Multiple sequence alignment - TraesCS1B01G258600

Loading Multiple Alignment...

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 TraesCS1B01G258600 chr1B 100.000 3815 0 0 1 3815 455986945 455983131 0.000000e+00 7046.0
1 TraesCS1B01G258600 chr1B 86.957 69 9 0 604 672 681799411 681799479 1.140000e-10 78.7
2 TraesCS1B01G258600 chr1B 89.130 46 4 1 599 643 681799526 681799481 5.320000e-04 56.5
3 TraesCS1B01G258600 chr1D 95.780 2867 96 10 750 3602 340525506 340522651 0.000000e+00 4601.0
4 TraesCS1B01G258600 chr1D 85.897 780 70 19 1 765 340526550 340525796 0.000000e+00 795.0
5 TraesCS1B01G258600 chr1D 83.544 158 12 3 3610 3753 182052338 182052181 6.650000e-28 135.0
6 TraesCS1B01G258600 chr1D 96.610 59 2 0 3609 3667 379922594 379922652 8.720000e-17 99.0
7 TraesCS1B01G258600 chr1D 93.023 43 0 2 3712 3754 279120553 279120592 4.120000e-05 60.2
8 TraesCS1B01G258600 chr1A 94.477 2897 109 19 750 3607 440074860 440071976 0.000000e+00 4416.0
9 TraesCS1B01G258600 chr1A 84.272 515 54 11 254 765 440075579 440075089 9.590000e-131 477.0
10 TraesCS1B01G258600 chr1A 87.455 279 18 2 1 262 440076168 440075890 4.790000e-79 305.0
11 TraesCS1B01G258600 chr1A 96.923 65 2 0 3609 3673 546237438 546237502 4.030000e-20 110.0
12 TraesCS1B01G258600 chr1A 86.207 87 9 2 604 687 587666977 587666891 1.460000e-14 91.6
13 TraesCS1B01G258600 chr5D 84.375 160 10 6 3610 3754 2786283 2786442 3.970000e-30 143.0
14 TraesCS1B01G258600 chr5D 96.923 65 2 0 3609 3673 446576043 446575979 4.030000e-20 110.0
15 TraesCS1B01G258600 chr5D 94.828 58 2 1 619 676 324101087 324101031 5.250000e-14 89.8
16 TraesCS1B01G258600 chr5A 83.125 160 11 8 3609 3753 112319397 112319555 8.600000e-27 132.0
17 TraesCS1B01G258600 chr6B 98.413 63 1 0 3609 3671 698032092 698032154 1.120000e-20 111.0
18 TraesCS1B01G258600 chr4B 96.970 66 2 0 3609 3674 85939383 85939318 1.120000e-20 111.0
19 TraesCS1B01G258600 chr4B 96.923 65 2 0 3609 3673 496964680 496964616 4.030000e-20 110.0
20 TraesCS1B01G258600 chrUn 96.923 65 2 0 3609 3673 175473804 175473868 4.030000e-20 110.0
21 TraesCS1B01G258600 chr6D 96.923 65 2 0 3609 3673 86728347 86728411 4.030000e-20 110.0
22 TraesCS1B01G258600 chr7D 80.588 170 8 9 3609 3754 480055889 480055721 1.450000e-19 108.0
23 TraesCS1B01G258600 chr3D 95.385 65 3 0 3609 3673 42401917 42401853 1.870000e-18 104.0
24 TraesCS1B01G258600 chr3D 89.412 85 5 3 3674 3754 291224076 291224160 1.870000e-18 104.0
25 TraesCS1B01G258600 chr3D 93.023 43 0 2 3712 3754 420536955 420536994 4.120000e-05 60.2
26 TraesCS1B01G258600 chr2D 88.235 85 6 3 3674 3754 154634232 154634148 8.720000e-17 99.0
27 TraesCS1B01G258600 chr2D 93.023 43 0 2 3712 3754 602420938 602420899 4.120000e-05 60.2
28 TraesCS1B01G258600 chr3A 86.420 81 7 3 3678 3754 172969211 172969131 6.790000e-13 86.1


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 TraesCS1B01G258600 chr1B 455983131 455986945 3814 True 7046.000000 7046 100.000000 1 3815 1 chr1B.!!$R1 3814
1 TraesCS1B01G258600 chr1D 340522651 340526550 3899 True 2698.000000 4601 90.838500 1 3602 2 chr1D.!!$R2 3601
2 TraesCS1B01G258600 chr1A 440071976 440076168 4192 True 1732.666667 4416 88.734667 1 3607 3 chr1A.!!$R2 3606

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
863 1512 0.552848 ACCCAATCAATCCTCCGCAT 59.447 50.000 0.00 0.0 0.00 4.73 F
864 1513 1.063717 ACCCAATCAATCCTCCGCATT 60.064 47.619 0.00 0.0 0.00 3.56 F
2379 3041 0.830648 TCCCCGATGTTGTCATCCTC 59.169 55.000 3.17 0.0 45.32 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2196 2858 0.584396 GATTTGTGAACACGGCGTCA 59.416 50.000 10.85 1.75 0.0 4.35 R
2469 3131 1.131126 CGCAACCTCACTTTAGCCATG 59.869 52.381 0.00 0.00 0.0 3.66 R
3611 4305 0.185175 AGTCCCTGGAACCAAACACC 59.815 55.000 0.00 0.00 0.0 4.16 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
59 60 4.220602 TCCATTTCGACTTCTCATCTGACA 59.779 41.667 0.00 0.00 0.00 3.58
86 104 2.143925 GCTATCCCGGCTTTGTCATAC 58.856 52.381 0.00 0.00 0.00 2.39
113 131 1.270907 AGATGGACCTGACACTCACC 58.729 55.000 0.00 0.00 0.00 4.02
148 166 3.900966 TGTCAATCCTCCTGTGATCAG 57.099 47.619 0.00 0.00 41.01 2.90
161 179 4.818005 CCTGTGATCAGTATTGCTTATGCA 59.182 41.667 0.00 0.00 42.56 3.96
215 233 4.021456 GGCTGTTAGGGCAAAACATTAGTT 60.021 41.667 4.61 0.00 40.40 2.24
263 600 5.250200 GTTCTACATGGGTATGGTGTTTGA 58.750 41.667 0.00 0.00 38.66 2.69
282 622 3.930336 TGAAGCGAAGACAATGTGAGAT 58.070 40.909 0.00 0.00 0.00 2.75
297 637 4.700700 TGTGAGATAGATTGTGGCATCAG 58.299 43.478 0.00 0.00 0.00 2.90
314 654 4.319766 GCATCAGTTGGTTGTGTCTAACAG 60.320 45.833 0.00 0.00 40.74 3.16
344 684 6.183360 ACAACAAACTCTTGAGAAATCTTGGG 60.183 38.462 4.49 1.39 36.33 4.12
361 701 7.630242 ATCTTGGGTATCACAAAATGTACAG 57.370 36.000 0.33 0.00 0.00 2.74
415 755 7.066887 TGTGACATAATTCCTGCGTATCAAAAT 59.933 33.333 0.00 0.00 0.00 1.82
417 757 9.283768 TGACATAATTCCTGCGTATCAAAATAT 57.716 29.630 0.00 0.00 0.00 1.28
424 764 8.589335 TTCCTGCGTATCAAAATATAAGAGTC 57.411 34.615 0.00 0.00 0.00 3.36
425 765 7.722363 TCCTGCGTATCAAAATATAAGAGTCA 58.278 34.615 0.00 0.00 0.00 3.41
426 766 7.867909 TCCTGCGTATCAAAATATAAGAGTCAG 59.132 37.037 0.00 0.00 0.00 3.51
427 767 7.867909 CCTGCGTATCAAAATATAAGAGTCAGA 59.132 37.037 0.00 0.00 0.00 3.27
428 768 9.416794 CTGCGTATCAAAATATAAGAGTCAGAT 57.583 33.333 0.00 0.00 0.00 2.90
429 769 9.764363 TGCGTATCAAAATATAAGAGTCAGATT 57.236 29.630 0.00 0.00 0.00 2.40
469 809 8.738645 ATATTTTGACACAGAGGGAGTATTTC 57.261 34.615 0.00 0.00 0.00 2.17
472 812 3.056821 TGACACAGAGGGAGTATTTCACG 60.057 47.826 0.00 0.00 33.09 4.35
496 836 3.322191 ACCCACCTAACCAAACATGTT 57.678 42.857 4.92 4.92 0.00 2.71
513 853 2.649516 TGTTAAGTCACGGTTACGACG 58.350 47.619 0.00 0.00 44.60 5.12
543 883 8.185505 GGACAAACACACAACTAAATTTAGACA 58.814 33.333 27.92 0.00 34.84 3.41
545 885 9.730420 ACAAACACACAACTAAATTTAGACATC 57.270 29.630 27.92 0.00 34.84 3.06
561 901 9.775854 ATTTAGACATCTCATTCTAACCATGAG 57.224 33.333 0.00 3.88 46.32 2.90
573 913 2.097160 CATGAGCTGAACGTGCGC 59.903 61.111 0.00 0.00 35.28 6.09
588 928 1.090728 TGCGCAAACAAGTCACAAGA 58.909 45.000 8.16 0.00 0.00 3.02
589 929 1.675483 TGCGCAAACAAGTCACAAGAT 59.325 42.857 8.16 0.00 0.00 2.40
610 951 8.939929 CAAGATTTTCTCTCTGCAAATACTACA 58.060 33.333 0.00 0.00 31.03 2.74
662 1005 4.928020 GCTAAACTAGCCTACAAAACGACT 59.072 41.667 0.00 0.00 45.95 4.18
700 1043 5.361571 TGAGGGAGTATAACGTTCTGCATAA 59.638 40.000 2.82 0.00 0.00 1.90
758 1406 1.135228 CGGCTCCAAATAAAAACCCCG 60.135 52.381 0.00 0.00 0.00 5.73
764 1413 4.633175 TCCAAATAAAAACCCCGAAAAGC 58.367 39.130 0.00 0.00 0.00 3.51
783 1432 1.923899 CATATGCATTTTGTGGCGCA 58.076 45.000 10.83 0.00 39.01 6.09
784 1433 2.269172 CATATGCATTTTGTGGCGCAA 58.731 42.857 10.83 9.85 38.01 4.85
785 1434 1.993542 TATGCATTTTGTGGCGCAAG 58.006 45.000 13.78 3.91 38.47 4.01
863 1512 0.552848 ACCCAATCAATCCTCCGCAT 59.447 50.000 0.00 0.00 0.00 4.73
864 1513 1.063717 ACCCAATCAATCCTCCGCATT 60.064 47.619 0.00 0.00 0.00 3.56
865 1514 1.610522 CCCAATCAATCCTCCGCATTC 59.389 52.381 0.00 0.00 0.00 2.67
1115 1777 4.426313 GGACCCCAAGAAGCCCGG 62.426 72.222 0.00 0.00 0.00 5.73
1179 1841 2.567049 CTCGGCGTCGTCTTCCTT 59.433 61.111 10.18 0.00 37.69 3.36
1257 1919 2.202932 CAGCATTACCTCGGCGCT 60.203 61.111 7.64 0.00 0.00 5.92
1395 2057 1.112916 CCAACCCCACCAACTTCACC 61.113 60.000 0.00 0.00 0.00 4.02
1522 2184 3.939939 TCACCAAGCTGAGCGCCA 61.940 61.111 2.29 0.10 40.39 5.69
1554 2216 2.664851 TTCACGTTCTGGGCGCTG 60.665 61.111 7.64 1.03 0.00 5.18
1916 2578 2.357034 GCTCGCCAGGAACGACAA 60.357 61.111 0.00 0.00 35.35 3.18
2028 2690 1.299976 GGAGAGCAACGGATGGGTT 59.700 57.895 0.00 0.00 0.00 4.11
2151 2813 1.599047 CATCCGCAACCTCCTGACT 59.401 57.895 0.00 0.00 0.00 3.41
2196 2858 3.649986 GCAGTGACACGCCGCTTT 61.650 61.111 10.16 0.00 0.00 3.51
2211 2873 2.010670 CTTTGACGCCGTGTTCACA 58.989 52.632 0.00 0.00 0.00 3.58
2220 2882 1.604604 CCGTGTTCACAAATCCCAGT 58.395 50.000 3.87 0.00 0.00 4.00
2262 2924 2.542020 TCACAAGCATCTTCAACGGA 57.458 45.000 0.00 0.00 0.00 4.69
2379 3041 0.830648 TCCCCGATGTTGTCATCCTC 59.169 55.000 3.17 0.00 45.32 3.71
2482 3144 0.739462 CGGCGTCATGGCTAAAGTGA 60.739 55.000 0.00 0.00 42.02 3.41
2592 3254 5.121380 ACAAGATGGAGCTATTCAATGGT 57.879 39.130 0.00 0.00 0.00 3.55
2821 3483 4.401519 CCATCTGCAATGGATGAAACTCTT 59.598 41.667 17.90 0.00 42.02 2.85
2853 3517 1.195448 CTCGGTAAGTTTGTGCAGCTG 59.805 52.381 10.11 10.11 0.00 4.24
2869 3533 5.179368 GTGCAGCTGAATTGTGTAAACTAGA 59.821 40.000 20.43 0.00 0.00 2.43
3008 3672 3.919216 AGCTATGTCGCTGTTATGATCC 58.081 45.455 0.00 0.00 39.16 3.36
3040 3704 0.317479 CCAGGAAGGTCGAAGTTCGT 59.683 55.000 23.67 5.47 41.35 3.85
3058 3722 1.465387 CGTTCGATCGGAGCTAGCTAT 59.535 52.381 19.38 7.84 0.00 2.97
3066 3730 1.620819 CGGAGCTAGCTATGGGTGAAT 59.379 52.381 19.38 0.00 0.00 2.57
3142 3806 4.148079 TGCAATTTGAGTGGGTCATGTTA 58.852 39.130 0.00 0.00 34.17 2.41
3244 3916 0.535102 AGTGCCTTCAGGTGTTTCCG 60.535 55.000 0.00 0.00 41.99 4.30
3303 3975 1.881973 GTGAGCTGCCTGATTTGAACA 59.118 47.619 0.00 0.00 0.00 3.18
3304 3976 2.095364 GTGAGCTGCCTGATTTGAACAG 60.095 50.000 0.00 0.00 35.43 3.16
3306 3978 1.884579 AGCTGCCTGATTTGAACAGTG 59.115 47.619 0.00 0.00 34.04 3.66
3307 3979 1.881973 GCTGCCTGATTTGAACAGTGA 59.118 47.619 0.00 0.00 34.04 3.41
3308 3980 2.095364 GCTGCCTGATTTGAACAGTGAG 60.095 50.000 0.00 0.00 34.04 3.51
3447 4125 7.813148 GCTGTCTTAGTAATCTAATTATGCCGA 59.187 37.037 0.00 0.00 35.87 5.54
3517 4211 9.372369 AGAAAGTTTAGTACTATGTCAGATTGC 57.628 33.333 2.79 0.00 35.54 3.56
3557 4251 6.425114 TCTTACTCTGTTCATTCTTGTTCAGC 59.575 38.462 0.00 0.00 0.00 4.26
3625 4319 4.191243 GGGGGTGTTTGGTTCCAG 57.809 61.111 0.00 0.00 0.00 3.86
3626 4320 1.533033 GGGGGTGTTTGGTTCCAGG 60.533 63.158 0.00 0.00 0.00 4.45
3627 4321 1.533033 GGGGTGTTTGGTTCCAGGG 60.533 63.158 0.00 0.00 0.00 4.45
3628 4322 1.539665 GGGTGTTTGGTTCCAGGGA 59.460 57.895 0.00 0.00 0.00 4.20
3629 4323 0.826256 GGGTGTTTGGTTCCAGGGAC 60.826 60.000 0.00 0.00 0.00 4.46
3630 4324 0.185175 GGTGTTTGGTTCCAGGGACT 59.815 55.000 0.00 0.00 43.88 3.85
3631 4325 1.411074 GGTGTTTGGTTCCAGGGACTT 60.411 52.381 0.00 0.00 34.60 3.01
3632 4326 2.384828 GTGTTTGGTTCCAGGGACTTT 58.615 47.619 0.00 0.00 34.60 2.66
3633 4327 2.764010 GTGTTTGGTTCCAGGGACTTTT 59.236 45.455 0.00 0.00 34.60 2.27
3634 4328 3.196901 GTGTTTGGTTCCAGGGACTTTTT 59.803 43.478 0.00 0.00 34.60 1.94
3673 4367 7.597288 AAAAAGTCCCTAGCAAACTAAACAT 57.403 32.000 0.00 0.00 0.00 2.71
3674 4368 7.597288 AAAAGTCCCTAGCAAACTAAACATT 57.403 32.000 0.00 0.00 0.00 2.71
3675 4369 7.597288 AAAGTCCCTAGCAAACTAAACATTT 57.403 32.000 0.00 0.00 0.00 2.32
3676 4370 6.575162 AGTCCCTAGCAAACTAAACATTTG 57.425 37.500 0.00 0.00 39.57 2.32
3687 4381 8.871686 CAAACTAAACATTTGCTAAAAGTCCT 57.128 30.769 0.00 0.00 30.77 3.85
3688 4382 9.313118 CAAACTAAACATTTGCTAAAAGTCCTT 57.687 29.630 0.00 0.00 30.77 3.36
3691 4385 9.569122 ACTAAACATTTGCTAAAAGTCCTTAGA 57.431 29.630 11.46 0.00 31.59 2.10
3694 4388 6.914259 ACATTTGCTAAAAGTCCTTAGAAGC 58.086 36.000 0.00 0.00 31.59 3.86
3695 4389 6.490040 ACATTTGCTAAAAGTCCTTAGAAGCA 59.510 34.615 6.73 6.73 31.59 3.91
3696 4390 5.941948 TTGCTAAAAGTCCTTAGAAGCAC 57.058 39.130 9.21 0.00 31.59 4.40
3697 4391 5.228945 TGCTAAAAGTCCTTAGAAGCACT 57.771 39.130 6.73 0.00 31.59 4.40
3698 4392 5.238583 TGCTAAAAGTCCTTAGAAGCACTC 58.761 41.667 6.73 0.00 31.59 3.51
3699 4393 4.632251 GCTAAAAGTCCTTAGAAGCACTCC 59.368 45.833 0.00 0.00 31.59 3.85
3700 4394 4.984146 AAAAGTCCTTAGAAGCACTCCT 57.016 40.909 0.00 0.00 0.00 3.69
3701 4395 4.984146 AAAGTCCTTAGAAGCACTCCTT 57.016 40.909 0.00 0.00 36.19 3.36
3702 4396 3.971245 AGTCCTTAGAAGCACTCCTTG 57.029 47.619 0.00 0.00 32.78 3.61
3703 4397 3.511477 AGTCCTTAGAAGCACTCCTTGA 58.489 45.455 0.00 0.00 32.78 3.02
3704 4398 3.904339 AGTCCTTAGAAGCACTCCTTGAA 59.096 43.478 0.00 0.00 32.78 2.69
3705 4399 4.348168 AGTCCTTAGAAGCACTCCTTGAAA 59.652 41.667 0.00 0.00 32.78 2.69
3706 4400 4.693095 GTCCTTAGAAGCACTCCTTGAAAG 59.307 45.833 0.00 0.00 32.78 2.62
3707 4401 4.348168 TCCTTAGAAGCACTCCTTGAAAGT 59.652 41.667 0.00 0.00 32.78 2.66
3708 4402 5.066593 CCTTAGAAGCACTCCTTGAAAGTT 58.933 41.667 0.00 0.00 32.78 2.66
3709 4403 5.532779 CCTTAGAAGCACTCCTTGAAAGTTT 59.467 40.000 0.00 0.00 32.78 2.66
3710 4404 6.039829 CCTTAGAAGCACTCCTTGAAAGTTTT 59.960 38.462 0.00 0.00 32.78 2.43
3711 4405 5.921962 AGAAGCACTCCTTGAAAGTTTTT 57.078 34.783 0.00 0.00 32.78 1.94
3756 4450 7.800300 AAAAATCCTAGGACTAGAGAACAGT 57.200 36.000 15.42 0.00 35.21 3.55
3757 4451 8.896722 AAAAATCCTAGGACTAGAGAACAGTA 57.103 34.615 15.42 0.00 35.21 2.74
3758 4452 9.495382 AAAAATCCTAGGACTAGAGAACAGTAT 57.505 33.333 15.42 0.00 35.21 2.12
3759 4453 8.472007 AAATCCTAGGACTAGAGAACAGTATG 57.528 38.462 15.42 0.00 37.48 2.39
3760 4454 6.578313 TCCTAGGACTAGAGAACAGTATGT 57.422 41.667 7.62 0.00 43.53 2.29
3761 4455 6.593807 TCCTAGGACTAGAGAACAGTATGTC 58.406 44.000 7.62 0.00 41.73 3.06
3762 4456 5.766174 CCTAGGACTAGAGAACAGTATGTCC 59.234 48.000 1.05 0.00 41.73 4.02
3763 4457 6.358178 CTAGGACTAGAGAACAGTATGTCCA 58.642 44.000 11.13 0.00 41.73 4.02
3764 4458 6.485313 CTAGGACTAGAGAACAGTATGTCCAG 59.515 46.154 11.13 4.02 41.73 3.86
3765 4459 7.636192 CTAGGACTAGAGAACAGTATGTCCAGA 60.636 44.444 11.13 0.00 41.73 3.86
3796 4490 3.582714 CCCACTTGGCTGATCTTTTTC 57.417 47.619 0.00 0.00 0.00 2.29
3797 4491 2.892852 CCCACTTGGCTGATCTTTTTCA 59.107 45.455 0.00 0.00 0.00 2.69
3798 4492 3.512724 CCCACTTGGCTGATCTTTTTCAT 59.487 43.478 0.00 0.00 0.00 2.57
3799 4493 4.020839 CCCACTTGGCTGATCTTTTTCATT 60.021 41.667 0.00 0.00 0.00 2.57
3800 4494 5.166398 CCACTTGGCTGATCTTTTTCATTC 58.834 41.667 0.00 0.00 0.00 2.67
3801 4495 5.047519 CCACTTGGCTGATCTTTTTCATTCT 60.048 40.000 0.00 0.00 0.00 2.40
3802 4496 6.091437 CACTTGGCTGATCTTTTTCATTCTC 58.909 40.000 0.00 0.00 0.00 2.87
3803 4497 6.008960 ACTTGGCTGATCTTTTTCATTCTCT 58.991 36.000 0.00 0.00 0.00 3.10
3804 4498 6.492772 ACTTGGCTGATCTTTTTCATTCTCTT 59.507 34.615 0.00 0.00 0.00 2.85
3805 4499 6.263516 TGGCTGATCTTTTTCATTCTCTTG 57.736 37.500 0.00 0.00 0.00 3.02
3806 4500 5.100943 GGCTGATCTTTTTCATTCTCTTGC 58.899 41.667 0.00 0.00 0.00 4.01
3807 4501 4.792189 GCTGATCTTTTTCATTCTCTTGCG 59.208 41.667 0.00 0.00 0.00 4.85
3808 4502 5.300969 TGATCTTTTTCATTCTCTTGCGG 57.699 39.130 0.00 0.00 0.00 5.69
3809 4503 5.003160 TGATCTTTTTCATTCTCTTGCGGA 58.997 37.500 0.00 0.00 0.00 5.54
3810 4504 5.122869 TGATCTTTTTCATTCTCTTGCGGAG 59.877 40.000 0.00 0.70 43.12 4.63
3811 4505 3.753272 TCTTTTTCATTCTCTTGCGGAGG 59.247 43.478 6.66 0.00 42.10 4.30
3812 4506 2.859165 TTTCATTCTCTTGCGGAGGT 57.141 45.000 6.66 0.00 42.10 3.85
3813 4507 2.386661 TTCATTCTCTTGCGGAGGTC 57.613 50.000 6.66 0.00 42.10 3.85
3814 4508 1.266178 TCATTCTCTTGCGGAGGTCA 58.734 50.000 6.66 0.00 42.10 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 1.966451 GTTGAGAAGGTGTGGCCGG 60.966 63.158 0.00 0.00 43.70 6.13
59 60 1.696097 AAGCCGGGATAGCCAACGAT 61.696 55.000 2.18 0.00 35.15 3.73
86 104 3.941483 GTGTCAGGTCCATCTAACAATGG 59.059 47.826 0.00 0.00 46.44 3.16
113 131 6.118170 AGGATTGACAATGAGATGTTACTGG 58.882 40.000 5.14 0.00 32.57 4.00
195 213 9.482627 CAAATAAACTAATGTTTTGCCCTAACA 57.517 29.630 0.00 0.00 43.13 2.41
215 233 2.093658 GGTGTCCGCCTCTCTCAAATAA 60.094 50.000 0.00 0.00 0.00 1.40
263 600 5.330455 TCTATCTCACATTGTCTTCGCTT 57.670 39.130 0.00 0.00 0.00 4.68
282 622 3.719268 ACCAACTGATGCCACAATCTA 57.281 42.857 0.00 0.00 0.00 1.98
297 637 5.756347 TGTGATACTGTTAGACACAACCAAC 59.244 40.000 0.00 0.00 38.28 3.77
314 654 8.778358 AGATTTCTCAAGAGTTTGTTGTGATAC 58.222 33.333 0.00 0.00 35.73 2.24
377 717 6.403200 GGAATTATGTCACACGCTTTGTATGT 60.403 38.462 0.00 0.00 35.67 2.29
383 723 3.119849 GCAGGAATTATGTCACACGCTTT 60.120 43.478 0.00 0.00 0.00 3.51
453 793 3.594603 ACGTGAAATACTCCCTCTGTG 57.405 47.619 0.00 0.00 0.00 3.66
456 796 4.831710 GGGTATACGTGAAATACTCCCTCT 59.168 45.833 0.00 0.00 31.71 3.69
469 809 3.891422 TTGGTTAGGTGGGTATACGTG 57.109 47.619 0.00 0.00 0.00 4.49
472 812 5.503002 ACATGTTTGGTTAGGTGGGTATAC 58.497 41.667 0.00 0.00 0.00 1.47
496 836 2.095768 CCTTCGTCGTAACCGTGACTTA 60.096 50.000 0.00 0.00 32.93 2.24
513 853 5.570234 TTTAGTTGTGTGTTTGTCCCTTC 57.430 39.130 0.00 0.00 0.00 3.46
561 901 1.531522 CTTGTTTGCGCACGTTCAGC 61.532 55.000 11.12 0.00 0.00 4.26
573 913 7.642978 CAGAGAGAAAATCTTGTGACTTGTTTG 59.357 37.037 0.00 0.00 38.84 2.93
676 1019 3.093814 TGCAGAACGTTATACTCCCTCA 58.906 45.455 0.00 0.00 0.00 3.86
708 1051 4.568592 GGACATGGGACTGAGATTTTTCCT 60.569 45.833 0.00 0.00 0.00 3.36
758 1406 4.492895 CGCCACAAAATGCATATGCTTTTC 60.493 41.667 30.56 20.64 44.29 2.29
764 1413 1.923899 TGCGCCACAAAATGCATATG 58.076 45.000 4.18 5.16 31.31 1.78
783 1432 2.859165 TTGGATCTTCTGTTCCGCTT 57.141 45.000 0.00 0.00 35.38 4.68
784 1433 3.274288 GAATTGGATCTTCTGTTCCGCT 58.726 45.455 0.00 0.00 35.38 5.52
785 1434 2.030946 CGAATTGGATCTTCTGTTCCGC 59.969 50.000 0.00 0.00 35.38 5.54
786 1435 2.030946 GCGAATTGGATCTTCTGTTCCG 59.969 50.000 0.00 0.00 35.38 4.30
787 1436 3.009723 TGCGAATTGGATCTTCTGTTCC 58.990 45.455 0.00 0.00 33.70 3.62
788 1437 3.484229 CGTGCGAATTGGATCTTCTGTTC 60.484 47.826 0.00 0.00 0.00 3.18
1155 1817 3.680338 GACGACGCCGAGGAAGGAC 62.680 68.421 0.00 0.00 39.50 3.85
1293 1955 3.246112 CTGGTGGGGTCGGGAACA 61.246 66.667 0.00 0.00 0.00 3.18
1296 1958 4.974438 AAGCTGGTGGGGTCGGGA 62.974 66.667 0.00 0.00 0.00 5.14
1522 2184 1.401148 CGTGAACTCGTGAATCTCGGT 60.401 52.381 4.86 0.00 0.00 4.69
1611 2273 3.319198 GACTTCCACGCCTCCCCA 61.319 66.667 0.00 0.00 0.00 4.96
1916 2578 1.977009 TCGTCCACATCCTCGCACT 60.977 57.895 0.00 0.00 0.00 4.40
2028 2690 2.126071 GAGCAGTGCGCCGAGTAA 60.126 61.111 10.00 0.00 44.04 2.24
2151 2813 0.941542 CCTCAACGCCAAGAACGAAA 59.058 50.000 0.00 0.00 0.00 3.46
2196 2858 0.584396 GATTTGTGAACACGGCGTCA 59.416 50.000 10.85 1.75 0.00 4.35
2211 2873 2.044946 GGCTCGCCACTGGGATTT 60.045 61.111 2.41 0.00 35.59 2.17
2262 2924 2.816087 GTTCATGCTCATGTTCCAGTGT 59.184 45.455 9.41 0.00 39.72 3.55
2379 3041 1.676746 CATCATGGAGGCCAGAGTTG 58.323 55.000 5.01 0.00 36.75 3.16
2469 3131 1.131126 CGCAACCTCACTTTAGCCATG 59.869 52.381 0.00 0.00 0.00 3.66
2592 3254 1.203287 CTCATCTTCTCCACGAGCACA 59.797 52.381 0.00 0.00 0.00 4.57
2821 3483 1.207089 CTTACCGAGCATGGAACCAGA 59.793 52.381 0.69 0.00 0.00 3.86
2853 3517 9.465985 GCTATCCTACTCTAGTTTACACAATTC 57.534 37.037 0.00 0.00 0.00 2.17
2869 3533 2.032620 CAGTTCCGTGGCTATCCTACT 58.967 52.381 0.00 0.00 0.00 2.57
3008 3672 4.232878 CCTGGCCGGCTAGAGCAG 62.233 72.222 38.41 28.15 44.36 4.24
3040 3704 1.813178 CCATAGCTAGCTCCGATCGAA 59.187 52.381 23.26 0.28 0.00 3.71
3043 3707 1.203523 CACCCATAGCTAGCTCCGATC 59.796 57.143 23.26 0.00 0.00 3.69
3044 3708 1.203063 TCACCCATAGCTAGCTCCGAT 60.203 52.381 23.26 6.58 0.00 4.18
3045 3709 0.185175 TCACCCATAGCTAGCTCCGA 59.815 55.000 23.26 3.87 0.00 4.55
3046 3710 1.040646 TTCACCCATAGCTAGCTCCG 58.959 55.000 23.26 13.43 0.00 4.63
3058 3722 6.816616 TTACATGTACCTGATATTCACCCA 57.183 37.500 4.68 0.00 0.00 4.51
3128 3792 3.627395 TGGACATAACATGACCCACTC 57.373 47.619 0.00 0.00 43.12 3.51
3142 3806 5.011329 ACTGAAGAATGCAAACATTGGACAT 59.989 36.000 0.00 0.00 46.59 3.06
3244 3916 4.448210 ACACATCAACCCGGAACATATAC 58.552 43.478 0.73 0.00 0.00 1.47
3303 3975 2.614987 GGCTTCATCAAGACAGCTCACT 60.615 50.000 0.00 0.00 37.63 3.41
3304 3976 1.736681 GGCTTCATCAAGACAGCTCAC 59.263 52.381 0.00 0.00 37.63 3.51
3306 3978 2.105006 TGGCTTCATCAAGACAGCTC 57.895 50.000 0.00 0.00 43.33 4.09
3432 4110 5.794894 CACCTACCTCGGCATAATTAGATT 58.205 41.667 0.00 0.00 0.00 2.40
3445 4123 2.315925 ATTGTCATGCACCTACCTCG 57.684 50.000 0.00 0.00 0.00 4.63
3447 4125 2.308570 TCCAATTGTCATGCACCTACCT 59.691 45.455 4.43 0.00 0.00 3.08
3517 4211 4.338682 AGAGTAAGATTACTGGCTACGGTG 59.661 45.833 9.90 0.00 43.64 4.94
3557 4251 1.003839 TCCAGCCTTACAAGCCACG 60.004 57.895 0.00 0.00 0.00 4.94
3608 4302 1.533033 CCTGGAACCAAACACCCCC 60.533 63.158 0.00 0.00 0.00 5.40
3609 4303 1.533033 CCCTGGAACCAAACACCCC 60.533 63.158 0.00 0.00 0.00 4.95
3610 4304 0.826256 GTCCCTGGAACCAAACACCC 60.826 60.000 0.00 0.00 0.00 4.61
3611 4305 0.185175 AGTCCCTGGAACCAAACACC 59.815 55.000 0.00 0.00 0.00 4.16
3612 4306 2.067365 AAGTCCCTGGAACCAAACAC 57.933 50.000 0.00 0.00 0.00 3.32
3613 4307 2.838637 AAAGTCCCTGGAACCAAACA 57.161 45.000 0.00 0.00 0.00 2.83
3649 4343 7.597288 ATGTTTAGTTTGCTAGGGACTTTTT 57.403 32.000 0.00 0.00 41.75 1.94
3650 4344 7.597288 AATGTTTAGTTTGCTAGGGACTTTT 57.403 32.000 0.00 0.00 41.75 2.27
3651 4345 7.433680 CAAATGTTTAGTTTGCTAGGGACTTT 58.566 34.615 0.00 0.00 32.94 2.66
3652 4346 6.981722 CAAATGTTTAGTTTGCTAGGGACTT 58.018 36.000 0.00 0.00 32.94 3.01
3653 4347 6.575162 CAAATGTTTAGTTTGCTAGGGACT 57.425 37.500 0.00 0.00 34.41 3.85
3662 4356 8.871686 AGGACTTTTAGCAAATGTTTAGTTTG 57.128 30.769 0.00 0.00 39.08 2.93
3665 4359 9.569122 TCTAAGGACTTTTAGCAAATGTTTAGT 57.431 29.630 0.00 0.00 32.01 2.24
3668 4362 7.867909 GCTTCTAAGGACTTTTAGCAAATGTTT 59.132 33.333 0.00 0.00 32.01 2.83
3669 4363 7.014230 TGCTTCTAAGGACTTTTAGCAAATGTT 59.986 33.333 10.79 0.00 32.01 2.71
3670 4364 6.490040 TGCTTCTAAGGACTTTTAGCAAATGT 59.510 34.615 10.79 0.00 32.01 2.71
3671 4365 6.803807 GTGCTTCTAAGGACTTTTAGCAAATG 59.196 38.462 7.07 0.00 43.15 2.32
3672 4366 6.914259 GTGCTTCTAAGGACTTTTAGCAAAT 58.086 36.000 7.07 0.00 43.15 2.32
3673 4367 6.313744 GTGCTTCTAAGGACTTTTAGCAAA 57.686 37.500 7.07 0.00 43.15 3.68
3674 4368 5.941948 GTGCTTCTAAGGACTTTTAGCAA 57.058 39.130 7.07 1.75 43.15 3.91
3683 4377 3.963428 TCAAGGAGTGCTTCTAAGGAC 57.037 47.619 6.27 6.27 46.33 3.85
3684 4378 4.348168 ACTTTCAAGGAGTGCTTCTAAGGA 59.652 41.667 15.20 0.15 0.00 3.36
3685 4379 4.646572 ACTTTCAAGGAGTGCTTCTAAGG 58.353 43.478 15.20 7.76 0.00 2.69
3686 4380 6.625873 AAACTTTCAAGGAGTGCTTCTAAG 57.374 37.500 11.31 11.31 0.00 2.18
3687 4381 7.404671 AAAAACTTTCAAGGAGTGCTTCTAA 57.595 32.000 0.00 0.00 0.00 2.10
3689 4383 5.921962 AAAAACTTTCAAGGAGTGCTTCT 57.078 34.783 0.00 0.00 0.00 2.85
3732 4426 7.800300 ACTGTTCTCTAGTCCTAGGATTTTT 57.200 36.000 16.27 4.11 34.06 1.94
3733 4427 8.919145 CATACTGTTCTCTAGTCCTAGGATTTT 58.081 37.037 16.27 6.69 34.06 1.82
3734 4428 8.062536 ACATACTGTTCTCTAGTCCTAGGATTT 58.937 37.037 16.27 9.33 34.06 2.17
3735 4429 7.588169 ACATACTGTTCTCTAGTCCTAGGATT 58.412 38.462 16.27 13.96 34.06 3.01
3736 4430 7.156694 ACATACTGTTCTCTAGTCCTAGGAT 57.843 40.000 16.27 6.84 34.06 3.24
3737 4431 6.409464 GGACATACTGTTCTCTAGTCCTAGGA 60.409 46.154 7.62 7.62 40.57 2.94
3738 4432 5.766174 GGACATACTGTTCTCTAGTCCTAGG 59.234 48.000 0.82 0.82 40.57 3.02
3739 4433 6.358178 TGGACATACTGTTCTCTAGTCCTAG 58.642 44.000 0.00 0.00 43.31 3.02
3740 4434 6.158169 TCTGGACATACTGTTCTCTAGTCCTA 59.842 42.308 0.00 0.00 43.31 2.94
3741 4435 5.044772 TCTGGACATACTGTTCTCTAGTCCT 60.045 44.000 0.00 0.00 43.31 3.85
3742 4436 5.194432 TCTGGACATACTGTTCTCTAGTCC 58.806 45.833 0.00 0.00 43.24 3.85
3743 4437 6.761099 TTCTGGACATACTGTTCTCTAGTC 57.239 41.667 0.00 0.00 0.00 2.59
3744 4438 7.540474 TTTTCTGGACATACTGTTCTCTAGT 57.460 36.000 0.00 0.00 0.00 2.57
3776 4470 2.892852 TGAAAAAGATCAGCCAAGTGGG 59.107 45.455 0.00 0.00 40.85 4.61
3777 4471 4.796038 ATGAAAAAGATCAGCCAAGTGG 57.204 40.909 0.00 0.00 38.53 4.00
3778 4472 6.022163 AGAATGAAAAAGATCAGCCAAGTG 57.978 37.500 0.00 0.00 31.76 3.16
3779 4473 6.008960 AGAGAATGAAAAAGATCAGCCAAGT 58.991 36.000 0.00 0.00 31.76 3.16
3780 4474 6.512342 AGAGAATGAAAAAGATCAGCCAAG 57.488 37.500 0.00 0.00 31.76 3.61
3781 4475 6.684686 CAAGAGAATGAAAAAGATCAGCCAA 58.315 36.000 0.00 0.00 31.76 4.52
3782 4476 5.336213 GCAAGAGAATGAAAAAGATCAGCCA 60.336 40.000 0.00 0.00 31.76 4.75
3783 4477 5.100943 GCAAGAGAATGAAAAAGATCAGCC 58.899 41.667 0.00 0.00 31.76 4.85
3784 4478 4.792189 CGCAAGAGAATGAAAAAGATCAGC 59.208 41.667 0.00 0.00 43.02 4.26
3785 4479 5.122869 TCCGCAAGAGAATGAAAAAGATCAG 59.877 40.000 0.00 0.00 43.02 2.90
3786 4480 5.003160 TCCGCAAGAGAATGAAAAAGATCA 58.997 37.500 0.00 0.00 43.02 2.92
3787 4481 5.448360 CCTCCGCAAGAGAATGAAAAAGATC 60.448 44.000 2.33 0.00 46.50 2.75
3788 4482 4.397417 CCTCCGCAAGAGAATGAAAAAGAT 59.603 41.667 2.33 0.00 46.50 2.40
3789 4483 3.753272 CCTCCGCAAGAGAATGAAAAAGA 59.247 43.478 2.33 0.00 46.50 2.52
3790 4484 3.503748 ACCTCCGCAAGAGAATGAAAAAG 59.496 43.478 2.33 0.00 46.50 2.27
3791 4485 3.486383 ACCTCCGCAAGAGAATGAAAAA 58.514 40.909 2.33 0.00 46.50 1.94
3792 4486 3.074412 GACCTCCGCAAGAGAATGAAAA 58.926 45.455 2.33 0.00 46.50 2.29
3793 4487 2.038426 TGACCTCCGCAAGAGAATGAAA 59.962 45.455 2.33 0.00 46.50 2.69
3794 4488 1.623311 TGACCTCCGCAAGAGAATGAA 59.377 47.619 2.33 0.00 46.50 2.57
3795 4489 1.266178 TGACCTCCGCAAGAGAATGA 58.734 50.000 2.33 0.00 46.50 2.57
3796 4490 3.840831 TGACCTCCGCAAGAGAATG 57.159 52.632 2.33 0.00 46.50 2.67


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

AutoCloner maintained by Alex Coulton.