Multiple sequence alignment - TraesCS7D01G118200

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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 TraesCS7D01G118200 chr7D 100.000 2615 0 0 1 2615 73118201 73115587 0.000000e+00 4830.0
1 TraesCS7D01G118200 chr7D 90.625 640 47 10 1069 1704 71812577 71813207 0.000000e+00 837.0
2 TraesCS7D01G118200 chr7D 91.823 587 37 7 1069 1648 71864511 71863929 0.000000e+00 808.0
3 TraesCS7D01G118200 chr7D 81.690 355 43 15 1718 2066 72217032 72217370 2.560000e-70 276.0
4 TraesCS7D01G118200 chr7D 80.000 350 50 10 2208 2541 72218316 72218661 9.350000e-60 241.0
5 TraesCS7D01G118200 chr7A 89.388 1649 136 29 23 1648 77149047 77150679 0.000000e+00 2039.0
6 TraesCS7D01G118200 chr7A 87.356 1392 109 36 766 2117 77194613 77195977 0.000000e+00 1533.0
7 TraesCS7D01G118200 chr7A 93.220 59 4 0 2321 2379 77197207 77197265 1.290000e-13 87.9
8 TraesCS7D01G118200 chr7A 97.143 35 1 0 2336 2370 77197171 77197205 2.810000e-05 60.2
9 TraesCS7D01G118200 chr7B 82.901 1310 155 46 800 2066 15298113 15299396 0.000000e+00 1114.0
10 TraesCS7D01G118200 chr7B 90.395 583 47 8 1071 1648 14866443 14865865 0.000000e+00 758.0
11 TraesCS7D01G118200 chr7B 82.198 455 58 10 2175 2615 15300269 15300714 1.140000e-98 370.0
12 TraesCS7D01G118200 chr7B 84.211 399 28 4 2175 2541 15020099 15020494 3.200000e-94 355.0
13 TraesCS7D01G118200 chr7B 79.355 465 68 9 2175 2615 15269432 15269892 4.230000e-78 302.0
14 TraesCS7D01G118200 chr7B 82.471 348 34 8 2175 2498 15071679 15072023 1.980000e-71 279.0
15 TraesCS7D01G118200 chrUn 92.637 584 37 3 1071 1648 82605062 82604479 0.000000e+00 835.0
16 TraesCS7D01G118200 chrUn 90.267 637 50 8 1071 1704 84331098 84330471 0.000000e+00 822.0
17 TraesCS7D01G118200 chrUn 92.473 558 42 0 1068 1625 82565941 82566498 0.000000e+00 798.0
18 TraesCS7D01G118200 chr1B 72.642 424 89 16 118 538 384237372 384237771 5.910000e-22 115.0


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 TraesCS7D01G118200 chr7D 73115587 73118201 2614 True 4830.000000 4830 100.0000 1 2615 1 chr7D.!!$R2 2614
1 TraesCS7D01G118200 chr7D 71812577 71813207 630 False 837.000000 837 90.6250 1069 1704 1 chr7D.!!$F1 635
2 TraesCS7D01G118200 chr7D 71863929 71864511 582 True 808.000000 808 91.8230 1069 1648 1 chr7D.!!$R1 579
3 TraesCS7D01G118200 chr7D 72217032 72218661 1629 False 258.500000 276 80.8450 1718 2541 2 chr7D.!!$F2 823
4 TraesCS7D01G118200 chr7A 77149047 77150679 1632 False 2039.000000 2039 89.3880 23 1648 1 chr7A.!!$F1 1625
5 TraesCS7D01G118200 chr7A 77194613 77197265 2652 False 560.366667 1533 92.5730 766 2379 3 chr7A.!!$F2 1613
6 TraesCS7D01G118200 chr7B 14865865 14866443 578 True 758.000000 758 90.3950 1071 1648 1 chr7B.!!$R1 577
7 TraesCS7D01G118200 chr7B 15298113 15300714 2601 False 742.000000 1114 82.5495 800 2615 2 chr7B.!!$F4 1815
8 TraesCS7D01G118200 chrUn 82604479 82605062 583 True 835.000000 835 92.6370 1071 1648 1 chrUn.!!$R1 577
9 TraesCS7D01G118200 chrUn 84330471 84331098 627 True 822.000000 822 90.2670 1071 1704 1 chrUn.!!$R2 633
10 TraesCS7D01G118200 chrUn 82565941 82566498 557 False 798.000000 798 92.4730 1068 1625 1 chrUn.!!$F1 557

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
152 154 0.03601 CGAGAGGGCCTGACAACATT 60.036 55.0 12.95 0.0 0.0 2.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2141 3297 0.169672 TCGTTGCTGCCTACTCGTAC 59.83 55.0 0.0 0.0 0.0 3.67 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
21 22 3.214123 CTCGACCGGCCCGATGTA 61.214 66.667 18.03 0.00 35.35 2.29
65 66 4.301027 GCTATGGACGCCCTCCGG 62.301 72.222 0.00 0.00 43.03 5.14
82 83 1.613630 GGAGGTGGCTGAGAAGGGA 60.614 63.158 0.00 0.00 0.00 4.20
143 145 4.361971 TGTCGGACGAGAGGGCCT 62.362 66.667 5.25 5.25 0.00 5.19
152 154 0.036010 CGAGAGGGCCTGACAACATT 60.036 55.000 12.95 0.00 0.00 2.71
159 161 2.267351 CCTGACAACATTGCCCGCA 61.267 57.895 0.00 0.00 0.00 5.69
201 204 3.375472 GACGCCCCGGACCGTTATT 62.375 63.158 18.09 0.00 37.87 1.40
204 207 1.377594 GCCCCGGACCGTTATTTGT 60.378 57.895 13.94 0.00 0.00 2.83
213 216 0.169451 CCGTTATTTGTTGTCGCCCC 59.831 55.000 0.00 0.00 0.00 5.80
221 224 1.067582 GTTGTCGCCCCGATCTAGG 59.932 63.158 0.00 0.00 38.42 3.02
265 268 2.094545 GGAAAGCAACCACATCCATGTC 60.095 50.000 0.00 0.00 39.39 3.06
274 277 3.450817 ACCACATCCATGTCGAAGTCATA 59.549 43.478 0.00 0.00 39.39 2.15
275 278 4.053983 CCACATCCATGTCGAAGTCATAG 58.946 47.826 0.00 0.00 39.39 2.23
282 285 3.211803 TGTCGAAGTCATAGTTGTCGG 57.788 47.619 0.00 0.00 32.68 4.79
287 290 3.259902 GAAGTCATAGTTGTCGGAACCC 58.740 50.000 0.00 0.00 0.00 4.11
335 339 3.531059 TCAGATTGGGAAGAAGAAGGGA 58.469 45.455 0.00 0.00 0.00 4.20
337 341 3.009473 CAGATTGGGAAGAAGAAGGGACA 59.991 47.826 0.00 0.00 0.00 4.02
342 346 2.499693 GGGAAGAAGAAGGGACAGAGAG 59.500 54.545 0.00 0.00 0.00 3.20
344 348 3.447229 GGAAGAAGAAGGGACAGAGAGAG 59.553 52.174 0.00 0.00 0.00 3.20
354 358 0.178950 ACAGAGAGAGTGGAGTGGCA 60.179 55.000 0.00 0.00 0.00 4.92
360 364 0.546267 AGAGTGGAGTGGCATGGAGT 60.546 55.000 0.00 0.00 0.00 3.85
371 375 1.195115 GCATGGAGTGGTCTGAGGTA 58.805 55.000 0.00 0.00 0.00 3.08
374 378 3.006323 GCATGGAGTGGTCTGAGGTATAG 59.994 52.174 0.00 0.00 0.00 1.31
383 387 5.128827 GTGGTCTGAGGTATAGGTTTCATCA 59.871 44.000 0.00 0.00 0.00 3.07
385 389 5.598830 GGTCTGAGGTATAGGTTTCATCAGA 59.401 44.000 4.98 4.98 43.37 3.27
395 399 9.606631 GTATAGGTTTCATCAGATTGGGATATC 57.393 37.037 0.00 0.00 0.00 1.63
406 410 2.512910 TGGGATATCTGTGGGGTCAT 57.487 50.000 2.05 0.00 0.00 3.06
442 446 3.986006 GGCCTGACGTGACGGACA 61.986 66.667 10.66 8.41 0.00 4.02
443 447 2.028484 GCCTGACGTGACGGACAA 59.972 61.111 10.66 0.00 0.00 3.18
485 496 4.381398 CGCCTCATATCCTTCCTACATCTG 60.381 50.000 0.00 0.00 0.00 2.90
491 502 0.471617 CCTTCCTACATCTGGGCTGG 59.528 60.000 0.00 0.00 0.00 4.85
494 505 3.242867 CTTCCTACATCTGGGCTGGATA 58.757 50.000 0.00 0.00 0.00 2.59
503 514 0.768221 TGGGCTGGATATGAGGGGTC 60.768 60.000 0.00 0.00 0.00 4.46
504 515 0.474660 GGGCTGGATATGAGGGGTCT 60.475 60.000 0.00 0.00 0.00 3.85
507 518 1.762827 GCTGGATATGAGGGGTCTGGA 60.763 57.143 0.00 0.00 0.00 3.86
543 554 2.672996 CCGGTTTGAGGTGCCCAG 60.673 66.667 0.00 0.00 0.00 4.45
551 562 1.142748 GAGGTGCCCAGATGAGTCG 59.857 63.158 0.00 0.00 0.00 4.18
556 567 1.464997 GTGCCCAGATGAGTCGTTTTC 59.535 52.381 0.00 0.00 0.00 2.29
571 582 3.068590 TCGTTTTCTTCTTACCGGTCAGT 59.931 43.478 12.40 0.00 0.00 3.41
617 628 2.361610 ATTTGGGGCGCCTGACTG 60.362 61.111 28.56 0.00 0.00 3.51
642 653 4.938226 AGAAGCTTTTACATTCTCTTCCGG 59.062 41.667 0.00 0.00 32.62 5.14
650 661 2.305927 ACATTCTCTTCCGGGTCAATGT 59.694 45.455 0.00 6.95 31.19 2.71
713 725 1.602377 CTGAATTCCGGGGAAATACGC 59.398 52.381 0.00 0.00 37.69 4.42
715 727 1.332686 GAATTCCGGGGAAATACGCAC 59.667 52.381 0.00 0.00 37.69 5.34
737 750 4.145876 TCAGCAAATTAAACGAGCACAG 57.854 40.909 0.00 0.00 0.00 3.66
753 766 7.097192 ACGAGCACAGATTAGAAATTGTTCTA 58.903 34.615 0.00 0.00 42.53 2.10
776 789 2.674380 CTGGCCCACTCACCAAGC 60.674 66.667 0.00 0.00 34.96 4.01
857 872 0.326618 ATCCCTCCCTGATCCAACGT 60.327 55.000 0.00 0.00 0.00 3.99
908 925 2.586357 GCGAAGATCCGGCCAGAC 60.586 66.667 2.24 0.00 0.00 3.51
940 957 1.484240 CCTCTCGAAATTCTCAGGCCT 59.516 52.381 0.00 0.00 0.00 5.19
962 982 2.186826 GCCATCGTCCAAATCCCCG 61.187 63.158 0.00 0.00 0.00 5.73
974 995 0.551396 AATCCCCGCCCCTTCTTAAG 59.449 55.000 0.00 0.00 0.00 1.85
1008 1034 1.579429 GCGAATCCCCACAACACAC 59.421 57.895 0.00 0.00 0.00 3.82
1047 1073 1.333619 CCAAAGAAGACAACACCACCG 59.666 52.381 0.00 0.00 0.00 4.94
1048 1074 1.021968 AAAGAAGACAACACCACCGC 58.978 50.000 0.00 0.00 0.00 5.68
1049 1075 0.180406 AAGAAGACAACACCACCGCT 59.820 50.000 0.00 0.00 0.00 5.52
1050 1076 0.249911 AGAAGACAACACCACCGCTC 60.250 55.000 0.00 0.00 0.00 5.03
1051 1077 1.557443 GAAGACAACACCACCGCTCG 61.557 60.000 0.00 0.00 0.00 5.03
1053 1079 4.235762 ACAACACCACCGCTCGCT 62.236 61.111 0.00 0.00 0.00 4.93
1055 1081 3.923864 AACACCACCGCTCGCTCA 61.924 61.111 0.00 0.00 0.00 4.26
1056 1082 3.454587 AACACCACCGCTCGCTCAA 62.455 57.895 0.00 0.00 0.00 3.02
1057 1083 3.114616 CACCACCGCTCGCTCAAG 61.115 66.667 0.00 0.00 0.00 3.02
1058 1084 3.616721 ACCACCGCTCGCTCAAGT 61.617 61.111 0.00 0.00 0.00 3.16
1066 1093 2.604686 TCGCTCAAGTCCCCAGCT 60.605 61.111 0.00 0.00 0.00 4.24
1533 1571 3.498774 AGCTGTTCTTGTCCTGTGATT 57.501 42.857 0.00 0.00 0.00 2.57
1536 1574 3.653344 CTGTTCTTGTCCTGTGATTCGA 58.347 45.455 0.00 0.00 0.00 3.71
1545 1583 3.498397 GTCCTGTGATTCGAATGTGTGTT 59.502 43.478 16.96 0.00 0.00 3.32
1547 1585 3.498018 CCTGTGATTCGAATGTGTGTTGA 59.502 43.478 16.96 0.00 0.00 3.18
1602 1642 3.383505 TCGTCTGTTCCTATGTATGGTGG 59.616 47.826 0.00 0.00 0.00 4.61
1687 1730 5.488341 TCTACTGTTTGCTACTTCATTCCC 58.512 41.667 0.00 0.00 0.00 3.97
1726 1806 2.227194 TGCAGTCATGGATGCATGATC 58.773 47.619 29.41 22.04 46.97 2.92
1782 1862 5.457473 CGTGGTCTGTTATTTTTGTTTGGTC 59.543 40.000 0.00 0.00 0.00 4.02
1824 1906 2.695359 TGCACGTTTCTACAGGGATTC 58.305 47.619 0.00 0.00 0.00 2.52
1846 1928 3.303990 CGGTGAATCCAATTATGCCTTCG 60.304 47.826 0.00 0.00 35.57 3.79
1859 1941 0.449388 GCCTTCGGCTCTGTTTGATG 59.551 55.000 0.00 0.00 46.69 3.07
1869 1951 4.094590 GGCTCTGTTTGATGTGATTCTGAG 59.905 45.833 0.00 0.00 0.00 3.35
1976 2059 8.746922 TCAAATTTGCAAAGAATGTGATCTAC 57.253 30.769 18.19 0.00 28.31 2.59
1991 2074 6.647229 TGTGATCTACTTCATCTGCATTTCT 58.353 36.000 0.00 0.00 0.00 2.52
1992 2075 6.760298 TGTGATCTACTTCATCTGCATTTCTC 59.240 38.462 0.00 0.00 0.00 2.87
1995 2078 6.535963 TCTACTTCATCTGCATTTCTCAGA 57.464 37.500 0.00 0.00 43.79 3.27
2007 2090 7.281774 TCTGCATTTCTCAGATCTTGTTAATCC 59.718 37.037 0.00 0.00 35.81 3.01
2043 2126 4.523943 GGATGCTATGTTTGGCCAATGATA 59.476 41.667 21.26 16.45 0.00 2.15
2117 2200 5.931724 TGCTCTGTTATTCTTCATTCGTTGA 59.068 36.000 0.00 0.00 0.00 3.18
2118 2201 6.091305 TGCTCTGTTATTCTTCATTCGTTGAG 59.909 38.462 0.00 0.00 35.27 3.02
2120 2203 6.697395 TCTGTTATTCTTCATTCGTTGAGGA 58.303 36.000 0.26 0.26 38.57 3.71
2122 2205 5.874810 TGTTATTCTTCATTCGTTGAGGAGG 59.125 40.000 3.94 0.00 41.04 4.30
2123 2206 4.559862 ATTCTTCATTCGTTGAGGAGGT 57.440 40.909 3.94 0.00 41.04 3.85
2124 2207 3.319137 TCTTCATTCGTTGAGGAGGTG 57.681 47.619 0.26 0.00 35.68 4.00
2125 2208 1.734465 CTTCATTCGTTGAGGAGGTGC 59.266 52.381 0.00 0.00 33.37 5.01
2127 2210 1.347707 TCATTCGTTGAGGAGGTGCTT 59.652 47.619 0.00 0.00 0.00 3.91
2128 2211 1.734465 CATTCGTTGAGGAGGTGCTTC 59.266 52.381 0.00 0.00 0.00 3.86
2129 2212 0.756294 TTCGTTGAGGAGGTGCTTCA 59.244 50.000 0.00 0.00 0.00 3.02
2132 2215 1.734465 CGTTGAGGAGGTGCTTCATTC 59.266 52.381 0.00 0.00 32.14 2.67
2133 2216 2.783135 GTTGAGGAGGTGCTTCATTCA 58.217 47.619 0.00 0.00 32.14 2.57
2134 2217 3.350833 GTTGAGGAGGTGCTTCATTCAT 58.649 45.455 0.00 0.00 32.14 2.57
2139 3295 4.298626 AGGAGGTGCTTCATTCATAGGTA 58.701 43.478 0.00 0.00 0.00 3.08
2141 3297 4.503991 GGAGGTGCTTCATTCATAGGTAGG 60.504 50.000 0.00 0.00 0.00 3.18
2153 3309 3.392285 TCATAGGTAGGTACGAGTAGGCA 59.608 47.826 0.00 0.00 0.00 4.75
2154 3310 2.345124 AGGTAGGTACGAGTAGGCAG 57.655 55.000 0.00 0.00 0.00 4.85
2157 3313 1.747355 GTAGGTACGAGTAGGCAGCAA 59.253 52.381 0.00 0.00 0.00 3.91
2158 3314 0.531200 AGGTACGAGTAGGCAGCAAC 59.469 55.000 0.00 0.00 0.00 4.17
2159 3315 0.801067 GGTACGAGTAGGCAGCAACG 60.801 60.000 0.00 0.00 0.00 4.10
2163 3319 0.101399 CGAGTAGGCAGCAACGATCT 59.899 55.000 0.00 0.00 0.00 2.75
2165 3321 0.176680 AGTAGGCAGCAACGATCTGG 59.823 55.000 0.00 0.00 32.41 3.86
2166 3322 0.175760 GTAGGCAGCAACGATCTGGA 59.824 55.000 0.00 0.00 32.41 3.86
2167 3323 1.123077 TAGGCAGCAACGATCTGGAT 58.877 50.000 0.00 0.00 32.41 3.41
2168 3324 0.463295 AGGCAGCAACGATCTGGATG 60.463 55.000 0.00 0.00 32.41 3.51
2169 3325 0.462581 GGCAGCAACGATCTGGATGA 60.463 55.000 0.00 0.00 32.41 2.92
2170 3326 0.935898 GCAGCAACGATCTGGATGAG 59.064 55.000 0.00 0.00 32.41 2.90
2172 3328 2.481969 GCAGCAACGATCTGGATGAGTA 60.482 50.000 0.00 0.00 32.41 2.59
2173 3329 3.801638 GCAGCAACGATCTGGATGAGTAT 60.802 47.826 0.00 0.00 32.41 2.12
2179 3886 4.219115 ACGATCTGGATGAGTATTCCACT 58.781 43.478 0.00 0.00 38.35 4.00
2182 3889 5.707764 CGATCTGGATGAGTATTCCACTAGA 59.292 44.000 0.00 0.00 38.35 2.43
2185 3892 7.733773 TCTGGATGAGTATTCCACTAGAAAA 57.266 36.000 0.00 0.00 38.35 2.29
2227 3934 2.676076 GCCATGTTGAACACCATGAAC 58.324 47.619 12.58 2.83 40.70 3.18
2236 3943 0.534877 ACACCATGAACTTGCGAGCA 60.535 50.000 0.00 0.00 0.00 4.26
2240 3947 0.110056 CATGAACTTGCGAGCACCAC 60.110 55.000 0.00 0.00 0.00 4.16
2241 3948 1.237285 ATGAACTTGCGAGCACCACC 61.237 55.000 0.00 0.00 0.00 4.61
2242 3949 1.891919 GAACTTGCGAGCACCACCA 60.892 57.895 0.00 0.00 0.00 4.17
2286 3993 1.174078 TTGAGCAGGTGCCACACATG 61.174 55.000 7.94 7.94 46.88 3.21
2294 4001 1.888512 GGTGCCACACATGACAGATTT 59.111 47.619 0.00 0.00 35.86 2.17
2309 4022 7.887996 TGACAGATTTGCCAATTATTTTGAC 57.112 32.000 0.00 0.00 0.00 3.18
2315 4028 8.949177 AGATTTGCCAATTATTTTGACCATTTC 58.051 29.630 0.00 0.00 0.00 2.17
2316 4029 8.866970 ATTTGCCAATTATTTTGACCATTTCT 57.133 26.923 0.00 0.00 0.00 2.52
2392 4119 2.447244 AGGAAGAGTTCGCTTGACAG 57.553 50.000 0.00 0.00 0.00 3.51
2393 4120 0.793250 GGAAGAGTTCGCTTGACAGC 59.207 55.000 0.00 0.00 43.41 4.40
2402 4129 2.467826 GCTTGACAGCCTCGATGCC 61.468 63.158 9.21 0.00 40.61 4.40
2406 4133 3.746949 GACAGCCTCGATGCCCTGG 62.747 68.421 9.21 0.00 0.00 4.45
2448 4175 2.291365 TCATTCTGGCCAATGTCGATG 58.709 47.619 15.50 9.44 35.56 3.84
2460 4187 4.494484 CAATGTCGATGGTGTACAGAGAA 58.506 43.478 0.00 0.00 0.00 2.87
2462 4189 4.371855 TGTCGATGGTGTACAGAGAATC 57.628 45.455 0.00 0.00 0.00 2.52
2471 4198 2.991190 TGTACAGAGAATCGCCGAAAAC 59.009 45.455 0.00 0.00 42.67 2.43
2472 4199 2.163818 ACAGAGAATCGCCGAAAACA 57.836 45.000 0.00 0.00 42.67 2.83
2473 4200 1.798813 ACAGAGAATCGCCGAAAACAC 59.201 47.619 0.00 0.00 42.67 3.32
2474 4201 2.069273 CAGAGAATCGCCGAAAACACT 58.931 47.619 0.00 0.00 42.67 3.55
2499 4226 2.421399 GGGAAGCTGGCCTGCAATC 61.421 63.158 32.96 27.71 34.99 2.67
2503 4230 1.538687 AAGCTGGCCTGCAATCCAAC 61.539 55.000 32.96 4.55 34.99 3.77
2511 4238 0.165944 CTGCAATCCAACCGAACGAC 59.834 55.000 0.00 0.00 0.00 4.34
2551 4278 8.084684 AGCTGTAAAATTCAGAAAATTCAGACC 58.915 33.333 0.00 0.00 35.20 3.85
2552 4279 7.061094 GCTGTAAAATTCAGAAAATTCAGACCG 59.939 37.037 0.00 0.00 35.20 4.79
2553 4280 7.936584 TGTAAAATTCAGAAAATTCAGACCGT 58.063 30.769 0.00 0.00 0.00 4.83
2554 4281 7.860373 TGTAAAATTCAGAAAATTCAGACCGTG 59.140 33.333 0.00 0.00 0.00 4.94
2555 4282 3.896648 TTCAGAAAATTCAGACCGTGC 57.103 42.857 0.00 0.00 0.00 5.34
2556 4283 2.844946 TCAGAAAATTCAGACCGTGCA 58.155 42.857 0.00 0.00 0.00 4.57
2557 4284 2.548057 TCAGAAAATTCAGACCGTGCAC 59.452 45.455 6.82 6.82 0.00 4.57
2558 4285 2.549754 CAGAAAATTCAGACCGTGCACT 59.450 45.455 16.19 0.00 0.00 4.40
2559 4286 3.745975 CAGAAAATTCAGACCGTGCACTA 59.254 43.478 16.19 0.00 0.00 2.74
2560 4287 3.746492 AGAAAATTCAGACCGTGCACTAC 59.254 43.478 16.19 6.00 0.00 2.73
2604 4331 0.250553 TTCCTTTACCACTGGTGCCG 60.251 55.000 11.32 0.00 36.19 5.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 2.349672 TTTACATCGGGCCGGTCGA 61.350 57.895 27.98 20.61 41.04 4.20
6 7 2.169146 GTTTACATCGGGCCGGTCG 61.169 63.158 27.98 16.22 0.00 4.79
7 8 2.169146 CGTTTACATCGGGCCGGTC 61.169 63.158 27.98 5.27 0.00 4.79
8 9 2.125431 CGTTTACATCGGGCCGGT 60.125 61.111 27.98 18.59 0.00 5.28
9 10 1.881252 CTCGTTTACATCGGGCCGG 60.881 63.158 27.98 13.85 0.00 6.13
10 11 1.881252 CCTCGTTTACATCGGGCCG 60.881 63.158 22.51 22.51 0.00 6.13
11 12 1.523032 CCCTCGTTTACATCGGGCC 60.523 63.158 0.00 0.00 0.00 5.80
12 13 4.120085 CCCTCGTTTACATCGGGC 57.880 61.111 0.00 0.00 0.00 6.13
13 14 0.179056 ATGCCCTCGTTTACATCGGG 60.179 55.000 0.00 0.00 37.97 5.14
14 15 0.937304 CATGCCCTCGTTTACATCGG 59.063 55.000 0.00 0.00 0.00 4.18
15 16 1.860950 CTCATGCCCTCGTTTACATCG 59.139 52.381 0.00 0.00 0.00 3.84
16 17 1.599542 GCTCATGCCCTCGTTTACATC 59.400 52.381 0.00 0.00 0.00 3.06
17 18 1.065491 TGCTCATGCCCTCGTTTACAT 60.065 47.619 0.00 0.00 38.71 2.29
18 19 0.323302 TGCTCATGCCCTCGTTTACA 59.677 50.000 0.00 0.00 38.71 2.41
19 20 0.727398 GTGCTCATGCCCTCGTTTAC 59.273 55.000 0.00 0.00 38.71 2.01
20 21 0.392461 GGTGCTCATGCCCTCGTTTA 60.392 55.000 0.00 0.00 38.71 2.01
21 22 1.675641 GGTGCTCATGCCCTCGTTT 60.676 57.895 0.00 0.00 38.71 3.60
65 66 1.599576 GTCCCTTCTCAGCCACCTC 59.400 63.158 0.00 0.00 0.00 3.85
71 72 4.475135 GCCCCGTCCCTTCTCAGC 62.475 72.222 0.00 0.00 0.00 4.26
82 83 1.306654 TCCAGATAGGTTGCCCCGT 60.307 57.895 0.00 0.00 38.74 5.28
126 127 4.361971 AGGCCCTCTCGTCCGACA 62.362 66.667 0.00 0.00 0.00 4.35
128 129 4.043100 TCAGGCCCTCTCGTCCGA 62.043 66.667 0.00 0.00 0.00 4.55
133 134 0.036010 AATGTTGTCAGGCCCTCTCG 60.036 55.000 0.00 0.00 0.00 4.04
143 145 1.528076 AGTGCGGGCAATGTTGTCA 60.528 52.632 0.00 0.00 33.59 3.58
192 195 1.135888 GGGCGACAACAAATAACGGTC 60.136 52.381 0.00 0.00 0.00 4.79
194 197 0.169451 GGGGCGACAACAAATAACGG 59.831 55.000 0.00 0.00 0.00 4.44
201 204 0.174845 CTAGATCGGGGCGACAACAA 59.825 55.000 0.00 0.00 39.18 2.83
204 207 2.792947 GCCTAGATCGGGGCGACAA 61.793 63.158 14.37 0.00 39.18 3.18
213 216 4.685026 CCGGTCGCGCCTAGATCG 62.685 72.222 15.78 9.15 41.46 3.69
247 250 1.167851 CGACATGGATGTGGTTGCTT 58.832 50.000 0.00 0.00 41.95 3.91
251 254 2.038426 TGACTTCGACATGGATGTGGTT 59.962 45.455 0.00 0.00 41.95 3.67
265 268 2.921754 GGTTCCGACAACTATGACTTCG 59.078 50.000 0.00 0.00 0.00 3.79
282 285 3.730761 CAGCAGCAGCACGGGTTC 61.731 66.667 3.17 0.00 45.49 3.62
290 293 4.724602 TCGTCCGACAGCAGCAGC 62.725 66.667 0.00 0.00 42.56 5.25
302 305 3.574396 TCCCAATCTGATCTATGTCGTCC 59.426 47.826 0.00 0.00 0.00 4.79
303 306 4.855715 TCCCAATCTGATCTATGTCGTC 57.144 45.455 0.00 0.00 0.00 4.20
335 339 0.178950 TGCCACTCCACTCTCTCTGT 60.179 55.000 0.00 0.00 0.00 3.41
337 341 1.193323 CATGCCACTCCACTCTCTCT 58.807 55.000 0.00 0.00 0.00 3.10
342 346 0.392193 CACTCCATGCCACTCCACTC 60.392 60.000 0.00 0.00 0.00 3.51
344 348 1.377725 CCACTCCATGCCACTCCAC 60.378 63.158 0.00 0.00 0.00 4.02
354 358 3.207777 ACCTATACCTCAGACCACTCCAT 59.792 47.826 0.00 0.00 0.00 3.41
360 364 5.277250 TGATGAAACCTATACCTCAGACCA 58.723 41.667 0.00 0.00 0.00 4.02
371 375 8.460317 AGATATCCCAATCTGATGAAACCTAT 57.540 34.615 0.00 0.00 34.87 2.57
383 387 2.982488 GACCCCACAGATATCCCAATCT 59.018 50.000 0.00 0.00 36.64 2.40
385 389 2.787956 TGACCCCACAGATATCCCAAT 58.212 47.619 0.00 0.00 0.00 3.16
395 399 1.039233 GGCCATCAATGACCCCACAG 61.039 60.000 0.00 0.00 0.00 3.66
427 431 2.022129 GCTTGTCCGTCACGTCAGG 61.022 63.158 0.00 0.00 0.00 3.86
454 458 2.122989 ATATGAGGCGGTCCGGGT 60.123 61.111 14.38 0.00 37.47 5.28
459 463 1.343069 AGGAAGGATATGAGGCGGTC 58.657 55.000 0.00 0.00 0.00 4.79
460 464 2.249139 GTAGGAAGGATATGAGGCGGT 58.751 52.381 0.00 0.00 0.00 5.68
485 496 0.474660 AGACCCCTCATATCCAGCCC 60.475 60.000 0.00 0.00 0.00 5.19
491 502 1.346068 GCTGTCCAGACCCCTCATATC 59.654 57.143 0.00 0.00 0.00 1.63
494 505 1.997874 GGCTGTCCAGACCCCTCAT 60.998 63.158 0.00 0.00 0.00 2.90
504 515 0.400213 CTAAACACCTGGGCTGTCCA 59.600 55.000 0.00 0.00 44.79 4.02
507 518 1.767692 CCCTAAACACCTGGGCTGT 59.232 57.895 0.00 0.00 33.88 4.40
543 554 4.326548 CCGGTAAGAAGAAAACGACTCATC 59.673 45.833 0.00 0.00 0.00 2.92
551 562 4.210746 GTCACTGACCGGTAAGAAGAAAAC 59.789 45.833 26.69 9.62 0.00 2.43
556 567 2.365408 GGTCACTGACCGGTAAGAAG 57.635 55.000 26.69 16.76 43.14 2.85
578 589 0.038526 GTCTCAAAAGTCCGAGCGGA 60.039 55.000 7.66 7.66 42.90 5.54
579 590 1.014564 GGTCTCAAAAGTCCGAGCGG 61.015 60.000 1.74 1.74 0.00 5.52
580 591 2.446341 GGTCTCAAAAGTCCGAGCG 58.554 57.895 0.00 0.00 0.00 5.03
617 628 6.036191 CCGGAAGAGAATGTAAAAGCTTCTAC 59.964 42.308 0.00 0.00 33.95 2.59
704 716 3.764885 ATTTGCTGAGTGCGTATTTCC 57.235 42.857 0.00 0.00 46.63 3.13
713 725 3.908382 GTGCTCGTTTAATTTGCTGAGTG 59.092 43.478 0.00 0.00 0.00 3.51
715 727 4.083855 TCTGTGCTCGTTTAATTTGCTGAG 60.084 41.667 0.00 0.00 0.00 3.35
737 750 7.475840 CCAGGTTGCTAGAACAATTTCTAATC 58.524 38.462 0.00 0.00 42.61 1.75
753 766 3.177884 TGAGTGGGCCAGGTTGCT 61.178 61.111 6.40 0.00 0.00 3.91
776 789 1.091771 ATCCGTGGCAGCATTTCTCG 61.092 55.000 0.00 0.00 0.00 4.04
875 890 4.415332 GCGCCACGAAGGACGAGA 62.415 66.667 0.00 0.00 45.77 4.04
906 923 2.007608 CGAGAGGAAATTTTCGGGGTC 58.992 52.381 3.17 0.00 0.00 4.46
908 925 2.396590 TCGAGAGGAAATTTTCGGGG 57.603 50.000 9.45 0.00 34.08 5.73
940 957 2.125310 ATTTGGACGATGGCGCGA 60.125 55.556 12.10 0.00 42.48 5.87
950 967 3.296842 AAGGGGCGGGGATTTGGAC 62.297 63.158 0.00 0.00 0.00 4.02
962 982 1.379977 GGGTGGCTTAAGAAGGGGC 60.380 63.158 6.67 0.00 0.00 5.80
992 1016 1.862602 GCGGTGTGTTGTGGGGATTC 61.863 60.000 0.00 0.00 0.00 2.52
1029 1055 1.021968 GCGGTGGTGTTGTCTTCTTT 58.978 50.000 0.00 0.00 0.00 2.52
1047 1073 2.125350 CTGGGGACTTGAGCGAGC 60.125 66.667 0.00 0.00 0.00 5.03
1048 1074 2.125350 GCTGGGGACTTGAGCGAG 60.125 66.667 0.00 0.00 0.00 5.03
1049 1075 2.604686 AGCTGGGGACTTGAGCGA 60.605 61.111 0.00 0.00 37.81 4.93
1050 1076 2.125350 GAGCTGGGGACTTGAGCG 60.125 66.667 0.00 0.00 37.81 5.03
1051 1077 2.270527 GGAGCTGGGGACTTGAGC 59.729 66.667 0.00 0.00 0.00 4.26
1053 1079 1.306141 ATCGGAGCTGGGGACTTGA 60.306 57.895 0.00 0.00 0.00 3.02
1055 1081 2.370445 CCATCGGAGCTGGGGACTT 61.370 63.158 0.00 0.00 0.00 3.01
1056 1082 2.765807 CCATCGGAGCTGGGGACT 60.766 66.667 0.00 0.00 0.00 3.85
1057 1083 4.554036 GCCATCGGAGCTGGGGAC 62.554 72.222 0.00 0.00 34.16 4.46
1509 1547 3.062763 CACAGGACAAGAACAGCTACTG 58.937 50.000 0.00 0.00 37.52 2.74
1533 1571 1.202639 AGGCACTCAACACACATTCGA 60.203 47.619 0.00 0.00 0.00 3.71
1602 1642 2.634982 TTGCCATTTCATTCGAGCAC 57.365 45.000 0.00 0.00 0.00 4.40
1687 1730 3.226346 CAACCATTGCAGAATCACAGG 57.774 47.619 0.00 0.00 0.00 4.00
1782 1862 3.354089 AAAAACCTGAATCACACAGCG 57.646 42.857 0.00 0.00 34.47 5.18
1824 1906 3.303990 CGAAGGCATAATTGGATTCACCG 60.304 47.826 0.00 0.00 42.61 4.94
1846 1928 4.005650 TCAGAATCACATCAAACAGAGCC 58.994 43.478 0.00 0.00 0.00 4.70
1855 1937 7.092891 ACCCAACTATAACTCAGAATCACATCA 60.093 37.037 0.00 0.00 0.00 3.07
1859 1941 6.316390 CCAACCCAACTATAACTCAGAATCAC 59.684 42.308 0.00 0.00 0.00 3.06
1869 1951 5.105917 CCACATCAACCAACCCAACTATAAC 60.106 44.000 0.00 0.00 0.00 1.89
1991 2074 6.875726 CACAGAACTGGATTAACAAGATCTGA 59.124 38.462 19.44 0.00 36.25 3.27
1992 2075 6.875726 TCACAGAACTGGATTAACAAGATCTG 59.124 38.462 14.50 14.50 38.14 2.90
1995 2078 7.121759 CCAATCACAGAACTGGATTAACAAGAT 59.878 37.037 13.67 0.00 32.85 2.40
2007 2090 4.880120 ACATAGCATCCAATCACAGAACTG 59.120 41.667 0.00 0.00 0.00 3.16
2043 2126 6.251471 GGACAATAATCATTCCCAGGATGAT 58.749 40.000 0.00 0.00 39.69 2.45
2117 2200 3.118531 ACCTATGAATGAAGCACCTCCT 58.881 45.455 0.00 0.00 0.00 3.69
2118 2201 3.567478 ACCTATGAATGAAGCACCTCC 57.433 47.619 0.00 0.00 0.00 4.30
2120 2203 4.040755 ACCTACCTATGAATGAAGCACCT 58.959 43.478 0.00 0.00 0.00 4.00
2122 2205 4.982916 CGTACCTACCTATGAATGAAGCAC 59.017 45.833 0.00 0.00 0.00 4.40
2123 2206 4.891168 TCGTACCTACCTATGAATGAAGCA 59.109 41.667 0.00 0.00 0.00 3.91
2124 2207 5.009811 ACTCGTACCTACCTATGAATGAAGC 59.990 44.000 0.00 0.00 0.00 3.86
2125 2208 6.636562 ACTCGTACCTACCTATGAATGAAG 57.363 41.667 0.00 0.00 0.00 3.02
2127 2210 6.236409 CCTACTCGTACCTACCTATGAATGA 58.764 44.000 0.00 0.00 0.00 2.57
2128 2211 5.106237 GCCTACTCGTACCTACCTATGAATG 60.106 48.000 0.00 0.00 0.00 2.67
2129 2212 5.008980 GCCTACTCGTACCTACCTATGAAT 58.991 45.833 0.00 0.00 0.00 2.57
2132 2215 3.748083 TGCCTACTCGTACCTACCTATG 58.252 50.000 0.00 0.00 0.00 2.23
2133 2216 3.810033 GCTGCCTACTCGTACCTACCTAT 60.810 52.174 0.00 0.00 0.00 2.57
2134 2217 2.486191 GCTGCCTACTCGTACCTACCTA 60.486 54.545 0.00 0.00 0.00 3.08
2139 3295 0.531200 GTTGCTGCCTACTCGTACCT 59.469 55.000 0.00 0.00 0.00 3.08
2141 3297 0.169672 TCGTTGCTGCCTACTCGTAC 59.830 55.000 0.00 0.00 0.00 3.67
2153 3309 4.502259 GGAATACTCATCCAGATCGTTGCT 60.502 45.833 0.00 0.00 36.92 3.91
2154 3310 3.743396 GGAATACTCATCCAGATCGTTGC 59.257 47.826 0.00 0.00 36.92 4.17
2163 3319 6.349300 GCTTTTCTAGTGGAATACTCATCCA 58.651 40.000 0.00 0.00 44.58 3.41
2165 3321 5.463724 CGGCTTTTCTAGTGGAATACTCATC 59.536 44.000 0.00 0.00 40.89 2.92
2166 3322 5.360591 CGGCTTTTCTAGTGGAATACTCAT 58.639 41.667 0.00 0.00 40.89 2.90
2167 3323 4.382685 CCGGCTTTTCTAGTGGAATACTCA 60.383 45.833 0.00 0.00 40.89 3.41
2168 3324 4.120589 CCGGCTTTTCTAGTGGAATACTC 58.879 47.826 0.00 0.00 40.89 2.59
2169 3325 3.118371 CCCGGCTTTTCTAGTGGAATACT 60.118 47.826 0.00 0.00 43.56 2.12
2170 3326 3.203716 CCCGGCTTTTCTAGTGGAATAC 58.796 50.000 0.00 0.00 33.53 1.89
2172 3328 1.633945 ACCCGGCTTTTCTAGTGGAAT 59.366 47.619 0.00 0.00 33.53 3.01
2173 3329 1.061546 ACCCGGCTTTTCTAGTGGAA 58.938 50.000 0.00 0.00 0.00 3.53
2179 3886 0.251073 GGTGCTACCCGGCTTTTCTA 59.749 55.000 0.00 0.00 30.04 2.10
2203 3910 1.081242 GGTGTTCAACATGGCGCTG 60.081 57.895 7.64 0.00 0.00 5.18
2204 3911 0.895100 ATGGTGTTCAACATGGCGCT 60.895 50.000 7.64 0.00 0.00 5.92
2227 3934 1.210931 CATTGGTGGTGCTCGCAAG 59.789 57.895 0.00 0.00 0.00 4.01
2236 3943 0.756442 ACTTGCACAGCATTGGTGGT 60.756 50.000 19.20 5.03 38.76 4.16
2240 3947 0.242825 CAGGACTTGCACAGCATTGG 59.757 55.000 0.00 0.00 38.76 3.16
2241 3948 3.786809 CAGGACTTGCACAGCATTG 57.213 52.632 0.00 0.00 38.76 2.82
2286 3993 6.873076 TGGTCAAAATAATTGGCAAATCTGTC 59.127 34.615 3.01 0.00 0.00 3.51
2287 3994 6.767456 TGGTCAAAATAATTGGCAAATCTGT 58.233 32.000 3.01 0.00 0.00 3.41
2288 3995 7.852971 ATGGTCAAAATAATTGGCAAATCTG 57.147 32.000 3.01 0.00 0.00 2.90
2289 3996 8.866970 AAATGGTCAAAATAATTGGCAAATCT 57.133 26.923 3.01 0.00 0.00 2.40
2294 4001 8.133024 ACTAGAAATGGTCAAAATAATTGGCA 57.867 30.769 0.00 0.00 0.00 4.92
2392 4119 4.554036 GTCCCAGGGCATCGAGGC 62.554 72.222 14.84 14.84 43.27 4.70
2393 4120 4.227134 CGTCCCAGGGCATCGAGG 62.227 72.222 0.00 0.00 0.00 4.63
2406 4133 3.637273 ACCTCCAACCTGGCGTCC 61.637 66.667 0.00 0.00 37.47 4.79
2412 4139 4.157289 CAGAATGATTTCACCTCCAACCTG 59.843 45.833 0.00 0.00 39.69 4.00
2448 4175 0.454600 TCGGCGATTCTCTGTACACC 59.545 55.000 4.99 0.00 0.00 4.16
2460 4187 2.332654 GCCCAGTGTTTTCGGCGAT 61.333 57.895 11.76 0.00 0.00 4.58
2487 4214 2.703798 CGGTTGGATTGCAGGCCAG 61.704 63.158 5.01 0.00 35.23 4.85
2490 4217 1.212751 GTTCGGTTGGATTGCAGGC 59.787 57.895 0.00 0.00 0.00 4.85
2495 4222 0.796312 CTGGTCGTTCGGTTGGATTG 59.204 55.000 0.00 0.00 0.00 2.67
2499 4226 0.666577 GAGACTGGTCGTTCGGTTGG 60.667 60.000 0.00 0.00 34.09 3.77
2503 4230 0.314302 AACAGAGACTGGTCGTTCGG 59.686 55.000 0.00 0.00 35.51 4.30
2511 4238 6.861065 TTTTACAGCTAAAACAGAGACTGG 57.139 37.500 0.00 0.00 35.51 4.00
2543 4270 3.402628 AAAGTAGTGCACGGTCTGAAT 57.597 42.857 12.01 0.00 0.00 2.57
2545 4272 2.902705 AAAAGTAGTGCACGGTCTGA 57.097 45.000 12.01 0.00 0.00 3.27
2583 4310 2.312390 GGCACCAGTGGTAAAGGAAAA 58.688 47.619 16.22 0.00 32.11 2.29
2584 4311 1.816183 CGGCACCAGTGGTAAAGGAAA 60.816 52.381 16.22 0.00 32.11 3.13
2586 4313 1.373435 CGGCACCAGTGGTAAAGGA 59.627 57.895 16.22 0.00 32.11 3.36
2587 4314 2.332654 GCGGCACCAGTGGTAAAGG 61.333 63.158 16.22 3.43 32.11 3.11
2588 4315 2.332654 GGCGGCACCAGTGGTAAAG 61.333 63.158 16.22 9.98 38.86 1.85


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

AutoCloner maintained by Alex Coulton.