Multiple sequence alignment - TraesCS3B01G146500

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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 TraesCS3B01G146500 chr3B 100.000 2554 0 0 1 2554 136451413 136448860 0.000000e+00 4717.0
1 TraesCS3B01G146500 chr3B 100.000 524 0 0 2989 3512 136448425 136447902 0.000000e+00 968.0
2 TraesCS3B01G146500 chr3A 95.960 1782 59 8 779 2554 102625193 102623419 0.000000e+00 2880.0
3 TraesCS3B01G146500 chr3A 90.441 680 59 4 1 675 102626189 102625511 0.000000e+00 891.0
4 TraesCS3B01G146500 chr3A 81.068 206 20 8 3014 3200 102623242 102623037 2.820000e-31 147.0
5 TraesCS3B01G146500 chr3D 95.697 1743 68 6 816 2554 86343147 86341408 0.000000e+00 2796.0
6 TraesCS3B01G146500 chr3D 77.486 533 59 24 2989 3508 86340752 86340268 2.690000e-66 263.0
7 TraesCS3B01G146500 chr1A 98.680 682 9 0 1500 2181 300942739 300943420 0.000000e+00 1210.0
8 TraesCS3B01G146500 chr7A 93.098 681 15 13 1500 2180 180640857 180641505 0.000000e+00 968.0
9 TraesCS3B01G146500 chr7A 76.280 1387 268 36 1088 2448 1690817 1692168 0.000000e+00 682.0
10 TraesCS3B01G146500 chr7D 79.086 1138 187 36 1093 2206 625615362 625616472 0.000000e+00 736.0
11 TraesCS3B01G146500 chr7D 76.744 1419 243 56 1064 2446 2000000 1998633 0.000000e+00 712.0
12 TraesCS3B01G146500 chr7D 76.157 1405 271 41 1070 2445 30761253 30759884 0.000000e+00 680.0
13 TraesCS3B01G146500 chr4A 76.207 1408 264 45 1070 2445 697970055 697971423 0.000000e+00 678.0
14 TraesCS3B01G146500 chr4A 78.980 490 75 17 1387 1864 232507464 232507937 3.400000e-80 309.0
15 TraesCS3B01G146500 chr7B 79.091 220 44 2 2230 2448 682372983 682372765 2.180000e-32 150.0
16 TraesCS3B01G146500 chr7B 83.607 61 6 4 3176 3233 600844335 600844394 2.000000e-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 TraesCS3B01G146500 chr3B 136447902 136451413 3511 True 2842.5 4717 100.000000 1 3512 2 chr3B.!!$R1 3511
1 TraesCS3B01G146500 chr3A 102623037 102626189 3152 True 1306.0 2880 89.156333 1 3200 3 chr3A.!!$R1 3199
2 TraesCS3B01G146500 chr3D 86340268 86343147 2879 True 1529.5 2796 86.591500 816 3508 2 chr3D.!!$R1 2692
3 TraesCS3B01G146500 chr1A 300942739 300943420 681 False 1210.0 1210 98.680000 1500 2181 1 chr1A.!!$F1 681
4 TraesCS3B01G146500 chr7A 180640857 180641505 648 False 968.0 968 93.098000 1500 2180 1 chr7A.!!$F2 680
5 TraesCS3B01G146500 chr7A 1690817 1692168 1351 False 682.0 682 76.280000 1088 2448 1 chr7A.!!$F1 1360
6 TraesCS3B01G146500 chr7D 625615362 625616472 1110 False 736.0 736 79.086000 1093 2206 1 chr7D.!!$F1 1113
7 TraesCS3B01G146500 chr7D 1998633 2000000 1367 True 712.0 712 76.744000 1064 2446 1 chr7D.!!$R1 1382
8 TraesCS3B01G146500 chr7D 30759884 30761253 1369 True 680.0 680 76.157000 1070 2445 1 chr7D.!!$R2 1375
9 TraesCS3B01G146500 chr4A 697970055 697971423 1368 False 678.0 678 76.207000 1070 2445 1 chr4A.!!$F2 1375

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
92 93 0.252881 TGTGATCCTCTCCTTGGCCT 60.253 55.0 3.32 0.0 0.00 5.19 F
95 96 0.399806 GATCCTCTCCTTGGCCTCCT 60.400 60.0 3.32 0.0 0.00 3.69 F
688 694 0.942962 ACGATACGAGTTCGGCTAGG 59.057 55.0 6.48 0.0 44.95 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1365 1628 1.621317 TGGCCGTCACAGTCAATAGAA 59.379 47.619 0.00 0.00 0.00 2.10 R
2411 2701 1.422179 CTCGTCGTCTAGCTCGAGCA 61.422 60.000 36.87 22.05 45.16 4.26 R
3006 3528 6.578944 TGGCGAGTGAATAATGTAAGTATGT 58.421 36.000 0.00 0.00 0.00 2.29 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
69 70 0.650512 GGTTGATGTGTATGCGGTCG 59.349 55.000 0.00 0.00 0.00 4.79
71 72 1.996898 GTTGATGTGTATGCGGTCGAA 59.003 47.619 0.00 0.00 0.00 3.71
82 83 0.931005 GCGGTCGAATTGTGATCCTC 59.069 55.000 0.00 0.00 0.00 3.71
92 93 0.252881 TGTGATCCTCTCCTTGGCCT 60.253 55.000 3.32 0.00 0.00 5.19
95 96 0.399806 GATCCTCTCCTTGGCCTCCT 60.400 60.000 3.32 0.00 0.00 3.69
103 104 3.054361 TCTCCTTGGCCTCCTAAAATCAC 60.054 47.826 3.32 0.00 0.00 3.06
110 111 3.381590 GGCCTCCTAAAATCACCATTGAC 59.618 47.826 0.00 0.00 33.38 3.18
119 120 2.696989 TCACCATTGACGATCATGCT 57.303 45.000 0.00 0.00 0.00 3.79
146 147 5.551760 ACCATTTTGAAGTCATCATCGTC 57.448 39.130 0.00 0.00 38.03 4.20
157 158 3.383185 GTCATCATCGTCTTCTTCCTCCT 59.617 47.826 0.00 0.00 0.00 3.69
162 163 1.636519 TCGTCTTCTTCCTCCTCCTCT 59.363 52.381 0.00 0.00 0.00 3.69
163 164 2.021457 CGTCTTCTTCCTCCTCCTCTC 58.979 57.143 0.00 0.00 0.00 3.20
164 165 2.384828 GTCTTCTTCCTCCTCCTCTCC 58.615 57.143 0.00 0.00 0.00 3.71
165 166 2.024369 GTCTTCTTCCTCCTCCTCTCCT 60.024 54.545 0.00 0.00 0.00 3.69
166 167 2.243736 TCTTCTTCCTCCTCCTCTCCTC 59.756 54.545 0.00 0.00 0.00 3.71
173 178 1.149627 CCTCCTCTCCTCCGACGAT 59.850 63.158 0.00 0.00 0.00 3.73
217 222 4.899502 TCTTTCAACCTCTTCATCTGGAC 58.100 43.478 0.00 0.00 0.00 4.02
224 229 7.461749 TCAACCTCTTCATCTGGACTAAAAAT 58.538 34.615 0.00 0.00 0.00 1.82
230 235 6.813649 TCTTCATCTGGACTAAAAATGACTCG 59.186 38.462 0.00 0.00 0.00 4.18
266 271 6.395426 AAAATGAGATGAAAGAAGCACACA 57.605 33.333 0.00 0.00 0.00 3.72
291 297 0.981183 ATCACCTAGGCAAACCGTCA 59.019 50.000 9.30 0.00 42.76 4.35
328 334 1.448540 GAGGTGTCATGGTCCGCTG 60.449 63.158 0.00 0.00 0.00 5.18
329 335 3.127533 GGTGTCATGGTCCGCTGC 61.128 66.667 0.00 0.00 0.00 5.25
339 345 4.680237 TCCGCTGCCCACGTTGAG 62.680 66.667 0.00 0.00 0.00 3.02
350 356 3.125316 GCCCACGTTGAGCATATATTAGC 59.875 47.826 0.00 0.00 0.00 3.09
352 358 3.367932 CCACGTTGAGCATATATTAGCGG 59.632 47.826 0.00 0.00 35.48 5.52
354 360 4.447724 CACGTTGAGCATATATTAGCGGTT 59.552 41.667 0.00 0.00 35.48 4.44
356 362 4.684242 CGTTGAGCATATATTAGCGGTTGA 59.316 41.667 0.00 0.00 35.48 3.18
359 365 3.585862 AGCATATATTAGCGGTTGACGG 58.414 45.455 0.00 0.00 44.51 4.79
362 368 1.125633 ATATTAGCGGTTGACGGGGT 58.874 50.000 0.00 0.00 44.51 4.95
394 400 1.066573 CGGAAGTGGACAGAGATGCTT 60.067 52.381 0.00 0.00 0.00 3.91
429 435 3.650369 GCCTCTTTTTGGCGACGA 58.350 55.556 0.00 0.00 41.03 4.20
536 542 2.022129 GTTGACAGTGAGGCGTCGG 61.022 63.158 0.00 0.00 34.78 4.79
537 543 2.495409 TTGACAGTGAGGCGTCGGT 61.495 57.895 0.00 0.00 34.78 4.69
539 545 2.910479 ACAGTGAGGCGTCGGTGA 60.910 61.111 13.09 0.00 0.00 4.02
575 581 1.414897 CGAAAGTAACGCTGGCGAC 59.585 57.895 21.77 10.07 42.83 5.19
609 615 4.280929 GGAGTGGCCAAACTTTTTACTCAT 59.719 41.667 7.24 0.00 35.88 2.90
615 621 4.155280 GCCAAACTTTTTACTCATCGGCTA 59.845 41.667 0.00 0.00 33.03 3.93
620 626 4.222145 ACTTTTTACTCATCGGCTAGGTGA 59.778 41.667 0.00 0.00 37.72 4.02
622 628 1.688772 TACTCATCGGCTAGGTGACC 58.311 55.000 0.00 0.00 34.48 4.02
639 645 3.007290 GTGACCGGGTATATTTAGGGGTC 59.993 52.174 6.32 0.53 42.10 4.46
645 651 3.171528 GGTATATTTAGGGGTCGAGGCT 58.828 50.000 0.00 0.00 0.00 4.58
661 667 5.586643 GTCGAGGCTGATAAATTTTTCCTCT 59.413 40.000 0.00 0.00 37.17 3.69
662 668 5.817816 TCGAGGCTGATAAATTTTTCCTCTC 59.182 40.000 0.00 4.84 37.17 3.20
675 681 9.603298 AAATTTTTCCTCTCGTAAAAACGATAC 57.397 29.630 0.59 0.00 41.56 2.24
676 682 5.997732 TTTCCTCTCGTAAAAACGATACG 57.002 39.130 0.59 0.00 45.60 3.06
683 689 4.142445 CGTAAAAACGATACGAGTTCGG 57.858 45.455 6.48 0.00 46.81 4.30
684 690 3.538258 CGTAAAAACGATACGAGTTCGGC 60.538 47.826 6.48 0.00 46.81 5.54
685 691 2.358939 AAAACGATACGAGTTCGGCT 57.641 45.000 6.48 0.00 44.95 5.52
686 692 3.492421 AAAACGATACGAGTTCGGCTA 57.508 42.857 6.48 0.00 44.95 3.93
687 693 2.752144 AACGATACGAGTTCGGCTAG 57.248 50.000 6.48 0.00 44.95 3.42
688 694 0.942962 ACGATACGAGTTCGGCTAGG 59.057 55.000 6.48 0.00 44.95 3.02
689 695 0.942962 CGATACGAGTTCGGCTAGGT 59.057 55.000 6.48 0.00 44.95 3.08
690 696 2.138320 CGATACGAGTTCGGCTAGGTA 58.862 52.381 6.48 0.00 44.95 3.08
691 697 2.096516 CGATACGAGTTCGGCTAGGTAC 60.097 54.545 6.48 0.00 44.95 3.34
692 698 2.401583 TACGAGTTCGGCTAGGTACA 57.598 50.000 6.48 0.00 44.95 2.90
693 699 1.538047 ACGAGTTCGGCTAGGTACAA 58.462 50.000 6.48 0.00 44.95 2.41
694 700 1.471684 ACGAGTTCGGCTAGGTACAAG 59.528 52.381 6.48 0.00 44.95 3.16
695 701 1.471684 CGAGTTCGGCTAGGTACAAGT 59.528 52.381 0.00 0.00 35.37 3.16
696 702 2.094854 CGAGTTCGGCTAGGTACAAGTT 60.095 50.000 0.00 0.00 35.37 2.66
697 703 3.127548 CGAGTTCGGCTAGGTACAAGTTA 59.872 47.826 0.00 0.00 35.37 2.24
698 704 4.670347 GAGTTCGGCTAGGTACAAGTTAG 58.330 47.826 0.00 0.00 0.00 2.34
731 737 3.988517 CCGAATTTATCCTCCTCTAACGC 59.011 47.826 0.00 0.00 0.00 4.84
736 742 1.108132 ATCCTCCTCTAACGCCGGAC 61.108 60.000 5.05 0.00 0.00 4.79
755 761 3.444388 GGACAGAGATCGGTTAGAGTTGT 59.556 47.826 0.00 0.00 0.00 3.32
757 763 3.444388 ACAGAGATCGGTTAGAGTTGTCC 59.556 47.826 0.00 0.00 0.00 4.02
774 780 1.464997 GTCCCGAGCAGTTCAAACATC 59.535 52.381 0.00 0.00 0.00 3.06
777 783 2.932614 CCCGAGCAGTTCAAACATCTAG 59.067 50.000 0.00 0.00 0.00 2.43
787 1032 7.361201 GCAGTTCAAACATCTAGATGCAAAGTA 60.361 37.037 28.86 10.47 42.39 2.24
811 1056 6.123651 AGCACTAGACTACACAGCTTATAGT 58.876 40.000 0.00 1.75 31.79 2.12
812 1057 6.603997 AGCACTAGACTACACAGCTTATAGTT 59.396 38.462 0.00 0.00 29.25 2.24
813 1058 6.693545 GCACTAGACTACACAGCTTATAGTTG 59.306 42.308 0.00 0.00 32.33 3.16
814 1059 7.415318 GCACTAGACTACACAGCTTATAGTTGA 60.415 40.741 0.00 0.00 30.50 3.18
819 1064 7.976734 AGACTACACAGCTTATAGTTGATTGAC 59.023 37.037 3.45 0.00 30.50 3.18
932 1177 6.542821 TCCTTGAACATTCAGTCAGGTAAAT 58.457 36.000 9.59 0.00 38.61 1.40
934 1179 8.328758 TCCTTGAACATTCAGTCAGGTAAATAT 58.671 33.333 9.59 0.00 38.61 1.28
985 1236 4.235372 ACCCTATAAATCTAGTGCAGCCT 58.765 43.478 0.00 0.00 0.00 4.58
1362 1625 2.594592 GCCGTTGTTGGGTGCTCT 60.595 61.111 0.00 0.00 0.00 4.09
1365 1628 1.101049 CCGTTGTTGGGTGCTCTGTT 61.101 55.000 0.00 0.00 0.00 3.16
2421 2711 3.147595 ATGGCGGTGCTCGAGCTA 61.148 61.111 35.27 20.40 42.43 3.32
3011 3533 6.270096 GTTGGTCATTAGCGAGTTACATAC 57.730 41.667 0.00 0.00 0.00 2.39
3069 3602 9.113838 CATTAGTGATAGTTAGAGGTTGCATTT 57.886 33.333 0.00 0.00 0.00 2.32
3104 3637 7.040755 TCACCAATAACTGTCATGTTTAAGGTG 60.041 37.037 0.00 0.00 40.62 4.00
3133 3666 9.185192 GGAATCAAAGTTTTCTCACAATAGTTG 57.815 33.333 0.00 0.00 0.00 3.16
3164 3703 3.278574 CGCCCTGAGTTTGGATTAATCA 58.721 45.455 17.07 1.07 0.00 2.57
3172 3711 9.143631 CCTGAGTTTGGATTAATCAATTTTCAC 57.856 33.333 17.07 4.00 0.00 3.18
3182 3721 8.742554 ATTAATCAATTTTCACGTGAAGGAAC 57.257 30.769 28.21 0.00 35.21 3.62
3209 3752 1.081174 AGGGAAGGAAGGAGATCACCA 59.919 52.381 12.05 0.00 0.00 4.17
3212 3755 2.840651 GGAAGGAAGGAGATCACCAGAA 59.159 50.000 12.05 0.00 0.00 3.02
3222 3765 2.646798 AGATCACCAGAAAAGCCCTCTT 59.353 45.455 0.00 0.00 0.00 2.85
3226 3769 1.202940 ACCAGAAAAGCCCTCTTGGTC 60.203 52.381 0.00 0.00 36.04 4.02
3229 3772 3.054065 CCAGAAAAGCCCTCTTGGTCTAT 60.054 47.826 0.00 0.00 36.04 1.98
3230 3773 4.195416 CAGAAAAGCCCTCTTGGTCTATC 58.805 47.826 0.00 0.00 36.04 2.08
3231 3774 4.080638 CAGAAAAGCCCTCTTGGTCTATCT 60.081 45.833 0.00 0.00 36.04 1.98
3232 3775 4.538089 AGAAAAGCCCTCTTGGTCTATCTT 59.462 41.667 0.00 0.00 36.04 2.40
3233 3776 4.936685 AAAGCCCTCTTGGTCTATCTTT 57.063 40.909 0.00 0.00 36.04 2.52
3276 3831 4.104086 TGGGTATATCTTAGGATGGCAGG 58.896 47.826 0.00 0.00 33.71 4.85
3296 3851 3.261897 AGGCGACCCCATTATCTATCTTG 59.738 47.826 0.00 0.00 35.39 3.02
3309 3864 1.211567 TATCTTGGGGTGTGTGGGGG 61.212 60.000 0.00 0.00 0.00 5.40
3317 3872 2.529136 TGTGTGGGGGTGAGGGAG 60.529 66.667 0.00 0.00 0.00 4.30
3318 3873 2.203938 GTGTGGGGGTGAGGGAGA 60.204 66.667 0.00 0.00 0.00 3.71
3319 3874 2.122729 TGTGGGGGTGAGGGAGAG 59.877 66.667 0.00 0.00 0.00 3.20
3320 3875 2.450243 GTGGGGGTGAGGGAGAGA 59.550 66.667 0.00 0.00 0.00 3.10
3321 3876 1.687493 GTGGGGGTGAGGGAGAGAG 60.687 68.421 0.00 0.00 0.00 3.20
3322 3877 2.041405 GGGGGTGAGGGAGAGAGG 60.041 72.222 0.00 0.00 0.00 3.69
3323 3878 2.637640 GGGGGTGAGGGAGAGAGGA 61.638 68.421 0.00 0.00 0.00 3.71
3324 3879 1.075600 GGGGTGAGGGAGAGAGGAG 60.076 68.421 0.00 0.00 0.00 3.69
3325 3880 1.075600 GGGTGAGGGAGAGAGGAGG 60.076 68.421 0.00 0.00 0.00 4.30
3326 3881 1.075600 GGTGAGGGAGAGAGGAGGG 60.076 68.421 0.00 0.00 0.00 4.30
3327 3882 1.585651 GGTGAGGGAGAGAGGAGGGA 61.586 65.000 0.00 0.00 0.00 4.20
3328 3883 0.106217 GTGAGGGAGAGAGGAGGGAG 60.106 65.000 0.00 0.00 0.00 4.30
3329 3884 0.253868 TGAGGGAGAGAGGAGGGAGA 60.254 60.000 0.00 0.00 0.00 3.71
3330 3885 0.478507 GAGGGAGAGAGGAGGGAGAG 59.521 65.000 0.00 0.00 0.00 3.20
3331 3886 0.047176 AGGGAGAGAGGAGGGAGAGA 59.953 60.000 0.00 0.00 0.00 3.10
3332 3887 0.478507 GGGAGAGAGGAGGGAGAGAG 59.521 65.000 0.00 0.00 0.00 3.20
3333 3888 0.478507 GGAGAGAGGAGGGAGAGAGG 59.521 65.000 0.00 0.00 0.00 3.69
3334 3889 1.222567 GAGAGAGGAGGGAGAGAGGT 58.777 60.000 0.00 0.00 0.00 3.85
3335 3890 0.926293 AGAGAGGAGGGAGAGAGGTG 59.074 60.000 0.00 0.00 0.00 4.00
3340 3895 1.612395 GGAGGGAGAGAGGTGTGCAG 61.612 65.000 0.00 0.00 0.00 4.41
3342 3897 2.267324 GGAGAGAGGTGTGCAGGC 59.733 66.667 0.00 0.00 0.00 4.85
3345 3900 1.534959 AGAGAGGTGTGCAGGCTCA 60.535 57.895 0.00 0.00 0.00 4.26
3357 3912 2.305635 TGCAGGCTCACCAGATAAGAAA 59.694 45.455 0.00 0.00 39.06 2.52
3358 3913 3.054139 TGCAGGCTCACCAGATAAGAAAT 60.054 43.478 0.00 0.00 39.06 2.17
3359 3914 3.950395 GCAGGCTCACCAGATAAGAAATT 59.050 43.478 0.00 0.00 39.06 1.82
3367 3922 6.122277 TCACCAGATAAGAAATTGGTCATCC 58.878 40.000 0.00 0.00 41.81 3.51
3371 3926 4.412199 AGATAAGAAATTGGTCATCCCCGA 59.588 41.667 0.00 0.00 0.00 5.14
3372 3927 3.449746 AAGAAATTGGTCATCCCCGAA 57.550 42.857 0.00 0.00 0.00 4.30
3410 3966 2.939022 GGCAGCAACACGACAGTC 59.061 61.111 0.00 0.00 0.00 3.51
3414 3970 1.007271 AGCAACACGACAGTCGAGG 60.007 57.895 29.53 21.15 43.74 4.63
3416 3972 1.658114 CAACACGACAGTCGAGGGA 59.342 57.895 29.53 0.00 43.74 4.20
3420 3976 1.977544 ACGACAGTCGAGGGAAGGG 60.978 63.158 29.53 0.00 43.74 3.95
3423 3979 4.148825 CAGTCGAGGGAAGGGCGG 62.149 72.222 0.00 0.00 0.00 6.13
3451 4007 4.457496 CTGTCACGGGAGCGCCAT 62.457 66.667 9.31 0.00 35.15 4.40
3454 4010 3.700970 TCACGGGAGCGCCATCAA 61.701 61.111 9.31 0.00 35.15 2.57
3455 4011 3.197790 CACGGGAGCGCCATCAAG 61.198 66.667 9.31 0.00 35.15 3.02
3466 4022 3.436924 CATCAAGCGCAGGCAGCA 61.437 61.111 11.47 0.00 46.13 4.41
3473 4029 2.825387 CGCAGGCAGCATAGGCAA 60.825 61.111 0.67 0.00 46.13 4.52
3474 4030 2.409055 CGCAGGCAGCATAGGCAAA 61.409 57.895 0.67 0.00 46.13 3.68
3482 4038 2.480759 GCAGCATAGGCAAATGGTTCAG 60.481 50.000 0.67 0.00 44.61 3.02
3486 4042 2.573340 GGCAAATGGTTCAGCCGG 59.427 61.111 0.00 0.00 41.21 6.13
3508 4064 3.247056 TTGCGGGCGGTTCAGATCA 62.247 57.895 0.00 0.00 0.00 2.92
3509 4065 2.435938 GCGGGCGGTTCAGATCAA 60.436 61.111 0.00 0.00 0.00 2.57
3510 4066 2.038269 GCGGGCGGTTCAGATCAAA 61.038 57.895 0.00 0.00 0.00 2.69
3511 4067 1.982073 GCGGGCGGTTCAGATCAAAG 61.982 60.000 0.00 0.00 0.00 2.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 6.115446 TGCCAAGATTACGAGAGATCATTTT 58.885 36.000 0.00 0.00 0.00 1.82
38 39 3.181482 ACACATCAACCGAGATAGAGCAG 60.181 47.826 0.00 0.00 0.00 4.24
39 40 2.760650 ACACATCAACCGAGATAGAGCA 59.239 45.455 0.00 0.00 0.00 4.26
69 70 2.948315 GCCAAGGAGAGGATCACAATTC 59.052 50.000 0.00 0.00 37.82 2.17
71 72 1.213926 GGCCAAGGAGAGGATCACAAT 59.786 52.381 0.00 0.00 37.82 2.71
82 83 3.282885 GTGATTTTAGGAGGCCAAGGAG 58.717 50.000 5.01 0.00 0.00 3.69
92 93 5.739959 TGATCGTCAATGGTGATTTTAGGA 58.260 37.500 0.00 0.00 35.80 2.94
95 96 5.589855 AGCATGATCGTCAATGGTGATTTTA 59.410 36.000 0.00 0.00 35.80 1.52
103 104 3.060272 GTCGTTAGCATGATCGTCAATGG 60.060 47.826 0.00 0.00 0.00 3.16
110 111 4.033932 TCAAAATGGTCGTTAGCATGATCG 59.966 41.667 0.00 0.00 42.93 3.69
119 120 6.183360 CGATGATGACTTCAAAATGGTCGTTA 60.183 38.462 0.00 0.00 38.03 3.18
146 147 2.666317 GAGGAGAGGAGGAGGAAGAAG 58.334 57.143 0.00 0.00 0.00 2.85
157 158 2.172082 TCTTTATCGTCGGAGGAGAGGA 59.828 50.000 6.55 1.52 39.03 3.71
162 163 2.092538 AGGACTCTTTATCGTCGGAGGA 60.093 50.000 2.53 2.53 0.00 3.71
163 164 2.291190 GAGGACTCTTTATCGTCGGAGG 59.709 54.545 0.00 0.00 0.00 4.30
164 165 2.032722 CGAGGACTCTTTATCGTCGGAG 60.033 54.545 8.73 0.00 45.81 4.63
165 166 1.938577 CGAGGACTCTTTATCGTCGGA 59.061 52.381 8.73 0.00 45.81 4.55
166 167 2.386501 CGAGGACTCTTTATCGTCGG 57.613 55.000 8.73 0.00 45.81 4.79
173 178 6.361433 AGAGATGATCTTCGAGGACTCTTTA 58.639 40.000 8.92 0.00 32.99 1.85
279 285 1.134175 CAAGTGTTTGACGGTTTGCCT 59.866 47.619 0.00 0.00 36.36 4.75
291 297 2.551912 CGCCGCCCTTCAAGTGTTT 61.552 57.895 0.00 0.00 0.00 2.83
314 320 4.408821 GGGCAGCGGACCATGACA 62.409 66.667 2.80 0.00 44.16 3.58
328 334 3.125316 GCTAATATATGCTCAACGTGGGC 59.875 47.826 3.28 3.28 46.11 5.36
329 335 3.367932 CGCTAATATATGCTCAACGTGGG 59.632 47.826 0.00 0.00 0.00 4.61
339 345 2.671396 CCCGTCAACCGCTAATATATGC 59.329 50.000 0.00 0.00 34.38 3.14
350 356 0.533308 TCTCAAAACCCCGTCAACCG 60.533 55.000 0.00 0.00 0.00 4.44
352 358 1.539827 CCATCTCAAAACCCCGTCAAC 59.460 52.381 0.00 0.00 0.00 3.18
354 360 0.608035 GCCATCTCAAAACCCCGTCA 60.608 55.000 0.00 0.00 0.00 4.35
356 362 1.304134 GGCCATCTCAAAACCCCGT 60.304 57.895 0.00 0.00 0.00 5.28
359 365 0.610785 TTCCGGCCATCTCAAAACCC 60.611 55.000 2.24 0.00 0.00 4.11
362 368 1.533625 CACTTCCGGCCATCTCAAAA 58.466 50.000 2.24 0.00 0.00 2.44
394 400 2.175931 AGGCTCGGATCTTCTTCCTCTA 59.824 50.000 0.00 0.00 33.30 2.43
429 435 3.061231 TTGCCGCCGCATCATTGT 61.061 55.556 0.00 0.00 46.67 2.71
481 487 2.517598 TCGACTTCGAGCAAGTTGC 58.482 52.632 20.44 20.44 46.10 4.17
491 497 3.175240 CACCGCTGCTCGACTTCG 61.175 66.667 0.00 0.00 41.67 3.79
492 498 1.803519 CTCACCGCTGCTCGACTTC 60.804 63.158 0.00 0.00 41.67 3.01
514 520 0.180406 ACGCCTCACTGTCAACCTTT 59.820 50.000 0.00 0.00 0.00 3.11
536 542 0.685097 TGACTAGCCACCACCTTCAC 59.315 55.000 0.00 0.00 0.00 3.18
537 543 0.685097 GTGACTAGCCACCACCTTCA 59.315 55.000 0.00 0.00 0.00 3.02
559 565 1.007038 TCGTCGCCAGCGTTACTTT 60.007 52.632 12.32 0.00 40.74 2.66
575 581 2.594962 GCCACTCCACGTTGTGTCG 61.595 63.158 10.79 0.00 32.76 4.35
597 603 4.222145 TCACCTAGCCGATGAGTAAAAAGT 59.778 41.667 0.00 0.00 0.00 2.66
598 604 4.567159 GTCACCTAGCCGATGAGTAAAAAG 59.433 45.833 0.00 0.00 0.00 2.27
615 621 3.245441 CCCTAAATATACCCGGTCACCT 58.755 50.000 0.00 0.00 0.00 4.00
620 626 2.158325 TCGACCCCTAAATATACCCGGT 60.158 50.000 0.00 0.00 0.00 5.28
622 628 2.494870 CCTCGACCCCTAAATATACCCG 59.505 54.545 0.00 0.00 0.00 5.28
624 630 3.056035 CAGCCTCGACCCCTAAATATACC 60.056 52.174 0.00 0.00 0.00 2.73
625 631 3.830755 TCAGCCTCGACCCCTAAATATAC 59.169 47.826 0.00 0.00 0.00 1.47
639 645 5.277058 CGAGAGGAAAAATTTATCAGCCTCG 60.277 44.000 14.02 12.80 43.86 4.63
661 667 3.845775 CCGAACTCGTATCGTTTTTACGA 59.154 43.478 2.66 2.66 46.52 3.43
662 668 3.538258 GCCGAACTCGTATCGTTTTTACG 60.538 47.826 0.00 0.00 42.83 3.18
674 680 1.471684 CTTGTACCTAGCCGAACTCGT 59.528 52.381 0.00 0.00 37.74 4.18
675 681 1.471684 ACTTGTACCTAGCCGAACTCG 59.528 52.381 0.00 0.00 39.44 4.18
676 682 3.589495 AACTTGTACCTAGCCGAACTC 57.411 47.619 0.00 0.00 0.00 3.01
677 683 4.338879 TCTAACTTGTACCTAGCCGAACT 58.661 43.478 0.00 0.00 0.00 3.01
678 684 4.397417 TCTCTAACTTGTACCTAGCCGAAC 59.603 45.833 0.00 0.00 0.00 3.95
679 685 4.592942 TCTCTAACTTGTACCTAGCCGAA 58.407 43.478 0.00 0.00 0.00 4.30
680 686 4.226427 TCTCTAACTTGTACCTAGCCGA 57.774 45.455 0.00 0.00 0.00 5.54
681 687 4.202030 CCTTCTCTAACTTGTACCTAGCCG 60.202 50.000 0.00 0.00 0.00 5.52
682 688 4.099727 CCCTTCTCTAACTTGTACCTAGCC 59.900 50.000 0.00 0.00 0.00 3.93
683 689 4.710865 ACCCTTCTCTAACTTGTACCTAGC 59.289 45.833 0.00 0.00 0.00 3.42
684 690 7.147932 GGTTACCCTTCTCTAACTTGTACCTAG 60.148 44.444 0.00 0.00 0.00 3.02
685 691 6.665248 GGTTACCCTTCTCTAACTTGTACCTA 59.335 42.308 0.00 0.00 0.00 3.08
686 692 5.483231 GGTTACCCTTCTCTAACTTGTACCT 59.517 44.000 0.00 0.00 0.00 3.08
687 693 5.623141 CGGTTACCCTTCTCTAACTTGTACC 60.623 48.000 0.00 0.00 0.00 3.34
688 694 5.183904 TCGGTTACCCTTCTCTAACTTGTAC 59.816 44.000 0.00 0.00 0.00 2.90
689 695 5.324409 TCGGTTACCCTTCTCTAACTTGTA 58.676 41.667 0.00 0.00 0.00 2.41
690 696 4.154942 TCGGTTACCCTTCTCTAACTTGT 58.845 43.478 0.00 0.00 0.00 3.16
691 697 4.796038 TCGGTTACCCTTCTCTAACTTG 57.204 45.455 0.00 0.00 0.00 3.16
692 698 6.370186 AATTCGGTTACCCTTCTCTAACTT 57.630 37.500 0.00 0.00 0.00 2.66
693 699 6.370186 AAATTCGGTTACCCTTCTCTAACT 57.630 37.500 0.00 0.00 0.00 2.24
694 700 7.440556 GGATAAATTCGGTTACCCTTCTCTAAC 59.559 40.741 0.00 0.00 0.00 2.34
695 701 7.346436 AGGATAAATTCGGTTACCCTTCTCTAA 59.654 37.037 0.00 0.00 0.00 2.10
696 702 6.842807 AGGATAAATTCGGTTACCCTTCTCTA 59.157 38.462 0.00 0.00 0.00 2.43
697 703 5.666265 AGGATAAATTCGGTTACCCTTCTCT 59.334 40.000 0.00 0.00 0.00 3.10
698 704 5.926663 AGGATAAATTCGGTTACCCTTCTC 58.073 41.667 0.00 0.00 0.00 2.87
723 729 1.002251 GATCTCTGTCCGGCGTTAGAG 60.002 57.143 19.67 19.67 38.36 2.43
736 742 3.181485 GGGACAACTCTAACCGATCTCTG 60.181 52.174 0.00 0.00 0.00 3.35
755 761 1.347707 AGATGTTTGAACTGCTCGGGA 59.652 47.619 0.00 0.00 0.00 5.14
757 763 3.849911 TCTAGATGTTTGAACTGCTCGG 58.150 45.455 0.00 0.00 0.00 4.63
774 780 6.142818 AGTCTAGTGCTACTTTGCATCTAG 57.857 41.667 14.11 14.11 45.23 2.43
777 783 5.517054 GTGTAGTCTAGTGCTACTTTGCATC 59.483 44.000 19.81 0.00 45.23 3.91
787 1032 6.123651 ACTATAAGCTGTGTAGTCTAGTGCT 58.876 40.000 0.00 0.00 28.54 4.40
794 1039 7.976734 AGTCAATCAACTATAAGCTGTGTAGTC 59.023 37.037 6.44 0.00 33.33 2.59
811 1056 8.970702 GCCGCTGCTTTTGATTAGTCAATCAA 62.971 42.308 8.36 8.36 44.62 2.57
812 1057 4.142622 CCGCTGCTTTTGATTAGTCAATCA 60.143 41.667 1.06 0.00 46.96 2.57
813 1058 4.346129 CCGCTGCTTTTGATTAGTCAATC 58.654 43.478 1.06 0.00 43.49 2.67
814 1059 3.428045 GCCGCTGCTTTTGATTAGTCAAT 60.428 43.478 1.06 0.00 38.12 2.57
819 1064 1.739466 TCTGCCGCTGCTTTTGATTAG 59.261 47.619 0.70 0.00 38.71 1.73
834 1079 3.746492 ACGTGAGAGTTAACAAATCTGCC 59.254 43.478 8.61 0.00 35.72 4.85
932 1177 3.354948 AACTGAATGTGCTCTGCCATA 57.645 42.857 0.00 0.00 0.00 2.74
934 1179 1.985473 AAACTGAATGTGCTCTGCCA 58.015 45.000 0.00 0.00 0.00 4.92
985 1236 1.309950 GACGTGATCGATCCAGGAGA 58.690 55.000 22.31 0.00 40.62 3.71
1362 1625 3.064207 GCCGTCACAGTCAATAGAAACA 58.936 45.455 0.00 0.00 0.00 2.83
1365 1628 1.621317 TGGCCGTCACAGTCAATAGAA 59.379 47.619 0.00 0.00 0.00 2.10
2411 2701 1.422179 CTCGTCGTCTAGCTCGAGCA 61.422 60.000 36.87 22.05 45.16 4.26
2520 2811 9.436957 TGGCTTAACTTTTGTGAAATGTTTTAA 57.563 25.926 5.86 0.00 38.92 1.52
2522 2813 7.913674 TGGCTTAACTTTTGTGAAATGTTTT 57.086 28.000 5.86 0.00 38.92 2.43
2526 2817 9.437045 GAAATTTGGCTTAACTTTTGTGAAATG 57.563 29.630 0.00 0.00 0.00 2.32
2527 2818 8.334632 CGAAATTTGGCTTAACTTTTGTGAAAT 58.665 29.630 0.00 0.00 0.00 2.17
2528 2819 7.680062 CGAAATTTGGCTTAACTTTTGTGAAA 58.320 30.769 0.00 0.00 0.00 2.69
3003 3525 8.485591 GGCGAGTGAATAATGTAAGTATGTAAC 58.514 37.037 0.00 0.00 0.00 2.50
3004 3526 8.198778 TGGCGAGTGAATAATGTAAGTATGTAA 58.801 33.333 0.00 0.00 0.00 2.41
3005 3527 7.718525 TGGCGAGTGAATAATGTAAGTATGTA 58.281 34.615 0.00 0.00 0.00 2.29
3006 3528 6.578944 TGGCGAGTGAATAATGTAAGTATGT 58.421 36.000 0.00 0.00 0.00 2.29
3007 3529 7.410835 CGATGGCGAGTGAATAATGTAAGTATG 60.411 40.741 0.00 0.00 40.82 2.39
3009 3531 5.918576 CGATGGCGAGTGAATAATGTAAGTA 59.081 40.000 0.00 0.00 40.82 2.24
3011 3533 4.982295 TCGATGGCGAGTGAATAATGTAAG 59.018 41.667 0.00 0.00 42.51 2.34
3058 3583 4.445385 GTGACATGTGAAAAATGCAACCTC 59.555 41.667 1.15 0.00 33.78 3.85
3064 3597 6.646240 AGTTATTGGTGACATGTGAAAAATGC 59.354 34.615 1.15 0.00 42.32 3.56
3069 3602 5.825151 TGACAGTTATTGGTGACATGTGAAA 59.175 36.000 1.15 0.00 42.32 2.69
3104 3637 5.514274 TGTGAGAAAACTTTGATTCCACC 57.486 39.130 0.00 0.00 31.46 4.61
3133 3666 2.685850 ACTCAGGGCGGTTTACATAC 57.314 50.000 0.00 0.00 0.00 2.39
3142 3675 2.122783 TTAATCCAAACTCAGGGCGG 57.877 50.000 0.00 0.00 0.00 6.13
3164 3703 2.287368 GCCGTTCCTTCACGTGAAAATT 60.287 45.455 29.32 0.00 38.57 1.82
3172 3711 4.367023 TCCGGCCGTTCCTTCACG 62.367 66.667 26.12 5.01 40.02 4.35
3182 3721 4.162690 CTTCCTTCCCTCCGGCCG 62.163 72.222 21.04 21.04 0.00 6.13
3201 3744 2.273619 AGAGGGCTTTTCTGGTGATCT 58.726 47.619 0.00 0.00 0.00 2.75
3259 3814 2.234908 GTCGCCTGCCATCCTAAGATAT 59.765 50.000 0.00 0.00 0.00 1.63
3271 3826 1.600916 GATAATGGGGTCGCCTGCC 60.601 63.158 7.55 0.00 0.00 4.85
3276 3831 3.600388 CCAAGATAGATAATGGGGTCGC 58.400 50.000 0.00 0.00 0.00 5.19
3296 3851 3.966543 CTCACCCCCACACACCCC 61.967 72.222 0.00 0.00 0.00 4.95
3298 3853 3.966543 CCCTCACCCCCACACACC 61.967 72.222 0.00 0.00 0.00 4.16
3309 3864 0.106217 CTCCCTCCTCTCTCCCTCAC 60.106 65.000 0.00 0.00 0.00 3.51
3317 3872 0.629058 ACACCTCTCTCCCTCCTCTC 59.371 60.000 0.00 0.00 0.00 3.20
3318 3873 0.334676 CACACCTCTCTCCCTCCTCT 59.665 60.000 0.00 0.00 0.00 3.69
3319 3874 1.326951 GCACACCTCTCTCCCTCCTC 61.327 65.000 0.00 0.00 0.00 3.71
3320 3875 1.305718 GCACACCTCTCTCCCTCCT 60.306 63.158 0.00 0.00 0.00 3.69
3321 3876 1.610673 TGCACACCTCTCTCCCTCC 60.611 63.158 0.00 0.00 0.00 4.30
3322 3877 1.612395 CCTGCACACCTCTCTCCCTC 61.612 65.000 0.00 0.00 0.00 4.30
3323 3878 1.611851 CCTGCACACCTCTCTCCCT 60.612 63.158 0.00 0.00 0.00 4.20
3324 3879 2.985456 CCTGCACACCTCTCTCCC 59.015 66.667 0.00 0.00 0.00 4.30
3325 3880 2.237534 GAGCCTGCACACCTCTCTCC 62.238 65.000 0.00 0.00 0.00 3.71
3326 3881 1.217779 GAGCCTGCACACCTCTCTC 59.782 63.158 0.00 0.00 0.00 3.20
3327 3882 1.534959 TGAGCCTGCACACCTCTCT 60.535 57.895 5.44 0.00 0.00 3.10
3328 3883 1.375268 GTGAGCCTGCACACCTCTC 60.375 63.158 8.28 0.00 38.63 3.20
3329 3884 2.746359 GTGAGCCTGCACACCTCT 59.254 61.111 8.28 0.00 38.63 3.69
3333 3888 0.250234 TATCTGGTGAGCCTGCACAC 59.750 55.000 10.67 10.67 40.52 3.82
3334 3889 0.983467 TTATCTGGTGAGCCTGCACA 59.017 50.000 0.00 0.00 40.52 4.57
3335 3890 1.208052 TCTTATCTGGTGAGCCTGCAC 59.792 52.381 0.00 0.00 38.05 4.57
3340 3895 4.273318 ACCAATTTCTTATCTGGTGAGCC 58.727 43.478 0.00 0.00 40.69 4.70
3342 3897 6.261826 GGATGACCAATTTCTTATCTGGTGAG 59.738 42.308 0.00 0.00 42.27 3.51
3345 3900 5.449553 GGGATGACCAATTTCTTATCTGGT 58.550 41.667 0.00 0.00 44.90 4.00
3348 3903 4.412199 TCGGGGATGACCAATTTCTTATCT 59.588 41.667 0.00 0.00 42.91 1.98
3357 3912 3.112263 TCTAACTTCGGGGATGACCAAT 58.888 45.455 0.00 0.00 42.91 3.16
3358 3913 2.500098 CTCTAACTTCGGGGATGACCAA 59.500 50.000 0.00 0.00 42.91 3.67
3359 3914 2.108168 CTCTAACTTCGGGGATGACCA 58.892 52.381 0.00 0.00 42.91 4.02
3367 3922 1.413077 GACCATCCCTCTAACTTCGGG 59.587 57.143 0.00 0.00 39.41 5.14
3371 3926 2.389715 CCTCGACCATCCCTCTAACTT 58.610 52.381 0.00 0.00 0.00 2.66
3372 3927 2.030045 GCCTCGACCATCCCTCTAACT 61.030 57.143 0.00 0.00 0.00 2.24
3395 3951 1.278172 CCTCGACTGTCGTGTTGCTG 61.278 60.000 27.16 9.94 41.35 4.41
3396 3952 1.007271 CCTCGACTGTCGTGTTGCT 60.007 57.895 27.16 0.00 41.35 3.91
3404 3960 2.579738 GCCCTTCCCTCGACTGTC 59.420 66.667 0.00 0.00 0.00 3.51
3428 3984 4.803426 CTCCCGTGACAGCCTCGC 62.803 72.222 0.00 0.00 0.00 5.03
3429 3985 4.803426 GCTCCCGTGACAGCCTCG 62.803 72.222 0.00 0.00 0.00 4.63
3430 3986 4.803426 CGCTCCCGTGACAGCCTC 62.803 72.222 0.00 0.00 31.37 4.70
3434 3990 4.457496 ATGGCGCTCCCGTGACAG 62.457 66.667 7.64 0.00 42.98 3.51
3435 3991 4.451150 GATGGCGCTCCCGTGACA 62.451 66.667 7.64 0.00 44.05 3.58
3451 4007 1.816679 CTATGCTGCCTGCGCTTGA 60.817 57.895 9.73 0.00 46.63 3.02
3459 4015 0.032813 ACCATTTGCCTATGCTGCCT 60.033 50.000 0.00 0.00 38.71 4.75
3463 4019 1.753073 GCTGAACCATTTGCCTATGCT 59.247 47.619 0.00 0.00 38.71 3.79
3466 4022 1.392589 CGGCTGAACCATTTGCCTAT 58.607 50.000 0.00 0.00 42.90 2.57
3473 4029 3.860930 AACCGCCGGCTGAACCATT 62.861 57.895 25.71 4.76 39.03 3.16
3474 4030 4.344865 AACCGCCGGCTGAACCAT 62.345 61.111 25.71 0.00 39.03 3.55
3493 4049 2.089854 CTTTGATCTGAACCGCCCG 58.910 57.895 0.00 0.00 0.00 6.13


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

AutoCloner maintained by Alex Coulton.