Multiple sequence alignment - TraesCS2B01G106500

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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 TraesCS2B01G106500 chr2B 100.000 3265 0 0 1 3265 67542847 67539583 0.000000e+00 6030.0
1 TraesCS2B01G106500 chr2B 89.163 1541 103 34 749 2251 67659227 67657713 0.000000e+00 1862.0
2 TraesCS2B01G106500 chr2B 88.346 1493 104 27 749 2224 67464285 67465724 0.000000e+00 1729.0
3 TraesCS2B01G106500 chr2B 87.568 925 68 18 702 1613 67423973 67424863 0.000000e+00 1027.0
4 TraesCS2B01G106500 chr2B 92.321 599 44 1 2667 3265 484609574 484608978 0.000000e+00 850.0
5 TraesCS2B01G106500 chr2B 82.864 391 23 22 2016 2378 67424874 67425248 8.800000e-81 311.0
6 TraesCS2B01G106500 chr2B 77.237 514 77 23 1 502 67661965 67661480 6.950000e-67 265.0
7 TraesCS2B01G106500 chr2B 81.761 318 34 11 1 314 67456740 67457037 9.050000e-61 244.0
8 TraesCS2B01G106500 chr2B 94.286 70 4 0 2467 2536 67433494 67433425 1.240000e-19 108.0
9 TraesCS2B01G106500 chr2B 82.308 130 3 1 2538 2667 67433384 67433275 9.640000e-16 95.3
10 TraesCS2B01G106500 chr2D 87.360 1962 122 60 407 2304 38636688 38638587 0.000000e+00 2134.0
11 TraesCS2B01G106500 chr2D 87.722 1686 123 38 583 2224 40903518 40901873 0.000000e+00 1890.0
12 TraesCS2B01G106500 chr2D 87.218 1682 122 46 583 2205 38782912 38781265 0.000000e+00 1829.0
13 TraesCS2B01G106500 chr2D 87.325 1641 105 50 521 2137 38678118 38679679 0.000000e+00 1783.0
14 TraesCS2B01G106500 chr2D 90.968 919 71 7 1206 2117 40849918 40850831 0.000000e+00 1227.0
15 TraesCS2B01G106500 chr2D 88.243 723 46 21 1596 2302 38685834 38685135 0.000000e+00 828.0
16 TraesCS2B01G106500 chr2D 91.639 598 50 0 2668 3265 609574690 609575287 0.000000e+00 828.0
17 TraesCS2B01G106500 chr2D 83.815 346 30 9 2337 2662 38781010 38780671 4.090000e-79 305.0
18 TraesCS2B01G106500 chr2D 83.136 338 32 12 1 314 38741341 38741005 5.330000e-73 285.0
19 TraesCS2B01G106500 chr2D 80.412 194 25 8 2346 2537 38671000 38671182 5.680000e-28 135.0
20 TraesCS2B01G106500 chr2A 88.043 1773 121 45 521 2250 43457913 43459637 0.000000e+00 2015.0
21 TraesCS2B01G106500 chr2A 89.322 1386 93 31 845 2208 43429477 43430829 0.000000e+00 1688.0
22 TraesCS2B01G106500 chr2A 89.936 934 60 17 1369 2298 43484026 43483123 0.000000e+00 1173.0
23 TraesCS2B01G106500 chr2A 83.540 644 64 24 749 1376 43489719 43489102 6.120000e-157 564.0
24 TraesCS2B01G106500 chr2A 82.623 305 24 20 521 816 43429197 43429481 3.250000e-60 243.0
25 TraesCS2B01G106500 chr2A 86.937 222 21 4 2446 2667 43460078 43460291 3.250000e-60 243.0
26 TraesCS2B01G106500 chr2A 84.977 213 20 6 2337 2546 43481047 43480844 4.270000e-49 206.0
27 TraesCS2B01G106500 chr2A 92.105 76 6 0 2461 2536 43463432 43463507 1.240000e-19 108.0
28 TraesCS2B01G106500 chr2A 90.000 80 3 2 520 599 44073127 44073053 7.460000e-17 99.0
29 TraesCS2B01G106500 chr1B 91.820 599 45 3 2668 3265 549450877 549451472 0.000000e+00 832.0
30 TraesCS2B01G106500 chr1B 89.535 602 56 4 2669 3265 654649603 654650202 0.000000e+00 756.0
31 TraesCS2B01G106500 chr6B 90.970 598 51 3 2668 3265 20088624 20089218 0.000000e+00 802.0
32 TraesCS2B01G106500 chr6A 90.333 600 57 1 2667 3265 435593790 435593191 0.000000e+00 785.0
33 TraesCS2B01G106500 chr5B 89.816 599 60 1 2667 3265 37466822 37466225 0.000000e+00 767.0
34 TraesCS2B01G106500 chr7D 89.316 599 63 1 2667 3265 565529767 565529170 0.000000e+00 750.0
35 TraesCS2B01G106500 chr6D 89.280 597 62 2 2669 3265 276399337 276398743 0.000000e+00 747.0


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 TraesCS2B01G106500 chr2B 67539583 67542847 3264 True 6030.000000 6030 100.000000 1 3265 1 chr2B.!!$R1 3264
1 TraesCS2B01G106500 chr2B 67464285 67465724 1439 False 1729.000000 1729 88.346000 749 2224 1 chr2B.!!$F2 1475
2 TraesCS2B01G106500 chr2B 67657713 67661965 4252 True 1063.500000 1862 83.200000 1 2251 2 chr2B.!!$R4 2250
3 TraesCS2B01G106500 chr2B 484608978 484609574 596 True 850.000000 850 92.321000 2667 3265 1 chr2B.!!$R2 598
4 TraesCS2B01G106500 chr2B 67423973 67425248 1275 False 669.000000 1027 85.216000 702 2378 2 chr2B.!!$F3 1676
5 TraesCS2B01G106500 chr2D 38636688 38638587 1899 False 2134.000000 2134 87.360000 407 2304 1 chr2D.!!$F1 1897
6 TraesCS2B01G106500 chr2D 40901873 40903518 1645 True 1890.000000 1890 87.722000 583 2224 1 chr2D.!!$R3 1641
7 TraesCS2B01G106500 chr2D 38678118 38679679 1561 False 1783.000000 1783 87.325000 521 2137 1 chr2D.!!$F3 1616
8 TraesCS2B01G106500 chr2D 40849918 40850831 913 False 1227.000000 1227 90.968000 1206 2117 1 chr2D.!!$F4 911
9 TraesCS2B01G106500 chr2D 38780671 38782912 2241 True 1067.000000 1829 85.516500 583 2662 2 chr2D.!!$R4 2079
10 TraesCS2B01G106500 chr2D 38685135 38685834 699 True 828.000000 828 88.243000 1596 2302 1 chr2D.!!$R1 706
11 TraesCS2B01G106500 chr2D 609574690 609575287 597 False 828.000000 828 91.639000 2668 3265 1 chr2D.!!$F5 597
12 TraesCS2B01G106500 chr2A 43429197 43430829 1632 False 965.500000 1688 85.972500 521 2208 2 chr2A.!!$F1 1687
13 TraesCS2B01G106500 chr2A 43457913 43463507 5594 False 788.666667 2015 89.028333 521 2667 3 chr2A.!!$F2 2146
14 TraesCS2B01G106500 chr2A 43480844 43484026 3182 True 689.500000 1173 87.456500 1369 2546 2 chr2A.!!$R3 1177
15 TraesCS2B01G106500 chr2A 43489102 43489719 617 True 564.000000 564 83.540000 749 1376 1 chr2A.!!$R1 627
16 TraesCS2B01G106500 chr1B 549450877 549451472 595 False 832.000000 832 91.820000 2668 3265 1 chr1B.!!$F1 597
17 TraesCS2B01G106500 chr1B 654649603 654650202 599 False 756.000000 756 89.535000 2669 3265 1 chr1B.!!$F2 596
18 TraesCS2B01G106500 chr6B 20088624 20089218 594 False 802.000000 802 90.970000 2668 3265 1 chr6B.!!$F1 597
19 TraesCS2B01G106500 chr6A 435593191 435593790 599 True 785.000000 785 90.333000 2667 3265 1 chr6A.!!$R1 598
20 TraesCS2B01G106500 chr5B 37466225 37466822 597 True 767.000000 767 89.816000 2667 3265 1 chr5B.!!$R1 598
21 TraesCS2B01G106500 chr7D 565529170 565529767 597 True 750.000000 750 89.316000 2667 3265 1 chr7D.!!$R1 598
22 TraesCS2B01G106500 chr6D 276398743 276399337 594 True 747.000000 747 89.280000 2669 3265 1 chr6D.!!$R1 596

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
609 2453 0.179073 ATTCTTGACCTGGCGATCGG 60.179 55.0 18.3 2.04 0.0 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2436 7024 0.250727 CCAGAGTTTTTCCCGGCTGA 60.251 55.0 0.0 0.0 0.0 4.26 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
60 61 0.397564 TGTTGCACATCAGGAGAGCA 59.602 50.000 0.00 0.00 0.00 4.26
79 80 3.255888 AGCAACATCTGAGACGTGACTAA 59.744 43.478 0.00 0.00 0.00 2.24
84 85 3.917329 TCTGAGACGTGACTAACTTGG 57.083 47.619 0.00 0.00 0.00 3.61
104 112 7.616313 ACTTGGTTCTTTTCTATACCTGAGAG 58.384 38.462 0.00 0.00 0.00 3.20
106 114 5.483937 TGGTTCTTTTCTATACCTGAGAGCA 59.516 40.000 0.00 0.00 0.00 4.26
111 119 2.852449 TCTATACCTGAGAGCAGACGG 58.148 52.381 0.00 0.00 45.17 4.79
116 124 2.457598 ACCTGAGAGCAGACGGAAATA 58.542 47.619 0.00 0.00 45.17 1.40
122 130 4.520874 TGAGAGCAGACGGAAATATAGAGG 59.479 45.833 0.00 0.00 0.00 3.69
123 131 3.257127 AGAGCAGACGGAAATATAGAGGC 59.743 47.826 0.00 0.00 0.00 4.70
125 133 3.388024 AGCAGACGGAAATATAGAGGCAA 59.612 43.478 0.00 0.00 0.00 4.52
126 134 3.743396 GCAGACGGAAATATAGAGGCAAG 59.257 47.826 0.00 0.00 0.00 4.01
127 135 3.743396 CAGACGGAAATATAGAGGCAAGC 59.257 47.826 0.00 0.00 0.00 4.01
129 137 4.127171 GACGGAAATATAGAGGCAAGCAA 58.873 43.478 0.00 0.00 0.00 3.91
130 138 4.523083 ACGGAAATATAGAGGCAAGCAAA 58.477 39.130 0.00 0.00 0.00 3.68
131 139 4.947388 ACGGAAATATAGAGGCAAGCAAAA 59.053 37.500 0.00 0.00 0.00 2.44
132 140 5.417580 ACGGAAATATAGAGGCAAGCAAAAA 59.582 36.000 0.00 0.00 0.00 1.94
133 141 5.973565 CGGAAATATAGAGGCAAGCAAAAAG 59.026 40.000 0.00 0.00 0.00 2.27
134 142 6.183360 CGGAAATATAGAGGCAAGCAAAAAGA 60.183 38.462 0.00 0.00 0.00 2.52
135 143 7.547227 GGAAATATAGAGGCAAGCAAAAAGAA 58.453 34.615 0.00 0.00 0.00 2.52
136 144 8.200120 GGAAATATAGAGGCAAGCAAAAAGAAT 58.800 33.333 0.00 0.00 0.00 2.40
137 145 8.937634 AAATATAGAGGCAAGCAAAAAGAATG 57.062 30.769 0.00 0.00 0.00 2.67
138 146 3.036075 AGAGGCAAGCAAAAAGAATGC 57.964 42.857 0.00 0.00 44.15 3.56
139 147 2.366266 AGAGGCAAGCAAAAAGAATGCA 59.634 40.909 0.00 0.00 46.22 3.96
140 148 2.735134 GAGGCAAGCAAAAAGAATGCAG 59.265 45.455 0.00 0.00 46.22 4.41
141 149 1.196127 GGCAAGCAAAAAGAATGCAGC 59.804 47.619 0.00 4.62 46.22 5.25
142 150 2.140717 GCAAGCAAAAAGAATGCAGCT 58.859 42.857 0.00 0.00 46.22 4.24
143 151 3.319755 GCAAGCAAAAAGAATGCAGCTA 58.680 40.909 0.00 0.00 46.22 3.32
144 152 3.367025 GCAAGCAAAAAGAATGCAGCTAG 59.633 43.478 0.00 0.00 46.22 3.42
145 153 3.227810 AGCAAAAAGAATGCAGCTAGC 57.772 42.857 6.62 6.62 46.22 3.42
205 213 4.314961 TGTGCGCTCAAATATATGTAGGG 58.685 43.478 10.16 0.00 0.00 3.53
225 233 4.058817 GGGATGATTAGCTCAAACTACGG 58.941 47.826 0.00 0.00 37.44 4.02
227 235 4.745620 GGATGATTAGCTCAAACTACGGAC 59.254 45.833 0.00 0.00 37.44 4.79
233 241 1.625616 CTCAAACTACGGACGCGAAT 58.374 50.000 15.93 0.00 0.00 3.34
234 242 1.320555 CTCAAACTACGGACGCGAATG 59.679 52.381 15.93 3.52 0.00 2.67
235 243 1.068402 TCAAACTACGGACGCGAATGA 60.068 47.619 15.93 0.28 0.00 2.57
236 244 1.924524 CAAACTACGGACGCGAATGAT 59.075 47.619 15.93 0.00 0.00 2.45
237 245 3.110358 CAAACTACGGACGCGAATGATA 58.890 45.455 15.93 0.00 0.00 2.15
239 247 2.996155 ACTACGGACGCGAATGATAAG 58.004 47.619 15.93 3.54 0.00 1.73
246 254 4.209288 CGGACGCGAATGATAAGAAGAAAT 59.791 41.667 15.93 0.00 0.00 2.17
269 277 3.191539 GTGCTGCACGCCTCTAGC 61.192 66.667 17.93 0.00 38.05 3.42
286 294 6.054295 CCTCTAGCTTCTTATTGCAGTCAAT 58.946 40.000 0.00 0.00 44.52 2.57
287 295 6.018098 CCTCTAGCTTCTTATTGCAGTCAATG 60.018 42.308 0.00 0.00 42.50 2.82
300 308 1.202568 AGTCAATGCGCTGCAGCTATA 60.203 47.619 34.22 20.92 43.65 1.31
315 323 3.085443 GCTATAGCTCTGCTGTTTCGA 57.915 47.619 17.75 0.00 40.10 3.71
316 324 3.049206 GCTATAGCTCTGCTGTTTCGAG 58.951 50.000 17.75 0.00 40.10 4.04
317 325 3.243234 GCTATAGCTCTGCTGTTTCGAGA 60.243 47.826 17.75 0.00 40.10 4.04
319 327 1.252175 AGCTCTGCTGTTTCGAGAGA 58.748 50.000 0.00 0.00 37.57 3.10
320 328 1.202114 AGCTCTGCTGTTTCGAGAGAG 59.798 52.381 0.00 0.00 38.58 3.20
321 329 1.201181 GCTCTGCTGTTTCGAGAGAGA 59.799 52.381 4.10 0.00 43.69 3.10
322 330 2.731968 GCTCTGCTGTTTCGAGAGAGAG 60.732 54.545 4.10 8.17 43.69 3.20
323 331 2.746904 CTCTGCTGTTTCGAGAGAGAGA 59.253 50.000 4.10 3.79 43.69 3.10
324 332 2.746904 TCTGCTGTTTCGAGAGAGAGAG 59.253 50.000 4.10 0.00 43.69 3.20
325 333 2.746904 CTGCTGTTTCGAGAGAGAGAGA 59.253 50.000 4.10 0.00 43.69 3.10
326 334 2.746904 TGCTGTTTCGAGAGAGAGAGAG 59.253 50.000 4.10 0.00 43.69 3.20
327 335 3.006940 GCTGTTTCGAGAGAGAGAGAGA 58.993 50.000 4.10 0.00 43.69 3.10
328 336 3.438781 GCTGTTTCGAGAGAGAGAGAGAA 59.561 47.826 4.10 0.00 43.69 2.87
329 337 4.096382 GCTGTTTCGAGAGAGAGAGAGAAT 59.904 45.833 4.10 0.00 43.69 2.40
332 340 7.172532 GCTGTTTCGAGAGAGAGAGAGAATATA 59.827 40.741 4.10 0.00 43.69 0.86
337 345 9.647797 TTCGAGAGAGAGAGAGAATATACATAC 57.352 37.037 0.00 0.00 43.69 2.39
338 346 7.971722 TCGAGAGAGAGAGAGAATATACATACG 59.028 40.741 0.00 0.00 34.84 3.06
339 347 7.253983 CGAGAGAGAGAGAGAATATACATACGC 60.254 44.444 0.00 0.00 0.00 4.42
340 348 7.620880 AGAGAGAGAGAGAATATACATACGCT 58.379 38.462 0.00 0.00 0.00 5.07
341 349 7.764443 AGAGAGAGAGAGAATATACATACGCTC 59.236 40.741 0.00 0.00 0.00 5.03
342 350 7.620880 AGAGAGAGAGAATATACATACGCTCT 58.379 38.462 0.00 0.00 40.83 4.09
346 354 6.189677 AGAGAATATACATACGCTCTCTGC 57.810 41.667 0.00 0.00 38.52 4.26
350 359 6.659668 AGAATATACATACGCTCTCTGCCTAA 59.340 38.462 0.00 0.00 38.78 2.69
361 370 4.760204 GCTCTCTGCCTAAAGTTTTACCAA 59.240 41.667 0.00 0.00 35.15 3.67
362 371 5.106515 GCTCTCTGCCTAAAGTTTTACCAAG 60.107 44.000 0.00 0.00 35.15 3.61
372 381 9.720769 CCTAAAGTTTTACCAAGAAGATCTACA 57.279 33.333 0.00 0.00 0.00 2.74
441 451 2.166829 CCTGCTGACTGAGACACTACT 58.833 52.381 0.00 0.00 0.00 2.57
442 452 2.094803 CCTGCTGACTGAGACACTACTG 60.095 54.545 0.00 0.00 0.00 2.74
443 453 2.816672 CTGCTGACTGAGACACTACTGA 59.183 50.000 0.00 0.00 0.00 3.41
457 467 0.888619 TACTGACTCAGCCACGGAAG 59.111 55.000 5.92 0.00 34.37 3.46
512 526 0.394192 TGTGCAGTGCAAGACTAGCT 59.606 50.000 21.67 0.00 41.47 3.32
514 528 2.037121 TGTGCAGTGCAAGACTAGCTAA 59.963 45.455 21.67 0.00 41.47 3.09
515 529 3.067106 GTGCAGTGCAAGACTAGCTAAA 58.933 45.455 21.67 0.00 41.47 1.85
546 2382 4.732442 GCTCGGTAAACGTGATTACTCTAC 59.268 45.833 9.39 0.00 44.69 2.59
547 2383 4.897224 TCGGTAAACGTGATTACTCTACG 58.103 43.478 9.39 5.53 44.69 3.51
551 2387 5.004156 GGTAAACGTGATTACTCTACGCTTG 59.996 44.000 9.39 0.00 41.19 4.01
552 2388 2.527100 ACGTGATTACTCTACGCTTGC 58.473 47.619 0.00 0.00 41.19 4.01
559 2395 1.517257 CTCTACGCTTGCCTCGGTG 60.517 63.158 0.00 0.00 0.00 4.94
568 2404 2.643551 CTTGCCTCGGTGGTTAATCAT 58.356 47.619 0.00 0.00 38.35 2.45
569 2405 2.036958 TGCCTCGGTGGTTAATCATG 57.963 50.000 0.00 0.00 38.35 3.07
570 2406 1.557371 TGCCTCGGTGGTTAATCATGA 59.443 47.619 0.00 0.00 38.35 3.07
571 2407 1.940613 GCCTCGGTGGTTAATCATGAC 59.059 52.381 0.00 0.00 38.35 3.06
602 2442 4.401925 AGAAAAGGTGATTCTTGACCTGG 58.598 43.478 0.00 0.00 42.03 4.45
603 2443 2.206576 AAGGTGATTCTTGACCTGGC 57.793 50.000 0.00 0.00 42.03 4.85
609 2453 0.179073 ATTCTTGACCTGGCGATCGG 60.179 55.000 18.30 2.04 0.00 4.18
617 2461 1.359117 CTGGCGATCGGACATACGT 59.641 57.895 18.30 0.00 28.99 3.57
618 2462 0.589708 CTGGCGATCGGACATACGTA 59.410 55.000 18.30 0.00 28.99 3.57
619 2463 0.308684 TGGCGATCGGACATACGTAC 59.691 55.000 18.30 0.00 34.94 3.67
620 2464 0.590195 GGCGATCGGACATACGTACT 59.410 55.000 18.30 0.00 34.94 2.73
621 2465 1.662309 GGCGATCGGACATACGTACTG 60.662 57.143 18.30 0.31 34.94 2.74
622 2466 1.003116 GCGATCGGACATACGTACTGT 60.003 52.381 18.30 3.84 34.94 3.55
623 2467 2.221749 GCGATCGGACATACGTACTGTA 59.778 50.000 18.30 0.00 37.49 2.74
624 2468 3.792294 CGATCGGACATACGTACTGTAC 58.208 50.000 7.38 7.90 35.44 2.90
638 2662 7.113704 ACGTACTGTACTACAAAGAAAATGC 57.886 36.000 15.35 0.00 0.00 3.56
643 2667 8.165239 ACTGTACTACAAAGAAAATGCATCAA 57.835 30.769 0.00 0.00 0.00 2.57
647 2675 9.243637 GTACTACAAAGAAAATGCATCAAACAA 57.756 29.630 0.00 0.00 0.00 2.83
657 2685 1.720852 GCATCAAACAATGTGAACGGC 59.279 47.619 0.00 0.00 0.00 5.68
658 2686 2.327568 CATCAAACAATGTGAACGGCC 58.672 47.619 0.00 0.00 0.00 6.13
659 2687 1.393603 TCAAACAATGTGAACGGCCA 58.606 45.000 2.24 0.00 0.00 5.36
660 2688 1.066303 TCAAACAATGTGAACGGCCAC 59.934 47.619 2.24 0.00 37.55 5.01
737 2801 2.801162 CGAGCAGTGACGTCCGTG 60.801 66.667 14.12 11.36 0.00 4.94
811 2885 5.476599 TGAGGGTCAAACCACAATGAATTAG 59.523 40.000 0.00 0.00 41.02 1.73
911 3010 1.305219 ACGGTGCCAAATGTCATCCG 61.305 55.000 6.79 6.79 41.77 4.18
990 3143 2.607635 CCTATAAAATGACGTGCGTGCT 59.392 45.455 0.67 0.00 0.00 4.40
1036 3203 3.220110 CATCCATCCATAGCTGCAAGTT 58.780 45.455 1.02 0.00 35.30 2.66
1052 3220 3.612479 GCAAGTTTCACACATCATCACCC 60.612 47.826 0.00 0.00 0.00 4.61
1053 3221 2.426522 AGTTTCACACATCATCACCCG 58.573 47.619 0.00 0.00 0.00 5.28
1105 3281 3.195698 GACTTCATGCCCGCCGAC 61.196 66.667 0.00 0.00 0.00 4.79
1204 3405 2.436292 CAGCAGCACAGGAGGCTC 60.436 66.667 5.78 5.78 40.23 4.70
1311 3512 2.164663 TGATTGCCGACATCGACGC 61.165 57.895 2.09 0.00 43.02 5.19
1312 3513 2.125713 ATTGCCGACATCGACGCA 60.126 55.556 2.09 1.89 43.02 5.24
1444 3645 4.657824 CACGGGCGACTGGACGTT 62.658 66.667 0.04 0.00 42.76 3.99
1744 3963 4.250305 ACCAAGAACGCGGCCTGT 62.250 61.111 12.47 0.00 0.00 4.00
1861 4080 4.856607 GACGAGGAAGAGGGCGCG 62.857 72.222 0.00 0.00 0.00 6.86
1891 4113 3.138798 GTGAGCGCGGAGGAGGTA 61.139 66.667 8.83 0.00 0.00 3.08
2178 4426 3.001634 CCGCATGCATGAACTGTACTTAG 59.998 47.826 30.64 0.00 0.00 2.18
2201 4453 9.720769 TTAGATTAATTATAGGTTGGCACTAGC 57.279 33.333 0.00 0.00 41.10 3.42
2267 4797 3.875727 CCTGATGAGTGGTTCATGTGATC 59.124 47.826 0.00 0.00 46.51 2.92
2276 4812 4.336433 GTGGTTCATGTGATCAACTATGGG 59.664 45.833 0.00 0.00 0.00 4.00
2360 6948 1.811359 AGTGACGCAGGAGTAGTACAC 59.189 52.381 2.52 0.00 0.00 2.90
2389 6977 3.948086 GACTGACGGTGCGGACGAG 62.948 68.421 0.00 0.00 34.93 4.18
2432 7020 1.208052 ACTGACACACTGTGCAGTTCT 59.792 47.619 22.87 9.67 42.97 3.01
2433 7021 2.283298 CTGACACACTGTGCAGTTCTT 58.717 47.619 18.21 0.00 40.20 2.52
2434 7022 2.679837 CTGACACACTGTGCAGTTCTTT 59.320 45.455 18.21 0.00 40.20 2.52
2435 7023 2.677836 TGACACACTGTGCAGTTCTTTC 59.322 45.455 9.20 0.00 40.20 2.62
2436 7024 2.939103 GACACACTGTGCAGTTCTTTCT 59.061 45.455 9.20 0.00 40.20 2.52
2437 7025 2.939103 ACACACTGTGCAGTTCTTTCTC 59.061 45.455 9.20 0.00 40.20 2.87
2440 7028 2.032204 CACTGTGCAGTTCTTTCTCAGC 60.032 50.000 1.57 0.00 40.20 4.26
2444 7033 1.301677 GCAGTTCTTTCTCAGCCGGG 61.302 60.000 2.18 0.00 0.00 5.73
2450 7039 2.227194 TCTTTCTCAGCCGGGAAAAAC 58.773 47.619 2.18 0.00 32.17 2.43
2531 7121 5.351233 TGTAGTAAAAACCATGTGAAGCG 57.649 39.130 0.00 0.00 0.00 4.68
2560 7169 2.697363 CGATGCGAATGTCACATCAAC 58.303 47.619 0.00 0.00 36.11 3.18
2574 7183 5.463724 GTCACATCAACCTAAGATCGATTCC 59.536 44.000 0.00 0.00 0.00 3.01
2585 7194 0.846015 ATCGATTCCATCTGGGCCAA 59.154 50.000 8.04 0.00 36.21 4.52
2605 7214 2.418083 CCAAGCCAAATCGCCCCTC 61.418 63.158 0.00 0.00 0.00 4.30
2631 7240 7.682628 TGTGTACTTAATTAGCTTGGTAACCT 58.317 34.615 0.00 0.00 0.00 3.50
2639 7248 1.866853 GCTTGGTAACCTGTGGCTGC 61.867 60.000 0.00 0.00 0.00 5.25
2832 8326 3.763557 ATCCAAATGATGAAGGGGTGT 57.236 42.857 0.00 0.00 30.54 4.16
2841 8335 1.525175 TGAAGGGGTGTAAACTGGGT 58.475 50.000 0.00 0.00 0.00 4.51
2880 8374 7.202047 CCTCTCACCTAAGCCTAACATCTAAAT 60.202 40.741 0.00 0.00 0.00 1.40
2933 8544 1.376037 GGGCTCAAACCGGTCTGAG 60.376 63.158 29.95 29.95 41.71 3.35
2991 9518 4.142513 GGTCCATCTTCAGAGCAAATTGAC 60.143 45.833 0.00 0.00 0.00 3.18
3004 9531 3.733684 GCAAATTGACGTGACAACCTTGT 60.734 43.478 0.00 0.00 45.65 3.16
3023 9555 2.123251 AGGTCCTCCGCCATCGAT 60.123 61.111 0.00 0.00 39.05 3.59
3126 9658 2.750637 ACGCGAGTCCATCTCCGT 60.751 61.111 15.93 0.00 44.19 4.69
3222 9755 3.785122 AAGGTTCCCAAAGCGGCGT 62.785 57.895 9.37 0.00 37.95 5.68
3240 10319 1.270147 CGTCTTCAAGAAGGGAACGGT 60.270 52.381 9.73 0.00 38.88 4.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 2.607631 TCGTTTTCCAGAGAACCGTT 57.392 45.000 0.00 0.00 31.67 4.44
24 25 3.484229 GCAACATCGATCGTTTTCCAGAG 60.484 47.826 15.94 0.00 0.00 3.35
25 26 2.415168 GCAACATCGATCGTTTTCCAGA 59.585 45.455 15.94 0.00 0.00 3.86
28 29 2.095969 TGTGCAACATCGATCGTTTTCC 60.096 45.455 15.94 1.58 45.67 3.13
54 55 2.095008 TCACGTCTCAGATGTTGCTCTC 60.095 50.000 0.00 0.00 28.28 3.20
60 61 5.223382 CAAGTTAGTCACGTCTCAGATGTT 58.777 41.667 0.00 0.00 28.28 2.71
79 80 7.554959 TCTCAGGTATAGAAAAGAACCAAGT 57.445 36.000 0.00 0.00 34.29 3.16
84 85 6.754675 GTCTGCTCTCAGGTATAGAAAAGAAC 59.245 42.308 0.00 0.00 40.69 3.01
104 112 3.386768 TGCCTCTATATTTCCGTCTGC 57.613 47.619 0.00 0.00 0.00 4.26
106 114 3.388024 TGCTTGCCTCTATATTTCCGTCT 59.612 43.478 0.00 0.00 0.00 4.18
111 119 9.028185 CATTCTTTTTGCTTGCCTCTATATTTC 57.972 33.333 0.00 0.00 0.00 2.17
116 124 4.221262 TGCATTCTTTTTGCTTGCCTCTAT 59.779 37.500 0.00 0.00 40.77 1.98
122 130 2.140717 AGCTGCATTCTTTTTGCTTGC 58.859 42.857 1.02 0.00 40.77 4.01
123 131 3.367025 GCTAGCTGCATTCTTTTTGCTTG 59.633 43.478 7.70 0.00 40.77 4.01
125 133 3.227810 GCTAGCTGCATTCTTTTTGCT 57.772 42.857 7.70 0.00 40.77 3.91
141 149 4.747108 GCCCGATACATTATGCTATGCTAG 59.253 45.833 0.00 0.00 0.00 3.42
142 150 4.405680 AGCCCGATACATTATGCTATGCTA 59.594 41.667 0.00 0.00 0.00 3.49
143 151 3.198635 AGCCCGATACATTATGCTATGCT 59.801 43.478 0.00 0.00 0.00 3.79
144 152 3.535561 AGCCCGATACATTATGCTATGC 58.464 45.455 0.00 0.00 0.00 3.14
145 153 5.050490 GGTAGCCCGATACATTATGCTATG 58.950 45.833 0.00 0.00 34.25 2.23
146 154 4.714802 TGGTAGCCCGATACATTATGCTAT 59.285 41.667 0.00 0.00 34.25 2.97
147 155 4.090819 TGGTAGCCCGATACATTATGCTA 58.909 43.478 0.00 0.00 0.00 3.49
148 156 2.903784 TGGTAGCCCGATACATTATGCT 59.096 45.455 0.00 0.00 0.00 3.79
149 157 3.328382 TGGTAGCCCGATACATTATGC 57.672 47.619 0.00 0.00 0.00 3.14
150 158 5.487433 TGATTGGTAGCCCGATACATTATG 58.513 41.667 0.00 0.00 34.74 1.90
151 159 5.755409 TGATTGGTAGCCCGATACATTAT 57.245 39.130 0.00 0.00 34.74 1.28
152 160 5.554437 TTGATTGGTAGCCCGATACATTA 57.446 39.130 0.00 0.00 34.74 1.90
153 161 4.431416 TTGATTGGTAGCCCGATACATT 57.569 40.909 0.00 0.00 34.74 2.71
154 162 4.326826 CATTGATTGGTAGCCCGATACAT 58.673 43.478 0.00 0.00 34.74 2.29
155 163 3.738982 CATTGATTGGTAGCCCGATACA 58.261 45.455 0.00 0.00 34.74 2.29
156 164 2.484264 GCATTGATTGGTAGCCCGATAC 59.516 50.000 0.00 0.00 34.74 2.24
157 165 2.778299 GCATTGATTGGTAGCCCGATA 58.222 47.619 0.00 0.00 34.74 2.92
205 213 4.441415 CGTCCGTAGTTTGAGCTAATCATC 59.559 45.833 0.00 0.00 37.89 2.92
225 233 5.435557 CCATTTCTTCTTATCATTCGCGTC 58.564 41.667 5.77 0.00 0.00 5.19
227 235 4.273480 ACCCATTTCTTCTTATCATTCGCG 59.727 41.667 0.00 0.00 0.00 5.87
233 241 3.938963 GCACGACCCATTTCTTCTTATCA 59.061 43.478 0.00 0.00 0.00 2.15
234 242 4.034510 CAGCACGACCCATTTCTTCTTATC 59.965 45.833 0.00 0.00 0.00 1.75
235 243 3.941483 CAGCACGACCCATTTCTTCTTAT 59.059 43.478 0.00 0.00 0.00 1.73
236 244 3.334691 CAGCACGACCCATTTCTTCTTA 58.665 45.455 0.00 0.00 0.00 2.10
237 245 2.154462 CAGCACGACCCATTTCTTCTT 58.846 47.619 0.00 0.00 0.00 2.52
239 247 0.169009 GCAGCACGACCCATTTCTTC 59.831 55.000 0.00 0.00 0.00 2.87
300 308 1.202114 CTCTCTCGAAACAGCAGAGCT 59.798 52.381 0.00 0.00 40.77 4.09
314 322 7.764443 AGCGTATGTATATTCTCTCTCTCTCTC 59.236 40.741 0.00 0.00 0.00 3.20
315 323 7.620880 AGCGTATGTATATTCTCTCTCTCTCT 58.379 38.462 0.00 0.00 0.00 3.10
316 324 7.764443 AGAGCGTATGTATATTCTCTCTCTCTC 59.236 40.741 0.00 0.00 0.00 3.20
317 325 7.620880 AGAGCGTATGTATATTCTCTCTCTCT 58.379 38.462 0.00 0.00 0.00 3.10
319 327 7.843490 GAGAGCGTATGTATATTCTCTCTCT 57.157 40.000 14.65 5.85 41.77 3.10
322 330 6.255215 GCAGAGAGCGTATGTATATTCTCTC 58.745 44.000 16.86 16.86 44.00 3.20
323 331 6.189677 GCAGAGAGCGTATGTATATTCTCT 57.810 41.667 0.00 0.00 41.36 3.10
338 346 4.324267 TGGTAAAACTTTAGGCAGAGAGC 58.676 43.478 0.00 0.00 44.65 4.09
339 347 6.231211 TCTTGGTAAAACTTTAGGCAGAGAG 58.769 40.000 0.00 0.00 0.00 3.20
340 348 6.182507 TCTTGGTAAAACTTTAGGCAGAGA 57.817 37.500 0.00 0.00 0.00 3.10
341 349 6.710744 TCTTCTTGGTAAAACTTTAGGCAGAG 59.289 38.462 0.00 0.00 0.00 3.35
342 350 6.597562 TCTTCTTGGTAAAACTTTAGGCAGA 58.402 36.000 0.00 0.00 0.00 4.26
343 351 6.877611 TCTTCTTGGTAAAACTTTAGGCAG 57.122 37.500 0.00 0.00 0.00 4.85
344 352 7.231467 AGATCTTCTTGGTAAAACTTTAGGCA 58.769 34.615 0.00 0.00 0.00 4.75
345 353 7.689446 AGATCTTCTTGGTAAAACTTTAGGC 57.311 36.000 0.00 0.00 0.00 3.93
346 354 9.720769 TGTAGATCTTCTTGGTAAAACTTTAGG 57.279 33.333 0.00 0.00 0.00 2.69
350 359 9.628500 ACTTTGTAGATCTTCTTGGTAAAACTT 57.372 29.630 0.00 0.00 0.00 2.66
441 451 2.343758 GCTTCCGTGGCTGAGTCA 59.656 61.111 0.00 0.00 0.00 3.41
442 452 2.029844 GTGCTTCCGTGGCTGAGTC 61.030 63.158 0.00 0.00 0.00 3.36
443 453 2.031163 GTGCTTCCGTGGCTGAGT 59.969 61.111 0.00 0.00 0.00 3.41
462 472 2.530497 AAGTTGCAAGACGCGCGAA 61.530 52.632 39.36 16.83 46.97 4.70
489 503 0.313043 AGTCTTGCACTGCACATTGC 59.687 50.000 2.26 6.06 45.29 3.56
514 528 2.679336 ACGTTTACCGAGCTGTGTTTTT 59.321 40.909 0.00 0.00 40.70 1.94
515 529 2.031191 CACGTTTACCGAGCTGTGTTTT 59.969 45.455 0.00 0.00 40.70 2.43
546 2382 1.024579 ATTAACCACCGAGGCAAGCG 61.025 55.000 0.00 0.00 43.14 4.68
547 2383 0.733150 GATTAACCACCGAGGCAAGC 59.267 55.000 0.00 0.00 43.14 4.01
551 2387 1.940613 GTCATGATTAACCACCGAGGC 59.059 52.381 0.00 0.00 43.14 4.70
552 2388 3.118775 TCAGTCATGATTAACCACCGAGG 60.119 47.826 0.00 0.00 45.67 4.63
559 2395 5.734720 TCTCCAAGTCAGTCATGATTAACC 58.265 41.667 0.00 0.00 37.87 2.85
568 2404 3.454447 TCACCTTTTCTCCAAGTCAGTCA 59.546 43.478 0.00 0.00 0.00 3.41
569 2405 4.073293 TCACCTTTTCTCCAAGTCAGTC 57.927 45.455 0.00 0.00 0.00 3.51
570 2406 4.713792 ATCACCTTTTCTCCAAGTCAGT 57.286 40.909 0.00 0.00 0.00 3.41
571 2407 5.312079 AGAATCACCTTTTCTCCAAGTCAG 58.688 41.667 0.00 0.00 0.00 3.51
602 2442 1.003116 ACAGTACGTATGTCCGATCGC 60.003 52.381 10.32 0.00 0.00 4.58
603 2443 3.492383 AGTACAGTACGTATGTCCGATCG 59.508 47.826 8.51 8.51 31.20 3.69
609 2453 8.955061 TTTCTTTGTAGTACAGTACGTATGTC 57.045 34.615 12.06 6.67 31.20 3.06
617 2461 8.840833 TGATGCATTTTCTTTGTAGTACAGTA 57.159 30.769 0.00 0.00 0.00 2.74
618 2462 7.744087 TGATGCATTTTCTTTGTAGTACAGT 57.256 32.000 0.00 0.00 0.00 3.55
619 2463 8.905702 GTTTGATGCATTTTCTTTGTAGTACAG 58.094 33.333 0.00 0.00 0.00 2.74
620 2464 8.409371 TGTTTGATGCATTTTCTTTGTAGTACA 58.591 29.630 0.00 0.00 0.00 2.90
621 2465 8.795786 TGTTTGATGCATTTTCTTTGTAGTAC 57.204 30.769 0.00 0.00 0.00 2.73
622 2466 9.979578 ATTGTTTGATGCATTTTCTTTGTAGTA 57.020 25.926 0.00 0.00 0.00 1.82
623 2467 8.767085 CATTGTTTGATGCATTTTCTTTGTAGT 58.233 29.630 0.00 0.00 0.00 2.73
624 2468 8.767085 ACATTGTTTGATGCATTTTCTTTGTAG 58.233 29.630 0.00 0.00 0.00 2.74
638 2662 2.288091 TGGCCGTTCACATTGTTTGATG 60.288 45.455 0.00 0.00 0.00 3.07
643 2667 0.667993 CTGTGGCCGTTCACATTGTT 59.332 50.000 0.00 0.00 45.26 2.83
667 2695 1.028868 GGTCAACTGATGCCAGCCTC 61.029 60.000 0.00 0.00 44.16 4.70
680 2708 0.535102 CATATCCCGGGCTGGTCAAC 60.535 60.000 18.49 0.00 35.15 3.18
737 2801 2.474359 GAGAGCGATGTATGCATGTCAC 59.526 50.000 10.16 0.00 35.07 3.67
811 2885 9.310716 GTTAATCTGGTGGTACTAATTCTGTAC 57.689 37.037 11.17 11.17 39.43 2.90
887 2986 0.521735 GACATTTGGCACCGTCTTCC 59.478 55.000 0.00 0.00 0.00 3.46
967 3120 3.062909 GCACGCACGTCATTTTATAGGAA 59.937 43.478 0.00 0.00 0.00 3.36
990 3143 3.458163 GTGGGACGGGATCGAGCA 61.458 66.667 1.84 0.00 40.11 4.26
1036 3203 1.018752 CGCGGGTGATGATGTGTGAA 61.019 55.000 0.00 0.00 0.00 3.18
1204 3405 3.406595 GATGGCCACCTTCCCCTCG 62.407 68.421 8.16 0.00 0.00 4.63
1435 3636 0.464036 TGTTGCAGAGAACGTCCAGT 59.536 50.000 0.00 0.00 0.00 4.00
1444 3645 2.664851 CCGGCGTTGTTGCAGAGA 60.665 61.111 6.01 0.00 36.28 3.10
1831 4050 2.994995 TCGTCCTCGCCATGGTGT 60.995 61.111 24.28 0.00 36.96 4.16
1891 4113 0.758685 CCATCTCCTCCGCCTTCTCT 60.759 60.000 0.00 0.00 0.00 3.10
2003 4225 2.668550 GAGGTTGTGCCCGGACAC 60.669 66.667 14.79 14.79 41.10 3.67
2005 4227 4.309950 ACGAGGTTGTGCCCGGAC 62.310 66.667 0.73 0.00 38.26 4.79
2178 4426 6.092259 CCGCTAGTGCCAACCTATAATTAATC 59.908 42.308 0.00 0.00 35.36 1.75
2201 4453 5.009811 AGCAGCTAATTACTCCTACTTACCG 59.990 44.000 0.00 0.00 0.00 4.02
2267 4797 1.923356 ACCAGGCAAACCCATAGTTG 58.077 50.000 0.00 0.00 39.19 3.16
2276 4812 3.796717 CGAAGAAGAAAAACCAGGCAAAC 59.203 43.478 0.00 0.00 0.00 2.93
2360 6948 1.213013 CGTCAGTCCCGAACAGGAG 59.787 63.158 0.00 0.00 45.00 3.69
2389 6977 0.819259 TGCCTCCAACACTCAACAGC 60.819 55.000 0.00 0.00 0.00 4.40
2391 6979 0.819259 GCTGCCTCCAACACTCAACA 60.819 55.000 0.00 0.00 0.00 3.33
2432 7020 2.158667 AGAGTTTTTCCCGGCTGAGAAA 60.159 45.455 0.00 0.00 0.00 2.52
2433 7021 1.420138 AGAGTTTTTCCCGGCTGAGAA 59.580 47.619 0.00 0.00 0.00 2.87
2434 7022 1.056660 AGAGTTTTTCCCGGCTGAGA 58.943 50.000 0.00 0.00 0.00 3.27
2435 7023 1.160137 CAGAGTTTTTCCCGGCTGAG 58.840 55.000 0.00 0.00 0.00 3.35
2436 7024 0.250727 CCAGAGTTTTTCCCGGCTGA 60.251 55.000 0.00 0.00 0.00 4.26
2437 7025 1.866853 GCCAGAGTTTTTCCCGGCTG 61.867 60.000 0.00 0.00 40.24 4.85
2440 7028 0.821711 TGTGCCAGAGTTTTTCCCGG 60.822 55.000 0.00 0.00 0.00 5.73
2444 7033 4.836125 TCATTCTGTGCCAGAGTTTTTC 57.164 40.909 5.26 0.00 41.75 2.29
2450 7039 3.247886 CGATGAATCATTCTGTGCCAGAG 59.752 47.826 0.00 0.00 41.75 3.35
2511 7101 5.543714 TCTCGCTTCACATGGTTTTTACTA 58.456 37.500 0.00 0.00 0.00 1.82
2515 7105 4.853924 ATTCTCGCTTCACATGGTTTTT 57.146 36.364 0.00 0.00 0.00 1.94
2543 7152 2.183478 AGGTTGATGTGACATTCGCA 57.817 45.000 0.00 0.00 41.54 5.10
2585 7194 3.070576 GGGCGATTTGGCTTGGCT 61.071 61.111 0.00 0.00 44.11 4.75
2596 7205 2.154567 TAAGTACACAGAGGGGCGAT 57.845 50.000 0.00 0.00 0.00 4.58
2597 7206 1.927487 TTAAGTACACAGAGGGGCGA 58.073 50.000 0.00 0.00 0.00 5.54
2605 7214 7.822822 AGGTTACCAAGCTAATTAAGTACACAG 59.177 37.037 3.51 0.00 37.49 3.66
2631 7240 2.591923 TCCAATAAACAAGCAGCCACA 58.408 42.857 0.00 0.00 0.00 4.17
2639 7248 7.874940 TCAGTCAAACAGATCCAATAAACAAG 58.125 34.615 0.00 0.00 0.00 3.16
2690 7362 2.688666 AGATGCAGAGGCCGGGAA 60.689 61.111 2.18 0.00 40.13 3.97
2841 8335 3.052109 AGGTGAGAGGTATGGGTATGTGA 60.052 47.826 0.00 0.00 0.00 3.58
2933 8544 2.730672 GACGACACATGTGAGCGCC 61.731 63.158 31.94 21.42 36.17 6.53
3004 9531 2.928988 ATCGATGGCGGAGGACCTGA 62.929 60.000 0.00 0.00 38.28 3.86
3023 9555 1.098712 GTGGAGGTTGTCGTTTGGCA 61.099 55.000 0.00 0.00 0.00 4.92
3071 9603 2.860293 CATCGTGGTGGCGTCAAC 59.140 61.111 0.00 0.00 0.00 3.18
3126 9658 1.735018 CATGGATTTACGTCCGTTGCA 59.265 47.619 0.00 0.00 41.35 4.08
3222 9755 1.542547 GCACCGTTCCCTTCTTGAAGA 60.543 52.381 11.53 0.00 0.00 2.87


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

AutoCloner maintained by Alex Coulton.