Multiple sequence alignment - TraesCS6D01G333000

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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 TraesCS6D01G333000 chr6D 100.000 2780 0 0 1 2780 435710668 435713447 0.000000e+00 5134
1 TraesCS6D01G333000 chr6D 89.125 754 71 9 1222 1964 435749971 435750724 0.000000e+00 928
2 TraesCS6D01G333000 chr6D 83.122 1025 98 50 780 1778 435963503 435962528 0.000000e+00 865
3 TraesCS6D01G333000 chr6D 86.441 767 58 20 801 1539 435763535 435764283 0.000000e+00 798
4 TraesCS6D01G333000 chr6D 87.387 555 51 11 607 1152 435749414 435749958 1.090000e-173 619
5 TraesCS6D01G333000 chr6D 94.366 213 11 1 1986 2197 435750820 435751032 2.670000e-85 326
6 TraesCS6D01G333000 chr6D 92.793 222 13 3 664 883 435810490 435810270 4.470000e-83 318
7 TraesCS6D01G333000 chr6B 91.796 1292 63 16 642 1913 658476991 658478259 0.000000e+00 1759
8 TraesCS6D01G333000 chr6B 91.802 1293 60 18 642 1913 658495777 658497044 0.000000e+00 1759
9 TraesCS6D01G333000 chr6B 91.641 1292 65 16 642 1913 658514927 658516195 0.000000e+00 1748
10 TraesCS6D01G333000 chr6B 84.711 968 92 28 607 1539 658530152 658531098 0.000000e+00 917
11 TraesCS6D01G333000 chr6B 82.115 1135 129 42 780 1898 658578687 658577611 0.000000e+00 904
12 TraesCS6D01G333000 chr6B 84.132 605 62 14 1988 2591 658478405 658478976 3.130000e-154 555
13 TraesCS6D01G333000 chr6B 84.132 605 62 14 1988 2591 658516341 658516912 3.130000e-154 555
14 TraesCS6D01G333000 chr6B 83.967 605 63 14 1988 2591 658497190 658497761 1.460000e-152 549
15 TraesCS6D01G333000 chr6B 90.730 356 26 3 1613 1962 658531132 658531486 4.190000e-128 468
16 TraesCS6D01G333000 chr6B 76.637 565 70 42 774 1284 658402725 658403281 3.550000e-64 255
17 TraesCS6D01G333000 chrUn 92.243 954 41 11 642 1585 389578176 389577246 0.000000e+00 1321
18 TraesCS6D01G333000 chrUn 92.515 815 30 9 779 1585 465805809 465805018 0.000000e+00 1138
19 TraesCS6D01G333000 chr6A 86.930 1140 79 38 852 1964 582511134 582512230 0.000000e+00 1216
20 TraesCS6D01G333000 chr6A 82.125 1393 147 57 607 1960 582516032 582517361 0.000000e+00 1099
21 TraesCS6D01G333000 chr6A 84.753 892 84 28 1 865 582508683 582509549 0.000000e+00 846
22 TraesCS6D01G333000 chr6A 88.350 618 59 9 1222 1831 582631211 582630599 0.000000e+00 730
23 TraesCS6D01G333000 chr6A 85.135 592 58 15 1331 1913 582920906 582920336 1.860000e-161 579
24 TraesCS6D01G333000 chr6A 90.347 404 34 4 1990 2392 582512334 582512733 2.450000e-145 525
25 TraesCS6D01G333000 chr6A 89.516 248 22 2 940 1183 582631462 582631215 7.480000e-81 311
26 TraesCS6D01G333000 chr6A 89.732 224 19 4 664 885 582633113 582632892 1.630000e-72 283
27 TraesCS6D01G333000 chr2D 90.289 484 46 1 1 484 190599813 190600295 1.400000e-177 632
28 TraesCS6D01G333000 chr2D 90.126 476 46 1 9 484 372703012 372702538 3.930000e-173 617
29 TraesCS6D01G333000 chr2D 88.660 485 49 4 1 484 490819771 490820250 1.110000e-163 586
30 TraesCS6D01G333000 chr7D 88.484 521 50 6 1 515 511647996 511648512 3.040000e-174 621
31 TraesCS6D01G333000 chr7D 88.406 483 55 1 4 486 203946561 203947042 5.160000e-162 580
32 TraesCS6D01G333000 chr7B 89.937 477 46 2 1 477 540776451 540776925 5.090000e-172 614
33 TraesCS6D01G333000 chr4A 89.004 482 51 2 4 484 648473178 648472698 1.840000e-166 595
34 TraesCS6D01G333000 chr5B 88.797 482 52 2 4 484 508816823 508816343 8.580000e-165 590
35 TraesCS6D01G333000 chr4D 88.406 483 51 4 4 484 67273246 67272767 6.680000e-161 577


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 TraesCS6D01G333000 chr6D 435710668 435713447 2779 False 5134.000000 5134 100.000000 1 2780 1 chr6D.!!$F1 2779
1 TraesCS6D01G333000 chr6D 435962528 435963503 975 True 865.000000 865 83.122000 780 1778 1 chr6D.!!$R2 998
2 TraesCS6D01G333000 chr6D 435763535 435764283 748 False 798.000000 798 86.441000 801 1539 1 chr6D.!!$F2 738
3 TraesCS6D01G333000 chr6D 435749414 435751032 1618 False 624.333333 928 90.292667 607 2197 3 chr6D.!!$F3 1590
4 TraesCS6D01G333000 chr6B 658476991 658478976 1985 False 1157.000000 1759 87.964000 642 2591 2 chr6B.!!$F2 1949
5 TraesCS6D01G333000 chr6B 658495777 658497761 1984 False 1154.000000 1759 87.884500 642 2591 2 chr6B.!!$F3 1949
6 TraesCS6D01G333000 chr6B 658514927 658516912 1985 False 1151.500000 1748 87.886500 642 2591 2 chr6B.!!$F4 1949
7 TraesCS6D01G333000 chr6B 658577611 658578687 1076 True 904.000000 904 82.115000 780 1898 1 chr6B.!!$R1 1118
8 TraesCS6D01G333000 chr6B 658530152 658531486 1334 False 692.500000 917 87.720500 607 1962 2 chr6B.!!$F5 1355
9 TraesCS6D01G333000 chr6B 658402725 658403281 556 False 255.000000 255 76.637000 774 1284 1 chr6B.!!$F1 510
10 TraesCS6D01G333000 chrUn 389577246 389578176 930 True 1321.000000 1321 92.243000 642 1585 1 chrUn.!!$R1 943
11 TraesCS6D01G333000 chrUn 465805018 465805809 791 True 1138.000000 1138 92.515000 779 1585 1 chrUn.!!$R2 806
12 TraesCS6D01G333000 chr6A 582508683 582517361 8678 False 921.500000 1216 86.038750 1 2392 4 chr6A.!!$F1 2391
13 TraesCS6D01G333000 chr6A 582920336 582920906 570 True 579.000000 579 85.135000 1331 1913 1 chr6A.!!$R1 582
14 TraesCS6D01G333000 chr6A 582630599 582633113 2514 True 441.333333 730 89.199333 664 1831 3 chr6A.!!$R2 1167
15 TraesCS6D01G333000 chr7D 511647996 511648512 516 False 621.000000 621 88.484000 1 515 1 chr7D.!!$F2 514

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
234 236 0.098376 ATCCGTACTGCGTCTTCGAC 59.902 55.0 0.0 0.0 39.71 4.2 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2133 5412 0.59411 TTTCGGTGGTGCGGATTTTC 59.406 50.0 0.0 0.0 0.0 2.29 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
65 66 2.125106 GGAAGCCATCCGCGTTCT 60.125 61.111 4.92 0.00 44.76 3.01
151 153 4.511246 CCATGCCCGGACTGCCAT 62.511 66.667 0.73 0.00 0.00 4.40
178 180 1.344763 AGGAGAAGGAGGACAACAACG 59.655 52.381 0.00 0.00 0.00 4.10
186 188 2.315386 GGACAACAACGGCGAGGAC 61.315 63.158 16.62 0.00 0.00 3.85
191 193 2.357517 CAACGGCGAGGACAGCTT 60.358 61.111 16.62 0.00 34.52 3.74
192 194 2.048127 AACGGCGAGGACAGCTTC 60.048 61.111 16.62 0.00 34.52 3.86
196 198 2.876645 GCGAGGACAGCTTCGACG 60.877 66.667 9.64 8.63 45.33 5.12
198 200 1.512310 CGAGGACAGCTTCGACGAC 60.512 63.158 0.00 0.00 45.33 4.34
209 211 1.568025 TCGACGACGAGCATATCCG 59.432 57.895 5.75 0.00 43.81 4.18
218 220 1.893786 AGCATATCCGGCTCGATCC 59.106 57.895 0.00 0.00 36.81 3.36
225 227 2.353607 CGGCTCGATCCGTACTGC 60.354 66.667 19.25 0.00 44.18 4.40
226 228 2.353607 GGCTCGATCCGTACTGCG 60.354 66.667 0.00 0.00 40.95 5.18
227 229 2.408022 GCTCGATCCGTACTGCGT 59.592 61.111 0.00 0.00 39.32 5.24
228 230 1.654743 GCTCGATCCGTACTGCGTC 60.655 63.158 0.00 0.00 39.32 5.19
229 231 2.015382 CTCGATCCGTACTGCGTCT 58.985 57.895 0.00 0.00 39.32 4.18
230 232 0.377554 CTCGATCCGTACTGCGTCTT 59.622 55.000 0.00 0.00 39.32 3.01
231 233 0.376152 TCGATCCGTACTGCGTCTTC 59.624 55.000 0.00 0.00 39.32 2.87
232 234 0.924363 CGATCCGTACTGCGTCTTCG 60.924 60.000 0.00 0.00 39.32 3.79
233 235 0.376152 GATCCGTACTGCGTCTTCGA 59.624 55.000 0.00 0.00 39.71 3.71
234 236 0.098376 ATCCGTACTGCGTCTTCGAC 59.902 55.000 0.00 0.00 39.71 4.20
235 237 1.513586 CCGTACTGCGTCTTCGACC 60.514 63.158 0.00 0.00 39.71 4.79
266 268 3.119096 GAAGGACGACAAGGGCGC 61.119 66.667 0.00 0.00 0.00 6.53
315 317 4.018870 TGAACTCCACCATAGCCAAACATA 60.019 41.667 0.00 0.00 0.00 2.29
316 318 3.886123 ACTCCACCATAGCCAAACATAC 58.114 45.455 0.00 0.00 0.00 2.39
349 351 2.493278 AGTCCAATGGCATGTTTAGTGC 59.507 45.455 0.00 0.00 41.78 4.40
354 356 0.597568 TGGCATGTTTAGTGCAGTGC 59.402 50.000 8.58 8.58 44.25 4.40
366 368 1.884926 GCAGTGCGATGGAGTAGCC 60.885 63.158 0.00 0.00 37.10 3.93
368 370 2.279517 GTGCGATGGAGTAGCCGG 60.280 66.667 0.00 0.00 40.66 6.13
375 377 0.755698 ATGGAGTAGCCGGACGATGT 60.756 55.000 5.05 0.00 40.66 3.06
376 378 1.065928 GGAGTAGCCGGACGATGTG 59.934 63.158 5.05 0.00 0.00 3.21
438 440 7.505258 TGAAATATGATAATTGAGGTGTCCGA 58.495 34.615 0.00 0.00 0.00 4.55
449 451 6.433847 TTGAGGTGTCCGAATATGGATTAT 57.566 37.500 0.00 0.00 40.91 1.28
471 473 2.249844 TTTTTGAGGAGTGTCCGGTC 57.750 50.000 0.00 0.00 42.75 4.79
473 475 0.679505 TTTGAGGAGTGTCCGGTCAG 59.320 55.000 0.19 0.00 42.75 3.51
476 478 2.048127 GGAGTGTCCGGTCAGTGC 60.048 66.667 14.00 12.84 0.00 4.40
494 496 3.508840 CCGCGGATGTTTGAGGGC 61.509 66.667 24.07 0.00 0.00 5.19
496 498 3.508840 GCGGATGTTTGAGGGCCG 61.509 66.667 0.00 0.00 44.47 6.13
498 500 2.674754 GGATGTTTGAGGGCCGGA 59.325 61.111 5.05 0.00 0.00 5.14
499 501 1.227383 GGATGTTTGAGGGCCGGAT 59.773 57.895 5.05 0.00 0.00 4.18
501 503 1.474330 GATGTTTGAGGGCCGGATTT 58.526 50.000 5.05 0.00 0.00 2.17
502 504 1.134946 GATGTTTGAGGGCCGGATTTG 59.865 52.381 5.05 0.00 0.00 2.32
518 538 0.320073 TTTGTAAGTCCGGCTGGTCG 60.320 55.000 12.43 0.00 36.30 4.79
529 549 1.446966 GCTGGTCGGTCAGAGAAGC 60.447 63.158 9.52 0.00 36.93 3.86
564 584 1.298488 GAGGATCGGTTCGACGCTC 60.298 63.158 0.00 0.00 39.18 5.03
569 589 0.100146 ATCGGTTCGACGCTCTTACC 59.900 55.000 0.00 0.00 39.18 2.85
581 611 5.506815 CGACGCTCTTACCCTGTATTCAATA 60.507 44.000 0.00 0.00 0.00 1.90
583 613 6.456501 ACGCTCTTACCCTGTATTCAATATC 58.543 40.000 0.00 0.00 0.00 1.63
676 710 6.865834 AATGCATGGGTTTGGTCTATTTTA 57.134 33.333 0.00 0.00 0.00 1.52
719 754 5.464168 CGACAATTCCAGCTTTCATTTTCT 58.536 37.500 0.00 0.00 0.00 2.52
927 2572 4.137872 GCCCGCACACGTAGGCTA 62.138 66.667 8.70 0.00 41.67 3.93
928 2573 2.574929 CCCGCACACGTAGGCTAA 59.425 61.111 0.00 0.00 37.70 3.09
929 2574 1.143183 CCCGCACACGTAGGCTAAT 59.857 57.895 0.00 0.00 37.70 1.73
930 2575 0.461339 CCCGCACACGTAGGCTAATT 60.461 55.000 0.00 0.00 37.70 1.40
931 2576 0.650512 CCGCACACGTAGGCTAATTG 59.349 55.000 0.00 0.00 37.70 2.32
932 2577 1.355971 CGCACACGTAGGCTAATTGT 58.644 50.000 0.00 0.00 33.53 2.71
933 2578 1.323534 CGCACACGTAGGCTAATTGTC 59.676 52.381 0.00 0.00 33.53 3.18
1045 4104 2.880890 AGCAAGACAACACACCAGATTC 59.119 45.455 0.00 0.00 0.00 2.52
1319 4442 5.995282 TGCTTGTTGCTAACACTAGTTGTAT 59.005 36.000 0.00 0.00 41.97 2.29
1345 4471 2.481185 TGCGTGTTTCCCGTTTAGATTC 59.519 45.455 0.00 0.00 0.00 2.52
1358 4484 6.974622 CCCGTTTAGATTCTGAATGAAAATGG 59.025 38.462 23.26 23.26 38.29 3.16
1386 4517 3.669122 CGACTGAATTTTCTCGTTCGTCT 59.331 43.478 0.00 0.00 31.76 4.18
1518 4653 4.269523 GGGCAGCAGGGTCACACA 62.270 66.667 0.00 0.00 0.00 3.72
1767 4929 9.851686 ATAATAAGATGGAGATGCAGTAAAACA 57.148 29.630 0.00 0.00 0.00 2.83
1819 4981 7.834068 TGTAATATCTGAGTTCTGAGTTTGC 57.166 36.000 0.00 0.00 0.00 3.68
1822 4984 2.487934 TCTGAGTTCTGAGTTTGCTGC 58.512 47.619 0.00 0.00 0.00 5.25
1826 4988 3.181466 TGAGTTCTGAGTTTGCTGCACTA 60.181 43.478 0.00 0.00 0.00 2.74
1848 5022 5.138125 AGAATTTGGGTTGCTTGTATGTG 57.862 39.130 0.00 0.00 0.00 3.21
1885 5059 5.414765 TGTACTCTGTACTTCGATGTGTGAT 59.585 40.000 13.80 0.00 0.00 3.06
1921 5109 4.129380 CACTGTGTATGTATGGGGATGTG 58.871 47.826 0.00 0.00 0.00 3.21
1926 5114 5.168569 GTGTATGTATGGGGATGTGTATCG 58.831 45.833 0.00 0.00 33.98 2.92
1966 5244 3.726291 TTGCCCTTTTACTTGAGCAAC 57.274 42.857 0.00 0.00 35.46 4.17
1980 5259 9.651913 TTACTTGAGCAACTTTTGAAAATTTCT 57.348 25.926 7.29 0.00 0.00 2.52
1982 5261 9.305925 ACTTGAGCAACTTTTGAAAATTTCTAG 57.694 29.630 7.29 4.78 0.00 2.43
1983 5262 8.647143 TTGAGCAACTTTTGAAAATTTCTAGG 57.353 30.769 7.29 0.00 0.00 3.02
1984 5263 6.701400 TGAGCAACTTTTGAAAATTTCTAGGC 59.299 34.615 7.29 2.10 0.00 3.93
1985 5264 6.581712 AGCAACTTTTGAAAATTTCTAGGCA 58.418 32.000 7.29 0.00 0.00 4.75
1986 5265 7.047271 AGCAACTTTTGAAAATTTCTAGGCAA 58.953 30.769 7.29 0.00 0.00 4.52
1987 5266 7.716560 AGCAACTTTTGAAAATTTCTAGGCAAT 59.283 29.630 7.29 0.00 0.00 3.56
1988 5267 8.344831 GCAACTTTTGAAAATTTCTAGGCAATT 58.655 29.630 7.29 0.00 0.00 2.32
2133 5412 1.009829 GAGTGCATAGCGACCAAAGG 58.990 55.000 0.00 0.00 0.00 3.11
2141 5421 1.165270 AGCGACCAAAGGAAAATCCG 58.835 50.000 0.00 0.00 42.75 4.18
2263 5544 4.939439 ACACCGATGAATGTTTTACCTACC 59.061 41.667 0.00 0.00 0.00 3.18
2270 5551 6.325919 TGAATGTTTTACCTACCTGCAAAG 57.674 37.500 0.00 0.00 0.00 2.77
2271 5552 5.830991 TGAATGTTTTACCTACCTGCAAAGT 59.169 36.000 0.00 0.00 0.00 2.66
2276 5557 6.153000 TGTTTTACCTACCTGCAAAGTTTTCA 59.847 34.615 0.00 0.00 0.00 2.69
2284 5565 6.610075 ACCTGCAAAGTTTTCATAATGGAT 57.390 33.333 0.00 0.00 0.00 3.41
2328 5609 7.231115 AGGGCAATAAAAACAAAATCAATGCTT 59.769 29.630 0.00 0.00 0.00 3.91
2361 5642 8.146479 AGTCTTTTTGGAGCATTTGATTTTTC 57.854 30.769 0.00 0.00 0.00 2.29
2362 5643 7.042523 AGTCTTTTTGGAGCATTTGATTTTTCG 60.043 33.333 0.00 0.00 0.00 3.46
2371 5652 4.260948 GCATTTGATTTTTCGTTTTGCCCA 60.261 37.500 0.00 0.00 0.00 5.36
2373 5654 4.392921 TTGATTTTTCGTTTTGCCCAGA 57.607 36.364 0.00 0.00 0.00 3.86
2374 5655 3.976169 TGATTTTTCGTTTTGCCCAGAG 58.024 40.909 0.00 0.00 0.00 3.35
2377 5658 0.951558 TTTCGTTTTGCCCAGAGCTC 59.048 50.000 5.27 5.27 44.23 4.09
2380 5661 1.856265 CGTTTTGCCCAGAGCTCCAC 61.856 60.000 10.93 0.00 44.23 4.02
2469 6026 9.796062 CGGACATAATTGTTTGATTTTTCTTTG 57.204 29.630 0.00 0.00 35.79 2.77
2521 6078 2.771943 TCGGGATTAGAAGCTCCATGTT 59.228 45.455 0.00 0.00 32.90 2.71
2531 6088 0.323725 GCTCCATGTTCACCCACCAT 60.324 55.000 0.00 0.00 0.00 3.55
2538 6095 5.046735 TCCATGTTCACCCACCATTTAATTG 60.047 40.000 0.00 0.00 0.00 2.32
2583 6140 5.402270 TCTCGAATACATATGAATGTGCGTG 59.598 40.000 10.38 6.48 45.99 5.34
2592 6149 7.874940 ACATATGAATGTGCGTGCTTTATATT 58.125 30.769 10.38 0.00 44.79 1.28
2598 6155 8.454894 TGAATGTGCGTGCTTTATATTAAAGAA 58.545 29.630 10.42 0.00 0.00 2.52
2599 6156 8.841444 AATGTGCGTGCTTTATATTAAAGAAG 57.159 30.769 10.42 3.09 0.00 2.85
2600 6157 7.603963 TGTGCGTGCTTTATATTAAAGAAGA 57.396 32.000 10.42 0.00 0.00 2.87
2601 6158 7.684670 TGTGCGTGCTTTATATTAAAGAAGAG 58.315 34.615 10.42 0.41 0.00 2.85
2603 6160 8.058915 GTGCGTGCTTTATATTAAAGAAGAGAG 58.941 37.037 10.42 0.00 0.00 3.20
2604 6161 7.224753 TGCGTGCTTTATATTAAAGAAGAGAGG 59.775 37.037 10.42 0.00 0.00 3.69
2606 6163 7.171678 CGTGCTTTATATTAAAGAAGAGAGGGG 59.828 40.741 10.42 0.00 0.00 4.79
2607 6164 7.445707 GTGCTTTATATTAAAGAAGAGAGGGGG 59.554 40.741 10.42 0.00 0.00 5.40
2628 6185 3.267974 GCAAAGAGCCCTTCCACG 58.732 61.111 0.00 0.00 37.23 4.94
2629 6186 1.302511 GCAAAGAGCCCTTCCACGA 60.303 57.895 0.00 0.00 37.23 4.35
2630 6187 1.578206 GCAAAGAGCCCTTCCACGAC 61.578 60.000 0.00 0.00 37.23 4.34
2631 6188 1.004918 AAAGAGCCCTTCCACGACG 60.005 57.895 0.00 0.00 0.00 5.12
2633 6190 4.452733 GAGCCCTTCCACGACGGG 62.453 72.222 0.00 0.00 43.10 5.28
2636 6193 2.428622 CCCTTCCACGACGGGTTT 59.571 61.111 0.00 0.00 36.51 3.27
2637 6194 1.672898 CCCTTCCACGACGGGTTTA 59.327 57.895 0.00 0.00 36.51 2.01
2638 6195 0.390735 CCCTTCCACGACGGGTTTAG 60.391 60.000 0.00 0.00 36.51 1.85
2654 6211 7.542025 ACGGGTTTAGTAGTTCTTACATACAG 58.458 38.462 0.00 0.00 34.56 2.74
2655 6212 6.474751 CGGGTTTAGTAGTTCTTACATACAGC 59.525 42.308 0.00 0.00 34.56 4.40
2661 6218 6.631962 AGTAGTTCTTACATACAGCCAACTC 58.368 40.000 0.00 0.00 34.56 3.01
2664 6221 5.045578 AGTTCTTACATACAGCCAACTCCAT 60.046 40.000 0.00 0.00 0.00 3.41
2670 6227 2.036256 AGCCAACTCCATGCCCAC 59.964 61.111 0.00 0.00 0.00 4.61
2675 6232 0.962356 CAACTCCATGCCCACTCCAC 60.962 60.000 0.00 0.00 0.00 4.02
2684 6241 0.108756 GCCCACTCCACGTCTAAGTC 60.109 60.000 0.00 0.00 0.00 3.01
2692 6249 6.405953 CCACTCCACGTCTAAGTCAATCTATT 60.406 42.308 0.00 0.00 0.00 1.73
2715 6272 1.593296 AACTCCTCGCGTCACTACCC 61.593 60.000 5.77 0.00 0.00 3.69
2732 6290 3.091633 ACCCACCGTTAGAGCTACTAA 57.908 47.619 0.00 0.00 38.56 2.24
2740 6298 7.201803 CCACCGTTAGAGCTACTAAGAAACTAT 60.202 40.741 6.04 0.00 41.07 2.12
2742 6300 7.555554 ACCGTTAGAGCTACTAAGAAACTATCA 59.444 37.037 6.04 0.00 41.07 2.15
2748 6306 8.417884 AGAGCTACTAAGAAACTATCAATGTCC 58.582 37.037 0.00 0.00 0.00 4.02
2749 6307 7.203910 AGCTACTAAGAAACTATCAATGTCCG 58.796 38.462 0.00 0.00 0.00 4.79
2750 6308 6.979238 GCTACTAAGAAACTATCAATGTCCGT 59.021 38.462 0.00 0.00 0.00 4.69
2751 6309 7.167801 GCTACTAAGAAACTATCAATGTCCGTC 59.832 40.741 0.00 0.00 0.00 4.79
2761 6319 5.679734 ATCAATGTCCGTCTTGATAATGC 57.320 39.130 0.00 0.00 39.64 3.56
2765 6323 0.531974 TCCGTCTTGATAATGCCCGC 60.532 55.000 0.00 0.00 0.00 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 2.125350 GCTTCCTCCTCTGTGGCG 60.125 66.667 0.00 0.00 35.26 5.69
40 41 1.333636 CGGATGGCTTCCTCCTCTGT 61.334 60.000 16.47 0.00 42.99 3.41
62 63 3.210227 TGCCGTTTCTTCACAATGAGAA 58.790 40.909 0.00 0.00 0.00 2.87
63 64 2.807967 CTGCCGTTTCTTCACAATGAGA 59.192 45.455 0.00 0.00 0.00 3.27
65 66 1.266718 GCTGCCGTTTCTTCACAATGA 59.733 47.619 0.00 0.00 0.00 2.57
139 141 2.202932 CTTCGATGGCAGTCCGGG 60.203 66.667 0.00 0.00 34.14 5.73
145 147 0.826715 TTCTCCTCCTTCGATGGCAG 59.173 55.000 12.42 10.24 0.00 4.85
151 153 1.000496 TCCTCCTTCTCCTCCTTCGA 59.000 55.000 0.00 0.00 0.00 3.71
178 180 2.507324 GTCGAAGCTGTCCTCGCC 60.507 66.667 0.58 0.00 0.00 5.54
186 188 0.248094 TATGCTCGTCGTCGAAGCTG 60.248 55.000 17.37 8.12 45.61 4.24
191 193 1.568025 CGGATATGCTCGTCGTCGA 59.432 57.895 4.42 4.42 44.12 4.20
192 194 1.440518 CCGGATATGCTCGTCGTCG 60.441 63.158 0.00 0.00 38.55 5.12
196 198 4.561731 GAGCCGGATATGCTCGTC 57.438 61.111 5.05 0.00 45.05 4.20
209 211 2.353607 CGCAGTACGGATCGAGCC 60.354 66.667 10.41 10.41 38.44 4.70
246 248 2.342279 CCCTTGTCGTCCTTCGCA 59.658 61.111 0.00 0.00 39.67 5.10
248 250 2.809601 CGCCCTTGTCGTCCTTCG 60.810 66.667 0.00 0.00 41.41 3.79
333 335 2.353011 GCACTGCACTAAACATGCCATT 60.353 45.455 0.00 0.00 42.69 3.16
337 339 0.516877 TCGCACTGCACTAAACATGC 59.483 50.000 1.11 0.00 43.68 4.06
349 351 1.589993 CGGCTACTCCATCGCACTG 60.590 63.158 0.00 0.00 34.01 3.66
354 356 1.516365 ATCGTCCGGCTACTCCATCG 61.516 60.000 0.00 0.00 34.01 3.84
366 368 2.430075 TCGCACACACATCGTCCG 60.430 61.111 0.00 0.00 0.00 4.79
368 370 1.728074 TCGTCGCACACACATCGTC 60.728 57.895 0.00 0.00 0.00 4.20
375 377 0.585838 TAACTACGTCGTCGCACACA 59.414 50.000 0.00 0.00 41.18 3.72
376 378 0.970606 GTAACTACGTCGTCGCACAC 59.029 55.000 0.00 0.00 41.18 3.82
383 385 7.859377 CCATATAAACTCATGTAACTACGTCGT 59.141 37.037 2.21 2.21 0.00 4.34
414 416 7.962964 TCGGACACCTCAATTATCATATTTC 57.037 36.000 0.00 0.00 0.00 2.17
460 462 2.048127 GGCACTGACCGGACACTC 60.048 66.667 9.46 0.00 0.00 3.51
471 473 3.055719 AAACATCCGCGGGCACTG 61.056 61.111 27.83 19.29 38.10 3.66
473 475 3.039202 CTCAAACATCCGCGGGCAC 62.039 63.158 27.83 0.00 0.00 5.01
476 478 2.824041 CCCTCAAACATCCGCGGG 60.824 66.667 27.83 13.23 0.00 6.13
484 486 0.178975 ACAAATCCGGCCCTCAAACA 60.179 50.000 0.00 0.00 0.00 2.83
496 498 1.339727 ACCAGCCGGACTTACAAATCC 60.340 52.381 5.05 0.00 35.59 3.01
498 500 1.674817 CGACCAGCCGGACTTACAAAT 60.675 52.381 5.05 0.00 35.59 2.32
499 501 0.320073 CGACCAGCCGGACTTACAAA 60.320 55.000 5.05 0.00 35.59 2.83
501 503 2.967397 CGACCAGCCGGACTTACA 59.033 61.111 5.05 0.00 35.59 2.41
529 549 6.310960 CGATCCTCGATAACATGTTAGAGAG 58.689 44.000 28.46 28.46 43.74 3.20
535 555 4.369182 GAACCGATCCTCGATAACATGTT 58.631 43.478 16.68 16.68 43.74 2.71
536 556 3.550233 CGAACCGATCCTCGATAACATGT 60.550 47.826 0.00 0.00 43.74 3.21
537 557 2.980476 CGAACCGATCCTCGATAACATG 59.020 50.000 0.00 0.00 43.74 3.21
538 558 2.882761 TCGAACCGATCCTCGATAACAT 59.117 45.455 5.38 0.00 43.74 2.71
539 559 2.032550 GTCGAACCGATCCTCGATAACA 59.967 50.000 11.12 0.00 45.08 2.41
540 560 2.648426 GTCGAACCGATCCTCGATAAC 58.352 52.381 11.12 0.00 45.08 1.89
541 561 1.262417 CGTCGAACCGATCCTCGATAA 59.738 52.381 11.12 0.00 45.08 1.75
542 562 0.863799 CGTCGAACCGATCCTCGATA 59.136 55.000 11.12 0.00 45.08 2.92
543 563 1.647629 CGTCGAACCGATCCTCGAT 59.352 57.895 11.12 0.00 45.08 3.59
545 565 2.651232 GCGTCGAACCGATCCTCG 60.651 66.667 0.00 1.15 38.42 4.63
557 577 2.098607 TGAATACAGGGTAAGAGCGTCG 59.901 50.000 0.00 0.00 0.00 5.12
560 580 6.692486 AGATATTGAATACAGGGTAAGAGCG 58.308 40.000 0.00 0.00 0.00 5.03
656 688 6.872920 TGAATAAAATAGACCAAACCCATGC 58.127 36.000 0.00 0.00 0.00 4.06
676 710 2.095263 CGGCATGGAACGAAAACTGAAT 60.095 45.455 0.00 0.00 0.00 2.57
719 754 4.796312 GCAAAAGTCGTCTTGTTTGCTTTA 59.204 37.500 18.42 0.00 40.91 1.85
925 2570 0.602905 GATCGCCGGGGGACAATTAG 60.603 60.000 19.63 0.00 0.00 1.73
926 2571 1.338890 TGATCGCCGGGGGACAATTA 61.339 55.000 19.63 0.00 0.00 1.40
927 2572 1.994885 ATGATCGCCGGGGGACAATT 61.995 55.000 19.63 0.00 0.00 2.32
928 2573 1.125093 TATGATCGCCGGGGGACAAT 61.125 55.000 19.63 14.42 0.00 2.71
929 2574 1.125093 ATATGATCGCCGGGGGACAA 61.125 55.000 19.63 7.93 0.00 3.18
930 2575 1.535444 ATATGATCGCCGGGGGACA 60.535 57.895 19.63 18.12 0.00 4.02
931 2576 1.218316 GATATGATCGCCGGGGGAC 59.782 63.158 19.63 13.11 0.00 4.46
932 2577 1.987855 GGATATGATCGCCGGGGGA 60.988 63.158 19.63 16.73 0.00 4.81
933 2578 2.584608 GGATATGATCGCCGGGGG 59.415 66.667 19.63 4.42 0.00 5.40
1045 4104 6.647481 CAGATGCTGATCTTGATTCTCTTAGG 59.353 42.308 0.00 0.00 36.75 2.69
1327 4453 5.934935 TTCAGAATCTAAACGGGAAACAC 57.065 39.130 0.00 0.00 0.00 3.32
1345 4471 6.025896 CAGTCGTTGATCCATTTTCATTCAG 58.974 40.000 0.00 0.00 0.00 3.02
1358 4484 5.517037 ACGAGAAAATTCAGTCGTTGATC 57.483 39.130 5.06 0.00 42.81 2.92
1386 4517 3.969312 TGCCATCATCCTCAGACTATCAA 59.031 43.478 0.00 0.00 0.00 2.57
1518 4653 2.671070 CCAGTGCCGGTCATTCCT 59.329 61.111 1.90 0.00 0.00 3.36
1689 4843 1.888436 CTCAAGTAGCTGCCGTGGGA 61.888 60.000 0.00 0.00 0.00 4.37
1693 4847 0.969894 AACTCTCAAGTAGCTGCCGT 59.030 50.000 0.00 0.00 33.48 5.68
1767 4929 4.101741 AGCTAGCTCACTTTATTTCGGGAT 59.898 41.667 12.68 0.00 0.00 3.85
1819 4981 2.821969 AGCAACCCAAATTCTAGTGCAG 59.178 45.455 0.00 0.00 0.00 4.41
1822 4984 4.853924 ACAAGCAACCCAAATTCTAGTG 57.146 40.909 0.00 0.00 0.00 2.74
1826 4988 4.561326 GCACATACAAGCAACCCAAATTCT 60.561 41.667 0.00 0.00 0.00 2.40
1848 5022 1.293963 GAGTACAAAACGTCCCGGGC 61.294 60.000 18.49 10.58 0.00 6.13
1898 5073 4.037222 ACATCCCCATACATACACAGTGA 58.963 43.478 7.81 0.00 0.00 3.41
1979 5258 6.677781 TCGATACTTCCAAAAATTGCCTAG 57.322 37.500 0.00 0.00 0.00 3.02
1980 5259 7.455641 TTTCGATACTTCCAAAAATTGCCTA 57.544 32.000 0.00 0.00 0.00 3.93
1981 5260 5.975693 TTCGATACTTCCAAAAATTGCCT 57.024 34.783 0.00 0.00 0.00 4.75
1982 5261 7.414814 TTTTTCGATACTTCCAAAAATTGCC 57.585 32.000 0.00 0.00 0.00 4.52
1986 5265 9.366216 GCCTTATTTTTCGATACTTCCAAAAAT 57.634 29.630 8.40 8.40 40.12 1.82
1987 5266 8.361139 TGCCTTATTTTTCGATACTTCCAAAAA 58.639 29.630 0.00 0.00 33.46 1.94
1988 5267 7.810759 GTGCCTTATTTTTCGATACTTCCAAAA 59.189 33.333 0.00 0.00 0.00 2.44
1989 5268 7.040340 TGTGCCTTATTTTTCGATACTTCCAAA 60.040 33.333 0.00 0.00 0.00 3.28
1990 5269 6.431543 TGTGCCTTATTTTTCGATACTTCCAA 59.568 34.615 0.00 0.00 0.00 3.53
2133 5412 0.594110 TTTCGGTGGTGCGGATTTTC 59.406 50.000 0.00 0.00 0.00 2.29
2141 5421 2.357952 AGAAGAAAACTTTCGGTGGTGC 59.642 45.455 0.00 0.00 41.92 5.01
2237 5518 4.215399 AGGTAAAACATTCATCGGTGTGTG 59.785 41.667 0.00 0.00 0.00 3.82
2244 5525 4.634004 TGCAGGTAGGTAAAACATTCATCG 59.366 41.667 0.00 0.00 0.00 3.84
2263 5544 8.712285 ATCAATCCATTATGAAAACTTTGCAG 57.288 30.769 0.00 0.00 0.00 4.41
2276 5557 7.784073 TGACCACCACAAATATCAATCCATTAT 59.216 33.333 0.00 0.00 0.00 1.28
2284 5565 3.696045 CCCTGACCACCACAAATATCAA 58.304 45.455 0.00 0.00 0.00 2.57
2297 5578 5.359194 TTTTGTTTTTATTGCCCTGACCA 57.641 34.783 0.00 0.00 0.00 4.02
2328 5609 9.044150 CAAATGCTCCAAAAAGACTAATTTTGA 57.956 29.630 12.10 2.11 45.96 2.69
2343 5624 6.713520 CAAAACGAAAAATCAAATGCTCCAA 58.286 32.000 0.00 0.00 0.00 3.53
2361 5642 1.600636 TGGAGCTCTGGGCAAAACG 60.601 57.895 14.64 0.00 44.79 3.60
2362 5643 1.856265 CGTGGAGCTCTGGGCAAAAC 61.856 60.000 14.64 0.00 44.79 2.43
2371 5652 3.244215 TGAAATCACTTTCGTGGAGCTCT 60.244 43.478 14.64 0.00 43.10 4.09
2373 5654 3.126001 TGAAATCACTTTCGTGGAGCT 57.874 42.857 0.00 0.00 43.10 4.09
2374 5655 4.008539 GATGAAATCACTTTCGTGGAGC 57.991 45.455 0.00 0.00 44.70 4.70
2443 6000 9.796062 CAAAGAAAAATCAAACAATTATGTCCG 57.204 29.630 0.00 0.00 39.40 4.79
2465 6022 7.489113 GCACCCATATGAACAGTAAAATCAAAG 59.511 37.037 3.65 0.00 0.00 2.77
2469 6026 6.449635 TGCACCCATATGAACAGTAAAATC 57.550 37.500 3.65 0.00 0.00 2.17
2485 6042 0.396435 CCCGAGCTTATATGCACCCA 59.604 55.000 12.65 0.00 34.99 4.51
2521 6078 7.617329 TGTATGAATCAATTAAATGGTGGGTGA 59.383 33.333 0.00 0.00 0.00 4.02
2560 6117 5.602516 CACGCACATTCATATGTATTCGAG 58.397 41.667 1.90 0.00 43.07 4.04
2562 6119 4.084380 AGCACGCACATTCATATGTATTCG 60.084 41.667 1.90 5.03 43.07 3.34
2570 6127 9.877137 CTTTAATATAAAGCACGCACATTCATA 57.123 29.630 0.00 0.00 0.00 2.15
2572 6129 7.980062 TCTTTAATATAAAGCACGCACATTCA 58.020 30.769 5.23 0.00 0.00 2.57
2573 6130 8.835467 TTCTTTAATATAAAGCACGCACATTC 57.165 30.769 5.23 0.00 0.00 2.67
2583 6140 7.987750 CCCCCTCTCTTCTTTAATATAAAGC 57.012 40.000 5.23 0.00 0.00 3.51
2612 6169 1.291877 CGTCGTGGAAGGGCTCTTTG 61.292 60.000 0.00 0.00 32.52 2.77
2625 6182 3.565905 AGAACTACTAAACCCGTCGTG 57.434 47.619 0.00 0.00 0.00 4.35
2626 6183 4.518970 TGTAAGAACTACTAAACCCGTCGT 59.481 41.667 0.00 0.00 0.00 4.34
2627 6184 5.046910 TGTAAGAACTACTAAACCCGTCG 57.953 43.478 0.00 0.00 0.00 5.12
2628 6185 7.538575 TGTATGTAAGAACTACTAAACCCGTC 58.461 38.462 0.00 0.00 0.00 4.79
2629 6186 7.466746 TGTATGTAAGAACTACTAAACCCGT 57.533 36.000 0.00 0.00 0.00 5.28
2630 6187 6.474751 GCTGTATGTAAGAACTACTAAACCCG 59.525 42.308 0.00 0.00 0.00 5.28
2631 6188 6.760298 GGCTGTATGTAAGAACTACTAAACCC 59.240 42.308 0.00 0.00 0.00 4.11
2633 6190 8.654215 GTTGGCTGTATGTAAGAACTACTAAAC 58.346 37.037 0.00 0.00 0.00 2.01
2636 6193 7.147949 GGAGTTGGCTGTATGTAAGAACTACTA 60.148 40.741 0.00 0.00 0.00 1.82
2637 6194 6.351117 GGAGTTGGCTGTATGTAAGAACTACT 60.351 42.308 0.00 0.00 0.00 2.57
2638 6195 5.811100 GGAGTTGGCTGTATGTAAGAACTAC 59.189 44.000 0.00 0.00 0.00 2.73
2654 6211 2.036256 AGTGGGCATGGAGTTGGC 59.964 61.111 0.00 0.00 41.20 4.52
2655 6212 1.379044 GGAGTGGGCATGGAGTTGG 60.379 63.158 0.00 0.00 0.00 3.77
2661 6218 1.613317 TAGACGTGGAGTGGGCATGG 61.613 60.000 0.00 0.00 0.00 3.66
2664 6221 0.830444 ACTTAGACGTGGAGTGGGCA 60.830 55.000 0.00 0.00 0.00 5.36
2670 6227 5.460419 GCAATAGATTGACTTAGACGTGGAG 59.540 44.000 6.43 0.00 40.14 3.86
2675 6232 7.380065 GGAGTTAGCAATAGATTGACTTAGACG 59.620 40.741 6.43 0.00 40.14 4.18
2684 6241 3.426859 CGCGAGGAGTTAGCAATAGATTG 59.573 47.826 0.00 0.00 40.66 2.67
2692 6249 1.211969 GTGACGCGAGGAGTTAGCA 59.788 57.895 15.93 0.00 0.00 3.49
2715 6272 5.952033 AGTTTCTTAGTAGCTCTAACGGTG 58.048 41.667 0.00 0.00 35.17 4.94
2732 6290 6.037786 TCAAGACGGACATTGATAGTTTCT 57.962 37.500 0.00 0.00 30.67 2.52
2740 6298 3.876914 GGCATTATCAAGACGGACATTGA 59.123 43.478 0.00 0.00 39.59 2.57
2742 6300 3.214328 GGGCATTATCAAGACGGACATT 58.786 45.455 0.00 0.00 0.00 2.71
2747 6305 1.507141 GGCGGGCATTATCAAGACGG 61.507 60.000 0.00 0.00 0.00 4.79
2748 6306 1.831389 CGGCGGGCATTATCAAGACG 61.831 60.000 0.00 0.00 0.00 4.18
2749 6307 0.814010 ACGGCGGGCATTATCAAGAC 60.814 55.000 13.24 0.00 0.00 3.01
2750 6308 0.531974 GACGGCGGGCATTATCAAGA 60.532 55.000 13.24 0.00 0.00 3.02
2751 6309 0.532862 AGACGGCGGGCATTATCAAG 60.533 55.000 13.24 0.00 0.00 3.02
2761 6319 1.595382 GATCATGGAAGACGGCGGG 60.595 63.158 13.24 0.00 0.00 6.13


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

AutoCloner maintained by Alex Coulton.