Multiple sequence alignment - TraesCS1B01G304000

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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 TraesCS1B01G304000 chr1B 100.000 2813 0 0 1 2813 526262798 526259986 0.000000e+00 5195.0
1 TraesCS1B01G304000 chr1B 80.552 689 88 26 998 1667 526272318 526271657 3.260000e-134 488.0
2 TraesCS1B01G304000 chr1B 76.816 647 135 13 1021 1661 526291398 526290761 1.600000e-92 350.0
3 TraesCS1B01G304000 chr1D 92.000 975 61 6 767 1734 394950602 394949638 0.000000e+00 1352.0
4 TraesCS1B01G304000 chr1D 83.994 656 63 19 1744 2360 394949444 394948792 2.410000e-165 592.0
5 TraesCS1B01G304000 chr1D 81.395 688 92 22 998 1667 395055332 395054663 1.920000e-146 529.0
6 TraesCS1B01G304000 chr1D 77.728 669 135 11 998 1661 395410623 395409964 5.650000e-107 398.0
7 TraesCS1B01G304000 chr1D 84.231 260 34 5 2542 2799 394896095 394895841 2.160000e-61 246.0
8 TraesCS1B01G304000 chr1D 91.525 177 15 0 998 1174 395382444 395382268 7.780000e-61 244.0
9 TraesCS1B01G304000 chr1A 91.572 973 59 6 767 1736 489289239 489288287 0.000000e+00 1321.0
10 TraesCS1B01G304000 chr1A 86.157 549 39 15 1744 2272 489287654 489287123 2.450000e-155 558.0
11 TraesCS1B01G304000 chr1A 81.991 683 91 23 998 1667 489325619 489324956 4.100000e-153 551.0
12 TraesCS1B01G304000 chr1A 80.556 684 99 25 998 1667 489383672 489383009 1.950000e-136 496.0
13 TraesCS1B01G304000 chr1A 84.598 435 49 14 2388 2813 489286959 489286534 1.560000e-112 416.0
14 TraesCS1B01G304000 chr1A 79.470 151 16 4 2079 2228 489324311 489324175 2.980000e-15 93.5
15 TraesCS1B01G304000 chr3A 99.038 728 7 0 1 728 519218541 519217814 0.000000e+00 1306.0
16 TraesCS1B01G304000 chr3A 94.505 728 40 0 1 728 735708897 735708170 0.000000e+00 1123.0
17 TraesCS1B01G304000 chr3A 94.595 37 2 0 723 759 735707985 735708021 1.090000e-04 58.4
18 TraesCS1B01G304000 chr2B 98.901 728 8 0 1 728 118829755 118829028 0.000000e+00 1301.0
19 TraesCS1B01G304000 chr2B 92.683 41 3 0 719 759 118828840 118828880 3.030000e-05 60.2
20 TraesCS1B01G304000 chr2B 100.000 28 0 0 1295 1322 708183727 708183754 5.000000e-03 52.8
21 TraesCS1B01G304000 chr6B 98.626 728 10 0 1 728 619401820 619402547 0.000000e+00 1290.0
22 TraesCS1B01G304000 chr6B 80.132 151 30 0 1051 1201 62001328 62001478 2.290000e-21 113.0
23 TraesCS1B01G304000 chr6B 97.368 38 1 0 722 759 619402733 619402696 6.500000e-07 65.8
24 TraesCS1B01G304000 chr5B 98.077 728 14 0 1 728 572895856 572896583 0.000000e+00 1267.0
25 TraesCS1B01G304000 chr5B 82.336 702 119 3 31 731 245722458 245721761 3.100000e-169 604.0
26 TraesCS1B01G304000 chr5B 100.000 34 0 0 726 759 572896765 572896732 2.340000e-06 63.9
27 TraesCS1B01G304000 chr4B 96.986 730 20 1 1 728 599372000 599372729 0.000000e+00 1225.0
28 TraesCS1B01G304000 chr4B 100.000 34 0 0 726 759 599372911 599372878 2.340000e-06 63.9
29 TraesCS1B01G304000 chr3D 89.543 679 68 3 49 725 449332206 449332883 0.000000e+00 857.0
30 TraesCS1B01G304000 chrUn 94.621 409 21 1 320 728 74509462 74509869 1.420000e-177 632.0
31 TraesCS1B01G304000 chr6A 93.827 324 20 0 1 324 578167026 578167349 3.260000e-134 488.0
32 TraesCS1B01G304000 chr6A 100.000 28 0 0 1295 1322 33967424 33967451 5.000000e-03 52.8
33 TraesCS1B01G304000 chr7B 97.059 34 1 0 726 759 518337045 518337012 1.090000e-04 58.4
34 TraesCS1B01G304000 chr6D 100.000 28 0 0 1295 1322 28683277 28683250 5.000000e-03 52.8
35 TraesCS1B01G304000 chr2D 100.000 28 0 0 1295 1322 586571658 586571685 5.000000e-03 52.8
36 TraesCS1B01G304000 chr2D 100.000 28 0 0 1295 1322 586769319 586769346 5.000000e-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 TraesCS1B01G304000 chr1B 526259986 526262798 2812 True 5195.00 5195 100.000000 1 2813 1 chr1B.!!$R1 2812
1 TraesCS1B01G304000 chr1B 526271657 526272318 661 True 488.00 488 80.552000 998 1667 1 chr1B.!!$R2 669
2 TraesCS1B01G304000 chr1B 526290761 526291398 637 True 350.00 350 76.816000 1021 1661 1 chr1B.!!$R3 640
3 TraesCS1B01G304000 chr1D 394948792 394950602 1810 True 972.00 1352 87.997000 767 2360 2 chr1D.!!$R5 1593
4 TraesCS1B01G304000 chr1D 395054663 395055332 669 True 529.00 529 81.395000 998 1667 1 chr1D.!!$R2 669
5 TraesCS1B01G304000 chr1D 395409964 395410623 659 True 398.00 398 77.728000 998 1661 1 chr1D.!!$R4 663
6 TraesCS1B01G304000 chr1A 489286534 489289239 2705 True 765.00 1321 87.442333 767 2813 3 chr1A.!!$R2 2046
7 TraesCS1B01G304000 chr1A 489383009 489383672 663 True 496.00 496 80.556000 998 1667 1 chr1A.!!$R1 669
8 TraesCS1B01G304000 chr1A 489324175 489325619 1444 True 322.25 551 80.730500 998 2228 2 chr1A.!!$R3 1230
9 TraesCS1B01G304000 chr3A 519217814 519218541 727 True 1306.00 1306 99.038000 1 728 1 chr3A.!!$R1 727
10 TraesCS1B01G304000 chr3A 735708170 735708897 727 True 1123.00 1123 94.505000 1 728 1 chr3A.!!$R2 727
11 TraesCS1B01G304000 chr2B 118829028 118829755 727 True 1301.00 1301 98.901000 1 728 1 chr2B.!!$R1 727
12 TraesCS1B01G304000 chr6B 619401820 619402547 727 False 1290.00 1290 98.626000 1 728 1 chr6B.!!$F2 727
13 TraesCS1B01G304000 chr5B 572895856 572896583 727 False 1267.00 1267 98.077000 1 728 1 chr5B.!!$F1 727
14 TraesCS1B01G304000 chr5B 245721761 245722458 697 True 604.00 604 82.336000 31 731 1 chr5B.!!$R1 700
15 TraesCS1B01G304000 chr4B 599372000 599372729 729 False 1225.00 1225 96.986000 1 728 1 chr4B.!!$F1 727
16 TraesCS1B01G304000 chr3D 449332206 449332883 677 False 857.00 857 89.543000 49 725 1 chr3D.!!$F1 676

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
922 926 0.110509 TCGTTCCGTTCGTCTTCTCG 60.111 55.0 0.0 0.0 0.0 4.04 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2625 3430 1.003839 ATCAACCAAAGAGCGCCGA 60.004 52.632 2.29 0.0 0.0 5.54 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
294 295 1.647334 TTCACCGTTTGGACCCCCTT 61.647 55.000 0.00 0.00 39.21 3.95
654 656 7.382110 TCATAAGCCTTGCTCATATCTAGTTC 58.618 38.462 0.00 0.00 38.25 3.01
728 732 3.565764 TCTCATAAGCAAGGATGGTGG 57.434 47.619 0.00 0.00 37.35 4.61
731 735 4.130118 CTCATAAGCAAGGATGGTGGTAC 58.870 47.826 0.00 0.00 37.35 3.34
732 736 3.780294 TCATAAGCAAGGATGGTGGTACT 59.220 43.478 0.00 0.00 37.35 2.73
733 737 2.789409 AAGCAAGGATGGTGGTACTC 57.211 50.000 0.00 0.00 37.35 2.59
734 738 1.656587 AGCAAGGATGGTGGTACTCA 58.343 50.000 0.00 0.00 35.55 3.41
735 739 2.200081 AGCAAGGATGGTGGTACTCAT 58.800 47.619 0.00 0.00 35.55 2.90
736 740 2.171448 AGCAAGGATGGTGGTACTCATC 59.829 50.000 12.60 12.60 38.33 2.92
739 743 1.507140 GGATGGTGGTACTCATCCCA 58.493 55.000 21.76 11.58 46.11 4.37
740 744 1.843851 GGATGGTGGTACTCATCCCAA 59.156 52.381 21.76 0.00 46.11 4.12
741 745 2.241176 GGATGGTGGTACTCATCCCAAA 59.759 50.000 21.76 0.00 46.11 3.28
742 746 3.545703 GATGGTGGTACTCATCCCAAAG 58.454 50.000 10.92 0.00 35.14 2.77
743 747 1.633432 TGGTGGTACTCATCCCAAAGG 59.367 52.381 0.00 0.00 31.17 3.11
744 748 1.633945 GGTGGTACTCATCCCAAAGGT 59.366 52.381 0.00 0.00 31.17 3.50
745 749 2.041216 GGTGGTACTCATCCCAAAGGTT 59.959 50.000 0.00 0.00 31.17 3.50
746 750 3.344515 GTGGTACTCATCCCAAAGGTTC 58.655 50.000 0.00 0.00 31.17 3.62
747 751 2.027561 TGGTACTCATCCCAAAGGTTCG 60.028 50.000 0.00 0.00 0.00 3.95
748 752 2.629051 GTACTCATCCCAAAGGTTCGG 58.371 52.381 0.00 0.00 0.00 4.30
749 753 1.358152 ACTCATCCCAAAGGTTCGGA 58.642 50.000 0.00 0.00 0.00 4.55
750 754 1.702957 ACTCATCCCAAAGGTTCGGAA 59.297 47.619 0.00 0.00 0.00 4.30
751 755 2.084546 CTCATCCCAAAGGTTCGGAAC 58.915 52.381 12.41 12.41 0.00 3.62
760 764 0.908180 AGGTTCGGAACCCGGATCTT 60.908 55.000 31.05 12.26 44.67 2.40
761 765 2.845878 AGGTTCGGAACCCGGATCTTC 61.846 57.143 31.05 7.89 44.67 2.87
763 767 2.585247 CGGAACCCGGATCTTCGC 60.585 66.667 0.73 0.00 44.15 4.70
764 768 2.203029 GGAACCCGGATCTTCGCC 60.203 66.667 0.73 0.00 0.00 5.54
765 769 2.582436 GAACCCGGATCTTCGCCA 59.418 61.111 0.73 0.00 0.00 5.69
830 834 8.827177 TCAGTAATTTTGTAACGATTGAGACT 57.173 30.769 0.00 0.00 0.00 3.24
879 883 4.044426 GGCGCCAGATTGAAAATATGAAC 58.956 43.478 24.80 0.00 0.00 3.18
880 884 4.044426 GCGCCAGATTGAAAATATGAACC 58.956 43.478 0.00 0.00 0.00 3.62
881 885 4.282068 CGCCAGATTGAAAATATGAACCG 58.718 43.478 0.00 0.00 0.00 4.44
882 886 4.044426 GCCAGATTGAAAATATGAACCGC 58.956 43.478 0.00 0.00 0.00 5.68
922 926 0.110509 TCGTTCCGTTCGTCTTCTCG 60.111 55.000 0.00 0.00 0.00 4.04
1205 1213 2.435059 GCTCGGCTTCCTCCACAC 60.435 66.667 0.00 0.00 0.00 3.82
1254 1269 2.203182 ACCACGGACTTCCTCCCA 59.797 61.111 0.00 0.00 35.21 4.37
1334 1349 1.878734 CCTCCTCCGGTACTTCGATAC 59.121 57.143 0.00 0.00 0.00 2.24
1618 1649 5.287170 TGTTGAGATTGAAATCAGCTTCG 57.713 39.130 5.86 0.00 37.89 3.79
1638 1672 3.384789 TCGCTATGATGCCTAGTGTTCTT 59.615 43.478 0.00 0.00 0.00 2.52
1672 1706 3.181454 GCTCTATTTCCCCATTTCGAGGA 60.181 47.826 0.00 0.00 0.00 3.71
1679 1713 6.509523 TTTCCCCATTTCGAGGAACTATAT 57.490 37.500 2.75 0.00 41.55 0.86
1736 1788 2.743183 GCCTAGACATTCATCTGCCGTT 60.743 50.000 0.00 0.00 0.00 4.44
1739 1791 2.783135 AGACATTCATCTGCCGTTGTT 58.217 42.857 0.00 0.00 0.00 2.83
1740 1792 3.149196 AGACATTCATCTGCCGTTGTTT 58.851 40.909 0.00 0.00 0.00 2.83
1774 2454 2.725312 GCTCCATCGAGGGCACTGA 61.725 63.158 12.24 0.00 36.55 3.41
1821 2501 3.378427 TGGCACCTATATGATCGATCTCG 59.622 47.826 25.02 9.35 41.45 4.04
1898 2578 1.133136 TGGGCACTCTATCCCTACCTC 60.133 57.143 0.00 0.00 43.04 3.85
1922 2602 3.958798 GCTTCTACAGTCCACCAGGTATA 59.041 47.826 0.00 0.00 35.89 1.47
1925 2615 6.267014 GCTTCTACAGTCCACCAGGTATATTA 59.733 42.308 0.00 0.00 35.89 0.98
1926 2616 7.592885 TTCTACAGTCCACCAGGTATATTAC 57.407 40.000 0.00 0.00 35.89 1.89
1927 2617 6.919158 TCTACAGTCCACCAGGTATATTACT 58.081 40.000 0.00 0.00 35.89 2.24
1928 2618 8.049165 TCTACAGTCCACCAGGTATATTACTA 57.951 38.462 0.00 0.00 35.89 1.82
1975 2695 9.627123 TTTGGGAATATATTTCAGTTCTAGTGG 57.373 33.333 6.09 0.00 0.00 4.00
1976 2696 7.745717 TGGGAATATATTTCAGTTCTAGTGGG 58.254 38.462 6.09 0.00 0.00 4.61
1978 2698 8.606830 GGGAATATATTTCAGTTCTAGTGGGAT 58.393 37.037 6.09 0.00 0.00 3.85
2031 2751 6.206243 CCTTAAGATGCATGGTTTCATCCTAG 59.794 42.308 2.46 3.85 39.79 3.02
2038 2758 5.125900 TGCATGGTTTCATCCTAGTGAATTG 59.874 40.000 0.00 0.00 37.88 2.32
2045 2765 7.148239 GGTTTCATCCTAGTGAATTGGTACTTG 60.148 40.741 0.00 0.00 37.88 3.16
2073 2793 2.912956 TGGTTCTTCACTTAGCAGGGAT 59.087 45.455 0.00 0.00 30.17 3.85
2077 2797 2.700897 TCTTCACTTAGCAGGGATAGGC 59.299 50.000 0.00 0.00 30.17 3.93
2082 2802 1.412710 CTTAGCAGGGATAGGCGTTGA 59.587 52.381 0.00 0.00 34.54 3.18
2144 2864 2.223665 GCATAAATCTCAAGCAGGCCAC 60.224 50.000 5.01 0.00 0.00 5.01
2145 2865 3.285484 CATAAATCTCAAGCAGGCCACT 58.715 45.455 5.01 0.00 0.00 4.00
2149 2869 0.694771 TCTCAAGCAGGCCACTCAAT 59.305 50.000 5.01 0.00 0.00 2.57
2214 2938 4.523943 TGGGTTTTGAGTTTGATGGATGAG 59.476 41.667 0.00 0.00 0.00 2.90
2242 2966 7.095187 GGAGAGTTGTGTTATGTCTTGTTAAGG 60.095 40.741 0.00 0.00 0.00 2.69
2272 2996 5.639506 TCTCTGTTCTTGTTAAGCATGCTAC 59.360 40.000 23.00 17.17 0.00 3.58
2279 3003 7.880160 TCTTGTTAAGCATGCTACCAATATT 57.120 32.000 23.00 4.92 0.00 1.28
2283 3007 8.378172 TGTTAAGCATGCTACCAATATTCTAC 57.622 34.615 23.00 4.94 0.00 2.59
2284 3008 7.444183 TGTTAAGCATGCTACCAATATTCTACC 59.556 37.037 23.00 0.00 0.00 3.18
2285 3009 4.911390 AGCATGCTACCAATATTCTACCC 58.089 43.478 21.21 0.00 0.00 3.69
2287 3011 4.263506 GCATGCTACCAATATTCTACCCCT 60.264 45.833 11.37 0.00 0.00 4.79
2288 3012 4.974645 TGCTACCAATATTCTACCCCTG 57.025 45.455 0.00 0.00 0.00 4.45
2291 3085 5.248477 TGCTACCAATATTCTACCCCTGATC 59.752 44.000 0.00 0.00 0.00 2.92
2302 3096 5.219739 TCTACCCCTGATCTCATTAAAGCT 58.780 41.667 0.00 0.00 0.00 3.74
2304 3098 4.786425 ACCCCTGATCTCATTAAAGCTTC 58.214 43.478 0.00 0.00 0.00 3.86
2318 3114 1.613836 AGCTTCTGAAGGTTGCCTTG 58.386 50.000 15.86 0.00 44.82 3.61
2331 3127 4.892934 AGGTTGCCTTGTGTCTAAAAATCA 59.107 37.500 0.00 0.00 0.00 2.57
2361 3157 8.241471 CAAGTTTTGCGCGTAATAACTATAAG 57.759 34.615 24.95 16.59 0.00 1.73
2362 3158 7.529880 AGTTTTGCGCGTAATAACTATAAGT 57.470 32.000 24.13 11.01 0.00 2.24
2363 3159 7.967178 AGTTTTGCGCGTAATAACTATAAGTT 58.033 30.769 24.13 8.91 41.97 2.66
2364 3160 8.112449 AGTTTTGCGCGTAATAACTATAAGTTC 58.888 33.333 24.13 3.60 39.51 3.01
2365 3161 7.522901 TTTGCGCGTAATAACTATAAGTTCA 57.477 32.000 11.23 0.00 39.51 3.18
2366 3162 7.703298 TTGCGCGTAATAACTATAAGTTCAT 57.297 32.000 5.23 0.00 39.51 2.57
2367 3163 7.329438 TGCGCGTAATAACTATAAGTTCATC 57.671 36.000 8.43 0.00 39.51 2.92
2368 3164 7.143340 TGCGCGTAATAACTATAAGTTCATCT 58.857 34.615 8.43 0.00 39.51 2.90
2369 3165 7.325338 TGCGCGTAATAACTATAAGTTCATCTC 59.675 37.037 8.43 0.00 39.51 2.75
2370 3166 7.201333 GCGCGTAATAACTATAAGTTCATCTCC 60.201 40.741 8.43 0.00 39.51 3.71
2371 3167 7.806487 CGCGTAATAACTATAAGTTCATCTCCA 59.194 37.037 0.00 0.00 39.51 3.86
2372 3168 9.472361 GCGTAATAACTATAAGTTCATCTCCAA 57.528 33.333 0.00 0.00 39.51 3.53
2422 3218 2.352817 TGCAAACTGCCATGCATGA 58.647 47.368 28.31 8.14 46.87 3.07
2432 3229 1.159285 CCATGCATGAACGACACAGT 58.841 50.000 28.31 0.00 0.00 3.55
2437 3234 3.000041 TGCATGAACGACACAGTAATCC 59.000 45.455 0.00 0.00 0.00 3.01
2438 3235 3.000041 GCATGAACGACACAGTAATCCA 59.000 45.455 0.00 0.00 0.00 3.41
2439 3236 3.062639 GCATGAACGACACAGTAATCCAG 59.937 47.826 0.00 0.00 0.00 3.86
2443 3240 6.032956 TGAACGACACAGTAATCCAGTAAT 57.967 37.500 0.00 0.00 0.00 1.89
2467 3264 4.911390 AGAATCAACTTACCTCCTGTTGG 58.089 43.478 0.00 0.00 40.75 3.77
2468 3265 4.597507 AGAATCAACTTACCTCCTGTTGGA 59.402 41.667 0.00 0.00 40.75 3.53
2469 3266 4.993705 ATCAACTTACCTCCTGTTGGAA 57.006 40.909 0.00 0.00 42.66 3.53
2470 3267 4.351874 TCAACTTACCTCCTGTTGGAAG 57.648 45.455 0.00 0.00 42.66 3.46
2471 3268 3.714798 TCAACTTACCTCCTGTTGGAAGT 59.285 43.478 0.00 0.00 42.66 3.01
2472 3269 4.065789 CAACTTACCTCCTGTTGGAAGTC 58.934 47.826 0.00 0.00 42.66 3.01
2490 3289 2.092699 AGTCTTCCAGGGCTAATGCTTC 60.093 50.000 0.00 0.00 39.59 3.86
2515 3314 5.468072 AGCTATTCCGTGAACATGATGAATC 59.532 40.000 0.00 0.00 0.00 2.52
2550 3349 5.636123 TCCAACTTAAGCATGGGTTTAAGA 58.364 37.500 21.56 4.34 45.37 2.10
2552 3351 6.152661 TCCAACTTAAGCATGGGTTTAAGATG 59.847 38.462 21.56 13.15 45.37 2.90
2553 3352 6.071391 CCAACTTAAGCATGGGTTTAAGATGT 60.071 38.462 16.59 1.57 45.37 3.06
2554 3353 7.378181 CAACTTAAGCATGGGTTTAAGATGTT 58.622 34.615 15.00 1.54 45.37 2.71
2556 3355 6.493458 ACTTAAGCATGGGTTTAAGATGTTGT 59.507 34.615 15.00 0.00 45.37 3.32
2557 3356 5.391312 AAGCATGGGTTTAAGATGTTGTC 57.609 39.130 0.00 0.00 0.00 3.18
2559 3358 3.427503 GCATGGGTTTAAGATGTTGTCCG 60.428 47.826 0.00 0.00 0.00 4.79
2560 3359 3.495434 TGGGTTTAAGATGTTGTCCGT 57.505 42.857 0.00 0.00 0.00 4.69
2561 3360 3.822940 TGGGTTTAAGATGTTGTCCGTT 58.177 40.909 0.00 0.00 0.00 4.44
2625 3430 8.565416 GTTATTTGTTAAGCTACAGGTTTGTCT 58.435 33.333 0.00 0.00 38.76 3.41
2627 3432 4.304110 TGTTAAGCTACAGGTTTGTCTCG 58.696 43.478 0.00 0.00 38.76 4.04
2628 3433 2.457366 AAGCTACAGGTTTGTCTCGG 57.543 50.000 0.00 0.00 38.76 4.63
2629 3434 0.037232 AGCTACAGGTTTGTCTCGGC 60.037 55.000 0.00 0.00 38.76 5.54
2641 3446 1.667830 TCTCGGCGCTCTTTGGTTG 60.668 57.895 7.64 0.00 0.00 3.77
2644 3449 1.135315 CGGCGCTCTTTGGTTGATG 59.865 57.895 7.64 0.00 0.00 3.07
2647 3452 1.474077 GGCGCTCTTTGGTTGATGATT 59.526 47.619 7.64 0.00 0.00 2.57
2648 3453 2.478539 GGCGCTCTTTGGTTGATGATTC 60.479 50.000 7.64 0.00 0.00 2.52
2655 3460 5.481105 TCTTTGGTTGATGATTCAATTGGC 58.519 37.500 5.42 0.00 43.49 4.52
2672 3477 1.542472 TGGCTGTGTGCATCTTTGATG 59.458 47.619 0.00 3.42 45.15 3.07
2680 3485 5.817296 TGTGTGCATCTTTGATGTATAGGTC 59.183 40.000 8.98 0.00 0.00 3.85
2681 3486 5.817296 GTGTGCATCTTTGATGTATAGGTCA 59.183 40.000 8.98 0.00 0.00 4.02
2682 3487 6.018425 GTGTGCATCTTTGATGTATAGGTCAG 60.018 42.308 8.98 0.00 0.00 3.51
2683 3488 5.468072 GTGCATCTTTGATGTATAGGTCAGG 59.532 44.000 8.98 0.00 0.00 3.86
2684 3489 5.130975 TGCATCTTTGATGTATAGGTCAGGT 59.869 40.000 8.98 0.00 0.00 4.00
2700 3505 7.016153 AGGTCAGGTGTGAATTCTATTGTTA 57.984 36.000 7.05 0.00 33.27 2.41
2730 3535 6.800072 TGGTTTGGAAGGTTGTAAAGAATT 57.200 33.333 0.00 0.00 0.00 2.17
2731 3536 7.899648 TGGTTTGGAAGGTTGTAAAGAATTA 57.100 32.000 0.00 0.00 0.00 1.40
2733 3538 8.198778 TGGTTTGGAAGGTTGTAAAGAATTAAC 58.801 33.333 0.00 0.00 0.00 2.01
2735 3540 9.758651 GTTTGGAAGGTTGTAAAGAATTAACAT 57.241 29.630 0.00 0.00 0.00 2.71
2794 3599 5.997129 TGTGCTGTCATACAATCTTCAAGAA 59.003 36.000 0.00 0.00 0.00 2.52
2796 3601 7.175467 TGTGCTGTCATACAATCTTCAAGAATT 59.825 33.333 0.00 0.00 0.00 2.17
2797 3602 7.695618 GTGCTGTCATACAATCTTCAAGAATTC 59.304 37.037 0.00 0.00 0.00 2.17
2798 3603 7.391275 TGCTGTCATACAATCTTCAAGAATTCA 59.609 33.333 8.44 0.00 0.00 2.57
2799 3604 7.695618 GCTGTCATACAATCTTCAAGAATTCAC 59.304 37.037 8.44 0.00 0.00 3.18
2801 3606 7.148423 TGTCATACAATCTTCAAGAATTCACGG 60.148 37.037 8.44 0.00 0.00 4.94
2802 3607 7.064609 GTCATACAATCTTCAAGAATTCACGGA 59.935 37.037 8.44 0.00 0.00 4.69
2804 3609 6.187125 ACAATCTTCAAGAATTCACGGATG 57.813 37.500 8.44 4.72 0.00 3.51
2805 3610 4.889832 ATCTTCAAGAATTCACGGATGC 57.110 40.909 8.44 0.00 0.00 3.91
2806 3611 3.942829 TCTTCAAGAATTCACGGATGCT 58.057 40.909 8.44 0.00 0.00 3.79
2807 3612 3.935203 TCTTCAAGAATTCACGGATGCTC 59.065 43.478 8.44 0.00 0.00 4.26
2809 3614 1.328680 CAAGAATTCACGGATGCTCGG 59.671 52.381 8.44 0.00 0.00 4.63
2811 3616 1.066143 AGAATTCACGGATGCTCGGTT 60.066 47.619 8.44 0.00 0.00 4.44
2812 3617 1.062587 GAATTCACGGATGCTCGGTTG 59.937 52.381 0.00 0.00 0.00 3.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 4.262592 GGAAAGGGTTTTGTCTACTACCGA 60.263 45.833 0.00 0.00 0.00 4.69
15 16 5.067954 GCTTGGAAAGGGTTTTGTCTACTA 58.932 41.667 0.00 0.00 46.35 1.82
294 295 2.580962 TGGTGATGCAAGCAAGTGTTA 58.419 42.857 0.00 0.00 28.10 2.41
654 656 1.556911 AGGATGCTTATATGGCCCTCG 59.443 52.381 0.00 0.00 0.00 4.63
728 732 2.235402 TCCGAACCTTTGGGATGAGTAC 59.765 50.000 0.00 0.00 32.17 2.73
731 735 2.084546 GTTCCGAACCTTTGGGATGAG 58.915 52.381 0.00 0.00 37.40 2.90
732 736 2.194201 GTTCCGAACCTTTGGGATGA 57.806 50.000 0.00 0.00 37.40 2.92
747 751 2.203029 GGCGAAGATCCGGGTTCC 60.203 66.667 0.00 0.00 0.00 3.62
748 752 1.078708 TTGGCGAAGATCCGGGTTC 60.079 57.895 0.00 1.55 0.00 3.62
749 753 1.078426 CTTGGCGAAGATCCGGGTT 60.078 57.895 1.62 0.00 0.00 4.11
750 754 2.240162 GACTTGGCGAAGATCCGGGT 62.240 60.000 16.00 0.00 32.98 5.28
751 755 1.521681 GACTTGGCGAAGATCCGGG 60.522 63.158 16.00 0.00 32.98 5.73
752 756 1.521681 GGACTTGGCGAAGATCCGG 60.522 63.158 16.00 0.00 32.98 5.14
753 757 0.108138 AAGGACTTGGCGAAGATCCG 60.108 55.000 16.00 0.00 35.85 4.18
754 758 2.115343 AAAGGACTTGGCGAAGATCC 57.885 50.000 16.00 16.43 33.17 3.36
755 759 5.819825 ATAAAAAGGACTTGGCGAAGATC 57.180 39.130 16.00 8.68 32.98 2.75
756 760 7.881775 AATATAAAAAGGACTTGGCGAAGAT 57.118 32.000 16.00 0.00 32.98 2.40
757 761 7.696992 AAATATAAAAAGGACTTGGCGAAGA 57.303 32.000 16.00 0.00 32.98 2.87
758 762 8.026607 TCAAAATATAAAAAGGACTTGGCGAAG 58.973 33.333 6.95 6.95 35.07 3.79
759 763 7.887381 TCAAAATATAAAAAGGACTTGGCGAA 58.113 30.769 0.00 0.00 0.00 4.70
760 764 7.455641 TCAAAATATAAAAAGGACTTGGCGA 57.544 32.000 0.00 0.00 0.00 5.54
761 765 8.702163 AATCAAAATATAAAAAGGACTTGGCG 57.298 30.769 0.00 0.00 0.00 5.69
879 883 1.341369 GAAAATTTCGGCGGTTGCGG 61.341 55.000 7.21 0.00 44.10 5.69
880 884 0.386731 AGAAAATTTCGGCGGTTGCG 60.387 50.000 7.21 0.00 44.10 4.85
881 885 1.336877 GAGAAAATTTCGGCGGTTGC 58.663 50.000 7.21 0.00 41.71 4.17
882 886 1.602191 CGAGAAAATTTCGGCGGTTG 58.398 50.000 7.21 0.00 34.56 3.77
943 947 2.359975 GCTGCTAGGGTTGCGGTT 60.360 61.111 0.00 0.00 38.90 4.44
947 951 1.380380 AATGGGCTGCTAGGGTTGC 60.380 57.895 0.00 0.00 0.00 4.17
981 985 0.820074 TCGTTTGTGGCCGGTGATTT 60.820 50.000 1.90 0.00 0.00 2.17
982 986 0.608035 ATCGTTTGTGGCCGGTGATT 60.608 50.000 1.90 0.00 0.00 2.57
1074 1082 4.698625 AGGTTCCCGGGCTCGTCT 62.699 66.667 18.49 5.69 33.95 4.18
1164 1172 2.741211 GGCGTTCGGTGGAAGTCC 60.741 66.667 0.00 0.00 31.49 3.85
1216 1231 1.154150 GGACGAACTCGGTGTACGG 60.154 63.158 3.88 0.00 44.95 4.02
1217 1232 1.154150 GGGACGAACTCGGTGTACG 60.154 63.158 3.88 0.00 44.95 3.67
1218 1233 1.213799 GGGGACGAACTCGGTGTAC 59.786 63.158 3.88 0.00 44.95 2.90
1219 1234 1.228521 TGGGGACGAACTCGGTGTA 60.229 57.895 3.88 0.00 44.95 2.90
1220 1235 2.522436 TGGGGACGAACTCGGTGT 60.522 61.111 3.88 0.00 44.95 4.16
1221 1236 2.048503 GTGGGGACGAACTCGGTG 60.049 66.667 3.88 0.00 44.95 4.94
1254 1269 2.516460 AGTAGATCGGGCTCGCGT 60.516 61.111 0.00 0.00 36.13 6.01
1334 1349 3.554692 GCGGCATGTTCTCGTCCG 61.555 66.667 0.00 0.00 42.68 4.79
1338 1353 1.203928 CTAAGAGCGGCATGTTCTCG 58.796 55.000 1.45 0.00 37.13 4.04
1618 1649 4.446371 ACAAGAACACTAGGCATCATAGC 58.554 43.478 0.00 0.00 0.00 2.97
1638 1672 1.374343 AATAGAGCGCGTCTCCGACA 61.374 55.000 21.48 9.41 42.90 4.35
1708 1757 4.334759 CAGATGAATGTCTAGGCAGGTTTG 59.665 45.833 2.27 0.00 0.00 2.93
1710 1759 3.683847 GCAGATGAATGTCTAGGCAGGTT 60.684 47.826 2.27 0.00 0.00 3.50
1711 1760 2.158842 GCAGATGAATGTCTAGGCAGGT 60.159 50.000 2.27 0.00 0.00 4.00
1736 1788 1.292061 CGACCAACTCCGTTGAAACA 58.708 50.000 8.21 0.00 45.28 2.83
1739 1791 1.595929 GCCGACCAACTCCGTTGAA 60.596 57.895 8.21 0.00 45.28 2.69
1740 1792 2.029964 GCCGACCAACTCCGTTGA 59.970 61.111 8.21 0.00 45.28 3.18
1754 2434 4.899239 GTGCCCTCGATGGAGCCG 62.899 72.222 11.34 0.00 39.06 5.52
1774 2454 4.052159 TCCGTGATTGCAAAAACAATGT 57.948 36.364 1.71 0.00 40.31 2.71
1821 2501 3.258228 GCTCCTTCAAGCTTAGTGACTC 58.742 50.000 0.00 0.00 39.27 3.36
1867 2547 6.407525 GGGATAGAGTGCCCATGTAATATCTC 60.408 46.154 0.00 0.00 44.07 2.75
1898 2578 1.066573 CCTGGTGGACTGTAGAAGCTG 60.067 57.143 0.00 0.00 34.57 4.24
1928 2618 9.487790 CCCAAATCACAACTACATGTAAAAATT 57.512 29.630 7.06 0.00 30.84 1.82
1971 2691 9.975218 ACATTCACTACTTTATTTTATCCCACT 57.025 29.630 0.00 0.00 0.00 4.00
1986 2706 6.561519 AAGGCCTAATACACATTCACTACT 57.438 37.500 5.16 0.00 0.00 2.57
1988 2708 8.313944 TCTTAAGGCCTAATACACATTCACTA 57.686 34.615 5.16 0.00 0.00 2.74
2002 2722 3.951563 AACCATGCATCTTAAGGCCTA 57.048 42.857 5.16 0.00 0.00 3.93
2005 2725 4.500375 GGATGAAACCATGCATCTTAAGGC 60.500 45.833 0.00 0.00 40.49 4.35
2031 2751 6.981722 ACCAGATTTTCAAGTACCAATTCAC 58.018 36.000 0.00 0.00 0.00 3.18
2038 2758 6.486993 AGTGAAGAACCAGATTTTCAAGTACC 59.513 38.462 0.00 0.00 31.98 3.34
2045 2765 6.348868 CCTGCTAAGTGAAGAACCAGATTTTC 60.349 42.308 0.00 0.00 0.00 2.29
2073 2793 1.079127 GCTTCAGCCTCAACGCCTA 60.079 57.895 0.00 0.00 34.31 3.93
2077 2797 1.129998 CTTGATGCTTCAGCCTCAACG 59.870 52.381 13.61 8.03 45.88 4.10
2082 2802 2.434428 CTTCACTTGATGCTTCAGCCT 58.566 47.619 2.23 0.00 41.18 4.58
2144 2864 5.357314 AGCAATCTGAACTTCCATGATTGAG 59.643 40.000 21.10 7.31 43.68 3.02
2145 2865 5.124936 CAGCAATCTGAACTTCCATGATTGA 59.875 40.000 21.10 0.00 43.68 2.57
2149 2869 4.025040 ACAGCAATCTGAACTTCCATGA 57.975 40.909 0.00 0.00 42.95 3.07
2214 2938 3.983044 AGACATAACACAACTCTCCCC 57.017 47.619 0.00 0.00 0.00 4.81
2242 2966 4.449405 GCTTAACAAGAACAGAGACAGGTC 59.551 45.833 0.00 0.00 0.00 3.85
2272 2996 6.633325 ATGAGATCAGGGGTAGAATATTGG 57.367 41.667 0.00 0.00 0.00 3.16
2279 3003 5.219739 AGCTTTAATGAGATCAGGGGTAGA 58.780 41.667 0.00 0.00 0.00 2.59
2283 3007 4.820716 CAGAAGCTTTAATGAGATCAGGGG 59.179 45.833 0.00 0.00 0.00 4.79
2284 3008 5.678583 TCAGAAGCTTTAATGAGATCAGGG 58.321 41.667 0.00 0.00 0.00 4.45
2285 3009 6.260493 CCTTCAGAAGCTTTAATGAGATCAGG 59.740 42.308 0.00 5.98 0.00 3.86
2287 3011 6.715280 ACCTTCAGAAGCTTTAATGAGATCA 58.285 36.000 0.00 0.00 0.00 2.92
2288 3012 7.470900 CAACCTTCAGAAGCTTTAATGAGATC 58.529 38.462 0.00 0.00 0.00 2.75
2291 3085 5.397326 GCAACCTTCAGAAGCTTTAATGAG 58.603 41.667 0.00 0.00 0.00 2.90
2302 3096 2.092429 AGACACAAGGCAACCTTCAGAA 60.092 45.455 0.00 0.00 42.67 3.02
2304 3098 1.972872 AGACACAAGGCAACCTTCAG 58.027 50.000 0.00 0.00 42.67 3.02
2318 3114 7.755582 AAACTTGCAGTTGATTTTTAGACAC 57.244 32.000 2.88 0.00 38.66 3.67
2345 3141 7.806487 TGGAGATGAACTTATAGTTATTACGCG 59.194 37.037 3.53 3.53 38.80 6.01
2378 3174 5.852282 AGCAGTGTCCAAACATAGTTTTT 57.148 34.783 0.00 0.00 37.81 1.94
2379 3175 5.048713 GCTAGCAGTGTCCAAACATAGTTTT 60.049 40.000 10.63 0.00 37.81 2.43
2380 3176 4.455877 GCTAGCAGTGTCCAAACATAGTTT 59.544 41.667 10.63 0.00 37.81 2.66
2381 3177 4.003648 GCTAGCAGTGTCCAAACATAGTT 58.996 43.478 10.63 0.00 37.81 2.24
2382 3178 3.261897 AGCTAGCAGTGTCCAAACATAGT 59.738 43.478 18.83 0.00 37.81 2.12
2383 3179 3.620374 CAGCTAGCAGTGTCCAAACATAG 59.380 47.826 18.83 0.00 37.81 2.23
2386 3182 1.882912 CAGCTAGCAGTGTCCAAACA 58.117 50.000 18.83 0.00 0.00 2.83
2422 3218 6.032956 TCATTACTGGATTACTGTGTCGTT 57.967 37.500 0.00 0.00 33.02 3.85
2432 3229 9.832445 GGTAAGTTGATTCTCATTACTGGATTA 57.168 33.333 0.00 0.00 28.15 1.75
2437 3234 7.493971 CAGGAGGTAAGTTGATTCTCATTACTG 59.506 40.741 0.00 0.00 28.15 2.74
2438 3235 7.181125 ACAGGAGGTAAGTTGATTCTCATTACT 59.819 37.037 0.00 0.00 28.15 2.24
2439 3236 7.331791 ACAGGAGGTAAGTTGATTCTCATTAC 58.668 38.462 0.00 0.00 0.00 1.89
2443 3240 5.513094 CCAACAGGAGGTAAGTTGATTCTCA 60.513 44.000 6.13 0.00 43.93 3.27
2464 3261 6.928773 GCATTAGCCCTGGAAGACTTCCAA 62.929 50.000 31.68 19.46 46.80 3.53
2467 3264 2.092699 AGCATTAGCCCTGGAAGACTTC 60.093 50.000 6.66 6.66 43.56 3.01
2468 3265 1.918957 AGCATTAGCCCTGGAAGACTT 59.081 47.619 0.00 0.00 43.56 3.01
2469 3266 1.589414 AGCATTAGCCCTGGAAGACT 58.411 50.000 0.00 0.00 43.56 3.24
2470 3267 2.293170 GAAGCATTAGCCCTGGAAGAC 58.707 52.381 0.00 0.00 43.56 3.01
2471 3268 1.915489 TGAAGCATTAGCCCTGGAAGA 59.085 47.619 0.00 0.00 43.56 2.87
2472 3269 2.295885 CTGAAGCATTAGCCCTGGAAG 58.704 52.381 0.00 0.00 43.56 3.46
2490 3289 4.122046 TCATCATGTTCACGGAATAGCTG 58.878 43.478 0.00 0.00 0.00 4.24
2515 3314 6.582636 TGCTTAAGTTGGATCACATAGTAGG 58.417 40.000 4.02 0.00 0.00 3.18
2552 3351 1.658994 TCAAGTGGTCAACGGACAAC 58.341 50.000 0.00 0.00 46.55 3.32
2553 3352 2.631160 ATCAAGTGGTCAACGGACAA 57.369 45.000 0.00 0.00 46.17 3.18
2554 3353 3.755112 TTATCAAGTGGTCAACGGACA 57.245 42.857 0.00 0.00 46.17 4.02
2556 3355 4.647611 ACATTTATCAAGTGGTCAACGGA 58.352 39.130 0.00 0.00 0.00 4.69
2557 3356 5.371115 AACATTTATCAAGTGGTCAACGG 57.629 39.130 0.00 0.00 0.00 4.44
2559 3358 7.648142 TCTCAAACATTTATCAAGTGGTCAAC 58.352 34.615 0.00 0.00 0.00 3.18
2560 3359 7.815840 TCTCAAACATTTATCAAGTGGTCAA 57.184 32.000 0.00 0.00 0.00 3.18
2561 3360 9.685276 ATATCTCAAACATTTATCAAGTGGTCA 57.315 29.630 0.00 0.00 0.00 4.02
2592 3397 8.237267 CCTGTAGCTTAACAAATAACAGGAAAG 58.763 37.037 17.85 0.00 43.36 2.62
2625 3430 1.003839 ATCAACCAAAGAGCGCCGA 60.004 52.632 2.29 0.00 0.00 5.54
2627 3432 1.098050 ATCATCAACCAAAGAGCGCC 58.902 50.000 2.29 0.00 0.00 6.53
2628 3433 2.162208 TGAATCATCAACCAAAGAGCGC 59.838 45.455 0.00 0.00 30.99 5.92
2629 3434 4.424061 TTGAATCATCAACCAAAGAGCG 57.576 40.909 0.00 0.00 40.59 5.03
2641 3446 3.184541 GCACACAGCCAATTGAATCATC 58.815 45.455 7.12 0.00 37.23 2.92
2644 3449 2.728690 TGCACACAGCCAATTGAATC 57.271 45.000 7.12 0.00 44.83 2.52
2647 3452 1.913778 AGATGCACACAGCCAATTGA 58.086 45.000 7.12 0.00 44.83 2.57
2648 3453 2.734606 CAAAGATGCACACAGCCAATTG 59.265 45.455 0.00 0.00 44.83 2.32
2655 3460 5.819379 ACCTATACATCAAAGATGCACACAG 59.181 40.000 6.90 0.00 0.00 3.66
2672 3477 8.204836 ACAATAGAATTCACACCTGACCTATAC 58.795 37.037 8.44 0.00 0.00 1.47
2700 3505 7.604657 TTACAACCTTCCAAACCAATACAAT 57.395 32.000 0.00 0.00 0.00 2.71
2709 3514 9.758651 ATGTTAATTCTTTACAACCTTCCAAAC 57.241 29.630 0.00 0.00 0.00 2.93
2766 3571 4.627611 AGATTGTATGACAGCACATTGC 57.372 40.909 0.00 0.00 45.46 3.56
2767 3572 6.185852 TGAAGATTGTATGACAGCACATTG 57.814 37.500 0.00 0.00 0.00 2.82
2778 3583 7.307493 TCCGTGAATTCTTGAAGATTGTATG 57.693 36.000 7.05 0.00 0.00 2.39
2781 3586 5.392380 GCATCCGTGAATTCTTGAAGATTGT 60.392 40.000 7.05 0.00 0.00 2.71
2794 3599 2.767536 CAACCGAGCATCCGTGAAT 58.232 52.632 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.