Multiple sequence alignment - TraesCS7B01G223700

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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 TraesCS7B01G223700 chr7B 100.000 6672 0 0 1 6672 422936105 422929434 0.000000e+00 12321.0
1 TraesCS7B01G223700 chr7B 95.745 94 4 0 6088 6181 422929965 422929872 1.160000e-32 152.0
2 TraesCS7B01G223700 chr7B 95.745 94 4 0 6141 6234 422930018 422929925 1.160000e-32 152.0
3 TraesCS7B01G223700 chr7B 82.081 173 18 4 3768 3927 382607707 382607535 1.170000e-27 135.0
4 TraesCS7B01G223700 chr7B 94.737 38 1 1 575 612 386556252 386556288 2.600000e-04 58.4
5 TraesCS7B01G223700 chr7A 93.593 5884 256 55 1 5829 468466271 468460454 0.000000e+00 8665.0
6 TraesCS7B01G223700 chr7A 94.675 507 26 1 5339 5845 467652134 467651629 0.000000e+00 785.0
7 TraesCS7B01G223700 chr7A 85.544 588 57 11 6090 6672 467651283 467650719 2.070000e-164 590.0
8 TraesCS7B01G223700 chr7A 86.292 445 46 10 5846 6279 467651587 467651147 2.820000e-128 470.0
9 TraesCS7B01G223700 chr7A 96.732 153 5 0 6082 6234 467651397 467651245 8.590000e-64 255.0
10 TraesCS7B01G223700 chr7A 89.908 109 9 2 6127 6234 467651405 467651298 9.020000e-29 139.0
11 TraesCS7B01G223700 chr7A 100.000 32 0 0 5846 5877 468460409 468460378 7.230000e-05 60.2
12 TraesCS7B01G223700 chr7D 95.695 2741 96 11 2976 5703 408369325 408366594 0.000000e+00 4388.0
13 TraesCS7B01G223700 chr7D 97.143 1610 26 9 1251 2859 408370920 408369330 0.000000e+00 2700.0
14 TraesCS7B01G223700 chr7D 89.560 613 56 4 1 612 408374610 408374005 0.000000e+00 771.0
15 TraesCS7B01G223700 chr7D 90.112 536 49 2 6141 6672 408365694 408365159 0.000000e+00 693.0
16 TraesCS7B01G223700 chr7D 90.591 372 7 9 807 1178 408371821 408371478 1.010000e-127 468.0
17 TraesCS7B01G223700 chr7D 87.719 342 30 9 5846 6181 408365936 408365601 8.110000e-104 388.0
18 TraesCS7B01G223700 chr7D 92.929 198 14 0 612 809 408373047 408372850 8.470000e-74 289.0
19 TraesCS7B01G223700 chr2D 77.009 448 85 12 6194 6627 26022810 26023253 2.400000e-59 241.0
20 TraesCS7B01G223700 chr2D 79.355 155 21 6 3764 3908 646596036 646596189 1.530000e-16 99.0
21 TraesCS7B01G223700 chr2D 90.196 51 5 0 6057 6107 104276259 104276309 4.320000e-07 67.6
22 TraesCS7B01G223700 chr1A 83.333 180 16 5 3768 3933 134962282 134962103 3.220000e-33 154.0
23 TraesCS7B01G223700 chr1A 94.872 39 1 1 577 615 449858335 449858298 7.230000e-05 60.2
24 TraesCS7B01G223700 chr3B 76.389 288 56 8 6342 6621 257239653 257239370 1.940000e-30 145.0
25 TraesCS7B01G223700 chr3B 79.245 159 29 4 3768 3926 150655640 150655486 2.540000e-19 108.0
26 TraesCS7B01G223700 chr3D 79.747 158 26 4 3770 3926 100224992 100224840 7.070000e-20 110.0
27 TraesCS7B01G223700 chr3D 91.304 46 3 1 577 622 169682315 169682271 2.010000e-05 62.1
28 TraesCS7B01G223700 chr3D 89.796 49 1 3 568 615 398269010 398268965 7.230000e-05 60.2
29 TraesCS7B01G223700 chr2A 83.673 98 9 2 3765 3862 42399367 42399457 1.190000e-12 86.1
30 TraesCS7B01G223700 chr5B 92.727 55 4 0 3764 3818 566681398 566681452 5.550000e-11 80.5
31 TraesCS7B01G223700 chr6A 89.831 59 6 0 3804 3862 169207951 169208009 7.170000e-10 76.8
32 TraesCS7B01G223700 chr5A 92.000 50 2 2 569 618 372158619 372158572 1.200000e-07 69.4
33 TraesCS7B01G223700 chr5A 96.875 32 1 0 6075 6106 699779003 699779034 3.000000e-03 54.7
34 TraesCS7B01G223700 chr3A 90.196 51 4 1 6194 6244 12936673 12936722 1.550000e-06 65.8
35 TraesCS7B01G223700 chr4A 97.368 38 0 1 575 612 626283640 626283676 5.590000e-06 63.9
36 TraesCS7B01G223700 chrUn 92.308 39 1 2 577 615 112408730 112408694 3.000000e-03 54.7


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 TraesCS7B01G223700 chr7B 422929434 422936105 6671 True 12321.000000 12321 100.000000 1 6672 1 chr7B.!!$R2 6671
1 TraesCS7B01G223700 chr7A 468460378 468466271 5893 True 4362.600000 8665 96.796500 1 5877 2 chr7A.!!$R2 5876
2 TraesCS7B01G223700 chr7A 467650719 467652134 1415 True 447.800000 785 90.630200 5339 6672 5 chr7A.!!$R1 1333
3 TraesCS7B01G223700 chr7D 408365159 408374610 9451 True 1385.285714 4388 91.964143 1 6672 7 chr7D.!!$R1 6671

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
28 29 0.039618 TTTCCCATGACTTCCCCTGC 59.960 55.000 0.00 0.0 0.00 4.85 F
1056 3053 0.105709 CTCCCTCTCTCTTCCCCCTC 60.106 65.000 0.00 0.0 0.00 4.30 F
1057 3054 1.074850 CCCTCTCTCTTCCCCCTCC 60.075 68.421 0.00 0.0 0.00 4.30 F
1059 3056 1.074850 CTCTCTCTTCCCCCTCCCC 60.075 68.421 0.00 0.0 0.00 4.81 F
1060 3057 1.550374 TCTCTCTTCCCCCTCCCCT 60.550 63.158 0.00 0.0 0.00 4.79 F
2661 5163 0.469331 TCCCCCAGTACTATGAGGCG 60.469 60.000 0.00 0.0 0.00 5.52 F
3195 5707 1.420138 ACGAGGTATTTATGGGGCTGG 59.580 52.381 0.00 0.0 0.00 4.85 F
4106 6651 1.069049 GCCTTTTGCACCATCAGTTGT 59.931 47.619 0.00 0.0 40.77 3.32 F
5113 7665 0.394899 CACCTCAGGGGCCTTTCATC 60.395 60.000 0.84 0.0 39.10 2.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1069 3066 0.104144 TCAGTGGGAAGGGAAGGGAA 60.104 55.000 0.00 0.0 0.00 3.97 R
1873 4356 2.097110 TGGTGACAGTAACAGGGAGT 57.903 50.000 0.00 0.0 35.01 3.85 R
2022 4505 2.346284 TAACCCCAAACACCGCAGCT 62.346 55.000 0.00 0.0 0.00 4.24 R
2496 4998 2.365582 ACACAACTGTCCTCCAACAAC 58.634 47.619 0.00 0.0 0.00 3.32 R
3039 5551 5.107109 TGACAACATTTGGACAATTCGAG 57.893 39.130 0.00 0.0 34.12 4.04 R
3805 6343 1.208776 ACCCACCCAGTAGCGATTAAC 59.791 52.381 0.00 0.0 0.00 2.01 R
4473 7021 1.282157 AGGGAAAACGGATAAGCAGCT 59.718 47.619 0.00 0.0 0.00 4.24 R
5233 7785 0.464013 CAGGCAAGCATCCAGAGGAG 60.464 60.000 0.00 0.0 34.05 3.69 R
6206 9345 0.394216 TGGCAGCCACCACATACATC 60.394 55.000 11.22 0.0 33.75 3.06 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
28 29 0.039618 TTTCCCATGACTTCCCCTGC 59.960 55.000 0.00 0.00 0.00 4.85
32 33 1.450312 CATGACTTCCCCTGCGTCC 60.450 63.158 0.00 0.00 0.00 4.79
46 47 0.250770 GCGTCCTCCTTTTCCCTTGT 60.251 55.000 0.00 0.00 0.00 3.16
52 53 2.623416 CCTCCTTTTCCCTTGTTGTGAC 59.377 50.000 0.00 0.00 0.00 3.67
55 56 1.336755 CTTTTCCCTTGTTGTGACCCG 59.663 52.381 0.00 0.00 0.00 5.28
71 72 1.142262 ACCCGCACCCATAATTCCTAC 59.858 52.381 0.00 0.00 0.00 3.18
101 103 6.303054 TCATTTAGACCATCACAAGACCAAA 58.697 36.000 0.00 0.00 0.00 3.28
166 168 6.470235 CCGTGCAATTGATTTAATGAGAGTTC 59.530 38.462 10.34 0.00 0.00 3.01
168 170 7.315142 GTGCAATTGATTTAATGAGAGTTCCA 58.685 34.615 10.34 0.00 0.00 3.53
177 179 4.387026 AATGAGAGTTCCATTTCCACCA 57.613 40.909 0.00 0.00 30.72 4.17
222 224 9.787532 AACATCATACGTTTTGATAATTTGGAG 57.212 29.630 11.87 2.82 32.63 3.86
230 232 8.085296 ACGTTTTGATAATTTGGAGTGCAATTA 58.915 29.630 0.00 0.41 31.11 1.40
240 242 5.818136 TGGAGTGCAATTATGAAACTAGC 57.182 39.130 0.00 0.00 0.00 3.42
254 256 6.174720 TGAAACTAGCCCTTAGTCATATGG 57.825 41.667 2.13 0.00 41.80 2.74
297 299 8.429641 AGACCAAGTACTTCTCTTCAAAATGTA 58.570 33.333 4.77 0.00 0.00 2.29
313 315 6.882140 TCAAAATGTAAGTTATCCACCGACAT 59.118 34.615 0.00 0.00 34.20 3.06
321 323 5.118990 AGTTATCCACCGACATTTCAGATG 58.881 41.667 0.00 0.00 0.00 2.90
348 350 5.440610 CCTCTAATTGTTGGCCAATAGAGT 58.559 41.667 32.58 20.82 43.04 3.24
364 366 6.147164 CCAATAGAGTAAGAGTTCGCAAACAA 59.853 38.462 0.00 0.00 37.88 2.83
369 371 8.149973 AGAGTAAGAGTTCGCAAACAAAATTA 57.850 30.769 0.00 0.00 37.88 1.40
447 449 0.385029 TTTTTCATGTGCTGCAGCGT 59.615 45.000 32.11 18.65 45.83 5.07
499 501 4.685169 TCATCCGCAAAAAGAAGATGTC 57.315 40.909 0.00 0.00 36.54 3.06
529 531 2.474816 GAGCGCTCCGACAGATTTATT 58.525 47.619 27.22 0.00 0.00 1.40
530 532 3.552273 GGAGCGCTCCGACAGATTTATTA 60.552 47.826 38.78 0.00 40.36 0.98
539 543 7.982354 GCTCCGACAGATTTATTAGCCTTATAT 59.018 37.037 0.00 0.00 0.00 0.86
540 544 9.522804 CTCCGACAGATTTATTAGCCTTATATC 57.477 37.037 0.00 0.00 0.00 1.63
626 1588 4.760204 AGGGAGTATGTTGCACAAACTTAC 59.240 41.667 5.38 5.38 44.21 2.34
630 1592 5.432885 GTATGTTGCACAAACTTACTGGT 57.567 39.130 0.00 0.00 42.21 4.00
639 1601 5.679906 CACAAACTTACTGGTCTGAAATCG 58.320 41.667 0.00 0.00 0.00 3.34
678 1640 3.716431 AGGATTTTTGGGATGAGCACAT 58.284 40.909 0.00 0.00 39.67 3.21
735 1697 5.480073 CCATTGTGAAAGAAATCCCTAACCA 59.520 40.000 0.00 0.00 0.00 3.67
759 1721 8.400947 CCACTTTGATTACATCATCCTTAACAG 58.599 37.037 0.00 0.00 39.39 3.16
799 1762 2.164338 GAAAATGGCCGGAAACCACTA 58.836 47.619 5.05 0.00 40.82 2.74
838 2832 6.098266 AGCCAAAACAAAGGAAGTAAGACAAT 59.902 34.615 0.00 0.00 0.00 2.71
997 2994 5.961395 GCAAAATGAGAAATTGCATCGAT 57.039 34.783 4.96 0.00 46.57 3.59
1024 3021 5.192927 TGCAAATAACCTCACCTTCCATAG 58.807 41.667 0.00 0.00 0.00 2.23
1040 3037 2.555227 CCATAGCCCTCTCTCTCTCTCC 60.555 59.091 0.00 0.00 0.00 3.71
1049 3046 3.713764 CTCTCTCTCTCTCCCTCTCTCTT 59.286 52.174 0.00 0.00 0.00 2.85
1050 3047 3.711704 TCTCTCTCTCTCCCTCTCTCTTC 59.288 52.174 0.00 0.00 0.00 2.87
1052 3049 1.850345 TCTCTCTCCCTCTCTCTTCCC 59.150 57.143 0.00 0.00 0.00 3.97
1053 3050 0.930726 TCTCTCCCTCTCTCTTCCCC 59.069 60.000 0.00 0.00 0.00 4.81
1055 3052 0.556380 TCTCCCTCTCTCTTCCCCCT 60.556 60.000 0.00 0.00 0.00 4.79
1056 3053 0.105709 CTCCCTCTCTCTTCCCCCTC 60.106 65.000 0.00 0.00 0.00 4.30
1057 3054 1.074850 CCCTCTCTCTTCCCCCTCC 60.075 68.421 0.00 0.00 0.00 4.30
1058 3055 1.074850 CCTCTCTCTTCCCCCTCCC 60.075 68.421 0.00 0.00 0.00 4.30
1059 3056 1.074850 CTCTCTCTTCCCCCTCCCC 60.075 68.421 0.00 0.00 0.00 4.81
1060 3057 1.550374 TCTCTCTTCCCCCTCCCCT 60.550 63.158 0.00 0.00 0.00 4.79
1064 3061 3.711782 CTTCCCCCTCCCCTCCCT 61.712 72.222 0.00 0.00 0.00 4.20
1069 3066 3.711782 CCCTCCCCTCCCTTCCCT 61.712 72.222 0.00 0.00 0.00 4.20
1211 3208 5.106908 GCGTGCTATGTTCTCTTCTCTTTTT 60.107 40.000 0.00 0.00 0.00 1.94
1337 3819 5.464965 AAAGACGCGATACTTATGGTTTG 57.535 39.130 15.93 0.00 0.00 2.93
1749 4231 4.387598 TCCCCGTATTTTCTTTCGTGAAA 58.612 39.130 0.00 0.00 34.55 2.69
1758 4240 6.443934 TTTTCTTTCGTGAAAGGTGAATCA 57.556 33.333 19.25 0.00 45.80 2.57
1799 4281 4.877378 TCTTCTTGGCATGCTGATTTTT 57.123 36.364 18.92 0.00 0.00 1.94
1873 4356 5.744171 TCCTCGAATGATCCATTTTTCTCA 58.256 37.500 0.00 0.00 33.90 3.27
1983 4466 7.495934 ACTTTATGCTGTCATGGTGAGTTATAC 59.504 37.037 0.00 0.00 34.22 1.47
2198 4699 1.556373 CCTGGTGCCCTGATCACTGA 61.556 60.000 0.00 0.00 34.97 3.41
2225 4727 7.448748 TTTTATAAAAGAGAACACAGAGGGC 57.551 36.000 6.54 0.00 0.00 5.19
2226 4728 2.278332 AAAAGAGAACACAGAGGGCC 57.722 50.000 0.00 0.00 0.00 5.80
2384 4886 4.261801 GGTGCTATTTCTTCCAGCTGTTA 58.738 43.478 13.81 0.00 36.26 2.41
2450 4952 4.889409 GTCATTGATAATGGGCTTCTTCCA 59.111 41.667 2.09 0.00 39.38 3.53
2496 4998 3.971032 AGGTGACTTCTTTTTCGCTTG 57.029 42.857 0.00 0.00 37.44 4.01
2520 5022 1.053424 TGGAGGACAGTTGTGTACCC 58.947 55.000 0.00 0.00 38.47 3.69
2661 5163 0.469331 TCCCCCAGTACTATGAGGCG 60.469 60.000 0.00 0.00 0.00 5.52
2881 5383 7.931407 TGCAATAATATCTGTTGGTCGTTCTAT 59.069 33.333 0.00 0.00 0.00 1.98
2882 5384 8.223769 GCAATAATATCTGTTGGTCGTTCTATG 58.776 37.037 0.00 0.00 0.00 2.23
2883 5385 9.476202 CAATAATATCTGTTGGTCGTTCTATGA 57.524 33.333 0.00 0.00 0.00 2.15
2886 5388 8.964476 AATATCTGTTGGTCGTTCTATGATTT 57.036 30.769 0.00 0.00 0.00 2.17
2887 5389 6.668541 ATCTGTTGGTCGTTCTATGATTTG 57.331 37.500 0.00 0.00 0.00 2.32
2888 5390 5.547465 TCTGTTGGTCGTTCTATGATTTGT 58.453 37.500 0.00 0.00 0.00 2.83
2889 5391 5.408299 TCTGTTGGTCGTTCTATGATTTGTG 59.592 40.000 0.00 0.00 0.00 3.33
2891 5393 3.669536 TGGTCGTTCTATGATTTGTGCA 58.330 40.909 0.00 0.00 0.00 4.57
3039 5551 2.246719 AGTCTGCTGGTGTGAAGTTC 57.753 50.000 0.00 0.00 0.00 3.01
3046 5558 2.808543 GCTGGTGTGAAGTTCTCGAATT 59.191 45.455 4.17 0.00 0.00 2.17
3192 5704 2.158871 TGACACGAGGTATTTATGGGGC 60.159 50.000 0.00 0.00 0.00 5.80
3195 5707 1.420138 ACGAGGTATTTATGGGGCTGG 59.580 52.381 0.00 0.00 0.00 4.85
3228 5741 2.779430 TCATCTGCAACCTGTATCCCAT 59.221 45.455 0.00 0.00 0.00 4.00
3240 5753 6.006449 ACCTGTATCCCATCTTTGAATATGC 58.994 40.000 0.00 0.00 0.00 3.14
3241 5754 6.183361 ACCTGTATCCCATCTTTGAATATGCT 60.183 38.462 0.00 0.00 0.00 3.79
3259 5772 9.328721 GAATATGCTTTAATTTTGTTTTGTGCC 57.671 29.630 0.00 0.00 0.00 5.01
3335 5848 6.183360 GCATTCCAGTCTCTATGCTCAAAAAT 60.183 38.462 0.00 0.00 40.08 1.82
3359 5872 4.250464 CGTGACTAAACCTTTCATGCCTA 58.750 43.478 0.00 0.00 0.00 3.93
3523 6040 8.967664 TTCTGGTTATTGTATATGGTGTTACC 57.032 34.615 0.00 0.00 39.22 2.85
3555 6073 9.444600 GTTTCAATTAGGACTAGGACATGTAAA 57.555 33.333 0.00 0.00 0.00 2.01
3581 6099 3.213506 TGGATGTCAAGGTGTGTTTGAG 58.786 45.455 0.00 0.00 35.39 3.02
3589 6107 1.493022 AGGTGTGTTTGAGGGCTGTTA 59.507 47.619 0.00 0.00 0.00 2.41
3786 6324 5.263599 TCAATGTTCCAAATATCAGCCAGT 58.736 37.500 0.00 0.00 0.00 4.00
3787 6325 5.716228 TCAATGTTCCAAATATCAGCCAGTT 59.284 36.000 0.00 0.00 0.00 3.16
3788 6326 6.889177 TCAATGTTCCAAATATCAGCCAGTTA 59.111 34.615 0.00 0.00 0.00 2.24
3789 6327 7.395772 TCAATGTTCCAAATATCAGCCAGTTAA 59.604 33.333 0.00 0.00 0.00 2.01
3790 6328 7.902920 ATGTTCCAAATATCAGCCAGTTAAT 57.097 32.000 0.00 0.00 0.00 1.40
3791 6329 7.333528 TGTTCCAAATATCAGCCAGTTAATC 57.666 36.000 0.00 0.00 0.00 1.75
3792 6330 6.038161 TGTTCCAAATATCAGCCAGTTAATCG 59.962 38.462 0.00 0.00 0.00 3.34
3793 6331 5.063204 TCCAAATATCAGCCAGTTAATCGG 58.937 41.667 0.00 0.00 0.00 4.18
3818 6356 3.064958 TCTCCGTCAGTTAATCGCTACTG 59.935 47.826 0.00 0.00 42.41 2.74
3895 6433 1.613317 TACCCAGCACCCGACTGATG 61.613 60.000 0.00 0.00 37.32 3.07
4071 6616 7.151999 TGCGACAAATATATTGTTTCCTGTT 57.848 32.000 0.00 0.00 31.96 3.16
4072 6617 7.026562 TGCGACAAATATATTGTTTCCTGTTG 58.973 34.615 0.00 4.03 31.96 3.33
4094 6639 7.545265 TGTTGTGATTATCTAATTGCCTTTTGC 59.455 33.333 0.00 0.00 41.77 3.68
4105 6650 1.787012 GCCTTTTGCACCATCAGTTG 58.213 50.000 0.00 0.00 40.77 3.16
4106 6651 1.069049 GCCTTTTGCACCATCAGTTGT 59.931 47.619 0.00 0.00 40.77 3.32
4149 6694 9.268268 ACTTTTCTGTGTTTCAGTATAATTCGA 57.732 29.630 0.00 0.00 43.97 3.71
4253 6798 8.871125 CCATTACTTACATCCTCAACTATAGGT 58.129 37.037 4.43 0.00 35.48 3.08
4352 6899 5.775701 ACCTACTGTGAACTCTTACATCAGT 59.224 40.000 0.00 0.00 38.10 3.41
4473 7021 5.900123 TCAAGGTAAGGGTTCAATTTTTGGA 59.100 36.000 0.00 0.00 0.00 3.53
4481 7029 4.262420 GGGTTCAATTTTTGGAGCTGCTTA 60.262 41.667 6.82 0.00 36.87 3.09
4600 7149 9.650714 TTATAACTACTTGCTAGGGATGAAGTA 57.349 33.333 0.00 0.00 31.25 2.24
4696 7245 1.536766 CACCCAACTACGACGACAGTA 59.463 52.381 0.00 0.00 0.00 2.74
4818 7367 5.048013 CCTTCTTACCAAATTTCCTGTCACC 60.048 44.000 0.00 0.00 0.00 4.02
4822 7371 1.812571 CCAAATTTCCTGTCACCGGAG 59.187 52.381 9.46 0.00 0.00 4.63
4849 7398 1.685180 GCGGAAGGGGAAGGCTTTATT 60.685 52.381 0.00 0.00 0.00 1.40
4897 7446 3.057736 CCATCGTTTCGATCTATACCCGT 60.058 47.826 1.58 0.00 45.19 5.28
5113 7665 0.394899 CACCTCAGGGGCCTTTCATC 60.395 60.000 0.84 0.00 39.10 2.92
5206 7758 8.893727 GCAGTGATTGGTATATACAGTTCTTTT 58.106 33.333 14.70 0.00 0.00 2.27
5240 7792 7.901029 TCTTTATTAGTATGGATGCTCCTCTG 58.099 38.462 4.21 0.00 37.46 3.35
5255 7807 3.145551 CTGGATGCTTGCCTGGCC 61.146 66.667 17.53 0.00 0.00 5.36
5276 7830 3.123050 CGGCGATACATTGATCTGTTCA 58.877 45.455 0.00 0.00 0.00 3.18
5549 8103 0.386838 GCACTTGCCTCTGCTTTTGT 59.613 50.000 0.00 0.00 38.71 2.83
5765 8797 4.154195 ACATCGTTCCTTACACATTCTTGC 59.846 41.667 0.00 0.00 0.00 4.01
5945 9020 3.507162 TGTCCATGTCCACAAAGTCAT 57.493 42.857 0.00 0.00 0.00 3.06
6069 9152 0.442699 GTTGTCCGTCTTCAATCGCC 59.557 55.000 0.00 0.00 0.00 5.54
6072 9155 2.509336 CCGTCTTCAATCGCCGCT 60.509 61.111 0.00 0.00 0.00 5.52
6206 9345 4.301505 CCAACCATGGTGAGGTCG 57.698 61.111 20.60 2.99 42.18 4.79
6210 9349 0.984230 AACCATGGTGAGGTCGATGT 59.016 50.000 20.60 0.00 38.76 3.06
6212 9351 2.398588 ACCATGGTGAGGTCGATGTAT 58.601 47.619 18.99 0.00 32.90 2.29
6333 9505 4.883354 GGCCGCCCATGAGGAAGG 62.883 72.222 0.00 2.82 38.24 3.46
6400 9573 2.109387 CCACCAACGTCGGGTTCA 59.891 61.111 9.00 0.00 36.49 3.18
6431 9604 2.003548 GGGGCTCCTCCATCACCTT 61.004 63.158 0.00 0.00 36.21 3.50
6509 9682 2.043248 GTCGAGGCCCTCCCACTA 60.043 66.667 4.85 0.00 35.39 2.74
6571 9747 3.522731 CAGCTCCTCCTCGACGGG 61.523 72.222 0.00 0.00 0.00 5.28
6638 9814 4.903010 AAGCGCACGTGAACCCGT 62.903 61.111 22.23 1.42 42.87 5.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 2.929043 AGGGGAAGTCATGGGAAAAGAT 59.071 45.455 0.00 0.00 0.00 2.40
28 29 1.880027 CAACAAGGGAAAAGGAGGACG 59.120 52.381 0.00 0.00 0.00 4.79
32 33 2.623416 GGTCACAACAAGGGAAAAGGAG 59.377 50.000 0.00 0.00 0.00 3.69
52 53 1.420138 AGTAGGAATTATGGGTGCGGG 59.580 52.381 0.00 0.00 0.00 6.13
55 56 5.221722 TGAGATGAGTAGGAATTATGGGTGC 60.222 44.000 0.00 0.00 0.00 5.01
71 72 7.224362 GTCTTGTGATGGTCTAAATGAGATGAG 59.776 40.741 0.00 0.00 36.29 2.90
86 87 2.292828 ACCCTTTGGTCTTGTGATGG 57.707 50.000 0.00 0.00 43.06 3.51
130 132 4.269183 TCAATTGCACGGTCTATTCCAAT 58.731 39.130 0.00 0.00 0.00 3.16
141 143 5.883661 ACTCTCATTAAATCAATTGCACGG 58.116 37.500 0.00 0.00 0.00 4.94
222 224 5.582689 AAGGGCTAGTTTCATAATTGCAC 57.417 39.130 0.00 0.00 0.00 4.57
230 232 6.745474 GCCATATGACTAAGGGCTAGTTTCAT 60.745 42.308 3.65 0.00 41.17 2.57
238 240 1.819753 TGGCCATATGACTAAGGGCT 58.180 50.000 0.00 0.00 45.97 5.19
240 242 3.307975 CCAGATGGCCATATGACTAAGGG 60.308 52.174 36.26 17.61 32.07 3.95
264 266 5.262804 AGAGAAGTACTTGGTCTTACCGAT 58.737 41.667 14.14 0.00 42.58 4.18
273 275 8.974060 TTACATTTTGAAGAGAAGTACTTGGT 57.026 30.769 14.14 0.00 0.00 3.67
297 299 5.160607 TCTGAAATGTCGGTGGATAACTT 57.839 39.130 0.00 0.00 0.00 2.66
313 315 4.922206 ACAATTAGAGGCCACATCTGAAA 58.078 39.130 5.01 0.00 0.00 2.69
348 350 8.800031 GTGTTTAATTTTGTTTGCGAACTCTTA 58.200 29.630 17.65 7.40 36.70 2.10
364 366 7.787028 TCTAAACCCAGCAAAGTGTTTAATTT 58.213 30.769 0.00 0.00 34.01 1.82
369 371 4.532834 TCTCTAAACCCAGCAAAGTGTTT 58.467 39.130 0.00 0.00 35.32 2.83
432 434 1.739196 GAGACGCTGCAGCACATGA 60.739 57.895 36.03 0.00 42.21 3.07
499 501 1.227497 GGAGCGCTCCTGGAATCTG 60.227 63.158 42.50 0.00 46.16 2.90
539 543 8.578308 TCGAAACGTACTTTCTCTATTTTTGA 57.422 30.769 12.75 0.00 36.80 2.69
540 544 9.302773 CTTCGAAACGTACTTTCTCTATTTTTG 57.697 33.333 0.00 0.00 36.80 2.44
583 587 7.728981 ACTCCCTCCGTCTCATAATATAAAAGA 59.271 37.037 0.00 0.00 0.00 2.52
586 590 8.967918 CATACTCCCTCCGTCTCATAATATAAA 58.032 37.037 0.00 0.00 0.00 1.40
626 1588 1.066573 AGCTCACCGATTTCAGACCAG 60.067 52.381 0.00 0.00 0.00 4.00
627 1589 0.976641 AGCTCACCGATTTCAGACCA 59.023 50.000 0.00 0.00 0.00 4.02
630 1592 2.688507 GTGAAGCTCACCGATTTCAGA 58.311 47.619 5.33 0.00 41.37 3.27
678 1640 9.378551 GGCGGATTATGTCAATGATACTATTAA 57.621 33.333 0.00 0.00 0.00 1.40
703 1665 4.852134 TTCTTTCACAATGGTGTCATGG 57.148 40.909 0.00 0.00 45.45 3.66
759 1721 5.705609 TTCTTTCAGACAAATTGGGCTAC 57.294 39.130 0.00 0.00 0.00 3.58
838 2832 8.291032 ACGAAATTACAACCGAAAATGACAATA 58.709 29.630 0.00 0.00 0.00 1.90
851 2845 8.875803 TCATATCTTGTGTACGAAATTACAACC 58.124 33.333 0.00 0.00 33.73 3.77
994 2991 6.377327 AGGTGAGGTTATTTGCAAATATCG 57.623 37.500 27.83 0.00 31.47 2.92
997 2994 6.013379 TGGAAGGTGAGGTTATTTGCAAATA 58.987 36.000 24.63 24.63 0.00 1.40
1024 3021 0.178990 GAGGGAGAGAGAGAGAGGGC 60.179 65.000 0.00 0.00 0.00 5.19
1040 3037 1.074850 GGGAGGGGGAAGAGAGAGG 60.075 68.421 0.00 0.00 0.00 3.69
1049 3046 3.707189 GAAGGGAGGGGAGGGGGA 61.707 72.222 0.00 0.00 0.00 4.81
1050 3047 4.845307 GGAAGGGAGGGGAGGGGG 62.845 77.778 0.00 0.00 0.00 5.40
1052 3049 3.289454 AAGGGAAGGGAGGGGAGGG 62.289 68.421 0.00 0.00 0.00 4.30
1053 3050 1.694525 GAAGGGAAGGGAGGGGAGG 60.695 68.421 0.00 0.00 0.00 4.30
1055 3052 2.459710 GGAAGGGAAGGGAGGGGA 59.540 66.667 0.00 0.00 0.00 4.81
1056 3053 2.696504 GGGAAGGGAAGGGAGGGG 60.697 72.222 0.00 0.00 0.00 4.79
1057 3054 1.230314 AAGGGAAGGGAAGGGAGGG 60.230 63.158 0.00 0.00 0.00 4.30
1058 3055 1.282653 GGAAGGGAAGGGAAGGGAGG 61.283 65.000 0.00 0.00 0.00 4.30
1059 3056 1.282653 GGGAAGGGAAGGGAAGGGAG 61.283 65.000 0.00 0.00 0.00 4.30
1060 3057 1.230182 GGGAAGGGAAGGGAAGGGA 60.230 63.158 0.00 0.00 0.00 4.20
1064 3061 0.849540 GGGAAGGGAAGGGAAGGGAA 60.850 60.000 0.00 0.00 0.00 3.97
1069 3066 0.104144 TCAGTGGGAAGGGAAGGGAA 60.104 55.000 0.00 0.00 0.00 3.97
1337 3819 3.777465 TCGTACACAGAGGCACTAATC 57.223 47.619 0.00 0.00 41.55 1.75
1742 4224 4.893608 TCAGATTGATTCACCTTTCACGA 58.106 39.130 0.00 0.00 0.00 4.35
1743 4225 5.391310 CCTTCAGATTGATTCACCTTTCACG 60.391 44.000 0.00 0.00 0.00 4.35
1749 4231 3.681034 CGCTCCTTCAGATTGATTCACCT 60.681 47.826 0.00 0.00 0.00 4.00
1758 4240 1.115467 ACCGATCGCTCCTTCAGATT 58.885 50.000 10.32 0.00 0.00 2.40
1799 4281 5.191722 ACCTAAGAGCCATGGATGTCTAAAA 59.808 40.000 18.40 2.88 0.00 1.52
1873 4356 2.097110 TGGTGACAGTAACAGGGAGT 57.903 50.000 0.00 0.00 35.01 3.85
1931 4414 2.770164 TTCTTGCTCCTGCTTCCTAC 57.230 50.000 0.00 0.00 40.48 3.18
2022 4505 2.346284 TAACCCCAAACACCGCAGCT 62.346 55.000 0.00 0.00 0.00 4.24
2224 4726 3.954258 ACAGACAAAAGCATATTAGGGGC 59.046 43.478 0.00 0.00 0.00 5.80
2225 4727 4.202050 GCACAGACAAAAGCATATTAGGGG 60.202 45.833 0.00 0.00 0.00 4.79
2226 4728 4.496341 CGCACAGACAAAAGCATATTAGGG 60.496 45.833 0.00 0.00 0.00 3.53
2384 4886 5.129980 TCCACAGTTATTCATGAGCATCTCT 59.870 40.000 0.00 0.00 34.92 3.10
2496 4998 2.365582 ACACAACTGTCCTCCAACAAC 58.634 47.619 0.00 0.00 0.00 3.32
2715 5217 5.437289 TTTGTTGCAGTACATGGAAGAAG 57.563 39.130 0.00 0.00 42.19 2.85
2881 5383 7.043961 TGTAAGGTTGTTAATGCACAAATCA 57.956 32.000 0.00 0.00 38.40 2.57
2882 5384 7.651704 ACTTGTAAGGTTGTTAATGCACAAATC 59.348 33.333 0.00 0.00 38.40 2.17
2883 5385 7.496747 ACTTGTAAGGTTGTTAATGCACAAAT 58.503 30.769 0.00 0.00 38.40 2.32
2886 5388 6.458232 AACTTGTAAGGTTGTTAATGCACA 57.542 33.333 0.00 0.00 0.00 4.57
2887 5389 7.645402 AGTAACTTGTAAGGTTGTTAATGCAC 58.355 34.615 0.00 0.00 0.00 4.57
2888 5390 7.811117 AGTAACTTGTAAGGTTGTTAATGCA 57.189 32.000 0.00 0.00 0.00 3.96
2889 5391 8.996271 AGTAGTAACTTGTAAGGTTGTTAATGC 58.004 33.333 0.00 0.00 29.00 3.56
2891 5393 9.716531 GGAGTAGTAACTTGTAAGGTTGTTAAT 57.283 33.333 0.00 0.00 35.56 1.40
2973 5482 5.180304 GCTATATACCAAAAAGAGCAGCTCC 59.820 44.000 19.40 1.14 0.00 4.70
3039 5551 5.107109 TGACAACATTTGGACAATTCGAG 57.893 39.130 0.00 0.00 34.12 4.04
3046 5558 6.096141 ACTTGTGTAATGACAACATTTGGACA 59.904 34.615 0.00 0.00 43.17 4.02
3192 5704 7.412853 GTTGCAGATGAAATGATTACTACCAG 58.587 38.462 0.00 0.00 0.00 4.00
3195 5707 7.066284 ACAGGTTGCAGATGAAATGATTACTAC 59.934 37.037 2.33 0.00 0.00 2.73
3240 5753 9.260002 AGATACTGGCACAAAACAAAATTAAAG 57.740 29.630 0.00 0.00 38.70 1.85
3241 5754 9.606631 AAGATACTGGCACAAAACAAAATTAAA 57.393 25.926 0.00 0.00 38.70 1.52
3287 5800 7.466455 ATGCGAACATGTTAGCTTCATTAGAAG 60.466 37.037 33.78 1.01 43.63 2.85
3310 5823 3.465742 TGAGCATAGAGACTGGAATGC 57.534 47.619 0.00 0.00 43.97 3.56
3335 5848 3.071479 GCATGAAAGGTTTAGTCACGGA 58.929 45.455 0.00 0.00 0.00 4.69
3382 5895 6.839134 TCAGAAGGAGCCATGTTTATACTAGA 59.161 38.462 0.00 0.00 0.00 2.43
3431 5944 2.237143 GGATGGTGAGAGGTGTCAATGA 59.763 50.000 0.00 0.00 0.00 2.57
3523 6040 6.318900 GTCCTAGTCCTAATTGAAACCATTGG 59.681 42.308 0.00 0.00 0.00 3.16
3581 6099 4.072131 TCAAGTCAGAAATGTAACAGCCC 58.928 43.478 0.00 0.00 0.00 5.19
3792 6330 2.128035 CGATTAACTGACGGAGATGCC 58.872 52.381 0.00 0.00 0.00 4.40
3793 6331 1.523095 GCGATTAACTGACGGAGATGC 59.477 52.381 0.00 0.00 0.00 3.91
3794 6332 3.085443 AGCGATTAACTGACGGAGATG 57.915 47.619 0.00 0.00 0.00 2.90
3795 6333 3.884091 AGTAGCGATTAACTGACGGAGAT 59.116 43.478 0.00 0.00 0.00 2.75
3796 6334 3.064958 CAGTAGCGATTAACTGACGGAGA 59.935 47.826 0.00 0.00 44.79 3.71
3797 6335 3.364062 CAGTAGCGATTAACTGACGGAG 58.636 50.000 0.00 0.00 44.79 4.63
3798 6336 2.098607 CCAGTAGCGATTAACTGACGGA 59.901 50.000 5.18 0.00 44.79 4.69
3799 6337 2.460918 CCAGTAGCGATTAACTGACGG 58.539 52.381 5.18 0.00 44.79 4.79
3800 6338 2.159282 ACCCAGTAGCGATTAACTGACG 60.159 50.000 5.18 0.00 44.79 4.35
3801 6339 3.187700 CACCCAGTAGCGATTAACTGAC 58.812 50.000 5.18 0.00 44.79 3.51
3802 6340 2.167693 CCACCCAGTAGCGATTAACTGA 59.832 50.000 5.18 0.00 44.79 3.41
3803 6341 2.550978 CCACCCAGTAGCGATTAACTG 58.449 52.381 0.00 0.00 42.25 3.16
3804 6342 1.485066 CCCACCCAGTAGCGATTAACT 59.515 52.381 0.00 0.00 0.00 2.24
3805 6343 1.208776 ACCCACCCAGTAGCGATTAAC 59.791 52.381 0.00 0.00 0.00 2.01
3895 6433 3.325135 AGGATATAGCTAACTGGTGCCAC 59.675 47.826 0.00 0.00 0.00 5.01
4028 6573 5.065218 GTCGCATCACAGGAATTATCTTGTT 59.935 40.000 0.00 0.00 42.67 2.83
4049 6594 8.233868 TCACAACAGGAAACAATATATTTGTCG 58.766 33.333 0.00 0.00 0.00 4.35
4094 6639 3.627123 TCAGAACAACACAACTGATGGTG 59.373 43.478 0.00 0.00 40.79 4.17
4102 6647 2.161410 TGCACTGTCAGAACAACACAAC 59.839 45.455 6.91 0.00 34.24 3.32
4103 6648 2.161410 GTGCACTGTCAGAACAACACAA 59.839 45.455 10.32 0.00 35.46 3.33
4104 6649 1.737236 GTGCACTGTCAGAACAACACA 59.263 47.619 10.32 0.00 35.46 3.72
4105 6650 2.009774 AGTGCACTGTCAGAACAACAC 58.990 47.619 20.97 7.03 35.54 3.32
4106 6651 2.401583 AGTGCACTGTCAGAACAACA 57.598 45.000 20.97 0.00 34.24 3.33
4149 6694 5.564550 ACTTCCATGACACTAGATGCTTTT 58.435 37.500 0.00 0.00 0.00 2.27
4253 6798 4.645535 AGAAAATAACTGCTGCAGTCAGA 58.354 39.130 33.00 21.81 44.62 3.27
4352 6899 2.703536 TGCTCCCTACAGAACAGAAACA 59.296 45.455 0.00 0.00 0.00 2.83
4473 7021 1.282157 AGGGAAAACGGATAAGCAGCT 59.718 47.619 0.00 0.00 0.00 4.24
4481 7029 2.586648 AAGAAGCAGGGAAAACGGAT 57.413 45.000 0.00 0.00 0.00 4.18
4600 7149 7.441836 TCAATTCTATACATTGCGATACCACT 58.558 34.615 0.00 0.00 32.49 4.00
4630 7179 1.419387 ACAAGAACCTTCTGCAGCTCT 59.581 47.619 9.47 2.70 37.65 4.09
4696 7245 3.639094 CGTCCTCCTTGAGATTAGATGGT 59.361 47.826 0.00 0.00 0.00 3.55
4791 7340 4.089361 CAGGAAATTTGGTAAGAAGGCCT 58.911 43.478 0.00 0.00 0.00 5.19
4818 7367 2.507992 CTTCCGCAGTCTGCTCCG 60.508 66.667 22.13 9.76 42.25 4.63
4822 7371 3.254024 TTCCCCTTCCGCAGTCTGC 62.254 63.158 15.22 15.22 40.69 4.26
4849 7398 1.893137 ACTCGTCTATGTGGTCTTGCA 59.107 47.619 0.00 0.00 0.00 4.08
4897 7446 4.838152 GGCGGCGCATCTTCTCCA 62.838 66.667 34.36 0.00 0.00 3.86
5060 7609 1.880340 GCCGTCCATGCTCTTCTCG 60.880 63.158 0.00 0.00 0.00 4.04
5082 7631 2.936032 GAGGTGGCCAGGGAGGTT 60.936 66.667 5.11 0.00 40.61 3.50
5083 7632 4.270153 TGAGGTGGCCAGGGAGGT 62.270 66.667 5.11 0.00 40.61 3.85
5085 7634 3.406200 CCTGAGGTGGCCAGGGAG 61.406 72.222 5.11 0.00 45.66 4.30
5233 7785 0.464013 CAGGCAAGCATCCAGAGGAG 60.464 60.000 0.00 0.00 34.05 3.69
5255 7807 3.123050 TGAACAGATCAATGTATCGCCG 58.877 45.455 0.00 0.00 34.30 6.46
5302 7856 3.245658 TGTCAGTAGGAACTAGGAAGGCT 60.246 47.826 0.00 0.00 44.14 4.58
5410 7964 1.821241 CTGACAGCACAACACCGACG 61.821 60.000 0.00 0.00 0.00 5.12
5549 8103 8.250332 ACAGAAAACTCAAAAGAACAAAGCATA 58.750 29.630 0.00 0.00 0.00 3.14
5687 8241 6.881065 GCCATAGAGATCCAACATGCTTAATA 59.119 38.462 0.00 0.00 0.00 0.98
5691 8245 3.137913 AGCCATAGAGATCCAACATGCTT 59.862 43.478 0.00 0.00 0.00 3.91
5710 8741 0.680280 TGACTGACGAGGTAGGAGCC 60.680 60.000 0.00 0.00 0.00 4.70
5783 8816 1.950909 CGTTGGAGTTGGCCTAACAAA 59.049 47.619 16.93 8.10 41.88 2.83
5784 8817 1.600023 CGTTGGAGTTGGCCTAACAA 58.400 50.000 16.93 8.06 41.88 2.83
5823 8857 2.561569 GACGACCCCAAATGGACATAG 58.438 52.381 0.00 0.00 37.39 2.23
5831 8865 2.514803 CAGAAAAGGACGACCCCAAAT 58.485 47.619 0.00 0.00 36.73 2.32
5836 8870 1.534729 AATGCAGAAAAGGACGACCC 58.465 50.000 0.00 0.00 36.73 4.46
5925 9000 3.148412 CATGACTTTGTGGACATGGACA 58.852 45.455 0.00 0.00 37.18 4.02
5945 9020 8.811017 TCAGGTTTATTTTCAATATTTCAGCCA 58.189 29.630 0.00 0.00 0.00 4.75
6042 9125 3.712881 GACGGACAACACGGCAGC 61.713 66.667 0.00 0.00 39.67 5.25
6044 9127 1.593209 GAAGACGGACAACACGGCA 60.593 57.895 0.00 0.00 43.13 5.69
6051 9134 1.011968 CGGCGATTGAAGACGGACAA 61.012 55.000 0.00 0.00 36.29 3.18
6069 9152 3.384014 GACGACGAGGAGGACAGCG 62.384 68.421 0.00 0.00 0.00 5.18
6072 9155 1.001269 ATGGACGACGAGGAGGACA 60.001 57.895 0.00 0.00 0.00 4.02
6082 9165 1.153823 CGACCTCACCATGGACGAC 60.154 63.158 21.47 3.68 43.24 4.34
6206 9345 0.394216 TGGCAGCCACCACATACATC 60.394 55.000 11.22 0.00 33.75 3.06
6210 9349 0.473755 CCTATGGCAGCCACCACATA 59.526 55.000 19.10 3.59 44.17 2.29
6212 9351 2.230653 ACCTATGGCAGCCACCACA 61.231 57.895 19.10 1.06 44.17 4.17
6331 9503 1.380785 CAGCCCACCATCATTGCCT 60.381 57.895 0.00 0.00 0.00 4.75
6333 9505 1.682451 ATGCAGCCCACCATCATTGC 61.682 55.000 0.00 0.00 0.00 3.56
6431 9604 0.772124 AAAGCTGGAGGTCAAGGGGA 60.772 55.000 0.00 0.00 0.00 4.81
6477 9650 1.931841 CTCGACTTCATGATGGCACTG 59.068 52.381 14.35 0.00 0.00 3.66
6480 9653 0.462581 GCCTCGACTTCATGATGGCA 60.463 55.000 14.35 0.00 38.79 4.92
6529 9702 1.689575 GGAGGGTGCTCATGGACTCTA 60.690 57.143 0.00 0.00 45.61 2.43
6571 9747 2.361610 CACCACCTCCCACCATGC 60.362 66.667 0.00 0.00 0.00 4.06


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

AutoCloner maintained by Alex Coulton.