Multiple sequence alignment - TraesCS4A01G468900

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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 TraesCS4A01G468900 chr4A 100.000 3565 0 0 1 3565 730885685 730889249 0.000000e+00 6584.0
1 TraesCS4A01G468900 chr4A 96.168 2636 95 6 568 3201 730279367 730281998 0.000000e+00 4303.0
2 TraesCS4A01G468900 chr4A 91.839 2181 140 20 905 3073 730787010 730784856 0.000000e+00 3007.0
3 TraesCS4A01G468900 chr4A 90.775 1767 124 18 1444 3201 730193841 730192105 0.000000e+00 2324.0
4 TraesCS4A01G468900 chr4A 90.961 1217 97 5 1561 2766 728851006 728852220 0.000000e+00 1626.0
5 TraesCS4A01G468900 chr4A 93.934 544 27 3 905 1444 730199164 730198623 0.000000e+00 817.0
6 TraesCS4A01G468900 chr4A 93.567 513 31 2 56 567 686632586 686632075 0.000000e+00 763.0
7 TraesCS4A01G468900 chr4A 93.640 456 28 1 113 567 659730226 659730681 0.000000e+00 680.0
8 TraesCS4A01G468900 chr4A 92.308 247 17 1 3241 3485 730282339 730282585 2.040000e-92 350.0
9 TraesCS4A01G468900 chr4A 91.429 245 19 1 3241 3483 730191763 730191519 5.700000e-88 335.0
10 TraesCS4A01G468900 chr4A 89.671 213 21 1 570 782 730790908 730790697 1.630000e-68 270.0
11 TraesCS4A01G468900 chr4A 92.754 69 5 0 905 973 728850406 728850474 2.260000e-17 100.0
12 TraesCS4A01G468900 chr4A 85.507 69 9 1 834 902 584037903 584037970 1.780000e-08 71.3
13 TraesCS4A01G468900 chr7A 91.086 2255 161 17 957 3198 9411275 9413502 0.000000e+00 3014.0
14 TraesCS4A01G468900 chr7A 91.093 247 20 1 3241 3485 9413837 9414083 2.050000e-87 333.0
15 TraesCS4A01G468900 chr7D 90.878 1754 124 21 1456 3201 8982152 8983877 0.000000e+00 2320.0
16 TraesCS4A01G468900 chr7D 91.677 1586 114 13 1625 3201 8988517 8990093 0.000000e+00 2182.0
17 TraesCS4A01G468900 chr7D 93.292 1133 67 4 1618 2741 9378349 9379481 0.000000e+00 1663.0
18 TraesCS4A01G468900 chr7D 93.485 614 30 4 957 1563 9377737 9378347 0.000000e+00 904.0
19 TraesCS4A01G468900 chr7D 92.832 558 40 0 904 1461 8981105 8981662 0.000000e+00 809.0
20 TraesCS4A01G468900 chr7D 91.379 464 34 4 1119 1582 8985509 8985966 6.500000e-177 630.0
21 TraesCS4A01G468900 chr7D 86.605 433 54 4 2770 3201 9379482 9379911 3.220000e-130 475.0
22 TraesCS4A01G468900 chr7D 94.694 245 11 1 3241 3483 8990412 8990656 2.600000e-101 379.0
23 TraesCS4A01G468900 chr7D 92.713 247 16 1 3241 3485 8984219 8984465 4.380000e-94 355.0
24 TraesCS4A01G468900 chr7D 90.254 236 14 5 3241 3475 9380256 9380483 2.080000e-77 300.0
25 TraesCS4A01G468900 chr5D 86.489 1014 121 12 1616 2619 445719892 445718885 0.000000e+00 1099.0
26 TraesCS4A01G468900 chr5D 89.292 551 49 5 902 1445 445720742 445720195 0.000000e+00 682.0
27 TraesCS4A01G468900 chrUn 100.000 442 0 0 712 1153 475916668 475917109 0.000000e+00 817.0
28 TraesCS4A01G468900 chrUn 91.493 529 30 7 55 582 383553822 383554336 0.000000e+00 713.0
29 TraesCS4A01G468900 chr6B 94.990 519 23 3 60 575 46511548 46511030 0.000000e+00 811.0
30 TraesCS4A01G468900 chr6B 94.872 507 24 2 62 567 383421104 383420599 0.000000e+00 791.0
31 TraesCS4A01G468900 chr6B 100.000 31 0 0 2778 2808 460923980 460923950 1.380000e-04 58.4
32 TraesCS4A01G468900 chr1B 94.685 508 26 1 54 560 489905061 489905568 0.000000e+00 787.0
33 TraesCS4A01G468900 chr1B 92.759 511 37 0 62 572 32226543 32226033 0.000000e+00 739.0
34 TraesCS4A01G468900 chr5B 92.979 527 17 7 52 568 53669363 53668847 0.000000e+00 750.0
35 TraesCS4A01G468900 chr5A 90.208 480 41 3 971 1444 563376435 563375956 3.910000e-174 621.0
36 TraesCS4A01G468900 chr5A 93.878 49 3 0 853 901 485616166 485616214 1.370000e-09 75.0
37 TraesCS4A01G468900 chr3B 95.129 349 14 1 60 405 773171807 773172155 6.730000e-152 547.0
38 TraesCS4A01G468900 chr3B 91.781 292 17 6 306 595 743614066 743613780 1.990000e-107 399.0
39 TraesCS4A01G468900 chr3B 91.781 292 17 6 306 595 743691610 743691324 1.990000e-107 399.0
40 TraesCS4A01G468900 chr6A 84.138 435 49 9 2769 3201 604452116 604452532 1.540000e-108 403.0
41 TraesCS4A01G468900 chr1D 82.322 379 55 12 2796 3170 334464363 334464733 5.740000e-83 318.0
42 TraesCS4A01G468900 chr6D 93.056 72 5 0 836 907 12259963 12260034 4.870000e-19 106.0
43 TraesCS4A01G468900 chr6D 90.769 65 6 0 836 900 318993723 318993787 1.760000e-13 87.9
44 TraesCS4A01G468900 chr2B 93.151 73 4 1 3493 3564 402214086 402214158 4.870000e-19 106.0
45 TraesCS4A01G468900 chr3D 81.905 105 13 4 804 902 84474027 84474131 2.280000e-12 84.2
46 TraesCS4A01G468900 chr4D 94.000 50 3 0 853 902 16454777 16454728 3.820000e-10 76.8
47 TraesCS4A01G468900 chr7B 100.000 36 0 0 858 893 703998132 703998097 2.300000e-07 67.6


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 TraesCS4A01G468900 chr4A 730885685 730889249 3564 False 6584.0 6584 100.000000 1 3565 1 chr4A.!!$F3 3564
1 TraesCS4A01G468900 chr4A 730279367 730282585 3218 False 2326.5 4303 94.238000 568 3485 2 chr4A.!!$F5 2917
2 TraesCS4A01G468900 chr4A 730784856 730790908 6052 True 1638.5 3007 90.755000 570 3073 2 chr4A.!!$R4 2503
3 TraesCS4A01G468900 chr4A 730191519 730193841 2322 True 1329.5 2324 91.102000 1444 3483 2 chr4A.!!$R3 2039
4 TraesCS4A01G468900 chr4A 728850406 728852220 1814 False 863.0 1626 91.857500 905 2766 2 chr4A.!!$F4 1861
5 TraesCS4A01G468900 chr4A 730198623 730199164 541 True 817.0 817 93.934000 905 1444 1 chr4A.!!$R2 539
6 TraesCS4A01G468900 chr4A 686632075 686632586 511 True 763.0 763 93.567000 56 567 1 chr4A.!!$R1 511
7 TraesCS4A01G468900 chr7A 9411275 9414083 2808 False 1673.5 3014 91.089500 957 3485 2 chr7A.!!$F1 2528
8 TraesCS4A01G468900 chr7D 8981105 8990656 9551 False 1112.5 2320 92.362167 904 3485 6 chr7D.!!$F1 2581
9 TraesCS4A01G468900 chr7D 9377737 9380483 2746 False 835.5 1663 90.909000 957 3475 4 chr7D.!!$F2 2518
10 TraesCS4A01G468900 chr5D 445718885 445720742 1857 True 890.5 1099 87.890500 902 2619 2 chr5D.!!$R1 1717
11 TraesCS4A01G468900 chrUn 383553822 383554336 514 False 713.0 713 91.493000 55 582 1 chrUn.!!$F1 527
12 TraesCS4A01G468900 chr6B 46511030 46511548 518 True 811.0 811 94.990000 60 575 1 chr6B.!!$R1 515
13 TraesCS4A01G468900 chr6B 383420599 383421104 505 True 791.0 791 94.872000 62 567 1 chr6B.!!$R2 505
14 TraesCS4A01G468900 chr1B 489905061 489905568 507 False 787.0 787 94.685000 54 560 1 chr1B.!!$F1 506
15 TraesCS4A01G468900 chr1B 32226033 32226543 510 True 739.0 739 92.759000 62 572 1 chr1B.!!$R1 510
16 TraesCS4A01G468900 chr5B 53668847 53669363 516 True 750.0 750 92.979000 52 568 1 chr5B.!!$R1 516

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
460 471 1.202031 GCTTGTGTAGCGCGCTAATTT 60.202 47.619 39.73 18.95 40.71 1.82 F
1153 4740 0.613260 CCCCGTCATCCACTTCTTCA 59.387 55.000 0.00 0.00 0.00 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2196 12665 0.106819 GCCTTCATCACCAGCTCCAT 60.107 55.0 0.0 0.0 0.00 3.41 R
2878 13359 0.662619 CAAAGGCTTCTGCAACACGA 59.337 50.0 0.0 0.0 41.91 4.35 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
29 30 9.447157 ACCCAATAAAAATTGAATGTTACATGG 57.553 29.630 0.00 0.00 33.55 3.66
30 31 8.397148 CCCAATAAAAATTGAATGTTACATGGC 58.603 33.333 0.00 0.00 33.55 4.40
31 32 8.944029 CCAATAAAAATTGAATGTTACATGGCA 58.056 29.630 0.00 0.00 33.55 4.92
32 33 9.757859 CAATAAAAATTGAATGTTACATGGCAC 57.242 29.630 0.00 0.00 33.55 5.01
286 288 4.712337 GGAGTGAGAAAGGGATGAGAAGTA 59.288 45.833 0.00 0.00 0.00 2.24
304 306 2.429971 AGTAAGAACTAGGGTTAGCCGC 59.570 50.000 0.00 0.00 35.58 6.53
333 335 6.294361 TCTCGTGGGAGAATCTGATAAAAA 57.706 37.500 0.00 0.00 46.11 1.94
338 340 7.123697 TCGTGGGAGAATCTGATAAAAAGAGTA 59.876 37.037 0.00 0.00 33.73 2.59
407 418 6.647334 TTATTTCAGTTTTGCATGGTCTGA 57.353 33.333 0.00 0.00 34.08 3.27
408 419 3.988379 TTCAGTTTTGCATGGTCTGAC 57.012 42.857 0.00 0.00 35.36 3.51
442 453 7.669098 CGTTACAATGTTACAACGTTATAGCT 58.331 34.615 10.66 0.00 39.04 3.32
460 471 1.202031 GCTTGTGTAGCGCGCTAATTT 60.202 47.619 39.73 18.95 40.71 1.82
1153 4740 0.613260 CCCCGTCATCCACTTCTTCA 59.387 55.000 0.00 0.00 0.00 3.02
1201 4788 3.454573 CGCCTGTACTACGGGGCA 61.455 66.667 14.88 0.00 44.90 5.36
1287 4874 4.406173 CTCGCCGTCGACTGCACT 62.406 66.667 27.83 0.00 40.21 4.40
1428 5015 1.756950 TATCCTCGACTGCCCGCTT 60.757 57.895 0.00 0.00 0.00 4.68
1744 5991 1.437573 CTATCGCGGAGGTTGCTCA 59.562 57.895 6.13 0.00 0.00 4.26
1873 6126 2.171237 ACGATGATGTGGTGGACATGAT 59.829 45.455 0.00 0.00 45.90 2.45
1922 6175 0.901827 TGCACCGCTCCTTCTTCATA 59.098 50.000 0.00 0.00 0.00 2.15
1977 6230 2.202610 CGTCGGCTCTCAATCGCA 60.203 61.111 0.00 0.00 0.00 5.10
2196 12665 0.673333 CAACCATGTGAGCTACGCCA 60.673 55.000 0.00 0.00 0.00 5.69
2256 12725 0.535335 GTACATCCTCTCCGTGGCAA 59.465 55.000 0.00 0.00 0.00 4.52
2583 13053 4.005650 GTGATCTGCCATCTGAGTTGAAA 58.994 43.478 0.00 0.00 0.00 2.69
2637 13116 5.620206 TCAAAGCTTGTACCTGAAATCTCA 58.380 37.500 0.00 0.00 0.00 3.27
2702 13181 5.221382 CCAAAGGATGGGAGCATGATTTAAG 60.221 44.000 0.00 0.00 46.27 1.85
2731 13210 9.678260 ATTAATAAAGATAGTCATGATGGCCTC 57.322 33.333 3.32 0.00 0.00 4.70
2738 13217 2.080536 CATGATGGCCTCCCCCTCA 61.081 63.158 3.32 0.00 41.62 3.86
2739 13218 1.309013 ATGATGGCCTCCCCCTCAA 60.309 57.895 3.32 0.00 40.90 3.02
2775 13255 9.203163 AGAATACTATATATCTAGGGTTGTGCC 57.797 37.037 0.74 0.00 0.00 5.01
2878 13359 4.319177 GTCCTCACTACTGCAACAAAGAT 58.681 43.478 0.00 0.00 0.00 2.40
3006 13487 4.401022 AGAACTTCTGCAACATGGATGAA 58.599 39.130 0.00 0.00 0.00 2.57
3007 13488 4.458295 AGAACTTCTGCAACATGGATGAAG 59.542 41.667 0.00 6.54 37.50 3.02
3030 13514 7.867445 AGTTGCAGAATTTATTTTGTAACGG 57.133 32.000 15.77 0.00 45.35 4.44
3060 13544 2.109739 AGCGCACCGTTGTTGTTGA 61.110 52.632 11.47 0.00 0.00 3.18
3174 13674 2.028484 GACCTGACGGTGTCGCAA 59.972 61.111 0.00 0.00 45.73 4.85
3218 13998 1.073284 GGTACGTGGGCCCATAATGAT 59.927 52.381 31.45 12.47 0.00 2.45
3234 14014 7.256439 CCCATAATGATGAGTGGAAGACATAGA 60.256 40.741 0.00 0.00 34.73 1.98
3235 14015 7.601886 CCATAATGATGAGTGGAAGACATAGAC 59.398 40.741 0.00 0.00 34.73 2.59
3236 14016 6.805016 AATGATGAGTGGAAGACATAGACT 57.195 37.500 0.00 0.00 0.00 3.24
3238 14018 7.904558 ATGATGAGTGGAAGACATAGACTTA 57.095 36.000 0.00 0.00 0.00 2.24
3239 14019 7.101652 TGATGAGTGGAAGACATAGACTTAC 57.898 40.000 0.00 0.00 0.00 2.34
3278 14093 9.784531 CTTTTCCCATATATCTGTATCAACACT 57.215 33.333 0.00 0.00 0.00 3.55
3333 14148 7.601886 GTCATCCATTGGATCTACTTCATGTAG 59.398 40.741 15.50 0.00 40.98 2.74
3348 14163 0.901827 TGTAGCGGCTGAGAATTGGA 59.098 50.000 13.86 0.00 0.00 3.53
3353 14168 1.269448 GCGGCTGAGAATTGGAAAACA 59.731 47.619 0.00 0.00 0.00 2.83
3397 14214 3.695830 TCTTGTGTTGTACCAGATCCC 57.304 47.619 0.00 0.00 0.00 3.85
3485 14302 9.775854 ATTTCCATGTCATGTTTTAATGTTGAA 57.224 25.926 11.84 1.69 0.00 2.69
3486 14303 8.586570 TTCCATGTCATGTTTTAATGTTGAAC 57.413 30.769 11.84 0.00 0.00 3.18
3487 14304 7.950512 TCCATGTCATGTTTTAATGTTGAACT 58.049 30.769 11.84 0.00 0.00 3.01
3488 14305 8.420222 TCCATGTCATGTTTTAATGTTGAACTT 58.580 29.630 11.84 0.00 0.00 2.66
3489 14306 8.702438 CCATGTCATGTTTTAATGTTGAACTTC 58.298 33.333 11.84 0.00 0.00 3.01
3490 14307 7.906611 TGTCATGTTTTAATGTTGAACTTCG 57.093 32.000 0.00 0.00 0.00 3.79
3491 14308 6.416455 TGTCATGTTTTAATGTTGAACTTCGC 59.584 34.615 0.00 0.00 0.00 4.70
3492 14309 5.918011 TCATGTTTTAATGTTGAACTTCGCC 59.082 36.000 0.00 0.00 0.00 5.54
3493 14310 5.508200 TGTTTTAATGTTGAACTTCGCCT 57.492 34.783 0.00 0.00 0.00 5.52
3494 14311 6.621316 TGTTTTAATGTTGAACTTCGCCTA 57.379 33.333 0.00 0.00 0.00 3.93
3495 14312 7.209471 TGTTTTAATGTTGAACTTCGCCTAT 57.791 32.000 0.00 0.00 0.00 2.57
3496 14313 7.081349 TGTTTTAATGTTGAACTTCGCCTATG 58.919 34.615 0.00 0.00 0.00 2.23
3497 14314 6.811253 TTTAATGTTGAACTTCGCCTATGT 57.189 33.333 0.00 0.00 0.00 2.29
3498 14315 6.811253 TTAATGTTGAACTTCGCCTATGTT 57.189 33.333 0.00 0.00 0.00 2.71
3499 14316 4.685169 ATGTTGAACTTCGCCTATGTTG 57.315 40.909 0.00 0.00 0.00 3.33
3500 14317 3.472652 TGTTGAACTTCGCCTATGTTGT 58.527 40.909 0.00 0.00 0.00 3.32
3501 14318 3.496884 TGTTGAACTTCGCCTATGTTGTC 59.503 43.478 0.00 0.00 0.00 3.18
3502 14319 3.678056 TGAACTTCGCCTATGTTGTCT 57.322 42.857 0.00 0.00 0.00 3.41
3503 14320 3.325870 TGAACTTCGCCTATGTTGTCTG 58.674 45.455 0.00 0.00 0.00 3.51
3504 14321 3.006430 TGAACTTCGCCTATGTTGTCTGA 59.994 43.478 0.00 0.00 0.00 3.27
3505 14322 3.678056 ACTTCGCCTATGTTGTCTGAA 57.322 42.857 0.00 0.00 0.00 3.02
3506 14323 3.326747 ACTTCGCCTATGTTGTCTGAAC 58.673 45.455 0.00 0.00 0.00 3.18
3507 14324 3.244078 ACTTCGCCTATGTTGTCTGAACA 60.244 43.478 0.00 0.00 34.31 3.18
3508 14325 3.610040 TCGCCTATGTTGTCTGAACAT 57.390 42.857 5.45 5.45 42.82 2.71
3509 14326 4.729227 TCGCCTATGTTGTCTGAACATA 57.271 40.909 6.98 6.98 40.87 2.29
3514 14331 2.093306 TGTTGTCTGAACATAGCCGG 57.907 50.000 0.00 0.00 34.73 6.13
3515 14332 1.346395 TGTTGTCTGAACATAGCCGGT 59.654 47.619 1.90 0.00 34.73 5.28
3516 14333 2.000447 GTTGTCTGAACATAGCCGGTC 59.000 52.381 1.90 0.00 34.73 4.79
3517 14334 0.535335 TGTCTGAACATAGCCGGTCC 59.465 55.000 1.90 0.00 0.00 4.46
3518 14335 0.179081 GTCTGAACATAGCCGGTCCC 60.179 60.000 1.90 0.00 0.00 4.46
3519 14336 0.616395 TCTGAACATAGCCGGTCCCA 60.616 55.000 1.90 0.00 0.00 4.37
3520 14337 0.251916 CTGAACATAGCCGGTCCCAA 59.748 55.000 1.90 0.00 0.00 4.12
3521 14338 0.251916 TGAACATAGCCGGTCCCAAG 59.748 55.000 1.90 0.00 0.00 3.61
3522 14339 0.463833 GAACATAGCCGGTCCCAAGG 60.464 60.000 1.90 0.00 0.00 3.61
3533 14350 2.761160 CCCAAGGCCGGGTAAAGT 59.239 61.111 14.46 0.00 41.83 2.66
3534 14351 1.076014 CCCAAGGCCGGGTAAAGTT 59.924 57.895 14.46 0.00 41.83 2.66
3535 14352 1.248101 CCCAAGGCCGGGTAAAGTTG 61.248 60.000 14.46 3.23 41.83 3.16
3536 14353 1.248101 CCAAGGCCGGGTAAAGTTGG 61.248 60.000 2.18 5.13 0.00 3.77
3537 14354 0.250989 CAAGGCCGGGTAAAGTTGGA 60.251 55.000 2.18 0.00 0.00 3.53
3538 14355 0.037734 AAGGCCGGGTAAAGTTGGAG 59.962 55.000 2.18 0.00 0.00 3.86
3539 14356 1.378119 GGCCGGGTAAAGTTGGAGG 60.378 63.158 2.18 0.00 0.00 4.30
3540 14357 1.378119 GCCGGGTAAAGTTGGAGGG 60.378 63.158 2.18 0.00 0.00 4.30
3541 14358 2.072366 CCGGGTAAAGTTGGAGGGT 58.928 57.895 0.00 0.00 0.00 4.34
3542 14359 0.402887 CCGGGTAAAGTTGGAGGGTT 59.597 55.000 0.00 0.00 0.00 4.11
3543 14360 1.530323 CGGGTAAAGTTGGAGGGTTG 58.470 55.000 0.00 0.00 0.00 3.77
3544 14361 1.202842 CGGGTAAAGTTGGAGGGTTGT 60.203 52.381 0.00 0.00 0.00 3.32
3545 14362 2.235891 GGGTAAAGTTGGAGGGTTGTG 58.764 52.381 0.00 0.00 0.00 3.33
3546 14363 2.158579 GGGTAAAGTTGGAGGGTTGTGA 60.159 50.000 0.00 0.00 0.00 3.58
3547 14364 3.499745 GGGTAAAGTTGGAGGGTTGTGAT 60.500 47.826 0.00 0.00 0.00 3.06
3548 14365 4.263594 GGGTAAAGTTGGAGGGTTGTGATA 60.264 45.833 0.00 0.00 0.00 2.15
3549 14366 4.941873 GGTAAAGTTGGAGGGTTGTGATAG 59.058 45.833 0.00 0.00 0.00 2.08
3550 14367 3.721087 AAGTTGGAGGGTTGTGATAGG 57.279 47.619 0.00 0.00 0.00 2.57
3551 14368 1.282157 AGTTGGAGGGTTGTGATAGGC 59.718 52.381 0.00 0.00 0.00 3.93
3552 14369 1.282157 GTTGGAGGGTTGTGATAGGCT 59.718 52.381 0.00 0.00 0.00 4.58
3553 14370 1.668826 TGGAGGGTTGTGATAGGCTT 58.331 50.000 0.00 0.00 0.00 4.35
3554 14371 1.281867 TGGAGGGTTGTGATAGGCTTG 59.718 52.381 0.00 0.00 0.00 4.01
3555 14372 1.408822 GGAGGGTTGTGATAGGCTTGG 60.409 57.143 0.00 0.00 0.00 3.61
3556 14373 0.034089 AGGGTTGTGATAGGCTTGGC 60.034 55.000 0.00 0.00 0.00 4.52
3557 14374 1.376609 GGGTTGTGATAGGCTTGGCG 61.377 60.000 0.00 0.00 0.00 5.69
3558 14375 0.392461 GGTTGTGATAGGCTTGGCGA 60.392 55.000 0.00 0.00 0.00 5.54
3559 14376 0.727398 GTTGTGATAGGCTTGGCGAC 59.273 55.000 0.00 0.00 0.00 5.19
3560 14377 0.392461 TTGTGATAGGCTTGGCGACC 60.392 55.000 0.00 0.00 0.00 4.79
3561 14378 1.220749 GTGATAGGCTTGGCGACCA 59.779 57.895 0.00 0.00 0.00 4.02
3562 14379 0.392461 GTGATAGGCTTGGCGACCAA 60.392 55.000 10.28 10.28 41.69 3.67
3563 14380 0.392461 TGATAGGCTTGGCGACCAAC 60.392 55.000 7.15 5.37 38.75 3.77
3564 14381 0.392461 GATAGGCTTGGCGACCAACA 60.392 55.000 7.15 0.00 38.75 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 9.499479 TGTGCCATGTAACATTCAATTTTTATT 57.501 25.926 0.00 0.00 0.00 1.40
8 9 9.499479 TTGTGCCATGTAACATTCAATTTTTAT 57.501 25.926 0.00 0.00 0.00 1.40
9 10 8.893219 TTGTGCCATGTAACATTCAATTTTTA 57.107 26.923 0.00 0.00 0.00 1.52
10 11 7.798596 TTGTGCCATGTAACATTCAATTTTT 57.201 28.000 0.00 0.00 0.00 1.94
11 12 7.982761 ATTGTGCCATGTAACATTCAATTTT 57.017 28.000 0.00 0.00 0.00 1.82
12 13 8.093307 TGTATTGTGCCATGTAACATTCAATTT 58.907 29.630 0.00 0.00 0.00 1.82
13 14 7.609960 TGTATTGTGCCATGTAACATTCAATT 58.390 30.769 0.00 0.00 0.00 2.32
14 15 7.167924 TGTATTGTGCCATGTAACATTCAAT 57.832 32.000 0.00 0.00 0.00 2.57
15 16 6.581171 TGTATTGTGCCATGTAACATTCAA 57.419 33.333 0.00 0.00 0.00 2.69
16 17 6.772360 ATGTATTGTGCCATGTAACATTCA 57.228 33.333 0.00 0.00 0.00 2.57
17 18 8.477984 AAAATGTATTGTGCCATGTAACATTC 57.522 30.769 0.00 0.00 35.61 2.67
18 19 8.845413 AAAAATGTATTGTGCCATGTAACATT 57.155 26.923 0.00 0.00 37.60 2.71
53 54 9.195831 GCGCGCTATTTAAAATATTGAGTATAC 57.804 33.333 26.67 0.00 0.00 1.47
54 55 9.146984 AGCGCGCTATTTAAAATATTGAGTATA 57.853 29.630 35.79 0.00 0.00 1.47
55 56 8.029642 AGCGCGCTATTTAAAATATTGAGTAT 57.970 30.769 35.79 0.00 0.00 2.12
56 57 7.416154 AGCGCGCTATTTAAAATATTGAGTA 57.584 32.000 35.79 0.00 0.00 2.59
57 58 6.300354 AGCGCGCTATTTAAAATATTGAGT 57.700 33.333 35.79 0.18 0.00 3.41
286 288 1.569653 AGCGGCTAACCCTAGTTCTT 58.430 50.000 0.00 0.00 37.42 2.52
304 306 3.067461 CAGATTCTCCCACGAGACCTAAG 59.933 52.174 0.00 0.00 45.01 2.18
333 335 4.080687 ACGACCACTAGCTTTCTTACTCT 58.919 43.478 0.00 0.00 0.00 3.24
338 340 1.002087 CCCACGACCACTAGCTTTCTT 59.998 52.381 0.00 0.00 0.00 2.52
442 453 1.059979 CGAAATTAGCGCGCTACACAA 59.940 47.619 38.48 26.89 0.00 3.33
481 492 3.242673 ACGTTACGTTTTGGCAAAATCGA 60.243 39.130 33.14 22.11 39.67 3.59
705 716 8.283992 CACACTCAAAATAAACCGTTATGTGTA 58.716 33.333 0.00 0.00 33.45 2.90
710 721 8.385898 TCTTCACACTCAAAATAAACCGTTAT 57.614 30.769 0.00 0.00 0.00 1.89
1201 4788 4.530857 GAGCACCGCCGCTATGGT 62.531 66.667 0.00 0.00 44.01 3.55
1661 5908 2.169144 CTGTATCCTCACAGCCATGACA 59.831 50.000 0.00 0.00 39.54 3.58
1922 6175 2.444895 GAGATCTCCCGCCACCCT 60.445 66.667 12.00 0.00 0.00 4.34
1977 6230 2.367567 TGACCTCGAAGTTGGTAGCTTT 59.632 45.455 0.00 0.00 35.92 3.51
2196 12665 0.106819 GCCTTCATCACCAGCTCCAT 60.107 55.000 0.00 0.00 0.00 3.41
2490 12959 3.566322 TCGTTAACAAACTTGTCCATGGG 59.434 43.478 13.02 0.00 41.31 4.00
2583 13053 5.097742 TGAAACCGTGATACCAGATGATT 57.902 39.130 0.00 0.00 0.00 2.57
2878 13359 0.662619 CAAAGGCTTCTGCAACACGA 59.337 50.000 0.00 0.00 41.91 4.35
3006 13487 7.653647 TCCGTTACAAAATAAATTCTGCAACT 58.346 30.769 0.00 0.00 0.00 3.16
3007 13488 7.861176 TCCGTTACAAAATAAATTCTGCAAC 57.139 32.000 0.00 0.00 0.00 4.17
3030 13514 2.815211 TGCGCTGCGACATCCTTC 60.815 61.111 28.07 5.61 0.00 3.46
3174 13674 1.476291 GGTCCCCGTCACAGAAGTTTT 60.476 52.381 0.00 0.00 0.00 2.43
3201 13701 0.843309 TCATCATTATGGGCCCACGT 59.157 50.000 31.51 16.26 33.61 4.49
3202 13702 1.202806 ACTCATCATTATGGGCCCACG 60.203 52.381 31.51 16.57 37.04 4.94
3218 13998 5.562506 CGTAAGTCTATGTCTTCCACTCA 57.437 43.478 0.00 0.00 0.00 3.41
3234 14014 2.914379 GCTGGTGCTCAACGTAAGT 58.086 52.632 0.00 0.00 45.52 2.24
3333 14148 1.269448 TGTTTTCCAATTCTCAGCCGC 59.731 47.619 0.00 0.00 0.00 6.53
3348 14163 3.011119 TGACGGCTACAACTTGTGTTTT 58.989 40.909 4.57 0.00 41.98 2.43
3353 14168 2.299013 TGATCTGACGGCTACAACTTGT 59.701 45.455 0.00 0.00 0.00 3.16
3485 14302 3.244078 TGTTCAGACAACATAGGCGAAGT 60.244 43.478 0.00 0.00 31.49 3.01
3486 14303 3.325870 TGTTCAGACAACATAGGCGAAG 58.674 45.455 0.00 0.00 31.49 3.79
3487 14304 3.394674 TGTTCAGACAACATAGGCGAA 57.605 42.857 0.00 0.00 31.49 4.70
3488 14305 3.610040 ATGTTCAGACAACATAGGCGA 57.390 42.857 0.00 0.00 38.94 5.54
3493 14310 3.196901 ACCGGCTATGTTCAGACAACATA 59.803 43.478 0.00 6.93 40.87 2.29
3494 14311 2.027192 ACCGGCTATGTTCAGACAACAT 60.027 45.455 0.00 5.37 42.82 2.71
3495 14312 1.346395 ACCGGCTATGTTCAGACAACA 59.654 47.619 0.00 0.00 39.66 3.33
3496 14313 2.000447 GACCGGCTATGTTCAGACAAC 59.000 52.381 0.00 0.00 39.66 3.32
3497 14314 1.066430 GGACCGGCTATGTTCAGACAA 60.066 52.381 0.00 0.00 39.66 3.18
3498 14315 0.535335 GGACCGGCTATGTTCAGACA 59.465 55.000 0.00 0.00 40.71 3.41
3499 14316 0.179081 GGGACCGGCTATGTTCAGAC 60.179 60.000 0.00 0.00 0.00 3.51
3500 14317 0.616395 TGGGACCGGCTATGTTCAGA 60.616 55.000 0.00 0.00 0.00 3.27
3501 14318 0.251916 TTGGGACCGGCTATGTTCAG 59.748 55.000 0.00 0.00 0.00 3.02
3502 14319 0.251916 CTTGGGACCGGCTATGTTCA 59.748 55.000 0.00 0.00 0.00 3.18
3503 14320 0.463833 CCTTGGGACCGGCTATGTTC 60.464 60.000 0.00 0.00 0.00 3.18
3504 14321 1.607612 CCTTGGGACCGGCTATGTT 59.392 57.895 0.00 0.00 0.00 2.71
3505 14322 3.043999 GCCTTGGGACCGGCTATGT 62.044 63.158 0.00 0.00 40.16 2.29
3506 14323 2.203209 GCCTTGGGACCGGCTATG 60.203 66.667 0.00 0.00 40.16 2.23
3507 14324 3.489513 GGCCTTGGGACCGGCTAT 61.490 66.667 0.00 0.00 42.43 2.97
3517 14334 1.248101 CCAACTTTACCCGGCCTTGG 61.248 60.000 0.00 3.47 0.00 3.61
3518 14335 0.250989 TCCAACTTTACCCGGCCTTG 60.251 55.000 0.00 0.00 0.00 3.61
3519 14336 0.037734 CTCCAACTTTACCCGGCCTT 59.962 55.000 0.00 0.00 0.00 4.35
3520 14337 1.683441 CTCCAACTTTACCCGGCCT 59.317 57.895 0.00 0.00 0.00 5.19
3521 14338 1.378119 CCTCCAACTTTACCCGGCC 60.378 63.158 0.00 0.00 0.00 6.13
3522 14339 1.378119 CCCTCCAACTTTACCCGGC 60.378 63.158 0.00 0.00 0.00 6.13
3523 14340 0.402887 AACCCTCCAACTTTACCCGG 59.597 55.000 0.00 0.00 0.00 5.73
3524 14341 1.202842 ACAACCCTCCAACTTTACCCG 60.203 52.381 0.00 0.00 0.00 5.28
3525 14342 2.158579 TCACAACCCTCCAACTTTACCC 60.159 50.000 0.00 0.00 0.00 3.69
3526 14343 3.217681 TCACAACCCTCCAACTTTACC 57.782 47.619 0.00 0.00 0.00 2.85
3527 14344 4.941873 CCTATCACAACCCTCCAACTTTAC 59.058 45.833 0.00 0.00 0.00 2.01
3528 14345 4.566907 GCCTATCACAACCCTCCAACTTTA 60.567 45.833 0.00 0.00 0.00 1.85
3529 14346 3.814316 GCCTATCACAACCCTCCAACTTT 60.814 47.826 0.00 0.00 0.00 2.66
3530 14347 2.290960 GCCTATCACAACCCTCCAACTT 60.291 50.000 0.00 0.00 0.00 2.66
3531 14348 1.282157 GCCTATCACAACCCTCCAACT 59.718 52.381 0.00 0.00 0.00 3.16
3532 14349 1.282157 AGCCTATCACAACCCTCCAAC 59.718 52.381 0.00 0.00 0.00 3.77
3533 14350 1.668826 AGCCTATCACAACCCTCCAA 58.331 50.000 0.00 0.00 0.00 3.53
3534 14351 1.281867 CAAGCCTATCACAACCCTCCA 59.718 52.381 0.00 0.00 0.00 3.86
3535 14352 1.408822 CCAAGCCTATCACAACCCTCC 60.409 57.143 0.00 0.00 0.00 4.30
3536 14353 2.019156 GCCAAGCCTATCACAACCCTC 61.019 57.143 0.00 0.00 0.00 4.30
3537 14354 0.034089 GCCAAGCCTATCACAACCCT 60.034 55.000 0.00 0.00 0.00 4.34
3538 14355 1.376609 CGCCAAGCCTATCACAACCC 61.377 60.000 0.00 0.00 0.00 4.11
3539 14356 0.392461 TCGCCAAGCCTATCACAACC 60.392 55.000 0.00 0.00 0.00 3.77
3540 14357 0.727398 GTCGCCAAGCCTATCACAAC 59.273 55.000 0.00 0.00 0.00 3.32
3541 14358 0.392461 GGTCGCCAAGCCTATCACAA 60.392 55.000 0.00 0.00 0.00 3.33
3542 14359 1.220749 GGTCGCCAAGCCTATCACA 59.779 57.895 0.00 0.00 0.00 3.58
3543 14360 0.392461 TTGGTCGCCAAGCCTATCAC 60.392 55.000 7.15 0.00 38.75 3.06
3544 14361 0.392461 GTTGGTCGCCAAGCCTATCA 60.392 55.000 10.94 0.00 44.82 2.15
3545 14362 0.392461 TGTTGGTCGCCAAGCCTATC 60.392 55.000 10.94 0.99 44.82 2.08
3546 14363 1.682849 TGTTGGTCGCCAAGCCTAT 59.317 52.632 10.94 0.00 44.82 2.57
3547 14364 3.152865 TGTTGGTCGCCAAGCCTA 58.847 55.556 10.94 0.00 44.82 3.93


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

AutoCloner maintained by Alex Coulton.