Multiple sequence alignment - TraesCS3B01G599800

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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 TraesCS3B01G599800 chr3B 100.000 5527 0 0 1 5527 820671721 820677247 0.000000e+00 10207
1 TraesCS3B01G599800 chr3B 94.696 2451 101 7 1056 3482 820791998 820794443 0.000000e+00 3779
2 TraesCS3B01G599800 chr3B 95.575 2034 69 4 1425 3438 820502726 820504758 0.000000e+00 3238
3 TraesCS3B01G599800 chr3B 89.401 1670 128 27 3867 5503 820598189 820599842 0.000000e+00 2058
4 TraesCS3B01G599800 chr3B 91.232 1437 94 15 3867 5290 820760656 820762073 0.000000e+00 1927
5 TraesCS3B01G599800 chr3B 88.820 1449 129 8 3867 5292 820794923 820796361 0.000000e+00 1748
6 TraesCS3B01G599800 chr3B 92.363 969 61 4 4562 5524 820505980 820506941 0.000000e+00 1367
7 TraesCS3B01G599800 chr3B 87.692 1040 79 16 4468 5472 820717877 820718902 0.000000e+00 1166
8 TraesCS3B01G599800 chr3B 89.551 890 65 16 4653 5524 820772041 820772920 0.000000e+00 1103
9 TraesCS3B01G599800 chr3B 94.290 683 27 3 2746 3418 820716308 820716988 0.000000e+00 1035
10 TraesCS3B01G599800 chr3B 90.087 686 31 4 3221 3870 820597471 820598155 0.000000e+00 856
11 TraesCS3B01G599800 chr3B 88.089 722 75 7 4817 5527 820554512 820555233 0.000000e+00 846
12 TraesCS3B01G599800 chr3B 96.226 477 18 0 2746 3222 820596913 820597389 0.000000e+00 782
13 TraesCS3B01G599800 chr3B 90.164 549 39 9 3867 4400 820505355 820505903 0.000000e+00 701
14 TraesCS3B01G599800 chr3B 92.506 387 28 1 3949 4335 820717440 820717825 2.250000e-153 553
15 TraesCS3B01G599800 chr3B 87.696 447 55 0 4838 5284 820774027 820774473 6.340000e-144 521
16 TraesCS3B01G599800 chr3B 82.561 453 66 11 5080 5527 820599386 820599830 2.410000e-103 387
17 TraesCS3B01G599800 chr3B 91.197 284 21 2 3590 3872 820794612 820794892 3.120000e-102 383
18 TraesCS3B01G599800 chr3B 88.189 254 22 4 3492 3745 820760125 820760370 4.190000e-76 296
19 TraesCS3B01G599800 chr3B 86.691 278 14 7 1060 1336 826096584 826096839 2.520000e-73 287
20 TraesCS3B01G599800 chr3B 89.151 212 17 3 4494 4705 820554189 820554394 5.490000e-65 259
21 TraesCS3B01G599800 chr3B 88.942 208 22 1 3570 3777 820717083 820717289 7.110000e-64 255
22 TraesCS3B01G599800 chr3B 78.426 394 78 5 5080 5472 820506464 820506851 3.310000e-62 250
23 TraesCS3B01G599800 chr3B 91.765 170 12 1 3489 3656 820505019 820505188 9.260000e-58 235
24 TraesCS3B01G599800 chr3B 92.908 141 6 2 3733 3872 820760489 820760626 9.390000e-48 202
25 TraesCS3B01G599800 chr3B 94.118 119 6 1 3364 3482 820504758 820504875 4.400000e-41 180
26 TraesCS3B01G599800 chr3B 94.545 110 6 0 4510 4619 820771935 820772044 2.650000e-38 171
27 TraesCS3B01G599800 chr3B 92.233 103 7 1 4225 4327 820553967 820554068 1.600000e-30 145
28 TraesCS3B01G599800 chr3B 85.841 113 16 0 20 132 780676890 780677002 2.700000e-23 121
29 TraesCS3B01G599800 chr3D 94.634 2143 89 5 1358 3482 609623921 609626055 0.000000e+00 3297
30 TraesCS3B01G599800 chr3D 90.914 1684 109 20 3875 5527 609626353 609628023 0.000000e+00 2222
31 TraesCS3B01G599800 chr3D 89.789 284 16 6 1056 1336 612887223 612886950 8.810000e-93 351
32 TraesCS3B01G599800 chr3D 89.503 181 15 2 3519 3695 609626056 609626236 5.570000e-55 226
33 TraesCS3B01G599800 chr3D 95.181 83 4 0 3788 3870 609626236 609626318 1.250000e-26 132
34 TraesCS3B01G599800 chr3A 95.056 1881 71 9 1358 3221 743189671 743191546 0.000000e+00 2939
35 TraesCS3B01G599800 chr3A 85.163 1530 149 24 3872 5366 743192391 743193877 0.000000e+00 1496
36 TraesCS3B01G599800 chr3A 84.311 682 60 15 3221 3864 743191588 743192260 1.690000e-174 623
37 TraesCS3B01G599800 chr3A 90.391 281 15 8 1060 1336 747613293 747613021 5.260000e-95 359
38 TraesCS3B01G599800 chr1D 97.264 1060 28 1 1 1060 372412953 372414011 0.000000e+00 1796
39 TraesCS3B01G599800 chr1D 89.598 423 41 2 402 821 23638988 23639410 8.150000e-148 534
40 TraesCS3B01G599800 chr1D 90.476 126 12 0 2658 2783 453118382 453118257 3.420000e-37 167
41 TraesCS3B01G599800 chr1D 85.161 155 15 6 2914 3061 372871710 372871863 9.590000e-33 152
42 TraesCS3B01G599800 chr7D 96.990 1063 32 0 1 1063 51733692 51734754 0.000000e+00 1786
43 TraesCS3B01G599800 chr7D 91.353 717 45 8 348 1062 459922214 459922915 0.000000e+00 965
44 TraesCS3B01G599800 chr7D 91.857 307 23 2 1 307 459921905 459922209 1.420000e-115 427
45 TraesCS3B01G599800 chr7B 92.279 531 35 3 489 1017 159523568 159524094 0.000000e+00 749
46 TraesCS3B01G599800 chr7B 90.796 402 32 4 402 800 25425500 25425899 2.930000e-147 532
47 TraesCS3B01G599800 chr5B 92.162 421 28 4 405 821 480247918 480247499 1.710000e-164 590
48 TraesCS3B01G599800 chr4B 91.962 423 30 3 402 821 667983605 667983184 1.710000e-164 590
49 TraesCS3B01G599800 chr4B 86.726 113 15 0 20 132 373533014 373533126 5.810000e-25 126
50 TraesCS3B01G599800 chr4B 85.841 113 16 0 20 132 373534465 373534353 2.700000e-23 121
51 TraesCS3B01G599800 chr4D 91.443 409 31 3 402 806 456677482 456677074 4.840000e-155 558
52 TraesCS3B01G599800 chr4A 90.244 410 34 5 402 806 68454877 68454469 1.050000e-146 531
53 TraesCS3B01G599800 chr4A 89.441 161 17 0 910 1070 68454456 68454296 2.610000e-48 204
54 TraesCS3B01G599800 chr4A 86.726 113 15 0 20 132 688703450 688703338 5.810000e-25 126
55 TraesCS3B01G599800 chr5A 82.310 407 66 4 3870 4274 626250385 626249983 1.140000e-91 348
56 TraesCS3B01G599800 chr5A 85.635 181 25 1 869 1049 568577578 568577757 7.310000e-44 189
57 TraesCS3B01G599800 chr5A 87.611 113 14 0 20 132 579206483 579206595 1.250000e-26 132
58 TraesCS3B01G599800 chr5A 85.841 113 16 0 20 132 580194574 580194462 2.700000e-23 121
59 TraesCS3B01G599800 chr5D 78.519 405 67 14 3861 4254 501062850 501063245 1.190000e-61 248
60 TraesCS3B01G599800 chr2B 89.610 154 15 1 910 1063 746373944 746373792 1.570000e-45 195
61 TraesCS3B01G599800 chr1B 87.898 157 19 0 2658 2814 623552531 623552375 9.450000e-43 185
62 TraesCS3B01G599800 chr6D 87.162 148 13 3 141 288 199584887 199585028 4.430000e-36 163


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 TraesCS3B01G599800 chr3B 820671721 820677247 5526 False 10207.000000 10207 100.000000 1 5527 1 chr3B.!!$F2 5526
1 TraesCS3B01G599800 chr3B 820791998 820796361 4363 False 1970.000000 3779 91.571000 1056 5292 3 chr3B.!!$F10 4236
2 TraesCS3B01G599800 chr3B 820596913 820599842 2929 False 1020.750000 2058 89.568750 2746 5527 4 chr3B.!!$F6 2781
3 TraesCS3B01G599800 chr3B 820502726 820506941 4215 False 995.166667 3238 90.401833 1425 5524 6 chr3B.!!$F4 4099
4 TraesCS3B01G599800 chr3B 820760125 820762073 1948 False 808.333333 1927 90.776333 3492 5290 3 chr3B.!!$F8 1798
5 TraesCS3B01G599800 chr3B 820716308 820718902 2594 False 752.250000 1166 90.857500 2746 5472 4 chr3B.!!$F7 2726
6 TraesCS3B01G599800 chr3B 820771935 820774473 2538 False 598.333333 1103 90.597333 4510 5524 3 chr3B.!!$F9 1014
7 TraesCS3B01G599800 chr3B 820553967 820555233 1266 False 416.666667 846 89.824333 4225 5527 3 chr3B.!!$F5 1302
8 TraesCS3B01G599800 chr3D 609623921 609628023 4102 False 1469.250000 3297 92.558000 1358 5527 4 chr3D.!!$F1 4169
9 TraesCS3B01G599800 chr3A 743189671 743193877 4206 False 1686.000000 2939 88.176667 1358 5366 3 chr3A.!!$F1 4008
10 TraesCS3B01G599800 chr1D 372412953 372414011 1058 False 1796.000000 1796 97.264000 1 1060 1 chr1D.!!$F2 1059
11 TraesCS3B01G599800 chr7D 51733692 51734754 1062 False 1786.000000 1786 96.990000 1 1063 1 chr7D.!!$F1 1062
12 TraesCS3B01G599800 chr7D 459921905 459922915 1010 False 696.000000 965 91.605000 1 1062 2 chr7D.!!$F2 1061
13 TraesCS3B01G599800 chr7B 159523568 159524094 526 False 749.000000 749 92.279000 489 1017 1 chr7B.!!$F2 528
14 TraesCS3B01G599800 chr4A 68454296 68454877 581 True 367.500000 531 89.842500 402 1070 2 chr4A.!!$R2 668

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
57 58 1.024579 CCTGCGGTAGAATTGGCGTT 61.025 55.0 0.00 0.00 0.00 4.84 F
1182 1191 0.475906 AAGGCAGCTTCCTGTCACTT 59.524 50.0 5.40 0.00 46.14 3.16 F
2222 2253 0.249868 TGCACCACTTCCGAAGTCTG 60.250 55.0 10.98 10.23 40.46 3.51 F
3352 3471 0.446222 GCGACTGGCGAAAATGCTTA 59.554 50.0 7.31 0.00 44.57 3.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1488 1499 0.038166 ATACCACAGGTTGTGCAGGG 59.962 55.0 3.72 0.0 46.51 4.45 R
2254 2285 0.674895 CAGCTACACCTCTGGTTGGC 60.675 60.0 0.00 0.0 31.02 4.52 R
4016 4750 1.238439 CCGGCATATCCATTGACACC 58.762 55.0 0.00 0.0 34.01 4.16 R
5131 6079 0.036875 ACAAGTACTTGCCAGAGCCC 59.963 55.0 30.97 0.0 44.03 5.19 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
57 58 1.024579 CCTGCGGTAGAATTGGCGTT 61.025 55.000 0.00 0.00 0.00 4.84
133 134 2.764314 CGCGGCCATCAAAAGGAGG 61.764 63.158 2.24 0.00 0.00 4.30
179 180 2.202756 GGAGGTCGGCTAAGTGCG 60.203 66.667 0.00 0.00 44.05 5.34
203 205 1.582610 TTGTGGAAGGAATTCGCCGC 61.583 55.000 13.94 13.94 0.00 6.53
204 206 2.437716 TGGAAGGAATTCGCCGCC 60.438 61.111 0.00 0.00 0.00 6.13
374 376 1.070758 GAGATCTTAATCGGCTGGCCA 59.929 52.381 4.71 4.71 36.97 5.36
700 707 6.811665 CAGGACAGACGTCACTGATATTTTTA 59.188 38.462 19.50 0.00 44.54 1.52
704 711 6.037172 ACAGACGTCACTGATATTTTTATGGC 59.963 38.462 19.50 0.00 40.63 4.40
723 730 1.202132 GCCATTTTTAGCGTCGCATCA 60.202 47.619 21.09 0.52 0.00 3.07
782 789 7.011482 CCAAGTTATCTGTTGTATGCCTAACTC 59.989 40.741 0.00 0.00 30.06 3.01
859 868 6.129874 GGGAAGGGTTAGCTTTTATGATCTT 58.870 40.000 0.00 0.00 0.00 2.40
861 870 7.778382 GGGAAGGGTTAGCTTTTATGATCTTAA 59.222 37.037 0.00 0.00 0.00 1.85
895 904 3.258372 ACTCGGTGATGCTACTCTTTTGA 59.742 43.478 0.00 0.00 0.00 2.69
1107 1116 5.433712 TGTACATTACCTTACCCCAATGGAT 59.566 40.000 0.00 0.00 38.00 3.41
1118 1127 5.206905 ACCCCAATGGATTTAAGCTAACT 57.793 39.130 0.00 0.00 38.00 2.24
1138 1147 0.884704 GGTTCCGCTTTGCTGACTGA 60.885 55.000 0.00 0.00 0.00 3.41
1154 1163 1.339727 ACTGATAACGGAGGGCCAAAC 60.340 52.381 6.18 0.00 0.00 2.93
1182 1191 0.475906 AAGGCAGCTTCCTGTCACTT 59.524 50.000 5.40 0.00 46.14 3.16
1185 1194 1.597742 GCAGCTTCCTGTCACTTCAA 58.402 50.000 0.00 0.00 41.26 2.69
1211 1220 1.744522 TGGTACAGCTATTCGTGCGTA 59.255 47.619 0.00 0.00 35.28 4.42
1212 1221 2.223409 TGGTACAGCTATTCGTGCGTAG 60.223 50.000 0.00 0.00 35.28 3.51
1213 1222 2.223433 GGTACAGCTATTCGTGCGTAGT 60.223 50.000 0.00 0.00 35.28 2.73
1235 1244 3.132289 TGGTCCGACAGAATAGGATTGTC 59.868 47.826 0.00 0.00 38.23 3.18
1435 1444 2.223572 GCTCTTGTTTCTGTGTTGGTGG 60.224 50.000 0.00 0.00 0.00 4.61
1493 1506 7.603180 AATTTATTTTATCCTTCTCCCCTGC 57.397 36.000 0.00 0.00 0.00 4.85
1686 1700 2.808543 GGATACAATTAAGGAGCCTGCG 59.191 50.000 0.00 0.00 0.00 5.18
2219 2250 2.423577 GTTATGCACCACTTCCGAAGT 58.576 47.619 8.03 8.03 44.06 3.01
2222 2253 0.249868 TGCACCACTTCCGAAGTCTG 60.250 55.000 10.98 10.23 40.46 3.51
2285 2316 2.093658 GGTGTAGCTGATTCCTCCGAAA 60.094 50.000 0.00 0.00 0.00 3.46
2286 2317 3.432326 GGTGTAGCTGATTCCTCCGAAAT 60.432 47.826 0.00 0.00 0.00 2.17
2585 2619 1.808945 CTGCACCACTTGTTCAGGATC 59.191 52.381 0.00 0.00 34.95 3.36
2625 2659 3.634910 GCAAGGGTTTCTTTTACCACTCA 59.365 43.478 0.00 0.00 37.40 3.41
3032 3068 5.296151 TCTTCAGGTTCACTTTCATCACT 57.704 39.130 0.00 0.00 0.00 3.41
3103 3139 1.068541 GCAAAACTTCACCCGGACATC 60.069 52.381 0.73 0.00 0.00 3.06
3213 3249 6.436847 AGAAGGTAACCAGACTCTTAACCTAC 59.563 42.308 0.00 0.00 37.17 3.18
3273 3392 8.607459 CAAATTAGGAACTGATCTGACACATAC 58.393 37.037 6.60 0.00 41.52 2.39
3352 3471 0.446222 GCGACTGGCGAAAATGCTTA 59.554 50.000 7.31 0.00 44.57 3.09
3568 3912 3.941483 TGCATAGAAAGGAGTAAGCAAGC 59.059 43.478 0.00 0.00 0.00 4.01
3731 4301 6.839124 TCAGACATTTAAAGGCACATGATT 57.161 33.333 0.00 0.00 0.00 2.57
3917 4624 7.039223 ACCTTCAAAGATCATCTTCAAAAGCAT 60.039 33.333 0.00 0.00 35.27 3.79
3925 4656 4.763279 TCATCTTCAAAAGCATGAGCAGAA 59.237 37.500 0.00 0.00 45.49 3.02
3932 4663 2.687700 AGCATGAGCAGAACGAAGAT 57.312 45.000 0.00 0.00 45.49 2.40
4016 4750 1.274167 AGCAATGCCAATGTTCACCTG 59.726 47.619 0.00 0.00 0.00 4.00
4052 4786 0.803768 CGGTGACCTTCAGCATCGAG 60.804 60.000 0.00 0.00 44.51 4.04
4221 4955 2.729194 AGCTCCTGAACAGAGTCGTAT 58.271 47.619 3.19 0.00 0.00 3.06
4280 5015 4.620982 AGTTTGGTTCAAATGCTACTTGC 58.379 39.130 0.00 0.00 35.74 4.01
4361 5112 9.408648 ACATCTTTTTACCACCTTATATTCCTG 57.591 33.333 0.00 0.00 0.00 3.86
4368 5119 6.636454 ACCACCTTATATTCCTGTTCTCAA 57.364 37.500 0.00 0.00 0.00 3.02
4371 5122 6.016777 CCACCTTATATTCCTGTTCTCAATGC 60.017 42.308 0.00 0.00 0.00 3.56
4696 5470 7.964604 TCCAAGAAACTAGTAAAGAGAAAGC 57.035 36.000 0.00 0.00 0.00 3.51
4771 5623 4.502604 GCTAACGATATAGGCCTCACCAAA 60.503 45.833 9.68 0.00 43.14 3.28
4803 5655 3.264845 GCCTCCCCAACCCCAAGA 61.265 66.667 0.00 0.00 0.00 3.02
4809 5661 1.234529 CCCAACCCCAAGAAACCCA 59.765 57.895 0.00 0.00 0.00 4.51
5058 6003 2.107552 TGGTGGGTTCCTCTTTGGTAAG 59.892 50.000 0.00 0.00 37.07 2.34
5059 6004 2.554564 GGTGGGTTCCTCTTTGGTAAGG 60.555 54.545 0.00 0.00 37.07 2.69
5060 6005 2.374170 GTGGGTTCCTCTTTGGTAAGGA 59.626 50.000 0.00 0.00 39.94 3.36
5061 6006 3.010250 GTGGGTTCCTCTTTGGTAAGGAT 59.990 47.826 0.00 0.00 41.26 3.24
5062 6007 3.010138 TGGGTTCCTCTTTGGTAAGGATG 59.990 47.826 0.00 0.00 41.26 3.51
5063 6008 3.010250 GGGTTCCTCTTTGGTAAGGATGT 59.990 47.826 0.00 0.00 41.26 3.06
5064 6009 4.262617 GGTTCCTCTTTGGTAAGGATGTC 58.737 47.826 0.00 0.00 41.26 3.06
5065 6010 4.262617 GTTCCTCTTTGGTAAGGATGTCC 58.737 47.826 0.00 0.00 41.26 4.02
5066 6011 3.526899 TCCTCTTTGGTAAGGATGTCCA 58.473 45.455 1.30 0.00 36.75 4.02
5067 6012 3.913799 TCCTCTTTGGTAAGGATGTCCAA 59.086 43.478 1.30 0.00 36.75 3.53
5068 6013 4.010349 CCTCTTTGGTAAGGATGTCCAAC 58.990 47.826 1.30 0.00 40.32 3.77
5069 6014 4.263506 CCTCTTTGGTAAGGATGTCCAACT 60.264 45.833 1.30 0.00 40.32 3.16
5070 6015 4.906618 TCTTTGGTAAGGATGTCCAACTC 58.093 43.478 1.30 0.00 40.32 3.01
5071 6016 4.597507 TCTTTGGTAAGGATGTCCAACTCT 59.402 41.667 1.30 0.00 40.32 3.24
5072 6017 3.981071 TGGTAAGGATGTCCAACTCTG 57.019 47.619 1.30 0.00 38.89 3.35
5073 6018 2.571653 TGGTAAGGATGTCCAACTCTGG 59.428 50.000 1.30 0.00 45.08 3.86
5074 6019 2.633488 GTAAGGATGTCCAACTCTGGC 58.367 52.381 1.30 0.00 43.17 4.85
5075 6020 1.067295 AAGGATGTCCAACTCTGGCA 58.933 50.000 1.30 0.00 43.17 4.92
5076 6021 1.067295 AGGATGTCCAACTCTGGCAA 58.933 50.000 1.30 0.00 43.17 4.52
5077 6022 1.004044 AGGATGTCCAACTCTGGCAAG 59.996 52.381 1.30 0.00 43.17 4.01
5078 6023 1.271597 GGATGTCCAACTCTGGCAAGT 60.272 52.381 0.00 0.00 43.17 3.16
5079 6024 2.508526 GATGTCCAACTCTGGCAAGTT 58.491 47.619 8.59 8.59 43.17 2.66
5080 6025 1.967319 TGTCCAACTCTGGCAAGTTC 58.033 50.000 10.70 3.71 43.17 3.01
5081 6026 1.490490 TGTCCAACTCTGGCAAGTTCT 59.510 47.619 10.70 0.00 43.17 3.01
5082 6027 2.092429 TGTCCAACTCTGGCAAGTTCTT 60.092 45.455 10.70 0.00 43.17 2.52
5083 6028 2.952310 GTCCAACTCTGGCAAGTTCTTT 59.048 45.455 10.70 0.00 43.17 2.52
5084 6029 2.951642 TCCAACTCTGGCAAGTTCTTTG 59.048 45.455 10.70 3.46 43.17 2.77
5085 6030 2.689983 CCAACTCTGGCAAGTTCTTTGT 59.310 45.455 10.70 0.00 37.38 2.83
5086 6031 3.882888 CCAACTCTGGCAAGTTCTTTGTA 59.117 43.478 10.70 0.00 37.38 2.41
5087 6032 4.338118 CCAACTCTGGCAAGTTCTTTGTAA 59.662 41.667 10.70 0.00 37.38 2.41
5111 6059 3.196040 TCCAATGGAGATGGCAAGC 57.804 52.632 0.00 0.00 37.88 4.01
5145 6093 4.451150 CGCGGGCTCTGGCAAGTA 62.451 66.667 0.00 0.00 40.87 2.24
5298 6315 5.238583 GTTGTTGGTTAGCATCTCTAGTGT 58.761 41.667 0.00 0.00 0.00 3.55
5317 6433 0.105760 TCCATGGCAGGTTGTTGGTT 60.106 50.000 6.96 0.00 0.00 3.67
5327 6443 2.375174 AGGTTGTTGGTTAGCATCTCCA 59.625 45.455 0.00 0.00 0.00 3.86
5333 6449 0.464554 GGTTAGCATCTCCAGTGGCC 60.465 60.000 3.51 0.00 0.00 5.36
5337 6453 1.826921 GCATCTCCAGTGGCCATGG 60.827 63.158 21.71 21.71 39.33 3.66
5340 6456 2.280404 ATCTCCAGTGGCCATGGCAG 62.280 60.000 36.56 23.92 44.11 4.85
5351 6467 0.758123 CCATGGCAGGTTGTTGGTTT 59.242 50.000 0.00 0.00 0.00 3.27
5436 6555 1.817087 ATCATCTCCCATGGCTCTGT 58.183 50.000 6.09 0.00 0.00 3.41
5442 6561 0.904865 TCCCATGGCTCTGTCTCGTT 60.905 55.000 6.09 0.00 0.00 3.85
5454 6609 1.079503 GTCTCGTTCTCCATGGCAAC 58.920 55.000 6.96 11.34 0.00 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
57 58 3.072468 CCGTCTTGCCGGTCCCTA 61.072 66.667 1.90 0.00 43.07 3.53
133 134 4.389576 CCTCAAACTGCCGCACGC 62.390 66.667 0.00 0.00 38.31 5.34
179 180 1.200020 CGAATTCCTTCCACAACAGCC 59.800 52.381 0.00 0.00 0.00 4.85
307 309 2.366533 TCTACAAAAACACACCGGCAA 58.633 42.857 0.00 0.00 0.00 4.52
374 376 1.392710 CCTGTATCCCGCGACTCCTT 61.393 60.000 8.23 0.00 0.00 3.36
700 707 0.100503 GCGACGCTAAAAATGGCCAT 59.899 50.000 14.09 14.09 0.00 4.40
704 711 2.159585 TGTGATGCGACGCTAAAAATGG 60.160 45.455 22.08 0.00 0.00 3.16
723 730 2.498481 CCATGAGTGCCATTCCATTTGT 59.502 45.455 0.00 0.00 31.94 2.83
782 789 4.265073 AGCCAATAGAACTACAAAGCCAG 58.735 43.478 0.00 0.00 0.00 4.85
824 831 1.305549 CCCTTCCCAAGCAAGGCAT 60.306 57.895 0.00 0.00 39.43 4.40
859 868 3.096541 CGAGTTCAACGCGGTCTTA 57.903 52.632 12.47 0.00 37.75 2.10
895 904 6.071278 GGTAGGAAGAAACACTCACTCTGTAT 60.071 42.308 0.00 0.00 0.00 2.29
1107 1116 3.412237 AGCGGAACCAGTTAGCTTAAA 57.588 42.857 0.00 0.00 34.49 1.52
1118 1127 1.148273 AGTCAGCAAAGCGGAACCA 59.852 52.632 0.00 0.00 34.22 3.67
1138 1147 1.684869 CCATGTTTGGCCCTCCGTTAT 60.685 52.381 0.00 0.00 35.85 1.89
1154 1163 1.030457 GAAGCTGCCTTCCATCCATG 58.970 55.000 0.00 0.00 41.30 3.66
1174 1183 5.056480 TGTACCATGTCTTTGAAGTGACAG 58.944 41.667 8.54 0.91 44.85 3.51
1182 1191 5.109210 CGAATAGCTGTACCATGTCTTTGA 58.891 41.667 0.00 0.00 0.00 2.69
1185 1194 4.433615 CACGAATAGCTGTACCATGTCTT 58.566 43.478 0.00 0.00 0.00 3.01
1211 1220 2.526888 TCCTATTCTGTCGGACCACT 57.473 50.000 5.55 0.00 0.00 4.00
1212 1221 3.118738 ACAATCCTATTCTGTCGGACCAC 60.119 47.826 5.55 0.00 0.00 4.16
1213 1222 3.104512 ACAATCCTATTCTGTCGGACCA 58.895 45.455 5.55 0.00 0.00 4.02
1435 1444 5.367945 TCACCATTCACTAGGGGAAATAC 57.632 43.478 0.00 0.00 33.51 1.89
1474 1483 3.269381 TGTGCAGGGGAGAAGGATAAAAT 59.731 43.478 0.00 0.00 0.00 1.82
1488 1499 0.038166 ATACCACAGGTTGTGCAGGG 59.962 55.000 3.72 0.00 46.51 4.45
1628 1642 3.493699 CCGGATAATCACCTTAGGCGAAA 60.494 47.826 0.00 0.00 0.00 3.46
1632 1646 3.139077 CAACCGGATAATCACCTTAGGC 58.861 50.000 9.46 0.00 0.00 3.93
1686 1700 4.016444 TCCAAATAATCAAGGACTGTGCC 58.984 43.478 0.00 0.00 0.00 5.01
1691 1705 8.917088 CACCAAATATCCAAATAATCAAGGACT 58.083 33.333 0.00 0.00 32.04 3.85
1928 1942 9.778741 TTTTGAATTCTTCTAGCTGTTCTTCTA 57.221 29.630 7.05 0.00 0.00 2.10
2254 2285 0.674895 CAGCTACACCTCTGGTTGGC 60.675 60.000 0.00 0.00 31.02 4.52
2285 2316 6.703607 CCAGATTCAGCGTCAGAATTAGTAAT 59.296 38.462 0.00 0.00 35.93 1.89
2286 2317 6.042777 CCAGATTCAGCGTCAGAATTAGTAA 58.957 40.000 0.00 0.00 35.93 2.24
2585 2619 1.290203 GCACATGATGTCTGTACCGG 58.710 55.000 0.00 0.00 0.00 5.28
2625 2659 7.428826 CAATTTAGGTTTTCTCTCAAAGCTGT 58.571 34.615 7.89 0.00 42.92 4.40
3032 3068 4.287067 AGACAACTTCAAGGGCAAGAGATA 59.713 41.667 0.00 0.00 0.00 1.98
3085 3121 1.519408 CGATGTCCGGGTGAAGTTTT 58.481 50.000 0.00 0.00 33.91 2.43
3103 3139 4.032104 GGTAGTGGTCGTACAAAATAAGCG 59.968 45.833 0.00 0.00 0.00 4.68
3213 3249 9.431887 TGCATGAAACTAAGTAACTAGTAAAGG 57.568 33.333 0.00 0.00 31.72 3.11
3387 3516 3.539604 CAAGAGCAACCTCCTATTCCTG 58.460 50.000 0.00 0.00 38.96 3.86
3393 3595 1.279271 GGAAGCAAGAGCAACCTCCTA 59.721 52.381 0.00 0.00 45.49 2.94
3506 3845 9.528018 TCATCACAAAGACATTCCTTTTTAAAC 57.472 29.630 0.00 0.00 34.41 2.01
3515 3854 7.327761 CAGTTGAAATCATCACAAAGACATTCC 59.672 37.037 0.00 0.00 37.92 3.01
3917 4624 4.941873 TCTGTACTATCTTCGTTCTGCTCA 59.058 41.667 0.00 0.00 0.00 4.26
3925 4656 4.521639 TGTTGTGGTCTGTACTATCTTCGT 59.478 41.667 0.00 0.00 0.00 3.85
3932 4663 2.294233 GTCGGTGTTGTGGTCTGTACTA 59.706 50.000 0.00 0.00 0.00 1.82
4016 4750 1.238439 CCGGCATATCCATTGACACC 58.762 55.000 0.00 0.00 34.01 4.16
4061 4795 2.282391 AATCGCCAGCACAAGCCA 60.282 55.556 0.00 0.00 43.56 4.75
4085 4819 1.839424 TCGAAGTGCTCAGGATCTCA 58.161 50.000 0.00 0.00 0.00 3.27
4202 4936 2.539953 CGATACGACTCTGTTCAGGAGC 60.540 54.545 0.00 0.00 34.46 4.70
4221 4955 1.964223 GCCCCTTCACTCTATGATCGA 59.036 52.381 0.00 0.00 37.11 3.59
4280 5015 7.764695 TGTACAATGATTTACAGTATCCACG 57.235 36.000 0.00 0.00 0.00 4.94
4318 5053 5.360649 AGATGTTTACTCTAAAGCCCTCC 57.639 43.478 0.00 0.00 0.00 4.30
4563 5326 9.708222 GATTTATCAACTGTACAATGTCATCAC 57.292 33.333 0.00 0.00 0.00 3.06
4711 5563 9.218440 CCTGGTTTTTGACATGCTTATTTTTAT 57.782 29.630 0.00 0.00 0.00 1.40
4712 5564 8.207545 ACCTGGTTTTTGACATGCTTATTTTTA 58.792 29.630 0.00 0.00 0.00 1.52
4713 5565 7.053498 ACCTGGTTTTTGACATGCTTATTTTT 58.947 30.769 0.00 0.00 0.00 1.94
4714 5566 6.591001 ACCTGGTTTTTGACATGCTTATTTT 58.409 32.000 0.00 0.00 0.00 1.82
4967 5822 2.421739 CCCTAACGCGGAGATGGG 59.578 66.667 12.47 10.75 0.00 4.00
5060 6005 9.962289 TACAAAGAACTTGCCAGAGTTGGACAT 62.962 40.741 0.00 0.00 46.80 3.06
5061 6006 8.761258 TACAAAGAACTTGCCAGAGTTGGACA 62.761 42.308 0.00 0.00 46.80 4.02
5062 6007 5.699932 ACAAAGAACTTGCCAGAGTTGGAC 61.700 45.833 0.00 0.00 46.80 4.02
5063 6008 3.624707 ACAAAGAACTTGCCAGAGTTGGA 60.625 43.478 0.00 0.00 46.80 3.53
5065 6010 5.499139 TTACAAAGAACTTGCCAGAGTTG 57.501 39.130 2.43 0.00 39.84 3.16
5066 6011 4.580580 CCTTACAAAGAACTTGCCAGAGTT 59.419 41.667 0.00 0.00 42.31 3.01
5067 6012 4.137543 CCTTACAAAGAACTTGCCAGAGT 58.862 43.478 0.00 0.00 38.75 3.24
5068 6013 4.389374 TCCTTACAAAGAACTTGCCAGAG 58.611 43.478 0.00 0.00 38.75 3.35
5069 6014 4.431416 TCCTTACAAAGAACTTGCCAGA 57.569 40.909 0.00 0.00 38.75 3.86
5070 6015 5.006386 AGATCCTTACAAAGAACTTGCCAG 58.994 41.667 0.00 0.00 38.75 4.85
5071 6016 4.985538 AGATCCTTACAAAGAACTTGCCA 58.014 39.130 0.00 0.00 38.75 4.92
5072 6017 4.396478 GGAGATCCTTACAAAGAACTTGCC 59.604 45.833 0.00 0.00 38.75 4.52
5073 6018 5.003804 TGGAGATCCTTACAAAGAACTTGC 58.996 41.667 0.00 0.00 36.25 4.01
5074 6019 7.362401 CCATTGGAGATCCTTACAAAGAACTTG 60.362 40.741 0.00 0.00 37.74 3.16
5075 6020 6.660949 CCATTGGAGATCCTTACAAAGAACTT 59.339 38.462 0.00 0.00 36.82 2.66
5076 6021 6.012508 TCCATTGGAGATCCTTACAAAGAACT 60.013 38.462 0.00 0.00 36.82 3.01
5077 6022 6.180472 TCCATTGGAGATCCTTACAAAGAAC 58.820 40.000 0.00 0.00 36.82 3.01
5078 6023 6.387192 TCCATTGGAGATCCTTACAAAGAA 57.613 37.500 0.00 0.00 36.82 2.52
5111 6059 3.715854 CGGAGACCGTTACCAAGAG 57.284 57.895 1.80 0.00 42.73 2.85
5131 6079 0.036875 ACAAGTACTTGCCAGAGCCC 59.963 55.000 30.97 0.00 44.03 5.19
5145 6093 3.157087 CCATTGCAGACCCTTAACAAGT 58.843 45.455 0.00 0.00 0.00 3.16
5174 6122 5.578727 CACTGGAGATGCTTACTAACAACTC 59.421 44.000 0.00 0.00 35.59 3.01
5298 6315 0.105760 AACCAACAACCTGCCATGGA 60.106 50.000 18.40 0.00 35.16 3.41
5317 6433 0.471191 CATGGCCACTGGAGATGCTA 59.529 55.000 8.16 0.00 0.00 3.49
5327 6443 2.283388 CAACCTGCCATGGCCACT 60.283 61.111 33.44 12.72 41.09 4.00
5333 6449 1.868469 CAAACCAACAACCTGCCATG 58.132 50.000 0.00 0.00 0.00 3.66
5337 6453 1.069049 AGATGCAAACCAACAACCTGC 59.931 47.619 0.00 0.00 0.00 4.85
5340 6456 1.686052 TGGAGATGCAAACCAACAACC 59.314 47.619 7.28 0.00 0.00 3.77
5351 6467 1.077285 CATGGCCACTGGAGATGCA 60.077 57.895 8.16 0.00 0.00 3.96
5436 6555 0.389817 CGTTGCCATGGAGAACGAGA 60.390 55.000 31.04 2.59 44.04 4.04
5442 6561 0.465705 GGAGATCGTTGCCATGGAGA 59.534 55.000 18.40 9.03 0.00 3.71
5454 6609 1.339610 GACCAGAGTCATGGGAGATCG 59.660 57.143 11.73 0.00 45.25 3.69


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

AutoCloner maintained by Alex Coulton.