Multiple sequence alignment - TraesCS1B01G072800

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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 TraesCS1B01G072800 chr1B 100.000 2563 0 0 1 2563 57111917 57109355 0.000000e+00 4734
1 TraesCS1B01G072800 chr1B 81.461 534 87 11 1690 2220 22517690 22517166 6.550000e-116 427
2 TraesCS1B01G072800 chr1B 81.273 534 88 11 1690 2220 22397745 22397221 3.050000e-114 422
3 TraesCS1B01G072800 chr1B 80.899 534 90 11 1690 2220 22457758 22457234 6.600000e-111 411
4 TraesCS1B01G072800 chr7B 96.482 796 27 1 798 1592 407386988 407387783 0.000000e+00 1314
5 TraesCS1B01G072800 chr5B 95.975 795 31 1 798 1591 642595502 642594708 0.000000e+00 1290
6 TraesCS1B01G072800 chr5B 94.364 763 39 3 840 1599 451532131 451531370 0.000000e+00 1168
7 TraesCS1B01G072800 chr5B 83.852 836 112 12 1693 2522 137108615 137107797 0.000000e+00 774
8 TraesCS1B01G072800 chr6B 95.739 798 27 5 1 798 706818037 706818827 0.000000e+00 1279
9 TraesCS1B01G072800 chr6B 94.856 797 35 4 1 797 706811156 706811946 0.000000e+00 1240
10 TraesCS1B01G072800 chr6B 94.486 798 37 5 1 798 427522761 427523551 0.000000e+00 1223
11 TraesCS1B01G072800 chr4B 94.875 800 33 6 1 799 646821140 646820348 0.000000e+00 1243
12 TraesCS1B01G072800 chr4B 94.605 797 37 4 1 797 48842875 48842085 0.000000e+00 1229
13 TraesCS1B01G072800 chr4B 94.486 798 37 5 1 797 646828002 646827211 0.000000e+00 1223
14 TraesCS1B01G072800 chr5D 94.424 807 40 4 798 1599 378151172 378151978 0.000000e+00 1236
15 TraesCS1B01G072800 chr5D 83.610 842 105 18 1689 2520 458483598 458484416 0.000000e+00 760
16 TraesCS1B01G072800 chr5D 82.402 841 114 17 1690 2522 549788769 549789583 0.000000e+00 702
17 TraesCS1B01G072800 chr3B 94.862 798 30 9 1 797 802945907 802945120 0.000000e+00 1236
18 TraesCS1B01G072800 chr3B 83.208 530 75 12 1690 2214 309404172 309404692 8.300000e-130 473
19 TraesCS1B01G072800 chr2B 94.479 797 39 3 1 797 80165463 80166254 0.000000e+00 1223
20 TraesCS1B01G072800 chr2B 94.214 795 43 3 798 1591 310898298 310899090 0.000000e+00 1210
21 TraesCS1B01G072800 chr3A 94.361 798 39 5 1 797 694131183 694130391 0.000000e+00 1219
22 TraesCS1B01G072800 chr2A 94.221 796 42 4 798 1591 550182323 550183116 0.000000e+00 1212
23 TraesCS1B01G072800 chr2A 93.711 795 48 2 798 1591 348050478 348051271 0.000000e+00 1190
24 TraesCS1B01G072800 chr1D 93.836 795 45 4 798 1591 142663428 142664219 0.000000e+00 1194
25 TraesCS1B01G072800 chr6A 92.839 796 53 4 798 1592 155746817 155746025 0.000000e+00 1151
26 TraesCS1B01G072800 chr5A 83.656 826 111 12 1702 2522 651530752 651529946 0.000000e+00 756
27 TraesCS1B01G072800 chr5A 82.959 845 115 13 1690 2522 680523554 680522727 0.000000e+00 736


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 TraesCS1B01G072800 chr1B 57109355 57111917 2562 True 4734 4734 100.000 1 2563 1 chr1B.!!$R4 2562
1 TraesCS1B01G072800 chr1B 22517166 22517690 524 True 427 427 81.461 1690 2220 1 chr1B.!!$R3 530
2 TraesCS1B01G072800 chr1B 22397221 22397745 524 True 422 422 81.273 1690 2220 1 chr1B.!!$R1 530
3 TraesCS1B01G072800 chr1B 22457234 22457758 524 True 411 411 80.899 1690 2220 1 chr1B.!!$R2 530
4 TraesCS1B01G072800 chr7B 407386988 407387783 795 False 1314 1314 96.482 798 1592 1 chr7B.!!$F1 794
5 TraesCS1B01G072800 chr5B 642594708 642595502 794 True 1290 1290 95.975 798 1591 1 chr5B.!!$R3 793
6 TraesCS1B01G072800 chr5B 451531370 451532131 761 True 1168 1168 94.364 840 1599 1 chr5B.!!$R2 759
7 TraesCS1B01G072800 chr5B 137107797 137108615 818 True 774 774 83.852 1693 2522 1 chr5B.!!$R1 829
8 TraesCS1B01G072800 chr6B 706818037 706818827 790 False 1279 1279 95.739 1 798 1 chr6B.!!$F3 797
9 TraesCS1B01G072800 chr6B 706811156 706811946 790 False 1240 1240 94.856 1 797 1 chr6B.!!$F2 796
10 TraesCS1B01G072800 chr6B 427522761 427523551 790 False 1223 1223 94.486 1 798 1 chr6B.!!$F1 797
11 TraesCS1B01G072800 chr4B 646820348 646821140 792 True 1243 1243 94.875 1 799 1 chr4B.!!$R2 798
12 TraesCS1B01G072800 chr4B 48842085 48842875 790 True 1229 1229 94.605 1 797 1 chr4B.!!$R1 796
13 TraesCS1B01G072800 chr4B 646827211 646828002 791 True 1223 1223 94.486 1 797 1 chr4B.!!$R3 796
14 TraesCS1B01G072800 chr5D 378151172 378151978 806 False 1236 1236 94.424 798 1599 1 chr5D.!!$F1 801
15 TraesCS1B01G072800 chr5D 458483598 458484416 818 False 760 760 83.610 1689 2520 1 chr5D.!!$F2 831
16 TraesCS1B01G072800 chr5D 549788769 549789583 814 False 702 702 82.402 1690 2522 1 chr5D.!!$F3 832
17 TraesCS1B01G072800 chr3B 802945120 802945907 787 True 1236 1236 94.862 1 797 1 chr3B.!!$R1 796
18 TraesCS1B01G072800 chr3B 309404172 309404692 520 False 473 473 83.208 1690 2214 1 chr3B.!!$F1 524
19 TraesCS1B01G072800 chr2B 80165463 80166254 791 False 1223 1223 94.479 1 797 1 chr2B.!!$F1 796
20 TraesCS1B01G072800 chr2B 310898298 310899090 792 False 1210 1210 94.214 798 1591 1 chr2B.!!$F2 793
21 TraesCS1B01G072800 chr3A 694130391 694131183 792 True 1219 1219 94.361 1 797 1 chr3A.!!$R1 796
22 TraesCS1B01G072800 chr2A 550182323 550183116 793 False 1212 1212 94.221 798 1591 1 chr2A.!!$F2 793
23 TraesCS1B01G072800 chr2A 348050478 348051271 793 False 1190 1190 93.711 798 1591 1 chr2A.!!$F1 793
24 TraesCS1B01G072800 chr1D 142663428 142664219 791 False 1194 1194 93.836 798 1591 1 chr1D.!!$F1 793
25 TraesCS1B01G072800 chr6A 155746025 155746817 792 True 1151 1151 92.839 798 1592 1 chr6A.!!$R1 794
26 TraesCS1B01G072800 chr5A 651529946 651530752 806 True 756 756 83.656 1702 2522 1 chr5A.!!$R1 820
27 TraesCS1B01G072800 chr5A 680522727 680523554 827 True 736 736 82.959 1690 2522 1 chr5A.!!$R2 832

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
293 294 0.042131 TGAATCCTACTCCCGGTGGT 59.958 55.0 0.0 0.62 0.0 4.16 F
634 637 0.108520 TAACGGTGCTTGGATCGGTC 60.109 55.0 0.0 0.00 0.0 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1102 1108 0.040425 AACGCGGCTTCAACATTCAC 60.040 50.0 12.47 0.0 0.0 3.18 R
2440 2481 0.398696 TGGCAAGTACGACATGGGTT 59.601 50.0 0.00 0.0 0.0 4.11 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
75 76 1.402787 GGGAGTTACGGGAATACGGA 58.597 55.000 0.00 0.00 38.39 4.69
213 214 3.054728 CCTCCTTCCTTCCCTTCTCTTTC 60.055 52.174 0.00 0.00 0.00 2.62
293 294 0.042131 TGAATCCTACTCCCGGTGGT 59.958 55.000 0.00 0.62 0.00 4.16
308 310 2.092212 CGGTGGTAGTAGGACTCCCTAA 60.092 54.545 0.00 0.00 46.06 2.69
309 311 3.625716 CGGTGGTAGTAGGACTCCCTAAA 60.626 52.174 0.00 0.00 46.06 1.85
327 329 3.606662 GGGCGCGCCATAGAGAGA 61.607 66.667 46.88 0.00 37.98 3.10
388 390 2.361610 GGCACCCCATGGACACAG 60.362 66.667 15.22 0.00 34.81 3.66
515 518 3.244044 TGAACATCAAGATCGTCACCACA 60.244 43.478 0.00 0.00 0.00 4.17
604 607 0.874607 ACGTGTGTCAAGAACTCGGC 60.875 55.000 0.00 0.00 38.48 5.54
634 637 0.108520 TAACGGTGCTTGGATCGGTC 60.109 55.000 0.00 0.00 0.00 4.79
638 641 1.144057 GTGCTTGGATCGGTCGGAT 59.856 57.895 0.00 0.00 38.35 4.18
658 661 2.403259 TCGTGAAGACGTACGACTACA 58.597 47.619 24.41 13.28 46.20 2.74
661 664 3.181527 CGTGAAGACGTACGACTACATCA 60.182 47.826 24.41 18.00 42.54 3.07
662 665 4.667415 CGTGAAGACGTACGACTACATCAA 60.667 45.833 24.41 4.49 42.54 2.57
665 668 2.094894 AGACGTACGACTACATCAACCG 59.905 50.000 24.41 0.00 0.00 4.44
672 675 1.389106 GACTACATCAACCGCGTTGTC 59.611 52.381 16.97 5.64 43.23 3.18
673 676 1.269883 ACTACATCAACCGCGTTGTCA 60.270 47.619 16.97 4.13 43.23 3.58
674 677 1.999735 CTACATCAACCGCGTTGTCAT 59.000 47.619 16.97 5.85 43.23 3.06
688 691 2.658373 TGTCATAACGCTTCCGCTTA 57.342 45.000 0.00 0.00 38.22 3.09
689 692 2.962125 TGTCATAACGCTTCCGCTTAA 58.038 42.857 0.00 0.00 38.22 1.85
900 905 7.732222 AGAATTAAACATTAAGGGCATCCAA 57.268 32.000 0.00 0.00 34.83 3.53
971 976 1.691976 ACGTCAACTGGTCCATGAAGA 59.308 47.619 13.39 0.00 0.00 2.87
1026 1032 3.387397 GGCTCGTGCTATAACGGTAAAT 58.613 45.455 9.61 0.00 43.73 1.40
1043 1049 8.896320 ACGGTAAATTATGTCAATGCATACTA 57.104 30.769 0.00 0.00 31.77 1.82
1050 1056 9.860650 AATTATGTCAATGCATACTACCCTAAA 57.139 29.630 0.00 0.00 31.77 1.85
1102 1108 2.173569 CCTCCTAGGGGATTTGTGAAGG 59.826 54.545 11.40 0.20 41.36 3.46
1113 1119 5.221422 GGGATTTGTGAAGGTGAATGTTGAA 60.221 40.000 0.00 0.00 0.00 2.69
1155 1161 4.980702 CAAGGTGCAGCTGGGGCA 62.981 66.667 20.97 4.15 41.70 5.36
1375 1382 1.285641 GCCGCAGCTGCAGTTTTTA 59.714 52.632 36.03 0.00 42.21 1.52
1617 1628 9.665264 CTAGTGTTAACAAAATCTCAAGTTTCC 57.335 33.333 10.51 0.00 0.00 3.13
1618 1629 8.293699 AGTGTTAACAAAATCTCAAGTTTCCT 57.706 30.769 10.51 0.00 0.00 3.36
1619 1630 8.406297 AGTGTTAACAAAATCTCAAGTTTCCTC 58.594 33.333 10.51 0.00 0.00 3.71
1620 1631 8.188139 GTGTTAACAAAATCTCAAGTTTCCTCA 58.812 33.333 10.51 0.00 0.00 3.86
1621 1632 8.912988 TGTTAACAAAATCTCAAGTTTCCTCAT 58.087 29.630 5.64 0.00 0.00 2.90
1622 1633 9.399403 GTTAACAAAATCTCAAGTTTCCTCATC 57.601 33.333 0.00 0.00 0.00 2.92
1623 1634 7.830099 AACAAAATCTCAAGTTTCCTCATCT 57.170 32.000 0.00 0.00 0.00 2.90
1624 1635 8.924511 AACAAAATCTCAAGTTTCCTCATCTA 57.075 30.769 0.00 0.00 0.00 1.98
1625 1636 8.924511 ACAAAATCTCAAGTTTCCTCATCTAA 57.075 30.769 0.00 0.00 0.00 2.10
1626 1637 9.354673 ACAAAATCTCAAGTTTCCTCATCTAAA 57.645 29.630 0.00 0.00 0.00 1.85
1627 1638 9.617975 CAAAATCTCAAGTTTCCTCATCTAAAC 57.382 33.333 0.00 0.00 36.13 2.01
1628 1639 7.602517 AATCTCAAGTTTCCTCATCTAAACG 57.397 36.000 0.00 0.00 39.90 3.60
1629 1640 6.097915 TCTCAAGTTTCCTCATCTAAACGT 57.902 37.500 0.00 0.00 39.90 3.99
1630 1641 5.926542 TCTCAAGTTTCCTCATCTAAACGTG 59.073 40.000 0.00 0.00 42.59 4.49
1631 1642 5.849510 TCAAGTTTCCTCATCTAAACGTGA 58.150 37.500 10.91 10.91 45.37 4.35
1632 1643 5.694910 TCAAGTTTCCTCATCTAAACGTGAC 59.305 40.000 10.91 0.00 43.91 3.67
1633 1644 5.209818 AGTTTCCTCATCTAAACGTGACA 57.790 39.130 0.00 0.00 39.90 3.58
1634 1645 5.794894 AGTTTCCTCATCTAAACGTGACAT 58.205 37.500 0.00 0.00 39.90 3.06
1635 1646 6.931838 AGTTTCCTCATCTAAACGTGACATA 58.068 36.000 0.00 0.00 39.90 2.29
1636 1647 7.556844 AGTTTCCTCATCTAAACGTGACATAT 58.443 34.615 0.00 0.00 39.90 1.78
1637 1648 7.707035 AGTTTCCTCATCTAAACGTGACATATC 59.293 37.037 0.00 0.00 39.90 1.63
1638 1649 6.961360 TCCTCATCTAAACGTGACATATCT 57.039 37.500 0.00 0.00 0.00 1.98
1639 1650 7.348080 TCCTCATCTAAACGTGACATATCTT 57.652 36.000 0.00 0.00 0.00 2.40
1640 1651 8.459911 TCCTCATCTAAACGTGACATATCTTA 57.540 34.615 0.00 0.00 0.00 2.10
1641 1652 9.078990 TCCTCATCTAAACGTGACATATCTTAT 57.921 33.333 0.00 0.00 0.00 1.73
1642 1653 9.347934 CCTCATCTAAACGTGACATATCTTATC 57.652 37.037 0.00 0.00 0.00 1.75
1645 1656 9.899226 CATCTAAACGTGACATATCTTATCTCA 57.101 33.333 0.00 0.00 0.00 3.27
1674 1685 8.421249 AAAAACCTGACATATCTTTGATGGAA 57.579 30.769 0.00 0.00 0.00 3.53
1675 1686 8.599624 AAAACCTGACATATCTTTGATGGAAT 57.400 30.769 0.00 0.00 0.00 3.01
1676 1687 7.578310 AACCTGACATATCTTTGATGGAATG 57.422 36.000 0.00 0.00 0.00 2.67
1677 1688 6.066690 ACCTGACATATCTTTGATGGAATGG 58.933 40.000 0.00 0.00 0.00 3.16
1678 1689 5.475909 CCTGACATATCTTTGATGGAATGGG 59.524 44.000 0.00 0.00 0.00 4.00
1679 1690 6.017211 TGACATATCTTTGATGGAATGGGT 57.983 37.500 0.00 0.00 0.00 4.51
1680 1691 5.829391 TGACATATCTTTGATGGAATGGGTG 59.171 40.000 0.00 0.00 0.00 4.61
1681 1692 5.142639 ACATATCTTTGATGGAATGGGTGG 58.857 41.667 0.00 0.00 0.00 4.61
1682 1693 3.763557 ATCTTTGATGGAATGGGTGGT 57.236 42.857 0.00 0.00 0.00 4.16
1683 1694 2.806434 TCTTTGATGGAATGGGTGGTG 58.194 47.619 0.00 0.00 0.00 4.17
1684 1695 1.826720 CTTTGATGGAATGGGTGGTGG 59.173 52.381 0.00 0.00 0.00 4.61
1685 1696 0.783206 TTGATGGAATGGGTGGTGGT 59.217 50.000 0.00 0.00 0.00 4.16
1686 1697 0.783206 TGATGGAATGGGTGGTGGTT 59.217 50.000 0.00 0.00 0.00 3.67
1687 1698 1.185315 GATGGAATGGGTGGTGGTTG 58.815 55.000 0.00 0.00 0.00 3.77
1688 1699 0.783206 ATGGAATGGGTGGTGGTTGA 59.217 50.000 0.00 0.00 0.00 3.18
1699 1711 3.181485 GGTGGTGGTTGATTTTCGACAAA 60.181 43.478 0.00 0.00 32.35 2.83
1755 1771 1.564622 CGACCTCTGCAACAACACG 59.435 57.895 0.00 0.00 0.00 4.49
1758 1774 0.107897 ACCTCTGCAACAACACGACA 60.108 50.000 0.00 0.00 0.00 4.35
1771 1787 1.733041 ACGACACCGCGATCAACTG 60.733 57.895 8.23 0.00 39.95 3.16
1839 1868 9.971922 AGAACAAAAGAGAAAAACCAAGATATG 57.028 29.630 0.00 0.00 0.00 1.78
1854 1883 5.178061 CAAGATATGAGGCACACAGTAACA 58.822 41.667 0.00 0.00 29.06 2.41
1857 1886 6.418101 AGATATGAGGCACACAGTAACAAAT 58.582 36.000 0.00 0.00 29.06 2.32
1883 1912 2.066262 CATCAACCACTACCGTGACAC 58.934 52.381 0.00 0.00 43.97 3.67
1892 1921 1.750341 TACCGTGACACCACACAGGG 61.750 60.000 0.00 0.00 43.34 4.45
1907 1938 0.035458 CAGGGTGCGAGAAGGTTCTT 59.965 55.000 0.00 0.00 37.73 2.52
1914 1945 2.878406 TGCGAGAAGGTTCTTCAAAAGG 59.122 45.455 9.87 0.00 37.73 3.11
1942 1973 6.539649 TCTTCAGGAAGATAAAAACACACG 57.460 37.500 7.62 0.00 42.06 4.49
2025 2061 4.192429 ACTGGGCAAAATTCTATGCAAC 57.808 40.909 11.47 5.82 44.32 4.17
2033 2069 1.959042 ATTCTATGCAACGCCCTCAG 58.041 50.000 0.00 0.00 0.00 3.35
2117 2158 3.662759 TTTCACCCTGAAACTCCAGTT 57.337 42.857 0.00 0.00 41.02 3.16
2120 2161 3.583228 TCACCCTGAAACTCCAGTTCTA 58.417 45.455 0.00 0.00 37.25 2.10
2184 2225 2.752807 AACCGCTTGACCACCACCT 61.753 57.895 0.00 0.00 0.00 4.00
2195 2236 2.558359 GACCACCACCTTTCATTCCTTG 59.442 50.000 0.00 0.00 0.00 3.61
2210 2251 6.484288 TCATTCCTTGTATCCTTGACAATGT 58.516 36.000 0.00 0.00 36.27 2.71
2226 2267 3.352524 GTCGACCAGACCACTCGT 58.647 61.111 3.51 0.00 43.95 4.18
2227 2268 1.658673 GTCGACCAGACCACTCGTT 59.341 57.895 3.51 0.00 43.95 3.85
2289 2330 4.775236 ACATCTCAGAATGTCTTTAGCCC 58.225 43.478 0.00 0.00 34.84 5.19
2293 2334 4.020573 TCTCAGAATGTCTTTAGCCCGAAA 60.021 41.667 0.00 0.00 37.40 3.46
2319 2360 3.561313 GGGCTTTCCAACCTCTATTCACA 60.561 47.826 0.00 0.00 35.00 3.58
2321 2362 4.072131 GCTTTCCAACCTCTATTCACACA 58.928 43.478 0.00 0.00 0.00 3.72
2332 2373 7.624549 ACCTCTATTCACACACATAGTTGATT 58.375 34.615 0.00 0.00 0.00 2.57
2346 2387 4.555348 AGTTGATTAACGCGACCAAAAA 57.445 36.364 15.93 0.00 41.71 1.94
2355 2396 0.380378 GCGACCAAAAACTGTGCTCA 59.620 50.000 0.00 0.00 0.00 4.26
2356 2397 1.001378 GCGACCAAAAACTGTGCTCAT 60.001 47.619 0.00 0.00 0.00 2.90
2357 2398 2.225491 GCGACCAAAAACTGTGCTCATA 59.775 45.455 0.00 0.00 0.00 2.15
2358 2399 3.810373 CGACCAAAAACTGTGCTCATAC 58.190 45.455 0.00 0.00 0.00 2.39
2359 2400 3.498397 CGACCAAAAACTGTGCTCATACT 59.502 43.478 0.00 0.00 0.00 2.12
2360 2401 4.611355 CGACCAAAAACTGTGCTCATACTG 60.611 45.833 0.00 0.00 0.00 2.74
2361 2402 4.207165 ACCAAAAACTGTGCTCATACTGT 58.793 39.130 0.00 0.00 34.72 3.55
2362 2403 4.036734 ACCAAAAACTGTGCTCATACTGTG 59.963 41.667 0.00 0.00 33.74 3.66
2363 2404 3.904136 AAAACTGTGCTCATACTGTGC 57.096 42.857 0.00 0.00 37.38 4.57
2364 2405 2.847327 AACTGTGCTCATACTGTGCT 57.153 45.000 3.27 0.00 37.71 4.40
2365 2406 2.376808 ACTGTGCTCATACTGTGCTC 57.623 50.000 3.27 0.70 37.71 4.26
2440 2481 3.983420 CAAGGGCCCCTCCAGCAA 61.983 66.667 21.43 0.00 36.21 3.91
2448 2489 1.077265 CCCTCCAGCAAACCCATGT 59.923 57.895 0.00 0.00 0.00 3.21
2452 2493 0.687920 TCCAGCAAACCCATGTCGTA 59.312 50.000 0.00 0.00 0.00 3.43
2469 2510 2.093500 TCGTACTTGCCATCAGCTGATT 60.093 45.455 26.70 13.59 44.23 2.57
2471 2512 4.060900 CGTACTTGCCATCAGCTGATTAT 58.939 43.478 26.70 4.20 44.23 1.28
2484 2527 6.189859 TCAGCTGATTATGAACTTGGGAAAT 58.810 36.000 13.74 0.00 0.00 2.17
2511 2554 3.018856 CCCATCAATTGTCTAGCTGCAA 58.981 45.455 5.13 0.00 0.00 4.08
2534 2577 3.134127 GCCACCGCCTTGGATGAC 61.134 66.667 2.29 0.00 42.00 3.06
2535 2578 2.350895 CCACCGCCTTGGATGACA 59.649 61.111 0.00 0.00 42.00 3.58
2536 2579 1.077501 CCACCGCCTTGGATGACAT 60.078 57.895 0.00 0.00 42.00 3.06
2537 2580 1.097547 CCACCGCCTTGGATGACATC 61.098 60.000 6.91 6.91 42.00 3.06
2538 2581 0.107508 CACCGCCTTGGATGACATCT 60.108 55.000 14.95 0.00 42.00 2.90
2539 2582 0.620556 ACCGCCTTGGATGACATCTT 59.379 50.000 14.95 0.00 42.00 2.40
2540 2583 1.303309 CCGCCTTGGATGACATCTTC 58.697 55.000 14.95 0.35 42.00 2.87
2541 2584 0.933097 CGCCTTGGATGACATCTTCG 59.067 55.000 14.95 7.83 0.00 3.79
2542 2585 1.740380 CGCCTTGGATGACATCTTCGT 60.740 52.381 14.95 0.00 0.00 3.85
2543 2586 1.936547 GCCTTGGATGACATCTTCGTC 59.063 52.381 14.95 0.00 39.31 4.20
2544 2587 2.419297 GCCTTGGATGACATCTTCGTCT 60.419 50.000 14.95 0.00 39.87 4.18
2545 2588 3.866651 CCTTGGATGACATCTTCGTCTT 58.133 45.455 14.95 0.00 39.87 3.01
2546 2589 3.868077 CCTTGGATGACATCTTCGTCTTC 59.132 47.826 14.95 0.00 39.87 2.87
2547 2590 4.498241 CTTGGATGACATCTTCGTCTTCA 58.502 43.478 14.95 0.00 40.22 3.02
2548 2591 4.535526 TGGATGACATCTTCGTCTTCAA 57.464 40.909 14.95 0.00 40.22 2.69
2549 2592 5.089970 TGGATGACATCTTCGTCTTCAAT 57.910 39.130 14.95 0.00 40.22 2.57
2550 2593 5.491070 TGGATGACATCTTCGTCTTCAATT 58.509 37.500 14.95 0.00 40.22 2.32
2551 2594 5.582269 TGGATGACATCTTCGTCTTCAATTC 59.418 40.000 14.95 0.00 40.22 2.17
2552 2595 5.276584 GGATGACATCTTCGTCTTCAATTCG 60.277 44.000 14.95 0.00 40.22 3.34
2553 2596 4.556233 TGACATCTTCGTCTTCAATTCGT 58.444 39.130 0.00 0.00 36.82 3.85
2554 2597 4.988540 TGACATCTTCGTCTTCAATTCGTT 59.011 37.500 0.00 0.00 36.82 3.85
2555 2598 6.153756 TGACATCTTCGTCTTCAATTCGTTA 58.846 36.000 0.00 0.00 36.82 3.18
2556 2599 6.811665 TGACATCTTCGTCTTCAATTCGTTAT 59.188 34.615 0.00 0.00 36.82 1.89
2557 2600 7.009265 TGACATCTTCGTCTTCAATTCGTTATC 59.991 37.037 0.00 0.00 36.82 1.75
2558 2601 6.255887 ACATCTTCGTCTTCAATTCGTTATCC 59.744 38.462 0.00 0.00 0.00 2.59
2559 2602 5.716094 TCTTCGTCTTCAATTCGTTATCCA 58.284 37.500 0.00 0.00 0.00 3.41
2560 2603 5.575606 TCTTCGTCTTCAATTCGTTATCCAC 59.424 40.000 0.00 0.00 0.00 4.02
2561 2604 4.178540 TCGTCTTCAATTCGTTATCCACC 58.821 43.478 0.00 0.00 0.00 4.61
2562 2605 3.000078 CGTCTTCAATTCGTTATCCACCG 60.000 47.826 0.00 0.00 0.00 4.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
75 76 4.141158 CCAATAAGGCCCAATACTTCTCCT 60.141 45.833 0.00 0.00 0.00 3.69
213 214 1.205055 GTAGGAGACAAGGAAGGGGG 58.795 60.000 0.00 0.00 0.00 5.40
274 275 0.042131 ACCACCGGGAGTAGGATTCA 59.958 55.000 6.32 0.00 38.05 2.57
308 310 3.154473 TCTCTATGGCGCGCCCTT 61.154 61.111 44.42 33.41 34.56 3.95
309 311 3.610669 CTCTCTATGGCGCGCCCT 61.611 66.667 44.42 37.34 34.56 5.19
429 432 2.783510 AGGTGTAATATTGTGGAGGGGG 59.216 50.000 0.00 0.00 0.00 5.40
439 442 7.817962 GCTACAATATGACCGAGGTGTAATATT 59.182 37.037 0.00 4.41 0.00 1.28
532 535 1.746991 CAAAGCTTCGGGGAGGAGC 60.747 63.158 0.00 0.00 0.00 4.70
641 644 4.378770 GGTTGATGTAGTCGTACGTCTTCA 60.379 45.833 19.61 19.79 43.23 3.02
658 661 1.392168 CGTTATGACAACGCGGTTGAT 59.608 47.619 22.26 12.10 45.28 2.57
688 691 0.321653 ACGTACCCTCGTAGACCGTT 60.322 55.000 0.00 0.00 42.35 4.44
689 692 0.535335 TACGTACCCTCGTAGACCGT 59.465 55.000 0.00 0.00 43.80 4.83
942 947 2.431057 GACCAGTTGACGTCTATCCCAT 59.569 50.000 17.92 0.00 0.00 4.00
971 976 8.891671 AGTTTGATTTGCATCATGTAACTTTT 57.108 26.923 0.00 0.00 35.68 2.27
1026 1032 7.444183 GCTTTAGGGTAGTATGCATTGACATAA 59.556 37.037 3.54 2.07 34.41 1.90
1043 1049 1.975660 TTTGCGAGTTGCTTTAGGGT 58.024 45.000 3.50 0.00 46.63 4.34
1050 1056 1.455383 CCCCTGTTTTGCGAGTTGCT 61.455 55.000 3.50 0.00 46.63 3.91
1102 1108 0.040425 AACGCGGCTTCAACATTCAC 60.040 50.000 12.47 0.00 0.00 3.18
1113 1119 0.941463 GATCATGATCGAACGCGGCT 60.941 55.000 19.55 0.00 38.28 5.52
1155 1161 4.823364 TCCCTTATCATCTCTCAGGACT 57.177 45.455 0.00 0.00 0.00 3.85
1599 1610 7.830099 AGATGAGGAAACTTGAGATTTTGTT 57.170 32.000 0.00 0.00 44.43 2.83
1600 1611 8.924511 TTAGATGAGGAAACTTGAGATTTTGT 57.075 30.769 0.00 0.00 44.43 2.83
1601 1612 9.617975 GTTTAGATGAGGAAACTTGAGATTTTG 57.382 33.333 0.00 0.00 44.43 2.44
1602 1613 8.507249 CGTTTAGATGAGGAAACTTGAGATTTT 58.493 33.333 0.00 0.00 44.43 1.82
1603 1614 7.661847 ACGTTTAGATGAGGAAACTTGAGATTT 59.338 33.333 0.00 0.00 44.43 2.17
1604 1615 7.118390 CACGTTTAGATGAGGAAACTTGAGATT 59.882 37.037 0.00 0.00 44.43 2.40
1605 1616 6.591834 CACGTTTAGATGAGGAAACTTGAGAT 59.408 38.462 0.00 0.00 44.43 2.75
1606 1617 5.926542 CACGTTTAGATGAGGAAACTTGAGA 59.073 40.000 0.00 0.00 44.43 3.27
1607 1618 5.926542 TCACGTTTAGATGAGGAAACTTGAG 59.073 40.000 3.43 0.00 44.43 3.02
1608 1619 5.694910 GTCACGTTTAGATGAGGAAACTTGA 59.305 40.000 3.43 3.43 44.43 3.02
1609 1620 5.465390 TGTCACGTTTAGATGAGGAAACTTG 59.535 40.000 0.00 0.00 44.43 3.16
1610 1621 5.607477 TGTCACGTTTAGATGAGGAAACTT 58.393 37.500 0.00 0.00 44.43 2.66
1612 1623 7.707035 AGATATGTCACGTTTAGATGAGGAAAC 59.293 37.037 0.00 0.00 33.17 2.78
1613 1624 7.782049 AGATATGTCACGTTTAGATGAGGAAA 58.218 34.615 0.00 0.00 0.00 3.13
1614 1625 7.348080 AGATATGTCACGTTTAGATGAGGAA 57.652 36.000 0.00 0.00 0.00 3.36
1615 1626 6.961360 AGATATGTCACGTTTAGATGAGGA 57.039 37.500 0.00 0.00 0.00 3.71
1616 1627 9.347934 GATAAGATATGTCACGTTTAGATGAGG 57.652 37.037 0.00 0.00 0.00 3.86
1619 1630 9.899226 TGAGATAAGATATGTCACGTTTAGATG 57.101 33.333 0.00 0.00 0.00 2.90
1649 1660 8.421249 TTCCATCAAAGATATGTCAGGTTTTT 57.579 30.769 0.00 0.00 0.00 1.94
1650 1661 8.472413 CATTCCATCAAAGATATGTCAGGTTTT 58.528 33.333 0.00 0.00 0.00 2.43
1651 1662 7.069085 CCATTCCATCAAAGATATGTCAGGTTT 59.931 37.037 0.00 0.00 0.00 3.27
1652 1663 6.548622 CCATTCCATCAAAGATATGTCAGGTT 59.451 38.462 0.00 0.00 0.00 3.50
1653 1664 6.066690 CCATTCCATCAAAGATATGTCAGGT 58.933 40.000 0.00 0.00 0.00 4.00
1654 1665 5.475909 CCCATTCCATCAAAGATATGTCAGG 59.524 44.000 0.00 0.00 0.00 3.86
1655 1666 6.016527 CACCCATTCCATCAAAGATATGTCAG 60.017 42.308 0.00 0.00 0.00 3.51
1656 1667 5.829391 CACCCATTCCATCAAAGATATGTCA 59.171 40.000 0.00 0.00 0.00 3.58
1657 1668 5.242393 CCACCCATTCCATCAAAGATATGTC 59.758 44.000 0.00 0.00 0.00 3.06
1658 1669 5.142639 CCACCCATTCCATCAAAGATATGT 58.857 41.667 0.00 0.00 0.00 2.29
1659 1670 5.010314 CACCACCCATTCCATCAAAGATATG 59.990 44.000 0.00 0.00 0.00 1.78
1660 1671 5.142639 CACCACCCATTCCATCAAAGATAT 58.857 41.667 0.00 0.00 0.00 1.63
1661 1672 4.535781 CACCACCCATTCCATCAAAGATA 58.464 43.478 0.00 0.00 0.00 1.98
1662 1673 3.368248 CACCACCCATTCCATCAAAGAT 58.632 45.455 0.00 0.00 0.00 2.40
1663 1674 2.557229 CCACCACCCATTCCATCAAAGA 60.557 50.000 0.00 0.00 0.00 2.52
1664 1675 1.826720 CCACCACCCATTCCATCAAAG 59.173 52.381 0.00 0.00 0.00 2.77
1665 1676 1.148867 ACCACCACCCATTCCATCAAA 59.851 47.619 0.00 0.00 0.00 2.69
1666 1677 0.783206 ACCACCACCCATTCCATCAA 59.217 50.000 0.00 0.00 0.00 2.57
1667 1678 0.783206 AACCACCACCCATTCCATCA 59.217 50.000 0.00 0.00 0.00 3.07
1668 1679 1.185315 CAACCACCACCCATTCCATC 58.815 55.000 0.00 0.00 0.00 3.51
1669 1680 0.783206 TCAACCACCACCCATTCCAT 59.217 50.000 0.00 0.00 0.00 3.41
1670 1681 0.783206 ATCAACCACCACCCATTCCA 59.217 50.000 0.00 0.00 0.00 3.53
1671 1682 1.937191 AATCAACCACCACCCATTCC 58.063 50.000 0.00 0.00 0.00 3.01
1672 1683 3.613910 CGAAAATCAACCACCACCCATTC 60.614 47.826 0.00 0.00 0.00 2.67
1673 1684 2.298729 CGAAAATCAACCACCACCCATT 59.701 45.455 0.00 0.00 0.00 3.16
1674 1685 1.892474 CGAAAATCAACCACCACCCAT 59.108 47.619 0.00 0.00 0.00 4.00
1675 1686 1.133761 TCGAAAATCAACCACCACCCA 60.134 47.619 0.00 0.00 0.00 4.51
1676 1687 1.268625 GTCGAAAATCAACCACCACCC 59.731 52.381 0.00 0.00 0.00 4.61
1677 1688 1.950909 TGTCGAAAATCAACCACCACC 59.049 47.619 0.00 0.00 0.00 4.61
1678 1689 3.701532 TTGTCGAAAATCAACCACCAC 57.298 42.857 0.00 0.00 0.00 4.16
1679 1690 3.067461 CCTTTGTCGAAAATCAACCACCA 59.933 43.478 0.00 0.00 0.00 4.17
1680 1691 3.067601 ACCTTTGTCGAAAATCAACCACC 59.932 43.478 0.00 0.00 0.00 4.61
1681 1692 4.301637 ACCTTTGTCGAAAATCAACCAC 57.698 40.909 0.00 0.00 0.00 4.16
1682 1693 6.642707 ATTACCTTTGTCGAAAATCAACCA 57.357 33.333 0.00 0.00 0.00 3.67
1724 1739 1.482593 AGAGGTCGGGTGAACATGATC 59.517 52.381 0.00 0.00 32.76 2.92
1729 1745 1.691195 TTGCAGAGGTCGGGTGAACA 61.691 55.000 0.00 0.00 32.76 3.18
1732 1748 1.691195 TTGTTGCAGAGGTCGGGTGA 61.691 55.000 0.00 0.00 0.00 4.02
1755 1771 1.078759 CTCCAGTTGATCGCGGTGTC 61.079 60.000 6.13 2.96 0.00 3.67
1758 1774 2.579201 CCTCCAGTTGATCGCGGT 59.421 61.111 6.13 0.00 0.00 5.68
1817 1843 7.543520 GCCTCATATCTTGGTTTTTCTCTTTTG 59.456 37.037 0.00 0.00 0.00 2.44
1822 1851 5.415701 TGTGCCTCATATCTTGGTTTTTCTC 59.584 40.000 0.00 0.00 0.00 2.87
1837 1866 4.396166 GCTATTTGTTACTGTGTGCCTCAT 59.604 41.667 0.00 0.00 0.00 2.90
1839 1868 3.751175 TGCTATTTGTTACTGTGTGCCTC 59.249 43.478 0.00 0.00 0.00 4.70
1854 1883 4.394920 CGGTAGTGGTTGATGTTGCTATTT 59.605 41.667 0.00 0.00 0.00 1.40
1857 1886 2.300723 ACGGTAGTGGTTGATGTTGCTA 59.699 45.455 0.00 0.00 0.00 3.49
1883 1912 1.669115 CTTCTCGCACCCTGTGTGG 60.669 63.158 7.82 0.17 45.55 4.17
1892 1921 3.304057 CCTTTTGAAGAACCTTCTCGCAC 60.304 47.826 8.02 0.00 36.28 5.34
1907 1938 3.830744 TCCTGAAGACGTTCCTTTTGA 57.169 42.857 0.00 0.00 0.00 2.69
1942 1973 2.214181 ATCCGGCGACAGTGACACTC 62.214 60.000 9.30 0.00 0.00 3.51
2002 2033 4.888326 TGCATAGAATTTTGCCCAGTTT 57.112 36.364 6.53 0.00 38.08 2.66
2033 2069 4.217754 TGTTTCAACATCGTTACCTTGC 57.782 40.909 0.00 0.00 33.17 4.01
2058 2094 1.134946 GTTGGTCATACCTGGCAATGC 59.865 52.381 0.00 0.00 39.58 3.56
2117 2158 5.020795 TGGTGGTGCTAATTCAGTACTAGA 58.979 41.667 0.00 0.00 39.62 2.43
2120 2161 4.634012 TTGGTGGTGCTAATTCAGTACT 57.366 40.909 0.00 0.00 39.62 2.73
2184 2225 7.451255 ACATTGTCAAGGATACAAGGAATGAAA 59.549 33.333 3.86 0.00 40.17 2.69
2195 2236 3.857052 TGGTCGACATTGTCAAGGATAC 58.143 45.455 18.91 4.72 32.09 2.24
2210 2251 1.267806 GTTAACGAGTGGTCTGGTCGA 59.732 52.381 0.00 0.00 37.16 4.20
2310 2351 9.083080 CGTTAATCAACTATGTGTGTGAATAGA 57.917 33.333 0.00 0.00 31.93 1.98
2314 2355 5.388994 CGCGTTAATCAACTATGTGTGTGAA 60.389 40.000 0.00 0.00 32.09 3.18
2319 2360 3.615496 GGTCGCGTTAATCAACTATGTGT 59.385 43.478 5.77 0.00 32.09 3.72
2321 2362 3.852286 TGGTCGCGTTAATCAACTATGT 58.148 40.909 5.77 0.00 32.09 2.29
2332 2373 1.268133 GCACAGTTTTTGGTCGCGTTA 60.268 47.619 5.77 0.00 0.00 3.18
2363 2404 2.868583 CCCGACAACAAGCTCATATGAG 59.131 50.000 25.64 25.64 44.75 2.90
2364 2405 2.905075 CCCGACAACAAGCTCATATGA 58.095 47.619 5.07 5.07 0.00 2.15
2365 2406 1.331756 GCCCGACAACAAGCTCATATG 59.668 52.381 0.00 0.00 0.00 1.78
2409 2450 1.549203 CCCTTGACATGGGTTTCAGG 58.451 55.000 16.71 0.00 39.82 3.86
2440 2481 0.398696 TGGCAAGTACGACATGGGTT 59.601 50.000 0.00 0.00 0.00 4.11
2448 2489 0.894835 TCAGCTGATGGCAAGTACGA 59.105 50.000 13.74 0.00 44.79 3.43
2452 2493 4.160642 TCATAATCAGCTGATGGCAAGT 57.839 40.909 29.34 15.09 44.79 3.16
2484 2527 5.591472 CAGCTAGACAATTGATGGGATTCAA 59.409 40.000 13.59 0.00 39.77 2.69
2493 2536 2.679837 CGGTTGCAGCTAGACAATTGAT 59.320 45.455 13.59 2.70 0.00 2.57
2497 2540 1.442769 CACGGTTGCAGCTAGACAAT 58.557 50.000 0.00 0.00 0.00 2.71
2503 2546 3.947459 TGGCCACGGTTGCAGCTA 61.947 61.111 0.00 0.00 0.00 3.32
2522 2565 0.933097 CGAAGATGTCATCCAAGGCG 59.067 55.000 9.29 3.17 0.00 5.52
2523 2566 1.936547 GACGAAGATGTCATCCAAGGC 59.063 52.381 9.29 0.00 38.75 4.35
2524 2567 3.533606 AGACGAAGATGTCATCCAAGG 57.466 47.619 9.29 0.00 41.41 3.61
2525 2568 4.498241 TGAAGACGAAGATGTCATCCAAG 58.502 43.478 9.29 3.70 41.41 3.61
2526 2569 4.535526 TGAAGACGAAGATGTCATCCAA 57.464 40.909 9.29 0.00 41.41 3.53
2527 2570 4.535526 TTGAAGACGAAGATGTCATCCA 57.464 40.909 9.29 0.00 41.41 3.41
2528 2571 5.276584 CGAATTGAAGACGAAGATGTCATCC 60.277 44.000 9.29 0.00 41.41 3.51
2529 2572 5.289675 ACGAATTGAAGACGAAGATGTCATC 59.710 40.000 4.52 4.52 41.41 2.92
2530 2573 5.171476 ACGAATTGAAGACGAAGATGTCAT 58.829 37.500 0.00 0.00 41.41 3.06
2531 2574 4.556233 ACGAATTGAAGACGAAGATGTCA 58.444 39.130 0.00 0.00 41.41 3.58
2532 2575 5.517037 AACGAATTGAAGACGAAGATGTC 57.483 39.130 0.00 0.00 39.21 3.06
2533 2576 6.255887 GGATAACGAATTGAAGACGAAGATGT 59.744 38.462 0.00 0.00 0.00 3.06
2534 2577 6.255670 TGGATAACGAATTGAAGACGAAGATG 59.744 38.462 0.00 0.00 0.00 2.90
2535 2578 6.255887 GTGGATAACGAATTGAAGACGAAGAT 59.744 38.462 0.00 0.00 0.00 2.40
2536 2579 5.575606 GTGGATAACGAATTGAAGACGAAGA 59.424 40.000 0.00 0.00 0.00 2.87
2537 2580 5.220416 GGTGGATAACGAATTGAAGACGAAG 60.220 44.000 0.00 0.00 0.00 3.79
2538 2581 4.628333 GGTGGATAACGAATTGAAGACGAA 59.372 41.667 0.00 0.00 0.00 3.85
2539 2582 4.178540 GGTGGATAACGAATTGAAGACGA 58.821 43.478 0.00 0.00 0.00 4.20
2540 2583 3.000078 CGGTGGATAACGAATTGAAGACG 60.000 47.826 0.00 0.00 0.00 4.18
2541 2584 4.516092 CGGTGGATAACGAATTGAAGAC 57.484 45.455 0.00 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.