Multiple sequence alignment - TraesCS2B01G603500

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS2B01G603500 chr2B 100.000 3494 0 0 1 3494 785292041 785288548 0.000000e+00 6453.0
1 TraesCS2B01G603500 chr2B 94.220 346 17 2 1942 2287 788845286 788844944 3.090000e-145 525.0
2 TraesCS2B01G603500 chr2B 96.648 179 6 0 1702 1880 788846914 788846736 7.330000e-77 298.0
3 TraesCS2B01G603500 chr2B 95.187 187 6 2 1702 1888 746164891 746164708 3.410000e-75 292.0
4 TraesCS2B01G603500 chr2B 94.186 86 5 0 2202 2287 746164378 746164293 7.870000e-27 132.0
5 TraesCS2B01G603500 chr2B 97.297 37 1 0 1909 1945 788846746 788846710 2.910000e-06 63.9
6 TraesCS2B01G603500 chr2B 94.444 36 2 0 1696 1731 746164432 746164397 4.870000e-04 56.5
7 TraesCS2B01G603500 chr2D 93.600 2250 65 37 559 2777 649616979 649614778 0.000000e+00 3284.0
8 TraesCS2B01G603500 chr2D 87.778 720 38 18 2819 3494 649614403 649613690 0.000000e+00 797.0
9 TraesCS2B01G603500 chr2D 90.635 598 40 10 1702 2287 164280091 164280684 0.000000e+00 780.0
10 TraesCS2B01G603500 chr2D 79.004 281 21 9 104 382 649617282 649617038 1.300000e-34 158.0
11 TraesCS2B01G603500 chr2D 95.556 45 2 0 2778 2822 649614464 649614420 4.840000e-09 73.1
12 TraesCS2B01G603500 chr2A 92.770 1964 64 28 533 2487 775208465 775210359 0.000000e+00 2769.0
13 TraesCS2B01G603500 chr2A 86.207 290 19 7 2867 3146 775211040 775211318 9.480000e-76 294.0
14 TraesCS2B01G603500 chr2A 88.108 185 13 4 103 285 775206689 775206866 9.830000e-51 211.0
15 TraesCS2B01G603500 chr2A 96.190 105 2 1 1 103 38568995 38569099 1.670000e-38 171.0
16 TraesCS2B01G603500 chr2A 81.279 219 16 7 278 492 775207033 775207230 1.680000e-33 154.0
17 TraesCS2B01G603500 chr2A 77.869 122 17 8 2643 2762 775210528 775210641 2.250000e-07 67.6
18 TraesCS2B01G603500 chr3B 88.571 595 51 12 1705 2287 794285647 794285058 0.000000e+00 706.0
19 TraesCS2B01G603500 chr3B 94.416 197 8 1 1702 1898 487555882 487555689 2.040000e-77 300.0
20 TraesCS2B01G603500 chr3B 94.495 109 3 2 1 109 765781739 765781634 7.760000e-37 165.0
21 TraesCS2B01G603500 chr3B 94.186 86 5 0 2202 2287 487555595 487555510 7.870000e-27 132.0
22 TraesCS2B01G603500 chr5B 99.065 107 0 1 1 106 568815837 568815943 1.280000e-44 191.0
23 TraesCS2B01G603500 chr7B 97.170 106 2 1 1 105 750151669 750151564 9.970000e-41 178.0
24 TraesCS2B01G603500 chr3D 97.143 105 3 0 1 105 83730824 83730720 9.970000e-41 178.0
25 TraesCS2B01G603500 chr5D 95.455 110 4 1 1 109 466658193 466658084 1.290000e-39 174.0
26 TraesCS2B01G603500 chr5D 90.698 129 8 2 1 125 495289923 495290051 6.000000e-38 169.0
27 TraesCS2B01G603500 chr1B 96.190 105 4 0 1 105 676855941 676855837 4.640000e-39 172.0
28 TraesCS2B01G603500 chr1B 95.918 98 4 0 1702 1799 36276412 36276315 3.610000e-35 159.0
29 TraesCS2B01G603500 chr1B 94.444 36 2 0 2159 2194 36276316 36276281 4.870000e-04 56.5
30 TraesCS2B01G603500 chr6B 96.117 103 1 1 1 103 82728322 82728223 7.760000e-37 165.0
31 TraesCS2B01G603500 chr6B 96.774 31 1 0 998 1028 652171160 652171130 6.000000e-03 52.8


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2B01G603500 chr2B 785288548 785292041 3493 True 6453.000000 6453 100.0000 1 3494 1 chr2B.!!$R1 3493
1 TraesCS2B01G603500 chr2B 788844944 788846914 1970 True 295.633333 525 96.0550 1702 2287 3 chr2B.!!$R3 585
2 TraesCS2B01G603500 chr2D 649613690 649617282 3592 True 1078.025000 3284 88.9845 104 3494 4 chr2D.!!$R1 3390
3 TraesCS2B01G603500 chr2D 164280091 164280684 593 False 780.000000 780 90.6350 1702 2287 1 chr2D.!!$F1 585
4 TraesCS2B01G603500 chr2A 775206689 775211318 4629 False 699.120000 2769 85.2466 103 3146 5 chr2A.!!$F2 3043
5 TraesCS2B01G603500 chr3B 794285058 794285647 589 True 706.000000 706 88.5710 1705 2287 1 chr3B.!!$R2 582

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
856 2248 0.108138 CTCCCCACCGTCTGTCAATC 60.108 60.0 0.0 0.0 0.0 2.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2586 5426 0.031857 CATGCCTGCCTCTACTCTCG 59.968 60.0 0.0 0.0 0.0 4.04 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 1.696063 TCTACCTGTATGGGTACGCC 58.304 55.000 7.55 0.31 40.48 5.68
20 21 0.313043 CTACCTGTATGGGTACGCCG 59.687 60.000 7.55 0.00 40.48 6.46
21 22 1.737355 TACCTGTATGGGTACGCCGC 61.737 60.000 7.55 0.00 40.48 6.53
22 23 2.497293 CTGTATGGGTACGCCGCA 59.503 61.111 7.55 3.13 40.68 5.69
24 25 0.315886 CTGTATGGGTACGCCGCATA 59.684 55.000 7.55 7.95 44.23 3.14
26 27 1.286570 TATGGGTACGCCGCATACG 59.713 57.895 7.55 0.00 44.23 3.06
37 38 3.110178 GCATACGGCGCGGGATAC 61.110 66.667 19.75 7.31 0.00 2.24
39 40 3.289834 ATACGGCGCGGGATACGT 61.290 61.111 19.75 15.41 46.52 3.57
40 41 2.848858 ATACGGCGCGGGATACGTT 61.849 57.895 19.75 0.00 46.52 3.99
41 42 1.514678 ATACGGCGCGGGATACGTTA 61.515 55.000 19.75 0.86 46.52 3.18
42 43 1.719725 TACGGCGCGGGATACGTTAA 61.720 55.000 19.75 0.00 46.52 2.01
43 44 2.297912 CGGCGCGGGATACGTTAAG 61.298 63.158 8.83 0.00 46.52 1.85
44 45 2.592222 GGCGCGGGATACGTTAAGC 61.592 63.158 8.83 0.00 46.52 3.09
45 46 1.879430 GCGCGGGATACGTTAAGCA 60.879 57.895 8.83 0.00 46.52 3.91
46 47 1.922189 CGCGGGATACGTTAAGCAC 59.078 57.895 0.00 0.00 46.52 4.40
47 48 1.485032 CGCGGGATACGTTAAGCACC 61.485 60.000 0.00 0.00 46.52 5.01
48 49 1.485032 GCGGGATACGTTAAGCACCG 61.485 60.000 0.00 1.04 46.52 4.94
49 50 0.179129 CGGGATACGTTAAGCACCGT 60.179 55.000 0.00 0.00 40.87 4.83
50 51 1.065401 CGGGATACGTTAAGCACCGTA 59.935 52.381 0.00 0.00 42.95 4.02
52 53 3.054878 GGGATACGTTAAGCACCGTATG 58.945 50.000 12.06 0.00 46.82 2.39
62 63 3.344064 CACCGTATGCCCAAAATGC 57.656 52.632 0.00 0.00 0.00 3.56
63 64 0.179113 CACCGTATGCCCAAAATGCC 60.179 55.000 0.00 0.00 0.00 4.40
64 65 1.326951 ACCGTATGCCCAAAATGCCC 61.327 55.000 0.00 0.00 0.00 5.36
65 66 1.042559 CCGTATGCCCAAAATGCCCT 61.043 55.000 0.00 0.00 0.00 5.19
66 67 0.823460 CGTATGCCCAAAATGCCCTT 59.177 50.000 0.00 0.00 0.00 3.95
67 68 2.028130 CGTATGCCCAAAATGCCCTTA 58.972 47.619 0.00 0.00 0.00 2.69
68 69 2.627699 CGTATGCCCAAAATGCCCTTAT 59.372 45.455 0.00 0.00 0.00 1.73
69 70 3.823873 CGTATGCCCAAAATGCCCTTATA 59.176 43.478 0.00 0.00 0.00 0.98
70 71 4.320935 CGTATGCCCAAAATGCCCTTATAC 60.321 45.833 0.00 0.00 0.00 1.47
71 72 2.028130 TGCCCAAAATGCCCTTATACG 58.972 47.619 0.00 0.00 0.00 3.06
72 73 2.028876 GCCCAAAATGCCCTTATACGT 58.971 47.619 0.00 0.00 0.00 3.57
73 74 2.429250 GCCCAAAATGCCCTTATACGTT 59.571 45.455 0.00 0.00 0.00 3.99
74 75 3.633065 GCCCAAAATGCCCTTATACGTTA 59.367 43.478 0.00 0.00 0.00 3.18
75 76 4.098196 GCCCAAAATGCCCTTATACGTTAA 59.902 41.667 0.00 0.00 0.00 2.01
76 77 5.735070 GCCCAAAATGCCCTTATACGTTAAG 60.735 44.000 0.00 1.90 0.00 1.85
77 78 5.278604 CCAAAATGCCCTTATACGTTAAGC 58.721 41.667 0.00 0.00 0.00 3.09
78 79 5.278604 CAAAATGCCCTTATACGTTAAGCC 58.721 41.667 0.00 0.00 0.00 4.35
79 80 2.228138 TGCCCTTATACGTTAAGCCG 57.772 50.000 0.00 0.00 0.00 5.52
80 81 1.202557 TGCCCTTATACGTTAAGCCGG 60.203 52.381 0.00 0.00 0.00 6.13
81 82 1.875157 GCCCTTATACGTTAAGCCGGG 60.875 57.143 2.18 0.00 0.00 5.73
82 83 1.270465 CCCTTATACGTTAAGCCGGGG 60.270 57.143 2.18 0.00 0.00 5.73
83 84 1.270465 CCTTATACGTTAAGCCGGGGG 60.270 57.143 2.18 0.00 0.00 5.40
97 98 2.267961 GGGGGTGTACCGAAGCAG 59.732 66.667 0.00 0.00 41.60 4.24
98 99 2.288025 GGGGGTGTACCGAAGCAGA 61.288 63.158 0.00 0.00 41.60 4.26
99 100 1.079336 GGGGTGTACCGAAGCAGAC 60.079 63.158 0.00 0.00 41.60 3.51
100 101 1.079336 GGGTGTACCGAAGCAGACC 60.079 63.158 0.00 0.00 36.71 3.85
101 102 1.542187 GGGTGTACCGAAGCAGACCT 61.542 60.000 0.00 0.00 36.71 3.85
102 103 0.108756 GGTGTACCGAAGCAGACCTC 60.109 60.000 0.00 0.00 0.00 3.85
148 151 0.748005 TTGCCGCCTCTGCTAATTCC 60.748 55.000 0.00 0.00 34.43 3.01
151 154 0.598680 CCGCCTCTGCTAATTCCGAG 60.599 60.000 0.00 0.00 34.43 4.63
198 201 2.501223 GATATGGATTCGGCGCCGGA 62.501 60.000 44.95 40.78 40.25 5.14
219 222 0.388659 AGCCTTTGTTTGCGCATGAA 59.611 45.000 12.75 0.00 0.00 2.57
225 229 2.063156 TGTTTGCGCATGAATTCACC 57.937 45.000 12.75 4.08 0.00 4.02
246 250 2.587753 GCCCGCACGCAGCTAATA 60.588 61.111 0.00 0.00 42.61 0.98
247 251 2.177580 GCCCGCACGCAGCTAATAA 61.178 57.895 0.00 0.00 42.61 1.40
248 252 1.934463 CCCGCACGCAGCTAATAAG 59.066 57.895 0.00 0.00 42.61 1.73
249 253 0.810031 CCCGCACGCAGCTAATAAGT 60.810 55.000 0.00 0.00 42.61 2.24
250 254 1.006832 CCGCACGCAGCTAATAAGTT 58.993 50.000 0.00 0.00 42.61 2.66
251 255 1.267532 CCGCACGCAGCTAATAAGTTG 60.268 52.381 0.00 0.00 42.61 3.16
252 256 1.658596 CGCACGCAGCTAATAAGTTGA 59.341 47.619 0.00 0.00 42.61 3.18
253 257 2.093625 CGCACGCAGCTAATAAGTTGAA 59.906 45.455 0.00 0.00 42.61 2.69
263 267 6.367969 CAGCTAATAAGTTGAAGGTGTACGTT 59.632 38.462 0.00 0.00 36.10 3.99
296 474 1.277557 GGGCATGGTAGCTGGATCTAG 59.722 57.143 0.86 0.86 34.17 2.43
354 532 3.651645 CTGTGTCAGCAGCCAGTG 58.348 61.111 0.00 0.00 0.00 3.66
382 560 0.948623 CCCGTTCACACGCATGAGAA 60.949 55.000 2.50 0.00 45.72 2.87
383 561 1.078709 CCGTTCACACGCATGAGAAT 58.921 50.000 2.50 0.00 45.72 2.40
384 562 1.201954 CCGTTCACACGCATGAGAATG 60.202 52.381 2.50 5.34 45.72 2.67
385 563 1.726248 CGTTCACACGCATGAGAATGA 59.274 47.619 6.33 3.41 42.06 2.57
386 564 2.222663 CGTTCACACGCATGAGAATGAG 60.223 50.000 6.33 0.00 42.06 2.90
387 565 2.995939 GTTCACACGCATGAGAATGAGA 59.004 45.455 2.50 0.00 37.68 3.27
388 566 3.531934 TCACACGCATGAGAATGAGAT 57.468 42.857 2.50 0.00 0.00 2.75
389 567 3.192466 TCACACGCATGAGAATGAGATG 58.808 45.455 2.50 0.00 0.00 2.90
449 631 9.883142 AGAAGAAATTTATAGGATGGATCGATC 57.117 33.333 17.36 17.36 0.00 3.69
450 632 8.709386 AAGAAATTTATAGGATGGATCGATCG 57.291 34.615 18.81 9.36 0.00 3.69
451 633 8.067751 AGAAATTTATAGGATGGATCGATCGA 57.932 34.615 21.86 21.86 0.00 3.59
452 634 7.976734 AGAAATTTATAGGATGGATCGATCGAC 59.023 37.037 22.06 14.00 0.00 4.20
492 674 1.153489 CAGTCACCGCATCCTCCTG 60.153 63.158 0.00 0.00 0.00 3.86
504 694 0.693049 TCCTCCTGTTCCTTTCCAGC 59.307 55.000 0.00 0.00 0.00 4.85
512 702 0.675633 TTCCTTTCCAGCAGCAAAGC 59.324 50.000 0.00 0.00 0.00 3.51
514 704 0.390124 CCTTTCCAGCAGCAAAGCAA 59.610 50.000 0.00 0.00 36.85 3.91
515 705 1.202557 CCTTTCCAGCAGCAAAGCAAA 60.203 47.619 0.00 0.00 36.85 3.68
516 706 2.132762 CTTTCCAGCAGCAAAGCAAAG 58.867 47.619 0.00 0.00 36.85 2.77
517 707 0.249573 TTCCAGCAGCAAAGCAAAGC 60.250 50.000 0.00 0.00 36.85 3.51
519 709 0.320421 CCAGCAGCAAAGCAAAGCAT 60.320 50.000 0.00 0.00 36.85 3.79
520 710 1.067425 CCAGCAGCAAAGCAAAGCATA 60.067 47.619 0.00 0.00 36.85 3.14
521 711 1.990563 CAGCAGCAAAGCAAAGCATAC 59.009 47.619 0.00 0.00 36.85 2.39
522 712 1.614903 AGCAGCAAAGCAAAGCATACA 59.385 42.857 0.00 0.00 36.85 2.29
524 714 2.347452 GCAGCAAAGCAAAGCATACATG 59.653 45.455 0.00 0.00 0.00 3.21
525 715 3.840468 CAGCAAAGCAAAGCATACATGA 58.160 40.909 0.00 0.00 0.00 3.07
527 717 4.267690 CAGCAAAGCAAAGCATACATGATG 59.732 41.667 0.00 0.00 38.73 3.07
528 718 4.158949 AGCAAAGCAAAGCATACATGATGA 59.841 37.500 0.00 0.00 37.82 2.92
529 719 4.266976 GCAAAGCAAAGCATACATGATGAC 59.733 41.667 0.00 0.00 37.82 3.06
530 720 5.647589 CAAAGCAAAGCATACATGATGACT 58.352 37.500 0.00 0.00 37.82 3.41
531 721 4.895224 AGCAAAGCATACATGATGACTG 57.105 40.909 0.00 0.00 37.82 3.51
534 724 4.142534 GCAAAGCATACATGATGACTGTGT 60.143 41.667 0.00 0.00 37.82 3.72
546 1914 1.484240 TGACTGTGTGTGGATGTGTGA 59.516 47.619 0.00 0.00 0.00 3.58
586 1962 4.477975 CGGAGCCGACCGTGTCTC 62.478 72.222 2.00 0.00 46.70 3.36
778 2160 2.579787 CCGTGTCGTCTCCATCGC 60.580 66.667 0.00 0.00 0.00 4.58
807 2189 1.351017 GACCCATCAAGTCCAGTCCAA 59.649 52.381 0.00 0.00 0.00 3.53
854 2246 2.879233 GCTCCCCACCGTCTGTCAA 61.879 63.158 0.00 0.00 0.00 3.18
855 2247 1.983224 CTCCCCACCGTCTGTCAAT 59.017 57.895 0.00 0.00 0.00 2.57
856 2248 0.108138 CTCCCCACCGTCTGTCAATC 60.108 60.000 0.00 0.00 0.00 2.67
858 2250 1.447838 CCCACCGTCTGTCAATCCG 60.448 63.158 0.00 0.00 0.00 4.18
868 2260 1.765314 CTGTCAATCCGATCCTCCCTT 59.235 52.381 0.00 0.00 0.00 3.95
904 2296 4.581824 CCAAGCAAGGCACATATACTCATT 59.418 41.667 0.00 0.00 0.00 2.57
911 2303 7.637229 CAAGGCACATATACTCATTTCTCAAG 58.363 38.462 0.00 0.00 0.00 3.02
922 2314 3.387374 TCATTTCTCAAGCCCAAGCAAAA 59.613 39.130 0.00 0.00 43.56 2.44
923 2315 3.457610 TTTCTCAAGCCCAAGCAAAAG 57.542 42.857 0.00 0.00 43.56 2.27
924 2316 0.675633 TCTCAAGCCCAAGCAAAAGC 59.324 50.000 0.00 0.00 43.56 3.51
925 2317 0.320160 CTCAAGCCCAAGCAAAAGCC 60.320 55.000 0.00 0.00 43.56 4.35
926 2318 1.047596 TCAAGCCCAAGCAAAAGCCA 61.048 50.000 0.00 0.00 43.56 4.75
927 2319 0.179051 CAAGCCCAAGCAAAAGCCAA 60.179 50.000 0.00 0.00 43.56 4.52
937 2329 0.249996 CAAAAGCCAAGCCAACCCAG 60.250 55.000 0.00 0.00 0.00 4.45
1021 2413 4.081030 CGATGCCGATGCCGATGC 62.081 66.667 0.00 0.00 38.22 3.91
1022 2414 3.730761 GATGCCGATGCCGATGCC 61.731 66.667 0.00 0.00 38.22 4.40
2424 5252 0.610174 TCCAGCAGCAGAACTACCAG 59.390 55.000 0.00 0.00 0.00 4.00
2488 5316 4.086178 CCTGCTCGTCGTCGTCGT 62.086 66.667 11.41 0.00 38.33 4.34
2489 5317 2.571096 CTGCTCGTCGTCGTCGTC 60.571 66.667 11.41 6.00 38.33 4.20
2490 5318 4.419957 TGCTCGTCGTCGTCGTCG 62.420 66.667 14.18 14.18 46.06 5.12
2531 5359 4.459089 GCGAGCTGGACTGGGACC 62.459 72.222 0.00 0.00 0.00 4.46
2619 5462 0.527817 GGCATGCTCGCTTACGTACT 60.528 55.000 18.92 0.00 41.18 2.73
2635 5486 8.014517 GCTTACGTACTGTACTATACTGAATCC 58.985 40.741 15.35 0.00 31.20 3.01
2641 5505 6.982852 ACTGTACTATACTGAATCCAATCCG 58.017 40.000 0.00 0.00 0.00 4.18
2674 5538 0.107703 TGACAGATTAAGCTGCCCGG 60.108 55.000 20.30 0.00 39.51 5.73
2695 5559 2.112928 TGCAGGCAGCTTTCGGAA 59.887 55.556 2.86 0.00 45.94 4.30
2696 5560 1.303561 TGCAGGCAGCTTTCGGAAT 60.304 52.632 2.86 0.00 45.94 3.01
2697 5561 0.895100 TGCAGGCAGCTTTCGGAATT 60.895 50.000 2.86 0.00 45.94 2.17
2698 5562 0.179153 GCAGGCAGCTTTCGGAATTC 60.179 55.000 0.00 0.00 41.15 2.17
2699 5563 0.097674 CAGGCAGCTTTCGGAATTCG 59.902 55.000 0.00 0.00 40.90 3.34
2700 5564 1.026718 AGGCAGCTTTCGGAATTCGG 61.027 55.000 6.67 6.67 39.77 4.30
2701 5565 1.024579 GGCAGCTTTCGGAATTCGGA 61.025 55.000 11.36 11.36 39.77 4.55
2702 5566 1.017387 GCAGCTTTCGGAATTCGGAT 58.983 50.000 15.56 0.00 39.77 4.18
2703 5567 1.268234 GCAGCTTTCGGAATTCGGATG 60.268 52.381 15.56 11.90 39.77 3.51
2708 5572 1.651987 TTCGGAATTCGGATGCAGAC 58.348 50.000 15.56 0.00 39.77 3.51
2768 5638 4.102649 AGCAATAAATAAAAGCGAACGGC 58.897 39.130 0.00 0.00 44.05 5.68
2778 5648 4.059459 CGAACGGCACTGCGTGTC 62.059 66.667 9.76 6.84 35.75 3.67
2779 5649 2.661866 GAACGGCACTGCGTGTCT 60.662 61.111 10.63 0.00 35.84 3.41
2866 6224 7.171508 TGAACAGAGTTAATCAAGCTTGTACTG 59.828 37.037 25.19 21.89 0.00 2.74
2867 6225 6.525629 ACAGAGTTAATCAAGCTTGTACTGT 58.474 36.000 25.19 22.39 0.00 3.55
2868 6226 6.425114 ACAGAGTTAATCAAGCTTGTACTGTG 59.575 38.462 27.67 27.67 33.51 3.66
2954 6339 2.035321 CGTTTGGTTGCTGGGTGTTTAT 59.965 45.455 0.00 0.00 0.00 1.40
2955 6340 3.491792 CGTTTGGTTGCTGGGTGTTTATT 60.492 43.478 0.00 0.00 0.00 1.40
2956 6341 4.261656 CGTTTGGTTGCTGGGTGTTTATTA 60.262 41.667 0.00 0.00 0.00 0.98
2959 6344 5.398603 TGGTTGCTGGGTGTTTATTAATG 57.601 39.130 0.00 0.00 0.00 1.90
2968 6353 4.947388 GGGTGTTTATTAATGCTCTCACCA 59.053 41.667 20.47 0.00 43.74 4.17
3169 6594 1.203287 TGGATCTCTGCACTGTTCGAG 59.797 52.381 0.00 0.00 0.00 4.04
3170 6595 1.276415 GATCTCTGCACTGTTCGAGC 58.724 55.000 0.00 0.00 0.00 5.03
3174 6602 1.599071 CTCTGCACTGTTCGAGCAAAA 59.401 47.619 2.85 0.00 38.75 2.44
3197 6625 2.419457 AGAGGGATGGATCTCTGCAT 57.581 50.000 0.00 0.00 37.86 3.96
3210 6638 0.388520 TCTGCATGTCTCCAACGACG 60.389 55.000 0.00 0.00 36.71 5.12
3229 6657 2.171701 GCGACGGGCGTGTAAAAC 59.828 61.111 4.64 0.00 43.41 2.43
3230 6658 2.312436 GCGACGGGCGTGTAAAACT 61.312 57.895 4.64 0.00 43.41 2.66
3231 6659 1.834458 GCGACGGGCGTGTAAAACTT 61.834 55.000 4.64 0.00 43.41 2.66
3303 6731 0.322187 AATTACTTGGCCGAGCGGTT 60.322 50.000 20.81 9.06 37.65 4.44
3318 6746 1.021202 CGGTTGTGCAGAGGTTTTCA 58.979 50.000 0.00 0.00 0.00 2.69
3332 6760 8.286097 GCAGAGGTTTTCAGATACTATAAATGC 58.714 37.037 0.00 0.00 0.00 3.56
3344 6772 7.725397 AGATACTATAAATGCTTGAATTGGCCA 59.275 33.333 0.00 0.00 0.00 5.36
3349 6777 9.199982 CTATAAATGCTTGAATTGGCCATTTAG 57.800 33.333 6.09 6.02 31.84 1.85
3351 6779 5.881923 ATGCTTGAATTGGCCATTTAGAT 57.118 34.783 6.09 0.00 0.00 1.98
3352 6780 5.013568 TGCTTGAATTGGCCATTTAGATG 57.986 39.130 6.09 3.63 0.00 2.90
3353 6781 3.805971 GCTTGAATTGGCCATTTAGATGC 59.194 43.478 6.09 9.67 31.67 3.91
3354 6782 3.713858 TGAATTGGCCATTTAGATGCG 57.286 42.857 6.09 0.00 31.67 4.73
3355 6783 3.286353 TGAATTGGCCATTTAGATGCGA 58.714 40.909 6.09 0.00 31.67 5.10
3357 6785 3.715628 ATTGGCCATTTAGATGCGAAC 57.284 42.857 6.09 0.00 31.67 3.95
3358 6786 1.013596 TGGCCATTTAGATGCGAACG 58.986 50.000 0.00 0.00 31.67 3.95
3369 6798 1.939934 GATGCGAACGGAATGGATTGA 59.060 47.619 0.00 0.00 0.00 2.57
3375 6804 4.060900 CGAACGGAATGGATTGATCATCT 58.939 43.478 0.00 0.00 31.67 2.90
3386 6815 2.820059 TGATCATCTCCGTATGTGGC 57.180 50.000 0.00 0.00 0.00 5.01
3429 6858 9.604626 CAACAAAATTTTGCAAACAAGTTTCTA 57.395 25.926 26.94 0.00 41.79 2.10
3440 6869 7.018235 GCAAACAAGTTTCTAGAAGCATCTAC 58.982 38.462 19.87 8.15 37.10 2.59
3444 6873 6.651225 ACAAGTTTCTAGAAGCATCTACAACC 59.349 38.462 19.87 0.00 37.10 3.77
3449 6878 5.382616 TCTAGAAGCATCTACAACCGGATA 58.617 41.667 9.46 0.00 37.10 2.59
3450 6879 5.831525 TCTAGAAGCATCTACAACCGGATAA 59.168 40.000 9.46 0.00 37.10 1.75
3452 6881 3.470645 AGCATCTACAACCGGATAACC 57.529 47.619 9.46 0.00 0.00 2.85
3453 6882 2.769663 AGCATCTACAACCGGATAACCA 59.230 45.455 9.46 0.00 35.59 3.67
3456 6885 4.578928 GCATCTACAACCGGATAACCATTT 59.421 41.667 9.46 0.00 35.59 2.32
3457 6886 5.277828 GCATCTACAACCGGATAACCATTTC 60.278 44.000 9.46 0.00 35.59 2.17
3458 6887 5.687166 TCTACAACCGGATAACCATTTCT 57.313 39.130 9.46 0.00 35.59 2.52
3459 6888 5.424757 TCTACAACCGGATAACCATTTCTG 58.575 41.667 9.46 0.00 35.59 3.02
3460 6889 2.752903 ACAACCGGATAACCATTTCTGC 59.247 45.455 9.46 0.00 35.59 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.696063 GGCGTACCCATACAGGTAGA 58.304 55.000 0.00 0.00 43.09 2.59
1 2 0.313043 CGGCGTACCCATACAGGTAG 59.687 60.000 0.00 0.00 43.09 3.18
3 4 3.085119 GCGGCGTACCCATACAGGT 62.085 63.158 9.37 0.00 44.37 4.00
5 6 0.315886 TATGCGGCGTACCCATACAG 59.684 55.000 9.37 0.00 31.62 2.74
6 7 0.032403 GTATGCGGCGTACCCATACA 59.968 55.000 22.12 6.33 43.06 2.29
7 8 1.005294 CGTATGCGGCGTACCCATAC 61.005 60.000 22.84 19.06 41.70 2.39
8 9 1.286570 CGTATGCGGCGTACCCATA 59.713 57.895 22.84 4.74 31.62 2.74
9 10 2.028484 CGTATGCGGCGTACCCAT 59.972 61.111 22.84 5.83 33.19 4.00
20 21 3.110178 GTATCCCGCGCCGTATGC 61.110 66.667 0.00 0.00 0.00 3.14
21 22 2.803670 CGTATCCCGCGCCGTATG 60.804 66.667 0.00 0.00 0.00 2.39
22 23 1.514678 TAACGTATCCCGCGCCGTAT 61.515 55.000 0.00 0.00 41.42 3.06
23 24 1.719725 TTAACGTATCCCGCGCCGTA 61.720 55.000 0.00 0.00 41.42 4.02
24 25 2.941964 CTTAACGTATCCCGCGCCGT 62.942 60.000 0.00 0.51 41.42 5.68
25 26 2.278726 TTAACGTATCCCGCGCCG 60.279 61.111 0.00 0.00 41.42 6.46
26 27 2.592222 GCTTAACGTATCCCGCGCC 61.592 63.158 0.00 0.00 41.42 6.53
27 28 1.879430 TGCTTAACGTATCCCGCGC 60.879 57.895 0.00 0.00 41.42 6.86
28 29 1.485032 GGTGCTTAACGTATCCCGCG 61.485 60.000 0.00 0.00 41.42 6.46
29 30 1.485032 CGGTGCTTAACGTATCCCGC 61.485 60.000 0.00 0.00 41.42 6.13
30 31 0.179129 ACGGTGCTTAACGTATCCCG 60.179 55.000 0.00 0.00 42.15 5.14
31 32 2.869233 TACGGTGCTTAACGTATCCC 57.131 50.000 0.00 0.00 43.79 3.85
44 45 0.179113 GGCATTTTGGGCATACGGTG 60.179 55.000 0.00 0.00 0.00 4.94
45 46 1.326951 GGGCATTTTGGGCATACGGT 61.327 55.000 0.00 0.00 34.52 4.83
46 47 1.042559 AGGGCATTTTGGGCATACGG 61.043 55.000 0.00 0.00 34.52 4.02
47 48 0.823460 AAGGGCATTTTGGGCATACG 59.177 50.000 0.00 0.00 34.52 3.06
48 49 4.320935 CGTATAAGGGCATTTTGGGCATAC 60.321 45.833 0.00 0.00 34.52 2.39
49 50 3.823873 CGTATAAGGGCATTTTGGGCATA 59.176 43.478 0.00 0.00 34.52 3.14
50 51 2.627699 CGTATAAGGGCATTTTGGGCAT 59.372 45.455 0.00 0.00 34.52 4.40
51 52 2.028130 CGTATAAGGGCATTTTGGGCA 58.972 47.619 0.00 0.00 34.52 5.36
52 53 2.028876 ACGTATAAGGGCATTTTGGGC 58.971 47.619 0.00 0.00 0.00 5.36
53 54 5.735070 GCTTAACGTATAAGGGCATTTTGGG 60.735 44.000 14.90 0.00 0.00 4.12
54 55 5.278604 GCTTAACGTATAAGGGCATTTTGG 58.721 41.667 14.90 0.00 0.00 3.28
55 56 5.278604 GGCTTAACGTATAAGGGCATTTTG 58.721 41.667 14.90 0.00 0.00 2.44
56 57 4.035909 CGGCTTAACGTATAAGGGCATTTT 59.964 41.667 14.90 0.00 0.00 1.82
57 58 3.562557 CGGCTTAACGTATAAGGGCATTT 59.437 43.478 14.90 0.00 0.00 2.32
58 59 3.135994 CGGCTTAACGTATAAGGGCATT 58.864 45.455 14.90 0.00 0.00 3.56
59 60 2.549349 CCGGCTTAACGTATAAGGGCAT 60.549 50.000 14.90 0.00 0.00 4.40
60 61 1.202557 CCGGCTTAACGTATAAGGGCA 60.203 52.381 14.90 0.00 0.00 5.36
61 62 1.505425 CCGGCTTAACGTATAAGGGC 58.495 55.000 14.90 5.69 0.00 5.19
62 63 1.270465 CCCCGGCTTAACGTATAAGGG 60.270 57.143 14.90 11.22 37.42 3.95
63 64 1.270465 CCCCCGGCTTAACGTATAAGG 60.270 57.143 14.90 4.43 0.00 2.69
64 65 2.159327 CCCCCGGCTTAACGTATAAG 57.841 55.000 0.00 11.04 0.00 1.73
80 81 2.267961 CTGCTTCGGTACACCCCC 59.732 66.667 0.00 0.00 0.00 5.40
81 82 1.079336 GTCTGCTTCGGTACACCCC 60.079 63.158 0.00 0.00 0.00 4.95
82 83 1.079336 GGTCTGCTTCGGTACACCC 60.079 63.158 0.00 0.00 0.00 4.61
83 84 0.108756 GAGGTCTGCTTCGGTACACC 60.109 60.000 0.00 0.00 0.00 4.16
84 85 0.889306 AGAGGTCTGCTTCGGTACAC 59.111 55.000 0.00 0.00 0.00 2.90
85 86 1.629043 AAGAGGTCTGCTTCGGTACA 58.371 50.000 0.00 0.00 0.00 2.90
86 87 2.745515 AAAGAGGTCTGCTTCGGTAC 57.254 50.000 0.00 0.00 0.00 3.34
87 88 3.764237 AAAAAGAGGTCTGCTTCGGTA 57.236 42.857 0.00 0.00 0.00 4.02
88 89 2.640316 AAAAAGAGGTCTGCTTCGGT 57.360 45.000 0.00 0.00 0.00 4.69
148 151 3.498676 GACACACTCCTTGTCCTCG 57.501 57.895 0.00 0.00 37.93 4.63
198 201 0.598158 CATGCGCAAACAAAGGCTGT 60.598 50.000 17.11 0.00 41.27 4.40
201 204 1.431496 ATTCATGCGCAAACAAAGGC 58.569 45.000 17.11 0.00 0.00 4.35
219 222 4.778143 GTGCGGGCCTCGGTGAAT 62.778 66.667 14.29 0.00 39.69 2.57
243 247 5.861727 AGGAACGTACACCTTCAACTTATT 58.138 37.500 0.00 0.00 31.95 1.40
246 250 3.832615 AGGAACGTACACCTTCAACTT 57.167 42.857 0.00 0.00 31.95 2.66
247 251 3.893813 ACTAGGAACGTACACCTTCAACT 59.106 43.478 12.74 0.00 37.68 3.16
248 252 4.248691 ACTAGGAACGTACACCTTCAAC 57.751 45.455 12.74 0.00 37.68 3.18
249 253 4.501915 CCAACTAGGAACGTACACCTTCAA 60.502 45.833 12.74 0.00 41.22 2.69
250 254 3.006110 CCAACTAGGAACGTACACCTTCA 59.994 47.826 12.74 0.00 41.22 3.02
251 255 3.582780 CCAACTAGGAACGTACACCTTC 58.417 50.000 12.74 0.00 41.22 3.46
252 256 2.301009 CCCAACTAGGAACGTACACCTT 59.699 50.000 12.74 0.00 41.22 3.50
253 257 1.897802 CCCAACTAGGAACGTACACCT 59.102 52.381 12.27 12.27 41.22 4.00
287 465 3.999663 GGCCGAATTCAATCTAGATCCAG 59.000 47.826 5.51 0.00 0.00 3.86
289 467 2.996621 CGGCCGAATTCAATCTAGATCC 59.003 50.000 24.07 0.00 0.00 3.36
296 474 3.609409 GCTATTTCCGGCCGAATTCAATC 60.609 47.826 30.73 5.31 0.00 2.67
347 525 2.599597 GGATGGGATGCACTGGCT 59.400 61.111 0.00 0.00 41.91 4.75
348 526 2.520260 GGGATGGGATGCACTGGC 60.520 66.667 0.00 0.00 41.68 4.85
350 528 1.077501 AACGGGATGGGATGCACTG 60.078 57.895 0.00 0.00 0.00 3.66
351 529 1.224592 GAACGGGATGGGATGCACT 59.775 57.895 0.00 0.00 0.00 4.40
352 530 1.077787 TGAACGGGATGGGATGCAC 60.078 57.895 0.00 0.00 0.00 4.57
353 531 1.077787 GTGAACGGGATGGGATGCA 60.078 57.895 0.00 0.00 0.00 3.96
354 532 1.077787 TGTGAACGGGATGGGATGC 60.078 57.895 0.00 0.00 0.00 3.91
355 533 1.089481 CGTGTGAACGGGATGGGATG 61.089 60.000 0.00 0.00 0.00 3.51
356 534 1.220749 CGTGTGAACGGGATGGGAT 59.779 57.895 0.00 0.00 0.00 3.85
357 535 2.660206 CGTGTGAACGGGATGGGA 59.340 61.111 0.00 0.00 0.00 4.37
358 536 3.124921 GCGTGTGAACGGGATGGG 61.125 66.667 0.00 0.00 0.00 4.00
359 537 1.745115 ATGCGTGTGAACGGGATGG 60.745 57.895 0.00 0.00 0.00 3.51
360 538 1.018752 TCATGCGTGTGAACGGGATG 61.019 55.000 5.68 0.00 0.00 3.51
361 539 0.740868 CTCATGCGTGTGAACGGGAT 60.741 55.000 5.68 0.00 0.00 3.85
382 560 0.982852 TCCAAGGACGGCCATCTCAT 60.983 55.000 11.69 0.00 36.29 2.90
383 561 0.982852 ATCCAAGGACGGCCATCTCA 60.983 55.000 11.69 0.00 36.29 3.27
384 562 0.181350 AATCCAAGGACGGCCATCTC 59.819 55.000 11.69 0.00 36.29 2.75
385 563 0.107017 CAATCCAAGGACGGCCATCT 60.107 55.000 11.69 0.00 36.29 2.90
386 564 1.103398 CCAATCCAAGGACGGCCATC 61.103 60.000 11.69 0.00 36.29 3.51
387 565 1.076777 CCAATCCAAGGACGGCCAT 60.077 57.895 11.69 0.00 36.29 4.40
388 566 1.570857 ATCCAATCCAAGGACGGCCA 61.571 55.000 11.69 0.00 38.13 5.36
389 567 1.103398 CATCCAATCCAAGGACGGCC 61.103 60.000 0.00 0.00 38.13 6.13
437 619 0.109689 GTCGGTCGATCGATCCATCC 60.110 60.000 25.41 15.84 41.40 3.51
492 674 1.603931 GCTTTGCTGCTGGAAAGGAAC 60.604 52.381 29.43 15.41 47.00 3.62
504 694 3.840468 TCATGTATGCTTTGCTTTGCTG 58.160 40.909 0.00 0.00 0.00 4.41
512 702 5.106436 ACACACAGTCATCATGTATGCTTTG 60.106 40.000 0.00 4.19 35.38 2.77
514 704 4.393990 CACACACAGTCATCATGTATGCTT 59.606 41.667 0.00 0.00 35.38 3.91
515 705 3.937079 CACACACAGTCATCATGTATGCT 59.063 43.478 0.00 0.00 35.38 3.79
516 706 3.064408 CCACACACAGTCATCATGTATGC 59.936 47.826 0.00 0.00 35.38 3.14
517 707 4.506758 TCCACACACAGTCATCATGTATG 58.493 43.478 0.00 0.00 36.88 2.39
519 709 4.020307 ACATCCACACACAGTCATCATGTA 60.020 41.667 0.00 0.00 0.00 2.29
520 710 3.244665 ACATCCACACACAGTCATCATGT 60.245 43.478 0.00 0.00 0.00 3.21
521 711 3.126343 CACATCCACACACAGTCATCATG 59.874 47.826 0.00 0.00 0.00 3.07
522 712 3.244665 ACACATCCACACACAGTCATCAT 60.245 43.478 0.00 0.00 0.00 2.45
524 714 2.481568 CACACATCCACACACAGTCATC 59.518 50.000 0.00 0.00 0.00 2.92
525 715 2.104622 TCACACATCCACACACAGTCAT 59.895 45.455 0.00 0.00 0.00 3.06
527 717 1.867233 GTCACACATCCACACACAGTC 59.133 52.381 0.00 0.00 0.00 3.51
528 718 1.806247 CGTCACACATCCACACACAGT 60.806 52.381 0.00 0.00 0.00 3.55
529 719 0.861185 CGTCACACATCCACACACAG 59.139 55.000 0.00 0.00 0.00 3.66
530 720 0.531753 CCGTCACACATCCACACACA 60.532 55.000 0.00 0.00 0.00 3.72
531 721 0.531974 ACCGTCACACATCCACACAC 60.532 55.000 0.00 0.00 0.00 3.82
534 724 1.596752 GCACCGTCACACATCCACA 60.597 57.895 0.00 0.00 0.00 4.17
546 1914 4.002506 TGGACGCTCATGCACCGT 62.003 61.111 0.00 0.00 39.64 4.83
586 1962 3.932289 GGTCGTCCGTGACTGTTG 58.068 61.111 3.15 0.00 38.91 3.33
807 2189 4.504514 CCATGATGACTCGAAGGATTGGAT 60.505 45.833 0.00 0.00 30.68 3.41
854 2246 0.178918 GGAGGAAGGGAGGATCGGAT 60.179 60.000 0.00 0.00 34.37 4.18
855 2247 1.233369 GGAGGAAGGGAGGATCGGA 59.767 63.158 0.00 0.00 34.37 4.55
856 2248 1.839296 GGGAGGAAGGGAGGATCGG 60.839 68.421 0.00 0.00 34.37 4.18
858 2250 0.472925 GGAGGGAGGAAGGGAGGATC 60.473 65.000 0.00 0.00 0.00 3.36
868 2260 2.231380 GCTTGGGTTGGAGGGAGGA 61.231 63.158 0.00 0.00 0.00 3.71
904 2296 1.069049 GCTTTTGCTTGGGCTTGAGAA 59.931 47.619 0.00 0.00 43.35 2.87
911 2303 1.962822 GCTTGGCTTTTGCTTGGGC 60.963 57.895 0.00 0.00 46.54 5.36
940 2332 2.095516 GGTTTTAAGCAGAGCAGAGTGC 60.096 50.000 0.00 0.00 45.46 4.40
942 2334 2.106511 TGGGTTTTAAGCAGAGCAGAGT 59.893 45.455 0.00 0.00 0.00 3.24
1083 2475 4.404098 GGGATCGTGGTGGGCGTT 62.404 66.667 0.00 0.00 0.00 4.84
1874 3269 2.813179 GCGTACTGCATCTTGCCGG 61.813 63.158 0.00 0.00 44.23 6.13
1876 3271 2.703409 CGCGTACTGCATCTTGCC 59.297 61.111 0.00 0.00 44.23 4.52
1877 3272 2.021931 GCGCGTACTGCATCTTGC 59.978 61.111 8.43 0.00 46.97 4.01
1878 3273 2.703409 GGCGCGTACTGCATCTTG 59.297 61.111 8.43 0.00 46.97 3.02
1879 3274 2.885644 CGGCGCGTACTGCATCTT 60.886 61.111 8.43 0.00 46.97 2.40
2062 4890 2.044650 CGTCGGGTCCAGGTAGGA 60.045 66.667 0.00 0.00 46.75 2.94
2188 5016 3.136123 CATGGTCTTGGCGCCCTG 61.136 66.667 26.77 16.96 0.00 4.45
2189 5017 4.431131 CCATGGTCTTGGCGCCCT 62.431 66.667 26.77 0.00 0.00 5.19
2424 5252 0.323178 TCTCCAGGTCGTACTCCACC 60.323 60.000 6.71 2.79 0.00 4.61
2478 5306 2.276306 GCCTACGACGACGACGAC 60.276 66.667 25.15 7.02 42.66 4.34
2488 5316 0.106619 GAGGAGGAAGGAGCCTACGA 60.107 60.000 0.00 0.00 44.10 3.43
2489 5317 1.448922 CGAGGAGGAAGGAGCCTACG 61.449 65.000 0.00 0.00 44.10 3.51
2490 5318 1.740332 GCGAGGAGGAAGGAGCCTAC 61.740 65.000 0.00 0.00 38.73 3.18
2586 5426 0.031857 CATGCCTGCCTCTACTCTCG 59.968 60.000 0.00 0.00 0.00 4.04
2611 5454 8.962884 TGGATTCAGTATAGTACAGTACGTAA 57.037 34.615 5.02 0.00 0.00 3.18
2619 5462 5.836898 ACCGGATTGGATTCAGTATAGTACA 59.163 40.000 9.46 0.00 42.00 2.90
2635 5486 4.069304 TCACTAACTTTTCCACCGGATTG 58.931 43.478 9.46 0.00 0.00 2.67
2641 5505 7.573283 GCTTAATCTGTCACTAACTTTTCCACC 60.573 40.741 0.00 0.00 0.00 4.61
2674 5538 2.558313 GAAAGCTGCCTGCACGAC 59.442 61.111 0.00 0.00 45.94 4.34
2695 5559 2.919043 GGGGGTCTGCATCCGAAT 59.081 61.111 0.00 0.00 0.00 3.34
2696 5560 3.781307 CGGGGGTCTGCATCCGAA 61.781 66.667 6.71 0.00 44.69 4.30
2708 5572 0.320073 TAATATCGAAAGCGCGGGGG 60.320 55.000 8.83 0.00 37.46 5.40
2773 5643 3.483558 GCAAAAGAGCAAAAGAAGACACG 59.516 43.478 0.00 0.00 0.00 4.49
2777 5647 5.036737 CGAAAGCAAAAGAGCAAAAGAAGA 58.963 37.500 0.00 0.00 36.85 2.87
2778 5648 4.207841 CCGAAAGCAAAAGAGCAAAAGAAG 59.792 41.667 0.00 0.00 36.85 2.85
2779 5649 4.111916 CCGAAAGCAAAAGAGCAAAAGAA 58.888 39.130 0.00 0.00 36.85 2.52
2866 6224 1.206371 ACGCATCTACTAACCACCCAC 59.794 52.381 0.00 0.00 0.00 4.61
2867 6225 1.479323 GACGCATCTACTAACCACCCA 59.521 52.381 0.00 0.00 0.00 4.51
2868 6226 1.479323 TGACGCATCTACTAACCACCC 59.521 52.381 0.00 0.00 0.00 4.61
2954 6339 8.758829 TCTAATTCTAGTTGGTGAGAGCATTAA 58.241 33.333 0.00 0.00 0.00 1.40
2955 6340 8.306313 TCTAATTCTAGTTGGTGAGAGCATTA 57.694 34.615 0.00 0.00 0.00 1.90
2956 6341 7.187824 TCTAATTCTAGTTGGTGAGAGCATT 57.812 36.000 0.00 0.00 0.00 3.56
2959 6344 5.465056 GCATCTAATTCTAGTTGGTGAGAGC 59.535 44.000 0.00 0.00 0.00 4.09
2968 6353 4.455606 GCACAGGGCATCTAATTCTAGTT 58.544 43.478 0.00 0.00 43.97 2.24
3038 6431 2.513897 GCATGGGTCAGGGTACGC 60.514 66.667 0.77 0.77 0.00 4.42
3063 6470 2.898840 CAGGTAGCAGCCGCCATG 60.899 66.667 5.72 0.00 39.83 3.66
3087 6494 0.110056 GAGCTGTGCACATTGAACGG 60.110 55.000 22.00 7.87 0.00 4.44
3088 6495 0.110056 GGAGCTGTGCACATTGAACG 60.110 55.000 22.00 8.67 0.00 3.95
3146 6563 2.159128 CGAACAGTGCAGAGATCCATCT 60.159 50.000 0.00 0.00 40.50 2.90
3147 6564 2.159184 TCGAACAGTGCAGAGATCCATC 60.159 50.000 0.00 0.00 0.00 3.51
3148 6565 1.827344 TCGAACAGTGCAGAGATCCAT 59.173 47.619 0.00 0.00 0.00 3.41
3174 6602 3.267812 TGCAGAGATCCATCCCTCTTTTT 59.732 43.478 0.00 0.00 37.64 1.94
3179 6607 1.698532 ACATGCAGAGATCCATCCCTC 59.301 52.381 0.00 0.00 0.00 4.30
3181 6609 1.698532 AGACATGCAGAGATCCATCCC 59.301 52.381 0.00 0.00 0.00 3.85
3191 6619 0.388520 CGTCGTTGGAGACATGCAGA 60.389 55.000 0.00 0.00 42.32 4.26
3214 6642 5.555069 CGAATATAAGTTTTACACGCCCGTC 60.555 44.000 0.00 0.00 0.00 4.79
3229 6657 7.308782 ACCTGCAAGAAGTTTCGAATATAAG 57.691 36.000 0.00 0.00 34.07 1.73
3230 6658 7.681939 AACCTGCAAGAAGTTTCGAATATAA 57.318 32.000 0.00 0.00 34.07 0.98
3231 6659 7.681939 AAACCTGCAAGAAGTTTCGAATATA 57.318 32.000 0.00 0.00 34.07 0.86
3286 6714 1.669760 CAACCGCTCGGCCAAGTAA 60.670 57.895 8.41 0.00 39.32 2.24
3303 6731 4.623932 AGTATCTGAAAACCTCTGCACA 57.376 40.909 0.00 0.00 0.00 4.57
3318 6746 7.725397 TGGCCAATTCAAGCATTTATAGTATCT 59.275 33.333 0.61 0.00 0.00 1.98
3332 6760 4.046462 CGCATCTAAATGGCCAATTCAAG 58.954 43.478 10.96 2.76 33.19 3.02
3344 6772 3.804036 TCCATTCCGTTCGCATCTAAAT 58.196 40.909 0.00 0.00 0.00 1.40
3349 6777 1.939934 TCAATCCATTCCGTTCGCATC 59.060 47.619 0.00 0.00 0.00 3.91
3351 6779 1.939934 GATCAATCCATTCCGTTCGCA 59.060 47.619 0.00 0.00 0.00 5.10
3352 6780 1.939934 TGATCAATCCATTCCGTTCGC 59.060 47.619 0.00 0.00 0.00 4.70
3353 6781 4.060900 AGATGATCAATCCATTCCGTTCG 58.939 43.478 0.00 0.00 35.72 3.95
3354 6782 4.453819 GGAGATGATCAATCCATTCCGTTC 59.546 45.833 20.23 1.74 35.72 3.95
3355 6783 4.392940 GGAGATGATCAATCCATTCCGTT 58.607 43.478 20.23 0.00 35.72 4.44
3357 6785 2.998670 CGGAGATGATCAATCCATTCCG 59.001 50.000 23.13 18.53 37.81 4.30
3358 6786 4.013267 ACGGAGATGATCAATCCATTCC 57.987 45.455 23.13 12.90 35.72 3.01
3369 6798 1.345741 CCAGCCACATACGGAGATGAT 59.654 52.381 1.74 0.00 0.00 2.45
3375 6804 1.078497 CAAGCCAGCCACATACGGA 60.078 57.895 0.00 0.00 0.00 4.69
3429 6858 4.443034 GGTTATCCGGTTGTAGATGCTTCT 60.443 45.833 0.00 7.35 35.90 2.85
3440 6869 2.099098 GGCAGAAATGGTTATCCGGTTG 59.901 50.000 0.00 0.00 36.30 3.77
3444 6873 1.318576 GGGGCAGAAATGGTTATCCG 58.681 55.000 0.00 0.00 36.30 4.18
3449 6878 1.055849 GTTTGGGGGCAGAAATGGTT 58.944 50.000 0.00 0.00 0.00 3.67
3450 6879 0.105246 TGTTTGGGGGCAGAAATGGT 60.105 50.000 0.00 0.00 0.00 3.55
3452 6881 0.321346 GGTGTTTGGGGGCAGAAATG 59.679 55.000 0.00 0.00 0.00 2.32
3453 6882 0.835971 GGGTGTTTGGGGGCAGAAAT 60.836 55.000 0.00 0.00 0.00 2.17
3456 6885 4.278513 CGGGTGTTTGGGGGCAGA 62.279 66.667 0.00 0.00 0.00 4.26
3457 6886 4.278513 TCGGGTGTTTGGGGGCAG 62.279 66.667 0.00 0.00 0.00 4.85
3458 6887 4.278513 CTCGGGTGTTTGGGGGCA 62.279 66.667 0.00 0.00 0.00 5.36
3459 6888 4.280019 ACTCGGGTGTTTGGGGGC 62.280 66.667 0.00 0.00 0.00 5.80
3460 6889 2.282180 CACTCGGGTGTTTGGGGG 60.282 66.667 7.44 0.00 38.54 5.40


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.