Multiple sequence alignment - TraesCS3A01G251900

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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 TraesCS3A01G251900 chr3A 100.000 3722 0 0 1 3722 471819336 471815615 0.000000e+00 6874.0
1 TraesCS3A01G251900 chr3D 92.449 3059 141 24 455 3478 352950392 352947389 0.000000e+00 4287.0
2 TraesCS3A01G251900 chr3D 89.956 458 44 2 4 459 352950960 352950503 1.150000e-164 590.0
3 TraesCS3A01G251900 chr3D 74.178 213 41 10 5 217 301976146 301976344 3.990000e-10 76.8
4 TraesCS3A01G251900 chr3B 94.763 2177 73 19 871 3045 452104989 452102852 0.000000e+00 3350.0
5 TraesCS3A01G251900 chr3B 86.471 340 32 6 3388 3722 452102393 452102063 9.830000e-96 361.0
6 TraesCS3A01G251900 chr3B 88.362 232 21 4 3158 3383 452102740 452102509 1.320000e-69 274.0
7 TraesCS3A01G251900 chr3B 97.500 40 1 0 3381 3420 452102435 452102396 6.670000e-08 69.4
8 TraesCS3A01G251900 chr7B 74.194 248 56 7 456 699 709554548 709554791 3.060000e-16 97.1
9 TraesCS3A01G251900 chr7B 77.885 104 21 2 107 210 679498200 679498301 3.100000e-06 63.9
10 TraesCS3A01G251900 chr1D 90.196 51 5 0 169 219 62440537 62440487 2.400000e-07 67.6
11 TraesCS3A01G251900 chr7A 85.455 55 8 0 155 209 91399937 91399991 1.440000e-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 TraesCS3A01G251900 chr3A 471815615 471819336 3721 True 6874.0 6874 100.0000 1 3722 1 chr3A.!!$R1 3721
1 TraesCS3A01G251900 chr3D 352947389 352950960 3571 True 2438.5 4287 91.2025 4 3478 2 chr3D.!!$R1 3474
2 TraesCS3A01G251900 chr3B 452102063 452104989 2926 True 1013.6 3350 91.7740 871 3722 4 chr3B.!!$R1 2851

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
630 748 0.179006 GGGATGGTGAGGATTGGAGC 60.179 60.0 0.00 0.0 0.00 4.70 F
2023 2149 0.036388 GTTCCGCCAGATGGAGTTGA 60.036 55.0 2.18 0.0 36.72 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2238 2364 0.108138 AGTATGCGGCCTTGAGTGTC 60.108 55.0 0.0 0.0 0.0 3.67 R
3586 3876 0.744414 ACGGCCTGTCATCCATTTCG 60.744 55.0 0.0 0.0 0.0 3.46 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
43 44 5.517322 AATCTAGTCTAAATCTTCGCCGT 57.483 39.130 0.00 0.00 0.00 5.68
44 45 6.630444 AATCTAGTCTAAATCTTCGCCGTA 57.370 37.500 0.00 0.00 0.00 4.02
45 46 6.630444 ATCTAGTCTAAATCTTCGCCGTAA 57.370 37.500 0.00 0.00 0.00 3.18
55 56 0.595588 TTCGCCGTAACCGTACTTGA 59.404 50.000 0.00 0.00 0.00 3.02
66 67 1.553248 CCGTACTTGATGTTCCCTCCA 59.447 52.381 0.00 0.00 0.00 3.86
74 75 1.839994 GATGTTCCCTCCATGTCCTCA 59.160 52.381 0.00 0.00 0.00 3.86
76 77 1.839994 TGTTCCCTCCATGTCCTCATC 59.160 52.381 0.00 0.00 31.15 2.92
83 84 4.241555 ATGTCCTCATCCGGCGGC 62.242 66.667 23.83 5.69 0.00 6.53
112 113 1.737793 ACGCAAATTGAAGATCCGGTC 59.262 47.619 0.00 0.00 0.00 4.79
113 114 1.737236 CGCAAATTGAAGATCCGGTCA 59.263 47.619 0.00 0.00 0.00 4.02
142 143 5.162936 TGAGATAGGGTAGGACATGAGACAT 60.163 44.000 0.00 0.00 0.00 3.06
143 144 6.045577 TGAGATAGGGTAGGACATGAGACATA 59.954 42.308 0.00 0.00 0.00 2.29
149 150 5.133941 GGTAGGACATGAGACATAGACTGA 58.866 45.833 0.00 0.00 0.00 3.41
152 153 3.957497 GGACATGAGACATAGACTGACCT 59.043 47.826 0.00 0.00 0.00 3.85
167 168 2.203070 CCTACATGGGGCACGAGC 60.203 66.667 0.00 0.00 41.10 5.03
189 190 0.396435 CCGCCATCTTACATGCCCTA 59.604 55.000 0.00 0.00 0.00 3.53
209 210 2.181021 CTTCCTCGTCGGAACCCG 59.819 66.667 0.00 0.00 46.80 5.28
219 220 1.295423 CGGAACCCGTGACCTGAAT 59.705 57.895 0.00 0.00 42.73 2.57
223 224 0.320421 AACCCGTGACCTGAATGTCG 60.320 55.000 0.00 0.00 38.11 4.35
225 226 1.079819 CCGTGACCTGAATGTCGCT 60.080 57.895 0.00 0.00 42.27 4.93
262 264 4.720902 TAGACGTGGACGGGCGGA 62.721 66.667 0.00 0.00 44.95 5.54
283 285 1.202927 CCTCATCCAAGGTGGTTGTGT 60.203 52.381 5.48 0.00 38.18 3.72
297 299 3.681835 GTGTGACTCCGGCTCCGT 61.682 66.667 7.59 0.00 37.81 4.69
318 320 3.371021 CTCTGTCGTGAGGGCTGT 58.629 61.111 0.00 0.00 0.00 4.40
320 322 2.126307 CTGTCGTGAGGGCTGTCG 60.126 66.667 0.00 0.00 0.00 4.35
321 323 4.357947 TGTCGTGAGGGCTGTCGC 62.358 66.667 0.00 0.00 0.00 5.19
343 345 1.684049 CTCCCTCGTCCTCTGCCTT 60.684 63.158 0.00 0.00 0.00 4.35
377 379 0.433492 CTCGCGTCTACAAACCAACG 59.567 55.000 5.77 0.00 38.13 4.10
393 395 1.320344 AACGCCTCGACTCCATAGCA 61.320 55.000 0.00 0.00 0.00 3.49
395 397 1.448119 CGCCTCGACTCCATAGCAGA 61.448 60.000 0.00 0.00 0.00 4.26
416 418 2.584391 GGTCGTGAGGGAAGCCACT 61.584 63.158 0.00 0.00 0.00 4.00
429 432 0.824759 AGCCACTATTGACCTCGACC 59.175 55.000 0.00 0.00 0.00 4.79
487 605 2.747460 GCAACGGAGAGCCATGCA 60.747 61.111 0.00 0.00 42.91 3.96
492 610 2.202987 GGAGAGCCATGCAGACGG 60.203 66.667 0.00 0.00 0.00 4.79
502 620 2.037620 ATGCAGACGGCCATCTCCTC 62.038 60.000 0.00 0.00 43.89 3.71
503 621 2.725312 GCAGACGGCCATCTCCTCA 61.725 63.158 0.00 0.00 36.11 3.86
504 622 1.142748 CAGACGGCCATCTCCTCAC 59.857 63.158 0.00 0.00 0.00 3.51
505 623 2.060980 AGACGGCCATCTCCTCACC 61.061 63.158 2.24 0.00 0.00 4.02
507 625 4.227134 CGGCCATCTCCTCACCGG 62.227 72.222 2.24 0.00 40.18 5.28
541 659 0.325296 AGGCCCTAGTTGACGGATCA 60.325 55.000 0.00 0.00 0.00 2.92
543 661 1.112113 GCCCTAGTTGACGGATCAGA 58.888 55.000 0.00 0.00 35.83 3.27
545 663 2.656002 CCCTAGTTGACGGATCAGAGA 58.344 52.381 0.00 0.00 35.83 3.10
569 687 1.326213 CGGAGTCAGATCCACTGCCT 61.326 60.000 7.97 0.00 45.38 4.75
574 692 0.610174 TCAGATCCACTGCCTGACAC 59.390 55.000 0.00 0.00 45.38 3.67
578 696 1.188219 ATCCACTGCCTGACACGTCT 61.188 55.000 0.00 0.00 0.00 4.18
579 697 1.665916 CCACTGCCTGACACGTCTG 60.666 63.158 0.00 0.00 0.00 3.51
595 713 0.516001 TCTGAGACGGTCGAAGTTCG 59.484 55.000 19.23 19.23 42.10 3.95
617 735 1.704007 GGAGAGGAGCTTGGGGATGG 61.704 65.000 0.00 0.00 0.00 3.51
618 736 0.985490 GAGAGGAGCTTGGGGATGGT 60.985 60.000 0.00 0.00 0.00 3.55
620 738 1.229951 AGGAGCTTGGGGATGGTGA 60.230 57.895 0.00 0.00 0.00 4.02
630 748 0.179006 GGGATGGTGAGGATTGGAGC 60.179 60.000 0.00 0.00 0.00 4.70
643 761 0.690192 TTGGAGCGGAATGGAGTGAA 59.310 50.000 0.00 0.00 0.00 3.18
645 763 2.115427 TGGAGCGGAATGGAGTGAATA 58.885 47.619 0.00 0.00 0.00 1.75
646 764 2.705658 TGGAGCGGAATGGAGTGAATAT 59.294 45.455 0.00 0.00 0.00 1.28
656 774 6.774656 GGAATGGAGTGAATATGGTTTGATCT 59.225 38.462 0.00 0.00 0.00 2.75
658 776 6.312141 TGGAGTGAATATGGTTTGATCTGA 57.688 37.500 0.00 0.00 0.00 3.27
663 781 7.170965 AGTGAATATGGTTTGATCTGAAGTGT 58.829 34.615 0.00 0.00 0.00 3.55
664 782 8.321353 AGTGAATATGGTTTGATCTGAAGTGTA 58.679 33.333 0.00 0.00 0.00 2.90
672 790 8.321353 TGGTTTGATCTGAAGTGTAGATATTGT 58.679 33.333 0.00 0.00 35.14 2.71
691 809 4.079980 TGTTGAATATATGTGGGGTCGG 57.920 45.455 0.00 0.00 0.00 4.79
699 817 3.703127 GTGGGGTCGGAGTGGGTC 61.703 72.222 0.00 0.00 0.00 4.46
703 821 1.987855 GGGTCGGAGTGGGTCATGA 60.988 63.158 0.00 0.00 0.00 3.07
711 829 0.327480 AGTGGGTCATGATGGGCCTA 60.327 55.000 4.53 0.00 0.00 3.93
719 837 0.321671 ATGATGGGCCTAATCCGACG 59.678 55.000 4.53 0.00 0.00 5.12
720 838 1.004918 GATGGGCCTAATCCGACGG 60.005 63.158 7.84 7.84 0.00 4.79
749 867 3.516615 GCATCTGAGCGTCCTTATATCC 58.483 50.000 0.00 0.00 0.00 2.59
750 868 3.056536 GCATCTGAGCGTCCTTATATCCA 60.057 47.826 0.00 0.00 0.00 3.41
752 870 3.833732 TCTGAGCGTCCTTATATCCACT 58.166 45.455 0.00 0.00 0.00 4.00
753 871 4.215908 TCTGAGCGTCCTTATATCCACTT 58.784 43.478 0.00 0.00 0.00 3.16
756 874 4.038042 TGAGCGTCCTTATATCCACTTCAG 59.962 45.833 0.00 0.00 0.00 3.02
761 879 6.366332 GCGTCCTTATATCCACTTCAGTTATG 59.634 42.308 0.00 0.00 0.00 1.90
762 880 6.868864 CGTCCTTATATCCACTTCAGTTATGG 59.131 42.308 0.00 0.00 34.58 2.74
763 881 7.162082 GTCCTTATATCCACTTCAGTTATGGG 58.838 42.308 0.00 0.00 34.03 4.00
766 884 2.787473 TCCACTTCAGTTATGGGCTG 57.213 50.000 0.00 0.00 34.03 4.85
771 889 3.313526 CACTTCAGTTATGGGCTGCATAC 59.686 47.826 0.50 0.00 34.21 2.39
780 898 1.517832 GGCTGCATACGAGAGGTGT 59.482 57.895 0.50 0.00 0.00 4.16
782 900 1.281899 GCTGCATACGAGAGGTGTTC 58.718 55.000 0.00 0.00 0.00 3.18
789 907 3.031660 CGAGAGGTGTTCGTTAGCC 57.968 57.895 0.00 0.00 33.57 3.93
817 937 4.096231 CGTTTGCCAGATTTGTCATATCCA 59.904 41.667 0.16 0.00 0.00 3.41
820 940 3.953612 TGCCAGATTTGTCATATCCAACC 59.046 43.478 0.16 0.00 0.00 3.77
822 942 4.202050 GCCAGATTTGTCATATCCAACCAC 60.202 45.833 0.16 0.00 0.00 4.16
838 958 4.679197 CCAACCACGTGACATATTTTTGTG 59.321 41.667 19.30 0.00 0.00 3.33
869 989 1.134310 CCGGGCGTTTAGGACCTTTAT 60.134 52.381 0.00 0.00 30.57 1.40
940 1064 6.702716 TTCTTATTTGTGGTTTTCTTCCGT 57.297 33.333 0.00 0.00 0.00 4.69
941 1065 6.702716 TCTTATTTGTGGTTTTCTTCCGTT 57.297 33.333 0.00 0.00 0.00 4.44
985 1109 9.557061 GTAGAGAGAAACCTTAAAGAAAAAGGA 57.443 33.333 8.79 0.00 45.41 3.36
986 1110 8.684386 AGAGAGAAACCTTAAAGAAAAAGGAG 57.316 34.615 8.79 0.00 45.41 3.69
987 1111 8.495260 AGAGAGAAACCTTAAAGAAAAAGGAGA 58.505 33.333 8.79 0.00 45.41 3.71
988 1112 9.121658 GAGAGAAACCTTAAAGAAAAAGGAGAA 57.878 33.333 8.79 0.00 45.41 2.87
989 1113 9.126151 AGAGAAACCTTAAAGAAAAAGGAGAAG 57.874 33.333 8.79 0.00 45.41 2.85
990 1114 9.121658 GAGAAACCTTAAAGAAAAAGGAGAAGA 57.878 33.333 8.79 0.00 45.41 2.87
991 1115 9.126151 AGAAACCTTAAAGAAAAAGGAGAAGAG 57.874 33.333 8.79 0.00 45.41 2.85
993 1117 9.475620 AAACCTTAAAGAAAAAGGAGAAGAGAA 57.524 29.630 8.79 0.00 45.41 2.87
994 1118 9.475620 AACCTTAAAGAAAAAGGAGAAGAGAAA 57.524 29.630 8.79 0.00 45.41 2.52
995 1119 9.475620 ACCTTAAAGAAAAAGGAGAAGAGAAAA 57.524 29.630 8.79 0.00 45.41 2.29
1000 1124 8.410673 AAGAAAAAGGAGAAGAGAAAATACCC 57.589 34.615 0.00 0.00 0.00 3.69
1029 1153 4.454728 AAACGTATCCTTGGTACGCTTA 57.545 40.909 6.81 0.00 46.46 3.09
1030 1154 3.427161 ACGTATCCTTGGTACGCTTAC 57.573 47.619 6.81 0.00 46.46 2.34
1031 1155 2.223340 ACGTATCCTTGGTACGCTTACG 60.223 50.000 6.81 0.00 46.46 3.18
1070 1194 2.547855 CCAATAACAGATCCGATCCGCA 60.548 50.000 4.67 0.00 0.00 5.69
1127 1253 2.171659 GTCTTCTCCCCCAAATCTCTCC 59.828 54.545 0.00 0.00 0.00 3.71
1395 1521 4.755507 GTCTCCCTCCCCGACGGT 62.756 72.222 13.94 0.00 0.00 4.83
1941 2067 1.545706 GCTTCTCCCGTCTTGGTCCT 61.546 60.000 0.00 0.00 35.15 3.85
1944 2070 2.678934 TCCCGTCTTGGTCCTCGG 60.679 66.667 0.00 0.00 42.22 4.63
2001 2127 4.547367 GATGCGCCGCTTACCCCT 62.547 66.667 11.67 0.00 0.00 4.79
2023 2149 0.036388 GTTCCGCCAGATGGAGTTGA 60.036 55.000 2.18 0.00 36.72 3.18
2082 2208 3.419759 GCAAGGTACGTGGTGGCG 61.420 66.667 0.00 0.00 38.52 5.69
2202 2328 4.479619 CAGATTTCTGCAGCTTTTACACC 58.520 43.478 9.47 0.00 37.15 4.16
2238 2364 2.159653 GCTGAACAATGCCAACTACTCG 60.160 50.000 0.00 0.00 0.00 4.18
2330 2456 2.951269 TGATTGTGGCCAAGCAGAG 58.049 52.632 7.24 0.00 41.75 3.35
2409 2535 0.110486 TCAAGTTTGGCCCTGGAGAC 59.890 55.000 0.00 0.00 0.00 3.36
2790 2917 6.061441 ACATTCAGTGTGTATGGTTCAAAGA 58.939 36.000 0.00 0.00 40.28 2.52
2826 2954 6.280643 GCACTCAGTTTACCAAGGAATTTTT 58.719 36.000 0.00 0.00 0.00 1.94
2878 3006 4.204799 AGTACCCTTGTGTTTTGAGGTTC 58.795 43.478 0.00 0.00 0.00 3.62
2886 3014 7.094762 CCCTTGTGTTTTGAGGTTCTAACTATC 60.095 40.741 0.00 0.00 0.00 2.08
2893 3021 5.599999 TGAGGTTCTAACTATCTGGCTTC 57.400 43.478 0.00 0.00 0.00 3.86
2920 3048 7.429340 GTCGATTTATGACATTCACCATTGTTC 59.571 37.037 0.00 0.00 36.37 3.18
2952 3080 4.163427 TGCCCCAAAATTTGATGTCCTTA 58.837 39.130 7.37 0.00 0.00 2.69
3025 3153 7.090319 TGCTATCATATGAGGTGGGTTTATT 57.910 36.000 11.78 0.00 0.00 1.40
3094 3261 5.098211 GCATCAATAAGCCTCTTTGTCAAC 58.902 41.667 0.00 0.00 0.00 3.18
3109 3276 0.038166 TCAACCTTGTGGCATCCTCC 59.962 55.000 0.00 0.00 36.63 4.30
3131 3298 5.559427 CCCCCTCTTTTGTTTTTGTTTTG 57.441 39.130 0.00 0.00 0.00 2.44
3132 3299 5.007034 CCCCCTCTTTTGTTTTTGTTTTGT 58.993 37.500 0.00 0.00 0.00 2.83
3133 3300 5.475220 CCCCCTCTTTTGTTTTTGTTTTGTT 59.525 36.000 0.00 0.00 0.00 2.83
3134 3301 6.015856 CCCCCTCTTTTGTTTTTGTTTTGTTT 60.016 34.615 0.00 0.00 0.00 2.83
3135 3302 7.429633 CCCCTCTTTTGTTTTTGTTTTGTTTT 58.570 30.769 0.00 0.00 0.00 2.43
3249 3420 7.343574 TGACATTACATAGTCTAAGGCACCTTA 59.656 37.037 8.80 8.80 37.06 2.69
3263 3434 4.412199 AGGCACCTTATTAGATGTTAGCCA 59.588 41.667 0.00 0.00 40.72 4.75
3300 3472 6.909550 TTAGTTGCCCAATTAGATTGTGTT 57.090 33.333 0.58 0.00 38.59 3.32
3307 3481 7.731054 TGCCCAATTAGATTGTGTTTAAACTT 58.269 30.769 18.72 2.17 38.59 2.66
3308 3482 7.655328 TGCCCAATTAGATTGTGTTTAAACTTG 59.345 33.333 18.72 10.94 38.59 3.16
3351 3525 4.278170 TGATAAGTGAAAACAGCCCAACAG 59.722 41.667 0.00 0.00 0.00 3.16
3354 3528 2.689983 AGTGAAAACAGCCCAACAGAAG 59.310 45.455 0.00 0.00 0.00 2.85
3421 3673 5.743636 ATTCATGGTGGTTGCAAAAGTAT 57.256 34.783 0.00 0.00 0.00 2.12
3450 3736 0.401738 TCCCTTGCAAACTCTGGAGG 59.598 55.000 0.00 0.00 0.00 4.30
3480 3766 2.894765 TCTGTGGTCGGACACTAATGAA 59.105 45.455 10.76 0.00 41.84 2.57
3482 3768 4.020573 TCTGTGGTCGGACACTAATGAATT 60.021 41.667 10.76 0.00 41.84 2.17
3483 3769 4.000325 TGTGGTCGGACACTAATGAATTG 59.000 43.478 10.76 0.00 41.84 2.32
3485 3771 4.330074 GTGGTCGGACACTAATGAATTGAG 59.670 45.833 10.76 0.00 38.32 3.02
3486 3772 3.309954 GGTCGGACACTAATGAATTGAGC 59.690 47.826 10.76 0.00 0.00 4.26
3510 3798 5.637006 TTTATCATGGGTTACACAGTTGC 57.363 39.130 0.00 0.00 0.00 4.17
3531 3819 3.063045 GCTAAGTACGGTATGGTTTGTGC 59.937 47.826 0.00 0.00 0.00 4.57
3558 3846 4.142447 CCCTTCATGCAACTTTCTCTGATG 60.142 45.833 0.00 0.00 0.00 3.07
3570 3858 1.203287 TCTCTGATGAGTGAAGTGCCG 59.797 52.381 0.00 0.00 40.98 5.69
3574 3864 0.247736 GATGAGTGAAGTGCCGGTCT 59.752 55.000 1.90 0.00 0.00 3.85
3586 3876 2.892425 CGGTCTTGCGGCCTGATC 60.892 66.667 0.00 0.00 0.00 2.92
3596 3886 0.870393 CGGCCTGATCGAAATGGATG 59.130 55.000 0.00 0.00 0.00 3.51
3600 3890 2.547211 GCCTGATCGAAATGGATGACAG 59.453 50.000 0.00 0.00 0.00 3.51
3639 3929 4.313020 AAATCTTGAGTTCCTCCATGCT 57.687 40.909 0.00 0.00 0.00 3.79
3640 3930 2.775911 TCTTGAGTTCCTCCATGCTG 57.224 50.000 0.00 0.00 0.00 4.41
3641 3931 1.093159 CTTGAGTTCCTCCATGCTGC 58.907 55.000 0.00 0.00 0.00 5.25
3642 3932 0.694771 TTGAGTTCCTCCATGCTGCT 59.305 50.000 0.00 0.00 0.00 4.24
3643 3933 0.694771 TGAGTTCCTCCATGCTGCTT 59.305 50.000 0.00 0.00 0.00 3.91
3656 3946 4.217118 CCATGCTGCTTCTTTTAGTGAAGT 59.783 41.667 0.00 0.00 41.94 3.01
3663 3953 6.112734 TGCTTCTTTTAGTGAAGTGTCTCAA 58.887 36.000 0.00 0.00 41.94 3.02
3664 3954 6.597672 TGCTTCTTTTAGTGAAGTGTCTCAAA 59.402 34.615 0.00 0.00 41.94 2.69
3672 3962 4.080863 AGTGAAGTGTCTCAAAAGTCCAGT 60.081 41.667 0.00 0.00 0.00 4.00
3674 3964 5.123979 GTGAAGTGTCTCAAAAGTCCAGTTT 59.876 40.000 0.00 0.00 0.00 2.66
3681 3971 6.128007 TGTCTCAAAAGTCCAGTTTCTGTTTC 60.128 38.462 0.00 0.00 0.00 2.78
3684 3974 6.620678 TCAAAAGTCCAGTTTCTGTTTCTTG 58.379 36.000 0.00 0.00 0.00 3.02
3686 3976 4.503714 AGTCCAGTTTCTGTTTCTTGGA 57.496 40.909 0.00 0.00 0.00 3.53
3687 3977 5.053978 AGTCCAGTTTCTGTTTCTTGGAT 57.946 39.130 0.00 0.00 0.00 3.41
3688 3978 4.823989 AGTCCAGTTTCTGTTTCTTGGATG 59.176 41.667 0.00 0.00 0.00 3.51
3690 3980 4.141274 TCCAGTTTCTGTTTCTTGGATGGA 60.141 41.667 0.00 0.00 0.00 3.41
3691 3981 4.022849 CCAGTTTCTGTTTCTTGGATGGAC 60.023 45.833 0.00 0.00 0.00 4.02
3692 3982 3.815401 AGTTTCTGTTTCTTGGATGGACG 59.185 43.478 0.00 0.00 0.00 4.79
3718 4008 6.998968 ACTCATCCAAAAGCTAGAAGAATG 57.001 37.500 0.00 0.00 0.00 2.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.322664 AGATTTTACGTTGCATTTGATTGGAT 58.677 30.769 0.00 0.00 0.00 3.41
1 2 6.686630 AGATTTTACGTTGCATTTGATTGGA 58.313 32.000 0.00 0.00 0.00 3.53
2 3 6.949578 AGATTTTACGTTGCATTTGATTGG 57.050 33.333 0.00 0.00 0.00 3.16
6 7 7.667043 AGACTAGATTTTACGTTGCATTTGA 57.333 32.000 0.00 0.00 0.00 2.69
43 44 3.196254 GGAGGGAACATCAAGTACGGTTA 59.804 47.826 0.00 0.00 0.00 2.85
44 45 2.027469 GGAGGGAACATCAAGTACGGTT 60.027 50.000 0.00 0.00 0.00 4.44
45 46 1.553704 GGAGGGAACATCAAGTACGGT 59.446 52.381 0.00 0.00 0.00 4.83
55 56 1.971149 TGAGGACATGGAGGGAACAT 58.029 50.000 0.00 0.00 0.00 2.71
66 67 4.241555 GCCGCCGGATGAGGACAT 62.242 66.667 7.68 0.00 39.67 3.06
96 97 2.356135 CGGTGACCGGATCTTCAATTT 58.644 47.619 17.80 0.00 44.15 1.82
112 113 2.820787 GTCCTACCCTATCTCATCGGTG 59.179 54.545 0.00 0.00 0.00 4.94
113 114 2.445905 TGTCCTACCCTATCTCATCGGT 59.554 50.000 0.00 0.00 0.00 4.69
117 118 5.162936 TGTCTCATGTCCTACCCTATCTCAT 60.163 44.000 0.00 0.00 0.00 2.90
122 123 6.046168 AGTCTATGTCTCATGTCCTACCCTAT 59.954 42.308 0.00 0.00 0.00 2.57
142 143 1.007842 TGCCCCATGTAGGTCAGTCTA 59.992 52.381 1.34 0.00 34.66 2.59
143 144 0.252696 TGCCCCATGTAGGTCAGTCT 60.253 55.000 1.34 0.00 34.66 3.24
149 150 3.031417 GCTCGTGCCCCATGTAGGT 62.031 63.158 0.00 0.00 34.66 3.08
167 168 2.896801 GCATGTAAGATGGCGGCGG 61.897 63.158 9.78 0.00 0.00 6.13
209 210 0.320771 ACCAGCGACATTCAGGTCAC 60.321 55.000 0.00 0.00 37.66 3.67
219 220 2.596338 TCACCTCGACCAGCGACA 60.596 61.111 0.00 0.00 45.59 4.35
223 224 1.395826 ATAGCCTCACCTCGACCAGC 61.396 60.000 0.00 0.00 0.00 4.85
225 226 0.033503 TCATAGCCTCACCTCGACCA 60.034 55.000 0.00 0.00 0.00 4.02
321 323 4.824515 AGAGGACGAGGGAGGCCG 62.825 72.222 0.00 0.00 0.00 6.13
363 365 0.788391 CGAGGCGTTGGTTTGTAGAC 59.212 55.000 0.00 0.00 0.00 2.59
366 368 0.390124 AGTCGAGGCGTTGGTTTGTA 59.610 50.000 0.00 0.00 0.00 2.41
371 373 0.968901 TATGGAGTCGAGGCGTTGGT 60.969 55.000 0.00 0.00 0.00 3.67
377 379 0.031449 GTCTGCTATGGAGTCGAGGC 59.969 60.000 0.00 0.00 0.00 4.70
393 395 1.977544 CTTCCCTCACGACCCGTCT 60.978 63.158 0.00 0.00 38.32 4.18
395 397 3.692406 GCTTCCCTCACGACCCGT 61.692 66.667 0.00 0.00 42.36 5.28
416 418 1.389609 GCTCCGGGTCGAGGTCAATA 61.390 60.000 0.00 0.00 0.00 1.90
444 447 4.778143 GGAGTGCGGCGTTCCCAT 62.778 66.667 9.37 0.00 0.00 4.00
464 582 4.821589 GCTCTCCGTTGCTCCCGG 62.822 72.222 0.00 0.00 46.83 5.73
472 590 1.078848 GTCTGCATGGCTCTCCGTT 60.079 57.895 0.00 0.00 34.14 4.44
473 591 2.581354 GTCTGCATGGCTCTCCGT 59.419 61.111 0.00 0.00 34.14 4.69
487 605 2.060980 GGTGAGGAGATGGCCGTCT 61.061 63.158 27.92 27.92 0.00 4.18
492 610 4.554036 GGCCGGTGAGGAGATGGC 62.554 72.222 1.90 0.00 45.00 4.40
495 613 3.461773 CGTGGCCGGTGAGGAGAT 61.462 66.667 1.90 0.00 45.00 2.75
506 624 3.365265 CTTGTCCCTTGCGTGGCC 61.365 66.667 0.00 0.00 0.00 5.36
507 625 3.365265 CCTTGTCCCTTGCGTGGC 61.365 66.667 0.00 0.00 0.00 5.01
527 645 5.559991 CGAGATTCTCTGATCCGTCAACTAG 60.560 48.000 11.75 0.00 33.05 2.57
541 659 3.117701 TGGATCTGACTCCGAGATTCTCT 60.118 47.826 11.75 0.00 38.21 3.10
543 661 2.955660 GTGGATCTGACTCCGAGATTCT 59.044 50.000 1.33 0.00 38.21 2.40
545 663 2.692557 CAGTGGATCTGACTCCGAGATT 59.307 50.000 1.33 0.00 46.27 2.40
578 696 1.081641 GCGAACTTCGACCGTCTCA 60.082 57.895 15.43 0.00 43.74 3.27
579 697 1.800713 GGCGAACTTCGACCGTCTC 60.801 63.158 15.43 0.00 43.36 3.36
585 703 1.514443 CTCTCCGGCGAACTTCGAC 60.514 63.158 15.43 11.35 46.24 4.20
586 704 2.697761 CCTCTCCGGCGAACTTCGA 61.698 63.158 15.43 0.00 43.74 3.71
589 707 3.007973 GCTCCTCTCCGGCGAACTT 62.008 63.158 9.30 0.00 0.00 2.66
595 713 4.168291 CCCAAGCTCCTCTCCGGC 62.168 72.222 0.00 0.00 0.00 6.13
617 735 1.303309 CATTCCGCTCCAATCCTCAC 58.697 55.000 0.00 0.00 0.00 3.51
618 736 0.181114 CCATTCCGCTCCAATCCTCA 59.819 55.000 0.00 0.00 0.00 3.86
620 738 0.471617 CTCCATTCCGCTCCAATCCT 59.528 55.000 0.00 0.00 0.00 3.24
630 748 4.881273 TCAAACCATATTCACTCCATTCCG 59.119 41.667 0.00 0.00 0.00 4.30
645 763 9.334947 CAATATCTACACTTCAGATCAAACCAT 57.665 33.333 0.00 0.00 34.58 3.55
646 764 8.321353 ACAATATCTACACTTCAGATCAAACCA 58.679 33.333 0.00 0.00 34.58 3.67
664 782 7.824289 CGACCCCACATATATTCAACAATATCT 59.176 37.037 0.00 0.00 36.68 1.98
670 788 3.712218 TCCGACCCCACATATATTCAACA 59.288 43.478 0.00 0.00 0.00 3.33
672 790 3.971305 ACTCCGACCCCACATATATTCAA 59.029 43.478 0.00 0.00 0.00 2.69
691 809 1.152881 GGCCCATCATGACCCACTC 60.153 63.158 0.00 0.00 0.00 3.51
699 817 1.813513 GTCGGATTAGGCCCATCATG 58.186 55.000 13.35 6.34 0.00 3.07
703 821 2.516888 CCCGTCGGATTAGGCCCAT 61.517 63.158 14.39 0.00 0.00 4.00
711 829 2.180017 CGTTCGTCCCGTCGGATT 59.820 61.111 14.39 0.00 41.40 3.01
719 837 2.167861 GCTCAGATGCGTTCGTCCC 61.168 63.158 0.00 0.00 0.00 4.46
720 838 3.389206 GCTCAGATGCGTTCGTCC 58.611 61.111 0.00 0.00 0.00 4.79
734 852 4.038162 ACTGAAGTGGATATAAGGACGCTC 59.962 45.833 0.00 0.00 0.00 5.03
741 859 6.652481 CAGCCCATAACTGAAGTGGATATAAG 59.348 42.308 0.00 0.00 37.32 1.73
749 867 1.825090 TGCAGCCCATAACTGAAGTG 58.175 50.000 0.00 0.00 37.32 3.16
750 868 2.814805 ATGCAGCCCATAACTGAAGT 57.185 45.000 0.00 0.00 37.32 3.01
752 870 2.169561 TCGTATGCAGCCCATAACTGAA 59.830 45.455 0.00 0.00 38.11 3.02
753 871 1.760029 TCGTATGCAGCCCATAACTGA 59.240 47.619 0.00 0.00 38.11 3.41
756 874 2.408050 CTCTCGTATGCAGCCCATAAC 58.592 52.381 0.00 0.00 38.11 1.89
761 879 1.227380 CACCTCTCGTATGCAGCCC 60.227 63.158 0.00 0.00 0.00 5.19
762 880 0.108138 AACACCTCTCGTATGCAGCC 60.108 55.000 0.00 0.00 0.00 4.85
763 881 1.281899 GAACACCTCTCGTATGCAGC 58.718 55.000 0.00 0.00 0.00 5.25
771 889 0.458025 GGGCTAACGAACACCTCTCG 60.458 60.000 0.00 0.00 42.06 4.04
780 898 1.071814 AAACGCCTGGGCTAACGAA 59.928 52.632 10.04 0.00 39.32 3.85
782 900 2.867472 CAAACGCCTGGGCTAACG 59.133 61.111 10.04 0.00 39.32 3.18
804 924 4.394920 GTCACGTGGTTGGATATGACAAAT 59.605 41.667 17.00 0.00 37.11 2.32
809 929 3.904800 ATGTCACGTGGTTGGATATGA 57.095 42.857 17.00 0.00 0.00 2.15
817 937 4.202060 TGCACAAAAATATGTCACGTGGTT 60.202 37.500 17.00 3.36 0.00 3.67
820 940 3.913763 CCTGCACAAAAATATGTCACGTG 59.086 43.478 9.94 9.94 0.00 4.49
822 942 2.916716 GCCTGCACAAAAATATGTCACG 59.083 45.455 0.00 0.00 0.00 4.35
869 989 3.258372 AGCATCTACAACCGAACTCTTCA 59.742 43.478 0.00 0.00 0.00 3.02
913 1037 9.289303 CGGAAGAAAACCACAAATAAGAATATG 57.711 33.333 0.00 0.00 0.00 1.78
915 1039 8.398878 ACGGAAGAAAACCACAAATAAGAATA 57.601 30.769 0.00 0.00 0.00 1.75
917 1041 6.702716 ACGGAAGAAAACCACAAATAAGAA 57.297 33.333 0.00 0.00 0.00 2.52
940 1064 7.197703 TCTCTACATCACGCGATATTACAAAA 58.802 34.615 15.93 0.00 0.00 2.44
941 1065 6.731164 TCTCTACATCACGCGATATTACAAA 58.269 36.000 15.93 0.00 0.00 2.83
995 1119 9.292195 CCAAGGATACGTTTATTTATTGGGTAT 57.708 33.333 0.00 0.00 46.39 2.73
996 1120 8.273605 ACCAAGGATACGTTTATTTATTGGGTA 58.726 33.333 0.00 0.00 46.39 3.69
997 1121 7.120716 ACCAAGGATACGTTTATTTATTGGGT 58.879 34.615 0.00 0.00 46.39 4.51
998 1122 7.576861 ACCAAGGATACGTTTATTTATTGGG 57.423 36.000 0.00 0.00 46.39 4.12
999 1123 8.277713 CGTACCAAGGATACGTTTATTTATTGG 58.722 37.037 0.00 2.70 40.39 3.16
1000 1124 7.795272 GCGTACCAAGGATACGTTTATTTATTG 59.205 37.037 16.63 0.00 45.65 1.90
1029 1153 3.171528 GGGCTACCTATTCCCTATTCGT 58.828 50.000 0.00 0.00 37.08 3.85
1030 1154 3.170717 TGGGCTACCTATTCCCTATTCG 58.829 50.000 0.00 0.00 40.69 3.34
1031 1155 5.780958 ATTGGGCTACCTATTCCCTATTC 57.219 43.478 0.00 0.00 40.69 1.75
1127 1253 0.541863 ATCGGCTGTAGGGTTTGAGG 59.458 55.000 0.00 0.00 0.00 3.86
1810 1936 0.322816 GCCTGCCAGATGTTCTCCAA 60.323 55.000 0.00 0.00 0.00 3.53
1941 2067 2.814604 CGGCTCATGGTCATCCGA 59.185 61.111 4.24 0.00 42.43 4.55
1944 2070 2.528743 CGTGCGGCTCATGGTCATC 61.529 63.158 0.00 0.00 0.00 2.92
2001 2127 2.609299 TCCATCTGGCGGAACCCA 60.609 61.111 0.00 0.00 37.83 4.51
2023 2149 0.607489 GTGACTGCTGCAACATCCCT 60.607 55.000 3.02 0.00 0.00 4.20
2082 2208 4.142227 ACATCAAGCTCATCAAAATCTGGC 60.142 41.667 0.00 0.00 0.00 4.85
2121 2247 2.286425 ACCACATCCTCCTGGGGG 60.286 66.667 6.15 6.15 44.54 5.40
2238 2364 0.108138 AGTATGCGGCCTTGAGTGTC 60.108 55.000 0.00 0.00 0.00 3.67
2330 2456 3.483574 CGCGTTGAACACATCATAGTTCC 60.484 47.826 0.00 0.00 42.57 3.62
2409 2535 1.151668 GATAATAGTGCAGCTGCCCG 58.848 55.000 34.64 0.00 41.18 6.13
2790 2917 7.178274 TGGTAAACTGAGTGCCATCATAAAATT 59.822 33.333 0.00 0.00 0.00 1.82
2878 3006 3.965292 TCGACGAAGCCAGATAGTTAG 57.035 47.619 0.00 0.00 0.00 2.34
2886 3014 3.186909 TGTCATAAATCGACGAAGCCAG 58.813 45.455 0.00 0.00 36.11 4.85
2893 3021 5.657470 ATGGTGAATGTCATAAATCGACG 57.343 39.130 0.00 0.00 36.11 5.12
2920 3048 5.129155 TCAAATTTTGGGGCATTCTAGATGG 59.871 40.000 9.18 0.00 0.00 3.51
2952 3080 8.752005 ACAAGTAATACAGATTTGCATACCAT 57.248 30.769 0.00 0.00 0.00 3.55
3025 3153 9.685276 ATAAGAACATCCAAGTCATCAAACATA 57.315 29.630 0.00 0.00 0.00 2.29
3109 3276 5.007034 ACAAAACAAAAACAAAAGAGGGGG 58.993 37.500 0.00 0.00 0.00 5.40
3113 3280 8.265315 GGCAAAAACAAAACAAAAACAAAAGAG 58.735 29.630 0.00 0.00 0.00 2.85
3114 3281 7.222805 GGGCAAAAACAAAACAAAAACAAAAGA 59.777 29.630 0.00 0.00 0.00 2.52
3120 3287 5.524284 ACAGGGCAAAAACAAAACAAAAAC 58.476 33.333 0.00 0.00 0.00 2.43
3126 3293 4.249661 TGAAGACAGGGCAAAAACAAAAC 58.750 39.130 0.00 0.00 0.00 2.43
3127 3294 4.543590 TGAAGACAGGGCAAAAACAAAA 57.456 36.364 0.00 0.00 0.00 2.44
3128 3295 4.543590 TTGAAGACAGGGCAAAAACAAA 57.456 36.364 0.00 0.00 0.00 2.83
3129 3296 4.543590 TTTGAAGACAGGGCAAAAACAA 57.456 36.364 0.00 0.00 0.00 2.83
3130 3297 4.161189 TGATTTGAAGACAGGGCAAAAACA 59.839 37.500 0.00 0.00 35.44 2.83
3131 3298 4.507756 GTGATTTGAAGACAGGGCAAAAAC 59.492 41.667 0.00 0.00 35.44 2.43
3132 3299 4.405358 AGTGATTTGAAGACAGGGCAAAAA 59.595 37.500 0.00 0.00 35.44 1.94
3133 3300 3.960102 AGTGATTTGAAGACAGGGCAAAA 59.040 39.130 0.00 0.00 35.44 2.44
3134 3301 3.318839 CAGTGATTTGAAGACAGGGCAAA 59.681 43.478 0.00 0.00 36.15 3.68
3135 3302 2.886523 CAGTGATTTGAAGACAGGGCAA 59.113 45.455 0.00 0.00 0.00 4.52
3249 3420 7.557358 TGATGTGAACATTGGCTAACATCTAAT 59.443 33.333 17.36 0.00 42.68 1.73
3263 3434 5.245751 TGGGCAACTAAATGATGTGAACATT 59.754 36.000 0.00 0.00 39.25 2.71
3300 3472 5.929992 CAGGTCAGGAATACGACAAGTTTAA 59.070 40.000 0.00 0.00 33.66 1.52
3307 3481 2.225382 TCCAGGTCAGGAATACGACA 57.775 50.000 0.00 0.00 33.93 4.35
3351 3525 6.108687 GGATTTGAAATCCAATCAACCCTTC 58.891 40.000 27.42 0.00 36.57 3.46
3354 3528 5.419239 TGGATTTGAAATCCAATCAACCC 57.581 39.130 31.41 8.13 44.54 4.11
3421 3673 2.687935 GTTTGCAAGGGAACTCTGTTGA 59.312 45.455 0.00 0.00 42.68 3.18
3466 3752 4.471904 AGCTCAATTCATTAGTGTCCGA 57.528 40.909 0.00 0.00 0.00 4.55
3480 3766 6.663093 TGTGTAACCCATGATAAAAGCTCAAT 59.337 34.615 0.00 0.00 34.36 2.57
3482 3768 5.565509 TGTGTAACCCATGATAAAAGCTCA 58.434 37.500 0.00 0.00 34.36 4.26
3483 3769 5.648092 ACTGTGTAACCCATGATAAAAGCTC 59.352 40.000 0.00 0.00 34.36 4.09
3485 3771 5.897377 ACTGTGTAACCCATGATAAAAGC 57.103 39.130 0.00 0.00 34.36 3.51
3486 3772 6.071952 AGCAACTGTGTAACCCATGATAAAAG 60.072 38.462 0.00 0.00 34.36 2.27
3510 3798 4.247258 TGCACAAACCATACCGTACTTAG 58.753 43.478 0.00 0.00 0.00 2.18
3558 3846 1.569479 GCAAGACCGGCACTTCACTC 61.569 60.000 0.00 0.00 0.00 3.51
3570 3858 2.852495 TTCGATCAGGCCGCAAGACC 62.852 60.000 0.00 0.00 43.02 3.85
3574 3864 1.375853 CCATTTCGATCAGGCCGCAA 61.376 55.000 0.00 0.00 0.00 4.85
3586 3876 0.744414 ACGGCCTGTCATCCATTTCG 60.744 55.000 0.00 0.00 0.00 3.46
3639 3929 5.670485 TGAGACACTTCACTAAAAGAAGCA 58.330 37.500 0.00 0.00 44.87 3.91
3640 3930 6.604735 TTGAGACACTTCACTAAAAGAAGC 57.395 37.500 0.00 0.00 44.87 3.86
3641 3931 8.669243 ACTTTTGAGACACTTCACTAAAAGAAG 58.331 33.333 11.96 0.00 46.08 2.85
3642 3932 8.561738 ACTTTTGAGACACTTCACTAAAAGAA 57.438 30.769 11.96 0.00 31.56 2.52
3643 3933 7.280205 GGACTTTTGAGACACTTCACTAAAAGA 59.720 37.037 11.96 0.00 31.56 2.52
3656 3946 4.843728 ACAGAAACTGGACTTTTGAGACA 58.156 39.130 0.00 0.00 35.51 3.41
3663 3953 5.261216 TCCAAGAAACAGAAACTGGACTTT 58.739 37.500 0.00 0.00 35.51 2.66
3664 3954 4.855340 TCCAAGAAACAGAAACTGGACTT 58.145 39.130 0.00 0.00 35.51 3.01
3672 3962 3.146066 CCGTCCATCCAAGAAACAGAAA 58.854 45.455 0.00 0.00 0.00 2.52
3674 3964 1.974957 TCCGTCCATCCAAGAAACAGA 59.025 47.619 0.00 0.00 0.00 3.41
3681 3971 2.555199 GATGAGTTCCGTCCATCCAAG 58.445 52.381 0.00 0.00 32.68 3.61
3692 3982 5.491982 TCTTCTAGCTTTTGGATGAGTTCC 58.508 41.667 0.00 0.00 45.69 3.62


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

AutoCloner maintained by Alex Coulton.