Multiple sequence alignment - TraesCS6D01G250900

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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 TraesCS6D01G250900 chr6D 100.000 2708 0 0 1 2708 354838354 354835647 0.000000e+00 5001.0
1 TraesCS6D01G250900 chr6D 91.139 79 5 2 2594 2672 429354547 429354471 3.690000e-19 106.0
2 TraesCS6D01G250900 chr6B 94.008 1235 34 14 695 1909 523206164 523207378 0.000000e+00 1834.0
3 TraesCS6D01G250900 chr6B 89.668 271 26 2 372 640 523205647 523205917 7.180000e-91 344.0
4 TraesCS6D01G250900 chr6B 85.043 234 25 7 36 262 523204180 523204410 2.100000e-56 230.0
5 TraesCS6D01G250900 chr6A 97.050 1017 18 5 828 1835 486976222 486977235 0.000000e+00 1701.0
6 TraesCS6D01G250900 chr6A 85.185 594 69 8 1964 2545 486978269 486978855 2.320000e-165 592.0
7 TraesCS6D01G250900 chr6A 90.291 412 24 5 317 712 486975790 486976201 2.390000e-145 525.0
8 TraesCS6D01G250900 chr6A 92.377 223 15 1 1 221 486967673 486967895 1.560000e-82 316.0
9 TraesCS6D01G250900 chr6A 85.612 139 13 4 2543 2674 486978885 486979023 3.640000e-29 139.0
10 TraesCS6D01G250900 chr6A 91.000 100 5 3 1866 1961 486977221 486977320 6.080000e-27 132.0
11 TraesCS6D01G250900 chr4A 83.457 538 77 8 2006 2542 80852974 80853500 8.710000e-135 490.0
12 TraesCS6D01G250900 chr4A 83.054 478 64 9 2068 2533 1133575 1134047 4.170000e-113 418.0
13 TraesCS6D01G250900 chr4A 91.139 79 7 0 2594 2672 63750135 63750057 1.030000e-19 108.0
14 TraesCS6D01G250900 chr4A 90.123 81 7 1 2593 2673 564696615 564696536 1.330000e-18 104.0
15 TraesCS6D01G250900 chr5A 82.095 592 87 12 1966 2542 527397786 527398373 3.130000e-134 488.0
16 TraesCS6D01G250900 chr1D 81.588 592 92 10 1965 2542 364067792 364067204 8.770000e-130 473.0
17 TraesCS6D01G250900 chr7A 82.407 540 86 6 2006 2541 718513124 718512590 1.900000e-126 462.0
18 TraesCS6D01G250900 chr7A 83.158 285 37 4 2266 2539 696635784 696635500 1.610000e-62 250.0
19 TraesCS6D01G250900 chr7A 91.250 80 6 1 2594 2673 232336873 232336951 1.030000e-19 108.0
20 TraesCS6D01G250900 chr7A 89.286 84 6 3 2590 2672 620860161 620860080 4.770000e-18 102.0
21 TraesCS6D01G250900 chr7A 88.372 86 7 3 2590 2673 64372347 64372431 1.720000e-17 100.0
22 TraesCS6D01G250900 chr4D 83.665 502 67 11 2008 2497 344128783 344128285 2.460000e-125 459.0
23 TraesCS6D01G250900 chr4D 75.581 258 38 12 12 245 121437057 121437313 1.330000e-18 104.0
24 TraesCS6D01G250900 chr2D 82.890 526 75 6 2008 2521 641490310 641489788 2.460000e-125 459.0
25 TraesCS6D01G250900 chr2D 78.924 223 31 12 26 243 37044337 37044548 1.310000e-28 137.0
26 TraesCS6D01G250900 chr3D 82.674 531 77 7 2006 2524 530410730 530410203 8.840000e-125 457.0
27 TraesCS6D01G250900 chr3D 84.038 426 64 3 2006 2429 121875447 121875870 9.030000e-110 407.0
28 TraesCS6D01G250900 chr3D 84.000 425 64 3 2006 2428 121797050 121797472 3.250000e-109 405.0
29 TraesCS6D01G250900 chr3D 93.750 48 3 0 822 869 23840331 23840378 3.740000e-09 73.1
30 TraesCS6D01G250900 chr3D 100.000 28 0 0 26 53 15002839 15002812 5.000000e-03 52.8
31 TraesCS6D01G250900 chr3A 82.874 508 72 8 2050 2544 696617183 696617688 2.470000e-120 442.0
32 TraesCS6D01G250900 chr5D 81.748 515 87 5 2010 2520 500488204 500488715 8.960000e-115 424.0
33 TraesCS6D01G250900 chr5B 81.723 476 81 3 2067 2541 399797592 399798062 2.530000e-105 392.0
34 TraesCS6D01G250900 chr4B 81.944 216 34 3 2327 2542 529860991 529861201 7.700000e-41 178.0
35 TraesCS6D01G250900 chr2B 77.826 230 33 14 26 250 63837545 63837329 2.830000e-25 126.0
36 TraesCS6D01G250900 chr3B 92.593 81 5 1 2594 2674 790172194 790172115 6.130000e-22 115.0
37 TraesCS6D01G250900 chr3B 91.667 48 4 0 822 869 41508317 41508270 1.740000e-07 67.6
38 TraesCS6D01G250900 chr7B 91.250 80 6 1 2594 2673 718781207 718781129 1.030000e-19 108.0
39 TraesCS6D01G250900 chr1B 100.000 40 0 0 136 175 207264926 207264965 1.040000e-09 75.0


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 TraesCS6D01G250900 chr6D 354835647 354838354 2707 True 5001.000000 5001 100.0000 1 2708 1 chr6D.!!$R1 2707
1 TraesCS6D01G250900 chr6B 523204180 523207378 3198 False 802.666667 1834 89.5730 36 1909 3 chr6B.!!$F1 1873
2 TraesCS6D01G250900 chr6A 486975790 486979023 3233 False 617.800000 1701 89.8276 317 2674 5 chr6A.!!$F2 2357
3 TraesCS6D01G250900 chr4A 80852974 80853500 526 False 490.000000 490 83.4570 2006 2542 1 chr4A.!!$F2 536
4 TraesCS6D01G250900 chr5A 527397786 527398373 587 False 488.000000 488 82.0950 1966 2542 1 chr5A.!!$F1 576
5 TraesCS6D01G250900 chr1D 364067204 364067792 588 True 473.000000 473 81.5880 1965 2542 1 chr1D.!!$R1 577
6 TraesCS6D01G250900 chr7A 718512590 718513124 534 True 462.000000 462 82.4070 2006 2541 1 chr7A.!!$R3 535
7 TraesCS6D01G250900 chr2D 641489788 641490310 522 True 459.000000 459 82.8900 2008 2521 1 chr2D.!!$R1 513
8 TraesCS6D01G250900 chr3D 530410203 530410730 527 True 457.000000 457 82.6740 2006 2524 1 chr3D.!!$R2 518
9 TraesCS6D01G250900 chr3A 696617183 696617688 505 False 442.000000 442 82.8740 2050 2544 1 chr3A.!!$F1 494
10 TraesCS6D01G250900 chr5D 500488204 500488715 511 False 424.000000 424 81.7480 2010 2520 1 chr5D.!!$F1 510

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
276 282 0.039798 TGACGACGGTCCGAAGAAAG 60.04 55.0 20.51 4.7 42.73 2.62 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2082 4477 0.322187 GCCCCTGCGAGGACTAAAAA 60.322 55.0 4.0 0.0 37.67 1.94 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
21 22 4.278975 GACTCCTCACTTCCATGTTTCT 57.721 45.455 0.00 0.00 0.00 2.52
22 23 3.999663 GACTCCTCACTTCCATGTTTCTG 59.000 47.826 0.00 0.00 0.00 3.02
23 24 3.648067 ACTCCTCACTTCCATGTTTCTGA 59.352 43.478 0.00 0.00 0.00 3.27
24 25 4.103153 ACTCCTCACTTCCATGTTTCTGAA 59.897 41.667 0.00 0.00 0.00 3.02
25 26 4.645535 TCCTCACTTCCATGTTTCTGAAG 58.354 43.478 7.00 7.00 40.96 3.02
26 27 4.347876 TCCTCACTTCCATGTTTCTGAAGA 59.652 41.667 13.52 0.00 39.01 2.87
27 28 5.065914 CCTCACTTCCATGTTTCTGAAGAA 58.934 41.667 13.52 0.00 39.01 2.52
28 29 5.532406 CCTCACTTCCATGTTTCTGAAGAAA 59.468 40.000 13.52 1.31 41.29 2.52
29 30 6.293845 CCTCACTTCCATGTTTCTGAAGAAAG 60.294 42.308 13.52 10.02 43.82 2.62
30 31 6.356556 TCACTTCCATGTTTCTGAAGAAAGA 58.643 36.000 13.52 5.48 43.82 2.52
31 32 6.828273 TCACTTCCATGTTTCTGAAGAAAGAA 59.172 34.615 13.52 5.64 43.82 2.52
32 33 7.339212 TCACTTCCATGTTTCTGAAGAAAGAAA 59.661 33.333 13.52 0.00 43.82 2.52
33 34 8.139989 CACTTCCATGTTTCTGAAGAAAGAAAT 58.860 33.333 13.52 0.00 45.37 2.17
34 35 8.355913 ACTTCCATGTTTCTGAAGAAAGAAATC 58.644 33.333 13.52 0.00 45.37 2.17
37 38 6.210185 CCATGTTTCTGAAGAAAGAAATCCCT 59.790 38.462 5.74 0.00 45.37 4.20
45 46 4.263018 AGAAAGAAATCCCTTGCAAAGC 57.737 40.909 0.00 0.00 44.44 3.51
69 70 9.421806 AGCAATCAACGAAAATCAAATAAATCA 57.578 25.926 0.00 0.00 0.00 2.57
71 72 9.956797 CAATCAACGAAAATCAAATAAATCACC 57.043 29.630 0.00 0.00 0.00 4.02
72 73 9.703892 AATCAACGAAAATCAAATAAATCACCA 57.296 25.926 0.00 0.00 0.00 4.17
138 139 8.370940 TCAAGTCACATCATATCCTTCCTTATC 58.629 37.037 0.00 0.00 0.00 1.75
155 158 5.012893 CCTTATCTTTGCCTATGGATTCCC 58.987 45.833 0.00 0.00 0.00 3.97
157 160 4.821532 ATCTTTGCCTATGGATTCCCTT 57.178 40.909 0.00 0.00 0.00 3.95
159 162 3.117512 TCTTTGCCTATGGATTCCCTTCC 60.118 47.826 0.00 0.00 36.24 3.46
161 164 1.149101 GCCTATGGATTCCCTTCCCA 58.851 55.000 0.00 0.00 34.67 4.37
166 169 1.153539 TGGATTCCCTTCCCACAACA 58.846 50.000 0.00 0.00 34.67 3.33
180 183 7.395190 TTCCCACAACATATCTCAATTTCAG 57.605 36.000 0.00 0.00 0.00 3.02
187 190 8.404000 ACAACATATCTCAATTTCAGCTCAATC 58.596 33.333 0.00 0.00 0.00 2.67
188 191 8.403236 CAACATATCTCAATTTCAGCTCAATCA 58.597 33.333 0.00 0.00 0.00 2.57
189 192 8.155821 ACATATCTCAATTTCAGCTCAATCAG 57.844 34.615 0.00 0.00 0.00 2.90
190 193 7.991460 ACATATCTCAATTTCAGCTCAATCAGA 59.009 33.333 0.00 0.00 0.00 3.27
220 226 7.649533 TCTACATCGGACCACTAGAATAAAA 57.350 36.000 0.00 0.00 0.00 1.52
227 233 4.341235 GGACCACTAGAATAAAATTGCCCC 59.659 45.833 0.00 0.00 0.00 5.80
229 235 6.335781 ACCACTAGAATAAAATTGCCCCTA 57.664 37.500 0.00 0.00 0.00 3.53
232 238 7.287696 ACCACTAGAATAAAATTGCCCCTATTG 59.712 37.037 0.00 0.00 0.00 1.90
252 258 1.468054 GCAATGCACGGGTTCATTCTC 60.468 52.381 0.00 0.00 31.15 2.87
253 259 1.811965 CAATGCACGGGTTCATTCTCA 59.188 47.619 0.00 0.00 31.15 3.27
254 260 2.198827 ATGCACGGGTTCATTCTCAA 57.801 45.000 0.00 0.00 0.00 3.02
256 262 0.804989 GCACGGGTTCATTCTCAAGG 59.195 55.000 0.00 0.00 0.00 3.61
257 263 1.882352 GCACGGGTTCATTCTCAAGGT 60.882 52.381 0.00 0.00 0.00 3.50
258 264 1.806542 CACGGGTTCATTCTCAAGGTG 59.193 52.381 0.00 0.00 0.00 4.00
259 265 1.697432 ACGGGTTCATTCTCAAGGTGA 59.303 47.619 0.00 0.00 0.00 4.02
260 266 2.076863 CGGGTTCATTCTCAAGGTGAC 58.923 52.381 0.00 0.00 0.00 3.67
262 268 2.289444 GGGTTCATTCTCAAGGTGACGA 60.289 50.000 0.00 0.00 0.00 4.20
263 269 2.737252 GGTTCATTCTCAAGGTGACGAC 59.263 50.000 0.00 0.00 0.00 4.34
265 271 1.067846 TCATTCTCAAGGTGACGACGG 60.068 52.381 0.00 0.00 0.00 4.79
268 274 1.080705 CTCAAGGTGACGACGGTCC 60.081 63.158 1.91 0.00 42.73 4.46
269 275 2.430244 CAAGGTGACGACGGTCCG 60.430 66.667 10.48 10.48 42.73 4.79
271 277 2.195567 AAGGTGACGACGGTCCGAA 61.196 57.895 20.51 0.00 42.73 4.30
272 278 2.126580 GGTGACGACGGTCCGAAG 60.127 66.667 20.51 13.49 42.73 3.79
274 280 1.283793 GTGACGACGGTCCGAAGAA 59.716 57.895 20.51 2.92 42.73 2.52
275 281 0.318107 GTGACGACGGTCCGAAGAAA 60.318 55.000 20.51 0.00 42.73 2.52
276 282 0.039798 TGACGACGGTCCGAAGAAAG 60.040 55.000 20.51 4.70 42.73 2.62
277 283 1.342796 GACGACGGTCCGAAGAAAGC 61.343 60.000 20.51 0.00 37.19 3.51
281 287 1.667830 CGGTCCGAAGAAAGCAGCA 60.668 57.895 4.91 0.00 0.00 4.41
282 288 1.227999 CGGTCCGAAGAAAGCAGCAA 61.228 55.000 4.91 0.00 0.00 3.91
283 289 0.238553 GGTCCGAAGAAAGCAGCAAC 59.761 55.000 0.00 0.00 0.00 4.17
284 290 0.238553 GTCCGAAGAAAGCAGCAACC 59.761 55.000 0.00 0.00 0.00 3.77
296 328 3.084786 AGCAGCAACCAATAGGACTTTC 58.915 45.455 0.00 0.00 38.69 2.62
297 329 3.084786 GCAGCAACCAATAGGACTTTCT 58.915 45.455 0.00 0.00 38.69 2.52
305 337 7.201741 GCAACCAATAGGACTTTCTTAATCCTC 60.202 40.741 0.00 0.00 42.08 3.71
306 338 7.757242 ACCAATAGGACTTTCTTAATCCTCT 57.243 36.000 0.00 0.00 42.08 3.69
307 339 7.797062 ACCAATAGGACTTTCTTAATCCTCTC 58.203 38.462 0.00 0.00 42.08 3.20
308 340 7.625682 ACCAATAGGACTTTCTTAATCCTCTCT 59.374 37.037 0.00 0.00 42.08 3.10
309 341 8.490311 CCAATAGGACTTTCTTAATCCTCTCTT 58.510 37.037 0.00 0.00 42.08 2.85
310 342 9.541143 CAATAGGACTTTCTTAATCCTCTCTTC 57.459 37.037 0.00 0.00 42.08 2.87
311 343 6.553953 AGGACTTTCTTAATCCTCTCTTCC 57.446 41.667 0.00 0.00 38.55 3.46
312 344 6.268414 AGGACTTTCTTAATCCTCTCTTCCT 58.732 40.000 0.00 0.00 38.55 3.36
313 345 6.733334 AGGACTTTCTTAATCCTCTCTTCCTT 59.267 38.462 0.00 0.00 38.55 3.36
314 346 7.238723 AGGACTTTCTTAATCCTCTCTTCCTTT 59.761 37.037 0.00 0.00 38.55 3.11
315 347 7.551262 GGACTTTCTTAATCCTCTCTTCCTTTC 59.449 40.741 0.00 0.00 0.00 2.62
316 348 7.978925 ACTTTCTTAATCCTCTCTTCCTTTCA 58.021 34.615 0.00 0.00 0.00 2.69
317 349 8.100164 ACTTTCTTAATCCTCTCTTCCTTTCAG 58.900 37.037 0.00 0.00 0.00 3.02
318 350 7.798710 TTCTTAATCCTCTCTTCCTTTCAGA 57.201 36.000 0.00 0.00 0.00 3.27
418 1605 8.964772 GGTACTACTAAGTTTGTAAGATCCTGA 58.035 37.037 0.00 0.00 37.15 3.86
504 1691 2.430244 CCACGTCGTCAACCCTCG 60.430 66.667 0.00 0.00 0.00 4.63
599 1804 6.438741 TGGAGCTCTAATTTCTCTCTCTTTGA 59.561 38.462 14.64 0.00 0.00 2.69
621 1826 4.752879 TCAGTAGGGTTGCGCGCC 62.753 66.667 30.77 14.42 0.00 6.53
768 2183 8.828688 AAAAACATTCTAGCGTTCTTAGTACT 57.171 30.769 0.00 0.00 0.00 2.73
769 2184 7.813852 AAACATTCTAGCGTTCTTAGTACTG 57.186 36.000 5.39 0.00 0.00 2.74
770 2185 6.512342 ACATTCTAGCGTTCTTAGTACTGT 57.488 37.500 5.39 0.00 0.00 3.55
771 2186 6.553524 ACATTCTAGCGTTCTTAGTACTGTC 58.446 40.000 5.39 0.00 0.00 3.51
772 2187 6.150641 ACATTCTAGCGTTCTTAGTACTGTCA 59.849 38.462 5.39 0.00 0.00 3.58
773 2188 6.754702 TTCTAGCGTTCTTAGTACTGTCAT 57.245 37.500 5.39 0.00 0.00 3.06
774 2189 6.120378 TCTAGCGTTCTTAGTACTGTCATG 57.880 41.667 5.39 0.00 0.00 3.07
775 2190 5.878669 TCTAGCGTTCTTAGTACTGTCATGA 59.121 40.000 5.39 0.00 0.00 3.07
776 2191 5.584253 AGCGTTCTTAGTACTGTCATGAT 57.416 39.130 5.39 0.00 0.00 2.45
777 2192 5.967088 AGCGTTCTTAGTACTGTCATGATT 58.033 37.500 5.39 0.00 0.00 2.57
778 2193 5.807520 AGCGTTCTTAGTACTGTCATGATTG 59.192 40.000 5.39 0.00 0.00 2.67
779 2194 5.805486 GCGTTCTTAGTACTGTCATGATTGA 59.195 40.000 5.39 0.00 0.00 2.57
780 2195 6.477033 GCGTTCTTAGTACTGTCATGATTGAT 59.523 38.462 5.39 0.00 33.56 2.57
781 2196 7.010552 GCGTTCTTAGTACTGTCATGATTGATT 59.989 37.037 5.39 0.00 33.56 2.57
782 2197 9.516314 CGTTCTTAGTACTGTCATGATTGATTA 57.484 33.333 5.39 0.00 33.56 1.75
883 2298 3.854784 GCAAACGAAGAAAAGAGCAGCAT 60.855 43.478 0.00 0.00 0.00 3.79
893 2308 2.267174 AGAGCAGCATTGACAGTTGT 57.733 45.000 0.00 0.00 0.00 3.32
918 2333 0.250467 GGCACTGGCAGTTGAGAAGA 60.250 55.000 19.43 0.00 43.71 2.87
919 2334 1.597742 GCACTGGCAGTTGAGAAGAA 58.402 50.000 19.43 0.00 40.72 2.52
920 2335 1.534595 GCACTGGCAGTTGAGAAGAAG 59.465 52.381 19.43 4.34 40.72 2.85
1730 3164 4.033684 GCAGCATCAGTGAATTCGAAATC 58.966 43.478 0.00 3.61 0.00 2.17
1733 3167 3.242543 GCATCAGTGAATTCGAAATCGCT 60.243 43.478 20.80 20.80 39.60 4.93
1844 3279 1.888512 ACGCCATGTTTCATTGCTTCT 59.111 42.857 0.00 0.00 0.00 2.85
1848 3283 4.418392 GCCATGTTTCATTGCTTCTACTG 58.582 43.478 0.00 0.00 0.00 2.74
1904 3339 7.227512 GGACTTATTGAATCTTTGGATGTCGAT 59.772 37.037 0.00 0.00 31.75 3.59
1922 3359 5.052238 TGTCGATTGTATGTTATAACGCACG 60.052 40.000 10.92 9.93 0.00 5.34
1929 3366 7.343614 TGTATGTTATAACGCACGTAACAAA 57.656 32.000 12.38 2.07 40.47 2.83
1961 3398 8.123445 ACTAAGTGTAAAACGTGTTCTAAGTG 57.877 34.615 0.00 0.00 0.00 3.16
1962 3399 6.973229 AAGTGTAAAACGTGTTCTAAGTGT 57.027 33.333 0.00 0.00 0.00 3.55
1984 4368 1.341156 AAGCCTTCCTCCCCTCGATG 61.341 60.000 0.00 0.00 0.00 3.84
2065 4460 4.222847 GGTGCCTCGGATCCGGTC 62.223 72.222 32.79 21.23 40.25 4.79
2082 4477 1.062352 GGTCAGTGGATAGGTAGGGGT 60.062 57.143 0.00 0.00 0.00 4.95
2159 4554 0.179070 GTCTTCCTGGCTTCGATCCC 60.179 60.000 2.26 0.00 0.00 3.85
2162 4558 0.988145 TTCCTGGCTTCGATCCCCAT 60.988 55.000 2.26 0.00 0.00 4.00
2177 4573 1.129811 CCCCATAAGTTCGTTCGTTGC 59.870 52.381 0.00 0.00 0.00 4.17
2213 4609 2.234908 AGCTTCGGTGTAGATTCTTGCT 59.765 45.455 0.00 0.00 0.00 3.91
2224 4620 1.683917 GATTCTTGCTAGCTCCTCGGA 59.316 52.381 17.23 2.41 0.00 4.55
2392 4788 4.003788 CGACAAGGTCAGGCCGGT 62.004 66.667 1.90 0.00 43.70 5.28
2470 4886 6.441924 AGGTGATCCATGAACCTCGATATAAT 59.558 38.462 0.00 0.00 40.34 1.28
2607 5058 1.006758 TGGATGTACTCCCTCCGTTCT 59.993 52.381 8.36 0.00 44.23 3.01
2616 5067 8.716674 TGTACTCCCTCCGTTCTTAAATATAT 57.283 34.615 0.00 0.00 0.00 0.86
2674 5132 6.183360 ACGAAGCAAAATAAGTGAATCTACGG 60.183 38.462 0.00 0.00 0.00 4.02
2675 5133 6.035650 CGAAGCAAAATAAGTGAATCTACGGA 59.964 38.462 0.00 0.00 0.00 4.69
2676 5134 7.412563 CGAAGCAAAATAAGTGAATCTACGGAA 60.413 37.037 0.00 0.00 0.00 4.30
2677 5135 7.308782 AGCAAAATAAGTGAATCTACGGAAG 57.691 36.000 0.00 0.00 0.00 3.46
2678 5136 5.965918 GCAAAATAAGTGAATCTACGGAAGC 59.034 40.000 0.00 0.00 0.00 3.86
2679 5137 6.183360 GCAAAATAAGTGAATCTACGGAAGCT 60.183 38.462 0.00 0.00 0.00 3.74
2680 5138 7.402640 CAAAATAAGTGAATCTACGGAAGCTC 58.597 38.462 0.00 0.00 0.00 4.09
2681 5139 5.854010 ATAAGTGAATCTACGGAAGCTCA 57.146 39.130 0.00 0.00 0.00 4.26
2682 5140 4.744795 AAGTGAATCTACGGAAGCTCAT 57.255 40.909 0.00 0.00 0.00 2.90
2683 5141 4.052159 AGTGAATCTACGGAAGCTCATG 57.948 45.455 0.00 0.00 0.00 3.07
2684 5142 3.449018 AGTGAATCTACGGAAGCTCATGT 59.551 43.478 0.00 0.00 0.00 3.21
2685 5143 3.553511 GTGAATCTACGGAAGCTCATGTG 59.446 47.826 0.00 0.00 0.00 3.21
2686 5144 2.231215 ATCTACGGAAGCTCATGTGC 57.769 50.000 11.79 11.79 0.00 4.57
2687 5145 1.186200 TCTACGGAAGCTCATGTGCT 58.814 50.000 16.33 16.33 46.40 4.40
2688 5146 2.375146 TCTACGGAAGCTCATGTGCTA 58.625 47.619 21.70 5.91 43.24 3.49
2689 5147 2.359214 TCTACGGAAGCTCATGTGCTAG 59.641 50.000 21.70 17.33 43.24 3.42
2690 5148 0.460987 ACGGAAGCTCATGTGCTAGC 60.461 55.000 21.70 16.08 43.24 3.42
2694 5152 1.440893 AGCTCATGTGCTAGCTCGG 59.559 57.895 20.22 8.94 45.92 4.63
2695 5153 1.593750 GCTCATGTGCTAGCTCGGG 60.594 63.158 17.23 8.58 35.80 5.14
2696 5154 2.021068 GCTCATGTGCTAGCTCGGGA 62.021 60.000 17.23 12.31 35.80 5.14
2697 5155 0.678395 CTCATGTGCTAGCTCGGGAT 59.322 55.000 17.23 0.00 0.00 3.85
2698 5156 1.889170 CTCATGTGCTAGCTCGGGATA 59.111 52.381 17.23 0.00 0.00 2.59
2699 5157 2.495270 CTCATGTGCTAGCTCGGGATAT 59.505 50.000 17.23 0.00 0.00 1.63
2700 5158 2.232208 TCATGTGCTAGCTCGGGATATG 59.768 50.000 17.23 11.31 0.00 1.78
2701 5159 1.704641 TGTGCTAGCTCGGGATATGT 58.295 50.000 17.23 0.00 0.00 2.29
2702 5160 1.341209 TGTGCTAGCTCGGGATATGTG 59.659 52.381 17.23 0.00 0.00 3.21
2703 5161 0.318441 TGCTAGCTCGGGATATGTGC 59.682 55.000 17.23 0.00 0.00 4.57
2704 5162 0.318441 GCTAGCTCGGGATATGTGCA 59.682 55.000 7.70 0.00 0.00 4.57
2705 5163 1.066573 GCTAGCTCGGGATATGTGCAT 60.067 52.381 7.70 0.00 0.00 3.96
2706 5164 2.886081 CTAGCTCGGGATATGTGCATC 58.114 52.381 0.00 0.00 0.00 3.91
2707 5165 1.051008 AGCTCGGGATATGTGCATCA 58.949 50.000 0.00 0.00 0.00 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.999663 CAGAAACATGGAAGTGAGGAGTC 59.000 47.826 0.00 0.00 0.00 3.36
1 2 3.648067 TCAGAAACATGGAAGTGAGGAGT 59.352 43.478 0.00 0.00 0.00 3.85
2 3 4.277515 TCAGAAACATGGAAGTGAGGAG 57.722 45.455 0.00 0.00 0.00 3.69
3 4 4.347876 TCTTCAGAAACATGGAAGTGAGGA 59.652 41.667 0.00 0.00 39.19 3.71
4 5 4.645535 TCTTCAGAAACATGGAAGTGAGG 58.354 43.478 0.00 0.00 39.19 3.86
5 6 6.484643 TCTTTCTTCAGAAACATGGAAGTGAG 59.515 38.462 0.00 3.44 38.94 3.51
6 7 6.356556 TCTTTCTTCAGAAACATGGAAGTGA 58.643 36.000 0.00 0.00 38.94 3.41
7 8 6.624352 TCTTTCTTCAGAAACATGGAAGTG 57.376 37.500 0.00 0.00 38.94 3.16
8 9 7.645058 TTTCTTTCTTCAGAAACATGGAAGT 57.355 32.000 0.00 0.00 37.77 3.01
9 10 7.811713 GGATTTCTTTCTTCAGAAACATGGAAG 59.188 37.037 0.00 0.00 43.88 3.46
10 11 7.255942 GGGATTTCTTTCTTCAGAAACATGGAA 60.256 37.037 0.00 0.00 43.88 3.53
11 12 6.209391 GGGATTTCTTTCTTCAGAAACATGGA 59.791 38.462 0.00 0.00 43.88 3.41
12 13 6.210185 AGGGATTTCTTTCTTCAGAAACATGG 59.790 38.462 0.00 0.00 43.88 3.66
13 14 7.224522 AGGGATTTCTTTCTTCAGAAACATG 57.775 36.000 0.00 0.00 43.88 3.21
14 15 7.664758 CAAGGGATTTCTTTCTTCAGAAACAT 58.335 34.615 0.00 0.00 43.88 2.71
15 16 6.461509 GCAAGGGATTTCTTTCTTCAGAAACA 60.462 38.462 0.00 0.00 43.88 2.83
16 17 5.923114 GCAAGGGATTTCTTTCTTCAGAAAC 59.077 40.000 0.00 0.00 43.88 2.78
17 18 5.598005 TGCAAGGGATTTCTTTCTTCAGAAA 59.402 36.000 2.07 2.07 44.90 2.52
18 19 5.139727 TGCAAGGGATTTCTTTCTTCAGAA 58.860 37.500 0.00 0.00 0.00 3.02
19 20 4.728772 TGCAAGGGATTTCTTTCTTCAGA 58.271 39.130 0.00 0.00 0.00 3.27
20 21 5.458041 TTGCAAGGGATTTCTTTCTTCAG 57.542 39.130 0.00 0.00 0.00 3.02
21 22 5.739935 GCTTTGCAAGGGATTTCTTTCTTCA 60.740 40.000 10.89 0.00 0.00 3.02
22 23 4.687948 GCTTTGCAAGGGATTTCTTTCTTC 59.312 41.667 10.89 0.00 0.00 2.87
23 24 4.101430 TGCTTTGCAAGGGATTTCTTTCTT 59.899 37.500 10.89 0.00 34.76 2.52
24 25 3.642848 TGCTTTGCAAGGGATTTCTTTCT 59.357 39.130 10.89 0.00 34.76 2.52
25 26 3.993920 TGCTTTGCAAGGGATTTCTTTC 58.006 40.909 10.89 0.00 34.76 2.62
26 27 4.420522 TTGCTTTGCAAGGGATTTCTTT 57.579 36.364 10.89 0.00 43.99 2.52
45 46 9.956797 GGTGATTTATTTGATTTTCGTTGATTG 57.043 29.630 0.00 0.00 0.00 2.67
85 86 9.401873 GTTGACTTTGTTGTTTTACTACAAGTT 57.598 29.630 6.86 0.32 42.71 2.66
91 92 9.005777 ACTTGAGTTGACTTTGTTGTTTTACTA 57.994 29.630 0.00 0.00 0.00 1.82
93 94 7.806014 TGACTTGAGTTGACTTTGTTGTTTTAC 59.194 33.333 0.00 0.00 0.00 2.01
138 139 3.225940 GGAAGGGAATCCATAGGCAAAG 58.774 50.000 0.09 0.00 39.42 2.77
155 158 7.395190 TGAAATTGAGATATGTTGTGGGAAG 57.605 36.000 0.00 0.00 0.00 3.46
157 160 5.357878 GCTGAAATTGAGATATGTTGTGGGA 59.642 40.000 0.00 0.00 0.00 4.37
159 162 6.094464 TGAGCTGAAATTGAGATATGTTGTGG 59.906 38.462 0.00 0.00 0.00 4.17
161 164 7.692460 TTGAGCTGAAATTGAGATATGTTGT 57.308 32.000 0.00 0.00 0.00 3.32
166 169 8.430431 TCTCTGATTGAGCTGAAATTGAGATAT 58.570 33.333 9.64 0.00 42.38 1.63
180 183 6.073873 CCGATGTAGATTTTCTCTGATTGAGC 60.074 42.308 0.00 0.00 42.38 4.26
187 190 4.806247 GTGGTCCGATGTAGATTTTCTCTG 59.194 45.833 0.00 0.00 35.28 3.35
188 191 4.712337 AGTGGTCCGATGTAGATTTTCTCT 59.288 41.667 0.00 0.00 38.06 3.10
189 192 5.012328 AGTGGTCCGATGTAGATTTTCTC 57.988 43.478 0.00 0.00 0.00 2.87
190 193 5.892119 TCTAGTGGTCCGATGTAGATTTTCT 59.108 40.000 0.00 0.00 0.00 2.52
191 194 6.145338 TCTAGTGGTCCGATGTAGATTTTC 57.855 41.667 0.00 0.00 0.00 2.29
196 202 7.649533 TTTTATTCTAGTGGTCCGATGTAGA 57.350 36.000 0.00 0.00 0.00 2.59
201 207 5.531287 GGCAATTTTATTCTAGTGGTCCGAT 59.469 40.000 0.00 0.00 0.00 4.18
203 209 4.036380 GGGCAATTTTATTCTAGTGGTCCG 59.964 45.833 0.00 0.00 0.00 4.79
204 210 4.341235 GGGGCAATTTTATTCTAGTGGTCC 59.659 45.833 0.00 0.00 0.00 4.46
227 233 1.472082 TGAACCCGTGCATTGCAATAG 59.528 47.619 13.94 7.98 41.47 1.73
229 235 0.896923 ATGAACCCGTGCATTGCAAT 59.103 45.000 13.94 5.99 41.47 3.56
232 238 0.527565 AGAATGAACCCGTGCATTGC 59.472 50.000 5.76 0.46 35.05 3.56
252 258 2.410638 TTCGGACCGTCGTCACCTTG 62.411 60.000 14.79 0.00 41.13 3.61
253 259 2.138656 CTTCGGACCGTCGTCACCTT 62.139 60.000 14.79 0.00 41.13 3.50
254 260 2.595463 TTCGGACCGTCGTCACCT 60.595 61.111 14.79 0.00 41.13 4.00
256 262 0.318107 TTTCTTCGGACCGTCGTCAC 60.318 55.000 14.79 0.00 41.13 3.67
257 263 0.039798 CTTTCTTCGGACCGTCGTCA 60.040 55.000 14.79 0.00 41.13 4.35
258 264 1.342796 GCTTTCTTCGGACCGTCGTC 61.343 60.000 14.79 0.00 38.38 4.20
259 265 1.372623 GCTTTCTTCGGACCGTCGT 60.373 57.895 14.79 0.00 0.00 4.34
260 266 1.344942 CTGCTTTCTTCGGACCGTCG 61.345 60.000 14.79 6.31 0.00 5.12
262 268 1.668151 GCTGCTTTCTTCGGACCGT 60.668 57.895 14.79 0.00 0.00 4.83
263 269 1.227999 TTGCTGCTTTCTTCGGACCG 61.228 55.000 7.84 7.84 0.00 4.79
265 271 0.238553 GGTTGCTGCTTTCTTCGGAC 59.761 55.000 0.00 0.00 0.00 4.79
268 274 2.712057 ATTGGTTGCTGCTTTCTTCG 57.288 45.000 0.00 0.00 0.00 3.79
269 275 3.758554 TCCTATTGGTTGCTGCTTTCTTC 59.241 43.478 0.00 0.00 34.23 2.87
271 277 3.084786 GTCCTATTGGTTGCTGCTTTCT 58.915 45.455 0.00 0.00 34.23 2.52
272 278 3.084786 AGTCCTATTGGTTGCTGCTTTC 58.915 45.455 0.00 0.00 34.23 2.62
274 280 2.887151 AGTCCTATTGGTTGCTGCTT 57.113 45.000 0.00 0.00 34.23 3.91
275 281 2.887151 AAGTCCTATTGGTTGCTGCT 57.113 45.000 0.00 0.00 34.23 4.24
276 282 3.084786 AGAAAGTCCTATTGGTTGCTGC 58.915 45.455 0.00 0.00 34.23 5.25
277 283 6.817765 TTAAGAAAGTCCTATTGGTTGCTG 57.182 37.500 0.00 0.00 34.23 4.41
281 287 8.164057 AGAGGATTAAGAAAGTCCTATTGGTT 57.836 34.615 0.00 0.00 42.27 3.67
282 288 7.625682 AGAGAGGATTAAGAAAGTCCTATTGGT 59.374 37.037 0.00 0.00 42.27 3.67
283 289 8.028652 AGAGAGGATTAAGAAAGTCCTATTGG 57.971 38.462 0.00 0.00 42.27 3.16
284 290 9.541143 GAAGAGAGGATTAAGAAAGTCCTATTG 57.459 37.037 0.00 0.00 42.27 1.90
344 376 3.691049 ACCACTTCGTCAACACATTTG 57.309 42.857 0.00 0.00 0.00 2.32
345 377 3.242608 CGAACCACTTCGTCAACACATTT 60.243 43.478 0.00 0.00 43.68 2.32
364 396 9.211485 GGCCTTATATAGCAACTTAATAACGAA 57.789 33.333 0.00 0.00 0.00 3.85
418 1605 3.587061 TGACTGAGGGATAACAACATGGT 59.413 43.478 0.00 0.00 0.00 3.55
504 1691 2.202756 GGATGACGACCTGCGGAC 60.203 66.667 0.00 0.00 46.49 4.79
599 1804 1.296715 CGCAACCCTACTGAAGCCT 59.703 57.895 0.00 0.00 0.00 4.58
621 1826 4.440127 GCTGCAAATGCCCCACCG 62.440 66.667 2.46 0.00 41.18 4.94
747 2162 6.150641 TGACAGTACTAAGAACGCTAGAATGT 59.849 38.462 0.00 0.00 0.00 2.71
748 2163 6.552629 TGACAGTACTAAGAACGCTAGAATG 58.447 40.000 0.00 0.00 0.00 2.67
755 2170 5.805486 TCAATCATGACAGTACTAAGAACGC 59.195 40.000 0.00 0.00 0.00 4.84
820 2235 9.619316 CATACACATCGTTTCCTCAATTTTTAA 57.381 29.630 0.00 0.00 0.00 1.52
865 2280 3.058639 GTCAATGCTGCTCTTTTCTTCGT 60.059 43.478 0.00 0.00 0.00 3.85
883 2298 0.254462 TGCCCACTCACAACTGTCAA 59.746 50.000 0.00 0.00 0.00 3.18
893 2308 2.756042 AACTGCCAGTGCCCACTCA 61.756 57.895 0.00 0.00 40.20 3.41
920 2335 8.847307 TATGAGGTCCATAGAGGTGTGTACCC 62.847 50.000 0.00 0.00 41.04 3.69
1730 3164 5.510671 ACAGACAACAAAGAATTACAAGCG 58.489 37.500 0.00 0.00 0.00 4.68
1733 3167 7.773864 TCGTACAGACAACAAAGAATTACAA 57.226 32.000 0.00 0.00 0.00 2.41
1844 3279 3.971305 TCTTGGAAGAGAACAACCCAGTA 59.029 43.478 0.00 0.00 0.00 2.74
1869 3304 8.954350 CAAAGATTCAATAAGTCCAAGATGAGT 58.046 33.333 0.00 0.00 0.00 3.41
1870 3305 8.404000 CCAAAGATTCAATAAGTCCAAGATGAG 58.596 37.037 0.00 0.00 0.00 2.90
1904 3339 6.941218 TGTTACGTGCGTTATAACATACAA 57.059 33.333 15.67 3.09 34.65 2.41
1929 3366 6.752168 ACACGTTTTACACTTAGTACATCCT 58.248 36.000 0.00 0.00 30.91 3.24
1961 3398 1.407025 CGAGGGGAGGAAGGCTTTTAC 60.407 57.143 0.00 0.00 0.00 2.01
1962 3399 0.909623 CGAGGGGAGGAAGGCTTTTA 59.090 55.000 0.00 0.00 0.00 1.52
2065 4460 4.586306 AAAAACCCCTACCTATCCACTG 57.414 45.455 0.00 0.00 0.00 3.66
2082 4477 0.322187 GCCCCTGCGAGGACTAAAAA 60.322 55.000 4.00 0.00 37.67 1.94
2159 4554 1.722464 TCGCAACGAACGAACTTATGG 59.278 47.619 0.14 0.00 36.44 2.74
2162 4558 1.722464 CCATCGCAACGAACGAACTTA 59.278 47.619 0.14 0.00 43.71 2.24
2177 4573 2.667137 GAAGCTCCGTCTAATCCATCG 58.333 52.381 0.00 0.00 0.00 3.84
2224 4620 1.697982 AGAAACCTTAACCTCACCGCT 59.302 47.619 0.00 0.00 0.00 5.52
2229 4625 2.624838 ACGACGAGAAACCTTAACCTCA 59.375 45.455 0.00 0.00 0.00 3.86
2392 4788 0.681887 TCGCCACTCTCATACCGGAA 60.682 55.000 9.46 0.00 0.00 4.30
2420 4836 2.282391 ATTGCTGCCGCCAGAACA 60.282 55.556 0.00 0.00 41.77 3.18
2432 4848 2.420129 GGATCACCTAACGACCATTGCT 60.420 50.000 0.00 0.00 0.00 3.91
2474 4890 9.744468 GAAGTACAAAACACCTCAAACATAATT 57.256 29.630 0.00 0.00 0.00 1.40
2546 4997 7.730364 TCCATCAAGTCAAAGAACTTAACTC 57.270 36.000 0.00 0.00 37.38 3.01
2553 5004 7.202016 TGTTGTATCCATCAAGTCAAAGAAC 57.798 36.000 0.00 0.00 0.00 3.01
2641 5099 8.181487 TCACTTATTTTGCTTCGTATGTAGTC 57.819 34.615 0.00 0.00 0.00 2.59
2644 5102 9.378551 AGATTCACTTATTTTGCTTCGTATGTA 57.621 29.630 0.00 0.00 0.00 2.29
2648 5106 7.009815 CCGTAGATTCACTTATTTTGCTTCGTA 59.990 37.037 0.00 0.00 0.00 3.43
2651 5109 7.303634 TCCGTAGATTCACTTATTTTGCTTC 57.696 36.000 0.00 0.00 0.00 3.86
2652 5110 7.626452 GCTTCCGTAGATTCACTTATTTTGCTT 60.626 37.037 0.00 0.00 0.00 3.91
2677 5135 1.593750 CCCGAGCTAGCACATGAGC 60.594 63.158 18.83 7.07 39.08 4.26
2678 5136 0.678395 ATCCCGAGCTAGCACATGAG 59.322 55.000 18.83 0.15 0.00 2.90
2679 5137 1.995376 TATCCCGAGCTAGCACATGA 58.005 50.000 18.83 10.10 0.00 3.07
2680 5138 2.028658 ACATATCCCGAGCTAGCACATG 60.029 50.000 18.83 12.03 0.00 3.21
2681 5139 2.028658 CACATATCCCGAGCTAGCACAT 60.029 50.000 18.83 3.10 0.00 3.21
2682 5140 1.341209 CACATATCCCGAGCTAGCACA 59.659 52.381 18.83 0.00 0.00 4.57
2683 5141 1.937108 GCACATATCCCGAGCTAGCAC 60.937 57.143 18.83 10.18 0.00 4.40
2684 5142 0.318441 GCACATATCCCGAGCTAGCA 59.682 55.000 18.83 0.00 0.00 3.49
2685 5143 0.318441 TGCACATATCCCGAGCTAGC 59.682 55.000 6.62 6.62 0.00 3.42
2686 5144 2.232208 TGATGCACATATCCCGAGCTAG 59.768 50.000 0.00 0.00 0.00 3.42
2687 5145 2.247358 TGATGCACATATCCCGAGCTA 58.753 47.619 0.00 0.00 0.00 3.32
2688 5146 1.051008 TGATGCACATATCCCGAGCT 58.949 50.000 0.00 0.00 0.00 4.09
2689 5147 3.612517 TGATGCACATATCCCGAGC 57.387 52.632 0.00 0.00 0.00 5.03


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

AutoCloner maintained by Alex Coulton.