Multiple sequence alignment - TraesCS5B01G099400

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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 TraesCS5B01G099400 chr5B 100.000 5582 0 0 1 5582 132298203 132292622 0.000000e+00 10309.0
1 TraesCS5B01G099400 chr5B 97.107 242 7 0 3240 3481 132294723 132294482 5.210000e-110 409.0
2 TraesCS5B01G099400 chr5B 97.107 242 7 0 3481 3722 132294964 132294723 5.210000e-110 409.0
3 TraesCS5B01G099400 chr5B 93.407 182 12 0 4346 4527 132293822 132293641 2.560000e-68 270.0
4 TraesCS5B01G099400 chr5B 93.407 182 12 0 4382 4563 132293858 132293677 2.560000e-68 270.0
5 TraesCS5B01G099400 chr5B 83.871 155 23 2 5276 5429 283985787 283985634 4.510000e-31 147.0
6 TraesCS5B01G099400 chr5B 97.561 41 1 0 5219 5259 132292945 132292905 2.790000e-08 71.3
7 TraesCS5B01G099400 chr5B 97.561 41 1 0 5259 5299 132292985 132292945 2.790000e-08 71.3
8 TraesCS5B01G099400 chr5A 92.599 2932 130 37 550 3446 129610308 129607429 0.000000e+00 4132.0
9 TraesCS5B01G099400 chr5A 94.357 1081 47 4 3428 4507 129607415 129606348 0.000000e+00 1646.0
10 TraesCS5B01G099400 chr5A 91.482 904 50 13 4376 5260 129606104 129605209 0.000000e+00 1218.0
11 TraesCS5B01G099400 chr5A 84.843 574 56 12 10 552 129620095 129619522 2.940000e-152 549.0
12 TraesCS5B01G099400 chr5A 97.934 242 5 0 3240 3481 129607362 129607121 2.400000e-113 420.0
13 TraesCS5B01G099400 chr5A 93.237 207 14 0 3481 3687 129607635 129607429 7.030000e-79 305.0
14 TraesCS5B01G099400 chr5A 90.659 182 17 0 4346 4527 129606098 129605917 5.590000e-60 243.0
15 TraesCS5B01G099400 chr5A 98.148 54 1 0 3669 3722 129607415 129607362 1.660000e-15 95.3
16 TraesCS5B01G099400 chr5D 95.713 1796 59 9 1969 3756 119493952 119492167 0.000000e+00 2874.0
17 TraesCS5B01G099400 chr5D 90.271 1881 105 30 105 1930 119495804 119493947 0.000000e+00 2388.0
18 TraesCS5B01G099400 chr5D 90.641 951 53 20 4317 5260 119491045 119490124 0.000000e+00 1230.0
19 TraesCS5B01G099400 chr5D 92.750 800 42 2 3753 4552 119492075 119491292 0.000000e+00 1142.0
20 TraesCS5B01G099400 chr5D 96.281 242 9 0 3240 3481 119492442 119492201 1.130000e-106 398.0
21 TraesCS5B01G099400 chr5D 95.868 242 9 1 3481 3722 119492682 119492442 1.890000e-104 390.0
22 TraesCS5B01G099400 chr5D 94.505 182 10 0 4346 4527 119490980 119490799 1.180000e-71 281.0
23 TraesCS5B01G099400 chr5D 93.407 182 12 0 4382 4563 119491016 119490835 2.560000e-68 270.0
24 TraesCS5B01G099400 chr4B 77.634 465 76 10 1 452 540459413 540459862 2.000000e-64 257.0
25 TraesCS5B01G099400 chr2D 86.550 171 23 0 5259 5429 600565633 600565463 7.380000e-44 189.0
26 TraesCS5B01G099400 chr7A 91.473 129 11 0 5301 5429 721594859 721594987 1.600000e-40 178.0
27 TraesCS5B01G099400 chr7A 90.000 130 12 1 5301 5430 721664410 721664538 3.460000e-37 167.0
28 TraesCS5B01G099400 chr4D 84.118 170 25 1 5259 5428 51078998 51079165 4.470000e-36 163.0
29 TraesCS5B01G099400 chr2B 86.667 135 17 1 5295 5429 98288464 98288597 1.250000e-31 148.0
30 TraesCS5B01G099400 chr7D 88.983 118 13 0 5312 5429 626054690 626054807 4.510000e-31 147.0
31 TraesCS5B01G099400 chr3B 81.657 169 30 1 5261 5429 352029885 352029718 7.540000e-29 139.0
32 TraesCS5B01G099400 chr6D 86.400 125 13 4 5311 5434 340211779 340211658 3.510000e-27 134.0


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 TraesCS5B01G099400 chr5B 132292622 132298203 5581 True 10309.000000 10309 100.000000 1 5582 1 chr5B.!!$R1 5581
1 TraesCS5B01G099400 chr5B 132292905 132294964 2059 True 250.100000 409 96.025000 3240 5299 6 chr5B.!!$R3 2059
2 TraesCS5B01G099400 chr5A 129605209 129610308 5099 True 1151.328571 4132 94.059429 550 5260 7 chr5A.!!$R2 4710
3 TraesCS5B01G099400 chr5A 129619522 129620095 573 True 549.000000 549 84.843000 10 552 1 chr5A.!!$R1 542
4 TraesCS5B01G099400 chr5D 119490124 119495804 5680 True 1121.625000 2874 93.679500 105 5260 8 chr5D.!!$R1 5155

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
582 623 0.033504 GTGGTTGAGAGGCTTCGTCA 59.966 55.000 0.00 0.00 0.00 4.35 F
1132 1189 0.179026 CCTCCGATCTCAGTACCCGA 60.179 60.000 0.00 0.00 0.00 5.14 F
1594 1670 1.662044 CACCAAAGCCCAGCACTTC 59.338 57.895 0.00 0.00 0.00 3.01 F
2970 3060 0.535780 AGCTAGCACTTGTGCTGCAA 60.536 50.000 31.09 15.37 45.81 4.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1439 1509 3.808466 TGGTGCAAGCATTTACAACAA 57.192 38.095 0.00 0.0 40.88 2.83 R
2468 2556 3.986996 ATGCATTTAAGGGCTTTGCTT 57.013 38.095 0.00 0.0 34.47 3.91 R
3132 3224 3.255642 GGAGATAAAGCAGTTTGCCAACA 59.744 43.478 3.22 0.0 46.52 3.33 R
4998 6088 2.422127 ACCCAACAGAAGAAAACACACG 59.578 45.455 0.00 0.0 0.00 4.49 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
68 69 2.440409 CAGCTTTCCTATGCACTGGTT 58.560 47.619 6.69 0.00 0.00 3.67
70 71 2.307098 AGCTTTCCTATGCACTGGTTCT 59.693 45.455 6.69 0.00 0.00 3.01
79 80 0.875059 GCACTGGTTCTAGCACCAAC 59.125 55.000 15.38 4.64 46.60 3.77
92 93 1.147600 ACCAACAGACACCGGTTCC 59.852 57.895 2.97 0.00 0.00 3.62
114 115 2.158900 AGCACCGATAGCAGCATAACTT 60.159 45.455 0.00 0.00 36.91 2.66
133 134 2.026301 CTAGGACGTAGCAGCGCC 59.974 66.667 2.29 0.00 34.88 6.53
167 168 4.640690 ACCGGCCAGTGGAGGAGT 62.641 66.667 25.29 9.42 0.00 3.85
172 173 1.673665 GCCAGTGGAGGAGTTGCAG 60.674 63.158 15.20 0.00 0.00 4.41
177 178 4.400961 GGAGGAGTTGCAGCCGCT 62.401 66.667 0.00 0.00 39.64 5.52
212 213 0.039035 ATCCGGCAAGGGCAAAGTTA 59.961 50.000 0.00 0.00 43.71 2.24
251 272 1.619654 CTGCATCTGTTTTGGGGTGA 58.380 50.000 0.00 0.00 0.00 4.02
295 316 3.188786 GCAACCGCGGCTAGAGTG 61.189 66.667 28.58 14.63 0.00 3.51
355 377 0.901124 GTCCTCCTCTGCAGATGTGT 59.099 55.000 18.63 0.00 0.00 3.72
365 387 0.036732 GCAGATGTGTGTCTTCCCCA 59.963 55.000 0.00 0.00 0.00 4.96
420 442 2.942710 CGACATCGTGGTTGTAGTTCT 58.057 47.619 0.00 0.00 34.11 3.01
447 469 1.680314 TTGGTTGCAGCACACCACA 60.680 52.632 21.98 13.89 31.71 4.17
453 475 2.203001 CAGCACACCACACACCGA 60.203 61.111 0.00 0.00 0.00 4.69
457 479 3.148963 ACACCACACACCGACCGA 61.149 61.111 0.00 0.00 0.00 4.69
459 481 3.148963 ACCACACACCGACCGACA 61.149 61.111 0.00 0.00 0.00 4.35
460 482 2.107343 CCACACACCGACCGACAA 59.893 61.111 0.00 0.00 0.00 3.18
461 483 1.521906 CCACACACCGACCGACAAA 60.522 57.895 0.00 0.00 0.00 2.83
462 484 1.639534 CACACACCGACCGACAAAC 59.360 57.895 0.00 0.00 0.00 2.93
463 485 1.084935 CACACACCGACCGACAAACA 61.085 55.000 0.00 0.00 0.00 2.83
464 486 0.391395 ACACACCGACCGACAAACAA 60.391 50.000 0.00 0.00 0.00 2.83
467 489 0.727970 CACCGACCGACAAACAACAA 59.272 50.000 0.00 0.00 0.00 2.83
468 490 1.011333 ACCGACCGACAAACAACAAG 58.989 50.000 0.00 0.00 0.00 3.16
469 491 0.306533 CCGACCGACAAACAACAAGG 59.693 55.000 0.00 0.00 0.00 3.61
470 492 0.316689 CGACCGACAAACAACAAGGC 60.317 55.000 0.00 0.00 0.00 4.35
480 512 2.175202 AACAACAAGGCAGTTGGTCAA 58.825 42.857 21.49 0.00 45.82 3.18
492 524 0.179032 TTGGTCAAGGCTTCAAGCGA 60.179 50.000 2.54 0.00 43.62 4.93
496 528 2.280797 AAGGCTTCAAGCGACGCA 60.281 55.556 23.70 0.00 43.62 5.24
567 608 3.368116 CGGGAGATAAGAAAACGAGTGGT 60.368 47.826 0.00 0.00 0.00 4.16
582 623 0.033504 GTGGTTGAGAGGCTTCGTCA 59.966 55.000 0.00 0.00 0.00 4.35
608 649 6.366340 AGATAAGAACGAGAGATAAGGGACA 58.634 40.000 0.00 0.00 0.00 4.02
614 655 1.409427 GAGAGATAAGGGACACGTGGG 59.591 57.143 21.57 0.00 0.00 4.61
633 674 0.245539 GCTGACTACGTGGTGGCTAA 59.754 55.000 10.14 0.00 0.00 3.09
646 687 1.153628 GGCTAACGAGTGATGCGGT 60.154 57.895 0.00 0.00 0.00 5.68
662 703 0.999406 CGGTAGCAAATCTCGTGTGG 59.001 55.000 0.00 0.00 0.00 4.17
666 707 2.086054 AGCAAATCTCGTGTGGTCTC 57.914 50.000 0.00 0.00 0.00 3.36
696 737 2.509336 CCGGGAACTAGCAGTGCG 60.509 66.667 10.00 0.00 0.00 5.34
716 757 0.394216 TTGTTGATCAGATGGCCCGG 60.394 55.000 0.00 0.00 0.00 5.73
763 804 1.778027 CGACCGGCCAGAAACGTTTT 61.778 55.000 15.89 2.49 0.00 2.43
788 829 8.940768 TCATTTCTGATATGTACAAATCGTGA 57.059 30.769 0.00 0.00 0.00 4.35
805 846 9.848172 CAAATCGTGAGTTTTAAATTGAAAAGG 57.152 29.630 0.58 0.00 32.18 3.11
809 850 9.640963 TCGTGAGTTTTAAATTGAAAAGGAAAA 57.359 25.926 0.58 0.00 0.00 2.29
857 908 0.241481 GCGGCCTCTCCTCGTATAAG 59.759 60.000 0.00 0.00 0.00 1.73
980 1031 3.706373 CCTAGCCACCACCAGCGT 61.706 66.667 0.00 0.00 0.00 5.07
1132 1189 0.179026 CCTCCGATCTCAGTACCCGA 60.179 60.000 0.00 0.00 0.00 5.14
1594 1670 1.662044 CACCAAAGCCCAGCACTTC 59.338 57.895 0.00 0.00 0.00 3.01
1607 1683 3.062763 CAGCACTTCGAGAACAACATCT 58.937 45.455 0.00 0.00 0.00 2.90
1656 1741 3.559238 AACAATGGCTTCATCGTCAAC 57.441 42.857 0.00 0.00 0.00 3.18
1663 1748 2.477375 GGCTTCATCGTCAACGTTACAA 59.523 45.455 0.00 0.00 40.80 2.41
1676 1761 5.049954 TCAACGTTACAAACCATGCTTCTAC 60.050 40.000 0.00 0.00 0.00 2.59
1679 1764 5.144359 CGTTACAAACCATGCTTCTACAAC 58.856 41.667 0.00 0.00 0.00 3.32
1735 1820 7.102346 AGATCAGAAAATCACGAGTTCAATCT 58.898 34.615 0.00 0.00 0.00 2.40
1736 1821 7.605691 AGATCAGAAAATCACGAGTTCAATCTT 59.394 33.333 0.00 0.00 29.16 2.40
1737 1822 7.121974 TCAGAAAATCACGAGTTCAATCTTC 57.878 36.000 0.00 0.00 0.00 2.87
1738 1823 6.931281 TCAGAAAATCACGAGTTCAATCTTCT 59.069 34.615 0.00 0.00 0.00 2.85
1739 1824 7.116948 TCAGAAAATCACGAGTTCAATCTTCTC 59.883 37.037 0.00 0.00 0.00 2.87
1740 1825 7.117523 CAGAAAATCACGAGTTCAATCTTCTCT 59.882 37.037 0.00 0.00 0.00 3.10
1830 1915 2.610479 CCTTCTTCTGTGTTGAGCGCTA 60.610 50.000 11.50 0.00 0.00 4.26
1915 2000 3.308595 TGTAGCACTTTGTCAGTTTGTCG 59.691 43.478 0.00 0.00 30.92 4.35
1928 2013 3.857665 CAGTTTGTCGATGCGTACTGTAT 59.142 43.478 0.00 0.00 0.00 2.29
1963 2048 8.788806 CATAATTGTTCAGTAAGTGGTTACCAA 58.211 33.333 5.33 0.00 39.65 3.67
2374 2461 3.264574 GGGCACACCTTAATGAGCA 57.735 52.632 1.78 0.00 37.86 4.26
2495 2583 3.927476 AGCCCTTAAATGCATAATGGGT 58.073 40.909 23.41 14.79 35.79 4.51
2525 2614 9.979270 TTTACTTTTTGTTACAATTGCACATTG 57.021 25.926 5.05 15.58 35.29 2.82
2556 2645 9.807649 ATTGCTTCACTTGGAATTGTTAATATC 57.192 29.630 0.00 0.00 34.32 1.63
2557 2646 8.347004 TGCTTCACTTGGAATTGTTAATATCA 57.653 30.769 0.00 0.00 34.32 2.15
2762 2852 7.810282 CCCAGAACTATTGTATTGAGTATCGAG 59.190 40.741 0.00 0.00 38.61 4.04
2779 2869 7.268586 AGTATCGAGACATTATTTGCAGAACT 58.731 34.615 13.45 0.00 0.00 3.01
2865 2955 5.074929 ACATGCAAGGGGATAATGAAGGATA 59.925 40.000 0.00 0.00 0.00 2.59
2938 3028 7.451255 ACAATACAACCTTCCTTGAATGAATGA 59.549 33.333 0.00 0.00 0.00 2.57
2948 3038 9.971922 CTTCCTTGAATGAATGAAAACTAACTT 57.028 29.630 0.00 0.00 0.00 2.66
2970 3060 0.535780 AGCTAGCACTTGTGCTGCAA 60.536 50.000 31.09 15.37 45.81 4.08
2997 3088 8.237267 CACTCCTTCATTTGAATACCAACTTAC 58.763 37.037 0.00 0.00 33.85 2.34
4998 6088 1.168714 GGGAGGTGCATCACTGAAAC 58.831 55.000 0.00 0.00 34.40 2.78
4999 6089 0.798776 GGAGGTGCATCACTGAAACG 59.201 55.000 0.00 0.00 34.40 3.60
5000 6090 1.512926 GAGGTGCATCACTGAAACGT 58.487 50.000 0.00 0.00 34.40 3.99
5001 6091 1.195448 GAGGTGCATCACTGAAACGTG 59.805 52.381 0.00 0.00 34.40 4.49
5005 6095 2.013400 TGCATCACTGAAACGTGTGTT 58.987 42.857 3.96 0.00 40.98 3.32
5299 6403 5.596845 TGCAAATTTGGAGAGGTAAAACAC 58.403 37.500 19.47 0.00 0.00 3.32
5300 6404 4.679654 GCAAATTTGGAGAGGTAAAACACG 59.320 41.667 19.47 0.00 0.00 4.49
5301 6405 5.506649 GCAAATTTGGAGAGGTAAAACACGA 60.507 40.000 19.47 0.00 0.00 4.35
5302 6406 5.941948 AATTTGGAGAGGTAAAACACGAG 57.058 39.130 0.00 0.00 0.00 4.18
5303 6407 4.675976 TTTGGAGAGGTAAAACACGAGA 57.324 40.909 0.00 0.00 0.00 4.04
5304 6408 4.884668 TTGGAGAGGTAAAACACGAGAT 57.115 40.909 0.00 0.00 0.00 2.75
5305 6409 5.988310 TTGGAGAGGTAAAACACGAGATA 57.012 39.130 0.00 0.00 0.00 1.98
5306 6410 6.540438 TTGGAGAGGTAAAACACGAGATAT 57.460 37.500 0.00 0.00 0.00 1.63
5307 6411 7.649533 TTGGAGAGGTAAAACACGAGATATA 57.350 36.000 0.00 0.00 0.00 0.86
5308 6412 7.649533 TGGAGAGGTAAAACACGAGATATAA 57.350 36.000 0.00 0.00 0.00 0.98
5309 6413 8.070034 TGGAGAGGTAAAACACGAGATATAAA 57.930 34.615 0.00 0.00 0.00 1.40
5310 6414 8.533657 TGGAGAGGTAAAACACGAGATATAAAA 58.466 33.333 0.00 0.00 0.00 1.52
5311 6415 9.374838 GGAGAGGTAAAACACGAGATATAAAAA 57.625 33.333 0.00 0.00 0.00 1.94
5373 6477 9.950496 AAAAGAGACAACTACAATAGATGATGT 57.050 29.630 0.67 0.00 33.37 3.06
5394 6498 8.615211 TGATGTAAATTGATGATGTAGAAGTGC 58.385 33.333 0.00 0.00 0.00 4.40
5395 6499 7.920160 TGTAAATTGATGATGTAGAAGTGCA 57.080 32.000 0.00 0.00 0.00 4.57
5396 6500 8.334263 TGTAAATTGATGATGTAGAAGTGCAA 57.666 30.769 0.00 0.00 0.00 4.08
5397 6501 8.236586 TGTAAATTGATGATGTAGAAGTGCAAC 58.763 33.333 0.00 0.00 0.00 4.17
5446 6550 3.525268 AAAAATAGAATTGGGCGGCTG 57.475 42.857 9.56 0.00 0.00 4.85
5447 6551 2.435372 AAATAGAATTGGGCGGCTGA 57.565 45.000 9.56 0.00 0.00 4.26
5448 6552 1.972872 AATAGAATTGGGCGGCTGAG 58.027 50.000 9.56 0.00 0.00 3.35
5449 6553 0.536006 ATAGAATTGGGCGGCTGAGC 60.536 55.000 9.56 0.00 0.00 4.26
5450 6554 2.923426 TAGAATTGGGCGGCTGAGCG 62.923 60.000 9.56 0.00 38.18 5.03
5463 6567 4.884257 GAGCGGCGGCGACCATAA 62.884 66.667 36.87 0.00 46.35 1.90
5467 6571 3.560278 GGCGGCGACCATAACGTG 61.560 66.667 12.98 0.00 0.00 4.49
5480 6584 4.489249 ACGTGGCGTTCTAATCGG 57.511 55.556 0.00 0.00 36.35 4.18
5481 6585 1.153706 ACGTGGCGTTCTAATCGGG 60.154 57.895 0.00 0.00 36.35 5.14
5482 6586 1.881252 CGTGGCGTTCTAATCGGGG 60.881 63.158 0.00 0.00 0.00 5.73
5483 6587 2.178235 GTGGCGTTCTAATCGGGGC 61.178 63.158 0.00 0.00 0.00 5.80
5484 6588 2.965462 GGCGTTCTAATCGGGGCG 60.965 66.667 0.00 0.00 0.00 6.13
5485 6589 2.965462 GCGTTCTAATCGGGGCGG 60.965 66.667 0.00 0.00 0.00 6.13
5486 6590 2.965462 CGTTCTAATCGGGGCGGC 60.965 66.667 0.00 0.00 0.00 6.53
5487 6591 2.188469 GTTCTAATCGGGGCGGCA 59.812 61.111 12.47 0.00 0.00 5.69
5488 6592 1.887707 GTTCTAATCGGGGCGGCAG 60.888 63.158 12.47 4.04 0.00 4.85
5489 6593 3.750373 TTCTAATCGGGGCGGCAGC 62.750 63.158 12.47 0.00 44.18 5.25
5506 6610 2.912025 CCACGGGGCAAAAGCTGT 60.912 61.111 0.00 0.00 0.00 4.40
5507 6611 2.336088 CACGGGGCAAAAGCTGTG 59.664 61.111 0.00 0.00 0.00 3.66
5508 6612 2.912025 ACGGGGCAAAAGCTGTGG 60.912 61.111 0.00 0.00 0.00 4.17
5509 6613 3.683937 CGGGGCAAAAGCTGTGGG 61.684 66.667 0.00 0.00 0.00 4.61
5510 6614 2.203625 GGGGCAAAAGCTGTGGGA 60.204 61.111 0.00 0.00 0.00 4.37
5511 6615 2.574018 GGGGCAAAAGCTGTGGGAC 61.574 63.158 0.00 0.00 0.00 4.46
5512 6616 2.644992 GGCAAAAGCTGTGGGACG 59.355 61.111 0.00 0.00 0.00 4.79
5513 6617 2.644992 GCAAAAGCTGTGGGACGG 59.355 61.111 0.00 0.00 0.00 4.79
5514 6618 2.919494 GCAAAAGCTGTGGGACGGG 61.919 63.158 0.00 0.00 0.00 5.28
5515 6619 2.115266 AAAAGCTGTGGGACGGGG 59.885 61.111 0.00 0.00 0.00 5.73
5516 6620 4.660938 AAAGCTGTGGGACGGGGC 62.661 66.667 0.00 0.00 0.00 5.80
5535 6639 4.265056 GCGGTGGGTGTGGAGGTT 62.265 66.667 0.00 0.00 0.00 3.50
5536 6640 2.281484 CGGTGGGTGTGGAGGTTG 60.281 66.667 0.00 0.00 0.00 3.77
5537 6641 2.115266 GGTGGGTGTGGAGGTTGG 59.885 66.667 0.00 0.00 0.00 3.77
5538 6642 2.115266 GTGGGTGTGGAGGTTGGG 59.885 66.667 0.00 0.00 0.00 4.12
5539 6643 3.897122 TGGGTGTGGAGGTTGGGC 61.897 66.667 0.00 0.00 0.00 5.36
5542 6646 4.265056 GTGTGGAGGTTGGGCGGT 62.265 66.667 0.00 0.00 0.00 5.68
5543 6647 4.263572 TGTGGAGGTTGGGCGGTG 62.264 66.667 0.00 0.00 0.00 4.94
5547 6651 4.660938 GAGGTTGGGCGGTGGCTT 62.661 66.667 0.00 0.00 39.81 4.35
5548 6652 4.974721 AGGTTGGGCGGTGGCTTG 62.975 66.667 0.00 0.00 39.81 4.01
5550 6654 3.977244 GTTGGGCGGTGGCTTGTG 61.977 66.667 0.00 0.00 39.81 3.33
5551 6655 4.196778 TTGGGCGGTGGCTTGTGA 62.197 61.111 0.00 0.00 39.81 3.58
5552 6656 4.641645 TGGGCGGTGGCTTGTGAG 62.642 66.667 0.00 0.00 39.81 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.178947 TCTTGGTTTTCGGCCCCAAT 60.179 50.000 10.43 0.00 37.60 3.16
1 2 0.178947 ATCTTGGTTTTCGGCCCCAA 60.179 50.000 9.71 9.71 36.80 4.12
2 3 0.699399 TATCTTGGTTTTCGGCCCCA 59.301 50.000 0.00 0.00 0.00 4.96
3 4 1.340697 ACTATCTTGGTTTTCGGCCCC 60.341 52.381 0.00 0.00 0.00 5.80
4 5 2.124277 ACTATCTTGGTTTTCGGCCC 57.876 50.000 0.00 0.00 0.00 5.80
5 6 3.870274 ACTACTATCTTGGTTTTCGGCC 58.130 45.455 0.00 0.00 0.00 6.13
6 7 4.507021 GCTACTACTATCTTGGTTTTCGGC 59.493 45.833 0.00 0.00 0.00 5.54
7 8 5.657474 TGCTACTACTATCTTGGTTTTCGG 58.343 41.667 0.00 0.00 0.00 4.30
8 9 7.591006 TTTGCTACTACTATCTTGGTTTTCG 57.409 36.000 0.00 0.00 0.00 3.46
40 41 3.519510 TGCATAGGAAAGCTGGAACTAGT 59.480 43.478 0.00 0.00 0.00 2.57
68 69 0.317160 CGGTGTCTGTTGGTGCTAGA 59.683 55.000 0.00 0.00 0.00 2.43
70 71 1.369692 CCGGTGTCTGTTGGTGCTA 59.630 57.895 0.00 0.00 0.00 3.49
79 80 1.961277 GTGCTGGAACCGGTGTCTG 60.961 63.158 8.52 8.91 0.00 3.51
92 93 1.528586 GTTATGCTGCTATCGGTGCTG 59.471 52.381 0.00 0.00 0.00 4.41
148 149 2.852075 TCCTCCACTGGCCGGTTT 60.852 61.111 16.73 0.00 0.00 3.27
167 168 1.676678 CTACTCCCTAGCGGCTGCAA 61.677 60.000 21.93 0.00 46.23 4.08
172 173 1.529713 AGCTCTACTCCCTAGCGGC 60.530 63.158 0.00 0.00 41.19 6.53
177 178 1.819697 CGGATGCAGCTCTACTCCCTA 60.820 57.143 0.22 0.00 0.00 3.53
212 213 4.379243 CTGCCACTCGCGGGTTCT 62.379 66.667 10.11 0.00 40.51 3.01
239 260 0.260230 TCCAGCTTCACCCCAAAACA 59.740 50.000 0.00 0.00 0.00 2.83
295 316 1.741770 ACTCGCCGATTGCAACTCC 60.742 57.895 0.00 0.00 41.33 3.85
315 336 1.519455 CTAGCCCGTTCAGCTTCGG 60.519 63.158 12.92 12.92 45.42 4.30
355 377 1.052617 TGTGACGAATGGGGAAGACA 58.947 50.000 0.00 0.00 0.00 3.41
417 439 2.192861 CAACCAACAGGCCGCAGAA 61.193 57.895 0.00 0.00 0.00 3.02
447 469 0.391395 TGTTGTTTGTCGGTCGGTGT 60.391 50.000 0.00 0.00 0.00 4.16
453 475 0.738389 CTGCCTTGTTGTTTGTCGGT 59.262 50.000 0.00 0.00 0.00 4.69
457 479 1.899142 ACCAACTGCCTTGTTGTTTGT 59.101 42.857 11.52 2.84 44.01 2.83
459 481 2.175202 TGACCAACTGCCTTGTTGTTT 58.825 42.857 11.52 1.45 44.01 2.83
460 482 1.846007 TGACCAACTGCCTTGTTGTT 58.154 45.000 11.52 0.31 44.01 2.83
461 483 1.750778 CTTGACCAACTGCCTTGTTGT 59.249 47.619 11.52 2.96 44.01 3.32
462 484 1.067516 CCTTGACCAACTGCCTTGTTG 59.932 52.381 7.18 7.18 44.81 3.33
463 485 1.402787 CCTTGACCAACTGCCTTGTT 58.597 50.000 0.00 0.00 0.00 2.83
464 486 1.109323 GCCTTGACCAACTGCCTTGT 61.109 55.000 0.00 0.00 0.00 3.16
467 489 0.538287 GAAGCCTTGACCAACTGCCT 60.538 55.000 0.00 0.00 0.00 4.75
468 490 0.823356 TGAAGCCTTGACCAACTGCC 60.823 55.000 0.00 0.00 0.00 4.85
469 491 1.000938 CTTGAAGCCTTGACCAACTGC 60.001 52.381 0.00 0.00 0.00 4.40
470 492 1.000938 GCTTGAAGCCTTGACCAACTG 60.001 52.381 5.74 0.00 34.48 3.16
480 512 3.044305 GTGCGTCGCTTGAAGCCT 61.044 61.111 19.50 0.00 45.11 4.58
496 528 1.374758 CTCTCTTTTGAGCCGCCGT 60.375 57.895 0.00 0.00 45.83 5.68
567 608 1.911057 TCTCTGACGAAGCCTCTCAA 58.089 50.000 0.00 0.00 0.00 3.02
582 623 6.713450 GTCCCTTATCTCTCGTTCTTATCTCT 59.287 42.308 0.00 0.00 0.00 3.10
614 655 0.245539 TTAGCCACCACGTAGTCAGC 59.754 55.000 0.00 0.00 41.61 4.26
633 674 3.284336 TGCTACCGCATCACTCGT 58.716 55.556 0.00 0.00 42.25 4.18
646 687 2.094182 GGAGACCACACGAGATTTGCTA 60.094 50.000 0.00 0.00 0.00 3.49
650 691 1.254026 TCGGAGACCACACGAGATTT 58.746 50.000 0.00 0.00 32.29 2.17
687 728 2.068519 CTGATCAACAACGCACTGCTA 58.931 47.619 0.00 0.00 0.00 3.49
696 737 0.734889 CGGGCCATCTGATCAACAAC 59.265 55.000 4.39 0.00 0.00 3.32
763 804 8.940768 TCACGATTTGTACATATCAGAAATGA 57.059 30.769 21.40 14.33 0.00 2.57
809 850 2.036089 GGTCTCTCACCGTCAGTTCTTT 59.964 50.000 0.00 0.00 34.56 2.52
810 851 1.614413 GGTCTCTCACCGTCAGTTCTT 59.386 52.381 0.00 0.00 34.56 2.52
811 852 1.249407 GGTCTCTCACCGTCAGTTCT 58.751 55.000 0.00 0.00 34.56 3.01
857 908 3.133365 AAGGTGGTGGGTGGTCTGC 62.133 63.158 0.00 0.00 0.00 4.26
980 1031 4.880426 GGATCGGGGGAGGGAGCA 62.880 72.222 0.00 0.00 0.00 4.26
991 1042 1.337260 GGAATCGGACATGAGGATCGG 60.337 57.143 0.00 0.00 38.61 4.18
1070 1121 3.213402 GAGACGGGGAGCTCTCGG 61.213 72.222 25.13 22.60 0.00 4.63
1132 1189 3.403038 CAAACGATCAGAAACCAGACCT 58.597 45.455 0.00 0.00 0.00 3.85
1439 1509 3.808466 TGGTGCAAGCATTTACAACAA 57.192 38.095 0.00 0.00 40.88 2.83
1594 1670 6.202937 GTGGAGAGTATAGATGTTGTTCTCG 58.797 44.000 0.00 0.00 32.44 4.04
1607 1683 5.942977 TCCCTAATGAGGTGGAGAGTATA 57.057 43.478 0.00 0.00 41.95 1.47
1627 1703 5.973565 CGATGAAGCCATTGTTTTAGAATCC 59.026 40.000 0.00 0.00 32.09 3.01
1628 1704 6.555315 ACGATGAAGCCATTGTTTTAGAATC 58.445 36.000 0.00 0.00 43.17 2.52
1629 1705 6.150976 TGACGATGAAGCCATTGTTTTAGAAT 59.849 34.615 0.00 0.00 45.12 2.40
1630 1706 5.471797 TGACGATGAAGCCATTGTTTTAGAA 59.528 36.000 0.00 0.00 45.12 2.10
1631 1707 5.000591 TGACGATGAAGCCATTGTTTTAGA 58.999 37.500 0.00 0.00 45.12 2.10
1632 1708 5.295431 TGACGATGAAGCCATTGTTTTAG 57.705 39.130 0.00 0.00 45.12 1.85
1633 1709 5.457140 GTTGACGATGAAGCCATTGTTTTA 58.543 37.500 0.00 0.00 45.12 1.52
1634 1710 4.298332 GTTGACGATGAAGCCATTGTTTT 58.702 39.130 0.00 0.00 45.12 2.43
1656 1741 5.049680 AGTTGTAGAAGCATGGTTTGTAACG 60.050 40.000 12.13 0.00 0.00 3.18
1663 1748 4.623932 TCTGAGTTGTAGAAGCATGGTT 57.376 40.909 10.50 10.50 0.00 3.67
1679 1764 8.494347 CACTGAACTCTAAACAAATCTTCTGAG 58.506 37.037 0.00 0.00 0.00 3.35
1695 1780 9.956640 ATTTTCTGATCTTAATCACTGAACTCT 57.043 29.630 0.00 0.00 36.98 3.24
1780 1865 5.393787 CCCCACACATTGATTCAGATGAAAG 60.394 44.000 12.67 7.12 37.61 2.62
1830 1915 6.755542 CTAGAATAGGAAGGTCCAGGATTT 57.244 41.667 0.00 0.00 39.61 2.17
1915 2000 5.769367 TGAGATTGGTATACAGTACGCATC 58.231 41.667 5.01 0.00 0.00 3.91
1963 2048 9.200817 ACAATTTATGGGTGAAATAACATAGCT 57.799 29.630 0.00 0.00 0.00 3.32
2088 2173 7.976135 TTTCCTTCTTTCTCTCAGAATCTTG 57.024 36.000 0.00 0.00 33.67 3.02
2374 2461 4.591321 TTTCTATTTCTGGTGAGCCCAT 57.409 40.909 0.00 0.00 44.15 4.00
2468 2556 3.986996 ATGCATTTAAGGGCTTTGCTT 57.013 38.095 0.00 0.00 34.47 3.91
2495 2583 8.436200 GTGCAATTGTAACAAAAAGTAAACACA 58.564 29.630 7.40 0.00 0.00 3.72
2525 2614 5.754890 ACAATTCCAAGTGAAGCAATGAAAC 59.245 36.000 0.00 0.00 36.14 2.78
2762 2852 6.437928 TGACAACAGTTCTGCAAATAATGTC 58.562 36.000 0.00 0.00 35.30 3.06
2779 2869 7.611079 TCATCCAATCACTGAAATATGACAACA 59.389 33.333 0.00 0.00 0.00 3.33
2865 2955 7.780271 AGAAACTTTCTGACCAAAGGAACTATT 59.220 33.333 3.07 0.00 36.49 1.73
2938 3028 6.318900 ACAAGTGCTAGCTCAAAGTTAGTTTT 59.681 34.615 17.23 0.00 32.44 2.43
2970 3060 6.306987 AGTTGGTATTCAAATGAAGGAGTGT 58.693 36.000 1.98 0.00 37.48 3.55
2997 3088 8.618702 ATTTCCTGCAAGACATAGAATGATAG 57.381 34.615 0.00 0.00 34.07 2.08
3132 3224 3.255642 GGAGATAAAGCAGTTTGCCAACA 59.744 43.478 3.22 0.00 46.52 3.33
4998 6088 2.422127 ACCCAACAGAAGAAAACACACG 59.578 45.455 0.00 0.00 0.00 4.49
4999 6089 3.428862 CCACCCAACAGAAGAAAACACAC 60.429 47.826 0.00 0.00 0.00 3.82
5000 6090 2.757868 CCACCCAACAGAAGAAAACACA 59.242 45.455 0.00 0.00 0.00 3.72
5001 6091 2.758423 ACCACCCAACAGAAGAAAACAC 59.242 45.455 0.00 0.00 0.00 3.32
5005 6095 1.476110 CCGACCACCCAACAGAAGAAA 60.476 52.381 0.00 0.00 0.00 2.52
5008 6098 0.884704 CACCGACCACCCAACAGAAG 60.885 60.000 0.00 0.00 0.00 2.85
5011 6101 2.124507 ATCCACCGACCACCCAACAG 62.125 60.000 0.00 0.00 0.00 3.16
5347 6451 9.950496 ACATCATCTATTGTAGTTGTCTCTTTT 57.050 29.630 0.00 0.00 0.00 2.27
5368 6472 8.615211 GCACTTCTACATCATCAATTTACATCA 58.385 33.333 0.00 0.00 0.00 3.07
5369 6473 8.615211 TGCACTTCTACATCATCAATTTACATC 58.385 33.333 0.00 0.00 0.00 3.06
5370 6474 8.510243 TGCACTTCTACATCATCAATTTACAT 57.490 30.769 0.00 0.00 0.00 2.29
5371 6475 7.920160 TGCACTTCTACATCATCAATTTACA 57.080 32.000 0.00 0.00 0.00 2.41
5372 6476 8.454106 AGTTGCACTTCTACATCATCAATTTAC 58.546 33.333 0.00 0.00 0.00 2.01
5373 6477 8.565896 AGTTGCACTTCTACATCATCAATTTA 57.434 30.769 0.00 0.00 0.00 1.40
5374 6478 7.458409 AGTTGCACTTCTACATCATCAATTT 57.542 32.000 0.00 0.00 0.00 1.82
5375 6479 7.458409 AAGTTGCACTTCTACATCATCAATT 57.542 32.000 0.00 0.00 31.77 2.32
5389 6493 6.457355 TGCATCATTTATTGAAGTTGCACTT 58.543 32.000 0.00 0.00 40.94 3.16
5390 6494 6.028146 TGCATCATTTATTGAAGTTGCACT 57.972 33.333 0.00 0.00 40.94 4.40
5391 6495 6.709145 TTGCATCATTTATTGAAGTTGCAC 57.291 33.333 4.14 0.00 43.82 4.57
5392 6496 7.148390 CCATTTGCATCATTTATTGAAGTTGCA 60.148 33.333 0.00 0.00 42.96 4.08
5393 6497 7.064847 TCCATTTGCATCATTTATTGAAGTTGC 59.935 33.333 0.00 0.00 38.03 4.17
5394 6498 8.481974 TCCATTTGCATCATTTATTGAAGTTG 57.518 30.769 0.00 0.00 38.03 3.16
5395 6499 8.533657 TCTCCATTTGCATCATTTATTGAAGTT 58.466 29.630 0.00 0.00 38.03 2.66
5396 6500 8.070034 TCTCCATTTGCATCATTTATTGAAGT 57.930 30.769 0.00 0.00 38.03 3.01
5397 6501 8.978539 CATCTCCATTTGCATCATTTATTGAAG 58.021 33.333 0.00 0.00 38.03 3.02
5398 6502 8.479689 ACATCTCCATTTGCATCATTTATTGAA 58.520 29.630 0.00 0.00 38.03 2.69
5399 6503 8.014070 ACATCTCCATTTGCATCATTTATTGA 57.986 30.769 0.00 0.00 39.12 2.57
5400 6504 9.752961 TTACATCTCCATTTGCATCATTTATTG 57.247 29.630 0.00 0.00 0.00 1.90
5429 6533 1.972872 CTCAGCCGCCCAATTCTATT 58.027 50.000 0.00 0.00 0.00 1.73
5431 6535 1.153168 GCTCAGCCGCCCAATTCTA 60.153 57.895 0.00 0.00 0.00 2.10
5432 6536 2.439156 GCTCAGCCGCCCAATTCT 60.439 61.111 0.00 0.00 0.00 2.40
5433 6537 3.880846 CGCTCAGCCGCCCAATTC 61.881 66.667 0.00 0.00 0.00 2.17
5446 6550 4.884257 TTATGGTCGCCGCCGCTC 62.884 66.667 0.00 0.00 0.00 5.03
5450 6554 3.560278 CACGTTATGGTCGCCGCC 61.560 66.667 0.00 0.00 0.00 6.13
5451 6555 3.560278 CCACGTTATGGTCGCCGC 61.560 66.667 0.00 0.00 44.46 6.53
5463 6567 1.153706 CCCGATTAGAACGCCACGT 60.154 57.895 0.00 0.00 43.97 4.49
5464 6568 1.881252 CCCCGATTAGAACGCCACG 60.881 63.158 0.00 0.00 0.00 4.94
5465 6569 2.178235 GCCCCGATTAGAACGCCAC 61.178 63.158 0.00 0.00 0.00 5.01
5466 6570 2.188469 GCCCCGATTAGAACGCCA 59.812 61.111 0.00 0.00 0.00 5.69
5467 6571 2.965462 CGCCCCGATTAGAACGCC 60.965 66.667 0.00 0.00 0.00 5.68
5468 6572 2.965462 CCGCCCCGATTAGAACGC 60.965 66.667 0.00 0.00 0.00 4.84
5469 6573 2.965462 GCCGCCCCGATTAGAACG 60.965 66.667 0.00 0.00 0.00 3.95
5470 6574 1.887707 CTGCCGCCCCGATTAGAAC 60.888 63.158 0.00 0.00 0.00 3.01
5471 6575 2.504032 CTGCCGCCCCGATTAGAA 59.496 61.111 0.00 0.00 0.00 2.10
5472 6576 4.235762 GCTGCCGCCCCGATTAGA 62.236 66.667 0.00 0.00 0.00 2.10
5497 6601 2.268076 CCCCGTCCCACAGCTTTTG 61.268 63.158 0.00 0.00 0.00 2.44
5498 6602 2.115266 CCCCGTCCCACAGCTTTT 59.885 61.111 0.00 0.00 0.00 2.27
5499 6603 4.660938 GCCCCGTCCCACAGCTTT 62.661 66.667 0.00 0.00 0.00 3.51
5518 6622 4.265056 AACCTCCACACCCACCGC 62.265 66.667 0.00 0.00 0.00 5.68
5519 6623 2.281484 CAACCTCCACACCCACCG 60.281 66.667 0.00 0.00 0.00 4.94
5520 6624 2.115266 CCAACCTCCACACCCACC 59.885 66.667 0.00 0.00 0.00 4.61
5521 6625 2.115266 CCCAACCTCCACACCCAC 59.885 66.667 0.00 0.00 0.00 4.61
5522 6626 3.897122 GCCCAACCTCCACACCCA 61.897 66.667 0.00 0.00 0.00 4.51
5525 6629 4.265056 ACCGCCCAACCTCCACAC 62.265 66.667 0.00 0.00 0.00 3.82
5526 6630 4.263572 CACCGCCCAACCTCCACA 62.264 66.667 0.00 0.00 0.00 4.17
5530 6634 4.660938 AAGCCACCGCCCAACCTC 62.661 66.667 0.00 0.00 34.57 3.85
5531 6635 4.974721 CAAGCCACCGCCCAACCT 62.975 66.667 0.00 0.00 34.57 3.50
5533 6637 3.977244 CACAAGCCACCGCCCAAC 61.977 66.667 0.00 0.00 34.57 3.77
5534 6638 4.196778 TCACAAGCCACCGCCCAA 62.197 61.111 0.00 0.00 34.57 4.12
5535 6639 4.641645 CTCACAAGCCACCGCCCA 62.642 66.667 0.00 0.00 34.57 5.36
5541 6645 3.730761 CTGCCGCTCACAAGCCAC 61.731 66.667 0.00 0.00 46.34 5.01


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

AutoCloner maintained by Alex Coulton.