Multiple sequence alignment - TraesCS3B01G055900

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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 TraesCS3B01G055900 chr3B 100.000 5075 0 0 1 5075 29595234 29590160 0.000000e+00 9372.0
1 TraesCS3B01G055900 chr3B 91.110 2801 192 27 2308 5074 30091649 30088872 0.000000e+00 3740.0
2 TraesCS3B01G055900 chr3B 94.685 1844 94 4 2769 4610 30409435 30411276 0.000000e+00 2859.0
3 TraesCS3B01G055900 chr3B 91.601 1643 91 7 615 2233 30406946 30408565 0.000000e+00 2226.0
4 TraesCS3B01G055900 chr3B 94.725 1308 43 8 654 1957 30093339 30092054 0.000000e+00 2010.0
5 TraesCS3B01G055900 chr3B 89.047 1616 122 21 2573 4152 29379793 29381389 0.000000e+00 1953.0
6 TraesCS3B01G055900 chr3B 89.886 880 62 15 905 1768 29640843 29641711 0.000000e+00 1107.0
7 TraesCS3B01G055900 chr3B 81.068 1273 135 50 3842 5061 29787730 29788949 0.000000e+00 918.0
8 TraesCS3B01G055900 chr3B 92.751 538 39 0 2270 2807 30408903 30409440 0.000000e+00 778.0
9 TraesCS3B01G055900 chr3B 82.940 381 53 8 4700 5074 30411328 30411702 2.930000e-87 333.0
10 TraesCS3B01G055900 chr3B 86.620 284 35 3 3622 3903 29354645 29354363 1.370000e-80 311.0
11 TraesCS3B01G055900 chr3B 72.409 772 160 36 1063 1808 29528900 29528156 4.010000e-46 196.0
12 TraesCS3B01G055900 chr3B 94.444 126 7 0 615 740 29640719 29640844 1.440000e-45 195.0
13 TraesCS3B01G055900 chr3B 96.552 58 1 1 1882 1938 30092056 30091999 1.500000e-15 95.3
14 TraesCS3B01G055900 chr3D 91.963 2837 197 15 2261 5074 18659298 18662126 0.000000e+00 3947.0
15 TraesCS3B01G055900 chr3D 92.501 1907 111 12 2430 4318 18926509 18928401 0.000000e+00 2700.0
16 TraesCS3B01G055900 chr3D 94.508 1311 65 6 606 1911 18657739 18659047 0.000000e+00 2015.0
17 TraesCS3B01G055900 chr3D 92.609 1096 65 7 895 1980 18911019 18912108 0.000000e+00 1561.0
18 TraesCS3B01G055900 chr3D 91.653 623 38 7 1 615 358192629 358192013 0.000000e+00 850.0
19 TraesCS3B01G055900 chr3D 90.641 577 51 3 2321 2894 18740563 18741139 0.000000e+00 763.0
20 TraesCS3B01G055900 chr3D 93.014 501 30 5 1475 1972 18739710 18740208 0.000000e+00 726.0
21 TraesCS3B01G055900 chr3D 95.516 223 9 1 2019 2240 498438494 498438716 6.250000e-94 355.0
22 TraesCS3B01G055900 chr3D 94.886 176 9 0 618 793 18910839 18911014 5.010000e-70 276.0
23 TraesCS3B01G055900 chr3D 86.957 184 23 1 4613 4796 18932525 18932707 6.660000e-49 206.0
24 TraesCS3B01G055900 chr3D 74.194 279 53 13 929 1201 18778982 18779247 1.160000e-16 99.0
25 TraesCS3B01G055900 chr3A 94.134 1824 99 4 2350 4172 26195553 26197369 0.000000e+00 2769.0
26 TraesCS3B01G055900 chr3A 91.430 1657 106 19 2573 4203 26141561 26143207 0.000000e+00 2241.0
27 TraesCS3B01G055900 chr3A 93.595 1374 75 7 614 1982 26194104 26195469 0.000000e+00 2037.0
28 TraesCS3B01G055900 chr3A 80.426 235 35 4 1062 1286 26247052 26247285 8.740000e-38 169.0
29 TraesCS3B01G055900 chr7A 92.013 626 37 6 1 619 128144185 128143566 0.000000e+00 867.0
30 TraesCS3B01G055900 chr7A 95.516 223 9 1 2019 2240 200013553 200013331 6.250000e-94 355.0
31 TraesCS3B01G055900 chr4B 91.479 622 40 7 1 615 215915843 215916458 0.000000e+00 843.0
32 TraesCS3B01G055900 chr4B 89.297 626 50 9 1 616 344650630 344650012 0.000000e+00 769.0
33 TraesCS3B01G055900 chr2B 91.332 623 39 9 2 616 66713059 66712444 0.000000e+00 837.0
34 TraesCS3B01G055900 chr2B 90.560 625 43 9 1 615 760254216 760254834 0.000000e+00 813.0
35 TraesCS3B01G055900 chr2B 89.228 622 53 7 1 615 690728492 690729106 0.000000e+00 765.0
36 TraesCS3B01G055900 chr2B 89.600 500 36 7 1 490 697570284 697570777 5.580000e-174 621.0
37 TraesCS3B01G055900 chr1A 89.904 624 44 8 1 617 492263183 492263794 0.000000e+00 785.0
38 TraesCS3B01G055900 chr1A 86.301 73 10 0 2308 2380 552963257 552963185 4.210000e-11 80.5
39 TraesCS3B01G055900 chr4A 88.604 623 56 8 2 617 651226262 651225648 0.000000e+00 743.0
40 TraesCS3B01G055900 chr4A 80.488 123 21 3 2258 2379 626304686 626304806 1.950000e-14 91.6
41 TraesCS3B01G055900 chr5A 91.348 497 30 7 1 490 437204032 437204522 0.000000e+00 667.0
42 TraesCS3B01G055900 chr5A 89.873 79 8 0 2301 2379 305569581 305569503 8.990000e-18 102.0
43 TraesCS3B01G055900 chr6B 89.800 500 34 8 1 490 484659449 484658957 4.310000e-175 625.0
44 TraesCS3B01G055900 chr6B 95.964 223 7 2 2019 2240 264979630 264979409 1.340000e-95 361.0
45 TraesCS3B01G055900 chr6B 95.516 223 9 1 2019 2240 128896562 128896340 6.250000e-94 355.0
46 TraesCS3B01G055900 chr7B 95.516 223 9 1 2019 2240 698133190 698132968 6.250000e-94 355.0
47 TraesCS3B01G055900 chr6D 95.516 223 8 2 2019 2240 430474780 430474559 6.250000e-94 355.0
48 TraesCS3B01G055900 chr2D 95.516 223 9 1 2019 2240 18020268 18020046 6.250000e-94 355.0
49 TraesCS3B01G055900 chr1B 95.516 223 8 2 2019 2240 49755810 49755589 6.250000e-94 355.0
50 TraesCS3B01G055900 chr1B 88.764 267 22 4 360 619 432380259 432380524 2.280000e-83 320.0
51 TraesCS3B01G055900 chr1B 86.842 76 9 1 2304 2379 652787498 652787424 3.260000e-12 84.2
52 TraesCS3B01G055900 chrUn 95.089 224 9 2 2019 2240 246703575 246703352 8.080000e-93 351.0
53 TraesCS3B01G055900 chr5B 83.824 136 13 7 515 646 325726295 325726165 2.480000e-23 121.0
54 TraesCS3B01G055900 chr2A 82.946 129 20 2 2252 2379 445714553 445714680 1.150000e-21 115.0


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 TraesCS3B01G055900 chr3B 29590160 29595234 5074 True 9372.000000 9372 100.00000 1 5075 1 chr3B.!!$R3 5074
1 TraesCS3B01G055900 chr3B 29379793 29381389 1596 False 1953.000000 1953 89.04700 2573 4152 1 chr3B.!!$F1 1579
2 TraesCS3B01G055900 chr3B 30088872 30093339 4467 True 1948.433333 3740 94.12900 654 5074 3 chr3B.!!$R4 4420
3 TraesCS3B01G055900 chr3B 30406946 30411702 4756 False 1549.000000 2859 90.49425 615 5074 4 chr3B.!!$F4 4459
4 TraesCS3B01G055900 chr3B 29787730 29788949 1219 False 918.000000 918 81.06800 3842 5061 1 chr3B.!!$F2 1219
5 TraesCS3B01G055900 chr3B 29640719 29641711 992 False 651.000000 1107 92.16500 615 1768 2 chr3B.!!$F3 1153
6 TraesCS3B01G055900 chr3D 18657739 18662126 4387 False 2981.000000 3947 93.23550 606 5074 2 chr3D.!!$F5 4468
7 TraesCS3B01G055900 chr3D 18926509 18928401 1892 False 2700.000000 2700 92.50100 2430 4318 1 chr3D.!!$F2 1888
8 TraesCS3B01G055900 chr3D 18910839 18912108 1269 False 918.500000 1561 93.74750 618 1980 2 chr3D.!!$F7 1362
9 TraesCS3B01G055900 chr3D 358192013 358192629 616 True 850.000000 850 91.65300 1 615 1 chr3D.!!$R1 614
10 TraesCS3B01G055900 chr3D 18739710 18741139 1429 False 744.500000 763 91.82750 1475 2894 2 chr3D.!!$F6 1419
11 TraesCS3B01G055900 chr3A 26194104 26197369 3265 False 2403.000000 2769 93.86450 614 4172 2 chr3A.!!$F3 3558
12 TraesCS3B01G055900 chr3A 26141561 26143207 1646 False 2241.000000 2241 91.43000 2573 4203 1 chr3A.!!$F1 1630
13 TraesCS3B01G055900 chr7A 128143566 128144185 619 True 867.000000 867 92.01300 1 619 1 chr7A.!!$R1 618
14 TraesCS3B01G055900 chr4B 215915843 215916458 615 False 843.000000 843 91.47900 1 615 1 chr4B.!!$F1 614
15 TraesCS3B01G055900 chr4B 344650012 344650630 618 True 769.000000 769 89.29700 1 616 1 chr4B.!!$R1 615
16 TraesCS3B01G055900 chr2B 66712444 66713059 615 True 837.000000 837 91.33200 2 616 1 chr2B.!!$R1 614
17 TraesCS3B01G055900 chr2B 760254216 760254834 618 False 813.000000 813 90.56000 1 615 1 chr2B.!!$F3 614
18 TraesCS3B01G055900 chr2B 690728492 690729106 614 False 765.000000 765 89.22800 1 615 1 chr2B.!!$F1 614
19 TraesCS3B01G055900 chr1A 492263183 492263794 611 False 785.000000 785 89.90400 1 617 1 chr1A.!!$F1 616
20 TraesCS3B01G055900 chr4A 651225648 651226262 614 True 743.000000 743 88.60400 2 617 1 chr4A.!!$R1 615

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
329 330 0.889306 GGTTGTAGAGTGTCGGCTCT 59.111 55.0 0.0 0.0 46.49 4.09 F
2026 2252 0.551396 GTAGGGCAGGGGCAATACTT 59.449 55.0 0.0 0.0 43.71 2.24 F
2242 2476 0.033208 TGATCCACTTCATTGCCCCC 60.033 55.0 0.0 0.0 0.00 5.40 F
2304 2839 0.389426 GGACCAATACAGCGTCGTGT 60.389 55.0 0.0 0.0 34.21 4.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2118 2344 0.033699 AAGCATCCTCCCTTTGCTCC 60.034 55.000 0.00 0.00 45.54 4.70 R
3423 4057 1.534595 GCGATGCCAAGTGCTATTTGG 60.535 52.381 9.26 9.26 46.28 3.28 R
3608 4242 3.567478 ATCCAATGGTACCTCTTGCTC 57.433 47.619 14.36 0.00 0.00 4.26 R
4270 4927 3.243359 ACCAAACACATGAATCACCCT 57.757 42.857 0.00 0.00 0.00 4.34 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
130 131 2.904866 GGCAGTGTCGTTGGCCAA 60.905 61.111 16.05 16.05 45.70 4.52
213 214 4.324991 GGGTGTCGGCTCCGGTTT 62.325 66.667 8.59 0.00 40.25 3.27
217 218 2.668550 GTCGGCTCCGGTTTGCTT 60.669 61.111 8.59 0.00 40.25 3.91
329 330 0.889306 GGTTGTAGAGTGTCGGCTCT 59.111 55.000 0.00 0.00 46.49 4.09
340 341 4.069232 CGGCTCTGGTTGCTCGGA 62.069 66.667 0.00 0.00 0.00 4.55
392 393 4.735132 CGTGGTCGGCGTGGATGT 62.735 66.667 6.85 0.00 0.00 3.06
393 394 2.358247 GTGGTCGGCGTGGATGTT 60.358 61.111 6.85 0.00 0.00 2.71
394 395 2.047655 TGGTCGGCGTGGATGTTC 60.048 61.111 6.85 0.00 0.00 3.18
395 396 2.818274 GGTCGGCGTGGATGTTCC 60.818 66.667 6.85 0.00 36.96 3.62
444 453 2.063015 ATGGGTTGCTTGGGTGACGA 62.063 55.000 0.00 0.00 0.00 4.20
498 509 2.127270 GCGTGTGTTGATGGTGCG 60.127 61.111 0.00 0.00 0.00 5.34
513 524 2.126346 GCGTTGTTGAGGGCATGC 60.126 61.111 9.90 9.90 0.00 4.06
597 608 5.759273 TGAATGAAAGTGGCAAATCTTTTGG 59.241 36.000 3.47 0.00 34.60 3.28
608 619 5.504392 GCAAATCTTTTGGCTTGTTTCAAG 58.496 37.500 5.28 5.28 0.00 3.02
713 724 5.549347 TCGGTATCACCTCTCATCTAGTAC 58.451 45.833 0.00 0.00 35.66 2.73
718 729 4.794334 TCACCTCTCATCTAGTACCTTCC 58.206 47.826 0.00 0.00 0.00 3.46
922 937 1.154225 GCATCCGTTCTTTGCCACG 60.154 57.895 0.00 0.00 36.12 4.94
954 969 4.667161 GCATGATCACCAATTTTGTTTGCG 60.667 41.667 0.00 0.00 0.00 4.85
1053 1068 4.621087 GTTTGGTGGCTGCCCCCT 62.621 66.667 21.05 0.00 0.00 4.79
1221 1236 4.448732 TGCTATAATAACAGCACTGCATCG 59.551 41.667 3.30 0.00 42.68 3.84
1549 1587 1.523711 CATCACGACCGGATTGGGG 60.524 63.158 9.46 0.00 44.64 4.96
1572 1610 2.124736 GCCAGCTACGCCATGGAA 60.125 61.111 18.40 0.00 36.09 3.53
1814 1855 5.411669 CCTACTCGAACCAAGCAAATTAGTT 59.588 40.000 0.00 0.00 0.00 2.24
1821 1862 6.523201 CGAACCAAGCAAATTAGTTATGTCAC 59.477 38.462 0.00 0.00 0.00 3.67
2026 2252 0.551396 GTAGGGCAGGGGCAATACTT 59.449 55.000 0.00 0.00 43.71 2.24
2063 2289 0.808755 AAATGCATTTCGACCCCGTC 59.191 50.000 18.99 0.00 37.05 4.79
2069 2295 2.026641 CATTTCGACCCCGTCCTAGTA 58.973 52.381 0.00 0.00 37.05 1.82
2094 2320 2.114411 ATTTCGTGGCACCGGGTT 59.886 55.556 12.86 0.00 0.00 4.11
2118 2344 2.553904 GCTGAACCATCTATGATGGGGG 60.554 54.545 24.84 14.68 43.32 5.40
2133 2359 2.009302 GGGGGAGCAAAGGGAGGAT 61.009 63.158 0.00 0.00 0.00 3.24
2158 2384 6.486993 TGCTTAGATAAGAGAATACGCTCTCA 59.513 38.462 11.15 0.00 44.18 3.27
2160 2386 7.520776 GCTTAGATAAGAGAATACGCTCTCACA 60.521 40.741 11.15 0.96 44.18 3.58
2165 2391 1.405463 AGAATACGCTCTCACATCGCA 59.595 47.619 0.00 0.00 0.00 5.10
2198 2432 1.395262 GCTCTACCAGCGAGAAAAAGC 59.605 52.381 0.00 0.00 38.76 3.51
2206 2440 1.275471 GCGAGAAAAAGCGTTTGGCC 61.275 55.000 0.00 0.00 45.17 5.36
2208 2442 0.663269 GAGAAAAAGCGTTTGGCCCG 60.663 55.000 0.00 0.00 45.17 6.13
2209 2443 1.104577 AGAAAAAGCGTTTGGCCCGA 61.105 50.000 0.00 0.00 45.17 5.14
2233 2467 5.185828 AGCCAAAAATAGGTTGATCCACTTC 59.814 40.000 0.00 0.00 39.02 3.01
2234 2468 5.047377 GCCAAAAATAGGTTGATCCACTTCA 60.047 40.000 0.00 0.00 39.02 3.02
2235 2469 6.351286 GCCAAAAATAGGTTGATCCACTTCAT 60.351 38.462 0.00 0.00 39.02 2.57
2236 2470 7.614494 CCAAAAATAGGTTGATCCACTTCATT 58.386 34.615 0.00 0.00 39.02 2.57
2237 2471 7.546667 CCAAAAATAGGTTGATCCACTTCATTG 59.453 37.037 0.00 0.00 39.02 2.82
2238 2472 5.841957 AATAGGTTGATCCACTTCATTGC 57.158 39.130 0.00 0.00 39.02 3.56
2239 2473 2.450476 AGGTTGATCCACTTCATTGCC 58.550 47.619 0.00 0.00 39.02 4.52
2240 2474 1.478105 GGTTGATCCACTTCATTGCCC 59.522 52.381 0.00 0.00 35.97 5.36
2241 2475 1.478105 GTTGATCCACTTCATTGCCCC 59.522 52.381 0.00 0.00 0.00 5.80
2242 2476 0.033208 TGATCCACTTCATTGCCCCC 60.033 55.000 0.00 0.00 0.00 5.40
2279 2814 2.409975 GAAAAATGACGTCCAGACCGA 58.590 47.619 14.12 0.00 0.00 4.69
2297 2832 1.146358 GACGAGCGGACCAATACAGC 61.146 60.000 0.00 0.00 0.00 4.40
2298 2833 2.230940 CGAGCGGACCAATACAGCG 61.231 63.158 0.00 0.00 34.06 5.18
2299 2834 1.153628 GAGCGGACCAATACAGCGT 60.154 57.895 0.00 0.00 34.06 5.07
2304 2839 0.389426 GGACCAATACAGCGTCGTGT 60.389 55.000 0.00 0.00 34.21 4.49
2379 2923 3.477582 TCCGTGTTGGAGATGCCA 58.522 55.556 0.00 0.00 43.74 4.92
2460 3006 9.265901 CTATTTTGACCTACATGACATCTTAGG 57.734 37.037 14.50 14.50 37.67 2.69
2491 3037 5.582269 CGGTTTTGATGTGATGTCAGTCTAT 59.418 40.000 0.00 0.00 0.00 1.98
2495 3041 7.601073 TTTGATGTGATGTCAGTCTATTGAC 57.399 36.000 0.00 0.00 46.02 3.18
2524 3071 7.543756 TCCCATTCGAGTTAAAATTTTGATCC 58.456 34.615 13.76 1.26 0.00 3.36
2533 3080 9.353999 GAGTTAAAATTTTGATCCGCTTATGTT 57.646 29.630 13.76 0.00 0.00 2.71
2597 3146 4.996122 TGCCATGGTTCATTTTCATGTTTC 59.004 37.500 14.67 0.00 37.24 2.78
2763 3323 8.262601 TCCATACTTTGATGCTATCTAAAGGA 57.737 34.615 15.93 12.05 34.57 3.36
2835 3458 8.726870 AATGGCATGAAATTTAAAGATTCCTG 57.273 30.769 0.00 12.47 0.00 3.86
3011 3645 5.585047 ACCGACATAAGCAAAAGATTAGTCC 59.415 40.000 0.00 0.00 0.00 3.85
3207 3841 2.505407 AGATGGCTATGTGGTTGCTGTA 59.495 45.455 0.00 0.00 0.00 2.74
3234 3868 3.964031 TCCTAAAAGCTTCCAAAGGCAAA 59.036 39.130 0.00 0.00 0.00 3.68
3301 3935 6.403049 TCACATATTAACATTGTCGGTCTGT 58.597 36.000 0.00 0.00 0.00 3.41
3303 3937 6.960992 CACATATTAACATTGTCGGTCTGTTG 59.039 38.462 0.00 0.00 35.00 3.33
3608 4242 2.415010 CATCCTCTCTGTCGCCGG 59.585 66.667 0.00 0.00 0.00 6.13
3749 4383 8.061920 AGGAAGGATAAATAAAGGAAAAGGGAG 58.938 37.037 0.00 0.00 0.00 4.30
3760 4394 3.712218 AGGAAAAGGGAGTACAGATAGCC 59.288 47.826 0.00 0.00 0.00 3.93
3854 4488 4.749323 CCTTGAAGAGGCCATGCA 57.251 55.556 5.01 0.00 39.09 3.96
3858 4492 2.037511 CCTTGAAGAGGCCATGCAAAAA 59.962 45.455 5.01 0.00 39.09 1.94
3950 4584 7.649533 TTGATATGTTGGAAAAGAGCATCAT 57.350 32.000 0.00 0.00 37.82 2.45
3951 4585 8.750515 TTGATATGTTGGAAAAGAGCATCATA 57.249 30.769 0.00 0.00 37.82 2.15
4199 4856 0.247460 CGTGTCTCTCAGAATGGCCA 59.753 55.000 8.56 8.56 36.16 5.36
4221 4878 6.486657 GCCAGGCTGTTTGAGATTATTGTATA 59.513 38.462 14.43 0.00 0.00 1.47
4376 5037 1.133809 ACAAGCAGTTAGGGGCCTCA 61.134 55.000 4.79 0.00 0.00 3.86
4377 5038 0.038166 CAAGCAGTTAGGGGCCTCAA 59.962 55.000 4.79 0.00 0.00 3.02
4396 5057 1.223187 AAAACCCAGTAAGCGTCGTG 58.777 50.000 0.00 0.00 0.00 4.35
4415 5076 4.588951 TCGTGGAGCATCTATTCTAACCAT 59.411 41.667 0.00 0.00 33.73 3.55
4449 5110 7.360946 CGACCCTACAAAATTAAGAAACCTGAG 60.361 40.741 0.00 0.00 0.00 3.35
4459 5120 0.935196 GAAACCTGAGTGCGTCGTTT 59.065 50.000 0.00 0.00 0.00 3.60
4468 5129 4.515107 GCGTCGTTTTGAAGCTGG 57.485 55.556 0.00 0.00 46.89 4.85
4476 5137 3.128589 TCGTTTTGAAGCTGGATATTGCC 59.871 43.478 0.00 0.00 0.00 4.52
4507 5168 7.293073 ACATGCCCAGATTGAAGTATCTTATT 58.707 34.615 0.00 0.00 32.60 1.40
4509 5170 7.141758 TGCCCAGATTGAAGTATCTTATTCT 57.858 36.000 0.00 0.00 32.60 2.40
4645 5326 0.684535 TCTTGGCGACCACTCAATCA 59.315 50.000 0.00 0.00 30.78 2.57
4716 5397 1.982395 CCCTACTCCTGGCACGACA 60.982 63.158 0.00 0.00 0.00 4.35
4743 5424 4.147322 CTGCCGCGCCGTTACTTG 62.147 66.667 0.00 0.00 0.00 3.16
4777 5459 2.761213 CAGGGCCCAGCATTTCCC 60.761 66.667 27.56 0.00 39.05 3.97
4783 5465 2.595095 CCAGCATTTCCCGCCCTA 59.405 61.111 0.00 0.00 0.00 3.53
4853 5554 0.037882 CTGAGAGGCTCTTCGTTGCA 60.038 55.000 19.80 9.71 0.00 4.08
4875 5576 1.019673 GGTCACGATGGTAGCTACGA 58.980 55.000 17.48 14.47 0.00 3.43
4886 5587 0.174845 TAGCTACGAAATGCAGCGGT 59.825 50.000 10.49 0.40 40.29 5.68
4888 5589 1.358725 GCTACGAAATGCAGCGGTGA 61.359 55.000 20.69 3.85 0.00 4.02
4898 5600 4.393155 AGCGGTGATGGCGCAGAA 62.393 61.111 10.83 0.00 35.00 3.02
4912 5614 1.605058 GCAGAAGGAGGTAGCACGGA 61.605 60.000 0.00 0.00 0.00 4.69
4918 5620 1.775459 AGGAGGTAGCACGGAGAGATA 59.225 52.381 0.00 0.00 0.00 1.98
5041 5748 1.028905 TTTCCCCGTTCACTGCAAAG 58.971 50.000 0.00 0.00 0.00 2.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
147 148 3.771160 GACATCCACGCCGACCCT 61.771 66.667 0.00 0.00 0.00 4.34
183 184 0.738412 GACACCCAACCACCGTATCG 60.738 60.000 0.00 0.00 0.00 2.92
184 185 0.738412 CGACACCCAACCACCGTATC 60.738 60.000 0.00 0.00 0.00 2.24
185 186 1.294138 CGACACCCAACCACCGTAT 59.706 57.895 0.00 0.00 0.00 3.06
186 187 2.735883 CGACACCCAACCACCGTA 59.264 61.111 0.00 0.00 0.00 4.02
213 214 1.597854 CAGCTTCGTCACCCAAGCA 60.598 57.895 8.51 0.00 46.37 3.91
217 218 2.338620 CGTCAGCTTCGTCACCCA 59.661 61.111 0.00 0.00 0.00 4.51
273 274 2.097056 GCTCCGACGTACAGACAAAAAC 60.097 50.000 0.00 0.00 0.00 2.43
377 378 2.047655 GAACATCCACGCCGACCA 60.048 61.111 0.00 0.00 0.00 4.02
395 396 1.068474 CTACAACCAAGACCGAAGCG 58.932 55.000 0.00 0.00 0.00 4.68
498 509 0.664166 CAACGCATGCCCTCAACAAC 60.664 55.000 13.15 0.00 0.00 3.32
954 969 0.954452 CAACAAGACACAGAAGGGGC 59.046 55.000 0.00 0.00 0.00 5.80
1053 1068 2.441348 TCAGCCCCGACGAGCATA 60.441 61.111 11.58 0.00 0.00 3.14
1104 1119 3.574952 AGGTTGCCACACCTGCTA 58.425 55.556 0.00 0.00 46.22 3.49
2063 2289 4.508124 GCCACGAAATGATTGAGTACTAGG 59.492 45.833 0.00 0.00 0.00 3.02
2069 2295 1.812571 GGTGCCACGAAATGATTGAGT 59.187 47.619 0.00 0.00 0.00 3.41
2118 2344 0.033699 AAGCATCCTCCCTTTGCTCC 60.034 55.000 0.00 0.00 45.54 4.70
2123 2349 6.146760 TCTCTTATCTAAGCATCCTCCCTTT 58.853 40.000 0.00 0.00 33.40 3.11
2133 2359 6.486993 TGAGAGCGTATTCTCTTATCTAAGCA 59.513 38.462 12.63 0.00 43.05 3.91
2174 2401 2.656560 TTCTCGCTGGTAGAGCTTTC 57.343 50.000 0.00 0.00 46.64 2.62
2206 2440 3.066760 GGATCAACCTATTTTTGGCTCGG 59.933 47.826 0.00 0.00 35.41 4.63
2208 2442 4.706962 AGTGGATCAACCTATTTTTGGCTC 59.293 41.667 0.00 0.00 39.86 4.70
2209 2443 4.677182 AGTGGATCAACCTATTTTTGGCT 58.323 39.130 0.00 0.00 39.86 4.75
2218 2452 3.620488 GGCAATGAAGTGGATCAACCTA 58.380 45.455 0.00 0.00 39.86 3.08
2246 2480 2.817258 TCATTTTTCCCACTAACGCTGG 59.183 45.455 0.00 0.00 0.00 4.85
2247 2481 3.666902 CGTCATTTTTCCCACTAACGCTG 60.667 47.826 0.00 0.00 0.00 5.18
2248 2482 2.482721 CGTCATTTTTCCCACTAACGCT 59.517 45.455 0.00 0.00 0.00 5.07
2249 2483 2.224784 ACGTCATTTTTCCCACTAACGC 59.775 45.455 0.00 0.00 32.48 4.84
2250 2484 3.120442 GGACGTCATTTTTCCCACTAACG 60.120 47.826 18.91 0.00 35.20 3.18
2251 2485 3.816523 TGGACGTCATTTTTCCCACTAAC 59.183 43.478 18.91 0.00 0.00 2.34
2252 2486 4.069304 CTGGACGTCATTTTTCCCACTAA 58.931 43.478 18.91 0.00 0.00 2.24
2253 2487 3.325425 TCTGGACGTCATTTTTCCCACTA 59.675 43.478 18.91 0.00 0.00 2.74
2254 2488 2.105821 TCTGGACGTCATTTTTCCCACT 59.894 45.455 18.91 0.00 0.00 4.00
2255 2489 2.225727 GTCTGGACGTCATTTTTCCCAC 59.774 50.000 18.91 0.00 0.00 4.61
2256 2490 2.500229 GTCTGGACGTCATTTTTCCCA 58.500 47.619 18.91 2.82 0.00 4.37
2257 2491 1.810755 GGTCTGGACGTCATTTTTCCC 59.189 52.381 18.91 3.61 0.00 3.97
2258 2492 1.463444 CGGTCTGGACGTCATTTTTCC 59.537 52.381 18.91 10.25 0.00 3.13
2259 2493 2.157085 GTCGGTCTGGACGTCATTTTTC 59.843 50.000 18.91 0.00 0.00 2.29
2279 2814 1.153628 GCTGTATTGGTCCGCTCGT 60.154 57.895 0.00 0.00 0.00 4.18
2297 2832 1.778591 GTTTTGCCATCAAACACGACG 59.221 47.619 0.00 0.00 41.48 5.12
2298 2833 2.533942 GTGTTTTGCCATCAAACACGAC 59.466 45.455 11.69 0.00 41.48 4.34
2299 2834 2.803451 GTGTTTTGCCATCAAACACGA 58.197 42.857 11.69 0.00 41.48 4.35
2304 2839 1.268794 CGGACGTGTTTTGCCATCAAA 60.269 47.619 0.00 0.00 40.17 2.69
2407 2953 2.233186 TCTCTCAACATGTCAGCTCAGG 59.767 50.000 0.00 0.00 0.00 3.86
2460 3006 4.454504 ACATCACATCAAAACCGGTAGTTC 59.545 41.667 8.00 0.00 37.88 3.01
2491 3037 3.502123 AACTCGAATGGGAAAGGTCAA 57.498 42.857 0.00 0.00 0.00 3.18
2495 3041 7.870445 TCAAAATTTTAACTCGAATGGGAAAGG 59.130 33.333 2.44 0.00 0.00 3.11
2533 3080 6.200286 GCAACTAGCTATTAGAAATACACGCA 59.800 38.462 0.00 0.00 41.15 5.24
2539 3086 6.423905 CCAAGCGCAACTAGCTATTAGAAATA 59.576 38.462 11.47 0.00 45.31 1.40
2824 3447 8.713971 TCTAATACAGCCATTCAGGAATCTTTA 58.286 33.333 0.00 0.00 41.22 1.85
2835 3458 8.910351 ACTATCCTTTTCTAATACAGCCATTC 57.090 34.615 0.00 0.00 0.00 2.67
3011 3645 4.077822 AGTCTGCTTTGGGAGAATGAAAG 58.922 43.478 0.00 0.00 41.42 2.62
3018 3652 2.024176 TACCAGTCTGCTTTGGGAGA 57.976 50.000 0.00 0.00 38.82 3.71
3234 3868 3.989056 CTCCTTTAGGAACTCCTCTCCT 58.011 50.000 0.27 0.00 44.77 3.69
3252 3886 2.887152 CCTACCAATGCTAATTGCCTCC 59.113 50.000 0.00 0.00 41.66 4.30
3301 3935 3.320826 GCTCCTTCTAAGCAAAAACCCAA 59.679 43.478 0.00 0.00 39.61 4.12
3303 3937 3.157881 AGCTCCTTCTAAGCAAAAACCC 58.842 45.455 0.00 0.00 42.35 4.11
3397 4031 7.773690 GTGTAACTTGTCCCATCCAATAACTAT 59.226 37.037 0.00 0.00 0.00 2.12
3423 4057 1.534595 GCGATGCCAAGTGCTATTTGG 60.535 52.381 9.26 9.26 46.28 3.28
3608 4242 3.567478 ATCCAATGGTACCTCTTGCTC 57.433 47.619 14.36 0.00 0.00 4.26
3749 4383 4.122776 CACATCACTTGGGCTATCTGTAC 58.877 47.826 0.00 0.00 0.00 2.90
3760 4394 5.243730 AGTTTGGGAAATACACATCACTTGG 59.756 40.000 0.00 0.00 0.00 3.61
4172 4829 5.402398 CATTCTGAGAGACACGATGTAACA 58.598 41.667 0.00 0.00 0.00 2.41
4221 4878 7.259882 TGTTTTGACTCGTATGTCCGTATTAT 58.740 34.615 0.00 0.00 36.21 1.28
4270 4927 3.243359 ACCAAACACATGAATCACCCT 57.757 42.857 0.00 0.00 0.00 4.34
4362 5023 1.893137 GGTTTTTGAGGCCCCTAACTG 59.107 52.381 0.00 0.00 0.00 3.16
4376 5037 1.600485 CACGACGCTTACTGGGTTTTT 59.400 47.619 0.00 0.00 42.14 1.94
4377 5038 1.223187 CACGACGCTTACTGGGTTTT 58.777 50.000 0.00 0.00 42.14 2.43
4396 5057 5.012561 AGGTCATGGTTAGAATAGATGCTCC 59.987 44.000 0.00 0.00 0.00 4.70
4415 5076 1.707106 TTTGTAGGGTCGTCAGGTCA 58.293 50.000 0.00 0.00 0.00 4.02
4449 5110 0.657368 CCAGCTTCAAAACGACGCAC 60.657 55.000 0.00 0.00 41.27 5.34
4459 5120 1.024271 GCGGCAATATCCAGCTTCAA 58.976 50.000 0.00 0.00 0.00 2.69
4507 5168 7.335673 TGCTGATTTTATATGTTTGGTTCGAGA 59.664 33.333 0.00 0.00 0.00 4.04
4509 5170 7.335673 TCTGCTGATTTTATATGTTTGGTTCGA 59.664 33.333 0.00 0.00 0.00 3.71
4645 5326 3.769300 GAGGGAAAATGGTGGTGCTATTT 59.231 43.478 0.00 0.00 39.49 1.40
4711 5392 1.301716 GCAGGGTGATGTGTGTCGT 60.302 57.895 0.00 0.00 0.00 4.34
4714 5395 2.032528 CGGCAGGGTGATGTGTGT 59.967 61.111 0.00 0.00 0.00 3.72
4742 5423 2.933287 AAGGTGATGTCGGGGGCA 60.933 61.111 0.00 0.00 0.00 5.36
4743 5424 2.124695 GAAGGTGATGTCGGGGGC 60.125 66.667 0.00 0.00 0.00 5.80
4747 5428 1.450312 GCCCTGAAGGTGATGTCGG 60.450 63.158 0.00 0.00 38.26 4.79
4806 5507 1.018752 CCACGTGATCGCATGGTGAA 61.019 55.000 19.30 0.00 41.18 3.18
4807 5508 1.447663 CCACGTGATCGCATGGTGA 60.448 57.895 19.30 0.00 41.18 4.02
4808 5509 3.092403 CCACGTGATCGCATGGTG 58.908 61.111 19.30 9.17 41.18 4.17
4809 5510 2.819595 GCCACGTGATCGCATGGT 60.820 61.111 21.43 1.40 41.18 3.55
4853 5554 0.394762 TAGCTACCATCGTGACCCGT 60.395 55.000 0.00 0.00 37.94 5.28
4872 5573 1.647545 CCATCACCGCTGCATTTCGT 61.648 55.000 0.00 0.00 0.00 3.85
4875 5576 2.887360 GCCATCACCGCTGCATTT 59.113 55.556 0.00 0.00 0.00 2.32
4886 5587 0.975556 TACCTCCTTCTGCGCCATCA 60.976 55.000 4.18 0.00 0.00 3.07
4888 5589 1.826024 CTACCTCCTTCTGCGCCAT 59.174 57.895 4.18 0.00 0.00 4.40
4895 5596 0.331954 TCTCCGTGCTACCTCCTTCT 59.668 55.000 0.00 0.00 0.00 2.85
4898 5600 0.553819 ATCTCTCCGTGCTACCTCCT 59.446 55.000 0.00 0.00 0.00 3.69
4912 5614 1.081108 GATTCGCCGCGCTATCTCT 60.081 57.895 8.21 0.00 0.00 3.10
4953 5656 1.210931 CTGCCATTGTGTTGCTCGG 59.789 57.895 0.00 0.00 0.00 4.63
4984 5691 2.870372 CAAGTGTTAGGCTGCCGC 59.130 61.111 13.96 8.44 0.00 6.53
4989 5696 3.254166 CACAAATCTGCAAGTGTTAGGCT 59.746 43.478 0.00 0.00 33.76 4.58


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

AutoCloner maintained by Alex Coulton.