Multiple sequence alignment - TraesCS3A01G221400

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 TraesCS3A01G221400 chr3A 100.000 3818 0 0 1 3818 411265294 411261477 0.000000e+00 7051.0
1 TraesCS3A01G221400 chr3D 95.698 3208 96 23 570 3748 316814883 316818077 0.000000e+00 5121.0
2 TraesCS3A01G221400 chr3D 91.040 346 20 8 1 337 316814288 316814631 1.250000e-124 457.0
3 TraesCS3A01G221400 chr3B 95.841 2717 71 9 563 3249 402452831 402450127 0.000000e+00 4353.0
4 TraesCS3A01G221400 chr3B 93.436 259 15 2 1 257 402453653 402453395 2.150000e-102 383.0
5 TraesCS3A01G221400 chr3B 90.533 169 12 4 3250 3415 402450073 402449906 1.790000e-53 220.0
6 TraesCS3A01G221400 chr3B 100.000 29 0 0 280 308 402453363 402453335 2.000000e-03 54.7
7 TraesCS3A01G221400 chr7B 97.450 353 9 0 1582 1934 736624033 736623681 1.520000e-168 603.0
8 TraesCS3A01G221400 chr7B 96.053 76 3 0 1985 2060 736623687 736623612 1.440000e-24 124.0
9 TraesCS3A01G221400 chr7A 91.667 48 4 0 1580 1627 553996614 553996661 2.460000e-07 67.6


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 TraesCS3A01G221400 chr3A 411261477 411265294 3817 True 7051.000 7051 100.0000 1 3818 1 chr3A.!!$R1 3817
1 TraesCS3A01G221400 chr3D 316814288 316818077 3789 False 2789.000 5121 93.3690 1 3748 2 chr3D.!!$F1 3747
2 TraesCS3A01G221400 chr3B 402449906 402453653 3747 True 1252.675 4353 94.9525 1 3415 4 chr3B.!!$R1 3414

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
274 277 0.382636 CGCACGAGTGAAACGTTTCC 60.383 55.0 32.14 23.98 45.86 3.13 F
411 521 0.457851 CTGGCCAAACGGTCACAAAA 59.542 50.0 7.01 0.00 31.55 2.44 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2085 2369 1.215647 GATCGTGCCGAGGAACACT 59.784 57.895 0.59 0.0 39.91 3.55 R
2995 3299 3.009584 AGAACTTGATCAACCTCTTCCCC 59.990 47.826 3.38 0.0 0.00 4.81 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
55 56 3.803082 CCTGCGCGGTCAATGGTG 61.803 66.667 16.49 0.00 0.00 4.17
85 86 1.982073 GAAAATCTCTGCACCCCGCG 61.982 60.000 0.00 0.00 46.97 6.46
174 175 0.753848 AAAGACCAACAACCCACCCG 60.754 55.000 0.00 0.00 0.00 5.28
223 226 1.540797 CGTTAGGTCACCGGTGGAAAA 60.541 52.381 33.40 19.24 0.00 2.29
270 273 3.688330 CGCGCACGAGTGAAACGT 61.688 61.111 8.75 0.00 45.86 3.99
271 274 2.624264 GCGCACGAGTGAAACGTT 59.376 55.556 0.30 0.00 45.86 3.99
272 275 1.011574 GCGCACGAGTGAAACGTTT 60.012 52.632 14.57 14.57 45.86 3.60
273 276 0.985416 GCGCACGAGTGAAACGTTTC 60.985 55.000 29.72 29.72 45.86 2.78
274 277 0.382636 CGCACGAGTGAAACGTTTCC 60.383 55.000 32.14 23.98 45.86 3.13
275 278 0.935196 GCACGAGTGAAACGTTTCCT 59.065 50.000 32.14 27.40 45.86 3.36
276 279 1.329599 GCACGAGTGAAACGTTTCCTT 59.670 47.619 32.14 22.23 45.86 3.36
278 281 3.729762 GCACGAGTGAAACGTTTCCTTTT 60.730 43.478 32.14 17.82 45.86 2.27
308 320 7.637709 TCTGAATTCGTTCGTTCCATATATG 57.362 36.000 5.68 5.68 0.00 1.78
331 371 6.446318 TGATTTGTGCATTTGGACTAAGTTC 58.554 36.000 3.85 0.00 35.16 3.01
332 372 5.843673 TTTGTGCATTTGGACTAAGTTCA 57.156 34.783 3.85 0.00 37.28 3.18
333 373 6.403866 TTTGTGCATTTGGACTAAGTTCAT 57.596 33.333 3.85 0.00 37.28 2.57
334 374 5.375417 TGTGCATTTGGACTAAGTTCATG 57.625 39.130 3.85 0.00 37.28 3.07
335 375 5.069318 TGTGCATTTGGACTAAGTTCATGA 58.931 37.500 3.85 0.00 37.28 3.07
336 376 5.181811 TGTGCATTTGGACTAAGTTCATGAG 59.818 40.000 3.85 0.00 37.28 2.90
339 379 5.163581 GCATTTGGACTAAGTTCATGAGCAT 60.164 40.000 12.41 2.17 0.00 3.79
344 421 3.599343 ACTAAGTTCATGAGCATCGCAA 58.401 40.909 12.41 0.00 38.61 4.85
345 422 3.620374 ACTAAGTTCATGAGCATCGCAAG 59.380 43.478 12.41 0.00 38.61 4.01
364 474 5.504665 CGCAAGGCAAGATAGTGATTTTAGG 60.505 44.000 0.00 0.00 0.00 2.69
406 516 1.187087 AAAAACTGGCCAAACGGTCA 58.813 45.000 7.01 0.00 35.17 4.02
407 517 0.458260 AAAACTGGCCAAACGGTCAC 59.542 50.000 7.01 0.00 31.55 3.67
408 518 0.681564 AAACTGGCCAAACGGTCACA 60.682 50.000 7.01 0.00 31.55 3.58
409 519 0.681564 AACTGGCCAAACGGTCACAA 60.682 50.000 7.01 0.00 31.55 3.33
410 520 0.681564 ACTGGCCAAACGGTCACAAA 60.682 50.000 7.01 0.00 31.55 2.83
411 521 0.457851 CTGGCCAAACGGTCACAAAA 59.542 50.000 7.01 0.00 31.55 2.44
412 522 0.895530 TGGCCAAACGGTCACAAAAA 59.104 45.000 0.61 0.00 31.55 1.94
413 523 1.482593 TGGCCAAACGGTCACAAAAAT 59.517 42.857 0.61 0.00 31.55 1.82
414 524 2.093447 TGGCCAAACGGTCACAAAAATT 60.093 40.909 0.61 0.00 31.55 1.82
415 525 3.132289 TGGCCAAACGGTCACAAAAATTA 59.868 39.130 0.61 0.00 31.55 1.40
416 526 4.120589 GGCCAAACGGTCACAAAAATTAA 58.879 39.130 0.00 0.00 0.00 1.40
417 527 4.571176 GGCCAAACGGTCACAAAAATTAAA 59.429 37.500 0.00 0.00 0.00 1.52
418 528 5.064834 GGCCAAACGGTCACAAAAATTAAAA 59.935 36.000 0.00 0.00 0.00 1.52
419 529 6.403309 GGCCAAACGGTCACAAAAATTAAAAA 60.403 34.615 0.00 0.00 0.00 1.94
420 530 6.684979 GCCAAACGGTCACAAAAATTAAAAAG 59.315 34.615 0.00 0.00 0.00 2.27
421 531 7.183433 CCAAACGGTCACAAAAATTAAAAAGG 58.817 34.615 0.00 0.00 0.00 3.11
422 532 7.064728 CCAAACGGTCACAAAAATTAAAAAGGA 59.935 33.333 0.00 0.00 0.00 3.36
423 533 7.528481 AACGGTCACAAAAATTAAAAAGGAC 57.472 32.000 0.00 0.00 0.00 3.85
424 534 6.044046 ACGGTCACAAAAATTAAAAAGGACC 58.956 36.000 0.00 0.00 39.05 4.46
425 535 6.519353 GGTCACAAAAATTAAAAAGGACCG 57.481 37.500 0.00 0.00 33.74 4.79
426 536 6.274579 GGTCACAAAAATTAAAAAGGACCGA 58.725 36.000 0.00 0.00 33.74 4.69
427 537 6.419710 GGTCACAAAAATTAAAAAGGACCGAG 59.580 38.462 0.00 0.00 33.74 4.63
428 538 6.419710 GTCACAAAAATTAAAAAGGACCGAGG 59.580 38.462 0.00 0.00 0.00 4.63
429 539 5.176774 CACAAAAATTAAAAAGGACCGAGGC 59.823 40.000 0.00 0.00 0.00 4.70
430 540 3.842732 AAATTAAAAAGGACCGAGGCG 57.157 42.857 0.00 0.00 0.00 5.52
447 557 3.253955 GGCACGACACATGGACAC 58.746 61.111 0.00 0.00 0.00 3.67
448 558 2.325082 GGCACGACACATGGACACC 61.325 63.158 0.00 0.00 0.00 4.16
449 559 2.325082 GCACGACACATGGACACCC 61.325 63.158 0.00 0.00 0.00 4.61
451 561 1.070786 ACGACACATGGACACCCAC 59.929 57.895 0.00 0.00 46.98 4.61
452 562 1.070615 CGACACATGGACACCCACA 59.929 57.895 0.00 0.00 46.98 4.17
453 563 0.533978 CGACACATGGACACCCACAA 60.534 55.000 0.00 0.00 46.98 3.33
454 564 1.686355 GACACATGGACACCCACAAA 58.314 50.000 0.00 0.00 46.98 2.83
455 565 2.028130 GACACATGGACACCCACAAAA 58.972 47.619 0.00 0.00 46.98 2.44
456 566 2.428890 GACACATGGACACCCACAAAAA 59.571 45.455 0.00 0.00 46.98 1.94
457 567 3.037549 ACACATGGACACCCACAAAAAT 58.962 40.909 0.00 0.00 46.98 1.82
458 568 4.219115 ACACATGGACACCCACAAAAATA 58.781 39.130 0.00 0.00 46.98 1.40
459 569 4.837860 ACACATGGACACCCACAAAAATAT 59.162 37.500 0.00 0.00 46.98 1.28
460 570 5.306678 ACACATGGACACCCACAAAAATATT 59.693 36.000 0.00 0.00 46.98 1.28
461 571 6.495181 ACACATGGACACCCACAAAAATATTA 59.505 34.615 0.00 0.00 46.98 0.98
462 572 7.015682 ACACATGGACACCCACAAAAATATTAA 59.984 33.333 0.00 0.00 46.98 1.40
463 573 7.545265 CACATGGACACCCACAAAAATATTAAG 59.455 37.037 0.00 0.00 46.98 1.85
469 579 9.150348 GACACCCACAAAAATATTAAGAAATGG 57.850 33.333 0.00 0.00 0.00 3.16
494 731 7.470935 GTGTAACCATTAACCCCAAATACTT 57.529 36.000 0.00 0.00 0.00 2.24
501 738 8.053355 ACCATTAACCCCAAATACTTCTCTTAG 58.947 37.037 0.00 0.00 0.00 2.18
506 743 3.309954 CCCAAATACTTCTCTTAGCGTGC 59.690 47.826 0.00 0.00 0.00 5.34
509 746 2.941453 TACTTCTCTTAGCGTGCCTG 57.059 50.000 0.00 0.00 0.00 4.85
524 761 3.672511 CGTGCCTGTACTCTGTATTCGTT 60.673 47.826 0.00 0.00 0.00 3.85
525 762 3.858238 GTGCCTGTACTCTGTATTCGTTC 59.142 47.826 0.00 0.00 0.00 3.95
531 768 6.341880 TGTACTCTGTATTCGTTCGAGTAG 57.658 41.667 0.00 0.00 37.73 2.57
532 769 4.275838 ACTCTGTATTCGTTCGAGTAGC 57.724 45.455 0.00 0.00 33.53 3.58
533 770 3.688185 ACTCTGTATTCGTTCGAGTAGCA 59.312 43.478 0.00 0.80 33.53 3.49
534 771 4.335874 ACTCTGTATTCGTTCGAGTAGCAT 59.664 41.667 0.00 0.00 33.53 3.79
535 772 5.526479 ACTCTGTATTCGTTCGAGTAGCATA 59.474 40.000 0.00 0.00 33.53 3.14
538 775 5.882553 TGTATTCGTTCGAGTAGCATACAA 58.117 37.500 11.59 1.23 46.26 2.41
541 778 8.130469 TGTATTCGTTCGAGTAGCATACAATAA 58.870 33.333 11.59 0.00 46.26 1.40
542 779 9.125906 GTATTCGTTCGAGTAGCATACAATAAT 57.874 33.333 8.26 0.00 46.26 1.28
545 782 8.723777 TCGTTCGAGTAGCATACAATAATAAG 57.276 34.615 0.00 0.00 46.26 1.73
546 783 7.325338 TCGTTCGAGTAGCATACAATAATAAGC 59.675 37.037 0.00 0.00 46.26 3.09
547 784 7.326305 CGTTCGAGTAGCATACAATAATAAGCT 59.674 37.037 0.00 0.00 46.26 3.74
549 786 9.841880 TTCGAGTAGCATACAATAATAAGCTAG 57.158 33.333 0.00 0.00 46.26 3.42
551 788 9.066939 CGAGTAGCATACAATAATAAGCTAGTG 57.933 37.037 0.00 0.00 46.26 2.74
552 789 9.915629 GAGTAGCATACAATAATAAGCTAGTGT 57.084 33.333 0.00 0.00 46.26 3.55
641 909 0.608640 GAGTTGATCAGTCCCGGTGT 59.391 55.000 0.00 0.00 0.00 4.16
644 912 1.549170 GTTGATCAGTCCCGGTGTACT 59.451 52.381 0.00 0.00 0.00 2.73
867 1146 1.606668 ACCACACAGCAAACATTACGG 59.393 47.619 0.00 0.00 0.00 4.02
1104 1388 1.747367 CGAGACGAGGGCTCTGTCT 60.747 63.158 15.76 15.76 41.99 3.41
1416 1700 2.101380 GTCGAGGAGTCGCTGCTC 59.899 66.667 15.04 15.04 46.39 4.26
1521 1805 4.719369 GTCGCGCACTCGAGGGTT 62.719 66.667 17.64 0.00 39.34 4.11
1956 2240 4.710167 TCGCCCTCGTCCTCGTCA 62.710 66.667 0.00 0.00 38.33 4.35
2980 3284 7.058525 TCCGATTAGGCCGATAAGATTATCTA 58.941 38.462 10.11 0.00 40.77 1.98
3080 3384 7.509141 ACAATGCAATTTATGGATGATACGA 57.491 32.000 0.00 0.00 39.46 3.43
3100 3404 9.737025 GATACGAAATTGCGAATAGGTAAATAC 57.263 33.333 14.14 0.00 34.83 1.89
3101 3405 7.781548 ACGAAATTGCGAATAGGTAAATACT 57.218 32.000 14.14 0.00 34.83 2.12
3102 3406 8.876275 ACGAAATTGCGAATAGGTAAATACTA 57.124 30.769 14.14 0.00 34.83 1.82
3103 3407 8.975439 ACGAAATTGCGAATAGGTAAATACTAG 58.025 33.333 14.14 0.00 34.83 2.57
3197 3507 2.322772 TGGGTGTGTTCCTTCCCAA 58.677 52.632 0.00 0.00 45.66 4.12
3201 3511 1.133915 GGTGTGTTCCTTCCCAACTCA 60.134 52.381 0.00 0.00 0.00 3.41
3202 3512 2.650322 GTGTGTTCCTTCCCAACTCAA 58.350 47.619 0.00 0.00 31.07 3.02
3249 3559 5.698832 TGGATTTTGCAATTTGTCTAGTCG 58.301 37.500 0.00 0.00 0.00 4.18
3251 3561 6.016693 TGGATTTTGCAATTTGTCTAGTCGAA 60.017 34.615 0.00 0.00 0.00 3.71
3252 3562 6.524586 GGATTTTGCAATTTGTCTAGTCGAAG 59.475 38.462 0.00 0.00 0.00 3.79
3253 3563 5.356882 TTTGCAATTTGTCTAGTCGAAGG 57.643 39.130 0.00 0.00 0.00 3.46
3254 3564 2.742053 TGCAATTTGTCTAGTCGAAGGC 59.258 45.455 0.00 8.49 0.00 4.35
3255 3565 2.222819 GCAATTTGTCTAGTCGAAGGCG 60.223 50.000 0.00 0.00 36.95 5.52
3257 3567 2.806608 TTTGTCTAGTCGAAGGCGTT 57.193 45.000 0.00 0.00 36.95 4.84
3299 3664 3.304324 GCTGAGAAAAGCAAGACCAAGTC 60.304 47.826 0.00 0.00 43.01 3.01
3300 3665 3.214328 TGAGAAAAGCAAGACCAAGTCC 58.786 45.455 0.00 0.00 32.18 3.85
3335 3701 1.677052 GAAAAAGTACGGGCAACACCA 59.323 47.619 0.00 0.00 42.05 4.17
3372 3738 5.851720 ACATGCCTAATCTGTATCTGTCTG 58.148 41.667 0.00 0.00 0.00 3.51
3472 3841 4.556699 CGACAGATCCACGCAATATGACTA 60.557 45.833 0.00 0.00 0.00 2.59
3476 3845 5.403766 CAGATCCACGCAATATGACTAACTC 59.596 44.000 0.00 0.00 0.00 3.01
3484 3853 5.172232 CGCAATATGACTAACTCGTCTCTTG 59.828 44.000 0.00 0.00 35.00 3.02
3490 3859 7.820044 ATGACTAACTCGTCTCTTGATTTTC 57.180 36.000 0.00 0.00 35.00 2.29
3528 3897 0.909610 TTTCCCTCCGGCTGAGATGT 60.910 55.000 7.57 0.00 44.42 3.06
3605 3976 9.046296 CAAACTAGTCTTGTCTGTTCTTATGTT 57.954 33.333 0.00 0.00 0.00 2.71
3622 3993 0.040958 GTTCAGCAAGCTGGTCGTTG 60.041 55.000 20.78 0.00 43.75 4.10
3623 3994 0.179059 TTCAGCAAGCTGGTCGTTGA 60.179 50.000 20.78 0.00 43.75 3.18
3624 3995 0.035317 TCAGCAAGCTGGTCGTTGAT 59.965 50.000 20.78 0.00 43.75 2.57
3625 3996 1.275010 TCAGCAAGCTGGTCGTTGATA 59.725 47.619 20.78 0.00 43.75 2.15
3626 3997 1.394917 CAGCAAGCTGGTCGTTGATAC 59.605 52.381 14.10 0.00 40.17 2.24
3717 4088 2.816672 TGAATGCCGTATTTGAGCACAA 59.183 40.909 0.00 0.00 39.77 3.33
3748 4119 0.028505 GGCGAATACTGCTGCACATG 59.971 55.000 0.00 0.00 0.00 3.21
3749 4120 1.009078 GCGAATACTGCTGCACATGA 58.991 50.000 0.00 0.00 0.00 3.07
3750 4121 1.004185 GCGAATACTGCTGCACATGAG 60.004 52.381 0.00 0.00 0.00 2.90
3751 4122 1.004185 CGAATACTGCTGCACATGAGC 60.004 52.381 8.32 8.32 36.95 4.26
3752 4123 2.286872 GAATACTGCTGCACATGAGCT 58.713 47.619 16.24 0.00 37.35 4.09
3753 4124 3.461061 GAATACTGCTGCACATGAGCTA 58.539 45.455 16.24 0.33 37.35 3.32
3754 4125 2.591571 TACTGCTGCACATGAGCTAG 57.408 50.000 16.24 13.15 37.35 3.42
3755 4126 0.743701 ACTGCTGCACATGAGCTAGC 60.744 55.000 22.65 22.65 38.36 3.42
3756 4127 0.743345 CTGCTGCACATGAGCTAGCA 60.743 55.000 26.83 26.83 42.23 3.49
3757 4128 0.321830 TGCTGCACATGAGCTAGCAA 60.322 50.000 26.68 16.64 41.85 3.91
3758 4129 0.377554 GCTGCACATGAGCTAGCAAG 59.622 55.000 23.68 12.54 38.04 4.01
3759 4130 1.735386 CTGCACATGAGCTAGCAAGT 58.265 50.000 18.83 6.52 36.44 3.16
3760 4131 2.082231 CTGCACATGAGCTAGCAAGTT 58.918 47.619 18.83 0.00 36.44 2.66
3761 4132 2.486982 CTGCACATGAGCTAGCAAGTTT 59.513 45.455 18.83 0.00 36.44 2.66
3762 4133 2.227149 TGCACATGAGCTAGCAAGTTTG 59.773 45.455 18.83 9.24 33.48 2.93
3763 4134 2.415090 GCACATGAGCTAGCAAGTTTGG 60.415 50.000 18.83 1.68 0.00 3.28
3764 4135 3.076621 CACATGAGCTAGCAAGTTTGGA 58.923 45.455 18.83 0.00 0.00 3.53
3765 4136 3.503363 CACATGAGCTAGCAAGTTTGGAA 59.497 43.478 18.83 0.00 0.00 3.53
3766 4137 4.157289 CACATGAGCTAGCAAGTTTGGAAT 59.843 41.667 18.83 0.00 0.00 3.01
3767 4138 5.355071 CACATGAGCTAGCAAGTTTGGAATA 59.645 40.000 18.83 0.00 0.00 1.75
3768 4139 6.039047 CACATGAGCTAGCAAGTTTGGAATAT 59.961 38.462 18.83 0.00 0.00 1.28
3769 4140 6.261826 ACATGAGCTAGCAAGTTTGGAATATC 59.738 38.462 18.83 0.98 0.00 1.63
3770 4141 5.126067 TGAGCTAGCAAGTTTGGAATATCC 58.874 41.667 18.83 0.00 36.96 2.59
3771 4142 5.104360 TGAGCTAGCAAGTTTGGAATATCCT 60.104 40.000 18.83 0.00 37.46 3.24
3772 4143 6.099701 TGAGCTAGCAAGTTTGGAATATCCTA 59.900 38.462 18.83 0.00 37.46 2.94
3773 4144 6.900194 AGCTAGCAAGTTTGGAATATCCTAA 58.100 36.000 18.83 0.00 37.46 2.69
3780 4151 4.132336 GTTTGGAATATCCTAACGGACCC 58.868 47.826 7.72 0.00 41.06 4.46
3781 4152 3.339713 TGGAATATCCTAACGGACCCT 57.660 47.619 0.00 0.00 43.51 4.34
3782 4153 3.236896 TGGAATATCCTAACGGACCCTC 58.763 50.000 0.00 0.00 43.51 4.30
3783 4154 2.230750 GGAATATCCTAACGGACCCTCG 59.769 54.545 0.00 0.00 43.51 4.63
3784 4155 2.671896 ATATCCTAACGGACCCTCGT 57.328 50.000 0.00 0.00 43.51 4.18
3790 4161 3.920196 ACGGACCCTCGTTGCGTT 61.920 61.111 0.00 0.00 37.85 4.84
3791 4162 2.259204 CGGACCCTCGTTGCGTTA 59.741 61.111 0.00 0.00 0.00 3.18
3792 4163 1.373246 CGGACCCTCGTTGCGTTAA 60.373 57.895 0.00 0.00 0.00 2.01
3793 4164 1.620413 CGGACCCTCGTTGCGTTAAC 61.620 60.000 0.00 0.00 35.90 2.01
3794 4165 0.320160 GGACCCTCGTTGCGTTAACT 60.320 55.000 3.71 0.00 37.13 2.24
3795 4166 1.505425 GACCCTCGTTGCGTTAACTT 58.495 50.000 3.71 0.00 37.13 2.66
3796 4167 1.193874 GACCCTCGTTGCGTTAACTTG 59.806 52.381 3.71 0.00 37.13 3.16
3797 4168 1.223187 CCCTCGTTGCGTTAACTTGT 58.777 50.000 3.71 0.00 37.13 3.16
3798 4169 1.193874 CCCTCGTTGCGTTAACTTGTC 59.806 52.381 3.71 0.00 37.13 3.18
3799 4170 2.132762 CCTCGTTGCGTTAACTTGTCT 58.867 47.619 3.71 0.00 37.13 3.41
3800 4171 2.542595 CCTCGTTGCGTTAACTTGTCTT 59.457 45.455 3.71 0.00 37.13 3.01
3801 4172 3.001939 CCTCGTTGCGTTAACTTGTCTTT 59.998 43.478 3.71 0.00 37.13 2.52
3802 4173 4.495184 CCTCGTTGCGTTAACTTGTCTTTT 60.495 41.667 3.71 0.00 37.13 2.27
3803 4174 4.580528 TCGTTGCGTTAACTTGTCTTTTC 58.419 39.130 3.71 0.00 37.13 2.29
3804 4175 4.330620 TCGTTGCGTTAACTTGTCTTTTCT 59.669 37.500 3.71 0.00 37.13 2.52
3805 4176 5.025826 CGTTGCGTTAACTTGTCTTTTCTT 58.974 37.500 3.71 0.00 37.13 2.52
3806 4177 5.510323 CGTTGCGTTAACTTGTCTTTTCTTT 59.490 36.000 3.71 0.00 37.13 2.52
3807 4178 6.033091 CGTTGCGTTAACTTGTCTTTTCTTTT 59.967 34.615 3.71 0.00 37.13 2.27
3808 4179 7.409980 CGTTGCGTTAACTTGTCTTTTCTTTTT 60.410 33.333 3.71 0.00 37.13 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
55 56 2.559440 AGAGATTTTCTGATGAGCGGC 58.441 47.619 0.00 0.00 33.93 6.53
174 175 2.872858 GGTCCGATTTGATCTAACCTGC 59.127 50.000 0.00 0.00 32.15 4.85
253 256 2.674365 AAACGTTTCACTCGTGCGCG 62.674 55.000 14.79 14.79 41.38 6.86
257 260 3.668596 AAAGGAAACGTTTCACTCGTG 57.331 42.857 34.79 0.00 41.38 4.35
259 262 4.408694 ACAAAAAGGAAACGTTTCACTCG 58.591 39.130 34.79 21.92 41.27 4.18
260 263 6.699895 AAACAAAAAGGAAACGTTTCACTC 57.300 33.333 34.79 21.43 41.27 3.51
261 264 6.926826 AGAAAACAAAAAGGAAACGTTTCACT 59.073 30.769 34.79 26.84 41.27 3.41
262 265 7.007117 CAGAAAACAAAAAGGAAACGTTTCAC 58.993 34.615 34.79 25.39 41.27 3.18
263 266 6.924060 TCAGAAAACAAAAAGGAAACGTTTCA 59.076 30.769 34.79 11.87 41.27 2.69
264 267 7.341024 TCAGAAAACAAAAAGGAAACGTTTC 57.659 32.000 28.83 28.83 41.27 2.78
265 268 7.716768 TTCAGAAAACAAAAAGGAAACGTTT 57.283 28.000 14.57 14.57 44.07 3.60
266 269 7.899178 ATTCAGAAAACAAAAAGGAAACGTT 57.101 28.000 0.00 0.00 0.00 3.99
267 270 7.201401 CGAATTCAGAAAACAAAAAGGAAACGT 60.201 33.333 6.22 0.00 0.00 3.99
270 273 8.541133 AACGAATTCAGAAAACAAAAAGGAAA 57.459 26.923 6.22 0.00 0.00 3.13
271 274 7.008810 CGAACGAATTCAGAAAACAAAAAGGAA 59.991 33.333 6.22 0.00 34.14 3.36
272 275 6.470877 CGAACGAATTCAGAAAACAAAAAGGA 59.529 34.615 6.22 0.00 34.14 3.36
273 276 6.252655 ACGAACGAATTCAGAAAACAAAAAGG 59.747 34.615 6.22 0.00 34.14 3.11
274 277 7.204737 ACGAACGAATTCAGAAAACAAAAAG 57.795 32.000 6.22 0.00 34.14 2.27
275 278 7.201367 GGAACGAACGAATTCAGAAAACAAAAA 60.201 33.333 6.22 0.00 34.14 1.94
276 279 6.251801 GGAACGAACGAATTCAGAAAACAAAA 59.748 34.615 6.22 0.00 34.14 2.44
278 281 5.163744 TGGAACGAACGAATTCAGAAAACAA 60.164 36.000 6.22 0.00 34.14 2.83
308 320 6.446318 TGAACTTAGTCCAAATGCACAAATC 58.554 36.000 0.00 0.00 0.00 2.17
331 371 0.248498 CTTGCCTTGCGATGCTCATG 60.248 55.000 2.72 0.00 0.00 3.07
332 372 0.393402 TCTTGCCTTGCGATGCTCAT 60.393 50.000 2.72 0.00 0.00 2.90
333 373 0.393402 ATCTTGCCTTGCGATGCTCA 60.393 50.000 2.72 0.00 0.00 4.26
334 374 1.530293 CTATCTTGCCTTGCGATGCTC 59.470 52.381 2.72 0.00 0.00 4.26
335 375 1.134280 ACTATCTTGCCTTGCGATGCT 60.134 47.619 2.72 0.00 0.00 3.79
336 376 1.003116 CACTATCTTGCCTTGCGATGC 60.003 52.381 0.00 0.00 0.00 3.91
339 379 2.988010 ATCACTATCTTGCCTTGCGA 57.012 45.000 0.00 0.00 0.00 5.10
344 421 7.337942 CAGTTTCCTAAAATCACTATCTTGCCT 59.662 37.037 0.00 0.00 0.00 4.75
345 422 7.415653 CCAGTTTCCTAAAATCACTATCTTGCC 60.416 40.741 0.00 0.00 0.00 4.52
387 497 1.134936 GTGACCGTTTGGCCAGTTTTT 60.135 47.619 5.11 0.00 39.70 1.94
388 498 0.458260 GTGACCGTTTGGCCAGTTTT 59.542 50.000 5.11 0.00 39.70 2.43
389 499 0.681564 TGTGACCGTTTGGCCAGTTT 60.682 50.000 5.11 0.00 39.70 2.66
390 500 0.681564 TTGTGACCGTTTGGCCAGTT 60.682 50.000 5.11 0.00 39.70 3.16
391 501 0.681564 TTTGTGACCGTTTGGCCAGT 60.682 50.000 5.11 0.00 39.70 4.00
392 502 0.457851 TTTTGTGACCGTTTGGCCAG 59.542 50.000 5.11 0.00 39.70 4.85
393 503 0.895530 TTTTTGTGACCGTTTGGCCA 59.104 45.000 0.00 0.00 39.70 5.36
394 504 2.232756 ATTTTTGTGACCGTTTGGCC 57.767 45.000 0.00 0.00 39.70 5.36
395 505 5.720261 TTTAATTTTTGTGACCGTTTGGC 57.280 34.783 0.00 0.00 39.70 4.52
396 506 7.064728 TCCTTTTTAATTTTTGTGACCGTTTGG 59.935 33.333 0.00 0.00 42.84 3.28
397 507 7.900864 GTCCTTTTTAATTTTTGTGACCGTTTG 59.099 33.333 0.00 0.00 0.00 2.93
398 508 7.064847 GGTCCTTTTTAATTTTTGTGACCGTTT 59.935 33.333 0.00 0.00 31.45 3.60
399 509 6.535865 GGTCCTTTTTAATTTTTGTGACCGTT 59.464 34.615 0.00 0.00 31.45 4.44
400 510 6.044046 GGTCCTTTTTAATTTTTGTGACCGT 58.956 36.000 0.00 0.00 31.45 4.83
401 511 6.519353 GGTCCTTTTTAATTTTTGTGACCG 57.481 37.500 0.00 0.00 31.45 4.79
402 512 6.274579 TCGGTCCTTTTTAATTTTTGTGACC 58.725 36.000 0.00 0.00 37.09 4.02
403 513 6.419710 CCTCGGTCCTTTTTAATTTTTGTGAC 59.580 38.462 0.00 0.00 0.00 3.67
404 514 6.508777 CCTCGGTCCTTTTTAATTTTTGTGA 58.491 36.000 0.00 0.00 0.00 3.58
405 515 5.176774 GCCTCGGTCCTTTTTAATTTTTGTG 59.823 40.000 0.00 0.00 0.00 3.33
406 516 5.294356 GCCTCGGTCCTTTTTAATTTTTGT 58.706 37.500 0.00 0.00 0.00 2.83
407 517 4.384547 CGCCTCGGTCCTTTTTAATTTTTG 59.615 41.667 0.00 0.00 0.00 2.44
408 518 4.552355 CGCCTCGGTCCTTTTTAATTTTT 58.448 39.130 0.00 0.00 0.00 1.94
409 519 3.057104 CCGCCTCGGTCCTTTTTAATTTT 60.057 43.478 0.00 0.00 42.73 1.82
410 520 2.490509 CCGCCTCGGTCCTTTTTAATTT 59.509 45.455 0.00 0.00 42.73 1.82
411 521 2.089201 CCGCCTCGGTCCTTTTTAATT 58.911 47.619 0.00 0.00 42.73 1.40
412 522 1.746470 CCGCCTCGGTCCTTTTTAAT 58.254 50.000 0.00 0.00 42.73 1.40
413 523 3.236604 CCGCCTCGGTCCTTTTTAA 57.763 52.632 0.00 0.00 42.73 1.52
425 535 3.490759 CATGTGTCGTGCCGCCTC 61.491 66.667 0.00 0.00 0.00 4.70
428 538 3.788766 GTCCATGTGTCGTGCCGC 61.789 66.667 0.00 0.00 0.00 6.53
429 539 2.356913 TGTCCATGTGTCGTGCCG 60.357 61.111 0.00 0.00 0.00 5.69
430 540 2.325082 GGTGTCCATGTGTCGTGCC 61.325 63.158 0.00 0.00 0.00 5.01
431 541 2.325082 GGGTGTCCATGTGTCGTGC 61.325 63.158 0.00 0.00 0.00 5.34
432 542 1.070615 TGGGTGTCCATGTGTCGTG 59.929 57.895 0.00 0.00 38.32 4.35
433 543 1.070786 GTGGGTGTCCATGTGTCGT 59.929 57.895 0.00 0.00 46.09 4.34
434 544 0.533978 TTGTGGGTGTCCATGTGTCG 60.534 55.000 0.00 0.00 46.09 4.35
435 545 1.686355 TTTGTGGGTGTCCATGTGTC 58.314 50.000 0.00 0.00 46.09 3.67
436 546 2.151502 TTTTGTGGGTGTCCATGTGT 57.848 45.000 0.00 0.00 46.09 3.72
437 547 3.749665 ATTTTTGTGGGTGTCCATGTG 57.250 42.857 0.00 0.00 46.09 3.21
438 548 7.453126 TCTTAATATTTTTGTGGGTGTCCATGT 59.547 33.333 0.00 0.00 46.09 3.21
439 549 7.835822 TCTTAATATTTTTGTGGGTGTCCATG 58.164 34.615 0.00 0.00 46.09 3.66
440 550 8.429237 TTCTTAATATTTTTGTGGGTGTCCAT 57.571 30.769 0.00 0.00 46.09 3.41
441 551 7.841282 TTCTTAATATTTTTGTGGGTGTCCA 57.159 32.000 0.00 0.00 41.58 4.02
442 552 9.150348 CATTTCTTAATATTTTTGTGGGTGTCC 57.850 33.333 0.00 0.00 0.00 4.02
443 553 9.150348 CCATTTCTTAATATTTTTGTGGGTGTC 57.850 33.333 0.00 0.00 0.00 3.67
444 554 8.100164 CCCATTTCTTAATATTTTTGTGGGTGT 58.900 33.333 11.91 0.00 38.16 4.16
445 555 8.491331 CCCATTTCTTAATATTTTTGTGGGTG 57.509 34.615 11.91 0.00 38.16 4.61
447 557 8.100164 ACACCCATTTCTTAATATTTTTGTGGG 58.900 33.333 15.83 15.83 46.18 4.61
469 579 5.953548 AGTATTTGGGGTTAATGGTTACACC 59.046 40.000 0.00 0.00 38.36 4.16
471 581 7.471890 AGAAGTATTTGGGGTTAATGGTTACA 58.528 34.615 0.00 0.00 0.00 2.41
482 719 3.518303 ACGCTAAGAGAAGTATTTGGGGT 59.482 43.478 0.00 0.00 0.00 4.95
492 729 2.164624 AGTACAGGCACGCTAAGAGAAG 59.835 50.000 0.00 0.00 0.00 2.85
493 730 2.163815 GAGTACAGGCACGCTAAGAGAA 59.836 50.000 0.00 0.00 0.00 2.87
494 731 1.743958 GAGTACAGGCACGCTAAGAGA 59.256 52.381 0.00 0.00 0.00 3.10
501 738 2.194271 GAATACAGAGTACAGGCACGC 58.806 52.381 0.00 0.00 0.00 5.34
506 743 4.094590 ACTCGAACGAATACAGAGTACAGG 59.905 45.833 0.00 0.00 40.00 4.00
509 746 5.196825 GCTACTCGAACGAATACAGAGTAC 58.803 45.833 0.00 0.00 41.68 2.73
524 761 9.011095 ACTAGCTTATTATTGTATGCTACTCGA 57.989 33.333 0.00 0.00 36.70 4.04
525 762 9.066939 CACTAGCTTATTATTGTATGCTACTCG 57.933 37.037 0.00 0.00 36.70 4.18
545 782 6.861572 TGCTGTATCAAATCGTATACACTAGC 59.138 38.462 3.32 0.00 34.47 3.42
546 783 8.972262 ATGCTGTATCAAATCGTATACACTAG 57.028 34.615 3.32 0.00 34.47 2.57
547 784 8.793592 AGATGCTGTATCAAATCGTATACACTA 58.206 33.333 8.45 0.00 38.31 2.74
549 786 7.875316 AGATGCTGTATCAAATCGTATACAC 57.125 36.000 8.45 0.00 38.31 2.90
552 789 9.124807 CGTTTAGATGCTGTATCAAATCGTATA 57.875 33.333 8.45 0.00 38.31 1.47
554 791 7.197703 TCGTTTAGATGCTGTATCAAATCGTA 58.802 34.615 8.45 0.00 38.31 3.43
555 792 6.040247 TCGTTTAGATGCTGTATCAAATCGT 58.960 36.000 8.45 0.00 38.31 3.73
556 793 6.510746 TCGTTTAGATGCTGTATCAAATCG 57.489 37.500 8.45 7.52 38.31 3.34
745 1014 1.859302 AGGGTTTTGCTGTGTTTCCA 58.141 45.000 0.00 0.00 0.00 3.53
755 1024 2.801699 CGGGAGTTTTCAAGGGTTTTGC 60.802 50.000 0.00 0.00 0.00 3.68
867 1146 2.047830 CCTCTCCCCCTTATGTACACC 58.952 57.143 0.00 0.00 0.00 4.16
1132 1416 1.738099 CCCGCAAGAAGGACGACAG 60.738 63.158 0.00 0.00 43.02 3.51
2085 2369 1.215647 GATCGTGCCGAGGAACACT 59.784 57.895 0.59 0.00 39.91 3.55
2995 3299 3.009584 AGAACTTGATCAACCTCTTCCCC 59.990 47.826 3.38 0.00 0.00 4.81
3197 3507 2.092429 TGTGACAGCTTCCCTTTTGAGT 60.092 45.455 0.00 0.00 0.00 3.41
3201 3511 3.837355 AGAATGTGACAGCTTCCCTTTT 58.163 40.909 0.00 0.00 0.00 2.27
3202 3512 3.515602 AGAATGTGACAGCTTCCCTTT 57.484 42.857 0.00 0.00 0.00 3.11
3210 3520 4.510038 AATCCAACAAGAATGTGACAGC 57.490 40.909 0.00 0.00 40.46 4.40
3211 3521 5.176223 GCAAAATCCAACAAGAATGTGACAG 59.824 40.000 0.00 0.00 40.46 3.51
3249 3559 0.874175 GCCCACAAACAAACGCCTTC 60.874 55.000 0.00 0.00 0.00 3.46
3251 3561 1.608717 TTGCCCACAAACAAACGCCT 61.609 50.000 0.00 0.00 31.21 5.52
3252 3562 1.151172 CTTGCCCACAAACAAACGCC 61.151 55.000 0.00 0.00 34.74 5.68
3253 3563 1.151172 CCTTGCCCACAAACAAACGC 61.151 55.000 0.00 0.00 34.74 4.84
3254 3564 0.529555 CCCTTGCCCACAAACAAACG 60.530 55.000 0.00 0.00 34.74 3.60
3255 3565 0.179059 CCCCTTGCCCACAAACAAAC 60.179 55.000 0.00 0.00 34.74 2.93
3257 3567 0.261991 TACCCCTTGCCCACAAACAA 59.738 50.000 0.00 0.00 34.74 2.83
3299 3664 4.755123 ACTTTTTCATCACTTACGACTGGG 59.245 41.667 0.00 0.00 0.00 4.45
3300 3665 5.924475 ACTTTTTCATCACTTACGACTGG 57.076 39.130 0.00 0.00 0.00 4.00
3335 3701 1.237285 GCATGTTTCCGACCTGCTGT 61.237 55.000 0.00 0.00 43.83 4.40
3425 3794 3.461843 GCTGAGCGAACAAAACCAG 57.538 52.632 0.00 0.00 0.00 4.00
3472 3841 4.617959 TCACGAAAATCAAGAGACGAGTT 58.382 39.130 0.00 0.00 0.00 3.01
3476 3845 4.859245 TCTCATCACGAAAATCAAGAGACG 59.141 41.667 0.00 0.00 0.00 4.18
3490 3859 6.986817 AGGGAAAATGTTAGTATCTCATCACG 59.013 38.462 0.00 0.00 0.00 4.35
3574 3943 8.738645 AGAACAGACAAGACTAGTTTGAAAAT 57.261 30.769 18.56 3.08 0.00 1.82
3595 3966 3.503748 ACCAGCTTGCTGAACATAAGAAC 59.496 43.478 22.50 0.00 0.00 3.01
3605 3976 0.035317 ATCAACGACCAGCTTGCTGA 59.965 50.000 22.50 2.81 0.00 4.26
3641 4012 4.826274 TTATCTGCCTACTTGTGCTCTT 57.174 40.909 0.00 0.00 0.00 2.85
3643 4014 4.513318 GGAATTATCTGCCTACTTGTGCTC 59.487 45.833 0.00 0.00 0.00 4.26
3737 4108 0.743345 TGCTAGCTCATGTGCAGCAG 60.743 55.000 27.52 19.57 39.86 4.24
3740 4111 1.735386 ACTTGCTAGCTCATGTGCAG 58.265 50.000 20.92 15.86 36.75 4.41
3748 4119 5.372373 AGGATATTCCAAACTTGCTAGCTC 58.628 41.667 17.23 0.00 39.61 4.09
3749 4120 5.379706 AGGATATTCCAAACTTGCTAGCT 57.620 39.130 17.23 0.00 39.61 3.32
3750 4121 6.292919 CGTTAGGATATTCCAAACTTGCTAGC 60.293 42.308 8.10 8.10 39.61 3.42
3751 4122 6.202954 CCGTTAGGATATTCCAAACTTGCTAG 59.797 42.308 0.00 0.00 39.61 3.42
3752 4123 6.053005 CCGTTAGGATATTCCAAACTTGCTA 58.947 40.000 0.00 0.00 39.61 3.49
3753 4124 4.881850 CCGTTAGGATATTCCAAACTTGCT 59.118 41.667 0.00 0.00 39.61 3.91
3754 4125 4.879545 TCCGTTAGGATATTCCAAACTTGC 59.120 41.667 0.00 0.00 42.75 4.01
3773 4144 2.086251 TTAACGCAACGAGGGTCCGT 62.086 55.000 0.00 0.00 43.40 4.69
3774 4145 1.373246 TTAACGCAACGAGGGTCCG 60.373 57.895 0.00 0.00 43.40 4.79
3775 4146 0.320160 AGTTAACGCAACGAGGGTCC 60.320 55.000 0.00 0.00 43.40 4.46
3776 4147 1.193874 CAAGTTAACGCAACGAGGGTC 59.806 52.381 0.00 0.00 43.40 4.46
3777 4148 1.223187 CAAGTTAACGCAACGAGGGT 58.777 50.000 0.00 0.00 46.58 4.34
3778 4149 1.193874 GACAAGTTAACGCAACGAGGG 59.806 52.381 0.00 0.00 42.35 4.30
3779 4150 2.132762 AGACAAGTTAACGCAACGAGG 58.867 47.619 0.00 0.00 42.35 4.63
3780 4151 3.854286 AAGACAAGTTAACGCAACGAG 57.146 42.857 0.00 0.00 42.35 4.18
3781 4152 4.330620 AGAAAAGACAAGTTAACGCAACGA 59.669 37.500 0.00 0.00 42.35 3.85
3782 4153 4.584394 AGAAAAGACAAGTTAACGCAACG 58.416 39.130 0.00 0.00 42.35 4.10
3783 4154 6.864560 AAAGAAAAGACAAGTTAACGCAAC 57.135 33.333 0.00 0.00 37.41 4.17
3784 4155 7.876896 AAAAAGAAAAGACAAGTTAACGCAA 57.123 28.000 0.00 0.00 0.00 4.85


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

AutoCloner maintained by Alex Coulton.