Multiple sequence alignment - TraesCS6B01G350300

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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 TraesCS6B01G350300 chr6B 100.000 5350 0 0 2432 7781 615322410 615317061 0.000000e+00 9880
1 TraesCS6B01G350300 chr6B 90.623 3530 268 49 2605 6091 208186586 208190095 0.000000e+00 4626
2 TraesCS6B01G350300 chr6B 90.555 3515 282 42 2607 6092 491281371 491284864 0.000000e+00 4606
3 TraesCS6B01G350300 chr6B 90.356 3515 287 40 2607 6092 491050891 491054382 0.000000e+00 4566
4 TraesCS6B01G350300 chr6B 100.000 1858 0 0 1 1858 615324841 615322984 0.000000e+00 3432
5 TraesCS6B01G350300 chr6B 88.111 614 62 9 1212 1817 707045347 707044737 0.000000e+00 719
6 TraesCS6B01G350300 chr7B 92.402 3343 224 25 2770 6091 32436965 32440298 0.000000e+00 4739
7 TraesCS6B01G350300 chr7B 91.372 3419 245 39 2701 6091 214008770 214005374 0.000000e+00 4634
8 TraesCS6B01G350300 chr7B 87.253 659 65 17 1211 1857 724017555 724016904 0.000000e+00 734
9 TraesCS6B01G350300 chr7B 86.082 661 71 20 1210 1857 724010091 724009439 0.000000e+00 691
10 TraesCS6B01G350300 chr7B 86.741 626 71 12 1210 1827 505101401 505102022 0.000000e+00 686
11 TraesCS6B01G350300 chr7B 86.207 638 75 12 1212 1844 131669288 131668659 0.000000e+00 678
12 TraesCS6B01G350300 chr7B 78.539 671 93 41 1210 1858 199203145 199202504 2.040000e-105 394
13 TraesCS6B01G350300 chr7B 74.687 798 144 47 2629 3393 507323129 507323901 1.270000e-77 302
14 TraesCS6B01G350300 chr7B 73.587 867 160 58 2606 3432 504164266 504165103 1.290000e-67 268
15 TraesCS6B01G350300 chr4B 91.116 3467 270 31 2651 6090 473757802 473754347 0.000000e+00 4662
16 TraesCS6B01G350300 chr4B 86.715 2755 286 48 2606 5320 421138969 421141683 0.000000e+00 2987
17 TraesCS6B01G350300 chr4B 86.322 658 73 16 1210 1856 350330694 350331345 0.000000e+00 701
18 TraesCS6B01G350300 chr4B 87.237 619 64 13 1209 1817 170192827 170192214 0.000000e+00 691
19 TraesCS6B01G350300 chr4B 74.650 856 163 46 2606 3432 540451666 540452496 5.820000e-86 329
20 TraesCS6B01G350300 chr4B 74.023 870 159 54 2605 3432 359418890 359418046 7.640000e-75 292
21 TraesCS6B01G350300 chr3B 91.216 3438 253 39 2686 6092 548378684 548382103 0.000000e+00 4630
22 TraesCS6B01G350300 chr3B 91.482 3381 245 34 2739 6091 276507705 276504340 0.000000e+00 4608
23 TraesCS6B01G350300 chr3B 85.779 661 72 15 1212 1858 680208910 680209562 0.000000e+00 680
24 TraesCS6B01G350300 chr2B 90.759 3506 252 54 2628 6091 667349138 667352613 0.000000e+00 4614
25 TraesCS6B01G350300 chr2B 97.404 1695 39 2 6091 7781 244703254 244704947 0.000000e+00 2881
26 TraesCS6B01G350300 chr2B 97.227 1695 42 2 6091 7781 244761624 244759931 0.000000e+00 2865
27 TraesCS6B01G350300 chr2B 95.993 1697 51 5 6091 7781 424683187 424681502 0.000000e+00 2741
28 TraesCS6B01G350300 chr2B 97.362 1213 31 1 1 1212 244762831 244761619 0.000000e+00 2061
29 TraesCS6B01G350300 chr2B 96.950 1213 35 2 1 1212 244702048 244703259 0.000000e+00 2034
30 TraesCS6B01G350300 chr2B 93.863 1222 51 5 1 1212 424684389 424683182 0.000000e+00 1820
31 TraesCS6B01G350300 chr2B 85.281 659 81 14 1210 1857 420838939 420839592 0.000000e+00 665
32 TraesCS6B01G350300 chr2B 74.505 859 157 52 2606 3432 281997871 281998699 4.530000e-82 316
33 TraesCS6B01G350300 chr7D 97.109 1695 41 3 6091 7781 474678775 474680465 0.000000e+00 2852
34 TraesCS6B01G350300 chr7D 94.926 1222 37 6 1 1212 474677574 474678780 0.000000e+00 1890
35 TraesCS6B01G350300 chr1B 96.047 1695 56 2 6091 7781 530762295 530760608 0.000000e+00 2748
36 TraesCS6B01G350300 chr1B 95.929 1695 54 4 6091 7781 95493871 95495554 0.000000e+00 2734
37 TraesCS6B01G350300 chr1B 94.763 1222 40 5 1 1212 95492669 95493876 0.000000e+00 1881
38 TraesCS6B01G350300 chr1B 94.108 1222 47 6 1 1212 530763496 530762290 0.000000e+00 1834
39 TraesCS6B01G350300 chr5B 95.932 1696 62 4 6091 7781 629226737 629225044 0.000000e+00 2743
40 TraesCS6B01G350300 chr1A 95.811 1695 60 2 6091 7781 409611064 409612751 0.000000e+00 2726
41 TraesCS6B01G350300 chr2A 95.752 1695 61 2 6091 7781 374485503 374487190 0.000000e+00 2721
42 TraesCS6B01G350300 chr2A 95.575 1695 62 4 6091 7781 628571636 628573321 0.000000e+00 2702
43 TraesCS6B01G350300 chr2A 94.522 1223 42 6 1 1212 628570433 628571641 0.000000e+00 1864
44 TraesCS6B01G350300 chr2A 94.358 1223 44 6 1 1212 628647586 628646378 0.000000e+00 1853
45 TraesCS6B01G350300 chr2A 94.272 1222 44 7 1 1212 374484303 374485508 0.000000e+00 1845
46 TraesCS6B01G350300 chr2A 94.026 1222 49 5 1 1212 161527498 161528705 0.000000e+00 1831
47 TraesCS6B01G350300 chr5A 92.962 1222 59 6 1 1212 272285349 272286553 0.000000e+00 1755
48 TraesCS6B01G350300 chr7A 92.182 1228 65 8 1 1216 607607093 607608301 0.000000e+00 1707
49 TraesCS6B01G350300 chr6A 95.794 737 21 2 1 727 610988362 610989098 0.000000e+00 1181
50 TraesCS6B01G350300 chr6A 95.794 737 21 2 1 727 611014448 611015184 0.000000e+00 1181
51 TraesCS6B01G350300 chr6A 95.664 738 21 2 1 727 610963880 610964617 0.000000e+00 1175
52 TraesCS6B01G350300 chr6A 92.653 490 21 3 724 1212 610964798 610965273 0.000000e+00 691
53 TraesCS6B01G350300 chr6A 92.653 490 21 3 724 1212 611015365 611015840 0.000000e+00 691
54 TraesCS6B01G350300 chr6A 92.449 490 22 3 724 1212 610981354 610981829 0.000000e+00 686


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 TraesCS6B01G350300 chr6B 615317061 615324841 7780 True 6656.0 9880 100.0000 1 7781 2 chr6B.!!$R2 7780
1 TraesCS6B01G350300 chr6B 208186586 208190095 3509 False 4626.0 4626 90.6230 2605 6091 1 chr6B.!!$F1 3486
2 TraesCS6B01G350300 chr6B 491281371 491284864 3493 False 4606.0 4606 90.5550 2607 6092 1 chr6B.!!$F3 3485
3 TraesCS6B01G350300 chr6B 491050891 491054382 3491 False 4566.0 4566 90.3560 2607 6092 1 chr6B.!!$F2 3485
4 TraesCS6B01G350300 chr6B 707044737 707045347 610 True 719.0 719 88.1110 1212 1817 1 chr6B.!!$R1 605
5 TraesCS6B01G350300 chr7B 32436965 32440298 3333 False 4739.0 4739 92.4020 2770 6091 1 chr7B.!!$F1 3321
6 TraesCS6B01G350300 chr7B 214005374 214008770 3396 True 4634.0 4634 91.3720 2701 6091 1 chr7B.!!$R3 3390
7 TraesCS6B01G350300 chr7B 724016904 724017555 651 True 734.0 734 87.2530 1211 1857 1 chr7B.!!$R5 646
8 TraesCS6B01G350300 chr7B 724009439 724010091 652 True 691.0 691 86.0820 1210 1857 1 chr7B.!!$R4 647
9 TraesCS6B01G350300 chr7B 505101401 505102022 621 False 686.0 686 86.7410 1210 1827 1 chr7B.!!$F3 617
10 TraesCS6B01G350300 chr7B 131668659 131669288 629 True 678.0 678 86.2070 1212 1844 1 chr7B.!!$R1 632
11 TraesCS6B01G350300 chr7B 199202504 199203145 641 True 394.0 394 78.5390 1210 1858 1 chr7B.!!$R2 648
12 TraesCS6B01G350300 chr7B 507323129 507323901 772 False 302.0 302 74.6870 2629 3393 1 chr7B.!!$F4 764
13 TraesCS6B01G350300 chr7B 504164266 504165103 837 False 268.0 268 73.5870 2606 3432 1 chr7B.!!$F2 826
14 TraesCS6B01G350300 chr4B 473754347 473757802 3455 True 4662.0 4662 91.1160 2651 6090 1 chr4B.!!$R3 3439
15 TraesCS6B01G350300 chr4B 421138969 421141683 2714 False 2987.0 2987 86.7150 2606 5320 1 chr4B.!!$F2 2714
16 TraesCS6B01G350300 chr4B 350330694 350331345 651 False 701.0 701 86.3220 1210 1856 1 chr4B.!!$F1 646
17 TraesCS6B01G350300 chr4B 170192214 170192827 613 True 691.0 691 87.2370 1209 1817 1 chr4B.!!$R1 608
18 TraesCS6B01G350300 chr4B 540451666 540452496 830 False 329.0 329 74.6500 2606 3432 1 chr4B.!!$F3 826
19 TraesCS6B01G350300 chr4B 359418046 359418890 844 True 292.0 292 74.0230 2605 3432 1 chr4B.!!$R2 827
20 TraesCS6B01G350300 chr3B 548378684 548382103 3419 False 4630.0 4630 91.2160 2686 6092 1 chr3B.!!$F1 3406
21 TraesCS6B01G350300 chr3B 276504340 276507705 3365 True 4608.0 4608 91.4820 2739 6091 1 chr3B.!!$R1 3352
22 TraesCS6B01G350300 chr3B 680208910 680209562 652 False 680.0 680 85.7790 1212 1858 1 chr3B.!!$F2 646
23 TraesCS6B01G350300 chr2B 667349138 667352613 3475 False 4614.0 4614 90.7590 2628 6091 1 chr2B.!!$F3 3463
24 TraesCS6B01G350300 chr2B 244759931 244762831 2900 True 2463.0 2865 97.2945 1 7781 2 chr2B.!!$R1 7780
25 TraesCS6B01G350300 chr2B 244702048 244704947 2899 False 2457.5 2881 97.1770 1 7781 2 chr2B.!!$F4 7780
26 TraesCS6B01G350300 chr2B 424681502 424684389 2887 True 2280.5 2741 94.9280 1 7781 2 chr2B.!!$R2 7780
27 TraesCS6B01G350300 chr2B 420838939 420839592 653 False 665.0 665 85.2810 1210 1857 1 chr2B.!!$F2 647
28 TraesCS6B01G350300 chr2B 281997871 281998699 828 False 316.0 316 74.5050 2606 3432 1 chr2B.!!$F1 826
29 TraesCS6B01G350300 chr7D 474677574 474680465 2891 False 2371.0 2852 96.0175 1 7781 2 chr7D.!!$F1 7780
30 TraesCS6B01G350300 chr1B 95492669 95495554 2885 False 2307.5 2734 95.3460 1 7781 2 chr1B.!!$F1 7780
31 TraesCS6B01G350300 chr1B 530760608 530763496 2888 True 2291.0 2748 95.0775 1 7781 2 chr1B.!!$R1 7780
32 TraesCS6B01G350300 chr5B 629225044 629226737 1693 True 2743.0 2743 95.9320 6091 7781 1 chr5B.!!$R1 1690
33 TraesCS6B01G350300 chr1A 409611064 409612751 1687 False 2726.0 2726 95.8110 6091 7781 1 chr1A.!!$F1 1690
34 TraesCS6B01G350300 chr2A 374484303 374487190 2887 False 2283.0 2721 95.0120 1 7781 2 chr2A.!!$F2 7780
35 TraesCS6B01G350300 chr2A 628570433 628573321 2888 False 2283.0 2702 95.0485 1 7781 2 chr2A.!!$F3 7780
36 TraesCS6B01G350300 chr2A 628646378 628647586 1208 True 1853.0 1853 94.3580 1 1212 1 chr2A.!!$R1 1211
37 TraesCS6B01G350300 chr2A 161527498 161528705 1207 False 1831.0 1831 94.0260 1 1212 1 chr2A.!!$F1 1211
38 TraesCS6B01G350300 chr5A 272285349 272286553 1204 False 1755.0 1755 92.9620 1 1212 1 chr5A.!!$F1 1211
39 TraesCS6B01G350300 chr7A 607607093 607608301 1208 False 1707.0 1707 92.1820 1 1216 1 chr7A.!!$F1 1215
40 TraesCS6B01G350300 chr6A 610988362 610989098 736 False 1181.0 1181 95.7940 1 727 1 chr6A.!!$F2 726
41 TraesCS6B01G350300 chr6A 611014448 611015840 1392 False 936.0 1181 94.2235 1 1212 2 chr6A.!!$F4 1211
42 TraesCS6B01G350300 chr6A 610963880 610965273 1393 False 933.0 1175 94.1585 1 1212 2 chr6A.!!$F3 1211

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
664 670 0.321671 TCACCTCCTACAAGCAGTGC 59.678 55.000 7.13 7.13 0.00 4.40 F
1400 1613 1.096386 AATCTAGACCTCTCGCGCGT 61.096 55.000 30.98 10.20 0.00 6.01 F
1738 1958 0.323360 CTCCCCCTCCATTTTTCGCA 60.323 55.000 0.00 0.00 0.00 5.10 F
2629 2871 2.124151 GATCCACAAGGCCGCCAT 60.124 61.111 13.15 0.00 33.74 4.40 F
2727 2995 2.943033 CGAAGTCCCCGAAATATTTGCT 59.057 45.455 5.17 0.00 0.00 3.91 F
4386 4701 1.852942 TGTTGTGTGCTTCTCTCGAC 58.147 50.000 0.00 0.00 0.00 4.20 F
4846 5170 0.400594 ACTCTTGCCGCCCTAGTTTT 59.599 50.000 0.00 0.00 0.00 2.43 F
6262 6605 0.698818 AGGCCAAACTGTAGAAGGGG 59.301 55.000 5.01 0.00 0.00 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1652 1870 0.110373 GTTTTCGCCCACACGATCAC 60.110 55.000 0.00 0.00 42.54 3.06 R
2593 2835 0.317799 CTGATCCAGATCCAGAGCCG 59.682 60.000 5.22 0.00 37.02 5.52 R
3435 3712 0.807496 GGCATGTTGGAGAGCTTGTC 59.193 55.000 0.00 0.00 0.00 3.18 R
4386 4701 1.083015 CGCAACGAAACGGGAACTG 60.083 57.895 0.00 0.00 42.99 3.16 R
4599 4916 1.661341 GTTAGAGGCTGACATGGCAG 58.339 55.000 25.09 25.09 38.91 4.85 R
5809 6149 0.826715 CCCCTGATCGAAGAAGCAGA 59.173 55.000 0.00 0.00 42.86 4.26 R
6524 6869 0.604073 TGCAGCCACATCACCATTTG 59.396 50.000 0.00 0.00 0.00 2.32 R
7277 7632 0.179004 TCGCCCTTCTTTTGGAGCAA 60.179 50.000 0.00 0.00 0.00 3.91 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
79 80 3.815809 CCAACACACCTTACTTCTTGGA 58.184 45.455 0.00 0.00 30.17 3.53
212 213 3.069158 TCGAACGGGGATTAGGAATCTTC 59.931 47.826 0.00 0.00 38.01 2.87
468 469 2.804986 TGCTCATCAAATGTGGGCTA 57.195 45.000 0.00 0.00 0.00 3.93
664 670 0.321671 TCACCTCCTACAAGCAGTGC 59.678 55.000 7.13 7.13 0.00 4.40
788 991 9.730420 GGTACATTAACATACAATGTGGAAATC 57.270 33.333 10.20 0.00 44.30 2.17
812 1015 6.556495 TCCAGAAGATAGAGCATAGTGGAATT 59.444 38.462 0.00 0.00 0.00 2.17
817 1020 7.609097 AGATAGAGCATAGTGGAATTCAAGA 57.391 36.000 7.93 0.00 0.00 3.02
1141 1345 3.124921 GTTGCATGGGACGACCGG 61.125 66.667 0.00 0.00 44.64 5.28
1206 1410 1.729586 AGTCACACCCTAAAGCTGGA 58.270 50.000 0.00 0.00 0.00 3.86
1207 1411 2.054799 AGTCACACCCTAAAGCTGGAA 58.945 47.619 0.00 0.00 0.00 3.53
1208 1412 2.441750 AGTCACACCCTAAAGCTGGAAA 59.558 45.455 0.00 0.00 0.00 3.13
1400 1613 1.096386 AATCTAGACCTCTCGCGCGT 61.096 55.000 30.98 10.20 0.00 6.01
1471 1685 2.868253 GGAATGGACCGAGGTTTGG 58.132 57.895 0.00 0.00 0.00 3.28
1493 1707 1.486726 GAGTGGCCTTGGTATAGCACT 59.513 52.381 3.32 0.00 0.00 4.40
1601 1819 2.311854 ATCCCAGCACCCCTCCAAG 61.312 63.158 0.00 0.00 0.00 3.61
1619 1837 3.440127 CAAGGTGGACCAATAACCCATT 58.560 45.455 0.00 0.00 38.89 3.16
1652 1870 2.097918 CTCTCGGTCGTTCGGTCG 59.902 66.667 1.08 0.00 0.00 4.79
1738 1958 0.323360 CTCCCCCTCCATTTTTCGCA 60.323 55.000 0.00 0.00 0.00 5.10
1753 1977 3.924114 TTCGCAGATGAATCCCCTAAA 57.076 42.857 0.00 0.00 35.04 1.85
2506 2748 4.222847 CCGCTAGGCTTCCCCGAC 62.223 72.222 0.00 0.00 39.21 4.79
2507 2749 4.222847 CGCTAGGCTTCCCCGACC 62.223 72.222 0.00 0.00 39.21 4.79
2508 2750 3.862991 GCTAGGCTTCCCCGACCC 61.863 72.222 0.00 0.00 39.21 4.46
2509 2751 3.162154 CTAGGCTTCCCCGACCCC 61.162 72.222 0.00 0.00 39.21 4.95
2629 2871 2.124151 GATCCACAAGGCCGCCAT 60.124 61.111 13.15 0.00 33.74 4.40
2727 2995 2.943033 CGAAGTCCCCGAAATATTTGCT 59.057 45.455 5.17 0.00 0.00 3.91
2730 2998 4.718940 AGTCCCCGAAATATTTGCTTTG 57.281 40.909 5.17 0.00 0.00 2.77
2737 3005 4.236935 CGAAATATTTGCTTTGTGTGCCT 58.763 39.130 5.17 0.00 0.00 4.75
2763 3031 5.533528 TGTTCATTGCATCATATCTCCTTGG 59.466 40.000 0.00 0.00 0.00 3.61
2851 3122 4.066490 CCATTGTGCCATGTTTGTTTGAT 58.934 39.130 0.00 0.00 0.00 2.57
3106 3381 3.753272 TGTTTTGCTAGGCTGAATCTGTC 59.247 43.478 0.00 0.00 0.00 3.51
3130 3405 7.223971 GTCATTTCGTGATGCTATGTAAACCTA 59.776 37.037 0.00 0.00 39.48 3.08
3137 3412 7.155328 GTGATGCTATGTAAACCTACTGCTAT 58.845 38.462 0.00 0.00 0.00 2.97
3156 3431 9.429359 ACTGCTATAAGTCATTCTATGCATAAC 57.571 33.333 8.00 2.65 0.00 1.89
3173 3448 5.130975 TGCATAACCTGGAGATGTTCACTAT 59.869 40.000 0.00 0.00 0.00 2.12
3242 3517 6.099125 TGGTTGCAATTATAGCCTACTGTAGA 59.901 38.462 16.22 0.00 0.00 2.59
3351 3628 3.973305 TGATCCATGCACCCTATGAACTA 59.027 43.478 0.00 0.00 0.00 2.24
3362 3639 3.494048 CCCTATGAACTAGCTCTTGCCAG 60.494 52.174 0.00 0.00 40.80 4.85
3534 3811 5.565509 TGGATGCTACCATGTTTTCTGTTA 58.434 37.500 0.00 0.00 34.77 2.41
3546 3823 9.492973 CCATGTTTTCTGTTAATCTTTGGAATT 57.507 29.630 0.00 0.00 0.00 2.17
3682 3982 8.097038 TGATGTTATTTCTGCTAAGTCTGAAGT 58.903 33.333 0.00 0.00 0.00 3.01
3690 3990 7.658179 TCTGCTAAGTCTGAAGTTGTTATTG 57.342 36.000 0.00 0.00 0.00 1.90
3703 4003 7.763528 TGAAGTTGTTATTGTTTGCAATCTTGT 59.236 29.630 0.00 0.00 43.61 3.16
3743 4043 7.712639 GCATGTTCTAGTGATTTCTGGAGATAA 59.287 37.037 0.00 0.00 0.00 1.75
3773 4073 6.697019 GTGTTCATGTTTTGTCATGCTTTACT 59.303 34.615 0.00 0.00 43.18 2.24
3953 4264 5.910637 TGAAACTTGCTTGATTTTGCATC 57.089 34.783 0.00 0.00 39.07 3.91
3961 4272 6.579666 TGCTTGATTTTGCATCTAGTTTCT 57.420 33.333 0.00 0.00 33.94 2.52
4125 4437 8.470805 ACTAGAATTTCGTGTAGATCATCTTGT 58.529 33.333 0.00 0.00 0.00 3.16
4127 4439 8.190888 AGAATTTCGTGTAGATCATCTTGTTC 57.809 34.615 0.00 0.00 0.00 3.18
4386 4701 1.852942 TGTTGTGTGCTTCTCTCGAC 58.147 50.000 0.00 0.00 0.00 4.20
4474 4789 5.977489 TCTTCTTCATGGACTCGTTCTTA 57.023 39.130 0.00 0.00 0.00 2.10
4523 4838 2.520069 CGCTACCCTGGATCTCACTAT 58.480 52.381 0.00 0.00 0.00 2.12
4524 4839 2.230025 CGCTACCCTGGATCTCACTATG 59.770 54.545 0.00 0.00 0.00 2.23
4599 4916 0.884514 GCTCTTCAAGCCTCCCAAAC 59.115 55.000 0.00 0.00 45.92 2.93
4663 4980 2.081462 GTTGCTTGGCTATGTTACCGT 58.919 47.619 0.00 0.00 0.00 4.83
4706 5024 2.853281 GCGTTGTTAGTTGCAGGTGAAC 60.853 50.000 0.00 0.00 0.00 3.18
4707 5025 2.353269 CGTTGTTAGTTGCAGGTGAACA 59.647 45.455 0.00 0.00 0.00 3.18
4708 5026 3.546020 CGTTGTTAGTTGCAGGTGAACAG 60.546 47.826 5.91 0.00 32.05 3.16
4812 5135 0.466124 GGAAGACTCGGCCTTATGCT 59.534 55.000 0.00 0.00 40.92 3.79
4846 5170 0.400594 ACTCTTGCCGCCCTAGTTTT 59.599 50.000 0.00 0.00 0.00 2.43
4879 5203 3.057174 GTGTTATGTTCCCGGATTTTGCA 60.057 43.478 0.73 0.00 0.00 4.08
4889 5213 2.422127 CCGGATTTTGCATTCCTTACGT 59.578 45.455 0.00 0.00 0.00 3.57
5124 5453 3.577667 CAACTTGGATTACGTCGGTACA 58.422 45.455 0.00 0.00 0.00 2.90
5334 5664 1.004745 CATGGGCTAAGTTGGGACACT 59.995 52.381 0.00 0.00 39.29 3.55
5367 5697 0.818040 AACTTTCGAAAGCCGTGCCT 60.818 50.000 32.49 12.68 39.63 4.75
5448 5780 4.491234 ACGAATTAAAACGCATCAACCA 57.509 36.364 0.00 0.00 0.00 3.67
5563 5896 5.585445 ACTTCTTGATCATTGCTAGCTTCAG 59.415 40.000 17.23 3.55 0.00 3.02
5637 5971 1.088340 ATGCTTAGTCGCTGCTGCAG 61.088 55.000 24.80 24.80 39.64 4.41
5651 5985 1.160137 CTGCAGCCTCACCACTTTAC 58.840 55.000 0.00 0.00 0.00 2.01
5696 6031 3.653164 TGCTAGTCTTGATACCCATGGA 58.347 45.455 15.22 0.00 0.00 3.41
5770 6106 3.006967 AGGTACAGGTTATGCGATGATCC 59.993 47.826 0.00 0.00 0.00 3.36
5795 6131 1.062206 GAGAGCGATGCTTGCTTGC 59.938 57.895 0.00 0.00 44.18 4.01
5796 6132 2.277120 GAGCGATGCTTGCTTGCG 60.277 61.111 0.00 0.00 44.18 4.85
5800 6136 1.207339 CGATGCTTGCTTGCGTTGA 59.793 52.632 5.41 0.00 35.85 3.18
5801 6137 0.791983 CGATGCTTGCTTGCGTTGAG 60.792 55.000 5.41 0.00 35.85 3.02
5809 6149 2.288666 TGCTTGCGTTGAGTTCTTCTT 58.711 42.857 0.00 0.00 0.00 2.52
5812 6152 3.605692 GCTTGCGTTGAGTTCTTCTTCTG 60.606 47.826 0.00 0.00 0.00 3.02
5837 6177 3.117093 TCTTCGATCAGGGGATAGGTTCT 60.117 47.826 0.00 0.00 32.67 3.01
5898 6238 5.417266 TGAGTTTCTGTTTGTGTTTCATCCA 59.583 36.000 0.00 0.00 0.00 3.41
6016 6358 5.664294 ATGATATCCAACTTGCAAAAGCA 57.336 34.783 0.00 0.00 0.00 3.91
6084 6427 3.134804 AGGATAGTATCGCATATTGGGCC 59.865 47.826 0.00 0.00 0.00 5.80
6254 6597 5.067283 CACTTTAACTTGTAGGCCAAACTGT 59.933 40.000 5.01 3.74 31.20 3.55
6262 6605 0.698818 AGGCCAAACTGTAGAAGGGG 59.301 55.000 5.01 0.00 0.00 4.79
6607 6952 3.137360 GGATGAGAGGAATAAGCCAAGGT 59.863 47.826 0.00 0.00 0.00 3.50
6718 7063 2.536066 TCAAGATCCCTGAGAACCGAA 58.464 47.619 0.00 0.00 0.00 4.30
6794 7139 7.622081 TGAAATGGAATAACTCAGGTACTCCTA 59.378 37.037 0.00 0.00 43.07 2.94
6832 7178 5.477607 TGTTACTAAACTCCTTGCTAGCA 57.522 39.130 14.93 14.93 36.51 3.49
6884 7233 7.040478 TGCTGCAGTAAAGACATTATTTTCTGT 60.040 33.333 16.64 0.00 37.37 3.41
6885 7234 7.272084 GCTGCAGTAAAGACATTATTTTCTGTG 59.728 37.037 16.64 3.18 37.37 3.66
6944 7293 9.289782 AGTTCTTTTGCAAACTATTAGACTGAT 57.710 29.630 12.39 0.00 34.05 2.90
7028 7377 2.017049 ACACAGGTTGACAAGTGCTTC 58.983 47.619 6.08 0.00 35.47 3.86
7119 7470 7.790782 TGCCTTGTCCCTAGAAAATAAAAAT 57.209 32.000 0.00 0.00 0.00 1.82
7277 7632 7.255625 GGTTTCAAAAAGCAGGAGTTCTAAGAT 60.256 37.037 0.00 0.00 0.00 2.40
7285 7640 4.836825 CAGGAGTTCTAAGATTGCTCCAA 58.163 43.478 10.91 0.00 45.92 3.53
7363 7718 4.782156 AGGCTTCATATCTATTCTCTGGGG 59.218 45.833 0.00 0.00 0.00 4.96
7364 7719 4.080638 GGCTTCATATCTATTCTCTGGGGG 60.081 50.000 0.00 0.00 0.00 5.40
7367 7722 6.466470 GCTTCATATCTATTCTCTGGGGGTTT 60.466 42.308 0.00 0.00 0.00 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 2.355716 CCAGATAAAACTTGCCCGGAGA 60.356 50.000 0.73 0.00 0.00 3.71
79 80 0.388907 CCGAACACCACGATACGGTT 60.389 55.000 0.00 0.00 33.25 4.44
622 628 3.119101 TGCTCTATCCCTTTCGACAACTC 60.119 47.826 0.00 0.00 0.00 3.01
664 670 0.820871 CCCTCTCCTCCTCTTTGTCG 59.179 60.000 0.00 0.00 0.00 4.35
788 991 5.798125 TTCCACTATGCTCTATCTTCTGG 57.202 43.478 0.00 0.00 0.00 3.86
812 1015 5.994054 CCACAAGATCTTTCTCAAGTCTTGA 59.006 40.000 14.54 14.54 42.90 3.02
817 1020 5.559148 AGTCCACAAGATCTTTCTCAAGT 57.441 39.130 4.86 0.00 0.00 3.16
906 1109 6.373005 TCTGGTGGAATTTCTTCACTATCA 57.627 37.500 5.98 0.00 32.70 2.15
998 1202 6.294473 TGCTTCCTTATCTCTTTGATCATCC 58.706 40.000 0.00 0.00 36.65 3.51
1118 1322 2.147958 GTCGTCCCATGCAACAAGTAA 58.852 47.619 0.00 0.00 0.00 2.24
1206 1410 0.037160 ATCCGGGGCGTTACAACTTT 59.963 50.000 0.00 0.00 0.00 2.66
1207 1411 0.037160 AATCCGGGGCGTTACAACTT 59.963 50.000 0.00 0.00 0.00 2.66
1208 1412 0.392060 GAATCCGGGGCGTTACAACT 60.392 55.000 0.00 0.00 0.00 3.16
1372 1585 2.022934 GAGGTCTAGATTCCGAACGGT 58.977 52.381 12.93 0.00 36.47 4.83
1414 1627 1.939934 CTCACGAAAACAAGGTCTGCA 59.060 47.619 0.00 0.00 0.00 4.41
1415 1628 1.334149 GCTCACGAAAACAAGGTCTGC 60.334 52.381 0.00 0.00 0.00 4.26
1471 1685 0.880718 GCTATACCAAGGCCACTCGC 60.881 60.000 5.01 0.00 0.00 5.03
1601 1819 3.094484 TGAATGGGTTATTGGTCCACC 57.906 47.619 0.00 0.00 32.90 4.61
1619 1837 0.846427 AGAGCATGGAGGGGGTTTGA 60.846 55.000 0.00 0.00 0.00 2.69
1652 1870 0.110373 GTTTTCGCCCACACGATCAC 60.110 55.000 0.00 0.00 42.54 3.06
1738 1958 3.653352 GGCTAGGTTTAGGGGATTCATCT 59.347 47.826 0.00 0.00 0.00 2.90
1753 1977 1.075896 CGGAGGAAGGAGGCTAGGT 60.076 63.158 0.00 0.00 0.00 3.08
2489 2731 4.222847 GTCGGGGAAGCCTAGCGG 62.223 72.222 0.00 0.00 0.00 5.52
2490 2732 4.222847 GGTCGGGGAAGCCTAGCG 62.223 72.222 0.00 0.00 0.00 4.26
2491 2733 3.862991 GGGTCGGGGAAGCCTAGC 61.863 72.222 0.00 0.00 33.89 3.42
2492 2734 3.162154 GGGGTCGGGGAAGCCTAG 61.162 72.222 0.00 0.00 37.00 3.02
2589 2831 4.247380 CAGATCCAGAGCCGGGCC 62.247 72.222 17.02 7.43 0.00 5.80
2590 2832 4.247380 CCAGATCCAGAGCCGGGC 62.247 72.222 12.11 12.11 0.00 6.13
2591 2833 1.825281 GATCCAGATCCAGAGCCGGG 61.825 65.000 2.18 0.00 31.76 5.73
2592 2834 1.117749 TGATCCAGATCCAGAGCCGG 61.118 60.000 0.00 0.00 37.02 6.13
2593 2835 0.317799 CTGATCCAGATCCAGAGCCG 59.682 60.000 5.22 0.00 37.02 5.52
2594 2836 1.714541 TCTGATCCAGATCCAGAGCC 58.285 55.000 5.22 0.00 35.39 4.70
2619 2861 3.061848 CGTTTGGATGGCGGCCTT 61.062 61.111 21.46 14.55 0.00 4.35
2679 2927 1.762708 ATACCCTGCGAAAACATGGG 58.237 50.000 0.00 0.00 43.26 4.00
2684 2942 4.598062 GCAGAAATATACCCTGCGAAAAC 58.402 43.478 0.00 0.00 42.92 2.43
2707 2973 4.983671 AAGCAAATATTTCGGGGACTTC 57.016 40.909 0.00 0.00 0.00 3.01
2727 2995 3.320256 TGCAATGAACATAGGCACACAAA 59.680 39.130 9.03 0.00 0.00 2.83
2730 2998 3.129113 TGATGCAATGAACATAGGCACAC 59.871 43.478 13.39 11.59 35.19 3.82
2737 3005 7.392393 CCAAGGAGATATGATGCAATGAACATA 59.608 37.037 0.00 0.00 0.00 2.29
2763 3031 1.063174 CGCACAAAATGGAGCTAGAGC 59.937 52.381 0.00 0.00 42.49 4.09
2815 3086 5.105797 TGGCACAATGGAATGAAATGTAGAC 60.106 40.000 0.00 0.00 31.92 2.59
2851 3122 4.239428 TGATTCAGGCATCAAGATGGAA 57.761 40.909 11.66 7.28 39.16 3.53
3106 3381 6.363577 AGGTTTACATAGCATCACGAAATG 57.636 37.500 0.00 0.00 0.00 2.32
3130 3405 9.429359 GTTATGCATAGAATGACTTATAGCAGT 57.571 33.333 6.50 0.00 32.59 4.40
3137 3412 7.290014 TCTCCAGGTTATGCATAGAATGACTTA 59.710 37.037 6.50 0.00 0.00 2.24
3156 3431 4.102210 ACATCCATAGTGAACATCTCCAGG 59.898 45.833 0.00 0.00 0.00 4.45
3173 3448 9.241919 AGAATGACATGTATAACAAAACATCCA 57.758 29.630 0.00 0.00 34.12 3.41
3208 3483 0.837260 AATTGCAACCAGGGGCATGT 60.837 50.000 0.00 0.00 40.17 3.21
3351 3628 1.077858 GCTAAGCCTGGCAAGAGCT 60.078 57.895 22.65 0.00 41.70 4.09
3362 3639 6.442513 AAGACATGTTTATGAAGCTAAGCC 57.557 37.500 0.00 0.00 37.73 4.35
3432 3709 2.082231 CATGTTGGAGAGCTTGTCCAG 58.918 52.381 16.09 4.38 45.00 3.86
3435 3712 0.807496 GGCATGTTGGAGAGCTTGTC 59.193 55.000 0.00 0.00 0.00 3.18
3444 3721 5.895636 CAACAATAAGTAGGCATGTTGGA 57.104 39.130 8.63 0.00 44.29 3.53
3534 3811 8.390921 TCCTTTACTGACCTAATTCCAAAGATT 58.609 33.333 0.00 0.00 0.00 2.40
3546 3823 7.133133 AGAACAAAAGTCCTTTACTGACCTA 57.867 36.000 0.00 0.00 38.88 3.08
3682 3982 7.710044 ACATGACAAGATTGCAAACAATAACAA 59.290 29.630 1.71 0.00 46.59 2.83
3690 3990 5.971895 AAACACATGACAAGATTGCAAAC 57.028 34.783 1.71 0.00 0.00 2.93
3715 4015 6.381133 TCTCCAGAAATCACTAGAACATGCTA 59.619 38.462 0.00 0.00 0.00 3.49
3773 4073 5.981088 AAAAGCATGGACATGATGTACAA 57.019 34.783 15.39 0.00 45.60 2.41
3961 4272 9.368674 CAAAACAAGGATGCAACATGATAATAA 57.631 29.630 0.00 0.00 0.00 1.40
4386 4701 1.083015 CGCAACGAAACGGGAACTG 60.083 57.895 0.00 0.00 42.99 3.16
4599 4916 1.661341 GTTAGAGGCTGACATGGCAG 58.339 55.000 25.09 25.09 38.91 4.85
4706 5024 1.759299 CCACCATGGGGCAATCCTG 60.759 63.158 18.09 1.93 37.90 3.86
4707 5025 1.935400 TCCACCATGGGGCAATCCT 60.935 57.895 18.09 0.00 38.32 3.24
4708 5026 1.758122 GTCCACCATGGGGCAATCC 60.758 63.158 18.09 0.00 38.32 3.01
4776 5099 5.045797 AGTCTTCCACCCTTTACCAAGTATC 60.046 44.000 0.00 0.00 0.00 2.24
4812 5135 3.367910 GCAAGAGTGGAACAAAACACCAA 60.368 43.478 0.00 0.00 44.16 3.67
4846 5170 3.429272 GGAACATAACACCGGTATGACGA 60.429 47.826 20.21 0.00 35.47 4.20
4879 5203 1.700739 TCACCCAACCACGTAAGGAAT 59.299 47.619 0.00 0.00 46.39 3.01
4889 5213 2.291930 GGTCCCATAAATCACCCAACCA 60.292 50.000 0.00 0.00 0.00 3.67
5124 5453 2.626743 ACCGGATAAGCTAAGCGTACAT 59.373 45.455 9.46 0.00 0.00 2.29
5334 5664 2.882137 CGAAAGTTTAAACCCTGCAGGA 59.118 45.455 34.91 11.56 39.89 3.86
5367 5697 1.152984 CCATCTGCCCATAACCGCA 60.153 57.895 0.00 0.00 0.00 5.69
5448 5780 1.080093 CCATCACGGCTACACACGT 60.080 57.895 0.00 0.00 45.25 4.49
5637 5971 1.001269 GGGGGTAAAGTGGTGAGGC 60.001 63.158 0.00 0.00 0.00 4.70
5651 5985 2.888490 GCTTAAAGGGAAAGGAAGGGGG 60.888 54.545 0.00 0.00 0.00 5.40
5696 6031 2.681976 CGAGGACTCAGCAATCCCATTT 60.682 50.000 0.00 0.00 35.38 2.32
5787 6123 2.289002 AGAAGAACTCAACGCAAGCAAG 59.711 45.455 0.00 0.00 45.62 4.01
5795 6131 4.054671 AGAAGCAGAAGAAGAACTCAACG 58.945 43.478 0.00 0.00 0.00 4.10
5796 6132 5.332959 CGAAGAAGCAGAAGAAGAACTCAAC 60.333 44.000 0.00 0.00 0.00 3.18
5800 6136 4.592485 TCGAAGAAGCAGAAGAAGAACT 57.408 40.909 0.00 0.00 0.00 3.01
5801 6137 4.926238 TGATCGAAGAAGCAGAAGAAGAAC 59.074 41.667 0.00 0.00 43.58 3.01
5809 6149 0.826715 CCCCTGATCGAAGAAGCAGA 59.173 55.000 0.00 0.00 42.86 4.26
5812 6152 2.028567 CCTATCCCCTGATCGAAGAAGC 60.029 54.545 0.00 0.00 43.58 3.86
5898 6238 5.991933 ACATAAGAGCATCATCCGACTAT 57.008 39.130 0.00 0.00 37.82 2.12
6016 6358 7.667219 ACCAAGGATAGAATCGCATATTGAAAT 59.333 33.333 0.00 0.00 0.00 2.17
6029 6372 3.151542 AGGTCCCACCAAGGATAGAAT 57.848 47.619 0.00 0.00 41.95 2.40
6084 6427 5.289434 GGCTTTTGTCTTGAACTTTTGTCAG 59.711 40.000 0.00 0.00 0.00 3.51
6222 6565 6.151144 GGCCTACAAGTTAAAGTGACAATCAT 59.849 38.462 0.00 0.00 0.00 2.45
6254 6597 5.224441 AGGTGAAGTTATATGCCCCTTCTA 58.776 41.667 0.00 0.00 35.47 2.10
6523 6868 0.738412 GCAGCCACATCACCATTTGC 60.738 55.000 0.00 0.00 0.00 3.68
6524 6869 0.604073 TGCAGCCACATCACCATTTG 59.396 50.000 0.00 0.00 0.00 2.32
6525 6870 1.340088 TTGCAGCCACATCACCATTT 58.660 45.000 0.00 0.00 0.00 2.32
6607 6952 6.769134 TTTGATAGAGTACTCATCCACGAA 57.231 37.500 24.44 12.91 0.00 3.85
6718 7063 3.760684 GGTCTGGCACTCATGAAAATCTT 59.239 43.478 0.00 0.00 0.00 2.40
6832 7178 6.567050 CAGCAGCAATAACATGGACTAAATT 58.433 36.000 0.00 0.00 0.00 1.82
6944 7293 8.871629 TTCAAGCAAAGTATTCCTATAACCAA 57.128 30.769 0.00 0.00 0.00 3.67
7028 7377 3.948473 TCAGCCTAGACTAGCTACAACAG 59.052 47.826 3.76 0.00 37.18 3.16
7119 7470 6.994496 CCTCTGATCTATGTTAAAAGCATCCA 59.006 38.462 0.00 0.00 0.00 3.41
7277 7632 0.179004 TCGCCCTTCTTTTGGAGCAA 60.179 50.000 0.00 0.00 0.00 3.91
7285 7640 4.081050 GCACCTTCGCCCTTCTTT 57.919 55.556 0.00 0.00 0.00 2.52


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

AutoCloner maintained by Alex Coulton.