Multiple sequence alignment - TraesCS7D01G310400

Loading Multiple Alignment...

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 TraesCS7D01G310400 chr7D 100.000 3360 0 0 1 3360 393619100 393615741 0.000000e+00 6205.0
1 TraesCS7D01G310400 chr7D 94.305 755 36 3 6 759 614261585 614260837 0.000000e+00 1149.0
2 TraesCS7D01G310400 chr7D 100.000 38 0 0 2044 2081 393617018 393616981 1.670000e-08 71.3
3 TraesCS7D01G310400 chr7D 100.000 38 0 0 2083 2120 393617057 393617020 1.670000e-08 71.3
4 TraesCS7D01G310400 chr7D 87.273 55 5 2 2708 2760 121937401 121937347 1.010000e-05 62.1
5 TraesCS7D01G310400 chr7D 84.127 63 9 1 2699 2761 265692618 265692557 3.620000e-05 60.2
6 TraesCS7D01G310400 chr7A 91.012 1235 60 23 2148 3360 446363611 446362406 0.000000e+00 1618.0
7 TraesCS7D01G310400 chr7A 94.152 171 3 2 799 969 446363852 446363689 1.550000e-63 254.0
8 TraesCS7D01G310400 chr7A 91.139 79 6 1 2759 2836 412554020 412553942 4.580000e-19 106.0
9 TraesCS7D01G310400 chr7A 90.000 80 7 1 2759 2837 623623346 623623267 5.930000e-18 102.0
10 TraesCS7D01G310400 chr7B 95.548 921 31 7 760 1676 393403495 393402581 0.000000e+00 1465.0
11 TraesCS7D01G310400 chr7B 94.737 741 31 5 1830 2567 393400699 393399964 0.000000e+00 1146.0
12 TraesCS7D01G310400 chr7B 100.000 63 0 0 1769 1831 393400923 393400861 2.120000e-22 117.0
13 TraesCS7D01G310400 chr7B 88.889 81 9 0 2757 2837 557946156 557946076 2.130000e-17 100.0
14 TraesCS7D01G310400 chr7B 100.000 38 0 0 2044 2081 393400446 393400409 1.670000e-08 71.3
15 TraesCS7D01G310400 chr7B 100.000 38 0 0 2083 2120 393400485 393400448 1.670000e-08 71.3
16 TraesCS7D01G310400 chr2D 96.728 764 23 1 1 762 81293017 81292254 0.000000e+00 1271.0
17 TraesCS7D01G310400 chr2B 96.711 760 23 1 1 758 110489257 110488498 0.000000e+00 1264.0
18 TraesCS7D01G310400 chr2B 94.286 105 6 0 1670 1774 713407067 713407171 9.650000e-36 161.0
19 TraesCS7D01G310400 chr2B 92.661 109 6 2 1673 1779 584129500 584129392 4.490000e-34 156.0
20 TraesCS7D01G310400 chr2B 87.037 54 5 2 2706 2757 178708991 178709044 3.620000e-05 60.2
21 TraesCS7D01G310400 chr3A 96.583 761 24 2 1 759 10256769 10257529 0.000000e+00 1260.0
22 TraesCS7D01G310400 chr5A 95.817 765 30 2 1 763 7485721 7486485 0.000000e+00 1234.0
23 TraesCS7D01G310400 chr5A 95.921 760 28 3 1 758 660187767 660187009 0.000000e+00 1229.0
24 TraesCS7D01G310400 chr5A 96.429 56 1 1 2859 2913 502803545 502803490 1.280000e-14 91.6
25 TraesCS7D01G310400 chr5A 96.429 56 1 1 2859 2913 675524295 675524240 1.280000e-14 91.6
26 TraesCS7D01G310400 chr6D 95.641 757 30 1 1 757 17757759 17757006 0.000000e+00 1212.0
27 TraesCS7D01G310400 chr4A 94.785 767 37 3 1 765 376659201 376659966 0.000000e+00 1192.0
28 TraesCS7D01G310400 chr2A 94.474 760 28 4 1 758 762332053 762331306 0.000000e+00 1158.0
29 TraesCS7D01G310400 chr2A 95.050 101 5 0 1672 1772 68155923 68155823 3.470000e-35 159.0
30 TraesCS7D01G310400 chr2A 91.250 80 6 1 2759 2837 435675625 435675704 1.270000e-19 108.0
31 TraesCS7D01G310400 chr2A 85.185 54 6 2 2706 2757 131706176 131706229 2.000000e-03 54.7
32 TraesCS7D01G310400 chr6A 97.980 99 2 0 1675 1773 381087504 381087602 4.460000e-39 172.0
33 TraesCS7D01G310400 chr6A 96.970 99 3 0 1674 1772 459468671 459468573 2.070000e-37 167.0
34 TraesCS7D01G310400 chr6A 98.077 52 1 0 2859 2910 515649888 515649939 1.280000e-14 91.6
35 TraesCS7D01G310400 chr1D 95.960 99 4 0 1675 1773 225936852 225936950 9.650000e-36 161.0
36 TraesCS7D01G310400 chr3B 94.231 104 6 0 1669 1772 560117295 560117398 3.470000e-35 159.0
37 TraesCS7D01G310400 chr3B 89.362 47 5 0 2711 2757 685063074 685063120 3.620000e-05 60.2
38 TraesCS7D01G310400 chr3B 86.792 53 6 1 2708 2760 481620015 481619964 1.300000e-04 58.4
39 TraesCS7D01G310400 chr6B 93.458 107 5 2 1674 1778 714093238 714093132 1.250000e-34 158.0
40 TraesCS7D01G310400 chr6B 92.105 76 6 0 2759 2834 605015704 605015779 1.270000e-19 108.0
41 TraesCS7D01G310400 chr6B 90.123 81 8 0 2757 2837 356597434 356597514 4.580000e-19 106.0
42 TraesCS7D01G310400 chr5B 91.453 117 7 2 1670 1786 295217365 295217252 1.250000e-34 158.0
43 TraesCS7D01G310400 chr3D 92.000 75 6 0 2761 2835 560644367 560644441 4.580000e-19 106.0
44 TraesCS7D01G310400 chr1B 89.024 82 9 0 2756 2837 465942285 465942366 5.930000e-18 102.0
45 TraesCS7D01G310400 chr1B 87.273 55 5 1 2708 2760 150361158 150361104 1.010000e-05 62.1
46 TraesCS7D01G310400 chr1B 87.273 55 5 2 2708 2760 618697633 618697579 1.010000e-05 62.1
47 TraesCS7D01G310400 chr1A 90.000 80 7 1 2759 2837 288238889 288238968 5.930000e-18 102.0
48 TraesCS7D01G310400 chr1A 96.552 58 1 1 2859 2915 577393618 577393675 9.920000e-16 95.3
49 TraesCS7D01G310400 chrUn 96.552 58 1 1 2859 2915 23538089 23538146 9.920000e-16 95.3
50 TraesCS7D01G310400 chr4B 98.182 55 0 1 2859 2912 543286646 543286592 9.920000e-16 95.3
51 TraesCS7D01G310400 chr4B 93.548 62 2 2 2859 2918 205024945 205024884 1.280000e-14 91.6
52 TraesCS7D01G310400 chr5D 96.429 56 1 1 2859 2913 548396384 548396329 1.280000e-14 91.6


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 TraesCS7D01G310400 chr7D 393615741 393619100 3359 True 2115.866667 6205 100.000 1 3360 3 chr7D.!!$R4 3359
1 TraesCS7D01G310400 chr7D 614260837 614261585 748 True 1149.000000 1149 94.305 6 759 1 chr7D.!!$R3 753
2 TraesCS7D01G310400 chr7A 446362406 446363852 1446 True 936.000000 1618 92.582 799 3360 2 chr7A.!!$R3 2561
3 TraesCS7D01G310400 chr7B 393399964 393403495 3531 True 574.120000 1465 98.057 760 2567 5 chr7B.!!$R2 1807
4 TraesCS7D01G310400 chr2D 81292254 81293017 763 True 1271.000000 1271 96.728 1 762 1 chr2D.!!$R1 761
5 TraesCS7D01G310400 chr2B 110488498 110489257 759 True 1264.000000 1264 96.711 1 758 1 chr2B.!!$R1 757
6 TraesCS7D01G310400 chr3A 10256769 10257529 760 False 1260.000000 1260 96.583 1 759 1 chr3A.!!$F1 758
7 TraesCS7D01G310400 chr5A 7485721 7486485 764 False 1234.000000 1234 95.817 1 763 1 chr5A.!!$F1 762
8 TraesCS7D01G310400 chr5A 660187009 660187767 758 True 1229.000000 1229 95.921 1 758 1 chr5A.!!$R2 757
9 TraesCS7D01G310400 chr6D 17757006 17757759 753 True 1212.000000 1212 95.641 1 757 1 chr6D.!!$R1 756
10 TraesCS7D01G310400 chr4A 376659201 376659966 765 False 1192.000000 1192 94.785 1 765 1 chr4A.!!$F1 764
11 TraesCS7D01G310400 chr2A 762331306 762332053 747 True 1158.000000 1158 94.474 1 758 1 chr2A.!!$R2 757

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
789 791 0.872388 GCTTTGGTGTTACCGACAGG 59.128 55.0 0.00 0.0 42.58 4.00 F
1197 1204 0.233848 CCAAGTACCACAACGCGAAC 59.766 55.0 15.93 0.0 0.00 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2291 4027 1.145759 CCATCATCGTCGGTGGTTCG 61.146 60.0 5.5 0.0 0.00 3.95 R
2981 4748 0.389426 GCACAATGCAGCTTCCCTTG 60.389 55.0 0.0 0.0 44.26 3.61 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
41 42 3.897657 ACCCTTCCGGATGATCTACTA 57.102 47.619 18.51 0.00 34.64 1.82
114 115 2.532843 ACTTGTGGTGGATACGTAGGT 58.467 47.619 0.08 0.00 42.51 3.08
283 285 5.473039 ACTAAATGTTGATGCAGCCTTTTC 58.527 37.500 0.00 0.00 0.00 2.29
388 390 1.528076 TGGCGGCGGATGCAATTAT 60.528 52.632 9.78 0.00 45.35 1.28
399 401 3.129287 GGATGCAATTATAATGGAGGCGG 59.871 47.826 3.86 0.00 0.00 6.13
449 451 4.162509 GCCAACTCTCTAGGACTAAACCAT 59.837 45.833 0.00 0.00 0.00 3.55
622 624 3.958147 AAGCGGCGCATGTGCTAGT 62.958 57.895 35.02 11.95 38.17 2.57
631 633 3.125316 GCGCATGTGCTAGTTAACTTCTT 59.875 43.478 23.77 0.00 39.32 2.52
633 635 4.201724 CGCATGTGCTAGTTAACTTCTTCC 60.202 45.833 14.49 0.00 39.32 3.46
789 791 0.872388 GCTTTGGTGTTACCGACAGG 59.128 55.000 0.00 0.00 42.58 4.00
797 799 1.067142 TGTTACCGACAGGATGCACTC 60.067 52.381 0.00 0.00 42.53 3.51
823 826 1.493861 TCTGAGGCTGCAGATTAGCT 58.506 50.000 20.43 0.00 39.84 3.32
877 884 7.839200 AGCCCAGTATTAGTTGGTATGAAAAAT 59.161 33.333 0.00 0.00 32.40 1.82
952 959 2.523168 AAACCCCAAAGCCCACCG 60.523 61.111 0.00 0.00 0.00 4.94
1039 1046 2.736978 CACGATCCTTCTTCTCATCGG 58.263 52.381 5.28 0.00 41.97 4.18
1040 1047 1.067821 ACGATCCTTCTTCTCATCGGC 59.932 52.381 5.28 0.00 41.97 5.54
1064 1071 2.185608 GCCTTCTCTCCTCCACGC 59.814 66.667 0.00 0.00 0.00 5.34
1111 1118 1.445095 CCGCTTGGATCTCCTCCTG 59.555 63.158 0.00 0.00 45.21 3.86
1197 1204 0.233848 CCAAGTACCACAACGCGAAC 59.766 55.000 15.93 0.00 0.00 3.95
1603 1610 5.357878 AGCAACATTTCGTCCACATATGAAT 59.642 36.000 10.38 0.00 0.00 2.57
1615 1622 7.569408 CGTCCACATATGAATTCGATCGAAATT 60.569 37.037 32.11 24.42 37.69 1.82
1676 1683 5.449107 ACATCAGACCACCGTACATATAC 57.551 43.478 0.00 0.00 0.00 1.47
1678 1685 5.241064 ACATCAGACCACCGTACATATACTC 59.759 44.000 0.00 0.00 0.00 2.59
1679 1686 4.139786 TCAGACCACCGTACATATACTCC 58.860 47.826 0.00 0.00 0.00 3.85
1680 1687 3.255149 CAGACCACCGTACATATACTCCC 59.745 52.174 0.00 0.00 0.00 4.30
1681 1688 3.139770 AGACCACCGTACATATACTCCCT 59.860 47.826 0.00 0.00 0.00 4.20
1683 1690 2.824341 CCACCGTACATATACTCCCTCC 59.176 54.545 0.00 0.00 0.00 4.30
1684 1691 2.486982 CACCGTACATATACTCCCTCCG 59.513 54.545 0.00 0.00 0.00 4.63
1685 1692 2.107204 ACCGTACATATACTCCCTCCGT 59.893 50.000 0.00 0.00 0.00 4.69
1686 1693 2.746362 CCGTACATATACTCCCTCCGTC 59.254 54.545 0.00 0.00 0.00 4.79
1688 1695 2.305858 ACATATACTCCCTCCGTCCC 57.694 55.000 0.00 0.00 0.00 4.46
1692 1699 1.961133 ATACTCCCTCCGTCCCAAAA 58.039 50.000 0.00 0.00 0.00 2.44
1693 1700 1.961133 TACTCCCTCCGTCCCAAAAT 58.039 50.000 0.00 0.00 0.00 1.82
1694 1701 1.961133 ACTCCCTCCGTCCCAAAATA 58.039 50.000 0.00 0.00 0.00 1.40
1695 1702 2.271777 ACTCCCTCCGTCCCAAAATAA 58.728 47.619 0.00 0.00 0.00 1.40
1696 1703 2.238898 ACTCCCTCCGTCCCAAAATAAG 59.761 50.000 0.00 0.00 0.00 1.73
1697 1704 2.238898 CTCCCTCCGTCCCAAAATAAGT 59.761 50.000 0.00 0.00 0.00 2.24
1698 1705 2.026636 TCCCTCCGTCCCAAAATAAGTG 60.027 50.000 0.00 0.00 0.00 3.16
1699 1706 2.290705 CCCTCCGTCCCAAAATAAGTGT 60.291 50.000 0.00 0.00 0.00 3.55
1700 1707 3.007635 CCTCCGTCCCAAAATAAGTGTC 58.992 50.000 0.00 0.00 0.00 3.67
1702 1709 3.933332 CTCCGTCCCAAAATAAGTGTCTC 59.067 47.826 0.00 0.00 0.00 3.36
1703 1710 3.325425 TCCGTCCCAAAATAAGTGTCTCA 59.675 43.478 0.00 0.00 0.00 3.27
1704 1711 4.069304 CCGTCCCAAAATAAGTGTCTCAA 58.931 43.478 0.00 0.00 0.00 3.02
1706 1713 4.755123 CGTCCCAAAATAAGTGTCTCAACT 59.245 41.667 0.00 0.00 0.00 3.16
1709 1716 7.041644 CGTCCCAAAATAAGTGTCTCAACTTTA 60.042 37.037 0.00 0.00 40.77 1.85
1710 1717 8.793592 GTCCCAAAATAAGTGTCTCAACTTTAT 58.206 33.333 0.00 0.00 40.77 1.40
1746 1753 9.269453 AGTACAAAGTTGTAATAAGGTCAAGAC 57.731 33.333 5.49 0.00 44.46 3.01
1748 1755 7.927048 ACAAAGTTGTAATAAGGTCAAGACAC 58.073 34.615 2.29 0.00 40.16 3.67
1750 1757 8.621286 CAAAGTTGTAATAAGGTCAAGACACTT 58.379 33.333 2.29 5.99 0.00 3.16
1751 1758 9.841295 AAAGTTGTAATAAGGTCAAGACACTTA 57.159 29.630 2.29 7.78 32.63 2.24
1765 3309 4.860022 AGACACTTATTTTGGGATGGAGG 58.140 43.478 0.00 0.00 0.00 4.30
1766 3310 3.954258 GACACTTATTTTGGGATGGAGGG 59.046 47.826 0.00 0.00 0.00 4.30
1767 3311 3.596046 ACACTTATTTTGGGATGGAGGGA 59.404 43.478 0.00 0.00 0.00 4.20
1946 3681 4.631377 CGTATCTGTCATTTGTGGTGTCAT 59.369 41.667 0.00 0.00 0.00 3.06
2275 4011 5.063204 GGTCCATATCCATTTGACGATGAA 58.937 41.667 0.00 0.00 0.00 2.57
2280 4016 2.710377 TCCATTTGACGATGAACAGGG 58.290 47.619 0.00 0.00 0.00 4.45
2291 4027 1.079057 GAACAGGGGTCGAAGGAGC 60.079 63.158 0.00 0.00 39.95 4.70
2514 4252 2.772515 GACTTGGCTAGGTAGGGTGAAT 59.227 50.000 0.20 0.00 0.00 2.57
2539 4277 4.773674 TCATGCATCTTTGGGATTGAAAGT 59.226 37.500 0.00 0.00 33.04 2.66
2540 4278 4.789012 TGCATCTTTGGGATTGAAAGTC 57.211 40.909 0.00 0.00 33.04 3.01
2549 4287 3.217626 GGGATTGAAAGTCCTGCTATGG 58.782 50.000 0.00 0.00 36.00 2.74
2580 4318 7.286215 TGTACCTAGTATATCTCAAAGCACC 57.714 40.000 0.00 0.00 0.00 5.01
2600 4354 2.736721 CCGTGTGAGTGTGTAATTCTGG 59.263 50.000 0.00 0.00 0.00 3.86
2630 4384 1.042229 AGTTTGCTGCAATGGCTCAA 58.958 45.000 16.77 0.00 41.91 3.02
2631 4385 1.142474 GTTTGCTGCAATGGCTCAAC 58.858 50.000 16.77 5.64 41.91 3.18
2772 4528 1.377612 GGACTAAGGCCCCGTTTGT 59.622 57.895 0.00 0.00 0.00 2.83
2777 4533 1.268625 CTAAGGCCCCGTTTGTTTCAC 59.731 52.381 0.00 0.00 0.00 3.18
2799 4555 0.610174 TCTGCGACCAGATTCAGCTT 59.390 50.000 0.00 0.00 42.98 3.74
2800 4556 1.002430 TCTGCGACCAGATTCAGCTTT 59.998 47.619 0.00 0.00 42.98 3.51
2801 4557 1.129998 CTGCGACCAGATTCAGCTTTG 59.870 52.381 0.00 0.00 41.77 2.77
2802 4558 0.179179 GCGACCAGATTCAGCTTTGC 60.179 55.000 0.00 0.00 0.00 3.68
2803 4559 0.449388 CGACCAGATTCAGCTTTGCC 59.551 55.000 0.00 0.00 0.00 4.52
2804 4560 1.538047 GACCAGATTCAGCTTTGCCA 58.462 50.000 0.00 0.00 0.00 4.92
2805 4561 1.471684 GACCAGATTCAGCTTTGCCAG 59.528 52.381 0.00 0.00 0.00 4.85
2806 4562 1.202976 ACCAGATTCAGCTTTGCCAGT 60.203 47.619 0.00 0.00 0.00 4.00
2807 4563 1.201647 CCAGATTCAGCTTTGCCAGTG 59.798 52.381 0.00 0.00 0.00 3.66
2808 4564 2.156917 CAGATTCAGCTTTGCCAGTGA 58.843 47.619 0.00 0.00 0.00 3.41
2809 4565 2.555325 CAGATTCAGCTTTGCCAGTGAA 59.445 45.455 0.00 0.00 33.61 3.18
2810 4566 2.818432 AGATTCAGCTTTGCCAGTGAAG 59.182 45.455 0.00 0.00 32.64 3.02
2811 4567 0.670162 TTCAGCTTTGCCAGTGAAGC 59.330 50.000 6.89 6.89 46.57 3.86
2850 4616 1.204467 CAAACAGTGCCACTTTGGTGT 59.796 47.619 0.00 0.00 40.46 4.16
2851 4617 0.817013 AACAGTGCCACTTTGGTGTG 59.183 50.000 0.00 0.00 40.46 3.82
2887 4654 5.105392 GCAATCCACAGGTGATTAAAATCCA 60.105 40.000 0.00 0.00 34.50 3.41
2891 4658 4.414852 CACAGGTGATTAAAATCCAAGCG 58.585 43.478 0.00 0.00 34.50 4.68
2933 4700 8.090831 GGGCCTAATAATCTTTTCATCCATTTC 58.909 37.037 0.84 0.00 0.00 2.17
2945 4712 9.798994 CTTTTCATCCATTTCTATTTTGAGAGG 57.201 33.333 0.00 0.00 0.00 3.69
2948 4715 7.405292 TCATCCATTTCTATTTTGAGAGGTGT 58.595 34.615 0.00 0.00 0.00 4.16
2958 4725 8.644216 TCTATTTTGAGAGGTGTAGTGTGTAAA 58.356 33.333 0.00 0.00 0.00 2.01
2959 4726 9.268268 CTATTTTGAGAGGTGTAGTGTGTAAAA 57.732 33.333 0.00 0.00 0.00 1.52
2960 4727 6.913873 TTTGAGAGGTGTAGTGTGTAAAAC 57.086 37.500 0.00 0.00 0.00 2.43
2994 4761 0.106268 TTTGGTCAAGGGAAGCTGCA 60.106 50.000 1.02 0.00 0.00 4.41
3028 4795 1.072331 AGGAAACACACGGAGCTGATT 59.928 47.619 0.00 0.00 0.00 2.57
3094 4861 2.047679 GCAGCTGCAAGAACAAAGAG 57.952 50.000 33.36 0.00 41.59 2.85
3116 4883 1.895131 TCATTTTCCCCTCTGCTTTGC 59.105 47.619 0.00 0.00 0.00 3.68
3223 4992 4.751767 TTGCAGTGGTTCCAAAATTCTT 57.248 36.364 0.00 0.00 0.00 2.52
3225 4994 3.703556 TGCAGTGGTTCCAAAATTCTTCA 59.296 39.130 0.00 0.00 0.00 3.02
3260 5029 7.594714 CATATACTACTCCGTATATGGATGCC 58.405 42.308 14.21 0.00 46.86 4.40
3261 5030 4.048970 ACTACTCCGTATATGGATGCCT 57.951 45.455 14.21 0.84 37.41 4.75
3262 5031 3.764434 ACTACTCCGTATATGGATGCCTG 59.236 47.826 14.21 5.02 37.41 4.85
3263 5032 2.889512 ACTCCGTATATGGATGCCTGA 58.110 47.619 14.21 0.00 37.41 3.86
3264 5033 3.445008 ACTCCGTATATGGATGCCTGAT 58.555 45.455 14.21 0.00 37.41 2.90
3265 5034 3.196469 ACTCCGTATATGGATGCCTGATG 59.804 47.826 14.21 2.94 37.41 3.07
3266 5035 3.440127 TCCGTATATGGATGCCTGATGA 58.560 45.455 9.78 0.00 31.53 2.92
3285 5054 7.976734 CCTGATGAAAAAGATTACTCGTCTAGT 59.023 37.037 0.00 0.00 42.62 2.57
3301 5070 4.624452 CGTCTAGTAGAAAAGAAAACCGGG 59.376 45.833 6.32 0.00 0.00 5.73
3331 5100 1.450025 CGACTAGGAAAACCAAGGGC 58.550 55.000 0.00 0.00 0.00 5.19
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
52 53 6.265577 AGTGCTTGTTTGAAGTTGACATTAC 58.734 36.000 0.00 0.00 0.00 1.89
114 115 2.282407 CGGCTCATCATGTGTCATTCA 58.718 47.619 0.00 0.00 0.00 2.57
219 220 4.620803 CGGCTTACACCATTTAGTCTCTGT 60.621 45.833 0.00 0.00 0.00 3.41
300 302 2.484287 ATAACAGCCGCAGTTGCCCT 62.484 55.000 11.13 0.00 37.91 5.19
622 624 9.985730 TCGACTTATTACAAAGGAAGAAGTTAA 57.014 29.630 3.77 0.00 38.20 2.01
631 633 7.837863 ACTGAGATTCGACTTATTACAAAGGA 58.162 34.615 0.00 0.00 0.00 3.36
633 635 8.383619 CCAACTGAGATTCGACTTATTACAAAG 58.616 37.037 0.00 0.00 0.00 2.77
770 772 0.872388 CCTGTCGGTAACACCAAAGC 59.128 55.000 0.00 0.00 38.47 3.51
823 826 2.494530 GGCCACCGGAAACAGCAAA 61.495 57.895 9.46 0.00 0.00 3.68
877 884 9.826574 CTAGTACTACAATTGGGCTTACATTTA 57.173 33.333 10.83 0.00 0.00 1.40
1016 1023 1.173913 TGAGAAGAAGGATCGTGCGA 58.826 50.000 0.00 0.00 0.00 5.10
1023 1030 1.202627 GCTGCCGATGAGAAGAAGGAT 60.203 52.381 0.00 0.00 0.00 3.24
1039 1046 2.817396 GAGAGAAGGCGGTGCTGC 60.817 66.667 0.00 0.00 0.00 5.25
1040 1047 2.125350 GGAGAGAAGGCGGTGCTG 60.125 66.667 0.00 0.00 0.00 4.41
1603 1610 4.937696 TTGCTGCTTAATTTCGATCGAA 57.062 36.364 25.96 25.96 0.00 3.71
1615 1622 1.541147 GTGGCATGAGTTTGCTGCTTA 59.459 47.619 0.00 0.00 42.38 3.09
1676 1683 2.238898 ACTTATTTTGGGACGGAGGGAG 59.761 50.000 0.00 0.00 0.00 4.30
1678 1685 2.290705 ACACTTATTTTGGGACGGAGGG 60.291 50.000 0.00 0.00 0.00 4.30
1679 1686 3.007635 GACACTTATTTTGGGACGGAGG 58.992 50.000 0.00 0.00 0.00 4.30
1680 1687 3.933332 GAGACACTTATTTTGGGACGGAG 59.067 47.826 0.00 0.00 0.00 4.63
1681 1688 3.325425 TGAGACACTTATTTTGGGACGGA 59.675 43.478 0.00 0.00 0.00 4.69
1683 1690 4.755123 AGTTGAGACACTTATTTTGGGACG 59.245 41.667 0.00 0.00 0.00 4.79
1684 1691 6.635030 AAGTTGAGACACTTATTTTGGGAC 57.365 37.500 0.00 0.00 35.10 4.46
1685 1692 8.934023 ATAAAGTTGAGACACTTATTTTGGGA 57.066 30.769 0.00 0.00 35.87 4.37
1724 1731 8.154649 AGTGTCTTGACCTTATTACAACTTTG 57.845 34.615 0.00 0.00 0.00 2.77
1725 1732 8.747538 AAGTGTCTTGACCTTATTACAACTTT 57.252 30.769 0.00 0.00 0.00 2.66
1732 1739 9.238368 CCCAAAATAAGTGTCTTGACCTTATTA 57.762 33.333 22.33 9.86 39.33 0.98
1733 1740 7.947890 TCCCAAAATAAGTGTCTTGACCTTATT 59.052 33.333 19.52 19.52 41.02 1.40
1734 1741 7.466804 TCCCAAAATAAGTGTCTTGACCTTAT 58.533 34.615 13.60 13.60 33.86 1.73
1735 1742 6.843752 TCCCAAAATAAGTGTCTTGACCTTA 58.156 36.000 11.29 11.29 0.00 2.69
1736 1743 5.701224 TCCCAAAATAAGTGTCTTGACCTT 58.299 37.500 0.00 4.52 0.00 3.50
1737 1744 5.319043 TCCCAAAATAAGTGTCTTGACCT 57.681 39.130 0.00 0.00 0.00 3.85
1738 1745 5.105756 CCATCCCAAAATAAGTGTCTTGACC 60.106 44.000 0.00 0.00 0.00 4.02
1739 1746 5.710099 TCCATCCCAAAATAAGTGTCTTGAC 59.290 40.000 0.00 0.00 0.00 3.18
1740 1747 5.886609 TCCATCCCAAAATAAGTGTCTTGA 58.113 37.500 0.00 0.00 0.00 3.02
1741 1748 5.126061 CCTCCATCCCAAAATAAGTGTCTTG 59.874 44.000 0.00 0.00 0.00 3.02
1742 1749 5.264395 CCTCCATCCCAAAATAAGTGTCTT 58.736 41.667 0.00 0.00 0.00 3.01
1743 1750 4.325344 CCCTCCATCCCAAAATAAGTGTCT 60.325 45.833 0.00 0.00 0.00 3.41
1744 1751 3.954258 CCCTCCATCCCAAAATAAGTGTC 59.046 47.826 0.00 0.00 0.00 3.67
1745 1752 3.596046 TCCCTCCATCCCAAAATAAGTGT 59.404 43.478 0.00 0.00 0.00 3.55
1746 1753 4.210331 CTCCCTCCATCCCAAAATAAGTG 58.790 47.826 0.00 0.00 0.00 3.16
1748 1755 4.526438 ACTCCCTCCATCCCAAAATAAG 57.474 45.455 0.00 0.00 0.00 1.73
1750 1757 6.621931 TGTAATACTCCCTCCATCCCAAAATA 59.378 38.462 0.00 0.00 0.00 1.40
1751 1758 5.435041 TGTAATACTCCCTCCATCCCAAAAT 59.565 40.000 0.00 0.00 0.00 1.82
1752 1759 4.791334 TGTAATACTCCCTCCATCCCAAAA 59.209 41.667 0.00 0.00 0.00 2.44
1753 1760 4.376223 TGTAATACTCCCTCCATCCCAAA 58.624 43.478 0.00 0.00 0.00 3.28
1754 1761 3.973973 CTGTAATACTCCCTCCATCCCAA 59.026 47.826 0.00 0.00 0.00 4.12
1755 1762 3.208922 TCTGTAATACTCCCTCCATCCCA 59.791 47.826 0.00 0.00 0.00 4.37
1765 3309 7.224949 GGTTCAATTGCTACTCTGTAATACTCC 59.775 40.741 0.00 0.00 0.00 3.85
1766 3310 7.764443 TGGTTCAATTGCTACTCTGTAATACTC 59.236 37.037 0.00 0.00 0.00 2.59
1767 3311 7.620880 TGGTTCAATTGCTACTCTGTAATACT 58.379 34.615 0.00 0.00 0.00 2.12
2275 4011 3.382832 CGCTCCTTCGACCCCTGT 61.383 66.667 0.00 0.00 0.00 4.00
2280 4016 1.737008 GTGGTTCGCTCCTTCGACC 60.737 63.158 0.00 0.00 38.30 4.79
2291 4027 1.145759 CCATCATCGTCGGTGGTTCG 61.146 60.000 5.50 0.00 0.00 3.95
2514 4252 5.741962 TTCAATCCCAAAGATGCATGAAA 57.258 34.783 2.46 0.00 34.56 2.69
2539 4277 5.155161 AGGTACATAACATCCATAGCAGGA 58.845 41.667 0.00 0.00 43.01 3.86
2540 4278 5.489792 AGGTACATAACATCCATAGCAGG 57.510 43.478 0.00 0.00 0.00 4.85
2580 4318 3.390135 ACCAGAATTACACACTCACACG 58.610 45.455 0.00 0.00 0.00 4.49
2600 4354 1.202076 GCAGCAAACTGGCGATTCTAC 60.202 52.381 0.00 0.00 44.63 2.59
2630 4384 3.009723 CCAATAGAAGAACACATGGCGT 58.990 45.455 0.00 0.00 0.00 5.68
2631 4385 3.270027 TCCAATAGAAGAACACATGGCG 58.730 45.455 0.00 0.00 0.00 5.69
2719 4473 6.925610 ATTAATTGTCGCAGCTTCAATAGA 57.074 33.333 10.81 5.35 32.52 1.98
2720 4474 7.747799 CCATATTAATTGTCGCAGCTTCAATAG 59.252 37.037 10.81 0.00 32.52 1.73
2777 4533 1.329906 GCTGAATCTGGTCGCAGAATG 59.670 52.381 0.00 0.00 39.69 2.67
2804 4560 5.319453 TCAAATTCCAGATTCAGCTTCACT 58.681 37.500 0.00 0.00 0.00 3.41
2805 4561 5.633830 TCAAATTCCAGATTCAGCTTCAC 57.366 39.130 0.00 0.00 0.00 3.18
2806 4562 6.040729 TGTTTCAAATTCCAGATTCAGCTTCA 59.959 34.615 0.00 0.00 0.00 3.02
2807 4563 6.449698 TGTTTCAAATTCCAGATTCAGCTTC 58.550 36.000 0.00 0.00 0.00 3.86
2808 4564 6.409524 TGTTTCAAATTCCAGATTCAGCTT 57.590 33.333 0.00 0.00 0.00 3.74
2809 4565 6.409524 TTGTTTCAAATTCCAGATTCAGCT 57.590 33.333 0.00 0.00 0.00 4.24
2810 4566 6.479660 TGTTTGTTTCAAATTCCAGATTCAGC 59.520 34.615 0.00 0.00 0.00 4.26
2811 4567 7.707893 ACTGTTTGTTTCAAATTCCAGATTCAG 59.292 33.333 13.95 8.88 0.00 3.02
2824 4580 3.951775 AAGTGGCACTGTTTGTTTCAA 57.048 38.095 22.83 0.00 0.00 2.69
2850 4616 1.144708 TGGATTGCTTCAGGTTCACCA 59.855 47.619 0.00 0.00 38.89 4.17
2851 4617 1.541588 GTGGATTGCTTCAGGTTCACC 59.458 52.381 0.00 0.00 0.00 4.02
2887 4654 2.223572 CCTGTTTGTTTCAGCTTCGCTT 60.224 45.455 0.00 0.00 36.40 4.68
2891 4658 1.269778 GGCCCTGTTTGTTTCAGCTTC 60.270 52.381 0.00 0.00 0.00 3.86
2933 4700 8.827177 TTTACACACTACACCTCTCAAAATAG 57.173 34.615 0.00 0.00 0.00 1.73
2973 4740 1.620323 GCAGCTTCCCTTGACCAAAAT 59.380 47.619 0.00 0.00 0.00 1.82
2980 4747 1.250328 CACAATGCAGCTTCCCTTGA 58.750 50.000 1.18 0.00 0.00 3.02
2981 4748 0.389426 GCACAATGCAGCTTCCCTTG 60.389 55.000 0.00 0.00 44.26 3.61
2994 4761 3.503748 GTGTTTCCTCTAAGCTGCACAAT 59.496 43.478 1.02 0.00 0.00 2.71
3086 4853 5.302823 CAGAGGGGAAAATGAACTCTTTGTT 59.697 40.000 0.00 0.00 42.38 2.83
3094 4861 3.862264 GCAAAGCAGAGGGGAAAATGAAC 60.862 47.826 0.00 0.00 0.00 3.18
3102 4869 0.677731 CATTCGCAAAGCAGAGGGGA 60.678 55.000 0.00 0.00 0.00 4.81
3132 4899 1.472082 TGCCAATTTGTGTATCGCCAG 59.528 47.619 0.00 0.00 0.00 4.85
3136 4903 3.190327 TGGAACTGCCAATTTGTGTATCG 59.810 43.478 0.00 0.00 45.87 2.92
3180 4947 6.349280 GCAAAACATAGCCATGAGTTACAAGA 60.349 38.462 0.00 0.00 35.96 3.02
3181 4948 5.801947 GCAAAACATAGCCATGAGTTACAAG 59.198 40.000 0.00 0.00 35.96 3.16
3183 4950 4.764308 TGCAAAACATAGCCATGAGTTACA 59.236 37.500 0.00 0.00 35.96 2.41
3190 4959 2.231964 ACCACTGCAAAACATAGCCATG 59.768 45.455 0.00 0.00 38.21 3.66
3248 5017 7.750229 TCTTTTTCATCAGGCATCCATATAC 57.250 36.000 0.00 0.00 0.00 1.47
3249 5018 8.945195 AATCTTTTTCATCAGGCATCCATATA 57.055 30.769 0.00 0.00 0.00 0.86
3250 5019 7.850935 AATCTTTTTCATCAGGCATCCATAT 57.149 32.000 0.00 0.00 0.00 1.78
3251 5020 8.000709 AGTAATCTTTTTCATCAGGCATCCATA 58.999 33.333 0.00 0.00 0.00 2.74
3252 5021 6.837568 AGTAATCTTTTTCATCAGGCATCCAT 59.162 34.615 0.00 0.00 0.00 3.41
3253 5022 6.189859 AGTAATCTTTTTCATCAGGCATCCA 58.810 36.000 0.00 0.00 0.00 3.41
3254 5023 6.512415 CGAGTAATCTTTTTCATCAGGCATCC 60.512 42.308 0.00 0.00 0.00 3.51
3255 5024 6.037610 ACGAGTAATCTTTTTCATCAGGCATC 59.962 38.462 0.00 0.00 0.00 3.91
3256 5025 5.882557 ACGAGTAATCTTTTTCATCAGGCAT 59.117 36.000 0.00 0.00 0.00 4.40
3257 5026 5.245531 ACGAGTAATCTTTTTCATCAGGCA 58.754 37.500 0.00 0.00 0.00 4.75
3258 5027 5.582665 AGACGAGTAATCTTTTTCATCAGGC 59.417 40.000 0.00 0.00 0.00 4.85
3259 5028 7.976734 ACTAGACGAGTAATCTTTTTCATCAGG 59.023 37.037 0.00 0.00 36.27 3.86
3260 5029 8.918961 ACTAGACGAGTAATCTTTTTCATCAG 57.081 34.615 0.00 0.00 36.27 2.90
3285 5054 3.559811 GGGTAGCCCGGTTTTCTTTTCTA 60.560 47.826 0.00 0.00 32.13 2.10
3286 5055 2.511659 GGTAGCCCGGTTTTCTTTTCT 58.488 47.619 0.00 0.00 0.00 2.52
3287 5056 1.542915 GGGTAGCCCGGTTTTCTTTTC 59.457 52.381 0.00 0.00 32.13 2.29
3301 5070 0.473326 TCCTAGTCGGAGAGGGTAGC 59.527 60.000 6.14 0.00 36.95 3.58
3331 5100 5.070313 TGAAGAAAATGGGGAAAAGTTCAGG 59.930 40.000 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.