Multiple sequence alignment - TraesCS2D01G456700

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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 TraesCS2D01G456700 chr2D 100.000 4115 0 0 1 4115 564437424 564441538 0.000000e+00 7600
1 TraesCS2D01G456700 chr2D 94.449 2414 104 9 774 3181 564476074 564478463 0.000000e+00 3688
2 TraesCS2D01G456700 chr2D 81.312 2028 288 55 798 2804 564418499 564420456 0.000000e+00 1561
3 TraesCS2D01G456700 chr2D 88.790 1240 111 15 1890 3115 564071994 564070769 0.000000e+00 1495
4 TraesCS2D01G456700 chr2D 95.596 772 26 4 1 770 564475272 564476037 0.000000e+00 1230
5 TraesCS2D01G456700 chr2D 85.507 483 35 5 3357 3832 564478661 564479115 4.810000e-129 472
6 TraesCS2D01G456700 chr2D 93.333 90 5 1 3186 3275 564478574 564478662 9.280000e-27 132
7 TraesCS2D01G456700 chr2B 92.021 2519 175 17 774 3275 675533853 675536362 0.000000e+00 3515
8 TraesCS2D01G456700 chr2B 82.594 2344 345 45 794 3115 675524653 675526955 0.000000e+00 2010
9 TraesCS2D01G456700 chr2B 88.502 1235 121 11 1890 3115 675334063 675332841 0.000000e+00 1474
10 TraesCS2D01G456700 chr2B 94.682 771 34 3 1 770 675533052 675533816 0.000000e+00 1190
11 TraesCS2D01G456700 chr2B 89.212 482 43 4 3357 3832 675536361 675536839 9.850000e-166 593
12 TraesCS2D01G456700 chr2B 94.488 127 3 2 3846 3968 675536991 675537117 4.200000e-45 193
13 TraesCS2D01G456700 chr2B 81.604 212 35 2 325 532 675524348 675524559 5.470000e-39 172
14 TraesCS2D01G456700 chr2B 90.110 91 8 1 4026 4115 675695681 675695771 2.600000e-22 117
15 TraesCS2D01G456700 chr2A 83.812 2335 322 35 798 3115 705264438 705266733 0.000000e+00 2167
16 TraesCS2D01G456700 chr2A 88.145 1240 119 15 1890 3115 704754679 704753454 0.000000e+00 1450
17 TraesCS2D01G456700 chr2A 88.732 994 98 6 774 1757 705268337 705269326 0.000000e+00 1203
18 TraesCS2D01G456700 chr2A 92.436 780 37 8 1 770 705267533 705268300 0.000000e+00 1094
19 TraesCS2D01G456700 chr2A 89.103 624 58 6 2046 2667 705342857 705343472 0.000000e+00 767
20 TraesCS2D01G456700 chr4B 91.304 1219 94 9 2058 3275 22488520 22487313 0.000000e+00 1653
21 TraesCS2D01G456700 chr4B 94.509 1038 56 1 917 1953 22440902 22439865 0.000000e+00 1600
22 TraesCS2D01G456700 chr4B 91.352 1087 77 9 1949 3033 22438650 22437579 0.000000e+00 1471
23 TraesCS2D01G456700 chr4B 93.433 670 30 5 1 668 22442741 22442084 0.000000e+00 981
24 TraesCS2D01G456700 chr4B 90.167 478 33 6 3365 3832 22487312 22486839 9.780000e-171 610
25 TraesCS2D01G456700 chr4B 90.741 216 8 3 774 981 22441110 22440899 1.130000e-70 278
26 TraesCS2D01G456700 chr4B 91.391 151 11 2 3967 4115 22486530 22486380 5.390000e-49 206
27 TraesCS2D01G456700 chr4B 95.200 125 5 1 3845 3968 22486689 22486565 3.250000e-46 196
28 TraesCS2D01G456700 chr4B 94.737 114 5 1 661 773 22441257 22441144 4.230000e-40 176
29 TraesCS2D01G456700 chr4B 78.947 171 29 7 3604 3770 580383260 580383093 4.350000e-20 110
30 TraesCS2D01G456700 chr7A 81.909 1006 148 25 799 1784 9683569 9682578 0.000000e+00 819
31 TraesCS2D01G456700 chr7A 85.714 161 20 3 3614 3773 75478410 75478568 2.540000e-37 167
32 TraesCS2D01G456700 chr7D 81.741 942 143 17 862 1785 10056883 10057813 0.000000e+00 760
33 TraesCS2D01G456700 chr4A 80.259 1003 167 17 799 1784 729152349 729153337 0.000000e+00 726
34 TraesCS2D01G456700 chr4A 85.535 159 21 2 3614 3771 239640034 239639877 9.150000e-37 165
35 TraesCS2D01G456700 chr6D 86.875 160 21 0 3614 3773 455560024 455559865 3.270000e-41 180
36 TraesCS2D01G456700 chr6D 94.286 105 5 1 3269 3372 65497175 65497071 4.260000e-35 159
37 TraesCS2D01G456700 chr5A 85.714 161 21 2 3614 3773 512201901 512202060 7.070000e-38 169
38 TraesCS2D01G456700 chr5A 88.696 115 10 2 3245 3359 629924940 629925051 1.990000e-28 137
39 TraesCS2D01G456700 chr6A 85.625 160 21 2 3614 3772 602445411 602445253 2.540000e-37 167
40 TraesCS2D01G456700 chr6A 85.535 159 21 2 3614 3771 604219493 604219336 9.150000e-37 165
41 TraesCS2D01G456700 chr3D 98.864 88 1 0 3274 3361 336539180 336539267 1.530000e-34 158
42 TraesCS2D01G456700 chr3B 98.864 88 1 0 3274 3361 138269219 138269306 1.530000e-34 158
43 TraesCS2D01G456700 chr5B 96.774 93 3 0 3269 3361 289565425 289565517 5.510000e-34 156
44 TraesCS2D01G456700 chr5B 94.845 97 5 0 3273 3369 504177758 504177854 7.120000e-33 152
45 TraesCS2D01G456700 chr5D 94.000 100 5 1 3273 3372 238555671 238555769 2.560000e-32 150
46 TraesCS2D01G456700 chr5D 93.878 98 6 0 3264 3361 545281904 545281807 9.220000e-32 148
47 TraesCS2D01G456700 chr1A 93.939 99 4 1 3266 3364 388834908 388835004 9.220000e-32 148


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 TraesCS2D01G456700 chr2D 564437424 564441538 4114 False 7600.00 7600 100.000000 1 4115 1 chr2D.!!$F2 4114
1 TraesCS2D01G456700 chr2D 564418499 564420456 1957 False 1561.00 1561 81.312000 798 2804 1 chr2D.!!$F1 2006
2 TraesCS2D01G456700 chr2D 564070769 564071994 1225 True 1495.00 1495 88.790000 1890 3115 1 chr2D.!!$R1 1225
3 TraesCS2D01G456700 chr2D 564475272 564479115 3843 False 1380.50 3688 92.221250 1 3832 4 chr2D.!!$F3 3831
4 TraesCS2D01G456700 chr2B 675332841 675334063 1222 True 1474.00 1474 88.502000 1890 3115 1 chr2B.!!$R1 1225
5 TraesCS2D01G456700 chr2B 675533052 675537117 4065 False 1372.75 3515 92.600750 1 3968 4 chr2B.!!$F3 3967
6 TraesCS2D01G456700 chr2B 675524348 675526955 2607 False 1091.00 2010 82.099000 325 3115 2 chr2B.!!$F2 2790
7 TraesCS2D01G456700 chr2A 705264438 705269326 4888 False 1488.00 2167 88.326667 1 3115 3 chr2A.!!$F2 3114
8 TraesCS2D01G456700 chr2A 704753454 704754679 1225 True 1450.00 1450 88.145000 1890 3115 1 chr2A.!!$R1 1225
9 TraesCS2D01G456700 chr2A 705342857 705343472 615 False 767.00 767 89.103000 2046 2667 1 chr2A.!!$F1 621
10 TraesCS2D01G456700 chr4B 22437579 22442741 5162 True 901.20 1600 92.954400 1 3033 5 chr4B.!!$R2 3032
11 TraesCS2D01G456700 chr4B 22486380 22488520 2140 True 666.25 1653 92.015500 2058 4115 4 chr4B.!!$R3 2057
12 TraesCS2D01G456700 chr7A 9682578 9683569 991 True 819.00 819 81.909000 799 1784 1 chr7A.!!$R1 985
13 TraesCS2D01G456700 chr7D 10056883 10057813 930 False 760.00 760 81.741000 862 1785 1 chr7D.!!$F1 923
14 TraesCS2D01G456700 chr4A 729152349 729153337 988 False 726.00 726 80.259000 799 1784 1 chr4A.!!$F1 985

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
849 1756 2.433868 ATAGTATTGGCCGCTGTACG 57.566 50.0 0.00 0.0 43.15 3.67 F
1035 2022 0.037326 CCAGCAGCCTGTCGAACTTA 60.037 55.0 0.00 0.0 37.38 2.24 F
1119 2115 0.106918 ACCCCAACTTCAACGCAAGA 60.107 50.0 0.00 0.0 43.62 3.02 F
2347 4608 0.322648 CACACCAGAGCTCACATGGA 59.677 55.0 23.41 0.0 37.54 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2347 4608 0.178068 ATGATCTTGTACCGCCGCTT 59.822 50.000 0.0 0.0 0.00 4.68 R
2445 4706 0.809636 CCGCATCCAGCATCACGTTA 60.810 55.000 0.0 0.0 46.13 3.18 R
3039 5314 1.672356 CCCTCCCGTGAACAGCAAG 60.672 63.158 0.0 0.0 0.00 4.01 R
3702 6100 0.035439 GAAGCCCACCCGATTGAAGA 60.035 55.000 0.0 0.0 0.00 2.87 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
168 170 5.023533 TCTTCCATGTTAAGCGCTAGATT 57.976 39.130 12.05 0.00 0.00 2.40
202 204 7.384439 TGAGGATAATTCAAAATACGCACAA 57.616 32.000 0.00 0.00 0.00 3.33
212 214 8.942338 TTCAAAATACGCACAATAGAGATAGT 57.058 30.769 0.00 0.00 0.00 2.12
213 215 8.942338 TCAAAATACGCACAATAGAGATAGTT 57.058 30.769 0.00 0.00 0.00 2.24
214 216 9.378551 TCAAAATACGCACAATAGAGATAGTTT 57.621 29.630 0.00 0.00 0.00 2.66
215 217 9.988350 CAAAATACGCACAATAGAGATAGTTTT 57.012 29.630 0.00 0.00 0.00 2.43
275 277 9.807921 TGTAATCATAGAGAAACTTTCCCTTTT 57.192 29.630 0.00 0.00 0.00 2.27
335 338 6.418819 CCTTTGTTCTTTGATTGTAACAGCTG 59.581 38.462 13.48 13.48 33.70 4.24
339 342 5.050644 TCTTTGATTGTAACAGCTGCATG 57.949 39.130 15.27 0.00 0.00 4.06
369 372 5.537300 TCTACATTGACTAGGCATCTTCC 57.463 43.478 0.00 0.00 0.00 3.46
372 375 5.121380 ACATTGACTAGGCATCTTCCATT 57.879 39.130 0.00 0.00 0.00 3.16
547 553 5.648092 CCCTCTTTTAATCTGGTACCACTTG 59.352 44.000 11.60 1.20 0.00 3.16
598 604 5.608449 TCTACATTCATGAGGCATCTTCAG 58.392 41.667 0.00 0.00 0.00 3.02
758 1622 7.147880 CCCTCTTTTAATCCGTCTCTAGAGAAA 60.148 40.741 23.96 12.83 39.48 2.52
846 1753 3.206150 CAGAAATAGTATTGGCCGCTGT 58.794 45.455 0.00 0.00 0.00 4.40
847 1754 4.377021 CAGAAATAGTATTGGCCGCTGTA 58.623 43.478 0.00 0.00 0.00 2.74
848 1755 4.211374 CAGAAATAGTATTGGCCGCTGTAC 59.789 45.833 0.00 0.00 0.00 2.90
849 1756 2.433868 ATAGTATTGGCCGCTGTACG 57.566 50.000 0.00 0.00 43.15 3.67
900 1815 4.994852 TCTTCCAAGTATTTGTCAACTCCG 59.005 41.667 0.00 0.00 32.21 4.63
1035 2022 0.037326 CCAGCAGCCTGTCGAACTTA 60.037 55.000 0.00 0.00 37.38 2.24
1051 2038 5.874810 TCGAACTTATTCTGCATAGCTTGTT 59.125 36.000 0.00 0.00 32.12 2.83
1119 2115 0.106918 ACCCCAACTTCAACGCAAGA 60.107 50.000 0.00 0.00 43.62 3.02
1137 2133 4.381292 GCAAGAAACAGGGATGATTTCAGG 60.381 45.833 0.00 0.00 35.26 3.86
1358 2373 3.445096 GCCTTTGTGCTCACCAATAATCT 59.555 43.478 0.00 0.00 0.00 2.40
1360 2375 4.418392 CTTTGTGCTCACCAATAATCTGC 58.582 43.478 0.00 0.00 0.00 4.26
1503 2518 3.287445 GGCAACCATGTCGGCATT 58.713 55.556 0.00 0.00 39.03 3.56
1817 2838 0.875059 GTCAAAGTTGGAAGAGGGCG 59.125 55.000 0.00 0.00 0.00 6.13
1862 2889 5.270083 TCTCGTTACATTGCTTGTGTTTTG 58.730 37.500 3.49 0.00 39.48 2.44
1867 2894 8.343366 TCGTTACATTGCTTGTGTTTTGTATAA 58.657 29.630 3.49 0.00 39.48 0.98
1943 2970 1.275291 CTACCGCAACCTGGAGAAGAA 59.725 52.381 0.00 0.00 0.00 2.52
2151 4397 0.603569 GAGAGAAGGAGTTCGTGGCA 59.396 55.000 0.00 0.00 37.79 4.92
2230 4476 1.302033 CACAAGAAGGGCGAGCTGT 60.302 57.895 0.00 0.00 0.00 4.40
2298 4544 2.347490 GCCAGAGAAAGGACCGCA 59.653 61.111 0.00 0.00 0.00 5.69
2347 4608 0.322648 CACACCAGAGCTCACATGGA 59.677 55.000 23.41 0.00 37.54 3.41
3153 5428 1.448985 GATTGCCTTGTACTGCCGAA 58.551 50.000 0.00 0.00 0.00 4.30
3227 5607 4.158025 TCTCCTCTGGACGAGTTTGTTATC 59.842 45.833 0.00 0.00 38.11 1.75
3262 5642 6.607019 TGGGAACAAAGTTTGTAATCTACCT 58.393 36.000 21.14 3.39 44.59 3.08
3279 5659 7.784470 ATCTACCTTAATGACAGATACTCCC 57.216 40.000 0.00 0.00 0.00 4.30
3280 5660 6.923670 TCTACCTTAATGACAGATACTCCCT 58.076 40.000 0.00 0.00 0.00 4.20
3281 5661 7.005296 TCTACCTTAATGACAGATACTCCCTC 58.995 42.308 0.00 0.00 0.00 4.30
3282 5662 4.902448 ACCTTAATGACAGATACTCCCTCC 59.098 45.833 0.00 0.00 0.00 4.30
3283 5663 4.021894 CCTTAATGACAGATACTCCCTCCG 60.022 50.000 0.00 0.00 0.00 4.63
3284 5664 2.757894 ATGACAGATACTCCCTCCGT 57.242 50.000 0.00 0.00 0.00 4.69
3285 5665 2.054232 TGACAGATACTCCCTCCGTC 57.946 55.000 0.00 0.00 0.00 4.79
3286 5666 1.320507 GACAGATACTCCCTCCGTCC 58.679 60.000 0.00 0.00 0.00 4.79
3287 5667 0.106116 ACAGATACTCCCTCCGTCCC 60.106 60.000 0.00 0.00 0.00 4.46
3288 5668 0.106167 CAGATACTCCCTCCGTCCCA 60.106 60.000 0.00 0.00 0.00 4.37
3289 5669 0.861155 AGATACTCCCTCCGTCCCAT 59.139 55.000 0.00 0.00 0.00 4.00
3290 5670 2.071372 AGATACTCCCTCCGTCCCATA 58.929 52.381 0.00 0.00 0.00 2.74
3291 5671 2.449730 AGATACTCCCTCCGTCCCATAA 59.550 50.000 0.00 0.00 0.00 1.90
3292 5672 3.077695 AGATACTCCCTCCGTCCCATAAT 59.922 47.826 0.00 0.00 0.00 1.28
3293 5673 4.294168 AGATACTCCCTCCGTCCCATAATA 59.706 45.833 0.00 0.00 0.00 0.98
3294 5674 3.562108 ACTCCCTCCGTCCCATAATAT 57.438 47.619 0.00 0.00 0.00 1.28
3295 5675 4.687262 ACTCCCTCCGTCCCATAATATA 57.313 45.455 0.00 0.00 0.00 0.86
3296 5676 5.019657 ACTCCCTCCGTCCCATAATATAA 57.980 43.478 0.00 0.00 0.00 0.98
3297 5677 5.024118 ACTCCCTCCGTCCCATAATATAAG 58.976 45.833 0.00 0.00 0.00 1.73
3298 5678 5.222484 ACTCCCTCCGTCCCATAATATAAGA 60.222 44.000 0.00 0.00 0.00 2.10
3299 5679 5.657446 TCCCTCCGTCCCATAATATAAGAA 58.343 41.667 0.00 0.00 0.00 2.52
3300 5680 5.482878 TCCCTCCGTCCCATAATATAAGAAC 59.517 44.000 0.00 0.00 0.00 3.01
3301 5681 5.408356 CCTCCGTCCCATAATATAAGAACG 58.592 45.833 0.00 0.00 0.00 3.95
3302 5682 5.047519 CCTCCGTCCCATAATATAAGAACGT 60.048 44.000 0.00 0.00 0.00 3.99
3303 5683 6.409524 TCCGTCCCATAATATAAGAACGTT 57.590 37.500 0.00 0.00 0.00 3.99
3304 5684 6.819284 TCCGTCCCATAATATAAGAACGTTT 58.181 36.000 0.46 0.00 0.00 3.60
3305 5685 7.274447 TCCGTCCCATAATATAAGAACGTTTT 58.726 34.615 0.46 0.00 0.00 2.43
3306 5686 7.769970 TCCGTCCCATAATATAAGAACGTTTTT 59.230 33.333 9.22 9.22 0.00 1.94
3307 5687 7.853929 CCGTCCCATAATATAAGAACGTTTTTG 59.146 37.037 13.87 0.00 0.00 2.44
3308 5688 8.605746 CGTCCCATAATATAAGAACGTTTTTGA 58.394 33.333 13.87 2.81 0.00 2.69
3309 5689 9.712359 GTCCCATAATATAAGAACGTTTTTGAC 57.288 33.333 13.87 5.89 0.00 3.18
3310 5690 9.451002 TCCCATAATATAAGAACGTTTTTGACA 57.549 29.630 13.87 0.01 0.00 3.58
3311 5691 9.498307 CCCATAATATAAGAACGTTTTTGACAC 57.502 33.333 13.87 0.00 0.00 3.67
3317 5697 7.781548 ATAAGAACGTTTTTGACACTACACT 57.218 32.000 13.87 0.00 0.00 3.55
3318 5698 8.876275 ATAAGAACGTTTTTGACACTACACTA 57.124 30.769 13.87 0.00 0.00 2.74
3319 5699 6.823678 AGAACGTTTTTGACACTACACTAG 57.176 37.500 0.46 0.00 0.00 2.57
3320 5700 6.335777 AGAACGTTTTTGACACTACACTAGT 58.664 36.000 0.46 0.00 40.28 2.57
3331 5711 3.800531 ACTACACTAGTGCCAAAAACGT 58.199 40.909 22.90 2.45 37.69 3.99
3332 5712 4.193865 ACTACACTAGTGCCAAAAACGTT 58.806 39.130 22.90 0.00 37.69 3.99
3333 5713 3.685836 ACACTAGTGCCAAAAACGTTC 57.314 42.857 22.90 0.00 0.00 3.95
3334 5714 3.275999 ACACTAGTGCCAAAAACGTTCT 58.724 40.909 22.90 0.00 0.00 3.01
3335 5715 3.692593 ACACTAGTGCCAAAAACGTTCTT 59.307 39.130 22.90 0.00 0.00 2.52
3336 5716 4.877251 ACACTAGTGCCAAAAACGTTCTTA 59.123 37.500 22.90 0.00 0.00 2.10
3337 5717 5.529800 ACACTAGTGCCAAAAACGTTCTTAT 59.470 36.000 22.90 0.00 0.00 1.73
3338 5718 6.707161 ACACTAGTGCCAAAAACGTTCTTATA 59.293 34.615 22.90 0.00 0.00 0.98
3339 5719 7.389607 ACACTAGTGCCAAAAACGTTCTTATAT 59.610 33.333 22.90 0.00 0.00 0.86
3340 5720 8.234546 CACTAGTGCCAAAAACGTTCTTATATT 58.765 33.333 10.54 0.00 0.00 1.28
3341 5721 9.439500 ACTAGTGCCAAAAACGTTCTTATATTA 57.561 29.630 0.00 0.00 0.00 0.98
3344 5724 8.188139 AGTGCCAAAAACGTTCTTATATTATGG 58.812 33.333 0.00 3.63 0.00 2.74
3345 5725 7.434013 GTGCCAAAAACGTTCTTATATTATGGG 59.566 37.037 0.00 0.00 0.00 4.00
3346 5726 7.339721 TGCCAAAAACGTTCTTATATTATGGGA 59.660 33.333 0.00 1.11 0.00 4.37
3347 5727 7.646526 GCCAAAAACGTTCTTATATTATGGGAC 59.353 37.037 0.00 0.00 0.00 4.46
3404 5784 5.163933 GGCATCTTTCGTCGTTACATTGTTA 60.164 40.000 0.00 0.00 0.00 2.41
3427 5807 0.242017 GCATTGCCTCGAACTTGCTT 59.758 50.000 0.00 0.00 0.00 3.91
3440 5826 5.010922 TCGAACTTGCTTAGTGTTTAGGGTA 59.989 40.000 0.00 0.00 37.12 3.69
3517 5903 7.318141 AGCATCATTTCTTTTATGAAGGTGTG 58.682 34.615 0.00 0.00 35.77 3.82
3592 5981 4.512484 CCCATGGTTGTTGTTGTTTTTCT 58.488 39.130 11.73 0.00 0.00 2.52
3681 6079 3.152341 CTGTGCCCAGAGTTTGAATCTT 58.848 45.455 0.00 0.00 41.50 2.40
3684 6082 4.072131 GTGCCCAGAGTTTGAATCTTGTA 58.928 43.478 0.00 0.00 0.00 2.41
3702 6100 6.698380 TCTTGTAGGAAGCGAATTTCTAGTT 58.302 36.000 0.00 0.00 29.01 2.24
3818 6217 5.573380 ATTCATCCTAGGCATAGCTTTGA 57.427 39.130 8.49 0.00 0.00 2.69
3833 6232 8.400947 GCATAGCTTTGATTTTCTATGACTTGA 58.599 33.333 8.49 0.00 40.25 3.02
3842 6241 7.779798 TGATTTTCTATGACTTGAATTAGGGGG 59.220 37.037 0.00 0.00 0.00 5.40
3847 6955 2.109128 TGACTTGAATTAGGGGGTGCAA 59.891 45.455 0.00 0.00 0.00 4.08
4016 7880 1.589716 AAAGACTTGGCGCATGCTCC 61.590 55.000 20.04 20.04 42.25 4.70
4056 7921 6.813649 TCTTCGGCATACTTATCTTCATATGC 59.186 38.462 6.54 6.54 45.98 3.14
4074 7939 4.689612 ATGCAATCGACTATGTAACCCT 57.310 40.909 0.00 0.00 0.00 4.34
4076 7941 5.196341 TGCAATCGACTATGTAACCCTAG 57.804 43.478 0.00 0.00 0.00 3.02
4085 7950 5.400870 ACTATGTAACCCTAGGTACCATCC 58.599 45.833 15.94 0.00 33.12 3.51
4086 7951 3.780516 TGTAACCCTAGGTACCATCCA 57.219 47.619 15.94 0.00 33.12 3.41
4095 7960 5.482878 CCCTAGGTACCATCCACGTTTATAT 59.517 44.000 15.94 0.00 0.00 0.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
217 219 9.569122 TTGGAGTAATCTAGTTTGCTTAAACTT 57.431 29.630 10.28 0.00 42.48 2.66
218 220 9.220767 CTTGGAGTAATCTAGTTTGCTTAAACT 57.779 33.333 9.94 9.94 44.46 2.66
219 221 9.216117 TCTTGGAGTAATCTAGTTTGCTTAAAC 57.784 33.333 5.73 0.00 0.00 2.01
275 277 5.960811 TCAAATATTTGCAAGTTATCCCCCA 59.039 36.000 21.15 0.00 38.05 4.96
335 338 4.697352 AGTCAATGTAGAACTTGTCCATGC 59.303 41.667 0.00 0.00 0.00 4.06
339 342 4.870991 GCCTAGTCAATGTAGAACTTGTCC 59.129 45.833 0.00 0.00 0.00 4.02
394 397 2.100749 CCTGAACAACCTGGGTCAAAAC 59.899 50.000 0.00 0.00 0.00 2.43
474 480 7.026562 TGTTGAACAAGTAAAACAGTCACATG 58.973 34.615 0.00 0.00 0.00 3.21
547 553 3.249080 TCTTTGCGGCTGTTACAACTTAC 59.751 43.478 0.00 0.00 0.00 2.34
758 1622 1.897802 CAGCAAGAGCATCCCCTTTTT 59.102 47.619 0.00 0.00 45.49 1.94
770 1635 3.708890 TGTGCAAAATGTTCAGCAAGAG 58.291 40.909 0.00 0.00 38.91 2.85
846 1753 2.291209 TGGGACTTGTCAGGTACGTA 57.709 50.000 3.08 0.00 0.00 3.57
847 1754 1.640917 ATGGGACTTGTCAGGTACGT 58.359 50.000 0.00 0.00 0.00 3.57
848 1755 2.028476 TCAATGGGACTTGTCAGGTACG 60.028 50.000 3.08 0.00 0.00 3.67
849 1756 3.335579 GTCAATGGGACTTGTCAGGTAC 58.664 50.000 3.08 0.00 43.46 3.34
900 1815 2.999739 TTTCAACACGGACGAGGGGC 63.000 60.000 0.00 0.00 0.00 5.80
1051 2038 1.208052 GCCTAGGATGACAACAGCTGA 59.792 52.381 23.35 0.00 32.57 4.26
1119 2115 4.739793 TGAACCTGAAATCATCCCTGTTT 58.260 39.130 0.00 0.00 0.00 2.83
1503 2518 5.970317 AAGATTTGATGCTGTTGATGTCA 57.030 34.783 0.00 0.00 0.00 3.58
1817 2838 2.803133 GCCAAAAGCACCTTTCTCCAAC 60.803 50.000 0.00 0.00 42.97 3.77
1862 2889 4.022329 ACAGCCCAGCAAACAAACTTATAC 60.022 41.667 0.00 0.00 0.00 1.47
1867 2894 1.136891 GAACAGCCCAGCAAACAAACT 59.863 47.619 0.00 0.00 0.00 2.66
1943 2970 1.141881 GGACCATGTGCGTCGATCT 59.858 57.895 0.00 0.00 0.00 2.75
2151 4397 0.969149 TGCTGATCGTGTTCACCTCT 59.031 50.000 0.00 0.00 0.00 3.69
2230 4476 3.057033 GGGAAGTACTCGTAGACAAGCAA 60.057 47.826 0.00 0.00 0.00 3.91
2298 4544 1.725557 CCGACATGGACGAGGACGAT 61.726 60.000 14.36 0.00 42.00 3.73
2347 4608 0.178068 ATGATCTTGTACCGCCGCTT 59.822 50.000 0.00 0.00 0.00 4.68
2445 4706 0.809636 CCGCATCCAGCATCACGTTA 60.810 55.000 0.00 0.00 46.13 3.18
3039 5314 1.672356 CCCTCCCGTGAACAGCAAG 60.672 63.158 0.00 0.00 0.00 4.01
3153 5428 3.003275 CACAAGCAAACCGTAGTCAACAT 59.997 43.478 0.00 0.00 0.00 2.71
3227 5607 0.882927 TTGTTCCCAGCTCGTTTCGG 60.883 55.000 0.00 0.00 0.00 4.30
3262 5642 4.543689 ACGGAGGGAGTATCTGTCATTAA 58.456 43.478 0.00 0.00 30.27 1.40
3273 5653 4.687262 ATATTATGGGACGGAGGGAGTA 57.313 45.455 0.00 0.00 0.00 2.59
3274 5654 3.562108 ATATTATGGGACGGAGGGAGT 57.438 47.619 0.00 0.00 0.00 3.85
3275 5655 5.269991 TCTTATATTATGGGACGGAGGGAG 58.730 45.833 0.00 0.00 0.00 4.30
3276 5656 5.279562 TCTTATATTATGGGACGGAGGGA 57.720 43.478 0.00 0.00 0.00 4.20
3277 5657 5.623824 CGTTCTTATATTATGGGACGGAGGG 60.624 48.000 0.00 0.00 0.00 4.30
3278 5658 5.047519 ACGTTCTTATATTATGGGACGGAGG 60.048 44.000 13.18 0.00 0.00 4.30
3279 5659 6.022163 ACGTTCTTATATTATGGGACGGAG 57.978 41.667 13.18 0.00 0.00 4.63
3280 5660 6.409524 AACGTTCTTATATTATGGGACGGA 57.590 37.500 0.00 0.00 0.00 4.69
3281 5661 7.486802 AAAACGTTCTTATATTATGGGACGG 57.513 36.000 0.00 1.76 0.00 4.79
3282 5662 8.605746 TCAAAAACGTTCTTATATTATGGGACG 58.394 33.333 0.00 9.33 0.00 4.79
3283 5663 9.712359 GTCAAAAACGTTCTTATATTATGGGAC 57.288 33.333 0.00 0.00 0.00 4.46
3284 5664 9.451002 TGTCAAAAACGTTCTTATATTATGGGA 57.549 29.630 0.00 0.00 0.00 4.37
3285 5665 9.498307 GTGTCAAAAACGTTCTTATATTATGGG 57.502 33.333 0.00 0.00 0.00 4.00
3291 5671 9.485206 AGTGTAGTGTCAAAAACGTTCTTATAT 57.515 29.630 0.00 0.00 0.00 0.86
3292 5672 8.876275 AGTGTAGTGTCAAAAACGTTCTTATA 57.124 30.769 0.00 0.00 0.00 0.98
3293 5673 7.781548 AGTGTAGTGTCAAAAACGTTCTTAT 57.218 32.000 0.00 0.00 0.00 1.73
3294 5674 7.975616 ACTAGTGTAGTGTCAAAAACGTTCTTA 59.024 33.333 0.00 0.00 37.69 2.10
3295 5675 6.815142 ACTAGTGTAGTGTCAAAAACGTTCTT 59.185 34.615 0.00 0.00 37.69 2.52
3296 5676 6.335777 ACTAGTGTAGTGTCAAAAACGTTCT 58.664 36.000 0.00 0.00 37.69 3.01
3297 5677 6.579491 ACTAGTGTAGTGTCAAAAACGTTC 57.421 37.500 0.00 0.00 37.69 3.95
3310 5690 3.800531 ACGTTTTTGGCACTAGTGTAGT 58.199 40.909 23.44 9.54 40.28 2.73
3311 5691 4.510340 AGAACGTTTTTGGCACTAGTGTAG 59.490 41.667 23.44 8.99 0.00 2.74
3312 5692 4.444536 AGAACGTTTTTGGCACTAGTGTA 58.555 39.130 23.44 10.89 0.00 2.90
3313 5693 3.275999 AGAACGTTTTTGGCACTAGTGT 58.724 40.909 23.44 0.00 0.00 3.55
3314 5694 3.963383 AGAACGTTTTTGGCACTAGTG 57.037 42.857 18.93 18.93 0.00 2.74
3315 5695 7.916914 ATATAAGAACGTTTTTGGCACTAGT 57.083 32.000 13.87 0.00 0.00 2.57
3318 5698 8.188139 CCATAATATAAGAACGTTTTTGGCACT 58.812 33.333 13.87 0.00 0.00 4.40
3319 5699 7.434013 CCCATAATATAAGAACGTTTTTGGCAC 59.566 37.037 13.87 0.00 0.00 5.01
3320 5700 7.339721 TCCCATAATATAAGAACGTTTTTGGCA 59.660 33.333 13.87 0.01 0.00 4.92
3321 5701 7.646526 GTCCCATAATATAAGAACGTTTTTGGC 59.353 37.037 13.87 0.00 0.00 4.52
3322 5702 8.679100 TGTCCCATAATATAAGAACGTTTTTGG 58.321 33.333 13.87 5.54 0.00 3.28
3323 5703 9.716507 CTGTCCCATAATATAAGAACGTTTTTG 57.283 33.333 13.87 0.00 0.00 2.44
3324 5704 9.675464 TCTGTCCCATAATATAAGAACGTTTTT 57.325 29.630 9.22 9.22 0.00 1.94
3325 5705 9.326413 CTCTGTCCCATAATATAAGAACGTTTT 57.674 33.333 0.46 0.00 0.00 2.43
3326 5706 7.931948 CCTCTGTCCCATAATATAAGAACGTTT 59.068 37.037 0.46 0.00 0.00 3.60
3327 5707 7.442656 CCTCTGTCCCATAATATAAGAACGTT 58.557 38.462 0.00 0.00 0.00 3.99
3328 5708 6.014499 CCCTCTGTCCCATAATATAAGAACGT 60.014 42.308 0.00 0.00 0.00 3.99
3329 5709 6.210784 TCCCTCTGTCCCATAATATAAGAACG 59.789 42.308 0.00 0.00 0.00 3.95
3330 5710 7.235812 ACTCCCTCTGTCCCATAATATAAGAAC 59.764 40.741 0.00 0.00 0.00 3.01
3331 5711 7.313731 ACTCCCTCTGTCCCATAATATAAGAA 58.686 38.462 0.00 0.00 0.00 2.52
3332 5712 6.875469 ACTCCCTCTGTCCCATAATATAAGA 58.125 40.000 0.00 0.00 0.00 2.10
3333 5713 7.896496 ACTACTCCCTCTGTCCCATAATATAAG 59.104 40.741 0.00 0.00 0.00 1.73
3334 5714 7.776745 ACTACTCCCTCTGTCCCATAATATAA 58.223 38.462 0.00 0.00 0.00 0.98
3335 5715 7.358255 ACTACTCCCTCTGTCCCATAATATA 57.642 40.000 0.00 0.00 0.00 0.86
3336 5716 6.234404 ACTACTCCCTCTGTCCCATAATAT 57.766 41.667 0.00 0.00 0.00 1.28
3337 5717 5.681494 ACTACTCCCTCTGTCCCATAATA 57.319 43.478 0.00 0.00 0.00 0.98
3338 5718 4.561254 ACTACTCCCTCTGTCCCATAAT 57.439 45.455 0.00 0.00 0.00 1.28
3339 5719 4.030913 CAACTACTCCCTCTGTCCCATAA 58.969 47.826 0.00 0.00 0.00 1.90
3340 5720 3.630054 CCAACTACTCCCTCTGTCCCATA 60.630 52.174 0.00 0.00 0.00 2.74
3341 5721 2.472029 CAACTACTCCCTCTGTCCCAT 58.528 52.381 0.00 0.00 0.00 4.00
3342 5722 1.552486 CCAACTACTCCCTCTGTCCCA 60.552 57.143 0.00 0.00 0.00 4.37
3343 5723 1.196012 CCAACTACTCCCTCTGTCCC 58.804 60.000 0.00 0.00 0.00 4.46
3344 5724 1.939980 ACCAACTACTCCCTCTGTCC 58.060 55.000 0.00 0.00 0.00 4.02
3345 5725 5.068855 GGTATAACCAACTACTCCCTCTGTC 59.931 48.000 0.00 0.00 38.42 3.51
3346 5726 4.961099 GGTATAACCAACTACTCCCTCTGT 59.039 45.833 0.00 0.00 38.42 3.41
3347 5727 5.069251 CAGGTATAACCAACTACTCCCTCTG 59.931 48.000 0.00 0.00 41.95 3.35
3348 5728 5.209659 CAGGTATAACCAACTACTCCCTCT 58.790 45.833 0.00 0.00 41.95 3.69
3349 5729 4.344390 CCAGGTATAACCAACTACTCCCTC 59.656 50.000 0.00 0.00 41.95 4.30
3350 5730 4.296056 CCAGGTATAACCAACTACTCCCT 58.704 47.826 0.00 0.00 41.95 4.20
3351 5731 3.181457 GCCAGGTATAACCAACTACTCCC 60.181 52.174 0.00 0.00 41.95 4.30
3352 5732 3.453353 TGCCAGGTATAACCAACTACTCC 59.547 47.826 0.00 0.00 41.95 3.85
3353 5733 4.748277 TGCCAGGTATAACCAACTACTC 57.252 45.455 0.00 0.00 41.95 2.59
3354 5734 5.045140 ACAATGCCAGGTATAACCAACTACT 60.045 40.000 0.00 0.00 41.95 2.57
3355 5735 5.190677 ACAATGCCAGGTATAACCAACTAC 58.809 41.667 0.00 0.00 41.95 2.73
3440 5826 6.926630 TTGAAGGCTATATTGTGGGTTTTT 57.073 33.333 0.00 0.00 0.00 1.94
3450 5836 6.012745 GGATCCAACCATTGAAGGCTATATT 58.987 40.000 6.95 0.00 0.00 1.28
3549 5935 5.128919 GGGCATCAACTATCTCTTGACAAT 58.871 41.667 0.00 0.00 30.46 2.71
3592 5981 5.234329 TCAAGCGAACAAAACAACAAACAAA 59.766 32.000 0.00 0.00 0.00 2.83
3643 6041 0.538057 CAGGGTGCACCACTGTGATT 60.538 55.000 35.78 8.65 45.76 2.57
3644 6042 1.073722 CAGGGTGCACCACTGTGAT 59.926 57.895 35.78 10.40 45.76 3.06
3681 6079 6.282199 AGAACTAGAAATTCGCTTCCTACA 57.718 37.500 0.00 0.00 0.00 2.74
3684 6082 5.794894 TGAAGAACTAGAAATTCGCTTCCT 58.205 37.500 0.00 0.00 31.71 3.36
3702 6100 0.035439 GAAGCCCACCCGATTGAAGA 60.035 55.000 0.00 0.00 0.00 2.87
3818 6217 7.561356 CACCCCCTAATTCAAGTCATAGAAAAT 59.439 37.037 0.00 0.00 0.00 1.82
3833 6232 1.967779 GTGTGTTTGCACCCCCTAATT 59.032 47.619 0.00 0.00 44.65 1.40
3834 6233 1.146982 AGTGTGTTTGCACCCCCTAAT 59.853 47.619 0.00 0.00 44.65 1.73
3837 6236 0.110486 CTAGTGTGTTTGCACCCCCT 59.890 55.000 0.00 0.00 44.65 4.79
3838 6237 0.109723 TCTAGTGTGTTTGCACCCCC 59.890 55.000 0.00 0.00 44.65 5.40
3839 6238 1.071699 TCTCTAGTGTGTTTGCACCCC 59.928 52.381 0.00 0.00 44.65 4.95
3842 6241 3.304559 CGCTATCTCTAGTGTGTTTGCAC 59.695 47.826 0.00 0.00 45.44 4.57
3847 6955 6.684686 TGTTAAACGCTATCTCTAGTGTGTT 58.315 36.000 0.02 0.00 45.67 3.32
3975 7838 2.452064 GGATTCATCCGGGGCCTGA 61.452 63.158 15.75 6.32 37.19 3.86
4016 7880 2.171567 CGAAGATGCATTCGTGCTTTG 58.828 47.619 13.09 6.19 45.37 2.77
4031 7895 6.813649 GCATATGAAGATAAGTATGCCGAAGA 59.186 38.462 6.97 0.00 42.06 2.87
4032 7896 6.591448 TGCATATGAAGATAAGTATGCCGAAG 59.409 38.462 6.97 0.00 45.38 3.79
4056 7921 5.786264 ACCTAGGGTTACATAGTCGATTG 57.214 43.478 14.81 0.00 27.29 2.67
4059 7924 4.165950 TGGTACCTAGGGTTACATAGTCGA 59.834 45.833 14.81 0.00 37.09 4.20
4074 7939 7.309990 GGCTTATATAAACGTGGATGGTACCTA 60.310 40.741 14.36 0.00 0.00 3.08
4076 7941 5.640783 GGCTTATATAAACGTGGATGGTACC 59.359 44.000 4.43 4.43 0.00 3.34
4085 7950 3.986277 ACCCTCGGCTTATATAAACGTG 58.014 45.455 14.95 13.10 0.00 4.49
4086 7951 4.141869 ACAACCCTCGGCTTATATAAACGT 60.142 41.667 14.95 0.00 0.00 3.99
4095 7960 0.609662 GGTGTACAACCCTCGGCTTA 59.390 55.000 0.00 0.00 44.02 3.09


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

AutoCloner maintained by Alex Coulton.