Multiple sequence alignment - TraesCS2D01G050500

Loading Multiple Alignment...

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 TraesCS2D01G050500 chr2D 100.000 3161 0 0 1 3161 18735222 18738382 0.000000e+00 5838
1 TraesCS2D01G050500 chr2D 82.689 543 73 14 1721 2246 18750763 18750225 2.220000e-126 462
2 TraesCS2D01G050500 chr2D 81.292 449 56 8 3 427 13053427 13052983 3.910000e-89 339
3 TraesCS2D01G050500 chr2D 88.384 198 23 0 244 441 12975930 12975733 4.070000e-59 239
4 TraesCS2D01G050500 chrUn 96.266 2678 69 15 508 3161 258069581 258066911 0.000000e+00 4362
5 TraesCS2D01G050500 chrUn 96.266 2678 69 15 508 3161 265987554 265990224 0.000000e+00 4362
6 TraesCS2D01G050500 chrUn 95.989 2443 67 15 508 2926 236195919 236193484 0.000000e+00 3940
7 TraesCS2D01G050500 chrUn 89.710 2381 153 50 817 3161 12639882 12637558 0.000000e+00 2955
8 TraesCS2D01G050500 chrUn 89.600 2375 158 47 822 3161 236203178 236200858 0.000000e+00 2935
9 TraesCS2D01G050500 chrUn 89.528 2120 148 33 728 2789 236203299 236201196 0.000000e+00 2617
10 TraesCS2D01G050500 chrUn 85.598 368 46 4 80 444 12640284 12639921 2.300000e-101 379
11 TraesCS2D01G050500 chr2A 96.191 2678 71 15 508 3161 20039566 20042236 0.000000e+00 4351
12 TraesCS2D01G050500 chr2A 84.341 364 53 3 75 437 15097563 15097203 1.390000e-93 353
13 TraesCS2D01G050500 chr2A 84.066 364 54 3 75 437 15113350 15112990 6.490000e-92 348
14 TraesCS2D01G050500 chr2B 96.993 2361 43 15 821 3161 30538160 30540512 0.000000e+00 3941
15 TraesCS2D01G050500 chr2B 91.055 2236 154 17 850 3063 30545443 30547654 0.000000e+00 2979
16 TraesCS2D01G050500 chr2B 91.330 1165 80 13 2003 3159 30548809 30549960 0.000000e+00 1572
17 TraesCS2D01G050500 chr2B 79.225 1213 188 48 998 2175 30569891 30568708 0.000000e+00 785
18 TraesCS2D01G050500 chr2B 89.524 105 6 3 728 829 30538001 30538103 9.200000e-26 128
19 TraesCS2D01G050500 chr2B 91.358 81 5 2 430 509 298515706 298515627 3.330000e-20 110
20 TraesCS2D01G050500 chr2B 88.764 89 8 2 424 511 25232590 25232677 1.200000e-19 108
21 TraesCS2D01G050500 chr2B 84.071 113 14 1 728 836 30545285 30545397 4.310000e-19 106
22 TraesCS2D01G050500 chr2B 90.244 82 6 2 443 523 708353511 708353431 4.310000e-19 106
23 TraesCS2D01G050500 chr4D 85.095 369 47 7 74 439 26915324 26914961 1.380000e-98 370
24 TraesCS2D01G050500 chr4B 81.140 456 62 13 1 439 39253072 39252624 8.390000e-91 344
25 TraesCS2D01G050500 chr4B 90.361 83 6 2 440 520 645475586 645475668 1.200000e-19 108
26 TraesCS2D01G050500 chr1B 94.170 223 11 2 507 728 621998665 621998444 3.910000e-89 339
27 TraesCS2D01G050500 chr1B 90.123 81 6 2 444 523 460271920 460271841 1.550000e-18 104
28 TraesCS2D01G050500 chr1D 93.665 221 14 0 507 727 308197765 308197545 6.540000e-87 331
29 TraesCS2D01G050500 chr1D 92.308 221 17 0 507 727 308198355 308198575 6.580000e-82 315
30 TraesCS2D01G050500 chr5A 92.342 222 17 0 507 728 652057203 652057424 1.830000e-82 316
31 TraesCS2D01G050500 chr4A 92.760 221 13 3 507 727 23595484 23595267 1.830000e-82 316
32 TraesCS2D01G050500 chr6B 81.918 365 58 6 74 437 481045003 481044646 5.120000e-78 302
33 TraesCS2D01G050500 chr6D 81.627 332 51 6 107 437 339689207 339689529 1.870000e-67 267
34 TraesCS2D01G050500 chr1A 90.476 84 6 2 441 523 498800910 498800992 3.330000e-20 110
35 TraesCS2D01G050500 chr7B 90.361 83 6 2 442 523 570221401 570221320 1.200000e-19 108
36 TraesCS2D01G050500 chr7A 90.244 82 6 2 443 523 353214273 353214353 4.310000e-19 106
37 TraesCS2D01G050500 chr5D 90.123 81 6 2 444 523 375171732 375171811 1.550000e-18 104


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 TraesCS2D01G050500 chr2D 18735222 18738382 3160 False 5838.000000 5838 100.000000 1 3161 1 chr2D.!!$F1 3160
1 TraesCS2D01G050500 chr2D 18750225 18750763 538 True 462.000000 462 82.689000 1721 2246 1 chr2D.!!$R3 525
2 TraesCS2D01G050500 chrUn 258066911 258069581 2670 True 4362.000000 4362 96.266000 508 3161 1 chrUn.!!$R2 2653
3 TraesCS2D01G050500 chrUn 265987554 265990224 2670 False 4362.000000 4362 96.266000 508 3161 1 chrUn.!!$F1 2653
4 TraesCS2D01G050500 chrUn 236193484 236195919 2435 True 3940.000000 3940 95.989000 508 2926 1 chrUn.!!$R1 2418
5 TraesCS2D01G050500 chrUn 236200858 236203299 2441 True 2776.000000 2935 89.564000 728 3161 2 chrUn.!!$R4 2433
6 TraesCS2D01G050500 chrUn 12637558 12640284 2726 True 1667.000000 2955 87.654000 80 3161 2 chrUn.!!$R3 3081
7 TraesCS2D01G050500 chr2A 20039566 20042236 2670 False 4351.000000 4351 96.191000 508 3161 1 chr2A.!!$F1 2653
8 TraesCS2D01G050500 chr2B 30538001 30540512 2511 False 2034.500000 3941 93.258500 728 3161 2 chr2B.!!$F2 2433
9 TraesCS2D01G050500 chr2B 30545285 30549960 4675 False 1552.333333 2979 88.818667 728 3159 3 chr2B.!!$F3 2431
10 TraesCS2D01G050500 chr2B 30568708 30569891 1183 True 785.000000 785 79.225000 998 2175 1 chr2B.!!$R1 1177

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
44 45 0.039074 AGCAAGTTCGACGAGACCAG 60.039 55.0 0.0 0.0 0.0 4.00 F
183 184 0.100861 GTCTCTACCGCTGCACTACC 59.899 60.0 0.0 0.0 0.0 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1513 1633 0.821517 TTCCAGTACATGACGCGGAT 59.178 50.000 12.47 0.0 35.27 4.18 R
2573 2717 4.193865 TCAATACAGATGACCATGCAGTG 58.806 43.478 0.00 0.0 0.00 3.66 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 2.168621 CGTGCAGCAAGTTCGACG 59.831 61.111 0.00 0.00 0.00 5.12
38 39 2.300066 CGTGCAGCAAGTTCGACGA 61.300 57.895 0.00 0.00 0.00 4.20
39 40 1.488957 GTGCAGCAAGTTCGACGAG 59.511 57.895 0.00 0.00 0.00 4.18
40 41 0.939577 GTGCAGCAAGTTCGACGAGA 60.940 55.000 0.00 0.00 0.00 4.04
41 42 0.939577 TGCAGCAAGTTCGACGAGAC 60.940 55.000 0.00 0.00 0.00 3.36
42 43 1.618640 GCAGCAAGTTCGACGAGACC 61.619 60.000 0.00 0.00 0.00 3.85
43 44 0.318699 CAGCAAGTTCGACGAGACCA 60.319 55.000 0.00 0.00 0.00 4.02
44 45 0.039074 AGCAAGTTCGACGAGACCAG 60.039 55.000 0.00 0.00 0.00 4.00
45 46 1.009389 GCAAGTTCGACGAGACCAGG 61.009 60.000 0.00 0.00 0.00 4.45
46 47 0.388649 CAAGTTCGACGAGACCAGGG 60.389 60.000 0.00 0.00 0.00 4.45
47 48 0.538977 AAGTTCGACGAGACCAGGGA 60.539 55.000 0.00 0.00 0.00 4.20
48 49 0.961358 AGTTCGACGAGACCAGGGAG 60.961 60.000 0.00 0.00 0.00 4.30
49 50 0.959372 GTTCGACGAGACCAGGGAGA 60.959 60.000 0.00 0.00 0.00 3.71
50 51 0.959372 TTCGACGAGACCAGGGAGAC 60.959 60.000 0.00 0.00 0.00 3.36
62 63 2.046217 GGAGACCCTTTGGCCGAC 60.046 66.667 0.00 0.00 33.59 4.79
63 64 2.046217 GAGACCCTTTGGCCGACC 60.046 66.667 0.00 0.00 33.59 4.79
72 73 2.933287 TGGCCGACCACCAAGGAT 60.933 61.111 0.00 0.00 42.67 3.24
73 74 2.124695 GGCCGACCACCAAGGATC 60.125 66.667 0.00 0.00 41.22 3.36
74 75 2.670148 GGCCGACCACCAAGGATCT 61.670 63.158 0.00 0.00 41.22 2.75
75 76 1.153349 GCCGACCACCAAGGATCTC 60.153 63.158 0.00 0.00 41.22 2.75
76 77 1.522569 CCGACCACCAAGGATCTCC 59.477 63.158 0.00 0.00 41.22 3.71
77 78 1.141881 CGACCACCAAGGATCTCCG 59.858 63.158 0.00 0.00 41.22 4.63
78 79 1.153349 GACCACCAAGGATCTCCGC 60.153 63.158 0.00 0.00 41.22 5.54
93 94 3.049674 CGCGAGGCAAAAGAGGCA 61.050 61.111 0.00 0.00 36.37 4.75
103 104 1.131883 CAAAAGAGGCATTCGAGGCAG 59.868 52.381 12.38 0.00 36.37 4.85
104 105 0.393537 AAAGAGGCATTCGAGGCAGG 60.394 55.000 12.38 0.00 36.37 4.85
111 112 1.406069 GCATTCGAGGCAGGAGAAGAA 60.406 52.381 6.30 0.00 0.00 2.52
119 120 3.775654 AGGAGAAGAAGGCGCCGG 61.776 66.667 23.20 0.00 0.00 6.13
176 177 1.465387 CGCCTATAGTCTCTACCGCTG 59.535 57.143 0.00 0.00 0.00 5.18
178 179 2.505405 CCTATAGTCTCTACCGCTGCA 58.495 52.381 0.00 0.00 0.00 4.41
183 184 0.100861 GTCTCTACCGCTGCACTACC 59.899 60.000 0.00 0.00 0.00 3.18
190 191 1.582937 CGCTGCACTACCGAGTACG 60.583 63.158 0.00 0.00 33.32 3.67
221 223 4.339814 CGTCAAGCCCTAGAGAGTTTAGAT 59.660 45.833 0.00 0.00 0.00 1.98
290 292 3.767131 TGATGAACTCCGGTGAACTATGA 59.233 43.478 11.17 0.00 0.00 2.15
298 300 2.159296 CCGGTGAACTATGATGACGTGA 60.159 50.000 0.00 0.00 0.00 4.35
303 305 5.408604 GGTGAACTATGATGACGTGAAGTTT 59.591 40.000 0.00 0.00 0.00 2.66
347 350 3.845781 ATATTGGATCTGTTCTGCCGT 57.154 42.857 0.00 0.00 0.00 5.68
350 353 2.109126 GGATCTGTTCTGCCGTGCC 61.109 63.158 0.00 0.00 0.00 5.01
373 376 1.698714 CGCGGTACCCCAAATTCGTC 61.699 60.000 6.25 0.00 0.00 4.20
376 379 2.677613 GCGGTACCCCAAATTCGTCTTA 60.678 50.000 6.25 0.00 0.00 2.10
377 380 3.800531 CGGTACCCCAAATTCGTCTTAT 58.199 45.455 6.25 0.00 0.00 1.73
378 381 4.740334 GCGGTACCCCAAATTCGTCTTATA 60.740 45.833 6.25 0.00 0.00 0.98
383 386 5.866207 ACCCCAAATTCGTCTTATAGGATC 58.134 41.667 0.00 0.00 0.00 3.36
386 389 6.166982 CCCAAATTCGTCTTATAGGATCTCC 58.833 44.000 0.00 0.00 0.00 3.71
401 404 4.884164 AGGATCTCCTAAAGGAAATTTGCG 59.116 41.667 3.87 0.00 46.48 4.85
403 406 4.028993 TCTCCTAAAGGAAATTTGCGGT 57.971 40.909 3.87 0.00 44.91 5.68
404 407 5.168647 TCTCCTAAAGGAAATTTGCGGTA 57.831 39.130 3.87 0.29 44.91 4.02
405 408 4.939439 TCTCCTAAAGGAAATTTGCGGTAC 59.061 41.667 3.87 0.00 44.91 3.34
407 410 3.181504 CCTAAAGGAAATTTGCGGTACCG 60.182 47.826 30.06 30.06 39.02 4.02
421 424 1.929169 GGTACCGCGTTTTACAGGATC 59.071 52.381 4.92 0.00 0.00 3.36
441 444 4.177537 TCTGCTAGAGATGCTCTAAGGT 57.822 45.455 5.75 0.00 41.74 3.50
442 445 4.541705 TCTGCTAGAGATGCTCTAAGGTT 58.458 43.478 5.75 0.00 41.74 3.50
443 446 4.340666 TCTGCTAGAGATGCTCTAAGGTTG 59.659 45.833 5.75 0.00 41.74 3.77
444 447 3.386078 TGCTAGAGATGCTCTAAGGTTGG 59.614 47.826 5.75 0.00 41.74 3.77
445 448 3.639094 GCTAGAGATGCTCTAAGGTTGGA 59.361 47.826 5.75 0.00 41.74 3.53
446 449 4.261994 GCTAGAGATGCTCTAAGGTTGGAG 60.262 50.000 5.75 0.00 41.74 3.86
447 450 3.718723 AGAGATGCTCTAAGGTTGGAGT 58.281 45.455 5.15 0.00 39.28 3.85
448 451 4.873010 AGAGATGCTCTAAGGTTGGAGTA 58.127 43.478 5.15 1.12 39.28 2.59
449 452 5.463154 AGAGATGCTCTAAGGTTGGAGTAT 58.537 41.667 6.41 6.41 42.08 2.12
450 453 5.902431 AGAGATGCTCTAAGGTTGGAGTATT 59.098 40.000 7.84 0.49 40.18 1.89
451 454 6.385467 AGAGATGCTCTAAGGTTGGAGTATTT 59.615 38.462 7.84 3.26 40.18 1.40
452 455 6.963322 AGATGCTCTAAGGTTGGAGTATTTT 58.037 36.000 7.84 0.00 40.18 1.82
453 456 8.090788 AGATGCTCTAAGGTTGGAGTATTTTA 57.909 34.615 7.84 0.00 40.18 1.52
454 457 8.548877 AGATGCTCTAAGGTTGGAGTATTTTAA 58.451 33.333 7.84 0.00 40.18 1.52
455 458 9.174166 GATGCTCTAAGGTTGGAGTATTTTAAA 57.826 33.333 7.84 0.00 40.18 1.52
456 459 8.927675 TGCTCTAAGGTTGGAGTATTTTAAAA 57.072 30.769 2.51 2.51 37.99 1.52
457 460 9.357161 TGCTCTAAGGTTGGAGTATTTTAAAAA 57.643 29.630 4.44 0.00 37.99 1.94
479 482 5.722021 AAACTACCACAATTCATGGAACC 57.278 39.130 11.51 0.00 39.87 3.62
480 483 3.343617 ACTACCACAATTCATGGAACCG 58.656 45.455 11.51 1.19 39.87 4.44
481 484 2.286365 ACCACAATTCATGGAACCGT 57.714 45.000 11.51 0.00 39.87 4.83
482 485 1.885887 ACCACAATTCATGGAACCGTG 59.114 47.619 11.51 6.71 39.87 4.94
483 486 1.402720 CCACAATTCATGGAACCGTGC 60.403 52.381 8.06 0.00 39.87 5.34
484 487 0.887933 ACAATTCATGGAACCGTGCC 59.112 50.000 8.06 0.00 33.28 5.01
485 488 1.176527 CAATTCATGGAACCGTGCCT 58.823 50.000 8.06 0.00 33.28 4.75
486 489 2.290641 ACAATTCATGGAACCGTGCCTA 60.291 45.455 8.06 0.00 33.28 3.93
487 490 2.038387 ATTCATGGAACCGTGCCTAC 57.962 50.000 8.06 0.00 33.28 3.18
488 491 0.687920 TTCATGGAACCGTGCCTACA 59.312 50.000 8.06 0.00 33.28 2.74
489 492 0.687920 TCATGGAACCGTGCCTACAA 59.312 50.000 8.06 0.00 33.28 2.41
490 493 1.072489 TCATGGAACCGTGCCTACAAA 59.928 47.619 8.06 0.00 33.28 2.83
491 494 1.199097 CATGGAACCGTGCCTACAAAC 59.801 52.381 0.00 0.00 0.00 2.93
492 495 0.470766 TGGAACCGTGCCTACAAACT 59.529 50.000 0.00 0.00 0.00 2.66
493 496 1.693062 TGGAACCGTGCCTACAAACTA 59.307 47.619 0.00 0.00 0.00 2.24
494 497 2.071540 GGAACCGTGCCTACAAACTAC 58.928 52.381 0.00 0.00 0.00 2.73
495 498 2.071540 GAACCGTGCCTACAAACTACC 58.928 52.381 0.00 0.00 0.00 3.18
496 499 1.050204 ACCGTGCCTACAAACTACCA 58.950 50.000 0.00 0.00 0.00 3.25
497 500 1.270465 ACCGTGCCTACAAACTACCAC 60.270 52.381 0.00 0.00 0.00 4.16
498 501 1.001633 CCGTGCCTACAAACTACCACT 59.998 52.381 0.00 0.00 0.00 4.00
499 502 2.549349 CCGTGCCTACAAACTACCACTT 60.549 50.000 0.00 0.00 0.00 3.16
500 503 3.135994 CGTGCCTACAAACTACCACTTT 58.864 45.455 0.00 0.00 0.00 2.66
501 504 4.309099 CGTGCCTACAAACTACCACTTTA 58.691 43.478 0.00 0.00 0.00 1.85
502 505 4.151157 CGTGCCTACAAACTACCACTTTAC 59.849 45.833 0.00 0.00 0.00 2.01
503 506 4.151157 GTGCCTACAAACTACCACTTTACG 59.849 45.833 0.00 0.00 0.00 3.18
504 507 4.039004 TGCCTACAAACTACCACTTTACGA 59.961 41.667 0.00 0.00 0.00 3.43
505 508 4.990426 GCCTACAAACTACCACTTTACGAA 59.010 41.667 0.00 0.00 0.00 3.85
506 509 5.640783 GCCTACAAACTACCACTTTACGAAT 59.359 40.000 0.00 0.00 0.00 3.34
510 513 9.940166 CTACAAACTACCACTTTACGAATTTTT 57.060 29.630 0.00 0.00 0.00 1.94
585 588 5.106712 CCAACTAGTCAGAAATGCGCTTAAA 60.107 40.000 9.73 0.00 0.00 1.52
597 600 3.216147 GCGCTTAAAAGAGCCAAATCA 57.784 42.857 0.00 0.00 44.63 2.57
612 615 4.776743 CCAAATCAGACACTTTTCAGACG 58.223 43.478 0.00 0.00 0.00 4.18
614 617 5.200454 CAAATCAGACACTTTTCAGACGTG 58.800 41.667 0.00 0.00 34.92 4.49
623 626 5.413523 ACACTTTTCAGACGTGGTAGTTTTT 59.586 36.000 0.00 0.00 33.13 1.94
673 676 6.103330 AGTTTTCCGCACAAATTTGTAAAGT 58.897 32.000 22.87 17.66 39.91 2.66
694 697 2.071540 GGTAGTTTGTAGGCACGGTTC 58.928 52.381 0.00 0.00 0.00 3.62
703 706 0.322322 AGGCACGGTTCCACGAATTA 59.678 50.000 0.00 0.00 37.61 1.40
891 969 2.367567 GTGGACCCACTTGTCAGAGTAA 59.632 50.000 11.73 0.00 43.12 2.24
897 975 8.550159 GGACCCACTTGTCAGAGTAATACTCG 62.550 50.000 14.05 9.65 39.76 4.18
909 987 4.035814 AGTAATACTCGGGCTAGGGTTTT 58.964 43.478 0.00 0.00 0.00 2.43
914 992 2.841881 ACTCGGGCTAGGGTTTTCATTA 59.158 45.455 0.00 0.00 0.00 1.90
917 995 2.294979 GGGCTAGGGTTTTCATTACCG 58.705 52.381 0.00 0.00 36.49 4.02
918 996 1.674441 GGCTAGGGTTTTCATTACCGC 59.326 52.381 0.00 0.00 36.49 5.68
919 997 2.640184 GCTAGGGTTTTCATTACCGCT 58.360 47.619 0.00 0.00 36.49 5.52
920 998 3.014623 GCTAGGGTTTTCATTACCGCTT 58.985 45.455 0.00 0.00 36.49 4.68
921 999 3.181500 GCTAGGGTTTTCATTACCGCTTG 60.181 47.826 0.00 0.00 36.49 4.01
922 1000 2.167662 AGGGTTTTCATTACCGCTTGG 58.832 47.619 0.00 0.00 36.49 3.61
924 1002 1.403647 GGTTTTCATTACCGCTTGGGC 60.404 52.381 0.00 0.00 40.62 5.36
925 1003 0.892063 TTTTCATTACCGCTTGGGCC 59.108 50.000 0.00 0.00 40.62 5.80
926 1004 1.309499 TTTCATTACCGCTTGGGCCG 61.309 55.000 0.00 0.00 40.62 6.13
927 1005 2.124901 CATTACCGCTTGGGCCGA 60.125 61.111 0.00 0.00 40.62 5.54
928 1006 1.525995 CATTACCGCTTGGGCCGAT 60.526 57.895 0.00 0.00 40.62 4.18
929 1007 1.525995 ATTACCGCTTGGGCCGATG 60.526 57.895 0.00 0.00 40.62 3.84
930 1008 4.849310 TACCGCTTGGGCCGATGC 62.849 66.667 14.69 14.69 40.62 3.91
934 1012 2.517875 GCTTGGGCCGATGCTGAT 60.518 61.111 16.99 0.00 37.74 2.90
935 1013 2.550101 GCTTGGGCCGATGCTGATC 61.550 63.158 16.99 0.00 37.74 2.92
938 1030 4.996434 GGGCCGATGCTGATCCCG 62.996 72.222 0.00 0.00 37.74 5.14
976 1069 1.000771 CCCGTCTCCACTCTCCTCA 60.001 63.158 0.00 0.00 0.00 3.86
994 1087 1.006043 TCAACTCCACCAAAACCACCA 59.994 47.619 0.00 0.00 0.00 4.17
995 1088 1.408702 CAACTCCACCAAAACCACCAG 59.591 52.381 0.00 0.00 0.00 4.00
1513 1633 1.779061 GCACCAACCTTCAGGGGAGA 61.779 60.000 0.00 0.00 40.27 3.71
2207 2345 5.238432 TGATTTCGCGCCATGTTAAATCTAT 59.762 36.000 20.69 0.00 37.42 1.98
2369 2513 2.419673 TGCGTGGCACTCATATTTTCTG 59.580 45.455 16.72 0.00 31.71 3.02
2494 2638 6.596497 TCTTAATTTGGATCGTTAGGTGGTTC 59.404 38.462 0.00 0.00 0.00 3.62
2573 2717 7.421530 TTTTCTGAATATGTTATAGAGCGGC 57.578 36.000 0.00 0.00 0.00 6.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 2.970974 GAACTTGCTGCACGCCCTC 61.971 63.158 0.00 0.00 38.05 4.30
16 17 2.980233 GAACTTGCTGCACGCCCT 60.980 61.111 0.00 0.00 38.05 5.19
17 18 4.389576 CGAACTTGCTGCACGCCC 62.390 66.667 0.00 0.00 38.05 6.13
18 19 3.345808 TCGAACTTGCTGCACGCC 61.346 61.111 0.00 0.00 38.05 5.68
19 20 2.127609 GTCGAACTTGCTGCACGC 60.128 61.111 0.00 1.70 39.77 5.34
20 21 2.168621 CGTCGAACTTGCTGCACG 59.831 61.111 0.00 2.38 0.00 5.34
21 22 0.939577 TCTCGTCGAACTTGCTGCAC 60.940 55.000 0.00 0.00 0.00 4.57
22 23 0.939577 GTCTCGTCGAACTTGCTGCA 60.940 55.000 0.00 0.00 0.00 4.41
23 24 1.618640 GGTCTCGTCGAACTTGCTGC 61.619 60.000 0.00 0.00 0.00 5.25
24 25 0.318699 TGGTCTCGTCGAACTTGCTG 60.319 55.000 0.00 0.00 0.00 4.41
25 26 0.039074 CTGGTCTCGTCGAACTTGCT 60.039 55.000 0.00 0.00 0.00 3.91
26 27 1.009389 CCTGGTCTCGTCGAACTTGC 61.009 60.000 0.00 0.00 0.00 4.01
27 28 0.388649 CCCTGGTCTCGTCGAACTTG 60.389 60.000 0.00 0.00 0.00 3.16
28 29 0.538977 TCCCTGGTCTCGTCGAACTT 60.539 55.000 0.00 0.00 0.00 2.66
29 30 0.961358 CTCCCTGGTCTCGTCGAACT 60.961 60.000 0.00 0.00 0.00 3.01
30 31 0.959372 TCTCCCTGGTCTCGTCGAAC 60.959 60.000 0.00 0.00 0.00 3.95
31 32 0.959372 GTCTCCCTGGTCTCGTCGAA 60.959 60.000 0.00 0.00 0.00 3.71
32 33 1.376942 GTCTCCCTGGTCTCGTCGA 60.377 63.158 0.00 0.00 0.00 4.20
33 34 2.408241 GGTCTCCCTGGTCTCGTCG 61.408 68.421 0.00 0.00 0.00 5.12
34 35 2.053277 GGGTCTCCCTGGTCTCGTC 61.053 68.421 0.00 0.00 41.34 4.20
35 36 2.037527 GGGTCTCCCTGGTCTCGT 59.962 66.667 0.00 0.00 41.34 4.18
44 45 3.327404 TCGGCCAAAGGGTCTCCC 61.327 66.667 2.24 0.00 45.90 4.30
45 46 2.046217 GTCGGCCAAAGGGTCTCC 60.046 66.667 2.24 0.00 36.31 3.71
46 47 2.046217 GGTCGGCCAAAGGGTCTC 60.046 66.667 0.00 0.00 36.31 3.36
47 48 2.852075 TGGTCGGCCAAAGGGTCT 60.852 61.111 6.10 0.00 42.83 3.85
55 56 2.933287 ATCCTTGGTGGTCGGCCA 60.933 61.111 3.51 3.51 43.73 5.36
56 57 2.124695 GATCCTTGGTGGTCGGCC 60.125 66.667 0.00 0.00 37.07 6.13
57 58 1.153349 GAGATCCTTGGTGGTCGGC 60.153 63.158 0.00 0.00 37.07 5.54
58 59 1.522569 GGAGATCCTTGGTGGTCGG 59.477 63.158 0.00 0.00 37.07 4.79
59 60 1.141881 CGGAGATCCTTGGTGGTCG 59.858 63.158 0.00 0.00 37.07 4.79
60 61 1.153349 GCGGAGATCCTTGGTGGTC 60.153 63.158 0.00 0.00 37.07 4.02
61 62 2.990479 GCGGAGATCCTTGGTGGT 59.010 61.111 0.00 0.00 37.07 4.16
62 63 2.202932 CGCGGAGATCCTTGGTGG 60.203 66.667 0.00 0.00 37.10 4.61
63 64 1.227089 CTCGCGGAGATCCTTGGTG 60.227 63.158 6.13 0.00 0.00 4.17
64 65 2.427245 CCTCGCGGAGATCCTTGGT 61.427 63.158 6.13 0.00 0.00 3.67
65 66 2.419198 CCTCGCGGAGATCCTTGG 59.581 66.667 6.13 0.00 0.00 3.61
66 67 2.279784 GCCTCGCGGAGATCCTTG 60.280 66.667 6.13 0.00 0.00 3.61
67 68 1.899437 TTTGCCTCGCGGAGATCCTT 61.899 55.000 6.13 0.00 0.00 3.36
68 69 1.899437 TTTTGCCTCGCGGAGATCCT 61.899 55.000 6.13 0.00 0.00 3.24
69 70 1.432270 CTTTTGCCTCGCGGAGATCC 61.432 60.000 6.13 0.00 0.00 3.36
70 71 0.460284 TCTTTTGCCTCGCGGAGATC 60.460 55.000 6.13 0.00 0.00 2.75
71 72 0.460987 CTCTTTTGCCTCGCGGAGAT 60.461 55.000 6.13 0.00 0.00 2.75
72 73 1.079819 CTCTTTTGCCTCGCGGAGA 60.080 57.895 6.13 0.00 0.00 3.71
73 74 2.103042 CCTCTTTTGCCTCGCGGAG 61.103 63.158 6.13 1.57 0.00 4.63
74 75 2.047274 CCTCTTTTGCCTCGCGGA 60.047 61.111 6.13 0.00 0.00 5.54
75 76 3.804193 GCCTCTTTTGCCTCGCGG 61.804 66.667 6.13 0.00 0.00 6.46
76 77 1.926511 AATGCCTCTTTTGCCTCGCG 61.927 55.000 0.00 0.00 0.00 5.87
77 78 0.179153 GAATGCCTCTTTTGCCTCGC 60.179 55.000 0.00 0.00 0.00 5.03
78 79 0.097674 CGAATGCCTCTTTTGCCTCG 59.902 55.000 0.00 0.00 0.00 4.63
93 94 1.484240 CCTTCTTCTCCTGCCTCGAAT 59.516 52.381 0.00 0.00 0.00 3.34
129 130 4.479993 CCCTCCTTGGCTGCCTCG 62.480 72.222 21.03 10.36 0.00 4.63
134 135 1.915078 CTGGTACCCCTCCTTGGCTG 61.915 65.000 10.07 0.00 0.00 4.85
135 136 1.616628 CTGGTACCCCTCCTTGGCT 60.617 63.158 10.07 0.00 0.00 4.75
153 154 1.733360 CGGTAGAGACTATAGGCGAGC 59.267 57.143 4.43 1.30 0.00 5.03
159 160 3.142951 AGTGCAGCGGTAGAGACTATAG 58.857 50.000 0.00 0.00 0.00 1.31
161 162 2.060050 AGTGCAGCGGTAGAGACTAT 57.940 50.000 0.00 0.00 0.00 2.12
176 177 0.376502 GAGGTCGTACTCGGTAGTGC 59.623 60.000 0.00 0.00 36.36 4.40
178 179 2.079925 GTTGAGGTCGTACTCGGTAGT 58.920 52.381 0.00 0.00 40.39 2.73
183 184 0.514255 TGACGTTGAGGTCGTACTCG 59.486 55.000 0.00 0.00 41.64 4.18
190 191 0.606604 TAGGGCTTGACGTTGAGGTC 59.393 55.000 0.00 0.00 37.45 3.85
249 251 7.748031 TCATCACACATTTAAACACACAAAC 57.252 32.000 0.00 0.00 0.00 2.93
250 252 8.031864 AGTTCATCACACATTTAAACACACAAA 58.968 29.630 0.00 0.00 0.00 2.83
257 259 5.048991 ACCGGAGTTCATCACACATTTAAAC 60.049 40.000 9.46 0.00 0.00 2.01
259 261 4.454161 CACCGGAGTTCATCACACATTTAA 59.546 41.667 9.46 0.00 0.00 1.52
331 334 1.375908 GCACGGCAGAACAGATCCA 60.376 57.895 0.00 0.00 0.00 3.41
362 365 6.014156 AGGAGATCCTATAAGACGAATTTGGG 60.014 42.308 0.00 0.00 46.48 4.12
363 366 6.998802 AGGAGATCCTATAAGACGAATTTGG 58.001 40.000 0.00 0.00 46.48 3.28
377 380 6.055588 CGCAAATTTCCTTTAGGAGATCCTA 58.944 40.000 4.42 4.42 46.48 2.94
383 386 4.095932 GGTACCGCAAATTTCCTTTAGGAG 59.904 45.833 0.00 0.00 46.36 3.69
386 389 4.011058 CGGTACCGCAAATTTCCTTTAG 57.989 45.455 23.44 0.00 0.00 1.85
400 403 0.388391 TCCTGTAAAACGCGGTACCG 60.388 55.000 30.06 30.06 43.09 4.02
401 404 1.929169 GATCCTGTAAAACGCGGTACC 59.071 52.381 12.47 0.16 0.00 3.34
403 406 2.883574 CAGATCCTGTAAAACGCGGTA 58.116 47.619 12.47 0.00 0.00 4.02
404 407 1.722011 CAGATCCTGTAAAACGCGGT 58.278 50.000 12.47 0.00 0.00 5.68
405 408 0.373716 GCAGATCCTGTAAAACGCGG 59.626 55.000 12.47 0.00 33.43 6.46
407 410 3.782046 TCTAGCAGATCCTGTAAAACGC 58.218 45.455 0.00 0.00 33.43 4.84
408 411 5.250235 TCTCTAGCAGATCCTGTAAAACG 57.750 43.478 0.00 0.00 33.43 3.60
409 412 5.465056 GCATCTCTAGCAGATCCTGTAAAAC 59.535 44.000 0.00 0.00 40.20 2.43
410 413 5.365025 AGCATCTCTAGCAGATCCTGTAAAA 59.635 40.000 0.00 0.00 40.20 1.52
411 414 4.898265 AGCATCTCTAGCAGATCCTGTAAA 59.102 41.667 0.00 0.00 40.20 2.01
412 415 4.478203 AGCATCTCTAGCAGATCCTGTAA 58.522 43.478 0.00 0.00 40.20 2.41
413 416 4.078537 GAGCATCTCTAGCAGATCCTGTA 58.921 47.826 2.22 0.00 40.20 2.74
414 417 2.892852 GAGCATCTCTAGCAGATCCTGT 59.107 50.000 2.22 0.00 40.20 4.00
415 418 3.581024 GAGCATCTCTAGCAGATCCTG 57.419 52.381 2.22 0.00 40.20 3.86
455 458 6.521162 GGTTCCATGAATTGTGGTAGTTTTT 58.479 36.000 0.00 0.00 37.96 1.94
456 459 5.278758 CGGTTCCATGAATTGTGGTAGTTTT 60.279 40.000 0.00 0.00 37.96 2.43
457 460 4.217550 CGGTTCCATGAATTGTGGTAGTTT 59.782 41.667 0.00 0.00 37.96 2.66
458 461 3.756434 CGGTTCCATGAATTGTGGTAGTT 59.244 43.478 0.00 0.00 37.96 2.24
459 462 3.244770 ACGGTTCCATGAATTGTGGTAGT 60.245 43.478 0.00 1.79 37.96 2.73
460 463 3.126858 CACGGTTCCATGAATTGTGGTAG 59.873 47.826 0.00 1.33 37.96 3.18
461 464 3.078097 CACGGTTCCATGAATTGTGGTA 58.922 45.455 0.00 0.00 37.96 3.25
462 465 1.885887 CACGGTTCCATGAATTGTGGT 59.114 47.619 0.00 0.00 37.96 4.16
463 466 1.402720 GCACGGTTCCATGAATTGTGG 60.403 52.381 0.00 0.87 38.11 4.17
464 467 1.402720 GGCACGGTTCCATGAATTGTG 60.403 52.381 0.00 0.00 34.77 3.33
465 468 0.887933 GGCACGGTTCCATGAATTGT 59.112 50.000 0.00 0.00 0.00 2.71
466 469 1.176527 AGGCACGGTTCCATGAATTG 58.823 50.000 0.00 0.00 0.00 2.32
467 470 2.290641 TGTAGGCACGGTTCCATGAATT 60.291 45.455 0.00 0.00 0.00 2.17
468 471 1.280710 TGTAGGCACGGTTCCATGAAT 59.719 47.619 0.00 0.00 0.00 2.57
469 472 0.687920 TGTAGGCACGGTTCCATGAA 59.312 50.000 0.00 0.00 0.00 2.57
470 473 0.687920 TTGTAGGCACGGTTCCATGA 59.312 50.000 0.00 0.00 0.00 3.07
471 474 1.199097 GTTTGTAGGCACGGTTCCATG 59.801 52.381 0.00 0.00 0.00 3.66
472 475 1.073284 AGTTTGTAGGCACGGTTCCAT 59.927 47.619 0.00 0.00 0.00 3.41
473 476 0.470766 AGTTTGTAGGCACGGTTCCA 59.529 50.000 0.00 0.00 0.00 3.53
474 477 2.071540 GTAGTTTGTAGGCACGGTTCC 58.928 52.381 0.00 0.00 0.00 3.62
475 478 2.071540 GGTAGTTTGTAGGCACGGTTC 58.928 52.381 0.00 0.00 0.00 3.62
476 479 1.417145 TGGTAGTTTGTAGGCACGGTT 59.583 47.619 0.00 0.00 0.00 4.44
477 480 1.050204 TGGTAGTTTGTAGGCACGGT 58.950 50.000 0.00 0.00 0.00 4.83
478 481 1.001633 AGTGGTAGTTTGTAGGCACGG 59.998 52.381 0.00 0.00 0.00 4.94
479 482 2.450609 AGTGGTAGTTTGTAGGCACG 57.549 50.000 0.00 0.00 0.00 5.34
480 483 4.151157 CGTAAAGTGGTAGTTTGTAGGCAC 59.849 45.833 0.00 0.00 0.00 5.01
481 484 4.039004 TCGTAAAGTGGTAGTTTGTAGGCA 59.961 41.667 0.00 0.00 0.00 4.75
482 485 4.559153 TCGTAAAGTGGTAGTTTGTAGGC 58.441 43.478 0.00 0.00 0.00 3.93
483 486 7.662604 AATTCGTAAAGTGGTAGTTTGTAGG 57.337 36.000 0.00 0.00 0.00 3.18
484 487 9.940166 AAAAATTCGTAAAGTGGTAGTTTGTAG 57.060 29.630 0.00 0.00 0.00 2.74
485 488 9.719279 CAAAAATTCGTAAAGTGGTAGTTTGTA 57.281 29.630 0.00 0.00 0.00 2.41
486 489 8.460428 TCAAAAATTCGTAAAGTGGTAGTTTGT 58.540 29.630 0.00 0.00 0.00 2.83
487 490 8.844441 TCAAAAATTCGTAAAGTGGTAGTTTG 57.156 30.769 0.00 0.00 0.00 2.93
488 491 9.511144 CTTCAAAAATTCGTAAAGTGGTAGTTT 57.489 29.630 0.00 0.00 0.00 2.66
489 492 8.895737 TCTTCAAAAATTCGTAAAGTGGTAGTT 58.104 29.630 0.00 0.00 0.00 2.24
490 493 8.441312 TCTTCAAAAATTCGTAAAGTGGTAGT 57.559 30.769 0.00 0.00 0.00 2.73
491 494 9.724839 TTTCTTCAAAAATTCGTAAAGTGGTAG 57.275 29.630 0.00 0.00 0.00 3.18
493 496 8.989653 TTTTCTTCAAAAATTCGTAAAGTGGT 57.010 26.923 0.00 0.00 0.00 4.16
494 497 9.683651 GTTTTTCTTCAAAAATTCGTAAAGTGG 57.316 29.630 0.00 0.00 42.22 4.00
499 502 9.738832 CCCTAGTTTTTCTTCAAAAATTCGTAA 57.261 29.630 0.00 0.00 42.22 3.18
500 503 9.122779 TCCCTAGTTTTTCTTCAAAAATTCGTA 57.877 29.630 0.00 0.00 42.22 3.43
501 504 7.919091 GTCCCTAGTTTTTCTTCAAAAATTCGT 59.081 33.333 0.00 0.00 42.22 3.85
502 505 7.381408 GGTCCCTAGTTTTTCTTCAAAAATTCG 59.619 37.037 0.00 0.00 42.22 3.34
503 506 7.656137 GGGTCCCTAGTTTTTCTTCAAAAATTC 59.344 37.037 0.00 0.00 42.22 2.17
504 507 7.506114 GGGTCCCTAGTTTTTCTTCAAAAATT 58.494 34.615 0.00 0.00 42.22 1.82
505 508 6.239204 CGGGTCCCTAGTTTTTCTTCAAAAAT 60.239 38.462 6.29 0.00 42.22 1.82
506 509 5.068067 CGGGTCCCTAGTTTTTCTTCAAAAA 59.932 40.000 6.29 0.00 38.84 1.94
510 513 2.974099 TCGGGTCCCTAGTTTTTCTTCA 59.026 45.455 6.29 0.00 0.00 3.02
561 564 2.350522 AGCGCATTTCTGACTAGTTGG 58.649 47.619 11.47 0.00 0.00 3.77
585 588 4.889409 TGAAAAGTGTCTGATTTGGCTCTT 59.111 37.500 0.00 0.00 0.00 2.85
596 599 2.550978 ACCACGTCTGAAAAGTGTCTG 58.449 47.619 0.00 0.00 35.81 3.51
597 600 2.981859 ACCACGTCTGAAAAGTGTCT 57.018 45.000 0.00 0.00 35.81 3.41
655 658 3.712187 ACCACTTTACAAATTTGTGCGG 58.288 40.909 29.72 22.61 42.31 5.69
656 659 5.516090 ACTACCACTTTACAAATTTGTGCG 58.484 37.500 29.72 19.89 42.31 5.34
673 676 1.050204 ACCGTGCCTACAAACTACCA 58.950 50.000 0.00 0.00 0.00 3.25
818 831 4.430137 TTGCAAAATCTCATCAGCACTC 57.570 40.909 0.00 0.00 0.00 3.51
891 969 2.474112 TGAAAACCCTAGCCCGAGTAT 58.526 47.619 0.00 0.00 0.00 2.12
897 975 2.294979 CGGTAATGAAAACCCTAGCCC 58.705 52.381 0.00 0.00 33.10 5.19
899 977 2.640184 AGCGGTAATGAAAACCCTAGC 58.360 47.619 0.00 0.00 33.10 3.42
909 987 1.978455 ATCGGCCCAAGCGGTAATGA 61.978 55.000 0.00 0.00 41.24 2.57
917 995 2.517875 ATCAGCATCGGCCCAAGC 60.518 61.111 0.00 0.00 42.56 4.01
918 996 1.895707 GGATCAGCATCGGCCCAAG 60.896 63.158 0.00 0.00 42.56 3.61
919 997 2.192979 GGATCAGCATCGGCCCAA 59.807 61.111 0.00 0.00 42.56 4.12
920 998 3.877450 GGGATCAGCATCGGCCCA 61.877 66.667 0.00 0.00 42.56 5.36
921 999 4.996434 CGGGATCAGCATCGGCCC 62.996 72.222 0.00 0.00 42.56 5.80
922 1000 4.996434 CCGGGATCAGCATCGGCC 62.996 72.222 0.00 0.00 42.56 6.13
924 1002 4.996434 GGCCGGGATCAGCATCGG 62.996 72.222 2.18 0.00 44.70 4.18
926 1004 4.996434 CCGGCCGGGATCAGCATC 62.996 72.222 37.42 0.00 38.47 3.91
976 1069 1.687996 CCTGGTGGTTTTGGTGGAGTT 60.688 52.381 0.00 0.00 0.00 3.01
995 1088 4.162690 AACGGAGGAGCATCGGCC 62.163 66.667 0.00 0.00 42.56 6.13
1513 1633 0.821517 TTCCAGTACATGACGCGGAT 59.178 50.000 12.47 0.00 35.27 4.18
2573 2717 4.193865 TCAATACAGATGACCATGCAGTG 58.806 43.478 0.00 0.00 0.00 3.66


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

AutoCloner maintained by Alex Coulton.