Multiple sequence alignment - TraesCS3D01G403000

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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 TraesCS3D01G403000 chr3D 100.000 3183 0 0 1 3183 517009539 517006357 0.000000e+00 5879.0
1 TraesCS3D01G403000 chr3D 89.100 578 63 0 1584 2161 4481984 4482561 0.000000e+00 719.0
2 TraesCS3D01G403000 chr3D 88.040 602 72 0 1584 2185 4866763 4866162 0.000000e+00 713.0
3 TraesCS3D01G403000 chr3D 85.217 460 55 6 960 1416 4869636 4869187 8.040000e-126 460.0
4 TraesCS3D01G403000 chr3D 93.358 271 18 0 1275 1545 4481443 4481713 4.950000e-108 401.0
5 TraesCS3D01G403000 chr3D 85.811 148 19 1 960 1105 4479815 4479962 4.250000e-34 156.0
6 TraesCS3D01G403000 chr3D 100.000 32 0 0 2188 2219 517155667 517155636 3.430000e-05 60.2
7 TraesCS3D01G403000 chr3B 92.127 1664 79 18 624 2253 680235528 680237173 0.000000e+00 2300.0
8 TraesCS3D01G403000 chr3B 89.528 869 76 10 2277 3141 144099048 144098191 0.000000e+00 1086.0
9 TraesCS3D01G403000 chr3B 89.228 557 50 8 2251 2804 670292923 670293472 0.000000e+00 688.0
10 TraesCS3D01G403000 chr3A 92.468 1580 68 17 717 2253 652831880 652830309 0.000000e+00 2211.0
11 TraesCS3D01G403000 chr3A 94.495 545 28 1 1 543 740311198 740310654 0.000000e+00 839.0
12 TraesCS3D01G403000 chr3A 85.283 829 74 24 747 1570 652911293 652910508 0.000000e+00 811.0
13 TraesCS3D01G403000 chr3A 89.515 639 56 6 1584 2219 652910459 652909829 0.000000e+00 798.0
14 TraesCS3D01G403000 chr6D 91.357 914 65 8 2277 3180 427268352 427269261 0.000000e+00 1238.0
15 TraesCS3D01G403000 chr6D 91.902 778 55 6 2410 3180 445651177 445651953 0.000000e+00 1081.0
16 TraesCS3D01G403000 chr6D 94.495 545 25 3 1 543 402564642 402564101 0.000000e+00 835.0
17 TraesCS3D01G403000 chr7D 90.278 936 80 8 2249 3180 7701352 7700424 0.000000e+00 1214.0
18 TraesCS3D01G403000 chr7D 94.843 543 26 2 2 543 525707999 525708540 0.000000e+00 846.0
19 TraesCS3D01G403000 chr7D 94.312 545 29 1 1 543 14573905 14573361 0.000000e+00 833.0
20 TraesCS3D01G403000 chr7D 93.945 545 31 1 1 543 137764980 137764436 0.000000e+00 822.0
21 TraesCS3D01G403000 chr4B 90.011 931 78 9 2253 3180 552824612 552825530 0.000000e+00 1190.0
22 TraesCS3D01G403000 chr4B 90.391 895 71 8 2277 3166 599913111 599913995 0.000000e+00 1162.0
23 TraesCS3D01G403000 chr4A 89.491 904 75 11 2279 3180 742776915 742777800 0.000000e+00 1125.0
24 TraesCS3D01G403000 chr7B 89.046 849 78 11 2335 3180 559007640 559006804 0.000000e+00 1038.0
25 TraesCS3D01G403000 chr1B 85.855 912 111 11 2277 3180 550979538 550980439 0.000000e+00 953.0
26 TraesCS3D01G403000 chr2D 84.079 917 111 25 2278 3180 628641676 628642571 0.000000e+00 852.0
27 TraesCS3D01G403000 chr2D 94.679 545 25 3 1 543 573965489 573964947 0.000000e+00 843.0
28 TraesCS3D01G403000 chr4D 94.679 545 26 2 1 543 435223769 435224312 0.000000e+00 843.0
29 TraesCS3D01G403000 chr4D 94.128 545 29 2 1 543 381553394 381552851 0.000000e+00 826.0
30 TraesCS3D01G403000 chrUn 94.171 549 30 1 1 547 103386259 103386807 0.000000e+00 835.0
31 TraesCS3D01G403000 chrUn 86.478 636 78 3 1584 2219 35356526 35355899 0.000000e+00 691.0
32 TraesCS3D01G403000 chrUn 86.478 636 78 3 1584 2219 263314765 263314138 0.000000e+00 691.0
33 TraesCS3D01G403000 chrUn 88.867 503 43 5 960 1459 35357163 35356671 9.760000e-170 606.0
34 TraesCS3D01G403000 chrUn 88.867 503 43 5 960 1459 263315402 263314910 9.760000e-170 606.0


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 TraesCS3D01G403000 chr3D 517006357 517009539 3182 True 5879.000000 5879 100.0000 1 3183 1 chr3D.!!$R1 3182
1 TraesCS3D01G403000 chr3D 4866162 4869636 3474 True 586.500000 713 86.6285 960 2185 2 chr3D.!!$R3 1225
2 TraesCS3D01G403000 chr3D 4479815 4482561 2746 False 425.333333 719 89.4230 960 2161 3 chr3D.!!$F1 1201
3 TraesCS3D01G403000 chr3B 680235528 680237173 1645 False 2300.000000 2300 92.1270 624 2253 1 chr3B.!!$F2 1629
4 TraesCS3D01G403000 chr3B 144098191 144099048 857 True 1086.000000 1086 89.5280 2277 3141 1 chr3B.!!$R1 864
5 TraesCS3D01G403000 chr3B 670292923 670293472 549 False 688.000000 688 89.2280 2251 2804 1 chr3B.!!$F1 553
6 TraesCS3D01G403000 chr3A 652830309 652831880 1571 True 2211.000000 2211 92.4680 717 2253 1 chr3A.!!$R1 1536
7 TraesCS3D01G403000 chr3A 740310654 740311198 544 True 839.000000 839 94.4950 1 543 1 chr3A.!!$R2 542
8 TraesCS3D01G403000 chr3A 652909829 652911293 1464 True 804.500000 811 87.3990 747 2219 2 chr3A.!!$R3 1472
9 TraesCS3D01G403000 chr6D 427268352 427269261 909 False 1238.000000 1238 91.3570 2277 3180 1 chr6D.!!$F1 903
10 TraesCS3D01G403000 chr6D 445651177 445651953 776 False 1081.000000 1081 91.9020 2410 3180 1 chr6D.!!$F2 770
11 TraesCS3D01G403000 chr6D 402564101 402564642 541 True 835.000000 835 94.4950 1 543 1 chr6D.!!$R1 542
12 TraesCS3D01G403000 chr7D 7700424 7701352 928 True 1214.000000 1214 90.2780 2249 3180 1 chr7D.!!$R1 931
13 TraesCS3D01G403000 chr7D 525707999 525708540 541 False 846.000000 846 94.8430 2 543 1 chr7D.!!$F1 541
14 TraesCS3D01G403000 chr7D 14573361 14573905 544 True 833.000000 833 94.3120 1 543 1 chr7D.!!$R2 542
15 TraesCS3D01G403000 chr7D 137764436 137764980 544 True 822.000000 822 93.9450 1 543 1 chr7D.!!$R3 542
16 TraesCS3D01G403000 chr4B 552824612 552825530 918 False 1190.000000 1190 90.0110 2253 3180 1 chr4B.!!$F1 927
17 TraesCS3D01G403000 chr4B 599913111 599913995 884 False 1162.000000 1162 90.3910 2277 3166 1 chr4B.!!$F2 889
18 TraesCS3D01G403000 chr4A 742776915 742777800 885 False 1125.000000 1125 89.4910 2279 3180 1 chr4A.!!$F1 901
19 TraesCS3D01G403000 chr7B 559006804 559007640 836 True 1038.000000 1038 89.0460 2335 3180 1 chr7B.!!$R1 845
20 TraesCS3D01G403000 chr1B 550979538 550980439 901 False 953.000000 953 85.8550 2277 3180 1 chr1B.!!$F1 903
21 TraesCS3D01G403000 chr2D 628641676 628642571 895 False 852.000000 852 84.0790 2278 3180 1 chr2D.!!$F1 902
22 TraesCS3D01G403000 chr2D 573964947 573965489 542 True 843.000000 843 94.6790 1 543 1 chr2D.!!$R1 542
23 TraesCS3D01G403000 chr4D 435223769 435224312 543 False 843.000000 843 94.6790 1 543 1 chr4D.!!$F1 542
24 TraesCS3D01G403000 chr4D 381552851 381553394 543 True 826.000000 826 94.1280 1 543 1 chr4D.!!$R1 542
25 TraesCS3D01G403000 chrUn 103386259 103386807 548 False 835.000000 835 94.1710 1 547 1 chrUn.!!$F1 546
26 TraesCS3D01G403000 chrUn 35355899 35357163 1264 True 648.500000 691 87.6725 960 2219 2 chrUn.!!$R1 1259
27 TraesCS3D01G403000 chrUn 263314138 263315402 1264 True 648.500000 691 87.6725 960 2219 2 chrUn.!!$R2 1259

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
559 565 0.03392 GCTTTGACCAAAGGCCCTTG 59.966 55.0 20.17 7.15 45.85 3.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2210 5903 0.10741 GGACACCAGTCACACCACAA 60.107 55.0 0.0 0.0 46.8 3.33 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
172 173 4.286808 TGAACTTCAAGATGGACTCCATGA 59.713 41.667 15.78 5.55 45.26 3.07
255 257 4.084013 CCTCTTTTGCGTAATGAACTTCGT 60.084 41.667 0.00 0.00 0.00 3.85
385 389 1.101049 CCCGAGCAAAACCCGCATAT 61.101 55.000 0.00 0.00 0.00 1.78
386 390 0.738389 CCGAGCAAAACCCGCATATT 59.262 50.000 0.00 0.00 0.00 1.28
466 472 0.684479 ATCTGTGCTAGTCCTCGCCA 60.684 55.000 0.00 0.00 0.00 5.69
480 486 3.972276 GCCAGCCCGCAAAAACGA 61.972 61.111 0.00 0.00 34.06 3.85
508 514 1.264672 GAACTGCAAACGCGTTTTGT 58.735 45.000 33.05 26.17 45.70 2.83
512 518 1.517475 GCAAACGCGTTTTGTGGGT 60.517 52.632 33.05 9.53 45.70 4.51
514 520 0.179161 CAAACGCGTTTTGTGGGTCA 60.179 50.000 33.05 0.00 39.96 4.02
524 530 3.902881 TTTGTGGGTCAACATTTTGCT 57.097 38.095 0.00 0.00 35.61 3.91
527 533 1.686052 GTGGGTCAACATTTTGCTGGA 59.314 47.619 0.00 0.00 32.17 3.86
531 537 3.119352 GGGTCAACATTTTGCTGGATCTC 60.119 47.826 0.00 0.00 32.17 2.75
543 549 2.433970 GCTGGATCTCCTAGAGTTGCTT 59.566 50.000 0.00 0.00 36.82 3.91
547 553 4.081420 TGGATCTCCTAGAGTTGCTTTGAC 60.081 45.833 0.00 0.00 36.82 3.18
548 554 3.963428 TCTCCTAGAGTTGCTTTGACC 57.037 47.619 0.00 0.00 0.00 4.02
549 555 3.239449 TCTCCTAGAGTTGCTTTGACCA 58.761 45.455 0.00 0.00 0.00 4.02
550 556 3.646162 TCTCCTAGAGTTGCTTTGACCAA 59.354 43.478 0.00 0.00 0.00 3.67
551 557 4.102524 TCTCCTAGAGTTGCTTTGACCAAA 59.897 41.667 0.00 0.00 0.00 3.28
553 559 3.503748 CCTAGAGTTGCTTTGACCAAAGG 59.496 47.826 20.17 6.23 45.85 3.11
554 560 1.683385 AGAGTTGCTTTGACCAAAGGC 59.317 47.619 20.17 14.03 45.85 4.35
555 561 0.752658 AGTTGCTTTGACCAAAGGCC 59.247 50.000 20.17 0.00 45.85 5.19
556 562 0.249868 GTTGCTTTGACCAAAGGCCC 60.250 55.000 20.17 7.76 45.85 5.80
557 563 0.398381 TTGCTTTGACCAAAGGCCCT 60.398 50.000 20.17 0.00 45.85 5.19
558 564 0.398381 TGCTTTGACCAAAGGCCCTT 60.398 50.000 20.17 0.00 45.85 3.95
559 565 0.033920 GCTTTGACCAAAGGCCCTTG 59.966 55.000 20.17 7.15 45.85 3.61
571 577 3.579302 CCCTTGGAGCCACACCCA 61.579 66.667 0.00 0.00 0.00 4.51
572 578 2.034687 CCTTGGAGCCACACCCAG 59.965 66.667 0.00 0.00 33.43 4.45
573 579 2.833913 CCTTGGAGCCACACCCAGT 61.834 63.158 0.00 0.00 33.43 4.00
574 580 1.488705 CCTTGGAGCCACACCCAGTA 61.489 60.000 0.00 0.00 33.43 2.74
575 581 0.321653 CTTGGAGCCACACCCAGTAC 60.322 60.000 0.00 0.00 33.43 2.73
576 582 1.057275 TTGGAGCCACACCCAGTACA 61.057 55.000 0.00 0.00 33.43 2.90
577 583 0.840288 TGGAGCCACACCCAGTACAT 60.840 55.000 0.00 0.00 0.00 2.29
578 584 1.200519 GGAGCCACACCCAGTACATA 58.799 55.000 0.00 0.00 0.00 2.29
579 585 1.139058 GGAGCCACACCCAGTACATAG 59.861 57.143 0.00 0.00 0.00 2.23
580 586 0.541863 AGCCACACCCAGTACATAGC 59.458 55.000 0.00 0.00 0.00 2.97
581 587 0.251916 GCCACACCCAGTACATAGCA 59.748 55.000 0.00 0.00 0.00 3.49
582 588 2.012051 GCCACACCCAGTACATAGCAC 61.012 57.143 0.00 0.00 0.00 4.40
583 589 1.406887 CCACACCCAGTACATAGCACC 60.407 57.143 0.00 0.00 0.00 5.01
584 590 0.909623 ACACCCAGTACATAGCACCC 59.090 55.000 0.00 0.00 0.00 4.61
585 591 0.180406 CACCCAGTACATAGCACCCC 59.820 60.000 0.00 0.00 0.00 4.95
586 592 0.986550 ACCCAGTACATAGCACCCCC 60.987 60.000 0.00 0.00 0.00 5.40
587 593 0.694444 CCCAGTACATAGCACCCCCT 60.694 60.000 0.00 0.00 0.00 4.79
588 594 1.213296 CCAGTACATAGCACCCCCTT 58.787 55.000 0.00 0.00 0.00 3.95
589 595 1.141053 CCAGTACATAGCACCCCCTTC 59.859 57.143 0.00 0.00 0.00 3.46
590 596 2.119495 CAGTACATAGCACCCCCTTCT 58.881 52.381 0.00 0.00 0.00 2.85
591 597 2.119495 AGTACATAGCACCCCCTTCTG 58.881 52.381 0.00 0.00 0.00 3.02
592 598 2.116238 GTACATAGCACCCCCTTCTGA 58.884 52.381 0.00 0.00 0.00 3.27
593 599 0.912486 ACATAGCACCCCCTTCTGAC 59.088 55.000 0.00 0.00 0.00 3.51
594 600 0.181350 CATAGCACCCCCTTCTGACC 59.819 60.000 0.00 0.00 0.00 4.02
595 601 0.044855 ATAGCACCCCCTTCTGACCT 59.955 55.000 0.00 0.00 0.00 3.85
596 602 0.617820 TAGCACCCCCTTCTGACCTC 60.618 60.000 0.00 0.00 0.00 3.85
597 603 2.224159 GCACCCCCTTCTGACCTCA 61.224 63.158 0.00 0.00 0.00 3.86
598 604 1.986413 CACCCCCTTCTGACCTCAG 59.014 63.158 0.00 0.00 45.08 3.35
599 605 1.229658 ACCCCCTTCTGACCTCAGG 60.230 63.158 2.45 0.00 43.91 3.86
600 606 1.081092 CCCCCTTCTGACCTCAGGA 59.919 63.158 0.00 0.00 43.91 3.86
601 607 1.268283 CCCCCTTCTGACCTCAGGAC 61.268 65.000 0.00 0.00 43.91 3.85
602 608 1.268283 CCCCTTCTGACCTCAGGACC 61.268 65.000 0.00 0.00 43.91 4.46
603 609 0.252467 CCCTTCTGACCTCAGGACCT 60.252 60.000 0.00 0.00 43.91 3.85
604 610 0.901124 CCTTCTGACCTCAGGACCTG 59.099 60.000 15.99 15.99 43.91 4.00
605 611 0.248843 CTTCTGACCTCAGGACCTGC 59.751 60.000 17.33 3.19 43.91 4.85
606 612 1.194781 TTCTGACCTCAGGACCTGCC 61.195 60.000 17.33 6.37 43.91 4.85
607 613 2.607750 TGACCTCAGGACCTGCCC 60.608 66.667 17.33 6.03 37.37 5.36
608 614 2.284995 GACCTCAGGACCTGCCCT 60.285 66.667 17.33 0.33 37.37 5.19
613 619 3.644606 CAGGACCTGCCCTGCACT 61.645 66.667 8.99 0.00 46.16 4.40
614 620 3.644606 AGGACCTGCCCTGCACTG 61.645 66.667 0.00 0.00 37.37 3.66
616 622 4.648626 GACCTGCCCTGCACTGCA 62.649 66.667 3.11 3.11 33.79 4.41
617 623 4.962836 ACCTGCCCTGCACTGCAC 62.963 66.667 0.00 0.00 33.79 4.57
618 624 4.655647 CCTGCCCTGCACTGCACT 62.656 66.667 0.00 0.00 33.79 4.40
619 625 2.348620 CTGCCCTGCACTGCACTA 59.651 61.111 0.00 0.00 33.79 2.74
620 626 1.744368 CTGCCCTGCACTGCACTAG 60.744 63.158 0.00 0.00 33.79 2.57
621 627 2.437359 GCCCTGCACTGCACTAGG 60.437 66.667 0.00 2.74 33.79 3.02
622 628 3.072476 CCCTGCACTGCACTAGGT 58.928 61.111 0.00 0.00 33.79 3.08
663 669 0.250513 CTAGCACACAGGAACCCCTC 59.749 60.000 0.00 0.00 42.02 4.30
697 705 2.191128 AAAAGCTAGCACACAGGAGG 57.809 50.000 18.83 0.00 0.00 4.30
888 900 3.112075 CGAACGCCACGAGCACAT 61.112 61.111 0.00 0.00 44.04 3.21
900 913 0.459237 GAGCACATGACTCCGGACAG 60.459 60.000 0.00 0.00 0.00 3.51
982 1002 0.247974 GCAGCGAGCAAGCACAATAG 60.248 55.000 6.21 0.00 44.79 1.73
989 1009 4.615949 CGAGCAAGCACAATAGTCTATCT 58.384 43.478 0.00 0.00 0.00 1.98
1218 1244 3.142393 CGGCTCCTCAATCCGGAT 58.858 61.111 12.38 12.38 39.52 4.18
1287 2666 2.067197 CGAGGACTGGGGGTTCTTT 58.933 57.895 0.00 0.00 33.05 2.52
1337 2716 1.825474 GACCGTGGAGGAGATGAAGAA 59.175 52.381 0.00 0.00 45.00 2.52
1545 3807 4.398319 ACCCTTCCACATTCAAGTAAGTG 58.602 43.478 0.00 0.00 0.00 3.16
1634 5323 4.463186 GGACTTGCTTGGAGAACTACTCTA 59.537 45.833 0.00 0.00 44.37 2.43
1657 5346 2.521708 GTGCAAAGGGTGGCAGGT 60.522 61.111 0.00 0.00 41.35 4.00
1999 5688 2.329614 GGTGGTTAACGCACGCCAT 61.330 57.895 16.18 0.00 34.96 4.40
2034 5723 1.372997 CGACGTTCCACAGTGGGAG 60.373 63.158 20.14 13.10 38.32 4.30
2108 5797 0.109226 GTACAGGAGTGTCAGCGTCC 60.109 60.000 0.00 0.00 38.19 4.79
2113 5802 1.666011 GAGTGTCAGCGTCCAGGAA 59.334 57.895 0.00 0.00 0.00 3.36
2210 5903 5.213891 TGATAGCAATACATGGTCATCGT 57.786 39.130 0.00 0.00 40.93 3.73
2211 5904 5.610398 TGATAGCAATACATGGTCATCGTT 58.390 37.500 0.00 0.00 40.93 3.85
2212 5905 5.466393 TGATAGCAATACATGGTCATCGTTG 59.534 40.000 0.00 0.00 40.93 4.10
2213 5906 3.609853 AGCAATACATGGTCATCGTTGT 58.390 40.909 0.00 0.00 33.56 3.32
2214 5907 3.374988 AGCAATACATGGTCATCGTTGTG 59.625 43.478 0.00 0.00 33.56 3.33
2215 5908 3.487376 GCAATACATGGTCATCGTTGTGG 60.487 47.826 0.00 0.00 0.00 4.17
2216 5909 3.627395 ATACATGGTCATCGTTGTGGT 57.373 42.857 0.00 0.00 0.00 4.16
2219 5912 1.197492 CATGGTCATCGTTGTGGTGTG 59.803 52.381 0.00 0.00 0.00 3.82
2220 5913 0.466124 TGGTCATCGTTGTGGTGTGA 59.534 50.000 0.00 0.00 0.00 3.58
2221 5914 0.865769 GGTCATCGTTGTGGTGTGAC 59.134 55.000 0.00 0.00 38.69 3.67
2272 5978 4.783621 GCATCTCCACCAGCCGCA 62.784 66.667 0.00 0.00 0.00 5.69
2273 5979 2.046023 CATCTCCACCAGCCGCAA 60.046 61.111 0.00 0.00 0.00 4.85
2274 5980 1.675310 CATCTCCACCAGCCGCAAA 60.675 57.895 0.00 0.00 0.00 3.68
2307 6021 2.573609 GAATACAGCGCCGGGTGAGT 62.574 60.000 12.72 11.26 44.37 3.41
2479 6214 2.315925 GCACATAGCCTGCTTCTACA 57.684 50.000 0.00 0.00 37.23 2.74
2628 6418 1.305297 TGCCTCGGTGATGTCCTCT 60.305 57.895 0.00 0.00 0.00 3.69
2651 6441 2.178521 CGTCTGAGCGTAGGCGTT 59.821 61.111 8.75 0.00 46.35 4.84
2715 6505 2.276201 AGCGCGATGTTGTATTTAGCA 58.724 42.857 12.10 0.00 0.00 3.49
2814 6604 1.456165 GCGAAGAACTGTTCCTCGTTC 59.544 52.381 30.69 20.30 43.58 3.95
2954 6744 0.696501 GGGAAAGGTGCCAACTCCTA 59.303 55.000 0.00 0.00 38.87 2.94
2958 6748 0.698238 AAGGTGCCAACTCCTATGCA 59.302 50.000 0.00 0.00 38.87 3.96
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
172 173 1.136984 GTCGATCTTCACTCGGCGT 59.863 57.895 6.85 0.00 36.78 5.68
255 257 1.711298 CAGTTTGCGCGCGAATAAAAA 59.289 42.857 34.36 21.04 0.00 1.94
341 344 2.409651 GCAACGACCCGCAAACAA 59.590 55.556 0.00 0.00 0.00 2.83
424 428 0.549469 GACCCCAAACGGACCCATAT 59.451 55.000 0.00 0.00 0.00 1.78
427 431 2.448931 AGACCCCAAACGGACCCA 60.449 61.111 0.00 0.00 0.00 4.51
466 472 1.496934 CAAAATCGTTTTTGCGGGCT 58.503 45.000 16.37 0.00 43.67 5.19
508 514 2.079170 TCCAGCAAAATGTTGACCCA 57.921 45.000 0.00 0.00 36.83 4.51
512 518 4.038271 AGGAGATCCAGCAAAATGTTGA 57.962 40.909 0.00 0.00 36.15 3.18
514 520 5.045286 ACTCTAGGAGATCCAGCAAAATGTT 60.045 40.000 0.92 0.00 38.89 2.71
524 530 4.081420 GTCAAAGCAACTCTAGGAGATCCA 60.081 45.833 0.92 0.00 38.89 3.41
527 533 3.840666 TGGTCAAAGCAACTCTAGGAGAT 59.159 43.478 1.31 0.00 33.32 2.75
531 537 3.503748 CCTTTGGTCAAAGCAACTCTAGG 59.496 47.826 15.73 0.00 44.76 3.02
543 549 0.178964 CTCCAAGGGCCTTTGGTCAA 60.179 55.000 37.48 22.69 46.23 3.18
554 560 3.574074 CTGGGTGTGGCTCCAAGGG 62.574 68.421 0.00 0.00 31.97 3.95
555 561 1.488705 TACTGGGTGTGGCTCCAAGG 61.489 60.000 0.00 0.00 30.65 3.61
556 562 0.321653 GTACTGGGTGTGGCTCCAAG 60.322 60.000 0.00 0.00 31.97 3.61
557 563 1.057275 TGTACTGGGTGTGGCTCCAA 61.057 55.000 0.00 0.00 31.97 3.53
558 564 0.840288 ATGTACTGGGTGTGGCTCCA 60.840 55.000 0.00 0.00 0.00 3.86
559 565 1.139058 CTATGTACTGGGTGTGGCTCC 59.861 57.143 0.00 0.00 0.00 4.70
560 566 1.473434 GCTATGTACTGGGTGTGGCTC 60.473 57.143 0.00 0.00 0.00 4.70
561 567 0.541863 GCTATGTACTGGGTGTGGCT 59.458 55.000 0.00 0.00 0.00 4.75
562 568 0.251916 TGCTATGTACTGGGTGTGGC 59.748 55.000 0.00 0.00 0.00 5.01
563 569 1.406887 GGTGCTATGTACTGGGTGTGG 60.407 57.143 0.00 0.00 0.00 4.17
564 570 1.406887 GGGTGCTATGTACTGGGTGTG 60.407 57.143 0.00 0.00 0.00 3.82
565 571 0.909623 GGGTGCTATGTACTGGGTGT 59.090 55.000 0.00 0.00 0.00 4.16
566 572 0.180406 GGGGTGCTATGTACTGGGTG 59.820 60.000 0.00 0.00 0.00 4.61
567 573 0.986550 GGGGGTGCTATGTACTGGGT 60.987 60.000 0.00 0.00 0.00 4.51
568 574 0.694444 AGGGGGTGCTATGTACTGGG 60.694 60.000 0.00 0.00 0.00 4.45
569 575 1.141053 GAAGGGGGTGCTATGTACTGG 59.859 57.143 0.00 0.00 0.00 4.00
570 576 2.119495 AGAAGGGGGTGCTATGTACTG 58.881 52.381 0.00 0.00 0.00 2.74
571 577 2.119495 CAGAAGGGGGTGCTATGTACT 58.881 52.381 0.00 0.00 0.00 2.73
572 578 2.116238 TCAGAAGGGGGTGCTATGTAC 58.884 52.381 0.00 0.00 0.00 2.90
573 579 2.116238 GTCAGAAGGGGGTGCTATGTA 58.884 52.381 0.00 0.00 0.00 2.29
574 580 0.912486 GTCAGAAGGGGGTGCTATGT 59.088 55.000 0.00 0.00 0.00 2.29
575 581 0.181350 GGTCAGAAGGGGGTGCTATG 59.819 60.000 0.00 0.00 0.00 2.23
576 582 0.044855 AGGTCAGAAGGGGGTGCTAT 59.955 55.000 0.00 0.00 0.00 2.97
577 583 0.617820 GAGGTCAGAAGGGGGTGCTA 60.618 60.000 0.00 0.00 0.00 3.49
578 584 1.920835 GAGGTCAGAAGGGGGTGCT 60.921 63.158 0.00 0.00 0.00 4.40
579 585 2.190488 CTGAGGTCAGAAGGGGGTGC 62.190 65.000 0.22 0.00 46.59 5.01
580 586 1.557269 CCTGAGGTCAGAAGGGGGTG 61.557 65.000 8.64 0.00 46.59 4.61
581 587 1.229658 CCTGAGGTCAGAAGGGGGT 60.230 63.158 8.64 0.00 46.59 4.95
582 588 1.081092 TCCTGAGGTCAGAAGGGGG 59.919 63.158 8.64 0.00 46.59 5.40
583 589 1.268283 GGTCCTGAGGTCAGAAGGGG 61.268 65.000 8.64 0.00 46.59 4.79
584 590 0.252467 AGGTCCTGAGGTCAGAAGGG 60.252 60.000 8.64 0.00 46.59 3.95
585 591 0.901124 CAGGTCCTGAGGTCAGAAGG 59.099 60.000 14.26 0.00 46.59 3.46
586 592 0.248843 GCAGGTCCTGAGGTCAGAAG 59.751 60.000 23.77 0.00 46.59 2.85
587 593 1.194781 GGCAGGTCCTGAGGTCAGAA 61.195 60.000 23.77 0.00 46.59 3.02
588 594 1.610673 GGCAGGTCCTGAGGTCAGA 60.611 63.158 23.77 0.00 46.59 3.27
589 595 2.664081 GGGCAGGTCCTGAGGTCAG 61.664 68.421 23.77 0.00 43.40 3.51
590 596 2.607750 GGGCAGGTCCTGAGGTCA 60.608 66.667 23.77 0.00 32.44 4.02
591 597 2.284995 AGGGCAGGTCCTGAGGTC 60.285 66.667 23.77 4.32 35.47 3.85
597 603 3.644606 CAGTGCAGGGCAGGTCCT 61.645 66.667 0.00 0.00 40.08 3.85
599 605 4.648626 TGCAGTGCAGGGCAGGTC 62.649 66.667 15.37 0.00 40.08 3.85
600 606 4.962836 GTGCAGTGCAGGGCAGGT 62.963 66.667 20.42 0.00 40.08 4.00
601 607 3.258228 TAGTGCAGTGCAGGGCAGG 62.258 63.158 20.42 0.00 40.08 4.85
602 608 1.744368 CTAGTGCAGTGCAGGGCAG 60.744 63.158 20.42 9.30 40.08 4.85
603 609 2.348620 CTAGTGCAGTGCAGGGCA 59.651 61.111 20.42 8.06 40.08 5.36
604 610 2.437359 CCTAGTGCAGTGCAGGGC 60.437 66.667 20.42 7.12 40.08 5.19
605 611 0.674895 GAACCTAGTGCAGTGCAGGG 60.675 60.000 20.42 21.74 40.08 4.45
606 612 0.674895 GGAACCTAGTGCAGTGCAGG 60.675 60.000 20.42 18.90 40.08 4.85
607 613 0.322975 AGGAACCTAGTGCAGTGCAG 59.677 55.000 20.42 9.47 40.08 4.41
608 614 0.764890 AAGGAACCTAGTGCAGTGCA 59.235 50.000 15.37 15.37 35.60 4.57
609 615 1.002544 AGAAGGAACCTAGTGCAGTGC 59.997 52.381 8.58 8.58 0.00 4.40
610 616 3.764434 TCTAGAAGGAACCTAGTGCAGTG 59.236 47.826 3.69 0.00 36.06 3.66
611 617 4.048970 TCTAGAAGGAACCTAGTGCAGT 57.951 45.455 0.00 0.00 36.06 4.40
612 618 6.491745 TGATATCTAGAAGGAACCTAGTGCAG 59.508 42.308 3.98 0.00 36.06 4.41
613 619 6.373759 TGATATCTAGAAGGAACCTAGTGCA 58.626 40.000 3.98 0.00 36.06 4.57
614 620 6.902771 TGATATCTAGAAGGAACCTAGTGC 57.097 41.667 3.98 0.00 36.06 4.40
615 621 9.308000 AGATTGATATCTAGAAGGAACCTAGTG 57.692 37.037 3.98 0.00 39.36 2.74
681 689 2.664081 GCCCTCCTGTGTGCTAGCT 61.664 63.158 17.23 0.00 0.00 3.32
682 690 2.124942 GCCCTCCTGTGTGCTAGC 60.125 66.667 8.10 8.10 0.00 3.42
696 704 0.394352 AAGGGAATCACATCACGCCC 60.394 55.000 0.00 0.00 35.79 6.13
697 705 1.017387 GAAGGGAATCACATCACGCC 58.983 55.000 0.00 0.00 0.00 5.68
888 900 0.391597 GTTTGTCCTGTCCGGAGTCA 59.608 55.000 3.06 0.00 44.20 3.41
982 1002 4.590918 TCCATCGGATCAGGTAGATAGAC 58.409 47.826 0.00 0.00 37.00 2.59
989 1009 1.780919 TCTCCTCCATCGGATCAGGTA 59.219 52.381 10.85 1.40 31.43 3.08
1087 1112 4.083862 GAGGAGGGTGGGCGTGAC 62.084 72.222 0.00 0.00 0.00 3.67
1337 2716 2.893637 CGAAGAATCCCATGACGTTCT 58.106 47.619 0.00 0.00 32.62 3.01
1425 3687 1.716826 GCTCCTCCGAGACGACGAAT 61.717 60.000 0.00 0.00 38.52 3.34
1545 3807 8.950210 TGATTTTCTTCTGTCAGTTGATTATCC 58.050 33.333 0.00 0.00 0.00 2.59
1634 5323 2.113139 CACCCTTTGCACCTCCGT 59.887 61.111 0.00 0.00 0.00 4.69
1657 5346 3.013327 ATGGCTCCCAGCAGCTCA 61.013 61.111 0.00 0.00 44.75 4.26
1999 5688 2.106938 GCGATGGACATCCGCTCA 59.893 61.111 16.27 0.00 39.43 4.26
2108 5797 2.868583 CCACGAGCTTCACATATTCCTG 59.131 50.000 0.00 0.00 0.00 3.86
2113 5802 2.101582 GGAGACCACGAGCTTCACATAT 59.898 50.000 0.00 0.00 0.00 1.78
2210 5903 0.107410 GGACACCAGTCACACCACAA 60.107 55.000 0.00 0.00 46.80 3.33
2211 5904 1.268283 TGGACACCAGTCACACCACA 61.268 55.000 0.00 0.00 46.80 4.17
2212 5905 0.814010 GTGGACACCAGTCACACCAC 60.814 60.000 0.00 0.00 46.80 4.16
2213 5906 0.980754 AGTGGACACCAGTCACACCA 60.981 55.000 0.00 0.00 46.80 4.17
2214 5907 1.045407 TAGTGGACACCAGTCACACC 58.955 55.000 1.15 0.00 46.80 4.16
2215 5908 2.902705 TTAGTGGACACCAGTCACAC 57.097 50.000 1.15 0.00 46.80 3.82
2216 5909 2.769663 ACTTTAGTGGACACCAGTCACA 59.230 45.455 1.15 0.00 46.80 3.58
2219 5912 3.069729 ACAGACTTTAGTGGACACCAGTC 59.930 47.826 14.52 14.52 44.21 3.51
2220 5913 3.039011 ACAGACTTTAGTGGACACCAGT 58.961 45.455 0.00 0.00 40.67 4.00
2221 5914 3.753294 ACAGACTTTAGTGGACACCAG 57.247 47.619 0.00 0.00 32.34 4.00
2272 5978 6.523201 CGCTGTATTCTGATTTTTAGCGTTTT 59.477 34.615 0.00 0.00 45.25 2.43
2273 5979 6.021596 CGCTGTATTCTGATTTTTAGCGTTT 58.978 36.000 0.00 0.00 45.25 3.60
2274 5980 5.560148 CGCTGTATTCTGATTTTTAGCGTT 58.440 37.500 0.00 0.00 45.25 4.84
2375 6089 1.864711 GAAATATAACGCGCCTGCTGA 59.135 47.619 5.73 0.00 39.65 4.26
2628 6418 1.792301 CTACGCTCAGACGTCGGAA 59.208 57.895 18.91 3.91 44.43 4.30
2651 6441 2.180017 GCGACGAGCGGTTCCTTA 59.820 61.111 0.00 0.00 41.29 2.69
2731 6521 0.175760 GCCTATCGTGAGGACAAGCA 59.824 55.000 9.22 0.00 39.15 3.91
2814 6604 0.379669 GCTTCCCGCAAGACATCATG 59.620 55.000 0.00 0.00 43.02 3.07
2976 6766 4.504858 GTTAGGACATGAACTTCACCGAT 58.495 43.478 0.00 0.00 0.00 4.18


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

AutoCloner maintained by Alex Coulton.