Multiple sequence alignment - TraesCS5A01G198800

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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 TraesCS5A01G198800 chr5A 100.000 4542 0 0 1 4542 403700252 403704793 0.000000e+00 8388
1 TraesCS5A01G198800 chr5A 96.552 87 0 3 3921 4005 702081582 702081667 1.700000e-29 141
2 TraesCS5A01G198800 chr5A 93.478 92 4 2 3909 3999 402213978 402214068 7.930000e-28 135
3 TraesCS5A01G198800 chr5D 91.545 4246 194 70 1 4202 310033028 310037152 0.000000e+00 5699
4 TraesCS5A01G198800 chr5D 93.631 314 10 3 4232 4542 310037138 310037444 1.150000e-125 460
5 TraesCS5A01G198800 chr5D 96.552 87 1 2 3913 3997 102283068 102282982 4.740000e-30 143
6 TraesCS5A01G198800 chr5B 94.196 2843 128 17 774 3613 355902136 355904944 0.000000e+00 4301
7 TraesCS5A01G198800 chr5B 85.112 712 52 29 87 778 355901419 355902096 0.000000e+00 678
8 TraesCS5A01G198800 chr5B 85.533 629 54 21 3608 4202 355910207 355910832 1.390000e-174 623
9 TraesCS5A01G198800 chr5B 93.312 314 14 2 4232 4542 355910818 355911127 1.490000e-124 457
10 TraesCS5A01G198800 chrUn 86.709 158 21 0 1383 1540 11818654 11818811 4.670000e-40 176
11 TraesCS5A01G198800 chrUn 86.709 158 21 0 1383 1540 11821200 11821357 4.670000e-40 176
12 TraesCS5A01G198800 chrUn 86.709 158 21 0 1383 1540 385071643 385071800 4.670000e-40 176
13 TraesCS5A01G198800 chrUn 86.076 158 22 0 1383 1540 377579916 377579759 2.170000e-38 171
14 TraesCS5A01G198800 chr7D 94.624 93 3 2 3926 4018 590446777 590446687 4.740000e-30 143
15 TraesCS5A01G198800 chr4D 92.929 99 5 2 3921 4019 505968137 505968233 4.740000e-30 143
16 TraesCS5A01G198800 chr3B 96.552 87 1 2 3926 4010 826657713 826657627 4.740000e-30 143
17 TraesCS5A01G198800 chr1D 97.561 82 2 0 3920 4001 47880383 47880464 1.700000e-29 141
18 TraesCS5A01G198800 chr1B 100.000 76 0 0 3925 4000 511213969 511213894 1.700000e-29 141


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 TraesCS5A01G198800 chr5A 403700252 403704793 4541 False 8388.0 8388 100.0000 1 4542 1 chr5A.!!$F2 4541
1 TraesCS5A01G198800 chr5D 310033028 310037444 4416 False 3079.5 5699 92.5880 1 4542 2 chr5D.!!$F1 4541
2 TraesCS5A01G198800 chr5B 355901419 355904944 3525 False 2489.5 4301 89.6540 87 3613 2 chr5B.!!$F1 3526
3 TraesCS5A01G198800 chr5B 355910207 355911127 920 False 540.0 623 89.4225 3608 4542 2 chr5B.!!$F2 934

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
305 316 0.036010 ACTCTATGCCAGGTGTGCAC 60.036 55.0 10.75 10.75 42.38 4.57 F
1357 1433 0.187117 TCGAGGAGATCCAGGATGCT 59.813 55.0 6.70 3.83 38.89 3.79 F
1358 1434 0.317799 CGAGGAGATCCAGGATGCTG 59.682 60.0 6.70 7.35 38.89 4.41 F
2251 2327 0.866061 CCGCTACATTCAGTCCGTCG 60.866 60.0 0.00 0.00 0.00 5.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2276 2352 0.104120 TGCGCCACGATGTAGCTAAT 59.896 50.000 4.18 0.0 0.00 1.73 R
3234 3310 0.185416 TAGCTAGGAGAAGGGGACGG 59.815 60.000 0.00 0.0 0.00 4.79 R
3262 3338 5.158494 TGTACGATGTACTGTGCTTACTTG 58.842 41.667 8.41 0.0 0.00 3.16 R
4079 4198 0.108186 CCGCAGAATGGAGCACTGTA 60.108 55.000 0.00 0.0 35.86 2.74 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
46 47 8.976986 ACTACCGATTAACAACTTACTTAGTG 57.023 34.615 0.00 0.00 37.12 2.74
47 48 8.579863 ACTACCGATTAACAACTTACTTAGTGT 58.420 33.333 0.00 0.00 37.12 3.55
49 50 8.976986 ACCGATTAACAACTTACTTAGTGTAG 57.023 34.615 0.00 0.00 37.12 2.74
50 51 7.543520 ACCGATTAACAACTTACTTAGTGTAGC 59.456 37.037 0.00 0.00 37.12 3.58
51 52 7.009907 CCGATTAACAACTTACTTAGTGTAGCC 59.990 40.741 0.00 0.00 37.12 3.93
52 53 7.758528 CGATTAACAACTTACTTAGTGTAGCCT 59.241 37.037 0.00 0.00 37.12 4.58
53 54 8.773404 ATTAACAACTTACTTAGTGTAGCCTG 57.227 34.615 0.00 0.00 37.12 4.85
54 55 4.566987 ACAACTTACTTAGTGTAGCCTGC 58.433 43.478 0.00 0.00 37.12 4.85
55 56 4.283722 ACAACTTACTTAGTGTAGCCTGCT 59.716 41.667 0.00 0.00 37.12 4.24
56 57 5.479375 ACAACTTACTTAGTGTAGCCTGCTA 59.521 40.000 0.00 0.00 37.12 3.49
57 58 6.014840 ACAACTTACTTAGTGTAGCCTGCTAA 60.015 38.462 0.00 0.00 37.12 3.09
58 59 6.793505 ACTTACTTAGTGTAGCCTGCTAAT 57.206 37.500 0.00 0.00 35.19 1.73
64 65 2.354656 TAGCCTGCTAATCGCGCG 60.355 61.111 26.76 26.76 43.27 6.86
114 116 3.918220 GCACGCGCGAATCTCCAG 61.918 66.667 39.36 15.22 0.00 3.86
119 122 2.109126 GCGCGAATCTCCAGGCTTT 61.109 57.895 12.10 0.00 0.00 3.51
138 141 1.152881 GGTGAGGCCATGGGATGAC 60.153 63.158 15.13 0.00 37.17 3.06
163 166 4.854784 TCGATCGCTGCTCGGTGC 62.855 66.667 11.09 0.00 43.25 5.01
226 229 3.423154 CAGCCGTCGCCCAAAGTC 61.423 66.667 0.00 0.00 34.57 3.01
227 230 3.936203 AGCCGTCGCCCAAAGTCA 61.936 61.111 0.00 0.00 34.57 3.41
228 231 2.746277 GCCGTCGCCCAAAGTCAT 60.746 61.111 0.00 0.00 0.00 3.06
229 232 1.448893 GCCGTCGCCCAAAGTCATA 60.449 57.895 0.00 0.00 0.00 2.15
230 233 0.814010 GCCGTCGCCCAAAGTCATAT 60.814 55.000 0.00 0.00 0.00 1.78
239 249 4.566759 CGCCCAAAGTCATATGTATATCCG 59.433 45.833 1.90 0.00 0.00 4.18
305 316 0.036010 ACTCTATGCCAGGTGTGCAC 60.036 55.000 10.75 10.75 42.38 4.57
349 360 1.361668 GCACGTACGTCTACCCGAGA 61.362 60.000 19.94 0.00 0.00 4.04
420 437 2.735762 GCACGACTGTACCATCTTCCTC 60.736 54.545 0.00 0.00 0.00 3.71
454 471 0.509929 GTCGGTTGCGTAGACCAAAC 59.490 55.000 5.91 0.00 36.99 2.93
537 560 1.801178 CTCTTCCTCGTTCACAAAGCC 59.199 52.381 0.00 0.00 0.00 4.35
581 611 6.248433 TCAAGGAATCCATCTTACTTTTGCT 58.752 36.000 0.61 0.00 26.22 3.91
582 612 6.375455 TCAAGGAATCCATCTTACTTTTGCTC 59.625 38.462 0.61 0.00 26.22 4.26
583 613 4.878397 AGGAATCCATCTTACTTTTGCTCG 59.122 41.667 0.61 0.00 0.00 5.03
584 614 4.636206 GGAATCCATCTTACTTTTGCTCGT 59.364 41.667 0.00 0.00 0.00 4.18
585 615 5.123979 GGAATCCATCTTACTTTTGCTCGTT 59.876 40.000 0.00 0.00 0.00 3.85
586 616 6.349363 GGAATCCATCTTACTTTTGCTCGTTT 60.349 38.462 0.00 0.00 0.00 3.60
587 617 5.356882 TCCATCTTACTTTTGCTCGTTTG 57.643 39.130 0.00 0.00 0.00 2.93
588 618 4.819630 TCCATCTTACTTTTGCTCGTTTGT 59.180 37.500 0.00 0.00 0.00 2.83
589 619 5.049680 TCCATCTTACTTTTGCTCGTTTGTC 60.050 40.000 0.00 0.00 0.00 3.18
590 620 4.806342 TCTTACTTTTGCTCGTTTGTCC 57.194 40.909 0.00 0.00 0.00 4.02
591 621 3.562557 TCTTACTTTTGCTCGTTTGTCCC 59.437 43.478 0.00 0.00 0.00 4.46
592 622 2.052782 ACTTTTGCTCGTTTGTCCCT 57.947 45.000 0.00 0.00 0.00 4.20
593 623 1.947456 ACTTTTGCTCGTTTGTCCCTC 59.053 47.619 0.00 0.00 0.00 4.30
594 624 1.946768 CTTTTGCTCGTTTGTCCCTCA 59.053 47.619 0.00 0.00 0.00 3.86
595 625 2.045561 TTTGCTCGTTTGTCCCTCAA 57.954 45.000 0.00 0.00 0.00 3.02
596 626 2.045561 TTGCTCGTTTGTCCCTCAAA 57.954 45.000 0.00 0.00 42.79 2.69
597 627 2.045561 TGCTCGTTTGTCCCTCAAAA 57.954 45.000 0.00 0.00 45.84 2.44
598 628 2.370349 TGCTCGTTTGTCCCTCAAAAA 58.630 42.857 0.00 0.00 45.84 1.94
599 629 2.098443 TGCTCGTTTGTCCCTCAAAAAC 59.902 45.455 0.00 0.00 45.84 2.43
600 630 2.357952 GCTCGTTTGTCCCTCAAAAACT 59.642 45.455 0.00 0.00 45.84 2.66
601 631 3.181490 GCTCGTTTGTCCCTCAAAAACTT 60.181 43.478 0.00 0.00 45.84 2.66
602 632 4.676986 GCTCGTTTGTCCCTCAAAAACTTT 60.677 41.667 0.00 0.00 45.84 2.66
603 633 5.394224 TCGTTTGTCCCTCAAAAACTTTT 57.606 34.783 0.00 0.00 45.84 2.27
604 634 5.164954 TCGTTTGTCCCTCAAAAACTTTTG 58.835 37.500 8.35 8.35 45.84 2.44
628 658 6.741992 TTCGTCTGAACATAAAGATTGCAT 57.258 33.333 0.00 0.00 0.00 3.96
629 659 6.349973 TCGTCTGAACATAAAGATTGCATC 57.650 37.500 0.00 0.00 0.00 3.91
630 660 5.294306 TCGTCTGAACATAAAGATTGCATCC 59.706 40.000 0.00 0.00 0.00 3.51
726 756 0.816421 TCCGGACATGCATGCATCAG 60.816 55.000 30.07 21.61 33.90 2.90
729 759 0.952280 GGACATGCATGCATCAGAGG 59.048 55.000 30.07 20.17 33.90 3.69
730 760 0.311165 GACATGCATGCATCAGAGGC 59.689 55.000 30.07 17.57 33.90 4.70
735 768 1.100510 GCATGCATCAGAGGCTCAAA 58.899 50.000 18.26 4.13 0.00 2.69
811 885 4.184079 TCATCATCATCATGGAGCTACG 57.816 45.455 0.00 0.00 0.00 3.51
871 945 1.090052 GCGTTCCTATCCACTGGTGC 61.090 60.000 0.00 0.00 0.00 5.01
920 994 3.499737 GTCCGCATCCCACGCTTG 61.500 66.667 0.00 0.00 0.00 4.01
921 995 4.776322 TCCGCATCCCACGCTTGG 62.776 66.667 1.29 1.29 43.50 3.61
962 1036 1.784856 CTGTCTGGTAACACGTGTTCG 59.215 52.381 35.40 21.55 46.17 3.95
988 1062 2.553172 CCTCTATAAGTACGCGCCTCTT 59.447 50.000 5.73 11.06 0.00 2.85
1004 1078 3.572255 GCCTCTTGGTATCCTCTCACTAG 59.428 52.174 0.00 0.00 35.27 2.57
1018 1092 5.593502 CCTCTCACTAGGAATTACTTACCGT 59.406 44.000 0.00 0.00 39.15 4.83
1030 1104 1.617357 ACTTACCGTCCACCTCTCAAC 59.383 52.381 0.00 0.00 0.00 3.18
1039 1113 1.277557 CCACCTCTCAACCTCTCTTGG 59.722 57.143 0.00 0.00 0.00 3.61
1054 1128 4.335416 TCTCTTGGGCTTACTCCATTTTG 58.665 43.478 0.00 0.00 33.82 2.44
1065 1141 1.373246 CCATTTTGTGCGCCCACTG 60.373 57.895 4.18 0.00 42.54 3.66
1120 1196 4.916293 TCATCAGCGATGCCGGCC 62.916 66.667 26.77 8.57 39.63 6.13
1222 1298 4.896829 CCGCTCCTCGCCTCCCTA 62.897 72.222 0.00 0.00 36.73 3.53
1225 1301 1.758906 GCTCCTCGCCTCCCTAGTT 60.759 63.158 0.00 0.00 0.00 2.24
1234 1310 1.187087 CCTCCCTAGTTTCGCTCACT 58.813 55.000 0.00 0.00 0.00 3.41
1240 1316 0.388134 TAGTTTCGCTCACTGCCGAC 60.388 55.000 0.00 0.00 38.78 4.79
1354 1430 1.153539 TCCTCGAGGAGATCCAGGAT 58.846 55.000 30.49 0.00 39.78 3.24
1357 1433 0.187117 TCGAGGAGATCCAGGATGCT 59.813 55.000 6.70 3.83 38.89 3.79
1358 1434 0.317799 CGAGGAGATCCAGGATGCTG 59.682 60.000 6.70 7.35 38.89 4.41
1692 1768 7.455008 ACGGTCTATCATGGATACCTTTAAGAT 59.545 37.037 0.00 0.00 0.00 2.40
1836 1912 3.832171 CGACGAGAACAGCAGCGC 61.832 66.667 0.00 0.00 0.00 5.92
1856 1932 1.676014 CGGTGGTCCTCCTCAACAATC 60.676 57.143 8.34 0.00 34.23 2.67
2251 2327 0.866061 CCGCTACATTCAGTCCGTCG 60.866 60.000 0.00 0.00 0.00 5.12
2377 2453 2.380410 GCACAGCGTGTTCTACCGG 61.380 63.158 0.00 0.00 35.75 5.28
2425 2501 2.113774 TGGTTGCTGTGCCTCCTG 59.886 61.111 0.00 0.00 0.00 3.86
2558 2634 1.443872 GACATCGTCAACGTCGGCT 60.444 57.895 2.09 0.00 40.80 5.52
2596 2672 2.746277 AACGCCGTGGCCATTCTC 60.746 61.111 9.72 0.00 37.98 2.87
2977 3053 3.663176 CACTGCGTGGGGTTGCTG 61.663 66.667 1.40 0.00 36.29 4.41
2981 3057 4.947147 GCGTGGGGTTGCTGGTCA 62.947 66.667 0.00 0.00 0.00 4.02
3148 3224 4.803426 GAGCTGACCAGGCCGTCG 62.803 72.222 0.00 0.00 35.40 5.12
3262 3338 3.418047 CTTCTCCTAGCTAGCTAGTCCC 58.582 54.545 37.50 5.72 43.22 4.46
3297 3373 2.159099 ACATCGTACAGCGTGATGGATT 60.159 45.455 11.01 0.00 42.91 3.01
3324 3400 3.937706 ACCATTTTTGCTCTCGATCTCAG 59.062 43.478 0.00 0.00 0.00 3.35
3383 3459 1.077169 GTTCCTCCCCACCATTCCTTT 59.923 52.381 0.00 0.00 0.00 3.11
3416 3492 2.739292 CCGCTATTGCTATACACGTGT 58.261 47.619 26.52 26.52 36.97 4.49
3422 3498 6.745907 CGCTATTGCTATACACGTGTATACAT 59.254 38.462 34.01 27.20 41.18 2.29
3423 3499 7.906527 CGCTATTGCTATACACGTGTATACATA 59.093 37.037 34.01 26.97 41.18 2.29
3424 3500 9.007252 GCTATTGCTATACACGTGTATACATAC 57.993 37.037 34.01 24.95 41.18 2.39
3473 3550 6.204688 ACACCTTTGTTGTACATATCTGTGTG 59.795 38.462 13.40 10.58 32.13 3.82
3492 3569 4.037923 GTGTGGAATTGGATTGTGTGTTCT 59.962 41.667 0.00 0.00 0.00 3.01
3513 3590 6.475596 TCTCTCTGATGATTTGAGTGCATA 57.524 37.500 0.00 0.00 0.00 3.14
3587 3664 3.186409 TCTCGCTCGAAAATGAAAACCTG 59.814 43.478 0.00 0.00 0.00 4.00
3593 3670 3.004315 TCGAAAATGAAAACCTGGACTGC 59.996 43.478 0.00 0.00 0.00 4.40
3731 3814 3.806625 ACAGCTCAAGCACACAAAAAT 57.193 38.095 4.59 0.00 45.16 1.82
3741 3824 7.958674 TCAAGCACACAAAAATTTCTTTGTAC 58.041 30.769 7.71 2.64 45.51 2.90
3757 3840 6.548171 TCTTTGTACGTTTCTTTTCCACAAG 58.452 36.000 0.00 0.00 0.00 3.16
3858 3941 7.741785 TGTCCAATTTAAAGAACTCTACTCCA 58.258 34.615 0.00 0.00 0.00 3.86
3870 3953 1.762957 TCTACTCCATAGTGGGCTTGC 59.237 52.381 0.00 0.00 38.32 4.01
3873 3956 2.124570 CCATAGTGGGCTTGCGCT 60.125 61.111 9.73 0.65 32.67 5.92
3877 3960 1.051812 ATAGTGGGCTTGCGCTAGAT 58.948 50.000 23.12 2.85 36.09 1.98
3887 3970 0.030773 TGCGCTAGATAGTGAAGGCG 59.969 55.000 9.73 0.00 44.40 5.52
3891 3974 2.535984 CGCTAGATAGTGAAGGCGTTTG 59.464 50.000 0.00 0.00 38.20 2.93
3893 3976 3.307242 GCTAGATAGTGAAGGCGTTTGTG 59.693 47.826 0.00 0.00 0.00 3.33
3898 3985 3.188159 AGTGAAGGCGTTTGTGTAGAA 57.812 42.857 0.00 0.00 0.00 2.10
3900 3987 3.311596 AGTGAAGGCGTTTGTGTAGAAAC 59.688 43.478 0.00 0.00 33.27 2.78
3923 4014 5.695816 ACGCATAAATTTCATTTTGCACACT 59.304 32.000 0.00 0.00 36.74 3.55
4011 4102 0.388520 GTGGGCGCTGGTTGATTTTC 60.389 55.000 7.64 0.00 0.00 2.29
4013 4104 1.154035 GGCGCTGGTTGATTTTCCG 60.154 57.895 7.64 0.00 0.00 4.30
4014 4105 1.579429 GCGCTGGTTGATTTTCCGT 59.421 52.632 0.00 0.00 0.00 4.69
4016 4107 1.601914 GCGCTGGTTGATTTTCCGTTT 60.602 47.619 0.00 0.00 0.00 3.60
4017 4108 2.738135 CGCTGGTTGATTTTCCGTTTT 58.262 42.857 0.00 0.00 0.00 2.43
4038 4136 7.378728 CGTTTTGTCTCCTATTTTGAACTTTCC 59.621 37.037 0.00 0.00 0.00 3.13
4062 4160 7.710475 TCCTTTCATTCATGGTTTCTGTTTTTC 59.290 33.333 0.00 0.00 0.00 2.29
4067 4165 9.447157 TCATTCATGGTTTCTGTTTTTCTTTTT 57.553 25.926 0.00 0.00 0.00 1.94
4099 4219 2.110967 CAGTGCTCCATTCTGCGGG 61.111 63.158 0.00 0.00 0.00 6.13
4113 4233 2.037251 TCTGCGGGCTAATCATTCTACC 59.963 50.000 0.00 0.00 0.00 3.18
4164 4284 6.109359 ACTGAGCAGATGGTTTGAGTAATAC 58.891 40.000 4.21 0.00 0.00 1.89
4189 4310 2.036933 GCGACGAGCTTTTTGTCAAAG 58.963 47.619 0.00 0.00 44.04 2.77
4198 4319 6.304208 CGAGCTTTTTGTCAAAGAATAGAAGC 59.696 38.462 16.93 16.93 37.75 3.86
4199 4320 7.042797 AGCTTTTTGTCAAAGAATAGAAGCA 57.957 32.000 22.70 0.00 39.39 3.91
4200 4321 7.144000 AGCTTTTTGTCAAAGAATAGAAGCAG 58.856 34.615 22.70 0.00 39.39 4.24
4201 4322 6.128982 GCTTTTTGTCAAAGAATAGAAGCAGC 60.129 38.462 18.65 1.88 37.50 5.25
4202 4323 6.639632 TTTTGTCAAAGAATAGAAGCAGCT 57.360 33.333 0.00 0.00 0.00 4.24
4203 4324 6.639632 TTTGTCAAAGAATAGAAGCAGCTT 57.360 33.333 7.60 7.60 0.00 3.74
4204 4325 5.869753 TGTCAAAGAATAGAAGCAGCTTC 57.130 39.130 25.46 25.46 40.45 3.86
4205 4326 4.389992 TGTCAAAGAATAGAAGCAGCTTCG 59.610 41.667 26.14 11.81 44.34 3.79
4206 4327 4.390297 GTCAAAGAATAGAAGCAGCTTCGT 59.610 41.667 26.14 17.56 44.34 3.85
4207 4328 4.389992 TCAAAGAATAGAAGCAGCTTCGTG 59.610 41.667 26.14 16.60 44.34 4.35
4208 4329 2.275318 AGAATAGAAGCAGCTTCGTGC 58.725 47.619 26.14 18.41 44.34 5.34
4217 4338 3.231501 GCTTCGTGCGTCTTCGTT 58.768 55.556 0.00 0.00 39.49 3.85
4218 4339 1.128015 GCTTCGTGCGTCTTCGTTC 59.872 57.895 0.00 0.00 39.49 3.95
4219 4340 1.773496 CTTCGTGCGTCTTCGTTCC 59.227 57.895 0.00 0.00 39.49 3.62
4220 4341 0.937699 CTTCGTGCGTCTTCGTTCCA 60.938 55.000 0.00 0.00 39.49 3.53
4221 4342 0.528033 TTCGTGCGTCTTCGTTCCAA 60.528 50.000 0.00 0.00 39.49 3.53
4222 4343 0.528033 TCGTGCGTCTTCGTTCCAAA 60.528 50.000 0.00 0.00 39.49 3.28
4223 4344 0.302288 CGTGCGTCTTCGTTCCAAAA 59.698 50.000 0.00 0.00 39.49 2.44
4224 4345 1.267632 CGTGCGTCTTCGTTCCAAAAA 60.268 47.619 0.00 0.00 39.49 1.94
4252 4373 3.435105 AGAATAGAAGCAGCAGACGAG 57.565 47.619 0.00 0.00 0.00 4.18
4304 4425 4.356442 ATGCAAACCAACGGCGCC 62.356 61.111 19.07 19.07 0.00 6.53
4385 4506 1.436195 CTTGACCGGGTGTGTGTGTG 61.436 60.000 3.30 0.00 0.00 3.82
4386 4507 2.186602 TTGACCGGGTGTGTGTGTGT 62.187 55.000 3.30 0.00 0.00 3.72
4428 4549 3.490759 CGCATCGCTCGCCTGTTT 61.491 61.111 0.00 0.00 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 8.109705 TGTTAATCGGTAGTAATCCGCTATTA 57.890 34.615 0.00 0.00 46.49 0.98
30 31 6.014840 AGCAGGCTACACTAAGTAAGTTGTTA 60.015 38.462 0.00 0.00 35.76 2.41
53 54 2.586773 GGAAGGACGCGCGATTAGC 61.587 63.158 39.36 21.17 43.95 3.09
54 55 1.949631 GGGAAGGACGCGCGATTAG 60.950 63.158 39.36 7.37 0.00 1.73
55 56 2.105528 GGGAAGGACGCGCGATTA 59.894 61.111 39.36 0.00 0.00 1.75
64 65 1.957765 GCCTACTGGACGGGAAGGAC 61.958 65.000 6.12 0.00 34.57 3.85
75 76 0.463295 TCTACTCCGTCGCCTACTGG 60.463 60.000 0.00 0.00 0.00 4.00
121 124 4.567318 GTCATCCCATGGCCTCAC 57.433 61.111 6.09 0.00 0.00 3.51
138 141 2.880879 CAGCGATCGACCACACGG 60.881 66.667 21.57 0.00 38.77 4.94
143 146 4.193334 CCGAGCAGCGATCGACCA 62.193 66.667 21.57 0.00 44.55 4.02
146 149 4.854784 GCACCGAGCAGCGATCGA 62.855 66.667 21.57 0.00 44.55 3.59
214 217 5.581085 GGATATACATATGACTTTGGGCGAC 59.419 44.000 10.38 0.00 0.00 5.19
331 342 0.649475 CTCTCGGGTAGACGTACGTG 59.351 60.000 28.16 10.39 34.94 4.49
349 360 2.034878 TCATGGAGATCGTAAGCTGCT 58.965 47.619 0.00 0.00 37.18 4.24
420 437 2.789917 GACGCATGCAGCAGAAGG 59.210 61.111 19.57 0.50 46.13 3.46
483 505 1.032114 CAAACCCTCTTCATCGGGGC 61.032 60.000 0.00 0.00 45.07 5.80
557 587 6.248433 AGCAAAAGTAAGATGGATTCCTTGA 58.752 36.000 3.95 0.00 0.00 3.02
581 611 5.394224 AAAAGTTTTTGAGGGACAAACGA 57.606 34.783 0.00 0.00 46.32 3.85
604 634 6.684555 GATGCAATCTTTATGTTCAGACGAAC 59.315 38.462 0.00 0.00 45.08 3.95
616 646 4.474303 TGGGATGGGATGCAATCTTTAT 57.526 40.909 1.17 0.00 44.71 1.40
625 655 0.108585 ACGTACATGGGATGGGATGC 59.891 55.000 0.00 0.00 33.60 3.91
626 656 1.882912 CACGTACATGGGATGGGATG 58.117 55.000 0.00 0.00 33.60 3.51
627 657 0.108585 GCACGTACATGGGATGGGAT 59.891 55.000 0.00 0.00 33.60 3.85
628 658 0.980754 AGCACGTACATGGGATGGGA 60.981 55.000 0.00 0.00 33.60 4.37
629 659 0.532862 GAGCACGTACATGGGATGGG 60.533 60.000 0.00 0.00 33.60 4.00
630 660 0.177836 TGAGCACGTACATGGGATGG 59.822 55.000 0.00 0.00 33.60 3.51
698 728 3.111853 TGCATGTCCGGATTGATAGAC 57.888 47.619 18.57 0.39 0.00 2.59
729 759 3.442100 GATTTGTGCTATGGCTTTGAGC 58.558 45.455 1.68 0.00 41.46 4.26
730 760 3.488047 CGGATTTGTGCTATGGCTTTGAG 60.488 47.826 1.68 0.00 39.59 3.02
735 768 3.275617 TTACGGATTTGTGCTATGGCT 57.724 42.857 1.68 0.00 39.59 4.75
744 777 7.989416 TTGGACTTTCTTATTACGGATTTGT 57.011 32.000 0.00 0.00 0.00 2.83
811 885 1.986575 GCATGGCAGCTTCTTCGTCC 61.987 60.000 0.00 0.00 0.00 4.79
871 945 4.082523 ACACGTGGAGCCCGATGG 62.083 66.667 21.57 0.00 0.00 3.51
906 980 0.813610 TAATCCAAGCGTGGGATGCG 60.814 55.000 19.08 0.00 44.30 4.73
915 989 1.672881 CTGCTTCCCTTAATCCAAGCG 59.327 52.381 7.52 0.00 43.55 4.68
918 992 2.041620 AGCACTGCTTCCCTTAATCCAA 59.958 45.455 0.00 0.00 33.89 3.53
919 993 1.635487 AGCACTGCTTCCCTTAATCCA 59.365 47.619 0.00 0.00 33.89 3.41
920 994 2.293170 GAGCACTGCTTCCCTTAATCC 58.707 52.381 4.67 0.00 39.88 3.01
921 995 2.293170 GGAGCACTGCTTCCCTTAATC 58.707 52.381 4.67 0.00 39.88 1.75
922 996 2.426842 GGAGCACTGCTTCCCTTAAT 57.573 50.000 4.67 0.00 39.88 1.40
923 997 3.957288 GGAGCACTGCTTCCCTTAA 57.043 52.632 4.67 0.00 39.88 1.85
929 1003 0.673022 CAGACAGGGAGCACTGCTTC 60.673 60.000 4.67 2.23 39.88 3.86
930 1004 1.374190 CAGACAGGGAGCACTGCTT 59.626 57.895 4.67 0.00 39.88 3.91
931 1005 2.591072 CCAGACAGGGAGCACTGCT 61.591 63.158 2.22 2.22 43.88 4.24
932 1006 1.544825 TACCAGACAGGGAGCACTGC 61.545 60.000 0.00 0.00 43.89 4.40
933 1007 0.976641 TTACCAGACAGGGAGCACTG 59.023 55.000 0.00 0.00 43.89 3.66
962 1036 1.199558 CGCGTACTTATAGAGGAGGCC 59.800 57.143 0.00 0.00 45.36 5.19
988 1062 6.923670 AGTAATTCCTAGTGAGAGGATACCA 58.076 40.000 0.00 0.00 45.25 3.25
1004 1078 3.450096 AGAGGTGGACGGTAAGTAATTCC 59.550 47.826 0.00 0.00 0.00 3.01
1008 1082 3.159213 TGAGAGGTGGACGGTAAGTAA 57.841 47.619 0.00 0.00 0.00 2.24
1009 1083 2.821969 GTTGAGAGGTGGACGGTAAGTA 59.178 50.000 0.00 0.00 0.00 2.24
1010 1084 1.617357 GTTGAGAGGTGGACGGTAAGT 59.383 52.381 0.00 0.00 0.00 2.24
1011 1085 1.067071 GGTTGAGAGGTGGACGGTAAG 60.067 57.143 0.00 0.00 0.00 2.34
1016 1090 0.528470 GAGAGGTTGAGAGGTGGACG 59.472 60.000 0.00 0.00 0.00 4.79
1018 1092 2.251818 CAAGAGAGGTTGAGAGGTGGA 58.748 52.381 0.00 0.00 0.00 4.02
1030 1104 1.573108 TGGAGTAAGCCCAAGAGAGG 58.427 55.000 0.00 0.00 0.00 3.69
1039 1113 1.732405 GCGCACAAAATGGAGTAAGCC 60.732 52.381 0.30 0.00 0.00 4.35
1711 1787 1.789078 GCACCCGCATCACATCATCC 61.789 60.000 0.00 0.00 38.36 3.51
1836 1912 0.324943 ATTGTTGAGGAGGACCACCG 59.675 55.000 1.88 0.00 41.83 4.94
1856 1932 0.249120 TACACCAGGAACGCCATCAG 59.751 55.000 0.00 0.00 36.29 2.90
2276 2352 0.104120 TGCGCCACGATGTAGCTAAT 59.896 50.000 4.18 0.00 0.00 1.73
2558 2634 4.069232 CTGCGTCTCGGCCTTGGA 62.069 66.667 0.00 0.00 0.00 3.53
2596 2672 1.529418 GCGTTCGACGAGAGGTAGAAG 60.529 57.143 10.82 0.00 46.05 2.85
2972 3048 2.270257 GGCACAGCATGACCAGCAA 61.270 57.895 0.00 0.00 39.69 3.91
3085 3161 3.793144 GACCGCGCCTTCTTGCAG 61.793 66.667 0.00 0.00 0.00 4.41
3234 3310 0.185416 TAGCTAGGAGAAGGGGACGG 59.815 60.000 0.00 0.00 0.00 4.79
3262 3338 5.158494 TGTACGATGTACTGTGCTTACTTG 58.842 41.667 8.41 0.00 0.00 3.16
3383 3459 3.737266 GCAATAGCGGCGTAGTATAACAA 59.263 43.478 9.37 0.00 0.00 2.83
3416 3492 8.914011 ACTGCAACTCTAATCTGTGTATGTATA 58.086 33.333 0.00 0.00 0.00 1.47
3422 3498 6.288294 ACAAACTGCAACTCTAATCTGTGTA 58.712 36.000 0.00 0.00 0.00 2.90
3423 3499 5.126067 ACAAACTGCAACTCTAATCTGTGT 58.874 37.500 0.00 0.00 0.00 3.72
3424 3500 5.679734 ACAAACTGCAACTCTAATCTGTG 57.320 39.130 0.00 0.00 0.00 3.66
3425 3501 6.765989 TGTTACAAACTGCAACTCTAATCTGT 59.234 34.615 0.00 0.00 0.00 3.41
3426 3502 7.072030 GTGTTACAAACTGCAACTCTAATCTG 58.928 38.462 0.00 0.00 0.00 2.90
3427 3503 6.204882 GGTGTTACAAACTGCAACTCTAATCT 59.795 38.462 0.00 0.00 0.00 2.40
3473 3550 5.006386 AGAGAGAACACACAATCCAATTCC 58.994 41.667 0.00 0.00 0.00 3.01
3492 3569 7.012989 CCATTTATGCACTCAAATCATCAGAGA 59.987 37.037 0.00 0.00 33.69 3.10
3513 3590 6.139679 TCCCACAACTATCTTCTTCCATTT 57.860 37.500 0.00 0.00 0.00 2.32
3587 3664 2.749076 TGCAATCATGTAAGTGCAGTCC 59.251 45.455 5.52 0.00 41.85 3.85
3593 3670 8.424274 TCTGTAATACTGCAATCATGTAAGTG 57.576 34.615 0.00 0.00 31.06 3.16
3731 3814 6.910995 TGTGGAAAAGAAACGTACAAAGAAA 58.089 32.000 0.00 0.00 0.00 2.52
3741 3824 4.993905 ACCTTTCTTGTGGAAAAGAAACG 58.006 39.130 7.78 7.22 46.26 3.60
3873 3956 4.530710 ACACAAACGCCTTCACTATCTA 57.469 40.909 0.00 0.00 0.00 1.98
3877 3960 4.325028 TTCTACACAAACGCCTTCACTA 57.675 40.909 0.00 0.00 0.00 2.74
3887 3970 8.276060 TGAAATTTATGCGTTTCTACACAAAC 57.724 30.769 0.00 0.00 35.80 2.93
3910 3997 0.961019 GGGCTGAGTGTGCAAAATGA 59.039 50.000 0.00 0.00 0.00 2.57
3923 4014 0.612174 AACTGAGCTAGACGGGCTGA 60.612 55.000 0.00 0.00 40.40 4.26
4004 4095 7.519032 AAATAGGAGACAAAACGGAAAATCA 57.481 32.000 0.00 0.00 0.00 2.57
4006 4097 7.947282 TCAAAATAGGAGACAAAACGGAAAAT 58.053 30.769 0.00 0.00 0.00 1.82
4011 4102 6.313744 AGTTCAAAATAGGAGACAAAACGG 57.686 37.500 0.00 0.00 0.00 4.44
4013 4104 8.414003 AGGAAAGTTCAAAATAGGAGACAAAAC 58.586 33.333 0.00 0.00 0.00 2.43
4014 4105 8.533569 AGGAAAGTTCAAAATAGGAGACAAAA 57.466 30.769 0.00 0.00 0.00 2.44
4016 4107 8.533569 AAAGGAAAGTTCAAAATAGGAGACAA 57.466 30.769 0.00 0.00 0.00 3.18
4017 4108 7.777910 TGAAAGGAAAGTTCAAAATAGGAGACA 59.222 33.333 0.00 0.00 32.13 3.41
4038 4136 8.652810 AGAAAAACAGAAACCATGAATGAAAG 57.347 30.769 0.00 0.00 0.00 2.62
4072 4170 4.278170 CAGAATGGAGCACTGTACCAAAAA 59.722 41.667 0.00 0.00 37.24 1.94
4073 4171 3.820467 CAGAATGGAGCACTGTACCAAAA 59.180 43.478 0.00 0.00 37.24 2.44
4074 4172 3.411446 CAGAATGGAGCACTGTACCAAA 58.589 45.455 0.00 0.00 37.24 3.28
4075 4173 2.875672 GCAGAATGGAGCACTGTACCAA 60.876 50.000 0.00 0.00 37.24 3.67
4076 4174 1.339055 GCAGAATGGAGCACTGTACCA 60.339 52.381 0.00 0.00 35.86 3.25
4079 4198 0.108186 CCGCAGAATGGAGCACTGTA 60.108 55.000 0.00 0.00 35.86 2.74
4083 4202 2.593468 TAGCCCGCAGAATGGAGCAC 62.593 60.000 0.00 0.00 35.86 4.40
4099 4219 5.523916 ACATCGTTGTGGTAGAATGATTAGC 59.476 40.000 0.00 0.00 33.85 3.09
4189 4310 1.005557 CGCACGAAGCTGCTTCTATTC 60.006 52.381 32.42 19.98 42.61 1.75
4198 4319 1.548973 AACGAAGACGCACGAAGCTG 61.549 55.000 0.00 0.00 43.96 4.24
4199 4320 1.276145 GAACGAAGACGCACGAAGCT 61.276 55.000 0.00 0.00 43.96 3.74
4200 4321 1.128015 GAACGAAGACGCACGAAGC 59.872 57.895 0.00 0.00 43.96 3.86
4201 4322 0.937699 TGGAACGAAGACGCACGAAG 60.938 55.000 0.00 0.00 43.96 3.79
4202 4323 0.528033 TTGGAACGAAGACGCACGAA 60.528 50.000 0.00 0.00 43.96 3.85
4203 4324 0.528033 TTTGGAACGAAGACGCACGA 60.528 50.000 0.00 0.00 43.96 4.35
4204 4325 0.302288 TTTTGGAACGAAGACGCACG 59.698 50.000 0.00 0.00 43.96 5.34
4205 4326 2.461897 TTTTTGGAACGAAGACGCAC 57.538 45.000 0.00 0.00 43.96 5.34
4222 4343 7.446625 TCTGCTGCTTCTATTCTTCTTCTTTTT 59.553 33.333 0.00 0.00 0.00 1.94
4223 4344 6.939163 TCTGCTGCTTCTATTCTTCTTCTTTT 59.061 34.615 0.00 0.00 0.00 2.27
4224 4345 6.371271 GTCTGCTGCTTCTATTCTTCTTCTTT 59.629 38.462 0.00 0.00 0.00 2.52
4225 4346 5.874261 GTCTGCTGCTTCTATTCTTCTTCTT 59.126 40.000 0.00 0.00 0.00 2.52
4226 4347 5.418676 GTCTGCTGCTTCTATTCTTCTTCT 58.581 41.667 0.00 0.00 0.00 2.85
4227 4348 4.267452 CGTCTGCTGCTTCTATTCTTCTTC 59.733 45.833 0.00 0.00 0.00 2.87
4228 4349 4.081972 TCGTCTGCTGCTTCTATTCTTCTT 60.082 41.667 0.00 0.00 0.00 2.52
4229 4350 3.445450 TCGTCTGCTGCTTCTATTCTTCT 59.555 43.478 0.00 0.00 0.00 2.85
4230 4351 3.775202 TCGTCTGCTGCTTCTATTCTTC 58.225 45.455 0.00 0.00 0.00 2.87
4231 4352 3.430098 CCTCGTCTGCTGCTTCTATTCTT 60.430 47.826 0.00 0.00 0.00 2.52
4232 4353 2.100584 CCTCGTCTGCTGCTTCTATTCT 59.899 50.000 0.00 0.00 0.00 2.40
4233 4354 2.099921 TCCTCGTCTGCTGCTTCTATTC 59.900 50.000 0.00 0.00 0.00 1.75
4234 4355 2.100584 CTCCTCGTCTGCTGCTTCTATT 59.899 50.000 0.00 0.00 0.00 1.73
4235 4356 1.680735 CTCCTCGTCTGCTGCTTCTAT 59.319 52.381 0.00 0.00 0.00 1.98
4236 4357 1.098869 CTCCTCGTCTGCTGCTTCTA 58.901 55.000 0.00 0.00 0.00 2.10
4237 4358 1.889454 CTCCTCGTCTGCTGCTTCT 59.111 57.895 0.00 0.00 0.00 2.85
4238 4359 1.809209 GCTCCTCGTCTGCTGCTTC 60.809 63.158 0.00 0.00 0.00 3.86
4239 4360 0.967887 TAGCTCCTCGTCTGCTGCTT 60.968 55.000 0.00 0.00 37.62 3.91
4240 4361 1.379176 TAGCTCCTCGTCTGCTGCT 60.379 57.895 0.00 0.00 37.62 4.24
4241 4362 1.065600 CTAGCTCCTCGTCTGCTGC 59.934 63.158 0.00 0.00 37.62 5.25
4242 4363 0.380378 GACTAGCTCCTCGTCTGCTG 59.620 60.000 0.00 0.00 37.62 4.41
4252 4373 3.589495 AACTACCGTTTGACTAGCTCC 57.411 47.619 0.00 0.00 0.00 4.70
4304 4425 1.426816 CGTGGCTGCTCTGCTGTATG 61.427 60.000 0.00 0.00 0.00 2.39
4329 4450 4.755614 GCTCTGCTTGCACGCTGC 62.756 66.667 16.80 13.45 45.29 5.25
4385 4506 1.206578 CGTGAACCGTGATTGGCAC 59.793 57.895 0.00 0.00 44.21 5.01
4386 4507 3.649096 CGTGAACCGTGATTGGCA 58.351 55.556 0.00 0.00 0.00 4.92
4423 4544 5.597813 ACTCACGCTAATCAAAGAAACAG 57.402 39.130 0.00 0.00 0.00 3.16
4428 4549 8.248253 TGATTAACTACTCACGCTAATCAAAGA 58.752 33.333 0.00 0.00 36.52 2.52


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

AutoCloner maintained by Alex Coulton.