Multiple sequence alignment - TraesCS6D01G340900

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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 TraesCS6D01G340900 chr6D 100.000 2889 0 0 919 3807 440015539 440012651 0.000000e+00 5336.0
1 TraesCS6D01G340900 chr6D 96.018 1758 56 4 1218 2963 439922051 439920296 0.000000e+00 2846.0
2 TraesCS6D01G340900 chr6D 81.463 1845 252 57 1176 2957 84084253 84086070 0.000000e+00 1430.0
3 TraesCS6D01G340900 chr6D 100.000 520 0 0 1 520 440016457 440015938 0.000000e+00 961.0
4 TraesCS6D01G340900 chr6D 83.638 1039 150 11 1171 2206 440210782 440209761 0.000000e+00 959.0
5 TraesCS6D01G340900 chr6D 87.859 453 24 3 75 520 439922984 439922556 1.580000e-138 503.0
6 TraesCS6D01G340900 chr6D 82.158 482 50 12 989 1440 440221237 440220762 7.720000e-102 381.0
7 TraesCS6D01G340900 chr6D 83.275 287 40 5 1180 1459 466528621 466528336 1.360000e-64 257.0
8 TraesCS6D01G340900 chr6D 84.524 252 29 7 276 520 440221627 440221379 1.370000e-59 241.0
9 TraesCS6D01G340900 chr6D 84.141 227 27 3 919 1142 439922415 439922195 1.070000e-50 211.0
10 TraesCS6D01G340900 chr6D 83.333 138 19 2 927 1061 440210905 440210769 1.440000e-24 124.0
11 TraesCS6D01G340900 chr6D 80.597 134 19 6 391 520 466552373 466552243 3.130000e-16 97.1
12 TraesCS6D01G340900 chr6B 94.476 2082 76 6 919 2963 665162599 665160520 0.000000e+00 3171.0
13 TraesCS6D01G340900 chr6B 83.814 1526 196 26 1471 2953 95237329 95235812 0.000000e+00 1402.0
14 TraesCS6D01G340900 chr6B 91.572 878 24 7 2963 3807 661551892 661552752 0.000000e+00 1166.0
15 TraesCS6D01G340900 chr6B 81.931 1295 170 20 943 2180 665132552 665131265 0.000000e+00 1037.0
16 TraesCS6D01G340900 chr6B 80.919 1284 172 34 976 2200 665425867 665424598 0.000000e+00 946.0
17 TraesCS6D01G340900 chr6B 81.722 941 146 17 1783 2705 142099020 142098088 0.000000e+00 761.0
18 TraesCS6D01G340900 chr6B 89.047 493 32 10 49 520 665133189 665132698 3.270000e-165 592.0
19 TraesCS6D01G340900 chr6B 86.722 482 37 11 49 520 665037793 665037329 9.430000e-141 510.0
20 TraesCS6D01G340900 chr6B 86.866 434 33 3 1031 1440 665417743 665417310 7.450000e-127 464.0
21 TraesCS6D01G340900 chr6B 93.092 304 20 1 218 520 665163001 665162698 9.700000e-121 444.0
22 TraesCS6D01G340900 chr6B 84.683 457 39 13 68 520 665418395 665417966 9.770000e-116 427.0
23 TraesCS6D01G340900 chr6B 93.578 109 5 2 3700 3807 718633697 718633804 1.090000e-35 161.0
24 TraesCS6D01G340900 chr6B 91.111 45 3 1 1105 1149 665132242 665132199 4.110000e-05 60.2
25 TraesCS6D01G340900 chr6B 100.000 29 0 0 4 32 635078414 635078386 2.000000e-03 54.7
26 TraesCS6D01G340900 chr7A 82.035 1848 259 38 1177 2963 219396886 219398721 0.000000e+00 1506.0
27 TraesCS6D01G340900 chr7A 76.498 217 42 5 288 497 219396319 219396533 4.020000e-20 110.0
28 TraesCS6D01G340900 chr2D 81.617 1855 232 62 1180 2963 493883339 493881523 0.000000e+00 1435.0
29 TraesCS6D01G340900 chr2A 82.325 1703 228 45 1171 2815 639694708 639696395 0.000000e+00 1410.0
30 TraesCS6D01G340900 chr2A 86.952 889 54 26 2963 3807 387610695 387611565 0.000000e+00 942.0
31 TraesCS6D01G340900 chr2A 93.823 599 17 7 3218 3807 8024231 8024818 0.000000e+00 883.0
32 TraesCS6D01G340900 chr2A 97.753 267 5 1 2951 3217 8023934 8024199 3.470000e-125 459.0
33 TraesCS6D01G340900 chr6A 81.115 1668 235 44 1346 2957 101315185 101316828 0.000000e+00 1262.0
34 TraesCS6D01G340900 chr6A 82.129 1315 168 28 943 2200 588355030 588353726 0.000000e+00 1064.0
35 TraesCS6D01G340900 chr6A 80.906 1037 155 19 1171 2206 588410968 588409974 0.000000e+00 778.0
36 TraesCS6D01G340900 chr6A 92.355 484 24 7 49 520 588355661 588355179 0.000000e+00 676.0
37 TraesCS6D01G340900 chr6A 82.000 750 97 20 2239 2953 52466234 52466980 1.510000e-168 603.0
38 TraesCS6D01G340900 chr6A 88.095 294 24 3 3459 3749 614422420 614422705 4.710000e-89 339.0
39 TraesCS6D01G340900 chr6A 82.270 141 19 3 927 1061 588411095 588410955 2.400000e-22 117.0
40 TraesCS6D01G340900 chr6A 89.333 75 8 0 3343 3417 614415570 614415644 1.130000e-15 95.3
41 TraesCS6D01G340900 chr6A 93.333 45 2 1 1105 1149 588354720 588354677 8.830000e-07 65.8
42 TraesCS6D01G340900 chr7B 88.377 456 38 7 3343 3792 651552496 651552050 5.600000e-148 534.0
43 TraesCS6D01G340900 chr7B 86.275 51 6 1 4 53 424552150 424552100 2.000000e-03 54.7
44 TraesCS6D01G340900 chr7B 96.875 32 0 1 1 32 397446454 397446424 7.000000e-03 52.8
45 TraesCS6D01G340900 chr3B 88.184 457 38 8 3343 3792 744317703 744317256 7.240000e-147 531.0
46 TraesCS6D01G340900 chr3B 92.233 103 7 1 3218 3320 744318670 744318569 1.100000e-30 145.0
47 TraesCS6D01G340900 chr1D 91.517 389 21 6 3344 3730 26160203 26160581 3.370000e-145 525.0
48 TraesCS6D01G340900 chr1D 93.204 103 6 1 3218 3320 26159208 26159309 2.370000e-32 150.0
49 TraesCS6D01G340900 chr4A 90.588 255 17 4 3557 3806 636326911 636326659 7.880000e-87 331.0
50 TraesCS6D01G340900 chr4A 86.154 260 34 2 1180 1438 661022490 661022232 2.900000e-71 279.0
51 TraesCS6D01G340900 chr2B 91.026 78 6 1 430 506 246570456 246570533 1.870000e-18 104.0
52 TraesCS6D01G340900 chr1A 94.444 36 2 0 5 40 4700487 4700522 5.310000e-04 56.5
53 TraesCS6D01G340900 chr1B 86.275 51 6 1 4 53 564691683 564691633 2.000000e-03 54.7
54 TraesCS6D01G340900 chrUn 96.875 32 0 1 1 32 287443345 287443315 7.000000e-03 52.8
55 TraesCS6D01G340900 chr4B 96.875 32 0 1 1 32 317289968 317289938 7.000000e-03 52.8
56 TraesCS6D01G340900 chr4B 96.875 32 0 1 1 32 317290163 317290193 7.000000e-03 52.8
57 TraesCS6D01G340900 chr3D 92.105 38 2 1 1 38 210615206 210615170 7.000000e-03 52.8


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 TraesCS6D01G340900 chr6D 440012651 440016457 3806 True 3148.500000 5336 100.000000 1 3807 2 chr6D.!!$R4 3806
1 TraesCS6D01G340900 chr6D 84084253 84086070 1817 False 1430.000000 1430 81.463000 1176 2957 1 chr6D.!!$F1 1781
2 TraesCS6D01G340900 chr6D 439920296 439922984 2688 True 1186.666667 2846 89.339333 75 2963 3 chr6D.!!$R3 2888
3 TraesCS6D01G340900 chr6D 440209761 440210905 1144 True 541.500000 959 83.485500 927 2206 2 chr6D.!!$R5 1279
4 TraesCS6D01G340900 chr6D 440220762 440221627 865 True 311.000000 381 83.341000 276 1440 2 chr6D.!!$R6 1164
5 TraesCS6D01G340900 chr6B 665160520 665163001 2481 True 1807.500000 3171 93.784000 218 2963 2 chr6B.!!$R7 2745
6 TraesCS6D01G340900 chr6B 95235812 95237329 1517 True 1402.000000 1402 83.814000 1471 2953 1 chr6B.!!$R1 1482
7 TraesCS6D01G340900 chr6B 661551892 661552752 860 False 1166.000000 1166 91.572000 2963 3807 1 chr6B.!!$F1 844
8 TraesCS6D01G340900 chr6B 665424598 665425867 1269 True 946.000000 946 80.919000 976 2200 1 chr6B.!!$R5 1224
9 TraesCS6D01G340900 chr6B 142098088 142099020 932 True 761.000000 761 81.722000 1783 2705 1 chr6B.!!$R2 922
10 TraesCS6D01G340900 chr6B 665131265 665133189 1924 True 563.066667 1037 87.363000 49 2180 3 chr6B.!!$R6 2131
11 TraesCS6D01G340900 chr6B 665417310 665418395 1085 True 445.500000 464 85.774500 68 1440 2 chr6B.!!$R8 1372
12 TraesCS6D01G340900 chr7A 219396319 219398721 2402 False 808.000000 1506 79.266500 288 2963 2 chr7A.!!$F1 2675
13 TraesCS6D01G340900 chr2D 493881523 493883339 1816 True 1435.000000 1435 81.617000 1180 2963 1 chr2D.!!$R1 1783
14 TraesCS6D01G340900 chr2A 639694708 639696395 1687 False 1410.000000 1410 82.325000 1171 2815 1 chr2A.!!$F2 1644
15 TraesCS6D01G340900 chr2A 387610695 387611565 870 False 942.000000 942 86.952000 2963 3807 1 chr2A.!!$F1 844
16 TraesCS6D01G340900 chr2A 8023934 8024818 884 False 671.000000 883 95.788000 2951 3807 2 chr2A.!!$F3 856
17 TraesCS6D01G340900 chr6A 101315185 101316828 1643 False 1262.000000 1262 81.115000 1346 2957 1 chr6A.!!$F2 1611
18 TraesCS6D01G340900 chr6A 52466234 52466980 746 False 603.000000 603 82.000000 2239 2953 1 chr6A.!!$F1 714
19 TraesCS6D01G340900 chr6A 588353726 588355661 1935 True 601.933333 1064 89.272333 49 2200 3 chr6A.!!$R1 2151
20 TraesCS6D01G340900 chr6A 588409974 588411095 1121 True 447.500000 778 81.588000 927 2206 2 chr6A.!!$R2 1279
21 TraesCS6D01G340900 chr3B 744317256 744318670 1414 True 338.000000 531 90.208500 3218 3792 2 chr3B.!!$R1 574
22 TraesCS6D01G340900 chr1D 26159208 26160581 1373 False 337.500000 525 92.360500 3218 3730 2 chr1D.!!$F1 512

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
37 38 0.253347 TGGGAAGGAGGGAGAAGCAT 60.253 55.0 0.0 0.0 0.00 3.79 F
939 970 0.950555 TAAGTGCAGCTCAGGCGTTG 60.951 55.0 0.0 0.0 44.37 4.10 F
1694 1899 0.034616 CCTGCCGATCTCCTCCAATC 59.965 60.0 0.0 0.0 0.00 2.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1067 1166 1.137086 CCATGAGGACGAATCGAAGGT 59.863 52.381 10.55 0.0 36.89 3.50 R
2629 2861 0.597568 CCGCATGTTCCACAACACAT 59.402 50.000 0.00 0.0 45.47 3.21 R
3662 4866 1.262950 CAAATTCGCAACGGTGACTCA 59.737 47.619 3.55 0.0 32.18 3.41 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 4.320608 AATGCGTGCCTTATATTTTGGG 57.679 40.909 0.00 0.00 0.00 4.12
22 23 3.006112 TGCGTGCCTTATATTTTGGGA 57.994 42.857 0.00 0.00 0.00 4.37
23 24 3.357203 TGCGTGCCTTATATTTTGGGAA 58.643 40.909 0.00 0.00 0.00 3.97
24 25 3.380004 TGCGTGCCTTATATTTTGGGAAG 59.620 43.478 0.00 0.00 0.00 3.46
25 26 3.243401 GCGTGCCTTATATTTTGGGAAGG 60.243 47.826 0.00 0.00 41.26 3.46
26 27 4.204012 CGTGCCTTATATTTTGGGAAGGA 58.796 43.478 3.71 0.00 40.88 3.36
27 28 4.275936 CGTGCCTTATATTTTGGGAAGGAG 59.724 45.833 3.71 0.00 40.88 3.69
28 29 4.584743 GTGCCTTATATTTTGGGAAGGAGG 59.415 45.833 3.71 0.00 40.88 4.30
29 30 4.152647 GCCTTATATTTTGGGAAGGAGGG 58.847 47.826 3.71 0.00 40.88 4.30
30 31 4.141018 GCCTTATATTTTGGGAAGGAGGGA 60.141 45.833 3.71 0.00 40.88 4.20
31 32 5.635120 CCTTATATTTTGGGAAGGAGGGAG 58.365 45.833 0.00 0.00 40.88 4.30
32 33 5.372661 CCTTATATTTTGGGAAGGAGGGAGA 59.627 44.000 0.00 0.00 40.88 3.71
33 34 6.126185 CCTTATATTTTGGGAAGGAGGGAGAA 60.126 42.308 0.00 0.00 40.88 2.87
34 35 3.746792 ATTTTGGGAAGGAGGGAGAAG 57.253 47.619 0.00 0.00 0.00 2.85
35 36 0.698818 TTTGGGAAGGAGGGAGAAGC 59.301 55.000 0.00 0.00 0.00 3.86
36 37 0.475632 TTGGGAAGGAGGGAGAAGCA 60.476 55.000 0.00 0.00 0.00 3.91
37 38 0.253347 TGGGAAGGAGGGAGAAGCAT 60.253 55.000 0.00 0.00 0.00 3.79
38 39 1.009552 TGGGAAGGAGGGAGAAGCATA 59.990 52.381 0.00 0.00 0.00 3.14
39 40 2.127708 GGGAAGGAGGGAGAAGCATAA 58.872 52.381 0.00 0.00 0.00 1.90
40 41 2.105649 GGGAAGGAGGGAGAAGCATAAG 59.894 54.545 0.00 0.00 0.00 1.73
41 42 3.041946 GGAAGGAGGGAGAAGCATAAGA 58.958 50.000 0.00 0.00 0.00 2.10
42 43 3.456277 GGAAGGAGGGAGAAGCATAAGAA 59.544 47.826 0.00 0.00 0.00 2.52
43 44 4.080299 GGAAGGAGGGAGAAGCATAAGAAA 60.080 45.833 0.00 0.00 0.00 2.52
44 45 4.769345 AGGAGGGAGAAGCATAAGAAAG 57.231 45.455 0.00 0.00 0.00 2.62
45 46 4.107820 AGGAGGGAGAAGCATAAGAAAGT 58.892 43.478 0.00 0.00 0.00 2.66
46 47 4.538089 AGGAGGGAGAAGCATAAGAAAGTT 59.462 41.667 0.00 0.00 0.00 2.66
47 48 4.878971 GGAGGGAGAAGCATAAGAAAGTTC 59.121 45.833 0.00 0.00 0.00 3.01
48 49 5.491982 GAGGGAGAAGCATAAGAAAGTTCA 58.508 41.667 0.00 0.00 0.00 3.18
49 50 5.880901 AGGGAGAAGCATAAGAAAGTTCAA 58.119 37.500 0.00 0.00 0.00 2.69
50 51 6.306987 AGGGAGAAGCATAAGAAAGTTCAAA 58.693 36.000 0.00 0.00 0.00 2.69
51 52 6.777580 AGGGAGAAGCATAAGAAAGTTCAAAA 59.222 34.615 0.00 0.00 0.00 2.44
52 53 7.287696 AGGGAGAAGCATAAGAAAGTTCAAAAA 59.712 33.333 0.00 0.00 0.00 1.94
166 173 2.298661 CCACCACCACTCTACCCCC 61.299 68.421 0.00 0.00 0.00 5.40
179 187 1.833055 TACCCCCTGACATCCCCTGT 61.833 60.000 0.00 0.00 42.15 4.00
242 250 3.386237 ACTCTCCTCCGCTGCCAC 61.386 66.667 0.00 0.00 0.00 5.01
347 367 2.244946 GGGGGAAATAATCTCGCGC 58.755 57.895 0.00 0.00 31.04 6.86
381 407 4.096984 CGGGAGAAGATTTGATTTCCTTGG 59.903 45.833 0.00 0.00 0.00 3.61
385 411 4.465305 AGAAGATTTGATTTCCTTGGGCAG 59.535 41.667 0.00 0.00 0.00 4.85
411 437 2.101750 GGAAGAGAGGAGGTCGATTTCC 59.898 54.545 9.48 9.48 31.22 3.13
459 489 6.743575 AAGGAGTGATTTTTATTCGGAGTG 57.256 37.500 0.00 0.00 0.00 3.51
467 497 5.666969 TTTTTATTCGGAGTGTGTCTGTG 57.333 39.130 0.00 0.00 32.66 3.66
468 498 4.330944 TTTATTCGGAGTGTGTCTGTGT 57.669 40.909 0.00 0.00 32.66 3.72
939 970 0.950555 TAAGTGCAGCTCAGGCGTTG 60.951 55.000 0.00 0.00 44.37 4.10
991 1087 5.148651 ACGTTAAGGCTACTTGTTGATCT 57.851 39.130 0.00 0.00 37.53 2.75
992 1088 5.169295 ACGTTAAGGCTACTTGTTGATCTC 58.831 41.667 0.00 0.00 37.53 2.75
1067 1166 3.500448 TGTGCCTGATGTTTGTCCTTA 57.500 42.857 0.00 0.00 0.00 2.69
1107 1206 1.468736 GCTAGGCTGCTGATTTGTTGC 60.469 52.381 0.00 0.00 0.00 4.17
1112 1214 2.874086 GGCTGCTGATTTGTTGCTTTTT 59.126 40.909 0.00 0.00 0.00 1.94
1154 1280 1.737735 CAGCTCGCAATGGTCGTCA 60.738 57.895 0.00 0.00 0.00 4.35
1489 1694 3.842925 AACCGTGCCGTGGCTCATT 62.843 57.895 12.84 3.29 42.51 2.57
1665 1870 8.653036 AGATTATAACGGAGAAGGCTTATAGT 57.347 34.615 0.00 0.00 0.00 2.12
1669 1874 3.362706 ACGGAGAAGGCTTATAGTGACA 58.637 45.455 0.00 0.00 0.00 3.58
1694 1899 0.034616 CCTGCCGATCTCCTCCAATC 59.965 60.000 0.00 0.00 0.00 2.67
1737 1942 3.499737 GGTGCTTGTCCGGATGCG 61.500 66.667 7.81 0.00 0.00 4.73
1789 1994 4.553330 AATATGAGGTTCGGTGAACAGT 57.447 40.909 11.39 0.00 43.54 3.55
1861 2066 0.467384 CCATTGCGACTCAGGGATCT 59.533 55.000 0.00 0.00 0.00 2.75
1959 2164 5.605534 CTGATATGTCTACCCAAACTCCAG 58.394 45.833 0.00 0.00 0.00 3.86
2057 2265 1.270625 CCTCACTAAAGTTGGCGTCCA 60.271 52.381 0.00 0.00 0.00 4.02
2200 2418 9.096160 CATTCTCACTCTATGATGGTTATATGC 57.904 37.037 0.00 0.00 36.48 3.14
2209 2431 9.333724 TCTATGATGGTTATATGCAGCAATATG 57.666 33.333 0.00 0.00 0.00 1.78
2242 2464 5.163301 TGGGTCTTATCTTATCTGCCAGTTC 60.163 44.000 0.00 0.00 0.00 3.01
2309 2538 2.649531 TCGGTCACAGATTTGGGTTT 57.350 45.000 0.00 0.00 0.00 3.27
2541 2773 0.601311 GCAGACGTGAAGTGGAAGCT 60.601 55.000 0.00 0.00 0.00 3.74
2568 2800 3.365767 GCTCCTGATTTCAAGCACAAGAC 60.366 47.826 0.47 0.00 31.77 3.01
2629 2861 6.533723 ACGACAATTTTAAGCGATACATCAGA 59.466 34.615 0.00 0.00 0.00 3.27
2695 2927 3.560251 AGGAAGCTGTGTGGGCGT 61.560 61.111 0.00 0.00 34.52 5.68
2713 2966 2.540157 GCGTTGTGGTGACAAGGTTTAC 60.540 50.000 8.82 0.00 45.65 2.01
2816 3070 6.150474 TCACTTCCGGTCCTAATTGAAAAATC 59.850 38.462 0.00 0.00 0.00 2.17
2844 3116 9.929180 TTGGCATGATAGTCTTATATGTAGTTC 57.071 33.333 0.00 0.00 0.00 3.01
2854 3126 8.915036 AGTCTTATATGTAGTTCGGAAATCACT 58.085 33.333 0.00 0.00 0.00 3.41
2900 3187 6.381994 AGGAGTTCCATAATTCCGTAGTTACA 59.618 38.462 0.28 0.00 44.23 2.41
2977 3264 0.179056 AAATACTAGCATGCCCGCGT 60.179 50.000 15.66 8.93 36.85 6.01
3422 4622 4.928263 TGATGTGATCCATTGTTACCCAA 58.072 39.130 0.00 0.00 37.49 4.12
3423 4623 5.517924 TGATGTGATCCATTGTTACCCAAT 58.482 37.500 0.00 0.00 44.73 3.16
3424 4624 6.667661 TGATGTGATCCATTGTTACCCAATA 58.332 36.000 0.00 0.00 41.93 1.90
3425 4625 6.545666 TGATGTGATCCATTGTTACCCAATAC 59.454 38.462 0.00 0.00 41.93 1.89
3426 4626 5.197451 TGTGATCCATTGTTACCCAATACC 58.803 41.667 0.00 0.00 41.93 2.73
3427 4627 4.583073 GTGATCCATTGTTACCCAATACCC 59.417 45.833 0.00 0.00 41.93 3.69
3428 4628 4.230733 TGATCCATTGTTACCCAATACCCA 59.769 41.667 0.00 0.00 41.93 4.51
3539 4741 7.194607 ACCAGATCTATAAATCATTGTTGCG 57.805 36.000 0.00 0.00 0.00 4.85
3541 4743 7.041780 ACCAGATCTATAAATCATTGTTGCGTC 60.042 37.037 0.00 0.00 0.00 5.19
3597 4800 3.436243 TCTCCTCTTTCTCTTGACCCTC 58.564 50.000 0.00 0.00 0.00 4.30
3799 5009 7.343833 AGTTCCAATCTGCAAAATATGAAGGAT 59.656 33.333 0.00 0.00 35.12 3.24
3800 5010 8.632679 GTTCCAATCTGCAAAATATGAAGGATA 58.367 33.333 0.00 0.00 35.12 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 3.243401 CCTTCCCAAAATATAAGGCACGC 60.243 47.826 0.00 0.00 32.66 5.34
7 8 4.141018 TCCCTCCTTCCCAAAATATAAGGC 60.141 45.833 0.00 0.00 38.70 4.35
8 9 5.372661 TCTCCCTCCTTCCCAAAATATAAGG 59.627 44.000 0.00 0.00 39.93 2.69
9 10 6.515512 TCTCCCTCCTTCCCAAAATATAAG 57.484 41.667 0.00 0.00 0.00 1.73
10 11 6.637261 GCTTCTCCCTCCTTCCCAAAATATAA 60.637 42.308 0.00 0.00 0.00 0.98
11 12 5.163088 GCTTCTCCCTCCTTCCCAAAATATA 60.163 44.000 0.00 0.00 0.00 0.86
12 13 4.386873 GCTTCTCCCTCCTTCCCAAAATAT 60.387 45.833 0.00 0.00 0.00 1.28
13 14 3.053619 GCTTCTCCCTCCTTCCCAAAATA 60.054 47.826 0.00 0.00 0.00 1.40
14 15 2.291865 GCTTCTCCCTCCTTCCCAAAAT 60.292 50.000 0.00 0.00 0.00 1.82
15 16 1.075536 GCTTCTCCCTCCTTCCCAAAA 59.924 52.381 0.00 0.00 0.00 2.44
16 17 0.698818 GCTTCTCCCTCCTTCCCAAA 59.301 55.000 0.00 0.00 0.00 3.28
18 19 0.253347 ATGCTTCTCCCTCCTTCCCA 60.253 55.000 0.00 0.00 0.00 4.37
19 20 1.807814 TATGCTTCTCCCTCCTTCCC 58.192 55.000 0.00 0.00 0.00 3.97
21 22 4.762289 TTCTTATGCTTCTCCCTCCTTC 57.238 45.455 0.00 0.00 0.00 3.46
22 23 4.538089 ACTTTCTTATGCTTCTCCCTCCTT 59.462 41.667 0.00 0.00 0.00 3.36
23 24 4.107820 ACTTTCTTATGCTTCTCCCTCCT 58.892 43.478 0.00 0.00 0.00 3.69
24 25 4.495690 ACTTTCTTATGCTTCTCCCTCC 57.504 45.455 0.00 0.00 0.00 4.30
25 26 5.491982 TGAACTTTCTTATGCTTCTCCCTC 58.508 41.667 0.00 0.00 0.00 4.30
26 27 5.505181 TGAACTTTCTTATGCTTCTCCCT 57.495 39.130 0.00 0.00 0.00 4.20
27 28 6.575162 TTTGAACTTTCTTATGCTTCTCCC 57.425 37.500 0.00 0.00 0.00 4.30
51 52 2.430694 GGTTCCTCTTGTGCCACTTTTT 59.569 45.455 0.00 0.00 0.00 1.94
52 53 2.031870 GGTTCCTCTTGTGCCACTTTT 58.968 47.619 0.00 0.00 0.00 2.27
53 54 1.064017 TGGTTCCTCTTGTGCCACTTT 60.064 47.619 0.00 0.00 0.00 2.66
54 55 0.550914 TGGTTCCTCTTGTGCCACTT 59.449 50.000 0.00 0.00 0.00 3.16
55 56 0.773644 ATGGTTCCTCTTGTGCCACT 59.226 50.000 0.00 0.00 31.47 4.00
56 57 2.359900 CTATGGTTCCTCTTGTGCCAC 58.640 52.381 0.00 0.00 31.47 5.01
57 58 1.340017 GCTATGGTTCCTCTTGTGCCA 60.340 52.381 0.00 0.00 0.00 4.92
58 59 1.383523 GCTATGGTTCCTCTTGTGCC 58.616 55.000 0.00 0.00 0.00 5.01
59 60 1.383523 GGCTATGGTTCCTCTTGTGC 58.616 55.000 0.00 0.00 0.00 4.57
60 61 1.207089 TCGGCTATGGTTCCTCTTGTG 59.793 52.381 0.00 0.00 0.00 3.33
61 62 1.568504 TCGGCTATGGTTCCTCTTGT 58.431 50.000 0.00 0.00 0.00 3.16
62 63 2.366916 AGATCGGCTATGGTTCCTCTTG 59.633 50.000 0.00 0.00 0.00 3.02
63 64 2.683768 AGATCGGCTATGGTTCCTCTT 58.316 47.619 0.00 0.00 0.00 2.85
64 65 2.366916 CAAGATCGGCTATGGTTCCTCT 59.633 50.000 0.00 0.00 0.00 3.69
65 66 2.760374 CAAGATCGGCTATGGTTCCTC 58.240 52.381 0.00 0.00 0.00 3.71
66 67 1.202698 GCAAGATCGGCTATGGTTCCT 60.203 52.381 5.31 0.00 0.00 3.36
166 173 0.392193 GCTGTCACAGGGGATGTCAG 60.392 60.000 7.00 0.00 41.41 3.51
179 187 1.159905 TTGGGTAGGGAGGCTGTCA 59.840 57.895 0.00 0.00 0.00 3.58
242 250 4.344865 CGGGGTTGACACAGGGGG 62.345 72.222 0.00 0.00 0.00 5.40
381 407 0.681564 TCCTCTCTTCCTCGACTGCC 60.682 60.000 0.00 0.00 0.00 4.85
385 411 1.385528 GACCTCCTCTCTTCCTCGAC 58.614 60.000 0.00 0.00 0.00 4.20
459 489 5.345202 CGGATTACAACTTCTACACAGACAC 59.655 44.000 0.00 0.00 0.00 3.67
467 497 5.530712 GAGGATCCGGATTACAACTTCTAC 58.469 45.833 20.22 0.19 0.00 2.59
468 498 5.786264 GAGGATCCGGATTACAACTTCTA 57.214 43.478 20.22 0.00 0.00 2.10
939 970 6.885314 CCTTATTGGATCTGTGACAACAGCC 61.885 48.000 0.91 0.00 45.32 4.85
991 1087 1.820519 GCTTTGGTTCATGGCTGATGA 59.179 47.619 0.00 0.00 39.47 2.92
992 1088 1.468565 CGCTTTGGTTCATGGCTGATG 60.469 52.381 0.00 0.00 0.00 3.07
1067 1166 1.137086 CCATGAGGACGAATCGAAGGT 59.863 52.381 10.55 0.00 36.89 3.50
1107 1206 8.296799 TCTGCATTGCATTTAACAGTAAAAAG 57.703 30.769 12.53 0.00 38.13 2.27
1112 1214 7.600960 TGATTTCTGCATTGCATTTAACAGTA 58.399 30.769 12.53 0.00 38.13 2.74
1154 1280 2.073816 GCACACTTACATTACGCCTGT 58.926 47.619 0.00 0.00 0.00 4.00
1489 1694 4.199310 GTGCCCAAGATGCTATCAGTTAA 58.801 43.478 0.00 0.00 0.00 2.01
1694 1899 8.430063 CAACAAAATTATTGAACAGCTTAGCAG 58.570 33.333 7.07 0.00 0.00 4.24
1789 1994 2.575735 TGCTGAGGATGTTTGGGATGTA 59.424 45.455 0.00 0.00 0.00 2.29
1861 2066 4.893608 TGTTCTACTTGCAGCACAGAATA 58.106 39.130 13.70 9.90 0.00 1.75
1959 2164 4.154195 CACCAATTATTATAGCTCACCCGC 59.846 45.833 0.00 0.00 0.00 6.13
2156 2368 8.341173 GTGAGAATGGACAGATATGATTCAAAC 58.659 37.037 0.00 0.00 0.00 2.93
2200 2418 5.882557 AGACCCACTTAAGTTCATATTGCTG 59.117 40.000 5.07 0.00 0.00 4.41
2209 2431 9.535878 CAGATAAGATAAGACCCACTTAAGTTC 57.464 37.037 5.07 1.24 43.15 3.01
2242 2464 7.558137 GCAAGTTGCATATAAATCAAATTCCG 58.442 34.615 22.90 0.00 44.26 4.30
2309 2538 2.165437 GCATTTTCGGGCATTCTGGTAA 59.835 45.455 0.00 0.00 0.00 2.85
2541 2773 5.683681 TGTGCTTGAAATCAGGAGCATATA 58.316 37.500 11.69 2.03 45.69 0.86
2568 2800 1.761784 AGATGGTGAGCTTAGCCAGAG 59.238 52.381 5.13 0.00 35.56 3.35
2629 2861 0.597568 CCGCATGTTCCACAACACAT 59.402 50.000 0.00 0.00 45.47 3.21
2695 2927 3.367646 TGGTAAACCTTGTCACCACAA 57.632 42.857 0.02 0.00 40.40 3.33
2713 2966 4.060900 CAGTCCGTGGATATCTTGATTGG 58.939 47.826 2.05 0.00 0.00 3.16
2816 3070 9.881649 ACTACATATAAGACTATCATGCCAATG 57.118 33.333 0.00 0.00 34.88 2.82
2829 3083 9.530633 AAGTGATTTCCGAACTACATATAAGAC 57.469 33.333 0.00 0.00 0.00 3.01
2854 3126 7.403231 ACTCCTTCCAACTAAAGATGATAGGAA 59.597 37.037 9.74 0.00 31.94 3.36
2891 3178 6.087820 GCAAGAGTACAGACTTTGTAACTACG 59.912 42.308 0.00 0.00 43.61 3.51
2900 3187 4.103311 AGGGAAAGCAAGAGTACAGACTTT 59.897 41.667 0.00 0.00 35.45 2.66
2934 3221 9.629878 TTTCCTCAATTAGGTAACAAGTACAAA 57.370 29.630 0.00 0.00 46.62 2.83
3076 3363 9.533253 ACTTTCCTTTTTGTGATTACAATCTTG 57.467 29.630 3.63 0.00 45.56 3.02
3234 3555 4.829872 TTACCATTTCATCACGGGTACT 57.170 40.909 0.00 0.00 34.05 2.73
3539 4741 5.414144 AGGCTAGCATTCTCTTTCTTTTGAC 59.586 40.000 18.24 0.00 0.00 3.18
3541 4743 5.638783 CAGGCTAGCATTCTCTTTCTTTTG 58.361 41.667 18.24 0.00 0.00 2.44
3597 4800 4.430423 GCGCGGCTTCAAGACACG 62.430 66.667 8.83 0.00 0.00 4.49
3661 4865 1.808411 AATTCGCAACGGTGACTCAT 58.192 45.000 3.55 0.00 32.18 2.90
3662 4866 1.262950 CAAATTCGCAACGGTGACTCA 59.737 47.619 3.55 0.00 32.18 3.41


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

AutoCloner maintained by Alex Coulton.