Multiple sequence alignment - TraesCS3D01G273200

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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 TraesCS3D01G273200 chr3D 100.000 4417 0 0 1 4417 378921983 378926399 0.000000e+00 8157.0
1 TraesCS3D01G273200 chr3D 100.000 31 0 0 3941 3971 451374005 451373975 1.720000e-04 58.4
2 TraesCS3D01G273200 chr3A 94.161 3100 134 29 778 3855 502836235 502839309 0.000000e+00 4678.0
3 TraesCS3D01G273200 chr3A 93.394 439 21 4 3968 4398 502839312 502839750 1.040000e-180 643.0
4 TraesCS3D01G273200 chr3A 84.810 553 36 24 16 536 502835630 502836166 3.050000e-141 512.0
5 TraesCS3D01G273200 chr3A 96.226 53 2 0 704 756 502836185 502836237 2.190000e-13 87.9
6 TraesCS3D01G273200 chr3B 93.779 2347 83 21 16 2325 494069347 494071667 0.000000e+00 3467.0
7 TraesCS3D01G273200 chr3B 93.198 838 26 20 2983 3800 494072911 494073737 0.000000e+00 1203.0
8 TraesCS3D01G273200 chr3B 94.530 585 21 3 2350 2934 494071660 494072233 0.000000e+00 893.0
9 TraesCS3D01G273200 chr3B 94.444 450 20 3 3968 4417 494073768 494074212 0.000000e+00 688.0
10 TraesCS3D01G273200 chr3B 95.604 91 3 1 3845 3935 64541117 64541028 1.280000e-30 145.0
11 TraesCS3D01G273200 chr3B 100.000 29 0 0 3938 3966 492208367 492208339 2.000000e-03 54.7
12 TraesCS3D01G273200 chr1B 97.701 87 1 1 3849 3935 420658897 420658812 9.900000e-32 148.0
13 TraesCS3D01G273200 chr1B 95.455 88 4 0 3847 3934 90698033 90697946 1.660000e-29 141.0
14 TraesCS3D01G273200 chr1B 89.524 105 7 4 3833 3935 368411212 368411314 3.590000e-26 130.0
15 TraesCS3D01G273200 chr1B 100.000 29 0 0 3938 3966 39849943 39849971 2.000000e-03 54.7
16 TraesCS3D01G273200 chr2D 92.000 100 6 2 3837 3935 392090446 392090544 5.960000e-29 139.0
17 TraesCS3D01G273200 chr2B 91.837 98 6 2 3838 3935 397939363 397939458 7.710000e-28 135.0
18 TraesCS3D01G273200 chr2B 88.182 110 9 4 3827 3935 752488050 752488156 1.290000e-25 128.0
19 TraesCS3D01G273200 chr2B 96.970 33 0 1 3935 3967 397990390 397990421 2.000000e-03 54.7
20 TraesCS3D01G273200 chr2B 94.118 34 2 0 3939 3972 674033351 674033318 8.000000e-03 52.8
21 TraesCS3D01G273200 chrUn 92.553 94 6 1 3842 3935 22130826 22130734 2.770000e-27 134.0
22 TraesCS3D01G273200 chrUn 96.923 65 2 0 3850 3914 12894000 12894064 4.670000e-20 110.0
23 TraesCS3D01G273200 chr7B 86.325 117 14 2 3850 3966 503865960 503865846 4.640000e-25 126.0
24 TraesCS3D01G273200 chr2A 96.923 65 2 0 3850 3914 39712063 39712127 4.670000e-20 110.0
25 TraesCS3D01G273200 chr4A 100.000 29 0 0 3938 3966 552149443 552149471 2.000000e-03 54.7


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 TraesCS3D01G273200 chr3D 378921983 378926399 4416 False 8157.000 8157 100.00000 1 4417 1 chr3D.!!$F1 4416
1 TraesCS3D01G273200 chr3A 502835630 502839750 4120 False 1480.225 4678 92.14775 16 4398 4 chr3A.!!$F1 4382
2 TraesCS3D01G273200 chr3B 494069347 494074212 4865 False 1562.750 3467 93.98775 16 4417 4 chr3B.!!$F1 4401

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
982 1059 0.242825 CATCCATCCATTGCATCGGC 59.757 55.0 0.00 0.0 41.68 5.54 F
2682 2767 0.097674 AATGCTGCGCGAAGATTGTC 59.902 50.0 21.09 0.0 0.00 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2796 2881 0.373716 GGCCGAAGCTGTAAACATCG 59.626 55.0 0.0 0.0 39.73 3.84 R
3954 4687 0.034283 ACTCTACCACTCCCTCCGTC 60.034 60.0 0.0 0.0 0.00 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
103 109 4.678743 AACAAAGGCGGGGAGGGC 62.679 66.667 0.00 0.00 0.00 5.19
198 209 3.171388 CCCCCTTCCATCCCTCCG 61.171 72.222 0.00 0.00 0.00 4.63
236 255 4.308458 CGCTCCACCCACGTCCAA 62.308 66.667 0.00 0.00 0.00 3.53
237 256 2.112297 GCTCCACCCACGTCCAAA 59.888 61.111 0.00 0.00 0.00 3.28
284 307 2.516225 GCCCGATTCTTTCCCCCG 60.516 66.667 0.00 0.00 0.00 5.73
452 508 2.422093 GGTTTCAGATTAGGAGGGCCAG 60.422 54.545 6.18 0.00 36.29 4.85
483 539 1.158434 TTTGGATACCGGTTGCGTTC 58.842 50.000 15.04 2.37 0.00 3.95
538 599 2.725008 GAGGTCTCCCGATCGCTG 59.275 66.667 10.32 2.78 35.12 5.18
541 602 4.593864 GTCTCCCGATCGCTGCCC 62.594 72.222 10.32 0.00 0.00 5.36
565 626 2.538141 CCTCCCCCTGTTTCCTGCA 61.538 63.158 0.00 0.00 0.00 4.41
566 627 1.693640 CTCCCCCTGTTTCCTGCAT 59.306 57.895 0.00 0.00 0.00 3.96
567 628 0.682209 CTCCCCCTGTTTCCTGCATG 60.682 60.000 0.00 0.00 0.00 4.06
568 629 1.077265 CCCCCTGTTTCCTGCATGT 59.923 57.895 0.00 0.00 0.00 3.21
569 630 1.252904 CCCCCTGTTTCCTGCATGTG 61.253 60.000 0.00 0.00 0.00 3.21
607 668 0.307760 CGCACGCCTCTGTTTTTCTT 59.692 50.000 0.00 0.00 0.00 2.52
625 686 4.681978 GCCTGCACGGTTCCTCGT 62.682 66.667 4.45 0.00 44.91 4.18
644 705 3.010138 TCGTTCCAATTTGATCCCTCCTT 59.990 43.478 0.00 0.00 0.00 3.36
647 708 4.953781 TCCAATTTGATCCCTCCTTCTT 57.046 40.909 0.00 0.00 0.00 2.52
775 852 4.517815 GCGGCGGTCCACGGAATA 62.518 66.667 9.78 0.00 44.51 1.75
812 889 1.260033 GAATTCAGAGCAATCGAGGCG 59.740 52.381 0.00 0.00 36.08 5.52
828 905 0.733150 GGCGTGCCATAAGAAGAACC 59.267 55.000 5.89 0.00 35.81 3.62
917 994 3.117398 TCGTCCAGGTTCCTATAAGCCTA 60.117 47.826 0.00 0.00 0.00 3.93
924 1001 6.935208 CCAGGTTCCTATAAGCCTAATAACAC 59.065 42.308 0.00 0.00 0.00 3.32
982 1059 0.242825 CATCCATCCATTGCATCGGC 59.757 55.000 0.00 0.00 41.68 5.54
1047 1124 2.722201 GCGGACGAGGTTCTCCCAT 61.722 63.158 0.00 0.00 34.66 4.00
1188 1265 1.374947 CTTCGAGCCCAGGACCAAA 59.625 57.895 0.00 0.00 0.00 3.28
1221 1298 2.533232 AACCCGGTCCCCATTCCA 60.533 61.111 0.00 0.00 0.00 3.53
1430 1507 3.254024 TTCAGGACCCGAGCAAGGC 62.254 63.158 0.00 0.00 0.00 4.35
1467 1544 0.178944 TCGAGTTCTCCTTCCACCCA 60.179 55.000 0.00 0.00 0.00 4.51
1722 1802 2.810012 GCGCCGGAAATCTTCGTCC 61.810 63.158 5.05 0.00 0.00 4.79
1841 1921 0.793250 GCAGAGAAGGTGCTCGAAAC 59.207 55.000 0.00 0.00 39.87 2.78
1977 2057 0.681564 AGCCTGACGTCGAGGAAGAT 60.682 55.000 27.67 13.33 31.48 2.40
2065 2145 4.804139 AGCATCGAAACGTCATTAAGGTAG 59.196 41.667 0.00 0.00 0.00 3.18
2066 2146 4.565564 GCATCGAAACGTCATTAAGGTAGT 59.434 41.667 0.00 0.00 0.00 2.73
2067 2147 5.745294 GCATCGAAACGTCATTAAGGTAGTA 59.255 40.000 0.00 0.00 0.00 1.82
2086 2166 5.476091 AGTAACTTCCTGAGTTTCCTCTG 57.524 43.478 0.00 0.00 46.34 3.35
2215 2297 0.107831 ACGTTTAGCCTTGTGCCAGA 59.892 50.000 0.00 0.00 42.71 3.86
2223 2305 1.740025 GCCTTGTGCCAGATGACTTAC 59.260 52.381 0.00 0.00 0.00 2.34
2278 2360 5.958987 ACTAAGTTTCCATCAGTACCTAGCT 59.041 40.000 0.00 0.00 0.00 3.32
2281 2363 6.128138 AGTTTCCATCAGTACCTAGCTTTT 57.872 37.500 0.00 0.00 0.00 2.27
2282 2364 7.253905 AGTTTCCATCAGTACCTAGCTTTTA 57.746 36.000 0.00 0.00 0.00 1.52
2283 2365 7.331791 AGTTTCCATCAGTACCTAGCTTTTAG 58.668 38.462 0.00 0.00 0.00 1.85
2284 2366 6.869206 TTCCATCAGTACCTAGCTTTTAGT 57.131 37.500 0.00 0.00 0.00 2.24
2287 2369 6.439375 TCCATCAGTACCTAGCTTTTAGTTCA 59.561 38.462 0.00 0.00 0.00 3.18
2288 2370 6.758886 CCATCAGTACCTAGCTTTTAGTTCAG 59.241 42.308 0.00 0.00 0.00 3.02
2290 2372 5.778750 TCAGTACCTAGCTTTTAGTTCAGGT 59.221 40.000 5.88 5.88 39.63 4.00
2309 2391 0.389296 TGTGTTCCTACGTCATGCCG 60.389 55.000 0.00 0.00 0.00 5.69
2389 2471 3.955471 ACGTGATCCCATCTTTGATGTT 58.045 40.909 6.78 0.00 0.00 2.71
2540 2622 4.937781 GCACAAGCAAGAGCACAG 57.062 55.556 0.00 0.00 45.49 3.66
2643 2725 0.245539 ATCGTGACGTGAAACCGGAT 59.754 50.000 9.46 0.00 0.00 4.18
2664 2746 6.001460 GGATAACATCATATTTGACGGGGAA 58.999 40.000 0.00 0.00 33.85 3.97
2665 2747 6.659242 GGATAACATCATATTTGACGGGGAAT 59.341 38.462 0.00 0.00 33.85 3.01
2666 2748 5.772825 AACATCATATTTGACGGGGAATG 57.227 39.130 0.00 0.00 33.85 2.67
2667 2749 3.569701 ACATCATATTTGACGGGGAATGC 59.430 43.478 0.00 0.00 33.85 3.56
2682 2767 0.097674 AATGCTGCGCGAAGATTGTC 59.902 50.000 21.09 0.00 0.00 3.18
2709 2794 0.940833 GAATAGCCTGCGAAGAAGCC 59.059 55.000 0.00 0.00 36.02 4.35
2760 2845 0.250209 CCTTCAGATGGATGGCTCCG 60.250 60.000 0.00 0.00 45.37 4.63
2796 2881 2.912020 ACCCTATGGTCGGAAGGTC 58.088 57.895 0.00 0.00 43.06 3.85
2934 3019 1.351017 GTCCCATTTCTGTCCCTGTCA 59.649 52.381 0.00 0.00 0.00 3.58
2935 3020 1.630369 TCCCATTTCTGTCCCTGTCAG 59.370 52.381 0.00 0.00 0.00 3.51
2985 3321 7.872113 ATACAAATTTTCCAGATGGAGAGAC 57.128 36.000 1.13 0.00 46.36 3.36
2986 3322 5.634118 ACAAATTTTCCAGATGGAGAGACA 58.366 37.500 1.13 0.00 46.36 3.41
2987 3323 6.251471 ACAAATTTTCCAGATGGAGAGACAT 58.749 36.000 1.13 0.00 46.36 3.06
2989 3325 7.890127 ACAAATTTTCCAGATGGAGAGACATTA 59.110 33.333 1.13 0.00 46.36 1.90
2990 3326 8.404000 CAAATTTTCCAGATGGAGAGACATTAG 58.596 37.037 1.13 0.00 46.36 1.73
2991 3327 5.620738 TTTCCAGATGGAGAGACATTAGG 57.379 43.478 1.13 0.00 46.36 2.69
2992 3328 2.968574 TCCAGATGGAGAGACATTAGGC 59.031 50.000 0.00 0.00 39.78 3.93
2993 3329 2.702478 CCAGATGGAGAGACATTAGGCA 59.298 50.000 0.00 0.00 37.39 4.75
2997 3333 3.827008 TGGAGAGACATTAGGCATGAC 57.173 47.619 0.00 0.00 36.24 3.06
3003 3720 4.880120 AGAGACATTAGGCATGACATTGTG 59.120 41.667 0.00 0.00 36.24 3.33
3016 3733 5.503662 TGACATTGTGCATATGGACATTC 57.496 39.130 27.79 22.65 45.59 2.67
3023 3740 9.537192 CATTGTGCATATGGACATTCTTTTAAT 57.463 29.630 27.79 14.39 45.59 1.40
3110 3835 6.016777 TGCTTTCTGAGAAGAAGAAAATGACC 60.017 38.462 0.00 0.00 41.74 4.02
3111 3836 6.016777 GCTTTCTGAGAAGAAGAAAATGACCA 60.017 38.462 0.00 0.00 41.74 4.02
3112 3837 6.867662 TTCTGAGAAGAAGAAAATGACCAC 57.132 37.500 0.00 0.00 30.79 4.16
3113 3838 5.308825 TCTGAGAAGAAGAAAATGACCACC 58.691 41.667 0.00 0.00 0.00 4.61
3114 3839 5.047566 TGAGAAGAAGAAAATGACCACCA 57.952 39.130 0.00 0.00 0.00 4.17
3617 4349 1.354031 TGCCTATGCAAAGTCCCTGAA 59.646 47.619 0.00 0.00 46.66 3.02
3618 4350 2.224992 TGCCTATGCAAAGTCCCTGAAA 60.225 45.455 0.00 0.00 46.66 2.69
3665 4397 5.065859 TGAATGTTTGTTGTCATTGACTCGT 59.934 36.000 17.26 1.45 34.92 4.18
3676 4408 6.053005 TGTCATTGACTCGTCCTTTTTAACT 58.947 36.000 17.26 0.00 33.15 2.24
3684 4416 5.535406 ACTCGTCCTTTTTAACTCTGAGAGA 59.465 40.000 17.71 0.00 33.32 3.10
3704 4436 7.445402 TGAGAGAGTCCAAAAGAAAAATCGAAT 59.555 33.333 0.00 0.00 0.00 3.34
3834 4567 2.305635 TGAGCAGAGCACCTTCCAATTA 59.694 45.455 0.00 0.00 0.00 1.40
3855 4588 7.781548 ATTATTGTCGTTGTATTGTACTCCC 57.218 36.000 0.00 0.00 0.00 4.30
3856 4589 4.877378 TTGTCGTTGTATTGTACTCCCT 57.123 40.909 0.00 0.00 0.00 4.20
3857 4590 4.445452 TGTCGTTGTATTGTACTCCCTC 57.555 45.455 0.00 0.00 0.00 4.30
3858 4591 3.194116 TGTCGTTGTATTGTACTCCCTCC 59.806 47.826 0.00 0.00 0.00 4.30
3859 4592 3.194116 GTCGTTGTATTGTACTCCCTCCA 59.806 47.826 0.00 0.00 0.00 3.86
3860 4593 4.028131 TCGTTGTATTGTACTCCCTCCAT 58.972 43.478 0.00 0.00 0.00 3.41
3861 4594 4.098960 TCGTTGTATTGTACTCCCTCCATC 59.901 45.833 0.00 0.00 0.00 3.51
3862 4595 4.704965 GTTGTATTGTACTCCCTCCATCC 58.295 47.826 0.00 0.00 0.00 3.51
3863 4596 3.314693 TGTATTGTACTCCCTCCATCCC 58.685 50.000 0.00 0.00 0.00 3.85
3864 4597 2.587060 ATTGTACTCCCTCCATCCCA 57.413 50.000 0.00 0.00 0.00 4.37
3865 4598 2.352561 TTGTACTCCCTCCATCCCAA 57.647 50.000 0.00 0.00 0.00 4.12
3866 4599 2.352561 TGTACTCCCTCCATCCCAAA 57.647 50.000 0.00 0.00 0.00 3.28
3867 4600 2.638325 TGTACTCCCTCCATCCCAAAA 58.362 47.619 0.00 0.00 0.00 2.44
3868 4601 3.197983 TGTACTCCCTCCATCCCAAAAT 58.802 45.455 0.00 0.00 0.00 1.82
3869 4602 4.376223 TGTACTCCCTCCATCCCAAAATA 58.624 43.478 0.00 0.00 0.00 1.40
3870 4603 4.791334 TGTACTCCCTCCATCCCAAAATAA 59.209 41.667 0.00 0.00 0.00 1.40
3871 4604 4.526438 ACTCCCTCCATCCCAAAATAAG 57.474 45.455 0.00 0.00 0.00 1.73
3872 4605 3.858638 ACTCCCTCCATCCCAAAATAAGT 59.141 43.478 0.00 0.00 0.00 2.24
3873 4606 4.210331 CTCCCTCCATCCCAAAATAAGTG 58.790 47.826 0.00 0.00 0.00 3.16
3874 4607 3.596046 TCCCTCCATCCCAAAATAAGTGT 59.404 43.478 0.00 0.00 0.00 3.55
3875 4608 3.954258 CCCTCCATCCCAAAATAAGTGTC 59.046 47.826 0.00 0.00 0.00 3.67
3876 4609 4.325344 CCCTCCATCCCAAAATAAGTGTCT 60.325 45.833 0.00 0.00 0.00 3.41
3877 4610 5.264395 CCTCCATCCCAAAATAAGTGTCTT 58.736 41.667 0.00 0.00 0.00 3.01
3878 4611 5.126061 CCTCCATCCCAAAATAAGTGTCTTG 59.874 44.000 0.00 0.00 0.00 3.02
3879 4612 5.886609 TCCATCCCAAAATAAGTGTCTTGA 58.113 37.500 0.00 0.00 0.00 3.02
3880 4613 5.945784 TCCATCCCAAAATAAGTGTCTTGAG 59.054 40.000 0.00 0.00 0.00 3.02
3881 4614 5.711976 CCATCCCAAAATAAGTGTCTTGAGT 59.288 40.000 0.00 0.00 0.00 3.41
3882 4615 6.209391 CCATCCCAAAATAAGTGTCTTGAGTT 59.791 38.462 0.00 0.00 0.00 3.01
3883 4616 7.255942 CCATCCCAAAATAAGTGTCTTGAGTTT 60.256 37.037 0.00 0.00 0.00 2.66
3884 4617 8.792633 CATCCCAAAATAAGTGTCTTGAGTTTA 58.207 33.333 0.00 0.00 0.00 2.01
3885 4618 8.391075 TCCCAAAATAAGTGTCTTGAGTTTAG 57.609 34.615 0.00 0.00 0.00 1.85
3886 4619 7.996644 TCCCAAAATAAGTGTCTTGAGTTTAGT 59.003 33.333 0.00 0.00 0.00 2.24
3887 4620 9.280174 CCCAAAATAAGTGTCTTGAGTTTAGTA 57.720 33.333 0.00 0.00 0.00 1.82
3896 4629 9.174166 AGTGTCTTGAGTTTAGTACAAATTTGT 57.826 29.630 25.99 25.99 44.86 2.83
3923 4656 9.857957 ACTAGAGCTAGTACAAAATTAAGACAC 57.142 33.333 8.35 0.00 43.98 3.67
3938 4671 9.596308 AAATTAAGACACTTATTTTAGGGTGGT 57.404 29.630 0.00 0.00 30.19 4.16
3940 4673 9.901172 ATTAAGACACTTATTTTAGGGTGGTAG 57.099 33.333 0.00 0.00 30.19 3.18
3941 4674 7.563724 AAGACACTTATTTTAGGGTGGTAGA 57.436 36.000 0.00 0.00 30.19 2.59
3942 4675 6.944096 AGACACTTATTTTAGGGTGGTAGAC 58.056 40.000 0.00 0.00 30.19 2.59
3943 4676 6.499350 AGACACTTATTTTAGGGTGGTAGACA 59.501 38.462 0.00 0.00 30.19 3.41
3956 4689 5.874895 GTGGTAGACACTTATTTTGGGAC 57.125 43.478 0.00 0.00 46.72 4.46
3957 4690 4.390909 GTGGTAGACACTTATTTTGGGACG 59.609 45.833 0.00 0.00 46.72 4.79
3958 4691 3.937079 GGTAGACACTTATTTTGGGACGG 59.063 47.826 0.00 0.00 0.00 4.79
3959 4692 4.322953 GGTAGACACTTATTTTGGGACGGA 60.323 45.833 0.00 0.00 0.00 4.69
3960 4693 3.939066 AGACACTTATTTTGGGACGGAG 58.061 45.455 0.00 0.00 0.00 4.63
3961 4694 3.007635 GACACTTATTTTGGGACGGAGG 58.992 50.000 0.00 0.00 0.00 4.30
3962 4695 2.290705 ACACTTATTTTGGGACGGAGGG 60.291 50.000 0.00 0.00 0.00 4.30
3963 4696 2.026636 CACTTATTTTGGGACGGAGGGA 60.027 50.000 0.00 0.00 0.00 4.20
3964 4697 2.238898 ACTTATTTTGGGACGGAGGGAG 59.761 50.000 0.00 0.00 0.00 4.30
3965 4698 1.961133 TATTTTGGGACGGAGGGAGT 58.039 50.000 0.00 0.00 0.00 3.85
3966 4699 0.328258 ATTTTGGGACGGAGGGAGTG 59.672 55.000 0.00 0.00 0.00 3.51
3996 4729 2.747396 TGCCAAGGTGAATTGAATGC 57.253 45.000 0.00 0.00 31.55 3.56
4000 4733 3.056322 GCCAAGGTGAATTGAATGCTTCT 60.056 43.478 0.00 0.00 31.55 2.85
4111 4852 8.602328 CATTTTGCAACATTAACTCTTCAAACA 58.398 29.630 0.00 0.00 0.00 2.83
4113 4854 6.691754 TGCAACATTAACTCTTCAAACAGA 57.308 33.333 0.00 0.00 0.00 3.41
4160 4901 1.410517 CGACCTGGTATCACTGCAGAT 59.589 52.381 23.35 7.26 0.00 2.90
4188 4929 3.003897 GCCGTTTTGACCAATCAACACTA 59.996 43.478 5.16 0.00 44.66 2.74
4209 4950 6.758416 CACTATGATGCAAACTACTCAGCTTA 59.242 38.462 0.00 0.00 0.00 3.09
4357 5099 2.661176 TCCTCTACCCCAGTCCATTT 57.339 50.000 0.00 0.00 0.00 2.32
4405 5147 4.013267 ACTGAAGCTGCACAGTATCTTT 57.987 40.909 23.42 5.53 44.06 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.821600 TGCCCTCTGCGTTGTAAAATAAA 59.178 39.130 0.00 0.00 45.60 1.40
1 2 3.413327 TGCCCTCTGCGTTGTAAAATAA 58.587 40.909 0.00 0.00 45.60 1.40
2 3 3.006940 CTGCCCTCTGCGTTGTAAAATA 58.993 45.455 0.00 0.00 45.60 1.40
3 4 1.812571 CTGCCCTCTGCGTTGTAAAAT 59.187 47.619 0.00 0.00 45.60 1.82
4 5 1.202710 TCTGCCCTCTGCGTTGTAAAA 60.203 47.619 0.00 0.00 45.60 1.52
5 6 0.394938 TCTGCCCTCTGCGTTGTAAA 59.605 50.000 0.00 0.00 45.60 2.01
6 7 0.037326 CTCTGCCCTCTGCGTTGTAA 60.037 55.000 0.00 0.00 45.60 2.41
7 8 1.591703 CTCTGCCCTCTGCGTTGTA 59.408 57.895 0.00 0.00 45.60 2.41
8 9 2.345244 CTCTGCCCTCTGCGTTGT 59.655 61.111 0.00 0.00 45.60 3.32
9 10 2.249413 ATCCTCTGCCCTCTGCGTTG 62.249 60.000 0.00 0.00 45.60 4.10
10 11 1.557269 AATCCTCTGCCCTCTGCGTT 61.557 55.000 0.00 0.00 45.60 4.84
11 12 1.965754 GAATCCTCTGCCCTCTGCGT 61.966 60.000 0.00 0.00 45.60 5.24
12 13 1.227497 GAATCCTCTGCCCTCTGCG 60.227 63.158 0.00 0.00 45.60 5.18
13 14 0.545646 AAGAATCCTCTGCCCTCTGC 59.454 55.000 0.00 0.00 41.77 4.26
14 15 1.140652 GGAAGAATCCTCTGCCCTCTG 59.859 57.143 0.00 0.00 41.32 3.35
70 76 3.790089 TTGTTCCTCTTCCTTTCTCCC 57.210 47.619 0.00 0.00 0.00 4.30
120 127 0.670546 CACCGAACGAATCCAGCAGT 60.671 55.000 0.00 0.00 0.00 4.40
452 508 3.066760 CGGTATCCAAATCCAAAAGGAGC 59.933 47.826 0.00 0.00 32.91 4.70
469 525 2.816520 GCCGAACGCAACCGGTAT 60.817 61.111 8.00 0.00 46.84 2.73
548 609 0.682209 CATGCAGGAAACAGGGGGAG 60.682 60.000 0.00 0.00 0.00 4.30
556 617 3.192001 ACATCACATCACATGCAGGAAAC 59.808 43.478 4.84 0.00 0.00 2.78
565 626 5.064325 CGAGAACAATCACATCACATCACAT 59.936 40.000 0.00 0.00 0.00 3.21
566 627 4.389687 CGAGAACAATCACATCACATCACA 59.610 41.667 0.00 0.00 0.00 3.58
567 628 4.726021 GCGAGAACAATCACATCACATCAC 60.726 45.833 0.00 0.00 0.00 3.06
568 629 3.371898 GCGAGAACAATCACATCACATCA 59.628 43.478 0.00 0.00 0.00 3.07
569 630 3.371898 TGCGAGAACAATCACATCACATC 59.628 43.478 0.00 0.00 0.00 3.06
607 668 4.680237 CGAGGAACCGTGCAGGCA 62.680 66.667 0.00 0.00 46.52 4.75
625 686 4.953781 AGAAGGAGGGATCAAATTGGAA 57.046 40.909 0.00 0.00 0.00 3.53
644 705 1.223187 GGTTTCCGAACGCAAGAAGA 58.777 50.000 0.00 0.00 43.62 2.87
703 776 2.526077 TCGCGAGATCAATACACACAC 58.474 47.619 3.71 0.00 33.31 3.82
812 889 3.596214 TCTTCGGTTCTTCTTATGGCAC 58.404 45.455 0.00 0.00 0.00 5.01
828 905 0.035056 ACATTTGCTCCCCCTCTTCG 60.035 55.000 0.00 0.00 0.00 3.79
917 994 1.614385 CGAGTCGCTGACGTGTTATT 58.386 50.000 0.00 0.00 41.18 1.40
982 1059 4.530857 GCCGACCGACCAGATGGG 62.531 72.222 3.48 0.00 44.81 4.00
1047 1124 3.296836 TTGGAGCGGACGACGGAA 61.297 61.111 0.00 0.00 44.51 4.30
1211 1288 0.704076 CCTTGTCCTTGGAATGGGGA 59.296 55.000 0.00 0.00 0.00 4.81
1221 1298 0.034059 CACTCAGCGACCTTGTCCTT 59.966 55.000 0.00 0.00 0.00 3.36
1467 1544 1.815196 CCTCATGCTCTGCTCGTCT 59.185 57.895 0.00 0.00 0.00 4.18
1650 1727 1.059584 TGGCCTCCTTGAACACCTCA 61.060 55.000 3.32 0.00 0.00 3.86
1841 1921 1.361668 CTTGCGATCCACCGTCCAAG 61.362 60.000 0.00 0.00 0.00 3.61
1968 2048 1.591059 CAGCTCCGCATCTTCCTCG 60.591 63.158 0.00 0.00 0.00 4.63
1977 2057 3.381333 CTGAGATGCCAGCTCCGCA 62.381 63.158 7.61 7.43 41.28 5.69
2049 2129 7.601508 CAGGAAGTTACTACCTTAATGACGTTT 59.398 37.037 0.00 0.00 31.06 3.60
2086 2166 5.314923 TGCCTGAAACTGAATATTTCTGC 57.685 39.130 0.00 0.00 37.05 4.26
2139 2221 7.704789 AATTTCATCAGCTGTTTCAAACTTC 57.295 32.000 14.67 0.00 0.00 3.01
2278 2360 5.051816 CGTAGGAACACACCTGAACTAAAA 58.948 41.667 0.00 0.00 40.81 1.52
2281 2363 3.225104 ACGTAGGAACACACCTGAACTA 58.775 45.455 0.00 0.00 40.81 2.24
2282 2364 2.035576 GACGTAGGAACACACCTGAACT 59.964 50.000 0.00 0.00 40.81 3.01
2283 2365 2.223876 TGACGTAGGAACACACCTGAAC 60.224 50.000 0.00 0.00 40.81 3.18
2284 2366 2.033372 TGACGTAGGAACACACCTGAA 58.967 47.619 0.00 0.00 40.81 3.02
2287 2369 1.337823 GCATGACGTAGGAACACACCT 60.338 52.381 0.00 0.00 43.32 4.00
2288 2370 1.076332 GCATGACGTAGGAACACACC 58.924 55.000 0.00 0.00 0.00 4.16
2290 2372 0.389296 CGGCATGACGTAGGAACACA 60.389 55.000 14.35 0.00 0.00 3.72
2309 2391 4.637534 TGGTCATACAGGACTACTACGTTC 59.362 45.833 0.00 0.00 37.91 3.95
2389 2471 9.853555 AATAATTGACTTTGTTTTGCGATGATA 57.146 25.926 0.00 0.00 0.00 2.15
2395 2477 7.116090 TGGATCAATAATTGACTTTGTTTTGCG 59.884 33.333 0.00 0.00 43.48 4.85
2434 2516 2.229792 TGCTCCAACCAGCTACAAAAG 58.770 47.619 0.00 0.00 40.39 2.27
2469 2551 1.078759 CGGTGATGACGCAGAAGACC 61.079 60.000 0.00 0.00 0.00 3.85
2540 2622 3.340814 TCTTGTCCAAAGGCAGAGATC 57.659 47.619 0.00 0.00 0.00 2.75
2643 2725 5.240623 GCATTCCCCGTCAAATATGATGTTA 59.759 40.000 0.00 0.00 40.36 2.41
2667 2749 0.647410 AATCGACAATCTTCGCGCAG 59.353 50.000 8.75 0.00 38.95 5.18
2673 2758 6.038714 AGGCTATTCCAAAATCGACAATCTTC 59.961 38.462 0.00 0.00 37.29 2.87
2682 2767 1.939934 TCGCAGGCTATTCCAAAATCG 59.060 47.619 0.00 0.00 37.29 3.34
2709 2794 0.965866 TCGCCAGAGGGTCACAGTAG 60.966 60.000 0.00 0.00 36.17 2.57
2760 2845 2.424956 GGGTTTGTGCTTCATCATCTCC 59.575 50.000 0.00 0.00 0.00 3.71
2790 2875 3.060895 CGAAGCTGTAAACATCGACCTTC 59.939 47.826 0.00 0.00 35.65 3.46
2796 2881 0.373716 GGCCGAAGCTGTAAACATCG 59.626 55.000 0.00 0.00 39.73 3.84
2967 3303 6.599445 CCTAATGTCTCTCCATCTGGAAAAT 58.401 40.000 0.00 0.00 44.91 1.82
2985 3321 3.786516 TGCACAATGTCATGCCTAATG 57.213 42.857 0.00 0.00 41.33 1.90
2986 3322 5.047590 CCATATGCACAATGTCATGCCTAAT 60.048 40.000 9.39 0.00 41.33 1.73
2987 3323 4.278919 CCATATGCACAATGTCATGCCTAA 59.721 41.667 9.39 0.00 41.33 2.69
2989 3325 2.626266 CCATATGCACAATGTCATGCCT 59.374 45.455 9.39 0.00 41.33 4.75
2990 3326 2.624364 TCCATATGCACAATGTCATGCC 59.376 45.455 9.39 0.00 41.33 4.40
2991 3327 3.067040 TGTCCATATGCACAATGTCATGC 59.933 43.478 0.00 0.00 42.40 4.06
2992 3328 4.904253 TGTCCATATGCACAATGTCATG 57.096 40.909 0.00 0.00 0.00 3.07
2993 3329 5.831525 AGAATGTCCATATGCACAATGTCAT 59.168 36.000 3.01 9.93 0.00 3.06
2997 3333 8.929827 TTAAAAGAATGTCCATATGCACAATG 57.070 30.769 3.01 0.00 0.00 2.82
3081 3806 4.000331 TCTTCTTCTCAGAAAGCACAGG 58.000 45.455 0.00 0.00 38.63 4.00
3110 3835 6.930164 TCACATTCTGAAAATGGAAATTGGTG 59.070 34.615 0.00 0.00 32.14 4.17
3111 3836 7.065120 TCACATTCTGAAAATGGAAATTGGT 57.935 32.000 0.00 0.00 32.14 3.67
3112 3837 6.592607 CCTCACATTCTGAAAATGGAAATTGG 59.407 38.462 0.00 0.00 32.14 3.16
3113 3838 6.091713 GCCTCACATTCTGAAAATGGAAATTG 59.908 38.462 0.00 0.00 32.14 2.32
3114 3839 6.168389 GCCTCACATTCTGAAAATGGAAATT 58.832 36.000 0.00 0.00 32.14 1.82
3499 4225 6.670695 AATACAAGCAAATGGGACTCTTTT 57.329 33.333 0.00 0.00 0.00 2.27
3501 4227 5.539955 ACAAATACAAGCAAATGGGACTCTT 59.460 36.000 0.00 0.00 0.00 2.85
3503 4229 5.391312 ACAAATACAAGCAAATGGGACTC 57.609 39.130 0.00 0.00 0.00 3.36
3543 4273 4.223953 TGAACCCAGAGAAGTACTTCACT 58.776 43.478 31.80 28.16 41.84 3.41
3544 4274 4.602340 TGAACCCAGAGAAGTACTTCAC 57.398 45.455 31.80 26.59 41.84 3.18
3545 4275 4.654262 AGTTGAACCCAGAGAAGTACTTCA 59.346 41.667 31.80 10.70 41.84 3.02
3546 4276 5.216614 AGTTGAACCCAGAGAAGTACTTC 57.783 43.478 25.24 25.24 39.78 3.01
3622 4354 7.491682 ACATTCAAGCACAAAAACAGAGTATT 58.508 30.769 0.00 0.00 0.00 1.89
3676 4408 6.425114 CGATTTTTCTTTTGGACTCTCTCAGA 59.575 38.462 0.00 0.00 0.00 3.27
3684 4416 7.422399 TCGAAATTCGATTTTTCTTTTGGACT 58.578 30.769 14.59 0.00 44.82 3.85
3685 4417 7.617533 TCGAAATTCGATTTTTCTTTTGGAC 57.382 32.000 14.59 0.00 44.82 4.02
3704 4436 2.549349 GCCAGGTGTACTTCCTTCGAAA 60.549 50.000 0.00 0.00 32.37 3.46
3709 4441 0.475828 AGGGCCAGGTGTACTTCCTT 60.476 55.000 6.18 0.00 32.37 3.36
3795 4528 4.756642 TGCTCAGTTAACTTCTCCACATTG 59.243 41.667 5.07 0.00 0.00 2.82
3834 4567 5.416271 AGGGAGTACAATACAACGACAAT 57.584 39.130 0.00 0.00 0.00 2.71
3855 4588 5.945784 TCAAGACACTTATTTTGGGATGGAG 59.054 40.000 0.00 0.00 0.00 3.86
3856 4589 5.886609 TCAAGACACTTATTTTGGGATGGA 58.113 37.500 0.00 0.00 0.00 3.41
3857 4590 5.711976 ACTCAAGACACTTATTTTGGGATGG 59.288 40.000 0.00 0.00 0.00 3.51
3858 4591 6.824305 ACTCAAGACACTTATTTTGGGATG 57.176 37.500 0.00 0.00 0.00 3.51
3859 4592 7.839680 AAACTCAAGACACTTATTTTGGGAT 57.160 32.000 0.00 0.00 0.00 3.85
3860 4593 7.996644 ACTAAACTCAAGACACTTATTTTGGGA 59.003 33.333 0.00 0.00 0.00 4.37
3861 4594 8.166422 ACTAAACTCAAGACACTTATTTTGGG 57.834 34.615 0.00 0.00 0.00 4.12
3870 4603 9.174166 ACAAATTTGTACTAAACTCAAGACACT 57.826 29.630 22.10 0.00 40.16 3.55
3912 4645 9.596308 ACCACCCTAAAATAAGTGTCTTAATTT 57.404 29.630 7.42 7.42 0.00 1.82
3914 4647 9.901172 CTACCACCCTAAAATAAGTGTCTTAAT 57.099 33.333 0.00 0.00 0.00 1.40
3915 4648 9.103582 TCTACCACCCTAAAATAAGTGTCTTAA 57.896 33.333 0.00 0.00 0.00 1.85
3916 4649 8.534496 GTCTACCACCCTAAAATAAGTGTCTTA 58.466 37.037 0.00 0.00 0.00 2.10
3917 4650 7.016858 TGTCTACCACCCTAAAATAAGTGTCTT 59.983 37.037 0.00 0.00 0.00 3.01
3918 4651 6.499350 TGTCTACCACCCTAAAATAAGTGTCT 59.501 38.462 0.00 0.00 0.00 3.41
3919 4652 6.592994 GTGTCTACCACCCTAAAATAAGTGTC 59.407 42.308 0.00 0.00 38.18 3.67
3920 4653 6.271624 AGTGTCTACCACCCTAAAATAAGTGT 59.728 38.462 0.00 0.00 45.74 3.55
3921 4654 6.708285 AGTGTCTACCACCCTAAAATAAGTG 58.292 40.000 0.00 0.00 45.74 3.16
3922 4655 6.947376 AGTGTCTACCACCCTAAAATAAGT 57.053 37.500 0.00 0.00 45.74 2.24
3923 4656 9.901172 AATAAGTGTCTACCACCCTAAAATAAG 57.099 33.333 0.00 0.00 45.74 1.73
3926 4659 9.020731 CAAAATAAGTGTCTACCACCCTAAAAT 57.979 33.333 0.00 0.00 45.74 1.82
3927 4660 7.449086 CCAAAATAAGTGTCTACCACCCTAAAA 59.551 37.037 0.00 0.00 45.74 1.52
3928 4661 6.943718 CCAAAATAAGTGTCTACCACCCTAAA 59.056 38.462 0.00 0.00 45.74 1.85
3929 4662 6.478129 CCAAAATAAGTGTCTACCACCCTAA 58.522 40.000 0.00 0.00 45.74 2.69
3930 4663 5.045432 CCCAAAATAAGTGTCTACCACCCTA 60.045 44.000 0.00 0.00 45.74 3.53
3931 4664 4.263771 CCCAAAATAAGTGTCTACCACCCT 60.264 45.833 0.00 0.00 45.74 4.34
3932 4665 4.014406 CCCAAAATAAGTGTCTACCACCC 58.986 47.826 0.00 0.00 45.74 4.61
3933 4666 4.698780 GTCCCAAAATAAGTGTCTACCACC 59.301 45.833 0.00 0.00 45.74 4.61
3934 4667 4.390909 CGTCCCAAAATAAGTGTCTACCAC 59.609 45.833 0.00 0.00 44.89 4.16
3935 4668 4.563993 CCGTCCCAAAATAAGTGTCTACCA 60.564 45.833 0.00 0.00 0.00 3.25
3936 4669 3.937079 CCGTCCCAAAATAAGTGTCTACC 59.063 47.826 0.00 0.00 0.00 3.18
3937 4670 4.824289 TCCGTCCCAAAATAAGTGTCTAC 58.176 43.478 0.00 0.00 0.00 2.59
3938 4671 4.081309 CCTCCGTCCCAAAATAAGTGTCTA 60.081 45.833 0.00 0.00 0.00 2.59
3939 4672 3.307480 CCTCCGTCCCAAAATAAGTGTCT 60.307 47.826 0.00 0.00 0.00 3.41
3940 4673 3.007635 CCTCCGTCCCAAAATAAGTGTC 58.992 50.000 0.00 0.00 0.00 3.67
3941 4674 2.290705 CCCTCCGTCCCAAAATAAGTGT 60.291 50.000 0.00 0.00 0.00 3.55
3942 4675 2.026636 TCCCTCCGTCCCAAAATAAGTG 60.027 50.000 0.00 0.00 0.00 3.16
3943 4676 2.238898 CTCCCTCCGTCCCAAAATAAGT 59.761 50.000 0.00 0.00 0.00 2.24
3944 4677 2.238898 ACTCCCTCCGTCCCAAAATAAG 59.761 50.000 0.00 0.00 0.00 1.73
3945 4678 2.026636 CACTCCCTCCGTCCCAAAATAA 60.027 50.000 0.00 0.00 0.00 1.40
3946 4679 1.557832 CACTCCCTCCGTCCCAAAATA 59.442 52.381 0.00 0.00 0.00 1.40
3947 4680 0.328258 CACTCCCTCCGTCCCAAAAT 59.672 55.000 0.00 0.00 0.00 1.82
3948 4681 1.758592 CACTCCCTCCGTCCCAAAA 59.241 57.895 0.00 0.00 0.00 2.44
3949 4682 2.221299 CCACTCCCTCCGTCCCAAA 61.221 63.158 0.00 0.00 0.00 3.28
3950 4683 2.096707 TACCACTCCCTCCGTCCCAA 62.097 60.000 0.00 0.00 0.00 4.12
3951 4684 2.509931 CTACCACTCCCTCCGTCCCA 62.510 65.000 0.00 0.00 0.00 4.37
3952 4685 1.757340 CTACCACTCCCTCCGTCCC 60.757 68.421 0.00 0.00 0.00 4.46
3953 4686 0.752376 CTCTACCACTCCCTCCGTCC 60.752 65.000 0.00 0.00 0.00 4.79
3954 4687 0.034283 ACTCTACCACTCCCTCCGTC 60.034 60.000 0.00 0.00 0.00 4.79
3955 4688 0.323542 CACTCTACCACTCCCTCCGT 60.324 60.000 0.00 0.00 0.00 4.69
3956 4689 1.038130 CCACTCTACCACTCCCTCCG 61.038 65.000 0.00 0.00 0.00 4.63
3957 4690 0.335361 TCCACTCTACCACTCCCTCC 59.665 60.000 0.00 0.00 0.00 4.30
3958 4691 2.035632 CATCCACTCTACCACTCCCTC 58.964 57.143 0.00 0.00 0.00 4.30
3959 4692 1.967274 GCATCCACTCTACCACTCCCT 60.967 57.143 0.00 0.00 0.00 4.20
3960 4693 0.466124 GCATCCACTCTACCACTCCC 59.534 60.000 0.00 0.00 0.00 4.30
3961 4694 0.466124 GGCATCCACTCTACCACTCC 59.534 60.000 0.00 0.00 0.00 3.85
3962 4695 1.195115 TGGCATCCACTCTACCACTC 58.805 55.000 0.00 0.00 0.00 3.51
3963 4696 1.556911 CTTGGCATCCACTCTACCACT 59.443 52.381 0.00 0.00 30.78 4.00
3964 4697 1.407437 CCTTGGCATCCACTCTACCAC 60.407 57.143 0.00 0.00 30.78 4.16
3965 4698 0.911769 CCTTGGCATCCACTCTACCA 59.088 55.000 0.00 0.00 30.78 3.25
3966 4699 0.912486 ACCTTGGCATCCACTCTACC 59.088 55.000 0.00 0.00 30.78 3.18
4020 4761 9.099454 GAAGAGTTGATGGACGAAAAATATACT 57.901 33.333 0.00 0.00 0.00 2.12
4023 4764 7.390440 TGTGAAGAGTTGATGGACGAAAAATAT 59.610 33.333 0.00 0.00 0.00 1.28
4111 4852 3.896272 AGACGAGGGACTAAACTTGTTCT 59.104 43.478 0.00 0.00 41.55 3.01
4113 4854 3.640029 TGAGACGAGGGACTAAACTTGTT 59.360 43.478 0.00 0.00 41.55 2.83
4160 4901 1.945354 TTGGTCAAAACGGCGCCAAA 61.945 50.000 28.98 0.77 36.42 3.28
4188 4929 7.225538 GTGTATAAGCTGAGTAGTTTGCATCAT 59.774 37.037 0.00 0.00 0.00 2.45
4209 4950 8.677148 ACTACTGTTTTGAAGTTGATGTGTAT 57.323 30.769 0.00 0.00 0.00 2.29
4293 5035 4.223144 AGGGGTAGCTGACATTTTTGTTT 58.777 39.130 0.00 0.00 0.00 2.83


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

AutoCloner maintained by Alex Coulton.