Multiple sequence alignment - TraesCS6D01G361800

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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 TraesCS6D01G361800 chr6D 100.000 2534 0 0 1 2534 452710810 452708277 0.000000e+00 4680.0
1 TraesCS6D01G361800 chr6D 83.837 563 45 22 1074 1614 452623536 452622998 6.300000e-136 494.0
2 TraesCS6D01G361800 chr6D 86.217 341 31 8 1292 1624 452641652 452641320 3.100000e-94 355.0
3 TraesCS6D01G361800 chr6D 83.268 257 28 7 1647 1901 452592602 452592359 3.280000e-54 222.0
4 TraesCS6D01G361800 chr6D 82.353 255 18 9 1030 1280 452641985 452641754 1.990000e-46 196.0
5 TraesCS6D01G361800 chr6B 90.899 1736 72 45 861 2534 687413703 687411992 0.000000e+00 2252.0
6 TraesCS6D01G361800 chr6B 86.756 521 40 13 1015 1507 687372435 687371916 1.020000e-153 553.0
7 TraesCS6D01G361800 chr6B 92.032 251 15 3 1058 1303 687367117 687366867 5.190000e-92 348.0
8 TraesCS6D01G361800 chr6B 87.823 271 26 4 1009 1278 687108210 687108474 6.810000e-81 311.0
9 TraesCS6D01G361800 chr6B 82.721 272 27 9 1292 1563 687317749 687317498 9.120000e-55 224.0
10 TraesCS6D01G361800 chr6B 94.118 68 4 0 861 928 687318423 687318356 1.240000e-18 104.0
11 TraesCS6D01G361800 chr6B 92.647 68 5 0 861 928 687108039 687108106 5.770000e-17 99.0
12 TraesCS6D01G361800 chr6A 78.252 1407 181 64 1044 2372 598326993 598325634 0.000000e+00 787.0
13 TraesCS6D01G361800 chr6A 78.252 1407 181 65 1044 2372 598461077 598459718 0.000000e+00 787.0
14 TraesCS6D01G361800 chr6A 78.196 1408 181 67 1044 2372 598253709 598252349 0.000000e+00 784.0
15 TraesCS6D01G361800 chr6A 77.983 1408 184 66 1044 2372 598521008 598519648 0.000000e+00 767.0
16 TraesCS6D01G361800 chr6A 84.364 825 79 26 1 809 598597965 598597175 0.000000e+00 763.0
17 TraesCS6D01G361800 chr6A 77.825 1407 188 70 1044 2372 598568796 598567436 0.000000e+00 756.0
18 TraesCS6D01G361800 chr6A 83.654 624 56 29 1009 1614 598576250 598575655 1.710000e-151 545.0
19 TraesCS6D01G361800 chr6A 77.711 664 75 34 1292 1901 598212506 598211862 3.120000e-89 339.0
20 TraesCS6D01G361800 chr6A 81.979 283 21 15 1375 1638 598207504 598207233 1.970000e-51 213.0
21 TraesCS6D01G361800 chr6A 80.357 224 27 7 1647 1869 598207189 598206982 1.210000e-33 154.0
22 TraesCS6D01G361800 chrUn 94.286 210 9 1 1041 1250 341387582 341387788 4.070000e-83 318.0
23 TraesCS6D01G361800 chr7A 83.333 78 9 3 782 859 71161839 71161912 4.520000e-08 69.4
24 TraesCS6D01G361800 chr7A 88.679 53 6 0 808 860 37236564 37236512 5.850000e-07 65.8
25 TraesCS6D01G361800 chr7A 94.737 38 2 0 808 845 37210332 37210295 2.720000e-05 60.2
26 TraesCS6D01G361800 chr7A 94.737 38 2 0 808 845 37351162 37351125 2.720000e-05 60.2
27 TraesCS6D01G361800 chr4A 89.091 55 6 0 806 860 686565894 686565948 4.520000e-08 69.4
28 TraesCS6D01G361800 chr4A 86.207 58 8 0 808 865 686585159 686585216 2.100000e-06 63.9


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 TraesCS6D01G361800 chr6D 452708277 452710810 2533 True 4680.0 4680 100.000 1 2534 1 chr6D.!!$R3 2533
1 TraesCS6D01G361800 chr6D 452622998 452623536 538 True 494.0 494 83.837 1074 1614 1 chr6D.!!$R2 540
2 TraesCS6D01G361800 chr6D 452641320 452641985 665 True 275.5 355 84.285 1030 1624 2 chr6D.!!$R4 594
3 TraesCS6D01G361800 chr6B 687411992 687413703 1711 True 2252.0 2252 90.899 861 2534 1 chr6B.!!$R3 1673
4 TraesCS6D01G361800 chr6B 687371916 687372435 519 True 553.0 553 86.756 1015 1507 1 chr6B.!!$R2 492
5 TraesCS6D01G361800 chr6A 598325634 598326993 1359 True 787.0 787 78.252 1044 2372 1 chr6A.!!$R3 1328
6 TraesCS6D01G361800 chr6A 598459718 598461077 1359 True 787.0 787 78.252 1044 2372 1 chr6A.!!$R4 1328
7 TraesCS6D01G361800 chr6A 598252349 598253709 1360 True 784.0 784 78.196 1044 2372 1 chr6A.!!$R2 1328
8 TraesCS6D01G361800 chr6A 598519648 598521008 1360 True 767.0 767 77.983 1044 2372 1 chr6A.!!$R5 1328
9 TraesCS6D01G361800 chr6A 598597175 598597965 790 True 763.0 763 84.364 1 809 1 chr6A.!!$R8 808
10 TraesCS6D01G361800 chr6A 598567436 598568796 1360 True 756.0 756 77.825 1044 2372 1 chr6A.!!$R6 1328
11 TraesCS6D01G361800 chr6A 598575655 598576250 595 True 545.0 545 83.654 1009 1614 1 chr6A.!!$R7 605
12 TraesCS6D01G361800 chr6A 598211862 598212506 644 True 339.0 339 77.711 1292 1901 1 chr6A.!!$R1 609

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
971 990 0.321653 CGGTAACCTCTTTGCCAGCT 60.322 55.0 0.0 0.0 39.94 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1968 2222 1.277842 TGCTAAAATGGGTCAGCGAGA 59.722 47.619 0.0 0.0 36.81 4.04 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
51 53 6.875972 AGTCCATACTTGAACTATTCACCT 57.124 37.500 0.00 0.00 39.87 4.00
55 57 6.051717 CCATACTTGAACTATTCACCTCCTG 58.948 44.000 0.00 0.00 39.87 3.86
56 58 4.559862 ACTTGAACTATTCACCTCCTGG 57.440 45.455 0.00 0.00 39.87 4.45
69 71 5.145564 TCACCTCCTGGTATCCTAACATAC 58.854 45.833 0.00 0.00 46.60 2.39
112 114 3.998099 GGAGTACCCGATAGTAACCAC 57.002 52.381 0.00 0.00 0.00 4.16
148 150 7.504926 TTACCCAGTCATTATTAGGAAGTGT 57.495 36.000 0.00 0.00 0.00 3.55
170 172 6.609616 GTGTTATCAAAATCCCCCAATTCCTA 59.390 38.462 0.00 0.00 0.00 2.94
174 176 9.959693 TTATCAAAATCCCCCAATTCCTATTTA 57.040 29.630 0.00 0.00 0.00 1.40
179 181 1.886542 CCCCAATTCCTATTTAGCGCC 59.113 52.381 2.29 0.00 0.00 6.53
197 199 3.831715 GCCTTAAGCGCCATTTATAGG 57.168 47.619 2.29 7.59 0.00 2.57
211 215 7.610305 CGCCATTTATAGGATATTGGGTTAACT 59.390 37.037 5.42 0.00 0.00 2.24
212 216 8.739972 GCCATTTATAGGATATTGGGTTAACTG 58.260 37.037 5.42 0.00 0.00 3.16
213 217 9.243105 CCATTTATAGGATATTGGGTTAACTGG 57.757 37.037 5.42 0.00 0.00 4.00
214 218 9.807921 CATTTATAGGATATTGGGTTAACTGGT 57.192 33.333 5.42 0.00 0.00 4.00
219 223 1.627864 ATTGGGTTAACTGGTGCACC 58.372 50.000 29.67 29.67 0.00 5.01
235 239 2.750237 CCAGGTAGCAAACGGGCC 60.750 66.667 0.00 0.00 0.00 5.80
252 256 1.687563 GCCGGGCCATGTAAGTATTT 58.312 50.000 8.12 0.00 0.00 1.40
282 286 2.807837 CGGTTTTGTAGGTTCGGAAGGT 60.808 50.000 0.00 0.00 0.00 3.50
295 299 0.826256 GGAAGGTTTCTTTGGGCGGT 60.826 55.000 0.00 0.00 32.52 5.68
309 313 1.411246 GGGCGGTTTTTCCTTCTGTTT 59.589 47.619 0.00 0.00 0.00 2.83
321 325 3.070446 TCCTTCTGTTTTTCTAGTGCGGA 59.930 43.478 0.00 0.00 0.00 5.54
329 333 4.419522 TTTTCTAGTGCGGATTTTGCTC 57.580 40.909 0.00 0.00 0.00 4.26
330 334 2.760634 TCTAGTGCGGATTTTGCTCA 57.239 45.000 0.00 0.00 0.00 4.26
331 335 3.052455 TCTAGTGCGGATTTTGCTCAA 57.948 42.857 0.00 0.00 0.00 3.02
339 343 4.389382 TGCGGATTTTGCTCAATTTTCATG 59.611 37.500 0.00 0.00 0.00 3.07
342 346 6.256321 GCGGATTTTGCTCAATTTTCATGTAT 59.744 34.615 0.00 0.00 0.00 2.29
400 404 6.473758 ACTTAGTTCCTAATCCACAAACTCC 58.526 40.000 0.00 0.00 32.71 3.85
408 412 7.010160 TCCTAATCCACAAACTCCTTTTCAAT 58.990 34.615 0.00 0.00 0.00 2.57
413 417 9.492973 AATCCACAAACTCCTTTTCAATTTATG 57.507 29.630 0.00 0.00 0.00 1.90
415 419 7.288852 TCCACAAACTCCTTTTCAATTTATGGA 59.711 33.333 0.00 0.00 0.00 3.41
416 420 7.384932 CCACAAACTCCTTTTCAATTTATGGAC 59.615 37.037 0.00 0.00 0.00 4.02
421 429 9.764363 AACTCCTTTTCAATTTATGGACTTTTC 57.236 29.630 0.00 0.00 0.00 2.29
426 434 9.336171 CTTTTCAATTTATGGACTTTTCCCAAA 57.664 29.630 0.00 0.00 42.01 3.28
464 472 6.148645 TCAAATGCATGAACTTTTAGCTCGTA 59.851 34.615 0.00 0.00 0.00 3.43
469 477 7.367285 TGCATGAACTTTTAGCTCGTAATTTT 58.633 30.769 0.00 0.00 0.00 1.82
664 678 7.532682 TTTTCCAATTCAAGAACCTTTTTCG 57.467 32.000 0.00 0.00 0.00 3.46
669 683 6.019075 CCAATTCAAGAACCTTTTTCGTTTCC 60.019 38.462 0.00 0.00 0.00 3.13
670 684 4.281525 TCAAGAACCTTTTTCGTTTCCG 57.718 40.909 0.00 0.00 0.00 4.30
671 685 2.768833 AGAACCTTTTTCGTTTCCGC 57.231 45.000 0.00 0.00 0.00 5.54
673 687 2.424246 AGAACCTTTTTCGTTTCCGCAA 59.576 40.909 0.00 0.00 0.00 4.85
674 688 2.943449 ACCTTTTTCGTTTCCGCAAA 57.057 40.000 0.00 0.00 0.00 3.68
675 689 3.233684 ACCTTTTTCGTTTCCGCAAAA 57.766 38.095 0.00 0.00 36.96 2.44
679 694 4.960953 CCTTTTTCGTTTCCGCAAAATTTG 59.039 37.500 0.57 0.57 38.24 2.32
823 838 9.956720 GTAGTACTCCGTATATGTTAATGTTGT 57.043 33.333 0.00 0.00 0.00 3.32
825 840 9.956720 AGTACTCCGTATATGTTAATGTTGTAC 57.043 33.333 0.00 0.00 0.00 2.90
826 841 9.956720 GTACTCCGTATATGTTAATGTTGTACT 57.043 33.333 0.00 0.00 0.00 2.73
837 852 7.970102 TGTTAATGTTGTACTAGAAGAAGGGT 58.030 34.615 0.00 0.00 0.00 4.34
838 853 7.876068 TGTTAATGTTGTACTAGAAGAAGGGTG 59.124 37.037 0.00 0.00 0.00 4.61
839 854 6.681729 AATGTTGTACTAGAAGAAGGGTGA 57.318 37.500 0.00 0.00 0.00 4.02
840 855 6.681729 ATGTTGTACTAGAAGAAGGGTGAA 57.318 37.500 0.00 0.00 0.00 3.18
841 856 6.488769 TGTTGTACTAGAAGAAGGGTGAAA 57.511 37.500 0.00 0.00 0.00 2.69
842 857 7.074653 TGTTGTACTAGAAGAAGGGTGAAAT 57.925 36.000 0.00 0.00 0.00 2.17
843 858 8.197592 TGTTGTACTAGAAGAAGGGTGAAATA 57.802 34.615 0.00 0.00 0.00 1.40
844 859 8.311836 TGTTGTACTAGAAGAAGGGTGAAATAG 58.688 37.037 0.00 0.00 0.00 1.73
845 860 6.875076 TGTACTAGAAGAAGGGTGAAATAGC 58.125 40.000 0.00 0.00 0.00 2.97
846 861 5.012328 ACTAGAAGAAGGGTGAAATAGCG 57.988 43.478 0.00 0.00 0.00 4.26
847 862 4.710375 ACTAGAAGAAGGGTGAAATAGCGA 59.290 41.667 0.00 0.00 0.00 4.93
848 863 4.762289 AGAAGAAGGGTGAAATAGCGAT 57.238 40.909 0.00 0.00 0.00 4.58
849 864 4.446371 AGAAGAAGGGTGAAATAGCGATG 58.554 43.478 0.00 0.00 0.00 3.84
850 865 3.914426 AGAAGGGTGAAATAGCGATGT 57.086 42.857 0.00 0.00 0.00 3.06
851 866 4.222124 AGAAGGGTGAAATAGCGATGTT 57.778 40.909 0.00 0.00 0.00 2.71
852 867 4.589908 AGAAGGGTGAAATAGCGATGTTT 58.410 39.130 0.00 0.00 0.00 2.83
853 868 4.636206 AGAAGGGTGAAATAGCGATGTTTC 59.364 41.667 14.96 14.96 35.45 2.78
854 869 3.279434 AGGGTGAAATAGCGATGTTTCC 58.721 45.455 18.32 10.54 34.29 3.13
855 870 3.054361 AGGGTGAAATAGCGATGTTTCCT 60.054 43.478 18.32 7.91 34.29 3.36
856 871 3.065371 GGGTGAAATAGCGATGTTTCCTG 59.935 47.826 18.32 0.00 34.29 3.86
857 872 3.938963 GGTGAAATAGCGATGTTTCCTGA 59.061 43.478 18.32 0.00 34.29 3.86
858 873 4.576463 GGTGAAATAGCGATGTTTCCTGAT 59.424 41.667 18.32 0.00 34.29 2.90
859 874 5.758296 GGTGAAATAGCGATGTTTCCTGATA 59.242 40.000 18.32 0.00 34.29 2.15
879 894 3.677648 GGTGTGCCTTGCCTGCAG 61.678 66.667 6.78 6.78 39.87 4.41
889 904 0.321919 TTGCCTGCAGAGCTACAAGG 60.322 55.000 17.39 0.00 0.00 3.61
907 922 4.184629 CAAGGTACTGATTCCTCCTTTCG 58.815 47.826 0.00 0.00 40.86 3.46
928 943 3.417069 TGTGCTACACATTTACTGCCT 57.583 42.857 0.00 0.00 39.62 4.75
944 963 1.320507 GCCTCGCCTAACTAGCTAGT 58.679 55.000 20.95 20.95 38.39 2.57
945 964 2.158711 TGCCTCGCCTAACTAGCTAGTA 60.159 50.000 26.29 13.46 34.99 1.82
946 965 3.083293 GCCTCGCCTAACTAGCTAGTAT 58.917 50.000 26.29 17.69 34.99 2.12
947 966 3.119779 GCCTCGCCTAACTAGCTAGTATG 60.120 52.174 26.29 19.86 34.99 2.39
948 967 3.119779 CCTCGCCTAACTAGCTAGTATGC 60.120 52.174 26.29 24.09 34.99 3.14
949 968 3.483421 TCGCCTAACTAGCTAGTATGCA 58.517 45.455 26.29 15.24 34.99 3.96
950 969 3.502595 TCGCCTAACTAGCTAGTATGCAG 59.497 47.826 26.29 20.60 34.99 4.41
951 970 3.580731 GCCTAACTAGCTAGTATGCAGC 58.419 50.000 26.29 19.32 39.41 5.25
952 971 3.615351 GCCTAACTAGCTAGTATGCAGCC 60.615 52.174 26.29 8.13 39.99 4.85
953 972 2.802787 AACTAGCTAGTATGCAGCCG 57.197 50.000 26.29 0.00 39.99 5.52
954 973 0.962489 ACTAGCTAGTATGCAGCCGG 59.038 55.000 24.97 0.00 39.99 6.13
955 974 0.962489 CTAGCTAGTATGCAGCCGGT 59.038 55.000 12.92 0.00 39.99 5.28
956 975 2.160205 CTAGCTAGTATGCAGCCGGTA 58.840 52.381 12.92 0.00 39.99 4.02
957 976 1.410004 AGCTAGTATGCAGCCGGTAA 58.590 50.000 1.90 0.00 39.99 2.85
958 977 1.068741 AGCTAGTATGCAGCCGGTAAC 59.931 52.381 1.90 0.00 39.99 2.50
959 978 1.872653 GCTAGTATGCAGCCGGTAACC 60.873 57.143 1.90 0.00 32.68 2.85
960 979 1.687123 CTAGTATGCAGCCGGTAACCT 59.313 52.381 1.90 0.00 0.00 3.50
961 980 0.464452 AGTATGCAGCCGGTAACCTC 59.536 55.000 1.90 0.00 0.00 3.85
962 981 0.464452 GTATGCAGCCGGTAACCTCT 59.536 55.000 1.90 0.00 0.00 3.69
963 982 1.134491 GTATGCAGCCGGTAACCTCTT 60.134 52.381 1.90 0.00 0.00 2.85
964 983 0.328258 ATGCAGCCGGTAACCTCTTT 59.672 50.000 1.90 0.00 0.00 2.52
965 984 0.605319 TGCAGCCGGTAACCTCTTTG 60.605 55.000 1.90 0.00 0.00 2.77
966 985 1.923227 GCAGCCGGTAACCTCTTTGC 61.923 60.000 1.90 0.00 0.00 3.68
967 986 1.002502 AGCCGGTAACCTCTTTGCC 60.003 57.895 1.90 0.00 36.63 4.52
968 987 1.302993 GCCGGTAACCTCTTTGCCA 60.303 57.895 1.90 0.00 39.94 4.92
969 988 1.305930 GCCGGTAACCTCTTTGCCAG 61.306 60.000 1.90 0.00 39.94 4.85
970 989 1.305930 CCGGTAACCTCTTTGCCAGC 61.306 60.000 0.00 0.00 39.94 4.85
971 990 0.321653 CGGTAACCTCTTTGCCAGCT 60.322 55.000 0.00 0.00 39.94 4.24
972 991 1.454201 GGTAACCTCTTTGCCAGCTC 58.546 55.000 0.00 0.00 39.72 4.09
973 992 1.079503 GTAACCTCTTTGCCAGCTCG 58.920 55.000 0.00 0.00 0.00 5.03
974 993 0.685097 TAACCTCTTTGCCAGCTCGT 59.315 50.000 0.00 0.00 0.00 4.18
975 994 0.886490 AACCTCTTTGCCAGCTCGTG 60.886 55.000 0.00 0.00 0.00 4.35
976 995 2.684843 CCTCTTTGCCAGCTCGTGC 61.685 63.158 0.07 0.07 40.05 5.34
977 996 1.962822 CTCTTTGCCAGCTCGTGCA 60.963 57.895 12.58 0.00 42.74 4.57
978 997 2.180131 CTCTTTGCCAGCTCGTGCAC 62.180 60.000 12.58 6.82 42.74 4.57
979 998 3.584250 CTTTGCCAGCTCGTGCACG 62.584 63.158 32.76 32.76 42.74 5.34
1028 1083 1.617850 ACAGCACAGAGACAGAGAAGG 59.382 52.381 0.00 0.00 0.00 3.46
1055 1111 2.434428 CAGCCAAGCAAAGTGAGAGAT 58.566 47.619 0.00 0.00 0.00 2.75
1070 1129 1.340889 AGAGATCAAGAGAGATGGCGC 59.659 52.381 0.00 0.00 0.00 6.53
1195 1257 1.075970 AGGATCTGCTGCCGGACTA 60.076 57.895 5.05 0.00 0.00 2.59
1213 1275 0.251922 TACAGCCACCGACTTACCCT 60.252 55.000 0.00 0.00 0.00 4.34
1214 1276 1.218316 CAGCCACCGACTTACCCTC 59.782 63.158 0.00 0.00 0.00 4.30
1255 1317 7.739444 TCCTCCACCATTGGTAATCTATCTATT 59.261 37.037 8.31 0.00 44.35 1.73
1262 1327 9.376075 CCATTGGTAATCTATCTATTGCTGTAG 57.624 37.037 0.00 0.00 0.00 2.74
1629 1827 4.690748 ACAACGAATGATGTACTGTTGAGG 59.309 41.667 9.59 0.00 39.11 3.86
1719 1943 1.540707 ACCAAACGGTTCACAAACGTT 59.459 42.857 6.25 6.25 36.16 3.99
1735 1960 5.518487 ACAAACGTTTTTCGATCTTGCATTT 59.482 32.000 11.66 0.00 42.86 2.32
1837 2072 5.209818 TCGCGAGTATATCCCAAAAGAAT 57.790 39.130 3.71 0.00 0.00 2.40
1886 2130 1.540267 TTGGCCAGATACCAAAACCG 58.460 50.000 5.11 0.00 44.11 4.44
1962 2216 9.790389 ACGTTTCTAGTATTAGAGACAGAAATG 57.210 33.333 13.95 10.85 39.69 2.32
1963 2217 8.747666 CGTTTCTAGTATTAGAGACAGAAATGC 58.252 37.037 13.95 0.00 39.69 3.56
1966 2220 7.640852 TCTAGTATTAGAGACAGAAATGCGAC 58.359 38.462 0.00 0.00 32.21 5.19
1968 2222 6.868622 AGTATTAGAGACAGAAATGCGACTT 58.131 36.000 0.00 0.00 0.00 3.01
1969 2223 6.975772 AGTATTAGAGACAGAAATGCGACTTC 59.024 38.462 0.00 0.00 0.00 3.01
1971 2225 3.843999 AGAGACAGAAATGCGACTTCTC 58.156 45.455 0.00 0.00 30.58 2.87
2022 2290 7.861176 TTCTCGTTTTATGTAAAAACATGGC 57.139 32.000 12.34 0.00 39.42 4.40
2333 2617 4.335735 AATGAAGGACCCATTTGGATCA 57.664 40.909 0.00 0.00 37.39 2.92
2419 2704 6.041423 AGGAAGTTTGAATTAAAGGCATGG 57.959 37.500 0.00 0.00 0.00 3.66
2518 2803 1.015607 GCAAAAGCTTTGCCCCATCG 61.016 55.000 13.54 0.00 39.38 3.84
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 9.739276 TGAATAGTTCAAGTATGGACTTCAATT 57.261 29.630 0.00 0.00 43.16 2.32
33 34 6.240549 CCAGGAGGTGAATAGTTCAAGTAT 57.759 41.667 0.00 0.00 42.15 2.12
51 53 7.073208 TGATCAAGTATGTTAGGATACCAGGA 58.927 38.462 0.00 0.00 30.20 3.86
95 97 3.290710 TCTGGTGGTTACTATCGGGTAC 58.709 50.000 0.00 0.00 0.00 3.34
101 103 5.871396 TGAAGGATCTGGTGGTTACTATC 57.129 43.478 0.00 0.00 0.00 2.08
112 114 3.455910 TGACTGGGTAATGAAGGATCTGG 59.544 47.826 0.00 0.00 0.00 3.86
148 150 8.868404 AAATAGGAATTGGGGGATTTTGATAA 57.132 30.769 0.00 0.00 0.00 1.75
179 181 7.201732 CCCAATATCCTATAAATGGCGCTTAAG 60.202 40.741 7.64 0.00 0.00 1.85
190 192 7.722285 GCACCAGTTAACCCAATATCCTATAAA 59.278 37.037 0.88 0.00 0.00 1.40
197 199 3.380320 GGTGCACCAGTTAACCCAATATC 59.620 47.826 31.23 0.00 35.64 1.63
211 215 0.821711 GTTTGCTACCTGGTGCACCA 60.822 55.000 35.49 35.49 45.30 4.17
212 216 1.852067 CGTTTGCTACCTGGTGCACC 61.852 60.000 29.67 29.67 39.05 5.01
213 217 1.574428 CGTTTGCTACCTGGTGCAC 59.426 57.895 19.02 8.80 39.05 4.57
214 218 1.599518 CCGTTTGCTACCTGGTGCA 60.600 57.895 10.23 14.10 37.42 4.57
219 223 3.124921 CGGCCCGTTTGCTACCTG 61.125 66.667 0.00 0.00 0.00 4.00
235 239 3.945285 ACAAGAAATACTTACATGGCCCG 59.055 43.478 0.00 0.00 37.03 6.13
238 242 6.422223 CGATGACAAGAAATACTTACATGGC 58.578 40.000 0.00 0.00 37.03 4.40
252 256 4.345859 ACCTACAAAACCGATGACAAGA 57.654 40.909 0.00 0.00 0.00 3.02
282 286 2.112190 AGGAAAAACCGCCCAAAGAAA 58.888 42.857 0.00 0.00 44.74 2.52
295 299 6.262601 CGCACTAGAAAAACAGAAGGAAAAA 58.737 36.000 0.00 0.00 0.00 1.94
309 313 3.407698 TGAGCAAAATCCGCACTAGAAA 58.592 40.909 0.00 0.00 0.00 2.52
361 365 7.694093 AGGAACTAAGTTCTGGAATCTGAAAT 58.306 34.615 0.00 0.00 41.70 2.17
380 384 5.584551 AAGGAGTTTGTGGATTAGGAACT 57.415 39.130 0.00 0.00 46.37 3.01
413 417 7.566760 AAAAACATGAATTTGGGAAAAGTCC 57.433 32.000 0.00 0.00 44.10 3.85
439 447 5.048782 ACGAGCTAAAAGTTCATGCATTTGA 60.049 36.000 0.00 0.00 0.00 2.69
440 448 5.156355 ACGAGCTAAAAGTTCATGCATTTG 58.844 37.500 0.00 0.00 0.00 2.32
477 485 7.890127 ACTCATGAATCTGGAAAAGTTTATGGA 59.110 33.333 0.00 0.00 0.00 3.41
478 486 8.059798 ACTCATGAATCTGGAAAAGTTTATGG 57.940 34.615 0.00 0.00 0.00 2.74
645 659 6.933130 GGAAACGAAAAAGGTTCTTGAATTG 58.067 36.000 0.00 0.00 37.91 2.32
811 826 8.603304 ACCCTTCTTCTAGTACAACATTAACAT 58.397 33.333 0.00 0.00 0.00 2.71
812 827 7.876068 CACCCTTCTTCTAGTACAACATTAACA 59.124 37.037 0.00 0.00 0.00 2.41
813 828 8.092687 TCACCCTTCTTCTAGTACAACATTAAC 58.907 37.037 0.00 0.00 0.00 2.01
814 829 8.197592 TCACCCTTCTTCTAGTACAACATTAA 57.802 34.615 0.00 0.00 0.00 1.40
815 830 7.786046 TCACCCTTCTTCTAGTACAACATTA 57.214 36.000 0.00 0.00 0.00 1.90
816 831 6.681729 TCACCCTTCTTCTAGTACAACATT 57.318 37.500 0.00 0.00 0.00 2.71
817 832 6.681729 TTCACCCTTCTTCTAGTACAACAT 57.318 37.500 0.00 0.00 0.00 2.71
818 833 6.488769 TTTCACCCTTCTTCTAGTACAACA 57.511 37.500 0.00 0.00 0.00 3.33
819 834 7.278203 GCTATTTCACCCTTCTTCTAGTACAAC 59.722 40.741 0.00 0.00 0.00 3.32
820 835 7.328737 GCTATTTCACCCTTCTTCTAGTACAA 58.671 38.462 0.00 0.00 0.00 2.41
821 836 6.405508 CGCTATTTCACCCTTCTTCTAGTACA 60.406 42.308 0.00 0.00 0.00 2.90
822 837 5.978322 CGCTATTTCACCCTTCTTCTAGTAC 59.022 44.000 0.00 0.00 0.00 2.73
823 838 5.889853 TCGCTATTTCACCCTTCTTCTAGTA 59.110 40.000 0.00 0.00 0.00 1.82
824 839 4.710375 TCGCTATTTCACCCTTCTTCTAGT 59.290 41.667 0.00 0.00 0.00 2.57
825 840 5.263968 TCGCTATTTCACCCTTCTTCTAG 57.736 43.478 0.00 0.00 0.00 2.43
826 841 5.128827 ACATCGCTATTTCACCCTTCTTCTA 59.871 40.000 0.00 0.00 0.00 2.10
827 842 4.080863 ACATCGCTATTTCACCCTTCTTCT 60.081 41.667 0.00 0.00 0.00 2.85
828 843 4.192317 ACATCGCTATTTCACCCTTCTTC 58.808 43.478 0.00 0.00 0.00 2.87
829 844 4.222124 ACATCGCTATTTCACCCTTCTT 57.778 40.909 0.00 0.00 0.00 2.52
830 845 3.914426 ACATCGCTATTTCACCCTTCT 57.086 42.857 0.00 0.00 0.00 2.85
831 846 4.201920 GGAAACATCGCTATTTCACCCTTC 60.202 45.833 0.00 0.00 36.69 3.46
832 847 3.694566 GGAAACATCGCTATTTCACCCTT 59.305 43.478 0.00 0.00 36.69 3.95
833 848 3.054361 AGGAAACATCGCTATTTCACCCT 60.054 43.478 0.00 0.00 36.69 4.34
834 849 3.065371 CAGGAAACATCGCTATTTCACCC 59.935 47.826 0.00 0.00 36.69 4.61
835 850 3.938963 TCAGGAAACATCGCTATTTCACC 59.061 43.478 0.00 0.00 36.69 4.02
836 851 5.741388 ATCAGGAAACATCGCTATTTCAC 57.259 39.130 0.00 0.00 36.69 3.18
837 852 6.479990 CACTATCAGGAAACATCGCTATTTCA 59.520 38.462 0.00 0.00 36.69 2.69
838 853 6.073548 CCACTATCAGGAAACATCGCTATTTC 60.074 42.308 0.00 0.00 34.65 2.17
839 854 5.760253 CCACTATCAGGAAACATCGCTATTT 59.240 40.000 0.00 0.00 0.00 1.40
840 855 5.163301 ACCACTATCAGGAAACATCGCTATT 60.163 40.000 0.00 0.00 0.00 1.73
841 856 4.345257 ACCACTATCAGGAAACATCGCTAT 59.655 41.667 0.00 0.00 0.00 2.97
842 857 3.704566 ACCACTATCAGGAAACATCGCTA 59.295 43.478 0.00 0.00 0.00 4.26
843 858 2.501723 ACCACTATCAGGAAACATCGCT 59.498 45.455 0.00 0.00 0.00 4.93
844 859 2.609459 CACCACTATCAGGAAACATCGC 59.391 50.000 0.00 0.00 0.00 4.58
845 860 3.618594 CACACCACTATCAGGAAACATCG 59.381 47.826 0.00 0.00 0.00 3.84
846 861 3.375299 GCACACCACTATCAGGAAACATC 59.625 47.826 0.00 0.00 0.00 3.06
847 862 3.347216 GCACACCACTATCAGGAAACAT 58.653 45.455 0.00 0.00 0.00 2.71
848 863 2.552155 GGCACACCACTATCAGGAAACA 60.552 50.000 0.00 0.00 35.26 2.83
849 864 2.084546 GGCACACCACTATCAGGAAAC 58.915 52.381 0.00 0.00 35.26 2.78
850 865 1.985159 AGGCACACCACTATCAGGAAA 59.015 47.619 0.00 0.00 39.06 3.13
851 866 1.656587 AGGCACACCACTATCAGGAA 58.343 50.000 0.00 0.00 39.06 3.36
852 867 1.278985 CAAGGCACACCACTATCAGGA 59.721 52.381 0.00 0.00 39.06 3.86
853 868 1.742761 CAAGGCACACCACTATCAGG 58.257 55.000 0.00 0.00 39.06 3.86
854 869 1.089920 GCAAGGCACACCACTATCAG 58.910 55.000 0.00 0.00 39.06 2.90
855 870 0.322456 GGCAAGGCACACCACTATCA 60.322 55.000 0.00 0.00 39.06 2.15
856 871 0.035056 AGGCAAGGCACACCACTATC 60.035 55.000 0.00 0.00 39.06 2.08
857 872 0.322816 CAGGCAAGGCACACCACTAT 60.323 55.000 0.00 0.00 39.06 2.12
858 873 1.073025 CAGGCAAGGCACACCACTA 59.927 57.895 0.00 0.00 39.06 2.74
859 874 2.203394 CAGGCAAGGCACACCACT 60.203 61.111 0.00 0.00 39.06 4.00
879 894 4.202172 GGAGGAATCAGTACCTTGTAGCTC 60.202 50.000 0.00 0.00 36.57 4.09
889 904 3.927142 CACACGAAAGGAGGAATCAGTAC 59.073 47.826 0.00 0.00 0.00 2.73
921 936 1.030457 GCTAGTTAGGCGAGGCAGTA 58.970 55.000 0.00 0.00 0.00 2.74
924 939 1.319541 CTAGCTAGTTAGGCGAGGCA 58.680 55.000 12.92 0.00 34.52 4.75
927 942 3.502595 TGCATACTAGCTAGTTAGGCGAG 59.497 47.826 30.40 13.66 37.73 5.03
928 943 3.483421 TGCATACTAGCTAGTTAGGCGA 58.517 45.455 30.40 12.74 37.73 5.54
944 963 1.200519 AAGAGGTTACCGGCTGCATA 58.799 50.000 0.00 0.00 0.00 3.14
945 964 0.328258 AAAGAGGTTACCGGCTGCAT 59.672 50.000 0.00 0.00 0.00 3.96
946 965 0.605319 CAAAGAGGTTACCGGCTGCA 60.605 55.000 0.00 0.00 0.00 4.41
947 966 1.923227 GCAAAGAGGTTACCGGCTGC 61.923 60.000 0.00 0.44 0.00 5.25
948 967 1.305930 GGCAAAGAGGTTACCGGCTG 61.306 60.000 0.00 0.00 0.00 4.85
949 968 1.002502 GGCAAAGAGGTTACCGGCT 60.003 57.895 0.00 0.00 0.00 5.52
950 969 1.302993 TGGCAAAGAGGTTACCGGC 60.303 57.895 0.00 0.00 0.00 6.13
951 970 1.305930 GCTGGCAAAGAGGTTACCGG 61.306 60.000 0.00 0.00 0.00 5.28
952 971 0.321653 AGCTGGCAAAGAGGTTACCG 60.322 55.000 0.00 0.00 0.00 4.02
953 972 1.454201 GAGCTGGCAAAGAGGTTACC 58.546 55.000 0.00 0.00 0.00 2.85
954 973 1.079503 CGAGCTGGCAAAGAGGTTAC 58.920 55.000 0.00 0.00 0.00 2.50
955 974 0.685097 ACGAGCTGGCAAAGAGGTTA 59.315 50.000 0.00 0.00 0.00 2.85
956 975 0.886490 CACGAGCTGGCAAAGAGGTT 60.886 55.000 0.00 0.00 0.00 3.50
957 976 1.302033 CACGAGCTGGCAAAGAGGT 60.302 57.895 0.00 0.00 0.00 3.85
958 977 2.684843 GCACGAGCTGGCAAAGAGG 61.685 63.158 0.00 0.00 37.91 3.69
959 978 1.962822 TGCACGAGCTGGCAAAGAG 60.963 57.895 6.36 0.00 42.74 2.85
960 979 2.110835 TGCACGAGCTGGCAAAGA 59.889 55.556 6.36 0.00 42.74 2.52
961 980 2.253452 GTGCACGAGCTGGCAAAG 59.747 61.111 0.00 0.00 42.45 2.77
962 981 3.648982 CGTGCACGAGCTGGCAAA 61.649 61.111 34.93 0.00 42.45 3.68
975 994 2.652548 GCATAATTGTGCACCGTGC 58.347 52.632 20.86 16.93 44.43 5.34
1003 1022 6.488344 CCTTCTCTGTCTCTGTGCTGTATATA 59.512 42.308 0.00 0.00 0.00 0.86
1011 1030 0.390998 GCCCTTCTCTGTCTCTGTGC 60.391 60.000 0.00 0.00 0.00 4.57
1055 1111 1.552799 TTGGGCGCCATCTCTCTTGA 61.553 55.000 30.85 0.00 31.53 3.02
1070 1129 4.447342 AGCGGGGAATGCCTTGGG 62.447 66.667 0.00 0.00 0.00 4.12
1195 1257 1.535687 AGGGTAAGTCGGTGGCTGT 60.536 57.895 0.00 0.00 0.00 4.40
1213 1275 3.731728 GAGTGGGCATGGGCAGGA 61.732 66.667 0.00 0.00 43.71 3.86
1214 1276 4.828296 GGAGTGGGCATGGGCAGG 62.828 72.222 0.00 0.00 43.71 4.85
1255 1317 6.416631 AATCATGAGAGATTAGCTACAGCA 57.583 37.500 0.09 0.00 37.44 4.41
1262 1327 5.537188 ACGGAGAAATCATGAGAGATTAGC 58.463 41.667 0.09 0.00 37.24 3.09
1467 1631 2.997315 CTGCCTGGACCTGGACGA 60.997 66.667 21.06 3.18 0.00 4.20
1530 1700 8.902806 TGACAACTTCACACAGATTTTATTCTT 58.097 29.630 0.00 0.00 0.00 2.52
1629 1827 8.837389 GGATAAACTTGTATATGTCCCAACTTC 58.163 37.037 0.00 0.00 0.00 3.01
1701 1925 4.620248 GAAAAACGTTTGTGAACCGTTTG 58.380 39.130 15.46 0.00 39.73 2.93
1709 1933 4.032355 GCAAGATCGAAAAACGTTTGTGA 58.968 39.130 15.46 12.83 43.13 3.58
1719 1943 6.073494 TCAGTACGAAAATGCAAGATCGAAAA 60.073 34.615 20.55 6.93 38.59 2.29
1735 1960 6.693978 CGACCATGTACATTTATCAGTACGAA 59.306 38.462 5.37 0.00 42.62 3.85
1837 2072 2.319025 TGGGATGTAGATATCGGCCA 57.681 50.000 2.24 0.00 0.00 5.36
1966 2220 2.352960 GCTAAAATGGGTCAGCGAGAAG 59.647 50.000 0.00 0.00 0.00 2.85
1968 2222 1.277842 TGCTAAAATGGGTCAGCGAGA 59.722 47.619 0.00 0.00 36.81 4.04
1969 2223 1.737838 TGCTAAAATGGGTCAGCGAG 58.262 50.000 0.00 0.00 36.81 5.03
1971 2225 3.296322 TTTTGCTAAAATGGGTCAGCG 57.704 42.857 0.00 0.00 36.81 5.18
2333 2617 7.068702 TGCATAATTCATATGAAACTCCCCTT 58.931 34.615 21.50 11.85 43.52 3.95
2419 2704 4.701956 ATACATAAGTTTGCAGTGTGCC 57.298 40.909 0.00 0.00 44.23 5.01
2504 2789 2.172717 ACTAATACGATGGGGCAAAGCT 59.827 45.455 0.00 0.00 0.00 3.74


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

AutoCloner maintained by Alex Coulton.