Multiple sequence alignment - TraesCS3B01G405200

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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 TraesCS3B01G405200 chr3B 100.000 2894 0 0 1 2894 640663578 640666471 0.000000e+00 5345.0
1 TraesCS3B01G405200 chr3B 84.106 906 140 4 995 1898 640832258 640833161 0.000000e+00 872.0
2 TraesCS3B01G405200 chr3B 83.075 904 147 5 995 1895 640700705 640701605 0.000000e+00 817.0
3 TraesCS3B01G405200 chr3B 93.182 88 6 0 2350 2437 640665884 640665971 2.340000e-26 130.0
4 TraesCS3B01G405200 chr3B 93.182 88 6 0 2307 2394 640665927 640666014 2.340000e-26 130.0
5 TraesCS3B01G405200 chr3B 79.255 188 20 13 116 289 803519810 803519628 2.360000e-21 113.0
6 TraesCS3B01G405200 chr3D 90.242 1404 121 9 995 2395 480125308 480126698 0.000000e+00 1820.0
7 TraesCS3B01G405200 chr3D 87.968 989 72 12 30 1001 480124323 480125281 0.000000e+00 1123.0
8 TraesCS3B01G405200 chr3D 84.031 908 137 7 995 1898 480375815 480376718 0.000000e+00 867.0
9 TraesCS3B01G405200 chr3D 83.698 914 144 5 985 1895 480157912 480158823 0.000000e+00 857.0
10 TraesCS3B01G405200 chr3D 90.811 555 38 9 2350 2894 480126611 480127162 0.000000e+00 730.0
11 TraesCS3B01G405200 chr3D 84.229 279 40 2 30 305 69508435 69508712 4.750000e-68 268.0
12 TraesCS3B01G405200 chr3D 85.484 124 17 1 2583 2705 336588374 336588251 8.420000e-26 128.0
13 TraesCS3B01G405200 chr3A 87.071 1485 161 18 602 2076 623200028 623201491 0.000000e+00 1650.0
14 TraesCS3B01G405200 chr3A 89.764 1104 95 13 995 2085 623197009 623198107 0.000000e+00 1397.0
15 TraesCS3B01G405200 chr3A 80.839 1096 181 24 828 1898 623389445 623390536 0.000000e+00 833.0
16 TraesCS3B01G405200 chr3A 80.892 1099 172 25 828 1895 623354308 623355399 0.000000e+00 832.0
17 TraesCS3B01G405200 chr3A 93.985 266 15 1 720 985 623196695 623196959 4.490000e-108 401.0
18 TraesCS3B01G405200 chr3A 87.539 321 31 3 2076 2395 623219655 623219967 2.120000e-96 363.0
19 TraesCS3B01G405200 chr3A 87.281 228 15 3 392 607 623194199 623194424 6.190000e-62 248.0
20 TraesCS3B01G405200 chr3A 91.150 113 6 3 2350 2460 623219879 623219989 1.800000e-32 150.0
21 TraesCS3B01G405200 chr3A 97.826 46 1 0 2307 2352 623219922 623219967 2.390000e-11 80.5
22 TraesCS3B01G405200 chr4B 82.394 284 44 3 30 310 108357475 108357195 2.880000e-60 243.0
23 TraesCS3B01G405200 chr4B 83.333 120 19 1 2586 2704 22880717 22880598 3.050000e-20 110.0
24 TraesCS3B01G405200 chr5A 82.206 281 44 2 30 307 702566898 702567175 1.340000e-58 237.0
25 TraesCS3B01G405200 chr2D 80.573 314 44 11 26 330 351984507 351984202 2.900000e-55 226.0
26 TraesCS3B01G405200 chr2D 79.225 284 56 1 31 311 351986195 351985912 8.180000e-46 195.0
27 TraesCS3B01G405200 chr2D 83.803 142 19 3 78 217 292295977 292295838 6.510000e-27 132.0
28 TraesCS3B01G405200 chr2A 83.060 183 26 4 128 310 365286923 365286746 8.300000e-36 161.0
29 TraesCS3B01G405200 chr2A 76.786 280 40 13 43 305 619807471 619807742 1.810000e-27 134.0
30 TraesCS3B01G405200 chr5D 89.423 104 10 1 2601 2704 241361741 241361639 2.340000e-26 130.0
31 TraesCS3B01G405200 chr7D 90.323 93 8 1 2583 2674 567987071 567986979 1.410000e-23 121.0
32 TraesCS3B01G405200 chr7A 84.821 112 15 2 2601 2711 26034460 26034570 8.480000e-21 111.0
33 TraesCS3B01G405200 chr5B 86.408 103 13 1 2602 2704 447185040 447184939 8.480000e-21 111.0
34 TraesCS3B01G405200 chr2B 85.437 103 12 2 2602 2704 358048019 358048118 1.420000e-18 104.0
35 TraesCS3B01G405200 chr2B 94.444 36 0 2 570 603 744178434 744178469 1.000000e-03 54.7
36 TraesCS3B01G405200 chr1B 81.600 125 18 5 2582 2703 62792990 62793112 6.600000e-17 99.0


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 TraesCS3B01G405200 chr3B 640663578 640666471 2893 False 1868.333333 5345 95.454667 1 2894 3 chr3B.!!$F3 2893
1 TraesCS3B01G405200 chr3B 640832258 640833161 903 False 872.000000 872 84.106000 995 1898 1 chr3B.!!$F2 903
2 TraesCS3B01G405200 chr3B 640700705 640701605 900 False 817.000000 817 83.075000 995 1895 1 chr3B.!!$F1 900
3 TraesCS3B01G405200 chr3D 480124323 480127162 2839 False 1224.333333 1820 89.673667 30 2894 3 chr3D.!!$F4 2864
4 TraesCS3B01G405200 chr3D 480375815 480376718 903 False 867.000000 867 84.031000 995 1898 1 chr3D.!!$F3 903
5 TraesCS3B01G405200 chr3D 480157912 480158823 911 False 857.000000 857 83.698000 985 1895 1 chr3D.!!$F2 910
6 TraesCS3B01G405200 chr3A 623194199 623201491 7292 False 924.000000 1650 89.525250 392 2085 4 chr3A.!!$F3 1693
7 TraesCS3B01G405200 chr3A 623389445 623390536 1091 False 833.000000 833 80.839000 828 1898 1 chr3A.!!$F2 1070
8 TraesCS3B01G405200 chr3A 623354308 623355399 1091 False 832.000000 832 80.892000 828 1895 1 chr3A.!!$F1 1067
9 TraesCS3B01G405200 chr2D 351984202 351986195 1993 True 210.500000 226 79.899000 26 330 2 chr2D.!!$R2 304

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
112 928 0.321996 GGAGAAGGAGACCGTTGCTT 59.678 55.0 0.0 0.0 0.0 3.91 F
1341 4405 0.317436 GCAGCTACGGACTCTCATCG 60.317 60.0 0.0 0.0 0.0 3.84 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1484 4548 0.037232 GCTCTTTAGGTCTGTGGCGT 60.037 55.0 0.00 0.00 0.00 5.68 R
2182 8652 0.397941 ATGGACCTGCATACCGGATG 59.602 55.0 9.46 9.09 38.73 3.51 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 2.737830 TCATGTGGCGGTCGTTGA 59.262 55.556 0.00 0.00 0.00 3.18
18 19 1.666553 TCATGTGGCGGTCGTTGAC 60.667 57.895 0.00 0.00 0.00 3.18
19 20 2.736995 ATGTGGCGGTCGTTGACG 60.737 61.111 0.00 0.00 41.45 4.35
111 927 1.545706 GGGAGAAGGAGACCGTTGCT 61.546 60.000 0.00 0.00 0.00 3.91
112 928 0.321996 GGAGAAGGAGACCGTTGCTT 59.678 55.000 0.00 0.00 0.00 3.91
153 969 2.105930 GAGTAGCAGCGCCTCCTG 59.894 66.667 2.29 0.00 35.93 3.86
154 970 2.681778 AGTAGCAGCGCCTCCTGT 60.682 61.111 2.29 0.00 35.28 4.00
180 996 0.458669 TCTCCGGCTACATTTCGTCC 59.541 55.000 0.00 0.00 0.00 4.79
226 1045 4.648626 ACGACGACGACCCTCCCA 62.649 66.667 15.32 0.00 42.66 4.37
376 1198 8.882415 TTATAAACCCGATGAACTATGTCTTC 57.118 34.615 0.00 0.00 0.00 2.87
390 1213 1.002430 TGTCTTCTGGGTCAGATGCAC 59.998 52.381 0.00 3.57 40.39 4.57
416 1239 5.989477 TGTCCTATTAACCATGTGGAGAAG 58.011 41.667 5.96 0.00 38.94 2.85
503 1338 3.132289 GGCTACTACAGTTGTGGATAGCA 59.868 47.826 20.24 0.00 37.59 3.49
533 1368 2.842462 TGTCCGGTCACTGCCAGT 60.842 61.111 0.00 0.00 0.00 4.00
550 1385 1.599518 GTGGGCATGTCCGAACACA 60.600 57.895 12.67 0.00 38.48 3.72
553 1388 0.392998 GGGCATGTCCGAACACATCT 60.393 55.000 0.00 0.00 38.48 2.90
613 1448 6.715347 TGTAGATGCTCTAAGACTGCATAA 57.285 37.500 0.00 0.00 45.90 1.90
656 1914 4.090819 GAGTAGAAAACAGAGGAGAGGGT 58.909 47.826 0.00 0.00 0.00 4.34
666 1924 3.817647 CAGAGGAGAGGGTTCAGTTTTTG 59.182 47.826 0.00 0.00 0.00 2.44
685 1943 4.804608 TTGTTGTACGTCTTGTTGATGG 57.195 40.909 0.00 0.00 36.05 3.51
734 3738 4.864806 GTGATCTGAACGCACTCTGATTTA 59.135 41.667 0.00 0.00 35.02 1.40
735 3739 4.864806 TGATCTGAACGCACTCTGATTTAC 59.135 41.667 0.00 0.00 35.02 2.01
736 3740 4.521130 TCTGAACGCACTCTGATTTACT 57.479 40.909 0.00 0.00 0.00 2.24
737 3741 5.638596 TCTGAACGCACTCTGATTTACTA 57.361 39.130 0.00 0.00 0.00 1.82
738 3742 6.020971 TCTGAACGCACTCTGATTTACTAA 57.979 37.500 0.00 0.00 0.00 2.24
739 3743 6.631016 TCTGAACGCACTCTGATTTACTAAT 58.369 36.000 0.00 0.00 0.00 1.73
740 3744 7.768240 TCTGAACGCACTCTGATTTACTAATA 58.232 34.615 0.00 0.00 0.00 0.98
741 3745 7.915923 TCTGAACGCACTCTGATTTACTAATAG 59.084 37.037 0.00 0.00 0.00 1.73
742 3746 7.544622 TGAACGCACTCTGATTTACTAATAGT 58.455 34.615 0.00 0.00 0.00 2.12
743 3747 8.033038 TGAACGCACTCTGATTTACTAATAGTT 58.967 33.333 0.00 0.00 0.00 2.24
744 3748 8.773404 AACGCACTCTGATTTACTAATAGTTT 57.227 30.769 0.00 0.00 0.00 2.66
788 3792 7.049620 CGAGTAAATTACGCAAAGAGATTACG 58.950 38.462 7.59 0.00 33.90 3.18
872 3889 1.284982 CGACGGCAGGAAAGTCACTG 61.285 60.000 0.00 0.00 37.76 3.66
926 3946 7.067737 ACACTATAAAAATCCAAACATACCCGG 59.932 37.037 0.00 0.00 0.00 5.73
947 3970 4.618927 CGGCATCCATCACAACTCAAAATT 60.619 41.667 0.00 0.00 0.00 1.82
999 4063 2.312140 TCTACTCCTTCCTGTACCAGCT 59.688 50.000 0.00 0.00 0.00 4.24
1272 4336 2.092538 CCAGAGCAAGGACATCCAATCT 60.093 50.000 0.00 0.00 38.89 2.40
1280 4344 1.466856 GACATCCAATCTTGCCAGCA 58.533 50.000 0.00 0.00 0.00 4.41
1281 4345 1.820519 GACATCCAATCTTGCCAGCAA 59.179 47.619 4.78 4.78 0.00 3.91
1332 4396 3.138798 GGAGACGGCAGCTACGGA 61.139 66.667 13.60 0.00 35.23 4.69
1341 4405 0.317436 GCAGCTACGGACTCTCATCG 60.317 60.000 0.00 0.00 0.00 3.84
1380 4444 2.357154 GGTTGCCATGTACCTCTGGAAT 60.357 50.000 9.69 0.00 34.24 3.01
1484 4548 2.876091 CGCTAAGTTCTGGAACGATCA 58.124 47.619 7.67 0.00 45.50 2.92
1491 4555 1.374125 CTGGAACGATCACGCCACA 60.374 57.895 0.00 0.00 43.96 4.17
1502 4566 1.272490 TCACGCCACAGACCTAAAGAG 59.728 52.381 0.00 0.00 0.00 2.85
1623 4687 2.416701 CGACTTTGTTTGGGTGCAGTTT 60.417 45.455 0.00 0.00 0.00 2.66
1806 8275 1.221840 GCTTCCGCTGATCAAGGGA 59.778 57.895 14.72 12.32 41.34 4.20
1807 8276 0.392998 GCTTCCGCTGATCAAGGGAA 60.393 55.000 20.27 20.27 41.34 3.97
1831 8300 2.315925 CAAGTATGGAGGCGTCATGT 57.684 50.000 8.91 0.00 0.00 3.21
1844 8313 3.581755 GCGTCATGTTGTGGTCTAAGTA 58.418 45.455 0.00 0.00 0.00 2.24
1898 8367 4.025040 TCAAGAGCCATGTGTGATTCTT 57.975 40.909 0.00 0.00 32.00 2.52
1903 8372 5.809001 AGAGCCATGTGTGATTCTTCTTAA 58.191 37.500 0.00 0.00 0.00 1.85
1931 8400 4.330944 TGGCCTAGTATTTATGTGTCCG 57.669 45.455 3.32 0.00 0.00 4.79
1939 8408 5.416947 AGTATTTATGTGTCCGTTGTCCTC 58.583 41.667 0.00 0.00 0.00 3.71
1976 8446 6.676950 TGCGTTAATTGTTTGAGATGTCATT 58.323 32.000 0.00 0.00 30.85 2.57
1977 8447 6.581919 TGCGTTAATTGTTTGAGATGTCATTG 59.418 34.615 0.00 0.00 30.85 2.82
2030 8500 7.464273 TGAGGAGATATGCATCCATTGTAAAT 58.536 34.615 0.19 0.00 38.12 1.40
2031 8501 8.605065 TGAGGAGATATGCATCCATTGTAAATA 58.395 33.333 0.19 0.00 38.12 1.40
2032 8502 9.624373 GAGGAGATATGCATCCATTGTAAATAT 57.376 33.333 0.19 0.00 38.12 1.28
2091 8561 5.755375 AGTCTCATATTACAATCAAGCACCG 59.245 40.000 0.00 0.00 0.00 4.94
2106 8576 3.067106 AGCACCGTGACATACTTTTCTG 58.933 45.455 1.65 0.00 0.00 3.02
2115 8585 8.573885 CCGTGACATACTTTTCTGGTATATCTA 58.426 37.037 0.00 0.00 28.14 1.98
2144 8614 7.548075 AGTTACTTTTACGATCACCCAGTTATG 59.452 37.037 0.00 0.00 0.00 1.90
2146 8616 4.829872 TTTACGATCACCCAGTTATGGT 57.170 40.909 0.00 0.00 46.10 3.55
2147 8617 2.981859 ACGATCACCCAGTTATGGTC 57.018 50.000 0.00 0.00 46.10 4.02
2148 8618 2.467880 ACGATCACCCAGTTATGGTCT 58.532 47.619 0.00 0.00 46.10 3.85
2149 8619 2.168521 ACGATCACCCAGTTATGGTCTG 59.831 50.000 0.00 0.00 46.10 3.51
2150 8620 2.168521 CGATCACCCAGTTATGGTCTGT 59.831 50.000 0.00 0.00 46.10 3.41
2151 8621 3.738281 CGATCACCCAGTTATGGTCTGTC 60.738 52.174 0.00 0.00 46.10 3.51
2154 8624 3.587061 TCACCCAGTTATGGTCTGTCATT 59.413 43.478 0.00 0.00 46.10 2.57
2156 8626 4.156556 CACCCAGTTATGGTCTGTCATTTG 59.843 45.833 0.00 0.00 46.10 2.32
2171 8641 3.742369 GTCATTTGACATTTGGCAACCTG 59.258 43.478 0.00 3.23 43.85 4.00
2174 8644 4.478206 TTTGACATTTGGCAACCTGAAA 57.522 36.364 14.11 6.80 43.85 2.69
2182 8652 5.715434 TTTGGCAACCTGAAAGTATAACC 57.285 39.130 0.00 0.00 0.00 2.85
2198 8668 1.830145 ACCATCCGGTATGCAGGTC 59.170 57.895 0.00 0.00 46.71 3.85
2201 8671 0.397941 CATCCGGTATGCAGGTCCAT 59.602 55.000 0.00 0.00 0.00 3.41
2202 8672 0.397941 ATCCGGTATGCAGGTCCATG 59.602 55.000 0.00 0.00 0.00 3.66
2226 8696 7.164122 TGATATTCTCATGGTCTAAAGATGCC 58.836 38.462 0.00 0.00 0.00 4.40
2228 8698 4.412796 TCTCATGGTCTAAAGATGCCAG 57.587 45.455 0.00 0.00 34.18 4.85
2234 8704 5.235850 TGGTCTAAAGATGCCAGTAAACA 57.764 39.130 0.00 0.00 0.00 2.83
2238 8708 7.552687 TGGTCTAAAGATGCCAGTAAACATTAG 59.447 37.037 0.00 0.00 0.00 1.73
2241 8711 6.780457 AAAGATGCCAGTAAACATTAGCAT 57.220 33.333 0.00 0.00 43.25 3.79
2250 8720 9.099454 GCCAGTAAACATTAGCATATCCTATAC 57.901 37.037 0.00 0.00 0.00 1.47
2317 8788 8.747538 ATACACACATACTACATCACTACTCA 57.252 34.615 0.00 0.00 0.00 3.41
2318 8789 7.646548 ACACACATACTACATCACTACTCAT 57.353 36.000 0.00 0.00 0.00 2.90
2319 8790 7.484140 ACACACATACTACATCACTACTCATG 58.516 38.462 0.00 0.00 0.00 3.07
2320 8791 6.419116 CACACATACTACATCACTACTCATGC 59.581 42.308 0.00 0.00 0.00 4.06
2321 8792 5.923114 CACATACTACATCACTACTCATGCC 59.077 44.000 0.00 0.00 0.00 4.40
2322 8793 5.598417 ACATACTACATCACTACTCATGCCA 59.402 40.000 0.00 0.00 0.00 4.92
2323 8794 4.392921 ACTACATCACTACTCATGCCAC 57.607 45.455 0.00 0.00 0.00 5.01
2324 8795 2.698855 ACATCACTACTCATGCCACC 57.301 50.000 0.00 0.00 0.00 4.61
2325 8796 2.191400 ACATCACTACTCATGCCACCT 58.809 47.619 0.00 0.00 0.00 4.00
2326 8797 2.573462 ACATCACTACTCATGCCACCTT 59.427 45.455 0.00 0.00 0.00 3.50
2327 8798 3.774766 ACATCACTACTCATGCCACCTTA 59.225 43.478 0.00 0.00 0.00 2.69
2328 8799 4.410228 ACATCACTACTCATGCCACCTTAT 59.590 41.667 0.00 0.00 0.00 1.73
2329 8800 4.672587 TCACTACTCATGCCACCTTATC 57.327 45.455 0.00 0.00 0.00 1.75
2330 8801 4.030216 TCACTACTCATGCCACCTTATCA 58.970 43.478 0.00 0.00 0.00 2.15
2331 8802 4.469586 TCACTACTCATGCCACCTTATCAA 59.530 41.667 0.00 0.00 0.00 2.57
2332 8803 5.045942 TCACTACTCATGCCACCTTATCAAA 60.046 40.000 0.00 0.00 0.00 2.69
2333 8804 5.295292 CACTACTCATGCCACCTTATCAAAG 59.705 44.000 0.00 0.00 0.00 2.77
2334 8805 4.574674 ACTCATGCCACCTTATCAAAGA 57.425 40.909 0.00 0.00 34.37 2.52
2335 8806 4.265073 ACTCATGCCACCTTATCAAAGAC 58.735 43.478 0.00 0.00 34.37 3.01
2336 8807 3.620488 TCATGCCACCTTATCAAAGACC 58.380 45.455 0.00 0.00 34.37 3.85
2337 8808 2.507407 TGCCACCTTATCAAAGACCC 57.493 50.000 0.00 0.00 34.37 4.46
2338 8809 1.707989 TGCCACCTTATCAAAGACCCA 59.292 47.619 0.00 0.00 34.37 4.51
2339 8810 2.092323 GCCACCTTATCAAAGACCCAC 58.908 52.381 0.00 0.00 34.37 4.61
2340 8811 2.723273 CCACCTTATCAAAGACCCACC 58.277 52.381 0.00 0.00 34.37 4.61
2341 8812 2.308866 CCACCTTATCAAAGACCCACCT 59.691 50.000 0.00 0.00 34.37 4.00
2342 8813 3.610911 CACCTTATCAAAGACCCACCTC 58.389 50.000 0.00 0.00 34.37 3.85
2343 8814 3.009033 CACCTTATCAAAGACCCACCTCA 59.991 47.826 0.00 0.00 34.37 3.86
2344 8815 3.655777 ACCTTATCAAAGACCCACCTCAA 59.344 43.478 0.00 0.00 34.37 3.02
2345 8816 4.010349 CCTTATCAAAGACCCACCTCAAC 58.990 47.826 0.00 0.00 34.37 3.18
2346 8817 4.506625 CCTTATCAAAGACCCACCTCAACA 60.507 45.833 0.00 0.00 34.37 3.33
2347 8818 3.814504 ATCAAAGACCCACCTCAACAT 57.185 42.857 0.00 0.00 0.00 2.71
2348 8819 2.862541 TCAAAGACCCACCTCAACATG 58.137 47.619 0.00 0.00 0.00 3.21
2361 8832 4.080695 ACCTCAACATGCATCACTACTCAT 60.081 41.667 0.00 0.00 0.00 2.90
2371 8842 1.827344 TCACTACTCATGCCACCTCAG 59.173 52.381 0.00 0.00 0.00 3.35
2419 8890 3.159213 ACTCATGCCACCTCATCAAAA 57.841 42.857 0.00 0.00 0.00 2.44
2422 8893 1.134907 CATGCCACCTCATCAAAAGCC 60.135 52.381 0.00 0.00 0.00 4.35
2428 8899 1.147817 ACCTCATCAAAAGCCCACCTT 59.852 47.619 0.00 0.00 34.51 3.50
2437 8908 1.256812 AAGCCCACCTTAACATGCAC 58.743 50.000 0.00 0.00 30.18 4.57
2496 8974 8.727100 ATCTCAACATTCACATATCCTACCTA 57.273 34.615 0.00 0.00 0.00 3.08
2528 9006 4.025813 GTCACCACAACATGCATTGAAAAC 60.026 41.667 7.04 0.00 33.57 2.43
2667 9148 9.706691 TCGTTATAGATACATCCATTTCTTTCC 57.293 33.333 0.00 0.00 0.00 3.13
2677 9236 2.923020 CCATTTCTTTCCATTTTCGCGG 59.077 45.455 6.13 0.00 0.00 6.46
2687 9246 2.851824 CCATTTTCGCGGCAAGTAATTC 59.148 45.455 6.13 0.00 0.00 2.17
2688 9247 3.497118 CATTTTCGCGGCAAGTAATTCA 58.503 40.909 6.13 0.00 0.00 2.57
2809 9772 2.551270 GACTTCCACAGCAACGCG 59.449 61.111 3.53 3.53 0.00 6.01
2864 9827 7.117812 CCAACAACAATATAGATACCGTGATCC 59.882 40.741 0.00 0.00 0.00 3.36
2865 9828 7.540474 ACAACAATATAGATACCGTGATCCT 57.460 36.000 0.00 0.00 0.00 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.666553 GTCAACGACCGCCACATGA 60.667 57.895 0.00 0.00 0.00 3.07
2 3 2.736995 CGTCAACGACCGCCACAT 60.737 61.111 0.00 0.00 43.02 3.21
12 13 2.386491 CATCGTCGTGCGTCAACG 59.614 61.111 0.00 0.00 44.92 4.10
13 14 2.093983 GCATCGTCGTGCGTCAAC 59.906 61.111 4.48 0.00 42.13 3.18
14 15 3.109547 GGCATCGTCGTGCGTCAA 61.110 61.111 11.75 0.00 45.97 3.18
15 16 4.050934 AGGCATCGTCGTGCGTCA 62.051 61.111 11.75 0.00 45.97 4.35
17 18 4.796231 GGAGGCATCGTCGTGCGT 62.796 66.667 12.51 12.51 45.97 5.24
19 20 4.492160 TCGGAGGCATCGTCGTGC 62.492 66.667 10.20 10.20 44.31 5.34
20 21 2.579787 GTCGGAGGCATCGTCGTG 60.580 66.667 0.00 0.00 0.00 4.35
21 22 4.175489 CGTCGGAGGCATCGTCGT 62.175 66.667 9.79 0.00 35.31 4.34
23 24 3.982372 TTGCGTCGGAGGCATCGTC 62.982 63.158 24.01 0.38 38.88 4.20
24 25 3.989698 CTTGCGTCGGAGGCATCGT 62.990 63.158 24.01 0.00 38.88 3.73
26 27 1.447838 TTCTTGCGTCGGAGGCATC 60.448 57.895 24.01 0.00 38.88 3.91
27 28 1.741770 GTTCTTGCGTCGGAGGCAT 60.742 57.895 24.01 0.00 38.88 4.40
28 29 2.357034 GTTCTTGCGTCGGAGGCA 60.357 61.111 20.30 20.30 37.19 4.75
204 1020 4.451652 GGGTCGTCGTCGTCGTCC 62.452 72.222 16.72 16.72 38.33 4.79
226 1045 2.423898 CCCTGTACGCATCGGAGGT 61.424 63.158 0.00 0.00 0.00 3.85
307 1129 2.129555 AATGCAGAGGCGGAGTTGGT 62.130 55.000 0.00 0.00 45.35 3.67
357 1179 3.133003 CCAGAAGACATAGTTCATCGGGT 59.867 47.826 0.00 0.00 0.00 5.28
358 1180 3.493350 CCCAGAAGACATAGTTCATCGGG 60.493 52.174 0.00 0.00 0.00 5.14
361 1183 5.127845 TCTGACCCAGAAGACATAGTTCATC 59.872 44.000 0.00 0.00 37.57 2.92
363 1185 4.416516 TCTGACCCAGAAGACATAGTTCA 58.583 43.478 0.00 0.00 37.57 3.18
376 1198 2.484417 GGACATAGTGCATCTGACCCAG 60.484 54.545 0.00 0.00 0.00 4.45
390 1213 7.303182 TCTCCACATGGTTAATAGGACATAG 57.697 40.000 0.00 0.00 36.34 2.23
416 1239 7.445900 TGTAGATCAACATCGAACGATAAAC 57.554 36.000 9.33 1.57 33.75 2.01
464 1299 2.126502 CATTTGCCCGCACCGAAC 60.127 61.111 0.00 0.00 0.00 3.95
533 1368 0.676466 GATGTGTTCGGACATGCCCA 60.676 55.000 0.00 0.00 36.67 5.36
550 1385 1.071314 TCCCCCAAACACCCACAGAT 61.071 55.000 0.00 0.00 0.00 2.90
553 1388 2.009882 AGTCCCCCAAACACCCACA 61.010 57.895 0.00 0.00 0.00 4.17
613 1448 0.252012 AGAGTACCAGGCAGAGCACT 60.252 55.000 0.00 0.00 0.00 4.40
656 1914 6.243811 ACAAGACGTACAACAAAAACTGAA 57.756 33.333 0.00 0.00 0.00 3.02
666 1924 4.806342 AACCATCAACAAGACGTACAAC 57.194 40.909 0.00 0.00 0.00 3.32
685 1943 1.405121 CCCTACCGTGCTAGACCAAAC 60.405 57.143 0.00 0.00 0.00 2.93
872 3889 3.702478 GCGTCATGGAGGCTTTTTC 57.298 52.632 3.86 0.00 39.86 2.29
926 3946 5.346822 GTGAATTTTGAGTTGTGATGGATGC 59.653 40.000 0.00 0.00 0.00 3.91
947 3970 2.917227 TGAGGAGGTGCGCTGTGA 60.917 61.111 9.73 0.00 0.00 3.58
967 3990 4.411212 AGGAAGGAGTAGAGACTAGAGACC 59.589 50.000 0.00 0.00 35.45 3.85
1280 4344 2.113243 GAGGACCTTGACACCGCCTT 62.113 60.000 0.00 0.00 0.00 4.35
1281 4345 2.526873 AGGACCTTGACACCGCCT 60.527 61.111 0.00 0.00 0.00 5.52
1332 4396 1.758514 ATCACCGGGCGATGAGAGT 60.759 57.895 6.32 0.00 0.00 3.24
1380 4444 2.983791 GTGCCGCCCAGGTAGTTA 59.016 61.111 0.00 0.00 43.70 2.24
1461 4525 1.359459 CGTTCCAGAACTTAGCGCCC 61.359 60.000 2.29 0.00 39.08 6.13
1467 4531 2.602878 GCGTGATCGTTCCAGAACTTA 58.397 47.619 8.77 0.00 39.08 2.24
1484 4548 0.037232 GCTCTTTAGGTCTGTGGCGT 60.037 55.000 0.00 0.00 0.00 5.68
1502 4566 0.803117 GCCACCGTTCTTTCCTAAGC 59.197 55.000 0.00 0.00 0.00 3.09
1596 4660 2.680841 CACCCAAACAAAGTCGAACAGA 59.319 45.455 0.00 0.00 0.00 3.41
1623 4687 1.213182 TGGCACTCTGGGTTGTTGTAA 59.787 47.619 0.00 0.00 0.00 2.41
1806 8275 1.077716 GCCTCCATACTTGGGCGTT 60.078 57.895 0.00 0.00 43.81 4.84
1807 8276 2.590092 GCCTCCATACTTGGGCGT 59.410 61.111 0.00 0.00 43.81 5.68
1821 8290 0.973632 TAGACCACAACATGACGCCT 59.026 50.000 0.00 0.00 0.00 5.52
1831 8300 4.314961 TCGTCGTAGTACTTAGACCACAA 58.685 43.478 18.66 5.62 0.00 3.33
1844 8313 1.022982 TCCAGTGCGATCGTCGTAGT 61.023 55.000 17.81 1.40 42.81 2.73
1898 8367 5.630415 ATACTAGGCCAAGCACATTAAGA 57.370 39.130 5.01 0.00 0.00 2.10
1903 8372 5.532406 CACATAAATACTAGGCCAAGCACAT 59.468 40.000 5.01 0.00 0.00 3.21
1931 8400 5.403766 CGCATGATACTATGAAGAGGACAAC 59.596 44.000 0.00 0.00 0.00 3.32
1939 8408 9.935682 AAACAATTAACGCATGATACTATGAAG 57.064 29.630 0.00 0.00 0.00 3.02
1976 8446 3.257375 CCGGTATGCTAGCTACCAATACA 59.743 47.826 28.01 6.22 38.88 2.29
1977 8447 3.257624 ACCGGTATGCTAGCTACCAATAC 59.742 47.826 28.01 20.93 38.88 1.89
2064 8534 9.277783 GGTGCTTGATTGTAATATGAGACTTAT 57.722 33.333 0.00 0.00 0.00 1.73
2071 8541 5.293324 GTCACGGTGCTTGATTGTAATATGA 59.707 40.000 2.51 0.00 0.00 2.15
2076 8546 2.839975 TGTCACGGTGCTTGATTGTAA 58.160 42.857 2.51 0.00 0.00 2.41
2083 8553 3.498397 AGAAAAGTATGTCACGGTGCTTG 59.502 43.478 2.51 0.00 0.00 4.01
2084 8554 3.498397 CAGAAAAGTATGTCACGGTGCTT 59.502 43.478 2.51 0.00 0.00 3.91
2115 8585 7.618137 ACTGGGTGATCGTAAAAGTAACTTAT 58.382 34.615 0.00 0.00 0.00 1.73
2118 8588 5.479124 ACTGGGTGATCGTAAAAGTAACT 57.521 39.130 0.00 0.00 0.00 2.24
2149 8619 3.742369 CAGGTTGCCAAATGTCAAATGAC 59.258 43.478 6.60 6.60 44.97 3.06
2150 8620 3.640498 TCAGGTTGCCAAATGTCAAATGA 59.360 39.130 0.00 0.00 0.00 2.57
2151 8621 3.992643 TCAGGTTGCCAAATGTCAAATG 58.007 40.909 0.00 0.00 0.00 2.32
2154 8624 3.450457 ACTTTCAGGTTGCCAAATGTCAA 59.550 39.130 0.00 0.00 0.00 3.18
2156 8626 3.733443 ACTTTCAGGTTGCCAAATGTC 57.267 42.857 0.00 0.00 0.00 3.06
2182 8652 0.397941 ATGGACCTGCATACCGGATG 59.602 55.000 9.46 9.09 38.73 3.51
2201 8671 7.164122 GGCATCTTTAGACCATGAGAATATCA 58.836 38.462 0.00 0.00 43.70 2.15
2202 8672 7.164122 TGGCATCTTTAGACCATGAGAATATC 58.836 38.462 0.00 0.00 0.00 1.63
2263 8733 9.862371 TGAGAGAATTAAGTAGTGAAGATCAAC 57.138 33.333 0.00 0.00 0.00 3.18
2291 8762 9.841295 TGAGTAGTGATGTAGTATGTGTGTATA 57.159 33.333 0.00 0.00 0.00 1.47
2294 8765 7.484140 CATGAGTAGTGATGTAGTATGTGTGT 58.516 38.462 0.00 0.00 0.00 3.72
2306 8777 2.996249 AGGTGGCATGAGTAGTGATG 57.004 50.000 0.00 0.00 0.00 3.07
2307 8778 4.655649 TGATAAGGTGGCATGAGTAGTGAT 59.344 41.667 0.00 0.00 0.00 3.06
2308 8779 4.030216 TGATAAGGTGGCATGAGTAGTGA 58.970 43.478 0.00 0.00 0.00 3.41
2309 8780 4.406648 TGATAAGGTGGCATGAGTAGTG 57.593 45.455 0.00 0.00 0.00 2.74
2310 8781 5.189736 TCTTTGATAAGGTGGCATGAGTAGT 59.810 40.000 0.00 0.00 32.02 2.73
2311 8782 5.525378 GTCTTTGATAAGGTGGCATGAGTAG 59.475 44.000 0.00 0.00 32.02 2.57
2312 8783 5.428253 GTCTTTGATAAGGTGGCATGAGTA 58.572 41.667 0.00 0.00 32.02 2.59
2313 8784 4.265073 GTCTTTGATAAGGTGGCATGAGT 58.735 43.478 0.00 0.00 32.02 3.41
2314 8785 3.629398 GGTCTTTGATAAGGTGGCATGAG 59.371 47.826 0.00 0.00 32.02 2.90
2315 8786 3.620488 GGTCTTTGATAAGGTGGCATGA 58.380 45.455 0.00 0.00 32.02 3.07
2316 8787 2.689983 GGGTCTTTGATAAGGTGGCATG 59.310 50.000 0.00 0.00 32.02 4.06
2317 8788 2.311542 TGGGTCTTTGATAAGGTGGCAT 59.688 45.455 0.00 0.00 32.02 4.40
2318 8789 1.707989 TGGGTCTTTGATAAGGTGGCA 59.292 47.619 0.00 0.00 32.02 4.92
2319 8790 2.092323 GTGGGTCTTTGATAAGGTGGC 58.908 52.381 0.00 0.00 32.02 5.01
2320 8791 2.308866 AGGTGGGTCTTTGATAAGGTGG 59.691 50.000 0.00 0.00 32.02 4.61
2321 8792 3.009033 TGAGGTGGGTCTTTGATAAGGTG 59.991 47.826 0.00 0.00 32.02 4.00
2322 8793 3.256704 TGAGGTGGGTCTTTGATAAGGT 58.743 45.455 0.00 0.00 32.02 3.50
2323 8794 4.010349 GTTGAGGTGGGTCTTTGATAAGG 58.990 47.826 0.00 0.00 32.02 2.69
2324 8795 4.651778 TGTTGAGGTGGGTCTTTGATAAG 58.348 43.478 0.00 0.00 0.00 1.73
2325 8796 4.715534 TGTTGAGGTGGGTCTTTGATAA 57.284 40.909 0.00 0.00 0.00 1.75
2326 8797 4.588899 CATGTTGAGGTGGGTCTTTGATA 58.411 43.478 0.00 0.00 0.00 2.15
2327 8798 3.424703 CATGTTGAGGTGGGTCTTTGAT 58.575 45.455 0.00 0.00 0.00 2.57
2328 8799 2.862541 CATGTTGAGGTGGGTCTTTGA 58.137 47.619 0.00 0.00 0.00 2.69
2329 8800 1.270550 GCATGTTGAGGTGGGTCTTTG 59.729 52.381 0.00 0.00 0.00 2.77
2330 8801 1.133513 TGCATGTTGAGGTGGGTCTTT 60.134 47.619 0.00 0.00 0.00 2.52
2331 8802 0.478072 TGCATGTTGAGGTGGGTCTT 59.522 50.000 0.00 0.00 0.00 3.01
2332 8803 0.700564 ATGCATGTTGAGGTGGGTCT 59.299 50.000 0.00 0.00 0.00 3.85
2333 8804 1.098050 GATGCATGTTGAGGTGGGTC 58.902 55.000 2.46 0.00 0.00 4.46
2334 8805 0.405198 TGATGCATGTTGAGGTGGGT 59.595 50.000 2.46 0.00 0.00 4.51
2335 8806 0.813184 GTGATGCATGTTGAGGTGGG 59.187 55.000 2.46 0.00 0.00 4.61
2336 8807 1.830279 AGTGATGCATGTTGAGGTGG 58.170 50.000 2.46 0.00 0.00 4.61
2337 8808 3.603532 AGTAGTGATGCATGTTGAGGTG 58.396 45.455 2.46 0.00 0.00 4.00
2338 8809 3.261643 TGAGTAGTGATGCATGTTGAGGT 59.738 43.478 2.46 0.00 0.00 3.85
2339 8810 3.865446 TGAGTAGTGATGCATGTTGAGG 58.135 45.455 2.46 0.00 0.00 3.86
2340 8811 4.260661 GCATGAGTAGTGATGCATGTTGAG 60.261 45.833 16.07 0.00 43.75 3.02
2341 8812 3.624410 GCATGAGTAGTGATGCATGTTGA 59.376 43.478 16.07 0.00 43.75 3.18
2342 8813 3.242969 GGCATGAGTAGTGATGCATGTTG 60.243 47.826 21.34 0.00 45.70 3.33
2343 8814 2.947652 GGCATGAGTAGTGATGCATGTT 59.052 45.455 21.34 0.00 45.70 2.71
2344 8815 2.092807 TGGCATGAGTAGTGATGCATGT 60.093 45.455 21.34 0.00 45.70 3.21
2345 8816 2.289820 GTGGCATGAGTAGTGATGCATG 59.710 50.000 21.34 8.17 45.70 4.06
2346 8817 2.569059 GTGGCATGAGTAGTGATGCAT 58.431 47.619 21.34 0.00 45.70 3.96
2347 8818 1.407299 GGTGGCATGAGTAGTGATGCA 60.407 52.381 21.34 7.08 45.70 3.96
2348 8819 1.134280 AGGTGGCATGAGTAGTGATGC 60.134 52.381 13.04 13.04 43.60 3.91
2361 8832 2.598394 GCCTTTGCTGAGGTGGCA 60.598 61.111 7.60 0.00 42.79 4.92
2386 8857 2.947652 GGCATGAGTAGTGATGCATGTT 59.052 45.455 21.34 0.00 45.70 2.71
2419 8890 0.960364 CGTGCATGTTAAGGTGGGCT 60.960 55.000 0.00 0.00 0.00 5.19
2422 8893 0.521291 CACCGTGCATGTTAAGGTGG 59.479 55.000 20.88 6.90 46.15 4.61
2481 8959 8.783660 ACTCTTTGATTAGGTAGGATATGTGA 57.216 34.615 0.00 0.00 0.00 3.58
2496 8974 4.261741 GCATGTTGTGGTGACTCTTTGATT 60.262 41.667 0.00 0.00 0.00 2.57
2505 8983 3.367992 TTCAATGCATGTTGTGGTGAC 57.632 42.857 0.00 0.00 0.00 3.67
2667 9148 3.497118 TGAATTACTTGCCGCGAAAATG 58.503 40.909 8.23 0.00 0.00 2.32
2677 9236 2.673368 CACTCCGTCCTGAATTACTTGC 59.327 50.000 0.00 0.00 0.00 4.01
2687 9246 4.920640 ATTGTATACTCACTCCGTCCTG 57.079 45.455 4.17 0.00 0.00 3.86
2688 9247 6.069331 ACATATTGTATACTCACTCCGTCCT 58.931 40.000 4.17 0.00 0.00 3.85
2774 9333 5.909610 GGAAGTCGCTGCAATATATTTCAAC 59.090 40.000 0.00 0.00 0.00 3.18
2779 9742 4.450976 TGTGGAAGTCGCTGCAATATATT 58.549 39.130 0.00 0.00 0.00 1.28
2809 9772 6.811253 TCATATAATTAAATGACACCCCGC 57.189 37.500 0.00 0.00 0.00 6.13
2856 9819 3.942130 TGATATACTGCAGGATCACGG 57.058 47.619 16.72 0.00 0.00 4.94
2857 9820 6.625362 ACTTATGATATACTGCAGGATCACG 58.375 40.000 16.72 14.53 31.41 4.35
2864 9827 6.763355 AGACCCAACTTATGATATACTGCAG 58.237 40.000 13.48 13.48 0.00 4.41
2865 9828 6.747414 AGACCCAACTTATGATATACTGCA 57.253 37.500 0.00 0.00 0.00 4.41


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

AutoCloner maintained by Alex Coulton.