Multiple sequence alignment - TraesCS4A01G103000

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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 TraesCS4A01G103000 chr4A 100.000 7715 0 0 1 7715 115796348 115788634 0.000000e+00 14248.0
1 TraesCS4A01G103000 chr4A 79.503 483 86 11 7222 7696 901532 901055 1.600000e-86 331.0
2 TraesCS4A01G103000 chr4D 94.894 5464 175 44 174 5584 349182598 349188010 0.000000e+00 8449.0
3 TraesCS4A01G103000 chr4D 95.721 2010 69 5 5719 7715 349188000 349190005 0.000000e+00 3219.0
4 TraesCS4A01G103000 chr4D 79.917 483 84 11 7222 7696 630999 630522 7.410000e-90 342.0
5 TraesCS4A01G103000 chr4D 86.260 131 4 2 1 117 349182116 349182246 6.280000e-26 130.0
6 TraesCS4A01G103000 chr4D 95.349 43 2 0 133 175 349182283 349182325 1.390000e-07 69.4
7 TraesCS4A01G103000 chr4B 95.033 4288 154 35 60 4300 431787880 431792155 0.000000e+00 6684.0
8 TraesCS4A01G103000 chr4B 94.364 3123 108 29 4624 7715 431792689 431795774 0.000000e+00 4730.0
9 TraesCS4A01G103000 chr4B 94.915 354 9 3 4299 4644 431792315 431792667 5.260000e-151 545.0
10 TraesCS4A01G103000 chr4B 79.710 483 85 11 7222 7696 1243724 1244201 3.450000e-88 337.0
11 TraesCS4A01G103000 chr4B 77.083 432 83 14 7224 7647 654131546 654131123 1.290000e-57 235.0
12 TraesCS4A01G103000 chr4B 100.000 36 0 0 1 36 431787847 431787882 5.000000e-07 67.6
13 TraesCS4A01G103000 chr6A 92.656 1171 64 5 3159 4318 222558382 222557223 0.000000e+00 1666.0
14 TraesCS4A01G103000 chr7B 92.694 657 28 4 3668 4318 706224766 706225408 0.000000e+00 929.0
15 TraesCS4A01G103000 chr6B 92.237 657 30 6 3668 4318 119107589 119106948 0.000000e+00 911.0
16 TraesCS4A01G103000 chr1B 77.204 1316 267 26 1135 2436 44072049 44070753 0.000000e+00 737.0
17 TraesCS4A01G103000 chr1B 80.465 215 40 2 1336 1548 371475558 371475772 6.190000e-36 163.0
18 TraesCS4A01G103000 chr1D 76.841 1317 270 28 1135 2436 27900278 27898982 0.000000e+00 710.0
19 TraesCS4A01G103000 chr1A 76.780 1292 265 28 1160 2436 28762227 28760956 0.000000e+00 691.0
20 TraesCS4A01G103000 chr3B 84.848 396 45 13 2074 2465 311115050 311115434 1.210000e-102 385.0
21 TraesCS4A01G103000 chr3B 81.919 271 41 6 7437 7703 142722112 142722378 1.010000e-53 222.0
22 TraesCS4A01G103000 chr3B 75.912 411 94 5 1336 1743 769467584 769467992 1.010000e-48 206.0
23 TraesCS4A01G103000 chr3B 92.086 139 8 1 5539 5674 201519331 201519469 7.900000e-45 193.0
24 TraesCS4A01G103000 chr3A 83.770 382 49 10 2063 2440 336858505 336858877 4.430000e-92 350.0
25 TraesCS4A01G103000 chr3A 82.288 271 40 6 7437 7703 546572111 546572377 2.170000e-55 228.0
26 TraesCS4A01G103000 chr3A 82.114 246 36 6 1239 1483 692344733 692344971 3.650000e-48 204.0
27 TraesCS4A01G103000 chr5A 77.083 480 100 10 7222 7696 540054425 540053951 1.280000e-67 268.0
28 TraesCS4A01G103000 chr3D 83.333 306 32 12 2197 2500 216472760 216472472 1.650000e-66 265.0
29 TraesCS4A01G103000 chrUn 92.086 139 8 1 5539 5674 93419693 93419555 7.900000e-45 193.0
30 TraesCS4A01G103000 chrUn 92.086 139 8 1 5539 5674 383640630 383640492 7.900000e-45 193.0
31 TraesCS4A01G103000 chrUn 92.086 139 8 1 5539 5674 449523338 449523476 7.900000e-45 193.0
32 TraesCS4A01G103000 chr7A 92.086 139 8 1 5539 5674 201369671 201369533 7.900000e-45 193.0
33 TraesCS4A01G103000 chr5D 92.086 139 8 1 5539 5674 6196770 6196632 7.900000e-45 193.0
34 TraesCS4A01G103000 chr5D 92.086 139 8 1 5539 5674 503210564 503210702 7.900000e-45 193.0
35 TraesCS4A01G103000 chr5D 92.086 139 8 1 5539 5674 560877124 560877262 7.900000e-45 193.0
36 TraesCS4A01G103000 chr5D 90.667 75 6 1 1336 1409 88351902 88351828 1.770000e-16 99.0


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 TraesCS4A01G103000 chr4A 115788634 115796348 7714 True 14248.00 14248 100.000 1 7715 1 chr4A.!!$R2 7714
1 TraesCS4A01G103000 chr4D 349182116 349190005 7889 False 2966.85 8449 93.056 1 7715 4 chr4D.!!$F1 7714
2 TraesCS4A01G103000 chr4B 431787847 431795774 7927 False 3006.65 6684 96.078 1 7715 4 chr4B.!!$F2 7714
3 TraesCS4A01G103000 chr6A 222557223 222558382 1159 True 1666.00 1666 92.656 3159 4318 1 chr6A.!!$R1 1159
4 TraesCS4A01G103000 chr7B 706224766 706225408 642 False 929.00 929 92.694 3668 4318 1 chr7B.!!$F1 650
5 TraesCS4A01G103000 chr6B 119106948 119107589 641 True 911.00 911 92.237 3668 4318 1 chr6B.!!$R1 650
6 TraesCS4A01G103000 chr1B 44070753 44072049 1296 True 737.00 737 77.204 1135 2436 1 chr1B.!!$R1 1301
7 TraesCS4A01G103000 chr1D 27898982 27900278 1296 True 710.00 710 76.841 1135 2436 1 chr1D.!!$R1 1301
8 TraesCS4A01G103000 chr1A 28760956 28762227 1271 True 691.00 691 76.780 1160 2436 1 chr1A.!!$R1 1276

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
820 1162 0.451783 GAATCCACACCACCAATCGC 59.548 55.000 0.00 0.0 0.00 4.58 F
1752 2120 1.146041 TGCAGTCTGTGTGGTGACC 59.854 57.895 0.93 0.0 34.02 4.02 F
2172 2541 1.480954 TGCTCCGATAAGACAGGAACC 59.519 52.381 0.00 0.0 33.10 3.62 F
2632 3008 0.984995 GGCTCCCTGGTGGATATACC 59.015 60.000 0.00 0.0 44.07 2.73 F
3067 3447 1.001520 TGTCATTGTCCACCGTACCAG 59.998 52.381 0.00 0.0 0.00 4.00 F
4783 5401 0.396974 TTGTCTGCCTGGCCAAAGTT 60.397 50.000 17.53 0.0 0.00 2.66 F
4849 5467 1.438651 TGTTAGCCGTTCTCACATGC 58.561 50.000 0.00 0.0 0.00 4.06 F
6236 6868 0.396435 TTCTGGCAATGTCGGTGTCT 59.604 50.000 0.00 0.0 0.00 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2172 2541 0.401738 ACATCTGGTTGGTGGTCAGG 59.598 55.000 0.00 0.00 0.00 3.86 R
2586 2962 1.068474 CTCGACCAAAACCTAGCACG 58.932 55.000 0.00 0.00 0.00 5.34 R
3043 3423 4.080807 TGGTACGGTGGACAATGACAATAT 60.081 41.667 0.00 0.00 0.00 1.28 R
4560 5129 0.032615 AGTAGAGGCAGGACAGGGAG 60.033 60.000 0.00 0.00 0.00 4.30 R
4849 5467 0.946221 GGTCACAAGTCCACTCTGCG 60.946 60.000 0.00 0.00 0.00 5.18 R
5915 6547 0.332632 TTCCCAGGAAAGAGCCATGG 59.667 55.000 7.63 7.63 0.00 3.66 R
6368 7000 1.101049 AGCACCGTCCCACAAACTTG 61.101 55.000 0.00 0.00 0.00 3.16 R
7382 8045 1.442184 CGTGTCTCAGGAACGGTCG 60.442 63.158 0.00 0.00 33.77 4.79 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
359 670 4.705519 CCGGCAGCCACAAAAGCG 62.706 66.667 13.30 0.00 34.64 4.68
377 690 3.512516 GCACGCCCCTCTCAATGC 61.513 66.667 0.00 0.00 0.00 3.56
381 694 2.045926 GCCCCTCTCAATGCGTGT 60.046 61.111 0.00 0.00 0.00 4.49
382 695 2.401766 GCCCCTCTCAATGCGTGTG 61.402 63.158 0.00 0.00 0.00 3.82
425 738 3.471354 GGTACAGTGGCACATACCC 57.529 57.895 28.05 16.62 44.52 3.69
426 739 0.461339 GGTACAGTGGCACATACCCG 60.461 60.000 28.05 11.13 44.52 5.28
428 741 0.978151 TACAGTGGCACATACCCGTT 59.022 50.000 21.41 0.00 44.52 4.44
430 743 1.002624 AGTGGCACATACCCGTTGG 60.003 57.895 21.41 0.00 44.52 3.77
431 744 1.003112 GTGGCACATACCCGTTGGA 60.003 57.895 13.86 0.00 44.52 3.53
434 747 2.112815 GCACATACCCGTTGGAGGC 61.113 63.158 0.00 0.00 34.81 4.70
504 817 1.377536 GTCAAGCAAGGCATCTCTCC 58.622 55.000 0.00 0.00 0.00 3.71
559 872 7.994425 AATTAACCATTCGCCACATATCATA 57.006 32.000 0.00 0.00 0.00 2.15
560 873 8.579850 AATTAACCATTCGCCACATATCATAT 57.420 30.769 0.00 0.00 0.00 1.78
561 874 7.609760 TTAACCATTCGCCACATATCATATC 57.390 36.000 0.00 0.00 0.00 1.63
562 875 4.183865 ACCATTCGCCACATATCATATCG 58.816 43.478 0.00 0.00 0.00 2.92
563 876 4.081697 ACCATTCGCCACATATCATATCGA 60.082 41.667 0.00 0.00 0.00 3.59
566 879 6.456047 CCATTCGCCACATATCATATCGAAAG 60.456 42.308 3.74 0.63 37.86 2.62
567 880 5.134202 TCGCCACATATCATATCGAAAGT 57.866 39.130 0.00 0.00 0.00 2.66
568 881 4.923281 TCGCCACATATCATATCGAAAGTG 59.077 41.667 0.00 0.00 0.00 3.16
569 882 4.091945 CGCCACATATCATATCGAAAGTGG 59.908 45.833 6.71 6.71 42.38 4.00
596 909 2.584143 CGCCACGATAACGACCCC 60.584 66.667 0.00 0.00 42.66 4.95
597 910 2.202974 GCCACGATAACGACCCCC 60.203 66.667 0.00 0.00 42.66 5.40
621 935 1.738099 CGCTGACGAAAGGTCCCAG 60.738 63.158 0.00 0.00 45.46 4.45
631 945 1.264749 AAGGTCCCAGCTCATACGCA 61.265 55.000 0.00 0.00 0.00 5.24
632 946 1.050988 AGGTCCCAGCTCATACGCAT 61.051 55.000 0.00 0.00 0.00 4.73
654 968 1.648720 CACCCGCAGACACACAAAG 59.351 57.895 0.00 0.00 0.00 2.77
663 977 2.614057 CAGACACACAAAGGTCCAAGAC 59.386 50.000 0.00 0.00 34.58 3.01
678 1000 3.673484 GACGACGAACCACCCGGA 61.673 66.667 0.73 0.00 35.59 5.14
816 1158 2.226330 CTTTCGAATCCACACCACCAA 58.774 47.619 0.00 0.00 0.00 3.67
818 1160 2.107950 TCGAATCCACACCACCAATC 57.892 50.000 0.00 0.00 0.00 2.67
819 1161 0.726827 CGAATCCACACCACCAATCG 59.273 55.000 0.00 0.00 0.00 3.34
820 1162 0.451783 GAATCCACACCACCAATCGC 59.548 55.000 0.00 0.00 0.00 4.58
823 1165 2.034066 CACACCACCAATCGCCCT 59.966 61.111 0.00 0.00 0.00 5.19
825 1167 2.224159 ACACCACCAATCGCCCTCT 61.224 57.895 0.00 0.00 0.00 3.69
959 1327 1.740905 GAACCCTAGGTAGGAGCGC 59.259 63.158 8.29 0.00 46.63 5.92
1737 2105 1.653667 CATTGTCAACGGCAGTGCA 59.346 52.632 18.61 0.00 0.00 4.57
1752 2120 1.146041 TGCAGTCTGTGTGGTGACC 59.854 57.895 0.93 0.00 34.02 4.02
1914 2282 3.252215 TCTTGGTTTGGCTCATTAACGTG 59.748 43.478 0.00 0.00 0.00 4.49
2172 2541 1.480954 TGCTCCGATAAGACAGGAACC 59.519 52.381 0.00 0.00 33.10 3.62
2226 2595 2.037847 GCAATTGGGAGGTGGCCT 59.962 61.111 3.32 0.00 36.03 5.19
2541 2917 7.755822 ACGACACTGTCTCTATTTCATTAACTC 59.244 37.037 7.58 0.00 0.00 3.01
2544 2920 7.542477 ACACTGTCTCTATTTCATTAACTCACG 59.458 37.037 0.00 0.00 0.00 4.35
2586 2962 7.076842 ACTGTTGAGTGATTGTATTATGCAC 57.923 36.000 0.00 0.00 0.00 4.57
2591 2967 4.191544 AGTGATTGTATTATGCACGTGCT 58.808 39.130 37.59 25.63 42.66 4.40
2632 3008 0.984995 GGCTCCCTGGTGGATATACC 59.015 60.000 0.00 0.00 44.07 2.73
2912 3292 9.774742 GAAGGTATTTGGAATAATTCATATCGC 57.225 33.333 0.00 0.00 0.00 4.58
2932 3312 5.730550 TCGCTTAGTTCTGTTGTGGATTAT 58.269 37.500 0.00 0.00 0.00 1.28
2947 3327 7.263100 TGTGGATTATCATATGTTGCACTTC 57.737 36.000 16.40 3.99 0.00 3.01
2969 3349 8.204836 ACTTCTGTATTTCAAGTTGTCTAGTGT 58.795 33.333 2.11 0.00 0.00 3.55
2973 3353 8.583810 TGTATTTCAAGTTGTCTAGTGTGTAC 57.416 34.615 2.11 0.00 0.00 2.90
2978 3358 7.477144 TCAAGTTGTCTAGTGTGTACAAATG 57.523 36.000 0.00 0.00 35.08 2.32
3041 3421 5.489249 TGTAACGCTGGAAATAACATACCA 58.511 37.500 0.00 0.00 0.00 3.25
3043 3423 7.273712 TGTAACGCTGGAAATAACATACCATA 58.726 34.615 0.00 0.00 0.00 2.74
3067 3447 1.001520 TGTCATTGTCCACCGTACCAG 59.998 52.381 0.00 0.00 0.00 4.00
3073 3453 2.290464 TGTCCACCGTACCAGTTTTTG 58.710 47.619 0.00 0.00 0.00 2.44
3078 3458 1.314730 CCGTACCAGTTTTTGTGCCT 58.685 50.000 0.00 0.00 0.00 4.75
3499 3887 2.777832 ACAAGGAAGATCTGGCAGAC 57.222 50.000 21.37 13.66 0.00 3.51
3607 3996 4.654091 ATTCTGTGGTTTTGTTGGTCTG 57.346 40.909 0.00 0.00 0.00 3.51
3636 4025 3.008485 AGACCTTCTCACTCCATGGAAAC 59.992 47.826 17.00 0.00 0.00 2.78
3666 4055 6.737254 AATAAATATGCGGTCCTAATTCGG 57.263 37.500 0.00 0.00 0.00 4.30
3678 4067 3.689161 TCCTAATTCGGAAACTGCATGTG 59.311 43.478 0.00 0.00 0.00 3.21
3806 4195 5.133221 ACAGGTGATAACAAAGAAACAGCT 58.867 37.500 0.00 0.00 36.72 4.24
3901 4290 6.777782 AGGAATTTATGGCTCTTCCTGATAG 58.222 40.000 2.03 0.00 44.45 2.08
4229 4634 4.156922 ACCTTCTGACATCTCAAGAGTACG 59.843 45.833 0.00 0.00 0.00 3.67
4259 4664 4.201950 GGCTGCACCTAATCACTTTACATG 60.202 45.833 0.50 0.00 34.51 3.21
4387 4954 7.493971 AGTTGTTTTATGTAATGTTTGCTGCAA 59.506 29.630 11.69 11.69 0.00 4.08
4430 4997 5.034200 TCATCAACCCCTAAGGCTACTTTA 58.966 41.667 0.00 0.00 40.58 1.85
4441 5008 7.272978 CCTAAGGCTACTTTACTGCTGAATAA 58.727 38.462 0.00 0.00 38.14 1.40
4444 5011 6.292150 AGGCTACTTTACTGCTGAATAATCC 58.708 40.000 0.00 0.00 0.00 3.01
4448 5015 7.227512 GCTACTTTACTGCTGAATAATCCATGT 59.772 37.037 0.00 0.00 0.00 3.21
4560 5129 6.705825 ACCTTTCTGTTTTGATTTAATGGTGC 59.294 34.615 0.00 0.00 0.00 5.01
4576 5145 2.686835 GCTCCCTGTCCTGCCTCT 60.687 66.667 0.00 0.00 0.00 3.69
4613 5182 7.742556 TTGTGAAATGTGTTACTCATGATGA 57.257 32.000 0.00 0.00 0.00 2.92
4695 5313 8.882415 ATGAAAGGTATAAATCGACACGTATT 57.118 30.769 0.00 0.00 0.00 1.89
4783 5401 0.396974 TTGTCTGCCTGGCCAAAGTT 60.397 50.000 17.53 0.00 0.00 2.66
4801 5419 5.675684 AAGTTTTGGAAGTTGGAACACAT 57.324 34.783 0.00 0.00 39.29 3.21
4849 5467 1.438651 TGTTAGCCGTTCTCACATGC 58.561 50.000 0.00 0.00 0.00 4.06
4873 5491 3.561725 CAGAGTGGACTTGTGACCTTTTC 59.438 47.826 0.00 0.00 0.00 2.29
5143 5761 1.798223 TCGAACATTGGAGAAGTTGCG 59.202 47.619 0.00 0.00 0.00 4.85
5357 5975 9.284968 GCTACATGGTATGTTTTCCTGTATATT 57.715 33.333 0.00 0.00 41.63 1.28
5445 6063 3.979495 ACTGTGTTCTACGTAGCTTTTCG 59.021 43.478 18.00 7.32 0.00 3.46
5453 6071 2.968675 ACGTAGCTTTTCGGCAATAGT 58.031 42.857 0.00 0.00 34.17 2.12
5516 6134 2.796593 GCACTTCCACAACAAGCATTTC 59.203 45.455 0.00 0.00 0.00 2.17
5588 6206 3.703556 TCAACTGGGAGATGCTTCTCTAG 59.296 47.826 24.20 22.66 46.46 2.43
5601 6219 5.953571 TGCTTCTCTAGAGTGTCCCATATA 58.046 41.667 19.21 0.00 0.00 0.86
5603 6221 6.435591 TGCTTCTCTAGAGTGTCCCATATATG 59.564 42.308 19.21 5.68 0.00 1.78
5605 6223 7.362574 GCTTCTCTAGAGTGTCCCATATATGTC 60.363 44.444 19.21 1.79 0.00 3.06
5606 6224 7.336475 TCTCTAGAGTGTCCCATATATGTCT 57.664 40.000 19.21 8.79 0.00 3.41
5608 6226 7.667635 TCTCTAGAGTGTCCCATATATGTCTTG 59.332 40.741 19.21 7.64 0.00 3.02
5615 6237 8.589338 AGTGTCCCATATATGTCTTGTATCTTC 58.411 37.037 11.73 0.00 0.00 2.87
5620 6242 7.281774 CCCATATATGTCTTGTATCTTCCATGC 59.718 40.741 11.73 0.00 0.00 4.06
5621 6243 7.010830 CCATATATGTCTTGTATCTTCCATGCG 59.989 40.741 11.73 0.00 0.00 4.73
5622 6244 3.885724 TGTCTTGTATCTTCCATGCGA 57.114 42.857 0.00 0.00 0.00 5.10
5630 6252 4.391830 TGTATCTTCCATGCGAAAACTGTC 59.608 41.667 0.00 0.00 0.00 3.51
5643 6265 6.204688 TGCGAAAACTGTCAATTCTCATAAGT 59.795 34.615 0.00 0.00 0.00 2.24
5650 6272 8.908786 ACTGTCAATTCTCATAAGTTCTTCAA 57.091 30.769 0.00 0.00 0.00 2.69
5707 6329 9.661563 TTGTATACATTGAGGACTTACGAAAAT 57.338 29.630 6.36 0.00 0.00 1.82
5762 6384 4.114794 GTCTTTTGGCACATCATTATGGC 58.885 43.478 0.00 0.00 39.30 4.40
5769 6391 4.102996 TGGCACATCATTATGGCTCTTCTA 59.897 41.667 0.00 0.00 41.74 2.10
5786 6417 5.126067 TCTTCTAGCCCTATTGATTTGTGC 58.874 41.667 0.00 0.00 0.00 4.57
5830 6461 5.824904 ATGAATGGATGCAGTTGTACTTC 57.175 39.130 0.00 0.00 0.00 3.01
5915 6547 6.591935 TGGAATCTTTATCATCTGGTACACC 58.408 40.000 0.00 0.00 0.00 4.16
6089 6721 1.017387 CTTGCGATTACTTCCAGGGC 58.983 55.000 0.00 0.00 0.00 5.19
6119 6751 0.853530 AAGCAACAACCCTCTCCCTT 59.146 50.000 0.00 0.00 0.00 3.95
6236 6868 0.396435 TTCTGGCAATGTCGGTGTCT 59.604 50.000 0.00 0.00 0.00 3.41
6251 6883 3.653344 GGTGTCTTTTGGGCTTCATTTC 58.347 45.455 0.00 0.00 0.00 2.17
6311 6943 2.380064 TTGTGCCCCTCAGTTTCAAT 57.620 45.000 0.00 0.00 0.00 2.57
6368 7000 2.478200 GGTTCTCATCGACGAGGTTCTC 60.478 54.545 8.88 0.06 33.59 2.87
6380 7012 2.484770 CGAGGTTCTCAAGTTTGTGGGA 60.485 50.000 0.00 0.00 0.00 4.37
6436 7068 3.429684 GGAAAGCGGAAGGAAGAGTAGAG 60.430 52.174 0.00 0.00 0.00 2.43
6458 7090 8.415950 AGAGGGTAGTGATTGAGTATTAGATG 57.584 38.462 0.00 0.00 0.00 2.90
6600 7232 8.169839 TCGAGTTTAACAGACTCATTTATTCG 57.830 34.615 6.60 0.00 42.85 3.34
6659 7291 2.463752 ACAGCATGATTTCTTGCCCAT 58.536 42.857 13.09 0.00 44.97 4.00
6701 7334 9.453572 TCACTTATATCCATGAAATATTCTGCC 57.546 33.333 0.00 0.00 0.00 4.85
6757 7400 0.798776 GTCTCGGCCTTGTTCACATG 59.201 55.000 0.00 0.00 0.00 3.21
6798 7452 0.601311 CTGGAGTATAAGCCGCTGCC 60.601 60.000 0.00 0.00 38.69 4.85
6799 7453 1.048724 TGGAGTATAAGCCGCTGCCT 61.049 55.000 0.00 0.00 38.69 4.75
6825 7485 6.752168 TCTGCCGATCATATACATATCCATG 58.248 40.000 0.00 0.00 38.21 3.66
6861 7521 6.808008 TTGTGAAATCAGGAGAATCTGTTC 57.192 37.500 0.00 0.00 36.25 3.18
6877 7537 4.091549 TCTGTTCCTCCTTATTGGTACGT 58.908 43.478 0.00 0.00 37.07 3.57
6878 7538 4.529377 TCTGTTCCTCCTTATTGGTACGTT 59.471 41.667 0.00 0.00 37.07 3.99
6879 7539 5.716228 TCTGTTCCTCCTTATTGGTACGTTA 59.284 40.000 0.00 0.00 37.07 3.18
6890 7550 9.403110 CCTTATTGGTACGTTATACATCACTAC 57.597 37.037 0.00 0.00 0.00 2.73
6891 7551 9.403110 CTTATTGGTACGTTATACATCACTACC 57.597 37.037 0.00 0.00 0.00 3.18
6911 7571 9.666626 CACTACCTGATATAACTTTCTTCTACG 57.333 37.037 0.00 0.00 0.00 3.51
6983 7646 5.739752 TTGACATATACATGTGCTTCAGC 57.260 39.130 9.11 0.00 45.58 4.26
6995 7658 1.864711 TGCTTCAGCTTGTACAACGTC 59.135 47.619 3.59 0.00 42.66 4.34
7111 7774 3.857854 GTCATGGCAGCAGCGTCG 61.858 66.667 0.00 0.00 43.41 5.12
7150 7813 0.900647 ACAGGCTACGCTGAACCTCT 60.901 55.000 0.00 0.00 0.00 3.69
7435 8098 2.765807 AGGCTCACCATCTCCCGG 60.766 66.667 0.00 0.00 39.06 5.73
7657 8320 1.522580 GGCCATGAAGCTCTCGTCC 60.523 63.158 0.00 0.00 0.00 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
129 144 4.082517 GCAAAAGAGGAATTCTGGAAGGTC 60.083 45.833 5.23 0.00 35.91 3.85
359 670 2.825836 CATTGAGAGGGGCGTGCC 60.826 66.667 1.16 1.16 0.00 5.01
371 684 0.888736 CCTTGACCCACACGCATTGA 60.889 55.000 0.00 0.00 0.00 2.57
373 686 2.268076 GCCTTGACCCACACGCATT 61.268 57.895 0.00 0.00 0.00 3.56
374 687 2.672996 GCCTTGACCCACACGCAT 60.673 61.111 0.00 0.00 0.00 4.73
375 688 3.825160 GAGCCTTGACCCACACGCA 62.825 63.158 0.00 0.00 0.00 5.24
377 690 2.738521 CGAGCCTTGACCCACACG 60.739 66.667 0.00 0.00 0.00 4.49
381 694 3.706373 GCCTCGAGCCTTGACCCA 61.706 66.667 6.99 0.00 34.35 4.51
382 695 4.821589 CGCCTCGAGCCTTGACCC 62.822 72.222 6.99 0.00 38.78 4.46
410 723 0.605319 CAACGGGTATGTGCCACTGT 60.605 55.000 0.00 0.00 0.00 3.55
504 817 4.461198 GGTAAGGTATGGGGTTCTTGATG 58.539 47.826 0.00 0.00 0.00 3.07
544 857 5.405269 CACTTTCGATATGATATGTGGCGAA 59.595 40.000 0.00 0.00 34.93 4.70
559 872 2.358267 CGGCTAGTACTCCACTTTCGAT 59.642 50.000 0.00 0.00 38.80 3.59
560 873 1.741706 CGGCTAGTACTCCACTTTCGA 59.258 52.381 0.00 0.00 38.80 3.71
561 874 1.798079 GCGGCTAGTACTCCACTTTCG 60.798 57.143 0.00 0.00 38.80 3.46
562 875 1.471153 GGCGGCTAGTACTCCACTTTC 60.471 57.143 0.00 0.00 38.80 2.62
563 876 0.535797 GGCGGCTAGTACTCCACTTT 59.464 55.000 0.00 0.00 38.80 2.66
566 879 1.141234 GTGGCGGCTAGTACTCCAC 59.859 63.158 11.43 13.24 40.13 4.02
567 880 2.412323 CGTGGCGGCTAGTACTCCA 61.412 63.158 11.43 0.00 0.00 3.86
568 881 1.453762 ATCGTGGCGGCTAGTACTCC 61.454 60.000 11.43 0.00 0.00 3.85
569 882 1.233019 TATCGTGGCGGCTAGTACTC 58.767 55.000 11.43 0.00 0.00 2.59
613 926 1.050988 ATGCGTATGAGCTGGGACCT 61.051 55.000 0.00 0.00 38.13 3.85
621 935 1.598130 GGTGGGGATGCGTATGAGC 60.598 63.158 0.00 0.00 37.71 4.26
631 945 3.717294 GTGTCTGCGGGTGGGGAT 61.717 66.667 0.00 0.00 0.00 3.85
654 968 0.942884 GTGGTTCGTCGTCTTGGACC 60.943 60.000 0.00 0.00 33.30 4.46
678 1000 2.884087 AATAGTACGCTGCGCACGCT 62.884 55.000 23.51 16.26 42.51 5.07
693 1030 2.579207 TCGCGACAGGGAAGAAATAG 57.421 50.000 3.71 0.00 36.33 1.73
816 1158 0.325671 TGGGAGAAGAAGAGGGCGAT 60.326 55.000 0.00 0.00 0.00 4.58
818 1160 1.219393 GTGGGAGAAGAAGAGGGCG 59.781 63.158 0.00 0.00 0.00 6.13
819 1161 1.604915 GGTGGGAGAAGAAGAGGGC 59.395 63.158 0.00 0.00 0.00 5.19
820 1162 0.547712 TGGGTGGGAGAAGAAGAGGG 60.548 60.000 0.00 0.00 0.00 4.30
823 1165 1.201429 GGCTGGGTGGGAGAAGAAGA 61.201 60.000 0.00 0.00 0.00 2.87
825 1167 2.231380 GGGCTGGGTGGGAGAAGAA 61.231 63.158 0.00 0.00 0.00 2.52
931 1290 2.751436 TAGGGTTCCCGTCCGTCG 60.751 66.667 1.91 0.00 39.52 5.12
932 1291 2.421399 CCTAGGGTTCCCGTCCGTC 61.421 68.421 0.00 0.00 0.00 4.79
933 1292 1.863155 TACCTAGGGTTCCCGTCCGT 61.863 60.000 14.81 1.06 37.09 4.69
934 1293 1.076777 TACCTAGGGTTCCCGTCCG 60.077 63.158 14.81 0.00 37.09 4.79
935 1294 0.758310 CCTACCTAGGGTTCCCGTCC 60.758 65.000 14.81 0.00 39.86 4.79
959 1327 1.335496 GAGATTCGAACGGAGAGGAGG 59.665 57.143 0.00 0.00 0.00 4.30
988 1356 2.421248 CCTTGCCCATTTGTTTTGTGGT 60.421 45.455 0.00 0.00 0.00 4.16
1617 1985 0.540830 AAGAGGTCTCGCCAGTGAGT 60.541 55.000 8.01 0.00 40.61 3.41
1737 2105 1.046472 TTCCGGTCACCACACAGACT 61.046 55.000 0.00 0.00 35.18 3.24
1914 2282 5.695424 ACTCCCAGGTAAGGAAATACTTC 57.305 43.478 0.00 0.00 31.49 3.01
2172 2541 0.401738 ACATCTGGTTGGTGGTCAGG 59.598 55.000 0.00 0.00 0.00 3.86
2226 2595 8.653191 TCAACCTTAAAGTTCCTAAGTGTATCA 58.347 33.333 0.00 0.00 0.00 2.15
2474 2850 8.723942 AATTAGAGTGTAGAATTGGCAAGTAG 57.276 34.615 5.96 0.00 0.00 2.57
2516 2892 7.755373 TGAGTTAATGAAATAGAGACAGTGTCG 59.245 37.037 17.40 0.00 37.67 4.35
2541 2917 8.025243 ACAGTACAAGTGATAAAATTACCGTG 57.975 34.615 0.00 0.00 0.00 4.94
2586 2962 1.068474 CTCGACCAAAACCTAGCACG 58.932 55.000 0.00 0.00 0.00 5.34
2591 2967 4.076394 CCCATTTTCTCGACCAAAACCTA 58.924 43.478 0.63 0.00 0.00 3.08
2744 3124 6.622896 GCACCCTTCAAACAACATAGATACAC 60.623 42.308 0.00 0.00 0.00 2.90
2752 3132 2.362077 GACAGCACCCTTCAAACAACAT 59.638 45.455 0.00 0.00 0.00 2.71
2932 3312 7.920160 TGAAATACAGAAGTGCAACATATGA 57.080 32.000 10.38 0.00 41.43 2.15
2947 3327 7.715265 ACACACTAGACAACTTGAAATACAG 57.285 36.000 0.00 0.00 0.00 2.74
2973 3353 8.785946 AGCCAAATTCCAGAAAAATAACATTTG 58.214 29.630 0.00 0.00 32.52 2.32
3004 3384 7.653647 TCCAGCGTTACAAAGAATAAAATGTT 58.346 30.769 0.00 0.00 0.00 2.71
3018 3398 5.489249 TGGTATGTTATTTCCAGCGTTACA 58.511 37.500 0.00 0.00 0.00 2.41
3023 3403 8.946085 ACAATATATGGTATGTTATTTCCAGCG 58.054 33.333 0.00 0.00 33.33 5.18
3041 3421 6.183361 TGGTACGGTGGACAATGACAATATAT 60.183 38.462 0.00 0.00 0.00 0.86
3043 3423 4.080807 TGGTACGGTGGACAATGACAATAT 60.081 41.667 0.00 0.00 0.00 1.28
3067 3447 5.011090 AGAGAAAAGGAAGGCACAAAAAC 57.989 39.130 0.00 0.00 0.00 2.43
3073 3453 4.339530 AGTTTCAAGAGAAAAGGAAGGCAC 59.660 41.667 0.00 0.00 44.75 5.01
3078 3458 5.070685 GCCCTAGTTTCAAGAGAAAAGGAA 58.929 41.667 9.25 0.00 44.75 3.36
3499 3887 6.688637 TCTTCTCCATCATATGTTGCAAAG 57.311 37.500 0.00 9.99 0.00 2.77
3579 3968 6.016276 ACCAACAAAACCACAGAATATCAGAC 60.016 38.462 0.00 0.00 0.00 3.51
3636 4025 8.827177 TTAGGACCGCATATTTATTTACAGAG 57.173 34.615 0.00 0.00 0.00 3.35
3664 4053 4.219033 GTTAAAGACACATGCAGTTTCCG 58.781 43.478 0.00 0.00 0.00 4.30
3666 4055 6.437928 TGATGTTAAAGACACATGCAGTTTC 58.562 36.000 0.00 0.00 42.04 2.78
3901 4290 5.693555 CCTGTTTGCCTCAAAATCTTCTTTC 59.306 40.000 0.00 0.00 35.03 2.62
4210 4615 3.687125 ACCGTACTCTTGAGATGTCAGA 58.313 45.455 4.49 0.00 32.98 3.27
4252 4657 8.504815 CAAAATGGATTCAATTGCACATGTAAA 58.495 29.630 0.00 0.00 0.00 2.01
4259 4664 7.171337 ACACTAACAAAATGGATTCAATTGCAC 59.829 33.333 0.00 0.00 31.22 4.57
4387 4954 7.333323 TGATGAGTAACAGATCATTGTGATGT 58.667 34.615 0.00 0.00 37.20 3.06
4430 4997 8.046708 TGTTACTAACATGGATTATTCAGCAGT 58.953 33.333 0.00 0.00 36.25 4.40
4441 5008 8.758829 TGTATCTTGAGTGTTACTAACATGGAT 58.241 33.333 4.93 7.30 44.35 3.41
4444 5011 8.757164 TGTGTATCTTGAGTGTTACTAACATG 57.243 34.615 4.93 0.00 44.35 3.21
4560 5129 0.032615 AGTAGAGGCAGGACAGGGAG 60.033 60.000 0.00 0.00 0.00 4.30
4576 5145 8.458573 ACACATTTCACAAAAAGGATACAGTA 57.541 30.769 0.00 0.00 41.41 2.74
4613 5182 2.211250 AGCATGCATTCACAGAAGGT 57.789 45.000 21.98 0.00 0.00 3.50
4685 5303 2.365948 GCAATGCATGAATACGTGTCG 58.634 47.619 0.00 0.00 35.65 4.35
4849 5467 0.946221 GGTCACAAGTCCACTCTGCG 60.946 60.000 0.00 0.00 0.00 5.18
4873 5491 6.058183 CCTAACACATCATAAGGAGAAAGGG 58.942 44.000 0.00 0.00 0.00 3.95
5021 5639 9.061610 CAAACGAAATGGTTAAAACATAGCTAG 57.938 33.333 0.00 0.00 0.00 3.42
5143 5761 1.868519 GCCGACGTGAGGAATATGGAC 60.869 57.143 10.56 0.00 0.00 4.02
5357 5975 3.334583 GGATACTTGAGGAAGTGCACA 57.665 47.619 21.04 0.00 42.66 4.57
5432 6050 4.114058 ACTATTGCCGAAAAGCTACGTA 57.886 40.909 0.00 0.00 0.00 3.57
5475 6093 6.534634 AGTGCTGACTCTTTATAAGGTGTTT 58.465 36.000 4.11 0.00 0.00 2.83
5601 6219 4.406648 TCGCATGGAAGATACAAGACAT 57.593 40.909 0.00 0.00 0.00 3.06
5603 6221 5.122396 AGTTTTCGCATGGAAGATACAAGAC 59.878 40.000 0.00 0.00 35.70 3.01
5605 6223 5.106555 ACAGTTTTCGCATGGAAGATACAAG 60.107 40.000 0.00 0.00 35.70 3.16
5606 6224 4.759693 ACAGTTTTCGCATGGAAGATACAA 59.240 37.500 0.00 0.00 35.70 2.41
5608 6226 4.391830 TGACAGTTTTCGCATGGAAGATAC 59.608 41.667 0.00 0.00 35.70 2.24
5615 6237 4.161333 GAGAATTGACAGTTTTCGCATGG 58.839 43.478 0.00 0.00 0.00 3.66
5620 6242 8.499162 AGAACTTATGAGAATTGACAGTTTTCG 58.501 33.333 0.00 0.00 0.00 3.46
5643 6265 7.287061 TGGACCTTTTGAGTAAGATTGAAGAA 58.713 34.615 0.00 0.00 0.00 2.52
5686 6308 8.786826 AATCATTTTCGTAAGTCCTCAATGTA 57.213 30.769 0.00 0.00 39.48 2.29
5687 6309 7.687941 AATCATTTTCGTAAGTCCTCAATGT 57.312 32.000 0.00 0.00 39.48 2.71
5688 6310 8.970691 AAAATCATTTTCGTAAGTCCTCAATG 57.029 30.769 0.00 0.00 39.48 2.82
5689 6311 9.626045 GAAAAATCATTTTCGTAAGTCCTCAAT 57.374 29.630 0.00 0.00 43.47 2.57
5700 6322 9.194101 AGCTATGCTGGGAAAAATCATTTTCGT 62.194 37.037 0.00 0.00 44.94 3.85
5707 6329 3.701040 GGAAGCTATGCTGGGAAAAATCA 59.299 43.478 0.00 0.00 39.62 2.57
5762 6384 5.238214 GCACAAATCAATAGGGCTAGAAGAG 59.762 44.000 0.00 0.00 0.00 2.85
5769 6391 3.091633 AGTGCACAAATCAATAGGGCT 57.908 42.857 21.04 0.00 0.00 5.19
5830 6461 9.033481 ACACACATGTTCATAAATTTCAAACAG 57.967 29.630 14.44 10.61 34.46 3.16
5915 6547 0.332632 TTCCCAGGAAAGAGCCATGG 59.667 55.000 7.63 7.63 0.00 3.66
6089 6721 3.059257 GGGTTGTTGCTTTTATTTTGCCG 60.059 43.478 0.00 0.00 0.00 5.69
6119 6751 3.390967 TCTCAATGGACACCAAGACAGAA 59.609 43.478 0.00 0.00 36.95 3.02
6236 6868 4.840115 AGGATCAAGAAATGAAGCCCAAAA 59.160 37.500 0.00 0.00 42.54 2.44
6251 6883 2.969628 AAGGCACGTAGAGGATCAAG 57.030 50.000 0.00 0.00 37.82 3.02
6311 6943 1.810151 GCTACGACCAAAAGCCATTCA 59.190 47.619 0.00 0.00 0.00 2.57
6368 7000 1.101049 AGCACCGTCCCACAAACTTG 61.101 55.000 0.00 0.00 0.00 3.16
6436 7068 6.166982 GCCATCTAATACTCAATCACTACCC 58.833 44.000 0.00 0.00 0.00 3.69
6458 7090 3.468140 GTCTACTCCCCCGTGGCC 61.468 72.222 0.00 0.00 0.00 5.36
6647 7279 3.834231 ACTGCAGTAAATGGGCAAGAAAT 59.166 39.130 20.16 0.00 37.06 2.17
6701 7334 1.446907 GAGGTGTCACTGCATTCAGG 58.553 55.000 2.35 0.00 44.54 3.86
6757 7400 3.929610 GGATGAGTATAAGCAGAATCGCC 59.070 47.826 0.00 0.00 0.00 5.54
6798 7452 6.264067 TGGATATGTATATGATCGGCAGAGAG 59.736 42.308 0.00 0.00 0.00 3.20
6799 7453 6.129179 TGGATATGTATATGATCGGCAGAGA 58.871 40.000 0.00 0.00 0.00 3.10
6825 7485 6.385649 TGATTTCACAAAAGTAACCTCACC 57.614 37.500 0.00 0.00 0.00 4.02
6861 7521 7.597743 GTGATGTATAACGTACCAATAAGGAGG 59.402 40.741 0.00 0.00 41.22 4.30
6890 7550 9.582431 TTTCACGTAGAAGAAAGTTATATCAGG 57.418 33.333 0.00 0.00 37.57 3.86
6911 7571 6.252281 TGACAAACGATGTACAAACTTTCAC 58.748 36.000 0.00 0.00 44.12 3.18
6983 7646 1.121967 GCTTCGTCGACGTTGTACAAG 59.878 52.381 34.40 27.93 40.80 3.16
6995 7658 0.798776 AGCCAAAAGATGCTTCGTCG 59.201 50.000 0.00 0.00 32.94 5.12
7150 7813 3.587933 GTGCCCGTGAAAACGCCA 61.588 61.111 0.00 0.00 0.00 5.69
7382 8045 1.442184 CGTGTCTCAGGAACGGTCG 60.442 63.158 0.00 0.00 33.77 4.79
7414 8077 2.191641 GAGATGGTGAGCCTGGCC 59.808 66.667 16.57 7.66 35.27 5.36
7468 8131 2.046507 GTCCTGCTGGAGGTGCTG 60.047 66.667 13.36 0.00 44.16 4.41
7657 8320 1.450312 GTCGGCCAACATCCTCCTG 60.450 63.158 2.24 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.