Multiple sequence alignment - TraesCS2A01G576600

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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 TraesCS2A01G576600 chr2A 100.000 4780 0 0 1 4780 770415485 770410706 0.000000e+00 8828.0
1 TraesCS2A01G576600 chr2A 95.982 896 29 2 624 1519 770425122 770424234 0.000000e+00 1448.0
2 TraesCS2A01G576600 chr2A 93.682 918 29 7 624 1519 770463249 770462339 0.000000e+00 1347.0
3 TraesCS2A01G576600 chr2A 92.950 922 30 12 624 1519 770430114 770429202 0.000000e+00 1310.0
4 TraesCS2A01G576600 chr2A 97.243 544 14 1 46 589 770425910 770425368 0.000000e+00 920.0
5 TraesCS2A01G576600 chr2A 92.751 469 16 4 121 589 770463945 770463495 0.000000e+00 662.0
6 TraesCS2A01G576600 chr2A 97.865 281 6 0 309 589 770430640 770430360 2.000000e-133 486.0
7 TraesCS2A01G576600 chr2A 97.761 268 6 0 46 313 770439657 770439390 3.370000e-126 462.0
8 TraesCS2A01G576600 chr2A 98.000 50 0 1 1 50 112078883 112078835 8.520000e-13 86.1
9 TraesCS2A01G576600 chr2D 93.308 3721 136 44 629 4274 645049323 645045641 0.000000e+00 5387.0
10 TraesCS2A01G576600 chr2D 88.889 540 11 19 4280 4780 645045381 645044852 1.890000e-173 619.0
11 TraesCS2A01G576600 chr2B 90.638 3119 173 64 1723 4780 790440787 790443847 0.000000e+00 4032.0
12 TraesCS2A01G576600 chr2B 90.057 523 25 11 628 1126 790439656 790440175 0.000000e+00 652.0
13 TraesCS2A01G576600 chr2B 86.542 483 31 14 1280 1728 790440278 790440760 7.140000e-138 501.0
14 TraesCS2A01G576600 chr2B 84.348 115 9 2 46 151 790439356 790439470 2.350000e-18 104.0
15 TraesCS2A01G576600 chr4B 90.055 181 17 1 1337 1516 356438533 356438713 2.880000e-57 233.0
16 TraesCS2A01G576600 chr4B 100.000 47 0 0 1 47 437846572 437846526 2.370000e-13 87.9
17 TraesCS2A01G576600 chrUn 100.000 47 0 0 1 47 430577141 430577187 2.370000e-13 87.9
18 TraesCS2A01G576600 chr6A 100.000 47 0 0 1 47 6946349 6946303 2.370000e-13 87.9
19 TraesCS2A01G576600 chr5B 100.000 47 0 0 1 47 696051277 696051231 2.370000e-13 87.9
20 TraesCS2A01G576600 chr4A 100.000 47 0 0 1 47 543386908 543386954 2.370000e-13 87.9
21 TraesCS2A01G576600 chr4A 100.000 47 0 0 1 47 589436929 589436883 2.370000e-13 87.9
22 TraesCS2A01G576600 chr4A 100.000 47 0 0 1 47 681642668 681642622 2.370000e-13 87.9
23 TraesCS2A01G576600 chr7B 96.154 52 1 1 1 52 302026984 302027034 3.070000e-12 84.2


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 TraesCS2A01G576600 chr2A 770410706 770415485 4779 True 8828.00 8828 100.00000 1 4780 1 chr2A.!!$R2 4779
1 TraesCS2A01G576600 chr2A 770424234 770430640 6406 True 1041.00 1448 96.01000 46 1519 4 chr2A.!!$R4 1473
2 TraesCS2A01G576600 chr2A 770462339 770463945 1606 True 1004.50 1347 93.21650 121 1519 2 chr2A.!!$R5 1398
3 TraesCS2A01G576600 chr2D 645044852 645049323 4471 True 3003.00 5387 91.09850 629 4780 2 chr2D.!!$R1 4151
4 TraesCS2A01G576600 chr2B 790439356 790443847 4491 False 1322.25 4032 87.89625 46 4780 4 chr2B.!!$F1 4734

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
41 42 0.249911 AGCTTGATTATCCGGGCGTC 60.250 55.000 0.00 0.00 0.00 5.19 F
42 43 0.531974 GCTTGATTATCCGGGCGTCA 60.532 55.000 0.00 0.00 0.00 4.35 F
603 5298 1.043816 CGTGGGTAGCCTGAGATCAT 58.956 55.000 13.11 0.00 0.00 2.45 F
604 5299 1.414181 CGTGGGTAGCCTGAGATCATT 59.586 52.381 13.11 0.00 0.00 2.57 F
626 5549 2.928036 TGTCCTCCTCCTTGAGATCA 57.072 50.000 0.00 0.00 34.11 2.92 F
2143 7245 3.132925 GCATTTGTTTCACTGCCATGTT 58.867 40.909 0.00 0.00 0.00 2.71 F
3295 8412 0.383491 GAAAGTGACGACGACGACGA 60.383 55.000 25.15 1.77 42.66 4.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1788 6886 0.249120 TCATGTTCCCAGCCAGTACG 59.751 55.000 0.00 0.0 0.00 3.67 R
1964 7065 3.067320 GCACCCTGAGGAAAATATCAAGC 59.933 47.826 0.00 0.0 36.73 4.01 R
2550 7664 4.772624 AGAGGAATACAAGTGCACTGTAGA 59.227 41.667 22.49 6.8 0.00 2.59 R
2757 7871 5.488341 ACAACCATGAAACGCTAGATAACT 58.512 37.500 0.00 0.0 0.00 2.24 R
2780 7895 6.540551 TGTAAGATATGCAGAAACGGCAATAA 59.459 34.615 0.00 0.0 45.60 1.40 R
3458 8575 0.320374 CCAGCGGAGTGAGTGGTAAA 59.680 55.000 0.00 0.0 0.00 2.01 R
4336 9753 0.670162 TGCTTTGCTTTCACTCTGGC 59.330 50.000 0.00 0.0 0.00 4.85 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
25 26 6.621394 TCATTAGTAGGGGATTACTGTAGCT 58.379 40.000 0.00 0.00 35.57 3.32
27 28 6.726490 TTAGTAGGGGATTACTGTAGCTTG 57.274 41.667 0.00 0.00 35.57 4.01
29 30 5.468658 AGTAGGGGATTACTGTAGCTTGAT 58.531 41.667 0.00 0.00 32.78 2.57
30 31 5.905913 AGTAGGGGATTACTGTAGCTTGATT 59.094 40.000 0.00 0.00 32.78 2.57
31 32 7.073854 AGTAGGGGATTACTGTAGCTTGATTA 58.926 38.462 0.00 0.00 32.78 1.75
32 33 7.735321 AGTAGGGGATTACTGTAGCTTGATTAT 59.265 37.037 0.00 0.00 32.78 1.28
33 34 7.010339 AGGGGATTACTGTAGCTTGATTATC 57.990 40.000 0.00 0.00 0.00 1.75
34 35 6.013293 AGGGGATTACTGTAGCTTGATTATCC 60.013 42.308 0.00 0.00 0.00 2.59
35 36 5.869888 GGGATTACTGTAGCTTGATTATCCG 59.130 44.000 0.00 0.00 31.87 4.18
36 37 5.869888 GGATTACTGTAGCTTGATTATCCGG 59.130 44.000 0.00 0.00 0.00 5.14
37 38 3.753294 ACTGTAGCTTGATTATCCGGG 57.247 47.619 0.00 0.00 0.00 5.73
38 39 2.224305 ACTGTAGCTTGATTATCCGGGC 60.224 50.000 0.00 0.00 0.00 6.13
40 41 1.045407 TAGCTTGATTATCCGGGCGT 58.955 50.000 0.00 0.00 0.00 5.68
41 42 0.249911 AGCTTGATTATCCGGGCGTC 60.250 55.000 0.00 0.00 0.00 5.19
42 43 0.531974 GCTTGATTATCCGGGCGTCA 60.532 55.000 0.00 0.00 0.00 4.35
43 44 1.217882 CTTGATTATCCGGGCGTCAC 58.782 55.000 0.00 0.00 0.00 3.67
317 5012 1.440938 TTTGTGAGCGGGAACAACGG 61.441 55.000 0.00 0.00 36.08 4.44
352 5047 2.881403 GCATCAGATGTGAAAGGGGTGT 60.881 50.000 12.18 0.00 35.88 4.16
502 5197 7.907389 AGTGGTAAAAGATGTGTCTCTTGATA 58.093 34.615 0.00 0.00 35.67 2.15
599 5294 3.449227 CGCGTGGGTAGCCTGAGA 61.449 66.667 13.11 0.00 0.00 3.27
601 5296 1.068250 GCGTGGGTAGCCTGAGATC 59.932 63.158 13.11 0.00 0.00 2.75
602 5297 1.676678 GCGTGGGTAGCCTGAGATCA 61.677 60.000 13.11 0.00 0.00 2.92
603 5298 1.043816 CGTGGGTAGCCTGAGATCAT 58.956 55.000 13.11 0.00 0.00 2.45
604 5299 1.414181 CGTGGGTAGCCTGAGATCATT 59.586 52.381 13.11 0.00 0.00 2.57
606 5301 3.682718 CGTGGGTAGCCTGAGATCATTTT 60.683 47.826 13.11 0.00 0.00 1.82
607 5302 4.273318 GTGGGTAGCCTGAGATCATTTTT 58.727 43.478 13.11 0.00 0.00 1.94
608 5303 4.096984 GTGGGTAGCCTGAGATCATTTTTG 59.903 45.833 13.11 0.00 0.00 2.44
609 5304 4.263905 TGGGTAGCCTGAGATCATTTTTGT 60.264 41.667 13.11 0.00 0.00 2.83
610 5305 4.336713 GGGTAGCCTGAGATCATTTTTGTC 59.663 45.833 2.95 0.00 0.00 3.18
614 5537 3.379688 GCCTGAGATCATTTTTGTCCTCC 59.620 47.826 0.00 0.00 0.00 4.30
617 5540 4.848357 TGAGATCATTTTTGTCCTCCTCC 58.152 43.478 0.00 0.00 0.00 4.30
618 5541 4.537688 TGAGATCATTTTTGTCCTCCTCCT 59.462 41.667 0.00 0.00 0.00 3.69
622 5545 4.655963 TCATTTTTGTCCTCCTCCTTGAG 58.344 43.478 0.00 0.00 0.00 3.02
623 5546 4.350816 TCATTTTTGTCCTCCTCCTTGAGA 59.649 41.667 0.00 0.00 34.11 3.27
625 5548 4.559862 TTTTGTCCTCCTCCTTGAGATC 57.440 45.455 0.00 0.00 34.11 2.75
626 5549 2.928036 TGTCCTCCTCCTTGAGATCA 57.072 50.000 0.00 0.00 34.11 2.92
1142 6122 4.489771 CCGGCCGCCTCCTTCAAT 62.490 66.667 22.85 0.00 0.00 2.57
1304 6324 4.062293 TCTTTCGTGTCCATACAAACTGG 58.938 43.478 0.00 0.00 37.36 4.00
1696 6751 6.067263 TGCTTTACAAGTTACAACATCACC 57.933 37.500 0.00 0.00 0.00 4.02
1788 6886 4.367450 GACACATCTCTCAGCTGTAATCC 58.633 47.826 14.67 0.00 0.00 3.01
1869 6970 5.067674 TCAAAGCAGCAGTTTAACTTCATGT 59.932 36.000 0.00 0.00 0.00 3.21
2047 7149 5.529800 TGGTTTTCTAGAAACTTGGTAGCAC 59.470 40.000 17.51 9.43 0.00 4.40
2143 7245 3.132925 GCATTTGTTTCACTGCCATGTT 58.867 40.909 0.00 0.00 0.00 2.71
2263 7374 5.178252 CCTTGATTAGGTAGCATCGACAATG 59.822 44.000 0.00 0.00 39.39 2.82
2449 7563 8.432805 TCATATGGACTTTCTTATCCTTCCTTC 58.567 37.037 2.13 0.00 35.86 3.46
2451 7565 6.642733 TGGACTTTCTTATCCTTCCTTCAT 57.357 37.500 0.00 0.00 35.86 2.57
2460 7574 8.293027 TCTTATCCTTCCTTCATTGGGATAAT 57.707 34.615 11.51 0.00 43.56 1.28
2505 7619 5.159209 CAAGCATAAGAGTTGGCAGAAAAG 58.841 41.667 0.00 0.00 0.00 2.27
2514 7628 5.595952 AGAGTTGGCAGAAAAGAGAAAACAT 59.404 36.000 0.00 0.00 0.00 2.71
2550 7664 8.630054 TTTATTATTGCTTGTGTACCTGAAGT 57.370 30.769 0.00 0.00 0.00 3.01
2757 7871 3.498481 GCTGCCTTGGGAATATCCATGTA 60.498 47.826 0.00 0.00 38.64 2.29
2780 7895 5.488341 AGTTATCTAGCGTTTCATGGTTGT 58.512 37.500 0.00 0.00 0.00 3.32
2788 7903 2.914214 CGTTTCATGGTTGTTATTGCCG 59.086 45.455 0.00 0.00 0.00 5.69
2811 7926 7.384115 GCCGTTTCTGCATATCTTACATAGTTA 59.616 37.037 0.00 0.00 0.00 2.24
2842 7957 8.866093 TGAGGATATGATTTATTTACACGGAGA 58.134 33.333 0.00 0.00 0.00 3.71
2866 7981 3.535280 TCCAAGGGCAAACAAAACTTC 57.465 42.857 0.00 0.00 0.00 3.01
2920 8035 5.593909 TGATCCTTTGTGATGACAGTGTTTT 59.406 36.000 0.00 0.00 32.26 2.43
2935 8050 5.221303 ACAGTGTTTTGTGCTGCTTAATGAT 60.221 36.000 0.00 0.00 33.87 2.45
3213 8330 3.251972 GGGTTTTCACTTCAGAGCTTCAG 59.748 47.826 0.00 0.00 0.00 3.02
3294 8411 0.655337 TGAAAGTGACGACGACGACG 60.655 55.000 17.60 17.60 42.66 5.12
3295 8412 0.383491 GAAAGTGACGACGACGACGA 60.383 55.000 25.15 1.77 42.66 4.20
3296 8413 0.655626 AAAGTGACGACGACGACGAC 60.656 55.000 25.15 19.21 42.66 4.34
3305 8422 2.799916 GACGACGACGCCTGTGAC 60.800 66.667 7.30 0.00 43.96 3.67
3336 8453 4.471726 GCTCACATGCGCACAGGC 62.472 66.667 14.90 9.66 0.00 4.85
3458 8575 1.933247 CCACCGTTGCAAAATGTTGT 58.067 45.000 0.00 0.00 37.06 3.32
3521 8638 4.778415 TTCCGCGCGTCTGCTCTC 62.778 66.667 29.95 0.00 39.65 3.20
3545 8662 2.515398 CACCCTGACAAGCACCCA 59.485 61.111 0.00 0.00 0.00 4.51
3562 8679 1.339151 CCCAGGCTCTTCACAGGTAAC 60.339 57.143 0.00 0.00 0.00 2.50
3563 8680 1.339151 CCAGGCTCTTCACAGGTAACC 60.339 57.143 0.00 0.00 37.17 2.85
3564 8681 0.608640 AGGCTCTTCACAGGTAACCG 59.391 55.000 0.00 0.00 37.17 4.44
3565 8682 0.606604 GGCTCTTCACAGGTAACCGA 59.393 55.000 0.00 0.00 37.17 4.69
3566 8683 1.672145 GGCTCTTCACAGGTAACCGAC 60.672 57.143 0.00 0.00 37.17 4.79
3590 8707 0.388649 CCGACTCTGAGGTGGTTTCG 60.389 60.000 9.85 7.76 0.00 3.46
3743 8860 1.794785 CAAGCTGTGCGTCAATGCG 60.795 57.895 0.00 0.00 37.81 4.73
3791 8908 0.876342 CCGCGTGATAAGCCTCTTCC 60.876 60.000 4.92 0.00 0.00 3.46
3792 8909 0.103208 CGCGTGATAAGCCTCTTCCT 59.897 55.000 0.00 0.00 0.00 3.36
3793 8910 1.471676 CGCGTGATAAGCCTCTTCCTT 60.472 52.381 0.00 0.00 0.00 3.36
3794 8911 2.205911 GCGTGATAAGCCTCTTCCTTC 58.794 52.381 0.00 0.00 0.00 3.46
3821 8938 1.581934 CGTGGTGTTCTGAAGCTTGA 58.418 50.000 2.10 0.00 0.00 3.02
3842 8971 1.135139 GAACGCTATCAGCTGACCTCA 59.865 52.381 20.97 3.72 39.60 3.86
3886 9020 3.372206 AGAAAATCGTTCCATCTCTTGCG 59.628 43.478 0.00 0.00 0.00 4.85
3969 9115 8.084590 TCCTTTCTTGAGTATTCGTTTTCTTC 57.915 34.615 0.00 0.00 0.00 2.87
3970 9116 7.713507 TCCTTTCTTGAGTATTCGTTTTCTTCA 59.286 33.333 0.00 0.00 0.00 3.02
3977 9123 9.706691 TTGAGTATTCGTTTTCTTCAACTAGAT 57.293 29.630 0.00 0.00 0.00 1.98
4009 9155 4.428845 AGCCAAGCTCCCAACATG 57.571 55.556 0.00 0.00 30.62 3.21
4088 9235 4.178545 AGCTGTAACAACAAATGATGGC 57.821 40.909 0.00 0.00 0.00 4.40
4112 9264 9.813446 GGCTATTTCATTTCATCTCTTGATTTT 57.187 29.630 0.00 0.00 33.34 1.82
4124 9276 6.405278 TCTCTTGATTTTGAAAGGGGAAAC 57.595 37.500 0.00 0.00 0.00 2.78
4130 9282 9.336171 CTTGATTTTGAAAGGGGAAACAAAATA 57.664 29.630 13.87 3.06 46.03 1.40
4184 9340 5.944007 TGAAAGCTCCCCTGTTAGTATTTTC 59.056 40.000 0.00 0.00 0.00 2.29
4198 9354 4.973168 AGTATTTTCCAGTGTTGCTCTCA 58.027 39.130 0.00 0.00 0.00 3.27
4199 9355 4.999950 AGTATTTTCCAGTGTTGCTCTCAG 59.000 41.667 0.00 0.00 0.00 3.35
4200 9356 3.558931 TTTTCCAGTGTTGCTCTCAGA 57.441 42.857 0.00 0.00 0.00 3.27
4201 9357 3.777106 TTTCCAGTGTTGCTCTCAGAT 57.223 42.857 0.00 0.00 0.00 2.90
4202 9358 2.756840 TCCAGTGTTGCTCTCAGATG 57.243 50.000 0.00 0.00 0.00 2.90
4219 9375 8.709272 TCTCAGATGAGATGTGATTCTTATCT 57.291 34.615 8.46 3.65 45.09 1.98
4223 9379 9.142515 CAGATGAGATGTGATTCTTATCTTAGC 57.857 37.037 6.13 0.00 42.99 3.09
4230 9386 5.977725 TGTGATTCTTATCTTAGCGTAGTGC 59.022 40.000 0.00 0.00 46.98 4.40
4245 9401 6.204075 GCGTAGTGCACATTTTAGATAGAG 57.796 41.667 21.04 0.00 45.45 2.43
4264 9422 9.111519 AGATAGAGGAAGATCTCAGATAGTACA 57.888 37.037 0.00 0.00 36.30 2.90
4336 9753 4.074259 TGATGAATTGATGATTAGGCCGG 58.926 43.478 0.00 0.00 0.00 6.13
4337 9754 2.229792 TGAATTGATGATTAGGCCGGC 58.770 47.619 21.18 21.18 0.00 6.13
4338 9755 1.541588 GAATTGATGATTAGGCCGGCC 59.458 52.381 39.29 39.29 0.00 6.13
4339 9756 0.478072 ATTGATGATTAGGCCGGCCA 59.522 50.000 45.13 28.44 38.92 5.36
4340 9757 0.179020 TTGATGATTAGGCCGGCCAG 60.179 55.000 45.13 0.00 38.92 4.85
4341 9758 1.053835 TGATGATTAGGCCGGCCAGA 61.054 55.000 45.13 32.85 38.92 3.86
4342 9759 0.321122 GATGATTAGGCCGGCCAGAG 60.321 60.000 45.13 0.00 38.92 3.35
4343 9760 1.056700 ATGATTAGGCCGGCCAGAGT 61.057 55.000 45.13 29.48 38.92 3.24
4344 9761 1.227674 GATTAGGCCGGCCAGAGTG 60.228 63.158 45.13 0.00 38.92 3.51
4345 9762 1.686325 GATTAGGCCGGCCAGAGTGA 61.686 60.000 45.13 23.45 38.92 3.41
4346 9763 1.271840 ATTAGGCCGGCCAGAGTGAA 61.272 55.000 45.13 27.28 38.92 3.18
4347 9764 1.485294 TTAGGCCGGCCAGAGTGAAA 61.485 55.000 45.13 23.47 38.92 2.69
4348 9765 1.899437 TAGGCCGGCCAGAGTGAAAG 61.899 60.000 45.13 0.00 38.92 2.62
4349 9766 3.435186 GCCGGCCAGAGTGAAAGC 61.435 66.667 18.11 0.00 0.00 3.51
4371 9788 1.602311 AGCAAAGCAGAGTTGGTCAG 58.398 50.000 0.00 0.00 31.22 3.51
4424 9853 1.892474 GAATGTTGGTAGGCAGGCAAA 59.108 47.619 0.00 0.00 0.00 3.68
4430 9859 1.098050 GGTAGGCAGGCAAACAGATG 58.902 55.000 0.00 0.00 0.00 2.90
4575 10039 0.047176 AGAGAGGAGGAGGAGGAGGA 59.953 60.000 0.00 0.00 0.00 3.71
4576 10040 0.478507 GAGAGGAGGAGGAGGAGGAG 59.521 65.000 0.00 0.00 0.00 3.69
4577 10041 0.998945 AGAGGAGGAGGAGGAGGAGG 60.999 65.000 0.00 0.00 0.00 4.30
4578 10042 0.996762 GAGGAGGAGGAGGAGGAGGA 60.997 65.000 0.00 0.00 0.00 3.71
4579 10043 0.998945 AGGAGGAGGAGGAGGAGGAG 60.999 65.000 0.00 0.00 0.00 3.69
4580 10044 1.541672 GAGGAGGAGGAGGAGGAGG 59.458 68.421 0.00 0.00 0.00 4.30
4581 10045 0.996762 GAGGAGGAGGAGGAGGAGGA 60.997 65.000 0.00 0.00 0.00 3.71
4582 10046 0.998945 AGGAGGAGGAGGAGGAGGAG 60.999 65.000 0.00 0.00 0.00 3.69
4583 10047 0.996762 GGAGGAGGAGGAGGAGGAGA 60.997 65.000 0.00 0.00 0.00 3.71
4584 10048 0.930726 GAGGAGGAGGAGGAGGAGAA 59.069 60.000 0.00 0.00 0.00 2.87
4585 10049 0.933700 AGGAGGAGGAGGAGGAGAAG 59.066 60.000 0.00 0.00 0.00 2.85
4586 10050 0.105709 GGAGGAGGAGGAGGAGAAGG 60.106 65.000 0.00 0.00 0.00 3.46
4721 10208 0.320374 TGAACTTGGCGAGGTAGGTG 59.680 55.000 6.71 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.249715 AGCTACAGTAATCCCCTACTAATGAT 58.750 38.462 0.00 0.00 30.77 2.45
1 2 6.621394 AGCTACAGTAATCCCCTACTAATGA 58.379 40.000 0.00 0.00 30.77 2.57
2 3 6.919775 AGCTACAGTAATCCCCTACTAATG 57.080 41.667 0.00 0.00 30.77 1.90
4 5 6.437755 TCAAGCTACAGTAATCCCCTACTAA 58.562 40.000 0.00 0.00 30.77 2.24
5 6 6.022107 TCAAGCTACAGTAATCCCCTACTA 57.978 41.667 0.00 0.00 30.77 1.82
7 8 5.810080 ATCAAGCTACAGTAATCCCCTAC 57.190 43.478 0.00 0.00 0.00 3.18
8 9 7.180408 GGATAATCAAGCTACAGTAATCCCCTA 59.820 40.741 0.00 0.00 0.00 3.53
9 10 6.013293 GGATAATCAAGCTACAGTAATCCCCT 60.013 42.308 0.00 0.00 0.00 4.79
10 11 6.174049 GGATAATCAAGCTACAGTAATCCCC 58.826 44.000 0.00 0.00 0.00 4.81
13 14 5.869888 CCCGGATAATCAAGCTACAGTAATC 59.130 44.000 0.73 0.00 0.00 1.75
15 16 4.502604 GCCCGGATAATCAAGCTACAGTAA 60.503 45.833 0.73 0.00 0.00 2.24
16 17 3.006537 GCCCGGATAATCAAGCTACAGTA 59.993 47.826 0.73 0.00 0.00 2.74
17 18 2.224305 GCCCGGATAATCAAGCTACAGT 60.224 50.000 0.73 0.00 0.00 3.55
18 19 2.417719 GCCCGGATAATCAAGCTACAG 58.582 52.381 0.73 0.00 0.00 2.74
19 20 1.270094 CGCCCGGATAATCAAGCTACA 60.270 52.381 0.73 0.00 0.00 2.74
20 21 1.270147 ACGCCCGGATAATCAAGCTAC 60.270 52.381 0.73 0.00 0.00 3.58
21 22 1.000506 GACGCCCGGATAATCAAGCTA 59.999 52.381 0.73 0.00 0.00 3.32
22 23 0.249911 GACGCCCGGATAATCAAGCT 60.250 55.000 0.73 0.00 0.00 3.74
25 26 0.537653 TGTGACGCCCGGATAATCAA 59.462 50.000 0.73 0.00 0.00 2.57
27 28 1.798813 GATTGTGACGCCCGGATAATC 59.201 52.381 0.73 0.00 0.00 1.75
29 30 0.528901 CGATTGTGACGCCCGGATAA 60.529 55.000 0.73 0.00 0.00 1.75
30 31 1.066752 CGATTGTGACGCCCGGATA 59.933 57.895 0.73 0.00 0.00 2.59
31 32 2.202878 CGATTGTGACGCCCGGAT 60.203 61.111 0.73 0.00 0.00 4.18
32 33 3.350909 CTCGATTGTGACGCCCGGA 62.351 63.158 0.73 0.00 0.00 5.14
33 34 2.885644 CTCGATTGTGACGCCCGG 60.886 66.667 0.00 0.00 0.00 5.73
34 35 3.554692 GCTCGATTGTGACGCCCG 61.555 66.667 0.00 0.00 0.00 6.13
35 36 3.195698 GGCTCGATTGTGACGCCC 61.196 66.667 0.00 0.00 34.75 6.13
36 37 0.529773 TATGGCTCGATTGTGACGCC 60.530 55.000 2.80 2.80 41.06 5.68
37 38 0.855349 CTATGGCTCGATTGTGACGC 59.145 55.000 0.00 0.00 0.00 5.19
38 39 2.209838 ACTATGGCTCGATTGTGACG 57.790 50.000 0.00 0.00 0.00 4.35
40 41 3.057526 CCGATACTATGGCTCGATTGTGA 60.058 47.826 3.63 0.00 34.41 3.58
41 42 3.245797 CCGATACTATGGCTCGATTGTG 58.754 50.000 3.63 0.00 34.41 3.33
42 43 2.891580 ACCGATACTATGGCTCGATTGT 59.108 45.455 3.63 0.00 34.41 2.71
43 44 3.577649 ACCGATACTATGGCTCGATTG 57.422 47.619 3.63 0.00 34.41 2.67
191 4886 1.147473 CTGTGCAACGCTACACATCA 58.853 50.000 5.57 0.00 45.18 3.07
352 5047 0.252761 TCGCCATCATCTTGCTTCCA 59.747 50.000 0.00 0.00 0.00 3.53
462 5157 0.321564 CCACTCAGCCGGATGTTTCA 60.322 55.000 20.97 0.00 0.00 2.69
502 5197 3.782443 GACCTTCACCCCGGCGAT 61.782 66.667 9.30 0.00 0.00 4.58
589 5284 5.189180 AGGACAAAAATGATCTCAGGCTAC 58.811 41.667 0.00 0.00 0.00 3.58
590 5285 5.431765 GAGGACAAAAATGATCTCAGGCTA 58.568 41.667 0.00 0.00 0.00 3.93
591 5286 4.268359 GAGGACAAAAATGATCTCAGGCT 58.732 43.478 0.00 0.00 0.00 4.58
592 5287 3.379688 GGAGGACAAAAATGATCTCAGGC 59.620 47.826 0.00 0.00 0.00 4.85
593 5288 4.853007 AGGAGGACAAAAATGATCTCAGG 58.147 43.478 0.00 0.00 0.00 3.86
595 5290 4.537688 AGGAGGAGGACAAAAATGATCTCA 59.462 41.667 0.00 0.00 0.00 3.27
597 5292 5.014544 TCAAGGAGGAGGACAAAAATGATCT 59.985 40.000 0.00 0.00 0.00 2.75
599 5294 5.014544 TCTCAAGGAGGAGGACAAAAATGAT 59.985 40.000 0.00 0.00 35.58 2.45
601 5296 4.655963 TCTCAAGGAGGAGGACAAAAATG 58.344 43.478 0.00 0.00 35.58 2.32
602 5297 5.014544 TGATCTCAAGGAGGAGGACAAAAAT 59.985 40.000 0.00 0.00 35.58 1.82
603 5298 4.350816 TGATCTCAAGGAGGAGGACAAAAA 59.649 41.667 0.00 0.00 35.58 1.94
604 5299 3.909995 TGATCTCAAGGAGGAGGACAAAA 59.090 43.478 0.00 0.00 35.58 2.44
606 5301 3.190383 TGATCTCAAGGAGGAGGACAA 57.810 47.619 0.00 0.00 35.58 3.18
607 5302 2.928036 TGATCTCAAGGAGGAGGACA 57.072 50.000 0.00 0.00 35.58 4.02
608 5303 4.769345 AAATGATCTCAAGGAGGAGGAC 57.231 45.455 0.00 0.00 35.58 3.85
609 5304 5.786121 AAAAATGATCTCAAGGAGGAGGA 57.214 39.130 0.00 0.00 35.58 3.71
785 5743 1.120530 CCTACCCACGCACCTCTATT 58.879 55.000 0.00 0.00 0.00 1.73
786 5744 0.260816 TCCTACCCACGCACCTCTAT 59.739 55.000 0.00 0.00 0.00 1.98
787 5745 0.395311 CTCCTACCCACGCACCTCTA 60.395 60.000 0.00 0.00 0.00 2.43
788 5746 1.682684 CTCCTACCCACGCACCTCT 60.683 63.158 0.00 0.00 0.00 3.69
789 5747 1.255667 TTCTCCTACCCACGCACCTC 61.256 60.000 0.00 0.00 0.00 3.85
790 5748 0.834687 TTTCTCCTACCCACGCACCT 60.835 55.000 0.00 0.00 0.00 4.00
1136 6116 2.042979 TGGGAAAAGAGGGGGATTGAAG 59.957 50.000 0.00 0.00 0.00 3.02
1137 6117 2.077803 TGGGAAAAGAGGGGGATTGAA 58.922 47.619 0.00 0.00 0.00 2.69
1140 6120 3.568780 GGAAATGGGAAAAGAGGGGGATT 60.569 47.826 0.00 0.00 0.00 3.01
1141 6121 2.023015 GGAAATGGGAAAAGAGGGGGAT 60.023 50.000 0.00 0.00 0.00 3.85
1142 6122 1.361197 GGAAATGGGAAAAGAGGGGGA 59.639 52.381 0.00 0.00 0.00 4.81
1304 6324 5.007136 GCATCTACTACAGCTTCCAATTGAC 59.993 44.000 7.12 0.00 0.00 3.18
1696 6751 7.935755 ACATATATGAGAAGAACATGAACAGGG 59.064 37.037 19.63 0.00 0.00 4.45
1788 6886 0.249120 TCATGTTCCCAGCCAGTACG 59.751 55.000 0.00 0.00 0.00 3.67
1964 7065 3.067320 GCACCCTGAGGAAAATATCAAGC 59.933 47.826 0.00 0.00 36.73 4.01
2087 7189 5.426504 AGAGGTGCTCAATTACATTCTGAG 58.573 41.667 0.00 0.00 39.69 3.35
2143 7245 6.458232 TTGAGTTTGCTTTGGCTACTAAAA 57.542 33.333 0.00 0.00 39.59 1.52
2263 7374 7.775561 ACCCATTAGAACTATCTCAAAATCACC 59.224 37.037 0.00 0.00 37.10 4.02
2291 7405 7.981789 TCGCTCATATTTCTGTTGAAGAGTTAT 59.018 33.333 0.00 0.00 35.91 1.89
2427 7541 6.642733 TGAAGGAAGGATAAGAAAGTCCAT 57.357 37.500 0.00 0.00 36.96 3.41
2430 7544 6.319911 CCCAATGAAGGAAGGATAAGAAAGTC 59.680 42.308 0.00 0.00 0.00 3.01
2433 7547 6.401537 TCCCAATGAAGGAAGGATAAGAAA 57.598 37.500 0.00 0.00 0.00 2.52
2449 7563 8.791327 AAACTTTTGCCTTAATTATCCCAATG 57.209 30.769 0.00 0.00 0.00 2.82
2460 7574 7.042119 GCTTGCAGAAATAAACTTTTGCCTTAA 60.042 33.333 0.00 0.00 0.00 1.85
2505 7619 5.665916 AAATGGATGGTGGATGTTTTCTC 57.334 39.130 0.00 0.00 0.00 2.87
2514 7628 6.610830 ACAAGCAATAATAAATGGATGGTGGA 59.389 34.615 0.00 0.00 0.00 4.02
2550 7664 4.772624 AGAGGAATACAAGTGCACTGTAGA 59.227 41.667 22.49 6.80 0.00 2.59
2757 7871 5.488341 ACAACCATGAAACGCTAGATAACT 58.512 37.500 0.00 0.00 0.00 2.24
2780 7895 6.540551 TGTAAGATATGCAGAAACGGCAATAA 59.459 34.615 0.00 0.00 45.60 1.40
2842 7957 3.263170 AGTTTTGTTTGCCCTTGGAACTT 59.737 39.130 0.00 0.00 0.00 2.66
2849 7964 4.441495 GCTGTAGAAGTTTTGTTTGCCCTT 60.441 41.667 0.00 0.00 0.00 3.95
2866 7981 7.941919 TCATATAGTTGAGTTGTAGGCTGTAG 58.058 38.462 0.00 0.00 0.00 2.74
2905 8020 3.365832 CAGCACAAAACACTGTCATCAC 58.634 45.455 0.00 0.00 0.00 3.06
2911 8026 4.097741 TCATTAAGCAGCACAAAACACTGT 59.902 37.500 0.00 0.00 33.87 3.55
2920 8035 6.573664 ACAAAACTATCATTAAGCAGCACA 57.426 33.333 0.00 0.00 0.00 4.57
3213 8330 1.794222 CCCGTCTGAATCCAAACGC 59.206 57.895 0.00 0.00 33.95 4.84
3275 8392 0.655337 CGTCGTCGTCGTCACTTTCA 60.655 55.000 3.67 0.00 38.33 2.69
3281 8398 4.707840 GCGTCGTCGTCGTCGTCA 62.708 66.667 19.72 0.00 46.29 4.35
3300 8417 4.539083 AACGCCGGCTGTGTCACA 62.539 61.111 26.68 5.36 36.45 3.58
3336 8453 0.967380 GGTGGCAATCCAAGGGTGAG 60.967 60.000 0.00 0.00 45.53 3.51
3458 8575 0.320374 CCAGCGGAGTGAGTGGTAAA 59.680 55.000 0.00 0.00 0.00 2.01
3545 8662 0.608640 CGGTTACCTGTGAAGAGCCT 59.391 55.000 0.00 0.00 0.00 4.58
3562 8679 3.812019 CAGAGTCGGTCGGGTCGG 61.812 72.222 0.00 0.00 0.00 4.79
3563 8680 2.745100 TCAGAGTCGGTCGGGTCG 60.745 66.667 0.00 0.00 0.00 4.79
3564 8681 2.408241 CCTCAGAGTCGGTCGGGTC 61.408 68.421 0.00 0.00 0.00 4.46
3565 8682 2.361357 CCTCAGAGTCGGTCGGGT 60.361 66.667 0.00 0.00 0.00 5.28
3566 8683 2.361357 ACCTCAGAGTCGGTCGGG 60.361 66.667 0.00 3.42 0.00 5.14
3590 8707 4.044426 GCATCTGTTGTTGGTTCAACTTC 58.956 43.478 11.36 5.85 45.26 3.01
3638 8755 4.088496 GCATATGTGTTTTCGCAAGTTGAC 59.912 41.667 7.16 0.00 43.76 3.18
3743 8860 1.344942 CGGTGCAGAGCGAGTTGTAC 61.345 60.000 0.00 0.00 46.19 2.90
3842 8971 1.626654 CCAAATTCACGCGCTCGAGT 61.627 55.000 15.13 0.00 39.41 4.18
3925 9067 1.606668 GAACAAACAACAGATGCGGGA 59.393 47.619 0.00 0.00 0.00 5.14
3969 9115 6.238320 GCTCTGTTGGCTCAAATATCTAGTTG 60.238 42.308 0.00 0.00 33.00 3.16
3970 9116 5.819901 GCTCTGTTGGCTCAAATATCTAGTT 59.180 40.000 0.00 0.00 0.00 2.24
3977 9123 2.877097 TGGCTCTGTTGGCTCAAATA 57.123 45.000 0.00 0.00 0.00 1.40
4008 9154 7.629157 TGTTACAACATAATCTCCTTCCATCA 58.371 34.615 0.00 0.00 33.17 3.07
4039 9185 7.592533 GCAATGGTAGTAAATATGATTGTGCTG 59.407 37.037 0.00 0.00 0.00 4.41
4112 9264 7.625469 ACAAGTTTATTTTGTTTCCCCTTTCA 58.375 30.769 0.00 0.00 35.32 2.69
4124 9276 8.129161 TGTTGCATTCAGACAAGTTTATTTTG 57.871 30.769 0.00 0.00 0.00 2.44
4168 9324 4.918588 ACACTGGAAAATACTAACAGGGG 58.081 43.478 0.00 0.00 36.91 4.79
4171 9327 6.428159 AGAGCAACACTGGAAAATACTAACAG 59.572 38.462 0.00 0.00 35.40 3.16
4184 9340 2.233186 TCTCATCTGAGAGCAACACTGG 59.767 50.000 5.80 0.00 45.48 4.00
4198 9354 8.028354 CGCTAAGATAAGAATCACATCTCATCT 58.972 37.037 0.00 0.00 36.21 2.90
4199 9355 7.812191 ACGCTAAGATAAGAATCACATCTCATC 59.188 37.037 0.00 0.00 34.28 2.92
4200 9356 7.665690 ACGCTAAGATAAGAATCACATCTCAT 58.334 34.615 0.00 0.00 34.28 2.90
4201 9357 7.043961 ACGCTAAGATAAGAATCACATCTCA 57.956 36.000 0.00 0.00 34.28 3.27
4202 9358 8.293867 ACTACGCTAAGATAAGAATCACATCTC 58.706 37.037 0.00 0.00 34.28 2.75
4219 9375 7.485810 TCTATCTAAAATGTGCACTACGCTAA 58.514 34.615 19.41 0.00 43.06 3.09
4223 9379 6.504398 TCCTCTATCTAAAATGTGCACTACG 58.496 40.000 19.41 0.85 0.00 3.51
4230 9386 9.695526 CTGAGATCTTCCTCTATCTAAAATGTG 57.304 37.037 0.00 0.00 32.60 3.21
4238 9394 9.111519 TGTACTATCTGAGATCTTCCTCTATCT 57.888 37.037 0.00 0.00 35.15 1.98
4239 9395 9.733556 TTGTACTATCTGAGATCTTCCTCTATC 57.266 37.037 0.00 0.00 34.38 2.08
4240 9396 9.515226 GTTGTACTATCTGAGATCTTCCTCTAT 57.485 37.037 0.00 0.00 34.38 1.98
4241 9397 8.495260 TGTTGTACTATCTGAGATCTTCCTCTA 58.505 37.037 0.00 0.00 34.38 2.43
4244 9400 7.962995 TTGTTGTACTATCTGAGATCTTCCT 57.037 36.000 0.00 0.00 0.00 3.36
4263 9421 6.947258 TCGCATCACACATCTATAATTGTTG 58.053 36.000 0.00 0.00 0.00 3.33
4264 9422 7.227314 ACATCGCATCACACATCTATAATTGTT 59.773 33.333 0.00 0.00 0.00 2.83
4274 9432 3.310501 TCAATCACATCGCATCACACATC 59.689 43.478 0.00 0.00 0.00 3.06
4336 9753 0.670162 TGCTTTGCTTTCACTCTGGC 59.330 50.000 0.00 0.00 0.00 4.85
4337 9754 3.378339 CTTTGCTTTGCTTTCACTCTGG 58.622 45.455 0.00 0.00 0.00 3.86
4338 9755 2.793232 GCTTTGCTTTGCTTTCACTCTG 59.207 45.455 0.00 0.00 0.00 3.35
4339 9756 2.428171 TGCTTTGCTTTGCTTTCACTCT 59.572 40.909 0.00 0.00 0.00 3.24
4340 9757 2.793232 CTGCTTTGCTTTGCTTTCACTC 59.207 45.455 0.00 0.00 0.00 3.51
4341 9758 2.428171 TCTGCTTTGCTTTGCTTTCACT 59.572 40.909 0.00 0.00 0.00 3.41
4342 9759 2.793232 CTCTGCTTTGCTTTGCTTTCAC 59.207 45.455 0.00 0.00 0.00 3.18
4343 9760 2.428171 ACTCTGCTTTGCTTTGCTTTCA 59.572 40.909 0.00 0.00 0.00 2.69
4344 9761 3.089573 ACTCTGCTTTGCTTTGCTTTC 57.910 42.857 0.00 0.00 0.00 2.62
4345 9762 3.192466 CAACTCTGCTTTGCTTTGCTTT 58.808 40.909 0.00 0.00 0.00 3.51
4346 9763 2.482490 CCAACTCTGCTTTGCTTTGCTT 60.482 45.455 0.00 0.00 0.00 3.91
4347 9764 1.068127 CCAACTCTGCTTTGCTTTGCT 59.932 47.619 0.00 0.00 0.00 3.91
4348 9765 1.202452 ACCAACTCTGCTTTGCTTTGC 60.202 47.619 0.00 0.00 0.00 3.68
4349 9766 2.099592 TGACCAACTCTGCTTTGCTTTG 59.900 45.455 0.00 0.00 0.00 2.77
4371 9788 2.291741 GGATCTTCGTTGGCCATGATTC 59.708 50.000 6.09 5.77 0.00 2.52
4413 9838 1.350684 TGACATCTGTTTGCCTGCCTA 59.649 47.619 0.00 0.00 0.00 3.93
4424 9853 2.968574 ACCAAGAGTGAGTGACATCTGT 59.031 45.455 0.00 0.00 0.00 3.41
4466 9903 1.006922 GCAAGCAGCACCCAGAAAC 60.007 57.895 0.00 0.00 44.79 2.78
4575 10039 2.225908 ACCACCATTACCTTCTCCTCCT 60.226 50.000 0.00 0.00 0.00 3.69
4576 10040 2.197465 ACCACCATTACCTTCTCCTCC 58.803 52.381 0.00 0.00 0.00 4.30
4577 10041 3.181464 GCTACCACCATTACCTTCTCCTC 60.181 52.174 0.00 0.00 0.00 3.71
4578 10042 2.772515 GCTACCACCATTACCTTCTCCT 59.227 50.000 0.00 0.00 0.00 3.69
4579 10043 2.772515 AGCTACCACCATTACCTTCTCC 59.227 50.000 0.00 0.00 0.00 3.71
4580 10044 4.039366 CCTAGCTACCACCATTACCTTCTC 59.961 50.000 0.00 0.00 0.00 2.87
4581 10045 3.967987 CCTAGCTACCACCATTACCTTCT 59.032 47.826 0.00 0.00 0.00 2.85
4582 10046 3.494573 GCCTAGCTACCACCATTACCTTC 60.495 52.174 0.00 0.00 0.00 3.46
4583 10047 2.438392 GCCTAGCTACCACCATTACCTT 59.562 50.000 0.00 0.00 0.00 3.50
4584 10048 2.047830 GCCTAGCTACCACCATTACCT 58.952 52.381 0.00 0.00 0.00 3.08
4585 10049 2.047830 AGCCTAGCTACCACCATTACC 58.952 52.381 0.00 0.00 36.99 2.85
4586 10050 3.258622 CCTAGCCTAGCTACCACCATTAC 59.741 52.174 0.00 0.00 40.44 1.89
4721 10208 3.701604 CTACCAGGAGCCGCACGAC 62.702 68.421 0.00 0.00 0.00 4.34


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

AutoCloner maintained by Alex Coulton.