Multiple sequence alignment - TraesCS7A01G089900

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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 TraesCS7A01G089900 chr7A 100.000 2575 0 0 1 2575 54854494 54851920 0.000000e+00 4756.0
1 TraesCS7A01G089900 chr7A 97.243 653 16 2 1846 2498 5855824 5855174 0.000000e+00 1105.0
2 TraesCS7A01G089900 chr4A 93.666 821 49 2 1027 1847 666952813 666951996 0.000000e+00 1225.0
3 TraesCS7A01G089900 chr4A 95.532 649 29 0 1854 2502 598589598 598588950 0.000000e+00 1038.0
4 TraesCS7A01G089900 chr4A 92.308 650 48 2 1849 2498 733536756 733536109 0.000000e+00 922.0
5 TraesCS7A01G089900 chr4A 80.505 831 130 20 1027 1851 731006894 731006090 2.190000e-170 608.0
6 TraesCS7A01G089900 chr4A 84.158 606 50 23 366 952 666953383 666952805 1.740000e-151 545.0
7 TraesCS7A01G089900 chr4A 72.391 594 137 22 1264 1839 532208641 532209225 2.050000e-36 163.0
8 TraesCS7A01G089900 chr4A 87.692 130 9 2 130 259 666953509 666953387 7.430000e-31 145.0
9 TraesCS7A01G089900 chr4A 90.805 87 2 1 2495 2575 666952000 666951914 7.530000e-21 111.0
10 TraesCS7A01G089900 chr2A 97.252 655 17 1 1846 2500 207643594 207642941 0.000000e+00 1109.0
11 TraesCS7A01G089900 chr5A 95.699 651 28 0 1846 2496 492629096 492629746 0.000000e+00 1048.0
12 TraesCS7A01G089900 chr5A 95.597 636 22 1 1863 2498 340812301 340811672 0.000000e+00 1014.0
13 TraesCS7A01G089900 chr5A 92.012 651 48 4 1849 2498 470178587 470179234 0.000000e+00 911.0
14 TraesCS7A01G089900 chr5D 92.627 651 45 3 1849 2498 457668716 457669364 0.000000e+00 933.0
15 TraesCS7A01G089900 chr5D 84.933 823 103 13 1028 1845 4054842 4054036 0.000000e+00 813.0
16 TraesCS7A01G089900 chr5D 82.759 696 98 16 1158 1851 27355404 27354729 3.670000e-168 601.0
17 TraesCS7A01G089900 chr5D 81.250 192 36 0 1635 1826 449040087 449039896 3.430000e-34 156.0
18 TraesCS7A01G089900 chr5D 93.548 62 4 0 952 1013 192545119 192545058 2.730000e-15 93.5
19 TraesCS7A01G089900 chr5D 86.747 83 7 4 953 1034 350376832 350376911 3.530000e-14 89.8
20 TraesCS7A01G089900 chr5D 85.714 84 9 3 952 1034 385924156 385924075 4.570000e-13 86.1
21 TraesCS7A01G089900 chr7D 95.076 589 27 2 364 952 52483469 52482883 0.000000e+00 926.0
22 TraesCS7A01G089900 chr7D 96.000 550 21 1 1027 1575 52355652 52355103 0.000000e+00 893.0
23 TraesCS7A01G089900 chr7D 93.189 602 28 4 364 952 52356245 52355644 0.000000e+00 872.0
24 TraesCS7A01G089900 chr7D 93.412 425 24 3 1269 1693 52475419 52474999 6.050000e-176 627.0
25 TraesCS7A01G089900 chr7D 96.071 280 8 1 1568 1847 52354928 52354652 1.090000e-123 453.0
26 TraesCS7A01G089900 chr7D 95.851 241 10 0 1029 1269 52482889 52482649 8.640000e-105 390.0
27 TraesCS7A01G089900 chr7D 83.202 381 14 12 1 363 52356510 52356162 1.160000e-78 303.0
28 TraesCS7A01G089900 chr7D 95.882 170 7 0 1678 1847 52474416 52474247 2.520000e-70 276.0
29 TraesCS7A01G089900 chr7D 93.103 174 4 2 87 259 52483636 52483470 5.500000e-62 248.0
30 TraesCS7A01G089900 chr7D 92.941 85 2 1 2495 2575 52354656 52354572 1.250000e-23 121.0
31 TraesCS7A01G089900 chr7D 92.857 84 3 2 2495 2575 52474251 52474168 4.500000e-23 119.0
32 TraesCS7A01G089900 chr7D 84.615 91 8 4 950 1035 606689289 606689200 4.570000e-13 86.1
33 TraesCS7A01G089900 chr3B 91.975 648 45 5 1850 2497 111731430 111732070 0.000000e+00 902.0
34 TraesCS7A01G089900 chr3B 83.705 448 71 2 1113 1560 544835430 544835875 3.060000e-114 422.0
35 TraesCS7A01G089900 chr3B 85.609 271 39 0 1027 1297 544927742 544928012 4.190000e-73 285.0
36 TraesCS7A01G089900 chr3B 84.821 112 17 0 391 502 544926795 544926906 2.090000e-21 113.0
37 TraesCS7A01G089900 chr3B 90.385 52 5 0 1027 1078 544835374 544835425 4.600000e-08 69.4
38 TraesCS7A01G089900 chr5B 84.615 819 103 14 1036 1851 19744999 19744201 0.000000e+00 793.0
39 TraesCS7A01G089900 chr3D 84.142 536 81 4 1027 1560 418560621 418561154 1.370000e-142 516.0
40 TraesCS7A01G089900 chr3D 82.022 534 84 5 1027 1560 418443204 418443725 6.540000e-121 444.0
41 TraesCS7A01G089900 chr3D 86.747 83 7 4 954 1034 603950589 603950669 3.530000e-14 89.8
42 TraesCS7A01G089900 chr4D 87.952 83 6 4 952 1032 464136648 464136728 7.590000e-16 95.3
43 TraesCS7A01G089900 chr1D 85.714 84 8 4 954 1035 81469555 81469474 4.570000e-13 86.1
44 TraesCS7A01G089900 chrUn 90.476 63 6 0 1113 1175 438151007 438151069 1.640000e-12 84.2
45 TraesCS7A01G089900 chrUn 90.385 52 5 0 1027 1078 438150951 438151002 4.600000e-08 69.4
46 TraesCS7A01G089900 chr6D 85.366 82 8 4 956 1035 34185684 34185605 5.910000e-12 82.4
47 TraesCS7A01G089900 chr2D 85.185 81 9 3 956 1035 22834791 22834713 2.120000e-11 80.5


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 TraesCS7A01G089900 chr7A 54851920 54854494 2574 True 4756.000000 4756 100.000000 1 2575 1 chr7A.!!$R2 2574
1 TraesCS7A01G089900 chr7A 5855174 5855824 650 True 1105.000000 1105 97.243000 1846 2498 1 chr7A.!!$R1 652
2 TraesCS7A01G089900 chr4A 598588950 598589598 648 True 1038.000000 1038 95.532000 1854 2502 1 chr4A.!!$R1 648
3 TraesCS7A01G089900 chr4A 733536109 733536756 647 True 922.000000 922 92.308000 1849 2498 1 chr4A.!!$R3 649
4 TraesCS7A01G089900 chr4A 731006090 731006894 804 True 608.000000 608 80.505000 1027 1851 1 chr4A.!!$R2 824
5 TraesCS7A01G089900 chr4A 666951914 666953509 1595 True 506.500000 1225 89.080250 130 2575 4 chr4A.!!$R4 2445
6 TraesCS7A01G089900 chr2A 207642941 207643594 653 True 1109.000000 1109 97.252000 1846 2500 1 chr2A.!!$R1 654
7 TraesCS7A01G089900 chr5A 492629096 492629746 650 False 1048.000000 1048 95.699000 1846 2496 1 chr5A.!!$F2 650
8 TraesCS7A01G089900 chr5A 340811672 340812301 629 True 1014.000000 1014 95.597000 1863 2498 1 chr5A.!!$R1 635
9 TraesCS7A01G089900 chr5A 470178587 470179234 647 False 911.000000 911 92.012000 1849 2498 1 chr5A.!!$F1 649
10 TraesCS7A01G089900 chr5D 457668716 457669364 648 False 933.000000 933 92.627000 1849 2498 1 chr5D.!!$F2 649
11 TraesCS7A01G089900 chr5D 4054036 4054842 806 True 813.000000 813 84.933000 1028 1845 1 chr5D.!!$R1 817
12 TraesCS7A01G089900 chr5D 27354729 27355404 675 True 601.000000 601 82.759000 1158 1851 1 chr5D.!!$R2 693
13 TraesCS7A01G089900 chr7D 52354572 52356510 1938 True 528.400000 893 92.280600 1 2575 5 chr7D.!!$R2 2574
14 TraesCS7A01G089900 chr7D 52482649 52483636 987 True 521.333333 926 94.676667 87 1269 3 chr7D.!!$R4 1182
15 TraesCS7A01G089900 chr7D 52474168 52475419 1251 True 340.666667 627 94.050333 1269 2575 3 chr7D.!!$R3 1306
16 TraesCS7A01G089900 chr3B 111731430 111732070 640 False 902.000000 902 91.975000 1850 2497 1 chr3B.!!$F1 647
17 TraesCS7A01G089900 chr3B 544835374 544835875 501 False 245.700000 422 87.045000 1027 1560 2 chr3B.!!$F2 533
18 TraesCS7A01G089900 chr5B 19744201 19744999 798 True 793.000000 793 84.615000 1036 1851 1 chr5B.!!$R1 815
19 TraesCS7A01G089900 chr3D 418560621 418561154 533 False 516.000000 516 84.142000 1027 1560 1 chr3D.!!$F2 533
20 TraesCS7A01G089900 chr3D 418443204 418443725 521 False 444.000000 444 82.022000 1027 1560 1 chr3D.!!$F1 533

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
319 320 0.166814 GCCAGCGAAATATCCGATGC 59.833 55.0 9.37 3.55 41.44 3.91 F
1011 1049 0.104855 TCAGAGTGATGCATACGGCC 59.895 55.0 0.00 0.00 43.89 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1227 1269 1.225855 TGGCAGCGTCAACTTAAGTG 58.774 50.000 9.34 3.91 0.0 3.16 R
2437 3270 4.919168 TCAATCAAGGTAGTACAACGAACG 59.081 41.667 2.06 0.00 0.0 3.95 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
26 27 9.209175 GTAGACAGACAATGAGAAAAGTGTAAT 57.791 33.333 0.00 0.00 0.00 1.89
47 48 2.815647 CTTTCCCCTCTCGCACGC 60.816 66.667 0.00 0.00 0.00 5.34
66 67 2.297701 GCTCTCTCCTCACCTACTCTG 58.702 57.143 0.00 0.00 0.00 3.35
67 68 2.356741 GCTCTCTCCTCACCTACTCTGT 60.357 54.545 0.00 0.00 0.00 3.41
68 69 3.876156 GCTCTCTCCTCACCTACTCTGTT 60.876 52.174 0.00 0.00 0.00 3.16
69 70 3.945285 CTCTCTCCTCACCTACTCTGTTC 59.055 52.174 0.00 0.00 0.00 3.18
70 71 3.589735 TCTCTCCTCACCTACTCTGTTCT 59.410 47.826 0.00 0.00 0.00 3.01
71 72 4.043561 TCTCTCCTCACCTACTCTGTTCTT 59.956 45.833 0.00 0.00 0.00 2.52
72 73 4.337145 TCTCCTCACCTACTCTGTTCTTC 58.663 47.826 0.00 0.00 0.00 2.87
73 74 3.432378 TCCTCACCTACTCTGTTCTTCC 58.568 50.000 0.00 0.00 0.00 3.46
74 75 2.498078 CCTCACCTACTCTGTTCTTCCC 59.502 54.545 0.00 0.00 0.00 3.97
75 76 2.498078 CTCACCTACTCTGTTCTTCCCC 59.502 54.545 0.00 0.00 0.00 4.81
76 77 2.111972 TCACCTACTCTGTTCTTCCCCT 59.888 50.000 0.00 0.00 0.00 4.79
77 78 2.907042 CACCTACTCTGTTCTTCCCCTT 59.093 50.000 0.00 0.00 0.00 3.95
78 79 4.094476 CACCTACTCTGTTCTTCCCCTTA 58.906 47.826 0.00 0.00 0.00 2.69
79 80 4.081586 CACCTACTCTGTTCTTCCCCTTAC 60.082 50.000 0.00 0.00 0.00 2.34
80 81 3.451540 CCTACTCTGTTCTTCCCCTTACC 59.548 52.174 0.00 0.00 0.00 2.85
81 82 2.267192 ACTCTGTTCTTCCCCTTACCC 58.733 52.381 0.00 0.00 0.00 3.69
82 83 1.560146 CTCTGTTCTTCCCCTTACCCC 59.440 57.143 0.00 0.00 0.00 4.95
83 84 1.153565 TCTGTTCTTCCCCTTACCCCT 59.846 52.381 0.00 0.00 0.00 4.79
84 85 1.560146 CTGTTCTTCCCCTTACCCCTC 59.440 57.143 0.00 0.00 0.00 4.30
85 86 1.153565 TGTTCTTCCCCTTACCCCTCT 59.846 52.381 0.00 0.00 0.00 3.69
124 125 0.470268 ATCTCCTCTAGTTCGGGCCC 60.470 60.000 13.57 13.57 0.00 5.80
197 198 4.594367 CAGAGGACTGCAGTCTGC 57.406 61.111 38.17 30.08 44.20 4.26
248 249 1.534595 GGACTGCAGTTGAGCTTCTTG 59.465 52.381 22.65 0.00 34.99 3.02
264 265 4.499183 CTTCTTGAGGTAATCGCTTCAGT 58.501 43.478 0.00 0.00 0.00 3.41
267 268 1.899814 TGAGGTAATCGCTTCAGTGGT 59.100 47.619 0.00 0.00 0.00 4.16
294 295 4.332268 CAGCTGAGCTTTCTTCAGGTAATC 59.668 45.833 8.42 0.00 39.77 1.75
295 296 3.625313 GCTGAGCTTTCTTCAGGTAATCC 59.375 47.826 0.00 0.00 32.55 3.01
296 297 4.195416 CTGAGCTTTCTTCAGGTAATCCC 58.805 47.826 0.00 0.00 0.00 3.85
297 298 3.587061 TGAGCTTTCTTCAGGTAATCCCA 59.413 43.478 0.00 0.00 34.66 4.37
298 299 4.228210 TGAGCTTTCTTCAGGTAATCCCAT 59.772 41.667 0.00 0.00 34.66 4.00
299 300 5.196695 GAGCTTTCTTCAGGTAATCCCATT 58.803 41.667 0.00 0.00 34.66 3.16
300 301 4.952335 AGCTTTCTTCAGGTAATCCCATTG 59.048 41.667 0.00 0.00 34.66 2.82
301 302 4.440663 GCTTTCTTCAGGTAATCCCATTGC 60.441 45.833 0.00 0.00 34.66 3.56
302 303 3.297134 TCTTCAGGTAATCCCATTGCC 57.703 47.619 0.00 0.00 44.29 4.52
303 304 2.580322 TCTTCAGGTAATCCCATTGCCA 59.420 45.455 6.20 0.00 46.08 4.92
304 305 2.734755 TCAGGTAATCCCATTGCCAG 57.265 50.000 6.20 0.00 46.08 4.85
305 306 1.035139 CAGGTAATCCCATTGCCAGC 58.965 55.000 6.20 0.00 46.08 4.85
306 307 0.466189 AGGTAATCCCATTGCCAGCG 60.466 55.000 6.20 0.00 46.08 5.18
307 308 0.465460 GGTAATCCCATTGCCAGCGA 60.465 55.000 0.00 0.00 43.53 4.93
308 309 1.388547 GTAATCCCATTGCCAGCGAA 58.611 50.000 0.00 0.00 0.00 4.70
309 310 1.748493 GTAATCCCATTGCCAGCGAAA 59.252 47.619 0.00 0.00 0.00 3.46
310 311 1.488390 AATCCCATTGCCAGCGAAAT 58.512 45.000 0.00 0.00 0.00 2.17
311 312 2.363306 ATCCCATTGCCAGCGAAATA 57.637 45.000 0.00 0.00 0.00 1.40
312 313 2.363306 TCCCATTGCCAGCGAAATAT 57.637 45.000 0.00 0.00 0.00 1.28
313 314 2.229792 TCCCATTGCCAGCGAAATATC 58.770 47.619 0.00 0.00 0.00 1.63
314 315 1.270550 CCCATTGCCAGCGAAATATCC 59.729 52.381 0.00 0.00 0.00 2.59
315 316 1.069022 CCATTGCCAGCGAAATATCCG 60.069 52.381 0.00 0.00 0.00 4.18
316 317 1.872952 CATTGCCAGCGAAATATCCGA 59.127 47.619 2.16 0.00 0.00 4.55
317 318 2.254546 TTGCCAGCGAAATATCCGAT 57.745 45.000 2.16 0.00 0.00 4.18
318 319 1.511850 TGCCAGCGAAATATCCGATG 58.488 50.000 8.25 8.25 42.29 3.84
319 320 0.166814 GCCAGCGAAATATCCGATGC 59.833 55.000 9.37 3.55 41.44 3.91
320 321 1.511850 CCAGCGAAATATCCGATGCA 58.488 50.000 9.37 0.00 41.44 3.96
321 322 2.079158 CCAGCGAAATATCCGATGCAT 58.921 47.619 0.00 0.00 41.44 3.96
322 323 2.159612 CCAGCGAAATATCCGATGCATG 60.160 50.000 2.46 0.00 41.44 4.06
323 324 2.738314 CAGCGAAATATCCGATGCATGA 59.262 45.455 2.46 0.00 36.64 3.07
324 325 3.373130 CAGCGAAATATCCGATGCATGAT 59.627 43.478 2.46 4.11 36.64 2.45
325 326 4.005650 AGCGAAATATCCGATGCATGATT 58.994 39.130 2.46 0.00 0.00 2.57
326 327 4.093514 GCGAAATATCCGATGCATGATTG 58.906 43.478 2.46 0.00 0.00 2.67
342 343 7.905031 GCATGATTGCTGTCTTTAGTTAATC 57.095 36.000 0.00 0.00 45.77 1.75
343 344 7.475015 GCATGATTGCTGTCTTTAGTTAATCA 58.525 34.615 0.00 0.00 45.77 2.57
344 345 8.133627 GCATGATTGCTGTCTTTAGTTAATCAT 58.866 33.333 0.00 0.00 45.77 2.45
345 346 9.447040 CATGATTGCTGTCTTTAGTTAATCATG 57.553 33.333 17.32 17.32 44.05 3.07
346 347 7.475015 TGATTGCTGTCTTTAGTTAATCATGC 58.525 34.615 0.00 0.00 33.09 4.06
347 348 7.337689 TGATTGCTGTCTTTAGTTAATCATGCT 59.662 33.333 0.00 0.00 33.09 3.79
348 349 6.426980 TGCTGTCTTTAGTTAATCATGCTG 57.573 37.500 0.00 0.00 0.00 4.41
349 350 5.163723 TGCTGTCTTTAGTTAATCATGCTGC 60.164 40.000 0.00 0.00 0.00 5.25
350 351 5.065731 GCTGTCTTTAGTTAATCATGCTGCT 59.934 40.000 0.00 0.00 0.00 4.24
351 352 6.404074 GCTGTCTTTAGTTAATCATGCTGCTT 60.404 38.462 0.00 0.00 0.00 3.91
352 353 7.076842 TGTCTTTAGTTAATCATGCTGCTTC 57.923 36.000 0.00 0.00 0.00 3.86
353 354 6.881065 TGTCTTTAGTTAATCATGCTGCTTCT 59.119 34.615 0.00 0.00 0.00 2.85
354 355 7.391554 TGTCTTTAGTTAATCATGCTGCTTCTT 59.608 33.333 0.00 0.00 0.00 2.52
355 356 8.239998 GTCTTTAGTTAATCATGCTGCTTCTTT 58.760 33.333 0.00 0.00 0.00 2.52
356 357 9.448438 TCTTTAGTTAATCATGCTGCTTCTTTA 57.552 29.630 0.00 0.00 0.00 1.85
359 360 6.952743 AGTTAATCATGCTGCTTCTTTATCG 58.047 36.000 0.00 0.00 0.00 2.92
362 363 3.599343 TCATGCTGCTTCTTTATCGTGT 58.401 40.909 0.00 0.00 0.00 4.49
480 482 2.553028 GGACCAATCATCCACACAGTGT 60.553 50.000 0.00 0.00 36.15 3.55
705 736 9.530633 GAATATTTATTGAGTCTAACCTCGTGT 57.469 33.333 0.00 0.00 34.04 4.49
867 903 7.954666 ATCTAAGAGCCAGATCTAATAGACC 57.045 40.000 0.00 0.00 0.00 3.85
943 981 4.283337 TGGATCACCGAACTATTACCTCA 58.717 43.478 0.00 0.00 39.42 3.86
944 982 4.098960 TGGATCACCGAACTATTACCTCAC 59.901 45.833 0.00 0.00 39.42 3.51
945 983 4.098960 GGATCACCGAACTATTACCTCACA 59.901 45.833 0.00 0.00 0.00 3.58
946 984 5.394883 GGATCACCGAACTATTACCTCACAA 60.395 44.000 0.00 0.00 0.00 3.33
947 985 5.471556 TCACCGAACTATTACCTCACAAA 57.528 39.130 0.00 0.00 0.00 2.83
948 986 5.856156 TCACCGAACTATTACCTCACAAAA 58.144 37.500 0.00 0.00 0.00 2.44
949 987 6.289834 TCACCGAACTATTACCTCACAAAAA 58.710 36.000 0.00 0.00 0.00 1.94
950 988 6.425721 TCACCGAACTATTACCTCACAAAAAG 59.574 38.462 0.00 0.00 0.00 2.27
951 989 6.204108 CACCGAACTATTACCTCACAAAAAGT 59.796 38.462 0.00 0.00 0.00 2.66
952 990 6.769341 ACCGAACTATTACCTCACAAAAAGTT 59.231 34.615 0.00 0.00 0.00 2.66
953 991 7.283807 ACCGAACTATTACCTCACAAAAAGTTT 59.716 33.333 0.00 0.00 0.00 2.66
954 992 8.132995 CCGAACTATTACCTCACAAAAAGTTTT 58.867 33.333 0.00 0.00 0.00 2.43
955 993 9.511144 CGAACTATTACCTCACAAAAAGTTTTT 57.489 29.630 7.79 7.79 0.00 1.94
980 1018 6.751157 TTTCTTTTCGAAAAGGGTTTATCCC 58.249 36.000 37.27 0.00 45.10 3.85
981 1019 6.239373 TTTCTTTTCGAAAAGGGTTTATCCCC 60.239 38.462 37.27 0.00 45.47 4.81
989 1027 3.808984 GGTTTATCCCCTGCCTCTG 57.191 57.895 0.00 0.00 0.00 3.35
990 1028 0.466372 GGTTTATCCCCTGCCTCTGC 60.466 60.000 0.00 0.00 38.26 4.26
1010 1048 1.797046 CATCAGAGTGATGCATACGGC 59.203 52.381 0.00 0.00 46.37 5.68
1011 1049 0.104855 TCAGAGTGATGCATACGGCC 59.895 55.000 0.00 0.00 43.89 6.13
1012 1050 0.179076 CAGAGTGATGCATACGGCCA 60.179 55.000 2.24 0.00 43.89 5.36
1013 1051 0.541392 AGAGTGATGCATACGGCCAA 59.459 50.000 2.24 0.00 43.89 4.52
1014 1052 1.141657 AGAGTGATGCATACGGCCAAT 59.858 47.619 2.24 0.00 43.89 3.16
1015 1053 1.949525 GAGTGATGCATACGGCCAATT 59.050 47.619 2.24 0.00 43.89 2.32
1016 1054 3.138304 GAGTGATGCATACGGCCAATTA 58.862 45.455 2.24 0.00 43.89 1.40
1017 1055 2.878406 AGTGATGCATACGGCCAATTAC 59.122 45.455 2.24 0.00 43.89 1.89
1018 1056 2.031157 GTGATGCATACGGCCAATTACC 60.031 50.000 2.24 0.00 43.89 2.85
1019 1057 2.158682 TGATGCATACGGCCAATTACCT 60.159 45.455 2.24 0.00 43.89 3.08
1020 1058 1.961793 TGCATACGGCCAATTACCTC 58.038 50.000 2.24 0.00 43.89 3.85
1021 1059 1.210722 TGCATACGGCCAATTACCTCA 59.789 47.619 2.24 0.00 43.89 3.86
1022 1060 1.602377 GCATACGGCCAATTACCTCAC 59.398 52.381 2.24 0.00 36.11 3.51
1023 1061 2.912771 CATACGGCCAATTACCTCACA 58.087 47.619 2.24 0.00 0.00 3.58
1024 1062 3.275143 CATACGGCCAATTACCTCACAA 58.725 45.455 2.24 0.00 0.00 3.33
1025 1063 2.279935 ACGGCCAATTACCTCACAAA 57.720 45.000 2.24 0.00 0.00 2.83
1039 1077 5.407502 ACCTCACAAAACAAAAAGTACTGC 58.592 37.500 0.00 0.00 0.00 4.40
1227 1269 4.143030 CGTCTTGATCATGGTTTCTGTGAC 60.143 45.833 8.60 0.00 0.00 3.67
1314 1356 3.181507 TGTGAAGAAGCTTTGCGATATGC 60.182 43.478 0.00 0.00 46.70 3.14
1337 1379 8.529424 TGCTTGATATGGATGAGAAGAAATTT 57.471 30.769 0.00 0.00 0.00 1.82
1367 1409 1.428448 TTCGTTGTCTGATGAAGGCG 58.572 50.000 0.00 0.00 30.85 5.52
1369 1411 0.716108 CGTTGTCTGATGAAGGCGAC 59.284 55.000 0.00 0.00 40.98 5.19
1380 1422 1.052287 GAAGGCGACGCACAAAAATG 58.948 50.000 23.09 0.00 0.00 2.32
1381 1423 0.665835 AAGGCGACGCACAAAAATGA 59.334 45.000 23.09 0.00 0.00 2.57
1411 1453 5.510520 GGTTCCTAGGATATTGCTCTGACAG 60.511 48.000 13.57 0.00 0.00 3.51
1428 1470 3.396276 TGACAGACAAGGGGAAATGGTAA 59.604 43.478 0.00 0.00 0.00 2.85
1527 1570 0.177141 TAAGCACATCACCGGTAGGC 59.823 55.000 6.87 6.91 42.76 3.93
1633 1868 3.304057 CCAACTTTCTGCTCTCCGTTTTC 60.304 47.826 0.00 0.00 0.00 2.29
1769 2602 6.477033 CCGGCAAATATACTGCTAGATGATAC 59.523 42.308 9.02 0.00 39.82 2.24
2046 2879 0.172352 CTGCTCAGGAAGACGAGACC 59.828 60.000 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 1.078528 TGCGAGAGGGGAAAGGAGA 59.921 57.895 0.00 0.00 0.00 3.71
47 48 3.644966 ACAGAGTAGGTGAGGAGAGAG 57.355 52.381 0.00 0.00 0.00 3.20
66 67 1.968278 AGAGGGGTAAGGGGAAGAAC 58.032 55.000 0.00 0.00 0.00 3.01
67 68 2.275466 CAAGAGGGGTAAGGGGAAGAA 58.725 52.381 0.00 0.00 0.00 2.52
68 69 1.153565 ACAAGAGGGGTAAGGGGAAGA 59.846 52.381 0.00 0.00 0.00 2.87
69 70 1.670059 ACAAGAGGGGTAAGGGGAAG 58.330 55.000 0.00 0.00 0.00 3.46
70 71 1.990327 GAACAAGAGGGGTAAGGGGAA 59.010 52.381 0.00 0.00 0.00 3.97
71 72 1.153565 AGAACAAGAGGGGTAAGGGGA 59.846 52.381 0.00 0.00 0.00 4.81
72 73 1.670059 AGAACAAGAGGGGTAAGGGG 58.330 55.000 0.00 0.00 0.00 4.79
73 74 2.026169 GGAAGAACAAGAGGGGTAAGGG 60.026 54.545 0.00 0.00 0.00 3.95
74 75 2.913617 AGGAAGAACAAGAGGGGTAAGG 59.086 50.000 0.00 0.00 0.00 2.69
75 76 3.368531 CGAGGAAGAACAAGAGGGGTAAG 60.369 52.174 0.00 0.00 0.00 2.34
76 77 2.565834 CGAGGAAGAACAAGAGGGGTAA 59.434 50.000 0.00 0.00 0.00 2.85
77 78 2.176889 CGAGGAAGAACAAGAGGGGTA 58.823 52.381 0.00 0.00 0.00 3.69
78 79 0.977395 CGAGGAAGAACAAGAGGGGT 59.023 55.000 0.00 0.00 0.00 4.95
79 80 1.267121 TCGAGGAAGAACAAGAGGGG 58.733 55.000 0.00 0.00 0.00 4.79
80 81 3.526534 GAATCGAGGAAGAACAAGAGGG 58.473 50.000 0.00 0.00 0.00 4.30
81 82 3.196685 AGGAATCGAGGAAGAACAAGAGG 59.803 47.826 0.00 0.00 0.00 3.69
82 83 4.081972 TGAGGAATCGAGGAAGAACAAGAG 60.082 45.833 0.00 0.00 0.00 2.85
83 84 3.832490 TGAGGAATCGAGGAAGAACAAGA 59.168 43.478 0.00 0.00 0.00 3.02
84 85 4.193826 TGAGGAATCGAGGAAGAACAAG 57.806 45.455 0.00 0.00 0.00 3.16
85 86 4.467795 AGATGAGGAATCGAGGAAGAACAA 59.532 41.667 0.00 0.00 40.54 2.83
124 125 4.556233 TGTCTAGACGTGGATTTTGTCAG 58.444 43.478 17.85 0.00 35.09 3.51
191 192 0.686224 AAGAAGCTCAGCTGCAGACT 59.314 50.000 20.43 11.55 39.62 3.24
192 193 2.376808 TAAGAAGCTCAGCTGCAGAC 57.623 50.000 20.43 9.11 39.62 3.51
193 194 2.354503 CCTTAAGAAGCTCAGCTGCAGA 60.355 50.000 20.43 0.00 39.62 4.26
194 195 2.008329 CCTTAAGAAGCTCAGCTGCAG 58.992 52.381 7.62 10.11 39.62 4.41
195 196 1.349026 ACCTTAAGAAGCTCAGCTGCA 59.651 47.619 7.62 0.00 39.62 4.41
196 197 2.106477 ACCTTAAGAAGCTCAGCTGC 57.894 50.000 9.47 0.00 39.62 5.25
197 198 4.505922 CGATTACCTTAAGAAGCTCAGCTG 59.494 45.833 7.63 7.63 39.62 4.24
248 249 2.166664 AGACCACTGAAGCGATTACCTC 59.833 50.000 0.00 0.00 0.00 3.85
264 265 0.604780 GAAAGCTCAGCTGCAGACCA 60.605 55.000 20.43 0.00 39.62 4.02
267 268 1.071228 TGAAGAAAGCTCAGCTGCAGA 59.929 47.619 20.43 0.00 39.62 4.26
294 295 1.270550 GGATATTTCGCTGGCAATGGG 59.729 52.381 0.00 0.00 0.00 4.00
295 296 1.069022 CGGATATTTCGCTGGCAATGG 60.069 52.381 0.00 0.00 0.00 3.16
296 297 1.872952 TCGGATATTTCGCTGGCAATG 59.127 47.619 0.00 0.00 0.00 2.82
297 298 2.254546 TCGGATATTTCGCTGGCAAT 57.745 45.000 0.00 0.00 0.00 3.56
298 299 1.872952 CATCGGATATTTCGCTGGCAA 59.127 47.619 0.00 0.00 0.00 4.52
299 300 1.511850 CATCGGATATTTCGCTGGCA 58.488 50.000 0.00 0.00 0.00 4.92
300 301 0.166814 GCATCGGATATTTCGCTGGC 59.833 55.000 0.00 0.00 0.00 4.85
301 302 1.511850 TGCATCGGATATTTCGCTGG 58.488 50.000 0.00 0.00 0.00 4.85
302 303 2.738314 TCATGCATCGGATATTTCGCTG 59.262 45.455 0.00 0.00 0.00 5.18
303 304 3.044235 TCATGCATCGGATATTTCGCT 57.956 42.857 0.00 0.00 0.00 4.93
304 305 4.093514 CAATCATGCATCGGATATTTCGC 58.906 43.478 0.00 0.00 0.00 4.70
319 320 9.447040 CATGATTAACTAAAGACAGCAATCATG 57.553 33.333 15.79 15.79 43.42 3.07
320 321 8.133627 GCATGATTAACTAAAGACAGCAATCAT 58.866 33.333 0.00 0.00 39.35 2.45
321 322 7.337689 AGCATGATTAACTAAAGACAGCAATCA 59.662 33.333 0.00 0.00 35.98 2.57
322 323 7.642978 CAGCATGATTAACTAAAGACAGCAATC 59.357 37.037 0.00 0.00 39.69 2.67
323 324 7.478322 CAGCATGATTAACTAAAGACAGCAAT 58.522 34.615 0.00 0.00 39.69 3.56
324 325 6.623549 GCAGCATGATTAACTAAAGACAGCAA 60.624 38.462 0.00 0.00 39.69 3.91
325 326 5.163723 GCAGCATGATTAACTAAAGACAGCA 60.164 40.000 0.00 0.00 39.69 4.41
326 327 5.065731 AGCAGCATGATTAACTAAAGACAGC 59.934 40.000 0.00 0.00 39.69 4.40
327 328 6.674694 AGCAGCATGATTAACTAAAGACAG 57.325 37.500 0.00 0.00 39.69 3.51
340 341 4.194640 ACACGATAAAGAAGCAGCATGAT 58.805 39.130 0.00 0.00 39.69 2.45
341 342 3.599343 ACACGATAAAGAAGCAGCATGA 58.401 40.909 0.00 0.00 39.69 3.07
342 343 3.371898 TGACACGATAAAGAAGCAGCATG 59.628 43.478 0.00 0.00 40.87 4.06
343 344 3.599343 TGACACGATAAAGAAGCAGCAT 58.401 40.909 0.00 0.00 0.00 3.79
344 345 3.038788 TGACACGATAAAGAAGCAGCA 57.961 42.857 0.00 0.00 0.00 4.41
345 346 4.606457 AATGACACGATAAAGAAGCAGC 57.394 40.909 0.00 0.00 0.00 5.25
380 382 5.472478 TCATGCATGCAGGAGAAGATATTTC 59.528 40.000 29.68 0.00 32.71 2.17
496 498 6.379417 ACTTCTCAGAATTCCAATGGGATTTC 59.621 38.462 7.32 13.80 46.67 2.17
628 631 4.136796 TGGTTCTCAGTCCAACAAATCAG 58.863 43.478 0.00 0.00 0.00 2.90
971 1009 0.466372 GCAGAGGCAGGGGATAAACC 60.466 60.000 0.00 0.00 40.72 3.27
972 1010 3.102090 GCAGAGGCAGGGGATAAAC 57.898 57.895 0.00 0.00 40.72 2.01
991 1029 1.270518 GGCCGTATGCATCACTCTGAT 60.271 52.381 0.19 0.00 43.89 2.90
992 1030 0.104855 GGCCGTATGCATCACTCTGA 59.895 55.000 0.19 0.00 43.89 3.27
993 1031 0.179076 TGGCCGTATGCATCACTCTG 60.179 55.000 0.19 0.00 43.89 3.35
994 1032 0.541392 TTGGCCGTATGCATCACTCT 59.459 50.000 0.19 0.00 43.89 3.24
995 1033 1.597742 ATTGGCCGTATGCATCACTC 58.402 50.000 0.19 0.00 43.89 3.51
996 1034 2.057137 AATTGGCCGTATGCATCACT 57.943 45.000 0.19 0.00 43.89 3.41
997 1035 2.031157 GGTAATTGGCCGTATGCATCAC 60.031 50.000 0.19 0.00 43.89 3.06
998 1036 2.158682 AGGTAATTGGCCGTATGCATCA 60.159 45.455 0.19 0.00 43.89 3.07
999 1037 2.484264 GAGGTAATTGGCCGTATGCATC 59.516 50.000 0.19 0.00 43.89 3.91
1000 1038 2.158682 TGAGGTAATTGGCCGTATGCAT 60.159 45.455 3.79 3.79 43.89 3.96
1001 1039 1.210722 TGAGGTAATTGGCCGTATGCA 59.789 47.619 0.00 0.00 43.89 3.96
1002 1040 1.602377 GTGAGGTAATTGGCCGTATGC 59.398 52.381 0.00 0.00 40.16 3.14
1003 1041 2.912771 TGTGAGGTAATTGGCCGTATG 58.087 47.619 0.00 0.00 0.00 2.39
1004 1042 3.637911 TTGTGAGGTAATTGGCCGTAT 57.362 42.857 0.00 0.00 0.00 3.06
1005 1043 3.420300 TTTGTGAGGTAATTGGCCGTA 57.580 42.857 0.00 0.00 0.00 4.02
1006 1044 2.279935 TTTGTGAGGTAATTGGCCGT 57.720 45.000 0.00 0.00 0.00 5.68
1007 1045 2.294791 TGTTTTGTGAGGTAATTGGCCG 59.705 45.455 0.00 0.00 0.00 6.13
1008 1046 4.329462 TTGTTTTGTGAGGTAATTGGCC 57.671 40.909 0.00 0.00 0.00 5.36
1009 1047 6.315144 ACTTTTTGTTTTGTGAGGTAATTGGC 59.685 34.615 0.00 0.00 0.00 4.52
1010 1048 7.841915 ACTTTTTGTTTTGTGAGGTAATTGG 57.158 32.000 0.00 0.00 0.00 3.16
1011 1049 9.581099 AGTACTTTTTGTTTTGTGAGGTAATTG 57.419 29.630 0.00 0.00 0.00 2.32
1012 1050 9.581099 CAGTACTTTTTGTTTTGTGAGGTAATT 57.419 29.630 0.00 0.00 0.00 1.40
1013 1051 7.704899 GCAGTACTTTTTGTTTTGTGAGGTAAT 59.295 33.333 0.00 0.00 0.00 1.89
1014 1052 7.030768 GCAGTACTTTTTGTTTTGTGAGGTAA 58.969 34.615 0.00 0.00 0.00 2.85
1015 1053 6.151312 TGCAGTACTTTTTGTTTTGTGAGGTA 59.849 34.615 0.00 0.00 0.00 3.08
1016 1054 5.047660 TGCAGTACTTTTTGTTTTGTGAGGT 60.048 36.000 0.00 0.00 0.00 3.85
1017 1055 5.406649 TGCAGTACTTTTTGTTTTGTGAGG 58.593 37.500 0.00 0.00 0.00 3.86
1018 1056 5.004726 GCTGCAGTACTTTTTGTTTTGTGAG 59.995 40.000 16.64 0.00 0.00 3.51
1019 1057 4.862018 GCTGCAGTACTTTTTGTTTTGTGA 59.138 37.500 16.64 0.00 0.00 3.58
1020 1058 4.259371 CGCTGCAGTACTTTTTGTTTTGTG 60.259 41.667 16.64 0.00 0.00 3.33
1021 1059 3.857093 CGCTGCAGTACTTTTTGTTTTGT 59.143 39.130 16.64 0.00 0.00 2.83
1022 1060 3.857093 ACGCTGCAGTACTTTTTGTTTTG 59.143 39.130 16.64 0.00 0.00 2.44
1023 1061 4.104696 ACGCTGCAGTACTTTTTGTTTT 57.895 36.364 16.64 0.00 0.00 2.43
1024 1062 3.775661 ACGCTGCAGTACTTTTTGTTT 57.224 38.095 16.64 0.00 0.00 2.83
1025 1063 5.238650 AGAATACGCTGCAGTACTTTTTGTT 59.761 36.000 16.64 0.00 0.00 2.83
1039 1077 5.842843 CGCTTTCATCAAATAGAATACGCTG 59.157 40.000 0.00 0.00 0.00 5.18
1227 1269 1.225855 TGGCAGCGTCAACTTAAGTG 58.774 50.000 9.34 3.91 0.00 3.16
1367 1409 3.223157 CCGTACTTCATTTTTGTGCGTC 58.777 45.455 0.00 0.00 37.93 5.19
1369 1411 3.262135 ACCGTACTTCATTTTTGTGCG 57.738 42.857 0.00 0.00 38.97 5.34
1380 1422 5.010820 AGCAATATCCTAGGAACCGTACTTC 59.989 44.000 17.30 0.00 0.00 3.01
1381 1423 4.900054 AGCAATATCCTAGGAACCGTACTT 59.100 41.667 17.30 0.00 0.00 2.24
1411 1453 3.056821 GCAGTTTACCATTTCCCCTTGTC 60.057 47.826 0.00 0.00 0.00 3.18
1428 1470 1.947456 GACAAGTTTTCCCTCGCAGTT 59.053 47.619 0.00 0.00 0.00 3.16
1527 1570 4.094739 TGAACCAAATACATGCGACATCAG 59.905 41.667 0.00 0.00 0.00 2.90
1581 1807 5.718649 TTTGAGAAACTTGAAGTCGTCAG 57.281 39.130 0.00 0.00 37.61 3.51
1582 1808 6.984474 AGTATTTGAGAAACTTGAAGTCGTCA 59.016 34.615 0.00 0.00 0.00 4.35
1583 1809 7.409465 AGTATTTGAGAAACTTGAAGTCGTC 57.591 36.000 0.00 0.00 0.00 4.20
1584 1810 8.882415 TTAGTATTTGAGAAACTTGAAGTCGT 57.118 30.769 0.00 0.00 0.00 4.34
1585 1811 9.582223 GTTTAGTATTTGAGAAACTTGAAGTCG 57.418 33.333 0.00 0.00 0.00 4.18
1633 1868 7.440556 CCATTCAAGTCCACAAGATACATCTAG 59.559 40.741 0.00 0.00 35.76 2.43
1710 2543 2.979813 GTGAACGATGTGATTTTGGTGC 59.020 45.455 0.00 0.00 0.00 5.01
1769 2602 4.095410 TCAGCAATTTTCGGCAACATAG 57.905 40.909 0.00 0.00 0.00 2.23
2437 3270 4.919168 TCAATCAAGGTAGTACAACGAACG 59.081 41.667 2.06 0.00 0.00 3.95
2502 3335 6.201806 GTCATAGCAAGCTTACATAGTTCCAG 59.798 42.308 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.