Multiple sequence alignment - TraesCS5A01G376000

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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 TraesCS5A01G376000 chr5A 100.000 6513 0 0 1 6513 573754168 573760680 0.000000e+00 12028.0
1 TraesCS5A01G376000 chr5A 99.833 599 1 0 2452 3050 174601590 174600992 0.000000e+00 1101.0
2 TraesCS5A01G376000 chr5A 92.828 739 49 1 1 739 600200980 600201714 0.000000e+00 1068.0
3 TraesCS5A01G376000 chr5A 89.054 740 79 2 1 739 227127962 227128700 0.000000e+00 917.0
4 TraesCS5A01G376000 chr5A 87.912 91 6 3 749 839 573676268 573676353 1.160000e-17 102.0
5 TraesCS5A01G376000 chr5A 85.714 91 13 0 3196 3286 522102221 522102311 5.380000e-16 97.1
6 TraesCS5A01G376000 chr5D 92.825 3345 146 39 3052 6339 454803272 454806579 0.000000e+00 4761.0
7 TraesCS5A01G376000 chr5D 94.894 940 27 7 1532 2451 454802157 454803095 0.000000e+00 1450.0
8 TraesCS5A01G376000 chr5D 88.593 789 54 14 776 1530 454801272 454802058 0.000000e+00 926.0
9 TraesCS5A01G376000 chr5B 89.512 3280 216 43 3298 6513 556949236 556952451 0.000000e+00 4034.0
10 TraesCS5A01G376000 chr5B 99.833 599 1 0 2452 3050 48316275 48315677 0.000000e+00 1101.0
11 TraesCS5A01G376000 chr5B 85.442 838 90 16 1639 2451 556947926 556948756 0.000000e+00 843.0
12 TraesCS5A01G376000 chr5B 86.289 547 26 18 737 1246 556947128 556947662 3.430000e-152 549.0
13 TraesCS5A01G376000 chr5B 88.288 111 10 3 3076 3183 556948969 556949079 5.300000e-26 130.0
14 TraesCS5A01G376000 chr3A 95.670 739 31 1 1 739 574922465 574923202 0.000000e+00 1186.0
15 TraesCS5A01G376000 chr3A 86.239 109 13 2 3189 3296 78190503 78190610 4.130000e-22 117.0
16 TraesCS5A01G376000 chr7A 95.399 739 33 1 1 739 602991294 602992031 0.000000e+00 1175.0
17 TraesCS5A01G376000 chr7A 88.991 109 12 0 3185 3293 21353774 21353882 1.140000e-27 135.0
18 TraesCS5A01G376000 chr2D 93.919 740 42 3 1 739 566770223 566770960 0.000000e+00 1114.0
19 TraesCS5A01G376000 chr2A 99.834 601 1 0 2450 3050 602799679 602799079 0.000000e+00 1105.0
20 TraesCS5A01G376000 chr2A 99.833 599 1 0 2452 3050 518944211 518943613 0.000000e+00 1101.0
21 TraesCS5A01G376000 chr6B 99.833 599 1 0 2452 3050 606303260 606302662 0.000000e+00 1101.0
22 TraesCS5A01G376000 chr6B 86.739 739 98 0 1 739 9009669 9008931 0.000000e+00 822.0
23 TraesCS5A01G376000 chr4B 99.833 599 1 0 2452 3050 5372863 5373461 0.000000e+00 1101.0
24 TraesCS5A01G376000 chr3B 99.833 599 1 0 2452 3050 389957595 389958193 0.000000e+00 1101.0
25 TraesCS5A01G376000 chr3B 99.668 602 1 1 2449 3050 610171984 610172584 0.000000e+00 1099.0
26 TraesCS5A01G376000 chr3B 86.739 739 98 0 1 739 7157813 7157075 0.000000e+00 822.0
27 TraesCS5A01G376000 chr1B 99.833 599 1 0 2452 3050 451910458 451911056 0.000000e+00 1101.0
28 TraesCS5A01G376000 chr3D 88.949 742 78 3 1 739 584471072 584470332 0.000000e+00 913.0
29 TraesCS5A01G376000 chr7B 87.688 731 84 4 11 739 639358122 639357396 0.000000e+00 846.0
30 TraesCS5A01G376000 chr4A 86.087 115 12 3 3187 3300 5466221 5466332 3.190000e-23 121.0


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 TraesCS5A01G376000 chr5A 573754168 573760680 6512 False 12028 12028 100.00000 1 6513 1 chr5A.!!$F4 6512
1 TraesCS5A01G376000 chr5A 174600992 174601590 598 True 1101 1101 99.83300 2452 3050 1 chr5A.!!$R1 598
2 TraesCS5A01G376000 chr5A 600200980 600201714 734 False 1068 1068 92.82800 1 739 1 chr5A.!!$F5 738
3 TraesCS5A01G376000 chr5A 227127962 227128700 738 False 917 917 89.05400 1 739 1 chr5A.!!$F1 738
4 TraesCS5A01G376000 chr5D 454801272 454806579 5307 False 2379 4761 92.10400 776 6339 3 chr5D.!!$F1 5563
5 TraesCS5A01G376000 chr5B 556947128 556952451 5323 False 1389 4034 87.38275 737 6513 4 chr5B.!!$F1 5776
6 TraesCS5A01G376000 chr5B 48315677 48316275 598 True 1101 1101 99.83300 2452 3050 1 chr5B.!!$R1 598
7 TraesCS5A01G376000 chr3A 574922465 574923202 737 False 1186 1186 95.67000 1 739 1 chr3A.!!$F2 738
8 TraesCS5A01G376000 chr7A 602991294 602992031 737 False 1175 1175 95.39900 1 739 1 chr7A.!!$F2 738
9 TraesCS5A01G376000 chr2D 566770223 566770960 737 False 1114 1114 93.91900 1 739 1 chr2D.!!$F1 738
10 TraesCS5A01G376000 chr2A 602799079 602799679 600 True 1105 1105 99.83400 2450 3050 1 chr2A.!!$R2 600
11 TraesCS5A01G376000 chr2A 518943613 518944211 598 True 1101 1101 99.83300 2452 3050 1 chr2A.!!$R1 598
12 TraesCS5A01G376000 chr6B 606302662 606303260 598 True 1101 1101 99.83300 2452 3050 1 chr6B.!!$R2 598
13 TraesCS5A01G376000 chr6B 9008931 9009669 738 True 822 822 86.73900 1 739 1 chr6B.!!$R1 738
14 TraesCS5A01G376000 chr4B 5372863 5373461 598 False 1101 1101 99.83300 2452 3050 1 chr4B.!!$F1 598
15 TraesCS5A01G376000 chr3B 389957595 389958193 598 False 1101 1101 99.83300 2452 3050 1 chr3B.!!$F1 598
16 TraesCS5A01G376000 chr3B 610171984 610172584 600 False 1099 1099 99.66800 2449 3050 1 chr3B.!!$F2 601
17 TraesCS5A01G376000 chr3B 7157075 7157813 738 True 822 822 86.73900 1 739 1 chr3B.!!$R1 738
18 TraesCS5A01G376000 chr1B 451910458 451911056 598 False 1101 1101 99.83300 2452 3050 1 chr1B.!!$F1 598
19 TraesCS5A01G376000 chr3D 584470332 584471072 740 True 913 913 88.94900 1 739 1 chr3D.!!$R1 738
20 TraesCS5A01G376000 chr7B 639357396 639358122 726 True 846 846 87.68800 11 739 1 chr7B.!!$R1 728

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
837 852 0.168568 GTTCACTCCGTCTCCGTCTC 59.831 60.0 0.00 0.0 0.00 3.36 F
1315 1375 0.816825 ACCTGTGAGTGCTTGCAGTG 60.817 55.0 7.75 0.0 0.00 3.66 F
3068 3254 0.719465 GAATGTGGCGTTCACCTACG 59.281 55.0 8.20 0.0 45.48 3.51 F
4111 4360 0.839946 TCTAGGGAATTGCAGGGAGC 59.160 55.0 0.00 0.0 45.96 4.70 F
4444 4697 1.114627 GGCCCCAAGATCAATTGACC 58.885 55.0 11.07 0.0 31.55 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2549 2735 0.549950 AGCTTGCTATCCATGTGCCT 59.450 50.000 0.0 0.0 0.00 4.75 R
3283 3477 2.621556 TTTTAAGGCCCTGCTTGGAT 57.378 45.000 0.0 0.0 38.35 3.41 R
4184 4433 0.611200 CGGTGACCCAGACCATGTTA 59.389 55.000 0.0 0.0 32.45 2.41 R
5059 5341 1.021390 CGCCCCAGTCTGCAAAGTAG 61.021 60.000 0.0 0.0 0.00 2.57 R
5933 6235 1.144936 GGTCAGATTGCTCGGAGGG 59.855 63.158 7.2 0.0 0.00 4.30 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
27 28 6.334296 AGGGATTGATCTGGGAAGTATATCA 58.666 40.000 0.00 0.00 0.00 2.15
70 71 1.547820 CGACTCCGGATCATCCATCAT 59.452 52.381 3.57 0.00 35.91 2.45
272 273 6.810941 CCTCTTGGAAGCCTGAAACAGGAA 62.811 50.000 20.11 5.55 44.55 3.36
385 386 3.067470 TCTCCCAGACTCTATCCCTCAT 58.933 50.000 0.00 0.00 0.00 2.90
473 481 2.105477 AGACTCATTGTGCACCTGAAGT 59.895 45.455 15.69 12.67 0.00 3.01
474 482 2.880890 GACTCATTGTGCACCTGAAGTT 59.119 45.455 15.69 4.77 0.00 2.66
475 483 3.290710 ACTCATTGTGCACCTGAAGTTT 58.709 40.909 15.69 0.00 0.00 2.66
476 484 3.701040 ACTCATTGTGCACCTGAAGTTTT 59.299 39.130 15.69 0.00 0.00 2.43
562 572 6.677913 CATTGTTTATTTTCTGTCCGGAAGT 58.322 36.000 5.23 0.00 0.00 3.01
573 583 4.768448 TCTGTCCGGAAGTGTTACAATAGA 59.232 41.667 5.23 0.00 0.00 1.98
670 680 1.276622 AGATGGTTAACGGCTGGAGT 58.723 50.000 0.00 0.00 0.00 3.85
746 756 1.095807 GGCACGAAAGGCATAGGACC 61.096 60.000 0.00 0.00 0.00 4.46
820 835 0.179156 ACGTCGATGGCGTATTCGTT 60.179 50.000 9.90 0.00 41.06 3.85
833 848 0.170561 ATTCGTTCACTCCGTCTCCG 59.829 55.000 0.00 0.00 0.00 4.63
834 849 1.168407 TTCGTTCACTCCGTCTCCGT 61.168 55.000 0.00 0.00 0.00 4.69
835 850 1.154263 CGTTCACTCCGTCTCCGTC 60.154 63.158 0.00 0.00 0.00 4.79
836 851 1.575576 CGTTCACTCCGTCTCCGTCT 61.576 60.000 0.00 0.00 0.00 4.18
837 852 0.168568 GTTCACTCCGTCTCCGTCTC 59.831 60.000 0.00 0.00 0.00 3.36
838 853 0.959372 TTCACTCCGTCTCCGTCTCC 60.959 60.000 0.00 0.00 0.00 3.71
848 863 1.202663 TCTCCGTCTCCACCGATCTAG 60.203 57.143 0.00 0.00 0.00 2.43
919 957 2.441164 AGCGTCAGAGCCGATCCT 60.441 61.111 0.00 0.00 38.01 3.24
1010 1063 1.452833 GGTGAGCCATGGAGAAGCC 60.453 63.158 18.40 6.48 34.09 4.35
1169 1222 5.022021 CCTTCGCTCGTAATTTGATTTCAC 58.978 41.667 0.00 0.00 0.00 3.18
1179 1232 7.270365 TCGTAATTTGATTTCACTTCGATTTGC 59.730 33.333 0.00 0.00 0.00 3.68
1285 1344 2.128771 AGGTTGTTTGTGTCTGCAGT 57.871 45.000 14.67 0.00 0.00 4.40
1286 1345 3.275617 AGGTTGTTTGTGTCTGCAGTA 57.724 42.857 14.67 1.04 0.00 2.74
1297 1356 2.166459 TGTCTGCAGTAGTATGCCTCAC 59.834 50.000 14.67 0.00 45.91 3.51
1315 1375 0.816825 ACCTGTGAGTGCTTGCAGTG 60.817 55.000 7.75 0.00 0.00 3.66
1421 1485 5.462398 GGTAGATGATGTGAATTCGGTGTAC 59.538 44.000 0.04 0.00 0.00 2.90
1428 1492 4.951254 TGTGAATTCGGTGTACTCTTTGA 58.049 39.130 0.04 0.00 0.00 2.69
1432 1496 8.471609 TGTGAATTCGGTGTACTCTTTGATATA 58.528 33.333 0.04 0.00 0.00 0.86
1434 1498 9.476202 TGAATTCGGTGTACTCTTTGATATATG 57.524 33.333 0.04 0.00 0.00 1.78
1435 1499 9.692749 GAATTCGGTGTACTCTTTGATATATGA 57.307 33.333 0.00 0.00 0.00 2.15
1437 1501 9.698309 ATTCGGTGTACTCTTTGATATATGAAG 57.302 33.333 0.00 0.00 0.00 3.02
1438 1502 8.234136 TCGGTGTACTCTTTGATATATGAAGT 57.766 34.615 0.00 0.00 0.00 3.01
1476 1540 2.818132 CCTGACTGCCCGGAGATC 59.182 66.667 0.73 0.00 0.00 2.75
1530 1594 6.602803 TGGCATTCACATTTCACAGTACATAT 59.397 34.615 0.00 0.00 0.00 1.78
1569 1731 5.308825 TGAAGAAGGAAAATCTGTGTCCTC 58.691 41.667 0.00 0.00 41.03 3.71
1591 1754 7.446013 TCCTCCAACATAATTACTTGTTTTCGT 59.554 33.333 2.37 0.00 33.93 3.85
1635 1798 5.650543 AGTTGTGAAGCTTTTTAACTGGTG 58.349 37.500 17.09 0.00 0.00 4.17
1643 1806 6.670695 AGCTTTTTAACTGGTGAATGGATT 57.329 33.333 0.00 0.00 0.00 3.01
1849 2018 1.766494 TTGATTCATCTGGCCGCATT 58.234 45.000 0.00 0.00 0.00 3.56
1855 2024 5.534278 TGATTCATCTGGCCGCATTAAATTA 59.466 36.000 0.00 0.00 0.00 1.40
2038 2211 1.467342 GCGGTTGTTAGTGATGGTTCC 59.533 52.381 0.00 0.00 0.00 3.62
2052 2225 5.574443 GTGATGGTTCCGTACTACTGTTTAC 59.426 44.000 0.00 0.00 0.00 2.01
2180 2354 7.389232 TGTTAGTGATGACTGATGAGTTCAAT 58.611 34.615 0.00 0.00 32.78 2.57
2188 2362 9.545105 GATGACTGATGAGTTCAATCTAGAAAT 57.455 33.333 0.00 0.00 31.81 2.17
2189 2363 8.939201 TGACTGATGAGTTCAATCTAGAAATC 57.061 34.615 0.00 0.00 41.53 2.17
2194 2368 7.550551 TGATGAGTTCAATCTAGAAATCGCTTT 59.449 33.333 0.00 0.00 43.42 3.51
2298 2472 5.048013 TGCTATGCTTCTACTATATGTGCGT 60.048 40.000 0.00 0.00 0.00 5.24
2373 2559 3.788227 TGTCTCCACTGTTTGCCTATT 57.212 42.857 0.00 0.00 0.00 1.73
2434 2620 2.659063 CCGTGCATCCCTGTCCAGA 61.659 63.158 0.00 0.00 0.00 3.86
3050 3236 2.212652 CATCCGGCTTTGATTCGATGA 58.787 47.619 0.00 0.00 0.00 2.92
3068 3254 0.719465 GAATGTGGCGTTCACCTACG 59.281 55.000 8.20 0.00 45.48 3.51
3085 3277 4.142138 ACCTACGCTAACCTTGATTCTCAG 60.142 45.833 0.00 0.00 0.00 3.35
3130 3322 5.946942 AAGGATTGCACTGAGATTCTAGA 57.053 39.130 0.00 0.00 0.00 2.43
3283 3477 4.749099 GCAGCACACAAAATTTACATCCAA 59.251 37.500 0.00 0.00 0.00 3.53
3289 3483 7.360269 GCACACAAAATTTACATCCAATCCAAG 60.360 37.037 0.00 0.00 0.00 3.61
3395 3631 3.146066 AGTGGTCATAGCTTGCGAAAAA 58.854 40.909 0.00 0.00 0.00 1.94
3475 3718 9.574516 GTATATAATTTCTCAGAACCCACCAAT 57.425 33.333 0.00 0.00 0.00 3.16
3607 3851 1.053424 ACGTGCCACTTTCCCTCTTA 58.947 50.000 0.00 0.00 0.00 2.10
3608 3852 1.270678 ACGTGCCACTTTCCCTCTTAC 60.271 52.381 0.00 0.00 0.00 2.34
3782 4026 7.062749 AGATTTATCCTTAGTACGCCAATGA 57.937 36.000 0.00 0.00 0.00 2.57
3826 4073 6.478344 CCTTGATAGAGTTGTATGAGCTGTTC 59.522 42.308 0.00 0.00 0.00 3.18
3866 4113 5.123936 GGGTAATTTGACTACTCCATCCAC 58.876 45.833 0.00 0.00 0.00 4.02
4000 4249 7.977789 TTCTTGAGACAAAGTTGCACATATA 57.022 32.000 0.00 0.00 0.00 0.86
4054 4303 6.657836 AAGGATAACGGTATTTCAGTTTCG 57.342 37.500 0.00 0.00 36.09 3.46
4060 4309 5.996669 ACGGTATTTCAGTTTCGAAAGTT 57.003 34.783 15.54 4.33 38.24 2.66
4104 4353 3.084786 ACAACAGCTTCTAGGGAATTGC 58.915 45.455 0.00 0.00 0.00 3.56
4111 4360 0.839946 TCTAGGGAATTGCAGGGAGC 59.160 55.000 0.00 0.00 45.96 4.70
4164 4413 5.221641 GGGGTTTAAGTTCCTGATTTTGCTT 60.222 40.000 0.00 0.00 0.00 3.91
4165 4414 5.926542 GGGTTTAAGTTCCTGATTTTGCTTC 59.073 40.000 0.00 0.00 0.00 3.86
4166 4415 5.629435 GGTTTAAGTTCCTGATTTTGCTTCG 59.371 40.000 0.00 0.00 0.00 3.79
4172 4421 2.552315 TCCTGATTTTGCTTCGTTGTCC 59.448 45.455 0.00 0.00 0.00 4.02
4182 4431 1.466167 CTTCGTTGTCCTCATGCCAAG 59.534 52.381 0.00 0.00 0.00 3.61
4184 4433 1.278985 TCGTTGTCCTCATGCCAAGAT 59.721 47.619 0.00 0.00 0.00 2.40
4298 4547 7.963981 CAGTAATGGATATTGCTGGTATTACG 58.036 38.462 9.37 0.00 46.74 3.18
4435 4688 2.799576 TTGGTACTGGCCCCAAGAT 58.200 52.632 7.07 0.00 35.84 2.40
4444 4697 1.114627 GGCCCCAAGATCAATTGACC 58.885 55.000 11.07 0.00 31.55 4.02
4446 4699 2.027385 GCCCCAAGATCAATTGACCTC 58.973 52.381 11.07 5.58 31.55 3.85
4478 4731 2.372074 TATGGCCCCGAGGACCAAC 61.372 63.158 0.00 0.00 42.80 3.77
4498 4751 3.294750 CATGCCAGCCATGTTGCT 58.705 55.556 0.00 0.00 45.05 3.91
4632 4890 5.011023 GGAAGATTGACTTGGACCACAAAAT 59.989 40.000 0.00 0.00 38.91 1.82
4691 4949 7.654022 TTTCCCAAGTAAATTGAAGTCTTGT 57.346 32.000 0.00 0.00 41.83 3.16
4761 5019 3.390135 TGTGAGCTTCCAAGTTTAGTCG 58.610 45.455 0.00 0.00 0.00 4.18
4933 5214 4.770795 TCTCACTTAGGGCATTTTAGCTC 58.229 43.478 0.00 0.00 34.37 4.09
4934 5215 4.225042 TCTCACTTAGGGCATTTTAGCTCA 59.775 41.667 0.00 0.00 37.50 4.26
4935 5216 4.517285 TCACTTAGGGCATTTTAGCTCAG 58.483 43.478 0.00 0.00 37.50 3.35
4948 5229 5.897377 TTTAGCTCAGGAAACATTTAGGC 57.103 39.130 0.00 0.00 0.00 3.93
4956 5237 2.760092 GGAAACATTTAGGCTGGCATCA 59.240 45.455 3.38 0.00 0.00 3.07
4960 5241 4.395959 ACATTTAGGCTGGCATCAATTG 57.604 40.909 3.38 0.00 0.00 2.32
5040 5321 5.238650 CAGTAGAAGTTTTCGGAATTGTGGT 59.761 40.000 0.00 0.00 34.02 4.16
5059 5341 6.226052 TGTGGTCTAATGATCATCATACTGC 58.774 40.000 9.06 5.51 35.76 4.40
5235 5517 0.247736 AGCTGAGGTACCTTCTTGCG 59.752 55.000 17.53 2.55 0.00 4.85
5333 5616 3.107601 ACGGGATGATTCTCTTCTCCAA 58.892 45.455 0.00 0.00 0.00 3.53
5515 5799 5.780282 TCTTGAAACTCCTCTGGAATAGTCA 59.220 40.000 0.00 0.00 0.00 3.41
5614 5898 7.373493 ACAAGCTATCTTCATCCTTTGTTTTG 58.627 34.615 0.00 0.00 0.00 2.44
5616 5900 5.713861 AGCTATCTTCATCCTTTGTTTTGCT 59.286 36.000 0.00 0.00 0.00 3.91
5696 5981 7.038587 TGTGTACATAACTGGACTTGGTAGATT 60.039 37.037 0.00 0.00 37.11 2.40
5753 6038 4.000988 AGATGGACACCACGTAATTGTTC 58.999 43.478 0.00 0.00 35.80 3.18
5824 6109 6.873605 TGTTTGTAAGATCTAGTGTGACATGG 59.126 38.462 0.00 0.00 0.00 3.66
5893 6194 5.196341 CAATGTGCATTGCCTATCTGAAT 57.804 39.130 11.33 0.00 41.27 2.57
5959 6261 0.107945 AGCAATCTGACCTCGCTTCC 60.108 55.000 0.00 0.00 0.00 3.46
5973 6275 2.158769 TCGCTTCCATATGGTTGCATCT 60.159 45.455 27.73 0.00 35.49 2.90
5994 6296 2.231964 TGATTTGATTGTCAAGCAGGGC 59.768 45.455 3.40 0.00 37.70 5.19
6004 6306 2.603008 AGCAGGGCTGGTTGTTGT 59.397 55.556 0.00 0.00 38.24 3.32
6030 6332 3.934068 TCCTTTTCGTTAGGGCAGTTAG 58.066 45.455 0.00 0.00 33.41 2.34
6033 6335 1.272807 TTCGTTAGGGCAGTTAGGCT 58.727 50.000 0.00 0.00 43.56 4.58
6097 6406 8.867112 ACGATAATGAACTAACAACGATGTAT 57.133 30.769 0.00 0.00 39.40 2.29
6155 6465 8.391075 TGCAAAGTATTTAGTTCAGCTTAAGT 57.609 30.769 4.02 0.00 35.03 2.24
6156 6466 8.846211 TGCAAAGTATTTAGTTCAGCTTAAGTT 58.154 29.630 4.02 0.00 35.03 2.66
6190 6501 2.291930 TGCGGGGAAATTATGAGGGTTT 60.292 45.455 0.00 0.00 0.00 3.27
6209 6520 5.186198 GGTTTGTGGCTATAGACAATGACT 58.814 41.667 10.67 0.00 32.99 3.41
6212 6523 4.030216 TGTGGCTATAGACAATGACTGGA 58.970 43.478 10.67 0.00 32.99 3.86
6306 6617 3.895656 CCTATCTTCGAATAGGGTGGACA 59.104 47.826 14.61 0.00 43.13 4.02
6309 6620 2.496070 TCTTCGAATAGGGTGGACACTG 59.504 50.000 0.00 0.00 0.00 3.66
6327 6638 6.882678 GGACACTGTGTACCCTTATTAACATT 59.117 38.462 14.31 0.00 0.00 2.71
6350 6661 2.474410 AAATGTCGGAAGTGAGGGAC 57.526 50.000 0.00 0.00 0.00 4.46
6364 6675 0.743345 AGGGACTTTTATCGTGGCGC 60.743 55.000 0.00 0.00 27.25 6.53
6414 6725 1.213537 GCACATTGCTCACGCCAAT 59.786 52.632 0.00 0.00 40.96 3.16
6420 6731 0.310543 TTGCTCACGCCAATTCACAC 59.689 50.000 0.00 0.00 34.43 3.82
6421 6732 1.210155 GCTCACGCCAATTCACACC 59.790 57.895 0.00 0.00 0.00 4.16
6436 6747 4.217754 TCACACCGTTTTCAATTGCTAC 57.782 40.909 0.00 0.00 0.00 3.58
6446 6757 7.066525 CCGTTTTCAATTGCTACCCTATTCTTA 59.933 37.037 0.00 0.00 0.00 2.10
6487 6798 8.908786 TCTTGATTCTCTTTTCTGCTTTTCTA 57.091 30.769 0.00 0.00 0.00 2.10
6492 6803 9.824534 GATTCTCTTTTCTGCTTTTCTAGAAAG 57.175 33.333 17.05 12.56 42.08 2.62
6502 6813 7.171678 TCTGCTTTTCTAGAAAGAACTTACTGC 59.828 37.037 17.05 11.50 41.48 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 6.143206 TGAAGGTGATATACTTCCCAGATCA 58.857 40.000 0.00 0.00 41.78 2.92
27 28 5.351458 GTTGAGTGCAAGAATTTTGAAGGT 58.649 37.500 0.00 0.00 34.01 3.50
272 273 6.670027 CCCAGGCTATACCAGTCTATTCTATT 59.330 42.308 0.00 0.00 36.98 1.73
284 285 2.076184 GGTGGCCCAGGCTATACCA 61.076 63.158 18.79 3.61 43.14 3.25
385 386 9.268268 ACTCAAAGAACGACACTTTCAAATATA 57.732 29.630 0.00 0.00 35.74 0.86
473 481 0.178984 GGGACGGGGTGAAGGAAAAA 60.179 55.000 0.00 0.00 0.00 1.94
474 482 1.063654 AGGGACGGGGTGAAGGAAAA 61.064 55.000 0.00 0.00 0.00 2.29
475 483 1.063654 AAGGGACGGGGTGAAGGAAA 61.064 55.000 0.00 0.00 0.00 3.13
476 484 0.178897 TAAGGGACGGGGTGAAGGAA 60.179 55.000 0.00 0.00 0.00 3.36
515 524 5.649395 TGCAAAGTCATCCATCTTCTTTAGG 59.351 40.000 0.00 0.00 0.00 2.69
598 608 0.685097 GACTAGTGTGGAGGGTGCAA 59.315 55.000 0.00 0.00 0.00 4.08
643 653 6.053005 CCAGCCGTTAACCATCTTCTATTTA 58.947 40.000 0.00 0.00 0.00 1.40
676 686 0.106519 GGCAGGTATCAAGGTGGCAT 60.107 55.000 0.00 0.00 35.63 4.40
746 756 1.808411 AGATTGTGTGGGCTTGTACG 58.192 50.000 0.00 0.00 0.00 3.67
833 848 0.308376 GCGTCTAGATCGGTGGAGAC 59.692 60.000 13.92 0.00 35.91 3.36
834 849 0.818445 GGCGTCTAGATCGGTGGAGA 60.818 60.000 13.92 0.00 0.00 3.71
835 850 0.820074 AGGCGTCTAGATCGGTGGAG 60.820 60.000 13.92 0.00 0.00 3.86
836 851 0.818445 GAGGCGTCTAGATCGGTGGA 60.818 60.000 13.92 0.00 0.00 4.02
837 852 0.820074 AGAGGCGTCTAGATCGGTGG 60.820 60.000 7.25 0.00 0.00 4.61
838 853 0.589223 GAGAGGCGTCTAGATCGGTG 59.411 60.000 9.29 0.00 30.97 4.94
848 863 3.063084 AGTGGACGGAGAGGCGTC 61.063 66.667 0.00 0.00 34.71 5.19
897 935 3.826754 CGGCTCTGACGCTGGCTA 61.827 66.667 0.00 0.00 32.64 3.93
919 957 2.713967 GCGAGGTTACGGGGCTGTA 61.714 63.158 0.00 0.00 0.00 2.74
967 1019 4.753662 TCCTCCCCCTCGTCGTGG 62.754 72.222 6.36 6.36 0.00 4.94
1169 1222 1.428448 TGTGTCGGAGCAAATCGAAG 58.572 50.000 0.00 0.00 37.14 3.79
1179 1232 2.732366 CGGTATTCTCATGTGTCGGAG 58.268 52.381 0.00 0.00 0.00 4.63
1257 1316 6.183360 GCAGACACAAACAACCTATGATACTC 60.183 42.308 0.00 0.00 0.00 2.59
1297 1356 1.947013 CACTGCAAGCACTCACAGG 59.053 57.895 0.00 0.00 37.60 4.00
1315 1375 0.523519 GCTCTAAACCAAGCACCAGC 59.476 55.000 0.00 0.00 38.42 4.85
1428 1492 7.070821 ACCCGACTTTCAGGTTACTTCATATAT 59.929 37.037 0.00 0.00 0.00 0.86
1432 1496 3.326880 ACCCGACTTTCAGGTTACTTCAT 59.673 43.478 0.00 0.00 0.00 2.57
1434 1498 3.397849 ACCCGACTTTCAGGTTACTTC 57.602 47.619 0.00 0.00 0.00 3.01
1435 1499 3.118149 ACAACCCGACTTTCAGGTTACTT 60.118 43.478 0.00 0.00 41.97 2.24
1436 1500 2.436911 ACAACCCGACTTTCAGGTTACT 59.563 45.455 0.00 0.00 41.97 2.24
1437 1501 2.546789 CACAACCCGACTTTCAGGTTAC 59.453 50.000 0.00 0.00 41.97 2.50
1438 1502 2.841215 CACAACCCGACTTTCAGGTTA 58.159 47.619 0.00 0.00 41.97 2.85
1489 1553 3.560636 TGCCACCTAGAAATTCTAGCC 57.439 47.619 21.35 11.17 43.89 3.93
1517 1581 9.990360 TCAACTTGTAAGAATATGTACTGTGAA 57.010 29.630 0.00 0.00 0.00 3.18
1530 1594 7.279615 TCCTTCTTCATGTCAACTTGTAAGAA 58.720 34.615 14.91 14.91 32.87 2.52
1569 1731 8.964420 ATCACGAAAACAAGTAATTATGTTGG 57.036 30.769 5.44 2.44 39.57 3.77
1635 1798 7.506938 TCCCAGATTTCTATCCAAAATCCATTC 59.493 37.037 5.26 0.00 41.82 2.67
1643 1806 7.661437 CGATAACATCCCAGATTTCTATCCAAA 59.339 37.037 0.00 0.00 0.00 3.28
1808 1971 5.987019 AACTATTAGGGGCCAAAGTATGA 57.013 39.130 4.39 0.00 0.00 2.15
1982 2152 2.554032 ACCATCACTTAACAGCAGCAAC 59.446 45.455 0.00 0.00 0.00 4.17
2038 2211 6.417044 GGTATGCTCATGTAAACAGTAGTACG 59.583 42.308 0.00 0.00 0.00 3.67
2180 2354 8.408743 GCTTAACTCTAAAAGCGATTTCTAGA 57.591 34.615 0.00 8.22 38.80 2.43
2259 2433 7.977853 AGAAGCATAGCACTTGGAATTTTTATG 59.022 33.333 0.00 0.00 0.00 1.90
2373 2559 6.169094 TGCAAAGAGGAAAACAATCAAACAA 58.831 32.000 0.00 0.00 0.00 2.83
2434 2620 2.831526 GTTGTAACCATTTCAGGGGCAT 59.168 45.455 0.00 0.00 0.00 4.40
2549 2735 0.549950 AGCTTGCTATCCATGTGCCT 59.450 50.000 0.00 0.00 0.00 4.75
3130 3322 6.017109 CACATTCTACAGCTGTTTTAGGTTGT 60.017 38.462 27.06 18.27 34.17 3.32
3171 3364 5.418840 CAGGGCCTAACATGTACTTGATTTT 59.581 40.000 5.28 2.64 0.00 1.82
3283 3477 2.621556 TTTTAAGGCCCTGCTTGGAT 57.378 45.000 0.00 0.00 38.35 3.41
3289 3483 6.961360 ATAGAGTAAATTTTAAGGCCCTGC 57.039 37.500 0.00 0.00 0.00 4.85
3395 3631 7.332926 CACATGTAAGAATGAGAGCACTTAACT 59.667 37.037 0.00 0.00 0.00 2.24
3475 3718 1.879575 AGCCAATAGGGTACAGAGCA 58.120 50.000 0.00 0.00 45.70 4.26
3668 3912 2.852748 CGTAGCGAGTATATCTGCCAC 58.147 52.381 0.00 0.00 0.00 5.01
3716 3960 9.658799 GCATGCTTAATTGGAGAATAGAGTATA 57.341 33.333 11.37 0.00 0.00 1.47
3720 3964 6.872628 TGCATGCTTAATTGGAGAATAGAG 57.127 37.500 20.33 0.00 0.00 2.43
3782 4026 8.599624 ATCAAGGAAATCAGACCAATAACAAT 57.400 30.769 0.00 0.00 0.00 2.71
3792 4036 9.039870 CATACAACTCTATCAAGGAAATCAGAC 57.960 37.037 0.00 0.00 0.00 3.51
3841 4088 5.251932 TGGATGGAGTAGTCAAATTACCCAA 59.748 40.000 0.00 0.00 30.51 4.12
4024 4273 9.020731 ACTGAAATACCGTTATCCTTTGAAATT 57.979 29.630 0.00 0.00 0.00 1.82
4038 4287 5.277634 CCAACTTTCGAAACTGAAATACCGT 60.278 40.000 6.47 0.00 37.24 4.83
4041 4290 6.956047 AGTCCAACTTTCGAAACTGAAATAC 58.044 36.000 6.47 0.33 37.24 1.89
4054 4303 2.029918 GCATGGGTGAAGTCCAACTTTC 60.030 50.000 0.00 0.00 38.80 2.62
4060 4309 1.685224 GAGGCATGGGTGAAGTCCA 59.315 57.895 0.00 0.00 38.82 4.02
4104 4353 1.376543 CAGTTGTGCTATGCTCCCTG 58.623 55.000 0.00 0.00 0.00 4.45
4131 4380 6.492087 TCAGGAACTTAAACCCCAAGTAATTG 59.508 38.462 0.00 0.00 34.60 2.32
4164 4413 0.684535 TCTTGGCATGAGGACAACGA 59.315 50.000 0.00 0.00 40.44 3.85
4165 4414 1.742761 ATCTTGGCATGAGGACAACG 58.257 50.000 9.09 0.00 40.44 4.10
4166 4415 4.009675 TGTTATCTTGGCATGAGGACAAC 58.990 43.478 14.86 12.52 40.44 3.32
4172 4421 4.275196 CAGACCATGTTATCTTGGCATGAG 59.725 45.833 9.09 0.00 41.62 2.90
4182 4431 2.741878 CGGTGACCCAGACCATGTTATC 60.742 54.545 0.00 0.00 32.45 1.75
4184 4433 0.611200 CGGTGACCCAGACCATGTTA 59.389 55.000 0.00 0.00 32.45 2.41
4444 4697 2.941415 GCCATACCTCCAACCTTGTGAG 60.941 54.545 0.00 0.00 0.00 3.51
4446 4699 1.463674 GCCATACCTCCAACCTTGTG 58.536 55.000 0.00 0.00 0.00 3.33
4478 4731 1.138036 CAACATGGCTGGCATGTCG 59.862 57.895 38.78 29.63 41.85 4.35
4498 4751 2.716424 ACCTTCCCTCCATTTCAACTCA 59.284 45.455 0.00 0.00 0.00 3.41
4921 5202 4.725790 ATGTTTCCTGAGCTAAAATGCC 57.274 40.909 0.00 0.00 0.00 4.40
4933 5214 2.170166 TGCCAGCCTAAATGTTTCCTG 58.830 47.619 0.00 0.00 0.00 3.86
4934 5215 2.603075 TGCCAGCCTAAATGTTTCCT 57.397 45.000 0.00 0.00 0.00 3.36
4935 5216 2.760092 TGATGCCAGCCTAAATGTTTCC 59.240 45.455 0.00 0.00 0.00 3.13
4956 5237 4.893424 ACACAAGTCTAACAACGCAATT 57.107 36.364 0.00 0.00 0.00 2.32
4960 5241 6.071463 CAGAATTACACAAGTCTAACAACGC 58.929 40.000 0.00 0.00 36.99 4.84
5040 5321 9.702494 CAAAGTAGCAGTATGATGATCATTAGA 57.298 33.333 13.81 0.00 39.69 2.10
5059 5341 1.021390 CGCCCCAGTCTGCAAAGTAG 61.021 60.000 0.00 0.00 0.00 2.57
5235 5517 8.311650 TGACACTTTAGAAGAAGAATAAGCAC 57.688 34.615 0.00 0.00 0.00 4.40
5287 5569 5.869888 AGATAGACAAAACGGCACTAGAAAG 59.130 40.000 0.00 0.00 0.00 2.62
5333 5616 7.304497 AGAGGTACAGTTCAAATAACACTCT 57.696 36.000 0.00 0.00 0.00 3.24
5574 5858 3.911661 GCTTGTTGCTTCACTTCTCAT 57.088 42.857 0.00 0.00 38.95 2.90
5616 5900 7.160049 TGGAAGAATAAATGCTGCAATTTTCA 58.840 30.769 6.36 0.00 32.16 2.69
5671 5956 6.276832 TCTACCAAGTCCAGTTATGTACAC 57.723 41.667 0.00 0.00 0.00 2.90
5753 6038 1.956629 AACCCTACAGCGACCATCCG 61.957 60.000 0.00 0.00 0.00 4.18
5824 6109 5.170748 CCAGATTACCATTTGTTTTCTGGC 58.829 41.667 3.36 0.00 42.80 4.85
5913 6215 1.391485 GCATAGCTGCCGTAATCATCG 59.609 52.381 0.00 0.00 42.88 3.84
5933 6235 1.144936 GGTCAGATTGCTCGGAGGG 59.855 63.158 7.20 0.00 0.00 4.30
5959 6261 7.207383 ACAATCAAATCAGATGCAACCATATG 58.793 34.615 0.00 0.00 41.01 1.78
5973 6275 2.231964 GCCCTGCTTGACAATCAAATCA 59.768 45.455 0.00 0.00 35.73 2.57
5994 6296 4.739716 CGAAAAGGAATTCACAACAACCAG 59.260 41.667 7.93 0.00 0.00 4.00
6004 6306 3.756434 CTGCCCTAACGAAAAGGAATTCA 59.244 43.478 7.93 0.00 36.08 2.57
6030 6332 8.913656 GTTAGTTCATTATCGTATACTTCAGCC 58.086 37.037 0.56 0.00 0.00 4.85
6033 6335 9.961265 CTGGTTAGTTCATTATCGTATACTTCA 57.039 33.333 0.56 0.00 0.00 3.02
6034 6336 9.962783 ACTGGTTAGTTCATTATCGTATACTTC 57.037 33.333 0.56 0.00 31.66 3.01
6042 6344 6.281405 AGCCTAACTGGTTAGTTCATTATCG 58.719 40.000 16.24 2.89 43.53 2.92
6165 6475 2.362077 CCTCATAATTTCCCCGCAAAGG 59.638 50.000 0.00 0.00 40.63 3.11
6190 6501 4.030216 TCCAGTCATTGTCTATAGCCACA 58.970 43.478 0.00 0.00 0.00 4.17
6209 6520 2.171840 GTGAGCTCTACACCTCTTCCA 58.828 52.381 16.19 0.00 32.84 3.53
6212 6523 1.178276 CCGTGAGCTCTACACCTCTT 58.822 55.000 16.19 0.00 35.17 2.85
6231 6542 2.354259 CCTTGCAATGTCTCTCACTCC 58.646 52.381 0.00 0.00 0.00 3.85
6282 6593 4.773149 GTCCACCCTATTCGAAGATAGGAT 59.227 45.833 21.44 6.19 38.90 3.24
6333 6644 1.645710 AAGTCCCTCACTTCCGACAT 58.354 50.000 0.00 0.00 42.07 3.06
6339 6650 3.933332 CCACGATAAAAGTCCCTCACTTC 59.067 47.826 0.00 0.00 45.32 3.01
6343 6654 1.404986 CGCCACGATAAAAGTCCCTCA 60.405 52.381 0.00 0.00 0.00 3.86
6364 6675 4.992319 TGTTGAGGGTACATAACTTGTTCG 59.008 41.667 0.00 0.00 39.87 3.95
6366 6677 7.648039 TTTTGTTGAGGGTACATAACTTGTT 57.352 32.000 0.00 0.00 39.87 2.83
6414 6725 3.791973 AGCAATTGAAAACGGTGTGAA 57.208 38.095 10.34 0.00 0.00 3.18
6420 6731 5.357032 AGAATAGGGTAGCAATTGAAAACGG 59.643 40.000 10.34 0.00 0.00 4.44
6421 6732 6.436843 AGAATAGGGTAGCAATTGAAAACG 57.563 37.500 10.34 0.00 0.00 3.60
6454 6765 9.683069 GCAGAAAAGAGAATCAAGAAAAATACA 57.317 29.630 0.00 0.00 37.82 2.29
6455 6766 9.905171 AGCAGAAAAGAGAATCAAGAAAAATAC 57.095 29.630 0.00 0.00 37.82 1.89
6459 6770 9.305925 GAAAAGCAGAAAAGAGAATCAAGAAAA 57.694 29.630 0.00 0.00 37.82 2.29
6467 6778 9.566432 TCTTTCTAGAAAAGCAGAAAAGAGAAT 57.434 29.630 18.25 0.00 39.58 2.40
6487 6798 4.020662 CAGAGGGAGCAGTAAGTTCTTTCT 60.021 45.833 0.00 0.00 0.00 2.52


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

AutoCloner maintained by Alex Coulton.