Multiple sequence alignment - TraesCS3D01G310900

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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 TraesCS3D01G310900 chr3D 100.000 2858 0 0 1 2858 425153271 425150414 0.000000e+00 5278.0
1 TraesCS3D01G310900 chr3D 96.325 517 13 5 1 512 214959193 214959708 0.000000e+00 845.0
2 TraesCS3D01G310900 chr3D 90.756 119 9 2 485 602 214959613 214959730 1.060000e-34 158.0
3 TraesCS3D01G310900 chr3D 100.000 40 0 0 2430 2469 565081507 565081546 1.100000e-09 75.0
4 TraesCS3D01G310900 chr3B 90.505 1843 110 20 622 2431 555245392 555243582 0.000000e+00 2374.0
5 TraesCS3D01G310900 chr3B 90.825 1722 107 25 740 2431 555156373 555154673 0.000000e+00 2257.0
6 TraesCS3D01G310900 chr3B 100.000 41 0 0 704 744 555156428 555156388 3.050000e-10 76.8
7 TraesCS3D01G310900 chr3A 93.589 1591 56 14 603 2185 562913982 562915534 0.000000e+00 2331.0
8 TraesCS3D01G310900 chr3A 96.943 1374 36 5 1362 2733 563394892 563396261 0.000000e+00 2300.0
9 TraesCS3D01G310900 chr3A 90.377 769 29 10 603 1367 563388715 563389442 0.000000e+00 968.0
10 TraesCS3D01G310900 chr3A 96.705 516 13 3 1 512 660861320 660860805 0.000000e+00 856.0
11 TraesCS3D01G310900 chr3A 95.918 98 4 0 506 603 749289022 749289119 2.950000e-35 159.0
12 TraesCS3D01G310900 chr6D 97.093 516 11 3 1 512 464214235 464213720 0.000000e+00 867.0
13 TraesCS3D01G310900 chr6D 97.938 97 2 0 506 602 464213794 464213698 4.900000e-38 169.0
14 TraesCS3D01G310900 chr6D 95.960 99 4 0 506 604 86664470 86664568 8.190000e-36 161.0
15 TraesCS3D01G310900 chr6D 95.960 99 4 0 506 604 232765830 232765928 8.190000e-36 161.0
16 TraesCS3D01G310900 chr7D 96.512 516 14 3 1 512 114467802 114468317 0.000000e+00 850.0
17 TraesCS3D01G310900 chr7D 96.325 517 15 3 1 513 151540598 151541114 0.000000e+00 846.0
18 TraesCS3D01G310900 chr7D 77.400 500 107 6 1598 2094 607109873 607110369 2.790000e-75 292.0
19 TraesCS3D01G310900 chr5D 96.505 515 15 2 1 512 404194280 404193766 0.000000e+00 848.0
20 TraesCS3D01G310900 chr2D 96.132 517 14 5 1 512 70391409 70391924 0.000000e+00 839.0
21 TraesCS3D01G310900 chr2D 95.938 517 15 5 1 512 623949803 623950318 0.000000e+00 833.0
22 TraesCS3D01G310900 chr2D 76.695 236 50 3 1039 1270 621841436 621841670 2.990000e-25 126.0
23 TraesCS3D01G310900 chr1A 95.938 517 16 3 1 512 579858707 579858191 0.000000e+00 833.0
24 TraesCS3D01G310900 chr1A 95.960 99 4 0 506 604 579858265 579858167 8.190000e-36 161.0
25 TraesCS3D01G310900 chr7B 78.302 1166 228 20 1023 2171 690904474 690905631 0.000000e+00 728.0
26 TraesCS3D01G310900 chr7B 79.298 570 104 8 1522 2082 692283389 692282825 1.240000e-103 387.0
27 TraesCS3D01G310900 chr7B 78.114 562 112 7 1547 2099 692339888 692339329 2.110000e-91 346.0
28 TraesCS3D01G310900 chr7B 73.837 860 191 25 1040 1886 691276783 691275945 7.690000e-81 311.0
29 TraesCS3D01G310900 chr7A 76.571 1225 245 27 1023 2218 698729469 698730680 4.020000e-178 634.0
30 TraesCS3D01G310900 chr7A 77.805 820 163 8 1425 2229 699066863 699067678 3.310000e-134 488.0
31 TraesCS3D01G310900 chr1D 96.000 100 4 0 506 605 464934642 464934543 2.280000e-36 163.0
32 TraesCS3D01G310900 chr2B 95.918 98 4 0 506 603 731216728 731216631 2.950000e-35 159.0
33 TraesCS3D01G310900 chr4D 92.593 108 8 0 506 613 414330471 414330578 3.810000e-34 156.0


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 TraesCS3D01G310900 chr3D 425150414 425153271 2857 True 5278.0 5278 100.0000 1 2858 1 chr3D.!!$R1 2857
1 TraesCS3D01G310900 chr3D 214959193 214959730 537 False 501.5 845 93.5405 1 602 2 chr3D.!!$F2 601
2 TraesCS3D01G310900 chr3B 555243582 555245392 1810 True 2374.0 2374 90.5050 622 2431 1 chr3B.!!$R1 1809
3 TraesCS3D01G310900 chr3B 555154673 555156428 1755 True 1166.9 2257 95.4125 704 2431 2 chr3B.!!$R2 1727
4 TraesCS3D01G310900 chr3A 562913982 562915534 1552 False 2331.0 2331 93.5890 603 2185 1 chr3A.!!$F1 1582
5 TraesCS3D01G310900 chr3A 563394892 563396261 1369 False 2300.0 2300 96.9430 1362 2733 1 chr3A.!!$F3 1371
6 TraesCS3D01G310900 chr3A 563388715 563389442 727 False 968.0 968 90.3770 603 1367 1 chr3A.!!$F2 764
7 TraesCS3D01G310900 chr3A 660860805 660861320 515 True 856.0 856 96.7050 1 512 1 chr3A.!!$R1 511
8 TraesCS3D01G310900 chr6D 464213698 464214235 537 True 518.0 867 97.5155 1 602 2 chr6D.!!$R1 601
9 TraesCS3D01G310900 chr7D 114467802 114468317 515 False 850.0 850 96.5120 1 512 1 chr7D.!!$F1 511
10 TraesCS3D01G310900 chr7D 151540598 151541114 516 False 846.0 846 96.3250 1 513 1 chr7D.!!$F2 512
11 TraesCS3D01G310900 chr5D 404193766 404194280 514 True 848.0 848 96.5050 1 512 1 chr5D.!!$R1 511
12 TraesCS3D01G310900 chr2D 70391409 70391924 515 False 839.0 839 96.1320 1 512 1 chr2D.!!$F1 511
13 TraesCS3D01G310900 chr2D 623949803 623950318 515 False 833.0 833 95.9380 1 512 1 chr2D.!!$F3 511
14 TraesCS3D01G310900 chr1A 579858167 579858707 540 True 497.0 833 95.9490 1 604 2 chr1A.!!$R1 603
15 TraesCS3D01G310900 chr7B 690904474 690905631 1157 False 728.0 728 78.3020 1023 2171 1 chr7B.!!$F1 1148
16 TraesCS3D01G310900 chr7B 692282825 692283389 564 True 387.0 387 79.2980 1522 2082 1 chr7B.!!$R2 560
17 TraesCS3D01G310900 chr7B 692339329 692339888 559 True 346.0 346 78.1140 1547 2099 1 chr7B.!!$R3 552
18 TraesCS3D01G310900 chr7B 691275945 691276783 838 True 311.0 311 73.8370 1040 1886 1 chr7B.!!$R1 846
19 TraesCS3D01G310900 chr7A 698729469 698730680 1211 False 634.0 634 76.5710 1023 2218 1 chr7A.!!$F1 1195
20 TraesCS3D01G310900 chr7A 699066863 699067678 815 False 488.0 488 77.8050 1425 2229 1 chr7A.!!$F2 804

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
565 574 0.108585 ACAGAACGTGTGGGCAGATT 59.891 50.0 0.00 0.00 38.28 2.40 F
595 604 0.438445 CACACGTGTGGCAGTTATCG 59.562 55.0 35.65 10.61 42.10 2.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1654 1777 1.447314 GGCCGTAGAACTTCACCCG 60.447 63.158 0.0 0.0 0.0 5.28 R
2593 2755 2.353610 GCAATGCCTCTGTTGGGGG 61.354 63.158 0.0 0.0 0.0 5.40 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
66 68 2.108970 GCCTAGTGTTAGTAGGTGGCT 58.891 52.381 10.53 0.00 42.16 4.75
94 96 7.504403 TCCTAAAGTTTTGAAATCATGGCAAA 58.496 30.769 0.00 0.00 0.00 3.68
406 412 1.089978 TGTAAGAGGGACTGGGAGGA 58.910 55.000 0.00 0.00 41.55 3.71
411 417 1.988846 AGAGGGACTGGGAGGAAAAAG 59.011 52.381 0.00 0.00 41.55 2.27
460 469 2.698855 ACATACAGACATGTGGGCTC 57.301 50.000 1.15 0.00 40.79 4.70
513 522 3.625764 GCAGATTTCTTAACGCCCACATA 59.374 43.478 0.00 0.00 0.00 2.29
514 523 4.495844 GCAGATTTCTTAACGCCCACATAC 60.496 45.833 0.00 0.00 0.00 2.39
515 524 4.634004 CAGATTTCTTAACGCCCACATACA 59.366 41.667 0.00 0.00 0.00 2.29
516 525 4.876107 AGATTTCTTAACGCCCACATACAG 59.124 41.667 0.00 0.00 0.00 2.74
517 526 3.965379 TTCTTAACGCCCACATACAGA 57.035 42.857 0.00 0.00 0.00 3.41
518 527 3.241067 TCTTAACGCCCACATACAGAC 57.759 47.619 0.00 0.00 0.00 3.51
519 528 2.563620 TCTTAACGCCCACATACAGACA 59.436 45.455 0.00 0.00 0.00 3.41
520 529 3.196901 TCTTAACGCCCACATACAGACAT 59.803 43.478 0.00 0.00 0.00 3.06
521 530 1.737838 AACGCCCACATACAGACATG 58.262 50.000 0.00 0.00 0.00 3.21
522 531 0.613260 ACGCCCACATACAGACATGT 59.387 50.000 0.00 0.00 43.76 3.21
528 537 2.698855 ACATACAGACATGTGGGCTC 57.301 50.000 1.15 0.00 40.79 4.70
529 538 1.134699 ACATACAGACATGTGGGCTCG 60.135 52.381 1.15 0.00 40.79 5.03
530 539 1.134699 CATACAGACATGTGGGCTCGT 60.135 52.381 1.15 0.00 40.79 4.18
531 540 0.530744 TACAGACATGTGGGCTCGTC 59.469 55.000 1.15 0.00 40.79 4.20
532 541 1.448540 CAGACATGTGGGCTCGTCC 60.449 63.158 1.15 0.00 0.00 4.79
533 542 1.610673 AGACATGTGGGCTCGTCCT 60.611 57.895 1.15 0.00 34.39 3.85
534 543 1.153549 GACATGTGGGCTCGTCCTC 60.154 63.158 1.15 0.00 34.39 3.71
535 544 1.608717 GACATGTGGGCTCGTCCTCT 61.609 60.000 1.15 0.00 34.39 3.69
536 545 1.194781 ACATGTGGGCTCGTCCTCTT 61.195 55.000 0.00 0.00 34.39 2.85
537 546 0.824109 CATGTGGGCTCGTCCTCTTA 59.176 55.000 0.00 0.00 34.39 2.10
538 547 1.115467 ATGTGGGCTCGTCCTCTTAG 58.885 55.000 0.00 0.00 34.39 2.18
539 548 0.970937 TGTGGGCTCGTCCTCTTAGG 60.971 60.000 0.00 0.00 36.46 2.69
540 549 2.058595 TGGGCTCGTCCTCTTAGGC 61.059 63.158 0.00 0.00 34.61 3.93
541 550 2.058595 GGGCTCGTCCTCTTAGGCA 61.059 63.158 0.00 0.00 37.53 4.75
542 551 1.142097 GGCTCGTCCTCTTAGGCAC 59.858 63.158 0.00 0.00 34.61 5.01
543 552 1.142097 GCTCGTCCTCTTAGGCACC 59.858 63.158 0.00 0.00 34.61 5.01
544 553 1.605058 GCTCGTCCTCTTAGGCACCA 61.605 60.000 0.00 0.00 34.61 4.17
545 554 0.173708 CTCGTCCTCTTAGGCACCAC 59.826 60.000 0.00 0.00 34.61 4.16
546 555 0.541063 TCGTCCTCTTAGGCACCACA 60.541 55.000 0.00 0.00 34.61 4.17
547 556 0.389948 CGTCCTCTTAGGCACCACAC 60.390 60.000 0.00 0.00 34.61 3.82
548 557 0.685097 GTCCTCTTAGGCACCACACA 59.315 55.000 0.00 0.00 34.61 3.72
549 558 0.976641 TCCTCTTAGGCACCACACAG 59.023 55.000 0.00 0.00 34.61 3.66
550 559 0.976641 CCTCTTAGGCACCACACAGA 59.023 55.000 0.00 0.00 0.00 3.41
551 560 1.347707 CCTCTTAGGCACCACACAGAA 59.652 52.381 0.00 0.00 0.00 3.02
552 561 2.417719 CTCTTAGGCACCACACAGAAC 58.582 52.381 0.00 0.00 0.00 3.01
553 562 1.148310 CTTAGGCACCACACAGAACG 58.852 55.000 0.00 0.00 0.00 3.95
554 563 0.466543 TTAGGCACCACACAGAACGT 59.533 50.000 0.00 0.00 0.00 3.99
563 572 3.226242 ACAGAACGTGTGGGCAGA 58.774 55.556 0.00 0.00 38.28 4.26
564 573 1.754745 ACAGAACGTGTGGGCAGAT 59.245 52.632 0.00 0.00 38.28 2.90
565 574 0.108585 ACAGAACGTGTGGGCAGATT 59.891 50.000 0.00 0.00 38.28 2.40
566 575 1.238439 CAGAACGTGTGGGCAGATTT 58.762 50.000 0.00 0.00 0.00 2.17
567 576 1.197721 CAGAACGTGTGGGCAGATTTC 59.802 52.381 0.00 0.00 0.00 2.17
568 577 1.072331 AGAACGTGTGGGCAGATTTCT 59.928 47.619 0.00 0.00 0.00 2.52
569 578 1.880027 GAACGTGTGGGCAGATTTCTT 59.120 47.619 0.00 0.00 0.00 2.52
570 579 2.851263 ACGTGTGGGCAGATTTCTTA 57.149 45.000 0.00 0.00 0.00 2.10
571 580 3.134574 ACGTGTGGGCAGATTTCTTAA 57.865 42.857 0.00 0.00 0.00 1.85
572 581 2.812011 ACGTGTGGGCAGATTTCTTAAC 59.188 45.455 0.00 0.00 0.00 2.01
573 582 2.159707 CGTGTGGGCAGATTTCTTAACG 60.160 50.000 0.00 0.00 0.00 3.18
574 583 1.810151 TGTGGGCAGATTTCTTAACGC 59.190 47.619 0.00 0.00 0.00 4.84
575 584 1.132453 GTGGGCAGATTTCTTAACGCC 59.868 52.381 0.00 0.00 38.85 5.68
577 586 1.459450 GGCAGATTTCTTAACGCCCA 58.541 50.000 0.00 0.00 33.31 5.36
578 587 1.132453 GGCAGATTTCTTAACGCCCAC 59.868 52.381 0.00 0.00 33.31 4.61
579 588 1.810151 GCAGATTTCTTAACGCCCACA 59.190 47.619 0.00 0.00 0.00 4.17
580 589 2.414161 GCAGATTTCTTAACGCCCACAC 60.414 50.000 0.00 0.00 0.00 3.82
581 590 2.073816 AGATTTCTTAACGCCCACACG 58.926 47.619 0.00 0.00 39.50 4.49
595 604 0.438445 CACACGTGTGGCAGTTATCG 59.562 55.000 35.65 10.61 42.10 2.92
596 605 0.669318 ACACGTGTGGCAGTTATCGG 60.669 55.000 22.71 0.00 34.19 4.18
597 606 1.740296 ACGTGTGGCAGTTATCGGC 60.740 57.895 0.00 0.00 0.00 5.54
598 607 2.798501 CGTGTGGCAGTTATCGGCG 61.799 63.158 0.00 0.00 35.70 6.46
599 608 1.740296 GTGTGGCAGTTATCGGCGT 60.740 57.895 6.85 0.00 35.70 5.68
600 609 1.447140 TGTGGCAGTTATCGGCGTC 60.447 57.895 6.85 0.00 35.70 5.19
601 610 2.171725 GTGGCAGTTATCGGCGTCC 61.172 63.158 6.85 0.00 35.70 4.79
886 931 6.367422 CCTAACAGCTCAAACAAAACAAAACA 59.633 34.615 0.00 0.00 0.00 2.83
887 932 6.610741 AACAGCTCAAACAAAACAAAACAA 57.389 29.167 0.00 0.00 0.00 2.83
888 933 6.610741 ACAGCTCAAACAAAACAAAACAAA 57.389 29.167 0.00 0.00 0.00 2.83
889 934 7.020914 ACAGCTCAAACAAAACAAAACAAAA 57.979 28.000 0.00 0.00 0.00 2.44
968 1059 4.925576 CCCGAATCGCCTCGTCCG 62.926 72.222 0.00 0.00 37.11 4.79
1228 1319 3.555917 AGGACTACGTTTCAGTCTTCG 57.444 47.619 14.81 0.00 41.78 3.79
1339 1439 2.363795 TCCCCAGCCAGTACGAGG 60.364 66.667 3.30 3.30 0.00 4.63
1368 1468 4.326548 GTGTTTAACTCCGCTGATGACTAC 59.673 45.833 0.00 0.00 0.00 2.73
1592 1702 4.187694 GAGGGATCTGATGTGTCTTTCAC 58.812 47.826 0.00 0.00 46.31 3.18
1811 1946 4.811024 TGACGATGAGTATGAAGAAATGGC 59.189 41.667 0.00 0.00 0.00 4.40
2087 2223 2.164624 GGAGAAAGCAGCTAAGACTCGA 59.835 50.000 0.00 0.00 0.00 4.04
2169 2321 2.776536 AGCAATCTGGGATTAGTCTGCT 59.223 45.455 0.00 0.00 34.32 4.24
2185 2337 8.677148 TTAGTCTGCTTATTTCTTGTGTTCTT 57.323 30.769 0.00 0.00 0.00 2.52
2218 2370 9.297586 CTTTTGTAAAAGGGTAAGTTTCTCAAC 57.702 33.333 8.81 0.00 41.23 3.18
2733 2895 6.841229 TGATCTCCCAGTAGAGTGTAAATCAT 59.159 38.462 0.00 0.00 35.28 2.45
2734 2896 7.345653 TGATCTCCCAGTAGAGTGTAAATCATT 59.654 37.037 0.00 0.00 35.28 2.57
2735 2897 7.496346 TCTCCCAGTAGAGTGTAAATCATTT 57.504 36.000 0.00 0.00 35.28 2.32
2736 2898 7.918076 TCTCCCAGTAGAGTGTAAATCATTTT 58.082 34.615 0.00 0.00 35.28 1.82
2737 2899 8.383175 TCTCCCAGTAGAGTGTAAATCATTTTT 58.617 33.333 0.00 0.00 35.28 1.94
2762 2924 9.757227 TTTTTCGGTGTATCATTTCAAGATTTT 57.243 25.926 0.00 0.00 0.00 1.82
2763 2925 8.741101 TTTCGGTGTATCATTTCAAGATTTTG 57.259 30.769 0.00 0.00 35.57 2.44
2764 2926 6.321717 TCGGTGTATCATTTCAAGATTTTGC 58.678 36.000 0.00 0.00 34.21 3.68
2765 2927 5.516339 CGGTGTATCATTTCAAGATTTTGCC 59.484 40.000 0.00 0.00 34.21 4.52
2766 2928 5.812127 GGTGTATCATTTCAAGATTTTGCCC 59.188 40.000 0.00 0.00 34.21 5.36
2767 2929 5.812127 GTGTATCATTTCAAGATTTTGCCCC 59.188 40.000 0.00 0.00 34.21 5.80
2768 2930 3.979101 TCATTTCAAGATTTTGCCCCC 57.021 42.857 0.00 0.00 34.21 5.40
2769 2931 3.246301 TCATTTCAAGATTTTGCCCCCA 58.754 40.909 0.00 0.00 34.21 4.96
2770 2932 3.649981 TCATTTCAAGATTTTGCCCCCAA 59.350 39.130 0.00 0.00 34.21 4.12
2771 2933 4.289148 TCATTTCAAGATTTTGCCCCCAAT 59.711 37.500 0.00 0.00 34.21 3.16
2772 2934 4.720775 TTTCAAGATTTTGCCCCCAATT 57.279 36.364 0.00 0.00 34.21 2.32
2773 2935 5.832539 TTTCAAGATTTTGCCCCCAATTA 57.167 34.783 0.00 0.00 34.21 1.40
2774 2936 4.817318 TCAAGATTTTGCCCCCAATTAC 57.183 40.909 0.00 0.00 34.21 1.89
2775 2937 4.424842 TCAAGATTTTGCCCCCAATTACT 58.575 39.130 0.00 0.00 34.21 2.24
2776 2938 4.843516 TCAAGATTTTGCCCCCAATTACTT 59.156 37.500 0.00 0.00 34.21 2.24
2777 2939 5.309282 TCAAGATTTTGCCCCCAATTACTTT 59.691 36.000 0.00 0.00 34.21 2.66
2778 2940 5.841267 AGATTTTGCCCCCAATTACTTTT 57.159 34.783 0.00 0.00 0.00 2.27
2779 2941 6.199557 AGATTTTGCCCCCAATTACTTTTT 57.800 33.333 0.00 0.00 0.00 1.94
2799 2961 2.543777 TTTGAAACTGTCGAGAGGGG 57.456 50.000 14.79 0.00 0.00 4.79
2800 2962 0.685097 TTGAAACTGTCGAGAGGGGG 59.315 55.000 14.79 0.00 0.00 5.40
2823 2985 3.283020 GGGGTCCCCAACTGAATTC 57.717 57.895 23.53 0.00 44.65 2.17
2824 2986 0.407918 GGGGTCCCCAACTGAATTCA 59.592 55.000 23.53 8.12 44.65 2.57
2825 2987 1.007118 GGGGTCCCCAACTGAATTCAT 59.993 52.381 23.53 0.00 44.65 2.57
2826 2988 2.559705 GGGGTCCCCAACTGAATTCATT 60.560 50.000 23.53 0.00 44.65 2.57
2827 2989 3.173151 GGGTCCCCAACTGAATTCATTT 58.827 45.455 8.96 6.93 35.81 2.32
2828 2990 4.349365 GGGTCCCCAACTGAATTCATTTA 58.651 43.478 8.96 0.00 35.81 1.40
2829 2991 4.775253 GGGTCCCCAACTGAATTCATTTAA 59.225 41.667 8.96 0.00 35.81 1.52
2830 2992 5.247337 GGGTCCCCAACTGAATTCATTTAAA 59.753 40.000 8.96 0.00 35.81 1.52
2831 2993 6.239743 GGGTCCCCAACTGAATTCATTTAAAA 60.240 38.462 8.96 0.00 35.81 1.52
2832 2994 7.220740 GGTCCCCAACTGAATTCATTTAAAAA 58.779 34.615 8.96 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
66 68 7.450014 TGCCATGATTTCAAAACTTTAGGAGTA 59.550 33.333 0.00 0.00 37.72 2.59
94 96 1.276421 GTGTGGTCTGGTCTACTGCAT 59.724 52.381 0.00 0.00 0.00 3.96
406 412 2.200337 GCCCACACGCCTCCTTTTT 61.200 57.895 0.00 0.00 0.00 1.94
460 469 0.389948 GTGTGGTGCCTAAGAGGACG 60.390 60.000 0.00 0.00 37.67 4.79
513 522 1.293498 GACGAGCCCACATGTCTGT 59.707 57.895 0.00 0.00 35.44 3.41
514 523 1.448540 GGACGAGCCCACATGTCTG 60.449 63.158 0.00 0.00 0.00 3.51
515 524 1.608717 GAGGACGAGCCCACATGTCT 61.609 60.000 0.00 0.00 37.37 3.41
516 525 1.153549 GAGGACGAGCCCACATGTC 60.154 63.158 0.00 0.00 37.37 3.06
517 526 1.194781 AAGAGGACGAGCCCACATGT 61.195 55.000 0.00 0.00 37.37 3.21
518 527 0.824109 TAAGAGGACGAGCCCACATG 59.176 55.000 0.00 0.00 37.37 3.21
519 528 1.115467 CTAAGAGGACGAGCCCACAT 58.885 55.000 0.00 0.00 37.37 3.21
520 529 0.970937 CCTAAGAGGACGAGCCCACA 60.971 60.000 0.00 0.00 37.67 4.17
521 530 1.817209 CCTAAGAGGACGAGCCCAC 59.183 63.158 0.00 0.00 37.67 4.61
522 531 2.058595 GCCTAAGAGGACGAGCCCA 61.059 63.158 0.00 0.00 37.67 5.36
523 532 2.058595 TGCCTAAGAGGACGAGCCC 61.059 63.158 0.00 0.00 37.67 5.19
524 533 1.142097 GTGCCTAAGAGGACGAGCC 59.858 63.158 0.00 0.00 37.67 4.70
525 534 1.142097 GGTGCCTAAGAGGACGAGC 59.858 63.158 0.00 0.00 37.67 5.03
526 535 0.173708 GTGGTGCCTAAGAGGACGAG 59.826 60.000 0.00 0.00 37.67 4.18
527 536 0.541063 TGTGGTGCCTAAGAGGACGA 60.541 55.000 0.00 0.00 37.67 4.20
528 537 0.389948 GTGTGGTGCCTAAGAGGACG 60.390 60.000 0.00 0.00 37.67 4.79
529 538 0.685097 TGTGTGGTGCCTAAGAGGAC 59.315 55.000 0.00 0.00 37.67 3.85
530 539 0.976641 CTGTGTGGTGCCTAAGAGGA 59.023 55.000 0.00 0.00 37.67 3.71
531 540 0.976641 TCTGTGTGGTGCCTAAGAGG 59.023 55.000 0.00 0.00 38.80 3.69
532 541 2.417719 GTTCTGTGTGGTGCCTAAGAG 58.582 52.381 0.00 0.00 0.00 2.85
533 542 1.270094 CGTTCTGTGTGGTGCCTAAGA 60.270 52.381 0.00 0.00 0.00 2.10
534 543 1.148310 CGTTCTGTGTGGTGCCTAAG 58.852 55.000 0.00 0.00 0.00 2.18
535 544 0.466543 ACGTTCTGTGTGGTGCCTAA 59.533 50.000 0.00 0.00 0.00 2.69
536 545 0.249699 CACGTTCTGTGTGGTGCCTA 60.250 55.000 0.00 0.00 43.88 3.93
537 546 1.523711 CACGTTCTGTGTGGTGCCT 60.524 57.895 0.00 0.00 43.88 4.75
538 547 3.022287 CACGTTCTGTGTGGTGCC 58.978 61.111 0.00 0.00 43.88 5.01
546 555 0.108585 AATCTGCCCACACGTTCTGT 59.891 50.000 0.00 0.00 0.00 3.41
547 556 1.197721 GAAATCTGCCCACACGTTCTG 59.802 52.381 0.00 0.00 0.00 3.02
548 557 1.072331 AGAAATCTGCCCACACGTTCT 59.928 47.619 0.00 0.00 0.00 3.01
549 558 1.523758 AGAAATCTGCCCACACGTTC 58.476 50.000 0.00 0.00 0.00 3.95
550 559 1.981256 AAGAAATCTGCCCACACGTT 58.019 45.000 0.00 0.00 0.00 3.99
551 560 2.812011 GTTAAGAAATCTGCCCACACGT 59.188 45.455 0.00 0.00 0.00 4.49
552 561 2.159707 CGTTAAGAAATCTGCCCACACG 60.160 50.000 0.00 0.00 0.00 4.49
553 562 2.414161 GCGTTAAGAAATCTGCCCACAC 60.414 50.000 0.00 0.00 0.00 3.82
554 563 1.810151 GCGTTAAGAAATCTGCCCACA 59.190 47.619 0.00 0.00 0.00 4.17
555 564 1.132453 GGCGTTAAGAAATCTGCCCAC 59.868 52.381 0.00 0.00 36.51 4.61
556 565 1.459450 GGCGTTAAGAAATCTGCCCA 58.541 50.000 0.00 0.00 36.51 5.36
558 567 1.132453 GTGGGCGTTAAGAAATCTGCC 59.868 52.381 1.85 1.85 41.72 4.85
559 568 1.810151 TGTGGGCGTTAAGAAATCTGC 59.190 47.619 0.00 0.00 0.00 4.26
560 569 2.159707 CGTGTGGGCGTTAAGAAATCTG 60.160 50.000 0.00 0.00 0.00 2.90
561 570 2.073816 CGTGTGGGCGTTAAGAAATCT 58.926 47.619 0.00 0.00 0.00 2.40
562 571 1.802365 ACGTGTGGGCGTTAAGAAATC 59.198 47.619 0.00 0.00 43.04 2.17
563 572 1.533731 CACGTGTGGGCGTTAAGAAAT 59.466 47.619 7.58 0.00 43.83 2.17
564 573 0.938713 CACGTGTGGGCGTTAAGAAA 59.061 50.000 7.58 0.00 43.83 2.52
565 574 0.179078 ACACGTGTGGGCGTTAAGAA 60.179 50.000 22.71 0.00 43.83 2.52
566 575 0.876777 CACACGTGTGGGCGTTAAGA 60.877 55.000 35.65 0.00 43.83 2.10
567 576 1.567537 CACACGTGTGGGCGTTAAG 59.432 57.895 35.65 11.35 43.83 1.85
568 577 3.720531 CACACGTGTGGGCGTTAA 58.279 55.556 35.65 0.00 43.83 2.01
576 585 0.438445 CGATAACTGCCACACGTGTG 59.562 55.000 36.13 36.13 45.23 3.82
577 586 0.669318 CCGATAACTGCCACACGTGT 60.669 55.000 17.22 17.22 0.00 4.49
578 587 1.966493 GCCGATAACTGCCACACGTG 61.966 60.000 15.48 15.48 0.00 4.49
579 588 1.740296 GCCGATAACTGCCACACGT 60.740 57.895 0.00 0.00 0.00 4.49
580 589 2.798501 CGCCGATAACTGCCACACG 61.799 63.158 0.00 0.00 0.00 4.49
581 590 1.693083 GACGCCGATAACTGCCACAC 61.693 60.000 0.00 0.00 0.00 3.82
582 591 1.447140 GACGCCGATAACTGCCACA 60.447 57.895 0.00 0.00 0.00 4.17
583 592 2.171725 GGACGCCGATAACTGCCAC 61.172 63.158 0.00 0.00 0.00 5.01
584 593 1.895020 AAGGACGCCGATAACTGCCA 61.895 55.000 0.00 0.00 0.00 4.92
585 594 0.743345 AAAGGACGCCGATAACTGCC 60.743 55.000 0.00 0.00 0.00 4.85
586 595 1.084289 AAAAGGACGCCGATAACTGC 58.916 50.000 0.00 0.00 0.00 4.40
587 596 2.343101 TCAAAAGGACGCCGATAACTG 58.657 47.619 0.00 0.00 0.00 3.16
588 597 2.232941 TCTCAAAAGGACGCCGATAACT 59.767 45.455 0.00 0.00 0.00 2.24
589 598 2.613691 TCTCAAAAGGACGCCGATAAC 58.386 47.619 0.00 0.00 0.00 1.89
590 599 3.322211 TTCTCAAAAGGACGCCGATAA 57.678 42.857 0.00 0.00 0.00 1.75
591 600 3.194861 CATTCTCAAAAGGACGCCGATA 58.805 45.455 0.00 0.00 0.00 2.92
592 601 2.009774 CATTCTCAAAAGGACGCCGAT 58.990 47.619 0.00 0.00 0.00 4.18
593 602 1.438651 CATTCTCAAAAGGACGCCGA 58.561 50.000 0.00 0.00 0.00 5.54
594 603 0.179189 GCATTCTCAAAAGGACGCCG 60.179 55.000 0.00 0.00 0.00 6.46
595 604 1.135575 CAGCATTCTCAAAAGGACGCC 60.136 52.381 0.00 0.00 0.00 5.68
596 605 1.730446 GCAGCATTCTCAAAAGGACGC 60.730 52.381 0.00 0.00 0.00 5.19
597 606 1.808945 AGCAGCATTCTCAAAAGGACG 59.191 47.619 0.00 0.00 0.00 4.79
598 607 3.080319 AGAGCAGCATTCTCAAAAGGAC 58.920 45.455 0.00 0.00 27.72 3.85
599 608 3.430042 AGAGCAGCATTCTCAAAAGGA 57.570 42.857 0.00 0.00 27.72 3.36
600 609 4.516365 AAAGAGCAGCATTCTCAAAAGG 57.484 40.909 0.00 0.00 27.72 3.11
601 610 5.751990 ACAAAAAGAGCAGCATTCTCAAAAG 59.248 36.000 0.00 0.00 27.72 2.27
887 932 1.459592 CGAGGCGATTCGTGAGTTTTT 59.540 47.619 8.03 0.00 35.91 1.94
888 933 1.068474 CGAGGCGATTCGTGAGTTTT 58.932 50.000 8.03 0.00 35.91 2.43
889 934 1.352156 GCGAGGCGATTCGTGAGTTT 61.352 55.000 8.03 0.00 42.38 2.66
938 1020 4.772231 TCGGGAGGAGGGGAACGG 62.772 72.222 0.00 0.00 0.00 4.44
939 1021 2.029307 GATTCGGGAGGAGGGGAACG 62.029 65.000 0.00 0.00 0.00 3.95
940 1022 1.830836 GATTCGGGAGGAGGGGAAC 59.169 63.158 0.00 0.00 0.00 3.62
941 1023 1.760875 CGATTCGGGAGGAGGGGAA 60.761 63.158 0.00 0.00 0.00 3.97
1228 1319 0.522180 TTCTCGGTCTTGAGCTCGAC 59.478 55.000 9.64 11.02 35.90 4.20
1339 1439 1.495951 CGGAGTTAAACACCAGCGC 59.504 57.895 0.00 0.00 0.00 5.92
1368 1468 2.103042 GTAGCCCGAGCAGCAGTTG 61.103 63.158 0.00 0.00 43.56 3.16
1592 1702 2.633488 GGAAAATCTCCTCCTTGACCG 58.367 52.381 0.00 0.00 41.61 4.79
1654 1777 1.447314 GGCCGTAGAACTTCACCCG 60.447 63.158 0.00 0.00 0.00 5.28
1811 1946 2.774799 GGCCACCGCAAATGCCTAG 61.775 63.158 0.00 0.00 40.77 3.02
2087 2223 7.108841 TCTACGGTCAGCATACTAAATTCTT 57.891 36.000 0.00 0.00 0.00 2.52
2218 2370 4.026558 CCAATGACATCGAAGACATACACG 60.027 45.833 6.07 0.00 42.51 4.49
2540 2702 5.353394 TGTATAAGGGACACATGAGGAAC 57.647 43.478 0.00 0.00 0.00 3.62
2593 2755 2.353610 GCAATGCCTCTGTTGGGGG 61.354 63.158 0.00 0.00 0.00 5.40
2617 2779 0.908910 ACACGATGGCAGGTAATGGA 59.091 50.000 0.00 0.00 0.00 3.41
2736 2898 9.757227 AAAATCTTGAAATGATACACCGAAAAA 57.243 25.926 0.00 0.00 29.61 1.94
2737 2899 9.190858 CAAAATCTTGAAATGATACACCGAAAA 57.809 29.630 0.00 0.00 34.14 2.29
2738 2900 7.328249 GCAAAATCTTGAAATGATACACCGAAA 59.672 33.333 0.00 0.00 34.14 3.46
2739 2901 6.806249 GCAAAATCTTGAAATGATACACCGAA 59.194 34.615 0.00 0.00 34.14 4.30
2740 2902 6.321717 GCAAAATCTTGAAATGATACACCGA 58.678 36.000 0.00 0.00 34.14 4.69
2741 2903 5.516339 GGCAAAATCTTGAAATGATACACCG 59.484 40.000 0.00 0.00 34.14 4.94
2742 2904 5.812127 GGGCAAAATCTTGAAATGATACACC 59.188 40.000 0.00 0.00 34.14 4.16
2743 2905 5.812127 GGGGCAAAATCTTGAAATGATACAC 59.188 40.000 0.00 0.00 34.14 2.90
2744 2906 5.104982 GGGGGCAAAATCTTGAAATGATACA 60.105 40.000 0.00 0.00 34.14 2.29
2745 2907 5.104982 TGGGGGCAAAATCTTGAAATGATAC 60.105 40.000 0.00 0.00 34.14 2.24
2746 2908 5.028802 TGGGGGCAAAATCTTGAAATGATA 58.971 37.500 0.00 0.00 34.14 2.15
2747 2909 3.845398 TGGGGGCAAAATCTTGAAATGAT 59.155 39.130 0.00 0.00 34.14 2.45
2748 2910 3.246301 TGGGGGCAAAATCTTGAAATGA 58.754 40.909 0.00 0.00 34.14 2.57
2749 2911 3.699411 TGGGGGCAAAATCTTGAAATG 57.301 42.857 0.00 0.00 34.14 2.32
2750 2912 4.932911 ATTGGGGGCAAAATCTTGAAAT 57.067 36.364 0.00 0.00 34.14 2.17
2751 2913 4.720775 AATTGGGGGCAAAATCTTGAAA 57.279 36.364 0.00 0.00 34.14 2.69
2752 2914 4.843516 AGTAATTGGGGGCAAAATCTTGAA 59.156 37.500 0.00 0.00 34.14 2.69
2753 2915 4.424842 AGTAATTGGGGGCAAAATCTTGA 58.575 39.130 0.00 0.00 34.14 3.02
2754 2916 4.824479 AGTAATTGGGGGCAAAATCTTG 57.176 40.909 0.00 0.00 35.49 3.02
2755 2917 5.841267 AAAGTAATTGGGGGCAAAATCTT 57.159 34.783 0.00 0.00 0.00 2.40
2756 2918 5.841267 AAAAGTAATTGGGGGCAAAATCT 57.159 34.783 0.00 0.00 0.00 2.40
2778 2940 3.211045 CCCCTCTCGACAGTTTCAAAAA 58.789 45.455 0.00 0.00 0.00 1.94
2779 2941 2.486548 CCCCCTCTCGACAGTTTCAAAA 60.487 50.000 0.00 0.00 0.00 2.44
2780 2942 1.071699 CCCCCTCTCGACAGTTTCAAA 59.928 52.381 0.00 0.00 0.00 2.69
2781 2943 0.685097 CCCCCTCTCGACAGTTTCAA 59.315 55.000 0.00 0.00 0.00 2.69
2782 2944 2.362242 CCCCCTCTCGACAGTTTCA 58.638 57.895 0.00 0.00 0.00 2.69


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

AutoCloner maintained by Alex Coulton.