Multiple sequence alignment - TraesCS2A01G032200

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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 TraesCS2A01G032200 chr2A 100.000 3341 0 0 1 3341 14731418 14728078 0.000000e+00 6170.0
1 TraesCS2A01G032200 chr2A 92.422 2481 158 21 572 3034 14712252 14709784 0.000000e+00 3513.0
2 TraesCS2A01G032200 chr2A 90.244 2132 155 32 757 2861 14703810 14701705 0.000000e+00 2736.0
3 TraesCS2A01G032200 chr2A 89.168 1911 177 22 645 2533 14721447 14719545 0.000000e+00 2355.0
4 TraesCS2A01G032200 chr2A 88.889 1782 144 29 771 2534 14740757 14739012 0.000000e+00 2145.0
5 TraesCS2A01G032200 chr2A 91.498 988 77 6 1011 1996 14683500 14682518 0.000000e+00 1352.0
6 TraesCS2A01G032200 chr2A 86.957 736 70 14 2016 2727 14682452 14681719 0.000000e+00 804.0
7 TraesCS2A01G032200 chr2A 89.426 331 23 7 2886 3214 14701470 14701150 1.120000e-109 407.0
8 TraesCS2A01G032200 chr2A 95.758 165 7 0 3169 3333 14708954 14708790 1.980000e-67 267.0
9 TraesCS2A01G032200 chr2A 94.326 141 7 1 7 147 14712883 14712744 7.260000e-52 215.0
10 TraesCS2A01G032200 chr2A 94.574 129 7 0 3206 3334 14695339 14695211 2.030000e-47 200.0
11 TraesCS2A01G032200 chr2A 77.231 325 43 19 14 320 14704320 14704009 9.590000e-36 161.0
12 TraesCS2A01G032200 chr2A 88.800 125 13 1 14 138 14721941 14721818 5.770000e-33 152.0
13 TraesCS2A01G032200 chr2A 82.081 173 25 6 3 171 14692518 14692348 3.470000e-30 143.0
14 TraesCS2A01G032200 chr2A 90.164 61 6 0 313 373 733925375 733925315 2.760000e-11 80.5
15 TraesCS2A01G032200 chr2A 92.308 39 3 0 319 357 699975303 699975341 4.660000e-04 56.5
16 TraesCS2A01G032200 chr2B 93.916 1841 101 8 699 2533 20146289 20148124 0.000000e+00 2769.0
17 TraesCS2A01G032200 chr2B 88.437 467 37 9 2875 3341 32141387 32141836 6.300000e-152 547.0
18 TraesCS2A01G032200 chr2B 91.789 341 20 6 164 501 20145771 20146106 5.050000e-128 468.0
19 TraesCS2A01G032200 chr2B 84.314 204 23 4 2576 2779 20148188 20148382 1.220000e-44 191.0
20 TraesCS2A01G032200 chr2D 88.166 1876 180 25 645 2489 12632773 12630909 0.000000e+00 2196.0
21 TraesCS2A01G032200 chr2D 88.997 1336 130 14 679 2007 12626936 12625611 0.000000e+00 1637.0
22 TraesCS2A01G032200 chr2D 87.364 736 67 12 2016 2727 12625534 12624801 0.000000e+00 821.0
23 TraesCS2A01G032200 chr2D 88.224 501 43 8 2841 3341 19384852 19385336 4.800000e-163 584.0
24 TraesCS2A01G032200 chr2D 84.740 557 58 15 2794 3341 19395740 19396278 1.760000e-147 532.0
25 TraesCS2A01G032200 chr2D 88.060 201 22 2 3140 3340 19569350 19569548 1.550000e-58 237.0
26 TraesCS2A01G032200 chr2D 85.890 163 18 4 14 171 12627567 12627405 5.730000e-38 169.0
27 TraesCS2A01G032200 chr2D 86.029 136 16 2 3 138 12633273 12633141 3.470000e-30 143.0
28 TraesCS2A01G032200 chr5D 80.206 1652 272 44 859 2478 438438826 438437198 0.000000e+00 1188.0
29 TraesCS2A01G032200 chr5B 79.975 1628 271 39 859 2450 533035456 533033848 0.000000e+00 1149.0
30 TraesCS2A01G032200 chr5B 80.321 996 170 24 975 1956 533018708 533017725 0.000000e+00 730.0
31 TraesCS2A01G032200 chr3D 88.732 355 30 7 2986 3340 589661361 589661017 3.080000e-115 425.0
32 TraesCS2A01G032200 chrUn 89.007 282 18 10 2875 3156 16709788 16709520 1.490000e-88 337.0
33 TraesCS2A01G032200 chrUn 89.007 282 18 10 2875 3156 259845124 259845392 1.490000e-88 337.0
34 TraesCS2A01G032200 chrUn 89.007 282 18 10 2875 3156 305383308 305383576 1.490000e-88 337.0
35 TraesCS2A01G032200 chrUn 88.776 196 20 1 3146 3341 16706482 16706289 4.310000e-59 239.0
36 TraesCS2A01G032200 chrUn 86.747 83 9 1 3259 3341 16724118 16724038 1.280000e-14 91.6
37 TraesCS2A01G032200 chr4A 92.857 42 3 0 317 358 603947575 603947616 1.000000e-05 62.1
38 TraesCS2A01G032200 chr6D 92.683 41 3 0 316 356 61722309 61722269 3.600000e-05 60.2
39 TraesCS2A01G032200 chr7A 92.500 40 3 0 318 357 680681677 680681716 1.290000e-04 58.4
40 TraesCS2A01G032200 chr7A 96.970 33 1 0 325 357 93921791 93921759 4.660000e-04 56.5


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 TraesCS2A01G032200 chr2A 14728078 14731418 3340 True 6170.000000 6170 100.000000 1 3341 1 chr2A.!!$R1 3340
1 TraesCS2A01G032200 chr2A 14739012 14740757 1745 True 2145.000000 2145 88.889000 771 2534 1 chr2A.!!$R2 1763
2 TraesCS2A01G032200 chr2A 14708790 14712883 4093 True 1331.666667 3513 94.168667 7 3333 3 chr2A.!!$R7 3326
3 TraesCS2A01G032200 chr2A 14719545 14721941 2396 True 1253.500000 2355 88.984000 14 2533 2 chr2A.!!$R8 2519
4 TraesCS2A01G032200 chr2A 14701150 14704320 3170 True 1101.333333 2736 85.633667 14 3214 3 chr2A.!!$R6 3200
5 TraesCS2A01G032200 chr2A 14681719 14683500 1781 True 1078.000000 1352 89.227500 1011 2727 2 chr2A.!!$R4 1716
6 TraesCS2A01G032200 chr2B 20145771 20148382 2611 False 1142.666667 2769 90.006333 164 2779 3 chr2B.!!$F2 2615
7 TraesCS2A01G032200 chr2D 12624801 12633273 8472 True 993.200000 2196 87.289200 3 2727 5 chr2D.!!$R1 2724
8 TraesCS2A01G032200 chr2D 19395740 19396278 538 False 532.000000 532 84.740000 2794 3341 1 chr2D.!!$F2 547
9 TraesCS2A01G032200 chr5D 438437198 438438826 1628 True 1188.000000 1188 80.206000 859 2478 1 chr5D.!!$R1 1619
10 TraesCS2A01G032200 chr5B 533033848 533035456 1608 True 1149.000000 1149 79.975000 859 2450 1 chr5B.!!$R2 1591
11 TraesCS2A01G032200 chr5B 533017725 533018708 983 True 730.000000 730 80.321000 975 1956 1 chr5B.!!$R1 981
12 TraesCS2A01G032200 chrUn 16706289 16709788 3499 True 288.000000 337 88.891500 2875 3341 2 chrUn.!!$R2 466

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
522 683 0.028902 GCAGTTTGGTTCGTGTCCAC 59.971 55.0 0.0 0.0 34.45 4.02 F
568 729 0.178990 AGGACTCCAACCAAACTGCC 60.179 55.0 0.0 0.0 0.00 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2221 8380 1.449070 GACGATTGGGGTCCGGAAC 60.449 63.158 12.37 12.37 0.0 3.62 R
2556 8756 2.435805 AGAGTGGCTGAGAAGAACAACA 59.564 45.455 0.00 0.00 0.0 3.33 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 67 1.656587 TACAGTGAGGATTGGGCTGT 58.343 50.000 0.00 0.00 42.25 4.40
88 89 3.315191 TCAGTTTTAGCAAGTGTTCTGGC 59.685 43.478 0.00 0.00 40.72 4.85
140 142 5.429681 AATTTAAAGGTGCATTTACCCCC 57.570 39.130 0.00 0.00 41.83 5.40
158 169 1.133482 CCCCGCCCCTCTCATAAAAAT 60.133 52.381 0.00 0.00 0.00 1.82
162 178 4.506625 CCCGCCCCTCTCATAAAAATGATA 60.507 45.833 0.00 0.00 0.00 2.15
208 354 8.596293 ACCATGTAAAATCATGAAATCCTTTGT 58.404 29.630 0.00 0.00 45.41 2.83
243 389 7.769220 ACTAGAGCAAATCATGAAATCTTTGG 58.231 34.615 17.09 6.46 30.55 3.28
323 481 6.605471 TCACAATGGACAATGTACTACTCT 57.395 37.500 0.00 0.00 0.00 3.24
386 544 6.531021 CGGAGGGAGTACCAAATAATATTGT 58.469 40.000 0.00 0.00 43.89 2.71
411 569 3.140707 TCCACATGCCAGGGAAATCATAT 59.859 43.478 0.00 0.00 0.00 1.78
412 570 3.257375 CCACATGCCAGGGAAATCATATG 59.743 47.826 0.00 0.00 0.00 1.78
421 579 5.649395 CCAGGGAAATCATATGCGATATTGT 59.351 40.000 0.00 0.00 0.00 2.71
442 602 4.576873 TGTCGGTTTCATAAAACAAGAGCA 59.423 37.500 0.00 0.00 45.44 4.26
447 607 5.695816 GGTTTCATAAAACAAGAGCAATGCA 59.304 36.000 8.35 0.00 45.44 3.96
462 622 3.731867 GCAATGCAGTGTTACCATGCTAC 60.732 47.826 16.47 0.00 40.62 3.58
489 650 0.969894 GGTCTCGAGGATATGGGTGG 59.030 60.000 13.56 0.00 0.00 4.61
497 658 0.779997 GGATATGGGTGGGCCTGATT 59.220 55.000 4.53 0.00 34.45 2.57
498 659 1.548582 GGATATGGGTGGGCCTGATTG 60.549 57.143 4.53 0.00 34.45 2.67
499 660 1.425066 GATATGGGTGGGCCTGATTGA 59.575 52.381 4.53 0.00 34.45 2.57
500 661 0.846015 TATGGGTGGGCCTGATTGAG 59.154 55.000 4.53 0.00 34.45 3.02
501 662 0.920763 ATGGGTGGGCCTGATTGAGA 60.921 55.000 4.53 0.00 34.45 3.27
502 663 1.225704 GGGTGGGCCTGATTGAGAG 59.774 63.158 4.53 0.00 34.45 3.20
503 664 1.225704 GGTGGGCCTGATTGAGAGG 59.774 63.158 4.53 0.00 0.00 3.69
511 672 2.089980 CCTGATTGAGAGGCAGTTTGG 58.910 52.381 0.00 0.00 0.00 3.28
512 673 2.553904 CCTGATTGAGAGGCAGTTTGGT 60.554 50.000 0.00 0.00 0.00 3.67
513 674 3.152341 CTGATTGAGAGGCAGTTTGGTT 58.848 45.455 0.00 0.00 0.00 3.67
514 675 3.149196 TGATTGAGAGGCAGTTTGGTTC 58.851 45.455 0.00 0.00 0.00 3.62
515 676 1.593196 TTGAGAGGCAGTTTGGTTCG 58.407 50.000 0.00 0.00 0.00 3.95
516 677 0.468226 TGAGAGGCAGTTTGGTTCGT 59.532 50.000 0.00 0.00 0.00 3.85
517 678 0.868406 GAGAGGCAGTTTGGTTCGTG 59.132 55.000 0.00 0.00 0.00 4.35
518 679 0.180406 AGAGGCAGTTTGGTTCGTGT 59.820 50.000 0.00 0.00 0.00 4.49
519 680 0.586802 GAGGCAGTTTGGTTCGTGTC 59.413 55.000 0.00 0.00 0.00 3.67
520 681 0.818040 AGGCAGTTTGGTTCGTGTCC 60.818 55.000 0.00 0.00 0.00 4.02
521 682 1.098712 GGCAGTTTGGTTCGTGTCCA 61.099 55.000 0.00 0.00 0.00 4.02
522 683 0.028902 GCAGTTTGGTTCGTGTCCAC 59.971 55.000 0.00 0.00 34.45 4.02
523 684 1.374560 CAGTTTGGTTCGTGTCCACA 58.625 50.000 0.00 0.00 34.45 4.17
524 685 1.330521 CAGTTTGGTTCGTGTCCACAG 59.669 52.381 0.00 0.00 34.45 3.66
525 686 1.065709 AGTTTGGTTCGTGTCCACAGT 60.066 47.619 0.00 0.00 34.45 3.55
526 687 1.741145 GTTTGGTTCGTGTCCACAGTT 59.259 47.619 0.00 0.00 34.45 3.16
527 688 1.374560 TTGGTTCGTGTCCACAGTTG 58.625 50.000 0.00 0.00 34.45 3.16
528 689 1.092921 TGGTTCGTGTCCACAGTTGC 61.093 55.000 0.00 0.00 0.00 4.17
529 690 1.275657 GTTCGTGTCCACAGTTGCG 59.724 57.895 0.00 0.00 0.00 4.85
530 691 1.153529 TTCGTGTCCACAGTTGCGT 60.154 52.632 0.00 0.00 0.00 5.24
531 692 1.425267 TTCGTGTCCACAGTTGCGTG 61.425 55.000 0.00 0.00 36.61 5.34
532 693 2.327940 GTGTCCACAGTTGCGTGC 59.672 61.111 0.00 0.00 35.47 5.34
533 694 2.899838 TGTCCACAGTTGCGTGCC 60.900 61.111 0.00 0.00 35.47 5.01
534 695 2.591715 GTCCACAGTTGCGTGCCT 60.592 61.111 0.00 0.00 35.47 4.75
535 696 2.591429 TCCACAGTTGCGTGCCTG 60.591 61.111 0.00 0.00 35.47 4.85
536 697 3.663176 CCACAGTTGCGTGCCTGG 61.663 66.667 3.71 0.00 35.47 4.45
537 698 2.901840 CACAGTTGCGTGCCTGGT 60.902 61.111 0.00 0.00 32.90 4.00
538 699 1.596752 CACAGTTGCGTGCCTGGTA 60.597 57.895 0.00 0.00 32.90 3.25
539 700 1.147376 ACAGTTGCGTGCCTGGTAA 59.853 52.632 0.00 0.00 32.90 2.85
540 701 0.250727 ACAGTTGCGTGCCTGGTAAT 60.251 50.000 0.00 0.00 32.90 1.89
541 702 0.447801 CAGTTGCGTGCCTGGTAATC 59.552 55.000 0.00 0.00 0.00 1.75
542 703 0.324943 AGTTGCGTGCCTGGTAATCT 59.675 50.000 0.00 0.00 0.00 2.40
543 704 1.165270 GTTGCGTGCCTGGTAATCTT 58.835 50.000 0.00 0.00 0.00 2.40
544 705 1.539827 GTTGCGTGCCTGGTAATCTTT 59.460 47.619 0.00 0.00 0.00 2.52
545 706 1.904287 TGCGTGCCTGGTAATCTTTT 58.096 45.000 0.00 0.00 0.00 2.27
546 707 1.539388 TGCGTGCCTGGTAATCTTTTG 59.461 47.619 0.00 0.00 0.00 2.44
547 708 1.539827 GCGTGCCTGGTAATCTTTTGT 59.460 47.619 0.00 0.00 0.00 2.83
548 709 2.414161 GCGTGCCTGGTAATCTTTTGTC 60.414 50.000 0.00 0.00 0.00 3.18
549 710 2.811431 CGTGCCTGGTAATCTTTTGTCA 59.189 45.455 0.00 0.00 0.00 3.58
550 711 3.120199 CGTGCCTGGTAATCTTTTGTCAG 60.120 47.826 0.00 0.00 0.00 3.51
551 712 3.191371 GTGCCTGGTAATCTTTTGTCAGG 59.809 47.826 0.00 0.00 43.20 3.86
552 713 3.073798 TGCCTGGTAATCTTTTGTCAGGA 59.926 43.478 10.90 0.00 43.05 3.86
553 714 3.440522 GCCTGGTAATCTTTTGTCAGGAC 59.559 47.826 10.90 0.00 43.05 3.85
554 715 4.807643 GCCTGGTAATCTTTTGTCAGGACT 60.808 45.833 10.90 0.00 43.05 3.85
555 716 4.938226 CCTGGTAATCTTTTGTCAGGACTC 59.062 45.833 0.00 0.00 43.05 3.36
556 717 4.906618 TGGTAATCTTTTGTCAGGACTCC 58.093 43.478 0.65 0.00 0.00 3.85
557 718 4.349636 TGGTAATCTTTTGTCAGGACTCCA 59.650 41.667 0.00 0.00 0.00 3.86
558 719 5.163141 TGGTAATCTTTTGTCAGGACTCCAA 60.163 40.000 0.00 0.00 0.00 3.53
559 720 5.181433 GGTAATCTTTTGTCAGGACTCCAAC 59.819 44.000 0.00 0.00 0.00 3.77
560 721 3.208747 TCTTTTGTCAGGACTCCAACC 57.791 47.619 0.00 0.00 0.00 3.77
561 722 2.507886 TCTTTTGTCAGGACTCCAACCA 59.492 45.455 0.00 0.00 0.00 3.67
562 723 3.053991 TCTTTTGTCAGGACTCCAACCAA 60.054 43.478 0.00 0.00 0.00 3.67
563 724 3.374042 TTTGTCAGGACTCCAACCAAA 57.626 42.857 0.00 0.53 0.00 3.28
564 725 2.341846 TGTCAGGACTCCAACCAAAC 57.658 50.000 0.00 0.00 0.00 2.93
565 726 1.843851 TGTCAGGACTCCAACCAAACT 59.156 47.619 0.00 0.00 0.00 2.66
566 727 2.222027 GTCAGGACTCCAACCAAACTG 58.778 52.381 0.00 0.00 0.00 3.16
567 728 0.954452 CAGGACTCCAACCAAACTGC 59.046 55.000 0.00 0.00 0.00 4.40
568 729 0.178990 AGGACTCCAACCAAACTGCC 60.179 55.000 0.00 0.00 0.00 4.85
569 730 1.179174 GGACTCCAACCAAACTGCCC 61.179 60.000 0.00 0.00 0.00 5.36
570 731 1.152546 ACTCCAACCAAACTGCCCC 60.153 57.895 0.00 0.00 0.00 5.80
611 772 0.268869 ATGGGGATGAGGAGGTAGCA 59.731 55.000 0.00 0.00 0.00 3.49
661 822 8.596293 AGAAACATTATTTCCCAACACATGAAT 58.404 29.630 0.00 0.00 0.00 2.57
743 963 5.268544 CGAAGTGCCTCATGAATTATGTTG 58.731 41.667 0.00 0.00 38.01 3.33
746 966 5.439721 AGTGCCTCATGAATTATGTTGCTA 58.560 37.500 0.00 0.00 38.01 3.49
755 975 6.772360 TGAATTATGTTGCTATGGCTTTGA 57.228 33.333 1.68 0.00 39.59 2.69
756 976 7.350744 TGAATTATGTTGCTATGGCTTTGAT 57.649 32.000 1.68 0.00 39.59 2.57
757 977 7.428020 TGAATTATGTTGCTATGGCTTTGATC 58.572 34.615 1.68 0.00 39.59 2.92
794 1020 0.948678 CGAACACCAACGGTTCCAAT 59.051 50.000 0.00 0.00 41.16 3.16
904 1132 3.059634 TCAAAAAGTGGAGAAAACGCG 57.940 42.857 3.53 3.53 0.00 6.01
957 1185 7.059156 CCTCTTATGAACTTGATGAAGGGAAT 58.941 38.462 0.00 0.00 32.95 3.01
971 1199 0.529992 GGGAATCGTCACCGTGATCC 60.530 60.000 4.13 7.38 35.01 3.36
1023 1251 2.362077 GTCCATGGCAACTCACAACTTT 59.638 45.455 6.96 0.00 37.61 2.66
1078 1306 7.682501 GCTTTGGCAAAGTTTACAAGGTAACTA 60.683 37.037 33.45 0.00 43.65 2.24
1167 1416 3.739401 ACCTTCAAATTGTCTAGGGGG 57.261 47.619 13.08 0.00 0.00 5.40
1378 1627 4.097892 GGATGCTACCCTTTTTGGTACATG 59.902 45.833 0.00 0.00 39.30 3.21
1511 1776 9.449719 CGGTTTAATATAATCAAAGGGATAGCT 57.550 33.333 0.00 0.00 34.28 3.32
1516 1781 8.933522 AATATAATCAAAGGGATAGCTAGGGA 57.066 34.615 0.00 0.00 34.28 4.20
1546 1811 3.703001 TCTCCACCAAGATTCAAGACC 57.297 47.619 0.00 0.00 0.00 3.85
1566 1831 7.348080 AGACCGACAATAATTCATAGAGACA 57.652 36.000 0.00 0.00 0.00 3.41
1592 1857 4.773323 AGCTGGAAATGTTTTGCTAGAC 57.227 40.909 0.00 0.00 0.00 2.59
1630 1895 4.021102 AGATAGCGGATTTTGGTATGGG 57.979 45.455 0.00 0.00 30.66 4.00
1877 7947 8.545472 ACTATTAGAGGTTGTAACTGGCATTAA 58.455 33.333 0.00 0.00 0.00 1.40
2044 8199 1.993956 TGGGTTGTTTCAGTCATGGG 58.006 50.000 0.00 0.00 0.00 4.00
2211 8370 2.496070 TGTGTTCGTCCTAGAGAATGGG 59.504 50.000 0.00 0.00 0.00 4.00
2316 8475 3.942748 AGACTTCCGCAAACAGTTTTACA 59.057 39.130 0.00 0.00 0.00 2.41
2452 8616 6.714278 TCAGAAGTCATCATCTTTGAATGGA 58.286 36.000 0.00 0.00 34.96 3.41
2555 8755 1.140052 TGGACACAAGTGATTCGGTGT 59.860 47.619 7.28 0.00 46.31 4.16
2556 8756 2.218603 GGACACAAGTGATTCGGTGTT 58.781 47.619 7.28 0.00 43.91 3.32
2569 8769 3.254470 TCGGTGTTGTTGTTCTTCTCA 57.746 42.857 0.00 0.00 0.00 3.27
2671 8871 1.210478 ACTGAGGTGAAGTGTGCAAGT 59.790 47.619 0.00 0.00 0.00 3.16
2789 8989 5.244626 GGTTTAGTACAGGTCCTGAGTACAA 59.755 44.000 26.18 11.57 40.32 2.41
2792 8992 3.769844 AGTACAGGTCCTGAGTACAATGG 59.230 47.826 26.18 0.00 40.32 3.16
2832 9032 0.394565 GTCTTGTGGGCAGTCAGTCT 59.605 55.000 0.00 0.00 0.00 3.24
3071 9914 1.337260 GCACCCTATCCTAGACATGCG 60.337 57.143 0.00 0.00 0.00 4.73
3237 13302 9.866655 ATTTGTGCCTAGGAGATTTAATTATCA 57.133 29.630 14.75 0.00 0.00 2.15
3293 13359 0.818938 ATGCGCTTTGATTGCCATCA 59.181 45.000 9.73 0.00 37.67 3.07
3300 13366 2.832643 TTGATTGCCATCAGGTCCAT 57.167 45.000 0.24 0.00 40.66 3.41
3304 13370 4.401022 TGATTGCCATCAGGTCCATATTC 58.599 43.478 0.00 0.00 34.22 1.75
3333 13399 4.440525 CGCCTTCCTTTTGCATGAATGTAT 60.441 41.667 0.00 0.00 0.00 2.29
3334 13400 5.221028 CGCCTTCCTTTTGCATGAATGTATA 60.221 40.000 0.00 0.00 0.00 1.47
3335 13401 6.211515 GCCTTCCTTTTGCATGAATGTATAG 58.788 40.000 0.00 0.00 0.00 1.31
3336 13402 6.183360 GCCTTCCTTTTGCATGAATGTATAGT 60.183 38.462 0.00 0.00 0.00 2.12
3337 13403 7.013274 GCCTTCCTTTTGCATGAATGTATAGTA 59.987 37.037 0.00 0.00 0.00 1.82
3338 13404 8.902806 CCTTCCTTTTGCATGAATGTATAGTAA 58.097 33.333 0.00 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 7.571892 TGTTGCAATGCATATACGTAACATAG 58.428 34.615 9.39 0.00 38.76 2.23
3 4 6.370433 TGTTGCAATGCATATACGTAACAT 57.630 33.333 9.39 0.00 38.76 2.71
4 5 5.220758 CCTGTTGCAATGCATATACGTAACA 60.221 40.000 9.39 6.85 38.76 2.41
5 6 5.204833 CCTGTTGCAATGCATATACGTAAC 58.795 41.667 9.39 1.75 38.76 2.50
66 67 3.315191 GCCAGAACACTTGCTAAAACTGA 59.685 43.478 0.00 0.00 0.00 3.41
88 89 2.775890 CCAAGGCTATGCATAGGAGTG 58.224 52.381 30.14 10.25 0.00 3.51
140 142 2.930950 TCATTTTTATGAGAGGGGCGG 58.069 47.619 0.00 0.00 0.00 6.13
142 144 6.015180 TGCAATATCATTTTTATGAGAGGGGC 60.015 38.462 0.00 0.00 33.59 5.80
208 354 7.815549 TCATGATTTGCTCTAGTTTTACGTGTA 59.184 33.333 0.00 0.00 0.00 2.90
239 385 3.078097 TGCTCTAGTTTTATGCGCCAAA 58.922 40.909 4.18 1.96 0.00 3.28
241 387 2.394930 TGCTCTAGTTTTATGCGCCA 57.605 45.000 4.18 0.00 0.00 5.69
243 389 6.255215 TGTTATTTGCTCTAGTTTTATGCGC 58.745 36.000 0.00 0.00 0.00 6.09
323 481 5.803461 CACGACACTTATTTTGGATCGTAGA 59.197 40.000 0.00 0.00 39.14 2.59
386 544 1.367346 TTTCCCTGGCATGTGGACTA 58.633 50.000 0.00 0.00 0.00 2.59
421 579 5.759506 TTGCTCTTGTTTTATGAAACCGA 57.240 34.783 10.29 6.39 43.57 4.69
497 658 0.468226 ACGAACCAAACTGCCTCTCA 59.532 50.000 0.00 0.00 0.00 3.27
498 659 0.868406 CACGAACCAAACTGCCTCTC 59.132 55.000 0.00 0.00 0.00 3.20
499 660 0.180406 ACACGAACCAAACTGCCTCT 59.820 50.000 0.00 0.00 0.00 3.69
500 661 0.586802 GACACGAACCAAACTGCCTC 59.413 55.000 0.00 0.00 0.00 4.70
501 662 0.818040 GGACACGAACCAAACTGCCT 60.818 55.000 0.00 0.00 0.00 4.75
502 663 1.098712 TGGACACGAACCAAACTGCC 61.099 55.000 0.00 0.00 34.25 4.85
503 664 0.028902 GTGGACACGAACCAAACTGC 59.971 55.000 0.00 0.00 39.22 4.40
504 665 1.330521 CTGTGGACACGAACCAAACTG 59.669 52.381 0.00 0.00 39.22 3.16
505 666 1.065709 ACTGTGGACACGAACCAAACT 60.066 47.619 0.00 0.00 39.22 2.66
506 667 1.375551 ACTGTGGACACGAACCAAAC 58.624 50.000 0.00 0.00 39.22 2.93
507 668 1.740585 CAACTGTGGACACGAACCAAA 59.259 47.619 0.00 0.00 39.22 3.28
508 669 1.374560 CAACTGTGGACACGAACCAA 58.625 50.000 0.00 0.00 39.22 3.67
509 670 1.092921 GCAACTGTGGACACGAACCA 61.093 55.000 0.00 0.00 34.84 3.67
510 671 1.647084 GCAACTGTGGACACGAACC 59.353 57.895 0.00 0.00 0.00 3.62
511 672 1.275657 CGCAACTGTGGACACGAAC 59.724 57.895 0.00 0.00 0.00 3.95
512 673 1.153529 ACGCAACTGTGGACACGAA 60.154 52.632 0.00 0.00 0.00 3.85
513 674 1.880796 CACGCAACTGTGGACACGA 60.881 57.895 0.00 0.00 36.20 4.35
514 675 2.625906 CACGCAACTGTGGACACG 59.374 61.111 0.00 0.00 36.20 4.49
515 676 2.327940 GCACGCAACTGTGGACAC 59.672 61.111 0.00 0.00 40.26 3.67
516 677 2.899838 GGCACGCAACTGTGGACA 60.900 61.111 0.00 0.00 40.26 4.02
517 678 2.591715 AGGCACGCAACTGTGGAC 60.592 61.111 0.00 0.00 40.26 4.02
518 679 2.591429 CAGGCACGCAACTGTGGA 60.591 61.111 0.00 0.00 40.26 4.02
519 680 3.663176 CCAGGCACGCAACTGTGG 61.663 66.667 0.00 0.00 40.26 4.17
520 681 1.163420 TTACCAGGCACGCAACTGTG 61.163 55.000 0.00 0.00 42.81 3.66
521 682 0.250727 ATTACCAGGCACGCAACTGT 60.251 50.000 0.00 0.00 32.90 3.55
522 683 0.447801 GATTACCAGGCACGCAACTG 59.552 55.000 0.00 0.00 34.54 3.16
523 684 0.324943 AGATTACCAGGCACGCAACT 59.675 50.000 0.00 0.00 0.00 3.16
524 685 1.165270 AAGATTACCAGGCACGCAAC 58.835 50.000 0.00 0.00 0.00 4.17
525 686 1.904287 AAAGATTACCAGGCACGCAA 58.096 45.000 0.00 0.00 0.00 4.85
526 687 1.539388 CAAAAGATTACCAGGCACGCA 59.461 47.619 0.00 0.00 0.00 5.24
527 688 1.539827 ACAAAAGATTACCAGGCACGC 59.460 47.619 0.00 0.00 0.00 5.34
528 689 2.811431 TGACAAAAGATTACCAGGCACG 59.189 45.455 0.00 0.00 0.00 5.34
529 690 3.191371 CCTGACAAAAGATTACCAGGCAC 59.809 47.826 0.00 0.00 33.42 5.01
530 691 3.073798 TCCTGACAAAAGATTACCAGGCA 59.926 43.478 0.00 0.00 37.29 4.75
531 692 3.440522 GTCCTGACAAAAGATTACCAGGC 59.559 47.826 0.00 0.00 37.29 4.85
532 693 4.911390 AGTCCTGACAAAAGATTACCAGG 58.089 43.478 0.00 0.00 38.05 4.45
533 694 4.938226 GGAGTCCTGACAAAAGATTACCAG 59.062 45.833 0.41 0.00 0.00 4.00
534 695 4.349636 TGGAGTCCTGACAAAAGATTACCA 59.650 41.667 11.33 0.00 0.00 3.25
535 696 4.906618 TGGAGTCCTGACAAAAGATTACC 58.093 43.478 11.33 0.00 0.00 2.85
536 697 5.181433 GGTTGGAGTCCTGACAAAAGATTAC 59.819 44.000 11.33 0.00 0.00 1.89
537 698 5.163141 TGGTTGGAGTCCTGACAAAAGATTA 60.163 40.000 11.33 0.00 0.00 1.75
538 699 4.145052 GGTTGGAGTCCTGACAAAAGATT 58.855 43.478 11.33 0.00 0.00 2.40
539 700 3.138283 TGGTTGGAGTCCTGACAAAAGAT 59.862 43.478 11.33 0.00 0.00 2.40
540 701 2.507886 TGGTTGGAGTCCTGACAAAAGA 59.492 45.455 11.33 0.00 0.00 2.52
541 702 2.930950 TGGTTGGAGTCCTGACAAAAG 58.069 47.619 11.33 0.00 0.00 2.27
542 703 3.374042 TTGGTTGGAGTCCTGACAAAA 57.626 42.857 11.33 5.37 0.00 2.44
543 704 3.020984 GTTTGGTTGGAGTCCTGACAAA 58.979 45.455 11.33 14.60 0.00 2.83
544 705 2.241176 AGTTTGGTTGGAGTCCTGACAA 59.759 45.455 11.33 9.52 0.00 3.18
545 706 1.843851 AGTTTGGTTGGAGTCCTGACA 59.156 47.619 11.33 3.45 0.00 3.58
546 707 2.222027 CAGTTTGGTTGGAGTCCTGAC 58.778 52.381 11.33 9.08 0.00 3.51
547 708 1.476833 GCAGTTTGGTTGGAGTCCTGA 60.477 52.381 11.33 0.00 0.00 3.86
548 709 0.954452 GCAGTTTGGTTGGAGTCCTG 59.046 55.000 11.33 0.00 0.00 3.86
549 710 0.178990 GGCAGTTTGGTTGGAGTCCT 60.179 55.000 11.33 0.00 0.00 3.85
550 711 1.179174 GGGCAGTTTGGTTGGAGTCC 61.179 60.000 0.73 0.73 0.00 3.85
551 712 1.179174 GGGGCAGTTTGGTTGGAGTC 61.179 60.000 0.00 0.00 0.00 3.36
552 713 1.152546 GGGGCAGTTTGGTTGGAGT 60.153 57.895 0.00 0.00 0.00 3.85
553 714 1.153756 AGGGGCAGTTTGGTTGGAG 59.846 57.895 0.00 0.00 0.00 3.86
554 715 1.152567 CAGGGGCAGTTTGGTTGGA 60.153 57.895 0.00 0.00 0.00 3.53
555 716 1.152567 TCAGGGGCAGTTTGGTTGG 60.153 57.895 0.00 0.00 0.00 3.77
556 717 0.468029 ACTCAGGGGCAGTTTGGTTG 60.468 55.000 0.00 0.00 0.00 3.77
557 718 0.468029 CACTCAGGGGCAGTTTGGTT 60.468 55.000 0.00 0.00 0.00 3.67
558 719 1.151450 CACTCAGGGGCAGTTTGGT 59.849 57.895 0.00 0.00 0.00 3.67
559 720 2.270986 GCACTCAGGGGCAGTTTGG 61.271 63.158 0.00 0.00 0.00 3.28
560 721 1.529010 TGCACTCAGGGGCAGTTTG 60.529 57.895 0.00 0.00 34.58 2.93
561 722 1.529244 GTGCACTCAGGGGCAGTTT 60.529 57.895 10.32 0.00 41.35 2.66
562 723 2.113986 GTGCACTCAGGGGCAGTT 59.886 61.111 10.32 0.00 41.35 3.16
563 724 2.072874 ATTGTGCACTCAGGGGCAGT 62.073 55.000 19.41 0.00 41.35 4.40
564 725 1.303888 ATTGTGCACTCAGGGGCAG 60.304 57.895 19.41 0.00 41.35 4.85
565 726 1.604308 CATTGTGCACTCAGGGGCA 60.604 57.895 19.41 0.00 37.77 5.36
566 727 2.998279 GCATTGTGCACTCAGGGGC 61.998 63.158 19.41 9.30 44.26 5.80
567 728 3.281240 GCATTGTGCACTCAGGGG 58.719 61.111 19.41 2.96 44.26 4.79
611 772 0.622665 CTTTGCATCCCCCTCTCACT 59.377 55.000 0.00 0.00 0.00 3.41
684 845 5.981088 ATGATAAACTTGACAATGTGGCA 57.019 34.783 0.00 0.00 30.30 4.92
743 963 3.760684 CCCCTTATGATCAAAGCCATAGC 59.239 47.826 0.00 0.00 40.32 2.97
746 966 3.052642 ACACCCCTTATGATCAAAGCCAT 60.053 43.478 0.00 0.00 0.00 4.40
755 975 2.158813 CGCCTAACACACCCCTTATGAT 60.159 50.000 0.00 0.00 0.00 2.45
756 976 1.208535 CGCCTAACACACCCCTTATGA 59.791 52.381 0.00 0.00 0.00 2.15
757 977 1.208535 TCGCCTAACACACCCCTTATG 59.791 52.381 0.00 0.00 0.00 1.90
904 1132 7.014615 ACCTATGCCATCCAATGATAAACTTTC 59.985 37.037 0.00 0.00 0.00 2.62
1023 1251 7.819644 CATGTCCAATCTTACATGTTTCAGAA 58.180 34.615 2.30 0.00 45.08 3.02
1141 1389 6.719829 CCCCTAGACAATTTGAAGGTAAAACT 59.280 38.462 2.79 0.00 0.00 2.66
1167 1416 3.003378 GCAACTTCTTGACCACCTAACAC 59.997 47.826 0.00 0.00 0.00 3.32
1378 1627 5.525012 TGATATGATGTTGTGTTGCTAGAGC 59.475 40.000 0.00 0.00 42.50 4.09
1511 1776 5.347124 TGGTGGAGATAAAGAAGTTCCCTA 58.653 41.667 0.00 0.00 0.00 3.53
1516 1781 7.461749 TGAATCTTGGTGGAGATAAAGAAGTT 58.538 34.615 0.00 0.00 35.37 2.66
1566 1831 4.964593 AGCAAAACATTTCCAGCTTTCAT 58.035 34.783 0.00 0.00 0.00 2.57
1592 1857 4.574013 GCTATCTTGGGTTTCATCTCTGTG 59.426 45.833 0.00 0.00 0.00 3.66
1630 1895 2.158813 TGGTTATCGCCAAAGATCCTCC 60.159 50.000 0.00 0.00 35.25 4.30
1877 7947 4.642885 TGGTTTGACCATTCGAGTTTCTTT 59.357 37.500 0.00 0.00 44.79 2.52
2044 8199 2.222027 CCGCCCTTCTTTCCACATATC 58.778 52.381 0.00 0.00 0.00 1.63
2211 8370 1.668151 GTCCGGAACTGTGGTGCTC 60.668 63.158 5.23 0.00 0.00 4.26
2221 8380 1.449070 GACGATTGGGGTCCGGAAC 60.449 63.158 12.37 12.37 0.00 3.62
2316 8475 3.105283 ACGCCCCTCTATTTCAGTAAGT 58.895 45.455 0.00 0.00 0.00 2.24
2452 8616 4.284746 TCAGGCCCAAAACGGAATAAAAAT 59.715 37.500 0.00 0.00 36.56 1.82
2514 8680 7.865385 TGTCCAATAAGTACTGAATTTTGTTGC 59.135 33.333 0.00 0.00 0.00 4.17
2555 8755 3.118261 AGAGTGGCTGAGAAGAACAACAA 60.118 43.478 0.00 0.00 0.00 2.83
2556 8756 2.435805 AGAGTGGCTGAGAAGAACAACA 59.564 45.455 0.00 0.00 0.00 3.33
2671 8871 3.138304 ACTTCAAAGCTGCGTATGAACA 58.862 40.909 11.77 0.00 0.00 3.18
2789 8989 0.777446 AACAGGCCAGGTACAACCAT 59.223 50.000 5.01 0.00 41.95 3.55
2792 8992 2.028876 ACAAAACAGGCCAGGTACAAC 58.971 47.619 5.01 0.00 0.00 3.32
2832 9032 6.419413 CGTTTGCAGGCTTTAGTCAAATTTTA 59.581 34.615 0.00 0.00 0.00 1.52
2862 9068 8.397148 GTCAAATTTTGTGTCCAATCATTTTGT 58.603 29.630 8.89 0.00 28.51 2.83
3003 9431 9.526713 GCTGGTGACATATCTACTCATTATATG 57.473 37.037 0.00 0.00 41.51 1.78
3026 9454 3.560481 TGCACCATGTTTTTCAATTGCTG 59.440 39.130 0.00 0.00 33.30 4.41
3060 9903 6.035435 GCATTCATCTTATACGCATGTCTAGG 59.965 42.308 0.00 0.00 0.00 3.02
3071 9914 6.460123 CCAACCACCAAGCATTCATCTTATAC 60.460 42.308 0.00 0.00 0.00 1.47
3278 13344 1.135721 GGACCTGATGGCAATCAAAGC 59.864 52.381 5.04 0.00 42.28 3.51
3293 13359 2.050269 CGGGCTCGAATATGGACCT 58.950 57.895 0.00 0.00 39.00 3.85
3300 13366 1.335132 AAGGAAGGCGGGCTCGAATA 61.335 55.000 12.03 0.00 39.00 1.75
3304 13370 2.359975 AAAAGGAAGGCGGGCTCG 60.360 61.111 0.00 0.00 39.81 5.03


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

AutoCloner maintained by Alex Coulton.