Multiple sequence alignment - TraesCS4B01G010100

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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 TraesCS4B01G010100 chr4B 100.000 4877 0 0 2217 7093 6640758 6635882 0.000000e+00 9007.0
1 TraesCS4B01G010100 chr4B 93.699 2920 153 7 3891 6785 6538503 6535590 0.000000e+00 4344.0
2 TraesCS4B01G010100 chr4B 100.000 2017 0 0 1 2017 6642974 6640958 0.000000e+00 3725.0
3 TraesCS4B01G010100 chr4B 96.681 1898 41 6 136 2017 6542110 6540219 0.000000e+00 3136.0
4 TraesCS4B01G010100 chr4B 95.895 1681 61 7 2220 3898 6540202 6538528 0.000000e+00 2715.0
5 TraesCS4B01G010100 chr4B 92.857 308 21 1 6787 7093 6517158 6516851 5.050000e-121 446.0
6 TraesCS4B01G010100 chr4B 79.412 408 78 4 2420 2825 377950820 377950417 4.190000e-72 283.0
7 TraesCS4B01G010100 chr4B 78.261 207 36 6 4035 4232 64081139 64080933 2.690000e-24 124.0
8 TraesCS4B01G010100 chr4B 89.157 83 0 3 1 83 6542479 6542406 2.110000e-15 95.3
9 TraesCS4B01G010100 chr4A 94.835 1665 83 3 3851 5512 599491314 599489650 0.000000e+00 2595.0
10 TraesCS4B01G010100 chr4A 93.427 1643 63 14 2240 3853 599496991 599495365 0.000000e+00 2394.0
11 TraesCS4B01G010100 chr4A 90.097 1030 51 19 6092 7093 599483048 599482042 0.000000e+00 1290.0
12 TraesCS4B01G010100 chr4A 91.948 385 24 4 5725 6104 599487439 599487057 3.770000e-147 532.0
13 TraesCS4B01G010100 chr4A 94.077 287 10 2 1738 2017 599497467 599497181 5.080000e-116 429.0
14 TraesCS4B01G010100 chr4A 94.500 200 9 2 5510 5707 599487862 599487663 2.490000e-79 307.0
15 TraesCS4B01G010100 chr4A 100.000 29 0 0 5704 5732 599487677 599487649 4.000000e-03 54.7
16 TraesCS4B01G010100 chr5D 82.637 1244 192 21 4332 5564 446277959 446279189 0.000000e+00 1079.0
17 TraesCS4B01G010100 chr5D 79.459 740 100 27 3190 3895 446277212 446277933 1.790000e-130 477.0
18 TraesCS4B01G010100 chr5D 82.815 547 61 21 1123 1648 446275547 446276081 6.480000e-125 459.0
19 TraesCS4B01G010100 chr5D 77.947 526 96 14 2279 2796 51229486 51229999 1.920000e-80 311.0
20 TraesCS4B01G010100 chr5D 78.471 497 84 17 2279 2765 51305873 51306356 3.220000e-78 303.0
21 TraesCS4B01G010100 chr5D 81.293 294 36 12 2828 3105 446276801 446277091 3.330000e-53 220.0
22 TraesCS4B01G010100 chr7D 81.797 1291 180 46 4465 5732 32380033 32378775 0.000000e+00 1031.0
23 TraesCS4B01G010100 chr7D 79.820 555 96 13 2281 2825 98997898 98997350 2.400000e-104 390.0
24 TraesCS4B01G010100 chr7D 75.253 691 119 30 3179 3836 32380962 32380291 1.510000e-71 281.0
25 TraesCS4B01G010100 chr7D 86.916 214 24 3 2526 2738 80239576 80239786 3.310000e-58 237.0
26 TraesCS4B01G010100 chr5A 82.317 1148 168 28 4497 5629 563842153 563843280 0.000000e+00 963.0
27 TraesCS4B01G010100 chr5A 77.991 1095 150 52 627 1648 563839148 563840224 2.830000e-168 603.0
28 TraesCS4B01G010100 chr5A 81.505 319 50 8 5880 6190 563843309 563843626 3.280000e-63 254.0
29 TraesCS4B01G010100 chr7B 77.467 537 108 9 2286 2822 43245324 43245847 6.910000e-80 309.0
30 TraesCS4B01G010100 chr7B 87.324 213 24 2 2526 2738 27481334 27481543 2.560000e-59 241.0
31 TraesCS4B01G010100 chr4D 77.158 556 107 14 2280 2827 314659613 314659070 8.940000e-79 305.0
32 TraesCS4B01G010100 chrUn 82.682 179 27 3 4550 4726 89367061 89366885 9.530000e-34 156.0
33 TraesCS4B01G010100 chrUn 82.682 179 27 3 4550 4726 298794595 298794419 9.530000e-34 156.0
34 TraesCS4B01G010100 chr1D 74.608 319 73 7 2511 2827 381373109 381373421 4.460000e-27 134.0
35 TraesCS4B01G010100 chr6B 86.111 72 6 3 2276 2345 245724401 245724332 2.740000e-09 75.0


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 TraesCS4B01G010100 chr4B 6635882 6642974 7092 True 6366.000000 9007 100.000000 1 7093 2 chr4B.!!$R5 7092
1 TraesCS4B01G010100 chr4B 6535590 6542479 6889 True 2572.575000 4344 93.858000 1 6785 4 chr4B.!!$R4 6784
2 TraesCS4B01G010100 chr4A 599495365 599497467 2102 True 1411.500000 2394 93.752000 1738 3853 2 chr4A.!!$R3 2115
3 TraesCS4B01G010100 chr4A 599482042 599483048 1006 True 1290.000000 1290 90.097000 6092 7093 1 chr4A.!!$R1 1001
4 TraesCS4B01G010100 chr4A 599487057 599491314 4257 True 872.175000 2595 95.320750 3851 6104 4 chr4A.!!$R2 2253
5 TraesCS4B01G010100 chr5D 446275547 446279189 3642 False 558.750000 1079 81.551000 1123 5564 4 chr5D.!!$F3 4441
6 TraesCS4B01G010100 chr5D 51229486 51229999 513 False 311.000000 311 77.947000 2279 2796 1 chr5D.!!$F1 517
7 TraesCS4B01G010100 chr7D 32378775 32380962 2187 True 656.000000 1031 78.525000 3179 5732 2 chr7D.!!$R2 2553
8 TraesCS4B01G010100 chr7D 98997350 98997898 548 True 390.000000 390 79.820000 2281 2825 1 chr7D.!!$R1 544
9 TraesCS4B01G010100 chr5A 563839148 563843626 4478 False 606.666667 963 80.604333 627 6190 3 chr5A.!!$F1 5563
10 TraesCS4B01G010100 chr7B 43245324 43245847 523 False 309.000000 309 77.467000 2286 2822 1 chr7B.!!$F2 536
11 TraesCS4B01G010100 chr4D 314659070 314659613 543 True 305.000000 305 77.158000 2280 2827 1 chr4D.!!$R1 547

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
120 121 0.110010 CACGCACACACACACAAACA 60.110 50.000 0.00 0.00 0.00 2.83 F
121 122 0.593618 ACGCACACACACACAAACAA 59.406 45.000 0.00 0.00 0.00 2.83 F
226 470 0.739462 TGCGCCAGTCGGAATAGTTG 60.739 55.000 4.18 0.00 38.94 3.16 F
1322 1630 0.811219 GCGACATGCAGTGCTATGGA 60.811 55.000 22.84 3.93 45.45 3.41 F
1323 1631 0.933097 CGACATGCAGTGCTATGGAC 59.067 55.000 22.84 17.14 0.00 4.02 F
2488 3116 1.599542 GCGTGCTCTTTTGTCAGAAGT 59.400 47.619 3.25 0.00 0.00 3.01 F
2728 3356 1.891011 GCCCGGAATCTTGTTCCCTTT 60.891 52.381 0.73 0.00 35.17 3.11 F
4646 5657 0.966920 GGAGACCTTCCTGTCGTCAA 59.033 55.000 0.00 0.00 43.16 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1289 1597 1.878522 GTCGCTGCGGTGATCGATT 60.879 57.895 23.03 0.00 42.43 3.34 R
1305 1613 1.938577 CTGTCCATAGCACTGCATGTC 59.061 52.381 3.30 2.61 0.00 3.06 R
1857 2459 3.068165 TCTGTGTGTGTCTTGGTCAGTAG 59.932 47.826 0.00 0.00 0.00 2.57 R
2664 3292 0.323629 TCACCCTACGCCTTTGGAAG 59.676 55.000 0.00 0.00 0.00 3.46 R
2889 3754 0.466189 CCACAACCAGCTCAACCTGT 60.466 55.000 0.00 0.00 0.00 4.00 R
3986 4979 1.852157 ATTTCGGCCTCCTTGGAGCA 61.852 55.000 11.01 0.00 38.35 4.26 R
4668 5679 4.949856 GGAAATGGATCTTGGAAAGTGCTA 59.050 41.667 0.00 0.00 46.34 3.49 R
6328 9393 1.561542 AGGGTGCTTAATCCTCCTGTG 59.438 52.381 0.00 0.00 31.62 3.66 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
33 34 2.280865 GGCCTGGTATGCGGTAGC 60.281 66.667 0.00 0.00 45.41 3.58
43 44 2.877691 GCGGTAGCAGGGCAAAAG 59.122 61.111 0.00 0.00 44.35 2.27
84 85 9.826574 TTCATGTACATAGTAAGTTTATGACCC 57.173 33.333 8.32 0.00 33.68 4.46
85 86 8.426489 TCATGTACATAGTAAGTTTATGACCCC 58.574 37.037 8.32 0.00 33.68 4.95
86 87 7.128234 TGTACATAGTAAGTTTATGACCCCC 57.872 40.000 0.00 0.00 33.68 5.40
115 116 4.589700 CCGCACGCACACACACAC 62.590 66.667 0.00 0.00 0.00 3.82
116 117 3.858989 CGCACGCACACACACACA 61.859 61.111 0.00 0.00 0.00 3.72
117 118 2.482831 GCACGCACACACACACAA 59.517 55.556 0.00 0.00 0.00 3.33
118 119 1.154131 GCACGCACACACACACAAA 60.154 52.632 0.00 0.00 0.00 2.83
119 120 1.402479 GCACGCACACACACACAAAC 61.402 55.000 0.00 0.00 0.00 2.93
120 121 0.110010 CACGCACACACACACAAACA 60.110 50.000 0.00 0.00 0.00 2.83
121 122 0.593618 ACGCACACACACACAAACAA 59.406 45.000 0.00 0.00 0.00 2.83
122 123 1.201181 ACGCACACACACACAAACAAT 59.799 42.857 0.00 0.00 0.00 2.71
123 124 1.845568 CGCACACACACACAAACAATC 59.154 47.619 0.00 0.00 0.00 2.67
124 125 1.845568 GCACACACACACAAACAATCG 59.154 47.619 0.00 0.00 0.00 3.34
125 126 2.477021 GCACACACACACAAACAATCGA 60.477 45.455 0.00 0.00 0.00 3.59
126 127 3.752731 CACACACACACAAACAATCGAA 58.247 40.909 0.00 0.00 0.00 3.71
127 128 4.350346 CACACACACACAAACAATCGAAT 58.650 39.130 0.00 0.00 0.00 3.34
128 129 4.204775 CACACACACACAAACAATCGAATG 59.795 41.667 0.00 0.00 0.00 2.67
129 130 3.180189 CACACACACAAACAATCGAATGC 59.820 43.478 0.00 0.00 0.00 3.56
130 131 2.725723 CACACACAAACAATCGAATGCC 59.274 45.455 0.00 0.00 0.00 4.40
131 132 1.978097 CACACAAACAATCGAATGCCG 59.022 47.619 0.00 0.00 40.25 5.69
183 427 1.425066 TGCCACTGGAACAAAGAGGAT 59.575 47.619 0.00 0.00 38.70 3.24
224 468 1.141881 CTGCGCCAGTCGGAATAGT 59.858 57.895 4.18 0.00 38.28 2.12
226 470 0.739462 TGCGCCAGTCGGAATAGTTG 60.739 55.000 4.18 0.00 38.94 3.16
305 549 5.481105 TCCATCCATTGAAATGCAAACTTC 58.519 37.500 0.00 0.00 40.48 3.01
362 606 6.801539 TGATTTCAGCTGTACCTAAAGTTG 57.198 37.500 14.67 0.00 0.00 3.16
443 687 1.467035 GGGTATATACGGCTCTTCGCG 60.467 57.143 0.00 0.00 40.44 5.87
645 889 7.839680 TGTCTATCAAGCATCCATACTTAGA 57.160 36.000 0.00 0.00 0.00 2.10
654 898 5.426833 AGCATCCATACTTAGAGAAACCAGT 59.573 40.000 0.00 0.00 0.00 4.00
804 1048 4.832248 ACTTGTCTCTTGTCTGTTCACAA 58.168 39.130 0.00 0.00 34.99 3.33
863 1118 7.966812 ACTATAAGAGTATCAACCATGCATCA 58.033 34.615 0.00 0.00 36.27 3.07
970 1250 5.817988 TCTTCTACATATTCAGGTTCGTCG 58.182 41.667 0.00 0.00 0.00 5.12
985 1268 3.532892 TCGTCGCTCGATCCTTATTAC 57.467 47.619 0.00 0.00 44.01 1.89
1053 1345 1.550976 GGAAAGACCATCCTCGTCACT 59.449 52.381 0.00 0.00 38.79 3.41
1068 1360 2.024414 GTCACTGGCTCAACTGGTTTT 58.976 47.619 0.00 0.00 0.00 2.43
1087 1379 6.481644 TGGTTTTCTTGGAAAATGTATGCAAC 59.518 34.615 8.38 0.00 0.00 4.17
1275 1583 4.932146 ACACAGGTAAAGTTGAAATGTGC 58.068 39.130 10.00 0.00 40.05 4.57
1305 1613 1.136529 CAATAATCGATCACCGCAGCG 60.137 52.381 8.18 8.18 38.37 5.18
1321 1629 1.645455 GCGACATGCAGTGCTATGG 59.355 57.895 22.84 11.51 45.45 2.74
1322 1630 0.811219 GCGACATGCAGTGCTATGGA 60.811 55.000 22.84 3.93 45.45 3.41
1323 1631 0.933097 CGACATGCAGTGCTATGGAC 59.067 55.000 22.84 17.14 0.00 4.02
1324 1632 1.740043 CGACATGCAGTGCTATGGACA 60.740 52.381 22.84 2.64 0.00 4.02
1325 1633 1.938577 GACATGCAGTGCTATGGACAG 59.061 52.381 22.84 7.11 0.00 3.51
1757 2354 4.563061 TCGAAGTCTTACTAAGCAAACCC 58.437 43.478 0.00 0.00 0.00 4.11
2295 2908 7.725844 AGATACCCAGATTTTGTTTTCAAGACT 59.274 33.333 0.00 0.00 41.09 3.24
2488 3116 1.599542 GCGTGCTCTTTTGTCAGAAGT 59.400 47.619 3.25 0.00 0.00 3.01
2521 3149 3.347216 CTCTCGTTCCAAATGGTCCAAT 58.653 45.455 0.00 0.00 36.34 3.16
2664 3292 5.169295 AGATTAAGCCACTCGTTGACTAAC 58.831 41.667 0.00 0.00 0.00 2.34
2715 3343 1.901464 GAAAAGGTGCAGCCCGGAA 60.901 57.895 13.29 0.00 38.26 4.30
2728 3356 1.891011 GCCCGGAATCTTGTTCCCTTT 60.891 52.381 0.73 0.00 35.17 3.11
2729 3357 2.525368 CCCGGAATCTTGTTCCCTTTT 58.475 47.619 0.73 0.00 35.17 2.27
2770 3398 2.033448 GTTCGGCCACCCACATCA 59.967 61.111 2.24 0.00 0.00 3.07
2889 3754 7.118723 ACATGCTATCCCTGAAAAAGACATAA 58.881 34.615 0.00 0.00 0.00 1.90
2899 3764 6.072112 TGAAAAAGACATAACAGGTTGAGC 57.928 37.500 0.00 0.00 0.00 4.26
3068 3948 4.326826 TGCAAAGAAGTGTCCTAATCTGG 58.673 43.478 0.00 0.00 0.00 3.86
3097 3977 5.222079 TGCTTCATGTTTCTACTGGTACA 57.778 39.130 0.00 0.00 0.00 2.90
3173 4086 9.938280 ATATGTTTAGCCAACTATAATAGCGAA 57.062 29.630 0.00 0.00 36.21 4.70
3270 4185 2.961526 ATCACTACAGCCTGGTTACG 57.038 50.000 0.00 0.00 0.00 3.18
3339 4254 4.070009 TGAACTCACAGCGTCTAAGAGTA 58.930 43.478 11.07 0.18 38.51 2.59
3512 4429 7.872113 AGAGCTATCTTGGTAAAAGGAATTG 57.128 36.000 0.00 0.00 28.57 2.32
3563 4491 6.024552 ACATACCATTTTCACATGACCAAC 57.975 37.500 0.00 0.00 0.00 3.77
3778 4736 5.045066 ACCATTATAGATCATGGCTCATGCT 60.045 40.000 9.21 1.66 43.52 3.79
3986 4979 4.713792 AGTGAGGATTTTTGTCTCCTGT 57.286 40.909 0.00 0.00 42.02 4.00
4110 5103 7.063426 ACGTGTGTGTATAGTTTCATGATGAAG 59.937 37.037 8.01 0.00 37.70 3.02
4218 5212 7.541783 TGCAGCTCACATAAAAATGTATTTCAC 59.458 33.333 0.00 0.00 32.74 3.18
4247 5241 8.867097 TGAAACTTTACTGACAGTATAAGTCCT 58.133 33.333 26.08 20.61 34.30 3.85
4251 5245 9.531158 ACTTTACTGACAGTATAAGTCCTTACT 57.469 33.333 23.29 10.25 32.16 2.24
4283 5277 9.353999 GTGTAGGTTTTTCCATGATATTTTGAC 57.646 33.333 0.00 0.00 39.02 3.18
4333 5327 5.083122 TCAAAATCCAGGCTCCAATTTACA 58.917 37.500 0.00 0.00 0.00 2.41
4646 5657 0.966920 GGAGACCTTCCTGTCGTCAA 59.033 55.000 0.00 0.00 43.16 3.18
4668 5679 6.325545 TCAATATTCGACCTACCATGGTAACT 59.674 38.462 24.59 12.76 41.00 2.24
4853 5868 8.177119 ACTGAGTTTTGCTATAATTGTTTCCA 57.823 30.769 0.00 0.00 0.00 3.53
5069 6099 0.907704 AGGTTCCTGCGGACATGGTA 60.908 55.000 0.00 0.00 0.00 3.25
5144 6174 4.074259 TCATTTACAATGTGTGCTCAGCT 58.926 39.130 0.00 0.00 0.00 4.24
5291 6324 4.726021 GCTTTATTCCGCGCATATCTGATG 60.726 45.833 8.75 0.00 0.00 3.07
5328 6361 5.028549 ACCACTTGAGGTACATGATCATC 57.971 43.478 4.86 0.00 40.98 2.92
5335 6368 5.351458 TGAGGTACATGATCATCTGTTTCG 58.649 41.667 4.86 0.00 0.00 3.46
5366 6399 8.358895 TCATTTATACACATGCCAATATTGTGG 58.641 33.333 14.25 1.81 43.88 4.17
5469 6502 6.969828 TTTTGTGGGTTGTTTTCACAATAC 57.030 33.333 8.60 0.00 46.43 1.89
5474 6507 6.547880 TGTGGGTTGTTTTCACAATACTACAT 59.452 34.615 0.00 0.00 44.85 2.29
5558 8381 3.251484 TCTTCAAAGGATGGTGAGGTCT 58.749 45.455 0.00 0.00 0.00 3.85
5771 8824 6.742559 AAAAGTAGTATGGGGTCGTATCAT 57.257 37.500 0.00 0.00 0.00 2.45
5782 8835 3.753272 GGGTCGTATCATGCATTATGCTT 59.247 43.478 18.44 9.28 45.31 3.91
5793 8846 5.970317 TGCATTATGCTTATCCCTTCATG 57.030 39.130 18.44 0.00 45.31 3.07
5799 8852 4.853468 TGCTTATCCCTTCATGTGGTTA 57.147 40.909 0.00 0.00 0.00 2.85
5806 8859 3.139397 TCCCTTCATGTGGTTACCAACTT 59.861 43.478 5.33 0.00 34.18 2.66
5849 8902 4.576053 TCATGCACACATAAGATTAGTGGC 59.424 41.667 0.00 0.00 37.58 5.01
5876 8929 8.981647 GCGATTTCATTCCATTTATTTATTGCT 58.018 29.630 0.00 0.00 0.00 3.91
5933 8987 8.045507 TGTTCTTATCTCTGAAGCTTTGATGAT 58.954 33.333 0.00 5.88 0.00 2.45
5942 8996 6.256539 TCTGAAGCTTTGATGATACGAACATC 59.743 38.462 0.00 11.78 42.81 3.06
6086 9144 1.548719 GGCCGCAAAAATAAGGGAAGT 59.451 47.619 0.00 0.00 0.00 3.01
6094 9152 7.700656 CCGCAAAAATAAGGGAAGTGTATAAAG 59.299 37.037 0.00 0.00 0.00 1.85
6147 9212 3.567164 AGAACAAGCATCTTGTCCAACAG 59.433 43.478 11.99 0.00 0.00 3.16
6328 9393 7.378966 TGATCATAGATCCAACCGAAGAATAC 58.621 38.462 4.69 0.00 0.00 1.89
6400 9465 2.837532 GTTGCATCAACATTTGGGGT 57.162 45.000 4.95 0.00 43.09 4.95
6417 9482 8.536175 CATTTGGGGTGGTAAATAAAAGTATGT 58.464 33.333 0.00 0.00 0.00 2.29
6489 9554 2.729360 TGTTGTTCTTGACTACGATGCG 59.271 45.455 0.00 0.00 36.89 4.73
6498 9563 0.601558 ACTACGATGCGTCAACCACT 59.398 50.000 6.75 0.00 41.54 4.00
6533 9598 2.232941 TCGAAAATTCTACTCCAGCCGT 59.767 45.455 0.00 0.00 0.00 5.68
6600 9666 3.323691 AGTTTTCCCTTATGTTTGGTGGC 59.676 43.478 0.00 0.00 0.00 5.01
6662 9752 3.179830 GTCCATCACAGTCGTACATGTC 58.820 50.000 0.00 0.00 0.00 3.06
6705 9795 8.795786 TCAACATTCGTTTTAAAAGATTCCAG 57.204 30.769 0.00 0.00 31.13 3.86
6741 9831 4.389374 AGGTCTCACACACGAAATTGAAT 58.611 39.130 0.00 0.00 0.00 2.57
6750 9840 5.525745 ACACACGAAATTGAATAGACACACA 59.474 36.000 0.00 0.00 0.00 3.72
6751 9841 6.037720 ACACACGAAATTGAATAGACACACAA 59.962 34.615 0.00 0.00 0.00 3.33
6753 9843 7.430793 CACACGAAATTGAATAGACACACAAAA 59.569 33.333 0.00 0.00 0.00 2.44
6804 9894 5.377478 GCCAAGGTTACCTAAGCTGAATAT 58.623 41.667 15.67 0.00 42.60 1.28
6827 9917 5.988287 TGTGATACTGCCATTGTAGATCAA 58.012 37.500 0.00 0.00 40.53 2.57
6849 9939 7.282585 TCAAAGCTACTTGGCATCACTTATAT 58.717 34.615 0.00 0.00 34.17 0.86
6854 9944 7.012704 AGCTACTTGGCATCACTTATATGTTTG 59.987 37.037 0.00 0.00 34.17 2.93
6919 10009 6.027749 CGGCAGAACCTTGTGTAATAATTTC 58.972 40.000 0.00 0.00 35.61 2.17
6928 10018 7.094377 ACCTTGTGTAATAATTTCGCAAGTGAT 60.094 33.333 18.22 6.82 43.62 3.06
6935 10025 4.889832 AATTTCGCAAGTGATCTGATCC 57.110 40.909 14.71 6.61 39.48 3.36
6953 10043 2.229792 TCCTGTTGGACATCAGTTTGC 58.770 47.619 8.95 0.00 37.46 3.68
6954 10044 1.270550 CCTGTTGGACATCAGTTTGCC 59.729 52.381 8.95 0.00 34.57 4.52
6956 10046 0.240945 GTTGGACATCAGTTTGCCGG 59.759 55.000 0.00 0.00 0.00 6.13
6980 10070 7.148656 CGGGAAATTTGTGTCACCAATTTATTC 60.149 37.037 21.45 15.43 0.00 1.75
7062 10152 4.021016 ACTGAAGGAGTACAATGACTGACC 60.021 45.833 0.00 0.00 30.86 4.02
7073 10163 6.515272 ACAATGACTGACCCAAATAATGTC 57.485 37.500 0.00 0.00 0.00 3.06
7074 10164 6.009589 ACAATGACTGACCCAAATAATGTCA 58.990 36.000 0.00 0.00 37.45 3.58
7082 10172 7.926018 ACTGACCCAAATAATGTCAACTTTTTC 59.074 33.333 0.00 0.00 38.45 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 0.542702 ACACATCCCCTTTTGCCCTG 60.543 55.000 0.00 0.00 0.00 4.45
35 36 1.272480 ACTACACATCCCCTTTTGCCC 60.272 52.381 0.00 0.00 0.00 5.36
36 37 2.215942 ACTACACATCCCCTTTTGCC 57.784 50.000 0.00 0.00 0.00 4.52
37 38 5.417580 TGAAATACTACACATCCCCTTTTGC 59.582 40.000 0.00 0.00 0.00 3.68
38 39 7.122650 ACATGAAATACTACACATCCCCTTTTG 59.877 37.037 0.00 0.00 0.00 2.44
39 40 7.182060 ACATGAAATACTACACATCCCCTTTT 58.818 34.615 0.00 0.00 0.00 2.27
40 41 6.731467 ACATGAAATACTACACATCCCCTTT 58.269 36.000 0.00 0.00 0.00 3.11
41 42 6.327386 ACATGAAATACTACACATCCCCTT 57.673 37.500 0.00 0.00 0.00 3.95
42 43 5.975988 ACATGAAATACTACACATCCCCT 57.024 39.130 0.00 0.00 0.00 4.79
43 44 6.588204 TGTACATGAAATACTACACATCCCC 58.412 40.000 0.00 0.00 0.00 4.81
98 99 4.589700 GTGTGTGTGTGCGTGCGG 62.590 66.667 0.00 0.00 0.00 5.69
99 100 2.840955 TTTGTGTGTGTGTGCGTGCG 62.841 55.000 0.00 0.00 0.00 5.34
100 101 1.154131 TTTGTGTGTGTGTGCGTGC 60.154 52.632 0.00 0.00 0.00 5.34
101 102 0.110010 TGTTTGTGTGTGTGTGCGTG 60.110 50.000 0.00 0.00 0.00 5.34
102 103 0.593618 TTGTTTGTGTGTGTGTGCGT 59.406 45.000 0.00 0.00 0.00 5.24
103 104 1.845568 GATTGTTTGTGTGTGTGTGCG 59.154 47.619 0.00 0.00 0.00 5.34
104 105 1.845568 CGATTGTTTGTGTGTGTGTGC 59.154 47.619 0.00 0.00 0.00 4.57
105 106 3.397405 TCGATTGTTTGTGTGTGTGTG 57.603 42.857 0.00 0.00 0.00 3.82
106 107 4.350346 CATTCGATTGTTTGTGTGTGTGT 58.650 39.130 0.00 0.00 0.00 3.72
107 108 3.180189 GCATTCGATTGTTTGTGTGTGTG 59.820 43.478 8.93 0.00 0.00 3.82
108 109 3.371168 GCATTCGATTGTTTGTGTGTGT 58.629 40.909 8.93 0.00 0.00 3.72
109 110 2.725723 GGCATTCGATTGTTTGTGTGTG 59.274 45.455 8.93 0.00 0.00 3.82
110 111 2.604373 CGGCATTCGATTGTTTGTGTGT 60.604 45.455 8.93 0.00 42.43 3.72
111 112 1.978097 CGGCATTCGATTGTTTGTGTG 59.022 47.619 8.93 0.00 42.43 3.82
112 113 1.876799 TCGGCATTCGATTGTTTGTGT 59.123 42.857 8.93 0.00 43.74 3.72
113 114 2.610219 TCGGCATTCGATTGTTTGTG 57.390 45.000 8.93 0.00 43.74 3.33
123 124 0.933097 CTGGTTGAGATCGGCATTCG 59.067 55.000 0.00 0.00 40.90 3.34
124 125 0.659957 GCTGGTTGAGATCGGCATTC 59.340 55.000 0.00 0.00 35.49 2.67
125 126 1.091771 CGCTGGTTGAGATCGGCATT 61.092 55.000 0.00 0.00 35.14 3.56
126 127 1.522355 CGCTGGTTGAGATCGGCAT 60.522 57.895 0.00 0.00 35.14 4.40
127 128 2.125552 CGCTGGTTGAGATCGGCA 60.126 61.111 0.00 0.00 35.14 5.69
128 129 2.167861 GTCGCTGGTTGAGATCGGC 61.168 63.158 0.00 0.00 0.00 5.54
129 130 1.874019 CGTCGCTGGTTGAGATCGG 60.874 63.158 0.00 0.00 0.00 4.18
130 131 0.456142 TTCGTCGCTGGTTGAGATCG 60.456 55.000 0.00 0.00 0.00 3.69
131 132 0.992802 GTTCGTCGCTGGTTGAGATC 59.007 55.000 0.00 0.00 0.00 2.75
132 133 0.603569 AGTTCGTCGCTGGTTGAGAT 59.396 50.000 0.00 0.00 0.00 2.75
133 134 1.068748 GTAGTTCGTCGCTGGTTGAGA 60.069 52.381 0.00 0.00 0.00 3.27
134 135 1.337821 GTAGTTCGTCGCTGGTTGAG 58.662 55.000 0.00 0.00 0.00 3.02
183 427 2.184020 CTCCTTCATCGCCACACCCA 62.184 60.000 0.00 0.00 0.00 4.51
224 468 0.687757 ATCACTCCCGCTCTAGCCAA 60.688 55.000 0.00 0.00 37.91 4.52
226 470 1.365633 CATCACTCCCGCTCTAGCC 59.634 63.158 0.00 0.00 37.91 3.93
362 606 5.465724 CGGGTCAGTATTTTATCTTAGTGGC 59.534 44.000 0.00 0.00 0.00 5.01
443 687 2.092375 AGTATAAGCTGCCTTGGGTTCC 60.092 50.000 0.00 0.00 32.47 3.62
508 752 8.702819 GTTTACATATAACTCTCACTAGGGGTT 58.297 37.037 0.00 0.00 0.00 4.11
608 852 9.807649 ATGCTTGATAGACATTGGTTATTTTTC 57.192 29.630 0.00 0.00 0.00 2.29
645 889 7.333672 CCTAAAGTAATTAAGCGACTGGTTTCT 59.666 37.037 0.00 0.00 37.03 2.52
654 898 4.873827 CAGGTGCCTAAAGTAATTAAGCGA 59.126 41.667 0.00 0.00 34.29 4.93
804 1048 0.542702 CATTTGGGTGGGCCTTGAGT 60.543 55.000 4.53 0.00 34.45 3.41
863 1118 3.777522 AGGATGCTAGCTTAGGTCTTGTT 59.222 43.478 17.23 0.00 0.00 2.83
970 1250 2.035576 ACCGTGGTAATAAGGATCGAGC 59.964 50.000 0.00 0.00 0.00 5.03
985 1268 2.655364 CATCGCGAGCTACCGTGG 60.655 66.667 16.66 0.00 40.13 4.94
1053 1345 2.031120 CCAAGAAAACCAGTTGAGCCA 58.969 47.619 0.00 0.00 0.00 4.75
1068 1360 6.007076 TGGTAGTTGCATACATTTTCCAAGA 58.993 36.000 0.21 0.00 0.00 3.02
1087 1379 7.385205 GGCAAGTGTTAGATGTGTATATGGTAG 59.615 40.741 0.00 0.00 0.00 3.18
1275 1583 4.905866 GTGATCGATTATTGAATGCAACGG 59.094 41.667 0.00 0.00 36.72 4.44
1289 1597 1.878522 GTCGCTGCGGTGATCGATT 60.879 57.895 23.03 0.00 42.43 3.34
1305 1613 1.938577 CTGTCCATAGCACTGCATGTC 59.061 52.381 3.30 2.61 0.00 3.06
1320 1628 6.335777 ACGTTAGTGTTATTATGTCCTGTCC 58.664 40.000 0.00 0.00 0.00 4.02
1321 1629 7.823149 AACGTTAGTGTTATTATGTCCTGTC 57.177 36.000 0.00 0.00 0.00 3.51
1322 1630 8.742777 TCTAACGTTAGTGTTATTATGTCCTGT 58.257 33.333 29.36 0.00 34.07 4.00
1323 1631 9.745880 ATCTAACGTTAGTGTTATTATGTCCTG 57.254 33.333 29.36 4.40 34.07 3.86
1324 1632 9.745880 CATCTAACGTTAGTGTTATTATGTCCT 57.254 33.333 29.36 0.00 34.07 3.85
1325 1633 9.525409 ACATCTAACGTTAGTGTTATTATGTCC 57.475 33.333 29.36 0.00 36.80 4.02
1649 1991 6.769512 ACCTTGTAAAAGATAGCTGAAGTGA 58.230 36.000 0.00 0.00 0.00 3.41
1696 2195 4.933505 TGGACTTTGCAAAATGTGATCA 57.066 36.364 13.84 0.00 0.00 2.92
1757 2354 5.579384 AATTGAAAACACATGAACATGCG 57.421 34.783 13.71 7.81 42.39 4.73
1857 2459 3.068165 TCTGTGTGTGTCTTGGTCAGTAG 59.932 47.826 0.00 0.00 0.00 2.57
2284 2897 5.248870 TCTTTTGGCTCAGTCTTGAAAAC 57.751 39.130 0.00 0.00 31.69 2.43
2521 3149 2.356432 CCTCCCTCACAATGCTCATTCA 60.356 50.000 0.00 0.00 0.00 2.57
2664 3292 0.323629 TCACCCTACGCCTTTGGAAG 59.676 55.000 0.00 0.00 0.00 3.46
2728 3356 0.998928 TCTATGCCCCCTCTGCAAAA 59.001 50.000 0.00 0.00 42.92 2.44
2729 3357 1.133699 CATCTATGCCCCCTCTGCAAA 60.134 52.381 0.00 0.00 42.92 3.68
2848 3476 4.703897 AGCATGTACGTAGGCAATATGTT 58.296 39.130 14.09 0.00 35.23 2.71
2853 3481 3.306780 GGGATAGCATGTACGTAGGCAAT 60.307 47.826 14.09 0.47 0.00 3.56
2889 3754 0.466189 CCACAACCAGCTCAACCTGT 60.466 55.000 0.00 0.00 0.00 4.00
2899 3764 4.020218 TGACTTCTATCCTTCCACAACCAG 60.020 45.833 0.00 0.00 0.00 4.00
3068 3948 6.583806 CCAGTAGAAACATGAAGCAACAATTC 59.416 38.462 0.00 0.00 0.00 2.17
3097 3977 7.399245 AAAGGGCATGTATAAATAAACACGT 57.601 32.000 0.00 0.00 0.00 4.49
3128 4008 6.604171 ACATATATGCACTCATCTTTTCCCA 58.396 36.000 12.79 0.00 34.22 4.37
3270 4185 3.406764 ACTCAGCTTCAATGTCCAAGTC 58.593 45.455 0.00 0.00 0.00 3.01
3339 4254 7.009179 TCTCCAATGATTTGTCTGAACTACT 57.991 36.000 0.00 0.00 0.00 2.57
3587 4525 8.813643 AAACAAGTGTACTTAGATGACTGTAC 57.186 34.615 0.00 0.00 36.69 2.90
3724 4673 2.838736 AGGTGGCAGCGTTTGATATAG 58.161 47.619 11.51 0.00 0.00 1.31
3808 4766 6.431543 ACCATTTTAAACGTATGACATGTGGA 59.568 34.615 1.15 0.00 0.00 4.02
3898 4858 6.025749 AGGCTAGCTTTGATTTGTTAAACC 57.974 37.500 15.72 0.00 0.00 3.27
3944 4936 8.514330 TCACTTGGTAAATTTGTCTACTGTTT 57.486 30.769 0.00 0.00 0.00 2.83
3964 4957 4.823989 CACAGGAGACAAAAATCCTCACTT 59.176 41.667 0.00 0.00 44.30 3.16
3986 4979 1.852157 ATTTCGGCCTCCTTGGAGCA 61.852 55.000 11.01 0.00 38.35 4.26
4164 5158 8.556213 AAAAATTCATGCATTTCTAGCACATT 57.444 26.923 3.74 0.00 45.95 2.71
4194 5188 8.028354 TGGTGAAATACATTTTTATGTGAGCTG 58.972 33.333 0.00 0.00 36.08 4.24
4218 5212 9.436957 ACTTATACTGTCAGTAAAGTTTCATGG 57.563 33.333 21.98 7.48 33.89 3.66
4247 5241 8.788806 CATGGAAAAACCTACACACATAAGTAA 58.211 33.333 0.00 0.00 39.86 2.24
4250 5244 7.447374 TCATGGAAAAACCTACACACATAAG 57.553 36.000 0.00 0.00 39.86 1.73
4251 5245 9.693739 ATATCATGGAAAAACCTACACACATAA 57.306 29.630 0.00 0.00 39.86 1.90
4304 5298 6.678568 TTGGAGCCTGGATTTTGAAAATTA 57.321 33.333 4.46 0.00 0.00 1.40
4333 5327 5.717178 ACACACTATCCAGAGTAGTTGATGT 59.283 40.000 0.00 0.00 30.24 3.06
4456 5452 6.587226 GCAAATGAATAATGTTGTCTGAGCAA 59.413 34.615 0.00 0.00 0.00 3.91
4457 5453 6.094719 GCAAATGAATAATGTTGTCTGAGCA 58.905 36.000 0.00 0.00 0.00 4.26
4646 5657 6.071503 GCTAGTTACCATGGTAGGTCGAATAT 60.072 42.308 23.40 6.70 42.06 1.28
4668 5679 4.949856 GGAAATGGATCTTGGAAAGTGCTA 59.050 41.667 0.00 0.00 46.34 3.49
4853 5868 6.776116 ACAATCATAGCATCAATTGTCCTGAT 59.224 34.615 5.13 3.69 37.72 2.90
5069 6099 1.737793 GCTACCAGCGTTGCATTTACT 59.262 47.619 0.00 0.00 40.05 2.24
5144 6174 1.546773 CCCGTCAATGGGTTTTGGAGA 60.547 52.381 0.00 0.00 44.76 3.71
5291 6324 3.821421 AGTGGTAGCTTATACACCAGC 57.179 47.619 5.52 2.15 42.84 4.85
5366 6399 9.614792 AAAGTATGAGTCCCTTCATAATACAAC 57.385 33.333 0.00 0.00 40.64 3.32
5469 6502 7.970384 TGTATCTTCGGTTTTGCTTAATGTAG 58.030 34.615 0.00 0.00 0.00 2.74
5474 6507 8.573035 AGAAATTGTATCTTCGGTTTTGCTTAA 58.427 29.630 0.00 0.00 0.00 1.85
5636 8462 7.379750 GGAACTAGACAAGTCTGTAGTCAAAT 58.620 38.462 12.77 0.00 40.71 2.32
5694 8530 9.880157 CTATCTACTAGTACTCCACTAATCTCC 57.120 40.741 0.00 0.00 39.28 3.71
5695 8531 9.880157 CCTATCTACTAGTACTCCACTAATCTC 57.120 40.741 0.00 0.00 39.28 2.75
5696 8532 8.828751 CCCTATCTACTAGTACTCCACTAATCT 58.171 40.741 0.00 0.00 39.28 2.40
5738 8791 7.292319 ACCCCATACTACTTTTTAGTTTGTGT 58.708 34.615 0.00 0.00 0.00 3.72
5740 8793 6.652062 CGACCCCATACTACTTTTTAGTTTGT 59.348 38.462 0.00 0.00 0.00 2.83
5782 8835 4.538490 AGTTGGTAACCACATGAAGGGATA 59.462 41.667 0.00 0.00 30.78 2.59
5793 8846 6.820152 AGTAATTATCGGAAGTTGGTAACCAC 59.180 38.462 0.00 0.00 30.78 4.16
5799 8852 6.295719 ACTGAGTAATTATCGGAAGTTGGT 57.704 37.500 9.40 0.00 0.00 3.67
5806 8859 8.147704 TGCATGAATAACTGAGTAATTATCGGA 58.852 33.333 0.00 0.00 0.00 4.55
5849 8902 7.946237 GCAATAAATAAATGGAATGAAATCGCG 59.054 33.333 0.00 0.00 0.00 5.87
5933 8987 3.830178 TCCTCAACCTTCTGATGTTCGTA 59.170 43.478 0.00 0.00 0.00 3.43
5942 8996 3.710209 ACTTCCATCCTCAACCTTCTG 57.290 47.619 0.00 0.00 0.00 3.02
6003 9058 4.712476 GAGTGCCAGTCCATAGATTTGAT 58.288 43.478 0.00 0.00 0.00 2.57
6086 9144 7.848128 AGAAAGATCCCGTTCTTCTTTATACA 58.152 34.615 0.00 0.00 39.22 2.29
6094 9152 6.986817 TCATGAATAGAAAGATCCCGTTCTTC 59.013 38.462 8.68 3.79 40.63 2.87
6100 9158 7.792374 TTTTCTCATGAATAGAAAGATCCCG 57.208 36.000 8.19 0.00 42.30 5.14
6280 9345 8.684386 TCATTTATTTCCACAACACTGAACTA 57.316 30.769 0.00 0.00 0.00 2.24
6328 9393 1.561542 AGGGTGCTTAATCCTCCTGTG 59.438 52.381 0.00 0.00 31.62 3.66
6533 9598 4.269183 CTCCATTACAATAAGGCACACCA 58.731 43.478 0.00 0.00 39.06 4.17
6542 9607 6.472016 TCACTGACTTGCTCCATTACAATAA 58.528 36.000 0.00 0.00 0.00 1.40
6600 9666 3.274288 GGAGCAGTCAACAGAAATAGGG 58.726 50.000 0.00 0.00 0.00 3.53
6662 9752 2.621338 TGAAGGCGAGTAATGAAGCAG 58.379 47.619 0.00 0.00 0.00 4.24
6705 9795 5.580297 GTGTGAGACCTCATCTTTCTGATTC 59.420 44.000 2.78 0.00 42.18 2.52
6753 9843 8.474025 TGTCCAAGACAATACATTTGTTCTTTT 58.526 29.630 0.00 0.00 39.78 2.27
6757 9847 6.381801 CCTGTCCAAGACAATACATTTGTTC 58.618 40.000 0.00 0.00 42.26 3.18
6804 9894 5.612725 TGATCTACAATGGCAGTATCACA 57.387 39.130 0.00 0.00 0.00 3.58
6827 9917 6.595682 ACATATAAGTGATGCCAAGTAGCTT 58.404 36.000 0.00 0.00 0.00 3.74
6849 9939 9.973450 AATAACTGTTGTGCAATATTACAAACA 57.027 25.926 2.69 9.48 38.40 2.83
6889 9979 0.255890 ACAAGGTTCTGCCGCCATAT 59.744 50.000 0.00 0.00 43.70 1.78
6919 10009 2.306341 ACAGGATCAGATCACTTGCG 57.694 50.000 12.66 0.00 0.00 4.85
6928 10018 3.176411 ACTGATGTCCAACAGGATCAGA 58.824 45.455 17.50 0.00 39.39 3.27
6935 10025 1.069022 CGGCAAACTGATGTCCAACAG 60.069 52.381 3.32 3.32 39.65 3.16
6953 10043 1.323412 TGGTGACACAAATTTCCCGG 58.677 50.000 8.08 0.00 33.40 5.73
6954 10044 3.658757 ATTGGTGACACAAATTTCCCG 57.341 42.857 8.08 0.00 42.67 5.14
6956 10046 8.831715 AGAATAAATTGGTGACACAAATTTCC 57.168 30.769 28.86 20.64 42.67 3.13
7034 10124 7.819415 TCAGTCATTGTACTCCTTCAGTATTTG 59.181 37.037 0.00 0.00 39.90 2.32
7040 10130 4.499183 GGTCAGTCATTGTACTCCTTCAG 58.501 47.826 0.00 0.00 0.00 3.02
7041 10131 3.260884 GGGTCAGTCATTGTACTCCTTCA 59.739 47.826 0.00 0.00 0.00 3.02
7048 10138 7.120579 TGACATTATTTGGGTCAGTCATTGTAC 59.879 37.037 0.00 0.00 36.69 2.90
7062 10152 7.922505 TGACGAAAAAGTTGACATTATTTGG 57.077 32.000 0.00 0.00 0.00 3.28


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

AutoCloner maintained by Alex Coulton.