Multiple sequence alignment - TraesCS2D01G329600

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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 TraesCS2D01G329600 chr2D 100.000 5682 0 0 1416 7097 422783796 422778115 0.000000e+00 10493.0
1 TraesCS2D01G329600 chr2D 100.000 1121 0 0 1 1121 422785211 422784091 0.000000e+00 2071.0
2 TraesCS2D01G329600 chr2D 100.000 684 0 0 6414 7097 106237458 106236775 0.000000e+00 1264.0
3 TraesCS2D01G329600 chr2D 100.000 683 0 0 6415 7097 592136861 592137543 0.000000e+00 1262.0
4 TraesCS2D01G329600 chr2D 95.859 652 25 1 1 650 579068130 579068781 0.000000e+00 1053.0
5 TraesCS2D01G329600 chr2D 100.000 28 0 0 4058 4085 422781121 422781094 1.300000e-02 52.8
6 TraesCS2D01G329600 chr2D 100.000 28 0 0 4091 4118 422781154 422781127 1.300000e-02 52.8
7 TraesCS2D01G329600 chr2A 94.453 3371 108 28 1416 4725 569215634 569212282 0.000000e+00 5116.0
8 TraesCS2D01G329600 chr2A 93.439 1829 82 18 4603 6412 569212281 569210472 0.000000e+00 2678.0
9 TraesCS2D01G329600 chr2A 88.306 248 10 8 835 1081 569216099 569215870 5.420000e-71 279.0
10 TraesCS2D01G329600 chr2A 94.286 35 1 1 4085 4118 569212982 569212948 1.300000e-02 52.8
11 TraesCS2D01G329600 chr2B 95.328 3125 86 26 2314 5393 495170866 495167757 0.000000e+00 4907.0
12 TraesCS2D01G329600 chr2B 92.842 936 46 12 5462 6384 495167663 495166736 0.000000e+00 1338.0
13 TraesCS2D01G329600 chr2B 90.618 938 43 10 1416 2312 495171881 495170948 0.000000e+00 1203.0
14 TraesCS2D01G329600 chr2B 93.728 287 18 0 835 1121 495172195 495171909 1.410000e-116 431.0
15 TraesCS2D01G329600 chr2B 94.286 35 1 1 4085 4118 495169126 495169092 1.300000e-02 52.8
16 TraesCS2D01G329600 chr4A 100.000 687 0 0 6411 7097 85145654 85144968 0.000000e+00 1269.0
17 TraesCS2D01G329600 chr4A 100.000 686 0 0 6412 7097 84922888 84923573 0.000000e+00 1267.0
18 TraesCS2D01G329600 chr4A 100.000 683 0 0 6415 7097 85183978 85183296 0.000000e+00 1262.0
19 TraesCS2D01G329600 chr3B 100.000 686 0 0 6412 7097 613815716 613815031 0.000000e+00 1267.0
20 TraesCS2D01G329600 chr3B 90.191 785 74 3 1 785 621142336 621143117 0.000000e+00 1020.0
21 TraesCS2D01G329600 chr1B 99.711 692 2 0 6406 7097 424524740 424525431 0.000000e+00 1267.0
22 TraesCS2D01G329600 chr6B 100.000 684 0 0 6414 7097 712670462 712669779 0.000000e+00 1264.0
23 TraesCS2D01G329600 chr3D 99.418 687 4 0 6411 7097 443944471 443945157 0.000000e+00 1247.0
24 TraesCS2D01G329600 chr3D 92.201 795 49 3 1 784 545699790 545700582 0.000000e+00 1112.0
25 TraesCS2D01G329600 chr6D 93.000 800 44 3 1 788 301787816 301787017 0.000000e+00 1157.0
26 TraesCS2D01G329600 chr6D 92.028 715 51 5 1 714 386329252 386329961 0.000000e+00 1000.0
27 TraesCS2D01G329600 chr7D 93.458 749 37 2 10 747 572188469 572187722 0.000000e+00 1101.0
28 TraesCS2D01G329600 chr7D 91.454 784 60 4 1 784 250317213 250317989 0.000000e+00 1070.0
29 TraesCS2D01G329600 chr5B 90.306 784 74 2 1 783 118941594 118942376 0.000000e+00 1026.0
30 TraesCS2D01G329600 chr7B 89.043 794 84 3 1 794 453116063 453115273 0.000000e+00 981.0
31 TraesCS2D01G329600 chr7B 89.158 784 72 8 1 784 659648753 659649523 0.000000e+00 965.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2D01G329600 chr2D 422778115 422785211 7096 True 3167.40 10493 100.0000 1 7097 4 chr2D.!!$R2 7096
1 TraesCS2D01G329600 chr2D 106236775 106237458 683 True 1264.00 1264 100.0000 6414 7097 1 chr2D.!!$R1 683
2 TraesCS2D01G329600 chr2D 592136861 592137543 682 False 1262.00 1262 100.0000 6415 7097 1 chr2D.!!$F2 682
3 TraesCS2D01G329600 chr2D 579068130 579068781 651 False 1053.00 1053 95.8590 1 650 1 chr2D.!!$F1 649
4 TraesCS2D01G329600 chr2A 569210472 569216099 5627 True 2031.45 5116 92.6210 835 6412 4 chr2A.!!$R1 5577
5 TraesCS2D01G329600 chr2B 495166736 495172195 5459 True 1586.36 4907 93.3604 835 6384 5 chr2B.!!$R1 5549
6 TraesCS2D01G329600 chr4A 85144968 85145654 686 True 1269.00 1269 100.0000 6411 7097 1 chr4A.!!$R1 686
7 TraesCS2D01G329600 chr4A 84922888 84923573 685 False 1267.00 1267 100.0000 6412 7097 1 chr4A.!!$F1 685
8 TraesCS2D01G329600 chr4A 85183296 85183978 682 True 1262.00 1262 100.0000 6415 7097 1 chr4A.!!$R2 682
9 TraesCS2D01G329600 chr3B 613815031 613815716 685 True 1267.00 1267 100.0000 6412 7097 1 chr3B.!!$R1 685
10 TraesCS2D01G329600 chr3B 621142336 621143117 781 False 1020.00 1020 90.1910 1 785 1 chr3B.!!$F1 784
11 TraesCS2D01G329600 chr1B 424524740 424525431 691 False 1267.00 1267 99.7110 6406 7097 1 chr1B.!!$F1 691
12 TraesCS2D01G329600 chr6B 712669779 712670462 683 True 1264.00 1264 100.0000 6414 7097 1 chr6B.!!$R1 683
13 TraesCS2D01G329600 chr3D 443944471 443945157 686 False 1247.00 1247 99.4180 6411 7097 1 chr3D.!!$F1 686
14 TraesCS2D01G329600 chr3D 545699790 545700582 792 False 1112.00 1112 92.2010 1 784 1 chr3D.!!$F2 783
15 TraesCS2D01G329600 chr6D 301787017 301787816 799 True 1157.00 1157 93.0000 1 788 1 chr6D.!!$R1 787
16 TraesCS2D01G329600 chr6D 386329252 386329961 709 False 1000.00 1000 92.0280 1 714 1 chr6D.!!$F1 713
17 TraesCS2D01G329600 chr7D 572187722 572188469 747 True 1101.00 1101 93.4580 10 747 1 chr7D.!!$R1 737
18 TraesCS2D01G329600 chr7D 250317213 250317989 776 False 1070.00 1070 91.4540 1 784 1 chr7D.!!$F1 783
19 TraesCS2D01G329600 chr5B 118941594 118942376 782 False 1026.00 1026 90.3060 1 783 1 chr5B.!!$F1 782
20 TraesCS2D01G329600 chr7B 453115273 453116063 790 True 981.00 981 89.0430 1 794 1 chr7B.!!$R1 793
21 TraesCS2D01G329600 chr7B 659648753 659649523 770 False 965.00 965 89.1580 1 784 1 chr7B.!!$F1 783

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
561 562 0.033228 TTCGGCTTGCAAAACCATGG 59.967 50.000 11.19 11.19 0.00 3.66 F
826 842 0.179073 AATCTGGATCGCTCCGTTGG 60.179 55.000 0.03 0.00 45.37 3.77 F
1586 1624 0.396811 GCACTGGTCAGGGTTGTAGT 59.603 55.000 1.97 0.00 33.42 2.73 F
1630 1668 2.065993 ATGTCGTCAGGAGTGTTTCG 57.934 50.000 0.00 0.00 0.00 3.46 F
2390 2528 2.076100 TGCTAGAAATGCAACTCACGG 58.924 47.619 0.00 0.00 37.51 4.94 F
4114 4266 1.608055 TGCTGCATTGTGTAAGTGCT 58.392 45.000 0.00 0.00 39.52 4.40 F
5539 5939 0.249741 ACTAATGCCGGCACCGATAC 60.250 55.000 35.50 0.00 42.83 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2090 2148 0.175989 GTCCCTTAGCTGAGGAACCG 59.824 60.000 25.55 9.02 39.25 4.44 R
2810 2949 0.517316 GGAAGACGGTTGTGTGATGC 59.483 55.000 0.00 0.00 0.00 3.91 R
3292 3431 1.133598 TGGCACTACGATAAGTGGACG 59.866 52.381 15.47 0.00 45.75 4.79 R
3582 3726 7.546667 CACATTCTCATCTGGGTTAAAATTTGG 59.453 37.037 0.00 0.00 0.00 3.28 R
4375 4570 0.394352 AATCCATTCGCCACTGGGAC 60.394 55.000 0.00 0.00 35.59 4.46 R
5949 6352 0.106335 CGGCATCATCTTCTGGCTCT 59.894 55.000 0.00 0.00 35.91 4.09 R
6395 6820 0.810016 AGTAGGAAACTCCTCGCGTC 59.190 55.000 5.77 0.00 45.66 5.19 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
21 22 3.849953 GCGCTCGCCGGTGTTTAG 61.850 66.667 16.01 6.35 37.44 1.85
91 92 5.518847 CGACCACAACTACGACAAATGATAT 59.481 40.000 0.00 0.00 0.00 1.63
95 96 8.038944 ACCACAACTACGACAAATGATATTACT 58.961 33.333 0.00 0.00 0.00 2.24
104 105 6.315144 CGACAAATGATATTACTTGGGTGACA 59.685 38.462 0.00 0.00 0.00 3.58
156 157 0.768622 ACAATCCCCAACCTTGTCGA 59.231 50.000 0.00 0.00 0.00 4.20
283 284 0.176680 ATACCTGGAGCACGCAGAAG 59.823 55.000 0.00 0.00 0.00 2.85
497 498 5.280654 ACTGCAAAATGATTTGGTTGAGT 57.719 34.783 0.00 0.00 44.93 3.41
501 502 8.028938 ACTGCAAAATGATTTGGTTGAGTATAC 58.971 33.333 0.00 0.00 44.93 1.47
557 558 4.303282 TCTTTTATTCGGCTTGCAAAACC 58.697 39.130 0.00 4.20 0.00 3.27
561 562 0.033228 TTCGGCTTGCAAAACCATGG 59.967 50.000 11.19 11.19 0.00 3.66
691 707 4.954970 CGGCCAGCCAACCACACT 62.955 66.667 9.78 0.00 35.37 3.55
740 756 2.417719 GCTGCCGACCCATATCTAAAG 58.582 52.381 0.00 0.00 0.00 1.85
817 833 7.891183 AGAACGGATAAAATAATCTGGATCG 57.109 36.000 0.00 0.00 36.69 3.69
818 834 6.369065 AGAACGGATAAAATAATCTGGATCGC 59.631 38.462 0.00 0.00 36.69 4.58
819 835 5.794894 ACGGATAAAATAATCTGGATCGCT 58.205 37.500 0.00 0.00 36.69 4.93
820 836 5.869888 ACGGATAAAATAATCTGGATCGCTC 59.130 40.000 0.00 0.00 36.69 5.03
821 837 5.292101 CGGATAAAATAATCTGGATCGCTCC 59.708 44.000 0.00 0.00 42.45 4.70
822 838 5.292101 GGATAAAATAATCTGGATCGCTCCG 59.708 44.000 0.03 0.00 45.37 4.63
823 839 3.753294 AAATAATCTGGATCGCTCCGT 57.247 42.857 0.03 0.00 45.37 4.69
824 840 3.753294 AATAATCTGGATCGCTCCGTT 57.247 42.857 0.03 0.00 45.37 4.44
825 841 2.509052 TAATCTGGATCGCTCCGTTG 57.491 50.000 0.03 0.00 45.37 4.10
826 842 0.179073 AATCTGGATCGCTCCGTTGG 60.179 55.000 0.03 0.00 45.37 3.77
827 843 1.043116 ATCTGGATCGCTCCGTTGGA 61.043 55.000 0.03 0.00 45.37 3.53
844 860 2.889512 TGGAGTTGCTCTAACAGGAGA 58.110 47.619 0.00 0.00 41.88 3.71
872 888 8.032451 AGTATTGAAATTTCGGGTTACAAATGG 58.968 33.333 13.34 0.00 0.00 3.16
882 898 4.201910 CGGGTTACAAATGGCAAGTCATAG 60.202 45.833 0.00 0.00 0.00 2.23
930 947 3.304123 GGCAACGCACAAAACACACTATA 60.304 43.478 0.00 0.00 0.00 1.31
947 964 0.461516 ATAGAGGCGTCGTCGTCAGA 60.462 55.000 9.66 0.00 44.74 3.27
1459 1478 1.893315 CTCCCCCAGGGTTCTTATCA 58.107 55.000 4.22 0.00 44.74 2.15
1463 1482 0.909623 CCCAGGGTTCTTATCACCGT 59.090 55.000 0.00 0.00 34.79 4.83
1464 1483 1.406887 CCCAGGGTTCTTATCACCGTG 60.407 57.143 0.00 5.05 45.81 4.94
1538 1572 4.201910 TGCTTCGTATGCCTTGAAATTAGC 60.202 41.667 0.00 0.00 0.00 3.09
1545 1579 4.249638 TGCCTTGAAATTAGCCAGGTAT 57.750 40.909 0.00 0.00 0.00 2.73
1546 1580 4.609301 TGCCTTGAAATTAGCCAGGTATT 58.391 39.130 0.00 0.00 0.00 1.89
1586 1624 0.396811 GCACTGGTCAGGGTTGTAGT 59.603 55.000 1.97 0.00 33.42 2.73
1613 1651 4.176271 TGCGAGTCAGTTGATGTAGAATG 58.824 43.478 0.00 0.00 0.00 2.67
1618 1656 5.403246 AGTCAGTTGATGTAGAATGTCGTC 58.597 41.667 0.00 0.00 0.00 4.20
1630 1668 2.065993 ATGTCGTCAGGAGTGTTTCG 57.934 50.000 0.00 0.00 0.00 3.46
1688 1726 4.295051 GTCATGCTTCGTCCTTCTCTATC 58.705 47.826 0.00 0.00 0.00 2.08
1689 1727 4.037446 GTCATGCTTCGTCCTTCTCTATCT 59.963 45.833 0.00 0.00 0.00 1.98
1696 1734 5.425577 TCGTCCTTCTCTATCTTCGATTG 57.574 43.478 0.00 0.00 0.00 2.67
1699 1737 5.525199 GTCCTTCTCTATCTTCGATTGACC 58.475 45.833 0.00 0.00 0.00 4.02
1746 1784 5.682212 GCAAATTCTGTGGAAACAGGAAGTT 60.682 40.000 6.06 3.05 44.46 2.66
1750 1788 3.454447 TCTGTGGAAACAGGAAGTTCTGA 59.546 43.478 2.25 0.00 44.46 3.27
1920 1978 4.922206 TCCCATTAGTGATGACTTTTGCT 58.078 39.130 0.00 0.00 38.03 3.91
1974 2032 3.524095 TGGGTTCCTGACAATGAACAT 57.476 42.857 15.56 0.00 42.04 2.71
2090 2148 4.446371 CCAACTTCCACACTGATCTATCC 58.554 47.826 0.00 0.00 0.00 2.59
2189 2247 7.707467 AATTCTCATAAACCCTACATACCCT 57.293 36.000 0.00 0.00 0.00 4.34
2190 2248 6.494666 TTCTCATAAACCCTACATACCCTG 57.505 41.667 0.00 0.00 0.00 4.45
2252 2310 7.416213 CCGAATGCTGGGTAATAAAATCAAAGA 60.416 37.037 0.00 0.00 0.00 2.52
2390 2528 2.076100 TGCTAGAAATGCAACTCACGG 58.924 47.619 0.00 0.00 37.51 4.94
2666 2805 8.025445 ACAAAATGGAAAATTTCTCATCTCTCG 58.975 33.333 5.65 0.48 0.00 4.04
2681 2820 4.237976 TCTCTCGACCTCATTCCTAAGT 57.762 45.455 0.00 0.00 0.00 2.24
2705 2844 9.377312 AGTAATAGAGCTCACTTCAAATTTCTC 57.623 33.333 17.77 0.00 0.00 2.87
2776 2915 6.212955 TGCCTGCTGTAAATTTTCTACAAAC 58.787 36.000 0.00 0.00 0.00 2.93
2810 2949 5.981915 TCATCTGCATCTTTGAGAATAGACG 59.018 40.000 0.00 0.00 0.00 4.18
2884 3023 6.772716 TCCTTTCTGCACTCTTTTTATTGACT 59.227 34.615 0.00 0.00 0.00 3.41
3292 3431 6.422400 GTGGTATAGCTGAATACTCTTCAAGC 59.578 42.308 0.00 0.00 33.62 4.01
3393 3537 6.418057 TTGTATGTGCAATTTTCTTCCCTT 57.582 33.333 0.00 0.00 0.00 3.95
3402 3546 8.620416 GTGCAATTTTCTTCCCTTGTTTTTATT 58.380 29.630 0.00 0.00 0.00 1.40
3582 3726 4.647424 TCAAGGAACCAAACATGACAAC 57.353 40.909 0.00 0.00 0.00 3.32
3679 3823 5.009110 TGTTCATTTCTTTGGTTCACGCATA 59.991 36.000 0.00 0.00 0.00 3.14
3727 3871 6.704819 ACAATCGTGTTCTTTCAAATTTTGC 58.295 32.000 4.19 0.00 32.58 3.68
3739 3883 4.786507 TCAAATTTTGCACATCTGTCTCG 58.213 39.130 4.19 0.00 0.00 4.04
3805 3949 3.777106 ACTCTGCTTTTGTCCATCAGA 57.223 42.857 0.00 0.00 33.35 3.27
3895 4047 4.620723 TGATCTAGGCCCCATTCGTATAT 58.379 43.478 0.00 0.00 0.00 0.86
3954 4106 3.277715 TGCATTCTCGCATTTACCATCA 58.722 40.909 0.00 0.00 36.86 3.07
4007 4159 9.982651 TCATTCTAATATAGTGCCACTTAAGTC 57.017 33.333 1.02 0.00 0.00 3.01
4107 4259 3.733236 GCATGATGCTGCATTGTGT 57.267 47.368 17.36 0.00 40.96 3.72
4108 4260 2.855660 GCATGATGCTGCATTGTGTA 57.144 45.000 17.36 2.13 40.96 2.90
4109 4261 3.153676 GCATGATGCTGCATTGTGTAA 57.846 42.857 17.36 0.00 40.96 2.41
4110 4262 3.113322 GCATGATGCTGCATTGTGTAAG 58.887 45.455 17.36 4.50 40.96 2.34
4111 4263 3.428452 GCATGATGCTGCATTGTGTAAGT 60.428 43.478 17.36 0.00 40.96 2.24
4112 4264 3.835378 TGATGCTGCATTGTGTAAGTG 57.165 42.857 17.36 0.00 0.00 3.16
4113 4265 2.095110 TGATGCTGCATTGTGTAAGTGC 60.095 45.455 17.36 0.17 39.26 4.40
4114 4266 1.608055 TGCTGCATTGTGTAAGTGCT 58.392 45.000 0.00 0.00 39.52 4.40
4115 4267 1.955778 TGCTGCATTGTGTAAGTGCTT 59.044 42.857 0.00 0.00 39.52 3.91
4163 4358 6.512297 TGTGTATGCGTATATTCAGTGTGAT 58.488 36.000 0.00 0.00 0.00 3.06
4674 4992 7.862372 TGCTAATCTCACTGTTCAATTTTTGAC 59.138 33.333 0.00 0.00 39.87 3.18
5086 5404 6.426587 AGTGCATTAATAACTCCAGGACATT 58.573 36.000 0.00 0.00 0.00 2.71
5140 5458 0.749454 CCAATGGCTAGCCTCCACAC 60.749 60.000 33.07 6.63 36.26 3.82
5163 5481 4.462834 CGGCCTCTGATATTACTGGTATGA 59.537 45.833 0.00 0.00 0.00 2.15
5182 5500 9.661563 TGGTATGAATCATAACCGGATAATTAC 57.338 33.333 15.00 0.00 33.49 1.89
5362 5683 5.997129 TGTCAATTGTTCATCAGCTTCACTA 59.003 36.000 5.13 0.00 0.00 2.74
5389 5788 7.012610 GCCGCATTAGTTTTAGTTTATCCCTTA 59.987 37.037 0.00 0.00 0.00 2.69
5406 5805 6.963083 TCCCTTAAAATTTTCAAGAACCGA 57.037 33.333 6.72 2.51 0.00 4.69
5415 5814 6.986904 ATTTTCAAGAACCGAACTCTATCC 57.013 37.500 0.00 0.00 0.00 2.59
5448 5848 8.102676 TGAGAAATGTTCACTTCAATAGGATCA 58.897 33.333 0.00 0.00 0.00 2.92
5481 5881 2.485426 TCTCTTCCAATGCTGCTTTTCG 59.515 45.455 0.00 0.00 0.00 3.46
5539 5939 0.249741 ACTAATGCCGGCACCGATAC 60.250 55.000 35.50 0.00 42.83 2.24
5545 5945 2.279517 CGGCACCGATACCTCTGC 60.280 66.667 2.01 0.00 42.83 4.26
5682 6082 1.570347 CTCTCGAGGATCCTACGGCG 61.570 65.000 24.19 19.37 0.00 6.46
5685 6085 2.618219 CGAGGATCCTACGGCGAGG 61.618 68.421 16.16 16.32 38.03 4.63
5728 6128 4.634443 AGGACAATGCGGTAAGATGTTAAC 59.366 41.667 0.00 0.00 0.00 2.01
5739 6139 1.134670 AGATGTTAACGAGCCAGCCTC 60.135 52.381 0.26 0.00 37.22 4.70
5749 6149 2.818274 CCAGCCTCGCGGTTTACC 60.818 66.667 6.13 0.00 0.00 2.85
5961 6364 1.965754 GCGTCCCAGAGCCAGAAGAT 61.966 60.000 0.00 0.00 0.00 2.40
6213 6626 1.375908 TCATCCCGTTGCTGCTGTC 60.376 57.895 0.00 0.00 0.00 3.51
6250 6663 1.230324 GAGCCACTCTGTTGGTGTTC 58.770 55.000 0.00 0.00 39.09 3.18
6280 6693 1.090728 TGCAGTTTTTGTGCAGTCGA 58.909 45.000 0.00 0.00 45.96 4.20
6304 6717 2.103094 GGCATGATGGCACTAGTCAGTA 59.897 50.000 14.60 0.00 43.14 2.74
6307 6720 4.681781 GCATGATGGCACTAGTCAGTACTT 60.682 45.833 0.00 0.00 37.15 2.24
6308 6721 5.451937 GCATGATGGCACTAGTCAGTACTTA 60.452 44.000 0.00 0.00 37.15 2.24
6378 6799 2.359531 AGTCGATGGCACTAGCTTAGTC 59.640 50.000 0.00 0.00 41.70 2.59
6387 6812 3.126514 GCACTAGCTTAGTCTGTGTCGTA 59.873 47.826 0.00 0.00 36.76 3.43
6395 6820 2.438411 AGTCTGTGTCGTAGGGAAGAG 58.562 52.381 0.00 0.00 0.00 2.85
6399 6824 0.179169 GTGTCGTAGGGAAGAGACGC 60.179 60.000 0.00 0.00 36.54 5.19
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
91 92 7.567250 TGAGGATAGATATTGTCACCCAAGTAA 59.433 37.037 0.00 0.00 36.25 2.24
95 96 5.905331 ACTGAGGATAGATATTGTCACCCAA 59.095 40.000 0.00 0.00 37.49 4.12
123 124 4.288366 TGGGGATTGTCTTGACAATAGTGA 59.712 41.667 23.64 9.98 40.08 3.41
156 157 4.769488 GGGCAAATCTTTTCCTCTTCTCTT 59.231 41.667 0.00 0.00 0.00 2.85
283 284 0.392193 CAGTCATCACCTCCCACAGC 60.392 60.000 0.00 0.00 0.00 4.40
497 498 1.474320 GCCAACATGAGCCCACGTATA 60.474 52.381 0.00 0.00 0.00 1.47
501 502 2.267351 TTGCCAACATGAGCCCACG 61.267 57.895 0.00 0.00 0.00 4.94
561 562 8.926715 AGCCGAATAAAAATAAAAATGTCTCC 57.073 30.769 0.00 0.00 0.00 3.71
683 699 1.616725 CCCATATGTGCCAGTGTGGTT 60.617 52.381 1.24 0.00 40.46 3.67
684 700 0.034186 CCCATATGTGCCAGTGTGGT 60.034 55.000 1.24 0.00 40.46 4.16
689 705 1.526887 CCGACCCATATGTGCCAGT 59.473 57.895 1.24 0.00 0.00 4.00
691 707 2.191908 GCCGACCCATATGTGCCA 59.808 61.111 1.24 0.00 0.00 4.92
793 809 6.369065 GCGATCCAGATTATTTTATCCGTTCT 59.631 38.462 0.00 0.00 0.00 3.01
794 810 6.369065 AGCGATCCAGATTATTTTATCCGTTC 59.631 38.462 0.00 0.00 0.00 3.95
795 811 6.231211 AGCGATCCAGATTATTTTATCCGTT 58.769 36.000 0.00 0.00 0.00 4.44
796 812 5.794894 AGCGATCCAGATTATTTTATCCGT 58.205 37.500 0.00 0.00 0.00 4.69
797 813 5.292101 GGAGCGATCCAGATTATTTTATCCG 59.708 44.000 16.44 0.00 0.00 4.18
798 814 5.292101 CGGAGCGATCCAGATTATTTTATCC 59.708 44.000 21.44 0.00 0.00 2.59
799 815 5.869888 ACGGAGCGATCCAGATTATTTTATC 59.130 40.000 21.44 0.00 0.00 1.75
800 816 5.794894 ACGGAGCGATCCAGATTATTTTAT 58.205 37.500 21.44 0.00 0.00 1.40
801 817 5.209818 ACGGAGCGATCCAGATTATTTTA 57.790 39.130 21.44 0.00 0.00 1.52
802 818 4.073293 ACGGAGCGATCCAGATTATTTT 57.927 40.909 21.44 0.00 0.00 1.82
803 819 3.753294 ACGGAGCGATCCAGATTATTT 57.247 42.857 21.44 0.00 0.00 1.40
804 820 3.393800 CAACGGAGCGATCCAGATTATT 58.606 45.455 21.44 0.58 0.00 1.40
805 821 2.289072 CCAACGGAGCGATCCAGATTAT 60.289 50.000 21.44 0.00 0.00 1.28
806 822 1.068588 CCAACGGAGCGATCCAGATTA 59.931 52.381 21.44 0.00 0.00 1.75
807 823 0.179073 CCAACGGAGCGATCCAGATT 60.179 55.000 21.44 7.79 0.00 2.40
808 824 1.043116 TCCAACGGAGCGATCCAGAT 61.043 55.000 21.44 4.51 0.00 2.90
809 825 1.667154 CTCCAACGGAGCGATCCAGA 61.667 60.000 21.44 9.37 43.29 3.86
810 826 1.227089 CTCCAACGGAGCGATCCAG 60.227 63.158 21.44 14.75 43.29 3.86
811 827 2.892640 CTCCAACGGAGCGATCCA 59.107 61.111 21.44 0.00 43.29 3.41
819 835 1.689813 TGTTAGAGCAACTCCAACGGA 59.310 47.619 2.34 0.00 35.48 4.69
820 836 2.069273 CTGTTAGAGCAACTCCAACGG 58.931 52.381 1.31 1.31 35.48 4.44
821 837 2.069273 CCTGTTAGAGCAACTCCAACG 58.931 52.381 2.34 0.00 35.48 4.10
822 838 3.006967 TCTCCTGTTAGAGCAACTCCAAC 59.993 47.826 0.00 0.00 38.05 3.77
823 839 3.239449 TCTCCTGTTAGAGCAACTCCAA 58.761 45.455 0.00 0.00 38.05 3.53
824 840 2.828520 CTCTCCTGTTAGAGCAACTCCA 59.171 50.000 0.00 0.00 36.84 3.86
825 841 3.093057 TCTCTCCTGTTAGAGCAACTCC 58.907 50.000 0.00 0.00 42.36 3.85
826 842 3.761752 ACTCTCTCCTGTTAGAGCAACTC 59.238 47.826 0.00 0.00 42.50 3.01
827 843 3.773560 ACTCTCTCCTGTTAGAGCAACT 58.226 45.455 0.00 0.00 42.50 3.16
828 844 5.845391 ATACTCTCTCCTGTTAGAGCAAC 57.155 43.478 0.00 0.00 42.50 4.17
829 845 5.952347 TCAATACTCTCTCCTGTTAGAGCAA 59.048 40.000 0.00 0.00 42.50 3.91
830 846 5.510430 TCAATACTCTCTCCTGTTAGAGCA 58.490 41.667 0.00 0.00 42.50 4.26
831 847 6.458232 TTCAATACTCTCTCCTGTTAGAGC 57.542 41.667 0.00 0.00 42.50 4.09
832 848 9.883142 AAATTTCAATACTCTCTCCTGTTAGAG 57.117 33.333 0.00 0.00 43.72 2.43
833 849 9.877178 GAAATTTCAATACTCTCTCCTGTTAGA 57.123 33.333 13.40 0.00 0.00 2.10
844 860 7.989416 TTGTAACCCGAAATTTCAATACTCT 57.011 32.000 17.99 0.00 0.00 3.24
872 888 1.846782 CACGTAGCGACTATGACTTGC 59.153 52.381 11.45 0.00 0.00 4.01
910 926 5.337219 TCTATAGTGTGTTTTGTGCGTTG 57.663 39.130 0.00 0.00 0.00 4.10
930 947 2.358369 TCTGACGACGACGCCTCT 60.358 61.111 7.30 0.00 43.96 3.69
1085 1102 2.427575 CGCCGATCTCGATGACGG 60.428 66.667 16.22 16.22 46.74 4.79
1446 1465 1.369625 GCACGGTGATAAGAACCCTG 58.630 55.000 13.29 0.00 33.88 4.45
1538 1572 1.344438 TCGCCTGAGCATAATACCTGG 59.656 52.381 0.00 0.00 39.83 4.45
1545 1579 0.461548 CAGAGGTCGCCTGAGCATAA 59.538 55.000 2.98 0.00 45.10 1.90
1546 1580 0.684479 ACAGAGGTCGCCTGAGCATA 60.684 55.000 2.98 0.00 45.10 3.14
1586 1624 2.289631 ACATCAACTGACTCGCAATCCA 60.290 45.455 0.00 0.00 0.00 3.41
1613 1651 1.849097 AACGAAACACTCCTGACGAC 58.151 50.000 0.00 0.00 0.00 4.34
1618 1656 5.479716 ACAGTAAAAACGAAACACTCCTG 57.520 39.130 0.00 0.00 0.00 3.86
1630 1668 4.615541 GCATCAAGCGGTTACAGTAAAAAC 59.384 41.667 0.00 0.00 0.00 2.43
1654 1692 1.423056 GCATGACGCTGAGCTCAAC 59.577 57.895 18.85 12.84 37.77 3.18
1676 1714 5.067936 TGGTCAATCGAAGATAGAGAAGGAC 59.932 44.000 0.00 0.00 45.12 3.85
1688 1726 4.058124 TGAGAACAGTTGGTCAATCGAAG 58.942 43.478 0.00 0.00 33.22 3.79
1689 1727 4.058124 CTGAGAACAGTTGGTCAATCGAA 58.942 43.478 0.00 0.00 39.11 3.71
1696 1734 1.694696 AGGACCTGAGAACAGTTGGTC 59.305 52.381 10.76 10.76 42.05 4.02
1699 1737 1.071385 AGCAGGACCTGAGAACAGTTG 59.929 52.381 26.25 0.00 42.05 3.16
1920 1978 5.934043 CACACTCACTATCTCATGGTTTCAA 59.066 40.000 0.00 0.00 0.00 2.69
2090 2148 0.175989 GTCCCTTAGCTGAGGAACCG 59.824 60.000 25.55 9.02 39.25 4.44
2189 2247 4.022416 GGCACATGTGTTTAATGAAGGACA 60.022 41.667 26.01 0.00 0.00 4.02
2190 2248 4.022416 TGGCACATGTGTTTAATGAAGGAC 60.022 41.667 26.01 5.32 0.00 3.85
2252 2310 7.226523 GGAACACAAAATGTAGCTTCCAAATTT 59.773 33.333 0.00 0.00 42.31 1.82
2259 2317 5.453567 AAGGGAACACAAAATGTAGCTTC 57.546 39.130 0.00 0.00 42.31 3.86
2390 2528 5.187967 TCTTTCTCAGGTGGAAGTTAGATCC 59.812 44.000 0.00 0.00 37.48 3.36
2654 2793 3.634448 GGAATGAGGTCGAGAGATGAGAA 59.366 47.826 0.00 0.00 45.19 2.87
2666 2805 7.231722 TGAGCTCTATTACTTAGGAATGAGGTC 59.768 40.741 24.82 24.82 43.65 3.85
2681 2820 9.950496 AAGAGAAATTTGAAGTGAGCTCTATTA 57.050 29.630 16.19 0.00 31.78 0.98
2705 2844 6.360681 CGCTTAAACATCTTTGAGGTTTGAAG 59.639 38.462 17.00 15.61 44.36 3.02
2776 2915 3.542648 AGATGCAGATGACACCATTCTG 58.457 45.455 0.00 0.25 34.25 3.02
2810 2949 0.517316 GGAAGACGGTTGTGTGATGC 59.483 55.000 0.00 0.00 0.00 3.91
3071 3210 6.455360 TTCATCAATAAGCAGAATGGAACC 57.545 37.500 0.00 0.00 35.86 3.62
3292 3431 1.133598 TGGCACTACGATAAGTGGACG 59.866 52.381 15.47 0.00 45.75 4.79
3402 3546 8.758829 ACATGATCTAGTCACCACAAATACTTA 58.241 33.333 0.00 0.00 40.28 2.24
3582 3726 7.546667 CACATTCTCATCTGGGTTAAAATTTGG 59.453 37.037 0.00 0.00 0.00 3.28
3727 3871 2.427095 TCCATGGTACGAGACAGATGTG 59.573 50.000 12.58 0.00 0.00 3.21
3739 3883 2.790433 TCCTGTTTGCTTCCATGGTAC 58.210 47.619 12.58 2.98 0.00 3.34
3805 3949 4.411540 AGTGATAGCAAGATCCCATCAAGT 59.588 41.667 0.00 0.00 0.00 3.16
3954 4106 5.665812 TCCATACAAAGACAGCCTTACCTAT 59.334 40.000 0.00 0.00 34.00 2.57
4007 4159 6.469782 AAGGGACCATTTGTGCATATAAAG 57.530 37.500 0.00 0.00 36.96 1.85
4049 4201 0.815095 TGCAGCATCATGGCAAGAAG 59.185 50.000 0.00 0.00 34.05 2.85
4050 4202 1.480789 ATGCAGCATCATGGCAAGAA 58.519 45.000 0.52 0.00 41.43 2.52
4051 4203 1.136110 CAATGCAGCATCATGGCAAGA 59.864 47.619 8.77 0.00 41.43 3.02
4094 4246 2.165167 AGCACTTACACAATGCAGCAT 58.835 42.857 0.52 0.52 41.97 3.79
4095 4247 1.608055 AGCACTTACACAATGCAGCA 58.392 45.000 0.00 0.00 41.97 4.41
4096 4248 2.712057 AAGCACTTACACAATGCAGC 57.288 45.000 0.00 0.00 41.97 5.25
4097 4249 6.421377 TGTATAAGCACTTACACAATGCAG 57.579 37.500 0.00 0.00 41.97 4.41
4098 4250 6.809630 TTGTATAAGCACTTACACAATGCA 57.190 33.333 9.58 0.00 37.48 3.96
4099 4251 8.687824 ATTTTGTATAAGCACTTACACAATGC 57.312 30.769 13.39 0.00 40.68 3.56
4102 4254 9.672086 GACAATTTTGTATAAGCACTTACACAA 57.328 29.630 9.58 9.58 39.72 3.33
4103 4255 9.062524 AGACAATTTTGTATAAGCACTTACACA 57.937 29.630 0.00 0.00 42.43 3.72
4108 4260 9.502091 TCACTAGACAATTTTGTATAAGCACTT 57.498 29.630 0.00 0.00 42.43 3.16
4109 4261 9.672673 ATCACTAGACAATTTTGTATAAGCACT 57.327 29.630 0.00 0.00 42.43 4.40
4215 4410 5.717078 AGCTGCAATTCAAGATCTTTCAA 57.283 34.783 4.86 2.03 0.00 2.69
4309 4504 9.567776 TTTCCTCAGTTGACATAAGTATCAAAA 57.432 29.630 0.00 0.00 36.62 2.44
4375 4570 0.394352 AATCCATTCGCCACTGGGAC 60.394 55.000 0.00 0.00 35.59 4.46
4674 4992 1.453155 ACAGAGGCGCACAATTTAGG 58.547 50.000 10.83 0.00 0.00 2.69
4965 5283 3.076621 TCAATGACACTGCCATCTTCAC 58.923 45.455 0.00 0.00 0.00 3.18
5086 5404 1.231958 GGTGGCAAAACGACCATCGA 61.232 55.000 5.04 0.00 46.01 3.59
5140 5458 4.462834 TCATACCAGTAATATCAGAGGCCG 59.537 45.833 0.00 0.00 0.00 6.13
5362 5683 5.298527 GGGATAAACTAAAACTAATGCGGCT 59.701 40.000 0.00 0.00 0.00 5.52
5389 5788 8.297426 GGATAGAGTTCGGTTCTTGAAAATTTT 58.703 33.333 2.28 2.28 0.00 1.82
5392 5791 6.712276 AGGATAGAGTTCGGTTCTTGAAAAT 58.288 36.000 0.00 0.00 0.00 1.82
5406 5805 6.097554 ACATTTCTCACGATGAGGATAGAGTT 59.902 38.462 12.89 0.00 44.39 3.01
5415 5814 5.406477 TGAAGTGAACATTTCTCACGATGAG 59.594 40.000 10.40 8.24 46.38 2.90
5448 5848 2.329267 TGGAAGAGACACCATCACTGT 58.671 47.619 0.00 0.00 0.00 3.55
5539 5939 1.201647 CTGGCACAAAAGATGCAGAGG 59.798 52.381 0.00 0.00 45.27 3.69
5545 5945 1.069022 CGTCACCTGGCACAAAAGATG 60.069 52.381 0.00 0.00 38.70 2.90
5682 6082 1.344438 TGGACGTATGCATGGATCCTC 59.656 52.381 14.23 2.81 0.00 3.71
5685 6085 2.238942 TGTGGACGTATGCATGGATC 57.761 50.000 10.16 3.40 0.00 3.36
5710 6110 3.308866 GCTCGTTAACATCTTACCGCATT 59.691 43.478 6.39 0.00 0.00 3.56
5739 6139 1.977594 GAGGTGCATGGTAAACCGCG 61.978 60.000 0.00 0.00 39.07 6.46
5749 6149 2.304056 ACTGGAGGGGAGGTGCATG 61.304 63.158 0.00 0.00 0.00 4.06
5811 6211 1.228245 TCAGGCACTTGTGGCTTCC 60.228 57.895 24.05 7.01 43.13 3.46
5949 6352 0.106335 CGGCATCATCTTCTGGCTCT 59.894 55.000 0.00 0.00 35.91 4.09
6058 6467 1.524863 CCGAAGATCCGATACCGCCT 61.525 60.000 0.00 0.00 0.00 5.52
6060 6469 1.733399 GCCGAAGATCCGATACCGC 60.733 63.158 0.00 0.00 0.00 5.68
6130 6539 4.657824 CGAGGCGGTTCACCACGT 62.658 66.667 0.00 0.00 36.65 4.49
6156 6565 1.403514 GCAGACCTCTCTGTACACAGC 60.404 57.143 4.43 0.00 45.30 4.40
6213 6626 3.634910 GGCTCCTCTAGTCTAAGGAACAG 59.365 52.174 10.28 3.61 41.09 3.16
6280 6693 2.092267 TGACTAGTGCCATCATGCCATT 60.092 45.455 0.00 0.00 0.00 3.16
6378 6799 1.130749 CGTCTCTTCCCTACGACACAG 59.869 57.143 0.00 0.00 38.89 3.66
6387 6812 1.751162 CTCCTCGCGTCTCTTCCCT 60.751 63.158 5.77 0.00 0.00 4.20
6395 6820 0.810016 AGTAGGAAACTCCTCGCGTC 59.190 55.000 5.77 0.00 45.66 5.19
6399 6824 4.271661 AGGAAGTAGTAGGAAACTCCTCG 58.728 47.826 0.00 0.00 45.66 4.63


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

AutoCloner maintained by Alex Coulton.