Multiple sequence alignment - TraesCS5B01G526500

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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 TraesCS5B01G526500 chr5B 100.000 2858 0 0 1 2858 685658765 685655908 0.000000e+00 5278.0
1 TraesCS5B01G526500 chr5B 82.662 1142 163 23 738 1862 685692052 685690929 0.000000e+00 979.0
2 TraesCS5B01G526500 chr5B 87.805 656 56 13 2206 2858 335746797 335746163 0.000000e+00 747.0
3 TraesCS5B01G526500 chr5B 86.923 130 13 4 799 928 685607964 685608089 2.970000e-30 143.0
4 TraesCS5B01G526500 chr5D 92.628 2116 121 16 102 2205 543829727 543831819 0.000000e+00 3011.0
5 TraesCS5B01G526500 chr5D 82.109 1375 204 22 848 2205 543776468 543777817 0.000000e+00 1138.0
6 TraesCS5B01G526500 chr5D 82.753 1148 154 27 738 1862 543816925 543818051 0.000000e+00 983.0
7 TraesCS5B01G526500 chr5D 80.426 1221 201 26 657 1867 543771622 543772814 0.000000e+00 896.0
8 TraesCS5B01G526500 chr5D 82.058 797 114 14 657 1451 543803300 543804069 0.000000e+00 652.0
9 TraesCS5B01G526500 chr5D 81.291 604 101 9 1288 1882 544149690 544150290 1.990000e-131 479.0
10 TraesCS5B01G526500 chr5D 80.569 211 27 6 1901 2106 543818045 543818246 1.770000e-32 150.0
11 TraesCS5B01G526500 chr5D 74.648 284 50 17 831 1107 544491242 544491510 3.890000e-19 106.0
12 TraesCS5B01G526500 chr4A 92.740 1281 85 5 932 2206 625265272 625263994 0.000000e+00 1844.0
13 TraesCS5B01G526500 chr4A 82.344 1314 190 25 857 2151 625368238 625366948 0.000000e+00 1103.0
14 TraesCS5B01G526500 chr4A 82.897 1146 156 23 738 1862 625282392 625281266 0.000000e+00 994.0
15 TraesCS5B01G526500 chr4A 80.213 1218 202 26 657 1863 625373046 625371857 0.000000e+00 878.0
16 TraesCS5B01G526500 chr4A 89.818 550 35 13 384 930 625265761 625265230 0.000000e+00 686.0
17 TraesCS5B01G526500 chr4A 80.177 792 119 20 672 1451 625322566 625321801 2.490000e-155 558.0
18 TraesCS5B01G526500 chr4A 76.437 696 128 14 1288 1972 624351233 624351903 7.580000e-91 344.0
19 TraesCS5B01G526500 chr4A 95.146 103 2 3 1 103 598529764 598529665 2.950000e-35 159.0
20 TraesCS5B01G526500 chr4A 80.597 201 27 4 1914 2109 625281261 625281068 8.250000e-31 145.0
21 TraesCS5B01G526500 chr1D 88.855 655 51 8 2206 2857 457163112 457163747 0.000000e+00 785.0
22 TraesCS5B01G526500 chr4B 88.567 656 52 12 2206 2858 5024994 5025629 0.000000e+00 774.0
23 TraesCS5B01G526500 chr4B 100.000 88 0 0 1 88 472492540 472492627 2.280000e-36 163.0
24 TraesCS5B01G526500 chr4B 98.876 89 1 0 1 89 525501001 525501089 2.950000e-35 159.0
25 TraesCS5B01G526500 chr4B 96.875 96 1 2 1 96 647694735 647694642 2.950000e-35 159.0
26 TraesCS5B01G526500 chr4B 96.809 94 3 0 1 94 28685333 28685240 1.060000e-34 158.0
27 TraesCS5B01G526500 chr6D 88.012 659 60 13 2203 2858 48859629 48860271 0.000000e+00 761.0
28 TraesCS5B01G526500 chr6D 89.223 399 20 11 2462 2857 76060859 76061237 7.160000e-131 477.0
29 TraesCS5B01G526500 chr6D 97.778 90 2 0 1 90 269930090 269930179 3.810000e-34 156.0
30 TraesCS5B01G526500 chr2D 87.671 657 60 11 2205 2858 435275031 435274393 0.000000e+00 745.0
31 TraesCS5B01G526500 chr2D 88.571 385 40 4 2470 2852 8602506 8602888 5.580000e-127 464.0
32 TraesCS5B01G526500 chr3A 87.690 658 56 11 2205 2858 726548178 726547542 0.000000e+00 743.0
33 TraesCS5B01G526500 chr3A 83.964 661 91 14 2205 2858 341663261 341662609 1.120000e-173 619.0
34 TraesCS5B01G526500 chr3A 96.040 101 2 2 1 101 35634676 35634578 2.280000e-36 163.0
35 TraesCS5B01G526500 chr6B 87.237 666 63 9 2198 2858 76487265 76487913 0.000000e+00 739.0
36 TraesCS5B01G526500 chr6B 86.170 658 69 11 2205 2858 553419642 553419003 0.000000e+00 691.0
37 TraesCS5B01G526500 chr6B 100.000 90 0 0 1 90 63236327 63236238 1.760000e-37 167.0
38 TraesCS5B01G526500 chr6B 100.000 90 0 0 1 90 204560916 204561005 1.760000e-37 167.0
39 TraesCS5B01G526500 chr6B 100.000 90 0 0 1 90 505165636 505165547 1.760000e-37 167.0
40 TraesCS5B01G526500 chr6B 100.000 90 0 0 1 90 711658910 711658821 1.760000e-37 167.0
41 TraesCS5B01G526500 chr6B 94.495 109 3 3 1 109 273891594 273891699 6.330000e-37 165.0
42 TraesCS5B01G526500 chr6A 87.519 657 58 10 2206 2858 597838739 597839375 0.000000e+00 737.0
43 TraesCS5B01G526500 chr6A 100.000 88 0 0 1 88 604893234 604893147 2.280000e-36 163.0
44 TraesCS5B01G526500 chr6A 98.889 90 1 0 1 90 119756940 119757029 8.190000e-36 161.0
45 TraesCS5B01G526500 chr6A 98.889 90 0 1 1 89 558027906 558027817 2.950000e-35 159.0
46 TraesCS5B01G526500 chr6A 97.778 90 2 0 1 90 12430130 12430219 3.810000e-34 156.0
47 TraesCS5B01G526500 chr2A 87.405 659 57 11 2206 2858 660553208 660553846 0.000000e+00 734.0
48 TraesCS5B01G526500 chr1B 87.289 653 62 7 2206 2855 614281226 614281860 0.000000e+00 726.0
49 TraesCS5B01G526500 chr1B 86.910 657 62 12 2206 2858 73859712 73859076 0.000000e+00 715.0
50 TraesCS5B01G526500 chr1B 88.439 346 22 4 2515 2858 17826396 17826067 4.440000e-108 401.0
51 TraesCS5B01G526500 chr1B 100.000 91 0 0 1 91 277163314 277163224 4.900000e-38 169.0
52 TraesCS5B01G526500 chr1B 98.913 92 1 0 1 92 614567746 614567837 6.330000e-37 165.0
53 TraesCS5B01G526500 chr1B 98.913 92 0 1 1 91 171263504 171263595 2.280000e-36 163.0
54 TraesCS5B01G526500 chr1B 100.000 88 0 0 1 88 215010660 215010573 2.280000e-36 163.0
55 TraesCS5B01G526500 chr1B 96.000 100 2 2 1 99 84424723 84424625 8.190000e-36 161.0
56 TraesCS5B01G526500 chr7B 86.718 655 68 9 2206 2858 579445372 579446009 0.000000e+00 710.0
57 TraesCS5B01G526500 chr7B 97.917 96 2 0 1 96 28889657 28889562 1.760000e-37 167.0
58 TraesCS5B01G526500 chr7A 98.000 100 1 1 1 100 723785239 723785141 3.790000e-39 172.0
59 TraesCS5B01G526500 chr5A 100.000 91 0 0 1 91 662540371 662540461 4.900000e-38 169.0
60 TraesCS5B01G526500 chr5A 97.917 96 0 2 1 96 391972229 391972322 6.330000e-37 165.0
61 TraesCS5B01G526500 chrUn 97.917 96 1 1 1 96 87248774 87248868 6.330000e-37 165.0
62 TraesCS5B01G526500 chrUn 97.917 96 1 1 1 96 235064633 235064727 6.330000e-37 165.0
63 TraesCS5B01G526500 chrUn 96.703 91 3 0 1 91 47475021 47475111 4.930000e-33 152.0
64 TraesCS5B01G526500 chrUn 97.727 88 2 0 1 88 465884410 465884323 4.930000e-33 152.0
65 TraesCS5B01G526500 chrUn 96.629 89 3 0 1 89 211914878 211914966 6.380000e-32 148.0
66 TraesCS5B01G526500 chrUn 96.629 89 3 0 1 89 309511659 309511747 6.380000e-32 148.0
67 TraesCS5B01G526500 chrUn 96.629 89 3 0 1 89 321023965 321023877 6.380000e-32 148.0
68 TraesCS5B01G526500 chrUn 97.647 85 2 0 1 85 231816897 231816813 2.290000e-31 147.0
69 TraesCS5B01G526500 chrUn 96.591 88 3 0 1 88 431646892 431646805 2.290000e-31 147.0
70 TraesCS5B01G526500 chrUn 96.591 88 3 0 1 88 447950894 447950807 2.290000e-31 147.0
71 TraesCS5B01G526500 chrUn 86.408 103 9 4 831 928 271849065 271848963 1.080000e-19 108.0
72 TraesCS5B01G526500 chrUn 84.694 98 10 4 836 928 478701580 478701483 3.030000e-15 93.5
73 TraesCS5B01G526500 chr1A 98.889 90 1 0 1 90 343662122 343662033 8.190000e-36 161.0
74 TraesCS5B01G526500 chr1A 98.864 88 1 0 1 88 532275896 532275809 1.060000e-34 158.0
75 TraesCS5B01G526500 chr1A 97.727 88 2 0 1 88 291241694 291241781 4.930000e-33 152.0
76 TraesCS5B01G526500 chr1A 96.667 90 3 0 1 90 119732889 119732800 1.770000e-32 150.0
77 TraesCS5B01G526500 chr1A 74.825 286 50 15 831 1110 569486561 569486292 3.010000e-20 110.0
78 TraesCS5B01G526500 chr1A 74.825 286 50 15 831 1110 569499050 569498781 3.010000e-20 110.0
79 TraesCS5B01G526500 chr1A 74.825 286 50 15 831 1110 569509584 569509315 3.010000e-20 110.0
80 TraesCS5B01G526500 chr1A 74.825 286 50 15 831 1110 569521854 569521585 3.010000e-20 110.0


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 TraesCS5B01G526500 chr5B 685655908 685658765 2857 True 5278.0 5278 100.0000 1 2858 1 chr5B.!!$R2 2857
1 TraesCS5B01G526500 chr5B 685690929 685692052 1123 True 979.0 979 82.6620 738 1862 1 chr5B.!!$R3 1124
2 TraesCS5B01G526500 chr5B 335746163 335746797 634 True 747.0 747 87.8050 2206 2858 1 chr5B.!!$R1 652
3 TraesCS5B01G526500 chr5D 543829727 543831819 2092 False 3011.0 3011 92.6280 102 2205 1 chr5D.!!$F2 2103
4 TraesCS5B01G526500 chr5D 543771622 543777817 6195 False 1017.0 1138 81.2675 657 2205 2 chr5D.!!$F5 1548
5 TraesCS5B01G526500 chr5D 543803300 543804069 769 False 652.0 652 82.0580 657 1451 1 chr5D.!!$F1 794
6 TraesCS5B01G526500 chr5D 543816925 543818246 1321 False 566.5 983 81.6610 738 2106 2 chr5D.!!$F6 1368
7 TraesCS5B01G526500 chr5D 544149690 544150290 600 False 479.0 479 81.2910 1288 1882 1 chr5D.!!$F3 594
8 TraesCS5B01G526500 chr4A 625263994 625265761 1767 True 1265.0 1844 91.2790 384 2206 2 chr4A.!!$R3 1822
9 TraesCS5B01G526500 chr4A 625366948 625373046 6098 True 990.5 1103 81.2785 657 2151 2 chr4A.!!$R5 1494
10 TraesCS5B01G526500 chr4A 625281068 625282392 1324 True 569.5 994 81.7470 738 2109 2 chr4A.!!$R4 1371
11 TraesCS5B01G526500 chr4A 625321801 625322566 765 True 558.0 558 80.1770 672 1451 1 chr4A.!!$R2 779
12 TraesCS5B01G526500 chr4A 624351233 624351903 670 False 344.0 344 76.4370 1288 1972 1 chr4A.!!$F1 684
13 TraesCS5B01G526500 chr1D 457163112 457163747 635 False 785.0 785 88.8550 2206 2857 1 chr1D.!!$F1 651
14 TraesCS5B01G526500 chr4B 5024994 5025629 635 False 774.0 774 88.5670 2206 2858 1 chr4B.!!$F1 652
15 TraesCS5B01G526500 chr6D 48859629 48860271 642 False 761.0 761 88.0120 2203 2858 1 chr6D.!!$F1 655
16 TraesCS5B01G526500 chr2D 435274393 435275031 638 True 745.0 745 87.6710 2205 2858 1 chr2D.!!$R1 653
17 TraesCS5B01G526500 chr3A 726547542 726548178 636 True 743.0 743 87.6900 2205 2858 1 chr3A.!!$R3 653
18 TraesCS5B01G526500 chr3A 341662609 341663261 652 True 619.0 619 83.9640 2205 2858 1 chr3A.!!$R2 653
19 TraesCS5B01G526500 chr6B 76487265 76487913 648 False 739.0 739 87.2370 2198 2858 1 chr6B.!!$F1 660
20 TraesCS5B01G526500 chr6B 553419003 553419642 639 True 691.0 691 86.1700 2205 2858 1 chr6B.!!$R3 653
21 TraesCS5B01G526500 chr6A 597838739 597839375 636 False 737.0 737 87.5190 2206 2858 1 chr6A.!!$F3 652
22 TraesCS5B01G526500 chr2A 660553208 660553846 638 False 734.0 734 87.4050 2206 2858 1 chr2A.!!$F1 652
23 TraesCS5B01G526500 chr1B 614281226 614281860 634 False 726.0 726 87.2890 2206 2855 1 chr1B.!!$F2 649
24 TraesCS5B01G526500 chr1B 73859076 73859712 636 True 715.0 715 86.9100 2206 2858 1 chr1B.!!$R2 652
25 TraesCS5B01G526500 chr7B 579445372 579446009 637 False 710.0 710 86.7180 2206 2858 1 chr7B.!!$F1 652

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
291 295 0.038166 ACCATTCGGCATCAGTGGTT 59.962 50.0 0.0 0.0 40.08 3.67 F
417 423 0.100503 GCGCTTCGGCATTTTACCAT 59.899 50.0 0.0 0.0 41.88 3.55 F
1320 5962 0.393808 ACAACAAACTGGTCGGCACT 60.394 50.0 0.0 0.0 0.00 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1422 6067 0.179134 AACGACCAGCTATGACGAGC 60.179 55.0 12.65 0.0 43.19 5.03 R
1431 6076 0.830444 TACCCAGTGAACGACCAGCT 60.830 55.0 0.00 0.0 0.00 4.24 R
2587 11949 0.179108 ATTCTTCGCACGGCTACCTC 60.179 55.0 0.00 0.0 0.00 3.85 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
29 30 1.314730 AAAAAGGTCGCCAATGTCGT 58.685 45.000 0.00 0.00 0.00 4.34
30 31 2.172851 AAAAGGTCGCCAATGTCGTA 57.827 45.000 0.00 0.00 0.00 3.43
31 32 2.172851 AAAGGTCGCCAATGTCGTAA 57.827 45.000 0.00 0.00 0.00 3.18
32 33 2.396590 AAGGTCGCCAATGTCGTAAT 57.603 45.000 0.00 0.00 0.00 1.89
33 34 3.530265 AAGGTCGCCAATGTCGTAATA 57.470 42.857 0.00 0.00 0.00 0.98
34 35 3.746045 AGGTCGCCAATGTCGTAATAT 57.254 42.857 0.00 0.00 0.00 1.28
35 36 4.067972 AGGTCGCCAATGTCGTAATATT 57.932 40.909 0.00 0.00 0.00 1.28
36 37 3.807622 AGGTCGCCAATGTCGTAATATTG 59.192 43.478 0.00 0.00 34.68 1.90
37 38 3.805422 GGTCGCCAATGTCGTAATATTGA 59.195 43.478 0.00 0.00 36.41 2.57
38 39 4.271533 GGTCGCCAATGTCGTAATATTGAA 59.728 41.667 0.00 0.00 36.41 2.69
39 40 5.195379 GTCGCCAATGTCGTAATATTGAAC 58.805 41.667 0.00 0.00 36.41 3.18
40 41 5.006358 GTCGCCAATGTCGTAATATTGAACT 59.994 40.000 0.00 0.00 36.41 3.01
41 42 5.233476 TCGCCAATGTCGTAATATTGAACTC 59.767 40.000 0.00 0.00 36.41 3.01
42 43 5.234329 CGCCAATGTCGTAATATTGAACTCT 59.766 40.000 0.00 0.00 36.41 3.24
43 44 6.238103 CGCCAATGTCGTAATATTGAACTCTT 60.238 38.462 0.00 0.00 36.41 2.85
44 45 7.042992 CGCCAATGTCGTAATATTGAACTCTTA 60.043 37.037 0.00 0.00 36.41 2.10
45 46 8.609176 GCCAATGTCGTAATATTGAACTCTTAA 58.391 33.333 0.00 0.00 36.41 1.85
59 60 5.977489 AACTCTTAAAGTTAATGTGGCCC 57.023 39.130 0.00 0.00 46.55 5.80
60 61 4.341487 ACTCTTAAAGTTAATGTGGCCCC 58.659 43.478 0.00 0.00 33.03 5.80
61 62 3.349022 TCTTAAAGTTAATGTGGCCCCG 58.651 45.455 0.00 0.00 0.00 5.73
62 63 2.883122 TAAAGTTAATGTGGCCCCGT 57.117 45.000 0.00 0.00 0.00 5.28
63 64 2.003937 AAAGTTAATGTGGCCCCGTT 57.996 45.000 0.00 0.00 0.00 4.44
64 65 1.253100 AAGTTAATGTGGCCCCGTTG 58.747 50.000 0.00 0.00 0.00 4.10
65 66 1.214325 GTTAATGTGGCCCCGTTGC 59.786 57.895 0.00 0.00 0.00 4.17
66 67 1.228583 TTAATGTGGCCCCGTTGCA 60.229 52.632 0.00 0.00 0.00 4.08
67 68 0.827925 TTAATGTGGCCCCGTTGCAA 60.828 50.000 0.00 0.00 0.00 4.08
68 69 1.528292 TAATGTGGCCCCGTTGCAAC 61.528 55.000 19.89 19.89 35.65 4.17
86 87 3.782042 GCACGGGCGTTCTTCTAG 58.218 61.111 0.00 0.00 0.00 2.43
87 88 1.080025 GCACGGGCGTTCTTCTAGT 60.080 57.895 0.00 0.00 0.00 2.57
88 89 0.171903 GCACGGGCGTTCTTCTAGTA 59.828 55.000 0.00 0.00 0.00 1.82
89 90 1.202382 GCACGGGCGTTCTTCTAGTAT 60.202 52.381 0.00 0.00 0.00 2.12
90 91 2.460918 CACGGGCGTTCTTCTAGTATG 58.539 52.381 0.00 0.00 0.00 2.39
91 92 2.097825 ACGGGCGTTCTTCTAGTATGT 58.902 47.619 0.00 0.00 0.00 2.29
92 93 2.098770 ACGGGCGTTCTTCTAGTATGTC 59.901 50.000 0.00 0.00 0.00 3.06
93 94 2.358267 CGGGCGTTCTTCTAGTATGTCT 59.642 50.000 0.00 0.00 0.00 3.41
94 95 3.181489 CGGGCGTTCTTCTAGTATGTCTT 60.181 47.826 0.00 0.00 0.00 3.01
95 96 4.036027 CGGGCGTTCTTCTAGTATGTCTTA 59.964 45.833 0.00 0.00 0.00 2.10
96 97 5.280164 GGGCGTTCTTCTAGTATGTCTTAC 58.720 45.833 0.00 0.00 0.00 2.34
97 98 5.163581 GGGCGTTCTTCTAGTATGTCTTACA 60.164 44.000 0.00 0.00 32.87 2.41
98 99 6.461231 GGGCGTTCTTCTAGTATGTCTTACAT 60.461 42.308 0.00 0.00 42.35 2.29
99 100 6.979238 GGCGTTCTTCTAGTATGTCTTACATT 59.021 38.462 0.00 0.00 39.88 2.71
100 101 7.043325 GGCGTTCTTCTAGTATGTCTTACATTG 60.043 40.741 0.00 0.00 39.88 2.82
115 116 9.772973 TGTCTTACATTGTAGACAATAAACTGT 57.227 29.630 18.52 5.84 45.60 3.55
122 123 8.598924 CATTGTAGACAATAAACTGTAGCAGAG 58.401 37.037 7.55 0.00 44.10 3.35
134 135 5.078411 CTGTAGCAGAGTACAGTCCATTT 57.922 43.478 0.00 0.00 43.39 2.32
147 148 7.928706 AGTACAGTCCATTTCTATGATTAGCAC 59.071 37.037 0.00 0.00 33.37 4.40
167 168 3.318839 CACTGTGCTTCCTCCATTTCAAA 59.681 43.478 0.00 0.00 0.00 2.69
216 217 7.656707 AAATTATGTTGCAATGAACAACTCC 57.343 32.000 0.59 0.00 46.03 3.85
219 220 3.286353 TGTTGCAATGAACAACTCCTCA 58.714 40.909 0.59 0.00 46.03 3.86
227 228 6.684686 CAATGAACAACTCCTCAATGACATT 58.315 36.000 0.00 0.00 0.00 2.71
245 249 9.528489 AATGACATTTACCTTATGTTTGGTAGT 57.472 29.630 0.00 0.00 39.61 2.73
252 256 4.081807 ACCTTATGTTTGGTAGTCTCGGTC 60.082 45.833 0.00 0.00 34.36 4.79
253 257 4.081862 CCTTATGTTTGGTAGTCTCGGTCA 60.082 45.833 0.00 0.00 0.00 4.02
255 259 4.553330 ATGTTTGGTAGTCTCGGTCAAT 57.447 40.909 0.00 0.00 0.00 2.57
256 260 4.345859 TGTTTGGTAGTCTCGGTCAATT 57.654 40.909 0.00 0.00 0.00 2.32
257 261 5.471556 TGTTTGGTAGTCTCGGTCAATTA 57.528 39.130 0.00 0.00 0.00 1.40
258 262 6.045072 TGTTTGGTAGTCTCGGTCAATTAT 57.955 37.500 0.00 0.00 0.00 1.28
261 265 5.018539 TGGTAGTCTCGGTCAATTATTGG 57.981 43.478 5.02 0.00 0.00 3.16
264 268 5.981915 GGTAGTCTCGGTCAATTATTGGTAC 59.018 44.000 5.02 0.00 0.00 3.34
284 288 2.228822 ACAAAACAGACCATTCGGCATC 59.771 45.455 0.00 0.00 34.57 3.91
286 290 1.742761 AACAGACCATTCGGCATCAG 58.257 50.000 0.00 0.00 34.57 2.90
291 295 0.038166 ACCATTCGGCATCAGTGGTT 59.962 50.000 0.00 0.00 40.08 3.67
314 319 7.753580 GGTTAGCTATACCAAAACAATGAACAC 59.246 37.037 15.90 0.00 35.67 3.32
315 320 8.512138 GTTAGCTATACCAAAACAATGAACACT 58.488 33.333 0.00 0.00 0.00 3.55
378 383 2.436542 ACGCCTAGCCAAATACCACATA 59.563 45.455 0.00 0.00 0.00 2.29
381 386 4.083324 CGCCTAGCCAAATACCACATATTG 60.083 45.833 0.00 0.00 33.53 1.90
417 423 0.100503 GCGCTTCGGCATTTTACCAT 59.899 50.000 0.00 0.00 41.88 3.55
422 428 5.753744 CGCTTCGGCATTTTACCATAATTA 58.246 37.500 0.00 0.00 41.88 1.40
424 430 6.305399 CGCTTCGGCATTTTACCATAATTATG 59.695 38.462 17.11 17.11 41.88 1.90
530 536 6.211384 CCATACCATGTCATCCACACTATCTA 59.789 42.308 0.00 0.00 38.04 1.98
531 537 7.093156 CCATACCATGTCATCCACACTATCTAT 60.093 40.741 0.00 0.00 38.04 1.98
532 538 8.971073 CATACCATGTCATCCACACTATCTATA 58.029 37.037 0.00 0.00 38.04 1.31
533 539 9.720874 ATACCATGTCATCCACACTATCTATAT 57.279 33.333 0.00 0.00 38.04 0.86
574 580 7.654116 TCTTTTGACGTCCGCATAATAATATCA 59.346 33.333 14.12 0.00 0.00 2.15
655 663 2.632377 CGCATGGGATCACTGTAACTT 58.368 47.619 3.11 0.00 0.00 2.66
692 700 7.225538 CGACAAAGCAATAATGGACTAGAAGAT 59.774 37.037 0.00 0.00 0.00 2.40
710 718 7.913674 AGAAGATGTTTGAATTGAGTAGGAC 57.086 36.000 0.00 0.00 0.00 3.85
761 771 2.220824 CGCATTTCAGTCGACACAAGAA 59.779 45.455 19.50 12.75 0.00 2.52
855 875 3.181482 TGCAACACATGGTTACAAACAGG 60.181 43.478 0.00 0.00 37.72 4.00
871 891 7.849804 ACAAACAGGCACACTATAAGATAAG 57.150 36.000 0.00 0.00 0.00 1.73
1021 1043 3.126879 CGAAATGCGGGCTGCTGA 61.127 61.111 20.66 0.00 46.63 4.26
1320 5962 0.393808 ACAACAAACTGGTCGGCACT 60.394 50.000 0.00 0.00 0.00 4.40
1389 6031 5.104527 TCTCTCGGATAATTCATTGGTTGGT 60.105 40.000 0.00 0.00 0.00 3.67
1422 6067 3.054802 AGAGTTTGATACAGCTCAAGGGG 60.055 47.826 0.00 0.00 36.55 4.79
1431 6076 0.687757 AGCTCAAGGGGCTCGTCATA 60.688 55.000 0.00 0.00 34.70 2.15
1451 10763 0.669625 GCTGGTCGTTCACTGGGTAC 60.670 60.000 0.00 0.00 0.00 3.34
1464 10776 4.223477 TCACTGGGTACGGCTTTTACTAAT 59.777 41.667 0.00 0.00 0.00 1.73
1479 10791 9.612620 GCTTTTACTAATATGCCATTGTATGTC 57.387 33.333 0.00 0.00 0.00 3.06
1515 10839 3.963383 ACACTCGATGAACAACCAAAC 57.037 42.857 0.00 0.00 0.00 2.93
1725 11049 3.882888 ACAATAACAATGCTGTATCCGGG 59.117 43.478 0.00 0.00 33.45 5.73
1865 11197 8.258007 AGTCGTAGGAGATGAATGATTTGTAAA 58.742 33.333 0.00 0.00 0.00 2.01
1906 11242 1.003355 ACGGAGCTCATGTGGTTGG 60.003 57.895 17.19 0.00 0.00 3.77
1932 11268 6.127814 CCAAGTTCAATGTAGCTCACAATCAT 60.128 38.462 0.00 0.00 41.55 2.45
1963 11300 4.634443 GGCCAATCGTGTTATGTAACTTCT 59.366 41.667 0.00 0.00 37.12 2.85
2041 11383 6.519382 TCTTACATGCTGACCTGAATATCAG 58.481 40.000 0.00 0.32 43.91 2.90
2047 11390 1.048601 GACCTGAATATCAGCGGGGA 58.951 55.000 1.79 0.00 42.98 4.81
2174 11517 5.951148 TGATGTTTTCTTATGCTGATTGGGA 59.049 36.000 0.00 0.00 0.00 4.37
2262 11610 3.660501 TGTATTGCTTGAGTCTCGTGT 57.339 42.857 0.00 0.00 0.00 4.49
2385 11737 1.214589 CCGAGGTCACAACGGTAGG 59.785 63.158 4.07 0.00 41.47 3.18
2448 11805 2.430367 GACACCCCCACACAGTCC 59.570 66.667 0.00 0.00 0.00 3.85
2584 11946 3.066190 TGGTCGAGGTAGCCGTGG 61.066 66.667 0.00 0.00 0.00 4.94
2585 11947 3.066814 GGTCGAGGTAGCCGTGGT 61.067 66.667 0.00 0.00 0.00 4.16
2586 11948 2.488820 GTCGAGGTAGCCGTGGTC 59.511 66.667 0.00 0.00 0.00 4.02
2587 11949 3.129502 TCGAGGTAGCCGTGGTCG 61.130 66.667 3.38 0.00 0.00 4.79
2588 11950 3.129502 CGAGGTAGCCGTGGTCGA 61.130 66.667 0.00 0.00 39.71 4.20
2589 11951 2.799371 GAGGTAGCCGTGGTCGAG 59.201 66.667 0.00 0.00 39.71 4.04
2590 11952 2.754658 AGGTAGCCGTGGTCGAGG 60.755 66.667 0.00 0.00 39.71 4.63
2591 11953 3.066814 GGTAGCCGTGGTCGAGGT 61.067 66.667 0.00 0.00 39.71 3.85
2592 11954 1.750399 GGTAGCCGTGGTCGAGGTA 60.750 63.158 0.00 0.00 39.71 3.08
2593 11955 1.722636 GGTAGCCGTGGTCGAGGTAG 61.723 65.000 0.00 0.00 39.71 3.18
2594 11956 2.117156 TAGCCGTGGTCGAGGTAGC 61.117 63.158 0.00 0.00 39.71 3.58
2595 11957 4.509737 GCCGTGGTCGAGGTAGCC 62.510 72.222 0.00 0.00 39.71 3.93
2596 11958 4.189188 CCGTGGTCGAGGTAGCCG 62.189 72.222 0.00 0.00 39.71 5.52
2597 11959 3.437795 CGTGGTCGAGGTAGCCGT 61.438 66.667 0.00 0.00 39.71 5.68
2598 11960 2.181021 GTGGTCGAGGTAGCCGTG 59.819 66.667 0.00 0.00 0.00 4.94
2662 12041 0.982852 AGGAAGTCGCCATGGATCCA 60.983 55.000 18.88 18.88 0.00 3.41
2814 12194 4.189580 ACCGGTGTTGCCAGCACT 62.190 61.111 6.12 0.00 39.05 4.40
2815 12195 2.031919 CCGGTGTTGCCAGCACTA 59.968 61.111 11.55 0.00 39.05 2.74
2838 12218 2.451132 CATGCGTAGACGAACGAAGAT 58.549 47.619 6.19 0.73 45.68 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 1.314730 ACGACATTGGCGACCTTTTT 58.685 45.000 20.74 0.00 0.00 1.94
11 12 2.172851 TACGACATTGGCGACCTTTT 57.827 45.000 20.74 0.00 0.00 2.27
12 13 2.172851 TTACGACATTGGCGACCTTT 57.827 45.000 20.74 0.00 0.00 3.11
13 14 2.396590 ATTACGACATTGGCGACCTT 57.603 45.000 20.74 0.00 0.00 3.50
14 15 3.746045 ATATTACGACATTGGCGACCT 57.254 42.857 20.74 4.55 0.00 3.85
15 16 3.805422 TCAATATTACGACATTGGCGACC 59.195 43.478 20.74 0.00 33.77 4.79
16 17 5.006358 AGTTCAATATTACGACATTGGCGAC 59.994 40.000 20.74 2.50 33.77 5.19
17 18 5.113383 AGTTCAATATTACGACATTGGCGA 58.887 37.500 20.74 0.00 33.77 5.54
18 19 5.234329 AGAGTTCAATATTACGACATTGGCG 59.766 40.000 11.09 11.09 33.77 5.69
19 20 6.604735 AGAGTTCAATATTACGACATTGGC 57.395 37.500 0.00 0.00 33.77 4.52
32 33 8.736244 GGCCACATTAACTTTAAGAGTTCAATA 58.264 33.333 0.00 0.00 45.40 1.90
33 34 7.309805 GGGCCACATTAACTTTAAGAGTTCAAT 60.310 37.037 4.39 4.32 45.40 2.57
34 35 6.015772 GGGCCACATTAACTTTAAGAGTTCAA 60.016 38.462 4.39 2.81 45.40 2.69
35 36 5.475564 GGGCCACATTAACTTTAAGAGTTCA 59.524 40.000 4.39 0.00 45.40 3.18
36 37 5.105877 GGGGCCACATTAACTTTAAGAGTTC 60.106 44.000 4.39 0.00 45.40 3.01
38 39 4.341487 GGGGCCACATTAACTTTAAGAGT 58.659 43.478 4.39 0.00 41.47 3.24
39 40 3.377172 CGGGGCCACATTAACTTTAAGAG 59.623 47.826 5.46 0.00 0.00 2.85
40 41 3.244981 ACGGGGCCACATTAACTTTAAGA 60.245 43.478 5.46 0.00 0.00 2.10
41 42 3.086282 ACGGGGCCACATTAACTTTAAG 58.914 45.455 5.46 0.00 0.00 1.85
42 43 3.157750 ACGGGGCCACATTAACTTTAA 57.842 42.857 5.46 0.00 0.00 1.52
43 44 2.820787 CAACGGGGCCACATTAACTTTA 59.179 45.455 5.46 0.00 0.00 1.85
44 45 1.616374 CAACGGGGCCACATTAACTTT 59.384 47.619 5.46 0.00 0.00 2.66
45 46 1.253100 CAACGGGGCCACATTAACTT 58.747 50.000 5.46 0.00 0.00 2.66
46 47 1.248101 GCAACGGGGCCACATTAACT 61.248 55.000 5.46 0.00 0.00 2.24
47 48 1.214325 GCAACGGGGCCACATTAAC 59.786 57.895 5.46 0.00 0.00 2.01
48 49 0.827925 TTGCAACGGGGCCACATTAA 60.828 50.000 5.46 0.00 0.00 1.40
49 50 1.228583 TTGCAACGGGGCCACATTA 60.229 52.632 5.46 0.00 0.00 1.90
50 51 2.522923 TTGCAACGGGGCCACATT 60.523 55.556 5.46 0.00 0.00 2.71
51 52 3.302344 GTTGCAACGGGGCCACAT 61.302 61.111 14.90 0.00 30.39 3.21
69 70 0.171903 TACTAGAAGAACGCCCGTGC 59.828 55.000 0.00 0.00 0.00 5.34
70 71 2.159282 ACATACTAGAAGAACGCCCGTG 60.159 50.000 0.00 0.00 0.00 4.94
71 72 2.097825 ACATACTAGAAGAACGCCCGT 58.902 47.619 0.00 0.00 0.00 5.28
72 73 2.358267 AGACATACTAGAAGAACGCCCG 59.642 50.000 0.00 0.00 0.00 6.13
73 74 4.388378 AAGACATACTAGAAGAACGCCC 57.612 45.455 0.00 0.00 0.00 6.13
74 75 5.888105 TGTAAGACATACTAGAAGAACGCC 58.112 41.667 0.00 0.00 35.42 5.68
75 76 7.488471 ACAATGTAAGACATACTAGAAGAACGC 59.512 37.037 0.00 0.00 37.97 4.84
76 77 8.912787 ACAATGTAAGACATACTAGAAGAACG 57.087 34.615 0.00 0.00 37.97 3.95
93 94 9.713713 TGCTACAGTTTATTGTCTACAATGTAA 57.286 29.630 16.68 9.07 45.34 2.41
94 95 9.366216 CTGCTACAGTTTATTGTCTACAATGTA 57.634 33.333 16.68 10.90 45.34 2.29
95 96 8.094548 TCTGCTACAGTTTATTGTCTACAATGT 58.905 33.333 16.68 10.40 38.55 2.71
96 97 8.479313 TCTGCTACAGTTTATTGTCTACAATG 57.521 34.615 16.68 5.44 38.55 2.82
97 98 8.314751 ACTCTGCTACAGTTTATTGTCTACAAT 58.685 33.333 12.61 12.61 39.88 2.71
98 99 7.667557 ACTCTGCTACAGTTTATTGTCTACAA 58.332 34.615 0.00 0.00 35.10 2.41
99 100 7.228314 ACTCTGCTACAGTTTATTGTCTACA 57.772 36.000 0.00 0.00 32.61 2.74
100 101 8.242053 TGTACTCTGCTACAGTTTATTGTCTAC 58.758 37.037 0.00 0.00 32.61 2.59
103 104 7.513190 CTGTACTCTGCTACAGTTTATTGTC 57.487 40.000 3.32 0.00 39.16 3.18
115 116 6.833933 TCATAGAAATGGACTGTACTCTGCTA 59.166 38.462 0.00 0.00 33.61 3.49
122 123 7.928706 AGTGCTAATCATAGAAATGGACTGTAC 59.071 37.037 0.00 0.00 33.61 2.90
129 130 5.755813 GCACAGTGCTAATCATAGAAATGG 58.244 41.667 18.92 0.00 37.13 3.16
147 148 4.589216 TTTTGAAATGGAGGAAGCACAG 57.411 40.909 0.00 0.00 0.00 3.66
192 193 7.444299 AGGAGTTGTTCATTGCAACATAATTT 58.556 30.769 0.00 0.00 46.09 1.82
196 197 5.069318 TGAGGAGTTGTTCATTGCAACATA 58.931 37.500 0.00 0.00 46.09 2.29
208 209 6.306987 AGGTAAATGTCATTGAGGAGTTGTT 58.693 36.000 0.00 0.00 0.00 2.83
213 214 8.511604 AACATAAGGTAAATGTCATTGAGGAG 57.488 34.615 0.00 0.00 36.56 3.69
216 217 8.522830 ACCAAACATAAGGTAAATGTCATTGAG 58.477 33.333 0.00 0.00 36.56 3.02
219 220 9.528489 ACTACCAAACATAAGGTAAATGTCATT 57.472 29.630 0.00 0.00 39.72 2.57
227 228 5.481473 ACCGAGACTACCAAACATAAGGTAA 59.519 40.000 0.00 0.00 39.72 2.85
245 249 6.711194 TGTTTTGTACCAATAATTGACCGAGA 59.289 34.615 0.00 0.00 0.00 4.04
252 256 9.139174 GAATGGTCTGTTTTGTACCAATAATTG 57.861 33.333 0.00 0.00 45.91 2.32
253 257 8.026607 CGAATGGTCTGTTTTGTACCAATAATT 58.973 33.333 0.00 0.00 45.91 1.40
255 259 6.072397 CCGAATGGTCTGTTTTGTACCAATAA 60.072 38.462 0.00 0.00 45.91 1.40
256 260 5.413213 CCGAATGGTCTGTTTTGTACCAATA 59.587 40.000 0.00 0.00 45.91 1.90
257 261 4.217550 CCGAATGGTCTGTTTTGTACCAAT 59.782 41.667 0.00 0.00 45.91 3.16
258 262 3.566322 CCGAATGGTCTGTTTTGTACCAA 59.434 43.478 0.00 0.00 45.91 3.67
261 265 2.550606 TGCCGAATGGTCTGTTTTGTAC 59.449 45.455 0.00 0.00 37.67 2.90
264 268 2.228582 TGATGCCGAATGGTCTGTTTTG 59.771 45.455 0.00 0.00 37.67 2.44
277 281 1.480789 TAGCTAACCACTGATGCCGA 58.519 50.000 0.00 0.00 0.00 5.54
284 288 6.811253 TTGTTTTGGTATAGCTAACCACTG 57.189 37.500 20.58 0.00 46.56 3.66
286 290 7.385778 TCATTGTTTTGGTATAGCTAACCAC 57.614 36.000 20.58 13.37 46.56 4.16
291 295 9.899661 ATAGTGTTCATTGTTTTGGTATAGCTA 57.100 29.630 0.00 0.00 0.00 3.32
359 364 4.321230 GCAATATGTGGTATTTGGCTAGGC 60.321 45.833 9.85 9.85 30.53 3.93
378 383 4.559300 GCGCCATCATTAATACCAAGCAAT 60.559 41.667 0.00 0.00 0.00 3.56
381 386 2.554032 AGCGCCATCATTAATACCAAGC 59.446 45.455 2.29 0.00 0.00 4.01
424 430 9.757227 AGCCGAATAATTCTATCTGATTATAGC 57.243 33.333 0.00 0.00 30.79 2.97
531 537 8.670135 CGTCAAAAGAAACAACACCCATATATA 58.330 33.333 0.00 0.00 0.00 0.86
532 538 7.175990 ACGTCAAAAGAAACAACACCCATATAT 59.824 33.333 0.00 0.00 0.00 0.86
533 539 6.487331 ACGTCAAAAGAAACAACACCCATATA 59.513 34.615 0.00 0.00 0.00 0.86
655 663 2.518112 TTTGTCGCCAGCTGCCAA 60.518 55.556 8.66 5.27 36.24 4.52
692 700 6.459573 GCAACTTGTCCTACTCAATTCAAACA 60.460 38.462 0.00 0.00 0.00 2.83
710 718 1.602311 AGACTCAAGCTGGCAACTTG 58.398 50.000 21.62 21.62 44.76 3.16
761 771 5.106515 CCCAATTCAAACGTGGTTTTTGTTT 60.107 36.000 0.00 0.00 33.10 2.83
855 875 5.991606 TGGTGCATCTTATCTTATAGTGTGC 59.008 40.000 0.00 0.00 0.00 4.57
871 891 1.181098 AACTGCTTGGGTGGTGCATC 61.181 55.000 0.00 0.00 36.07 3.91
951 973 2.254546 TTGAGGTGCAAGTGATTCGT 57.745 45.000 0.00 0.00 31.55 3.85
1021 1043 2.579860 AGAGGAATGCCAAGAACAGGAT 59.420 45.455 0.00 0.00 36.29 3.24
1320 5962 2.368548 CTCACCAATCCACGATGGGATA 59.631 50.000 1.92 0.00 46.96 2.59
1399 6041 4.187694 CCCTTGAGCTGTATCAAACTCTC 58.812 47.826 0.00 0.00 38.66 3.20
1422 6067 0.179134 AACGACCAGCTATGACGAGC 60.179 55.000 12.65 0.00 43.19 5.03
1431 6076 0.830444 TACCCAGTGAACGACCAGCT 60.830 55.000 0.00 0.00 0.00 4.24
1451 10763 6.072112 ACAATGGCATATTAGTAAAAGCCG 57.928 37.500 0.00 7.05 44.83 5.52
1479 10791 3.060003 CGAGTGTTCTTCTGTTGCTCTTG 60.060 47.826 0.00 0.00 0.00 3.02
1515 10839 3.317711 TGTTGTTGCTCCCAGTTATTGTG 59.682 43.478 0.00 0.00 0.00 3.33
1725 11049 4.624015 TCCCGGATACATTATTGTCGTTC 58.376 43.478 0.73 0.00 37.28 3.95
1865 11197 9.184403 CCGTCAAGGAAGATGGAAACAATTCAT 62.184 40.741 0.00 0.00 45.67 2.57
1906 11242 2.813754 TGTGAGCTACATTGAACTTGGC 59.186 45.455 0.00 0.00 33.42 4.52
1916 11252 4.400251 CCACCAAATGATTGTGAGCTACAT 59.600 41.667 0.00 0.00 39.48 2.29
2011 11349 7.792374 TTCAGGTCAGCATGTAAGATATTTC 57.208 36.000 0.00 0.00 37.40 2.17
2041 11383 3.984193 ATCAGCTGCAAGTCCCCGC 62.984 63.158 9.47 0.00 35.30 6.13
2047 11390 0.952497 CGTCCACATCAGCTGCAAGT 60.952 55.000 9.47 4.16 35.30 3.16
2370 11722 1.530013 CGTCCCTACCGTTGTGACCT 61.530 60.000 0.00 0.00 0.00 3.85
2371 11723 1.080298 CGTCCCTACCGTTGTGACC 60.080 63.158 0.00 0.00 0.00 4.02
2385 11737 2.126424 GTCTCACCGTCTGCGTCC 60.126 66.667 0.00 0.00 36.15 4.79
2440 11796 1.201647 CGTCGACCATTAGGACTGTGT 59.798 52.381 10.58 0.00 38.69 3.72
2584 11946 3.332493 TTCGCACGGCTACCTCGAC 62.332 63.158 0.00 0.00 0.00 4.20
2585 11947 3.047718 CTTCGCACGGCTACCTCGA 62.048 63.158 0.00 0.00 0.00 4.04
2586 11948 2.537792 TTCTTCGCACGGCTACCTCG 62.538 60.000 0.00 0.00 0.00 4.63
2587 11949 0.179108 ATTCTTCGCACGGCTACCTC 60.179 55.000 0.00 0.00 0.00 3.85
2588 11950 0.460284 CATTCTTCGCACGGCTACCT 60.460 55.000 0.00 0.00 0.00 3.08
2589 11951 2.006772 CATTCTTCGCACGGCTACC 58.993 57.895 0.00 0.00 0.00 3.18
2590 11952 1.348594 GCATTCTTCGCACGGCTAC 59.651 57.895 0.00 0.00 0.00 3.58
2591 11953 2.164663 CGCATTCTTCGCACGGCTA 61.165 57.895 0.00 0.00 0.00 3.93
2592 11954 3.490759 CGCATTCTTCGCACGGCT 61.491 61.111 0.00 0.00 0.00 5.52
2593 11955 4.520846 CCGCATTCTTCGCACGGC 62.521 66.667 0.00 0.00 37.05 5.68
2595 11957 2.096406 CACCGCATTCTTCGCACG 59.904 61.111 0.00 0.00 0.00 5.34
2596 11958 2.240612 GACCACCGCATTCTTCGCAC 62.241 60.000 0.00 0.00 0.00 5.34
2597 11959 2.031919 ACCACCGCATTCTTCGCA 59.968 55.556 0.00 0.00 0.00 5.10
2598 11960 2.785258 GACCACCGCATTCTTCGC 59.215 61.111 0.00 0.00 0.00 4.70
2654 12033 4.108299 TTGCGCCCGTGGATCCAT 62.108 61.111 19.62 0.00 0.00 3.41
2682 12061 2.438434 ACTGCGCCCATGCTAACC 60.438 61.111 4.18 0.00 35.36 2.85
2727 12107 0.798776 GCCTCGTCAACACCATCTTG 59.201 55.000 0.00 0.00 0.00 3.02
2814 12194 0.248336 CGTTCGTCTACGCATGCCTA 60.248 55.000 13.15 3.99 39.60 3.93
2815 12195 1.516386 CGTTCGTCTACGCATGCCT 60.516 57.895 13.15 2.75 39.60 4.75
2838 12218 2.307309 CGGCGCTTCGTCAACTTCA 61.307 57.895 7.64 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.