Multiple sequence alignment - TraesCS7D01G102600

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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 TraesCS7D01G102600 chr7D 100.000 1866 0 0 1814 3679 62170562 62172427 0.000000e+00 3446.0
1 TraesCS7D01G102600 chr7D 100.000 1548 0 0 1 1548 62168749 62170296 0.000000e+00 2859.0
2 TraesCS7D01G102600 chr7D 92.621 1843 118 5 1854 3679 62929858 62931699 0.000000e+00 2634.0
3 TraesCS7D01G102600 chr7D 86.870 754 85 8 792 1543 62928904 62929645 0.000000e+00 832.0
4 TraesCS7D01G102600 chr7D 81.561 743 118 11 1944 2672 181975934 181975197 2.450000e-166 595.0
5 TraesCS7D01G102600 chr7D 81.457 302 52 2 1958 2257 181845910 181845611 1.020000e-60 244.0
6 TraesCS7D01G102600 chr7D 83.721 258 38 3 274 527 263369193 263369450 1.320000e-59 241.0
7 TraesCS7D01G102600 chr7D 80.583 206 32 7 1344 1543 92276167 92276370 6.360000e-33 152.0
8 TraesCS7D01G102600 chr7D 91.111 90 1 2 752 840 62169465 62169548 8.350000e-22 115.0
9 TraesCS7D01G102600 chr7D 91.111 90 1 2 717 800 62169500 62169588 8.350000e-22 115.0
10 TraesCS7D01G102600 chr7D 87.879 99 8 4 574 671 110099193 110099288 3.000000e-21 113.0
11 TraesCS7D01G102600 chr7D 96.000 50 1 1 752 800 62928904 62928953 3.050000e-11 80.5
12 TraesCS7D01G102600 chr7D 81.319 91 13 3 2468 2555 181843360 181843271 1.830000e-08 71.3
13 TraesCS7D01G102600 chr7D 95.122 41 2 0 2473 2513 615902095 615902055 8.530000e-07 65.8
14 TraesCS7D01G102600 chr7A 94.706 1870 94 4 1814 3679 65505154 65507022 0.000000e+00 2900.0
15 TraesCS7D01G102600 chr7A 95.652 414 17 1 1133 1545 65504712 65505125 0.000000e+00 664.0
16 TraesCS7D01G102600 chr7A 82.353 714 119 7 1957 2669 189718517 189719224 6.750000e-172 614.0
17 TraesCS7D01G102600 chr7A 89.822 393 39 1 1 393 65503897 65504288 1.520000e-138 503.0
18 TraesCS7D01G102600 chr7A 91.386 267 18 2 348 613 65504287 65504549 9.710000e-96 361.0
19 TraesCS7D01G102600 chr7A 94.220 173 5 1 634 801 65504542 65504714 3.640000e-65 259.0
20 TraesCS7D01G102600 chr7A 79.341 334 55 11 204 527 68841375 68841704 4.780000e-54 222.0
21 TraesCS7D01G102600 chr7A 86.957 92 1 2 754 840 65504628 65504713 3.910000e-15 93.5
22 TraesCS7D01G102600 chr5A 85.196 331 43 4 1928 2253 479462117 479461788 5.890000e-88 335.0
23 TraesCS7D01G102600 chr5A 78.208 413 81 8 115 520 74531784 74531374 4.710000e-64 255.0
24 TraesCS7D01G102600 chr5D 86.242 298 39 2 1957 2253 379234797 379234501 4.580000e-84 322.0
25 TraesCS7D01G102600 chr5D 81.443 194 30 6 1347 1535 557143039 557143231 1.770000e-33 154.0
26 TraesCS7D01G102600 chr2D 80.471 425 74 7 112 527 445746864 445746440 2.130000e-82 316.0
27 TraesCS7D01G102600 chr5B 85.235 298 42 2 1957 2253 454907632 454907336 4.620000e-79 305.0
28 TraesCS7D01G102600 chr5B 77.262 431 80 13 104 520 87303256 87302830 1.710000e-58 237.0
29 TraesCS7D01G102600 chr4B 76.505 515 100 14 31 527 520518918 520518407 1.010000e-65 261.0
30 TraesCS7D01G102600 chr7B 80.795 302 54 2 1958 2257 150028720 150028421 2.210000e-57 233.0
31 TraesCS7D01G102600 chr1D 79.240 342 58 10 195 527 371216905 371216568 3.700000e-55 226.0
32 TraesCS7D01G102600 chr6B 76.244 442 88 13 99 527 665669425 665669862 6.190000e-53 219.0
33 TraesCS7D01G102600 chr2A 82.759 87 14 1 584 670 3755482 3755397 3.940000e-10 76.8
34 TraesCS7D01G102600 chr4A 94.737 38 1 1 591 628 598783360 598783324 1.430000e-04 58.4


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 TraesCS7D01G102600 chr7D 62168749 62172427 3678 False 1633.750000 3446 95.555500 1 3679 4 chr7D.!!$F4 3678
1 TraesCS7D01G102600 chr7D 62928904 62931699 2795 False 1182.166667 2634 91.830333 752 3679 3 chr7D.!!$F5 2927
2 TraesCS7D01G102600 chr7D 181975197 181975934 737 True 595.000000 595 81.561000 1944 2672 1 chr7D.!!$R1 728
3 TraesCS7D01G102600 chr7A 65503897 65507022 3125 False 796.750000 2900 92.123833 1 3679 6 chr7A.!!$F3 3678
4 TraesCS7D01G102600 chr7A 189718517 189719224 707 False 614.000000 614 82.353000 1957 2669 1 chr7A.!!$F2 712
5 TraesCS7D01G102600 chr4B 520518407 520518918 511 True 261.000000 261 76.505000 31 527 1 chr4B.!!$R1 496

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
918 981 0.037447 AAGGCCAGAGGTCTTTGCTC 59.963 55.0 5.01 0.00 46.43 4.26 F
996 1059 0.248702 TTTTGAGGGAAACGCGTTGC 60.249 50.0 27.34 24.67 0.00 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2274 2528 0.989602 TCTGGTACTCCACGGAGAGA 59.010 55.0 19.98 8.89 44.53 3.1 R
2680 2965 1.021390 GGAACACCAGCACCGATCTG 61.021 60.0 0.00 0.00 0.00 2.9 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
26 27 1.529244 GATGCATAGGCCCCACCAC 60.529 63.158 0.00 0.00 43.14 4.16
28 29 4.109675 GCATAGGCCCCACCACGT 62.110 66.667 0.00 0.00 43.14 4.49
39 40 1.528309 CACCACGTTCCTTGCCCTT 60.528 57.895 0.00 0.00 0.00 3.95
48 49 2.368548 GTTCCTTGCCCTTGGATTTGTT 59.631 45.455 0.00 0.00 31.76 2.83
59 60 1.623311 TGGATTTGTTCCTCTCTCGCA 59.377 47.619 0.00 0.00 45.68 5.10
65 66 0.526524 GTTCCTCTCTCGCACCATCG 60.527 60.000 0.00 0.00 0.00 3.84
89 90 1.413382 CGCAGAATCGGTAGATCTGC 58.587 55.000 15.10 15.10 44.74 4.26
165 169 2.514824 GGCCCGTCAATGCCTCTC 60.515 66.667 0.00 0.00 44.46 3.20
167 171 3.036429 GCCCGTCAATGCCTCTCCT 62.036 63.158 0.00 0.00 0.00 3.69
227 231 2.049433 ACTTGTCGGAGGTTCGCG 60.049 61.111 0.00 0.00 0.00 5.87
239 243 0.600782 GGTTCGCGGGTAAAGACACA 60.601 55.000 6.13 0.00 0.00 3.72
242 246 1.005394 CGCGGGTAAAGACACACCT 60.005 57.895 0.00 0.00 35.04 4.00
312 323 0.391228 TCAAAGTGCTACGACTGCCA 59.609 50.000 0.00 0.00 0.00 4.92
353 364 1.978455 TTCCACCACGCCAGAACACT 61.978 55.000 0.00 0.00 0.00 3.55
356 367 2.425592 CCACGCCAGAACACTCCA 59.574 61.111 0.00 0.00 0.00 3.86
410 465 4.515567 GGGTGAGTTCTTCTTTTGATTCGT 59.484 41.667 0.00 0.00 0.00 3.85
412 467 6.204108 GGGTGAGTTCTTCTTTTGATTCGTTA 59.796 38.462 0.00 0.00 0.00 3.18
425 481 9.929722 CTTTTGATTCGTTATAATTCGGATTCA 57.070 29.630 0.00 0.00 0.00 2.57
428 484 6.704050 TGATTCGTTATAATTCGGATTCAGCA 59.296 34.615 0.00 0.00 0.00 4.41
509 567 7.011857 GGCATTGGGAAGAAGAATATATCGATC 59.988 40.741 0.00 0.00 0.00 3.69
574 632 8.324191 TCCATTATATTTAGGGGATCAGCTAG 57.676 38.462 0.00 0.00 0.00 3.42
575 633 6.995091 CCATTATATTTAGGGGATCAGCTAGC 59.005 42.308 6.62 6.62 0.00 3.42
576 634 7.147408 CCATTATATTTAGGGGATCAGCTAGCT 60.147 40.741 12.68 12.68 0.00 3.32
577 635 8.928448 CATTATATTTAGGGGATCAGCTAGCTA 58.072 37.037 18.86 6.64 0.00 3.32
584 642 1.545875 GGATCAGCTAGCTAGGTCCGA 60.546 57.143 22.33 17.39 30.45 4.55
595 653 6.429385 GCTAGCTAGGTCCGACTAATACTTAA 59.571 42.308 22.10 0.00 0.00 1.85
622 680 9.856162 TGGAGTAAAAATACTTCACTAAAGGTT 57.144 29.630 0.00 0.00 39.47 3.50
630 688 5.874895 ACTTCACTAAAGGTTTATTCCGC 57.125 39.130 0.00 0.00 39.47 5.54
631 689 5.557866 ACTTCACTAAAGGTTTATTCCGCT 58.442 37.500 0.00 0.00 39.47 5.52
632 690 5.411669 ACTTCACTAAAGGTTTATTCCGCTG 59.588 40.000 0.00 0.00 39.47 5.18
633 691 5.155278 TCACTAAAGGTTTATTCCGCTGA 57.845 39.130 0.00 0.00 0.00 4.26
634 692 5.553123 TCACTAAAGGTTTATTCCGCTGAA 58.447 37.500 0.00 0.00 34.33 3.02
635 693 6.177610 TCACTAAAGGTTTATTCCGCTGAAT 58.822 36.000 8.49 8.49 43.56 2.57
636 694 7.332557 TCACTAAAGGTTTATTCCGCTGAATA 58.667 34.615 6.49 6.49 41.44 1.75
637 695 7.279313 TCACTAAAGGTTTATTCCGCTGAATAC 59.721 37.037 9.80 3.15 41.89 1.89
638 696 7.280205 CACTAAAGGTTTATTCCGCTGAATACT 59.720 37.037 9.80 2.62 41.89 2.12
639 697 7.827729 ACTAAAGGTTTATTCCGCTGAATACTT 59.172 33.333 9.80 7.88 41.89 2.24
640 698 6.679327 AAGGTTTATTCCGCTGAATACTTC 57.321 37.500 9.80 4.50 41.89 3.01
641 699 5.990668 AGGTTTATTCCGCTGAATACTTCT 58.009 37.500 9.80 5.49 41.89 2.85
642 700 6.415573 AGGTTTATTCCGCTGAATACTTCTT 58.584 36.000 9.80 0.00 41.89 2.52
643 701 6.884836 AGGTTTATTCCGCTGAATACTTCTTT 59.115 34.615 9.80 0.00 41.89 2.52
644 702 8.044908 AGGTTTATTCCGCTGAATACTTCTTTA 58.955 33.333 9.80 0.00 41.89 1.85
645 703 8.837389 GGTTTATTCCGCTGAATACTTCTTTAT 58.163 33.333 9.80 0.00 41.89 1.40
703 761 6.420903 ACGTGAATAAATGATATCACCGTCTG 59.579 38.462 7.78 2.40 39.13 3.51
719 777 3.489059 CCGTCTGTGTTGCTTTCAAATGT 60.489 43.478 0.00 0.00 33.37 2.71
798 861 2.401766 GCTGTTGGAGGATGGCGTG 61.402 63.158 0.00 0.00 0.00 5.34
799 862 1.746615 CTGTTGGAGGATGGCGTGG 60.747 63.158 0.00 0.00 0.00 4.94
800 863 2.184020 CTGTTGGAGGATGGCGTGGA 62.184 60.000 0.00 0.00 0.00 4.02
801 864 1.745489 GTTGGAGGATGGCGTGGAC 60.745 63.158 0.00 0.00 0.00 4.02
802 865 2.220586 TTGGAGGATGGCGTGGACA 61.221 57.895 0.00 0.00 0.00 4.02
803 866 1.773856 TTGGAGGATGGCGTGGACAA 61.774 55.000 0.00 0.00 0.00 3.18
804 867 1.450312 GGAGGATGGCGTGGACAAG 60.450 63.158 0.00 0.00 0.00 3.16
805 868 1.296715 GAGGATGGCGTGGACAAGT 59.703 57.895 0.00 0.00 0.00 3.16
806 869 0.535335 GAGGATGGCGTGGACAAGTA 59.465 55.000 0.00 0.00 0.00 2.24
807 870 0.981183 AGGATGGCGTGGACAAGTAA 59.019 50.000 0.00 0.00 0.00 2.24
808 871 1.349688 AGGATGGCGTGGACAAGTAAA 59.650 47.619 0.00 0.00 0.00 2.01
809 872 1.737793 GGATGGCGTGGACAAGTAAAG 59.262 52.381 0.00 0.00 0.00 1.85
810 873 2.614481 GGATGGCGTGGACAAGTAAAGA 60.614 50.000 0.00 0.00 0.00 2.52
811 874 2.851263 TGGCGTGGACAAGTAAAGAT 57.149 45.000 0.00 0.00 0.00 2.40
812 875 2.422597 TGGCGTGGACAAGTAAAGATG 58.577 47.619 0.00 0.00 0.00 2.90
813 876 2.037902 TGGCGTGGACAAGTAAAGATGA 59.962 45.455 0.00 0.00 0.00 2.92
814 877 3.270877 GGCGTGGACAAGTAAAGATGAT 58.729 45.455 0.00 0.00 0.00 2.45
815 878 3.063997 GGCGTGGACAAGTAAAGATGATG 59.936 47.826 0.00 0.00 0.00 3.07
816 879 3.485877 GCGTGGACAAGTAAAGATGATGC 60.486 47.826 0.00 0.00 0.00 3.91
817 880 3.684305 CGTGGACAAGTAAAGATGATGCA 59.316 43.478 0.00 0.00 0.00 3.96
818 881 4.154015 CGTGGACAAGTAAAGATGATGCAA 59.846 41.667 0.00 0.00 0.00 4.08
819 882 5.334802 CGTGGACAAGTAAAGATGATGCAAA 60.335 40.000 0.00 0.00 0.00 3.68
820 883 6.088824 GTGGACAAGTAAAGATGATGCAAAG 58.911 40.000 0.00 0.00 0.00 2.77
821 884 5.098211 GGACAAGTAAAGATGATGCAAAGC 58.902 41.667 0.00 0.00 0.00 3.51
822 885 5.105997 GGACAAGTAAAGATGATGCAAAGCT 60.106 40.000 0.00 0.00 0.00 3.74
823 886 5.706916 ACAAGTAAAGATGATGCAAAGCTG 58.293 37.500 0.00 0.00 0.00 4.24
824 887 5.242393 ACAAGTAAAGATGATGCAAAGCTGT 59.758 36.000 0.00 0.00 0.00 4.40
825 888 5.972107 AGTAAAGATGATGCAAAGCTGTT 57.028 34.783 0.00 0.00 0.00 3.16
826 889 5.706916 AGTAAAGATGATGCAAAGCTGTTG 58.293 37.500 0.00 0.00 0.00 3.33
835 898 0.529378 CAAAGCTGTTGGAGGATGGC 59.471 55.000 0.00 0.00 0.00 4.40
845 908 2.607750 AGGATGGCGTGGTGTCCT 60.608 61.111 0.00 0.00 36.29 3.85
853 916 0.788391 GCGTGGTGTCCTTTAACTCG 59.212 55.000 0.00 0.00 0.00 4.18
863 926 4.217118 TGTCCTTTAACTCGTCTACTGTCC 59.783 45.833 0.00 0.00 0.00 4.02
866 929 1.089920 TAACTCGTCTACTGTCCGCC 58.910 55.000 0.00 0.00 0.00 6.13
882 945 1.205657 CGCCACGCATAAATACGAGT 58.794 50.000 0.00 0.00 0.00 4.18
883 946 1.591158 CGCCACGCATAAATACGAGTT 59.409 47.619 0.00 0.00 0.00 3.01
884 947 2.596575 CGCCACGCATAAATACGAGTTG 60.597 50.000 0.00 0.00 0.00 3.16
918 981 0.037447 AAGGCCAGAGGTCTTTGCTC 59.963 55.000 5.01 0.00 46.43 4.26
924 987 2.028930 CCAGAGGTCTTTGCTCGTTAGT 60.029 50.000 0.00 0.00 0.00 2.24
925 988 2.989840 CAGAGGTCTTTGCTCGTTAGTG 59.010 50.000 0.00 0.00 0.00 2.74
928 991 1.508632 GTCTTTGCTCGTTAGTGCCA 58.491 50.000 0.00 0.00 36.14 4.92
944 1007 1.167851 GCCATCACACTTGCTAGCAA 58.832 50.000 27.67 27.67 0.00 3.91
950 1013 1.198637 CACACTTGCTAGCAAAGGAGC 59.801 52.381 28.95 0.00 39.25 4.70
951 1014 0.445436 CACTTGCTAGCAAAGGAGCG 59.555 55.000 28.95 18.86 41.83 5.03
954 1017 2.289444 ACTTGCTAGCAAAGGAGCGTAA 60.289 45.455 28.95 4.96 41.83 3.18
956 1019 1.001520 TGCTAGCAAAGGAGCGTAACA 59.998 47.619 16.84 0.00 41.83 2.41
957 1020 1.393883 GCTAGCAAAGGAGCGTAACAC 59.606 52.381 10.63 0.00 40.15 3.32
996 1059 0.248702 TTTTGAGGGAAACGCGTTGC 60.249 50.000 27.34 24.67 0.00 4.17
1012 1075 2.809601 GCGAGATGGTTGCGTCGT 60.810 61.111 0.00 0.00 34.87 4.34
1025 1088 3.034721 TGCGTCGTTATGGTTCTTCTT 57.965 42.857 0.00 0.00 0.00 2.52
1026 1089 2.991190 TGCGTCGTTATGGTTCTTCTTC 59.009 45.455 0.00 0.00 0.00 2.87
1027 1090 3.251571 GCGTCGTTATGGTTCTTCTTCT 58.748 45.455 0.00 0.00 0.00 2.85
1028 1091 3.060895 GCGTCGTTATGGTTCTTCTTCTG 59.939 47.826 0.00 0.00 0.00 3.02
1029 1092 3.612860 CGTCGTTATGGTTCTTCTTCTGG 59.387 47.826 0.00 0.00 0.00 3.86
1030 1093 3.371285 GTCGTTATGGTTCTTCTTCTGGC 59.629 47.826 0.00 0.00 0.00 4.85
1071 1134 3.002791 CCAAGTTTTCGCTCTCAGCATA 58.997 45.455 0.00 0.00 42.58 3.14
1120 1183 4.570874 GCCGGCCCAAGGATCTCC 62.571 72.222 18.11 0.00 0.00 3.71
1123 1186 2.998949 GGCCCAAGGATCTCCGTT 59.001 61.111 0.00 0.00 42.08 4.44
1175 1238 1.141665 CGACATCAGGCATCGGACA 59.858 57.895 0.00 0.00 32.22 4.02
1251 1314 4.135153 CCCACCAGACTCCGCGAG 62.135 72.222 8.23 5.77 35.52 5.03
1278 1341 5.314529 TCCGAAACGATCTCTAGGACATAT 58.685 41.667 0.00 0.00 0.00 1.78
1417 1481 6.367161 ACCCTTTTAGTGGCAGTTTTAGTTA 58.633 36.000 0.00 0.00 0.00 2.24
1422 1486 7.681939 TTTAGTGGCAGTTTTAGTTATGAGG 57.318 36.000 0.00 0.00 0.00 3.86
1444 1508 5.543790 AGGCAAGATTAAATGGTGGAAGTTT 59.456 36.000 0.00 0.00 0.00 2.66
1545 1799 4.485163 GACAAAATCGTTAGCAAATGCCT 58.515 39.130 0.94 0.00 43.38 4.75
2031 2285 2.186826 GGTGCTGGTGAACAACGCT 61.187 57.895 0.00 0.00 0.00 5.07
2178 2432 3.646715 GGCAGGGGTGCAGTGGTA 61.647 66.667 0.00 0.00 36.33 3.25
2270 2524 1.236616 TACGTCGCGGAGTTCTCCAA 61.237 55.000 17.48 1.44 0.00 3.53
2274 2528 0.894184 TCGCGGAGTTCTCCAAGAGT 60.894 55.000 17.48 0.00 0.00 3.24
2353 2607 1.450134 GTGGCGCTCACATCCATCA 60.450 57.895 19.85 0.00 45.39 3.07
2376 2644 4.798882 TGTCACCAGATTACCTTTGGTTT 58.201 39.130 0.00 0.00 42.36 3.27
2400 2668 1.811965 CGTGTTTGCAGATCCCATTCA 59.188 47.619 0.00 0.00 0.00 2.57
2402 2670 3.119388 CGTGTTTGCAGATCCCATTCATT 60.119 43.478 0.00 0.00 0.00 2.57
2411 2679 3.524789 AGATCCCATTCATTGTGGAGACA 59.475 43.478 0.00 0.00 39.12 3.41
2453 2721 3.804688 GAAGAACAGCTTCTTTCTTCGC 58.195 45.455 19.26 6.08 45.22 4.70
2623 2891 1.159285 CGGAATTTGCAGCACAGAGA 58.841 50.000 0.00 0.00 0.00 3.10
2642 2910 6.441924 ACAGAGACATCTTTAGGAGGATCAAA 59.558 38.462 0.00 0.00 31.27 2.69
2784 3070 3.259064 GTTGTGCCGAACTTAGAGCATA 58.741 45.455 0.00 0.00 37.60 3.14
2935 3221 9.875708 GGACCCTGATATCTATATCTACTGAAT 57.124 37.037 3.98 0.00 39.82 2.57
2960 3246 0.487772 ATAGGAGCACCCGGGATACT 59.512 55.000 32.02 21.09 40.87 2.12
3029 3315 2.041485 TCATTCTGGCAACCCAAGATCA 59.959 45.455 0.00 0.00 41.58 2.92
3075 3361 0.661552 CTCGAGCGAGACCCGAATTA 59.338 55.000 14.28 0.00 44.53 1.40
3096 3382 0.034477 ATCGAGGGTGCCCGAAAAAT 60.034 50.000 0.98 0.00 41.95 1.82
3105 3392 2.556622 GTGCCCGAAAAATCTCTCCAAA 59.443 45.455 0.00 0.00 0.00 3.28
3149 3436 0.103554 ACCTAACCCCCAACTTCCCT 60.104 55.000 0.00 0.00 0.00 4.20
3159 3446 1.691482 CCAACTTCCCTCGATCCCCTA 60.691 57.143 0.00 0.00 0.00 3.53
3244 3531 8.680001 TCTCGCACTACTAGAAAAACATATGTA 58.320 33.333 9.21 0.00 0.00 2.29
3370 3659 3.814268 TACCTCCACGTACGGCGC 61.814 66.667 21.06 0.00 46.11 6.53
3410 3699 6.452242 TGCTCGTTGTATAGAAAAAGACTCA 58.548 36.000 0.00 0.00 0.00 3.41
3645 3934 3.060000 ATCGCACCTCGTGGTCGA 61.060 61.111 23.36 23.36 46.60 4.20
3655 3944 2.577059 GTGGTCGAGCGGATTCCA 59.423 61.111 10.46 0.00 0.00 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 2.357517 GGGCCTATGCATCGTCCG 60.358 66.667 0.19 0.00 40.13 4.79
11 12 3.638592 AACGTGGTGGGGCCTATGC 62.639 63.158 0.84 0.00 38.35 3.14
26 27 1.067635 CAAATCCAAGGGCAAGGAACG 60.068 52.381 0.00 0.00 37.48 3.95
28 29 2.397044 ACAAATCCAAGGGCAAGGAA 57.603 45.000 0.00 0.00 37.48 3.36
48 49 2.775856 GCGATGGTGCGAGAGAGGA 61.776 63.158 0.00 0.00 0.00 3.71
65 66 4.884257 TACCGATTCTGCGCCGGC 62.884 66.667 19.07 19.07 46.54 6.13
106 107 2.480555 CATGGCAAAGGCGTCGTC 59.519 61.111 0.00 0.00 42.47 4.20
154 158 0.543277 ATGCGAAGGAGAGGCATTGA 59.457 50.000 0.00 0.00 44.45 2.57
165 169 1.789078 GCCATACCTGCATGCGAAGG 61.789 60.000 19.81 19.81 39.65 3.46
167 171 1.823470 GGCCATACCTGCATGCGAA 60.823 57.895 14.09 0.00 34.51 4.70
227 231 2.104281 ACAGTCAGGTGTGTCTTTACCC 59.896 50.000 0.00 0.00 37.70 3.69
292 301 1.001974 TGGCAGTCGTAGCACTTTGAT 59.998 47.619 0.00 0.00 0.00 2.57
339 350 1.669115 CTGGAGTGTTCTGGCGTGG 60.669 63.158 0.00 0.00 0.00 4.94
353 364 2.711009 ACTTGAAGAACACCCATCTGGA 59.289 45.455 0.00 0.00 37.39 3.86
356 367 2.158623 TGCACTTGAAGAACACCCATCT 60.159 45.455 0.00 0.00 0.00 2.90
395 450 9.373603 TCCGAATTATAACGAATCAAAAGAAGA 57.626 29.630 0.00 0.00 0.00 2.87
425 481 1.806542 CAATGAGCTACAAACGGTGCT 59.193 47.619 0.00 0.00 36.84 4.40
428 484 3.119849 GCAATCAATGAGCTACAAACGGT 60.120 43.478 0.00 0.00 0.00 4.83
574 632 6.208204 TCCATTAAGTATTAGTCGGACCTAGC 59.792 42.308 4.14 0.00 0.00 3.42
575 633 7.447853 ACTCCATTAAGTATTAGTCGGACCTAG 59.552 40.741 4.14 0.00 0.00 3.02
576 634 7.293073 ACTCCATTAAGTATTAGTCGGACCTA 58.707 38.462 4.14 0.00 0.00 3.08
577 635 6.134754 ACTCCATTAAGTATTAGTCGGACCT 58.865 40.000 4.14 0.00 0.00 3.85
613 671 7.336396 AGTATTCAGCGGAATAAACCTTTAGT 58.664 34.615 18.99 0.00 45.12 2.24
614 672 7.787725 AGTATTCAGCGGAATAAACCTTTAG 57.212 36.000 18.99 0.00 45.12 1.85
615 673 8.205131 GAAGTATTCAGCGGAATAAACCTTTA 57.795 34.615 18.99 0.00 45.12 1.85
617 675 6.679327 GAAGTATTCAGCGGAATAAACCTT 57.321 37.500 18.99 17.14 45.12 3.50
636 694 9.516546 AACCGAATCCTCTAAAAATAAAGAAGT 57.483 29.630 0.00 0.00 0.00 3.01
644 702 8.406297 GCAATTCTAACCGAATCCTCTAAAAAT 58.594 33.333 0.00 0.00 41.42 1.82
645 703 7.148137 GGCAATTCTAACCGAATCCTCTAAAAA 60.148 37.037 0.00 0.00 41.42 1.94
703 761 2.034675 CACGCACATTTGAAAGCAACAC 60.035 45.455 0.00 0.00 32.79 3.32
719 777 3.325870 CTCATCTTTACTTGTCCACGCA 58.674 45.455 0.00 0.00 0.00 5.24
798 861 5.098211 GCTTTGCATCATCTTTACTTGTCC 58.902 41.667 0.00 0.00 0.00 4.02
799 862 5.798934 CAGCTTTGCATCATCTTTACTTGTC 59.201 40.000 0.00 0.00 0.00 3.18
800 863 5.242393 ACAGCTTTGCATCATCTTTACTTGT 59.758 36.000 0.00 0.00 0.00 3.16
801 864 5.706916 ACAGCTTTGCATCATCTTTACTTG 58.293 37.500 0.00 0.00 0.00 3.16
802 865 5.972107 ACAGCTTTGCATCATCTTTACTT 57.028 34.783 0.00 0.00 0.00 2.24
803 866 5.336213 CCAACAGCTTTGCATCATCTTTACT 60.336 40.000 0.00 0.00 0.00 2.24
804 867 4.860907 CCAACAGCTTTGCATCATCTTTAC 59.139 41.667 0.00 0.00 0.00 2.01
805 868 4.766373 TCCAACAGCTTTGCATCATCTTTA 59.234 37.500 0.00 0.00 0.00 1.85
806 869 3.575256 TCCAACAGCTTTGCATCATCTTT 59.425 39.130 0.00 0.00 0.00 2.52
807 870 3.159472 TCCAACAGCTTTGCATCATCTT 58.841 40.909 0.00 0.00 0.00 2.40
808 871 2.753452 CTCCAACAGCTTTGCATCATCT 59.247 45.455 0.00 0.00 0.00 2.90
809 872 2.159282 CCTCCAACAGCTTTGCATCATC 60.159 50.000 0.00 0.00 0.00 2.92
810 873 1.822990 CCTCCAACAGCTTTGCATCAT 59.177 47.619 0.00 0.00 0.00 2.45
811 874 1.202915 TCCTCCAACAGCTTTGCATCA 60.203 47.619 0.00 0.00 0.00 3.07
812 875 1.538047 TCCTCCAACAGCTTTGCATC 58.462 50.000 0.00 0.00 0.00 3.91
813 876 1.822990 CATCCTCCAACAGCTTTGCAT 59.177 47.619 0.00 0.00 0.00 3.96
814 877 1.250328 CATCCTCCAACAGCTTTGCA 58.750 50.000 0.00 0.00 0.00 4.08
815 878 0.529378 CCATCCTCCAACAGCTTTGC 59.471 55.000 0.00 0.00 0.00 3.68
816 879 0.529378 GCCATCCTCCAACAGCTTTG 59.471 55.000 0.00 0.00 0.00 2.77
817 880 0.962356 CGCCATCCTCCAACAGCTTT 60.962 55.000 0.00 0.00 0.00 3.51
818 881 1.377725 CGCCATCCTCCAACAGCTT 60.378 57.895 0.00 0.00 0.00 3.74
819 882 2.270205 CGCCATCCTCCAACAGCT 59.730 61.111 0.00 0.00 0.00 4.24
820 883 2.045926 ACGCCATCCTCCAACAGC 60.046 61.111 0.00 0.00 0.00 4.40
821 884 1.746615 CCACGCCATCCTCCAACAG 60.747 63.158 0.00 0.00 0.00 3.16
822 885 2.350895 CCACGCCATCCTCCAACA 59.649 61.111 0.00 0.00 0.00 3.33
823 886 2.040544 CACCACGCCATCCTCCAAC 61.041 63.158 0.00 0.00 0.00 3.77
824 887 2.350895 CACCACGCCATCCTCCAA 59.649 61.111 0.00 0.00 0.00 3.53
825 888 2.927856 ACACCACGCCATCCTCCA 60.928 61.111 0.00 0.00 0.00 3.86
826 889 2.125106 GACACCACGCCATCCTCC 60.125 66.667 0.00 0.00 0.00 4.30
835 898 2.056577 GACGAGTTAAAGGACACCACG 58.943 52.381 0.00 0.00 0.00 4.94
845 908 2.095059 GGCGGACAGTAGACGAGTTAAA 60.095 50.000 0.00 0.00 0.00 1.52
853 916 2.506438 GCGTGGCGGACAGTAGAC 60.506 66.667 0.00 0.00 0.00 2.59
863 926 1.205657 ACTCGTATTTATGCGTGGCG 58.794 50.000 7.09 0.00 37.19 5.69
866 929 2.596575 CGGCAACTCGTATTTATGCGTG 60.597 50.000 0.40 1.10 37.88 5.34
899 962 0.037447 GAGCAAAGACCTCTGGCCTT 59.963 55.000 3.32 0.00 0.00 4.35
900 963 1.682257 GAGCAAAGACCTCTGGCCT 59.318 57.895 3.32 0.00 0.00 5.19
903 966 2.028930 ACTAACGAGCAAAGACCTCTGG 60.029 50.000 0.00 0.00 0.00 3.86
924 987 2.858622 GCTAGCAAGTGTGATGGCA 58.141 52.632 10.63 0.00 45.99 4.92
925 988 1.167851 TTGCTAGCAAGTGTGATGGC 58.832 50.000 26.06 0.00 46.80 4.40
928 991 3.341823 CTCCTTTGCTAGCAAGTGTGAT 58.658 45.455 27.82 0.00 37.24 3.06
951 1014 3.717350 AAATAGCTCGCAACGTGTTAC 57.283 42.857 0.00 0.00 0.00 2.50
994 1057 2.809174 CGACGCAACCATCTCGCA 60.809 61.111 0.00 0.00 0.00 5.10
996 1059 1.255342 CATAACGACGCAACCATCTCG 59.745 52.381 0.00 0.00 0.00 4.04
1004 1067 3.034721 AGAAGAACCATAACGACGCAA 57.965 42.857 0.00 0.00 0.00 4.85
1012 1075 3.873801 GCCAGCCAGAAGAAGAACCATAA 60.874 47.826 0.00 0.00 0.00 1.90
1048 1111 1.462670 GCTGAGAGCGAAAACTTGGAG 59.537 52.381 0.00 0.00 0.00 3.86
1120 1183 1.447838 AGGCTCCGTATGTGCAACG 60.448 57.895 2.41 2.41 42.39 4.10
1123 1186 2.584064 CCAGGCTCCGTATGTGCA 59.416 61.111 0.00 0.00 35.15 4.57
1158 1221 1.224075 CATGTCCGATGCCTGATGTC 58.776 55.000 0.00 0.00 0.00 3.06
1175 1238 1.992519 GAGCTCCAGGGACATGGCAT 61.993 60.000 0.87 0.00 40.41 4.40
1237 1300 1.077357 AGATCTCGCGGAGTCTGGT 60.077 57.895 6.13 0.00 0.00 4.00
1251 1314 4.066490 TCCTAGAGATCGTTTCGGAGATC 58.934 47.826 0.00 0.00 42.52 2.75
1278 1341 1.303561 GGTCTTGGTCTGCATGGCA 60.304 57.895 0.00 0.00 36.92 4.92
1417 1481 4.870636 TCCACCATTTAATCTTGCCTCAT 58.129 39.130 0.00 0.00 0.00 2.90
1422 1486 8.825667 TTAAAACTTCCACCATTTAATCTTGC 57.174 30.769 0.00 0.00 0.00 4.01
1471 1535 5.237815 TGTTCAGAGCGACATGATACTTTT 58.762 37.500 0.00 0.00 0.00 2.27
1477 1541 3.434641 CAGTTTGTTCAGAGCGACATGAT 59.565 43.478 0.00 0.00 0.00 2.45
1819 2073 1.087771 CAGTGTATTCGGGGAACGCC 61.088 60.000 0.00 0.00 43.86 5.68
1833 2087 1.087202 TTTGCAACTCGCGTCAGTGT 61.087 50.000 5.77 0.00 46.97 3.55
2175 2429 2.178235 GCCCGAGCCGATGTTTACC 61.178 63.158 0.00 0.00 0.00 2.85
2178 2432 2.125106 GAGCCCGAGCCGATGTTT 60.125 61.111 0.00 0.00 41.25 2.83
2270 2524 1.065272 GGTACTCCACGGAGAGACTCT 60.065 57.143 19.98 4.14 44.53 3.24
2274 2528 0.989602 TCTGGTACTCCACGGAGAGA 59.010 55.000 19.98 8.89 44.53 3.10
2353 2607 4.657814 ACCAAAGGTAATCTGGTGACAT 57.342 40.909 0.00 0.00 41.95 3.06
2376 2644 1.234821 GGGATCTGCAAACACGACAA 58.765 50.000 0.00 0.00 0.00 3.18
2400 2668 3.565307 ACACCATGTTTGTCTCCACAAT 58.435 40.909 0.00 0.00 42.28 2.71
2402 2670 2.571212 GACACCATGTTTGTCTCCACA 58.429 47.619 14.58 0.00 40.30 4.17
2411 2679 2.325082 GGCGCTCGACACCATGTTT 61.325 57.895 7.64 0.00 0.00 2.83
2448 2716 3.136123 CAGCACCCATGGGCGAAG 61.136 66.667 31.73 18.64 39.32 3.79
2525 2793 4.636435 CGGTGGGCGAAGTTGGGT 62.636 66.667 0.00 0.00 0.00 4.51
2623 2891 4.225267 ACGGTTTGATCCTCCTAAAGATGT 59.775 41.667 0.00 0.00 0.00 3.06
2680 2965 1.021390 GGAACACCAGCACCGATCTG 61.021 60.000 0.00 0.00 0.00 2.90
2935 3221 1.672854 CCGGGTGCTCCTATCGAACA 61.673 60.000 4.53 0.00 0.00 3.18
2960 3246 2.494530 GCCCCAAACGCCTTGTTCA 61.495 57.895 0.00 0.00 40.84 3.18
2983 3269 6.621316 TGCTTTTGTTCGGTCTATAAAACA 57.379 33.333 0.00 0.00 0.00 2.83
3029 3315 2.958016 GGTGTCGCGTGTGTTCGT 60.958 61.111 5.77 0.00 0.00 3.85
3096 3382 2.472029 GGGATCTGAGGTTTGGAGAGA 58.528 52.381 0.00 0.00 0.00 3.10
3105 3392 2.143419 GGCGATGGGGATCTGAGGT 61.143 63.158 0.00 0.00 0.00 3.85
3130 3417 0.103554 AGGGAAGTTGGGGGTTAGGT 60.104 55.000 0.00 0.00 0.00 3.08
3149 3436 3.134081 GGAAGAACAACATAGGGGATCGA 59.866 47.826 0.00 0.00 0.00 3.59
3159 3446 4.703897 TCAAGAACGAGGAAGAACAACAT 58.296 39.130 0.00 0.00 0.00 2.71
3244 3531 3.019564 GCATATGGAGAAACACAAGGCT 58.980 45.455 4.56 0.00 0.00 4.58
3410 3699 9.388506 CACACTCAGATTTCTCCTAAATACATT 57.611 33.333 0.00 0.00 0.00 2.71
3510 3799 4.610714 TGGCGCACGGCTTACACA 62.611 61.111 17.68 0.00 42.94 3.72
3645 3934 0.546122 TACTGGCAATGGAATCCGCT 59.454 50.000 0.00 0.00 0.00 5.52


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

AutoCloner maintained by Alex Coulton.