Multiple sequence alignment - TraesCS6B01G364900

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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 TraesCS6B01G364900 chr6B 100.000 3468 0 0 1 3468 636586879 636583412 0.000000e+00 6405
1 TraesCS6B01G364900 chr6B 89.891 2740 158 71 599 3261 636491236 636493933 0.000000e+00 3415
2 TraesCS6B01G364900 chr6B 92.857 1372 81 12 1126 2487 614582251 614583615 0.000000e+00 1975
3 TraesCS6B01G364900 chr6B 92.847 1370 82 11 1126 2487 614311883 614313244 0.000000e+00 1973
4 TraesCS6B01G364900 chr6B 92.784 1372 82 12 1126 2487 614437193 614438557 0.000000e+00 1969
5 TraesCS6B01G364900 chr6B 83.062 307 27 11 787 1093 614311539 614311820 4.440000e-64 255
6 TraesCS6B01G364900 chr6B 83.062 307 26 12 787 1093 614436850 614437130 4.440000e-64 255
7 TraesCS6B01G364900 chr6B 80.053 376 36 17 731 1093 614581839 614582188 3.460000e-60 243
8 TraesCS6B01G364900 chr6B 86.667 195 17 3 34 224 636490374 636490563 1.260000e-49 207
9 TraesCS6B01G364900 chr6B 87.313 134 12 4 2498 2629 614583661 614583791 7.760000e-32 148
10 TraesCS6B01G364900 chr6D 91.054 2135 116 26 604 2699 422205830 422203732 0.000000e+00 2815
11 TraesCS6B01G364900 chr6D 90.645 2063 115 42 698 2712 422190423 422192455 0.000000e+00 2669
12 TraesCS6B01G364900 chr6D 87.611 565 46 5 2771 3320 422203523 422202968 4.880000e-178 634
13 TraesCS6B01G364900 chr6D 87.987 308 32 3 787 1093 409346574 409346877 3.290000e-95 359
14 TraesCS6B01G364900 chr6D 88.265 196 13 6 37 228 422206573 422206384 3.480000e-55 226
15 TraesCS6B01G364900 chr6D 90.756 119 7 4 2498 2614 409348607 409348723 4.630000e-34 156
16 TraesCS6B01G364900 chr6A 92.074 1842 97 19 681 2487 564911004 564909177 0.000000e+00 2547
17 TraesCS6B01G364900 chr6A 91.725 1861 98 31 657 2487 564974508 564976342 0.000000e+00 2532
18 TraesCS6B01G364900 chr6A 93.811 1341 72 7 1152 2487 554824781 554826115 0.000000e+00 2006
19 TraesCS6B01G364900 chr6A 86.612 859 71 18 2501 3320 564909125 564908272 0.000000e+00 909
20 TraesCS6B01G364900 chr6A 82.702 607 27 26 37 590 564911671 564911090 5.240000e-128 468
21 TraesCS6B01G364900 chr6A 84.021 388 35 11 726 1092 554824033 554824414 7.120000e-92 348
22 TraesCS6B01G364900 chr6A 94.836 213 10 1 2501 2712 564907834 564907622 7.170000e-87 331
23 TraesCS6B01G364900 chr6A 87.168 226 18 10 2498 2712 564976392 564976617 2.670000e-61 246
24 TraesCS6B01G364900 chr6A 83.200 250 20 7 34 266 564973737 564973981 3.510000e-50 209
25 TraesCS6B01G364900 chr6A 83.626 171 19 7 2498 2663 554826161 554826327 6.000000e-33 152
26 TraesCS6B01G364900 chrUn 87.582 153 17 1 3318 3468 409687727 409687575 3.560000e-40 176
27 TraesCS6B01G364900 chrUn 86.928 153 18 1 3318 3468 409689169 409689017 1.660000e-38 171
28 TraesCS6B01G364900 chr7D 87.582 153 17 2 3318 3468 416234233 416234081 3.560000e-40 176
29 TraesCS6B01G364900 chr7D 86.093 151 20 1 3319 3468 141135525 141135375 9.960000e-36 161
30 TraesCS6B01G364900 chr4D 87.417 151 18 1 3316 3465 64390468 64390618 4.600000e-39 172
31 TraesCS6B01G364900 chr3B 86.755 151 19 1 3319 3468 379305242 379305092 2.140000e-37 167
32 TraesCS6B01G364900 chr7B 85.535 159 21 2 3308 3465 611908953 611909110 7.700000e-37 165
33 TraesCS6B01G364900 chr4A 86.755 151 17 2 3316 3465 673962811 673962959 7.700000e-37 165
34 TraesCS6B01G364900 chr3A 86.577 149 19 1 3318 3465 600923077 600923225 2.770000e-36 163


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 TraesCS6B01G364900 chr6B 636583412 636586879 3467 True 6405.000000 6405 100.000000 1 3468 1 chr6B.!!$R1 3467
1 TraesCS6B01G364900 chr6B 636490374 636493933 3559 False 1811.000000 3415 88.279000 34 3261 2 chr6B.!!$F4 3227
2 TraesCS6B01G364900 chr6B 614311539 614313244 1705 False 1114.000000 1973 87.954500 787 2487 2 chr6B.!!$F1 1700
3 TraesCS6B01G364900 chr6B 614436850 614438557 1707 False 1112.000000 1969 87.923000 787 2487 2 chr6B.!!$F2 1700
4 TraesCS6B01G364900 chr6B 614581839 614583791 1952 False 788.666667 1975 86.741000 731 2629 3 chr6B.!!$F3 1898
5 TraesCS6B01G364900 chr6D 422190423 422192455 2032 False 2669.000000 2669 90.645000 698 2712 1 chr6D.!!$F1 2014
6 TraesCS6B01G364900 chr6D 422202968 422206573 3605 True 1225.000000 2815 88.976667 37 3320 3 chr6D.!!$R1 3283
7 TraesCS6B01G364900 chr6D 409346574 409348723 2149 False 257.500000 359 89.371500 787 2614 2 chr6D.!!$F2 1827
8 TraesCS6B01G364900 chr6A 564907622 564911671 4049 True 1063.750000 2547 89.056000 37 3320 4 chr6A.!!$R1 3283
9 TraesCS6B01G364900 chr6A 564973737 564976617 2880 False 995.666667 2532 87.364333 34 2712 3 chr6A.!!$F2 2678
10 TraesCS6B01G364900 chr6A 554824033 554826327 2294 False 835.333333 2006 87.152667 726 2663 3 chr6A.!!$F1 1937

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
171 179 0.030908 CCCGAGATAACGTCTCTGGC 59.969 60.0 5.41 0.0 46.87 4.85 F
694 1242 0.249398 CCCTAGCTAGTTTGGCGTGT 59.751 55.0 19.31 0.0 34.52 4.49 F
965 1582 0.467384 CCATCAGTTCTCCATCGCCT 59.533 55.0 0.00 0.0 0.00 5.52 F
1348 2328 0.938713 CGTCCAAGTACGGCAACAAA 59.061 50.0 0.00 0.0 39.19 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1123 1768 2.025898 TCAAAACTCGGTCCAAAACCC 58.974 47.619 0.00 0.0 46.27 4.11 R
2245 3240 0.676736 GGCGATCGATCTCCTCCTTT 59.323 55.000 24.13 0.0 0.00 3.11 R
2282 3277 1.200760 TCACTGTGTATGCCCTGCCT 61.201 55.000 7.79 0.0 0.00 4.75 R
2712 3760 1.878953 CCCCCTTTGGTCGATATTCG 58.121 55.000 0.00 0.0 42.10 3.34 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
19 20 2.831685 TCGTATCTTGTGTGGCACTT 57.168 45.000 19.83 0.00 35.11 3.16
20 21 3.945981 TCGTATCTTGTGTGGCACTTA 57.054 42.857 19.83 4.68 35.11 2.24
21 22 3.845178 TCGTATCTTGTGTGGCACTTAG 58.155 45.455 19.83 12.69 35.11 2.18
22 23 3.257375 TCGTATCTTGTGTGGCACTTAGT 59.743 43.478 19.83 2.90 35.11 2.24
23 24 4.460034 TCGTATCTTGTGTGGCACTTAGTA 59.540 41.667 19.83 2.10 35.11 1.82
24 25 4.798907 CGTATCTTGTGTGGCACTTAGTAG 59.201 45.833 19.83 8.97 35.11 2.57
25 26 3.678056 TCTTGTGTGGCACTTAGTAGG 57.322 47.619 19.83 3.06 35.11 3.18
26 27 3.236047 TCTTGTGTGGCACTTAGTAGGA 58.764 45.455 19.83 5.31 35.11 2.94
27 28 3.838317 TCTTGTGTGGCACTTAGTAGGAT 59.162 43.478 19.83 0.00 35.11 3.24
28 29 3.887621 TGTGTGGCACTTAGTAGGATC 57.112 47.619 19.83 0.00 35.11 3.36
29 30 2.500098 TGTGTGGCACTTAGTAGGATCC 59.500 50.000 19.83 2.48 35.11 3.36
30 31 2.766828 GTGTGGCACTTAGTAGGATCCT 59.233 50.000 20.48 20.48 0.00 3.24
31 32 3.958798 GTGTGGCACTTAGTAGGATCCTA 59.041 47.826 18.00 18.00 0.00 2.94
32 33 4.038162 GTGTGGCACTTAGTAGGATCCTAG 59.962 50.000 22.30 14.39 0.00 3.02
39 40 6.461788 GCACTTAGTAGGATCCTAGTTTCCTG 60.462 46.154 29.92 20.44 42.38 3.86
65 66 0.456824 CAGTGCAGCGTGACGTCTAT 60.457 55.000 17.92 0.00 0.00 1.98
93 97 1.988956 GGGCATGGTGGCAATTGGA 60.989 57.895 7.72 0.00 45.76 3.53
118 126 0.725784 CATCGGAAACACACTTGCGC 60.726 55.000 0.00 0.00 39.66 6.09
146 154 2.476619 AGTTGAGTCAGTTCGATTTGCG 59.523 45.455 0.00 0.00 42.69 4.85
156 164 3.122323 GATTTGCGTTCGCCCCGA 61.122 61.111 14.44 0.00 0.00 5.14
171 179 0.030908 CCCGAGATAACGTCTCTGGC 59.969 60.000 5.41 0.00 46.87 4.85
172 180 3.282867 CCCGAGATAACGTCTCTGGCC 62.283 61.905 0.00 0.00 46.87 5.36
313 590 1.609555 CTGCGACATACTCCTACCCTC 59.390 57.143 0.00 0.00 0.00 4.30
314 591 1.064240 TGCGACATACTCCTACCCTCA 60.064 52.381 0.00 0.00 0.00 3.86
315 592 1.337387 GCGACATACTCCTACCCTCAC 59.663 57.143 0.00 0.00 0.00 3.51
316 593 1.602851 CGACATACTCCTACCCTCACG 59.397 57.143 0.00 0.00 0.00 4.35
317 594 2.744166 CGACATACTCCTACCCTCACGA 60.744 54.545 0.00 0.00 0.00 4.35
318 595 3.488363 GACATACTCCTACCCTCACGAT 58.512 50.000 0.00 0.00 0.00 3.73
331 608 3.254060 CCTCACGATCACGAACTGAATT 58.746 45.455 0.00 0.00 42.66 2.17
366 708 4.508551 TGAATACTCGGACTGGGTACTA 57.491 45.455 0.00 0.00 0.00 1.82
367 709 4.202441 TGAATACTCGGACTGGGTACTAC 58.798 47.826 0.00 0.00 0.00 2.73
368 710 4.080129 TGAATACTCGGACTGGGTACTACT 60.080 45.833 0.00 0.00 0.00 2.57
371 713 2.015587 CTCGGACTGGGTACTACTCAC 58.984 57.143 0.00 0.00 0.00 3.51
372 714 1.101331 CGGACTGGGTACTACTCACC 58.899 60.000 0.00 0.00 35.15 4.02
529 916 1.207329 GCCCCTGATCTTACGAACTGT 59.793 52.381 0.00 0.00 0.00 3.55
563 962 1.375908 GACCCTCATTGCAGTGCGA 60.376 57.895 7.70 7.70 0.00 5.10
590 989 4.881850 AGCCGAAACCTTTTCGATTGATAT 59.118 37.500 19.82 0.00 43.97 1.63
591 990 5.007724 AGCCGAAACCTTTTCGATTGATATC 59.992 40.000 19.82 0.00 43.97 1.63
594 1027 5.896432 CGAAACCTTTTCGATTGATATCACG 59.104 40.000 14.39 7.15 43.97 4.35
596 1029 3.560068 ACCTTTTCGATTGATATCACGCC 59.440 43.478 4.48 0.00 0.00 5.68
597 1030 3.058914 CCTTTTCGATTGATATCACGCCC 60.059 47.826 4.48 0.00 0.00 6.13
633 1080 1.805120 GCTCGTAACCACACACACACT 60.805 52.381 0.00 0.00 0.00 3.55
634 1081 2.544277 GCTCGTAACCACACACACACTA 60.544 50.000 0.00 0.00 0.00 2.74
635 1082 3.859627 GCTCGTAACCACACACACACTAT 60.860 47.826 0.00 0.00 0.00 2.12
636 1083 4.304110 CTCGTAACCACACACACACTATT 58.696 43.478 0.00 0.00 0.00 1.73
637 1084 4.300803 TCGTAACCACACACACACTATTC 58.699 43.478 0.00 0.00 0.00 1.75
640 1087 3.788227 ACCACACACACACTATTCCAT 57.212 42.857 0.00 0.00 0.00 3.41
681 1229 3.349927 ACGGTGTTTATTTTCCCCTAGC 58.650 45.455 0.00 0.00 0.00 3.42
683 1231 4.225717 ACGGTGTTTATTTTCCCCTAGCTA 59.774 41.667 0.00 0.00 0.00 3.32
685 1233 5.628433 CGGTGTTTATTTTCCCCTAGCTAGT 60.628 44.000 19.31 1.63 0.00 2.57
687 1235 6.662234 GGTGTTTATTTTCCCCTAGCTAGTTT 59.338 38.462 19.31 0.00 0.00 2.66
688 1236 7.362660 GGTGTTTATTTTCCCCTAGCTAGTTTG 60.363 40.741 19.31 7.44 0.00 2.93
689 1237 6.661805 TGTTTATTTTCCCCTAGCTAGTTTGG 59.338 38.462 19.31 15.59 0.00 3.28
690 1238 2.801077 TTTCCCCTAGCTAGTTTGGC 57.199 50.000 19.31 0.00 0.00 4.52
691 1239 0.539986 TTCCCCTAGCTAGTTTGGCG 59.460 55.000 19.31 7.98 34.52 5.69
692 1240 0.616679 TCCCCTAGCTAGTTTGGCGT 60.617 55.000 19.31 0.00 34.52 5.68
693 1241 0.462047 CCCCTAGCTAGTTTGGCGTG 60.462 60.000 19.31 1.49 34.52 5.34
694 1242 0.249398 CCCTAGCTAGTTTGGCGTGT 59.751 55.000 19.31 0.00 34.52 4.49
695 1243 1.359848 CCTAGCTAGTTTGGCGTGTG 58.640 55.000 19.31 0.00 34.52 3.82
696 1244 1.067142 CCTAGCTAGTTTGGCGTGTGA 60.067 52.381 19.31 0.00 34.52 3.58
937 1554 1.064003 AATACCTGGCCAGACACACA 58.936 50.000 34.91 11.92 0.00 3.72
963 1580 2.540265 ATCCATCAGTTCTCCATCGC 57.460 50.000 0.00 0.00 0.00 4.58
965 1582 0.467384 CCATCAGTTCTCCATCGCCT 59.533 55.000 0.00 0.00 0.00 5.52
983 1600 1.538950 CCTTCTTCCAAAGCACAGCTC 59.461 52.381 0.00 0.00 38.25 4.09
1144 2120 3.074504 GGTTTTGGACCGAGTTTTGAC 57.925 47.619 0.00 0.00 39.00 3.18
1153 2133 2.158957 ACCGAGTTTTGACTTCTGCTGA 60.159 45.455 0.00 0.00 0.00 4.26
1192 2172 1.228657 GGGAGTCGTGGAAGCACAAC 61.229 60.000 0.00 0.00 0.00 3.32
1348 2328 0.938713 CGTCCAAGTACGGCAACAAA 59.061 50.000 0.00 0.00 39.19 2.83
2152 3138 7.653713 TCATCGTATCTAAATTGCTCTTCTTCC 59.346 37.037 0.00 0.00 0.00 3.46
2178 3173 9.289303 CTTTTTCGTTCATATAAGAAACCATGG 57.711 33.333 11.19 11.19 33.06 3.66
2245 3240 1.209504 CATTTCTTCGACTGGGGCCTA 59.790 52.381 0.84 0.00 0.00 3.93
2282 3277 1.555075 GCCTAGTGTCAATCAGGACCA 59.445 52.381 0.00 0.00 36.97 4.02
2449 3444 1.442769 CACACGGCAAAGACTATGCT 58.557 50.000 0.00 0.00 43.34 3.79
2614 3653 5.938125 AGTGTTTTCGCTACTCATGGTTTAT 59.062 36.000 0.00 0.00 39.04 1.40
2643 3682 3.619729 TCGTTGACCAAAAATTGCGTAC 58.380 40.909 0.00 0.00 0.00 3.67
2721 3769 2.832563 TGCCTTTGCATCGAATATCGA 58.167 42.857 4.80 4.80 44.54 3.59
2722 3770 2.543848 TGCCTTTGCATCGAATATCGAC 59.456 45.455 4.39 0.00 42.95 4.20
2723 3771 4.596269 TGCCTTTGCATCGAATATCGACC 61.596 47.826 4.39 0.49 42.95 4.79
2764 3836 6.040391 TGAATGGGAACTTCGACAATTTCTTT 59.960 34.615 0.00 0.00 0.00 2.52
2766 3838 6.554334 TGGGAACTTCGACAATTTCTTTAG 57.446 37.500 0.00 0.00 0.00 1.85
2805 3991 7.658179 TGAGCAAAAACAGAGTACATAGAAG 57.342 36.000 0.00 0.00 0.00 2.85
2808 3994 8.089115 AGCAAAAACAGAGTACATAGAAGAAC 57.911 34.615 0.00 0.00 0.00 3.01
2810 3996 9.204570 GCAAAAACAGAGTACATAGAAGAACTA 57.795 33.333 0.00 0.00 35.42 2.24
2895 4102 5.006552 GCAATGCACACAAAACTAAACATGT 59.993 36.000 0.00 0.00 0.00 3.21
2939 4146 3.125829 GTGCTCAAAATCATCTTCGCAGA 59.874 43.478 0.00 0.00 0.00 4.26
2940 4147 3.752747 TGCTCAAAATCATCTTCGCAGAA 59.247 39.130 0.00 0.00 45.90 3.02
2941 4148 4.216042 TGCTCAAAATCATCTTCGCAGAAA 59.784 37.500 0.00 0.00 45.90 2.52
2942 4149 5.106038 TGCTCAAAATCATCTTCGCAGAAAT 60.106 36.000 0.00 0.00 45.90 2.17
2943 4150 5.454877 GCTCAAAATCATCTTCGCAGAAATC 59.545 40.000 0.00 0.00 45.90 2.17
2944 4151 6.499234 TCAAAATCATCTTCGCAGAAATCA 57.501 33.333 0.00 0.00 45.90 2.57
2945 4152 6.317088 TCAAAATCATCTTCGCAGAAATCAC 58.683 36.000 0.00 0.00 45.90 3.06
2946 4153 5.885230 AAATCATCTTCGCAGAAATCACA 57.115 34.783 0.00 0.00 45.90 3.58
2947 4154 5.885230 AATCATCTTCGCAGAAATCACAA 57.115 34.783 0.00 0.00 45.90 3.33
2950 4157 4.152938 TCATCTTCGCAGAAATCACAACAG 59.847 41.667 0.00 0.00 45.90 3.16
2986 4202 1.900486 ACGGGGAGAAGTTCTTCGAAT 59.100 47.619 22.15 3.43 0.00 3.34
3003 4219 3.245048 TCGAATGCATGCACGTTACATAG 59.755 43.478 25.37 7.17 0.00 2.23
3071 4291 4.020573 ACATAGATTTGTTCGACCAGTCCA 60.021 41.667 0.00 0.00 0.00 4.02
3079 4299 1.334160 TCGACCAGTCCAAGTTGCTA 58.666 50.000 0.00 0.00 0.00 3.49
3188 4409 0.994995 CTTCGCTCAATCACTCGTGG 59.005 55.000 0.00 0.00 0.00 4.94
3196 4417 4.791411 GCTCAATCACTCGTGGTAGATCTC 60.791 50.000 0.00 0.00 0.00 2.75
3200 4421 2.014857 CACTCGTGGTAGATCTCCGAA 58.985 52.381 0.00 0.00 0.00 4.30
3261 4495 2.885266 TCAGACGCTTAGAACAGACACT 59.115 45.455 0.00 0.00 0.00 3.55
3263 4497 3.426859 CAGACGCTTAGAACAGACACTTG 59.573 47.826 0.00 0.00 0.00 3.16
3274 4508 6.010850 AGAACAGACACTTGACCATCTAGTA 58.989 40.000 0.00 0.00 30.99 1.82
3275 4509 6.493802 AGAACAGACACTTGACCATCTAGTAA 59.506 38.462 0.00 0.00 30.99 2.24
3305 4539 7.926555 CACGATCCACAAGAGTAATAGGTTAAT 59.073 37.037 0.00 0.00 0.00 1.40
3332 4566 9.877178 TTAATTCTCAACTACTCTCTCCATTTC 57.123 33.333 0.00 0.00 0.00 2.17
3333 4567 7.732222 ATTCTCAACTACTCTCTCCATTTCT 57.268 36.000 0.00 0.00 0.00 2.52
3334 4568 8.830915 ATTCTCAACTACTCTCTCCATTTCTA 57.169 34.615 0.00 0.00 0.00 2.10
3335 4569 8.651589 TTCTCAACTACTCTCTCCATTTCTAA 57.348 34.615 0.00 0.00 0.00 2.10
3336 4570 8.651589 TCTCAACTACTCTCTCCATTTCTAAA 57.348 34.615 0.00 0.00 0.00 1.85
3337 4571 8.524487 TCTCAACTACTCTCTCCATTTCTAAAC 58.476 37.037 0.00 0.00 0.00 2.01
3342 4576 8.474025 ACTACTCTCTCCATTTCTAAACATCAG 58.526 37.037 0.00 0.00 0.00 2.90
3344 4578 7.327214 ACTCTCTCCATTTCTAAACATCAGTC 58.673 38.462 0.00 0.00 0.00 3.51
3345 4579 7.180051 ACTCTCTCCATTTCTAAACATCAGTCT 59.820 37.037 0.00 0.00 0.00 3.24
3346 4580 7.911651 TCTCTCCATTTCTAAACATCAGTCTT 58.088 34.615 0.00 0.00 0.00 3.01
3347 4581 8.378565 TCTCTCCATTTCTAAACATCAGTCTTT 58.621 33.333 0.00 0.00 0.00 2.52
3348 4582 8.924511 TCTCCATTTCTAAACATCAGTCTTTT 57.075 30.769 0.00 0.00 0.00 2.27
3365 4599 8.163408 TCAGTCTTTTAGAGATTTCAATTGGGA 58.837 33.333 5.42 0.00 36.61 4.37
3366 4600 8.239998 CAGTCTTTTAGAGATTTCAATTGGGAC 58.760 37.037 5.42 0.00 36.61 4.46
3368 4602 9.449719 GTCTTTTAGAGATTTCAATTGGGACTA 57.550 33.333 5.42 0.00 36.61 2.59
3369 4603 9.449719 TCTTTTAGAGATTTCAATTGGGACTAC 57.550 33.333 5.42 0.00 0.00 2.73
3370 4604 9.231297 CTTTTAGAGATTTCAATTGGGACTACA 57.769 33.333 5.42 0.00 0.00 2.74
3371 4605 9.753674 TTTTAGAGATTTCAATTGGGACTACAT 57.246 29.630 5.42 0.00 0.00 2.29
3374 4608 7.861629 AGAGATTTCAATTGGGACTACATACA 58.138 34.615 5.42 0.00 0.00 2.29
3375 4609 7.989741 AGAGATTTCAATTGGGACTACATACAG 59.010 37.037 5.42 0.00 0.00 2.74
3376 4610 7.861629 AGATTTCAATTGGGACTACATACAGA 58.138 34.615 5.42 0.00 0.00 3.41
3378 4612 7.864108 TTTCAATTGGGACTACATACAGATG 57.136 36.000 5.42 0.00 39.16 2.90
3380 4614 7.669089 TCAATTGGGACTACATACAGATGTA 57.331 36.000 5.42 0.00 44.77 2.29
3381 4615 8.262601 TCAATTGGGACTACATACAGATGTAT 57.737 34.615 5.42 0.00 45.42 2.29
3382 4616 9.374711 TCAATTGGGACTACATACAGATGTATA 57.625 33.333 5.42 0.00 45.42 1.47
3419 4653 7.934855 AGAGTGTAGATTCATTCATTTTGCT 57.065 32.000 0.00 0.00 0.00 3.91
3421 4655 9.624373 AGAGTGTAGATTCATTCATTTTGCTAT 57.376 29.630 0.00 0.00 0.00 2.97
3422 4656 9.661187 GAGTGTAGATTCATTCATTTTGCTATG 57.339 33.333 0.00 0.00 0.00 2.23
3423 4657 9.182214 AGTGTAGATTCATTCATTTTGCTATGT 57.818 29.630 0.00 0.00 0.00 2.29
3428 4662 8.635328 AGATTCATTCATTTTGCTATGTATGCA 58.365 29.630 0.00 0.00 34.90 3.96
3441 4675 9.737844 TTGCTATGTATGCAATCCATATTAGAA 57.262 29.630 0.00 0.00 44.24 2.10
3442 4676 9.910267 TGCTATGTATGCAATCCATATTAGAAT 57.090 29.630 0.00 0.00 38.60 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.831685 AAGTGCCACACAAGATACGA 57.168 45.000 0.00 0.00 36.74 3.43
1 2 3.585862 ACTAAGTGCCACACAAGATACG 58.414 45.455 0.00 0.00 36.74 3.06
2 3 5.105473 TCCTACTAAGTGCCACACAAGATAC 60.105 44.000 0.00 0.00 36.74 2.24
3 4 5.020795 TCCTACTAAGTGCCACACAAGATA 58.979 41.667 0.00 0.00 36.74 1.98
4 5 3.838317 TCCTACTAAGTGCCACACAAGAT 59.162 43.478 0.00 0.00 36.74 2.40
5 6 3.236047 TCCTACTAAGTGCCACACAAGA 58.764 45.455 0.00 0.00 36.74 3.02
6 7 3.678056 TCCTACTAAGTGCCACACAAG 57.322 47.619 0.00 0.13 36.74 3.16
7 8 3.055385 GGATCCTACTAAGTGCCACACAA 60.055 47.826 3.84 0.00 36.74 3.33
8 9 2.500098 GGATCCTACTAAGTGCCACACA 59.500 50.000 3.84 0.00 36.74 3.72
9 10 2.766828 AGGATCCTACTAAGTGCCACAC 59.233 50.000 14.27 0.00 34.10 3.82
10 11 3.116096 AGGATCCTACTAAGTGCCACA 57.884 47.619 14.27 0.00 0.00 4.17
11 12 4.216708 ACTAGGATCCTACTAAGTGCCAC 58.783 47.826 18.00 0.00 0.00 5.01
12 13 4.537945 ACTAGGATCCTACTAAGTGCCA 57.462 45.455 18.00 0.00 0.00 4.92
13 14 5.221481 GGAAACTAGGATCCTACTAAGTGCC 60.221 48.000 18.00 15.66 32.75 5.01
14 15 5.599242 AGGAAACTAGGATCCTACTAAGTGC 59.401 44.000 18.00 11.15 44.24 4.40
15 16 6.041069 CCAGGAAACTAGGATCCTACTAAGTG 59.959 46.154 18.00 9.45 44.26 3.16
16 17 6.068379 TCCAGGAAACTAGGATCCTACTAAGT 60.068 42.308 18.00 13.04 44.26 2.24
17 18 6.374588 TCCAGGAAACTAGGATCCTACTAAG 58.625 44.000 18.00 12.36 44.26 2.18
18 19 6.351317 TCCAGGAAACTAGGATCCTACTAA 57.649 41.667 18.00 0.00 44.26 2.24
19 20 6.351317 TTCCAGGAAACTAGGATCCTACTA 57.649 41.667 18.00 0.00 44.26 1.82
20 21 4.901785 TCCAGGAAACTAGGATCCTACT 57.098 45.455 18.00 10.02 44.26 2.57
21 22 7.070821 TGTTATTCCAGGAAACTAGGATCCTAC 59.929 40.741 18.00 7.93 44.26 3.18
22 23 7.136885 TGTTATTCCAGGAAACTAGGATCCTA 58.863 38.462 20.53 20.53 44.26 2.94
24 25 6.126739 ACTGTTATTCCAGGAAACTAGGATCC 60.127 42.308 5.81 2.48 40.21 3.36
25 26 6.763610 CACTGTTATTCCAGGAAACTAGGATC 59.236 42.308 5.81 0.00 40.21 3.36
26 27 6.653989 CACTGTTATTCCAGGAAACTAGGAT 58.346 40.000 5.81 0.00 40.21 3.24
27 28 5.570844 GCACTGTTATTCCAGGAAACTAGGA 60.571 44.000 5.81 0.00 40.21 2.94
28 29 4.636206 GCACTGTTATTCCAGGAAACTAGG 59.364 45.833 5.81 0.00 40.21 3.02
29 30 5.245531 TGCACTGTTATTCCAGGAAACTAG 58.754 41.667 5.81 5.39 40.21 2.57
30 31 5.235850 TGCACTGTTATTCCAGGAAACTA 57.764 39.130 5.81 0.00 40.21 2.24
31 32 4.074970 CTGCACTGTTATTCCAGGAAACT 58.925 43.478 5.81 0.00 46.44 2.66
32 33 3.366374 GCTGCACTGTTATTCCAGGAAAC 60.366 47.826 5.81 1.11 36.75 2.78
39 40 1.128692 GTCACGCTGCACTGTTATTCC 59.871 52.381 0.00 0.00 0.00 3.01
65 66 1.489481 CACCATGCCCTCTAGAGTCA 58.511 55.000 18.42 15.14 0.00 3.41
93 97 3.703001 AGTGTGTTTCCGATGGAGATT 57.297 42.857 0.00 0.00 31.21 2.40
118 126 4.112634 TCGAACTGACTCAACTGAACAAG 58.887 43.478 0.00 0.00 0.00 3.16
146 154 0.869028 GACGTTATCTCGGGGCGAAC 60.869 60.000 0.00 0.00 34.74 3.95
156 164 0.461961 GCTGGCCAGAGACGTTATCT 59.538 55.000 37.21 0.00 41.91 1.98
313 590 3.920412 TGAGAATTCAGTTCGTGATCGTG 59.080 43.478 8.44 0.00 41.84 4.35
314 591 4.174411 TGAGAATTCAGTTCGTGATCGT 57.826 40.909 8.44 0.00 41.84 3.73
315 592 4.085873 CGATGAGAATTCAGTTCGTGATCG 60.086 45.833 8.44 3.13 41.84 3.69
316 593 5.037385 TCGATGAGAATTCAGTTCGTGATC 58.963 41.667 17.65 2.91 41.84 2.92
317 594 4.998788 TCGATGAGAATTCAGTTCGTGAT 58.001 39.130 17.65 0.00 41.84 3.06
318 595 4.434713 TCGATGAGAATTCAGTTCGTGA 57.565 40.909 17.65 2.63 41.84 4.35
331 608 5.205565 CGAGTATTCATTCGTTCGATGAGA 58.794 41.667 0.00 0.00 32.44 3.27
366 708 5.880901 ACTGGACATAAATTTCTGGTGAGT 58.119 37.500 8.28 3.97 0.00 3.41
367 709 6.824305 AACTGGACATAAATTTCTGGTGAG 57.176 37.500 8.28 3.46 0.00 3.51
368 710 7.595819 AAAACTGGACATAAATTTCTGGTGA 57.404 32.000 8.28 0.00 0.00 4.02
371 713 7.915397 CGGATAAAACTGGACATAAATTTCTGG 59.085 37.037 8.28 0.00 0.00 3.86
372 714 7.432252 GCGGATAAAACTGGACATAAATTTCTG 59.568 37.037 0.00 0.00 0.00 3.02
374 716 6.695713 GGCGGATAAAACTGGACATAAATTTC 59.304 38.462 0.00 0.00 0.00 2.17
375 717 6.379988 AGGCGGATAAAACTGGACATAAATTT 59.620 34.615 0.00 0.00 0.00 1.82
376 718 5.891551 AGGCGGATAAAACTGGACATAAATT 59.108 36.000 0.00 0.00 0.00 1.82
529 916 2.092646 AGGGTCAGTTGTGCTGTAACAA 60.093 45.455 0.00 0.00 45.23 2.83
563 962 2.567985 TCGAAAAGGTTTCGGCTTTCT 58.432 42.857 19.61 0.00 41.78 2.52
590 989 2.161855 TCGTCTACTAAAAGGGCGTGA 58.838 47.619 0.00 0.00 0.00 4.35
591 990 2.642139 TCGTCTACTAAAAGGGCGTG 57.358 50.000 0.00 0.00 0.00 5.34
594 1027 2.158943 AGCCATCGTCTACTAAAAGGGC 60.159 50.000 0.00 0.00 39.14 5.19
596 1029 3.372954 CGAGCCATCGTCTACTAAAAGG 58.627 50.000 0.00 0.00 44.09 3.11
633 1080 7.122650 CCTTTCTAGCAGTGGAAAAATGGAATA 59.877 37.037 0.00 0.00 33.19 1.75
634 1081 6.071165 CCTTTCTAGCAGTGGAAAAATGGAAT 60.071 38.462 0.00 0.00 33.19 3.01
635 1082 5.243730 CCTTTCTAGCAGTGGAAAAATGGAA 59.756 40.000 0.00 0.00 33.19 3.53
636 1083 4.766891 CCTTTCTAGCAGTGGAAAAATGGA 59.233 41.667 0.00 0.00 33.19 3.41
637 1084 4.766891 TCCTTTCTAGCAGTGGAAAAATGG 59.233 41.667 0.00 0.00 33.19 3.16
640 1087 3.813166 CGTCCTTTCTAGCAGTGGAAAAA 59.187 43.478 0.00 0.00 33.19 1.94
681 1229 2.061773 CTCACTCACACGCCAAACTAG 58.938 52.381 0.00 0.00 0.00 2.57
683 1231 0.178068 ACTCACTCACACGCCAAACT 59.822 50.000 0.00 0.00 0.00 2.66
685 1233 1.134521 AGAACTCACTCACACGCCAAA 60.135 47.619 0.00 0.00 0.00 3.28
687 1235 0.249447 CAGAACTCACTCACACGCCA 60.249 55.000 0.00 0.00 0.00 5.69
688 1236 0.032130 TCAGAACTCACTCACACGCC 59.968 55.000 0.00 0.00 0.00 5.68
689 1237 1.413382 CTCAGAACTCACTCACACGC 58.587 55.000 0.00 0.00 0.00 5.34
690 1238 1.609072 TCCTCAGAACTCACTCACACG 59.391 52.381 0.00 0.00 0.00 4.49
691 1239 3.735237 TTCCTCAGAACTCACTCACAC 57.265 47.619 0.00 0.00 0.00 3.82
692 1240 4.590647 AGAATTCCTCAGAACTCACTCACA 59.409 41.667 0.65 0.00 30.53 3.58
693 1241 5.146010 AGAATTCCTCAGAACTCACTCAC 57.854 43.478 0.65 0.00 30.53 3.51
694 1242 4.835056 TGAGAATTCCTCAGAACTCACTCA 59.165 41.667 0.65 0.00 46.38 3.41
695 1243 5.398603 TGAGAATTCCTCAGAACTCACTC 57.601 43.478 0.65 0.00 46.38 3.51
738 1286 2.435234 GCACCGGCCAATACGACA 60.435 61.111 0.00 0.00 0.00 4.35
759 1311 1.680522 GGAGCCAGCCTTCGATGAGA 61.681 60.000 0.00 0.00 0.00 3.27
963 1580 1.538950 GAGCTGTGCTTTGGAAGAAGG 59.461 52.381 0.00 0.00 39.88 3.46
965 1582 1.229428 CGAGCTGTGCTTTGGAAGAA 58.771 50.000 0.00 0.00 39.88 2.52
1123 1768 2.025898 TCAAAACTCGGTCCAAAACCC 58.974 47.619 0.00 0.00 46.27 4.11
1144 2120 2.357881 TGCCGCACTCAGCAGAAG 60.358 61.111 0.00 0.00 46.13 2.85
1153 2133 2.193536 GTTGAAACCCTGCCGCACT 61.194 57.895 0.00 0.00 0.00 4.40
1192 2172 2.030958 GAAGTTGTACCACCCGCCG 61.031 63.158 0.00 0.00 0.00 6.46
1246 2226 2.125912 AGCCAGACGTGCGTGATC 60.126 61.111 0.67 0.00 0.00 2.92
1348 2328 3.308014 GAGGGACTTGAGCTGCGCT 62.308 63.158 9.73 2.68 41.55 5.92
2152 3138 9.289303 CCATGGTTTCTTATATGAACGAAAAAG 57.711 33.333 2.57 0.00 0.00 2.27
2178 3173 9.013490 CAATTATTTTTCATCAGTTCGGTCATC 57.987 33.333 0.00 0.00 0.00 2.92
2245 3240 0.676736 GGCGATCGATCTCCTCCTTT 59.323 55.000 24.13 0.00 0.00 3.11
2282 3277 1.200760 TCACTGTGTATGCCCTGCCT 61.201 55.000 7.79 0.00 0.00 4.75
2333 3328 3.132289 TCGATCTCGGCAAGGTAAAGATT 59.868 43.478 0.00 0.00 40.29 2.40
2586 3623 5.938125 ACCATGAGTAGCGAAAACACTATTT 59.062 36.000 0.00 0.00 0.00 1.40
2591 3628 4.483476 AAACCATGAGTAGCGAAAACAC 57.517 40.909 0.00 0.00 0.00 3.32
2594 3631 7.624360 ATGAATAAACCATGAGTAGCGAAAA 57.376 32.000 0.00 0.00 0.00 2.29
2614 3653 6.456181 GCAATTTTTGGTCAACGAACAATGAA 60.456 34.615 0.00 0.00 39.10 2.57
2712 3760 1.878953 CCCCCTTTGGTCGATATTCG 58.121 55.000 0.00 0.00 42.10 3.34
2895 4102 5.355071 CACTTTGTTATTCTGCTGCCTATGA 59.645 40.000 0.00 0.00 0.00 2.15
2939 4146 6.949352 ATTTCTCTGTGACTGTTGTGATTT 57.051 33.333 0.00 0.00 0.00 2.17
2940 4147 7.933577 TCTTATTTCTCTGTGACTGTTGTGATT 59.066 33.333 0.00 0.00 0.00 2.57
2941 4148 7.386299 GTCTTATTTCTCTGTGACTGTTGTGAT 59.614 37.037 0.00 0.00 0.00 3.06
2942 4149 6.701841 GTCTTATTTCTCTGTGACTGTTGTGA 59.298 38.462 0.00 0.00 0.00 3.58
2943 4150 6.346120 CGTCTTATTTCTCTGTGACTGTTGTG 60.346 42.308 0.00 0.00 0.00 3.33
2944 4151 5.692204 CGTCTTATTTCTCTGTGACTGTTGT 59.308 40.000 0.00 0.00 0.00 3.32
2945 4152 5.119279 CCGTCTTATTTCTCTGTGACTGTTG 59.881 44.000 0.00 0.00 0.00 3.33
2946 4153 5.230942 CCGTCTTATTTCTCTGTGACTGTT 58.769 41.667 0.00 0.00 0.00 3.16
2947 4154 4.322049 CCCGTCTTATTTCTCTGTGACTGT 60.322 45.833 0.00 0.00 0.00 3.55
2950 4157 3.194968 TCCCCGTCTTATTTCTCTGTGAC 59.805 47.826 0.00 0.00 0.00 3.67
2986 4202 2.394930 ACCTATGTAACGTGCATGCA 57.605 45.000 18.46 18.46 0.00 3.96
3079 4299 4.940046 CCAAACAGATCATAGAGTTGTGCT 59.060 41.667 0.00 0.00 0.00 4.40
3160 4380 4.021894 AGTGATTGAGCGAAGTCTAAGTGT 60.022 41.667 0.00 0.00 0.00 3.55
3188 4409 4.158025 TCTGTGAAGGTTTCGGAGATCTAC 59.842 45.833 0.00 0.00 35.04 2.59
3196 4417 2.561569 ACAAGTCTGTGAAGGTTTCGG 58.438 47.619 0.00 0.00 33.30 4.30
3200 4421 3.871594 CGAAGAACAAGTCTGTGAAGGTT 59.128 43.478 0.00 0.00 36.40 3.50
3261 4495 5.079689 TCGTGCATTTACTAGATGGTCAA 57.920 39.130 0.00 0.00 0.00 3.18
3263 4497 4.686554 GGATCGTGCATTTACTAGATGGTC 59.313 45.833 0.00 0.00 0.00 4.02
3274 4508 2.783135 ACTCTTGTGGATCGTGCATTT 58.217 42.857 0.00 0.00 0.00 2.32
3275 4509 2.479566 ACTCTTGTGGATCGTGCATT 57.520 45.000 0.00 0.00 0.00 3.56
3310 4544 8.651589 TTAGAAATGGAGAGAGTAGTTGAGAA 57.348 34.615 0.00 0.00 0.00 2.87
3320 4554 7.555087 AGACTGATGTTTAGAAATGGAGAGAG 58.445 38.462 0.00 0.00 0.00 3.20
3322 4556 8.558973 AAAGACTGATGTTTAGAAATGGAGAG 57.441 34.615 0.00 0.00 0.00 3.20
3323 4557 8.924511 AAAAGACTGATGTTTAGAAATGGAGA 57.075 30.769 0.00 0.00 0.00 3.71
3337 4571 9.784680 CCAATTGAAATCTCTAAAAGACTGATG 57.215 33.333 7.12 0.00 36.65 3.07
3342 4576 8.341892 AGTCCCAATTGAAATCTCTAAAAGAC 57.658 34.615 7.12 0.00 36.65 3.01
3344 4578 9.231297 TGTAGTCCCAATTGAAATCTCTAAAAG 57.769 33.333 7.12 0.00 0.00 2.27
3345 4579 9.753674 ATGTAGTCCCAATTGAAATCTCTAAAA 57.246 29.630 7.12 0.00 0.00 1.52
3347 4581 9.832445 GTATGTAGTCCCAATTGAAATCTCTAA 57.168 33.333 7.12 0.00 0.00 2.10
3348 4582 8.988060 TGTATGTAGTCCCAATTGAAATCTCTA 58.012 33.333 7.12 0.00 0.00 2.43
3351 4585 7.861629 TCTGTATGTAGTCCCAATTGAAATCT 58.138 34.615 7.12 2.69 0.00 2.40
3352 4586 8.562892 CATCTGTATGTAGTCCCAATTGAAATC 58.437 37.037 7.12 0.00 0.00 2.17
3353 4587 8.055181 ACATCTGTATGTAGTCCCAATTGAAAT 58.945 33.333 7.12 0.00 44.66 2.17
3355 4589 6.957631 ACATCTGTATGTAGTCCCAATTGAA 58.042 36.000 7.12 0.00 44.66 2.69
3356 4590 6.560003 ACATCTGTATGTAGTCCCAATTGA 57.440 37.500 7.12 0.00 44.66 2.57
3395 4629 7.934855 AGCAAAATGAATGAATCTACACTCT 57.065 32.000 0.00 0.00 0.00 3.24
3397 4631 9.182214 ACATAGCAAAATGAATGAATCTACACT 57.818 29.630 1.26 0.00 0.00 3.55
3402 4636 8.635328 TGCATACATAGCAAAATGAATGAATCT 58.365 29.630 1.26 0.00 39.39 2.40
3403 4637 8.806177 TGCATACATAGCAAAATGAATGAATC 57.194 30.769 1.26 0.00 39.39 2.52
3416 4650 9.910267 ATTCTAATATGGATTGCATACATAGCA 57.090 29.630 0.00 0.00 39.34 3.49


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

AutoCloner maintained by Alex Coulton.