Multiple sequence alignment - TraesCS2B01G429500

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 TraesCS2B01G429500 chr2B 100.000 2663 0 0 1 2663 616933463 616936125 0.000000e+00 4918.0
1 TraesCS2B01G429500 chr2B 75.180 278 63 6 1133 1407 290519726 290520000 2.780000e-25 126.0
2 TraesCS2B01G429500 chr2B 90.625 64 6 0 426 489 612461640 612461577 4.720000e-13 86.1
3 TraesCS2B01G429500 chr2A 90.528 2006 120 30 699 2663 668242307 668244283 0.000000e+00 2588.0
4 TraesCS2B01G429500 chr2A 89.498 438 30 10 1 427 668241625 668242057 8.390000e-150 540.0
5 TraesCS2B01G429500 chr2A 81.459 329 55 6 2319 2642 470243133 470243460 5.650000e-67 265.0
6 TraesCS2B01G429500 chr2D 89.115 1718 97 37 507 2166 523027836 523029521 0.000000e+00 2054.0
7 TraesCS2B01G429500 chr2D 90.058 513 48 3 2149 2660 523123739 523124249 0.000000e+00 662.0
8 TraesCS2B01G429500 chr2D 90.433 439 25 11 1 427 523027404 523027837 1.790000e-156 562.0
9 TraesCS2B01G429500 chr2D 82.081 346 56 6 2319 2659 352209120 352209464 9.330000e-75 291.0
10 TraesCS2B01G429500 chr6B 83.273 275 46 0 1129 1403 502484423 502484149 1.220000e-63 254.0
11 TraesCS2B01G429500 chr6B 78.767 292 55 7 2374 2659 468253856 468253566 3.500000e-44 189.0
12 TraesCS2B01G429500 chr6B 86.875 160 19 2 1509 1667 502483350 502483192 7.580000e-41 178.0
13 TraesCS2B01G429500 chr6D 82.909 275 47 0 1129 1403 320228156 320228430 5.690000e-62 248.0
14 TraesCS2B01G429500 chr6D 85.897 156 20 2 1510 1664 320229175 320229329 5.900000e-37 165.0
15 TraesCS2B01G429500 chr6A 82.182 275 49 0 1129 1403 457685918 457686192 1.230000e-58 237.0
16 TraesCS2B01G429500 chr6A 87.179 156 18 2 1510 1664 457686958 457687112 2.720000e-40 176.0
17 TraesCS2B01G429500 chr6A 77.211 294 56 11 2374 2659 413108631 413108921 7.630000e-36 161.0
18 TraesCS2B01G429500 chr6A 94.643 56 2 1 418 472 558454904 558454849 4.720000e-13 86.1
19 TraesCS2B01G429500 chr6A 94.643 56 2 1 418 472 558458989 558458934 4.720000e-13 86.1
20 TraesCS2B01G429500 chr7A 76.338 355 71 12 2318 2663 620536101 620536451 7.580000e-41 178.0
21 TraesCS2B01G429500 chr7B 77.627 295 56 10 2369 2659 418733210 418732922 1.270000e-38 171.0
22 TraesCS2B01G429500 chr5B 76.061 330 72 7 2318 2643 523182828 523183154 5.900000e-37 165.0
23 TraesCS2B01G429500 chr5B 98.039 51 1 0 419 469 142712563 142712513 3.650000e-14 89.8
24 TraesCS2B01G429500 chr5B 97.561 41 1 0 467 507 71906625 71906665 1.320000e-08 71.3
25 TraesCS2B01G429500 chr4B 80.556 180 29 5 1227 1403 475811240 475811416 1.660000e-27 134.0
26 TraesCS2B01G429500 chr4A 80.328 183 30 5 1224 1403 68689364 68689543 1.660000e-27 134.0
27 TraesCS2B01G429500 chr4D 80.000 180 30 5 1227 1403 387441775 387441951 7.740000e-26 128.0
28 TraesCS2B01G429500 chr3B 92.308 91 5 2 426 516 321594223 321594135 7.740000e-26 128.0
29 TraesCS2B01G429500 chr3B 97.561 41 1 0 467 507 86950650 86950690 1.320000e-08 71.3
30 TraesCS2B01G429500 chrUn 96.226 53 1 1 418 469 138274127 138274179 4.720000e-13 86.1
31 TraesCS2B01G429500 chrUn 96.226 53 1 1 418 469 138486767 138486819 4.720000e-13 86.1
32 TraesCS2B01G429500 chrUn 94.643 56 2 1 418 472 171110563 171110508 4.720000e-13 86.1
33 TraesCS2B01G429500 chrUn 94.643 56 2 1 418 472 172121628 172121573 4.720000e-13 86.1


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 TraesCS2B01G429500 chr2B 616933463 616936125 2662 False 4918.0 4918 100.0000 1 2663 1 chr2B.!!$F2 2662
1 TraesCS2B01G429500 chr2A 668241625 668244283 2658 False 1564.0 2588 90.0130 1 2663 2 chr2A.!!$F2 2662
2 TraesCS2B01G429500 chr2D 523027404 523029521 2117 False 1308.0 2054 89.7740 1 2166 2 chr2D.!!$F3 2165
3 TraesCS2B01G429500 chr2D 523123739 523124249 510 False 662.0 662 90.0580 2149 2660 1 chr2D.!!$F2 511
4 TraesCS2B01G429500 chr6B 502483192 502484423 1231 True 216.0 254 85.0740 1129 1667 2 chr6B.!!$R2 538
5 TraesCS2B01G429500 chr6D 320228156 320229329 1173 False 206.5 248 84.4030 1129 1664 2 chr6D.!!$F1 535
6 TraesCS2B01G429500 chr6A 457685918 457687112 1194 False 206.5 237 84.6805 1129 1664 2 chr6A.!!$F2 535

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
715 750 0.107643 GTAGCCAGGGATGGAGCTTC 59.892 60.0 0.00 0.0 36.79 3.86 F
1452 2326 0.036577 TCTCTTTCTGCAGCCTGCTC 60.037 55.0 18.96 0.0 45.31 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1617 2494 0.178767 CCAATGTCATCTCGCTGGGA 59.821 55.0 0.0 0.0 0.0 4.37 R
2586 3490 0.179129 CGGGCATTTCACCAAGCATC 60.179 55.0 0.0 0.0 0.0 3.91 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
31 32 2.694628 TGGTGCAACTGAATTTCTGCTT 59.305 40.909 2.04 0.26 36.74 3.91
32 33 3.888323 TGGTGCAACTGAATTTCTGCTTA 59.112 39.130 2.04 0.00 36.74 3.09
33 34 4.022935 TGGTGCAACTGAATTTCTGCTTAG 60.023 41.667 2.04 0.00 36.74 2.18
34 35 4.022849 GGTGCAACTGAATTTCTGCTTAGT 60.023 41.667 0.00 0.00 36.74 2.24
35 36 5.181245 GGTGCAACTGAATTTCTGCTTAGTA 59.819 40.000 0.00 0.00 36.74 1.82
36 37 6.310197 GTGCAACTGAATTTCTGCTTAGTAG 58.690 40.000 9.63 0.00 35.78 2.57
37 38 9.884653 GGTGCAACTGAATTTCTGCTTAGTAGC 62.885 44.444 0.00 0.00 42.17 3.58
52 55 2.259618 AGTAGCGTGCAGTTCATTACG 58.740 47.619 0.00 0.00 39.37 3.18
56 59 0.999406 CGTGCAGTTCATTACGGGAG 59.001 55.000 0.00 0.00 33.27 4.30
276 282 6.538945 AAGGAAAACAAGCTCCAAAAGTTA 57.461 33.333 0.00 0.00 33.83 2.24
328 334 5.871531 TTTTTGTAGTGTACGTCGAGAAC 57.128 39.130 0.00 0.00 0.00 3.01
349 355 4.848357 ACGATCATCTTCCTGGACAATTT 58.152 39.130 0.00 0.00 0.00 1.82
351 357 5.124457 ACGATCATCTTCCTGGACAATTTTG 59.876 40.000 0.00 0.00 0.00 2.44
352 358 4.789012 TCATCTTCCTGGACAATTTTGC 57.211 40.909 0.00 0.00 0.00 3.68
353 359 4.151121 TCATCTTCCTGGACAATTTTGCA 58.849 39.130 0.00 0.00 0.00 4.08
361 370 3.911868 TGGACAATTTTGCAAGGAATCG 58.088 40.909 0.00 0.00 0.00 3.34
377 386 3.871594 GGAATCGCAGCTGTGTAACTTAT 59.128 43.478 25.68 8.98 38.04 1.73
378 387 4.332819 GGAATCGCAGCTGTGTAACTTATT 59.667 41.667 25.68 16.63 38.04 1.40
380 389 6.036735 GGAATCGCAGCTGTGTAACTTATTAA 59.963 38.462 25.68 3.83 38.04 1.40
382 391 5.716094 TCGCAGCTGTGTAACTTATTAAGA 58.284 37.500 25.68 0.00 38.04 2.10
383 392 5.805486 TCGCAGCTGTGTAACTTATTAAGAG 59.195 40.000 25.68 0.00 38.04 2.85
386 399 7.010552 CGCAGCTGTGTAACTTATTAAGAGAAT 59.989 37.037 19.30 0.00 38.04 2.40
413 426 3.055167 TCTGTCTACCATGTGATGTTGGG 60.055 47.826 0.00 0.00 37.32 4.12
425 438 6.005066 TGTGATGTTGGGAAGATGTCATAT 57.995 37.500 0.00 0.00 0.00 1.78
426 439 7.135591 TGTGATGTTGGGAAGATGTCATATA 57.864 36.000 0.00 0.00 0.00 0.86
427 440 6.992123 TGTGATGTTGGGAAGATGTCATATAC 59.008 38.462 0.00 0.00 0.00 1.47
428 441 7.147497 TGTGATGTTGGGAAGATGTCATATACT 60.147 37.037 0.00 0.00 0.00 2.12
429 442 7.386299 GTGATGTTGGGAAGATGTCATATACTC 59.614 40.741 0.00 0.00 0.00 2.59
430 443 6.174720 TGTTGGGAAGATGTCATATACTCC 57.825 41.667 0.00 0.00 0.00 3.85
431 444 5.071788 TGTTGGGAAGATGTCATATACTCCC 59.928 44.000 9.48 9.48 35.56 4.30
432 445 5.093236 TGGGAAGATGTCATATACTCCCT 57.907 43.478 15.29 0.00 35.98 4.20
433 446 5.476983 TGGGAAGATGTCATATACTCCCTT 58.523 41.667 15.29 0.77 35.98 3.95
434 447 5.544176 TGGGAAGATGTCATATACTCCCTTC 59.456 44.000 15.29 8.50 35.98 3.46
435 448 5.336849 GGGAAGATGTCATATACTCCCTTCG 60.337 48.000 9.22 0.00 33.40 3.79
436 449 5.244178 GGAAGATGTCATATACTCCCTTCGT 59.756 44.000 0.00 0.00 33.40 3.85
437 450 5.968528 AGATGTCATATACTCCCTTCGTC 57.031 43.478 0.00 0.00 0.00 4.20
438 451 4.767928 AGATGTCATATACTCCCTTCGTCC 59.232 45.833 0.00 0.00 0.00 4.79
439 452 2.882761 TGTCATATACTCCCTTCGTCCG 59.117 50.000 0.00 0.00 0.00 4.79
440 453 2.228343 GTCATATACTCCCTTCGTCCGG 59.772 54.545 0.00 0.00 0.00 5.14
441 454 2.107031 TCATATACTCCCTTCGTCCGGA 59.893 50.000 0.00 0.00 0.00 5.14
442 455 2.734755 TATACTCCCTTCGTCCGGAA 57.265 50.000 5.23 0.00 0.00 4.30
443 456 1.856629 ATACTCCCTTCGTCCGGAAA 58.143 50.000 5.23 0.00 33.34 3.13
444 457 1.856629 TACTCCCTTCGTCCGGAAAT 58.143 50.000 5.23 0.00 33.34 2.17
445 458 1.856629 ACTCCCTTCGTCCGGAAATA 58.143 50.000 5.23 0.00 33.34 1.40
446 459 1.479730 ACTCCCTTCGTCCGGAAATAC 59.520 52.381 5.23 0.00 33.34 1.89
447 460 1.755380 CTCCCTTCGTCCGGAAATACT 59.245 52.381 5.23 0.00 33.34 2.12
448 461 2.167900 CTCCCTTCGTCCGGAAATACTT 59.832 50.000 5.23 0.00 33.34 2.24
449 462 2.093869 TCCCTTCGTCCGGAAATACTTG 60.094 50.000 5.23 0.00 33.34 3.16
450 463 2.354403 CCCTTCGTCCGGAAATACTTGT 60.354 50.000 5.23 0.00 33.34 3.16
451 464 2.928116 CCTTCGTCCGGAAATACTTGTC 59.072 50.000 5.23 0.00 33.34 3.18
452 465 3.581755 CTTCGTCCGGAAATACTTGTCA 58.418 45.455 5.23 0.00 33.34 3.58
453 466 3.880047 TCGTCCGGAAATACTTGTCAT 57.120 42.857 5.23 0.00 0.00 3.06
454 467 4.196626 TCGTCCGGAAATACTTGTCATT 57.803 40.909 5.23 0.00 0.00 2.57
455 468 3.930229 TCGTCCGGAAATACTTGTCATTG 59.070 43.478 5.23 0.00 0.00 2.82
456 469 3.930229 CGTCCGGAAATACTTGTCATTGA 59.070 43.478 5.23 0.00 0.00 2.57
457 470 4.390603 CGTCCGGAAATACTTGTCATTGAA 59.609 41.667 5.23 0.00 0.00 2.69
458 471 5.106869 CGTCCGGAAATACTTGTCATTGAAA 60.107 40.000 5.23 0.00 0.00 2.69
459 472 6.403200 CGTCCGGAAATACTTGTCATTGAAAT 60.403 38.462 5.23 0.00 0.00 2.17
460 473 6.747280 GTCCGGAAATACTTGTCATTGAAATG 59.253 38.462 5.23 0.00 37.75 2.32
461 474 6.035843 CCGGAAATACTTGTCATTGAAATGG 58.964 40.000 0.00 0.00 37.03 3.16
462 475 6.127758 CCGGAAATACTTGTCATTGAAATGGA 60.128 38.462 0.00 0.00 37.03 3.41
463 476 7.416664 CCGGAAATACTTGTCATTGAAATGGAT 60.417 37.037 0.00 0.00 37.03 3.41
464 477 7.433131 CGGAAATACTTGTCATTGAAATGGATG 59.567 37.037 3.31 0.00 37.03 3.51
465 478 8.253113 GGAAATACTTGTCATTGAAATGGATGT 58.747 33.333 3.31 2.77 37.03 3.06
484 497 7.338800 GGATGTATCCATTTTGATGACAACT 57.661 36.000 6.03 0.00 46.38 3.16
485 498 8.450578 GGATGTATCCATTTTGATGACAACTA 57.549 34.615 6.03 0.00 46.38 2.24
486 499 8.902806 GGATGTATCCATTTTGATGACAACTAA 58.097 33.333 6.03 0.00 46.38 2.24
490 503 9.736023 GTATCCATTTTGATGACAACTAATTCC 57.264 33.333 0.00 0.00 35.63 3.01
491 504 7.773489 TCCATTTTGATGACAACTAATTCCA 57.227 32.000 0.00 0.00 35.63 3.53
492 505 7.829725 TCCATTTTGATGACAACTAATTCCAG 58.170 34.615 0.00 0.00 35.63 3.86
493 506 7.669304 TCCATTTTGATGACAACTAATTCCAGA 59.331 33.333 0.00 0.00 35.63 3.86
494 507 8.472413 CCATTTTGATGACAACTAATTCCAGAT 58.528 33.333 0.00 0.00 35.63 2.90
495 508 9.297586 CATTTTGATGACAACTAATTCCAGATG 57.702 33.333 0.00 0.00 35.63 2.90
496 509 7.395190 TTTGATGACAACTAATTCCAGATGG 57.605 36.000 0.00 0.00 35.63 3.51
497 510 6.312141 TGATGACAACTAATTCCAGATGGA 57.688 37.500 0.00 0.00 43.73 3.41
498 511 6.351711 TGATGACAACTAATTCCAGATGGAG 58.648 40.000 1.13 0.00 46.36 3.86
499 512 5.102953 TGACAACTAATTCCAGATGGAGG 57.897 43.478 1.13 0.00 46.36 4.30
500 513 4.080356 TGACAACTAATTCCAGATGGAGGG 60.080 45.833 1.13 0.00 46.36 4.30
501 514 4.111577 ACAACTAATTCCAGATGGAGGGA 58.888 43.478 1.13 0.00 46.36 4.20
502 515 4.164988 ACAACTAATTCCAGATGGAGGGAG 59.835 45.833 1.13 3.54 46.36 4.30
503 516 4.014273 ACTAATTCCAGATGGAGGGAGT 57.986 45.455 1.13 4.12 46.36 3.85
504 517 5.157770 ACTAATTCCAGATGGAGGGAGTA 57.842 43.478 1.13 0.00 46.36 2.59
505 518 4.902448 ACTAATTCCAGATGGAGGGAGTAC 59.098 45.833 1.13 0.00 46.36 2.73
517 530 7.995488 AGATGGAGGGAGTACTAATTTGAAATG 59.005 37.037 0.00 0.00 0.00 2.32
518 531 5.885912 TGGAGGGAGTACTAATTTGAAATGC 59.114 40.000 0.00 0.00 0.00 3.56
533 546 2.715749 AATGCCTGATCGTCCATCAA 57.284 45.000 0.00 0.00 41.25 2.57
545 558 3.634910 TCGTCCATCAATCCTCATTACGA 59.365 43.478 0.00 0.00 34.80 3.43
548 561 5.573282 CGTCCATCAATCCTCATTACGATAC 59.427 44.000 0.00 0.00 0.00 2.24
553 566 5.286438 TCAATCCTCATTACGATACGGTTG 58.714 41.667 0.00 0.00 0.00 3.77
585 605 4.552166 GTGATCATAAATCACGGGGTTG 57.448 45.455 0.00 0.00 38.97 3.77
591 611 2.547299 AAATCACGGGGTTGTACGAA 57.453 45.000 0.00 0.00 0.00 3.85
616 636 0.250234 GATGTGCCTGTGTCTGGCTA 59.750 55.000 16.13 7.94 46.43 3.93
620 640 2.103094 TGTGCCTGTGTCTGGCTATATC 59.897 50.000 16.13 5.41 46.43 1.63
624 644 3.643763 CCTGTGTCTGGCTATATCGTTC 58.356 50.000 0.00 0.00 0.00 3.95
630 650 3.060473 GTCTGGCTATATCGTTCGTTTGC 60.060 47.826 0.00 0.00 0.00 3.68
632 652 1.191647 GGCTATATCGTTCGTTTGCCG 59.808 52.381 0.00 0.00 38.13 5.69
636 656 1.676438 TATCGTTCGTTTGCCGTCGC 61.676 55.000 0.00 0.00 37.94 5.19
655 676 1.148310 CTTCGTCCAAATCGCAGTGT 58.852 50.000 0.00 0.00 0.00 3.55
672 693 1.159713 TGTTGCAGCAAGTCACGAGG 61.160 55.000 8.49 0.00 0.00 4.63
673 694 1.597854 TTGCAGCAAGTCACGAGGG 60.598 57.895 2.83 0.00 0.00 4.30
698 733 1.877637 AATGTTGCTGTGCTGTCGTA 58.122 45.000 0.00 0.00 0.00 3.43
713 748 2.136878 CGTAGCCAGGGATGGAGCT 61.137 63.158 0.00 0.00 39.37 4.09
715 750 0.107643 GTAGCCAGGGATGGAGCTTC 59.892 60.000 0.00 0.00 36.79 3.86
716 751 1.402896 TAGCCAGGGATGGAGCTTCG 61.403 60.000 0.00 0.00 36.79 3.79
719 754 0.830648 CCAGGGATGGAGCTTCGTTA 59.169 55.000 0.00 0.00 0.00 3.18
720 755 1.473434 CCAGGGATGGAGCTTCGTTAC 60.473 57.143 0.00 0.00 0.00 2.50
721 756 1.207089 CAGGGATGGAGCTTCGTTACA 59.793 52.381 0.00 0.00 0.00 2.41
722 757 1.482593 AGGGATGGAGCTTCGTTACAG 59.517 52.381 0.00 0.00 0.00 2.74
723 758 1.473434 GGGATGGAGCTTCGTTACAGG 60.473 57.143 0.00 0.00 0.00 4.00
724 759 1.291132 GATGGAGCTTCGTTACAGGC 58.709 55.000 0.00 0.00 0.00 4.85
725 760 0.613260 ATGGAGCTTCGTTACAGGCA 59.387 50.000 0.00 0.00 0.00 4.75
730 765 3.426292 GGAGCTTCGTTACAGGCATTTTC 60.426 47.826 0.00 0.00 0.00 2.29
731 766 2.159627 AGCTTCGTTACAGGCATTTTCG 59.840 45.455 0.00 0.00 0.00 3.46
732 767 2.727916 GCTTCGTTACAGGCATTTTCGG 60.728 50.000 0.00 0.00 0.00 4.30
737 808 0.742990 TACAGGCATTTTCGGAGGCG 60.743 55.000 0.00 0.00 0.00 5.52
739 810 1.097547 CAGGCATTTTCGGAGGCGAT 61.098 55.000 0.00 0.00 0.00 4.58
772 847 4.767255 GTGTGGAGCGCCTCTGGG 62.767 72.222 8.34 0.00 34.31 4.45
991 1086 3.003378 CGTGGAAAGAAGAGAAAACCCAC 59.997 47.826 0.00 0.00 39.38 4.61
1080 1178 4.022416 CGATCCTTTTGGTTGGTTGATTGA 60.022 41.667 0.00 0.00 41.38 2.57
1093 1192 6.395426 TGGTTGATTGATTGATAATGAGGC 57.605 37.500 0.00 0.00 0.00 4.70
1099 1198 3.396560 TGATTGATAATGAGGCGCTCTG 58.603 45.455 7.64 0.00 0.00 3.35
1424 1929 1.524621 GACCCGTCCATCCATGCAG 60.525 63.158 0.00 0.00 0.00 4.41
1440 2314 1.339438 TGCAGGCATGGTCTCTCTTTC 60.339 52.381 0.00 0.00 0.00 2.62
1445 2319 2.008329 GCATGGTCTCTCTTTCTGCAG 58.992 52.381 7.63 7.63 0.00 4.41
1452 2326 0.036577 TCTCTTTCTGCAGCCTGCTC 60.037 55.000 18.96 0.00 45.31 4.26
1454 2328 0.321387 TCTTTCTGCAGCCTGCTCTG 60.321 55.000 18.96 8.30 45.31 3.35
1460 2334 3.420606 CAGCCTGCTCTGCACACG 61.421 66.667 0.00 0.00 33.79 4.49
1461 2335 3.933722 AGCCTGCTCTGCACACGT 61.934 61.111 0.00 0.00 33.79 4.49
1462 2336 3.720193 GCCTGCTCTGCACACGTG 61.720 66.667 15.48 15.48 33.79 4.49
1463 2337 3.046087 CCTGCTCTGCACACGTGG 61.046 66.667 21.57 10.05 33.79 4.94
1464 2338 3.720193 CTGCTCTGCACACGTGGC 61.720 66.667 21.57 19.77 33.79 5.01
1498 2375 3.190849 CGATCTGTGGTGGCTGCG 61.191 66.667 0.00 0.00 0.00 5.18
1617 2494 4.479993 GAGCTGCAGGCCACCGAT 62.480 66.667 17.12 0.00 43.05 4.18
1632 2509 1.735973 CGATCCCAGCGAGATGACA 59.264 57.895 0.00 0.00 0.00 3.58
1639 2516 0.926155 CAGCGAGATGACATTGGACG 59.074 55.000 0.00 0.00 0.00 4.79
1693 2576 2.739996 CGCTCCTTCCAGGCTCCAT 61.740 63.158 0.00 0.00 34.61 3.41
1778 2664 3.720193 CGTCGTCGGTGTCGGAGT 61.720 66.667 0.00 0.00 36.95 3.85
1978 2866 4.499040 CACGAAAAGACAAACATTGTGGTC 59.501 41.667 11.82 11.82 45.52 4.02
1992 2880 1.064758 TGTGGTCTGTTTTGCTCCTGT 60.065 47.619 0.00 0.00 0.00 4.00
2007 2895 3.620966 GCTCCTGTTCTCCTTATGTGCTT 60.621 47.826 0.00 0.00 0.00 3.91
2018 2906 5.136828 TCCTTATGTGCTTGTTCCAAAAGA 58.863 37.500 0.00 0.00 0.00 2.52
2031 2919 1.203994 CCAAAAGAAGCCCTCATGCTG 59.796 52.381 0.00 0.00 41.80 4.41
2077 2965 6.183360 CGCATTTGTCTTCTGCTAGTGATTTA 60.183 38.462 0.00 0.00 33.75 1.40
2114 3005 8.506437 CAAAGTTATGAATGCTAGAGTGAAACA 58.494 33.333 0.00 0.00 41.43 2.83
2224 3124 0.250124 TTTGTCATCCAACGCCGTCT 60.250 50.000 0.00 0.00 31.20 4.18
2231 3131 2.809174 CAACGCCGTCTGCATCGA 60.809 61.111 11.98 0.00 41.33 3.59
2288 3190 1.152830 GGAAGCAAACTGGGGGTGA 59.847 57.895 0.00 0.00 0.00 4.02
2314 3217 0.036105 GGGGTTTGTGGTAGTACGGG 60.036 60.000 0.00 0.00 0.00 5.28
2316 3219 1.015607 GGTTTGTGGTAGTACGGGCG 61.016 60.000 0.00 0.00 0.00 6.13
2342 3245 1.224039 CGTAGGACTCCGACTCCCT 59.776 63.158 6.75 0.00 0.00 4.20
2351 3254 3.636231 CGACTCCCTTGGCCCACA 61.636 66.667 0.00 0.00 0.00 4.17
2370 3273 1.293683 ACAAAACCCCACCAGGACCT 61.294 55.000 0.00 0.00 38.24 3.85
2414 3317 0.628668 ATGCATCCCCTTCCCTCCTT 60.629 55.000 0.00 0.00 0.00 3.36
2418 3321 2.805827 ATCCCCTTCCCTCCTTGCCA 62.806 60.000 0.00 0.00 0.00 4.92
2470 3374 1.988406 GCCCTTCCAGGACCTACGT 60.988 63.158 0.00 0.00 37.67 3.57
2478 3382 0.675837 CAGGACCTACGTGACCTCGA 60.676 60.000 0.00 0.00 36.62 4.04
2511 3415 2.038269 CGCCACACCGTTTGCCTAT 61.038 57.895 0.00 0.00 0.00 2.57
2536 3440 1.606889 GGTCCACACCTCTCGTCCT 60.607 63.158 0.00 0.00 40.00 3.85
2543 3447 3.068691 CCTCTCGTCCTTCCGCCA 61.069 66.667 0.00 0.00 0.00 5.69
2612 3516 0.170339 GGTGAAATGCCCGTGCTAAC 59.830 55.000 0.00 0.00 38.71 2.34
2647 3551 5.801350 TCTTTGAAGCAATGGATTCGTAG 57.199 39.130 0.00 0.00 42.27 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 3.431856 CGTAATGAACTGCACGCTACTA 58.568 45.455 0.00 0.00 0.00 1.82
32 33 2.259618 CGTAATGAACTGCACGCTACT 58.740 47.619 0.00 0.00 0.00 2.57
33 34 1.323534 CCGTAATGAACTGCACGCTAC 59.676 52.381 0.00 0.00 33.19 3.58
34 35 1.635844 CCGTAATGAACTGCACGCTA 58.364 50.000 0.00 0.00 33.19 4.26
35 36 1.019278 CCCGTAATGAACTGCACGCT 61.019 55.000 0.00 0.00 33.19 5.07
36 37 1.017177 TCCCGTAATGAACTGCACGC 61.017 55.000 0.00 0.00 33.19 5.34
37 38 0.999406 CTCCCGTAATGAACTGCACG 59.001 55.000 0.00 0.00 0.00 5.34
52 55 4.888038 AAACAAGTAAACACGAACTCCC 57.112 40.909 0.00 0.00 0.00 4.30
56 59 7.426169 ACGACAAATAAACAAGTAAACACGAAC 59.574 33.333 0.00 0.00 0.00 3.95
100 103 5.087323 GGTAGTCTCCCTCCATATTCATCA 58.913 45.833 0.00 0.00 0.00 3.07
101 104 5.087323 TGGTAGTCTCCCTCCATATTCATC 58.913 45.833 0.00 0.00 0.00 2.92
276 282 8.716909 CGGCATTGTTTAACCAAAGAATTTTAT 58.283 29.630 0.00 0.00 35.93 1.40
328 334 5.575957 CAAAATTGTCCAGGAAGATGATCG 58.424 41.667 0.00 0.00 0.00 3.69
349 355 0.890542 ACAGCTGCGATTCCTTGCAA 60.891 50.000 15.27 0.00 41.30 4.08
351 357 1.136147 CACAGCTGCGATTCCTTGC 59.864 57.895 15.27 0.00 0.00 4.01
352 358 1.725641 TACACAGCTGCGATTCCTTG 58.274 50.000 15.27 4.24 0.00 3.61
353 359 2.076863 GTTACACAGCTGCGATTCCTT 58.923 47.619 15.27 0.00 0.00 3.36
361 370 7.596749 TTCTCTTAATAAGTTACACAGCTGC 57.403 36.000 15.27 0.00 0.00 5.25
380 389 8.762645 TCACATGGTAGACAGATAAAATTCTCT 58.237 33.333 0.00 0.00 0.00 3.10
382 391 9.334947 CATCACATGGTAGACAGATAAAATTCT 57.665 33.333 0.00 0.00 0.00 2.40
383 392 9.113838 ACATCACATGGTAGACAGATAAAATTC 57.886 33.333 0.00 0.00 33.60 2.17
386 399 7.336679 CCAACATCACATGGTAGACAGATAAAA 59.663 37.037 0.00 0.00 33.60 1.52
388 401 6.348498 CCAACATCACATGGTAGACAGATAA 58.652 40.000 0.00 0.00 33.60 1.75
400 413 4.011698 TGACATCTTCCCAACATCACATG 58.988 43.478 0.00 0.00 0.00 3.21
401 414 4.305539 TGACATCTTCCCAACATCACAT 57.694 40.909 0.00 0.00 0.00 3.21
404 417 7.379059 AGTATATGACATCTTCCCAACATCA 57.621 36.000 0.00 0.00 0.00 3.07
413 426 6.334102 ACGAAGGGAGTATATGACATCTTC 57.666 41.667 0.00 0.00 32.24 2.87
425 438 1.856629 ATTTCCGGACGAAGGGAGTA 58.143 50.000 1.83 0.00 33.01 2.59
426 439 1.479730 GTATTTCCGGACGAAGGGAGT 59.520 52.381 1.83 0.00 33.01 3.85
427 440 1.755380 AGTATTTCCGGACGAAGGGAG 59.245 52.381 1.83 0.00 33.01 4.30
428 441 1.856629 AGTATTTCCGGACGAAGGGA 58.143 50.000 1.83 0.00 0.00 4.20
429 442 2.277084 CAAGTATTTCCGGACGAAGGG 58.723 52.381 1.83 0.00 0.00 3.95
430 443 2.928116 GACAAGTATTTCCGGACGAAGG 59.072 50.000 1.83 0.00 0.00 3.46
431 444 3.581755 TGACAAGTATTTCCGGACGAAG 58.418 45.455 1.83 0.00 0.00 3.79
432 445 3.663995 TGACAAGTATTTCCGGACGAA 57.336 42.857 1.83 0.00 0.00 3.85
433 446 3.880047 ATGACAAGTATTTCCGGACGA 57.120 42.857 1.83 0.00 0.00 4.20
434 447 3.930229 TCAATGACAAGTATTTCCGGACG 59.070 43.478 1.83 0.00 0.00 4.79
435 448 5.873179 TTCAATGACAAGTATTTCCGGAC 57.127 39.130 1.83 0.00 0.00 4.79
436 449 6.127758 CCATTTCAATGACAAGTATTTCCGGA 60.128 38.462 0.00 0.00 38.70 5.14
437 450 6.035843 CCATTTCAATGACAAGTATTTCCGG 58.964 40.000 0.00 0.00 38.70 5.14
438 451 6.851609 TCCATTTCAATGACAAGTATTTCCG 58.148 36.000 0.81 0.00 38.70 4.30
439 452 8.253113 ACATCCATTTCAATGACAAGTATTTCC 58.747 33.333 0.81 0.00 38.70 3.13
443 456 9.071276 GGATACATCCATTTCAATGACAAGTAT 57.929 33.333 3.26 4.50 46.38 2.12
444 457 8.450578 GGATACATCCATTTCAATGACAAGTA 57.549 34.615 3.26 0.37 46.38 2.24
445 458 7.338800 GGATACATCCATTTCAATGACAAGT 57.661 36.000 3.26 0.00 46.38 3.16
464 477 9.736023 GGAATTAGTTGTCATCAAAATGGATAC 57.264 33.333 0.00 0.00 35.20 2.24
465 478 9.473007 TGGAATTAGTTGTCATCAAAATGGATA 57.527 29.630 0.00 0.00 35.20 2.59
466 479 8.365060 TGGAATTAGTTGTCATCAAAATGGAT 57.635 30.769 0.00 0.00 35.20 3.41
467 480 7.669304 TCTGGAATTAGTTGTCATCAAAATGGA 59.331 33.333 0.00 0.00 35.20 3.41
468 481 7.829725 TCTGGAATTAGTTGTCATCAAAATGG 58.170 34.615 0.00 0.00 35.20 3.16
469 482 9.297586 CATCTGGAATTAGTTGTCATCAAAATG 57.702 33.333 0.00 0.00 35.20 2.32
470 483 8.472413 CCATCTGGAATTAGTTGTCATCAAAAT 58.528 33.333 0.00 0.00 37.39 1.82
471 484 7.669304 TCCATCTGGAATTAGTTGTCATCAAAA 59.331 33.333 0.00 0.00 42.18 2.44
472 485 7.174413 TCCATCTGGAATTAGTTGTCATCAAA 58.826 34.615 0.00 0.00 42.18 2.69
473 486 6.720309 TCCATCTGGAATTAGTTGTCATCAA 58.280 36.000 0.00 0.00 42.18 2.57
474 487 6.312141 TCCATCTGGAATTAGTTGTCATCA 57.688 37.500 0.00 0.00 42.18 3.07
475 488 5.762218 CCTCCATCTGGAATTAGTTGTCATC 59.238 44.000 0.00 0.00 44.91 2.92
476 489 5.398353 CCCTCCATCTGGAATTAGTTGTCAT 60.398 44.000 0.00 0.00 44.91 3.06
477 490 4.080356 CCCTCCATCTGGAATTAGTTGTCA 60.080 45.833 0.00 0.00 44.91 3.58
478 491 4.164221 TCCCTCCATCTGGAATTAGTTGTC 59.836 45.833 0.00 0.00 44.91 3.18
479 492 4.111577 TCCCTCCATCTGGAATTAGTTGT 58.888 43.478 0.00 0.00 44.91 3.32
480 493 4.164988 ACTCCCTCCATCTGGAATTAGTTG 59.835 45.833 0.00 0.00 44.91 3.16
481 494 4.375313 ACTCCCTCCATCTGGAATTAGTT 58.625 43.478 0.00 0.00 44.91 2.24
482 495 4.014273 ACTCCCTCCATCTGGAATTAGT 57.986 45.455 0.00 1.53 44.91 2.24
483 496 5.151454 AGTACTCCCTCCATCTGGAATTAG 58.849 45.833 0.00 0.95 44.91 1.73
484 497 5.157770 AGTACTCCCTCCATCTGGAATTA 57.842 43.478 0.00 0.00 44.91 1.40
485 498 4.014273 AGTACTCCCTCCATCTGGAATT 57.986 45.455 0.00 0.00 44.91 2.17
486 499 3.715648 AGTACTCCCTCCATCTGGAAT 57.284 47.619 0.00 0.00 44.91 3.01
487 500 4.620086 TTAGTACTCCCTCCATCTGGAA 57.380 45.455 0.00 0.00 44.91 3.53
488 501 4.834406 ATTAGTACTCCCTCCATCTGGA 57.166 45.455 0.00 0.00 43.08 3.86
489 502 5.366768 TCAAATTAGTACTCCCTCCATCTGG 59.633 44.000 0.00 0.00 0.00 3.86
490 503 6.485830 TCAAATTAGTACTCCCTCCATCTG 57.514 41.667 0.00 0.00 0.00 2.90
491 504 7.510675 TTTCAAATTAGTACTCCCTCCATCT 57.489 36.000 0.00 0.00 0.00 2.90
492 505 7.255277 GCATTTCAAATTAGTACTCCCTCCATC 60.255 40.741 0.00 0.00 0.00 3.51
493 506 6.547510 GCATTTCAAATTAGTACTCCCTCCAT 59.452 38.462 0.00 0.00 0.00 3.41
494 507 5.885912 GCATTTCAAATTAGTACTCCCTCCA 59.114 40.000 0.00 0.00 0.00 3.86
495 508 5.299531 GGCATTTCAAATTAGTACTCCCTCC 59.700 44.000 0.00 0.00 0.00 4.30
496 509 6.038714 CAGGCATTTCAAATTAGTACTCCCTC 59.961 42.308 0.00 0.00 0.00 4.30
497 510 5.888161 CAGGCATTTCAAATTAGTACTCCCT 59.112 40.000 0.00 0.00 0.00 4.20
498 511 5.885912 TCAGGCATTTCAAATTAGTACTCCC 59.114 40.000 0.00 0.00 0.00 4.30
499 512 7.519008 CGATCAGGCATTTCAAATTAGTACTCC 60.519 40.741 0.00 0.00 0.00 3.85
500 513 7.011482 ACGATCAGGCATTTCAAATTAGTACTC 59.989 37.037 0.00 0.00 0.00 2.59
501 514 6.823689 ACGATCAGGCATTTCAAATTAGTACT 59.176 34.615 0.00 0.00 0.00 2.73
502 515 7.016361 ACGATCAGGCATTTCAAATTAGTAC 57.984 36.000 0.00 0.00 0.00 2.73
503 516 6.260050 GGACGATCAGGCATTTCAAATTAGTA 59.740 38.462 0.00 0.00 0.00 1.82
504 517 5.066505 GGACGATCAGGCATTTCAAATTAGT 59.933 40.000 0.00 0.00 0.00 2.24
505 518 5.066375 TGGACGATCAGGCATTTCAAATTAG 59.934 40.000 0.00 0.00 0.00 1.73
517 530 1.071385 AGGATTGATGGACGATCAGGC 59.929 52.381 0.21 0.00 42.24 4.85
518 531 2.366590 TGAGGATTGATGGACGATCAGG 59.633 50.000 0.21 0.00 42.24 3.86
533 546 3.069016 TGCAACCGTATCGTAATGAGGAT 59.931 43.478 0.00 0.00 34.59 3.24
569 582 3.523547 TCGTACAACCCCGTGATTTATG 58.476 45.455 0.00 0.00 0.00 1.90
570 583 3.891422 TCGTACAACCCCGTGATTTAT 57.109 42.857 0.00 0.00 0.00 1.40
571 584 3.324993 GTTCGTACAACCCCGTGATTTA 58.675 45.455 0.00 0.00 0.00 1.40
573 586 1.799544 GTTCGTACAACCCCGTGATT 58.200 50.000 0.00 0.00 0.00 2.57
574 587 0.388907 CGTTCGTACAACCCCGTGAT 60.389 55.000 0.00 0.00 0.00 3.06
578 598 2.432972 CCCGTTCGTACAACCCCG 60.433 66.667 0.00 0.00 0.00 5.73
585 605 2.795389 GCACATCGCCCGTTCGTAC 61.795 63.158 0.00 0.00 32.94 3.67
630 650 1.708027 GATTTGGACGAAGCGACGG 59.292 57.895 9.92 0.00 37.61 4.79
632 652 1.058903 GCGATTTGGACGAAGCGAC 59.941 57.895 13.50 2.16 40.55 5.19
636 656 1.148310 ACACTGCGATTTGGACGAAG 58.852 50.000 0.00 0.00 41.59 3.79
655 676 1.597854 CCCTCGTGACTTGCTGCAA 60.598 57.895 15.16 15.16 0.00 4.08
698 733 2.739996 CGAAGCTCCATCCCTGGCT 61.740 63.158 0.00 0.00 42.80 4.75
713 748 2.739913 CTCCGAAAATGCCTGTAACGAA 59.260 45.455 0.00 0.00 0.00 3.85
715 750 1.396996 CCTCCGAAAATGCCTGTAACG 59.603 52.381 0.00 0.00 0.00 3.18
716 751 1.132453 GCCTCCGAAAATGCCTGTAAC 59.868 52.381 0.00 0.00 0.00 2.50
719 754 2.040544 CGCCTCCGAAAATGCCTGT 61.041 57.895 0.00 0.00 36.29 4.00
720 755 1.745115 TCGCCTCCGAAAATGCCTG 60.745 57.895 0.00 0.00 41.17 4.85
721 756 2.668632 TCGCCTCCGAAAATGCCT 59.331 55.556 0.00 0.00 41.17 4.75
730 765 1.938657 ATCCATCGCTATCGCCTCCG 61.939 60.000 0.00 0.00 35.26 4.63
731 766 0.459237 CATCCATCGCTATCGCCTCC 60.459 60.000 0.00 0.00 35.26 4.30
732 767 0.459237 CCATCCATCGCTATCGCCTC 60.459 60.000 0.00 0.00 35.26 4.70
737 808 0.687354 ACCACCCATCCATCGCTATC 59.313 55.000 0.00 0.00 0.00 2.08
739 810 0.980754 ACACCACCCATCCATCGCTA 60.981 55.000 0.00 0.00 0.00 4.26
797 876 2.147387 AAGCACGTCCCCTCCTTGT 61.147 57.895 0.00 0.00 0.00 3.16
991 1086 2.821366 GCTCACCATGGCTGACGG 60.821 66.667 13.04 5.57 0.00 4.79
1080 1178 2.105477 ACCAGAGCGCCTCATTATCAAT 59.895 45.455 2.29 0.00 32.06 2.57
1093 1192 1.132262 ACAACAACAACAACCAGAGCG 59.868 47.619 0.00 0.00 0.00 5.03
1099 1198 4.051922 TCACACAAACAACAACAACAACC 58.948 39.130 0.00 0.00 0.00 3.77
1241 1340 4.320456 ACCACCACCTGCTGCGAG 62.320 66.667 0.00 0.00 0.00 5.03
1411 1515 4.593033 ATGCCTGCATGGATGGAC 57.407 55.556 3.36 0.57 38.35 4.02
1424 1929 1.339438 TGCAGAAAGAGAGACCATGCC 60.339 52.381 0.00 0.00 0.00 4.40
1445 2319 3.720193 CACGTGTGCAGAGCAGGC 61.720 66.667 7.58 0.00 40.08 4.85
1473 2347 2.607187 CCACCACAGATCGTTCACTAC 58.393 52.381 0.00 0.00 0.00 2.73
1498 2375 4.107051 GGACCTGCATGCACGCAC 62.107 66.667 18.46 10.62 36.86 5.34
1617 2494 0.178767 CCAATGTCATCTCGCTGGGA 59.821 55.000 0.00 0.00 0.00 4.37
1632 2509 1.375523 GGCCTTGACGACGTCCAAT 60.376 57.895 24.33 0.00 0.00 3.16
1667 2544 0.253044 CTGGAAGGAGCGATGGGAAA 59.747 55.000 0.00 0.00 0.00 3.13
1711 2594 0.393077 AGGTACGTAGGGCATGATGC 59.607 55.000 9.33 9.33 44.08 3.91
1717 2600 4.137872 GCGCAGGTACGTAGGGCA 62.138 66.667 14.78 0.00 40.46 5.36
1778 2664 2.735259 AGTTTACAAGGAGGGGGAGA 57.265 50.000 0.00 0.00 0.00 3.71
1856 2742 4.098501 CAGCAACAAGGGGGAAATAAGATC 59.901 45.833 0.00 0.00 0.00 2.75
1941 2829 4.214545 TCTTTTCGTGAATAATTGCCGTGT 59.785 37.500 0.00 0.00 0.00 4.49
1949 2837 8.967218 CACAATGTTTGTCTTTTCGTGAATAAT 58.033 29.630 0.00 0.00 43.23 1.28
1978 2866 2.856222 AGGAGAACAGGAGCAAAACAG 58.144 47.619 0.00 0.00 0.00 3.16
1992 2880 4.365514 TGGAACAAGCACATAAGGAGAA 57.634 40.909 0.00 0.00 31.92 2.87
2007 2895 2.746279 TGAGGGCTTCTTTTGGAACA 57.254 45.000 0.00 0.00 0.00 3.18
2031 2919 5.407387 TGCGTCTAAACTTTTGGATAGTGTC 59.593 40.000 0.00 0.00 30.29 3.67
2083 2971 8.514594 CACTCTAGCATTCATAACTTTGGAAAA 58.485 33.333 0.00 0.00 0.00 2.29
2084 2972 7.882791 TCACTCTAGCATTCATAACTTTGGAAA 59.117 33.333 0.00 0.00 0.00 3.13
2224 3124 2.296814 CTGGTCCACGGATCGATGCA 62.297 60.000 17.54 0.00 0.00 3.96
2298 3201 1.015607 CCGCCCGTACTACCACAAAC 61.016 60.000 0.00 0.00 0.00 2.93
2316 3219 4.509737 GAGTCCTACGTGGCGGCC 62.510 72.222 13.32 13.32 35.26 6.13
2323 3226 1.077858 GGGAGTCGGAGTCCTACGT 60.078 63.158 26.66 0.00 37.84 3.57
2342 3245 2.066999 GGGGTTTTGTGTGGGCCAA 61.067 57.895 8.40 0.00 0.00 4.52
2351 3254 1.231928 GGTCCTGGTGGGGTTTTGT 59.768 57.895 0.00 0.00 35.33 2.83
2370 3273 1.306141 AGGAAGGGATGGAGACGCA 60.306 57.895 0.00 0.00 0.00 5.24
2470 3374 2.649034 GTGAAGCGGTCGAGGTCA 59.351 61.111 0.00 0.00 0.00 4.02
2536 3440 2.357760 GGTACTTGCGTGGCGGAA 60.358 61.111 0.00 0.00 35.65 4.30
2543 3447 2.125269 GGCGGATGGTACTTGCGT 60.125 61.111 10.68 0.00 0.00 5.24
2586 3490 0.179129 CGGGCATTTCACCAAGCATC 60.179 55.000 0.00 0.00 0.00 3.91


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

AutoCloner maintained by Alex Coulton.