Multiple sequence alignment - TraesCS2B01G351500

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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 TraesCS2B01G351500 chr2B 100.000 2537 0 0 1 2537 500456219 500453683 0.000000e+00 4686
1 TraesCS2B01G351500 chr2B 86.264 182 23 2 2 181 258092785 258092966 1.990000e-46 196
2 TraesCS2B01G351500 chr2B 93.443 122 6 2 1732 1852 234641216 234641336 2.010000e-41 180
3 TraesCS2B01G351500 chr2B 88.136 118 13 1 1732 1848 15389615 15389732 3.400000e-29 139
4 TraesCS2B01G351500 chr2D 93.577 903 42 8 845 1734 425159195 425158296 0.000000e+00 1332
5 TraesCS2B01G351500 chr2D 85.798 683 95 2 1856 2537 275732254 275732935 0.000000e+00 723
6 TraesCS2B01G351500 chr2D 88.235 187 19 3 6 191 176939772 176939956 1.180000e-53 220
7 TraesCS2B01G351500 chr2A 94.348 867 40 3 828 1688 563202307 563203170 0.000000e+00 1321
8 TraesCS2B01G351500 chr4A 97.313 670 18 0 1 670 672108687 672109356 0.000000e+00 1138
9 TraesCS2B01G351500 chr4A 82.443 262 32 11 551 810 169827871 169827622 1.530000e-52 217
10 TraesCS2B01G351500 chr4A 88.034 117 11 3 1732 1846 610458765 610458880 4.400000e-28 135
11 TraesCS2B01G351500 chr3D 86.569 685 86 5 1856 2537 50603315 50602634 0.000000e+00 750
12 TraesCS2B01G351500 chr3D 84.751 682 103 1 1856 2537 476815013 476814333 0.000000e+00 682
13 TraesCS2B01G351500 chr3B 84.604 682 103 2 1856 2537 473488226 473487547 0.000000e+00 676
14 TraesCS2B01G351500 chr3B 86.719 128 11 6 1734 1859 678169266 678169143 1.220000e-28 137
15 TraesCS2B01G351500 chr7D 84.425 687 101 4 1856 2537 470908324 470909009 0.000000e+00 671
16 TraesCS2B01G351500 chr7D 83.588 262 29 10 551 810 206107131 206106882 1.520000e-57 233
17 TraesCS2B01G351500 chr7D 86.885 122 12 4 1732 1851 477147178 477147059 1.580000e-27 134
18 TraesCS2B01G351500 chr1A 84.187 683 103 3 1856 2537 214690386 214689708 0.000000e+00 658
19 TraesCS2B01G351500 chr1A 83.455 683 110 2 1856 2537 187776501 187777181 1.280000e-177 632
20 TraesCS2B01G351500 chr1B 83.871 682 110 0 1856 2537 188250742 188250061 0.000000e+00 651
21 TraesCS2B01G351500 chr1B 88.670 203 22 1 609 810 277317405 277317203 1.950000e-61 246
22 TraesCS2B01G351500 chr1B 84.874 238 30 5 574 810 587905611 587905379 4.220000e-58 235
23 TraesCS2B01G351500 chr1B 86.667 150 18 2 43 191 565997620 565997472 5.610000e-37 165
24 TraesCS2B01G351500 chr1B 79.581 191 26 13 5 188 587906082 587905898 9.530000e-25 124
25 TraesCS2B01G351500 chr4D 82.673 681 116 2 1858 2537 183480804 183480125 1.000000e-168 603
26 TraesCS2B01G351500 chr4D 89.394 264 21 7 550 810 99781710 99781451 2.430000e-85 326
27 TraesCS2B01G351500 chr4D 86.400 125 12 5 1732 1852 11133793 11133916 5.690000e-27 132
28 TraesCS2B01G351500 chr4D 86.777 121 12 4 1731 1849 465072862 465072980 5.690000e-27 132
29 TraesCS2B01G351500 chr4D 85.156 128 15 3 1727 1851 213411980 213412106 7.370000e-26 128
30 TraesCS2B01G351500 chr6D 86.292 569 58 11 1 551 415235076 415234510 3.610000e-168 601
31 TraesCS2B01G351500 chr4B 82.680 485 65 14 1 476 159338853 159339327 1.820000e-111 412
32 TraesCS2B01G351500 chr4B 88.550 262 27 3 550 810 159339469 159339728 5.270000e-82 315
33 TraesCS2B01G351500 chr6B 88.550 262 27 3 550 810 606059838 606060097 5.270000e-82 315
34 TraesCS2B01G351500 chr6B 88.182 220 23 2 550 768 620185392 620185175 2.500000e-65 259
35 TraesCS2B01G351500 chr3A 91.905 210 16 1 602 810 32991339 32991130 2.470000e-75 292
36 TraesCS2B01G351500 chr3A 91.005 189 10 2 322 503 32993918 32993730 5.420000e-62 248
37 TraesCS2B01G351500 chr3A 96.053 152 6 0 12 163 32997093 32996942 5.420000e-62 248
38 TraesCS2B01G351500 chr3A 88.000 150 10 4 184 325 32996649 32996500 1.210000e-38 171
39 TraesCS2B01G351500 chr3A 79.006 181 33 5 632 810 598872833 598873010 4.430000e-23 119
40 TraesCS2B01G351500 chr1D 83.030 165 21 4 1 162 313167974 313168134 2.630000e-30 143
41 TraesCS2B01G351500 chr5A 87.705 122 10 5 1732 1851 550504897 550505015 1.220000e-28 137
42 TraesCS2B01G351500 chr5A 78.689 183 32 7 5 184 452075042 452074864 5.740000e-22 115


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 TraesCS2B01G351500 chr2B 500453683 500456219 2536 True 4686.00 4686 100.00000 1 2537 1 chr2B.!!$R1 2536
1 TraesCS2B01G351500 chr2D 425158296 425159195 899 True 1332.00 1332 93.57700 845 1734 1 chr2D.!!$R1 889
2 TraesCS2B01G351500 chr2D 275732254 275732935 681 False 723.00 723 85.79800 1856 2537 1 chr2D.!!$F2 681
3 TraesCS2B01G351500 chr2A 563202307 563203170 863 False 1321.00 1321 94.34800 828 1688 1 chr2A.!!$F1 860
4 TraesCS2B01G351500 chr4A 672108687 672109356 669 False 1138.00 1138 97.31300 1 670 1 chr4A.!!$F2 669
5 TraesCS2B01G351500 chr3D 50602634 50603315 681 True 750.00 750 86.56900 1856 2537 1 chr3D.!!$R1 681
6 TraesCS2B01G351500 chr3D 476814333 476815013 680 True 682.00 682 84.75100 1856 2537 1 chr3D.!!$R2 681
7 TraesCS2B01G351500 chr3B 473487547 473488226 679 True 676.00 676 84.60400 1856 2537 1 chr3B.!!$R1 681
8 TraesCS2B01G351500 chr7D 470908324 470909009 685 False 671.00 671 84.42500 1856 2537 1 chr7D.!!$F1 681
9 TraesCS2B01G351500 chr1A 214689708 214690386 678 True 658.00 658 84.18700 1856 2537 1 chr1A.!!$R1 681
10 TraesCS2B01G351500 chr1A 187776501 187777181 680 False 632.00 632 83.45500 1856 2537 1 chr1A.!!$F1 681
11 TraesCS2B01G351500 chr1B 188250061 188250742 681 True 651.00 651 83.87100 1856 2537 1 chr1B.!!$R1 681
12 TraesCS2B01G351500 chr4D 183480125 183480804 679 True 603.00 603 82.67300 1858 2537 1 chr4D.!!$R2 679
13 TraesCS2B01G351500 chr6D 415234510 415235076 566 True 601.00 601 86.29200 1 551 1 chr6D.!!$R1 550
14 TraesCS2B01G351500 chr4B 159338853 159339728 875 False 363.50 412 85.61500 1 810 2 chr4B.!!$F1 809
15 TraesCS2B01G351500 chr3A 32991130 32997093 5963 True 239.75 292 91.74075 12 810 4 chr3A.!!$R1 798

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
816 6061 0.261696 GGGTGCCCATGGGTTAGATT 59.738 55.0 31.58 0.0 37.65 2.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1844 7105 0.387929 TAATCACTCCATCGGCGACC 59.612 55.0 13.76 0.0 0.0 4.79 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
39 40 0.609957 TTTGACCGGGTCGAGCTCTA 60.610 55.000 21.52 0.00 34.95 2.43
129 130 4.189580 CCCATGCCCGAACCCGAT 62.190 66.667 0.00 0.00 38.22 4.18
553 5714 6.761714 ACCAAGAGCGATCGAAAATAAATACT 59.238 34.615 21.57 1.26 0.00 2.12
736 5981 3.042059 ACCCTACCCATGACTAATCGT 57.958 47.619 0.00 0.00 0.00 3.73
747 5992 5.356426 CATGACTAATCGTGTTACCCATCA 58.644 41.667 0.00 0.00 37.12 3.07
749 5994 4.707934 TGACTAATCGTGTTACCCATCAGA 59.292 41.667 0.00 0.00 0.00 3.27
755 6000 4.084287 TCGTGTTACCCATCAGACTTACT 58.916 43.478 0.00 0.00 0.00 2.24
759 6004 6.183360 CGTGTTACCCATCAGACTTACTCATA 60.183 42.308 0.00 0.00 0.00 2.15
770 6015 8.996651 TCAGACTTACTCATAGGTGAATATGA 57.003 34.615 0.00 0.00 39.33 2.15
792 6037 1.843851 GACCCATACCCTGTCCATTCA 59.156 52.381 0.00 0.00 0.00 2.57
811 6056 4.360405 GTCGGGTGCCCATGGGTT 62.360 66.667 31.58 0.00 37.65 4.11
812 6057 2.611172 TCGGGTGCCCATGGGTTA 60.611 61.111 31.58 18.47 37.65 2.85
813 6058 2.124320 CGGGTGCCCATGGGTTAG 60.124 66.667 31.58 14.91 37.65 2.34
814 6059 2.675242 CGGGTGCCCATGGGTTAGA 61.675 63.158 31.58 11.03 37.65 2.10
815 6060 1.930520 GGGTGCCCATGGGTTAGAT 59.069 57.895 31.58 0.00 37.65 1.98
816 6061 0.261696 GGGTGCCCATGGGTTAGATT 59.738 55.000 31.58 0.00 37.65 2.40
817 6062 1.402787 GGTGCCCATGGGTTAGATTG 58.597 55.000 31.58 4.22 37.65 2.67
818 6063 0.746659 GTGCCCATGGGTTAGATTGC 59.253 55.000 31.58 15.01 37.65 3.56
819 6064 0.334335 TGCCCATGGGTTAGATTGCA 59.666 50.000 31.58 17.50 37.65 4.08
820 6065 1.035139 GCCCATGGGTTAGATTGCAG 58.965 55.000 31.58 2.09 37.65 4.41
821 6066 1.696063 CCCATGGGTTAGATTGCAGG 58.304 55.000 23.93 0.00 0.00 4.85
822 6067 1.696063 CCATGGGTTAGATTGCAGGG 58.304 55.000 2.85 0.00 0.00 4.45
823 6068 1.063717 CCATGGGTTAGATTGCAGGGT 60.064 52.381 2.85 0.00 0.00 4.34
824 6069 2.624029 CCATGGGTTAGATTGCAGGGTT 60.624 50.000 2.85 0.00 0.00 4.11
825 6070 2.214376 TGGGTTAGATTGCAGGGTTG 57.786 50.000 0.00 0.00 0.00 3.77
826 6071 1.707989 TGGGTTAGATTGCAGGGTTGA 59.292 47.619 0.00 0.00 0.00 3.18
827 6072 2.290896 TGGGTTAGATTGCAGGGTTGAG 60.291 50.000 0.00 0.00 0.00 3.02
828 6073 2.026262 GGGTTAGATTGCAGGGTTGAGA 60.026 50.000 0.00 0.00 0.00 3.27
829 6074 3.010420 GGTTAGATTGCAGGGTTGAGAC 58.990 50.000 0.00 0.00 0.00 3.36
830 6075 3.010420 GTTAGATTGCAGGGTTGAGACC 58.990 50.000 0.00 0.00 45.75 3.85
840 6085 3.691342 TTGAGACCTGGCCCGTCG 61.691 66.667 12.95 0.00 35.33 5.12
875 6120 2.577059 GACAATCCCGTCTGCCGA 59.423 61.111 0.00 0.00 39.56 5.54
950 6195 2.225963 CCTCGAATAGCTACCACCTACG 59.774 54.545 0.00 0.00 0.00 3.51
1044 6290 2.776370 TACCGTTCCTCCTCCACGCT 62.776 60.000 0.00 0.00 32.43 5.07
1104 6350 2.032223 CTGCTGTGCTGCTCCACT 59.968 61.111 0.00 0.00 36.68 4.00
1312 6558 1.766069 AATCGTTGTTGCGGAAAAGC 58.234 45.000 0.00 0.00 37.71 3.51
1368 6614 4.089239 TGCGGGCTTGACGGCATA 62.089 61.111 4.56 0.00 41.00 3.14
1401 6647 1.122019 ACCCGCAGTTCAGGAAGTCT 61.122 55.000 0.00 0.00 0.00 3.24
1440 6686 3.379445 ACGGACGGCGTCTGGATT 61.379 61.111 41.53 25.17 42.66 3.01
1449 6695 1.943340 GGCGTCTGGATTGATTTCTCC 59.057 52.381 0.00 0.00 0.00 3.71
1519 6765 2.224209 GGGGAGCGATTTATCCGAGAAA 60.224 50.000 0.00 0.00 36.38 2.52
1568 6814 4.408182 AGCTGATCCTTTAGTAATGCGT 57.592 40.909 0.00 0.00 0.00 5.24
1569 6815 4.122776 AGCTGATCCTTTAGTAATGCGTG 58.877 43.478 0.00 0.00 0.00 5.34
1570 6816 3.871594 GCTGATCCTTTAGTAATGCGTGT 59.128 43.478 0.00 0.00 0.00 4.49
1574 6820 7.534085 TGATCCTTTAGTAATGCGTGTAAAG 57.466 36.000 8.01 8.01 33.89 1.85
1598 6844 9.696917 AAGATGTTGTATGTTTTGAAATCCTTC 57.303 29.630 0.00 0.00 0.00 3.46
1601 6847 7.484975 TGTTGTATGTTTTGAAATCCTTCGTT 58.515 30.769 0.00 0.00 33.94 3.85
1696 6955 8.570068 TCTAGTTTGGTTTAGTCTGTTTGTTT 57.430 30.769 0.00 0.00 0.00 2.83
1704 6963 7.612633 TGGTTTAGTCTGTTTGTTTTAGTCCTT 59.387 33.333 0.00 0.00 0.00 3.36
1717 6978 5.845391 TTTAGTCCTTTGTTTGTCTTGGG 57.155 39.130 0.00 0.00 0.00 4.12
1724 6985 5.659079 TCCTTTGTTTGTCTTGGGTTTATGT 59.341 36.000 0.00 0.00 0.00 2.29
1734 6995 6.938030 TGTCTTGGGTTTATGTAGGTGTTTAG 59.062 38.462 0.00 0.00 0.00 1.85
1735 6996 7.163441 GTCTTGGGTTTATGTAGGTGTTTAGA 58.837 38.462 0.00 0.00 0.00 2.10
1736 6997 7.333672 GTCTTGGGTTTATGTAGGTGTTTAGAG 59.666 40.741 0.00 0.00 0.00 2.43
1737 6998 5.493809 TGGGTTTATGTAGGTGTTTAGAGC 58.506 41.667 0.00 0.00 0.00 4.09
1738 6999 5.013287 TGGGTTTATGTAGGTGTTTAGAGCA 59.987 40.000 0.00 0.00 0.00 4.26
1739 7000 6.120220 GGGTTTATGTAGGTGTTTAGAGCAT 58.880 40.000 0.00 0.00 0.00 3.79
1740 7001 6.260271 GGGTTTATGTAGGTGTTTAGAGCATC 59.740 42.308 0.00 0.00 0.00 3.91
1751 7012 4.116878 GAGCATCTCCAGCCGTTC 57.883 61.111 0.00 0.00 0.00 3.95
1752 7013 1.880340 GAGCATCTCCAGCCGTTCG 60.880 63.158 0.00 0.00 0.00 3.95
1753 7014 2.892425 GCATCTCCAGCCGTTCGG 60.892 66.667 6.90 6.90 0.00 4.30
1772 7033 4.183858 CCCCAGGGCGGCGATAAA 62.184 66.667 12.98 0.00 0.00 1.40
1773 7034 2.124487 CCCAGGGCGGCGATAAAA 60.124 61.111 12.98 0.00 0.00 1.52
1774 7035 1.751162 CCCAGGGCGGCGATAAAAA 60.751 57.895 12.98 0.00 0.00 1.94
1775 7036 1.724582 CCCAGGGCGGCGATAAAAAG 61.725 60.000 12.98 0.00 0.00 2.27
1776 7037 1.064134 CAGGGCGGCGATAAAAAGC 59.936 57.895 12.98 0.00 0.00 3.51
1782 7043 4.690159 GCGATAAAAAGCCGCCTG 57.310 55.556 0.00 0.00 42.77 4.85
1783 7044 1.064134 GCGATAAAAAGCCGCCTGG 59.936 57.895 0.00 0.00 42.77 4.45
1784 7045 1.727467 CGATAAAAAGCCGCCTGGG 59.273 57.895 0.00 0.00 39.58 4.45
1785 7046 1.724582 CGATAAAAAGCCGCCTGGGG 61.725 60.000 3.33 3.33 35.78 4.96
1786 7047 1.381191 ATAAAAAGCCGCCTGGGGG 60.381 57.895 24.52 24.52 38.76 5.40
1787 7048 2.163021 ATAAAAAGCCGCCTGGGGGT 62.163 55.000 28.18 14.78 40.11 4.95
1788 7049 4.994756 AAAAGCCGCCTGGGGGTG 62.995 66.667 28.18 7.12 42.41 4.61
1802 7063 3.284449 GGTGAACCGGCGCAAGTT 61.284 61.111 10.83 12.36 41.68 2.66
1803 7064 2.719354 GTGAACCGGCGCAAGTTT 59.281 55.556 10.83 0.00 41.68 2.66
1804 7065 1.657181 GTGAACCGGCGCAAGTTTG 60.657 57.895 10.83 0.00 41.68 2.93
1805 7066 2.050442 GAACCGGCGCAAGTTTGG 60.050 61.111 10.83 2.92 41.68 3.28
1806 7067 4.279043 AACCGGCGCAAGTTTGGC 62.279 61.111 10.83 0.00 41.68 4.52
1813 7074 4.026226 GCAAGTTTGGCGTTTGGG 57.974 55.556 0.00 0.00 0.00 4.12
1814 7075 1.594021 GCAAGTTTGGCGTTTGGGG 60.594 57.895 0.00 0.00 0.00 4.96
1815 7076 1.068921 CAAGTTTGGCGTTTGGGGG 59.931 57.895 0.00 0.00 0.00 5.40
1816 7077 2.802724 AAGTTTGGCGTTTGGGGGC 61.803 57.895 0.00 0.00 0.00 5.80
1817 7078 4.656117 GTTTGGCGTTTGGGGGCG 62.656 66.667 0.00 0.00 0.00 6.13
1818 7079 4.896829 TTTGGCGTTTGGGGGCGA 62.897 61.111 0.00 0.00 0.00 5.54
1822 7083 3.733960 GCGTTTGGGGGCGACTTC 61.734 66.667 0.00 0.00 0.00 3.01
1823 7084 3.419759 CGTTTGGGGGCGACTTCG 61.420 66.667 0.00 0.00 43.27 3.79
1824 7085 2.281276 GTTTGGGGGCGACTTCGT 60.281 61.111 0.00 0.00 42.22 3.85
1825 7086 2.031465 TTTGGGGGCGACTTCGTC 59.969 61.111 0.00 0.00 44.28 4.20
1831 7092 3.692406 GGCGACTTCGTCCCCAGT 61.692 66.667 0.00 0.00 42.22 4.00
1832 7093 2.126031 GCGACTTCGTCCCCAGTC 60.126 66.667 0.00 0.00 42.22 3.51
1834 7095 3.363351 GACTTCGTCCCCAGTCGT 58.637 61.111 0.00 0.00 30.51 4.34
1835 7096 1.212229 GACTTCGTCCCCAGTCGTC 59.788 63.158 0.00 0.00 30.51 4.20
1836 7097 2.178521 CTTCGTCCCCAGTCGTCG 59.821 66.667 0.00 0.00 0.00 5.12
1837 7098 3.966026 CTTCGTCCCCAGTCGTCGC 62.966 68.421 0.00 0.00 0.00 5.19
1844 7105 4.742201 CCAGTCGTCGCCCACCAG 62.742 72.222 0.00 0.00 0.00 4.00
1845 7106 4.742201 CAGTCGTCGCCCACCAGG 62.742 72.222 0.00 0.00 39.47 4.45
1847 7108 4.736896 GTCGTCGCCCACCAGGTC 62.737 72.222 0.00 0.00 38.26 3.85
1854 7115 4.838152 CCCACCAGGTCGCCGATG 62.838 72.222 0.00 0.00 0.00 3.84
1860 7121 2.362503 AGGTCGCCGATGGAGTGA 60.363 61.111 0.00 0.00 0.00 3.41
1875 7136 8.620416 CCGATGGAGTGATTATCAAAACATTTA 58.380 33.333 0.00 0.00 0.00 1.40
1926 7187 4.232221 GACTAAGTTACAGCACTGCGTTA 58.768 43.478 0.00 0.00 0.00 3.18
1928 7189 5.235516 ACTAAGTTACAGCACTGCGTTAAT 58.764 37.500 0.00 0.00 0.00 1.40
1932 7193 6.165659 AGTTACAGCACTGCGTTAATAAAG 57.834 37.500 0.00 0.00 0.00 1.85
1943 7204 5.090083 TGCGTTAATAAAGCGAATGAAACC 58.910 37.500 6.45 0.00 0.00 3.27
2064 7325 5.189180 ACAGGGAGCTCATACTGAAATTTC 58.811 41.667 28.14 11.41 35.08 2.17
2092 7353 1.580994 GGGGCCATGTCCCTAAACCT 61.581 60.000 12.49 0.00 45.53 3.50
2147 7408 2.490685 GAAGAGGACCGACTCCGC 59.509 66.667 0.00 0.00 45.10 5.54
2152 7413 3.681835 GGACCGACTCCGCAGTGT 61.682 66.667 0.00 0.00 30.63 3.55
2163 7424 1.140052 TCCGCAGTGTCAAAGGAAAGA 59.860 47.619 0.00 0.00 0.00 2.52
2292 7558 1.290134 AGGGAAGGCCAAAGAGTAGG 58.710 55.000 5.01 0.00 35.15 3.18
2323 7589 8.498575 TCCTAAGAAGAAGATAGATCAGTCTGA 58.501 37.037 4.68 4.68 35.87 3.27
2324 7590 9.130661 CCTAAGAAGAAGATAGATCAGTCTGAA 57.869 37.037 6.64 0.00 35.87 3.02
2387 7653 4.722361 AGACGAAGAGGGTAACTTGATC 57.278 45.455 0.00 0.00 0.00 2.92
2453 7719 1.739562 CCGTGAAGGTCAGCTGAGC 60.740 63.158 33.42 33.42 42.47 4.26
2495 7761 3.999663 ACGAAGATGAAGAAAAGGCAGAG 59.000 43.478 0.00 0.00 0.00 3.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 40 2.586425 CTATTCGGGCATGGGTTTGAT 58.414 47.619 0.00 0.00 0.00 2.57
129 130 1.613928 TGATGGGTCGGGTTGCCTA 60.614 57.895 0.00 0.00 0.00 3.93
348 3223 2.571757 CTCGCCTAGCCGTGTTGA 59.428 61.111 0.00 0.00 0.00 3.18
553 5714 1.745115 GCACCCAGTAGCGATGCAA 60.745 57.895 0.00 0.00 36.30 4.08
672 5917 1.383109 TCGCCTGATGGGTCATCCT 60.383 57.895 5.57 0.00 39.87 3.24
675 5920 2.746375 GGGTCGCCTGATGGGTCAT 61.746 63.158 0.00 0.00 37.43 3.06
736 5981 6.323996 CCTATGAGTAAGTCTGATGGGTAACA 59.676 42.308 0.00 0.00 34.70 2.41
747 5992 7.720074 TCGTCATATTCACCTATGAGTAAGTCT 59.280 37.037 0.00 0.00 38.47 3.24
749 5994 7.255520 GGTCGTCATATTCACCTATGAGTAAGT 60.256 40.741 0.00 0.00 38.47 2.24
755 6000 4.219919 TGGGTCGTCATATTCACCTATGA 58.780 43.478 0.00 0.00 36.11 2.15
759 6004 3.323979 GGTATGGGTCGTCATATTCACCT 59.676 47.826 0.00 0.00 32.93 4.00
770 6015 0.326238 ATGGACAGGGTATGGGTCGT 60.326 55.000 0.00 0.00 32.39 4.34
810 6055 3.350219 GGTCTCAACCCTGCAATCTAA 57.650 47.619 0.00 0.00 39.93 2.10
812 6057 3.965888 GGTCTCAACCCTGCAATCT 57.034 52.632 0.00 0.00 39.93 2.40
821 6066 3.607370 GACGGGCCAGGTCTCAACC 62.607 68.421 16.57 0.00 46.87 3.77
822 6067 2.047179 GACGGGCCAGGTCTCAAC 60.047 66.667 16.57 0.00 0.00 3.18
823 6068 3.691342 CGACGGGCCAGGTCTCAA 61.691 66.667 20.07 0.00 32.24 3.02
840 6085 2.170273 GCTTTGTTCGACGACGGC 59.830 61.111 7.55 0.00 40.21 5.68
875 6120 4.379243 CGGAGCGGGCACAGAAGT 62.379 66.667 0.00 0.00 0.00 3.01
915 6160 5.402867 GCTATTCGAGGAAGAAACTTATCCG 59.597 44.000 0.00 0.00 38.31 4.18
950 6195 1.080434 GTGCGTGAGGGAGTGACTC 60.080 63.158 3.47 3.47 35.55 3.36
1094 6340 2.423898 TAGGCGGTAGTGGAGCAGC 61.424 63.158 0.00 0.00 0.00 5.25
1312 6558 1.875576 GCGTGGATGATAGGCAAGGAG 60.876 57.143 0.00 0.00 0.00 3.69
1365 6611 2.699954 GGGTGCCTATCGACCATTATG 58.300 52.381 0.00 0.00 33.48 1.90
1368 6614 1.445942 CGGGTGCCTATCGACCATT 59.554 57.895 0.00 0.00 33.48 3.16
1401 6647 1.063616 CGAACGACGAAGAGGCATCTA 59.936 52.381 0.00 0.00 45.77 1.98
1440 6686 3.055094 GGCACTTCTGGTAGGAGAAATCA 60.055 47.826 0.00 0.00 31.52 2.57
1449 6695 0.108615 CACGGAGGCACTTCTGGTAG 60.109 60.000 0.00 0.00 41.55 3.18
1512 6758 3.058224 AGGTTCGCTTGAAATTTTCTCGG 60.058 43.478 10.33 2.47 32.31 4.63
1519 6765 2.029918 GCCTTCAGGTTCGCTTGAAATT 60.030 45.455 0.00 0.00 41.62 1.82
1574 6820 7.807907 ACGAAGGATTTCAAAACATACAACATC 59.192 33.333 0.00 0.00 32.67 3.06
1696 6955 4.862371 ACCCAAGACAAACAAAGGACTAA 58.138 39.130 0.00 0.00 0.00 2.24
1704 6963 6.039941 CACCTACATAAACCCAAGACAAACAA 59.960 38.462 0.00 0.00 0.00 2.83
1717 6978 7.224949 GGAGATGCTCTAAACACCTACATAAAC 59.775 40.741 0.00 0.00 0.00 2.01
1724 6985 3.133003 GCTGGAGATGCTCTAAACACCTA 59.867 47.826 0.00 0.00 0.00 3.08
1734 6995 1.880340 CGAACGGCTGGAGATGCTC 60.880 63.158 0.00 0.00 0.00 4.26
1735 6996 2.185350 CGAACGGCTGGAGATGCT 59.815 61.111 0.00 0.00 0.00 3.79
1736 6997 2.892425 CCGAACGGCTGGAGATGC 60.892 66.667 0.00 0.00 0.00 3.91
1756 7017 1.724582 CTTTTTATCGCCGCCCTGGG 61.725 60.000 8.86 8.86 38.63 4.45
1757 7018 1.727467 CTTTTTATCGCCGCCCTGG 59.273 57.895 0.00 0.00 42.50 4.45
1758 7019 1.064134 GCTTTTTATCGCCGCCCTG 59.936 57.895 0.00 0.00 0.00 4.45
1759 7020 2.119029 GGCTTTTTATCGCCGCCCT 61.119 57.895 0.00 0.00 36.45 5.19
1760 7021 2.411701 GGCTTTTTATCGCCGCCC 59.588 61.111 0.00 0.00 36.45 6.13
1766 7027 1.724582 CCCCAGGCGGCTTTTTATCG 61.725 60.000 9.66 0.00 0.00 2.92
1767 7028 1.391933 CCCCCAGGCGGCTTTTTATC 61.392 60.000 9.66 0.00 0.00 1.75
1768 7029 1.381191 CCCCCAGGCGGCTTTTTAT 60.381 57.895 9.66 0.00 0.00 1.40
1769 7030 2.036572 CCCCCAGGCGGCTTTTTA 59.963 61.111 9.66 0.00 0.00 1.52
1770 7031 4.233558 ACCCCCAGGCGGCTTTTT 62.234 61.111 9.66 0.00 36.11 1.94
1771 7032 4.994756 CACCCCCAGGCGGCTTTT 62.995 66.667 9.66 0.00 36.11 2.27
1785 7046 2.841160 AAACTTGCGCCGGTTCACC 61.841 57.895 4.18 0.00 0.00 4.02
1786 7047 1.657181 CAAACTTGCGCCGGTTCAC 60.657 57.895 4.18 0.00 0.00 3.18
1787 7048 2.718731 CAAACTTGCGCCGGTTCA 59.281 55.556 4.18 0.00 0.00 3.18
1788 7049 2.050442 CCAAACTTGCGCCGGTTC 60.050 61.111 4.18 0.00 0.00 3.62
1789 7050 4.279043 GCCAAACTTGCGCCGGTT 62.279 61.111 4.18 7.14 0.00 4.44
1796 7057 1.594021 CCCCAAACGCCAAACTTGC 60.594 57.895 0.00 0.00 0.00 4.01
1797 7058 1.068921 CCCCCAAACGCCAAACTTG 59.931 57.895 0.00 0.00 0.00 3.16
1798 7059 2.802724 GCCCCCAAACGCCAAACTT 61.803 57.895 0.00 0.00 0.00 2.66
1799 7060 3.230990 GCCCCCAAACGCCAAACT 61.231 61.111 0.00 0.00 0.00 2.66
1800 7061 4.656117 CGCCCCCAAACGCCAAAC 62.656 66.667 0.00 0.00 0.00 2.93
1801 7062 4.896829 TCGCCCCCAAACGCCAAA 62.897 61.111 0.00 0.00 0.00 3.28
1805 7066 3.733960 GAAGTCGCCCCCAAACGC 61.734 66.667 0.00 0.00 0.00 4.84
1806 7067 3.419759 CGAAGTCGCCCCCAAACG 61.420 66.667 0.00 0.00 0.00 3.60
1807 7068 2.281276 ACGAAGTCGCCCCCAAAC 60.281 61.111 0.00 0.00 44.43 2.93
1819 7080 2.178521 CGACGACTGGGGACGAAG 59.821 66.667 0.00 0.00 34.97 3.79
1820 7081 4.047059 GCGACGACTGGGGACGAA 62.047 66.667 0.00 0.00 34.97 3.85
1827 7088 4.742201 CTGGTGGGCGACGACTGG 62.742 72.222 2.57 0.00 39.30 4.00
1828 7089 4.742201 CCTGGTGGGCGACGACTG 62.742 72.222 2.57 0.00 39.30 3.51
1830 7091 4.736896 GACCTGGTGGGCGACGAC 62.737 72.222 2.82 0.00 39.10 4.34
1837 7098 4.838152 CATCGGCGACCTGGTGGG 62.838 72.222 13.76 0.00 41.89 4.61
1838 7099 4.838152 CCATCGGCGACCTGGTGG 62.838 72.222 18.96 15.45 39.83 4.61
1839 7100 3.723235 CTCCATCGGCGACCTGGTG 62.723 68.421 24.33 19.55 32.73 4.17
1840 7101 3.461773 CTCCATCGGCGACCTGGT 61.462 66.667 24.33 0.00 32.73 4.00
1841 7102 3.461773 ACTCCATCGGCGACCTGG 61.462 66.667 20.71 20.71 0.00 4.45
1842 7103 2.021068 ATCACTCCATCGGCGACCTG 62.021 60.000 13.76 7.79 0.00 4.00
1843 7104 1.330655 AATCACTCCATCGGCGACCT 61.331 55.000 13.76 0.00 0.00 3.85
1844 7105 0.387929 TAATCACTCCATCGGCGACC 59.612 55.000 13.76 0.00 0.00 4.79
1845 7106 2.288213 TGATAATCACTCCATCGGCGAC 60.288 50.000 13.76 0.00 0.00 5.19
1846 7107 1.960689 TGATAATCACTCCATCGGCGA 59.039 47.619 13.87 13.87 0.00 5.54
1847 7108 2.438868 TGATAATCACTCCATCGGCG 57.561 50.000 0.00 0.00 0.00 6.46
1848 7109 4.335315 TGTTTTGATAATCACTCCATCGGC 59.665 41.667 0.00 0.00 0.00 5.54
1849 7110 6.624352 ATGTTTTGATAATCACTCCATCGG 57.376 37.500 0.00 0.00 0.00 4.18
1853 7114 8.748412 CCCTTAAATGTTTTGATAATCACTCCA 58.252 33.333 0.00 0.00 0.00 3.86
1854 7115 7.706607 GCCCTTAAATGTTTTGATAATCACTCC 59.293 37.037 0.00 0.00 0.00 3.85
1860 7121 7.334171 GCAAGTGCCCTTAAATGTTTTGATAAT 59.666 33.333 0.00 0.00 34.31 1.28
1875 7136 2.203337 TCGCTTGCAAGTGCCCTT 60.203 55.556 30.73 0.00 41.18 3.95
1877 7138 4.043200 GGTCGCTTGCAAGTGCCC 62.043 66.667 30.73 26.98 41.18 5.36
1926 7187 5.253330 TCTCAGGGTTTCATTCGCTTTATT 58.747 37.500 0.00 0.00 0.00 1.40
1928 7189 4.020573 TCTCTCAGGGTTTCATTCGCTTTA 60.021 41.667 0.00 0.00 0.00 1.85
1932 7193 2.386661 TCTCTCAGGGTTTCATTCGC 57.613 50.000 0.00 0.00 0.00 4.70
1943 7204 4.052159 ACGCTGAATGTAATCTCTCAGG 57.948 45.455 0.00 0.00 36.60 3.86
2028 7289 2.660802 CCTGTACCGGACGCCTTT 59.339 61.111 9.46 0.00 0.00 3.11
2087 7348 3.718434 TGGCTATCTCCATCATCAGGTTT 59.282 43.478 0.00 0.00 0.00 3.27
2092 7353 2.560105 CGAGTGGCTATCTCCATCATCA 59.440 50.000 0.00 0.00 38.57 3.07
2147 7408 5.601662 TCTGTAGTCTTTCCTTTGACACTG 58.398 41.667 0.00 0.00 35.81 3.66
2152 7413 5.780282 TCAGGATCTGTAGTCTTTCCTTTGA 59.220 40.000 0.00 0.00 34.59 2.69
2163 7424 2.509166 TCGGTGTCAGGATCTGTAGT 57.491 50.000 0.00 0.00 32.61 2.73
2292 7558 6.555360 TGATCTATCTTCTTCTTAGGAACCCC 59.445 42.308 0.00 0.00 0.00 4.95
2323 7589 3.306780 CGGTAAGTCCAAGACATCCTGTT 60.307 47.826 0.00 0.00 34.60 3.16
2324 7590 2.233922 CGGTAAGTCCAAGACATCCTGT 59.766 50.000 0.00 0.00 34.60 4.00
2387 7653 3.930848 GTCGAGTGGTATGTTTGGGTAAG 59.069 47.826 0.00 0.00 0.00 2.34
2495 7761 1.318576 CATTGGCCTTCGGGTAATCC 58.681 55.000 3.32 0.00 37.45 3.01
2509 7775 1.843368 AATCACCAGAGTGGCATTGG 58.157 50.000 12.36 12.36 42.67 3.16


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

AutoCloner maintained by Alex Coulton.