Multiple sequence alignment - TraesCS7D01G462500

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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 TraesCS7D01G462500 chr7D 100.000 2939 0 0 1 2939 578039264 578042202 0.000000e+00 5428.0
1 TraesCS7D01G462500 chr7D 96.585 615 11 4 4 613 62955489 62954880 0.000000e+00 1011.0
2 TraesCS7D01G462500 chr7D 90.826 327 30 0 1033 1359 578467198 578467524 3.480000e-119 438.0
3 TraesCS7D01G462500 chr7D 80.546 586 78 17 1443 2004 578467677 578468250 4.530000e-113 418.0
4 TraesCS7D01G462500 chr7D 87.465 359 33 5 1536 1882 577984525 577984883 1.270000e-108 403.0
5 TraesCS7D01G462500 chr7D 88.750 320 22 10 2519 2837 578053961 578054267 2.140000e-101 379.0
6 TraesCS7D01G462500 chr7D 85.593 354 51 0 1006 1359 578012217 578012570 3.580000e-99 372.0
7 TraesCS7D01G462500 chr7D 88.235 272 18 11 567 832 62954828 62954565 2.200000e-81 313.0
8 TraesCS7D01G462500 chr7D 79.282 362 56 4 1006 1366 577782233 577781890 4.900000e-58 235.0
9 TraesCS7D01G462500 chr7D 92.079 101 5 3 2830 2929 514348286 514348188 3.950000e-29 139.0
10 TraesCS7D01G462500 chr7D 92.958 71 5 0 2019 2089 578468298 578468368 1.440000e-18 104.0
11 TraesCS7D01G462500 chr7D 100.000 41 0 0 2050 2090 578053193 578053233 3.140000e-10 76.8
12 TraesCS7D01G462500 chr7A 94.745 628 17 6 1 613 62258818 62258192 0.000000e+00 963.0
13 TraesCS7D01G462500 chr7A 91.790 609 34 7 6 607 586951631 586951032 0.000000e+00 833.0
14 TraesCS7D01G462500 chr7A 97.051 373 11 0 2567 2939 670277263 670276891 1.920000e-176 628.0
15 TraesCS7D01G462500 chr7A 85.876 354 50 0 1006 1359 670553778 670554131 7.690000e-101 377.0
16 TraesCS7D01G462500 chr7A 85.475 358 45 4 1006 1359 670284077 670283723 1.660000e-97 366.0
17 TraesCS7D01G462500 chr7A 79.006 543 91 10 1447 1975 670283566 670283033 1.680000e-92 350.0
18 TraesCS7D01G462500 chr7A 87.805 287 26 8 561 839 62258164 62257879 7.850000e-86 327.0
19 TraesCS7D01G462500 chr7A 94.565 184 9 1 600 782 586950952 586950769 1.720000e-72 283.0
20 TraesCS7D01G462500 chr7A 88.889 162 14 4 679 839 50345613 50345455 2.310000e-46 196.0
21 TraesCS7D01G462500 chr7A 94.505 91 5 0 2839 2929 204607947 204608037 1.100000e-29 141.0
22 TraesCS7D01G462500 chr7A 92.632 95 7 0 2839 2933 20733014 20732920 1.420000e-28 137.0
23 TraesCS7D01G462500 chr7B 85.738 596 40 15 1930 2520 641605431 641605986 3.260000e-164 588.0
24 TraesCS7D01G462500 chr7B 82.965 634 62 20 1448 2077 641878718 641878127 5.580000e-147 531.0
25 TraesCS7D01G462500 chr7B 87.853 354 43 0 1006 1359 642264808 642265161 1.630000e-112 416.0
26 TraesCS7D01G462500 chr7B 84.444 360 50 4 1006 1359 641603625 641603984 1.680000e-92 350.0
27 TraesCS7D01G462500 chr7B 87.189 281 25 5 2089 2363 641878076 641877801 2.840000e-80 309.0
28 TraesCS7D01G462500 chr7B 95.808 167 7 0 2521 2687 641606024 641606190 1.340000e-68 270.0
29 TraesCS7D01G462500 chr7B 83.922 255 15 12 859 1101 641883241 641883001 1.370000e-53 220.0
30 TraesCS7D01G462500 chr7B 92.000 150 12 0 1087 1236 641882313 641882164 8.250000e-51 211.0
31 TraesCS7D01G462500 chr7B 83.028 218 31 4 2623 2840 642061291 642061080 2.990000e-45 193.0
32 TraesCS7D01G462500 chr7B 77.165 381 35 26 2397 2741 641877685 641877321 1.080000e-39 174.0
33 TraesCS7D01G462500 chr7B 93.827 81 5 0 1279 1359 641878962 641878882 3.980000e-24 122.0
34 TraesCS7D01G462500 chr7B 91.837 49 4 0 1227 1275 641880978 641880930 5.260000e-08 69.4
35 TraesCS7D01G462500 chr4A 92.239 335 20 4 248 577 696226054 696225721 1.230000e-128 470.0
36 TraesCS7D01G462500 chr4A 92.121 330 22 4 248 574 706525458 706525786 2.060000e-126 462.0
37 TraesCS7D01G462500 chr4A 87.558 217 19 5 600 810 641770990 641771204 8.140000e-61 244.0
38 TraesCS7D01G462500 chr4A 87.264 212 20 5 606 814 696225349 696225142 4.900000e-58 235.0
39 TraesCS7D01G462500 chr4A 84.649 228 22 6 561 776 656079830 656080056 6.380000e-52 215.0
40 TraesCS7D01G462500 chr4A 86.243 189 11 8 432 613 718360298 718360118 1.080000e-44 191.0
41 TraesCS7D01G462500 chr2D 91.892 333 19 7 248 574 91204053 91204383 2.670000e-125 459.0
42 TraesCS7D01G462500 chr1D 86.631 187 11 7 665 839 7282971 7282787 8.310000e-46 195.0
43 TraesCS7D01G462500 chr3D 87.662 154 15 3 679 832 593265672 593265523 3.010000e-40 176.0
44 TraesCS7D01G462500 chr3A 86.164 159 22 0 1754 1912 663463461 663463619 3.890000e-39 172.0
45 TraesCS7D01G462500 chr3A 91.089 101 9 0 2830 2930 37821422 37821322 1.420000e-28 137.0
46 TraesCS7D01G462500 chr2B 97.701 87 2 0 2839 2925 564875739 564875825 1.820000e-32 150.0
47 TraesCS7D01G462500 chr2A 97.647 85 2 0 2841 2925 14754785 14754869 2.360000e-31 147.0
48 TraesCS7D01G462500 chr5D 93.684 95 6 0 2840 2934 137915337 137915243 3.050000e-30 143.0
49 TraesCS7D01G462500 chr1B 94.565 92 4 1 2839 2930 282278213 282278123 1.100000e-29 141.0


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 TraesCS7D01G462500 chr7D 578039264 578042202 2938 False 5428.000000 5428 100.000000 1 2939 1 chr7D.!!$F3 2938
1 TraesCS7D01G462500 chr7D 62954565 62955489 924 True 662.000000 1011 92.410000 4 832 2 chr7D.!!$R3 828
2 TraesCS7D01G462500 chr7D 578467198 578468368 1170 False 320.000000 438 88.110000 1033 2089 3 chr7D.!!$F5 1056
3 TraesCS7D01G462500 chr7D 578053193 578054267 1074 False 227.900000 379 94.375000 2050 2837 2 chr7D.!!$F4 787
4 TraesCS7D01G462500 chr7A 62257879 62258818 939 True 645.000000 963 91.275000 1 839 2 chr7A.!!$R4 838
5 TraesCS7D01G462500 chr7A 586950769 586951631 862 True 558.000000 833 93.177500 6 782 2 chr7A.!!$R5 776
6 TraesCS7D01G462500 chr7A 670283033 670284077 1044 True 358.000000 366 82.240500 1006 1975 2 chr7A.!!$R6 969
7 TraesCS7D01G462500 chr7B 641603625 641606190 2565 False 402.666667 588 88.663333 1006 2687 3 chr7B.!!$F2 1681
8 TraesCS7D01G462500 chr7B 641877321 641883241 5920 True 233.771429 531 86.986429 859 2741 7 chr7B.!!$R2 1882
9 TraesCS7D01G462500 chr4A 696225142 696226054 912 True 352.500000 470 89.751500 248 814 2 chr4A.!!$R2 566

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
992 1389 0.959372 CTTTCCCCTCAGCAGCACAG 60.959 60.0 0.0 0.0 0.0 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2483 8144 0.107752 TTACCCGGCGAATTACCCAC 60.108 55.0 9.3 0.0 0.0 4.61 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
163 164 2.228841 GAGGGTGGATGGGTGCCAAT 62.229 60.000 0.00 0.00 36.95 3.16
508 521 6.823286 TTTGGATTGTGAGGGAGATATACA 57.177 37.500 0.00 0.00 0.00 2.29
874 1259 7.672983 TGGCTAACTGAGATTTACTTGAAAG 57.327 36.000 0.00 0.00 0.00 2.62
909 1302 5.939883 ACTGAAATTTAGCAGCAGATGTGTA 59.060 36.000 9.99 0.00 35.57 2.90
911 1304 7.770433 ACTGAAATTTAGCAGCAGATGTGTATA 59.230 33.333 9.99 0.00 35.57 1.47
912 1305 8.681486 TGAAATTTAGCAGCAGATGTGTATAT 57.319 30.769 0.00 0.00 0.00 0.86
921 1318 6.643388 CAGCAGATGTGTATATATAAGGCCA 58.357 40.000 5.01 0.00 0.00 5.36
925 1322 7.044181 CAGATGTGTATATATAAGGCCACCTG 58.956 42.308 5.01 6.17 32.13 4.00
930 1327 7.290481 TGTGTATATATAAGGCCACCTGTGTTA 59.710 37.037 5.01 0.00 32.13 2.41
956 1353 1.577729 TCCTGTCCATCCCTCATCTCT 59.422 52.381 0.00 0.00 0.00 3.10
957 1354 1.969923 CCTGTCCATCCCTCATCTCTC 59.030 57.143 0.00 0.00 0.00 3.20
958 1355 2.426121 CCTGTCCATCCCTCATCTCTCT 60.426 54.545 0.00 0.00 0.00 3.10
959 1356 3.307506 CTGTCCATCCCTCATCTCTCTT 58.692 50.000 0.00 0.00 0.00 2.85
960 1357 4.478203 CTGTCCATCCCTCATCTCTCTTA 58.522 47.826 0.00 0.00 0.00 2.10
961 1358 4.219115 TGTCCATCCCTCATCTCTCTTAC 58.781 47.826 0.00 0.00 0.00 2.34
962 1359 4.078922 TGTCCATCCCTCATCTCTCTTACT 60.079 45.833 0.00 0.00 0.00 2.24
963 1360 4.522789 GTCCATCCCTCATCTCTCTTACTC 59.477 50.000 0.00 0.00 0.00 2.59
964 1361 4.168871 TCCATCCCTCATCTCTCTTACTCA 59.831 45.833 0.00 0.00 0.00 3.41
965 1362 4.523943 CCATCCCTCATCTCTCTTACTCAG 59.476 50.000 0.00 0.00 0.00 3.35
971 1368 5.656416 CCTCATCTCTCTTACTCAGTTCCTT 59.344 44.000 0.00 0.00 0.00 3.36
977 1374 5.542779 TCTCTTACTCAGTTCCTTGCTTTC 58.457 41.667 0.00 0.00 0.00 2.62
981 1378 1.074566 CTCAGTTCCTTGCTTTCCCCT 59.925 52.381 0.00 0.00 0.00 4.79
990 1387 2.338785 GCTTTCCCCTCAGCAGCAC 61.339 63.158 0.00 0.00 35.95 4.40
991 1388 1.073722 CTTTCCCCTCAGCAGCACA 59.926 57.895 0.00 0.00 0.00 4.57
992 1389 0.959372 CTTTCCCCTCAGCAGCACAG 60.959 60.000 0.00 0.00 0.00 3.66
996 1393 2.814341 CCTCAGCAGCACAGCTCG 60.814 66.667 0.00 0.00 44.54 5.03
997 1394 2.048409 CTCAGCAGCACAGCTCGT 60.048 61.111 0.00 0.00 44.54 4.18
998 1395 2.048784 TCAGCAGCACAGCTCGTC 60.049 61.111 0.00 0.00 44.54 4.20
1083 1480 4.052229 AAGACCCTCCGCGTCGTG 62.052 66.667 4.92 0.00 35.33 4.35
1180 2277 1.458588 ATCTCCCGCTCCCTCTTCC 60.459 63.158 0.00 0.00 0.00 3.46
1277 5542 2.439883 GGTCGCCTACCTCCTCGT 60.440 66.667 0.00 0.00 45.75 4.18
1359 5630 4.471726 GTCACCGACGACCGCGAT 62.472 66.667 8.23 0.00 41.64 4.58
1395 5705 2.366972 ATCCCCAGGTTCCGAGGG 60.367 66.667 13.09 13.09 42.44 4.30
1543 5895 2.258591 GTGAGAAGAGCGGCGTGA 59.741 61.111 9.37 0.00 0.00 4.35
1557 5909 4.752879 GTGAAGCTGGCGCGGGTA 62.753 66.667 8.83 0.00 42.32 3.69
1600 5955 2.362760 TGTACTTCGCCGGGGCTA 60.363 61.111 14.85 3.20 39.32 3.93
1601 5956 2.416260 GTACTTCGCCGGGGCTAG 59.584 66.667 14.85 15.36 39.32 3.42
1686 6047 3.200593 GCCCTGCACATGAGCGAG 61.201 66.667 10.61 8.70 37.31 5.03
1957 7158 4.803426 AGCTCGGCGGCGAAGAAG 62.803 66.667 33.90 23.02 37.29 2.85
1986 7204 3.532155 CGGCCGGAGAGGAGAAGG 61.532 72.222 20.10 0.00 45.00 3.46
1987 7205 3.855853 GGCCGGAGAGGAGAAGGC 61.856 72.222 5.05 0.00 45.00 4.35
1988 7206 3.077556 GCCGGAGAGGAGAAGGCA 61.078 66.667 5.05 0.00 46.48 4.75
1989 7207 2.896443 CCGGAGAGGAGAAGGCAC 59.104 66.667 0.00 0.00 45.00 5.01
1990 7208 1.684049 CCGGAGAGGAGAAGGCACT 60.684 63.158 0.00 0.00 45.00 4.40
1991 7209 0.395862 CCGGAGAGGAGAAGGCACTA 60.396 60.000 0.00 0.00 45.00 2.74
1992 7210 1.028905 CGGAGAGGAGAAGGCACTAG 58.971 60.000 0.00 0.00 38.49 2.57
1993 7211 1.408969 GGAGAGGAGAAGGCACTAGG 58.591 60.000 0.00 0.00 38.49 3.02
1994 7212 1.063567 GGAGAGGAGAAGGCACTAGGA 60.064 57.143 0.00 0.00 38.49 2.94
1995 7213 2.306847 GAGAGGAGAAGGCACTAGGAG 58.693 57.143 0.00 0.00 38.49 3.69
1996 7214 1.926665 AGAGGAGAAGGCACTAGGAGA 59.073 52.381 0.00 0.00 38.49 3.71
1997 7215 2.313342 AGAGGAGAAGGCACTAGGAGAA 59.687 50.000 0.00 0.00 38.49 2.87
1998 7216 2.693074 GAGGAGAAGGCACTAGGAGAAG 59.307 54.545 0.00 0.00 38.49 2.85
1999 7217 1.138069 GGAGAAGGCACTAGGAGAAGC 59.862 57.143 0.00 0.00 38.49 3.86
2000 7218 0.820871 AGAAGGCACTAGGAGAAGCG 59.179 55.000 0.00 0.00 38.49 4.68
2001 7219 0.808060 GAAGGCACTAGGAGAAGCGC 60.808 60.000 0.00 0.00 38.49 5.92
2038 7290 0.311790 TTAATCCTACGTAGCGCCCG 59.688 55.000 17.41 14.67 0.00 6.13
2161 7498 3.892588 TGTACCCAACCAAACCAAGAATC 59.107 43.478 0.00 0.00 0.00 2.52
2171 7510 8.773645 CAACCAAACCAAGAATCTTTAATTTCC 58.226 33.333 0.00 0.00 0.00 3.13
2227 7567 6.430451 GGATATGTCGATTTGATGGTTGTTC 58.570 40.000 0.00 0.00 0.00 3.18
2261 7601 4.410099 TCAAATGAACTTGGGAGCTTGAT 58.590 39.130 0.00 0.00 0.00 2.57
2262 7602 4.460382 TCAAATGAACTTGGGAGCTTGATC 59.540 41.667 0.00 0.00 0.00 2.92
2263 7603 2.099141 TGAACTTGGGAGCTTGATCG 57.901 50.000 0.00 0.00 0.00 3.69
2264 7604 1.623311 TGAACTTGGGAGCTTGATCGA 59.377 47.619 0.00 0.00 0.00 3.59
2276 7616 3.722147 GCTTGATCGAGCTCCTTTGATA 58.278 45.455 25.22 0.00 39.57 2.15
2378 7996 9.787532 TTGAAGTACTCAAATTCTCAAAAACAG 57.212 29.630 0.00 0.00 41.21 3.16
2464 8123 0.539669 ACTAACAAGTTGGGCTGGGC 60.540 55.000 7.96 0.00 0.00 5.36
2478 8139 4.382320 GGGCGCGTTGGACCAGTA 62.382 66.667 8.43 0.00 0.00 2.74
2479 8140 2.813908 GGCGCGTTGGACCAGTAG 60.814 66.667 8.43 0.00 0.00 2.57
2480 8141 2.048503 GCGCGTTGGACCAGTAGT 60.049 61.111 8.43 0.00 0.00 2.73
2481 8142 2.380410 GCGCGTTGGACCAGTAGTG 61.380 63.158 8.43 0.00 0.00 2.74
2510 8171 3.678915 ATTCGCCGGGTAAAATAAACG 57.321 42.857 2.18 0.00 0.00 3.60
2629 8328 8.911918 TTCCAAAGATAAGCAAACTTACACTA 57.088 30.769 0.00 0.00 41.12 2.74
2675 8389 4.264253 CAAAGCAATGACTACTCCATCCA 58.736 43.478 0.00 0.00 0.00 3.41
2682 8397 4.927267 TGACTACTCCATCCATTTTGGT 57.073 40.909 0.00 0.00 39.03 3.67
2687 8402 5.726793 ACTACTCCATCCATTTTGGTAGAGT 59.273 40.000 15.11 15.11 41.43 3.24
2719 8437 4.803098 TGAGGAGTAAAAGCTACTGTCC 57.197 45.455 0.00 0.00 27.85 4.02
2728 8446 5.948992 AAAAGCTACTGTCCAGTCATTTC 57.051 39.130 2.65 0.00 42.54 2.17
2729 8447 4.623932 AAGCTACTGTCCAGTCATTTCA 57.376 40.909 2.65 0.00 42.54 2.69
2730 8448 4.199432 AGCTACTGTCCAGTCATTTCAG 57.801 45.455 2.65 0.00 42.54 3.02
2741 8459 9.300681 TGTCCAGTCATTTCAGAATTTCTATTT 57.699 29.630 0.00 0.00 0.00 1.40
2822 8540 8.134895 GGAAATAAATATTGCATCAGGAAACGA 58.865 33.333 0.00 0.00 0.00 3.85
2828 8546 4.909696 TTGCATCAGGAAACGAGAAAAA 57.090 36.364 0.00 0.00 0.00 1.94
2830 8548 5.452078 TGCATCAGGAAACGAGAAAAATT 57.548 34.783 0.00 0.00 0.00 1.82
2831 8549 6.567687 TGCATCAGGAAACGAGAAAAATTA 57.432 33.333 0.00 0.00 0.00 1.40
2833 8551 7.601856 TGCATCAGGAAACGAGAAAAATTATT 58.398 30.769 0.00 0.00 0.00 1.40
2834 8552 7.541783 TGCATCAGGAAACGAGAAAAATTATTG 59.458 33.333 0.00 0.00 0.00 1.90
2836 8554 9.624697 CATCAGGAAACGAGAAAAATTATTGAA 57.375 29.630 0.00 0.00 0.00 2.69
2837 8555 9.626045 ATCAGGAAACGAGAAAAATTATTGAAC 57.374 29.630 0.00 0.00 0.00 3.18
2838 8556 8.846211 TCAGGAAACGAGAAAAATTATTGAACT 58.154 29.630 0.00 0.00 0.00 3.01
2839 8557 8.905702 CAGGAAACGAGAAAAATTATTGAACTG 58.094 33.333 0.00 0.00 0.00 3.16
2840 8558 8.630037 AGGAAACGAGAAAAATTATTGAACTGT 58.370 29.630 0.00 0.00 0.00 3.55
2841 8559 9.887406 GGAAACGAGAAAAATTATTGAACTGTA 57.113 29.630 0.00 0.00 0.00 2.74
2845 8563 8.718734 ACGAGAAAAATTATTGAACTGTACTCC 58.281 33.333 0.00 0.00 0.00 3.85
2846 8564 8.175716 CGAGAAAAATTATTGAACTGTACTCCC 58.824 37.037 0.00 0.00 0.00 4.30
2847 8565 9.232473 GAGAAAAATTATTGAACTGTACTCCCT 57.768 33.333 0.00 0.00 0.00 4.20
2848 8566 9.232473 AGAAAAATTATTGAACTGTACTCCCTC 57.768 33.333 0.00 0.00 0.00 4.30
2849 8567 9.232473 GAAAAATTATTGAACTGTACTCCCTCT 57.768 33.333 0.00 0.00 0.00 3.69
2850 8568 8.567285 AAAATTATTGAACTGTACTCCCTCTG 57.433 34.615 0.00 0.00 0.00 3.35
2851 8569 6.875972 ATTATTGAACTGTACTCCCTCTGT 57.124 37.500 0.00 0.00 0.00 3.41
2852 8570 7.973048 ATTATTGAACTGTACTCCCTCTGTA 57.027 36.000 0.00 0.00 0.00 2.74
2853 8571 7.786046 TTATTGAACTGTACTCCCTCTGTAA 57.214 36.000 0.00 0.00 0.00 2.41
2854 8572 6.681729 ATTGAACTGTACTCCCTCTGTAAA 57.318 37.500 0.00 0.00 0.00 2.01
2855 8573 6.681729 TTGAACTGTACTCCCTCTGTAAAT 57.318 37.500 0.00 0.00 0.00 1.40
2856 8574 6.681729 TGAACTGTACTCCCTCTGTAAATT 57.318 37.500 0.00 0.00 0.00 1.82
2857 8575 7.786046 TGAACTGTACTCCCTCTGTAAATTA 57.214 36.000 0.00 0.00 0.00 1.40
2858 8576 8.197592 TGAACTGTACTCCCTCTGTAAATTAA 57.802 34.615 0.00 0.00 0.00 1.40
2859 8577 8.822805 TGAACTGTACTCCCTCTGTAAATTAAT 58.177 33.333 0.00 0.00 0.00 1.40
2868 8586 9.360093 CTCCCTCTGTAAATTAATATAAGAGCG 57.640 37.037 9.98 4.77 0.00 5.03
2869 8587 8.867097 TCCCTCTGTAAATTAATATAAGAGCGT 58.133 33.333 9.98 0.00 0.00 5.07
2870 8588 9.490379 CCCTCTGTAAATTAATATAAGAGCGTT 57.510 33.333 9.98 0.00 0.00 4.84
2886 8604 9.953697 ATAAGAGCGTTTAGATCACTACTTTAG 57.046 33.333 0.00 0.00 37.82 1.85
2887 8605 7.393841 AGAGCGTTTAGATCACTACTTTAGT 57.606 36.000 0.00 0.00 37.82 2.24
2888 8606 8.503458 AGAGCGTTTAGATCACTACTTTAGTA 57.497 34.615 0.00 0.00 37.82 1.82
2889 8607 8.954350 AGAGCGTTTAGATCACTACTTTAGTAA 58.046 33.333 0.00 0.00 37.82 2.24
2890 8608 9.733219 GAGCGTTTAGATCACTACTTTAGTAAT 57.267 33.333 0.00 0.00 37.23 1.89
2891 8609 9.733219 AGCGTTTAGATCACTACTTTAGTAATC 57.267 33.333 0.00 0.00 37.23 1.75
2892 8610 8.966194 GCGTTTAGATCACTACTTTAGTAATCC 58.034 37.037 0.00 0.00 37.23 3.01
2897 8615 8.928270 AGATCACTACTTTAGTAATCCAAACG 57.072 34.615 0.00 0.00 37.23 3.60
2898 8616 6.956299 TCACTACTTTAGTAATCCAAACGC 57.044 37.500 0.00 0.00 37.23 4.84
2899 8617 6.694447 TCACTACTTTAGTAATCCAAACGCT 58.306 36.000 0.00 0.00 37.23 5.07
2900 8618 6.810182 TCACTACTTTAGTAATCCAAACGCTC 59.190 38.462 0.00 0.00 37.23 5.03
2901 8619 6.812160 CACTACTTTAGTAATCCAAACGCTCT 59.188 38.462 0.00 0.00 37.23 4.09
2902 8620 7.331193 CACTACTTTAGTAATCCAAACGCTCTT 59.669 37.037 0.00 0.00 37.23 2.85
2903 8621 8.526147 ACTACTTTAGTAATCCAAACGCTCTTA 58.474 33.333 0.00 0.00 37.23 2.10
2904 8622 9.530633 CTACTTTAGTAATCCAAACGCTCTTAT 57.469 33.333 0.00 0.00 0.00 1.73
2916 8634 9.653287 TCCAAACGCTCTTATATTAGATTATGG 57.347 33.333 0.00 0.00 0.00 2.74
2917 8635 9.653287 CCAAACGCTCTTATATTAGATTATGGA 57.347 33.333 0.00 0.00 0.00 3.41
2919 8637 9.877178 AAACGCTCTTATATTAGATTATGGAGG 57.123 33.333 0.00 0.00 0.00 4.30
2920 8638 8.012957 ACGCTCTTATATTAGATTATGGAGGG 57.987 38.462 0.00 0.00 35.06 4.30
2921 8639 7.839705 ACGCTCTTATATTAGATTATGGAGGGA 59.160 37.037 0.00 0.00 34.22 4.20
2922 8640 8.356657 CGCTCTTATATTAGATTATGGAGGGAG 58.643 40.741 0.00 0.00 33.23 4.30
2923 8641 9.207868 GCTCTTATATTAGATTATGGAGGGAGT 57.792 37.037 0.00 0.00 0.00 3.85
2934 8652 9.629878 AGATTATGGAGGGAGTATATTACTACG 57.370 37.037 0.00 0.00 40.68 3.51
2935 8653 7.636150 TTATGGAGGGAGTATATTACTACGC 57.364 40.000 0.00 0.00 40.68 4.42
2936 8654 5.252586 TGGAGGGAGTATATTACTACGCT 57.747 43.478 0.00 0.00 40.68 5.07
2937 8655 5.008331 TGGAGGGAGTATATTACTACGCTG 58.992 45.833 0.00 0.00 40.68 5.18
2938 8656 4.142425 GGAGGGAGTATATTACTACGCTGC 60.142 50.000 0.00 0.00 40.68 5.25
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
163 164 2.887783 GTCCATGCTTCCTCGATCTAGA 59.112 50.000 0.00 0.00 0.00 2.43
441 450 2.182827 TCTCTCTCCTGTTGTGATGGG 58.817 52.381 0.00 0.00 0.00 4.00
523 537 4.370776 TCCCCCAATCTCTTATGTTCTCA 58.629 43.478 0.00 0.00 0.00 3.27
674 803 9.886132 GACCAAATTATTACGGTATAGATCCAT 57.114 33.333 0.00 0.00 0.00 3.41
843 1228 9.740710 AAGTAAATCTCAGTTAGCCAATACTTT 57.259 29.630 0.00 0.00 0.00 2.66
844 1229 9.167311 CAAGTAAATCTCAGTTAGCCAATACTT 57.833 33.333 0.00 0.00 31.94 2.24
845 1230 8.540388 TCAAGTAAATCTCAGTTAGCCAATACT 58.460 33.333 0.00 0.00 0.00 2.12
846 1231 8.718102 TCAAGTAAATCTCAGTTAGCCAATAC 57.282 34.615 0.00 0.00 0.00 1.89
847 1232 9.733556 TTTCAAGTAAATCTCAGTTAGCCAATA 57.266 29.630 0.00 0.00 0.00 1.90
848 1233 8.635765 TTTCAAGTAAATCTCAGTTAGCCAAT 57.364 30.769 0.00 0.00 0.00 3.16
849 1234 7.936847 TCTTTCAAGTAAATCTCAGTTAGCCAA 59.063 33.333 0.00 0.00 0.00 4.52
850 1235 7.450074 TCTTTCAAGTAAATCTCAGTTAGCCA 58.550 34.615 0.00 0.00 0.00 4.75
851 1236 7.907214 TCTTTCAAGTAAATCTCAGTTAGCC 57.093 36.000 0.00 0.00 0.00 3.93
855 1240 9.956720 CACATTTCTTTCAAGTAAATCTCAGTT 57.043 29.630 0.00 0.00 0.00 3.16
856 1241 8.571336 CCACATTTCTTTCAAGTAAATCTCAGT 58.429 33.333 0.00 0.00 0.00 3.41
857 1242 7.540055 GCCACATTTCTTTCAAGTAAATCTCAG 59.460 37.037 0.00 0.00 0.00 3.35
874 1259 4.558860 GCTAAATTTCAGTCGCCACATTTC 59.441 41.667 0.00 0.00 0.00 2.17
880 1265 1.468520 GCTGCTAAATTTCAGTCGCCA 59.531 47.619 8.27 0.00 33.09 5.69
909 1302 6.557253 TGTCTAACACAGGTGGCCTTATATAT 59.443 38.462 3.32 0.00 34.19 0.86
911 1304 4.719773 TGTCTAACACAGGTGGCCTTATAT 59.280 41.667 3.32 0.00 34.19 0.86
912 1305 4.098155 TGTCTAACACAGGTGGCCTTATA 58.902 43.478 3.32 0.00 34.19 0.98
916 1309 2.848608 TGTCTAACACAGGTGGCCT 58.151 52.632 3.32 0.00 34.19 5.19
936 1333 1.577729 AGAGATGAGGGATGGACAGGA 59.422 52.381 0.00 0.00 0.00 3.86
956 1353 4.505039 GGGAAAGCAAGGAACTGAGTAAGA 60.505 45.833 0.00 0.00 40.86 2.10
957 1354 3.753797 GGGAAAGCAAGGAACTGAGTAAG 59.246 47.826 0.00 0.00 40.86 2.34
958 1355 3.497942 GGGGAAAGCAAGGAACTGAGTAA 60.498 47.826 0.00 0.00 40.86 2.24
959 1356 2.039879 GGGGAAAGCAAGGAACTGAGTA 59.960 50.000 0.00 0.00 40.86 2.59
960 1357 1.202940 GGGGAAAGCAAGGAACTGAGT 60.203 52.381 0.00 0.00 40.86 3.41
961 1358 1.074566 AGGGGAAAGCAAGGAACTGAG 59.925 52.381 0.00 0.00 40.86 3.35
962 1359 1.073923 GAGGGGAAAGCAAGGAACTGA 59.926 52.381 0.00 0.00 40.86 3.41
963 1360 1.202927 TGAGGGGAAAGCAAGGAACTG 60.203 52.381 0.00 0.00 40.86 3.16
965 1362 1.539157 CTGAGGGGAAAGCAAGGAAC 58.461 55.000 0.00 0.00 0.00 3.62
971 1368 2.034687 GCTGCTGAGGGGAAAGCA 59.965 61.111 0.00 0.00 46.84 3.91
977 1374 3.972971 GAGCTGTGCTGCTGAGGGG 62.973 68.421 8.27 0.00 44.17 4.79
981 1378 2.048784 GACGAGCTGTGCTGCTGA 60.049 61.111 8.27 0.00 44.17 4.26
1121 2218 0.392193 CAGGGTGAGCATGGTCACTC 60.392 60.000 41.07 39.99 46.81 3.51
1262 3563 0.818445 GATGACGAGGAGGTAGGCGA 60.818 60.000 0.00 0.00 0.00 5.54
1268 3569 1.367599 GACGACGATGACGAGGAGGT 61.368 60.000 0.00 0.00 42.66 3.85
1277 5542 1.934220 GAGCCACTGGACGACGATGA 61.934 60.000 0.00 0.00 0.00 2.92
1303 5568 0.108424 GAGAAGACGCAGCAGATGGT 60.108 55.000 0.00 0.00 0.00 3.55
1306 5571 1.140589 CGGAGAAGACGCAGCAGAT 59.859 57.895 0.00 0.00 0.00 2.90
1307 5572 2.201436 GACGGAGAAGACGCAGCAGA 62.201 60.000 0.00 0.00 34.00 4.26
1310 5575 2.876645 CGACGGAGAAGACGCAGC 60.877 66.667 0.00 0.00 34.00 5.25
1374 5657 0.689745 CTCGGAACCTGGGGATGGTA 60.690 60.000 0.00 0.00 36.69 3.25
1378 5661 2.366972 CCCTCGGAACCTGGGGAT 60.367 66.667 10.78 0.00 41.25 3.85
1580 5935 3.751246 CCCCGGCGAAGTACACGA 61.751 66.667 9.30 0.00 0.00 4.35
1600 5955 2.360350 CACCAAGCCGATGTGCCT 60.360 61.111 0.00 0.00 0.00 4.75
1601 5956 2.672996 ACACCAAGCCGATGTGCC 60.673 61.111 0.00 0.00 33.30 5.01
1672 6033 2.172372 GCTCCTCGCTCATGTGCAG 61.172 63.158 18.98 14.10 35.14 4.41
1891 7081 2.097954 TCTTGCACACAAAGAACAGCAG 59.902 45.455 0.00 0.00 34.74 4.24
1943 7136 2.431942 GAACTTCTTCGCCGCCGA 60.432 61.111 0.00 0.00 42.66 5.54
1987 7205 1.690219 ATGGGGCGCTTCTCCTAGTG 61.690 60.000 7.64 0.00 0.00 2.74
1988 7206 1.383248 ATGGGGCGCTTCTCCTAGT 60.383 57.895 7.64 0.00 0.00 2.57
1989 7207 1.070445 CATGGGGCGCTTCTCCTAG 59.930 63.158 7.64 0.00 0.00 3.02
1990 7208 2.443394 CCATGGGGCGCTTCTCCTA 61.443 63.158 7.64 0.00 0.00 2.94
1991 7209 3.801997 CCATGGGGCGCTTCTCCT 61.802 66.667 7.64 0.00 0.00 3.69
1992 7210 2.666596 CTACCATGGGGCGCTTCTCC 62.667 65.000 18.09 0.00 37.90 3.71
1993 7211 1.227674 CTACCATGGGGCGCTTCTC 60.228 63.158 18.09 0.00 37.90 2.87
1994 7212 1.995626 ACTACCATGGGGCGCTTCT 60.996 57.895 18.09 0.00 37.90 2.85
1995 7213 1.819632 CACTACCATGGGGCGCTTC 60.820 63.158 18.09 0.00 37.90 3.86
1996 7214 2.272146 CACTACCATGGGGCGCTT 59.728 61.111 18.09 0.00 37.90 4.68
1997 7215 3.009115 ACACTACCATGGGGCGCT 61.009 61.111 18.09 0.00 37.90 5.92
1998 7216 2.513897 GACACTACCATGGGGCGC 60.514 66.667 18.09 0.00 37.90 6.53
1999 7217 1.153369 CAGACACTACCATGGGGCG 60.153 63.158 18.09 6.16 37.90 6.13
2000 7218 0.839946 ATCAGACACTACCATGGGGC 59.160 55.000 18.09 0.00 37.90 5.80
2001 7219 4.771114 TTAATCAGACACTACCATGGGG 57.229 45.455 18.09 11.03 41.29 4.96
2161 7498 8.286191 AGTAGAATGGCAAGAGGAAATTAAAG 57.714 34.615 0.00 0.00 0.00 1.85
2171 7510 8.228035 AGTTACTAGTAGTAGAATGGCAAGAG 57.772 38.462 11.68 0.00 31.47 2.85
2248 7588 2.687842 GCTCGATCAAGCTCCCAAG 58.312 57.895 0.00 0.00 39.27 3.61
2385 8003 2.845659 TGATTTCTCTAAGGGGCTGGA 58.154 47.619 0.00 0.00 0.00 3.86
2387 8005 4.594920 TCCTATGATTTCTCTAAGGGGCTG 59.405 45.833 0.00 0.00 0.00 4.85
2388 8006 4.832492 TCCTATGATTTCTCTAAGGGGCT 58.168 43.478 0.00 0.00 0.00 5.19
2389 8007 5.072464 AGTTCCTATGATTTCTCTAAGGGGC 59.928 44.000 0.00 0.00 0.00 5.80
2391 8009 7.610580 AGAGTTCCTATGATTTCTCTAAGGG 57.389 40.000 0.00 0.00 31.73 3.95
2421 8044 5.428457 TGCAGGATAAGAAGACAAATCCCTA 59.572 40.000 0.00 0.00 38.99 3.53
2464 8123 1.736645 CCACTACTGGTCCAACGCG 60.737 63.158 3.53 3.53 32.03 6.01
2478 8139 1.301954 GGCGAATTACCCACCCACT 59.698 57.895 0.00 0.00 0.00 4.00
2479 8140 2.110352 CGGCGAATTACCCACCCAC 61.110 63.158 0.00 0.00 0.00 4.61
2480 8141 2.269562 CGGCGAATTACCCACCCA 59.730 61.111 0.00 0.00 0.00 4.51
2481 8142 2.515290 CCGGCGAATTACCCACCC 60.515 66.667 9.30 0.00 0.00 4.61
2482 8143 1.970352 TACCCGGCGAATTACCCACC 61.970 60.000 9.30 0.00 0.00 4.61
2483 8144 0.107752 TTACCCGGCGAATTACCCAC 60.108 55.000 9.30 0.00 0.00 4.61
2484 8145 0.617413 TTTACCCGGCGAATTACCCA 59.383 50.000 9.30 0.00 0.00 4.51
2485 8146 1.748950 TTTTACCCGGCGAATTACCC 58.251 50.000 9.30 0.00 0.00 3.69
2488 8149 4.495514 GCGTTTATTTTACCCGGCGAATTA 60.496 41.667 9.30 0.00 0.00 1.40
2491 8152 1.130186 GCGTTTATTTTACCCGGCGAA 59.870 47.619 9.30 0.00 0.00 4.70
2510 8171 1.008309 TTTTTACCCGTGCGCTTGC 60.008 52.632 9.73 0.00 39.78 4.01
2682 8397 2.023404 TCCTCATGCCTTGGGTACTCTA 60.023 50.000 0.00 0.00 0.00 2.43
2687 8402 2.561209 TACTCCTCATGCCTTGGGTA 57.439 50.000 0.00 0.00 0.00 3.69
2753 8471 9.851686 AAGCATGACAAATATATCTCAAGGTTA 57.148 29.630 0.00 0.00 0.00 2.85
2791 8509 7.717436 TCCTGATGCAATATTTATTTCCGTACA 59.283 33.333 0.00 0.00 0.00 2.90
2795 8513 7.113404 CGTTTCCTGATGCAATATTTATTTCCG 59.887 37.037 0.00 0.00 0.00 4.30
2801 8519 7.857734 TTCTCGTTTCCTGATGCAATATTTA 57.142 32.000 0.00 0.00 0.00 1.40
2822 8540 9.232473 GAGGGAGTACAGTTCAATAATTTTTCT 57.768 33.333 0.00 0.00 0.00 2.52
2828 8546 6.875972 ACAGAGGGAGTACAGTTCAATAAT 57.124 37.500 0.00 0.00 0.00 1.28
2830 8548 7.786046 TTTACAGAGGGAGTACAGTTCAATA 57.214 36.000 0.00 0.00 0.00 1.90
2831 8549 6.681729 TTTACAGAGGGAGTACAGTTCAAT 57.318 37.500 0.00 0.00 0.00 2.57
2833 8551 6.681729 AATTTACAGAGGGAGTACAGTTCA 57.318 37.500 0.00 0.00 0.00 3.18
2842 8560 9.360093 CGCTCTTATATTAATTTACAGAGGGAG 57.640 37.037 20.74 5.24 40.49 4.30
2843 8561 8.867097 ACGCTCTTATATTAATTTACAGAGGGA 58.133 33.333 25.54 1.67 40.49 4.20
2844 8562 9.490379 AACGCTCTTATATTAATTTACAGAGGG 57.510 33.333 21.96 21.96 42.53 4.30
2860 8578 9.953697 CTAAAGTAGTGATCTAAACGCTCTTAT 57.046 33.333 0.00 0.00 0.00 1.73
2861 8579 8.954350 ACTAAAGTAGTGATCTAAACGCTCTTA 58.046 33.333 0.00 0.00 37.69 2.10
2862 8580 7.828712 ACTAAAGTAGTGATCTAAACGCTCTT 58.171 34.615 0.00 0.00 37.69 2.85
2863 8581 7.393841 ACTAAAGTAGTGATCTAAACGCTCT 57.606 36.000 0.00 0.00 37.69 4.09
2864 8582 9.733219 ATTACTAAAGTAGTGATCTAAACGCTC 57.267 33.333 0.00 0.00 39.81 5.03
2865 8583 9.733219 GATTACTAAAGTAGTGATCTAAACGCT 57.267 33.333 11.11 0.00 44.10 5.07
2866 8584 8.966194 GGATTACTAAAGTAGTGATCTAAACGC 58.034 37.037 15.64 0.72 45.72 4.84
2872 8590 7.491696 GCGTTTGGATTACTAAAGTAGTGATCT 59.508 37.037 15.64 0.00 45.72 2.75
2873 8591 7.491696 AGCGTTTGGATTACTAAAGTAGTGATC 59.508 37.037 10.27 10.27 45.72 2.92
2874 8592 7.328737 AGCGTTTGGATTACTAAAGTAGTGAT 58.671 34.615 0.00 0.00 39.81 3.06
2875 8593 6.694447 AGCGTTTGGATTACTAAAGTAGTGA 58.306 36.000 0.00 0.00 39.81 3.41
2876 8594 6.812160 AGAGCGTTTGGATTACTAAAGTAGTG 59.188 38.462 0.00 0.00 39.81 2.74
2877 8595 6.932947 AGAGCGTTTGGATTACTAAAGTAGT 58.067 36.000 0.00 0.00 42.68 2.73
2878 8596 7.829378 AAGAGCGTTTGGATTACTAAAGTAG 57.171 36.000 0.00 0.00 0.00 2.57
2890 8608 9.653287 CCATAATCTAATATAAGAGCGTTTGGA 57.347 33.333 0.00 0.00 0.00 3.53
2891 8609 9.653287 TCCATAATCTAATATAAGAGCGTTTGG 57.347 33.333 0.00 0.00 0.00 3.28
2893 8611 9.877178 CCTCCATAATCTAATATAAGAGCGTTT 57.123 33.333 0.00 0.00 0.00 3.60
2894 8612 8.478877 CCCTCCATAATCTAATATAAGAGCGTT 58.521 37.037 0.00 0.00 0.00 4.84
2895 8613 7.839705 TCCCTCCATAATCTAATATAAGAGCGT 59.160 37.037 0.00 0.00 0.00 5.07
2896 8614 8.239038 TCCCTCCATAATCTAATATAAGAGCG 57.761 38.462 0.00 0.00 0.00 5.03
2897 8615 9.207868 ACTCCCTCCATAATCTAATATAAGAGC 57.792 37.037 0.00 0.00 0.00 4.09
2908 8626 9.629878 CGTAGTAATATACTCCCTCCATAATCT 57.370 37.037 0.00 0.00 40.14 2.40
2909 8627 8.351461 GCGTAGTAATATACTCCCTCCATAATC 58.649 40.741 0.00 0.00 40.14 1.75
2910 8628 8.060075 AGCGTAGTAATATACTCCCTCCATAAT 58.940 37.037 0.00 0.00 40.14 1.28
2911 8629 7.338703 CAGCGTAGTAATATACTCCCTCCATAA 59.661 40.741 0.00 0.00 40.14 1.90
2912 8630 6.827251 CAGCGTAGTAATATACTCCCTCCATA 59.173 42.308 0.00 0.00 40.14 2.74
2913 8631 5.652891 CAGCGTAGTAATATACTCCCTCCAT 59.347 44.000 0.00 0.00 40.14 3.41
2914 8632 5.008331 CAGCGTAGTAATATACTCCCTCCA 58.992 45.833 0.00 0.00 40.14 3.86
2915 8633 4.142425 GCAGCGTAGTAATATACTCCCTCC 60.142 50.000 0.00 0.00 40.14 4.30
2916 8634 4.984205 GCAGCGTAGTAATATACTCCCTC 58.016 47.826 0.00 0.00 40.14 4.30


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

AutoCloner maintained by Alex Coulton.