Multiple sequence alignment - TraesCS2B01G150300

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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 TraesCS2B01G150300 chr2B 100.000 3434 0 0 1 3434 116849112 116845679 0.000000e+00 6342
1 TraesCS2B01G150300 chr2B 91.351 555 41 3 2580 3128 53452726 53452173 0.000000e+00 752
2 TraesCS2B01G150300 chr2B 90.317 568 46 5 2569 3128 359867866 359868432 0.000000e+00 736
3 TraesCS2B01G150300 chr2B 81.127 408 75 2 2028 2434 615578808 615579214 3.300000e-85 326
4 TraesCS2B01G150300 chr2B 88.770 187 20 1 977 1162 669469625 669469439 9.590000e-56 228
5 TraesCS2B01G150300 chr2A 94.451 1658 62 4 867 2521 75656672 75655042 0.000000e+00 2525
6 TraesCS2B01G150300 chr2A 85.992 514 40 12 218 716 75657159 75656663 3.930000e-144 521
7 TraesCS2B01G150300 chr2A 81.127 408 75 2 2028 2434 667943208 667943614 3.300000e-85 326
8 TraesCS2B01G150300 chr2A 73.623 944 192 43 1016 1935 667942235 667943145 9.250000e-81 311
9 TraesCS2B01G150300 chr2A 79.635 329 58 8 2035 2359 667965277 667965600 9.590000e-56 228
10 TraesCS2B01G150300 chr2D 94.033 1659 52 7 867 2521 75760945 75759330 0.000000e+00 2471
11 TraesCS2B01G150300 chr2D 92.946 1602 72 10 867 2460 75674753 75676321 0.000000e+00 2294
12 TraesCS2B01G150300 chr2D 96.279 860 25 2 2580 3434 434927565 434928422 0.000000e+00 1404
13 TraesCS2B01G150300 chr2D 90.932 397 33 3 2 397 75761626 75761232 6.530000e-147 531
14 TraesCS2B01G150300 chr2D 74.866 935 182 40 1014 1930 522897794 522898693 3.240000e-100 375
15 TraesCS2B01G150300 chr2D 81.553 412 72 4 2025 2434 522630697 522631106 1.530000e-88 337
16 TraesCS2B01G150300 chr2D 72.959 943 200 42 1016 1935 522629727 522630637 9.390000e-71 278
17 TraesCS2B01G150300 chr6B 98.030 863 15 2 2571 3433 155478634 155477774 0.000000e+00 1498
18 TraesCS2B01G150300 chr6B 93.421 152 10 0 716 867 659210814 659210663 3.450000e-55 226
19 TraesCS2B01G150300 chr4A 95.255 864 25 6 2580 3433 728975003 728975860 0.000000e+00 1354
20 TraesCS2B01G150300 chr3A 94.240 868 44 5 2573 3434 486354490 486355357 0.000000e+00 1321
21 TraesCS2B01G150300 chr3A 93.968 862 45 3 2580 3434 42040890 42041751 0.000000e+00 1297
22 TraesCS2B01G150300 chr3A 92.258 155 11 1 716 870 568452786 568452633 5.770000e-53 219
23 TraesCS2B01G150300 chr7A 94.200 862 42 4 2580 3434 541485 542345 0.000000e+00 1308
24 TraesCS2B01G150300 chr7A 98.089 157 2 1 714 870 376625331 376625176 4.370000e-69 272
25 TraesCS2B01G150300 chr4D 94.200 862 43 3 2580 3434 418512733 418511872 0.000000e+00 1308
26 TraesCS2B01G150300 chr1B 93.155 862 52 3 2580 3434 437561107 437561968 0.000000e+00 1258
27 TraesCS2B01G150300 chr1B 92.126 127 10 0 716 842 510985966 510986092 2.720000e-41 180
28 TraesCS2B01G150300 chr6D 92.691 862 50 6 2580 3434 87137831 87138686 0.000000e+00 1230
29 TraesCS2B01G150300 chr6D 92.053 151 12 0 717 867 354403503 354403653 2.680000e-51 213
30 TraesCS2B01G150300 chr5B 92.424 396 27 3 2569 2963 629274577 629274184 2.310000e-156 562
31 TraesCS2B01G150300 chr5B 91.919 396 29 3 2569 2963 629357147 629356754 5.010000e-153 551
32 TraesCS2B01G150300 chr5B 90.397 302 27 2 2576 2877 283954507 283954208 2.480000e-106 396
33 TraesCS2B01G150300 chr7D 74.736 1421 253 75 1016 2395 573987030 573988385 3.900000e-149 538
34 TraesCS2B01G150300 chr7B 74.595 1421 258 75 1016 2395 633251938 633253296 2.350000e-146 529
35 TraesCS2B01G150300 chr5D 81.304 460 49 16 1 430 65903889 65903437 4.250000e-89 339
36 TraesCS2B01G150300 chr3D 100.000 151 0 0 716 866 183740623 183740773 2.610000e-71 279
37 TraesCS2B01G150300 chr5A 79.054 444 56 20 1 430 55161786 55161366 1.570000e-68 270
38 TraesCS2B01G150300 chr5A 92.810 153 11 0 714 866 688965488 688965336 4.460000e-54 222
39 TraesCS2B01G150300 chr1D 96.078 153 6 0 716 868 460733736 460733888 2.050000e-62 250
40 TraesCS2B01G150300 chr6A 95.425 153 5 2 715 866 107221587 107221436 3.420000e-60 243


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 TraesCS2B01G150300 chr2B 116845679 116849112 3433 True 6342.0 6342 100.0000 1 3434 1 chr2B.!!$R2 3433
1 TraesCS2B01G150300 chr2B 53452173 53452726 553 True 752.0 752 91.3510 2580 3128 1 chr2B.!!$R1 548
2 TraesCS2B01G150300 chr2B 359867866 359868432 566 False 736.0 736 90.3170 2569 3128 1 chr2B.!!$F1 559
3 TraesCS2B01G150300 chr2A 75655042 75657159 2117 True 1523.0 2525 90.2215 218 2521 2 chr2A.!!$R1 2303
4 TraesCS2B01G150300 chr2A 667942235 667943614 1379 False 318.5 326 77.3750 1016 2434 2 chr2A.!!$F2 1418
5 TraesCS2B01G150300 chr2D 75674753 75676321 1568 False 2294.0 2294 92.9460 867 2460 1 chr2D.!!$F1 1593
6 TraesCS2B01G150300 chr2D 75759330 75761626 2296 True 1501.0 2471 92.4825 2 2521 2 chr2D.!!$R1 2519
7 TraesCS2B01G150300 chr2D 434927565 434928422 857 False 1404.0 1404 96.2790 2580 3434 1 chr2D.!!$F2 854
8 TraesCS2B01G150300 chr2D 522897794 522898693 899 False 375.0 375 74.8660 1014 1930 1 chr2D.!!$F3 916
9 TraesCS2B01G150300 chr2D 522629727 522631106 1379 False 307.5 337 77.2560 1016 2434 2 chr2D.!!$F4 1418
10 TraesCS2B01G150300 chr6B 155477774 155478634 860 True 1498.0 1498 98.0300 2571 3433 1 chr6B.!!$R1 862
11 TraesCS2B01G150300 chr4A 728975003 728975860 857 False 1354.0 1354 95.2550 2580 3433 1 chr4A.!!$F1 853
12 TraesCS2B01G150300 chr3A 486354490 486355357 867 False 1321.0 1321 94.2400 2573 3434 1 chr3A.!!$F2 861
13 TraesCS2B01G150300 chr3A 42040890 42041751 861 False 1297.0 1297 93.9680 2580 3434 1 chr3A.!!$F1 854
14 TraesCS2B01G150300 chr7A 541485 542345 860 False 1308.0 1308 94.2000 2580 3434 1 chr7A.!!$F1 854
15 TraesCS2B01G150300 chr4D 418511872 418512733 861 True 1308.0 1308 94.2000 2580 3434 1 chr4D.!!$R1 854
16 TraesCS2B01G150300 chr1B 437561107 437561968 861 False 1258.0 1258 93.1550 2580 3434 1 chr1B.!!$F1 854
17 TraesCS2B01G150300 chr6D 87137831 87138686 855 False 1230.0 1230 92.6910 2580 3434 1 chr6D.!!$F1 854
18 TraesCS2B01G150300 chr7D 573987030 573988385 1355 False 538.0 538 74.7360 1016 2395 1 chr7D.!!$F1 1379
19 TraesCS2B01G150300 chr7B 633251938 633253296 1358 False 529.0 529 74.5950 1016 2395 1 chr7B.!!$F1 1379

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
807 953 0.100503 AACAGTTGTCTGCAAACCGC 59.899 50.0 0.0 0.0 44.77 5.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2538 2735 0.243907 CGAGTCAAGGACGGTCATGT 59.756 55.0 10.76 0.0 37.67 3.21 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 1.463674 GGGCAAGGGTGTTCACTATG 58.536 55.000 2.98 1.98 0.00 2.23
22 23 2.290323 GGCAAGGGTGTTCACTATGTCT 60.290 50.000 2.98 0.00 0.00 3.41
29 30 2.939103 GTGTTCACTATGTCTGATGCCC 59.061 50.000 0.00 0.00 0.00 5.36
65 66 8.422973 TTTCAACTCAAATTTGGAGTGATTTG 57.577 30.769 17.90 13.29 44.50 2.32
81 82 5.687285 AGTGATTTGAGATTTGTTTTGTCGC 59.313 36.000 0.00 0.00 0.00 5.19
86 87 1.944024 AGATTTGTTTTGTCGCGTGGA 59.056 42.857 5.77 0.00 0.00 4.02
88 89 1.088306 TTTGTTTTGTCGCGTGGACT 58.912 45.000 5.77 0.00 46.24 3.85
96 97 3.853831 TGTCGCGTGGACTTTATCTTA 57.146 42.857 5.77 0.00 46.24 2.10
97 98 4.177165 TGTCGCGTGGACTTTATCTTAA 57.823 40.909 5.77 0.00 46.24 1.85
110 111 6.166982 ACTTTATCTTAAGCGAGCTTTGAGT 58.833 36.000 15.90 6.99 37.47 3.41
151 152 7.834068 TTCTTAATGGAGAAGTTGAGAATCG 57.166 36.000 0.00 0.00 32.41 3.34
168 169 6.919662 TGAGAATCGTTTCGTACTTTTGTACT 59.080 34.615 0.72 0.00 45.37 2.73
256 258 9.106070 GTTTTAGGTCTCTTCTTTTCAAGTGTA 57.894 33.333 0.00 0.00 0.00 2.90
277 279 0.169451 CGCCCGGTAAATTTCCACAC 59.831 55.000 0.00 0.00 0.00 3.82
290 292 9.476202 GTAAATTTCCACACTTTTAATCAGCTT 57.524 29.630 0.00 0.00 0.00 3.74
306 308 0.804989 GCTTGACAGCTACCGCATTT 59.195 50.000 0.00 0.00 43.51 2.32
317 319 6.202954 ACAGCTACCGCATTTTATAGATGAAC 59.797 38.462 2.66 0.00 35.21 3.18
322 324 7.259290 ACCGCATTTTATAGATGAACGAAAT 57.741 32.000 0.00 0.00 0.00 2.17
324 326 7.132213 CCGCATTTTATAGATGAACGAAATGT 58.868 34.615 0.00 0.00 37.03 2.71
346 348 5.705441 TGTCTCAAAGAACAACTCAACAAGT 59.295 36.000 0.00 0.00 41.10 3.16
357 359 6.177610 ACAACTCAACAAGTAGGACTCAAAA 58.822 36.000 0.00 0.00 37.17 2.44
364 366 6.927294 ACAAGTAGGACTCAAAACTGAAAG 57.073 37.500 0.00 0.00 42.29 2.62
382 385 1.101049 AGTGTTTCACGCCTTGGGTG 61.101 55.000 5.05 5.05 45.77 4.61
397 400 6.492254 GCCTTGGGTGTTATTTTAAGATACG 58.508 40.000 0.00 0.00 0.00 3.06
398 401 6.316890 GCCTTGGGTGTTATTTTAAGATACGA 59.683 38.462 0.00 0.00 0.00 3.43
404 512 9.550811 GGGTGTTATTTTAAGATACGAAAGTTG 57.449 33.333 0.00 0.00 46.40 3.16
423 531 8.723942 AAAGTTGCAAATACCAAATGTTACAA 57.276 26.923 0.00 0.00 0.00 2.41
450 558 8.207545 ACTGTTTCTTATAGTCTTCATCATCCC 58.792 37.037 0.00 0.00 0.00 3.85
457 565 4.148128 AGTCTTCATCATCCCATCACAC 57.852 45.455 0.00 0.00 0.00 3.82
475 583 4.456911 TCACACCATTTGAGCAGAATTCTC 59.543 41.667 4.57 0.94 0.00 2.87
511 649 0.664761 CCTGCGCGGATTGAAATGAT 59.335 50.000 20.25 0.00 33.16 2.45
542 680 3.131396 ACAACTGAAGCTAACCTGAACG 58.869 45.455 0.00 0.00 0.00 3.95
583 721 9.678941 CTTTTTAGGAACCTGAACAAAGATAAC 57.321 33.333 3.36 0.00 0.00 1.89
585 723 5.223449 AGGAACCTGAACAAAGATAACGA 57.777 39.130 0.00 0.00 0.00 3.85
614 752 0.103755 TCATCATCTCGTCAGCTGGC 59.896 55.000 15.13 12.04 0.00 4.85
641 779 6.094048 TCTGGCATCTTAAATTGCAGAGTAAC 59.906 38.462 10.47 0.00 40.66 2.50
688 834 4.435518 CGGGAACATGTTAATGTGAACGAG 60.436 45.833 11.95 0.00 46.58 4.18
716 862 5.822519 AGCAGACGGAGCAATAATTTAATCA 59.177 36.000 0.00 0.00 0.00 2.57
717 863 6.017605 AGCAGACGGAGCAATAATTTAATCAG 60.018 38.462 0.00 0.00 0.00 2.90
718 864 6.138761 CAGACGGAGCAATAATTTAATCAGC 58.861 40.000 0.00 0.00 0.00 4.26
719 865 5.822519 AGACGGAGCAATAATTTAATCAGCA 59.177 36.000 0.00 0.00 0.00 4.41
720 866 5.821204 ACGGAGCAATAATTTAATCAGCAC 58.179 37.500 0.00 0.00 0.00 4.40
721 867 5.590259 ACGGAGCAATAATTTAATCAGCACT 59.410 36.000 0.00 0.00 0.00 4.40
722 868 5.911280 CGGAGCAATAATTTAATCAGCACTG 59.089 40.000 0.00 0.00 0.00 3.66
723 869 5.689068 GGAGCAATAATTTAATCAGCACTGC 59.311 40.000 0.00 0.00 0.00 4.40
724 870 6.460676 GGAGCAATAATTTAATCAGCACTGCT 60.461 38.462 0.00 0.00 40.77 4.24
725 871 7.255242 GGAGCAATAATTTAATCAGCACTGCTA 60.255 37.037 2.39 0.00 36.40 3.49
726 872 8.174733 AGCAATAATTTAATCAGCACTGCTAT 57.825 30.769 2.39 0.00 36.40 2.97
727 873 9.288576 AGCAATAATTTAATCAGCACTGCTATA 57.711 29.630 2.39 0.00 36.40 1.31
728 874 9.334693 GCAATAATTTAATCAGCACTGCTATAC 57.665 33.333 2.39 0.00 36.40 1.47
742 888 3.882444 TGCTATACAGACGACAGTAGGT 58.118 45.455 0.00 0.00 0.00 3.08
743 889 5.027293 TGCTATACAGACGACAGTAGGTA 57.973 43.478 0.00 0.00 0.00 3.08
744 890 5.055144 TGCTATACAGACGACAGTAGGTAG 58.945 45.833 0.00 0.00 0.00 3.18
745 891 5.163374 TGCTATACAGACGACAGTAGGTAGA 60.163 44.000 0.00 0.00 0.00 2.59
746 892 5.177327 GCTATACAGACGACAGTAGGTAGAC 59.823 48.000 0.00 0.00 0.00 2.59
747 893 2.344950 ACAGACGACAGTAGGTAGACG 58.655 52.381 0.00 0.00 0.00 4.18
748 894 2.028658 ACAGACGACAGTAGGTAGACGA 60.029 50.000 0.00 0.00 0.00 4.20
749 895 3.196463 CAGACGACAGTAGGTAGACGAT 58.804 50.000 0.00 0.00 0.00 3.73
750 896 3.622163 CAGACGACAGTAGGTAGACGATT 59.378 47.826 0.00 0.00 0.00 3.34
751 897 4.807834 CAGACGACAGTAGGTAGACGATTA 59.192 45.833 0.00 0.00 0.00 1.75
752 898 5.466058 CAGACGACAGTAGGTAGACGATTAT 59.534 44.000 0.00 0.00 0.00 1.28
753 899 6.018098 CAGACGACAGTAGGTAGACGATTATT 60.018 42.308 0.00 0.00 0.00 1.40
754 900 6.018098 AGACGACAGTAGGTAGACGATTATTG 60.018 42.308 0.00 0.00 0.00 1.90
755 901 5.819379 ACGACAGTAGGTAGACGATTATTGA 59.181 40.000 0.00 0.00 0.00 2.57
756 902 6.317140 ACGACAGTAGGTAGACGATTATTGAA 59.683 38.462 0.00 0.00 0.00 2.69
757 903 6.632035 CGACAGTAGGTAGACGATTATTGAAC 59.368 42.308 0.00 0.00 0.00 3.18
758 904 6.493116 ACAGTAGGTAGACGATTATTGAACG 58.507 40.000 0.00 0.00 0.00 3.95
759 905 6.317140 ACAGTAGGTAGACGATTATTGAACGA 59.683 38.462 0.00 0.00 0.00 3.85
760 906 6.632035 CAGTAGGTAGACGATTATTGAACGAC 59.368 42.308 0.00 0.00 0.00 4.34
761 907 5.571784 AGGTAGACGATTATTGAACGACA 57.428 39.130 0.00 0.00 0.00 4.35
762 908 5.957798 AGGTAGACGATTATTGAACGACAA 58.042 37.500 0.00 0.00 42.95 3.18
764 910 6.696148 AGGTAGACGATTATTGAACGACAATC 59.304 38.462 13.56 3.64 44.77 2.67
765 911 5.968387 AGACGATTATTGAACGACAATCC 57.032 39.130 13.56 6.49 44.77 3.01
766 912 5.416083 AGACGATTATTGAACGACAATCCA 58.584 37.500 13.56 5.56 44.77 3.41
767 913 6.049149 AGACGATTATTGAACGACAATCCAT 58.951 36.000 13.56 8.98 44.77 3.41
768 914 6.538742 AGACGATTATTGAACGACAATCCATT 59.461 34.615 13.56 1.88 44.77 3.16
769 915 7.065803 AGACGATTATTGAACGACAATCCATTT 59.934 33.333 13.56 1.61 44.77 2.32
770 916 8.203937 ACGATTATTGAACGACAATCCATTTA 57.796 30.769 13.56 0.00 44.77 1.40
771 917 8.670135 ACGATTATTGAACGACAATCCATTTAA 58.330 29.630 13.56 5.15 44.77 1.52
772 918 9.158364 CGATTATTGAACGACAATCCATTTAAG 57.842 33.333 13.56 0.00 44.77 1.85
773 919 8.856490 ATTATTGAACGACAATCCATTTAAGC 57.144 30.769 13.56 0.00 44.77 3.09
774 920 4.695217 TGAACGACAATCCATTTAAGCC 57.305 40.909 0.00 0.00 0.00 4.35
775 921 3.126171 TGAACGACAATCCATTTAAGCCG 59.874 43.478 0.00 0.00 0.00 5.52
776 922 2.706890 ACGACAATCCATTTAAGCCGT 58.293 42.857 0.00 0.00 0.00 5.68
777 923 2.676342 ACGACAATCCATTTAAGCCGTC 59.324 45.455 0.00 0.00 0.00 4.79
778 924 2.031683 CGACAATCCATTTAAGCCGTCC 59.968 50.000 0.00 0.00 0.00 4.79
779 925 3.013921 GACAATCCATTTAAGCCGTCCA 58.986 45.455 0.00 0.00 0.00 4.02
780 926 3.631250 ACAATCCATTTAAGCCGTCCAT 58.369 40.909 0.00 0.00 0.00 3.41
781 927 3.381272 ACAATCCATTTAAGCCGTCCATG 59.619 43.478 0.00 0.00 0.00 3.66
782 928 1.388547 TCCATTTAAGCCGTCCATGC 58.611 50.000 0.00 0.00 0.00 4.06
783 929 1.102154 CCATTTAAGCCGTCCATGCA 58.898 50.000 0.00 0.00 0.00 3.96
784 930 1.682854 CCATTTAAGCCGTCCATGCAT 59.317 47.619 0.00 0.00 0.00 3.96
785 931 2.544277 CCATTTAAGCCGTCCATGCATG 60.544 50.000 20.19 20.19 0.00 4.06
789 935 3.451004 GCCGTCCATGCATGGCAA 61.451 61.111 36.47 20.89 46.48 4.52
790 936 3.704908 GCCGTCCATGCATGGCAAC 62.705 63.158 36.47 28.64 46.48 4.17
801 947 4.653893 TGGCAACAGTTGTCTGCA 57.346 50.000 18.62 0.00 46.17 4.41
802 948 2.879372 TGGCAACAGTTGTCTGCAA 58.121 47.368 18.62 0.00 46.17 4.08
803 949 1.180907 TGGCAACAGTTGTCTGCAAA 58.819 45.000 18.62 0.00 46.17 3.68
804 950 1.135141 TGGCAACAGTTGTCTGCAAAC 60.135 47.619 18.62 0.00 46.17 2.93
805 951 1.559831 GCAACAGTTGTCTGCAAACC 58.440 50.000 14.88 0.00 44.77 3.27
806 952 1.826327 CAACAGTTGTCTGCAAACCG 58.174 50.000 4.99 0.00 44.77 4.44
807 953 0.100503 AACAGTTGTCTGCAAACCGC 59.899 50.000 0.00 0.00 44.77 5.68
808 954 0.748005 ACAGTTGTCTGCAAACCGCT 60.748 50.000 0.00 0.00 44.77 5.52
809 955 0.317269 CAGTTGTCTGCAAACCGCTG 60.317 55.000 0.00 0.00 43.06 5.18
810 956 1.008538 GTTGTCTGCAAACCGCTGG 60.009 57.895 0.00 0.00 43.06 4.85
811 957 1.153066 TTGTCTGCAAACCGCTGGA 60.153 52.632 1.50 0.00 43.06 3.86
812 958 0.537143 TTGTCTGCAAACCGCTGGAT 60.537 50.000 1.50 0.00 43.06 3.41
813 959 1.236616 TGTCTGCAAACCGCTGGATG 61.237 55.000 1.50 2.20 43.06 3.51
814 960 1.675310 TCTGCAAACCGCTGGATGG 60.675 57.895 1.50 0.00 43.06 3.51
815 961 1.675310 CTGCAAACCGCTGGATGGA 60.675 57.895 1.50 1.63 43.06 3.41
816 962 1.926511 CTGCAAACCGCTGGATGGAC 61.927 60.000 1.50 0.00 43.06 4.02
817 963 2.700773 GCAAACCGCTGGATGGACC 61.701 63.158 1.50 0.00 37.77 4.46
825 971 3.397906 TGGATGGACCATCGTGCA 58.602 55.556 24.94 16.08 45.16 4.57
826 972 1.682257 TGGATGGACCATCGTGCAA 59.318 52.632 24.94 8.06 44.18 4.08
827 973 0.392863 TGGATGGACCATCGTGCAAG 60.393 55.000 24.94 0.00 44.18 4.01
828 974 1.097547 GGATGGACCATCGTGCAAGG 61.098 60.000 24.94 0.00 44.18 3.61
829 975 1.077501 ATGGACCATCGTGCAAGGG 60.078 57.895 0.00 0.00 44.18 3.95
830 976 1.852157 ATGGACCATCGTGCAAGGGT 61.852 55.000 0.00 0.00 44.18 4.34
831 977 3.730160 ATGGACCATCGTGCAAGGGTC 62.730 57.143 12.76 12.76 44.18 4.46
832 978 2.047274 ACCATCGTGCAAGGGTCG 60.047 61.111 0.00 0.00 0.00 4.79
833 979 2.047274 CCATCGTGCAAGGGTCGT 60.047 61.111 0.00 0.00 0.00 4.34
834 980 1.671054 CCATCGTGCAAGGGTCGTT 60.671 57.895 0.00 0.00 0.00 3.85
835 981 1.635663 CCATCGTGCAAGGGTCGTTC 61.636 60.000 0.00 0.00 0.00 3.95
836 982 0.948623 CATCGTGCAAGGGTCGTTCA 60.949 55.000 0.00 0.00 0.00 3.18
837 983 0.949105 ATCGTGCAAGGGTCGTTCAC 60.949 55.000 0.00 0.00 0.00 3.18
838 984 2.604174 CGTGCAAGGGTCGTTCACC 61.604 63.158 0.00 0.00 45.97 4.02
848 994 3.009301 GGTCGTTCACCCTATATGTCG 57.991 52.381 0.00 0.00 39.69 4.35
849 995 2.360165 GGTCGTTCACCCTATATGTCGT 59.640 50.000 0.00 0.00 39.69 4.34
850 996 3.369385 GTCGTTCACCCTATATGTCGTG 58.631 50.000 0.00 0.00 0.00 4.35
851 997 3.018856 TCGTTCACCCTATATGTCGTGT 58.981 45.455 0.00 0.00 0.00 4.49
852 998 3.113322 CGTTCACCCTATATGTCGTGTG 58.887 50.000 0.00 0.00 0.00 3.82
853 999 3.428452 CGTTCACCCTATATGTCGTGTGT 60.428 47.826 0.00 0.00 0.00 3.72
854 1000 4.201940 CGTTCACCCTATATGTCGTGTGTA 60.202 45.833 0.00 0.00 0.00 2.90
855 1001 4.906065 TCACCCTATATGTCGTGTGTAC 57.094 45.455 0.00 0.00 0.00 2.90
856 1002 4.271661 TCACCCTATATGTCGTGTGTACA 58.728 43.478 0.00 0.00 0.00 2.90
857 1003 4.337274 TCACCCTATATGTCGTGTGTACAG 59.663 45.833 0.00 0.00 0.00 2.74
858 1004 3.067742 ACCCTATATGTCGTGTGTACAGC 59.932 47.826 0.00 0.00 0.00 4.40
859 1005 3.067601 CCCTATATGTCGTGTGTACAGCA 59.932 47.826 0.00 0.00 0.00 4.41
860 1006 4.290969 CCTATATGTCGTGTGTACAGCAG 58.709 47.826 0.00 0.00 0.00 4.24
861 1007 3.868757 ATATGTCGTGTGTACAGCAGT 57.131 42.857 0.00 0.00 0.00 4.40
862 1008 2.526304 ATGTCGTGTGTACAGCAGTT 57.474 45.000 0.00 0.00 0.00 3.16
863 1009 2.303163 TGTCGTGTGTACAGCAGTTT 57.697 45.000 0.00 0.00 0.00 2.66
864 1010 2.198406 TGTCGTGTGTACAGCAGTTTC 58.802 47.619 0.00 0.00 0.00 2.78
865 1011 1.189446 GTCGTGTGTACAGCAGTTTCG 59.811 52.381 0.00 0.00 0.00 3.46
938 1091 2.772287 CGAAAGCTCTGTCTTTTCCCT 58.228 47.619 0.00 0.00 36.50 4.20
1846 2040 2.812609 CGACGTCGTCTCTCCGGA 60.813 66.667 29.08 2.93 34.11 5.14
1856 2050 3.071206 TCTCCGGACAGAGCAGGC 61.071 66.667 0.00 0.00 33.66 4.85
2325 2522 3.976490 ATCGGAGGAAGGGGCGACA 62.976 63.158 0.00 0.00 0.00 4.35
2496 2693 2.661537 CGCAACGTGGAGCTGTGA 60.662 61.111 0.00 0.00 0.00 3.58
2521 2718 7.775053 AAGTTAAAGATCCATGGCTGTTTAA 57.225 32.000 20.71 20.71 0.00 1.52
2522 2719 7.158099 AGTTAAAGATCCATGGCTGTTTAAC 57.842 36.000 33.05 33.05 39.21 2.01
2523 2720 6.152831 AGTTAAAGATCCATGGCTGTTTAACC 59.847 38.462 34.61 24.73 39.51 2.85
2524 2721 2.643551 AGATCCATGGCTGTTTAACCG 58.356 47.619 6.96 0.00 0.00 4.44
2525 2722 1.065551 GATCCATGGCTGTTTAACCGC 59.934 52.381 6.96 2.89 0.00 5.68
2526 2723 0.037590 TCCATGGCTGTTTAACCGCT 59.962 50.000 6.96 0.00 0.00 5.52
2527 2724 0.451783 CCATGGCTGTTTAACCGCTC 59.548 55.000 10.98 2.97 0.00 5.03
2528 2725 1.453155 CATGGCTGTTTAACCGCTCT 58.547 50.000 10.98 0.00 0.00 4.09
2529 2726 1.812571 CATGGCTGTTTAACCGCTCTT 59.187 47.619 10.98 0.00 0.00 2.85
2530 2727 1.234821 TGGCTGTTTAACCGCTCTTG 58.765 50.000 10.98 0.00 0.00 3.02
2531 2728 1.202710 TGGCTGTTTAACCGCTCTTGA 60.203 47.619 10.98 0.00 0.00 3.02
2532 2729 1.877443 GGCTGTTTAACCGCTCTTGAA 59.123 47.619 10.98 0.00 0.00 2.69
2533 2730 2.095718 GGCTGTTTAACCGCTCTTGAAG 60.096 50.000 10.98 0.00 0.00 3.02
2534 2731 2.806244 GCTGTTTAACCGCTCTTGAAGA 59.194 45.455 4.29 0.00 0.00 2.87
2535 2732 3.120511 GCTGTTTAACCGCTCTTGAAGAG 60.121 47.826 17.59 17.59 45.04 2.85
2536 2733 4.058817 CTGTTTAACCGCTCTTGAAGAGT 58.941 43.478 22.01 6.21 44.12 3.24
2545 2742 2.999355 GCTCTTGAAGAGTGACATGACC 59.001 50.000 22.01 0.01 44.12 4.02
2546 2743 3.249091 CTCTTGAAGAGTGACATGACCG 58.751 50.000 13.93 0.00 37.57 4.79
2547 2744 2.628178 TCTTGAAGAGTGACATGACCGT 59.372 45.455 0.00 0.00 0.00 4.83
2548 2745 2.724977 TGAAGAGTGACATGACCGTC 57.275 50.000 0.00 0.00 36.40 4.79
2549 2746 1.272490 TGAAGAGTGACATGACCGTCC 59.728 52.381 0.00 0.00 34.88 4.79
2550 2747 1.546476 GAAGAGTGACATGACCGTCCT 59.454 52.381 0.00 0.00 34.88 3.85
2551 2748 1.633774 AGAGTGACATGACCGTCCTT 58.366 50.000 0.00 0.00 34.88 3.36
2552 2749 1.273606 AGAGTGACATGACCGTCCTTG 59.726 52.381 0.00 0.00 34.88 3.61
2553 2750 1.272490 GAGTGACATGACCGTCCTTGA 59.728 52.381 0.00 0.00 34.88 3.02
2554 2751 1.000955 AGTGACATGACCGTCCTTGAC 59.999 52.381 0.00 1.34 34.88 3.18
2555 2752 1.000955 GTGACATGACCGTCCTTGACT 59.999 52.381 0.00 0.00 34.88 3.41
2556 2753 1.272490 TGACATGACCGTCCTTGACTC 59.728 52.381 0.00 0.00 34.88 3.36
2557 2754 0.243907 ACATGACCGTCCTTGACTCG 59.756 55.000 0.00 0.00 0.00 4.18
2558 2755 0.526211 CATGACCGTCCTTGACTCGA 59.474 55.000 0.00 0.00 0.00 4.04
2559 2756 0.811915 ATGACCGTCCTTGACTCGAG 59.188 55.000 11.84 11.84 0.00 4.04
2560 2757 1.153997 GACCGTCCTTGACTCGAGC 60.154 63.158 13.61 6.11 0.00 5.03
2561 2758 1.587933 GACCGTCCTTGACTCGAGCT 61.588 60.000 13.61 0.00 0.00 4.09
2562 2759 0.322277 ACCGTCCTTGACTCGAGCTA 60.322 55.000 13.61 0.00 0.00 3.32
2563 2760 0.809385 CCGTCCTTGACTCGAGCTAA 59.191 55.000 13.61 7.06 0.00 3.09
2564 2761 1.467713 CCGTCCTTGACTCGAGCTAAC 60.468 57.143 13.61 2.45 0.00 2.34
2565 2762 1.467713 CGTCCTTGACTCGAGCTAACC 60.468 57.143 13.61 0.00 0.00 2.85
2566 2763 1.544691 GTCCTTGACTCGAGCTAACCA 59.455 52.381 13.61 0.04 0.00 3.67
2567 2764 1.819288 TCCTTGACTCGAGCTAACCAG 59.181 52.381 13.61 3.33 0.00 4.00
2568 2765 1.546476 CCTTGACTCGAGCTAACCAGT 59.454 52.381 13.61 0.00 0.00 4.00
2569 2766 2.600731 CTTGACTCGAGCTAACCAGTG 58.399 52.381 13.61 0.00 0.00 3.66
2570 2767 1.617322 TGACTCGAGCTAACCAGTGT 58.383 50.000 13.61 0.00 0.00 3.55
2571 2768 1.961394 TGACTCGAGCTAACCAGTGTT 59.039 47.619 13.61 0.00 38.52 3.32
2572 2769 3.151554 TGACTCGAGCTAACCAGTGTTA 58.848 45.455 13.61 0.00 35.87 2.41
2573 2770 3.762288 TGACTCGAGCTAACCAGTGTTAT 59.238 43.478 13.61 0.00 36.40 1.89
2574 2771 4.142447 TGACTCGAGCTAACCAGTGTTATC 60.142 45.833 13.61 0.00 36.40 1.75
2575 2772 3.762288 ACTCGAGCTAACCAGTGTTATCA 59.238 43.478 13.61 0.00 36.40 2.15
2576 2773 4.106029 TCGAGCTAACCAGTGTTATCAC 57.894 45.455 0.00 0.00 44.15 3.06
2577 2774 3.508402 TCGAGCTAACCAGTGTTATCACA 59.492 43.478 6.70 0.00 46.01 3.58
2717 2914 1.269448 GAAGCCGCATTTTCTCACCAA 59.731 47.619 0.00 0.00 0.00 3.67
2992 3194 4.141088 ACATGTCCTTAATCCTGCATCCAT 60.141 41.667 0.00 0.00 0.00 3.41
3000 3202 0.402887 TCCTGCATCCATAGCCCATG 59.597 55.000 0.00 0.00 0.00 3.66
3359 3570 6.519382 ACTTAGTTGTACTTCAAGTGGTACC 58.481 40.000 4.43 4.43 39.67 3.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.271926 ACATAGTGAACACCCTTGCCC 60.272 52.381 1.11 0.00 0.00 5.36
19 20 1.506493 CTTATCGCAGGGCATCAGAC 58.494 55.000 0.00 0.00 0.00 3.51
22 23 0.181114 AAGCTTATCGCAGGGCATCA 59.819 50.000 0.00 0.00 42.61 3.07
29 30 4.668576 TTGAGTTGAAAGCTTATCGCAG 57.331 40.909 0.00 0.00 42.61 5.18
65 66 2.032377 TCCACGCGACAAAACAAATCTC 60.032 45.455 15.93 0.00 0.00 2.75
67 68 2.041244 GTCCACGCGACAAAACAAATC 58.959 47.619 15.93 0.00 41.54 2.17
81 82 3.243177 GCTCGCTTAAGATAAAGTCCACG 59.757 47.826 6.67 0.00 0.00 4.94
86 87 6.091441 CACTCAAAGCTCGCTTAAGATAAAGT 59.909 38.462 6.67 6.13 34.84 2.66
88 89 5.932303 ACACTCAAAGCTCGCTTAAGATAAA 59.068 36.000 6.67 0.00 34.84 1.40
96 97 3.467803 ACTTAACACTCAAAGCTCGCTT 58.532 40.909 0.00 0.00 37.98 4.68
97 98 3.113260 ACTTAACACTCAAAGCTCGCT 57.887 42.857 0.00 0.00 0.00 4.93
136 137 5.857517 AGTACGAAACGATTCTCAACTTCTC 59.142 40.000 3.81 0.00 33.17 2.87
138 139 6.449448 AAGTACGAAACGATTCTCAACTTC 57.551 37.500 3.81 0.00 30.30 3.01
151 152 8.831000 AAAATGTCAGTACAAAAGTACGAAAC 57.169 30.769 0.00 0.00 39.58 2.78
209 210 2.551721 CCATGACAAGCAGACAAGGTCT 60.552 50.000 0.00 0.00 44.44 3.85
290 292 5.270893 TCTATAAAATGCGGTAGCTGTCA 57.729 39.130 0.00 0.00 45.42 3.58
306 308 9.869757 TCTTTGAGACATTTCGTTCATCTATAA 57.130 29.630 0.00 0.00 0.00 0.98
317 319 6.048073 TGAGTTGTTCTTTGAGACATTTCG 57.952 37.500 0.00 0.00 0.00 3.46
322 324 5.705441 ACTTGTTGAGTTGTTCTTTGAGACA 59.295 36.000 0.00 0.00 33.92 3.41
324 326 6.538742 CCTACTTGTTGAGTTGTTCTTTGAGA 59.461 38.462 0.00 0.00 39.86 3.27
346 348 6.882140 TGAAACACTTTCAGTTTTGAGTCCTA 59.118 34.615 0.00 0.00 44.21 2.94
364 366 1.358759 CACCCAAGGCGTGAAACAC 59.641 57.895 0.76 0.00 35.74 3.32
397 400 8.359060 TGTAACATTTGGTATTTGCAACTTTC 57.641 30.769 0.00 0.00 0.00 2.62
398 401 8.723942 TTGTAACATTTGGTATTTGCAACTTT 57.276 26.923 0.00 0.00 0.00 2.66
404 512 7.707774 ACAGTTTGTAACATTTGGTATTTGC 57.292 32.000 0.00 0.00 0.00 3.68
423 531 9.606631 GGATGATGAAGACTATAAGAAACAGTT 57.393 33.333 0.00 0.00 0.00 3.16
431 539 7.601886 GTGTGATGGGATGATGAAGACTATAAG 59.398 40.741 0.00 0.00 0.00 1.73
437 545 3.209410 GGTGTGATGGGATGATGAAGAC 58.791 50.000 0.00 0.00 0.00 3.01
448 556 1.475280 CTGCTCAAATGGTGTGATGGG 59.525 52.381 0.00 0.00 0.00 4.00
450 558 4.713824 ATTCTGCTCAAATGGTGTGATG 57.286 40.909 0.00 0.00 0.00 3.07
457 565 3.359033 TGGGAGAATTCTGCTCAAATGG 58.641 45.455 24.03 0.00 34.50 3.16
475 583 1.153005 GGCTCAGCTCCATCTTGGG 60.153 63.158 0.00 0.00 38.32 4.12
511 649 1.948611 GCTTCAGTTGTTATGCCGGGA 60.949 52.381 2.18 0.00 0.00 5.14
550 688 8.356000 TGTTCAGGTTCCTAAAAAGAAAAAGA 57.644 30.769 0.00 0.00 0.00 2.52
552 690 9.430623 CTTTGTTCAGGTTCCTAAAAAGAAAAA 57.569 29.630 0.00 0.00 0.00 1.94
568 706 8.648557 TCTGATAATCGTTATCTTTGTTCAGG 57.351 34.615 14.56 0.00 41.99 3.86
583 721 7.025963 TGACGAGATGATGATTCTGATAATCG 58.974 38.462 0.00 0.00 0.00 3.34
585 723 6.812656 GCTGACGAGATGATGATTCTGATAAT 59.187 38.462 0.00 0.00 0.00 1.28
614 752 3.374988 TCTGCAATTTAAGATGCCAGACG 59.625 43.478 10.84 0.00 41.87 4.18
665 811 3.433957 TCGTTCACATTAACATGTTCCCG 59.566 43.478 15.85 6.92 41.16 5.14
688 834 2.586258 TATTGCTCCGTCTGCTCTTC 57.414 50.000 0.00 0.00 0.00 2.87
716 862 2.092323 TGTCGTCTGTATAGCAGTGCT 58.908 47.619 23.44 23.44 45.23 4.40
717 863 2.159366 ACTGTCGTCTGTATAGCAGTGC 60.159 50.000 7.13 7.13 45.23 4.40
718 864 3.766676 ACTGTCGTCTGTATAGCAGTG 57.233 47.619 0.00 0.00 45.23 3.66
719 865 3.878103 CCTACTGTCGTCTGTATAGCAGT 59.122 47.826 0.00 0.00 45.23 4.40
720 866 3.878103 ACCTACTGTCGTCTGTATAGCAG 59.122 47.826 0.44 0.00 46.34 4.24
721 867 3.882444 ACCTACTGTCGTCTGTATAGCA 58.118 45.455 0.44 0.00 0.00 3.49
722 868 5.177327 GTCTACCTACTGTCGTCTGTATAGC 59.823 48.000 0.44 0.00 0.00 2.97
723 869 5.401972 CGTCTACCTACTGTCGTCTGTATAG 59.598 48.000 0.44 1.90 0.00 1.31
724 870 5.067805 TCGTCTACCTACTGTCGTCTGTATA 59.932 44.000 0.44 0.00 0.00 1.47
725 871 4.118410 CGTCTACCTACTGTCGTCTGTAT 58.882 47.826 0.44 0.00 0.00 2.29
726 872 3.193479 TCGTCTACCTACTGTCGTCTGTA 59.807 47.826 0.19 0.19 0.00 2.74
727 873 2.028658 TCGTCTACCTACTGTCGTCTGT 60.029 50.000 0.00 0.00 0.00 3.41
728 874 2.614779 TCGTCTACCTACTGTCGTCTG 58.385 52.381 0.00 0.00 0.00 3.51
729 875 3.540314 ATCGTCTACCTACTGTCGTCT 57.460 47.619 0.00 0.00 0.00 4.18
730 876 5.921004 ATAATCGTCTACCTACTGTCGTC 57.079 43.478 0.00 0.00 0.00 4.20
731 877 5.819379 TCAATAATCGTCTACCTACTGTCGT 59.181 40.000 0.00 0.00 0.00 4.34
732 878 6.296365 TCAATAATCGTCTACCTACTGTCG 57.704 41.667 0.00 0.00 0.00 4.35
733 879 6.632035 CGTTCAATAATCGTCTACCTACTGTC 59.368 42.308 0.00 0.00 0.00 3.51
734 880 6.317140 TCGTTCAATAATCGTCTACCTACTGT 59.683 38.462 0.00 0.00 0.00 3.55
735 881 6.632035 GTCGTTCAATAATCGTCTACCTACTG 59.368 42.308 0.00 0.00 0.00 2.74
736 882 6.317140 TGTCGTTCAATAATCGTCTACCTACT 59.683 38.462 0.00 0.00 0.00 2.57
737 883 6.489675 TGTCGTTCAATAATCGTCTACCTAC 58.510 40.000 0.00 0.00 0.00 3.18
738 884 6.682423 TGTCGTTCAATAATCGTCTACCTA 57.318 37.500 0.00 0.00 0.00 3.08
739 885 5.571784 TGTCGTTCAATAATCGTCTACCT 57.428 39.130 0.00 0.00 0.00 3.08
740 886 6.074463 GGATTGTCGTTCAATAATCGTCTACC 60.074 42.308 8.11 0.00 45.49 3.18
741 887 6.474427 TGGATTGTCGTTCAATAATCGTCTAC 59.526 38.462 8.11 0.00 45.49 2.59
742 888 6.566141 TGGATTGTCGTTCAATAATCGTCTA 58.434 36.000 8.11 0.00 45.49 2.59
743 889 5.416083 TGGATTGTCGTTCAATAATCGTCT 58.584 37.500 8.11 0.00 45.49 4.18
744 890 5.712217 TGGATTGTCGTTCAATAATCGTC 57.288 39.130 8.11 0.00 45.49 4.20
745 891 6.677781 AATGGATTGTCGTTCAATAATCGT 57.322 33.333 8.11 2.61 45.49 3.73
746 892 9.158364 CTTAAATGGATTGTCGTTCAATAATCG 57.842 33.333 8.11 0.00 45.49 3.34
747 893 8.958043 GCTTAAATGGATTGTCGTTCAATAATC 58.042 33.333 8.11 0.00 45.49 1.75
748 894 7.920682 GGCTTAAATGGATTGTCGTTCAATAAT 59.079 33.333 8.11 4.33 45.49 1.28
749 895 7.254852 GGCTTAAATGGATTGTCGTTCAATAA 58.745 34.615 8.11 2.64 45.49 1.40
750 896 6.457663 CGGCTTAAATGGATTGTCGTTCAATA 60.458 38.462 8.11 0.00 45.49 1.90
752 898 4.378978 CGGCTTAAATGGATTGTCGTTCAA 60.379 41.667 0.00 0.00 40.53 2.69
753 899 3.126171 CGGCTTAAATGGATTGTCGTTCA 59.874 43.478 0.00 0.00 0.00 3.18
754 900 3.126343 ACGGCTTAAATGGATTGTCGTTC 59.874 43.478 0.00 0.00 0.00 3.95
755 901 3.078837 ACGGCTTAAATGGATTGTCGTT 58.921 40.909 0.00 0.00 0.00 3.85
756 902 2.676342 GACGGCTTAAATGGATTGTCGT 59.324 45.455 0.00 0.00 0.00 4.34
757 903 2.031683 GGACGGCTTAAATGGATTGTCG 59.968 50.000 0.00 0.00 0.00 4.35
758 904 3.013921 TGGACGGCTTAAATGGATTGTC 58.986 45.455 0.00 0.00 0.00 3.18
759 905 3.080300 TGGACGGCTTAAATGGATTGT 57.920 42.857 0.00 0.00 0.00 2.71
760 906 3.796504 GCATGGACGGCTTAAATGGATTG 60.797 47.826 0.00 0.00 0.00 2.67
761 907 2.362077 GCATGGACGGCTTAAATGGATT 59.638 45.455 0.00 0.00 0.00 3.01
762 908 1.956477 GCATGGACGGCTTAAATGGAT 59.044 47.619 0.00 0.00 0.00 3.41
763 909 1.340502 TGCATGGACGGCTTAAATGGA 60.341 47.619 0.00 0.00 0.00 3.41
764 910 1.102154 TGCATGGACGGCTTAAATGG 58.898 50.000 0.00 0.00 0.00 3.16
765 911 2.734670 CATGCATGGACGGCTTAAATG 58.265 47.619 19.40 0.00 0.00 2.32
778 924 1.271379 AGACAACTGTTGCCATGCATG 59.729 47.619 20.19 20.19 38.76 4.06
779 925 1.271379 CAGACAACTGTTGCCATGCAT 59.729 47.619 19.82 0.00 39.11 3.96
780 926 0.669619 CAGACAACTGTTGCCATGCA 59.330 50.000 19.82 0.00 39.11 3.96
781 927 0.665369 GCAGACAACTGTTGCCATGC 60.665 55.000 19.82 20.76 45.04 4.06
782 928 0.669619 TGCAGACAACTGTTGCCATG 59.330 50.000 19.82 15.85 45.04 3.66
783 929 1.401761 TTGCAGACAACTGTTGCCAT 58.598 45.000 19.82 0.96 45.04 4.40
784 930 1.135141 GTTTGCAGACAACTGTTGCCA 60.135 47.619 19.82 9.51 45.04 4.92
785 931 1.559831 GTTTGCAGACAACTGTTGCC 58.440 50.000 19.82 9.66 45.04 4.52
786 932 1.559831 GGTTTGCAGACAACTGTTGC 58.440 50.000 19.82 12.59 45.04 4.17
787 933 1.826327 CGGTTTGCAGACAACTGTTG 58.174 50.000 18.44 18.44 45.04 3.33
788 934 0.100503 GCGGTTTGCAGACAACTGTT 59.899 50.000 9.87 0.00 45.04 3.16
789 935 1.727467 GCGGTTTGCAGACAACTGT 59.273 52.632 9.87 0.00 45.04 3.55
790 936 4.614673 GCGGTTTGCAGACAACTG 57.385 55.556 9.87 6.95 45.45 3.16
799 945 2.700773 GGTCCATCCAGCGGTTTGC 61.701 63.158 0.00 0.00 46.98 3.68
800 946 1.303236 TGGTCCATCCAGCGGTTTG 60.303 57.895 0.00 0.00 41.93 2.93
801 947 3.166434 TGGTCCATCCAGCGGTTT 58.834 55.556 0.00 0.00 41.93 3.27
809 955 1.097547 CCTTGCACGATGGTCCATCC 61.098 60.000 23.58 11.99 37.57 3.51
810 956 1.097547 CCCTTGCACGATGGTCCATC 61.098 60.000 20.45 20.45 37.50 3.51
811 957 1.077501 CCCTTGCACGATGGTCCAT 60.078 57.895 3.26 3.26 0.00 3.41
812 958 2.350895 CCCTTGCACGATGGTCCA 59.649 61.111 0.00 0.00 0.00 4.02
813 959 1.745489 GACCCTTGCACGATGGTCC 60.745 63.158 10.55 0.00 41.14 4.46
814 960 2.100631 CGACCCTTGCACGATGGTC 61.101 63.158 11.32 11.32 43.07 4.02
815 961 2.047274 CGACCCTTGCACGATGGT 60.047 61.111 0.00 0.00 0.00 3.55
816 962 1.635663 GAACGACCCTTGCACGATGG 61.636 60.000 0.24 0.00 0.00 3.51
817 963 0.948623 TGAACGACCCTTGCACGATG 60.949 55.000 0.24 0.00 0.00 3.84
818 964 0.949105 GTGAACGACCCTTGCACGAT 60.949 55.000 0.24 0.00 0.00 3.73
819 965 1.593209 GTGAACGACCCTTGCACGA 60.593 57.895 0.24 0.00 0.00 4.35
820 966 2.604174 GGTGAACGACCCTTGCACG 61.604 63.158 0.00 0.00 39.10 5.34
821 967 3.340789 GGTGAACGACCCTTGCAC 58.659 61.111 0.00 0.00 39.10 4.57
828 974 2.360165 ACGACATATAGGGTGAACGACC 59.640 50.000 0.00 0.00 45.28 4.79
829 975 3.181493 ACACGACATATAGGGTGAACGAC 60.181 47.826 0.00 0.00 34.59 4.34
830 976 3.018856 ACACGACATATAGGGTGAACGA 58.981 45.455 0.00 0.00 34.59 3.85
831 977 3.113322 CACACGACATATAGGGTGAACG 58.887 50.000 0.00 0.00 34.59 3.95
832 978 4.119442 ACACACGACATATAGGGTGAAC 57.881 45.455 12.52 0.00 34.59 3.18
833 979 4.705991 TGTACACACGACATATAGGGTGAA 59.294 41.667 12.52 0.00 34.59 3.18
834 980 4.271661 TGTACACACGACATATAGGGTGA 58.728 43.478 12.52 0.00 34.59 4.02
835 981 4.607955 CTGTACACACGACATATAGGGTG 58.392 47.826 0.00 6.02 36.50 4.61
836 982 3.067742 GCTGTACACACGACATATAGGGT 59.932 47.826 0.00 0.00 0.00 4.34
837 983 3.067601 TGCTGTACACACGACATATAGGG 59.932 47.826 0.00 0.00 0.00 3.53
838 984 4.202020 ACTGCTGTACACACGACATATAGG 60.202 45.833 0.00 0.00 0.00 2.57
839 985 4.921547 ACTGCTGTACACACGACATATAG 58.078 43.478 0.00 0.00 0.00 1.31
840 986 4.976224 ACTGCTGTACACACGACATATA 57.024 40.909 0.00 0.00 0.00 0.86
841 987 3.868757 ACTGCTGTACACACGACATAT 57.131 42.857 0.00 0.00 0.00 1.78
842 988 3.653539 AACTGCTGTACACACGACATA 57.346 42.857 0.00 0.00 0.00 2.29
843 989 2.526304 AACTGCTGTACACACGACAT 57.474 45.000 0.00 0.00 0.00 3.06
844 990 2.198406 GAAACTGCTGTACACACGACA 58.802 47.619 0.00 0.00 0.00 4.35
845 991 1.189446 CGAAACTGCTGTACACACGAC 59.811 52.381 0.00 0.00 0.00 4.34
846 992 1.202325 ACGAAACTGCTGTACACACGA 60.202 47.619 0.00 0.00 0.00 4.35
847 993 1.205657 ACGAAACTGCTGTACACACG 58.794 50.000 0.00 2.16 0.00 4.49
848 994 4.985044 ATTACGAAACTGCTGTACACAC 57.015 40.909 0.00 0.00 0.00 3.82
849 995 5.994887 AAATTACGAAACTGCTGTACACA 57.005 34.783 0.00 0.00 0.00 3.72
850 996 8.440833 AGATTAAATTACGAAACTGCTGTACAC 58.559 33.333 0.00 0.00 0.00 2.90
851 997 8.440059 CAGATTAAATTACGAAACTGCTGTACA 58.560 33.333 0.00 0.00 0.00 2.90
852 998 7.903431 CCAGATTAAATTACGAAACTGCTGTAC 59.097 37.037 0.00 0.00 0.00 2.90
853 999 7.413657 GCCAGATTAAATTACGAAACTGCTGTA 60.414 37.037 0.00 0.00 0.00 2.74
854 1000 6.622896 GCCAGATTAAATTACGAAACTGCTGT 60.623 38.462 0.00 0.00 0.00 4.40
855 1001 5.739161 GCCAGATTAAATTACGAAACTGCTG 59.261 40.000 0.00 0.00 0.00 4.41
856 1002 5.447279 CGCCAGATTAAATTACGAAACTGCT 60.447 40.000 0.00 0.00 0.00 4.24
857 1003 4.728608 CGCCAGATTAAATTACGAAACTGC 59.271 41.667 0.00 0.00 0.00 4.40
858 1004 5.864986 ACGCCAGATTAAATTACGAAACTG 58.135 37.500 0.00 0.00 0.00 3.16
859 1005 5.640357 TGACGCCAGATTAAATTACGAAACT 59.360 36.000 0.00 0.00 0.00 2.66
860 1006 5.731263 GTGACGCCAGATTAAATTACGAAAC 59.269 40.000 0.00 0.00 0.00 2.78
861 1007 5.444877 CGTGACGCCAGATTAAATTACGAAA 60.445 40.000 0.00 0.00 0.00 3.46
862 1008 4.031991 CGTGACGCCAGATTAAATTACGAA 59.968 41.667 0.00 0.00 0.00 3.85
863 1009 3.548668 CGTGACGCCAGATTAAATTACGA 59.451 43.478 0.00 0.00 0.00 3.43
864 1010 3.845683 CGTGACGCCAGATTAAATTACG 58.154 45.455 0.00 0.00 0.00 3.18
887 1033 3.812019 ACTAGTCGCCACTCGCCG 61.812 66.667 0.00 0.00 38.27 6.46
938 1091 0.108804 CGGGCTCGCTTTTGACTCTA 60.109 55.000 0.00 0.00 0.00 2.43
1446 1626 2.256158 CCGACGTTGTAGGACGCA 59.744 61.111 1.30 0.00 46.47 5.24
1665 1854 4.689549 TGGCCGTCGGAGGAGGAA 62.690 66.667 17.49 0.00 0.00 3.36
1802 1996 1.269883 ACGAAATGTACAGCACCGACA 60.270 47.619 13.92 0.00 0.00 4.35
1846 2040 3.073735 CTCCCTCGCCTGCTCTGT 61.074 66.667 0.00 0.00 0.00 3.41
2291 2488 3.905705 GATCGCATCGCCCTCTCGG 62.906 68.421 0.00 0.00 0.00 4.63
2472 2669 1.358725 GCTCCACGTTGCGCATCTAA 61.359 55.000 12.75 0.00 0.00 2.10
2496 2693 6.670695 AAACAGCCATGGATCTTTAACTTT 57.329 33.333 18.40 0.00 0.00 2.66
2521 2718 1.040646 TGTCACTCTTCAAGAGCGGT 58.959 50.000 14.81 0.00 46.12 5.68
2522 2719 1.998315 CATGTCACTCTTCAAGAGCGG 59.002 52.381 14.81 7.31 46.12 5.52
2523 2720 2.665537 GTCATGTCACTCTTCAAGAGCG 59.334 50.000 14.81 5.09 46.12 5.03
2524 2721 2.999355 GGTCATGTCACTCTTCAAGAGC 59.001 50.000 14.81 0.00 46.12 4.09
2526 2723 2.628178 ACGGTCATGTCACTCTTCAAGA 59.372 45.455 0.00 0.00 0.00 3.02
2527 2724 2.989840 GACGGTCATGTCACTCTTCAAG 59.010 50.000 2.62 0.00 38.75 3.02
2528 2725 2.288825 GGACGGTCATGTCACTCTTCAA 60.289 50.000 10.76 0.00 40.72 2.69
2529 2726 1.272490 GGACGGTCATGTCACTCTTCA 59.728 52.381 10.76 0.00 40.72 3.02
2530 2727 1.546476 AGGACGGTCATGTCACTCTTC 59.454 52.381 10.76 0.00 40.72 2.87
2531 2728 1.633774 AGGACGGTCATGTCACTCTT 58.366 50.000 10.76 0.00 40.72 2.85
2532 2729 1.273606 CAAGGACGGTCATGTCACTCT 59.726 52.381 10.76 0.00 40.72 3.24
2533 2730 1.272490 TCAAGGACGGTCATGTCACTC 59.728 52.381 10.76 0.00 40.72 3.51
2534 2731 1.000955 GTCAAGGACGGTCATGTCACT 59.999 52.381 10.76 0.00 40.72 3.41
2535 2732 1.000955 AGTCAAGGACGGTCATGTCAC 59.999 52.381 10.76 4.15 40.72 3.67
2536 2733 1.272490 GAGTCAAGGACGGTCATGTCA 59.728 52.381 10.76 0.00 40.72 3.58
2537 2734 1.732732 CGAGTCAAGGACGGTCATGTC 60.733 57.143 10.76 6.42 37.67 3.06
2538 2735 0.243907 CGAGTCAAGGACGGTCATGT 59.756 55.000 10.76 0.00 37.67 3.21
2539 2736 0.526211 TCGAGTCAAGGACGGTCATG 59.474 55.000 10.76 8.49 37.67 3.07
2540 2737 0.811915 CTCGAGTCAAGGACGGTCAT 59.188 55.000 10.76 0.00 37.67 3.06
2541 2738 1.863662 GCTCGAGTCAAGGACGGTCA 61.864 60.000 15.13 0.00 37.67 4.02
2542 2739 1.153997 GCTCGAGTCAAGGACGGTC 60.154 63.158 15.13 0.00 37.67 4.79
2543 2740 0.322277 TAGCTCGAGTCAAGGACGGT 60.322 55.000 15.13 0.00 37.67 4.83
2544 2741 0.809385 TTAGCTCGAGTCAAGGACGG 59.191 55.000 15.13 0.00 37.67 4.79
2545 2742 1.467713 GGTTAGCTCGAGTCAAGGACG 60.468 57.143 15.13 0.00 37.67 4.79
2546 2743 1.544691 TGGTTAGCTCGAGTCAAGGAC 59.455 52.381 15.13 4.84 0.00 3.85
2547 2744 1.819288 CTGGTTAGCTCGAGTCAAGGA 59.181 52.381 15.13 0.00 0.00 3.36
2548 2745 1.546476 ACTGGTTAGCTCGAGTCAAGG 59.454 52.381 15.13 1.79 0.00 3.61
2549 2746 2.029828 ACACTGGTTAGCTCGAGTCAAG 60.030 50.000 15.13 7.89 0.00 3.02
2550 2747 1.961394 ACACTGGTTAGCTCGAGTCAA 59.039 47.619 15.13 5.52 0.00 3.18
2551 2748 1.617322 ACACTGGTTAGCTCGAGTCA 58.383 50.000 15.13 0.00 0.00 3.41
2552 2749 2.726832 AACACTGGTTAGCTCGAGTC 57.273 50.000 15.13 6.52 34.87 3.36
2553 2750 3.762288 TGATAACACTGGTTAGCTCGAGT 59.238 43.478 15.13 3.51 44.24 4.18
2554 2751 4.106197 GTGATAACACTGGTTAGCTCGAG 58.894 47.826 8.45 8.45 44.24 4.04
2555 2752 3.508402 TGTGATAACACTGGTTAGCTCGA 59.492 43.478 4.65 0.00 44.24 4.04
2556 2753 3.845178 TGTGATAACACTGGTTAGCTCG 58.155 45.455 4.65 0.00 44.24 5.03
2557 2754 6.574350 AGTATGTGATAACACTGGTTAGCTC 58.426 40.000 4.65 2.17 44.24 4.09
2558 2755 6.546428 AGTATGTGATAACACTGGTTAGCT 57.454 37.500 4.65 0.00 44.24 3.32
2559 2756 7.713750 TCTAGTATGTGATAACACTGGTTAGC 58.286 38.462 4.65 0.00 46.07 3.09
2560 2757 9.684448 CATCTAGTATGTGATAACACTGGTTAG 57.316 37.037 4.65 2.84 46.07 2.34
2561 2758 9.416284 TCATCTAGTATGTGATAACACTGGTTA 57.584 33.333 4.65 0.00 46.07 2.85
2562 2759 8.198109 GTCATCTAGTATGTGATAACACTGGTT 58.802 37.037 4.65 0.00 46.07 3.67
2563 2760 7.561722 AGTCATCTAGTATGTGATAACACTGGT 59.438 37.037 4.65 0.00 46.07 4.00
2564 2761 7.946207 AGTCATCTAGTATGTGATAACACTGG 58.054 38.462 4.65 0.00 46.07 4.00
2565 2762 7.800847 CGAGTCATCTAGTATGTGATAACACTG 59.199 40.741 4.65 0.00 46.07 3.66
2566 2763 7.499563 ACGAGTCATCTAGTATGTGATAACACT 59.500 37.037 4.65 0.00 46.07 3.55
2567 2764 7.640852 ACGAGTCATCTAGTATGTGATAACAC 58.359 38.462 0.00 0.00 46.09 3.32
2568 2765 7.803279 ACGAGTCATCTAGTATGTGATAACA 57.197 36.000 0.00 0.00 0.00 2.41
2569 2766 7.113684 GCAACGAGTCATCTAGTATGTGATAAC 59.886 40.741 0.00 0.00 0.00 1.89
2570 2767 7.139392 GCAACGAGTCATCTAGTATGTGATAA 58.861 38.462 0.00 0.00 0.00 1.75
2571 2768 6.565999 CGCAACGAGTCATCTAGTATGTGATA 60.566 42.308 0.00 0.00 0.00 2.15
2572 2769 5.524284 GCAACGAGTCATCTAGTATGTGAT 58.476 41.667 0.00 0.00 0.00 3.06
2573 2770 4.495844 CGCAACGAGTCATCTAGTATGTGA 60.496 45.833 0.00 0.00 0.00 3.58
2574 2771 3.726235 CGCAACGAGTCATCTAGTATGTG 59.274 47.826 0.00 0.00 0.00 3.21
2575 2772 3.792459 GCGCAACGAGTCATCTAGTATGT 60.792 47.826 0.30 0.00 0.00 2.29
2576 2773 2.721603 GCGCAACGAGTCATCTAGTATG 59.278 50.000 0.30 0.00 0.00 2.39
2577 2774 2.287668 GGCGCAACGAGTCATCTAGTAT 60.288 50.000 10.83 0.00 0.00 2.12
2705 2902 8.599624 ATCCATGTTAGATTTGGTGAGAAAAT 57.400 30.769 0.00 0.00 0.00 1.82
2828 3025 7.294584 TCTCTTGGACCTTTAGATTTCCAAAA 58.705 34.615 3.65 0.00 45.36 2.44
2992 3194 3.088532 GGTGTTGAAACATCATGGGCTA 58.911 45.455 1.53 0.00 41.59 3.93
3000 3202 7.156876 TCATGGATTTAGGTGTTGAAACATC 57.843 36.000 0.00 0.00 41.59 3.06
3075 3277 4.323104 GCACAAGAATGTAGTCCTTCTCCT 60.323 45.833 0.00 0.00 37.82 3.69
3359 3570 2.107950 TGGCTTAGTTTCATGTCCCG 57.892 50.000 0.00 0.00 0.00 5.14


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

AutoCloner maintained by Alex Coulton.