Multiple sequence alignment - TraesCS4A01G048700

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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 TraesCS4A01G048700 chr4A 100.000 5892 0 0 1 5892 39524460 39518569 0.000000e+00 10881.0
1 TraesCS4A01G048700 chr4A 89.216 102 7 2 3908 4005 15761588 15761487 2.230000e-24 124.0
2 TraesCS4A01G048700 chr4D 92.426 2931 121 43 1 2859 425245192 425248093 0.000000e+00 4089.0
3 TraesCS4A01G048700 chr4D 94.042 1712 50 28 4167 5856 425249562 425251243 0.000000e+00 2549.0
4 TraesCS4A01G048700 chr4D 96.918 876 26 1 2858 3733 425248339 425249213 0.000000e+00 1467.0
5 TraesCS4A01G048700 chr4B 94.020 2040 59 23 840 2859 520907493 520909489 0.000000e+00 3033.0
6 TraesCS4A01G048700 chr4B 93.251 1704 72 30 4167 5855 520911143 520912818 0.000000e+00 2470.0
7 TraesCS4A01G048700 chr4B 92.857 1092 35 8 2858 3932 520909733 520910798 0.000000e+00 1544.0
8 TraesCS4A01G048700 chr4B 88.087 831 66 21 4852 5663 228028771 228029587 0.000000e+00 955.0
9 TraesCS4A01G048700 chr4B 89.178 730 48 22 1 721 520906402 520907109 0.000000e+00 881.0
10 TraesCS4A01G048700 chr4B 91.579 190 12 2 3977 4163 520910904 520911092 5.860000e-65 259.0
11 TraesCS4A01G048700 chr4B 89.796 98 6 3 3908 4001 11736926 11736829 8.020000e-24 122.0
12 TraesCS4A01G048700 chr4B 87.879 99 9 3 3904 4001 38362947 38363043 4.830000e-21 113.0
13 TraesCS4A01G048700 chr4B 88.312 77 5 2 3789 3862 4715182 4715107 8.130000e-14 89.8
14 TraesCS4A01G048700 chr7A 88.942 832 56 23 4852 5663 290243744 290244559 0.000000e+00 994.0
15 TraesCS4A01G048700 chr7B 88.755 827 56 23 4858 5663 653448086 653448896 0.000000e+00 977.0
16 TraesCS4A01G048700 chr7B 88.115 833 62 22 4852 5663 653602646 653603462 0.000000e+00 955.0
17 TraesCS4A01G048700 chr7B 88.029 827 62 23 4858 5663 653515806 653516616 0.000000e+00 944.0
18 TraesCS4A01G048700 chr2A 88.109 841 55 26 4852 5663 614698615 614697791 0.000000e+00 957.0
19 TraesCS4A01G048700 chr2A 88.889 72 4 2 3790 3861 18609652 18609719 1.050000e-12 86.1
20 TraesCS4A01G048700 chr2B 87.981 832 65 23 4852 5663 693977519 693976703 0.000000e+00 950.0
21 TraesCS4A01G048700 chr2B 91.667 228 11 3 4852 5072 693990902 693990676 5.730000e-80 309.0
22 TraesCS4A01G048700 chr2B 84.685 111 13 3 3904 4013 710325626 710325519 2.250000e-19 108.0
23 TraesCS4A01G048700 chr2B 89.474 76 4 1 3791 3862 91631308 91631383 6.290000e-15 93.5
24 TraesCS4A01G048700 chr2B 89.189 74 2 3 3794 3862 91631379 91631307 2.930000e-13 87.9
25 TraesCS4A01G048700 chr1A 86.372 565 43 21 4964 5506 11267244 11266692 2.370000e-163 586.0
26 TraesCS4A01G048700 chr1A 89.172 157 4 7 4852 5008 11267402 11267259 3.630000e-42 183.0
27 TraesCS4A01G048700 chr5D 88.182 110 11 2 3899 4006 134780496 134780605 4.790000e-26 130.0
28 TraesCS4A01G048700 chr1B 90.426 94 8 1 3908 4001 368223027 368223119 8.020000e-24 122.0
29 TraesCS4A01G048700 chrUn 89.474 95 7 3 3908 4001 26701824 26701916 3.730000e-22 117.0
30 TraesCS4A01G048700 chrUn 89.744 78 2 3 3789 3861 215727633 215727709 1.750000e-15 95.3
31 TraesCS4A01G048700 chrUn 86.111 72 5 2 3791 3862 34213231 34213297 8.190000e-09 73.1
32 TraesCS4A01G048700 chr5A 87.755 98 11 1 3904 4001 410509938 410510034 4.830000e-21 113.0
33 TraesCS4A01G048700 chr5A 91.667 72 2 2 3794 3861 21453251 21453322 4.860000e-16 97.1
34 TraesCS4A01G048700 chr3B 85.981 107 13 2 3897 4001 794105854 794105960 4.830000e-21 113.0
35 TraesCS4A01G048700 chr3B 80.435 92 10 7 3791 3874 269249757 269249848 4.930000e-06 63.9
36 TraesCS4A01G048700 chr7D 87.500 80 5 2 3790 3864 225203156 225203077 2.930000e-13 87.9
37 TraesCS4A01G048700 chr7D 81.250 80 10 3 3794 3868 121199829 121199750 6.380000e-05 60.2
38 TraesCS4A01G048700 chr7D 83.824 68 6 3 3791 3853 121788918 121788985 6.380000e-05 60.2
39 TraesCS4A01G048700 chr2D 87.342 79 5 2 3788 3861 422751571 422751493 1.050000e-12 86.1
40 TraesCS4A01G048700 chr3D 85.714 84 4 4 3795 3871 119114422 119114504 1.360000e-11 82.4
41 TraesCS4A01G048700 chr3A 87.838 74 4 1 3795 3868 108469188 108469256 1.360000e-11 82.4
42 TraesCS4A01G048700 chr3A 81.818 88 9 6 3794 3874 238688700 238688613 3.810000e-07 67.6
43 TraesCS4A01G048700 chr6A 85.526 76 3 5 3794 3868 15702829 15702761 8.190000e-09 73.1
44 TraesCS4A01G048700 chr6D 84.211 76 4 5 3791 3865 14725179 14725247 3.810000e-07 67.6


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 TraesCS4A01G048700 chr4A 39518569 39524460 5891 True 10881.000000 10881 100.000 1 5892 1 chr4A.!!$R2 5891
1 TraesCS4A01G048700 chr4D 425245192 425251243 6051 False 2701.666667 4089 94.462 1 5856 3 chr4D.!!$F1 5855
2 TraesCS4A01G048700 chr4B 520906402 520912818 6416 False 1637.400000 3033 92.177 1 5855 5 chr4B.!!$F3 5854
3 TraesCS4A01G048700 chr4B 228028771 228029587 816 False 955.000000 955 88.087 4852 5663 1 chr4B.!!$F2 811
4 TraesCS4A01G048700 chr7A 290243744 290244559 815 False 994.000000 994 88.942 4852 5663 1 chr7A.!!$F1 811
5 TraesCS4A01G048700 chr7B 653448086 653448896 810 False 977.000000 977 88.755 4858 5663 1 chr7B.!!$F1 805
6 TraesCS4A01G048700 chr7B 653602646 653603462 816 False 955.000000 955 88.115 4852 5663 1 chr7B.!!$F3 811
7 TraesCS4A01G048700 chr7B 653515806 653516616 810 False 944.000000 944 88.029 4858 5663 1 chr7B.!!$F2 805
8 TraesCS4A01G048700 chr2A 614697791 614698615 824 True 957.000000 957 88.109 4852 5663 1 chr2A.!!$R1 811
9 TraesCS4A01G048700 chr2B 693976703 693977519 816 True 950.000000 950 87.981 4852 5663 1 chr2B.!!$R2 811
10 TraesCS4A01G048700 chr1A 11266692 11267402 710 True 384.500000 586 87.772 4852 5506 2 chr1A.!!$R1 654

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
641 695 0.035056 AAGCAAAGATCCCCCAGACG 60.035 55.0 0.00 0.00 0.00 4.18 F
691 745 0.391228 GCGGCCAAAGGAAAAGGAAA 59.609 50.0 2.24 0.00 0.00 3.13 F
1770 2103 0.955919 CGAGGTTCTGGCAGGAAACC 60.956 60.0 23.68 23.68 33.76 3.27 F
2611 2961 0.443869 CGCCGGTCTGTTGAATCAAG 59.556 55.0 1.90 0.00 0.00 3.02 F
3804 4437 0.325602 TGTTGTATTCCCACCGTCCC 59.674 55.0 0.00 0.00 0.00 4.46 F
3805 4438 0.325602 GTTGTATTCCCACCGTCCCA 59.674 55.0 0.00 0.00 0.00 4.37 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2580 2930 0.110373 GACCGGCGCAAACTTAAGTG 60.110 55.000 10.83 0.00 0.00 3.16 R
2593 2943 0.169009 GCTTGATTCAACAGACCGGC 59.831 55.000 0.00 0.00 0.00 6.13 R
2656 3006 1.406539 CAATTGCATGCCAGTCTACCC 59.593 52.381 16.68 0.00 0.00 3.69 R
4405 5155 0.102300 AACGCAGGCCTGTTTTTCAC 59.898 50.000 32.81 13.99 0.00 3.18 R
4646 5398 0.391130 TCGCAAGCTCATACACCACC 60.391 55.000 0.00 0.00 37.18 4.61 R
5018 5846 0.536687 ATCGGTCGAGCGGATTAGGA 60.537 55.000 33.60 15.39 34.04 2.94 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
33 38 5.627499 AACCAGTATTACAGCATTGTGTG 57.373 39.130 0.00 0.00 38.23 3.82
91 99 4.050553 ACCGAACATTGCAACATTTCTTG 58.949 39.130 0.00 0.00 0.00 3.02
127 136 1.523154 TTTGCGCACCTCATTCCCAC 61.523 55.000 11.12 0.00 0.00 4.61
134 143 1.142688 ACCTCATTCCCACCAAGGCT 61.143 55.000 0.00 0.00 35.39 4.58
150 159 1.812571 AGGCTATCAAAGTTGGTTGCG 59.187 47.619 4.96 0.00 40.22 4.85
164 174 3.827625 TGGTTGCGGAATTATTTTCACG 58.172 40.909 0.00 0.00 0.00 4.35
181 191 5.418310 TTCACGAGTGAAAGAAAATCACC 57.582 39.130 15.39 0.00 46.60 4.02
265 287 2.244946 GGGAACGTCACTTTCCAGC 58.755 57.895 14.70 0.00 43.96 4.85
266 288 0.250338 GGGAACGTCACTTTCCAGCT 60.250 55.000 14.70 0.00 43.96 4.24
267 289 1.594331 GGAACGTCACTTTCCAGCTT 58.406 50.000 8.20 0.00 42.04 3.74
268 290 2.549349 GGGAACGTCACTTTCCAGCTTA 60.549 50.000 14.70 0.00 43.96 3.09
269 291 3.135994 GGAACGTCACTTTCCAGCTTAA 58.864 45.455 8.20 0.00 42.04 1.85
270 292 3.186613 GGAACGTCACTTTCCAGCTTAAG 59.813 47.826 8.20 0.00 42.04 1.85
271 293 3.470645 ACGTCACTTTCCAGCTTAAGT 57.529 42.857 4.02 0.00 35.06 2.24
300 322 5.596836 TTGACAAGATGAAGCACCTTTTT 57.403 34.783 0.00 0.00 0.00 1.94
312 334 8.729805 TGAAGCACCTTTTTCAATTGTTATTT 57.270 26.923 5.13 0.00 30.84 1.40
314 336 9.650371 GAAGCACCTTTTTCAATTGTTATTTTC 57.350 29.630 5.13 0.00 0.00 2.29
346 370 8.674263 TTCTCTCCTAGTAGTCTATTAAACCG 57.326 38.462 0.00 0.00 0.00 4.44
376 400 5.237815 TCATTCGTTTCAGACATAAGCTGT 58.762 37.500 0.00 0.00 42.15 4.40
398 422 4.979943 TGCTCAACATTGTCAAACAGAA 57.020 36.364 0.00 0.00 0.00 3.02
399 423 4.923893 TGCTCAACATTGTCAAACAGAAG 58.076 39.130 0.00 0.00 0.00 2.85
400 424 4.639755 TGCTCAACATTGTCAAACAGAAGA 59.360 37.500 0.00 0.00 0.00 2.87
418 442 9.931210 AACAGAAGAAAAACTATTACTCAAACG 57.069 29.630 0.00 0.00 0.00 3.60
441 465 4.798574 CCCATTTCTCGAAAGTTCAAAGG 58.201 43.478 0.00 0.00 33.32 3.11
450 474 3.366374 CGAAAGTTCAAAGGCCATTCTCC 60.366 47.826 5.01 0.00 0.00 3.71
475 499 4.842380 AGTTACCCCACTTAGAAGCTGTTA 59.158 41.667 0.00 0.00 0.00 2.41
476 500 3.697619 ACCCCACTTAGAAGCTGTTAC 57.302 47.619 0.00 0.00 0.00 2.50
482 507 6.713450 CCCCACTTAGAAGCTGTTACTAAAAA 59.287 38.462 0.00 0.00 0.00 1.94
532 560 9.635520 AGCATTGTAATCAAATCAAAGAAGAAG 57.364 29.630 0.00 0.00 37.11 2.85
578 610 1.883275 CAGAGTAGATAGAGTGCGGGG 59.117 57.143 0.00 0.00 0.00 5.73
641 695 0.035056 AAGCAAAGATCCCCCAGACG 60.035 55.000 0.00 0.00 0.00 4.18
648 702 0.468226 GATCCCCCAGACGCAATACA 59.532 55.000 0.00 0.00 0.00 2.29
682 736 1.809567 AAGAGCAAAGCGGCCAAAGG 61.810 55.000 2.24 0.00 0.00 3.11
687 741 1.501169 CAAAGCGGCCAAAGGAAAAG 58.499 50.000 2.24 0.00 0.00 2.27
688 742 0.392706 AAAGCGGCCAAAGGAAAAGG 59.607 50.000 2.24 0.00 0.00 3.11
689 743 0.469144 AAGCGGCCAAAGGAAAAGGA 60.469 50.000 2.24 0.00 0.00 3.36
691 745 0.391228 GCGGCCAAAGGAAAAGGAAA 59.609 50.000 2.24 0.00 0.00 3.13
692 746 1.001974 GCGGCCAAAGGAAAAGGAAAT 59.998 47.619 2.24 0.00 0.00 2.17
699 755 6.166279 GCCAAAGGAAAAGGAAATAGGAAAG 58.834 40.000 0.00 0.00 0.00 2.62
812 870 2.230266 TGCTGTAACTACACTGCATCGA 59.770 45.455 4.03 0.00 45.04 3.59
813 871 2.854777 GCTGTAACTACACTGCATCGAG 59.145 50.000 0.00 0.00 41.49 4.04
826 884 1.811428 CATCGAGAGTTCGTACCACG 58.189 55.000 0.00 0.00 46.72 4.94
847 1165 1.220236 CCTCATCCTTCCTCCTCCTCT 59.780 57.143 0.00 0.00 0.00 3.69
1182 1512 2.360852 TCCTCCACCTCGTCGACC 60.361 66.667 10.58 0.00 0.00 4.79
1344 1677 4.180946 CGGAGCCTCTCGGTGTCG 62.181 72.222 0.00 0.00 37.82 4.35
1770 2103 0.955919 CGAGGTTCTGGCAGGAAACC 60.956 60.000 23.68 23.68 33.76 3.27
1779 2112 2.193536 GCAGGAAACCAACAGCCGT 61.194 57.895 0.00 0.00 0.00 5.68
1989 2322 2.860062 GCAAATGCGCCATCTATCATC 58.140 47.619 4.18 0.00 0.00 2.92
2207 2540 7.935520 TGTTCAAATGTTGATAGCTTGTTGTA 58.064 30.769 0.00 0.00 39.84 2.41
2227 2560 9.321562 TGTTGTAAAACCTAAGTTCACTCTAAG 57.678 33.333 0.00 0.00 34.19 2.18
2324 2660 8.707839 TGCTTGCTTAATATTTTTACTGCAAAC 58.292 29.630 0.00 0.00 38.44 2.93
2328 2664 7.327275 TGCTTAATATTTTTACTGCAAACGTGG 59.673 33.333 0.00 0.00 0.00 4.94
2352 2688 7.092444 TGGGGTAATTCTGGGATAATATGCTAG 60.092 40.741 0.00 0.00 0.00 3.42
2353 2689 7.283329 GGGTAATTCTGGGATAATATGCTAGG 58.717 42.308 5.42 0.00 30.25 3.02
2354 2690 7.127339 GGGTAATTCTGGGATAATATGCTAGGA 59.873 40.741 5.42 0.00 30.25 2.94
2355 2691 7.988028 GGTAATTCTGGGATAATATGCTAGGAC 59.012 40.741 5.42 0.46 30.25 3.85
2356 2692 7.821134 AATTCTGGGATAATATGCTAGGACT 57.179 36.000 5.42 0.00 30.25 3.85
2357 2693 7.821134 ATTCTGGGATAATATGCTAGGACTT 57.179 36.000 5.42 0.00 30.25 3.01
2358 2694 6.611613 TCTGGGATAATATGCTAGGACTTG 57.388 41.667 5.42 0.00 30.25 3.16
2359 2695 6.084738 TCTGGGATAATATGCTAGGACTTGT 58.915 40.000 5.42 0.00 30.25 3.16
2360 2696 6.558775 TCTGGGATAATATGCTAGGACTTGTT 59.441 38.462 5.42 0.00 30.25 2.83
2361 2697 7.733047 TCTGGGATAATATGCTAGGACTTGTTA 59.267 37.037 5.42 0.00 30.25 2.41
2364 2700 7.819900 GGGATAATATGCTAGGACTTGTTACTG 59.180 40.741 0.00 0.00 0.00 2.74
2369 2705 5.073311 TGCTAGGACTTGTTACTGATCAC 57.927 43.478 0.00 0.00 0.00 3.06
2372 2720 6.607600 TGCTAGGACTTGTTACTGATCACTAT 59.392 38.462 0.00 0.00 0.00 2.12
2398 2746 5.529060 ACATTTAGTATTTGCTAGCTGCCTC 59.471 40.000 17.23 4.13 42.00 4.70
2424 2772 9.846248 CTTTCAGGATAATGGTTAGTTTTTCAG 57.154 33.333 0.00 0.00 0.00 3.02
2549 2899 7.607991 GGAGATAAGGAGAATCTTTGAACACAA 59.392 37.037 0.00 0.00 34.28 3.33
2593 2943 4.944962 TCCATCATCACTTAAGTTTGCG 57.055 40.909 5.07 0.00 0.00 4.85
2611 2961 0.443869 CGCCGGTCTGTTGAATCAAG 59.556 55.000 1.90 0.00 0.00 3.02
2656 3006 0.739462 TGGACATAGTTGAAGGCGCG 60.739 55.000 0.00 0.00 0.00 6.86
2659 3009 1.449601 CATAGTTGAAGGCGCGGGT 60.450 57.895 8.83 0.00 0.00 5.28
2690 3040 4.517952 TGCAATTGTGGGTGTATGAAAG 57.482 40.909 7.40 0.00 0.00 2.62
2734 3084 9.959721 TTATTCATTAACATCTAGGCCCTATTC 57.040 33.333 0.00 0.00 0.00 1.75
2824 3176 9.152327 TGAGAACAAGGAGATACTAATGATGAT 57.848 33.333 0.00 0.00 0.00 2.45
2917 3516 8.292448 CGCTAAAATTGGCAAATATAGAGATGT 58.708 33.333 3.01 0.00 33.91 3.06
2958 3557 9.897744 TTGTAAAGCTATCTTTTGATGAAACTG 57.102 29.630 0.00 0.00 42.21 3.16
2961 3560 5.947443 AGCTATCTTTTGATGAAACTGCAC 58.053 37.500 0.00 0.00 39.88 4.57
2969 3568 7.648908 TCTTTTGATGAAACTGCACTGTATTTG 59.351 33.333 0.00 0.00 0.00 2.32
3209 3808 5.642165 TCTTAGGGGAGAGGTATGTGATAC 58.358 45.833 0.00 0.00 35.00 2.24
3543 4142 1.352622 TGCCCAAGGTGTGAAGGAGT 61.353 55.000 0.00 0.00 0.00 3.85
3587 4186 2.035530 TGCATACAATGGCATCGTCA 57.964 45.000 0.00 0.00 34.58 4.35
3797 4430 6.718912 TGATTTCTCATTGTGTTGTATTCCCA 59.281 34.615 0.00 0.00 0.00 4.37
3800 4433 3.078097 TCATTGTGTTGTATTCCCACCG 58.922 45.455 0.00 0.00 0.00 4.94
3801 4434 2.642154 TTGTGTTGTATTCCCACCGT 57.358 45.000 0.00 0.00 0.00 4.83
3802 4435 2.172851 TGTGTTGTATTCCCACCGTC 57.827 50.000 0.00 0.00 0.00 4.79
3803 4436 1.270947 TGTGTTGTATTCCCACCGTCC 60.271 52.381 0.00 0.00 0.00 4.79
3804 4437 0.325602 TGTTGTATTCCCACCGTCCC 59.674 55.000 0.00 0.00 0.00 4.46
3805 4438 0.325602 GTTGTATTCCCACCGTCCCA 59.674 55.000 0.00 0.00 0.00 4.37
3806 4439 1.065647 TTGTATTCCCACCGTCCCAA 58.934 50.000 0.00 0.00 0.00 4.12
3807 4440 1.065647 TGTATTCCCACCGTCCCAAA 58.934 50.000 0.00 0.00 0.00 3.28
3808 4441 1.424302 TGTATTCCCACCGTCCCAAAA 59.576 47.619 0.00 0.00 0.00 2.44
3809 4442 2.041891 TGTATTCCCACCGTCCCAAAAT 59.958 45.455 0.00 0.00 0.00 1.82
3810 4443 3.266254 TGTATTCCCACCGTCCCAAAATA 59.734 43.478 0.00 0.00 0.00 1.40
3811 4444 2.973983 TTCCCACCGTCCCAAAATAA 57.026 45.000 0.00 0.00 0.00 1.40
3812 4445 2.500392 TCCCACCGTCCCAAAATAAG 57.500 50.000 0.00 0.00 0.00 1.73
3813 4446 1.706305 TCCCACCGTCCCAAAATAAGT 59.294 47.619 0.00 0.00 0.00 2.24
3814 4447 1.816224 CCCACCGTCCCAAAATAAGTG 59.184 52.381 0.00 0.00 0.00 3.16
3815 4448 2.510613 CCACCGTCCCAAAATAAGTGT 58.489 47.619 0.00 0.00 0.00 3.55
3816 4449 2.486592 CCACCGTCCCAAAATAAGTGTC 59.513 50.000 0.00 0.00 0.00 3.67
3817 4450 3.408634 CACCGTCCCAAAATAAGTGTCT 58.591 45.455 0.00 0.00 0.00 3.41
3818 4451 3.435671 CACCGTCCCAAAATAAGTGTCTC 59.564 47.826 0.00 0.00 0.00 3.36
3819 4452 3.071892 ACCGTCCCAAAATAAGTGTCTCA 59.928 43.478 0.00 0.00 0.00 3.27
3820 4453 4.069304 CCGTCCCAAAATAAGTGTCTCAA 58.931 43.478 0.00 0.00 0.00 3.02
3821 4454 4.083484 CCGTCCCAAAATAAGTGTCTCAAC 60.083 45.833 0.00 0.00 0.00 3.18
3822 4455 4.755123 CGTCCCAAAATAAGTGTCTCAACT 59.245 41.667 0.00 0.00 0.00 3.16
3823 4456 5.238650 CGTCCCAAAATAAGTGTCTCAACTT 59.761 40.000 0.00 0.00 42.89 2.66
3824 4457 6.238648 CGTCCCAAAATAAGTGTCTCAACTTT 60.239 38.462 0.00 0.00 40.77 2.66
3825 4458 7.041644 CGTCCCAAAATAAGTGTCTCAACTTTA 60.042 37.037 0.00 0.00 40.77 1.85
3826 4459 8.290325 GTCCCAAAATAAGTGTCTCAACTTTAG 58.710 37.037 0.00 0.00 40.77 1.85
3827 4460 7.996644 TCCCAAAATAAGTGTCTCAACTTTAGT 59.003 33.333 0.00 0.00 40.77 2.24
3828 4461 9.280174 CCCAAAATAAGTGTCTCAACTTTAGTA 57.720 33.333 0.00 0.00 40.77 1.82
3853 4486 3.326880 AGAGACACTTATTTTGGGACGGT 59.673 43.478 0.00 0.00 0.00 4.83
3869 4502 4.220163 GGGACGGTGGGAGTATAAGATAAG 59.780 50.000 0.00 0.00 0.00 1.73
3916 4549 7.880623 TGTACCTCTTAGTTATTACTCCCTCT 58.119 38.462 0.00 0.00 35.78 3.69
3919 4552 7.880623 ACCTCTTAGTTATTACTCCCTCTGTA 58.119 38.462 0.00 0.00 35.78 2.74
3920 4553 8.342270 ACCTCTTAGTTATTACTCCCTCTGTAA 58.658 37.037 0.00 0.00 35.78 2.41
3921 4554 9.198475 CCTCTTAGTTATTACTCCCTCTGTAAA 57.802 37.037 0.00 0.00 35.78 2.01
3934 4567 8.425703 ACTCCCTCTGTAAAGAAATATAAGAGC 58.574 37.037 0.00 0.00 0.00 4.09
3935 4568 7.434492 TCCCTCTGTAAAGAAATATAAGAGCG 58.566 38.462 0.00 0.00 0.00 5.03
3954 4587 7.393841 AGAGCGTTTAGATCACTACTTTAGT 57.606 36.000 0.00 0.00 37.82 2.24
3969 4663 5.161943 ACTTTAGTGATCTAAACGCCCTT 57.838 39.130 0.00 0.00 40.05 3.95
3971 4665 6.885922 ACTTTAGTGATCTAAACGCCCTTAT 58.114 36.000 0.00 0.00 40.05 1.73
3973 4667 8.142551 ACTTTAGTGATCTAAACGCCCTTATAG 58.857 37.037 0.00 0.00 40.05 1.31
3974 4668 4.884247 AGTGATCTAAACGCCCTTATAGC 58.116 43.478 0.00 0.00 0.00 2.97
3975 4669 4.589374 AGTGATCTAAACGCCCTTATAGCT 59.411 41.667 0.00 0.00 0.00 3.32
3985 4679 8.549338 AAACGCCCTTATAGCTCTTATATTTC 57.451 34.615 0.00 0.00 0.00 2.17
3986 4680 7.483580 ACGCCCTTATAGCTCTTATATTTCT 57.516 36.000 0.00 0.00 0.00 2.52
3987 4681 7.908453 ACGCCCTTATAGCTCTTATATTTCTT 58.092 34.615 0.00 0.00 0.00 2.52
3988 4682 8.376270 ACGCCCTTATAGCTCTTATATTTCTTT 58.624 33.333 0.00 0.00 0.00 2.52
4049 4746 7.262048 TGCGGTGGATTTTAATAATCCTTTTC 58.738 34.615 20.52 12.74 45.01 2.29
4122 4819 8.380742 TCCTACTTCTGTCAGATATTTTTCCT 57.619 34.615 2.68 0.00 0.00 3.36
4297 5044 5.590259 GCTAATTGCTTTCTGATCCCTGTTA 59.410 40.000 0.00 0.00 38.95 2.41
4405 5155 4.684242 TGTAATTACACTTGACAGTCTGCG 59.316 41.667 14.35 0.00 0.00 5.18
4455 5205 5.008331 AGACCTACAGTTCTGTTGTCGATA 58.992 41.667 19.47 0.00 31.78 2.92
4456 5206 5.652891 AGACCTACAGTTCTGTTGTCGATAT 59.347 40.000 19.47 8.21 31.78 1.63
4464 5214 7.173218 ACAGTTCTGTTGTCGATATTGAATGTT 59.827 33.333 0.00 0.00 0.00 2.71
4475 5225 2.798976 TTGAATGTTGTCTGCTTGCC 57.201 45.000 0.00 0.00 0.00 4.52
4489 5239 2.159254 TGCTTGCCTCTTTTGTGAACAC 60.159 45.455 0.00 0.00 0.00 3.32
4490 5240 2.799562 GCTTGCCTCTTTTGTGAACACC 60.800 50.000 2.46 0.00 0.00 4.16
4560 5312 0.716108 GCGGACTGTCAAGACATTCG 59.284 55.000 10.38 12.40 40.56 3.34
4604 5356 5.083122 TGTGGCAATCTCCCATTTCTTAAA 58.917 37.500 0.00 0.00 34.34 1.52
4646 5398 2.266055 GTGGAGGGGACAAGCTCG 59.734 66.667 0.00 0.00 0.00 5.03
4745 5497 1.937108 GCAGCGATACATGTAGGGAGC 60.937 57.143 11.91 12.80 0.00 4.70
4791 5543 9.388506 CAGTTCTGGACATTGTTTAGATAATCT 57.611 33.333 5.21 0.00 0.00 2.40
5018 5846 1.705997 GGGTGTGAAGTGTGTCCCCT 61.706 60.000 0.00 0.00 0.00 4.79
5223 6052 0.654472 GCTTGCTTGTTGTCGTCGTG 60.654 55.000 0.00 0.00 0.00 4.35
5337 6166 6.498304 CGGAGATTTGTTTTCCCTTATCATG 58.502 40.000 0.00 0.00 0.00 3.07
5358 6187 3.662623 CTGCTCGTGCTGCATGTGC 62.663 63.158 31.16 31.16 39.86 4.57
5415 6251 4.506654 TCTCTGCTTGTTGTAACGAAACTC 59.493 41.667 0.00 0.00 0.00 3.01
5418 6254 3.311322 TGCTTGTTGTAACGAAACTCTGG 59.689 43.478 0.00 0.00 0.00 3.86
5435 6271 0.393448 TGGTACTTACGCTGGTTGCA 59.607 50.000 0.00 0.00 43.06 4.08
5536 6401 4.653868 TGTTAAATGTGGTACGGGATGTT 58.346 39.130 0.00 0.00 0.00 2.71
5637 6502 0.588252 CTTCACAGGCAAACCGACAG 59.412 55.000 0.00 0.00 42.76 3.51
5640 6505 0.249868 CACAGGCAAACCGACAGAGA 60.250 55.000 0.00 0.00 42.76 3.10
5651 6516 1.592400 CGACAGAGAAGGCCACCGTA 61.592 60.000 5.01 0.00 0.00 4.02
5856 6721 1.452145 GGCGTTTGTTGGCTCTGGAA 61.452 55.000 0.00 0.00 0.00 3.53
5857 6722 0.317854 GCGTTTGTTGGCTCTGGAAC 60.318 55.000 0.00 0.00 0.00 3.62
5858 6723 1.021202 CGTTTGTTGGCTCTGGAACA 58.979 50.000 0.00 0.00 0.00 3.18
5859 6724 1.403679 CGTTTGTTGGCTCTGGAACAA 59.596 47.619 0.00 0.00 39.67 2.83
5860 6725 2.159310 CGTTTGTTGGCTCTGGAACAAA 60.159 45.455 8.27 8.27 45.34 2.83
5862 6727 4.543590 TTTGTTGGCTCTGGAACAAAAA 57.456 36.364 9.53 0.00 44.84 1.94
5863 6728 3.518634 TGTTGGCTCTGGAACAAAAAC 57.481 42.857 0.00 0.00 38.70 2.43
5864 6729 2.828520 TGTTGGCTCTGGAACAAAAACA 59.171 40.909 0.00 0.00 38.70 2.83
5865 6730 3.119173 TGTTGGCTCTGGAACAAAAACAG 60.119 43.478 0.00 0.00 38.70 3.16
5866 6731 2.031120 TGGCTCTGGAACAAAAACAGG 58.969 47.619 0.00 0.00 38.70 4.00
5867 6732 2.031870 GGCTCTGGAACAAAAACAGGT 58.968 47.619 0.00 0.00 38.70 4.00
5868 6733 2.034685 GGCTCTGGAACAAAAACAGGTC 59.965 50.000 0.00 0.00 38.70 3.85
5869 6734 2.952310 GCTCTGGAACAAAAACAGGTCT 59.048 45.455 0.00 0.00 38.70 3.85
5870 6735 3.381590 GCTCTGGAACAAAAACAGGTCTT 59.618 43.478 0.00 0.00 38.70 3.01
5871 6736 4.142160 GCTCTGGAACAAAAACAGGTCTTT 60.142 41.667 0.00 0.00 38.70 2.52
5872 6737 5.323371 TCTGGAACAAAAACAGGTCTTTG 57.677 39.130 0.00 0.00 38.70 2.77
5873 6738 4.770010 TCTGGAACAAAAACAGGTCTTTGT 59.230 37.500 0.00 0.00 45.35 2.83
5874 6739 5.946972 TCTGGAACAAAAACAGGTCTTTGTA 59.053 36.000 4.46 0.00 43.25 2.41
5875 6740 6.605594 TCTGGAACAAAAACAGGTCTTTGTAT 59.394 34.615 4.46 0.00 43.25 2.29
5876 6741 6.801575 TGGAACAAAAACAGGTCTTTGTATC 58.198 36.000 4.46 5.18 43.25 2.24
5877 6742 6.605594 TGGAACAAAAACAGGTCTTTGTATCT 59.394 34.615 4.46 0.00 43.25 1.98
5878 6743 7.123547 TGGAACAAAAACAGGTCTTTGTATCTT 59.876 33.333 4.46 0.00 43.25 2.40
5879 6744 7.648112 GGAACAAAAACAGGTCTTTGTATCTTC 59.352 37.037 4.46 0.00 43.25 2.87
5880 6745 7.639113 ACAAAAACAGGTCTTTGTATCTTCA 57.361 32.000 2.21 0.00 42.47 3.02
5881 6746 8.062065 ACAAAAACAGGTCTTTGTATCTTCAA 57.938 30.769 2.21 0.00 42.47 2.69
5882 6747 8.190784 ACAAAAACAGGTCTTTGTATCTTCAAG 58.809 33.333 2.21 0.00 42.47 3.02
5883 6748 8.405531 CAAAAACAGGTCTTTGTATCTTCAAGA 58.594 33.333 0.00 0.00 0.00 3.02
5884 6749 8.519799 AAAACAGGTCTTTGTATCTTCAAGAA 57.480 30.769 0.00 0.00 0.00 2.52
5885 6750 8.519799 AAACAGGTCTTTGTATCTTCAAGAAA 57.480 30.769 0.00 0.00 0.00 2.52
5886 6751 8.519799 AACAGGTCTTTGTATCTTCAAGAAAA 57.480 30.769 0.00 0.00 0.00 2.29
5887 6752 8.519799 ACAGGTCTTTGTATCTTCAAGAAAAA 57.480 30.769 0.00 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 5.648092 ACAATGCTGTAATACTGGTTTCTCC 59.352 40.000 0.00 0.00 32.54 3.71
112 121 1.303236 TTGGTGGGAATGAGGTGCG 60.303 57.895 0.00 0.00 0.00 5.34
127 136 3.614870 GCAACCAACTTTGATAGCCTTGG 60.615 47.826 0.00 0.00 36.53 3.61
134 143 6.767524 ATAATTCCGCAACCAACTTTGATA 57.232 33.333 0.00 0.00 0.00 2.15
164 174 5.591099 TGCTTTGGTGATTTTCTTTCACTC 58.409 37.500 4.07 0.00 42.48 3.51
181 191 3.218398 GTTTCGTCTCGTCAATGCTTTG 58.782 45.455 5.99 5.99 0.00 2.77
239 249 2.434185 TGACGTTCCCGCAGATGC 60.434 61.111 0.00 0.00 37.70 3.91
260 282 7.500892 TCTTGTCAATTTGTTACTTAAGCTGGA 59.499 33.333 1.29 0.00 0.00 3.86
261 283 7.648142 TCTTGTCAATTTGTTACTTAAGCTGG 58.352 34.615 1.29 0.00 0.00 4.85
262 284 9.121517 CATCTTGTCAATTTGTTACTTAAGCTG 57.878 33.333 1.29 0.00 0.00 4.24
263 285 9.066892 TCATCTTGTCAATTTGTTACTTAAGCT 57.933 29.630 1.29 0.00 0.00 3.74
264 286 9.677567 TTCATCTTGTCAATTTGTTACTTAAGC 57.322 29.630 1.29 0.00 0.00 3.09
266 288 9.677567 GCTTCATCTTGTCAATTTGTTACTTAA 57.322 29.630 0.00 0.00 0.00 1.85
267 289 8.845227 TGCTTCATCTTGTCAATTTGTTACTTA 58.155 29.630 0.00 0.00 0.00 2.24
268 290 7.649306 GTGCTTCATCTTGTCAATTTGTTACTT 59.351 33.333 0.00 0.00 0.00 2.24
269 291 7.141363 GTGCTTCATCTTGTCAATTTGTTACT 58.859 34.615 0.00 0.00 0.00 2.24
270 292 6.363357 GGTGCTTCATCTTGTCAATTTGTTAC 59.637 38.462 0.00 0.00 0.00 2.50
271 293 6.265196 AGGTGCTTCATCTTGTCAATTTGTTA 59.735 34.615 0.00 0.00 0.00 2.41
312 334 8.887264 AGACTACTAGGAGAGAAAAGAATGAA 57.113 34.615 9.61 0.00 0.00 2.57
320 342 9.118300 CGGTTTAATAGACTACTAGGAGAGAAA 57.882 37.037 9.61 0.00 31.78 2.52
333 355 8.021973 CGAATGATAGCTACGGTTTAATAGACT 58.978 37.037 0.00 0.00 0.00 3.24
334 356 7.806960 ACGAATGATAGCTACGGTTTAATAGAC 59.193 37.037 0.00 0.00 0.00 2.59
346 370 8.575565 TTATGTCTGAAACGAATGATAGCTAC 57.424 34.615 0.00 0.00 0.00 3.58
376 400 4.979943 TCTGTTTGACAATGTTGAGCAA 57.020 36.364 0.00 1.49 0.00 3.91
398 422 5.766174 TGGGCGTTTGAGTAATAGTTTTTCT 59.234 36.000 0.00 0.00 0.00 2.52
399 423 6.004408 TGGGCGTTTGAGTAATAGTTTTTC 57.996 37.500 0.00 0.00 0.00 2.29
400 424 6.584185 ATGGGCGTTTGAGTAATAGTTTTT 57.416 33.333 0.00 0.00 0.00 1.94
418 442 3.915437 TTGAACTTTCGAGAAATGGGC 57.085 42.857 0.00 0.00 0.00 5.36
441 465 1.005450 TGGGGTAACTTGGAGAATGGC 59.995 52.381 0.00 0.00 0.00 4.40
450 474 4.003648 CAGCTTCTAAGTGGGGTAACTTG 58.996 47.826 0.00 0.00 40.58 3.16
522 550 5.664457 AGCCAACCTTTTTCTTCTTCTTTG 58.336 37.500 0.00 0.00 0.00 2.77
529 557 4.309933 CCATCAAGCCAACCTTTTTCTTC 58.690 43.478 0.00 0.00 0.00 2.87
532 560 2.871637 GCCCATCAAGCCAACCTTTTTC 60.872 50.000 0.00 0.00 0.00 2.29
598 630 3.699894 CTCTCTGCCCTGCCGTGT 61.700 66.667 0.00 0.00 0.00 4.49
622 676 0.035056 CGTCTGGGGGATCTTTGCTT 60.035 55.000 0.00 0.00 0.00 3.91
641 695 8.330302 TCTTGTTTTACTCGTTTTTGTATTGC 57.670 30.769 0.00 0.00 0.00 3.56
648 702 6.034577 GCTTTGCTCTTGTTTTACTCGTTTTT 59.965 34.615 0.00 0.00 0.00 1.94
682 736 4.096532 CGCCTCCTTTCCTATTTCCTTTTC 59.903 45.833 0.00 0.00 0.00 2.29
687 741 1.309950 GCGCCTCCTTTCCTATTTCC 58.690 55.000 0.00 0.00 0.00 3.13
688 742 1.943340 CTGCGCCTCCTTTCCTATTTC 59.057 52.381 4.18 0.00 0.00 2.17
689 743 1.559682 TCTGCGCCTCCTTTCCTATTT 59.440 47.619 4.18 0.00 0.00 1.40
691 745 1.204146 TTCTGCGCCTCCTTTCCTAT 58.796 50.000 4.18 0.00 0.00 2.57
692 746 0.981183 TTTCTGCGCCTCCTTTCCTA 59.019 50.000 4.18 0.00 0.00 2.94
699 755 2.121538 GGGGATTTTCTGCGCCTCC 61.122 63.158 4.18 1.17 34.57 4.30
786 844 2.009774 CAGTGTAGTTACAGCATGGGC 58.990 52.381 0.00 0.00 43.62 5.36
812 870 0.892358 TGAGGCGTGGTACGAACTCT 60.892 55.000 19.42 7.12 46.05 3.24
813 871 0.172803 ATGAGGCGTGGTACGAACTC 59.827 55.000 5.44 11.44 46.05 3.01
826 884 0.399806 AGGAGGAGGAAGGATGAGGC 60.400 60.000 0.00 0.00 0.00 4.70
897 1218 1.677637 GCCCTCTACCTCTTCCACCG 61.678 65.000 0.00 0.00 0.00 4.94
898 1219 1.677637 CGCCCTCTACCTCTTCCACC 61.678 65.000 0.00 0.00 0.00 4.61
900 1221 2.058595 GCGCCCTCTACCTCTTCCA 61.059 63.158 0.00 0.00 0.00 3.53
1182 1512 2.800581 CGAGGACGACGAGGACGAG 61.801 68.421 0.00 0.00 41.06 4.18
1344 1677 0.547954 AGAAGGACTCCCCCTGGAAC 60.548 60.000 0.00 0.00 41.17 3.62
1770 2103 2.738147 CCTTCGTAGACGGCTGTTG 58.262 57.895 0.00 0.00 39.67 3.33
1779 2112 1.651240 CGTCCGGAAGCCTTCGTAGA 61.651 60.000 5.23 0.00 0.00 2.59
1845 2178 1.926511 GCAGCCTCGGTGACATTTGG 61.927 60.000 0.00 0.00 32.22 3.28
2207 2540 9.847224 TGAAATCTTAGAGTGAACTTAGGTTTT 57.153 29.630 0.00 0.00 32.49 2.43
2227 2560 5.065731 CCTATCAGAGGCACAAAGTGAAATC 59.934 44.000 0.58 0.00 38.96 2.17
2231 2564 3.616956 CCTATCAGAGGCACAAAGTGA 57.383 47.619 0.58 0.00 38.96 3.41
2324 2660 3.849563 TTATCCCAGAATTACCCCACG 57.150 47.619 0.00 0.00 0.00 4.94
2328 2664 7.127339 TCCTAGCATATTATCCCAGAATTACCC 59.873 40.741 0.00 0.00 0.00 3.69
2352 2688 6.631016 TGTCATAGTGATCAGTAACAAGTCC 58.369 40.000 14.15 0.48 0.00 3.85
2353 2689 8.709386 AATGTCATAGTGATCAGTAACAAGTC 57.291 34.615 14.15 4.34 0.00 3.01
2366 2702 9.261180 GCTAGCAAATACTAAATGTCATAGTGA 57.739 33.333 10.63 0.00 35.34 3.41
2367 2703 9.265901 AGCTAGCAAATACTAAATGTCATAGTG 57.734 33.333 18.83 0.00 35.34 2.74
2369 2705 8.226448 GCAGCTAGCAAATACTAAATGTCATAG 58.774 37.037 18.83 0.00 44.79 2.23
2372 2720 6.363577 GCAGCTAGCAAATACTAAATGTCA 57.636 37.500 18.83 0.00 44.79 3.58
2386 2734 0.251354 CCTGAAAGAGGCAGCTAGCA 59.749 55.000 18.83 0.00 40.88 3.49
2398 2746 9.846248 CTGAAAAACTAACCATTATCCTGAAAG 57.154 33.333 0.00 0.00 0.00 2.62
2410 2758 8.918202 ATCAATGTAGACTGAAAAACTAACCA 57.082 30.769 0.00 0.00 0.00 3.67
2424 2772 8.834465 ACAAATCATCTGCTAATCAATGTAGAC 58.166 33.333 0.00 0.00 0.00 2.59
2549 2899 9.353431 TGGATACTTTATACATGTGAAATGCAT 57.647 29.630 9.11 0.00 37.61 3.96
2580 2930 0.110373 GACCGGCGCAAACTTAAGTG 60.110 55.000 10.83 0.00 0.00 3.16
2593 2943 0.169009 GCTTGATTCAACAGACCGGC 59.831 55.000 0.00 0.00 0.00 6.13
2656 3006 1.406539 CAATTGCATGCCAGTCTACCC 59.593 52.381 16.68 0.00 0.00 3.69
2659 3009 2.093890 CCACAATTGCATGCCAGTCTA 58.906 47.619 16.68 0.00 0.00 2.59
2734 3084 4.696877 TGTTGAGCTGTGATCCATACTTTG 59.303 41.667 0.00 0.00 0.00 2.77
2824 3176 7.148103 TGCAATTCGTTTGAGATGGATAATCAA 60.148 33.333 5.27 0.00 37.53 2.57
2888 3487 6.205784 TCTATATTTGCCAATTTTAGCGTGC 58.794 36.000 0.00 0.00 0.00 5.34
2935 3534 8.023128 GTGCAGTTTCATCAAAAGATAGCTTTA 58.977 33.333 6.37 0.00 43.32 1.85
2958 3557 6.966021 TGTAAGAAGTTTCCAAATACAGTGC 58.034 36.000 0.00 0.00 0.00 4.40
2961 3560 8.081633 TGCAATGTAAGAAGTTTCCAAATACAG 58.918 33.333 0.00 0.00 0.00 2.74
2969 3568 4.503741 TGCTGCAATGTAAGAAGTTTCC 57.496 40.909 0.00 0.00 0.00 3.13
3209 3808 8.749841 AGCAATAAGATAAGCTATGTAACTCG 57.250 34.615 0.00 0.00 35.19 4.18
3332 3931 5.381757 ACATGAGACCACTCCTCTAGATAC 58.618 45.833 0.00 0.00 41.99 2.24
3543 4142 3.244078 ACATCAACCGCTGAGTTAACAGA 60.244 43.478 8.61 0.00 39.94 3.41
3584 4183 7.491048 ACCTTTGACAACAAATTACACATTGAC 59.509 33.333 0.00 0.00 43.64 3.18
3587 4186 6.257630 GCACCTTTGACAACAAATTACACATT 59.742 34.615 0.00 0.00 43.64 2.71
3717 4316 7.224297 GGATGGAGCTTATATTTGTGGACTTA 58.776 38.462 0.00 0.00 0.00 2.24
3792 4425 2.108601 ACTTATTTTGGGACGGTGGGAA 59.891 45.455 0.00 0.00 0.00 3.97
3797 4430 3.071892 TGAGACACTTATTTTGGGACGGT 59.928 43.478 0.00 0.00 0.00 4.83
3800 4433 6.635030 AAGTTGAGACACTTATTTTGGGAC 57.365 37.500 0.00 0.00 35.10 4.46
3801 4434 7.996644 ACTAAAGTTGAGACACTTATTTTGGGA 59.003 33.333 0.00 0.00 35.87 4.37
3802 4435 8.166422 ACTAAAGTTGAGACACTTATTTTGGG 57.834 34.615 0.00 0.00 35.87 4.12
3808 4441 9.915629 CTCTTGTACTAAAGTTGAGACACTTAT 57.084 33.333 0.00 0.00 35.87 1.73
3809 4442 9.128404 TCTCTTGTACTAAAGTTGAGACACTTA 57.872 33.333 0.00 0.00 35.87 2.24
3810 4443 7.921745 GTCTCTTGTACTAAAGTTGAGACACTT 59.078 37.037 18.96 0.00 44.60 3.16
3811 4444 7.427214 GTCTCTTGTACTAAAGTTGAGACACT 58.573 38.462 18.96 0.00 44.60 3.55
3812 4445 7.626144 GTCTCTTGTACTAAAGTTGAGACAC 57.374 40.000 18.96 1.85 44.60 3.67
3814 4447 7.427214 AGTGTCTCTTGTACTAAAGTTGAGAC 58.573 38.462 18.01 18.01 45.11 3.36
3815 4448 7.584122 AGTGTCTCTTGTACTAAAGTTGAGA 57.416 36.000 0.00 0.00 0.00 3.27
3816 4449 9.915629 ATAAGTGTCTCTTGTACTAAAGTTGAG 57.084 33.333 0.00 0.00 37.56 3.02
3822 4455 9.280174 CCCAAAATAAGTGTCTCTTGTACTAAA 57.720 33.333 0.00 0.00 37.56 1.85
3823 4456 8.653191 TCCCAAAATAAGTGTCTCTTGTACTAA 58.347 33.333 0.00 0.00 37.56 2.24
3824 4457 8.092687 GTCCCAAAATAAGTGTCTCTTGTACTA 58.907 37.037 0.00 0.00 37.56 1.82
3825 4458 6.935208 GTCCCAAAATAAGTGTCTCTTGTACT 59.065 38.462 0.00 0.00 37.56 2.73
3826 4459 6.128634 CGTCCCAAAATAAGTGTCTCTTGTAC 60.129 42.308 0.00 0.00 37.56 2.90
3827 4460 5.929992 CGTCCCAAAATAAGTGTCTCTTGTA 59.070 40.000 0.00 0.00 37.56 2.41
3828 4461 4.755123 CGTCCCAAAATAAGTGTCTCTTGT 59.245 41.667 0.00 0.00 37.56 3.16
3829 4462 4.154195 CCGTCCCAAAATAAGTGTCTCTTG 59.846 45.833 0.00 0.00 37.56 3.02
3830 4463 4.202430 ACCGTCCCAAAATAAGTGTCTCTT 60.202 41.667 0.00 0.00 39.89 2.85
3831 4464 3.326880 ACCGTCCCAAAATAAGTGTCTCT 59.673 43.478 0.00 0.00 0.00 3.10
3853 4486 5.131977 TGCCAAAGCTTATCTTATACTCCCA 59.868 40.000 0.00 0.00 40.80 4.37
3893 4526 7.880623 ACAGAGGGAGTAATAACTAAGAGGTA 58.119 38.462 0.00 0.00 35.56 3.08
3944 4577 5.421374 AGGGCGTTTAGATCACTAAAGTAGT 59.579 40.000 0.00 0.00 45.42 2.73
3945 4578 5.903810 AGGGCGTTTAGATCACTAAAGTAG 58.096 41.667 0.00 0.00 45.42 2.57
3946 4579 5.927281 AGGGCGTTTAGATCACTAAAGTA 57.073 39.130 0.00 0.00 45.42 2.24
3947 4580 4.820894 AGGGCGTTTAGATCACTAAAGT 57.179 40.909 0.00 0.00 45.42 2.66
3948 4581 7.116519 GCTATAAGGGCGTTTAGATCACTAAAG 59.883 40.741 0.00 0.00 45.42 1.85
3949 4582 6.927381 GCTATAAGGGCGTTTAGATCACTAAA 59.073 38.462 0.00 0.00 43.52 1.85
3951 4584 5.773680 AGCTATAAGGGCGTTTAGATCACTA 59.226 40.000 0.00 0.00 34.52 2.74
3952 4585 4.589374 AGCTATAAGGGCGTTTAGATCACT 59.411 41.667 0.00 0.00 34.52 3.41
3954 4587 4.833380 AGAGCTATAAGGGCGTTTAGATCA 59.167 41.667 19.36 0.00 31.26 2.92
3955 4588 5.394224 AGAGCTATAAGGGCGTTTAGATC 57.606 43.478 14.03 14.03 34.52 2.75
3956 4589 5.810080 AAGAGCTATAAGGGCGTTTAGAT 57.190 39.130 0.00 0.00 34.52 1.98
3958 4591 9.654663 AAATATAAGAGCTATAAGGGCGTTTAG 57.345 33.333 0.00 1.88 34.52 1.85
3959 4592 9.649167 GAAATATAAGAGCTATAAGGGCGTTTA 57.351 33.333 0.00 0.00 34.52 2.01
3961 4594 7.908453 AGAAATATAAGAGCTATAAGGGCGTT 58.092 34.615 0.00 0.00 34.52 4.84
3971 4665 9.656323 TCCCTCTGTAAAGAAATATAAGAGCTA 57.344 33.333 0.00 0.00 0.00 3.32
3973 4667 8.425703 ACTCCCTCTGTAAAGAAATATAAGAGC 58.574 37.037 0.00 0.00 0.00 4.09
3985 4679 9.274206 GCCTTAATAAATACTCCCTCTGTAAAG 57.726 37.037 0.00 0.00 0.00 1.85
3986 4680 8.999895 AGCCTTAATAAATACTCCCTCTGTAAA 58.000 33.333 0.00 0.00 0.00 2.01
3987 4681 8.562949 AGCCTTAATAAATACTCCCTCTGTAA 57.437 34.615 0.00 0.00 0.00 2.41
3988 4682 8.011290 AGAGCCTTAATAAATACTCCCTCTGTA 58.989 37.037 0.00 0.00 0.00 2.74
3991 4685 6.847036 ACAGAGCCTTAATAAATACTCCCTCT 59.153 38.462 0.00 0.00 0.00 3.69
4001 4695 6.037830 GCAATACCGAACAGAGCCTTAATAAA 59.962 38.462 0.00 0.00 0.00 1.40
4049 4746 1.068541 GGGCAAAAGCTGGTTAAGACG 60.069 52.381 0.00 0.00 0.00 4.18
4184 4929 9.293404 ACTATGTCATACGACCTTAATAAGCTA 57.707 33.333 0.00 0.00 41.85 3.32
4185 4930 8.179509 ACTATGTCATACGACCTTAATAAGCT 57.820 34.615 0.00 0.00 41.85 3.74
4186 4931 8.298140 AGACTATGTCATACGACCTTAATAAGC 58.702 37.037 0.00 0.00 41.85 3.09
4187 4932 9.613957 CAGACTATGTCATACGACCTTAATAAG 57.386 37.037 0.00 0.00 41.85 1.73
4188 4933 9.128404 ACAGACTATGTCATACGACCTTAATAA 57.872 33.333 0.00 0.00 37.75 1.40
4189 4934 8.687292 ACAGACTATGTCATACGACCTTAATA 57.313 34.615 0.00 0.00 37.75 0.98
4190 4935 7.584122 ACAGACTATGTCATACGACCTTAAT 57.416 36.000 0.00 0.00 37.75 1.40
4297 5044 7.255590 GCTGCCCACTTGTCATTATGTATTTAT 60.256 37.037 0.00 0.00 0.00 1.40
4405 5155 0.102300 AACGCAGGCCTGTTTTTCAC 59.898 50.000 32.81 13.99 0.00 3.18
4455 5205 2.895404 AGGCAAGCAGACAACATTCAAT 59.105 40.909 0.00 0.00 0.00 2.57
4456 5206 2.294233 GAGGCAAGCAGACAACATTCAA 59.706 45.455 0.00 0.00 0.00 2.69
4464 5214 1.677576 CACAAAAGAGGCAAGCAGACA 59.322 47.619 0.00 0.00 0.00 3.41
4475 5225 2.023673 TGCCAGGTGTTCACAAAAGAG 58.976 47.619 5.32 0.00 0.00 2.85
4489 5239 6.299141 AGTGTAATTACATCCTATTGCCAGG 58.701 40.000 20.72 0.00 38.63 4.45
4490 5240 7.498900 TCAAGTGTAATTACATCCTATTGCCAG 59.501 37.037 20.72 3.28 38.63 4.85
4560 5312 5.911280 CACAAGAAACTCATTGACATGACAC 59.089 40.000 0.00 0.00 34.22 3.67
4604 5356 9.045745 ACCTGGGTCAATAAAATTTATGACAAT 57.954 29.630 22.61 8.77 43.02 2.71
4624 5376 2.531685 TTGTCCCCTCCACCTGGG 60.532 66.667 0.00 0.00 44.19 4.45
4646 5398 0.391130 TCGCAAGCTCATACACCACC 60.391 55.000 0.00 0.00 37.18 4.61
4745 5497 5.308825 ACTGAACCAAAGGTCATAGAAGTG 58.691 41.667 0.00 0.00 33.12 3.16
4791 5543 7.078851 CGTTGCAATGTATGTAAGGTTAACAA 58.921 34.615 10.65 0.00 35.58 2.83
4874 5626 4.248859 CTGATCTACCACTGTGTTTGGAG 58.751 47.826 7.08 0.00 37.58 3.86
5018 5846 0.536687 ATCGGTCGAGCGGATTAGGA 60.537 55.000 33.60 15.39 34.04 2.94
5104 5933 3.064324 CCGCAGGCAAAAGAGGGG 61.064 66.667 0.00 0.00 46.14 4.79
5337 6166 2.435586 ATGCAGCACGAGCAGGTC 60.436 61.111 7.77 0.00 46.36 3.85
5358 6187 2.107950 TCCAGGATTAACAACGCAGG 57.892 50.000 0.00 0.00 0.00 4.85
5415 6251 1.076332 GCAACCAGCGTAAGTACCAG 58.924 55.000 0.00 0.00 41.68 4.00
5435 6271 1.484038 GCTCAGAGTCAGAGGTCCAT 58.516 55.000 13.80 0.00 33.72 3.41
5536 6401 0.837691 ACACACCTCAGCAGGATCCA 60.838 55.000 15.82 0.00 43.65 3.41
5637 6502 2.582978 GGGTACGGTGGCCTTCTC 59.417 66.667 3.32 0.00 0.00 2.87
5835 6700 1.576421 CAGAGCCAACAAACGCCTC 59.424 57.895 0.00 0.00 0.00 4.70
5856 6721 7.639113 TGAAGATACAAAGACCTGTTTTTGT 57.361 32.000 18.91 18.91 45.73 2.83
5857 6722 8.405531 TCTTGAAGATACAAAGACCTGTTTTTG 58.594 33.333 10.67 10.67 39.62 2.44
5858 6723 8.519799 TCTTGAAGATACAAAGACCTGTTTTT 57.480 30.769 0.00 0.00 0.00 1.94
5859 6724 8.519799 TTCTTGAAGATACAAAGACCTGTTTT 57.480 30.769 0.00 0.00 0.00 2.43
5860 6725 8.519799 TTTCTTGAAGATACAAAGACCTGTTT 57.480 30.769 0.00 0.00 0.00 2.83
5861 6726 8.519799 TTTTCTTGAAGATACAAAGACCTGTT 57.480 30.769 0.00 0.00 0.00 3.16
5862 6727 8.519799 TTTTTCTTGAAGATACAAAGACCTGT 57.480 30.769 0.00 0.00 0.00 4.00


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

AutoCloner maintained by Alex Coulton.