Multiple sequence alignment - TraesCS1A01G126800

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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 TraesCS1A01G126800 chr1A 100.000 3723 0 0 1 3723 153336577 153340299 0.000000e+00 6876.0
1 TraesCS1A01G126800 chr1B 95.370 2311 71 23 546 2841 200297829 200300118 0.000000e+00 3642.0
2 TraesCS1A01G126800 chr1B 97.005 868 12 8 2866 3721 200300109 200300974 0.000000e+00 1447.0
3 TraesCS1A01G126800 chr1D 95.086 1852 57 21 547 2382 138785067 138783234 0.000000e+00 2885.0
4 TraesCS1A01G126800 chr1D 96.744 860 11 4 2868 3723 138782753 138781907 0.000000e+00 1417.0
5 TraesCS1A01G126800 chr1D 98.739 476 6 0 2364 2839 138783221 138782746 0.000000e+00 846.0
6 TraesCS1A01G126800 chr1D 96.610 59 2 0 1992 2050 254402434 254402492 8.510000e-17 99.0
7 TraesCS1A01G126800 chrUn 88.807 545 49 5 4 546 324122666 324122132 0.000000e+00 658.0
8 TraesCS1A01G126800 chrUn 88.807 545 49 5 4 546 353963737 353963203 0.000000e+00 658.0
9 TraesCS1A01G126800 chrUn 96.610 59 2 0 1992 2050 458727174 458727232 8.510000e-17 99.0
10 TraesCS1A01G126800 chr7B 87.259 518 49 8 45 545 439011839 439011322 3.220000e-160 575.0
11 TraesCS1A01G126800 chr2B 89.877 326 31 2 221 544 215197780 215198105 5.750000e-113 418.0
12 TraesCS1A01G126800 chr2B 84.507 71 6 5 480 547 789287005 789286937 8.630000e-07 65.8
13 TraesCS1A01G126800 chr5D 94.286 105 4 2 1855 1958 399614623 399614520 3.850000e-35 159.0
14 TraesCS1A01G126800 chr5D 96.610 59 2 0 1992 2050 6184614 6184556 8.510000e-17 99.0
15 TraesCS1A01G126800 chr5D 96.610 59 2 0 1992 2050 483807258 483807200 8.510000e-17 99.0
16 TraesCS1A01G126800 chr5D 96.610 59 2 0 1992 2050 503283626 503283684 8.510000e-17 99.0
17 TraesCS1A01G126800 chr5B 94.286 105 4 2 1855 1958 479726936 479726833 3.850000e-35 159.0
18 TraesCS1A01G126800 chr5B 84.058 69 6 5 480 545 425387030 425387096 1.120000e-05 62.1
19 TraesCS1A01G126800 chr4D 91.589 107 7 2 1853 1958 32019555 32019450 3.000000e-31 147.0
20 TraesCS1A01G126800 chr4D 91.589 107 7 2 1853 1958 32019737 32019632 3.000000e-31 147.0
21 TraesCS1A01G126800 chr6A 91.429 105 7 2 1853 1956 47466893 47466790 3.880000e-30 143.0
22 TraesCS1A01G126800 chr6A 83.824 68 6 5 480 544 77157600 77157665 4.020000e-05 60.2
23 TraesCS1A01G126800 chr3B 91.429 105 7 2 1855 1958 399973219 399973116 3.880000e-30 143.0
24 TraesCS1A01G126800 chr3B 98.246 57 1 0 2105 2161 822040407 822040351 2.370000e-17 100.0
25 TraesCS1A01G126800 chr3B 98.246 57 1 0 2105 2161 822068497 822068441 2.370000e-17 100.0
26 TraesCS1A01G126800 chr3B 94.000 50 2 1 2050 2099 581959219 581959267 1.430000e-09 75.0
27 TraesCS1A01G126800 chr3B 84.932 73 6 5 480 549 684914530 684914600 6.670000e-08 69.4
28 TraesCS1A01G126800 chr2D 93.000 100 4 3 1854 1951 534928650 534928748 3.880000e-30 143.0
29 TraesCS1A01G126800 chr7A 98.246 57 1 0 2105 2161 575311308 575311252 2.370000e-17 100.0
30 TraesCS1A01G126800 chr7A 98.077 52 1 0 2050 2101 574973570 574973519 1.420000e-14 91.6
31 TraesCS1A01G126800 chr6D 96.667 60 2 0 1991 2050 429819876 429819935 2.370000e-17 100.0
32 TraesCS1A01G126800 chr6D 96.610 59 2 0 1992 2050 45515243 45515185 8.510000e-17 99.0
33 TraesCS1A01G126800 chr3A 98.246 57 1 0 2105 2161 671093559 671093615 2.370000e-17 100.0
34 TraesCS1A01G126800 chr3A 93.103 58 4 0 2050 2107 585018029 585017972 6.630000e-13 86.1
35 TraesCS1A01G126800 chr3D 96.000 50 1 1 2050 2099 444053635 444053683 3.080000e-11 80.5
36 TraesCS1A01G126800 chr5A 84.286 70 6 5 480 546 588844429 588844496 3.100000e-06 63.9


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 TraesCS1A01G126800 chr1A 153336577 153340299 3722 False 6876.0 6876 100.000000 1 3723 1 chr1A.!!$F1 3722
1 TraesCS1A01G126800 chr1B 200297829 200300974 3145 False 2544.5 3642 96.187500 546 3721 2 chr1B.!!$F1 3175
2 TraesCS1A01G126800 chr1D 138781907 138785067 3160 True 1716.0 2885 96.856333 547 3723 3 chr1D.!!$R1 3176
3 TraesCS1A01G126800 chrUn 324122132 324122666 534 True 658.0 658 88.807000 4 546 1 chrUn.!!$R1 542
4 TraesCS1A01G126800 chrUn 353963203 353963737 534 True 658.0 658 88.807000 4 546 1 chrUn.!!$R2 542
5 TraesCS1A01G126800 chr7B 439011322 439011839 517 True 575.0 575 87.259000 45 545 1 chr7B.!!$R1 500

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
474 500 0.039978 AACGCGCGAGATGATAGGAG 60.040 55.0 39.36 1.99 0.00 3.69 F
518 544 0.236187 CGCTCGACTCCTCCGAATAG 59.764 60.0 0.00 0.00 35.48 1.73 F
522 548 0.317103 CGACTCCTCCGAATAGTGCG 60.317 60.0 0.00 0.00 0.00 5.34 F
523 549 0.595310 GACTCCTCCGAATAGTGCGC 60.595 60.0 0.00 0.00 0.00 6.09 F
1867 1919 0.040204 AGAATGAACCAGCCCCCTTG 59.960 55.0 0.00 0.00 0.00 3.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1327 1358 0.179189 GCCGAACAAGATCGCCAAAG 60.179 55.000 0.0 0.0 41.40 2.77 R
1413 1448 1.019278 AACAGTCGGCGCGATGAAAT 61.019 50.000 12.1 0.0 38.42 2.17 R
1445 1480 1.204467 ACCAAACCTGCAAACACAGTG 59.796 47.619 0.0 0.0 35.83 3.66 R
1912 1964 2.436109 CACAAGGTGGGGTCTGGG 59.564 66.667 0.0 0.0 0.00 4.45 R
3595 3688 0.033781 GCATTGTTTTGCCCAGCAGA 59.966 50.000 0.0 0.0 40.61 4.26 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
64 65 3.319198 GGCGGGAAGGTCCTCACA 61.319 66.667 0.00 0.00 36.57 3.58
69 70 0.329596 GGGAAGGTCCTCACAAGCAT 59.670 55.000 0.00 0.00 36.57 3.79
78 79 1.974249 CTCACAAGCATCGCGCACAT 61.974 55.000 8.75 0.00 46.13 3.21
121 122 1.213296 GGGGGAGCAGATGGTAGAAA 58.787 55.000 0.00 0.00 0.00 2.52
124 125 1.488393 GGGAGCAGATGGTAGAAAGCT 59.512 52.381 0.00 0.00 34.61 3.74
126 127 2.093235 GGAGCAGATGGTAGAAAGCTGT 60.093 50.000 0.00 0.00 31.61 4.40
195 197 0.823460 GAGCTGGTGGAGAGAGAAGG 59.177 60.000 0.00 0.00 0.00 3.46
317 319 2.669229 TCGACGACGGCACCTACA 60.669 61.111 7.55 0.00 40.21 2.74
384 401 2.246761 TATGGTTGGACGGGGCGAAG 62.247 60.000 0.00 0.00 0.00 3.79
390 407 2.735237 GACGGGGCGAAGGGATAG 59.265 66.667 0.00 0.00 0.00 2.08
391 408 1.831286 GACGGGGCGAAGGGATAGA 60.831 63.158 0.00 0.00 0.00 1.98
397 414 1.209747 GGGCGAAGGGATAGAAACAGT 59.790 52.381 0.00 0.00 0.00 3.55
400 417 3.335579 GCGAAGGGATAGAAACAGTTGT 58.664 45.455 0.00 0.00 0.00 3.32
401 418 3.125316 GCGAAGGGATAGAAACAGTTGTG 59.875 47.826 0.00 0.00 0.00 3.33
402 419 3.684788 CGAAGGGATAGAAACAGTTGTGG 59.315 47.826 0.00 0.00 0.00 4.17
403 420 4.652822 GAAGGGATAGAAACAGTTGTGGT 58.347 43.478 0.00 0.00 0.00 4.16
404 421 4.287766 AGGGATAGAAACAGTTGTGGTC 57.712 45.455 0.00 0.00 0.00 4.02
405 422 3.650942 AGGGATAGAAACAGTTGTGGTCA 59.349 43.478 0.00 0.00 0.00 4.02
406 423 4.289672 AGGGATAGAAACAGTTGTGGTCAT 59.710 41.667 0.00 0.00 0.00 3.06
407 424 4.636206 GGGATAGAAACAGTTGTGGTCATC 59.364 45.833 0.00 0.00 0.00 2.92
408 425 4.330074 GGATAGAAACAGTTGTGGTCATCG 59.670 45.833 0.00 0.00 0.00 3.84
409 426 3.469008 AGAAACAGTTGTGGTCATCGA 57.531 42.857 0.00 0.00 0.00 3.59
458 484 4.687464 GGTACCACCTGACCAACG 57.313 61.111 7.15 0.00 34.73 4.10
459 485 1.670083 GGTACCACCTGACCAACGC 60.670 63.158 7.15 0.00 34.73 4.84
460 486 2.025418 GTACCACCTGACCAACGCG 61.025 63.158 3.53 3.53 0.00 6.01
461 487 3.869473 TACCACCTGACCAACGCGC 62.869 63.158 5.73 0.00 0.00 6.86
465 491 4.717629 CCTGACCAACGCGCGAGA 62.718 66.667 39.36 11.44 0.00 4.04
466 492 2.507102 CTGACCAACGCGCGAGAT 60.507 61.111 39.36 16.34 0.00 2.75
467 493 2.792290 CTGACCAACGCGCGAGATG 61.792 63.158 39.36 28.59 0.00 2.90
468 494 2.506217 GACCAACGCGCGAGATGA 60.506 61.111 39.36 0.00 0.00 2.92
469 495 1.878522 GACCAACGCGCGAGATGAT 60.879 57.895 39.36 19.46 0.00 2.45
470 496 0.594028 GACCAACGCGCGAGATGATA 60.594 55.000 39.36 0.00 0.00 2.15
471 497 0.595053 ACCAACGCGCGAGATGATAG 60.595 55.000 39.36 19.45 0.00 2.08
472 498 1.278172 CCAACGCGCGAGATGATAGG 61.278 60.000 39.36 19.94 0.00 2.57
473 499 0.317854 CAACGCGCGAGATGATAGGA 60.318 55.000 39.36 0.00 0.00 2.94
474 500 0.039978 AACGCGCGAGATGATAGGAG 60.040 55.000 39.36 1.99 0.00 3.69
475 501 1.167155 ACGCGCGAGATGATAGGAGT 61.167 55.000 39.36 5.70 0.00 3.85
476 502 0.727457 CGCGCGAGATGATAGGAGTG 60.727 60.000 28.94 0.00 0.00 3.51
477 503 0.593618 GCGCGAGATGATAGGAGTGA 59.406 55.000 12.10 0.00 0.00 3.41
478 504 1.400888 GCGCGAGATGATAGGAGTGAG 60.401 57.143 12.10 0.00 0.00 3.51
479 505 2.147150 CGCGAGATGATAGGAGTGAGA 58.853 52.381 0.00 0.00 0.00 3.27
480 506 2.746904 CGCGAGATGATAGGAGTGAGAT 59.253 50.000 0.00 0.00 0.00 2.75
481 507 3.181511 CGCGAGATGATAGGAGTGAGATC 60.182 52.174 0.00 0.00 0.00 2.75
482 508 3.181511 GCGAGATGATAGGAGTGAGATCG 60.182 52.174 0.00 0.00 0.00 3.69
483 509 4.000325 CGAGATGATAGGAGTGAGATCGT 59.000 47.826 0.00 0.00 0.00 3.73
484 510 4.142924 CGAGATGATAGGAGTGAGATCGTG 60.143 50.000 0.00 0.00 0.00 4.35
485 511 3.505680 AGATGATAGGAGTGAGATCGTGC 59.494 47.826 0.00 0.00 0.00 5.34
486 512 1.604278 TGATAGGAGTGAGATCGTGCG 59.396 52.381 0.00 0.00 0.00 5.34
487 513 0.312416 ATAGGAGTGAGATCGTGCGC 59.688 55.000 0.00 0.00 0.00 6.09
488 514 1.725557 TAGGAGTGAGATCGTGCGCC 61.726 60.000 4.18 0.00 0.00 6.53
489 515 2.181777 GAGTGAGATCGTGCGCCA 59.818 61.111 4.18 0.00 0.00 5.69
490 516 1.875813 GAGTGAGATCGTGCGCCAG 60.876 63.158 4.18 0.00 0.00 4.85
491 517 2.887568 GTGAGATCGTGCGCCAGG 60.888 66.667 4.18 0.00 0.00 4.45
492 518 3.068064 TGAGATCGTGCGCCAGGA 61.068 61.111 4.18 4.74 32.83 3.86
493 519 2.279120 GAGATCGTGCGCCAGGAG 60.279 66.667 4.18 0.00 31.81 3.69
494 520 4.521062 AGATCGTGCGCCAGGAGC 62.521 66.667 8.52 8.52 35.33 4.70
515 541 3.132139 CCGCTCGACTCCTCCGAA 61.132 66.667 0.00 0.00 35.48 4.30
516 542 2.482333 CCGCTCGACTCCTCCGAAT 61.482 63.158 0.00 0.00 35.48 3.34
517 543 1.164662 CCGCTCGACTCCTCCGAATA 61.165 60.000 0.00 0.00 35.48 1.75
518 544 0.236187 CGCTCGACTCCTCCGAATAG 59.764 60.000 0.00 0.00 35.48 1.73
519 545 1.310904 GCTCGACTCCTCCGAATAGT 58.689 55.000 0.00 0.00 35.48 2.12
520 546 1.002251 GCTCGACTCCTCCGAATAGTG 60.002 57.143 0.00 0.00 35.48 2.74
521 547 1.002251 CTCGACTCCTCCGAATAGTGC 60.002 57.143 0.00 0.00 35.48 4.40
522 548 0.317103 CGACTCCTCCGAATAGTGCG 60.317 60.000 0.00 0.00 0.00 5.34
523 549 0.595310 GACTCCTCCGAATAGTGCGC 60.595 60.000 0.00 0.00 0.00 6.09
524 550 1.658717 CTCCTCCGAATAGTGCGCG 60.659 63.158 0.00 0.00 0.00 6.86
525 551 3.330853 CCTCCGAATAGTGCGCGC 61.331 66.667 27.26 27.26 0.00 6.86
526 552 3.682315 CTCCGAATAGTGCGCGCG 61.682 66.667 28.44 28.44 0.00 6.86
537 563 2.172419 GCGCGCGCACTTTTTAGA 59.828 55.556 46.11 0.00 41.49 2.10
538 564 1.439693 GCGCGCGCACTTTTTAGAA 60.440 52.632 46.11 0.00 41.49 2.10
539 565 0.793104 GCGCGCGCACTTTTTAGAAT 60.793 50.000 46.11 0.00 41.49 2.40
540 566 1.602191 CGCGCGCACTTTTTAGAATT 58.398 45.000 32.61 0.00 0.00 2.17
541 567 1.976045 CGCGCGCACTTTTTAGAATTT 59.024 42.857 32.61 0.00 0.00 1.82
542 568 3.157510 CGCGCGCACTTTTTAGAATTTA 58.842 40.909 32.61 0.00 0.00 1.40
543 569 3.235179 CGCGCGCACTTTTTAGAATTTAG 59.765 43.478 32.61 3.88 0.00 1.85
544 570 3.542310 GCGCGCACTTTTTAGAATTTAGG 59.458 43.478 29.10 0.00 0.00 2.69
594 620 1.069935 GAAGATAGCCCTGTCCGCC 59.930 63.158 0.00 0.00 0.00 6.13
731 758 8.229253 TCTAATAAACAACGCTCTAGTCCATA 57.771 34.615 0.00 0.00 0.00 2.74
760 787 1.016130 CACGCTCCATCGAAGCTTGT 61.016 55.000 2.10 0.00 37.62 3.16
994 1024 1.117150 GGCGGTGGGTATCTGAGTTA 58.883 55.000 0.00 0.00 0.00 2.24
1176 1206 2.751436 CACATCAAGGCCCCCGTG 60.751 66.667 0.00 0.00 34.41 4.94
1208 1238 2.395353 CCCCATCCTTTCCCTCCCC 61.395 68.421 0.00 0.00 0.00 4.81
1327 1358 2.353376 TCGTTTTGCTGCGCTTGC 60.353 55.556 9.73 14.07 39.78 4.01
1413 1448 0.904865 CCCGGGCAGATGGATAGCTA 60.905 60.000 8.08 0.00 0.00 3.32
1425 1460 1.661112 GGATAGCTATTTCATCGCGCC 59.339 52.381 7.87 0.00 0.00 6.53
1445 1480 3.181510 GCCGACTGTTTGATTCATGTACC 60.182 47.826 0.00 0.00 0.00 3.34
1470 1505 0.317854 GTTTGCAGGTTTGGTCGCTC 60.318 55.000 0.00 0.00 0.00 5.03
1581 1616 1.068585 GGTCAACGTCAAGACCGGT 59.931 57.895 6.92 6.92 44.23 5.28
1690 1725 0.603975 GCTCAGGGTTCGTGCTTTCT 60.604 55.000 0.00 0.00 0.00 2.52
1691 1726 1.337823 GCTCAGGGTTCGTGCTTTCTA 60.338 52.381 0.00 0.00 0.00 2.10
1692 1727 2.611518 CTCAGGGTTCGTGCTTTCTAG 58.388 52.381 0.00 0.00 0.00 2.43
1693 1728 1.968493 TCAGGGTTCGTGCTTTCTAGT 59.032 47.619 0.00 0.00 0.00 2.57
1694 1729 2.029290 TCAGGGTTCGTGCTTTCTAGTC 60.029 50.000 0.00 0.00 0.00 2.59
1695 1730 1.968493 AGGGTTCGTGCTTTCTAGTCA 59.032 47.619 0.00 0.00 0.00 3.41
1696 1731 2.567615 AGGGTTCGTGCTTTCTAGTCAT 59.432 45.455 0.00 0.00 0.00 3.06
1697 1732 3.008049 AGGGTTCGTGCTTTCTAGTCATT 59.992 43.478 0.00 0.00 0.00 2.57
1699 1734 4.933400 GGGTTCGTGCTTTCTAGTCATTTA 59.067 41.667 0.00 0.00 0.00 1.40
1700 1735 5.163884 GGGTTCGTGCTTTCTAGTCATTTAC 60.164 44.000 0.00 0.00 0.00 2.01
1737 1774 6.192970 ACTAGTGCCTAAATGCTCCATTAT 57.807 37.500 0.00 0.00 32.43 1.28
1740 1777 8.386264 ACTAGTGCCTAAATGCTCCATTATAAT 58.614 33.333 0.00 0.00 32.43 1.28
1741 1778 9.890629 CTAGTGCCTAAATGCTCCATTATAATA 57.109 33.333 0.00 0.00 32.43 0.98
1746 1783 9.305925 GCCTAAATGCTCCATTATAATAATTGC 57.694 33.333 0.00 2.00 32.43 3.56
1753 1790 9.618890 TGCTCCATTATAATAATTGCTAGATCC 57.381 33.333 0.00 0.00 0.00 3.36
1754 1791 9.844257 GCTCCATTATAATAATTGCTAGATCCT 57.156 33.333 0.00 0.00 0.00 3.24
1756 1793 9.618890 TCCATTATAATAATTGCTAGATCCTGC 57.381 33.333 0.00 1.08 0.00 4.85
1757 1794 9.399797 CCATTATAATAATTGCTAGATCCTGCA 57.600 33.333 6.18 6.18 37.42 4.41
1867 1919 0.040204 AGAATGAACCAGCCCCCTTG 59.960 55.000 0.00 0.00 0.00 3.61
1912 1964 3.201045 AGGCTGTCTAGAAATTCCCTTCC 59.799 47.826 0.00 0.00 0.00 3.46
2010 2062 2.869101 TGGGATTTCCACAACGATCA 57.131 45.000 0.00 0.00 41.46 2.92
2099 2152 5.629079 ACCGATTGGATCAAGAAGAAAAC 57.371 39.130 5.81 0.00 39.21 2.43
2141 2194 2.096819 TGGAAACTGTTGTGACGCTTTC 59.903 45.455 0.00 0.00 0.00 2.62
2161 2214 4.754667 GACGAAGGTCACCGGGGC 62.755 72.222 6.32 0.00 42.91 5.80
2285 2338 4.984161 CCTGCAGTTTTACAAAATCAGGTG 59.016 41.667 13.81 0.00 37.62 4.00
2422 2507 7.382898 ACCTTGCAAGAAGTTGAAAAGTTAAA 58.617 30.769 28.05 0.00 40.14 1.52
2448 2533 0.966875 TTGATGGACATGCCTGCACC 60.967 55.000 0.00 0.00 37.63 5.01
2490 2575 6.892485 TGTTTGATCCATACTGATCTGATGT 58.108 36.000 6.60 0.00 41.42 3.06
2832 2917 6.058183 CGGTAGATTCTCCATTTTCTTCCAT 58.942 40.000 0.00 0.00 0.00 3.41
2833 2918 7.217200 CGGTAGATTCTCCATTTTCTTCCATA 58.783 38.462 0.00 0.00 0.00 2.74
2834 2919 7.880195 CGGTAGATTCTCCATTTTCTTCCATAT 59.120 37.037 0.00 0.00 0.00 1.78
3302 3392 6.990341 TGTAATTGACATGATTGGTGAGAG 57.010 37.500 0.00 0.00 31.20 3.20
3519 3611 7.725818 AACTTGTAAGTACCTTTCTAAGCAC 57.274 36.000 0.00 0.00 38.57 4.40
3550 3642 3.700538 AGCCAAGGCATCACTTTCAATA 58.299 40.909 14.40 0.00 44.88 1.90
3628 3725 1.003262 CAATGCGGGAACTGTTTGCG 61.003 55.000 0.00 0.00 36.83 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.783621 CCTAGCCGGCTGCAGCAA 62.784 66.667 38.98 17.17 44.83 3.91
24 25 1.457831 GCTCCTCCACCGGTAGGAT 60.458 63.158 23.53 0.00 41.06 3.24
57 58 2.815211 GCGCGATGCTTGTGAGGA 60.815 61.111 12.10 0.00 41.73 3.71
64 65 4.183686 GCCATGTGCGCGATGCTT 62.184 61.111 12.10 0.00 46.63 3.91
78 79 2.349755 GCTACCCCAAAGACGCCA 59.650 61.111 0.00 0.00 0.00 5.69
85 86 4.090588 CGCCTCGGCTACCCCAAA 62.091 66.667 6.35 0.00 39.32 3.28
111 112 3.624861 CCATGTCACAGCTTTCTACCATC 59.375 47.826 0.00 0.00 0.00 3.51
116 117 1.675714 CGGCCATGTCACAGCTTTCTA 60.676 52.381 2.24 0.00 0.00 2.10
121 122 2.359107 CACGGCCATGTCACAGCT 60.359 61.111 2.24 0.00 0.00 4.24
195 197 3.925090 CGGCCACCGTATCCCTCC 61.925 72.222 2.24 0.00 42.73 4.30
214 216 2.134630 CTTCCCCAAGGCACTGCTCT 62.135 60.000 0.00 0.00 40.86 4.09
384 401 4.015872 TGACCACAACTGTTTCTATCCC 57.984 45.455 0.00 0.00 0.00 3.85
390 407 2.096218 GCTCGATGACCACAACTGTTTC 60.096 50.000 0.00 0.00 0.00 2.78
391 408 1.873591 GCTCGATGACCACAACTGTTT 59.126 47.619 0.00 0.00 0.00 2.83
397 414 2.434185 GCCGCTCGATGACCACAA 60.434 61.111 0.00 0.00 0.00 3.33
400 417 4.492160 GACGCCGCTCGATGACCA 62.492 66.667 2.25 0.00 41.67 4.02
424 450 4.016706 CTGGTCGGGGCGGTTTCT 62.017 66.667 0.00 0.00 0.00 2.52
455 481 0.039978 CTCCTATCATCTCGCGCGTT 60.040 55.000 30.98 13.31 0.00 4.84
457 483 0.727457 CACTCCTATCATCTCGCGCG 60.727 60.000 26.76 26.76 0.00 6.86
458 484 0.593618 TCACTCCTATCATCTCGCGC 59.406 55.000 0.00 0.00 0.00 6.86
459 485 2.147150 TCTCACTCCTATCATCTCGCG 58.853 52.381 0.00 0.00 0.00 5.87
460 486 3.181511 CGATCTCACTCCTATCATCTCGC 60.182 52.174 0.00 0.00 0.00 5.03
461 487 4.000325 ACGATCTCACTCCTATCATCTCG 59.000 47.826 0.00 0.00 0.00 4.04
462 488 4.379394 GCACGATCTCACTCCTATCATCTC 60.379 50.000 0.00 0.00 0.00 2.75
463 489 3.505680 GCACGATCTCACTCCTATCATCT 59.494 47.826 0.00 0.00 0.00 2.90
464 490 3.669290 CGCACGATCTCACTCCTATCATC 60.669 52.174 0.00 0.00 0.00 2.92
465 491 2.227626 CGCACGATCTCACTCCTATCAT 59.772 50.000 0.00 0.00 0.00 2.45
466 492 1.604278 CGCACGATCTCACTCCTATCA 59.396 52.381 0.00 0.00 0.00 2.15
467 493 1.664588 GCGCACGATCTCACTCCTATC 60.665 57.143 0.30 0.00 0.00 2.08
468 494 0.312416 GCGCACGATCTCACTCCTAT 59.688 55.000 0.30 0.00 0.00 2.57
469 495 1.725557 GGCGCACGATCTCACTCCTA 61.726 60.000 10.83 0.00 0.00 2.94
470 496 2.492090 GCGCACGATCTCACTCCT 59.508 61.111 0.30 0.00 0.00 3.69
471 497 2.583593 GGCGCACGATCTCACTCC 60.584 66.667 10.83 0.00 0.00 3.85
472 498 1.875813 CTGGCGCACGATCTCACTC 60.876 63.158 10.83 0.00 0.00 3.51
473 499 2.182791 CTGGCGCACGATCTCACT 59.817 61.111 10.83 0.00 0.00 3.41
474 500 2.887568 CCTGGCGCACGATCTCAC 60.888 66.667 10.83 0.00 0.00 3.51
475 501 3.068064 TCCTGGCGCACGATCTCA 61.068 61.111 10.83 0.00 0.00 3.27
476 502 2.279120 CTCCTGGCGCACGATCTC 60.279 66.667 10.83 0.00 0.00 2.75
477 503 4.521062 GCTCCTGGCGCACGATCT 62.521 66.667 10.83 0.00 0.00 2.75
498 524 1.164662 TATTCGGAGGAGTCGAGCGG 61.165 60.000 0.00 0.00 37.93 5.52
499 525 0.236187 CTATTCGGAGGAGTCGAGCG 59.764 60.000 0.00 0.00 37.93 5.03
500 526 1.002251 CACTATTCGGAGGAGTCGAGC 60.002 57.143 0.00 0.00 37.93 5.03
501 527 1.002251 GCACTATTCGGAGGAGTCGAG 60.002 57.143 0.00 0.00 37.93 4.04
502 528 1.022735 GCACTATTCGGAGGAGTCGA 58.977 55.000 0.00 0.00 34.62 4.20
503 529 0.317103 CGCACTATTCGGAGGAGTCG 60.317 60.000 0.00 0.00 0.00 4.18
504 530 0.595310 GCGCACTATTCGGAGGAGTC 60.595 60.000 0.30 0.00 0.00 3.36
505 531 1.437986 GCGCACTATTCGGAGGAGT 59.562 57.895 0.30 0.00 0.00 3.85
506 532 1.658717 CGCGCACTATTCGGAGGAG 60.659 63.158 8.75 0.00 0.00 3.69
507 533 2.411701 CGCGCACTATTCGGAGGA 59.588 61.111 8.75 0.00 0.00 3.71
508 534 3.330853 GCGCGCACTATTCGGAGG 61.331 66.667 29.10 0.00 0.00 4.30
509 535 3.682315 CGCGCGCACTATTCGGAG 61.682 66.667 32.61 6.38 0.00 4.63
520 546 0.793104 ATTCTAAAAAGTGCGCGCGC 60.793 50.000 45.02 45.02 42.35 6.86
521 547 1.602191 AATTCTAAAAAGTGCGCGCG 58.398 45.000 28.44 28.44 0.00 6.86
522 548 3.542310 CCTAAATTCTAAAAAGTGCGCGC 59.458 43.478 27.26 27.26 0.00 6.86
523 549 4.965062 TCCTAAATTCTAAAAAGTGCGCG 58.035 39.130 0.00 0.00 0.00 6.86
524 550 9.516314 AATAATCCTAAATTCTAAAAAGTGCGC 57.484 29.630 0.00 0.00 0.00 6.09
594 620 1.593006 CGCCAGCTAGGACAATAAACG 59.407 52.381 6.40 0.00 41.22 3.60
643 669 3.616956 ATCTTCGGTCATGTGACACAT 57.383 42.857 15.48 15.48 46.47 3.21
644 670 4.736126 ATATCTTCGGTCATGTGACACA 57.264 40.909 11.41 11.41 46.47 3.72
645 671 6.422776 AAAATATCTTCGGTCATGTGACAC 57.577 37.500 14.47 0.00 46.47 3.67
646 672 6.622679 GCAAAAATATCTTCGGTCATGTGACA 60.623 38.462 14.47 0.00 46.47 3.58
647 673 5.739161 GCAAAAATATCTTCGGTCATGTGAC 59.261 40.000 4.58 4.58 44.04 3.67
696 723 5.827568 GTTGTTTATTAGAACGACGGTGA 57.172 39.130 0.00 0.00 35.03 4.02
821 848 1.247567 ACAAAAATCTGCGGGGTGAG 58.752 50.000 0.00 0.00 0.00 3.51
988 1018 0.327924 CCCACCATGCCAGTAACTCA 59.672 55.000 0.00 0.00 0.00 3.41
1176 1206 4.083862 GGGGGTCTCACGAGGTGC 62.084 72.222 0.00 0.00 32.98 5.01
1215 1245 0.615850 AGGTACAGCAAAGGAGGAGC 59.384 55.000 0.00 0.00 0.00 4.70
1217 1247 2.708861 TGAAAGGTACAGCAAAGGAGGA 59.291 45.455 0.00 0.00 0.00 3.71
1327 1358 0.179189 GCCGAACAAGATCGCCAAAG 60.179 55.000 0.00 0.00 41.40 2.77
1413 1448 1.019278 AACAGTCGGCGCGATGAAAT 61.019 50.000 12.10 0.00 38.42 2.17
1425 1460 4.690748 AGTGGTACATGAATCAAACAGTCG 59.309 41.667 0.00 0.00 44.52 4.18
1445 1480 1.204467 ACCAAACCTGCAAACACAGTG 59.796 47.619 0.00 0.00 35.83 3.66
1470 1505 4.717629 TGGTCGAAGCTCCGCACG 62.718 66.667 0.00 0.00 33.74 5.34
1581 1616 2.662596 CTAGTTGTGGCCGGCAGA 59.337 61.111 30.85 11.68 0.00 4.26
1690 1725 9.463902 AGTAAGAAGTAGAGCAGTAAATGACTA 57.536 33.333 0.00 0.00 35.64 2.59
1691 1726 8.356000 AGTAAGAAGTAGAGCAGTAAATGACT 57.644 34.615 0.00 0.00 39.82 3.41
1692 1727 9.724839 CTAGTAAGAAGTAGAGCAGTAAATGAC 57.275 37.037 0.00 0.00 31.18 3.06
1693 1728 9.463902 ACTAGTAAGAAGTAGAGCAGTAAATGA 57.536 33.333 0.00 0.00 33.49 2.57
1694 1729 9.509855 CACTAGTAAGAAGTAGAGCAGTAAATG 57.490 37.037 0.00 0.00 33.49 2.32
1695 1730 8.192110 GCACTAGTAAGAAGTAGAGCAGTAAAT 58.808 37.037 0.00 0.00 41.93 1.40
1696 1731 7.362747 GGCACTAGTAAGAAGTAGAGCAGTAAA 60.363 40.741 0.00 0.00 43.27 2.01
1697 1732 6.095160 GGCACTAGTAAGAAGTAGAGCAGTAA 59.905 42.308 0.00 0.00 43.27 2.24
1699 1734 4.399934 GGCACTAGTAAGAAGTAGAGCAGT 59.600 45.833 0.00 0.00 43.27 4.40
1700 1735 4.642885 AGGCACTAGTAAGAAGTAGAGCAG 59.357 45.833 0.00 0.00 43.27 4.24
1744 1781 6.537355 AGCTATTATTTTGCAGGATCTAGCA 58.463 36.000 18.00 8.25 39.32 3.49
1747 1784 9.881649 CATCTAGCTATTATTTTGCAGGATCTA 57.118 33.333 0.00 0.00 0.00 1.98
1748 1785 7.336427 GCATCTAGCTATTATTTTGCAGGATCT 59.664 37.037 0.00 0.00 41.15 2.75
1749 1786 7.470900 GCATCTAGCTATTATTTTGCAGGATC 58.529 38.462 0.00 0.00 41.15 3.36
1750 1787 7.388460 GCATCTAGCTATTATTTTGCAGGAT 57.612 36.000 0.00 0.00 41.15 3.24
1751 1788 6.808008 GCATCTAGCTATTATTTTGCAGGA 57.192 37.500 0.00 0.00 41.15 3.86
1766 1803 4.749099 CAGACTTGTAATGGAGCATCTAGC 59.251 45.833 0.00 0.00 46.19 3.42
1867 1919 6.294731 CCTTTACCCCTGCATAATAATTCTGC 60.295 42.308 0.00 0.00 36.45 4.26
1883 1935 3.994931 TTTCTAGACAGCCTTTACCCC 57.005 47.619 0.00 0.00 0.00 4.95
1912 1964 2.436109 CACAAGGTGGGGTCTGGG 59.564 66.667 0.00 0.00 0.00 4.45
1952 2004 9.004231 AGACCATTATTAGTTCTAATGAAGGGT 57.996 33.333 18.65 18.65 38.35 4.34
2285 2338 4.275196 GTGTTCCTTCCTTAGTGGTCAAAC 59.725 45.833 0.00 0.00 37.07 2.93
2422 2507 4.571919 CAGGCATGTCCATCAACAAAAAT 58.428 39.130 8.58 0.00 37.29 1.82
2448 2533 7.065216 TCAAACAGAAGCTTAAAGATCATCG 57.935 36.000 0.00 0.00 0.00 3.84
2490 2575 6.127168 TGAGTAGTTCTGAAGAAGTGGAAACA 60.127 38.462 10.10 2.39 38.13 2.83
3302 3392 5.757850 ACACAGGAAAACTCAGACATTTC 57.242 39.130 0.00 0.00 33.38 2.17
3399 3489 2.415625 GCCAAGCAAGCATGAAAGAGAG 60.416 50.000 0.00 0.00 0.00 3.20
3519 3611 2.309528 TGCCTTGGCTTATCTACACG 57.690 50.000 13.18 0.00 0.00 4.49
3550 3642 5.483583 AGAAGTCATTTCAGGAGCTTCTAGT 59.516 40.000 0.00 0.00 40.27 2.57
3594 3687 1.787012 CATTGTTTTGCCCAGCAGAC 58.213 50.000 0.00 0.00 40.61 3.51
3595 3688 0.033781 GCATTGTTTTGCCCAGCAGA 59.966 50.000 0.00 0.00 40.61 4.26
3596 3689 1.286354 CGCATTGTTTTGCCCAGCAG 61.286 55.000 0.00 0.00 40.61 4.24
3628 3725 4.932146 ACCACACAAAATTACAAGCAGAC 58.068 39.130 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.