Multiple sequence alignment - TraesCS4B01G061500

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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 TraesCS4B01G061500 chr4B 100.000 2931 0 0 3104 6034 53041185 53038255 0.000000e+00 5413.0
1 TraesCS4B01G061500 chr4B 100.000 2896 0 0 1 2896 53044288 53041393 0.000000e+00 5349.0
2 TraesCS4B01G061500 chr4B 94.390 2941 134 22 3104 6034 52931872 52934791 0.000000e+00 4488.0
3 TraesCS4B01G061500 chr4B 97.674 2579 26 8 325 2896 52929287 52931838 0.000000e+00 4399.0
4 TraesCS4B01G061500 chr4B 89.578 2888 252 28 3104 5981 52401190 52404038 0.000000e+00 3620.0
5 TraesCS4B01G061500 chr4B 95.569 677 25 3 2133 2807 52817188 52817861 0.000000e+00 1079.0
6 TraesCS4B01G061500 chr4B 84.924 1121 67 41 738 1830 52399641 52400687 0.000000e+00 1040.0
7 TraesCS4B01G061500 chr4B 100.000 251 0 0 6365 6615 53037924 53037674 1.300000e-126 464.0
8 TraesCS4B01G061500 chr4B 92.260 323 22 2 1 323 52828740 52829059 7.820000e-124 455.0
9 TraesCS4B01G061500 chr4B 90.351 342 26 4 1219 1555 52406246 52406585 6.090000e-120 442.0
10 TraesCS4B01G061500 chr4B 86.630 359 39 5 3111 3461 52830170 52830527 8.040000e-104 388.0
11 TraesCS4B01G061500 chr4B 88.854 323 21 7 1 323 52818124 52818431 3.740000e-102 383.0
12 TraesCS4B01G061500 chr4B 85.237 359 44 6 3111 3461 52829309 52829666 1.750000e-95 361.0
13 TraesCS4B01G061500 chr4B 86.826 334 22 10 1 323 52398712 52399034 2.930000e-93 353.0
14 TraesCS4B01G061500 chr4B 91.270 252 18 4 6365 6615 52934839 52935087 2.280000e-89 340.0
15 TraesCS4B01G061500 chr4B 84.419 353 46 5 3117 3461 52818678 52819029 8.220000e-89 339.0
16 TraesCS4B01G061500 chr4B 95.522 201 9 0 1 201 52895866 52896066 8.270000e-84 322.0
17 TraesCS4B01G061500 chr4B 94.712 208 8 1 1 205 52413079 52413286 2.980000e-83 320.0
18 TraesCS4B01G061500 chr4B 89.904 208 19 1 1624 1829 52816784 52816991 3.930000e-67 267.0
19 TraesCS4B01G061500 chr4B 80.980 347 43 15 325 656 52399152 52399490 3.060000e-63 254.0
20 TraesCS4B01G061500 chr4B 85.950 242 27 7 6365 6602 52404127 52404365 1.100000e-62 252.0
21 TraesCS4B01G061500 chr4B 90.503 179 14 2 1878 2053 52400710 52400888 3.990000e-57 233.0
22 TraesCS4B01G061500 chr4B 90.395 177 14 2 1880 2053 52817017 52817193 5.160000e-56 230.0
23 TraesCS4B01G061500 chr4B 79.614 363 40 22 1053 1398 53015134 53014789 5.160000e-56 230.0
24 TraesCS4B01G061500 chr4B 95.238 126 6 0 198 323 52928026 52928151 4.050000e-47 200.0
25 TraesCS4B01G061500 chr4B 85.870 184 22 2 1246 1425 52939705 52939888 6.770000e-45 193.0
26 TraesCS4B01G061500 chr4B 85.870 184 22 2 1246 1425 53019585 53019402 6.770000e-45 193.0
27 TraesCS4B01G061500 chr4B 85.616 146 20 1 1053 1197 52939476 52939621 1.150000e-32 152.0
28 TraesCS4B01G061500 chr4B 85.616 146 20 1 1053 1197 53019814 53019669 1.150000e-32 152.0
29 TraesCS4B01G061500 chr4B 90.826 109 7 3 2029 2135 489910913 489911020 6.910000e-30 143.0
30 TraesCS4B01G061500 chr4B 83.544 79 9 4 5539 5615 645345074 645344998 3.310000e-08 71.3
31 TraesCS4B01G061500 chr4D 92.724 1979 122 12 3104 5075 36430537 36432500 0.000000e+00 2837.0
32 TraesCS4B01G061500 chr4D 89.814 913 65 9 5065 5975 36434028 36434914 0.000000e+00 1146.0
33 TraesCS4B01G061500 chr4D 90.409 636 47 11 2267 2896 36429877 36430504 0.000000e+00 824.0
34 TraesCS4B01G061500 chr4D 84.223 412 36 15 1645 2053 36429330 36429715 2.250000e-99 374.0
35 TraesCS4B01G061500 chr4D 85.886 333 22 13 1 319 36420831 36421152 1.370000e-86 331.0
36 TraesCS4B01G061500 chr4D 89.494 257 15 7 6365 6613 36434985 36435237 1.380000e-81 315.0
37 TraesCS4B01G061500 chr4D 81.287 342 40 14 1086 1419 36561616 36561941 8.510000e-64 255.0
38 TraesCS4B01G061500 chr4D 79.319 382 51 19 1053 1421 36464505 36464871 6.630000e-60 243.0
39 TraesCS4B01G061500 chr4D 78.517 391 68 9 5643 6029 499254110 499253732 6.630000e-60 243.0
40 TraesCS4B01G061500 chr4D 97.744 133 3 0 2133 2265 36429710 36429842 5.160000e-56 230.0
41 TraesCS4B01G061500 chr4D 78.022 364 65 11 5643 6001 6680755 6680402 1.440000e-51 215.0
42 TraesCS4B01G061500 chr4D 84.932 146 21 1 1053 1197 36446804 36446949 5.350000e-31 147.0
43 TraesCS4B01G061500 chr4A 85.972 2438 269 42 3104 5487 565838727 565836309 0.000000e+00 2540.0
44 TraesCS4B01G061500 chr4A 84.581 1122 83 38 772 1857 565840846 565839779 0.000000e+00 1031.0
45 TraesCS4B01G061500 chr4A 82.137 655 81 18 2264 2894 565839409 565838767 4.540000e-146 529.0
46 TraesCS4B01G061500 chr4A 94.118 323 16 1 1 323 565841846 565841527 7.710000e-134 488.0
47 TraesCS4B01G061500 chr4A 92.424 198 15 0 3 200 566291226 566291423 3.900000e-72 283.0
48 TraesCS4B01G061500 chr4A 73.727 746 153 28 3322 4050 565749243 565748524 1.100000e-62 252.0
49 TraesCS4B01G061500 chr4A 90.217 184 14 2 1877 2056 565839791 565839608 3.080000e-58 237.0
50 TraesCS4B01G061500 chr4A 86.486 185 21 2 1250 1430 565750337 565750153 4.050000e-47 200.0
51 TraesCS4B01G061500 chr4A 85.057 174 26 0 1261 1434 565761791 565761618 1.900000e-40 178.0
52 TraesCS4B01G061500 chr4A 94.118 102 5 1 2041 2142 681667426 681667326 3.190000e-33 154.0
53 TraesCS4B01G061500 chr4A 94.898 98 3 2 2045 2141 691017923 691017827 1.150000e-32 152.0
54 TraesCS4B01G061500 chr4A 82.895 152 19 6 1053 1197 565750579 565750428 5.380000e-26 130.0
55 TraesCS4B01G061500 chr7B 73.258 890 197 33 3184 4050 19889327 19890198 3.020000e-73 287.0
56 TraesCS4B01G061500 chr3D 80.601 366 59 10 5668 6029 445620906 445620549 8.450000e-69 272.0
57 TraesCS4B01G061500 chr3D 86.076 79 8 3 5535 5612 576310972 576311048 1.530000e-11 82.4
58 TraesCS4B01G061500 chrUn 79.235 366 63 10 5668 6029 46069714 46070070 6.630000e-60 243.0
59 TraesCS4B01G061500 chr6A 77.411 394 72 13 5645 6034 608085269 608085649 1.120000e-52 219.0
60 TraesCS4B01G061500 chr5B 77.027 370 77 7 5668 6034 681920539 681920903 8.700000e-49 206.0
61 TraesCS4B01G061500 chr5B 76.276 392 79 8 5646 6034 681919725 681920105 5.230000e-46 196.0
62 TraesCS4B01G061500 chr5B 90.244 123 10 2 6365 6485 526635992 526635870 6.870000e-35 159.0
63 TraesCS4B01G061500 chr5B 83.544 79 9 3 5540 5616 382564793 382564869 3.310000e-08 71.3
64 TraesCS4B01G061500 chr5D 79.070 301 57 6 5704 6001 342859083 342858786 1.120000e-47 202.0
65 TraesCS4B01G061500 chr1B 96.939 98 3 0 2042 2139 431457286 431457189 1.480000e-36 165.0
66 TraesCS4B01G061500 chr2D 90.164 122 11 1 6365 6486 100415820 100415700 2.470000e-34 158.0
67 TraesCS4B01G061500 chr2D 94.898 98 5 0 2038 2135 465573050 465572953 3.190000e-33 154.0
68 TraesCS4B01G061500 chr2D 88.000 125 13 2 6365 6489 451694019 451694141 5.350000e-31 147.0
69 TraesCS4B01G061500 chr2D 80.180 111 17 5 5539 5646 424832546 424832654 1.980000e-10 78.7
70 TraesCS4B01G061500 chr6B 94.175 103 5 1 2049 2151 238140989 238140888 8.880000e-34 156.0
71 TraesCS4B01G061500 chr6B 93.939 99 6 0 2042 2140 420861803 420861705 4.130000e-32 150.0
72 TraesCS4B01G061500 chr7D 97.701 87 2 0 2049 2135 311872850 311872936 4.130000e-32 150.0
73 TraesCS4B01G061500 chr7D 88.618 123 13 1 6365 6487 513314028 513313907 1.490000e-31 148.0
74 TraesCS4B01G061500 chr1A 88.618 123 13 1 6365 6487 556086398 556086519 1.490000e-31 148.0
75 TraesCS4B01G061500 chr5A 88.000 125 13 2 6365 6488 547713389 547713266 5.350000e-31 147.0
76 TraesCS4B01G061500 chr6D 88.889 63 7 0 5537 5599 265305215 265305277 1.980000e-10 78.7
77 TraesCS4B01G061500 chr6D 93.617 47 3 0 5539 5585 119991868 119991914 3.310000e-08 71.3
78 TraesCS4B01G061500 chr6D 90.000 40 4 0 422 461 265992278 265992317 1.200000e-02 52.8


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 TraesCS4B01G061500 chr4B 53037674 53044288 6614 True 3742.000000 5413 100.000000 1 6615 3 chr4B.!!$R4 6614
1 TraesCS4B01G061500 chr4B 52928026 52935087 7061 False 2356.750000 4488 94.643000 198 6615 4 chr4B.!!$F7 6417
2 TraesCS4B01G061500 chr4B 52398712 52406585 7873 False 884.857143 3620 87.016000 1 6602 7 chr4B.!!$F4 6601
3 TraesCS4B01G061500 chr4B 52816784 52819029 2245 False 459.600000 1079 89.828200 1 3461 5 chr4B.!!$F5 3460
4 TraesCS4B01G061500 chr4B 52828740 52830527 1787 False 401.333333 455 88.042333 1 3461 3 chr4B.!!$F6 3460
5 TraesCS4B01G061500 chr4D 36429330 36435237 5907 False 954.333333 2837 90.734667 1645 6613 6 chr4D.!!$F5 4968
6 TraesCS4B01G061500 chr4A 565836309 565841846 5537 True 965.000000 2540 87.405000 1 5487 5 chr4A.!!$R5 5486
7 TraesCS4B01G061500 chr7B 19889327 19890198 871 False 287.000000 287 73.258000 3184 4050 1 chr7B.!!$F1 866
8 TraesCS4B01G061500 chr5B 681919725 681920903 1178 False 201.000000 206 76.651500 5646 6034 2 chr5B.!!$F2 388

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
196 197 1.005394 CCTAAACGCCACGACCACT 60.005 57.895 0.0 0.0 0.0 4.00 F
275 297 2.026915 GGAAAATGGGGAAAATGCTGCT 60.027 45.455 0.0 0.0 0.0 4.24 F
279 301 2.897271 TGGGGAAAATGCTGCTTAGA 57.103 45.000 0.0 0.0 0.0 2.10 F
280 302 3.386932 TGGGGAAAATGCTGCTTAGAT 57.613 42.857 0.0 0.0 0.0 1.98 F
281 303 3.711863 TGGGGAAAATGCTGCTTAGATT 58.288 40.909 0.0 0.0 0.0 2.40 F
282 304 4.095946 TGGGGAAAATGCTGCTTAGATTT 58.904 39.130 0.0 0.0 0.0 2.17 F
2868 5035 2.236146 TGGTAATGATGTCTTGTCCGCT 59.764 45.455 0.0 0.0 0.0 5.52 F
4409 7530 0.252197 GGTGAGGGCGACTGGTTTAT 59.748 55.000 0.0 0.0 0.0 1.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1354 2676 1.227793 GGTGAGCCATAGGAGCAGC 60.228 63.158 0.00 0.0 34.09 5.25 R
2061 3421 6.345096 ACAAAGTTGGGTCATCTATTTTGG 57.655 37.500 0.00 0.0 0.00 3.28 R
2290 3717 8.085720 TGTGGAGCATATTTTTGATGTTTTTG 57.914 30.769 0.00 0.0 0.00 2.44 R
2812 4971 7.397892 TCTCTCACCTTTGTCTATGTTAGAG 57.602 40.000 0.00 0.0 35.04 2.43 R
2868 5035 9.328845 GGTTTTACCGATTTTGTCCTATATGTA 57.671 33.333 0.00 0.0 0.00 2.29 R
3121 5288 4.153411 TGGTGAAATTCCAAATTACCCGT 58.847 39.130 0.00 0.0 31.50 5.28 R
5600 10268 1.066143 CCTGTGTTAGATGGCTTCCGT 60.066 52.381 0.00 0.0 0.00 4.69 R
6513 11194 1.115326 GTTGCCTGCAGGGAGGTTTT 61.115 55.000 33.46 0.0 36.70 2.43 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
34 35 3.468063 GGGACGGTGAACCTCACT 58.532 61.111 6.74 0.00 46.19 3.41
143 144 2.048222 TCAAGGACAAGAGCGCCG 60.048 61.111 2.29 0.00 0.00 6.46
196 197 1.005394 CCTAAACGCCACGACCACT 60.005 57.895 0.00 0.00 0.00 4.00
267 289 3.352611 TTCCTTGGGAAAATGGGGAAA 57.647 42.857 0.00 0.00 38.93 3.13
269 291 3.880608 TCCTTGGGAAAATGGGGAAAAT 58.119 40.909 0.00 0.00 0.00 1.82
270 292 3.586618 TCCTTGGGAAAATGGGGAAAATG 59.413 43.478 0.00 0.00 0.00 2.32
271 293 3.346315 CTTGGGAAAATGGGGAAAATGC 58.654 45.455 0.00 0.00 0.00 3.56
273 295 2.305343 TGGGAAAATGGGGAAAATGCTG 59.695 45.455 0.00 0.00 0.00 4.41
274 296 2.358957 GGAAAATGGGGAAAATGCTGC 58.641 47.619 0.00 0.00 0.00 5.25
275 297 2.026915 GGAAAATGGGGAAAATGCTGCT 60.027 45.455 0.00 0.00 0.00 4.24
276 298 3.559811 GGAAAATGGGGAAAATGCTGCTT 60.560 43.478 0.00 0.00 0.00 3.91
277 299 4.323409 GGAAAATGGGGAAAATGCTGCTTA 60.323 41.667 0.00 0.00 0.00 3.09
278 300 4.476628 AAATGGGGAAAATGCTGCTTAG 57.523 40.909 0.00 0.00 0.00 2.18
279 301 2.897271 TGGGGAAAATGCTGCTTAGA 57.103 45.000 0.00 0.00 0.00 2.10
280 302 3.386932 TGGGGAAAATGCTGCTTAGAT 57.613 42.857 0.00 0.00 0.00 1.98
281 303 3.711863 TGGGGAAAATGCTGCTTAGATT 58.288 40.909 0.00 0.00 0.00 2.40
282 304 4.095946 TGGGGAAAATGCTGCTTAGATTT 58.904 39.130 0.00 0.00 0.00 2.17
323 345 4.222336 CCAGATGGGAGTAGAGATCAACT 58.778 47.826 0.00 0.00 40.01 3.16
324 346 4.653341 CCAGATGGGAGTAGAGATCAACTT 59.347 45.833 0.00 0.00 40.01 2.66
325 347 5.453057 CCAGATGGGAGTAGAGATCAACTTG 60.453 48.000 0.00 0.00 40.01 3.16
326 348 5.128499 CAGATGGGAGTAGAGATCAACTTGT 59.872 44.000 0.00 0.00 0.00 3.16
551 1719 9.524106 AAAAAGGTGTTTAAGGAGTTAAATTCG 57.476 29.630 0.00 0.00 39.69 3.34
585 1753 5.576128 CCCCAAAAATAGTTACTCCCTTCA 58.424 41.667 0.00 0.00 0.00 3.02
716 1897 5.215160 GCTGTACTTGGACAAAATCTTGTG 58.785 41.667 0.00 0.00 45.98 3.33
2061 3421 8.706521 AGAAGGTAATTATTACTCCCTCTGTTC 58.293 37.037 13.86 4.80 36.39 3.18
2290 3717 7.764443 TGGAGCTCACATTACTAACTTTATGTC 59.236 37.037 17.19 0.00 0.00 3.06
2812 4971 4.300189 TGTGTATGTTGTTGCCTCAAAC 57.700 40.909 0.00 0.00 0.00 2.93
2868 5035 2.236146 TGGTAATGATGTCTTGTCCGCT 59.764 45.455 0.00 0.00 0.00 5.52
2871 5038 3.610040 AATGATGTCTTGTCCGCTACA 57.390 42.857 0.00 0.00 35.88 2.74
2872 5039 3.827008 ATGATGTCTTGTCCGCTACAT 57.173 42.857 0.00 0.00 38.10 2.29
3147 5314 6.517529 CGGGTAATTTGGAATTTCACCAAGAA 60.518 38.462 0.00 0.00 46.05 2.52
3296 6337 6.377327 ACAATATAATGGAAAAGAGTGCGG 57.623 37.500 0.00 0.00 0.00 5.69
3461 6512 2.821969 GAGGTGATGCCACATTTGAACT 59.178 45.455 0.00 0.00 44.93 3.01
3553 6622 1.795286 GTGAAGAGTGCGGTGAAGAAG 59.205 52.381 0.00 0.00 0.00 2.85
3556 6625 0.753262 AGAGTGCGGTGAAGAAGTGT 59.247 50.000 0.00 0.00 0.00 3.55
3609 6678 5.710513 ATGTGTGTTGAAGTGTTGCATAT 57.289 34.783 0.00 0.00 0.00 1.78
3652 6750 9.755804 TTCATGTATTGCTTTGTTGTTATGAAA 57.244 25.926 0.00 0.00 30.58 2.69
3814 6912 6.609616 AGTTTTTGTTGGAAGAATCTACCCAA 59.390 34.615 11.40 11.40 36.43 4.12
3876 6974 4.961099 TGTCAGTCTCTCTTCATCCATGAT 59.039 41.667 0.00 0.00 36.56 2.45
4022 7134 4.582701 TTGGATGAACAACAACATGACC 57.417 40.909 0.00 0.00 0.00 4.02
4032 7144 4.887071 ACAACAACATGACCAGAAAAGCTA 59.113 37.500 0.00 0.00 0.00 3.32
4114 7227 7.445096 TGCATCCAAAGGTATCATTATGTAGTG 59.555 37.037 0.00 0.00 0.00 2.74
4304 7424 3.713858 TTGACATCAAGTGGTTTGCAG 57.286 42.857 0.00 0.00 36.70 4.41
4317 7437 5.767665 AGTGGTTTGCAGTAACATAACATCA 59.232 36.000 3.80 0.00 0.00 3.07
4322 7442 9.289303 GGTTTGCAGTAACATAACATCAAATAG 57.711 33.333 3.80 0.00 30.87 1.73
4402 7523 2.584391 GGTGAAGGTGAGGGCGACT 61.584 63.158 0.00 0.00 0.00 4.18
4409 7530 0.252197 GGTGAGGGCGACTGGTTTAT 59.748 55.000 0.00 0.00 0.00 1.40
4411 7532 2.483188 GGTGAGGGCGACTGGTTTATAG 60.483 54.545 0.00 0.00 0.00 1.31
4413 7534 2.037144 GAGGGCGACTGGTTTATAGGA 58.963 52.381 0.00 0.00 0.00 2.94
4414 7535 2.036089 GAGGGCGACTGGTTTATAGGAG 59.964 54.545 0.00 0.00 0.00 3.69
4518 7641 9.606631 AAGTGTATGGTTCTCTTTAGATGATTC 57.393 33.333 0.00 0.00 0.00 2.52
4540 7663 9.103861 GATTCCAAAGTTTTCATACCAAAACAA 57.896 29.630 10.54 0.00 45.16 2.83
4603 7729 6.468333 TTAATACGTACCATGTAGGAGCAA 57.532 37.500 0.00 0.00 41.22 3.91
4844 7974 3.670055 GTCACATTGGCTCAAAATGTTCG 59.330 43.478 0.00 0.00 43.94 3.95
4861 7991 3.749088 TGTTCGTTCGCACCTCATAATTT 59.251 39.130 0.00 0.00 0.00 1.82
4868 7998 7.493320 TCGTTCGCACCTCATAATTTAAACTAT 59.507 33.333 0.00 0.00 0.00 2.12
4874 8004 9.855021 GCACCTCATAATTTAAACTATTTGTGT 57.145 29.630 9.70 0.00 0.00 3.72
5168 9835 4.641396 CCACAGTGAAGGTGATCTTGTTA 58.359 43.478 0.62 0.00 38.54 2.41
5233 9901 6.666678 ACATGGTAGAGGTCATCATTCATTT 58.333 36.000 0.00 0.00 0.00 2.32
5412 10080 6.510746 TCTACATATGAAAAGATGAACGCG 57.489 37.500 10.38 3.53 0.00 6.01
5413 10081 4.536364 ACATATGAAAAGATGAACGCGG 57.464 40.909 12.47 0.00 0.00 6.46
5435 10103 8.311120 CGCGGTAATGATTTTAAATGAACTTTC 58.689 33.333 0.00 0.00 0.00 2.62
5498 10166 6.012683 AGCATCCATCAAGGCTAGATTTATCT 60.013 38.462 0.00 0.00 37.91 1.98
5531 10199 5.406649 TGAATGTGAATTAAATGGGCGAAC 58.593 37.500 0.00 0.00 0.00 3.95
5588 10256 1.410737 CCGCATACGTCCAGACAACG 61.411 60.000 0.00 0.00 45.37 4.10
5616 10284 2.614481 GGACAACGGAAGCCATCTAACA 60.614 50.000 0.00 0.00 0.00 2.41
5622 10290 2.615493 CGGAAGCCATCTAACACAGGTT 60.615 50.000 0.00 0.00 41.06 3.50
5633 10301 3.764237 AACACAGGTTTGTATCGGTCT 57.236 42.857 0.00 0.00 35.25 3.85
5639 10307 1.017177 GTTTGTATCGGTCTGCGGCA 61.017 55.000 1.29 1.29 0.00 5.69
5641 10309 1.884075 TTGTATCGGTCTGCGGCACT 61.884 55.000 0.00 0.00 0.00 4.40
5732 10404 0.318441 CTCAGGAAGACAAGACGGCA 59.682 55.000 0.00 0.00 0.00 5.69
5766 10438 2.581246 AGTTGGAATAAGGTTCTCCCCC 59.419 50.000 0.00 0.00 0.00 5.40
5818 10490 0.532862 CTATCAAAGGGCGCGTGGAT 60.533 55.000 8.43 11.19 0.00 3.41
5825 10497 3.353836 GGCGCGTGGATGTGTGTT 61.354 61.111 8.43 0.00 0.00 3.32
5936 10609 5.389520 TCAGATTGGATCCTTCGATCTACT 58.610 41.667 14.23 0.00 43.90 2.57
5986 10659 2.344592 AGGTGTGTTGGTCCTATTGGA 58.655 47.619 0.00 0.00 40.69 3.53
6001 10674 0.892755 TTGGACCTTAGCACGACGAT 59.107 50.000 0.00 0.00 0.00 3.73
6002 10675 0.892755 TGGACCTTAGCACGACGATT 59.107 50.000 0.00 0.00 0.00 3.34
6003 10676 2.093890 TGGACCTTAGCACGACGATTA 58.906 47.619 0.00 0.00 0.00 1.75
6004 10677 2.492881 TGGACCTTAGCACGACGATTAA 59.507 45.455 0.00 0.00 0.00 1.40
6007 10680 4.208666 GGACCTTAGCACGACGATTAATTC 59.791 45.833 0.00 0.00 0.00 2.17
6008 10681 5.007385 ACCTTAGCACGACGATTAATTCT 57.993 39.130 0.00 0.00 0.00 2.40
6017 10690 6.198403 GCACGACGATTAATTCTCAACTATCA 59.802 38.462 0.00 0.00 0.00 2.15
6414 11088 4.028131 TGGTCTACGGTTCTGGATGTAAT 58.972 43.478 0.00 0.00 0.00 1.89
6454 11130 4.997395 TCTTTGTACTTCCTTGACAGATGC 59.003 41.667 0.00 0.00 0.00 3.91
6513 11194 3.433343 TCTCCCGTGTGAACTACCATTA 58.567 45.455 0.00 0.00 0.00 1.90
6524 11206 5.414765 GTGAACTACCATTAAAACCTCCCTG 59.585 44.000 0.00 0.00 0.00 4.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 3.982241 GGTTCACCGTCCCGTCGT 61.982 66.667 0.00 0.00 0.00 4.34
32 33 0.105453 ATCGGTCCCATGAGGCTAGT 60.105 55.000 0.00 0.00 34.51 2.57
34 35 0.105709 TGATCGGTCCCATGAGGCTA 60.106 55.000 0.00 0.00 34.51 3.93
262 284 3.867493 GCAAATCTAAGCAGCATTTTCCC 59.133 43.478 0.00 0.00 0.00 3.97
263 285 4.752146 AGCAAATCTAAGCAGCATTTTCC 58.248 39.130 0.00 0.00 0.00 3.13
265 287 5.126707 AGCTAGCAAATCTAAGCAGCATTTT 59.873 36.000 18.83 0.00 37.36 1.82
266 288 4.643784 AGCTAGCAAATCTAAGCAGCATTT 59.356 37.500 18.83 0.00 37.36 2.32
267 289 4.205587 AGCTAGCAAATCTAAGCAGCATT 58.794 39.130 18.83 0.00 37.36 3.56
269 291 3.272574 AGCTAGCAAATCTAAGCAGCA 57.727 42.857 18.83 0.00 37.36 4.41
270 292 4.210955 CACTAGCTAGCAAATCTAAGCAGC 59.789 45.833 20.91 0.00 36.12 5.25
271 293 4.749099 CCACTAGCTAGCAAATCTAAGCAG 59.251 45.833 20.91 0.00 0.00 4.24
273 295 3.496507 GCCACTAGCTAGCAAATCTAAGC 59.503 47.826 20.91 5.40 38.99 3.09
274 296 4.509600 GTGCCACTAGCTAGCAAATCTAAG 59.490 45.833 20.91 4.87 44.23 2.18
275 297 4.162320 AGTGCCACTAGCTAGCAAATCTAA 59.838 41.667 20.91 0.00 44.23 2.10
276 298 3.706594 AGTGCCACTAGCTAGCAAATCTA 59.293 43.478 20.91 0.00 44.23 1.98
277 299 2.503356 AGTGCCACTAGCTAGCAAATCT 59.497 45.455 20.91 10.90 44.23 2.40
278 300 2.911484 AGTGCCACTAGCTAGCAAATC 58.089 47.619 20.91 8.88 44.23 2.17
279 301 3.012518 CAAGTGCCACTAGCTAGCAAAT 58.987 45.455 20.91 3.92 44.23 2.32
280 302 2.426522 CAAGTGCCACTAGCTAGCAAA 58.573 47.619 20.91 3.32 44.23 3.68
281 303 1.945819 GCAAGTGCCACTAGCTAGCAA 60.946 52.381 20.91 0.95 44.23 3.91
282 304 0.391661 GCAAGTGCCACTAGCTAGCA 60.392 55.000 20.91 11.31 44.23 3.49
323 345 6.037500 GCTTCATACAAGATGACTGCATACAA 59.962 38.462 0.00 0.00 34.11 2.41
324 346 5.525012 GCTTCATACAAGATGACTGCATACA 59.475 40.000 0.00 0.00 34.11 2.29
325 347 5.525012 TGCTTCATACAAGATGACTGCATAC 59.475 40.000 9.13 0.00 34.87 2.39
326 348 5.673514 TGCTTCATACAAGATGACTGCATA 58.326 37.500 9.13 0.00 34.87 3.14
551 1719 6.775594 ACTATTTTTGGGGCATCTCTAAAC 57.224 37.500 0.00 0.00 0.00 2.01
633 1808 8.239038 CAGAGTACTCCATCTGTCCTAAAATA 57.761 38.462 19.38 0.00 38.49 1.40
741 2018 6.260936 ACAAGTAGAGATGAAAAACCAGTGTG 59.739 38.462 0.00 0.00 0.00 3.82
1354 2676 1.227793 GGTGAGCCATAGGAGCAGC 60.228 63.158 0.00 0.00 34.09 5.25
2061 3421 6.345096 ACAAAGTTGGGTCATCTATTTTGG 57.655 37.500 0.00 0.00 0.00 3.28
2290 3717 8.085720 TGTGGAGCATATTTTTGATGTTTTTG 57.914 30.769 0.00 0.00 0.00 2.44
2812 4971 7.397892 TCTCTCACCTTTGTCTATGTTAGAG 57.602 40.000 0.00 0.00 35.04 2.43
2868 5035 9.328845 GGTTTTACCGATTTTGTCCTATATGTA 57.671 33.333 0.00 0.00 0.00 2.29
3121 5288 4.153411 TGGTGAAATTCCAAATTACCCGT 58.847 39.130 0.00 0.00 31.50 5.28
3147 5314 5.104485 GGTAAGTCCACATTACCTCCTCAAT 60.104 44.000 7.48 0.00 45.80 2.57
3296 6337 5.359576 TGGCAACAGAATAAATACATGGTCC 59.640 40.000 0.00 0.00 46.17 4.46
3553 6622 6.060136 GGGGGTAACATAATCTCCTTTACAC 58.940 44.000 0.00 0.00 39.74 2.90
3556 6625 4.970640 ACGGGGGTAACATAATCTCCTTTA 59.029 41.667 0.00 0.00 39.74 1.85
3682 6780 4.610333 TGAGCTGTGATAGAAGGGAAGTA 58.390 43.478 0.00 0.00 0.00 2.24
3876 6974 9.336171 TCGGAATTCATATATCAAATTGACACA 57.664 29.630 7.93 0.00 0.00 3.72
3893 6991 8.224389 ACATATTTCACATTCATCGGAATTCA 57.776 30.769 7.93 0.00 41.78 2.57
3926 7032 1.194772 GTTTGTGCTACGAGAACAGCC 59.805 52.381 0.00 0.00 34.69 4.85
4022 7134 3.812053 CCTTGATCCCGATAGCTTTTCTG 59.188 47.826 0.00 0.00 0.00 3.02
4032 7144 2.040178 GTGTACCTCCTTGATCCCGAT 58.960 52.381 0.00 0.00 0.00 4.18
4317 7437 7.291182 ACCATCCAACTGATACTAGCTCTATTT 59.709 37.037 0.00 0.00 30.56 1.40
4322 7442 4.946478 ACCATCCAACTGATACTAGCTC 57.054 45.455 0.00 0.00 30.56 4.09
4330 7450 1.271325 TGTCGCAACCATCCAACTGAT 60.271 47.619 0.00 0.00 0.00 2.90
4402 7523 7.622081 TCAGTTACCAATCTCTCCTATAAACCA 59.378 37.037 0.00 0.00 0.00 3.67
4409 7530 6.017192 AGTTGTCAGTTACCAATCTCTCCTA 58.983 40.000 0.00 0.00 0.00 2.94
4411 7532 5.153950 AGTTGTCAGTTACCAATCTCTCC 57.846 43.478 0.00 0.00 0.00 3.71
4413 7534 6.357367 ACAAAGTTGTCAGTTACCAATCTCT 58.643 36.000 0.00 0.00 36.50 3.10
4414 7535 6.619801 ACAAAGTTGTCAGTTACCAATCTC 57.380 37.500 0.00 0.00 36.50 2.75
4518 7641 8.726068 AGTTTTGTTTTGGTATGAAAACTTTGG 58.274 29.630 0.00 0.00 41.71 3.28
4540 7663 5.343307 AATCTCAACTTTGCACCAAGTTT 57.657 34.783 12.76 0.00 0.00 2.66
4717 7845 5.646793 TGGTATACTGCTCGGTATCTCATAC 59.353 44.000 2.25 0.00 34.65 2.39
4819 7949 5.633830 ACATTTTGAGCCAATGTGACTAG 57.366 39.130 0.00 0.00 42.17 2.57
4844 7974 9.783256 AAATAGTTTAAATTATGAGGTGCGAAC 57.217 29.630 4.19 0.00 0.00 3.95
4861 7991 3.058570 CCGCTGCACACACAAATAGTTTA 60.059 43.478 0.00 0.00 0.00 2.01
4868 7998 1.153269 TCTCCGCTGCACACACAAA 60.153 52.632 0.00 0.00 0.00 2.83
4874 8004 1.902765 ATCATGGTCTCCGCTGCACA 61.903 55.000 0.00 0.00 0.00 4.57
4876 8006 1.144716 GATCATGGTCTCCGCTGCA 59.855 57.895 0.00 0.00 0.00 4.41
4938 8068 6.072728 TCCATTCATCAACGATCGAAAAGTTT 60.073 34.615 24.34 0.59 0.00 2.66
5168 9835 4.652421 CCATGGACATGATTTGGAAAGGAT 59.348 41.667 5.56 0.00 41.20 3.24
5233 9901 1.213182 TGACCAGCACCCTGTACAAAA 59.787 47.619 0.00 0.00 37.38 2.44
5266 9934 4.142249 GCAAAACATTCTTTAGGCCGGTAT 60.142 41.667 1.90 0.00 0.00 2.73
5329 9997 8.152246 CAGAAAATAAAGTGGTCGGGGTATATA 58.848 37.037 0.00 0.00 0.00 0.86
5377 10045 9.378597 CTTTTCATATGTAGATGAAGAAATGCG 57.621 33.333 1.90 0.00 44.51 4.73
5435 10103 8.940952 CACCAAATCTTTCTAGGAAGAGTAAAG 58.059 37.037 18.39 10.56 38.90 1.85
5531 10199 2.359900 GTTGGAGATGCCCTAACACAG 58.640 52.381 0.00 0.00 34.97 3.66
5599 10267 2.615493 CCTGTGTTAGATGGCTTCCGTT 60.615 50.000 0.00 0.00 0.00 4.44
5600 10268 1.066143 CCTGTGTTAGATGGCTTCCGT 60.066 52.381 0.00 0.00 0.00 4.69
5616 10284 1.671850 CGCAGACCGATACAAACCTGT 60.672 52.381 0.00 0.00 40.02 4.00
5622 10290 1.447140 GTGCCGCAGACCGATACAA 60.447 57.895 0.00 0.00 40.02 2.41
5702 10371 2.805099 GTCTTCCTGAGCAGAACACAAG 59.195 50.000 0.00 0.00 0.00 3.16
5732 10404 1.192146 TCCAACTTCAGGTAGCCGCT 61.192 55.000 0.00 0.00 0.00 5.52
5818 10490 1.606668 GAGATCCGCCAAAAACACACA 59.393 47.619 0.00 0.00 0.00 3.72
5825 10497 1.376683 CCCGTGAGATCCGCCAAAA 60.377 57.895 0.00 0.00 0.00 2.44
5936 10609 1.141881 GCCGCCGATGAAGAGAAGA 59.858 57.895 0.00 0.00 0.00 2.87
5986 10659 5.007385 AGAATTAATCGTCGTGCTAAGGT 57.993 39.130 0.00 0.00 0.00 3.50
6003 10676 9.003658 CCTTGTTGTAGTTGATAGTTGAGAATT 57.996 33.333 0.00 0.00 0.00 2.17
6004 10677 8.157476 ACCTTGTTGTAGTTGATAGTTGAGAAT 58.843 33.333 0.00 0.00 0.00 2.40
6007 10680 7.730364 AACCTTGTTGTAGTTGATAGTTGAG 57.270 36.000 0.00 0.00 0.00 3.02
6008 10681 7.925993 CAAACCTTGTTGTAGTTGATAGTTGA 58.074 34.615 0.00 0.00 0.00 3.18
6427 11101 6.411376 TCTGTCAAGGAAGTACAAAGAACAA 58.589 36.000 0.00 0.00 0.00 2.83
6490 11168 1.548719 TGGTAGTTCACACGGGAGATG 59.451 52.381 0.00 0.00 0.00 2.90
6497 11178 5.106830 GGAGGTTTTAATGGTAGTTCACACG 60.107 44.000 0.00 0.00 0.00 4.49
6513 11194 1.115326 GTTGCCTGCAGGGAGGTTTT 61.115 55.000 33.46 0.00 36.70 2.43
6524 11206 3.996150 ATACTAATGCATGTTGCCTGC 57.004 42.857 0.00 0.00 44.23 4.85


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

AutoCloner maintained by Alex Coulton.