Multiple sequence alignment - TraesCS3D01G417600

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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 TraesCS3D01G417600 chr3D 100.000 3080 0 0 1 3080 529497504 529494425 0.000000e+00 5688
1 TraesCS3D01G417600 chr3D 89.399 1198 91 7 905 2099 529503848 529502684 0.000000e+00 1476
2 TraesCS3D01G417600 chr3D 87.597 129 14 2 2341 2469 498263820 498263694 6.880000e-32 148
3 TraesCS3D01G417600 chr3D 79.235 183 25 11 11 191 346057451 346057280 6.980000e-22 115
4 TraesCS3D01G417600 chr3A 94.829 1779 77 11 354 2123 663442456 663440684 0.000000e+00 2761
5 TraesCS3D01G417600 chr3A 90.218 1329 115 12 823 2143 663452127 663450806 0.000000e+00 1720
6 TraesCS3D01G417600 chr3A 89.857 838 58 9 1 830 663456536 663455718 0.000000e+00 1051
7 TraesCS3D01G417600 chr3A 91.346 208 18 0 153 360 663442850 663442643 5.030000e-73 285
8 TraesCS3D01G417600 chr3A 94.479 163 5 4 1 163 663444226 663444068 6.600000e-62 248
9 TraesCS3D01G417600 chr3A 89.076 119 6 1 2154 2265 663440460 663440342 1.150000e-29 141
10 TraesCS3D01G417600 chr3B 93.289 1520 83 9 708 2214 700073626 700072113 0.000000e+00 2224
11 TraesCS3D01G417600 chr3B 86.809 1501 139 29 855 2341 700234692 700236147 0.000000e+00 1620
12 TraesCS3D01G417600 chr3B 85.075 737 54 21 1 711 700074492 700073786 0.000000e+00 701
13 TraesCS3D01G417600 chr3B 80.874 183 22 10 11 191 803188767 803188596 6.930000e-27 132
14 TraesCS3D01G417600 chr7D 84.192 1126 165 10 972 2090 624769085 624770204 0.000000e+00 1081
15 TraesCS3D01G417600 chr7D 81.967 1098 165 20 1014 2082 48824893 48823800 0.000000e+00 900
16 TraesCS3D01G417600 chr7D 91.743 109 9 0 2361 2469 43386931 43386823 5.320000e-33 152
17 TraesCS3D01G417600 chr7D 79.235 183 25 11 11 191 460794883 460794712 6.980000e-22 115
18 TraesCS3D01G417600 chr7D 79.235 183 25 11 11 191 530757358 530757187 6.980000e-22 115
19 TraesCS3D01G417600 chr4A 83.688 1128 162 12 972 2081 604105237 604104114 0.000000e+00 1044
20 TraesCS3D01G417600 chr4A 92.480 625 31 7 2471 3080 618129370 618129993 0.000000e+00 880
21 TraesCS3D01G417600 chr5B 83.159 1146 166 16 973 2095 710608479 710609620 0.000000e+00 1022
22 TraesCS3D01G417600 chr5B 81.636 1100 146 30 1014 2085 711858984 711857913 0.000000e+00 861
23 TraesCS3D01G417600 chr5D 95.417 611 27 1 2471 3080 393901177 393901787 0.000000e+00 972
24 TraesCS3D01G417600 chr5D 92.097 620 38 2 2471 3080 364248560 364249178 0.000000e+00 863
25 TraesCS3D01G417600 chr5D 90.484 641 30 12 2471 3080 386212435 386211795 0.000000e+00 817
26 TraesCS3D01G417600 chr5D 76.605 966 176 35 1014 1963 558956975 558956044 1.280000e-133 486
27 TraesCS3D01G417600 chr2D 82.625 1082 151 20 1028 2089 13770230 13771294 0.000000e+00 922
28 TraesCS3D01G417600 chr2D 92.647 612 35 1 2479 3080 563305772 563305161 0.000000e+00 872
29 TraesCS3D01G417600 chr2D 92.105 114 6 3 2351 2462 480163331 480163219 1.140000e-34 158
30 TraesCS3D01G417600 chr2A 93.126 611 38 3 2471 3080 744276682 744277289 0.000000e+00 893
31 TraesCS3D01G417600 chr1D 92.545 617 35 2 2474 3080 475209239 475208624 0.000000e+00 874
32 TraesCS3D01G417600 chr1D 92.917 593 30 4 2498 3080 17121714 17122304 0.000000e+00 852
33 TraesCS3D01G417600 chr1D 89.831 354 15 6 2471 2804 99675867 99676219 4.720000e-118 435
34 TraesCS3D01G417600 chr1D 91.589 107 9 0 2356 2462 96949797 96949691 6.880000e-32 148
35 TraesCS3D01G417600 chr6D 91.774 620 39 8 2471 3080 77706887 77706270 0.000000e+00 852
36 TraesCS3D01G417600 chr6D 79.275 193 25 12 1 191 2162189 2162368 1.500000e-23 121
37 TraesCS3D01G417600 chr6A 91.774 620 31 5 2471 3080 22062914 22063523 0.000000e+00 845
38 TraesCS3D01G417600 chr6A 90.000 110 11 0 2360 2469 48520204 48520095 3.200000e-30 143
39 TraesCS3D01G417600 chr7A 91.883 579 37 3 2512 3080 470793908 470793330 0.000000e+00 800
40 TraesCS3D01G417600 chr7A 91.743 109 9 0 2355 2463 580506696 580506804 5.320000e-33 152
41 TraesCS3D01G417600 chr1B 90.300 567 43 3 2478 3034 431035056 431035620 0.000000e+00 732
42 TraesCS3D01G417600 chr7B 88.152 633 43 11 2479 3080 334803159 334803790 0.000000e+00 725
43 TraesCS3D01G417600 chr7B 93.269 104 6 1 2360 2462 663743411 663743514 5.320000e-33 152
44 TraesCS3D01G417600 chr4B 77.498 1071 168 39 1029 2049 3784899 3785946 2.660000e-160 575
45 TraesCS3D01G417600 chr4D 79.470 755 119 22 1016 1752 3260776 3260040 1.270000e-138 503
46 TraesCS3D01G417600 chr4D 80.144 277 43 6 1783 2050 3259970 3259697 2.420000e-46 196
47 TraesCS3D01G417600 chr6B 86.506 415 25 12 2478 2861 715319464 715319050 7.890000e-116 427
48 TraesCS3D01G417600 chr6B 81.281 203 28 6 1551 1752 187212916 187212723 4.110000e-34 156
49 TraesCS3D01G417600 chr6B 77.434 226 39 7 1789 2005 187212716 187212494 1.160000e-24 124
50 TraesCS3D01G417600 chr5A 93.137 102 7 0 2361 2462 467400017 467400118 1.910000e-32 150
51 TraesCS3D01G417600 chr5A 92.453 106 7 1 2357 2462 671866755 671866651 1.910000e-32 150


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 TraesCS3D01G417600 chr3D 529494425 529497504 3079 True 5688.00 5688 100.0000 1 3080 1 chr3D.!!$R3 3079
1 TraesCS3D01G417600 chr3D 529502684 529503848 1164 True 1476.00 1476 89.3990 905 2099 1 chr3D.!!$R4 1194
2 TraesCS3D01G417600 chr3A 663450806 663456536 5730 True 1385.50 1720 90.0375 1 2143 2 chr3A.!!$R2 2142
3 TraesCS3D01G417600 chr3A 663440342 663444226 3884 True 858.75 2761 92.4325 1 2265 4 chr3A.!!$R1 2264
4 TraesCS3D01G417600 chr3B 700234692 700236147 1455 False 1620.00 1620 86.8090 855 2341 1 chr3B.!!$F1 1486
5 TraesCS3D01G417600 chr3B 700072113 700074492 2379 True 1462.50 2224 89.1820 1 2214 2 chr3B.!!$R2 2213
6 TraesCS3D01G417600 chr7D 624769085 624770204 1119 False 1081.00 1081 84.1920 972 2090 1 chr7D.!!$F1 1118
7 TraesCS3D01G417600 chr7D 48823800 48824893 1093 True 900.00 900 81.9670 1014 2082 1 chr7D.!!$R2 1068
8 TraesCS3D01G417600 chr4A 604104114 604105237 1123 True 1044.00 1044 83.6880 972 2081 1 chr4A.!!$R1 1109
9 TraesCS3D01G417600 chr4A 618129370 618129993 623 False 880.00 880 92.4800 2471 3080 1 chr4A.!!$F1 609
10 TraesCS3D01G417600 chr5B 710608479 710609620 1141 False 1022.00 1022 83.1590 973 2095 1 chr5B.!!$F1 1122
11 TraesCS3D01G417600 chr5B 711857913 711858984 1071 True 861.00 861 81.6360 1014 2085 1 chr5B.!!$R1 1071
12 TraesCS3D01G417600 chr5D 393901177 393901787 610 False 972.00 972 95.4170 2471 3080 1 chr5D.!!$F2 609
13 TraesCS3D01G417600 chr5D 364248560 364249178 618 False 863.00 863 92.0970 2471 3080 1 chr5D.!!$F1 609
14 TraesCS3D01G417600 chr5D 386211795 386212435 640 True 817.00 817 90.4840 2471 3080 1 chr5D.!!$R1 609
15 TraesCS3D01G417600 chr5D 558956044 558956975 931 True 486.00 486 76.6050 1014 1963 1 chr5D.!!$R2 949
16 TraesCS3D01G417600 chr2D 13770230 13771294 1064 False 922.00 922 82.6250 1028 2089 1 chr2D.!!$F1 1061
17 TraesCS3D01G417600 chr2D 563305161 563305772 611 True 872.00 872 92.6470 2479 3080 1 chr2D.!!$R2 601
18 TraesCS3D01G417600 chr2A 744276682 744277289 607 False 893.00 893 93.1260 2471 3080 1 chr2A.!!$F1 609
19 TraesCS3D01G417600 chr1D 475208624 475209239 615 True 874.00 874 92.5450 2474 3080 1 chr1D.!!$R2 606
20 TraesCS3D01G417600 chr1D 17121714 17122304 590 False 852.00 852 92.9170 2498 3080 1 chr1D.!!$F1 582
21 TraesCS3D01G417600 chr6D 77706270 77706887 617 True 852.00 852 91.7740 2471 3080 1 chr6D.!!$R1 609
22 TraesCS3D01G417600 chr6A 22062914 22063523 609 False 845.00 845 91.7740 2471 3080 1 chr6A.!!$F1 609
23 TraesCS3D01G417600 chr7A 470793330 470793908 578 True 800.00 800 91.8830 2512 3080 1 chr7A.!!$R1 568
24 TraesCS3D01G417600 chr1B 431035056 431035620 564 False 732.00 732 90.3000 2478 3034 1 chr1B.!!$F1 556
25 TraesCS3D01G417600 chr7B 334803159 334803790 631 False 725.00 725 88.1520 2479 3080 1 chr7B.!!$F1 601
26 TraesCS3D01G417600 chr4B 3784899 3785946 1047 False 575.00 575 77.4980 1029 2049 1 chr4B.!!$F1 1020
27 TraesCS3D01G417600 chr4D 3259697 3260776 1079 True 349.50 503 79.8070 1016 2050 2 chr4D.!!$R1 1034

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
533 1961 1.662517 TGTGCGCAGAGAAGAAAACA 58.337 45.0 12.22 0.0 0.0 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2462 8054 0.607217 GGTTTCCCCCGTCACGAAAT 60.607 55.0 0.0 0.0 0.0 2.17 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
112 113 7.400599 TCTTTTGATGAAGCTAGCATTGATT 57.599 32.000 18.83 0.95 0.00 2.57
218 1447 6.061441 AGCCGATGATTCCATGTATTGTTAA 58.939 36.000 0.00 0.00 32.09 2.01
288 1522 6.809689 CGACGCTGGGTACATATCAAAATATA 59.190 38.462 0.00 0.00 0.00 0.86
311 1545 6.349973 ACATGATCACAAATAGTTGCTACG 57.650 37.500 2.17 0.00 38.39 3.51
533 1961 1.662517 TGTGCGCAGAGAAGAAAACA 58.337 45.000 12.22 0.00 0.00 2.83
543 1971 5.103000 CAGAGAAGAAAACACCGACGATAT 58.897 41.667 0.00 0.00 0.00 1.63
610 2039 8.786898 CCTTACCATATTTTAGTCATGACCATG 58.213 37.037 22.21 14.34 40.09 3.66
830 6045 4.819630 GTGTTCCACAATCCACAAGAGTTA 59.180 41.667 0.00 0.00 34.08 2.24
841 6056 6.445357 TCCACAAGAGTTAGTTTGGTTTTC 57.555 37.500 0.00 0.00 0.00 2.29
929 6145 4.219944 TCAGTAAAGAGCCACGACTACATT 59.780 41.667 0.00 0.00 0.00 2.71
963 6194 5.853282 CACAAACTGAATTCAAAGGATCGAC 59.147 40.000 9.88 0.00 0.00 4.20
964 6195 5.765182 ACAAACTGAATTCAAAGGATCGACT 59.235 36.000 9.88 0.00 0.00 4.18
965 6196 6.073003 ACAAACTGAATTCAAAGGATCGACTC 60.073 38.462 9.88 0.00 0.00 3.36
966 6197 5.152623 ACTGAATTCAAAGGATCGACTCA 57.847 39.130 9.88 0.00 0.00 3.41
967 6198 5.738909 ACTGAATTCAAAGGATCGACTCAT 58.261 37.500 9.88 0.00 0.00 2.90
968 6199 5.814705 ACTGAATTCAAAGGATCGACTCATC 59.185 40.000 9.88 0.00 0.00 2.92
1009 6242 0.186630 CCAATCATCCATGGCCTCCA 59.813 55.000 6.96 0.00 38.19 3.86
1331 6612 0.807667 CTGCGGAACTTCATCGAGGG 60.808 60.000 0.00 0.00 0.00 4.30
1519 6803 1.078143 GCAATCGCCCCAGAGTTCT 60.078 57.895 0.00 0.00 0.00 3.01
1701 7009 4.003788 ACCAAGCACTCCGACCCG 62.004 66.667 0.00 0.00 0.00 5.28
2218 7803 1.492599 TCCCAATGGCGATATTGTGGA 59.507 47.619 0.00 13.24 36.54 4.02
2221 7806 3.057315 CCCAATGGCGATATTGTGGATTC 60.057 47.826 0.00 0.00 36.54 2.52
2222 7807 3.569277 CCAATGGCGATATTGTGGATTCA 59.431 43.478 10.04 0.00 36.54 2.57
2224 7809 3.558931 TGGCGATATTGTGGATTCAGT 57.441 42.857 0.00 0.00 0.00 3.41
2225 7810 3.205338 TGGCGATATTGTGGATTCAGTG 58.795 45.455 0.00 0.00 0.00 3.66
2259 7851 7.001073 AGATAAGATTTAATTCCCTGAGGTGC 58.999 38.462 0.00 0.00 0.00 5.01
2265 7857 5.514500 TTAATTCCCTGAGGTGCTAACTT 57.486 39.130 0.00 0.00 0.00 2.66
2266 7858 6.630203 TTAATTCCCTGAGGTGCTAACTTA 57.370 37.500 0.00 0.00 0.00 2.24
2267 7859 3.975168 TTCCCTGAGGTGCTAACTTAC 57.025 47.619 0.00 0.00 0.00 2.34
2268 7860 2.897350 TCCCTGAGGTGCTAACTTACA 58.103 47.619 0.00 0.00 0.00 2.41
2269 7861 2.832129 TCCCTGAGGTGCTAACTTACAG 59.168 50.000 0.00 0.00 0.00 2.74
2270 7862 2.567615 CCCTGAGGTGCTAACTTACAGT 59.432 50.000 0.00 0.00 0.00 3.55
2271 7863 3.008049 CCCTGAGGTGCTAACTTACAGTT 59.992 47.826 0.00 0.00 41.97 3.16
2272 7864 4.222145 CCCTGAGGTGCTAACTTACAGTTA 59.778 45.833 0.00 0.00 39.51 2.24
2273 7865 5.169295 CCTGAGGTGCTAACTTACAGTTAC 58.831 45.833 0.00 0.00 39.51 2.50
2274 7866 5.279306 CCTGAGGTGCTAACTTACAGTTACA 60.279 44.000 0.00 0.00 39.51 2.41
2275 7867 5.779922 TGAGGTGCTAACTTACAGTTACAG 58.220 41.667 0.00 0.00 39.51 2.74
2279 7871 6.071503 AGGTGCTAACTTACAGTTACAGGTAG 60.072 42.308 0.00 0.00 39.51 3.18
2289 7881 9.886132 CTTACAGTTACAGGTAGGAAAACATAT 57.114 33.333 0.00 0.00 0.00 1.78
2290 7882 9.661563 TTACAGTTACAGGTAGGAAAACATATG 57.338 33.333 0.00 0.00 0.00 1.78
2291 7883 6.598064 ACAGTTACAGGTAGGAAAACATATGC 59.402 38.462 1.58 0.00 0.00 3.14
2297 7889 7.346471 ACAGGTAGGAAAACATATGCTAACAT 58.654 34.615 1.58 0.00 40.49 2.71
2303 7895 7.765307 AGGAAAACATATGCTAACATGAACTG 58.235 34.615 1.58 0.00 37.04 3.16
2305 7897 7.148086 GGAAAACATATGCTAACATGAACTGGA 60.148 37.037 1.58 0.00 37.04 3.86
2311 7903 5.627499 TGCTAACATGAACTGGAAATCAC 57.373 39.130 0.00 0.00 0.00 3.06
2312 7904 5.069318 TGCTAACATGAACTGGAAATCACA 58.931 37.500 0.00 0.00 0.00 3.58
2313 7905 5.181811 TGCTAACATGAACTGGAAATCACAG 59.818 40.000 0.00 0.00 41.64 3.66
2314 7906 5.412594 GCTAACATGAACTGGAAATCACAGA 59.587 40.000 0.00 0.00 39.24 3.41
2315 7907 5.954296 AACATGAACTGGAAATCACAGAG 57.046 39.130 0.00 0.00 39.24 3.35
2316 7908 3.755378 ACATGAACTGGAAATCACAGAGC 59.245 43.478 0.00 0.00 39.24 4.09
2317 7909 3.490439 TGAACTGGAAATCACAGAGCA 57.510 42.857 0.00 0.00 39.24 4.26
2318 7910 3.405831 TGAACTGGAAATCACAGAGCAG 58.594 45.455 0.00 0.00 39.24 4.24
2320 7912 1.093159 CTGGAAATCACAGAGCAGGC 58.907 55.000 0.00 0.00 38.20 4.85
2321 7913 0.401356 TGGAAATCACAGAGCAGGCA 59.599 50.000 0.00 0.00 0.00 4.75
2322 7914 1.005097 TGGAAATCACAGAGCAGGCAT 59.995 47.619 0.00 0.00 0.00 4.40
2341 7933 4.273318 GCATCTCCTACAAATTGAAGGGT 58.727 43.478 0.00 0.00 0.00 4.34
2342 7934 5.437060 GCATCTCCTACAAATTGAAGGGTA 58.563 41.667 0.00 0.00 0.00 3.69
2343 7935 5.885912 GCATCTCCTACAAATTGAAGGGTAA 59.114 40.000 0.00 0.00 0.00 2.85
2344 7936 6.038714 GCATCTCCTACAAATTGAAGGGTAAG 59.961 42.308 0.00 0.00 0.00 2.34
2345 7937 6.697641 TCTCCTACAAATTGAAGGGTAAGT 57.302 37.500 0.00 0.00 0.00 2.24
2346 7938 7.086685 TCTCCTACAAATTGAAGGGTAAGTT 57.913 36.000 0.00 0.00 0.00 2.66
2347 7939 8.209802 TCTCCTACAAATTGAAGGGTAAGTTA 57.790 34.615 0.00 0.00 0.00 2.24
2348 7940 8.832735 TCTCCTACAAATTGAAGGGTAAGTTAT 58.167 33.333 0.00 0.00 0.00 1.89
2349 7941 9.462606 CTCCTACAAATTGAAGGGTAAGTTATT 57.537 33.333 0.00 0.00 0.00 1.40
2350 7942 9.457436 TCCTACAAATTGAAGGGTAAGTTATTC 57.543 33.333 0.00 0.00 0.00 1.75
2351 7943 9.238368 CCTACAAATTGAAGGGTAAGTTATTCA 57.762 33.333 0.00 0.00 0.00 2.57
2370 7962 8.936864 GTTATTCATAATTTCATACTCCCTCCG 58.063 37.037 0.00 0.00 0.00 4.63
2371 7963 6.494666 TTCATAATTTCATACTCCCTCCGT 57.505 37.500 0.00 0.00 0.00 4.69
2372 7964 6.494666 TCATAATTTCATACTCCCTCCGTT 57.505 37.500 0.00 0.00 0.00 4.44
2373 7965 6.522054 TCATAATTTCATACTCCCTCCGTTC 58.478 40.000 0.00 0.00 0.00 3.95
2374 7966 3.840124 ATTTCATACTCCCTCCGTTCC 57.160 47.619 0.00 0.00 0.00 3.62
2375 7967 2.544844 TTCATACTCCCTCCGTTCCT 57.455 50.000 0.00 0.00 0.00 3.36
2376 7968 3.675348 TTCATACTCCCTCCGTTCCTA 57.325 47.619 0.00 0.00 0.00 2.94
2377 7969 3.675348 TCATACTCCCTCCGTTCCTAA 57.325 47.619 0.00 0.00 0.00 2.69
2378 7970 3.985127 TCATACTCCCTCCGTTCCTAAA 58.015 45.455 0.00 0.00 0.00 1.85
2379 7971 4.553678 TCATACTCCCTCCGTTCCTAAAT 58.446 43.478 0.00 0.00 0.00 1.40
2380 7972 5.708544 TCATACTCCCTCCGTTCCTAAATA 58.291 41.667 0.00 0.00 0.00 1.40
2381 7973 6.320518 TCATACTCCCTCCGTTCCTAAATAT 58.679 40.000 0.00 0.00 0.00 1.28
2382 7974 7.472741 TCATACTCCCTCCGTTCCTAAATATA 58.527 38.462 0.00 0.00 0.00 0.86
2383 7975 7.951806 TCATACTCCCTCCGTTCCTAAATATAA 59.048 37.037 0.00 0.00 0.00 0.98
2384 7976 6.667558 ACTCCCTCCGTTCCTAAATATAAG 57.332 41.667 0.00 0.00 0.00 1.73
2385 7977 6.141790 ACTCCCTCCGTTCCTAAATATAAGT 58.858 40.000 0.00 0.00 0.00 2.24
2386 7978 6.267242 ACTCCCTCCGTTCCTAAATATAAGTC 59.733 42.308 0.00 0.00 0.00 3.01
2387 7979 6.379579 TCCCTCCGTTCCTAAATATAAGTCT 58.620 40.000 0.00 0.00 0.00 3.24
2388 7980 6.267014 TCCCTCCGTTCCTAAATATAAGTCTG 59.733 42.308 0.00 0.00 0.00 3.51
2389 7981 6.041751 CCCTCCGTTCCTAAATATAAGTCTGT 59.958 42.308 0.00 0.00 0.00 3.41
2390 7982 7.418712 CCCTCCGTTCCTAAATATAAGTCTGTT 60.419 40.741 0.00 0.00 0.00 3.16
2391 7983 7.985752 CCTCCGTTCCTAAATATAAGTCTGTTT 59.014 37.037 0.00 0.00 0.00 2.83
2408 8000 8.410673 AGTCTGTTTAGAGATTTCACTGTAGA 57.589 34.615 0.00 0.00 32.48 2.59
2409 8001 8.519526 AGTCTGTTTAGAGATTTCACTGTAGAG 58.480 37.037 0.00 0.00 32.48 2.43
2410 8002 8.516234 GTCTGTTTAGAGATTTCACTGTAGAGA 58.484 37.037 0.00 0.00 32.48 3.10
2411 8003 8.516234 TCTGTTTAGAGATTTCACTGTAGAGAC 58.484 37.037 0.00 0.00 0.00 3.36
2412 8004 8.410673 TGTTTAGAGATTTCACTGTAGAGACT 57.589 34.615 0.00 0.00 0.00 3.24
2413 8005 9.516546 TGTTTAGAGATTTCACTGTAGAGACTA 57.483 33.333 0.00 0.00 0.00 2.59
2414 8006 9.777575 GTTTAGAGATTTCACTGTAGAGACTAC 57.222 37.037 0.00 0.00 0.00 2.73
2415 8007 9.516546 TTTAGAGATTTCACTGTAGAGACTACA 57.483 33.333 10.49 10.49 0.00 2.74
2416 8008 9.688091 TTAGAGATTTCACTGTAGAGACTACAT 57.312 33.333 11.21 0.00 0.00 2.29
2417 8009 8.588290 AGAGATTTCACTGTAGAGACTACATT 57.412 34.615 11.21 4.43 0.00 2.71
2418 8010 9.030452 AGAGATTTCACTGTAGAGACTACATTT 57.970 33.333 11.21 1.08 0.00 2.32
2419 8011 8.994429 AGATTTCACTGTAGAGACTACATTTG 57.006 34.615 11.21 11.25 0.00 2.32
2420 8012 8.037758 AGATTTCACTGTAGAGACTACATTTGG 58.962 37.037 11.21 3.96 0.00 3.28
2421 8013 6.911250 TTCACTGTAGAGACTACATTTGGA 57.089 37.500 11.21 5.26 0.00 3.53
2422 8014 7.482169 TTCACTGTAGAGACTACATTTGGAT 57.518 36.000 11.21 0.00 0.00 3.41
2423 8015 6.867550 TCACTGTAGAGACTACATTTGGATG 58.132 40.000 11.21 2.49 39.25 3.51
2425 8017 7.614192 TCACTGTAGAGACTACATTTGGATGTA 59.386 37.037 11.21 0.00 44.51 2.29
2426 8018 8.417106 CACTGTAGAGACTACATTTGGATGTAT 58.583 37.037 11.21 0.00 45.20 2.29
2427 8019 9.642343 ACTGTAGAGACTACATTTGGATGTATA 57.358 33.333 11.21 0.00 45.20 1.47
2775 8424 3.188786 GCGTCCTCATCGTGGCAC 61.189 66.667 7.79 7.79 0.00 5.01
2776 8425 2.573869 CGTCCTCATCGTGGCACT 59.426 61.111 16.72 0.00 0.00 4.40
2907 8556 3.668147 CCAATGGTGGTGGTCATCA 57.332 52.632 0.00 0.00 41.30 3.07
2951 8600 1.895798 GAGGCATGGTGATCGGATCTA 59.104 52.381 18.16 6.17 0.00 1.98
2965 8614 6.320926 TGATCGGATCTAGAGATTCATCATCC 59.679 42.308 18.16 0.00 34.37 3.51
2971 8620 5.963092 TCTAGAGATTCATCATCCAGTCCT 58.037 41.667 0.00 0.00 31.20 3.85
2973 8622 4.296912 AGAGATTCATCATCCAGTCCTGT 58.703 43.478 0.00 0.00 31.20 4.00
3001 8650 2.668632 GGGAGACATGGTTGCCGA 59.331 61.111 0.00 0.00 0.00 5.54
3073 8722 0.604073 TGGAGGCATCGTCGTGTAAA 59.396 50.000 0.00 0.00 0.00 2.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
238 1467 3.067742 GCTAATAGGCTGGAGTACGTCAA 59.932 47.826 0.00 0.00 0.00 3.18
239 1468 2.621998 GCTAATAGGCTGGAGTACGTCA 59.378 50.000 0.00 0.00 0.00 4.35
288 1522 6.106003 TCGTAGCAACTATTTGTGATCATGT 58.894 36.000 0.00 0.00 34.90 3.21
388 1816 4.473196 TGATGCCAGGATCTAAACCTTGTA 59.527 41.667 0.00 0.00 35.35 2.41
520 1948 2.739292 TCGTCGGTGTTTTCTTCTCTG 58.261 47.619 0.00 0.00 0.00 3.35
543 1971 1.274167 ACACGCAACCTTCTTCCGATA 59.726 47.619 0.00 0.00 0.00 2.92
559 1987 0.387202 TTTGGCCACAATCCAACACG 59.613 50.000 3.88 0.00 42.75 4.49
610 2039 5.514274 TGATCCAAACCAAGAACAAGTTC 57.486 39.130 4.82 4.82 39.78 3.01
830 6045 3.492482 CGGATTTGCTGGAAAACCAAACT 60.492 43.478 18.26 0.00 36.49 2.66
841 6056 1.202533 ACGTCTATCCGGATTTGCTGG 60.203 52.381 24.71 10.03 45.07 4.85
929 6145 2.708216 TCAGTTTGTGGAAGTGAGCA 57.292 45.000 0.00 0.00 41.60 4.26
963 6194 1.458445 CTTGTGCAGTGTGTCGATGAG 59.542 52.381 0.00 0.00 0.00 2.90
964 6195 1.501169 CTTGTGCAGTGTGTCGATGA 58.499 50.000 0.00 0.00 0.00 2.92
965 6196 0.110509 GCTTGTGCAGTGTGTCGATG 60.111 55.000 0.00 0.00 39.41 3.84
966 6197 0.250038 AGCTTGTGCAGTGTGTCGAT 60.250 50.000 0.00 0.00 42.74 3.59
967 6198 0.387565 TAGCTTGTGCAGTGTGTCGA 59.612 50.000 0.00 0.00 42.74 4.20
968 6199 0.786581 CTAGCTTGTGCAGTGTGTCG 59.213 55.000 0.00 0.00 42.74 4.35
969 6200 0.514691 GCTAGCTTGTGCAGTGTGTC 59.485 55.000 7.70 0.00 42.74 3.67
970 6201 0.107456 AGCTAGCTTGTGCAGTGTGT 59.893 50.000 12.68 0.00 42.74 3.72
1472 6753 3.097162 GGGGGATTTCCTCGGGCT 61.097 66.667 0.00 0.00 37.38 5.19
1549 6836 2.811317 CGACAGAAGCCCGAGCAC 60.811 66.667 0.00 0.00 43.56 4.40
1603 6905 4.796231 CTCTAGGCACGCGGCGTT 62.796 66.667 27.24 14.59 46.16 4.84
1701 7009 2.378028 GAGCACGGTGATGAAGCTC 58.622 57.895 13.29 6.23 43.95 4.09
2218 7803 7.876936 ATCTTATCTGCATTTCACACTGAAT 57.123 32.000 0.00 0.00 36.11 2.57
2225 7810 9.468532 GGGAATTAAATCTTATCTGCATTTCAC 57.531 33.333 0.00 0.00 0.00 3.18
2265 7857 7.767198 GCATATGTTTTCCTACCTGTAACTGTA 59.233 37.037 4.29 0.00 0.00 2.74
2266 7858 6.598064 GCATATGTTTTCCTACCTGTAACTGT 59.402 38.462 4.29 0.00 0.00 3.55
2267 7859 6.823689 AGCATATGTTTTCCTACCTGTAACTG 59.176 38.462 4.29 0.00 0.00 3.16
2268 7860 6.958767 AGCATATGTTTTCCTACCTGTAACT 58.041 36.000 4.29 0.00 0.00 2.24
2269 7861 8.610035 GTTAGCATATGTTTTCCTACCTGTAAC 58.390 37.037 4.29 0.00 0.00 2.50
2270 7862 8.322828 TGTTAGCATATGTTTTCCTACCTGTAA 58.677 33.333 4.29 0.00 0.00 2.41
2271 7863 7.853299 TGTTAGCATATGTTTTCCTACCTGTA 58.147 34.615 4.29 0.00 0.00 2.74
2272 7864 6.717289 TGTTAGCATATGTTTTCCTACCTGT 58.283 36.000 4.29 0.00 0.00 4.00
2273 7865 7.498900 TCATGTTAGCATATGTTTTCCTACCTG 59.501 37.037 4.29 0.00 33.30 4.00
2274 7866 7.573710 TCATGTTAGCATATGTTTTCCTACCT 58.426 34.615 4.29 0.00 33.30 3.08
2275 7867 7.801716 TCATGTTAGCATATGTTTTCCTACC 57.198 36.000 4.29 0.00 33.30 3.18
2279 7871 6.974622 CCAGTTCATGTTAGCATATGTTTTCC 59.025 38.462 4.29 0.00 33.30 3.13
2289 7881 5.069318 TGTGATTTCCAGTTCATGTTAGCA 58.931 37.500 0.00 0.00 0.00 3.49
2290 7882 5.412594 TCTGTGATTTCCAGTTCATGTTAGC 59.587 40.000 0.00 0.00 0.00 3.09
2291 7883 6.402983 GCTCTGTGATTTCCAGTTCATGTTAG 60.403 42.308 0.00 0.00 0.00 2.34
2297 7889 3.405831 CTGCTCTGTGATTTCCAGTTCA 58.594 45.455 0.00 0.00 0.00 3.18
2303 7895 1.674962 GATGCCTGCTCTGTGATTTCC 59.325 52.381 0.00 0.00 0.00 3.13
2305 7897 2.641305 GAGATGCCTGCTCTGTGATTT 58.359 47.619 0.00 0.00 0.00 2.17
2318 7910 3.633986 CCCTTCAATTTGTAGGAGATGCC 59.366 47.826 20.23 0.00 37.12 4.40
2320 7912 7.112779 ACTTACCCTTCAATTTGTAGGAGATG 58.887 38.462 20.23 12.59 37.12 2.90
2321 7913 7.272144 ACTTACCCTTCAATTTGTAGGAGAT 57.728 36.000 20.23 9.93 37.12 2.75
2322 7914 6.697641 ACTTACCCTTCAATTTGTAGGAGA 57.302 37.500 20.23 7.46 37.12 3.71
2344 7936 8.936864 CGGAGGGAGTATGAAATTATGAATAAC 58.063 37.037 0.00 0.00 0.00 1.89
2345 7937 8.656806 ACGGAGGGAGTATGAAATTATGAATAA 58.343 33.333 0.00 0.00 0.00 1.40
2346 7938 8.202461 ACGGAGGGAGTATGAAATTATGAATA 57.798 34.615 0.00 0.00 0.00 1.75
2347 7939 7.079451 ACGGAGGGAGTATGAAATTATGAAT 57.921 36.000 0.00 0.00 0.00 2.57
2348 7940 6.494666 ACGGAGGGAGTATGAAATTATGAA 57.505 37.500 0.00 0.00 0.00 2.57
2349 7941 6.463897 GGAACGGAGGGAGTATGAAATTATGA 60.464 42.308 0.00 0.00 0.00 2.15
2350 7942 5.701290 GGAACGGAGGGAGTATGAAATTATG 59.299 44.000 0.00 0.00 0.00 1.90
2351 7943 5.607171 AGGAACGGAGGGAGTATGAAATTAT 59.393 40.000 0.00 0.00 0.00 1.28
2352 7944 4.966805 AGGAACGGAGGGAGTATGAAATTA 59.033 41.667 0.00 0.00 0.00 1.40
2353 7945 3.780850 AGGAACGGAGGGAGTATGAAATT 59.219 43.478 0.00 0.00 0.00 1.82
2354 7946 3.385115 AGGAACGGAGGGAGTATGAAAT 58.615 45.455 0.00 0.00 0.00 2.17
2355 7947 2.829023 AGGAACGGAGGGAGTATGAAA 58.171 47.619 0.00 0.00 0.00 2.69
2356 7948 2.544844 AGGAACGGAGGGAGTATGAA 57.455 50.000 0.00 0.00 0.00 2.57
2357 7949 3.675348 TTAGGAACGGAGGGAGTATGA 57.325 47.619 0.00 0.00 0.00 2.15
2358 7950 4.957684 ATTTAGGAACGGAGGGAGTATG 57.042 45.455 0.00 0.00 0.00 2.39
2359 7951 7.954620 ACTTATATTTAGGAACGGAGGGAGTAT 59.045 37.037 0.00 0.00 0.00 2.12
2360 7952 7.300658 ACTTATATTTAGGAACGGAGGGAGTA 58.699 38.462 0.00 0.00 0.00 2.59
2361 7953 6.141790 ACTTATATTTAGGAACGGAGGGAGT 58.858 40.000 0.00 0.00 0.00 3.85
2362 7954 6.494146 AGACTTATATTTAGGAACGGAGGGAG 59.506 42.308 0.00 0.00 0.00 4.30
2363 7955 6.267014 CAGACTTATATTTAGGAACGGAGGGA 59.733 42.308 0.00 0.00 0.00 4.20
2364 7956 6.041751 ACAGACTTATATTTAGGAACGGAGGG 59.958 42.308 0.00 0.00 0.00 4.30
2365 7957 7.052142 ACAGACTTATATTTAGGAACGGAGG 57.948 40.000 0.00 0.00 0.00 4.30
2366 7958 8.943909 AAACAGACTTATATTTAGGAACGGAG 57.056 34.615 0.00 0.00 0.00 4.63
2382 7974 8.861086 TCTACAGTGAAATCTCTAAACAGACTT 58.139 33.333 0.00 0.00 0.00 3.01
2383 7975 8.410673 TCTACAGTGAAATCTCTAAACAGACT 57.589 34.615 0.00 0.00 0.00 3.24
2384 7976 8.516234 TCTCTACAGTGAAATCTCTAAACAGAC 58.484 37.037 0.00 0.00 0.00 3.51
2385 7977 8.516234 GTCTCTACAGTGAAATCTCTAAACAGA 58.484 37.037 0.00 0.00 0.00 3.41
2386 7978 8.519526 AGTCTCTACAGTGAAATCTCTAAACAG 58.480 37.037 0.00 0.00 0.00 3.16
2387 7979 8.410673 AGTCTCTACAGTGAAATCTCTAAACA 57.589 34.615 0.00 0.00 0.00 2.83
2388 7980 9.777575 GTAGTCTCTACAGTGAAATCTCTAAAC 57.222 37.037 0.00 0.00 0.00 2.01
2389 7981 9.516546 TGTAGTCTCTACAGTGAAATCTCTAAA 57.483 33.333 0.00 0.00 0.00 1.85
2390 7982 9.688091 ATGTAGTCTCTACAGTGAAATCTCTAA 57.312 33.333 13.65 0.00 0.00 2.10
2391 7983 9.688091 AATGTAGTCTCTACAGTGAAATCTCTA 57.312 33.333 13.65 0.00 0.00 2.43
2392 7984 8.588290 AATGTAGTCTCTACAGTGAAATCTCT 57.412 34.615 13.65 0.00 0.00 3.10
2393 7985 9.081997 CAAATGTAGTCTCTACAGTGAAATCTC 57.918 37.037 13.65 0.00 0.00 2.75
2394 7986 8.037758 CCAAATGTAGTCTCTACAGTGAAATCT 58.962 37.037 17.34 0.64 0.00 2.40
2395 7987 8.035394 TCCAAATGTAGTCTCTACAGTGAAATC 58.965 37.037 17.34 0.00 0.00 2.17
2396 7988 7.907389 TCCAAATGTAGTCTCTACAGTGAAAT 58.093 34.615 17.34 1.43 0.00 2.17
2397 7989 7.297936 TCCAAATGTAGTCTCTACAGTGAAA 57.702 36.000 17.34 8.35 0.00 2.69
2398 7990 6.911250 TCCAAATGTAGTCTCTACAGTGAA 57.089 37.500 17.34 3.19 0.00 3.18
2399 7991 6.437477 ACATCCAAATGTAGTCTCTACAGTGA 59.563 38.462 17.34 10.28 44.38 3.41
2400 7992 6.634805 ACATCCAAATGTAGTCTCTACAGTG 58.365 40.000 13.65 12.98 44.38 3.66
2401 7993 6.859112 ACATCCAAATGTAGTCTCTACAGT 57.141 37.500 13.65 9.28 44.38 3.55
2446 8038 8.218441 CGTCACGAAATAAAATGAGTGAACTTA 58.782 33.333 0.00 0.00 39.80 2.24
2447 8039 7.069569 CGTCACGAAATAAAATGAGTGAACTT 58.930 34.615 0.00 0.00 39.80 2.66
2448 8040 6.347402 CCGTCACGAAATAAAATGAGTGAACT 60.347 38.462 0.00 0.00 39.80 3.01
2449 8041 5.788531 CCGTCACGAAATAAAATGAGTGAAC 59.211 40.000 0.00 0.00 39.80 3.18
2450 8042 5.106869 CCCGTCACGAAATAAAATGAGTGAA 60.107 40.000 0.00 0.00 39.80 3.18
2451 8043 4.390603 CCCGTCACGAAATAAAATGAGTGA 59.609 41.667 0.00 0.00 36.43 3.41
2452 8044 4.436852 CCCCGTCACGAAATAAAATGAGTG 60.437 45.833 0.00 0.00 0.00 3.51
2453 8045 3.687698 CCCCGTCACGAAATAAAATGAGT 59.312 43.478 0.00 0.00 0.00 3.41
2454 8046 3.064820 CCCCCGTCACGAAATAAAATGAG 59.935 47.826 0.00 0.00 0.00 2.90
2455 8047 3.011119 CCCCCGTCACGAAATAAAATGA 58.989 45.455 0.00 0.00 0.00 2.57
2456 8048 3.011119 TCCCCCGTCACGAAATAAAATG 58.989 45.455 0.00 0.00 0.00 2.32
2457 8049 3.353370 TCCCCCGTCACGAAATAAAAT 57.647 42.857 0.00 0.00 0.00 1.82
2458 8050 2.855209 TCCCCCGTCACGAAATAAAA 57.145 45.000 0.00 0.00 0.00 1.52
2459 8051 2.813172 GTTTCCCCCGTCACGAAATAAA 59.187 45.455 0.00 0.00 0.00 1.40
2460 8052 2.425539 GTTTCCCCCGTCACGAAATAA 58.574 47.619 0.00 0.00 0.00 1.40
2461 8053 1.338960 GGTTTCCCCCGTCACGAAATA 60.339 52.381 0.00 0.00 0.00 1.40
2462 8054 0.607217 GGTTTCCCCCGTCACGAAAT 60.607 55.000 0.00 0.00 0.00 2.17
2463 8055 1.227913 GGTTTCCCCCGTCACGAAA 60.228 57.895 0.00 0.00 0.00 3.46
2464 8056 2.426887 GGTTTCCCCCGTCACGAA 59.573 61.111 0.00 0.00 0.00 3.85
2465 8057 3.628982 GGGTTTCCCCCGTCACGA 61.629 66.667 0.00 0.00 45.80 4.35
2775 8424 3.741476 GAGGGCAACGGCAAGCAG 61.741 66.667 0.00 0.00 43.71 4.24
2828 8477 3.958860 GTCCTGGCCAGCACCACT 61.959 66.667 28.39 0.00 35.33 4.00
2907 8556 0.387202 CGGCCATCTCTGACGAAGAT 59.613 55.000 2.24 0.00 33.29 2.40
2936 8585 5.328565 TGAATCTCTAGATCCGATCACCAT 58.671 41.667 11.01 0.00 32.75 3.55
2951 8600 4.296912 ACAGGACTGGATGATGAATCTCT 58.703 43.478 4.14 0.00 35.43 3.10
2965 8614 0.668706 CCAACTCGCAGACAGGACTG 60.669 60.000 0.00 0.00 40.43 3.51
2971 8620 1.533033 TCTCCCCAACTCGCAGACA 60.533 57.895 0.00 0.00 0.00 3.41
2973 8622 0.904865 ATGTCTCCCCAACTCGCAGA 60.905 55.000 0.00 0.00 0.00 4.26
3001 8650 1.862602 GCCAACGGCTCGGTTTTCAT 61.863 55.000 0.00 0.00 46.69 2.57


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

AutoCloner maintained by Alex Coulton.