Multiple sequence alignment - TraesCS2A01G134200

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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 TraesCS2A01G134200 chr2A 100.000 3112 0 0 1 3112 80614068 80617179 0.000000e+00 5747.0
1 TraesCS2A01G134200 chr2A 82.983 905 91 23 1383 2286 299511503 299510661 0.000000e+00 760.0
2 TraesCS2A01G134200 chr2A 82.873 905 92 27 1383 2286 460474261 460473419 0.000000e+00 754.0
3 TraesCS2A01G134200 chr2D 93.811 2359 97 14 788 3112 80034137 80036480 0.000000e+00 3502.0
4 TraesCS2A01G134200 chr2D 84.661 1004 86 30 1325 2327 232181939 232181003 0.000000e+00 939.0
5 TraesCS2A01G134200 chr2D 92.308 221 15 2 1 221 80033087 80033305 2.330000e-81 313.0
6 TraesCS2A01G134200 chr2D 100.000 29 0 0 567 595 471214590 471214618 2.000000e-03 54.7
7 TraesCS2A01G134200 chr2B 89.170 2373 153 43 787 3112 131581256 131583571 0.000000e+00 2863.0
8 TraesCS2A01G134200 chr2B 89.216 204 21 1 18 221 131580093 131580295 1.430000e-63 254.0
9 TraesCS2A01G134200 chr2B 100.000 29 0 0 567 595 550398194 550398222 2.000000e-03 54.7
10 TraesCS2A01G134200 chr3D 85.089 1006 79 29 1325 2327 497286932 497287869 0.000000e+00 961.0
11 TraesCS2A01G134200 chr3D 89.088 724 42 11 1325 2045 172532044 172531355 0.000000e+00 865.0
12 TraesCS2A01G134200 chr5D 84.363 1004 81 25 1325 2327 489746641 489745713 0.000000e+00 915.0
13 TraesCS2A01G134200 chr4D 86.501 726 58 13 1325 2045 200717251 200716561 0.000000e+00 761.0
14 TraesCS2A01G134200 chr7B 86.389 720 56 17 1325 2042 193199103 193199782 0.000000e+00 749.0
15 TraesCS2A01G134200 chr7B 82.635 334 30 4 1713 2045 680449150 680449456 1.420000e-68 270.0
16 TraesCS2A01G134200 chr7B 82.335 334 31 4 1713 2045 680417985 680418291 6.620000e-67 265.0
17 TraesCS2A01G134200 chr7B 88.517 209 18 2 2120 2327 193199831 193200034 6.660000e-62 248.0
18 TraesCS2A01G134200 chr7B 83.077 260 28 9 2079 2327 680449450 680449704 4.040000e-54 222.0
19 TraesCS2A01G134200 chr7A 84.690 725 71 22 1325 2045 667804162 667804850 0.000000e+00 688.0
20 TraesCS2A01G134200 chr7A 100.000 29 0 0 567 595 192986908 192986880 2.000000e-03 54.7
21 TraesCS2A01G134200 chr6B 82.635 334 30 4 1713 2045 519170392 519170698 1.420000e-68 270.0
22 TraesCS2A01G134200 chr4B 84.615 260 24 9 2079 2327 614205626 614205372 8.620000e-61 244.0
23 TraesCS2A01G134200 chr1B 84.231 260 25 8 2079 2327 34738228 34737974 4.010000e-59 239.0
24 TraesCS2A01G134200 chr4A 83.846 260 26 9 2079 2327 706767275 706767529 1.870000e-57 233.0
25 TraesCS2A01G134200 chr5B 83.462 260 27 8 2079 2327 20985867 20985613 8.680000e-56 228.0
26 TraesCS2A01G134200 chr6D 78.205 156 25 6 567 721 331250278 331250425 1.190000e-14 91.6


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 TraesCS2A01G134200 chr2A 80614068 80617179 3111 False 5747.0 5747 100.0000 1 3112 1 chr2A.!!$F1 3111
1 TraesCS2A01G134200 chr2A 299510661 299511503 842 True 760.0 760 82.9830 1383 2286 1 chr2A.!!$R1 903
2 TraesCS2A01G134200 chr2A 460473419 460474261 842 True 754.0 754 82.8730 1383 2286 1 chr2A.!!$R2 903
3 TraesCS2A01G134200 chr2D 80033087 80036480 3393 False 1907.5 3502 93.0595 1 3112 2 chr2D.!!$F2 3111
4 TraesCS2A01G134200 chr2D 232181003 232181939 936 True 939.0 939 84.6610 1325 2327 1 chr2D.!!$R1 1002
5 TraesCS2A01G134200 chr2B 131580093 131583571 3478 False 1558.5 2863 89.1930 18 3112 2 chr2B.!!$F2 3094
6 TraesCS2A01G134200 chr3D 497286932 497287869 937 False 961.0 961 85.0890 1325 2327 1 chr3D.!!$F1 1002
7 TraesCS2A01G134200 chr3D 172531355 172532044 689 True 865.0 865 89.0880 1325 2045 1 chr3D.!!$R1 720
8 TraesCS2A01G134200 chr5D 489745713 489746641 928 True 915.0 915 84.3630 1325 2327 1 chr5D.!!$R1 1002
9 TraesCS2A01G134200 chr4D 200716561 200717251 690 True 761.0 761 86.5010 1325 2045 1 chr4D.!!$R1 720
10 TraesCS2A01G134200 chr7B 193199103 193200034 931 False 498.5 749 87.4530 1325 2327 2 chr7B.!!$F2 1002
11 TraesCS2A01G134200 chr7B 680449150 680449704 554 False 246.0 270 82.8560 1713 2327 2 chr7B.!!$F3 614
12 TraesCS2A01G134200 chr7A 667804162 667804850 688 False 688.0 688 84.6900 1325 2045 1 chr7A.!!$F1 720

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
495 728 0.105760 ATGGAGTTTGGGTGCCAACA 60.106 50.0 0.0 0.0 43.82 3.33 F
1901 2440 0.036732 TGTTGCCTGACTGACCCATC 59.963 55.0 0.0 0.0 0.00 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1913 2452 0.039437 TTCCGAACAGAGAGACGCAC 60.039 55.0 0.0 0.0 0.00 5.34 R
2890 3489 2.223433 GGAAAGCCAGATGAGCAATTCG 60.223 50.0 0.0 0.0 32.35 3.34 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 5.011738 TGAACTTTTAGGTACACAGAGAGGG 59.988 44.000 0.00 0.00 0.00 4.30
39 40 4.805140 ACACAGAGAGGGAGATGAGATA 57.195 45.455 0.00 0.00 0.00 1.98
87 89 7.981142 TCACCCACGATTCTAAATGAAATTAC 58.019 34.615 0.00 0.00 33.67 1.89
102 104 9.658799 AAATGAAATTACGAGAATCTCTCTTGA 57.341 29.630 8.77 0.00 37.11 3.02
157 159 1.135717 TGCATGAAAATCGAAGTGGCG 60.136 47.619 0.00 0.00 0.00 5.69
253 477 7.710896 GCTTGAGGCTAAAATTACAAGATCAT 58.289 34.615 12.45 0.00 37.49 2.45
256 480 8.213518 TGAGGCTAAAATTACAAGATCATGAC 57.786 34.615 4.68 0.00 0.00 3.06
271 495 3.002791 TCATGACAAATCGTGAGAAGCC 58.997 45.455 0.00 0.00 44.38 4.35
285 509 0.651031 GAAGCCGTAATCGCCTCAAC 59.349 55.000 0.00 0.00 35.54 3.18
287 511 0.460284 AGCCGTAATCGCCTCAACAG 60.460 55.000 0.00 0.00 35.54 3.16
309 533 6.825721 ACAGGATTCCTTATCAACATGTTCTC 59.174 38.462 8.48 0.00 34.77 2.87
324 548 9.840427 CAACATGTTCTCTAAACCGAATATTTT 57.160 29.630 8.48 0.00 0.00 1.82
326 550 9.226606 ACATGTTCTCTAAACCGAATATTTTCA 57.773 29.630 0.00 0.00 0.00 2.69
395 620 1.591768 TCCCCATTCCTAGGACAACC 58.408 55.000 12.22 0.00 0.00 3.77
396 621 0.180406 CCCCATTCCTAGGACAACCG 59.820 60.000 12.22 0.00 41.83 4.44
404 629 1.656652 CTAGGACAACCGCATTCCTG 58.343 55.000 0.00 0.00 40.17 3.86
417 644 2.038295 GCATTCCTGGAATCCTCGATCT 59.962 50.000 18.87 0.00 28.87 2.75
421 648 2.961741 TCCTGGAATCCTCGATCTTCTG 59.038 50.000 0.00 0.00 0.00 3.02
432 660 2.092375 TCGATCTTCTGCCTCAGACCTA 60.092 50.000 0.00 0.00 40.46 3.08
458 686 4.155826 GCTACAACATGCCAATCTTACACA 59.844 41.667 0.00 0.00 0.00 3.72
462 690 3.002791 ACATGCCAATCTTACACACTCG 58.997 45.455 0.00 0.00 0.00 4.18
463 691 2.831685 TGCCAATCTTACACACTCGT 57.168 45.000 0.00 0.00 0.00 4.18
464 692 3.120321 TGCCAATCTTACACACTCGTT 57.880 42.857 0.00 0.00 0.00 3.85
465 693 2.805671 TGCCAATCTTACACACTCGTTG 59.194 45.455 0.00 0.00 0.00 4.10
475 708 7.431249 TCTTACACACTCGTTGATAAGAACTT 58.569 34.615 11.66 0.00 35.40 2.66
482 715 7.036220 CACTCGTTGATAAGAACTTATGGAGT 58.964 38.462 11.14 13.11 41.47 3.85
495 728 0.105760 ATGGAGTTTGGGTGCCAACA 60.106 50.000 0.00 0.00 43.82 3.33
500 733 0.179086 GTTTGGGTGCCAACAACAGG 60.179 55.000 0.00 0.00 43.82 4.00
510 743 3.402628 CCAACAACAGGCACTAGTACT 57.597 47.619 0.00 0.00 36.02 2.73
515 748 7.272978 CCAACAACAGGCACTAGTACTATTAT 58.727 38.462 2.33 0.00 36.02 1.28
516 749 8.418662 CCAACAACAGGCACTAGTACTATTATA 58.581 37.037 2.33 0.00 36.02 0.98
517 750 9.245962 CAACAACAGGCACTAGTACTATTATAC 57.754 37.037 2.33 0.00 36.02 1.47
518 751 8.763984 ACAACAGGCACTAGTACTATTATACT 57.236 34.615 2.33 0.00 36.02 2.12
519 752 8.848182 ACAACAGGCACTAGTACTATTATACTC 58.152 37.037 2.33 0.00 36.02 2.59
520 753 7.999450 ACAGGCACTAGTACTATTATACTCC 57.001 40.000 2.33 0.00 36.02 3.85
521 754 6.947158 ACAGGCACTAGTACTATTATACTCCC 59.053 42.308 2.33 0.00 36.02 4.30
522 755 7.176490 CAGGCACTAGTACTATTATACTCCCT 58.824 42.308 2.33 0.00 36.02 4.20
523 756 7.337436 CAGGCACTAGTACTATTATACTCCCTC 59.663 44.444 2.33 0.00 36.02 4.30
524 757 6.602803 GGCACTAGTACTATTATACTCCCTCC 59.397 46.154 2.33 0.00 36.74 4.30
525 758 6.315891 GCACTAGTACTATTATACTCCCTCCG 59.684 46.154 2.33 0.00 36.74 4.63
526 759 7.393216 CACTAGTACTATTATACTCCCTCCGT 58.607 42.308 2.33 0.00 36.74 4.69
527 760 7.333921 CACTAGTACTATTATACTCCCTCCGTG 59.666 44.444 2.33 0.00 36.74 4.94
528 761 6.445451 AGTACTATTATACTCCCTCCGTGA 57.555 41.667 0.00 0.00 28.86 4.35
529 762 6.237154 AGTACTATTATACTCCCTCCGTGAC 58.763 44.000 0.00 0.00 28.86 3.67
530 763 5.321934 ACTATTATACTCCCTCCGTGACT 57.678 43.478 0.00 0.00 0.00 3.41
531 764 5.703310 ACTATTATACTCCCTCCGTGACTT 58.297 41.667 0.00 0.00 0.00 3.01
532 765 6.845908 ACTATTATACTCCCTCCGTGACTTA 58.154 40.000 0.00 0.00 0.00 2.24
533 766 7.293073 ACTATTATACTCCCTCCGTGACTTAA 58.707 38.462 0.00 0.00 0.00 1.85
534 767 7.949006 ACTATTATACTCCCTCCGTGACTTAAT 59.051 37.037 0.00 0.00 0.00 1.40
535 768 9.458727 CTATTATACTCCCTCCGTGACTTAATA 57.541 37.037 0.00 0.00 0.00 0.98
536 769 8.896722 ATTATACTCCCTCCGTGACTTAATAT 57.103 34.615 0.00 0.00 0.00 1.28
537 770 9.986157 ATTATACTCCCTCCGTGACTTAATATA 57.014 33.333 0.00 0.00 0.00 0.86
538 771 9.812347 TTATACTCCCTCCGTGACTTAATATAA 57.188 33.333 0.00 0.00 0.00 0.98
539 772 6.651975 ACTCCCTCCGTGACTTAATATAAG 57.348 41.667 0.00 0.00 0.00 1.73
540 773 6.371278 ACTCCCTCCGTGACTTAATATAAGA 58.629 40.000 4.24 0.00 0.00 2.10
541 774 6.490721 ACTCCCTCCGTGACTTAATATAAGAG 59.509 42.308 4.24 0.00 0.00 2.85
542 775 5.243283 TCCCTCCGTGACTTAATATAAGAGC 59.757 44.000 4.24 0.00 0.00 4.09
543 776 5.154932 CCTCCGTGACTTAATATAAGAGCG 58.845 45.833 4.24 5.38 0.00 5.03
544 777 5.278364 CCTCCGTGACTTAATATAAGAGCGT 60.278 44.000 4.24 0.00 0.00 5.07
545 778 6.140303 TCCGTGACTTAATATAAGAGCGTT 57.860 37.500 4.24 0.00 0.00 4.84
546 779 6.567050 TCCGTGACTTAATATAAGAGCGTTT 58.433 36.000 4.24 0.00 0.00 3.60
547 780 7.037438 TCCGTGACTTAATATAAGAGCGTTTT 58.963 34.615 4.24 0.00 0.00 2.43
548 781 7.546667 TCCGTGACTTAATATAAGAGCGTTTTT 59.453 33.333 4.24 0.00 0.00 1.94
549 782 7.634817 CCGTGACTTAATATAAGAGCGTTTTTG 59.365 37.037 4.24 0.00 0.00 2.44
550 783 8.377681 CGTGACTTAATATAAGAGCGTTTTTGA 58.622 33.333 4.24 0.00 0.00 2.69
551 784 9.474249 GTGACTTAATATAAGAGCGTTTTTGAC 57.526 33.333 4.24 0.00 0.00 3.18
552 785 9.210329 TGACTTAATATAAGAGCGTTTTTGACA 57.790 29.630 4.24 0.00 0.00 3.58
553 786 9.474249 GACTTAATATAAGAGCGTTTTTGACAC 57.526 33.333 4.24 0.00 0.00 3.67
554 787 8.448615 ACTTAATATAAGAGCGTTTTTGACACC 58.551 33.333 4.24 0.00 0.00 4.16
555 788 8.556213 TTAATATAAGAGCGTTTTTGACACCT 57.444 30.769 0.00 0.00 0.00 4.00
556 789 9.656040 TTAATATAAGAGCGTTTTTGACACCTA 57.344 29.630 0.00 0.00 0.00 3.08
557 790 7.772332 ATATAAGAGCGTTTTTGACACCTAG 57.228 36.000 0.00 0.00 0.00 3.02
561 794 3.054878 AGCGTTTTTGACACCTAGTACG 58.945 45.455 0.00 0.00 0.00 3.67
571 804 4.019860 TGACACCTAGTACGGAGTTACTCT 60.020 45.833 12.41 0.00 37.78 3.24
674 939 4.270325 GTCCACTTATTTCAGTCCGTATGC 59.730 45.833 0.00 0.00 0.00 3.14
734 1164 6.596497 TGAACCGAGGGATTACATTTTAAGAC 59.404 38.462 0.00 0.00 0.00 3.01
795 1285 0.529378 CAGAAAGAGTTGCCATGGCC 59.471 55.000 33.44 19.25 41.09 5.36
945 1453 4.622260 ACAATTCCCCAACAAAATCCAG 57.378 40.909 0.00 0.00 0.00 3.86
1150 1666 2.960129 GAATCCGCCGTACCGCTG 60.960 66.667 4.69 0.00 0.00 5.18
1157 1674 2.358247 CCGTACCGCTGCTGGTTT 60.358 61.111 18.37 1.36 43.56 3.27
1158 1675 2.388232 CCGTACCGCTGCTGGTTTC 61.388 63.158 18.37 12.26 43.56 2.78
1159 1676 1.374252 CGTACCGCTGCTGGTTTCT 60.374 57.895 18.37 0.45 43.56 2.52
1160 1677 1.626654 CGTACCGCTGCTGGTTTCTG 61.627 60.000 18.37 5.89 43.56 3.02
1161 1678 1.003839 TACCGCTGCTGGTTTCTGG 60.004 57.895 18.37 3.31 43.56 3.86
1418 1938 1.132640 CTGCTAGTTCGCGGTTTGC 59.867 57.895 6.13 5.66 41.47 3.68
1445 1971 1.364626 GCCTGTCTTCTGTGGCGATG 61.365 60.000 0.00 0.00 35.79 3.84
1446 1972 1.364626 CCTGTCTTCTGTGGCGATGC 61.365 60.000 0.00 0.00 0.00 3.91
1447 1973 1.690283 CTGTCTTCTGTGGCGATGCG 61.690 60.000 0.00 0.00 0.00 4.73
1895 2434 4.206375 TCTGAAATTTGTTGCCTGACTGA 58.794 39.130 0.00 0.00 0.00 3.41
1898 2437 1.620822 ATTTGTTGCCTGACTGACCC 58.379 50.000 0.00 0.00 0.00 4.46
1901 2440 0.036732 TGTTGCCTGACTGACCCATC 59.963 55.000 0.00 0.00 0.00 3.51
1902 2441 0.326264 GTTGCCTGACTGACCCATCT 59.674 55.000 0.00 0.00 0.00 2.90
1903 2442 0.615331 TTGCCTGACTGACCCATCTC 59.385 55.000 0.00 0.00 0.00 2.75
1904 2443 0.252421 TGCCTGACTGACCCATCTCT 60.252 55.000 0.00 0.00 0.00 3.10
1905 2444 0.177604 GCCTGACTGACCCATCTCTG 59.822 60.000 0.00 0.00 0.00 3.35
1906 2445 1.566211 CCTGACTGACCCATCTCTGT 58.434 55.000 0.00 0.00 0.00 3.41
1907 2446 1.905215 CCTGACTGACCCATCTCTGTT 59.095 52.381 0.00 0.00 0.00 3.16
1908 2447 2.304180 CCTGACTGACCCATCTCTGTTT 59.696 50.000 0.00 0.00 0.00 2.83
1909 2448 3.332919 CTGACTGACCCATCTCTGTTTG 58.667 50.000 0.00 0.00 0.00 2.93
1910 2449 2.705658 TGACTGACCCATCTCTGTTTGT 59.294 45.455 0.00 0.00 0.00 2.83
1911 2450 3.244215 TGACTGACCCATCTCTGTTTGTC 60.244 47.826 0.00 0.00 0.00 3.18
1912 2451 2.039084 ACTGACCCATCTCTGTTTGTCC 59.961 50.000 0.00 0.00 0.00 4.02
1913 2452 1.001974 TGACCCATCTCTGTTTGTCCG 59.998 52.381 0.00 0.00 0.00 4.79
1914 2453 1.002087 GACCCATCTCTGTTTGTCCGT 59.998 52.381 0.00 0.00 0.00 4.69
1915 2454 1.270839 ACCCATCTCTGTTTGTCCGTG 60.271 52.381 0.00 0.00 0.00 4.94
1916 2455 0.798776 CCATCTCTGTTTGTCCGTGC 59.201 55.000 0.00 0.00 0.00 5.34
1917 2456 0.439985 CATCTCTGTTTGTCCGTGCG 59.560 55.000 0.00 0.00 0.00 5.34
1918 2457 0.033504 ATCTCTGTTTGTCCGTGCGT 59.966 50.000 0.00 0.00 0.00 5.24
1919 2458 0.596600 TCTCTGTTTGTCCGTGCGTC 60.597 55.000 0.00 0.00 0.00 5.19
1920 2459 0.597637 CTCTGTTTGTCCGTGCGTCT 60.598 55.000 0.00 0.00 0.00 4.18
1928 2467 0.729816 GTCCGTGCGTCTCTCTGTTC 60.730 60.000 0.00 0.00 0.00 3.18
2016 2599 3.443329 TCCGTATGTGTACATGGTACGTT 59.557 43.478 23.62 1.16 35.33 3.99
2049 2632 1.336440 CACAGTTTGCGTTGGAATGGA 59.664 47.619 0.00 0.00 0.00 3.41
2055 2638 2.721274 TGCGTTGGAATGGAAATGTG 57.279 45.000 0.00 0.00 0.00 3.21
2056 2639 1.271934 TGCGTTGGAATGGAAATGTGG 59.728 47.619 0.00 0.00 0.00 4.17
2057 2640 1.543802 GCGTTGGAATGGAAATGTGGA 59.456 47.619 0.00 0.00 0.00 4.02
2141 2734 5.869344 GCAATCAGTATAACTCACTGTCACA 59.131 40.000 2.70 0.00 43.21 3.58
2286 2880 5.982516 CACTCACAGCCTCAGTTCTATAATC 59.017 44.000 0.00 0.00 0.00 1.75
2368 2962 1.207089 CGATCAACTTGGTAGCCCAGA 59.793 52.381 0.00 0.00 43.15 3.86
2462 3058 3.643320 TCCCAGGCTTCTCATGTATACTG 59.357 47.826 4.17 0.58 0.00 2.74
2516 3112 6.569179 TGAAATGGTGAAGTTAAGTAAGCC 57.431 37.500 0.00 0.00 0.00 4.35
2648 3246 0.605589 CTAGCCTCCCCGCAGATAAG 59.394 60.000 0.00 0.00 0.00 1.73
2734 3332 7.230027 AGCTCTTGGATAGAAAGATAAATGGG 58.770 38.462 0.00 0.00 33.34 4.00
2762 3360 8.240682 AGTCGTATAGATAGCAGTTTCATGATC 58.759 37.037 0.00 0.00 0.00 2.92
2829 3427 5.631026 GCAAGAAGCACGAGAAATAATTGA 58.369 37.500 0.00 0.00 44.79 2.57
2890 3489 0.825840 TTGGGGTACTGGTTTGCAGC 60.826 55.000 0.00 0.00 0.00 5.25
3062 3662 2.508526 AGACATGTCTTTGCTTCCCAC 58.491 47.619 22.89 0.00 36.31 4.61
3079 3682 8.768397 TGCTTCCCACTGTATTATATATAAGGG 58.232 37.037 14.83 14.83 0.00 3.95
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 4.229812 TCATCTCCCTCTCTGTGTACCTAA 59.770 45.833 0.00 0.00 0.00 2.69
61 63 6.683974 ATTTCATTTAGAATCGTGGGTGAG 57.316 37.500 0.00 0.00 35.83 3.51
96 98 6.666417 GGATCATGATCCGATTTTTCAAGAG 58.334 40.000 33.48 0.00 46.84 2.85
120 122 4.156373 TCATGCATAAGTCCACAACACATG 59.844 41.667 0.00 0.00 34.99 3.21
157 159 1.694696 CCCTAGCCTTCACATACCTCC 59.305 57.143 0.00 0.00 0.00 4.30
231 455 7.828717 TGTCATGATCTTGTAATTTTAGCCTCA 59.171 33.333 0.00 0.00 0.00 3.86
253 477 1.270094 ACGGCTTCTCACGATTTGTCA 60.270 47.619 0.00 0.00 0.00 3.58
256 480 3.301835 CGATTACGGCTTCTCACGATTTG 60.302 47.826 0.00 0.00 35.72 2.32
270 494 0.174845 TCCTGTTGAGGCGATTACGG 59.825 55.000 0.00 0.00 39.57 4.02
271 495 2.225068 ATCCTGTTGAGGCGATTACG 57.775 50.000 0.00 0.00 39.57 3.18
285 509 7.052873 AGAGAACATGTTGATAAGGAATCCTG 58.947 38.462 17.58 0.00 32.13 3.86
287 511 8.964476 TTAGAGAACATGTTGATAAGGAATCC 57.036 34.615 17.58 0.00 33.22 3.01
324 548 9.979578 AACATTTGTGTTGATTTTAAGCTATGA 57.020 25.926 0.00 0.00 0.00 2.15
326 550 9.423061 GGAACATTTGTGTTGATTTTAAGCTAT 57.577 29.630 0.00 0.00 31.35 2.97
345 569 7.159372 CCGCCATTACTACTATTAGGAACATT 58.841 38.462 0.00 0.00 30.37 2.71
380 605 2.332063 ATGCGGTTGTCCTAGGAATG 57.668 50.000 14.65 2.85 0.00 2.67
395 620 0.104855 TCGAGGATTCCAGGAATGCG 59.895 55.000 23.92 20.08 43.45 4.73
396 621 2.038295 AGATCGAGGATTCCAGGAATGC 59.962 50.000 23.11 23.11 39.98 3.56
404 629 1.691434 AGGCAGAAGATCGAGGATTCC 59.309 52.381 0.00 0.00 0.00 3.01
417 644 0.898320 GCAGTAGGTCTGAGGCAGAA 59.102 55.000 0.00 0.00 46.27 3.02
421 648 1.475403 TGTAGCAGTAGGTCTGAGGC 58.525 55.000 0.00 0.00 46.27 4.70
432 660 3.077484 AGATTGGCATGTTGTAGCAGT 57.923 42.857 0.00 0.00 0.00 4.40
458 686 7.171630 ACTCCATAAGTTCTTATCAACGAGT 57.828 36.000 2.52 8.02 33.03 4.18
475 708 1.145945 TGTTGGCACCCAAACTCCATA 59.854 47.619 0.00 0.00 45.73 2.74
482 715 1.965754 GCCTGTTGTTGGCACCCAAA 61.966 55.000 0.00 0.00 45.73 3.28
495 728 7.450944 GGGAGTATAATAGTACTAGTGCCTGTT 59.549 40.741 12.98 8.38 35.14 3.16
500 733 6.315891 CGGAGGGAGTATAATAGTACTAGTGC 59.684 46.154 12.98 3.75 35.14 4.40
510 743 9.986157 ATATTAAGTCACGGAGGGAGTATAATA 57.014 33.333 0.00 0.00 0.00 0.98
515 748 7.520798 TCTTATATTAAGTCACGGAGGGAGTA 58.479 38.462 0.00 0.00 0.00 2.59
516 749 6.371278 TCTTATATTAAGTCACGGAGGGAGT 58.629 40.000 0.00 0.00 0.00 3.85
517 750 6.570764 GCTCTTATATTAAGTCACGGAGGGAG 60.571 46.154 0.00 0.00 0.00 4.30
518 751 5.243283 GCTCTTATATTAAGTCACGGAGGGA 59.757 44.000 0.00 0.00 0.00 4.20
519 752 5.471257 GCTCTTATATTAAGTCACGGAGGG 58.529 45.833 0.00 0.00 0.00 4.30
520 753 5.154932 CGCTCTTATATTAAGTCACGGAGG 58.845 45.833 0.00 0.00 0.00 4.30
521 754 5.759963 ACGCTCTTATATTAAGTCACGGAG 58.240 41.667 0.00 0.00 0.00 4.63
522 755 5.762825 ACGCTCTTATATTAAGTCACGGA 57.237 39.130 0.00 0.00 0.00 4.69
523 756 6.823678 AAACGCTCTTATATTAAGTCACGG 57.176 37.500 0.00 0.00 0.00 4.94
524 757 8.377681 TCAAAAACGCTCTTATATTAAGTCACG 58.622 33.333 0.00 0.00 0.00 4.35
525 758 9.474249 GTCAAAAACGCTCTTATATTAAGTCAC 57.526 33.333 0.00 0.00 0.00 3.67
526 759 9.210329 TGTCAAAAACGCTCTTATATTAAGTCA 57.790 29.630 0.00 0.00 0.00 3.41
527 760 9.474249 GTGTCAAAAACGCTCTTATATTAAGTC 57.526 33.333 0.00 0.00 35.42 3.01
528 761 8.448615 GGTGTCAAAAACGCTCTTATATTAAGT 58.551 33.333 0.00 0.00 38.49 2.24
529 762 8.665685 AGGTGTCAAAAACGCTCTTATATTAAG 58.334 33.333 0.00 0.00 38.49 1.85
530 763 8.556213 AGGTGTCAAAAACGCTCTTATATTAA 57.444 30.769 0.00 0.00 38.49 1.40
531 764 9.309516 CTAGGTGTCAAAAACGCTCTTATATTA 57.690 33.333 0.00 0.00 38.49 0.98
532 765 7.822822 ACTAGGTGTCAAAAACGCTCTTATATT 59.177 33.333 0.00 0.00 38.49 1.28
533 766 7.328737 ACTAGGTGTCAAAAACGCTCTTATAT 58.671 34.615 0.00 0.00 38.49 0.86
534 767 6.694447 ACTAGGTGTCAAAAACGCTCTTATA 58.306 36.000 0.00 0.00 38.49 0.98
535 768 5.548406 ACTAGGTGTCAAAAACGCTCTTAT 58.452 37.500 0.00 0.00 38.49 1.73
536 769 4.952460 ACTAGGTGTCAAAAACGCTCTTA 58.048 39.130 0.00 0.00 38.49 2.10
537 770 3.805207 ACTAGGTGTCAAAAACGCTCTT 58.195 40.909 0.00 0.00 38.49 2.85
538 771 3.470645 ACTAGGTGTCAAAAACGCTCT 57.529 42.857 0.00 0.00 38.49 4.09
539 772 3.120782 CGTACTAGGTGTCAAAAACGCTC 59.879 47.826 0.00 0.00 38.49 5.03
540 773 3.054878 CGTACTAGGTGTCAAAAACGCT 58.945 45.455 0.00 0.00 38.49 5.07
541 774 2.156310 CCGTACTAGGTGTCAAAAACGC 59.844 50.000 0.00 0.00 37.67 4.84
542 775 3.641648 TCCGTACTAGGTGTCAAAAACG 58.358 45.455 0.00 0.00 0.00 3.60
543 776 4.625028 ACTCCGTACTAGGTGTCAAAAAC 58.375 43.478 0.00 0.00 33.16 2.43
544 777 4.942761 ACTCCGTACTAGGTGTCAAAAA 57.057 40.909 0.00 0.00 33.16 1.94
545 778 4.942761 AACTCCGTACTAGGTGTCAAAA 57.057 40.909 0.00 0.00 37.04 2.44
546 779 5.072741 AGTAACTCCGTACTAGGTGTCAAA 58.927 41.667 0.00 0.00 37.04 2.69
547 780 4.655963 AGTAACTCCGTACTAGGTGTCAA 58.344 43.478 0.00 0.00 37.04 3.18
548 781 4.019860 AGAGTAACTCCGTACTAGGTGTCA 60.020 45.833 0.00 0.00 37.04 3.58
549 782 4.512484 AGAGTAACTCCGTACTAGGTGTC 58.488 47.826 0.00 0.00 37.04 3.67
550 783 4.224818 AGAGAGTAACTCCGTACTAGGTGT 59.775 45.833 0.00 0.00 45.96 4.16
551 784 4.768583 AGAGAGTAACTCCGTACTAGGTG 58.231 47.826 0.00 0.00 45.96 4.00
552 785 4.141733 GGAGAGAGTAACTCCGTACTAGGT 60.142 50.000 0.00 0.00 45.96 3.08
553 786 4.379652 GGAGAGAGTAACTCCGTACTAGG 58.620 52.174 0.00 0.00 45.96 3.02
561 794 5.831702 TTATGAACGGAGAGAGTAACTCC 57.168 43.478 0.00 0.00 45.96 3.85
650 915 5.661458 CATACGGACTGAAATAAGTGGACT 58.339 41.667 0.00 0.00 0.00 3.85
802 1292 2.687200 AGGCTGACATGCGGGGTA 60.687 61.111 0.00 0.00 0.00 3.69
1150 1666 0.315251 GGCAGAAACCAGAAACCAGC 59.685 55.000 0.00 0.00 0.00 4.85
1156 1673 1.896660 GTGCGGGCAGAAACCAGAA 60.897 57.895 0.00 0.00 0.00 3.02
1157 1674 2.281484 GTGCGGGCAGAAACCAGA 60.281 61.111 0.00 0.00 0.00 3.86
1158 1675 3.365265 GGTGCGGGCAGAAACCAG 61.365 66.667 0.00 0.00 32.69 4.00
1159 1676 4.966787 GGGTGCGGGCAGAAACCA 62.967 66.667 0.00 0.00 34.18 3.67
1286 1804 3.598715 TCGGACACGCACGACCTT 61.599 61.111 0.00 0.00 40.69 3.50
1418 1938 2.432628 GAAGACAGGCACGACGGG 60.433 66.667 0.00 0.00 0.00 5.28
1446 1972 3.699484 CCATCGATCAGCGCTGCG 61.699 66.667 32.44 28.46 40.61 5.18
1447 1973 2.098842 GAACCATCGATCAGCGCTGC 62.099 60.000 32.44 18.29 40.61 5.25
1448 1974 0.529337 AGAACCATCGATCAGCGCTG 60.529 55.000 31.53 31.53 40.61 5.18
1449 1975 0.529337 CAGAACCATCGATCAGCGCT 60.529 55.000 2.64 2.64 40.61 5.92
1895 2434 1.056660 ACGGACAAACAGAGATGGGT 58.943 50.000 0.00 0.00 0.00 4.51
1898 2437 0.439985 CGCACGGACAAACAGAGATG 59.560 55.000 0.00 0.00 0.00 2.90
1901 2440 0.597637 AGACGCACGGACAAACAGAG 60.598 55.000 0.00 0.00 0.00 3.35
1902 2441 0.596600 GAGACGCACGGACAAACAGA 60.597 55.000 0.00 0.00 0.00 3.41
1903 2442 0.597637 AGAGACGCACGGACAAACAG 60.598 55.000 0.00 0.00 0.00 3.16
1904 2443 0.596600 GAGAGACGCACGGACAAACA 60.597 55.000 0.00 0.00 0.00 2.83
1905 2444 0.318784 AGAGAGACGCACGGACAAAC 60.319 55.000 0.00 0.00 0.00 2.93
1906 2445 0.318699 CAGAGAGACGCACGGACAAA 60.319 55.000 0.00 0.00 0.00 2.83
1907 2446 1.285950 CAGAGAGACGCACGGACAA 59.714 57.895 0.00 0.00 0.00 3.18
1908 2447 1.452953 AACAGAGAGACGCACGGACA 61.453 55.000 0.00 0.00 0.00 4.02
1909 2448 0.729816 GAACAGAGAGACGCACGGAC 60.730 60.000 0.00 0.00 0.00 4.79
1910 2449 1.579932 GAACAGAGAGACGCACGGA 59.420 57.895 0.00 0.00 0.00 4.69
1911 2450 1.797933 CGAACAGAGAGACGCACGG 60.798 63.158 0.00 0.00 0.00 4.94
1912 2451 1.797933 CCGAACAGAGAGACGCACG 60.798 63.158 0.00 0.00 0.00 5.34
1913 2452 0.039437 TTCCGAACAGAGAGACGCAC 60.039 55.000 0.00 0.00 0.00 5.34
1914 2453 0.888619 ATTCCGAACAGAGAGACGCA 59.111 50.000 0.00 0.00 0.00 5.24
1915 2454 1.921230 GAATTCCGAACAGAGAGACGC 59.079 52.381 0.00 0.00 0.00 5.19
1916 2455 2.177977 CGAATTCCGAACAGAGAGACG 58.822 52.381 0.00 0.00 41.76 4.18
1917 2456 1.921230 GCGAATTCCGAACAGAGAGAC 59.079 52.381 0.00 0.00 41.76 3.36
1918 2457 1.544246 TGCGAATTCCGAACAGAGAGA 59.456 47.619 0.00 0.00 41.76 3.10
1919 2458 1.923204 CTGCGAATTCCGAACAGAGAG 59.077 52.381 0.00 0.00 41.76 3.20
1920 2459 1.404181 CCTGCGAATTCCGAACAGAGA 60.404 52.381 11.82 0.00 41.76 3.10
2016 2599 4.920340 CGCAAACTGTGTGGCATAAATTTA 59.080 37.500 0.00 0.00 33.83 1.40
2076 2659 5.163447 CCTTGAGCAATCATCATCCAAACAT 60.163 40.000 0.00 0.00 0.00 2.71
2141 2734 5.126061 CCTAACTGCATCTAAAGGTTGCATT 59.874 40.000 8.35 2.43 45.78 3.56
2497 3093 4.000988 CACGGCTTACTTAACTTCACCAT 58.999 43.478 0.00 0.00 0.00 3.55
2516 3112 2.858344 CCAACTCCTTCGCTATAACACG 59.142 50.000 0.00 0.00 0.00 4.49
2598 3196 1.448985 TCGATTAAACAGCAGGTGCC 58.551 50.000 0.00 0.00 43.38 5.01
2734 3332 8.504815 TCATGAAACTGCTATCTATACGACTAC 58.495 37.037 0.00 0.00 0.00 2.73
2890 3489 2.223433 GGAAAGCCAGATGAGCAATTCG 60.223 50.000 0.00 0.00 32.35 3.34
2926 3525 5.281693 TGAGACAATTTCAACAGCATACG 57.718 39.130 0.00 0.00 0.00 3.06
2962 3562 7.310664 ACTGAAGCACATGAAATAACTGAATG 58.689 34.615 0.00 0.00 0.00 2.67
2968 3568 7.593825 AGGTAAACTGAAGCACATGAAATAAC 58.406 34.615 0.00 0.00 0.00 1.89
3062 3662 6.169557 TGCCCGCCCTTATATATAATACAG 57.830 41.667 5.64 0.00 0.00 2.74


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

AutoCloner maintained by Alex Coulton.