Multiple sequence alignment - TraesCS2A01G324600

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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 TraesCS2A01G324600 chr2A 100.000 2714 0 0 1 2714 554576170 554578883 0.000000e+00 5012.0
1 TraesCS2A01G324600 chr2A 92.374 813 51 11 615 1423 460832093 460831288 0.000000e+00 1147.0
2 TraesCS2A01G324600 chr2A 92.227 759 55 4 1957 2713 522931922 522931166 0.000000e+00 1072.0
3 TraesCS2A01G324600 chr2A 89.359 827 78 10 1890 2712 261616299 261615479 0.000000e+00 1031.0
4 TraesCS2A01G324600 chr2A 89.010 828 81 10 1890 2713 261624179 261623358 0.000000e+00 1016.0
5 TraesCS2A01G324600 chr2A 89.418 567 51 9 999 1561 178416540 178417101 0.000000e+00 706.0
6 TraesCS2A01G324600 chr2A 95.489 399 14 4 82 479 551853218 551853613 3.810000e-178 634.0
7 TraesCS2A01G324600 chr2A 94.236 399 21 2 82 479 551845349 551845746 2.310000e-170 608.0
8 TraesCS2A01G324600 chr2A 91.083 157 11 3 846 1001 641657692 641657846 2.740000e-50 209.0
9 TraesCS2A01G324600 chr2A 87.640 178 13 4 1557 1734 178422806 178422974 5.930000e-47 198.0
10 TraesCS2A01G324600 chr2A 92.373 118 8 1 473 590 304841503 304841387 1.670000e-37 167.0
11 TraesCS2A01G324600 chr2A 92.405 79 3 3 1 78 87122645 87122569 2.860000e-20 110.0
12 TraesCS2A01G324600 chr2A 92.308 78 3 3 1 77 224332209 224332134 1.030000e-19 108.0
13 TraesCS2A01G324600 chr2A 89.744 78 4 4 1 77 166451605 166451679 2.220000e-16 97.1
14 TraesCS2A01G324600 chr2A 89.474 76 5 3 1 75 224396913 224396840 2.880000e-15 93.5
15 TraesCS2A01G324600 chr2A 88.462 78 5 4 1 77 166444023 166444097 1.030000e-14 91.6
16 TraesCS2A01G324600 chr3A 92.729 1788 85 16 104 1862 631462283 631464054 0.000000e+00 2540.0
17 TraesCS2A01G324600 chr3A 90.085 827 70 9 1890 2713 349002628 349001811 0.000000e+00 1062.0
18 TraesCS2A01G324600 chr3A 89.734 828 73 9 1890 2713 189837529 189836710 0.000000e+00 1048.0
19 TraesCS2A01G324600 chr3A 89.734 828 74 8 1890 2713 189845284 189844464 0.000000e+00 1048.0
20 TraesCS2A01G324600 chr3A 95.806 453 15 4 28 479 353636384 353635935 0.000000e+00 728.0
21 TraesCS2A01G324600 chr3A 95.238 399 16 3 82 479 169890294 169890690 1.770000e-176 628.0
22 TraesCS2A01G324600 chr3A 94.987 399 18 2 82 479 169898185 169898582 2.290000e-175 625.0
23 TraesCS2A01G324600 chr3A 95.312 128 6 0 458 585 94350239 94350366 1.270000e-48 204.0
24 TraesCS2A01G324600 chr3A 92.086 139 10 1 453 591 500266142 500266279 7.670000e-46 195.0
25 TraesCS2A01G324600 chr7A 94.577 1254 64 4 614 1865 286200859 286202110 0.000000e+00 1936.0
26 TraesCS2A01G324600 chr7A 93.840 1250 74 3 614 1861 286192534 286193782 0.000000e+00 1879.0
27 TraesCS2A01G324600 chr7A 93.229 827 51 5 1890 2713 481282476 481281652 0.000000e+00 1212.0
28 TraesCS2A01G324600 chr7A 92.874 828 53 6 1890 2713 481274448 481273623 0.000000e+00 1197.0
29 TraesCS2A01G324600 chr7A 91.288 815 57 12 612 1423 321665171 321665974 0.000000e+00 1099.0
30 TraesCS2A01G324600 chr7A 89.766 811 71 8 615 1423 420967819 420967019 0.000000e+00 1027.0
31 TraesCS2A01G324600 chr7A 94.486 399 20 2 82 479 214292868 214293265 4.970000e-172 614.0
32 TraesCS2A01G324600 chr7A 94.208 259 14 1 1605 1862 384112801 384113059 7.040000e-106 394.0
33 TraesCS2A01G324600 chr7A 74.603 378 54 33 2 345 390080615 390080984 7.890000e-26 128.0
34 TraesCS2A01G324600 chr7A 88.462 78 5 4 1 77 301854447 301854373 1.030000e-14 91.6
35 TraesCS2A01G324600 chr7A 88.312 77 7 2 1 77 301860360 301860286 1.030000e-14 91.6
36 TraesCS2A01G324600 chr7A 91.304 69 3 3 525 591 338692283 338692216 1.030000e-14 91.6
37 TraesCS2A01G324600 chr7A 85.556 90 7 5 1 89 379769181 379769097 3.720000e-14 89.8
38 TraesCS2A01G324600 chr7A 85.556 90 7 5 1 89 379777160 379777076 3.720000e-14 89.8
39 TraesCS2A01G324600 chr1A 93.365 1251 80 3 614 1862 116630611 116631860 0.000000e+00 1847.0
40 TraesCS2A01G324600 chr1A 93.791 1224 73 3 640 1861 116638927 116640149 0.000000e+00 1836.0
41 TraesCS2A01G324600 chr1A 92.083 821 47 10 1895 2713 458577510 458576706 0.000000e+00 1140.0
42 TraesCS2A01G324600 chr1A 91.521 743 58 5 996 1734 243660485 243661226 0.000000e+00 1018.0
43 TraesCS2A01G324600 chr1A 93.197 147 8 2 613 757 474637416 474637270 5.890000e-52 215.0
44 TraesCS2A01G324600 chr4A 95.431 394 15 3 88 479 193208737 193208345 2.290000e-175 625.0
45 TraesCS2A01G324600 chr4A 94.924 394 17 3 88 479 193200715 193200323 4.970000e-172 614.0
46 TraesCS2A01G324600 chr4A 94.250 400 19 4 82 479 340482611 340483008 2.310000e-170 608.0
47 TraesCS2A01G324600 chr4A 90.446 157 13 2 846 1001 330899910 330899755 3.540000e-49 206.0
48 TraesCS2A01G324600 chr6A 94.981 259 12 1 1605 1862 55911329 55911587 3.250000e-109 405.0
49 TraesCS2A01G324600 chr6A 94.203 138 8 0 463 600 317834711 317834574 7.610000e-51 211.0
50 TraesCS2A01G324600 chr5A 94.208 259 14 1 1605 1862 310382871 310382613 7.040000e-106 394.0
51 TraesCS2A01G324600 chr5A 88.235 68 5 3 479 544 136841769 136841703 8.060000e-11 78.7


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 TraesCS2A01G324600 chr2A 554576170 554578883 2713 False 5012 5012 100.000 1 2714 1 chr2A.!!$F7 2713
1 TraesCS2A01G324600 chr2A 460831288 460832093 805 True 1147 1147 92.374 615 1423 1 chr2A.!!$R7 808
2 TraesCS2A01G324600 chr2A 522931166 522931922 756 True 1072 1072 92.227 1957 2713 1 chr2A.!!$R8 756
3 TraesCS2A01G324600 chr2A 261615479 261616299 820 True 1031 1031 89.359 1890 2712 1 chr2A.!!$R4 822
4 TraesCS2A01G324600 chr2A 261623358 261624179 821 True 1016 1016 89.010 1890 2713 1 chr2A.!!$R5 823
5 TraesCS2A01G324600 chr2A 178416540 178417101 561 False 706 706 89.418 999 1561 1 chr2A.!!$F3 562
6 TraesCS2A01G324600 chr3A 631462283 631464054 1771 False 2540 2540 92.729 104 1862 1 chr3A.!!$F5 1758
7 TraesCS2A01G324600 chr3A 349001811 349002628 817 True 1062 1062 90.085 1890 2713 1 chr3A.!!$R3 823
8 TraesCS2A01G324600 chr3A 189836710 189837529 819 True 1048 1048 89.734 1890 2713 1 chr3A.!!$R1 823
9 TraesCS2A01G324600 chr3A 189844464 189845284 820 True 1048 1048 89.734 1890 2713 1 chr3A.!!$R2 823
10 TraesCS2A01G324600 chr7A 286200859 286202110 1251 False 1936 1936 94.577 614 1865 1 chr7A.!!$F3 1251
11 TraesCS2A01G324600 chr7A 286192534 286193782 1248 False 1879 1879 93.840 614 1861 1 chr7A.!!$F2 1247
12 TraesCS2A01G324600 chr7A 481281652 481282476 824 True 1212 1212 93.229 1890 2713 1 chr7A.!!$R8 823
13 TraesCS2A01G324600 chr7A 481273623 481274448 825 True 1197 1197 92.874 1890 2713 1 chr7A.!!$R7 823
14 TraesCS2A01G324600 chr7A 321665171 321665974 803 False 1099 1099 91.288 612 1423 1 chr7A.!!$F4 811
15 TraesCS2A01G324600 chr7A 420967019 420967819 800 True 1027 1027 89.766 615 1423 1 chr7A.!!$R6 808
16 TraesCS2A01G324600 chr1A 116630611 116631860 1249 False 1847 1847 93.365 614 1862 1 chr1A.!!$F1 1248
17 TraesCS2A01G324600 chr1A 116638927 116640149 1222 False 1836 1836 93.791 640 1861 1 chr1A.!!$F2 1221
18 TraesCS2A01G324600 chr1A 458576706 458577510 804 True 1140 1140 92.083 1895 2713 1 chr1A.!!$R1 818
19 TraesCS2A01G324600 chr1A 243660485 243661226 741 False 1018 1018 91.521 996 1734 1 chr1A.!!$F3 738

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
33 34 0.033781 GTGCCTCTTGCCATTTTGCA 59.966 50.0 0.0 0.0 40.16 4.08 F
1158 1187 0.687757 CTCAAGACCCATCCCCGAGA 60.688 60.0 0.0 0.0 0.00 4.04 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1305 1337 0.107831 TGGCCGAACAAGCTTACACT 59.892 50.000 0.0 0.0 0.0 3.55 R
2541 2581 1.062002 GCATATTGACGGAACACCACG 59.938 52.381 0.0 0.0 0.0 4.94 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
19 20 2.919666 GTTTGCATTACATCGTGCCT 57.080 45.000 0.00 0.00 40.56 4.75
20 21 2.785679 GTTTGCATTACATCGTGCCTC 58.214 47.619 0.00 0.00 40.56 4.70
21 22 2.401583 TTGCATTACATCGTGCCTCT 57.598 45.000 0.00 0.00 40.56 3.69
22 23 2.401583 TGCATTACATCGTGCCTCTT 57.598 45.000 0.00 0.00 40.56 2.85
23 24 2.009051 TGCATTACATCGTGCCTCTTG 58.991 47.619 0.00 0.00 40.56 3.02
24 25 1.268234 GCATTACATCGTGCCTCTTGC 60.268 52.381 0.00 0.00 41.77 4.01
25 26 1.331756 CATTACATCGTGCCTCTTGCC 59.668 52.381 0.00 0.00 40.16 4.52
26 27 0.323302 TTACATCGTGCCTCTTGCCA 59.677 50.000 0.00 0.00 40.16 4.92
27 28 0.541392 TACATCGTGCCTCTTGCCAT 59.459 50.000 0.00 0.00 40.16 4.40
28 29 0.322816 ACATCGTGCCTCTTGCCATT 60.323 50.000 0.00 0.00 40.16 3.16
29 30 0.813184 CATCGTGCCTCTTGCCATTT 59.187 50.000 0.00 0.00 40.16 2.32
30 31 1.203052 CATCGTGCCTCTTGCCATTTT 59.797 47.619 0.00 0.00 40.16 1.82
31 32 0.597568 TCGTGCCTCTTGCCATTTTG 59.402 50.000 0.00 0.00 40.16 2.44
32 33 1.010419 CGTGCCTCTTGCCATTTTGC 61.010 55.000 0.00 0.00 40.16 3.68
33 34 0.033781 GTGCCTCTTGCCATTTTGCA 59.966 50.000 0.00 0.00 40.16 4.08
34 35 0.978151 TGCCTCTTGCCATTTTGCAT 59.022 45.000 0.00 0.00 41.70 3.96
35 36 1.348366 TGCCTCTTGCCATTTTGCATT 59.652 42.857 0.00 0.00 41.70 3.56
36 37 2.224572 TGCCTCTTGCCATTTTGCATTT 60.225 40.909 0.00 0.00 41.70 2.32
37 38 2.417586 GCCTCTTGCCATTTTGCATTTC 59.582 45.455 0.00 0.00 41.70 2.17
38 39 3.666274 CCTCTTGCCATTTTGCATTTCA 58.334 40.909 0.00 0.00 41.70 2.69
39 40 4.258543 CCTCTTGCCATTTTGCATTTCAT 58.741 39.130 0.00 0.00 41.70 2.57
40 41 4.331717 CCTCTTGCCATTTTGCATTTCATC 59.668 41.667 0.00 0.00 41.70 2.92
41 42 4.895961 TCTTGCCATTTTGCATTTCATCA 58.104 34.783 0.00 0.00 41.70 3.07
42 43 5.492895 TCTTGCCATTTTGCATTTCATCAT 58.507 33.333 0.00 0.00 41.70 2.45
43 44 6.641474 TCTTGCCATTTTGCATTTCATCATA 58.359 32.000 0.00 0.00 41.70 2.15
44 45 7.104290 TCTTGCCATTTTGCATTTCATCATAA 58.896 30.769 0.00 0.00 41.70 1.90
45 46 7.771361 TCTTGCCATTTTGCATTTCATCATAAT 59.229 29.630 0.00 0.00 41.70 1.28
46 47 7.485418 TGCCATTTTGCATTTCATCATAATC 57.515 32.000 0.00 0.00 36.04 1.75
47 48 7.048512 TGCCATTTTGCATTTCATCATAATCA 58.951 30.769 0.00 0.00 36.04 2.57
48 49 7.717436 TGCCATTTTGCATTTCATCATAATCAT 59.283 29.630 0.00 0.00 36.04 2.45
49 50 8.227791 GCCATTTTGCATTTCATCATAATCATC 58.772 33.333 0.00 0.00 0.00 2.92
50 51 9.267084 CCATTTTGCATTTCATCATAATCATCA 57.733 29.630 0.00 0.00 0.00 3.07
53 54 9.825109 TTTTGCATTTCATCATAATCATCATGT 57.175 25.926 0.00 0.00 0.00 3.21
54 55 8.810652 TTGCATTTCATCATAATCATCATGTG 57.189 30.769 0.00 0.00 0.00 3.21
55 56 6.866248 TGCATTTCATCATAATCATCATGTGC 59.134 34.615 0.00 0.00 0.00 4.57
56 57 6.866248 GCATTTCATCATAATCATCATGTGCA 59.134 34.615 0.00 0.00 0.00 4.57
57 58 7.545615 GCATTTCATCATAATCATCATGTGCAT 59.454 33.333 0.00 0.00 0.00 3.96
58 59 9.423061 CATTTCATCATAATCATCATGTGCATT 57.577 29.630 0.00 0.00 0.00 3.56
59 60 8.810652 TTTCATCATAATCATCATGTGCATTG 57.189 30.769 0.00 0.00 0.00 2.82
60 61 7.519032 TCATCATAATCATCATGTGCATTGT 57.481 32.000 0.00 0.00 0.00 2.71
61 62 7.590279 TCATCATAATCATCATGTGCATTGTC 58.410 34.615 0.00 0.00 0.00 3.18
62 63 6.945938 TCATAATCATCATGTGCATTGTCA 57.054 33.333 0.00 0.00 0.00 3.58
63 64 7.519032 TCATAATCATCATGTGCATTGTCAT 57.481 32.000 0.00 0.00 0.00 3.06
64 65 8.624367 TCATAATCATCATGTGCATTGTCATA 57.376 30.769 0.00 0.00 0.00 2.15
65 66 9.238368 TCATAATCATCATGTGCATTGTCATAT 57.762 29.630 0.00 0.00 0.00 1.78
66 67 9.855021 CATAATCATCATGTGCATTGTCATATT 57.145 29.630 0.00 0.00 0.00 1.28
68 69 6.945938 TCATCATGTGCATTGTCATATTCA 57.054 33.333 0.00 0.00 0.00 2.57
69 70 7.519032 TCATCATGTGCATTGTCATATTCAT 57.481 32.000 0.00 0.00 0.00 2.57
70 71 7.367285 TCATCATGTGCATTGTCATATTCATG 58.633 34.615 0.00 0.00 34.62 3.07
71 72 5.525199 TCATGTGCATTGTCATATTCATGC 58.475 37.500 0.00 0.33 33.74 4.06
72 73 4.985538 TGTGCATTGTCATATTCATGCA 57.014 36.364 5.24 5.24 41.91 3.96
73 74 5.523438 TGTGCATTGTCATATTCATGCAT 57.477 34.783 11.30 0.00 45.07 3.96
74 75 5.285651 TGTGCATTGTCATATTCATGCATG 58.714 37.500 21.07 21.07 45.07 4.06
75 76 5.163499 TGTGCATTGTCATATTCATGCATGT 60.163 36.000 25.43 10.70 45.07 3.21
76 77 5.751509 GTGCATTGTCATATTCATGCATGTT 59.248 36.000 25.43 16.54 45.07 2.71
77 78 6.919115 GTGCATTGTCATATTCATGCATGTTA 59.081 34.615 25.43 18.02 45.07 2.41
78 79 6.919115 TGCATTGTCATATTCATGCATGTTAC 59.081 34.615 25.43 15.05 39.69 2.50
79 80 6.919115 GCATTGTCATATTCATGCATGTTACA 59.081 34.615 25.43 17.07 35.35 2.41
80 81 7.114388 GCATTGTCATATTCATGCATGTTACAG 59.886 37.037 25.43 14.14 35.35 2.74
81 82 7.628769 TTGTCATATTCATGCATGTTACAGT 57.371 32.000 25.43 6.48 31.73 3.55
82 83 7.018635 TGTCATATTCATGCATGTTACAGTG 57.981 36.000 25.43 16.74 31.73 3.66
83 84 6.598850 TGTCATATTCATGCATGTTACAGTGT 59.401 34.615 25.43 0.00 31.73 3.55
84 85 7.121020 TGTCATATTCATGCATGTTACAGTGTT 59.879 33.333 25.43 3.11 31.73 3.32
85 86 7.430211 GTCATATTCATGCATGTTACAGTGTTG 59.570 37.037 25.43 12.30 31.73 3.33
86 87 3.557577 TCATGCATGTTACAGTGTTGC 57.442 42.857 25.43 10.15 0.00 4.17
87 88 2.883386 TCATGCATGTTACAGTGTTGCA 59.117 40.909 25.43 19.63 46.22 4.08
89 90 3.285816 TGCATGTTACAGTGTTGCATG 57.714 42.857 23.91 23.91 38.32 4.06
91 92 3.564235 CATGTTACAGTGTTGCATGCT 57.436 42.857 20.33 0.00 32.03 3.79
92 93 3.495193 CATGTTACAGTGTTGCATGCTC 58.505 45.455 20.33 12.47 32.03 4.26
93 94 1.879380 TGTTACAGTGTTGCATGCTCC 59.121 47.619 20.33 9.69 0.00 4.70
94 95 1.879380 GTTACAGTGTTGCATGCTCCA 59.121 47.619 20.33 12.36 0.00 3.86
95 96 2.489329 GTTACAGTGTTGCATGCTCCAT 59.511 45.455 20.33 3.43 0.00 3.41
96 97 0.885879 ACAGTGTTGCATGCTCCATG 59.114 50.000 20.33 13.17 43.91 3.66
97 98 0.885879 CAGTGTTGCATGCTCCATGT 59.114 50.000 20.33 4.48 43.10 3.21
98 99 2.086094 CAGTGTTGCATGCTCCATGTA 58.914 47.619 20.33 0.00 43.10 2.29
99 100 2.686405 CAGTGTTGCATGCTCCATGTAT 59.314 45.455 20.33 1.16 43.10 2.29
100 101 2.686405 AGTGTTGCATGCTCCATGTATG 59.314 45.455 20.33 0.00 43.10 2.39
101 102 2.684374 GTGTTGCATGCTCCATGTATGA 59.316 45.455 20.33 0.00 43.10 2.15
102 103 3.317149 GTGTTGCATGCTCCATGTATGAT 59.683 43.478 20.33 0.00 43.10 2.45
122 123 1.419012 TCATGCATCATCACCTCCTCC 59.581 52.381 0.00 0.00 0.00 4.30
130 131 2.045047 TCATCACCTCCTCCTTCCTTCT 59.955 50.000 0.00 0.00 0.00 2.85
205 206 5.227569 TCTTTTCCTGATGCTAGTTCACA 57.772 39.130 0.00 0.00 0.00 3.58
232 233 5.106118 GCCTAAACCCTCTCTGTCAAATTTC 60.106 44.000 0.00 0.00 0.00 2.17
262 263 4.625607 TGAAGTTGTTTTGGTTGGGTTT 57.374 36.364 0.00 0.00 0.00 3.27
271 272 6.246163 TGTTTTGGTTGGGTTTAAAAATGGT 58.754 32.000 0.00 0.00 0.00 3.55
336 337 6.822442 TCCTTAAAAATTCCCAAACCACTTC 58.178 36.000 0.00 0.00 0.00 3.01
406 407 2.756760 CTCACATCCATTCCAAACCCTG 59.243 50.000 0.00 0.00 0.00 4.45
411 412 3.149005 TCCATTCCAAACCCTGTGTAC 57.851 47.619 0.00 0.00 0.00 2.90
503 504 1.460305 GATCCCAGCCAGGCCTCTA 60.460 63.158 8.22 0.00 35.39 2.43
654 680 2.515991 CGCCGCCAACACCCATAT 60.516 61.111 0.00 0.00 0.00 1.78
663 689 1.134753 CAACACCCATATGCACGCATT 59.865 47.619 10.23 0.00 37.82 3.56
685 711 1.513158 CCAGGAGACGTGCTCGATT 59.487 57.895 16.04 1.95 44.91 3.34
827 856 1.071471 CCCAACACCAACGAGCTCT 59.929 57.895 12.85 0.00 0.00 4.09
834 863 1.241990 ACCAACGAGCTCTGTCGCTA 61.242 55.000 12.85 0.00 44.06 4.26
901 930 3.062466 CTCTGGTCCGGCGTCTCA 61.062 66.667 6.01 0.00 0.00 3.27
1151 1180 2.514824 GGCGCCTCAAGACCCATC 60.515 66.667 22.15 0.00 0.00 3.51
1158 1187 0.687757 CTCAAGACCCATCCCCGAGA 60.688 60.000 0.00 0.00 0.00 4.04
1194 1223 1.672356 GCTTCGCCTCCTTGCTTCA 60.672 57.895 0.00 0.00 0.00 3.02
1231 1260 1.738099 CCACTTCACCTTCGCCTCG 60.738 63.158 0.00 0.00 0.00 4.63
1305 1337 1.074248 GGCCCCTCGTTTTTCCTCA 59.926 57.895 0.00 0.00 0.00 3.86
1306 1338 0.960861 GGCCCCTCGTTTTTCCTCAG 60.961 60.000 0.00 0.00 0.00 3.35
1310 1342 2.038033 CCCCTCGTTTTTCCTCAGTGTA 59.962 50.000 0.00 0.00 0.00 2.90
1330 1362 1.675641 GCTTGTTCGGCCATGGACT 60.676 57.895 18.40 0.00 0.00 3.85
1440 1473 1.217244 GTACCGACCACCGCATTCT 59.783 57.895 0.00 0.00 36.84 2.40
1748 1782 6.072064 CGACTACTTCCTTCTCCAAAGAACTA 60.072 42.308 0.00 0.00 36.59 2.24
1749 1783 7.523380 CGACTACTTCCTTCTCCAAAGAACTAA 60.523 40.741 0.00 0.00 36.59 2.24
1865 1899 4.398673 AGAATGACTACTTCCACTACCGTC 59.601 45.833 0.00 0.00 0.00 4.79
1866 1900 2.440409 TGACTACTTCCACTACCGTCC 58.560 52.381 0.00 0.00 0.00 4.79
1867 1901 2.040813 TGACTACTTCCACTACCGTCCT 59.959 50.000 0.00 0.00 0.00 3.85
1868 1902 2.422832 GACTACTTCCACTACCGTCCTG 59.577 54.545 0.00 0.00 0.00 3.86
1869 1903 2.224967 ACTACTTCCACTACCGTCCTGT 60.225 50.000 0.00 0.00 0.00 4.00
1870 1904 1.713297 ACTTCCACTACCGTCCTGTT 58.287 50.000 0.00 0.00 0.00 3.16
1871 1905 1.343465 ACTTCCACTACCGTCCTGTTG 59.657 52.381 0.00 0.00 0.00 3.33
1872 1906 1.616865 CTTCCACTACCGTCCTGTTGA 59.383 52.381 0.00 0.00 0.00 3.18
1873 1907 1.933021 TCCACTACCGTCCTGTTGAT 58.067 50.000 0.00 0.00 0.00 2.57
1874 1908 1.822990 TCCACTACCGTCCTGTTGATC 59.177 52.381 0.00 0.00 0.00 2.92
1875 1909 1.548719 CCACTACCGTCCTGTTGATCA 59.451 52.381 0.00 0.00 0.00 2.92
1876 1910 2.168521 CCACTACCGTCCTGTTGATCAT 59.831 50.000 0.00 0.00 0.00 2.45
1877 1911 3.448686 CACTACCGTCCTGTTGATCATC 58.551 50.000 0.00 0.00 0.00 2.92
1878 1912 2.099263 ACTACCGTCCTGTTGATCATCG 59.901 50.000 0.00 0.00 0.00 3.84
1879 1913 1.182667 ACCGTCCTGTTGATCATCGA 58.817 50.000 0.00 0.00 0.00 3.59
1880 1914 1.757118 ACCGTCCTGTTGATCATCGAT 59.243 47.619 0.00 0.00 0.00 3.59
1881 1915 2.130395 CCGTCCTGTTGATCATCGATG 58.870 52.381 19.61 19.61 0.00 3.84
1882 1916 2.223805 CCGTCCTGTTGATCATCGATGA 60.224 50.000 29.09 29.09 41.70 2.92
1883 1917 2.791560 CGTCCTGTTGATCATCGATGAC 59.208 50.000 29.49 21.75 40.03 3.06
1884 1918 3.126831 GTCCTGTTGATCATCGATGACC 58.873 50.000 29.49 21.75 40.03 4.02
1885 1919 2.130395 CCTGTTGATCATCGATGACCG 58.870 52.381 29.49 13.66 40.03 4.79
1903 1937 3.209410 ACCGATAGTACCACTACTTCCG 58.791 50.000 0.00 0.00 32.84 4.30
1998 2034 3.898529 GAAGGTATAACCATCGAGACGG 58.101 50.000 0.00 0.00 41.95 4.79
2048 2084 0.385974 GAAATGCTCGCGTTTGCACT 60.386 50.000 21.26 11.71 42.26 4.40
2092 2128 0.333312 TTCCCCGTTGCCATACCATT 59.667 50.000 0.00 0.00 0.00 3.16
2275 2312 2.855180 CCACGATGACAAATGCTTCAC 58.145 47.619 0.00 0.00 0.00 3.18
2335 2372 1.621107 CTTGCAAATGTCATCCGCAC 58.379 50.000 0.00 0.00 31.10 5.34
2409 2448 3.364460 TGCATATGGGGATTTATCGGG 57.636 47.619 4.56 0.00 0.00 5.14
2478 2518 8.456471 GGTATAGTTTTGTTATGTTTCACCTCC 58.544 37.037 0.00 0.00 0.00 4.30
2481 2521 6.126409 AGTTTTGTTATGTTTCACCTCCTGA 58.874 36.000 0.00 0.00 0.00 3.86
2486 2526 1.896220 TGTTTCACCTCCTGACATGC 58.104 50.000 0.00 0.00 0.00 4.06
2664 2710 6.263617 ACATGCATCATACTTGATTGTGCATA 59.736 34.615 12.57 0.00 46.64 3.14
2713 2759 7.817418 TTACTATGTTGTTTGCTTCTTTCCT 57.183 32.000 0.00 0.00 0.00 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.420022 AGAGGCACGATGTAATGCAAAC 59.580 45.455 0.00 0.00 43.93 2.93
1 2 2.710377 AGAGGCACGATGTAATGCAAA 58.290 42.857 0.00 0.00 43.93 3.68
3 4 2.009051 CAAGAGGCACGATGTAATGCA 58.991 47.619 0.00 0.00 43.93 3.96
4 5 1.268234 GCAAGAGGCACGATGTAATGC 60.268 52.381 0.00 0.00 43.97 3.56
5 6 2.744787 GCAAGAGGCACGATGTAATG 57.255 50.000 0.00 0.00 43.97 1.90
6 7 1.065491 TGGCAAGAGGCACGATGTAAT 60.065 47.619 0.00 0.00 46.46 1.89
7 8 0.323302 TGGCAAGAGGCACGATGTAA 59.677 50.000 0.00 0.00 46.46 2.41
8 9 1.979262 TGGCAAGAGGCACGATGTA 59.021 52.632 0.00 0.00 46.46 2.29
9 10 2.749682 TGGCAAGAGGCACGATGT 59.250 55.556 0.00 0.00 46.46 3.06
23 24 7.485418 TGATTATGATGAAATGCAAAATGGC 57.515 32.000 0.00 0.00 0.00 4.40
24 25 9.267084 TGATGATTATGATGAAATGCAAAATGG 57.733 29.630 0.00 0.00 0.00 3.16
27 28 9.825109 ACATGATGATTATGATGAAATGCAAAA 57.175 25.926 4.07 0.00 32.93 2.44
28 29 9.255304 CACATGATGATTATGATGAAATGCAAA 57.745 29.630 4.07 0.00 32.93 3.68
29 30 7.383843 GCACATGATGATTATGATGAAATGCAA 59.616 33.333 4.07 0.00 32.01 4.08
30 31 6.866248 GCACATGATGATTATGATGAAATGCA 59.134 34.615 4.07 0.00 32.01 3.96
31 32 6.866248 TGCACATGATGATTATGATGAAATGC 59.134 34.615 4.07 4.42 32.93 3.56
32 33 8.986477 ATGCACATGATGATTATGATGAAATG 57.014 30.769 4.07 0.00 32.93 2.32
33 34 9.423061 CAATGCACATGATGATTATGATGAAAT 57.577 29.630 4.07 0.00 32.93 2.17
34 35 8.417884 ACAATGCACATGATGATTATGATGAAA 58.582 29.630 4.07 0.00 32.93 2.69
35 36 7.947282 ACAATGCACATGATGATTATGATGAA 58.053 30.769 4.07 0.00 32.93 2.57
36 37 7.229707 TGACAATGCACATGATGATTATGATGA 59.770 33.333 4.07 0.00 32.93 2.92
37 38 7.367285 TGACAATGCACATGATGATTATGATG 58.633 34.615 4.07 0.00 34.54 3.07
38 39 7.519032 TGACAATGCACATGATGATTATGAT 57.481 32.000 4.07 0.00 0.00 2.45
39 40 6.945938 TGACAATGCACATGATGATTATGA 57.054 33.333 4.07 0.00 0.00 2.15
40 41 9.855021 AATATGACAATGCACATGATGATTATG 57.145 29.630 0.00 0.00 0.00 1.90
42 43 9.069082 TGAATATGACAATGCACATGATGATTA 57.931 29.630 0.00 0.00 0.00 1.75
43 44 7.947282 TGAATATGACAATGCACATGATGATT 58.053 30.769 0.00 2.94 0.00 2.57
44 45 7.519032 TGAATATGACAATGCACATGATGAT 57.481 32.000 0.00 0.69 0.00 2.45
45 46 6.945938 TGAATATGACAATGCACATGATGA 57.054 33.333 0.00 0.00 0.00 2.92
46 47 6.089417 GCATGAATATGACAATGCACATGATG 59.911 38.462 0.00 0.00 36.87 3.07
47 48 6.156519 GCATGAATATGACAATGCACATGAT 58.843 36.000 0.00 0.00 36.87 2.45
48 49 5.067936 TGCATGAATATGACAATGCACATGA 59.932 36.000 7.49 0.00 39.69 3.07
49 50 5.285651 TGCATGAATATGACAATGCACATG 58.714 37.500 7.49 0.00 39.69 3.21
50 51 5.523438 TGCATGAATATGACAATGCACAT 57.477 34.783 7.49 0.00 39.69 3.21
51 52 4.985538 TGCATGAATATGACAATGCACA 57.014 36.364 7.49 0.00 39.69 4.57
52 53 5.286438 ACATGCATGAATATGACAATGCAC 58.714 37.500 32.75 0.00 45.90 4.57
53 54 5.523438 ACATGCATGAATATGACAATGCA 57.477 34.783 32.75 12.76 46.89 3.96
54 55 6.919115 TGTAACATGCATGAATATGACAATGC 59.081 34.615 32.75 10.74 36.36 3.56
55 56 8.132995 ACTGTAACATGCATGAATATGACAATG 58.867 33.333 32.75 15.55 36.36 2.82
56 57 8.132995 CACTGTAACATGCATGAATATGACAAT 58.867 33.333 32.75 13.08 36.36 2.71
57 58 7.121020 ACACTGTAACATGCATGAATATGACAA 59.879 33.333 32.75 7.35 36.36 3.18
58 59 6.598850 ACACTGTAACATGCATGAATATGACA 59.401 34.615 32.75 21.35 36.36 3.58
59 60 7.019774 ACACTGTAACATGCATGAATATGAC 57.980 36.000 32.75 18.47 36.36 3.06
60 61 7.474190 CAACACTGTAACATGCATGAATATGA 58.526 34.615 32.75 13.76 36.36 2.15
61 62 6.197655 GCAACACTGTAACATGCATGAATATG 59.802 38.462 32.75 21.66 37.00 1.78
62 63 6.127675 TGCAACACTGTAACATGCATGAATAT 60.128 34.615 32.75 16.92 41.67 1.28
63 64 5.182760 TGCAACACTGTAACATGCATGAATA 59.817 36.000 32.75 20.62 41.67 1.75
64 65 4.022155 TGCAACACTGTAACATGCATGAAT 60.022 37.500 32.75 21.62 41.67 2.57
65 66 3.317430 TGCAACACTGTAACATGCATGAA 59.683 39.130 32.75 17.10 41.67 2.57
66 67 2.883386 TGCAACACTGTAACATGCATGA 59.117 40.909 32.75 9.00 41.67 3.07
67 68 3.285816 TGCAACACTGTAACATGCATG 57.714 42.857 25.09 25.09 41.67 4.06
71 72 3.495193 GAGCATGCAACACTGTAACATG 58.505 45.455 21.98 15.39 40.80 3.21
72 73 2.489329 GGAGCATGCAACACTGTAACAT 59.511 45.455 21.98 0.00 0.00 2.71
73 74 1.879380 GGAGCATGCAACACTGTAACA 59.121 47.619 21.98 0.00 0.00 2.41
74 75 1.879380 TGGAGCATGCAACACTGTAAC 59.121 47.619 21.98 0.00 28.48 2.50
75 76 2.268762 TGGAGCATGCAACACTGTAA 57.731 45.000 21.98 0.00 28.48 2.41
76 77 2.086094 CATGGAGCATGCAACACTGTA 58.914 47.619 21.98 0.00 42.43 2.74
77 78 0.885879 CATGGAGCATGCAACACTGT 59.114 50.000 21.98 0.00 42.43 3.55
78 79 0.885879 ACATGGAGCATGCAACACTG 59.114 50.000 21.98 17.64 42.43 3.66
79 80 2.495155 TACATGGAGCATGCAACACT 57.505 45.000 21.98 9.26 42.43 3.55
80 81 2.684374 TCATACATGGAGCATGCAACAC 59.316 45.455 21.98 7.22 42.43 3.32
81 82 3.002038 TCATACATGGAGCATGCAACA 57.998 42.857 21.98 18.20 42.43 3.33
82 83 3.566742 TGATCATACATGGAGCATGCAAC 59.433 43.478 21.98 12.62 42.43 4.17
83 84 3.822940 TGATCATACATGGAGCATGCAA 58.177 40.909 21.98 5.23 42.43 4.08
84 85 3.495434 TGATCATACATGGAGCATGCA 57.505 42.857 21.98 0.00 44.80 3.96
87 88 4.028993 TGCATGATCATACATGGAGCAT 57.971 40.909 8.15 0.00 45.14 3.79
88 89 3.495434 TGCATGATCATACATGGAGCA 57.505 42.857 8.15 9.12 45.14 4.26
99 100 2.709397 AGGAGGTGATGATGCATGATCA 59.291 45.455 22.85 22.85 45.43 2.92
100 101 3.336468 GAGGAGGTGATGATGCATGATC 58.664 50.000 18.11 18.11 0.00 2.92
101 102 2.040012 GGAGGAGGTGATGATGCATGAT 59.960 50.000 2.46 0.00 0.00 2.45
102 103 1.419012 GGAGGAGGTGATGATGCATGA 59.581 52.381 2.46 0.00 0.00 3.07
122 123 7.170489 GCCAAAATGAAAGAAAGAAGAAGGAAG 59.830 37.037 0.00 0.00 0.00 3.46
130 131 6.534793 GTCACTTGCCAAAATGAAAGAAAGAA 59.465 34.615 0.00 0.00 0.00 2.52
205 206 2.912956 TGACAGAGAGGGTTTAGGCATT 59.087 45.455 0.00 0.00 0.00 3.56
232 233 7.254522 CCAACCAAAACAACTTCAAATGATCTG 60.255 37.037 0.00 0.00 0.00 2.90
311 312 7.292356 AGAAGTGGTTTGGGAATTTTTAAGGAT 59.708 33.333 0.00 0.00 0.00 3.24
331 332 9.003658 AGAAATATGCCCGATTTAATAGAAGTG 57.996 33.333 0.00 0.00 0.00 3.16
336 337 8.110860 ACCAAGAAATATGCCCGATTTAATAG 57.889 34.615 0.00 0.00 0.00 1.73
411 412 9.994432 ATCGCATAAACAGAAATAGAAAGAAAG 57.006 29.630 0.00 0.00 0.00 2.62
446 447 9.753674 TCTCTCTCTCTCTCTTATTTTTCTCTT 57.246 33.333 0.00 0.00 0.00 2.85
452 453 8.772250 TCTCTCTCTCTCTCTCTCTCTTATTTT 58.228 37.037 0.00 0.00 0.00 1.82
458 459 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
459 460 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
460 461 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
461 462 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
462 463 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
463 464 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
464 465 5.136068 TCTCTCTCTCTCTCTCTCTCTCT 57.864 47.826 0.00 0.00 0.00 3.10
465 466 5.047377 GGATCTCTCTCTCTCTCTCTCTCTC 60.047 52.000 0.00 0.00 0.00 3.20
466 467 4.837860 GGATCTCTCTCTCTCTCTCTCTCT 59.162 50.000 0.00 0.00 0.00 3.10
467 468 4.020662 GGGATCTCTCTCTCTCTCTCTCTC 60.021 54.167 0.00 0.00 0.00 3.20
468 469 3.906846 GGGATCTCTCTCTCTCTCTCTCT 59.093 52.174 0.00 0.00 0.00 3.10
469 470 3.648067 TGGGATCTCTCTCTCTCTCTCTC 59.352 52.174 0.00 0.00 0.00 3.20
470 471 3.649981 CTGGGATCTCTCTCTCTCTCTCT 59.350 52.174 0.00 0.00 0.00 3.10
471 472 3.808618 GCTGGGATCTCTCTCTCTCTCTC 60.809 56.522 0.00 0.00 0.00 3.20
568 569 0.685785 CTCAGGGAGGTCAGCTGCTA 60.686 60.000 9.47 0.00 0.00 3.49
601 602 1.205460 GGGAGAGGGTTAGGGTTGCA 61.205 60.000 0.00 0.00 0.00 4.08
654 680 1.002746 TCCTGGCTTAATGCGTGCA 60.003 52.632 0.00 0.00 44.05 4.57
663 689 1.890894 GAGCACGTCTCCTGGCTTA 59.109 57.895 0.00 0.00 36.59 3.09
685 711 0.919780 TCGAAGAGAGAGGAGGGGGA 60.920 60.000 0.00 0.00 0.00 4.81
827 856 4.498520 GCGAGGCTGCTAGCGACA 62.499 66.667 10.77 0.00 43.62 4.35
894 923 1.882167 GGAGAGCAGCATGAGACGC 60.882 63.158 0.00 0.00 39.69 5.19
901 930 2.818132 GCGGTAGGAGAGCAGCAT 59.182 61.111 0.00 0.00 0.00 3.79
1151 1180 3.522731 CGAGCAGAGGTCTCGGGG 61.523 72.222 4.66 0.00 46.82 5.73
1292 1321 4.058817 AGCTTACACTGAGGAAAAACGAG 58.941 43.478 0.00 0.00 0.00 4.18
1293 1322 4.067972 AGCTTACACTGAGGAAAAACGA 57.932 40.909 0.00 0.00 0.00 3.85
1305 1337 0.107831 TGGCCGAACAAGCTTACACT 59.892 50.000 0.00 0.00 0.00 3.55
1306 1338 1.135689 CATGGCCGAACAAGCTTACAC 60.136 52.381 0.00 0.00 0.00 2.90
1310 1342 1.074775 TCCATGGCCGAACAAGCTT 59.925 52.632 6.96 0.00 0.00 3.74
1357 1389 3.831911 GGTGGATTTGGAGGAAACATGAA 59.168 43.478 0.00 0.00 0.00 2.57
1360 1392 2.041081 TCGGTGGATTTGGAGGAAACAT 59.959 45.455 0.00 0.00 0.00 2.71
1427 1460 1.234821 TGAAACAGAATGCGGTGGTC 58.765 50.000 0.00 0.00 42.53 4.02
1440 1473 4.075682 TCGGCCTTGACAAATATGAAACA 58.924 39.130 0.00 0.00 0.00 2.83
1488 1521 1.001633 GTAGTCGAACTTGAGGGGCAA 59.998 52.381 0.00 0.00 34.73 4.52
1586 1619 2.931512 TGTCACATCATCGAGCGTAA 57.068 45.000 0.00 0.00 0.00 3.18
1748 1782 2.896745 ACTTGACGGTTCCGTTACTT 57.103 45.000 17.90 1.14 43.08 2.24
1749 1783 2.747436 GAACTTGACGGTTCCGTTACT 58.253 47.619 17.90 1.89 43.08 2.24
1865 1899 2.130395 CGGTCATCGATGATCAACAGG 58.870 52.381 32.13 15.81 37.79 4.00
1866 1900 3.084070 TCGGTCATCGATGATCAACAG 57.916 47.619 32.13 20.01 43.74 3.16
1876 1910 4.202295 AGTAGTGGTACTATCGGTCATCGA 60.202 45.833 0.00 0.00 41.11 3.59
1877 1911 4.063689 AGTAGTGGTACTATCGGTCATCG 58.936 47.826 0.00 0.00 37.76 3.84
1878 1912 5.048852 GGAAGTAGTGGTACTATCGGTCATC 60.049 48.000 0.00 0.00 38.66 2.92
1879 1913 4.826183 GGAAGTAGTGGTACTATCGGTCAT 59.174 45.833 0.00 0.00 38.66 3.06
1880 1914 4.202441 GGAAGTAGTGGTACTATCGGTCA 58.798 47.826 0.00 0.00 38.66 4.02
1881 1915 3.249559 CGGAAGTAGTGGTACTATCGGTC 59.750 52.174 0.00 0.00 38.66 4.79
1882 1916 3.209410 CGGAAGTAGTGGTACTATCGGT 58.791 50.000 0.00 0.00 38.66 4.69
1883 1917 2.031333 GCGGAAGTAGTGGTACTATCGG 60.031 54.545 0.00 0.00 38.66 4.18
1884 1918 2.877168 AGCGGAAGTAGTGGTACTATCG 59.123 50.000 0.00 0.00 38.66 2.92
1885 1919 4.084118 CGTAGCGGAAGTAGTGGTACTATC 60.084 50.000 0.00 0.00 38.66 2.08
1886 1920 3.812053 CGTAGCGGAAGTAGTGGTACTAT 59.188 47.826 0.00 0.00 38.66 2.12
1887 1921 3.118775 TCGTAGCGGAAGTAGTGGTACTA 60.119 47.826 0.00 0.00 38.66 1.82
1888 1922 2.012673 CGTAGCGGAAGTAGTGGTACT 58.987 52.381 0.00 0.00 41.61 2.73
1998 2034 4.811761 GCGTTCATTCACGGGCGC 62.812 66.667 0.00 0.00 40.69 6.53
2048 2084 1.336440 CAAGAAAACATGTCGGGCACA 59.664 47.619 0.00 0.00 40.18 4.57
2092 2128 3.299977 CGGGTGTCCCACGAGACA 61.300 66.667 5.64 0.00 45.83 3.41
2322 2359 2.353357 ATCATGGTGCGGATGACATT 57.647 45.000 0.00 0.00 32.68 2.71
2405 2444 6.372185 CGAATATAACAAACAACAAACCCGA 58.628 36.000 0.00 0.00 0.00 5.14
2409 2448 5.346551 GGGCCGAATATAACAAACAACAAAC 59.653 40.000 0.00 0.00 0.00 2.93
2505 2545 3.869832 TCTCTCTCGGTTATGTACTCACG 59.130 47.826 0.00 0.00 0.00 4.35
2539 2579 3.513662 CATATTGACGGAACACCACGTA 58.486 45.455 0.00 0.00 44.24 3.57
2541 2581 1.062002 GCATATTGACGGAACACCACG 59.938 52.381 0.00 0.00 0.00 4.94
2664 2710 5.046448 ACAACCATCACATAAACATGGCATT 60.046 36.000 0.00 0.00 40.85 3.56


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

AutoCloner maintained by Alex Coulton.