Multiple sequence alignment - TraesCS2B01G162800

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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 TraesCS2B01G162800 chr2B 100.000 3218 0 0 1 3218 135357085 135360302 0.000000e+00 5943.0
1 TraesCS2B01G162800 chr2B 91.153 2611 154 44 511 3074 135197667 135200247 0.000000e+00 3470.0
2 TraesCS2B01G162800 chr2B 91.178 2437 142 37 736 3137 182153466 182151068 0.000000e+00 3241.0
3 TraesCS2B01G162800 chr2B 89.340 2167 132 57 714 2832 135463498 135465613 0.000000e+00 2630.0
4 TraesCS2B01G162800 chr2B 87.563 2171 143 61 704 2834 135126538 135128621 0.000000e+00 2396.0
5 TraesCS2B01G162800 chr2B 89.809 1727 140 20 887 2598 137814510 137812805 0.000000e+00 2182.0
6 TraesCS2B01G162800 chr2B 89.860 1716 137 24 896 2598 137349335 137347644 0.000000e+00 2170.0
7 TraesCS2B01G162800 chr2B 89.844 256 19 1 2889 3137 135515489 135515744 4.000000e-84 322.0
8 TraesCS2B01G162800 chr2B 98.413 63 1 0 3156 3218 182151081 182151019 9.440000e-21 111.0
9 TraesCS2B01G162800 chr2B 89.231 65 6 1 722 785 135238904 135238968 2.660000e-11 80.5
10 TraesCS2B01G162800 chr2D 93.178 2448 114 24 715 3137 83225052 83227471 0.000000e+00 3546.0
11 TraesCS2B01G162800 chr2D 90.990 2464 144 38 715 3137 83188233 83190659 0.000000e+00 3249.0
12 TraesCS2B01G162800 chr2D 92.323 2006 97 19 750 2740 83529794 83531757 0.000000e+00 2798.0
13 TraesCS2B01G162800 chr2D 90.095 1999 123 29 868 2848 127821397 127819456 0.000000e+00 2525.0
14 TraesCS2B01G162800 chr2D 87.800 459 27 13 1 432 83529146 83529602 7.960000e-141 510.0
15 TraesCS2B01G162800 chr2D 85.644 202 19 7 511 707 83529598 83529794 1.510000e-48 204.0
16 TraesCS2B01G162800 chr2D 92.045 88 7 0 427 514 512165927 512165840 1.210000e-24 124.0
17 TraesCS2B01G162800 chr2D 98.413 63 1 0 3156 3218 83190646 83190708 9.440000e-21 111.0
18 TraesCS2B01G162800 chr2D 96.875 64 1 1 3156 3218 83227458 83227521 4.390000e-19 106.0
19 TraesCS2B01G162800 chr2A 91.313 2072 131 28 865 2921 83984965 83987002 0.000000e+00 2784.0
20 TraesCS2B01G162800 chr2A 89.775 2044 146 29 868 2892 134867511 134865512 0.000000e+00 2558.0
21 TraesCS2B01G162800 chr2A 87.460 2201 147 67 656 2832 84143431 84145526 0.000000e+00 2416.0
22 TraesCS2B01G162800 chr2A 86.775 2155 166 57 704 2835 83989970 83992028 0.000000e+00 2290.0
23 TraesCS2B01G162800 chr2A 91.932 1066 68 9 1535 2598 84228932 84229981 0.000000e+00 1476.0
24 TraesCS2B01G162800 chr2A 89.347 291 21 7 1 290 84116105 84116386 1.100000e-94 357.0
25 TraesCS2B01G162800 chr2A 90.310 258 18 1 2873 3123 83992267 83992524 6.650000e-87 331.0
26 TraesCS2B01G162800 chr2A 91.257 183 12 1 2955 3137 83987003 83987181 2.480000e-61 246.0
27 TraesCS2B01G162800 chr2A 94.521 146 8 0 286 431 84141725 84141870 3.230000e-55 226.0
28 TraesCS2B01G162800 chr2A 91.083 157 11 3 511 664 84141870 84142026 3.250000e-50 209.0
29 TraesCS2B01G162800 chr2A 90.517 116 6 2 2580 2691 84231276 84231390 7.190000e-32 148.0
30 TraesCS2B01G162800 chr2A 98.413 63 1 0 3156 3218 83987168 83987230 9.440000e-21 111.0
31 TraesCS2B01G162800 chrUn 89.022 1339 93 17 511 1841 25420038 25418746 0.000000e+00 1609.0
32 TraesCS2B01G162800 chrUn 89.594 788 57 13 2366 3137 25418011 25417233 0.000000e+00 977.0
33 TraesCS2B01G162800 chrUn 93.779 434 23 2 1 432 25420465 25420034 0.000000e+00 649.0
34 TraesCS2B01G162800 chrUn 86.957 92 12 0 423 514 42479331 42479240 1.580000e-18 104.0
35 TraesCS2B01G162800 chrUn 93.750 64 3 1 3156 3218 25417246 25417183 9.500000e-16 95.3
36 TraesCS2B01G162800 chr5B 87.822 1125 104 17 896 2012 321478256 321477157 0.000000e+00 1288.0
37 TraesCS2B01G162800 chr7D 89.362 94 10 0 430 523 221683482 221683575 5.640000e-23 119.0
38 TraesCS2B01G162800 chr7B 86.275 102 13 1 416 516 684403208 684403309 3.390000e-20 110.0
39 TraesCS2B01G162800 chr7B 88.372 86 10 0 429 514 428965844 428965929 1.580000e-18 104.0
40 TraesCS2B01G162800 chr6D 88.636 88 10 0 427 514 190909272 190909359 1.220000e-19 108.0
41 TraesCS2B01G162800 chr5D 88.506 87 8 1 430 514 535136260 535136174 1.580000e-18 104.0
42 TraesCS2B01G162800 chr3A 88.372 86 10 0 429 514 507291489 507291574 1.580000e-18 104.0
43 TraesCS2B01G162800 chr3D 87.500 88 11 0 428 515 526192469 526192556 5.680000e-18 102.0


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 TraesCS2B01G162800 chr2B 135357085 135360302 3217 False 5943.000000 5943 100.000000 1 3218 1 chr2B.!!$F4 3217
1 TraesCS2B01G162800 chr2B 135197667 135200247 2580 False 3470.000000 3470 91.153000 511 3074 1 chr2B.!!$F2 2563
2 TraesCS2B01G162800 chr2B 135463498 135465613 2115 False 2630.000000 2630 89.340000 714 2832 1 chr2B.!!$F5 2118
3 TraesCS2B01G162800 chr2B 135126538 135128621 2083 False 2396.000000 2396 87.563000 704 2834 1 chr2B.!!$F1 2130
4 TraesCS2B01G162800 chr2B 137812805 137814510 1705 True 2182.000000 2182 89.809000 887 2598 1 chr2B.!!$R2 1711
5 TraesCS2B01G162800 chr2B 137347644 137349335 1691 True 2170.000000 2170 89.860000 896 2598 1 chr2B.!!$R1 1702
6 TraesCS2B01G162800 chr2B 182151019 182153466 2447 True 1676.000000 3241 94.795500 736 3218 2 chr2B.!!$R3 2482
7 TraesCS2B01G162800 chr2D 127819456 127821397 1941 True 2525.000000 2525 90.095000 868 2848 1 chr2D.!!$R1 1980
8 TraesCS2B01G162800 chr2D 83225052 83227521 2469 False 1826.000000 3546 95.026500 715 3218 2 chr2D.!!$F2 2503
9 TraesCS2B01G162800 chr2D 83188233 83190708 2475 False 1680.000000 3249 94.701500 715 3218 2 chr2D.!!$F1 2503
10 TraesCS2B01G162800 chr2D 83529146 83531757 2611 False 1170.666667 2798 88.589000 1 2740 3 chr2D.!!$F3 2739
11 TraesCS2B01G162800 chr2A 134865512 134867511 1999 True 2558.000000 2558 89.775000 868 2892 1 chr2A.!!$R1 2024
12 TraesCS2B01G162800 chr2A 83984965 83992524 7559 False 1152.400000 2784 91.613600 704 3218 5 chr2A.!!$F2 2514
13 TraesCS2B01G162800 chr2A 84141725 84145526 3801 False 950.333333 2416 91.021333 286 2832 3 chr2A.!!$F3 2546
14 TraesCS2B01G162800 chr2A 84228932 84231390 2458 False 812.000000 1476 91.224500 1535 2691 2 chr2A.!!$F4 1156
15 TraesCS2B01G162800 chrUn 25417183 25420465 3282 True 832.575000 1609 91.536250 1 3218 4 chrUn.!!$R2 3217
16 TraesCS2B01G162800 chr5B 321477157 321478256 1099 True 1288.000000 1288 87.822000 896 2012 1 chr5B.!!$R1 1116


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
942 2429 0.459585 GCGACAGCTGGTAATCCGAA 60.46 55.0 19.93 0.0 41.01 4.3 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2313 3834 0.096454 GCGTTCTTTATTTCGCGGCT 59.904 50.0 6.13 0.0 39.35 5.52 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
115 118 6.244552 TCTGCAATAGAGTTCATCCTTCAT 57.755 37.500 0.00 0.00 0.00 2.57
116 119 6.053650 TCTGCAATAGAGTTCATCCTTCATG 58.946 40.000 0.00 0.00 0.00 3.07
164 167 5.349061 AATGCAATTCATTTTCTCCCTCC 57.651 39.130 0.00 0.00 42.48 4.30
165 168 2.754552 TGCAATTCATTTTCTCCCTCCG 59.245 45.455 0.00 0.00 0.00 4.63
166 169 2.755103 GCAATTCATTTTCTCCCTCCGT 59.245 45.455 0.00 0.00 0.00 4.69
167 170 3.945285 GCAATTCATTTTCTCCCTCCGTA 59.055 43.478 0.00 0.00 0.00 4.02
168 171 4.580580 GCAATTCATTTTCTCCCTCCGTAT 59.419 41.667 0.00 0.00 0.00 3.06
169 172 5.067805 GCAATTCATTTTCTCCCTCCGTATT 59.932 40.000 0.00 0.00 0.00 1.89
358 387 7.003402 AGATCTGAAGCCTGTATCTTATTCC 57.997 40.000 0.00 0.00 0.00 3.01
368 397 6.461788 GCCTGTATCTTATTCCGAACTTCTCT 60.462 42.308 0.00 0.00 0.00 3.10
407 436 0.482446 TCCAGTTGCTCCATTGGGTT 59.518 50.000 2.09 0.00 34.93 4.11
434 463 9.036671 GTCTTTCAGAAGCATATTTAGTACTCC 57.963 37.037 0.00 0.00 32.75 3.85
435 464 8.982723 TCTTTCAGAAGCATATTTAGTACTCCT 58.017 33.333 0.00 0.00 32.75 3.69
436 465 9.606631 CTTTCAGAAGCATATTTAGTACTCCTT 57.393 33.333 0.00 0.00 0.00 3.36
437 466 9.959721 TTTCAGAAGCATATTTAGTACTCCTTT 57.040 29.630 0.00 0.00 0.00 3.11
438 467 9.959721 TTCAGAAGCATATTTAGTACTCCTTTT 57.040 29.630 0.00 0.00 0.00 2.27
439 468 9.383519 TCAGAAGCATATTTAGTACTCCTTTTG 57.616 33.333 0.00 0.00 0.00 2.44
440 469 9.167311 CAGAAGCATATTTAGTACTCCTTTTGT 57.833 33.333 0.00 0.00 0.00 2.83
441 470 9.384764 AGAAGCATATTTAGTACTCCTTTTGTC 57.615 33.333 0.00 0.00 0.00 3.18
442 471 8.507524 AAGCATATTTAGTACTCCTTTTGTCC 57.492 34.615 0.00 0.00 0.00 4.02
443 472 7.054751 AGCATATTTAGTACTCCTTTTGTCCC 58.945 38.462 0.00 0.00 0.00 4.46
444 473 6.826741 GCATATTTAGTACTCCTTTTGTCCCA 59.173 38.462 0.00 0.00 0.00 4.37
445 474 7.201705 GCATATTTAGTACTCCTTTTGTCCCAC 60.202 40.741 0.00 0.00 0.00 4.61
446 475 5.633655 TTTAGTACTCCTTTTGTCCCACA 57.366 39.130 0.00 0.00 0.00 4.17
447 476 5.633655 TTAGTACTCCTTTTGTCCCACAA 57.366 39.130 0.00 0.00 36.11 3.33
448 477 4.724279 AGTACTCCTTTTGTCCCACAAT 57.276 40.909 0.00 0.00 38.00 2.71
449 478 5.836024 AGTACTCCTTTTGTCCCACAATA 57.164 39.130 0.00 0.00 38.00 1.90
450 479 6.388619 AGTACTCCTTTTGTCCCACAATAT 57.611 37.500 0.00 0.00 38.00 1.28
451 480 7.504926 AGTACTCCTTTTGTCCCACAATATA 57.495 36.000 0.00 0.00 38.00 0.86
452 481 7.924541 AGTACTCCTTTTGTCCCACAATATAA 58.075 34.615 0.00 0.00 38.00 0.98
453 482 8.047310 AGTACTCCTTTTGTCCCACAATATAAG 58.953 37.037 0.00 0.00 38.00 1.73
454 483 7.027874 ACTCCTTTTGTCCCACAATATAAGA 57.972 36.000 2.29 0.00 38.00 2.10
455 484 6.884836 ACTCCTTTTGTCCCACAATATAAGAC 59.115 38.462 2.29 0.00 38.00 3.01
456 485 5.878116 TCCTTTTGTCCCACAATATAAGACG 59.122 40.000 2.29 0.00 38.00 4.18
457 486 5.646360 CCTTTTGTCCCACAATATAAGACGT 59.354 40.000 0.00 0.00 38.00 4.34
458 487 6.150474 CCTTTTGTCCCACAATATAAGACGTT 59.850 38.462 0.00 0.00 38.00 3.99
459 488 7.308951 CCTTTTGTCCCACAATATAAGACGTTT 60.309 37.037 0.00 0.00 38.00 3.60
460 489 7.513371 TTTGTCCCACAATATAAGACGTTTT 57.487 32.000 0.00 0.00 38.00 2.43
461 490 7.513371 TTGTCCCACAATATAAGACGTTTTT 57.487 32.000 0.00 0.00 32.34 1.94
462 491 6.904498 TGTCCCACAATATAAGACGTTTTTG 58.096 36.000 0.00 0.00 0.00 2.44
463 492 5.798434 GTCCCACAATATAAGACGTTTTTGC 59.202 40.000 0.00 0.00 0.00 3.68
464 493 5.473846 TCCCACAATATAAGACGTTTTTGCA 59.526 36.000 0.00 0.00 0.00 4.08
465 494 6.016192 TCCCACAATATAAGACGTTTTTGCAA 60.016 34.615 0.00 0.00 0.00 4.08
466 495 6.307800 CCCACAATATAAGACGTTTTTGCAAG 59.692 38.462 0.00 0.00 0.00 4.01
467 496 6.183359 CCACAATATAAGACGTTTTTGCAAGC 60.183 38.462 0.00 0.00 0.00 4.01
468 497 6.582295 CACAATATAAGACGTTTTTGCAAGCT 59.418 34.615 0.00 0.00 0.00 3.74
469 498 7.748683 CACAATATAAGACGTTTTTGCAAGCTA 59.251 33.333 0.00 0.00 0.00 3.32
470 499 8.293867 ACAATATAAGACGTTTTTGCAAGCTAA 58.706 29.630 0.00 0.00 0.00 3.09
471 500 8.575454 CAATATAAGACGTTTTTGCAAGCTAAC 58.425 33.333 0.00 5.28 0.00 2.34
472 501 4.364415 AAGACGTTTTTGCAAGCTAACA 57.636 36.364 16.37 0.00 0.00 2.41
473 502 4.568152 AGACGTTTTTGCAAGCTAACAT 57.432 36.364 16.37 5.95 0.00 2.71
474 503 5.682943 AGACGTTTTTGCAAGCTAACATA 57.317 34.783 16.37 0.00 0.00 2.29
475 504 5.689819 AGACGTTTTTGCAAGCTAACATAG 58.310 37.500 16.37 7.17 0.00 2.23
493 522 9.722056 CTAACATAGCTTGGAAAAACATGATAC 57.278 33.333 0.00 0.00 0.00 2.24
494 523 7.701539 ACATAGCTTGGAAAAACATGATACA 57.298 32.000 0.00 0.00 0.00 2.29
495 524 8.297470 ACATAGCTTGGAAAAACATGATACAT 57.703 30.769 0.00 0.00 0.00 2.29
496 525 8.752187 ACATAGCTTGGAAAAACATGATACATT 58.248 29.630 0.00 0.00 0.00 2.71
500 529 8.199449 AGCTTGGAAAAACATGATACATTATGG 58.801 33.333 0.00 0.00 0.00 2.74
501 530 7.439056 GCTTGGAAAAACATGATACATTATGGG 59.561 37.037 0.00 0.00 0.00 4.00
502 531 8.601047 TTGGAAAAACATGATACATTATGGGA 57.399 30.769 0.00 0.00 0.00 4.37
503 532 8.006298 TGGAAAAACATGATACATTATGGGAC 57.994 34.615 0.00 0.00 0.00 4.46
504 533 7.138736 GGAAAAACATGATACATTATGGGACG 58.861 38.462 0.00 0.00 0.00 4.79
505 534 6.633500 AAAACATGATACATTATGGGACGG 57.367 37.500 0.00 0.00 0.00 4.79
506 535 5.560722 AACATGATACATTATGGGACGGA 57.439 39.130 0.00 0.00 0.00 4.69
507 536 5.152623 ACATGATACATTATGGGACGGAG 57.847 43.478 0.00 0.00 0.00 4.63
508 537 4.020218 ACATGATACATTATGGGACGGAGG 60.020 45.833 0.00 0.00 0.00 4.30
509 538 2.903784 TGATACATTATGGGACGGAGGG 59.096 50.000 0.00 0.00 0.00 4.30
527 556 5.104652 CGGAGGGAGTAGAAGGGAAAAATTA 60.105 44.000 0.00 0.00 0.00 1.40
530 559 6.188407 AGGGAGTAGAAGGGAAAAATTAAGC 58.812 40.000 0.00 0.00 0.00 3.09
554 583 7.286316 AGCATGAAGGAGAACCATATTTTAAGG 59.714 37.037 0.00 0.00 38.94 2.69
555 584 7.470563 GCATGAAGGAGAACCATATTTTAAGGG 60.471 40.741 0.00 0.00 38.94 3.95
561 593 7.959152 AGGAGAACCATATTTTAAGGGGAAAAA 59.041 33.333 0.00 0.00 38.94 1.94
641 678 7.969690 TTTTATGGGATTGATACACATTGGT 57.030 32.000 0.00 0.00 33.27 3.67
702 2152 5.992829 TGCTTTTTGTACCAACGAATCTCTA 59.007 36.000 0.00 0.00 0.00 2.43
705 2155 7.416154 TTTTTGTACCAACGAATCTCTACTG 57.584 36.000 0.00 0.00 0.00 2.74
706 2156 5.717078 TTGTACCAACGAATCTCTACTGT 57.283 39.130 0.00 0.00 0.00 3.55
707 2157 5.055642 TGTACCAACGAATCTCTACTGTG 57.944 43.478 0.00 0.00 0.00 3.66
708 2158 4.521639 TGTACCAACGAATCTCTACTGTGT 59.478 41.667 0.00 0.00 0.00 3.72
709 2159 4.602340 ACCAACGAATCTCTACTGTGTT 57.398 40.909 0.00 0.00 0.00 3.32
710 2160 4.307432 ACCAACGAATCTCTACTGTGTTG 58.693 43.478 0.00 0.00 36.04 3.33
711 2161 4.038763 ACCAACGAATCTCTACTGTGTTGA 59.961 41.667 3.94 0.00 37.90 3.18
712 2162 4.623167 CCAACGAATCTCTACTGTGTTGAG 59.377 45.833 3.94 3.46 37.90 3.02
713 2163 5.461526 CAACGAATCTCTACTGTGTTGAGA 58.538 41.667 12.50 12.50 45.03 3.27
757 2236 7.294245 AGAAATTCATCAATAGGATCCAGAGGA 59.706 37.037 15.82 10.30 32.57 3.71
785 2269 7.664318 TCCAGGTTTTTAACTGAAGAATCCTAC 59.336 37.037 0.00 0.00 36.86 3.18
788 2272 9.642343 AGGTTTTTAACTGAAGAATCCTACTTT 57.358 29.630 0.00 0.00 0.00 2.66
808 2292 6.360618 ACTTTTGGACTGAGAAACTGAAGAT 58.639 36.000 0.00 0.00 0.00 2.40
811 2295 4.635223 TGGACTGAGAAACTGAAGATGTG 58.365 43.478 0.00 0.00 0.00 3.21
826 2310 6.645700 GAAGATGTGCTACTTCTTCTTCAG 57.354 41.667 22.88 0.00 46.90 3.02
840 2327 4.567558 TCTTCTTCAGTTAAAAACGACGCA 59.432 37.500 0.00 0.00 36.23 5.24
862 2349 3.078837 TCCGGAATTAAAACAGCTGGAC 58.921 45.455 19.93 0.00 0.00 4.02
942 2429 0.459585 GCGACAGCTGGTAATCCGAA 60.460 55.000 19.93 0.00 41.01 4.30
1018 2507 1.660167 CAGCTCCAATTCGATCTGCA 58.340 50.000 0.00 0.00 0.00 4.41
1019 2508 2.219458 CAGCTCCAATTCGATCTGCAT 58.781 47.619 0.00 0.00 0.00 3.96
1056 2551 1.399744 CCAGACCTAGGCACGCCATA 61.400 60.000 9.30 0.00 38.92 2.74
1739 3249 0.390472 GCCCGTGAAGAAGGTCTCTG 60.390 60.000 0.00 0.00 33.37 3.35
1752 3262 1.906824 TCTCTGGTCCCGTCGCTTT 60.907 57.895 0.00 0.00 0.00 3.51
1892 3402 1.134551 GCAAGGTTCCCAAGCAAAACA 60.135 47.619 0.00 0.00 0.00 2.83
1911 3421 0.527565 AAATCGCCATTGCCTGTCAC 59.472 50.000 0.00 0.00 0.00 3.67
1997 3511 8.475331 TTGCTAGTCTTTTATCTTCCTAAACG 57.525 34.615 0.00 0.00 0.00 3.60
2063 3577 6.716628 TCTGCACTTAATCACCAAGATTTCTT 59.283 34.615 0.00 0.00 44.48 2.52
2079 3593 7.830099 AGATTTCTTGTGTTCTTTGAATCCT 57.170 32.000 0.00 0.00 0.00 3.24
2305 3826 1.478137 GGCACGAGACATAGCGTAAG 58.522 55.000 0.00 0.00 38.92 2.34
2327 3848 2.368980 GCACTAGCCGCGAAATAAAG 57.631 50.000 8.23 0.00 33.58 1.85
2426 4147 1.032657 TGCCTAGCGTCTGGAGTCTC 61.033 60.000 0.00 0.00 0.00 3.36
2435 4156 1.892474 GTCTGGAGTCTCTGCTGACTT 59.108 52.381 16.22 0.00 46.11 3.01
2445 4166 6.529220 AGTCTCTGCTGACTTTCTTGTAAAT 58.471 36.000 2.59 0.00 44.01 1.40
2494 9317 2.673043 GCATTGGCATCTTGGTGAGTTG 60.673 50.000 0.00 0.00 40.72 3.16
2542 9365 3.804036 TGGTTAGTGAACTCTTGTGTGG 58.196 45.455 0.00 0.00 35.74 4.17
2691 9632 2.995939 TGAGCAGAGCATTTGAGTAACG 59.004 45.455 0.00 0.00 0.00 3.18
3115 10708 1.135721 GGGCATTGCTTGGAATCACTC 59.864 52.381 8.82 0.00 0.00 3.51
3141 10734 9.946165 CGATCTAATTTGTTACTTTTAATCCCC 57.054 33.333 0.00 0.00 0.00 4.81
3143 10736 8.283699 TCTAATTTGTTACTTTTAATCCCCCG 57.716 34.615 0.00 0.00 0.00 5.73
3194 10950 2.224079 GCGACAACATGCTCAGAAGAAA 59.776 45.455 0.00 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 4.129380 GACACCATTGCATGTATAGAGCA 58.871 43.478 0.00 0.00 36.32 4.26
33 34 4.024556 GTGACACCATTGCATGTATAGAGC 60.025 45.833 0.00 0.00 0.00 4.09
40 43 2.516906 TGATGTGACACCATTGCATGT 58.483 42.857 2.45 0.00 0.00 3.21
50 53 4.548494 TGCATGTTTTGATGATGTGACAC 58.452 39.130 0.00 0.00 0.00 3.67
53 56 5.394224 ACATGCATGTTTTGATGATGTGA 57.606 34.783 26.61 0.00 37.90 3.58
84 87 8.677300 GGATGAACTCTATTGCAGAAAATAACA 58.323 33.333 0.00 0.00 31.12 2.41
98 101 8.641498 AACAAAACATGAAGGATGAACTCTAT 57.359 30.769 0.00 0.00 35.80 1.98
115 118 6.506500 AATGTTGGCATTTCAAACAAAACA 57.493 29.167 0.00 0.00 42.19 2.83
335 364 5.866633 CGGAATAAGATACAGGCTTCAGATC 59.133 44.000 0.00 0.00 0.00 2.75
358 387 1.807142 GGGAAGCCAAAGAGAAGTTCG 59.193 52.381 0.00 0.00 0.00 3.95
368 397 2.286935 AGGAGGATAGGGAAGCCAAA 57.713 50.000 0.00 0.00 0.00 3.28
434 463 6.737254 ACGTCTTATATTGTGGGACAAAAG 57.263 37.500 0.00 0.00 39.85 2.27
435 464 7.513371 AAACGTCTTATATTGTGGGACAAAA 57.487 32.000 0.00 0.00 44.16 2.44
436 465 7.513371 AAAACGTCTTATATTGTGGGACAAA 57.487 32.000 0.00 0.00 44.16 2.83
437 466 7.364200 CAAAAACGTCTTATATTGTGGGACAA 58.636 34.615 0.00 0.00 44.16 3.18
438 467 6.568844 GCAAAAACGTCTTATATTGTGGGACA 60.569 38.462 0.00 0.00 0.00 4.02
439 468 5.798434 GCAAAAACGTCTTATATTGTGGGAC 59.202 40.000 0.00 0.00 0.00 4.46
440 469 5.473846 TGCAAAAACGTCTTATATTGTGGGA 59.526 36.000 0.00 0.00 0.00 4.37
441 470 5.704888 TGCAAAAACGTCTTATATTGTGGG 58.295 37.500 0.00 0.00 0.00 4.61
442 471 6.183359 GCTTGCAAAAACGTCTTATATTGTGG 60.183 38.462 0.00 0.00 0.00 4.17
443 472 6.582295 AGCTTGCAAAAACGTCTTATATTGTG 59.418 34.615 0.00 0.00 0.00 3.33
444 473 6.677913 AGCTTGCAAAAACGTCTTATATTGT 58.322 32.000 0.00 0.00 0.00 2.71
445 474 8.575454 GTTAGCTTGCAAAAACGTCTTATATTG 58.425 33.333 0.00 0.00 0.00 1.90
446 475 8.293867 TGTTAGCTTGCAAAAACGTCTTATATT 58.706 29.630 0.00 0.00 0.00 1.28
447 476 7.812648 TGTTAGCTTGCAAAAACGTCTTATAT 58.187 30.769 0.00 0.00 0.00 0.86
448 477 7.192148 TGTTAGCTTGCAAAAACGTCTTATA 57.808 32.000 0.00 0.00 0.00 0.98
449 478 6.067263 TGTTAGCTTGCAAAAACGTCTTAT 57.933 33.333 0.00 0.00 0.00 1.73
450 479 5.487153 TGTTAGCTTGCAAAAACGTCTTA 57.513 34.783 0.00 0.00 0.00 2.10
451 480 4.364415 TGTTAGCTTGCAAAAACGTCTT 57.636 36.364 0.00 0.00 0.00 3.01
452 481 4.568152 ATGTTAGCTTGCAAAAACGTCT 57.432 36.364 0.00 0.00 0.00 4.18
453 482 5.975138 CTATGTTAGCTTGCAAAAACGTC 57.025 39.130 13.85 0.43 0.00 4.34
467 496 9.722056 GTATCATGTTTTTCCAAGCTATGTTAG 57.278 33.333 0.00 0.00 0.00 2.34
468 497 9.237187 TGTATCATGTTTTTCCAAGCTATGTTA 57.763 29.630 0.00 0.00 0.00 2.41
469 498 8.121305 TGTATCATGTTTTTCCAAGCTATGTT 57.879 30.769 0.00 0.00 0.00 2.71
470 499 7.701539 TGTATCATGTTTTTCCAAGCTATGT 57.298 32.000 0.00 0.00 0.00 2.29
474 503 8.199449 CCATAATGTATCATGTTTTTCCAAGCT 58.801 33.333 0.00 0.00 0.00 3.74
475 504 7.439056 CCCATAATGTATCATGTTTTTCCAAGC 59.561 37.037 0.00 0.00 0.00 4.01
476 505 8.694540 TCCCATAATGTATCATGTTTTTCCAAG 58.305 33.333 0.00 0.00 0.00 3.61
477 506 8.474025 GTCCCATAATGTATCATGTTTTTCCAA 58.526 33.333 0.00 0.00 0.00 3.53
478 507 7.201776 CGTCCCATAATGTATCATGTTTTTCCA 60.202 37.037 0.00 0.00 0.00 3.53
479 508 7.138736 CGTCCCATAATGTATCATGTTTTTCC 58.861 38.462 0.00 0.00 0.00 3.13
480 509 7.012894 TCCGTCCCATAATGTATCATGTTTTTC 59.987 37.037 0.00 0.00 0.00 2.29
481 510 6.831353 TCCGTCCCATAATGTATCATGTTTTT 59.169 34.615 0.00 0.00 0.00 1.94
482 511 6.361433 TCCGTCCCATAATGTATCATGTTTT 58.639 36.000 0.00 0.00 0.00 2.43
483 512 5.935945 TCCGTCCCATAATGTATCATGTTT 58.064 37.500 0.00 0.00 0.00 2.83
484 513 5.513094 CCTCCGTCCCATAATGTATCATGTT 60.513 44.000 0.00 0.00 0.00 2.71
485 514 4.020218 CCTCCGTCCCATAATGTATCATGT 60.020 45.833 0.00 0.00 0.00 3.21
486 515 4.507710 CCTCCGTCCCATAATGTATCATG 58.492 47.826 0.00 0.00 0.00 3.07
487 516 3.519510 CCCTCCGTCCCATAATGTATCAT 59.480 47.826 0.00 0.00 0.00 2.45
488 517 2.903784 CCCTCCGTCCCATAATGTATCA 59.096 50.000 0.00 0.00 0.00 2.15
489 518 3.170717 TCCCTCCGTCCCATAATGTATC 58.829 50.000 0.00 0.00 0.00 2.24
490 519 3.173965 CTCCCTCCGTCCCATAATGTAT 58.826 50.000 0.00 0.00 0.00 2.29
491 520 2.090943 ACTCCCTCCGTCCCATAATGTA 60.091 50.000 0.00 0.00 0.00 2.29
492 521 1.344087 ACTCCCTCCGTCCCATAATGT 60.344 52.381 0.00 0.00 0.00 2.71
493 522 1.424638 ACTCCCTCCGTCCCATAATG 58.575 55.000 0.00 0.00 0.00 1.90
494 523 2.449730 TCTACTCCCTCCGTCCCATAAT 59.550 50.000 0.00 0.00 0.00 1.28
495 524 1.854939 TCTACTCCCTCCGTCCCATAA 59.145 52.381 0.00 0.00 0.00 1.90
496 525 1.526315 TCTACTCCCTCCGTCCCATA 58.474 55.000 0.00 0.00 0.00 2.74
497 526 0.635009 TTCTACTCCCTCCGTCCCAT 59.365 55.000 0.00 0.00 0.00 4.00
498 527 0.033405 CTTCTACTCCCTCCGTCCCA 60.033 60.000 0.00 0.00 0.00 4.37
499 528 0.756070 CCTTCTACTCCCTCCGTCCC 60.756 65.000 0.00 0.00 0.00 4.46
500 529 0.756070 CCCTTCTACTCCCTCCGTCC 60.756 65.000 0.00 0.00 0.00 4.79
501 530 0.258194 TCCCTTCTACTCCCTCCGTC 59.742 60.000 0.00 0.00 0.00 4.79
502 531 0.708802 TTCCCTTCTACTCCCTCCGT 59.291 55.000 0.00 0.00 0.00 4.69
503 532 1.861982 TTTCCCTTCTACTCCCTCCG 58.138 55.000 0.00 0.00 0.00 4.63
504 533 4.864483 ATTTTTCCCTTCTACTCCCTCC 57.136 45.455 0.00 0.00 0.00 4.30
505 534 6.319152 GCTTAATTTTTCCCTTCTACTCCCTC 59.681 42.308 0.00 0.00 0.00 4.30
506 535 6.188407 GCTTAATTTTTCCCTTCTACTCCCT 58.812 40.000 0.00 0.00 0.00 4.20
507 536 5.949952 TGCTTAATTTTTCCCTTCTACTCCC 59.050 40.000 0.00 0.00 0.00 4.30
508 537 7.339466 TCATGCTTAATTTTTCCCTTCTACTCC 59.661 37.037 0.00 0.00 0.00 3.85
509 538 8.281212 TCATGCTTAATTTTTCCCTTCTACTC 57.719 34.615 0.00 0.00 0.00 2.59
527 556 8.593945 TTAAAATATGGTTCTCCTTCATGCTT 57.406 30.769 0.00 0.00 34.23 3.91
530 559 7.014615 CCCCTTAAAATATGGTTCTCCTTCATG 59.985 40.741 0.00 0.00 34.23 3.07
757 2236 6.490381 GGATTCTTCAGTTAAAAACCTGGACT 59.510 38.462 0.00 0.00 0.00 3.85
785 2269 6.261826 ACATCTTCAGTTTCTCAGTCCAAAAG 59.738 38.462 0.00 0.00 0.00 2.27
788 2272 5.059161 CACATCTTCAGTTTCTCAGTCCAA 58.941 41.667 0.00 0.00 0.00 3.53
808 2292 8.395633 GTTTTTAACTGAAGAAGAAGTAGCACA 58.604 33.333 0.00 0.00 0.00 4.57
811 2295 7.792967 GTCGTTTTTAACTGAAGAAGAAGTAGC 59.207 37.037 0.00 0.00 0.00 3.58
824 2308 2.492001 CGGATGCGTCGTTTTTAACTG 58.508 47.619 0.00 0.00 0.00 3.16
825 2309 1.461897 CCGGATGCGTCGTTTTTAACT 59.538 47.619 5.72 0.00 0.00 2.24
826 2310 1.460359 TCCGGATGCGTCGTTTTTAAC 59.540 47.619 0.00 0.00 0.00 2.01
840 2327 3.694566 GTCCAGCTGTTTTAATTCCGGAT 59.305 43.478 13.81 0.00 0.00 4.18
862 2349 0.025513 GCAATCTCACGCGCTGTTAG 59.974 55.000 5.73 6.54 0.00 2.34
942 2429 1.211457 AGCTCCTGATTCTTGCCGAAT 59.789 47.619 0.00 0.00 44.87 3.34
1018 2507 0.764752 GAGATCGGGAAGGTGGGGAT 60.765 60.000 0.00 0.00 0.00 3.85
1019 2508 1.382695 GAGATCGGGAAGGTGGGGA 60.383 63.158 0.00 0.00 0.00 4.81
1703 3213 2.956194 CGCAACAGCATTGGCAGA 59.044 55.556 3.24 0.00 44.61 4.26
1739 3249 2.033194 CCTTGAAAGCGACGGGACC 61.033 63.158 0.00 0.00 0.00 4.46
1752 3262 1.512926 GACGAAAGAGCAAGCCTTGA 58.487 50.000 9.04 0.00 0.00 3.02
1804 3314 1.002087 GTCATCTTCTTCACACCGGGT 59.998 52.381 6.32 0.00 0.00 5.28
1892 3402 0.527565 GTGACAGGCAATGGCGATTT 59.472 50.000 0.00 0.00 41.39 2.17
2063 3577 5.192927 ACTGAACAGGATTCAAAGAACACA 58.807 37.500 6.76 0.00 0.00 3.72
2313 3834 0.096454 GCGTTCTTTATTTCGCGGCT 59.904 50.000 6.13 0.00 39.35 5.52
2319 3840 2.659757 GCAAACGGGCGTTCTTTATTTC 59.340 45.455 0.00 0.00 37.35 2.17
2327 3848 2.683859 GGGTAGCAAACGGGCGTTC 61.684 63.158 0.00 0.00 37.35 3.95
2494 9317 1.192534 CTCGTCGGAAACTGCAACTTC 59.807 52.381 0.00 0.00 0.00 3.01
2542 9365 2.227388 CTCAAAGCTTCACCCACACATC 59.773 50.000 0.00 0.00 0.00 3.06
3115 10708 9.946165 GGGGATTAAAAGTAACAAATTAGATCG 57.054 33.333 0.00 0.00 0.00 3.69
3155 10911 6.680874 TGTCGCTCCTTTAAAAGTAACAAA 57.319 33.333 0.00 0.00 0.00 2.83
3157 10913 5.585445 TGTTGTCGCTCCTTTAAAAGTAACA 59.415 36.000 0.00 0.00 0.00 2.41
3158 10914 6.051646 TGTTGTCGCTCCTTTAAAAGTAAC 57.948 37.500 0.00 0.00 0.00 2.50
3159 10915 6.664515 CATGTTGTCGCTCCTTTAAAAGTAA 58.335 36.000 0.00 0.00 0.00 2.24
3163 10919 3.568007 AGCATGTTGTCGCTCCTTTAAAA 59.432 39.130 0.00 0.00 31.16 1.52
3167 10923 3.329300 AGCATGTTGTCGCTCCTTT 57.671 47.368 0.00 0.00 31.16 3.11



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

AutoCloner maintained by Alex Coulton.