Multiple sequence alignment - TraesCS5D01G304300

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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 TraesCS5D01G304300 chr5D 100.000 5122 0 0 1 5122 399333302 399328181 0.000000e+00 9459.0
1 TraesCS5D01G304300 chr5B 89.708 3595 177 65 147 3653 479720369 479716880 0.000000e+00 4410.0
2 TraesCS5D01G304300 chr5B 92.698 1438 64 22 3699 5122 479716868 479715458 0.000000e+00 2036.0
3 TraesCS5D01G304300 chr5B 94.937 79 4 0 1 79 479720702 479720624 1.940000e-24 124.0
4 TraesCS5D01G304300 chr5A 89.772 3246 216 44 1289 4443 504959503 504956283 0.000000e+00 4048.0
5 TraesCS5D01G304300 chr5A 90.581 637 44 10 4490 5116 504956303 504955673 0.000000e+00 830.0
6 TraesCS5D01G304300 chr5A 90.991 555 26 6 745 1291 504960145 504959607 0.000000e+00 726.0
7 TraesCS5D01G304300 chr5A 88.809 277 19 9 449 718 504961558 504961287 3.820000e-86 329.0
8 TraesCS5D01G304300 chr5A 82.562 281 30 7 145 423 505016087 505015824 3.990000e-56 230.0
9 TraesCS5D01G304300 chr5A 85.507 138 17 3 429 563 505015787 505015650 1.920000e-29 141.0
10 TraesCS5D01G304300 chr3D 83.607 549 70 13 4490 5030 51685895 51686431 9.900000e-137 497.0
11 TraesCS5D01G304300 chr3B 82.601 546 75 12 4490 5029 82629009 82629540 1.000000e-126 464.0
12 TraesCS5D01G304300 chr7D 92.000 125 8 2 1006 1130 249793008 249792886 1.900000e-39 174.0
13 TraesCS5D01G304300 chr7B 89.600 125 11 2 1006 1130 226905651 226905529 1.910000e-34 158.0
14 TraesCS5D01G304300 chr7A 90.164 122 10 2 1006 1127 271375840 271375959 1.910000e-34 158.0
15 TraesCS5D01G304300 chr7A 94.444 54 3 0 4436 4489 316454709 316454762 3.290000e-12 84.2
16 TraesCS5D01G304300 chr4A 96.226 53 2 0 4437 4489 705816649 705816597 2.540000e-13 87.9
17 TraesCS5D01G304300 chr6B 95.918 49 2 0 4441 4489 415119584 415119632 4.250000e-11 80.5
18 TraesCS5D01G304300 chr2D 95.918 49 2 0 4441 4489 350750680 350750632 4.250000e-11 80.5
19 TraesCS5D01G304300 chr1D 95.918 49 2 0 4441 4489 345263393 345263345 4.250000e-11 80.5
20 TraesCS5D01G304300 chr1B 94.231 52 3 0 4438 4489 465702325 465702376 4.250000e-11 80.5
21 TraesCS5D01G304300 chr1A 94.231 52 3 0 4438 4489 123551359 123551410 4.250000e-11 80.5
22 TraesCS5D01G304300 chrUn 95.833 48 2 0 4442 4489 85312987 85312940 1.530000e-10 78.7


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 TraesCS5D01G304300 chr5D 399328181 399333302 5121 True 9459.00 9459 100.000000 1 5122 1 chr5D.!!$R1 5121
1 TraesCS5D01G304300 chr5B 479715458 479720702 5244 True 2190.00 4410 92.447667 1 5122 3 chr5B.!!$R1 5121
2 TraesCS5D01G304300 chr5A 504955673 504961558 5885 True 1483.25 4048 90.038250 449 5116 4 chr5A.!!$R1 4667
3 TraesCS5D01G304300 chr3D 51685895 51686431 536 False 497.00 497 83.607000 4490 5030 1 chr3D.!!$F1 540
4 TraesCS5D01G304300 chr3B 82629009 82629540 531 False 464.00 464 82.601000 4490 5029 1 chr3B.!!$F1 539

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
489 678 1.202927 TGGGCTAGCTTGCACTCTTTT 60.203 47.619 22.76 0.00 37.25 2.27 F
1320 2760 0.235926 GCACGCCACTCTGAAAGAAC 59.764 55.000 0.00 0.00 46.34 3.01 F
1850 3302 1.277557 CAGGACAGGGATAGCTATGCC 59.722 57.143 31.25 31.25 43.72 4.40 F
3095 4587 0.035439 AGGGGCATTACAGTGAACCG 60.035 55.000 0.00 0.00 0.00 4.44 F
3573 5122 1.785041 GATATGCGGCGCAACCATGT 61.785 55.000 39.46 23.39 43.62 3.21 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1551 3003 0.872021 GCGCGAGGAGGATGTAGTTG 60.872 60.0 12.10 0.0 0.00 3.16 R
2521 4000 0.436150 CGGCGATGACAAGCATATCG 59.564 55.0 0.00 0.0 44.65 2.92 R
3777 5330 0.107508 ACATCCAATCGACCTGCAGG 60.108 55.0 31.60 31.6 42.17 4.85 R
4013 5575 0.471780 TCTCTGTTGTGGCCTCCTCA 60.472 55.0 3.32 1.5 0.00 3.86 R
4449 6044 5.364157 TGTTTGGGGCTAAATACTTTGTTGT 59.636 36.0 0.00 0.0 0.00 3.32 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
62 63 3.193267 ACACAAGCAACACAATGTCAACT 59.807 39.130 0.00 0.00 0.00 3.16
81 82 9.569167 TGTCAACTTACGAATCACTTATTAGAG 57.431 33.333 0.00 0.00 0.00 2.43
82 83 9.784680 GTCAACTTACGAATCACTTATTAGAGA 57.215 33.333 0.00 0.00 0.00 3.10
84 85 9.239002 CAACTTACGAATCACTTATTAGAGAGG 57.761 37.037 0.00 0.00 0.00 3.69
85 86 7.942990 ACTTACGAATCACTTATTAGAGAGGG 58.057 38.462 0.00 0.00 0.00 4.30
86 87 5.793030 ACGAATCACTTATTAGAGAGGGG 57.207 43.478 0.00 0.00 0.00 4.79
87 88 4.589374 ACGAATCACTTATTAGAGAGGGGG 59.411 45.833 0.00 0.00 0.00 5.40
107 108 4.980573 GGGGGAAAGTACACATATATGCA 58.019 43.478 12.79 0.00 0.00 3.96
108 109 5.003804 GGGGGAAAGTACACATATATGCAG 58.996 45.833 12.79 8.26 0.00 4.41
109 110 5.221843 GGGGGAAAGTACACATATATGCAGA 60.222 44.000 12.79 0.00 0.00 4.26
110 111 6.296026 GGGGAAAGTACACATATATGCAGAA 58.704 40.000 12.79 0.00 0.00 3.02
111 112 6.428159 GGGGAAAGTACACATATATGCAGAAG 59.572 42.308 12.79 1.11 0.00 2.85
112 113 6.992715 GGGAAAGTACACATATATGCAGAAGT 59.007 38.462 12.79 6.61 0.00 3.01
134 293 6.074648 AGTAGAAGATATGGTTCCCTCTCTG 58.925 44.000 0.00 0.00 0.00 3.35
135 294 5.149584 AGAAGATATGGTTCCCTCTCTGA 57.850 43.478 0.00 0.00 0.00 3.27
136 295 5.725490 AGAAGATATGGTTCCCTCTCTGAT 58.275 41.667 0.00 0.00 0.00 2.90
137 296 6.868826 AGAAGATATGGTTCCCTCTCTGATA 58.131 40.000 0.00 0.00 0.00 2.15
138 297 6.723977 AGAAGATATGGTTCCCTCTCTGATAC 59.276 42.308 0.00 0.00 0.00 2.24
139 298 6.226272 AGATATGGTTCCCTCTCTGATACT 57.774 41.667 0.00 0.00 0.00 2.12
140 299 6.252995 AGATATGGTTCCCTCTCTGATACTC 58.747 44.000 0.00 0.00 0.00 2.59
141 300 3.757947 TGGTTCCCTCTCTGATACTCA 57.242 47.619 0.00 0.00 0.00 3.41
142 301 3.636679 TGGTTCCCTCTCTGATACTCAG 58.363 50.000 0.00 0.00 45.59 3.35
341 530 7.324178 GTGATATGTTTCCGGCTCTAATATCT 58.676 38.462 17.35 1.69 0.00 1.98
350 539 3.438087 CGGCTCTAATATCTTGGGCATTG 59.562 47.826 0.00 0.00 0.00 2.82
361 550 4.016444 TCTTGGGCATTGTCTGGATAAAC 58.984 43.478 0.00 0.00 0.00 2.01
374 563 4.646945 TCTGGATAAACCTGTGTTGCAAAA 59.353 37.500 0.00 0.00 39.86 2.44
375 564 5.127845 TCTGGATAAACCTGTGTTGCAAAAA 59.872 36.000 0.00 0.00 39.86 1.94
376 565 5.112686 TGGATAAACCTGTGTTGCAAAAAC 58.887 37.500 0.00 3.37 39.86 2.43
489 678 1.202927 TGGGCTAGCTTGCACTCTTTT 60.203 47.619 22.76 0.00 37.25 2.27
503 693 9.567848 CTTGCACTCTTTTGTTAGTTTAGAAAA 57.432 29.630 0.00 0.00 0.00 2.29
578 773 3.699067 CACCTGCAAGTTTTTGTGAGAG 58.301 45.455 0.00 0.00 36.65 3.20
758 2068 9.015367 ACTACATAGTACTAGATGATTTCGCAT 57.985 33.333 11.75 0.00 34.13 4.73
771 2081 3.197790 CGCATGAACTCTGCCGGG 61.198 66.667 2.18 0.00 36.24 5.73
778 2088 1.893919 GAACTCTGCCGGGAAGAGCT 61.894 60.000 28.80 19.22 44.22 4.09
1175 2509 0.394625 GTCTACTCCGCTGTCCCTCT 60.395 60.000 0.00 0.00 0.00 3.69
1181 2515 0.975556 TCCGCTGTCCCTCTGCAATA 60.976 55.000 0.00 0.00 40.30 1.90
1288 2622 7.008538 CACCATTCATAATTTCGTGACAACATG 59.991 37.037 0.00 0.00 0.00 3.21
1291 2625 9.553418 CATTCATAATTTCGTGACAACATGTAA 57.447 29.630 0.00 0.00 34.90 2.41
1320 2760 0.235926 GCACGCCACTCTGAAAGAAC 59.764 55.000 0.00 0.00 46.34 3.01
1337 2777 4.877323 AGAACGTCTGAACAAAAGGAAC 57.123 40.909 0.00 0.00 0.00 3.62
1375 2818 1.339610 CTCATGTGTTTCGGCCCAAAA 59.660 47.619 0.00 0.00 0.00 2.44
1390 2833 5.508994 CGGCCCAAAAGAAAAATTCTAGTGT 60.509 40.000 0.00 0.00 39.61 3.55
1422 2869 3.541996 TTGGCTCATCGCTTATTCTCA 57.458 42.857 0.00 0.00 39.13 3.27
1511 2963 3.624410 GCAGTGTTATGATCATGTCTGCA 59.376 43.478 29.20 16.65 43.99 4.41
1527 2979 2.053627 CTGCATTTTTCAGGCGTCAAC 58.946 47.619 0.00 0.00 0.00 3.18
1754 3206 9.638176 ATGCTCTAGTAAAATGAAATCTCCAAT 57.362 29.630 0.00 0.00 0.00 3.16
1780 3232 5.509498 TCCTAGTGGATTTCCCTGATTTTG 58.491 41.667 0.00 0.00 37.46 2.44
1781 3233 5.015178 TCCTAGTGGATTTCCCTGATTTTGT 59.985 40.000 0.00 0.00 37.46 2.83
1782 3234 5.716703 CCTAGTGGATTTCCCTGATTTTGTT 59.283 40.000 0.00 0.00 35.38 2.83
1783 3235 6.211384 CCTAGTGGATTTCCCTGATTTTGTTT 59.789 38.462 0.00 0.00 35.38 2.83
1850 3302 1.277557 CAGGACAGGGATAGCTATGCC 59.722 57.143 31.25 31.25 43.72 4.40
2091 3545 2.852413 CGATGCACTTACCGTTACTGAG 59.148 50.000 0.00 0.00 0.00 3.35
2101 3555 6.980978 ACTTACCGTTACTGAGATGAATGATG 59.019 38.462 0.00 0.00 0.00 3.07
2104 3558 4.747108 CCGTTACTGAGATGAATGATGTCC 59.253 45.833 0.00 0.00 0.00 4.02
2105 3559 5.452496 CCGTTACTGAGATGAATGATGTCCT 60.452 44.000 0.00 0.00 0.00 3.85
2106 3560 5.689514 CGTTACTGAGATGAATGATGTCCTC 59.310 44.000 0.00 0.00 0.00 3.71
2107 3561 4.686191 ACTGAGATGAATGATGTCCTCC 57.314 45.455 0.00 0.00 0.00 4.30
2114 3568 2.239654 TGAATGATGTCCTCCCAGTTCC 59.760 50.000 0.00 0.00 0.00 3.62
2116 3570 2.044793 TGATGTCCTCCCAGTTCCTT 57.955 50.000 0.00 0.00 0.00 3.36
2131 3585 6.142817 CCAGTTCCTTTAGTTTTTCATCACG 58.857 40.000 0.00 0.00 0.00 4.35
2135 3589 7.228706 AGTTCCTTTAGTTTTTCATCACGATGT 59.771 33.333 6.91 0.00 39.72 3.06
2156 3610 9.507280 CGATGTGTAATTAAGATGCTGAAATTT 57.493 29.630 0.00 0.00 0.00 1.82
2167 3621 4.475763 TGCTGAAATTTGCTTTGCATTG 57.524 36.364 0.00 0.00 38.76 2.82
2285 3742 2.093235 CACCTGGATCTTCCTCAAGACC 60.093 54.545 0.00 0.00 41.64 3.85
2315 3772 2.357517 AGGAAGCTGTTCGGCGTG 60.358 61.111 6.85 0.00 37.29 5.34
2375 3832 2.661866 GTGCACGCCTCTGAACGT 60.662 61.111 0.00 0.07 44.75 3.99
2491 3970 4.913335 ACATCACATGATCTTGGAATGC 57.087 40.909 17.84 0.00 31.21 3.56
2584 4063 2.579207 ATGTCACCGAGGTATCAACG 57.421 50.000 0.00 0.00 0.00 4.10
2588 4067 3.056393 TGTCACCGAGGTATCAACGAAAT 60.056 43.478 0.00 0.00 0.00 2.17
2593 4072 3.797256 CCGAGGTATCAACGAAATCTCAC 59.203 47.826 0.00 0.00 0.00 3.51
2698 4178 1.284198 AGCAGCAGGATTGAGGTGATT 59.716 47.619 0.00 0.00 35.37 2.57
2731 4211 6.398095 AGGTGTTTTTGGAGCAATTATAAGC 58.602 36.000 0.00 0.00 0.00 3.09
2788 4268 4.275689 TCACGAACTGTACTTTCTTCGGTA 59.724 41.667 14.72 4.66 39.83 4.02
2806 4286 6.476243 TCGGTAGTGCTTCAACTTAATTTC 57.524 37.500 0.00 0.00 0.00 2.17
2808 4288 6.483974 TCGGTAGTGCTTCAACTTAATTTCAA 59.516 34.615 0.00 0.00 0.00 2.69
2865 4348 6.153000 AGTCCGACATATGGAACTACATATCC 59.847 42.308 7.80 0.00 40.97 2.59
2882 4372 5.070180 ACATATCCATGTGAAGACTGAGGAG 59.930 44.000 0.00 0.00 43.89 3.69
2884 4374 1.406614 CCATGTGAAGACTGAGGAGGC 60.407 57.143 0.00 0.00 0.00 4.70
2894 4384 0.397941 CTGAGGAGGCAGTGAAACCA 59.602 55.000 0.00 0.00 37.80 3.67
3088 4580 6.064060 TCATTCTGATTTAGGGGCATTACAG 58.936 40.000 0.00 0.00 0.00 2.74
3095 4587 0.035439 AGGGGCATTACAGTGAACCG 60.035 55.000 0.00 0.00 0.00 4.44
3113 4605 2.829720 ACCGACTACAGCCATAGACAAA 59.170 45.455 0.00 0.00 0.00 2.83
3118 4610 7.014905 ACCGACTACAGCCATAGACAAATATAA 59.985 37.037 0.00 0.00 0.00 0.98
3119 4611 7.870954 CCGACTACAGCCATAGACAAATATAAA 59.129 37.037 0.00 0.00 0.00 1.40
3232 4775 7.339482 ACCTTCCAAATCTTATCAGAGGTTAC 58.661 38.462 0.00 0.00 31.27 2.50
3246 4789 6.711277 TCAGAGGTTACATGTTAAGCATCTT 58.289 36.000 2.30 0.00 35.19 2.40
3259 4802 6.072508 TGTTAAGCATCTTTCATCCAACTGAC 60.073 38.462 0.00 0.00 0.00 3.51
3264 4808 5.618640 GCATCTTTCATCCAACTGACACTTC 60.619 44.000 0.00 0.00 0.00 3.01
3265 4809 5.034852 TCTTTCATCCAACTGACACTTCA 57.965 39.130 0.00 0.00 0.00 3.02
3338 4882 4.328536 TGCTATTAAACATTCACCACGGT 58.671 39.130 0.00 0.00 0.00 4.83
3379 4923 9.830975 AAAATTTTATAGTTTTTCACACTGGCT 57.169 25.926 0.37 0.00 0.00 4.75
3459 5003 5.706447 TCTACTCCACAGTGCCTATTATCT 58.294 41.667 0.00 0.00 33.62 1.98
3485 5034 6.897966 TGAAGGTAGATCACTATCCTCTTGTT 59.102 38.462 0.00 0.00 32.86 2.83
3491 5040 6.638610 AGATCACTATCCTCTTGTTGTCAAG 58.361 40.000 0.00 2.05 41.19 3.02
3508 5057 4.573900 GTCAAGTTCATGACTGTCCTGAT 58.426 43.478 15.03 0.82 44.98 2.90
3509 5058 4.999950 GTCAAGTTCATGACTGTCCTGATT 59.000 41.667 15.03 6.40 44.98 2.57
3510 5059 5.471456 GTCAAGTTCATGACTGTCCTGATTT 59.529 40.000 15.03 10.59 44.98 2.17
3511 5060 6.016777 GTCAAGTTCATGACTGTCCTGATTTT 60.017 38.462 15.03 10.30 44.98 1.82
3512 5061 6.547141 TCAAGTTCATGACTGTCCTGATTTTT 59.453 34.615 15.03 8.34 39.00 1.94
3573 5122 1.785041 GATATGCGGCGCAACCATGT 61.785 55.000 39.46 23.39 43.62 3.21
3584 5133 2.223021 CGCAACCATGTTGAACCTATCG 60.223 50.000 10.94 0.00 0.00 2.92
3608 5157 2.927856 ACCTCCGACATGTGGGCA 60.928 61.111 21.24 9.87 0.00 5.36
3617 5166 3.009723 CGACATGTGGGCAGTTCTAATT 58.990 45.455 1.15 0.00 0.00 1.40
3653 5202 2.361757 CCATGAGAAGGTTTGTGCACAA 59.638 45.455 27.96 27.96 0.00 3.33
3667 5217 4.797471 TGTGCACAACAATTCTATCTTGC 58.203 39.130 19.28 0.00 35.24 4.01
3672 5222 5.688823 CACAACAATTCTATCTTGCGACAA 58.311 37.500 0.00 0.00 0.00 3.18
3674 5224 5.700832 ACAACAATTCTATCTTGCGACAAGA 59.299 36.000 19.64 19.64 0.00 3.02
3682 5232 7.295952 TCTATCTTGCGACAAGAGATTTTTC 57.704 36.000 21.13 0.00 32.68 2.29
3688 5238 5.519722 TGCGACAAGAGATTTTTCTTTTCC 58.480 37.500 0.00 0.00 35.28 3.13
3696 5246 7.150783 AGAGATTTTTCTTTTCCGATTCCTG 57.849 36.000 0.00 0.00 0.00 3.86
3763 5314 2.879756 GCTCTAACTGAACCAATGGGCA 60.880 50.000 3.55 0.12 37.90 5.36
3774 5327 2.174424 ACCAATGGGCACAAATTTTGGT 59.826 40.909 17.20 17.20 39.95 3.67
3777 5330 2.611225 TGGGCACAAATTTTGGTCAC 57.389 45.000 13.42 6.21 34.12 3.67
3813 5366 2.766970 TGTACTTTGTTGCTTTCGCC 57.233 45.000 0.00 0.00 34.43 5.54
3856 5409 8.841300 TCATCATCTACTCATACAAGTACTGTC 58.159 37.037 0.00 0.00 39.64 3.51
3858 5411 8.439993 TCATCTACTCATACAAGTACTGTCTC 57.560 38.462 0.00 0.00 39.64 3.36
3867 5420 5.615925 ACAAGTACTGTCTCCTTCAGTTT 57.384 39.130 0.00 0.00 42.50 2.66
3873 5426 4.589908 ACTGTCTCCTTCAGTTTGTGTTT 58.410 39.130 0.00 0.00 42.50 2.83
3903 5461 7.819900 CCTAAACATTCATGATAGCTACTACCC 59.180 40.741 0.00 0.00 0.00 3.69
4013 5575 0.322816 AGGTCACAGGCGCAATTGAT 60.323 50.000 10.83 0.00 0.00 2.57
4022 5584 2.028130 CGCAATTGATGAGGAGGCC 58.972 57.895 10.34 0.00 0.00 5.19
4023 5585 0.749091 CGCAATTGATGAGGAGGCCA 60.749 55.000 10.34 0.00 0.00 5.36
4025 5587 1.956636 GCAATTGATGAGGAGGCCACA 60.957 52.381 10.34 0.00 0.00 4.17
4036 5598 0.108585 GAGGCCACAACAGAGAACCA 59.891 55.000 5.01 0.00 0.00 3.67
4038 5600 1.507141 GGCCACAACAGAGAACCACG 61.507 60.000 0.00 0.00 0.00 4.94
4039 5601 1.507141 GCCACAACAGAGAACCACGG 61.507 60.000 0.00 0.00 0.00 4.94
4043 5605 3.530910 AACAGAGAACCACGGGGCG 62.531 63.158 1.73 0.00 37.90 6.13
4083 5648 1.757118 GAGAAGATGATGGACCGGACA 59.243 52.381 9.46 7.37 0.00 4.02
4237 5831 7.781056 ACTGGTTCATTCTACAATTGTTTTGT 58.219 30.769 17.78 0.00 36.49 2.83
4238 5832 8.908903 ACTGGTTCATTCTACAATTGTTTTGTA 58.091 29.630 17.78 0.00 34.11 2.41
4247 5841 9.743057 TTCTACAATTGTTTTGTAAACATGGAG 57.257 29.630 17.78 10.03 34.84 3.86
4248 5842 6.843069 ACAATTGTTTTGTAAACATGGAGC 57.157 33.333 4.92 0.00 0.00 4.70
4249 5843 6.344500 ACAATTGTTTTGTAAACATGGAGCA 58.656 32.000 4.92 0.00 0.00 4.26
4250 5844 6.820656 ACAATTGTTTTGTAAACATGGAGCAA 59.179 30.769 4.92 0.00 0.00 3.91
4251 5845 6.843069 ATTGTTTTGTAAACATGGAGCAAC 57.157 33.333 5.88 0.00 0.00 4.17
4252 5846 5.330455 TGTTTTGTAAACATGGAGCAACA 57.670 34.783 0.00 0.00 0.00 3.33
4253 5847 5.724328 TGTTTTGTAAACATGGAGCAACAA 58.276 33.333 0.00 0.00 0.00 2.83
4254 5848 6.344500 TGTTTTGTAAACATGGAGCAACAAT 58.656 32.000 0.00 0.00 0.00 2.71
4255 5849 6.257411 TGTTTTGTAAACATGGAGCAACAATG 59.743 34.615 0.00 0.00 0.00 2.82
4256 5850 4.517952 TGTAAACATGGAGCAACAATGG 57.482 40.909 0.00 0.00 0.00 3.16
4257 5851 3.894427 TGTAAACATGGAGCAACAATGGT 59.106 39.130 0.00 0.00 40.72 3.55
4258 5852 5.073428 TGTAAACATGGAGCAACAATGGTA 58.927 37.500 0.00 0.00 37.41 3.25
4259 5853 5.714333 TGTAAACATGGAGCAACAATGGTAT 59.286 36.000 0.00 0.00 37.41 2.73
4260 5854 5.743636 AAACATGGAGCAACAATGGTATT 57.256 34.783 0.00 0.00 37.41 1.89
4261 5855 4.724074 ACATGGAGCAACAATGGTATTG 57.276 40.909 0.00 0.28 37.41 1.90
4262 5856 3.448301 ACATGGAGCAACAATGGTATTGG 59.552 43.478 0.00 0.00 37.41 3.16
4263 5857 3.168035 TGGAGCAACAATGGTATTGGT 57.832 42.857 6.51 0.00 39.16 3.67
4264 5858 4.308526 TGGAGCAACAATGGTATTGGTA 57.691 40.909 6.51 0.00 36.70 3.25
4449 6044 6.348132 CGCCAAAGATGATACTACAACAACAA 60.348 38.462 0.00 0.00 0.00 2.83
4450 6045 6.801862 GCCAAAGATGATACTACAACAACAAC 59.198 38.462 0.00 0.00 0.00 3.32
4451 6046 7.521423 GCCAAAGATGATACTACAACAACAACA 60.521 37.037 0.00 0.00 0.00 3.33
4551 6146 3.507233 TCCAGTGATGAAAACCAGATTGC 59.493 43.478 0.00 0.00 0.00 3.56
4792 6401 6.072286 AGCTTCAAACTGGTCATGAAACATAG 60.072 38.462 0.00 0.00 33.08 2.23
4925 6534 4.280677 TGGGAAGAAACCAAACATGTGATC 59.719 41.667 0.00 0.00 34.44 2.92
4972 6582 2.298729 TCAGGTGGCTTGGTTTATTTGC 59.701 45.455 0.00 0.00 0.00 3.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
62 63 6.267014 CCCCCTCTCTAATAAGTGATTCGTAA 59.733 42.308 0.00 0.00 0.00 3.18
85 86 4.980573 TGCATATATGTGTACTTTCCCCC 58.019 43.478 14.14 0.00 0.00 5.40
86 87 5.865085 TCTGCATATATGTGTACTTTCCCC 58.135 41.667 14.14 0.00 0.00 4.81
87 88 6.992715 ACTTCTGCATATATGTGTACTTTCCC 59.007 38.462 14.14 0.00 0.00 3.97
88 89 9.197694 CTACTTCTGCATATATGTGTACTTTCC 57.802 37.037 14.14 0.00 0.00 3.13
89 90 9.967346 TCTACTTCTGCATATATGTGTACTTTC 57.033 33.333 14.14 0.00 0.00 2.62
91 92 9.973450 CTTCTACTTCTGCATATATGTGTACTT 57.027 33.333 14.14 0.00 0.00 2.24
92 93 9.355916 TCTTCTACTTCTGCATATATGTGTACT 57.644 33.333 14.14 0.00 0.00 2.73
101 102 8.317679 GGAACCATATCTTCTACTTCTGCATAT 58.682 37.037 0.00 0.00 0.00 1.78
102 103 7.671302 GGAACCATATCTTCTACTTCTGCATA 58.329 38.462 0.00 0.00 0.00 3.14
103 104 6.529220 GGAACCATATCTTCTACTTCTGCAT 58.471 40.000 0.00 0.00 0.00 3.96
104 105 5.918608 GGAACCATATCTTCTACTTCTGCA 58.081 41.667 0.00 0.00 0.00 4.41
134 293 0.248539 GGCGTCACGGTCTGAGTATC 60.249 60.000 0.00 0.00 0.00 2.24
135 294 0.963856 TGGCGTCACGGTCTGAGTAT 60.964 55.000 0.00 0.00 0.00 2.12
136 295 0.963856 ATGGCGTCACGGTCTGAGTA 60.964 55.000 0.00 0.00 0.00 2.59
137 296 2.276116 ATGGCGTCACGGTCTGAGT 61.276 57.895 0.00 0.00 0.00 3.41
138 297 1.807165 CATGGCGTCACGGTCTGAG 60.807 63.158 0.00 0.00 0.00 3.35
139 298 2.261361 CATGGCGTCACGGTCTGA 59.739 61.111 0.00 0.00 0.00 3.27
140 299 2.815211 CCATGGCGTCACGGTCTG 60.815 66.667 0.00 0.00 0.00 3.51
141 300 4.760047 GCCATGGCGTCACGGTCT 62.760 66.667 23.48 0.00 0.00 3.85
144 303 2.642996 TATCTGCCATGGCGTCACGG 62.643 60.000 30.87 15.88 45.51 4.94
321 510 5.308825 CCAAGATATTAGAGCCGGAAACAT 58.691 41.667 5.05 0.00 0.00 2.71
341 530 3.096092 GGTTTATCCAGACAATGCCCAA 58.904 45.455 0.00 0.00 35.97 4.12
350 539 3.146066 TGCAACACAGGTTTATCCAGAC 58.854 45.455 0.00 0.00 39.02 3.51
432 621 6.925211 TCACTCTCTTATTACAGAACTGGTG 58.075 40.000 6.76 0.00 34.19 4.17
433 622 7.540474 TTCACTCTCTTATTACAGAACTGGT 57.460 36.000 6.76 0.00 34.19 4.00
729 1831 9.976255 CGAAATCATCTAGTACTATGTAGTAGC 57.024 37.037 2.33 0.00 39.29 3.58
740 1842 6.920758 AGAGTTCATGCGAAATCATCTAGTAC 59.079 38.462 5.57 0.00 46.28 2.73
754 2064 3.197790 CCCGGCAGAGTTCATGCG 61.198 66.667 0.00 0.00 44.80 4.73
758 2068 1.975327 CTCTTCCCGGCAGAGTTCA 59.025 57.895 17.13 0.00 34.18 3.18
918 2245 1.133598 CCCACTCGTGTCGTATAGCAA 59.866 52.381 0.00 0.00 0.00 3.91
1288 2622 3.871594 AGTGGCGTGCTAGAATTCATTAC 59.128 43.478 8.44 0.60 0.00 1.89
1291 2625 2.169352 AGAGTGGCGTGCTAGAATTCAT 59.831 45.455 8.44 0.00 0.00 2.57
1320 2760 7.114811 CCAATAATTGTTCCTTTTGTTCAGACG 59.885 37.037 0.00 0.00 0.00 4.18
1337 2777 7.031372 CACATGAGAACTGGAACCAATAATTG 58.969 38.462 0.00 0.00 0.00 2.32
1375 2818 6.704493 TGCTCGTGTTACACTAGAATTTTTCT 59.296 34.615 19.11 0.00 43.72 2.52
1422 2869 3.080319 GGAGCAGAGAACAGAAGCAAAT 58.920 45.455 0.00 0.00 0.00 2.32
1551 3003 0.872021 GCGCGAGGAGGATGTAGTTG 60.872 60.000 12.10 0.00 0.00 3.16
1629 3081 4.142038 TCTCTTTTGGACAGTAAAAGGCC 58.858 43.478 0.00 0.00 42.51 5.19
1760 3212 7.610580 AAAACAAAATCAGGGAAATCCACTA 57.389 32.000 1.22 0.00 38.24 2.74
1780 3232 1.482531 GCATCGCACACGCAAAAAC 59.517 52.632 0.00 0.00 39.84 2.43
1781 3233 2.008168 CGCATCGCACACGCAAAAA 61.008 52.632 0.00 0.00 39.84 1.94
1782 3234 2.426588 CGCATCGCACACGCAAAA 60.427 55.556 0.00 0.00 39.84 2.44
1850 3302 5.234757 GTGAAGAGCAGCAGAATCAGAATAG 59.765 44.000 0.00 0.00 0.00 1.73
1939 3392 2.868583 CTGCTGATAGGAACATTCACGG 59.131 50.000 0.00 0.00 0.00 4.94
2073 3527 3.508402 TCATCTCAGTAACGGTAAGTGCA 59.492 43.478 0.00 0.00 0.00 4.57
2077 3531 6.980978 ACATCATTCATCTCAGTAACGGTAAG 59.019 38.462 0.00 0.00 0.00 2.34
2078 3532 6.873997 ACATCATTCATCTCAGTAACGGTAA 58.126 36.000 0.00 0.00 0.00 2.85
2091 3545 3.853355 ACTGGGAGGACATCATTCATC 57.147 47.619 0.00 0.00 0.00 2.92
2101 3555 4.368565 AAACTAAAGGAACTGGGAGGAC 57.631 45.455 0.00 0.00 40.86 3.85
2104 3558 6.490040 TGATGAAAAACTAAAGGAACTGGGAG 59.510 38.462 0.00 0.00 40.86 4.30
2105 3559 6.264518 GTGATGAAAAACTAAAGGAACTGGGA 59.735 38.462 0.00 0.00 40.86 4.37
2106 3560 6.447162 GTGATGAAAAACTAAAGGAACTGGG 58.553 40.000 0.00 0.00 40.86 4.45
2107 3561 6.017440 TCGTGATGAAAAACTAAAGGAACTGG 60.017 38.462 0.00 0.00 40.86 4.00
2114 3568 9.825972 ATTACACATCGTGATGAAAAACTAAAG 57.174 29.630 16.33 0.00 41.20 1.85
2135 3589 9.709495 AAAGCAAATTTCAGCATCTTAATTACA 57.291 25.926 3.62 0.00 0.00 2.41
2141 3595 5.539979 TGCAAAGCAAATTTCAGCATCTTA 58.460 33.333 3.62 0.00 34.76 2.10
2156 3610 5.003692 TGAACAGTTAACAATGCAAAGCA 57.996 34.783 8.61 0.00 44.86 3.91
2167 3621 7.797123 CCTTCACGACTTTTATGAACAGTTAAC 59.203 37.037 0.00 0.00 0.00 2.01
2285 3742 1.002087 AGCTTCCTCAACCCGTACTTG 59.998 52.381 0.00 0.00 0.00 3.16
2474 3953 2.361119 CAGGGCATTCCAAGATCATGTG 59.639 50.000 0.00 0.00 38.24 3.21
2491 3970 2.673523 CTGGGTCCTTCTGCAGGG 59.326 66.667 15.13 8.39 44.12 4.45
2521 4000 0.436150 CGGCGATGACAAGCATATCG 59.564 55.000 0.00 0.00 44.65 2.92
2584 4063 0.723981 GCGCTGACAGGTGAGATTTC 59.276 55.000 0.00 0.00 0.00 2.17
2588 4067 1.005748 CTTGCGCTGACAGGTGAGA 60.006 57.895 9.73 0.00 0.00 3.27
2593 4072 0.723414 CATACACTTGCGCTGACAGG 59.277 55.000 9.73 0.00 0.00 4.00
2698 4178 1.539388 CCAAAAACACCTAGCATCGCA 59.461 47.619 0.00 0.00 0.00 5.10
2731 4211 4.214119 CCAAAAGGATACATCTGTATGCCG 59.786 45.833 15.56 5.25 46.41 5.69
2852 4333 6.703607 CAGTCTTCACATGGATATGTAGTTCC 59.296 42.308 0.00 0.00 45.53 3.62
2865 4348 1.277273 TGCCTCCTCAGTCTTCACATG 59.723 52.381 0.00 0.00 0.00 3.21
2882 4372 3.801114 AAACTTTCTGGTTTCACTGCC 57.199 42.857 0.00 0.00 34.79 4.85
3088 4580 2.426024 TCTATGGCTGTAGTCGGTTCAC 59.574 50.000 0.00 0.00 0.00 3.18
3232 4775 6.750501 CAGTTGGATGAAAGATGCTTAACATG 59.249 38.462 0.00 0.00 39.84 3.21
3246 4789 4.149511 TGTGAAGTGTCAGTTGGATGAA 57.850 40.909 0.00 0.00 33.27 2.57
3359 4903 7.284489 ACAGAAAGCCAGTGTGAAAAACTATAA 59.716 33.333 0.00 0.00 25.60 0.98
3370 4914 3.340814 AGGATACAGAAAGCCAGTGTG 57.659 47.619 0.00 0.00 41.41 3.82
3459 5003 6.897966 ACAAGAGGATAGTGATCTACCTTCAA 59.102 38.462 0.00 0.00 32.22 2.69
3485 5034 3.387699 TCAGGACAGTCATGAACTTGACA 59.612 43.478 15.51 0.00 46.81 3.58
3541 5090 3.853671 GCCGCATATCTGAAACAAACAAG 59.146 43.478 0.00 0.00 0.00 3.16
3543 5092 2.159585 CGCCGCATATCTGAAACAAACA 60.160 45.455 0.00 0.00 0.00 2.83
3544 5093 2.440501 CGCCGCATATCTGAAACAAAC 58.559 47.619 0.00 0.00 0.00 2.93
3584 5133 0.247736 ACATGTCGGAGGTCAGAAGC 59.752 55.000 0.00 0.00 0.00 3.86
3608 5157 8.038944 TGGTAAGCAAAGATACGAATTAGAACT 58.961 33.333 0.00 0.00 0.00 3.01
3617 5166 5.592104 TCTCATGGTAAGCAAAGATACGA 57.408 39.130 0.00 0.00 0.00 3.43
3667 5217 5.985781 TCGGAAAAGAAAAATCTCTTGTCG 58.014 37.500 0.00 0.00 39.63 4.35
3672 5222 6.349694 GCAGGAATCGGAAAAGAAAAATCTCT 60.350 38.462 0.00 0.00 0.00 3.10
3674 5224 5.478332 AGCAGGAATCGGAAAAGAAAAATCT 59.522 36.000 0.00 0.00 0.00 2.40
3682 5232 4.503741 TTTTCAGCAGGAATCGGAAAAG 57.496 40.909 0.00 0.00 33.83 2.27
3688 5238 5.865552 ACAATTCAATTTTCAGCAGGAATCG 59.134 36.000 0.00 0.00 34.91 3.34
3696 5246 8.351495 TCACAGTAAACAATTCAATTTTCAGC 57.649 30.769 0.00 0.00 0.00 4.26
3763 5314 2.102925 CCTGCAGGTGACCAAAATTTGT 59.897 45.455 25.53 0.00 0.00 2.83
3777 5330 0.107508 ACATCCAATCGACCTGCAGG 60.108 55.000 31.60 31.60 42.17 4.85
3813 5366 1.236616 TGAGACCAATTGCAGTGCCG 61.237 55.000 13.72 0.00 0.00 5.69
3856 5409 2.623416 GGGGAAACACAAACTGAAGGAG 59.377 50.000 0.00 0.00 0.00 3.69
3858 5411 1.686587 GGGGGAAACACAAACTGAAGG 59.313 52.381 0.00 0.00 32.66 3.46
3873 5426 4.665009 AGCTATCATGAATGTTTAGGGGGA 59.335 41.667 0.00 0.00 0.00 4.81
3903 5461 0.532573 ACACTGTCAGGGTAGATGCG 59.467 55.000 5.76 0.00 23.74 4.73
4013 5575 0.471780 TCTCTGTTGTGGCCTCCTCA 60.472 55.000 3.32 1.50 0.00 3.86
4022 5584 0.884704 CCCCGTGGTTCTCTGTTGTG 60.885 60.000 0.00 0.00 0.00 3.33
4023 5585 1.450211 CCCCGTGGTTCTCTGTTGT 59.550 57.895 0.00 0.00 0.00 3.32
4025 5587 2.430367 GCCCCGTGGTTCTCTGTT 59.570 61.111 0.00 0.00 0.00 3.16
4055 5620 0.877649 CATCATCTTCTCCGGCACCG 60.878 60.000 1.02 1.02 39.44 4.94
4083 5648 1.227734 CCGACGGGGACTTGTTTGT 60.228 57.895 5.81 0.00 38.47 2.83
4125 5690 1.300931 GTTGGCAGCAGACAGTCGA 60.301 57.895 0.00 0.00 31.60 4.20
4237 5831 6.350864 CCAATACCATTGTTGCTCCATGTTTA 60.351 38.462 0.00 0.00 0.00 2.01
4238 5832 5.481105 CAATACCATTGTTGCTCCATGTTT 58.519 37.500 0.00 0.00 0.00 2.83
4241 5835 3.448301 ACCAATACCATTGTTGCTCCATG 59.552 43.478 0.00 0.00 0.00 3.66
4242 5836 3.711863 ACCAATACCATTGTTGCTCCAT 58.288 40.909 0.00 0.00 0.00 3.41
4243 5837 3.168035 ACCAATACCATTGTTGCTCCA 57.832 42.857 0.00 0.00 0.00 3.86
4244 5838 4.270008 ACTACCAATACCATTGTTGCTCC 58.730 43.478 0.00 0.00 0.00 4.70
4245 5839 5.897377 AACTACCAATACCATTGTTGCTC 57.103 39.130 0.00 0.00 0.00 4.26
4246 5840 7.768807 TTAAACTACCAATACCATTGTTGCT 57.231 32.000 0.00 0.00 0.00 3.91
4247 5841 8.247562 TCATTAAACTACCAATACCATTGTTGC 58.752 33.333 0.00 0.00 0.00 4.17
4250 5844 9.920946 AGATCATTAAACTACCAATACCATTGT 57.079 29.630 0.00 0.00 0.00 2.71
4255 5849 9.516314 GCAAAAGATCATTAAACTACCAATACC 57.484 33.333 0.00 0.00 0.00 2.73
4264 5858 8.946085 TCGTGATTAGCAAAAGATCATTAAACT 58.054 29.630 0.00 0.00 32.92 2.66
4288 5882 2.143925 GACAAAGTTCTGAACCCCTCG 58.856 52.381 16.48 4.56 0.00 4.63
4449 6044 5.364157 TGTTTGGGGCTAAATACTTTGTTGT 59.636 36.000 0.00 0.00 0.00 3.32
4450 6045 5.848406 TGTTTGGGGCTAAATACTTTGTTG 58.152 37.500 0.00 0.00 0.00 3.33
4451 6046 6.099125 ACTTGTTTGGGGCTAAATACTTTGTT 59.901 34.615 0.00 0.00 0.00 2.83
4551 6146 7.959651 GTGTTCAAGACATGTCTGCTATTTTAG 59.040 37.037 28.52 10.25 41.10 1.85
4750 6355 6.611613 TGAAGCTTCCTGGATACCATATAG 57.388 41.667 23.42 0.00 30.82 1.31
4752 6357 5.912149 TTGAAGCTTCCTGGATACCATAT 57.088 39.130 23.42 0.00 30.82 1.78


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

AutoCloner maintained by Alex Coulton.