Multiple sequence alignment - TraesCS1A01G050300

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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 TraesCS1A01G050300 chr1A 100.000 2810 0 0 1 2810 32185118 32187927 0.000000e+00 5190
1 TraesCS1A01G050300 chr1A 97.456 511 9 2 1 508 355554402 355553893 0.000000e+00 869
2 TraesCS1A01G050300 chr1A 97.065 511 11 2 1 508 32174327 32174836 0.000000e+00 857
3 TraesCS1A01G050300 chr1A 96.869 511 12 2 1 508 320886068 320885559 0.000000e+00 852
4 TraesCS1A01G050300 chr1A 96.869 511 12 2 1 508 448825177 448825686 0.000000e+00 852
5 TraesCS1A01G050300 chr1A 96.869 511 12 2 1 508 578802849 578803358 0.000000e+00 852
6 TraesCS1A01G050300 chr1A 78.526 312 50 13 2398 2706 517099138 517098841 3.700000e-44 189
7 TraesCS1A01G050300 chr1D 91.340 1582 88 24 601 2146 33603771 33605339 0.000000e+00 2117
8 TraesCS1A01G050300 chr1D 90.729 658 36 4 2176 2809 33605337 33605993 0.000000e+00 854
9 TraesCS1A01G050300 chr1D 77.707 314 53 13 2396 2706 420651745 420651446 2.880000e-40 176
10 TraesCS1A01G050300 chr1B 87.030 1889 157 40 980 2809 50987311 50989170 0.000000e+00 2050
11 TraesCS1A01G050300 chr1B 93.466 352 21 2 647 997 50986942 50987292 3.210000e-144 521
12 TraesCS1A01G050300 chr1B 91.549 355 28 2 644 997 50985518 50985871 3.250000e-134 488
13 TraesCS1A01G050300 chr1B 78.526 312 50 13 2398 2706 568965304 568965007 3.700000e-44 189
14 TraesCS1A01G050300 chr7A 97.065 511 11 2 1 508 249235390 249234881 0.000000e+00 857
15 TraesCS1A01G050300 chr7A 96.869 511 12 2 1 508 195111639 195111130 0.000000e+00 852
16 TraesCS1A01G050300 chr4A 97.065 511 11 2 1 508 34277766 34278275 0.000000e+00 857
17 TraesCS1A01G050300 chr3A 97.065 511 11 2 1 508 435765903 435765394 0.000000e+00 857


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 TraesCS1A01G050300 chr1A 32185118 32187927 2809 False 5190.000000 5190 100.000000 1 2810 1 chr1A.!!$F2 2809
1 TraesCS1A01G050300 chr1A 355553893 355554402 509 True 869.000000 869 97.456000 1 508 1 chr1A.!!$R2 507
2 TraesCS1A01G050300 chr1A 32174327 32174836 509 False 857.000000 857 97.065000 1 508 1 chr1A.!!$F1 507
3 TraesCS1A01G050300 chr1A 320885559 320886068 509 True 852.000000 852 96.869000 1 508 1 chr1A.!!$R1 507
4 TraesCS1A01G050300 chr1A 448825177 448825686 509 False 852.000000 852 96.869000 1 508 1 chr1A.!!$F3 507
5 TraesCS1A01G050300 chr1A 578802849 578803358 509 False 852.000000 852 96.869000 1 508 1 chr1A.!!$F4 507
6 TraesCS1A01G050300 chr1D 33603771 33605993 2222 False 1485.500000 2117 91.034500 601 2809 2 chr1D.!!$F1 2208
7 TraesCS1A01G050300 chr1B 50985518 50989170 3652 False 1019.666667 2050 90.681667 644 2809 3 chr1B.!!$F1 2165
8 TraesCS1A01G050300 chr7A 249234881 249235390 509 True 857.000000 857 97.065000 1 508 1 chr7A.!!$R2 507
9 TraesCS1A01G050300 chr7A 195111130 195111639 509 True 852.000000 852 96.869000 1 508 1 chr7A.!!$R1 507
10 TraesCS1A01G050300 chr4A 34277766 34278275 509 False 857.000000 857 97.065000 1 508 1 chr4A.!!$F1 507
11 TraesCS1A01G050300 chr3A 435765394 435765903 509 True 857.000000 857 97.065000 1 508 1 chr3A.!!$R1 507

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
556 560 0.039978 CAGCGGATAGAGCCTACACG 60.040 60.0 0.0 0.0 34.64 4.49 F
566 570 0.107831 AGCCTACACGAAACTTGCCA 59.892 50.0 0.0 0.0 0.00 4.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1778 3246 0.326264 GAGCAGGTTCATGACACCCT 59.674 55.000 18.00 11.22 34.44 4.34 R
2249 3763 1.663739 CTGCTGTTGCTGCCACAAT 59.336 52.632 7.99 0.00 40.48 2.71 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
169 173 6.933514 ACATTGAATGGTCTATTTGGGTTT 57.066 33.333 10.27 0.00 33.60 3.27
238 242 8.507524 GGTACCTAAAACTAAGCATTGATCTT 57.492 34.615 4.06 0.00 0.00 2.40
274 278 1.349542 CCGGTGGGGGATCATGGTTA 61.350 60.000 0.00 0.00 0.00 2.85
310 314 5.057149 GCTACAAATCATATGACCGGAAGT 58.943 41.667 9.46 4.22 0.00 3.01
491 495 7.011295 ACAATTTACTTTCCGTTCGTCAACTTA 59.989 33.333 0.00 0.00 0.00 2.24
504 508 4.051922 CGTCAACTTACTATCATGGGCTC 58.948 47.826 0.00 0.00 0.00 4.70
506 510 5.675538 GTCAACTTACTATCATGGGCTCTT 58.324 41.667 0.00 0.00 0.00 2.85
507 511 5.525378 GTCAACTTACTATCATGGGCTCTTG 59.475 44.000 0.00 0.00 0.00 3.02
508 512 5.189736 TCAACTTACTATCATGGGCTCTTGT 59.810 40.000 0.00 0.00 0.00 3.16
509 513 5.700402 ACTTACTATCATGGGCTCTTGTT 57.300 39.130 0.00 0.00 0.00 2.83
510 514 6.067217 ACTTACTATCATGGGCTCTTGTTT 57.933 37.500 0.00 0.00 0.00 2.83
511 515 5.882557 ACTTACTATCATGGGCTCTTGTTTG 59.117 40.000 0.00 0.00 0.00 2.93
512 516 4.307032 ACTATCATGGGCTCTTGTTTGT 57.693 40.909 0.00 0.00 0.00 2.83
513 517 4.265073 ACTATCATGGGCTCTTGTTTGTC 58.735 43.478 0.00 0.00 0.00 3.18
514 518 2.655090 TCATGGGCTCTTGTTTGTCA 57.345 45.000 0.00 0.00 0.00 3.58
515 519 2.507484 TCATGGGCTCTTGTTTGTCAG 58.493 47.619 0.00 0.00 0.00 3.51
516 520 2.158623 TCATGGGCTCTTGTTTGTCAGT 60.159 45.455 0.00 0.00 0.00 3.41
517 521 1.967319 TGGGCTCTTGTTTGTCAGTC 58.033 50.000 0.00 0.00 0.00 3.51
518 522 1.211703 TGGGCTCTTGTTTGTCAGTCA 59.788 47.619 0.00 0.00 0.00 3.41
519 523 2.158623 TGGGCTCTTGTTTGTCAGTCAT 60.159 45.455 0.00 0.00 0.00 3.06
520 524 2.485814 GGGCTCTTGTTTGTCAGTCATC 59.514 50.000 0.00 0.00 0.00 2.92
521 525 3.406764 GGCTCTTGTTTGTCAGTCATCT 58.593 45.455 0.00 0.00 0.00 2.90
522 526 3.817647 GGCTCTTGTTTGTCAGTCATCTT 59.182 43.478 0.00 0.00 0.00 2.40
523 527 4.083590 GGCTCTTGTTTGTCAGTCATCTTC 60.084 45.833 0.00 0.00 0.00 2.87
524 528 4.754114 GCTCTTGTTTGTCAGTCATCTTCT 59.246 41.667 0.00 0.00 0.00 2.85
525 529 5.107143 GCTCTTGTTTGTCAGTCATCTTCTC 60.107 44.000 0.00 0.00 0.00 2.87
526 530 5.300752 TCTTGTTTGTCAGTCATCTTCTCC 58.699 41.667 0.00 0.00 0.00 3.71
527 531 4.687901 TGTTTGTCAGTCATCTTCTCCA 57.312 40.909 0.00 0.00 0.00 3.86
528 532 4.380531 TGTTTGTCAGTCATCTTCTCCAC 58.619 43.478 0.00 0.00 0.00 4.02
529 533 3.685139 TTGTCAGTCATCTTCTCCACC 57.315 47.619 0.00 0.00 0.00 4.61
530 534 2.608623 TGTCAGTCATCTTCTCCACCA 58.391 47.619 0.00 0.00 0.00 4.17
531 535 2.564504 TGTCAGTCATCTTCTCCACCAG 59.435 50.000 0.00 0.00 0.00 4.00
532 536 2.828520 GTCAGTCATCTTCTCCACCAGA 59.171 50.000 0.00 0.00 0.00 3.86
533 537 3.450457 GTCAGTCATCTTCTCCACCAGAT 59.550 47.826 0.00 0.00 0.00 2.90
534 538 4.081198 GTCAGTCATCTTCTCCACCAGATT 60.081 45.833 0.00 0.00 0.00 2.40
535 539 4.161189 TCAGTCATCTTCTCCACCAGATTC 59.839 45.833 0.00 0.00 0.00 2.52
536 540 4.081254 CAGTCATCTTCTCCACCAGATTCA 60.081 45.833 0.00 0.00 0.00 2.57
537 541 4.081198 AGTCATCTTCTCCACCAGATTCAC 60.081 45.833 0.00 0.00 0.00 3.18
538 542 3.840078 TCATCTTCTCCACCAGATTCACA 59.160 43.478 0.00 0.00 0.00 3.58
539 543 3.969287 TCTTCTCCACCAGATTCACAG 57.031 47.619 0.00 0.00 0.00 3.66
540 544 2.027745 TCTTCTCCACCAGATTCACAGC 60.028 50.000 0.00 0.00 0.00 4.40
541 545 0.247460 TCTCCACCAGATTCACAGCG 59.753 55.000 0.00 0.00 0.00 5.18
542 546 0.742281 CTCCACCAGATTCACAGCGG 60.742 60.000 0.00 0.00 0.00 5.52
543 547 1.191489 TCCACCAGATTCACAGCGGA 61.191 55.000 0.00 0.00 0.00 5.54
544 548 0.107508 CCACCAGATTCACAGCGGAT 60.108 55.000 0.00 0.00 0.00 4.18
545 549 1.138859 CCACCAGATTCACAGCGGATA 59.861 52.381 0.00 0.00 0.00 2.59
546 550 2.477825 CACCAGATTCACAGCGGATAG 58.522 52.381 0.00 0.00 0.00 2.08
547 551 2.101415 CACCAGATTCACAGCGGATAGA 59.899 50.000 0.00 0.00 0.00 1.98
548 552 2.363680 ACCAGATTCACAGCGGATAGAG 59.636 50.000 0.00 0.00 0.00 2.43
549 553 2.402305 CAGATTCACAGCGGATAGAGC 58.598 52.381 0.00 0.00 0.00 4.09
550 554 1.342819 AGATTCACAGCGGATAGAGCC 59.657 52.381 0.00 0.00 34.64 4.70
551 555 1.342819 GATTCACAGCGGATAGAGCCT 59.657 52.381 0.00 0.00 34.64 4.58
552 556 2.067365 TTCACAGCGGATAGAGCCTA 57.933 50.000 0.00 0.00 34.64 3.93
553 557 1.319541 TCACAGCGGATAGAGCCTAC 58.680 55.000 0.00 0.00 34.64 3.18
554 558 1.032794 CACAGCGGATAGAGCCTACA 58.967 55.000 0.00 0.00 34.64 2.74
555 559 1.033574 ACAGCGGATAGAGCCTACAC 58.966 55.000 0.00 0.00 34.64 2.90
556 560 0.039978 CAGCGGATAGAGCCTACACG 60.040 60.000 0.00 0.00 34.64 4.49
557 561 0.179026 AGCGGATAGAGCCTACACGA 60.179 55.000 0.00 0.00 34.64 4.35
558 562 0.666913 GCGGATAGAGCCTACACGAA 59.333 55.000 0.00 0.00 0.00 3.85
559 563 1.066605 GCGGATAGAGCCTACACGAAA 59.933 52.381 0.00 0.00 0.00 3.46
560 564 2.728922 CGGATAGAGCCTACACGAAAC 58.271 52.381 0.00 0.00 0.00 2.78
561 565 2.358267 CGGATAGAGCCTACACGAAACT 59.642 50.000 0.00 0.00 0.00 2.66
562 566 3.181489 CGGATAGAGCCTACACGAAACTT 60.181 47.826 0.00 0.00 0.00 2.66
563 567 4.113354 GGATAGAGCCTACACGAAACTTG 58.887 47.826 0.00 0.00 0.00 3.16
564 568 1.797025 AGAGCCTACACGAAACTTGC 58.203 50.000 0.00 0.00 0.00 4.01
565 569 0.796927 GAGCCTACACGAAACTTGCC 59.203 55.000 0.00 0.00 0.00 4.52
566 570 0.107831 AGCCTACACGAAACTTGCCA 59.892 50.000 0.00 0.00 0.00 4.92
567 571 1.165270 GCCTACACGAAACTTGCCAT 58.835 50.000 0.00 0.00 0.00 4.40
568 572 2.027561 AGCCTACACGAAACTTGCCATA 60.028 45.455 0.00 0.00 0.00 2.74
569 573 2.351726 GCCTACACGAAACTTGCCATAG 59.648 50.000 0.00 0.00 0.00 2.23
570 574 3.596214 CCTACACGAAACTTGCCATAGT 58.404 45.455 0.00 0.00 0.00 2.12
571 575 3.370978 CCTACACGAAACTTGCCATAGTG 59.629 47.826 0.00 0.00 0.00 2.74
572 576 1.535462 ACACGAAACTTGCCATAGTGC 59.465 47.619 0.00 0.00 0.00 4.40
573 577 1.535028 CACGAAACTTGCCATAGTGCA 59.465 47.619 0.00 0.00 40.07 4.57
575 579 2.031157 ACGAAACTTGCCATAGTGCAAC 60.031 45.455 0.00 0.00 45.77 4.17
576 580 2.031245 CGAAACTTGCCATAGTGCAACA 60.031 45.455 0.00 0.00 45.77 3.33
577 581 3.308530 GAAACTTGCCATAGTGCAACAC 58.691 45.455 0.00 0.00 45.77 3.32
578 582 1.979855 ACTTGCCATAGTGCAACACA 58.020 45.000 0.00 0.00 45.77 3.72
579 583 1.881973 ACTTGCCATAGTGCAACACAG 59.118 47.619 0.00 0.00 45.77 3.66
580 584 1.200716 CTTGCCATAGTGCAACACAGG 59.799 52.381 0.00 0.62 45.77 4.00
581 585 0.399833 TGCCATAGTGCAACACAGGA 59.600 50.000 0.00 0.00 41.43 3.86
582 586 1.089920 GCCATAGTGCAACACAGGAG 58.910 55.000 0.00 0.00 41.43 3.69
583 587 1.611673 GCCATAGTGCAACACAGGAGT 60.612 52.381 0.00 0.00 41.43 3.85
597 601 5.980698 CACAGGAGTGCATATGTCTTAAG 57.019 43.478 4.29 0.00 39.21 1.85
598 602 4.813161 CACAGGAGTGCATATGTCTTAAGG 59.187 45.833 4.29 0.00 39.21 2.69
599 603 4.716784 ACAGGAGTGCATATGTCTTAAGGA 59.283 41.667 4.29 0.00 0.00 3.36
602 606 5.843421 AGGAGTGCATATGTCTTAAGGATCT 59.157 40.000 4.29 0.00 0.00 2.75
605 609 6.998802 AGTGCATATGTCTTAAGGATCTACC 58.001 40.000 4.29 0.00 39.35 3.18
608 612 7.880195 GTGCATATGTCTTAAGGATCTACCAAT 59.120 37.037 4.29 0.00 42.04 3.16
615 619 7.092891 TGTCTTAAGGATCTACCAATGACATGT 60.093 37.037 0.00 0.00 42.04 3.21
638 642 1.067364 TGCGTTTTAGAGTGTCCGTGA 59.933 47.619 0.00 0.00 0.00 4.35
641 645 3.922240 GCGTTTTAGAGTGTCCGTGATTA 59.078 43.478 0.00 0.00 0.00 1.75
642 646 4.386652 GCGTTTTAGAGTGTCCGTGATTAA 59.613 41.667 0.00 0.00 0.00 1.40
653 657 4.184629 GTCCGTGATTAACAGAGAATGCT 58.815 43.478 0.00 0.00 0.00 3.79
655 659 4.870426 TCCGTGATTAACAGAGAATGCTTC 59.130 41.667 0.00 0.00 0.00 3.86
675 679 2.238646 TCGCCAACCTCCATAGAAACAT 59.761 45.455 0.00 0.00 0.00 2.71
707 711 4.645535 TGATGCCATGCCTATCTTTAGTC 58.354 43.478 0.00 0.00 0.00 2.59
747 751 9.476761 GTTTGAAAAATCTGTGTGAATCAAAAC 57.523 29.630 0.00 0.00 0.00 2.43
751 755 5.458041 AATCTGTGTGAATCAAAACCAGG 57.542 39.130 0.00 0.00 0.00 4.45
759 763 5.835819 TGTGAATCAAAACCAGGTCCAATTA 59.164 36.000 0.00 0.00 0.00 1.40
760 764 6.496565 TGTGAATCAAAACCAGGTCCAATTAT 59.503 34.615 0.00 0.00 0.00 1.28
761 765 7.035612 GTGAATCAAAACCAGGTCCAATTATC 58.964 38.462 0.00 0.00 0.00 1.75
762 766 6.723515 TGAATCAAAACCAGGTCCAATTATCA 59.276 34.615 0.00 0.00 0.00 2.15
763 767 5.975693 TCAAAACCAGGTCCAATTATCAC 57.024 39.130 0.00 0.00 0.00 3.06
764 768 5.389520 TCAAAACCAGGTCCAATTATCACA 58.610 37.500 0.00 0.00 0.00 3.58
842 2268 5.355596 TGTTTGAACCAAAATCATCACCAC 58.644 37.500 0.00 0.00 35.03 4.16
860 2286 2.103736 GCGTCCGGGCTGTACTAC 59.896 66.667 3.66 0.00 0.00 2.73
870 2296 1.337387 GGCTGTACTACCAGATCCGAC 59.663 57.143 0.00 0.00 34.23 4.79
876 2302 2.351336 CTACCAGATCCGACGGCCAC 62.351 65.000 9.66 2.80 0.00 5.01
963 2392 1.075050 AGAGTAGAACCCACGGACTCA 59.925 52.381 0.00 0.00 39.20 3.41
1057 2525 3.636231 CCTCCACCGCCTTGTCCA 61.636 66.667 0.00 0.00 0.00 4.02
1058 2526 2.358737 CTCCACCGCCTTGTCCAC 60.359 66.667 0.00 0.00 0.00 4.02
1089 2557 2.726351 CCTCTCCTCCACCGCTTCC 61.726 68.421 0.00 0.00 0.00 3.46
1090 2558 2.683933 TCTCCTCCACCGCTTCCC 60.684 66.667 0.00 0.00 0.00 3.97
1127 2595 3.977244 CAACACCAACAGCCCCGC 61.977 66.667 0.00 0.00 0.00 6.13
1199 2667 2.037208 CCCGGCAAAGAACCCCAT 59.963 61.111 0.00 0.00 0.00 4.00
1723 3191 4.537688 AGATGATGAAGAAGAAGGGGTTCA 59.462 41.667 0.00 0.00 33.61 3.18
1724 3192 4.021102 TGATGAAGAAGAAGGGGTTCAC 57.979 45.455 0.00 0.00 31.94 3.18
1778 3246 2.361104 GCGGGGGCATGTCTTCAA 60.361 61.111 0.00 0.00 0.00 2.69
1818 3286 7.118723 TGCTCTTTGGAAAGTGATAATGGTAT 58.881 34.615 5.57 0.00 37.31 2.73
1834 3307 6.398234 AATGGTATGCACACTGTTTTGTTA 57.602 33.333 0.00 0.00 0.00 2.41
1840 3313 9.716507 GGTATGCACACTGTTTTGTTAATATAG 57.283 33.333 0.00 0.00 0.00 1.31
1841 3314 9.716507 GTATGCACACTGTTTTGTTAATATAGG 57.283 33.333 0.00 0.00 0.00 2.57
1842 3315 7.987750 TGCACACTGTTTTGTTAATATAGGA 57.012 32.000 0.00 0.00 0.00 2.94
1843 3316 7.812648 TGCACACTGTTTTGTTAATATAGGAC 58.187 34.615 0.00 0.00 0.00 3.85
1880 3357 4.927422 CCAATTGTTGGTTCGTAACTTGT 58.073 39.130 4.43 0.00 45.93 3.16
1932 3416 0.663153 GTTGTCTGTTGCACAGGACC 59.337 55.000 13.87 0.00 45.94 4.46
2002 3486 7.626446 AGTGTTTGAAGTTTGTTGTGTTTTTC 58.374 30.769 0.00 0.00 0.00 2.29
2003 3487 7.494298 AGTGTTTGAAGTTTGTTGTGTTTTTCT 59.506 29.630 0.00 0.00 0.00 2.52
2070 3554 9.919416 TGAAACTGATTCCCATTAATCATAGAA 57.081 29.630 0.00 0.00 43.16 2.10
2094 3604 9.347934 GAATCGTAGTGATGATAGTAATTCAGG 57.652 37.037 0.00 0.00 37.39 3.86
2156 3666 7.362056 GCTCTGAACTAGCATTGTTTTATCCAA 60.362 37.037 0.00 0.00 39.83 3.53
2238 3752 7.384932 CACTATCATGATCTTTATGGTTACGCA 59.615 37.037 12.53 0.00 0.00 5.24
2249 3763 6.745159 TTATGGTTACGCATTTTGAAGCTA 57.255 33.333 0.00 0.00 0.00 3.32
2305 3823 8.690203 TGGTGAAGAAGTATCTGATTCAAAAA 57.310 30.769 0.00 0.00 35.59 1.94
2336 3854 5.319453 ACAAAGATTTCATGCTTCCTCTCA 58.681 37.500 0.00 0.00 0.00 3.27
2337 3855 5.771666 ACAAAGATTTCATGCTTCCTCTCAA 59.228 36.000 0.00 0.00 0.00 3.02
2394 3913 6.594159 ACTGGATTTATCTTTGTTCTGTACCG 59.406 38.462 0.00 0.00 0.00 4.02
2452 3971 6.590292 GTGGTAATATATTGAGGGTGACATCG 59.410 42.308 8.28 0.00 46.19 3.84
2539 4070 3.120889 CGCGTGATGGTATGCTGATAAAG 60.121 47.826 0.00 0.00 0.00 1.85
2544 4075 6.481976 CGTGATGGTATGCTGATAAAGGTTTA 59.518 38.462 0.00 0.00 0.00 2.01
2598 4129 9.130661 TGTTATCATGGTAATATTTGACAAGGG 57.869 33.333 0.86 0.00 0.00 3.95
2606 4137 8.783903 TGGTAATATTTGACAAGGGGTAATAGT 58.216 33.333 0.00 0.00 0.00 2.12
2663 4195 4.634443 ACCCTTGTATTTTACTTGCTAGCG 59.366 41.667 10.77 0.00 0.00 4.26
2669 4201 4.696899 ATTTTACTTGCTAGCGTTTCCC 57.303 40.909 10.77 0.00 0.00 3.97
2686 4218 6.400568 CGTTTCCCTTTTACTCTGTATACCA 58.599 40.000 0.00 0.00 0.00 3.25
2712 4259 2.437359 ACAGCCATGCGGAAGAGC 60.437 61.111 0.00 0.00 37.71 4.09
2785 4338 1.556911 ACCATCCCAGTCTTAGCACTG 59.443 52.381 5.31 5.31 43.13 3.66
2798 4351 7.010552 CAGTCTTAGCACTGTACATTATGGAAC 59.989 40.741 0.00 0.00 39.26 3.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
238 242 1.950909 CCGGAAGCAAACACCTACAAA 59.049 47.619 0.00 0.00 0.00 2.83
274 278 1.676746 TTGTAGCTCCGCTATCGAGT 58.323 50.000 0.00 0.00 43.30 4.18
310 314 0.682852 CGTCCACCACCAAGTCCTTA 59.317 55.000 0.00 0.00 0.00 2.69
491 495 4.263462 TGACAAACAAGAGCCCATGATAGT 60.263 41.667 0.00 0.00 0.00 2.12
504 508 5.049818 GTGGAGAAGATGACTGACAAACAAG 60.050 44.000 0.00 0.00 0.00 3.16
506 510 4.380531 GTGGAGAAGATGACTGACAAACA 58.619 43.478 0.00 0.00 0.00 2.83
507 511 3.748568 GGTGGAGAAGATGACTGACAAAC 59.251 47.826 0.00 0.00 0.00 2.93
508 512 3.390967 TGGTGGAGAAGATGACTGACAAA 59.609 43.478 0.00 0.00 0.00 2.83
509 513 2.972021 TGGTGGAGAAGATGACTGACAA 59.028 45.455 0.00 0.00 0.00 3.18
510 514 2.564504 CTGGTGGAGAAGATGACTGACA 59.435 50.000 0.00 0.00 0.00 3.58
511 515 2.828520 TCTGGTGGAGAAGATGACTGAC 59.171 50.000 0.00 0.00 0.00 3.51
512 516 3.175438 TCTGGTGGAGAAGATGACTGA 57.825 47.619 0.00 0.00 0.00 3.41
513 517 4.081254 TGAATCTGGTGGAGAAGATGACTG 60.081 45.833 0.00 0.00 33.42 3.51
514 518 4.081198 GTGAATCTGGTGGAGAAGATGACT 60.081 45.833 0.00 0.00 33.42 3.41
515 519 4.187694 GTGAATCTGGTGGAGAAGATGAC 58.812 47.826 0.00 0.00 33.42 3.06
516 520 3.840078 TGTGAATCTGGTGGAGAAGATGA 59.160 43.478 0.00 0.00 33.42 2.92
517 521 4.190001 CTGTGAATCTGGTGGAGAAGATG 58.810 47.826 0.00 0.00 33.42 2.90
518 522 3.370315 GCTGTGAATCTGGTGGAGAAGAT 60.370 47.826 0.00 0.00 33.12 2.40
519 523 2.027745 GCTGTGAATCTGGTGGAGAAGA 60.028 50.000 0.00 0.00 33.12 2.87
520 524 2.354259 GCTGTGAATCTGGTGGAGAAG 58.646 52.381 0.00 0.00 33.12 2.85
521 525 1.338105 CGCTGTGAATCTGGTGGAGAA 60.338 52.381 0.00 0.00 33.12 2.87
522 526 0.247460 CGCTGTGAATCTGGTGGAGA 59.753 55.000 0.00 0.00 34.25 3.71
523 527 0.742281 CCGCTGTGAATCTGGTGGAG 60.742 60.000 0.00 0.00 0.00 3.86
524 528 1.191489 TCCGCTGTGAATCTGGTGGA 61.191 55.000 0.00 0.00 36.22 4.02
525 529 0.107508 ATCCGCTGTGAATCTGGTGG 60.108 55.000 0.00 0.00 0.00 4.61
526 530 2.101415 TCTATCCGCTGTGAATCTGGTG 59.899 50.000 0.00 0.00 0.00 4.17
527 531 2.363680 CTCTATCCGCTGTGAATCTGGT 59.636 50.000 0.00 0.00 0.00 4.00
528 532 2.865670 GCTCTATCCGCTGTGAATCTGG 60.866 54.545 0.00 0.00 0.00 3.86
529 533 2.402305 GCTCTATCCGCTGTGAATCTG 58.598 52.381 0.00 0.00 0.00 2.90
530 534 1.342819 GGCTCTATCCGCTGTGAATCT 59.657 52.381 0.00 0.00 0.00 2.40
531 535 1.342819 AGGCTCTATCCGCTGTGAATC 59.657 52.381 0.00 0.00 0.00 2.52
532 536 1.418334 AGGCTCTATCCGCTGTGAAT 58.582 50.000 0.00 0.00 0.00 2.57
533 537 1.681793 GTAGGCTCTATCCGCTGTGAA 59.318 52.381 0.00 0.00 0.00 3.18
534 538 1.319541 GTAGGCTCTATCCGCTGTGA 58.680 55.000 0.00 0.00 0.00 3.58
535 539 1.032794 TGTAGGCTCTATCCGCTGTG 58.967 55.000 0.00 0.00 0.00 3.66
536 540 1.033574 GTGTAGGCTCTATCCGCTGT 58.966 55.000 0.00 0.00 0.00 4.40
537 541 0.039978 CGTGTAGGCTCTATCCGCTG 60.040 60.000 0.00 0.00 0.00 5.18
538 542 0.179026 TCGTGTAGGCTCTATCCGCT 60.179 55.000 0.00 0.00 0.00 5.52
539 543 0.666913 TTCGTGTAGGCTCTATCCGC 59.333 55.000 0.00 0.00 0.00 5.54
540 544 2.358267 AGTTTCGTGTAGGCTCTATCCG 59.642 50.000 0.00 0.00 0.00 4.18
541 545 4.113354 CAAGTTTCGTGTAGGCTCTATCC 58.887 47.826 0.00 0.00 0.00 2.59
542 546 3.552294 GCAAGTTTCGTGTAGGCTCTATC 59.448 47.826 0.00 0.00 0.00 2.08
543 547 3.522553 GCAAGTTTCGTGTAGGCTCTAT 58.477 45.455 0.00 0.00 0.00 1.98
544 548 2.353406 GGCAAGTTTCGTGTAGGCTCTA 60.353 50.000 0.00 0.00 0.00 2.43
545 549 1.608283 GGCAAGTTTCGTGTAGGCTCT 60.608 52.381 0.00 0.00 0.00 4.09
546 550 0.796927 GGCAAGTTTCGTGTAGGCTC 59.203 55.000 0.00 0.00 0.00 4.70
547 551 0.107831 TGGCAAGTTTCGTGTAGGCT 59.892 50.000 0.00 0.00 0.00 4.58
548 552 1.165270 ATGGCAAGTTTCGTGTAGGC 58.835 50.000 0.00 0.00 0.00 3.93
549 553 3.370978 CACTATGGCAAGTTTCGTGTAGG 59.629 47.826 0.00 0.00 0.00 3.18
550 554 3.181520 GCACTATGGCAAGTTTCGTGTAG 60.182 47.826 0.00 0.00 0.00 2.74
551 555 2.739913 GCACTATGGCAAGTTTCGTGTA 59.260 45.455 0.00 0.00 0.00 2.90
552 556 1.535462 GCACTATGGCAAGTTTCGTGT 59.465 47.619 0.00 0.00 0.00 4.49
553 557 1.535028 TGCACTATGGCAAGTTTCGTG 59.465 47.619 0.00 0.00 41.65 4.35
554 558 1.890876 TGCACTATGGCAAGTTTCGT 58.109 45.000 0.00 0.00 41.65 3.85
562 566 0.399833 TCCTGTGTTGCACTATGGCA 59.600 50.000 0.00 0.00 43.19 4.92
563 567 1.089920 CTCCTGTGTTGCACTATGGC 58.910 55.000 0.00 0.00 35.11 4.40
564 568 2.079158 CACTCCTGTGTTGCACTATGG 58.921 52.381 0.00 1.64 39.24 2.74
565 569 1.466167 GCACTCCTGTGTTGCACTATG 59.534 52.381 0.00 0.00 45.44 2.23
566 570 1.072173 TGCACTCCTGTGTTGCACTAT 59.928 47.619 0.00 0.00 45.44 2.12
567 571 0.467804 TGCACTCCTGTGTTGCACTA 59.532 50.000 0.00 0.00 45.44 2.74
568 572 0.179009 ATGCACTCCTGTGTTGCACT 60.179 50.000 0.00 0.00 45.44 4.40
569 573 1.522668 TATGCACTCCTGTGTTGCAC 58.477 50.000 0.00 0.00 45.44 4.57
570 574 2.086094 CATATGCACTCCTGTGTTGCA 58.914 47.619 0.00 0.00 45.44 4.08
571 575 2.086869 ACATATGCACTCCTGTGTTGC 58.913 47.619 1.58 0.00 45.44 4.17
572 576 3.603532 AGACATATGCACTCCTGTGTTG 58.396 45.455 1.58 0.00 45.44 3.33
573 577 3.988976 AGACATATGCACTCCTGTGTT 57.011 42.857 1.58 0.00 45.44 3.32
574 578 3.988976 AAGACATATGCACTCCTGTGT 57.011 42.857 1.58 0.00 45.44 3.72
575 579 4.813161 CCTTAAGACATATGCACTCCTGTG 59.187 45.833 3.36 0.00 46.37 3.66
576 580 4.716784 TCCTTAAGACATATGCACTCCTGT 59.283 41.667 3.36 0.00 0.00 4.00
577 581 5.282055 TCCTTAAGACATATGCACTCCTG 57.718 43.478 3.36 0.00 0.00 3.86
578 582 5.843421 AGATCCTTAAGACATATGCACTCCT 59.157 40.000 3.36 0.00 0.00 3.69
579 583 6.107901 AGATCCTTAAGACATATGCACTCC 57.892 41.667 3.36 0.00 0.00 3.85
580 584 7.093992 GGTAGATCCTTAAGACATATGCACTC 58.906 42.308 3.36 0.00 0.00 3.51
581 585 6.554982 TGGTAGATCCTTAAGACATATGCACT 59.445 38.462 3.36 0.00 37.07 4.40
582 586 6.759272 TGGTAGATCCTTAAGACATATGCAC 58.241 40.000 3.36 0.00 37.07 4.57
583 587 6.994421 TGGTAGATCCTTAAGACATATGCA 57.006 37.500 3.36 0.00 37.07 3.96
584 588 8.097038 TCATTGGTAGATCCTTAAGACATATGC 58.903 37.037 3.36 0.00 37.07 3.14
585 589 9.429359 GTCATTGGTAGATCCTTAAGACATATG 57.571 37.037 3.36 0.00 37.07 1.78
586 590 9.159254 TGTCATTGGTAGATCCTTAAGACATAT 57.841 33.333 3.36 0.00 37.07 1.78
587 591 8.547481 TGTCATTGGTAGATCCTTAAGACATA 57.453 34.615 3.36 0.00 37.07 2.29
588 592 7.437713 TGTCATTGGTAGATCCTTAAGACAT 57.562 36.000 3.36 0.00 37.07 3.06
589 593 6.867519 TGTCATTGGTAGATCCTTAAGACA 57.132 37.500 3.36 0.00 37.07 3.41
590 594 7.275920 ACATGTCATTGGTAGATCCTTAAGAC 58.724 38.462 3.36 0.00 37.07 3.01
591 595 7.437713 ACATGTCATTGGTAGATCCTTAAGA 57.562 36.000 3.36 0.00 37.07 2.10
592 596 8.511604 AAACATGTCATTGGTAGATCCTTAAG 57.488 34.615 0.00 0.00 37.07 1.85
593 597 8.739039 CAAAACATGTCATTGGTAGATCCTTAA 58.261 33.333 13.76 0.00 37.07 1.85
594 598 7.148086 GCAAAACATGTCATTGGTAGATCCTTA 60.148 37.037 19.92 0.00 37.07 2.69
595 599 6.350445 GCAAAACATGTCATTGGTAGATCCTT 60.350 38.462 19.92 0.00 37.07 3.36
596 600 5.126061 GCAAAACATGTCATTGGTAGATCCT 59.874 40.000 19.92 0.00 37.07 3.24
597 601 5.343249 GCAAAACATGTCATTGGTAGATCC 58.657 41.667 19.92 4.30 0.00 3.36
598 602 5.030295 CGCAAAACATGTCATTGGTAGATC 58.970 41.667 19.92 6.79 0.00 2.75
599 603 4.458989 ACGCAAAACATGTCATTGGTAGAT 59.541 37.500 19.92 0.00 0.00 1.98
602 606 4.576216 AACGCAAAACATGTCATTGGTA 57.424 36.364 19.92 0.00 0.00 3.25
605 609 6.417635 ACTCTAAAACGCAAAACATGTCATTG 59.582 34.615 16.17 16.17 0.00 2.82
608 612 5.163703 ACACTCTAAAACGCAAAACATGTCA 60.164 36.000 0.00 0.00 0.00 3.58
615 619 2.937799 ACGGACACTCTAAAACGCAAAA 59.062 40.909 0.00 0.00 0.00 2.44
653 657 2.039216 TGTTTCTATGGAGGTTGGCGAA 59.961 45.455 0.00 0.00 0.00 4.70
655 659 2.107950 TGTTTCTATGGAGGTTGGCG 57.892 50.000 0.00 0.00 0.00 5.69
675 679 2.691526 GGCATGGCATCAAAGATCAAGA 59.308 45.455 15.47 0.00 0.00 3.02
747 751 3.701040 CCCTTTGTGATAATTGGACCTGG 59.299 47.826 0.00 0.00 0.00 4.45
751 755 3.699538 GACCCCCTTTGTGATAATTGGAC 59.300 47.826 0.00 0.00 0.00 4.02
759 763 0.036306 GTGTCGACCCCCTTTGTGAT 59.964 55.000 14.12 0.00 0.00 3.06
760 764 1.338890 TGTGTCGACCCCCTTTGTGA 61.339 55.000 14.12 0.00 0.00 3.58
761 765 1.147376 TGTGTCGACCCCCTTTGTG 59.853 57.895 14.12 0.00 0.00 3.33
762 766 1.147600 GTGTGTCGACCCCCTTTGT 59.852 57.895 14.12 0.00 0.00 2.83
763 767 1.959226 CGTGTGTCGACCCCCTTTG 60.959 63.158 14.12 0.00 42.86 2.77
764 768 2.424302 CGTGTGTCGACCCCCTTT 59.576 61.111 14.12 0.00 42.86 3.11
842 2268 3.511595 TAGTACAGCCCGGACGCG 61.512 66.667 0.73 3.53 0.00 6.01
860 2286 4.530857 GGTGGCCGTCGGATCTGG 62.531 72.222 17.49 0.00 0.00 3.86
876 2302 2.807631 GATGGCAAGCAAGCACACGG 62.808 60.000 0.00 0.00 35.83 4.94
902 2328 1.831736 ACCGATCCTTGGACTTGTAGG 59.168 52.381 0.00 0.00 0.00 3.18
1039 2507 4.410400 GGACAAGGCGGTGGAGGG 62.410 72.222 0.00 0.00 0.00 4.30
1116 2584 4.351054 AAGGAGGCGGGGCTGTTG 62.351 66.667 0.00 0.00 0.00 3.33
1127 2595 1.677966 TCGGACCAGTCGAAGGAGG 60.678 63.158 11.80 2.47 33.42 4.30
1176 2644 2.362375 TTCTTTGCCGGGGATGCC 60.362 61.111 2.18 0.00 0.00 4.40
1440 2908 2.822255 GGGCCAGCATTCGCGTAA 60.822 61.111 4.39 0.00 45.49 3.18
1518 2986 2.329614 GGCCATGGTGTACGCGTTT 61.330 57.895 20.78 0.00 0.00 3.60
1575 3043 4.569214 AGGTACTTGCCTGCCTCT 57.431 55.556 0.00 0.00 37.50 3.69
1723 3191 2.915659 TGCCTCCTCGTCCAACGT 60.916 61.111 0.00 0.00 43.14 3.99
1724 3192 2.125912 CTGCCTCCTCGTCCAACG 60.126 66.667 0.00 0.00 44.19 4.10
1778 3246 0.326264 GAGCAGGTTCATGACACCCT 59.674 55.000 18.00 11.22 34.44 4.34
1818 3286 7.445707 TGTCCTATATTAACAAAACAGTGTGCA 59.554 33.333 0.00 0.00 0.00 4.57
1834 3307 7.559533 TGGTTATGCAACAACATGTCCTATATT 59.440 33.333 14.39 0.00 36.29 1.28
1840 3313 3.932545 TGGTTATGCAACAACATGTCC 57.067 42.857 14.39 0.00 36.29 4.02
1841 3314 5.695816 ACAATTGGTTATGCAACAACATGTC 59.304 36.000 10.83 0.00 36.29 3.06
1842 3315 5.609423 ACAATTGGTTATGCAACAACATGT 58.391 33.333 10.83 0.00 36.29 3.21
1843 3316 6.364261 CAACAATTGGTTATGCAACAACATG 58.636 36.000 10.83 11.07 37.72 3.21
1871 3348 6.387465 TCAAGTAGAATCCTGACAAGTTACG 58.613 40.000 0.00 0.00 0.00 3.18
1876 3353 6.813649 TCGATTTCAAGTAGAATCCTGACAAG 59.186 38.462 0.00 0.00 35.83 3.16
1880 3357 7.824289 ACATTTCGATTTCAAGTAGAATCCTGA 59.176 33.333 0.00 0.00 35.83 3.86
1932 3416 2.434336 TGGAAGACAGGATATCAACCCG 59.566 50.000 4.83 0.00 0.00 5.28
2070 3554 8.410673 ACCTGAATTACTATCATCACTACGAT 57.589 34.615 0.00 0.00 33.27 3.73
2094 3604 7.377766 TCTTGCACAATACCTATTCTGAAAC 57.622 36.000 0.00 0.00 0.00 2.78
2238 3752 3.258872 TGCTGCCACAATAGCTTCAAAAT 59.741 39.130 0.00 0.00 40.52 1.82
2249 3763 1.663739 CTGCTGTTGCTGCCACAAT 59.336 52.632 7.99 0.00 40.48 2.71
2305 3823 9.374838 GGAAGCATGAAATCTTTGTATTTGAAT 57.625 29.630 0.00 0.00 0.00 2.57
2326 3844 7.442364 TGCTATGTTTATATGTTGAGAGGAAGC 59.558 37.037 0.00 0.00 0.00 3.86
2370 3888 6.594159 ACGGTACAGAACAAAGATAAATCCAG 59.406 38.462 0.00 0.00 0.00 3.86
2394 3913 9.455847 GAAATAAGGCATGAATGAAGATAACAC 57.544 33.333 0.00 0.00 0.00 3.32
2452 3971 9.741647 GATTTGATTATCAAGGATTCTGGTTTC 57.258 33.333 7.72 0.00 37.70 2.78
2486 4017 1.893801 CTCCGGTATATCCAGTGGGTC 59.106 57.143 9.92 0.00 35.57 4.46
2517 4048 2.064573 TATCAGCATACCATCACGCG 57.935 50.000 3.53 3.53 0.00 6.01
2598 4129 9.425577 GACTATGAGGCTATGAAAACTATTACC 57.574 37.037 0.00 0.00 0.00 2.85
2606 4137 7.618019 ACCTATGACTATGAGGCTATGAAAA 57.382 36.000 0.00 0.00 33.28 2.29
2663 4195 8.625786 TTTGGTATACAGAGTAAAAGGGAAAC 57.374 34.615 5.01 0.00 0.00 2.78
2669 4201 9.268268 TGTTCACTTTGGTATACAGAGTAAAAG 57.732 33.333 5.01 6.94 42.13 2.27
2686 4218 0.311790 CGCATGGCTGTGTTCACTTT 59.688 50.000 4.59 0.00 0.00 2.66
2712 4259 1.279271 AGGGGGAGAATCGTGAAAGTG 59.721 52.381 0.00 0.00 34.37 3.16
2716 4263 3.654273 AGATTAGGGGGAGAATCGTGAA 58.346 45.455 0.00 0.00 37.19 3.18
2774 4327 7.042335 AGTTCCATAATGTACAGTGCTAAGAC 58.958 38.462 5.98 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.