Multiple sequence alignment - TraesCS4A01G213200

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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 TraesCS4A01G213200 chr4A 100.000 2870 0 0 652 3521 511187608 511190477 0.000000e+00 5301.0
1 TraesCS4A01G213200 chr4A 100.000 347 0 0 1 347 511186957 511187303 2.960000e-180 641.0
2 TraesCS4A01G213200 chr4B 92.594 1958 93 25 774 2695 108672038 108670097 0.000000e+00 2765.0
3 TraesCS4A01G213200 chr4B 91.739 230 12 6 121 346 108672255 108672029 2.640000e-81 313.0
4 TraesCS4A01G213200 chr4D 93.761 1763 62 19 774 2505 77119957 77121702 0.000000e+00 2603.0
5 TraesCS4A01G213200 chr4D 91.885 801 43 10 793 1588 76600335 76599552 0.000000e+00 1099.0
6 TraesCS4A01G213200 chr4D 95.571 429 16 1 2111 2536 76599447 76599019 0.000000e+00 684.0
7 TraesCS4A01G213200 chr4D 89.677 155 8 5 185 335 77117644 77117794 1.290000e-44 191.0
8 TraesCS4A01G213200 chr4D 100.000 54 0 0 1602 1655 76599559 76599506 2.240000e-17 100.0
9 TraesCS4A01G213200 chr5A 89.939 825 83 0 2695 3519 535119500 535118676 0.000000e+00 1064.0
10 TraesCS4A01G213200 chr5A 86.804 826 107 2 2695 3520 315278301 315277478 0.000000e+00 920.0
11 TraesCS4A01G213200 chr5A 78.341 1025 192 17 1011 2014 503667650 503668665 1.380000e-178 636.0
12 TraesCS4A01G213200 chr1B 89.722 827 85 0 2695 3521 667916863 667916037 0.000000e+00 1057.0
13 TraesCS4A01G213200 chr1B 88.189 127 14 1 652 777 250062695 250062821 2.190000e-32 150.0
14 TraesCS4A01G213200 chr5B 89.855 828 73 8 2695 3520 115630561 115629743 0.000000e+00 1053.0
15 TraesCS4A01G213200 chr6D 88.983 826 88 3 2695 3519 192102016 192101193 0.000000e+00 1018.0
16 TraesCS4A01G213200 chr6D 87.638 817 100 1 2695 3511 160455992 160455177 0.000000e+00 948.0
17 TraesCS4A01G213200 chr6D 91.525 59 5 0 652 710 407213067 407213125 8.100000e-12 82.4
18 TraesCS4A01G213200 chr6D 90.698 43 2 1 743 785 487968 487928 4.910000e-04 56.5
19 TraesCS4A01G213200 chr5D 88.378 826 94 2 2695 3519 293093354 293094178 0.000000e+00 992.0
20 TraesCS4A01G213200 chr5D 77.500 1040 189 31 1011 2014 398576944 398577974 1.820000e-162 582.0
21 TraesCS4A01G213200 chr2D 87.606 823 100 2 2695 3516 214054434 214053613 0.000000e+00 953.0
22 TraesCS4A01G213200 chr2D 87.152 825 103 2 2695 3519 181583218 181584039 0.000000e+00 933.0
23 TraesCS4A01G213200 chr1D 91.597 119 7 3 658 775 374414921 374415037 1.010000e-35 161.0
24 TraesCS4A01G213200 chr1D 93.878 49 1 2 729 775 47934078 47934030 4.880000e-09 73.1
25 TraesCS4A01G213200 chr7D 89.516 124 11 2 652 774 500236370 500236248 4.710000e-34 156.0
26 TraesCS4A01G213200 chr7B 80.800 125 8 6 1 117 639048261 639048145 2.250000e-12 84.2
27 TraesCS4A01G213200 chr7A 80.469 128 6 10 1 117 667323435 667323316 2.910000e-11 80.5


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 TraesCS4A01G213200 chr4A 511186957 511190477 3520 False 2971.000000 5301 100.000000 1 3521 2 chr4A.!!$F1 3520
1 TraesCS4A01G213200 chr4B 108670097 108672255 2158 True 1539.000000 2765 92.166500 121 2695 2 chr4B.!!$R1 2574
2 TraesCS4A01G213200 chr4D 77117644 77121702 4058 False 1397.000000 2603 91.719000 185 2505 2 chr4D.!!$F1 2320
3 TraesCS4A01G213200 chr4D 76599019 76600335 1316 True 627.666667 1099 95.818667 793 2536 3 chr4D.!!$R1 1743
4 TraesCS4A01G213200 chr5A 535118676 535119500 824 True 1064.000000 1064 89.939000 2695 3519 1 chr5A.!!$R2 824
5 TraesCS4A01G213200 chr5A 315277478 315278301 823 True 920.000000 920 86.804000 2695 3520 1 chr5A.!!$R1 825
6 TraesCS4A01G213200 chr5A 503667650 503668665 1015 False 636.000000 636 78.341000 1011 2014 1 chr5A.!!$F1 1003
7 TraesCS4A01G213200 chr1B 667916037 667916863 826 True 1057.000000 1057 89.722000 2695 3521 1 chr1B.!!$R1 826
8 TraesCS4A01G213200 chr5B 115629743 115630561 818 True 1053.000000 1053 89.855000 2695 3520 1 chr5B.!!$R1 825
9 TraesCS4A01G213200 chr6D 192101193 192102016 823 True 1018.000000 1018 88.983000 2695 3519 1 chr6D.!!$R3 824
10 TraesCS4A01G213200 chr6D 160455177 160455992 815 True 948.000000 948 87.638000 2695 3511 1 chr6D.!!$R2 816
11 TraesCS4A01G213200 chr5D 293093354 293094178 824 False 992.000000 992 88.378000 2695 3519 1 chr5D.!!$F1 824
12 TraesCS4A01G213200 chr5D 398576944 398577974 1030 False 582.000000 582 77.500000 1011 2014 1 chr5D.!!$F2 1003
13 TraesCS4A01G213200 chr2D 214053613 214054434 821 True 953.000000 953 87.606000 2695 3516 1 chr2D.!!$R1 821
14 TraesCS4A01G213200 chr2D 181583218 181584039 821 False 933.000000 933 87.152000 2695 3519 1 chr2D.!!$F1 824

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
259 265 0.249120 TGGATCGCAGTTCGGACATT 59.751 50.0 0.0 0.0 39.05 2.71 F
1669 3432 0.036294 GCTGTCCTTCCACCAGTACC 60.036 60.0 0.0 0.0 0.00 3.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2240 4045 0.465705 CTTATTCTCCCCGCTGCTGA 59.534 55.0 0.00 0.00 0.0 4.26 R
2659 4470 0.034089 AGGGGTAGGAGCATGCAAAC 60.034 55.0 21.98 11.45 0.0 2.93 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
26 27 9.300681 ACCATTTATCATGTAATTGGGTAGATG 57.699 33.333 20.62 8.24 34.18 2.90
27 28 9.519191 CCATTTATCATGTAATTGGGTAGATGA 57.481 33.333 14.63 0.00 37.93 2.92
33 34 9.911788 ATCATGTAATTGGGTAGATGAATATCC 57.088 33.333 0.00 0.00 37.33 2.59
34 35 9.116080 TCATGTAATTGGGTAGATGAATATCCT 57.884 33.333 0.00 0.00 32.48 3.24
35 36 9.745018 CATGTAATTGGGTAGATGAATATCCTT 57.255 33.333 0.00 0.00 33.64 3.36
36 37 9.965902 ATGTAATTGGGTAGATGAATATCCTTC 57.034 33.333 0.00 0.00 33.64 3.46
37 38 9.170890 TGTAATTGGGTAGATGAATATCCTTCT 57.829 33.333 0.00 0.00 33.64 2.85
40 41 9.942526 AATTGGGTAGATGAATATCCTTCTTTT 57.057 29.630 0.00 0.00 33.64 2.27
66 67 8.922058 ATTCATACATCTCTTGTGAAATTTGC 57.078 30.769 0.00 0.00 39.48 3.68
67 68 7.692460 TCATACATCTCTTGTGAAATTTGCT 57.308 32.000 0.00 0.00 39.48 3.91
68 69 8.114331 TCATACATCTCTTGTGAAATTTGCTT 57.886 30.769 0.00 0.00 39.48 3.91
69 70 9.230122 TCATACATCTCTTGTGAAATTTGCTTA 57.770 29.630 0.00 0.00 39.48 3.09
73 74 9.199982 ACATCTCTTGTGAAATTTGCTTATTTG 57.800 29.630 0.00 0.00 37.11 2.32
74 75 9.414295 CATCTCTTGTGAAATTTGCTTATTTGA 57.586 29.630 0.00 0.00 0.00 2.69
76 77 9.985730 TCTCTTGTGAAATTTGCTTATTTGATT 57.014 25.926 0.00 0.00 0.00 2.57
140 141 4.278678 GTGCTTCACCTACATGTTATGC 57.721 45.455 2.30 0.38 0.00 3.14
158 159 3.782656 TGCATGGCATGATCTACTGAT 57.217 42.857 30.69 0.00 31.71 2.90
160 161 4.828829 TGCATGGCATGATCTACTGATAG 58.171 43.478 30.69 0.00 31.71 2.08
165 168 4.022849 TGGCATGATCTACTGATAGTGTCG 60.023 45.833 0.00 0.00 32.19 4.35
168 171 5.049060 GCATGATCTACTGATAGTGTCGTCT 60.049 44.000 0.00 0.00 32.19 4.18
172 175 5.926214 TCTACTGATAGTGTCGTCTATGC 57.074 43.478 0.00 0.00 31.71 3.14
234 240 2.031163 GTGCGCTTCACACCCTCT 59.969 61.111 9.73 0.00 44.98 3.69
259 265 0.249120 TGGATCGCAGTTCGGACATT 59.751 50.000 0.00 0.00 39.05 2.71
324 331 3.057033 GGAAGTGTAGTACGCCAGAGAAA 60.057 47.826 10.23 0.00 0.00 2.52
325 332 3.851976 AGTGTAGTACGCCAGAGAAAG 57.148 47.619 10.23 0.00 0.00 2.62
678 685 9.959721 AGAAAACATGTATATACTCCTTTGTGT 57.040 29.630 13.89 5.17 0.00 3.72
682 689 9.832445 AACATGTATATACTCCTTTGTGTTAGG 57.168 33.333 13.89 0.00 0.00 2.69
683 690 7.931948 ACATGTATATACTCCTTTGTGTTAGGC 59.068 37.037 13.89 0.00 32.59 3.93
699 825 7.954788 GTGTTAGGCACATTTTCCATTAAAA 57.045 32.000 0.00 0.00 46.91 1.52
725 851 6.863275 ACAGCTAAAATAGTTATGTTTGCCC 58.137 36.000 5.30 0.00 33.85 5.36
726 852 6.663523 ACAGCTAAAATAGTTATGTTTGCCCT 59.336 34.615 5.30 0.00 33.85 5.19
727 853 7.148069 ACAGCTAAAATAGTTATGTTTGCCCTC 60.148 37.037 5.30 0.00 33.85 4.30
729 855 5.932619 AAAATAGTTATGTTTGCCCTCCC 57.067 39.130 0.00 0.00 0.00 4.30
730 856 4.881157 AATAGTTATGTTTGCCCTCCCT 57.119 40.909 0.00 0.00 0.00 4.20
731 857 2.808906 AGTTATGTTTGCCCTCCCTC 57.191 50.000 0.00 0.00 0.00 4.30
732 858 2.279173 AGTTATGTTTGCCCTCCCTCT 58.721 47.619 0.00 0.00 0.00 3.69
734 860 3.456277 AGTTATGTTTGCCCTCCCTCTAG 59.544 47.826 0.00 0.00 0.00 2.43
735 861 0.548510 ATGTTTGCCCTCCCTCTAGC 59.451 55.000 0.00 0.00 0.00 3.42
736 862 1.224870 GTTTGCCCTCCCTCTAGCC 59.775 63.158 0.00 0.00 0.00 3.93
738 864 2.781258 TTTGCCCTCCCTCTAGCCCA 62.781 60.000 0.00 0.00 0.00 5.36
739 865 2.122189 GCCCTCCCTCTAGCCCAT 60.122 66.667 0.00 0.00 0.00 4.00
740 866 2.524204 GCCCTCCCTCTAGCCCATG 61.524 68.421 0.00 0.00 0.00 3.66
741 867 1.845205 CCCTCCCTCTAGCCCATGG 60.845 68.421 4.14 4.14 0.00 3.66
762 888 2.065899 CCCCCATAATTTCGGCTCAA 57.934 50.000 0.00 0.00 0.00 3.02
763 889 1.956477 CCCCCATAATTTCGGCTCAAG 59.044 52.381 0.00 0.00 0.00 3.02
764 890 1.338020 CCCCATAATTTCGGCTCAAGC 59.662 52.381 0.00 0.00 41.14 4.01
766 892 2.291741 CCCATAATTTCGGCTCAAGCTC 59.708 50.000 1.46 0.00 41.70 4.09
767 893 2.291741 CCATAATTTCGGCTCAAGCTCC 59.708 50.000 1.46 0.00 41.70 4.70
768 894 1.651987 TAATTTCGGCTCAAGCTCCG 58.348 50.000 5.25 5.25 46.52 4.63
769 895 1.648467 AATTTCGGCTCAAGCTCCGC 61.648 55.000 6.70 0.22 44.91 5.54
770 896 4.760047 TTCGGCTCAAGCTCCGCC 62.760 66.667 6.70 8.51 44.91 6.13
782 2512 2.280524 TCCGCCACTGTTCCGTTG 60.281 61.111 0.00 0.00 0.00 4.10
815 2549 1.021202 TGTTCCGTTGCTTGGAAGTG 58.979 50.000 5.32 0.00 45.76 3.16
820 2554 1.268539 CCGTTGCTTGGAAGTGAACAC 60.269 52.381 0.00 0.00 0.00 3.32
837 2571 0.728466 CACGTTCCGACTCGTCTTCC 60.728 60.000 0.00 0.00 38.23 3.46
838 2572 1.511464 CGTTCCGACTCGTCTTCCG 60.511 63.158 0.00 0.00 38.13 4.30
856 2590 4.773117 GACCGCGACCGACTCCAC 62.773 72.222 8.23 0.00 36.29 4.02
865 2599 0.896019 ACCGACTCCACCTCAGACTG 60.896 60.000 0.00 0.00 0.00 3.51
871 2605 0.752658 TCCACCTCAGACTGTGTGTG 59.247 55.000 19.40 16.81 32.87 3.82
872 2606 0.465705 CCACCTCAGACTGTGTGTGT 59.534 55.000 19.40 1.49 31.84 3.72
873 2607 1.575244 CACCTCAGACTGTGTGTGTG 58.425 55.000 15.36 12.83 40.83 3.82
874 2608 1.134699 CACCTCAGACTGTGTGTGTGT 60.135 52.381 16.26 8.03 40.40 3.72
876 2610 1.575244 CTCAGACTGTGTGTGTGTGG 58.425 55.000 4.77 0.00 40.40 4.17
886 2623 2.203082 TGTGTGTGGAGCTCGCTCT 61.203 57.895 17.48 0.00 42.38 4.09
953 2690 1.130140 TTCGTTCGTCGCGATTGAAA 58.870 45.000 22.85 10.24 38.21 2.69
977 2719 3.191669 TCACGATCTCTCTCTCGTTCTC 58.808 50.000 0.00 0.00 45.15 2.87
1524 3287 1.626654 CCAACGGCTTCTGCTACGTG 61.627 60.000 0.00 0.00 37.22 4.49
1669 3432 0.036294 GCTGTCCTTCCACCAGTACC 60.036 60.000 0.00 0.00 0.00 3.34
1673 3436 2.158726 TGTCCTTCCACCAGTACCAAAC 60.159 50.000 0.00 0.00 0.00 2.93
1677 3440 1.354101 TCCACCAGTACCAAACCGAT 58.646 50.000 0.00 0.00 0.00 4.18
2047 3840 4.790140 GCATGAACTCGTGATTGATCAAAC 59.210 41.667 13.09 10.68 38.75 2.93
2048 3841 5.617529 GCATGAACTCGTGATTGATCAAACA 60.618 40.000 13.09 13.50 38.75 2.83
2049 3842 5.342806 TGAACTCGTGATTGATCAAACAC 57.657 39.130 29.25 29.25 39.68 3.32
2395 4200 3.249973 CTCTGCCACGACGACGACA 62.250 63.158 15.32 8.11 42.66 4.35
2421 4229 5.567623 CGATGAAGAAGAAGAAGAAGACCCA 60.568 44.000 0.00 0.00 0.00 4.51
2516 4324 1.043816 CTATCGTCCTCTGCCATGGT 58.956 55.000 14.67 0.00 0.00 3.55
2560 4368 1.066716 CCATGCATGTGGAGGTTTTGG 60.067 52.381 24.58 2.94 42.02 3.28
2561 4369 1.066716 CATGCATGTGGAGGTTTTGGG 60.067 52.381 18.91 0.00 0.00 4.12
2564 4372 0.881118 CATGTGGAGGTTTTGGGTCG 59.119 55.000 0.00 0.00 0.00 4.79
2580 4388 2.032030 GGGTCGTGTCATTGTTCACTTG 60.032 50.000 10.84 0.00 33.07 3.16
2586 4394 5.469760 TCGTGTCATTGTTCACTTGATTCAT 59.530 36.000 10.84 0.00 33.07 2.57
2587 4395 6.017192 TCGTGTCATTGTTCACTTGATTCATT 60.017 34.615 10.84 0.00 33.07 2.57
2588 4396 6.303970 CGTGTCATTGTTCACTTGATTCATTC 59.696 38.462 10.84 0.00 33.07 2.67
2589 4397 7.140705 GTGTCATTGTTCACTTGATTCATTCA 58.859 34.615 0.00 0.00 0.00 2.57
2590 4398 7.811236 GTGTCATTGTTCACTTGATTCATTCAT 59.189 33.333 0.00 0.00 33.34 2.57
2611 4419 1.801512 GAACCGGCGAGCATTTTGC 60.802 57.895 9.30 0.00 45.46 3.68
2659 4470 1.608590 ACAGAAATCCAGTTTGTGCCG 59.391 47.619 0.00 0.00 42.99 5.69
2673 4484 3.903783 GCCGTTTGCATGCTCCTA 58.096 55.556 20.33 0.00 40.77 2.94
2674 4485 1.429423 GCCGTTTGCATGCTCCTAC 59.571 57.895 20.33 10.16 40.77 3.18
2675 4486 1.993369 GCCGTTTGCATGCTCCTACC 61.993 60.000 20.33 0.00 40.77 3.18
2676 4487 1.376609 CCGTTTGCATGCTCCTACCC 61.377 60.000 20.33 0.00 0.00 3.69
2677 4488 1.376609 CGTTTGCATGCTCCTACCCC 61.377 60.000 20.33 0.00 0.00 4.95
2678 4489 0.034089 GTTTGCATGCTCCTACCCCT 60.034 55.000 20.33 0.00 0.00 4.79
2679 4490 0.704076 TTTGCATGCTCCTACCCCTT 59.296 50.000 20.33 0.00 0.00 3.95
2680 4491 0.255890 TTGCATGCTCCTACCCCTTC 59.744 55.000 20.33 0.00 0.00 3.46
2681 4492 0.621571 TGCATGCTCCTACCCCTTCT 60.622 55.000 20.33 0.00 0.00 2.85
2682 4493 0.548510 GCATGCTCCTACCCCTTCTT 59.451 55.000 11.37 0.00 0.00 2.52
2683 4494 1.064389 GCATGCTCCTACCCCTTCTTT 60.064 52.381 11.37 0.00 0.00 2.52
2684 4495 2.172717 GCATGCTCCTACCCCTTCTTTA 59.827 50.000 11.37 0.00 0.00 1.85
2685 4496 3.181439 GCATGCTCCTACCCCTTCTTTAT 60.181 47.826 11.37 0.00 0.00 1.40
2686 4497 4.646572 CATGCTCCTACCCCTTCTTTATC 58.353 47.826 0.00 0.00 0.00 1.75
2687 4498 4.008916 TGCTCCTACCCCTTCTTTATCT 57.991 45.455 0.00 0.00 0.00 1.98
2688 4499 3.711704 TGCTCCTACCCCTTCTTTATCTG 59.288 47.826 0.00 0.00 0.00 2.90
2689 4500 3.712218 GCTCCTACCCCTTCTTTATCTGT 59.288 47.826 0.00 0.00 0.00 3.41
2690 4501 4.164413 GCTCCTACCCCTTCTTTATCTGTT 59.836 45.833 0.00 0.00 0.00 3.16
2691 4502 5.675538 CTCCTACCCCTTCTTTATCTGTTG 58.324 45.833 0.00 0.00 0.00 3.33
2692 4503 5.098663 TCCTACCCCTTCTTTATCTGTTGT 58.901 41.667 0.00 0.00 0.00 3.32
2693 4504 5.550403 TCCTACCCCTTCTTTATCTGTTGTT 59.450 40.000 0.00 0.00 0.00 2.83
2771 4583 2.306805 TCATGGTTGAAGGCTCTGATGT 59.693 45.455 0.00 0.00 0.00 3.06
2778 4590 5.163405 GGTTGAAGGCTCTGATGTAGACATA 60.163 44.000 0.00 0.00 36.57 2.29
2784 4596 6.015918 AGGCTCTGATGTAGACATAGCTAAT 58.984 40.000 13.08 0.00 36.32 1.73
2808 4620 7.259088 TCTTAAATTACTCCTCCTCTGCTTT 57.741 36.000 0.00 0.00 0.00 3.51
2851 4663 6.516739 AGATCAACTTCGACAAGAGTGATA 57.483 37.500 0.00 0.00 37.71 2.15
2889 4701 2.187946 CCGGCAGAGGCTTTCGAT 59.812 61.111 0.00 0.00 40.87 3.59
2925 4737 1.327690 ATTGTCGCCTCGGCTCCTTA 61.328 55.000 6.35 0.00 39.32 2.69
2934 4746 0.252103 TCGGCTCCTTACCCACTTCT 60.252 55.000 0.00 0.00 0.00 2.85
2971 4783 2.104530 GCGTCTCGAGGCTTACCC 59.895 66.667 16.21 0.00 38.98 3.69
3036 4848 3.953775 CCTTGGCAGGGTCGGTGT 61.954 66.667 7.63 0.00 36.36 4.16
3105 4917 3.513515 GTCTCCTCTTGTTCCTCATGAGT 59.486 47.826 21.11 0.00 42.87 3.41
3121 4933 4.040339 TCATGAGTTTCTACAGCCTTCACA 59.960 41.667 0.00 0.00 0.00 3.58
3168 4980 3.458118 ACATCCAATCCCGGTTCTATTGA 59.542 43.478 14.27 0.00 33.38 2.57
3170 4982 3.112263 TCCAATCCCGGTTCTATTGAGT 58.888 45.455 14.27 0.00 33.38 3.41
3347 5160 6.166982 GGTTATGGCTAGACATCATTAGGAC 58.833 44.000 16.26 3.87 32.39 3.85
3356 5169 7.755822 GCTAGACATCATTAGGACTAAATACCG 59.244 40.741 0.00 0.00 0.00 4.02
3452 5265 2.046314 CCTCCGCATTGGGACGTT 60.046 61.111 1.69 0.00 38.76 3.99
3469 5282 1.196127 CGTTCATATCGGTCGGATCGA 59.804 52.381 16.54 16.54 41.04 3.59
3489 5302 1.827344 AGATCAGCGACCATGTTCTGA 59.173 47.619 0.00 6.10 39.54 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 9.300681 CATCTACCCAATTACATGATAAATGGT 57.699 33.333 0.00 1.80 0.00 3.55
1 2 9.519191 TCATCTACCCAATTACATGATAAATGG 57.481 33.333 0.00 7.35 0.00 3.16
7 8 9.911788 GGATATTCATCTACCCAATTACATGAT 57.088 33.333 0.00 0.00 0.00 2.45
8 9 9.116080 AGGATATTCATCTACCCAATTACATGA 57.884 33.333 0.00 0.00 0.00 3.07
9 10 9.745018 AAGGATATTCATCTACCCAATTACATG 57.255 33.333 0.00 0.00 0.00 3.21
10 11 9.965902 GAAGGATATTCATCTACCCAATTACAT 57.034 33.333 0.00 0.00 0.00 2.29
11 12 9.170890 AGAAGGATATTCATCTACCCAATTACA 57.829 33.333 0.00 0.00 0.00 2.41
14 15 9.942526 AAAAGAAGGATATTCATCTACCCAATT 57.057 29.630 0.00 0.00 0.00 2.32
41 42 8.746530 AGCAAATTTCACAAGAGATGTATGAAT 58.253 29.630 0.00 0.00 41.46 2.57
42 43 8.114331 AGCAAATTTCACAAGAGATGTATGAA 57.886 30.769 0.00 0.00 41.46 2.57
43 44 7.692460 AGCAAATTTCACAAGAGATGTATGA 57.308 32.000 0.00 0.00 41.46 2.15
47 48 9.199982 CAAATAAGCAAATTTCACAAGAGATGT 57.800 29.630 0.00 0.00 45.34 3.06
48 49 9.414295 TCAAATAAGCAAATTTCACAAGAGATG 57.586 29.630 0.00 0.00 0.00 2.90
50 51 9.985730 AATCAAATAAGCAAATTTCACAAGAGA 57.014 25.926 0.00 0.00 0.00 3.10
118 119 6.663916 ATGCATAACATGTAGGTGAAGCACC 61.664 44.000 8.51 8.51 45.58 5.01
119 120 3.689161 TGCATAACATGTAGGTGAAGCAC 59.311 43.478 0.00 0.00 0.00 4.40
140 141 5.791666 ACACTATCAGTAGATCATGCCATG 58.208 41.667 0.00 0.00 35.67 3.66
157 158 4.261656 GCTACTTGGCATAGACGACACTAT 60.262 45.833 0.00 0.00 33.95 2.12
158 159 3.066342 GCTACTTGGCATAGACGACACTA 59.934 47.826 0.00 0.00 0.00 2.74
160 161 2.194271 GCTACTTGGCATAGACGACAC 58.806 52.381 0.00 0.00 0.00 3.67
165 168 1.136305 TGGACGCTACTTGGCATAGAC 59.864 52.381 0.00 0.00 0.00 2.59
168 171 3.832490 AGATATGGACGCTACTTGGCATA 59.168 43.478 0.00 0.00 0.00 3.14
172 175 4.592485 AAGAGATATGGACGCTACTTGG 57.408 45.455 0.00 0.00 0.00 3.61
229 235 1.045350 TGCGATCCAGGAGAAGAGGG 61.045 60.000 0.00 0.00 0.00 4.30
234 240 0.173481 CGAACTGCGATCCAGGAGAA 59.827 55.000 13.60 0.00 46.14 2.87
259 265 5.290493 AGACACATTAAAGTGACACCTCA 57.710 39.130 17.18 0.00 42.05 3.86
652 659 9.959721 ACACAAAGGAGTATATACATGTTTTCT 57.040 29.630 15.18 0.00 0.00 2.52
656 663 9.832445 CCTAACACAAAGGAGTATATACATGTT 57.168 33.333 15.18 13.35 36.08 2.71
658 665 7.931407 TGCCTAACACAAAGGAGTATATACATG 59.069 37.037 15.18 7.99 36.08 3.21
675 682 7.954788 TTTTAATGGAAAATGTGCCTAACAC 57.045 32.000 0.00 0.00 43.06 3.32
698 824 9.203421 GGCAAACATAACTATTTTAGCTGTTTT 57.797 29.630 0.00 0.00 35.69 2.43
699 825 7.817478 GGGCAAACATAACTATTTTAGCTGTTT 59.183 33.333 0.00 0.00 37.01 2.83
702 828 7.100458 AGGGCAAACATAACTATTTTAGCTG 57.900 36.000 0.00 0.00 0.00 4.24
704 830 6.461092 GGGAGGGCAAACATAACTATTTTAGC 60.461 42.308 0.00 0.00 0.00 3.09
712 838 2.279173 AGAGGGAGGGCAAACATAACT 58.721 47.619 0.00 0.00 0.00 2.24
714 840 2.172717 GCTAGAGGGAGGGCAAACATAA 59.827 50.000 0.00 0.00 0.00 1.90
715 841 1.768870 GCTAGAGGGAGGGCAAACATA 59.231 52.381 0.00 0.00 0.00 2.29
719 845 2.001269 GGGCTAGAGGGAGGGCAAA 61.001 63.158 0.00 0.00 0.00 3.68
721 847 3.039981 ATGGGCTAGAGGGAGGGCA 62.040 63.158 0.00 0.00 0.00 5.36
722 848 2.122189 ATGGGCTAGAGGGAGGGC 60.122 66.667 0.00 0.00 0.00 5.19
723 849 1.845205 CCATGGGCTAGAGGGAGGG 60.845 68.421 2.85 0.00 0.00 4.30
725 851 3.155750 GCCATGGGCTAGAGGGAG 58.844 66.667 15.13 0.00 46.69 4.30
743 869 1.956477 CTTGAGCCGAAATTATGGGGG 59.044 52.381 0.00 0.00 0.00 5.40
744 870 1.338020 GCTTGAGCCGAAATTATGGGG 59.662 52.381 0.00 0.00 34.31 4.96
746 872 2.291741 GGAGCTTGAGCCGAAATTATGG 59.708 50.000 0.00 0.00 43.38 2.74
747 873 3.615849 GGAGCTTGAGCCGAAATTATG 57.384 47.619 0.00 0.00 43.38 1.90
764 890 2.030562 AACGGAACAGTGGCGGAG 59.969 61.111 0.00 0.00 0.00 4.63
766 892 3.353836 CCAACGGAACAGTGGCGG 61.354 66.667 0.00 0.00 0.00 6.13
767 893 4.025401 GCCAACGGAACAGTGGCG 62.025 66.667 0.00 0.00 35.86 5.69
768 894 2.200170 GATGCCAACGGAACAGTGGC 62.200 60.000 6.96 6.96 45.19 5.01
769 895 1.875963 GATGCCAACGGAACAGTGG 59.124 57.895 0.00 0.00 0.00 4.00
770 896 0.948623 TCGATGCCAACGGAACAGTG 60.949 55.000 0.00 0.00 0.00 3.66
772 898 1.635663 GGTCGATGCCAACGGAACAG 61.636 60.000 0.00 0.00 0.00 3.16
782 2512 0.521735 GGAACAACTTGGTCGATGCC 59.478 55.000 0.62 0.00 34.15 4.40
856 2590 1.575244 CACACACACACAGTCTGAGG 58.425 55.000 6.91 0.68 0.00 3.86
865 2599 2.598632 GCGAGCTCCACACACACAC 61.599 63.158 8.47 0.00 0.00 3.82
871 2605 0.457851 ATGTAGAGCGAGCTCCACAC 59.542 55.000 23.98 17.69 44.64 3.82
872 2606 2.052782 TATGTAGAGCGAGCTCCACA 57.947 50.000 23.79 23.79 45.55 4.17
873 2607 3.425094 CGTATATGTAGAGCGAGCTCCAC 60.425 52.174 20.15 17.45 43.70 4.02
874 2608 2.742589 CGTATATGTAGAGCGAGCTCCA 59.257 50.000 20.15 12.92 43.70 3.86
876 2610 2.776330 GCGTATATGTAGAGCGAGCTC 58.224 52.381 16.63 16.63 43.03 4.09
977 2719 1.402968 CCATGGCTGGTTCTTGATTCG 59.597 52.381 0.00 0.00 37.79 3.34
1099 2844 1.380302 GCACCATGGAGTGTCCCTT 59.620 57.895 21.47 0.00 40.04 3.95
1380 3143 2.106566 CTCAGGCAGTACTCCATGAGT 58.893 52.381 18.30 1.94 45.54 3.41
1669 3432 0.808755 CCGGGGAAGAAATCGGTTTG 59.191 55.000 0.00 0.00 37.92 2.93
1673 3436 2.112815 GTGCCGGGGAAGAAATCGG 61.113 63.158 2.18 0.00 44.70 4.18
2047 3840 3.483574 CGTTTGCCATTAGAGTTAGCGTG 60.484 47.826 0.00 0.00 0.00 5.34
2048 3841 2.671396 CGTTTGCCATTAGAGTTAGCGT 59.329 45.455 0.00 0.00 0.00 5.07
2049 3842 2.927477 TCGTTTGCCATTAGAGTTAGCG 59.073 45.455 0.00 0.00 0.00 4.26
2050 3843 3.063588 GGTCGTTTGCCATTAGAGTTAGC 59.936 47.826 0.00 0.00 0.00 3.09
2052 3845 3.998341 GTGGTCGTTTGCCATTAGAGTTA 59.002 43.478 0.00 0.00 38.40 2.24
2053 3846 2.812011 GTGGTCGTTTGCCATTAGAGTT 59.188 45.455 0.00 0.00 38.40 3.01
2054 3847 2.038557 AGTGGTCGTTTGCCATTAGAGT 59.961 45.455 0.00 0.00 38.40 3.24
2055 3848 2.673368 GAGTGGTCGTTTGCCATTAGAG 59.327 50.000 0.00 0.00 38.40 2.43
2240 4045 0.465705 CTTATTCTCCCCGCTGCTGA 59.534 55.000 0.00 0.00 0.00 4.26
2395 4200 5.929415 GGTCTTCTTCTTCTTCTTCATCGTT 59.071 40.000 0.00 0.00 0.00 3.85
2421 4229 2.124819 CGCTGCAGCCTCTCCATT 60.125 61.111 32.07 0.00 37.91 3.16
2560 4368 2.869801 TCAAGTGAACAATGACACGACC 59.130 45.455 0.00 0.00 41.22 4.79
2561 4369 4.732285 ATCAAGTGAACAATGACACGAC 57.268 40.909 0.00 0.00 41.22 4.34
2564 4372 7.140705 TGAATGAATCAAGTGAACAATGACAC 58.859 34.615 7.07 7.07 34.30 3.67
2580 4388 2.480419 CGCCGGTTCCTATGAATGAATC 59.520 50.000 1.90 0.00 31.98 2.52
2586 4394 1.143183 GCTCGCCGGTTCCTATGAA 59.857 57.895 1.90 0.00 0.00 2.57
2587 4395 1.399744 ATGCTCGCCGGTTCCTATGA 61.400 55.000 1.90 0.00 0.00 2.15
2588 4396 0.532862 AATGCTCGCCGGTTCCTATG 60.533 55.000 1.90 0.00 0.00 2.23
2589 4397 0.180406 AAATGCTCGCCGGTTCCTAT 59.820 50.000 1.90 0.00 0.00 2.57
2590 4398 0.035820 AAAATGCTCGCCGGTTCCTA 60.036 50.000 1.90 0.00 0.00 2.94
2639 4450 1.608590 CGGCACAAACTGGATTTCTGT 59.391 47.619 0.00 0.00 0.00 3.41
2644 4455 1.537990 GCAAACGGCACAAACTGGATT 60.538 47.619 0.00 0.00 43.97 3.01
2659 4470 0.034089 AGGGGTAGGAGCATGCAAAC 60.034 55.000 21.98 11.45 0.00 2.93
2671 4482 5.880887 GGAACAACAGATAAAGAAGGGGTAG 59.119 44.000 0.00 0.00 0.00 3.18
2672 4483 5.311121 TGGAACAACAGATAAAGAAGGGGTA 59.689 40.000 0.00 0.00 31.92 3.69
2673 4484 4.105697 TGGAACAACAGATAAAGAAGGGGT 59.894 41.667 0.00 0.00 31.92 4.95
2674 4485 4.459337 GTGGAACAACAGATAAAGAAGGGG 59.541 45.833 0.00 0.00 44.16 4.79
2675 4486 5.316987 AGTGGAACAACAGATAAAGAAGGG 58.683 41.667 0.00 0.00 44.16 3.95
2676 4487 6.294176 CCAAGTGGAACAACAGATAAAGAAGG 60.294 42.308 0.00 0.00 44.16 3.46
2677 4488 6.672147 CCAAGTGGAACAACAGATAAAGAAG 58.328 40.000 0.00 0.00 44.16 2.85
2678 4489 5.009610 GCCAAGTGGAACAACAGATAAAGAA 59.990 40.000 0.18 0.00 44.16 2.52
2679 4490 4.518970 GCCAAGTGGAACAACAGATAAAGA 59.481 41.667 0.18 0.00 44.16 2.52
2680 4491 4.321230 GGCCAAGTGGAACAACAGATAAAG 60.321 45.833 0.00 0.00 44.16 1.85
2681 4492 3.572255 GGCCAAGTGGAACAACAGATAAA 59.428 43.478 0.00 0.00 44.16 1.40
2682 4493 3.153919 GGCCAAGTGGAACAACAGATAA 58.846 45.455 0.00 0.00 44.16 1.75
2683 4494 2.790433 GGCCAAGTGGAACAACAGATA 58.210 47.619 0.00 0.00 44.16 1.98
2684 4495 1.620822 GGCCAAGTGGAACAACAGAT 58.379 50.000 0.00 0.00 44.16 2.90
2685 4496 0.817634 CGGCCAAGTGGAACAACAGA 60.818 55.000 2.24 0.00 44.16 3.41
2686 4497 1.654220 CGGCCAAGTGGAACAACAG 59.346 57.895 2.24 0.00 44.16 3.16
2687 4498 1.826054 CCGGCCAAGTGGAACAACA 60.826 57.895 2.24 0.00 44.16 3.33
2688 4499 1.826487 ACCGGCCAAGTGGAACAAC 60.826 57.895 0.00 0.00 44.16 3.32
2689 4500 1.826054 CACCGGCCAAGTGGAACAA 60.826 57.895 13.93 0.00 44.16 2.83
2690 4501 2.203280 CACCGGCCAAGTGGAACA 60.203 61.111 13.93 0.00 41.43 3.18
2715 4526 1.138266 GCGTACTGGAGCAGGGAAATA 59.862 52.381 0.00 0.00 35.51 1.40
2778 4590 8.646900 CAGAGGAGGAGTAATTTAAGATTAGCT 58.353 37.037 0.00 0.00 0.00 3.32
2784 4596 6.875972 AAGCAGAGGAGGAGTAATTTAAGA 57.124 37.500 0.00 0.00 0.00 2.10
2793 4605 2.050144 TGTTGAAAGCAGAGGAGGAGT 58.950 47.619 0.00 0.00 0.00 3.85
2808 4620 2.655090 TGAGGCCAGACATTTGTTGA 57.345 45.000 5.01 0.00 0.00 3.18
2851 4663 2.636893 GAGAGTAGCCCATCACCATCAT 59.363 50.000 0.00 0.00 0.00 2.45
2884 4696 0.107410 AGGCGGTTGGCAATATCGAA 60.107 50.000 19.33 0.00 46.16 3.71
2889 4701 1.476085 CAATTCAGGCGGTTGGCAATA 59.524 47.619 1.92 0.00 46.16 1.90
2957 4769 0.614979 AGCAAGGGTAAGCCTCGAGA 60.615 55.000 15.71 0.00 34.45 4.04
2971 4783 0.179215 GTCGGACGCAAATCAGCAAG 60.179 55.000 0.00 0.00 0.00 4.01
3057 4869 2.102252 GAGCGAGGAGTTGATGAGGATT 59.898 50.000 0.00 0.00 0.00 3.01
3105 4917 3.496160 GGGTCTTGTGAAGGCTGTAGAAA 60.496 47.826 0.00 0.00 32.49 2.52
3121 4933 2.122768 GATCTCATGGTGGAGGGTCTT 58.877 52.381 0.00 0.00 35.58 3.01
3168 4980 3.139397 TCTGTTTGTTATGGTCCCCAACT 59.861 43.478 4.76 0.00 36.95 3.16
3170 4982 3.885976 TCTGTTTGTTATGGTCCCCAA 57.114 42.857 0.00 0.00 36.95 4.12
3347 5160 3.727146 GGCCACGCCGGTATTTAG 58.273 61.111 1.90 0.00 39.62 1.85
3452 5265 2.467566 TCTCGATCCGACCGATATGA 57.532 50.000 0.00 0.00 35.35 2.15
3469 5282 1.827344 TCAGAACATGGTCGCTGATCT 59.173 47.619 4.80 0.00 32.85 2.75


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

AutoCloner maintained by Alex Coulton.