Multiple sequence alignment - TraesCS1B01G132800

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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 TraesCS1B01G132800 chr1B 100.000 5566 0 0 1 5566 167714394 167719959 0.000000e+00 10279
1 TraesCS1B01G132800 chr1B 90.400 125 11 1 2569 2693 68073351 68073474 4.460000e-36 163
2 TraesCS1B01G132800 chr1A 92.693 3572 155 41 881 4414 114547947 114551450 0.000000e+00 5053
3 TraesCS1B01G132800 chr1A 93.242 1169 49 8 4413 5566 114551679 114552832 0.000000e+00 1694
4 TraesCS1B01G132800 chr1A 90.524 401 26 4 1 392 114546425 114546822 2.300000e-143 520
5 TraesCS1B01G132800 chr1A 89.342 319 24 5 389 702 114547158 114547471 5.230000e-105 392
6 TraesCS1B01G132800 chr1D 92.973 3259 177 22 2331 5560 110338664 110341899 0.000000e+00 4702
7 TraesCS1B01G132800 chr1D 92.333 1826 86 21 529 2328 110336837 110338634 0.000000e+00 2547
8 TraesCS1B01G132800 chr1D 91.501 553 26 12 3116 3661 488723193 488722655 0.000000e+00 741
9 TraesCS1B01G132800 chr1D 97.727 176 4 0 1 176 110336318 110336493 2.520000e-78 303
10 TraesCS1B01G132800 chr1D 92.000 125 9 1 2569 2693 48391337 48391460 2.060000e-39 174
11 TraesCS1B01G132800 chr3D 91.019 1080 72 14 2672 3745 226022244 226023304 0.000000e+00 1434
12 TraesCS1B01G132800 chr3D 95.472 265 6 3 1590 1852 573314671 573314411 8.620000e-113 418
13 TraesCS1B01G132800 chr3D 95.094 265 7 3 1590 1852 474128907 474128647 4.010000e-111 412
14 TraesCS1B01G132800 chr4D 92.132 788 43 10 2963 3745 12844366 12845139 0.000000e+00 1094
15 TraesCS1B01G132800 chr4D 92.377 223 14 2 2962 3184 197323870 197323651 1.160000e-81 315
16 TraesCS1B01G132800 chr4D 87.597 129 15 1 2569 2696 293386178 293386050 1.250000e-31 148
17 TraesCS1B01G132800 chr2D 91.381 789 48 10 2963 3745 467630531 467629757 0.000000e+00 1062
18 TraesCS1B01G132800 chr2D 95.094 265 7 3 1590 1852 573865162 573864902 4.010000e-111 412
19 TraesCS1B01G132800 chr2D 93.810 210 13 0 2672 2881 573508209 573508418 3.240000e-82 316
20 TraesCS1B01G132800 chrUn 90.241 789 48 15 2963 3745 71029993 71029228 0.000000e+00 1003
21 TraesCS1B01G132800 chrUn 90.241 789 48 15 2963 3745 408524110 408524875 0.000000e+00 1003
22 TraesCS1B01G132800 chrUn 83.651 630 60 24 1247 1852 331637494 331638104 2.270000e-153 553
23 TraesCS1B01G132800 chr3B 90.972 576 36 6 3175 3745 254543126 254542562 0.000000e+00 761
24 TraesCS1B01G132800 chr3B 89.080 522 43 6 2672 3192 254606290 254605782 2.190000e-178 636
25 TraesCS1B01G132800 chr7D 91.501 553 26 12 3116 3661 184789779 184789241 0.000000e+00 741
26 TraesCS1B01G132800 chr7D 95.849 265 5 3 1590 1852 177235491 177235231 1.850000e-114 424
27 TraesCS1B01G132800 chr7D 91.776 304 22 2 2672 2975 177235238 177234938 2.400000e-113 420
28 TraesCS1B01G132800 chr7D 89.600 125 12 1 2569 2693 530123876 530123999 2.080000e-34 158
29 TraesCS1B01G132800 chr6D 91.320 553 27 12 3116 3661 123583530 123584068 0.000000e+00 736
30 TraesCS1B01G132800 chr6D 94.776 268 8 3 1587 1852 453201273 453201536 4.010000e-111 412
31 TraesCS1B01G132800 chr3A 83.693 742 75 22 1109 1841 530061607 530062311 0.000000e+00 658
32 TraesCS1B01G132800 chr6A 83.333 744 51 26 1109 1841 86629678 86628997 2.200000e-173 619
33 TraesCS1B01G132800 chr6A 91.060 302 24 2 2672 2973 33173032 33172734 6.710000e-109 405
34 TraesCS1B01G132800 chr4A 84.302 688 50 25 1168 1841 201150630 201149987 2.200000e-173 619
35 TraesCS1B01G132800 chr4A 83.221 745 55 27 1109 1841 211667949 211668635 2.200000e-173 619
36 TraesCS1B01G132800 chr4A 88.281 128 14 1 2569 2696 231025461 231025335 9.660000e-33 152
37 TraesCS1B01G132800 chr5B 83.810 630 59 24 1247 1852 688472333 688471723 4.870000e-155 558
38 TraesCS1B01G132800 chr5B 83.433 501 43 22 1373 1852 688474941 688474460 3.980000e-116 429
39 TraesCS1B01G132800 chr2B 95.149 268 7 3 1587 1852 703576940 703577203 8.620000e-113 418
40 TraesCS1B01G132800 chr2B 94.776 268 8 3 1587 1852 2492798 2493061 4.010000e-111 412
41 TraesCS1B01G132800 chr2B 94.286 210 12 0 2672 2881 703577196 703577405 6.960000e-84 322
42 TraesCS1B01G132800 chr6B 94.762 210 11 0 2672 2881 353790671 353790880 1.500000e-85 327
43 TraesCS1B01G132800 chr2A 91.057 123 11 0 2571 2693 186406124 186406002 3.450000e-37 167
44 TraesCS1B01G132800 chr5A 88.281 128 15 0 2569 2696 82869920 82869793 2.690000e-33 154


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 TraesCS1B01G132800 chr1B 167714394 167719959 5565 False 10279.000000 10279 100.000000 1 5566 1 chr1B.!!$F2 5565
1 TraesCS1B01G132800 chr1A 114546425 114552832 6407 False 1914.750000 5053 91.450250 1 5566 4 chr1A.!!$F1 5565
2 TraesCS1B01G132800 chr1D 110336318 110341899 5581 False 2517.333333 4702 94.344333 1 5560 3 chr1D.!!$F2 5559
3 TraesCS1B01G132800 chr1D 488722655 488723193 538 True 741.000000 741 91.501000 3116 3661 1 chr1D.!!$R1 545
4 TraesCS1B01G132800 chr3D 226022244 226023304 1060 False 1434.000000 1434 91.019000 2672 3745 1 chr3D.!!$F1 1073
5 TraesCS1B01G132800 chr4D 12844366 12845139 773 False 1094.000000 1094 92.132000 2963 3745 1 chr4D.!!$F1 782
6 TraesCS1B01G132800 chr2D 467629757 467630531 774 True 1062.000000 1062 91.381000 2963 3745 1 chr2D.!!$R1 782
7 TraesCS1B01G132800 chrUn 71029228 71029993 765 True 1003.000000 1003 90.241000 2963 3745 1 chrUn.!!$R1 782
8 TraesCS1B01G132800 chrUn 408524110 408524875 765 False 1003.000000 1003 90.241000 2963 3745 1 chrUn.!!$F2 782
9 TraesCS1B01G132800 chrUn 331637494 331638104 610 False 553.000000 553 83.651000 1247 1852 1 chrUn.!!$F1 605
10 TraesCS1B01G132800 chr3B 254542562 254543126 564 True 761.000000 761 90.972000 3175 3745 1 chr3B.!!$R1 570
11 TraesCS1B01G132800 chr3B 254605782 254606290 508 True 636.000000 636 89.080000 2672 3192 1 chr3B.!!$R2 520
12 TraesCS1B01G132800 chr7D 184789241 184789779 538 True 741.000000 741 91.501000 3116 3661 1 chr7D.!!$R1 545
13 TraesCS1B01G132800 chr7D 177234938 177235491 553 True 422.000000 424 93.812500 1590 2975 2 chr7D.!!$R2 1385
14 TraesCS1B01G132800 chr6D 123583530 123584068 538 False 736.000000 736 91.320000 3116 3661 1 chr6D.!!$F1 545
15 TraesCS1B01G132800 chr3A 530061607 530062311 704 False 658.000000 658 83.693000 1109 1841 1 chr3A.!!$F1 732
16 TraesCS1B01G132800 chr6A 86628997 86629678 681 True 619.000000 619 83.333000 1109 1841 1 chr6A.!!$R2 732
17 TraesCS1B01G132800 chr4A 201149987 201150630 643 True 619.000000 619 84.302000 1168 1841 1 chr4A.!!$R1 673
18 TraesCS1B01G132800 chr4A 211667949 211668635 686 False 619.000000 619 83.221000 1109 1841 1 chr4A.!!$F1 732
19 TraesCS1B01G132800 chr5B 688471723 688474941 3218 True 493.500000 558 83.621500 1247 1852 2 chr5B.!!$R1 605

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
290 291 0.732538 GTTGAGCAAAATTCGGGCCG 60.733 55.000 22.51 22.51 0.00 6.13 F
292 293 1.154035 GAGCAAAATTCGGGCCGTG 60.154 57.895 27.32 17.44 0.00 4.94 F
1722 3106 1.149148 GACCGCTCTCAAGGTTTGTC 58.851 55.000 0.00 0.00 41.51 3.18 F
2091 3500 0.034337 CAAATTGCAAGCTGGCCACT 59.966 50.000 11.50 0.75 0.00 4.00 F
2520 3960 0.166814 CTGAGTGCCGCTAAAACTGC 59.833 55.000 0.00 0.00 0.00 4.40 F
3174 4634 0.911769 CCCTGTTCCCTCACATAGCA 59.088 55.000 0.00 0.00 0.00 3.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1649 3025 0.873054 CTGCGGCAATCCAGATCATC 59.127 55.0 3.44 0.0 0.00 2.92 R
1928 3336 1.109609 TGTCACATTTGTGCTGGCAA 58.890 45.0 5.81 0.0 45.25 4.52 R
3389 4867 0.333993 ATGAGTTGCTGATTGGGCCT 59.666 50.0 4.53 0.0 0.00 5.19 R
3390 4868 1.188863 AATGAGTTGCTGATTGGGCC 58.811 50.0 0.00 0.0 0.00 5.80 R
4267 5752 0.457443 TAGCACACAGATCTCCAGCG 59.543 55.0 0.00 0.0 0.00 5.18 R
4890 6609 0.388649 CAAGCTACGTTCGCTCAGGT 60.389 55.0 11.72 0.0 36.56 4.00 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
188 189 1.024271 CTGTGGTTGTTGTCCTGTGG 58.976 55.000 0.00 0.00 0.00 4.17
209 210 6.203145 TGTGGTTGAATTTGATGCTTCATTTG 59.797 34.615 2.75 0.00 31.83 2.32
235 236 9.937175 GATGAAGCTACATAAGGAAAATGTTAC 57.063 33.333 0.00 0.00 38.49 2.50
236 237 9.686683 ATGAAGCTACATAAGGAAAATGTTACT 57.313 29.630 0.00 0.00 38.49 2.24
248 249 6.018180 AGGAAAATGTTACTCGTTCTTCACAC 60.018 38.462 0.00 0.00 0.00 3.82
266 267 4.876679 TCACACGGTTTGAAACATTCTGTA 59.123 37.500 10.53 0.00 0.00 2.74
273 274 7.148137 ACGGTTTGAAACATTCTGTAAAGAGTT 60.148 33.333 10.53 0.00 0.00 3.01
274 275 7.165812 CGGTTTGAAACATTCTGTAAAGAGTTG 59.834 37.037 10.53 0.00 0.00 3.16
290 291 0.732538 GTTGAGCAAAATTCGGGCCG 60.733 55.000 22.51 22.51 0.00 6.13
292 293 1.154035 GAGCAAAATTCGGGCCGTG 60.154 57.895 27.32 17.44 0.00 4.94
308 309 2.937873 GCCGTGGCACCTTTCAGTAATA 60.938 50.000 12.86 0.00 41.49 0.98
347 364 5.671493 ACAATTTCCGGATGTCTAGTTAGG 58.329 41.667 4.15 0.00 0.00 2.69
379 396 1.269517 TGGTCAATTTTGCTGGCGTTC 60.270 47.619 0.00 0.00 0.00 3.95
410 766 2.413310 ATACAATTTCCGGACGCCTT 57.587 45.000 1.83 0.00 0.00 4.35
522 882 4.365514 TCATGTCAGTTTGCCTTCCTTA 57.634 40.909 0.00 0.00 0.00 2.69
532 932 2.000048 TGCCTTCCTTATTTCCCCTGT 59.000 47.619 0.00 0.00 0.00 4.00
618 1021 5.009631 AGAATTGACCGAACATGAAATCCA 58.990 37.500 0.00 0.00 0.00 3.41
625 1028 3.067180 CCGAACATGAAATCCAAGGGATG 59.933 47.826 0.00 0.00 42.27 3.51
747 1150 1.609580 CGGGGAGACGAACAAAATCCA 60.610 52.381 0.00 0.00 35.47 3.41
776 1179 3.103911 GTCGCCCACACGAACGAG 61.104 66.667 0.14 0.00 44.93 4.18
777 1180 3.598715 TCGCCCACACGAACGAGT 61.599 61.111 0.14 0.00 39.54 4.18
779 1182 2.654912 CGCCCACACGAACGAGTTC 61.655 63.158 5.93 5.93 36.29 3.01
865 1268 2.581246 ACATAAACCCCCTTCCTTCCTC 59.419 50.000 0.00 0.00 0.00 3.71
868 1271 2.696504 CCCCCTTCCTTCCTCCCC 60.697 72.222 0.00 0.00 0.00 4.81
884 1594 2.317378 CCCTCTTCCCCTTTCCCCC 61.317 68.421 0.00 0.00 0.00 5.40
1107 1817 3.187699 CTCCGCGCTGCTCGAGTAT 62.188 63.158 14.26 0.00 41.67 2.12
1537 2911 3.155998 CGTGAATTGTGATGCGAGTTTC 58.844 45.455 0.00 0.00 0.00 2.78
1588 2962 2.127232 GCGTGGAAAAGTCGCTGC 60.127 61.111 0.00 0.00 45.29 5.25
1649 3025 8.932791 AGTTTATATTGTGTAGGTTTCTTCGTG 58.067 33.333 0.00 0.00 0.00 4.35
1722 3106 1.149148 GACCGCTCTCAAGGTTTGTC 58.851 55.000 0.00 0.00 41.51 3.18
1845 3251 3.732721 GTGCATCAACTTTCTTGTTCTGC 59.267 43.478 0.00 0.00 36.74 4.26
1853 3259 7.497595 TCAACTTTCTTGTTCTGCTTCTAGTA 58.502 34.615 0.00 0.00 0.00 1.82
1884 3290 9.601217 GATTAATTGTTCTGCTTCTAGAGGTTA 57.399 33.333 3.55 0.00 0.00 2.85
1885 3292 8.773404 TTAATTGTTCTGCTTCTAGAGGTTAC 57.227 34.615 3.55 0.00 0.00 2.50
1937 3345 1.445582 GCTCAGCAATTGCCAGCAC 60.446 57.895 32.41 16.31 43.33 4.40
2024 3433 5.714333 TGAATAAATGCAAACCCTTCTGCTA 59.286 36.000 0.00 0.00 39.38 3.49
2091 3500 0.034337 CAAATTGCAAGCTGGCCACT 59.966 50.000 11.50 0.75 0.00 4.00
2133 3542 2.731968 CGTCTGCCCATGTAACATTTGC 60.732 50.000 0.00 0.00 0.00 3.68
2214 3627 5.469479 GGTTTGGTTGTCCTTTCATATGTG 58.531 41.667 1.90 0.00 34.23 3.21
2223 3636 4.342092 GTCCTTTCATATGTGGGGAAATGG 59.658 45.833 1.90 1.03 30.88 3.16
2254 3667 5.459107 ACAGCTAAGAGTAATTGATAACGCG 59.541 40.000 3.53 3.53 0.00 6.01
2282 3695 6.493802 TGGATGTCTAAGCCTATAAGACGATT 59.506 38.462 0.00 0.00 42.05 3.34
2328 3741 1.496060 ATGACCATGCCTCCTTACGA 58.504 50.000 0.00 0.00 0.00 3.43
2353 3793 3.978855 CACGAAGAACAACACGTAGATGA 59.021 43.478 0.00 0.00 37.22 2.92
2378 3818 0.175760 TGGCGCCTCACTGAACTATC 59.824 55.000 29.70 0.00 0.00 2.08
2389 3829 4.109050 CACTGAACTATCGAAGCCTCTTC 58.891 47.826 0.00 0.00 0.00 2.87
2485 3925 2.673043 GCTGTTGCTGATGGAACCAATG 60.673 50.000 0.00 0.00 42.72 2.82
2500 3940 1.039068 CAATGGCTGGTGTTTGTGGA 58.961 50.000 0.00 0.00 0.00 4.02
2520 3960 0.166814 CTGAGTGCCGCTAAAACTGC 59.833 55.000 0.00 0.00 0.00 4.40
2542 3982 2.290093 GCAGTGAGCCTCATAGCAATTC 59.710 50.000 14.15 0.00 37.23 2.17
2651 4091 2.445525 TGCCTTGTATAATCCTTCCCCC 59.554 50.000 0.00 0.00 0.00 5.40
2678 4118 1.627297 CCTGGGGTGGGAGCTTCTAC 61.627 65.000 0.00 0.00 0.00 2.59
2808 4265 5.878406 AGATAACTCCATTTGATCGTCCT 57.122 39.130 0.00 0.00 0.00 3.85
2809 4266 5.848406 AGATAACTCCATTTGATCGTCCTC 58.152 41.667 0.00 0.00 0.00 3.71
2810 4267 3.981071 AACTCCATTTGATCGTCCTCA 57.019 42.857 0.00 0.00 0.00 3.86
2811 4268 4.494091 AACTCCATTTGATCGTCCTCAT 57.506 40.909 0.00 0.00 0.00 2.90
2812 4269 5.614324 AACTCCATTTGATCGTCCTCATA 57.386 39.130 0.00 0.00 0.00 2.15
2813 4270 5.207110 ACTCCATTTGATCGTCCTCATAG 57.793 43.478 0.00 0.00 0.00 2.23
2814 4271 4.651503 ACTCCATTTGATCGTCCTCATAGT 59.348 41.667 0.00 0.00 0.00 2.12
2815 4272 4.948847 TCCATTTGATCGTCCTCATAGTG 58.051 43.478 0.00 0.00 0.00 2.74
2816 4273 4.649218 TCCATTTGATCGTCCTCATAGTGA 59.351 41.667 0.00 0.00 0.00 3.41
2817 4274 5.305386 TCCATTTGATCGTCCTCATAGTGAT 59.695 40.000 0.00 0.00 0.00 3.06
2818 4275 5.636965 CCATTTGATCGTCCTCATAGTGATC 59.363 44.000 0.00 0.00 36.77 2.92
2819 4276 6.453943 CATTTGATCGTCCTCATAGTGATCT 58.546 40.000 0.00 0.00 37.07 2.75
2820 4277 5.697473 TTGATCGTCCTCATAGTGATCTC 57.303 43.478 0.00 0.00 37.07 2.75
2821 4278 4.718961 TGATCGTCCTCATAGTGATCTCA 58.281 43.478 0.00 0.00 37.07 3.27
2822 4279 4.517075 TGATCGTCCTCATAGTGATCTCAC 59.483 45.833 2.01 2.01 46.77 3.51
2919 4376 4.036941 TCCCCTTTAAGTTAATGCGGTT 57.963 40.909 10.44 0.00 0.00 4.44
3112 4570 4.998051 TGCTTCCTCCAAAAGAAATACCT 58.002 39.130 0.00 0.00 0.00 3.08
3165 4625 3.053619 GTGAATGGTATTCCCTGTTCCCT 60.054 47.826 0.00 0.00 31.48 4.20
3170 4630 2.509964 GGTATTCCCTGTTCCCTCACAT 59.490 50.000 0.00 0.00 0.00 3.21
3171 4631 3.714798 GGTATTCCCTGTTCCCTCACATA 59.285 47.826 0.00 0.00 0.00 2.29
3172 4632 4.202367 GGTATTCCCTGTTCCCTCACATAG 60.202 50.000 0.00 0.00 0.00 2.23
3173 4633 1.204146 TCCCTGTTCCCTCACATAGC 58.796 55.000 0.00 0.00 0.00 2.97
3174 4634 0.911769 CCCTGTTCCCTCACATAGCA 59.088 55.000 0.00 0.00 0.00 3.49
3175 4635 1.492176 CCCTGTTCCCTCACATAGCAT 59.508 52.381 0.00 0.00 0.00 3.79
3176 4636 2.569059 CCTGTTCCCTCACATAGCATG 58.431 52.381 0.00 0.00 0.00 4.06
3177 4637 2.171237 CCTGTTCCCTCACATAGCATGA 59.829 50.000 0.00 0.00 0.00 3.07
3200 4660 2.592993 CCGTTTGGGGCCTCTCTGA 61.593 63.158 3.07 0.00 0.00 3.27
3272 4744 6.647334 TGGTTTTCTATGATGCACTCAAAA 57.353 33.333 0.00 0.00 37.44 2.44
3384 4857 2.647299 TGAGGCCCTTGGTCATTTCTTA 59.353 45.455 0.00 0.00 0.00 2.10
3389 4867 5.014202 GGCCCTTGGTCATTTCTTAAACTA 58.986 41.667 0.00 0.00 0.00 2.24
3390 4868 5.125578 GGCCCTTGGTCATTTCTTAAACTAG 59.874 44.000 0.00 0.00 0.00 2.57
3391 4869 5.125578 GCCCTTGGTCATTTCTTAAACTAGG 59.874 44.000 0.00 0.00 0.00 3.02
3392 4870 5.125578 CCCTTGGTCATTTCTTAAACTAGGC 59.874 44.000 0.00 0.00 0.00 3.93
3393 4871 5.125578 CCTTGGTCATTTCTTAAACTAGGCC 59.874 44.000 0.00 0.00 0.00 5.19
3401 4879 3.886123 TCTTAAACTAGGCCCAATCAGC 58.114 45.455 0.00 0.00 0.00 4.26
3436 4915 5.202640 GGAAAAACTTGACGATGTGTGTAC 58.797 41.667 0.00 0.00 0.00 2.90
3437 4916 4.806342 AAAACTTGACGATGTGTGTACC 57.194 40.909 0.00 0.00 0.00 3.34
3438 4917 3.746045 AACTTGACGATGTGTGTACCT 57.254 42.857 0.00 0.00 0.00 3.08
3559 5038 9.388506 ACCATTTCTATCTGTTCATAACTCTTG 57.611 33.333 0.00 0.00 0.00 3.02
3787 5271 5.102953 AGAGATGTACAGCCAAGCATTTA 57.897 39.130 7.66 0.00 0.00 1.40
3789 5273 6.125029 AGAGATGTACAGCCAAGCATTTATT 58.875 36.000 7.66 0.00 0.00 1.40
3983 5467 3.509575 GCATCAATGGTGGAAAAGGTACA 59.490 43.478 0.00 0.00 0.00 2.90
4267 5752 1.767759 ATGGTATGCAGGTTCTTGCC 58.232 50.000 4.58 0.00 43.43 4.52
4396 5884 3.133362 ACACCTTTGTCGTCTGGTTCTTA 59.867 43.478 0.00 0.00 0.00 2.10
4403 5891 3.745975 TGTCGTCTGGTTCTTAATGCTTG 59.254 43.478 0.00 0.00 0.00 4.01
4404 5892 3.746492 GTCGTCTGGTTCTTAATGCTTGT 59.254 43.478 0.00 0.00 0.00 3.16
4405 5893 4.213482 GTCGTCTGGTTCTTAATGCTTGTT 59.787 41.667 0.00 0.00 0.00 2.83
4406 5894 4.213270 TCGTCTGGTTCTTAATGCTTGTTG 59.787 41.667 0.00 0.00 0.00 3.33
4408 5896 3.255642 TCTGGTTCTTAATGCTTGTTGGC 59.744 43.478 0.00 0.00 0.00 4.52
4409 5897 2.961741 TGGTTCTTAATGCTTGTTGGCA 59.038 40.909 0.00 0.00 46.63 4.92
4429 6148 7.473735 TGGCATCTAACATTTACCAAATTGA 57.526 32.000 0.00 0.00 0.00 2.57
4451 6170 0.924090 CTTACCATCGCTCGCTGAAC 59.076 55.000 0.00 0.00 0.00 3.18
4615 6334 1.528824 CAGATGTTGGATCGCCCCT 59.471 57.895 0.00 0.00 0.00 4.79
4879 6598 8.267620 TGACCTTATACAAGATCACAAATGTG 57.732 34.615 7.22 7.22 39.51 3.21
4898 6617 1.269778 TGAACTCTTGACACCTGAGCG 60.270 52.381 0.00 0.00 0.00 5.03
4927 6646 3.181526 GCTTGTTGCTCGTACAATGAGAG 60.182 47.826 0.31 0.00 35.18 3.20
4967 6686 1.882912 TGCTTGTGTCACATGAGTCC 58.117 50.000 20.02 5.45 0.00 3.85
4971 6690 3.619733 GCTTGTGTCACATGAGTCCCATA 60.620 47.826 20.02 0.00 33.31 2.74
4973 6692 3.937814 TGTGTCACATGAGTCCCATAAC 58.062 45.455 0.18 0.00 33.31 1.89
5021 6741 5.796350 TTTAGTAATTTCAGCGAAGGAGC 57.204 39.130 0.00 0.00 37.41 4.70
5037 6757 3.094572 AGGAGCTGGGTTTGATTTGATG 58.905 45.455 0.00 0.00 0.00 3.07
5038 6758 2.417787 GGAGCTGGGTTTGATTTGATGC 60.418 50.000 0.00 0.00 0.00 3.91
5044 6764 1.669502 GGTTTGATTTGATGCAGCGCA 60.670 47.619 11.47 5.73 44.86 6.09
5045 6765 1.387756 GTTTGATTTGATGCAGCGCAC 59.612 47.619 11.47 0.68 43.04 5.34
5046 6766 0.597072 TTGATTTGATGCAGCGCACA 59.403 45.000 11.47 8.11 43.04 4.57
5091 6822 2.403259 GCACCGAAAATGAACCAAAGG 58.597 47.619 0.00 0.00 0.00 3.11
5111 6842 0.333993 AGGCAAGATGGCATGAACCT 59.666 50.000 3.81 3.23 46.46 3.50
5217 6949 4.201714 CCGACAGCACTAATGTGTGTAATG 60.202 45.833 0.00 0.00 45.44 1.90
5288 7020 0.767375 ACATCACAGGAAGGTGCACT 59.233 50.000 17.98 0.00 38.66 4.40
5289 7021 1.143684 ACATCACAGGAAGGTGCACTT 59.856 47.619 17.98 6.12 43.65 3.16
5290 7022 2.233271 CATCACAGGAAGGTGCACTTT 58.767 47.619 14.80 14.80 40.21 2.66
5291 7023 1.967319 TCACAGGAAGGTGCACTTTC 58.033 50.000 28.32 28.32 40.21 2.62
5295 7027 1.959848 GGAAGGTGCACTTTCCTGC 59.040 57.895 39.35 22.05 45.46 4.85
5296 7028 0.823356 GGAAGGTGCACTTTCCTGCA 60.823 55.000 39.35 0.00 45.46 4.41
5551 7289 2.095053 GCTGATTGTCTTCTTCCTTCGC 59.905 50.000 0.00 0.00 0.00 4.70
5560 7298 2.024176 TCTTCCTTCGCTTGTATGCC 57.976 50.000 0.00 0.00 0.00 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
188 189 8.246908 TCATCAAATGAAGCATCAAATTCAAC 57.753 30.769 0.00 0.00 38.80 3.18
209 210 9.937175 GTAACATTTTCCTTATGTAGCTTCATC 57.063 33.333 9.33 0.00 35.26 2.92
235 236 2.198406 TCAAACCGTGTGAAGAACGAG 58.802 47.619 0.00 0.00 43.68 4.18
236 237 2.296831 TCAAACCGTGTGAAGAACGA 57.703 45.000 0.00 0.00 43.68 3.85
266 267 3.552890 GCCCGAATTTTGCTCAACTCTTT 60.553 43.478 0.00 0.00 0.00 2.52
273 274 1.602323 ACGGCCCGAATTTTGCTCA 60.602 52.632 11.71 0.00 0.00 4.26
274 275 1.154035 CACGGCCCGAATTTTGCTC 60.154 57.895 11.71 0.00 0.00 4.26
290 291 5.897377 ACAATATTACTGAAAGGTGCCAC 57.103 39.130 0.00 0.00 39.30 5.01
292 293 6.509418 TCAACAATATTACTGAAAGGTGCC 57.491 37.500 0.00 0.00 39.30 5.01
308 309 7.250569 CGGAAATTGTATACTGCTTCAACAAT 58.749 34.615 4.17 0.00 41.29 2.71
347 364 5.585390 CAAAATTGACCAGCAGATGATACC 58.415 41.667 0.00 0.00 0.00 2.73
379 396 8.074972 GTCCGGAAATTGTATACTACTCTACTG 58.925 40.741 5.23 0.00 0.00 2.74
410 766 3.425094 CGAAACAACCAACTGAACGAACA 60.425 43.478 0.00 0.00 0.00 3.18
489 849 9.023967 GGCAAACTGACATGAATGTTATATTTC 57.976 33.333 0.00 0.00 41.95 2.17
498 858 3.508793 AGGAAGGCAAACTGACATGAATG 59.491 43.478 0.00 0.00 0.00 2.67
522 882 4.600062 GAACCATCAACTACAGGGGAAAT 58.400 43.478 0.00 0.00 0.00 2.17
532 932 4.837093 AGGGATTTCGAACCATCAACTA 57.163 40.909 11.04 0.00 0.00 2.24
605 1008 5.418576 AGCCATCCCTTGGATTTCATGTTC 61.419 45.833 0.00 0.00 43.17 3.18
618 1021 0.912487 TCCCAACGTAGCCATCCCTT 60.912 55.000 0.00 0.00 0.00 3.95
625 1028 1.227176 GACCGATCCCAACGTAGCC 60.227 63.158 0.00 0.00 0.00 3.93
628 1031 1.067425 CAACAGACCGATCCCAACGTA 60.067 52.381 0.00 0.00 0.00 3.57
690 1093 2.863401 TCGATGGTCGTCTATTGGTG 57.137 50.000 0.00 0.00 41.35 4.17
721 1124 2.362120 TTCGTCTCCCCGGGTCTC 60.362 66.667 21.85 5.94 0.00 3.36
730 1133 3.551551 CGTTTGGATTTTGTTCGTCTCC 58.448 45.455 0.00 0.00 0.00 3.71
759 1162 3.103911 CTCGTTCGTGTGGGCGAC 61.104 66.667 0.00 0.00 40.85 5.19
865 1268 2.317378 GGGGAAAGGGGAAGAGGGG 61.317 68.421 0.00 0.00 0.00 4.79
1537 2911 2.757896 CACAACGAAATGGATCGAACG 58.242 47.619 3.47 0.00 45.48 3.95
1588 2962 2.886862 ACTCGCCATCATCTTCTGAG 57.113 50.000 0.00 0.00 37.28 3.35
1649 3025 0.873054 CTGCGGCAATCCAGATCATC 59.127 55.000 3.44 0.00 0.00 2.92
1859 3265 9.384764 GTAACCTCTAGAAGCAGAACAATTAAT 57.615 33.333 0.00 0.00 0.00 1.40
1867 3273 5.542635 TCCAAAGTAACCTCTAGAAGCAGAA 59.457 40.000 0.00 0.00 0.00 3.02
1869 3275 5.407407 TCCAAAGTAACCTCTAGAAGCAG 57.593 43.478 0.00 0.00 0.00 4.24
1884 3290 7.943079 TGATCAACAATATGACATCCAAAGT 57.057 32.000 0.00 0.00 30.82 2.66
1885 3292 8.410912 ACATGATCAACAATATGACATCCAAAG 58.589 33.333 0.00 0.00 30.82 2.77
1928 3336 1.109609 TGTCACATTTGTGCTGGCAA 58.890 45.000 5.81 0.00 45.25 4.52
2024 3433 2.574018 TAGCTGTGCCGCTGACAGT 61.574 57.895 11.36 3.23 42.47 3.55
2214 3627 2.024414 GCTGTACACATCCATTTCCCC 58.976 52.381 0.00 0.00 0.00 4.81
2223 3636 8.879342 ATCAATTACTCTTAGCTGTACACATC 57.121 34.615 0.00 0.00 0.00 3.06
2254 3667 6.809196 CGTCTTATAGGCTTAGACATCCATTC 59.191 42.308 18.18 0.00 38.52 2.67
2282 3695 6.990349 GTGGATTATTCTCGGAGTTGGAATAA 59.010 38.462 4.69 8.42 42.32 1.40
2328 3741 5.112220 TCTACGTGTTGTTCTTCGTGTAT 57.888 39.130 0.00 0.00 37.66 2.29
2353 3793 2.418368 TCAGTGAGGCGCCAATTATT 57.582 45.000 31.54 6.18 0.00 1.40
2378 3818 1.748493 AGTCTAGCTGAAGAGGCTTCG 59.252 52.381 0.00 0.00 40.74 3.79
2389 3829 0.372679 CATGTGCGCAAGTCTAGCTG 59.627 55.000 14.00 0.00 41.68 4.24
2485 3925 0.465460 TCAGTCCACAAACACCAGCC 60.465 55.000 0.00 0.00 0.00 4.85
2500 3940 1.512926 CAGTTTTAGCGGCACTCAGT 58.487 50.000 1.45 0.00 0.00 3.41
2520 3960 0.460811 TTGCTATGAGGCTCACTGCG 60.461 55.000 27.08 15.59 44.05 5.18
2542 3982 2.221169 TGCTTCCTTAATGGCGCATAG 58.779 47.619 10.83 0.00 37.16 2.23
2549 3989 1.747355 CACAGCCTGCTTCCTTAATGG 59.253 52.381 0.00 0.00 37.10 3.16
2609 4049 2.066340 CCTTACCCCTGCACAGTGA 58.934 57.895 4.15 0.00 0.00 3.41
2803 4245 4.544651 CATGTGAGATCACTATGAGGACG 58.455 47.826 13.74 0.00 46.55 4.79
2808 4265 9.082313 TCTTATAAGCATGTGAGATCACTATGA 57.918 33.333 20.11 7.87 46.55 2.15
2809 4266 9.356433 CTCTTATAAGCATGTGAGATCACTATG 57.644 37.037 13.74 14.65 46.55 2.23
2810 4267 8.034215 GCTCTTATAAGCATGTGAGATCACTAT 58.966 37.037 13.74 5.90 43.19 2.12
2811 4268 7.232330 AGCTCTTATAAGCATGTGAGATCACTA 59.768 37.037 13.74 1.75 44.58 2.74
2812 4269 6.041865 AGCTCTTATAAGCATGTGAGATCACT 59.958 38.462 13.74 0.00 44.58 3.41
2813 4270 6.145858 CAGCTCTTATAAGCATGTGAGATCAC 59.854 42.308 7.67 6.01 45.00 3.06
2814 4271 6.221659 CAGCTCTTATAAGCATGTGAGATCA 58.778 40.000 7.67 0.00 45.00 2.92
2815 4272 5.638657 CCAGCTCTTATAAGCATGTGAGATC 59.361 44.000 7.67 0.00 45.00 2.75
2816 4273 5.306419 TCCAGCTCTTATAAGCATGTGAGAT 59.694 40.000 7.67 0.00 45.00 2.75
2817 4274 4.651045 TCCAGCTCTTATAAGCATGTGAGA 59.349 41.667 7.67 0.00 45.00 3.27
2818 4275 4.953667 TCCAGCTCTTATAAGCATGTGAG 58.046 43.478 7.67 0.59 45.00 3.51
2819 4276 5.357742 TTCCAGCTCTTATAAGCATGTGA 57.642 39.130 7.67 0.00 45.00 3.58
2820 4277 5.355071 TGTTTCCAGCTCTTATAAGCATGTG 59.645 40.000 7.67 2.94 45.00 3.21
2821 4278 5.355350 GTGTTTCCAGCTCTTATAAGCATGT 59.645 40.000 7.67 0.00 45.00 3.21
2822 4279 5.587844 AGTGTTTCCAGCTCTTATAAGCATG 59.412 40.000 7.67 6.11 45.00 4.06
2830 4287 5.246203 ACATCTACAGTGTTTCCAGCTCTTA 59.754 40.000 0.00 0.00 0.00 2.10
2860 4317 8.093307 AGTTACATTCTAGAGCACATATCCATG 58.907 37.037 0.00 0.00 38.21 3.66
2919 4376 8.227791 GCTGAAGATCTTGTTTAATTGACGTTA 58.772 33.333 14.00 0.00 0.00 3.18
3014 4471 8.958119 AACACGTGAATGGTGAATACTATTAT 57.042 30.769 25.01 0.00 38.01 1.28
3165 4625 4.406648 AACGGAGAATCATGCTATGTGA 57.593 40.909 0.00 0.00 36.25 3.58
3170 4630 2.421388 CCCCAAACGGAGAATCATGCTA 60.421 50.000 0.00 0.00 36.25 3.49
3171 4631 1.683011 CCCCAAACGGAGAATCATGCT 60.683 52.381 0.00 0.00 36.25 3.79
3172 4632 0.740737 CCCCAAACGGAGAATCATGC 59.259 55.000 0.00 0.00 36.25 4.06
3173 4633 0.740737 GCCCCAAACGGAGAATCATG 59.259 55.000 0.00 0.00 36.25 3.07
3174 4634 0.395724 GGCCCCAAACGGAGAATCAT 60.396 55.000 0.00 0.00 36.25 2.45
3175 4635 1.001393 GGCCCCAAACGGAGAATCA 60.001 57.895 0.00 0.00 36.25 2.57
3176 4636 0.748367 GAGGCCCCAAACGGAGAATC 60.748 60.000 0.00 0.00 0.00 2.52
3177 4637 1.208165 AGAGGCCCCAAACGGAGAAT 61.208 55.000 0.00 0.00 0.00 2.40
3246 4717 8.523915 TTTGAGTGCATCATAGAAAACCATAT 57.476 30.769 0.00 0.00 37.89 1.78
3384 4857 2.171003 GTTGCTGATTGGGCCTAGTTT 58.829 47.619 4.53 0.00 0.00 2.66
3389 4867 0.333993 ATGAGTTGCTGATTGGGCCT 59.666 50.000 4.53 0.00 0.00 5.19
3390 4868 1.188863 AATGAGTTGCTGATTGGGCC 58.811 50.000 0.00 0.00 0.00 5.80
3391 4869 2.028748 ACAAATGAGTTGCTGATTGGGC 60.029 45.455 0.00 0.00 41.31 5.36
3392 4870 3.581755 CACAAATGAGTTGCTGATTGGG 58.418 45.455 0.00 0.00 41.31 4.12
3393 4871 3.256383 TCCACAAATGAGTTGCTGATTGG 59.744 43.478 0.00 0.00 41.31 3.16
3401 4879 6.237542 CGTCAAGTTTTTCCACAAATGAGTTG 60.238 38.462 0.00 0.00 43.43 3.16
3436 4915 4.398044 ACAAAACAGAACACACAGGTAAGG 59.602 41.667 0.00 0.00 0.00 2.69
3437 4916 5.560966 ACAAAACAGAACACACAGGTAAG 57.439 39.130 0.00 0.00 0.00 2.34
3438 4917 5.968528 AACAAAACAGAACACACAGGTAA 57.031 34.783 0.00 0.00 0.00 2.85
3528 5007 5.823209 TGAACAGATAGAAATGGTGCATG 57.177 39.130 0.00 0.00 0.00 4.06
3559 5038 2.561478 TTTTGAGGGCAGTGGTAGTC 57.439 50.000 0.00 0.00 0.00 2.59
3564 5044 5.185635 TGATTAGAAATTTTGAGGGCAGTGG 59.814 40.000 0.00 0.00 0.00 4.00
3983 5467 9.807921 TTAAGAAATGAAACAAGGGAACTAGAT 57.192 29.630 0.00 0.00 42.68 1.98
4267 5752 0.457443 TAGCACACAGATCTCCAGCG 59.543 55.000 0.00 0.00 0.00 5.18
4403 5891 7.816995 TCAATTTGGTAAATGTTAGATGCCAAC 59.183 33.333 0.00 0.00 34.72 3.77
4404 5892 7.901029 TCAATTTGGTAAATGTTAGATGCCAA 58.099 30.769 0.00 0.00 33.35 4.52
4405 5893 7.473735 TCAATTTGGTAAATGTTAGATGCCA 57.526 32.000 0.00 0.00 0.00 4.92
4406 5894 8.655970 GTTTCAATTTGGTAAATGTTAGATGCC 58.344 33.333 0.00 0.00 0.00 4.40
4417 6136 6.864165 GCGATGGTAAGTTTCAATTTGGTAAA 59.136 34.615 0.00 0.00 0.00 2.01
4429 6148 1.067142 TCAGCGAGCGATGGTAAGTTT 60.067 47.619 8.33 0.00 31.68 2.66
4435 6154 2.507102 CGTTCAGCGAGCGATGGT 60.507 61.111 8.33 0.00 44.77 3.55
4436 6155 2.202610 TCGTTCAGCGAGCGATGG 60.203 61.111 8.33 0.00 45.68 3.51
4451 6170 3.197790 CGCTCCAACCTGCCATCG 61.198 66.667 0.00 0.00 0.00 3.84
4529 6248 1.364901 GAGGGTCGTTGAACCGTCA 59.635 57.895 10.09 0.00 45.53 4.35
4615 6334 2.355108 GCAGGCTGATGGAGAGTAACAA 60.355 50.000 20.86 0.00 0.00 2.83
4757 6476 8.478877 AGTTATTTCGTCATAACAATCCTCTCT 58.521 33.333 16.59 0.00 40.69 3.10
4838 6557 9.638239 GTATAAGGTCAATTCTGAATTTTGCAA 57.362 29.630 12.74 0.00 31.88 4.08
4879 6598 1.000163 TCGCTCAGGTGTCAAGAGTTC 60.000 52.381 0.00 0.00 0.00 3.01
4890 6609 0.388649 CAAGCTACGTTCGCTCAGGT 60.389 55.000 11.72 0.00 36.56 4.00
4940 6659 4.338964 TCATGTGACACAAGCAAGAAACAT 59.661 37.500 13.23 0.00 0.00 2.71
4947 6666 2.221169 GGACTCATGTGACACAAGCAA 58.779 47.619 13.23 0.00 0.00 3.91
4967 6686 2.738743 AGGTGGCAAGAATGGTTATGG 58.261 47.619 0.00 0.00 0.00 2.74
4971 6690 6.440328 ACATATTTTAGGTGGCAAGAATGGTT 59.560 34.615 0.00 0.00 0.00 3.67
4973 6692 6.322201 AGACATATTTTAGGTGGCAAGAATGG 59.678 38.462 0.00 0.00 0.00 3.16
5011 6730 1.302832 CAAACCCAGCTCCTTCGCT 60.303 57.895 0.00 0.00 41.90 4.93
5021 6741 2.613691 GCTGCATCAAATCAAACCCAG 58.386 47.619 0.00 0.00 0.00 4.45
5027 6747 0.597072 TGTGCGCTGCATCAAATCAA 59.403 45.000 9.73 0.00 41.91 2.57
5037 6757 1.330306 CAAAACATACTGTGCGCTGC 58.670 50.000 9.73 1.68 0.00 5.25
5038 6758 1.069022 AGCAAAACATACTGTGCGCTG 60.069 47.619 9.73 2.21 41.90 5.18
5044 6764 3.221771 TGGAGCAAGCAAAACATACTGT 58.778 40.909 0.00 0.00 0.00 3.55
5045 6765 3.503363 TCTGGAGCAAGCAAAACATACTG 59.497 43.478 0.00 0.00 0.00 2.74
5046 6766 3.754965 TCTGGAGCAAGCAAAACATACT 58.245 40.909 0.00 0.00 0.00 2.12
5091 6822 0.743097 GGTTCATGCCATCTTGCCTC 59.257 55.000 0.00 0.00 0.00 4.70
5111 6842 2.727544 GCTTTTGCCTTGCCGTCA 59.272 55.556 0.00 0.00 40.15 4.35
5162 6894 1.410882 TGTTTGCCTGCTACCCAAAAC 59.589 47.619 0.00 0.00 31.11 2.43
5217 6949 6.300354 ACTATTCAACAGCACACAACTAAC 57.700 37.500 0.00 0.00 0.00 2.34
5288 7020 4.922206 ACAGGATATTCTTGTGCAGGAAA 58.078 39.130 1.01 0.00 35.26 3.13
5289 7021 4.574674 ACAGGATATTCTTGTGCAGGAA 57.425 40.909 0.00 0.00 35.26 3.36
5290 7022 4.574674 AACAGGATATTCTTGTGCAGGA 57.425 40.909 0.00 0.00 36.77 3.86
5291 7023 5.278169 GCATAACAGGATATTCTTGTGCAGG 60.278 44.000 0.75 0.00 36.77 4.85
5292 7024 5.278169 GGCATAACAGGATATTCTTGTGCAG 60.278 44.000 6.73 0.00 36.77 4.41
5293 7025 4.580167 GGCATAACAGGATATTCTTGTGCA 59.420 41.667 6.73 0.00 36.77 4.57
5294 7026 4.319766 CGGCATAACAGGATATTCTTGTGC 60.320 45.833 0.00 0.00 36.77 4.57
5295 7027 4.214119 CCGGCATAACAGGATATTCTTGTG 59.786 45.833 0.00 0.00 36.77 3.33
5296 7028 4.102524 TCCGGCATAACAGGATATTCTTGT 59.897 41.667 0.00 0.00 38.40 3.16
5297 7029 4.641396 TCCGGCATAACAGGATATTCTTG 58.359 43.478 0.00 0.00 37.77 3.02
5359 7091 0.944386 TCTTTCAGTTCAGGCAACGC 59.056 50.000 0.00 0.00 46.39 4.84
5443 7179 8.682936 ACTAGCTATATTGTTTTCCTTGATGG 57.317 34.615 0.00 0.00 37.10 3.51
5513 7251 4.517952 TCAGCATGGTTTGGTTGTAATG 57.482 40.909 0.00 0.00 36.16 1.90


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

AutoCloner maintained by Alex Coulton.