Multiple sequence alignment - TraesCS1A01G079700

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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 TraesCS1A01G079700 chr1A 100.000 4108 0 0 1 4108 62610517 62614624 0.000000e+00 7587.0
1 TraesCS1A01G079700 chr1B 92.622 3456 138 46 1 3390 104463549 104466953 0.000000e+00 4861.0
2 TraesCS1A01G079700 chr1B 95.011 441 20 2 3668 4108 104467259 104467697 0.000000e+00 691.0
3 TraesCS1A01G079700 chr1B 85.366 82 8 3 2703 2784 162282035 162281958 9.460000e-12 82.4
4 TraesCS1A01G079700 chr1B 88.136 59 5 2 2640 2697 555633687 555633630 7.370000e-08 69.4
5 TraesCS1A01G079700 chr1B 91.837 49 3 1 3560 3608 12439946 12439993 2.650000e-07 67.6
6 TraesCS1A01G079700 chr1B 95.122 41 1 1 2700 2740 635936513 635936552 3.430000e-06 63.9
7 TraesCS1A01G079700 chr1D 95.214 1776 54 11 931 2687 63633610 63635373 0.000000e+00 2780.0
8 TraesCS1A01G079700 chr1D 88.519 1411 84 40 2757 4103 63635411 63636807 0.000000e+00 1637.0
9 TraesCS1A01G079700 chr1D 92.474 877 40 6 1 875 63632778 63633630 0.000000e+00 1230.0
10 TraesCS1A01G079700 chr1D 89.474 57 6 0 2641 2697 403331679 403331735 5.700000e-09 73.1
11 TraesCS1A01G079700 chr1D 95.455 44 1 1 3560 3603 394488500 394488542 7.370000e-08 69.4
12 TraesCS1A01G079700 chr4D 98.113 53 1 0 2645 2697 417934341 417934289 4.370000e-15 93.5
13 TraesCS1A01G079700 chr4D 100.000 39 0 0 2703 2741 417934327 417934289 5.700000e-09 73.1
14 TraesCS1A01G079700 chr7D 97.778 45 1 0 3564 3608 60676601 60676557 1.220000e-10 78.7
15 TraesCS1A01G079700 chr3D 83.750 80 13 0 2968 3047 144291490 144291569 4.400000e-10 76.8
16 TraesCS1A01G079700 chr3D 81.609 87 16 0 2959 3045 192058869 192058955 5.700000e-09 73.1
17 TraesCS1A01G079700 chr3A 80.612 98 19 0 2968 3065 262522792 262522695 4.400000e-10 76.8
18 TraesCS1A01G079700 chr3A 80.899 89 17 0 2959 3047 163923979 163924067 2.050000e-08 71.3
19 TraesCS1A01G079700 chr3B 92.593 54 1 2 2644 2697 136446376 136446426 1.580000e-09 75.0
20 TraesCS1A01G079700 chr2B 97.674 43 1 0 3566 3608 136171369 136171327 1.580000e-09 75.0
21 TraesCS1A01G079700 chr2B 95.238 42 1 1 2700 2741 169856165 169856205 9.530000e-07 65.8
22 TraesCS1A01G079700 chr2B 100.000 29 0 0 1954 1982 265219152 265219180 2.000000e-03 54.7
23 TraesCS1A01G079700 chr2A 92.453 53 3 1 2645 2697 10381991 10382042 1.580000e-09 75.0
24 TraesCS1A01G079700 chr2A 100.000 29 0 0 1954 1982 262576672 262576700 2.000000e-03 54.7
25 TraesCS1A01G079700 chr6B 95.556 45 2 0 3564 3608 255535465 255535421 5.700000e-09 73.1
26 TraesCS1A01G079700 chr5D 88.525 61 6 1 2637 2697 18085008 18085067 5.700000e-09 73.1
27 TraesCS1A01G079700 chr5D 100.000 39 0 0 2703 2741 59945824 59945786 5.700000e-09 73.1
28 TraesCS1A01G079700 chr5D 82.927 82 6 5 2704 2784 547069900 547069974 2.650000e-07 67.6
29 TraesCS1A01G079700 chr5B 95.556 45 2 0 3564 3608 384594859 384594903 5.700000e-09 73.1
30 TraesCS1A01G079700 chr5A 100.000 39 0 0 2703 2741 48467145 48467107 5.700000e-09 73.1
31 TraesCS1A01G079700 chr2D 95.556 45 2 0 3564 3608 391259008 391259052 5.700000e-09 73.1
32 TraesCS1A01G079700 chr4B 97.619 42 0 1 2700 2741 30729191 30729231 2.050000e-08 71.3
33 TraesCS1A01G079700 chr4B 89.474 57 4 2 2642 2697 564673360 564673415 2.050000e-08 71.3


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 TraesCS1A01G079700 chr1A 62610517 62614624 4107 False 7587.000000 7587 100.0000 1 4108 1 chr1A.!!$F1 4107
1 TraesCS1A01G079700 chr1B 104463549 104467697 4148 False 2776.000000 4861 93.8165 1 4108 2 chr1B.!!$F3 4107
2 TraesCS1A01G079700 chr1D 63632778 63636807 4029 False 1882.333333 2780 92.0690 1 4103 3 chr1D.!!$F3 4102

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
615 623 0.035152 CTCCCTTGCTGCATGTACCA 60.035 55.000 1.84 0.00 0.00 3.25 F
897 909 1.079819 CCACTAGTCCTGTGGCACG 60.080 63.158 13.77 7.78 46.73 5.34 F
2666 2705 0.032813 TCCCTCCGTCCGGAATTACT 60.033 55.000 5.23 0.00 44.66 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2597 2636 2.420372 GGCAAGCTTAGTAAGTTCCAGC 59.580 50.0 11.51 10.05 0.0 4.85 R
2697 2736 0.373716 GCGTCAAGTAATTCCTGGCG 59.626 55.0 4.50 4.50 0.0 5.69 R
4073 4319 0.693049 GGGAGAAGAGGGACAAGCAA 59.307 55.0 0.00 0.00 0.0 3.91 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
24 25 4.739137 GCAAGAGTGAGTGAAGAACTGAGT 60.739 45.833 0.00 0.00 40.07 3.41
34 35 4.626081 AACTGAGTTGGCGCGCCT 62.626 61.111 45.79 30.36 36.94 5.52
62 63 2.026014 CAAGGTTGTTTGCGCGCT 59.974 55.556 33.29 5.92 0.00 5.92
119 124 9.988350 ATGCAAATTTAGAAGTAGTTATCGTTG 57.012 29.630 0.00 0.00 0.00 4.10
205 213 2.095919 GGCGGTTGCACTTGTTTACTAG 60.096 50.000 0.00 0.00 45.35 2.57
206 214 2.664698 GCGGTTGCACTTGTTTACTAGC 60.665 50.000 0.00 0.00 42.15 3.42
208 216 3.002862 CGGTTGCACTTGTTTACTAGCAA 59.997 43.478 0.00 0.00 39.38 3.91
209 217 4.496673 CGGTTGCACTTGTTTACTAGCAAA 60.497 41.667 0.00 0.00 42.69 3.68
211 219 5.458779 GGTTGCACTTGTTTACTAGCAAAAG 59.541 40.000 0.00 0.00 42.69 2.27
213 221 4.884744 TGCACTTGTTTACTAGCAAAAGGA 59.115 37.500 0.00 0.00 0.00 3.36
214 222 5.358442 TGCACTTGTTTACTAGCAAAAGGAA 59.642 36.000 0.00 0.00 0.00 3.36
215 223 5.915196 GCACTTGTTTACTAGCAAAAGGAAG 59.085 40.000 0.00 0.03 0.00 3.46
216 224 5.915196 CACTTGTTTACTAGCAAAAGGAAGC 59.085 40.000 0.00 0.00 0.00 3.86
217 225 5.592688 ACTTGTTTACTAGCAAAAGGAAGCA 59.407 36.000 0.00 0.00 29.60 3.91
282 290 9.368674 CACTGATAGCTGGATGAATAATCTAAG 57.631 37.037 0.00 0.00 35.43 2.18
292 300 7.710907 TGGATGAATAATCTAAGACGTTTCCAG 59.289 37.037 0.00 0.00 35.43 3.86
359 367 7.386299 CCTGTAGGATATTGACAAGTATCAAGC 59.614 40.741 14.31 0.00 38.58 4.01
458 466 2.961536 TCCAATCCTACCTGGGAAGA 57.038 50.000 0.00 0.00 39.02 2.87
459 467 3.438131 TCCAATCCTACCTGGGAAGAT 57.562 47.619 0.00 0.00 39.02 2.40
460 468 4.569676 TCCAATCCTACCTGGGAAGATA 57.430 45.455 0.00 0.00 39.02 1.98
563 571 3.737266 GGTGTGCACATGAGATTGTTTTG 59.263 43.478 24.69 0.00 0.00 2.44
603 611 3.686726 GTGTGATTTCTGTAGCTCCCTTG 59.313 47.826 0.00 0.00 0.00 3.61
615 623 0.035152 CTCCCTTGCTGCATGTACCA 60.035 55.000 1.84 0.00 0.00 3.25
621 629 3.562973 CCTTGCTGCATGTACCATAGAAG 59.437 47.826 1.84 0.00 0.00 2.85
622 630 4.445453 CTTGCTGCATGTACCATAGAAGA 58.555 43.478 1.84 0.00 0.00 2.87
623 631 4.486125 TGCTGCATGTACCATAGAAGAA 57.514 40.909 0.00 0.00 0.00 2.52
702 713 6.768483 TGAGATAGATACAGAGGAGAGAGTG 58.232 44.000 0.00 0.00 0.00 3.51
740 751 6.980397 GCAAAGTAGTGGGATAAAATGAATGG 59.020 38.462 0.00 0.00 0.00 3.16
746 757 4.829492 GTGGGATAAAATGAATGGAGAGGG 59.171 45.833 0.00 0.00 0.00 4.30
790 802 4.985538 AGCATTCCTTCACTTGTTTCCTA 58.014 39.130 0.00 0.00 0.00 2.94
832 844 2.290641 CCATTGGGGCCATTACGCTATA 60.291 50.000 4.39 0.00 0.00 1.31
891 903 3.772025 CCATTTCTCTCCACTAGTCCTGT 59.228 47.826 0.00 0.00 0.00 4.00
897 909 1.079819 CCACTAGTCCTGTGGCACG 60.080 63.158 13.77 7.78 46.73 5.34
915 927 4.569162 GGCACGTGCTATTAGTATTTGTCA 59.431 41.667 36.84 0.00 41.70 3.58
933 945 6.449635 TTGTCAGATATATGGCCACAAAAC 57.550 37.500 8.16 0.00 0.00 2.43
1139 1151 4.946160 ACAGGAATCAATACCCAGGAAA 57.054 40.909 0.00 0.00 0.00 3.13
1161 1173 6.759497 AACCATCCAGCAAGTAATAACTTC 57.241 37.500 0.00 0.00 44.28 3.01
1199 1211 5.121380 ACAATTCTATCATCTGCAACCCT 57.879 39.130 0.00 0.00 0.00 4.34
1211 1223 3.512329 TCTGCAACCCTATTTCTCGTACA 59.488 43.478 0.00 0.00 0.00 2.90
1212 1224 4.020928 TCTGCAACCCTATTTCTCGTACAA 60.021 41.667 0.00 0.00 0.00 2.41
1217 1229 6.674760 GCAACCCTATTTCTCGTACAACATTC 60.675 42.308 0.00 0.00 0.00 2.67
1241 1253 9.547753 TTCTACTTCTGTTGCCTGATAATATTC 57.452 33.333 0.00 0.00 0.00 1.75
1598 1610 8.777578 ACTTACATTCACAGGTATCTATGGTA 57.222 34.615 0.00 0.00 0.00 3.25
1625 1637 5.232463 AGGCTTAAGCATGAAAATGTTGTG 58.768 37.500 27.83 0.00 44.36 3.33
1649 1661 3.877508 AGTTGCTTGGTTACTGTCTTGAC 59.122 43.478 0.00 0.00 0.00 3.18
1797 1810 6.952773 TGGTGCAGTTAAGTTCTTATGTTT 57.047 33.333 0.00 0.00 0.00 2.83
1798 1811 6.734137 TGGTGCAGTTAAGTTCTTATGTTTG 58.266 36.000 0.00 0.00 0.00 2.93
1799 1812 6.544197 TGGTGCAGTTAAGTTCTTATGTTTGA 59.456 34.615 0.00 0.00 0.00 2.69
1800 1813 7.230510 TGGTGCAGTTAAGTTCTTATGTTTGAT 59.769 33.333 0.00 0.00 0.00 2.57
2379 2416 5.126061 CCTTTGGTGGATGGAATTCTAACAG 59.874 44.000 5.23 0.00 0.00 3.16
2387 2424 6.549364 TGGATGGAATTCTAACAGTTGTTTGT 59.451 34.615 5.23 0.00 39.31 2.83
2521 2558 2.031944 GCCTCTCTTGGTTTCGAAACAC 60.032 50.000 34.79 25.59 40.63 3.32
2528 2565 1.336440 TGGTTTCGAAACACTGCATGG 59.664 47.619 34.79 0.00 40.63 3.66
2609 2648 8.409358 AAATACTGATTTTGCTGGAACTTACT 57.591 30.769 0.00 0.00 30.77 2.24
2666 2705 0.032813 TCCCTCCGTCCGGAATTACT 60.033 55.000 5.23 0.00 44.66 2.24
2668 2707 1.472728 CCCTCCGTCCGGAATTACTTG 60.473 57.143 5.23 0.00 44.66 3.16
2669 2708 1.479323 CCTCCGTCCGGAATTACTTGA 59.521 52.381 5.23 0.00 44.66 3.02
2670 2709 2.537401 CTCCGTCCGGAATTACTTGAC 58.463 52.381 5.23 0.00 44.66 3.18
2671 2710 1.135315 TCCGTCCGGAATTACTTGACG 60.135 52.381 17.86 17.86 46.05 4.35
2672 2711 0.643820 CGTCCGGAATTACTTGACGC 59.356 55.000 5.23 0.00 41.71 5.19
2673 2712 1.734707 CGTCCGGAATTACTTGACGCT 60.735 52.381 5.23 0.00 41.71 5.07
2674 2713 1.925185 GTCCGGAATTACTTGACGCTC 59.075 52.381 5.23 0.00 0.00 5.03
2675 2714 1.546923 TCCGGAATTACTTGACGCTCA 59.453 47.619 0.00 0.00 0.00 4.26
2676 2715 2.028839 TCCGGAATTACTTGACGCTCAA 60.029 45.455 0.00 1.48 34.79 3.02
2677 2716 2.936498 CCGGAATTACTTGACGCTCAAT 59.064 45.455 0.00 0.00 35.59 2.57
2678 2717 3.001330 CCGGAATTACTTGACGCTCAATC 59.999 47.826 0.00 0.00 35.59 2.67
2679 2718 3.301835 CGGAATTACTTGACGCTCAATCG 60.302 47.826 1.76 0.00 35.59 3.34
2680 2719 3.001330 GGAATTACTTGACGCTCAATCGG 59.999 47.826 1.76 0.00 35.59 4.18
2681 2720 3.520290 ATTACTTGACGCTCAATCGGA 57.480 42.857 1.76 0.00 35.59 4.55
2682 2721 3.520290 TTACTTGACGCTCAATCGGAT 57.480 42.857 1.76 0.00 35.59 4.18
2683 2722 1.645034 ACTTGACGCTCAATCGGATG 58.355 50.000 0.00 0.00 35.59 3.51
2684 2723 1.066858 ACTTGACGCTCAATCGGATGT 60.067 47.619 0.00 0.00 35.59 3.06
2685 2724 2.165641 ACTTGACGCTCAATCGGATGTA 59.834 45.455 0.00 0.00 35.59 2.29
2686 2725 3.181475 ACTTGACGCTCAATCGGATGTAT 60.181 43.478 0.00 0.00 35.59 2.29
2687 2726 3.013276 TGACGCTCAATCGGATGTATC 57.987 47.619 0.00 0.00 0.00 2.24
2688 2727 2.623416 TGACGCTCAATCGGATGTATCT 59.377 45.455 0.00 0.00 0.00 1.98
2689 2728 3.818773 TGACGCTCAATCGGATGTATCTA 59.181 43.478 0.00 0.00 0.00 1.98
2690 2729 4.083271 TGACGCTCAATCGGATGTATCTAG 60.083 45.833 0.00 0.00 0.00 2.43
2691 2730 3.175152 CGCTCAATCGGATGTATCTAGC 58.825 50.000 0.00 0.00 0.00 3.42
2692 2731 3.366374 CGCTCAATCGGATGTATCTAGCA 60.366 47.826 0.00 0.00 0.00 3.49
2693 2732 3.923461 GCTCAATCGGATGTATCTAGCAC 59.077 47.826 0.00 0.00 0.00 4.40
2694 2733 4.321601 GCTCAATCGGATGTATCTAGCACT 60.322 45.833 0.00 0.00 0.00 4.40
2695 2734 5.106118 GCTCAATCGGATGTATCTAGCACTA 60.106 44.000 0.00 0.00 0.00 2.74
2696 2735 6.570571 GCTCAATCGGATGTATCTAGCACTAA 60.571 42.308 0.00 0.00 0.00 2.24
2697 2736 6.678878 TCAATCGGATGTATCTAGCACTAAC 58.321 40.000 0.00 0.00 0.00 2.34
2698 2737 4.744136 TCGGATGTATCTAGCACTAACG 57.256 45.455 0.00 0.00 0.00 3.18
2699 2738 3.058432 TCGGATGTATCTAGCACTAACGC 60.058 47.826 0.00 0.00 0.00 4.84
2700 2739 3.576648 GGATGTATCTAGCACTAACGCC 58.423 50.000 0.00 0.00 0.00 5.68
2701 2740 3.005472 GGATGTATCTAGCACTAACGCCA 59.995 47.826 0.00 0.00 0.00 5.69
2702 2741 3.710326 TGTATCTAGCACTAACGCCAG 57.290 47.619 0.00 0.00 0.00 4.85
2703 2742 2.361119 TGTATCTAGCACTAACGCCAGG 59.639 50.000 0.00 0.00 0.00 4.45
2704 2743 1.776662 ATCTAGCACTAACGCCAGGA 58.223 50.000 0.00 0.00 0.00 3.86
2705 2744 1.552578 TCTAGCACTAACGCCAGGAA 58.447 50.000 0.00 0.00 0.00 3.36
2706 2745 2.108168 TCTAGCACTAACGCCAGGAAT 58.892 47.619 0.00 0.00 0.00 3.01
2734 2773 3.966154 ACGCTCAAACGGATGTATCTAG 58.034 45.455 0.00 0.00 37.37 2.43
2740 2779 6.459670 TCAAACGGATGTATCTAGCACTAA 57.540 37.500 0.00 0.00 0.00 2.24
2741 2780 6.270815 TCAAACGGATGTATCTAGCACTAAC 58.729 40.000 0.00 0.00 0.00 2.34
2742 2781 4.485024 ACGGATGTATCTAGCACTAACG 57.515 45.455 0.00 0.00 0.00 3.18
2743 2782 3.235195 CGGATGTATCTAGCACTAACGC 58.765 50.000 0.00 0.00 0.00 4.84
2744 2783 3.576648 GGATGTATCTAGCACTAACGCC 58.423 50.000 0.00 0.00 0.00 5.68
2745 2784 3.256136 GGATGTATCTAGCACTAACGCCT 59.744 47.826 0.00 0.00 0.00 5.52
2746 2785 3.710326 TGTATCTAGCACTAACGCCTG 57.290 47.619 0.00 0.00 0.00 4.85
2747 2786 3.021695 TGTATCTAGCACTAACGCCTGT 58.978 45.455 0.00 0.00 0.00 4.00
2748 2787 3.446161 TGTATCTAGCACTAACGCCTGTT 59.554 43.478 0.00 0.00 42.19 3.16
2749 2788 2.649331 TCTAGCACTAACGCCTGTTC 57.351 50.000 0.00 0.00 39.54 3.18
2750 2789 1.135489 TCTAGCACTAACGCCTGTTCG 60.135 52.381 0.00 0.00 39.54 3.95
2751 2790 0.883153 TAGCACTAACGCCTGTTCGA 59.117 50.000 0.00 0.00 39.54 3.71
2752 2791 0.388649 AGCACTAACGCCTGTTCGAG 60.389 55.000 0.00 0.00 39.54 4.04
2753 2792 1.956620 GCACTAACGCCTGTTCGAGC 61.957 60.000 0.00 0.00 39.54 5.03
2755 2794 0.246635 ACTAACGCCTGTTCGAGCAT 59.753 50.000 1.26 0.00 39.54 3.79
2756 2795 0.647410 CTAACGCCTGTTCGAGCATG 59.353 55.000 1.26 0.67 39.54 4.06
2759 2798 1.737735 CGCCTGTTCGAGCATGTCA 60.738 57.895 1.26 0.00 0.00 3.58
2769 2831 5.106712 TGTTCGAGCATGTCAAAGTAATTCC 60.107 40.000 0.00 0.00 0.00 3.01
2771 2833 3.685058 GAGCATGTCAAAGTAATTCCGC 58.315 45.455 0.00 0.00 0.00 5.54
2798 2860 6.489361 CGGAGGGAGTACTAGCTAAGAATTTA 59.511 42.308 0.00 0.00 0.00 1.40
2823 2885 4.433186 TCCAGAAACTGTGTTTGTTGTG 57.567 40.909 0.10 0.00 0.00 3.33
2824 2886 3.192422 TCCAGAAACTGTGTTTGTTGTGG 59.808 43.478 0.10 0.29 35.40 4.17
2829 2891 3.988379 ACTGTGTTTGTTGTGGCATAG 57.012 42.857 0.00 0.00 0.00 2.23
2881 2964 9.469807 CCTACTACTGTGATTAACATCATTCTC 57.530 37.037 0.00 0.00 41.64 2.87
2894 2984 4.221482 ACATCATTCTCGGAGCATGCTATA 59.779 41.667 22.74 8.09 0.00 1.31
2904 2994 4.568359 CGGAGCATGCTATATGTCATAACC 59.432 45.833 22.74 11.77 0.00 2.85
2916 3006 5.871396 ATGTCATAACCAAGTCGAGGTAT 57.129 39.130 0.00 0.00 38.76 2.73
2921 3011 7.123098 TGTCATAACCAAGTCGAGGTATTCTTA 59.877 37.037 0.00 0.00 38.76 2.10
2924 3014 4.351127 ACCAAGTCGAGGTATTCTTAGGT 58.649 43.478 0.00 0.00 37.67 3.08
2925 3015 4.159879 ACCAAGTCGAGGTATTCTTAGGTG 59.840 45.833 0.00 0.00 37.67 4.00
2948 3038 2.890945 AGCCACTTGTAACACCATTTCC 59.109 45.455 0.00 0.00 0.00 3.13
3005 3095 0.662619 CGGCATTGTGCGTCCAATAT 59.337 50.000 2.11 0.00 46.21 1.28
3110 3200 2.511373 CATGCCGGACGCTAAGCA 60.511 61.111 5.05 0.00 40.00 3.91
3314 3407 5.312120 AGTACCTAGAACACTTGTCATCG 57.688 43.478 0.00 0.00 0.00 3.84
3335 3428 4.528596 TCGGACAGAGAGAAAAAGGAAGAT 59.471 41.667 0.00 0.00 0.00 2.40
3421 3536 9.447157 TTTCTCATTTTGTGTTGGATTTTTCTT 57.553 25.926 0.00 0.00 0.00 2.52
3490 3605 4.771114 TCTCAAACAGAAACAGAAGGGA 57.229 40.909 0.00 0.00 0.00 4.20
3494 3609 6.095440 TCTCAAACAGAAACAGAAGGGAAAAG 59.905 38.462 0.00 0.00 0.00 2.27
3512 3627 2.898729 AGGAGTCGCATAATGGACTG 57.101 50.000 6.38 0.00 43.23 3.51
3521 3636 3.002042 CGCATAATGGACTGAAGAAGCAG 59.998 47.826 0.00 0.00 41.63 4.24
3528 3643 4.836825 TGGACTGAAGAAGCAGGAATTAG 58.163 43.478 0.00 0.00 40.20 1.73
3530 3645 3.615155 ACTGAAGAAGCAGGAATTAGCC 58.385 45.455 0.00 0.00 40.20 3.93
3540 3655 6.001449 AGCAGGAATTAGCCATGTACTTTA 57.999 37.500 0.00 0.00 0.00 1.85
3541 3656 6.423182 AGCAGGAATTAGCCATGTACTTTAA 58.577 36.000 0.00 0.00 0.00 1.52
3618 3766 2.499289 ACAGAGGAAGTGGTAGATGCTG 59.501 50.000 0.00 0.00 0.00 4.41
3631 3779 6.752815 GTGGTAGATGCTGAAGAGTACTAAAC 59.247 42.308 0.00 0.00 0.00 2.01
3638 3786 7.534723 TGCTGAAGAGTACTAAACCTCTTAA 57.465 36.000 0.00 0.00 36.44 1.85
3713 3948 7.834803 AGTACAGGATTACAGTTAACTACCAC 58.165 38.462 8.04 0.00 0.00 4.16
3767 4002 3.700539 GGTCTAGAGGACTAAACCTGGAC 59.299 52.174 0.00 0.00 43.97 4.02
3852 4087 2.823747 ACAACGCTACTCCAGTACATGA 59.176 45.455 0.00 0.00 0.00 3.07
3959 4205 0.811616 GGACCATCACGACCAGCATC 60.812 60.000 0.00 0.00 0.00 3.91
3974 4220 4.141965 ATCGACATGCCGGCGACA 62.142 61.111 23.90 1.91 36.83 4.35
4073 4319 2.500910 CTGATCCTTGAGCTCCTTGAGT 59.499 50.000 12.15 0.00 31.39 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
49 50 0.981956 GGAAATAGCGCGCAAACAAC 59.018 50.000 35.10 18.49 0.00 3.32
62 63 2.354510 CTGAAATTGCGCGAGGGAAATA 59.645 45.455 12.10 0.00 0.00 1.40
205 213 4.451774 TGCAAATTATGTGCTTCCTTTTGC 59.548 37.500 8.95 9.77 44.59 3.68
206 214 6.203338 ACTTGCAAATTATGTGCTTCCTTTTG 59.797 34.615 8.95 0.00 42.69 2.44
208 216 5.697633 CACTTGCAAATTATGTGCTTCCTTT 59.302 36.000 8.95 0.00 42.69 3.11
209 217 5.221501 ACACTTGCAAATTATGTGCTTCCTT 60.222 36.000 13.86 0.00 42.69 3.36
211 219 4.559153 ACACTTGCAAATTATGTGCTTCC 58.441 39.130 13.86 0.00 42.69 3.46
213 221 5.599732 TGAACACTTGCAAATTATGTGCTT 58.400 33.333 13.86 8.66 42.69 3.91
214 222 5.199024 TGAACACTTGCAAATTATGTGCT 57.801 34.783 13.86 3.95 42.69 4.40
215 223 5.865552 AGATGAACACTTGCAAATTATGTGC 59.134 36.000 13.86 0.00 42.55 4.57
216 224 6.309494 CCAGATGAACACTTGCAAATTATGTG 59.691 38.462 12.70 12.70 35.09 3.21
217 225 6.015180 ACCAGATGAACACTTGCAAATTATGT 60.015 34.615 0.00 0.00 0.00 2.29
257 265 9.319060 TCTTAGATTATTCATCCAGCTATCAGT 57.681 33.333 0.00 0.00 31.20 3.41
282 290 2.006772 CATAGCGGCTGGAAACGTC 58.993 57.895 13.86 0.00 0.00 4.34
359 367 3.128764 ACAGCTCATTCTGCATCAACATG 59.871 43.478 0.00 0.00 37.59 3.21
516 524 3.564235 TCATGTGCAAACATTCTCTGC 57.436 42.857 0.00 0.00 36.60 4.26
582 590 3.869912 GCAAGGGAGCTACAGAAATCACA 60.870 47.826 0.00 0.00 0.00 3.58
596 604 0.035152 TGGTACATGCAGCAAGGGAG 60.035 55.000 0.00 0.00 0.00 4.30
615 623 4.070716 GCAGGTGCAGCATATTCTTCTAT 58.929 43.478 19.63 0.00 41.59 1.98
643 651 2.024414 GCCCATAAGTGAACCATGACC 58.976 52.381 0.00 0.00 0.00 4.02
702 713 4.214332 CACTACTTTGCTTCCCTTTGTCTC 59.786 45.833 0.00 0.00 0.00 3.36
740 751 5.099042 TGTACAGCTAAATTTCCCCTCTC 57.901 43.478 0.00 0.00 0.00 3.20
746 757 7.985476 TGCTTAAGATGTACAGCTAAATTTCC 58.015 34.615 15.12 0.62 33.15 3.13
790 802 9.506018 CAATGGGGAAATAGAAGTTGAATTTTT 57.494 29.630 0.00 0.00 0.00 1.94
832 844 9.823647 AGTTTCGATTCATACTTCATTCTGTAT 57.176 29.630 0.00 0.00 0.00 2.29
891 903 4.509616 ACAAATACTAATAGCACGTGCCA 58.490 39.130 35.51 24.95 43.38 4.92
893 905 5.518847 TCTGACAAATACTAATAGCACGTGC 59.481 40.000 32.79 32.79 42.49 5.34
915 927 6.900194 ACTGTAGTTTTGTGGCCATATATCT 58.100 36.000 9.72 8.74 0.00 1.98
924 936 5.494632 AACTGTAACTGTAGTTTTGTGGC 57.505 39.130 2.20 0.00 39.31 5.01
933 945 7.148689 GGAACATAAACGGAACTGTAACTGTAG 60.149 40.741 0.00 0.00 0.00 2.74
1139 1151 4.876107 CGAAGTTATTACTTGCTGGATGGT 59.124 41.667 1.04 0.00 44.51 3.55
1174 1186 7.293073 AGGGTTGCAGATGATAGAATTGTAAT 58.707 34.615 0.00 0.00 0.00 1.89
1190 1202 3.857052 TGTACGAGAAATAGGGTTGCAG 58.143 45.455 0.00 0.00 0.00 4.41
1199 1211 9.569167 CAGAAGTAGAATGTTGTACGAGAAATA 57.431 33.333 0.00 0.00 32.69 1.40
1211 1223 4.973168 TCAGGCAACAGAAGTAGAATGTT 58.027 39.130 0.00 0.00 37.64 2.71
1212 1224 4.623932 TCAGGCAACAGAAGTAGAATGT 57.376 40.909 0.00 0.00 41.41 2.71
1217 1229 8.893219 TGAATATTATCAGGCAACAGAAGTAG 57.107 34.615 0.00 0.00 34.90 2.57
1241 1253 6.716438 CAGATCAGTTGCAGTTCATTAGATG 58.284 40.000 0.00 0.00 0.00 2.90
1523 1535 5.654209 GCAGAATTCCTAAACAGGGAGAAAT 59.346 40.000 0.65 0.00 34.06 2.17
1527 1539 3.955471 TGCAGAATTCCTAAACAGGGAG 58.045 45.455 0.65 0.00 34.06 4.30
1574 1586 9.862371 GATACCATAGATACCTGTGAATGTAAG 57.138 37.037 0.00 0.00 33.90 2.34
1598 1610 6.290294 ACATTTTCATGCTTAAGCCTTGAT 57.710 33.333 24.30 8.54 41.18 2.57
1625 1637 3.127425 AGACAGTAACCAAGCAACTCC 57.873 47.619 0.00 0.00 0.00 3.85
2379 2416 4.794169 CCTGCCAGTGTATAACAAACAAC 58.206 43.478 0.00 0.00 0.00 3.32
2448 2485 3.140143 AGGATAGTCCCCTCCAAGTCTA 58.860 50.000 0.00 0.00 37.19 2.59
2528 2565 5.479306 TGATAACTGACAGACTGCTTAACC 58.521 41.667 10.08 0.00 0.00 2.85
2597 2636 2.420372 GGCAAGCTTAGTAAGTTCCAGC 59.580 50.000 11.51 10.05 0.00 4.85
2609 2648 6.992063 TTCAAAACAAAAATGGCAAGCTTA 57.008 29.167 0.00 0.00 0.00 3.09
2666 2705 2.951457 TACATCCGATTGAGCGTCAA 57.049 45.000 3.49 3.49 41.09 3.18
2668 2707 3.290308 AGATACATCCGATTGAGCGTC 57.710 47.619 0.00 0.00 0.00 5.19
2669 2708 3.366476 GCTAGATACATCCGATTGAGCGT 60.366 47.826 0.00 0.00 0.00 5.07
2670 2709 3.175152 GCTAGATACATCCGATTGAGCG 58.825 50.000 0.00 0.00 0.00 5.03
2671 2710 3.923461 GTGCTAGATACATCCGATTGAGC 59.077 47.826 0.00 0.00 0.00 4.26
2672 2711 5.384063 AGTGCTAGATACATCCGATTGAG 57.616 43.478 0.00 0.00 0.00 3.02
2673 2712 6.567891 CGTTAGTGCTAGATACATCCGATTGA 60.568 42.308 0.00 0.00 0.00 2.57
2674 2713 5.569441 CGTTAGTGCTAGATACATCCGATTG 59.431 44.000 0.00 0.00 0.00 2.67
2675 2714 5.700846 CGTTAGTGCTAGATACATCCGATT 58.299 41.667 0.00 0.00 0.00 3.34
2676 2715 4.379603 GCGTTAGTGCTAGATACATCCGAT 60.380 45.833 0.00 0.00 0.00 4.18
2677 2716 3.058432 GCGTTAGTGCTAGATACATCCGA 60.058 47.826 0.00 0.00 0.00 4.55
2678 2717 3.235195 GCGTTAGTGCTAGATACATCCG 58.765 50.000 0.00 0.00 0.00 4.18
2679 2718 3.005472 TGGCGTTAGTGCTAGATACATCC 59.995 47.826 0.00 0.00 34.52 3.51
2680 2719 4.230657 CTGGCGTTAGTGCTAGATACATC 58.769 47.826 0.00 0.00 45.36 3.06
2681 2720 3.005897 CCTGGCGTTAGTGCTAGATACAT 59.994 47.826 0.00 0.00 45.36 2.29
2682 2721 2.361119 CCTGGCGTTAGTGCTAGATACA 59.639 50.000 0.00 0.00 45.36 2.29
2683 2722 2.621998 TCCTGGCGTTAGTGCTAGATAC 59.378 50.000 0.00 0.00 45.36 2.24
2684 2723 2.940158 TCCTGGCGTTAGTGCTAGATA 58.060 47.619 0.00 0.00 45.36 1.98
2685 2724 1.776662 TCCTGGCGTTAGTGCTAGAT 58.223 50.000 0.00 0.00 45.36 1.98
2686 2725 1.552578 TTCCTGGCGTTAGTGCTAGA 58.447 50.000 0.00 0.00 45.36 2.43
2687 2726 2.604046 ATTCCTGGCGTTAGTGCTAG 57.396 50.000 0.00 0.00 42.51 3.42
2688 2727 3.449737 AGTAATTCCTGGCGTTAGTGCTA 59.550 43.478 0.00 0.00 34.52 3.49
2689 2728 2.236395 AGTAATTCCTGGCGTTAGTGCT 59.764 45.455 0.00 0.00 34.52 4.40
2690 2729 2.629051 AGTAATTCCTGGCGTTAGTGC 58.371 47.619 0.00 0.00 0.00 4.40
2691 2730 4.092968 GTCAAGTAATTCCTGGCGTTAGTG 59.907 45.833 0.00 0.00 0.00 2.74
2692 2731 4.251268 GTCAAGTAATTCCTGGCGTTAGT 58.749 43.478 0.00 0.00 0.00 2.24
2693 2732 3.306166 CGTCAAGTAATTCCTGGCGTTAG 59.694 47.826 0.00 0.00 0.00 2.34
2694 2733 3.255725 CGTCAAGTAATTCCTGGCGTTA 58.744 45.455 0.00 0.00 0.00 3.18
2695 2734 2.073816 CGTCAAGTAATTCCTGGCGTT 58.926 47.619 0.00 0.00 0.00 4.84
2696 2735 1.722011 CGTCAAGTAATTCCTGGCGT 58.278 50.000 0.00 0.00 0.00 5.68
2697 2736 0.373716 GCGTCAAGTAATTCCTGGCG 59.626 55.000 4.50 4.50 0.00 5.69
2698 2737 1.666189 GAGCGTCAAGTAATTCCTGGC 59.334 52.381 0.00 0.00 0.00 4.85
2699 2738 2.972625 TGAGCGTCAAGTAATTCCTGG 58.027 47.619 0.00 0.00 0.00 4.45
2700 2739 4.666655 CGTTTGAGCGTCAAGTAATTCCTG 60.667 45.833 1.72 0.00 37.70 3.86
2701 2740 3.432252 CGTTTGAGCGTCAAGTAATTCCT 59.568 43.478 1.72 0.00 37.70 3.36
2702 2741 3.424433 CCGTTTGAGCGTCAAGTAATTCC 60.424 47.826 1.72 0.00 37.70 3.01
2703 2742 3.430895 TCCGTTTGAGCGTCAAGTAATTC 59.569 43.478 1.72 0.00 37.70 2.17
2704 2743 3.395639 TCCGTTTGAGCGTCAAGTAATT 58.604 40.909 1.72 0.00 37.70 1.40
2705 2744 3.034721 TCCGTTTGAGCGTCAAGTAAT 57.965 42.857 1.72 0.00 37.70 1.89
2706 2745 2.512485 TCCGTTTGAGCGTCAAGTAA 57.488 45.000 1.72 0.00 37.70 2.24
2734 2773 1.956620 GCTCGAACAGGCGTTAGTGC 61.957 60.000 11.04 11.04 39.09 4.40
2740 2779 1.738099 GACATGCTCGAACAGGCGT 60.738 57.895 0.00 0.00 0.00 5.68
2741 2780 1.291184 TTGACATGCTCGAACAGGCG 61.291 55.000 0.00 0.00 0.00 5.52
2742 2781 0.874390 TTTGACATGCTCGAACAGGC 59.126 50.000 0.00 0.00 0.00 4.85
2743 2782 2.146342 ACTTTGACATGCTCGAACAGG 58.854 47.619 0.00 0.00 0.00 4.00
2744 2783 4.990543 TTACTTTGACATGCTCGAACAG 57.009 40.909 0.00 0.00 0.00 3.16
2745 2784 5.106712 GGAATTACTTTGACATGCTCGAACA 60.107 40.000 0.00 0.00 0.00 3.18
2746 2785 5.324697 GGAATTACTTTGACATGCTCGAAC 58.675 41.667 0.00 0.00 0.00 3.95
2747 2786 4.092821 CGGAATTACTTTGACATGCTCGAA 59.907 41.667 0.00 0.00 0.00 3.71
2748 2787 3.616821 CGGAATTACTTTGACATGCTCGA 59.383 43.478 0.00 0.00 0.00 4.04
2749 2788 3.785505 GCGGAATTACTTTGACATGCTCG 60.786 47.826 0.00 0.00 0.00 5.03
2750 2789 3.126858 TGCGGAATTACTTTGACATGCTC 59.873 43.478 0.00 0.00 0.00 4.26
2751 2790 3.081061 TGCGGAATTACTTTGACATGCT 58.919 40.909 0.00 0.00 0.00 3.79
2752 2791 3.171277 GTGCGGAATTACTTTGACATGC 58.829 45.455 0.00 0.00 0.00 4.06
2753 2792 3.416277 CGTGCGGAATTACTTTGACATG 58.584 45.455 0.00 0.00 0.00 3.21
2755 2794 1.801771 CCGTGCGGAATTACTTTGACA 59.198 47.619 4.35 0.00 37.50 3.58
2756 2795 2.070783 TCCGTGCGGAATTACTTTGAC 58.929 47.619 11.22 0.00 42.05 3.18
2759 2798 1.677820 CCCTCCGTGCGGAATTACTTT 60.678 52.381 14.53 0.00 44.66 2.66
2769 2831 2.023318 CTAGTACTCCCTCCGTGCG 58.977 63.158 0.00 0.00 0.00 5.34
2771 2833 2.634815 TAGCTAGTACTCCCTCCGTG 57.365 55.000 0.00 0.00 0.00 4.94
2798 2860 6.368516 CACAACAAACACAGTTTCTGGAAATT 59.631 34.615 0.00 0.00 35.51 1.82
2857 2940 8.135529 CCGAGAATGATGTTAATCACAGTAGTA 58.864 37.037 0.00 0.00 45.51 1.82
2881 2964 4.568359 GGTTATGACATATAGCATGCTCCG 59.432 45.833 26.57 13.43 0.00 4.63
2894 2984 5.871396 ATACCTCGACTTGGTTATGACAT 57.129 39.130 0.00 0.00 38.88 3.06
2904 2994 5.578005 TCACCTAAGAATACCTCGACTTG 57.422 43.478 0.00 0.00 0.00 3.16
2916 3006 3.857157 ACAAGTGGCTTCACCTAAGAA 57.143 42.857 0.00 0.00 42.13 2.52
2921 3011 2.572290 GTGTTACAAGTGGCTTCACCT 58.428 47.619 0.00 0.00 42.13 4.00
2924 3014 2.719531 TGGTGTTACAAGTGGCTTCA 57.280 45.000 0.00 0.00 0.00 3.02
2925 3015 4.546570 GAAATGGTGTTACAAGTGGCTTC 58.453 43.478 0.00 0.00 0.00 3.86
2948 3038 3.673746 TTCAAACAACACGCAGAAGAG 57.326 42.857 0.00 0.00 0.00 2.85
3110 3200 0.696501 ATACAAAAGGCCGGAGTGGT 59.303 50.000 5.05 0.00 41.21 4.16
3314 3407 9.892130 TTATTATCTTCCTTTTTCTCTCTGTCC 57.108 33.333 0.00 0.00 0.00 4.02
3321 3414 9.561270 GCAGTGTTTATTATCTTCCTTTTTCTC 57.439 33.333 0.00 0.00 0.00 2.87
3366 3459 2.290514 TGGAATCTGGACTTGGAAGCAG 60.291 50.000 0.00 0.00 0.00 4.24
3417 3532 6.547880 TGTTCCAAACAAGGCTATACAAAGAA 59.452 34.615 0.00 0.00 38.72 2.52
3421 3536 4.764823 CCTGTTCCAAACAAGGCTATACAA 59.235 41.667 0.00 0.00 41.61 2.41
3490 3605 3.941483 CAGTCCATTATGCGACTCCTTTT 59.059 43.478 11.51 0.00 37.23 2.27
3494 3609 2.890808 TCAGTCCATTATGCGACTCC 57.109 50.000 11.51 0.00 37.23 3.85
3512 3627 3.950395 ACATGGCTAATTCCTGCTTCTTC 59.050 43.478 0.00 0.00 0.00 2.87
3521 3636 9.289782 AGATCATTAAAGTACATGGCTAATTCC 57.710 33.333 0.00 0.00 0.00 3.01
3608 3756 6.097129 AGGTTTAGTACTCTTCAGCATCTACC 59.903 42.308 0.00 0.00 0.00 3.18
3609 3757 7.067737 AGAGGTTTAGTACTCTTCAGCATCTAC 59.932 40.741 0.00 0.00 41.05 2.59
3610 3758 7.120051 AGAGGTTTAGTACTCTTCAGCATCTA 58.880 38.462 0.00 0.00 41.05 1.98
3713 3948 1.664659 GCTCAGCTGCTAGTTCATGTG 59.335 52.381 9.47 0.00 0.00 3.21
3767 4002 1.130749 AGAGACCAGAATTCGTCGACG 59.869 52.381 31.30 31.30 41.45 5.12
3852 4087 4.998033 GCTCTGTAGTTTTAAGAAGCCAGT 59.002 41.667 0.00 0.00 0.00 4.00
3896 4131 6.037098 GCGTCATCTTGTGTAGAGAAGTTAT 58.963 40.000 0.00 0.00 36.02 1.89
3959 4205 3.418913 TTTGTCGCCGGCATGTCG 61.419 61.111 28.98 13.99 0.00 4.35
3974 4220 5.556915 TGGGAGAATGATACGTTCAAGTTT 58.443 37.500 0.00 0.00 38.03 2.66
4073 4319 0.693049 GGGAGAAGAGGGACAAGCAA 59.307 55.000 0.00 0.00 0.00 3.91


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

AutoCloner maintained by Alex Coulton.