Multiple sequence alignment - TraesCS4D01G310500

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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 TraesCS4D01G310500 chr4D 100.000 2480 0 0 1 2480 477557985 477560464 0.000000e+00 4580.0
1 TraesCS4D01G310500 chr4D 92.857 840 45 9 712 1549 477543847 477543021 0.000000e+00 1205.0
2 TraesCS4D01G310500 chr4D 84.135 208 17 10 1861 2067 500404954 500405146 1.170000e-43 187.0
3 TraesCS4D01G310500 chr4D 100.000 31 0 0 1550 1580 477543000 477542970 9.580000e-05 58.4
4 TraesCS4D01G310500 chr4A 90.060 1660 124 18 709 2347 684470862 684472501 0.000000e+00 2113.0
5 TraesCS4D01G310500 chr4A 93.113 697 33 7 904 1589 684449413 684448721 0.000000e+00 1007.0
6 TraesCS4D01G310500 chr4A 83.741 695 66 17 230 911 684450283 684449623 4.530000e-172 614.0
7 TraesCS4D01G310500 chr4A 80.137 292 46 11 2132 2421 567647782 567648063 8.990000e-50 207.0
8 TraesCS4D01G310500 chr4B 93.101 1348 75 9 255 1589 603147670 603149012 0.000000e+00 1958.0
9 TraesCS4D01G310500 chr4B 92.823 1254 60 15 310 1549 603037308 603038545 0.000000e+00 1790.0
10 TraesCS4D01G310500 chr4B 88.054 1331 102 24 232 1549 602894351 602893065 0.000000e+00 1524.0
11 TraesCS4D01G310500 chr4B 91.211 933 62 10 623 1549 602874061 602873143 0.000000e+00 1251.0
12 TraesCS4D01G310500 chr4B 85.492 834 96 13 1595 2424 603162629 603163441 0.000000e+00 846.0
13 TraesCS4D01G310500 chr4B 91.396 616 45 6 913 1525 603026249 603025639 0.000000e+00 837.0
14 TraesCS4D01G310500 chr4B 88.745 231 25 1 1 231 358899189 358898960 5.220000e-72 281.0
15 TraesCS4D01G310500 chr4B 87.981 208 16 4 709 915 603028906 603028707 1.150000e-58 237.0
16 TraesCS4D01G310500 chr4B 81.786 280 40 7 317 588 602874338 602874062 8.930000e-55 224.0
17 TraesCS4D01G310500 chr4B 94.805 77 4 0 1513 1589 603144486 603144410 1.200000e-23 121.0
18 TraesCS4D01G310500 chr4B 96.667 60 2 0 1522 1581 603160576 603160635 1.570000e-17 100.0
19 TraesCS4D01G310500 chr4B 96.491 57 2 0 1533 1589 603024394 603024338 7.300000e-16 95.3
20 TraesCS4D01G310500 chr4B 100.000 29 0 0 232 260 603147632 603147660 1.000000e-03 54.7
21 TraesCS4D01G310500 chr1A 83.732 879 87 29 676 1522 372287970 372287116 0.000000e+00 780.0
22 TraesCS4D01G310500 chr1A 90.517 232 19 3 1 230 96366845 96367075 1.110000e-78 303.0
23 TraesCS4D01G310500 chr1A 89.270 233 23 2 1 231 224095431 224095199 8.680000e-75 291.0
24 TraesCS4D01G310500 chr1A 89.412 85 7 2 2398 2480 368340190 368340106 3.370000e-19 106.0
25 TraesCS4D01G310500 chr1B 83.620 873 91 27 676 1522 401992740 401991894 0.000000e+00 773.0
26 TraesCS4D01G310500 chr1B 89.764 127 12 1 1944 2069 486780246 486780372 7.100000e-36 161.0
27 TraesCS4D01G310500 chr1B 81.928 166 24 6 2319 2480 606199468 606199631 4.300000e-28 135.0
28 TraesCS4D01G310500 chr1B 78.404 213 34 8 1861 2067 470536767 470536973 7.200000e-26 128.0
29 TraesCS4D01G310500 chr1B 98.551 69 1 0 2412 2480 212145981 212146049 3.350000e-24 122.0
30 TraesCS4D01G310500 chr1B 93.421 76 3 2 2407 2480 425862500 425862575 7.250000e-21 111.0
31 TraesCS4D01G310500 chr2B 91.810 232 18 1 1 231 665192579 665192810 3.080000e-84 322.0
32 TraesCS4D01G310500 chr6D 91.102 236 14 5 1 231 246044806 246045039 1.850000e-81 313.0
33 TraesCS4D01G310500 chr6D 92.500 80 6 0 2401 2480 371751931 371752010 5.600000e-22 115.0
34 TraesCS4D01G310500 chr7A 89.610 231 22 2 1 231 198009617 198009845 2.410000e-75 292.0
35 TraesCS4D01G310500 chr5A 89.030 237 24 2 1 235 64788315 64788079 2.410000e-75 292.0
36 TraesCS4D01G310500 chr5A 77.568 370 62 19 1715 2068 636598581 636598217 1.160000e-48 204.0
37 TraesCS4D01G310500 chr2A 87.879 231 22 2 1 231 568402427 568402651 1.460000e-67 267.0
38 TraesCS4D01G310500 chr2D 79.730 370 47 17 1718 2070 593036830 593037188 2.460000e-60 243.0
39 TraesCS4D01G310500 chr2D 81.132 212 32 4 1862 2067 506519073 506519282 1.970000e-36 163.0
40 TraesCS4D01G310500 chr5D 85.776 232 20 6 1 231 522500892 522501111 1.480000e-57 233.0
41 TraesCS4D01G310500 chr5D 95.833 72 2 1 2409 2480 301004171 301004241 5.600000e-22 115.0
42 TraesCS4D01G310500 chr6A 82.528 269 34 8 1808 2067 140207380 140207644 8.930000e-55 224.0
43 TraesCS4D01G310500 chr6A 87.209 86 6 5 1 83 13149284 13149201 2.630000e-15 93.5
44 TraesCS4D01G310500 chr7D 80.237 253 33 10 1830 2070 528033133 528032886 9.120000e-40 174.0
45 TraesCS4D01G310500 chr7D 86.275 102 14 0 2323 2424 42410670 42410771 7.250000e-21 111.0
46 TraesCS4D01G310500 chr1D 75.000 368 78 11 2066 2426 447450113 447450473 9.180000e-35 158.0
47 TraesCS4D01G310500 chr7B 100.000 66 0 0 2415 2480 736937360 736937425 3.350000e-24 122.0
48 TraesCS4D01G310500 chr3A 95.833 72 2 1 2409 2480 156205722 156205652 5.600000e-22 115.0
49 TraesCS4D01G310500 chr3A 93.590 78 1 4 2405 2480 392490199 392490124 2.020000e-21 113.0
50 TraesCS4D01G310500 chrUn 86.275 102 14 0 2323 2424 340092977 340092876 7.250000e-21 111.0


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 TraesCS4D01G310500 chr4D 477557985 477560464 2479 False 4580.000000 4580 100.0000 1 2480 1 chr4D.!!$F1 2479
1 TraesCS4D01G310500 chr4D 477542970 477543847 877 True 631.700000 1205 96.4285 712 1580 2 chr4D.!!$R1 868
2 TraesCS4D01G310500 chr4A 684470862 684472501 1639 False 2113.000000 2113 90.0600 709 2347 1 chr4A.!!$F2 1638
3 TraesCS4D01G310500 chr4A 684448721 684450283 1562 True 810.500000 1007 88.4270 230 1589 2 chr4A.!!$R1 1359
4 TraesCS4D01G310500 chr4B 603037308 603038545 1237 False 1790.000000 1790 92.8230 310 1549 1 chr4B.!!$F1 1239
5 TraesCS4D01G310500 chr4B 602893065 602894351 1286 True 1524.000000 1524 88.0540 232 1549 1 chr4B.!!$R2 1317
6 TraesCS4D01G310500 chr4B 603147632 603149012 1380 False 1006.350000 1958 96.5505 232 1589 2 chr4B.!!$F2 1357
7 TraesCS4D01G310500 chr4B 602873143 602874338 1195 True 737.500000 1251 86.4985 317 1549 2 chr4B.!!$R4 1232
8 TraesCS4D01G310500 chr4B 603160576 603163441 2865 False 473.000000 846 91.0795 1522 2424 2 chr4B.!!$F3 902
9 TraesCS4D01G310500 chr4B 603024338 603028906 4568 True 389.766667 837 91.9560 709 1589 3 chr4B.!!$R5 880
10 TraesCS4D01G310500 chr1A 372287116 372287970 854 True 780.000000 780 83.7320 676 1522 1 chr1A.!!$R3 846
11 TraesCS4D01G310500 chr1B 401991894 401992740 846 True 773.000000 773 83.6200 676 1522 1 chr1B.!!$R1 846

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
206 207 0.448197 CTTGAGACGACTAGCGAGCA 59.552 55.0 12.46 5.53 44.57 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2175 8213 0.250234 TTCTCTGGGGAATGCTCACG 59.75 55.0 0.0 0.0 0.0 4.35 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
61 62 8.492673 AAATACGTTCATATCTGTTCACATGT 57.507 30.769 0.00 0.00 0.00 3.21
62 63 9.594478 AAATACGTTCATATCTGTTCACATGTA 57.406 29.630 0.00 0.00 0.00 2.29
63 64 9.764363 AATACGTTCATATCTGTTCACATGTAT 57.236 29.630 0.00 0.00 0.00 2.29
64 65 7.468922 ACGTTCATATCTGTTCACATGTATG 57.531 36.000 0.00 0.00 0.00 2.39
65 66 6.018751 ACGTTCATATCTGTTCACATGTATGC 60.019 38.462 0.00 0.00 0.00 3.14
66 67 6.201615 CGTTCATATCTGTTCACATGTATGCT 59.798 38.462 0.00 0.00 0.00 3.79
67 68 7.254556 CGTTCATATCTGTTCACATGTATGCTT 60.255 37.037 0.00 0.00 0.00 3.91
68 69 8.400947 GTTCATATCTGTTCACATGTATGCTTT 58.599 33.333 0.00 0.00 0.00 3.51
69 70 8.510243 TCATATCTGTTCACATGTATGCTTTT 57.490 30.769 0.00 0.00 0.00 2.27
70 71 8.400186 TCATATCTGTTCACATGTATGCTTTTG 58.600 33.333 0.00 0.00 0.00 2.44
71 72 6.579666 ATCTGTTCACATGTATGCTTTTGT 57.420 33.333 0.00 0.00 0.00 2.83
72 73 7.686438 ATCTGTTCACATGTATGCTTTTGTA 57.314 32.000 0.00 0.00 0.00 2.41
73 74 7.132694 TCTGTTCACATGTATGCTTTTGTAG 57.867 36.000 0.00 0.00 0.00 2.74
74 75 6.710295 TCTGTTCACATGTATGCTTTTGTAGT 59.290 34.615 0.00 0.00 0.00 2.73
75 76 7.875554 TCTGTTCACATGTATGCTTTTGTAGTA 59.124 33.333 0.00 0.00 0.00 1.82
76 77 8.560355 TGTTCACATGTATGCTTTTGTAGTAT 57.440 30.769 0.00 0.00 33.44 2.12
77 78 9.008965 TGTTCACATGTATGCTTTTGTAGTATT 57.991 29.630 0.00 0.00 31.17 1.89
78 79 9.840427 GTTCACATGTATGCTTTTGTAGTATTT 57.160 29.630 0.00 0.00 31.17 1.40
88 89 8.996988 TGCTTTTGTAGTATTTTTCTTGTACG 57.003 30.769 0.00 0.00 0.00 3.67
89 90 8.614346 TGCTTTTGTAGTATTTTTCTTGTACGT 58.386 29.630 0.00 0.00 0.00 3.57
90 91 8.889000 GCTTTTGTAGTATTTTTCTTGTACGTG 58.111 33.333 0.00 0.00 0.00 4.49
91 92 9.377383 CTTTTGTAGTATTTTTCTTGTACGTGG 57.623 33.333 0.00 0.00 0.00 4.94
92 93 8.436046 TTTGTAGTATTTTTCTTGTACGTGGT 57.564 30.769 0.00 0.00 0.00 4.16
93 94 9.539825 TTTGTAGTATTTTTCTTGTACGTGGTA 57.460 29.630 0.00 0.00 0.00 3.25
94 95 8.519492 TGTAGTATTTTTCTTGTACGTGGTAC 57.481 34.615 0.00 0.00 39.24 3.34
95 96 8.359642 TGTAGTATTTTTCTTGTACGTGGTACT 58.640 33.333 0.00 0.00 39.49 2.73
96 97 9.196552 GTAGTATTTTTCTTGTACGTGGTACTT 57.803 33.333 0.00 0.00 39.49 2.24
97 98 8.667076 AGTATTTTTCTTGTACGTGGTACTTT 57.333 30.769 0.00 0.00 39.49 2.66
98 99 9.112725 AGTATTTTTCTTGTACGTGGTACTTTT 57.887 29.630 0.00 0.00 39.49 2.27
99 100 9.720667 GTATTTTTCTTGTACGTGGTACTTTTT 57.279 29.630 0.00 0.00 39.49 1.94
100 101 8.845942 ATTTTTCTTGTACGTGGTACTTTTTC 57.154 30.769 0.00 0.00 39.49 2.29
101 102 7.614124 TTTTCTTGTACGTGGTACTTTTTCT 57.386 32.000 0.00 0.00 39.49 2.52
102 103 8.715191 TTTTCTTGTACGTGGTACTTTTTCTA 57.285 30.769 0.00 0.00 39.49 2.10
103 104 8.715191 TTTCTTGTACGTGGTACTTTTTCTAA 57.285 30.769 0.00 0.00 39.49 2.10
104 105 8.891671 TTCTTGTACGTGGTACTTTTTCTAAT 57.108 30.769 0.00 0.00 39.49 1.73
105 106 8.891671 TCTTGTACGTGGTACTTTTTCTAATT 57.108 30.769 0.00 0.00 39.49 1.40
106 107 9.979578 TCTTGTACGTGGTACTTTTTCTAATTA 57.020 29.630 0.00 0.00 39.49 1.40
108 109 9.979578 TTGTACGTGGTACTTTTTCTAATTAGA 57.020 29.630 11.24 11.24 39.49 2.10
109 110 9.979578 TGTACGTGGTACTTTTTCTAATTAGAA 57.020 29.630 21.46 21.46 39.49 2.10
131 132 8.909423 AGAATTGTTTTATTAATTGGAGGGGA 57.091 30.769 0.00 0.00 0.00 4.81
132 133 8.758829 AGAATTGTTTTATTAATTGGAGGGGAC 58.241 33.333 0.00 0.00 0.00 4.46
133 134 8.442660 AATTGTTTTATTAATTGGAGGGGACA 57.557 30.769 0.00 0.00 0.00 4.02
134 135 7.857404 TTGTTTTATTAATTGGAGGGGACAA 57.143 32.000 0.00 0.00 0.00 3.18
135 136 7.857404 TGTTTTATTAATTGGAGGGGACAAA 57.143 32.000 0.00 0.00 0.00 2.83
136 137 8.442660 TGTTTTATTAATTGGAGGGGACAAAT 57.557 30.769 0.00 0.00 0.00 2.32
137 138 8.885346 TGTTTTATTAATTGGAGGGGACAAATT 58.115 29.630 0.00 0.00 0.00 1.82
173 174 8.613922 ATGGATTAGGGATCAAAATTTTCTGT 57.386 30.769 0.00 0.00 36.43 3.41
174 175 8.434589 TGGATTAGGGATCAAAATTTTCTGTT 57.565 30.769 0.00 0.00 36.43 3.16
175 176 8.879227 TGGATTAGGGATCAAAATTTTCTGTTT 58.121 29.630 0.00 0.00 36.43 2.83
176 177 9.725019 GGATTAGGGATCAAAATTTTCTGTTTT 57.275 29.630 0.00 0.00 36.43 2.43
181 182 8.367911 AGGGATCAAAATTTTCTGTTTTAGACC 58.632 33.333 0.00 0.00 34.43 3.85
182 183 7.328493 GGGATCAAAATTTTCTGTTTTAGACCG 59.672 37.037 0.00 0.00 34.43 4.79
183 184 7.328493 GGATCAAAATTTTCTGTTTTAGACCGG 59.672 37.037 0.00 0.00 34.43 5.28
184 185 5.980715 TCAAAATTTTCTGTTTTAGACCGGC 59.019 36.000 0.00 0.00 34.43 6.13
185 186 4.514781 AATTTTCTGTTTTAGACCGGCC 57.485 40.909 0.00 0.00 34.43 6.13
186 187 1.515081 TTTCTGTTTTAGACCGGCCG 58.485 50.000 21.04 21.04 34.43 6.13
187 188 0.952010 TTCTGTTTTAGACCGGCCGC 60.952 55.000 22.85 7.25 34.43 6.53
188 189 1.375523 CTGTTTTAGACCGGCCGCT 60.376 57.895 22.85 15.64 0.00 5.52
189 190 0.953960 CTGTTTTAGACCGGCCGCTT 60.954 55.000 22.85 8.79 0.00 4.68
190 191 1.231958 TGTTTTAGACCGGCCGCTTG 61.232 55.000 22.85 9.35 0.00 4.01
191 192 0.952010 GTTTTAGACCGGCCGCTTGA 60.952 55.000 22.85 0.94 0.00 3.02
192 193 0.672401 TTTTAGACCGGCCGCTTGAG 60.672 55.000 22.85 8.46 0.00 3.02
193 194 1.537814 TTTAGACCGGCCGCTTGAGA 61.538 55.000 22.85 0.21 0.00 3.27
194 195 2.221906 TTAGACCGGCCGCTTGAGAC 62.222 60.000 22.85 6.13 0.00 3.36
198 199 4.421479 CGGCCGCTTGAGACGACT 62.421 66.667 14.67 0.00 0.00 4.18
199 200 2.882876 GGCCGCTTGAGACGACTA 59.117 61.111 0.00 0.00 0.00 2.59
200 201 1.226717 GGCCGCTTGAGACGACTAG 60.227 63.158 0.00 0.00 0.00 2.57
201 202 1.874466 GCCGCTTGAGACGACTAGC 60.874 63.158 0.00 0.00 35.87 3.42
204 205 3.228085 GCTTGAGACGACTAGCGAG 57.772 57.895 12.46 0.00 44.57 5.03
205 206 0.863957 GCTTGAGACGACTAGCGAGC 60.864 60.000 12.46 7.29 44.57 5.03
206 207 0.448197 CTTGAGACGACTAGCGAGCA 59.552 55.000 12.46 5.53 44.57 4.26
207 208 0.448197 TTGAGACGACTAGCGAGCAG 59.552 55.000 12.46 0.00 44.57 4.24
225 226 4.708968 CCGGCCGCTCGCTAGATC 62.709 72.222 22.85 0.00 37.74 2.75
267 283 3.111484 TCACATGGAGGTAGCATAACCA 58.889 45.455 0.00 0.00 42.40 3.67
398 421 9.158233 CATTTTTCATGGCAAATAATGTTCTCT 57.842 29.630 0.00 0.00 0.00 3.10
424 448 2.315176 TGGCATGTTTAGTTGGCAAGT 58.685 42.857 12.91 12.91 44.30 3.16
452 480 8.748412 TGTCAAATCCATCCCAGTTTATTTTAG 58.252 33.333 0.00 0.00 0.00 1.85
458 486 7.610865 TCCATCCCAGTTTATTTTAGCAAAAG 58.389 34.615 0.00 0.00 33.22 2.27
627 656 1.590238 CTAATGAAGTCCAAGCGCTCG 59.410 52.381 12.06 0.00 0.00 5.03
758 803 3.046968 TGCTCAACTTGTTGCCGTATA 57.953 42.857 8.48 0.00 0.00 1.47
759 804 3.605634 TGCTCAACTTGTTGCCGTATAT 58.394 40.909 8.48 0.00 0.00 0.86
760 805 4.760878 TGCTCAACTTGTTGCCGTATATA 58.239 39.130 8.48 0.00 0.00 0.86
761 806 5.364778 TGCTCAACTTGTTGCCGTATATAT 58.635 37.500 8.48 0.00 0.00 0.86
770 815 5.779922 TGTTGCCGTATATATCTTCAGGAC 58.220 41.667 0.00 0.00 0.00 3.85
802 848 4.598036 AAACCATCAGTCCCTGATCATT 57.402 40.909 3.80 0.00 46.83 2.57
806 852 4.346418 ACCATCAGTCCCTGATCATTCTAC 59.654 45.833 3.80 0.00 46.83 2.59
861 914 1.540267 TGACAACCTAGCAGTCTCGAC 59.460 52.381 8.33 0.00 33.56 4.20
990 3731 6.281405 CCGGCTATAAATACAACACTCTCTT 58.719 40.000 0.00 0.00 0.00 2.85
1025 3777 1.497286 TCCCAAACCCAAAGCACTAGT 59.503 47.619 0.00 0.00 0.00 2.57
1026 3778 2.712087 TCCCAAACCCAAAGCACTAGTA 59.288 45.455 0.00 0.00 0.00 1.82
1027 3779 3.081804 CCCAAACCCAAAGCACTAGTAG 58.918 50.000 0.00 0.00 0.00 2.57
1233 4008 1.946650 GCAGTGCTCTATCGACGCC 60.947 63.158 8.18 0.00 0.00 5.68
1487 4262 2.124860 AGCCCATTAACGGACGCC 60.125 61.111 0.00 0.00 0.00 5.68
1690 7716 1.508632 TGCACGGTAGCTCTTTTCAC 58.491 50.000 0.00 0.00 34.99 3.18
1711 7737 8.659925 TTCACATTGTCCGTAGTAAGTAAAAA 57.340 30.769 0.00 0.00 0.00 1.94
1735 7761 0.814010 AAGAACAACTCCAACGCGCT 60.814 50.000 5.73 0.00 0.00 5.92
1758 7784 0.726452 TAAACGAACGCGCCATTTGC 60.726 50.000 5.73 0.00 42.48 3.68
1764 7790 2.871080 CGCGCCATTTGCTCGTTG 60.871 61.111 0.00 0.00 42.99 4.10
1848 7881 1.083489 CGCGTACACCCATTTCATGT 58.917 50.000 0.00 0.00 0.00 3.21
1857 7894 3.312421 CACCCATTTCATGTCCGTACATC 59.688 47.826 0.00 0.00 44.70 3.06
1858 7895 2.878406 CCCATTTCATGTCCGTACATCC 59.122 50.000 0.00 0.00 44.70 3.51
1859 7896 2.878406 CCATTTCATGTCCGTACATCCC 59.122 50.000 0.00 0.00 44.70 3.85
1880 7917 2.357327 ATTTTAAAAAGGTCCGCGGC 57.643 45.000 23.51 16.04 0.00 6.53
1885 7922 1.310216 AAAAAGGTCCGCGGCCATAC 61.310 55.000 31.19 20.73 0.00 2.39
1895 7932 1.859427 GCGGCCATACATCATGCCAG 61.859 60.000 2.24 0.00 33.09 4.85
1899 7936 0.535780 CCATACATCATGCCAGCGGT 60.536 55.000 0.00 0.00 32.84 5.68
1924 7961 0.745486 CATCGCCCAGAGTTCATGCA 60.745 55.000 0.00 0.00 0.00 3.96
1925 7962 0.182061 ATCGCCCAGAGTTCATGCAT 59.818 50.000 0.00 0.00 0.00 3.96
1951 7988 0.620030 TGTCAGCCATACATGCCAGT 59.380 50.000 0.00 0.00 0.00 4.00
2018 8055 0.674581 CGACACACATCCCAGCACAT 60.675 55.000 0.00 0.00 0.00 3.21
2085 8123 2.044946 GCGGGCATTTCCTCTGGT 60.045 61.111 0.00 0.00 34.39 4.00
2134 8172 1.526887 GGGCATTGAGGTCGATGGA 59.473 57.895 8.92 0.00 38.03 3.41
2173 8211 3.129502 CGCCACCATGCTCACCTG 61.130 66.667 0.00 0.00 0.00 4.00
2175 8213 2.753043 CCACCATGCTCACCTGCC 60.753 66.667 0.00 0.00 0.00 4.85
2219 8257 1.267121 GAGGCTTGCGGATAGGGATA 58.733 55.000 0.00 0.00 0.00 2.59
2234 8272 2.243736 AGGGATAAAAGCCGGGAATCAA 59.756 45.455 2.18 0.00 0.00 2.57
2243 8281 1.674322 CGGGAATCAAAGGCGTGGT 60.674 57.895 0.00 0.00 0.00 4.16
2248 8286 2.614481 GGAATCAAAGGCGTGGTAGACA 60.614 50.000 0.00 0.00 0.00 3.41
2275 8313 1.296715 GACTCCGGAAGTGCCACAT 59.703 57.895 5.23 0.00 38.74 3.21
2289 8327 1.026718 CCACATGAGGAAAGGCCGAC 61.027 60.000 2.50 0.00 43.43 4.79
2367 8405 2.447714 CCCTAGGAAGAGCAGGGCC 61.448 68.421 11.48 0.00 42.59 5.80
2369 8407 0.105453 CCTAGGAAGAGCAGGGCCTA 60.105 60.000 5.28 0.00 32.04 3.93
2383 8421 2.126228 CCTAACTCGTTGCCGCGA 60.126 61.111 8.23 0.02 39.22 5.87
2385 8423 1.731613 CTAACTCGTTGCCGCGACA 60.732 57.895 8.23 0.00 36.80 4.35
2389 8427 3.000080 CTCGTTGCCGCGACAACTC 62.000 63.158 30.65 10.77 46.21 3.01
2433 8471 3.134127 GCGGCGGCTGAAGGAAAT 61.134 61.111 14.15 0.00 35.83 2.17
2434 8472 1.817941 GCGGCGGCTGAAGGAAATA 60.818 57.895 14.15 0.00 35.83 1.40
2435 8473 1.166531 GCGGCGGCTGAAGGAAATAT 61.167 55.000 14.15 0.00 35.83 1.28
2436 8474 0.588252 CGGCGGCTGAAGGAAATATG 59.412 55.000 7.61 0.00 0.00 1.78
2437 8475 0.312102 GGCGGCTGAAGGAAATATGC 59.688 55.000 0.00 0.00 0.00 3.14
2438 8476 0.312102 GCGGCTGAAGGAAATATGCC 59.688 55.000 0.00 0.00 37.24 4.40
2439 8477 0.954452 CGGCTGAAGGAAATATGCCC 59.046 55.000 0.00 0.00 37.29 5.36
2440 8478 1.477558 CGGCTGAAGGAAATATGCCCT 60.478 52.381 0.00 0.00 37.29 5.19
2441 8479 2.224523 CGGCTGAAGGAAATATGCCCTA 60.225 50.000 0.00 0.00 37.29 3.53
2442 8480 3.416156 GGCTGAAGGAAATATGCCCTAG 58.584 50.000 0.00 0.00 34.81 3.02
2443 8481 3.073062 GGCTGAAGGAAATATGCCCTAGA 59.927 47.826 0.00 0.00 34.81 2.43
2444 8482 4.322567 GCTGAAGGAAATATGCCCTAGAG 58.677 47.826 0.00 0.00 31.36 2.43
2445 8483 4.805609 GCTGAAGGAAATATGCCCTAGAGG 60.806 50.000 0.00 0.00 39.47 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 9.594478 ACATGTGAACAGATATGAACGTATTTA 57.406 29.630 0.00 0.00 0.00 1.40
36 37 8.492673 ACATGTGAACAGATATGAACGTATTT 57.507 30.769 0.00 0.00 0.00 1.40
37 38 9.764363 ATACATGTGAACAGATATGAACGTATT 57.236 29.630 9.11 0.00 0.00 1.89
38 39 9.196552 CATACATGTGAACAGATATGAACGTAT 57.803 33.333 9.11 0.00 33.13 3.06
39 40 7.169140 GCATACATGTGAACAGATATGAACGTA 59.831 37.037 9.11 0.00 33.13 3.57
40 41 6.018751 GCATACATGTGAACAGATATGAACGT 60.019 38.462 9.11 0.00 33.13 3.99
41 42 6.201615 AGCATACATGTGAACAGATATGAACG 59.798 38.462 9.11 0.00 33.13 3.95
42 43 7.488187 AGCATACATGTGAACAGATATGAAC 57.512 36.000 9.11 0.00 33.13 3.18
43 44 8.510243 AAAGCATACATGTGAACAGATATGAA 57.490 30.769 9.11 0.00 33.13 2.57
44 45 8.400186 CAAAAGCATACATGTGAACAGATATGA 58.600 33.333 9.11 0.00 33.13 2.15
45 46 8.186163 ACAAAAGCATACATGTGAACAGATATG 58.814 33.333 9.11 2.51 33.85 1.78
46 47 8.284945 ACAAAAGCATACATGTGAACAGATAT 57.715 30.769 9.11 0.00 0.00 1.63
47 48 7.686438 ACAAAAGCATACATGTGAACAGATA 57.314 32.000 9.11 0.00 0.00 1.98
48 49 6.579666 ACAAAAGCATACATGTGAACAGAT 57.420 33.333 9.11 0.00 0.00 2.90
49 50 6.710295 ACTACAAAAGCATACATGTGAACAGA 59.290 34.615 9.11 0.00 0.00 3.41
50 51 6.902341 ACTACAAAAGCATACATGTGAACAG 58.098 36.000 9.11 0.00 0.00 3.16
51 52 6.875948 ACTACAAAAGCATACATGTGAACA 57.124 33.333 9.11 0.00 0.00 3.18
52 53 9.840427 AAATACTACAAAAGCATACATGTGAAC 57.160 29.630 9.11 0.00 0.00 3.18
62 63 9.607285 CGTACAAGAAAAATACTACAAAAGCAT 57.393 29.630 0.00 0.00 0.00 3.79
63 64 8.614346 ACGTACAAGAAAAATACTACAAAAGCA 58.386 29.630 0.00 0.00 0.00 3.91
64 65 8.889000 CACGTACAAGAAAAATACTACAAAAGC 58.111 33.333 0.00 0.00 0.00 3.51
65 66 9.377383 CCACGTACAAGAAAAATACTACAAAAG 57.623 33.333 0.00 0.00 0.00 2.27
66 67 8.891720 ACCACGTACAAGAAAAATACTACAAAA 58.108 29.630 0.00 0.00 0.00 2.44
67 68 8.436046 ACCACGTACAAGAAAAATACTACAAA 57.564 30.769 0.00 0.00 0.00 2.83
68 69 8.977505 GTACCACGTACAAGAAAAATACTACAA 58.022 33.333 0.00 0.00 38.71 2.41
69 70 8.359642 AGTACCACGTACAAGAAAAATACTACA 58.640 33.333 4.86 0.00 41.03 2.74
70 71 8.748380 AGTACCACGTACAAGAAAAATACTAC 57.252 34.615 4.86 0.00 41.03 2.73
71 72 9.762933 AAAGTACCACGTACAAGAAAAATACTA 57.237 29.630 4.86 0.00 41.03 1.82
72 73 8.667076 AAAGTACCACGTACAAGAAAAATACT 57.333 30.769 4.86 0.00 41.03 2.12
73 74 9.720667 AAAAAGTACCACGTACAAGAAAAATAC 57.279 29.630 4.86 0.00 41.03 1.89
74 75 9.934190 GAAAAAGTACCACGTACAAGAAAAATA 57.066 29.630 4.86 0.00 41.03 1.40
75 76 8.680001 AGAAAAAGTACCACGTACAAGAAAAAT 58.320 29.630 4.86 0.00 41.03 1.82
76 77 8.042944 AGAAAAAGTACCACGTACAAGAAAAA 57.957 30.769 4.86 0.00 41.03 1.94
77 78 7.614124 AGAAAAAGTACCACGTACAAGAAAA 57.386 32.000 4.86 0.00 41.03 2.29
78 79 8.715191 TTAGAAAAAGTACCACGTACAAGAAA 57.285 30.769 4.86 0.00 41.03 2.52
79 80 8.891671 ATTAGAAAAAGTACCACGTACAAGAA 57.108 30.769 4.86 0.00 41.03 2.52
80 81 8.891671 AATTAGAAAAAGTACCACGTACAAGA 57.108 30.769 4.86 0.00 41.03 3.02
82 83 9.979578 TCTAATTAGAAAAAGTACCACGTACAA 57.020 29.630 12.87 0.00 41.03 2.41
83 84 9.979578 TTCTAATTAGAAAAAGTACCACGTACA 57.020 29.630 22.73 0.00 38.96 2.90
105 106 9.998752 TCCCCTCCAATTAATAAAACAATTCTA 57.001 29.630 0.00 0.00 0.00 2.10
106 107 8.758829 GTCCCCTCCAATTAATAAAACAATTCT 58.241 33.333 0.00 0.00 0.00 2.40
107 108 8.536175 TGTCCCCTCCAATTAATAAAACAATTC 58.464 33.333 0.00 0.00 0.00 2.17
108 109 8.442660 TGTCCCCTCCAATTAATAAAACAATT 57.557 30.769 0.00 0.00 0.00 2.32
109 110 8.442660 TTGTCCCCTCCAATTAATAAAACAAT 57.557 30.769 0.00 0.00 0.00 2.71
110 111 7.857404 TTGTCCCCTCCAATTAATAAAACAA 57.143 32.000 0.00 0.00 0.00 2.83
111 112 7.857404 TTTGTCCCCTCCAATTAATAAAACA 57.143 32.000 0.00 0.00 0.00 2.83
147 148 9.713684 ACAGAAAATTTTGATCCCTAATCCATA 57.286 29.630 8.47 0.00 33.01 2.74
148 149 8.613922 ACAGAAAATTTTGATCCCTAATCCAT 57.386 30.769 8.47 0.00 33.01 3.41
149 150 8.434589 AACAGAAAATTTTGATCCCTAATCCA 57.565 30.769 8.47 0.00 33.01 3.41
150 151 9.725019 AAAACAGAAAATTTTGATCCCTAATCC 57.275 29.630 8.47 0.00 33.01 3.01
155 156 8.367911 GGTCTAAAACAGAAAATTTTGATCCCT 58.632 33.333 8.47 0.00 34.17 4.20
156 157 7.328493 CGGTCTAAAACAGAAAATTTTGATCCC 59.672 37.037 8.47 0.00 34.17 3.85
157 158 7.328493 CCGGTCTAAAACAGAAAATTTTGATCC 59.672 37.037 8.47 0.00 34.17 3.36
158 159 7.148804 GCCGGTCTAAAACAGAAAATTTTGATC 60.149 37.037 8.47 0.00 34.17 2.92
159 160 6.645003 GCCGGTCTAAAACAGAAAATTTTGAT 59.355 34.615 8.47 0.00 34.17 2.57
160 161 5.980715 GCCGGTCTAAAACAGAAAATTTTGA 59.019 36.000 8.47 0.00 34.17 2.69
161 162 5.176774 GGCCGGTCTAAAACAGAAAATTTTG 59.823 40.000 8.47 0.00 34.17 2.44
162 163 5.294356 GGCCGGTCTAAAACAGAAAATTTT 58.706 37.500 2.28 2.28 34.17 1.82
163 164 4.557895 CGGCCGGTCTAAAACAGAAAATTT 60.558 41.667 20.10 0.00 34.17 1.82
164 165 3.057806 CGGCCGGTCTAAAACAGAAAATT 60.058 43.478 20.10 0.00 34.17 1.82
165 166 2.486592 CGGCCGGTCTAAAACAGAAAAT 59.513 45.455 20.10 0.00 34.17 1.82
166 167 1.874872 CGGCCGGTCTAAAACAGAAAA 59.125 47.619 20.10 0.00 34.17 2.29
167 168 1.515081 CGGCCGGTCTAAAACAGAAA 58.485 50.000 20.10 0.00 34.17 2.52
168 169 0.952010 GCGGCCGGTCTAAAACAGAA 60.952 55.000 29.38 0.00 34.17 3.02
169 170 1.375013 GCGGCCGGTCTAAAACAGA 60.375 57.895 29.38 0.00 0.00 3.41
170 171 0.953960 AAGCGGCCGGTCTAAAACAG 60.954 55.000 32.52 0.00 0.00 3.16
171 172 1.071814 AAGCGGCCGGTCTAAAACA 59.928 52.632 32.52 0.00 0.00 2.83
172 173 0.952010 TCAAGCGGCCGGTCTAAAAC 60.952 55.000 32.52 8.89 0.00 2.43
173 174 0.672401 CTCAAGCGGCCGGTCTAAAA 60.672 55.000 32.52 13.10 0.00 1.52
174 175 1.079405 CTCAAGCGGCCGGTCTAAA 60.079 57.895 32.52 14.94 0.00 1.85
175 176 1.980232 TCTCAAGCGGCCGGTCTAA 60.980 57.895 32.52 17.53 0.00 2.10
176 177 2.361992 TCTCAAGCGGCCGGTCTA 60.362 61.111 32.52 20.20 0.00 2.59
177 178 4.070552 GTCTCAAGCGGCCGGTCT 62.071 66.667 32.52 15.71 0.00 3.85
181 182 2.921538 CTAGTCGTCTCAAGCGGCCG 62.922 65.000 24.05 24.05 34.09 6.13
182 183 1.226717 CTAGTCGTCTCAAGCGGCC 60.227 63.158 0.00 0.00 34.09 6.13
183 184 1.874466 GCTAGTCGTCTCAAGCGGC 60.874 63.158 0.00 0.00 0.00 6.53
184 185 4.386245 GCTAGTCGTCTCAAGCGG 57.614 61.111 0.00 0.00 0.00 5.52
186 187 0.863957 GCTCGCTAGTCGTCTCAAGC 60.864 60.000 6.49 4.61 39.67 4.01
187 188 0.448197 TGCTCGCTAGTCGTCTCAAG 59.552 55.000 6.49 0.00 39.67 3.02
188 189 0.448197 CTGCTCGCTAGTCGTCTCAA 59.552 55.000 6.49 0.00 39.67 3.02
189 190 1.983196 GCTGCTCGCTAGTCGTCTCA 61.983 60.000 6.49 3.58 39.67 3.27
190 191 1.298041 GCTGCTCGCTAGTCGTCTC 60.298 63.158 6.49 0.00 39.67 3.36
191 192 2.766400 GGCTGCTCGCTAGTCGTCT 61.766 63.158 0.00 0.00 39.67 4.18
192 193 2.278271 GGCTGCTCGCTAGTCGTC 60.278 66.667 0.00 2.18 39.67 4.20
193 194 4.180946 CGGCTGCTCGCTAGTCGT 62.181 66.667 0.00 0.00 38.38 4.34
194 195 4.914420 CCGGCTGCTCGCTAGTCG 62.914 72.222 0.00 7.88 42.50 4.18
208 209 4.708968 GATCTAGCGAGCGGCCGG 62.709 72.222 29.38 11.90 45.17 6.13
214 215 2.252855 CGGACCGATCTAGCGAGC 59.747 66.667 8.64 0.00 0.00 5.03
215 216 2.947542 CCGGACCGATCTAGCGAG 59.052 66.667 17.49 0.00 0.00 5.03
216 217 3.285215 GCCGGACCGATCTAGCGA 61.285 66.667 17.49 0.00 0.00 4.93
217 218 3.256716 GAGCCGGACCGATCTAGCG 62.257 68.421 17.49 0.00 0.00 4.26
218 219 1.735376 TTGAGCCGGACCGATCTAGC 61.735 60.000 17.49 9.91 0.00 3.42
219 220 0.962489 ATTGAGCCGGACCGATCTAG 59.038 55.000 17.49 0.00 0.00 2.43
220 221 2.281539 TATTGAGCCGGACCGATCTA 57.718 50.000 17.49 10.36 0.00 1.98
221 222 1.633774 ATATTGAGCCGGACCGATCT 58.366 50.000 17.49 12.01 0.00 2.75
222 223 2.069273 CAATATTGAGCCGGACCGATC 58.931 52.381 17.49 13.56 0.00 3.69
223 224 1.270839 CCAATATTGAGCCGGACCGAT 60.271 52.381 17.49 2.82 0.00 4.18
224 225 0.105964 CCAATATTGAGCCGGACCGA 59.894 55.000 17.49 0.00 0.00 4.69
225 226 0.179056 ACCAATATTGAGCCGGACCG 60.179 55.000 17.23 6.99 0.00 4.79
226 227 1.141053 AGACCAATATTGAGCCGGACC 59.859 52.381 17.23 0.00 0.00 4.46
227 228 2.158957 TGAGACCAATATTGAGCCGGAC 60.159 50.000 17.23 0.00 0.00 4.79
228 229 2.115427 TGAGACCAATATTGAGCCGGA 58.885 47.619 17.23 0.00 0.00 5.14
267 283 1.068741 GGAAGGTAAGCCGACATCGAT 59.931 52.381 2.09 0.00 43.02 3.59
398 421 3.355378 CCAACTAAACATGCCATCCTCA 58.645 45.455 0.00 0.00 0.00 3.86
424 448 8.837099 AAATAAACTGGGATGGATTTGACATA 57.163 30.769 0.00 0.00 0.00 2.29
508 536 9.970395 GCATGATAAATCTGACATTTTTATGGA 57.030 29.630 0.00 0.00 0.00 3.41
758 803 9.566432 GTTTTGGAATATCAGTCCTGAAGATAT 57.434 33.333 0.37 0.00 43.58 1.63
759 804 7.993183 GGTTTTGGAATATCAGTCCTGAAGATA 59.007 37.037 0.37 0.00 43.58 1.98
760 805 6.830838 GGTTTTGGAATATCAGTCCTGAAGAT 59.169 38.462 0.37 0.00 43.58 2.40
761 806 6.180472 GGTTTTGGAATATCAGTCCTGAAGA 58.820 40.000 0.37 0.00 43.58 2.87
770 815 5.300286 GGGACTGATGGTTTTGGAATATCAG 59.700 44.000 10.11 10.11 46.24 2.90
802 848 4.142337 TGTTTGATACGGCGAGATTGTAGA 60.142 41.667 16.62 0.00 0.00 2.59
806 852 4.335082 TTTGTTTGATACGGCGAGATTG 57.665 40.909 16.62 0.00 0.00 2.67
911 1188 1.128692 GCTGTTTGGCGTAGTAGCTTG 59.871 52.381 0.00 0.00 37.29 4.01
990 3731 0.913924 TGGGATGCATGAGAGCTTGA 59.086 50.000 2.46 0.00 34.99 3.02
1025 3777 2.168521 GTGTGCTTGAGTGGGATAGCTA 59.831 50.000 0.00 0.00 34.77 3.32
1026 3778 1.065854 GTGTGCTTGAGTGGGATAGCT 60.066 52.381 0.00 0.00 34.77 3.32
1027 3779 1.373570 GTGTGCTTGAGTGGGATAGC 58.626 55.000 0.00 0.00 0.00 2.97
1233 4008 1.021390 CGCACACCCTCAGCTTTAGG 61.021 60.000 5.05 5.05 0.00 2.69
1511 4296 2.997986 ACGTACGGATCGAAAGCAAATT 59.002 40.909 21.06 0.00 0.00 1.82
1690 7716 8.080083 AGTGTTTTTACTTACTACGGACAATG 57.920 34.615 0.00 0.00 0.00 2.82
1711 7737 2.870411 GCGTTGGAGTTGTTCTTAGTGT 59.130 45.455 0.00 0.00 0.00 3.55
1735 7761 0.668096 ATGGCGCGTTCGTTTAGTCA 60.668 50.000 8.43 0.00 38.14 3.41
1758 7784 1.268335 CCCAAACGGACAAACAACGAG 60.268 52.381 0.00 0.00 0.00 4.18
1824 7857 0.250381 AAATGGGTGTACGCGTTGGA 60.250 50.000 20.78 0.00 37.94 3.53
1848 7881 6.494146 ACCTTTTTAAAATTGGGATGTACGGA 59.506 34.615 18.64 0.00 0.00 4.69
1857 7894 2.990514 CGCGGACCTTTTTAAAATTGGG 59.009 45.455 18.64 15.01 0.00 4.12
1858 7895 2.990514 CCGCGGACCTTTTTAAAATTGG 59.009 45.455 24.07 15.00 0.00 3.16
1859 7896 2.410392 GCCGCGGACCTTTTTAAAATTG 59.590 45.455 33.48 0.00 0.00 2.32
1880 7917 0.535780 ACCGCTGGCATGATGTATGG 60.536 55.000 0.00 0.00 37.26 2.74
1885 7922 1.652563 CATGACCGCTGGCATGATG 59.347 57.895 18.43 0.00 38.51 3.07
1899 7936 1.913951 AACTCTGGGCGATGGCATGA 61.914 55.000 3.81 0.00 42.47 3.07
1924 7961 1.148949 TATGGCTGACATGGCGCAT 59.851 52.632 10.83 10.14 40.82 4.73
1925 7962 1.819208 GTATGGCTGACATGGCGCA 60.819 57.895 10.83 0.00 40.82 6.09
2000 8037 2.401583 TATGTGCTGGGATGTGTGTC 57.598 50.000 0.00 0.00 0.00 3.67
2116 8154 0.815615 GTCCATCGACCTCAATGCCC 60.816 60.000 0.00 0.00 32.40 5.36
2173 8211 2.825836 CTGGGGAATGCTCACGGC 60.826 66.667 0.00 0.00 42.22 5.68
2175 8213 0.250234 TTCTCTGGGGAATGCTCACG 59.750 55.000 0.00 0.00 0.00 4.35
2189 8227 0.606673 GCAAGCCTCCCGTTTTCTCT 60.607 55.000 0.00 0.00 0.00 3.10
2219 8257 0.608130 GCCTTTGATTCCCGGCTTTT 59.392 50.000 0.00 0.00 39.42 2.27
2234 8272 1.447838 CGCATGTCTACCACGCCTT 60.448 57.895 0.00 0.00 0.00 4.35
2239 8277 3.564027 GCGGCGCATGTCTACCAC 61.564 66.667 29.21 0.00 0.00 4.16
2243 8281 3.751401 GAGTCGCGGCGCATGTCTA 62.751 63.158 32.61 6.31 0.00 2.59
2275 8313 2.970639 CTCGTCGGCCTTTCCTCA 59.029 61.111 0.00 0.00 0.00 3.86
2329 8367 2.058125 TTAAACCCTGGCCAGCACGA 62.058 55.000 28.39 7.86 0.00 4.35
2383 8421 5.440610 AGAGGAAAACAATGTCAGAGTTGT 58.559 37.500 0.00 0.00 40.06 3.32
2385 8423 5.221126 GCAAGAGGAAAACAATGTCAGAGTT 60.221 40.000 0.00 0.00 0.00 3.01
2389 8427 4.037208 ACAGCAAGAGGAAAACAATGTCAG 59.963 41.667 0.00 0.00 0.00 3.51
2418 8456 0.312102 GCATATTTCCTTCAGCCGCC 59.688 55.000 0.00 0.00 0.00 6.13
2424 8462 4.982241 CCTCTAGGGCATATTTCCTTCA 57.018 45.455 0.00 0.00 34.75 3.02
2436 8474 8.637196 AATAACTTTATTATTGCCTCTAGGGC 57.363 34.615 13.60 13.60 44.71 5.19


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

AutoCloner maintained by Alex Coulton.