Multiple sequence alignment - TraesCS3A01G517500

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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 TraesCS3A01G517500 chr3A 100.000 3356 0 0 3472 6827 734524024 734520669 0.000000e+00 6198.0
1 TraesCS3A01G517500 chr3A 100.000 3004 0 0 1 3004 734527495 734524492 0.000000e+00 5548.0
2 TraesCS3A01G517500 chr3A 98.634 952 12 1 1 951 102757921 102758872 0.000000e+00 1685.0
3 TraesCS3A01G517500 chr3A 93.774 787 46 3 6040 6825 73871049 73871833 0.000000e+00 1179.0
4 TraesCS3A01G517500 chr3A 92.720 783 54 3 6044 6825 534530386 534531166 0.000000e+00 1127.0
5 TraesCS3A01G517500 chr3A 75.943 212 43 8 1595 1804 652907822 652908027 1.210000e-17 102.0
6 TraesCS3A01G517500 chr3A 89.796 49 4 1 3746 3793 674989490 674989442 2.060000e-05 62.1
7 TraesCS3A01G517500 chr3D 94.921 2599 72 15 3485 6030 604610689 604608098 0.000000e+00 4013.0
8 TraesCS3A01G517500 chr3D 93.851 1545 73 7 995 2534 604613329 604611802 0.000000e+00 2307.0
9 TraesCS3A01G517500 chr3D 91.667 336 28 0 2631 2966 604611647 604611312 3.730000e-127 466.0
10 TraesCS3A01G517500 chr3D 91.503 153 6 4 4718 4870 604610597 604610452 3.230000e-48 204.0
11 TraesCS3A01G517500 chr3B 94.155 1266 28 14 4749 5987 1788190 1789436 0.000000e+00 1886.0
12 TraesCS3A01G517500 chr3B 97.132 1011 14 7 1 996 373119085 373118075 0.000000e+00 1692.0
13 TraesCS3A01G517500 chr3B 88.196 1059 95 17 1494 2530 1784327 1785377 0.000000e+00 1236.0
14 TraesCS3A01G517500 chr3B 92.986 499 19 2 996 1493 1783883 1784366 0.000000e+00 713.0
15 TraesCS3A01G517500 chr3B 83.465 508 56 10 2522 3004 1785402 1785906 1.350000e-121 448.0
16 TraesCS3A01G517500 chr3B 90.541 222 18 2 3492 3713 1786159 1786377 2.410000e-74 291.0
17 TraesCS3A01G517500 chr3B 83.673 245 37 3 4135 4378 824908798 824909040 1.920000e-55 228.0
18 TraesCS3A01G517500 chr3B 83.673 245 37 3 4135 4378 825101714 825101956 1.920000e-55 228.0
19 TraesCS3A01G517500 chr3B 91.176 136 7 2 4735 4870 1786235 1786365 5.440000e-41 180.0
20 TraesCS3A01G517500 chr3B 95.604 91 3 1 4667 4756 1787943 1788033 1.980000e-30 145.0
21 TraesCS3A01G517500 chr6B 96.940 1013 16 7 1 998 717070723 717071735 0.000000e+00 1685.0
22 TraesCS3A01G517500 chr6B 97.899 952 19 1 1 951 679748694 679749645 0.000000e+00 1646.0
23 TraesCS3A01G517500 chr6B 97.689 952 21 1 1 951 637394074 637393123 0.000000e+00 1635.0
24 TraesCS3A01G517500 chr6B 79.339 121 25 0 3741 3861 75960567 75960447 1.220000e-12 86.1
25 TraesCS3A01G517500 chr1B 98.319 952 14 2 1 951 480225149 480226099 0.000000e+00 1668.0
26 TraesCS3A01G517500 chr1B 92.857 784 52 4 6044 6825 685736201 685735420 0.000000e+00 1134.0
27 TraesCS3A01G517500 chr1B 92.730 784 51 5 6044 6825 686222142 686222921 0.000000e+00 1127.0
28 TraesCS3A01G517500 chr1B 87.176 811 77 12 4668 5464 3272683 3273480 0.000000e+00 896.0
29 TraesCS3A01G517500 chr1B 86.133 512 59 7 5460 5970 3289420 3289920 6.020000e-150 542.0
30 TraesCS3A01G517500 chr1B 82.018 456 65 7 1019 1469 3269318 3269761 8.360000e-99 372.0
31 TraesCS3A01G517500 chr1B 87.662 154 18 1 3570 3723 3272752 3272904 1.960000e-40 178.0
32 TraesCS3A01G517500 chr5A 98.214 952 16 1 1 951 549363879 549364830 0.000000e+00 1663.0
33 TraesCS3A01G517500 chr7B 98.002 951 19 0 1 951 152066218 152067168 0.000000e+00 1652.0
34 TraesCS3A01G517500 chr7B 85.714 231 31 2 4148 4377 609816488 609816259 6.840000e-60 243.0
35 TraesCS3A01G517500 chr7B 90.909 44 4 0 1770 1813 655682399 655682442 7.390000e-05 60.2
36 TraesCS3A01G517500 chr1A 98.004 952 17 2 1 951 373270762 373271712 0.000000e+00 1652.0
37 TraesCS3A01G517500 chr1A 85.385 130 16 3 1684 1813 579996180 579996306 1.540000e-26 132.0
38 TraesCS3A01G517500 chr1D 86.491 1103 129 14 4876 5976 9275736 9276820 0.000000e+00 1194.0
39 TraesCS3A01G517500 chr1D 82.103 447 61 11 1029 1469 9272123 9272556 1.400000e-96 364.0
40 TraesCS3A01G517500 chr1D 86.154 195 21 3 4668 4862 9274843 9275031 8.980000e-49 206.0
41 TraesCS3A01G517500 chr1D 77.132 258 47 11 1578 1830 436328579 436328329 9.230000e-29 139.0
42 TraesCS3A01G517500 chr4A 93.893 786 46 2 6043 6827 595416754 595415970 0.000000e+00 1184.0
43 TraesCS3A01G517500 chr4A 74.038 312 65 11 1523 1830 239581540 239581241 5.600000e-21 113.0
44 TraesCS3A01G517500 chr7A 93.893 786 45 3 6043 6827 82126829 82126046 0.000000e+00 1182.0
45 TraesCS3A01G517500 chr7A 92.730 784 55 2 6043 6825 46688592 46689374 0.000000e+00 1131.0
46 TraesCS3A01G517500 chr7A 84.810 237 36 0 4138 4374 319765055 319764819 8.850000e-59 239.0
47 TraesCS3A01G517500 chr2D 93.248 785 51 2 6042 6825 642968604 642969387 0.000000e+00 1155.0
48 TraesCS3A01G517500 chr2D 81.179 441 61 6 1016 1452 454965023 454965445 1.100000e-87 335.0
49 TraesCS3A01G517500 chr2D 85.356 239 33 2 4138 4376 29841593 29841357 5.290000e-61 246.0
50 TraesCS3A01G517500 chr2D 91.954 87 2 3 5427 5508 635587959 635587873 4.330000e-22 117.0
51 TraesCS3A01G517500 chr2D 94.203 69 4 0 5940 6008 635587783 635587715 9.360000e-19 106.0
52 TraesCS3A01G517500 chr2D 96.552 58 0 2 5212 5269 635588013 635587958 2.030000e-15 95.3
53 TraesCS3A01G517500 chr5D 93.214 781 51 2 6043 6822 437333245 437334024 0.000000e+00 1147.0
54 TraesCS3A01G517500 chr5D 88.017 242 29 0 4135 4376 538171777 538171536 3.120000e-73 287.0
55 TraesCS3A01G517500 chr5D 78.774 212 38 7 1596 1804 212028597 212028804 1.190000e-27 135.0
56 TraesCS3A01G517500 chr2B 81.448 442 60 8 1016 1453 534707721 534708144 6.560000e-90 342.0
57 TraesCS3A01G517500 chr2B 86.667 60 6 2 3741 3799 142247003 142246945 1.590000e-06 65.8
58 TraesCS3A01G517500 chr2A 80.822 438 62 7 1019 1452 595345502 595345083 2.370000e-84 324.0
59 TraesCS3A01G517500 chr2A 95.161 62 3 0 939 1000 354042123 354042062 1.570000e-16 99.0
60 TraesCS3A01G517500 chr2A 86.154 65 9 0 3737 3801 598626178 598626242 3.420000e-08 71.3
61 TraesCS3A01G517500 chr6A 84.362 243 33 5 4138 4378 550253104 550253343 4.120000e-57 233.0
62 TraesCS3A01G517500 chr4B 83.884 242 37 2 4138 4378 652662143 652661903 5.330000e-56 230.0
63 TraesCS3A01G517500 chr4B 88.770 187 6 5 827 998 424977887 424977701 1.490000e-51 215.0
64 TraesCS3A01G517500 chr4B 81.897 116 21 0 1887 2002 100916341 100916226 1.570000e-16 99.0
65 TraesCS3A01G517500 chr7D 73.904 456 105 9 1857 2301 563891539 563891087 3.270000e-38 171.0
66 TraesCS3A01G517500 chr7D 78.689 122 22 4 2885 3004 108984822 108984703 2.040000e-10 78.7
67 TraesCS3A01G517500 chrUn 91.954 87 2 3 5427 5508 162244276 162244362 4.330000e-22 117.0
68 TraesCS3A01G517500 chrUn 95.652 69 3 0 5940 6008 162244452 162244520 2.010000e-20 111.0
69 TraesCS3A01G517500 chrUn 96.552 58 0 2 5212 5269 162244222 162244277 2.030000e-15 95.3
70 TraesCS3A01G517500 chr4D 82.203 118 20 1 2857 2974 4032977 4033093 4.360000e-17 100.0
71 TraesCS3A01G517500 chr5B 95.238 63 2 1 933 995 613627484 613627545 1.570000e-16 99.0
72 TraesCS3A01G517500 chr5B 89.474 57 6 0 1620 1676 653766743 653766799 9.500000e-09 73.1
73 TraesCS3A01G517500 chr5B 77.165 127 25 3 3747 3871 277623572 277623448 3.420000e-08 71.3
74 TraesCS3A01G517500 chr6D 78.289 152 24 4 1681 1824 472204298 472204148 9.430000e-14 89.8


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 TraesCS3A01G517500 chr3A 734520669 734527495 6826 True 5873.000000 6198 100.000000 1 6827 2 chr3A.!!$R2 6826
1 TraesCS3A01G517500 chr3A 102757921 102758872 951 False 1685.000000 1685 98.634000 1 951 1 chr3A.!!$F2 950
2 TraesCS3A01G517500 chr3A 73871049 73871833 784 False 1179.000000 1179 93.774000 6040 6825 1 chr3A.!!$F1 785
3 TraesCS3A01G517500 chr3A 534530386 534531166 780 False 1127.000000 1127 92.720000 6044 6825 1 chr3A.!!$F3 781
4 TraesCS3A01G517500 chr3D 604608098 604613329 5231 True 1747.500000 4013 92.985500 995 6030 4 chr3D.!!$R1 5035
5 TraesCS3A01G517500 chr3B 373118075 373119085 1010 True 1692.000000 1692 97.132000 1 996 1 chr3B.!!$R1 995
6 TraesCS3A01G517500 chr3B 1783883 1789436 5553 False 699.857143 1886 90.874714 996 5987 7 chr3B.!!$F3 4991
7 TraesCS3A01G517500 chr6B 717070723 717071735 1012 False 1685.000000 1685 96.940000 1 998 1 chr6B.!!$F2 997
8 TraesCS3A01G517500 chr6B 679748694 679749645 951 False 1646.000000 1646 97.899000 1 951 1 chr6B.!!$F1 950
9 TraesCS3A01G517500 chr6B 637393123 637394074 951 True 1635.000000 1635 97.689000 1 951 1 chr6B.!!$R2 950
10 TraesCS3A01G517500 chr1B 480225149 480226099 950 False 1668.000000 1668 98.319000 1 951 1 chr1B.!!$F2 950
11 TraesCS3A01G517500 chr1B 685735420 685736201 781 True 1134.000000 1134 92.857000 6044 6825 1 chr1B.!!$R1 781
12 TraesCS3A01G517500 chr1B 686222142 686222921 779 False 1127.000000 1127 92.730000 6044 6825 1 chr1B.!!$F3 781
13 TraesCS3A01G517500 chr1B 3289420 3289920 500 False 542.000000 542 86.133000 5460 5970 1 chr1B.!!$F1 510
14 TraesCS3A01G517500 chr1B 3269318 3273480 4162 False 482.000000 896 85.618667 1019 5464 3 chr1B.!!$F4 4445
15 TraesCS3A01G517500 chr5A 549363879 549364830 951 False 1663.000000 1663 98.214000 1 951 1 chr5A.!!$F1 950
16 TraesCS3A01G517500 chr7B 152066218 152067168 950 False 1652.000000 1652 98.002000 1 951 1 chr7B.!!$F1 950
17 TraesCS3A01G517500 chr1A 373270762 373271712 950 False 1652.000000 1652 98.004000 1 951 1 chr1A.!!$F1 950
18 TraesCS3A01G517500 chr1D 9272123 9276820 4697 False 588.000000 1194 84.916000 1029 5976 3 chr1D.!!$F1 4947
19 TraesCS3A01G517500 chr4A 595415970 595416754 784 True 1184.000000 1184 93.893000 6043 6827 1 chr4A.!!$R2 784
20 TraesCS3A01G517500 chr7A 82126046 82126829 783 True 1182.000000 1182 93.893000 6043 6827 1 chr7A.!!$R1 784
21 TraesCS3A01G517500 chr7A 46688592 46689374 782 False 1131.000000 1131 92.730000 6043 6825 1 chr7A.!!$F1 782
22 TraesCS3A01G517500 chr2D 642968604 642969387 783 False 1155.000000 1155 93.248000 6042 6825 1 chr2D.!!$F2 783
23 TraesCS3A01G517500 chr5D 437333245 437334024 779 False 1147.000000 1147 93.214000 6043 6822 1 chr5D.!!$F2 779

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
953 955 3.789224 CGAAGAAAAACCGGTTGAAAGTG 59.211 43.478 23.08 4.91 0.00 3.16 F
2635 4012 0.179097 GGCTACCTCTTTCTCGCTGG 60.179 60.000 0.00 0.00 0.00 4.85 F
2702 4079 0.182537 TTGTACCACTTGTGCCTGCT 59.817 50.000 0.00 0.00 0.00 4.24 F
2860 4237 0.323957 GACAAAGGGACGGTTAGCCT 59.676 55.000 0.00 0.00 0.00 4.58 F
3606 5110 0.463654 TACCATGCAGCCGGATGAAC 60.464 55.000 26.87 7.20 43.27 3.18 F
3809 5712 1.348036 ACCAGTGTCAAGCCTAAGACC 59.652 52.381 0.00 0.00 33.89 3.85 F
5324 10347 0.514255 CATGTCTGGCGTTGTGTCTG 59.486 55.000 0.00 0.00 0.00 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2874 4251 0.323957 AAACCAACTCCGGCCTCTAC 59.676 55.000 0.00 0.0 0.00 2.59 R
3782 5685 1.339055 GGCTTGACACTGGTGCTCATA 60.339 52.381 0.17 0.0 0.00 2.15 R
3809 5712 1.956477 CCCCAGTTCACCAAAGTTCAG 59.044 52.381 0.00 0.0 0.00 3.02 R
4362 7715 3.006217 ACAAAACAGTACTACCTCCGTCC 59.994 47.826 0.00 0.0 0.00 4.79 R
5133 10156 0.174162 GCTTGGATGACAACATGGCC 59.826 55.000 0.00 0.0 36.82 5.36 R
5338 10361 0.818445 GTGGGCTGATCAGATGGCAG 60.818 60.000 27.04 0.0 0.00 4.85 R
6482 11507 0.106318 GGCAAAGCAGGATCTCCCAT 60.106 55.000 0.00 0.0 37.41 4.00 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
72 73 3.791545 AGGTAGAGACTGAGGAAGGAGAT 59.208 47.826 0.00 0.00 0.00 2.75
477 478 7.039011 AGGGAAGGAAGGAAAATTGTGATTTAC 60.039 37.037 0.00 0.00 34.44 2.01
759 760 4.717877 TGGGTATTGTCAGCCAGATTATG 58.282 43.478 0.00 0.00 41.08 1.90
951 953 4.023739 ACGAAGAAAAACCGGTTGAAAG 57.976 40.909 23.08 11.25 0.00 2.62
953 955 3.789224 CGAAGAAAAACCGGTTGAAAGTG 59.211 43.478 23.08 4.91 0.00 3.16
1013 1029 2.169352 AGATATAGATGGGCATCACGGC 59.831 50.000 0.00 0.00 40.22 5.68
1017 1033 4.094646 ATGGGCATCACGGCGACA 62.095 61.111 16.62 0.00 42.43 4.35
1156 1172 3.795041 CTGAGGAGGCTGCCCCTG 61.795 72.222 26.82 13.79 46.60 4.45
1157 1173 4.337304 TGAGGAGGCTGCCCCTGA 62.337 66.667 26.82 18.93 46.60 3.86
1158 1174 3.478274 GAGGAGGCTGCCCCTGAG 61.478 72.222 26.82 0.00 46.60 3.35
1161 1177 3.478274 GAGGCTGCCCCTGAGGAG 61.478 72.222 16.57 0.00 46.60 3.69
1424 1444 3.431766 CGGACGAAATATCCTTCCCACTT 60.432 47.826 0.00 0.00 33.70 3.16
1562 1716 2.223479 ACAAATTTGCTTCAGCGTCGTT 60.223 40.909 18.12 0.00 45.83 3.85
1630 2931 0.819259 ATTCAACGCTGCCCGCATAT 60.819 50.000 0.00 0.00 41.76 1.78
1651 2952 9.369904 GCATATATTTCAACCACTGTTTCAATT 57.630 29.630 0.00 0.00 30.42 2.32
1662 2963 6.208599 ACCACTGTTTCAATTAAATGGACGAT 59.791 34.615 0.00 0.00 31.71 3.73
2014 3330 1.512694 GCTCCTTGCGGATTTTGGG 59.487 57.895 0.00 0.00 39.01 4.12
2178 3494 2.703798 GGTCGTACCGTGCCTGCTA 61.704 63.158 0.00 0.00 0.00 3.49
2221 3537 2.912987 ATACGACAGCCCTCGAGCCT 62.913 60.000 6.99 2.15 37.11 4.58
2270 3586 6.841229 TCTGAGGTAGTGAAAGATATGGACAT 59.159 38.462 0.00 0.00 0.00 3.06
2331 3647 2.809601 GCGGCGATGTTGACGAGT 60.810 61.111 12.98 0.00 45.34 4.18
2371 3687 4.681978 GTTGTGCGACGGGAGGCT 62.682 66.667 0.00 0.00 33.72 4.58
2405 3721 1.549243 TTGATGCGGTGGAGGCACTA 61.549 55.000 0.00 0.00 44.23 2.74
2498 3814 4.070552 GGCTCCTCCTTCACGCGT 62.071 66.667 5.58 5.58 0.00 6.01
2534 3850 2.659063 CGGGCCCATCTGACAGACA 61.659 63.158 24.92 0.00 0.00 3.41
2544 3893 3.081710 TCTGACAGACAATCGTCCCTA 57.918 47.619 0.00 0.00 43.73 3.53
2551 3900 1.480954 GACAATCGTCCCTAAGAGCCA 59.519 52.381 0.00 0.00 36.02 4.75
2578 3927 2.045634 GGAGATGTGGCTGCTGCA 60.046 61.111 17.89 0.88 41.91 4.41
2601 3950 2.102252 CTGCATCTACTTGTCCTCCTCC 59.898 54.545 0.00 0.00 0.00 4.30
2608 3957 0.677098 CTTGTCCTCCTCCTCGTCGA 60.677 60.000 0.00 0.00 0.00 4.20
2617 3966 1.066303 CCTCCTCGTCGAAAGAGATGG 59.934 57.143 18.83 14.58 43.49 3.51
2635 4012 0.179097 GGCTACCTCTTTCTCGCTGG 60.179 60.000 0.00 0.00 0.00 4.85
2658 4035 4.200283 CCAGAGAGCGAGGACGGC 62.200 72.222 0.00 0.00 40.15 5.68
2669 4046 4.585526 GGACGGCGCGATGATCCA 62.586 66.667 12.10 0.00 0.00 3.41
2702 4079 0.182537 TTGTACCACTTGTGCCTGCT 59.817 50.000 0.00 0.00 0.00 4.24
2748 4125 4.598894 CCGCTGGGCTCAGGATCG 62.599 72.222 17.16 10.52 41.19 3.69
2792 4169 2.893398 CTCGTGGAGGGGTAGTGC 59.107 66.667 0.00 0.00 0.00 4.40
2794 4171 4.814294 CGTGGAGGGGTAGTGCGC 62.814 72.222 0.00 0.00 0.00 6.09
2844 4221 2.139323 AGGCACGACCATACTAGACA 57.861 50.000 0.00 0.00 43.14 3.41
2860 4237 0.323957 GACAAAGGGACGGTTAGCCT 59.676 55.000 0.00 0.00 0.00 4.58
2874 4251 0.804364 TAGCCTGCTTCAATGCAACG 59.196 50.000 0.00 0.00 42.83 4.10
2878 4255 2.076100 CCTGCTTCAATGCAACGTAGA 58.924 47.619 0.00 0.00 42.83 2.59
2897 4274 1.072505 GGCCGGAGTTGGTTTCTCA 59.927 57.895 5.05 0.00 34.04 3.27
2922 4299 1.226773 GGCATCCGCATTGAAGCAC 60.227 57.895 0.00 0.00 41.24 4.40
2954 4331 3.690280 TCATGTCCGTCAGCGCCA 61.690 61.111 2.29 0.00 36.67 5.69
2971 4348 1.207488 CCACCCTCCCATCCAGTCAA 61.207 60.000 0.00 0.00 0.00 3.18
2977 4354 3.373438 CCCTCCCATCCAGTCAAATCATT 60.373 47.826 0.00 0.00 0.00 2.57
3498 4979 3.053291 GCACGGGCCGTTTGATGA 61.053 61.111 32.12 0.00 38.32 2.92
3598 5102 3.571401 AGCATAAAGAATACCATGCAGCC 59.429 43.478 8.00 0.00 44.90 4.85
3606 5110 0.463654 TACCATGCAGCCGGATGAAC 60.464 55.000 26.87 7.20 43.27 3.18
3624 5128 9.458374 CGGATGAACATAACAAAAAGTAAAAGT 57.542 29.630 0.00 0.00 0.00 2.66
3658 5162 1.657804 ACCAAGGTCTAAGGAGGGTG 58.342 55.000 0.00 0.00 0.00 4.61
3663 5167 1.940957 AGGTCTAAGGAGGGTGGAGAT 59.059 52.381 0.00 0.00 0.00 2.75
3686 5572 8.149647 AGATTTTCATTTATCACTTGGTGCAAA 58.850 29.630 0.00 0.00 32.98 3.68
3801 5704 2.099141 TATGAGCACCAGTGTCAAGC 57.901 50.000 0.00 0.00 0.00 4.01
3809 5712 1.348036 ACCAGTGTCAAGCCTAAGACC 59.652 52.381 0.00 0.00 33.89 3.85
3831 5734 2.176798 TGAACTTTGGTGAACTGGGGAT 59.823 45.455 0.00 0.00 0.00 3.85
3893 5796 7.323420 TCGATGGCTGAGTATATAATTGGAAG 58.677 38.462 0.00 0.00 0.00 3.46
3942 5845 5.830000 ATGTGATTCACCAATGTCTGATG 57.170 39.130 14.05 0.00 32.73 3.07
3961 5864 7.173218 GTCTGATGGACTCTTTCAACATACAAA 59.827 37.037 0.00 0.00 41.46 2.83
4166 7519 4.320870 TCCGTCTTGGTTTATTGGTCTTC 58.679 43.478 0.00 0.00 39.52 2.87
4168 7521 5.246656 TCCGTCTTGGTTTATTGGTCTTCTA 59.753 40.000 0.00 0.00 39.52 2.10
4169 7522 5.350640 CCGTCTTGGTTTATTGGTCTTCTAC 59.649 44.000 0.00 0.00 0.00 2.59
4265 7618 7.218773 CCAATGAAAACTATGTGCAAATACGAG 59.781 37.037 0.00 0.00 0.00 4.18
4271 7624 4.870426 ACTATGTGCAAATACGAGTCCAAG 59.130 41.667 0.00 0.00 0.00 3.61
4362 7715 4.482952 ACGAAGGGGACTAATAAACCAG 57.517 45.455 0.00 0.00 42.68 4.00
4470 7853 2.020720 TGCATACATACTTTTGCCCCG 58.979 47.619 0.00 0.00 34.20 5.73
4564 7947 3.201930 TGCCATGCCTCTTACCTATTTGA 59.798 43.478 0.00 0.00 0.00 2.69
4831 9162 3.275228 ACCAAGGTCTAAGGAGGGTAGAT 59.725 47.826 0.00 0.00 30.52 1.98
5133 10156 1.128200 TTGAGTACCATCCATCCCCG 58.872 55.000 0.00 0.00 0.00 5.73
5324 10347 0.514255 CATGTCTGGCGTTGTGTCTG 59.486 55.000 0.00 0.00 0.00 3.51
5338 10361 0.531974 TGTCTGTCTTTCACGTGGCC 60.532 55.000 17.00 0.00 0.00 5.36
5936 10960 2.901291 TCCCTTTTGCTAGGCCAAATT 58.099 42.857 5.01 0.00 34.92 1.82
5998 11022 1.341209 CCTTGTTTTGAGCAGTTCCCC 59.659 52.381 0.00 0.00 0.00 4.81
6015 11039 2.325082 CCAACACGCACTGGTAGCC 61.325 63.158 0.00 0.00 0.00 3.93
6130 11154 1.456518 CCTCTCTCTCCATCGGCCA 60.457 63.158 2.24 0.00 0.00 5.36
6200 11224 1.980036 TGTGTGGTAGGGTTAGGGTTC 59.020 52.381 0.00 0.00 0.00 3.62
6236 11260 2.668212 CCATTGCGGTGGTGTCGT 60.668 61.111 0.00 0.00 34.46 4.34
6239 11263 1.525077 ATTGCGGTGGTGTCGTGTT 60.525 52.632 0.00 0.00 0.00 3.32
6240 11264 0.249953 ATTGCGGTGGTGTCGTGTTA 60.250 50.000 0.00 0.00 0.00 2.41
6286 11310 1.507141 CGTTCAGGCGAGGCTTTTGT 61.507 55.000 0.00 0.00 0.00 2.83
6304 11328 1.271982 TGTCTTCGTCTAGGAGCCAGT 60.272 52.381 0.00 0.00 0.00 4.00
6308 11332 0.259065 TCGTCTAGGAGCCAGTGGAT 59.741 55.000 15.20 6.44 0.00 3.41
6335 11360 3.060615 CCGGGTCTCGTCGAGGTT 61.061 66.667 21.63 0.00 37.11 3.50
6336 11361 2.633509 CCGGGTCTCGTCGAGGTTT 61.634 63.158 21.63 0.00 37.11 3.27
6449 11474 3.514645 CTTGTTGGTATGATTTGCTGCC 58.485 45.455 0.00 0.00 0.00 4.85
6470 11495 2.755655 CGCTGTTCTTCTCCTTCCTCTA 59.244 50.000 0.00 0.00 0.00 2.43
6475 11500 5.519808 TGTTCTTCTCCTTCCTCTATGCTA 58.480 41.667 0.00 0.00 0.00 3.49
6478 11503 7.785028 TGTTCTTCTCCTTCCTCTATGCTAATA 59.215 37.037 0.00 0.00 0.00 0.98
6482 11507 6.853490 TCTCCTTCCTCTATGCTAATACTGA 58.147 40.000 0.00 0.00 0.00 3.41
6543 11568 1.142748 GCTGGACTGGTCGGATGAG 59.857 63.158 0.00 0.00 0.00 2.90
6600 11625 3.334691 CGGTACTCAAAGCCAAAGATGA 58.665 45.455 0.00 0.00 0.00 2.92
6643 11668 1.613836 GATTGATGTCCATGCCCTCC 58.386 55.000 0.00 0.00 0.00 4.30
6670 11695 3.142174 CTGGTGTCAAGAAAGGAGGAAC 58.858 50.000 0.00 0.00 0.00 3.62
6698 11723 0.951525 CGGCAATTGTACCGTGGTCA 60.952 55.000 14.30 0.00 44.46 4.02
6739 11764 3.679917 CGACTGGTTGCATATCCTTCTGT 60.680 47.826 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
72 73 2.359169 CCTCTTCCTGCGCCCTACA 61.359 63.158 4.18 0.00 0.00 2.74
477 478 6.749118 CAGAACTTTCCAAAACTTTGTCTGAG 59.251 38.462 10.46 3.14 36.62 3.35
960 976 8.531146 CCTAATGGACAAATTGGTTGAATAGTT 58.469 33.333 0.00 0.00 40.74 2.24
976 992 9.913310 CATCTATATCTCTACTCCTAATGGACA 57.087 37.037 0.00 0.00 37.46 4.02
1013 1029 4.680237 TTGCCCGCCTCACTGTCG 62.680 66.667 0.00 0.00 0.00 4.35
1017 1033 3.650950 ATGGTTGCCCGCCTCACT 61.651 61.111 0.00 0.00 0.00 3.41
1707 3008 7.138736 GGTGGAAATATCATCCGTTTTATGTG 58.861 38.462 3.73 0.00 39.98 3.21
1917 3233 3.443045 GGCGCCATCAACAGTGGG 61.443 66.667 24.80 0.00 37.22 4.61
2002 3318 1.378514 GAGCTCCCCAAAATCCGCA 60.379 57.895 0.87 0.00 0.00 5.69
2005 3321 0.684479 GGGTGAGCTCCCCAAAATCC 60.684 60.000 26.70 8.87 42.15 3.01
2014 3330 2.270527 GCCTTGAGGGTGAGCTCC 59.729 66.667 12.15 2.19 37.43 4.70
2126 3442 4.183686 CCGCTCCGCATTTGCCAG 62.184 66.667 0.00 0.00 37.91 4.85
2221 3537 1.473258 GCATTTATGGTGGTGCCTCA 58.527 50.000 0.00 0.00 38.35 3.86
2259 3575 4.103627 TCATGAAGGTGCATGTCCATATCT 59.896 41.667 10.70 0.00 44.59 1.98
2270 3586 1.815003 CCGCGATCATGAAGGTGCA 60.815 57.895 8.23 0.00 0.00 4.57
2371 3687 0.904865 ATCAAGGACGAGCCAGTGGA 60.905 55.000 15.20 0.00 40.02 4.02
2376 3692 2.125552 CGCATCAAGGACGAGCCA 60.126 61.111 0.00 0.00 40.02 4.75
2464 3780 2.108514 CCAGTCCATGATGCGCGTT 61.109 57.895 8.43 0.00 0.00 4.84
2530 3846 1.757699 GGCTCTTAGGGACGATTGTCT 59.242 52.381 12.89 0.00 44.83 3.41
2534 3850 0.831307 GGTGGCTCTTAGGGACGATT 59.169 55.000 0.00 0.00 0.00 3.34
2544 3893 2.286523 CCTCGTGGAGGTGGCTCTT 61.287 63.158 0.00 0.00 44.25 2.85
2578 3927 1.484240 GGAGGACAAGTAGATGCAGCT 59.516 52.381 10.44 10.44 0.00 4.24
2581 3930 2.111384 GGAGGAGGACAAGTAGATGCA 58.889 52.381 0.00 0.00 0.00 3.96
2584 3933 2.242708 ACGAGGAGGAGGACAAGTAGAT 59.757 50.000 0.00 0.00 0.00 1.98
2585 3934 1.634459 ACGAGGAGGAGGACAAGTAGA 59.366 52.381 0.00 0.00 0.00 2.59
2586 3935 2.018515 GACGAGGAGGAGGACAAGTAG 58.981 57.143 0.00 0.00 0.00 2.57
2587 3936 1.678123 CGACGAGGAGGAGGACAAGTA 60.678 57.143 0.00 0.00 0.00 2.24
2588 3937 0.961358 CGACGAGGAGGAGGACAAGT 60.961 60.000 0.00 0.00 0.00 3.16
2601 3950 2.541999 GGTAGCCATCTCTTTCGACGAG 60.542 54.545 0.00 4.86 0.00 4.18
2617 3966 0.533032 ACCAGCGAGAAAGAGGTAGC 59.467 55.000 0.00 0.00 0.00 3.58
2635 4012 2.716017 CCTCGCTCTCTGGGACCAC 61.716 68.421 0.00 0.00 33.86 4.16
2658 4035 1.300465 CCTCAGGTGGATCATCGCG 60.300 63.158 0.00 0.00 0.00 5.87
2661 4038 1.055040 CCCTCCTCAGGTGGATCATC 58.945 60.000 13.94 0.00 38.51 2.92
2669 4046 1.552719 GGTACAAGTCCCTCCTCAGGT 60.553 57.143 0.00 0.00 38.30 4.00
2702 4079 2.525629 TCCTGGTTCTCCGTGCCA 60.526 61.111 0.00 0.00 36.30 4.92
2748 4125 2.689034 CTCCCCCTCCCAGTCACC 60.689 72.222 0.00 0.00 0.00 4.02
2836 4213 3.445096 GCTAACCGTCCCTTTGTCTAGTA 59.555 47.826 0.00 0.00 0.00 1.82
2844 4221 1.002502 GCAGGCTAACCGTCCCTTT 60.003 57.895 0.00 0.00 42.76 3.11
2860 4237 2.076100 CCTCTACGTTGCATTGAAGCA 58.924 47.619 0.00 0.00 43.99 3.91
2874 4251 0.323957 AAACCAACTCCGGCCTCTAC 59.676 55.000 0.00 0.00 0.00 2.59
2878 4255 1.375326 GAGAAACCAACTCCGGCCT 59.625 57.895 0.00 0.00 0.00 5.19
2897 4274 3.329542 AATGCGGATGCCACGTCCT 62.330 57.895 4.43 0.00 41.78 3.85
2954 4331 1.566231 GATTTGACTGGATGGGAGGGT 59.434 52.381 0.00 0.00 0.00 4.34
3471 4848 1.656818 CGGCCCGTGCAAATCTTGAT 61.657 55.000 0.00 0.00 40.13 2.57
3472 4849 2.331893 CGGCCCGTGCAAATCTTGA 61.332 57.895 0.00 0.00 40.13 3.02
3473 4850 2.141122 AACGGCCCGTGCAAATCTTG 62.141 55.000 10.80 0.00 39.99 3.02
3474 4851 1.460273 AAACGGCCCGTGCAAATCTT 61.460 50.000 10.80 0.00 39.99 2.40
3475 4852 1.901464 AAACGGCCCGTGCAAATCT 60.901 52.632 10.80 0.00 39.99 2.40
3476 4853 1.732683 CAAACGGCCCGTGCAAATC 60.733 57.895 10.80 0.00 39.99 2.17
3477 4854 1.531739 ATCAAACGGCCCGTGCAAAT 61.532 50.000 10.80 0.00 39.99 2.32
3478 4855 2.196925 ATCAAACGGCCCGTGCAAA 61.197 52.632 10.80 0.00 39.99 3.68
3479 4856 2.596046 ATCAAACGGCCCGTGCAA 60.596 55.556 10.80 0.00 39.99 4.08
3480 4857 3.361158 CATCAAACGGCCCGTGCA 61.361 61.111 10.80 0.00 39.99 4.57
3481 4858 2.322999 GATCATCAAACGGCCCGTGC 62.323 60.000 10.80 0.00 39.99 5.34
3482 4859 1.721487 GATCATCAAACGGCCCGTG 59.279 57.895 10.80 0.00 39.99 4.94
3483 4860 1.813753 CGATCATCAAACGGCCCGT 60.814 57.895 1.02 1.02 43.97 5.28
3498 4979 3.813596 GGCATCTTCAACGCCGAT 58.186 55.556 0.00 0.00 35.79 4.18
3598 5102 9.458374 ACTTTTACTTTTTGTTATGTTCATCCG 57.542 29.630 0.00 0.00 0.00 4.18
3606 5110 9.301153 AGTGCTCAACTTTTACTTTTTGTTATG 57.699 29.630 0.00 0.00 34.57 1.90
3624 5128 2.161855 CTTGGTTATGGCAGTGCTCAA 58.838 47.619 16.11 9.13 0.00 3.02
3658 5162 6.753744 GCACCAAGTGATAAATGAAAATCTCC 59.246 38.462 0.00 0.00 35.23 3.71
3663 5167 8.149647 AGATTTGCACCAAGTGATAAATGAAAA 58.850 29.630 12.21 0.00 34.54 2.29
3706 5609 8.848474 AGCTAGCTACATTAGTTTCTTGAAAA 57.152 30.769 17.69 0.00 0.00 2.29
3723 5626 4.333649 GCATTCAATGACACAAGCTAGCTA 59.666 41.667 19.70 0.40 0.00 3.32
3724 5627 3.128242 GCATTCAATGACACAAGCTAGCT 59.872 43.478 12.68 12.68 0.00 3.32
3725 5628 3.119743 TGCATTCAATGACACAAGCTAGC 60.120 43.478 6.62 6.62 0.00 3.42
3726 5629 4.083164 TGTGCATTCAATGACACAAGCTAG 60.083 41.667 19.19 0.00 41.11 3.42
3727 5630 3.819902 TGTGCATTCAATGACACAAGCTA 59.180 39.130 19.19 2.93 41.11 3.32
3779 5682 3.064545 GCTTGACACTGGTGCTCATATTC 59.935 47.826 0.17 0.00 0.00 1.75
3780 5683 3.012518 GCTTGACACTGGTGCTCATATT 58.987 45.455 0.17 0.00 0.00 1.28
3782 5685 1.339055 GGCTTGACACTGGTGCTCATA 60.339 52.381 0.17 0.00 0.00 2.15
3793 5696 3.067833 GTTCAGGTCTTAGGCTTGACAC 58.932 50.000 17.77 0.00 35.11 3.67
3801 5704 4.351874 TCACCAAAGTTCAGGTCTTAGG 57.648 45.455 0.00 0.00 35.52 2.69
3809 5712 1.956477 CCCCAGTTCACCAAAGTTCAG 59.044 52.381 0.00 0.00 0.00 3.02
3831 5734 3.576982 CGATAGTTAGGAGGGCAATGGTA 59.423 47.826 0.00 0.00 0.00 3.25
3834 5737 4.058817 GTTCGATAGTTAGGAGGGCAATG 58.941 47.826 0.00 0.00 37.40 2.82
3842 5745 5.416083 CAACATGTGGTTCGATAGTTAGGA 58.584 41.667 0.00 0.00 37.72 2.94
3869 5772 6.036517 GCTTCCAATTATATACTCAGCCATCG 59.963 42.308 0.00 0.00 0.00 3.84
3871 5774 6.883217 CAGCTTCCAATTATATACTCAGCCAT 59.117 38.462 0.00 0.00 0.00 4.40
3893 5796 4.755266 TGGTTAGGACTTATTCTCCAGC 57.245 45.455 0.00 0.00 0.00 4.85
3942 5845 8.514594 TGATCAATTTGTATGTTGAAAGAGTCC 58.485 33.333 0.00 0.00 37.82 3.85
4166 7519 9.281075 GGCCAAAATTTTACACTAAATACGTAG 57.719 33.333 2.44 0.00 0.00 3.51
4168 7521 7.659186 TGGCCAAAATTTTACACTAAATACGT 58.341 30.769 0.61 0.00 0.00 3.57
4169 7522 8.696410 ATGGCCAAAATTTTACACTAAATACG 57.304 30.769 10.96 0.00 0.00 3.06
4242 7595 7.377766 ACTCGTATTTGCACATAGTTTTCAT 57.622 32.000 0.00 0.00 0.00 2.57
4321 7674 8.977505 CCTTCGTATTTTGTGTCAAATTTTGAT 58.022 29.630 14.54 0.44 42.47 2.57
4362 7715 3.006217 ACAAAACAGTACTACCTCCGTCC 59.994 47.826 0.00 0.00 0.00 4.79
4457 7839 4.086457 AGTTTGATTCGGGGCAAAAGTAT 58.914 39.130 0.00 0.00 35.95 2.12
4654 8056 7.996385 ACCATGTAATAATCACACCTTTTAGC 58.004 34.615 0.00 0.00 0.00 3.09
4831 9162 8.121305 AGTGCACCAAGTGATAAATGAAATTA 57.879 30.769 14.63 0.00 32.61 1.40
5133 10156 0.174162 GCTTGGATGACAACATGGCC 59.826 55.000 0.00 0.00 36.82 5.36
5195 10218 3.216800 AGCTTGAAGATGTCAACAGCAA 58.783 40.909 0.00 0.00 40.99 3.91
5324 10347 2.617274 GGCAGGCCACGTGAAAGAC 61.617 63.158 19.30 1.81 35.81 3.01
5338 10361 0.818445 GTGGGCTGATCAGATGGCAG 60.818 60.000 27.04 0.00 0.00 4.85
5757 10780 2.787473 AAGAGATGGCGATGGACAAA 57.213 45.000 0.00 0.00 32.52 2.83
5936 10960 4.072131 GTGCAGGAAATCAGGAGTAACAA 58.928 43.478 0.00 0.00 0.00 2.83
5998 11022 1.596752 TGGCTACCAGTGCGTGTTG 60.597 57.895 0.00 0.00 0.00 3.33
6030 11054 1.032657 CCGATCCTGACGAGGTCTGT 61.033 60.000 0.00 0.00 40.76 3.41
6031 11055 0.748367 TCCGATCCTGACGAGGTCTG 60.748 60.000 0.00 0.00 40.76 3.51
6032 11056 0.183971 ATCCGATCCTGACGAGGTCT 59.816 55.000 0.00 0.00 40.76 3.85
6033 11057 0.594110 GATCCGATCCTGACGAGGTC 59.406 60.000 0.00 0.00 40.76 3.85
6034 11058 1.167155 CGATCCGATCCTGACGAGGT 61.167 60.000 2.69 0.00 40.76 3.85
6035 11059 1.576920 CGATCCGATCCTGACGAGG 59.423 63.158 2.69 0.00 41.39 4.63
6036 11060 1.081774 GCGATCCGATCCTGACGAG 60.082 63.158 2.69 0.00 0.00 4.18
6037 11061 1.822186 TGCGATCCGATCCTGACGA 60.822 57.895 2.69 0.00 0.00 4.20
6038 11062 1.658717 GTGCGATCCGATCCTGACG 60.659 63.158 2.69 0.00 0.00 4.35
6039 11063 1.658717 CGTGCGATCCGATCCTGAC 60.659 63.158 2.69 0.00 0.00 3.51
6040 11064 1.786049 CTCGTGCGATCCGATCCTGA 61.786 60.000 2.69 0.00 33.27 3.86
6200 11224 4.504916 CTCGGCAGCGTCTCCCTG 62.505 72.222 0.00 0.00 0.00 4.45
6236 11260 4.224370 AGCCCGGAGAAACTTATTCTAACA 59.776 41.667 0.73 0.00 0.00 2.41
6239 11263 3.387050 GGAGCCCGGAGAAACTTATTCTA 59.613 47.826 0.73 0.00 0.00 2.10
6240 11264 2.170817 GGAGCCCGGAGAAACTTATTCT 59.829 50.000 0.73 0.00 0.00 2.40
6269 11293 0.108585 AGACAAAAGCCTCGCCTGAA 59.891 50.000 0.00 0.00 0.00 3.02
6286 11310 1.464734 CACTGGCTCCTAGACGAAGA 58.535 55.000 0.00 0.00 0.00 2.87
6304 11328 2.391130 CCCGGGGATCCCAAATCCA 61.391 63.158 32.07 0.00 45.83 3.41
6308 11332 1.999002 GAGACCCGGGGATCCCAAA 60.999 63.158 32.07 0.00 45.83 3.28
6335 11360 4.912395 AGCCACCAAAGCCCGCAA 62.912 61.111 0.00 0.00 0.00 4.85
6449 11474 1.548269 AGAGGAAGGAGAAGAACAGCG 59.452 52.381 0.00 0.00 0.00 5.18
6470 11495 5.189342 CAGGATCTCCCATCAGTATTAGCAT 59.811 44.000 0.00 0.00 37.41 3.79
6475 11500 3.596101 AGCAGGATCTCCCATCAGTATT 58.404 45.455 0.00 0.00 37.41 1.89
6478 11503 1.890552 AAGCAGGATCTCCCATCAGT 58.109 50.000 0.00 0.00 37.41 3.41
6482 11507 0.106318 GGCAAAGCAGGATCTCCCAT 60.106 55.000 0.00 0.00 37.41 4.00
6532 11557 0.809385 GAACTCGACTCATCCGACCA 59.191 55.000 0.00 0.00 32.18 4.02
6543 11568 2.265647 CGGAAGGAAGAGAACTCGAC 57.734 55.000 0.00 0.00 34.09 4.20
6600 11625 1.968017 CACCTGCAACAGCCGTCAT 60.968 57.895 0.00 0.00 0.00 3.06
6670 11695 4.781959 CAATTGCCGCCACGCTGG 62.782 66.667 0.00 0.25 41.55 4.85
6698 11723 3.189287 GTCGCAAACAGGTCATCATCTTT 59.811 43.478 0.00 0.00 0.00 2.52
6739 11764 4.422073 TCTTGAGAGAAGACCTTTGCAA 57.578 40.909 0.00 0.00 0.00 4.08
6744 11769 4.224818 CCCTGAATCTTGAGAGAAGACCTT 59.775 45.833 0.00 0.00 35.07 3.50
6745 11770 3.774216 CCCTGAATCTTGAGAGAAGACCT 59.226 47.826 0.00 0.00 35.07 3.85


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

AutoCloner maintained by Alex Coulton.