Multiple sequence alignment - TraesCS1A01G078400

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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 TraesCS1A01G078400 chr1A 100.000 3154 0 0 1 3154 61031277 61034430 0.000000e+00 5825.0
1 TraesCS1A01G078400 chr1A 96.207 1740 59 5 911 2647 61284052 61285787 0.000000e+00 2841.0
2 TraesCS1A01G078400 chr1A 93.298 1328 77 5 1324 2646 61341449 61342769 0.000000e+00 1949.0
3 TraesCS1A01G078400 chr1A 85.415 1001 124 17 1310 2295 62254283 62253290 0.000000e+00 1020.0
4 TraesCS1A01G078400 chr1A 83.479 799 132 0 1363 2161 61009399 61010197 0.000000e+00 745.0
5 TraesCS1A01G078400 chr1A 94.771 459 19 2 2189 2647 61158378 61158831 0.000000e+00 710.0
6 TraesCS1A01G078400 chr1A 87.751 498 35 8 758 1255 61340949 61341420 2.750000e-155 558.0
7 TraesCS1A01G078400 chr1A 87.327 505 36 11 2661 3154 61158816 61159303 1.280000e-153 553.0
8 TraesCS1A01G078400 chr1A 82.988 482 61 9 775 1255 62254920 62254459 1.750000e-112 416.0
9 TraesCS1A01G078400 chr1A 89.597 298 27 4 2322 2618 61252495 61252789 2.970000e-100 375.0
10 TraesCS1A01G078400 chr1A 89.420 293 27 4 2322 2613 61023278 61023567 1.790000e-97 366.0
11 TraesCS1A01G078400 chr1A 96.729 214 7 0 702 915 61269806 61270019 1.080000e-94 357.0
12 TraesCS1A01G078400 chr1A 92.797 236 17 0 2661 2896 61285772 61286007 3.010000e-90 342.0
13 TraesCS1A01G078400 chr1A 91.593 226 19 0 2661 2886 61342755 61342980 2.360000e-81 313.0
14 TraesCS1A01G078400 chr1A 86.232 138 18 1 2886 3023 61294844 61294980 7.050000e-32 148.0
15 TraesCS1A01G078400 chr1A 92.857 84 6 0 3071 3154 461055947 461055864 4.270000e-24 122.0
16 TraesCS1A01G078400 chr1A 93.056 72 5 0 2945 3016 61378441 61378512 4.300000e-19 106.0
17 TraesCS1A01G078400 chr1A 93.478 46 2 1 2250 2295 62249724 62249680 2.030000e-07 67.6
18 TraesCS1A01G078400 chr1D 92.316 1822 104 19 702 2515 62935460 62937253 0.000000e+00 2556.0
19 TraesCS1A01G078400 chr1D 86.787 999 110 16 1310 2295 63357325 63358314 0.000000e+00 1094.0
20 TraesCS1A01G078400 chr1D 82.805 442 53 14 823 1261 63356896 63357317 1.070000e-99 374.0
21 TraesCS1A01G078400 chr1D 87.821 312 30 2 2713 3016 62953021 62953332 2.990000e-95 359.0
22 TraesCS1A01G078400 chr1D 83.129 326 39 12 2324 2641 62930959 62931276 1.850000e-72 283.0
23 TraesCS1A01G078400 chr1D 93.443 122 7 1 2507 2627 62938682 62938803 2.500000e-41 180.0
24 TraesCS1A01G078400 chr1D 92.857 84 6 0 3071 3154 319068532 319068615 4.270000e-24 122.0
25 TraesCS1A01G078400 chr1D 91.667 84 7 0 3071 3154 452901849 452901766 1.990000e-22 117.0
26 TraesCS1A01G078400 chr1B 93.378 1495 92 4 988 2478 100541421 100542912 0.000000e+00 2206.0
27 TraesCS1A01G078400 chr1B 91.960 995 71 7 1310 2297 100631308 100632300 0.000000e+00 1386.0
28 TraesCS1A01G078400 chr1B 85.529 1002 121 19 1310 2295 101143252 101144245 0.000000e+00 1026.0
29 TraesCS1A01G078400 chr1B 94.376 569 28 3 1 568 9634735 9634170 0.000000e+00 870.0
30 TraesCS1A01G078400 chr1B 88.800 500 29 11 756 1255 100630813 100631285 3.500000e-164 588.0
31 TraesCS1A01G078400 chr1B 86.157 549 42 5 31 565 13532330 13532858 2.120000e-156 562.0
32 TraesCS1A01G078400 chr1B 94.562 331 17 1 2317 2647 100645745 100646074 7.800000e-141 510.0
33 TraesCS1A01G078400 chr1B 87.010 408 27 15 1 408 81755416 81755035 1.340000e-118 436.0
34 TraesCS1A01G078400 chr1B 88.043 368 29 10 2661 3016 100646059 100646423 3.760000e-114 422.0
35 TraesCS1A01G078400 chr1B 82.526 475 61 10 775 1248 101142773 101143226 6.340000e-107 398.0
36 TraesCS1A01G078400 chr1B 95.455 176 8 0 2472 2647 100553411 100553586 6.660000e-72 281.0
37 TraesCS1A01G078400 chr1B 87.129 202 13 3 2661 2857 100553571 100553764 1.900000e-52 217.0
38 TraesCS1A01G078400 chr1B 83.043 230 36 1 1019 1248 100422319 100422545 4.120000e-49 206.0
39 TraesCS1A01G078400 chr1B 92.000 150 7 1 751 900 100539625 100539769 4.120000e-49 206.0
40 TraesCS1A01G078400 chr1B 95.312 64 2 1 702 765 100539545 100539607 2.000000e-17 100.0
41 TraesCS1A01G078400 chr4A 98.934 563 4 2 1 562 589663318 589662757 0.000000e+00 1005.0
42 TraesCS1A01G078400 chr4A 92.029 138 7 3 569 704 552814817 552814952 1.150000e-44 191.0
43 TraesCS1A01G078400 chr6A 97.891 569 11 1 1 569 491036244 491036811 0.000000e+00 983.0
44 TraesCS1A01G078400 chr6A 86.308 577 55 10 1 569 99499 100059 9.670000e-170 606.0
45 TraesCS1A01G078400 chr5A 99.263 407 2 1 162 568 650679893 650679488 0.000000e+00 734.0
46 TraesCS1A01G078400 chr5A 91.971 137 9 2 569 704 649196152 649196017 1.150000e-44 191.0
47 TraesCS1A01G078400 chr5A 93.750 128 2 1 1 128 650680013 650679892 1.490000e-43 187.0
48 TraesCS1A01G078400 chrUn 86.364 198 24 3 379 574 461775547 461775351 2.460000e-51 213.0
49 TraesCS1A01G078400 chr2D 86.387 191 25 1 379 569 23110197 23110008 1.150000e-49 207.0
50 TraesCS1A01G078400 chr2D 91.971 137 9 2 569 704 284560041 284560176 1.150000e-44 191.0
51 TraesCS1A01G078400 chr2D 91.765 85 7 0 3070 3154 601982386 601982470 5.530000e-23 119.0
52 TraesCS1A01G078400 chr2D 87.037 54 4 3 2956 3008 617101048 617101099 1.220000e-04 58.4
53 TraesCS1A01G078400 chr2B 85.789 190 25 2 379 568 392036324 392036511 1.920000e-47 200.0
54 TraesCS1A01G078400 chr2B 89.000 100 9 2 3055 3154 126168492 126168395 4.270000e-24 122.0
55 TraesCS1A01G078400 chr7D 93.333 135 8 1 569 703 550550763 550550896 6.900000e-47 198.0
56 TraesCS1A01G078400 chr7D 92.857 84 6 0 3071 3154 1956694 1956777 4.270000e-24 122.0
57 TraesCS1A01G078400 chr2A 92.029 138 9 2 569 705 445710869 445710733 3.210000e-45 193.0
58 TraesCS1A01G078400 chr2A 83.333 144 23 1 421 564 749805709 749805567 7.100000e-27 132.0
59 TraesCS1A01G078400 chr2A 87.037 54 4 3 2956 3008 747272162 747272213 1.220000e-04 58.4
60 TraesCS1A01G078400 chr5D 91.971 137 9 2 569 704 324227895 324227760 1.150000e-44 191.0
61 TraesCS1A01G078400 chr3D 91.971 137 9 2 569 704 108290927 108291062 1.150000e-44 191.0
62 TraesCS1A01G078400 chr3D 91.667 84 7 0 3071 3154 79666604 79666687 1.990000e-22 117.0
63 TraesCS1A01G078400 chr3D 81.319 91 12 4 2980 3069 313816927 313816841 5.640000e-08 69.4
64 TraesCS1A01G078400 chr3B 91.971 137 10 1 569 705 29632205 29632340 1.150000e-44 191.0
65 TraesCS1A01G078400 chr3B 79.121 91 13 4 2980 3069 405783505 405783590 1.220000e-04 58.4
66 TraesCS1A01G078400 chr4D 91.367 139 10 2 569 706 367049373 367049236 4.150000e-44 189.0
67 TraesCS1A01G078400 chr4D 91.667 84 7 0 3071 3154 447293811 447293728 1.990000e-22 117.0
68 TraesCS1A01G078400 chr3A 82.418 91 12 3 2980 3069 416307138 416307051 3.370000e-10 76.8
69 TraesCS1A01G078400 chr7A 84.286 70 8 3 2968 3035 735953935 735954003 7.300000e-07 65.8
70 TraesCS1A01G078400 chr7B 84.375 64 7 2 2947 3008 687243051 687242989 3.400000e-05 60.2
71 TraesCS1A01G078400 chr7B 84.375 64 7 2 2947 3008 687685260 687685322 3.400000e-05 60.2
72 TraesCS1A01G078400 chr6D 78.351 97 12 8 2980 3069 183708550 183708456 2.000000e-03 54.7


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 TraesCS1A01G078400 chr1A 61031277 61034430 3153 False 5825.000000 5825 100.000000 1 3154 1 chr1A.!!$F3 3153
1 TraesCS1A01G078400 chr1A 61284052 61286007 1955 False 1591.500000 2841 94.502000 911 2896 2 chr1A.!!$F9 1985
2 TraesCS1A01G078400 chr1A 61340949 61342980 2031 False 940.000000 1949 90.880667 758 2886 3 chr1A.!!$F10 2128
3 TraesCS1A01G078400 chr1A 61009399 61010197 798 False 745.000000 745 83.479000 1363 2161 1 chr1A.!!$F1 798
4 TraesCS1A01G078400 chr1A 61158378 61159303 925 False 631.500000 710 91.049000 2189 3154 2 chr1A.!!$F8 965
5 TraesCS1A01G078400 chr1A 62249680 62254920 5240 True 501.200000 1020 87.293667 775 2295 3 chr1A.!!$R2 1520
6 TraesCS1A01G078400 chr1D 62935460 62938803 3343 False 1368.000000 2556 92.879500 702 2627 2 chr1D.!!$F4 1925
7 TraesCS1A01G078400 chr1D 63356896 63358314 1418 False 734.000000 1094 84.796000 823 2295 2 chr1D.!!$F5 1472
8 TraesCS1A01G078400 chr1B 100630813 100632300 1487 False 987.000000 1386 90.380000 756 2297 2 chr1B.!!$F5 1541
9 TraesCS1A01G078400 chr1B 9634170 9634735 565 True 870.000000 870 94.376000 1 568 1 chr1B.!!$R1 567
10 TraesCS1A01G078400 chr1B 100539545 100542912 3367 False 837.333333 2206 93.563333 702 2478 3 chr1B.!!$F3 1776
11 TraesCS1A01G078400 chr1B 101142773 101144245 1472 False 712.000000 1026 84.027500 775 2295 2 chr1B.!!$F7 1520
12 TraesCS1A01G078400 chr1B 13532330 13532858 528 False 562.000000 562 86.157000 31 565 1 chr1B.!!$F1 534
13 TraesCS1A01G078400 chr1B 100645745 100646423 678 False 466.000000 510 91.302500 2317 3016 2 chr1B.!!$F6 699
14 TraesCS1A01G078400 chr4A 589662757 589663318 561 True 1005.000000 1005 98.934000 1 562 1 chr4A.!!$R1 561
15 TraesCS1A01G078400 chr6A 491036244 491036811 567 False 983.000000 983 97.891000 1 569 1 chr6A.!!$F2 568
16 TraesCS1A01G078400 chr6A 99499 100059 560 False 606.000000 606 86.308000 1 569 1 chr6A.!!$F1 568
17 TraesCS1A01G078400 chr5A 650679488 650680013 525 True 460.500000 734 96.506500 1 568 2 chr5A.!!$R2 567

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
694 719 0.108898 CGCCCTGTGAACTGAGAGAG 60.109 60.000 0.0 0.0 0.0 3.2 F
696 721 1.204467 GCCCTGTGAACTGAGAGAGAG 59.796 57.143 0.0 0.0 0.0 3.2 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1821 3585 2.048597 TGCCGCGTAGAACCTGTG 60.049 61.111 4.92 0.0 0.0 3.66 R
2400 7803 2.348218 CCTTGTTTGTAGCGACGTGAAC 60.348 50.000 0.00 0.0 0.0 3.18 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
35 36 9.988815 GCTCAACCCTAACTGGATATATATATG 57.011 37.037 10.03 0.00 38.35 1.78
109 118 0.691413 GGGAGGGACGGAAGGAAGAT 60.691 60.000 0.00 0.00 0.00 2.40
419 435 4.263462 ACAAGGGAATTGACAGACATGCTA 60.263 41.667 0.00 0.00 41.83 3.49
569 594 4.213270 CACAATCACCGTAAAAGAGCTCAA 59.787 41.667 17.77 0.00 0.00 3.02
570 595 4.819630 ACAATCACCGTAAAAGAGCTCAAA 59.180 37.500 17.77 0.00 0.00 2.69
571 596 5.473504 ACAATCACCGTAAAAGAGCTCAAAT 59.526 36.000 17.77 3.35 0.00 2.32
572 597 6.016276 ACAATCACCGTAAAAGAGCTCAAATT 60.016 34.615 17.77 9.98 0.00 1.82
573 598 7.174253 ACAATCACCGTAAAAGAGCTCAAATTA 59.826 33.333 17.77 8.96 0.00 1.40
574 599 7.865706 ATCACCGTAAAAGAGCTCAAATTAT 57.134 32.000 17.77 0.00 0.00 1.28
575 600 8.958119 ATCACCGTAAAAGAGCTCAAATTATA 57.042 30.769 17.77 0.00 0.00 0.98
576 601 8.780846 TCACCGTAAAAGAGCTCAAATTATAA 57.219 30.769 17.77 0.00 0.00 0.98
577 602 9.221933 TCACCGTAAAAGAGCTCAAATTATAAA 57.778 29.630 17.77 0.00 0.00 1.40
578 603 9.274065 CACCGTAAAAGAGCTCAAATTATAAAC 57.726 33.333 17.77 2.25 0.00 2.01
579 604 8.173130 ACCGTAAAAGAGCTCAAATTATAAACG 58.827 33.333 17.77 12.72 0.00 3.60
580 605 8.173130 CCGTAAAAGAGCTCAAATTATAAACGT 58.827 33.333 17.77 0.00 0.00 3.99
581 606 9.537848 CGTAAAAGAGCTCAAATTATAAACGTT 57.462 29.630 17.77 0.00 0.00 3.99
583 608 8.655378 AAAAGAGCTCAAATTATAAACGTTCG 57.345 30.769 17.77 0.00 0.00 3.95
584 609 7.591006 AAGAGCTCAAATTATAAACGTTCGA 57.409 32.000 17.77 0.00 0.00 3.71
585 610 7.591006 AGAGCTCAAATTATAAACGTTCGAA 57.409 32.000 17.77 0.00 0.00 3.71
586 611 8.025243 AGAGCTCAAATTATAAACGTTCGAAA 57.975 30.769 17.77 0.00 0.00 3.46
587 612 8.500773 AGAGCTCAAATTATAAACGTTCGAAAA 58.499 29.630 17.77 0.00 0.00 2.29
588 613 9.274065 GAGCTCAAATTATAAACGTTCGAAAAT 57.726 29.630 9.40 0.00 0.00 1.82
596 621 9.977762 ATTATAAACGTTCGAAAATAGAACACC 57.022 29.630 0.00 0.00 45.93 4.16
597 622 5.996669 AAACGTTCGAAAATAGAACACCT 57.003 34.783 0.00 0.00 45.93 4.00
598 623 4.985044 ACGTTCGAAAATAGAACACCTG 57.015 40.909 0.00 0.00 45.93 4.00
599 624 4.624015 ACGTTCGAAAATAGAACACCTGA 58.376 39.130 0.00 0.00 45.93 3.86
600 625 5.051816 ACGTTCGAAAATAGAACACCTGAA 58.948 37.500 0.00 0.00 45.93 3.02
601 626 5.176958 ACGTTCGAAAATAGAACACCTGAAG 59.823 40.000 0.00 0.00 45.93 3.02
602 627 5.176958 CGTTCGAAAATAGAACACCTGAAGT 59.823 40.000 0.00 0.00 45.93 3.01
603 628 6.292703 CGTTCGAAAATAGAACACCTGAAGTT 60.293 38.462 0.00 0.00 45.93 2.66
604 629 7.415229 GTTCGAAAATAGAACACCTGAAGTTT 58.585 34.615 0.00 0.00 45.21 2.66
605 630 8.553696 GTTCGAAAATAGAACACCTGAAGTTTA 58.446 33.333 0.00 0.00 45.21 2.01
606 631 8.842358 TCGAAAATAGAACACCTGAAGTTTAT 57.158 30.769 0.00 0.00 0.00 1.40
607 632 9.932207 TCGAAAATAGAACACCTGAAGTTTATA 57.068 29.630 0.00 0.00 0.00 0.98
652 677 9.920946 ATATGACTTGTATTAGGTTGGTCAAAT 57.079 29.630 0.00 0.00 36.16 2.32
653 678 8.650143 ATGACTTGTATTAGGTTGGTCAAATT 57.350 30.769 0.00 0.00 36.16 1.82
654 679 7.881142 TGACTTGTATTAGGTTGGTCAAATTG 58.119 34.615 0.00 0.00 30.81 2.32
655 680 7.721842 TGACTTGTATTAGGTTGGTCAAATTGA 59.278 33.333 0.00 0.00 30.81 2.57
656 681 8.650143 ACTTGTATTAGGTTGGTCAAATTGAT 57.350 30.769 0.00 0.00 0.00 2.57
657 682 8.522830 ACTTGTATTAGGTTGGTCAAATTGATG 58.477 33.333 0.00 0.00 0.00 3.07
658 683 8.642935 TTGTATTAGGTTGGTCAAATTGATGA 57.357 30.769 0.00 0.00 0.00 2.92
659 684 8.821686 TGTATTAGGTTGGTCAAATTGATGAT 57.178 30.769 0.00 0.00 0.00 2.45
660 685 8.902806 TGTATTAGGTTGGTCAAATTGATGATC 58.097 33.333 0.00 0.00 0.00 2.92
661 686 9.125026 GTATTAGGTTGGTCAAATTGATGATCT 57.875 33.333 0.00 0.00 31.51 2.75
663 688 8.737168 TTAGGTTGGTCAAATTGATGATCTAG 57.263 34.615 0.00 0.00 31.51 2.43
664 689 6.125029 AGGTTGGTCAAATTGATGATCTAGG 58.875 40.000 0.00 0.00 31.51 3.02
665 690 6.069440 AGGTTGGTCAAATTGATGATCTAGGA 60.069 38.462 0.00 0.00 31.51 2.94
666 691 6.261826 GGTTGGTCAAATTGATGATCTAGGAG 59.738 42.308 0.00 0.00 31.51 3.69
667 692 6.566079 TGGTCAAATTGATGATCTAGGAGT 57.434 37.500 0.00 0.00 31.51 3.85
668 693 7.675161 TGGTCAAATTGATGATCTAGGAGTA 57.325 36.000 0.00 0.00 31.51 2.59
669 694 7.500992 TGGTCAAATTGATGATCTAGGAGTAC 58.499 38.462 0.00 0.00 31.51 2.73
670 695 6.642950 GGTCAAATTGATGATCTAGGAGTACG 59.357 42.308 0.00 0.00 0.00 3.67
671 696 7.203910 GTCAAATTGATGATCTAGGAGTACGT 58.796 38.462 0.00 0.00 0.00 3.57
672 697 7.168302 GTCAAATTGATGATCTAGGAGTACGTG 59.832 40.741 0.00 0.00 0.00 4.49
673 698 4.569761 TTGATGATCTAGGAGTACGTGC 57.430 45.455 0.00 0.00 0.00 5.34
674 699 3.551846 TGATGATCTAGGAGTACGTGCA 58.448 45.455 6.38 0.00 0.00 4.57
675 700 3.315470 TGATGATCTAGGAGTACGTGCAC 59.685 47.826 6.82 6.82 0.00 4.57
676 701 1.669265 TGATCTAGGAGTACGTGCACG 59.331 52.381 35.99 35.99 46.33 5.34
677 702 0.381089 ATCTAGGAGTACGTGCACGC 59.619 55.000 37.35 22.81 44.43 5.34
678 703 1.226603 CTAGGAGTACGTGCACGCC 60.227 63.158 37.35 28.75 44.43 5.68
679 704 2.609183 CTAGGAGTACGTGCACGCCC 62.609 65.000 37.35 29.53 44.43 6.13
680 705 4.065281 GGAGTACGTGCACGCCCT 62.065 66.667 37.35 30.92 44.43 5.19
681 706 2.809601 GAGTACGTGCACGCCCTG 60.810 66.667 37.35 13.22 44.43 4.45
682 707 3.569049 GAGTACGTGCACGCCCTGT 62.569 63.158 37.35 20.98 44.43 4.00
691 716 3.870955 ACGCCCTGTGAACTGAGA 58.129 55.556 0.00 0.00 0.00 3.27
692 717 1.668294 ACGCCCTGTGAACTGAGAG 59.332 57.895 0.00 0.00 0.00 3.20
693 718 0.827925 ACGCCCTGTGAACTGAGAGA 60.828 55.000 0.00 0.00 0.00 3.10
694 719 0.108898 CGCCCTGTGAACTGAGAGAG 60.109 60.000 0.00 0.00 0.00 3.20
695 720 1.261480 GCCCTGTGAACTGAGAGAGA 58.739 55.000 0.00 0.00 0.00 3.10
696 721 1.204467 GCCCTGTGAACTGAGAGAGAG 59.796 57.143 0.00 0.00 0.00 3.20
697 722 1.824230 CCCTGTGAACTGAGAGAGAGG 59.176 57.143 0.00 0.00 0.00 3.69
698 723 1.824230 CCTGTGAACTGAGAGAGAGGG 59.176 57.143 0.00 0.00 0.00 4.30
699 724 2.556336 CCTGTGAACTGAGAGAGAGGGA 60.556 54.545 0.00 0.00 0.00 4.20
700 725 2.754552 CTGTGAACTGAGAGAGAGGGAG 59.245 54.545 0.00 0.00 0.00 4.30
968 2608 1.737793 CAGCCCACGAAACTAATCCAC 59.262 52.381 0.00 0.00 0.00 4.02
984 2624 7.251704 CTAATCCACAATTAGTTGCTTCGAT 57.748 36.000 0.00 0.00 41.30 3.59
986 2626 6.851222 ATCCACAATTAGTTGCTTCGATAG 57.149 37.500 0.00 0.00 38.96 2.08
998 2638 4.048241 GCTTCGATAGTAAGCTTCCAGT 57.952 45.455 0.00 0.00 44.75 4.00
1119 2759 5.584551 AGTTTCTGAAGGTTGGGTTCTAT 57.415 39.130 0.00 0.00 0.00 1.98
1344 3106 4.102210 AGGTACCTGATCTGACCATTGATG 59.898 45.833 15.42 0.00 34.18 3.07
1579 3341 2.125310 CGGCGGCATCAACTACCA 60.125 61.111 10.53 0.00 0.00 3.25
1617 3379 3.405592 GACGGCCGCGTGTCTATCA 62.406 63.158 28.58 0.00 32.37 2.15
1659 3421 3.315140 TGCCATTCCCGACCGACA 61.315 61.111 0.00 0.00 0.00 4.35
1892 3656 2.291043 CCCTAGCGACCCCACAACT 61.291 63.158 0.00 0.00 0.00 3.16
2311 7703 6.096282 TCAAAAAGAGTTTTTCTTCCATCCGT 59.904 34.615 0.00 0.00 45.41 4.69
2647 9495 8.849168 TGTGTCAGATGATTAATTGTCTTGTTT 58.151 29.630 0.00 0.00 0.00 2.83
2648 9496 9.683069 GTGTCAGATGATTAATTGTCTTGTTTT 57.317 29.630 0.00 0.00 0.00 2.43
2672 9520 5.476091 TTTTTGCGGGGATTAATTGTCTT 57.524 34.783 0.00 0.00 0.00 3.01
2673 9521 4.448537 TTTGCGGGGATTAATTGTCTTG 57.551 40.909 0.00 0.00 0.00 3.02
2674 9522 3.080300 TGCGGGGATTAATTGTCTTGT 57.920 42.857 0.00 0.00 0.00 3.16
2675 9523 3.426615 TGCGGGGATTAATTGTCTTGTT 58.573 40.909 0.00 0.00 0.00 2.83
2680 9528 7.504238 TGCGGGGATTAATTGTCTTGTTAATAT 59.496 33.333 0.00 0.00 32.31 1.28
2736 9587 5.335897 GCACATCAATATTGCCGGTGAATAT 60.336 40.000 25.11 9.04 0.00 1.28
2817 9668 5.407502 CATGAATACACACTCGTACCTTCA 58.592 41.667 0.00 0.00 29.56 3.02
2820 9671 2.631418 ACACACTCGTACCTTCATCG 57.369 50.000 0.00 0.00 0.00 3.84
2872 9723 5.868454 TCTTCATCACAGGAATTGTTCTCA 58.132 37.500 0.00 0.00 38.16 3.27
2898 9755 8.347004 TCATCAGGATAGATAAGCTTACTGAG 57.653 38.462 20.36 14.71 34.86 3.35
2926 9783 5.004061 TCGATCGAACTTATAAACTTGCGTG 59.996 40.000 16.99 0.00 0.00 5.34
2973 9833 6.246163 TCCTCGCCTCACTTCATATATTCTA 58.754 40.000 0.00 0.00 0.00 2.10
2978 9838 6.326375 GCCTCACTTCATATATTCTACCTCG 58.674 44.000 0.00 0.00 0.00 4.63
3020 9891 8.635765 TGTTCTAACTTTTCCTAAATCTGCAT 57.364 30.769 0.00 0.00 0.00 3.96
3029 9900 8.856153 TTTTCCTAAATCTGCATGTGTTAGTA 57.144 30.769 0.00 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 1.571460 CTCGTTGCAGCACCTTCAC 59.429 57.895 0.00 0.00 0.00 3.18
109 118 3.995809 CTCTTCCCCTGCCCCCGTA 62.996 68.421 0.00 0.00 0.00 4.02
570 595 9.977762 GGTGTTCTATTTTCGAACGTTTATAAT 57.022 29.630 0.46 4.15 42.73 1.28
571 596 9.206870 AGGTGTTCTATTTTCGAACGTTTATAA 57.793 29.630 0.46 0.00 42.73 0.98
572 597 8.649841 CAGGTGTTCTATTTTCGAACGTTTATA 58.350 33.333 0.46 0.00 42.73 0.98
573 598 7.385752 TCAGGTGTTCTATTTTCGAACGTTTAT 59.614 33.333 0.46 0.00 42.73 1.40
574 599 6.700960 TCAGGTGTTCTATTTTCGAACGTTTA 59.299 34.615 0.46 0.00 42.73 2.01
575 600 5.524646 TCAGGTGTTCTATTTTCGAACGTTT 59.475 36.000 0.46 0.00 42.73 3.60
576 601 5.051816 TCAGGTGTTCTATTTTCGAACGTT 58.948 37.500 0.00 0.00 42.73 3.99
577 602 4.624015 TCAGGTGTTCTATTTTCGAACGT 58.376 39.130 0.00 0.00 42.73 3.99
578 603 5.176958 ACTTCAGGTGTTCTATTTTCGAACG 59.823 40.000 0.00 0.00 42.73 3.95
579 604 6.541111 ACTTCAGGTGTTCTATTTTCGAAC 57.459 37.500 0.00 0.00 40.79 3.95
580 605 7.562454 AAACTTCAGGTGTTCTATTTTCGAA 57.438 32.000 0.00 0.00 0.00 3.71
581 606 8.842358 ATAAACTTCAGGTGTTCTATTTTCGA 57.158 30.769 0.00 0.00 0.00 3.71
626 651 9.920946 ATTTGACCAACCTAATACAAGTCATAT 57.079 29.630 0.00 0.00 33.21 1.78
627 652 9.747898 AATTTGACCAACCTAATACAAGTCATA 57.252 29.630 0.00 0.00 33.21 2.15
628 653 8.522830 CAATTTGACCAACCTAATACAAGTCAT 58.477 33.333 0.00 0.00 33.21 3.06
629 654 7.721842 TCAATTTGACCAACCTAATACAAGTCA 59.278 33.333 0.00 0.00 0.00 3.41
630 655 8.106247 TCAATTTGACCAACCTAATACAAGTC 57.894 34.615 0.00 0.00 0.00 3.01
631 656 8.522830 CATCAATTTGACCAACCTAATACAAGT 58.477 33.333 0.15 0.00 0.00 3.16
632 657 8.739039 TCATCAATTTGACCAACCTAATACAAG 58.261 33.333 0.15 0.00 0.00 3.16
633 658 8.642935 TCATCAATTTGACCAACCTAATACAA 57.357 30.769 0.15 0.00 0.00 2.41
634 659 8.821686 ATCATCAATTTGACCAACCTAATACA 57.178 30.769 0.15 0.00 0.00 2.29
635 660 9.125026 AGATCATCAATTTGACCAACCTAATAC 57.875 33.333 0.15 0.00 0.00 1.89
637 662 9.347240 CTAGATCATCAATTTGACCAACCTAAT 57.653 33.333 0.15 0.00 0.00 1.73
638 663 7.775093 CCTAGATCATCAATTTGACCAACCTAA 59.225 37.037 0.15 0.00 0.00 2.69
639 664 7.127186 TCCTAGATCATCAATTTGACCAACCTA 59.873 37.037 0.15 0.46 0.00 3.08
640 665 6.069440 TCCTAGATCATCAATTTGACCAACCT 60.069 38.462 0.15 0.00 0.00 3.50
641 666 6.122277 TCCTAGATCATCAATTTGACCAACC 58.878 40.000 0.15 0.00 0.00 3.77
642 667 6.825721 ACTCCTAGATCATCAATTTGACCAAC 59.174 38.462 0.15 0.00 0.00 3.77
643 668 6.962182 ACTCCTAGATCATCAATTTGACCAA 58.038 36.000 0.15 0.00 0.00 3.67
644 669 6.566079 ACTCCTAGATCATCAATTTGACCA 57.434 37.500 0.15 0.00 0.00 4.02
645 670 6.642950 CGTACTCCTAGATCATCAATTTGACC 59.357 42.308 0.15 0.00 0.00 4.02
646 671 7.168302 CACGTACTCCTAGATCATCAATTTGAC 59.832 40.741 0.15 0.00 0.00 3.18
647 672 7.203218 CACGTACTCCTAGATCATCAATTTGA 58.797 38.462 0.75 0.75 0.00 2.69
648 673 6.074088 GCACGTACTCCTAGATCATCAATTTG 60.074 42.308 0.00 0.00 0.00 2.32
649 674 5.986135 GCACGTACTCCTAGATCATCAATTT 59.014 40.000 0.00 0.00 0.00 1.82
650 675 5.069119 TGCACGTACTCCTAGATCATCAATT 59.931 40.000 0.00 0.00 0.00 2.32
651 676 4.584743 TGCACGTACTCCTAGATCATCAAT 59.415 41.667 0.00 0.00 0.00 2.57
652 677 3.951680 TGCACGTACTCCTAGATCATCAA 59.048 43.478 0.00 0.00 0.00 2.57
653 678 3.315470 GTGCACGTACTCCTAGATCATCA 59.685 47.826 0.00 0.00 0.00 3.07
654 679 3.607310 CGTGCACGTACTCCTAGATCATC 60.607 52.174 30.50 0.00 34.11 2.92
655 680 2.290916 CGTGCACGTACTCCTAGATCAT 59.709 50.000 30.50 0.00 34.11 2.45
656 681 1.669265 CGTGCACGTACTCCTAGATCA 59.331 52.381 30.50 0.00 34.11 2.92
657 682 1.597445 GCGTGCACGTACTCCTAGATC 60.597 57.143 36.80 14.50 42.22 2.75
658 683 0.381089 GCGTGCACGTACTCCTAGAT 59.619 55.000 36.80 0.00 42.22 1.98
659 684 1.651240 GGCGTGCACGTACTCCTAGA 61.651 60.000 36.80 0.00 42.22 2.43
660 685 1.226603 GGCGTGCACGTACTCCTAG 60.227 63.158 36.80 9.58 42.22 3.02
661 686 2.703798 GGGCGTGCACGTACTCCTA 61.704 63.158 36.80 0.00 42.22 2.94
662 687 4.065281 GGGCGTGCACGTACTCCT 62.065 66.667 36.80 0.00 42.22 3.69
663 688 4.065281 AGGGCGTGCACGTACTCC 62.065 66.667 36.80 29.67 42.22 3.85
664 689 2.809601 CAGGGCGTGCACGTACTC 60.810 66.667 36.80 23.13 42.22 2.59
665 690 3.612681 ACAGGGCGTGCACGTACT 61.613 61.111 36.80 30.40 42.22 2.73
666 691 3.411351 CACAGGGCGTGCACGTAC 61.411 66.667 36.80 28.93 39.19 3.67
667 692 3.153270 TTCACAGGGCGTGCACGTA 62.153 57.895 36.80 13.57 45.92 3.57
668 693 4.539083 TTCACAGGGCGTGCACGT 62.539 61.111 36.80 17.90 45.92 4.49
669 694 4.012895 GTTCACAGGGCGTGCACG 62.013 66.667 34.01 34.01 45.92 5.34
670 695 2.591715 AGTTCACAGGGCGTGCAC 60.592 61.111 6.82 6.82 45.92 4.57
671 696 2.591429 CAGTTCACAGGGCGTGCA 60.591 61.111 7.17 0.00 45.92 4.57
672 697 2.280797 TCAGTTCACAGGGCGTGC 60.281 61.111 7.17 0.00 45.92 5.34
674 699 0.827925 TCTCTCAGTTCACAGGGCGT 60.828 55.000 0.00 0.00 0.00 5.68
675 700 0.108898 CTCTCTCAGTTCACAGGGCG 60.109 60.000 0.00 0.00 0.00 6.13
676 701 1.204467 CTCTCTCTCAGTTCACAGGGC 59.796 57.143 0.00 0.00 0.00 5.19
677 702 1.824230 CCTCTCTCTCAGTTCACAGGG 59.176 57.143 0.00 0.00 0.00 4.45
678 703 1.824230 CCCTCTCTCTCAGTTCACAGG 59.176 57.143 0.00 0.00 0.00 4.00
679 704 2.754552 CTCCCTCTCTCTCAGTTCACAG 59.245 54.545 0.00 0.00 0.00 3.66
680 705 2.109128 ACTCCCTCTCTCTCAGTTCACA 59.891 50.000 0.00 0.00 0.00 3.58
681 706 2.802719 ACTCCCTCTCTCTCAGTTCAC 58.197 52.381 0.00 0.00 0.00 3.18
682 707 3.589735 AGTACTCCCTCTCTCTCAGTTCA 59.410 47.826 0.00 0.00 0.00 3.18
683 708 4.196971 GAGTACTCCCTCTCTCTCAGTTC 58.803 52.174 12.13 0.00 0.00 3.01
684 709 3.053917 GGAGTACTCCCTCTCTCTCAGTT 60.054 52.174 28.87 0.00 43.94 3.16
685 710 2.508300 GGAGTACTCCCTCTCTCTCAGT 59.492 54.545 28.87 0.00 43.94 3.41
686 711 3.208747 GGAGTACTCCCTCTCTCTCAG 57.791 57.143 28.87 0.00 43.94 3.35
697 722 2.094649 CGTCAAGGAACTGGAGTACTCC 60.095 54.545 31.61 31.61 40.31 3.85
698 723 2.818432 TCGTCAAGGAACTGGAGTACTC 59.182 50.000 14.87 14.87 40.31 2.59
699 724 2.820787 CTCGTCAAGGAACTGGAGTACT 59.179 50.000 0.00 0.00 40.31 2.73
700 725 2.557490 ACTCGTCAAGGAACTGGAGTAC 59.443 50.000 0.00 0.00 40.31 2.73
769 826 1.272781 CTTGAAGACCAGATCGTCGC 58.727 55.000 0.00 0.00 38.56 5.19
984 2624 4.353777 ACCTCATGACTGGAAGCTTACTA 58.646 43.478 10.74 0.00 37.60 1.82
986 2626 3.618690 ACCTCATGACTGGAAGCTTAC 57.381 47.619 0.11 0.11 37.60 2.34
1659 3421 4.421479 CACGAGCTCCGCGACCTT 62.421 66.667 8.23 0.00 43.32 3.50
1821 3585 2.048597 TGCCGCGTAGAACCTGTG 60.049 61.111 4.92 0.00 0.00 3.66
2037 3801 2.363406 GGCCTGCCATGCCTTCTT 60.363 61.111 3.48 0.00 45.70 2.52
2400 7803 2.348218 CCTTGTTTGTAGCGACGTGAAC 60.348 50.000 0.00 0.00 0.00 3.18
2454 7861 5.419542 GTGCTAGTTTGGATGATCTACACA 58.580 41.667 0.00 0.00 0.00 3.72
2544 9388 8.349245 CCTGTGTATACATCTTCAACAAAACAA 58.651 33.333 9.18 0.00 35.97 2.83
2650 9498 5.221541 ACAAGACAATTAATCCCCGCAAAAA 60.222 36.000 0.00 0.00 0.00 1.94
2651 9499 4.282195 ACAAGACAATTAATCCCCGCAAAA 59.718 37.500 0.00 0.00 0.00 2.44
2652 9500 3.829601 ACAAGACAATTAATCCCCGCAAA 59.170 39.130 0.00 0.00 0.00 3.68
2653 9501 3.426615 ACAAGACAATTAATCCCCGCAA 58.573 40.909 0.00 0.00 0.00 4.85
2654 9502 3.080300 ACAAGACAATTAATCCCCGCA 57.920 42.857 0.00 0.00 0.00 5.69
2655 9503 5.570234 TTAACAAGACAATTAATCCCCGC 57.430 39.130 0.00 0.00 0.00 6.13
2736 9587 9.487442 TCTCCACCTACATGCATATATATACAA 57.513 33.333 0.00 0.00 0.00 2.41
2746 9597 1.541889 CGCATCTCCACCTACATGCAT 60.542 52.381 0.00 0.00 41.51 3.96
2754 9605 2.362503 TCCGTCGCATCTCCACCT 60.363 61.111 0.00 0.00 0.00 4.00
2798 9649 4.439700 CCGATGAAGGTACGAGTGTGTATT 60.440 45.833 0.00 0.00 0.00 1.89
2817 9668 2.914059 CTCCGGGTTGTAAATTCCGAT 58.086 47.619 0.00 0.00 44.43 4.18
2820 9671 1.828979 TGCTCCGGGTTGTAAATTCC 58.171 50.000 0.00 0.00 0.00 3.01
2872 9723 8.891985 TCAGTAAGCTTATCTATCCTGATGAT 57.108 34.615 9.88 0.00 37.49 2.45
2898 9755 4.618965 AGTTTATAAGTTCGATCGAGGGC 58.381 43.478 18.54 12.38 0.00 5.19
2934 9791 2.031069 GCGAGGATGAGAATAGTGCGTA 60.031 50.000 0.00 0.00 0.00 4.42
2938 9795 2.625314 TGAGGCGAGGATGAGAATAGTG 59.375 50.000 0.00 0.00 0.00 2.74
2973 9833 6.650120 ACATCTTATATTTGTGAACCGAGGT 58.350 36.000 0.00 0.00 0.00 3.85
3016 9876 6.625873 TGAACAAACATACTAACACATGCA 57.374 33.333 0.00 0.00 0.00 3.96
3020 9891 7.994425 ATGGATGAACAAACATACTAACACA 57.006 32.000 0.00 0.00 32.77 3.72
3059 9930 4.812653 ACACCCCGTCCTTAATATAGACT 58.187 43.478 0.00 0.00 0.00 3.24
3069 9940 3.308705 GGTCGACACCCCGTCCTT 61.309 66.667 18.91 0.00 42.07 3.36
3086 9957 2.260869 CCAGCTGTCCAACCAACGG 61.261 63.158 13.81 0.00 0.00 4.44
3088 9959 1.903404 CCCCAGCTGTCCAACCAAC 60.903 63.158 13.81 0.00 0.00 3.77


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

AutoCloner maintained by Alex Coulton.