Multiple sequence alignment - TraesCS1B01G444900

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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 TraesCS1B01G444900 chr1B 100.000 2593 0 0 1 2593 665129710 665132302 0.000000e+00 4789.0
1 TraesCS1B01G444900 chr1B 94.530 713 36 3 1 713 40423075 40422366 0.000000e+00 1098.0
2 TraesCS1B01G444900 chr1B 98.155 271 5 0 442 712 665124758 665125028 8.400000e-130 473.0
3 TraesCS1B01G444900 chr1B 95.361 194 7 2 2263 2454 37884253 37884446 9.010000e-80 307.0
4 TraesCS1B01G444900 chr1B 84.270 267 27 11 1978 2239 424436219 424436475 1.990000e-61 246.0
5 TraesCS1B01G444900 chr1A 93.159 1564 52 17 712 2266 574251458 574252975 0.000000e+00 2244.0
6 TraesCS1B01G444900 chr1A 90.521 211 19 1 1 210 247803512 247803722 7.070000e-71 278.0
7 TraesCS1B01G444900 chr1A 84.762 105 14 2 404 508 579175959 579175857 1.270000e-18 104.0
8 TraesCS1B01G444900 chr1A 94.872 39 2 0 76 114 386399532 386399494 7.750000e-06 62.1
9 TraesCS1B01G444900 chr1D 94.161 1490 45 11 783 2268 477759215 477760666 0.000000e+00 2231.0
10 TraesCS1B01G444900 chr1D 85.734 722 85 16 1 712 408881894 408882607 0.000000e+00 747.0
11 TraesCS1B01G444900 chr1D 85.417 720 91 11 1 712 1834968 1835681 0.000000e+00 736.0
12 TraesCS1B01G444900 chr1D 83.911 721 87 19 1 712 346191926 346192626 0.000000e+00 662.0
13 TraesCS1B01G444900 chr1D 79.779 272 50 4 444 712 346185184 346185453 2.630000e-45 193.0
14 TraesCS1B01G444900 chr1D 79.487 273 49 6 444 712 1828576 1828845 1.230000e-43 187.0
15 TraesCS1B01G444900 chr1D 76.838 272 46 7 444 712 408875173 408875430 1.250000e-28 137.0
16 TraesCS1B01G444900 chr1D 81.065 169 29 2 319 484 249327534 249327702 5.820000e-27 132.0
17 TraesCS1B01G444900 chr3B 94.142 717 42 0 1 717 93614043 93613327 0.000000e+00 1092.0
18 TraesCS1B01G444900 chr7D 85.814 719 90 10 1 712 30263044 30263757 0.000000e+00 752.0
19 TraesCS1B01G444900 chr7D 92.337 261 14 2 442 701 4193595 4193340 1.470000e-97 366.0
20 TraesCS1B01G444900 chr2D 85.535 719 92 10 1 712 614392190 614392903 0.000000e+00 741.0
21 TraesCS1B01G444900 chr2D 84.488 722 96 11 1 712 174425259 174425974 0.000000e+00 699.0
22 TraesCS1B01G444900 chr2D 84.680 718 87 16 1 708 527729080 527729784 0.000000e+00 695.0
23 TraesCS1B01G444900 chr2D 92.829 251 18 0 1 251 527676483 527676733 5.270000e-97 364.0
24 TraesCS1B01G444900 chr2D 80.813 443 68 13 276 708 527676821 527677256 5.350000e-87 331.0
25 TraesCS1B01G444900 chr2D 89.100 211 20 2 1 210 556044351 556044143 2.560000e-65 259.0
26 TraesCS1B01G444900 chr2D 81.250 272 46 4 444 712 614385461 614385730 5.620000e-52 215.0
27 TraesCS1B01G444900 chr2D 89.362 94 10 0 2175 2268 604059251 604059344 4.530000e-23 119.0
28 TraesCS1B01G444900 chr2D 86.567 67 8 1 207 272 574100871 574100937 3.580000e-09 73.1
29 TraesCS1B01G444900 chr7B 84.699 732 92 14 1 716 679451567 679450840 0.000000e+00 713.0
30 TraesCS1B01G444900 chr7B 96.296 189 7 0 2266 2454 17245694 17245506 6.970000e-81 311.0
31 TraesCS1B01G444900 chr7B 94.872 195 8 2 2261 2454 726571077 726571270 1.170000e-78 303.0
32 TraesCS1B01G444900 chr7B 94.857 175 4 2 2424 2593 702242021 702241847 4.250000e-68 268.0
33 TraesCS1B01G444900 chr7B 94.318 176 4 3 2424 2593 100717135 100717310 5.500000e-67 265.0
34 TraesCS1B01G444900 chr7B 94.318 176 4 3 2424 2593 721519803 721519628 5.500000e-67 265.0
35 TraesCS1B01G444900 chr7B 90.625 128 12 0 2141 2268 66505736 66505609 1.230000e-38 171.0
36 TraesCS1B01G444900 chr7B 90.588 85 3 3 2184 2268 26873600 26873679 9.810000e-20 108.0
37 TraesCS1B01G444900 chr5A 84.298 726 92 17 1 713 706071338 706070622 0.000000e+00 689.0
38 TraesCS1B01G444900 chr5A 82.711 723 91 25 1 712 651732901 651733600 1.710000e-171 612.0
39 TraesCS1B01G444900 chr5A 92.754 207 10 4 2251 2454 556772220 556772016 7.020000e-76 294.0
40 TraesCS1B01G444900 chr4A 96.330 327 10 2 2268 2593 723698509 723698184 1.060000e-148 536.0
41 TraesCS1B01G444900 chr5B 95.789 190 8 0 2265 2454 692132525 692132714 9.010000e-80 307.0
42 TraesCS1B01G444900 chr5B 95.312 192 9 0 2268 2459 689614780 689614589 3.240000e-79 305.0
43 TraesCS1B01G444900 chr5B 93.000 200 13 1 2261 2459 710848784 710848585 9.080000e-75 291.0
44 TraesCS1B01G444900 chr5B 93.370 181 5 4 2419 2593 545190057 545189878 7.120000e-66 261.0
45 TraesCS1B01G444900 chr5B 93.750 176 5 3 2424 2593 596685164 596685339 2.560000e-65 259.0
46 TraesCS1B01G444900 chr5B 92.778 180 7 3 2419 2593 691187553 691187375 3.310000e-64 255.0
47 TraesCS1B01G444900 chr3A 95.263 190 9 0 2265 2454 626441055 626441244 4.190000e-78 302.0
48 TraesCS1B01G444900 chr6B 94.886 176 3 3 2424 2593 576008058 576008233 1.180000e-68 270.0
49 TraesCS1B01G444900 chr6B 94.318 176 4 3 2424 2593 13614837 13614662 5.500000e-67 265.0
50 TraesCS1B01G444900 chr3D 80.292 274 46 6 444 712 604302493 604302763 1.570000e-47 200.0
51 TraesCS1B01G444900 chr3D 78.909 275 48 8 444 712 590437722 590437452 7.370000e-41 178.0
52 TraesCS1B01G444900 chr3D 78.400 125 21 5 73 194 361383042 361382921 2.770000e-10 76.8
53 TraesCS1B01G444900 chr3D 85.965 57 8 0 58 114 446486671 446486727 7.750000e-06 62.1
54 TraesCS1B01G444900 chr7A 88.800 125 14 0 2141 2265 169018953 169019077 1.240000e-33 154.0
55 TraesCS1B01G444900 chr6D 80.263 152 25 5 51 199 10354988 10355137 2.730000e-20 110.0


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 TraesCS1B01G444900 chr1B 665129710 665132302 2592 False 4789.0 4789 100.000 1 2593 1 chr1B.!!$F4 2592
1 TraesCS1B01G444900 chr1B 40422366 40423075 709 True 1098.0 1098 94.530 1 713 1 chr1B.!!$R1 712
2 TraesCS1B01G444900 chr1A 574251458 574252975 1517 False 2244.0 2244 93.159 712 2266 1 chr1A.!!$F2 1554
3 TraesCS1B01G444900 chr1D 477759215 477760666 1451 False 2231.0 2231 94.161 783 2268 1 chr1D.!!$F8 1485
4 TraesCS1B01G444900 chr1D 408881894 408882607 713 False 747.0 747 85.734 1 712 1 chr1D.!!$F7 711
5 TraesCS1B01G444900 chr1D 1834968 1835681 713 False 736.0 736 85.417 1 712 1 chr1D.!!$F2 711
6 TraesCS1B01G444900 chr1D 346191926 346192626 700 False 662.0 662 83.911 1 712 1 chr1D.!!$F5 711
7 TraesCS1B01G444900 chr3B 93613327 93614043 716 True 1092.0 1092 94.142 1 717 1 chr3B.!!$R1 716
8 TraesCS1B01G444900 chr7D 30263044 30263757 713 False 752.0 752 85.814 1 712 1 chr7D.!!$F1 711
9 TraesCS1B01G444900 chr2D 614392190 614392903 713 False 741.0 741 85.535 1 712 1 chr2D.!!$F6 711
10 TraesCS1B01G444900 chr2D 174425259 174425974 715 False 699.0 699 84.488 1 712 1 chr2D.!!$F1 711
11 TraesCS1B01G444900 chr2D 527729080 527729784 704 False 695.0 695 84.680 1 708 1 chr2D.!!$F2 707
12 TraesCS1B01G444900 chr2D 527676483 527677256 773 False 347.5 364 86.821 1 708 2 chr2D.!!$F7 707
13 TraesCS1B01G444900 chr7B 679450840 679451567 727 True 713.0 713 84.699 1 716 1 chr7B.!!$R3 715
14 TraesCS1B01G444900 chr5A 706070622 706071338 716 True 689.0 689 84.298 1 713 1 chr5A.!!$R2 712
15 TraesCS1B01G444900 chr5A 651732901 651733600 699 False 612.0 612 82.711 1 712 1 chr5A.!!$F1 711

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
590 665 0.179094 TCTCAAACCGTCGTTGTGCT 60.179 50.0 0.0 0.0 30.72 4.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2447 2545 0.102844 TTATTTAGCCGTCGGTCCCG 59.897 55.0 13.94 0.0 41.35 5.14 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
89 90 9.199982 CAAATAAAATCTTGTGACAATCTTGCT 57.800 29.630 0.00 0.00 0.00 3.91
120 121 5.865085 TCACTAAGTCTTTACCAGCAACAT 58.135 37.500 0.00 0.00 0.00 2.71
131 132 7.652909 TCTTTACCAGCAACATCATTTCAAAAG 59.347 33.333 0.00 0.00 0.00 2.27
134 135 5.051816 CCAGCAACATCATTTCAAAAGTGT 58.948 37.500 0.00 0.00 0.00 3.55
143 144 8.036575 ACATCATTTCAAAAGTGTATTCATGGG 58.963 33.333 0.00 0.00 0.00 4.00
536 605 4.201950 GGTCGTTAGAATCCTAGCGTTGTA 60.202 45.833 8.17 0.00 45.70 2.41
590 665 0.179094 TCTCAAACCGTCGTTGTGCT 60.179 50.000 0.00 0.00 30.72 4.40
668 750 8.826710 ACATATATAAACCTGAACACAACATCG 58.173 33.333 0.00 0.00 0.00 3.84
719 805 9.071276 TCTTTCTTGTTTCTCTTCAAATAGCAT 57.929 29.630 0.00 0.00 0.00 3.79
723 809 7.602644 TCTTGTTTCTCTTCAAATAGCATACGT 59.397 33.333 0.00 0.00 0.00 3.57
727 813 9.394477 GTTTCTCTTCAAATAGCATACGTTTTT 57.606 29.630 0.00 0.00 0.00 1.94
728 814 8.948853 TTCTCTTCAAATAGCATACGTTTTTG 57.051 30.769 0.00 0.00 0.00 2.44
729 815 7.526608 TCTCTTCAAATAGCATACGTTTTTGG 58.473 34.615 0.00 0.00 0.00 3.28
730 816 6.616947 TCTTCAAATAGCATACGTTTTTGGG 58.383 36.000 0.00 0.00 0.00 4.12
938 1029 2.203714 CTCCCGATCCCTCCCTCC 60.204 72.222 0.00 0.00 0.00 4.30
939 1030 3.837213 CTCCCGATCCCTCCCTCCC 62.837 73.684 0.00 0.00 0.00 4.30
940 1031 4.964241 CCCGATCCCTCCCTCCCC 62.964 77.778 0.00 0.00 0.00 4.81
1210 1301 4.270245 TCGAGGGGTAACGTTACAATTT 57.730 40.909 32.93 18.57 35.37 1.82
1211 1302 5.398603 TCGAGGGGTAACGTTACAATTTA 57.601 39.130 32.93 15.14 35.37 1.40
1212 1303 5.167845 TCGAGGGGTAACGTTACAATTTAC 58.832 41.667 32.93 18.01 35.37 2.01
1213 1304 4.031652 CGAGGGGTAACGTTACAATTTACG 59.968 45.833 32.93 24.83 43.08 3.18
1328 1419 2.504244 GAGGCGACGACGGACAAG 60.504 66.667 9.67 0.00 40.15 3.16
1329 1420 4.719369 AGGCGACGACGGACAAGC 62.719 66.667 9.67 0.00 40.15 4.01
1394 1485 3.519973 CTGCGAGGTGGTGCTGACA 62.520 63.158 0.00 0.00 32.47 3.58
1595 1686 1.002624 GCCCGAGAACCCATGAACA 60.003 57.895 0.00 0.00 0.00 3.18
1651 1745 5.772393 TCCCATCATCATCATCATCATCA 57.228 39.130 0.00 0.00 0.00 3.07
1666 1763 4.217983 TCATCATCATCTCATGACTCTCCG 59.782 45.833 0.00 0.00 43.01 4.63
1931 2028 4.151883 TCCAATCTGTTGCTTAAAGCCTT 58.848 39.130 0.00 0.00 41.51 4.35
1996 2093 0.322546 GTTCTCTTCCCCAACCGCAT 60.323 55.000 0.00 0.00 0.00 4.73
2026 2123 1.346722 ACGAGGAGGAAAAACCATCGT 59.653 47.619 0.00 0.00 43.96 3.73
2039 2136 3.155167 ATCGTCCCTTCCTCCGCC 61.155 66.667 0.00 0.00 0.00 6.13
2138 2236 3.555966 GCAGGTAGTTAGGATTGGCATT 58.444 45.455 0.00 0.00 0.00 3.56
2224 2322 2.307686 TCAATAAAGTCTCCCCGGCTTT 59.692 45.455 0.00 2.20 36.54 3.51
2268 2366 2.303022 TGAGAATCTTGTGGGAGTGGTC 59.697 50.000 0.00 0.00 34.92 4.02
2269 2367 2.303022 GAGAATCTTGTGGGAGTGGTCA 59.697 50.000 0.00 0.00 0.00 4.02
2270 2368 2.039084 AGAATCTTGTGGGAGTGGTCAC 59.961 50.000 0.00 0.00 34.71 3.67
2271 2369 1.734655 ATCTTGTGGGAGTGGTCACT 58.265 50.000 2.94 2.94 45.84 3.41
2272 2370 2.391926 TCTTGTGGGAGTGGTCACTA 57.608 50.000 3.35 0.00 42.66 2.74
2273 2371 2.248248 TCTTGTGGGAGTGGTCACTAG 58.752 52.381 3.35 0.00 42.66 2.57
2274 2372 1.971357 CTTGTGGGAGTGGTCACTAGT 59.029 52.381 3.35 0.00 42.66 2.57
2275 2373 2.984435 TGTGGGAGTGGTCACTAGTA 57.016 50.000 3.35 0.00 42.66 1.82
2276 2374 2.803956 TGTGGGAGTGGTCACTAGTAG 58.196 52.381 3.35 0.00 42.66 2.57
2277 2375 2.377531 TGTGGGAGTGGTCACTAGTAGA 59.622 50.000 3.59 0.00 42.66 2.59
2278 2376 3.181426 TGTGGGAGTGGTCACTAGTAGAA 60.181 47.826 3.59 0.00 42.66 2.10
2279 2377 3.830755 GTGGGAGTGGTCACTAGTAGAAA 59.169 47.826 3.59 0.00 42.66 2.52
2280 2378 4.282703 GTGGGAGTGGTCACTAGTAGAAAA 59.717 45.833 3.59 0.00 42.66 2.29
2281 2379 4.527038 TGGGAGTGGTCACTAGTAGAAAAG 59.473 45.833 3.59 0.00 42.66 2.27
2282 2380 4.081586 GGGAGTGGTCACTAGTAGAAAAGG 60.082 50.000 3.59 0.00 42.66 3.11
2283 2381 4.081586 GGAGTGGTCACTAGTAGAAAAGGG 60.082 50.000 3.59 0.00 42.66 3.95
2284 2382 3.838903 AGTGGTCACTAGTAGAAAAGGGG 59.161 47.826 3.59 0.00 40.43 4.79
2285 2383 3.055312 GTGGTCACTAGTAGAAAAGGGGG 60.055 52.174 3.59 0.00 0.00 5.40
2286 2384 2.093075 GGTCACTAGTAGAAAAGGGGGC 60.093 54.545 3.59 0.00 0.00 5.80
2287 2385 2.570302 GTCACTAGTAGAAAAGGGGGCA 59.430 50.000 3.59 0.00 0.00 5.36
2288 2386 3.008704 GTCACTAGTAGAAAAGGGGGCAA 59.991 47.826 3.59 0.00 0.00 4.52
2289 2387 3.653836 TCACTAGTAGAAAAGGGGGCAAA 59.346 43.478 3.59 0.00 0.00 3.68
2290 2388 4.010349 CACTAGTAGAAAAGGGGGCAAAG 58.990 47.826 3.59 0.00 0.00 2.77
2291 2389 2.604912 AGTAGAAAAGGGGGCAAAGG 57.395 50.000 0.00 0.00 0.00 3.11
2292 2390 1.787058 AGTAGAAAAGGGGGCAAAGGT 59.213 47.619 0.00 0.00 0.00 3.50
2293 2391 2.168496 GTAGAAAAGGGGGCAAAGGTC 58.832 52.381 0.00 0.00 0.00 3.85
2294 2392 0.178932 AGAAAAGGGGGCAAAGGTCC 60.179 55.000 0.00 0.00 38.40 4.46
2295 2393 0.471022 GAAAAGGGGGCAAAGGTCCA 60.471 55.000 0.00 0.00 42.08 4.02
2296 2394 0.471780 AAAAGGGGGCAAAGGTCCAG 60.472 55.000 0.00 0.00 42.08 3.86
2297 2395 2.386391 AAAGGGGGCAAAGGTCCAGG 62.386 60.000 0.00 0.00 42.08 4.45
2303 2401 3.966543 CAAAGGTCCAGGCCGGGT 61.967 66.667 22.25 0.00 34.36 5.28
2304 2402 3.647771 AAAGGTCCAGGCCGGGTC 61.648 66.667 22.25 16.31 34.36 4.46
2305 2403 4.974438 AAGGTCCAGGCCGGGTCA 62.974 66.667 22.25 0.00 34.36 4.02
2319 2417 1.146263 GGTCAGCCCATTAGTCCCG 59.854 63.158 0.00 0.00 0.00 5.14
2320 2418 1.146263 GTCAGCCCATTAGTCCCGG 59.854 63.158 0.00 0.00 0.00 5.73
2321 2419 1.306654 TCAGCCCATTAGTCCCGGT 60.307 57.895 0.00 0.00 0.00 5.28
2322 2420 0.912487 TCAGCCCATTAGTCCCGGTT 60.912 55.000 0.00 0.00 0.00 4.44
2323 2421 0.463833 CAGCCCATTAGTCCCGGTTC 60.464 60.000 0.00 0.00 0.00 3.62
2324 2422 0.912487 AGCCCATTAGTCCCGGTTCA 60.912 55.000 0.00 0.00 0.00 3.18
2325 2423 0.463833 GCCCATTAGTCCCGGTTCAG 60.464 60.000 0.00 0.00 0.00 3.02
2326 2424 0.909623 CCCATTAGTCCCGGTTCAGT 59.090 55.000 0.00 0.00 0.00 3.41
2327 2425 1.134491 CCCATTAGTCCCGGTTCAGTC 60.134 57.143 0.00 0.00 0.00 3.51
2328 2426 1.553248 CCATTAGTCCCGGTTCAGTCA 59.447 52.381 0.00 0.00 0.00 3.41
2329 2427 2.027561 CCATTAGTCCCGGTTCAGTCAA 60.028 50.000 0.00 0.00 0.00 3.18
2330 2428 3.262420 CATTAGTCCCGGTTCAGTCAAG 58.738 50.000 0.00 0.00 0.00 3.02
2331 2429 2.297698 TAGTCCCGGTTCAGTCAAGA 57.702 50.000 0.00 0.00 0.00 3.02
2332 2430 1.420430 AGTCCCGGTTCAGTCAAGAA 58.580 50.000 0.00 0.00 0.00 2.52
2333 2431 1.070289 AGTCCCGGTTCAGTCAAGAAC 59.930 52.381 0.00 0.00 45.50 3.01
2339 2437 1.509703 GTTCAGTCAAGAACCGGGAC 58.490 55.000 6.32 2.53 41.52 4.46
2340 2438 0.395312 TTCAGTCAAGAACCGGGACC 59.605 55.000 6.32 0.00 31.99 4.46
2341 2439 1.003718 CAGTCAAGAACCGGGACCC 60.004 63.158 6.32 0.00 31.99 4.46
2342 2440 1.460689 AGTCAAGAACCGGGACCCA 60.461 57.895 12.15 0.00 31.99 4.51
2343 2441 0.840722 AGTCAAGAACCGGGACCCAT 60.841 55.000 12.15 0.00 31.99 4.00
2344 2442 0.676782 GTCAAGAACCGGGACCCATG 60.677 60.000 12.15 3.12 0.00 3.66
2345 2443 1.378514 CAAGAACCGGGACCCATGG 60.379 63.158 12.15 4.14 0.00 3.66
2346 2444 2.612493 AAGAACCGGGACCCATGGG 61.612 63.158 30.23 30.23 42.03 4.00
2357 2455 2.444517 CCATGGGGGCATTGGACC 60.445 66.667 2.85 0.00 43.93 4.46
2363 2461 2.754254 GGGCATTGGACCCGGTTC 60.754 66.667 0.00 0.00 37.67 3.62
2364 2462 3.131478 GGCATTGGACCCGGTTCG 61.131 66.667 0.00 0.00 0.00 3.95
2365 2463 2.359478 GCATTGGACCCGGTTCGT 60.359 61.111 0.00 0.00 0.00 3.85
2366 2464 2.686816 GCATTGGACCCGGTTCGTG 61.687 63.158 0.00 0.00 0.00 4.35
2367 2465 1.004320 CATTGGACCCGGTTCGTGA 60.004 57.895 0.00 0.00 0.00 4.35
2368 2466 1.019278 CATTGGACCCGGTTCGTGAG 61.019 60.000 0.00 0.00 0.00 3.51
2369 2467 2.798148 ATTGGACCCGGTTCGTGAGC 62.798 60.000 0.00 0.00 0.00 4.26
2370 2468 4.754667 GGACCCGGTTCGTGAGCC 62.755 72.222 0.00 0.00 0.00 4.70
2371 2469 4.754667 GACCCGGTTCGTGAGCCC 62.755 72.222 0.00 0.00 0.00 5.19
2404 2502 4.101790 CCACGTGCGCCATTGGTC 62.102 66.667 10.91 0.00 0.00 4.02
2405 2503 4.101790 CACGTGCGCCATTGGTCC 62.102 66.667 4.18 0.00 0.00 4.46
2411 2509 3.131478 CGCCATTGGTCCCGGTTC 61.131 66.667 0.00 0.00 0.00 3.62
2412 2510 2.034999 GCCATTGGTCCCGGTTCA 59.965 61.111 0.00 0.00 0.00 3.18
2413 2511 1.379843 GCCATTGGTCCCGGTTCAT 60.380 57.895 0.00 0.00 0.00 2.57
2414 2512 1.384222 GCCATTGGTCCCGGTTCATC 61.384 60.000 0.00 0.00 0.00 2.92
2415 2513 0.255890 CCATTGGTCCCGGTTCATCT 59.744 55.000 0.00 0.00 0.00 2.90
2416 2514 1.382522 CATTGGTCCCGGTTCATCTG 58.617 55.000 0.00 0.00 0.00 2.90
2417 2515 0.255890 ATTGGTCCCGGTTCATCTGG 59.744 55.000 0.00 0.00 42.06 3.86
2418 2516 0.838554 TTGGTCCCGGTTCATCTGGA 60.839 55.000 0.00 0.00 45.09 3.86
2419 2517 1.221021 GGTCCCGGTTCATCTGGAC 59.779 63.158 0.00 0.00 45.09 4.02
2420 2518 1.221021 GTCCCGGTTCATCTGGACC 59.779 63.158 0.00 0.00 45.09 4.46
2421 2519 1.080354 TCCCGGTTCATCTGGACCT 59.920 57.895 0.00 0.00 45.09 3.85
2422 2520 0.546747 TCCCGGTTCATCTGGACCTT 60.547 55.000 0.00 0.00 45.09 3.50
2423 2521 0.328258 CCCGGTTCATCTGGACCTTT 59.672 55.000 0.00 0.00 45.09 3.11
2424 2522 1.271926 CCCGGTTCATCTGGACCTTTT 60.272 52.381 0.00 0.00 45.09 2.27
2425 2523 1.812571 CCGGTTCATCTGGACCTTTTG 59.187 52.381 6.11 0.00 45.09 2.44
2426 2524 3.458287 CCGGTTCATCTGGACCTTTTGG 61.458 54.545 6.11 0.00 45.09 3.28
2436 2534 2.676471 CCTTTTGGTCCCGGCTGG 60.676 66.667 3.88 3.88 34.07 4.85
2437 2535 2.115266 CTTTTGGTCCCGGCTGGT 59.885 61.111 11.58 0.00 34.77 4.00
2438 2536 2.203422 TTTTGGTCCCGGCTGGTG 60.203 61.111 11.58 1.93 34.77 4.17
2439 2537 3.801068 TTTTGGTCCCGGCTGGTGG 62.801 63.158 11.58 0.00 34.77 4.61
2450 2548 4.760047 CTGGTGGCTCGAACCGGG 62.760 72.222 6.32 0.00 40.86 5.73
2452 2550 4.754667 GGTGGCTCGAACCGGGAC 62.755 72.222 6.32 0.00 34.94 4.46
2453 2551 4.754667 GTGGCTCGAACCGGGACC 62.755 72.222 6.32 0.00 32.25 4.46
2456 2554 4.790861 GCTCGAACCGGGACCGAC 62.791 72.222 13.13 2.68 42.83 4.79
2457 2555 4.471726 CTCGAACCGGGACCGACG 62.472 72.222 13.13 14.09 42.83 5.12
2463 2561 3.762247 CCGGGACCGACGGCTAAA 61.762 66.667 15.39 0.00 45.34 1.85
2464 2562 2.497770 CGGGACCGACGGCTAAAT 59.502 61.111 15.39 0.00 42.83 1.40
2465 2563 1.735360 CGGGACCGACGGCTAAATA 59.265 57.895 15.39 0.00 42.83 1.40
2466 2564 0.102844 CGGGACCGACGGCTAAATAA 59.897 55.000 15.39 0.00 42.83 1.40
2467 2565 1.269936 CGGGACCGACGGCTAAATAAT 60.270 52.381 15.39 0.00 42.83 1.28
2468 2566 2.140717 GGGACCGACGGCTAAATAATG 58.859 52.381 15.39 0.00 0.00 1.90
2469 2567 2.224113 GGGACCGACGGCTAAATAATGA 60.224 50.000 15.39 0.00 0.00 2.57
2470 2568 3.460103 GGACCGACGGCTAAATAATGAA 58.540 45.455 15.39 0.00 0.00 2.57
2471 2569 3.872771 GGACCGACGGCTAAATAATGAAA 59.127 43.478 15.39 0.00 0.00 2.69
2472 2570 4.333372 GGACCGACGGCTAAATAATGAAAA 59.667 41.667 15.39 0.00 0.00 2.29
2473 2571 5.163733 GGACCGACGGCTAAATAATGAAAAA 60.164 40.000 15.39 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
89 90 7.041372 GCTGGTAAAGACTTAGTGAACAAATCA 60.041 37.037 0.00 0.00 35.05 2.57
120 121 7.773489 TCCCATGAATACACTTTTGAAATGA 57.227 32.000 0.00 0.00 0.00 2.57
131 132 6.428159 GTCTCATACCAATCCCATGAATACAC 59.572 42.308 0.00 0.00 0.00 2.90
134 135 5.542251 TCGTCTCATACCAATCCCATGAATA 59.458 40.000 0.00 0.00 0.00 1.75
143 144 4.808077 TCGTAGTCGTCTCATACCAATC 57.192 45.455 0.00 0.00 38.33 2.67
536 605 1.647629 CGCTATCTACTGCGTCGGT 59.352 57.895 0.00 0.00 46.09 4.69
668 750 5.901552 TGAAGTGAAAAGGGTGTTTTCATC 58.098 37.500 14.22 10.16 46.18 2.92
719 805 1.355916 GCACGCACCCAAAAACGTA 59.644 52.632 0.00 0.00 36.91 3.57
723 809 1.593750 GCATGCACGCACCCAAAAA 60.594 52.632 14.21 0.00 0.00 1.94
727 813 3.750155 CATGCATGCACGCACCCA 61.750 61.111 25.37 0.00 46.56 4.51
765 851 9.434420 CAGTTCATCTTCTTCAGAAAATAGTCT 57.566 33.333 0.00 0.00 34.16 3.24
767 853 9.784531 TTCAGTTCATCTTCTTCAGAAAATAGT 57.215 29.630 0.00 0.00 34.16 2.12
772 858 9.740239 CAAATTTCAGTTCATCTTCTTCAGAAA 57.260 29.630 0.00 0.00 34.16 2.52
773 859 9.123902 TCAAATTTCAGTTCATCTTCTTCAGAA 57.876 29.630 0.00 0.00 34.16 3.02
1107 1198 3.849951 CGGCAGGGGTCGCAGTAT 61.850 66.667 0.00 0.00 34.18 2.12
1154 1245 2.211026 GCGTACGTACCTTCGACGC 61.211 63.158 19.67 16.29 44.14 5.19
1182 1273 1.066605 ACGTTACCCCTCGATTCGATG 59.933 52.381 9.54 6.80 34.61 3.84
1183 1274 1.396653 ACGTTACCCCTCGATTCGAT 58.603 50.000 9.54 0.00 34.61 3.59
1184 1275 1.176527 AACGTTACCCCTCGATTCGA 58.823 50.000 8.70 8.70 0.00 3.71
1185 1276 2.159393 TGTAACGTTACCCCTCGATTCG 60.159 50.000 30.20 0.00 32.72 3.34
1186 1277 3.508744 TGTAACGTTACCCCTCGATTC 57.491 47.619 30.20 7.07 32.72 2.52
1187 1278 3.959535 TTGTAACGTTACCCCTCGATT 57.040 42.857 30.20 0.00 32.72 3.34
1188 1279 4.476628 AATTGTAACGTTACCCCTCGAT 57.523 40.909 30.20 11.79 32.72 3.59
1210 1301 1.317613 ACGTCACCCAACTGTACGTA 58.682 50.000 2.66 0.00 44.21 3.57
1211 1302 2.118132 ACGTCACCCAACTGTACGT 58.882 52.632 0.00 0.00 41.55 3.57
1212 1303 1.689959 GTACGTCACCCAACTGTACG 58.310 55.000 0.00 0.00 39.37 3.67
1213 1304 1.689959 CGTACGTCACCCAACTGTAC 58.310 55.000 7.22 0.00 33.74 2.90
1328 1419 0.462047 CGATCTTGTACCACCCCTGC 60.462 60.000 0.00 0.00 0.00 4.85
1329 1420 1.137086 CTCGATCTTGTACCACCCCTG 59.863 57.143 0.00 0.00 0.00 4.45
1394 1485 4.736896 GACGCGTCGGGGCTCTTT 62.737 66.667 25.19 0.00 0.00 2.52
1499 1590 0.748367 GGAAGAAGGCGATGGGGTTC 60.748 60.000 0.00 0.00 0.00 3.62
1577 1668 1.002624 TGTTCATGGGTTCTCGGGC 60.003 57.895 0.00 0.00 0.00 6.13
1595 1686 2.057922 GACTACATGGATGGGATGGGT 58.942 52.381 0.00 0.00 0.00 4.51
1651 1745 2.045561 ACGTCGGAGAGTCATGAGAT 57.954 50.000 0.00 0.00 36.95 2.75
1726 1823 8.703604 TTCGAGACAAAAAGATACCAATAGAG 57.296 34.615 0.00 0.00 0.00 2.43
1931 2028 2.978156 AAGGCTGAATCACCTCCAAA 57.022 45.000 5.16 0.00 34.31 3.28
1996 2093 2.046864 CCTCCTCGTTCGCCTCTCA 61.047 63.158 0.00 0.00 0.00 3.27
2042 2139 3.058160 CAGGGACCAGCGGCTTTG 61.058 66.667 0.00 0.00 0.00 2.77
2138 2236 4.041198 CCTAGACCCTAACACCAGAAAACA 59.959 45.833 0.00 0.00 0.00 2.83
2224 2322 2.125326 CACCGCCGAGATGGGACTA 61.125 63.158 0.00 0.00 38.63 2.59
2253 2351 2.248248 CTAGTGACCACTCCCACAAGA 58.752 52.381 5.87 0.00 42.54 3.02
2268 2366 3.713826 TTGCCCCCTTTTCTACTAGTG 57.286 47.619 5.39 0.00 0.00 2.74
2269 2367 3.010250 CCTTTGCCCCCTTTTCTACTAGT 59.990 47.826 0.00 0.00 0.00 2.57
2270 2368 3.010250 ACCTTTGCCCCCTTTTCTACTAG 59.990 47.826 0.00 0.00 0.00 2.57
2271 2369 2.990998 ACCTTTGCCCCCTTTTCTACTA 59.009 45.455 0.00 0.00 0.00 1.82
2272 2370 1.787058 ACCTTTGCCCCCTTTTCTACT 59.213 47.619 0.00 0.00 0.00 2.57
2273 2371 2.168496 GACCTTTGCCCCCTTTTCTAC 58.832 52.381 0.00 0.00 0.00 2.59
2274 2372 1.076513 GGACCTTTGCCCCCTTTTCTA 59.923 52.381 0.00 0.00 0.00 2.10
2275 2373 0.178932 GGACCTTTGCCCCCTTTTCT 60.179 55.000 0.00 0.00 0.00 2.52
2276 2374 0.471022 TGGACCTTTGCCCCCTTTTC 60.471 55.000 0.00 0.00 0.00 2.29
2277 2375 0.471780 CTGGACCTTTGCCCCCTTTT 60.472 55.000 0.00 0.00 0.00 2.27
2278 2376 1.156095 CTGGACCTTTGCCCCCTTT 59.844 57.895 0.00 0.00 0.00 3.11
2279 2377 2.854076 CTGGACCTTTGCCCCCTT 59.146 61.111 0.00 0.00 0.00 3.95
2280 2378 3.268032 CCTGGACCTTTGCCCCCT 61.268 66.667 0.00 0.00 0.00 4.79
2286 2384 3.920093 GACCCGGCCTGGACCTTTG 62.920 68.421 21.63 2.26 42.00 2.77
2287 2385 3.647771 GACCCGGCCTGGACCTTT 61.648 66.667 21.63 0.00 42.00 3.11
2288 2386 4.974438 TGACCCGGCCTGGACCTT 62.974 66.667 21.63 0.00 42.00 3.50
2301 2399 1.146263 CGGGACTAATGGGCTGACC 59.854 63.158 0.00 0.00 40.81 4.02
2302 2400 1.146263 CCGGGACTAATGGGCTGAC 59.854 63.158 0.00 0.00 0.00 3.51
2303 2401 0.912487 AACCGGGACTAATGGGCTGA 60.912 55.000 6.32 0.00 0.00 4.26
2304 2402 0.463833 GAACCGGGACTAATGGGCTG 60.464 60.000 6.32 0.00 0.00 4.85
2305 2403 0.912487 TGAACCGGGACTAATGGGCT 60.912 55.000 6.32 0.00 0.00 5.19
2306 2404 0.463833 CTGAACCGGGACTAATGGGC 60.464 60.000 6.32 0.00 0.00 5.36
2307 2405 0.909623 ACTGAACCGGGACTAATGGG 59.090 55.000 6.32 0.00 0.00 4.00
2308 2406 1.553248 TGACTGAACCGGGACTAATGG 59.447 52.381 6.32 0.00 0.00 3.16
2309 2407 3.056107 TCTTGACTGAACCGGGACTAATG 60.056 47.826 6.32 0.00 0.00 1.90
2310 2408 3.170717 TCTTGACTGAACCGGGACTAAT 58.829 45.455 6.32 0.00 0.00 1.73
2311 2409 2.600790 TCTTGACTGAACCGGGACTAA 58.399 47.619 6.32 0.00 0.00 2.24
2312 2410 2.297698 TCTTGACTGAACCGGGACTA 57.702 50.000 6.32 0.00 0.00 2.59
2313 2411 1.070289 GTTCTTGACTGAACCGGGACT 59.930 52.381 6.32 0.00 40.10 3.85
2314 2412 1.509703 GTTCTTGACTGAACCGGGAC 58.490 55.000 6.32 0.00 40.10 4.46
2320 2418 1.509703 GTCCCGGTTCTTGACTGAAC 58.490 55.000 0.00 0.00 43.88 3.18
2321 2419 0.395312 GGTCCCGGTTCTTGACTGAA 59.605 55.000 0.00 0.00 36.72 3.02
2322 2420 1.477685 GGGTCCCGGTTCTTGACTGA 61.478 60.000 0.00 0.00 36.72 3.41
2323 2421 1.003718 GGGTCCCGGTTCTTGACTG 60.004 63.158 0.00 0.00 0.00 3.51
2324 2422 0.840722 ATGGGTCCCGGTTCTTGACT 60.841 55.000 2.65 0.00 0.00 3.41
2325 2423 0.676782 CATGGGTCCCGGTTCTTGAC 60.677 60.000 2.65 0.00 0.00 3.18
2326 2424 1.682849 CATGGGTCCCGGTTCTTGA 59.317 57.895 2.65 0.00 0.00 3.02
2327 2425 1.378514 CCATGGGTCCCGGTTCTTG 60.379 63.158 2.85 0.00 0.00 3.02
2328 2426 2.612493 CCCATGGGTCCCGGTTCTT 61.612 63.158 23.93 0.00 0.00 2.52
2329 2427 3.015145 CCCATGGGTCCCGGTTCT 61.015 66.667 23.93 0.00 0.00 3.01
2330 2428 4.123545 CCCCATGGGTCCCGGTTC 62.124 72.222 29.33 0.00 38.25 3.62
2340 2438 2.444517 GGTCCAATGCCCCCATGG 60.445 66.667 4.14 4.14 37.09 3.66
2341 2439 2.444517 GGGTCCAATGCCCCCATG 60.445 66.667 1.18 0.00 40.26 3.66
2342 2440 4.141876 CGGGTCCAATGCCCCCAT 62.142 66.667 6.32 0.00 43.18 4.00
2345 2443 4.376170 AACCGGGTCCAATGCCCC 62.376 66.667 6.32 0.00 43.18 5.80
2346 2444 2.754254 GAACCGGGTCCAATGCCC 60.754 66.667 8.85 0.00 42.68 5.36
2347 2445 3.131478 CGAACCGGGTCCAATGCC 61.131 66.667 15.47 0.00 0.00 4.40
2348 2446 2.359478 ACGAACCGGGTCCAATGC 60.359 61.111 15.47 0.00 0.00 3.56
2349 2447 1.004320 TCACGAACCGGGTCCAATG 60.004 57.895 15.47 10.37 0.00 2.82
2350 2448 1.295423 CTCACGAACCGGGTCCAAT 59.705 57.895 15.47 0.00 0.00 3.16
2351 2449 2.738480 CTCACGAACCGGGTCCAA 59.262 61.111 15.47 0.00 0.00 3.53
2352 2450 3.998672 GCTCACGAACCGGGTCCA 61.999 66.667 15.47 0.00 0.00 4.02
2353 2451 4.754667 GGCTCACGAACCGGGTCC 62.755 72.222 15.47 0.00 0.00 4.46
2354 2452 4.754667 GGGCTCACGAACCGGGTC 62.755 72.222 10.31 10.31 0.00 4.46
2387 2485 4.101790 GACCAATGGCGCACGTGG 62.102 66.667 18.88 17.89 0.00 4.94
2388 2486 4.101790 GGACCAATGGCGCACGTG 62.102 66.667 12.28 12.28 0.00 4.49
2394 2492 3.131478 GAACCGGGACCAATGGCG 61.131 66.667 6.32 0.00 0.00 5.69
2395 2493 1.379843 ATGAACCGGGACCAATGGC 60.380 57.895 6.32 0.00 0.00 4.40
2396 2494 0.255890 AGATGAACCGGGACCAATGG 59.744 55.000 6.32 0.00 0.00 3.16
2397 2495 1.382522 CAGATGAACCGGGACCAATG 58.617 55.000 6.32 0.67 0.00 2.82
2398 2496 0.255890 CCAGATGAACCGGGACCAAT 59.744 55.000 6.32 0.00 0.00 3.16
2399 2497 0.838554 TCCAGATGAACCGGGACCAA 60.839 55.000 6.32 0.00 0.00 3.67
2400 2498 1.229368 TCCAGATGAACCGGGACCA 60.229 57.895 6.32 0.00 0.00 4.02
2401 2499 1.221021 GTCCAGATGAACCGGGACC 59.779 63.158 6.32 0.00 43.14 4.46
2402 2500 4.934989 GTCCAGATGAACCGGGAC 57.065 61.111 6.32 0.00 42.60 4.46
2403 2501 0.546747 AAGGTCCAGATGAACCGGGA 60.547 55.000 6.32 0.00 0.00 5.14
2404 2502 0.328258 AAAGGTCCAGATGAACCGGG 59.672 55.000 6.32 0.00 0.00 5.73
2405 2503 1.812571 CAAAAGGTCCAGATGAACCGG 59.187 52.381 0.00 0.00 0.00 5.28
2406 2504 1.812571 CCAAAAGGTCCAGATGAACCG 59.187 52.381 0.00 0.00 0.00 4.44
2407 2505 2.820197 GACCAAAAGGTCCAGATGAACC 59.180 50.000 3.27 0.00 33.21 3.62
2417 2515 1.971695 CAGCCGGGACCAAAAGGTC 60.972 63.158 2.18 6.11 38.09 3.85
2418 2516 2.115266 CAGCCGGGACCAAAAGGT 59.885 61.111 2.18 0.00 0.00 3.50
2419 2517 2.676471 CCAGCCGGGACCAAAAGG 60.676 66.667 2.18 0.00 40.01 3.11
2420 2518 2.115266 ACCAGCCGGGACCAAAAG 59.885 61.111 2.18 0.00 41.15 2.27
2421 2519 2.203422 CACCAGCCGGGACCAAAA 60.203 61.111 2.18 0.00 41.15 2.44
2422 2520 4.278513 CCACCAGCCGGGACCAAA 62.279 66.667 2.18 0.00 41.15 3.28
2433 2531 4.760047 CCCGGTTCGAGCCACCAG 62.760 72.222 19.03 0.00 33.36 4.00
2435 2533 4.754667 GTCCCGGTTCGAGCCACC 62.755 72.222 19.03 6.91 0.00 4.61
2436 2534 4.754667 GGTCCCGGTTCGAGCCAC 62.755 72.222 19.03 8.81 0.00 5.01
2439 2537 4.790861 GTCGGTCCCGGTTCGAGC 62.791 72.222 10.55 5.00 40.25 5.03
2440 2538 4.471726 CGTCGGTCCCGGTTCGAG 62.472 72.222 10.55 3.44 40.25 4.04
2447 2545 0.102844 TTATTTAGCCGTCGGTCCCG 59.897 55.000 13.94 0.00 41.35 5.14
2448 2546 2.140717 CATTATTTAGCCGTCGGTCCC 58.859 52.381 13.94 0.00 0.00 4.46
2449 2547 3.102052 TCATTATTTAGCCGTCGGTCC 57.898 47.619 13.94 0.00 0.00 4.46
2450 2548 5.473796 TTTTCATTATTTAGCCGTCGGTC 57.526 39.130 13.94 5.34 0.00 4.79
2451 2549 5.883503 TTTTTCATTATTTAGCCGTCGGT 57.116 34.783 13.94 2.30 0.00 4.69


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

AutoCloner maintained by Alex Coulton.