Multiple sequence alignment - TraesCS7B01G405800

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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 TraesCS7B01G405800 chr7B 100.000 2420 0 0 1 2420 674193345 674195764 0.000000e+00 4470
1 TraesCS7B01G405800 chr7B 86.624 927 97 15 715 1634 661998729 661999635 0.000000e+00 1000
2 TraesCS7B01G405800 chr7B 86.532 891 89 18 747 1630 661716435 661717301 0.000000e+00 952
3 TraesCS7B01G405800 chr7B 87.011 870 67 24 751 1589 662311719 662310865 0.000000e+00 939
4 TraesCS7B01G405800 chr7B 90.399 677 50 10 749 1420 662010203 662009537 0.000000e+00 876
5 TraesCS7B01G405800 chr7B 88.276 725 69 10 715 1431 661468876 661469592 0.000000e+00 854
6 TraesCS7B01G405800 chr7B 97.785 316 3 1 1630 1941 727232021 727232336 2.120000e-150 542
7 TraesCS7B01G405800 chr7B 97.880 283 4 1 1631 1911 674196105 674195823 2.800000e-134 488
8 TraesCS7B01G405800 chr7B 86.000 100 12 1 445 542 661911829 661911928 3.290000e-19 106
9 TraesCS7B01G405800 chr7B 87.097 93 11 1 433 525 661707457 661707548 1.180000e-18 104
10 TraesCS7B01G405800 chr7A 92.005 888 53 7 744 1630 689252000 689252870 0.000000e+00 1230
11 TraesCS7B01G405800 chr7A 89.231 715 65 8 715 1420 680264817 680264106 0.000000e+00 883
12 TraesCS7B01G405800 chr7A 87.945 730 69 15 733 1454 680244330 680245048 0.000000e+00 843
13 TraesCS7B01G405800 chr7A 92.908 141 7 2 433 570 689251735 689251875 4.080000e-48 202
14 TraesCS7B01G405800 chr7A 98.182 110 2 0 325 434 600791734 600791843 2.460000e-45 193
15 TraesCS7B01G405800 chr7A 93.182 88 6 0 239 326 689251646 689251733 1.950000e-26 130
16 TraesCS7B01G405800 chr7A 91.667 84 6 1 1 83 689250907 689250990 5.470000e-22 115
17 TraesCS7B01G405800 chr7D 90.517 928 49 20 714 1634 596092605 596093500 0.000000e+00 1190
18 TraesCS7B01G405800 chr7D 88.585 841 74 14 715 1552 588409031 588409852 0.000000e+00 1002
19 TraesCS7B01G405800 chr7D 85.091 939 95 29 715 1629 588472045 588471128 0.000000e+00 917
20 TraesCS7B01G405800 chr7D 96.923 130 4 0 433 562 596092408 596092537 4.050000e-53 219
21 TraesCS7B01G405800 chr7D 92.366 131 6 4 323 450 529685530 529685401 1.480000e-42 183
22 TraesCS7B01G405800 chr7D 92.857 126 6 3 317 439 579148690 579148815 1.910000e-41 180
23 TraesCS7B01G405800 chr7D 92.742 124 6 2 84 205 596090458 596090580 2.470000e-40 176
24 TraesCS7B01G405800 chr7D 85.714 161 21 2 781 940 588434093 588433934 4.140000e-38 169
25 TraesCS7B01G405800 chr7D 88.550 131 7 2 204 326 596092276 596092406 4.170000e-33 152
26 TraesCS7B01G405800 chr2B 98.077 520 3 5 1899 2418 153610885 153611397 0.000000e+00 898
27 TraesCS7B01G405800 chr2B 97.880 283 4 1 1631 1911 153611740 153611458 2.800000e-134 488
28 TraesCS7B01G405800 chr2A 99.154 473 4 0 1946 2418 3794507 3794979 0.000000e+00 852
29 TraesCS7B01G405800 chr3D 88.580 683 53 13 751 1431 455037637 455036978 0.000000e+00 806
30 TraesCS7B01G405800 chr3D 97.368 114 2 1 320 432 41211727 41211614 2.460000e-45 193
31 TraesCS7B01G405800 chr2D 96.617 473 16 0 1946 2418 5230317 5230789 0.000000e+00 785
32 TraesCS7B01G405800 chr2D 98.182 110 2 0 325 434 344879983 344879874 2.460000e-45 193
33 TraesCS7B01G405800 chr6B 98.718 390 3 1 1630 2017 539182231 539182620 0.000000e+00 691
34 TraesCS7B01G405800 chr6B 98.932 281 3 0 1631 1911 539183426 539183146 9.990000e-139 503
35 TraesCS7B01G405800 chr6B 97.578 289 5 1 1630 1918 11954215 11954501 6.010000e-136 494
36 TraesCS7B01G405800 chr6B 98.227 282 5 0 2137 2418 539182804 539183085 6.010000e-136 494
37 TraesCS7B01G405800 chr6B 88.384 198 23 0 1433 1630 637179819 637180016 3.110000e-59 239
38 TraesCS7B01G405800 chr6B 96.429 112 4 0 322 433 460495298 460495409 4.110000e-43 185
39 TraesCS7B01G405800 chr3B 96.805 313 4 3 1631 1941 142725938 142726246 3.570000e-143 518
40 TraesCS7B01G405800 chr3B 98.165 109 2 0 325 433 189150385 189150277 8.830000e-45 191
41 TraesCS7B01G405800 chr3A 98.221 281 3 1 1631 1909 741365764 741366044 7.780000e-135 490
42 TraesCS7B01G405800 chr6A 98.556 277 2 1 1631 1905 115344022 115343746 2.800000e-134 488
43 TraesCS7B01G405800 chr1B 87.940 199 22 2 1433 1630 468218431 468218234 1.450000e-57 233
44 TraesCS7B01G405800 chr5D 97.345 113 3 0 321 433 257163165 257163277 2.460000e-45 193
45 TraesCS7B01G405800 chr5D 97.273 110 3 0 325 434 399581790 399581681 1.140000e-43 187
46 TraesCS7B01G405800 chr5D 97.273 110 3 0 325 434 519979415 519979524 1.140000e-43 187
47 TraesCS7B01G405800 chr5B 97.321 112 3 0 325 436 632580522 632580633 8.830000e-45 191
48 TraesCS7B01G405800 chrUn 97.273 110 3 0 324 433 92940904 92940795 1.140000e-43 187
49 TraesCS7B01G405800 chrUn 96.330 109 4 0 325 433 100324815 100324923 1.910000e-41 180
50 TraesCS7B01G405800 chrUn 95.495 111 5 0 326 436 51053041 51053151 6.880000e-41 178
51 TraesCS7B01G405800 chrUn 96.296 108 4 0 326 433 87456450 87456557 6.880000e-41 178
52 TraesCS7B01G405800 chrUn 95.495 111 5 0 326 436 342353412 342353522 6.880000e-41 178
53 TraesCS7B01G405800 chrUn 94.737 114 6 0 326 439 347838625 347838512 6.880000e-41 178
54 TraesCS7B01G405800 chrUn 96.296 108 4 0 326 433 441816730 441816837 6.880000e-41 178
55 TraesCS7B01G405800 chrUn 95.370 108 5 0 325 432 77885266 77885373 3.200000e-39 172
56 TraesCS7B01G405800 chrUn 95.327 107 5 0 326 432 24771721 24771615 1.150000e-38 171
57 TraesCS7B01G405800 chrUn 94.545 110 6 0 325 434 102124654 102124545 1.150000e-38 171
58 TraesCS7B01G405800 chrUn 90.984 122 10 1 326 446 475962780 475962901 1.930000e-36 163
59 TraesCS7B01G405800 chr6D 97.273 110 3 0 325 434 128989374 128989265 1.140000e-43 187
60 TraesCS7B01G405800 chr6D 96.364 110 4 0 325 434 77986116 77986225 5.310000e-42 182
61 TraesCS7B01G405800 chr6D 96.396 111 3 1 325 434 262665048 262665158 5.310000e-42 182
62 TraesCS7B01G405800 chr6D 96.364 110 4 0 324 433 308219409 308219518 5.310000e-42 182
63 TraesCS7B01G405800 chr6D 97.196 107 3 0 326 432 397359922 397359816 5.310000e-42 182
64 TraesCS7B01G405800 chr4D 97.273 110 3 0 325 434 29093476 29093367 1.140000e-43 187
65 TraesCS7B01G405800 chr4D 97.273 110 3 0 325 434 333227490 333227599 1.140000e-43 187
66 TraesCS7B01G405800 chr4D 94.828 116 6 0 321 436 432559001 432558886 5.310000e-42 182
67 TraesCS7B01G405800 chr4B 95.726 117 3 2 321 435 87011416 87011532 1.140000e-43 187
68 TraesCS7B01G405800 chr4B 96.396 111 3 1 326 435 242910307 242910417 5.310000e-42 182
69 TraesCS7B01G405800 chr4B 94.737 114 5 1 320 432 428410774 428410661 2.470000e-40 176
70 TraesCS7B01G405800 chr1A 97.273 110 3 0 325 434 451750749 451750640 1.140000e-43 187
71 TraesCS7B01G405800 chr1A 94.118 119 6 1 317 435 584968567 584968684 1.910000e-41 180
72 TraesCS7B01G405800 chr1D 94.872 117 5 1 322 437 19774678 19774794 5.310000e-42 182


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 TraesCS7B01G405800 chr7B 674193345 674195764 2419 False 4470.00 4470 100.0000 1 2420 1 chr7B.!!$F6 2419
1 TraesCS7B01G405800 chr7B 661998729 661999635 906 False 1000.00 1000 86.6240 715 1634 1 chr7B.!!$F5 919
2 TraesCS7B01G405800 chr7B 661716435 661717301 866 False 952.00 952 86.5320 747 1630 1 chr7B.!!$F3 883
3 TraesCS7B01G405800 chr7B 662310865 662311719 854 True 939.00 939 87.0110 751 1589 1 chr7B.!!$R2 838
4 TraesCS7B01G405800 chr7B 662009537 662010203 666 True 876.00 876 90.3990 749 1420 1 chr7B.!!$R1 671
5 TraesCS7B01G405800 chr7B 661468876 661469592 716 False 854.00 854 88.2760 715 1431 1 chr7B.!!$F1 716
6 TraesCS7B01G405800 chr7A 680264106 680264817 711 True 883.00 883 89.2310 715 1420 1 chr7A.!!$R1 705
7 TraesCS7B01G405800 chr7A 680244330 680245048 718 False 843.00 843 87.9450 733 1454 1 chr7A.!!$F2 721
8 TraesCS7B01G405800 chr7A 689250907 689252870 1963 False 419.25 1230 92.4405 1 1630 4 chr7A.!!$F3 1629
9 TraesCS7B01G405800 chr7D 588409031 588409852 821 False 1002.00 1002 88.5850 715 1552 1 chr7D.!!$F2 837
10 TraesCS7B01G405800 chr7D 588471128 588472045 917 True 917.00 917 85.0910 715 1629 1 chr7D.!!$R3 914
11 TraesCS7B01G405800 chr7D 596090458 596093500 3042 False 434.25 1190 92.1830 84 1634 4 chr7D.!!$F3 1550
12 TraesCS7B01G405800 chr2B 153610885 153611397 512 False 898.00 898 98.0770 1899 2418 1 chr2B.!!$F1 519
13 TraesCS7B01G405800 chr3D 455036978 455037637 659 True 806.00 806 88.5800 751 1431 1 chr3D.!!$R2 680
14 TraesCS7B01G405800 chr6B 539182231 539183085 854 False 592.50 691 98.4725 1630 2418 2 chr6B.!!$F4 788

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
828 3093 0.605319 GGCTGGGATCGTGTCAAACA 60.605 55.0 0.0 0.0 0.0 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1640 3981 4.036971 TCCGTGAATTGTGGTAGTTTTTGG 59.963 41.667 0.0 0.0 0.0 3.28 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
56 57 6.193514 TGGTTGTATAGTCATTGCATTGTG 57.806 37.500 8.36 0.00 0.00 3.33
59 60 4.525996 TGTATAGTCATTGCATTGTGGCT 58.474 39.130 8.36 7.42 34.20 4.75
67 68 1.246056 TGCATTGTGGCTCTTCTGGC 61.246 55.000 0.00 0.00 34.04 4.85
77 78 1.481772 GCTCTTCTGGCACTCATCTCT 59.518 52.381 0.00 0.00 0.00 3.10
80 81 4.522405 GCTCTTCTGGCACTCATCTCTATA 59.478 45.833 0.00 0.00 0.00 1.31
81 82 5.185635 GCTCTTCTGGCACTCATCTCTATAT 59.814 44.000 0.00 0.00 0.00 0.86
82 83 6.587206 TCTTCTGGCACTCATCTCTATATG 57.413 41.667 0.00 0.00 0.00 1.78
83 84 4.797800 TCTGGCACTCATCTCTATATGC 57.202 45.455 0.00 0.00 0.00 3.14
85 86 5.574188 TCTGGCACTCATCTCTATATGCTA 58.426 41.667 0.00 0.00 33.57 3.49
91 505 6.756074 GCACTCATCTCTATATGCTATTGACC 59.244 42.308 0.00 0.00 0.00 4.02
150 568 8.446489 TGTTTAATTGTGTATTGAAATGCTCG 57.554 30.769 0.00 0.00 0.00 5.03
181 599 8.030106 AGTAGTACACTTGCTAGAATTGTTCTC 58.970 37.037 1.04 0.00 36.17 2.87
286 2484 2.047061 TGGTGGTGAGCAAGACTAACT 58.953 47.619 0.00 0.00 29.28 2.24
293 2499 3.999663 GTGAGCAAGACTAACTCTGCAAT 59.000 43.478 6.30 0.00 36.15 3.56
294 2500 4.453819 GTGAGCAAGACTAACTCTGCAATT 59.546 41.667 6.30 0.00 36.15 2.32
326 2532 8.251721 GGTGAAGACAAGCTCTCTAAACTTATA 58.748 37.037 0.00 0.00 0.00 0.98
327 2533 9.078753 GTGAAGACAAGCTCTCTAAACTTATAC 57.921 37.037 0.00 0.00 0.00 1.47
328 2534 9.026121 TGAAGACAAGCTCTCTAAACTTATACT 57.974 33.333 0.00 0.00 0.00 2.12
329 2535 9.511144 GAAGACAAGCTCTCTAAACTTATACTC 57.489 37.037 0.00 0.00 0.00 2.59
330 2536 8.002984 AGACAAGCTCTCTAAACTTATACTCC 57.997 38.462 0.00 0.00 0.00 3.85
331 2537 7.068962 AGACAAGCTCTCTAAACTTATACTCCC 59.931 40.741 0.00 0.00 0.00 4.30
332 2538 6.898521 ACAAGCTCTCTAAACTTATACTCCCT 59.101 38.462 0.00 0.00 0.00 4.20
333 2539 7.068962 ACAAGCTCTCTAAACTTATACTCCCTC 59.931 40.741 0.00 0.00 0.00 4.30
334 2540 6.072649 AGCTCTCTAAACTTATACTCCCTCC 58.927 44.000 0.00 0.00 0.00 4.30
335 2541 5.048573 GCTCTCTAAACTTATACTCCCTCCG 60.049 48.000 0.00 0.00 0.00 4.63
336 2542 6.011122 TCTCTAAACTTATACTCCCTCCGT 57.989 41.667 0.00 0.00 0.00 4.69
337 2543 6.430007 TCTCTAAACTTATACTCCCTCCGTT 58.570 40.000 0.00 0.00 0.00 4.44
338 2544 6.545298 TCTCTAAACTTATACTCCCTCCGTTC 59.455 42.308 0.00 0.00 0.00 3.95
339 2545 4.382345 AAACTTATACTCCCTCCGTTCG 57.618 45.455 0.00 0.00 0.00 3.95
340 2546 2.305009 ACTTATACTCCCTCCGTTCGG 58.695 52.381 4.74 4.74 0.00 4.30
341 2547 2.092212 ACTTATACTCCCTCCGTTCGGA 60.092 50.000 13.34 13.34 0.00 4.55
342 2548 2.734755 TATACTCCCTCCGTTCGGAA 57.265 50.000 14.79 0.00 33.41 4.30
343 2549 2.083628 ATACTCCCTCCGTTCGGAAT 57.916 50.000 14.79 2.14 33.41 3.01
344 2550 1.856629 TACTCCCTCCGTTCGGAATT 58.143 50.000 14.79 0.00 33.41 2.17
345 2551 1.856629 ACTCCCTCCGTTCGGAATTA 58.143 50.000 14.79 2.82 33.41 1.40
346 2552 1.479730 ACTCCCTCCGTTCGGAATTAC 59.520 52.381 14.79 0.00 33.41 1.89
347 2553 1.755380 CTCCCTCCGTTCGGAATTACT 59.245 52.381 14.79 0.00 33.41 2.24
348 2554 1.753073 TCCCTCCGTTCGGAATTACTC 59.247 52.381 14.79 0.00 33.41 2.59
349 2555 1.535437 CCCTCCGTTCGGAATTACTCG 60.535 57.143 14.79 1.97 33.41 4.18
350 2556 1.133790 CCTCCGTTCGGAATTACTCGT 59.866 52.381 14.79 0.00 33.41 4.18
351 2557 2.448219 CTCCGTTCGGAATTACTCGTC 58.552 52.381 14.79 0.00 33.41 4.20
352 2558 1.133025 TCCGTTCGGAATTACTCGTCC 59.867 52.381 11.66 0.00 0.00 4.79
353 2559 1.135315 CCGTTCGGAATTACTCGTCCA 60.135 52.381 5.19 0.00 33.10 4.02
354 2560 2.598589 CGTTCGGAATTACTCGTCCAA 58.401 47.619 0.00 0.00 33.10 3.53
355 2561 2.597305 CGTTCGGAATTACTCGTCCAAG 59.403 50.000 0.00 0.00 33.10 3.61
356 2562 3.671433 CGTTCGGAATTACTCGTCCAAGA 60.671 47.826 0.00 0.00 33.10 3.02
357 2563 4.240096 GTTCGGAATTACTCGTCCAAGAA 58.760 43.478 0.00 0.00 33.10 2.52
358 2564 4.524316 TCGGAATTACTCGTCCAAGAAA 57.476 40.909 0.00 0.00 33.10 2.52
359 2565 5.080969 TCGGAATTACTCGTCCAAGAAAT 57.919 39.130 0.00 0.00 33.10 2.17
360 2566 4.868171 TCGGAATTACTCGTCCAAGAAATG 59.132 41.667 0.00 0.00 33.10 2.32
361 2567 4.868171 CGGAATTACTCGTCCAAGAAATGA 59.132 41.667 0.00 0.00 33.10 2.57
362 2568 5.350365 CGGAATTACTCGTCCAAGAAATGAA 59.650 40.000 0.00 0.00 33.10 2.57
363 2569 6.037172 CGGAATTACTCGTCCAAGAAATGAAT 59.963 38.462 0.00 0.00 33.10 2.57
364 2570 7.189512 GGAATTACTCGTCCAAGAAATGAATG 58.810 38.462 0.00 0.00 33.79 2.67
365 2571 7.148239 GGAATTACTCGTCCAAGAAATGAATGT 60.148 37.037 0.00 0.00 33.79 2.71
366 2572 8.786826 AATTACTCGTCCAAGAAATGAATGTA 57.213 30.769 0.00 0.00 0.00 2.29
367 2573 8.964476 ATTACTCGTCCAAGAAATGAATGTAT 57.036 30.769 0.00 0.00 0.00 2.29
368 2574 6.910536 ACTCGTCCAAGAAATGAATGTATC 57.089 37.500 0.00 0.00 0.00 2.24
369 2575 6.644347 ACTCGTCCAAGAAATGAATGTATCT 58.356 36.000 0.00 0.00 0.00 1.98
370 2576 7.782049 ACTCGTCCAAGAAATGAATGTATCTA 58.218 34.615 0.00 0.00 0.00 1.98
371 2577 7.923344 ACTCGTCCAAGAAATGAATGTATCTAG 59.077 37.037 0.00 0.00 0.00 2.43
372 2578 8.007405 TCGTCCAAGAAATGAATGTATCTAGA 57.993 34.615 0.00 0.00 0.00 2.43
373 2579 8.642432 TCGTCCAAGAAATGAATGTATCTAGAT 58.358 33.333 10.73 10.73 0.00 1.98
374 2580 8.706936 CGTCCAAGAAATGAATGTATCTAGATG 58.293 37.037 15.79 0.00 0.00 2.90
375 2581 9.553064 GTCCAAGAAATGAATGTATCTAGATGT 57.447 33.333 15.79 0.00 0.00 3.06
397 2603 8.978874 ATGTATTTTAGTTGCAGATACATCCA 57.021 30.769 0.00 0.00 38.75 3.41
398 2604 8.978874 TGTATTTTAGTTGCAGATACATCCAT 57.021 30.769 0.00 0.00 30.60 3.41
399 2605 9.407380 TGTATTTTAGTTGCAGATACATCCATT 57.593 29.630 0.00 0.00 30.60 3.16
406 2612 8.523915 AGTTGCAGATACATCCATTTTTATGA 57.476 30.769 0.00 0.00 0.00 2.15
407 2613 8.408601 AGTTGCAGATACATCCATTTTTATGAC 58.591 33.333 0.00 0.00 0.00 3.06
408 2614 7.878547 TGCAGATACATCCATTTTTATGACA 57.121 32.000 0.00 0.00 0.00 3.58
409 2615 8.291191 TGCAGATACATCCATTTTTATGACAA 57.709 30.769 0.00 0.00 0.00 3.18
410 2616 8.407832 TGCAGATACATCCATTTTTATGACAAG 58.592 33.333 0.00 0.00 0.00 3.16
411 2617 8.408601 GCAGATACATCCATTTTTATGACAAGT 58.591 33.333 0.00 0.00 0.00 3.16
423 2629 8.716619 TTTTTATGACAAGTAATTTCGAACGG 57.283 30.769 0.00 0.00 0.00 4.44
424 2630 7.655236 TTTATGACAAGTAATTTCGAACGGA 57.345 32.000 0.00 0.00 0.00 4.69
425 2631 5.779806 ATGACAAGTAATTTCGAACGGAG 57.220 39.130 0.00 0.00 0.00 4.63
426 2632 3.991773 TGACAAGTAATTTCGAACGGAGG 59.008 43.478 0.00 0.00 0.00 4.30
427 2633 3.332034 ACAAGTAATTTCGAACGGAGGG 58.668 45.455 0.00 0.00 0.00 4.30
428 2634 3.007182 ACAAGTAATTTCGAACGGAGGGA 59.993 43.478 0.00 0.00 0.00 4.20
429 2635 3.521947 AGTAATTTCGAACGGAGGGAG 57.478 47.619 0.00 0.00 0.00 4.30
430 2636 2.830321 AGTAATTTCGAACGGAGGGAGT 59.170 45.455 0.00 0.00 0.00 3.85
431 2637 4.019174 AGTAATTTCGAACGGAGGGAGTA 58.981 43.478 0.00 0.00 0.00 2.59
556 2766 3.258872 TCCTGAAAGCAAAATGTCCATGG 59.741 43.478 4.97 4.97 0.00 3.66
562 2772 6.038050 TGAAAGCAAAATGTCCATGGAAAAAC 59.962 34.615 18.20 5.02 0.00 2.43
563 2773 5.033589 AGCAAAATGTCCATGGAAAAACA 57.966 34.783 18.20 11.52 0.00 2.83
564 2774 5.058490 AGCAAAATGTCCATGGAAAAACAG 58.942 37.500 18.20 7.04 0.00 3.16
565 2775 4.815846 GCAAAATGTCCATGGAAAAACAGT 59.184 37.500 18.20 7.27 0.00 3.55
566 2776 5.988561 GCAAAATGTCCATGGAAAAACAGTA 59.011 36.000 18.20 0.00 0.00 2.74
567 2777 6.481644 GCAAAATGTCCATGGAAAAACAGTAA 59.518 34.615 18.20 0.00 0.00 2.24
568 2778 7.518211 GCAAAATGTCCATGGAAAAACAGTAAC 60.518 37.037 18.20 0.44 0.00 2.50
569 2779 6.723298 AATGTCCATGGAAAAACAGTAACA 57.277 33.333 18.20 7.05 0.00 2.41
570 2780 6.916360 ATGTCCATGGAAAAACAGTAACAT 57.084 33.333 18.20 9.25 0.00 2.71
571 2781 6.723298 TGTCCATGGAAAAACAGTAACATT 57.277 33.333 18.20 0.00 0.00 2.71
572 2782 7.118496 TGTCCATGGAAAAACAGTAACATTT 57.882 32.000 18.20 0.00 0.00 2.32
573 2783 7.206687 TGTCCATGGAAAAACAGTAACATTTC 58.793 34.615 18.20 0.00 0.00 2.17
574 2784 7.069331 TGTCCATGGAAAAACAGTAACATTTCT 59.931 33.333 18.20 0.00 33.42 2.52
575 2785 7.926018 GTCCATGGAAAAACAGTAACATTTCTT 59.074 33.333 18.20 0.00 33.42 2.52
576 2786 8.482128 TCCATGGAAAAACAGTAACATTTCTTT 58.518 29.630 13.46 0.00 33.42 2.52
577 2787 9.108284 CCATGGAAAAACAGTAACATTTCTTTT 57.892 29.630 5.56 0.00 33.42 2.27
601 2811 9.911138 TTTTTAGAAACGGAAAACAGTAACTTT 57.089 25.926 0.00 0.00 0.00 2.66
602 2812 9.911138 TTTTAGAAACGGAAAACAGTAACTTTT 57.089 25.926 0.00 0.00 0.00 2.27
603 2813 9.911138 TTTAGAAACGGAAAACAGTAACTTTTT 57.089 25.926 0.00 0.00 0.00 1.94
635 2845 9.712305 TTTTGAGAAATGGAAAAACAGTAAACA 57.288 25.926 0.00 0.00 0.00 2.83
636 2846 8.925161 TTGAGAAATGGAAAAACAGTAAACAG 57.075 30.769 0.00 0.00 0.00 3.16
637 2847 8.062065 TGAGAAATGGAAAAACAGTAAACAGT 57.938 30.769 0.00 0.00 0.00 3.55
638 2848 8.527810 TGAGAAATGGAAAAACAGTAAACAGTT 58.472 29.630 0.00 0.00 0.00 3.16
639 2849 9.366216 GAGAAATGGAAAAACAGTAAACAGTTT 57.634 29.630 3.49 3.49 37.20 2.66
640 2850 9.719355 AGAAATGGAAAAACAGTAAACAGTTTT 57.281 25.926 3.25 9.70 43.99 2.43
680 2890 6.879458 AGAAAACACAGTGACAGTTTAACTCT 59.121 34.615 7.81 2.98 34.64 3.24
688 2898 8.211629 ACAGTGACAGTTTAACTCTAAATTCCT 58.788 33.333 0.00 0.00 29.86 3.36
693 2903 6.948309 ACAGTTTAACTCTAAATTCCTGCCAT 59.052 34.615 0.00 0.00 28.58 4.40
828 3093 0.605319 GGCTGGGATCGTGTCAAACA 60.605 55.000 0.00 0.00 0.00 2.83
957 3239 0.606401 CTCCCAGCGAAACACCACAT 60.606 55.000 0.00 0.00 0.00 3.21
976 3278 3.966026 CTCTCCCCGTCGACGCAAC 62.966 68.421 31.73 0.00 38.18 4.17
978 3280 4.651008 TCCCCGTCGACGCAACAC 62.651 66.667 31.73 0.00 38.18 3.32
1031 3337 2.646175 CGGAGAAGAAGCCGGTGGA 61.646 63.158 1.90 0.00 43.67 4.02
1121 3431 2.357517 CGGCGCTGACAAGAAGGT 60.358 61.111 11.90 0.00 0.00 3.50
1344 3654 3.382832 CAGACCTCCGTCCGCCTT 61.383 66.667 0.00 0.00 40.12 4.35
1481 3791 5.936054 TCTGTAGTTAGTTAGCTGTTCGTC 58.064 41.667 0.00 0.00 0.00 4.20
1482 3792 5.704515 TCTGTAGTTAGTTAGCTGTTCGTCT 59.295 40.000 0.00 0.00 0.00 4.18
1564 3905 5.749596 ATTCTGTCTCTGACTGTCTATCG 57.250 43.478 9.51 0.00 34.05 2.92
1615 3956 7.882271 ACATTTCTTGAGAGAGTTCTTGCTATT 59.118 33.333 0.00 0.00 32.53 1.73
1640 3981 5.001232 TCCTGCTTGTGTGGAGTATTTAAC 58.999 41.667 0.00 0.00 0.00 2.01
1712 4053 4.155280 CGATTTTGTCCCGAAAACTACCAT 59.845 41.667 0.00 0.00 0.00 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
56 57 0.540923 AGATGAGTGCCAGAAGAGCC 59.459 55.000 0.00 0.00 0.00 4.70
59 60 5.047448 GCATATAGAGATGAGTGCCAGAAGA 60.047 44.000 0.00 0.00 0.00 2.87
67 68 6.971756 CGGTCAATAGCATATAGAGATGAGTG 59.028 42.308 0.00 0.00 0.00 3.51
69 70 6.502652 CCGGTCAATAGCATATAGAGATGAG 58.497 44.000 0.00 0.00 0.00 2.90
77 78 7.494625 GCTAAAATAGCCGGTCAATAGCATATA 59.505 37.037 1.90 0.00 45.95 0.86
80 81 4.455877 GCTAAAATAGCCGGTCAATAGCAT 59.544 41.667 1.90 0.00 45.95 3.79
81 82 3.813166 GCTAAAATAGCCGGTCAATAGCA 59.187 43.478 1.90 0.00 45.95 3.49
82 83 4.406001 GCTAAAATAGCCGGTCAATAGC 57.594 45.455 1.90 6.83 45.95 2.97
91 505 7.681782 TCAATTCATTTGGAGCTAAAATAGCCG 60.682 37.037 5.78 0.00 43.02 5.52
127 545 9.123709 GAACGAGCATTTCAATACACAATTAAA 57.876 29.630 0.00 0.00 0.00 1.52
150 568 5.640189 TCTAGCAAGTGTACTACTGGAAC 57.360 43.478 0.00 0.00 40.26 3.62
254 2452 3.420893 CTCACCACCAAGATTTTAGCCA 58.579 45.455 0.00 0.00 0.00 4.75
284 2482 3.777106 TCACCAGAGAAATTGCAGAGT 57.223 42.857 0.00 0.00 0.00 3.24
286 2484 4.067896 GTCTTCACCAGAGAAATTGCAGA 58.932 43.478 0.00 0.00 29.34 4.26
293 2499 3.389329 AGAGCTTGTCTTCACCAGAGAAA 59.611 43.478 0.00 0.00 34.44 2.52
294 2500 2.968574 AGAGCTTGTCTTCACCAGAGAA 59.031 45.455 0.00 0.00 33.74 2.87
326 2532 1.479730 GTAATTCCGAACGGAGGGAGT 59.520 52.381 15.34 4.12 46.06 3.85
327 2533 1.755380 AGTAATTCCGAACGGAGGGAG 59.245 52.381 15.34 0.00 46.06 4.30
328 2534 1.753073 GAGTAATTCCGAACGGAGGGA 59.247 52.381 15.34 2.49 46.06 4.20
329 2535 1.535437 CGAGTAATTCCGAACGGAGGG 60.535 57.143 15.34 0.00 46.06 4.30
330 2536 1.133790 ACGAGTAATTCCGAACGGAGG 59.866 52.381 15.34 4.28 46.06 4.30
331 2537 2.448219 GACGAGTAATTCCGAACGGAG 58.552 52.381 15.34 5.60 46.06 4.63
332 2538 1.133025 GGACGAGTAATTCCGAACGGA 59.867 52.381 12.04 12.04 43.52 4.69
333 2539 1.135315 TGGACGAGTAATTCCGAACGG 60.135 52.381 6.94 6.94 0.00 4.44
334 2540 2.267188 TGGACGAGTAATTCCGAACG 57.733 50.000 0.00 0.00 0.00 3.95
335 2541 3.841643 TCTTGGACGAGTAATTCCGAAC 58.158 45.455 0.00 0.00 0.00 3.95
336 2542 4.524316 TTCTTGGACGAGTAATTCCGAA 57.476 40.909 0.00 0.00 0.00 4.30
337 2543 4.524316 TTTCTTGGACGAGTAATTCCGA 57.476 40.909 0.00 0.00 0.00 4.55
338 2544 4.868171 TCATTTCTTGGACGAGTAATTCCG 59.132 41.667 0.00 0.00 0.00 4.30
339 2545 6.737254 TTCATTTCTTGGACGAGTAATTCC 57.263 37.500 0.00 0.00 0.00 3.01
340 2546 7.752695 ACATTCATTTCTTGGACGAGTAATTC 58.247 34.615 0.00 0.00 0.00 2.17
341 2547 7.687941 ACATTCATTTCTTGGACGAGTAATT 57.312 32.000 0.00 0.00 0.00 1.40
342 2548 8.964476 ATACATTCATTTCTTGGACGAGTAAT 57.036 30.769 0.00 0.00 0.00 1.89
343 2549 8.258007 AGATACATTCATTTCTTGGACGAGTAA 58.742 33.333 0.00 0.00 0.00 2.24
344 2550 7.782049 AGATACATTCATTTCTTGGACGAGTA 58.218 34.615 0.00 0.00 0.00 2.59
345 2551 6.644347 AGATACATTCATTTCTTGGACGAGT 58.356 36.000 0.00 0.00 0.00 4.18
346 2552 8.138074 TCTAGATACATTCATTTCTTGGACGAG 58.862 37.037 0.00 0.00 0.00 4.18
347 2553 8.007405 TCTAGATACATTCATTTCTTGGACGA 57.993 34.615 0.00 0.00 0.00 4.20
348 2554 8.706936 CATCTAGATACATTCATTTCTTGGACG 58.293 37.037 4.54 0.00 0.00 4.79
349 2555 9.553064 ACATCTAGATACATTCATTTCTTGGAC 57.447 33.333 4.54 0.00 0.00 4.02
372 2578 8.978874 TGGATGTATCTGCAACTAAAATACAT 57.021 30.769 6.12 6.12 42.96 2.29
373 2579 8.978874 ATGGATGTATCTGCAACTAAAATACA 57.021 30.769 0.00 0.00 37.26 2.29
380 2586 9.625747 TCATAAAAATGGATGTATCTGCAACTA 57.374 29.630 0.00 0.00 0.00 2.24
381 2587 8.408601 GTCATAAAAATGGATGTATCTGCAACT 58.591 33.333 0.00 0.00 0.00 3.16
382 2588 8.190122 TGTCATAAAAATGGATGTATCTGCAAC 58.810 33.333 0.00 0.00 0.00 4.17
383 2589 8.291191 TGTCATAAAAATGGATGTATCTGCAA 57.709 30.769 0.00 0.00 0.00 4.08
384 2590 7.878547 TGTCATAAAAATGGATGTATCTGCA 57.121 32.000 0.00 0.00 0.00 4.41
385 2591 8.408601 ACTTGTCATAAAAATGGATGTATCTGC 58.591 33.333 0.00 0.00 0.00 4.26
397 2603 9.337091 CCGTTCGAAATTACTTGTCATAAAAAT 57.663 29.630 0.00 0.00 0.00 1.82
398 2604 8.557864 TCCGTTCGAAATTACTTGTCATAAAAA 58.442 29.630 0.00 0.00 0.00 1.94
399 2605 8.085720 TCCGTTCGAAATTACTTGTCATAAAA 57.914 30.769 0.00 0.00 0.00 1.52
400 2606 7.148540 CCTCCGTTCGAAATTACTTGTCATAAA 60.149 37.037 0.00 0.00 0.00 1.40
401 2607 6.311935 CCTCCGTTCGAAATTACTTGTCATAA 59.688 38.462 0.00 0.00 0.00 1.90
402 2608 5.808540 CCTCCGTTCGAAATTACTTGTCATA 59.191 40.000 0.00 0.00 0.00 2.15
403 2609 4.630069 CCTCCGTTCGAAATTACTTGTCAT 59.370 41.667 0.00 0.00 0.00 3.06
404 2610 3.991773 CCTCCGTTCGAAATTACTTGTCA 59.008 43.478 0.00 0.00 0.00 3.58
405 2611 3.370061 CCCTCCGTTCGAAATTACTTGTC 59.630 47.826 0.00 0.00 0.00 3.18
406 2612 3.007182 TCCCTCCGTTCGAAATTACTTGT 59.993 43.478 0.00 0.00 0.00 3.16
407 2613 3.592059 TCCCTCCGTTCGAAATTACTTG 58.408 45.455 0.00 0.00 0.00 3.16
408 2614 3.260128 ACTCCCTCCGTTCGAAATTACTT 59.740 43.478 0.00 0.00 0.00 2.24
409 2615 2.830321 ACTCCCTCCGTTCGAAATTACT 59.170 45.455 0.00 0.00 0.00 2.24
410 2616 3.242549 ACTCCCTCCGTTCGAAATTAC 57.757 47.619 0.00 0.00 0.00 1.89
411 2617 4.019174 AGTACTCCCTCCGTTCGAAATTA 58.981 43.478 0.00 0.00 0.00 1.40
412 2618 2.830321 AGTACTCCCTCCGTTCGAAATT 59.170 45.455 0.00 0.00 0.00 1.82
413 2619 2.454538 AGTACTCCCTCCGTTCGAAAT 58.545 47.619 0.00 0.00 0.00 2.17
414 2620 1.915141 AGTACTCCCTCCGTTCGAAA 58.085 50.000 0.00 0.00 0.00 3.46
415 2621 1.542915 CAAGTACTCCCTCCGTTCGAA 59.457 52.381 0.00 0.00 0.00 3.71
416 2622 1.171308 CAAGTACTCCCTCCGTTCGA 58.829 55.000 0.00 0.00 0.00 3.71
417 2623 0.458025 GCAAGTACTCCCTCCGTTCG 60.458 60.000 0.00 0.00 0.00 3.95
418 2624 0.896226 AGCAAGTACTCCCTCCGTTC 59.104 55.000 0.00 0.00 0.00 3.95
419 2625 2.226962 TAGCAAGTACTCCCTCCGTT 57.773 50.000 0.00 0.00 0.00 4.44
420 2626 2.308690 GATAGCAAGTACTCCCTCCGT 58.691 52.381 0.00 0.00 0.00 4.69
421 2627 2.307768 TGATAGCAAGTACTCCCTCCG 58.692 52.381 0.00 0.00 0.00 4.63
422 2628 3.898123 TCATGATAGCAAGTACTCCCTCC 59.102 47.826 0.00 0.00 0.00 4.30
423 2629 5.537300 TTCATGATAGCAAGTACTCCCTC 57.463 43.478 0.00 0.00 0.00 4.30
424 2630 5.957771 TTTCATGATAGCAAGTACTCCCT 57.042 39.130 0.00 0.00 0.00 4.20
425 2631 5.529060 CCTTTTCATGATAGCAAGTACTCCC 59.471 44.000 0.00 0.00 0.00 4.30
426 2632 6.349300 TCCTTTTCATGATAGCAAGTACTCC 58.651 40.000 0.00 0.00 0.00 3.85
427 2633 7.930865 AGATCCTTTTCATGATAGCAAGTACTC 59.069 37.037 0.00 0.00 0.00 2.59
428 2634 7.800092 AGATCCTTTTCATGATAGCAAGTACT 58.200 34.615 0.00 0.00 0.00 2.73
429 2635 8.341173 CAAGATCCTTTTCATGATAGCAAGTAC 58.659 37.037 0.00 0.00 0.00 2.73
430 2636 7.500227 CCAAGATCCTTTTCATGATAGCAAGTA 59.500 37.037 0.00 0.00 0.00 2.24
431 2637 6.320672 CCAAGATCCTTTTCATGATAGCAAGT 59.679 38.462 0.00 0.00 0.00 3.16
575 2785 9.911138 AAAGTTACTGTTTTCCGTTTCTAAAAA 57.089 25.926 0.00 0.00 0.00 1.94
576 2786 9.911138 AAAAGTTACTGTTTTCCGTTTCTAAAA 57.089 25.926 0.00 0.00 0.00 1.52
577 2787 9.911138 AAAAAGTTACTGTTTTCCGTTTCTAAA 57.089 25.926 0.00 0.00 0.00 1.85
609 2819 9.712305 TGTTTACTGTTTTTCCATTTCTCAAAA 57.288 25.926 0.00 0.00 0.00 2.44
610 2820 9.364989 CTGTTTACTGTTTTTCCATTTCTCAAA 57.635 29.630 0.00 0.00 0.00 2.69
611 2821 8.527810 ACTGTTTACTGTTTTTCCATTTCTCAA 58.472 29.630 0.00 0.00 0.00 3.02
612 2822 8.062065 ACTGTTTACTGTTTTTCCATTTCTCA 57.938 30.769 0.00 0.00 0.00 3.27
613 2823 8.926715 AACTGTTTACTGTTTTTCCATTTCTC 57.073 30.769 0.01 0.00 34.97 2.87
651 2861 8.974408 GTTAAACTGTCACTGTGTTTTCTTTTT 58.026 29.630 7.79 3.04 35.77 1.94
652 2862 8.357402 AGTTAAACTGTCACTGTGTTTTCTTTT 58.643 29.630 7.79 4.41 35.77 2.27
653 2863 7.882179 AGTTAAACTGTCACTGTGTTTTCTTT 58.118 30.769 7.79 3.72 35.77 2.52
654 2864 7.390718 AGAGTTAAACTGTCACTGTGTTTTCTT 59.609 33.333 7.79 0.85 35.77 2.52
655 2865 6.879458 AGAGTTAAACTGTCACTGTGTTTTCT 59.121 34.615 7.79 3.92 35.77 2.52
656 2866 7.073342 AGAGTTAAACTGTCACTGTGTTTTC 57.927 36.000 7.79 0.00 35.77 2.29
657 2867 8.556213 TTAGAGTTAAACTGTCACTGTGTTTT 57.444 30.769 7.79 6.26 35.77 2.43
658 2868 8.556213 TTTAGAGTTAAACTGTCACTGTGTTT 57.444 30.769 7.79 3.73 37.60 2.83
659 2869 8.732746 ATTTAGAGTTAAACTGTCACTGTGTT 57.267 30.769 7.79 0.00 31.90 3.32
660 2870 8.732746 AATTTAGAGTTAAACTGTCACTGTGT 57.267 30.769 7.79 0.00 31.90 3.72
661 2871 8.283291 GGAATTTAGAGTTAAACTGTCACTGTG 58.717 37.037 0.17 0.17 31.90 3.66
667 2877 6.430000 TGGCAGGAATTTAGAGTTAAACTGTC 59.570 38.462 0.00 0.00 31.13 3.51
674 2884 5.428457 TCTCCATGGCAGGAATTTAGAGTTA 59.572 40.000 6.96 0.00 37.20 2.24
680 2890 3.701040 GCTTTCTCCATGGCAGGAATTTA 59.299 43.478 6.96 0.00 37.20 1.40
688 2898 0.041535 ATTGGGCTTTCTCCATGGCA 59.958 50.000 6.96 0.00 33.82 4.92
693 2903 2.802719 GTACCAATTGGGCTTTCTCCA 58.197 47.619 27.89 0.00 42.05 3.86
731 2956 4.815108 GGAATGGTGGGCGGGGAC 62.815 72.222 0.00 0.00 0.00 4.46
783 3048 2.954684 GCTGTGGGTGATGGACGGA 61.955 63.158 0.00 0.00 0.00 4.69
814 3079 2.400399 TCGAGTTGTTTGACACGATCC 58.600 47.619 0.00 0.00 37.63 3.36
828 3093 2.722201 GGATCGGTGGCCTCGAGTT 61.722 63.158 22.01 10.33 40.09 3.01
957 3239 4.710167 TGCGTCGACGGGGAGAGA 62.710 66.667 36.13 0.00 40.23 3.10
982 3284 4.170062 CGATGCCGCTGGTTGCTG 62.170 66.667 0.00 0.00 40.11 4.41
983 3285 3.687321 ATCGATGCCGCTGGTTGCT 62.687 57.895 0.00 0.00 40.11 3.91
984 3286 3.204827 ATCGATGCCGCTGGTTGC 61.205 61.111 0.00 0.00 38.57 4.17
985 3287 2.711311 CATCGATGCCGCTGGTTG 59.289 61.111 13.37 0.00 35.37 3.77
1031 3337 0.973496 GGTCTTCTCGGCCTTCTCCT 60.973 60.000 0.00 0.00 0.00 3.69
1121 3431 4.636249 GCTCTTCTTGGACTTCTTCTTGA 58.364 43.478 0.00 0.00 0.00 3.02
1481 3791 6.183360 ACAGTTTGTGTTCAAGATGACAGAAG 60.183 38.462 0.00 0.00 34.94 2.85
1482 3792 5.647658 ACAGTTTGTGTTCAAGATGACAGAA 59.352 36.000 0.00 0.00 34.94 3.02
1564 3905 4.380128 GGGATCATGGTAAAAACCGAACAC 60.380 45.833 0.00 0.00 0.00 3.32
1615 3956 5.435686 AAATACTCCACACAAGCAGGATA 57.564 39.130 0.00 0.00 0.00 2.59
1640 3981 4.036971 TCCGTGAATTGTGGTAGTTTTTGG 59.963 41.667 0.00 0.00 0.00 3.28
1671 4012 8.460428 ACAAAATCGTAAAGTGGTAGTTTTTCA 58.540 29.630 0.00 0.00 0.00 2.69


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

AutoCloner maintained by Alex Coulton.