Multiple sequence alignment - TraesCS3A01G494000

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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 TraesCS3A01G494000 chr3A 100.000 5010 0 0 1 5010 720227117 720232126 0.000000e+00 9252.0
1 TraesCS3A01G494000 chr3A 94.488 2304 94 10 2728 5010 720076516 720078807 0.000000e+00 3520.0
2 TraesCS3A01G494000 chr3A 86.276 2339 221 41 2739 5010 719995154 719997459 0.000000e+00 2449.0
3 TraesCS3A01G494000 chr3A 91.934 1277 61 11 3772 5010 720221841 720223113 0.000000e+00 1749.0
4 TraesCS3A01G494000 chr3A 88.222 1350 125 17 3683 5010 719935996 719937333 0.000000e+00 1581.0
5 TraesCS3A01G494000 chr3A 87.363 1369 128 21 993 2336 720214331 720215679 0.000000e+00 1528.0
6 TraesCS3A01G494000 chr3A 90.111 1082 74 22 2503 3577 720215900 720216955 0.000000e+00 1375.0
7 TraesCS3A01G494000 chr3A 84.722 1440 146 30 587 1984 720074825 720076232 0.000000e+00 1373.0
8 TraesCS3A01G494000 chr3A 87.565 965 98 13 1000 1951 719932886 719933841 0.000000e+00 1098.0
9 TraesCS3A01G494000 chr3A 84.732 989 121 18 1000 1974 719991668 719992640 0.000000e+00 963.0
10 TraesCS3A01G494000 chr3A 83.182 1100 132 37 2549 3630 719934829 719935893 0.000000e+00 957.0
11 TraesCS3A01G494000 chr3A 91.419 303 18 5 1 299 720064049 720064347 4.670000e-110 409.0
12 TraesCS3A01G494000 chr3A 81.235 405 27 19 474 849 720213119 720213503 1.060000e-71 281.0
13 TraesCS3A01G494000 chr3A 82.353 289 25 13 70 355 720212745 720213010 1.400000e-55 228.0
14 TraesCS3A01G494000 chr3A 88.514 148 15 2 2364 2510 108379014 108378868 1.430000e-40 178.0
15 TraesCS3A01G494000 chr3A 83.851 161 15 7 1989 2148 720076276 720076426 5.230000e-30 143.0
16 TraesCS3A01G494000 chr3A 94.915 59 3 0 862 920 720213579 720213637 5.340000e-15 93.5
17 TraesCS3A01G494000 chr3A 91.803 61 5 0 2329 2389 720215842 720215902 8.940000e-13 86.1
18 TraesCS3A01G494000 chr3D 94.179 2302 109 14 2728 5010 590307371 590309666 0.000000e+00 3485.0
19 TraesCS3A01G494000 chr3D 86.404 2030 156 49 1 1977 590305120 590307082 0.000000e+00 2109.0
20 TraesCS3A01G494000 chr3D 88.814 1332 111 22 3703 5010 590204070 590205387 0.000000e+00 1600.0
21 TraesCS3A01G494000 chr3D 82.982 1422 181 28 1000 2385 590238347 590239743 0.000000e+00 1229.0
22 TraesCS3A01G494000 chr3D 86.515 964 98 16 1000 1957 590200509 590201446 0.000000e+00 1031.0
23 TraesCS3A01G494000 chr3D 85.408 932 122 8 3638 4560 588977705 588976779 0.000000e+00 955.0
24 TraesCS3A01G494000 chr3D 82.190 1050 137 33 2598 3630 590202929 590203945 0.000000e+00 857.0
25 TraesCS3A01G494000 chr3D 81.341 1104 146 40 2549 3630 590239820 590240885 0.000000e+00 843.0
26 TraesCS3A01G494000 chr3D 86.254 291 25 1 4735 5010 590241624 590241914 8.150000e-78 302.0
27 TraesCS3A01G494000 chr3D 83.019 159 16 7 1991 2148 590307135 590307283 3.150000e-27 134.0
28 TraesCS3A01G494000 chr3B 93.483 2317 103 16 2728 5010 789228041 789230343 0.000000e+00 3398.0
29 TraesCS3A01G494000 chr3B 86.228 2338 208 46 2738 5007 789220102 789222393 0.000000e+00 2429.0
30 TraesCS3A01G494000 chr3B 88.609 1352 116 21 3683 5010 789179645 789180982 0.000000e+00 1609.0
31 TraesCS3A01G494000 chr3B 86.929 1117 119 15 862 1974 789226711 789227804 0.000000e+00 1229.0
32 TraesCS3A01G494000 chr3B 87.150 965 113 6 1000 1956 789175921 789176882 0.000000e+00 1085.0
33 TraesCS3A01G494000 chr3B 84.232 983 133 8 1000 1974 789217810 789218778 0.000000e+00 937.0
34 TraesCS3A01G494000 chr3B 88.999 709 40 20 69 770 789225865 789226542 0.000000e+00 843.0
35 TraesCS3A01G494000 chr3B 84.819 718 76 22 2549 3255 789177429 789178124 0.000000e+00 691.0
36 TraesCS3A01G494000 chr3B 79.856 417 52 15 1989 2385 789176948 789177352 4.940000e-70 276.0
37 TraesCS3A01G494000 chr3B 86.124 209 26 3 2190 2398 789219142 789219347 6.530000e-54 222.0
38 TraesCS3A01G494000 chr3B 93.814 97 5 1 769 864 789226573 789226669 1.450000e-30 145.0
39 TraesCS3A01G494000 chr3B 95.714 70 3 0 1 70 789225539 789225608 4.100000e-21 113.0
40 TraesCS3A01G494000 chr2A 96.639 119 4 0 2386 2504 539014580 539014698 1.100000e-46 198.0
41 TraesCS3A01G494000 chr2A 95.041 121 6 0 2387 2507 729162120 729162000 1.840000e-44 191.0
42 TraesCS3A01G494000 chr1A 96.639 119 4 0 2386 2504 498452667 498452785 1.100000e-46 198.0
43 TraesCS3A01G494000 chr4D 95.200 125 5 1 2387 2511 55352441 55352564 3.960000e-46 196.0
44 TraesCS3A01G494000 chr4D 89.437 142 15 0 2364 2505 93458761 93458902 3.980000e-41 180.0
45 TraesCS3A01G494000 chr2B 96.610 118 4 0 2387 2504 657072114 657072231 3.960000e-46 196.0
46 TraesCS3A01G494000 chr2B 95.041 121 6 0 2385 2505 518048323 518048443 1.840000e-44 191.0
47 TraesCS3A01G494000 chr1B 93.798 129 7 1 2384 2512 17743405 17743532 5.120000e-45 193.0
48 TraesCS3A01G494000 chr5A 92.969 128 9 0 2383 2510 689428130 689428003 2.380000e-43 187.0
49 TraesCS3A01G494000 chr7A 92.913 127 9 0 2379 2505 721098225 721098351 8.560000e-43 185.0
50 TraesCS3A01G494000 chr5B 92.969 128 7 2 2381 2507 646478041 646478167 8.560000e-43 185.0


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 TraesCS3A01G494000 chr3A 720227117 720232126 5009 False 9252.000000 9252 100.000000 1 5010 1 chr3A.!!$F3 5009
1 TraesCS3A01G494000 chr3A 720221841 720223113 1272 False 1749.000000 1749 91.934000 3772 5010 1 chr3A.!!$F2 1238
2 TraesCS3A01G494000 chr3A 719991668 719997459 5791 False 1706.000000 2449 85.504000 1000 5010 2 chr3A.!!$F5 4010
3 TraesCS3A01G494000 chr3A 720074825 720078807 3982 False 1678.666667 3520 87.687000 587 5010 3 chr3A.!!$F6 4423
4 TraesCS3A01G494000 chr3A 719932886 719937333 4447 False 1212.000000 1581 86.323000 1000 5010 3 chr3A.!!$F4 4010
5 TraesCS3A01G494000 chr3A 720212745 720216955 4210 False 598.600000 1528 87.963333 70 3577 6 chr3A.!!$F7 3507
6 TraesCS3A01G494000 chr3D 590305120 590309666 4546 False 1909.333333 3485 87.867333 1 5010 3 chr3D.!!$F3 5009
7 TraesCS3A01G494000 chr3D 590200509 590205387 4878 False 1162.666667 1600 85.839667 1000 5010 3 chr3D.!!$F1 4010
8 TraesCS3A01G494000 chr3D 588976779 588977705 926 True 955.000000 955 85.408000 3638 4560 1 chr3D.!!$R1 922
9 TraesCS3A01G494000 chr3D 590238347 590241914 3567 False 791.333333 1229 83.525667 1000 5010 3 chr3D.!!$F2 4010
10 TraesCS3A01G494000 chr3B 789217810 789230343 12533 False 1164.500000 3398 89.440375 1 5010 8 chr3B.!!$F2 5009
11 TraesCS3A01G494000 chr3B 789175921 789180982 5061 False 915.250000 1609 85.108500 1000 5010 4 chr3B.!!$F1 4010

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
717 8742 0.108567 GTTCTCCTCCTCCTTGTCGC 60.109 60.0 0.00 0.0 0.00 5.19 F
1166 9991 0.036732 GACCTGGCTTGTCATCCACA 59.963 55.0 0.00 0.0 32.91 4.17 F
1627 10482 0.251832 AAGAGCCGACTTCTCCAGGA 60.252 55.0 0.00 0.0 0.00 3.86 F
2056 10977 0.329596 GGCAGATCCTTGGTTGGACT 59.670 55.0 0.00 0.0 39.17 3.85 F
2408 12137 0.395312 TCCCTTCGTCCGAAAAAGCT 59.605 50.0 3.52 0.0 33.34 3.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2485 13296 0.032813 ATACTCCCTCCGTCCGGAAA 60.033 55.000 5.23 0.0 44.66 3.13 R
2489 13300 0.750546 TCACATACTCCCTCCGTCCG 60.751 60.000 0.00 0.0 0.00 4.79 R
2611 14337 1.076513 GGCCCCCTTTGTCCTTAGAAA 59.923 52.381 0.00 0.0 0.00 2.52 R
3697 16967 1.891933 TGCCATCCATGGGAAGACTA 58.108 50.000 13.02 0.0 45.79 2.59 R
4058 17331 0.107703 TTCGGCTAACATCTGCCCAG 60.108 55.000 0.00 0.0 45.90 4.45 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
38 7768 7.931948 AGAAGACTTAATTATGGGATGGTTACG 59.068 37.037 3.66 0.00 0.00 3.18
57 7787 7.771361 TGGTTACGCTGATTCCTAAAATGAATA 59.229 33.333 0.00 0.00 32.74 1.75
80 8068 1.825090 CTGCAACTATCACTTGCCCA 58.175 50.000 0.91 0.00 42.91 5.36
112 8100 1.136305 GTATCTTAGCCGGTGCACTCA 59.864 52.381 17.98 0.00 41.13 3.41
115 8103 0.811616 CTTAGCCGGTGCACTCATCC 60.812 60.000 17.98 0.00 41.13 3.51
169 8158 9.849166 CCGGTTGATAATACAAACATAGTTTTT 57.151 29.630 0.00 0.00 37.32 1.94
335 8326 2.463653 CGAGTGTGTCGCAAAAATGTTG 59.536 45.455 0.00 0.00 43.03 3.33
400 8395 7.069331 TCTGTAAATTTTTCTTTGCAGAGGGAA 59.931 33.333 11.59 0.00 46.23 3.97
425 8420 5.871834 ACTACTACAATTTTACCACCAGCA 58.128 37.500 0.00 0.00 0.00 4.41
426 8421 6.300703 ACTACTACAATTTTACCACCAGCAA 58.699 36.000 0.00 0.00 0.00 3.91
435 8430 1.692411 ACCACCAGCAAGTTTTCCTC 58.308 50.000 0.00 0.00 0.00 3.71
460 8455 5.220681 GGTCTTGCGTCTAGATTTCCATTTC 60.221 44.000 0.00 0.00 0.00 2.17
463 8458 2.347661 GCGTCTAGATTTCCATTTCGCG 60.348 50.000 0.00 0.00 32.68 5.87
464 8459 2.218759 CGTCTAGATTTCCATTTCGCGG 59.781 50.000 6.13 0.00 0.00 6.46
637 8662 2.033757 AGCCCACTGAAGCAGCAG 59.966 61.111 0.00 4.50 41.63 4.24
638 8663 3.745803 GCCCACTGAAGCAGCAGC 61.746 66.667 5.82 0.00 39.51 5.25
717 8742 0.108567 GTTCTCCTCCTCCTTGTCGC 60.109 60.000 0.00 0.00 0.00 5.19
964 9752 0.930726 ACAAACTTGGGGAGGTGGAA 59.069 50.000 0.00 0.00 0.00 3.53
1123 9945 3.741344 CAGTTTCTACAAGTTCCCTGACG 59.259 47.826 0.00 0.00 0.00 4.35
1124 9946 3.640029 AGTTTCTACAAGTTCCCTGACGA 59.360 43.478 0.00 0.00 0.00 4.20
1149 9974 0.319641 GGTTCCTATCATCCGCGGAC 60.320 60.000 33.75 15.05 0.00 4.79
1166 9991 0.036732 GACCTGGCTTGTCATCCACA 59.963 55.000 0.00 0.00 32.91 4.17
1187 10012 1.707427 GATGGCCATGGTTATCCTCCT 59.293 52.381 26.56 0.00 34.23 3.69
1288 10125 0.736325 CACCTACGAAGCCAACCTCG 60.736 60.000 0.00 0.00 0.00 4.63
1361 10207 2.668212 CACCGACACCGTTGGCAT 60.668 61.111 0.02 0.00 40.62 4.40
1545 10391 4.473444 TCTCCAACCAGAATTTTCTTGCT 58.527 39.130 0.00 0.00 34.74 3.91
1622 10477 0.603569 TGGACAAGAGCCGACTTCTC 59.396 55.000 0.00 0.00 0.00 2.87
1627 10482 0.251832 AAGAGCCGACTTCTCCAGGA 60.252 55.000 0.00 0.00 0.00 3.86
1630 10485 1.045911 AGCCGACTTCTCCAGGATCC 61.046 60.000 2.48 2.48 0.00 3.36
1775 10636 4.796231 GACCGCCGACGACTGCAT 62.796 66.667 0.00 0.00 43.93 3.96
2013 10931 4.096190 AGCCACCATCCAAGAATATCAG 57.904 45.455 0.00 0.00 0.00 2.90
2056 10977 0.329596 GGCAGATCCTTGGTTGGACT 59.670 55.000 0.00 0.00 39.17 3.85
2060 10981 2.040278 CAGATCCTTGGTTGGACTTGGA 59.960 50.000 0.00 0.00 39.17 3.53
2061 10982 2.040412 AGATCCTTGGTTGGACTTGGAC 59.960 50.000 0.00 0.00 39.17 4.02
2062 10983 1.217916 TCCTTGGTTGGACTTGGACA 58.782 50.000 0.00 0.00 0.00 4.02
2063 10984 1.780309 TCCTTGGTTGGACTTGGACAT 59.220 47.619 0.00 0.00 0.00 3.06
2064 10985 1.888512 CCTTGGTTGGACTTGGACATG 59.111 52.381 0.00 0.00 0.00 3.21
2065 10986 1.888512 CTTGGTTGGACTTGGACATGG 59.111 52.381 0.00 0.00 0.00 3.66
2066 10987 0.539438 TGGTTGGACTTGGACATGGC 60.539 55.000 0.00 0.00 0.00 4.40
2067 10988 0.539438 GGTTGGACTTGGACATGGCA 60.539 55.000 0.00 0.00 0.00 4.92
2068 10989 0.598065 GTTGGACTTGGACATGGCAC 59.402 55.000 0.00 0.00 0.00 5.01
2069 10990 0.539438 TTGGACTTGGACATGGCACC 60.539 55.000 0.00 0.00 0.00 5.01
2070 10991 1.074775 GGACTTGGACATGGCACCA 59.925 57.895 0.00 2.39 0.00 4.17
2071 10992 1.244019 GGACTTGGACATGGCACCAC 61.244 60.000 0.00 0.00 35.81 4.16
2203 11258 1.130561 CGGATGATGCATGCAGCTATG 59.869 52.381 33.41 18.15 45.94 2.23
2331 11889 8.189460 AGTCTACGTAGTTGAAATATCCACTTC 58.811 37.037 21.53 0.00 44.69 3.01
2394 12123 5.896073 ATTAGCTTGCTACATACTCCCTT 57.104 39.130 1.37 0.00 0.00 3.95
2400 12129 1.001597 GCTACATACTCCCTTCGTCCG 60.002 57.143 0.00 0.00 0.00 4.79
2402 12131 1.843368 ACATACTCCCTTCGTCCGAA 58.157 50.000 1.81 1.81 0.00 4.30
2406 12135 2.165319 ACTCCCTTCGTCCGAAAAAG 57.835 50.000 3.52 4.23 33.34 2.27
2408 12137 0.395312 TCCCTTCGTCCGAAAAAGCT 59.605 50.000 3.52 0.00 33.34 3.74
2411 12140 1.602377 CCTTCGTCCGAAAAAGCTTGT 59.398 47.619 0.00 0.00 33.34 3.16
2415 12144 1.314730 GTCCGAAAAAGCTTGTCCCA 58.685 50.000 0.00 0.00 0.00 4.37
2418 12147 1.602920 CCGAAAAAGCTTGTCCCAAGC 60.603 52.381 18.69 18.69 43.31 4.01
2428 12157 3.873801 GCTTGTCCCAAGCTTATTCCTCA 60.874 47.826 18.97 0.00 40.01 3.86
2429 12158 4.335416 CTTGTCCCAAGCTTATTCCTCAA 58.665 43.478 0.00 0.18 0.00 3.02
2430 12159 4.380843 TGTCCCAAGCTTATTCCTCAAA 57.619 40.909 0.00 0.00 0.00 2.69
2431 12160 4.934356 TGTCCCAAGCTTATTCCTCAAAT 58.066 39.130 0.00 0.00 0.00 2.32
2432 12161 4.706476 TGTCCCAAGCTTATTCCTCAAATG 59.294 41.667 0.00 0.00 0.00 2.32
2433 12162 4.098501 GTCCCAAGCTTATTCCTCAAATGG 59.901 45.833 0.00 0.00 0.00 3.16
2434 12163 4.017591 TCCCAAGCTTATTCCTCAAATGGA 60.018 41.667 0.00 0.00 0.00 3.41
2435 12164 4.897670 CCCAAGCTTATTCCTCAAATGGAT 59.102 41.667 0.00 0.00 35.83 3.41
2436 12165 5.221382 CCCAAGCTTATTCCTCAAATGGATG 60.221 44.000 0.00 0.00 35.83 3.51
2437 12166 5.361857 CCAAGCTTATTCCTCAAATGGATGT 59.638 40.000 0.00 0.00 35.83 3.06
2440 12169 7.992754 AGCTTATTCCTCAAATGGATGTATC 57.007 36.000 0.00 0.00 35.83 2.24
2441 12170 7.753630 AGCTTATTCCTCAAATGGATGTATCT 58.246 34.615 0.00 0.00 35.83 1.98
2442 12171 8.884323 AGCTTATTCCTCAAATGGATGTATCTA 58.116 33.333 0.00 0.00 35.83 1.98
2443 12172 9.160496 GCTTATTCCTCAAATGGATGTATCTAG 57.840 37.037 0.00 0.00 35.83 2.43
2444 12173 9.160496 CTTATTCCTCAAATGGATGTATCTAGC 57.840 37.037 0.00 0.00 35.83 3.42
2445 12174 6.499106 TTCCTCAAATGGATGTATCTAGCA 57.501 37.500 0.00 0.00 35.83 3.49
2447 12176 5.604231 TCCTCAAATGGATGTATCTAGCACT 59.396 40.000 0.00 0.00 0.00 4.40
2448 12177 6.782494 TCCTCAAATGGATGTATCTAGCACTA 59.218 38.462 0.00 0.00 0.00 2.74
2449 12178 7.290014 TCCTCAAATGGATGTATCTAGCACTAA 59.710 37.037 0.00 0.00 0.00 2.24
2451 12180 8.023021 TCAAATGGATGTATCTAGCACTAACT 57.977 34.615 0.00 0.00 0.00 2.24
2452 12181 8.486210 TCAAATGGATGTATCTAGCACTAACTT 58.514 33.333 0.00 0.00 0.00 2.66
2453 12182 8.554528 CAAATGGATGTATCTAGCACTAACTTG 58.445 37.037 0.00 0.00 0.00 3.16
2454 12183 6.161855 TGGATGTATCTAGCACTAACTTGG 57.838 41.667 0.00 0.00 0.00 3.61
2455 12184 5.661312 TGGATGTATCTAGCACTAACTTGGT 59.339 40.000 0.00 0.00 0.00 3.67
2456 12185 5.986135 GGATGTATCTAGCACTAACTTGGTG 59.014 44.000 0.97 0.97 37.70 4.17
2473 13284 7.325660 ACTTGGTGCTAGATACATTCATTTG 57.674 36.000 0.00 0.00 0.00 2.32
2474 13285 7.112122 ACTTGGTGCTAGATACATTCATTTGA 58.888 34.615 0.00 0.00 0.00 2.69
2475 13286 7.281774 ACTTGGTGCTAGATACATTCATTTGAG 59.718 37.037 0.00 0.00 0.00 3.02
2476 13287 6.057533 TGGTGCTAGATACATTCATTTGAGG 58.942 40.000 0.00 0.00 0.00 3.86
2477 13288 5.471456 GGTGCTAGATACATTCATTTGAGGG 59.529 44.000 0.00 0.00 0.00 4.30
2478 13289 6.291377 GTGCTAGATACATTCATTTGAGGGA 58.709 40.000 0.00 0.00 0.00 4.20
2479 13290 6.203723 GTGCTAGATACATTCATTTGAGGGAC 59.796 42.308 0.00 0.00 0.00 4.46
2480 13291 6.126796 TGCTAGATACATTCATTTGAGGGACA 60.127 38.462 0.00 0.00 0.00 4.02
2482 13293 7.041508 GCTAGATACATTCATTTGAGGGACAAG 60.042 40.741 0.00 0.00 39.77 3.16
2483 13294 6.725364 AGATACATTCATTTGAGGGACAAGT 58.275 36.000 0.00 0.00 39.77 3.16
2484 13295 7.177878 AGATACATTCATTTGAGGGACAAGTT 58.822 34.615 0.00 0.00 39.77 2.66
2485 13296 7.671398 AGATACATTCATTTGAGGGACAAGTTT 59.329 33.333 0.00 0.00 39.77 2.66
2486 13297 6.484364 ACATTCATTTGAGGGACAAGTTTT 57.516 33.333 0.00 0.00 39.77 2.43
2489 13300 5.529581 TCATTTGAGGGACAAGTTTTTCC 57.470 39.130 0.00 0.00 39.77 3.13
2588 13468 7.860373 CGAAGAAAATGGTGTTTGTTGATAAGA 59.140 33.333 0.00 0.00 0.00 2.10
2591 13471 9.082313 AGAAAATGGTGTTTGTTGATAAGAGAT 57.918 29.630 0.00 0.00 0.00 2.75
2611 14337 8.710749 AGAGATAAGATGCTAGAGTCAGAATT 57.289 34.615 0.00 0.00 0.00 2.17
2615 14342 9.762933 GATAAGATGCTAGAGTCAGAATTTTCT 57.237 33.333 0.00 0.00 38.25 2.52
2620 14347 7.482169 TGCTAGAGTCAGAATTTTCTAAGGA 57.518 36.000 0.00 0.00 35.34 3.36
2977 15103 7.095144 CCTTAACGTTGTATATTTGTGTGTCCA 60.095 37.037 11.99 0.00 0.00 4.02
3069 15201 5.215252 TCGAGATTGGAAGACAAGAGTTT 57.785 39.130 0.00 0.00 43.48 2.66
3183 15315 6.597672 CCTGTCTACAAGGTAAATGCATTGTA 59.402 38.462 13.82 10.18 42.32 2.41
3458 16663 8.727100 TCTCCATTATATTATCGATGCCCTAT 57.273 34.615 8.54 2.61 0.00 2.57
3632 16847 7.275560 ACTCTTGATAAACATTTATTTTGCGCC 59.724 33.333 4.18 0.00 33.72 6.53
3662 16913 8.523915 TGCACTGAAATGGAATATTAAGACAT 57.476 30.769 0.00 0.00 0.00 3.06
3686 16956 7.440541 TTGTATTCGATATGTGACGTTGTAC 57.559 36.000 0.00 0.00 0.00 2.90
3696 16966 4.138290 TGTGACGTTGTACATCCCAAAAT 58.862 39.130 0.00 0.00 0.00 1.82
3697 16967 4.580995 TGTGACGTTGTACATCCCAAAATT 59.419 37.500 0.00 0.00 0.00 1.82
3698 16968 5.763698 TGTGACGTTGTACATCCCAAAATTA 59.236 36.000 0.00 0.00 0.00 1.40
3739 17012 7.302524 GCATGTGATTCATTTTCTGCAATTTT 58.697 30.769 0.00 0.00 34.09 1.82
4043 17316 4.318760 CGATCGTGTTTTGGCCATACTATG 60.319 45.833 6.09 5.26 0.00 2.23
4058 17331 6.367422 GCCATACTATGAAATGCACTCTCTAC 59.633 42.308 0.00 0.00 0.00 2.59
4061 17334 5.911752 ACTATGAAATGCACTCTCTACTGG 58.088 41.667 0.00 0.00 0.00 4.00
4109 17382 7.961351 TGGTTGATTGGAATAAAAGATGTGTT 58.039 30.769 0.00 0.00 0.00 3.32
4160 17433 0.108424 ATCTCCACAAGCACTCTCGC 60.108 55.000 0.00 0.00 0.00 5.03
4266 17539 6.813152 GCTAGCAAAAATTTTCAGCTCCAATA 59.187 34.615 25.19 12.74 34.61 1.90
4277 17550 5.296151 TCAGCTCCAATAATACTCAAGGG 57.704 43.478 0.00 0.00 0.00 3.95
4862 18157 7.472945 GCATACTTCAGCCTAAGGGTATCTAAA 60.473 40.741 0.00 0.00 34.45 1.85
4887 18197 8.423906 AGTAGATGAATCGGGTAATAATGACT 57.576 34.615 0.00 0.00 0.00 3.41
4910 18220 3.146618 ACCGTCTGCAGTAATAACGAG 57.853 47.619 22.20 15.45 35.45 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 7768 7.115947 GCAGCATTATTCATTTTAGGAATCAGC 59.884 37.037 0.00 0.00 36.45 4.26
80 8068 4.251268 GGCTAAGATACTTTGACCAACGT 58.749 43.478 0.00 0.00 0.00 3.99
112 8100 9.059023 ACTTTAGGTACAAAAAGAGGATAGGAT 57.941 33.333 20.07 0.00 37.15 3.24
293 8284 3.733236 GGCTCGCCGCACATATATA 57.267 52.632 0.00 0.00 41.67 0.86
314 8305 2.383298 ACATTTTTGCGACACACTCG 57.617 45.000 0.00 0.00 45.97 4.18
315 8306 2.216263 GCAACATTTTTGCGACACACTC 59.784 45.455 0.00 0.00 35.58 3.51
316 8307 2.192624 GCAACATTTTTGCGACACACT 58.807 42.857 0.00 0.00 35.58 3.55
317 8308 2.626462 GCAACATTTTTGCGACACAC 57.374 45.000 0.00 0.00 35.58 3.82
335 8326 4.370364 TCAGTGGTGTTCTTTTGAAAGC 57.630 40.909 0.00 0.00 40.53 3.51
383 8378 6.779860 AGTAGTATTCCCTCTGCAAAGAAAA 58.220 36.000 0.00 0.00 0.00 2.29
400 8395 7.626390 TGCTGGTGGTAAAATTGTAGTAGTAT 58.374 34.615 0.00 0.00 0.00 2.12
425 8420 1.226746 CGCAAGACCGAGGAAAACTT 58.773 50.000 0.00 0.00 43.02 2.66
426 8421 0.106149 ACGCAAGACCGAGGAAAACT 59.894 50.000 0.00 0.00 43.62 2.66
435 8430 2.194271 GGAAATCTAGACGCAAGACCG 58.806 52.381 0.00 0.00 43.62 4.79
460 8455 6.505039 AAGAAAACTGTTTTATTTTCCGCG 57.495 33.333 17.70 0.00 43.03 6.46
463 8458 8.402472 CCCCAAAAGAAAACTGTTTTATTTTCC 58.598 33.333 32.02 16.11 45.51 3.13
464 8459 7.913297 GCCCCAAAAGAAAACTGTTTTATTTTC 59.087 33.333 32.02 22.84 45.51 2.29
469 8464 5.046231 AGTGCCCCAAAAGAAAACTGTTTTA 60.046 36.000 17.70 0.00 31.94 1.52
637 8662 1.022735 TAGTGCCGACTAGCAGTAGC 58.977 55.000 0.00 0.00 44.58 3.58
638 8663 1.003759 CGTAGTGCCGACTAGCAGTAG 60.004 57.143 1.44 0.00 46.57 2.57
639 8664 1.012086 CGTAGTGCCGACTAGCAGTA 58.988 55.000 0.00 0.00 44.58 2.74
640 8665 0.675837 TCGTAGTGCCGACTAGCAGT 60.676 55.000 0.00 0.00 45.14 4.40
641 8666 0.028242 CTCGTAGTGCCGACTAGCAG 59.972 60.000 0.00 0.00 45.14 4.24
642 8667 0.392060 TCTCGTAGTGCCGACTAGCA 60.392 55.000 0.00 0.00 41.46 3.49
964 9752 6.441088 AGATAACTGGAAAACTTGAGGAGT 57.559 37.500 0.00 0.00 41.47 3.85
996 9784 4.022416 TGGAAAACACCAGCATACATCAAC 60.022 41.667 0.00 0.00 34.77 3.18
1123 9945 2.672478 CGGATGATAGGAACCGCATCTC 60.672 54.545 16.87 10.45 38.98 2.75
1124 9946 1.273606 CGGATGATAGGAACCGCATCT 59.726 52.381 16.87 0.00 38.98 2.90
1145 9970 1.450312 GGATGACAAGCCAGGTCCG 60.450 63.158 0.00 0.00 34.36 4.79
1149 9974 0.325933 TCTGTGGATGACAAGCCAGG 59.674 55.000 0.96 0.00 44.25 4.45
1166 9991 1.707427 GGAGGATAACCATGGCCATCT 59.293 52.381 17.61 8.05 38.94 2.90
1187 10012 4.465446 CGAGGGGCAGGAGGAGGA 62.465 72.222 0.00 0.00 0.00 3.71
1288 10125 0.907230 AGGGTGGTTGAGAGGAGCTC 60.907 60.000 4.71 4.71 44.21 4.09
1400 10246 3.059982 CAGAGGCGTTGGAGTCCA 58.940 61.111 8.12 8.12 0.00 4.02
1545 10391 6.693978 CGAGTATATTGTCATTGACGTTGGTA 59.306 38.462 11.97 1.66 34.95 3.25
1627 10482 3.476552 TCAGAAGCGTGAAAAACAGGAT 58.523 40.909 0.00 0.00 36.62 3.24
1630 10485 4.014847 TGTTCAGAAGCGTGAAAAACAG 57.985 40.909 1.38 0.00 38.17 3.16
2013 10931 5.561679 GGGAAGGATGAGAATTACATACCC 58.438 45.833 0.00 0.00 29.60 3.69
2056 10977 2.282110 CGGTGGTGCCATGTCCAA 60.282 61.111 0.00 0.00 36.97 3.53
2060 10981 2.672996 GAAGCGGTGGTGCCATGT 60.673 61.111 0.00 0.00 36.97 3.21
2061 10982 1.597797 ATTGAAGCGGTGGTGCCATG 61.598 55.000 0.00 0.00 36.97 3.66
2062 10983 0.899717 AATTGAAGCGGTGGTGCCAT 60.900 50.000 0.00 0.00 36.97 4.40
2063 10984 0.250945 TAATTGAAGCGGTGGTGCCA 60.251 50.000 0.00 0.00 36.97 4.92
2064 10985 0.451783 CTAATTGAAGCGGTGGTGCC 59.548 55.000 0.00 0.00 34.65 5.01
2065 10986 1.448985 TCTAATTGAAGCGGTGGTGC 58.551 50.000 0.00 0.00 0.00 5.01
2066 10987 3.689161 TGAATCTAATTGAAGCGGTGGTG 59.311 43.478 0.00 0.00 0.00 4.17
2067 10988 3.950397 TGAATCTAATTGAAGCGGTGGT 58.050 40.909 0.00 0.00 0.00 4.16
2068 10989 4.963276 TTGAATCTAATTGAAGCGGTGG 57.037 40.909 0.00 0.00 0.00 4.61
2069 10990 9.520204 AAATTATTGAATCTAATTGAAGCGGTG 57.480 29.630 0.00 0.00 31.03 4.94
2151 11073 5.659079 AGACAGAGGGAGTCGATAAAGAAAT 59.341 40.000 0.00 0.00 40.84 2.17
2162 11217 0.533032 CGGGAAAGACAGAGGGAGTC 59.467 60.000 0.00 0.00 36.26 3.36
2244 11299 8.919145 ACACAACTCTAATTAGCTAGCTCTTAT 58.081 33.333 23.26 10.69 0.00 1.73
2249 11304 7.176589 AGAACACAACTCTAATTAGCTAGCT 57.823 36.000 23.12 23.12 0.00 3.32
2331 11889 6.987386 AGATCTAACTATCGATTGTCCTTGG 58.013 40.000 12.86 0.63 0.00 3.61
2381 12110 2.569059 TCGGACGAAGGGAGTATGTAG 58.431 52.381 0.00 0.00 0.00 2.74
2394 12123 1.223187 GGACAAGCTTTTTCGGACGA 58.777 50.000 0.00 0.00 0.00 4.20
2408 12137 9.826959 TCCATTTGAGGAATAAGCTTGGGACAA 62.827 40.741 9.86 5.50 38.10 3.18
2411 12140 4.017591 TCCATTTGAGGAATAAGCTTGGGA 60.018 41.667 9.86 0.00 33.93 4.37
2415 12144 8.223330 AGATACATCCATTTGAGGAATAAGCTT 58.777 33.333 3.48 3.48 41.92 3.74
2418 12147 9.160496 GCTAGATACATCCATTTGAGGAATAAG 57.840 37.037 0.00 0.00 41.92 1.73
2419 12148 8.659527 TGCTAGATACATCCATTTGAGGAATAA 58.340 33.333 0.00 0.00 41.92 1.40
2420 12149 8.097038 GTGCTAGATACATCCATTTGAGGAATA 58.903 37.037 0.00 0.00 41.92 1.75
2423 12152 5.604231 AGTGCTAGATACATCCATTTGAGGA 59.396 40.000 0.00 0.00 43.01 3.71
2425 12154 8.147058 AGTTAGTGCTAGATACATCCATTTGAG 58.853 37.037 0.00 0.00 0.00 3.02
2428 12157 7.716998 CCAAGTTAGTGCTAGATACATCCATTT 59.283 37.037 0.00 0.00 0.00 2.32
2429 12158 7.147479 ACCAAGTTAGTGCTAGATACATCCATT 60.147 37.037 0.00 0.00 0.00 3.16
2430 12159 6.327626 ACCAAGTTAGTGCTAGATACATCCAT 59.672 38.462 0.00 0.00 0.00 3.41
2431 12160 5.661312 ACCAAGTTAGTGCTAGATACATCCA 59.339 40.000 0.00 0.00 0.00 3.41
2432 12161 5.986135 CACCAAGTTAGTGCTAGATACATCC 59.014 44.000 0.00 0.00 0.00 3.51
2444 12173 7.041721 TGAATGTATCTAGCACCAAGTTAGTG 58.958 38.462 0.00 0.00 38.30 2.74
2445 12174 7.182817 TGAATGTATCTAGCACCAAGTTAGT 57.817 36.000 0.00 0.00 33.25 2.24
2447 12176 8.892723 CAAATGAATGTATCTAGCACCAAGTTA 58.107 33.333 0.00 0.00 0.00 2.24
2448 12177 7.611467 TCAAATGAATGTATCTAGCACCAAGTT 59.389 33.333 0.00 0.00 0.00 2.66
2449 12178 7.112122 TCAAATGAATGTATCTAGCACCAAGT 58.888 34.615 0.00 0.00 0.00 3.16
2451 12180 6.543465 CCTCAAATGAATGTATCTAGCACCAA 59.457 38.462 0.00 0.00 0.00 3.67
2452 12181 6.057533 CCTCAAATGAATGTATCTAGCACCA 58.942 40.000 0.00 0.00 0.00 4.17
2453 12182 5.471456 CCCTCAAATGAATGTATCTAGCACC 59.529 44.000 0.00 0.00 0.00 5.01
2454 12183 6.203723 GTCCCTCAAATGAATGTATCTAGCAC 59.796 42.308 0.00 0.00 0.00 4.40
2455 12184 6.126796 TGTCCCTCAAATGAATGTATCTAGCA 60.127 38.462 0.00 0.00 0.00 3.49
2456 12185 6.291377 TGTCCCTCAAATGAATGTATCTAGC 58.709 40.000 0.00 0.00 0.00 3.42
2457 12186 7.989741 ACTTGTCCCTCAAATGAATGTATCTAG 59.010 37.037 0.00 0.00 35.48 2.43
2463 13274 6.484364 AAAACTTGTCCCTCAAATGAATGT 57.516 33.333 0.00 0.00 35.48 2.71
2466 13277 5.451242 CGGAAAAACTTGTCCCTCAAATGAA 60.451 40.000 0.00 0.00 35.48 2.57
2473 13284 1.878088 GTCCGGAAAAACTTGTCCCTC 59.122 52.381 5.23 0.00 0.00 4.30
2474 13285 1.812708 CGTCCGGAAAAACTTGTCCCT 60.813 52.381 5.23 0.00 0.00 4.20
2475 13286 0.589708 CGTCCGGAAAAACTTGTCCC 59.410 55.000 5.23 0.00 0.00 4.46
2476 13287 0.589708 CCGTCCGGAAAAACTTGTCC 59.410 55.000 5.23 0.00 37.50 4.02
2477 13288 1.529865 CTCCGTCCGGAAAAACTTGTC 59.470 52.381 5.23 0.00 44.66 3.18
2478 13289 1.589803 CTCCGTCCGGAAAAACTTGT 58.410 50.000 5.23 0.00 44.66 3.16
2479 13290 0.872388 CCTCCGTCCGGAAAAACTTG 59.128 55.000 5.23 0.00 44.66 3.16
2480 13291 0.250597 CCCTCCGTCCGGAAAAACTT 60.251 55.000 5.23 0.00 44.66 2.66
2482 13293 0.672711 CTCCCTCCGTCCGGAAAAAC 60.673 60.000 5.23 0.00 44.66 2.43
2483 13294 1.123246 ACTCCCTCCGTCCGGAAAAA 61.123 55.000 5.23 0.00 44.66 1.94
2484 13295 0.251742 TACTCCCTCCGTCCGGAAAA 60.252 55.000 5.23 0.00 44.66 2.29
2485 13296 0.032813 ATACTCCCTCCGTCCGGAAA 60.033 55.000 5.23 0.00 44.66 3.13
2486 13297 0.754217 CATACTCCCTCCGTCCGGAA 60.754 60.000 5.23 0.00 44.66 4.30
2489 13300 0.750546 TCACATACTCCCTCCGTCCG 60.751 60.000 0.00 0.00 0.00 4.79
2553 13433 9.619316 CAAACACCATTTTCTTCGTTATTCATA 57.381 29.630 0.00 0.00 0.00 2.15
2588 13468 9.762933 GAAAATTCTGACTCTAGCATCTTATCT 57.237 33.333 0.00 0.00 0.00 1.98
2611 14337 1.076513 GGCCCCCTTTGTCCTTAGAAA 59.923 52.381 0.00 0.00 0.00 2.52
2615 14342 1.539372 TCGGCCCCCTTTGTCCTTA 60.539 57.895 0.00 0.00 0.00 2.69
2800 14919 2.030893 GCAATAGCAATAATCCGCAGCA 60.031 45.455 0.00 0.00 41.58 4.41
2945 15071 6.033831 ACAAATATACAACGTTAAGGTCGACG 59.966 38.462 9.92 0.00 44.34 5.12
3271 16463 4.980573 AGATTGGGCTACTGTAAACAACA 58.019 39.130 0.00 0.00 36.42 3.33
3630 16845 3.042871 TCCATTTCAGTGCATTTTGGC 57.957 42.857 0.00 0.00 0.00 4.52
3662 16913 7.028361 TGTACAACGTCACATATCGAATACAA 58.972 34.615 0.00 0.00 0.00 2.41
3669 16920 3.734231 GGGATGTACAACGTCACATATCG 59.266 47.826 0.00 0.00 37.48 2.92
3679 16946 6.737254 AGACTAATTTTGGGATGTACAACG 57.263 37.500 0.00 0.00 0.00 4.10
3686 16956 5.069516 CCATGGGAAGACTAATTTTGGGATG 59.930 44.000 2.85 0.00 0.00 3.51
3696 16966 2.204463 TGCCATCCATGGGAAGACTAA 58.796 47.619 13.02 0.00 45.79 2.24
3697 16967 1.891933 TGCCATCCATGGGAAGACTA 58.108 50.000 13.02 0.00 45.79 2.59
3698 16968 2.713967 TGCCATCCATGGGAAGACT 58.286 52.632 13.02 0.00 45.79 3.24
4043 17316 2.284190 GCCCAGTAGAGAGTGCATTTC 58.716 52.381 0.00 0.00 0.00 2.17
4058 17331 0.107703 TTCGGCTAACATCTGCCCAG 60.108 55.000 0.00 0.00 45.90 4.45
4061 17334 3.153024 TGTTCGGCTAACATCTGCC 57.847 52.632 0.00 0.00 43.22 4.85
4160 17433 0.659427 CCCTGTGTATGATGCGCAAG 59.341 55.000 17.11 3.95 43.44 4.01
4266 17539 4.566488 CCTCTTTGTGCTCCCTTGAGTATT 60.566 45.833 0.00 0.00 40.95 1.89
4277 17550 0.890996 CCACCACCCTCTTTGTGCTC 60.891 60.000 0.00 0.00 32.30 4.26
4340 17613 7.153985 TCAAATTTTAAAGGTTGATCAGCTGG 58.846 34.615 15.13 0.00 31.79 4.85
4643 17938 4.044571 TCAAAACATCTTCCTCCTTCCCAT 59.955 41.667 0.00 0.00 0.00 4.00
4862 18157 8.423906 AGTCATTATTACCCGATTCATCTACT 57.576 34.615 0.00 0.00 0.00 2.57
4887 18197 5.058149 TCGTTATTACTGCAGACGGTTAA 57.942 39.130 23.35 8.52 36.55 2.01
4910 18220 1.134371 GGCTCCTCAGTGATGGTTACC 60.134 57.143 0.00 0.00 0.00 2.85


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

AutoCloner maintained by Alex Coulton.