Multiple sequence alignment - TraesCS3D01G138800

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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 TraesCS3D01G138800 chr3D 100.000 3596 0 0 1 3596 97613321 97609726 0.000000e+00 6641.0
1 TraesCS3D01G138800 chr3D 90.476 147 11 3 3271 3414 308822247 308822393 1.320000e-44 191.0
2 TraesCS3D01G138800 chr3B 93.830 2642 80 35 674 3273 148293458 148290858 0.000000e+00 3899.0
3 TraesCS3D01G138800 chr3B 91.556 450 37 1 1304 1752 485701206 485700757 1.420000e-173 619.0
4 TraesCS3D01G138800 chr3B 85.640 383 32 8 1 375 148295814 148295447 7.290000e-102 381.0
5 TraesCS3D01G138800 chr3B 95.732 164 6 1 3433 3596 148290860 148290698 2.750000e-66 263.0
6 TraesCS3D01G138800 chr3B 95.862 145 6 0 373 517 148295378 148295234 6.000000e-58 235.0
7 TraesCS3D01G138800 chr3B 97.436 78 2 0 506 583 148295212 148295135 2.250000e-27 134.0
8 TraesCS3D01G138800 chr3A 93.621 1944 84 15 951 2876 114772152 114770231 0.000000e+00 2867.0
9 TraesCS3D01G138800 chr3A 87.085 271 16 10 373 631 114772931 114772668 4.540000e-74 289.0
10 TraesCS3D01G138800 chr3A 87.660 235 18 7 3033 3257 114769781 114769548 2.750000e-66 263.0
11 TraesCS3D01G138800 chr3A 82.182 275 31 11 614 876 114772654 114772386 1.680000e-53 220.0
12 TraesCS3D01G138800 chr7B 92.667 450 30 2 1304 1752 356983550 356983103 0.000000e+00 645.0
13 TraesCS3D01G138800 chr7B 100.000 28 0 0 1696 1723 535225589 535225616 6.000000e-03 52.8
14 TraesCS3D01G138800 chr1A 91.111 450 24 5 1304 1752 469399213 469398779 2.390000e-166 595.0
15 TraesCS3D01G138800 chr1A 100.000 28 0 0 1265 1292 145199414 145199441 6.000000e-03 52.8
16 TraesCS3D01G138800 chr2A 88.488 443 36 5 1310 1752 106109557 106109130 4.110000e-144 521.0
17 TraesCS3D01G138800 chr2A 88.667 150 13 4 3271 3416 742751890 742752039 2.850000e-41 180.0
18 TraesCS3D01G138800 chr1D 91.213 239 20 1 1304 1541 270586282 270586044 1.250000e-84 324.0
19 TraesCS3D01G138800 chr2B 90.789 152 9 5 3271 3419 735406851 735406702 7.880000e-47 198.0
20 TraesCS3D01G138800 chr2B 88.889 153 14 3 3270 3419 506266836 506266684 6.130000e-43 185.0
21 TraesCS3D01G138800 chr2B 87.662 154 15 4 3267 3416 451929905 451930058 3.690000e-40 176.0
22 TraesCS3D01G138800 chr7D 88.816 152 15 2 3270 3419 480055891 480055740 6.130000e-43 185.0
23 TraesCS3D01G138800 chr7D 100.000 28 0 0 1696 1723 165334968 165334995 6.000000e-03 52.8
24 TraesCS3D01G138800 chr4A 87.117 163 17 4 3271 3429 635812212 635812374 7.930000e-42 182.0
25 TraesCS3D01G138800 chr2D 88.158 152 13 5 3270 3416 549605176 549605327 3.690000e-40 176.0
26 TraesCS3D01G138800 chr2D 88.158 152 13 5 3270 3416 550066586 550066737 3.690000e-40 176.0
27 TraesCS3D01G138800 chr7A 87.500 128 12 4 3273 3396 15602290 15602417 1.040000e-30 145.0
28 TraesCS3D01G138800 chr6D 100.000 28 0 0 1696 1723 126945961 126945934 6.000000e-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 TraesCS3D01G138800 chr3D 97609726 97613321 3595 True 6641.00 6641 100.000 1 3596 1 chr3D.!!$R1 3595
1 TraesCS3D01G138800 chr3B 148290698 148295814 5116 True 982.40 3899 93.700 1 3596 5 chr3B.!!$R2 3595
2 TraesCS3D01G138800 chr3A 114769548 114772931 3383 True 909.75 2867 87.637 373 3257 4 chr3A.!!$R1 2884

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
888 2651 0.267960 TTATCCCACTCCTCCCTCCC 59.732 60.0 0.00 0.0 0.0 4.30 F
2368 4302 1.766143 GCATTGCCTCTTCTACGCGG 61.766 60.0 12.47 0.0 0.0 6.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2433 4367 1.107114 CGCTCTCCATGTACACCTCT 58.893 55.0 0.0 0.0 0.0 3.69 R
3270 5568 0.105709 CCTGAAACCAAACACCCCCT 60.106 55.0 0.0 0.0 0.0 4.79 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
44 53 3.515502 ACGGAGATCACTTGGATTTGAGA 59.484 43.478 0.00 0.00 36.00 3.27
47 56 4.880696 GGAGATCACTTGGATTTGAGAAGG 59.119 45.833 0.00 0.00 36.00 3.46
90 99 1.450312 GCTTGTCCACGGCTGCTAT 60.450 57.895 0.00 0.00 0.00 2.97
106 115 2.947938 CTATGCCAGGAAGGTGCCGG 62.948 65.000 0.00 0.00 40.61 6.13
133 142 1.595993 CCCTCGACGTGACATCCACT 61.596 60.000 0.00 0.00 43.53 4.00
135 144 1.676529 CCTCGACGTGACATCCACTAT 59.323 52.381 0.00 0.00 43.53 2.12
144 153 4.383948 CGTGACATCCACTATGAATCATCG 59.616 45.833 0.00 0.00 43.53 3.84
161 170 2.027625 CGTTTCCGAGTGGTCTGGC 61.028 63.158 0.00 0.00 35.63 4.85
179 188 2.173141 CGCGACCGTGTACGTACA 59.827 61.111 24.10 24.10 37.74 2.90
189 198 2.284798 CGTGTACGTACATGAAATGCGG 60.285 50.000 34.35 12.64 44.02 5.69
197 206 2.772568 CATGAAATGCGGCGGATTTA 57.227 45.000 33.75 22.94 37.62 1.40
201 210 4.481930 TGAAATGCGGCGGATTTATTAG 57.518 40.909 33.75 0.00 0.00 1.73
209 218 1.818674 GCGGATTTATTAGGCATGGGG 59.181 52.381 0.00 0.00 0.00 4.96
308 317 0.893727 ATCGGCTGGTGTTTGGTTCC 60.894 55.000 0.00 0.00 0.00 3.62
309 318 2.903547 CGGCTGGTGTTTGGTTCCG 61.904 63.158 0.00 0.00 0.00 4.30
327 336 2.707192 GTTGCAAACGTACATGGCG 58.293 52.632 0.00 9.82 36.92 5.69
329 338 2.573167 GCAAACGTACATGGCGCG 60.573 61.111 0.00 0.00 0.00 6.86
330 339 2.097538 CAAACGTACATGGCGCGG 59.902 61.111 8.83 0.00 0.00 6.46
331 340 3.795342 AAACGTACATGGCGCGGC 61.795 61.111 27.61 27.61 0.00 6.53
357 366 0.467290 TCTTCCCCCAGTTGTGTTGC 60.467 55.000 0.00 0.00 0.00 4.17
628 770 6.183361 ACCCTTGCTATTTATCAGTTCCTAGG 60.183 42.308 0.82 0.82 0.00 3.02
631 773 7.442666 CCTTGCTATTTATCAGTTCCTAGGTTC 59.557 40.741 9.08 3.27 0.00 3.62
640 782 2.038164 AGTTCCTAGGTTCGGTTTGTCC 59.962 50.000 9.08 0.00 0.00 4.02
665 813 7.705752 CCGGATTAACTAGTCTCTTCTTTTACC 59.294 40.741 0.00 0.00 0.00 2.85
672 820 5.087391 AGTCTCTTCTTTTACCCGAATCC 57.913 43.478 0.00 0.00 0.00 3.01
677 825 6.374333 TCTCTTCTTTTACCCGAATCCATTTG 59.626 38.462 0.00 0.00 0.00 2.32
683 831 1.636519 ACCCGAATCCATTTGTACCCA 59.363 47.619 0.00 0.00 0.00 4.51
684 832 2.021457 CCCGAATCCATTTGTACCCAC 58.979 52.381 0.00 0.00 0.00 4.61
685 833 2.619332 CCCGAATCCATTTGTACCCACA 60.619 50.000 0.00 0.00 0.00 4.17
687 835 3.343617 CGAATCCATTTGTACCCACAGT 58.656 45.455 0.00 0.00 35.67 3.55
688 836 4.509616 CGAATCCATTTGTACCCACAGTA 58.490 43.478 0.00 0.00 35.67 2.74
755 2518 4.891992 AAAGAACTGCTGCCTAGAAGTA 57.108 40.909 0.00 0.00 42.24 2.24
756 2519 4.464069 AAGAACTGCTGCCTAGAAGTAG 57.536 45.455 0.00 8.34 42.24 2.57
760 2523 3.698289 ACTGCTGCCTAGAAGTAGTACA 58.302 45.455 12.32 0.00 41.22 2.90
761 2524 4.282496 ACTGCTGCCTAGAAGTAGTACAT 58.718 43.478 12.32 0.00 41.22 2.29
762 2525 4.098654 ACTGCTGCCTAGAAGTAGTACATG 59.901 45.833 12.32 0.00 41.22 3.21
765 2528 4.737946 GCTGCCTAGAAGTAGTACATGTGG 60.738 50.000 9.11 0.00 0.00 4.17
766 2529 3.132289 TGCCTAGAAGTAGTACATGTGGC 59.868 47.826 9.11 9.05 37.38 5.01
767 2530 3.385111 GCCTAGAAGTAGTACATGTGGCT 59.615 47.826 9.11 9.19 34.42 4.75
768 2531 4.500035 GCCTAGAAGTAGTACATGTGGCTC 60.500 50.000 9.11 0.00 34.42 4.70
769 2532 3.784701 AGAAGTAGTACATGTGGCTCG 57.215 47.619 9.11 0.00 0.00 5.03
770 2533 3.090037 AGAAGTAGTACATGTGGCTCGT 58.910 45.455 9.11 0.00 0.00 4.18
771 2534 2.941453 AGTAGTACATGTGGCTCGTG 57.059 50.000 9.11 7.20 38.86 4.35
772 2535 2.168496 AGTAGTACATGTGGCTCGTGT 58.832 47.619 17.44 17.44 46.50 4.49
773 2536 2.163815 AGTAGTACATGTGGCTCGTGTC 59.836 50.000 16.88 9.62 44.13 3.67
888 2651 0.267960 TTATCCCACTCCTCCCTCCC 59.732 60.000 0.00 0.00 0.00 4.30
1011 2933 3.869272 CGAGCAATGGAGGCGCAC 61.869 66.667 10.83 1.82 36.08 5.34
1059 2981 3.667282 CACAGCCACAGCCACAGC 61.667 66.667 0.00 0.00 41.25 4.40
1062 2984 4.962836 AGCCACAGCCACAGCCAC 62.963 66.667 0.00 0.00 41.25 5.01
1064 2986 3.289834 CCACAGCCACAGCCACAC 61.290 66.667 0.00 0.00 41.25 3.82
1065 2987 3.289834 CACAGCCACAGCCACACC 61.290 66.667 0.00 0.00 41.25 4.16
1066 2988 4.586235 ACAGCCACAGCCACACCC 62.586 66.667 0.00 0.00 41.25 4.61
1067 2989 4.584518 CAGCCACAGCCACACCCA 62.585 66.667 0.00 0.00 41.25 4.51
1119 3041 2.970974 GCGCACCTTCACCAAGCTC 61.971 63.158 0.30 0.00 0.00 4.09
1174 3108 4.101448 CCGGGCCCAAGGAGACAG 62.101 72.222 24.92 0.78 0.00 3.51
1175 3109 3.322466 CGGGCCCAAGGAGACAGT 61.322 66.667 24.92 0.00 0.00 3.55
1176 3110 2.671682 GGGCCCAAGGAGACAGTC 59.328 66.667 19.95 0.00 0.00 3.51
1230 3164 4.457496 AGCTCCATGGACGCCACG 62.457 66.667 24.08 11.21 35.80 4.94
1233 3167 4.429212 TCCATGGACGCCACGACG 62.429 66.667 11.44 0.00 35.80 5.12
1939 3873 2.593978 CAGCTGGGTGGGATCTGG 59.406 66.667 5.57 0.00 0.00 3.86
2368 4302 1.766143 GCATTGCCTCTTCTACGCGG 61.766 60.000 12.47 0.00 0.00 6.46
2625 4569 1.057851 AGAACCGTCCTGTTTGGGGA 61.058 55.000 0.00 0.00 36.20 4.81
2626 4570 0.037734 GAACCGTCCTGTTTGGGGAT 59.962 55.000 0.00 0.00 35.15 3.85
2628 4572 0.037734 ACCGTCCTGTTTGGGGATTC 59.962 55.000 0.00 0.00 35.15 2.52
2629 4573 0.679960 CCGTCCTGTTTGGGGATTCC 60.680 60.000 0.00 0.00 35.15 3.01
2794 4748 8.925700 GCGATGTGATCATAATATAAGTGACAA 58.074 33.333 0.00 0.00 34.06 3.18
2852 4806 4.025313 GTCTTCTTGTCTTGCAGTCTGTTC 60.025 45.833 0.93 0.00 0.00 3.18
2859 4813 4.214437 GTCTTGCAGTCTGTTCATTTTCG 58.786 43.478 0.93 0.00 0.00 3.46
2903 4857 2.866762 GTCTGATGGTAGCACCGAATTC 59.133 50.000 0.00 0.00 42.58 2.17
2914 4868 3.379372 AGCACCGAATTCCAGATGATTTG 59.621 43.478 0.00 0.00 0.00 2.32
2916 4870 4.731773 GCACCGAATTCCAGATGATTTGTC 60.732 45.833 0.00 0.00 0.00 3.18
2918 4895 3.002656 CCGAATTCCAGATGATTTGTCCG 59.997 47.826 0.00 0.00 0.00 4.79
2930 4907 0.748729 TTTGTCCGGCGTTCCAGTTT 60.749 50.000 6.01 0.00 0.00 2.66
2935 4912 1.208535 TCCGGCGTTCCAGTTTATGAT 59.791 47.619 6.01 0.00 0.00 2.45
3009 5021 0.955428 GATTCCCAGCTGCACGTTCA 60.955 55.000 8.66 0.00 0.00 3.18
3075 5364 0.746923 GAATCCCACGGCCAGTAACC 60.747 60.000 2.24 0.00 0.00 2.85
3259 5557 0.605319 TGCTGGCCTTTGTTACGAGG 60.605 55.000 3.32 0.94 36.09 4.63
3264 5562 0.955905 GCCTTTGTTACGAGGGCAAA 59.044 50.000 19.22 0.00 42.08 3.68
3265 5563 1.068541 GCCTTTGTTACGAGGGCAAAG 60.069 52.381 19.22 14.50 44.94 2.77
3266 5564 2.500229 CCTTTGTTACGAGGGCAAAGA 58.500 47.619 19.46 0.00 46.98 2.52
3267 5565 2.225727 CCTTTGTTACGAGGGCAAAGAC 59.774 50.000 19.46 0.00 46.98 3.01
3269 5567 2.623878 TGTTACGAGGGCAAAGACAA 57.376 45.000 0.00 0.00 0.00 3.18
3270 5568 2.920524 TGTTACGAGGGCAAAGACAAA 58.079 42.857 0.00 0.00 0.00 2.83
3271 5569 2.875933 TGTTACGAGGGCAAAGACAAAG 59.124 45.455 0.00 0.00 0.00 2.77
3272 5570 2.178912 TACGAGGGCAAAGACAAAGG 57.821 50.000 0.00 0.00 0.00 3.11
3273 5571 0.537371 ACGAGGGCAAAGACAAAGGG 60.537 55.000 0.00 0.00 0.00 3.95
3274 5572 1.244019 CGAGGGCAAAGACAAAGGGG 61.244 60.000 0.00 0.00 0.00 4.79
3275 5573 0.900182 GAGGGCAAAGACAAAGGGGG 60.900 60.000 0.00 0.00 0.00 5.40
3276 5574 1.152333 GGGCAAAGACAAAGGGGGT 60.152 57.895 0.00 0.00 0.00 4.95
3277 5575 1.471829 GGGCAAAGACAAAGGGGGTG 61.472 60.000 0.00 0.00 0.00 4.61
3278 5576 0.759060 GGCAAAGACAAAGGGGGTGT 60.759 55.000 0.00 0.00 0.00 4.16
3279 5577 1.119684 GCAAAGACAAAGGGGGTGTT 58.880 50.000 0.00 0.00 0.00 3.32
3280 5578 1.484653 GCAAAGACAAAGGGGGTGTTT 59.515 47.619 0.00 0.00 32.66 2.83
3281 5579 2.741553 GCAAAGACAAAGGGGGTGTTTG 60.742 50.000 9.85 9.85 46.37 2.93
3282 5580 1.788229 AAGACAAAGGGGGTGTTTGG 58.212 50.000 1.05 0.00 38.90 3.28
3283 5581 0.634465 AGACAAAGGGGGTGTTTGGT 59.366 50.000 1.05 0.00 38.90 3.67
3284 5582 1.007842 AGACAAAGGGGGTGTTTGGTT 59.992 47.619 1.05 0.00 38.90 3.67
3285 5583 1.834896 GACAAAGGGGGTGTTTGGTTT 59.165 47.619 1.05 0.00 38.90 3.27
3286 5584 1.834896 ACAAAGGGGGTGTTTGGTTTC 59.165 47.619 1.05 0.00 38.90 2.78
3287 5585 1.834263 CAAAGGGGGTGTTTGGTTTCA 59.166 47.619 0.00 0.00 32.26 2.69
3288 5586 1.788229 AAGGGGGTGTTTGGTTTCAG 58.212 50.000 0.00 0.00 0.00 3.02
3289 5587 0.105709 AGGGGGTGTTTGGTTTCAGG 60.106 55.000 0.00 0.00 0.00 3.86
3290 5588 1.118965 GGGGGTGTTTGGTTTCAGGG 61.119 60.000 0.00 0.00 0.00 4.45
3291 5589 0.105913 GGGGTGTTTGGTTTCAGGGA 60.106 55.000 0.00 0.00 0.00 4.20
3292 5590 1.482365 GGGGTGTTTGGTTTCAGGGAT 60.482 52.381 0.00 0.00 0.00 3.85
3293 5591 2.325484 GGGTGTTTGGTTTCAGGGATT 58.675 47.619 0.00 0.00 0.00 3.01
3294 5592 2.703536 GGGTGTTTGGTTTCAGGGATTT 59.296 45.455 0.00 0.00 0.00 2.17
3295 5593 3.135712 GGGTGTTTGGTTTCAGGGATTTT 59.864 43.478 0.00 0.00 0.00 1.82
3296 5594 4.384757 GGGTGTTTGGTTTCAGGGATTTTT 60.385 41.667 0.00 0.00 0.00 1.94
3336 5634 6.966534 AAGTCCCTAGCAAATCAAATATGG 57.033 37.500 0.00 0.00 0.00 2.74
3337 5635 5.388654 AGTCCCTAGCAAATCAAATATGGG 58.611 41.667 0.00 0.00 0.00 4.00
3338 5636 4.524328 GTCCCTAGCAAATCAAATATGGGG 59.476 45.833 0.00 0.00 33.35 4.96
3339 5637 4.418526 TCCCTAGCAAATCAAATATGGGGA 59.581 41.667 0.00 0.00 37.01 4.81
3340 5638 4.524328 CCCTAGCAAATCAAATATGGGGAC 59.476 45.833 0.00 0.00 32.50 4.46
3341 5639 5.388654 CCTAGCAAATCAAATATGGGGACT 58.611 41.667 0.00 0.00 0.00 3.85
3342 5640 5.835280 CCTAGCAAATCAAATATGGGGACTT 59.165 40.000 0.00 0.00 0.00 3.01
3343 5641 6.324770 CCTAGCAAATCAAATATGGGGACTTT 59.675 38.462 0.00 0.00 0.00 2.66
3344 5642 6.625532 AGCAAATCAAATATGGGGACTTTT 57.374 33.333 0.00 0.00 0.00 2.27
3345 5643 7.019656 AGCAAATCAAATATGGGGACTTTTT 57.980 32.000 0.00 0.00 0.00 1.94
3376 5674 8.419076 CTTTTTGCTAAAAGTCCTTAAAAGCA 57.581 30.769 20.79 6.73 43.34 3.91
3377 5675 8.956533 TTTTTGCTAAAAGTCCTTAAAAGCAT 57.043 26.923 1.76 0.00 0.00 3.79
3378 5676 8.587952 TTTTGCTAAAAGTCCTTAAAAGCATC 57.412 30.769 10.03 0.00 0.00 3.91
3379 5677 7.524717 TTGCTAAAAGTCCTTAAAAGCATCT 57.475 32.000 10.03 0.00 0.00 2.90
3380 5678 7.524717 TGCTAAAAGTCCTTAAAAGCATCTT 57.475 32.000 6.73 0.00 0.00 2.40
3381 5679 7.593825 TGCTAAAAGTCCTTAAAAGCATCTTC 58.406 34.615 6.73 0.00 0.00 2.87
3382 5680 7.448469 TGCTAAAAGTCCTTAAAAGCATCTTCT 59.552 33.333 6.73 0.00 0.00 2.85
3383 5681 8.300286 GCTAAAAGTCCTTAAAAGCATCTTCTT 58.700 33.333 0.00 0.00 0.00 2.52
3384 5682 9.617975 CTAAAAGTCCTTAAAAGCATCTTCTTG 57.382 33.333 0.00 0.00 0.00 3.02
3385 5683 7.823745 AAAGTCCTTAAAAGCATCTTCTTGA 57.176 32.000 0.00 0.00 0.00 3.02
3386 5684 7.823745 AAGTCCTTAAAAGCATCTTCTTGAA 57.176 32.000 0.00 0.00 0.00 2.69
3387 5685 7.823745 AGTCCTTAAAAGCATCTTCTTGAAA 57.176 32.000 0.00 0.00 0.00 2.69
3388 5686 7.880105 AGTCCTTAAAAGCATCTTCTTGAAAG 58.120 34.615 0.00 0.00 0.00 2.62
3389 5687 7.503902 AGTCCTTAAAAGCATCTTCTTGAAAGT 59.496 33.333 0.00 0.00 0.00 2.66
3390 5688 7.805542 GTCCTTAAAAGCATCTTCTTGAAAGTC 59.194 37.037 0.00 0.00 0.00 3.01
3391 5689 7.721399 TCCTTAAAAGCATCTTCTTGAAAGTCT 59.279 33.333 0.00 0.00 0.00 3.24
3392 5690 8.355913 CCTTAAAAGCATCTTCTTGAAAGTCTT 58.644 33.333 0.00 0.00 0.00 3.01
3393 5691 9.741647 CTTAAAAGCATCTTCTTGAAAGTCTTT 57.258 29.630 0.00 0.00 0.00 2.52
3425 5723 6.342338 GTCCTAAGACTAGAGAACCAAACA 57.658 41.667 0.00 0.00 40.10 2.83
3426 5724 6.157904 GTCCTAAGACTAGAGAACCAAACAC 58.842 44.000 0.00 0.00 40.10 3.32
3427 5725 5.245526 TCCTAAGACTAGAGAACCAAACACC 59.754 44.000 0.00 0.00 0.00 4.16
3428 5726 5.011738 CCTAAGACTAGAGAACCAAACACCA 59.988 44.000 0.00 0.00 0.00 4.17
3429 5727 4.338379 AGACTAGAGAACCAAACACCAC 57.662 45.455 0.00 0.00 0.00 4.16
3430 5728 3.071167 AGACTAGAGAACCAAACACCACC 59.929 47.826 0.00 0.00 0.00 4.61
3431 5729 3.046374 ACTAGAGAACCAAACACCACCT 58.954 45.455 0.00 0.00 0.00 4.00
3438 5736 0.322546 CCAAACACCACCTAGGCTCC 60.323 60.000 9.30 0.00 43.14 4.70
3448 5746 1.529309 CTAGGCTCCCCCTTTGCTC 59.471 63.158 0.00 0.00 43.06 4.26
3477 5775 3.275143 TGGCAATACGGTTGGTTCTATG 58.725 45.455 5.19 0.00 0.00 2.23
3538 5836 1.592939 GATCTCGAGAAAGGCGGCC 60.593 63.158 20.91 12.11 0.00 6.13
3578 5876 6.049955 TCGTGTGAAGGAAAAGGAAGATAT 57.950 37.500 0.00 0.00 0.00 1.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
47 56 4.148825 ACATGTCCCTCGCTCGCC 62.149 66.667 0.00 0.00 0.00 5.54
61 70 2.809601 GACAAGCCGCGACGACAT 60.810 61.111 8.23 0.00 0.00 3.06
109 118 4.477975 GTCACGTCGAGGGAGCGG 62.478 72.222 10.27 0.00 29.32 5.52
110 119 2.921538 GATGTCACGTCGAGGGAGCG 62.922 65.000 10.27 0.00 29.32 5.03
111 120 1.226717 GATGTCACGTCGAGGGAGC 60.227 63.158 10.27 0.00 29.32 4.70
112 121 1.313091 TGGATGTCACGTCGAGGGAG 61.313 60.000 10.27 1.85 29.32 4.30
113 122 1.303806 TGGATGTCACGTCGAGGGA 60.304 57.895 10.27 1.31 0.00 4.20
123 132 5.535753 ACGATGATTCATAGTGGATGTCA 57.464 39.130 11.07 0.00 36.84 3.58
144 153 1.671379 GGCCAGACCACTCGGAAAC 60.671 63.158 0.00 0.00 38.86 2.78
161 170 2.574212 GTACGTACACGGTCGCGG 60.574 66.667 20.67 0.00 44.95 6.46
164 173 2.245795 TTCATGTACGTACACGGTCG 57.754 50.000 29.54 15.56 44.95 4.79
173 182 1.701545 CCGCCGCATTTCATGTACGT 61.702 55.000 0.00 0.00 0.00 3.57
175 184 0.944386 ATCCGCCGCATTTCATGTAC 59.056 50.000 0.00 0.00 0.00 2.90
179 188 4.082787 CCTAATAAATCCGCCGCATTTCAT 60.083 41.667 0.00 0.00 0.00 2.57
189 198 1.818674 CCCCATGCCTAATAAATCCGC 59.181 52.381 0.00 0.00 0.00 5.54
209 218 1.008309 GTCTCGGCTATCCTCGCAC 60.008 63.158 0.00 0.00 0.00 5.34
288 297 0.240945 GAACCAAACACCAGCCGATG 59.759 55.000 0.00 0.00 0.00 3.84
289 298 0.893727 GGAACCAAACACCAGCCGAT 60.894 55.000 0.00 0.00 0.00 4.18
296 305 0.173708 TTGCAACGGAACCAAACACC 59.826 50.000 0.00 0.00 0.00 4.16
309 318 1.334288 GCGCCATGTACGTTTGCAAC 61.334 55.000 0.00 0.00 0.00 4.17
330 339 4.329545 TGGGGGAAGAGTGCGTGC 62.330 66.667 0.00 0.00 0.00 5.34
331 340 2.046892 CTGGGGGAAGAGTGCGTG 60.047 66.667 0.00 0.00 0.00 5.34
332 341 2.147387 AACTGGGGGAAGAGTGCGT 61.147 57.895 0.00 0.00 0.00 5.24
333 342 1.672356 CAACTGGGGGAAGAGTGCG 60.672 63.158 0.00 0.00 0.00 5.34
334 343 0.890996 CACAACTGGGGGAAGAGTGC 60.891 60.000 0.00 0.00 0.00 4.40
335 344 0.474184 ACACAACTGGGGGAAGAGTG 59.526 55.000 0.00 0.00 34.88 3.51
336 345 1.133792 CAACACAACTGGGGGAAGAGT 60.134 52.381 0.00 0.00 0.00 3.24
337 346 1.609208 CAACACAACTGGGGGAAGAG 58.391 55.000 0.00 0.00 0.00 2.85
338 347 0.467290 GCAACACAACTGGGGGAAGA 60.467 55.000 0.00 0.00 0.00 2.87
339 348 0.468029 AGCAACACAACTGGGGGAAG 60.468 55.000 0.00 0.00 0.00 3.46
340 349 0.032615 AAGCAACACAACTGGGGGAA 60.033 50.000 0.00 0.00 0.00 3.97
341 350 0.032615 AAAGCAACACAACTGGGGGA 60.033 50.000 0.00 0.00 0.00 4.81
342 351 0.104671 CAAAGCAACACAACTGGGGG 59.895 55.000 0.00 0.00 0.00 5.40
343 352 0.104671 CCAAAGCAACACAACTGGGG 59.895 55.000 0.00 0.00 0.00 4.96
344 353 0.530431 GCCAAAGCAACACAACTGGG 60.530 55.000 0.00 0.00 39.53 4.45
357 366 0.867086 CCAAACAAATGGCGCCAAAG 59.133 50.000 36.33 26.88 32.78 2.77
484 566 1.204312 GAACCGTTGAACTCAGCGC 59.796 57.895 10.09 0.00 46.76 5.92
550 665 1.202782 AGGATACGGCGAGCTCTCTTA 60.203 52.381 16.62 2.63 46.39 2.10
591 707 3.091318 CAAGGGTGCTGGATGCTAG 57.909 57.895 0.00 0.00 43.37 3.42
606 722 7.169982 CGAACCTAGGAACTGATAAATAGCAAG 59.830 40.741 17.98 0.00 41.52 4.01
607 723 6.984474 CGAACCTAGGAACTGATAAATAGCAA 59.016 38.462 17.98 0.00 41.52 3.91
640 782 7.705752 GGGTAAAAGAAGAGACTAGTTAATCCG 59.294 40.741 0.00 0.00 0.00 4.18
651 793 4.828829 TGGATTCGGGTAAAAGAAGAGAC 58.171 43.478 0.00 0.00 0.00 3.36
665 813 2.682856 CTGTGGGTACAAATGGATTCGG 59.317 50.000 0.00 0.00 36.14 4.30
672 820 6.024552 AGCAAATTACTGTGGGTACAAATG 57.975 37.500 0.00 0.00 36.14 2.32
677 825 4.156008 CCAGAAGCAAATTACTGTGGGTAC 59.844 45.833 0.00 0.00 0.00 3.34
739 2499 3.698289 TGTACTACTTCTAGGCAGCAGT 58.302 45.455 0.00 0.00 32.67 4.40
740 2500 4.098654 ACATGTACTACTTCTAGGCAGCAG 59.901 45.833 0.00 0.00 0.00 4.24
752 2515 2.163815 GACACGAGCCACATGTACTACT 59.836 50.000 0.00 0.00 0.00 2.57
753 2516 2.527100 GACACGAGCCACATGTACTAC 58.473 52.381 0.00 0.00 0.00 2.73
755 2518 0.109272 CGACACGAGCCACATGTACT 60.109 55.000 0.00 0.00 0.00 2.73
756 2519 0.388134 ACGACACGAGCCACATGTAC 60.388 55.000 0.00 0.00 0.00 2.90
760 2523 1.372997 GACACGACACGAGCCACAT 60.373 57.895 0.00 0.00 0.00 3.21
761 2524 2.027024 GACACGACACGAGCCACA 59.973 61.111 0.00 0.00 0.00 4.17
762 2525 1.344942 GATGACACGACACGAGCCAC 61.345 60.000 0.00 0.00 0.00 5.01
765 2528 2.152699 CCGATGACACGACACGAGC 61.153 63.158 0.00 0.00 35.09 5.03
766 2529 0.445043 TACCGATGACACGACACGAG 59.555 55.000 0.00 0.00 35.09 4.18
767 2530 0.445043 CTACCGATGACACGACACGA 59.555 55.000 0.00 0.00 35.09 4.35
768 2531 0.522705 CCTACCGATGACACGACACG 60.523 60.000 0.00 0.00 35.09 4.49
769 2532 0.806868 TCCTACCGATGACACGACAC 59.193 55.000 0.00 0.00 35.09 3.67
770 2533 1.092348 CTCCTACCGATGACACGACA 58.908 55.000 0.00 0.00 35.09 4.35
771 2534 0.248539 GCTCCTACCGATGACACGAC 60.249 60.000 0.00 0.00 35.09 4.34
772 2535 0.678684 TGCTCCTACCGATGACACGA 60.679 55.000 0.00 0.00 35.09 4.35
773 2536 0.525668 GTGCTCCTACCGATGACACG 60.526 60.000 0.00 0.00 0.00 4.49
909 2673 1.735920 GTGCTGTCTGTCTCTGCGG 60.736 63.158 0.00 0.00 33.56 5.69
910 2674 1.006922 TGTGCTGTCTGTCTCTGCG 60.007 57.895 0.00 0.00 33.56 5.18
1059 2981 4.584518 TGCTGCTGGTGGGTGTGG 62.585 66.667 0.00 0.00 0.00 4.17
1062 2984 4.960866 TGCTGCTGCTGGTGGGTG 62.961 66.667 17.00 0.00 40.48 4.61
1063 2985 4.655647 CTGCTGCTGCTGGTGGGT 62.656 66.667 17.00 0.00 40.48 4.51
1066 2988 3.738246 CTGCTGCTGCTGCTGGTG 61.738 66.667 27.67 13.98 40.48 4.17
1067 2989 3.486905 TTCTGCTGCTGCTGCTGGT 62.487 57.895 28.30 0.00 40.48 4.00
1338 3272 4.840005 CCGGCGGCCTTCTTCTCC 62.840 72.222 15.42 0.00 0.00 3.71
2433 4367 1.107114 CGCTCTCCATGTACACCTCT 58.893 55.000 0.00 0.00 0.00 3.69
2643 4587 4.485834 CAATCGTCGTCCGCCGGA 62.486 66.667 5.05 0.00 37.11 5.14
2794 4748 3.567164 GCATCATGGATCCGAACTGAAAT 59.433 43.478 7.39 0.00 0.00 2.17
2879 4833 1.621317 TCGGTGCTACCATCAGACAAA 59.379 47.619 6.21 0.00 38.47 2.83
2903 4857 0.744414 ACGCCGGACAAATCATCTGG 60.744 55.000 5.05 0.00 44.41 3.86
2914 4868 0.725117 CATAAACTGGAACGCCGGAC 59.275 55.000 5.05 0.00 43.76 4.79
2916 4870 1.597663 GATCATAAACTGGAACGCCGG 59.402 52.381 0.00 0.00 46.62 6.13
2918 4895 4.900635 AATGATCATAAACTGGAACGCC 57.099 40.909 9.04 0.00 0.00 5.68
2935 4912 7.337938 TGGTGCTATTATCAGACAGAAAATGA 58.662 34.615 0.00 0.00 0.00 2.57
2951 4928 9.023962 TGTTTAGATCAGAAATTTGGTGCTATT 57.976 29.630 0.00 0.00 0.00 1.73
2952 4929 8.579850 TGTTTAGATCAGAAATTTGGTGCTAT 57.420 30.769 0.00 0.00 0.00 2.97
2973 4985 4.156008 GGGAATCTGCGTATGAACTTGTTT 59.844 41.667 0.00 0.00 0.00 2.83
2975 4987 3.270877 GGGAATCTGCGTATGAACTTGT 58.729 45.455 0.00 0.00 0.00 3.16
3009 5021 1.275666 TCAGACCATGTTCACCGGAT 58.724 50.000 9.46 0.00 0.00 4.18
3259 5557 0.759060 ACACCCCCTTTGTCTTTGCC 60.759 55.000 0.00 0.00 0.00 4.52
3264 5562 0.634465 ACCAAACACCCCCTTTGTCT 59.366 50.000 0.00 0.00 0.00 3.41
3265 5563 1.491668 AACCAAACACCCCCTTTGTC 58.508 50.000 0.00 0.00 0.00 3.18
3266 5564 1.834896 GAAACCAAACACCCCCTTTGT 59.165 47.619 0.00 0.00 0.00 2.83
3267 5565 1.834263 TGAAACCAAACACCCCCTTTG 59.166 47.619 0.00 0.00 0.00 2.77
3269 5567 1.691163 CCTGAAACCAAACACCCCCTT 60.691 52.381 0.00 0.00 0.00 3.95
3270 5568 0.105709 CCTGAAACCAAACACCCCCT 60.106 55.000 0.00 0.00 0.00 4.79
3271 5569 1.118965 CCCTGAAACCAAACACCCCC 61.119 60.000 0.00 0.00 0.00 5.40
3272 5570 0.105913 TCCCTGAAACCAAACACCCC 60.106 55.000 0.00 0.00 0.00 4.95
3273 5571 2.009681 ATCCCTGAAACCAAACACCC 57.990 50.000 0.00 0.00 0.00 4.61
3274 5572 4.415881 AAAATCCCTGAAACCAAACACC 57.584 40.909 0.00 0.00 0.00 4.16
3310 5608 8.260114 CCATATTTGATTTGCTAGGGACTTTTT 58.740 33.333 0.00 0.00 41.75 1.94
3311 5609 7.147672 CCCATATTTGATTTGCTAGGGACTTTT 60.148 37.037 0.00 0.00 41.75 2.27
3312 5610 6.324770 CCCATATTTGATTTGCTAGGGACTTT 59.675 38.462 0.00 0.00 41.75 2.66
3313 5611 5.835280 CCCATATTTGATTTGCTAGGGACTT 59.165 40.000 0.00 0.00 41.75 3.01
3314 5612 5.388654 CCCATATTTGATTTGCTAGGGACT 58.611 41.667 0.00 0.00 46.37 3.85
3315 5613 4.524328 CCCCATATTTGATTTGCTAGGGAC 59.476 45.833 0.00 0.00 35.81 4.46
3316 5614 4.418526 TCCCCATATTTGATTTGCTAGGGA 59.581 41.667 0.00 0.00 37.50 4.20
3317 5615 4.524328 GTCCCCATATTTGATTTGCTAGGG 59.476 45.833 0.00 0.00 0.00 3.53
3318 5616 5.388654 AGTCCCCATATTTGATTTGCTAGG 58.611 41.667 0.00 0.00 0.00 3.02
3319 5617 6.966534 AAGTCCCCATATTTGATTTGCTAG 57.033 37.500 0.00 0.00 0.00 3.42
3320 5618 7.732222 AAAAGTCCCCATATTTGATTTGCTA 57.268 32.000 0.00 0.00 0.00 3.49
3321 5619 6.625532 AAAAGTCCCCATATTTGATTTGCT 57.374 33.333 0.00 0.00 0.00 3.91
3352 5650 8.956533 ATGCTTTTAAGGACTTTTAGCAAAAA 57.043 26.923 14.75 4.65 33.41 1.94
3353 5651 8.421002 AGATGCTTTTAAGGACTTTTAGCAAAA 58.579 29.630 14.75 5.17 33.41 2.44
3354 5652 7.951591 AGATGCTTTTAAGGACTTTTAGCAAA 58.048 30.769 14.75 0.00 33.41 3.68
3355 5653 7.524717 AGATGCTTTTAAGGACTTTTAGCAA 57.475 32.000 14.75 4.67 33.41 3.91
3356 5654 7.448469 AGAAGATGCTTTTAAGGACTTTTAGCA 59.552 33.333 13.77 13.77 0.00 3.49
3357 5655 7.821652 AGAAGATGCTTTTAAGGACTTTTAGC 58.178 34.615 0.00 0.00 0.00 3.09
3358 5656 9.617975 CAAGAAGATGCTTTTAAGGACTTTTAG 57.382 33.333 0.00 0.00 0.00 1.85
3359 5657 9.349713 TCAAGAAGATGCTTTTAAGGACTTTTA 57.650 29.630 0.00 0.00 0.00 1.52
3360 5658 8.237811 TCAAGAAGATGCTTTTAAGGACTTTT 57.762 30.769 0.00 0.00 0.00 2.27
3361 5659 7.823745 TCAAGAAGATGCTTTTAAGGACTTT 57.176 32.000 0.00 0.00 0.00 2.66
3362 5660 7.823745 TTCAAGAAGATGCTTTTAAGGACTT 57.176 32.000 0.00 0.00 0.00 3.01
3363 5661 7.503902 ACTTTCAAGAAGATGCTTTTAAGGACT 59.496 33.333 0.00 0.00 0.00 3.85
3364 5662 7.652727 ACTTTCAAGAAGATGCTTTTAAGGAC 58.347 34.615 0.00 0.00 0.00 3.85
3365 5663 7.721399 AGACTTTCAAGAAGATGCTTTTAAGGA 59.279 33.333 0.00 0.00 0.00 3.36
3366 5664 7.880105 AGACTTTCAAGAAGATGCTTTTAAGG 58.120 34.615 0.00 0.00 0.00 2.69
3367 5665 9.741647 AAAGACTTTCAAGAAGATGCTTTTAAG 57.258 29.630 0.00 0.00 0.00 1.85
3402 5700 6.157904 GTGTTTGGTTCTCTAGTCTTAGGAC 58.842 44.000 0.00 0.00 42.41 3.85
3403 5701 5.245526 GGTGTTTGGTTCTCTAGTCTTAGGA 59.754 44.000 0.00 0.00 0.00 2.94
3404 5702 5.011738 TGGTGTTTGGTTCTCTAGTCTTAGG 59.988 44.000 0.00 0.00 0.00 2.69
3405 5703 5.927115 GTGGTGTTTGGTTCTCTAGTCTTAG 59.073 44.000 0.00 0.00 0.00 2.18
3406 5704 5.221581 GGTGGTGTTTGGTTCTCTAGTCTTA 60.222 44.000 0.00 0.00 0.00 2.10
3407 5705 4.444449 GGTGGTGTTTGGTTCTCTAGTCTT 60.444 45.833 0.00 0.00 0.00 3.01
3408 5706 3.071167 GGTGGTGTTTGGTTCTCTAGTCT 59.929 47.826 0.00 0.00 0.00 3.24
3409 5707 3.071167 AGGTGGTGTTTGGTTCTCTAGTC 59.929 47.826 0.00 0.00 0.00 2.59
3410 5708 3.046374 AGGTGGTGTTTGGTTCTCTAGT 58.954 45.455 0.00 0.00 0.00 2.57
3411 5709 3.771577 AGGTGGTGTTTGGTTCTCTAG 57.228 47.619 0.00 0.00 0.00 2.43
3412 5710 3.581332 CCTAGGTGGTGTTTGGTTCTCTA 59.419 47.826 0.00 0.00 0.00 2.43
3413 5711 2.372172 CCTAGGTGGTGTTTGGTTCTCT 59.628 50.000 0.00 0.00 0.00 3.10
3414 5712 2.779506 CCTAGGTGGTGTTTGGTTCTC 58.220 52.381 0.00 0.00 0.00 2.87
3415 5713 1.202891 GCCTAGGTGGTGTTTGGTTCT 60.203 52.381 11.31 0.00 38.35 3.01
3416 5714 1.202891 AGCCTAGGTGGTGTTTGGTTC 60.203 52.381 11.31 0.00 38.35 3.62
3417 5715 0.850784 AGCCTAGGTGGTGTTTGGTT 59.149 50.000 11.31 0.00 38.35 3.67
3418 5716 0.400594 GAGCCTAGGTGGTGTTTGGT 59.599 55.000 11.31 0.00 38.35 3.67
3419 5717 0.322546 GGAGCCTAGGTGGTGTTTGG 60.323 60.000 11.31 0.00 38.35 3.28
3420 5718 0.322546 GGGAGCCTAGGTGGTGTTTG 60.323 60.000 11.31 0.00 38.35 2.93
3421 5719 1.498176 GGGGAGCCTAGGTGGTGTTT 61.498 60.000 11.31 0.00 38.35 2.83
3422 5720 1.923909 GGGGAGCCTAGGTGGTGTT 60.924 63.158 11.31 0.00 38.35 3.32
3423 5721 2.285442 GGGGAGCCTAGGTGGTGT 60.285 66.667 11.31 0.00 38.35 4.16
3424 5722 3.090532 GGGGGAGCCTAGGTGGTG 61.091 72.222 11.31 0.00 38.35 4.17
3425 5723 2.432567 AAAGGGGGAGCCTAGGTGGT 62.433 60.000 11.31 0.00 38.35 4.16
3426 5724 1.619669 AAAGGGGGAGCCTAGGTGG 60.620 63.158 11.31 0.00 39.35 4.61
3427 5725 1.609783 CAAAGGGGGAGCCTAGGTG 59.390 63.158 11.31 0.00 0.00 4.00
3428 5726 2.309504 GCAAAGGGGGAGCCTAGGT 61.310 63.158 11.31 0.00 0.00 3.08
3429 5727 1.988982 GAGCAAAGGGGGAGCCTAGG 61.989 65.000 3.67 3.67 0.00 3.02
3430 5728 1.274703 TGAGCAAAGGGGGAGCCTAG 61.275 60.000 0.00 0.00 0.00 3.02
3431 5729 1.229820 TGAGCAAAGGGGGAGCCTA 60.230 57.895 0.00 0.00 0.00 3.93
3448 5746 1.062365 CCGTATTGCCATGTGCGTG 59.938 57.895 0.00 0.00 45.60 5.34
3477 5775 7.327275 CAGAATCGTAGAATGGAGTATACAAGC 59.673 40.741 5.50 0.00 43.58 4.01
3526 5824 1.401905 CAATAAGTGGCCGCCTTTCTC 59.598 52.381 14.07 0.00 0.00 2.87
3538 5836 7.906611 TCACACGAAATCAAAACAATAAGTG 57.093 32.000 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.