Multiple sequence alignment - TraesCS2B01G309300

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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 TraesCS2B01G309300 chr2B 100.000 3705 0 0 1 3705 442332868 442329164 0.000000e+00 6842.0
1 TraesCS2B01G309300 chr2B 91.743 109 8 1 3131 3238 67548573 67548681 2.310000e-32 150.0
2 TraesCS2B01G309300 chr2B 92.000 100 7 1 3140 3238 550191668 550191569 4.990000e-29 139.0
3 TraesCS2B01G309300 chr2B 96.667 60 2 0 3307 3366 442329485 442329426 2.350000e-17 100.0
4 TraesCS2B01G309300 chr2B 96.667 60 2 0 3384 3443 442329562 442329503 2.350000e-17 100.0
5 TraesCS2B01G309300 chr2A 95.364 2351 92 10 802 3144 504553296 504555637 0.000000e+00 3722.0
6 TraesCS2B01G309300 chr2A 86.597 761 79 13 52 798 504552281 504553032 0.000000e+00 819.0
7 TraesCS2B01G309300 chr2A 95.541 471 11 3 3242 3705 504555634 504556101 0.000000e+00 745.0
8 TraesCS2B01G309300 chr2A 98.333 60 1 0 3384 3443 504555699 504555758 5.060000e-19 106.0
9 TraesCS2B01G309300 chr2A 95.000 60 3 0 3307 3366 504555776 504555835 1.100000e-15 95.3
10 TraesCS2B01G309300 chr2D 95.447 1208 40 7 811 2018 372806185 372804993 0.000000e+00 1912.0
11 TraesCS2B01G309300 chr2D 96.814 1130 32 1 2015 3144 372804734 372803609 0.000000e+00 1884.0
12 TraesCS2B01G309300 chr2D 93.705 826 41 4 1 816 372807901 372807077 0.000000e+00 1227.0
13 TraesCS2B01G309300 chr2D 91.489 470 17 3 3242 3705 372803612 372803160 3.140000e-175 625.0
14 TraesCS2B01G309300 chr2D 95.699 186 8 0 1399 1584 596152359 596152544 2.160000e-77 300.0
15 TraesCS2B01G309300 chr2D 98.148 54 1 0 3385 3438 372803546 372803493 1.100000e-15 95.3
16 TraesCS2B01G309300 chr7D 93.225 369 19 4 1365 1732 417790124 417789761 4.210000e-149 538.0
17 TraesCS2B01G309300 chr5B 95.098 102 4 1 3138 3238 549711106 549711005 3.830000e-35 159.0
18 TraesCS2B01G309300 chr5B 100.000 28 0 0 3490 3517 53662215 53662188 7.000000e-03 52.8
19 TraesCS2B01G309300 chr3B 95.098 102 4 1 3138 3238 702843597 702843496 3.830000e-35 159.0
20 TraesCS2B01G309300 chr3B 94.949 99 4 1 3141 3238 785320733 785320831 1.780000e-33 154.0
21 TraesCS2B01G309300 chr1A 94.949 99 4 1 3141 3238 548414093 548413995 1.780000e-33 154.0
22 TraesCS2B01G309300 chr1A 91.919 99 7 1 3141 3238 577474737 577474639 1.790000e-28 137.0
23 TraesCS2B01G309300 chr6A 93.269 104 5 2 3140 3241 559431736 559431633 6.410000e-33 152.0
24 TraesCS2B01G309300 chr6A 100.000 34 0 0 3487 3520 431145410 431145377 3.090000e-06 63.9
25 TraesCS2B01G309300 chr4A 91.919 99 7 1 3141 3238 563677090 563676992 1.790000e-28 137.0
26 TraesCS2B01G309300 chr4B 86.325 117 10 5 3141 3252 621917 621802 5.020000e-24 122.0
27 TraesCS2B01G309300 chr3A 88.000 100 10 2 3141 3238 90877949 90878048 2.340000e-22 117.0
28 TraesCS2B01G309300 chr7B 97.059 34 1 0 3487 3520 714311665 714311698 1.440000e-04 58.4
29 TraesCS2B01G309300 chr1D 94.737 38 0 1 3484 3519 11775364 11775327 1.440000e-04 58.4
30 TraesCS2B01G309300 chr6D 100.000 29 0 0 3491 3519 35662643 35662615 2.000000e-03 54.7
31 TraesCS2B01G309300 chr3D 92.308 39 1 1 3492 3530 66311979 66311943 2.000000e-03 54.7
32 TraesCS2B01G309300 chr5D 100.000 28 0 0 3487 3514 541578553 541578580 7.000000e-03 52.8


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 TraesCS2B01G309300 chr2B 442329164 442332868 3704 True 2347.333333 6842 97.7780 1 3705 3 chr2B.!!$R2 3704
1 TraesCS2B01G309300 chr2A 504552281 504556101 3820 False 1097.460000 3722 94.1670 52 3705 5 chr2A.!!$F1 3653
2 TraesCS2B01G309300 chr2D 372803160 372807901 4741 True 1148.660000 1912 95.1206 1 3705 5 chr2D.!!$R1 3704

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
520 530 1.029947 CATGAACGCCCCTTGGGTAC 61.030 60.0 4.84 0.0 46.51 3.34 F
1041 2214 0.325765 TATCCGATCCACCACCACCA 60.326 55.0 0.00 0.0 0.00 4.17 F
1689 2870 0.251341 AAACCTGCATTTCCGAGGCT 60.251 50.0 0.00 0.0 0.00 4.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1341 2522 0.252881 AGGGCTGGATCAAGGAGACA 60.253 55.000 0.00 0.00 0.00 3.41 R
2311 3754 1.813513 AATCCGAGGACTGCACAAAG 58.186 50.000 0.00 0.00 0.00 2.77 R
3179 4623 1.004044 AGGCTACTTTGCATGCTGTCT 59.996 47.619 20.33 6.02 34.04 3.41 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
28 29 8.438676 ACCAACAAATGCATACTATCTTCTAC 57.561 34.615 0.00 0.00 0.00 2.59
32 33 9.890629 AACAAATGCATACTATCTTCTACAGAA 57.109 29.630 0.00 0.00 34.16 3.02
37 38 7.436933 TGCATACTATCTTCTACAGAACATGG 58.563 38.462 0.00 0.00 34.16 3.66
92 93 6.524734 AGTTGTGAGATCAATGTGTGTAAGA 58.475 36.000 0.00 0.00 0.00 2.10
203 205 2.548057 CTCGCTCCAACTTACTTTGCAA 59.452 45.455 0.00 0.00 0.00 4.08
217 219 9.180678 ACTTACTTTGCAATGAAGTATTTTTCG 57.819 29.630 18.35 3.45 38.84 3.46
333 343 6.775142 TGGTTGAGGAATTTAAGTGACAATCA 59.225 34.615 0.00 0.00 0.00 2.57
497 507 6.264832 TGAAATGTTCTGTTGTGTTTGCTAG 58.735 36.000 0.00 0.00 0.00 3.42
520 530 1.029947 CATGAACGCCCCTTGGGTAC 61.030 60.000 4.84 0.00 46.51 3.34
522 532 1.377612 GAACGCCCCTTGGGTACTT 59.622 57.895 4.84 0.00 46.51 2.24
575 585 7.669304 TGTAACTCAAGGAAAATCCAATCATGA 59.331 33.333 0.00 0.00 39.61 3.07
582 592 8.715088 CAAGGAAAATCCAATCATGAGTTTTTC 58.285 33.333 17.22 17.22 39.61 2.29
666 679 5.822519 TCTTCCATGGATTATGTGCTACAAC 59.177 40.000 17.06 0.00 34.87 3.32
667 680 5.109500 TCCATGGATTATGTGCTACAACA 57.891 39.130 11.44 0.00 34.87 3.33
697 710 9.627395 TCGTCTCACAAAACTCAAATTTTAAAA 57.373 25.926 2.51 2.51 30.57 1.52
740 754 6.179756 TGTGGATGTTTACAAGATATGTGCT 58.820 36.000 0.00 0.00 43.77 4.40
997 2170 2.914097 GGTGCCACCAAGCAAGCT 60.914 61.111 9.55 0.00 46.19 3.74
998 2171 1.603455 GGTGCCACCAAGCAAGCTA 60.603 57.895 9.55 0.00 46.19 3.32
1039 2212 2.930826 AATATCCGATCCACCACCAC 57.069 50.000 0.00 0.00 0.00 4.16
1040 2213 1.056660 ATATCCGATCCACCACCACC 58.943 55.000 0.00 0.00 0.00 4.61
1041 2214 0.325765 TATCCGATCCACCACCACCA 60.326 55.000 0.00 0.00 0.00 4.17
1083 2264 0.897863 AACACCTGCGCTCTCTCTCT 60.898 55.000 9.73 0.00 0.00 3.10
1209 2390 2.683152 GCTACCGGAAGTACTCCTCTCA 60.683 54.545 9.46 0.00 42.85 3.27
1270 2451 3.986006 TCGTCCTTTCCACGCGCT 61.986 61.111 5.73 0.00 37.18 5.92
1345 2526 3.049674 CCGCACGTGGCAATGTCT 61.050 61.111 18.88 0.00 45.17 3.41
1349 2530 1.237285 GCACGTGGCAATGTCTCCTT 61.237 55.000 18.88 0.00 43.97 3.36
1354 2535 2.019984 GTGGCAATGTCTCCTTGATCC 58.980 52.381 0.00 0.00 0.00 3.36
1663 2844 2.681778 CCCTCACCGAGCTCACCT 60.682 66.667 15.40 0.00 0.00 4.00
1689 2870 0.251341 AAACCTGCATTTCCGAGGCT 60.251 50.000 0.00 0.00 0.00 4.58
1692 2873 1.748122 CTGCATTTCCGAGGCTGCT 60.748 57.895 0.00 0.00 35.66 4.24
1900 3081 2.368439 GTCTGAATGCAGCCATTACCA 58.632 47.619 0.00 0.00 41.60 3.25
2005 3186 6.468000 GCAGGTATTTTGCGTATTTCTGTTAC 59.532 38.462 0.00 0.00 0.00 2.50
2014 3195 3.676172 CGTATTTCTGTTACCGTCAGCAA 59.324 43.478 0.00 0.00 33.48 3.91
2022 3203 4.242475 TGTTACCGTCAGCAAGTATCTTG 58.758 43.478 5.28 5.28 0.00 3.02
2024 3205 3.238108 ACCGTCAGCAAGTATCTTGAG 57.762 47.619 12.77 5.22 0.00 3.02
2049 3492 3.808728 AGCAAGTTCAGCAAAGTGACTA 58.191 40.909 0.00 0.00 0.00 2.59
2237 3680 5.947663 TCCAGGTAATTTCCAGAACTTGAA 58.052 37.500 3.73 0.00 0.00 2.69
2311 3754 3.937706 CAGACCTTCCACTGATTCATCAC 59.062 47.826 0.00 0.00 36.38 3.06
2376 3819 3.296854 ACACCACTGTCTCTGACTACAA 58.703 45.455 0.00 0.00 33.15 2.41
2530 3973 2.969628 GGATTCAGTCCGAGATGTGT 57.030 50.000 0.00 0.00 37.23 3.72
2643 4086 0.307760 CAACGCAAGGACTTCACCAC 59.692 55.000 0.00 0.00 46.39 4.16
2665 4108 4.125703 CAGAAGGTGTGAATGCTCTATCC 58.874 47.826 0.00 0.00 0.00 2.59
2790 4233 3.244044 GCTGGCCTTTTGGTTATGTTCAA 60.244 43.478 3.32 0.00 42.99 2.69
2801 4244 8.430801 TTTGGTTATGTTCAATTGAGTTTTGG 57.569 30.769 8.41 0.00 0.00 3.28
2825 4268 6.344500 GCTCTAGATTCCAGACTCATTTTGA 58.656 40.000 0.00 0.00 0.00 2.69
2879 4322 9.430399 AGTTTACTATTAATGAGGTGGCTAGTA 57.570 33.333 0.00 0.00 0.00 1.82
2977 4421 1.264020 TGACTGTGAAGATTGTTGCGC 59.736 47.619 0.00 0.00 0.00 6.09
2981 4425 0.725784 GTGAAGATTGTTGCGCGTGG 60.726 55.000 8.43 0.00 0.00 4.94
3064 4508 0.108186 GGCTGGCCTTTTGGTTATGC 60.108 55.000 3.32 0.00 42.99 3.14
3073 4517 4.798574 CCTTTTGGTTATGCTCAGTTGAC 58.201 43.478 0.00 0.00 34.07 3.18
3144 4588 7.421530 TTCATGTTGCAGAAGTTTACTACTC 57.578 36.000 0.00 0.00 35.54 2.59
3145 4589 5.932303 TCATGTTGCAGAAGTTTACTACTCC 59.068 40.000 0.00 0.00 35.54 3.85
3146 4590 4.638304 TGTTGCAGAAGTTTACTACTCCC 58.362 43.478 0.00 0.00 35.54 4.30
3147 4591 4.347000 TGTTGCAGAAGTTTACTACTCCCT 59.653 41.667 0.00 0.00 35.54 4.20
3148 4592 4.803098 TGCAGAAGTTTACTACTCCCTC 57.197 45.455 0.00 0.00 35.54 4.30
3149 4593 4.417437 TGCAGAAGTTTACTACTCCCTCT 58.583 43.478 0.00 0.00 35.54 3.69
3150 4594 4.220821 TGCAGAAGTTTACTACTCCCTCTG 59.779 45.833 0.00 0.00 40.14 3.35
3151 4595 4.221041 GCAGAAGTTTACTACTCCCTCTGT 59.779 45.833 8.15 0.00 39.69 3.41
3152 4596 5.279556 GCAGAAGTTTACTACTCCCTCTGTT 60.280 44.000 8.15 0.00 39.69 3.16
3153 4597 6.391537 CAGAAGTTTACTACTCCCTCTGTTC 58.608 44.000 0.00 0.00 35.74 3.18
3154 4598 6.015350 CAGAAGTTTACTACTCCCTCTGTTCA 60.015 42.308 0.00 0.00 35.74 3.18
3155 4599 5.725325 AGTTTACTACTCCCTCTGTTCAC 57.275 43.478 0.00 0.00 28.23 3.18
3156 4600 5.145564 AGTTTACTACTCCCTCTGTTCACA 58.854 41.667 0.00 0.00 28.23 3.58
3157 4601 5.601313 AGTTTACTACTCCCTCTGTTCACAA 59.399 40.000 0.00 0.00 28.23 3.33
3158 4602 5.723672 TTACTACTCCCTCTGTTCACAAG 57.276 43.478 0.00 0.00 0.00 3.16
3159 4603 3.845860 ACTACTCCCTCTGTTCACAAGA 58.154 45.455 0.00 0.00 0.00 3.02
3160 4604 4.421131 ACTACTCCCTCTGTTCACAAGAT 58.579 43.478 0.00 0.00 0.00 2.40
3161 4605 5.580998 ACTACTCCCTCTGTTCACAAGATA 58.419 41.667 0.00 0.00 0.00 1.98
3162 4606 6.017192 ACTACTCCCTCTGTTCACAAGATAA 58.983 40.000 0.00 0.00 0.00 1.75
3163 4607 5.413309 ACTCCCTCTGTTCACAAGATAAG 57.587 43.478 0.00 0.00 0.00 1.73
3164 4608 4.223923 ACTCCCTCTGTTCACAAGATAAGG 59.776 45.833 0.00 0.00 0.00 2.69
3165 4609 3.055094 TCCCTCTGTTCACAAGATAAGGC 60.055 47.826 0.00 0.00 0.00 4.35
3166 4610 2.932614 CCTCTGTTCACAAGATAAGGCG 59.067 50.000 0.00 0.00 0.00 5.52
3167 4611 2.346803 TCTGTTCACAAGATAAGGCGC 58.653 47.619 0.00 0.00 0.00 6.53
3168 4612 2.028112 TCTGTTCACAAGATAAGGCGCT 60.028 45.455 7.64 0.00 0.00 5.92
3169 4613 2.076100 TGTTCACAAGATAAGGCGCTG 58.924 47.619 7.64 0.00 0.00 5.18
3170 4614 2.289382 TGTTCACAAGATAAGGCGCTGA 60.289 45.455 7.64 0.00 0.00 4.26
3171 4615 2.742053 GTTCACAAGATAAGGCGCTGAA 59.258 45.455 7.64 2.75 0.00 3.02
3172 4616 2.621338 TCACAAGATAAGGCGCTGAAG 58.379 47.619 7.64 0.00 0.00 3.02
3173 4617 2.233676 TCACAAGATAAGGCGCTGAAGA 59.766 45.455 7.64 0.00 0.00 2.87
3174 4618 3.002791 CACAAGATAAGGCGCTGAAGAA 58.997 45.455 7.64 0.00 0.00 2.52
3175 4619 3.624861 CACAAGATAAGGCGCTGAAGAAT 59.375 43.478 7.64 0.00 0.00 2.40
3176 4620 4.095483 CACAAGATAAGGCGCTGAAGAATT 59.905 41.667 7.64 0.00 0.00 2.17
3177 4621 4.702131 ACAAGATAAGGCGCTGAAGAATTT 59.298 37.500 7.64 0.00 0.00 1.82
3178 4622 5.163713 ACAAGATAAGGCGCTGAAGAATTTC 60.164 40.000 7.64 0.00 0.00 2.17
3179 4623 4.517285 AGATAAGGCGCTGAAGAATTTCA 58.483 39.130 7.64 0.00 40.92 2.69
3189 4633 4.430137 TGAAGAATTTCAGACAGCATGC 57.570 40.909 10.51 10.51 37.84 4.06
3190 4634 3.822167 TGAAGAATTTCAGACAGCATGCA 59.178 39.130 21.98 0.00 37.84 3.96
3191 4635 4.278919 TGAAGAATTTCAGACAGCATGCAA 59.721 37.500 21.98 3.36 37.84 4.08
3192 4636 4.859304 AGAATTTCAGACAGCATGCAAA 57.141 36.364 21.98 10.74 42.53 3.68
3193 4637 4.806330 AGAATTTCAGACAGCATGCAAAG 58.194 39.130 21.98 11.80 42.53 2.77
3194 4638 4.280174 AGAATTTCAGACAGCATGCAAAGT 59.720 37.500 21.98 15.18 42.53 2.66
3195 4639 5.474532 AGAATTTCAGACAGCATGCAAAGTA 59.525 36.000 21.98 0.33 42.53 2.24
3196 4640 4.754372 TTTCAGACAGCATGCAAAGTAG 57.246 40.909 21.98 11.10 42.53 2.57
3197 4641 2.079158 TCAGACAGCATGCAAAGTAGC 58.921 47.619 21.98 4.68 42.53 3.58
3198 4642 1.131883 CAGACAGCATGCAAAGTAGCC 59.868 52.381 21.98 3.99 42.53 3.93
3199 4643 1.004044 AGACAGCATGCAAAGTAGCCT 59.996 47.619 21.98 6.19 42.53 4.58
3200 4644 2.237143 AGACAGCATGCAAAGTAGCCTA 59.763 45.455 21.98 0.00 42.53 3.93
3201 4645 3.118112 AGACAGCATGCAAAGTAGCCTAT 60.118 43.478 21.98 0.00 42.53 2.57
3202 4646 3.624777 ACAGCATGCAAAGTAGCCTATT 58.375 40.909 21.98 0.00 42.53 1.73
3203 4647 4.019174 ACAGCATGCAAAGTAGCCTATTT 58.981 39.130 21.98 0.00 42.53 1.40
3204 4648 4.463891 ACAGCATGCAAAGTAGCCTATTTT 59.536 37.500 21.98 0.00 42.53 1.82
3205 4649 5.039333 CAGCATGCAAAGTAGCCTATTTTC 58.961 41.667 21.98 0.00 0.00 2.29
3206 4650 4.706476 AGCATGCAAAGTAGCCTATTTTCA 59.294 37.500 21.98 0.00 0.00 2.69
3207 4651 5.039333 GCATGCAAAGTAGCCTATTTTCAG 58.961 41.667 14.21 0.00 0.00 3.02
3208 4652 5.393461 GCATGCAAAGTAGCCTATTTTCAGT 60.393 40.000 14.21 0.00 0.00 3.41
3209 4653 6.624423 CATGCAAAGTAGCCTATTTTCAGTT 58.376 36.000 0.00 0.00 0.00 3.16
3210 4654 6.012658 TGCAAAGTAGCCTATTTTCAGTTG 57.987 37.500 0.00 0.00 0.00 3.16
3211 4655 5.534654 TGCAAAGTAGCCTATTTTCAGTTGT 59.465 36.000 0.00 0.00 0.00 3.32
3212 4656 6.086871 GCAAAGTAGCCTATTTTCAGTTGTC 58.913 40.000 0.00 0.00 0.00 3.18
3213 4657 6.072452 GCAAAGTAGCCTATTTTCAGTTGTCT 60.072 38.462 0.00 0.00 0.00 3.41
3214 4658 7.301054 CAAAGTAGCCTATTTTCAGTTGTCTG 58.699 38.462 0.00 0.00 42.54 3.51
3228 4672 7.857734 TCAGTTGTCTGAAATGACTTACAAA 57.142 32.000 0.00 0.00 46.17 2.83
3229 4673 8.275015 TCAGTTGTCTGAAATGACTTACAAAA 57.725 30.769 0.00 0.00 46.17 2.44
3230 4674 8.397906 TCAGTTGTCTGAAATGACTTACAAAAG 58.602 33.333 0.00 0.00 46.17 2.27
3231 4675 8.184192 CAGTTGTCTGAAATGACTTACAAAAGT 58.816 33.333 0.00 0.00 44.91 2.66
3232 4676 8.184192 AGTTGTCTGAAATGACTTACAAAAGTG 58.816 33.333 0.00 0.00 46.09 3.16
3233 4677 7.857734 TGTCTGAAATGACTTACAAAAGTGA 57.142 32.000 0.00 0.00 46.09 3.41
3234 4678 8.275015 TGTCTGAAATGACTTACAAAAGTGAA 57.725 30.769 0.00 0.00 46.09 3.18
3235 4679 8.181573 TGTCTGAAATGACTTACAAAAGTGAAC 58.818 33.333 0.00 0.00 46.09 3.18
3236 4680 7.373441 GTCTGAAATGACTTACAAAAGTGAACG 59.627 37.037 0.00 0.00 46.09 3.95
3237 4681 6.491394 TGAAATGACTTACAAAAGTGAACGG 58.509 36.000 0.00 0.00 46.09 4.44
3238 4682 5.432885 AATGACTTACAAAAGTGAACGGG 57.567 39.130 0.00 0.00 46.09 5.28
3239 4683 4.139859 TGACTTACAAAAGTGAACGGGA 57.860 40.909 0.00 0.00 46.09 5.14
3240 4684 4.124238 TGACTTACAAAAGTGAACGGGAG 58.876 43.478 0.00 0.00 46.09 4.30
3241 4685 4.124970 GACTTACAAAAGTGAACGGGAGT 58.875 43.478 0.00 0.00 46.09 3.85
3242 4686 5.163426 TGACTTACAAAAGTGAACGGGAGTA 60.163 40.000 0.00 0.00 46.09 2.59
3243 4687 5.052481 ACTTACAAAAGTGAACGGGAGTAC 58.948 41.667 0.00 0.00 44.40 2.73
3244 4688 3.832615 ACAAAAGTGAACGGGAGTACT 57.167 42.857 0.00 0.00 46.69 2.73
3249 4693 5.479124 AAAGTGAACGGGAGTACTTATGT 57.521 39.130 0.00 0.00 46.69 2.29
3250 4694 5.479124 AAGTGAACGGGAGTACTTATGTT 57.521 39.130 0.00 1.94 46.69 2.71
3324 4768 7.676004 TGTGGAGTTGTAGTCATTGATTTAGA 58.324 34.615 0.00 0.00 0.00 2.10
3549 4994 6.607735 ATTTTTGTGCTTTCCTTGTCATTG 57.392 33.333 0.00 0.00 0.00 2.82
3649 5100 5.635120 AGCATCTCCTTTTGGTTTAGTTCT 58.365 37.500 0.00 0.00 41.38 3.01
3700 5151 6.901081 TGTACTGTTATCATCCATCGATCT 57.099 37.500 0.00 0.00 0.00 2.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 8.046708 TGTAGAAGATAGTATGCATTTGTTGGT 58.953 33.333 3.54 0.00 0.00 3.67
28 29 4.019174 ACCTTTTAGATGCCCATGTTCTG 58.981 43.478 0.00 0.00 0.00 3.02
32 33 4.705023 GTGTAACCTTTTAGATGCCCATGT 59.295 41.667 0.00 0.00 0.00 3.21
37 38 5.414454 TGACATGTGTAACCTTTTAGATGCC 59.586 40.000 1.15 0.00 34.36 4.40
92 93 6.127366 CCCATGTGGCACTTATTTATCTTTGT 60.127 38.462 19.83 0.00 0.00 2.83
333 343 9.300681 TCAACTCAGAGATCCAACAAATTAAAT 57.699 29.630 3.79 0.00 0.00 1.40
497 507 1.595093 CCAAGGGGCGTTCATGTTCC 61.595 60.000 0.00 0.00 0.00 3.62
575 585 5.940192 TCATAACATGTCGCAGAAAAACT 57.060 34.783 0.00 0.00 39.69 2.66
582 592 3.879295 AGGGATTTCATAACATGTCGCAG 59.121 43.478 0.00 0.00 0.00 5.18
631 641 8.689061 CATAATCCATGGAAGAAGATGTTTTCA 58.311 33.333 20.67 0.00 0.00 2.69
642 655 5.628797 TGTAGCACATAATCCATGGAAGA 57.371 39.130 20.67 10.15 39.13 2.87
667 680 7.148239 AAAATTTGAGTTTTGTGAGACGAGAGT 60.148 33.333 0.00 0.00 37.14 3.24
955 2127 5.819991 TGCTCCCTTCTCATAAAGTTCAAT 58.180 37.500 0.00 0.00 0.00 2.57
960 2132 3.525199 ACCATGCTCCCTTCTCATAAAGT 59.475 43.478 0.00 0.00 0.00 2.66
989 2162 6.439636 TTCCATAGTCCATATAGCTTGCTT 57.560 37.500 0.00 0.00 0.00 3.91
991 2164 4.633565 GCTTCCATAGTCCATATAGCTTGC 59.366 45.833 0.00 0.00 0.00 4.01
992 2165 5.641209 GTGCTTCCATAGTCCATATAGCTTG 59.359 44.000 0.00 0.00 0.00 4.01
993 2166 5.280215 GGTGCTTCCATAGTCCATATAGCTT 60.280 44.000 0.00 0.00 35.97 3.74
994 2167 4.223923 GGTGCTTCCATAGTCCATATAGCT 59.776 45.833 0.00 0.00 35.97 3.32
995 2168 4.020218 TGGTGCTTCCATAGTCCATATAGC 60.020 45.833 0.00 0.00 41.93 2.97
996 2169 5.745312 TGGTGCTTCCATAGTCCATATAG 57.255 43.478 0.00 0.00 41.93 1.31
997 2170 6.508030 TTTGGTGCTTCCATAGTCCATATA 57.492 37.500 2.36 0.00 46.60 0.86
998 2171 5.387113 TTTGGTGCTTCCATAGTCCATAT 57.613 39.130 2.36 0.00 46.60 1.78
1075 2256 7.733773 TTTTAGAGAGAGAGAGAGAGAGAGA 57.266 40.000 0.00 0.00 0.00 3.10
1083 2264 5.011982 TGGGGTTTTTAGAGAGAGAGAGA 57.988 43.478 0.00 0.00 0.00 3.10
1209 2390 1.456705 GAGGCGGGAGAGGATGTCT 60.457 63.158 0.00 0.00 38.71 3.41
1335 2516 1.634973 TGGATCAAGGAGACATTGCCA 59.365 47.619 0.00 0.00 0.00 4.92
1341 2522 0.252881 AGGGCTGGATCAAGGAGACA 60.253 55.000 0.00 0.00 0.00 3.41
1601 2782 4.436998 CGTCGGAGAGGTGGCACC 62.437 72.222 29.32 29.32 36.95 5.01
1663 2844 1.611491 GGAAATGCAGGTTTCCGACAA 59.389 47.619 14.46 0.00 45.37 3.18
1908 3089 2.953821 GCAGTAAGCTTTGGCGCA 59.046 55.556 10.83 0.00 44.37 6.09
2005 3186 3.238108 ACTCAAGATACTTGCTGACGG 57.762 47.619 6.62 0.00 0.00 4.79
2014 3195 6.627065 GCTGAACTTGCTCTACTCAAGATACT 60.627 42.308 9.40 0.00 42.52 2.12
2022 3203 4.061596 ACTTTGCTGAACTTGCTCTACTC 58.938 43.478 0.00 0.00 0.00 2.59
2024 3205 3.809832 TCACTTTGCTGAACTTGCTCTAC 59.190 43.478 0.00 0.00 0.00 2.59
2049 3492 4.576463 GTGTATGAGCGAAAAATCCCATCT 59.424 41.667 0.00 0.00 0.00 2.90
2311 3754 1.813513 AATCCGAGGACTGCACAAAG 58.186 50.000 0.00 0.00 0.00 2.77
2376 3819 1.837439 TGATGGGATAACGCTTCTGGT 59.163 47.619 4.96 0.00 35.35 4.00
2530 3973 2.548904 CGTAACCCATTTTGGAACGTCA 59.451 45.455 0.00 0.00 40.96 4.35
2643 4086 4.125703 GGATAGAGCATTCACACCTTCTG 58.874 47.826 0.00 0.00 0.00 3.02
2665 4108 2.358247 CCACCGTCAAAGGGGTCG 60.358 66.667 0.00 0.00 33.23 4.79
2790 4233 5.819991 TGGAATCTAGAGCCAAAACTCAAT 58.180 37.500 13.22 0.00 39.26 2.57
2801 4244 6.257630 GTCAAAATGAGTCTGGAATCTAGAGC 59.742 42.308 0.00 0.00 0.00 4.09
2825 4268 5.536916 TCAACATGAAACCTTAAATTCCGGT 59.463 36.000 0.00 0.00 0.00 5.28
3064 4508 6.757897 ATCTAGAGTCTGAAGTCAACTGAG 57.242 41.667 1.86 0.00 0.00 3.35
3073 4517 9.996554 TCATAGTCTAGAATCTAGAGTCTGAAG 57.003 37.037 27.07 19.84 36.34 3.02
3144 4588 3.274288 GCCTTATCTTGTGAACAGAGGG 58.726 50.000 0.00 0.00 0.00 4.30
3145 4589 2.932614 CGCCTTATCTTGTGAACAGAGG 59.067 50.000 0.00 0.00 0.00 3.69
3146 4590 2.349886 GCGCCTTATCTTGTGAACAGAG 59.650 50.000 0.00 0.00 0.00 3.35
3147 4591 2.028112 AGCGCCTTATCTTGTGAACAGA 60.028 45.455 2.29 0.00 0.00 3.41
3148 4592 2.094894 CAGCGCCTTATCTTGTGAACAG 59.905 50.000 2.29 0.00 0.00 3.16
3149 4593 2.076100 CAGCGCCTTATCTTGTGAACA 58.924 47.619 2.29 0.00 0.00 3.18
3150 4594 2.346803 TCAGCGCCTTATCTTGTGAAC 58.653 47.619 2.29 0.00 0.00 3.18
3151 4595 2.760634 TCAGCGCCTTATCTTGTGAA 57.239 45.000 2.29 0.00 0.00 3.18
3152 4596 2.233676 TCTTCAGCGCCTTATCTTGTGA 59.766 45.455 2.29 0.00 0.00 3.58
3153 4597 2.621338 TCTTCAGCGCCTTATCTTGTG 58.379 47.619 2.29 0.00 0.00 3.33
3154 4598 3.334583 TTCTTCAGCGCCTTATCTTGT 57.665 42.857 2.29 0.00 0.00 3.16
3155 4599 4.889832 AATTCTTCAGCGCCTTATCTTG 57.110 40.909 2.29 0.00 0.00 3.02
3156 4600 4.943705 TGAAATTCTTCAGCGCCTTATCTT 59.056 37.500 2.29 0.00 36.62 2.40
3157 4601 4.517285 TGAAATTCTTCAGCGCCTTATCT 58.483 39.130 2.29 0.00 36.62 1.98
3158 4602 4.882671 TGAAATTCTTCAGCGCCTTATC 57.117 40.909 2.29 0.00 36.62 1.75
3168 4612 3.822167 TGCATGCTGTCTGAAATTCTTCA 59.178 39.130 20.33 0.00 39.30 3.02
3169 4613 4.430137 TGCATGCTGTCTGAAATTCTTC 57.570 40.909 20.33 0.00 0.00 2.87
3170 4614 4.859304 TTGCATGCTGTCTGAAATTCTT 57.141 36.364 20.33 0.00 0.00 2.52
3171 4615 4.280174 ACTTTGCATGCTGTCTGAAATTCT 59.720 37.500 20.33 0.00 0.00 2.40
3172 4616 4.553323 ACTTTGCATGCTGTCTGAAATTC 58.447 39.130 20.33 0.00 0.00 2.17
3173 4617 4.595762 ACTTTGCATGCTGTCTGAAATT 57.404 36.364 20.33 1.17 0.00 1.82
3174 4618 4.380233 GCTACTTTGCATGCTGTCTGAAAT 60.380 41.667 20.33 3.36 0.00 2.17
3175 4619 3.058016 GCTACTTTGCATGCTGTCTGAAA 60.058 43.478 20.33 8.76 0.00 2.69
3176 4620 2.485426 GCTACTTTGCATGCTGTCTGAA 59.515 45.455 20.33 0.00 0.00 3.02
3177 4621 2.079158 GCTACTTTGCATGCTGTCTGA 58.921 47.619 20.33 0.00 0.00 3.27
3178 4622 1.131883 GGCTACTTTGCATGCTGTCTG 59.868 52.381 20.33 11.82 34.04 3.51
3179 4623 1.004044 AGGCTACTTTGCATGCTGTCT 59.996 47.619 20.33 6.02 34.04 3.41
3180 4624 1.457346 AGGCTACTTTGCATGCTGTC 58.543 50.000 20.33 3.79 34.04 3.51
3181 4625 2.787473 TAGGCTACTTTGCATGCTGT 57.213 45.000 20.33 16.49 34.04 4.40
3182 4626 4.644103 AAATAGGCTACTTTGCATGCTG 57.356 40.909 20.33 11.45 34.04 4.41
3183 4627 4.706476 TGAAAATAGGCTACTTTGCATGCT 59.294 37.500 20.33 0.00 34.04 3.79
3184 4628 4.997565 TGAAAATAGGCTACTTTGCATGC 58.002 39.130 11.82 11.82 34.04 4.06
3185 4629 6.199937 ACTGAAAATAGGCTACTTTGCATG 57.800 37.500 5.59 5.83 34.04 4.06
3186 4630 6.209391 ACAACTGAAAATAGGCTACTTTGCAT 59.791 34.615 5.59 0.00 34.04 3.96
3187 4631 5.534654 ACAACTGAAAATAGGCTACTTTGCA 59.465 36.000 5.59 7.59 34.04 4.08
3188 4632 6.013842 ACAACTGAAAATAGGCTACTTTGC 57.986 37.500 5.59 3.58 0.00 3.68
3189 4633 7.301054 CAGACAACTGAAAATAGGCTACTTTG 58.699 38.462 5.59 0.00 46.03 2.77
3190 4634 7.440523 CAGACAACTGAAAATAGGCTACTTT 57.559 36.000 0.00 0.00 46.03 2.66
3205 4649 8.184192 ACTTTTGTAAGTCATTTCAGACAACTG 58.816 33.333 0.00 0.00 40.60 3.16
3206 4650 8.184192 CACTTTTGTAAGTCATTTCAGACAACT 58.816 33.333 0.00 0.00 42.67 3.16
3207 4651 8.181573 TCACTTTTGTAAGTCATTTCAGACAAC 58.818 33.333 0.00 0.00 42.67 3.32
3208 4652 8.275015 TCACTTTTGTAAGTCATTTCAGACAA 57.725 30.769 0.00 0.00 42.67 3.18
3209 4653 7.857734 TCACTTTTGTAAGTCATTTCAGACA 57.142 32.000 0.00 0.00 42.67 3.41
3210 4654 7.373441 CGTTCACTTTTGTAAGTCATTTCAGAC 59.627 37.037 0.00 0.00 42.67 3.51
3211 4655 7.406553 CGTTCACTTTTGTAAGTCATTTCAGA 58.593 34.615 0.00 0.00 42.67 3.27
3212 4656 6.632834 CCGTTCACTTTTGTAAGTCATTTCAG 59.367 38.462 0.00 0.00 42.67 3.02
3213 4657 6.459024 CCCGTTCACTTTTGTAAGTCATTTCA 60.459 38.462 0.00 0.00 42.67 2.69
3214 4658 5.912955 CCCGTTCACTTTTGTAAGTCATTTC 59.087 40.000 0.00 0.00 42.67 2.17
3215 4659 5.591067 TCCCGTTCACTTTTGTAAGTCATTT 59.409 36.000 0.00 0.00 42.67 2.32
3216 4660 5.127491 TCCCGTTCACTTTTGTAAGTCATT 58.873 37.500 0.00 0.00 42.67 2.57
3217 4661 4.710324 TCCCGTTCACTTTTGTAAGTCAT 58.290 39.130 0.00 0.00 42.67 3.06
3218 4662 4.124238 CTCCCGTTCACTTTTGTAAGTCA 58.876 43.478 0.00 0.00 42.67 3.41
3219 4663 4.124970 ACTCCCGTTCACTTTTGTAAGTC 58.875 43.478 0.00 0.00 42.67 3.01
3220 4664 4.146745 ACTCCCGTTCACTTTTGTAAGT 57.853 40.909 0.00 0.00 45.40 2.24
3221 4665 5.295152 AGTACTCCCGTTCACTTTTGTAAG 58.705 41.667 0.00 0.00 37.40 2.34
3222 4666 5.280654 AGTACTCCCGTTCACTTTTGTAA 57.719 39.130 0.00 0.00 0.00 2.41
3223 4667 4.942761 AGTACTCCCGTTCACTTTTGTA 57.057 40.909 0.00 0.00 0.00 2.41
3224 4668 3.832615 AGTACTCCCGTTCACTTTTGT 57.167 42.857 0.00 0.00 0.00 2.83
3225 4669 5.699458 ACATAAGTACTCCCGTTCACTTTTG 59.301 40.000 0.00 0.00 36.58 2.44
3226 4670 5.861727 ACATAAGTACTCCCGTTCACTTTT 58.138 37.500 0.00 0.00 33.47 2.27
3227 4671 5.479124 ACATAAGTACTCCCGTTCACTTT 57.521 39.130 0.00 0.00 33.47 2.66
3228 4672 5.221581 ACAACATAAGTACTCCCGTTCACTT 60.222 40.000 0.00 0.00 35.50 3.16
3229 4673 4.282703 ACAACATAAGTACTCCCGTTCACT 59.717 41.667 0.00 0.00 0.00 3.41
3230 4674 4.387862 CACAACATAAGTACTCCCGTTCAC 59.612 45.833 0.00 0.00 0.00 3.18
3231 4675 4.281435 TCACAACATAAGTACTCCCGTTCA 59.719 41.667 0.00 0.00 0.00 3.18
3232 4676 4.624452 GTCACAACATAAGTACTCCCGTTC 59.376 45.833 0.00 0.00 0.00 3.95
3233 4677 4.282703 AGTCACAACATAAGTACTCCCGTT 59.717 41.667 0.00 0.00 0.00 4.44
3234 4678 3.830755 AGTCACAACATAAGTACTCCCGT 59.169 43.478 0.00 0.00 0.00 5.28
3235 4679 4.451629 AGTCACAACATAAGTACTCCCG 57.548 45.455 0.00 0.00 0.00 5.14
3236 4680 6.527057 ACTAGTCACAACATAAGTACTCCC 57.473 41.667 0.00 0.00 0.00 4.30
3237 4681 7.272948 CGAAACTAGTCACAACATAAGTACTCC 59.727 40.741 0.00 0.00 0.00 3.85
3238 4682 7.201333 GCGAAACTAGTCACAACATAAGTACTC 60.201 40.741 0.00 0.00 0.00 2.59
3239 4683 6.585322 GCGAAACTAGTCACAACATAAGTACT 59.415 38.462 0.00 0.00 0.00 2.73
3240 4684 6.585322 AGCGAAACTAGTCACAACATAAGTAC 59.415 38.462 0.00 0.00 0.00 2.73
3241 4685 6.684686 AGCGAAACTAGTCACAACATAAGTA 58.315 36.000 0.00 0.00 0.00 2.24
3242 4686 5.539048 AGCGAAACTAGTCACAACATAAGT 58.461 37.500 0.00 0.00 0.00 2.24
3243 4687 6.073765 ACAAGCGAAACTAGTCACAACATAAG 60.074 38.462 0.00 0.00 0.00 1.73
3244 4688 5.756347 ACAAGCGAAACTAGTCACAACATAA 59.244 36.000 0.00 0.00 0.00 1.90
3249 4693 4.054780 AGACAAGCGAAACTAGTCACAA 57.945 40.909 0.00 0.00 0.00 3.33
3250 4694 3.728076 AGACAAGCGAAACTAGTCACA 57.272 42.857 0.00 0.00 0.00 3.58
3324 4768 4.816385 CACAGTGAAACCATTACACTCAGT 59.184 41.667 0.00 0.00 41.93 3.41
3462 4906 7.928307 TGTATTTCGTTACAGAGGTAGTAGT 57.072 36.000 0.00 0.00 0.00 2.73
3463 4907 9.798994 ATTTGTATTTCGTTACAGAGGTAGTAG 57.201 33.333 0.00 0.00 33.81 2.57
3464 4908 9.577110 CATTTGTATTTCGTTACAGAGGTAGTA 57.423 33.333 0.00 0.00 33.81 1.82
3549 4994 6.017852 GCTGATAAGGTTAAAGTATCAGGCAC 60.018 42.308 21.39 10.00 45.98 5.01


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

AutoCloner maintained by Alex Coulton.