Multiple sequence alignment - TraesCS1A01G055900

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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 TraesCS1A01G055900 chr1A 100.000 4239 0 0 1 4239 36622355 36618117 0.000000e+00 7829.0
1 TraesCS1A01G055900 chr1A 89.712 2187 110 45 1007 3152 31894864 31896976 0.000000e+00 2686.0
2 TraesCS1A01G055900 chr1A 93.487 952 39 8 1 951 31893227 31894156 0.000000e+00 1393.0
3 TraesCS1A01G055900 chr1A 86.842 190 19 3 3388 3576 31897085 31897269 1.540000e-49 207.0
4 TraesCS1A01G055900 chr1A 93.846 130 5 2 4044 4171 31900176 31900304 4.330000e-45 193.0
5 TraesCS1A01G055900 chr1A 91.011 89 6 1 3271 3357 154576869 154576781 7.450000e-23 119.0
6 TraesCS1A01G055900 chr1A 90.110 91 7 1 3269 3357 350017188 350017098 2.680000e-22 117.0
7 TraesCS1A01G055900 chr1A 76.923 195 24 15 3576 3768 31898980 31899155 1.620000e-14 91.6
8 TraesCS1A01G055900 chr1D 93.676 2372 102 22 1007 3361 37438785 37436445 0.000000e+00 3506.0
9 TraesCS1A01G055900 chr1D 95.067 892 28 7 3361 4239 37436480 37435592 0.000000e+00 1389.0
10 TraesCS1A01G055900 chr1D 83.465 1016 116 36 1 1002 37439884 37438907 0.000000e+00 898.0
11 TraesCS1A01G055900 chr1D 91.011 89 6 1 3271 3357 138347295 138347207 7.450000e-23 119.0
12 TraesCS1A01G055900 chr1D 89.011 91 8 1 3269 3357 277362612 277362522 1.250000e-20 111.0
13 TraesCS1A01G055900 chr1D 78.912 147 29 2 439 584 318512330 318512475 9.700000e-17 99.0
14 TraesCS1A01G055900 chr1D 92.857 42 0 3 3361 3401 3633181 3633142 1.650000e-04 58.4
15 TraesCS1A01G055900 chr1B 91.878 1933 94 21 1007 2922 57024465 57022579 0.000000e+00 2641.0
16 TraesCS1A01G055900 chr1B 90.723 1175 66 14 1311 2456 57070847 57069687 0.000000e+00 1526.0
17 TraesCS1A01G055900 chr1B 89.938 974 63 14 1504 2456 57045406 57044447 0.000000e+00 1223.0
18 TraesCS1A01G055900 chr1B 95.817 502 21 0 1007 1508 57051135 57050634 0.000000e+00 811.0
19 TraesCS1A01G055900 chr1B 78.624 814 89 37 1 788 57146023 57145269 1.070000e-125 460.0
20 TraesCS1A01G055900 chr1B 79.508 610 72 27 421 1009 57071662 57071085 6.650000e-103 385.0
21 TraesCS1A01G055900 chr1B 89.243 251 13 3 2454 2704 57068284 57068048 6.890000e-78 302.0
22 TraesCS1A01G055900 chr1B 88.845 251 14 3 2454 2704 57043045 57042809 3.200000e-76 296.0
23 TraesCS1A01G055900 chr1B 88.664 247 18 6 2702 2941 57067909 57067666 4.150000e-75 292.0
24 TraesCS1A01G055900 chr1B 88.259 247 19 6 2702 2941 57042670 57042427 1.930000e-73 287.0
25 TraesCS1A01G055900 chr1B 94.512 164 9 0 1007 1170 57071007 57070844 1.960000e-63 254.0
26 TraesCS1A01G055900 chr1B 78.111 434 53 31 3576 3994 57022001 57021595 1.970000e-58 237.0
27 TraesCS1A01G055900 chr1B 96.923 65 1 1 4039 4103 57021586 57021523 1.610000e-19 108.0
28 TraesCS1A01G055900 chr1B 91.489 47 2 2 3356 3402 678050870 678050826 3.540000e-06 63.9
29 TraesCS1A01G055900 chr4D 81.058 359 50 9 2611 2957 12320962 12320610 1.940000e-68 270.0
30 TraesCS1A01G055900 chr7A 90.355 197 13 4 2248 2444 465753347 465753157 1.960000e-63 254.0
31 TraesCS1A01G055900 chr6A 78.771 358 59 11 2611 2957 502509971 502509620 1.530000e-54 224.0
32 TraesCS1A01G055900 chr6A 88.393 112 13 0 2236 2347 142076439 142076550 7.390000e-28 135.0
33 TraesCS1A01G055900 chr6B 88.172 186 18 1 3391 3576 561143637 561143456 7.140000e-53 219.0
34 TraesCS1A01G055900 chr6B 87.634 186 19 1 3391 3576 561007975 561008156 3.320000e-51 213.0
35 TraesCS1A01G055900 chr6B 83.511 188 21 5 3391 3578 135132561 135132738 2.620000e-37 167.0
36 TraesCS1A01G055900 chr6B 80.193 207 22 7 2142 2348 543080203 543080390 2.060000e-28 137.0
37 TraesCS1A01G055900 chr6B 95.122 41 1 1 3356 3395 75264676 75264716 3.540000e-06 63.9
38 TraesCS1A01G055900 chr7B 89.565 115 10 2 2476 2588 508824582 508824468 1.230000e-30 145.0
39 TraesCS1A01G055900 chr7B 85.185 135 16 3 2476 2608 436751776 436751644 7.390000e-28 135.0
40 TraesCS1A01G055900 chr3B 85.926 135 17 2 2476 2608 572743285 572743419 4.420000e-30 143.0
41 TraesCS1A01G055900 chr3B 76.374 182 40 3 1864 2044 641805260 641805439 1.250000e-15 95.3
42 TraesCS1A01G055900 chr3B 100.000 31 0 0 1813 1843 771558308 771558278 1.650000e-04 58.4
43 TraesCS1A01G055900 chr3B 87.500 48 4 2 1794 1841 773569338 773569383 2.000000e-03 54.7
44 TraesCS1A01G055900 chr7D 85.821 134 13 3 2476 2608 420731669 420731541 2.060000e-28 137.0
45 TraesCS1A01G055900 chr5A 87.387 111 12 1 2238 2348 66827328 66827220 4.450000e-25 126.0
46 TraesCS1A01G055900 chr5A 100.000 34 0 0 3361 3394 3397736 3397703 3.540000e-06 63.9
47 TraesCS1A01G055900 chr4B 91.860 86 5 1 3274 3357 41531416 41531501 7.450000e-23 119.0
48 TraesCS1A01G055900 chr4B 100.000 34 0 0 3361 3394 587857335 587857368 3.540000e-06 63.9
49 TraesCS1A01G055900 chr4B 100.000 33 0 0 3361 3393 609505186 609505218 1.270000e-05 62.1
50 TraesCS1A01G055900 chr2D 90.698 86 6 1 3275 3358 86080997 86080912 3.460000e-21 113.0
51 TraesCS1A01G055900 chr6D 90.588 85 6 1 3275 3357 389976960 389976876 1.250000e-20 111.0
52 TraesCS1A01G055900 chr4A 89.011 91 8 1 3269 3357 27643520 27643610 1.250000e-20 111.0
53 TraesCS1A01G055900 chr3A 76.923 182 39 3 1864 2044 623777593 623777772 2.700000e-17 100.0
54 TraesCS1A01G055900 chr3D 75.824 182 41 3 1864 2044 480970003 480970182 5.840000e-14 89.8
55 TraesCS1A01G055900 chr3D 100.000 31 0 0 1813 1843 578259650 578259620 1.650000e-04 58.4
56 TraesCS1A01G055900 chr2B 95.238 42 0 2 3361 3402 247368591 247368630 9.840000e-07 65.8
57 TraesCS1A01G055900 chr2B 90.909 44 2 2 3361 3404 175632143 175632102 1.650000e-04 58.4


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 TraesCS1A01G055900 chr1A 36618117 36622355 4238 True 7829.000000 7829 100.000000 1 4239 1 chr1A.!!$R1 4238
1 TraesCS1A01G055900 chr1A 31893227 31900304 7077 False 914.120000 2686 88.162000 1 4171 5 chr1A.!!$F1 4170
2 TraesCS1A01G055900 chr1D 37435592 37439884 4292 True 1931.000000 3506 90.736000 1 4239 3 chr1D.!!$R4 4238
3 TraesCS1A01G055900 chr1B 57021523 57024465 2942 True 995.333333 2641 88.970667 1007 4103 3 chr1B.!!$R4 3096
4 TraesCS1A01G055900 chr1B 57050634 57051135 501 True 811.000000 811 95.817000 1007 1508 1 chr1B.!!$R1 501
5 TraesCS1A01G055900 chr1B 57042427 57045406 2979 True 602.000000 1223 89.014000 1504 2941 3 chr1B.!!$R5 1437
6 TraesCS1A01G055900 chr1B 57067666 57071662 3996 True 551.800000 1526 88.530000 421 2941 5 chr1B.!!$R6 2520
7 TraesCS1A01G055900 chr1B 57145269 57146023 754 True 460.000000 460 78.624000 1 788 1 chr1B.!!$R2 787

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
601 629 0.553819 TGCAAACCTACCAACCACCT 59.446 50.000 0.00 0.0 0.0 4.00 F
967 1017 0.589708 GTTTGCACAACGGGTAGGAC 59.410 55.000 0.00 0.0 0.0 3.85 F
1009 1723 1.000396 ACTCCAAGCCATCAAGCCC 60.000 57.895 0.00 0.0 0.0 5.19 F
2862 5180 0.539438 TGGACACAAGGAACCATGGC 60.539 55.000 13.04 0.0 0.0 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1607 2321 0.101939 CGAAGTAGGGGTAGGCGTTC 59.898 60.0 0.00 0.00 0.00 3.95 R
2852 5170 0.316204 GCATATGCTGCCATGGTTCC 59.684 55.0 20.64 2.11 45.66 3.62 R
2868 5186 1.028330 CATCAACAGGACAGCCGCAT 61.028 55.0 0.00 0.00 39.96 4.73 R
4033 8964 0.179702 TCCTGCAGCAGATGACCATC 59.820 55.0 24.90 1.90 38.09 3.51 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
201 202 6.151691 CACAACAAATTATCACCTTCCACAG 58.848 40.000 0.00 0.00 0.00 3.66
281 283 1.969923 CTCCAAATGCCCTTTCCACAA 59.030 47.619 0.00 0.00 0.00 3.33
311 313 4.091549 AGAACCTTCATGCATTTGGACAT 58.908 39.130 14.19 2.93 0.00 3.06
360 367 2.235016 GGAGATAGTCAGTCATCGGCT 58.765 52.381 0.00 0.00 0.00 5.52
505 533 2.298163 CTGGCATGCCAAAGAAAGAGTT 59.702 45.455 37.47 0.00 46.63 3.01
558 586 5.426504 CTTCTAGCATGATTGTGGTCTCTT 58.573 41.667 0.00 0.00 0.00 2.85
559 587 5.426689 TCTAGCATGATTGTGGTCTCTTT 57.573 39.130 0.00 0.00 0.00 2.52
600 628 1.339929 CTTGCAAACCTACCAACCACC 59.660 52.381 0.00 0.00 0.00 4.61
601 629 0.553819 TGCAAACCTACCAACCACCT 59.446 50.000 0.00 0.00 0.00 4.00
602 630 0.958822 GCAAACCTACCAACCACCTG 59.041 55.000 0.00 0.00 0.00 4.00
603 631 0.958822 CAAACCTACCAACCACCTGC 59.041 55.000 0.00 0.00 0.00 4.85
604 632 0.850784 AAACCTACCAACCACCTGCT 59.149 50.000 0.00 0.00 0.00 4.24
605 633 1.737199 AACCTACCAACCACCTGCTA 58.263 50.000 0.00 0.00 0.00 3.49
606 634 0.981943 ACCTACCAACCACCTGCTAC 59.018 55.000 0.00 0.00 0.00 3.58
612 640 0.951558 CAACCACCTGCTACCAACAC 59.048 55.000 0.00 0.00 0.00 3.32
838 869 1.447838 GCGCGAGGTGGATGAAAGA 60.448 57.895 12.10 0.00 0.00 2.52
846 877 1.065126 GGTGGATGAAAGACCAGAGGG 60.065 57.143 0.00 0.00 36.82 4.30
847 878 1.065126 GTGGATGAAAGACCAGAGGGG 60.065 57.143 0.00 0.00 44.81 4.79
858 889 1.985895 ACCAGAGGGGAAAAAGACGAT 59.014 47.619 0.00 0.00 41.15 3.73
865 896 2.290071 GGGGAAAAAGACGATGGACTGA 60.290 50.000 0.00 0.00 0.00 3.41
904 935 1.153489 CACCAGTGCCAGATCGGAG 60.153 63.158 7.64 0.00 36.56 4.63
952 984 7.826252 TCTCTAGGAAAGAAATCATCTGGTTTG 59.174 37.037 0.00 0.00 38.79 2.93
953 985 5.397142 AGGAAAGAAATCATCTGGTTTGC 57.603 39.130 0.00 0.00 38.79 3.68
954 986 4.834496 AGGAAAGAAATCATCTGGTTTGCA 59.166 37.500 0.00 0.00 38.79 4.08
956 988 5.509501 GGAAAGAAATCATCTGGTTTGCACA 60.510 40.000 0.00 0.00 38.79 4.57
957 989 5.534207 AAGAAATCATCTGGTTTGCACAA 57.466 34.783 0.00 0.00 38.79 3.33
958 990 4.874970 AGAAATCATCTGGTTTGCACAAC 58.125 39.130 0.00 0.00 36.88 3.32
967 1017 0.589708 GTTTGCACAACGGGTAGGAC 59.410 55.000 0.00 0.00 0.00 3.85
1002 1596 2.233566 TGAGCCCACTCCAAGCCAT 61.234 57.895 0.00 0.00 42.74 4.40
1003 1597 1.452833 GAGCCCACTCCAAGCCATC 60.453 63.158 0.00 0.00 36.90 3.51
1005 1599 1.304381 GCCCACTCCAAGCCATCAA 60.304 57.895 0.00 0.00 0.00 2.57
1009 1723 1.000396 ACTCCAAGCCATCAAGCCC 60.000 57.895 0.00 0.00 0.00 5.19
1139 1853 3.450115 CTCCCACCGACGACCTCC 61.450 72.222 0.00 0.00 0.00 4.30
1516 2230 4.849329 GCTCGCCACGTCCTACCG 62.849 72.222 0.00 0.00 0.00 4.02
1562 2276 2.681778 CTCCTCCCGGTGCTCTGT 60.682 66.667 0.00 0.00 0.00 3.41
1583 2297 1.586564 GATCCTCGACTTCCACGCG 60.587 63.158 3.53 3.53 0.00 6.01
1628 2342 2.416260 GCCTACCCCTACTTCGCG 59.584 66.667 0.00 0.00 0.00 5.87
1958 2690 1.351430 GCTGCGCGTCTACATGTTCA 61.351 55.000 8.43 0.00 0.00 3.18
2087 2827 2.040544 CAACGCCACCACCTCATCC 61.041 63.158 0.00 0.00 0.00 3.51
2209 2949 1.230324 GTGAGAGCTCCGCTTTTTGT 58.770 50.000 10.93 0.00 39.88 2.83
2309 3049 7.532682 TTGGATTAGTTTGCAAAGTTTTCAC 57.467 32.000 23.82 14.15 0.00 3.18
2330 3070 4.751098 CACGGTAAAAGTGTAGGCAAGTTA 59.249 41.667 0.00 0.00 35.08 2.24
2337 3077 7.412853 AAAAGTGTAGGCAAGTTAAAAAGGA 57.587 32.000 0.00 0.00 0.00 3.36
2370 3110 2.633967 TGCTTGGTGATGCCTTTTGATT 59.366 40.909 0.00 0.00 38.35 2.57
2372 3112 3.306225 GCTTGGTGATGCCTTTTGATTGA 60.306 43.478 0.00 0.00 38.35 2.57
2373 3113 3.940209 TGGTGATGCCTTTTGATTGAC 57.060 42.857 0.00 0.00 38.35 3.18
2374 3114 3.229293 TGGTGATGCCTTTTGATTGACA 58.771 40.909 0.00 0.00 38.35 3.58
2375 3115 3.256383 TGGTGATGCCTTTTGATTGACAG 59.744 43.478 0.00 0.00 38.35 3.51
2376 3116 3.248266 GTGATGCCTTTTGATTGACAGC 58.752 45.455 0.00 0.00 0.00 4.40
2416 3162 3.305608 GCATAAAGGAGCATGCCATTACC 60.306 47.826 15.66 10.41 41.36 2.85
2440 3186 6.073003 CCTGATCCAAAACTCTGTTTCTGTAC 60.073 42.308 0.00 0.00 0.00 2.90
2441 3187 6.353323 TGATCCAAAACTCTGTTTCTGTACA 58.647 36.000 0.00 0.00 0.00 2.90
2509 4666 5.419788 TCCATCTTTTTCTGAATGGGATGTG 59.580 40.000 17.35 12.42 0.00 3.21
2540 4697 4.260670 CGTTTTAGTGTGTTGTTCACTCG 58.739 43.478 1.82 0.00 46.27 4.18
2566 4723 6.971726 TCAGTCCGTATGTAGTCCATATTT 57.028 37.500 0.00 0.00 38.29 1.40
2760 5062 9.051679 TCATAAACGAGAAGAACAAATTCTGAA 57.948 29.630 0.00 0.00 44.82 3.02
2853 5171 3.723772 TGTGGACATGGACACAAGG 57.276 52.632 18.61 0.00 43.91 3.61
2854 5172 1.135960 TGTGGACATGGACACAAGGA 58.864 50.000 18.61 0.34 43.91 3.36
2855 5173 1.492599 TGTGGACATGGACACAAGGAA 59.507 47.619 18.61 0.03 43.91 3.36
2856 5174 1.880027 GTGGACATGGACACAAGGAAC 59.120 52.381 14.76 0.00 37.54 3.62
2857 5175 1.202879 TGGACATGGACACAAGGAACC 60.203 52.381 0.00 0.00 0.00 3.62
2858 5176 1.202879 GGACATGGACACAAGGAACCA 60.203 52.381 0.00 0.00 36.83 3.67
2859 5177 2.555227 GGACATGGACACAAGGAACCAT 60.555 50.000 0.00 0.00 42.83 3.55
2861 5179 2.220653 ATGGACACAAGGAACCATGG 57.779 50.000 11.19 11.19 40.91 3.66
2862 5180 0.539438 TGGACACAAGGAACCATGGC 60.539 55.000 13.04 0.00 0.00 4.40
2868 5186 1.005805 ACAAGGAACCATGGCAGCATA 59.994 47.619 13.04 0.00 0.00 3.14
2948 5290 4.023707 GCTTACATGGAAGGATATGTGTGC 60.024 45.833 19.45 0.00 37.98 4.57
3021 5368 3.214328 GGTTTCTTGAAGCCTGTCTTGA 58.786 45.455 8.66 0.00 34.56 3.02
3076 5423 2.306805 TCTCTCCAATCTGCCATGTTGT 59.693 45.455 0.00 0.00 0.00 3.32
3153 5515 6.978080 TCATTAAACCAGACACTTCTTTTTGC 59.022 34.615 0.00 0.00 0.00 3.68
3199 5561 6.323203 AGGTCAGTTGCATATATTGATTGC 57.677 37.500 0.00 0.00 36.91 3.56
3211 5573 7.307989 GCATATATTGATTGCCAAGTTACTCGT 60.308 37.037 0.00 0.00 38.31 4.18
3266 5688 4.762251 AGAAGCAATAGTTGAGACAAACCC 59.238 41.667 0.00 0.00 0.00 4.11
3267 5689 3.074412 AGCAATAGTTGAGACAAACCCG 58.926 45.455 0.00 0.00 0.00 5.28
3291 5713 6.517864 CGGTAAAATACTCCCTCCGTATCAAT 60.518 42.308 0.00 0.00 33.20 2.57
3323 5745 5.698089 ACGTTTTTGTAGTCTAGTTTAGCCC 59.302 40.000 0.00 0.00 0.00 5.19
3324 5746 5.121298 CGTTTTTGTAGTCTAGTTTAGCCCC 59.879 44.000 0.00 0.00 0.00 5.80
3350 5772 9.755064 CAAAACGTCTTATATTTTGGTACAGAG 57.245 33.333 0.00 0.00 42.39 3.35
3351 5773 8.488651 AAACGTCTTATATTTTGGTACAGAGG 57.511 34.615 0.00 0.00 42.39 3.69
3352 5774 7.179076 ACGTCTTATATTTTGGTACAGAGGT 57.821 36.000 0.00 0.00 42.39 3.85
3353 5775 8.297470 ACGTCTTATATTTTGGTACAGAGGTA 57.703 34.615 0.00 0.00 42.39 3.08
3354 5776 8.411683 ACGTCTTATATTTTGGTACAGAGGTAG 58.588 37.037 0.00 0.00 42.39 3.18
3355 5777 8.411683 CGTCTTATATTTTGGTACAGAGGTAGT 58.588 37.037 0.00 0.00 42.39 2.73
3364 5786 9.492973 TTTTGGTACAGAGGTAGTACATAAAAC 57.507 33.333 2.06 0.00 42.73 2.43
3365 5787 6.855836 TGGTACAGAGGTAGTACATAAAACG 58.144 40.000 2.06 0.00 42.73 3.60
3366 5788 6.434028 TGGTACAGAGGTAGTACATAAAACGT 59.566 38.462 2.06 0.00 42.73 3.99
3367 5789 6.969473 GGTACAGAGGTAGTACATAAAACGTC 59.031 42.308 2.06 0.00 42.73 4.34
3368 5790 6.830873 ACAGAGGTAGTACATAAAACGTCT 57.169 37.500 2.06 0.00 37.51 4.18
3369 5791 7.224522 ACAGAGGTAGTACATAAAACGTCTT 57.775 36.000 2.06 0.00 35.53 3.01
3370 5792 8.340618 ACAGAGGTAGTACATAAAACGTCTTA 57.659 34.615 2.06 0.00 35.53 2.10
3371 5793 8.964772 ACAGAGGTAGTACATAAAACGTCTTAT 58.035 33.333 2.06 0.00 35.53 1.73
3680 7813 8.795842 AGAGTAGTACATATCCACTACATAGC 57.204 38.462 18.84 9.68 46.26 2.97
3693 7826 8.577048 TCCACTACATAGCTGGTCTTATATAC 57.423 38.462 0.00 0.00 0.00 1.47
3705 7838 6.675565 TGGTCTTATATACTCCACACTACCA 58.324 40.000 0.00 0.00 0.00 3.25
3831 8762 1.819208 GCACACACCACACAGAGCA 60.819 57.895 0.00 0.00 0.00 4.26
3855 8786 6.889301 ATAGGTACTGCATCCAAAATGATG 57.111 37.500 0.00 0.00 41.90 3.07
3890 8821 6.183360 GGAAAGCATAGAGATGGACTGAAGTA 60.183 42.308 0.00 0.00 33.26 2.24
4062 8993 4.492494 TCTGCTGCAGGAATAATTCAGA 57.508 40.909 27.79 13.49 31.51 3.27
4098 9029 2.040412 AGCGGAAAGAGGAATGGTTTCT 59.960 45.455 0.00 0.00 31.96 2.52
4103 9034 3.441500 AAGAGGAATGGTTTCTGGGTC 57.558 47.619 0.00 0.00 32.16 4.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
174 175 5.010516 TGGAAGGTGATAATTTGTTGTGTGG 59.989 40.000 0.00 0.00 0.00 4.17
185 186 7.785028 TCTCTATACACTGTGGAAGGTGATAAT 59.215 37.037 13.09 0.00 37.22 1.28
201 202 7.161404 TGCAAATATGTGGGATCTCTATACAC 58.839 38.462 0.00 0.00 0.00 2.90
281 283 2.912956 TGCATGAAGGTTCTAGGAAGGT 59.087 45.455 0.00 0.00 0.00 3.50
311 313 7.040686 GCCAAAAGGTAACATGAAAAGTCTCTA 60.041 37.037 0.00 0.00 41.41 2.43
360 367 9.656323 AACTACCAATAGTGTCTATCCTCATTA 57.344 33.333 0.00 0.00 41.00 1.90
558 586 4.020543 GGGCAATACCAAGGTCATAACAA 58.979 43.478 0.00 0.00 42.05 2.83
559 587 3.268334 AGGGCAATACCAAGGTCATAACA 59.732 43.478 0.00 0.00 42.05 2.41
592 620 0.179004 TGTTGGTAGCAGGTGGTTGG 60.179 55.000 0.00 0.00 0.00 3.77
600 628 1.882912 TGCAGAAGTGTTGGTAGCAG 58.117 50.000 0.00 0.00 0.00 4.24
601 629 2.340210 TTGCAGAAGTGTTGGTAGCA 57.660 45.000 0.00 0.00 0.00 3.49
602 630 4.878397 AGATATTGCAGAAGTGTTGGTAGC 59.122 41.667 0.00 0.00 0.00 3.58
603 631 7.223582 CACTAGATATTGCAGAAGTGTTGGTAG 59.776 40.741 0.00 0.00 31.82 3.18
604 632 7.041721 CACTAGATATTGCAGAAGTGTTGGTA 58.958 38.462 0.00 0.00 31.82 3.25
605 633 5.877012 CACTAGATATTGCAGAAGTGTTGGT 59.123 40.000 0.00 0.00 31.82 3.67
606 634 5.220739 GCACTAGATATTGCAGAAGTGTTGG 60.221 44.000 0.00 0.00 38.68 3.77
698 727 0.951558 AGCCAAATGTCGTTGACACC 59.048 50.000 1.11 0.00 45.65 4.16
838 869 1.430992 TCGTCTTTTTCCCCTCTGGT 58.569 50.000 0.00 0.00 34.77 4.00
846 877 3.665190 ACTCAGTCCATCGTCTTTTTCC 58.335 45.455 0.00 0.00 0.00 3.13
847 878 5.444122 CAAACTCAGTCCATCGTCTTTTTC 58.556 41.667 0.00 0.00 0.00 2.29
858 889 0.035317 ATCGCAGCAAACTCAGTCCA 59.965 50.000 0.00 0.00 0.00 4.02
865 896 1.626654 CCGTTCGATCGCAGCAAACT 61.627 55.000 11.09 0.00 0.00 2.66
942 973 0.039256 CCCGTTGTGCAAACCAGATG 60.039 55.000 0.00 0.00 0.00 2.90
952 984 0.389948 CTCTGTCCTACCCGTTGTGC 60.390 60.000 0.00 0.00 0.00 4.57
953 985 0.389948 GCTCTGTCCTACCCGTTGTG 60.390 60.000 0.00 0.00 0.00 3.33
954 986 0.830444 TGCTCTGTCCTACCCGTTGT 60.830 55.000 0.00 0.00 0.00 3.32
956 988 0.542232 AGTGCTCTGTCCTACCCGTT 60.542 55.000 0.00 0.00 0.00 4.44
957 989 0.542232 AAGTGCTCTGTCCTACCCGT 60.542 55.000 0.00 0.00 0.00 5.28
958 990 0.108615 CAAGTGCTCTGTCCTACCCG 60.109 60.000 0.00 0.00 0.00 5.28
967 1017 1.970114 CACCTGGGCAAGTGCTCTG 60.970 63.158 4.52 3.82 43.37 3.35
1002 1596 2.507484 CATTGTCTTGTCAGGGCTTGA 58.493 47.619 0.00 0.00 0.00 3.02
1003 1597 1.068055 GCATTGTCTTGTCAGGGCTTG 60.068 52.381 0.00 0.00 0.00 4.01
1005 1599 0.610232 GGCATTGTCTTGTCAGGGCT 60.610 55.000 0.00 0.00 0.00 5.19
1009 1723 0.445436 GAGCGGCATTGTCTTGTCAG 59.555 55.000 1.45 0.00 0.00 3.51
1529 2243 0.831307 GGAGGTCCTTGCGGAAGTAT 59.169 55.000 15.93 0.00 42.08 2.12
1607 2321 0.101939 CGAAGTAGGGGTAGGCGTTC 59.898 60.000 0.00 0.00 0.00 3.95
1958 2690 2.061773 CATGTTCTCGTTGAAGAGCGT 58.938 47.619 0.00 0.00 38.12 5.07
1993 2725 2.579787 CCGTAGTTGCGCTCCGAG 60.580 66.667 9.73 0.00 0.00 4.63
2138 2878 3.299340 CTGTAGTAGCCGTTGTTCTGT 57.701 47.619 0.00 0.00 0.00 3.41
2290 3030 5.061920 ACCGTGAAAACTTTGCAAACTAA 57.938 34.783 8.05 0.00 0.00 2.24
2309 3049 5.927954 TTAACTTGCCTACACTTTTACCG 57.072 39.130 0.00 0.00 0.00 4.02
2355 3095 3.248266 GCTGTCAATCAAAAGGCATCAC 58.752 45.455 0.00 0.00 0.00 3.06
2370 3110 3.119319 TGATATTACCTTGGGGCTGTCA 58.881 45.455 0.00 0.00 35.63 3.58
2372 3112 3.181429 CCATGATATTACCTTGGGGCTGT 60.181 47.826 0.00 0.00 35.63 4.40
2373 3113 3.424703 CCATGATATTACCTTGGGGCTG 58.575 50.000 0.00 0.00 35.63 4.85
2374 3114 2.225117 GCCATGATATTACCTTGGGGCT 60.225 50.000 0.00 0.00 36.04 5.19
2375 3115 2.171003 GCCATGATATTACCTTGGGGC 58.829 52.381 0.00 0.00 35.63 5.80
2376 3116 3.524095 TGCCATGATATTACCTTGGGG 57.476 47.619 0.00 0.00 38.88 4.96
2414 3160 4.823989 CAGAAACAGAGTTTTGGATCAGGT 59.176 41.667 0.00 0.00 0.00 4.00
2416 3162 6.483307 TGTACAGAAACAGAGTTTTGGATCAG 59.517 38.462 0.00 0.00 0.00 2.90
2440 3186 8.908786 ATTACCATGGTTATGATGTCTTACTG 57.091 34.615 25.38 0.00 36.36 2.74
2441 3187 9.920946 AAATTACCATGGTTATGATGTCTTACT 57.079 29.630 25.38 0.00 36.36 2.24
2487 4644 5.107133 GCACATCCCATTCAGAAAAAGATG 58.893 41.667 13.98 13.98 36.55 2.90
2489 4646 4.151121 TGCACATCCCATTCAGAAAAAGA 58.849 39.130 0.00 0.00 0.00 2.52
2502 4659 0.810031 AACGCGTCTATGCACATCCC 60.810 55.000 14.44 0.00 34.15 3.85
2509 4666 2.410730 ACACACTAAAACGCGTCTATGC 59.589 45.455 14.44 0.00 0.00 3.14
2540 4697 4.445452 TGGACTACATACGGACTGAAAC 57.555 45.455 0.00 0.00 0.00 2.78
2760 5062 2.040813 AGCCAACATGAAGACAGGTCAT 59.959 45.455 0.00 0.00 40.18 3.06
2851 5169 1.991121 CATATGCTGCCATGGTTCCT 58.009 50.000 14.67 0.00 32.85 3.36
2852 5170 0.316204 GCATATGCTGCCATGGTTCC 59.684 55.000 20.64 2.11 45.66 3.62
2853 5171 3.879912 GCATATGCTGCCATGGTTC 57.120 52.632 20.64 3.34 45.66 3.62
2868 5186 1.028330 CATCAACAGGACAGCCGCAT 61.028 55.000 0.00 0.00 39.96 4.73
2948 5290 1.563410 AGAGGCTTCCTTCCTTCCATG 59.437 52.381 0.00 0.00 31.76 3.66
3046 5393 4.080863 GGCAGATTGGAGAGAAAGGAGTAA 60.081 45.833 0.00 0.00 0.00 2.24
3076 5423 7.424803 CAATTACAAGACCACATCAACTGAAA 58.575 34.615 0.00 0.00 0.00 2.69
3153 5515 6.381481 TTGCATTGCATGATTACTAGGAAG 57.619 37.500 12.95 0.00 38.76 3.46
3199 5561 1.270625 TGGAGCCAACGAGTAACTTGG 60.271 52.381 0.00 0.00 40.11 3.61
3211 5573 2.819608 GTGCTTTCTGTATTGGAGCCAA 59.180 45.455 4.15 4.15 40.47 4.52
3266 5688 4.279169 TGATACGGAGGGAGTATTTTACCG 59.721 45.833 0.00 0.00 43.61 4.02
3267 5689 5.796424 TGATACGGAGGGAGTATTTTACC 57.204 43.478 0.00 0.00 35.19 2.85
3324 5746 9.755064 CTCTGTACCAAAATATAAGACGTTTTG 57.245 33.333 0.83 0.74 40.63 2.44
3361 5783 9.886132 ACCTCTGTATCAAAATATAAGACGTTT 57.114 29.630 0.00 0.00 0.00 3.60
3376 5798 9.197306 ACAAACATATGTACTACCTCTGTATCA 57.803 33.333 9.21 0.00 0.00 2.15
3378 5800 9.817809 CAACAAACATATGTACTACCTCTGTAT 57.182 33.333 9.21 0.00 32.02 2.29
3379 5801 9.027202 TCAACAAACATATGTACTACCTCTGTA 57.973 33.333 9.21 0.00 32.02 2.74
3380 5802 7.903145 TCAACAAACATATGTACTACCTCTGT 58.097 34.615 9.21 0.74 32.02 3.41
3381 5803 8.771920 TTCAACAAACATATGTACTACCTCTG 57.228 34.615 9.21 0.00 32.02 3.35
3382 5804 9.436957 CTTTCAACAAACATATGTACTACCTCT 57.563 33.333 9.21 0.00 32.02 3.69
3383 5805 9.431887 TCTTTCAACAAACATATGTACTACCTC 57.568 33.333 9.21 0.00 32.02 3.85
3680 7813 6.776116 TGGTAGTGTGGAGTATATAAGACCAG 59.224 42.308 0.00 0.00 0.00 4.00
3693 7826 4.495422 GAGTATGTTGTGGTAGTGTGGAG 58.505 47.826 0.00 0.00 0.00 3.86
3705 7838 2.028748 ACCTTAACGCGGAGTATGTTGT 60.029 45.455 12.47 0.00 0.00 3.32
3742 7876 6.839124 AATGCATCTGTCACTGGAATTTTA 57.161 33.333 0.00 0.00 0.00 1.52
3798 8727 4.380867 GGTGTGTGCCCAATCTTTCATTAG 60.381 45.833 0.00 0.00 0.00 1.73
3831 8762 6.835488 ACATCATTTTGGATGCAGTACCTATT 59.165 34.615 3.23 0.00 46.81 1.73
3890 8821 3.766591 CAGAGCATATATTCCTCCGGTCT 59.233 47.826 0.00 1.82 0.00 3.85
4033 8964 0.179702 TCCTGCAGCAGATGACCATC 59.820 55.000 24.90 1.90 38.09 3.51
4035 8966 0.622136 ATTCCTGCAGCAGATGACCA 59.378 50.000 24.90 0.00 32.44 4.02
4062 8993 1.582610 CCGCTGCAATTTACACCCGT 61.583 55.000 0.00 0.00 0.00 5.28
4098 9029 1.075374 CTCATCCCAAAGGTTGACCCA 59.925 52.381 0.00 0.00 37.02 4.51
4103 9034 3.693085 CAGACATCTCATCCCAAAGGTTG 59.307 47.826 0.00 0.00 34.59 3.77


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

AutoCloner maintained by Alex Coulton.