Multiple sequence alignment - TraesCS4B01G114900

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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 TraesCS4B01G114900 chr4B 100.000 3276 0 0 1 3276 131168746 131165471 0.000000e+00 6050
1 TraesCS4B01G114900 chr4D 95.632 1740 49 6 714 2430 93347389 93345654 0.000000e+00 2767
2 TraesCS4B01G114900 chr4A 94.585 1736 56 14 772 2481 489082994 489084717 0.000000e+00 2651
3 TraesCS4B01G114900 chr3B 95.342 730 28 4 2548 3276 798202896 798202172 0.000000e+00 1155
4 TraesCS4B01G114900 chr3B 95.199 729 29 4 2548 3276 32986067 32986789 0.000000e+00 1147
5 TraesCS4B01G114900 chr3B 94.925 729 29 5 2548 3276 766594920 766595640 0.000000e+00 1134
6 TraesCS4B01G114900 chr6B 95.095 734 29 4 2543 3276 473645580 473644854 0.000000e+00 1149
7 TraesCS4B01G114900 chr6B 86.290 620 70 8 1 618 561645608 561646214 0.000000e+00 660
8 TraesCS4B01G114900 chr7B 95.205 730 24 6 2548 3276 165606619 165607338 0.000000e+00 1144
9 TraesCS4B01G114900 chr7B 94.787 729 30 3 2548 3276 740017125 740016405 0.000000e+00 1129
10 TraesCS4B01G114900 chr7B 93.700 746 45 2 2532 3276 699249073 699249817 0.000000e+00 1116
11 TraesCS4B01G114900 chr5B 94.687 734 34 4 2544 3276 641316604 641317333 0.000000e+00 1134
12 TraesCS4B01G114900 chr5B 94.332 741 36 6 2538 3276 421839979 421840715 0.000000e+00 1131
13 TraesCS4B01G114900 chr5B 83.929 112 8 8 523 632 646371733 646371630 7.480000e-17 99
14 TraesCS4B01G114900 chr1B 87.204 633 71 6 1 632 688397747 688398370 0.000000e+00 712
15 TraesCS4B01G114900 chr1B 83.201 631 85 14 1 625 52639074 52638459 2.860000e-155 558
16 TraesCS4B01G114900 chr1B 82.278 632 89 17 1 625 52554575 52553960 2.900000e-145 525
17 TraesCS4B01G114900 chr5A 81.677 644 89 20 1 635 534814596 534815219 2.920000e-140 508
18 TraesCS4B01G114900 chr7A 81.337 643 94 15 1 633 113455061 113455687 1.760000e-137 499
19 TraesCS4B01G114900 chr7A 82.283 587 88 11 50 632 541003473 541004047 8.170000e-136 494
20 TraesCS4B01G114900 chr2B 80.465 645 94 24 2 632 788225841 788226467 6.400000e-127 464
21 TraesCS4B01G114900 chr7D 80.511 626 102 14 15 635 423335229 423334619 2.300000e-126 462


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 TraesCS4B01G114900 chr4B 131165471 131168746 3275 True 6050 6050 100.000 1 3276 1 chr4B.!!$R1 3275
1 TraesCS4B01G114900 chr4D 93345654 93347389 1735 True 2767 2767 95.632 714 2430 1 chr4D.!!$R1 1716
2 TraesCS4B01G114900 chr4A 489082994 489084717 1723 False 2651 2651 94.585 772 2481 1 chr4A.!!$F1 1709
3 TraesCS4B01G114900 chr3B 798202172 798202896 724 True 1155 1155 95.342 2548 3276 1 chr3B.!!$R1 728
4 TraesCS4B01G114900 chr3B 32986067 32986789 722 False 1147 1147 95.199 2548 3276 1 chr3B.!!$F1 728
5 TraesCS4B01G114900 chr3B 766594920 766595640 720 False 1134 1134 94.925 2548 3276 1 chr3B.!!$F2 728
6 TraesCS4B01G114900 chr6B 473644854 473645580 726 True 1149 1149 95.095 2543 3276 1 chr6B.!!$R1 733
7 TraesCS4B01G114900 chr6B 561645608 561646214 606 False 660 660 86.290 1 618 1 chr6B.!!$F1 617
8 TraesCS4B01G114900 chr7B 165606619 165607338 719 False 1144 1144 95.205 2548 3276 1 chr7B.!!$F1 728
9 TraesCS4B01G114900 chr7B 740016405 740017125 720 True 1129 1129 94.787 2548 3276 1 chr7B.!!$R1 728
10 TraesCS4B01G114900 chr7B 699249073 699249817 744 False 1116 1116 93.700 2532 3276 1 chr7B.!!$F2 744
11 TraesCS4B01G114900 chr5B 641316604 641317333 729 False 1134 1134 94.687 2544 3276 1 chr5B.!!$F2 732
12 TraesCS4B01G114900 chr5B 421839979 421840715 736 False 1131 1131 94.332 2538 3276 1 chr5B.!!$F1 738
13 TraesCS4B01G114900 chr1B 688397747 688398370 623 False 712 712 87.204 1 632 1 chr1B.!!$F1 631
14 TraesCS4B01G114900 chr1B 52638459 52639074 615 True 558 558 83.201 1 625 1 chr1B.!!$R2 624
15 TraesCS4B01G114900 chr1B 52553960 52554575 615 True 525 525 82.278 1 625 1 chr1B.!!$R1 624
16 TraesCS4B01G114900 chr5A 534814596 534815219 623 False 508 508 81.677 1 635 1 chr5A.!!$F1 634
17 TraesCS4B01G114900 chr7A 113455061 113455687 626 False 499 499 81.337 1 633 1 chr7A.!!$F1 632
18 TraesCS4B01G114900 chr7A 541003473 541004047 574 False 494 494 82.283 50 632 1 chr7A.!!$F2 582
19 TraesCS4B01G114900 chr2B 788225841 788226467 626 False 464 464 80.465 2 632 1 chr2B.!!$F1 630
20 TraesCS4B01G114900 chr7D 423334619 423335229 610 True 462 462 80.511 15 635 1 chr7D.!!$R1 620

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
301 306 0.037697 TGGTTCGATCCGGTGACAAG 60.038 55.0 0.00 0.0 0.00 3.16 F
1267 1291 0.033796 TACTTCGAGATCCCGTGGGT 60.034 55.0 4.53 0.0 36.47 4.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2227 2251 0.249911 CGATCAGGATTCCCCGTTCC 60.250 60.0 0.00 0.0 40.87 3.62 R
2814 2873 0.391597 ACTCTGAAAAACCTCGCGGA 59.608 50.0 6.13 0.0 0.00 5.54 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
22 23 2.125912 CGACTTGACGCAGAGGGG 60.126 66.667 0.00 0.00 0.00 4.79
31 32 2.515901 GCAGAGGGGTGGTTGTGT 59.484 61.111 0.00 0.00 0.00 3.72
138 141 0.605860 AGTCGAGCACCTAGTGTCGT 60.606 55.000 14.62 1.09 37.84 4.34
179 182 2.418334 GGTCGGACCTGAGTTGGTTATC 60.418 54.545 19.92 0.00 41.00 1.75
181 184 1.831736 CGGACCTGAGTTGGTTATCCT 59.168 52.381 0.00 0.00 41.00 3.24
243 248 0.823769 TGCTCGGATATGCTCGGACT 60.824 55.000 0.00 0.00 0.00 3.85
299 304 0.174845 GATGGTTCGATCCGGTGACA 59.825 55.000 0.00 0.00 0.00 3.58
301 306 0.037697 TGGTTCGATCCGGTGACAAG 60.038 55.000 0.00 0.00 0.00 3.16
303 308 1.079405 TTCGATCCGGTGACAAGGC 60.079 57.895 0.00 0.00 0.00 4.35
380 385 2.886523 CAGTGGTGTCATGACATGGTTT 59.113 45.455 30.10 13.20 43.97 3.27
417 422 9.438291 GATCATTGTTTATAGTTTGTCGATTGG 57.562 33.333 0.00 0.00 0.00 3.16
440 455 4.979388 AGATCTGATCGCTTTGCTTTTTC 58.021 39.130 11.73 0.00 0.00 2.29
459 480 7.499321 TTTTTCTTTTCTCGCCTACACATAA 57.501 32.000 0.00 0.00 0.00 1.90
511 532 1.669184 CGTGTTATTTGTGTGCGTGG 58.331 50.000 0.00 0.00 0.00 4.94
521 542 1.096386 GTGTGCGTGGGTTGGTGTTA 61.096 55.000 0.00 0.00 0.00 2.41
534 555 1.072173 TGGTGTTAGCTGTGTGCATCT 59.928 47.619 0.00 0.00 45.94 2.90
564 585 2.980233 GGCTGGGTGTGTGCTCAC 60.980 66.667 11.94 11.94 44.08 3.51
565 586 2.111878 GCTGGGTGTGTGCTCACT 59.888 61.111 18.85 0.00 44.14 3.41
566 587 1.371183 GCTGGGTGTGTGCTCACTA 59.629 57.895 18.85 4.05 44.14 2.74
567 588 0.250295 GCTGGGTGTGTGCTCACTAA 60.250 55.000 18.85 0.00 44.14 2.24
568 589 1.611673 GCTGGGTGTGTGCTCACTAAT 60.612 52.381 18.85 0.00 44.14 1.73
569 590 2.350522 CTGGGTGTGTGCTCACTAATC 58.649 52.381 18.85 1.06 44.14 1.75
570 591 1.696884 TGGGTGTGTGCTCACTAATCA 59.303 47.619 18.85 9.70 44.14 2.57
571 592 2.076863 GGGTGTGTGCTCACTAATCAC 58.923 52.381 18.85 8.81 44.14 3.06
681 703 9.694137 ACAAGATGTAACTTCTAGTCAAAGTAC 57.306 33.333 0.00 0.00 35.96 2.73
682 704 9.141400 CAAGATGTAACTTCTAGTCAAAGTACC 57.859 37.037 0.00 0.00 35.96 3.34
683 705 8.418597 AGATGTAACTTCTAGTCAAAGTACCA 57.581 34.615 0.00 0.00 35.96 3.25
684 706 8.867097 AGATGTAACTTCTAGTCAAAGTACCAA 58.133 33.333 0.00 0.00 35.96 3.67
685 707 9.654663 GATGTAACTTCTAGTCAAAGTACCAAT 57.345 33.333 0.00 0.00 35.96 3.16
686 708 8.827177 TGTAACTTCTAGTCAAAGTACCAATG 57.173 34.615 0.00 0.00 35.96 2.82
687 709 8.644216 TGTAACTTCTAGTCAAAGTACCAATGA 58.356 33.333 0.00 0.00 35.96 2.57
688 710 9.654663 GTAACTTCTAGTCAAAGTACCAATGAT 57.345 33.333 0.00 0.00 35.96 2.45
689 711 8.553459 AACTTCTAGTCAAAGTACCAATGATG 57.447 34.615 0.00 0.00 35.96 3.07
690 712 6.595716 ACTTCTAGTCAAAGTACCAATGATGC 59.404 38.462 0.00 0.00 35.25 3.91
691 713 6.048732 TCTAGTCAAAGTACCAATGATGCA 57.951 37.500 0.00 0.00 0.00 3.96
692 714 6.653020 TCTAGTCAAAGTACCAATGATGCAT 58.347 36.000 0.00 0.00 0.00 3.96
693 715 7.791029 TCTAGTCAAAGTACCAATGATGCATA 58.209 34.615 0.00 0.00 0.00 3.14
694 716 8.432013 TCTAGTCAAAGTACCAATGATGCATAT 58.568 33.333 0.00 0.00 0.00 1.78
695 717 7.886629 AGTCAAAGTACCAATGATGCATATT 57.113 32.000 0.00 0.00 0.00 1.28
696 718 8.978874 AGTCAAAGTACCAATGATGCATATTA 57.021 30.769 0.00 0.00 0.00 0.98
697 719 9.060347 AGTCAAAGTACCAATGATGCATATTAG 57.940 33.333 0.00 0.00 0.00 1.73
698 720 9.056005 GTCAAAGTACCAATGATGCATATTAGA 57.944 33.333 0.00 0.00 0.00 2.10
699 721 9.276590 TCAAAGTACCAATGATGCATATTAGAG 57.723 33.333 0.00 0.00 0.00 2.43
700 722 8.509690 CAAAGTACCAATGATGCATATTAGAGG 58.490 37.037 0.00 0.00 0.00 3.69
701 723 7.321717 AGTACCAATGATGCATATTAGAGGT 57.678 36.000 0.00 6.23 0.00 3.85
702 724 7.749666 AGTACCAATGATGCATATTAGAGGTT 58.250 34.615 0.00 0.00 0.00 3.50
703 725 6.889301 ACCAATGATGCATATTAGAGGTTG 57.111 37.500 0.00 0.00 0.00 3.77
704 726 6.367983 ACCAATGATGCATATTAGAGGTTGT 58.632 36.000 0.00 0.00 0.00 3.32
705 727 6.488006 ACCAATGATGCATATTAGAGGTTGTC 59.512 38.462 0.00 0.00 0.00 3.18
706 728 6.713903 CCAATGATGCATATTAGAGGTTGTCT 59.286 38.462 0.00 0.00 39.59 3.41
707 729 7.879677 CCAATGATGCATATTAGAGGTTGTCTA 59.120 37.037 0.00 0.00 36.64 2.59
746 768 7.210873 ACTTCGAATATGGATAAGTTGAGTCC 58.789 38.462 0.00 0.00 0.00 3.85
755 777 5.874810 TGGATAAGTTGAGTCCGAAGATTTG 59.125 40.000 0.00 0.00 34.72 2.32
763 785 0.965363 TCCGAAGATTTGGGCAAGGC 60.965 55.000 0.00 0.00 32.26 4.35
993 1017 1.012086 CTTCGATCGACCCTCACGTA 58.988 55.000 19.26 0.00 0.00 3.57
1197 1221 2.022764 ATCGCGACATTGGTTGATCA 57.977 45.000 12.93 0.00 0.00 2.92
1267 1291 0.033796 TACTTCGAGATCCCGTGGGT 60.034 55.000 4.53 0.00 36.47 4.51
1406 1430 0.611062 TTCTCACCTCCATCGGTCGT 60.611 55.000 0.00 0.00 34.29 4.34
1685 1709 4.180946 CTCGAGTGGCTCCGGTCG 62.181 72.222 3.62 1.74 0.00 4.79
1883 1907 2.128035 GGAGAATACATTGACGCCGAG 58.872 52.381 0.00 0.00 0.00 4.63
1955 1979 2.202932 GCCATCGGCGACATCACT 60.203 61.111 13.76 0.00 39.62 3.41
2102 2126 2.742372 GCCATCACCGTCACGCTT 60.742 61.111 0.00 0.00 0.00 4.68
2145 2169 2.792290 CTGCCGTTCATGTCGCTCG 61.792 63.158 7.34 0.00 0.00 5.03
2224 2248 5.850046 AGGATGATGGGGATAAAAGGTAG 57.150 43.478 0.00 0.00 0.00 3.18
2225 2249 5.235534 AGGATGATGGGGATAAAAGGTAGT 58.764 41.667 0.00 0.00 0.00 2.73
2226 2250 6.399013 AGGATGATGGGGATAAAAGGTAGTA 58.601 40.000 0.00 0.00 0.00 1.82
2227 2251 6.502158 AGGATGATGGGGATAAAAGGTAGTAG 59.498 42.308 0.00 0.00 0.00 2.57
2253 2277 0.105039 GGAATCCTGATCGAGCGGTT 59.895 55.000 8.96 0.00 0.00 4.44
2362 2406 8.765219 GTGGAGTGATACATATGTTGTTGATAC 58.235 37.037 14.77 4.64 39.87 2.24
2482 2533 6.979238 AGAATACTACAGTTTTATCAGTCCGC 59.021 38.462 0.00 0.00 0.00 5.54
2483 2534 4.803098 ACTACAGTTTTATCAGTCCGCT 57.197 40.909 0.00 0.00 0.00 5.52
2484 2535 5.909621 ACTACAGTTTTATCAGTCCGCTA 57.090 39.130 0.00 0.00 0.00 4.26
2485 2536 5.648572 ACTACAGTTTTATCAGTCCGCTAC 58.351 41.667 0.00 0.00 0.00 3.58
2486 2537 4.530710 ACAGTTTTATCAGTCCGCTACA 57.469 40.909 0.00 0.00 0.00 2.74
2487 2538 4.890088 ACAGTTTTATCAGTCCGCTACAA 58.110 39.130 0.00 0.00 0.00 2.41
2488 2539 4.689345 ACAGTTTTATCAGTCCGCTACAAC 59.311 41.667 0.00 0.00 0.00 3.32
2489 2540 4.688879 CAGTTTTATCAGTCCGCTACAACA 59.311 41.667 0.00 0.00 0.00 3.33
2490 2541 5.351465 CAGTTTTATCAGTCCGCTACAACAT 59.649 40.000 0.00 0.00 0.00 2.71
2491 2542 6.533723 CAGTTTTATCAGTCCGCTACAACATA 59.466 38.462 0.00 0.00 0.00 2.29
2492 2543 6.534079 AGTTTTATCAGTCCGCTACAACATAC 59.466 38.462 0.00 0.00 0.00 2.39
2493 2544 2.953466 TCAGTCCGCTACAACATACC 57.047 50.000 0.00 0.00 0.00 2.73
2494 2545 2.453521 TCAGTCCGCTACAACATACCT 58.546 47.619 0.00 0.00 0.00 3.08
2495 2546 3.623703 TCAGTCCGCTACAACATACCTA 58.376 45.455 0.00 0.00 0.00 3.08
2496 2547 3.630769 TCAGTCCGCTACAACATACCTAG 59.369 47.826 0.00 0.00 0.00 3.02
2497 2548 2.361438 AGTCCGCTACAACATACCTAGC 59.639 50.000 0.00 0.00 0.00 3.42
2498 2549 2.100252 GTCCGCTACAACATACCTAGCA 59.900 50.000 0.00 0.00 33.78 3.49
2499 2550 2.761767 TCCGCTACAACATACCTAGCAA 59.238 45.455 0.00 0.00 33.78 3.91
2500 2551 3.196039 TCCGCTACAACATACCTAGCAAA 59.804 43.478 0.00 0.00 33.78 3.68
2501 2552 4.127171 CCGCTACAACATACCTAGCAAAT 58.873 43.478 0.00 0.00 33.78 2.32
2502 2553 4.024893 CCGCTACAACATACCTAGCAAATG 60.025 45.833 0.00 0.00 33.78 2.32
2503 2554 4.024893 CGCTACAACATACCTAGCAAATGG 60.025 45.833 0.00 0.00 33.78 3.16
2504 2555 4.275936 GCTACAACATACCTAGCAAATGGG 59.724 45.833 0.00 0.00 34.24 4.00
2505 2556 4.584638 ACAACATACCTAGCAAATGGGA 57.415 40.909 0.00 0.00 32.69 4.37
2506 2557 5.129368 ACAACATACCTAGCAAATGGGAT 57.871 39.130 0.00 0.00 32.69 3.85
2507 2558 5.518865 ACAACATACCTAGCAAATGGGATT 58.481 37.500 0.00 0.00 32.69 3.01
2508 2559 5.360714 ACAACATACCTAGCAAATGGGATTG 59.639 40.000 0.00 0.00 32.69 2.67
2509 2560 4.473444 ACATACCTAGCAAATGGGATTGG 58.527 43.478 0.00 0.00 32.69 3.16
2510 2561 4.079212 ACATACCTAGCAAATGGGATTGGT 60.079 41.667 0.00 0.00 43.03 3.67
2511 2562 3.473113 ACCTAGCAAATGGGATTGGTT 57.527 42.857 0.00 0.00 41.04 3.67
2512 2563 4.601406 ACCTAGCAAATGGGATTGGTTA 57.399 40.909 0.00 0.00 41.04 2.85
2513 2564 5.142806 ACCTAGCAAATGGGATTGGTTAT 57.857 39.130 0.00 0.00 41.04 1.89
2514 2565 6.274322 ACCTAGCAAATGGGATTGGTTATA 57.726 37.500 0.00 0.00 41.04 0.98
2515 2566 6.863322 ACCTAGCAAATGGGATTGGTTATAT 58.137 36.000 0.00 0.00 41.04 0.86
2516 2567 6.721208 ACCTAGCAAATGGGATTGGTTATATG 59.279 38.462 0.00 0.00 41.04 1.78
2517 2568 6.721208 CCTAGCAAATGGGATTGGTTATATGT 59.279 38.462 0.00 0.00 41.04 2.29
2518 2569 6.655078 AGCAAATGGGATTGGTTATATGTC 57.345 37.500 0.00 0.00 37.75 3.06
2519 2570 6.376248 AGCAAATGGGATTGGTTATATGTCT 58.624 36.000 0.00 0.00 37.75 3.41
2520 2571 6.840705 AGCAAATGGGATTGGTTATATGTCTT 59.159 34.615 0.00 0.00 37.75 3.01
2521 2572 7.345392 AGCAAATGGGATTGGTTATATGTCTTT 59.655 33.333 0.00 0.00 37.75 2.52
2522 2573 7.986889 GCAAATGGGATTGGTTATATGTCTTTT 59.013 33.333 0.00 0.00 0.00 2.27
2523 2574 9.533253 CAAATGGGATTGGTTATATGTCTTTTC 57.467 33.333 0.00 0.00 0.00 2.29
2524 2575 6.935741 TGGGATTGGTTATATGTCTTTTCG 57.064 37.500 0.00 0.00 0.00 3.46
2525 2576 6.654959 TGGGATTGGTTATATGTCTTTTCGA 58.345 36.000 0.00 0.00 0.00 3.71
2526 2577 6.765989 TGGGATTGGTTATATGTCTTTTCGAG 59.234 38.462 0.00 0.00 0.00 4.04
2527 2578 6.204882 GGGATTGGTTATATGTCTTTTCGAGG 59.795 42.308 0.00 0.00 0.00 4.63
2528 2579 6.766467 GGATTGGTTATATGTCTTTTCGAGGT 59.234 38.462 0.00 0.00 0.00 3.85
2529 2580 7.282450 GGATTGGTTATATGTCTTTTCGAGGTT 59.718 37.037 0.00 0.00 0.00 3.50
2530 2581 6.978343 TGGTTATATGTCTTTTCGAGGTTG 57.022 37.500 0.00 0.00 0.00 3.77
2572 2623 0.823356 AAGAGGCCGTGTGTTGCAAT 60.823 50.000 0.59 0.00 0.00 3.56
2678 2731 1.770749 ATTTGGGTTCCCGACGGTGA 61.771 55.000 13.94 7.06 0.00 4.02
2704 2757 2.682856 ACTGCTCACACAACGAAAATGT 59.317 40.909 0.00 0.00 0.00 2.71
2713 2766 9.605955 CTCACACAACGAAAATGTATTTGAATA 57.394 29.630 0.00 0.00 0.00 1.75
2717 2770 8.320295 CACAACGAAAATGTATTTGAATATGGC 58.680 33.333 0.00 0.00 0.00 4.40
2756 2815 2.695147 TCTCTCTCACACACACACACAT 59.305 45.455 0.00 0.00 0.00 3.21
2912 2972 2.651863 GCAATTTGGATCGCCGCG 60.652 61.111 6.39 6.39 36.79 6.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 2.966309 GCTGCCGCTACACAACCAC 61.966 63.158 0.00 0.00 0.00 4.16
138 141 0.619255 TAGGCTTTCACCCCGGATCA 60.619 55.000 0.73 0.00 0.00 2.92
162 165 3.610911 CAAGGATAACCAACTCAGGTCC 58.389 50.000 0.00 0.00 42.25 4.46
179 182 2.097680 AAAAATCGCCATTGCCAAGG 57.902 45.000 0.00 0.00 0.00 3.61
210 215 1.000385 CCGAGCAATGCCTTCAACAAA 60.000 47.619 0.00 0.00 0.00 2.83
256 261 3.690460 AGGCCACAATCTAGGTTTTCAG 58.310 45.455 5.01 0.00 0.00 3.02
417 422 4.612932 AAAAGCAAAGCGATCAGATCTC 57.387 40.909 8.82 0.20 0.00 2.75
440 455 6.747280 CCAAAATTATGTGTAGGCGAGAAAAG 59.253 38.462 0.00 0.00 0.00 2.27
480 501 6.017440 ACACAAATAACACGCTGACAAATAGT 60.017 34.615 0.00 0.00 0.00 2.12
490 511 0.941542 ACGCACACAAATAACACGCT 59.058 45.000 0.00 0.00 0.00 5.07
511 532 0.310854 GCACACAGCTAACACCAACC 59.689 55.000 0.00 0.00 41.15 3.77
521 542 5.179045 GCATAATTAAGATGCACACAGCT 57.821 39.130 16.47 0.00 46.79 4.24
534 555 3.053693 ACACCCAGCCTCTGCATAATTAA 60.054 43.478 0.00 0.00 41.13 1.40
550 571 4.828154 AGTGATTAGTGAGCACACACCCA 61.828 47.826 16.79 5.92 46.95 4.51
567 588 9.740239 GCATCATGAAAATACAAACATAGTGAT 57.260 29.630 0.00 0.00 0.00 3.06
568 589 8.959548 AGCATCATGAAAATACAAACATAGTGA 58.040 29.630 0.00 0.00 0.00 3.41
655 677 9.694137 GTACTTTGACTAGAAGTTACATCTTGT 57.306 33.333 4.59 4.59 38.28 3.16
656 678 9.141400 GGTACTTTGACTAGAAGTTACATCTTG 57.859 37.037 0.00 0.00 38.28 3.02
657 679 8.867097 TGGTACTTTGACTAGAAGTTACATCTT 58.133 33.333 0.00 0.00 38.28 2.40
658 680 8.418597 TGGTACTTTGACTAGAAGTTACATCT 57.581 34.615 0.00 0.00 38.28 2.90
659 681 9.654663 ATTGGTACTTTGACTAGAAGTTACATC 57.345 33.333 0.00 0.00 38.28 3.06
660 682 9.436957 CATTGGTACTTTGACTAGAAGTTACAT 57.563 33.333 0.00 0.00 38.28 2.29
661 683 8.644216 TCATTGGTACTTTGACTAGAAGTTACA 58.356 33.333 0.00 0.00 38.28 2.41
662 684 9.654663 ATCATTGGTACTTTGACTAGAAGTTAC 57.345 33.333 0.00 0.00 38.28 2.50
663 685 9.653287 CATCATTGGTACTTTGACTAGAAGTTA 57.347 33.333 0.00 0.00 38.28 2.24
664 686 7.119846 GCATCATTGGTACTTTGACTAGAAGTT 59.880 37.037 0.00 0.00 38.28 2.66
665 687 6.595716 GCATCATTGGTACTTTGACTAGAAGT 59.404 38.462 0.00 0.00 40.28 3.01
666 688 6.595326 TGCATCATTGGTACTTTGACTAGAAG 59.405 38.462 0.00 0.00 0.00 2.85
667 689 6.472016 TGCATCATTGGTACTTTGACTAGAA 58.528 36.000 0.00 0.00 0.00 2.10
668 690 6.048732 TGCATCATTGGTACTTTGACTAGA 57.951 37.500 0.00 0.00 0.00 2.43
669 691 6.932356 ATGCATCATTGGTACTTTGACTAG 57.068 37.500 0.00 0.00 0.00 2.57
670 692 8.978874 AATATGCATCATTGGTACTTTGACTA 57.021 30.769 0.19 0.00 0.00 2.59
671 693 7.886629 AATATGCATCATTGGTACTTTGACT 57.113 32.000 0.19 0.00 0.00 3.41
672 694 9.056005 TCTAATATGCATCATTGGTACTTTGAC 57.944 33.333 0.19 0.00 0.00 3.18
673 695 9.276590 CTCTAATATGCATCATTGGTACTTTGA 57.723 33.333 0.19 0.00 0.00 2.69
674 696 8.509690 CCTCTAATATGCATCATTGGTACTTTG 58.490 37.037 0.19 0.00 0.00 2.77
675 697 8.220559 ACCTCTAATATGCATCATTGGTACTTT 58.779 33.333 0.19 0.00 0.00 2.66
676 698 7.749666 ACCTCTAATATGCATCATTGGTACTT 58.250 34.615 0.19 0.00 0.00 2.24
677 699 7.321717 ACCTCTAATATGCATCATTGGTACT 57.678 36.000 0.19 0.00 0.00 2.73
678 700 7.445402 ACAACCTCTAATATGCATCATTGGTAC 59.555 37.037 0.19 0.00 0.00 3.34
679 701 7.517320 ACAACCTCTAATATGCATCATTGGTA 58.483 34.615 0.19 0.00 0.00 3.25
680 702 6.367983 ACAACCTCTAATATGCATCATTGGT 58.632 36.000 0.19 2.77 0.00 3.67
681 703 6.713903 AGACAACCTCTAATATGCATCATTGG 59.286 38.462 0.19 4.36 0.00 3.16
682 704 7.741027 AGACAACCTCTAATATGCATCATTG 57.259 36.000 0.19 0.40 0.00 2.82
683 705 9.851686 TTTAGACAACCTCTAATATGCATCATT 57.148 29.630 0.19 4.63 40.53 2.57
684 706 9.851686 TTTTAGACAACCTCTAATATGCATCAT 57.148 29.630 0.19 0.00 40.53 2.45
685 707 9.679661 TTTTTAGACAACCTCTAATATGCATCA 57.320 29.630 0.19 0.00 40.53 3.07
708 730 9.613428 TCCATATTCGAAGTAGATGACATTTTT 57.387 29.630 3.35 0.00 0.00 1.94
709 731 9.784531 ATCCATATTCGAAGTAGATGACATTTT 57.215 29.630 3.35 0.00 0.00 1.82
719 741 9.400638 GACTCAACTTATCCATATTCGAAGTAG 57.599 37.037 3.35 0.00 30.34 2.57
737 759 2.876079 GCCCAAATCTTCGGACTCAACT 60.876 50.000 0.00 0.00 0.00 3.16
738 760 1.468914 GCCCAAATCTTCGGACTCAAC 59.531 52.381 0.00 0.00 0.00 3.18
746 768 0.171903 CAGCCTTGCCCAAATCTTCG 59.828 55.000 0.00 0.00 0.00 3.79
755 777 2.440980 CCTTAGCCAGCCTTGCCC 60.441 66.667 0.00 0.00 0.00 5.36
781 803 1.314534 TGGAAGTCCGGCGATAACGA 61.315 55.000 9.30 0.00 39.46 3.85
885 909 1.863454 CAATGAGCTAGCTAACCTGCG 59.137 52.381 19.38 0.00 38.13 5.18
993 1017 1.056700 ACCAAGAGAGGTGCCTGTGT 61.057 55.000 0.00 0.00 41.30 3.72
1197 1221 7.027161 GGCGTATCACAAAATCAATAACAACT 58.973 34.615 0.00 0.00 0.00 3.16
1233 1257 2.284190 GAAGTACTCCTTCCTGCATGC 58.716 52.381 11.82 11.82 43.25 4.06
1284 1308 4.373116 CACCACCGTCGGGTCCAG 62.373 72.222 17.28 1.51 46.01 3.86
1562 1586 3.200887 GATGATCTCCGCCGCGAGT 62.201 63.158 15.93 0.00 0.00 4.18
1742 1766 1.584495 CTGTCCGTCGTGACCATCA 59.416 57.895 10.19 0.00 34.25 3.07
1745 1769 4.337060 CGCTGTCCGTCGTGACCA 62.337 66.667 10.19 1.01 34.25 4.02
1856 1880 4.045104 CGTCAATGTATTCTCCGAGGAAG 58.955 47.826 0.00 0.00 0.00 3.46
1865 1889 1.202533 CCCTCGGCGTCAATGTATTCT 60.203 52.381 6.85 0.00 0.00 2.40
2224 2248 1.492764 TCAGGATTCCCCGTTCCTAC 58.507 55.000 0.00 0.00 40.44 3.18
2225 2249 2.326428 GATCAGGATTCCCCGTTCCTA 58.674 52.381 0.00 0.00 40.44 2.94
2226 2250 1.132500 GATCAGGATTCCCCGTTCCT 58.868 55.000 0.00 0.00 43.24 3.36
2227 2251 0.249911 CGATCAGGATTCCCCGTTCC 60.250 60.000 0.00 0.00 40.87 3.62
2253 2277 1.396648 CGCACCAGCACATTAATTCGA 59.603 47.619 0.00 0.00 42.27 3.71
2288 2312 2.288091 CGAGAGCCTGATGAATCGATGT 60.288 50.000 0.00 0.00 32.13 3.06
2456 2504 8.133627 GCGGACTGATAAAACTGTAGTATTCTA 58.866 37.037 0.00 0.00 0.00 2.10
2458 2506 6.979238 AGCGGACTGATAAAACTGTAGTATTC 59.021 38.462 0.00 0.00 0.00 1.75
2460 2508 6.466885 AGCGGACTGATAAAACTGTAGTAT 57.533 37.500 0.00 0.00 0.00 2.12
2466 2517 4.688879 TGTTGTAGCGGACTGATAAAACTG 59.311 41.667 12.65 0.00 37.52 3.16
2481 2532 4.275936 CCCATTTGCTAGGTATGTTGTAGC 59.724 45.833 0.00 0.00 39.76 3.58
2482 2533 5.680619 TCCCATTTGCTAGGTATGTTGTAG 58.319 41.667 0.00 0.00 0.00 2.74
2483 2534 5.702065 TCCCATTTGCTAGGTATGTTGTA 57.298 39.130 0.00 0.00 0.00 2.41
2484 2535 4.584638 TCCCATTTGCTAGGTATGTTGT 57.415 40.909 0.00 0.00 0.00 3.32
2485 2536 5.221303 CCAATCCCATTTGCTAGGTATGTTG 60.221 44.000 0.00 0.00 0.00 3.33
2486 2537 4.895297 CCAATCCCATTTGCTAGGTATGTT 59.105 41.667 0.00 0.00 0.00 2.71
2487 2538 4.079212 ACCAATCCCATTTGCTAGGTATGT 60.079 41.667 0.00 0.00 0.00 2.29
2488 2539 4.473444 ACCAATCCCATTTGCTAGGTATG 58.527 43.478 0.00 0.00 0.00 2.39
2489 2540 4.814224 ACCAATCCCATTTGCTAGGTAT 57.186 40.909 0.00 0.00 0.00 2.73
2490 2541 4.601406 AACCAATCCCATTTGCTAGGTA 57.399 40.909 0.00 0.00 0.00 3.08
2491 2542 3.473113 AACCAATCCCATTTGCTAGGT 57.527 42.857 0.00 0.00 0.00 3.08
2492 2543 6.721208 ACATATAACCAATCCCATTTGCTAGG 59.279 38.462 0.00 0.00 0.00 3.02
2493 2544 7.667219 AGACATATAACCAATCCCATTTGCTAG 59.333 37.037 0.00 0.00 0.00 3.42
2494 2545 7.526041 AGACATATAACCAATCCCATTTGCTA 58.474 34.615 0.00 0.00 0.00 3.49
2495 2546 6.376248 AGACATATAACCAATCCCATTTGCT 58.624 36.000 0.00 0.00 0.00 3.91
2496 2547 6.655078 AGACATATAACCAATCCCATTTGC 57.345 37.500 0.00 0.00 0.00 3.68
2497 2548 9.533253 GAAAAGACATATAACCAATCCCATTTG 57.467 33.333 0.00 0.00 0.00 2.32
2498 2549 8.413229 CGAAAAGACATATAACCAATCCCATTT 58.587 33.333 0.00 0.00 0.00 2.32
2499 2550 7.777910 TCGAAAAGACATATAACCAATCCCATT 59.222 33.333 0.00 0.00 0.00 3.16
2500 2551 7.287061 TCGAAAAGACATATAACCAATCCCAT 58.713 34.615 0.00 0.00 0.00 4.00
2501 2552 6.654959 TCGAAAAGACATATAACCAATCCCA 58.345 36.000 0.00 0.00 0.00 4.37
2502 2553 6.204882 CCTCGAAAAGACATATAACCAATCCC 59.795 42.308 0.00 0.00 0.00 3.85
2503 2554 6.766467 ACCTCGAAAAGACATATAACCAATCC 59.234 38.462 0.00 0.00 0.00 3.01
2504 2555 7.787725 ACCTCGAAAAGACATATAACCAATC 57.212 36.000 0.00 0.00 0.00 2.67
2505 2556 7.415206 GCAACCTCGAAAAGACATATAACCAAT 60.415 37.037 0.00 0.00 0.00 3.16
2506 2557 6.128117 GCAACCTCGAAAAGACATATAACCAA 60.128 38.462 0.00 0.00 0.00 3.67
2507 2558 5.353123 GCAACCTCGAAAAGACATATAACCA 59.647 40.000 0.00 0.00 0.00 3.67
2508 2559 5.501897 CGCAACCTCGAAAAGACATATAACC 60.502 44.000 0.00 0.00 0.00 2.85
2509 2560 5.063060 ACGCAACCTCGAAAAGACATATAAC 59.937 40.000 0.00 0.00 0.00 1.89
2510 2561 5.172934 ACGCAACCTCGAAAAGACATATAA 58.827 37.500 0.00 0.00 0.00 0.98
2511 2562 4.751060 ACGCAACCTCGAAAAGACATATA 58.249 39.130 0.00 0.00 0.00 0.86
2512 2563 3.596214 ACGCAACCTCGAAAAGACATAT 58.404 40.909 0.00 0.00 0.00 1.78
2513 2564 3.034721 ACGCAACCTCGAAAAGACATA 57.965 42.857 0.00 0.00 0.00 2.29
2514 2565 1.878953 ACGCAACCTCGAAAAGACAT 58.121 45.000 0.00 0.00 0.00 3.06
2515 2566 2.129607 GTACGCAACCTCGAAAAGACA 58.870 47.619 0.00 0.00 0.00 3.41
2516 2567 1.458445 GGTACGCAACCTCGAAAAGAC 59.542 52.381 0.33 0.00 45.75 3.01
2517 2568 1.787012 GGTACGCAACCTCGAAAAGA 58.213 50.000 0.33 0.00 45.75 2.52
2541 2592 4.156008 ACACGGCCTCTTTTGCTAATAAAG 59.844 41.667 0.00 0.00 34.63 1.85
2546 2597 1.234821 CACACGGCCTCTTTTGCTAA 58.765 50.000 0.00 0.00 0.00 3.09
2558 2609 2.049248 CCCATTGCAACACACGGC 60.049 61.111 0.00 0.00 0.00 5.68
2582 2633 5.526846 TCGTTGGGTTAAGAACGTGTATTTT 59.473 36.000 11.85 0.00 44.18 1.82
2592 2645 1.411977 TCGTGGTCGTTGGGTTAAGAA 59.588 47.619 0.00 0.00 38.33 2.52
2604 2657 2.479650 GGTCTCGAGTCGTGGTCG 59.520 66.667 13.13 0.00 38.84 4.79
2664 2717 3.742357 GTGAGATCACCGTCGGGAACC 62.742 61.905 17.28 6.78 42.96 3.62
2678 2731 1.341209 TCGTTGTGTGAGCAGTGAGAT 59.659 47.619 0.00 0.00 0.00 2.75
2704 2757 6.542821 CCTTAGGACTGGCCATATTCAAATA 58.457 40.000 5.51 0.00 40.02 1.40
2713 2766 1.972660 GACGCCTTAGGACTGGCCAT 61.973 60.000 5.51 0.00 45.90 4.40
2717 2770 0.741915 GAGAGACGCCTTAGGACTGG 59.258 60.000 0.69 0.00 0.00 4.00
2814 2873 0.391597 ACTCTGAAAAACCTCGCGGA 59.608 50.000 6.13 0.00 0.00 5.54
2912 2972 2.609491 GGTCCATTTTTCTTTCGCACCC 60.609 50.000 0.00 0.00 0.00 4.61
3233 3299 9.517609 GTTCATCTATAAGTCATAACGAACTGT 57.482 33.333 0.00 0.00 0.00 3.55
3234 3300 9.737427 AGTTCATCTATAAGTCATAACGAACTG 57.263 33.333 0.00 0.00 38.26 3.16


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

AutoCloner maintained by Alex Coulton.