Multiple sequence alignment - TraesCS7D01G439000

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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 TraesCS7D01G439000 chr7D 100.000 2033 0 0 1 2033 558782461 558784493 0.000000e+00 3755.0
1 TraesCS7D01G439000 chr7D 100.000 303 0 0 2199 2501 558784659 558784961 6.040000e-156 560.0
2 TraesCS7D01G439000 chr6D 88.254 962 58 18 662 1595 767388 768322 0.000000e+00 1099.0
3 TraesCS7D01G439000 chr6D 91.029 379 32 2 624 1002 430010 429634 6.170000e-141 510.0
4 TraesCS7D01G439000 chr6D 90.617 373 22 5 990 1349 427696 427324 1.350000e-132 483.0
5 TraesCS7D01G439000 chr6D 91.000 300 27 0 2199 2498 789999 790298 3.000000e-109 405.0
6 TraesCS7D01G439000 chr6D 89.388 245 22 3 1787 2031 789716 789956 3.130000e-79 305.0
7 TraesCS7D01G439000 chr6D 87.218 266 28 4 2 265 430471 430210 5.230000e-77 298.0
8 TraesCS7D01G439000 chr6D 91.080 213 19 0 1377 1589 392101 391889 3.150000e-74 289.0
9 TraesCS7D01G439000 chr6D 83.396 265 24 11 2 256 393625 393371 6.960000e-56 228.0
10 TraesCS7D01G439000 chr6D 92.568 148 11 0 1159 1306 393282 393135 1.950000e-51 213.0
11 TraesCS7D01G439000 chr6D 92.035 113 8 1 520 631 767188 767300 9.260000e-35 158.0
12 TraesCS7D01G439000 chr6D 94.845 97 5 0 532 628 430184 430088 4.310000e-33 152.0
13 TraesCS7D01G439000 chr6D 93.548 62 4 0 201 262 767049 767110 2.650000e-15 93.5
14 TraesCS7D01G439000 chr6D 97.674 43 1 0 1198 1240 393371 393329 9.590000e-10 75.0
15 TraesCS7D01G439000 chr6D 97.436 39 1 0 945 983 393319 393281 1.610000e-07 67.6
16 TraesCS7D01G439000 chr6B 93.612 454 28 1 1155 1608 3104637 3105089 0.000000e+00 676.0
17 TraesCS7D01G439000 chr6B 89.378 386 37 1 1648 2033 3105210 3105591 1.350000e-132 483.0
18 TraesCS7D01G439000 chr6B 90.698 301 25 3 2199 2498 3105632 3105930 5.010000e-107 398.0
19 TraesCS7D01G439000 chr1A 94.643 56 3 0 2402 2457 581918509 581918564 1.230000e-13 87.9
20 TraesCS7D01G439000 chr7A 85.135 74 8 3 444 517 651756692 651756762 3.450000e-09 73.1
21 TraesCS7D01G439000 chr3B 88.235 51 4 2 444 493 8108042 8107993 2.690000e-05 60.2


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 TraesCS7D01G439000 chr7D 558782461 558784961 2500 False 2157.500000 3755 100.000000 1 2501 2 chr7D.!!$F1 2500
1 TraesCS7D01G439000 chr6D 767049 768322 1273 False 450.166667 1099 91.279000 201 1595 3 chr6D.!!$F1 1394
2 TraesCS7D01G439000 chr6D 427324 430471 3147 True 360.750000 510 90.927250 2 1349 4 chr6D.!!$R2 1347
3 TraesCS7D01G439000 chr6D 789716 790298 582 False 355.000000 405 90.194000 1787 2498 2 chr6D.!!$F2 711
4 TraesCS7D01G439000 chr6B 3104637 3105930 1293 False 519.000000 676 91.229333 1155 2498 3 chr6B.!!$F1 1343

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
276 279 0.098728 GTTTCGCGGGTCAATCCATG 59.901 55.0 6.13 0.0 38.11 3.66 F
652 655 0.316772 CGTCTACGGCATAGTCGTGG 60.317 60.0 6.94 3.9 45.67 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1410 3501 0.035630 GCATCTCACAGGAGCCAACT 60.036 55.0 0.0 0.0 41.13 3.16 R
1897 4069 0.251341 GCAAGAAAGGAAGCTGGGGA 60.251 55.0 0.0 0.0 0.00 4.81 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
37 38 4.969196 ATATCAGCGCGGCCACGG 62.969 66.667 16.11 0.00 41.36 4.94
63 66 3.724914 GAAGAAGGCCGGCGGAGAG 62.725 68.421 33.44 2.59 0.00 3.20
112 115 3.134127 GCTCGCCGGCCAAAAGAT 61.134 61.111 23.46 0.00 0.00 2.40
124 127 3.134458 GCCAAAAGATATGGAGACGGAG 58.866 50.000 0.00 0.00 40.56 4.63
127 130 1.343069 AAGATATGGAGACGGAGCCC 58.657 55.000 0.00 0.00 0.00 5.19
163 166 2.970324 GTGAACGCCCACGAAGCA 60.970 61.111 0.00 0.00 43.93 3.91
196 199 4.668289 GTGTTTTCTGGAACGACATGTTT 58.332 39.130 0.00 0.00 42.09 2.83
202 205 1.751351 TGGAACGACATGTTTGCCAAA 59.249 42.857 0.00 0.00 42.09 3.28
262 265 0.516877 TGCAGCCTTGAATCGTTTCG 59.483 50.000 2.00 0.00 34.39 3.46
265 268 1.226018 GCCTTGAATCGTTTCGCGG 60.226 57.895 6.13 8.47 41.72 6.46
266 269 1.423845 CCTTGAATCGTTTCGCGGG 59.576 57.895 6.13 0.00 41.72 6.13
269 272 0.600518 TTGAATCGTTTCGCGGGTCA 60.601 50.000 6.13 0.00 41.72 4.02
270 273 0.600518 TGAATCGTTTCGCGGGTCAA 60.601 50.000 6.13 0.00 41.72 3.18
271 274 0.725117 GAATCGTTTCGCGGGTCAAT 59.275 50.000 6.13 0.00 41.72 2.57
272 275 0.725117 AATCGTTTCGCGGGTCAATC 59.275 50.000 6.13 0.00 41.72 2.67
273 276 1.087771 ATCGTTTCGCGGGTCAATCC 61.088 55.000 6.13 0.00 41.72 3.01
276 279 0.098728 GTTTCGCGGGTCAATCCATG 59.901 55.000 6.13 0.00 38.11 3.66
277 280 1.653094 TTTCGCGGGTCAATCCATGC 61.653 55.000 6.13 0.00 38.11 4.06
278 281 2.811542 TTCGCGGGTCAATCCATGCA 62.812 55.000 6.13 0.00 38.49 3.96
279 282 2.800736 GCGGGTCAATCCATGCAC 59.199 61.111 0.00 0.00 38.46 4.57
283 286 1.656818 GGGTCAATCCATGCACACCG 61.657 60.000 0.00 0.00 38.11 4.94
284 287 1.137404 GTCAATCCATGCACACCGC 59.863 57.895 0.00 0.00 42.89 5.68
285 288 2.045708 TCAATCCATGCACACCGCC 61.046 57.895 0.00 0.00 41.33 6.13
286 289 2.755469 AATCCATGCACACCGCCC 60.755 61.111 0.00 0.00 41.33 6.13
287 290 3.286694 AATCCATGCACACCGCCCT 62.287 57.895 0.00 0.00 41.33 5.19
288 291 2.786512 AATCCATGCACACCGCCCTT 62.787 55.000 0.00 0.00 41.33 3.95
289 292 1.920734 ATCCATGCACACCGCCCTTA 61.921 55.000 0.00 0.00 41.33 2.69
290 293 1.677300 CCATGCACACCGCCCTTAA 60.677 57.895 0.00 0.00 41.33 1.85
291 294 1.506262 CATGCACACCGCCCTTAAC 59.494 57.895 0.00 0.00 41.33 2.01
293 296 0.960364 ATGCACACCGCCCTTAACTG 60.960 55.000 0.00 0.00 41.33 3.16
294 297 2.978018 GCACACCGCCCTTAACTGC 61.978 63.158 0.00 0.00 32.94 4.40
295 298 1.599518 CACACCGCCCTTAACTGCA 60.600 57.895 0.00 0.00 0.00 4.41
296 299 1.599797 ACACCGCCCTTAACTGCAC 60.600 57.895 0.00 0.00 0.00 4.57
297 300 1.599518 CACCGCCCTTAACTGCACA 60.600 57.895 0.00 0.00 0.00 4.57
298 301 1.599797 ACCGCCCTTAACTGCACAC 60.600 57.895 0.00 0.00 0.00 3.82
300 303 1.169661 CCGCCCTTAACTGCACACAA 61.170 55.000 0.00 0.00 0.00 3.33
313 316 5.381757 ACTGCACACAACCCTTAATTTCTA 58.618 37.500 0.00 0.00 0.00 2.10
314 317 6.010219 ACTGCACACAACCCTTAATTTCTAT 58.990 36.000 0.00 0.00 0.00 1.98
316 319 7.015195 ACTGCACACAACCCTTAATTTCTATTT 59.985 33.333 0.00 0.00 0.00 1.40
317 320 7.731054 TGCACACAACCCTTAATTTCTATTTT 58.269 30.769 0.00 0.00 0.00 1.82
318 321 8.207545 TGCACACAACCCTTAATTTCTATTTTT 58.792 29.630 0.00 0.00 0.00 1.94
319 322 9.699703 GCACACAACCCTTAATTTCTATTTTTA 57.300 29.630 0.00 0.00 0.00 1.52
399 402 8.322906 TCACAAAGTCTGATTATGTTTGTAGG 57.677 34.615 0.00 0.00 38.87 3.18
400 403 8.154203 TCACAAAGTCTGATTATGTTTGTAGGA 58.846 33.333 0.00 0.00 38.87 2.94
401 404 8.783093 CACAAAGTCTGATTATGTTTGTAGGAA 58.217 33.333 0.00 0.00 38.87 3.36
402 405 9.349713 ACAAAGTCTGATTATGTTTGTAGGAAA 57.650 29.630 0.00 0.00 39.07 3.13
432 435 5.902681 TCTACATTCAGAGTATCAAACCCG 58.097 41.667 0.00 0.00 37.82 5.28
433 436 4.553330 ACATTCAGAGTATCAAACCCGT 57.447 40.909 0.00 0.00 37.82 5.28
434 437 5.670792 ACATTCAGAGTATCAAACCCGTA 57.329 39.130 0.00 0.00 37.82 4.02
435 438 6.235231 ACATTCAGAGTATCAAACCCGTAT 57.765 37.500 0.00 0.00 37.82 3.06
436 439 6.281405 ACATTCAGAGTATCAAACCCGTATC 58.719 40.000 0.00 0.00 37.82 2.24
437 440 5.925506 TTCAGAGTATCAAACCCGTATCA 57.074 39.130 0.00 0.00 37.82 2.15
438 441 5.925506 TCAGAGTATCAAACCCGTATCAA 57.074 39.130 0.00 0.00 37.82 2.57
439 442 6.288941 TCAGAGTATCAAACCCGTATCAAA 57.711 37.500 0.00 0.00 37.82 2.69
440 443 6.103997 TCAGAGTATCAAACCCGTATCAAAC 58.896 40.000 0.00 0.00 37.82 2.93
441 444 5.293569 CAGAGTATCAAACCCGTATCAAACC 59.706 44.000 0.00 0.00 37.82 3.27
442 445 5.046159 AGAGTATCAAACCCGTATCAAACCA 60.046 40.000 0.00 0.00 37.82 3.67
443 446 5.562635 AGTATCAAACCCGTATCAAACCAA 58.437 37.500 0.00 0.00 0.00 3.67
444 447 6.184789 AGTATCAAACCCGTATCAAACCAAT 58.815 36.000 0.00 0.00 0.00 3.16
445 448 7.340256 AGTATCAAACCCGTATCAAACCAATA 58.660 34.615 0.00 0.00 0.00 1.90
446 449 7.830201 AGTATCAAACCCGTATCAAACCAATAA 59.170 33.333 0.00 0.00 0.00 1.40
447 450 6.256912 TCAAACCCGTATCAAACCAATAAC 57.743 37.500 0.00 0.00 0.00 1.89
448 451 6.005198 TCAAACCCGTATCAAACCAATAACT 58.995 36.000 0.00 0.00 0.00 2.24
449 452 6.490721 TCAAACCCGTATCAAACCAATAACTT 59.509 34.615 0.00 0.00 0.00 2.66
450 453 6.904463 AACCCGTATCAAACCAATAACTTT 57.096 33.333 0.00 0.00 0.00 2.66
451 454 7.999450 AACCCGTATCAAACCAATAACTTTA 57.001 32.000 0.00 0.00 0.00 1.85
452 455 7.999450 ACCCGTATCAAACCAATAACTTTAA 57.001 32.000 0.00 0.00 0.00 1.52
453 456 8.584063 ACCCGTATCAAACCAATAACTTTAAT 57.416 30.769 0.00 0.00 0.00 1.40
454 457 9.683870 ACCCGTATCAAACCAATAACTTTAATA 57.316 29.630 0.00 0.00 0.00 0.98
544 547 6.542005 TCTCTGCCGCAATTTTAATCATTCTA 59.458 34.615 0.00 0.00 0.00 2.10
581 584 1.124297 GTTACGTGCACTGTGATCGTG 59.876 52.381 27.32 10.89 36.24 4.35
628 631 1.746322 TTTCACCGACGGTAGCCACA 61.746 55.000 21.25 0.00 32.11 4.17
629 632 1.537814 TTCACCGACGGTAGCCACAT 61.538 55.000 21.25 0.00 32.11 3.21
630 633 1.809619 CACCGACGGTAGCCACATG 60.810 63.158 21.25 0.15 32.11 3.21
634 637 1.518572 GACGGTAGCCACATGGACG 60.519 63.158 0.87 2.89 37.39 4.79
637 640 1.898154 GGTAGCCACATGGACGTCT 59.102 57.895 16.46 0.00 37.39 4.18
638 641 1.108776 GGTAGCCACATGGACGTCTA 58.891 55.000 16.46 10.40 37.39 2.59
640 643 0.736636 TAGCCACATGGACGTCTACG 59.263 55.000 16.46 4.06 39.60 3.51
641 644 1.518572 GCCACATGGACGTCTACGG 60.519 63.158 16.46 12.04 38.63 4.02
650 653 2.772739 ACGTCTACGGCATAGTCGT 58.227 52.632 7.04 7.04 46.44 4.34
651 654 3.144300 CGTCTACGGCATAGTCGTG 57.856 57.895 6.94 0.00 45.67 4.35
652 655 0.316772 CGTCTACGGCATAGTCGTGG 60.317 60.000 6.94 3.90 45.67 4.94
654 657 1.299926 CTACGGCATAGTCGTGGCC 60.300 63.158 6.94 0.00 45.67 5.36
743 827 2.425312 CCAAGCAGGTTTGTACACACAA 59.575 45.455 13.84 0.00 42.93 3.33
766 850 2.510918 GGCCGCCTACTTCGTTCC 60.511 66.667 0.71 0.00 0.00 3.62
786 874 1.860676 GCGACGATACTATTTGGCCA 58.139 50.000 0.00 0.00 0.00 5.36
795 883 5.700832 CGATACTATTTGGCCAGCTTAATCA 59.299 40.000 5.11 0.00 0.00 2.57
836 931 2.291365 GTCATGTGCATGCATACAGGA 58.709 47.619 25.64 21.32 38.65 3.86
894 997 2.492019 TGCTATCTGTCGATCCAACG 57.508 50.000 0.00 0.00 0.00 4.10
1025 3086 1.353022 GTACCATGAAGGGACCACCAA 59.647 52.381 0.00 0.00 46.51 3.67
1040 3101 2.253452 CAACAAGCTCAGCACGCC 59.747 61.111 0.00 0.00 0.00 5.68
1053 3114 1.372087 GCACGCCAGAGCTAGCATTT 61.372 55.000 18.83 0.00 36.70 2.32
1102 3163 2.223971 ACGATCAGTGTGGAAGTCGTTT 60.224 45.455 0.00 0.00 38.98 3.60
1116 3177 0.464735 TCGTTTATGGGGATTGGCCG 60.465 55.000 0.00 0.00 37.63 6.13
1197 3275 1.317613 TGCTTGCATTTGAAGACGGT 58.682 45.000 0.00 0.00 0.00 4.83
1209 3287 7.148373 GCATTTGAAGACGGTAAATTACTACCA 60.148 37.037 2.96 0.00 41.38 3.25
1275 3353 4.047059 GTCGAACTCCGTCGGCCA 62.047 66.667 6.34 0.00 39.72 5.36
1350 3441 5.295787 GCGTATCAACAGGGAAAATGATGTA 59.704 40.000 0.00 0.00 34.54 2.29
1357 3448 6.078456 ACAGGGAAAATGATGTATGGAGAA 57.922 37.500 0.00 0.00 0.00 2.87
1362 3453 6.041296 GGGAAAATGATGTATGGAGAAATGCT 59.959 38.462 0.00 0.00 0.00 3.79
1378 3469 1.803334 TGCTGTAGCTTTTACACCCG 58.197 50.000 5.38 0.00 42.66 5.28
1395 3486 1.646189 CCGAGAAAGCAGGTAGAAGC 58.354 55.000 0.00 0.00 0.00 3.86
1404 3495 1.474307 AGGTAGAAGCCTGGGGACA 59.526 57.895 0.00 0.00 37.50 4.02
1410 3501 2.062636 AGAAGCCTGGGGACACTTAAA 58.937 47.619 0.00 0.00 35.60 1.52
1549 3640 6.050432 TTGGAGTTTAACGTGAACTACACAT 58.950 36.000 22.68 1.96 45.17 3.21
1598 3689 8.076714 ACATGCATGTAATAATGTTAGACTCG 57.923 34.615 30.50 0.00 39.68 4.18
1624 3749 4.436050 CGTGCATAGGATCAGTTGTTTGTC 60.436 45.833 0.00 0.00 0.00 3.18
1629 3754 6.621596 GCATAGGATCAGTTGTTTGTCTGTTC 60.622 42.308 0.00 0.00 33.89 3.18
1631 3756 5.440610 AGGATCAGTTGTTTGTCTGTTCTT 58.559 37.500 0.00 0.00 33.51 2.52
1637 3762 5.732647 CAGTTGTTTGTCTGTTCTTTACGTG 59.267 40.000 0.00 0.00 0.00 4.49
1640 3765 4.691685 TGTTTGTCTGTTCTTTACGTGTGT 59.308 37.500 0.00 0.00 0.00 3.72
1641 3766 5.868258 TGTTTGTCTGTTCTTTACGTGTGTA 59.132 36.000 0.00 0.00 0.00 2.90
1642 3767 5.954434 TTGTCTGTTCTTTACGTGTGTAC 57.046 39.130 0.00 0.00 0.00 2.90
1643 3768 4.362279 TGTCTGTTCTTTACGTGTGTACC 58.638 43.478 0.00 0.00 0.00 3.34
1644 3769 4.098349 TGTCTGTTCTTTACGTGTGTACCT 59.902 41.667 0.00 0.00 0.00 3.08
1645 3770 5.299028 TGTCTGTTCTTTACGTGTGTACCTA 59.701 40.000 0.00 0.00 0.00 3.08
1655 3827 3.567530 CGTGTGTACCTATTTCACGTCA 58.432 45.455 7.65 0.00 44.07 4.35
1706 3878 8.748412 CATTTTGATCCCTAGTTTACATTCCAA 58.252 33.333 0.00 0.00 0.00 3.53
1714 3886 7.060421 CCCTAGTTTACATTCCAACATGGTAT 58.940 38.462 0.00 0.00 39.03 2.73
1729 3901 7.941238 CCAACATGGTATCAGATTCTTAATCCT 59.059 37.037 0.00 0.00 33.87 3.24
1746 3918 0.318762 CCTAGTCCTATGCTTCCGCC 59.681 60.000 0.00 0.00 34.43 6.13
1758 3930 3.309436 TTCCGCCATGTCCACCGAG 62.309 63.158 0.00 0.00 0.00 4.63
1763 3935 2.509336 CATGTCCACCGAGTCCGC 60.509 66.667 0.00 0.00 0.00 5.54
1764 3936 2.994995 ATGTCCACCGAGTCCGCA 60.995 61.111 0.00 0.00 0.00 5.69
1772 3944 4.363990 CGAGTCCGCAGCTGGTGT 62.364 66.667 17.12 0.00 0.00 4.16
1773 3945 2.433318 GAGTCCGCAGCTGGTGTC 60.433 66.667 17.12 0.00 0.00 3.67
1778 3950 4.081030 CGCAGCTGGTGTCGCAAG 62.081 66.667 17.12 0.00 0.00 4.01
1781 3953 3.946201 AGCTGGTGTCGCAAGCCT 61.946 61.111 9.24 0.00 37.68 4.58
1811 3983 2.534990 CACCTCTCCCTCTTCTCTGTT 58.465 52.381 0.00 0.00 0.00 3.16
1843 4015 2.831526 GCTCTTCTGGTCTCTTCCTCTT 59.168 50.000 0.00 0.00 0.00 2.85
1869 4041 1.856629 CCTCCTTGCCAATCACCAAT 58.143 50.000 0.00 0.00 0.00 3.16
1887 4059 3.204526 CAATAGCCAGCTTCTTCCTCTG 58.795 50.000 0.00 0.00 0.00 3.35
1909 4081 2.543067 GATTGCGTCCCCAGCTTCCT 62.543 60.000 0.00 0.00 35.28 3.36
1910 4082 2.142292 ATTGCGTCCCCAGCTTCCTT 62.142 55.000 0.00 0.00 35.28 3.36
1911 4083 2.034221 GCGTCCCCAGCTTCCTTT 59.966 61.111 0.00 0.00 0.00 3.11
1925 4097 0.105224 TCCTTTCTTGCGTTCCACGA 59.895 50.000 0.00 0.00 46.05 4.35
1971 4143 1.807165 CCACCATGTGCGTCTCTCG 60.807 63.158 0.00 0.00 43.12 4.04
2001 4173 4.131596 TGAAGGGCACAAAACTACTGTAC 58.868 43.478 0.00 0.00 0.00 2.90
2244 4416 9.072375 CATGTTGACTATCTAGATAAGACCTCA 57.928 37.037 13.41 9.00 36.93 3.86
2266 4438 7.041780 CCTCACACACAAATATAAGGCTATGAC 60.042 40.741 0.00 0.00 0.00 3.06
2293 4465 9.388672 AGTAAAAGCTCATACCCATACCTATTA 57.611 33.333 5.50 0.00 0.00 0.98
2330 4502 6.399639 TTCAGCCTTAAAGGTTGTTAAAGG 57.600 37.500 0.00 0.00 45.52 3.11
2334 4506 4.585581 GCCTTAAAGGTTGTTAAAGGTCCA 59.414 41.667 0.00 0.00 37.80 4.02
2369 4542 2.663826 TTTCAGTTGCCACCAAACAC 57.336 45.000 0.00 0.00 31.68 3.32
2372 4545 1.748493 TCAGTTGCCACCAAACACTTC 59.252 47.619 0.00 0.00 31.68 3.01
2375 4548 2.831526 AGTTGCCACCAAACACTTCTTT 59.168 40.909 0.00 0.00 31.68 2.52
2387 4560 3.308401 ACACTTCTTTGGGAAAAGGCAT 58.692 40.909 0.00 0.00 33.07 4.40
2403 4576 7.040823 GGAAAAGGCATGAGAACCTTATCATAG 60.041 40.741 0.00 0.00 45.62 2.23
2417 4590 3.657015 ATCATAGTGCACATCCTCTCG 57.343 47.619 21.04 0.00 0.00 4.04
2467 4640 1.266989 GGAAAAAGGCACGAGAACCTG 59.733 52.381 0.00 0.00 36.07 4.00
2472 4645 0.687354 AGGCACGAGAACCTGATGTT 59.313 50.000 0.00 0.00 40.81 2.71
2476 4649 3.430929 GGCACGAGAACCTGATGTTATCT 60.431 47.826 0.00 0.00 41.90 1.98
2498 4671 2.100605 ACCAGATCTCAAAAGGCGTC 57.899 50.000 0.00 0.00 0.00 5.19
2499 4672 1.339151 ACCAGATCTCAAAAGGCGTCC 60.339 52.381 0.00 0.00 0.00 4.79
2500 4673 1.002366 CAGATCTCAAAAGGCGTCCG 58.998 55.000 0.00 0.00 0.00 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.307760 CGTCGTCAAAAAGCAAGCCT 59.692 50.000 0.00 0.00 0.00 4.58
37 38 2.391389 CGGCCTTCTTCCTCGTTGC 61.391 63.158 0.00 0.00 0.00 4.17
39 40 2.663196 CCGGCCTTCTTCCTCGTT 59.337 61.111 0.00 0.00 0.00 3.85
42 43 4.840005 CCGCCGGCCTTCTTCCTC 62.840 72.222 23.46 0.00 0.00 3.71
44 45 4.840005 CTCCGCCGGCCTTCTTCC 62.840 72.222 23.46 0.00 0.00 3.46
46 47 3.775654 CTCTCCGCCGGCCTTCTT 61.776 66.667 23.46 0.00 0.00 2.52
82 85 2.252260 CGAGCCAAGTTTGCCGTG 59.748 61.111 0.00 0.00 0.00 4.94
105 108 3.134458 GGCTCCGTCTCCATATCTTTTG 58.866 50.000 0.00 0.00 0.00 2.44
127 130 4.103103 TCTGTGCGCGACTCCTCG 62.103 66.667 12.10 0.00 43.28 4.63
128 131 2.505118 GTCTGTGCGCGACTCCTC 60.505 66.667 12.10 0.00 0.00 3.71
163 166 2.288030 CCAGAAAACACGGTAGAGACGT 60.288 50.000 0.00 0.00 46.82 4.34
172 175 1.292061 TGTCGTTCCAGAAAACACGG 58.708 50.000 0.00 0.00 33.39 4.94
177 180 3.490078 GGCAAACATGTCGTTCCAGAAAA 60.490 43.478 0.00 0.00 36.59 2.29
202 205 1.029947 CCCCGTAAGAGCCGCATTTT 61.030 55.000 0.00 0.00 43.02 1.82
214 217 0.527565 GCTTACTCGTGTCCCCGTAA 59.472 55.000 0.00 0.00 0.00 3.18
219 222 1.448013 GCTGGCTTACTCGTGTCCC 60.448 63.158 0.00 0.00 0.00 4.46
262 265 2.045708 TGTGCATGGATTGACCCGC 61.046 57.895 0.00 0.00 38.00 6.13
265 268 1.802636 CGGTGTGCATGGATTGACC 59.197 57.895 0.00 0.00 39.54 4.02
266 269 1.137404 GCGGTGTGCATGGATTGAC 59.863 57.895 0.00 0.00 45.45 3.18
276 279 2.978018 GCAGTTAAGGGCGGTGTGC 61.978 63.158 0.00 0.00 45.38 4.57
277 280 1.599518 TGCAGTTAAGGGCGGTGTG 60.600 57.895 0.00 0.00 0.00 3.82
278 281 1.599797 GTGCAGTTAAGGGCGGTGT 60.600 57.895 0.00 0.00 0.00 4.16
279 282 1.599518 TGTGCAGTTAAGGGCGGTG 60.600 57.895 0.00 0.00 0.00 4.94
283 286 0.313987 GGTTGTGTGCAGTTAAGGGC 59.686 55.000 0.00 0.00 0.00 5.19
284 287 0.958822 GGGTTGTGTGCAGTTAAGGG 59.041 55.000 0.00 0.00 0.00 3.95
285 288 1.981256 AGGGTTGTGTGCAGTTAAGG 58.019 50.000 0.00 0.00 0.00 2.69
286 289 5.705609 ATTAAGGGTTGTGTGCAGTTAAG 57.294 39.130 0.00 0.00 0.00 1.85
287 290 6.322712 AGAAATTAAGGGTTGTGTGCAGTTAA 59.677 34.615 0.00 0.00 0.00 2.01
288 291 5.830991 AGAAATTAAGGGTTGTGTGCAGTTA 59.169 36.000 0.00 0.00 0.00 2.24
289 292 4.649218 AGAAATTAAGGGTTGTGTGCAGTT 59.351 37.500 0.00 0.00 0.00 3.16
290 293 4.215109 AGAAATTAAGGGTTGTGTGCAGT 58.785 39.130 0.00 0.00 0.00 4.40
291 294 4.853924 AGAAATTAAGGGTTGTGTGCAG 57.146 40.909 0.00 0.00 0.00 4.41
293 296 8.601845 AAAAATAGAAATTAAGGGTTGTGTGC 57.398 30.769 0.00 0.00 0.00 4.57
373 376 8.783093 CCTACAAACATAATCAGACTTTGTGAA 58.217 33.333 0.00 0.00 36.12 3.18
374 377 8.154203 TCCTACAAACATAATCAGACTTTGTGA 58.846 33.333 0.00 0.00 36.12 3.58
375 378 8.322906 TCCTACAAACATAATCAGACTTTGTG 57.677 34.615 0.00 0.00 36.12 3.33
376 379 8.918202 TTCCTACAAACATAATCAGACTTTGT 57.082 30.769 0.00 0.00 38.35 2.83
406 409 8.307483 CGGGTTTGATACTCTGAATGTAGATAT 58.693 37.037 0.00 0.00 0.00 1.63
407 410 7.287005 ACGGGTTTGATACTCTGAATGTAGATA 59.713 37.037 0.00 0.00 0.00 1.98
408 411 6.098409 ACGGGTTTGATACTCTGAATGTAGAT 59.902 38.462 0.00 0.00 0.00 1.98
409 412 5.421056 ACGGGTTTGATACTCTGAATGTAGA 59.579 40.000 0.00 0.00 0.00 2.59
410 413 5.661458 ACGGGTTTGATACTCTGAATGTAG 58.339 41.667 0.00 0.00 0.00 2.74
411 414 5.670792 ACGGGTTTGATACTCTGAATGTA 57.329 39.130 0.00 0.00 0.00 2.29
412 415 4.553330 ACGGGTTTGATACTCTGAATGT 57.447 40.909 0.00 0.00 0.00 2.71
413 416 6.280643 TGATACGGGTTTGATACTCTGAATG 58.719 40.000 0.00 0.00 0.00 2.67
414 417 6.479972 TGATACGGGTTTGATACTCTGAAT 57.520 37.500 0.00 0.00 0.00 2.57
415 418 5.925506 TGATACGGGTTTGATACTCTGAA 57.074 39.130 0.00 0.00 0.00 3.02
416 419 5.925506 TTGATACGGGTTTGATACTCTGA 57.074 39.130 0.00 0.00 0.00 3.27
417 420 5.293569 GGTTTGATACGGGTTTGATACTCTG 59.706 44.000 0.00 0.00 0.00 3.35
418 421 5.046159 TGGTTTGATACGGGTTTGATACTCT 60.046 40.000 0.00 0.00 0.00 3.24
419 422 5.180271 TGGTTTGATACGGGTTTGATACTC 58.820 41.667 0.00 0.00 0.00 2.59
420 423 5.168647 TGGTTTGATACGGGTTTGATACT 57.831 39.130 0.00 0.00 0.00 2.12
421 424 5.883503 TTGGTTTGATACGGGTTTGATAC 57.116 39.130 0.00 0.00 0.00 2.24
422 425 7.830201 AGTTATTGGTTTGATACGGGTTTGATA 59.170 33.333 0.00 0.00 0.00 2.15
423 426 6.661805 AGTTATTGGTTTGATACGGGTTTGAT 59.338 34.615 0.00 0.00 0.00 2.57
424 427 6.005198 AGTTATTGGTTTGATACGGGTTTGA 58.995 36.000 0.00 0.00 0.00 2.69
425 428 6.262193 AGTTATTGGTTTGATACGGGTTTG 57.738 37.500 0.00 0.00 0.00 2.93
426 429 6.904463 AAGTTATTGGTTTGATACGGGTTT 57.096 33.333 0.00 0.00 0.00 3.27
427 430 6.904463 AAAGTTATTGGTTTGATACGGGTT 57.096 33.333 0.00 0.00 0.00 4.11
428 431 7.999450 TTAAAGTTATTGGTTTGATACGGGT 57.001 32.000 0.00 0.00 0.00 5.28
499 502 8.510505 GCAGAGATCTGTCTAAAGTCAAAATTT 58.489 33.333 0.00 0.00 45.45 1.82
500 503 7.120432 GGCAGAGATCTGTCTAAAGTCAAAATT 59.880 37.037 0.00 0.00 44.71 1.82
501 504 6.597280 GGCAGAGATCTGTCTAAAGTCAAAAT 59.403 38.462 0.00 0.00 44.71 1.82
502 505 5.934625 GGCAGAGATCTGTCTAAAGTCAAAA 59.065 40.000 0.00 0.00 44.71 2.44
503 506 5.482908 GGCAGAGATCTGTCTAAAGTCAAA 58.517 41.667 0.00 0.00 44.71 2.69
504 507 4.380973 CGGCAGAGATCTGTCTAAAGTCAA 60.381 45.833 12.29 0.00 45.86 3.18
505 508 3.129462 CGGCAGAGATCTGTCTAAAGTCA 59.871 47.826 12.29 0.00 45.86 3.41
506 509 3.701241 CGGCAGAGATCTGTCTAAAGTC 58.299 50.000 12.29 0.00 45.86 3.01
507 510 2.159170 GCGGCAGAGATCTGTCTAAAGT 60.159 50.000 12.29 0.00 45.86 2.66
508 511 2.159184 TGCGGCAGAGATCTGTCTAAAG 60.159 50.000 12.29 0.00 45.86 1.85
509 512 1.824852 TGCGGCAGAGATCTGTCTAAA 59.175 47.619 12.29 0.00 45.86 1.85
510 513 1.474330 TGCGGCAGAGATCTGTCTAA 58.526 50.000 12.29 0.00 45.86 2.10
511 514 1.474330 TTGCGGCAGAGATCTGTCTA 58.526 50.000 12.29 0.00 45.86 2.59
512 515 0.829333 ATTGCGGCAGAGATCTGTCT 59.171 50.000 12.29 0.00 45.86 3.41
513 516 1.661341 AATTGCGGCAGAGATCTGTC 58.339 50.000 0.00 8.00 45.45 3.51
514 517 2.119801 AAATTGCGGCAGAGATCTGT 57.880 45.000 0.00 0.00 45.45 3.41
515 518 4.621068 TTAAAATTGCGGCAGAGATCTG 57.379 40.909 0.00 5.45 46.40 2.90
516 519 4.883585 TGATTAAAATTGCGGCAGAGATCT 59.116 37.500 1.67 0.00 0.00 2.75
517 520 5.173774 TGATTAAAATTGCGGCAGAGATC 57.826 39.130 1.67 3.77 0.00 2.75
518 521 5.779529 ATGATTAAAATTGCGGCAGAGAT 57.220 34.783 1.67 0.00 0.00 2.75
522 525 7.864379 AGAATAGAATGATTAAAATTGCGGCAG 59.136 33.333 1.67 0.00 0.00 4.85
544 547 4.201891 ACGTAACGAAGTCAGCGATAGAAT 60.202 41.667 0.00 0.00 45.00 2.40
581 584 0.107654 AGGGATAGACGCTGCAAACC 60.108 55.000 0.00 0.00 40.28 3.27
628 631 1.607628 GACTATGCCGTAGACGTCCAT 59.392 52.381 13.01 10.52 37.74 3.41
629 632 1.019673 GACTATGCCGTAGACGTCCA 58.980 55.000 13.01 2.55 37.74 4.02
630 633 0.041488 CGACTATGCCGTAGACGTCC 60.041 60.000 13.01 0.00 41.50 4.79
634 637 0.594284 GCCACGACTATGCCGTAGAC 60.594 60.000 0.00 0.00 38.29 2.59
637 640 2.788640 GGGCCACGACTATGCCGTA 61.789 63.158 4.39 0.00 46.31 4.02
638 641 4.157120 GGGCCACGACTATGCCGT 62.157 66.667 4.39 0.00 46.31 5.68
652 655 4.856801 ATCCACCATGTCGCGGGC 62.857 66.667 6.13 0.00 0.00 6.13
654 657 2.173669 GTGATCCACCATGTCGCGG 61.174 63.158 6.13 0.00 0.00 6.46
656 659 0.447801 GTTGTGATCCACCATGTCGC 59.552 55.000 0.00 0.00 32.73 5.19
657 660 1.086696 GGTTGTGATCCACCATGTCG 58.913 55.000 0.00 0.00 32.73 4.35
658 661 1.086696 CGGTTGTGATCCACCATGTC 58.913 55.000 6.63 0.00 32.73 3.06
660 663 2.394930 TACGGTTGTGATCCACCATG 57.605 50.000 6.63 0.00 32.73 3.66
743 827 2.366972 AAGTAGGCGGCCAGGGAT 60.367 61.111 23.09 1.81 0.00 3.85
766 850 0.782384 GGCCAAATAGTATCGTCGCG 59.218 55.000 0.00 0.00 0.00 5.87
813 908 3.067601 CCTGTATGCATGCACATGACATT 59.932 43.478 25.37 7.00 41.20 2.71
836 931 3.741388 GCCTGTTAGTGCAAGATACGGAT 60.741 47.826 0.00 0.00 0.00 4.18
894 997 3.427243 CTTCAGATCAACCTCGACGTAC 58.573 50.000 0.00 0.00 0.00 3.67
1025 3086 2.667536 CTGGCGTGCTGAGCTTGT 60.668 61.111 5.83 0.00 34.52 3.16
1040 3101 0.737219 GTGGGCAAATGCTAGCTCTG 59.263 55.000 17.23 11.15 41.70 3.35
1053 3114 0.320683 CAGAGTTGACGATGTGGGCA 60.321 55.000 0.00 0.00 0.00 5.36
1102 3163 3.484806 ACGCGGCCAATCCCCATA 61.485 61.111 12.47 0.00 0.00 2.74
1116 3177 1.228657 AAACTCCTCGAAAGCCACGC 61.229 55.000 0.00 0.00 0.00 5.34
1197 3275 4.080469 TGGCCGTCCATTGGTAGTAATTTA 60.080 41.667 1.86 0.00 37.47 1.40
1275 3353 2.978156 TCTTCACCTTGGCCATCTTT 57.022 45.000 6.09 0.00 0.00 2.52
1284 3362 2.428888 GCTTTGGCTTCTTCACCTTG 57.571 50.000 0.00 0.00 35.22 3.61
1350 3441 5.945784 TGTAAAAGCTACAGCATTTCTCCAT 59.054 36.000 7.62 0.00 40.52 3.41
1357 3448 2.747446 CGGGTGTAAAAGCTACAGCATT 59.253 45.455 16.74 0.00 44.88 3.56
1362 3453 4.312443 CTTTCTCGGGTGTAAAAGCTACA 58.688 43.478 0.00 0.00 0.00 2.74
1395 3486 2.514803 CCAACTTTAAGTGTCCCCAGG 58.485 52.381 0.00 0.00 0.00 4.45
1404 3495 3.391296 TCTCACAGGAGCCAACTTTAAGT 59.609 43.478 0.00 0.00 41.13 2.24
1410 3501 0.035630 GCATCTCACAGGAGCCAACT 60.036 55.000 0.00 0.00 41.13 3.16
1549 3640 2.481969 CCTAGCTCTTTGTATGCGCTGA 60.482 50.000 9.73 0.00 32.49 4.26
1598 3689 1.328680 CAACTGATCCTATGCACGCAC 59.671 52.381 0.00 0.00 0.00 5.34
1624 3749 7.383029 TGAAATAGGTACACACGTAAAGAACAG 59.617 37.037 0.00 0.00 0.00 3.16
1629 3754 6.074398 CGTGAAATAGGTACACACGTAAAG 57.926 41.667 0.00 0.00 45.57 1.85
1637 3762 5.291128 CCTCAATGACGTGAAATAGGTACAC 59.709 44.000 0.00 0.00 0.00 2.90
1640 3765 5.163447 CCTCCTCAATGACGTGAAATAGGTA 60.163 44.000 0.00 0.00 0.00 3.08
1641 3766 4.383118 CCTCCTCAATGACGTGAAATAGGT 60.383 45.833 0.00 0.00 0.00 3.08
1642 3767 4.122776 CCTCCTCAATGACGTGAAATAGG 58.877 47.826 0.00 0.00 0.00 2.57
1643 3768 5.011090 TCCTCCTCAATGACGTGAAATAG 57.989 43.478 0.00 0.00 0.00 1.73
1644 3769 5.414789 TTCCTCCTCAATGACGTGAAATA 57.585 39.130 0.00 0.00 0.00 1.40
1645 3770 3.981071 TCCTCCTCAATGACGTGAAAT 57.019 42.857 0.00 0.00 0.00 2.17
1655 3827 6.040166 GCATTGTCATTGTATTCCTCCTCAAT 59.960 38.462 0.00 0.00 0.00 2.57
1706 3878 9.386122 ACTAGGATTAAGAATCTGATACCATGT 57.614 33.333 0.00 0.00 38.01 3.21
1714 3886 7.952930 AGCATAGGACTAGGATTAAGAATCTGA 59.047 37.037 0.00 0.00 38.01 3.27
1746 3918 2.509336 GCGGACTCGGTGGACATG 60.509 66.667 0.00 0.00 36.79 3.21
1763 3935 3.730761 GGCTTGCGACACCAGCTG 61.731 66.667 6.78 6.78 35.28 4.24
1764 3936 3.946201 AGGCTTGCGACACCAGCT 61.946 61.111 0.00 0.00 35.28 4.24
1787 3959 0.682855 AGAAGAGGGAGAGGTGCTCG 60.683 60.000 0.00 0.00 44.91 5.03
1788 3960 1.111277 GAGAAGAGGGAGAGGTGCTC 58.889 60.000 0.00 0.00 43.17 4.26
1800 3972 1.206849 GAGGAGGCCAACAGAGAAGAG 59.793 57.143 5.01 0.00 0.00 2.85
1811 3983 3.077556 GAAGAGCGGAGGAGGCCA 61.078 66.667 5.01 0.00 0.00 5.36
1869 4041 0.539051 GCAGAGGAAGAAGCTGGCTA 59.461 55.000 0.00 0.00 0.00 3.93
1887 4059 3.512516 GCTGGGGACGCAATCTGC 61.513 66.667 0.00 0.00 40.69 4.26
1897 4069 0.251341 GCAAGAAAGGAAGCTGGGGA 60.251 55.000 0.00 0.00 0.00 4.81
1925 4097 1.361668 GACATTCTCCACGCGCATGT 61.362 55.000 5.73 7.68 0.00 3.21
1971 4143 0.961019 TTGTGCCCTTCATGTCAAGC 59.039 50.000 0.00 0.00 0.00 4.01
2001 4173 2.563050 TTCTCCATGAGACTGCGCCG 62.563 60.000 4.18 0.00 38.51 6.46
2213 4385 5.736951 ATCTAGATAGTCAACATGGCTCC 57.263 43.478 2.53 0.00 32.64 4.70
2244 4416 7.338710 ACTGTCATAGCCTTATATTTGTGTGT 58.661 34.615 0.00 0.00 0.00 3.72
2266 4438 5.930135 AGGTATGGGTATGAGCTTTTACTG 58.070 41.667 0.00 0.00 0.00 2.74
2274 4446 8.329502 AGGATTTTAATAGGTATGGGTATGAGC 58.670 37.037 0.00 0.00 0.00 4.26
2293 4465 7.833285 TTAAGGCTGAAAACACTAGGATTTT 57.167 32.000 6.05 6.05 0.00 1.82
2311 4483 4.585581 TGGACCTTTAACAACCTTTAAGGC 59.414 41.667 11.45 0.00 39.63 4.35
2345 4517 4.187694 GTTTGGTGGCAACTGAAATTTCA 58.812 39.130 19.45 19.45 35.57 2.69
2353 4525 1.750778 AGAAGTGTTTGGTGGCAACTG 59.249 47.619 3.27 0.00 37.61 3.16
2369 4542 3.828451 TCTCATGCCTTTTCCCAAAGAAG 59.172 43.478 0.00 0.00 41.97 2.85
2372 4545 3.306294 GGTTCTCATGCCTTTTCCCAAAG 60.306 47.826 0.00 0.00 39.45 2.77
2375 4548 1.428912 AGGTTCTCATGCCTTTTCCCA 59.571 47.619 0.00 0.00 0.00 4.37
2387 4560 5.675684 TGTGCACTATGATAAGGTTCTCA 57.324 39.130 19.41 0.00 0.00 3.27
2403 4576 2.015736 ATTCACGAGAGGATGTGCAC 57.984 50.000 10.75 10.75 36.06 4.57
2417 4590 6.276847 AGTGATCCTGAGTTATCGAATTCAC 58.723 40.000 6.22 0.00 29.14 3.18
2472 4645 6.049149 CGCCTTTTGAGATCTGGTTTAGATA 58.951 40.000 0.00 0.00 46.12 1.98
2476 4649 4.000988 GACGCCTTTTGAGATCTGGTTTA 58.999 43.478 0.00 0.00 0.00 2.01


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

AutoCloner maintained by Alex Coulton.