Multiple sequence alignment - TraesCS3B01G269600

Loading Multiple Alignment...

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 TraesCS3B01G269600 chr3B 100.000 5034 0 0 1 5034 434346946 434341913 0.000000e+00 9297.0
1 TraesCS3B01G269600 chr3B 96.291 2750 79 9 1564 4299 512102128 512099388 0.000000e+00 4492.0
2 TraesCS3B01G269600 chr3B 93.331 2459 145 9 1682 4140 306886720 306889159 0.000000e+00 3615.0
3 TraesCS3B01G269600 chr3B 88.333 900 54 16 542 1405 512103015 512102131 0.000000e+00 1033.0
4 TraesCS3B01G269600 chr3B 93.548 620 17 8 4295 4913 512099354 512098757 0.000000e+00 902.0
5 TraesCS3B01G269600 chr3B 92.052 541 41 2 1 541 521562115 521561577 0.000000e+00 760.0
6 TraesCS3B01G269600 chr3B 100.000 36 0 0 1477 1512 434345542 434345507 3.250000e-07 67.6
7 TraesCS3B01G269600 chr7A 99.703 4373 10 1 541 4913 642148756 642153125 0.000000e+00 8000.0
8 TraesCS3B01G269600 chr7A 100.000 36 0 0 1477 1512 642149617 642149652 3.250000e-07 67.6
9 TraesCS3B01G269600 chr5B 97.882 2738 50 2 1564 4301 675602184 675599455 0.000000e+00 4728.0
10 TraesCS3B01G269600 chr5B 96.056 2764 71 16 1564 4299 23257946 23260699 0.000000e+00 4466.0
11 TraesCS3B01G269600 chr5B 95.736 1196 24 6 541 1728 623880353 623881529 0.000000e+00 1901.0
12 TraesCS3B01G269600 chr5B 95.401 1196 22 5 541 1728 627484638 627485808 0.000000e+00 1873.0
13 TraesCS3B01G269600 chr5B 94.771 937 17 5 3977 4913 627485801 627486705 0.000000e+00 1430.0
14 TraesCS3B01G269600 chr5B 94.664 937 18 5 3977 4913 623881522 623882426 0.000000e+00 1424.0
15 TraesCS3B01G269600 chr5B 93.634 864 31 6 542 1405 675603026 675602187 0.000000e+00 1269.0
16 TraesCS3B01G269600 chr5B 89.000 900 51 20 542 1405 23257056 23257943 0.000000e+00 1070.0
17 TraesCS3B01G269600 chr5B 96.452 620 21 1 4295 4913 675599423 675598804 0.000000e+00 1022.0
18 TraesCS3B01G269600 chr5B 93.548 620 17 8 4295 4913 23260733 23261330 0.000000e+00 902.0
19 TraesCS3B01G269600 chr5B 81.188 101 6 6 1350 1449 623881340 623881428 9.040000e-08 69.4
20 TraesCS3B01G269600 chr5B 81.188 101 6 6 1350 1449 627485619 627485707 9.040000e-08 69.4
21 TraesCS3B01G269600 chr5B 100.000 36 0 0 1477 1512 623881206 623881241 3.250000e-07 67.6
22 TraesCS3B01G269600 chr5B 100.000 36 0 0 1477 1512 627485485 627485520 3.250000e-07 67.6
23 TraesCS3B01G269600 chr5B 97.368 38 1 0 1412 1449 23257972 23258009 1.170000e-06 65.8
24 TraesCS3B01G269600 chr5B 97.368 38 1 0 1412 1449 675602158 675602121 1.170000e-06 65.8
25 TraesCS3B01G269600 chr5B 76.667 120 14 10 1513 1618 623881194 623881313 3.000000e-03 54.7
26 TraesCS3B01G269600 chr5B 76.667 120 14 10 1513 1618 627485473 627485592 3.000000e-03 54.7
27 TraesCS3B01G269600 chr1B 96.859 2738 78 1 1564 4301 570769565 570766836 0.000000e+00 4573.0
28 TraesCS3B01G269600 chr1B 90.417 887 41 13 540 1405 570770431 570769568 0.000000e+00 1127.0
29 TraesCS3B01G269600 chr1B 95.623 594 26 0 4321 4914 570766784 570766191 0.000000e+00 953.0
30 TraesCS3B01G269600 chr5A 96.035 2749 82 9 1564 4298 437838672 437841407 0.000000e+00 4447.0
31 TraesCS3B01G269600 chr5A 89.068 869 62 11 541 1405 437837830 437838669 0.000000e+00 1048.0
32 TraesCS3B01G269600 chr5A 89.256 605 24 4 4323 4913 437841464 437842041 0.000000e+00 719.0
33 TraesCS3B01G269600 chr2D 95.906 2467 92 2 1564 4022 261785958 261783493 0.000000e+00 3988.0
34 TraesCS3B01G269600 chr2D 88.353 850 62 17 542 1388 261786785 261785970 0.000000e+00 987.0
35 TraesCS3B01G269600 chr6A 99.662 2074 7 0 2840 4913 189534830 189536903 0.000000e+00 3792.0
36 TraesCS3B01G269600 chr6A 98.825 1277 4 1 542 1818 189532298 189533563 0.000000e+00 2265.0
37 TraesCS3B01G269600 chr6A 100.000 36 0 0 1477 1512 189533150 189533185 3.250000e-07 67.6
38 TraesCS3B01G269600 chr3A 90.324 1819 153 14 2464 4265 703415261 703413449 0.000000e+00 2362.0
39 TraesCS3B01G269600 chr3A 98.333 120 2 0 4914 5033 236447646 236447765 1.420000e-50 211.0
40 TraesCS3B01G269600 chr4A 93.978 1096 42 4 1564 2637 667659188 667658095 0.000000e+00 1637.0
41 TraesCS3B01G269600 chr4A 90.805 870 50 8 542 1405 667660036 667659191 0.000000e+00 1136.0
42 TraesCS3B01G269600 chr4A 96.296 594 22 0 4321 4914 667651196 667650603 0.000000e+00 976.0
43 TraesCS3B01G269600 chr4A 93.488 215 5 2 4087 4301 667651453 667651248 1.360000e-80 311.0
44 TraesCS3B01G269600 chr1D 90.856 853 55 10 557 1405 117407353 117408186 0.000000e+00 1122.0
45 TraesCS3B01G269600 chr1D 95.315 683 24 1 1564 2238 117408189 117408871 0.000000e+00 1077.0
46 TraesCS3B01G269600 chr1D 91.529 543 43 3 1 541 264613861 264613320 0.000000e+00 745.0
47 TraesCS3B01G269600 chr1D 97.521 121 3 0 4914 5034 106182786 106182906 1.840000e-49 207.0
48 TraesCS3B01G269600 chr1D 97.521 121 3 0 4914 5034 108974983 108975103 1.840000e-49 207.0
49 TraesCS3B01G269600 chr1D 97.521 121 3 0 4914 5034 218064842 218064722 1.840000e-49 207.0
50 TraesCS3B01G269600 chr1D 97.521 121 3 0 4914 5034 249879909 249880029 1.840000e-49 207.0
51 TraesCS3B01G269600 chr1D 97.521 121 3 0 4914 5034 329827211 329827331 1.840000e-49 207.0
52 TraesCS3B01G269600 chr1D 97.368 38 1 0 1412 1449 117408215 117408252 1.170000e-06 65.8
53 TraesCS3B01G269600 chr6B 92.449 543 37 3 1 541 292696755 292697295 0.000000e+00 773.0
54 TraesCS3B01G269600 chr6B 91.667 540 43 2 1 539 312293490 312294028 0.000000e+00 747.0
55 TraesCS3B01G269600 chr6B 91.312 541 47 0 1 541 666755339 666755879 0.000000e+00 739.0
56 TraesCS3B01G269600 chr4B 92.410 527 39 1 4 529 16371202 16370676 0.000000e+00 750.0
57 TraesCS3B01G269600 chr4B 91.713 543 42 3 1 541 283091123 283090582 0.000000e+00 750.0
58 TraesCS3B01G269600 chr4B 91.513 542 44 2 1 541 29923527 29922987 0.000000e+00 745.0
59 TraesCS3B01G269600 chr7B 91.360 544 42 5 1 541 210172891 210172350 0.000000e+00 739.0
60 TraesCS3B01G269600 chr4D 98.347 121 2 0 4914 5034 95212763 95212643 3.950000e-51 213.0
61 TraesCS3B01G269600 chr4D 96.774 124 3 1 4911 5034 208694271 208694149 6.610000e-49 206.0
62 TraesCS3B01G269600 chr6D 97.521 121 3 0 4914 5034 255572110 255572230 1.840000e-49 207.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3B01G269600 chr3B 434341913 434346946 5033 True 4682.300000 9297 100.000000 1 5034 2 chr3B.!!$R2 5033
1 TraesCS3B01G269600 chr3B 306886720 306889159 2439 False 3615.000000 3615 93.331000 1682 4140 1 chr3B.!!$F1 2458
2 TraesCS3B01G269600 chr3B 512098757 512103015 4258 True 2142.333333 4492 92.724000 542 4913 3 chr3B.!!$R3 4371
3 TraesCS3B01G269600 chr3B 521561577 521562115 538 True 760.000000 760 92.052000 1 541 1 chr3B.!!$R1 540
4 TraesCS3B01G269600 chr7A 642148756 642153125 4369 False 4033.800000 8000 99.851500 541 4913 2 chr7A.!!$F1 4372
5 TraesCS3B01G269600 chr5B 675598804 675603026 4222 True 1771.200000 4728 96.334000 542 4913 4 chr5B.!!$R1 4371
6 TraesCS3B01G269600 chr5B 23257056 23261330 4274 False 1625.950000 4466 93.993000 542 4913 4 chr5B.!!$F1 4371
7 TraesCS3B01G269600 chr5B 623880353 623882426 2073 False 703.340000 1901 89.651000 541 4913 5 chr5B.!!$F2 4372
8 TraesCS3B01G269600 chr5B 627484638 627486705 2067 False 698.940000 1873 89.605400 541 4913 5 chr5B.!!$F3 4372
9 TraesCS3B01G269600 chr1B 570766191 570770431 4240 True 2217.666667 4573 94.299667 540 4914 3 chr1B.!!$R1 4374
10 TraesCS3B01G269600 chr5A 437837830 437842041 4211 False 2071.333333 4447 91.453000 541 4913 3 chr5A.!!$F1 4372
11 TraesCS3B01G269600 chr2D 261783493 261786785 3292 True 2487.500000 3988 92.129500 542 4022 2 chr2D.!!$R1 3480
12 TraesCS3B01G269600 chr6A 189532298 189536903 4605 False 2041.533333 3792 99.495667 542 4913 3 chr6A.!!$F1 4371
13 TraesCS3B01G269600 chr3A 703413449 703415261 1812 True 2362.000000 2362 90.324000 2464 4265 1 chr3A.!!$R1 1801
14 TraesCS3B01G269600 chr4A 667658095 667660036 1941 True 1386.500000 1637 92.391500 542 2637 2 chr4A.!!$R2 2095
15 TraesCS3B01G269600 chr4A 667650603 667651453 850 True 643.500000 976 94.892000 4087 4914 2 chr4A.!!$R1 827
16 TraesCS3B01G269600 chr1D 117407353 117408871 1518 False 754.933333 1122 94.513000 557 2238 3 chr1D.!!$F5 1681
17 TraesCS3B01G269600 chr1D 264613320 264613861 541 True 745.000000 745 91.529000 1 541 1 chr1D.!!$R2 540
18 TraesCS3B01G269600 chr6B 292696755 292697295 540 False 773.000000 773 92.449000 1 541 1 chr6B.!!$F1 540
19 TraesCS3B01G269600 chr6B 312293490 312294028 538 False 747.000000 747 91.667000 1 539 1 chr6B.!!$F2 538
20 TraesCS3B01G269600 chr6B 666755339 666755879 540 False 739.000000 739 91.312000 1 541 1 chr6B.!!$F3 540
21 TraesCS3B01G269600 chr4B 16370676 16371202 526 True 750.000000 750 92.410000 4 529 1 chr4B.!!$R1 525
22 TraesCS3B01G269600 chr4B 283090582 283091123 541 True 750.000000 750 91.713000 1 541 1 chr4B.!!$R3 540
23 TraesCS3B01G269600 chr4B 29922987 29923527 540 True 745.000000 745 91.513000 1 541 1 chr4B.!!$R2 540
24 TraesCS3B01G269600 chr7B 210172350 210172891 541 True 739.000000 739 91.360000 1 541 1 chr7B.!!$R1 540

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
469 472 1.555477 CCAACAAGCGCGTTTCTTTT 58.445 45.000 4.81 0.0 0.0 2.27 F
510 514 2.027003 TGATGTCAATGATGCTCGCA 57.973 45.000 0.00 0.0 0.0 5.10 F
1982 2115 2.038557 AGGAAGTAAATGCCACGACAGT 59.961 45.455 0.00 0.0 0.0 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2725 2882 6.915786 AGATATCCAACTCTTTTAGCCCATT 58.084 36.0 0.0 0.0 0.00 3.16 R
3257 3637 0.674581 TGGATCAAGAGCAACAGCCG 60.675 55.0 0.0 0.0 0.00 5.52 R
4921 5377 7.486802 TGTGTTAGTCATATGCTTCATGATG 57.513 36.0 0.0 0.0 35.02 3.07 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
185 187 8.792633 CCATACTTCTGTAACTCCAAAAATTCA 58.207 33.333 0.00 0.00 31.80 2.57
192 194 9.581099 TCTGTAACTCCAAAAATTCAGAAAAAC 57.419 29.630 0.00 0.00 0.00 2.43
316 319 7.869800 AGTTTCTGTTTTTGCACAAAATCAAA 58.130 26.923 16.27 12.03 38.64 2.69
365 368 4.220602 AGGCTTTACTTGGCACTTTATTGG 59.779 41.667 0.00 0.00 0.00 3.16
461 464 2.250939 TTGTCTCCCAACAAGCGCG 61.251 57.895 0.00 0.00 34.31 6.86
469 472 1.555477 CCAACAAGCGCGTTTCTTTT 58.445 45.000 4.81 0.00 0.00 2.27
495 499 5.624344 CCTTTTAGCTAGGCATGATGATG 57.376 43.478 0.00 0.00 0.00 3.07
509 513 2.546789 TGATGATGTCAATGATGCTCGC 59.453 45.455 0.00 0.00 32.78 5.03
510 514 2.027003 TGATGTCAATGATGCTCGCA 57.973 45.000 0.00 0.00 0.00 5.10
511 515 2.567985 TGATGTCAATGATGCTCGCAT 58.432 42.857 3.70 3.70 39.69 4.73
512 516 3.731089 TGATGTCAATGATGCTCGCATA 58.269 40.909 4.10 0.00 36.70 3.14
513 517 4.128643 TGATGTCAATGATGCTCGCATAA 58.871 39.130 4.10 0.00 36.70 1.90
514 518 4.575645 TGATGTCAATGATGCTCGCATAAA 59.424 37.500 4.10 0.00 36.70 1.40
515 519 4.961435 TGTCAATGATGCTCGCATAAAA 57.039 36.364 4.10 0.00 36.70 1.52
516 520 4.912214 TGTCAATGATGCTCGCATAAAAG 58.088 39.130 4.10 0.00 36.70 2.27
517 521 4.635324 TGTCAATGATGCTCGCATAAAAGA 59.365 37.500 4.10 0.00 36.70 2.52
518 522 5.297527 TGTCAATGATGCTCGCATAAAAGAT 59.702 36.000 4.10 0.00 36.70 2.40
519 523 6.183360 TGTCAATGATGCTCGCATAAAAGATT 60.183 34.615 4.10 0.00 36.70 2.40
520 524 7.012232 TGTCAATGATGCTCGCATAAAAGATTA 59.988 33.333 4.10 0.00 36.70 1.75
521 525 7.533222 GTCAATGATGCTCGCATAAAAGATTAG 59.467 37.037 4.10 0.00 36.70 1.73
522 526 7.442062 TCAATGATGCTCGCATAAAAGATTAGA 59.558 33.333 4.10 0.00 36.70 2.10
523 527 7.734924 ATGATGCTCGCATAAAAGATTAGAA 57.265 32.000 4.10 0.00 36.70 2.10
524 528 7.734924 TGATGCTCGCATAAAAGATTAGAAT 57.265 32.000 4.10 0.00 36.70 2.40
525 529 8.158169 TGATGCTCGCATAAAAGATTAGAATT 57.842 30.769 4.10 0.00 36.70 2.17
526 530 8.071967 TGATGCTCGCATAAAAGATTAGAATTG 58.928 33.333 4.10 0.00 36.70 2.32
527 531 7.552458 TGCTCGCATAAAAGATTAGAATTGA 57.448 32.000 0.00 0.00 0.00 2.57
528 532 7.984391 TGCTCGCATAAAAGATTAGAATTGAA 58.016 30.769 0.00 0.00 0.00 2.69
529 533 7.910162 TGCTCGCATAAAAGATTAGAATTGAAC 59.090 33.333 0.00 0.00 0.00 3.18
530 534 8.125448 GCTCGCATAAAAGATTAGAATTGAACT 58.875 33.333 0.00 0.00 0.00 3.01
1107 1194 2.742372 GGTCGACGGCAGCAACAT 60.742 61.111 9.92 0.00 0.00 2.71
1982 2115 2.038557 AGGAAGTAAATGCCACGACAGT 59.961 45.455 0.00 0.00 0.00 3.55
2725 2882 7.676004 TCACATTCTGAACTTGATAGTTACCA 58.324 34.615 0.00 0.00 44.51 3.25
3257 3637 5.056894 AGCTTCAACATCTTGATCTTTGC 57.943 39.130 0.00 0.00 36.26 3.68
4921 5377 1.311651 GCCCAGGCTGAAAAGAGAGC 61.312 60.000 17.94 1.79 38.26 4.09
4922 5378 0.037303 CCCAGGCTGAAAAGAGAGCA 59.963 55.000 17.94 0.00 36.90 4.26
4923 5379 1.340795 CCCAGGCTGAAAAGAGAGCAT 60.341 52.381 17.94 0.00 36.90 3.79
4924 5380 2.015587 CCAGGCTGAAAAGAGAGCATC 58.984 52.381 17.94 0.00 36.90 3.91
4925 5381 2.617276 CCAGGCTGAAAAGAGAGCATCA 60.617 50.000 17.94 0.00 37.82 3.07
4926 5382 3.280295 CAGGCTGAAAAGAGAGCATCAT 58.720 45.455 9.42 0.00 37.82 2.45
4927 5383 3.065510 CAGGCTGAAAAGAGAGCATCATG 59.934 47.826 9.42 0.00 37.82 3.07
4928 5384 3.054582 AGGCTGAAAAGAGAGCATCATGA 60.055 43.478 0.00 0.00 37.82 3.07
4929 5385 3.693085 GGCTGAAAAGAGAGCATCATGAA 59.307 43.478 0.00 0.00 37.82 2.57
4930 5386 4.201930 GGCTGAAAAGAGAGCATCATGAAG 60.202 45.833 0.00 0.00 37.82 3.02
4931 5387 4.731193 GCTGAAAAGAGAGCATCATGAAGC 60.731 45.833 14.96 14.96 37.82 3.86
4932 5388 4.329392 TGAAAAGAGAGCATCATGAAGCA 58.671 39.130 23.62 0.00 37.82 3.91
4933 5389 4.948004 TGAAAAGAGAGCATCATGAAGCAT 59.052 37.500 23.62 12.40 37.82 3.79
4934 5390 6.117488 TGAAAAGAGAGCATCATGAAGCATA 58.883 36.000 23.62 0.00 37.82 3.14
4935 5391 6.771267 TGAAAAGAGAGCATCATGAAGCATAT 59.229 34.615 23.62 9.62 37.82 1.78
4936 5392 6.561737 AAAGAGAGCATCATGAAGCATATG 57.438 37.500 23.62 6.54 37.82 1.78
4937 5393 5.485209 AGAGAGCATCATGAAGCATATGA 57.515 39.130 23.62 0.00 38.76 2.15
4938 5394 5.239351 AGAGAGCATCATGAAGCATATGAC 58.761 41.667 23.62 9.33 37.38 3.06
4939 5395 5.012251 AGAGAGCATCATGAAGCATATGACT 59.988 40.000 23.62 12.33 37.38 3.41
4940 5396 6.210984 AGAGAGCATCATGAAGCATATGACTA 59.789 38.462 23.62 0.00 37.38 2.59
4941 5397 6.766429 AGAGCATCATGAAGCATATGACTAA 58.234 36.000 23.62 0.00 37.38 2.24
4942 5398 6.649973 AGAGCATCATGAAGCATATGACTAAC 59.350 38.462 23.62 2.88 37.38 2.34
4943 5399 6.293698 AGCATCATGAAGCATATGACTAACA 58.706 36.000 23.62 7.85 37.38 2.41
4944 5400 6.204301 AGCATCATGAAGCATATGACTAACAC 59.796 38.462 23.62 0.00 37.38 3.32
4945 5401 6.017687 GCATCATGAAGCATATGACTAACACA 60.018 38.462 17.64 3.61 37.38 3.72
4946 5402 7.308408 GCATCATGAAGCATATGACTAACACAT 60.308 37.037 17.64 5.44 37.38 3.21
4947 5403 8.565416 CATCATGAAGCATATGACTAACACATT 58.435 33.333 6.97 0.00 37.38 2.71
4948 5404 8.510243 TCATGAAGCATATGACTAACACATTT 57.490 30.769 6.97 0.00 30.03 2.32
4949 5405 9.612066 TCATGAAGCATATGACTAACACATTTA 57.388 29.630 6.97 0.00 30.03 1.40
4952 5408 9.448438 TGAAGCATATGACTAACACATTTAAGT 57.552 29.630 6.97 0.00 0.00 2.24
4953 5409 9.922305 GAAGCATATGACTAACACATTTAAGTC 57.078 33.333 6.97 0.00 39.04 3.01
4954 5410 9.672673 AAGCATATGACTAACACATTTAAGTCT 57.327 29.630 6.97 0.00 39.27 3.24
4959 5415 8.788325 ATGACTAACACATTTAAGTCTAACCC 57.212 34.615 0.00 0.00 39.27 4.11
4960 5416 7.737869 TGACTAACACATTTAAGTCTAACCCA 58.262 34.615 0.00 0.00 39.27 4.51
4961 5417 7.658575 TGACTAACACATTTAAGTCTAACCCAC 59.341 37.037 0.00 0.00 39.27 4.61
4962 5418 7.742767 ACTAACACATTTAAGTCTAACCCACT 58.257 34.615 0.00 0.00 0.00 4.00
4963 5419 8.215736 ACTAACACATTTAAGTCTAACCCACTT 58.784 33.333 0.00 0.00 37.80 3.16
4964 5420 7.506328 AACACATTTAAGTCTAACCCACTTC 57.494 36.000 0.00 0.00 35.63 3.01
4965 5421 6.002082 ACACATTTAAGTCTAACCCACTTCC 58.998 40.000 0.00 0.00 35.63 3.46
4966 5422 6.183361 ACACATTTAAGTCTAACCCACTTCCT 60.183 38.462 0.00 0.00 35.63 3.36
4967 5423 7.016858 ACACATTTAAGTCTAACCCACTTCCTA 59.983 37.037 0.00 0.00 35.63 2.94
4968 5424 8.047310 CACATTTAAGTCTAACCCACTTCCTAT 58.953 37.037 0.00 0.00 35.63 2.57
4969 5425 8.047310 ACATTTAAGTCTAACCCACTTCCTATG 58.953 37.037 0.00 0.00 35.63 2.23
4970 5426 4.489306 AAGTCTAACCCACTTCCTATGC 57.511 45.455 0.00 0.00 27.00 3.14
4971 5427 3.450904 AGTCTAACCCACTTCCTATGCA 58.549 45.455 0.00 0.00 0.00 3.96
4972 5428 4.040755 AGTCTAACCCACTTCCTATGCAT 58.959 43.478 3.79 3.79 0.00 3.96
4973 5429 5.216622 AGTCTAACCCACTTCCTATGCATA 58.783 41.667 6.20 6.20 0.00 3.14
4974 5430 5.305644 AGTCTAACCCACTTCCTATGCATAG 59.694 44.000 24.33 24.33 0.00 2.23
4986 5442 5.954296 CCTATGCATAGGGATTTTGTGAG 57.046 43.478 36.06 12.91 44.97 3.51
4987 5443 4.217118 CCTATGCATAGGGATTTTGTGAGC 59.783 45.833 36.06 0.00 44.97 4.26
4988 5444 3.084536 TGCATAGGGATTTTGTGAGCA 57.915 42.857 0.00 0.00 0.00 4.26
4989 5445 3.429492 TGCATAGGGATTTTGTGAGCAA 58.571 40.909 0.00 0.00 0.00 3.91
4990 5446 3.831333 TGCATAGGGATTTTGTGAGCAAA 59.169 39.130 0.00 0.00 42.25 3.68
4991 5447 4.176271 GCATAGGGATTTTGTGAGCAAAC 58.824 43.478 0.00 0.00 43.47 2.93
4992 5448 4.321899 GCATAGGGATTTTGTGAGCAAACA 60.322 41.667 0.00 0.00 43.47 2.83
4993 5449 5.782047 CATAGGGATTTTGTGAGCAAACAA 58.218 37.500 0.47 0.47 43.47 2.83
4994 5450 4.058721 AGGGATTTTGTGAGCAAACAAC 57.941 40.909 3.91 0.00 43.47 3.32
4995 5451 3.706086 AGGGATTTTGTGAGCAAACAACT 59.294 39.130 3.91 0.00 43.47 3.16
4996 5452 4.162131 AGGGATTTTGTGAGCAAACAACTT 59.838 37.500 3.91 0.00 43.47 2.66
4997 5453 5.362430 AGGGATTTTGTGAGCAAACAACTTA 59.638 36.000 3.91 0.00 43.47 2.24
4998 5454 6.041979 AGGGATTTTGTGAGCAAACAACTTAT 59.958 34.615 3.91 0.00 43.47 1.73
4999 5455 6.146021 GGGATTTTGTGAGCAAACAACTTATG 59.854 38.462 3.91 0.00 43.47 1.90
5000 5456 6.146021 GGATTTTGTGAGCAAACAACTTATGG 59.854 38.462 3.91 0.00 43.47 2.74
5001 5457 4.582701 TTGTGAGCAAACAACTTATGGG 57.417 40.909 0.47 0.00 35.16 4.00
5002 5458 3.826524 TGTGAGCAAACAACTTATGGGA 58.173 40.909 0.00 0.00 0.00 4.37
5003 5459 3.820467 TGTGAGCAAACAACTTATGGGAG 59.180 43.478 0.00 0.00 0.00 4.30
5004 5460 2.819608 TGAGCAAACAACTTATGGGAGC 59.180 45.455 0.00 0.00 0.00 4.70
5005 5461 2.819608 GAGCAAACAACTTATGGGAGCA 59.180 45.455 0.00 0.00 0.00 4.26
5006 5462 3.230134 AGCAAACAACTTATGGGAGCAA 58.770 40.909 0.00 0.00 0.00 3.91
5007 5463 3.256631 AGCAAACAACTTATGGGAGCAAG 59.743 43.478 0.00 0.00 0.00 4.01
5008 5464 3.255642 GCAAACAACTTATGGGAGCAAGA 59.744 43.478 0.00 0.00 0.00 3.02
5009 5465 4.616835 GCAAACAACTTATGGGAGCAAGAG 60.617 45.833 0.00 0.00 0.00 2.85
5010 5466 4.373156 AACAACTTATGGGAGCAAGAGT 57.627 40.909 0.00 0.00 0.00 3.24
5011 5467 3.944087 ACAACTTATGGGAGCAAGAGTC 58.056 45.455 0.00 0.00 0.00 3.36
5012 5468 3.327757 ACAACTTATGGGAGCAAGAGTCA 59.672 43.478 0.00 0.00 0.00 3.41
5013 5469 4.202461 ACAACTTATGGGAGCAAGAGTCAA 60.202 41.667 0.00 0.00 0.00 3.18
5014 5470 3.944087 ACTTATGGGAGCAAGAGTCAAC 58.056 45.455 0.00 0.00 0.00 3.18
5015 5471 3.584848 ACTTATGGGAGCAAGAGTCAACT 59.415 43.478 0.00 0.00 0.00 3.16
5016 5472 4.777896 ACTTATGGGAGCAAGAGTCAACTA 59.222 41.667 0.00 0.00 0.00 2.24
5017 5473 3.902881 ATGGGAGCAAGAGTCAACTAG 57.097 47.619 0.00 0.00 0.00 2.57
5018 5474 1.276421 TGGGAGCAAGAGTCAACTAGC 59.724 52.381 0.00 0.00 0.00 3.42
5019 5475 1.276421 GGGAGCAAGAGTCAACTAGCA 59.724 52.381 0.00 0.00 0.00 3.49
5020 5476 2.093235 GGGAGCAAGAGTCAACTAGCAT 60.093 50.000 0.00 0.00 0.00 3.79
5021 5477 3.133003 GGGAGCAAGAGTCAACTAGCATA 59.867 47.826 0.00 0.00 0.00 3.14
5022 5478 4.367450 GGAGCAAGAGTCAACTAGCATAG 58.633 47.826 0.00 0.00 46.50 2.23
5023 5479 4.367450 GAGCAAGAGTCAACTAGCATAGG 58.633 47.826 0.00 0.00 44.97 2.57
5024 5480 4.026744 AGCAAGAGTCAACTAGCATAGGA 58.973 43.478 0.00 0.00 44.97 2.94
5025 5481 4.467795 AGCAAGAGTCAACTAGCATAGGAA 59.532 41.667 0.00 0.00 44.97 3.36
5026 5482 4.808364 GCAAGAGTCAACTAGCATAGGAAG 59.192 45.833 0.00 0.00 44.97 3.46
5027 5483 5.355596 CAAGAGTCAACTAGCATAGGAAGG 58.644 45.833 0.00 0.00 44.97 3.46
5028 5484 3.386402 AGAGTCAACTAGCATAGGAAGGC 59.614 47.826 0.00 0.00 44.97 4.35
5029 5485 3.107601 AGTCAACTAGCATAGGAAGGCA 58.892 45.455 0.00 0.00 44.97 4.75
5030 5486 3.519510 AGTCAACTAGCATAGGAAGGCAA 59.480 43.478 0.00 0.00 44.97 4.52
5031 5487 4.019321 AGTCAACTAGCATAGGAAGGCAAA 60.019 41.667 0.00 0.00 44.97 3.68
5032 5488 4.700213 GTCAACTAGCATAGGAAGGCAAAA 59.300 41.667 0.00 0.00 44.97 2.44
5033 5489 4.700213 TCAACTAGCATAGGAAGGCAAAAC 59.300 41.667 0.00 0.00 44.97 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 9.917129 TGGAATACAGTATATATAACACCAACG 57.083 33.333 0.00 0.00 0.00 4.10
29 30 6.158695 ACCATGGAGAAGTTGGAATACAGTAT 59.841 38.462 21.47 0.00 34.52 2.12
316 319 5.846164 TGGGATAGTGTGGATGATAGTTGAT 59.154 40.000 0.00 0.00 0.00 2.57
395 398 5.744171 TGTGTGTCCACATGATTAAGCTAT 58.256 37.500 0.00 0.00 46.45 2.97
495 499 5.160699 TCTTTTATGCGAGCATCATTGAC 57.839 39.130 14.35 0.00 37.82 3.18
518 522 9.698309 CTGACTCTCTTTGTAGTTCAATTCTAA 57.302 33.333 0.00 0.00 35.84 2.10
519 523 7.815068 GCTGACTCTCTTTGTAGTTCAATTCTA 59.185 37.037 0.00 0.00 35.84 2.10
520 524 6.648725 GCTGACTCTCTTTGTAGTTCAATTCT 59.351 38.462 0.00 0.00 35.84 2.40
521 525 6.128418 GGCTGACTCTCTTTGTAGTTCAATTC 60.128 42.308 0.00 0.00 35.84 2.17
522 526 5.703130 GGCTGACTCTCTTTGTAGTTCAATT 59.297 40.000 0.00 0.00 35.84 2.32
523 527 5.012561 AGGCTGACTCTCTTTGTAGTTCAAT 59.987 40.000 0.00 0.00 35.84 2.57
524 528 4.345257 AGGCTGACTCTCTTTGTAGTTCAA 59.655 41.667 0.00 0.00 0.00 2.69
525 529 3.898123 AGGCTGACTCTCTTTGTAGTTCA 59.102 43.478 0.00 0.00 0.00 3.18
526 530 4.241681 CAGGCTGACTCTCTTTGTAGTTC 58.758 47.826 9.42 0.00 0.00 3.01
527 531 3.007398 CCAGGCTGACTCTCTTTGTAGTT 59.993 47.826 17.94 0.00 0.00 2.24
528 532 2.564947 CCAGGCTGACTCTCTTTGTAGT 59.435 50.000 17.94 0.00 0.00 2.73
529 533 2.093764 CCCAGGCTGACTCTCTTTGTAG 60.094 54.545 17.94 0.00 0.00 2.74
530 534 1.902508 CCCAGGCTGACTCTCTTTGTA 59.097 52.381 17.94 0.00 0.00 2.41
531 535 0.689623 CCCAGGCTGACTCTCTTTGT 59.310 55.000 17.94 0.00 0.00 2.83
532 536 0.676151 GCCCAGGCTGACTCTCTTTG 60.676 60.000 17.94 0.00 38.26 2.77
533 537 1.682257 GCCCAGGCTGACTCTCTTT 59.318 57.895 17.94 0.00 38.26 2.52
534 538 2.654079 CGCCCAGGCTGACTCTCTT 61.654 63.158 17.94 0.00 39.32 2.85
535 539 3.073735 CGCCCAGGCTGACTCTCT 61.074 66.667 17.94 0.00 39.32 3.10
536 540 2.844072 GAACGCCCAGGCTGACTCTC 62.844 65.000 17.94 2.00 39.32 3.20
537 541 2.925170 AACGCCCAGGCTGACTCT 60.925 61.111 17.94 0.00 39.32 3.24
538 542 2.435059 GAACGCCCAGGCTGACTC 60.435 66.667 17.94 3.28 39.32 3.36
1107 1194 3.123050 CACACTCACGTTGATCACTTGA 58.877 45.455 0.00 0.00 32.85 3.02
2725 2882 6.915786 AGATATCCAACTCTTTTAGCCCATT 58.084 36.000 0.00 0.00 0.00 3.16
3257 3637 0.674581 TGGATCAAGAGCAACAGCCG 60.675 55.000 0.00 0.00 0.00 5.52
4921 5377 7.486802 TGTGTTAGTCATATGCTTCATGATG 57.513 36.000 0.00 0.00 35.02 3.07
4922 5378 8.687292 AATGTGTTAGTCATATGCTTCATGAT 57.313 30.769 0.00 0.00 35.02 2.45
4923 5379 8.510243 AAATGTGTTAGTCATATGCTTCATGA 57.490 30.769 0.00 0.00 0.00 3.07
4926 5382 9.448438 ACTTAAATGTGTTAGTCATATGCTTCA 57.552 29.630 0.00 0.49 0.00 3.02
4927 5383 9.922305 GACTTAAATGTGTTAGTCATATGCTTC 57.078 33.333 0.00 0.00 37.53 3.86
4928 5384 9.672673 AGACTTAAATGTGTTAGTCATATGCTT 57.327 29.630 0.00 0.00 39.51 3.91
4933 5389 9.880157 GGGTTAGACTTAAATGTGTTAGTCATA 57.120 33.333 0.00 0.00 39.51 2.15
4934 5390 8.380099 TGGGTTAGACTTAAATGTGTTAGTCAT 58.620 33.333 0.00 0.00 39.51 3.06
4935 5391 7.658575 GTGGGTTAGACTTAAATGTGTTAGTCA 59.341 37.037 0.00 0.00 39.51 3.41
4936 5392 7.876582 AGTGGGTTAGACTTAAATGTGTTAGTC 59.123 37.037 0.00 0.00 37.79 2.59
4937 5393 7.742767 AGTGGGTTAGACTTAAATGTGTTAGT 58.257 34.615 0.00 0.00 0.00 2.24
4938 5394 8.617290 AAGTGGGTTAGACTTAAATGTGTTAG 57.383 34.615 0.00 0.00 31.72 2.34
4939 5395 7.662669 GGAAGTGGGTTAGACTTAAATGTGTTA 59.337 37.037 0.00 0.00 33.71 2.41
4940 5396 6.489022 GGAAGTGGGTTAGACTTAAATGTGTT 59.511 38.462 0.00 0.00 33.71 3.32
4941 5397 6.002082 GGAAGTGGGTTAGACTTAAATGTGT 58.998 40.000 0.00 0.00 33.71 3.72
4942 5398 6.238648 AGGAAGTGGGTTAGACTTAAATGTG 58.761 40.000 0.00 0.00 33.71 3.21
4943 5399 6.449830 AGGAAGTGGGTTAGACTTAAATGT 57.550 37.500 0.00 0.00 33.71 2.71
4944 5400 7.012421 GCATAGGAAGTGGGTTAGACTTAAATG 59.988 40.741 0.00 0.00 33.71 2.32
4945 5401 7.054751 GCATAGGAAGTGGGTTAGACTTAAAT 58.945 38.462 0.00 0.00 33.71 1.40
4946 5402 6.013206 TGCATAGGAAGTGGGTTAGACTTAAA 60.013 38.462 0.00 0.00 33.71 1.52
4947 5403 5.486063 TGCATAGGAAGTGGGTTAGACTTAA 59.514 40.000 0.00 0.00 33.71 1.85
4948 5404 5.027460 TGCATAGGAAGTGGGTTAGACTTA 58.973 41.667 0.00 0.00 33.71 2.24
4949 5405 3.844211 TGCATAGGAAGTGGGTTAGACTT 59.156 43.478 0.00 0.00 36.33 3.01
4950 5406 3.450904 TGCATAGGAAGTGGGTTAGACT 58.549 45.455 0.00 0.00 0.00 3.24
4951 5407 3.906720 TGCATAGGAAGTGGGTTAGAC 57.093 47.619 0.00 0.00 0.00 2.59
4952 5408 5.808366 CTATGCATAGGAAGTGGGTTAGA 57.192 43.478 23.70 0.00 0.00 2.10
4963 5419 9.708066 TTGCTCACAAAATCCCTATGCATAGGA 62.708 40.741 42.12 30.58 41.70 2.94
4964 5420 7.637743 TTGCTCACAAAATCCCTATGCATAGG 61.638 42.308 36.50 36.50 40.27 2.57
4965 5421 4.823442 TGCTCACAAAATCCCTATGCATAG 59.177 41.667 24.33 24.33 0.00 2.23
4966 5422 4.790937 TGCTCACAAAATCCCTATGCATA 58.209 39.130 6.20 6.20 0.00 3.14
4967 5423 3.634504 TGCTCACAAAATCCCTATGCAT 58.365 40.909 3.79 3.79 0.00 3.96
4968 5424 3.084536 TGCTCACAAAATCCCTATGCA 57.915 42.857 0.00 0.00 0.00 3.96
4969 5425 4.176271 GTTTGCTCACAAAATCCCTATGC 58.824 43.478 0.00 0.00 46.94 3.14
4970 5426 5.389859 TGTTTGCTCACAAAATCCCTATG 57.610 39.130 0.00 0.00 46.94 2.23
4971 5427 5.539955 AGTTGTTTGCTCACAAAATCCCTAT 59.460 36.000 3.21 0.00 46.94 2.57
4972 5428 4.892934 AGTTGTTTGCTCACAAAATCCCTA 59.107 37.500 3.21 0.00 46.94 3.53
4973 5429 3.706086 AGTTGTTTGCTCACAAAATCCCT 59.294 39.130 3.21 0.00 46.94 4.20
4974 5430 4.058721 AGTTGTTTGCTCACAAAATCCC 57.941 40.909 3.21 0.00 46.94 3.85
4975 5431 6.146021 CCATAAGTTGTTTGCTCACAAAATCC 59.854 38.462 3.21 0.00 46.94 3.01
4976 5432 6.146021 CCCATAAGTTGTTTGCTCACAAAATC 59.854 38.462 3.21 0.00 46.94 2.17
4977 5433 5.990996 CCCATAAGTTGTTTGCTCACAAAAT 59.009 36.000 3.21 0.00 46.94 1.82
4978 5434 5.127845 TCCCATAAGTTGTTTGCTCACAAAA 59.872 36.000 3.21 0.00 46.94 2.44
4979 5435 4.646945 TCCCATAAGTTGTTTGCTCACAAA 59.353 37.500 3.21 0.00 43.45 2.83
4980 5436 4.211125 TCCCATAAGTTGTTTGCTCACAA 58.789 39.130 0.00 0.00 34.15 3.33
4981 5437 3.820467 CTCCCATAAGTTGTTTGCTCACA 59.180 43.478 0.00 0.00 0.00 3.58
4982 5438 3.366374 GCTCCCATAAGTTGTTTGCTCAC 60.366 47.826 0.00 0.00 0.00 3.51
4983 5439 2.819608 GCTCCCATAAGTTGTTTGCTCA 59.180 45.455 0.00 0.00 0.00 4.26
4984 5440 2.819608 TGCTCCCATAAGTTGTTTGCTC 59.180 45.455 0.00 0.00 0.00 4.26
4985 5441 2.875296 TGCTCCCATAAGTTGTTTGCT 58.125 42.857 0.00 0.00 0.00 3.91
4986 5442 3.255642 TCTTGCTCCCATAAGTTGTTTGC 59.744 43.478 0.00 0.00 0.00 3.68
4987 5443 4.520492 ACTCTTGCTCCCATAAGTTGTTTG 59.480 41.667 0.00 0.00 0.00 2.93
4988 5444 4.729868 ACTCTTGCTCCCATAAGTTGTTT 58.270 39.130 0.00 0.00 0.00 2.83
4989 5445 4.202461 TGACTCTTGCTCCCATAAGTTGTT 60.202 41.667 0.00 0.00 0.00 2.83
4990 5446 3.327757 TGACTCTTGCTCCCATAAGTTGT 59.672 43.478 0.00 0.00 0.00 3.32
4991 5447 3.942829 TGACTCTTGCTCCCATAAGTTG 58.057 45.455 0.00 0.00 0.00 3.16
4992 5448 4.042187 AGTTGACTCTTGCTCCCATAAGTT 59.958 41.667 0.00 0.00 0.00 2.66
4993 5449 3.584848 AGTTGACTCTTGCTCCCATAAGT 59.415 43.478 0.00 0.00 0.00 2.24
4994 5450 4.213564 AGTTGACTCTTGCTCCCATAAG 57.786 45.455 0.00 0.00 0.00 1.73
4995 5451 4.383118 GCTAGTTGACTCTTGCTCCCATAA 60.383 45.833 0.00 0.00 34.44 1.90
4996 5452 3.133003 GCTAGTTGACTCTTGCTCCCATA 59.867 47.826 0.00 0.00 34.44 2.74
4997 5453 2.093235 GCTAGTTGACTCTTGCTCCCAT 60.093 50.000 0.00 0.00 34.44 4.00
4998 5454 1.276421 GCTAGTTGACTCTTGCTCCCA 59.724 52.381 0.00 0.00 34.44 4.37
4999 5455 1.276421 TGCTAGTTGACTCTTGCTCCC 59.724 52.381 0.00 0.00 37.17 4.30
5000 5456 2.751166 TGCTAGTTGACTCTTGCTCC 57.249 50.000 0.00 0.00 37.17 4.70
5001 5457 4.098654 TCCTATGCTAGTTGACTCTTGCTC 59.901 45.833 0.00 0.00 37.17 4.26
5002 5458 4.026744 TCCTATGCTAGTTGACTCTTGCT 58.973 43.478 0.00 0.00 37.17 3.91
5003 5459 4.392921 TCCTATGCTAGTTGACTCTTGC 57.607 45.455 0.00 0.00 36.89 4.01
5004 5460 5.355596 CCTTCCTATGCTAGTTGACTCTTG 58.644 45.833 0.00 0.00 0.00 3.02
5005 5461 4.141824 GCCTTCCTATGCTAGTTGACTCTT 60.142 45.833 0.00 0.00 0.00 2.85
5006 5462 3.386402 GCCTTCCTATGCTAGTTGACTCT 59.614 47.826 0.00 0.00 0.00 3.24
5007 5463 3.133003 TGCCTTCCTATGCTAGTTGACTC 59.867 47.826 0.00 0.00 0.00 3.36
5008 5464 3.107601 TGCCTTCCTATGCTAGTTGACT 58.892 45.455 0.00 0.00 0.00 3.41
5009 5465 3.543680 TGCCTTCCTATGCTAGTTGAC 57.456 47.619 0.00 0.00 0.00 3.18
5010 5466 4.568072 TTTGCCTTCCTATGCTAGTTGA 57.432 40.909 0.00 0.00 0.00 3.18
5011 5467 4.986622 GTTTTGCCTTCCTATGCTAGTTG 58.013 43.478 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.