Multiple sequence alignment - TraesCS3D01G442200

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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 TraesCS3D01G442200 chr3D 100.000 2591 0 0 1 2591 552417900 552415310 0.000000e+00 4785.0
1 TraesCS3D01G442200 chr3D 87.478 1118 78 29 494 1591 552289946 552288871 0.000000e+00 1232.0
2 TraesCS3D01G442200 chr3D 88.187 728 59 10 1643 2351 552424139 552423420 0.000000e+00 843.0
3 TraesCS3D01G442200 chr3D 88.784 633 57 6 960 1591 552424829 552424210 0.000000e+00 763.0
4 TraesCS3D01G442200 chr3D 85.784 619 66 15 991 1591 552576291 552575677 1.010000e-178 636.0
5 TraesCS3D01G442200 chr3D 80.964 851 105 32 778 1591 552727566 552728396 2.830000e-174 621.0
6 TraesCS3D01G442200 chr3D 90.323 124 6 1 8 125 552290654 552290531 9.600000e-35 158.0
7 TraesCS3D01G442200 chr3B 88.639 1646 129 29 975 2585 732857415 732855793 0.000000e+00 1951.0
8 TraesCS3D01G442200 chr3B 87.243 682 73 6 965 1643 732845769 732845099 0.000000e+00 765.0
9 TraesCS3D01G442200 chr3B 86.582 708 55 22 914 1591 732841727 732841030 0.000000e+00 745.0
10 TraesCS3D01G442200 chr3B 84.436 771 76 19 1643 2410 732844888 732844159 0.000000e+00 719.0
11 TraesCS3D01G442200 chr3B 87.170 530 58 5 1071 1591 733356529 733357057 6.170000e-166 593.0
12 TraesCS3D01G442200 chr3B 84.013 638 70 15 955 1579 733270857 733271475 3.720000e-163 584.0
13 TraesCS3D01G442200 chr3B 90.022 451 35 8 261 706 732842471 732842026 2.240000e-160 575.0
14 TraesCS3D01G442200 chr3B 83.505 388 31 13 441 817 732846395 732846030 5.340000e-87 331.0
15 TraesCS3D01G442200 chr3B 86.992 123 10 2 9 125 732842647 732842525 1.620000e-27 134.0
16 TraesCS3D01G442200 chr3A 86.199 1681 146 42 960 2586 688915889 688914241 0.000000e+00 1740.0
17 TraesCS3D01G442200 chr3A 86.674 878 62 18 914 1762 688907783 688906932 0.000000e+00 922.0
18 TraesCS3D01G442200 chr3A 85.320 906 70 29 914 1775 688899074 688898188 0.000000e+00 878.0
19 TraesCS3D01G442200 chr3A 85.971 613 62 9 991 1591 688978036 688977436 3.640000e-178 634.0
20 TraesCS3D01G442200 chr3A 88.454 537 46 9 1070 1591 689002906 689003441 3.640000e-178 634.0
21 TraesCS3D01G442200 chr3A 80.706 850 102 36 778 1591 688992816 688993639 2.850000e-169 604.0
22 TraesCS3D01G442200 chr3A 82.534 584 48 17 249 784 688899749 688899172 5.050000e-127 464.0
23 TraesCS3D01G442200 chr3A 90.984 244 22 0 2093 2336 688906460 688906217 1.920000e-86 329.0
24 TraesCS3D01G442200 chr3A 85.163 337 26 5 1793 2110 688906932 688906601 8.940000e-85 324.0
25 TraesCS3D01G442200 chr3A 87.215 219 15 5 622 831 688908015 688907801 1.200000e-58 237.0
26 TraesCS3D01G442200 chr3A 83.969 131 8 5 8 125 688911498 688911368 2.110000e-21 113.0
27 TraesCS3D01G442200 chr3A 97.143 35 1 0 824 858 688899174 688899140 2.780000e-05 60.2
28 TraesCS3D01G442200 chrUn 100.000 34 0 0 126 159 40107989 40108022 2.150000e-06 63.9
29 TraesCS3D01G442200 chrUn 97.297 37 1 0 126 162 67968526 67968490 2.150000e-06 63.9
30 TraesCS3D01G442200 chr5B 100.000 34 0 0 126 159 713148638 713148671 2.150000e-06 63.9
31 TraesCS3D01G442200 chr4B 97.297 37 1 0 126 162 209163437 209163401 2.150000e-06 63.9
32 TraesCS3D01G442200 chr4B 100.000 34 0 0 126 159 252956290 252956323 2.150000e-06 63.9
33 TraesCS3D01G442200 chr4A 97.297 37 1 0 126 162 435550851 435550815 2.150000e-06 63.9
34 TraesCS3D01G442200 chr2A 100.000 34 0 0 126 159 618276372 618276405 2.150000e-06 63.9
35 TraesCS3D01G442200 chr1B 100.000 34 0 0 126 159 338914562 338914595 2.150000e-06 63.9
36 TraesCS3D01G442200 chr1B 97.297 37 1 0 126 162 583514638 583514602 2.150000e-06 63.9


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3D01G442200 chr3D 552415310 552417900 2590 True 4785.000000 4785 100.000000 1 2591 1 chr3D.!!$R1 2590
1 TraesCS3D01G442200 chr3D 552423420 552424829 1409 True 803.000000 843 88.485500 960 2351 2 chr3D.!!$R4 1391
2 TraesCS3D01G442200 chr3D 552288871 552290654 1783 True 695.000000 1232 88.900500 8 1591 2 chr3D.!!$R3 1583
3 TraesCS3D01G442200 chr3D 552575677 552576291 614 True 636.000000 636 85.784000 991 1591 1 chr3D.!!$R2 600
4 TraesCS3D01G442200 chr3D 552727566 552728396 830 False 621.000000 621 80.964000 778 1591 1 chr3D.!!$F1 813
5 TraesCS3D01G442200 chr3B 732855793 732857415 1622 True 1951.000000 1951 88.639000 975 2585 1 chr3B.!!$R1 1610
6 TraesCS3D01G442200 chr3B 733356529 733357057 528 False 593.000000 593 87.170000 1071 1591 1 chr3B.!!$F2 520
7 TraesCS3D01G442200 chr3B 733270857 733271475 618 False 584.000000 584 84.013000 955 1579 1 chr3B.!!$F1 624
8 TraesCS3D01G442200 chr3B 732841030 732846395 5365 True 544.833333 765 86.463333 9 2410 6 chr3B.!!$R2 2401
9 TraesCS3D01G442200 chr3A 688977436 688978036 600 True 634.000000 634 85.971000 991 1591 1 chr3A.!!$R1 600
10 TraesCS3D01G442200 chr3A 689002906 689003441 535 False 634.000000 634 88.454000 1070 1591 1 chr3A.!!$F2 521
11 TraesCS3D01G442200 chr3A 688906217 688915889 9672 True 610.833333 1740 86.700667 8 2586 6 chr3A.!!$R3 2578
12 TraesCS3D01G442200 chr3A 688992816 688993639 823 False 604.000000 604 80.706000 778 1591 1 chr3A.!!$F1 813
13 TraesCS3D01G442200 chr3A 688898188 688899749 1561 True 467.400000 878 88.332333 249 1775 3 chr3A.!!$R2 1526

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
144 5473 0.605083 GGTCCGGTTTCTAACTCGGT 59.395 55.0 0.0 0.0 42.23 4.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2041 10930 0.1791 GCTAGCCATTCTCAGTGCGA 60.179 55.0 2.29 0.0 0.0 5.1 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
75 5397 1.532868 GTAGTTGCTGGTCTGCACAAG 59.467 52.381 2.05 0.00 43.20 3.16
94 5423 2.609610 TTCCCTCCCAACCTCCCG 60.610 66.667 0.00 0.00 0.00 5.14
104 5433 3.663419 ACCTCCCGGTTTTGTGGA 58.337 55.556 0.00 0.00 42.13 4.02
125 5454 3.733443 AGGCCTTGCTTTGTTTAACAG 57.267 42.857 0.00 0.00 0.00 3.16
126 5455 2.365293 AGGCCTTGCTTTGTTTAACAGG 59.635 45.455 0.00 0.00 0.00 4.00
127 5456 2.102420 GGCCTTGCTTTGTTTAACAGGT 59.898 45.455 0.00 0.00 0.00 4.00
128 5457 3.381045 GCCTTGCTTTGTTTAACAGGTC 58.619 45.455 0.00 0.00 0.00 3.85
129 5458 3.798889 GCCTTGCTTTGTTTAACAGGTCC 60.799 47.826 0.00 0.00 0.00 4.46
130 5459 3.550030 CCTTGCTTTGTTTAACAGGTCCG 60.550 47.826 0.00 0.00 0.00 4.79
131 5460 1.950909 TGCTTTGTTTAACAGGTCCGG 59.049 47.619 0.00 0.00 0.00 5.14
132 5461 1.951602 GCTTTGTTTAACAGGTCCGGT 59.048 47.619 0.00 0.00 0.00 5.28
133 5462 2.359848 GCTTTGTTTAACAGGTCCGGTT 59.640 45.455 12.28 12.28 0.00 4.44
134 5463 3.181484 GCTTTGTTTAACAGGTCCGGTTT 60.181 43.478 12.87 0.00 0.00 3.27
135 5464 4.603985 CTTTGTTTAACAGGTCCGGTTTC 58.396 43.478 12.87 5.35 0.00 2.78
136 5465 3.564053 TGTTTAACAGGTCCGGTTTCT 57.436 42.857 12.87 0.00 0.00 2.52
137 5466 4.686191 TGTTTAACAGGTCCGGTTTCTA 57.314 40.909 12.87 0.00 0.00 2.10
138 5467 5.033589 TGTTTAACAGGTCCGGTTTCTAA 57.966 39.130 12.87 0.00 0.00 2.10
139 5468 4.815846 TGTTTAACAGGTCCGGTTTCTAAC 59.184 41.667 12.87 13.92 0.00 2.34
140 5469 4.961438 TTAACAGGTCCGGTTTCTAACT 57.039 40.909 12.87 0.00 0.00 2.24
141 5470 3.397849 AACAGGTCCGGTTTCTAACTC 57.602 47.619 0.00 0.00 0.00 3.01
142 5471 1.271656 ACAGGTCCGGTTTCTAACTCG 59.728 52.381 0.00 0.00 0.00 4.18
143 5472 0.893447 AGGTCCGGTTTCTAACTCGG 59.107 55.000 0.00 10.99 42.65 4.63
144 5473 0.605083 GGTCCGGTTTCTAACTCGGT 59.395 55.000 0.00 0.00 42.23 4.69
145 5474 1.670967 GGTCCGGTTTCTAACTCGGTG 60.671 57.143 0.00 0.00 42.23 4.94
146 5475 1.270550 GTCCGGTTTCTAACTCGGTGA 59.729 52.381 0.00 0.85 42.23 4.02
147 5476 1.962807 TCCGGTTTCTAACTCGGTGAA 59.037 47.619 0.00 0.00 42.23 3.18
148 5477 2.564062 TCCGGTTTCTAACTCGGTGAAT 59.436 45.455 0.00 0.00 42.23 2.57
149 5478 3.007182 TCCGGTTTCTAACTCGGTGAATT 59.993 43.478 0.00 0.00 42.23 2.17
150 5479 3.124636 CCGGTTTCTAACTCGGTGAATTG 59.875 47.826 0.00 0.00 39.10 2.32
151 5480 3.124636 CGGTTTCTAACTCGGTGAATTGG 59.875 47.826 0.00 0.00 0.00 3.16
152 5481 4.070009 GGTTTCTAACTCGGTGAATTGGT 58.930 43.478 0.00 0.00 0.00 3.67
153 5482 5.240121 GGTTTCTAACTCGGTGAATTGGTA 58.760 41.667 0.00 0.00 0.00 3.25
154 5483 5.878669 GGTTTCTAACTCGGTGAATTGGTAT 59.121 40.000 0.00 0.00 0.00 2.73
155 5484 6.183360 GGTTTCTAACTCGGTGAATTGGTATG 60.183 42.308 0.00 0.00 0.00 2.39
156 5485 5.018539 TCTAACTCGGTGAATTGGTATGG 57.981 43.478 0.00 0.00 0.00 2.74
157 5486 3.713826 AACTCGGTGAATTGGTATGGT 57.286 42.857 0.00 0.00 0.00 3.55
158 5487 3.261981 ACTCGGTGAATTGGTATGGTC 57.738 47.619 0.00 0.00 0.00 4.02
159 5488 2.093128 ACTCGGTGAATTGGTATGGTCC 60.093 50.000 0.00 0.00 0.00 4.46
160 5489 1.134640 TCGGTGAATTGGTATGGTCCG 60.135 52.381 0.00 0.00 38.36 4.79
169 5498 0.751643 GGTATGGTCCGGCAGCATTT 60.752 55.000 19.03 4.77 40.52 2.32
182 5511 3.493176 GGCAGCATTTTCCTTGTGAGTTT 60.493 43.478 0.00 0.00 0.00 2.66
194 5530 7.672983 TCCTTGTGAGTTTGAAGCTAATTAG 57.327 36.000 8.20 8.20 0.00 1.73
199 5535 8.547967 TGTGAGTTTGAAGCTAATTAGTTAGG 57.452 34.615 13.91 0.00 38.19 2.69
201 5537 8.443937 GTGAGTTTGAAGCTAATTAGTTAGGTG 58.556 37.037 13.91 0.00 45.29 4.00
202 5538 7.606456 TGAGTTTGAAGCTAATTAGTTAGGTGG 59.394 37.037 13.91 0.00 45.29 4.61
203 5539 7.459234 AGTTTGAAGCTAATTAGTTAGGTGGT 58.541 34.615 13.91 0.00 45.29 4.16
205 5541 8.880750 GTTTGAAGCTAATTAGTTAGGTGGTAG 58.119 37.037 13.91 0.00 45.29 3.18
206 5542 6.579865 TGAAGCTAATTAGTTAGGTGGTAGC 58.420 40.000 13.91 0.00 45.29 3.58
207 5543 5.548181 AGCTAATTAGTTAGGTGGTAGCC 57.452 43.478 13.91 0.00 44.58 3.93
208 5544 4.038883 AGCTAATTAGTTAGGTGGTAGCCG 59.961 45.833 13.91 0.00 44.58 5.52
209 5545 4.038402 GCTAATTAGTTAGGTGGTAGCCGA 59.962 45.833 13.91 0.00 38.19 5.54
210 5546 5.279356 GCTAATTAGTTAGGTGGTAGCCGAT 60.279 44.000 13.91 0.00 38.19 4.18
211 5547 5.625568 AATTAGTTAGGTGGTAGCCGATT 57.374 39.130 0.00 0.00 0.00 3.34
212 5548 4.660789 TTAGTTAGGTGGTAGCCGATTC 57.339 45.455 0.00 0.00 0.00 2.52
213 5549 2.748388 AGTTAGGTGGTAGCCGATTCT 58.252 47.619 0.00 0.00 0.00 2.40
214 5550 3.105283 AGTTAGGTGGTAGCCGATTCTT 58.895 45.455 0.00 0.00 0.00 2.52
216 5552 1.568504 AGGTGGTAGCCGATTCTTCA 58.431 50.000 0.00 0.00 0.00 3.02
217 5553 1.482593 AGGTGGTAGCCGATTCTTCAG 59.517 52.381 0.00 0.00 0.00 3.02
218 5554 1.480954 GGTGGTAGCCGATTCTTCAGA 59.519 52.381 0.00 0.00 0.00 3.27
219 5555 2.093658 GGTGGTAGCCGATTCTTCAGAA 60.094 50.000 0.00 0.00 38.56 3.02
220 5556 3.432326 GGTGGTAGCCGATTCTTCAGAAT 60.432 47.826 1.47 1.47 46.54 2.40
221 5557 4.192317 GTGGTAGCCGATTCTTCAGAATT 58.808 43.478 3.54 0.00 44.14 2.17
222 5558 4.271291 GTGGTAGCCGATTCTTCAGAATTC 59.729 45.833 3.54 0.00 44.14 2.17
223 5559 3.491267 GGTAGCCGATTCTTCAGAATTCG 59.509 47.826 3.54 8.38 44.14 3.34
224 5560 3.526931 AGCCGATTCTTCAGAATTCGA 57.473 42.857 16.41 0.00 44.14 3.71
247 5655 7.590322 TCGATCTCAGTTTTATATAGTTCACGC 59.410 37.037 0.00 0.00 0.00 5.34
257 5671 5.667539 ATATAGTTCACGCTGCATATCCT 57.332 39.130 0.00 0.00 0.00 3.24
275 5689 2.439507 TCCTTTTTCTGTCAGAGCTGGT 59.560 45.455 2.12 0.00 0.00 4.00
303 5719 4.260538 GATTTCACTAATCCAGCAAGAGCG 60.261 45.833 0.00 0.00 40.33 5.03
361 5783 5.429957 AGCAGTTCTGCTTACTGAAAAAG 57.570 39.130 19.80 0.00 44.52 2.27
369 5791 9.353999 GTTCTGCTTACTGAAAAAGAAAAGAAA 57.646 29.630 0.00 0.00 35.76 2.52
371 5793 9.573133 TCTGCTTACTGAAAAAGAAAAGAAAAG 57.427 29.630 0.00 0.00 0.00 2.27
420 5842 6.424207 TGTGCGTACATAAAGTGATGTTGTTA 59.576 34.615 0.82 0.00 40.54 2.41
423 5845 8.813282 TGCGTACATAAAGTGATGTTGTTATAG 58.187 33.333 0.00 0.00 40.54 1.31
539 8919 1.152922 AAAACCGAACTGGCCCGAA 60.153 52.632 0.00 0.00 43.94 4.30
552 8935 4.278419 ACTGGCCCGAATGCTTAATTAATC 59.722 41.667 0.00 0.00 0.00 1.75
649 9226 8.202745 TCGCCAAAACAAAACAATCTATTTTT 57.797 26.923 0.00 0.00 0.00 1.94
715 9374 8.854979 TTTTAAACTTGATCTCACACATGTTG 57.145 30.769 0.00 0.00 35.60 3.33
855 9518 3.317150 GAGCATAAACAACTTTGGTGCC 58.683 45.455 0.00 0.00 34.95 5.01
873 9538 2.224281 TGCCGCACTATTCTATCCCAAG 60.224 50.000 0.00 0.00 0.00 3.61
905 9570 5.330455 TCACAACACTGCCATTAACAAAA 57.670 34.783 0.00 0.00 0.00 2.44
907 9572 5.982516 TCACAACACTGCCATTAACAAAATC 59.017 36.000 0.00 0.00 0.00 2.17
908 9573 5.177327 CACAACACTGCCATTAACAAAATCC 59.823 40.000 0.00 0.00 0.00 3.01
909 9574 5.163364 ACAACACTGCCATTAACAAAATCCA 60.163 36.000 0.00 0.00 0.00 3.41
910 9575 5.138125 ACACTGCCATTAACAAAATCCAG 57.862 39.130 0.00 0.00 0.00 3.86
911 9576 4.832266 ACACTGCCATTAACAAAATCCAGA 59.168 37.500 0.00 0.00 0.00 3.86
912 9577 5.163513 CACTGCCATTAACAAAATCCAGAC 58.836 41.667 0.00 0.00 0.00 3.51
949 9691 3.128188 CAGCAGCAGCAGAGCAGG 61.128 66.667 3.17 0.00 45.49 4.85
950 9692 4.411981 AGCAGCAGCAGAGCAGGG 62.412 66.667 3.17 0.00 45.49 4.45
1058 9825 0.106669 TCGTCCTCCGATGATCACCT 60.107 55.000 0.00 0.00 41.60 4.00
1237 10004 2.045926 GCAACGCCCTCATCAGGT 60.046 61.111 0.00 0.00 38.30 4.00
1269 10036 0.391661 GCTTCGGCATGTTCAGGAGA 60.392 55.000 0.00 0.00 41.33 3.71
1295 10092 1.457643 TCTGCCGGTATGAGGAGGG 60.458 63.158 1.90 0.00 0.00 4.30
1323 10123 4.903010 ACGGCGTGGTTCAGCGTT 62.903 61.111 13.76 0.00 0.00 4.84
1396 10196 2.076622 CTGCTACAGGATCGACGGGG 62.077 65.000 0.00 0.00 0.00 5.73
1431 10240 1.169577 CTGAGTACAGAGTGAGCGGT 58.830 55.000 0.00 0.00 46.03 5.68
1434 10243 2.082231 GAGTACAGAGTGAGCGGTGTA 58.918 52.381 0.00 0.00 0.00 2.90
1591 10400 1.081892 CATCAACCGCTCCTTGTGAG 58.918 55.000 0.00 0.00 44.47 3.51
1634 10481 2.378886 TCAGGTTCAGGTCTCTGTAGGA 59.621 50.000 0.00 0.00 41.59 2.94
1640 10487 2.563179 TCAGGTCTCTGTAGGAAGCAAC 59.437 50.000 0.00 0.00 41.59 4.17
1719 10587 7.644157 GTGACTCTTTTTGGTGTATGACTTTTC 59.356 37.037 0.00 0.00 0.00 2.29
1776 10646 7.820044 TTTCAACACAATGAAACAAGGTTAC 57.180 32.000 0.00 0.00 42.68 2.50
1779 10649 4.915704 ACACAATGAAACAAGGTTACACG 58.084 39.130 0.00 0.00 0.00 4.49
1809 10679 7.315247 TGTATAAATCTTTGGATGTGTTCGG 57.685 36.000 0.00 0.00 31.75 4.30
1902 10772 5.957771 TGTTAGCCTATGAGACTCCAATT 57.042 39.130 0.00 0.00 0.00 2.32
1957 10827 6.913170 TGAGAGGCATCAAAAATGTTTCTAC 58.087 36.000 0.00 0.00 0.00 2.59
2024 10913 3.193479 CAGTCACTACTCACTGGCATACA 59.807 47.826 0.00 0.00 37.04 2.29
2050 10939 0.649475 GCAGCAGTTATCGCACTGAG 59.351 55.000 11.97 5.87 46.29 3.35
2055 10944 2.286294 GCAGTTATCGCACTGAGAATGG 59.714 50.000 11.97 0.00 46.29 3.16
2059 10948 2.522836 ATCGCACTGAGAATGGCTAG 57.477 50.000 0.00 0.00 0.00 3.42
2063 10952 1.284657 CACTGAGAATGGCTAGCACG 58.715 55.000 18.24 0.00 0.00 5.34
2064 10953 1.134995 CACTGAGAATGGCTAGCACGA 60.135 52.381 18.24 0.00 0.00 4.35
2066 10955 2.200067 CTGAGAATGGCTAGCACGAAG 58.800 52.381 18.24 0.46 0.00 3.79
2076 10965 3.120511 GGCTAGCACGAAGAAGAAAGTTG 60.121 47.826 18.24 0.00 0.00 3.16
2078 10967 4.143221 GCTAGCACGAAGAAGAAAGTTGAG 60.143 45.833 10.63 0.00 0.00 3.02
2080 10969 4.192317 AGCACGAAGAAGAAAGTTGAGTT 58.808 39.130 0.00 0.00 0.00 3.01
2113 11162 5.003778 CACAACTTCAACGCAAAGAAGAAAG 59.996 40.000 13.86 7.07 42.95 2.62
2123 11172 3.221567 CAAAGAAGAAAGAAAGAGCGCG 58.778 45.455 0.00 0.00 0.00 6.86
2125 11174 0.517335 GAAGAAAGAAAGAGCGCGCG 60.517 55.000 28.44 28.44 0.00 6.86
2153 11202 0.677842 AGCCTACCAAAACGACGTCT 59.322 50.000 14.70 0.00 0.00 4.18
2336 11385 4.388469 CCCAAAAGGTTGCAATAATTCACG 59.612 41.667 0.59 0.00 33.01 4.35
2337 11386 4.388469 CCAAAAGGTTGCAATAATTCACGG 59.612 41.667 0.59 0.00 33.01 4.94
2382 11431 3.456380 AGTGGTGGCCAATATGAACTT 57.544 42.857 7.24 0.00 34.18 2.66
2427 11477 1.660242 AAATTGAGCCCATTTGCCCT 58.340 45.000 0.00 0.00 0.00 5.19
2450 11500 2.420568 GGTGCCTGGCCACATGATG 61.421 63.158 17.53 0.00 37.46 3.07
2451 11501 1.378911 GTGCCTGGCCACATGATGA 60.379 57.895 17.53 0.00 35.80 2.92
2454 11504 1.077285 CCTGGCCACATGATGAGCA 60.077 57.895 0.00 1.34 0.00 4.26
2458 11508 1.108776 GGCCACATGATGAGCAACAT 58.891 50.000 0.00 0.00 42.47 2.71
2467 11517 1.730501 ATGAGCAACATCACACTCGG 58.269 50.000 0.00 0.00 33.46 4.63
2471 11521 1.230635 GCAACATCACACTCGGCTGT 61.231 55.000 0.00 0.00 0.00 4.40
2476 11526 0.037882 ATCACACTCGGCTGTCAGTG 60.038 55.000 11.78 11.78 44.83 3.66
2481 11531 2.203640 TCGGCTGTCAGTGGACCT 60.204 61.111 0.93 0.00 43.65 3.85
2512 11563 3.005578 ACTCCACGTCTAGTTTGACCTTC 59.994 47.826 0.00 0.00 33.70 3.46
2527 11578 3.138283 TGACCTTCTCAAACCACCAATCT 59.862 43.478 0.00 0.00 0.00 2.40
2531 11582 1.425066 TCTCAAACCACCAATCTGGCT 59.575 47.619 0.00 0.00 42.67 4.75
2536 11587 1.450312 CCACCAATCTGGCTCGTCC 60.450 63.158 0.00 0.00 42.67 4.79
2537 11588 1.599047 CACCAATCTGGCTCGTCCT 59.401 57.895 0.00 0.00 42.67 3.85
2548 11599 2.038426 TGGCTCGTCCTTTTCATCAAGA 59.962 45.455 0.00 0.00 35.26 3.02
2554 11608 6.088616 GCTCGTCCTTTTCATCAAGATTTTTG 59.911 38.462 0.00 0.00 0.00 2.44
2555 11609 5.920273 TCGTCCTTTTCATCAAGATTTTTGC 59.080 36.000 0.00 0.00 0.00 3.68
2556 11610 5.922544 CGTCCTTTTCATCAAGATTTTTGCT 59.077 36.000 0.00 0.00 0.00 3.91
2557 11611 6.129009 CGTCCTTTTCATCAAGATTTTTGCTG 60.129 38.462 0.00 0.00 0.00 4.41
2560 11614 8.805175 TCCTTTTCATCAAGATTTTTGCTGATA 58.195 29.630 0.00 0.00 0.00 2.15
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
75 5397 2.677848 GGAGGTTGGGAGGGAAGC 59.322 66.667 0.00 0.00 0.00 3.86
94 5423 0.249868 GCAAGGCCTTCCACAAAACC 60.250 55.000 17.29 0.00 33.74 3.27
104 5433 3.181466 CCTGTTAAACAAAGCAAGGCCTT 60.181 43.478 13.78 13.78 0.00 4.35
125 5454 0.605083 ACCGAGTTAGAAACCGGACC 59.395 55.000 9.46 0.00 43.41 4.46
126 5455 1.270550 TCACCGAGTTAGAAACCGGAC 59.729 52.381 9.46 0.00 43.41 4.79
127 5456 1.619654 TCACCGAGTTAGAAACCGGA 58.380 50.000 9.46 0.00 43.41 5.14
128 5457 2.443887 TTCACCGAGTTAGAAACCGG 57.556 50.000 0.00 0.00 45.00 5.28
129 5458 3.124636 CCAATTCACCGAGTTAGAAACCG 59.875 47.826 0.00 0.00 0.00 4.44
130 5459 4.070009 ACCAATTCACCGAGTTAGAAACC 58.930 43.478 0.00 0.00 0.00 3.27
131 5460 6.183360 CCATACCAATTCACCGAGTTAGAAAC 60.183 42.308 0.00 0.00 0.00 2.78
132 5461 5.878116 CCATACCAATTCACCGAGTTAGAAA 59.122 40.000 0.00 0.00 0.00 2.52
133 5462 5.046159 ACCATACCAATTCACCGAGTTAGAA 60.046 40.000 0.00 0.00 0.00 2.10
134 5463 4.468510 ACCATACCAATTCACCGAGTTAGA 59.531 41.667 0.00 0.00 0.00 2.10
135 5464 4.766375 ACCATACCAATTCACCGAGTTAG 58.234 43.478 0.00 0.00 0.00 2.34
136 5465 4.383335 GGACCATACCAATTCACCGAGTTA 60.383 45.833 0.00 0.00 0.00 2.24
137 5466 3.606687 GACCATACCAATTCACCGAGTT 58.393 45.455 0.00 0.00 0.00 3.01
138 5467 2.093128 GGACCATACCAATTCACCGAGT 60.093 50.000 0.00 0.00 0.00 4.18
139 5468 2.561569 GGACCATACCAATTCACCGAG 58.438 52.381 0.00 0.00 0.00 4.63
140 5469 1.134640 CGGACCATACCAATTCACCGA 60.135 52.381 0.00 0.00 41.30 4.69
141 5470 1.295792 CGGACCATACCAATTCACCG 58.704 55.000 0.00 0.00 0.00 4.94
142 5471 1.675552 CCGGACCATACCAATTCACC 58.324 55.000 0.00 0.00 0.00 4.02
143 5472 1.021968 GCCGGACCATACCAATTCAC 58.978 55.000 5.05 0.00 0.00 3.18
144 5473 0.621082 TGCCGGACCATACCAATTCA 59.379 50.000 5.05 0.00 0.00 2.57
145 5474 1.308998 CTGCCGGACCATACCAATTC 58.691 55.000 5.05 0.00 0.00 2.17
146 5475 0.751643 GCTGCCGGACCATACCAATT 60.752 55.000 5.05 0.00 0.00 2.32
147 5476 1.152963 GCTGCCGGACCATACCAAT 60.153 57.895 5.05 0.00 0.00 3.16
148 5477 1.920734 ATGCTGCCGGACCATACCAA 61.921 55.000 5.05 0.00 0.00 3.67
149 5478 1.920734 AATGCTGCCGGACCATACCA 61.921 55.000 5.05 0.00 0.00 3.25
150 5479 0.751643 AAATGCTGCCGGACCATACC 60.752 55.000 5.05 0.00 0.00 2.73
151 5480 1.065551 GAAAATGCTGCCGGACCATAC 59.934 52.381 5.05 0.00 0.00 2.39
152 5481 1.388547 GAAAATGCTGCCGGACCATA 58.611 50.000 5.05 0.00 0.00 2.74
153 5482 1.322538 GGAAAATGCTGCCGGACCAT 61.323 55.000 5.05 0.00 0.00 3.55
154 5483 1.976474 GGAAAATGCTGCCGGACCA 60.976 57.895 5.05 0.00 0.00 4.02
155 5484 1.250840 AAGGAAAATGCTGCCGGACC 61.251 55.000 5.05 0.00 0.00 4.46
156 5485 0.109132 CAAGGAAAATGCTGCCGGAC 60.109 55.000 5.05 0.00 0.00 4.79
157 5486 0.539438 ACAAGGAAAATGCTGCCGGA 60.539 50.000 5.05 0.00 0.00 5.14
158 5487 0.388907 CACAAGGAAAATGCTGCCGG 60.389 55.000 0.00 0.00 0.00 6.13
159 5488 0.597568 TCACAAGGAAAATGCTGCCG 59.402 50.000 0.00 0.00 0.00 5.69
160 5489 1.615392 ACTCACAAGGAAAATGCTGCC 59.385 47.619 0.00 0.00 0.00 4.85
169 5498 6.959639 AATTAGCTTCAAACTCACAAGGAA 57.040 33.333 0.00 0.00 0.00 3.36
182 5511 6.407752 GGCTACCACCTAACTAATTAGCTTCA 60.408 42.308 12.54 0.00 37.12 3.02
194 5530 3.118884 TGAAGAATCGGCTACCACCTAAC 60.119 47.826 0.00 0.00 0.00 2.34
199 5535 2.961526 TCTGAAGAATCGGCTACCAC 57.038 50.000 0.00 0.00 31.55 4.16
200 5536 4.442706 GAATTCTGAAGAATCGGCTACCA 58.557 43.478 6.03 0.00 43.41 3.25
201 5537 3.491267 CGAATTCTGAAGAATCGGCTACC 59.509 47.826 6.03 0.00 43.41 3.18
202 5538 4.360563 TCGAATTCTGAAGAATCGGCTAC 58.639 43.478 17.27 4.21 43.41 3.58
203 5539 4.649088 TCGAATTCTGAAGAATCGGCTA 57.351 40.909 17.27 2.73 43.41 3.93
205 5541 4.054671 AGATCGAATTCTGAAGAATCGGC 58.945 43.478 17.27 12.20 43.41 5.54
206 5542 5.284864 TGAGATCGAATTCTGAAGAATCGG 58.715 41.667 17.27 9.43 43.41 4.18
207 5543 5.976534 ACTGAGATCGAATTCTGAAGAATCG 59.023 40.000 6.03 13.51 43.41 3.34
208 5544 7.769272 AACTGAGATCGAATTCTGAAGAATC 57.231 36.000 6.03 0.60 43.41 2.52
209 5545 8.558973 AAAACTGAGATCGAATTCTGAAGAAT 57.441 30.769 3.52 0.00 45.91 2.40
210 5546 7.969536 AAAACTGAGATCGAATTCTGAAGAA 57.030 32.000 3.52 0.00 38.56 2.52
220 5556 9.447040 CGTGAACTATATAAAACTGAGATCGAA 57.553 33.333 0.00 0.00 0.00 3.71
221 5557 7.590322 GCGTGAACTATATAAAACTGAGATCGA 59.410 37.037 0.00 0.00 0.00 3.59
222 5558 7.591795 AGCGTGAACTATATAAAACTGAGATCG 59.408 37.037 0.00 0.00 0.00 3.69
223 5559 8.695284 CAGCGTGAACTATATAAAACTGAGATC 58.305 37.037 0.00 0.00 0.00 2.75
224 5560 7.169982 GCAGCGTGAACTATATAAAACTGAGAT 59.830 37.037 0.00 0.00 0.00 2.75
240 5648 3.764885 AAAAGGATATGCAGCGTGAAC 57.235 42.857 0.00 0.00 0.00 3.18
242 5650 3.374988 CAGAAAAAGGATATGCAGCGTGA 59.625 43.478 0.00 0.00 0.00 4.35
243 5651 3.127548 ACAGAAAAAGGATATGCAGCGTG 59.872 43.478 0.00 0.00 0.00 5.34
244 5652 3.347216 ACAGAAAAAGGATATGCAGCGT 58.653 40.909 0.00 0.00 0.00 5.07
245 5653 3.374988 TGACAGAAAAAGGATATGCAGCG 59.625 43.478 0.00 0.00 0.00 5.18
247 5655 5.220815 GCTCTGACAGAAAAAGGATATGCAG 60.221 44.000 6.61 0.00 0.00 4.41
257 5671 2.575532 CCACCAGCTCTGACAGAAAAA 58.424 47.619 6.61 0.00 0.00 1.94
315 5731 7.811713 GCTTGAGAATAAGAAGCTGTGATTTTT 59.188 33.333 0.00 0.00 33.96 1.94
369 5791 7.903995 TGCAGAATTGAACAAAGTTTTTCTT 57.096 28.000 10.07 0.00 38.10 2.52
371 5793 8.177013 ACATTGCAGAATTGAACAAAGTTTTTC 58.823 29.630 0.00 0.00 0.00 2.29
377 5799 4.375606 CGCACATTGCAGAATTGAACAAAG 60.376 41.667 0.00 0.00 45.36 2.77
378 5800 3.490155 CGCACATTGCAGAATTGAACAAA 59.510 39.130 0.00 0.00 45.36 2.83
381 5803 2.664916 ACGCACATTGCAGAATTGAAC 58.335 42.857 0.00 0.00 45.36 3.18
386 5808 5.123820 ACTTTATGTACGCACATTGCAGAAT 59.876 36.000 6.58 0.00 45.36 2.40
420 5842 4.280929 GGCCCTCAACTTTGTTTTGTCTAT 59.719 41.667 0.00 0.00 0.00 1.98
423 5845 2.430694 AGGCCCTCAACTTTGTTTTGTC 59.569 45.455 0.00 0.00 0.00 3.18
539 8919 7.744087 TGCACCTAATCGATTAATTAAGCAT 57.256 32.000 18.08 3.97 0.00 3.79
552 8935 5.844004 AGGATAAGTACTTGCACCTAATCG 58.156 41.667 18.56 0.00 0.00 3.34
649 9226 8.024865 CGTACTATTTCGACCCATATATGTCAA 58.975 37.037 11.73 0.00 0.00 3.18
715 9374 4.114058 ACCACAATGTAATGCAATGCTC 57.886 40.909 6.82 0.00 31.33 4.26
855 9518 3.181465 ACACCTTGGGATAGAATAGTGCG 60.181 47.826 0.00 0.00 0.00 5.34
905 9570 4.043435 GGCCTATTTATTCAGGGTCTGGAT 59.957 45.833 0.00 0.00 33.72 3.41
907 9572 3.138283 TGGCCTATTTATTCAGGGTCTGG 59.862 47.826 3.32 0.00 32.15 3.86
908 9573 4.437682 TGGCCTATTTATTCAGGGTCTG 57.562 45.455 3.32 0.00 32.15 3.51
909 9574 5.201243 GTTTGGCCTATTTATTCAGGGTCT 58.799 41.667 3.32 0.00 32.15 3.85
910 9575 4.953579 TGTTTGGCCTATTTATTCAGGGTC 59.046 41.667 3.32 0.00 32.15 4.46
911 9576 4.941713 TGTTTGGCCTATTTATTCAGGGT 58.058 39.130 3.32 0.00 32.15 4.34
912 9577 4.202151 GCTGTTTGGCCTATTTATTCAGGG 60.202 45.833 3.32 0.00 32.15 4.45
953 9695 4.567385 CTCTGCTCGGCTCCGCTC 62.567 72.222 2.96 0.00 39.59 5.03
957 9699 1.886777 GATTGCTCTGCTCGGCTCC 60.887 63.158 0.00 0.00 0.00 4.70
1073 9840 2.514592 CCGTGTATGCCTGCCTGG 60.515 66.667 0.00 0.00 39.35 4.45
1083 9850 2.416836 CGACTTCATCCACACCGTGTAT 60.417 50.000 3.25 0.00 0.00 2.29
1237 10004 2.672996 GAAGCCCTTGCGCCTGAA 60.673 61.111 4.18 0.00 44.33 3.02
1269 10036 1.074471 ATACCGGCAGACCTCCCAT 60.074 57.895 0.00 0.00 0.00 4.00
1309 10109 4.072088 CCGAACGCTGAACCACGC 62.072 66.667 0.00 0.00 0.00 5.34
1413 10222 0.881796 CACCGCTCACTCTGTACTCA 59.118 55.000 0.00 0.00 0.00 3.41
1431 10240 1.663379 CCACGACCGAGCCATCTACA 61.663 60.000 0.00 0.00 0.00 2.74
1434 10243 4.148825 GCCACGACCGAGCCATCT 62.149 66.667 0.00 0.00 0.00 2.90
1591 10400 4.875561 ACTAGAAGAAGAGGGTCACAAC 57.124 45.455 0.00 0.00 0.00 3.32
1776 10646 7.315247 TCCAAAGATTTATACAATCACCGTG 57.685 36.000 0.00 0.00 0.00 4.94
1779 10649 8.686334 ACACATCCAAAGATTTATACAATCACC 58.314 33.333 9.07 0.00 0.00 4.02
1809 10679 6.093633 GGATAACACATAGACAACCTGGAAAC 59.906 42.308 0.00 0.00 0.00 2.78
1893 10763 8.841300 GGGATCATAAAGTCTTAAATTGGAGTC 58.159 37.037 0.00 0.00 0.00 3.36
1902 10772 7.252612 TCTGTGTGGGATCATAAAGTCTTAA 57.747 36.000 0.00 0.00 0.00 1.85
1957 10827 0.826715 TCTTCTCCAAGAGGCCGATG 59.173 55.000 0.00 0.00 33.38 3.84
1983 10872 3.940221 ACTGGCTAACGTTTTTGTGTGTA 59.060 39.130 5.91 0.00 0.00 2.90
2036 10925 2.169352 AGCCATTCTCAGTGCGATAACT 59.831 45.455 0.00 0.00 0.00 2.24
2039 10928 2.288457 GCTAGCCATTCTCAGTGCGATA 60.288 50.000 2.29 0.00 0.00 2.92
2040 10929 1.539929 GCTAGCCATTCTCAGTGCGAT 60.540 52.381 2.29 0.00 0.00 4.58
2041 10930 0.179100 GCTAGCCATTCTCAGTGCGA 60.179 55.000 2.29 0.00 0.00 5.10
2050 10939 2.893637 TCTTCTTCGTGCTAGCCATTC 58.106 47.619 13.29 0.00 0.00 2.67
2055 10944 3.741344 TCAACTTTCTTCTTCGTGCTAGC 59.259 43.478 8.10 8.10 0.00 3.42
2059 10948 4.274865 CAACTCAACTTTCTTCTTCGTGC 58.725 43.478 0.00 0.00 0.00 5.34
2063 10952 3.632145 TGCCCAACTCAACTTTCTTCTTC 59.368 43.478 0.00 0.00 0.00 2.87
2064 10953 3.381590 GTGCCCAACTCAACTTTCTTCTT 59.618 43.478 0.00 0.00 0.00 2.52
2066 10955 2.687935 TGTGCCCAACTCAACTTTCTTC 59.312 45.455 0.00 0.00 0.00 2.87
2080 10969 0.323816 TTGAAGTTGTGGTGTGCCCA 60.324 50.000 0.00 0.00 42.51 5.36
2113 11162 2.202058 GTTGACGCGCGCTCTTTC 60.202 61.111 32.58 20.19 0.00 2.62
2123 11172 0.391130 TGGTAGGCTGATGTTGACGC 60.391 55.000 0.00 0.00 0.00 5.19
2125 11174 3.364964 CGTTTTGGTAGGCTGATGTTGAC 60.365 47.826 0.00 0.00 0.00 3.18
2153 11202 2.141011 ATAAGGCTGGCAGTGGCACA 62.141 55.000 21.41 0.00 43.71 4.57
2222 11271 1.080025 GCGTACTGGTCTTCCGCTT 60.080 57.895 0.00 0.00 41.06 4.68
2242 11291 1.964891 CTATCTCCGTCGCCGCCTA 60.965 63.158 0.00 0.00 0.00 3.93
2336 11385 2.102588 ACGTATTGTACATCTCAGCCCC 59.897 50.000 0.00 0.00 0.00 5.80
2337 11386 3.123804 CACGTATTGTACATCTCAGCCC 58.876 50.000 0.00 0.00 0.00 5.19
2382 11431 4.468510 TCTTTTTCTCCGGTTATAGGCTCA 59.531 41.667 0.00 0.00 0.00 4.26
2450 11500 0.671781 AGCCGAGTGTGATGTTGCTC 60.672 55.000 0.00 0.00 0.00 4.26
2451 11501 0.952497 CAGCCGAGTGTGATGTTGCT 60.952 55.000 0.00 0.00 0.00 3.91
2454 11504 0.392706 TGACAGCCGAGTGTGATGTT 59.607 50.000 0.00 0.00 0.00 2.71
2458 11508 1.363807 CACTGACAGCCGAGTGTGA 59.636 57.895 1.25 0.00 35.78 3.58
2476 11526 3.000727 CGTGGAGTTGTATTTCAGGTCC 58.999 50.000 0.00 0.00 33.15 4.46
2481 11531 5.717078 ACTAGACGTGGAGTTGTATTTCA 57.283 39.130 0.00 0.00 0.00 2.69
2487 11537 3.492137 GGTCAAACTAGACGTGGAGTTGT 60.492 47.826 11.39 1.89 39.42 3.32
2512 11563 1.815003 GAGCCAGATTGGTGGTTTGAG 59.185 52.381 0.00 0.00 40.46 3.02
2527 11578 2.038426 TCTTGATGAAAAGGACGAGCCA 59.962 45.455 0.00 0.00 40.02 4.75
2531 11582 5.920273 GCAAAAATCTTGATGAAAAGGACGA 59.080 36.000 0.00 0.00 0.00 4.20


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

AutoCloner maintained by Alex Coulton.