Multiple sequence alignment - TraesCS2A01G568300

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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 TraesCS2A01G568300 chr2A 100.000 3146 0 0 1 3146 766711448 766708303 0.000000e+00 5810.0
1 TraesCS2A01G568300 chr2D 88.836 1890 120 36 697 2544 641608784 641606944 0.000000e+00 2237.0
2 TraesCS2A01G568300 chr2D 87.282 747 61 19 1556 2284 641957919 641957189 0.000000e+00 822.0
3 TraesCS2A01G568300 chr2D 85.732 806 73 18 777 1560 641959237 641958452 0.000000e+00 813.0
4 TraesCS2A01G568300 chr2D 86.613 747 66 19 1556 2284 597904040 597903310 0.000000e+00 795.0
5 TraesCS2A01G568300 chr2D 94.065 337 20 0 2810 3146 641606866 641606530 2.160000e-141 512.0
6 TraesCS2A01G568300 chr2D 85.872 453 52 8 777 1227 597922959 597922517 3.670000e-129 472.0
7 TraesCS2A01G568300 chr2D 91.186 295 12 3 1280 1560 597904893 597904599 3.810000e-104 388.0
8 TraesCS2A01G568300 chr2D 95.946 74 3 0 2635 2708 641606949 641606876 1.530000e-23 121.0
9 TraesCS2A01G568300 chr2D 100.000 28 0 0 670 697 641608835 641608808 6.000000e-03 52.8
10 TraesCS2A01G568300 chr2B 90.039 1285 83 23 1329 2571 800027597 800028878 0.000000e+00 1622.0
11 TraesCS2A01G568300 chr2B 92.147 573 30 10 669 1238 800026956 800027516 0.000000e+00 795.0
12 TraesCS2A01G568300 chr2B 85.277 686 59 22 1 677 800026277 800026929 0.000000e+00 669.0
13 TraesCS2A01G568300 chr2B 78.322 429 51 19 2602 3027 800028877 800029266 4.060000e-59 239.0
14 TraesCS2A01G568300 chr2B 84.810 79 9 2 241 317 24813243 24813320 3.360000e-10 76.8
15 TraesCS2A01G568300 chr7D 77.650 349 57 15 256 593 178282061 178282399 3.200000e-45 193.0
16 TraesCS2A01G568300 chr7D 84.247 146 19 4 309 453 637505084 637504942 4.230000e-29 139.0
17 TraesCS2A01G568300 chr7D 83.562 146 20 4 309 453 637436386 637436244 1.970000e-27 134.0
18 TraesCS2A01G568300 chr7D 86.486 111 14 1 344 453 637197826 637197716 1.530000e-23 121.0
19 TraesCS2A01G568300 chr7D 88.732 71 7 1 118 188 80707314 80707383 5.590000e-13 86.1
20 TraesCS2A01G568300 chr6D 79.343 213 32 10 290 499 357560561 357560358 4.230000e-29 139.0
21 TraesCS2A01G568300 chr6D 87.059 85 6 3 238 317 433692335 433692251 1.200000e-14 91.6
22 TraesCS2A01G568300 chr5A 81.871 171 22 9 290 455 11205913 11206079 5.470000e-28 135.0
23 TraesCS2A01G568300 chr5A 79.532 171 26 9 290 455 11154825 11154991 2.560000e-21 113.0
24 TraesCS2A01G568300 chr5A 79.532 171 26 9 290 455 11174227 11174393 2.560000e-21 113.0
25 TraesCS2A01G568300 chr5A 89.041 73 5 2 117 188 661218051 661218121 1.550000e-13 87.9
26 TraesCS2A01G568300 chr5D 84.252 127 13 6 117 241 319114809 319114688 1.980000e-22 117.0
27 TraesCS2A01G568300 chr5D 86.111 72 8 1 117 188 537661523 537661592 3.360000e-10 76.8
28 TraesCS2A01G568300 chr1B 80.645 124 13 9 217 333 21668632 21668751 5.590000e-13 86.1
29 TraesCS2A01G568300 chr1B 84.722 72 10 1 117 188 460571683 460571613 1.570000e-08 71.3
30 TraesCS2A01G568300 chr7A 87.500 72 8 1 117 188 608895579 608895509 7.230000e-12 82.4
31 TraesCS2A01G568300 chr3D 87.324 71 7 1 118 188 103613428 103613496 2.600000e-11 80.5
32 TraesCS2A01G568300 chr3A 86.111 72 8 1 117 188 523335629 523335698 3.360000e-10 76.8
33 TraesCS2A01G568300 chr7B 84.932 73 8 2 117 188 564377263 564377333 1.570000e-08 71.3
34 TraesCS2A01G568300 chr1A 86.667 60 5 3 258 316 435091699 435091756 2.620000e-06 63.9


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 TraesCS2A01G568300 chr2A 766708303 766711448 3145 True 5810.00 5810 100.00000 1 3146 1 chr2A.!!$R1 3145
1 TraesCS2A01G568300 chr2D 641957189 641959237 2048 True 817.50 822 86.50700 777 2284 2 chr2D.!!$R4 1507
2 TraesCS2A01G568300 chr2D 641606530 641608835 2305 True 730.70 2237 94.71175 670 3146 4 chr2D.!!$R3 2476
3 TraesCS2A01G568300 chr2D 597903310 597904893 1583 True 591.50 795 88.89950 1280 2284 2 chr2D.!!$R2 1004
4 TraesCS2A01G568300 chr2B 800026277 800029266 2989 False 831.25 1622 86.44625 1 3027 4 chr2B.!!$F2 3026

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
667 676 0.107165 AATTAGTTGCTCCCGCTCCC 60.107 55.0 0.00 0.00 36.97 4.30 F
1277 1370 0.034059 CCCTCCGATGAATTCTCCCG 59.966 60.0 7.05 7.27 0.00 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1662 2887 0.108138 CGACCACCCTCATGTCCTTC 60.108 60.0 0.00 0.0 0.0 3.46 R
2747 4037 0.039074 CCATCCCATCGCGTCTAGTC 60.039 60.0 5.77 0.0 0.0 2.59 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
39 42 7.486551 CGTCGAGATCTTCAAAAACTAGATTCT 59.513 37.037 0.00 0.00 0.00 2.40
40 43 8.591312 GTCGAGATCTTCAAAAACTAGATTCTG 58.409 37.037 0.00 0.00 0.00 3.02
105 109 0.881600 AACGGACGAAAACCCCGAAG 60.882 55.000 7.06 0.00 45.58 3.79
106 110 1.301165 CGGACGAAAACCCCGAAGT 60.301 57.895 0.00 0.00 45.58 3.01
155 159 2.029073 CACGGTTGTGCCTCTCGT 59.971 61.111 0.00 0.00 39.67 4.18
180 184 1.069765 ATAACCATGCCTCTCGCGG 59.930 57.895 6.13 0.00 42.08 6.46
188 192 2.101233 GCCTCTCGCGGAAGGAAAC 61.101 63.158 25.65 9.19 0.00 2.78
193 197 2.289547 CTCTCGCGGAAGGAAACAAAAA 59.710 45.455 6.13 0.00 0.00 1.94
254 258 2.293318 TGCCTGCCTCTCGTGGAAT 61.293 57.895 0.00 0.00 0.00 3.01
299 303 2.270352 TCGTTTTTGAGAGGCATGGT 57.730 45.000 0.00 0.00 0.00 3.55
336 340 2.898729 CATAACCATGCCTCTCTCGT 57.101 50.000 0.00 0.00 0.00 4.18
337 341 2.477825 CATAACCATGCCTCTCTCGTG 58.522 52.381 0.00 0.00 0.00 4.35
339 343 0.976641 AACCATGCCTCTCTCGTGAA 59.023 50.000 0.00 0.00 0.00 3.18
340 344 0.976641 ACCATGCCTCTCTCGTGAAA 59.023 50.000 0.00 0.00 0.00 2.69
341 345 1.066573 ACCATGCCTCTCTCGTGAAAG 60.067 52.381 0.00 0.00 0.00 2.62
342 346 1.005340 CATGCCTCTCTCGTGAAAGC 58.995 55.000 0.00 0.00 0.00 3.51
343 347 0.610174 ATGCCTCTCTCGTGAAAGCA 59.390 50.000 7.81 7.81 32.38 3.91
344 348 0.392706 TGCCTCTCTCGTGAAAGCAA 59.607 50.000 3.98 0.00 0.00 3.91
345 349 1.202639 TGCCTCTCTCGTGAAAGCAAA 60.203 47.619 3.98 0.00 0.00 3.68
346 350 1.873591 GCCTCTCTCGTGAAAGCAAAA 59.126 47.619 0.00 0.00 0.00 2.44
347 351 2.349912 GCCTCTCTCGTGAAAGCAAAAC 60.350 50.000 0.00 0.00 0.00 2.43
348 352 2.224314 CCTCTCTCGTGAAAGCAAAACC 59.776 50.000 0.00 0.00 0.00 3.27
349 353 3.134458 CTCTCTCGTGAAAGCAAAACCT 58.866 45.455 0.00 0.00 0.00 3.50
350 354 3.541632 TCTCTCGTGAAAGCAAAACCTT 58.458 40.909 0.00 0.00 0.00 3.50
351 355 3.312421 TCTCTCGTGAAAGCAAAACCTTG 59.688 43.478 0.00 0.00 35.49 3.61
373 377 6.817765 TGCTTATCACGGAAGAAAGAAAAT 57.182 33.333 0.00 0.00 0.00 1.82
383 387 7.913297 CACGGAAGAAAGAAAATAGAAAACACA 59.087 33.333 0.00 0.00 0.00 3.72
439 443 3.809990 CGAAAGCAAAACCGCGAC 58.190 55.556 8.23 0.00 36.85 5.19
440 444 1.278637 CGAAAGCAAAACCGCGACT 59.721 52.632 8.23 0.00 36.85 4.18
491 496 6.205784 TCGTGCAAGAAAAGAAATTCGAAAT 58.794 32.000 0.00 0.00 34.46 2.17
492 497 6.695278 TCGTGCAAGAAAAGAAATTCGAAATT 59.305 30.769 0.00 0.00 34.46 1.82
493 498 7.221838 TCGTGCAAGAAAAGAAATTCGAAATTT 59.778 29.630 0.00 3.62 34.46 1.82
494 499 7.845622 CGTGCAAGAAAAGAAATTCGAAATTTT 59.154 29.630 0.00 7.61 34.46 1.82
530 538 4.822350 AGCTAAGAAAGACAGGTGAAAACC 59.178 41.667 0.00 0.00 0.00 3.27
538 546 5.738619 AGACAGGTGAAAACCAAAAAGTT 57.261 34.783 0.00 0.00 0.00 2.66
539 547 5.720202 AGACAGGTGAAAACCAAAAAGTTC 58.280 37.500 0.00 0.00 0.00 3.01
540 548 5.245075 AGACAGGTGAAAACCAAAAAGTTCA 59.755 36.000 0.00 0.00 0.00 3.18
541 549 5.859495 ACAGGTGAAAACCAAAAAGTTCAA 58.141 33.333 0.00 0.00 32.12 2.69
577 585 0.455972 AAATCGAAAACGCATGCGGG 60.456 50.000 39.95 23.79 44.69 6.13
613 622 0.748005 GCGCTTTCAGCCTATCCCAA 60.748 55.000 0.00 0.00 38.18 4.12
615 624 2.091541 CGCTTTCAGCCTATCCCAAAA 58.908 47.619 0.00 0.00 38.18 2.44
643 652 2.038557 TGGAAGTCTTTAAAGGAGCGCT 59.961 45.455 11.27 11.27 0.00 5.92
644 653 2.673862 GGAAGTCTTTAAAGGAGCGCTC 59.326 50.000 29.38 29.38 0.00 5.03
666 675 2.484889 CTAATTAGTTGCTCCCGCTCC 58.515 52.381 4.18 0.00 36.97 4.70
667 676 0.107165 AATTAGTTGCTCCCGCTCCC 60.107 55.000 0.00 0.00 36.97 4.30
693 736 2.665000 GGCAGGCTCAGCAGTGTA 59.335 61.111 0.00 0.00 0.00 2.90
753 821 0.905357 CCGGCCCAGATAGAATAGGG 59.095 60.000 0.00 0.00 44.37 3.53
754 822 0.905357 CGGCCCAGATAGAATAGGGG 59.095 60.000 0.00 0.00 41.75 4.79
914 982 3.557595 CCTTTCCGTATAAAGCTGAGCTG 59.442 47.826 8.16 0.00 39.62 4.24
944 1012 0.539438 AGCCGCCAATCCAGTCAAAA 60.539 50.000 0.00 0.00 0.00 2.44
1027 1120 4.541482 CGACGCCGGCGCTACTAA 62.541 66.667 46.22 0.00 44.19 2.24
1194 1287 2.055042 CCTCGACCTCCAGGACCAG 61.055 68.421 0.00 0.00 38.94 4.00
1247 1340 1.705186 CAACCTTCCCCCTCTTCTTCA 59.295 52.381 0.00 0.00 0.00 3.02
1248 1341 2.310052 CAACCTTCCCCCTCTTCTTCAT 59.690 50.000 0.00 0.00 0.00 2.57
1249 1342 2.200955 ACCTTCCCCCTCTTCTTCATC 58.799 52.381 0.00 0.00 0.00 2.92
1258 1351 3.604582 CCTCTTCTTCATCTCCAACACC 58.395 50.000 0.00 0.00 0.00 4.16
1259 1352 3.604582 CTCTTCTTCATCTCCAACACCC 58.395 50.000 0.00 0.00 0.00 4.61
1271 1364 1.340991 CCAACACCCCTCCGATGAATT 60.341 52.381 0.00 0.00 0.00 2.17
1272 1365 2.017049 CAACACCCCTCCGATGAATTC 58.983 52.381 0.00 0.00 0.00 2.17
1273 1366 1.584724 ACACCCCTCCGATGAATTCT 58.415 50.000 7.05 0.00 0.00 2.40
1274 1367 1.486726 ACACCCCTCCGATGAATTCTC 59.513 52.381 7.05 1.29 0.00 2.87
1276 1369 0.398318 CCCCTCCGATGAATTCTCCC 59.602 60.000 7.05 0.00 0.00 4.30
1277 1370 0.034059 CCCTCCGATGAATTCTCCCG 59.966 60.000 7.05 7.27 0.00 5.14
1291 1402 1.535444 TCCCGTGCTCCTTCTTCCA 60.535 57.895 0.00 0.00 0.00 3.53
1292 1403 0.909610 TCCCGTGCTCCTTCTTCCAT 60.910 55.000 0.00 0.00 0.00 3.41
1293 1404 0.745845 CCCGTGCTCCTTCTTCCATG 60.746 60.000 0.00 0.00 0.00 3.66
1313 1424 1.866063 GCCCGATCTTGATCTGACGAC 60.866 57.143 8.70 0.00 0.00 4.34
1326 1437 3.082548 TCTGACGACCTCGATTCTTCTT 58.917 45.455 0.78 0.00 43.02 2.52
1662 2887 2.193248 GCCCCAATCCTCTTCGGG 59.807 66.667 0.00 0.00 38.52 5.14
1848 3077 3.310860 CTCCAAGGTCCCGTTCGGG 62.311 68.421 22.57 22.57 46.57 5.14
2058 3302 4.087892 CAGACACAGAGCCCCGGG 62.088 72.222 15.80 15.80 0.00 5.73
2150 3394 2.106684 GGCCGGGAAGGAGATAAAGAAT 59.893 50.000 2.18 0.00 45.00 2.40
2153 3397 4.058817 CCGGGAAGGAGATAAAGAATTCG 58.941 47.826 0.00 0.00 45.00 3.34
2157 3401 6.073548 CGGGAAGGAGATAAAGAATTCGATTG 60.074 42.308 0.00 0.00 0.00 2.67
2192 3444 8.354711 TGATGAGTTGAGAGATACTGTACTTT 57.645 34.615 0.00 0.00 0.00 2.66
2194 3446 9.944663 GATGAGTTGAGAGATACTGTACTTTAG 57.055 37.037 0.00 0.00 0.00 1.85
2231 3483 8.428536 GCTCATGTAGTATTAACGACATTCATC 58.571 37.037 2.11 0.00 46.06 2.92
2264 3531 7.030165 CCGATGTATTACTACCACTCATCATC 58.970 42.308 0.00 0.00 33.03 2.92
2265 3532 7.309194 CCGATGTATTACTACCACTCATCATCA 60.309 40.741 0.00 0.00 33.03 3.07
2266 3533 8.246871 CGATGTATTACTACCACTCATCATCAT 58.753 37.037 0.00 0.00 33.03 2.45
2269 3536 9.025041 TGTATTACTACCACTCATCATCATAGG 57.975 37.037 0.00 0.00 0.00 2.57
2344 3616 2.610219 TTGCGTTGGTTTGATGATCG 57.390 45.000 0.00 0.00 0.00 3.69
2354 3626 5.977635 TGGTTTGATGATCGACTACAATCT 58.022 37.500 0.00 0.00 0.00 2.40
2356 3628 5.277058 GGTTTGATGATCGACTACAATCTGC 60.277 44.000 0.00 0.00 0.00 4.26
2402 3687 6.422701 TGACCGCCGATTTCTAAATACTAATG 59.577 38.462 0.00 0.00 0.00 1.90
2499 3784 3.004752 ACAGCAAGAAGAGGTGTGTTT 57.995 42.857 0.00 0.00 45.05 2.83
2509 3794 5.762218 AGAAGAGGTGTGTTTCTTGATTCAG 59.238 40.000 0.00 0.00 33.97 3.02
2546 3835 0.746659 AACACAAGCCCTCAAACTGC 59.253 50.000 0.00 0.00 0.00 4.40
2558 3847 1.824230 TCAAACTGCCTGCAACTGTTT 59.176 42.857 14.72 14.72 39.02 2.83
2571 3860 0.818040 ACTGTTTGAACTGGGCGGTC 60.818 55.000 5.87 0.00 32.82 4.79
2572 3861 1.515521 CTGTTTGAACTGGGCGGTCC 61.516 60.000 0.00 0.00 0.00 4.46
2582 3871 3.771978 GGCGGTCCCAACACATTT 58.228 55.556 0.00 0.00 0.00 2.32
2583 3872 1.584495 GGCGGTCCCAACACATTTC 59.416 57.895 0.00 0.00 0.00 2.17
2584 3873 1.584495 GCGGTCCCAACACATTTCC 59.416 57.895 0.00 0.00 0.00 3.13
2585 3874 1.175983 GCGGTCCCAACACATTTCCA 61.176 55.000 0.00 0.00 0.00 3.53
2586 3875 1.544724 CGGTCCCAACACATTTCCAT 58.455 50.000 0.00 0.00 0.00 3.41
2587 3876 1.472480 CGGTCCCAACACATTTCCATC 59.528 52.381 0.00 0.00 0.00 3.51
2588 3877 1.824852 GGTCCCAACACATTTCCATCC 59.175 52.381 0.00 0.00 0.00 3.51
2589 3878 2.524306 GTCCCAACACATTTCCATCCA 58.476 47.619 0.00 0.00 0.00 3.41
2590 3879 2.896685 GTCCCAACACATTTCCATCCAA 59.103 45.455 0.00 0.00 0.00 3.53
2591 3880 2.896685 TCCCAACACATTTCCATCCAAC 59.103 45.455 0.00 0.00 0.00 3.77
2592 3881 2.899256 CCCAACACATTTCCATCCAACT 59.101 45.455 0.00 0.00 0.00 3.16
2593 3882 3.056607 CCCAACACATTTCCATCCAACTC 60.057 47.826 0.00 0.00 0.00 3.01
2594 3883 3.056607 CCAACACATTTCCATCCAACTCC 60.057 47.826 0.00 0.00 0.00 3.85
2595 3884 2.807676 ACACATTTCCATCCAACTCCC 58.192 47.619 0.00 0.00 0.00 4.30
2596 3885 2.102578 CACATTTCCATCCAACTCCCC 58.897 52.381 0.00 0.00 0.00 4.81
2597 3886 1.715931 ACATTTCCATCCAACTCCCCA 59.284 47.619 0.00 0.00 0.00 4.96
2598 3887 2.315763 ACATTTCCATCCAACTCCCCAT 59.684 45.455 0.00 0.00 0.00 4.00
2599 3888 2.826674 TTTCCATCCAACTCCCCATC 57.173 50.000 0.00 0.00 0.00 3.51
2600 3889 1.985622 TTCCATCCAACTCCCCATCT 58.014 50.000 0.00 0.00 0.00 2.90
2601 3890 1.216064 TCCATCCAACTCCCCATCTG 58.784 55.000 0.00 0.00 0.00 2.90
2602 3891 0.921896 CCATCCAACTCCCCATCTGT 59.078 55.000 0.00 0.00 0.00 3.41
2603 3892 1.133976 CCATCCAACTCCCCATCTGTC 60.134 57.143 0.00 0.00 0.00 3.51
2608 3897 2.162681 CAACTCCCCATCTGTCCAAAC 58.837 52.381 0.00 0.00 0.00 2.93
2612 3901 2.171448 CTCCCCATCTGTCCAAACCTAG 59.829 54.545 0.00 0.00 0.00 3.02
2616 3905 1.212935 CATCTGTCCAAACCTAGGGGG 59.787 57.143 14.81 11.73 41.89 5.40
2674 3964 3.331293 GGACACCCCGGATCCATT 58.669 61.111 13.41 0.00 32.35 3.16
2689 3979 1.702957 TCCATTCAAAACCTCTCCCGT 59.297 47.619 0.00 0.00 0.00 5.28
2722 4012 3.301554 CATGCCAACCGGTTGCCA 61.302 61.111 36.83 33.82 39.16 4.92
2729 4019 2.914908 AACCGGTTGCCACGCATTC 61.915 57.895 21.56 0.00 38.76 2.67
2771 4061 0.320771 GACGCGATGGGATGGCTATT 60.321 55.000 15.93 0.00 0.00 1.73
2773 4063 0.518636 CGCGATGGGATGGCTATTTG 59.481 55.000 0.00 0.00 0.00 2.32
2791 4081 3.258931 CCGCATGCACAACGGTTA 58.741 55.556 19.57 0.00 42.01 2.85
2792 4082 1.154301 CCGCATGCACAACGGTTAC 60.154 57.895 19.57 0.00 42.01 2.50
2793 4083 1.154301 CGCATGCACAACGGTTACC 60.154 57.895 19.57 0.00 0.00 2.85
2794 4084 1.211709 GCATGCACAACGGTTACCC 59.788 57.895 14.21 0.00 0.00 3.69
2896 4186 6.092748 CGCTATTTTATAATTGTCCATGCCC 58.907 40.000 0.00 0.00 0.00 5.36
2902 4192 0.965363 AATTGTCCATGCCCGACACC 60.965 55.000 3.12 0.00 39.89 4.16
2935 4225 3.382832 CCGTCGCTCCCACTCCTT 61.383 66.667 0.00 0.00 0.00 3.36
2962 4252 4.838152 CCACCTCCGCCATGACCG 62.838 72.222 0.00 0.00 0.00 4.79
3005 4295 1.523758 AACCTTACGGCAGAGCAAAG 58.476 50.000 0.00 0.00 0.00 2.77
3010 4300 0.320421 TACGGCAGAGCAAAGACACC 60.320 55.000 0.00 0.00 0.00 4.16
3056 4346 8.265055 AGTAAATCATCATTAGAGAAACCCGAA 58.735 33.333 0.00 0.00 0.00 4.30
3065 4355 8.630917 TCATTAGAGAAACCCGAATTACTCTAG 58.369 37.037 0.00 0.00 37.93 2.43
3074 4364 5.069251 ACCCGAATTACTCTAGTTGATCTGG 59.931 44.000 0.00 0.00 0.00 3.86
3117 4407 6.826668 TCAGTGGTTCATGAAGTTTCTAAGA 58.173 36.000 8.80 0.00 0.00 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 1.346365 TTTTGAAGATCTCGACGCGG 58.654 50.000 12.47 0.00 0.00 6.46
12 13 4.857588 TCTAGTTTTTGAAGATCTCGACGC 59.142 41.667 0.00 0.00 0.00 5.19
39 42 6.438259 TTTTCGTCAAAACCTATCAACACA 57.562 33.333 0.00 0.00 0.00 3.72
128 132 1.145377 ACAACCGTGCCTCTTTCGT 59.855 52.632 0.00 0.00 0.00 3.85
281 285 1.135972 CGACCATGCCTCTCAAAAACG 60.136 52.381 0.00 0.00 0.00 3.60
342 346 4.215399 TCTTCCGTGATAAGCAAGGTTTTG 59.785 41.667 0.00 0.00 45.18 2.44
343 347 4.394729 TCTTCCGTGATAAGCAAGGTTTT 58.605 39.130 0.00 0.00 45.18 2.43
344 348 4.015872 TCTTCCGTGATAAGCAAGGTTT 57.984 40.909 0.00 0.00 45.18 3.27
345 349 3.695830 TCTTCCGTGATAAGCAAGGTT 57.304 42.857 0.00 0.00 45.18 3.50
346 350 3.695830 TTCTTCCGTGATAAGCAAGGT 57.304 42.857 0.00 0.00 45.18 3.50
347 351 4.253685 TCTTTCTTCCGTGATAAGCAAGG 58.746 43.478 0.00 0.00 46.17 3.61
348 352 5.862924 TTCTTTCTTCCGTGATAAGCAAG 57.137 39.130 0.00 0.00 31.15 4.01
349 353 6.627395 TTTTCTTTCTTCCGTGATAAGCAA 57.373 33.333 0.00 0.00 0.00 3.91
350 354 6.817765 ATTTTCTTTCTTCCGTGATAAGCA 57.182 33.333 0.00 0.00 0.00 3.91
351 355 8.197988 TCTATTTTCTTTCTTCCGTGATAAGC 57.802 34.615 0.00 0.00 0.00 3.09
355 359 8.846211 TGTTTTCTATTTTCTTTCTTCCGTGAT 58.154 29.630 0.00 0.00 0.00 3.06
356 360 8.126700 GTGTTTTCTATTTTCTTTCTTCCGTGA 58.873 33.333 0.00 0.00 0.00 4.35
357 361 7.913297 TGTGTTTTCTATTTTCTTTCTTCCGTG 59.087 33.333 0.00 0.00 0.00 4.94
358 362 7.992008 TGTGTTTTCTATTTTCTTTCTTCCGT 58.008 30.769 0.00 0.00 0.00 4.69
391 395 0.391130 CCCATGCCTCTCGAAAACGA 60.391 55.000 0.00 0.00 0.00 3.85
426 430 2.022129 CGAGAGTCGCGGTTTTGCT 61.022 57.895 6.13 0.00 31.14 3.91
436 440 0.985549 CTTTTCTTCCGCGAGAGTCG 59.014 55.000 8.23 0.00 43.89 4.18
439 443 2.996621 ACATTCTTTTCTTCCGCGAGAG 59.003 45.455 8.23 4.80 0.00 3.20
440 444 2.736721 CACATTCTTTTCTTCCGCGAGA 59.263 45.455 8.23 0.00 0.00 4.04
492 497 3.880490 TCTTAGCTTCCGCACAAGAAAAA 59.120 39.130 0.00 0.00 36.88 1.94
493 498 3.472652 TCTTAGCTTCCGCACAAGAAAA 58.527 40.909 0.00 0.00 36.88 2.29
494 499 3.120321 TCTTAGCTTCCGCACAAGAAA 57.880 42.857 0.00 0.00 36.88 2.52
504 512 4.273148 TCACCTGTCTTTCTTAGCTTCC 57.727 45.455 0.00 0.00 0.00 3.46
505 513 6.431278 GTTTTCACCTGTCTTTCTTAGCTTC 58.569 40.000 0.00 0.00 0.00 3.86
510 518 7.469537 TTTTGGTTTTCACCTGTCTTTCTTA 57.530 32.000 0.00 0.00 44.61 2.10
520 528 7.809546 TTTTTGAACTTTTTGGTTTTCACCT 57.190 28.000 0.00 0.00 44.61 4.00
563 571 1.708822 ATTTTCCCGCATGCGTTTTC 58.291 45.000 35.55 0.00 37.81 2.29
613 622 7.791029 TCCTTTAAAGACTTCCAGCAATTTTT 58.209 30.769 16.98 0.00 0.00 1.94
615 624 6.517362 GCTCCTTTAAAGACTTCCAGCAATTT 60.517 38.462 16.98 0.00 0.00 1.82
621 630 2.416893 GCGCTCCTTTAAAGACTTCCAG 59.583 50.000 16.98 3.91 0.00 3.86
693 736 0.668401 CGACGGACGGCCTTTACTTT 60.668 55.000 5.33 0.00 38.46 2.66
753 821 2.927477 TCGTCAGTCGATTTGCATAACC 59.073 45.455 0.00 0.00 44.01 2.85
925 993 0.539438 TTTTGACTGGATTGGCGGCT 60.539 50.000 11.43 0.00 0.00 5.52
926 994 0.532115 ATTTTGACTGGATTGGCGGC 59.468 50.000 0.00 0.00 0.00 6.53
927 995 1.134946 GGATTTTGACTGGATTGGCGG 59.865 52.381 0.00 0.00 0.00 6.13
928 996 2.094675 AGGATTTTGACTGGATTGGCG 58.905 47.619 0.00 0.00 0.00 5.69
929 997 3.129988 CAGAGGATTTTGACTGGATTGGC 59.870 47.826 0.00 0.00 0.00 4.52
944 1012 1.463018 GGGGATCTGGGCAGAGGAT 60.463 63.158 0.00 0.00 41.33 3.24
1010 1103 4.541482 TTAGTAGCGCCGGCGTCG 62.541 66.667 45.02 22.76 46.35 5.12
1012 1105 4.503314 GGTTAGTAGCGCCGGCGT 62.503 66.667 45.02 33.46 46.35 5.68
1016 1109 2.649975 CGTCGGTTAGTAGCGCCG 60.650 66.667 2.29 0.00 44.52 6.46
1017 1110 1.298190 CTCGTCGGTTAGTAGCGCC 60.298 63.158 2.29 0.00 44.52 6.53
1018 1111 1.298190 CCTCGTCGGTTAGTAGCGC 60.298 63.158 0.00 0.00 44.52 5.92
1019 1112 1.354506 CCCTCGTCGGTTAGTAGCG 59.645 63.158 0.00 0.00 46.15 4.26
1020 1113 1.065436 GCCCTCGTCGGTTAGTAGC 59.935 63.158 0.00 0.00 0.00 3.58
1021 1114 1.030457 ATGCCCTCGTCGGTTAGTAG 58.970 55.000 0.00 0.00 0.00 2.57
1022 1115 0.742505 CATGCCCTCGTCGGTTAGTA 59.257 55.000 0.00 0.00 0.00 1.82
1023 1116 1.515954 CATGCCCTCGTCGGTTAGT 59.484 57.895 0.00 0.00 0.00 2.24
1024 1117 1.227263 CCATGCCCTCGTCGGTTAG 60.227 63.158 0.00 0.00 0.00 2.34
1025 1118 2.897207 CCATGCCCTCGTCGGTTA 59.103 61.111 0.00 0.00 0.00 2.85
1026 1119 4.778143 GCCATGCCCTCGTCGGTT 62.778 66.667 0.00 0.00 0.00 4.44
1247 1340 0.326618 ATCGGAGGGGTGTTGGAGAT 60.327 55.000 0.00 0.00 0.00 2.75
1248 1341 1.080354 ATCGGAGGGGTGTTGGAGA 59.920 57.895 0.00 0.00 0.00 3.71
1249 1342 1.221840 CATCGGAGGGGTGTTGGAG 59.778 63.158 0.00 0.00 0.00 3.86
1258 1351 0.034059 CGGGAGAATTCATCGGAGGG 59.966 60.000 8.44 0.00 0.00 4.30
1259 1352 0.753262 ACGGGAGAATTCATCGGAGG 59.247 55.000 8.44 0.00 0.00 4.30
1271 1364 1.258445 GGAAGAAGGAGCACGGGAGA 61.258 60.000 0.00 0.00 0.00 3.71
1272 1365 1.219393 GGAAGAAGGAGCACGGGAG 59.781 63.158 0.00 0.00 0.00 4.30
1273 1366 0.909610 ATGGAAGAAGGAGCACGGGA 60.910 55.000 0.00 0.00 0.00 5.14
1274 1367 0.745845 CATGGAAGAAGGAGCACGGG 60.746 60.000 0.00 0.00 0.00 5.28
1276 1369 1.372087 GGCATGGAAGAAGGAGCACG 61.372 60.000 0.00 0.00 0.00 5.34
1277 1370 1.034292 GGGCATGGAAGAAGGAGCAC 61.034 60.000 0.00 0.00 0.00 4.40
1291 1402 1.269988 CGTCAGATCAAGATCGGGCAT 60.270 52.381 13.61 0.00 42.48 4.40
1292 1403 0.103026 CGTCAGATCAAGATCGGGCA 59.897 55.000 13.61 0.00 42.48 5.36
1293 1404 0.385751 TCGTCAGATCAAGATCGGGC 59.614 55.000 9.71 7.41 42.48 6.13
1313 1424 2.797792 CGCTCTGGAAGAAGAATCGAGG 60.798 54.545 0.00 0.00 46.34 4.63
1650 2875 1.952621 TGTCCTTCCCGAAGAGGATT 58.047 50.000 6.01 0.00 45.00 3.01
1662 2887 0.108138 CGACCACCCTCATGTCCTTC 60.108 60.000 0.00 0.00 0.00 3.46
2014 3249 2.672307 GACAGCAGCAGCAGCCTT 60.672 61.111 6.10 0.00 45.49 4.35
2058 3302 2.815647 CTGAAAGAGACGCCGCCC 60.816 66.667 0.00 0.00 34.07 6.13
2068 3312 0.541998 TCGGTGGAGAGGCTGAAAGA 60.542 55.000 0.00 0.00 34.07 2.52
2150 3394 6.969366 ACTCATCATGTTTCAAACAATCGAA 58.031 32.000 7.14 0.00 45.86 3.71
2153 3397 8.077991 TCTCAACTCATCATGTTTCAAACAATC 58.922 33.333 7.14 0.00 45.86 2.67
2157 3401 7.194607 TCTCTCAACTCATCATGTTTCAAAC 57.805 36.000 0.00 0.00 0.00 2.93
2165 3409 7.939782 AGTACAGTATCTCTCAACTCATCATG 58.060 38.462 0.00 0.00 0.00 3.07
2192 3444 5.865085 ACTACATGAGCTCCAACAAAACTA 58.135 37.500 12.15 0.00 0.00 2.24
2194 3446 6.743575 ATACTACATGAGCTCCAACAAAAC 57.256 37.500 12.15 0.00 0.00 2.43
2231 3483 6.590292 GTGGTAGTAATACATCGGATGAATGG 59.410 42.308 23.98 0.00 0.00 3.16
2316 3588 4.130857 TCAAACCAACGCAATCAGAGTAA 58.869 39.130 0.00 0.00 0.00 2.24
2344 3616 1.863454 CATGAGCCGCAGATTGTAGTC 59.137 52.381 0.00 0.00 0.00 2.59
2354 3626 3.255395 TCTTTGAAATTTCATGAGCCGCA 59.745 39.130 21.10 1.34 37.00 5.69
2356 3628 5.514204 GTCATCTTTGAAATTTCATGAGCCG 59.486 40.000 21.10 14.52 37.00 5.52
2451 3736 6.870971 ACTTTATTTGCGGAGACAAAACTA 57.129 33.333 0.00 0.00 42.45 2.24
2499 3784 4.574892 TGCCGTAATGAACTGAATCAAGA 58.425 39.130 0.00 0.00 32.06 3.02
2509 3794 3.006940 TGTTGGAGATGCCGTAATGAAC 58.993 45.455 0.00 0.00 40.66 3.18
2546 3835 1.067516 CCCAGTTCAAACAGTTGCAGG 59.932 52.381 0.00 0.00 34.50 4.85
2571 3860 2.899256 AGTTGGATGGAAATGTGTTGGG 59.101 45.455 0.00 0.00 0.00 4.12
2572 3861 3.056607 GGAGTTGGATGGAAATGTGTTGG 60.057 47.826 0.00 0.00 0.00 3.77
2573 3862 3.056607 GGGAGTTGGATGGAAATGTGTTG 60.057 47.826 0.00 0.00 0.00 3.33
2574 3863 3.165071 GGGAGTTGGATGGAAATGTGTT 58.835 45.455 0.00 0.00 0.00 3.32
2575 3864 2.557452 GGGGAGTTGGATGGAAATGTGT 60.557 50.000 0.00 0.00 0.00 3.72
2576 3865 2.102578 GGGGAGTTGGATGGAAATGTG 58.897 52.381 0.00 0.00 0.00 3.21
2577 3866 1.715931 TGGGGAGTTGGATGGAAATGT 59.284 47.619 0.00 0.00 0.00 2.71
2578 3867 2.530460 TGGGGAGTTGGATGGAAATG 57.470 50.000 0.00 0.00 0.00 2.32
2579 3868 2.861317 AGATGGGGAGTTGGATGGAAAT 59.139 45.455 0.00 0.00 0.00 2.17
2580 3869 2.025037 CAGATGGGGAGTTGGATGGAAA 60.025 50.000 0.00 0.00 0.00 3.13
2581 3870 1.565759 CAGATGGGGAGTTGGATGGAA 59.434 52.381 0.00 0.00 0.00 3.53
2582 3871 1.216064 CAGATGGGGAGTTGGATGGA 58.784 55.000 0.00 0.00 0.00 3.41
2583 3872 0.921896 ACAGATGGGGAGTTGGATGG 59.078 55.000 0.00 0.00 0.00 3.51
2584 3873 1.133976 GGACAGATGGGGAGTTGGATG 60.134 57.143 0.00 0.00 0.00 3.51
2585 3874 1.216990 GGACAGATGGGGAGTTGGAT 58.783 55.000 0.00 0.00 0.00 3.41
2586 3875 0.178876 TGGACAGATGGGGAGTTGGA 60.179 55.000 0.00 0.00 0.00 3.53
2587 3876 0.698238 TTGGACAGATGGGGAGTTGG 59.302 55.000 0.00 0.00 0.00 3.77
2588 3877 2.162681 GTTTGGACAGATGGGGAGTTG 58.837 52.381 0.00 0.00 0.00 3.16
2589 3878 1.075536 GGTTTGGACAGATGGGGAGTT 59.924 52.381 0.00 0.00 0.00 3.01
2590 3879 0.698818 GGTTTGGACAGATGGGGAGT 59.301 55.000 0.00 0.00 0.00 3.85
2591 3880 0.995024 AGGTTTGGACAGATGGGGAG 59.005 55.000 0.00 0.00 0.00 4.30
2592 3881 2.196595 CTAGGTTTGGACAGATGGGGA 58.803 52.381 0.00 0.00 0.00 4.81
2593 3882 1.212935 CCTAGGTTTGGACAGATGGGG 59.787 57.143 0.00 0.00 0.00 4.96
2594 3883 1.212935 CCCTAGGTTTGGACAGATGGG 59.787 57.143 8.29 0.00 0.00 4.00
2595 3884 1.212935 CCCCTAGGTTTGGACAGATGG 59.787 57.143 8.29 0.00 0.00 3.51
2596 3885 1.212935 CCCCCTAGGTTTGGACAGATG 59.787 57.143 8.29 0.00 0.00 2.90
2597 3886 1.596496 CCCCCTAGGTTTGGACAGAT 58.404 55.000 8.29 0.00 0.00 2.90
2598 3887 3.098445 CCCCCTAGGTTTGGACAGA 57.902 57.895 8.29 0.00 0.00 3.41
2608 3897 2.617215 AAAGCCCCACCCCCTAGG 60.617 66.667 0.06 0.06 43.78 3.02
2630 3919 0.673437 ATGTGGCAAGGTTTGAACGG 59.327 50.000 0.00 0.00 0.00 4.44
2674 3964 1.072505 GGCACGGGAGAGGTTTTGA 59.927 57.895 0.00 0.00 0.00 2.69
2746 4036 0.386100 CATCCCATCGCGTCTAGTCG 60.386 60.000 5.77 4.95 0.00 4.18
2747 4037 0.039074 CCATCCCATCGCGTCTAGTC 60.039 60.000 5.77 0.00 0.00 2.59
2751 4041 1.188219 ATAGCCATCCCATCGCGTCT 61.188 55.000 5.77 0.00 0.00 4.18
2776 4066 4.859784 GGTAACCGTTGTGCATGC 57.140 55.556 11.82 11.82 0.00 4.06
2789 4079 3.315949 AGGCAGGCGAACGGGTAA 61.316 61.111 0.00 0.00 0.00 2.85
2790 4080 4.077184 CAGGCAGGCGAACGGGTA 62.077 66.667 0.00 0.00 0.00 3.69
2808 4098 0.109504 GCGCCAGTTTTTAATGCCGA 60.110 50.000 0.00 0.00 0.00 5.54
2822 4112 2.975799 GGTTTCTCCAACGCGCCA 60.976 61.111 5.73 0.00 36.05 5.69
2827 4117 1.070134 TCAGAGTGGGTTTCTCCAACG 59.930 52.381 0.00 0.00 44.63 4.10
2929 4219 0.394565 GTGGTGCAGTGAGAAGGAGT 59.605 55.000 0.00 0.00 0.00 3.85
2935 4225 2.574018 CGGAGGTGGTGCAGTGAGA 61.574 63.158 0.00 0.00 0.00 3.27
2962 4252 0.741221 CAGGTCACTTTAGGGCTCGC 60.741 60.000 0.00 0.00 0.00 5.03
3005 4295 2.948979 AGATGAGTCGAGAGATGGTGTC 59.051 50.000 0.00 0.00 45.19 3.67
3010 4300 7.722795 TTACTCTAAGATGAGTCGAGAGATG 57.277 40.000 13.66 0.00 45.07 2.90
3048 4338 7.042335 CAGATCAACTAGAGTAATTCGGGTTT 58.958 38.462 0.00 0.00 0.00 3.27
3065 4355 6.593382 GGAGCTGATCATTATACCAGATCAAC 59.407 42.308 0.00 0.00 45.18 3.18
3074 4364 7.361889 CACTGATTGGAGCTGATCATTATAC 57.638 40.000 0.00 0.00 32.31 1.47


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

AutoCloner maintained by Alex Coulton.