Multiple sequence alignment - TraesCS4A01G478200

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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 TraesCS4A01G478200 chr4A 100.000 3602 0 0 1 3602 735663302 735659701 0.000000e+00 6652
1 TraesCS4A01G478200 chr4A 83.967 2944 407 43 704 3600 735562253 735559328 0.000000e+00 2761
2 TraesCS4A01G478200 chr4A 83.684 2899 414 34 740 3598 735316797 735319676 0.000000e+00 2678
3 TraesCS4A01G478200 chr4A 83.055 2933 426 43 704 3600 736147740 736150637 0.000000e+00 2597
4 TraesCS4A01G478200 chr4A 82.661 2901 464 25 704 3595 735487496 735484626 0.000000e+00 2534
5 TraesCS4A01G478200 chr4A 82.722 2888 444 35 741 3592 735747621 735750489 0.000000e+00 2518
6 TraesCS4A01G478200 chr4A 82.665 2867 457 29 741 3596 735003911 735006748 0.000000e+00 2505
7 TraesCS4A01G478200 chr4A 82.308 2894 444 48 746 3598 736571227 736574093 0.000000e+00 2446
8 TraesCS4A01G478200 chr4A 82.280 2895 444 47 746 3598 734731150 734734017 0.000000e+00 2440
9 TraesCS4A01G478200 chr4A 82.913 2616 390 38 321 2900 734917494 734920088 0.000000e+00 2302
10 TraesCS4A01G478200 chr4A 81.273 2953 454 58 704 3600 736412843 736409934 0.000000e+00 2298
11 TraesCS4A01G478200 chr4A 81.635 2826 448 45 704 3475 735832120 735834928 0.000000e+00 2278
12 TraesCS4A01G478200 chr4A 83.806 1834 266 22 741 2566 734583122 734584932 0.000000e+00 1712
13 TraesCS4A01G478200 chr4A 94.655 711 24 9 1 708 734384901 734385600 0.000000e+00 1090
14 TraesCS4A01G478200 chr4A 82.293 1169 181 16 2437 3598 734482988 734484137 0.000000e+00 989
15 TraesCS4A01G478200 chr4A 80.135 1334 244 19 2273 3600 735778496 735779814 0.000000e+00 976
16 TraesCS4A01G478200 chr4A 84.751 682 99 3 15 694 735368191 735367513 0.000000e+00 678
17 TraesCS4A01G478200 chr4A 83.429 694 109 4 3 694 735776132 735776821 1.090000e-179 640
18 TraesCS4A01G478200 chr4A 83.779 598 92 2 99 694 736896591 736897185 2.430000e-156 562
19 TraesCS4A01G478200 chr4A 81.047 707 111 15 3 694 735316029 735316727 3.160000e-150 542
20 TraesCS4A01G478200 chr4A 87.443 438 54 1 258 694 734585118 734585555 1.490000e-138 503
21 TraesCS4A01G478200 chr4A 82.507 383 61 4 15 394 736471154 736470775 7.450000e-87 331
22 TraesCS4A01G478200 chr7D 82.558 2924 453 36 704 3592 5648929 5646028 0.000000e+00 2521
23 TraesCS4A01G478200 chr7D 81.728 2118 328 45 1513 3600 5665585 5663497 0.000000e+00 1712
24 TraesCS4A01G478200 chr7D 80.285 1334 244 17 2272 3600 5636023 5634704 0.000000e+00 989
25 TraesCS4A01G478200 chr7D 84.660 691 98 4 6 694 5638360 5637676 0.000000e+00 682
26 TraesCS4A01G478200 chr7D 84.457 682 101 3 15 694 5449383 5448705 0.000000e+00 667
27 TraesCS4A01G478200 chr7A 81.999 2911 457 36 740 3600 7321867 7318974 0.000000e+00 2410
28 TraesCS4A01G478200 chr7A 84.311 682 102 3 15 694 6928921 6928243 0.000000e+00 662


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 TraesCS4A01G478200 chr4A 735659701 735663302 3601 True 6652.0 6652 100.0000 1 3602 1 chr4A.!!$R4 3601
1 TraesCS4A01G478200 chr4A 735559328 735562253 2925 True 2761.0 2761 83.9670 704 3600 1 chr4A.!!$R3 2896
2 TraesCS4A01G478200 chr4A 736147740 736150637 2897 False 2597.0 2597 83.0550 704 3600 1 chr4A.!!$F8 2896
3 TraesCS4A01G478200 chr4A 735484626 735487496 2870 True 2534.0 2534 82.6610 704 3595 1 chr4A.!!$R2 2891
4 TraesCS4A01G478200 chr4A 735747621 735750489 2868 False 2518.0 2518 82.7220 741 3592 1 chr4A.!!$F6 2851
5 TraesCS4A01G478200 chr4A 735003911 735006748 2837 False 2505.0 2505 82.6650 741 3596 1 chr4A.!!$F5 2855
6 TraesCS4A01G478200 chr4A 736571227 736574093 2866 False 2446.0 2446 82.3080 746 3598 1 chr4A.!!$F9 2852
7 TraesCS4A01G478200 chr4A 734731150 734734017 2867 False 2440.0 2440 82.2800 746 3598 1 chr4A.!!$F3 2852
8 TraesCS4A01G478200 chr4A 734917494 734920088 2594 False 2302.0 2302 82.9130 321 2900 1 chr4A.!!$F4 2579
9 TraesCS4A01G478200 chr4A 736409934 736412843 2909 True 2298.0 2298 81.2730 704 3600 1 chr4A.!!$R5 2896
10 TraesCS4A01G478200 chr4A 735832120 735834928 2808 False 2278.0 2278 81.6350 704 3475 1 chr4A.!!$F7 2771
11 TraesCS4A01G478200 chr4A 735316029 735319676 3647 False 1610.0 2678 82.3655 3 3598 2 chr4A.!!$F12 3595
12 TraesCS4A01G478200 chr4A 734583122 734585555 2433 False 1107.5 1712 85.6245 258 2566 2 chr4A.!!$F11 2308
13 TraesCS4A01G478200 chr4A 734384901 734385600 699 False 1090.0 1090 94.6550 1 708 1 chr4A.!!$F1 707
14 TraesCS4A01G478200 chr4A 734482988 734484137 1149 False 989.0 989 82.2930 2437 3598 1 chr4A.!!$F2 1161
15 TraesCS4A01G478200 chr4A 735776132 735779814 3682 False 808.0 976 81.7820 3 3600 2 chr4A.!!$F13 3597
16 TraesCS4A01G478200 chr4A 735367513 735368191 678 True 678.0 678 84.7510 15 694 1 chr4A.!!$R1 679
17 TraesCS4A01G478200 chr4A 736896591 736897185 594 False 562.0 562 83.7790 99 694 1 chr4A.!!$F10 595
18 TraesCS4A01G478200 chr7D 5646028 5648929 2901 True 2521.0 2521 82.5580 704 3592 1 chr7D.!!$R2 2888
19 TraesCS4A01G478200 chr7D 5663497 5665585 2088 True 1712.0 1712 81.7280 1513 3600 1 chr7D.!!$R3 2087
20 TraesCS4A01G478200 chr7D 5634704 5638360 3656 True 835.5 989 82.4725 6 3600 2 chr7D.!!$R4 3594
21 TraesCS4A01G478200 chr7D 5448705 5449383 678 True 667.0 667 84.4570 15 694 1 chr7D.!!$R1 679
22 TraesCS4A01G478200 chr7A 7318974 7321867 2893 True 2410.0 2410 81.9990 740 3600 1 chr7A.!!$R2 2860
23 TraesCS4A01G478200 chr7A 6928243 6928921 678 True 662.0 662 84.3110 15 694 1 chr7A.!!$R1 679

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
333 352 1.259316 GCGTTAGCTTGAAATTGGCG 58.741 50.0 0.0 0.0 41.01 5.69 F
1065 1127 0.755686 GGGAGATCATCGAACCTGCT 59.244 55.0 0.0 0.0 0.00 4.24 F
2039 2168 1.167851 CGGAATTTCAAGAGGCTGCA 58.832 50.0 0.5 0.0 0.00 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1443 1508 0.039165 CTTTTGCCGCCAAAGGAGAC 60.039 55.0 8.71 0.00 41.58 3.36 R
2286 2471 0.039256 GCGAATTCAGCTTGCCAACA 60.039 50.0 6.22 0.00 0.00 3.33 R
3120 3582 0.392998 GCCCAATGCTCCTTCGAAGA 60.393 55.0 26.61 11.39 36.87 2.87 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
89 93 1.995542 AGGTCATTCCACACTCCCAAT 59.004 47.619 0.00 0.00 39.02 3.16
95 99 5.760253 GTCATTCCACACTCCCAATATAGTG 59.240 44.000 2.43 2.43 46.84 2.74
248 254 6.749923 AAGCAATTCTGGTTCTATCTTCAC 57.250 37.500 0.00 0.00 38.98 3.18
276 295 3.707102 TCAACCCAAAAAGTAAACCCTGG 59.293 43.478 0.00 0.00 0.00 4.45
333 352 1.259316 GCGTTAGCTTGAAATTGGCG 58.741 50.000 0.00 0.00 41.01 5.69
384 403 2.766263 TGATGCTTCAACCTACCTCGAT 59.234 45.455 0.00 0.00 0.00 3.59
501 520 3.007182 CCAAGTTGGACAAATGGCTTCAT 59.993 43.478 17.60 0.00 40.96 2.57
618 637 1.305219 CCAATGCGTCCACCGTCAAT 61.305 55.000 0.00 0.00 39.32 2.57
700 719 6.658816 TGAGAACAGAAAGCTAATTTGCCATA 59.341 34.615 8.30 0.00 0.00 2.74
723 772 9.288576 CATATAAAGGACTTCCATCAATTGCTA 57.711 33.333 0.00 0.00 38.89 3.49
725 774 6.705863 AAAGGACTTCCATCAATTGCTATC 57.294 37.500 0.00 0.00 38.89 2.08
752 801 3.885297 CCAGCTGGTTCTGGTTATAATGG 59.115 47.826 25.53 0.00 46.59 3.16
756 805 4.816925 GCTGGTTCTGGTTATAATGGAGAC 59.183 45.833 0.00 0.00 0.00 3.36
757 806 5.396884 GCTGGTTCTGGTTATAATGGAGACT 60.397 44.000 0.00 0.00 0.00 3.24
824 873 4.104102 ACCACCTCTGAAAGTAATTGGTCA 59.896 41.667 0.00 0.00 31.54 4.02
829 878 5.063944 CCTCTGAAAGTAATTGGTCATGACG 59.936 44.000 19.33 1.27 33.76 4.35
894 955 5.531659 TGCTATTACTGAGTCTAGTACAGCC 59.468 44.000 19.41 10.88 38.97 4.85
914 975 1.812571 CATGTACTCAGGTTTGGCCAC 59.187 52.381 3.88 0.00 40.61 5.01
933 994 2.624838 CACTGTTGGAGTTTGAGGCATT 59.375 45.455 0.00 0.00 29.75 3.56
955 1016 2.238521 GAAAATCCACCTTGGCACAGA 58.761 47.619 0.00 0.00 42.39 3.41
957 1018 2.134789 AATCCACCTTGGCACAGATC 57.865 50.000 0.00 0.00 42.39 2.75
977 1038 3.071479 TCGTTTACAATGACAAGAGGGC 58.929 45.455 0.00 0.00 0.00 5.19
994 1055 9.034800 ACAAGAGGGCAAAAGAATATTTTGATA 57.965 29.630 16.16 0.00 40.73 2.15
1059 1121 3.004419 GTCATACACGGGAGATCATCGAA 59.996 47.826 0.00 0.00 0.00 3.71
1060 1122 3.004419 TCATACACGGGAGATCATCGAAC 59.996 47.826 0.00 0.00 0.00 3.95
1065 1127 0.755686 GGGAGATCATCGAACCTGCT 59.244 55.000 0.00 0.00 0.00 4.24
1071 1134 3.196469 AGATCATCGAACCTGCTTCTCAA 59.804 43.478 0.00 0.00 0.00 3.02
1164 1228 3.552890 GGAAATTCCTGCTTGTGTTGGAC 60.553 47.826 4.46 0.00 32.53 4.02
1209 1273 3.753797 GTGAAAGAGAATGGGACCAACTC 59.246 47.826 15.96 15.96 35.41 3.01
1219 1283 2.043939 TGGGACCAACTCTTAGCTCCTA 59.956 50.000 0.00 0.00 0.00 2.94
1221 1285 3.070302 GGGACCAACTCTTAGCTCCTATG 59.930 52.174 0.00 0.00 0.00 2.23
1248 1312 3.820467 CACAACAGATGGGAAGCAAAGTA 59.180 43.478 0.00 0.00 32.54 2.24
1264 1329 6.407202 AGCAAAGTATTGGTAACTTCTCGAT 58.593 36.000 0.00 0.00 45.01 3.59
1280 1345 3.324846 TCTCGATGGGATACATTTCCAGG 59.675 47.826 0.00 0.00 40.72 4.45
1339 1404 7.443302 AAGATGGGAGATACTCAATTCTTGA 57.557 36.000 0.00 0.00 38.17 3.02
1340 1405 7.630005 AGATGGGAGATACTCAATTCTTGAT 57.370 36.000 0.00 0.00 39.30 2.57
1344 1409 7.730084 TGGGAGATACTCAATTCTTGATACTG 58.270 38.462 0.00 0.00 39.30 2.74
1423 1488 3.795688 TGGAAGATTTTGCAGAGGAGT 57.204 42.857 0.00 0.00 30.57 3.85
1499 1564 6.701400 CAGTTGAAAGGGAAAACAAATACCAG 59.299 38.462 0.00 0.00 0.00 4.00
1548 1613 5.234466 AGATTGACAAACTAAGTGAGCCT 57.766 39.130 0.00 0.00 0.00 4.58
1643 1708 1.892474 TCCAAAAGGCCACAAGTATGC 59.108 47.619 5.01 0.00 0.00 3.14
1774 1846 6.262601 TCTGTTTCGTTCTTTCAACCATTTC 58.737 36.000 0.00 0.00 0.00 2.17
1804 1933 7.454260 AGATACTATGTTATGCACGATCTCA 57.546 36.000 0.00 0.00 0.00 3.27
1808 1937 4.979564 ATGTTATGCACGATCTCATTCG 57.020 40.909 0.00 0.00 44.56 3.34
1823 1952 4.160439 TCTCATTCGTGACCTAGCAGAATT 59.840 41.667 0.00 0.00 30.10 2.17
1824 1953 4.183865 TCATTCGTGACCTAGCAGAATTG 58.816 43.478 0.00 0.00 30.10 2.32
1855 1984 7.559170 CCAAAGAGGAATACTTCAGATTGGAAT 59.441 37.037 0.00 0.00 41.22 3.01
1870 1999 5.882557 AGATTGGAATGTGATAAGGTGACAC 59.117 40.000 0.00 0.00 35.45 3.67
1884 2013 5.099042 AGGTGACACAAATACCATCTACC 57.901 43.478 8.08 0.00 36.94 3.18
1902 2031 3.422417 ACCGTTCGACATCTATCTGTG 57.578 47.619 0.00 0.00 0.00 3.66
1934 2063 5.261209 AGTATGAAGCAACACAAGCAAAA 57.739 34.783 0.00 0.00 0.00 2.44
1947 2076 4.326278 CACAAGCAAAATATCTGCAAGCTG 59.674 41.667 11.23 0.00 42.48 4.24
1949 2078 2.758979 AGCAAAATATCTGCAAGCTGCT 59.241 40.909 11.23 0.00 45.31 4.24
1951 2080 4.400251 AGCAAAATATCTGCAAGCTGCTTA 59.600 37.500 15.51 0.00 45.31 3.09
1969 2098 7.441157 AGCTGCTTAATTTACGCACTATTATCA 59.559 33.333 3.67 0.00 0.00 2.15
1977 2106 9.658799 AATTTACGCACTATTATCAGCATAGAT 57.341 29.630 0.00 0.00 0.00 1.98
2033 2162 8.438676 AATTGGATAGTACGGAATTTCAAGAG 57.561 34.615 0.00 0.00 0.00 2.85
2035 2164 4.750598 GGATAGTACGGAATTTCAAGAGGC 59.249 45.833 0.00 0.00 0.00 4.70
2039 2168 1.167851 CGGAATTTCAAGAGGCTGCA 58.832 50.000 0.50 0.00 0.00 4.41
2074 2211 8.756864 GTTTGTCATCTTATAGCAGTAGTAAGC 58.243 37.037 0.00 0.00 0.00 3.09
2123 2260 4.671766 GCACCTTCGGTATTTGAACATCAC 60.672 45.833 0.00 0.00 32.11 3.06
2130 2267 5.622770 GGTATTTGAACATCACCGAAACT 57.377 39.130 0.00 0.00 0.00 2.66
2145 2282 7.158697 TCACCGAAACTCTGATTTCTGAATTA 58.841 34.615 0.00 0.00 36.59 1.40
2173 2310 4.595762 TCACTGTGTACTCTTTACCACC 57.404 45.455 7.79 0.00 0.00 4.61
2178 2315 3.389983 TGTGTACTCTTTACCACCTGCTT 59.610 43.478 0.00 0.00 0.00 3.91
2179 2316 3.746492 GTGTACTCTTTACCACCTGCTTG 59.254 47.826 0.00 0.00 0.00 4.01
2182 2319 4.910458 ACTCTTTACCACCTGCTTGTAT 57.090 40.909 0.00 0.00 0.00 2.29
2186 2326 6.212791 ACTCTTTACCACCTGCTTGTATTAGA 59.787 38.462 0.00 0.00 0.00 2.10
2249 2389 6.509418 TTTAAGAAAGTTGCGGCATCTTAT 57.491 33.333 22.56 15.44 33.85 1.73
2251 2391 2.609459 AGAAAGTTGCGGCATCTTATCG 59.391 45.455 22.56 0.00 0.00 2.92
2252 2392 2.024176 AAGTTGCGGCATCTTATCGT 57.976 45.000 21.35 1.02 0.00 3.73
2253 2393 2.882927 AGTTGCGGCATCTTATCGTA 57.117 45.000 2.28 0.00 0.00 3.43
2254 2394 3.386768 AGTTGCGGCATCTTATCGTAT 57.613 42.857 2.28 0.00 0.00 3.06
2255 2395 3.318017 AGTTGCGGCATCTTATCGTATC 58.682 45.455 2.28 0.00 0.00 2.24
2258 2398 2.094700 TGCGGCATCTTATCGTATCCTC 60.095 50.000 0.00 0.00 0.00 3.71
2259 2399 2.164624 GCGGCATCTTATCGTATCCTCT 59.835 50.000 0.00 0.00 0.00 3.69
2264 2449 6.349445 CGGCATCTTATCGTATCCTCTAAAGT 60.349 42.308 0.00 0.00 0.00 2.66
2265 2450 7.379750 GGCATCTTATCGTATCCTCTAAAGTT 58.620 38.462 0.00 0.00 0.00 2.66
2284 2469 5.130292 AGTTGAACTGCATCAAATTCCTG 57.870 39.130 4.34 0.00 40.76 3.86
2286 2471 5.479375 AGTTGAACTGCATCAAATTCCTGAT 59.521 36.000 4.34 0.00 40.76 2.90
2300 2492 1.202915 TCCTGATGTTGGCAAGCTGAA 60.203 47.619 0.00 0.00 0.00 3.02
2313 2505 3.231965 CAAGCTGAATTCGCTTCAACAG 58.768 45.455 24.74 14.89 45.27 3.16
2327 2519 5.519927 CGCTTCAACAGTTGGAAGAATTTTT 59.480 36.000 20.71 0.00 42.39 1.94
2375 2567 3.411446 TGCAACAACTAAGGGACATGAG 58.589 45.455 0.00 0.00 0.00 2.90
2402 2594 6.231211 AGATTCGTGGAAGTTTAAGTGTCAT 58.769 36.000 0.00 0.00 0.00 3.06
2428 2620 2.479566 TGAGAATGTCACTGGGAAGC 57.520 50.000 0.00 0.00 0.00 3.86
2432 2624 3.873952 GAGAATGTCACTGGGAAGCATAC 59.126 47.826 0.00 0.00 0.00 2.39
2449 2641 5.818136 GCATACAGCCTTACAATCAAAGA 57.182 39.130 0.00 0.00 37.23 2.52
2452 2644 6.732154 CATACAGCCTTACAATCAAAGATGG 58.268 40.000 0.00 0.00 0.00 3.51
2471 2663 8.729805 AAGATGGATCAGAAAAGTCATCTTAC 57.270 34.615 14.22 0.00 44.82 2.34
2501 2694 1.895798 TCTTGTCTGGAGTTGCGAGAT 59.104 47.619 0.00 0.00 33.74 2.75
2505 2698 4.471904 TGTCTGGAGTTGCGAGATTAAT 57.528 40.909 0.00 0.00 33.74 1.40
2511 2704 7.224753 GTCTGGAGTTGCGAGATTAATATGAAA 59.775 37.037 0.00 0.00 33.74 2.69
2517 2710 7.443575 AGTTGCGAGATTAATATGAAAGCAGAT 59.556 33.333 0.00 0.00 33.51 2.90
2518 2711 7.734924 TGCGAGATTAATATGAAAGCAGATT 57.265 32.000 0.00 0.00 39.18 2.40
2519 2712 8.158169 TGCGAGATTAATATGAAAGCAGATTT 57.842 30.769 0.00 0.00 37.20 2.17
2520 2713 8.071967 TGCGAGATTAATATGAAAGCAGATTTG 58.928 33.333 0.00 0.00 37.20 2.32
2521 2714 8.285394 GCGAGATTAATATGAAAGCAGATTTGA 58.715 33.333 0.00 0.00 37.20 2.69
2538 2731 9.241317 GCAGATTTGAATGTGGATAATTTACAG 57.759 33.333 3.47 0.00 30.94 2.74
2593 3018 7.594758 CGCCTCAACTTGAAAATCTTTCAATTA 59.405 33.333 13.38 2.03 37.72 1.40
2764 3225 0.599558 CAATGTGCCACACCTGAAGG 59.400 55.000 0.00 0.00 42.17 3.46
2807 3269 6.127730 CCAGGCCTTAAAATGTTAAGTGTAGG 60.128 42.308 0.00 7.07 43.22 3.18
2840 3302 6.636850 CCACTGCTTATATTTATTTCCAACGC 59.363 38.462 0.00 0.00 0.00 4.84
2855 3317 2.015736 AACGCTGAGTTGGAGCATAG 57.984 50.000 0.00 0.00 42.39 2.23
2874 3336 5.590145 CATAGCGATCAGGGAGAGAATATG 58.410 45.833 0.00 0.00 0.00 1.78
2875 3337 2.830923 AGCGATCAGGGAGAGAATATGG 59.169 50.000 0.00 0.00 0.00 2.74
2880 3342 4.542906 TCAGGGAGAGAATATGGTGAGA 57.457 45.455 0.00 0.00 0.00 3.27
2941 3403 3.504906 GGTGGATGCAGGATCACATATTG 59.495 47.826 4.07 0.00 31.91 1.90
2943 3405 4.823442 GTGGATGCAGGATCACATATTGAA 59.177 41.667 4.07 0.00 37.92 2.69
2952 3414 7.262772 CAGGATCACATATTGAAAATGCACTT 58.737 34.615 0.00 0.00 37.92 3.16
2966 3428 7.282675 TGAAAATGCACTTTCATTGGAACATTT 59.717 29.630 18.68 0.00 39.74 2.32
2967 3429 7.571080 AAATGCACTTTCATTGGAACATTTT 57.429 28.000 0.00 0.00 39.30 1.82
2999 3461 8.459911 AAGAAGTTGATGATATTGATGCATGA 57.540 30.769 2.46 0.00 0.00 3.07
3089 3551 3.190744 GTGCATATCATCAAGGCATGGAG 59.809 47.826 0.00 0.00 36.79 3.86
3107 3569 1.201181 GAGACACTGTCACGAGCAGAT 59.799 52.381 11.80 0.54 37.40 2.90
3120 3582 2.223456 CGAGCAGATGATGAGACTCGTT 60.223 50.000 0.00 0.00 41.43 3.85
3122 3584 3.023119 AGCAGATGATGAGACTCGTTCT 58.977 45.455 0.00 0.00 37.23 3.01
3124 3586 3.796178 GCAGATGATGAGACTCGTTCTTC 59.204 47.826 0.00 5.96 33.22 2.87
3156 3618 0.035343 GGCTTCCACTGGTTCTACCC 60.035 60.000 0.00 0.00 37.50 3.69
3253 3715 4.460382 TGGCTTCATTGAAAAGTCTGATCC 59.540 41.667 0.01 0.00 29.68 3.36
3312 3774 0.036010 AGGTCCTCCTGCATTTGACG 60.036 55.000 0.00 0.00 43.33 4.35
3334 3796 2.568623 ACTTGAGGTGTTGTCCATCC 57.431 50.000 0.00 0.00 0.00 3.51
3404 3866 5.123027 CCTCTCTTTCAAATGTTAGTCTGGC 59.877 44.000 0.00 0.00 0.00 4.85
3408 3870 6.061441 TCTTTCAAATGTTAGTCTGGCTTCA 58.939 36.000 0.00 0.00 0.00 3.02
3471 3933 5.512232 GCCATTATCCCTTAAGAGTCTCAGG 60.512 48.000 3.36 10.34 0.00 3.86
3477 3939 6.342819 TCCCTTAAGAGTCTCAGGATAGAA 57.657 41.667 16.79 0.00 0.00 2.10
3480 3942 7.678598 TCCCTTAAGAGTCTCAGGATAGAAAAA 59.321 37.037 16.79 0.00 0.00 1.94
3510 3972 1.005340 GAGCTGAATTCCTCTGTGCG 58.995 55.000 2.27 0.00 0.00 5.34
3527 3989 4.864334 GGACTGGCCGCAGATGGG 62.864 72.222 0.00 0.00 0.00 4.00
3528 3990 3.785859 GACTGGCCGCAGATGGGA 61.786 66.667 0.00 0.00 0.00 4.37
3600 4062 8.345565 GGTAGCCTAACATCTGTTAAATCATTG 58.654 37.037 4.49 0.00 39.70 2.82
3601 4063 6.799512 AGCCTAACATCTGTTAAATCATTGC 58.200 36.000 4.49 0.00 39.70 3.56
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 5.644636 TGGAACGGATGTAGAAATAACCAAC 59.355 40.000 0.00 0.00 0.00 3.77
89 93 6.978659 CGATGGCAAAGACTAAGAACACTATA 59.021 38.462 0.00 0.00 0.00 1.31
95 99 4.246458 AGACGATGGCAAAGACTAAGAAC 58.754 43.478 0.00 0.00 0.00 3.01
199 203 8.807118 TCTAGACACAGTGATGAATAAGAAAGT 58.193 33.333 7.81 0.00 0.00 2.66
248 254 8.208224 AGGGTTTACTTTTTGGGTTGAATAAAG 58.792 33.333 0.00 0.00 33.27 1.85
276 295 0.893727 ACGCCACTTCCATTGGGTTC 60.894 55.000 2.09 0.00 34.35 3.62
333 352 2.479566 TCTTCAAGACAGGTGATGCC 57.520 50.000 0.00 0.00 37.58 4.40
384 403 1.303948 CTCATGGGCCATGTCCACA 59.696 57.895 38.04 22.27 41.42 4.17
476 495 1.341080 CCATTTGTCCAACTTGGGCT 58.659 50.000 13.62 0.00 44.07 5.19
501 520 4.348168 AGGTAGAAGCCTTCTTTGAGTTCA 59.652 41.667 13.04 0.00 41.14 3.18
606 625 4.499037 AAAAGCTTTATTGACGGTGGAC 57.501 40.909 13.10 0.00 0.00 4.02
610 629 6.322491 GCTTCATAAAAGCTTTATTGACGGT 58.678 36.000 13.10 0.00 40.01 4.83
613 632 7.699812 CAGAGGCTTCATAAAAGCTTTATTGAC 59.300 37.037 13.10 7.54 42.62 3.18
618 637 4.094887 CGCAGAGGCTTCATAAAAGCTTTA 59.905 41.667 13.10 1.49 42.62 1.85
700 719 7.449704 GGATAGCAATTGATGGAAGTCCTTTAT 59.550 37.037 10.34 0.00 36.82 1.40
752 801 1.523938 GTTATGGCGGGGCAGTCTC 60.524 63.158 0.45 0.00 0.00 3.36
756 805 0.751277 TTGATGTTATGGCGGGGCAG 60.751 55.000 0.45 0.00 0.00 4.85
757 806 0.106268 ATTGATGTTATGGCGGGGCA 60.106 50.000 0.00 0.00 0.00 5.36
829 878 8.779303 ACGATCTATTATATGATCACGATCCTC 58.221 37.037 0.00 0.00 39.06 3.71
864 913 6.857956 ACTAGACTCAGTAATAGCAGTTGTG 58.142 40.000 0.00 0.00 0.00 3.33
894 955 1.812571 GTGGCCAAACCTGAGTACATG 59.187 52.381 7.24 0.00 40.22 3.21
914 975 2.029649 CCAATGCCTCAAACTCCAACAG 60.030 50.000 0.00 0.00 0.00 3.16
933 994 1.337118 GTGCCAAGGTGGATTTTCCA 58.663 50.000 0.00 0.00 45.98 3.53
955 1016 3.689649 GCCCTCTTGTCATTGTAAACGAT 59.310 43.478 0.00 0.00 0.00 3.73
957 1018 2.811431 TGCCCTCTTGTCATTGTAAACG 59.189 45.455 0.00 0.00 0.00 3.60
994 1055 5.590259 GTGAGATGCTTACCCACATTGTTAT 59.410 40.000 0.00 0.00 0.00 1.89
1059 1121 1.005215 CATTCCCCTTGAGAAGCAGGT 59.995 52.381 0.00 0.00 0.00 4.00
1060 1122 1.760192 CATTCCCCTTGAGAAGCAGG 58.240 55.000 0.00 0.00 0.00 4.85
1182 1246 1.555075 TCCCATTCTCTTTCACTCCCG 59.445 52.381 0.00 0.00 0.00 5.14
1185 1249 3.703001 TGGTCCCATTCTCTTTCACTC 57.297 47.619 0.00 0.00 0.00 3.51
1209 1273 5.245531 TGTTGTGAAACCATAGGAGCTAAG 58.754 41.667 0.00 0.00 34.36 2.18
1219 1283 3.524095 TCCCATCTGTTGTGAAACCAT 57.476 42.857 0.00 0.00 34.36 3.55
1221 1285 2.029918 GCTTCCCATCTGTTGTGAAACC 60.030 50.000 0.00 0.00 34.36 3.27
1248 1312 5.365605 TGTATCCCATCGAGAAGTTACCAAT 59.634 40.000 0.00 0.00 0.00 3.16
1264 1329 1.922447 AGCACCTGGAAATGTATCCCA 59.078 47.619 0.00 0.00 38.82 4.37
1339 1404 2.794103 TGCATGGTGCTTGAACAGTAT 58.206 42.857 3.41 0.00 45.31 2.12
1340 1405 2.268762 TGCATGGTGCTTGAACAGTA 57.731 45.000 3.41 0.00 45.31 2.74
1344 1409 2.490903 AGAGAATGCATGGTGCTTGAAC 59.509 45.455 0.00 0.00 45.31 3.18
1420 1485 3.390135 GGCCAAGCCTTTTAACAAACTC 58.610 45.455 0.00 0.00 46.69 3.01
1443 1508 0.039165 CTTTTGCCGCCAAAGGAGAC 60.039 55.000 8.71 0.00 41.58 3.36
1548 1613 4.623932 ACTCCACAAAAGAGCACTCATA 57.376 40.909 0.00 0.00 34.56 2.15
1774 1846 6.868339 TCGTGCATAACATAGTATCTTCCATG 59.132 38.462 0.00 0.00 0.00 3.66
1779 1851 7.886338 TGAGATCGTGCATAACATAGTATCTT 58.114 34.615 0.00 0.00 0.00 2.40
1804 1933 2.939103 GCAATTCTGCTAGGTCACGAAT 59.061 45.455 0.00 0.00 45.74 3.34
1823 1952 6.384015 TCTGAAGTATTCCTCTTTGGATAGCA 59.616 38.462 0.00 0.00 46.93 3.49
1824 1953 6.821388 TCTGAAGTATTCCTCTTTGGATAGC 58.179 40.000 0.00 0.00 46.93 2.97
1827 1956 7.059156 CCAATCTGAAGTATTCCTCTTTGGAT 58.941 38.462 0.00 0.00 46.93 3.41
1839 1968 8.497745 ACCTTATCACATTCCAATCTGAAGTAT 58.502 33.333 0.00 0.00 0.00 2.12
1855 1984 5.870706 TGGTATTTGTGTCACCTTATCACA 58.129 37.500 0.00 0.00 39.76 3.58
1870 1999 4.426416 TGTCGAACGGTAGATGGTATTTG 58.574 43.478 0.00 0.00 0.00 2.32
1884 2013 1.775770 CGCACAGATAGATGTCGAACG 59.224 52.381 0.00 0.00 0.00 3.95
1902 2031 4.092821 TGTTGCTTCATACTATCAACACGC 59.907 41.667 0.00 0.00 41.12 5.34
1947 2076 7.572759 TGCTGATAATAGTGCGTAAATTAAGC 58.427 34.615 4.01 4.01 0.00 3.09
1951 2080 9.658799 ATCTATGCTGATAATAGTGCGTAAATT 57.341 29.630 0.00 0.00 0.00 1.82
1969 2098 7.138250 ACATCATCTATTAGGGGATCTATGCT 58.862 38.462 0.00 0.00 0.00 3.79
1977 2106 6.497259 GGTCACTTACATCATCTATTAGGGGA 59.503 42.308 0.00 0.00 0.00 4.81
2011 2140 5.684030 GCCTCTTGAAATTCCGTACTATCCA 60.684 44.000 0.00 0.00 0.00 3.41
2012 2141 4.750598 GCCTCTTGAAATTCCGTACTATCC 59.249 45.833 0.00 0.00 0.00 2.59
2017 2146 2.096013 GCAGCCTCTTGAAATTCCGTAC 59.904 50.000 0.00 0.00 0.00 3.67
2033 2162 3.689161 TGACAAACATAGTACATGCAGCC 59.311 43.478 0.00 0.00 0.00 4.85
2035 2164 6.915544 AGATGACAAACATAGTACATGCAG 57.084 37.500 0.00 0.00 39.56 4.41
2074 2211 1.538512 CTCACCAACACATTCTGGCAG 59.461 52.381 8.58 8.58 36.03 4.85
2084 2221 2.475200 GTGCTTCAACTCACCAACAC 57.525 50.000 0.00 0.00 0.00 3.32
2123 2260 6.371548 TGGTAATTCAGAAATCAGAGTTTCGG 59.628 38.462 0.00 0.00 41.74 4.30
2130 2267 8.324306 AGTGATCTTGGTAATTCAGAAATCAGA 58.676 33.333 0.00 0.00 0.00 3.27
2145 2282 5.552870 AAAGAGTACACAGTGATCTTGGT 57.447 39.130 7.81 0.00 30.90 3.67
2173 2310 5.627499 TTGCCAGTTTCTAATACAAGCAG 57.373 39.130 0.00 0.00 30.77 4.24
2178 2315 8.911918 TCTTAACTTTGCCAGTTTCTAATACA 57.088 30.769 3.86 0.00 43.89 2.29
2179 2316 9.000486 ACTCTTAACTTTGCCAGTTTCTAATAC 58.000 33.333 3.86 0.00 43.89 1.89
2182 2319 7.875327 AACTCTTAACTTTGCCAGTTTCTAA 57.125 32.000 3.86 0.00 43.89 2.10
2186 2326 5.109210 GCAAACTCTTAACTTTGCCAGTTT 58.891 37.500 3.86 0.00 43.89 2.66
2216 2356 5.116074 CGCAACTTTCTTAAATTGCAGAGTG 59.884 40.000 8.37 0.00 46.18 3.51
2249 2389 5.047590 TGCAGTTCAACTTTAGAGGATACGA 60.048 40.000 0.00 0.00 46.39 3.43
2251 2391 6.818644 TGATGCAGTTCAACTTTAGAGGATAC 59.181 38.462 0.00 0.00 0.00 2.24
2252 2392 6.946340 TGATGCAGTTCAACTTTAGAGGATA 58.054 36.000 0.00 0.00 0.00 2.59
2253 2393 5.809001 TGATGCAGTTCAACTTTAGAGGAT 58.191 37.500 0.00 0.00 0.00 3.24
2254 2394 5.227569 TGATGCAGTTCAACTTTAGAGGA 57.772 39.130 0.00 0.00 0.00 3.71
2255 2395 5.947228 TTGATGCAGTTCAACTTTAGAGG 57.053 39.130 0.00 0.00 30.82 3.69
2258 2398 7.327761 CAGGAATTTGATGCAGTTCAACTTTAG 59.672 37.037 2.20 0.00 35.42 1.85
2259 2399 7.014134 TCAGGAATTTGATGCAGTTCAACTTTA 59.986 33.333 2.20 0.00 35.42 1.85
2264 2449 5.716094 CATCAGGAATTTGATGCAGTTCAA 58.284 37.500 7.09 0.00 45.49 2.69
2265 2450 5.319140 CATCAGGAATTTGATGCAGTTCA 57.681 39.130 7.09 0.00 45.49 3.18
2284 2469 2.523015 CGAATTCAGCTTGCCAACATC 58.477 47.619 6.22 0.00 0.00 3.06
2286 2471 0.039256 GCGAATTCAGCTTGCCAACA 60.039 50.000 6.22 0.00 0.00 3.33
2287 2472 0.242017 AGCGAATTCAGCTTGCCAAC 59.758 50.000 15.86 0.00 43.24 3.77
2300 2492 3.476552 TCTTCCAACTGTTGAAGCGAAT 58.523 40.909 21.49 0.00 0.00 3.34
2327 2519 9.084533 ACTCATAACCCTTTTTATTTAGCACAA 57.915 29.630 0.00 0.00 0.00 3.33
2333 2525 9.699703 GTTGCAACTCATAACCCTTTTTATTTA 57.300 29.630 22.36 0.00 0.00 1.40
2375 2567 5.465724 ACACTTAAACTTCCACGAATCTCAC 59.534 40.000 0.00 0.00 0.00 3.51
2402 2594 6.373005 TCCCAGTGACATTCTCAAGATTTA 57.627 37.500 0.00 0.00 0.00 1.40
2428 2620 6.543465 TCCATCTTTGATTGTAAGGCTGTATG 59.457 38.462 0.00 0.00 0.00 2.39
2432 2624 5.591472 TGATCCATCTTTGATTGTAAGGCTG 59.409 40.000 0.00 0.00 0.00 4.85
2440 2632 7.823665 TGACTTTTCTGATCCATCTTTGATTG 58.176 34.615 0.00 0.00 0.00 2.67
2449 2641 6.962182 TGGTAAGATGACTTTTCTGATCCAT 58.038 36.000 0.00 0.00 37.53 3.41
2452 2644 7.913674 AGTTGGTAAGATGACTTTTCTGATC 57.086 36.000 0.00 0.00 37.53 2.92
2471 2663 2.486982 CTCCAGACAAGATGCAAGTTGG 59.513 50.000 14.10 9.89 0.00 3.77
2501 2694 9.806203 CCACATTCAAATCTGCTTTCATATTAA 57.194 29.630 0.00 0.00 0.00 1.40
2505 2698 7.649533 ATCCACATTCAAATCTGCTTTCATA 57.350 32.000 0.00 0.00 0.00 2.15
2511 2704 8.970020 TGTAAATTATCCACATTCAAATCTGCT 58.030 29.630 0.00 0.00 0.00 4.24
2519 2712 9.513906 TCTTCAACTGTAAATTATCCACATTCA 57.486 29.630 0.00 0.00 0.00 2.57
2523 2716 9.739276 AGAATCTTCAACTGTAAATTATCCACA 57.261 29.630 0.00 0.00 0.00 4.17
2538 2731 6.513066 GCATCAAGCCATCTAGAATCTTCAAC 60.513 42.308 0.00 0.00 37.23 3.18
2593 3018 9.374711 TGGATACTTTGAAGATTTTTAACCCTT 57.625 29.630 0.00 0.00 37.61 3.95
2601 3051 5.420104 CCAGCCTGGATACTTTGAAGATTTT 59.580 40.000 4.15 0.00 40.96 1.82
2613 3063 3.906720 TCAAGTAACCAGCCTGGATAC 57.093 47.619 19.90 20.14 43.60 2.24
2764 3225 4.036852 GCCTGGTTGAAGATAAGGTAATGC 59.963 45.833 0.00 0.00 0.00 3.56
2774 3235 5.086621 ACATTTTAAGGCCTGGTTGAAGAT 58.913 37.500 5.69 0.00 0.00 2.40
2780 3241 5.600898 ACACTTAACATTTTAAGGCCTGGTT 59.399 36.000 5.69 7.20 45.99 3.67
2840 3302 2.223900 TGATCGCTATGCTCCAACTCAG 60.224 50.000 0.00 0.00 0.00 3.35
2855 3317 2.564947 ACCATATTCTCTCCCTGATCGC 59.435 50.000 0.00 0.00 0.00 4.58
2874 3336 1.884235 CCAAGTGGTCTGTTCTCACC 58.116 55.000 0.00 0.00 32.29 4.02
2875 3337 1.230324 GCCAAGTGGTCTGTTCTCAC 58.770 55.000 0.00 0.00 37.57 3.51
2880 3342 1.133823 TGTGATGCCAAGTGGTCTGTT 60.134 47.619 0.00 0.00 37.57 3.16
2941 3403 6.790285 ATGTTCCAATGAAAGTGCATTTTC 57.210 33.333 23.54 23.54 36.39 2.29
2943 3405 7.571080 AAAATGTTCCAATGAAAGTGCATTT 57.429 28.000 0.00 0.00 36.12 2.32
2977 3439 8.404107 TCATCATGCATCAATATCATCAACTT 57.596 30.769 0.00 0.00 0.00 2.66
2999 3461 5.302568 AGGTTTTGAACATGTGACACATCAT 59.697 36.000 18.27 9.96 36.53 2.45
3062 3524 5.664294 TGCCTTGATGATATGCACTTTTT 57.336 34.783 0.00 0.00 0.00 1.94
3068 3530 3.073356 TCTCCATGCCTTGATGATATGCA 59.927 43.478 0.00 0.00 36.23 3.96
3089 3551 1.068264 TCATCTGCTCGTGACAGTGTC 60.068 52.381 16.68 16.68 36.50 3.67
3120 3582 0.392998 GCCCAATGCTCCTTCGAAGA 60.393 55.000 26.61 11.39 36.87 2.87
3122 3584 4.319133 GCCCAATGCTCCTTCGAA 57.681 55.556 0.00 0.00 36.87 3.71
3141 3603 1.552486 CCTGAGGGTAGAACCAGTGGA 60.552 57.143 18.40 0.00 41.02 4.02
3156 3618 9.528018 GAAAGATAAAGTCTATGAAGTCCTGAG 57.472 37.037 0.00 0.00 35.67 3.35
3302 3764 2.948979 ACCTCAAGTTTCGTCAAATGCA 59.051 40.909 0.00 0.00 0.00 3.96
3312 3774 3.253432 GGATGGACAACACCTCAAGTTTC 59.747 47.826 0.00 0.00 0.00 2.78
3334 3796 4.081476 TGACCTGAGACACCAGATATGTTG 60.081 45.833 0.00 0.00 36.29 3.33
3341 3803 3.099905 CCTAATGACCTGAGACACCAGA 58.900 50.000 0.00 0.00 36.29 3.86
3404 3866 4.397417 CCAACTCTAAAGAAGGGCATGAAG 59.603 45.833 0.00 0.00 0.00 3.02
3408 3870 2.041620 TGCCAACTCTAAAGAAGGGCAT 59.958 45.455 12.37 0.00 39.63 4.40
3443 3905 6.915786 AGACTCTTAAGGGATAATGGCAAAT 58.084 36.000 9.99 0.00 0.00 2.32
3471 3933 5.098211 GCTCCAAGCACACATTTTTCTATC 58.902 41.667 0.00 0.00 41.89 2.08
3477 3939 2.309613 TCAGCTCCAAGCACACATTTT 58.690 42.857 1.29 0.00 45.56 1.82
3480 3942 2.211250 ATTCAGCTCCAAGCACACAT 57.789 45.000 1.29 0.00 45.56 3.21
3510 3972 4.864334 CCCATCTGCGGCCAGTCC 62.864 72.222 2.24 0.00 40.09 3.85
3527 3989 7.642669 TCTGCAGCTGCTTATTACAATATTTC 58.357 34.615 36.61 4.71 42.66 2.17
3528 3990 7.572523 TCTGCAGCTGCTTATTACAATATTT 57.427 32.000 36.61 0.00 42.66 1.40
3559 4021 2.170607 GGCTACCAACAGATAAGCAGGA 59.829 50.000 0.00 0.00 34.85 3.86
3561 4023 3.550437 AGGCTACCAACAGATAAGCAG 57.450 47.619 0.00 0.00 34.85 4.24


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

AutoCloner maintained by Alex Coulton.