Multiple sequence alignment - TraesCS5A01G438100

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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 TraesCS5A01G438100 chr5A 100.000 4917 0 0 1 4917 619714454 619719370 0.000000e+00 9081.0
1 TraesCS5A01G438100 chr5A 82.655 467 45 14 4001 4433 619726484 619726948 9.990000e-102 381.0
2 TraesCS5A01G438100 chr5A 95.588 136 6 0 4603 4738 77084890 77084755 8.290000e-53 219.0
3 TraesCS5A01G438100 chr5A 90.698 129 8 3 2581 2708 619726247 619726372 8.460000e-38 169.0
4 TraesCS5A01G438100 chr5A 83.051 177 26 4 4743 4916 619753444 619753619 1.830000e-34 158.0
5 TraesCS5A01G438100 chr5A 88.571 105 12 0 3800 3904 619718211 619718315 1.440000e-25 128.0
6 TraesCS5A01G438100 chr5A 88.571 105 12 0 3758 3862 619718253 619718357 1.440000e-25 128.0
7 TraesCS5A01G438100 chr5A 94.118 68 4 0 4431 4498 23817593 23817526 2.420000e-18 104.0
8 TraesCS5A01G438100 chr5A 86.765 68 8 1 4495 4562 619726947 619727013 1.900000e-09 75.0
9 TraesCS5A01G438100 chr5B 94.645 4351 121 30 164 4433 612978414 612982733 0.000000e+00 6641.0
10 TraesCS5A01G438100 chr5B 84.235 1738 191 42 1504 3196 613081542 613083241 0.000000e+00 1615.0
11 TraesCS5A01G438100 chr5B 82.516 1121 141 34 1973 3061 613098120 613099217 0.000000e+00 933.0
12 TraesCS5A01G438100 chr5B 85.773 731 76 16 1504 2228 613097040 613097748 0.000000e+00 749.0
13 TraesCS5A01G438100 chr5B 96.875 192 3 2 4729 4917 612982841 612983032 7.940000e-83 318.0
14 TraesCS5A01G438100 chr5B 82.028 217 32 4 3892 4108 613108081 613108290 1.410000e-40 178.0
15 TraesCS5A01G438100 chr5B 81.567 217 33 4 3892 4108 613083998 613084207 6.540000e-39 172.0
16 TraesCS5A01G438100 chr5B 92.593 108 8 0 4495 4602 612982732 612982839 6.590000e-34 156.0
17 TraesCS5A01G438100 chr5B 86.667 105 14 0 3800 3904 612982020 612982124 3.110000e-22 117.0
18 TraesCS5A01G438100 chr5B 91.463 82 7 0 1394 1475 613044155 613044236 4.020000e-21 113.0
19 TraesCS5A01G438100 chr5D 94.927 3134 120 17 130 3233 495744995 495748119 0.000000e+00 4870.0
20 TraesCS5A01G438100 chr5D 96.439 1039 17 3 3213 4231 495748132 495749170 0.000000e+00 1696.0
21 TraesCS5A01G438100 chr5D 90.964 332 21 1 4269 4600 495749178 495749500 5.840000e-119 438.0
22 TraesCS5A01G438100 chr5D 97.368 190 4 1 4729 4917 495749504 495749693 6.140000e-84 322.0
23 TraesCS5A01G438100 chr5D 81.517 211 33 5 4709 4915 495782613 495782821 8.460000e-38 169.0
24 TraesCS5A01G438100 chr5D 90.000 130 3 5 1 129 495741841 495741961 5.090000e-35 159.0
25 TraesCS5A01G438100 chr5D 87.619 105 13 0 3800 3904 495748678 495748782 6.680000e-24 122.0
26 TraesCS5A01G438100 chr5D 87.619 105 13 0 3758 3862 495748720 495748824 6.680000e-24 122.0
27 TraesCS5A01G438100 chr3A 99.219 128 1 0 4603 4730 411879204 411879331 1.060000e-56 231.0
28 TraesCS5A01G438100 chr3A 98.462 130 2 0 4600 4729 38671378 38671249 3.830000e-56 230.0
29 TraesCS5A01G438100 chr4B 96.403 139 5 0 4597 4735 210282752 210282890 3.830000e-56 230.0
30 TraesCS5A01G438100 chr7A 97.037 135 4 0 4595 4729 77440675 77440541 1.380000e-55 228.0
31 TraesCS5A01G438100 chr1A 98.450 129 2 0 4601 4729 12159813 12159685 1.380000e-55 228.0
32 TraesCS5A01G438100 chr1A 95.312 64 3 0 4435 4498 290331271 290331208 8.710000e-18 102.0
33 TraesCS5A01G438100 chr2B 96.992 133 4 0 4598 4730 171995395 171995527 1.780000e-54 224.0
34 TraesCS5A01G438100 chr2B 83.036 112 17 2 261 371 541085991 541085881 3.130000e-17 100.0
35 TraesCS5A01G438100 chr6B 95.652 138 5 1 4593 4730 620850996 620850860 2.300000e-53 220.0
36 TraesCS5A01G438100 chr6A 97.656 128 3 0 4602 4729 594970513 594970386 2.300000e-53 220.0
37 TraesCS5A01G438100 chr1D 71.948 852 190 38 274 1101 81002229 81001403 2.320000e-48 204.0
38 TraesCS5A01G438100 chr1D 86.777 121 15 1 3991 4111 16547585 16547466 3.090000e-27 134.0
39 TraesCS5A01G438100 chr1D 87.288 118 14 1 3991 4108 124375662 124375778 3.090000e-27 134.0
40 TraesCS5A01G438100 chr1D 95.312 64 3 0 4432 4495 15516887 15516950 8.710000e-18 102.0
41 TraesCS5A01G438100 chr2A 82.915 199 29 4 241 435 602796839 602796642 1.820000e-39 174.0
42 TraesCS5A01G438100 chr2A 92.857 70 3 2 4431 4498 771521501 771521432 3.130000e-17 100.0
43 TraesCS5A01G438100 chr7D 87.288 118 14 1 3991 4108 27639510 27639626 3.090000e-27 134.0
44 TraesCS5A01G438100 chr7D 86.777 121 15 1 3991 4111 90997679 90997560 3.090000e-27 134.0
45 TraesCS5A01G438100 chr7D 86.777 121 15 1 3991 4111 576964813 576964694 3.090000e-27 134.0
46 TraesCS5A01G438100 chr7D 95.312 64 3 0 4435 4498 604972523 604972460 8.710000e-18 102.0
47 TraesCS5A01G438100 chr4A 98.438 64 1 0 4435 4498 456483177 456483240 4.020000e-21 113.0
48 TraesCS5A01G438100 chr6D 92.857 70 5 0 4426 4495 25612727 25612796 8.710000e-18 102.0
49 TraesCS5A01G438100 chr3B 95.312 64 3 0 4435 4498 636452108 636452045 8.710000e-18 102.0
50 TraesCS5A01G438100 chr3B 84.483 58 7 2 4405 4462 306576949 306577004 6.880000e-04 56.5
51 TraesCS5A01G438100 chr7B 90.541 74 7 0 4429 4502 296330821 296330894 1.130000e-16 99.0


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 TraesCS5A01G438100 chr5A 619714454 619719370 4916 False 3112.333333 9081 92.380667 1 4917 3 chr5A.!!$F2 4916
1 TraesCS5A01G438100 chr5A 619726247 619727013 766 False 208.333333 381 86.706000 2581 4562 3 chr5A.!!$F3 1981
2 TraesCS5A01G438100 chr5B 612978414 612983032 4618 False 1808.000000 6641 92.695000 164 4917 4 chr5B.!!$F3 4753
3 TraesCS5A01G438100 chr5B 613081542 613084207 2665 False 893.500000 1615 82.901000 1504 4108 2 chr5B.!!$F4 2604
4 TraesCS5A01G438100 chr5B 613097040 613099217 2177 False 841.000000 933 84.144500 1504 3061 2 chr5B.!!$F5 1557
5 TraesCS5A01G438100 chr5D 495741841 495749693 7852 False 1104.142857 4870 92.133714 1 4917 7 chr5D.!!$F2 4916
6 TraesCS5A01G438100 chr1D 81001403 81002229 826 True 204.000000 204 71.948000 274 1101 1 chr1D.!!$R2 827

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
954 4005 1.549170 GACCTCTTCAGCCGGAAACTA 59.451 52.381 5.05 0.0 34.44 2.24 F
1560 4629 1.040339 CGACAAGGAGGAGGAGGAGG 61.040 65.000 0.00 0.0 0.00 4.30 F
2147 5846 1.134220 TCCCTGGAATATTGTGTCGGC 60.134 52.381 0.00 0.0 0.00 5.54 F
2661 6377 1.276421 GAAGAGTCCTGGCAGCACTAA 59.724 52.381 11.87 0.0 0.00 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2275 5974 1.725641 TCTGTAGCAAAGCACATCCG 58.274 50.000 0.00 0.0 0.00 4.18 R
3447 7227 2.162408 GGAACGGAATTTTCTGAGCCAG 59.838 50.000 6.15 0.0 37.03 4.85 R
3645 7594 3.711190 TGATATTGCTTGCTCCAGGTCTA 59.289 43.478 0.00 0.0 0.00 2.59 R
4502 8622 0.108138 AGATGGCTGGCGACTGTAAC 60.108 55.000 0.00 0.0 0.00 2.50 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
115 116 7.660208 ACTGGACGTCAAAATATTTCTTAGTGT 59.340 33.333 18.91 0.00 0.00 3.55
118 119 7.270579 GGACGTCAAAATATTTCTTAGTGTTGC 59.729 37.037 18.91 0.00 0.00 4.17
178 3212 3.443681 GTGTCTCTCTCTCCTCTTTCAGG 59.556 52.174 0.00 0.00 45.15 3.86
183 3219 1.616628 TCTCCTCTTTCAGGCCCCC 60.617 63.158 0.00 0.00 43.08 5.40
211 3247 2.760477 CCCACATTTCCCCACCGA 59.240 61.111 0.00 0.00 0.00 4.69
574 3613 1.687123 ACCCTATTCGAATCACCGAGG 59.313 52.381 15.25 14.81 39.90 4.63
576 3615 2.029828 CCCTATTCGAATCACCGAGGAG 60.030 54.545 20.71 8.85 39.90 3.69
954 4005 1.549170 GACCTCTTCAGCCGGAAACTA 59.451 52.381 5.05 0.00 34.44 2.24
991 4042 3.679389 CCACCCATCCATCACTATAAGC 58.321 50.000 0.00 0.00 0.00 3.09
1049 4100 1.884497 CGCGAGTATGGAGGGATCTCT 60.884 57.143 0.00 0.00 39.86 3.10
1072 4126 4.436998 GCCTGTGGTCGACGGAGG 62.437 72.222 17.54 17.54 31.77 4.30
1385 4454 7.756272 TGCTGCAATTTGTTGATCATTTAGTAG 59.244 33.333 0.00 0.00 0.00 2.57
1443 4512 3.196254 GGGTGATGGTGCATTTTCTCAAT 59.804 43.478 0.00 0.00 0.00 2.57
1558 4627 1.682684 GCGACAAGGAGGAGGAGGA 60.683 63.158 0.00 0.00 0.00 3.71
1559 4628 1.671901 GCGACAAGGAGGAGGAGGAG 61.672 65.000 0.00 0.00 0.00 3.69
1560 4629 1.040339 CGACAAGGAGGAGGAGGAGG 61.040 65.000 0.00 0.00 0.00 4.30
1647 4716 2.774809 GCCCTTAAGGATGAGGACTTCT 59.225 50.000 23.74 0.00 38.24 2.85
1820 4889 9.117183 TCTCTTATGGATTCATCTTGATGTTTG 57.883 33.333 10.01 0.00 34.96 2.93
1978 5048 8.183536 TGTTATGATGTGTGAATTGTGATTAGC 58.816 33.333 0.00 0.00 0.00 3.09
1979 5049 8.400947 GTTATGATGTGTGAATTGTGATTAGCT 58.599 33.333 0.00 0.00 0.00 3.32
2147 5846 1.134220 TCCCTGGAATATTGTGTCGGC 60.134 52.381 0.00 0.00 0.00 5.54
2174 5873 2.702478 CTGATTCCCATGCTCTACCTCA 59.298 50.000 0.00 0.00 0.00 3.86
2185 5884 9.911788 CCCATGCTCTACCTCAAATTATATTAT 57.088 33.333 0.00 0.00 0.00 1.28
2311 6010 7.278135 TGCTACAGAAAGCTCTATCAAATCAT 58.722 34.615 0.00 0.00 43.19 2.45
2325 6024 9.895138 TCTATCAAATCATGATTCAGTGAAGAA 57.105 29.630 20.95 10.17 46.85 2.52
2353 6052 4.765339 ACCACCCAAAGTAATACTGAAAGC 59.235 41.667 0.00 0.00 37.60 3.51
2374 6073 4.215827 AGCGAAATAGTAGAGGGTATGTCG 59.784 45.833 0.00 0.00 38.76 4.35
2485 6189 6.946340 TCTTTATCTGTTCATACCTGCTGAA 58.054 36.000 0.00 0.00 0.00 3.02
2661 6377 1.276421 GAAGAGTCCTGGCAGCACTAA 59.724 52.381 11.87 0.00 0.00 2.24
2974 6700 6.552445 ATTGCTACAGTACTTGAATCCTCT 57.448 37.500 0.00 0.00 0.00 3.69
3012 6738 4.967442 GGGTGTTAGGGGTAGATCTTAGTT 59.033 45.833 0.00 0.00 0.00 2.24
3152 6898 4.279922 TGTATATGTGGTGACTGGGTATCG 59.720 45.833 0.00 0.00 0.00 2.92
3166 6912 3.454447 TGGGTATCGTCAACTTGGATCAT 59.546 43.478 0.00 0.00 0.00 2.45
3260 7040 3.056607 GCTGGTATGTTGCAGATTTTGGT 60.057 43.478 0.00 0.00 0.00 3.67
3464 7244 1.457346 AGCTGGCTCAGAAAATTCCG 58.543 50.000 6.40 0.00 32.44 4.30
3723 7786 2.274760 GGCTGCAGGCTGGATCTT 59.725 61.111 31.40 0.00 41.46 2.40
4062 8146 2.048444 ATGCTCTTCATGTCGGCATT 57.952 45.000 0.00 0.00 40.12 3.56
4260 8380 7.051000 ACAGATCTTAAAGCCCTAACATCTTC 58.949 38.462 0.00 0.00 0.00 2.87
4262 8382 7.554118 CAGATCTTAAAGCCCTAACATCTTCAA 59.446 37.037 0.00 0.00 0.00 2.69
4347 8467 5.386060 TGGTAGTATGTCCTCCACTCATAG 58.614 45.833 0.00 0.00 0.00 2.23
4348 8468 4.767928 GGTAGTATGTCCTCCACTCATAGG 59.232 50.000 0.00 0.00 0.00 2.57
4359 8479 2.107204 CCACTCATAGGCCCTGCTATTT 59.893 50.000 0.00 0.00 0.00 1.40
4410 8530 7.616313 AGTTCTCTCGATAACAGAATTCCTTT 58.384 34.615 0.65 0.00 0.00 3.11
4445 8565 4.008074 CTTTTCAAGCACTCCCTCTGTA 57.992 45.455 0.00 0.00 0.00 2.74
4446 8566 4.389374 CTTTTCAAGCACTCCCTCTGTAA 58.611 43.478 0.00 0.00 0.00 2.41
4447 8567 4.431416 TTTCAAGCACTCCCTCTGTAAA 57.569 40.909 0.00 0.00 0.00 2.01
4448 8568 3.685139 TCAAGCACTCCCTCTGTAAAG 57.315 47.619 0.00 0.00 0.00 1.85
4449 8569 3.239449 TCAAGCACTCCCTCTGTAAAGA 58.761 45.455 0.00 0.00 0.00 2.52
4459 8579 9.757227 CACTCCCTCTGTAAAGAAATATAAGAG 57.243 37.037 0.00 0.00 0.00 2.85
4460 8580 9.495382 ACTCCCTCTGTAAAGAAATATAAGAGT 57.505 33.333 0.00 0.00 0.00 3.24
4462 8582 9.488762 TCCCTCTGTAAAGAAATATAAGAGTGA 57.511 33.333 0.00 0.00 0.00 3.41
4473 8593 9.685828 AGAAATATAAGAGTGATCTAAACGCTC 57.314 33.333 0.00 0.00 42.81 5.03
4483 8603 8.819643 AGTGATCTAAACGCTCTTATATTTCC 57.180 34.615 0.00 0.00 0.00 3.13
4484 8604 8.643324 AGTGATCTAAACGCTCTTATATTTCCT 58.357 33.333 0.00 0.00 0.00 3.36
4485 8605 9.262358 GTGATCTAAACGCTCTTATATTTCCTT 57.738 33.333 0.00 0.00 0.00 3.36
4572 8692 1.668751 TGTGCGTGGTTCTTTTCTGAC 59.331 47.619 0.00 0.00 0.00 3.51
4610 8730 2.663826 CTGTTGTCAGCTACTCCCTC 57.336 55.000 0.00 0.00 34.79 4.30
4611 8731 1.205893 CTGTTGTCAGCTACTCCCTCC 59.794 57.143 0.00 0.00 34.79 4.30
4612 8732 0.173708 GTTGTCAGCTACTCCCTCCG 59.826 60.000 0.00 0.00 0.00 4.63
4613 8733 0.251653 TTGTCAGCTACTCCCTCCGT 60.252 55.000 0.00 0.00 0.00 4.69
4614 8734 0.251653 TGTCAGCTACTCCCTCCGTT 60.252 55.000 0.00 0.00 0.00 4.44
4615 8735 0.456628 GTCAGCTACTCCCTCCGTTC 59.543 60.000 0.00 0.00 0.00 3.95
4616 8736 0.683504 TCAGCTACTCCCTCCGTTCC 60.684 60.000 0.00 0.00 0.00 3.62
4617 8737 1.753463 AGCTACTCCCTCCGTTCCG 60.753 63.158 0.00 0.00 0.00 4.30
4618 8738 1.751927 GCTACTCCCTCCGTTCCGA 60.752 63.158 0.00 0.00 0.00 4.55
4619 8739 1.318158 GCTACTCCCTCCGTTCCGAA 61.318 60.000 0.00 0.00 0.00 4.30
4620 8740 1.400737 CTACTCCCTCCGTTCCGAAT 58.599 55.000 0.00 0.00 0.00 3.34
4621 8741 1.755380 CTACTCCCTCCGTTCCGAATT 59.245 52.381 0.00 0.00 0.00 2.17
4622 8742 1.856629 ACTCCCTCCGTTCCGAATTA 58.143 50.000 0.00 0.00 0.00 1.40
4623 8743 1.479730 ACTCCCTCCGTTCCGAATTAC 59.520 52.381 0.00 0.00 0.00 1.89
4624 8744 1.755380 CTCCCTCCGTTCCGAATTACT 59.245 52.381 0.00 0.00 0.00 2.24
4625 8745 2.167900 CTCCCTCCGTTCCGAATTACTT 59.832 50.000 0.00 0.00 0.00 2.24
4626 8746 2.093869 TCCCTCCGTTCCGAATTACTTG 60.094 50.000 0.00 0.00 0.00 3.16
4627 8747 2.354403 CCCTCCGTTCCGAATTACTTGT 60.354 50.000 0.00 0.00 0.00 3.16
4628 8748 2.928116 CCTCCGTTCCGAATTACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
4629 8749 3.368116 CCTCCGTTCCGAATTACTTGTCT 60.368 47.826 0.00 0.00 0.00 3.41
4630 8750 4.243270 CTCCGTTCCGAATTACTTGTCTT 58.757 43.478 0.00 0.00 0.00 3.01
4631 8751 5.389859 TCCGTTCCGAATTACTTGTCTTA 57.610 39.130 0.00 0.00 0.00 2.10
4632 8752 5.404946 TCCGTTCCGAATTACTTGTCTTAG 58.595 41.667 0.00 0.00 0.00 2.18
4633 8753 5.183713 TCCGTTCCGAATTACTTGTCTTAGA 59.816 40.000 0.00 0.00 0.00 2.10
4634 8754 6.040878 CCGTTCCGAATTACTTGTCTTAGAT 58.959 40.000 0.00 0.00 0.00 1.98
4635 8755 6.534079 CCGTTCCGAATTACTTGTCTTAGATT 59.466 38.462 0.00 0.00 0.00 2.40
4636 8756 7.064253 CCGTTCCGAATTACTTGTCTTAGATTT 59.936 37.037 0.00 0.00 0.00 2.17
4637 8757 7.898309 CGTTCCGAATTACTTGTCTTAGATTTG 59.102 37.037 0.00 0.00 0.00 2.32
4638 8758 8.718734 GTTCCGAATTACTTGTCTTAGATTTGT 58.281 33.333 0.00 0.00 0.00 2.83
4639 8759 8.475331 TCCGAATTACTTGTCTTAGATTTGTC 57.525 34.615 0.00 0.00 0.00 3.18
4640 8760 8.311836 TCCGAATTACTTGTCTTAGATTTGTCT 58.688 33.333 0.00 0.00 0.00 3.41
4641 8761 9.582431 CCGAATTACTTGTCTTAGATTTGTCTA 57.418 33.333 0.00 0.00 0.00 2.59
4648 8768 9.175312 ACTTGTCTTAGATTTGTCTAGATACGA 57.825 33.333 0.00 0.00 0.00 3.43
4651 8771 8.622157 TGTCTTAGATTTGTCTAGATACGAAGG 58.378 37.037 0.00 0.00 0.00 3.46
4652 8772 8.623030 GTCTTAGATTTGTCTAGATACGAAGGT 58.377 37.037 0.00 0.00 0.00 3.50
4653 8773 9.842775 TCTTAGATTTGTCTAGATACGAAGGTA 57.157 33.333 0.00 0.00 0.00 3.08
4669 8789 7.108841 ACGAAGGTATCTAGCACTAAAATGA 57.891 36.000 0.00 0.00 0.00 2.57
4670 8790 7.203910 ACGAAGGTATCTAGCACTAAAATGAG 58.796 38.462 0.00 0.00 0.00 2.90
4671 8791 7.147880 ACGAAGGTATCTAGCACTAAAATGAGT 60.148 37.037 0.00 0.00 0.00 3.41
4672 8792 7.380065 CGAAGGTATCTAGCACTAAAATGAGTC 59.620 40.741 0.00 0.00 0.00 3.36
4673 8793 7.906199 AGGTATCTAGCACTAAAATGAGTCT 57.094 36.000 0.00 0.00 0.00 3.24
4674 8794 8.998277 AGGTATCTAGCACTAAAATGAGTCTA 57.002 34.615 0.00 0.00 0.00 2.59
4675 8795 9.073475 AGGTATCTAGCACTAAAATGAGTCTAG 57.927 37.037 0.00 0.00 33.29 2.43
4676 8796 9.069082 GGTATCTAGCACTAAAATGAGTCTAGA 57.931 37.037 11.59 11.59 38.76 2.43
4680 8800 9.628500 TCTAGCACTAAAATGAGTCTAGATACA 57.372 33.333 0.00 0.00 34.65 2.29
4683 8803 8.364142 AGCACTAAAATGAGTCTAGATACATCC 58.636 37.037 12.66 0.00 0.00 3.51
4684 8804 7.327275 GCACTAAAATGAGTCTAGATACATCCG 59.673 40.741 12.66 6.68 0.00 4.18
4685 8805 8.353684 CACTAAAATGAGTCTAGATACATCCGT 58.646 37.037 12.66 7.10 0.00 4.69
4686 8806 9.570468 ACTAAAATGAGTCTAGATACATCCGTA 57.430 33.333 12.66 6.93 0.00 4.02
4692 8812 9.961264 ATGAGTCTAGATACATCCGTATTTAGA 57.039 33.333 0.00 8.15 43.95 2.10
4700 8820 8.647796 AGATACATCCGTATTTAGACAAATCCA 58.352 33.333 0.00 0.00 38.48 3.41
4701 8821 9.268268 GATACATCCGTATTTAGACAAATCCAA 57.732 33.333 0.00 0.00 38.48 3.53
4702 8822 7.553881 ACATCCGTATTTAGACAAATCCAAG 57.446 36.000 0.00 0.00 35.88 3.61
4703 8823 7.335627 ACATCCGTATTTAGACAAATCCAAGA 58.664 34.615 0.00 0.00 35.88 3.02
4704 8824 7.280205 ACATCCGTATTTAGACAAATCCAAGAC 59.720 37.037 0.00 0.00 35.88 3.01
4705 8825 6.703319 TCCGTATTTAGACAAATCCAAGACA 58.297 36.000 0.00 0.00 35.88 3.41
4706 8826 7.162761 TCCGTATTTAGACAAATCCAAGACAA 58.837 34.615 0.00 0.00 35.88 3.18
4707 8827 7.333423 TCCGTATTTAGACAAATCCAAGACAAG 59.667 37.037 0.00 0.00 35.88 3.16
4708 8828 7.119262 CCGTATTTAGACAAATCCAAGACAAGT 59.881 37.037 0.00 0.00 35.88 3.16
4709 8829 9.146984 CGTATTTAGACAAATCCAAGACAAGTA 57.853 33.333 0.00 0.00 35.88 2.24
4714 8834 7.133891 AGACAAATCCAAGACAAGTAATTCG 57.866 36.000 0.00 0.00 0.00 3.34
4715 8835 6.149474 AGACAAATCCAAGACAAGTAATTCGG 59.851 38.462 0.00 0.00 0.00 4.30
4716 8836 6.001460 ACAAATCCAAGACAAGTAATTCGGA 58.999 36.000 0.00 0.00 0.00 4.55
4717 8837 6.488683 ACAAATCCAAGACAAGTAATTCGGAA 59.511 34.615 0.00 0.00 0.00 4.30
4718 8838 6.496338 AATCCAAGACAAGTAATTCGGAAC 57.504 37.500 0.00 0.00 0.00 3.62
4754 8874 6.492087 AGAGACAGTAATCTAGTTATGGGCTC 59.508 42.308 0.00 0.00 35.33 4.70
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
75 76 6.751157 TGACGTCCAGTTAGAAATTCAACTA 58.249 36.000 14.12 0.00 33.29 2.24
115 116 3.527533 GTCACGTGTGATAATAGGGCAA 58.472 45.455 16.51 0.00 42.18 4.52
118 119 3.812156 TGGTCACGTGTGATAATAGGG 57.188 47.619 16.51 0.00 42.18 3.53
183 3219 0.255890 AAATGTGGGGAGTCGGGATG 59.744 55.000 0.00 0.00 0.00 3.51
211 3247 1.288752 CCGGTGGAATTTTGCGCTT 59.711 52.632 9.73 0.00 0.00 4.68
509 3548 3.363844 GAGTCGAGCACCTGGAGGC 62.364 68.421 0.00 3.59 39.32 4.70
807 3852 1.600916 GCAAGAGACAACGGGGCTT 60.601 57.895 0.00 0.00 0.00 4.35
954 4005 0.953960 GTGGCCCGTCGAACTTTGAT 60.954 55.000 0.00 0.00 0.00 2.57
1049 4100 1.891919 GTCGACCACAGGCAAAGCA 60.892 57.895 3.51 0.00 0.00 3.91
1089 4143 1.314534 TGCTTTCCATCCATGCCACG 61.315 55.000 0.00 0.00 0.00 4.94
1344 4413 9.911980 CAAATTGCAGCAGAGATAATATATACG 57.088 33.333 0.00 0.00 0.00 3.06
1385 4454 9.950680 CATCACCAACAATAATACTTACATTCC 57.049 33.333 0.00 0.00 0.00 3.01
1443 4512 4.955811 TCTCCAACTTGACAGCTCTTTA 57.044 40.909 0.00 0.00 0.00 1.85
1558 4627 1.306141 TCCACTTCCTCATCGGCCT 60.306 57.895 0.00 0.00 0.00 5.19
1559 4628 1.144936 CTCCACTTCCTCATCGGCC 59.855 63.158 0.00 0.00 0.00 6.13
1560 4629 1.522580 GCTCCACTTCCTCATCGGC 60.523 63.158 0.00 0.00 0.00 5.54
1647 4716 2.738521 GCAGTCTTCAGCGCCGAA 60.739 61.111 2.29 4.37 0.00 4.30
1820 4889 3.191162 TGCAGAGCAACAAATCACATACC 59.809 43.478 0.00 0.00 34.76 2.73
1851 4920 9.838339 ACTAAACTCATCTCCCAAAATACATAG 57.162 33.333 0.00 0.00 0.00 2.23
1978 5048 5.667539 TCCAGAGATACTCCAGTTTGAAG 57.332 43.478 0.00 0.00 0.00 3.02
1979 5049 5.485353 ACATCCAGAGATACTCCAGTTTGAA 59.515 40.000 0.00 0.00 0.00 2.69
2147 5846 4.686191 AGAGCATGGGAATCAGAAGTAG 57.314 45.455 0.00 0.00 0.00 2.57
2185 5884 8.026396 ACAAAGGTGTAAGAAGGTAGTAAAGA 57.974 34.615 0.00 0.00 35.72 2.52
2191 5890 7.876068 TGTGATAACAAAGGTGTAAGAAGGTAG 59.124 37.037 0.00 0.00 36.80 3.18
2275 5974 1.725641 TCTGTAGCAAAGCACATCCG 58.274 50.000 0.00 0.00 0.00 4.18
2311 6010 5.705441 GGTGGTTGTATTCTTCACTGAATCA 59.295 40.000 0.00 0.00 37.73 2.57
2325 6024 7.023171 TCAGTATTACTTTGGGTGGTTGTAT 57.977 36.000 0.00 0.00 0.00 2.29
2353 6052 4.023450 TGCGACATACCCTCTACTATTTCG 60.023 45.833 0.00 0.00 0.00 3.46
2374 6073 6.998673 AGTGTATAAGACTAAATGGGGAATGC 59.001 38.462 0.00 0.00 0.00 3.56
2485 6189 4.630644 TGAGAGGAAGAAATGCACTTCT 57.369 40.909 4.20 4.20 42.07 2.85
2661 6377 8.517062 AGCAGCAAAGAGTTTATATTTCTCAT 57.483 30.769 0.00 0.00 0.00 2.90
2974 6700 2.425592 CCCCAGAGACACACGCAA 59.574 61.111 0.00 0.00 0.00 4.85
3012 6738 4.813027 CCACCTAGCGTTCAAGTTAACTA 58.187 43.478 8.92 0.00 0.00 2.24
3166 6912 9.638239 GCATTACCAAACTGAATTATTCTTTGA 57.362 29.630 16.29 3.19 30.62 2.69
3260 7040 6.850752 AGGAAACTGAAAAAGGAAGAACAA 57.149 33.333 0.00 0.00 41.13 2.83
3447 7227 2.162408 GGAACGGAATTTTCTGAGCCAG 59.838 50.000 6.15 0.00 37.03 4.85
3464 7244 4.489306 ACTCTATAACCTTGGCTGGAAC 57.511 45.455 4.24 0.00 0.00 3.62
3645 7594 3.711190 TGATATTGCTTGCTCCAGGTCTA 59.289 43.478 0.00 0.00 0.00 2.59
4062 8146 5.560722 TTGACTCCTGAAACCTGTCATAA 57.439 39.130 0.00 0.00 37.47 1.90
4260 8380 4.022068 TGCTGTTGGATTCTAAGGCTTTTG 60.022 41.667 4.45 0.00 0.00 2.44
4262 8382 3.760684 CTGCTGTTGGATTCTAAGGCTTT 59.239 43.478 4.45 0.00 0.00 3.51
4347 8467 1.151679 GGAGGGAAATAGCAGGGCC 59.848 63.158 0.00 0.00 0.00 5.80
4348 8468 1.435256 TAGGAGGGAAATAGCAGGGC 58.565 55.000 0.00 0.00 0.00 5.19
4359 8479 6.956102 TTGTTACAGGTTTTATAGGAGGGA 57.044 37.500 0.00 0.00 0.00 4.20
4433 8553 9.757227 CTCTTATATTTCTTTACAGAGGGAGTG 57.243 37.037 0.00 0.00 0.00 3.51
4447 8567 9.685828 GAGCGTTTAGATCACTCTTATATTTCT 57.314 33.333 0.00 0.00 34.89 2.52
4448 8568 9.685828 AGAGCGTTTAGATCACTCTTATATTTC 57.314 33.333 0.00 0.00 37.82 2.17
4459 8579 8.819643 AGGAAATATAAGAGCGTTTAGATCAC 57.180 34.615 0.00 0.00 37.82 3.06
4466 8586 8.649973 CTCTGTAAGGAAATATAAGAGCGTTT 57.350 34.615 0.00 0.00 0.00 3.60
4482 8602 8.302515 TGTAACTAAATACTCCCTCTGTAAGG 57.697 38.462 0.00 0.00 45.77 2.69
4483 8603 8.968969 ACTGTAACTAAATACTCCCTCTGTAAG 58.031 37.037 0.00 0.00 0.00 2.34
4484 8604 8.890410 ACTGTAACTAAATACTCCCTCTGTAA 57.110 34.615 0.00 0.00 0.00 2.41
4485 8605 7.281774 CGACTGTAACTAAATACTCCCTCTGTA 59.718 40.741 0.00 0.00 0.00 2.74
4502 8622 0.108138 AGATGGCTGGCGACTGTAAC 60.108 55.000 0.00 0.00 0.00 2.50
4572 8692 2.910482 CAGCAATTCGATGAAAACACGG 59.090 45.455 0.00 0.00 30.38 4.94
4612 8732 8.718734 ACAAATCTAAGACAAGTAATTCGGAAC 58.281 33.333 0.00 0.00 0.00 3.62
4613 8733 8.842358 ACAAATCTAAGACAAGTAATTCGGAA 57.158 30.769 0.00 0.00 0.00 4.30
4614 8734 8.311836 AGACAAATCTAAGACAAGTAATTCGGA 58.688 33.333 0.00 0.00 31.46 4.55
4615 8735 8.480643 AGACAAATCTAAGACAAGTAATTCGG 57.519 34.615 0.00 0.00 31.46 4.30
4622 8742 9.175312 TCGTATCTAGACAAATCTAAGACAAGT 57.825 33.333 0.00 0.00 36.98 3.16
4625 8745 8.622157 CCTTCGTATCTAGACAAATCTAAGACA 58.378 37.037 0.00 0.00 36.98 3.41
4626 8746 8.623030 ACCTTCGTATCTAGACAAATCTAAGAC 58.377 37.037 0.00 0.00 36.98 3.01
4627 8747 8.749026 ACCTTCGTATCTAGACAAATCTAAGA 57.251 34.615 0.00 0.00 36.98 2.10
4643 8763 8.857098 TCATTTTAGTGCTAGATACCTTCGTAT 58.143 33.333 0.00 0.00 37.92 3.06
4644 8764 8.229253 TCATTTTAGTGCTAGATACCTTCGTA 57.771 34.615 0.00 0.00 0.00 3.43
4645 8765 7.108841 TCATTTTAGTGCTAGATACCTTCGT 57.891 36.000 0.00 0.00 0.00 3.85
4646 8766 7.203910 ACTCATTTTAGTGCTAGATACCTTCG 58.796 38.462 0.00 0.00 0.00 3.79
4647 8767 8.417884 AGACTCATTTTAGTGCTAGATACCTTC 58.582 37.037 0.00 0.00 0.00 3.46
4648 8768 8.312669 AGACTCATTTTAGTGCTAGATACCTT 57.687 34.615 0.00 0.00 0.00 3.50
4649 8769 7.906199 AGACTCATTTTAGTGCTAGATACCT 57.094 36.000 0.00 0.00 0.00 3.08
4650 8770 9.069082 TCTAGACTCATTTTAGTGCTAGATACC 57.931 37.037 0.00 0.00 34.69 2.73
4654 8774 9.628500 TGTATCTAGACTCATTTTAGTGCTAGA 57.372 33.333 0.00 0.00 38.76 2.43
4657 8777 8.364142 GGATGTATCTAGACTCATTTTAGTGCT 58.636 37.037 11.25 0.00 0.00 4.40
4658 8778 7.327275 CGGATGTATCTAGACTCATTTTAGTGC 59.673 40.741 11.25 0.00 0.00 4.40
4659 8779 8.353684 ACGGATGTATCTAGACTCATTTTAGTG 58.646 37.037 11.25 3.85 0.00 2.74
4660 8780 8.466617 ACGGATGTATCTAGACTCATTTTAGT 57.533 34.615 11.25 7.70 0.00 2.24
4666 8786 9.961264 TCTAAATACGGATGTATCTAGACTCAT 57.039 33.333 10.15 10.15 40.42 2.90
4674 8794 8.647796 TGGATTTGTCTAAATACGGATGTATCT 58.352 33.333 0.00 0.00 40.42 1.98
4675 8795 8.827177 TGGATTTGTCTAAATACGGATGTATC 57.173 34.615 0.00 0.00 40.42 2.24
4676 8796 9.273016 CTTGGATTTGTCTAAATACGGATGTAT 57.727 33.333 0.00 0.00 43.14 2.29
4677 8797 8.479689 TCTTGGATTTGTCTAAATACGGATGTA 58.520 33.333 0.00 0.00 39.54 2.29
4678 8798 7.280205 GTCTTGGATTTGTCTAAATACGGATGT 59.720 37.037 0.00 0.00 39.54 3.06
4679 8799 7.279981 TGTCTTGGATTTGTCTAAATACGGATG 59.720 37.037 0.00 0.00 39.54 3.51
4680 8800 7.335627 TGTCTTGGATTTGTCTAAATACGGAT 58.664 34.615 0.00 0.00 39.54 4.18
4681 8801 6.703319 TGTCTTGGATTTGTCTAAATACGGA 58.297 36.000 0.00 0.00 39.54 4.69
4682 8802 6.978343 TGTCTTGGATTTGTCTAAATACGG 57.022 37.500 0.00 0.00 39.54 4.02
4683 8803 8.029642 ACTTGTCTTGGATTTGTCTAAATACG 57.970 34.615 0.00 0.00 39.54 3.06
4688 8808 8.717821 CGAATTACTTGTCTTGGATTTGTCTAA 58.282 33.333 0.00 0.00 0.00 2.10
4689 8809 7.333423 CCGAATTACTTGTCTTGGATTTGTCTA 59.667 37.037 0.00 0.00 0.00 2.59
4690 8810 6.149474 CCGAATTACTTGTCTTGGATTTGTCT 59.851 38.462 0.00 0.00 0.00 3.41
4691 8811 6.148811 TCCGAATTACTTGTCTTGGATTTGTC 59.851 38.462 0.00 0.00 0.00 3.18
4692 8812 6.001460 TCCGAATTACTTGTCTTGGATTTGT 58.999 36.000 0.00 0.00 0.00 2.83
4693 8813 6.494893 TCCGAATTACTTGTCTTGGATTTG 57.505 37.500 0.00 0.00 0.00 2.32
4694 8814 6.348213 CGTTCCGAATTACTTGTCTTGGATTT 60.348 38.462 0.00 0.00 0.00 2.17
4695 8815 5.121768 CGTTCCGAATTACTTGTCTTGGATT 59.878 40.000 0.00 0.00 0.00 3.01
4696 8816 4.630069 CGTTCCGAATTACTTGTCTTGGAT 59.370 41.667 0.00 0.00 0.00 3.41
4697 8817 3.991773 CGTTCCGAATTACTTGTCTTGGA 59.008 43.478 0.00 0.00 0.00 3.53
4698 8818 3.124636 CCGTTCCGAATTACTTGTCTTGG 59.875 47.826 0.00 0.00 0.00 3.61
4699 8819 3.991773 TCCGTTCCGAATTACTTGTCTTG 59.008 43.478 0.00 0.00 0.00 3.02
4700 8820 4.243270 CTCCGTTCCGAATTACTTGTCTT 58.757 43.478 0.00 0.00 0.00 3.01
4701 8821 3.368116 CCTCCGTTCCGAATTACTTGTCT 60.368 47.826 0.00 0.00 0.00 3.41
4702 8822 2.928116 CCTCCGTTCCGAATTACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
4703 8823 2.354403 CCCTCCGTTCCGAATTACTTGT 60.354 50.000 0.00 0.00 0.00 3.16
4704 8824 2.093869 TCCCTCCGTTCCGAATTACTTG 60.094 50.000 0.00 0.00 0.00 3.16
4705 8825 2.167900 CTCCCTCCGTTCCGAATTACTT 59.832 50.000 0.00 0.00 0.00 2.24
4706 8826 1.755380 CTCCCTCCGTTCCGAATTACT 59.245 52.381 0.00 0.00 0.00 2.24
4707 8827 1.479730 ACTCCCTCCGTTCCGAATTAC 59.520 52.381 0.00 0.00 0.00 1.89
4708 8828 1.856629 ACTCCCTCCGTTCCGAATTA 58.143 50.000 0.00 0.00 0.00 1.40
4709 8829 1.856629 TACTCCCTCCGTTCCGAATT 58.143 50.000 0.00 0.00 0.00 2.17
4710 8830 1.755380 CTTACTCCCTCCGTTCCGAAT 59.245 52.381 0.00 0.00 0.00 3.34
4711 8831 1.180029 CTTACTCCCTCCGTTCCGAA 58.820 55.000 0.00 0.00 0.00 4.30
4712 8832 0.329261 TCTTACTCCCTCCGTTCCGA 59.671 55.000 0.00 0.00 0.00 4.55
4713 8833 0.739561 CTCTTACTCCCTCCGTTCCG 59.260 60.000 0.00 0.00 0.00 4.30
4714 8834 1.750206 GTCTCTTACTCCCTCCGTTCC 59.250 57.143 0.00 0.00 0.00 3.62
4715 8835 2.424246 CTGTCTCTTACTCCCTCCGTTC 59.576 54.545 0.00 0.00 0.00 3.95
4716 8836 2.225066 ACTGTCTCTTACTCCCTCCGTT 60.225 50.000 0.00 0.00 0.00 4.44
4717 8837 1.355043 ACTGTCTCTTACTCCCTCCGT 59.645 52.381 0.00 0.00 0.00 4.69
4718 8838 2.131776 ACTGTCTCTTACTCCCTCCG 57.868 55.000 0.00 0.00 0.00 4.63
4719 8839 5.451354 AGATTACTGTCTCTTACTCCCTCC 58.549 45.833 0.00 0.00 0.00 4.30
4720 8840 7.284820 ACTAGATTACTGTCTCTTACTCCCTC 58.715 42.308 0.00 0.00 0.00 4.30
4721 8841 7.215743 ACTAGATTACTGTCTCTTACTCCCT 57.784 40.000 0.00 0.00 0.00 4.20
4722 8842 7.885009 AACTAGATTACTGTCTCTTACTCCC 57.115 40.000 0.00 0.00 0.00 4.30
4725 8845 9.357161 CCCATAACTAGATTACTGTCTCTTACT 57.643 37.037 0.00 0.00 0.00 2.24
4726 8846 8.083462 GCCCATAACTAGATTACTGTCTCTTAC 58.917 40.741 0.00 0.00 0.00 2.34
4727 8847 8.005388 AGCCCATAACTAGATTACTGTCTCTTA 58.995 37.037 0.00 0.00 0.00 2.10
4754 8874 7.592885 AATTTTCCTGGTATCATCATCAAGG 57.407 36.000 0.00 0.00 0.00 3.61
4855 8975 8.697507 ATCTGAACCAGAACAGTAAAAAGAAT 57.302 30.769 0.43 0.00 44.04 2.40
4858 8980 8.017946 GCTAATCTGAACCAGAACAGTAAAAAG 58.982 37.037 0.43 0.00 44.04 2.27
4864 8986 4.899352 AGCTAATCTGAACCAGAACAGT 57.101 40.909 0.43 0.00 44.04 3.55


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

AutoCloner maintained by Alex Coulton.