Multiple sequence alignment - TraesCS2B01G035900

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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 TraesCS2B01G035900 chr2B 100.000 4022 0 0 1 4022 17161136 17165157 0.000000e+00 7428.0
1 TraesCS2B01G035900 chr2B 97.420 2984 56 6 808 3788 17458729 17461694 0.000000e+00 5064.0
2 TraesCS2B01G035900 chr2B 94.240 1389 49 7 1741 3128 17033325 17031967 0.000000e+00 2093.0
3 TraesCS2B01G035900 chr2B 94.891 1331 62 4 896 2223 17492139 17490812 0.000000e+00 2076.0
4 TraesCS2B01G035900 chr2B 97.781 721 16 0 1 721 17450245 17450965 0.000000e+00 1243.0
5 TraesCS2B01G035900 chr2B 94.239 677 32 4 3112 3788 17031925 17031256 0.000000e+00 1027.0
6 TraesCS2B01G035900 chr2B 94.764 573 29 1 2556 3128 17485952 17485381 0.000000e+00 891.0
7 TraesCS2B01G035900 chr2B 88.427 553 47 5 1 537 17495705 17495154 0.000000e+00 651.0
8 TraesCS2B01G035900 chr2B 95.000 280 9 2 2286 2565 17490775 17490501 6.170000e-118 435.0
9 TraesCS2B01G035900 chr2B 93.793 145 5 4 3112 3256 17485339 17485199 8.750000e-52 215.0
10 TraesCS2B01G035900 chr2B 81.496 254 36 5 1934 2183 17528966 17529212 8.820000e-47 198.0
11 TraesCS2B01G035900 chr2B 75.532 282 61 7 144 421 16969365 16969088 9.070000e-27 132.0
12 TraesCS2B01G035900 chr2B 77.293 229 44 7 208 432 17091663 17091439 1.170000e-25 128.0
13 TraesCS2B01G035900 chr2B 77.056 231 47 5 194 421 17202784 17203011 1.170000e-25 128.0
14 TraesCS2B01G035900 chr2B 89.888 89 7 2 612 700 17493168 17493082 3.290000e-21 113.0
15 TraesCS2B01G035900 chr2B 98.182 55 1 0 721 775 17458674 17458728 3.310000e-16 97.1
16 TraesCS2B01G035900 chr2D 91.911 1669 112 15 569 2231 11315109 11313458 0.000000e+00 2313.0
17 TraesCS2B01G035900 chr2D 92.281 855 60 4 2277 3128 11313441 11312590 0.000000e+00 1208.0
18 TraesCS2B01G035900 chr2D 87.072 789 86 9 945 1724 11389517 11390298 0.000000e+00 878.0
19 TraesCS2B01G035900 chr2D 85.274 747 99 9 985 1724 11169409 11168667 0.000000e+00 760.0
20 TraesCS2B01G035900 chr2D 84.552 725 100 11 985 1703 11309285 11308567 0.000000e+00 708.0
21 TraesCS2B01G035900 chr2D 90.494 547 35 6 7 537 11319829 11319284 0.000000e+00 706.0
22 TraesCS2B01G035900 chr2D 84.887 708 71 17 3112 3788 11312548 11311846 0.000000e+00 682.0
23 TraesCS2B01G035900 chr2D 88.223 484 56 1 54 537 11317929 11317447 9.690000e-161 577.0
24 TraesCS2B01G035900 chr2D 83.665 251 32 5 1934 2183 11168573 11168331 1.120000e-55 228.0
25 TraesCS2B01G035900 chrUn 89.534 1653 137 21 618 2252 345395690 345397324 0.000000e+00 2061.0
26 TraesCS2B01G035900 chrUn 91.369 1147 77 14 618 1757 409964849 409963718 0.000000e+00 1550.0
27 TraesCS2B01G035900 chrUn 91.601 631 49 3 2493 3123 463210718 463211344 0.000000e+00 869.0
28 TraesCS2B01G035900 chrUn 90.967 631 53 3 2493 3123 403133617 403132991 0.000000e+00 846.0
29 TraesCS2B01G035900 chrUn 91.104 607 50 3 2493 3099 472465365 472465967 0.000000e+00 819.0
30 TraesCS2B01G035900 chrUn 100.000 398 0 0 2865 3262 478980869 478981266 0.000000e+00 736.0
31 TraesCS2B01G035900 chrUn 91.387 476 37 3 2277 2752 449633131 449632660 0.000000e+00 649.0
32 TraesCS2B01G035900 chrUn 86.429 560 62 7 1704 2252 449633681 449633125 5.750000e-168 601.0
33 TraesCS2B01G035900 chrUn 89.004 482 33 13 618 1093 377867814 377867347 2.690000e-161 579.0
34 TraesCS2B01G035900 chrUn 92.663 368 26 1 2756 3123 433865566 433865932 2.750000e-146 529.0
35 TraesCS2B01G035900 chrUn 92.339 248 13 5 618 865 383847147 383847388 8.270000e-92 348.0
36 TraesCS2B01G035900 chrUn 83.665 251 35 3 1934 2184 313025838 313026082 8.690000e-57 231.0
37 TraesCS2B01G035900 chrUn 83.333 252 36 3 1934 2185 12511253 12511008 1.120000e-55 228.0
38 TraesCS2B01G035900 chrUn 78.333 120 14 6 3112 3228 403132944 403132834 2.590000e-07 67.6
39 TraesCS2B01G035900 chrUn 78.333 120 14 6 3112 3228 433865979 433866089 2.590000e-07 67.6
40 TraesCS2B01G035900 chrUn 90.909 44 2 2 3112 3155 463211391 463211432 1.560000e-04 58.4
41 TraesCS2B01G035900 chrUn 100.000 29 0 0 2277 2305 345397318 345397346 2.000000e-03 54.7
42 TraesCS2B01G035900 chr3D 84.485 767 107 10 963 1725 478540043 478539285 0.000000e+00 747.0
43 TraesCS2B01G035900 chr2A 89.945 547 38 7 7 537 11975199 11974654 0.000000e+00 689.0
44 TraesCS2B01G035900 chr2A 88.090 487 50 6 54 537 11705318 11704837 4.510000e-159 571.0
45 TraesCS2B01G035900 chr5B 98.058 206 3 1 3818 4022 314308575 314308780 1.370000e-94 357.0


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 TraesCS2B01G035900 chr2B 17161136 17165157 4021 False 7428.000000 7428 100.000000 1 4022 1 chr2B.!!$F1 4021
1 TraesCS2B01G035900 chr2B 17458674 17461694 3020 False 2580.550000 5064 97.801000 721 3788 2 chr2B.!!$F5 3067
2 TraesCS2B01G035900 chr2B 17031256 17033325 2069 True 1560.000000 2093 94.239500 1741 3788 2 chr2B.!!$R3 2047
3 TraesCS2B01G035900 chr2B 17450245 17450965 720 False 1243.000000 1243 97.781000 1 721 1 chr2B.!!$F3 720
4 TraesCS2B01G035900 chr2B 17490501 17495705 5204 True 818.750000 2076 92.051500 1 2565 4 chr2B.!!$R5 2564
5 TraesCS2B01G035900 chr2B 17485199 17485952 753 True 553.000000 891 94.278500 2556 3256 2 chr2B.!!$R4 700
6 TraesCS2B01G035900 chr2D 11308567 11319829 11262 True 1032.333333 2313 88.724667 7 3788 6 chr2D.!!$R2 3781
7 TraesCS2B01G035900 chr2D 11389517 11390298 781 False 878.000000 878 87.072000 945 1724 1 chr2D.!!$F1 779
8 TraesCS2B01G035900 chr2D 11168331 11169409 1078 True 494.000000 760 84.469500 985 2183 2 chr2D.!!$R1 1198
9 TraesCS2B01G035900 chrUn 409963718 409964849 1131 True 1550.000000 1550 91.369000 618 1757 1 chrUn.!!$R3 1139
10 TraesCS2B01G035900 chrUn 345395690 345397346 1656 False 1057.850000 2061 94.767000 618 2305 2 chrUn.!!$F5 1687
11 TraesCS2B01G035900 chrUn 472465365 472465967 602 False 819.000000 819 91.104000 2493 3099 1 chrUn.!!$F3 606
12 TraesCS2B01G035900 chrUn 449632660 449633681 1021 True 625.000000 649 88.908000 1704 2752 2 chrUn.!!$R5 1048
13 TraesCS2B01G035900 chrUn 463210718 463211432 714 False 463.700000 869 91.255000 2493 3155 2 chrUn.!!$F7 662
14 TraesCS2B01G035900 chrUn 403132834 403133617 783 True 456.800000 846 84.650000 2493 3228 2 chrUn.!!$R4 735
15 TraesCS2B01G035900 chrUn 433865566 433866089 523 False 298.300000 529 85.498000 2756 3228 2 chrUn.!!$F6 472
16 TraesCS2B01G035900 chr3D 478539285 478540043 758 True 747.000000 747 84.485000 963 1725 1 chr3D.!!$R1 762
17 TraesCS2B01G035900 chr2A 11974654 11975199 545 True 689.000000 689 89.945000 7 537 1 chr2A.!!$R2 530

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
237 2091 0.247736 GTTGATGAGGGAGCACGAGT 59.752 55.0 0.0 0.0 0.00 4.18 F
602 5188 0.251121 TGCCTTCCGCCTTCATCAAA 60.251 50.0 0.0 0.0 36.24 2.69 F
637 5223 1.108727 TGAGCACACCAAAAGCCCAG 61.109 55.0 0.0 0.0 0.00 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1786 7311 2.614259 ACTGAGTGAGTGAGGTCCAAT 58.386 47.619 0.00 0.0 31.75 3.16 R
2235 7768 5.730269 ACGACGTAATTTATAACCAATGCG 58.270 37.500 0.00 0.0 0.00 4.73 R
3262 8887 2.552155 GGATATCAATAGCCCACCGCAA 60.552 50.000 4.83 0.0 41.38 4.85 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
146 163 1.053835 TCCTGGTGGCTGAGAACACA 61.054 55.000 9.36 0.00 39.31 3.72
209 2063 2.361610 AAGCTGTCCGCCAATGGG 60.362 61.111 0.00 0.00 40.39 4.00
233 2087 2.777832 AGAAGTTGATGAGGGAGCAC 57.222 50.000 0.00 0.00 0.00 4.40
237 2091 0.247736 GTTGATGAGGGAGCACGAGT 59.752 55.000 0.00 0.00 0.00 4.18
249 2103 1.472276 GCACGAGTTAGACGCCATCG 61.472 60.000 0.00 0.00 42.43 3.84
268 2122 4.465632 TCGTGACACCTAATAATGCAGT 57.534 40.909 0.00 0.00 0.00 4.40
272 2126 5.117135 CGTGACACCTAATAATGCAGTATCG 59.883 44.000 7.20 2.10 0.00 2.92
275 2129 6.156748 ACACCTAATAATGCAGTATCGTCA 57.843 37.500 7.20 0.00 0.00 4.35
287 2141 0.459899 TATCGTCAGTGCTCGCCATT 59.540 50.000 3.34 0.00 0.00 3.16
290 2144 1.086067 CGTCAGTGCTCGCCATTGAT 61.086 55.000 4.87 0.00 41.44 2.57
365 2219 1.600636 TCTCTGCTTTGGCGGGTTG 60.601 57.895 0.00 0.00 44.44 3.77
380 2234 1.139095 GTTGAGAGGGTACGAGCCG 59.861 63.158 0.00 0.00 41.56 5.52
428 2282 1.555075 GAGCAGGTTACCATGGTCAGA 59.445 52.381 23.76 6.00 42.18 3.27
432 2286 3.559171 GCAGGTTACCATGGTCAGAAAGA 60.559 47.826 23.76 0.00 0.00 2.52
468 2322 2.868583 CCATAGAACTGACAATGCGGAG 59.131 50.000 0.00 0.00 0.00 4.63
473 2327 0.247736 ACTGACAATGCGGAGAGGTC 59.752 55.000 0.00 0.00 0.00 3.85
481 2335 2.261671 CGGAGAGGTCGTGTTGGG 59.738 66.667 0.00 0.00 0.00 4.12
486 2340 0.393077 AGAGGTCGTGTTGGGACTTG 59.607 55.000 0.00 0.00 34.82 3.16
499 2353 4.231718 TGGGACTTGTTTATTTTCGTGC 57.768 40.909 0.00 0.00 0.00 5.34
506 2360 3.958704 TGTTTATTTTCGTGCCACAGTG 58.041 40.909 0.00 0.00 0.00 3.66
523 2377 3.932710 ACAGTGTTTATGCACGTCTATGG 59.067 43.478 0.00 0.00 43.61 2.74
529 2383 5.932883 TGTTTATGCACGTCTATGGTGTAAA 59.067 36.000 0.00 0.00 37.70 2.01
530 2384 6.596106 TGTTTATGCACGTCTATGGTGTAAAT 59.404 34.615 0.00 0.00 37.70 1.40
531 2385 6.838198 TTATGCACGTCTATGGTGTAAATC 57.162 37.500 0.00 0.00 37.70 2.17
532 2386 4.195225 TGCACGTCTATGGTGTAAATCA 57.805 40.909 0.00 0.00 37.70 2.57
537 2391 6.468956 GCACGTCTATGGTGTAAATCATTTTG 59.531 38.462 0.00 0.00 37.70 2.44
538 2392 6.966632 CACGTCTATGGTGTAAATCATTTTGG 59.033 38.462 0.00 0.00 0.00 3.28
541 2395 6.751888 GTCTATGGTGTAAATCATTTTGGCAC 59.248 38.462 0.00 0.00 34.31 5.01
542 2396 5.743636 ATGGTGTAAATCATTTTGGCACT 57.256 34.783 10.16 0.00 34.89 4.40
543 2397 5.543507 TGGTGTAAATCATTTTGGCACTT 57.456 34.783 10.16 0.00 34.89 3.16
544 2398 5.537188 TGGTGTAAATCATTTTGGCACTTC 58.463 37.500 10.16 0.25 34.89 3.01
545 2399 4.621034 GGTGTAAATCATTTTGGCACTTCG 59.379 41.667 10.16 0.00 34.89 3.79
546 2400 5.219633 GTGTAAATCATTTTGGCACTTCGT 58.780 37.500 0.00 0.00 33.30 3.85
553 2418 6.811253 TCATTTTGGCACTTCGTTATTACT 57.189 33.333 0.00 0.00 0.00 2.24
559 2424 3.998341 GGCACTTCGTTATTACTGTTGGA 59.002 43.478 0.00 0.00 0.00 3.53
561 2426 5.813672 GGCACTTCGTTATTACTGTTGGATA 59.186 40.000 0.00 0.00 0.00 2.59
562 2427 6.018994 GGCACTTCGTTATTACTGTTGGATAG 60.019 42.308 0.00 0.00 0.00 2.08
565 2430 7.222224 CACTTCGTTATTACTGTTGGATAGACC 59.778 40.741 0.00 0.00 39.54 3.85
583 5169 7.711339 GGATAGACCGTCTTCATCTTTGTATTT 59.289 37.037 6.31 0.00 0.00 1.40
586 5172 4.156008 ACCGTCTTCATCTTTGTATTTGCC 59.844 41.667 0.00 0.00 0.00 4.52
592 5178 3.128589 TCATCTTTGTATTTGCCTTCCGC 59.871 43.478 0.00 0.00 38.31 5.54
602 5188 0.251121 TGCCTTCCGCCTTCATCAAA 60.251 50.000 0.00 0.00 36.24 2.69
606 5192 1.541147 CTTCCGCCTTCATCAAAAGCA 59.459 47.619 0.00 0.00 0.00 3.91
625 5211 2.873245 GCACAAGAAGAGGATGAGCACA 60.873 50.000 0.00 0.00 32.06 4.57
637 5223 1.108727 TGAGCACACCAAAAGCCCAG 61.109 55.000 0.00 0.00 0.00 4.45
703 6180 6.662616 CGCTTATGTTATGGAGGATCTTTTG 58.337 40.000 0.00 0.00 33.73 2.44
708 6185 9.527157 TTATGTTATGGAGGATCTTTTGAAACA 57.473 29.630 0.00 0.00 33.73 2.83
717 6194 6.395629 AGGATCTTTTGAAACAATGATGCAG 58.604 36.000 15.18 0.00 0.00 4.41
918 6406 4.003648 GTGCAGCTGGTCATACTTTACTT 58.996 43.478 17.12 0.00 0.00 2.24
1087 6596 1.895798 ACAGCTTCGAGTTCCATGAGA 59.104 47.619 0.00 0.00 0.00 3.27
1761 7284 2.432444 GTTTTGTCCCCATCACGATCA 58.568 47.619 0.00 0.00 0.00 2.92
3198 8814 7.977789 TGTTCTGTATATGTTGTTGACACAT 57.022 32.000 0.00 0.00 42.04 3.21
3199 8815 9.495572 TTGTTCTGTATATGTTGTTGACACATA 57.504 29.630 0.00 0.00 42.04 2.29
3200 8816 9.150348 TGTTCTGTATATGTTGTTGACACATAG 57.850 33.333 0.00 0.00 42.04 2.23
3262 8887 3.769739 TGCAGTACCACTCTGAAATGT 57.230 42.857 0.00 0.00 35.20 2.71
3276 8901 1.476488 GAAATGTTGCGGTGGGCTATT 59.524 47.619 0.00 0.00 44.05 1.73
3304 8929 1.619654 CCAAGGTGATCAAACTGGCA 58.380 50.000 0.00 0.00 0.00 4.92
3426 9051 3.543680 AGCGGCAATGTAACACTCTAT 57.456 42.857 1.45 0.00 0.00 1.98
3428 9053 2.936498 GCGGCAATGTAACACTCTATGT 59.064 45.455 0.00 0.00 46.42 2.29
3572 9198 5.539582 TTCGTTGAACATAAGTGGCATAC 57.460 39.130 0.00 0.00 0.00 2.39
3619 9245 3.615224 TTACAGTACCCCGAAATGGAC 57.385 47.619 0.00 0.00 42.00 4.02
3788 9445 6.984740 AAGCAACACAAACAATACATAACG 57.015 33.333 0.00 0.00 0.00 3.18
3790 9447 6.140110 AGCAACACAAACAATACATAACGAC 58.860 36.000 0.00 0.00 0.00 4.34
3792 9449 6.129561 GCAACACAAACAATACATAACGACAC 60.130 38.462 0.00 0.00 0.00 3.67
3793 9450 5.992729 ACACAAACAATACATAACGACACC 58.007 37.500 0.00 0.00 0.00 4.16
3794 9451 5.076765 CACAAACAATACATAACGACACCG 58.923 41.667 0.00 0.00 42.50 4.94
3795 9452 4.152759 ACAAACAATACATAACGACACCGG 59.847 41.667 0.00 0.00 40.78 5.28
3796 9453 3.872511 ACAATACATAACGACACCGGA 57.127 42.857 9.46 0.00 40.78 5.14
3797 9454 3.777478 ACAATACATAACGACACCGGAG 58.223 45.455 9.46 1.26 40.78 4.63
3798 9455 2.503920 ATACATAACGACACCGGAGC 57.496 50.000 9.46 0.00 40.78 4.70
3800 9457 0.108804 ACATAACGACACCGGAGCTG 60.109 55.000 9.46 0.00 40.78 4.24
3801 9458 0.108804 CATAACGACACCGGAGCTGT 60.109 55.000 9.46 0.69 40.78 4.40
3802 9459 0.606604 ATAACGACACCGGAGCTGTT 59.393 50.000 9.46 11.56 40.78 3.16
3803 9460 0.038892 TAACGACACCGGAGCTGTTC 60.039 55.000 9.46 0.00 40.78 3.18
3808 9465 1.669115 CACCGGAGCTGTTCCAGTG 60.669 63.158 9.46 11.71 45.41 3.66
3819 9476 2.474410 GTTCCAGTGAACGAAGGGAT 57.526 50.000 0.00 0.00 41.35 3.85
3820 9477 2.076863 GTTCCAGTGAACGAAGGGATG 58.923 52.381 0.00 0.00 41.35 3.51
3821 9478 0.613260 TCCAGTGAACGAAGGGATGG 59.387 55.000 0.00 0.00 0.00 3.51
3822 9479 1.026718 CCAGTGAACGAAGGGATGGC 61.027 60.000 0.00 0.00 0.00 4.40
3823 9480 0.036010 CAGTGAACGAAGGGATGGCT 60.036 55.000 0.00 0.00 0.00 4.75
3824 9481 0.250513 AGTGAACGAAGGGATGGCTC 59.749 55.000 0.00 0.00 0.00 4.70
3825 9482 1.084370 GTGAACGAAGGGATGGCTCG 61.084 60.000 0.00 0.00 38.53 5.03
3826 9483 2.125106 AACGAAGGGATGGCTCGC 60.125 61.111 0.00 0.00 36.03 5.03
3827 9484 3.682292 AACGAAGGGATGGCTCGCC 62.682 63.158 0.00 0.00 36.03 5.54
3828 9485 3.854669 CGAAGGGATGGCTCGCCT 61.855 66.667 9.65 0.00 34.99 5.52
3829 9486 2.110006 GAAGGGATGGCTCGCCTC 59.890 66.667 9.65 4.43 34.99 4.70
3830 9487 2.366167 AAGGGATGGCTCGCCTCT 60.366 61.111 9.65 0.00 34.99 3.69
3832 9489 4.292178 GGGATGGCTCGCCTCTCG 62.292 72.222 9.65 0.00 40.15 4.04
3834 9491 4.959596 GATGGCTCGCCTCTCGCC 62.960 72.222 9.65 0.00 44.02 5.54
3922 12381 1.074926 TCCTGATGCCCCTCTCCTC 60.075 63.158 0.00 0.00 0.00 3.71
3924 12383 1.074623 CTGATGCCCCTCTCCTCCT 60.075 63.158 0.00 0.00 0.00 3.69
3927 12386 3.765257 ATGCCCCTCTCCTCCTCGG 62.765 68.421 0.00 0.00 0.00 4.63
3929 12388 3.756783 CCCCTCTCCTCCTCGGGT 61.757 72.222 0.00 0.00 34.81 5.28
3931 12390 2.123640 CCTCTCCTCCTCGGGTCC 60.124 72.222 0.00 0.00 0.00 4.46
3933 12392 2.617538 TCTCCTCCTCGGGTCCCT 60.618 66.667 6.29 0.00 0.00 4.20
3934 12393 2.123640 CTCCTCCTCGGGTCCCTC 60.124 72.222 6.29 0.00 0.00 4.30
3935 12394 2.617538 TCCTCCTCGGGTCCCTCT 60.618 66.667 6.29 0.00 0.00 3.69
3936 12395 2.123640 CCTCCTCGGGTCCCTCTC 60.124 72.222 6.29 0.00 0.00 3.20
3938 12397 2.617538 TCCTCGGGTCCCTCTCCT 60.618 66.667 6.29 0.00 0.00 3.69
3940 12399 2.443016 CTCGGGTCCCTCTCCTGG 60.443 72.222 6.29 0.00 32.62 4.45
3941 12400 4.779733 TCGGGTCCCTCTCCTGGC 62.780 72.222 6.29 0.00 32.62 4.85
3942 12401 4.787280 CGGGTCCCTCTCCTGGCT 62.787 72.222 6.29 0.00 0.00 4.75
3943 12402 3.086600 GGGTCCCTCTCCTGGCTG 61.087 72.222 0.00 0.00 0.00 4.85
3944 12403 3.791586 GGTCCCTCTCCTGGCTGC 61.792 72.222 0.00 0.00 0.00 5.25
3945 12404 2.686835 GTCCCTCTCCTGGCTGCT 60.687 66.667 0.00 0.00 0.00 4.24
3946 12405 2.364842 TCCCTCTCCTGGCTGCTC 60.365 66.667 0.00 0.00 0.00 4.26
3947 12406 2.365370 CCCTCTCCTGGCTGCTCT 60.365 66.667 0.00 0.00 0.00 4.09
3949 12408 2.433994 CCTCTCCTGGCTGCTCTCC 61.434 68.421 0.00 0.00 0.00 3.71
3969 12428 2.657237 CGACGCTTCCTCAACCCT 59.343 61.111 0.00 0.00 0.00 4.34
3970 12429 1.446272 CGACGCTTCCTCAACCCTC 60.446 63.158 0.00 0.00 0.00 4.30
3971 12430 1.878656 CGACGCTTCCTCAACCCTCT 61.879 60.000 0.00 0.00 0.00 3.69
3973 12432 1.219393 CGCTTCCTCAACCCTCTCC 59.781 63.158 0.00 0.00 0.00 3.71
3974 12433 1.604915 GCTTCCTCAACCCTCTCCC 59.395 63.158 0.00 0.00 0.00 4.30
3975 12434 0.912006 GCTTCCTCAACCCTCTCCCT 60.912 60.000 0.00 0.00 0.00 4.20
3976 12435 1.199615 CTTCCTCAACCCTCTCCCTC 58.800 60.000 0.00 0.00 0.00 4.30
3978 12437 1.690985 CCTCAACCCTCTCCCTCCC 60.691 68.421 0.00 0.00 0.00 4.30
3979 12438 2.038975 TCAACCCTCTCCCTCCCG 59.961 66.667 0.00 0.00 0.00 5.14
3980 12439 2.284699 CAACCCTCTCCCTCCCGT 60.285 66.667 0.00 0.00 0.00 5.28
3981 12440 2.284699 AACCCTCTCCCTCCCGTG 60.285 66.667 0.00 0.00 0.00 4.94
3982 12441 3.925914 AACCCTCTCCCTCCCGTGG 62.926 68.421 0.00 0.00 0.00 4.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
209 2063 3.438434 GCTCCCTCATCAACTTCTTCAAC 59.562 47.826 0.00 0.00 0.00 3.18
249 2103 5.983720 ACGATACTGCATTATTAGGTGTCAC 59.016 40.000 0.00 0.00 0.00 3.67
268 2122 0.459899 AATGGCGAGCACTGACGATA 59.540 50.000 0.00 0.00 0.00 2.92
272 2126 0.376152 CATCAATGGCGAGCACTGAC 59.624 55.000 0.00 0.00 0.00 3.51
275 2129 4.230603 CCATCAATGGCGAGCACT 57.769 55.556 0.00 0.00 41.75 4.40
317 2171 4.028490 CCCAGCTTGCCGTACCCA 62.028 66.667 0.00 0.00 0.00 4.51
331 2185 4.589675 GACCAAACGGCACCCCCA 62.590 66.667 0.00 0.00 0.00 4.96
365 2219 2.188161 CCTCGGCTCGTACCCTCTC 61.188 68.421 0.00 0.00 0.00 3.20
380 2234 1.372748 CGCCATCTCGATCAGCCTC 60.373 63.158 0.00 0.00 0.00 4.70
416 2270 1.066430 GGCGTCTTTCTGACCATGGTA 60.066 52.381 19.80 0.00 42.49 3.25
468 2322 0.106149 ACAAGTCCCAACACGACCTC 59.894 55.000 0.00 0.00 0.00 3.85
473 2327 4.673311 CGAAAATAAACAAGTCCCAACACG 59.327 41.667 0.00 0.00 0.00 4.49
481 2335 4.602995 TGTGGCACGAAAATAAACAAGTC 58.397 39.130 13.77 0.00 0.00 3.01
486 2340 3.959943 ACACTGTGGCACGAAAATAAAC 58.040 40.909 13.77 0.00 0.00 2.01
499 2353 2.143122 AGACGTGCATAAACACTGTGG 58.857 47.619 13.09 0.00 38.45 4.17
506 2360 6.411630 TTTACACCATAGACGTGCATAAAC 57.588 37.500 0.00 0.00 34.45 2.01
523 2377 5.219633 ACGAAGTGCCAAAATGATTTACAC 58.780 37.500 9.36 9.36 42.51 2.90
529 2383 7.094377 ACAGTAATAACGAAGTGCCAAAATGAT 60.094 33.333 0.00 0.00 45.00 2.45
530 2384 6.205853 ACAGTAATAACGAAGTGCCAAAATGA 59.794 34.615 0.00 0.00 45.00 2.57
531 2385 6.378582 ACAGTAATAACGAAGTGCCAAAATG 58.621 36.000 0.00 0.00 45.00 2.32
532 2386 6.569179 ACAGTAATAACGAAGTGCCAAAAT 57.431 33.333 0.00 0.00 45.00 1.82
537 2391 3.998341 TCCAACAGTAATAACGAAGTGCC 59.002 43.478 0.00 0.00 45.00 5.01
538 2392 5.796350 ATCCAACAGTAATAACGAAGTGC 57.204 39.130 0.00 0.00 45.00 4.40
541 2395 6.417044 CGGTCTATCCAACAGTAATAACGAAG 59.583 42.308 0.00 0.00 35.57 3.79
542 2396 6.127647 ACGGTCTATCCAACAGTAATAACGAA 60.128 38.462 0.00 0.00 35.57 3.85
543 2397 5.357878 ACGGTCTATCCAACAGTAATAACGA 59.642 40.000 0.00 0.00 35.57 3.85
544 2398 5.585390 ACGGTCTATCCAACAGTAATAACG 58.415 41.667 0.00 0.00 35.57 3.18
545 2399 6.803642 AGACGGTCTATCCAACAGTAATAAC 58.196 40.000 9.33 0.00 35.57 1.89
546 2400 7.123098 TGAAGACGGTCTATCCAACAGTAATAA 59.877 37.037 11.71 0.00 35.57 1.40
553 2418 4.023980 AGATGAAGACGGTCTATCCAACA 58.976 43.478 11.71 5.93 35.57 3.33
559 2424 7.011482 GCAAATACAAAGATGAAGACGGTCTAT 59.989 37.037 11.71 1.77 0.00 1.98
561 2426 5.122396 GCAAATACAAAGATGAAGACGGTCT 59.878 40.000 4.45 4.45 0.00 3.85
562 2427 5.324697 GCAAATACAAAGATGAAGACGGTC 58.675 41.667 0.00 0.00 0.00 4.79
565 2430 5.551760 AGGCAAATACAAAGATGAAGACG 57.448 39.130 0.00 0.00 0.00 4.18
586 5172 1.541147 TGCTTTTGATGAAGGCGGAAG 59.459 47.619 0.00 0.00 42.81 3.46
592 5178 5.443185 TCTTCTTGTGCTTTTGATGAAGG 57.557 39.130 0.00 0.00 32.77 3.46
602 5188 2.039480 TGCTCATCCTCTTCTTGTGCTT 59.961 45.455 0.00 0.00 32.61 3.91
606 5192 2.289945 GGTGTGCTCATCCTCTTCTTGT 60.290 50.000 0.00 0.00 0.00 3.16
625 5211 0.261696 ACTTGGTCTGGGCTTTTGGT 59.738 50.000 0.00 0.00 0.00 3.67
637 5223 2.766828 AGGCTGGTAGTATCACTTGGTC 59.233 50.000 0.00 0.00 0.00 4.02
703 6180 6.921307 TCATTCATATGCTGCATCATTGTTTC 59.079 34.615 19.90 0.00 0.00 2.78
708 6185 6.041637 ACCTTTCATTCATATGCTGCATCATT 59.958 34.615 19.90 2.54 0.00 2.57
717 6194 7.975616 TCTTTTTAGCACCTTTCATTCATATGC 59.024 33.333 0.00 0.00 0.00 3.14
798 6275 3.005791 GCGGGAATCCTATGAAAATTGGG 59.994 47.826 0.00 0.00 0.00 4.12
918 6406 5.163794 GGCTAGTGCTCGTTGCTTTTAAATA 60.164 40.000 0.00 0.00 43.37 1.40
1087 6596 2.272146 GATGGCATCCACGGTGGT 59.728 61.111 25.53 11.27 39.03 4.16
1175 6684 4.704833 GCAGCAGCGGGTTGAGGA 62.705 66.667 0.00 0.00 0.00 3.71
1786 7311 2.614259 ACTGAGTGAGTGAGGTCCAAT 58.386 47.619 0.00 0.00 31.75 3.16
1860 7385 8.026607 TCAAAATCTCAAAATACCCGATCAAAC 58.973 33.333 0.00 0.00 0.00 2.93
1902 7427 6.036735 GCAAATAGCATGCTGAACATTTCAAT 59.963 34.615 30.42 8.47 44.79 2.57
2235 7768 5.730269 ACGACGTAATTTATAACCAATGCG 58.270 37.500 0.00 0.00 0.00 4.73
3262 8887 2.552155 GGATATCAATAGCCCACCGCAA 60.552 50.000 4.83 0.00 41.38 4.85
3276 8901 2.046292 TGATCACCTTGGCGGATATCA 58.954 47.619 4.83 0.00 36.10 2.15
3399 9024 0.325272 TTACATTGCCGCTACCCACA 59.675 50.000 0.00 0.00 0.00 4.17
3426 9051 2.325583 AGTGAAACCTCTTTGCGACA 57.674 45.000 0.00 0.00 37.80 4.35
3428 9053 1.333619 GCAAGTGAAACCTCTTTGCGA 59.666 47.619 0.00 0.00 37.80 5.10
3759 9416 7.518731 TGTATTGTTTGTGTTGCTTTCTTTC 57.481 32.000 0.00 0.00 0.00 2.62
3801 9458 1.003118 CCATCCCTTCGTTCACTGGAA 59.997 52.381 0.00 0.00 0.00 3.53
3802 9459 0.613260 CCATCCCTTCGTTCACTGGA 59.387 55.000 0.00 0.00 0.00 3.86
3803 9460 1.026718 GCCATCCCTTCGTTCACTGG 61.027 60.000 0.00 0.00 0.00 4.00
3805 9462 0.250513 GAGCCATCCCTTCGTTCACT 59.749 55.000 0.00 0.00 0.00 3.41
3806 9463 1.084370 CGAGCCATCCCTTCGTTCAC 61.084 60.000 0.00 0.00 0.00 3.18
3807 9464 1.218047 CGAGCCATCCCTTCGTTCA 59.782 57.895 0.00 0.00 0.00 3.18
3808 9465 2.174319 GCGAGCCATCCCTTCGTTC 61.174 63.158 0.00 0.00 36.74 3.95
3809 9466 2.125106 GCGAGCCATCCCTTCGTT 60.125 61.111 0.00 0.00 36.74 3.85
3810 9467 4.162690 GGCGAGCCATCCCTTCGT 62.163 66.667 9.58 0.00 36.74 3.85
3811 9468 3.798954 GAGGCGAGCCATCCCTTCG 62.799 68.421 17.18 0.00 38.92 3.79
3812 9469 2.110006 GAGGCGAGCCATCCCTTC 59.890 66.667 17.18 0.00 38.92 3.46
3813 9470 2.366167 AGAGGCGAGCCATCCCTT 60.366 61.111 17.18 0.00 38.92 3.95
3814 9471 2.841988 GAGAGGCGAGCCATCCCT 60.842 66.667 17.18 7.39 38.92 4.20
3815 9472 4.292178 CGAGAGGCGAGCCATCCC 62.292 72.222 17.18 2.61 44.57 3.85
3816 9473 4.959596 GCGAGAGGCGAGCCATCC 62.960 72.222 17.18 5.08 44.57 3.51
3901 12360 2.040043 AGAGGGGCATCAGGAGGG 60.040 66.667 0.00 0.00 0.00 4.30
3903 12362 1.074623 AGGAGAGGGGCATCAGGAG 60.075 63.158 0.00 0.00 0.00 3.69
3904 12363 1.074926 GAGGAGAGGGGCATCAGGA 60.075 63.158 0.00 0.00 0.00 3.86
3906 12365 1.074623 AGGAGGAGAGGGGCATCAG 60.075 63.158 0.00 0.00 0.00 2.90
3910 12369 4.465446 CCGAGGAGGAGAGGGGCA 62.465 72.222 0.00 0.00 45.00 5.36
3915 12374 2.123640 GGGACCCGAGGAGGAGAG 60.124 72.222 0.00 0.00 45.00 3.20
3916 12375 2.617538 AGGGACCCGAGGAGGAGA 60.618 66.667 4.40 0.00 45.00 3.71
3922 12381 2.443016 CAGGAGAGGGACCCGAGG 60.443 72.222 4.40 0.00 0.00 4.63
3924 12383 4.779733 GCCAGGAGAGGGACCCGA 62.780 72.222 4.40 0.00 0.00 5.14
3927 12386 3.791586 GCAGCCAGGAGAGGGACC 61.792 72.222 0.00 0.00 0.00 4.46
3928 12387 2.686835 AGCAGCCAGGAGAGGGAC 60.687 66.667 0.00 0.00 0.00 4.46
3929 12388 2.364842 GAGCAGCCAGGAGAGGGA 60.365 66.667 0.00 0.00 0.00 4.20
3931 12390 2.433994 GGAGAGCAGCCAGGAGAGG 61.434 68.421 0.00 0.00 0.00 3.69
3933 12392 2.757508 CGGAGAGCAGCCAGGAGA 60.758 66.667 0.00 0.00 0.00 3.71
3934 12393 3.847602 CCGGAGAGCAGCCAGGAG 61.848 72.222 0.00 0.00 0.00 3.69
3944 12403 4.856607 GGAAGCGTCGCCGGAGAG 62.857 72.222 14.86 4.15 33.68 3.20
3946 12405 4.856607 GAGGAAGCGTCGCCGGAG 62.857 72.222 14.86 0.00 33.68 4.63
3949 12408 3.479269 GTTGAGGAAGCGTCGCCG 61.479 66.667 14.86 0.00 37.07 6.46
3952 12411 1.446272 GAGGGTTGAGGAAGCGTCG 60.446 63.158 0.00 0.00 35.46 5.12
3953 12412 0.108567 GAGAGGGTTGAGGAAGCGTC 60.109 60.000 0.00 0.00 42.26 5.19
3956 12415 0.912006 AGGGAGAGGGTTGAGGAAGC 60.912 60.000 0.00 0.00 0.00 3.86
3957 12416 1.199615 GAGGGAGAGGGTTGAGGAAG 58.800 60.000 0.00 0.00 0.00 3.46
3958 12417 0.252742 GGAGGGAGAGGGTTGAGGAA 60.253 60.000 0.00 0.00 0.00 3.36
3959 12418 1.392534 GGAGGGAGAGGGTTGAGGA 59.607 63.158 0.00 0.00 0.00 3.71
3960 12419 1.690985 GGGAGGGAGAGGGTTGAGG 60.691 68.421 0.00 0.00 0.00 3.86
3961 12420 2.060980 CGGGAGGGAGAGGGTTGAG 61.061 68.421 0.00 0.00 0.00 3.02
3962 12421 2.038975 CGGGAGGGAGAGGGTTGA 59.961 66.667 0.00 0.00 0.00 3.18
3963 12422 2.284699 ACGGGAGGGAGAGGGTTG 60.285 66.667 0.00 0.00 0.00 3.77
3964 12423 2.284699 CACGGGAGGGAGAGGGTT 60.285 66.667 0.00 0.00 32.31 4.11
3965 12424 4.400251 CCACGGGAGGGAGAGGGT 62.400 72.222 0.00 0.00 32.31 4.34


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

AutoCloner maintained by Alex Coulton.