Multiple sequence alignment - TraesCS1A01G365400

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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 TraesCS1A01G365400 chr1A 100.000 2831 0 0 1 2831 544494425 544497255 0.000000e+00 5228.0
1 TraesCS1A01G365400 chr1B 92.583 1510 72 17 711 2207 614970041 614971523 0.000000e+00 2132.0
2 TraesCS1A01G365400 chr1B 91.898 469 21 10 1 453 614969549 614970016 8.550000e-180 640.0
3 TraesCS1A01G365400 chr1B 90.816 392 31 4 2442 2831 614972607 614972995 1.160000e-143 520.0
4 TraesCS1A01G365400 chr1B 100.000 29 0 0 2272 2300 645348133 645348161 1.000000e-03 54.7
5 TraesCS1A01G365400 chr1D 93.118 1424 61 9 717 2127 449312421 449313820 0.000000e+00 2052.0
6 TraesCS1A01G365400 chr1D 89.451 711 58 7 1 704 449311322 449312022 0.000000e+00 881.0
7 TraesCS1A01G365400 chr1D 95.556 45 2 0 2209 2253 318090004 318090048 3.910000e-09 73.1
8 TraesCS1A01G365400 chr7D 87.335 529 48 8 1164 1692 221986255 221985746 3.140000e-164 588.0
9 TraesCS1A01G365400 chr7D 86.604 530 48 12 1169 1693 53741739 53741228 5.290000e-157 564.0
10 TraesCS1A01G365400 chr7D 85.981 535 51 10 1164 1693 488105882 488106397 4.120000e-153 551.0
11 TraesCS1A01G365400 chr3D 86.981 530 45 7 1164 1693 53783129 53783634 2.450000e-160 575.0
12 TraesCS1A01G365400 chr3D 86.168 535 50 10 1164 1693 301332253 301332768 8.860000e-155 556.0
13 TraesCS1A01G365400 chr3D 85.981 535 49 14 1164 1693 141484650 141484137 1.480000e-152 549.0
14 TraesCS1A01G365400 chr3D 93.137 204 14 0 3 206 7122707 7122504 1.650000e-77 300.0
15 TraesCS1A01G365400 chr3D 85.714 238 34 0 467 704 346865475 346865238 4.680000e-63 252.0
16 TraesCS1A01G365400 chr2D 86.415 530 48 7 1164 1693 74144396 74144901 2.460000e-155 558.0
17 TraesCS1A01G365400 chr2D 92.308 39 1 2 2261 2299 575354212 575354176 1.000000e-03 54.7
18 TraesCS1A01G365400 chrUn 86.424 523 50 10 1169 1691 79581128 79581629 1.150000e-153 553.0
19 TraesCS1A01G365400 chr2A 85.094 530 60 7 1164 1693 186412442 186411932 8.990000e-145 523.0
20 TraesCS1A01G365400 chr2A 95.349 43 2 0 2211 2253 746836578 746836620 5.060000e-08 69.4
21 TraesCS1A01G365400 chr2A 93.023 43 3 0 2211 2253 694863803 694863761 2.350000e-06 63.9
22 TraesCS1A01G365400 chr3A 90.871 241 16 1 3 237 13190472 13190712 4.550000e-83 318.0
23 TraesCS1A01G365400 chr3A 85.714 238 34 0 467 704 41103267 41103030 4.680000e-63 252.0
24 TraesCS1A01G365400 chr3A 85.356 239 35 0 466 704 743686394 743686156 6.060000e-62 248.0
25 TraesCS1A01G365400 chr3B 89.388 245 17 3 3 238 8685261 8685017 1.650000e-77 300.0
26 TraesCS1A01G365400 chr4D 85.714 238 34 0 467 704 69179821 69179584 4.680000e-63 252.0
27 TraesCS1A01G365400 chr4D 86.036 222 29 2 484 704 122202347 122202127 1.310000e-58 237.0
28 TraesCS1A01G365400 chr4D 100.000 29 0 0 2272 2300 451274352 451274324 1.000000e-03 54.7
29 TraesCS1A01G365400 chr7A 84.937 239 34 2 467 704 675079753 675079990 1.010000e-59 241.0
30 TraesCS1A01G365400 chr7A 95.349 43 2 0 2211 2253 722380801 722380759 5.060000e-08 69.4
31 TraesCS1A01G365400 chr5A 84.711 242 36 1 463 704 578233730 578233490 1.010000e-59 241.0
32 TraesCS1A01G365400 chr5A 84.362 243 33 3 463 704 229576247 229576485 1.700000e-57 233.0
33 TraesCS1A01G365400 chr5D 95.349 43 2 0 2211 2253 273121464 273121422 5.060000e-08 69.4
34 TraesCS1A01G365400 chr6D 94.737 38 2 0 2214 2251 149646945 149646982 3.050000e-05 60.2
35 TraesCS1A01G365400 chr4A 100.000 31 0 0 2222 2252 739047999 739048029 1.100000e-04 58.4


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 TraesCS1A01G365400 chr1A 544494425 544497255 2830 False 5228.000000 5228 100.000000 1 2831 1 chr1A.!!$F1 2830
1 TraesCS1A01G365400 chr1B 614969549 614972995 3446 False 1097.333333 2132 91.765667 1 2831 3 chr1B.!!$F2 2830
2 TraesCS1A01G365400 chr1D 449311322 449313820 2498 False 1466.500000 2052 91.284500 1 2127 2 chr1D.!!$F2 2126
3 TraesCS1A01G365400 chr7D 221985746 221986255 509 True 588.000000 588 87.335000 1164 1692 1 chr7D.!!$R2 528
4 TraesCS1A01G365400 chr7D 53741228 53741739 511 True 564.000000 564 86.604000 1169 1693 1 chr7D.!!$R1 524
5 TraesCS1A01G365400 chr7D 488105882 488106397 515 False 551.000000 551 85.981000 1164 1693 1 chr7D.!!$F1 529
6 TraesCS1A01G365400 chr3D 53783129 53783634 505 False 575.000000 575 86.981000 1164 1693 1 chr3D.!!$F1 529
7 TraesCS1A01G365400 chr3D 301332253 301332768 515 False 556.000000 556 86.168000 1164 1693 1 chr3D.!!$F2 529
8 TraesCS1A01G365400 chr3D 141484137 141484650 513 True 549.000000 549 85.981000 1164 1693 1 chr3D.!!$R2 529
9 TraesCS1A01G365400 chr2D 74144396 74144901 505 False 558.000000 558 86.415000 1164 1693 1 chr2D.!!$F1 529
10 TraesCS1A01G365400 chrUn 79581128 79581629 501 False 553.000000 553 86.424000 1169 1691 1 chrUn.!!$F1 522
11 TraesCS1A01G365400 chr2A 186411932 186412442 510 True 523.000000 523 85.094000 1164 1693 1 chr2A.!!$R1 529

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
995 1416 0.038526 GCAGCAGCAGCAAGAAACAT 60.039 50.0 4.63 0.0 45.49 2.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2153 2609 0.179215 GATTTCACTCGGCGCAACTG 60.179 55.0 10.83 0.0 0.0 3.16 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
276 280 2.089980 AGATGCTGCTGATTGGTGAAC 58.910 47.619 0.00 0.00 0.00 3.18
403 419 4.159135 AGCCAAGCATAATTTCCAAGACAG 59.841 41.667 0.00 0.00 0.00 3.51
404 420 4.678840 GCCAAGCATAATTTCCAAGACAGG 60.679 45.833 0.00 0.00 0.00 4.00
437 454 5.597806 TGATAATATCCACGAGTTGTCCAC 58.402 41.667 0.00 0.00 0.00 4.02
473 501 6.930068 AGGTAACACAACAGTATACTTCCT 57.070 37.500 1.56 0.00 41.41 3.36
474 502 6.698380 AGGTAACACAACAGTATACTTCCTG 58.302 40.000 1.56 3.55 41.41 3.86
475 503 5.350640 GGTAACACAACAGTATACTTCCTGC 59.649 44.000 1.56 0.00 31.76 4.85
476 504 4.617253 ACACAACAGTATACTTCCTGCA 57.383 40.909 1.56 0.00 31.76 4.41
479 507 4.572389 CACAACAGTATACTTCCTGCATCC 59.428 45.833 1.56 0.00 31.76 3.51
480 508 4.225042 ACAACAGTATACTTCCTGCATCCA 59.775 41.667 1.56 0.00 31.76 3.41
482 510 3.134804 ACAGTATACTTCCTGCATCCACC 59.865 47.826 1.56 0.00 31.76 4.61
488 516 3.624777 ACTTCCTGCATCCACCAATAAG 58.375 45.455 0.00 0.00 0.00 1.73
490 518 3.003394 TCCTGCATCCACCAATAAGTG 57.997 47.619 0.00 0.00 37.51 3.16
494 522 4.260985 CTGCATCCACCAATAAGTGTACA 58.739 43.478 0.00 0.00 35.93 2.90
496 524 5.260424 TGCATCCACCAATAAGTGTACATT 58.740 37.500 0.00 0.00 35.93 2.71
508 536 9.341899 CAATAAGTGTACATTTAGCTTTTGTCC 57.658 33.333 15.04 0.00 0.00 4.02
509 537 6.952773 AAGTGTACATTTAGCTTTTGTCCA 57.047 33.333 1.14 0.00 0.00 4.02
510 538 6.952773 AGTGTACATTTAGCTTTTGTCCAA 57.047 33.333 0.00 0.00 0.00 3.53
511 539 7.341445 AGTGTACATTTAGCTTTTGTCCAAA 57.659 32.000 0.00 0.00 0.00 3.28
512 540 7.425606 AGTGTACATTTAGCTTTTGTCCAAAG 58.574 34.615 0.00 0.00 44.44 2.77
516 544 9.738832 GTACATTTAGCTTTTGTCCAAAGTTAA 57.261 29.630 0.00 2.71 42.96 2.01
524 552 9.713713 AGCTTTTGTCCAAAGTTAAAGTTTTAA 57.286 25.926 0.00 0.00 43.62 1.52
568 596 5.404466 AAAAAGTAGCAGCATTTATGGCA 57.596 34.783 0.00 0.00 0.00 4.92
569 597 4.376340 AAAGTAGCAGCATTTATGGCAC 57.624 40.909 0.00 0.00 0.00 5.01
577 605 6.507023 AGCAGCATTTATGGCACTAAATTAC 58.493 36.000 0.00 7.53 30.68 1.89
590 618 9.914834 TGGCACTAAATTACTATAACTGGATTT 57.085 29.630 0.00 0.00 0.00 2.17
643 671 8.648097 CCAATTTGATGTCGTATATACTACTGC 58.352 37.037 16.06 9.81 0.00 4.40
644 672 9.411801 CAATTTGATGTCGTATATACTACTGCT 57.588 33.333 16.06 4.15 0.00 4.24
645 673 9.627395 AATTTGATGTCGTATATACTACTGCTC 57.373 33.333 16.06 11.32 0.00 4.26
647 675 7.981102 TGATGTCGTATATACTACTGCTCTT 57.019 36.000 16.06 0.00 0.00 2.85
648 676 8.392372 TGATGTCGTATATACTACTGCTCTTT 57.608 34.615 16.06 0.00 0.00 2.52
650 678 9.119329 GATGTCGTATATACTACTGCTCTTTTG 57.881 37.037 16.06 0.00 0.00 2.44
651 679 7.423199 TGTCGTATATACTACTGCTCTTTTGG 58.577 38.462 16.06 0.00 0.00 3.28
652 680 7.283807 TGTCGTATATACTACTGCTCTTTTGGA 59.716 37.037 16.06 0.00 0.00 3.53
654 682 9.511272 TCGTATATACTACTGCTCTTTTGGATA 57.489 33.333 11.05 0.00 0.00 2.59
662 690 9.740710 ACTACTGCTCTTTTGGATAAATTTAGT 57.259 29.630 3.94 0.00 0.00 2.24
664 692 8.635765 ACTGCTCTTTTGGATAAATTTAGTCA 57.364 30.769 3.94 2.12 0.00 3.41
744 1158 3.461061 TCACTGAAGAACTCAACAGCAG 58.539 45.455 0.00 0.00 32.17 4.24
746 1160 2.216046 CTGAAGAACTCAACAGCAGCA 58.784 47.619 0.00 0.00 32.17 4.41
756 1170 0.684153 AACAGCAGCACAACCACCTT 60.684 50.000 0.00 0.00 0.00 3.50
860 1278 1.002087 AGAGGTTAGACCAAAGCCACG 59.998 52.381 0.00 0.00 41.95 4.94
891 1309 8.765517 AGATTCAGATTTGGGAGCAAATATTTT 58.234 29.630 0.00 0.00 35.18 1.82
904 1322 8.929746 GGAGCAAATATTTTTCAGAAAAGAAGG 58.070 33.333 8.34 0.50 38.09 3.46
964 1382 1.679153 GGAGGAAGACCAGATCGAGAC 59.321 57.143 0.00 0.00 38.94 3.36
995 1416 0.038526 GCAGCAGCAGCAAGAAACAT 60.039 50.000 4.63 0.00 45.49 2.71
997 1418 0.601558 AGCAGCAGCAAGAAACATGG 59.398 50.000 3.17 0.00 45.49 3.66
998 1419 1.012486 GCAGCAGCAAGAAACATGGC 61.012 55.000 0.00 0.00 41.58 4.40
1858 2305 3.117372 CGGAGTAAGATCGCCGGT 58.883 61.111 1.90 0.00 44.57 5.28
1863 2310 2.171725 GTAAGATCGCCGGTGGTGC 61.172 63.158 16.49 4.85 32.51 5.01
1864 2311 3.379865 TAAGATCGCCGGTGGTGCC 62.380 63.158 16.49 0.00 32.51 5.01
1894 2341 2.268920 GCATGTCGGCAAGGAGGA 59.731 61.111 0.00 0.00 0.00 3.71
1932 2379 4.838152 CGACCATGGCCACCGGAG 62.838 72.222 26.27 16.39 0.00 4.63
2026 2481 1.293963 CGTGGCCATGTCTGACTGTG 61.294 60.000 17.42 7.89 0.00 3.66
2072 2527 2.157738 ACAGAAGAGGCATGAGTTTGC 58.842 47.619 0.00 0.00 42.01 3.68
2091 2547 4.370364 TGCCTCCAATCTAAAAATTCGC 57.630 40.909 0.00 0.00 0.00 4.70
2093 2549 4.402155 TGCCTCCAATCTAAAAATTCGCAT 59.598 37.500 0.00 0.00 0.00 4.73
2094 2550 4.741676 GCCTCCAATCTAAAAATTCGCATG 59.258 41.667 0.00 0.00 0.00 4.06
2127 2583 8.999431 GTGAGATACAAATTTTCTTGTGTCCTA 58.001 33.333 8.90 0.00 44.23 2.94
2128 2584 8.999431 TGAGATACAAATTTTCTTGTGTCCTAC 58.001 33.333 8.90 3.92 44.23 3.18
2129 2585 8.336801 AGATACAAATTTTCTTGTGTCCTACC 57.663 34.615 8.90 0.00 44.23 3.18
2130 2586 5.784578 ACAAATTTTCTTGTGTCCTACCC 57.215 39.130 0.00 0.00 38.12 3.69
2131 2587 4.587262 ACAAATTTTCTTGTGTCCTACCCC 59.413 41.667 0.00 0.00 38.12 4.95
2132 2588 4.741928 AATTTTCTTGTGTCCTACCCCT 57.258 40.909 0.00 0.00 0.00 4.79
2133 2589 5.853572 AATTTTCTTGTGTCCTACCCCTA 57.146 39.130 0.00 0.00 0.00 3.53
2134 2590 4.903045 TTTTCTTGTGTCCTACCCCTAG 57.097 45.455 0.00 0.00 0.00 3.02
2135 2591 2.544844 TCTTGTGTCCTACCCCTAGG 57.455 55.000 0.06 0.06 41.19 3.02
2153 2609 5.534278 CCCTAGGTGTAGTTTAGGTACTAGC 59.466 48.000 8.29 0.00 44.25 3.42
2154 2610 6.125029 CCTAGGTGTAGTTTAGGTACTAGCA 58.875 44.000 0.00 0.00 44.25 3.49
2157 2613 6.015282 AGGTGTAGTTTAGGTACTAGCAGTT 58.985 40.000 0.00 0.00 44.25 3.16
2158 2614 6.071503 AGGTGTAGTTTAGGTACTAGCAGTTG 60.072 42.308 0.00 0.00 44.25 3.16
2161 2617 2.288961 TTAGGTACTAGCAGTTGCGC 57.711 50.000 0.00 0.00 44.25 6.09
2162 2618 0.458669 TAGGTACTAGCAGTTGCGCC 59.541 55.000 4.18 0.00 43.45 6.53
2163 2619 3.209228 TAGGTACTAGCAGTTGCGCCG 62.209 57.143 4.18 0.00 43.45 6.46
2207 2663 4.084433 CCAAAATGCAAATTGTGGTTCTCG 60.084 41.667 12.24 0.00 34.84 4.04
2208 2664 4.320608 AAATGCAAATTGTGGTTCTCGT 57.679 36.364 0.00 0.00 0.00 4.18
2209 2665 5.446143 AAATGCAAATTGTGGTTCTCGTA 57.554 34.783 0.00 0.00 0.00 3.43
2213 2669 5.242434 TGCAAATTGTGGTTCTCGTATACT 58.758 37.500 0.56 0.00 0.00 2.12
2216 2672 4.667519 ATTGTGGTTCTCGTATACTCCC 57.332 45.455 0.56 0.00 0.00 4.30
2219 2675 3.285484 GTGGTTCTCGTATACTCCCTCA 58.715 50.000 0.56 0.00 0.00 3.86
2220 2676 3.066481 GTGGTTCTCGTATACTCCCTCAC 59.934 52.174 0.56 0.00 0.00 3.51
2222 2678 4.164796 TGGTTCTCGTATACTCCCTCACTA 59.835 45.833 0.56 0.00 0.00 2.74
2223 2679 5.128919 GGTTCTCGTATACTCCCTCACTAA 58.871 45.833 0.56 0.00 0.00 2.24
2224 2680 5.591877 GGTTCTCGTATACTCCCTCACTAAA 59.408 44.000 0.56 0.00 0.00 1.85
2225 2681 6.264970 GGTTCTCGTATACTCCCTCACTAAAT 59.735 42.308 0.56 0.00 0.00 1.40
2226 2682 7.201893 GGTTCTCGTATACTCCCTCACTAAATT 60.202 40.741 0.56 0.00 0.00 1.82
2228 2684 8.985315 TCTCGTATACTCCCTCACTAAATTAA 57.015 34.615 0.56 0.00 0.00 1.40
2281 2810 8.834749 AGAAAGTACTTCTTGGTGATCTAAAC 57.165 34.615 8.95 0.00 41.97 2.01
2285 2814 4.642429 ACTTCTTGGTGATCTAAACGCTT 58.358 39.130 0.00 0.00 0.00 4.68
2289 2818 7.390718 ACTTCTTGGTGATCTAAACGCTTTTAT 59.609 33.333 0.00 0.00 0.00 1.40
2290 2819 8.780846 TTCTTGGTGATCTAAACGCTTTTATA 57.219 30.769 0.00 0.00 0.00 0.98
2291 2820 8.958119 TCTTGGTGATCTAAACGCTTTTATAT 57.042 30.769 0.00 0.00 0.00 0.86
2292 2821 9.391006 TCTTGGTGATCTAAACGCTTTTATATT 57.609 29.630 0.00 0.00 0.00 1.28
2294 2823 9.997482 TTGGTGATCTAAACGCTTTTATATTTC 57.003 29.630 0.00 0.00 0.00 2.17
2295 2824 8.617809 TGGTGATCTAAACGCTTTTATATTTCC 58.382 33.333 0.00 3.35 0.00 3.13
2296 2825 8.837389 GGTGATCTAAACGCTTTTATATTTCCT 58.163 33.333 0.00 0.00 0.00 3.36
2301 2830 9.585099 TCTAAACGCTTTTATATTTCCTTACGA 57.415 29.630 0.00 0.00 0.00 3.43
2304 2833 9.896263 AAACGCTTTTATATTTCCTTACGAAAA 57.104 25.926 0.00 0.00 43.61 2.29
2305 2834 9.896263 AACGCTTTTATATTTCCTTACGAAAAA 57.104 25.926 0.00 0.00 43.61 1.94
2327 2856 8.634475 AAAAAGTATCTGTTTTTCAAGAGCAC 57.366 30.769 0.00 0.00 32.82 4.40
2328 2857 6.942532 AAGTATCTGTTTTTCAAGAGCACA 57.057 33.333 0.00 0.00 0.00 4.57
2329 2858 6.305693 AGTATCTGTTTTTCAAGAGCACAC 57.694 37.500 0.00 0.00 0.00 3.82
2330 2859 5.822519 AGTATCTGTTTTTCAAGAGCACACA 59.177 36.000 0.00 0.00 0.00 3.72
2335 3582 6.531240 TCTGTTTTTCAAGAGCACACATTTTC 59.469 34.615 0.00 0.00 0.00 2.29
2349 3596 6.369005 CACACATTTTCTCTGCTTACTCAAG 58.631 40.000 0.00 0.00 34.66 3.02
2361 3608 6.778069 TCTGCTTACTCAAGGTAGCACTATAT 59.222 38.462 0.00 0.00 33.96 0.86
2392 3640 6.109359 AGAGCACTATTAGAACATCACCAAC 58.891 40.000 0.00 0.00 0.00 3.77
2399 3647 3.409026 AGAACATCACCAACAGGAGAC 57.591 47.619 0.00 0.00 0.00 3.36
2405 3653 4.202503 ACATCACCAACAGGAGACAGAAAT 60.203 41.667 0.00 0.00 0.00 2.17
2407 3655 3.648067 TCACCAACAGGAGACAGAAATCT 59.352 43.478 0.00 0.00 0.00 2.40
2410 3658 3.999663 CCAACAGGAGACAGAAATCTCAC 59.000 47.826 5.23 0.00 46.00 3.51
2413 3661 4.829968 ACAGGAGACAGAAATCTCACATG 58.170 43.478 5.23 0.00 46.00 3.21
2414 3662 4.529769 ACAGGAGACAGAAATCTCACATGA 59.470 41.667 0.00 0.00 46.00 3.07
2450 3757 5.708877 TCCCTTAACACGTTTATTTTGGG 57.291 39.130 0.00 0.00 0.00 4.12
2460 3767 4.189231 CGTTTATTTTGGGACGGAGAGAT 58.811 43.478 0.00 0.00 32.29 2.75
2464 3771 2.981859 TTTGGGACGGAGAGATTAGC 57.018 50.000 0.00 0.00 0.00 3.09
2510 3817 4.532834 ACAAAGGCTACAAAAGAAGACCA 58.467 39.130 0.00 0.00 0.00 4.02
2512 3819 5.598417 ACAAAGGCTACAAAAGAAGACCAAT 59.402 36.000 0.00 0.00 0.00 3.16
2513 3820 6.775629 ACAAAGGCTACAAAAGAAGACCAATA 59.224 34.615 0.00 0.00 0.00 1.90
2514 3821 6.819397 AAGGCTACAAAAGAAGACCAATAC 57.181 37.500 0.00 0.00 0.00 1.89
2515 3822 5.876357 AGGCTACAAAAGAAGACCAATACA 58.124 37.500 0.00 0.00 0.00 2.29
2516 3823 6.485171 AGGCTACAAAAGAAGACCAATACAT 58.515 36.000 0.00 0.00 0.00 2.29
2517 3824 6.375455 AGGCTACAAAAGAAGACCAATACATG 59.625 38.462 0.00 0.00 0.00 3.21
2518 3825 6.030228 GCTACAAAAGAAGACCAATACATGC 58.970 40.000 0.00 0.00 0.00 4.06
2520 3827 6.594788 ACAAAAGAAGACCAATACATGCAT 57.405 33.333 0.00 0.00 0.00 3.96
2521 3828 7.701539 ACAAAAGAAGACCAATACATGCATA 57.298 32.000 0.00 0.00 0.00 3.14
2522 3829 7.538575 ACAAAAGAAGACCAATACATGCATAC 58.461 34.615 0.00 0.00 0.00 2.39
2523 3830 6.699575 AAAGAAGACCAATACATGCATACC 57.300 37.500 0.00 0.00 0.00 2.73
2524 3831 5.372343 AGAAGACCAATACATGCATACCA 57.628 39.130 0.00 0.00 0.00 3.25
2525 3832 5.754782 AGAAGACCAATACATGCATACCAA 58.245 37.500 0.00 0.00 0.00 3.67
2526 3833 5.590259 AGAAGACCAATACATGCATACCAAC 59.410 40.000 0.00 0.00 0.00 3.77
2528 3835 6.247229 AGACCAATACATGCATACCAACTA 57.753 37.500 0.00 0.00 0.00 2.24
2529 3836 6.658849 AGACCAATACATGCATACCAACTAA 58.341 36.000 0.00 0.00 0.00 2.24
2589 3896 4.639726 TGGGTCACCACTAGCAGT 57.360 55.556 0.00 0.00 43.37 4.40
2653 3960 1.954382 GGTCTGAAACTTTCCCACCAC 59.046 52.381 11.63 0.00 32.98 4.16
2665 3973 1.595357 CCACCACCGACCTTCCTAC 59.405 63.158 0.00 0.00 0.00 3.18
2691 3999 2.582498 GGCACCGGTCGATTCTCG 60.582 66.667 2.59 0.00 42.10 4.04
2694 4002 1.874019 CACCGGTCGATTCTCGCTG 60.874 63.158 2.59 0.00 40.21 5.18
2697 4005 2.226896 CGGTCGATTCTCGCTGCTG 61.227 63.158 0.00 0.00 40.21 4.41
2742 4050 4.814294 CCCCTTCGCTCGTTCCCG 62.814 72.222 0.00 0.00 0.00 5.14
2745 4053 2.257371 CTTCGCTCGTTCCCGTCA 59.743 61.111 0.00 0.00 35.01 4.35
2784 4092 2.501128 CCCGCATCTGTCGTGGAT 59.499 61.111 0.00 0.00 36.02 3.41
2789 4097 2.586418 CATCTGTCGTGGATGCTCG 58.414 57.895 1.95 1.95 34.97 5.03
2793 4101 0.179100 CTGTCGTGGATGCTCGGAAT 60.179 55.000 8.82 0.00 0.00 3.01
2801 4109 2.652893 GATGCTCGGAATGTTGCGCC 62.653 60.000 4.18 0.00 41.99 6.53
2819 4127 3.365291 CTGTTCCCGCCGATTCCGA 62.365 63.158 0.00 0.00 38.22 4.55
2822 4130 3.668980 TTCCCGCCGATTCCGAACC 62.669 63.158 0.00 0.00 38.22 3.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
233 237 2.507324 GTCTTGAGCGTCTCCGGC 60.507 66.667 0.00 0.00 33.68 6.13
276 280 8.043710 ACTACAAGATCAAATTCTAGGAACAGG 58.956 37.037 0.00 0.00 0.00 4.00
403 419 8.771920 TCGTGGATATTATCATATTGTTGTCC 57.228 34.615 6.04 0.00 0.00 4.02
404 420 9.424319 ACTCGTGGATATTATCATATTGTTGTC 57.576 33.333 6.04 0.00 0.00 3.18
473 501 4.293662 TGTACACTTATTGGTGGATGCA 57.706 40.909 0.00 0.00 41.09 3.96
474 502 5.835113 AATGTACACTTATTGGTGGATGC 57.165 39.130 0.00 0.00 41.09 3.91
475 503 7.283127 AGCTAAATGTACACTTATTGGTGGATG 59.717 37.037 0.00 0.00 41.09 3.51
476 504 7.346471 AGCTAAATGTACACTTATTGGTGGAT 58.654 34.615 0.00 0.00 41.09 3.41
479 507 9.128107 CAAAAGCTAAATGTACACTTATTGGTG 57.872 33.333 0.00 0.00 42.34 4.17
480 508 8.856103 ACAAAAGCTAAATGTACACTTATTGGT 58.144 29.630 0.00 0.00 0.00 3.67
482 510 9.341899 GGACAAAAGCTAAATGTACACTTATTG 57.658 33.333 0.00 2.23 0.00 1.90
488 516 7.623268 CTTTGGACAAAAGCTAAATGTACAC 57.377 36.000 10.07 1.43 37.62 2.90
551 579 5.499139 TTTAGTGCCATAAATGCTGCTAC 57.501 39.130 0.00 0.00 0.00 3.58
552 580 6.713762 AATTTAGTGCCATAAATGCTGCTA 57.286 33.333 0.00 0.00 35.91 3.49
581 609 9.665719 AAACTACATTTCAAAACAAATCCAGTT 57.334 25.926 0.00 0.00 32.82 3.16
638 666 9.733556 TGACTAAATTTATCCAAAAGAGCAGTA 57.266 29.630 0.00 0.00 0.00 2.74
640 668 9.912634 TTTGACTAAATTTATCCAAAAGAGCAG 57.087 29.630 16.34 0.44 0.00 4.24
756 1170 1.300620 CTCCGTGTCACTTTCCGCA 60.301 57.895 0.65 0.00 0.00 5.69
848 1266 2.904866 TGGTGCGTGGCTTTGGTC 60.905 61.111 0.00 0.00 0.00 4.02
860 1278 2.686915 CTCCCAAATCTGAATCTGGTGC 59.313 50.000 3.34 0.00 0.00 5.01
891 1309 6.429385 GCTCTGAATTCTCCTTCTTTTCTGAA 59.571 38.462 7.05 0.00 0.00 3.02
904 1322 2.288458 GCATCTGCAGCTCTGAATTCTC 59.712 50.000 9.47 0.00 41.59 2.87
937 1355 2.977808 TCTGGTCTTCCTCCTTCAAGT 58.022 47.619 0.00 0.00 34.23 3.16
964 1382 2.007549 CTGCTGCTGCTCAATCTCG 58.992 57.895 17.00 0.00 40.48 4.04
1176 1597 2.861006 GCGAACTCCTTGGCGTTC 59.139 61.111 11.31 11.31 36.92 3.95
1932 2379 1.735920 CAGTCTCTCCGTGCAGCAC 60.736 63.158 16.21 16.21 0.00 4.40
1991 2438 2.179018 CGGGCGAAATGGTTGCAG 59.821 61.111 0.00 0.00 0.00 4.41
2026 2481 6.313658 TGCTGTATCACATTACAAGATCACAC 59.686 38.462 0.00 0.00 31.96 3.82
2072 2527 5.894807 ACATGCGAATTTTTAGATTGGAGG 58.105 37.500 0.00 0.00 0.00 4.30
2091 2547 9.993881 GAAAATTTGTATCTCACGAAAAACATG 57.006 29.630 0.00 0.00 34.12 3.21
2093 2549 9.796120 AAGAAAATTTGTATCTCACGAAAAACA 57.204 25.926 0.00 0.00 34.12 2.83
2128 2584 4.876580 AGTACCTAAACTACACCTAGGGG 58.123 47.826 10.33 10.33 37.17 4.79
2129 2585 5.534278 GCTAGTACCTAAACTACACCTAGGG 59.466 48.000 14.81 4.64 37.17 3.53
2130 2586 6.125029 TGCTAGTACCTAAACTACACCTAGG 58.875 44.000 7.41 7.41 38.56 3.02
2131 2587 6.827762 ACTGCTAGTACCTAAACTACACCTAG 59.172 42.308 0.00 0.00 0.00 3.02
2132 2588 6.725364 ACTGCTAGTACCTAAACTACACCTA 58.275 40.000 0.00 0.00 0.00 3.08
2133 2589 5.578073 ACTGCTAGTACCTAAACTACACCT 58.422 41.667 0.00 0.00 0.00 4.00
2134 2590 5.911378 ACTGCTAGTACCTAAACTACACC 57.089 43.478 0.00 0.00 0.00 4.16
2135 2591 5.575995 GCAACTGCTAGTACCTAAACTACAC 59.424 44.000 0.00 0.00 38.21 2.90
2136 2592 5.620654 CGCAACTGCTAGTACCTAAACTACA 60.621 44.000 0.00 0.00 39.32 2.74
2137 2593 4.797349 CGCAACTGCTAGTACCTAAACTAC 59.203 45.833 0.00 0.00 39.32 2.73
2153 2609 0.179215 GATTTCACTCGGCGCAACTG 60.179 55.000 10.83 0.00 0.00 3.16
2154 2610 0.602638 TGATTTCACTCGGCGCAACT 60.603 50.000 10.83 0.00 0.00 3.16
2157 2613 0.882484 TTGTGATTTCACTCGGCGCA 60.882 50.000 10.83 0.00 46.55 6.09
2158 2614 0.452784 GTTGTGATTTCACTCGGCGC 60.453 55.000 11.67 0.00 46.55 6.53
2161 2617 4.655027 CATGATGTTGTGATTTCACTCGG 58.345 43.478 11.67 0.00 46.55 4.63
2162 2618 4.093514 GCATGATGTTGTGATTTCACTCG 58.906 43.478 11.67 0.00 46.55 4.18
2163 2619 4.082625 TGGCATGATGTTGTGATTTCACTC 60.083 41.667 11.67 6.04 46.55 3.51
2165 2621 4.177165 TGGCATGATGTTGTGATTTCAC 57.823 40.909 0.00 3.72 46.59 3.18
2166 2622 4.868314 TTGGCATGATGTTGTGATTTCA 57.132 36.364 0.00 0.00 0.00 2.69
2167 2623 6.539324 CATTTTGGCATGATGTTGTGATTTC 58.461 36.000 0.00 0.00 0.00 2.17
2180 2636 3.253677 ACCACAATTTGCATTTTGGCATG 59.746 39.130 12.24 0.00 42.12 4.06
2258 2787 6.147328 GCGTTTAGATCACCAAGAAGTACTTT 59.853 38.462 10.02 0.00 36.61 2.66
2264 2793 5.613358 AAAGCGTTTAGATCACCAAGAAG 57.387 39.130 0.00 0.00 0.00 2.85
2270 2799 8.837389 AGGAAATATAAAAGCGTTTAGATCACC 58.163 33.333 11.74 15.47 31.44 4.02
2302 2831 8.250332 TGTGCTCTTGAAAAACAGATACTTTTT 58.750 29.630 0.00 0.00 34.27 1.94
2303 2832 7.702348 GTGTGCTCTTGAAAAACAGATACTTTT 59.298 33.333 0.00 0.00 0.00 2.27
2304 2833 7.148086 TGTGTGCTCTTGAAAAACAGATACTTT 60.148 33.333 0.00 0.00 0.00 2.66
2305 2834 6.318648 TGTGTGCTCTTGAAAAACAGATACTT 59.681 34.615 0.00 0.00 0.00 2.24
2307 2836 6.060028 TGTGTGCTCTTGAAAAACAGATAC 57.940 37.500 0.00 0.00 0.00 2.24
2308 2837 6.882610 ATGTGTGCTCTTGAAAAACAGATA 57.117 33.333 0.00 0.00 0.00 1.98
2311 2840 6.532657 AGAAAATGTGTGCTCTTGAAAAACAG 59.467 34.615 0.00 0.00 0.00 3.16
2312 2841 6.397272 AGAAAATGTGTGCTCTTGAAAAACA 58.603 32.000 0.00 0.00 0.00 2.83
2313 2842 6.753744 AGAGAAAATGTGTGCTCTTGAAAAAC 59.246 34.615 0.00 0.00 34.23 2.43
2314 2843 6.753279 CAGAGAAAATGTGTGCTCTTGAAAAA 59.247 34.615 0.00 0.00 35.66 1.94
2315 2844 6.267817 CAGAGAAAATGTGTGCTCTTGAAAA 58.732 36.000 0.00 0.00 35.66 2.29
2316 2845 5.734220 GCAGAGAAAATGTGTGCTCTTGAAA 60.734 40.000 0.00 0.00 35.66 2.69
2317 2846 4.261322 GCAGAGAAAATGTGTGCTCTTGAA 60.261 41.667 0.00 0.00 35.66 2.69
2318 2847 3.251729 GCAGAGAAAATGTGTGCTCTTGA 59.748 43.478 0.00 0.00 35.66 3.02
2319 2848 3.252701 AGCAGAGAAAATGTGTGCTCTTG 59.747 43.478 0.00 0.00 40.46 3.02
2322 2851 3.911661 AAGCAGAGAAAATGTGTGCTC 57.088 42.857 0.00 0.00 43.63 4.26
2324 2853 4.214119 TGAGTAAGCAGAGAAAATGTGTGC 59.786 41.667 0.00 0.00 0.00 4.57
2327 2856 5.471456 ACCTTGAGTAAGCAGAGAAAATGTG 59.529 40.000 0.00 0.00 32.40 3.21
2328 2857 5.625150 ACCTTGAGTAAGCAGAGAAAATGT 58.375 37.500 0.00 0.00 32.40 2.71
2329 2858 6.183360 GCTACCTTGAGTAAGCAGAGAAAATG 60.183 42.308 0.00 0.00 32.40 2.32
2330 2859 5.877564 GCTACCTTGAGTAAGCAGAGAAAAT 59.122 40.000 0.00 0.00 32.40 1.82
2335 3582 3.194542 AGTGCTACCTTGAGTAAGCAGAG 59.805 47.826 0.00 0.00 36.45 3.35
2367 3614 5.907207 TGGTGATGTTCTAATAGTGCTCTC 58.093 41.667 0.00 0.00 0.00 3.20
2368 3615 5.939764 TGGTGATGTTCTAATAGTGCTCT 57.060 39.130 0.00 0.00 0.00 4.09
2382 3630 2.329267 TCTGTCTCCTGTTGGTGATGT 58.671 47.619 0.00 0.00 38.03 3.06
2392 3640 5.082251 TCATGTGAGATTTCTGTCTCCTG 57.918 43.478 0.00 0.00 43.17 3.86
2427 3675 5.832060 TCCCAAAATAAACGTGTTAAGGGAA 59.168 36.000 13.71 4.17 38.56 3.97
2433 3681 4.384056 TCCGTCCCAAAATAAACGTGTTA 58.616 39.130 0.00 0.00 33.45 2.41
2434 3682 3.212685 TCCGTCCCAAAATAAACGTGTT 58.787 40.909 0.00 0.00 33.45 3.32
2435 3683 2.809696 CTCCGTCCCAAAATAAACGTGT 59.190 45.455 0.00 0.00 33.45 4.49
2436 3684 3.068560 TCTCCGTCCCAAAATAAACGTG 58.931 45.455 0.00 0.00 33.45 4.49
2437 3685 3.007182 TCTCTCCGTCCCAAAATAAACGT 59.993 43.478 0.00 0.00 33.45 3.99
2439 3687 6.238402 GCTAATCTCTCCGTCCCAAAATAAAC 60.238 42.308 0.00 0.00 0.00 2.01
2440 3688 5.820947 GCTAATCTCTCCGTCCCAAAATAAA 59.179 40.000 0.00 0.00 0.00 1.40
2450 3757 8.426881 AAGAATAAAAAGCTAATCTCTCCGTC 57.573 34.615 0.00 0.00 0.00 4.79
2460 3767 9.606631 TTTTGCTCCAAAAGAATAAAAAGCTAA 57.393 25.926 0.00 0.00 38.24 3.09
2504 3811 5.509498 AGTTGGTATGCATGTATTGGTCTT 58.491 37.500 10.16 0.00 0.00 3.01
2551 3858 9.975218 GACCCAAATATACCATTTCTATACCAT 57.025 33.333 0.00 0.00 0.00 3.55
2552 3859 8.950480 TGACCCAAATATACCATTTCTATACCA 58.050 33.333 0.00 0.00 0.00 3.25
2553 3860 9.227777 GTGACCCAAATATACCATTTCTATACC 57.772 37.037 0.00 0.00 0.00 2.73
2554 3861 9.227777 GGTGACCCAAATATACCATTTCTATAC 57.772 37.037 0.00 0.00 0.00 1.47
2600 3907 2.102252 GCTTCCATGGTTGTGGTTTTGA 59.898 45.455 12.58 0.00 40.27 2.69
2613 3920 1.479323 CAGACATTTGGGGCTTCCATG 59.521 52.381 0.45 0.00 46.52 3.66
2614 3921 1.620524 CCAGACATTTGGGGCTTCCAT 60.621 52.381 0.45 0.00 46.52 3.41
2653 3960 0.324460 AGGTGAGGTAGGAAGGTCGG 60.324 60.000 0.00 0.00 0.00 4.79
2784 4092 3.430862 GGCGCAACATTCCGAGCA 61.431 61.111 10.83 0.00 0.00 4.26
2789 4097 1.212751 GGAACAGGCGCAACATTCC 59.787 57.895 10.83 12.78 32.56 3.01
2801 4109 2.845752 TTCGGAATCGGCGGGAACAG 62.846 60.000 7.21 0.00 36.95 3.16


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

AutoCloner maintained by Alex Coulton.