Multiple sequence alignment - TraesCS6D01G038800

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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 TraesCS6D01G038800 chr6D 100.000 2270 0 0 1 2270 16160970 16158701 0.000000e+00 4193.0
1 TraesCS6D01G038800 chr6D 86.838 661 74 6 927 1587 367748633 367747986 0.000000e+00 726.0
2 TraesCS6D01G038800 chrUn 91.343 2033 113 24 100 2090 314596306 314594295 0.000000e+00 2721.0
3 TraesCS6D01G038800 chrUn 84.402 686 78 12 924 1580 358002660 358003345 0.000000e+00 647.0
4 TraesCS6D01G038800 chrUn 93.921 329 17 2 1764 2090 370994041 370994368 5.630000e-136 494.0
5 TraesCS6D01G038800 chrUn 94.180 189 6 4 2086 2270 314594266 314594079 1.330000e-72 283.0
6 TraesCS6D01G038800 chrUn 94.180 189 6 4 2086 2270 370994397 370994584 1.330000e-72 283.0
7 TraesCS6D01G038800 chr6B 90.640 2030 114 28 100 2090 27915985 27913993 0.000000e+00 2627.0
8 TraesCS6D01G038800 chr6B 94.180 189 6 4 2086 2270 27913964 27913777 1.330000e-72 283.0
9 TraesCS6D01G038800 chr6B 77.009 535 87 20 240 772 508533385 508532885 7.990000e-70 274.0
10 TraesCS6D01G038800 chr6B 93.878 49 3 0 152 200 487207073 487207025 8.700000e-10 75.0
11 TraesCS6D01G038800 chr4A 88.226 654 64 6 927 1580 734887052 734886412 0.000000e+00 769.0
12 TraesCS6D01G038800 chr4A 91.964 112 9 0 1469 1580 616975726 616975837 8.390000e-35 158.0
13 TraesCS6D01G038800 chr4A 80.531 113 21 1 408 520 595448329 595448218 4.020000e-13 86.1
14 TraesCS6D01G038800 chr3D 87.424 660 64 10 927 1580 51469716 51470362 0.000000e+00 741.0
15 TraesCS6D01G038800 chr3D 74.806 516 92 23 243 756 476503856 476503377 4.950000e-47 198.0
16 TraesCS6D01G038800 chr3D 100.000 103 0 0 1 103 2716667 2716769 8.280000e-45 191.0
17 TraesCS6D01G038800 chr3A 87.597 645 57 11 952 1580 704116992 704117629 0.000000e+00 726.0
18 TraesCS6D01G038800 chr3A 85.865 665 81 10 927 1583 737424289 737423630 0.000000e+00 695.0
19 TraesCS6D01G038800 chr3A 82.653 196 18 10 1400 1580 20014900 20015094 2.330000e-35 159.0
20 TraesCS6D01G038800 chr2B 92.239 451 33 2 929 1378 798711139 798710690 2.460000e-179 638.0
21 TraesCS6D01G038800 chr2B 72.032 497 109 20 275 765 506052648 506053120 1.100000e-23 121.0
22 TraesCS6D01G038800 chr2B 91.837 49 3 1 152 200 155052369 155052416 1.460000e-07 67.6
23 TraesCS6D01G038800 chr7A 86.301 365 41 5 1221 1585 554399160 554398805 2.730000e-104 388.0
24 TraesCS6D01G038800 chr7A 76.252 539 92 25 237 772 393325200 393325705 1.040000e-63 254.0
25 TraesCS6D01G038800 chr1A 82.836 268 31 9 1330 1583 169727788 169727522 2.270000e-55 226.0
26 TraesCS6D01G038800 chr1A 81.319 273 42 4 500 772 580932448 580932185 1.770000e-51 213.0
27 TraesCS6D01G038800 chr1A 74.651 430 93 13 248 673 94459786 94459369 2.320000e-40 176.0
28 TraesCS6D01G038800 chr1D 75.984 508 79 28 270 772 282131037 282130568 2.930000e-54 222.0
29 TraesCS6D01G038800 chr1D 100.000 103 0 0 1 103 452524328 452524430 8.280000e-45 191.0
30 TraesCS6D01G038800 chr1D 80.583 206 39 1 238 442 476447092 476447297 8.390000e-35 158.0
31 TraesCS6D01G038800 chr1B 75.486 514 86 25 248 757 666836099 666836576 4.910000e-52 215.0
32 TraesCS6D01G038800 chr1B 74.857 525 96 21 237 757 678869041 678868549 2.960000e-49 206.0
33 TraesCS6D01G038800 chr7D 100.000 103 0 0 1 103 49445802 49445904 8.280000e-45 191.0
34 TraesCS6D01G038800 chr7D 99.057 106 0 1 1 106 19123062 19123166 2.980000e-44 189.0
35 TraesCS6D01G038800 chr7D 97.273 110 2 1 1 109 551609494 551609385 3.850000e-43 185.0
36 TraesCS6D01G038800 chr7D 97.248 109 3 0 1 109 591135265 591135157 3.850000e-43 185.0
37 TraesCS6D01G038800 chr5D 100.000 103 0 0 1 103 476747294 476747396 8.280000e-45 191.0
38 TraesCS6D01G038800 chr5D 99.048 105 1 0 1 105 547264357 547264253 2.980000e-44 189.0
39 TraesCS6D01G038800 chr5D 97.248 109 3 0 1 109 565660864 565660756 3.850000e-43 185.0
40 TraesCS6D01G038800 chr5D 81.068 206 20 4 1400 1586 107622942 107622737 1.820000e-31 147.0
41 TraesCS6D01G038800 chr2A 80.608 263 36 11 1325 1583 690229859 690229608 2.980000e-44 189.0
42 TraesCS6D01G038800 chr2A 73.785 576 107 26 240 804 44796661 44797203 1.070000e-43 187.0
43 TraesCS6D01G038800 chr2A 83.010 206 16 5 1400 1586 669870071 669869866 3.880000e-38 169.0
44 TraesCS6D01G038800 chr4D 74.340 530 94 26 248 772 4936800 4936308 1.070000e-43 187.0
45 TraesCS6D01G038800 chr7B 73.732 552 100 23 264 804 586634417 586634934 8.330000e-40 174.0
46 TraesCS6D01G038800 chr7B 74.576 413 87 14 316 723 612331373 612331772 5.020000e-37 165.0
47 TraesCS6D01G038800 chr7B 72.300 426 94 16 392 804 533310165 533310579 6.630000e-21 111.0
48 TraesCS6D01G038800 chr5A 81.143 175 19 8 1412 1580 705283768 705283934 6.580000e-26 128.0
49 TraesCS6D01G038800 chr5A 74.317 366 60 22 237 596 107444078 107443741 8.510000e-25 124.0


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 TraesCS6D01G038800 chr6D 16158701 16160970 2269 True 4193.0 4193 100.0000 1 2270 1 chr6D.!!$R1 2269
1 TraesCS6D01G038800 chr6D 367747986 367748633 647 True 726.0 726 86.8380 927 1587 1 chr6D.!!$R2 660
2 TraesCS6D01G038800 chrUn 314594079 314596306 2227 True 1502.0 2721 92.7615 100 2270 2 chrUn.!!$R1 2170
3 TraesCS6D01G038800 chrUn 358002660 358003345 685 False 647.0 647 84.4020 924 1580 1 chrUn.!!$F1 656
4 TraesCS6D01G038800 chrUn 370994041 370994584 543 False 388.5 494 94.0505 1764 2270 2 chrUn.!!$F2 506
5 TraesCS6D01G038800 chr6B 27913777 27915985 2208 True 1455.0 2627 92.4100 100 2270 2 chr6B.!!$R3 2170
6 TraesCS6D01G038800 chr6B 508532885 508533385 500 True 274.0 274 77.0090 240 772 1 chr6B.!!$R2 532
7 TraesCS6D01G038800 chr4A 734886412 734887052 640 True 769.0 769 88.2260 927 1580 1 chr4A.!!$R2 653
8 TraesCS6D01G038800 chr3D 51469716 51470362 646 False 741.0 741 87.4240 927 1580 1 chr3D.!!$F2 653
9 TraesCS6D01G038800 chr3A 704116992 704117629 637 False 726.0 726 87.5970 952 1580 1 chr3A.!!$F2 628
10 TraesCS6D01G038800 chr3A 737423630 737424289 659 True 695.0 695 85.8650 927 1583 1 chr3A.!!$R1 656
11 TraesCS6D01G038800 chr7A 393325200 393325705 505 False 254.0 254 76.2520 237 772 1 chr7A.!!$F1 535

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
45 46 0.250858 TAGTCCCGGTTCGTGACTGA 60.251 55.0 17.52 2.93 43.49 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1903 2014 0.321387 TCTTGCTTCTCCTGCAGCAG 60.321 55.0 16.23 16.23 46.55 4.24 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
17 18 2.359478 GCACGAACCGGGACCAAT 60.359 61.111 6.32 0.00 28.17 3.16
18 19 2.686816 GCACGAACCGGGACCAATG 61.687 63.158 6.32 0.00 28.17 2.82
19 20 2.359478 ACGAACCGGGACCAATGC 60.359 61.111 6.32 0.00 0.00 3.56
20 21 2.046314 CGAACCGGGACCAATGCT 60.046 61.111 6.32 0.00 0.00 3.79
21 22 2.106683 CGAACCGGGACCAATGCTC 61.107 63.158 6.32 0.00 0.00 4.26
22 23 1.002624 GAACCGGGACCAATGCTCA 60.003 57.895 6.32 0.00 0.00 4.26
23 24 1.303317 AACCGGGACCAATGCTCAC 60.303 57.895 6.32 0.00 0.00 3.51
24 25 2.063015 AACCGGGACCAATGCTCACA 62.063 55.000 6.32 0.00 0.00 3.58
25 26 1.077501 CCGGGACCAATGCTCACAT 60.078 57.895 0.00 0.00 38.49 3.21
27 28 1.408127 CCGGGACCAATGCTCACATTA 60.408 52.381 0.00 0.00 44.83 1.90
28 29 1.942657 CGGGACCAATGCTCACATTAG 59.057 52.381 0.00 0.00 44.83 1.73
29 30 2.680805 CGGGACCAATGCTCACATTAGT 60.681 50.000 0.00 0.00 44.83 2.24
32 33 2.945668 GACCAATGCTCACATTAGTCCC 59.054 50.000 6.20 0.00 44.37 4.46
33 34 1.942657 CCAATGCTCACATTAGTCCCG 59.057 52.381 0.00 0.00 44.83 5.14
34 35 1.942657 CAATGCTCACATTAGTCCCGG 59.057 52.381 0.00 0.00 44.83 5.73
35 36 1.204146 ATGCTCACATTAGTCCCGGT 58.796 50.000 0.00 0.00 30.07 5.28
36 37 0.981183 TGCTCACATTAGTCCCGGTT 59.019 50.000 0.00 0.00 0.00 4.44
37 38 1.066430 TGCTCACATTAGTCCCGGTTC 60.066 52.381 0.00 0.00 0.00 3.62
38 39 1.922570 CTCACATTAGTCCCGGTTCG 58.077 55.000 0.00 0.00 0.00 3.95
39 40 1.203994 CTCACATTAGTCCCGGTTCGT 59.796 52.381 0.00 0.00 0.00 3.85
40 41 1.067425 TCACATTAGTCCCGGTTCGTG 60.067 52.381 0.00 0.00 0.00 4.35
41 42 1.067425 CACATTAGTCCCGGTTCGTGA 60.067 52.381 0.00 0.00 0.00 4.35
42 43 1.067354 ACATTAGTCCCGGTTCGTGAC 60.067 52.381 0.00 0.00 34.71 3.67
43 44 1.203994 CATTAGTCCCGGTTCGTGACT 59.796 52.381 13.76 13.76 45.32 3.41
44 45 0.599558 TTAGTCCCGGTTCGTGACTG 59.400 55.000 17.52 0.00 43.49 3.51
45 46 0.250858 TAGTCCCGGTTCGTGACTGA 60.251 55.000 17.52 2.93 43.49 3.41
46 47 1.111116 AGTCCCGGTTCGTGACTGAA 61.111 55.000 9.22 0.00 42.28 3.02
47 48 0.942884 GTCCCGGTTCGTGACTGAAC 60.943 60.000 0.00 10.38 45.91 3.18
51 52 3.946907 GTTCGTGACTGAACCGGG 58.053 61.111 6.32 0.00 41.88 5.73
52 53 1.364901 GTTCGTGACTGAACCGGGA 59.635 57.895 6.32 0.00 41.88 5.14
53 54 0.942884 GTTCGTGACTGAACCGGGAC 60.943 60.000 6.32 0.00 41.88 4.46
54 55 1.111116 TTCGTGACTGAACCGGGACT 61.111 55.000 6.32 0.00 0.00 3.85
55 56 0.250858 TCGTGACTGAACCGGGACTA 60.251 55.000 6.32 0.00 0.00 2.59
56 57 0.599558 CGTGACTGAACCGGGACTAA 59.400 55.000 6.32 0.00 0.00 2.24
57 58 1.203994 CGTGACTGAACCGGGACTAAT 59.796 52.381 6.32 0.00 0.00 1.73
58 59 2.618053 GTGACTGAACCGGGACTAATG 58.382 52.381 6.32 0.00 0.00 1.90
59 60 2.028385 GTGACTGAACCGGGACTAATGT 60.028 50.000 6.32 0.00 0.00 2.71
60 61 2.028476 TGACTGAACCGGGACTAATGTG 60.028 50.000 6.32 0.00 0.00 3.21
61 62 2.232941 GACTGAACCGGGACTAATGTGA 59.767 50.000 6.32 0.00 0.00 3.58
62 63 2.635915 ACTGAACCGGGACTAATGTGAA 59.364 45.455 6.32 0.00 0.00 3.18
63 64 3.263425 ACTGAACCGGGACTAATGTGAAT 59.737 43.478 6.32 0.00 0.00 2.57
64 65 4.468510 ACTGAACCGGGACTAATGTGAATA 59.531 41.667 6.32 0.00 0.00 1.75
65 66 5.130477 ACTGAACCGGGACTAATGTGAATAT 59.870 40.000 6.32 0.00 0.00 1.28
66 67 5.996644 TGAACCGGGACTAATGTGAATATT 58.003 37.500 6.32 0.00 0.00 1.28
67 68 5.820423 TGAACCGGGACTAATGTGAATATTG 59.180 40.000 6.32 0.00 0.00 1.90
68 69 4.134563 ACCGGGACTAATGTGAATATTGC 58.865 43.478 6.32 0.00 0.00 3.56
69 70 3.502211 CCGGGACTAATGTGAATATTGCC 59.498 47.826 0.00 0.00 0.00 4.52
70 71 3.502211 CGGGACTAATGTGAATATTGCCC 59.498 47.826 0.00 0.00 0.00 5.36
71 72 4.729868 GGGACTAATGTGAATATTGCCCT 58.270 43.478 0.00 0.00 30.77 5.19
72 73 4.520492 GGGACTAATGTGAATATTGCCCTG 59.480 45.833 0.00 0.00 30.77 4.45
73 74 5.133221 GGACTAATGTGAATATTGCCCTGT 58.867 41.667 0.00 0.00 0.00 4.00
74 75 5.009010 GGACTAATGTGAATATTGCCCTGTG 59.991 44.000 0.00 0.00 0.00 3.66
75 76 5.754782 ACTAATGTGAATATTGCCCTGTGA 58.245 37.500 0.00 0.00 0.00 3.58
76 77 4.989279 AATGTGAATATTGCCCTGTGAC 57.011 40.909 0.00 0.00 0.00 3.67
77 78 2.722094 TGTGAATATTGCCCTGTGACC 58.278 47.619 0.00 0.00 0.00 4.02
78 79 2.040947 TGTGAATATTGCCCTGTGACCA 59.959 45.455 0.00 0.00 0.00 4.02
79 80 3.088532 GTGAATATTGCCCTGTGACCAA 58.911 45.455 0.00 0.00 0.00 3.67
80 81 3.509575 GTGAATATTGCCCTGTGACCAAA 59.490 43.478 0.00 0.00 0.00 3.28
81 82 3.763360 TGAATATTGCCCTGTGACCAAAG 59.237 43.478 0.00 0.00 0.00 2.77
82 83 1.544724 TATTGCCCTGTGACCAAAGC 58.455 50.000 0.00 0.00 0.00 3.51
83 84 1.187567 ATTGCCCTGTGACCAAAGCC 61.188 55.000 0.00 0.00 0.00 4.35
84 85 2.991540 GCCCTGTGACCAAAGCCC 60.992 66.667 0.00 0.00 0.00 5.19
85 86 2.520458 CCCTGTGACCAAAGCCCA 59.480 61.111 0.00 0.00 0.00 5.36
86 87 1.604593 CCCTGTGACCAAAGCCCAG 60.605 63.158 0.00 0.00 0.00 4.45
87 88 1.151450 CCTGTGACCAAAGCCCAGT 59.849 57.895 0.00 0.00 0.00 4.00
88 89 0.468029 CCTGTGACCAAAGCCCAGTT 60.468 55.000 0.00 0.00 0.00 3.16
89 90 1.402787 CTGTGACCAAAGCCCAGTTT 58.597 50.000 0.00 0.00 0.00 2.66
90 91 1.756538 CTGTGACCAAAGCCCAGTTTT 59.243 47.619 0.00 0.00 0.00 2.43
91 92 1.754226 TGTGACCAAAGCCCAGTTTTC 59.246 47.619 0.00 0.00 0.00 2.29
92 93 2.031870 GTGACCAAAGCCCAGTTTTCT 58.968 47.619 0.00 0.00 0.00 2.52
93 94 3.219281 GTGACCAAAGCCCAGTTTTCTA 58.781 45.455 0.00 0.00 0.00 2.10
94 95 3.004419 GTGACCAAAGCCCAGTTTTCTAC 59.996 47.826 0.00 0.00 0.00 2.59
95 96 3.117663 TGACCAAAGCCCAGTTTTCTACT 60.118 43.478 0.00 0.00 37.68 2.57
96 97 4.103469 TGACCAAAGCCCAGTTTTCTACTA 59.897 41.667 0.00 0.00 34.56 1.82
97 98 4.652822 ACCAAAGCCCAGTTTTCTACTAG 58.347 43.478 0.00 0.00 34.56 2.57
98 99 4.104261 ACCAAAGCCCAGTTTTCTACTAGT 59.896 41.667 0.00 0.00 34.56 2.57
109 110 7.307989 CCAGTTTTCTACTAGTGTGGTCAAATG 60.308 40.741 5.39 0.91 34.56 2.32
180 181 1.595993 CGTCTCTCCTCCCAAGCGAA 61.596 60.000 0.00 0.00 0.00 4.70
326 328 3.753294 AGGATTGTGTTCTGTTCGAGT 57.247 42.857 0.00 0.00 0.00 4.18
387 389 2.443016 CCTGCCTAGAGCCCGTCT 60.443 66.667 0.00 0.00 42.71 4.18
426 428 2.615227 ATCGAAGGGCATGTGGAGGC 62.615 60.000 0.00 0.00 0.00 4.70
446 448 1.001269 TGTCTCCGGTGGATCTCGT 60.001 57.895 0.00 0.00 0.00 4.18
447 449 0.253894 TGTCTCCGGTGGATCTCGTA 59.746 55.000 0.00 0.00 0.00 3.43
474 476 4.774660 TGGTTAGTGGTTGTCTTTGGTA 57.225 40.909 0.00 0.00 0.00 3.25
596 598 2.953466 TGCGTTAGTCCTATGTGGTC 57.047 50.000 0.00 0.00 37.07 4.02
606 608 6.287589 AGTCCTATGTGGTCTTAAGTCTTG 57.712 41.667 1.63 0.00 37.07 3.02
607 609 6.017192 AGTCCTATGTGGTCTTAAGTCTTGA 58.983 40.000 1.63 0.00 37.07 3.02
619 621 5.518847 TCTTAAGTCTTGACACGACAACTTG 59.481 40.000 13.90 1.59 33.89 3.16
723 726 3.057104 TGATTGTAATCGTCGTCAGGTGT 60.057 43.478 0.00 0.00 38.26 4.16
724 727 2.341318 TGTAATCGTCGTCAGGTGTG 57.659 50.000 0.00 0.00 0.00 3.82
733 736 1.443872 GTCAGGTGTGGTCTACGCG 60.444 63.158 3.53 3.53 40.74 6.01
854 868 2.227388 CAGACAAGGCAAACACCATCTC 59.773 50.000 0.00 0.00 0.00 2.75
859 875 1.707427 AGGCAAACACCATCTCCTCTT 59.293 47.619 0.00 0.00 0.00 2.85
918 940 7.176515 TCTCTCTCTTGGATGATAGCAATCTAC 59.823 40.741 0.00 0.00 32.93 2.59
921 943 3.961480 TGGATGATAGCAATCTACGGG 57.039 47.619 0.00 0.00 32.93 5.28
922 944 3.506398 TGGATGATAGCAATCTACGGGA 58.494 45.455 0.00 0.00 32.93 5.14
923 945 3.901222 TGGATGATAGCAATCTACGGGAA 59.099 43.478 0.00 0.00 32.93 3.97
924 946 4.532126 TGGATGATAGCAATCTACGGGAAT 59.468 41.667 0.00 0.00 32.93 3.01
925 947 4.872691 GGATGATAGCAATCTACGGGAATG 59.127 45.833 0.00 0.00 32.93 2.67
950 972 6.651086 ACTCATCTGATGTTGATCTTGATGT 58.349 36.000 16.66 0.00 39.10 3.06
1175 1197 6.989169 AGGTCAACTATGTTGCAAGATAGATC 59.011 38.462 36.81 24.85 36.19 2.75
1229 1251 6.903516 AGGATATCTTGGACAATGTTGATCA 58.096 36.000 2.05 0.00 0.00 2.92
1242 1265 7.005902 ACAATGTTGATCATGATATTGCCCTA 58.994 34.615 21.14 0.80 36.81 3.53
1425 1450 9.669353 GCATTGTCCAACAATTATTATAGTCAG 57.331 33.333 2.65 0.00 45.80 3.51
1465 1504 4.629200 GTGTGGTTGAAAGTTGCAAATGAA 59.371 37.500 0.00 0.00 0.00 2.57
1660 1771 2.284331 TAGGCCCCGAACAGCAGA 60.284 61.111 0.00 0.00 0.00 4.26
1669 1780 1.136147 GAACAGCAGAGCATTGCCG 59.864 57.895 4.70 1.94 45.18 5.69
1674 1785 2.550101 GCAGAGCATTGCCGGATCC 61.550 63.158 5.05 0.00 38.13 3.36
1675 1786 1.895707 CAGAGCATTGCCGGATCCC 60.896 63.158 5.05 0.00 0.00 3.85
1683 1794 2.590859 GCCGGATCCCGCTTTACC 60.591 66.667 16.79 0.00 46.86 2.85
1691 1802 1.804326 CCCGCTTTACCGACGACTG 60.804 63.158 0.00 0.00 0.00 3.51
1707 1818 2.678934 TGGAGGGGACGGACGAAG 60.679 66.667 0.00 0.00 0.00 3.79
1710 1821 4.698625 AGGGGACGGACGAAGCCT 62.699 66.667 0.00 0.00 0.00 4.58
1730 1841 0.554305 TGGATCCAGCATCAGCCAAT 59.446 50.000 11.44 0.00 43.56 3.16
1738 1849 0.750546 GCATCAGCCAATGGAGCTCA 60.751 55.000 17.19 1.87 38.95 4.26
1751 1862 2.511600 GCTCACCGCGCCTACATT 60.512 61.111 0.00 0.00 0.00 2.71
1769 1880 2.941453 TTTGCTACTAGCGACTGGAG 57.059 50.000 3.59 0.00 46.26 3.86
1786 1897 1.273098 GGAGGAGGTGGGTCTGTAAGA 60.273 57.143 0.00 0.00 43.69 2.10
1804 1915 9.534565 TCTGTAAGATATAAGCTTGATTGTGAC 57.465 33.333 9.86 0.70 38.67 3.67
1887 1998 3.734902 GCAGGATGGGTTTTATCTTTGCG 60.735 47.826 0.00 0.00 35.86 4.85
1888 1999 3.023832 AGGATGGGTTTTATCTTTGCGG 58.976 45.455 0.00 0.00 0.00 5.69
1893 2004 2.094390 GGGTTTTATCTTTGCGGGGTTC 60.094 50.000 0.00 0.00 0.00 3.62
1903 2014 2.396590 TGCGGGGTTCTCTAATGTTC 57.603 50.000 0.00 0.00 0.00 3.18
1912 2023 3.257469 TCTCTAATGTTCTGCTGCAGG 57.743 47.619 27.79 11.18 31.51 4.85
1971 2084 4.511826 CGCACCTACAACTTTCTCTTTTCT 59.488 41.667 0.00 0.00 0.00 2.52
1973 2086 6.202226 GCACCTACAACTTTCTCTTTTCTTG 58.798 40.000 0.00 0.00 0.00 3.02
1974 2087 6.038271 GCACCTACAACTTTCTCTTTTCTTGA 59.962 38.462 0.00 0.00 0.00 3.02
2012 2125 7.606456 TGTCTATTTAGTTTGTGCTAAGGAAGG 59.394 37.037 0.00 0.00 33.16 3.46
2050 2163 5.070313 TGCTTTATCTTTTCTGTGGGCTTTT 59.930 36.000 0.00 0.00 0.00 2.27
2070 2183 7.062956 GGCTTTTATACTTTGTTTGGCACATAC 59.937 37.037 0.00 0.00 40.65 2.39
2094 2240 5.121811 CAAAATCTAGGGATGGTCAGTGAG 58.878 45.833 0.00 0.00 31.75 3.51
2109 2255 3.152341 CAGTGAGTGCCTTTTCCTTCAT 58.848 45.455 0.00 0.00 0.00 2.57
2113 2259 4.633565 GTGAGTGCCTTTTCCTTCATAGAG 59.366 45.833 0.00 0.00 0.00 2.43
2136 2282 3.050275 GGCTGCTGTGGGTCGTTC 61.050 66.667 0.00 0.00 0.00 3.95
2150 2296 1.483827 GTCGTTCTTTAGGGTAGGGGG 59.516 57.143 0.00 0.00 0.00 5.40
2186 2332 4.401925 CTGGTTCCTCAACTTCCTTTGAT 58.598 43.478 0.00 0.00 34.96 2.57
2219 2369 3.897505 CCCTGGAGACCAAGTTTTTGATT 59.102 43.478 0.00 0.00 36.36 2.57
2238 2388 5.481105 TGATTGATCAAAACATCCAAAGGC 58.519 37.500 13.09 0.00 33.08 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.359478 ATTGGTCCCGGTTCGTGC 60.359 61.111 0.00 0.00 0.00 5.34
1 2 2.686816 GCATTGGTCCCGGTTCGTG 61.687 63.158 0.00 0.00 0.00 4.35
3 4 2.046314 AGCATTGGTCCCGGTTCG 60.046 61.111 0.00 0.00 0.00 3.95
4 5 1.002624 TGAGCATTGGTCCCGGTTC 60.003 57.895 12.99 0.00 0.00 3.62
5 6 1.303317 GTGAGCATTGGTCCCGGTT 60.303 57.895 12.99 0.00 0.00 4.44
6 7 1.852157 ATGTGAGCATTGGTCCCGGT 61.852 55.000 12.99 0.00 29.54 5.28
7 8 0.680921 AATGTGAGCATTGGTCCCGG 60.681 55.000 12.99 0.00 43.12 5.73
8 9 1.942657 CTAATGTGAGCATTGGTCCCG 59.057 52.381 12.99 0.00 44.32 5.14
13 14 1.942657 CGGGACTAATGTGAGCATTGG 59.057 52.381 3.39 3.10 44.32 3.16
14 15 1.942657 CCGGGACTAATGTGAGCATTG 59.057 52.381 0.00 0.00 44.32 2.82
15 16 1.559682 ACCGGGACTAATGTGAGCATT 59.440 47.619 6.32 0.00 46.14 3.56
16 17 1.204146 ACCGGGACTAATGTGAGCAT 58.796 50.000 6.32 0.00 36.80 3.79
17 18 0.981183 AACCGGGACTAATGTGAGCA 59.019 50.000 6.32 0.00 0.00 4.26
18 19 1.653151 GAACCGGGACTAATGTGAGC 58.347 55.000 6.32 0.00 0.00 4.26
19 20 1.203994 ACGAACCGGGACTAATGTGAG 59.796 52.381 6.32 0.00 0.00 3.51
20 21 1.067425 CACGAACCGGGACTAATGTGA 60.067 52.381 6.32 0.00 28.17 3.58
21 22 1.067425 TCACGAACCGGGACTAATGTG 60.067 52.381 6.32 4.66 32.99 3.21
22 23 1.259609 TCACGAACCGGGACTAATGT 58.740 50.000 6.32 0.00 32.99 2.71
29 30 1.364901 GTTCAGTCACGAACCGGGA 59.635 57.895 6.32 0.00 39.52 5.14
30 31 3.946907 GTTCAGTCACGAACCGGG 58.053 61.111 6.32 0.00 39.52 5.73
34 35 0.942884 GTCCCGGTTCAGTCACGAAC 60.943 60.000 0.00 4.51 43.75 3.95
35 36 1.111116 AGTCCCGGTTCAGTCACGAA 61.111 55.000 0.00 0.00 0.00 3.85
36 37 0.250858 TAGTCCCGGTTCAGTCACGA 60.251 55.000 0.00 0.00 0.00 4.35
37 38 0.599558 TTAGTCCCGGTTCAGTCACG 59.400 55.000 0.00 0.00 0.00 4.35
38 39 2.028385 ACATTAGTCCCGGTTCAGTCAC 60.028 50.000 0.00 0.00 0.00 3.67
39 40 2.028476 CACATTAGTCCCGGTTCAGTCA 60.028 50.000 0.00 0.00 0.00 3.41
40 41 2.232941 TCACATTAGTCCCGGTTCAGTC 59.767 50.000 0.00 0.00 0.00 3.51
41 42 2.253610 TCACATTAGTCCCGGTTCAGT 58.746 47.619 0.00 0.00 0.00 3.41
42 43 3.328382 TTCACATTAGTCCCGGTTCAG 57.672 47.619 0.00 0.00 0.00 3.02
43 44 3.992943 ATTCACATTAGTCCCGGTTCA 57.007 42.857 0.00 0.00 0.00 3.18
44 45 5.277828 GCAATATTCACATTAGTCCCGGTTC 60.278 44.000 0.00 0.00 0.00 3.62
45 46 4.578928 GCAATATTCACATTAGTCCCGGTT 59.421 41.667 0.00 0.00 0.00 4.44
46 47 4.134563 GCAATATTCACATTAGTCCCGGT 58.865 43.478 0.00 0.00 0.00 5.28
47 48 3.502211 GGCAATATTCACATTAGTCCCGG 59.498 47.826 0.00 0.00 0.00 5.73
48 49 3.502211 GGGCAATATTCACATTAGTCCCG 59.498 47.826 0.00 0.00 0.00 5.14
49 50 4.520492 CAGGGCAATATTCACATTAGTCCC 59.480 45.833 0.00 0.00 0.00 4.46
50 51 5.009010 CACAGGGCAATATTCACATTAGTCC 59.991 44.000 0.00 0.00 0.00 3.85
51 52 5.822519 TCACAGGGCAATATTCACATTAGTC 59.177 40.000 0.00 0.00 0.00 2.59
52 53 5.590259 GTCACAGGGCAATATTCACATTAGT 59.410 40.000 0.00 0.00 0.00 2.24
53 54 5.009010 GGTCACAGGGCAATATTCACATTAG 59.991 44.000 0.00 0.00 0.00 1.73
54 55 4.887071 GGTCACAGGGCAATATTCACATTA 59.113 41.667 0.00 0.00 0.00 1.90
55 56 3.701040 GGTCACAGGGCAATATTCACATT 59.299 43.478 0.00 0.00 0.00 2.71
56 57 3.290710 GGTCACAGGGCAATATTCACAT 58.709 45.455 0.00 0.00 0.00 3.21
57 58 2.040947 TGGTCACAGGGCAATATTCACA 59.959 45.455 0.00 0.00 0.00 3.58
58 59 2.722094 TGGTCACAGGGCAATATTCAC 58.278 47.619 0.00 0.00 0.00 3.18
59 60 3.448093 TTGGTCACAGGGCAATATTCA 57.552 42.857 0.00 0.00 0.00 2.57
60 61 3.429410 GCTTTGGTCACAGGGCAATATTC 60.429 47.826 0.00 0.00 0.00 1.75
61 62 2.497273 GCTTTGGTCACAGGGCAATATT 59.503 45.455 0.00 0.00 0.00 1.28
62 63 2.102578 GCTTTGGTCACAGGGCAATAT 58.897 47.619 0.00 0.00 0.00 1.28
63 64 1.544724 GCTTTGGTCACAGGGCAATA 58.455 50.000 0.00 0.00 0.00 1.90
64 65 1.187567 GGCTTTGGTCACAGGGCAAT 61.188 55.000 0.00 0.00 0.00 3.56
65 66 1.832167 GGCTTTGGTCACAGGGCAA 60.832 57.895 0.00 0.00 0.00 4.52
66 67 2.203480 GGCTTTGGTCACAGGGCA 60.203 61.111 0.00 0.00 0.00 5.36
67 68 2.991540 GGGCTTTGGTCACAGGGC 60.992 66.667 0.00 0.00 0.00 5.19
68 69 1.604593 CTGGGCTTTGGTCACAGGG 60.605 63.158 0.00 0.00 0.00 4.45
69 70 0.468029 AACTGGGCTTTGGTCACAGG 60.468 55.000 0.00 0.00 33.63 4.00
70 71 1.402787 AAACTGGGCTTTGGTCACAG 58.597 50.000 0.00 0.00 35.40 3.66
71 72 1.754226 GAAAACTGGGCTTTGGTCACA 59.246 47.619 0.00 0.00 0.00 3.58
72 73 2.031870 AGAAAACTGGGCTTTGGTCAC 58.968 47.619 0.00 0.00 0.00 3.67
73 74 2.452600 AGAAAACTGGGCTTTGGTCA 57.547 45.000 0.00 0.00 0.00 4.02
74 75 3.487372 AGTAGAAAACTGGGCTTTGGTC 58.513 45.455 0.00 0.00 36.93 4.02
75 76 3.595190 AGTAGAAAACTGGGCTTTGGT 57.405 42.857 0.00 0.00 36.93 3.67
76 77 4.455877 CACTAGTAGAAAACTGGGCTTTGG 59.544 45.833 3.59 0.00 40.86 3.28
77 78 5.049405 CACACTAGTAGAAAACTGGGCTTTG 60.049 44.000 3.59 0.00 40.86 2.77
78 79 5.063880 CACACTAGTAGAAAACTGGGCTTT 58.936 41.667 3.59 0.00 40.86 3.51
79 80 4.505039 CCACACTAGTAGAAAACTGGGCTT 60.505 45.833 3.59 0.00 40.86 4.35
80 81 3.008049 CCACACTAGTAGAAAACTGGGCT 59.992 47.826 3.59 0.00 40.86 5.19
81 82 3.244457 ACCACACTAGTAGAAAACTGGGC 60.244 47.826 3.59 0.00 40.86 5.36
82 83 4.039973 TGACCACACTAGTAGAAAACTGGG 59.960 45.833 3.59 0.00 40.86 4.45
83 84 5.209818 TGACCACACTAGTAGAAAACTGG 57.790 43.478 3.59 3.47 42.21 4.00
84 85 7.576236 CATTTGACCACACTAGTAGAAAACTG 58.424 38.462 3.59 0.00 39.39 3.16
85 86 6.204882 GCATTTGACCACACTAGTAGAAAACT 59.795 38.462 3.59 0.00 42.62 2.66
86 87 6.371389 GCATTTGACCACACTAGTAGAAAAC 58.629 40.000 3.59 0.00 0.00 2.43
87 88 5.472137 GGCATTTGACCACACTAGTAGAAAA 59.528 40.000 3.59 0.00 0.00 2.29
88 89 5.001232 GGCATTTGACCACACTAGTAGAAA 58.999 41.667 3.59 0.00 0.00 2.52
89 90 4.041075 TGGCATTTGACCACACTAGTAGAA 59.959 41.667 3.59 0.00 30.29 2.10
90 91 3.580895 TGGCATTTGACCACACTAGTAGA 59.419 43.478 3.59 0.00 30.29 2.59
91 92 3.937814 TGGCATTTGACCACACTAGTAG 58.062 45.455 0.00 0.00 30.29 2.57
92 93 4.359434 TTGGCATTTGACCACACTAGTA 57.641 40.909 0.00 0.00 36.76 1.82
93 94 2.949177 TGGCATTTGACCACACTAGT 57.051 45.000 0.00 0.00 30.29 2.57
94 95 4.022068 ACATTTGGCATTTGACCACACTAG 60.022 41.667 4.41 0.00 36.76 2.57
95 96 3.894427 ACATTTGGCATTTGACCACACTA 59.106 39.130 4.41 0.00 36.76 2.74
96 97 2.699846 ACATTTGGCATTTGACCACACT 59.300 40.909 4.41 0.00 36.76 3.55
97 98 3.110447 ACATTTGGCATTTGACCACAC 57.890 42.857 4.41 0.00 36.76 3.82
98 99 3.726607 GAACATTTGGCATTTGACCACA 58.273 40.909 4.41 0.00 36.76 4.17
109 110 3.428862 CCAATAAGTCCCGAACATTTGGC 60.429 47.826 0.00 0.00 31.17 4.52
152 153 1.341778 GGAGGAGAGACGAAGGGGTAA 60.342 57.143 0.00 0.00 0.00 2.85
180 181 2.264794 GGAACCCTCGTCGCATGT 59.735 61.111 0.00 0.00 0.00 3.21
217 218 1.413767 CGAGACGAGGAACATTGGCG 61.414 60.000 0.00 0.00 0.00 5.69
387 389 5.105269 TCGATTATGCTAAACACACCACCTA 60.105 40.000 0.00 0.00 0.00 3.08
426 428 1.433879 GAGATCCACCGGAGACACG 59.566 63.158 9.46 0.00 34.05 4.49
446 448 5.836024 AGACAACCACTAACCAAATCCTA 57.164 39.130 0.00 0.00 0.00 2.94
447 449 4.724279 AGACAACCACTAACCAAATCCT 57.276 40.909 0.00 0.00 0.00 3.24
474 476 1.254284 GGGCGGATCCGATCAGATCT 61.254 60.000 37.64 0.00 42.02 2.75
596 598 5.728255 CAAGTTGTCGTGTCAAGACTTAAG 58.272 41.667 17.97 0.00 39.24 1.85
606 608 1.258982 CAGTCAGCAAGTTGTCGTGTC 59.741 52.381 4.48 0.00 0.00 3.67
607 609 1.290203 CAGTCAGCAAGTTGTCGTGT 58.710 50.000 4.48 0.00 0.00 4.49
619 621 6.787085 AACTTGTTGTAATAGACAGTCAGC 57.213 37.500 2.66 0.00 39.88 4.26
660 662 4.899239 GCCGTCATCAGCCCTCCG 62.899 72.222 0.00 0.00 0.00 4.63
703 706 3.250744 CACACCTGACGACGATTACAAT 58.749 45.455 0.00 0.00 0.00 2.71
709 712 0.894184 AGACCACACCTGACGACGAT 60.894 55.000 0.00 0.00 0.00 3.73
723 726 0.963856 ACATCCAGACGCGTAGACCA 60.964 55.000 13.97 0.00 0.00 4.02
724 727 1.019673 TACATCCAGACGCGTAGACC 58.980 55.000 13.97 0.00 0.00 3.85
854 868 3.513119 TGACCAGTCATGAGAGAAAGAGG 59.487 47.826 0.00 0.00 34.14 3.69
859 875 2.972021 TGGTTGACCAGTCATGAGAGAA 59.028 45.455 0.00 0.00 42.01 2.87
918 940 3.465742 ACATCAGATGAGTCATTCCCG 57.534 47.619 17.81 0.00 0.00 5.14
921 943 7.494952 TCAAGATCAACATCAGATGAGTCATTC 59.505 37.037 17.81 6.16 29.57 2.67
922 944 7.336396 TCAAGATCAACATCAGATGAGTCATT 58.664 34.615 17.81 0.00 29.57 2.57
923 945 6.885922 TCAAGATCAACATCAGATGAGTCAT 58.114 36.000 17.81 4.98 29.57 3.06
924 946 6.290294 TCAAGATCAACATCAGATGAGTCA 57.710 37.500 17.81 0.00 29.57 3.41
925 947 6.762187 ACATCAAGATCAACATCAGATGAGTC 59.238 38.462 17.81 8.73 41.66 3.36
950 972 6.817765 ACACTTTCAACTCAGAGACAAAAA 57.182 33.333 3.79 0.00 0.00 1.94
994 1016 2.094659 CGAGCGCCGACATCAAACT 61.095 57.895 2.29 0.00 41.76 2.66
1145 1167 4.829064 TGCAACATAGTTGACCTCAAAC 57.171 40.909 13.58 0.00 37.63 2.93
1175 1197 2.744787 GCACATAGCCAAGTCATTCG 57.255 50.000 0.00 0.00 37.23 3.34
1195 1217 4.450419 GTCCAAGATATCCTTCTCAATGCG 59.550 45.833 0.00 0.00 31.42 4.73
1229 1251 6.324512 TGCAAAGTCATTTAGGGCAATATCAT 59.675 34.615 0.00 0.00 0.00 2.45
1242 1265 5.591099 ACGTTTCTTGATGCAAAGTCATTT 58.409 33.333 0.00 0.00 0.00 2.32
1378 1403 9.528018 CAATGCCGTATTACCAAAGAAATAATT 57.472 29.630 0.00 0.00 0.00 1.40
1425 1450 7.173218 TCAACCACACATCTTTAGTTTGAGATC 59.827 37.037 0.00 0.00 30.43 2.75
1530 1640 1.080093 GAACTCGACGACATGGGCA 60.080 57.895 0.00 0.00 0.00 5.36
1610 1721 1.299850 GGAAGTGGCAACCAAACGC 60.300 57.895 0.00 0.00 34.18 4.84
1612 1723 1.299850 GCGGAAGTGGCAACCAAAC 60.300 57.895 0.00 0.00 34.18 2.93
1643 1754 2.284331 TCTGCTGTTCGGGGCCTA 60.284 61.111 0.84 0.00 0.00 3.93
1669 1780 1.590792 CGTCGGTAAAGCGGGATCC 60.591 63.158 1.92 1.92 0.00 3.36
1674 1785 1.804326 CCAGTCGTCGGTAAAGCGG 60.804 63.158 1.34 0.00 0.00 5.52
1675 1786 0.797249 CTCCAGTCGTCGGTAAAGCG 60.797 60.000 0.00 0.00 0.00 4.68
1683 1794 3.812019 CGTCCCCTCCAGTCGTCG 61.812 72.222 0.00 0.00 0.00 5.12
1691 1802 4.144703 GCTTCGTCCGTCCCCTCC 62.145 72.222 0.00 0.00 0.00 4.30
1707 1818 1.453762 GCTGATGCTGGATCCAAGGC 61.454 60.000 17.00 17.04 36.03 4.35
1710 1821 0.332293 TTGGCTGATGCTGGATCCAA 59.668 50.000 17.00 1.47 39.59 3.53
1738 1849 1.087771 GTAGCAAATGTAGGCGCGGT 61.088 55.000 8.83 0.00 34.54 5.68
1751 1862 1.103803 CCTCCAGTCGCTAGTAGCAA 58.896 55.000 21.70 0.00 42.58 3.91
1769 1880 5.279556 GCTTATATCTTACAGACCCACCTCC 60.280 48.000 0.00 0.00 0.00 4.30
1786 1897 4.450976 TGGCGTCACAATCAAGCTTATAT 58.549 39.130 0.00 0.00 0.00 0.86
1870 1981 2.107366 CCCCGCAAAGATAAAACCCAT 58.893 47.619 0.00 0.00 0.00 4.00
1871 1982 1.203075 ACCCCGCAAAGATAAAACCCA 60.203 47.619 0.00 0.00 0.00 4.51
1873 1984 2.823747 AGAACCCCGCAAAGATAAAACC 59.176 45.455 0.00 0.00 0.00 3.27
1887 1998 3.274288 CAGCAGAACATTAGAGAACCCC 58.726 50.000 0.00 0.00 0.00 4.95
1888 1999 2.680339 GCAGCAGAACATTAGAGAACCC 59.320 50.000 0.00 0.00 0.00 4.11
1893 2004 3.118847 TCTCCTGCAGCAGAACATTAGAG 60.119 47.826 24.90 18.17 32.44 2.43
1903 2014 0.321387 TCTTGCTTCTCCTGCAGCAG 60.321 55.000 16.23 16.23 46.55 4.24
1912 2023 3.054802 TGGATCCTTTCCTCTTGCTTCTC 60.055 47.826 14.23 0.00 45.68 2.87
1971 2084 9.023962 ACTAAATAGACAAAATCTGCCATTCAA 57.976 29.630 0.00 0.00 38.49 2.69
1973 2086 9.860898 AAACTAAATAGACAAAATCTGCCATTC 57.139 29.630 0.00 0.00 38.49 2.67
1974 2087 9.643693 CAAACTAAATAGACAAAATCTGCCATT 57.356 29.630 0.00 0.00 38.49 3.16
2012 2125 0.533951 AAAGCAAGGCCAGCTAATGC 59.466 50.000 21.22 13.02 42.53 3.56
2070 2183 4.080356 TCACTGACCATCCCTAGATTTTGG 60.080 45.833 0.00 0.00 0.00 3.28
2094 2240 6.575162 TTTTCTCTATGAAGGAAAAGGCAC 57.425 37.500 0.00 0.00 35.10 5.01
2109 2255 2.553028 CCCACAGCAGCCTTTTTCTCTA 60.553 50.000 0.00 0.00 0.00 2.43
2113 2259 0.315251 GACCCACAGCAGCCTTTTTC 59.685 55.000 0.00 0.00 0.00 2.29
2136 2282 1.353394 CCCTGCCCCCTACCCTAAAG 61.353 65.000 0.00 0.00 0.00 1.85
2150 2296 2.677875 CCAGGTTCCTTGCCCTGC 60.678 66.667 0.00 0.00 45.68 4.85
2186 2332 3.927322 TGGTCTCCAGGGGCTACTATATA 59.073 47.826 0.00 0.00 0.00 0.86
2219 2369 3.258872 CAGGCCTTTGGATGTTTTGATCA 59.741 43.478 0.00 0.00 0.00 2.92


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

AutoCloner maintained by Alex Coulton.