753--511783 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
511743 GTTTGATATT
511753 TATTTCAATCATAATA
1 TATTTCAATCATAATA
511769 TATTTCAATCATAAT
1 TATTTCAATCATAAT
511784 CTAAATGAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.42, C:0.13, G:0.00, T:0.45
Consensus pattern (16 bp):
TATTTCAATCATAATA
Found at i:512223 original size:31 final size:31
Alignment explanation
Indices: 512151--512223 Score: 78
Period size: 30 Copynumber: 2.4 Consensus size: 31
512141 ACAAATTGAT
* * * *
512151 CGTATAATTTTCCATAATTTTCAAATAGGTC
1 CGTATAACTTTCCAAAATTATCAAAAAGGTC
*
512182 CCTA-AACTTTCCTAAAATTAT-AAAAAGGTC
1 CGTATAACTTTCC-AAAATTATCAAAAAGGTC
512212 CGTATAACTTTC
1 CGTATAACTTTC
512224 TAAGTCTTGT
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
30 18 0.53
31 16 0.47
ACGTcount: A:0.36, C:0.19, G:0.08, T:0.37
Consensus pattern (31 bp):
CGTATAACTTTCCAAAATTATCAAAAAGGTC
Found at i:513254 original size:15 final size:15
Alignment explanation
Indices: 513234--513286 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
513224 CAGGATACAT
513234 AACTTTTGAAAATTA
1 AACTTTTGAAAATTA
****
513249 AACTTTTGGTCCTTA
1 AACTTTTGAAAATTA
513264 AACTTTT-AGAAATTA
1 AACTTTTGA-AAATTA
513279 AACTTTTG
1 AACTTTTG
513287 GTATCTAAAC
Statistics
Matches: 28, Mismatches: 8, Indels: 3
0.72 0.21 0.08
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.36, C:0.11, G:0.09, T:0.43
Consensus pattern (15 bp):
AACTTTTGAAAATTA
Found at i:514981 original size:15 final size:15
Alignment explanation
Indices: 514961--514995 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
514951 AAGGTTCCAC
*
514961 TAATATTTTTTCAGG
1 TAATATTTCTTCAGG
514976 TAATATTTCTTCAGG
1 TAATATTTCTTCAGG
514991 TAATA
1 TAATA
514996 GACAAGAATC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.31, C:0.09, G:0.11, T:0.49
Consensus pattern (15 bp):
TAATATTTCTTCAGG
Found at i:520140 original size:19 final size:19
Alignment explanation
Indices: 520116--520160 Score: 81
Period size: 19 Copynumber: 2.4 Consensus size: 19
520106 AAAAATCAAC
*
520116 TTAAATCTAATTATCCATA
1 TTAAATCTAATGATCCATA
520135 TTAAATCTAATGATCCATA
1 TTAAATCTAATGATCCATA
520154 TTAAATC
1 TTAAATC
520161 CTACCAATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.42, C:0.16, G:0.02, T:0.40
Consensus pattern (19 bp):
TTAAATCTAATGATCCATA
Found at i:521820 original size:56 final size:54
Alignment explanation
Indices: 521746--521851 Score: 142
Period size: 53 Copynumber: 1.9 Consensus size: 54
521736 GCTCATAGGC
521746 TTATTTTTACCAAAATACTTACCATTTAAATTCCATAAGCTCATAAGCTTATTATTA
1 TTATTTTTACCAAAATACTTACCA-TT--ATTCCATAAGCTCATAAGCTTATTATTA
* * * *
521803 TTATTTTT-TCAATATACTTGCCATTATTCCGTAAGCTCATAAGCTTATT
1 TTATTTTTACCAAAATACTTACCATTATTCCATAAGCTCATAAGCTTATT
521852 TGCATGGTTA
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
53 23 0.51
55 2 0.04
56 12 0.27
57 8 0.18
ACGTcount: A:0.32, C:0.18, G:0.06, T:0.44
Consensus pattern (54 bp):
TTATTTTTACCAAAATACTTACCATTATTCCATAAGCTCATAAGCTTATTATTA
Found at i:538702 original size:16 final size:15
Alignment explanation
Indices: 538670--538698 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
538660 AATTAGTAAT
538670 AAAAAAAACCTCACA
1 AAAAAAAACCTCACA
538685 AAAAAAAACCTCAC
1 AAAAAAAACCTCAC
538699 CAAACACTCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.66, C:0.28, G:0.00, T:0.07
Consensus pattern (15 bp):
AAAAAAAACCTCACA
Found at i:539005 original size:17 final size:17
Alignment explanation
Indices: 538983--539015 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
538973 TAAGAGTTGA
538983 TTTAATAAATGAACTAG
1 TTTAATAAATGAACTAG
*
539000 TTTAATTAATGAACTA
1 TTTAATAAATGAACTA
539016 CTTCACAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.45, C:0.06, G:0.09, T:0.39
Consensus pattern (17 bp):
TTTAATAAATGAACTAG
Found at i:543861 original size:8 final size:8
Alignment explanation
Indices: 543848--543872 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
543838 AAGCTAACCA
543848 AATTGAAT
1 AATTGAAT
543856 AATTGAAT
1 AATTGAAT
543864 AATTGAAT
1 AATTGAAT
543872 A
1 A
543873 TAAATATGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.52, C:0.00, G:0.12, T:0.36
Consensus pattern (8 bp):
AATTGAAT
Found at i:555547 original size:31 final size:31
Alignment explanation
Indices: 555464--555547 Score: 82
Period size: 32 Copynumber: 2.7 Consensus size: 31
555454 GAGTAACTCG
* *
555464 GGGCCTGC-GAGCCTACCCAAGACAATTCCTG
1 GGGCC-GCTGAGCCTACCCAAGAAAATTCCTA
* * *
555495 GGGCCACTAAGGCTTACCCAAGAAAATT-CTCA
1 GGGCCGCTGA-GCCTACCCAAGAAAATTCCT-A
555527 GGGCCGCTGAGCCTACCCAAG
1 GGGCCGCTGAGCCTACCCAAG
555548 GCTCGACTTA
Statistics
Matches: 42, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
30 1 0.02
31 18 0.43
32 23 0.55
ACGTcount: A:0.26, C:0.33, G:0.25, T:0.15
Consensus pattern (31 bp):
GGGCCGCTGAGCCTACCCAAGAAAATTCCTA
Found at i:556492 original size:28 final size:29
Alignment explanation
Indices: 556437--556521 Score: 145
Period size: 28 Copynumber: 3.0 Consensus size: 29
556427 AATTAATTAT
*
556437 GAAACTAACACCCTTTTAAAAATCTTTAC
1 GAAACTAACACCCTTTTAAAAATATTTAC
*
556466 GAAACTAACA-CCTTTTAAGAATATTTAC
1 GAAACTAACACCCTTTTAAAAATATTTAC
556494 GAAACTAACACCCTTTTAAAAATATTTA
1 GAAACTAACACCCTTTTAAAAATATTTA
556522 AAAAATAGAA
Statistics
Matches: 52, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
28 26 0.50
29 26 0.50
ACGTcount: A:0.44, C:0.20, G:0.05, T:0.32
Consensus pattern (29 bp):
GAAACTAACACCCTTTTAAAAATATTTAC
Found at i:556551 original size:57 final size:58
Alignment explanation
Indices: 556490--556636 Score: 172
Period size: 58 Copynumber: 2.6 Consensus size: 58
556480 TTAAGAATAT
556490 TTACGAAACTA-ACACCCTTTTAAAAATATTTA-AAAAATAGAATCGAACAGAAATTAA
1 TTACG-AACTAGACACCCTTTTAAAAATATTTACAAAAATAGAATCGAACAGAAATTAA
* * * * * *
556547 TTACGTATTAGGCACTCTTTTAAAAATATTTACAAAAATAGCATCGAACATAAATTAA
1 TTACGAACTAGACACCCTTTTAAAAATATTTACAAAAATAGAATCGAACAGAAATTAA
* * * * *
556605 TTACGTATTAGGCACTCTTTTAAAACTATTTA
1 TTACGAACTAGACACCCTTTTAAAAATATTTA
556637 TCGACAATCT
Statistics
Matches: 81, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
56 3 0.04
57 24 0.30
58 54 0.67
ACGTcount: A:0.45, C:0.14, G:0.08, T:0.33
Consensus pattern (58 bp):
TTACGAACTAGACACCCTTTTAAAAATATTTACAAAAATAGAATCGAACAGAAATTAA
Found at i:556602 original size:58 final size:57
Alignment explanation
Indices: 556506--556636 Score: 226
Period size: 58 Copynumber: 2.3 Consensus size: 57
556496 AACTAACACC
556506 CTTTTAAAAATATTTAAAAAATAGAATCGAACAGAAATTAATTACGTATTAGGCACT
1 CTTTTAAAAATATTTAAAAAATAGAATCGAACAGAAATTAATTACGTATTAGGCACT
* *
556563 CTTTTAAAAATATTTACAAAAATAGCATCGAACATAAATTAATTACGTATTAGGCACT
1 CTTTTAAAAATATTTA-AAAAATAGAATCGAACAGAAATTAATTACGTATTAGGCACT
*
556621 CTTTTAAAACTATTTA
1 CTTTTAAAAATATTTA
556637 TCGACAATCT
Statistics
Matches: 70, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
57 16 0.23
58 54 0.77
ACGTcount: A:0.45, C:0.12, G:0.08, T:0.34
Consensus pattern (57 bp):
CTTTTAAAAATATTTAAAAAATAGAATCGAACAGAAATTAATTACGTATTAGGCACT
Found at i:560084 original size:43 final size:44
Alignment explanation
Indices: 560014--560112 Score: 164
Period size: 43 Copynumber: 2.2 Consensus size: 44
560004 GTAAACCAGT
*
560014 ATCCAGAAATCATAAGTCGGGCAATCACACTTTACATTTTAGTAA
1 ATCCAG-AATCATAAGTCCGGCAATCACACTTTACATTTTAGTAA
*
560059 ATCCAGAATCATAAG-CCGGCAATCACACTTTACGTTTTAGTAA
1 ATCCAGAATCATAAGTCCGGCAATCACACTTTACATTTTAGTAA
560102 ATCCAGAATCA
1 ATCCAGAATCA
560113 GATAAATCAT
Statistics
Matches: 52, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
43 37 0.71
44 9 0.17
45 6 0.12
ACGTcount: A:0.37, C:0.22, G:0.13, T:0.27
Consensus pattern (44 bp):
ATCCAGAATCATAAGTCCGGCAATCACACTTTACATTTTAGTAA
Found at i:560797 original size:28 final size:29
Alignment explanation
Indices: 560755--560810 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 29
560745 AAATTAATTA
560755 TGAAACTAACACCCTTTTAAAAATATTTG
1 TGAAACTAACACCCTTTTAAAAATATTTG
560784 TGAAACTAA-ACCCTTTTAAAAATATTT
1 TGAAACTAACACCCTTTTAAAAATATTT
560811 TCAAAATATT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
28 18 0.67
29 9 0.33
ACGTcount: A:0.43, C:0.16, G:0.05, T:0.36
Consensus pattern (29 bp):
TGAAACTAACACCCTTTTAAAAATATTTG
Found at i:562077 original size:21 final size:20
Alignment explanation
Indices: 562053--562115 Score: 58
Period size: 21 Copynumber: 3.1 Consensus size: 20
562043 AATGTTACAA
562053 TAAAATATTAATTATGATAAT
1 TAAAATATTAATTAT-ATAAT
* * *
562074 TAAATTAATAA--ATATATT
1 TAAAATATTAATTATATAAT
*
562092 TAATATATTAATTATTATAAT
1 TAAAATATTAATTA-TATAAT
562113 TAA
1 TAA
562116 TATACTTTAT
Statistics
Matches: 32, Mismatches: 7, Indels: 6
0.71 0.16 0.13
Matches are distributed among these distances:
18 12 0.38
19 2 0.06
20 1 0.03
21 17 0.53
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (20 bp):
TAAAATATTAATTATATAAT
Found at i:562140 original size:22 final size:23
Alignment explanation
Indices: 562128--562274 Score: 166
Period size: 22 Copynumber: 6.7 Consensus size: 23
562118 TACTTTATAA
562128 TTAATACTTATAT-TTATATACT
1 TTAATACTTATATATTATATACT
562150 TTAATACTT-TATATTATATACT
1 TTAATACTTATATATTATATACT
*
562172 TTATTACTTATATACTT-TATA-T
1 TTAATACTTATATA-TTATATACT
562194 TTAATACTTATAT-TTATATACT
1 TTAATACTTATATATTATATACT
* * *
562216 TTAATACTTATAT-TCAAACACT
1 TTAATACTTATATATTATATACT
*
562238 TTATTACTT-TATATTATATA-T
1 TTAATACTTATATATTATATACT
*
562259 TTTATACTTTATATAT
1 TTAATAC-TTATATAT
562275 AAAGTACCAA
Statistics
Matches: 106, Mismatches: 11, Indels: 15
0.80 0.08 0.11
Matches are distributed among these distances:
20 2 0.02
21 16 0.15
22 73 0.69
23 13 0.12
24 2 0.02
ACGTcount: A:0.35, C:0.10, G:0.00, T:0.55
Consensus pattern (23 bp):
TTAATACTTATATATTATATACT
Found at i:562182 original size:7 final size:8
Alignment explanation
Indices: 562115--562228 Score: 92
Period size: 7 Copynumber: 15.5 Consensus size: 8
562105 ATTATAATTA
562115 ATATACTT
1 ATATACTT
*
562123 -TATAATT
1 ATATACTT
562130 A-ATACTT
1 ATATACTT
562137 ATAT--TT
1 ATATACTT
562143 ATATACTT
1 ATATACTT
562151 -TAATACTT
1 AT-ATACTT
562159 -TATA-TT
1 ATATACTT
562165 ATATACTT
1 ATATACTT
562173 -TATTACTT
1 ATA-TACTT
562181 ATATACTT
1 ATATACTT
*
562189 -TATATTT
1 ATATACTT
562196 A-ATACTT
1 ATATACTT
562203 ATAT--TT
1 ATATACTT
562209 ATATACTT
1 ATATACTT
562217 -TAATACTT
1 AT-ATACTT
562225 ATAT
1 ATAT
562229 TCAAACACTT
Statistics
Matches: 87, Mismatches: 4, Indels: 30
0.72 0.03 0.25
Matches are distributed among these distances:
6 14 0.16
7 35 0.40
8 35 0.40
9 3 0.03
ACGTcount: A:0.37, C:0.09, G:0.00, T:0.54
Consensus pattern (8 bp):
ATATACTT
Found at i:562198 original size:66 final size:66
Alignment explanation
Indices: 562115--562272 Score: 232
Period size: 66 Copynumber: 2.4 Consensus size: 66
562105 ATTATAATTA
* * *
562115 ATATACTTTATAATTAATACTTATATTTATATACTTTAATACTTTATATT-ATATACTTTATTAC
1 ATATACTTTATATTTAATACTTATATTTATATACTTTAATAC-TTATATTCAAACACTTTATTAC
562179 TT
65 TT
562181 ATATACTTTATATTTAATACTTATATTTATATACTTTAATACTTATATTCAAACACTTTATTACT
1 ATATACTTTATATTTAATACTTATATTTATATACTTTAATACTTATATTCAAACACTTTATTACT
562246 T
66 T
*
562247 -TATA-TTATATATTTTATACTTTATAT
1 ATATACTT-TATATTTAATAC-TTATAT
562273 ATAAAGTACC
Statistics
Matches: 85, Mismatches: 4, Indels: 6
0.89 0.04 0.06
Matches are distributed among these distances:
64 2 0.02
65 22 0.26
66 61 0.72
ACGTcount: A:0.36, C:0.09, G:0.00, T:0.54
Consensus pattern (66 bp):
ATATACTTTATATTTAATACTTATATTTATATACTTTAATACTTATATTCAAACACTTTATTACT
T
Found at i:562264 original size:14 final size:15
Alignment explanation
Indices: 562116--562274 Score: 75
Period size: 14 Copynumber: 10.9 Consensus size: 15
562106 TTATAATTAA
*
562116 TATACTT-TATAATT
1 TATACTTATATATTT
* *
562130 AATACTTATAT-TTA
1 TATACTTATATATTT
*
562144 TATACTT-TAATACTT
1 TATACTTAT-ATATTT
*
562159 TATA-TTATATACTT
1 TATACTTATATATTT
*
562173 TATTACTTATATACTT
1 TA-TACTTATATATTT
* *
562189 TATATTTA-ATA-CT
1 TATACTTATATATTT
*
562202 TATATTTATATACTTT
1 TATACTTATATA-TTT
* **
562218 AATACTTATAT-TCA
1 TATACTTATATATTT
* * *
562232 AACACTT-TATTACTT
1 TATACTTATA-TATTT
562247 TATA-TTATATATTT
1 TATACTTATATATTT
562261 TATACTTTATATAT
1 TATAC-TTATATAT
562275 AAAGTACCAA
Statistics
Matches: 111, Mismatches: 20, Indels: 26
0.71 0.13 0.17
Matches are distributed among these distances:
13 12 0.11
14 49 0.44
15 20 0.18
16 30 0.27
ACGTcount: A:0.36, C:0.09, G:0.00, T:0.55
Consensus pattern (15 bp):
TATACTTATATATTT
Found at i:562360 original size:33 final size:31
Alignment explanation
Indices: 562323--562388 Score: 114
Period size: 33 Copynumber: 2.1 Consensus size: 31
562313 AATTGAATAA
562323 ATTAAACAACACTTTATATACTTTATACTTTAT
1 ATTAAACAACACTTTAT-TACTTTATA-TTTAT
562356 ATTAAACAACACTTTATTACTTTATATTTAT
1 ATTAAACAACACTTTATTACTTTATATTTAT
562387 AT
1 AT
562389 ACTTTATACT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
31 7 0.21
32 9 0.27
33 17 0.52
ACGTcount: A:0.39, C:0.14, G:0.00, T:0.47
Consensus pattern (31 bp):
ATTAAACAACACTTTATTACTTTATATTTAT
Found at i:562391 original size:15 final size:16
Alignment explanation
Indices: 562333--562403 Score: 74
Period size: 16 Copynumber: 4.5 Consensus size: 16
562323 ATTAAACAAC
562333 ACTTTATATACTTTAT
1 ACTTTATATACTTTAT
**** *
562349 ACTTTATATTAAACAAC
1 ACTTTATA-TACTTTAT
562366 ACTTTAT-TACTTTAT
1 ACTTTATATACTTTAT
562381 A-TTTATATACTTTAT
1 ACTTTATATACTTTAT
562396 ACTTTATA
1 ACTTTATA
562404 CTAAGATGAC
Statistics
Matches: 42, Mismatches: 10, Indels: 6
0.72 0.17 0.10
Matches are distributed among these distances:
14 5 0.12
15 13 0.31
16 14 0.33
17 10 0.24
ACGTcount: A:0.35, C:0.13, G:0.00, T:0.52
Consensus pattern (16 bp):
ACTTTATATACTTTAT
Found at i:562398 original size:7 final size:7
Alignment explanation
Indices: 562366--562405 Score: 53
Period size: 7 Copynumber: 5.4 Consensus size: 7
562356 ATTAAACAAC
562366 ACTTTATT
1 ACTTTA-T
562374 ACTTTAT
1 ACTTTAT
*
562381 ATTTATAT
1 ACTT-TAT
562389 ACTTTAT
1 ACTTTAT
562396 ACTTTAT
1 ACTTTAT
562403 ACT
1 ACT
562406 AAGATGACAC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
7 17 0.59
8 12 0.41
ACGTcount: A:0.30, C:0.12, G:0.00, T:0.57
Consensus pattern (7 bp):
ACTTTAT
Found at i:563770 original size:8 final size:8
Alignment explanation
Indices: 563757--563798 Score: 54
Period size: 7 Copynumber: 5.6 Consensus size: 8
563747 ATACATGCAT
563757 CATATATA
1 CATATATA
563765 CATATATA
1 CATATATA
*
563773 CATACATA
1 CATATATA
563781 -ATATAT-
1 CATATATA
563787 CATATA-A
1 CATATATA
563794 CATAT
1 CATAT
563799 GTATCATACA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
7 15 0.50
8 15 0.50
ACGTcount: A:0.50, C:0.14, G:0.00, T:0.36
Consensus pattern (8 bp):
CATATATA
Found at i:563796 original size:17 final size:18
Alignment explanation
Indices: 563766--563821 Score: 55
Period size: 17 Copynumber: 3.2 Consensus size: 18
563756 TCATATATAC
*
563766 ATAT-ATACATACATAAT
1 ATATCATACACACATAAT
*
563783 ATATCATATA-ACAT-AT
1 ATATCATACACACATAAT
*
563799 GTATCATACACACATCAAT
1 ATATCATACACACAT-AAT
563818 ATAT
1 ATAT
563822 TTTTATAATA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
16 10 0.32
17 12 0.39
18 4 0.13
19 5 0.16
ACGTcount: A:0.48, C:0.16, G:0.02, T:0.34
Consensus pattern (18 bp):
ATATCATACACACATAAT
Found at i:564055 original size:7 final size:7
Alignment explanation
Indices: 564043--564094 Score: 59
Period size: 7 Copynumber: 7.4 Consensus size: 7
564033 AATACATATA
564043 TTAGGGT
1 TTAGGGT
564050 TTAGGGT
1 TTAGGGT
*
564057 TTAGTGT
1 TTAGGGT
*
564064 TTAGGAT
1 TTAGGGT
*
564071 TTAGGAT
1 TTAGGGT
*
564078 TTAGGAT
1 TTAGGGT
*
564085 TTAGAGT
1 TTAGGGT
564092 TTA
1 TTA
564095 AAGTTTCTAT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
7 40 1.00
ACGTcount: A:0.23, C:0.00, G:0.31, T:0.46
Consensus pattern (7 bp):
TTAGGGT
Found at i:564141 original size:2 final size:2
Alignment explanation
Indices: 564136--564175 Score: 53
Period size: 2 Copynumber: 19.0 Consensus size: 2
564126 TTATATAGTT
*
564136 TA TA TA TA TA TA TA TA TA TA TA TA GTT TA TA TA TA CTA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA -TA TA
564176 CATGGTTTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 31 0.91
3 3 0.09
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:564578 original size:21 final size:21
Alignment explanation
Indices: 564535--564586 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
564525 TCCATTTATA
**
564535 TTAGGGTTTATGGTTTATGGT
1 TTAGGGTTTATGGTTTAAAGT
*
564556 TTAGTGTTTATGGTTTAAAGT
1 TTAGGGTTTATGGTTTAAAGT
*
564577 TTAGGATTTA
1 TTAGGGTTTA
564587 GGGGTTATGA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.21, C:0.00, G:0.27, T:0.52
Consensus pattern (21 bp):
TTAGGGTTTATGGTTTAAAGT
Found at i:564610 original size:7 final size:7
Alignment explanation
Indices: 564535--564612 Score: 57
Period size: 7 Copynumber: 11.1 Consensus size: 7
564525 TCCATTTATA
564535 TTAGGGT
1 TTAGGGT
*
564542 TTATGGT
1 TTAGGGT
*
564549 TTATGGT
1 TTAGGGT
*
564556 TTAGTGT
1 TTAGGGT
*
564563 TTATGGT
1 TTAGGGT
**
564570 TTAAAGT
1 TTAGGGT
*
564577 TTAGGAT
1 TTAGGGT
*
564584 TTAGGGG
1 TTAGGGT
* **
564591 TTATGAA
1 TTAGGGT
564598 TTAGGGT
1 TTAGGGT
564605 TTAGGGT
1 TTAGGGT
564612 T
1 T
564613 GTTATAAAAC
Statistics
Matches: 53, Mismatches: 18, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
7 53 1.00
ACGTcount: A:0.21, C:0.00, G:0.32, T:0.47
Consensus pattern (7 bp):
TTAGGGT
Found at i:564888 original size:2 final size:2
Alignment explanation
Indices: 564877--564927 Score: 86
Period size: 2 Copynumber: 26.0 Consensus size: 2
564867 ATAGTGTTTC
564877 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
564918 TA TA TC TA TA
1 TA TA TA TA TA
564928 GATTACTTAT
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 45 0.98
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:565158 original size:12 final size:12
Alignment explanation
Indices: 565143--565167 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
565133 AATTTTTCTA
565143 TTCCCTCTAAAT
1 TTCCCTCTAAAT
565155 TTCCCTCTAAAT
1 TTCCCTCTAAAT
565167 T
1 T
565168 CTCAATTTCT
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:0.24, C:0.32, G:0.00, T:0.44
Consensus pattern (12 bp):
TTCCCTCTAAAT
Found at i:565416 original size:15 final size:15
Alignment explanation
Indices: 565398--565430 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
565388 ATAGTTTATA
565398 ATATAAATATAGTTT
1 ATATAAATATAGTTT
*
565413 ATATATATATAGTTT
1 ATATAAATATAGTTT
565428 ATA
1 ATA
565431 CATAAACTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.48
Consensus pattern (15 bp):
ATATAAATATAGTTT
Found at i:565419 original size:2 final size:2
Alignment explanation
Indices: 565394--565472 Score: 65
Period size: 2 Copynumber: 39.5 Consensus size: 2
565384 TTATATAGTT
* * * * *
565394 TA TA -A TA TA AA TA TA GTT TA TA TA TA TA TA GTT TA TA CA TA AA
1 TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA -TA TA TA TA TA TA
565437 CT- TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
565473 TTTTTTCAAT
Statistics
Matches: 61, Mismatches: 10, Indels: 12
0.73 0.12 0.14
Matches are distributed among these distances:
1 3 0.05
2 56 0.92
3 2 0.03
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.48
Consensus pattern (2 bp):
TA
Found at i:565447 original size:32 final size:31
Alignment explanation
Indices: 565363--565455 Score: 95
Period size: 32 Copynumber: 3.0 Consensus size: 31
565353 AAACATAATT
*
565363 TTTAT-ATATAACTTATAATA-AT-TATATAG
1 TTTATAATA-AACTTATATTATATATATATAG
*
565392 TTTATAATATAA-ATATAGTTTATATATATATAG
1 TTTATAATA-AACTTATA--TTATATATATATAG
565425 TTTATACATAAACTTATATTATATATATATA
1 TTTATA-ATAAACTTATATTATATATATATA
565456 TATATATATA
Statistics
Matches: 54, Mismatches: 3, Indels: 11
0.79 0.04 0.16
Matches are distributed among these distances:
29 9 0.17
30 6 0.11
31 2 0.04
32 15 0.28
33 15 0.28
34 7 0.13
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.48
Consensus pattern (31 bp):
TTTATAATAAACTTATATTATATATATATAG
Found at i:571008 original size:22 final size:21
Alignment explanation
Indices: 570966--571005 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
570956 GAGTTTATTT
*
570966 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
570987 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
571006 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:573121 original size:65 final size:64
Alignment explanation
Indices: 572973--573132 Score: 198
Period size: 65 Copynumber: 2.5 Consensus size: 64
572963 TGCACTAAGA
* * *
572973 GTGTATCGATGCATCAAGTGCATTCGATGTTTTAAAATAGCCAGAGTGCATTGATGCATGGCTG
1 GTGTATCGATGCATCAAATGCATTCGATGTTTTAAAATAGCCACAGTGCATCGATGCATGGCTG
* * * *
573037 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-ATCCTCAGTGCATCGGTGCATGG-T
1 GTGTATCGATGCATCAAATGCATTCGATGTTTT-A-AAATAGCCACAGTGCATCGATGCATGGCT
*
573100 AT
64 -G
*
573102 GTGTATCGATGCATGAAATGCATTCGATGTT
1 GTGTATCGATGCATCAAATGCATTCGATGTT
573133 CAATTTAATT
Statistics
Matches: 83, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
64 32 0.39
65 48 0.58
66 3 0.04
ACGTcount: A:0.26, C:0.17, G:0.24, T:0.33
Consensus pattern (64 bp):
GTGTATCGATGCATCAAATGCATTCGATGTTTTAAAATAGCCACAGTGCATCGATGCATGGCTG
Found at i:573180 original size:65 final size:63
Alignment explanation
Indices: 572977--573182 Score: 190
Period size: 65 Copynumber: 3.2 Consensus size: 63
572967 CTAAGAGTGT
* * *
572977 ATCGATGCATCAAGTGCATTCGATGTTT--TAAAATAGC-CAGAGTGCATTGATGCATGGCTGGT
1 ATCGATGCATCAAATGCATTCGATGTTTCATAAAAT--CTC--AGTGCATCGATGCATGGTTGGT
573039 GC
62 GC
*
573041 ATCGATGCATCAAATGCATTCGATGTTTTCATAAAATCCTCAGTGCATCGGTGCATGGTAT-GTG
1 ATCGATGCATCAAATGCATTCGATG-TTTCATAAAAT-CTCAGTGCATCGATGCATGGT-TGGTG
*
573105 T
63 C
* **
573106 ATCGATGCATGAAATGCATTCGATG-TTCAATTTAAT-TCATGGTGCATCGATGCATGGATTGGT
1 ATCGATGCATCAAATGCATTCGATGTTTC-ATAAAATCTCA--GTGCATCGATGCATGG-TTGGT
573169 GC
62 GC
*
573171 ATCGGTGCATCA
1 ATCGATGCATCA
573183 CTCTGAAAAA
Statistics
Matches: 119, Mismatches: 13, Indels: 19
0.79 0.09 0.13
Matches are distributed among these distances:
62 3 0.03
63 3 0.03
64 45 0.38
65 59 0.50
66 2 0.02
67 7 0.06
ACGTcount: A:0.26, C:0.17, G:0.24, T:0.32
Consensus pattern (63 bp):
ATCGATGCATCAAATGCATTCGATGTTTCATAAAATCTCAGTGCATCGATGCATGGTTGGTGC
Found at i:574909 original size:16 final size:14
Alignment explanation
Indices: 574885--574928 Score: 52
Period size: 14 Copynumber: 3.0 Consensus size: 14
574875 ATATAATTAG
*
574885 ATTTATTCTTATTTAT
1 ATTTTTTCTT-TTT-T
574901 ATTTTTTCTTTTTT
1 ATTTTTTCTTTTTT
*
574915 CTTTTTTCTTTTTT
1 ATTTTTTCTTTTTT
574929 TATGAGTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
14 14 0.54
15 3 0.12
16 9 0.35
ACGTcount: A:0.11, C:0.09, G:0.00, T:0.80
Consensus pattern (14 bp):
ATTTTTTCTTTTTT
Found at i:574914 original size:7 final size:7
Alignment explanation
Indices: 574902--574928 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
574892 CTTATTTATA
574902 TTTTTTC
1 TTTTTTC
574909 TTTTTTC
1 TTTTTTC
574916 TTTTTTC
1 TTTTTTC
574923 TTTTTT
1 TTTTTT
574929 TATGAGTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (7 bp):
TTTTTTC
Found at i:575334 original size:14 final size:15
Alignment explanation
Indices: 575303--575334 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
575293 AATACTTTTT
575303 AAAATAATTTTAAGA
1 AAAATAATTTTAAGA
575318 AAAATAATTTTAA-A
1 AAAATAATTTTAAGA
575332 AAA
1 AAA
575335 TAAAAAGTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (15 bp):
AAAATAATTTTAAGA
Found at i:575335 original size:13 final size:13
Alignment explanation
Indices: 575290--575337 Score: 53
Period size: 15 Copynumber: 3.6 Consensus size: 13
575280 TCGAATACCT
*
575290 AAAAATACTTTT-
1 AAAAATAATTTTA
*
575302 TAAAATAATTTTAA
1 AAAAATAATTTT-A
575316 GAAAAATAATTTTA
1 -AAAAATAATTTTA
575330 AAAAATAA
1 AAAAATAA
575338 AAAGTGATCC
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
12 10 0.33
13 8 0.27
14 1 0.03
15 11 0.37
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.35
Consensus pattern (13 bp):
AAAAATAATTTTA
Found at i:577659 original size:134 final size:133
Alignment explanation
Indices: 577436--577867 Score: 483
Period size: 134 Copynumber: 3.2 Consensus size: 133
577426 ATTGATATTT
* * * ** **
577436 TTCGTTGCTCTTTAGGAAGACCAAATCTGAAAGAAGAATAATATGCTCCACTACTCTTTAGAAGA
1 TTCGCTGCTCTTCAGGAAGACAAAATCTGAAAGAAGAATAATATGCTCTGCTACTCTTTAGGGGA
* * * * * * *
577501 GATCATACGCAAGAAATCTTTGATCCTCTTCTATGCTCTTCAAGAAATATTTAATCGAACTTGAT
66 GATCAGACTCGAGAAATATTTGATCCTCTTC-ATGCTCTTCAAGGAAGATTAAATCGAACTTGAT
577566 TTGC
130 TTGC
* * * *
577570 TTCGCTGCTCTTTAGGAATACAAAATCTGAAAGAAGAAGAATATGCTTTGCTACTCTTTAGGGGA
1 TTCGCTGCTCTTCAGGAAGACAAAATCTGAAAGAAGAATAATATGCTCTGCTACTCTTTAGGGGA
* * * * *
577635 GACCAGACTCGAGAAATATTTGATCCACTTCACTGCTCTTCAGGGAAGATTAAAACAAACTTGAT
66 GATCAGACTCGAGAAATATTTGATCCTCTTCA-TGCTCTTCAAGGAAGATTAAATCGAACTTGAT
577700 TTGC
130 TTGC
* * * * *
577704 TTCACTGCTCTTCAGGAATACCAAATCTGAAAGAAGAATAATCTGCTCTGCTACTCTTTAGGGAA
1 TTCGCTGCTCTTCAGGAAGACAAAATCTGAAAGAAGAATAATATGCTCTGCTACTCTTTAGGGGA
* * * * * *
577769 TATCAGACTTGAGAAAAAATTTGAT-CTAATTCGCTGCTCTTCAAGGAAGATTGAATCGAACTTG
66 GATCAGACTCGAG-AAATATTTGATCCT-CTTC-ATGCTCTTCAAGGAAGATTAAATCGAACTTG
577833 ATTTGC
128 ATTTGC
*
577839 TTCGCT-CTCTTCAAGAAGA-AAAATCTGAA
1 TTCGCTGCTCTTCAGGAAGACAAAATCTGAA
577868 GGTTTTAGAA
Statistics
Matches: 251, Mismatches: 43, Indels: 9
0.83 0.14 0.03
Matches are distributed among these distances:
133 10 0.04
134 191 0.76
135 50 0.20
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Consensus pattern (133 bp):
TTCGCTGCTCTTCAGGAAGACAAAATCTGAAAGAAGAATAATATGCTCTGCTACTCTTTAGGGGA
GATCAGACTCGAGAAATATTTGATCCTCTTCATGCTCTTCAAGGAAGATTAAATCGAACTTGATT
TGC
Found at i:578459 original size:45 final size:45
Alignment explanation
Indices: 578410--578653 Score: 265
Period size: 45 Copynumber: 5.4 Consensus size: 45
578400 AAATCGACTT
* * * *
578410 CTCTTCGTGAGAAAGTCAAGAAGAACAAAACTAAAATATTGAATC
1 CTCTTCGCGAGAAAGTCAAGAAGGACAACACTAAAAGATTGAATC
* * * * *
578455 CTCTTTGCGAGAAAGTCAAAAAGGGCAACACTAAAATATTGACTC
1 CTCTTCGCGAGAAAGTCAAGAAGGACAACACTAAAAGATTGAATC
*** * * * **
578500 CTCTTCAAAAGAAAGTCAAGAAAGACCATACCGAAAGATT-AACTC
1 CTCTTCGCGAGAAAGTCAAGAAGGACAACACTAAAAGATTGAA-TC
* *
578545 CACTTCGCGAGAAAGTCAAGAAGGACAACACTAAAAGATTGACTC
1 CTCTTCGCGAGAAAGTCAAGAAGGACAACACTAAAAGATTGAATC
* * *
578590 CACTTCGCGAGAAAGTCAAGAAGGACAACACTAAAAGATTGATTT
1 CTCTTCGCGAGAAAGTCAAGAAGGACAACACTAAAAGATTGAATC
*
578635 CTCTTCGCGATAAAGTCAA
1 CTCTTCGCGAGAAAGTCAA
578654 TATTTTTCTT
Statistics
Matches: 163, Mismatches: 34, Indels: 4
0.81 0.17 0.02
Matches are distributed among these distances:
44 1 0.01
45 161 0.99
46 1 0.01
ACGTcount: A:0.43, C:0.20, G:0.17, T:0.20
Consensus pattern (45 bp):
CTCTTCGCGAGAAAGTCAAGAAGGACAACACTAAAAGATTGAATC
Found at i:578704 original size:10 final size:10
Alignment explanation
Indices: 578687--578720 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
578677 TCAAATTTTG
578687 AAAAAAAAAT
1 AAAAAAAAAT
**
578697 TGAAAAAAAT
1 AAAAAAAAAT
578707 AAAAAAAAAT
1 AAAAAAAAAT
578717 AAAA
1 AAAA
578721 TATTTTCCTC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.85, C:0.00, G:0.03, T:0.12
Consensus pattern (10 bp):
AAAAAAAAAT
Found at i:581286 original size:15 final size:15
Alignment explanation
Indices: 581268--581348 Score: 57
Period size: 15 Copynumber: 5.8 Consensus size: 15
581258 ACTTTTATTT
581268 TTATAATTATTATAA
1 TTATAATTATTATAA
*
581283 TTATATTTATTATAA
1 TTATAATTATTATAA
*
581298 -TA-AA-TATTATAT
1 TTATAATTATTATAA
*
581310 TTATTA-TATTAT-A
1 TTATAATTATTATAA
**
581323 TT-TTTTTATTATAA
1 TTATAATTATTATAA
* *
581337 ATATTATTATTA
1 TTATAATTATTA
581349 CAAAATAGGC
Statistics
Matches: 53, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
12 9 0.17
13 11 0.21
14 11 0.21
15 22 0.42
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
TTATAATTATTATAA
Found at i:581300 original size:18 final size:19
Alignment explanation
Indices: 581273--581343 Score: 76
Period size: 18 Copynumber: 3.8 Consensus size: 19
581263 TATTTTTATA
*
581273 ATTATTATA-ATTATATTT
1 ATTATAATATATTATATTT
581291 ATTATAATAAATATTATATTT
1 ATTATAAT--ATATTATATTT
* *
581312 ATTATATTATATT-TTTTT
1 ATTATAATATATTATATTT
581330 ATTATAA-ATATTAT
1 ATTATAATATATTAT
581344 TATTACAAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
17 5 0.11
18 18 0.40
19 5 0.11
20 1 0.02
21 16 0.36
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
ATTATAATATATTATATTT
Found at i:581308 original size:36 final size:36
Alignment explanation
Indices: 581268--581348 Score: 110
Period size: 36 Copynumber: 2.2 Consensus size: 36
581258 ACTTTTATTT
581268 TTATAATTATTATAATTATA-TTTATTATAATAAATA
1 TTATAATTATTAT-ATTATATTTTATTATAATAAATA
* * *
581304 TTATATTTATTATATTATATTTTTTTATTATAAATA
1 TTATAATTATTATATTATATTTTATTATAATAAATA
*
581340 TTATTATTA
1 TTATAATTA
581349 CAAAATAGGC
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
35 6 0.15
36 33 0.85
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (36 bp):
TTATAATTATTATATTATATTTTATTATAATAAATA
Found at i:581320 original size:14 final size:13
Alignment explanation
Indices: 581301--581335 Score: 52
Period size: 14 Copynumber: 2.6 Consensus size: 13
581291 ATTATAATAA
581301 ATATTATATTTATT
1 ATATTATATTT-TT
581315 ATATTATATTTTT
1 ATATTATATTTTT
*
581328 TTATTATA
1 ATATTATA
581336 AATATTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 9 0.45
14 11 0.55
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (13 bp):
ATATTATATTTTT
Found at i:597118 original size:24 final size:25
Alignment explanation
Indices: 597068--597118 Score: 59
Period size: 25 Copynumber: 2.1 Consensus size: 25
597058 TCCCATTTTA
* * *
597068 TCCATTTTCTCTTCATTTCATCCTT
1 TCCATTTCCTCCTCATTTCAACCTT
*
597093 TCCATTTCCTCCTC-TTTCAACTTT
1 TCCATTTCCTCCTCATTTCAACCTT
597117 TC
1 TC
597119 TTAGTGGTCA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
24 10 0.45
25 12 0.55
ACGTcount: A:0.12, C:0.35, G:0.00, T:0.53
Consensus pattern (25 bp):
TCCATTTCCTCCTCATTTCAACCTT
Found at i:598925 original size:31 final size:31
Alignment explanation
Indices: 598873--598950 Score: 102
Period size: 31 Copynumber: 2.5 Consensus size: 31
598863 TACTAGTAAG
* *
598873 GTTGTATTCAGATAATACACAATATAGTCAA
1 GTTGAATTTAGATAATACACAATATAGTCAA
* *
598904 GTTGAATTTAGATAATGCACAATATAGTCAT
1 GTTGAATTTAGATAATACACAATATAGTCAA
* *
598935 GATGCATTTAGATAAT
1 GTTGAATTTAGATAAT
598951 CCATAGTACA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.35
Consensus pattern (31 bp):
GTTGAATTTAGATAATACACAATATAGTCAA
Found at i:600262 original size:22 final size:22
Alignment explanation
Indices: 600235--600276 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
600225 TTTTATACAT
*
600235 GTAGTATCGATACCCCTATGAA
1 GTAGTATCGATACCCATATGAA
600257 GTAGTATCGATACCCATATG
1 GTAGTATCGATACCCATATG
600277 CTCCCAGCAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.29
Consensus pattern (22 bp):
GTAGTATCGATACCCATATGAA
Found at i:601376 original size:27 final size:24
Alignment explanation
Indices: 601326--601376 Score: 66
Period size: 27 Copynumber: 2.0 Consensus size: 24
601316 TAGATCCAAT
*
601326 CCGATCCAAAAAAATAACCGAAAA
1 CCGATCCAAAAAAATAACCAAAAA
601350 CCGATCCAAAAAATCAATAACCAAAAA
1 CCGATCC-AAAAA--AATAACCAAAAA
601377 AAACTAATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 7 0.30
25 5 0.22
27 11 0.48
ACGTcount: A:0.59, C:0.25, G:0.06, T:0.10
Consensus pattern (24 bp):
CCGATCCAAAAAAATAACCAAAAA
Found at i:603256 original size:64 final size:65
Alignment explanation
Indices: 603181--603302 Score: 192
Period size: 64 Copynumber: 1.9 Consensus size: 65
603171 GCACTAAGGG
* *
603181 TGCACCGATGTATAAAATGCATTCGATG-TTTCAAACAAGCTTGAGTGCATCGATGCATGGTCTA
1 TGCACCGATGTATAAAATGCATTCGATGTTTTCAAACAAACCTGAGTGCATCGATGCATGGTCTA
* * *
603245 TGCATCGATGTATAAAATGCATTCGATGTTTTCATAGAAACCTGAGTGCATCGATGCA
1 TGCACCGATGTATAAAATGCATTCGATGTTTTCAAACAAACCTGAGTGCATCGATGCA
603303 AGGAAGTGCA
Statistics
Matches: 52, Mismatches: 5, Indels: 1
0.90 0.09 0.02
Matches are distributed among these distances:
64 27 0.52
65 25 0.48
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.30
Consensus pattern (65 bp):
TGCACCGATGTATAAAATGCATTCGATGTTTTCAAACAAACCTGAGTGCATCGATGCATGGTCTA
Found at i:606632 original size:54 final size:53
Alignment explanation
Indices: 606555--606898 Score: 402
Period size: 54 Copynumber: 6.4 Consensus size: 53
606545 GTGAATTCCA
* * *
606555 TGGGTTGCACAC-TAAGTGTCTATACGGTGGTTCATCAATATATGATGAATTATG
1 TGGGTTGCACACAT-AGTGCCTATACGGTCGTTCATCAACATATGATGAATT-TG
* * * *
606609 TGGTTTGTACACATGGTGCCTATACGGTCGTTCATAAACATATGATGAATTTCG
1 TGGGTTGCACACATAGTGCCTATACGGTCGTTCATCAACATATGATGAATTT-G
* * **
606663 TGGGTAGCACACATAGTGCCTATACGATCGTTCATCAACATATGATGAATTCCA
1 TGGGTTGCACACATAGTGCCTATACGGTCGTTCATCAACATATGATGAATT-TG
* * * *
606717 TGGGTTACTCACTTAGTGCCTATATGGTCGTTCATCAACATATGATGAATTTTG
1 TGGGTTGCACACATAGTGCCTATACGGTCGTTCATCAACATATGATGAA-TTTG
* *
606771 TGGGTTGCACACTTAGTGCCTAAACGGTCGTTCATCAACATATGATGAATTTG
1 TGGGTTGCACACATAGTGCCTATACGGTCGTTCATCAACATATGATGAATTTG
* * * *
606824 TGGGTTGCATACATAGTGCCTATATGGCCGTTCATTAACATATGATGAATTTTG
1 TGGGTTGCACACATAGTGCCTATACGGTCGTTCATCAACATATGATGAA-TTTG
* ** *
606878 TGGTTTATACAAATAGTGCCT
1 TGGGTTGCACACATAGTGCCT
606899 GTAATACACT
Statistics
Matches: 247, Mismatches: 38, Indels: 10
0.84 0.13 0.03
Matches are distributed among these distances:
53 48 0.19
54 196 0.79
55 3 0.01
ACGTcount: A:0.27, C:0.17, G:0.22, T:0.35
Consensus pattern (53 bp):
TGGGTTGCACACATAGTGCCTATACGGTCGTTCATCAACATATGATGAATTTG
Found at i:606754 original size:162 final size:161
Alignment explanation
Indices: 606546--606874 Score: 469
Period size: 162 Copynumber: 2.0 Consensus size: 161
606536 TACATCATAG
* * * *
606546 TGAATTCCATGGGTTGCACACTAAGTGTCTATACGGTGGTTCATCAATATATGATGAATTATGTG
1 TGAATTCCATGGGTTACACACTAAGTGCCTATACGGTCGTTCATCAACATATGATGAATTATGTG
* * * *
606611 GTTTGTACACATGGTGCCTATACGGTCGTTCATAAACATATGATGAATTTCGTGGGTAGCACACA
66 GGTTGCACACATAGTGCCTAAACGGTCGTTCATAAACATATGATGAATTT-GTGGGTAGCACACA
*
606676 TAGTGCCTATACGATCGTTCATCAACATATGA
130 TAGTGCCTATACGACCGTTCATCAACATATGA
* * * *
606708 TGAATTCCATGGGTTACTCACTTAGTGCCTATATGGTCGTTCATCAACATATGATGAATTTTGTG
1 TGAATTCCATGGGTTACACACTAAGTGCCTATACGGTCGTTCATCAACATATGATGAATTATGTG
* * * *
606773 GGTTGCACACTTAGTGCCTAAACGGTCGTTCATCAACATATGATGAATTTGTGGGTTGCATACAT
66 GGTTGCACACATAGTGCCTAAACGGTCGTTCATAAACATATGATGAATTTGTGGGTAGCACACAT
* * *
606838 AGTGCCTATATGGCCGTTCATTAACATATGA
131 AGTGCCTATACGACCGTTCATCAACATATGA
606869 TGAATT
1 TGAATT
606875 TTGTGGTTTA
Statistics
Matches: 147, Mismatches: 20, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
161 46 0.31
162 101 0.69
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.34
Consensus pattern (161 bp):
TGAATTCCATGGGTTACACACTAAGTGCCTATACGGTCGTTCATCAACATATGATGAATTATGTG
GGTTGCACACATAGTGCCTAAACGGTCGTTCATAAACATATGATGAATTTGTGGGTAGCACACAT
AGTGCCTATACGACCGTTCATCAACATATGA
Found at i:608343 original size:15 final size:15
Alignment explanation
Indices: 608317--608390 Score: 75
Period size: 15 Copynumber: 4.9 Consensus size: 15
608307 CATGTTAGAT
608317 ATAAAA-AAATAAAA
1 ATAAAATAAATAAAA
608331 ATAAAATAAAT-AAA
1 ATAAAATAAATAAAA
*
608345 TTCAAACA-AAATAAAA
1 AT-AAA-ATAAATAAAA
608361 AT-AAATAAAATAAAA
1 ATAAAAT-AAATAAAA
608376 ATAATAATAAATAAA
1 ATAA-AATAAATAAA
608391 TAAATAAAGC
Statistics
Matches: 50, Mismatches: 2, Indels: 14
0.76 0.03 0.21
Matches are distributed among these distances:
13 1 0.02
14 12 0.24
15 21 0.42
16 13 0.26
17 3 0.06
ACGTcount: A:0.77, C:0.03, G:0.00, T:0.20
Consensus pattern (15 bp):
ATAAAATAAATAAAA
Found at i:608361 original size:25 final size:23
Alignment explanation
Indices: 608327--608395 Score: 86
Period size: 25 Copynumber: 2.9 Consensus size: 23
608317 ATAAAAAAAT
608327 AAAAAT-AAAATAAATAAATTCAA
1 AAAAATAAAAATAAATAAATT-AA
*
608350 ACAAAATAAAAATAAATAAAATAA
1 A-AAAATAAAAATAAATAAATTAA
608374 AAATAATAATAAATAAATAAAT
1 AAA-AATAA-AAATAAATAAAT
608396 AAAGCATAGA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
23 3 0.08
24 13 0.32
25 24 0.60
ACGTcount: A:0.75, C:0.03, G:0.00, T:0.22
Consensus pattern (23 bp):
AAAAATAAAAATAAATAAATTAA
Found at i:609160 original size:37 final size:36
Alignment explanation
Indices: 609078--609213 Score: 161
Period size: 37 Copynumber: 3.8 Consensus size: 36
609068 GTGCTTGTGG
* * * * * *
609078 ATCCTATCTTTAGGAATTTAAATCTTAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAG-AAAATTCT
*
609115 ATCATATTTTTAGGAGTTTGAATCCTAGCAAAATGT-T
1 ATCCTATTTTTAGGAGTTTGAATCCTAG-AAAAT-TCT
609152 ATCCTATTTTTAGGAGTTTGAATCCT--AAAATTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGAAAATTCT
609186 ATCCTATTTTTAGGAGTTTGAATCCTAG
1 ATCCTATTTTTAGGAGTTTGAATCCTAG
609214 TAGGACGAAA
Statistics
Matches: 86, Mismatches: 9, Indels: 9
0.83 0.09 0.09
Matches are distributed among these distances:
33 1 0.01
34 32 0.37
37 52 0.60
38 1 0.01
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.42
Consensus pattern (36 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGAAAATTCT
Found at i:609189 original size:34 final size:35
Alignment explanation
Indices: 609112--609212 Score: 152
Period size: 34 Copynumber: 2.9 Consensus size: 35
609102 TTAGTAGAAC
*
609112 TCTATCATATTTTTAGGAGTTTGAATCCTAGCAAAATG
1 TCTATCCTATTTTTAGGAGTTTGAATCCT---AAAATG
609150 T-TATCCTATTTTTAGGAGTTTGAATCCTAAAAT-
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAAAATG
609183 TCTATCCTATTTTTAGGAGTTTGAATCCTA
1 TCTATCCTATTTTTAGGAGTTTGAATCCTA
609213 GTAGGACGAA
Statistics
Matches: 61, Mismatches: 1, Indels: 6
0.90 0.01 0.09
Matches are distributed among these distances:
33 1 0.02
34 33 0.54
37 26 0.43
38 1 0.02
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.44
Consensus pattern (35 bp):
TCTATCCTATTTTTAGGAGTTTGAATCCTAAAATG
Found at i:609742 original size:105 final size:106
Alignment explanation
Indices: 609528--609983 Score: 648
Period size: 105 Copynumber: 4.3 Consensus size: 106
609518 CATTGTTCCA
* * * ** *
609528 AGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGGAACCGGGAAATTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAAC
* *
609593 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
66 CAGCCGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTCG
* *
609634 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTG-TTGTTGACAAG
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAAC
* * *
609698 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
66 CAGCCGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTCG
*
609739 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTG-TTGTTGACAAA
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAAC
** *
609803 CAGTGGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCT-G
66 CAGCCGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTCG
* *
609843 AAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGAGAA
1 -AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* *
609908 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
65 CCAGCCGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTCG
* *
609950 AGTGCCACGATATCCTCCGTTGTGGAGTTGAAAT
1 AGT-CCA--ATATCCTTCGTTGTGAAGTTGAAAT
609984 CCAAGTATTG
Statistics
Matches: 316, Mismatches: 28, Indels: 9
0.90 0.08 0.03
Matches are distributed among these distances:
104 1 0.00
105 196 0.62
106 92 0.29
107 4 0.01
109 23 0.07
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.34
Consensus pattern (106 bp):
AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAAC
CAGCCGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTCG
Found at i:610645 original size:67 final size:65
Alignment explanation
Indices: 610514--610967 Score: 284
Period size: 65 Copynumber: 6.7 Consensus size: 65
610504 AAGATATCTA
* * * * **
610514 TTGTTTCATGAGAAACGGTCTCAAAGGAAACAAAATTATGTTTTAAGGGAAATAAATTTGAAGAT
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATT-TGTTTTAAGGGAAATAAATTCAAAGA-
610579 TT
64 TT
* *
610581 TGTGTTTCAAGAGTAACTGTCTCAAGGGAGACAAAATTTGTTTTAGGGGAAATAAATTCAAAGAT
1 T-TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAATAAATTCAAAGAT
610646 T
65 T
* ** * * *
610647 TTGTTTCAAGGGAAACTGTCTCAAGATAGACGAAATTTGTTTTAAGAGAAACTGTCTCAAGAGAG
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAA-----T--A-A-AT
* *
610712 ACAAA-ACT
57 TCAAAGATT
* * * * * * * * * * *
610720 TAGTTCCAAAAGCAACTGTCTCAAGGGAGACGAAATTTGTTTCAAAGAAAACATATTCAAATATT
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAATAAATTCAAAGATT
* * * * * *
610785 TTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTTATTTCAAGGGAAACTGTCTCAAGAGAG
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAA-----T--A-A-AT
*
610850 ACAAA-ATT
57 TCAAAGATT
* * * * * * *** *
610858 TTGTTTCAAGGGAAACTATCTCAAGAGAGACGAAATTTATTTCAAGGGAAATGTTTTCAATG-TT
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAATAAATTCAAAGATT
*
610922 TATGTTTCAAGAGAAATTGTCTCAAGGGAGACAAAATTTGTTTTAA
1 T-TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAA
610968 AAAAGCAATC
Statistics
Matches: 302, Mismatches: 63, Indels: 46
0.73 0.15 0.11
Matches are distributed among these distances:
64 11 0.04
65 122 0.40
66 4 0.01
67 24 0.08
68 32 0.11
70 1 0.00
72 2 0.01
73 96 0.32
74 10 0.03
ACGTcount: A:0.39, C:0.11, G:0.20, T:0.30
Consensus pattern (65 bp):
TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAATAAATTCAAAGATT
Found at i:610698 original size:36 final size:36
Alignment explanation
Indices: 610646--610908 Score: 254
Period size: 36 Copynumber: 7.4 Consensus size: 36
610636 ATTCAAAGAT
* *
610646 TTTGTTTCAAGGGAAACTGTCTCAAGATAGACGAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* *
610682 TTTGTTTTAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* * ** * * *
610718 CTTAGTTCCAAAAGCAACTGTCTCAAGGGAGACGAAA
1 -TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* * * * *
610755 TTTGTTTCAAAGAAAACATAT-TC-----A-A-ATAT
1 TTTGTTTCAAGGGAAAC-TGTCTCAAGAGAGACAAAA
*
610784 TTTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
*
610820 TTTATTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* *
610856 TTTTGTTTCAAGGGAAACTATCTCAAGAGAGACGAAA
1 -TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
*
610893 TTTATTTCAAGGGAAA
1 TTTGTTTCAAGGGAAA
610909 TGTTTTCAAT
Statistics
Matches: 186, Mismatches: 30, Indels: 22
0.78 0.13 0.09
Matches are distributed among these distances:
28 3 0.02
29 18 0.10
30 1 0.01
31 1 0.01
34 1 0.01
35 1 0.01
36 97 0.52
37 64 0.34
ACGTcount: A:0.40, C:0.14, G:0.19, T:0.27
Consensus pattern (36 bp):
TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
Found at i:610758 original size:138 final size:138
Alignment explanation
Indices: 610595--610967 Score: 469
Period size: 138 Copynumber: 2.7 Consensus size: 138
610585 TTTCAAGAGT
* * * *
610595 AACTGTCTCAAGGGAGACAAAATTTGTTTTAGGGGAAATAAATTCAAAGATTTTGTTTCAAGGGA
1 AACTGTCTCAAGGGAGACGAAATTTGTTTCAAGGGAAATATATTCAAAGATTTTGTTTCAAGGGA
* *
610660 AACTGTCTCAAGATAGACGAAATTTGTTTTAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTT
66 AACTGTCTCAAGAGAGACAAAATTTGTTTTAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTT
*
610725 CCAAAAGC
131 CCAAAAGA
* * * *
610733 AACTGTCTCAAGGGAGACGAAATTTGTTTCAAAGAAAACATATTCAAATATTTTGTTTCAAGGGA
1 AACTGTCTCAAGGGAGACGAAATTTGTTTCAAGGGAAATATATTCAAAGATTTTGTTTCAAGGGA
* * * * * *
610798 AACTATCTCAAGAGAGACAAAATTTATTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTTGTT
66 AACTGTCTCAAGAGAGACAAAATTTGTTTTAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTT
* **
610863 TCAAGGGA
131 CCAAAAGA
* * * * * * *
610871 AACTATCTCAAGAGAGACGAAATTTATTTCAAGGGAAATGTTTTCAATG-TTTATGTTTCAAGAG
1 AACTGTCTCAAGGGAGACGAAATTTGTTTCAAGGGAAATATATTCAAAGATTT-TGTTTCAAGGG
* *
610935 AAATTGTCTCAAGGGAGACAAAATTTGTTTTAA
65 AAACTGTCTCAAGAGAGACAAAATTTGTTTTAA
610968 AAAAGCAATC
Statistics
Matches: 198, Mismatches: 36, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
137 3 0.02
138 195 0.98
ACGTcount: A:0.39, C:0.12, G:0.19, T:0.29
Consensus pattern (138 bp):
AACTGTCTCAAGGGAGACGAAATTTGTTTCAAGGGAAATATATTCAAAGATTTTGTTTCAAGGGA
AACTGTCTCAAGAGAGACAAAATTTGTTTTAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTT
CCAAAAGA
Found at i:610815 original size:102 final size:102
Alignment explanation
Indices: 610682--610866 Score: 264
Period size: 102 Copynumber: 1.8 Consensus size: 102
610672 ATAGACGAAA
* * * *
610682 TTTGTTTTAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGCAACTGTCTCAAGGG
1 TTTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTA-TTCCAAAAGAAACTGTCTCAAGAG
*
610747 AGACGAAA-TTTGTTTCAAAGAAAACATATTCAAATAT
65 AGACAAAATTTTGTTTCAAAGAAAACATATTCAAATAT
* * * **
610784 TTTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTTATTTCAAGGGAAACTGTCTCAAGAGA
1 TTTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTATTCCAAAAGAAACTGTCTCAAGAGA
610849 GACAAAATTTTGTTTCAA
66 GACAAAATTTTGTTTCAA
610867 GGGAAACTAT
Statistics
Matches: 72, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
101 26 0.36
102 46 0.64
ACGTcount: A:0.40, C:0.14, G:0.17, T:0.29
Consensus pattern (102 bp):
TTTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTATTCCAAAAGAAACTGTCTCAAGAGA
GACAAAATTTTGTTTCAAAGAAAACATATTCAAATAT
Found at i:611357 original size:18 final size:18
Alignment explanation
Indices: 611330--611365 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
611320 TGTTGAATCC
* *
611330 CCAAAGATGCCTCAATAT
1 CCAAAAATGCCCCAATAT
611348 CCAAAAATGCCCCAATAT
1 CCAAAAATGCCCCAATAT
611366 TTGATGTTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.42, C:0.31, G:0.08, T:0.19
Consensus pattern (18 bp):
CCAAAAATGCCCCAATAT
Found at i:612462 original size:36 final size:33
Alignment explanation
Indices: 612422--612512 Score: 87
Period size: 36 Copynumber: 2.6 Consensus size: 33
612412 TGCATGTGCT
612422 TTTTGTTCCTCTTTCTTTTTGATTC-TTGTTTTTTCC
1 TTTTGTTCCT-TTTCTTTTT--TTCTTTGTTTTTT-C
* *
612458 TTTTGTTCTTGTTTCTCTTTTTTCTTTGTTTTTTT
1 TTTTGTTCCT-TTTCT-TTTTTTCTTTGTTTTTTC
612493 TTTTGCTT-CTTTTCTTTTTT
1 TTTTG-TTCCTTTTCTTTTTT
612513 CTTCTTGATT
Statistics
Matches: 48, Mismatches: 4, Indels: 9
0.79 0.07 0.15
Matches are distributed among these distances:
33 5 0.10
34 5 0.10
35 9 0.19
36 25 0.52
37 4 0.08
ACGTcount: A:0.01, C:0.15, G:0.08, T:0.76
Consensus pattern (33 bp):
TTTTGTTCCTTTTCTTTTTTTCTTTGTTTTTTC
Found at i:612468 original size:19 final size:19
Alignment explanation
Indices: 612433--612491 Score: 61
Period size: 20 Copynumber: 3.2 Consensus size: 19
612423 TTTGTTCCTC
*
612433 TTTCTTTTTGATTCTTGTTT
1 TTTCCTTTTG-TTCTTGTTT
612453 TTTCCTTTTGTTCTTG-TT
1 TTTCCTTTTGTTCTTGTTT
*
612471 TCT-CTTTT-TTCTTTGTTT
1 TTTCCTTTTGTTC-TTGTTT
612489 TTT
1 TTT
612492 TTTTTGCTTC
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
16 3 0.09
17 8 0.24
18 8 0.24
19 6 0.18
20 9 0.26
ACGTcount: A:0.02, C:0.14, G:0.08, T:0.76
Consensus pattern (19 bp):
TTTCCTTTTGTTCTTGTTT
Found at i:612486 original size:17 final size:15
Alignment explanation
Indices: 612452--612515 Score: 65
Period size: 16 Copynumber: 3.9 Consensus size: 15
612442 GATTCTTGTT
612452 TTTTCCTTTTGTTCTTG
1 TTTT-CTTTT-TTCTTG
612469 TTTCTCTTTTTTCTTTG
1 TTT-TCTTTTTTC-TTG
* *
612486 TTTTTTTTTTTGCTTC
1 TTTTCTTTTTT-CTTG
612502 TTTTCTTTTTTCTT
1 TTTTCTTTTTTCTT
612516 CTTGATTGGA
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
15 3 0.07
16 22 0.54
17 15 0.37
18 1 0.02
ACGTcount: A:0.00, C:0.16, G:0.06, T:0.78
Consensus pattern (15 bp):
TTTTCTTTTTTCTTG
Found at i:613676 original size:8 final size:8
Alignment explanation
Indices: 613660--613698 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
613650 AATGTAGATG
613660 AAAATGCA
1 AAAATGCA
*
613668 AAAAGGCA
1 AAAATGCA
613676 AAAATGC-
1 AAAATGCA
613683 AAAATGCA
1 AAAATGCA
*
613691 AGAATGCA
1 AAAATGCA
613699 TGAAATGTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
7 7 0.26
8 20 0.74
ACGTcount: A:0.59, C:0.13, G:0.18, T:0.10
Consensus pattern (8 bp):
AAAATGCA
Found at i:613686 original size:15 final size:15
Alignment explanation
Indices: 613660--613698 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
613650 AATGTAGATG
613660 AAAATGCAAAAAGGCA
1 AAAATGC-AAAAGGCA
*
613676 AAAATGCAAAATGCA
1 AAAATGCAAAAGGCA
*
613691 AGAATGCA
1 AAAATGCA
613699 TGAAATGTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 14 0.67
16 7 0.33
ACGTcount: A:0.59, C:0.13, G:0.18, T:0.10
Consensus pattern (15 bp):
AAAATGCAAAAGGCA
Found at i:616199 original size:8 final size:8
Alignment explanation
Indices: 616196--616278 Score: 76
Period size: 8 Copynumber: 9.5 Consensus size: 8
616186 ATAAAAAAAT
616196 AAAATAAA
1 AAAATAAA
616204 ATAAATAAA
1 A-AAATAAA
* *
616213 TAAATTCAACC
1 -AAAAT-AA-A
616224 AAAATAAAA
1 AAAAT-AAA
616233 AGAAATAAA
1 A-AAATAAA
*
616242 ATAATAAA
1 AAAATAAA
616250 AAAATAAAA
1 AAAAT-AAA
616259 AAAATAAA
1 AAAATAAA
616267 AAAATAAA
1 AAAATAAA
616275 AAAA
1 AAAA
616279 ACATAGAAAA
Statistics
Matches: 62, Mismatches: 7, Indels: 12
0.77 0.09 0.15
Matches are distributed among these distances:
8 26 0.42
9 23 0.37
10 13 0.21
ACGTcount: A:0.80, C:0.04, G:0.01, T:0.16
Consensus pattern (8 bp):
AAAATAAA
Found at i:616201 original size:5 final size:5
Alignment explanation
Indices: 616191--616279 Score: 66
Period size: 5 Copynumber: 18.8 Consensus size: 5
616181 TAGATATAAA
* * **
616191 AAAAT AAAAT AAAAT -AAAT -AAAT AAATT CAACC AAAAT AAAA- AGAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT A-AAAT
*
616239 AAAAT AATAAA AAAAT AAAA- AAAAT -AAA- AAAAT AAAA- AAAA
1 AAAAT AA-AAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
616280 CATAGAAAAA
Statistics
Matches: 68, Mismatches: 9, Indels: 15
0.74 0.10 0.16
Matches are distributed among these distances:
4 23 0.34
5 40 0.59
6 5 0.07
ACGTcount: A:0.80, C:0.03, G:0.01, T:0.16
Consensus pattern (5 bp):
AAAAT
Found at i:616252 original size:25 final size:25
Alignment explanation
Indices: 616188--616278 Score: 94
Period size: 25 Copynumber: 3.5 Consensus size: 25
616178 AGTTAGATAT
* *
616188 AAAAA-AATAAAATAAAATAAATAA
1 AAAAATAAAAAAATAAAAAAAATAA
* *
616212 ATAAATTCAACCAAAATAAAAAGAAATAA
1 A-AAAAT-AA-AAAAATAAAAA-AAATAA
*
616241 AATAATAAAAAAATAAAAAAAATAA
1 AAAAATAAAAAAATAAAAAAAATAA
616266 AAAAATAAAAAAA
1 AAAAATAAAAAAA
616279 ACATAGAAAA
Statistics
Matches: 55, Mismatches: 7, Indels: 9
0.77 0.10 0.13
Matches are distributed among these distances:
24 1 0.02
25 21 0.38
26 10 0.18
27 4 0.07
28 12 0.22
29 7 0.13
ACGTcount: A:0.80, C:0.03, G:0.01, T:0.15
Consensus pattern (25 bp):
AAAAATAAAAAAATAAAAAAAATAA
Found at i:616259 original size:17 final size:17
Alignment explanation
Indices: 616224--616276 Score: 74
Period size: 17 Copynumber: 3.2 Consensus size: 17
616214 AAATTCAACC
*
616224 AAAATAA-AAAGAAAT-
1 AAAATAATAAAAAAATA
616239 AAAATAATAAAAAAATA
1 AAAATAATAAAAAAATA
*
616256 AAAAAAATAAAAAAATA
1 AAAATAATAAAAAAATA
616273 AAAA
1 AAAA
616277 AAACATAGAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.21
16 7 0.21
17 20 0.59
ACGTcount: A:0.85, C:0.00, G:0.02, T:0.13
Consensus pattern (17 bp):
AAAATAATAAAAAAATA
Found at i:617004 original size:37 final size:36
Alignment explanation
Indices: 616954--617091 Score: 172
Period size: 37 Copynumber: 3.8 Consensus size: 36
616944 GTGCTTGTGG
* * * * *
616954 ATCCTATCTTTAGGAATTTAAATCTTAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTA-AAATCT
* *
616991 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATGTT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAAT-CT
*
617028 ATCCTATTTTTAGGAGTTTGAATCCTA--AAATTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAATCT
617062 ATCCTATTTTTAGGAGTTTGAATCCTAGTA
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTA
617092 GGACGAAAAA
Statistics
Matches: 89, Mismatches: 9, Indels: 7
0.85 0.09 0.07
Matches are distributed among these distances:
34 28 0.31
35 4 0.04
36 4 0.04
37 53 0.60
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.42
Consensus pattern (36 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAATCT
Found at i:617065 original size:34 final size:35
Alignment explanation
Indices: 616988--617088 Score: 161
Period size: 34 Copynumber: 2.9 Consensus size: 35
616978 TTAGTAGAAC
616988 TCTATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATG
1 TCTATCCTATTTTTAGGAGTTTGAATCCT---AAAATG
617026 T-TATCCTATTTTTAGGAGTTTGAATCCTAAAAT-
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAAAATG
617059 TCTATCCTATTTTTAGGAGTTTGAATCCTA
1 TCTATCCTATTTTTAGGAGTTTGAATCCTA
617089 GTAGGACGAA
Statistics
Matches: 62, Mismatches: 0, Indels: 6
0.91 0.00 0.09
Matches are distributed among these distances:
33 1 0.02
34 33 0.53
37 27 0.44
38 1 0.02
ACGTcount: A:0.28, C:0.15, G:0.14, T:0.44
Consensus pattern (35 bp):
TCTATCCTATTTTTAGGAGTTTGAATCCTAAAATG
Found at i:618211 original size:20 final size:20
Alignment explanation
Indices: 618183--618229 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
618173 GGTCAAGGTT
*
618183 TTTTCAAACTCAAACACAAG
1 TTTTCAAACTCAAACAAAAG
* *
618203 TTTTGAAACTCAATCAAAAG
1 TTTTCAAACTCAAACAAAAG
618223 -TTTCAAA
1 TTTTCAAA
618230 ACTTCTAGAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
19 6 0.26
20 17 0.74
ACGTcount: A:0.45, C:0.19, G:0.06, T:0.30
Consensus pattern (20 bp):
TTTTCAAACTCAAACAAAAG
Found at i:621229 original size:12 final size:13
Alignment explanation
Indices: 621213--621242 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
621203 AAATTAAACT
621213 TAAAGTTAAGGAG
1 TAAAGTTAAGGAG
621226 -AAAGTTAAGGAG
1 TAAAGTTAAGGAG
621238 TAAAG
1 TAAAG
621243 GTTGTCACCA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.50, C:0.00, G:0.30, T:0.20
Consensus pattern (13 bp):
TAAAGTTAAGGAG
Found at i:624284 original size:59 final size:60
Alignment explanation
Indices: 624127--624301 Score: 237
Period size: 60 Copynumber: 2.9 Consensus size: 60
624117 CCCCAAAACA
* * **
624127 ACATCCATAAGGACTTACCCTAGACCACTAAGATCTAGAAGTCCATTATCAAAGATACAG
1 ACATCCATAAGGACTTACCCTAGACCACTAAGATCTAGGAGTCCAATATGGAAGATACAG
**
624187 ACATCCATAAGGAGATACCCTAGACCACTAAGATCTAGGAGTCCAATATGGAAGATACA-
1 ACATCCATAAGGACTTACCCTAGACCACTAAGATCTAGGAGTCCAATATGGAAGATACAG
* * * *
624246 A-GTGTCATAAGGACTTACCTTAGATCACTAAGATCTAGGAGTCCAATATGGAAGAT
1 ACAT-CCATAAGGACTTACCCTAGACCACTAAGATCTAGGAGTCCAATATGGAAGAT
624302 CATAACAGGA
Statistics
Matches: 102, Mismatches: 12, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
58 1 0.01
59 48 0.47
60 53 0.52
ACGTcount: A:0.39, C:0.21, G:0.18, T:0.22
Consensus pattern (60 bp):
ACATCCATAAGGACTTACCCTAGACCACTAAGATCTAGGAGTCCAATATGGAAGATACAG
Found at i:627654 original size:24 final size:24
Alignment explanation
Indices: 627618--627673 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
627608 TCATTGCTAA
* **
627618 ACCTCACCTACGGTGAGGTCGACG
1 ACCTCACCCACGGCCAGGTCGACG
* *
627642 GCCTCACCCACGGCCTGGTCGACG
1 ACCTCACCCACGGCCAGGTCGACG
627666 ACCTCACC
1 ACCTCACC
627674 TAGTGTGCAT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.18, C:0.43, G:0.25, T:0.14
Consensus pattern (24 bp):
ACCTCACCCACGGCCAGGTCGACG
Found at i:628482 original size:60 final size:59
Alignment explanation
Indices: 628386--628521 Score: 139
Period size: 60 Copynumber: 2.3 Consensus size: 59
628376 CTCAAAACAG
* * ****
628386 GAATCCGTAAGGACTTACCCTAGACCACTAAGATCTAGGAGTTTGTTATGGAAAATACAA
1 GAATCCATAAGGACTTACCCTAGACCACTAAAATCTAGGAGTCCAATATGGAAAATA-AA
* * * * * *
628446 GAATCCATAAGGACTTATCGTATATCACTAAAATCTATGAGTCCAATATGGAAGATAAA
1 GAATCCATAAGGACTTACCCTAGACCACTAAAATCTAGGAGTCCAATATGGAAAATAAA
628505 -ACATCCATAAGGACTTA
1 GA-ATCCATAAGGACTTA
628522 GTATAGATCA
Statistics
Matches: 63, Mismatches: 12, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
58 1 0.02
59 17 0.27
60 45 0.71
ACGTcount: A:0.40, C:0.18, G:0.17, T:0.26
Consensus pattern (59 bp):
GAATCCATAAGGACTTACCCTAGACCACTAAAATCTAGGAGTCCAATATGGAAAATAAA
Done.