Multiple sequence alignment - TraesCS5D01G187000

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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 TraesCS5D01G187000 chr5D 100.000 2780 0 0 1 2780 289007685 289010464 0.000000e+00 5134
1 TraesCS5D01G187000 chr5D 87.626 1681 157 25 194 1844 288817728 288819387 0.000000e+00 1905
2 TraesCS5D01G187000 chr5D 94.530 585 14 1 2196 2780 285484793 285484227 0.000000e+00 887
3 TraesCS5D01G187000 chr5D 92.857 406 12 5 1858 2250 285485104 285484703 8.640000e-160 573
4 TraesCS5D01G187000 chr5D 73.993 1365 294 47 444 1787 288811089 288812413 5.350000e-137 497
5 TraesCS5D01G187000 chr5D 90.698 129 12 0 28 156 76160223 76160351 3.680000e-39 172
6 TraesCS5D01G187000 chr5D 88.000 100 11 1 1852 1950 551015086 551015185 1.750000e-22 117
7 TraesCS5D01G187000 chr5A 88.250 1617 150 18 255 1844 382291353 382292956 0.000000e+00 1897
8 TraesCS5D01G187000 chr5A 78.182 440 90 6 444 880 382284802 382285238 2.730000e-70 276
9 TraesCS5D01G187000 chr5B 87.984 1548 160 16 312 1844 328233429 328234965 0.000000e+00 1805
10 TraesCS5D01G187000 chr5B 73.815 1329 291 45 478 1787 328224604 328225894 9.010000e-130 473
11 TraesCS5D01G187000 chr5B 85.484 124 12 5 186 307 328233260 328233379 1.050000e-24 124
12 TraesCS5D01G187000 chr4D 96.158 937 21 6 1857 2780 454829472 454828538 0.000000e+00 1517
13 TraesCS5D01G187000 chr4D 90.998 511 27 7 2286 2778 483592017 483592526 0.000000e+00 671
14 TraesCS5D01G187000 chr4D 91.270 126 11 0 28 153 447038956 447039081 3.680000e-39 172
15 TraesCS5D01G187000 chr3D 81.637 1356 206 32 471 1800 610800301 610801639 0.000000e+00 1085
16 TraesCS5D01G187000 chr3D 85.200 250 12 13 1852 2085 33361038 33361278 1.660000e-57 233
17 TraesCS5D01G187000 chr3D 91.270 126 11 0 28 153 568066238 568066363 3.680000e-39 172
18 TraesCS5D01G187000 chr3B 80.826 1356 217 31 471 1800 828417041 828418379 0.000000e+00 1024
19 TraesCS5D01G187000 chr3B 80.568 1091 177 25 726 1800 828768055 828766984 0.000000e+00 808
20 TraesCS5D01G187000 chr3B 89.706 136 13 1 20 154 748784606 748784741 3.680000e-39 172
21 TraesCS5D01G187000 chr1D 97.949 585 12 0 2196 2780 379871036 379871620 0.000000e+00 1014
22 TraesCS5D01G187000 chr1D 89.904 416 16 6 1858 2250 379870714 379871126 1.910000e-141 512
23 TraesCS5D01G187000 chr1D 90.909 132 11 1 24 154 393087773 393087904 2.850000e-40 176
24 TraesCS5D01G187000 chr3A 79.522 1382 196 48 471 1806 745508845 745510185 0.000000e+00 904
25 TraesCS5D01G187000 chr3A 90.370 135 12 1 27 160 468726671 468726805 2.850000e-40 176
26 TraesCS5D01G187000 chr6B 94.600 500 25 2 2282 2780 675491777 675491279 0.000000e+00 773
27 TraesCS5D01G187000 chr6B 93.200 500 32 2 2282 2780 100510886 100511384 0.000000e+00 734
28 TraesCS5D01G187000 chr2B 94.611 501 23 3 2282 2780 40504676 40504178 0.000000e+00 773
29 TraesCS5D01G187000 chr2B 93.388 121 7 1 34 153 551567989 551567869 7.910000e-41 178
30 TraesCS5D01G187000 chr1A 93.600 500 30 2 2282 2780 71318675 71318177 0.000000e+00 745
31 TraesCS5D01G187000 chr2A 92.292 493 36 2 2286 2778 463646293 463646783 0.000000e+00 699
32 TraesCS5D01G187000 chr7B 88.376 585 30 12 2196 2780 502661620 502661074 0.000000e+00 669
33 TraesCS5D01G187000 chr7B 85.468 406 29 12 1863 2250 502661923 502661530 2.010000e-106 396
34 TraesCS5D01G187000 chr7B 85.468 406 29 12 1863 2250 502666364 502665971 2.010000e-106 396
35 TraesCS5D01G187000 chr7B 85.194 412 31 18 1858 2250 502670814 502670414 2.010000e-106 396
36 TraesCS5D01G187000 chr7B 84.236 406 34 13 1863 2250 502659778 502659385 4.370000e-98 368
37 TraesCS5D01G187000 chr7B 84.759 374 31 10 1893 2250 502664038 502663675 4.410000e-93 351
38 TraesCS5D01G187000 chr7B 84.492 374 32 10 1893 2250 502668479 502668116 2.050000e-91 346
39 TraesCS5D01G187000 chr7B 91.473 129 10 1 27 154 705715804 705715676 2.850000e-40 176
40 TraesCS5D01G187000 chr6D 86.777 242 12 9 1857 2085 233689369 233689135 4.600000e-63 252
41 TraesCS5D01G187000 chr6D 85.714 231 11 11 1869 2085 42505151 42505373 1.000000e-54 224
42 TraesCS5D01G187000 chr6D 84.774 243 13 10 1858 2085 344158400 344158633 3.600000e-54 222
43 TraesCS5D01G187000 chr2D 84.016 244 17 11 1857 2085 212010121 212009885 6.030000e-52 215
44 TraesCS5D01G187000 chr7D 83.471 242 18 9 1858 2084 525348876 525349110 3.630000e-49 206
45 TraesCS5D01G187000 chr7D 82.160 213 14 13 1887 2085 168066411 168066209 7.970000e-36 161
46 TraesCS5D01G187000 chr7A 90.226 133 11 2 27 157 426753984 426754116 3.680000e-39 172


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 TraesCS5D01G187000 chr5D 289007685 289010464 2779 False 5134.000000 5134 100.000000 1 2780 1 chr5D.!!$F4 2779
1 TraesCS5D01G187000 chr5D 288817728 288819387 1659 False 1905.000000 1905 87.626000 194 1844 1 chr5D.!!$F3 1650
2 TraesCS5D01G187000 chr5D 285484227 285485104 877 True 730.000000 887 93.693500 1858 2780 2 chr5D.!!$R1 922
3 TraesCS5D01G187000 chr5D 288811089 288812413 1324 False 497.000000 497 73.993000 444 1787 1 chr5D.!!$F2 1343
4 TraesCS5D01G187000 chr5A 382291353 382292956 1603 False 1897.000000 1897 88.250000 255 1844 1 chr5A.!!$F2 1589
5 TraesCS5D01G187000 chr5B 328233260 328234965 1705 False 964.500000 1805 86.734000 186 1844 2 chr5B.!!$F2 1658
6 TraesCS5D01G187000 chr5B 328224604 328225894 1290 False 473.000000 473 73.815000 478 1787 1 chr5B.!!$F1 1309
7 TraesCS5D01G187000 chr4D 454828538 454829472 934 True 1517.000000 1517 96.158000 1857 2780 1 chr4D.!!$R1 923
8 TraesCS5D01G187000 chr4D 483592017 483592526 509 False 671.000000 671 90.998000 2286 2778 1 chr4D.!!$F2 492
9 TraesCS5D01G187000 chr3D 610800301 610801639 1338 False 1085.000000 1085 81.637000 471 1800 1 chr3D.!!$F3 1329
10 TraesCS5D01G187000 chr3B 828417041 828418379 1338 False 1024.000000 1024 80.826000 471 1800 1 chr3B.!!$F2 1329
11 TraesCS5D01G187000 chr3B 828766984 828768055 1071 True 808.000000 808 80.568000 726 1800 1 chr3B.!!$R1 1074
12 TraesCS5D01G187000 chr1D 379870714 379871620 906 False 763.000000 1014 93.926500 1858 2780 2 chr1D.!!$F2 922
13 TraesCS5D01G187000 chr3A 745508845 745510185 1340 False 904.000000 904 79.522000 471 1806 1 chr3A.!!$F2 1335
14 TraesCS5D01G187000 chr7B 502659385 502670814 11429 True 417.428571 669 85.427571 1858 2780 7 chr7B.!!$R2 922

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
827 895 1.091771 GCAGGTCATGGGTGATCGTG 61.092 60.0 0.0 0.0 40.52 4.35 F
1029 1103 0.176910 GGAGAGGAGCTACCACTTGC 59.823 60.0 0.0 0.0 39.58 4.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1669 1794 1.003118 ACACGGATAAGCCACACATGT 59.997 47.619 0.00 0.00 35.94 3.21 R
2178 2342 1.139095 CGTGGCTTACTCGAGGGAC 59.861 63.158 18.41 9.21 38.27 4.46 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
30 31 7.664082 GCATCTGTACATGCTGTCTTATATT 57.336 36.000 13.10 0.00 45.03 1.28
31 32 7.737395 GCATCTGTACATGCTGTCTTATATTC 58.263 38.462 13.10 0.00 45.03 1.75
32 33 7.386025 GCATCTGTACATGCTGTCTTATATTCA 59.614 37.037 13.10 0.00 45.03 2.57
33 34 8.706936 CATCTGTACATGCTGTCTTATATTCAC 58.293 37.037 0.00 0.00 0.00 3.18
34 35 8.011844 TCTGTACATGCTGTCTTATATTCACT 57.988 34.615 0.00 0.00 0.00 3.41
35 36 8.138074 TCTGTACATGCTGTCTTATATTCACTC 58.862 37.037 0.00 0.00 0.00 3.51
36 37 7.210174 TGTACATGCTGTCTTATATTCACTCC 58.790 38.462 0.00 0.00 0.00 3.85
37 38 5.292765 ACATGCTGTCTTATATTCACTCCG 58.707 41.667 0.00 0.00 0.00 4.63
38 39 5.163405 ACATGCTGTCTTATATTCACTCCGT 60.163 40.000 0.00 0.00 0.00 4.69
39 40 5.339008 TGCTGTCTTATATTCACTCCGTT 57.661 39.130 0.00 0.00 0.00 4.44
40 41 5.348986 TGCTGTCTTATATTCACTCCGTTC 58.651 41.667 0.00 0.00 0.00 3.95
41 42 5.105513 TGCTGTCTTATATTCACTCCGTTCA 60.106 40.000 0.00 0.00 0.00 3.18
42 43 5.810587 GCTGTCTTATATTCACTCCGTTCAA 59.189 40.000 0.00 0.00 0.00 2.69
43 44 6.312918 GCTGTCTTATATTCACTCCGTTCAAA 59.687 38.462 0.00 0.00 0.00 2.69
44 45 7.148474 GCTGTCTTATATTCACTCCGTTCAAAA 60.148 37.037 0.00 0.00 0.00 2.44
45 46 8.610248 TGTCTTATATTCACTCCGTTCAAAAA 57.390 30.769 0.00 0.00 0.00 1.94
46 47 9.226606 TGTCTTATATTCACTCCGTTCAAAAAT 57.773 29.630 0.00 0.00 0.00 1.82
52 53 6.687081 TTCACTCCGTTCAAAAATACTTGT 57.313 33.333 0.00 0.00 0.00 3.16
53 54 6.295039 TCACTCCGTTCAAAAATACTTGTC 57.705 37.500 0.00 0.00 0.00 3.18
54 55 5.818336 TCACTCCGTTCAAAAATACTTGTCA 59.182 36.000 0.00 0.00 0.00 3.58
55 56 6.485313 TCACTCCGTTCAAAAATACTTGTCAT 59.515 34.615 0.00 0.00 0.00 3.06
56 57 7.012894 TCACTCCGTTCAAAAATACTTGTCATT 59.987 33.333 0.00 0.00 0.00 2.57
57 58 8.286800 CACTCCGTTCAAAAATACTTGTCATTA 58.713 33.333 0.00 0.00 0.00 1.90
58 59 8.842280 ACTCCGTTCAAAAATACTTGTCATTAA 58.158 29.630 0.00 0.00 0.00 1.40
59 60 9.672086 CTCCGTTCAAAAATACTTGTCATTAAA 57.328 29.630 0.00 0.00 0.00 1.52
145 146 9.443323 TTTTGATGATAAGTATTTTCGGACAGA 57.557 29.630 0.00 0.00 0.00 3.41
146 147 8.648557 TTGATGATAAGTATTTTCGGACAGAG 57.351 34.615 0.00 0.00 0.00 3.35
147 148 7.210174 TGATGATAAGTATTTTCGGACAGAGG 58.790 38.462 0.00 0.00 0.00 3.69
148 149 5.914033 TGATAAGTATTTTCGGACAGAGGG 58.086 41.667 0.00 0.00 0.00 4.30
149 150 5.659525 TGATAAGTATTTTCGGACAGAGGGA 59.340 40.000 0.00 0.00 0.00 4.20
150 151 4.473477 AAGTATTTTCGGACAGAGGGAG 57.527 45.455 0.00 0.00 0.00 4.30
151 152 3.442076 AGTATTTTCGGACAGAGGGAGT 58.558 45.455 0.00 0.00 0.00 3.85
152 153 4.607239 AGTATTTTCGGACAGAGGGAGTA 58.393 43.478 0.00 0.00 0.00 2.59
153 154 5.209659 AGTATTTTCGGACAGAGGGAGTAT 58.790 41.667 0.00 0.00 0.00 2.12
154 155 5.661759 AGTATTTTCGGACAGAGGGAGTATT 59.338 40.000 0.00 0.00 0.00 1.89
155 156 6.837568 AGTATTTTCGGACAGAGGGAGTATTA 59.162 38.462 0.00 0.00 0.00 0.98
156 157 6.555463 ATTTTCGGACAGAGGGAGTATTAA 57.445 37.500 0.00 0.00 0.00 1.40
157 158 6.555463 TTTTCGGACAGAGGGAGTATTAAT 57.445 37.500 0.00 0.00 0.00 1.40
158 159 6.555463 TTTCGGACAGAGGGAGTATTAATT 57.445 37.500 0.00 0.00 0.00 1.40
159 160 7.664552 TTTCGGACAGAGGGAGTATTAATTA 57.335 36.000 0.00 0.00 0.00 1.40
160 161 7.850935 TTCGGACAGAGGGAGTATTAATTAT 57.149 36.000 0.00 0.00 0.00 1.28
161 162 8.945195 TTCGGACAGAGGGAGTATTAATTATA 57.055 34.615 0.00 0.00 0.00 0.98
162 163 9.543231 TTCGGACAGAGGGAGTATTAATTATAT 57.457 33.333 0.00 0.00 0.00 0.86
163 164 8.967918 TCGGACAGAGGGAGTATTAATTATATG 58.032 37.037 0.00 0.00 0.00 1.78
164 165 8.967918 CGGACAGAGGGAGTATTAATTATATGA 58.032 37.037 0.00 0.00 0.00 2.15
166 167 9.790389 GACAGAGGGAGTATTAATTATATGACG 57.210 37.037 0.00 0.00 0.00 4.35
167 168 8.251721 ACAGAGGGAGTATTAATTATATGACGC 58.748 37.037 0.00 0.00 0.00 5.19
168 169 8.251026 CAGAGGGAGTATTAATTATATGACGCA 58.749 37.037 0.00 0.00 0.00 5.24
169 170 8.982723 AGAGGGAGTATTAATTATATGACGCAT 58.017 33.333 0.00 0.00 0.00 4.73
170 171 8.948631 AGGGAGTATTAATTATATGACGCATG 57.051 34.615 0.00 0.00 0.00 4.06
171 172 7.987458 AGGGAGTATTAATTATATGACGCATGG 59.013 37.037 0.00 0.00 0.00 3.66
172 173 7.254795 GGGAGTATTAATTATATGACGCATGGC 60.255 40.741 0.00 0.00 0.00 4.40
183 184 4.728058 GCATGGCGTGTTGTTTGT 57.272 50.000 8.75 0.00 0.00 2.83
184 185 3.855630 GCATGGCGTGTTGTTTGTA 57.144 47.368 8.75 0.00 0.00 2.41
190 191 3.958704 TGGCGTGTTGTTTGTATGAAAG 58.041 40.909 0.00 0.00 0.00 2.62
192 193 3.367607 GCGTGTTGTTTGTATGAAAGCA 58.632 40.909 0.00 0.00 0.00 3.91
201 202 6.370593 TGTTTGTATGAAAGCATCTTCGAAC 58.629 36.000 0.00 0.00 35.94 3.95
209 210 1.986575 GCATCTTCGAACTGGGCAGC 61.987 60.000 0.00 0.00 0.00 5.25
212 213 1.961277 CTTCGAACTGGGCAGCGTT 60.961 57.895 0.00 0.00 0.00 4.84
246 247 1.568025 GAAACCCGTTGACGAGCAC 59.432 57.895 4.91 0.00 43.02 4.40
272 275 1.815003 GCTAATCCAACTGCAGCAACT 59.185 47.619 15.27 0.00 32.46 3.16
273 276 2.415090 GCTAATCCAACTGCAGCAACTG 60.415 50.000 15.27 6.18 32.46 3.16
330 377 8.826710 TGTGACGAAGCTAATAAATAATCAAGG 58.173 33.333 0.00 0.00 0.00 3.61
355 402 5.477607 AACACTATACAAGTACAGCACCA 57.522 39.130 0.00 0.00 35.76 4.17
357 404 6.049955 ACACTATACAAGTACAGCACCATT 57.950 37.500 0.00 0.00 35.76 3.16
361 408 7.926018 CACTATACAAGTACAGCACCATTATCA 59.074 37.037 0.00 0.00 35.76 2.15
363 410 4.261801 ACAAGTACAGCACCATTATCACC 58.738 43.478 0.00 0.00 0.00 4.02
379 427 7.068593 CCATTATCACCATCTACAACACCATTT 59.931 37.037 0.00 0.00 0.00 2.32
384 432 7.047891 TCACCATCTACAACACCATTTCTATC 58.952 38.462 0.00 0.00 0.00 2.08
399 447 2.894731 TCTATCCCCATCTCTCGCATT 58.105 47.619 0.00 0.00 0.00 3.56
411 459 4.876125 TCTCTCGCATTCAAGATCATACC 58.124 43.478 0.00 0.00 0.00 2.73
423 471 2.975489 AGATCATACCGAGGAAGCCAAT 59.025 45.455 0.00 0.00 0.00 3.16
463 516 3.633986 CCCATGGCCAAAGAGAAAGATAC 59.366 47.826 10.96 0.00 0.00 2.24
581 640 2.064581 GTACCTCACCTCGCCCCAT 61.065 63.158 0.00 0.00 0.00 4.00
637 696 2.092291 GCCGCATCGTCGTTCAAGA 61.092 57.895 0.00 0.00 0.00 3.02
645 707 2.132762 TCGTCGTTCAAGAAAGCTTCC 58.867 47.619 0.00 0.00 30.14 3.46
648 710 1.873591 TCGTTCAAGAAAGCTTCCTGC 59.126 47.619 0.00 0.00 43.29 4.85
714 776 2.853430 ACCATAACCACACATCCCCTA 58.147 47.619 0.00 0.00 0.00 3.53
723 785 3.216800 CACACATCCCCTATTGATGGTG 58.783 50.000 5.36 6.41 43.10 4.17
724 786 2.233271 CACATCCCCTATTGATGGTGC 58.767 52.381 5.36 0.00 43.10 5.01
728 790 1.228245 CCCTATTGATGGTGCCCGG 60.228 63.158 0.00 0.00 0.00 5.73
747 809 1.609208 GCTCAGCTTTGTTCCTTCCA 58.391 50.000 0.00 0.00 0.00 3.53
820 888 1.562672 GGTGGTAGCAGGTCATGGGT 61.563 60.000 0.00 0.00 0.00 4.51
827 895 1.091771 GCAGGTCATGGGTGATCGTG 61.092 60.000 0.00 0.00 40.52 4.35
965 1039 4.637483 CGTGGAGCAAATGAAATACCAT 57.363 40.909 0.00 0.00 0.00 3.55
977 1051 8.423349 CAAATGAAATACCATCCATGTATTGGT 58.577 33.333 13.87 13.87 46.52 3.67
978 1052 9.653516 AAATGAAATACCATCCATGTATTGGTA 57.346 29.630 16.50 16.50 46.86 3.25
979 1053 9.653516 AATGAAATACCATCCATGTATTGGTAA 57.346 29.630 17.54 6.64 46.16 2.85
980 1054 9.827198 ATGAAATACCATCCATGTATTGGTAAT 57.173 29.630 17.54 10.20 46.16 1.89
981 1055 9.653516 TGAAATACCATCCATGTATTGGTAATT 57.346 29.630 17.54 15.91 46.16 1.40
982 1056 9.912634 GAAATACCATCCATGTATTGGTAATTG 57.087 33.333 17.36 0.00 46.16 2.32
996 1070 5.018539 TGGTAATTGGTGTATTCCTCGAG 57.981 43.478 5.13 5.13 0.00 4.04
997 1071 4.712829 TGGTAATTGGTGTATTCCTCGAGA 59.287 41.667 15.71 0.00 0.00 4.04
1011 1085 2.332104 CTCGAGAATATGCATGGTCGG 58.668 52.381 6.58 4.62 0.00 4.79
1026 1100 0.394625 GTCGGAGAGGAGCTACCACT 60.395 60.000 0.00 0.00 42.06 4.00
1029 1103 0.176910 GGAGAGGAGCTACCACTTGC 59.823 60.000 0.00 0.00 39.58 4.01
1134 1224 1.662044 CACAGCCAAGGCCTTTGTC 59.338 57.895 17.61 9.00 43.17 3.18
1144 1234 0.799393 GGCCTTTGTCTTCGAAGAGC 59.201 55.000 27.70 24.24 38.43 4.09
1147 1237 0.440371 CTTTGTCTTCGAAGAGCGCC 59.560 55.000 27.70 16.22 38.43 6.53
1151 1241 2.105128 CTTCGAAGAGCGCCGGAT 59.895 61.111 20.74 0.00 38.43 4.18
1174 1270 3.165160 AAGCGTGGCTGGTTCGTCT 62.165 57.895 0.00 0.00 39.62 4.18
1209 1323 2.242043 CACAAGCCTCAAATCCACCTT 58.758 47.619 0.00 0.00 0.00 3.50
1243 1360 3.002791 TCTCTGCATTTCATTGGTCGTC 58.997 45.455 0.00 0.00 0.00 4.20
1264 1381 5.182001 CGTCCATCATTTTCTCTTTTCTGGT 59.818 40.000 0.00 0.00 0.00 4.00
1312 1429 2.271944 AGCCTATAATTTCCGGTGGC 57.728 50.000 0.00 4.04 39.19 5.01
1359 1476 3.399181 GGCCACATCCGAGGGTCA 61.399 66.667 0.00 0.00 0.00 4.02
1374 1491 0.445436 GGTCAGCTTTGCGAGTCATG 59.555 55.000 0.00 0.00 0.00 3.07
1388 1511 4.260375 GCGAGTCATGGATATCAACAACAC 60.260 45.833 4.83 0.00 0.00 3.32
1429 1552 0.605319 CTTGCAGGGCGACAACCTTA 60.605 55.000 0.00 0.00 35.78 2.69
1453 1576 1.810151 TCTTTGCGCAAAGGACATACC 59.190 47.619 45.15 1.97 45.80 2.73
1508 1631 4.693283 CAATTAATGGAGGCTACTCGTGA 58.307 43.478 0.00 0.00 44.93 4.35
1531 1654 2.413142 GCAGGGCACAAGGATGAGC 61.413 63.158 0.00 0.00 41.75 4.26
1593 1716 2.343101 TCTATTGTGTTTTCTCCGGCG 58.657 47.619 0.00 0.00 0.00 6.46
1669 1794 4.201910 GCAAATACAAGGCGCATTCTTCTA 60.202 41.667 10.83 0.00 0.00 2.10
1844 1978 4.362279 AGCATCACAAAATGTTCACACAC 58.638 39.130 0.00 0.00 35.03 3.82
1845 1979 4.111198 GCATCACAAAATGTTCACACACA 58.889 39.130 0.00 0.00 35.03 3.72
1846 1980 4.026640 GCATCACAAAATGTTCACACACAC 60.027 41.667 0.00 0.00 35.03 3.82
1847 1981 4.773323 TCACAAAATGTTCACACACACA 57.227 36.364 0.00 0.00 35.03 3.72
1848 1982 4.480541 TCACAAAATGTTCACACACACAC 58.519 39.130 0.00 0.00 35.03 3.82
1849 1983 4.022849 TCACAAAATGTTCACACACACACA 60.023 37.500 0.00 0.00 35.03 3.72
1850 1984 4.089780 CACAAAATGTTCACACACACACAC 59.910 41.667 0.00 0.00 35.03 3.82
1851 1985 4.233005 CAAAATGTTCACACACACACACA 58.767 39.130 0.00 0.00 35.03 3.72
1852 1986 4.717233 AAATGTTCACACACACACACAT 57.283 36.364 0.00 0.00 35.03 3.21
1853 1987 5.826601 AAATGTTCACACACACACACATA 57.173 34.783 0.00 0.00 35.03 2.29
1854 1988 6.389830 AAATGTTCACACACACACACATAT 57.610 33.333 0.00 0.00 35.03 1.78
1855 1989 5.611796 ATGTTCACACACACACACATATC 57.388 39.130 0.00 0.00 35.03 1.63
1861 1995 7.639113 TCACACACACACACATATCTATCTA 57.361 36.000 0.00 0.00 0.00 1.98
1952 2101 1.886730 TACCTCCCACCTCCTCCCAG 61.887 65.000 0.00 0.00 0.00 4.45
2149 2312 1.265454 ACACCGTTCCTCTCCATCCC 61.265 60.000 0.00 0.00 0.00 3.85
2193 2357 1.751927 TCGGTCCCTCGAGTAAGCC 60.752 63.158 12.31 7.05 34.82 4.35
2194 2358 2.050350 CGGTCCCTCGAGTAAGCCA 61.050 63.158 12.31 0.00 0.00 4.75
2195 2359 1.516423 GGTCCCTCGAGTAAGCCAC 59.484 63.158 12.31 0.00 0.00 5.01
2388 2552 2.203640 TCGCTGAGTGGGTGGAGT 60.204 61.111 0.00 0.00 0.00 3.85
2477 4939 1.671054 CCGTCCTTCGTGGCACAAT 60.671 57.895 19.09 0.00 44.16 2.71
2724 7331 1.069513 TGTTGCTTGTACTACGCTGGT 59.930 47.619 0.00 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 5.292765 ACGGAGTGAATATAAGACAGCATG 58.707 41.667 0.00 0.00 42.51 4.06
16 17 5.537300 ACGGAGTGAATATAAGACAGCAT 57.463 39.130 0.00 0.00 42.51 3.79
17 18 5.105513 TGAACGGAGTGAATATAAGACAGCA 60.106 40.000 0.00 0.00 45.00 4.41
18 19 5.348986 TGAACGGAGTGAATATAAGACAGC 58.651 41.667 0.00 0.00 45.00 4.40
19 20 7.827819 TTTGAACGGAGTGAATATAAGACAG 57.172 36.000 0.00 0.00 45.00 3.51
20 21 8.610248 TTTTTGAACGGAGTGAATATAAGACA 57.390 30.769 0.00 0.00 45.00 3.41
26 27 9.010029 ACAAGTATTTTTGAACGGAGTGAATAT 57.990 29.630 0.00 0.00 45.00 1.28
27 28 8.385898 ACAAGTATTTTTGAACGGAGTGAATA 57.614 30.769 0.00 0.00 45.00 1.75
28 29 7.012894 TGACAAGTATTTTTGAACGGAGTGAAT 59.987 33.333 0.00 0.00 45.00 2.57
29 30 6.316640 TGACAAGTATTTTTGAACGGAGTGAA 59.683 34.615 0.00 0.00 45.00 3.18
30 31 5.818336 TGACAAGTATTTTTGAACGGAGTGA 59.182 36.000 0.00 0.00 45.00 3.41
31 32 6.055231 TGACAAGTATTTTTGAACGGAGTG 57.945 37.500 0.00 0.00 45.00 3.51
33 34 9.672086 TTTAATGACAAGTATTTTTGAACGGAG 57.328 29.630 0.00 0.00 0.00 4.63
119 120 9.443323 TCTGTCCGAAAATACTTATCATCAAAA 57.557 29.630 0.00 0.00 0.00 2.44
120 121 9.098355 CTCTGTCCGAAAATACTTATCATCAAA 57.902 33.333 0.00 0.00 0.00 2.69
121 122 7.710907 CCTCTGTCCGAAAATACTTATCATCAA 59.289 37.037 0.00 0.00 0.00 2.57
122 123 7.210174 CCTCTGTCCGAAAATACTTATCATCA 58.790 38.462 0.00 0.00 0.00 3.07
123 124 6.647067 CCCTCTGTCCGAAAATACTTATCATC 59.353 42.308 0.00 0.00 0.00 2.92
124 125 6.326583 TCCCTCTGTCCGAAAATACTTATCAT 59.673 38.462 0.00 0.00 0.00 2.45
125 126 5.659525 TCCCTCTGTCCGAAAATACTTATCA 59.340 40.000 0.00 0.00 0.00 2.15
126 127 6.158023 TCCCTCTGTCCGAAAATACTTATC 57.842 41.667 0.00 0.00 0.00 1.75
127 128 5.661759 ACTCCCTCTGTCCGAAAATACTTAT 59.338 40.000 0.00 0.00 0.00 1.73
128 129 5.021458 ACTCCCTCTGTCCGAAAATACTTA 58.979 41.667 0.00 0.00 0.00 2.24
129 130 3.838903 ACTCCCTCTGTCCGAAAATACTT 59.161 43.478 0.00 0.00 0.00 2.24
130 131 3.442076 ACTCCCTCTGTCCGAAAATACT 58.558 45.455 0.00 0.00 0.00 2.12
131 132 3.889520 ACTCCCTCTGTCCGAAAATAC 57.110 47.619 0.00 0.00 0.00 1.89
132 133 7.664552 TTAATACTCCCTCTGTCCGAAAATA 57.335 36.000 0.00 0.00 0.00 1.40
133 134 6.555463 TTAATACTCCCTCTGTCCGAAAAT 57.445 37.500 0.00 0.00 0.00 1.82
134 135 6.555463 ATTAATACTCCCTCTGTCCGAAAA 57.445 37.500 0.00 0.00 0.00 2.29
135 136 6.555463 AATTAATACTCCCTCTGTCCGAAA 57.445 37.500 0.00 0.00 0.00 3.46
136 137 7.850935 ATAATTAATACTCCCTCTGTCCGAA 57.149 36.000 0.00 0.00 0.00 4.30
137 138 8.967918 CATATAATTAATACTCCCTCTGTCCGA 58.032 37.037 0.00 0.00 0.00 4.55
138 139 8.967918 TCATATAATTAATACTCCCTCTGTCCG 58.032 37.037 0.00 0.00 0.00 4.79
140 141 9.790389 CGTCATATAATTAATACTCCCTCTGTC 57.210 37.037 0.00 0.00 0.00 3.51
141 142 8.251721 GCGTCATATAATTAATACTCCCTCTGT 58.748 37.037 0.00 0.00 0.00 3.41
142 143 8.251026 TGCGTCATATAATTAATACTCCCTCTG 58.749 37.037 0.00 0.00 0.00 3.35
143 144 8.362464 TGCGTCATATAATTAATACTCCCTCT 57.638 34.615 0.00 0.00 0.00 3.69
144 145 9.035607 CATGCGTCATATAATTAATACTCCCTC 57.964 37.037 0.00 0.00 0.00 4.30
145 146 7.987458 CCATGCGTCATATAATTAATACTCCCT 59.013 37.037 0.00 0.00 0.00 4.20
146 147 7.254795 GCCATGCGTCATATAATTAATACTCCC 60.255 40.741 0.00 0.00 0.00 4.30
147 148 7.630924 GCCATGCGTCATATAATTAATACTCC 58.369 38.462 0.00 0.00 0.00 3.85
166 167 1.984990 CATACAAACAACACGCCATGC 59.015 47.619 0.00 0.00 0.00 4.06
167 168 3.550950 TCATACAAACAACACGCCATG 57.449 42.857 0.00 0.00 0.00 3.66
168 169 4.545610 CTTTCATACAAACAACACGCCAT 58.454 39.130 0.00 0.00 0.00 4.40
169 170 3.793801 GCTTTCATACAAACAACACGCCA 60.794 43.478 0.00 0.00 0.00 5.69
170 171 2.724174 GCTTTCATACAAACAACACGCC 59.276 45.455 0.00 0.00 0.00 5.68
171 172 3.367607 TGCTTTCATACAAACAACACGC 58.632 40.909 0.00 0.00 0.00 5.34
172 173 5.451908 AGATGCTTTCATACAAACAACACG 58.548 37.500 0.00 0.00 31.96 4.49
173 174 6.086765 CGAAGATGCTTTCATACAAACAACAC 59.913 38.462 0.00 0.00 31.96 3.32
174 175 6.017523 TCGAAGATGCTTTCATACAAACAACA 60.018 34.615 0.00 0.00 31.96 3.33
175 176 6.370593 TCGAAGATGCTTTCATACAAACAAC 58.629 36.000 0.00 0.00 31.96 3.32
176 177 6.552859 TCGAAGATGCTTTCATACAAACAA 57.447 33.333 0.00 0.00 31.96 2.83
177 178 6.204688 AGTTCGAAGATGCTTTCATACAAACA 59.795 34.615 0.00 0.00 35.04 2.83
178 179 6.521133 CAGTTCGAAGATGCTTTCATACAAAC 59.479 38.462 0.00 0.00 35.04 2.93
179 180 6.348458 CCAGTTCGAAGATGCTTTCATACAAA 60.348 38.462 0.00 0.00 35.04 2.83
180 181 5.122239 CCAGTTCGAAGATGCTTTCATACAA 59.878 40.000 0.00 0.00 35.04 2.41
181 182 4.631377 CCAGTTCGAAGATGCTTTCATACA 59.369 41.667 0.00 0.00 35.04 2.29
182 183 4.034510 CCCAGTTCGAAGATGCTTTCATAC 59.965 45.833 0.00 0.00 35.04 2.39
183 184 4.191544 CCCAGTTCGAAGATGCTTTCATA 58.808 43.478 0.00 0.00 35.04 2.15
184 185 3.012518 CCCAGTTCGAAGATGCTTTCAT 58.987 45.455 0.00 0.00 35.04 2.57
190 191 1.986575 GCTGCCCAGTTCGAAGATGC 61.987 60.000 0.00 0.00 35.04 3.91
192 193 1.448540 CGCTGCCCAGTTCGAAGAT 60.449 57.895 0.00 0.00 35.04 2.40
212 213 3.304391 GGGTTTCGGTACATATACGCGTA 60.304 47.826 22.94 22.94 31.40 4.42
216 217 3.354089 ACGGGTTTCGGTACATATACG 57.646 47.619 0.00 0.00 44.45 3.06
218 219 4.681744 GTCAACGGGTTTCGGTACATATA 58.318 43.478 0.00 0.00 44.45 0.86
220 221 2.670789 CGTCAACGGGTTTCGGTACATA 60.671 50.000 0.00 0.00 44.45 2.29
221 222 1.799544 GTCAACGGGTTTCGGTACAT 58.200 50.000 0.00 0.00 44.45 2.29
222 223 0.597118 CGTCAACGGGTTTCGGTACA 60.597 55.000 0.00 0.00 44.45 2.90
223 224 0.318614 TCGTCAACGGGTTTCGGTAC 60.319 55.000 2.31 0.00 44.45 3.34
246 247 4.037089 TGCTGCAGTTGGATTAGCATATTG 59.963 41.667 16.64 0.00 39.26 1.90
330 377 7.262772 TGGTGCTGTACTTGTATAGTGTTATC 58.737 38.462 6.45 0.00 37.73 1.75
333 380 5.477607 TGGTGCTGTACTTGTATAGTGTT 57.522 39.130 6.45 0.00 37.73 3.32
338 385 7.147637 TGGTGATAATGGTGCTGTACTTGTATA 60.148 37.037 0.00 0.00 0.00 1.47
350 397 4.881273 TGTTGTAGATGGTGATAATGGTGC 59.119 41.667 0.00 0.00 0.00 5.01
355 402 8.055181 AGAAATGGTGTTGTAGATGGTGATAAT 58.945 33.333 0.00 0.00 0.00 1.28
357 404 6.957631 AGAAATGGTGTTGTAGATGGTGATA 58.042 36.000 0.00 0.00 0.00 2.15
361 408 6.357367 GGATAGAAATGGTGTTGTAGATGGT 58.643 40.000 0.00 0.00 0.00 3.55
363 410 5.765182 GGGGATAGAAATGGTGTTGTAGATG 59.235 44.000 0.00 0.00 0.00 2.90
379 427 2.612285 ATGCGAGAGATGGGGATAGA 57.388 50.000 0.00 0.00 0.00 1.98
384 432 1.139654 TCTTGAATGCGAGAGATGGGG 59.860 52.381 0.00 0.00 30.89 4.96
399 447 2.365617 GGCTTCCTCGGTATGATCTTGA 59.634 50.000 0.00 0.00 0.00 3.02
411 459 2.680312 TCAAGAGATTGGCTTCCTCG 57.320 50.000 0.00 0.00 32.52 4.63
423 471 1.825474 GGGAGTTGGTCGATCAAGAGA 59.175 52.381 12.34 0.00 0.00 3.10
463 516 2.805657 GCCATGCCGTTTACTACCCTAG 60.806 54.545 0.00 0.00 0.00 3.02
516 572 2.528743 GGATGTCATGCAGCGTCGG 61.529 63.158 0.00 0.00 33.59 4.79
633 692 1.069636 GTGACGCAGGAAGCTTTCTTG 60.070 52.381 3.86 3.19 42.61 3.02
637 696 1.609208 AATGTGACGCAGGAAGCTTT 58.391 45.000 0.00 0.00 42.61 3.51
645 707 1.586154 GGGGTGGAAATGTGACGCAG 61.586 60.000 0.00 0.00 0.00 5.18
648 710 0.538516 TTGGGGGTGGAAATGTGACG 60.539 55.000 0.00 0.00 0.00 4.35
651 713 1.554617 GGAATTGGGGGTGGAAATGTG 59.445 52.381 0.00 0.00 0.00 3.21
723 785 2.982744 GAACAAAGCTGAGCCGGGC 61.983 63.158 12.11 12.11 0.00 6.13
724 786 2.335712 GGAACAAAGCTGAGCCGGG 61.336 63.158 2.18 0.00 0.00 5.73
728 790 1.268079 GTGGAAGGAACAAAGCTGAGC 59.732 52.381 0.00 0.00 0.00 4.26
761 829 2.633488 GAGAAGTGGTGGCTATTGACC 58.367 52.381 0.00 0.00 0.00 4.02
806 874 0.752658 CGATCACCCATGACCTGCTA 59.247 55.000 0.00 0.00 37.79 3.49
827 895 1.527370 GAGGGTGTGGTGGCTATCC 59.473 63.158 0.00 0.00 0.00 2.59
976 1050 8.926710 CATATTCTCGAGGAATACACCAATTAC 58.073 37.037 13.56 0.00 45.97 1.89
977 1051 7.602644 GCATATTCTCGAGGAATACACCAATTA 59.397 37.037 13.56 0.00 45.97 1.40
978 1052 6.428159 GCATATTCTCGAGGAATACACCAATT 59.572 38.462 13.56 0.00 45.97 2.32
979 1053 5.934625 GCATATTCTCGAGGAATACACCAAT 59.065 40.000 13.56 4.11 45.97 3.16
980 1054 5.163353 TGCATATTCTCGAGGAATACACCAA 60.163 40.000 13.56 0.00 45.97 3.67
981 1055 4.343814 TGCATATTCTCGAGGAATACACCA 59.656 41.667 13.56 9.84 45.97 4.17
982 1056 4.883083 TGCATATTCTCGAGGAATACACC 58.117 43.478 13.56 7.85 45.97 4.16
996 1070 2.300152 TCCTCTCCGACCATGCATATTC 59.700 50.000 0.00 0.00 0.00 1.75
997 1071 2.301296 CTCCTCTCCGACCATGCATATT 59.699 50.000 0.00 0.00 0.00 1.28
1011 1085 0.179124 CGCAAGTGGTAGCTCCTCTC 60.179 60.000 0.00 0.00 38.87 3.20
1134 1224 2.105128 ATCCGGCGCTCTTCGAAG 59.895 61.111 19.35 19.35 41.67 3.79
1174 1270 3.279116 GTGCGTCACTTGCTGCCA 61.279 61.111 0.00 0.00 0.00 4.92
1209 1323 1.213430 TGCAGAGATTCCATGCCATGA 59.787 47.619 6.18 0.00 39.22 3.07
1243 1360 5.477984 TGGACCAGAAAAGAGAAAATGATGG 59.522 40.000 0.00 0.00 0.00 3.51
1264 1381 3.125656 AGGAATGGTCATCTTCCATGGA 58.874 45.455 11.44 11.44 43.85 3.41
1343 1460 2.187946 CTGACCCTCGGATGTGGC 59.812 66.667 0.00 0.00 0.00 5.01
1359 1476 2.988010 TATCCATGACTCGCAAAGCT 57.012 45.000 0.00 0.00 0.00 3.74
1374 1491 5.059404 CCAAGTTGGTGTTGTTGATATCC 57.941 43.478 14.21 0.00 31.35 2.59
1388 1511 2.600470 AACAACATGCACCAAGTTGG 57.400 45.000 20.76 20.76 44.13 3.77
1441 1564 2.872245 CGGTGCTATGGTATGTCCTTTG 59.128 50.000 0.00 0.00 37.07 2.77
1508 1631 2.085343 ATCCTTGTGCCCTGCCAGTT 62.085 55.000 0.00 0.00 0.00 3.16
1531 1654 3.306780 ATCTTGGTAGACCCACGAAAGTG 60.307 47.826 0.00 0.00 43.99 3.16
1593 1716 3.676291 GAGAATAGCCATGTCTCCTCC 57.324 52.381 0.00 0.00 33.16 4.30
1669 1794 1.003118 ACACGGATAAGCCACACATGT 59.997 47.619 0.00 0.00 35.94 3.21
1838 1972 9.399403 GTATAGATAGATATGTGTGTGTGTGTG 57.601 37.037 0.00 0.00 0.00 3.82
1861 1995 9.134055 GACTACCAACTAAGACATTAGGAGTAT 57.866 37.037 0.57 0.00 42.38 2.12
1932 2066 1.236026 TGGGAGGAGGTGGGAGGTAT 61.236 60.000 0.00 0.00 0.00 2.73
2178 2342 1.139095 CGTGGCTTACTCGAGGGAC 59.861 63.158 18.41 9.21 38.27 4.46
2442 2606 2.436115 GTTTCCTTCTCCGCCCCG 60.436 66.667 0.00 0.00 0.00 5.73
2724 7331 4.181309 TCACACGCATCAGTACATACAA 57.819 40.909 0.00 0.00 0.00 2.41


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

AutoCloner maintained by Alex Coulton.