Multiple sequence alignment - TraesCS7D01G358100

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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 TraesCS7D01G358100 chr7D 100.000 3188 0 0 1 3188 461146700 461143513 0.000000e+00 5888.0
1 TraesCS7D01G358100 chr7D 92.995 1299 72 9 1 1285 461197710 461196417 0.000000e+00 1877.0
2 TraesCS7D01G358100 chr7D 93.548 62 2 1 1 62 392052471 392052412 1.220000e-14 91.6
3 TraesCS7D01G358100 chr7B 92.325 1811 98 20 797 2602 483769320 483767546 0.000000e+00 2536.0
4 TraesCS7D01G358100 chr7A 91.840 1777 106 17 844 2619 538802200 538803938 0.000000e+00 2442.0
5 TraesCS7D01G358100 chr7A 86.328 256 24 4 2940 3185 538806242 538806496 5.240000e-68 268.0
6 TraesCS7D01G358100 chr7A 86.335 161 14 3 2758 2916 538806027 538806181 5.470000e-38 169.0
7 TraesCS7D01G358100 chr7A 93.443 61 2 1 1 61 264827144 264827086 4.380000e-14 89.8
8 TraesCS7D01G358100 chr1D 91.892 74 6 0 2684 2757 474351124 474351197 1.560000e-18 104.0
9 TraesCS7D01G358100 chr1D 86.076 79 11 0 2681 2759 279101460 279101382 5.670000e-13 86.1
10 TraesCS7D01G358100 chr5D 89.873 79 8 0 2681 2759 464070948 464070870 5.630000e-18 102.0
11 TraesCS7D01G358100 chr5A 88.095 84 8 2 2672 2754 613545384 613545302 7.280000e-17 99.0
12 TraesCS7D01G358100 chr5A 86.250 80 9 1 2679 2758 92177083 92177006 5.670000e-13 86.1
13 TraesCS7D01G358100 chr5A 86.250 80 10 1 2680 2759 410857509 410857587 5.670000e-13 86.1
14 TraesCS7D01G358100 chr3D 90.541 74 7 0 2681 2754 370115714 370115787 7.280000e-17 99.0
15 TraesCS7D01G358100 chr3D 94.915 59 1 1 1 59 558438622 558438678 1.220000e-14 91.6
16 TraesCS7D01G358100 chr4B 89.333 75 7 1 2681 2754 486282282 486282356 3.390000e-15 93.5
17 TraesCS7D01G358100 chr4A 86.905 84 10 1 2681 2763 76939763 76939846 3.390000e-15 93.5
18 TraesCS7D01G358100 chr4A 94.915 59 1 1 1 59 260415425 260415481 1.220000e-14 91.6
19 TraesCS7D01G358100 chr6A 94.915 59 1 1 1 59 554663320 554663376 1.220000e-14 91.6
20 TraesCS7D01G358100 chr6A 94.828 58 1 1 2 59 225926369 225926314 4.380000e-14 89.8
21 TraesCS7D01G358100 chr3A 93.548 62 2 1 1 62 295092385 295092444 1.220000e-14 91.6
22 TraesCS7D01G358100 chr2D 94.828 58 1 1 2 59 222212364 222212419 4.380000e-14 89.8


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 TraesCS7D01G358100 chr7D 461143513 461146700 3187 True 5888.000000 5888 100.000000 1 3188 1 chr7D.!!$R2 3187
1 TraesCS7D01G358100 chr7D 461196417 461197710 1293 True 1877.000000 1877 92.995000 1 1285 1 chr7D.!!$R3 1284
2 TraesCS7D01G358100 chr7B 483767546 483769320 1774 True 2536.000000 2536 92.325000 797 2602 1 chr7B.!!$R1 1805
3 TraesCS7D01G358100 chr7A 538802200 538806496 4296 False 959.666667 2442 88.167667 844 3185 3 chr7A.!!$F1 2341

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
619 633 0.668706 AGCGCCTGATGCTATTAGCG 60.669 55.0 2.29 6.63 46.26 4.26 F
1795 1811 0.179045 GAGGTATGCTGACCGGCAAT 60.179 55.0 0.00 0.00 45.68 3.56 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2155 2171 0.100682 CTGCAATCACCAGCATCAGC 59.899 55.0 0.0 0.0 40.42 4.26 R
3046 5121 0.671781 ATCACCAAGTGCTCTGCGAC 60.672 55.0 0.0 0.0 32.98 5.19 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
63 64 1.679032 GCTATTTTGACTGGAGGCGGT 60.679 52.381 0.00 0.00 0.00 5.68
167 181 1.296727 ATGTCGATCTCGTACGAGCA 58.703 50.000 34.92 26.89 41.71 4.26
217 231 3.059188 CAGAAACAACATTAGTTCGCCGT 60.059 43.478 0.00 0.00 35.28 5.68
361 375 2.076622 ATCGGGAGAGATTCGTGCCG 62.077 60.000 13.44 13.44 45.48 5.69
378 392 4.208686 GCGTAGTGCGGAGGGGAG 62.209 72.222 1.99 0.00 41.69 4.30
381 395 1.392710 CGTAGTGCGGAGGGGAGAAT 61.393 60.000 0.00 0.00 36.85 2.40
395 409 2.620367 GGGAGAATATGTTGTGTGGGCA 60.620 50.000 0.00 0.00 0.00 5.36
418 432 1.154016 CCGATGGCGCTAGGTATCG 60.154 63.158 7.64 14.55 41.35 2.92
425 439 2.254651 GCTAGGTATCGGCGTCGG 59.745 66.667 10.62 0.00 36.95 4.79
428 442 1.575576 CTAGGTATCGGCGTCGGAGG 61.576 65.000 10.62 0.00 36.95 4.30
453 467 1.532921 CCGCGAGCTACAAAGAGAGAG 60.533 57.143 8.23 0.00 0.00 3.20
492 506 3.477210 AGAGAAAGACAAAGAGCGGTT 57.523 42.857 0.00 0.00 0.00 4.44
494 508 4.561105 AGAGAAAGACAAAGAGCGGTTAG 58.439 43.478 0.00 0.00 0.00 2.34
501 515 1.725164 CAAAGAGCGGTTAGACGTTCC 59.275 52.381 0.00 0.00 43.76 3.62
511 525 1.344065 TAGACGTTCCCTTTCCTGCA 58.656 50.000 0.00 0.00 0.00 4.41
530 544 3.891977 TGCACTTGTTGGCCTTTATGTTA 59.108 39.130 3.32 0.00 0.00 2.41
538 552 4.345859 TGGCCTTTATGTTATACTCCCG 57.654 45.455 3.32 0.00 0.00 5.14
540 554 4.062991 GGCCTTTATGTTATACTCCCGTG 58.937 47.826 0.00 0.00 0.00 4.94
545 559 7.280652 GCCTTTATGTTATACTCCCGTGTAAAA 59.719 37.037 0.00 0.00 30.09 1.52
582 596 7.357287 GCGTTTACAAAGAAAGTACAAATGAGC 60.357 37.037 0.00 0.00 0.00 4.26
603 617 3.181552 GCGATTGCGTAGTTTCTATAGCG 60.182 47.826 0.00 0.00 40.36 4.26
604 618 3.181552 CGATTGCGTAGTTTCTATAGCGC 60.182 47.826 0.00 0.00 44.29 5.92
619 633 0.668706 AGCGCCTGATGCTATTAGCG 60.669 55.000 2.29 6.63 46.26 4.26
622 636 1.193203 CGCCTGATGCTATTAGCGTTG 59.807 52.381 11.58 8.00 46.26 4.10
646 660 6.748658 TGAAGATATAGACGGTAACACAAACG 59.251 38.462 0.00 0.00 0.00 3.60
656 670 5.466393 ACGGTAACACAAACGTTAAGCTAAT 59.534 36.000 0.00 0.00 35.90 1.73
751 766 5.358725 ACCGTTTCAGAAAAACCAACACTAT 59.641 36.000 0.00 0.00 0.00 2.12
767 782 0.877071 CTATGCTGCTAAATGGGCCG 59.123 55.000 0.00 0.00 0.00 6.13
865 880 2.421388 CGGGATCAGAAACCCTAATGCA 60.421 50.000 12.47 0.00 43.57 3.96
871 886 2.096496 CAGAAACCCTAATGCAGCGAAG 59.904 50.000 0.00 0.00 0.00 3.79
948 964 3.496875 CTCTGCGAGAGGGCCATCG 62.497 68.421 22.40 22.40 38.67 3.84
971 987 2.336088 CCAGCGGCTTGTTGGTTG 59.664 61.111 0.00 0.00 43.52 3.77
982 998 3.217626 CTTGTTGGTTGCTCTTCCTCTT 58.782 45.455 0.00 0.00 0.00 2.85
1110 1126 4.459089 GGCGAGGTGCTCCTGTCC 62.459 72.222 13.11 9.00 45.24 4.02
1407 1423 3.452786 CTCTCCTCGGCTCCGCAA 61.453 66.667 2.96 0.00 39.59 4.85
1509 1525 2.726351 GGGCTTCTCTCCGGACCTG 61.726 68.421 0.00 0.00 0.00 4.00
1674 1690 3.429085 CAATGCTTGCCACTTCGATTAC 58.571 45.455 0.00 0.00 0.00 1.89
1743 1759 2.358090 CCATGGCATAACAGAGGGGAAA 60.358 50.000 0.00 0.00 0.00 3.13
1767 1783 2.159393 GGTTTGCATCAGCTATTTCGCA 60.159 45.455 0.00 0.00 42.74 5.10
1789 1805 2.301346 CCAATTGGAGGTATGCTGACC 58.699 52.381 20.50 0.00 40.08 4.02
1795 1811 0.179045 GAGGTATGCTGACCGGCAAT 60.179 55.000 0.00 0.00 45.68 3.56
1872 1888 3.817647 AGAGCAAGTGGAAGTTTGATGAC 59.182 43.478 0.00 0.00 0.00 3.06
1883 1899 6.138761 GGAAGTTTGATGACGATAATGATGC 58.861 40.000 0.00 0.00 0.00 3.91
1928 1944 1.617536 AGGAGCATGGCAAGGAGGA 60.618 57.895 0.00 0.00 0.00 3.71
1979 1995 1.305381 AGGAGGAAGGGAGTGACGG 60.305 63.158 0.00 0.00 0.00 4.79
1986 2002 1.541310 AAGGGAGTGACGGCGATGAA 61.541 55.000 16.62 0.00 0.00 2.57
2034 2050 2.427095 TGTGAGGTATCTGTGTGATCGG 59.573 50.000 0.00 0.00 36.65 4.18
2144 2160 3.231818 TGAAGAAGGAAGAAGACGAGGT 58.768 45.455 0.00 0.00 0.00 3.85
2149 2165 1.896465 AGGAAGAAGACGAGGTTGAGG 59.104 52.381 0.00 0.00 0.00 3.86
2153 2169 0.603569 GAAGACGAGGTTGAGGCTGA 59.396 55.000 0.00 0.00 0.00 4.26
2154 2170 1.205893 GAAGACGAGGTTGAGGCTGAT 59.794 52.381 0.00 0.00 0.00 2.90
2155 2171 0.534412 AGACGAGGTTGAGGCTGATG 59.466 55.000 0.00 0.00 0.00 3.07
2225 2241 0.948678 TTTGGGTAAGTGTTCGCAGC 59.051 50.000 0.00 0.00 0.00 5.25
2247 2263 4.389077 GCACTGAGTATTCACCACTTACAC 59.611 45.833 0.00 0.00 0.00 2.90
2283 2304 4.574674 TTGGTGATACTGCTTCCTGAAT 57.425 40.909 0.00 0.00 0.00 2.57
2301 2322 6.000219 CCTGAATGTTCCGAATTCATATCCT 59.000 40.000 6.22 0.00 41.81 3.24
2302 2323 7.016170 TCCTGAATGTTCCGAATTCATATCCTA 59.984 37.037 6.22 0.00 41.81 2.94
2350 2371 3.508845 AACATTTGGGTGAGCTGTAGT 57.491 42.857 0.00 0.00 0.00 2.73
2387 2408 7.136822 TGATTTGATTAGGCCAGTGTAGTAT 57.863 36.000 5.01 0.00 0.00 2.12
2392 2413 4.771114 TTAGGCCAGTGTAGTATGCAAT 57.229 40.909 5.01 0.00 27.52 3.56
2431 2452 6.350103 ACCGGTGTTAATTTCCATTTGTTTT 58.650 32.000 6.12 0.00 0.00 2.43
2433 2454 7.128976 CCGGTGTTAATTTCCATTTGTTTTTG 58.871 34.615 0.00 0.00 0.00 2.44
2435 2456 8.178313 CGGTGTTAATTTCCATTTGTTTTTGTT 58.822 29.630 0.00 0.00 0.00 2.83
2495 2516 6.575162 TCTTTGATTTCTCTGGTTAAAGCC 57.425 37.500 0.00 0.00 0.00 4.35
2523 2544 3.884895 ACAGGTGAAATGTCAAGTCACA 58.115 40.909 16.76 0.00 42.81 3.58
2561 2582 5.807011 GCAAAGCTTACCATTTGGAAGTATG 59.193 40.000 0.00 5.41 36.99 2.39
2562 2583 6.572314 GCAAAGCTTACCATTTGGAAGTATGT 60.572 38.462 0.00 0.00 36.99 2.29
2591 2612 9.443283 CTTTGTAAGAGAAACACAGAAATCTTG 57.557 33.333 0.00 0.00 28.15 3.02
2615 2636 8.894409 TGCTGAATTTTATTATGTTCGACTTG 57.106 30.769 0.00 0.00 0.00 3.16
2623 2644 9.672086 TTTTATTATGTTCGACTTGGTTTCTTG 57.328 29.630 0.00 0.00 0.00 3.02
2625 2646 4.813296 ATGTTCGACTTGGTTTCTTGAC 57.187 40.909 0.00 0.00 0.00 3.18
2626 2647 3.869065 TGTTCGACTTGGTTTCTTGACT 58.131 40.909 0.00 0.00 0.00 3.41
2635 4671 5.819901 ACTTGGTTTCTTGACTTGAAGAGAG 59.180 40.000 0.00 0.00 33.50 3.20
2647 4683 4.100808 ACTTGAAGAGAGACACAGAAAGCT 59.899 41.667 0.00 0.00 0.00 3.74
2656 4692 1.212935 ACACAGAAAGCTGACCCAGTT 59.787 47.619 0.00 0.00 45.17 3.16
2662 4698 5.598417 ACAGAAAGCTGACCCAGTTAAAATT 59.402 36.000 0.00 0.00 45.17 1.82
2663 4699 6.098266 ACAGAAAGCTGACCCAGTTAAAATTT 59.902 34.615 0.00 0.00 45.17 1.82
2670 4706 5.596845 TGACCCAGTTAAAATTTGTGCTTC 58.403 37.500 0.00 0.00 0.00 3.86
2671 4707 5.127845 TGACCCAGTTAAAATTTGTGCTTCA 59.872 36.000 0.00 0.00 0.00 3.02
2688 4724 9.944376 TTGTGCTTCATTATATATTACTCCCTC 57.056 33.333 0.00 0.00 0.00 4.30
2689 4725 9.326489 TGTGCTTCATTATATATTACTCCCTCT 57.674 33.333 0.00 0.00 0.00 3.69
2690 4726 9.593134 GTGCTTCATTATATATTACTCCCTCTG 57.407 37.037 0.00 0.00 0.00 3.35
2691 4727 9.326489 TGCTTCATTATATATTACTCCCTCTGT 57.674 33.333 0.00 0.00 0.00 3.41
2707 4743 8.361139 ACTCCCTCTGTATCAAAATATAAGACG 58.639 37.037 0.00 0.00 0.00 4.18
2708 4744 7.152645 TCCCTCTGTATCAAAATATAAGACGC 58.847 38.462 0.00 0.00 0.00 5.19
2709 4745 6.369065 CCCTCTGTATCAAAATATAAGACGCC 59.631 42.308 0.00 0.00 0.00 5.68
2710 4746 7.155328 CCTCTGTATCAAAATATAAGACGCCT 58.845 38.462 0.00 0.00 0.00 5.52
2711 4747 7.657761 CCTCTGTATCAAAATATAAGACGCCTT 59.342 37.037 0.00 0.00 36.43 4.35
2712 4748 8.958119 TCTGTATCAAAATATAAGACGCCTTT 57.042 30.769 0.00 0.00 33.94 3.11
2713 4749 9.391006 TCTGTATCAAAATATAAGACGCCTTTT 57.609 29.630 0.00 0.00 33.94 2.27
2714 4750 9.438291 CTGTATCAAAATATAAGACGCCTTTTG 57.562 33.333 0.00 0.00 37.87 2.44
2715 4751 9.168451 TGTATCAAAATATAAGACGCCTTTTGA 57.832 29.630 10.17 10.17 44.91 2.69
2716 4752 9.434559 GTATCAAAATATAAGACGCCTTTTGAC 57.565 33.333 10.01 0.00 44.14 3.18
2717 4753 7.441890 TCAAAATATAAGACGCCTTTTGACA 57.558 32.000 5.03 0.00 39.55 3.58
2718 4754 8.050778 TCAAAATATAAGACGCCTTTTGACAT 57.949 30.769 5.03 0.00 39.55 3.06
2719 4755 8.519526 TCAAAATATAAGACGCCTTTTGACATT 58.480 29.630 5.03 0.00 39.55 2.71
2720 4756 9.781834 CAAAATATAAGACGCCTTTTGACATTA 57.218 29.630 0.00 0.00 38.46 1.90
2722 4758 9.950680 AAATATAAGACGCCTTTTGACATTATG 57.049 29.630 0.00 0.00 33.94 1.90
2723 4759 8.902540 ATATAAGACGCCTTTTGACATTATGA 57.097 30.769 0.00 0.00 33.94 2.15
2724 4760 4.946784 AGACGCCTTTTGACATTATGAC 57.053 40.909 0.00 0.00 0.00 3.06
2725 4761 4.323417 AGACGCCTTTTGACATTATGACA 58.677 39.130 0.00 0.00 0.00 3.58
2726 4762 4.393062 AGACGCCTTTTGACATTATGACAG 59.607 41.667 0.00 0.00 0.00 3.51
2727 4763 4.072131 ACGCCTTTTGACATTATGACAGT 58.928 39.130 0.00 0.00 0.00 3.55
2728 4764 4.083324 ACGCCTTTTGACATTATGACAGTG 60.083 41.667 0.00 0.00 0.00 3.66
2729 4765 4.083324 CGCCTTTTGACATTATGACAGTGT 60.083 41.667 0.00 0.00 0.00 3.55
2730 4766 5.393962 GCCTTTTGACATTATGACAGTGTC 58.606 41.667 16.68 16.68 41.90 3.67
2773 4809 3.498774 ATGGAGAAGTTTGCAGTGAGT 57.501 42.857 0.00 0.00 0.00 3.41
2776 4812 2.731976 GGAGAAGTTTGCAGTGAGTACG 59.268 50.000 0.00 0.00 0.00 3.67
2811 4847 5.316167 TGAAAGAACATGTAGGCAATGAGT 58.684 37.500 0.00 0.00 0.00 3.41
2815 4851 5.665459 AGAACATGTAGGCAATGAGTAGAC 58.335 41.667 0.00 0.00 0.00 2.59
2832 4868 8.974060 TGAGTAGACATTATATTTGGGTTTCC 57.026 34.615 0.00 0.00 0.00 3.13
2836 4872 9.274206 GTAGACATTATATTTGGGTTTCCTCTC 57.726 37.037 0.00 0.00 0.00 3.20
2919 4969 2.102588 AGTCACGGGAACATATGTAGGC 59.897 50.000 9.21 1.86 0.00 3.93
2930 4980 4.569943 ACATATGTAGGCTTCCTATTGCG 58.430 43.478 6.56 0.00 38.48 4.85
2935 4985 3.198200 TGTAGGCTTCCTATTGCGGTTAA 59.802 43.478 0.00 0.00 38.48 2.01
2936 4986 3.577805 AGGCTTCCTATTGCGGTTAAT 57.422 42.857 0.00 0.00 28.47 1.40
2937 4987 3.214328 AGGCTTCCTATTGCGGTTAATG 58.786 45.455 0.00 0.00 28.47 1.90
2938 4988 2.293399 GGCTTCCTATTGCGGTTAATGG 59.707 50.000 0.00 0.00 0.00 3.16
2939 4989 2.949644 GCTTCCTATTGCGGTTAATGGT 59.050 45.455 0.00 0.00 0.00 3.55
2941 4991 4.577283 GCTTCCTATTGCGGTTAATGGTTA 59.423 41.667 0.00 0.00 0.00 2.85
2943 4993 6.428771 GCTTCCTATTGCGGTTAATGGTTATA 59.571 38.462 0.00 0.00 0.00 0.98
2993 5067 3.450904 TGGTAGCAGATAGTTTGGGAGT 58.549 45.455 0.00 0.00 0.00 3.85
2998 5072 7.054751 GGTAGCAGATAGTTTGGGAGTTATTT 58.945 38.462 0.00 0.00 0.00 1.40
3001 5075 5.358160 GCAGATAGTTTGGGAGTTATTTGCT 59.642 40.000 0.00 0.00 33.38 3.91
3002 5076 6.127619 GCAGATAGTTTGGGAGTTATTTGCTT 60.128 38.462 0.00 0.00 33.38 3.91
3013 5088 6.021596 GGAGTTATTTGCTTGTATGTGTTCG 58.978 40.000 0.00 0.00 0.00 3.95
3035 5110 7.905604 TCGTTTGTCTTTGATGATCTAACAT 57.094 32.000 0.00 0.00 0.00 2.71
3038 5113 7.307694 GTTTGTCTTTGATGATCTAACATGCA 58.692 34.615 0.00 0.00 0.00 3.96
3046 5121 8.468720 TTGATGATCTAACATGCAAATTGTTG 57.531 30.769 13.21 0.00 37.81 3.33
3083 5167 3.194116 GTGATGAAATGGATGCACTGGTT 59.806 43.478 0.00 0.00 0.00 3.67
3106 5190 0.675837 GTTCTCCGTACTTTGGGGGC 60.676 60.000 0.00 0.00 0.00 5.80
3113 5197 0.317160 GTACTTTGGGGGCTGTTTGC 59.683 55.000 0.00 0.00 41.94 3.68
3142 5226 3.050275 GGTCCAGTGCGCCTGAAC 61.050 66.667 22.49 15.03 44.49 3.18
3162 5246 7.848223 TGAACTCAGGAATATGTATGTTGTG 57.152 36.000 0.00 0.00 0.00 3.33
3167 5251 6.883744 TCAGGAATATGTATGTTGTGCTACA 58.116 36.000 0.00 0.00 32.75 2.74
3171 5255 8.159447 AGGAATATGTATGTTGTGCTACATGAT 58.841 33.333 0.00 4.71 38.63 2.45
3185 5269 5.643348 TGCTACATGATTTCGTTCACTGAAT 59.357 36.000 0.00 0.00 0.00 2.57
3186 5270 5.961843 GCTACATGATTTCGTTCACTGAATG 59.038 40.000 0.00 4.78 0.00 2.67
3187 5271 5.947228 ACATGATTTCGTTCACTGAATGT 57.053 34.783 10.23 0.00 31.27 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 7.147302 ACAAGTATAGGGGATCAATTGTAGCTT 60.147 37.037 5.13 0.00 0.00 3.74
131 132 4.466370 TCGACATAATCTTTGTCCCTCACT 59.534 41.667 0.00 0.00 40.29 3.41
192 206 3.304391 GCGAACTAATGTTGTTTCTGGCA 60.304 43.478 0.00 0.00 36.39 4.92
217 231 2.202236 GAGCCACATGAGGGAGCCAA 62.202 60.000 11.42 0.00 0.00 4.52
225 239 2.480416 GGTCTACGAAGAGCCACATGAG 60.480 54.545 0.00 0.00 43.16 2.90
307 321 2.415776 CATGAACAATTTGGTGCCACC 58.584 47.619 7.01 7.01 39.22 4.61
317 331 4.141158 GGATCTACCTCCCCATGAACAATT 60.141 45.833 0.00 0.00 35.41 2.32
361 375 4.208686 CTCCCCTCCGCACTACGC 62.209 72.222 0.00 0.00 41.76 4.42
378 392 1.202177 CGCTGCCCACACAACATATTC 60.202 52.381 0.00 0.00 0.00 1.75
381 395 0.953471 GACGCTGCCCACACAACATA 60.953 55.000 0.00 0.00 0.00 2.29
411 425 2.905880 CCTCCGACGCCGATACCT 60.906 66.667 0.00 0.00 38.22 3.08
434 448 1.398739 TCTCTCTCTTTGTAGCTCGCG 59.601 52.381 0.00 0.00 0.00 5.87
438 452 4.040936 TGTCCTCTCTCTCTTTGTAGCT 57.959 45.455 0.00 0.00 0.00 3.32
453 467 2.365617 TCTATCCCATCGCTTTGTCCTC 59.634 50.000 0.00 0.00 0.00 3.71
492 506 1.001633 GTGCAGGAAAGGGAACGTCTA 59.998 52.381 0.00 0.00 0.00 2.59
494 508 0.250338 AGTGCAGGAAAGGGAACGTC 60.250 55.000 0.00 0.00 0.00 4.34
501 515 0.032540 GCCAACAAGTGCAGGAAAGG 59.967 55.000 0.00 0.00 0.00 3.11
511 525 6.602009 GGAGTATAACATAAAGGCCAACAAGT 59.398 38.462 5.01 0.00 0.00 3.16
565 579 5.393962 GCAATCGCTCATTTGTACTTTCTT 58.606 37.500 0.00 0.00 34.30 2.52
582 596 3.181552 GCGCTATAGAAACTACGCAATCG 60.182 47.826 13.16 0.59 45.25 3.34
603 617 2.483876 TCAACGCTAATAGCATCAGGC 58.516 47.619 13.15 0.00 42.58 4.85
604 618 4.371786 TCTTCAACGCTAATAGCATCAGG 58.628 43.478 13.15 0.00 42.58 3.86
619 633 8.378421 GTTTGTGTTACCGTCTATATCTTCAAC 58.622 37.037 0.00 0.00 0.00 3.18
622 636 6.749118 ACGTTTGTGTTACCGTCTATATCTTC 59.251 38.462 0.00 0.00 0.00 2.87
661 675 5.587443 GGGCGCTAGAGGAAAATAAAAACTA 59.413 40.000 7.64 0.00 0.00 2.24
663 677 4.157105 TGGGCGCTAGAGGAAAATAAAAAC 59.843 41.667 7.64 0.00 0.00 2.43
668 683 1.202651 GCTGGGCGCTAGAGGAAAATA 60.203 52.381 7.64 0.00 35.14 1.40
702 717 2.423446 GGGAACCGTTTAGGGCATAA 57.577 50.000 0.00 0.00 46.96 1.90
727 742 3.508402 AGTGTTGGTTTTTCTGAAACGGT 59.492 39.130 1.58 0.00 0.00 4.83
728 743 4.104696 AGTGTTGGTTTTTCTGAAACGG 57.895 40.909 1.58 0.00 0.00 4.44
729 744 5.173131 GCATAGTGTTGGTTTTTCTGAAACG 59.827 40.000 1.58 0.00 0.00 3.60
751 766 2.440065 CCGGCCCATTTAGCAGCA 60.440 61.111 0.00 0.00 0.00 4.41
767 782 2.825836 CTTGCGATGGAGTGGGCC 60.826 66.667 0.00 0.00 0.00 5.80
865 880 0.250901 ATTTGGCAGTCCACTTCGCT 60.251 50.000 0.00 0.00 43.33 4.93
871 886 2.489938 TGGAGTATTTGGCAGTCCAC 57.510 50.000 0.00 0.00 43.33 4.02
968 984 1.404851 CGGAGGAAGAGGAAGAGCAAC 60.405 57.143 0.00 0.00 0.00 4.17
969 985 0.898320 CGGAGGAAGAGGAAGAGCAA 59.102 55.000 0.00 0.00 0.00 3.91
970 986 1.608717 GCGGAGGAAGAGGAAGAGCA 61.609 60.000 0.00 0.00 0.00 4.26
971 987 1.142965 GCGGAGGAAGAGGAAGAGC 59.857 63.158 0.00 0.00 0.00 4.09
1110 1126 2.835431 AGGAGGATGGGCGACTCG 60.835 66.667 0.00 0.00 32.11 4.18
1534 1550 1.280421 GATGGAGAAGCTGTTGGTCCT 59.720 52.381 0.00 0.00 0.00 3.85
1743 1759 3.624861 CGAAATAGCTGATGCAAACCTCT 59.375 43.478 0.00 0.00 42.74 3.69
1767 1783 1.565759 TCAGCATACCTCCAATTGGCT 59.434 47.619 20.33 8.40 34.44 4.75
1872 1888 1.733912 CCATCACCGGCATCATTATCG 59.266 52.381 0.00 0.00 0.00 2.92
1883 1899 1.153168 GTGTCATCCCCATCACCGG 60.153 63.158 0.00 0.00 0.00 5.28
1928 1944 2.240414 TCATCACCACCATCTTCAGCAT 59.760 45.455 0.00 0.00 0.00 3.79
1979 1995 0.577269 CGGGAAATCGTCTTCATCGC 59.423 55.000 2.53 0.00 0.00 4.58
1986 2002 1.819632 GGCATGCGGGAAATCGTCT 60.820 57.895 12.44 0.00 0.00 4.18
2062 2078 1.301874 CGTTCGGTAAGGGTGGCAA 60.302 57.895 0.00 0.00 0.00 4.52
2144 2160 0.255033 AGCATCAGCATCAGCCTCAA 59.745 50.000 0.00 0.00 45.49 3.02
2149 2165 0.746923 TCACCAGCATCAGCATCAGC 60.747 55.000 0.00 0.00 45.49 4.26
2153 2169 0.744874 GCAATCACCAGCATCAGCAT 59.255 50.000 0.00 0.00 45.49 3.79
2154 2170 0.609681 TGCAATCACCAGCATCAGCA 60.610 50.000 0.00 0.00 45.49 4.41
2155 2171 0.100682 CTGCAATCACCAGCATCAGC 59.899 55.000 0.00 0.00 40.42 4.26
2217 2233 2.092838 GTGAATACTCAGTGCTGCGAAC 59.907 50.000 0.00 0.00 30.14 3.95
2221 2237 1.734465 GTGGTGAATACTCAGTGCTGC 59.266 52.381 0.00 0.00 30.14 5.25
2225 2241 5.784177 AGTGTAAGTGGTGAATACTCAGTG 58.216 41.667 0.00 0.00 30.14 3.66
2247 2263 3.538591 TCACCAATGCAGCAGATAGAAG 58.461 45.455 0.00 0.00 0.00 2.85
2283 2304 8.246430 ACTACTTAGGATATGAATTCGGAACA 57.754 34.615 0.04 0.00 0.00 3.18
2301 2322 9.854668 ATCTTGAGCTGACTAAGATACTACTTA 57.145 33.333 0.00 0.00 38.88 2.24
2302 2323 8.760980 ATCTTGAGCTGACTAAGATACTACTT 57.239 34.615 0.00 0.00 38.88 2.24
2317 2338 5.865552 CACCCAAATGTTTTATCTTGAGCTG 59.134 40.000 0.00 0.00 0.00 4.24
2318 2339 5.774690 TCACCCAAATGTTTTATCTTGAGCT 59.225 36.000 0.00 0.00 0.00 4.09
2319 2340 6.024552 TCACCCAAATGTTTTATCTTGAGC 57.975 37.500 0.00 0.00 0.00 4.26
2320 2341 6.071728 AGCTCACCCAAATGTTTTATCTTGAG 60.072 38.462 0.00 0.00 0.00 3.02
2350 2371 7.494211 CCTAATCAAATCATTCATTTCCTGCA 58.506 34.615 0.00 0.00 31.79 4.41
2387 2408 4.688021 GGTTAAGGTTGTTGTCAATTGCA 58.312 39.130 0.00 0.00 35.92 4.08
2392 2413 2.683867 CACCGGTTAAGGTTGTTGTCAA 59.316 45.455 2.97 0.00 43.00 3.18
2431 2452 9.622004 TTTCACACATTAAACTACGAAAAACAA 57.378 25.926 0.00 0.00 0.00 2.83
2466 2487 9.581289 TTTAACCAGAGAAATCAAAGATACCAA 57.419 29.630 0.00 0.00 0.00 3.67
2471 2492 6.721208 TGGCTTTAACCAGAGAAATCAAAGAT 59.279 34.615 0.00 0.00 33.75 2.40
2475 2496 6.723298 TTTGGCTTTAACCAGAGAAATCAA 57.277 33.333 0.00 0.00 41.82 2.57
2479 2500 6.153680 TGTTCTTTTGGCTTTAACCAGAGAAA 59.846 34.615 10.92 0.00 41.43 2.52
2495 2516 6.332630 ACTTGACATTTCACCTGTTCTTTTG 58.667 36.000 0.00 0.00 0.00 2.44
2523 2544 4.608948 AGCTTTGCTAGTCAAGTAGTGT 57.391 40.909 0.00 0.00 36.99 3.55
2567 2588 7.283127 AGCAAGATTTCTGTGTTTCTCTTACAA 59.717 33.333 0.00 0.00 0.00 2.41
2587 2608 8.946085 AGTCGAACATAATAAAATTCAGCAAGA 58.054 29.630 0.00 0.00 0.00 3.02
2591 2612 7.968405 ACCAAGTCGAACATAATAAAATTCAGC 59.032 33.333 0.00 0.00 0.00 4.26
2605 2626 3.869065 AGTCAAGAAACCAAGTCGAACA 58.131 40.909 0.00 0.00 0.00 3.18
2615 2636 5.235401 GTGTCTCTCTTCAAGTCAAGAAACC 59.765 44.000 0.00 0.00 31.86 3.27
2619 2640 4.889995 TCTGTGTCTCTCTTCAAGTCAAGA 59.110 41.667 0.00 0.00 0.00 3.02
2620 2641 5.193663 TCTGTGTCTCTCTTCAAGTCAAG 57.806 43.478 0.00 0.00 0.00 3.02
2621 2642 5.598416 TTCTGTGTCTCTCTTCAAGTCAA 57.402 39.130 0.00 0.00 0.00 3.18
2622 2643 5.595885 CTTTCTGTGTCTCTCTTCAAGTCA 58.404 41.667 0.00 0.00 0.00 3.41
2623 2644 4.447389 GCTTTCTGTGTCTCTCTTCAAGTC 59.553 45.833 0.00 0.00 0.00 3.01
2625 2646 4.448395 CAGCTTTCTGTGTCTCTCTTCAAG 59.552 45.833 0.00 0.00 35.61 3.02
2626 2647 4.100035 TCAGCTTTCTGTGTCTCTCTTCAA 59.900 41.667 0.00 0.00 41.10 2.69
2635 4671 1.202698 ACTGGGTCAGCTTTCTGTGTC 60.203 52.381 0.00 0.00 41.10 3.67
2647 4683 5.127845 TGAAGCACAAATTTTAACTGGGTCA 59.872 36.000 0.00 0.00 0.00 4.02
2648 4684 5.596845 TGAAGCACAAATTTTAACTGGGTC 58.403 37.500 0.00 0.00 0.00 4.46
2662 4698 9.944376 GAGGGAGTAATATATAATGAAGCACAA 57.056 33.333 0.00 0.00 0.00 3.33
2663 4699 9.326489 AGAGGGAGTAATATATAATGAAGCACA 57.674 33.333 0.00 0.00 0.00 4.57
2686 4722 8.594881 AAGGCGTCTTATATTTTGATACAGAG 57.405 34.615 0.00 0.00 0.00 3.35
2688 4724 9.438291 CAAAAGGCGTCTTATATTTTGATACAG 57.562 33.333 0.94 0.00 41.24 2.74
2689 4725 9.168451 TCAAAAGGCGTCTTATATTTTGATACA 57.832 29.630 0.94 0.00 42.06 2.29
2690 4726 9.434559 GTCAAAAGGCGTCTTATATTTTGATAC 57.565 33.333 14.81 3.14 45.94 2.24
2691 4727 9.168451 TGTCAAAAGGCGTCTTATATTTTGATA 57.832 29.630 14.81 10.64 45.94 2.15
2692 4728 8.050778 TGTCAAAAGGCGTCTTATATTTTGAT 57.949 30.769 14.81 0.00 45.94 2.57
2693 4729 7.441890 TGTCAAAAGGCGTCTTATATTTTGA 57.558 32.000 0.94 6.19 43.70 2.69
2694 4730 8.687824 AATGTCAAAAGGCGTCTTATATTTTG 57.312 30.769 0.94 3.51 40.50 2.44
2696 4732 9.950680 CATAATGTCAAAAGGCGTCTTATATTT 57.049 29.630 0.94 0.00 32.01 1.40
2697 4733 9.337396 TCATAATGTCAAAAGGCGTCTTATATT 57.663 29.630 0.94 0.25 32.01 1.28
2698 4734 8.774586 GTCATAATGTCAAAAGGCGTCTTATAT 58.225 33.333 0.94 0.00 32.01 0.86
2699 4735 7.766738 TGTCATAATGTCAAAAGGCGTCTTATA 59.233 33.333 0.94 0.00 32.01 0.98
2700 4736 6.597672 TGTCATAATGTCAAAAGGCGTCTTAT 59.402 34.615 0.94 0.00 32.01 1.73
2701 4737 5.935206 TGTCATAATGTCAAAAGGCGTCTTA 59.065 36.000 0.94 0.00 32.01 2.10
2702 4738 4.759693 TGTCATAATGTCAAAAGGCGTCTT 59.240 37.500 0.00 0.00 34.07 3.01
2703 4739 4.323417 TGTCATAATGTCAAAAGGCGTCT 58.677 39.130 0.00 0.00 0.00 4.18
2704 4740 4.154195 ACTGTCATAATGTCAAAAGGCGTC 59.846 41.667 0.00 0.00 0.00 5.19
2705 4741 4.072131 ACTGTCATAATGTCAAAAGGCGT 58.928 39.130 0.00 0.00 0.00 5.68
2706 4742 4.083324 ACACTGTCATAATGTCAAAAGGCG 60.083 41.667 0.00 0.00 0.00 5.52
2707 4743 5.376854 ACACTGTCATAATGTCAAAAGGC 57.623 39.130 0.00 0.00 0.00 4.35
2745 4781 9.023962 TCACTGCAAACTTCTCCATATTAAAAT 57.976 29.630 0.00 0.00 0.00 1.82
2746 4782 8.402798 TCACTGCAAACTTCTCCATATTAAAA 57.597 30.769 0.00 0.00 0.00 1.52
2747 4783 7.665559 ACTCACTGCAAACTTCTCCATATTAAA 59.334 33.333 0.00 0.00 0.00 1.52
2748 4784 7.168219 ACTCACTGCAAACTTCTCCATATTAA 58.832 34.615 0.00 0.00 0.00 1.40
2749 4785 6.711277 ACTCACTGCAAACTTCTCCATATTA 58.289 36.000 0.00 0.00 0.00 0.98
2750 4786 5.564550 ACTCACTGCAAACTTCTCCATATT 58.435 37.500 0.00 0.00 0.00 1.28
2751 4787 5.171339 ACTCACTGCAAACTTCTCCATAT 57.829 39.130 0.00 0.00 0.00 1.78
2752 4788 4.623932 ACTCACTGCAAACTTCTCCATA 57.376 40.909 0.00 0.00 0.00 2.74
2753 4789 3.498774 ACTCACTGCAAACTTCTCCAT 57.501 42.857 0.00 0.00 0.00 3.41
2754 4790 3.728845 GTACTCACTGCAAACTTCTCCA 58.271 45.455 0.00 0.00 0.00 3.86
2755 4791 2.731976 CGTACTCACTGCAAACTTCTCC 59.268 50.000 0.00 0.00 0.00 3.71
2756 4792 3.639538 TCGTACTCACTGCAAACTTCTC 58.360 45.455 0.00 0.00 0.00 2.87
2763 4799 1.732405 CGATGCTCGTACTCACTGCAA 60.732 52.381 0.00 0.00 36.10 4.08
2768 4804 3.857665 TCAAATTCGATGCTCGTACTCAC 59.142 43.478 5.66 0.00 41.35 3.51
2773 4809 5.407084 TGTTCTTTCAAATTCGATGCTCGTA 59.593 36.000 5.66 0.00 41.35 3.43
2776 4812 6.088824 ACATGTTCTTTCAAATTCGATGCTC 58.911 36.000 0.00 0.00 0.00 4.26
2783 4819 7.814107 TCATTGCCTACATGTTCTTTCAAATTC 59.186 33.333 2.30 0.00 0.00 2.17
2793 4829 5.419542 TGTCTACTCATTGCCTACATGTTC 58.580 41.667 2.30 0.00 0.00 3.18
2811 4847 8.148351 CGAGAGGAAACCCAAATATAATGTCTA 58.852 37.037 0.00 0.00 0.00 2.59
2832 4868 8.306680 TGTTTTGAAAGTATAGAAACCGAGAG 57.693 34.615 0.00 0.00 31.11 3.20
2836 4872 9.537848 GTGTATGTTTTGAAAGTATAGAAACCG 57.462 33.333 0.00 0.00 31.11 4.44
2879 4915 9.834628 CCGTGACTTTCTGCTAATTTAATTTAA 57.165 29.630 0.00 0.00 0.00 1.52
2880 4916 8.455682 CCCGTGACTTTCTGCTAATTTAATTTA 58.544 33.333 0.00 0.00 0.00 1.40
2881 4917 7.175990 TCCCGTGACTTTCTGCTAATTTAATTT 59.824 33.333 0.00 0.00 0.00 1.82
2882 4918 6.657541 TCCCGTGACTTTCTGCTAATTTAATT 59.342 34.615 0.00 0.00 0.00 1.40
2899 4935 2.102588 AGCCTACATATGTTCCCGTGAC 59.897 50.000 14.77 0.00 0.00 3.67
2919 4969 6.877611 ATAACCATTAACCGCAATAGGAAG 57.122 37.500 0.00 0.00 34.73 3.46
2936 4986 9.607988 CCACTACAGTTATCACAAATATAACCA 57.392 33.333 0.00 0.00 39.56 3.67
2937 4987 9.052759 CCCACTACAGTTATCACAAATATAACC 57.947 37.037 0.00 0.00 39.56 2.85
2938 4988 8.557029 GCCCACTACAGTTATCACAAATATAAC 58.443 37.037 0.00 0.00 39.20 1.89
2939 4989 8.268605 TGCCCACTACAGTTATCACAAATATAA 58.731 33.333 0.00 0.00 0.00 0.98
2941 4991 6.542370 GTGCCCACTACAGTTATCACAAATAT 59.458 38.462 0.00 0.00 0.00 1.28
2943 4993 4.700213 GTGCCCACTACAGTTATCACAAAT 59.300 41.667 0.00 0.00 0.00 2.32
2976 5050 5.358160 GCAAATAACTCCCAAACTATCTGCT 59.642 40.000 0.00 0.00 0.00 4.24
2993 5067 7.197017 ACAAACGAACACATACAAGCAAATAA 58.803 30.769 0.00 0.00 0.00 1.40
2998 5072 3.874543 AGACAAACGAACACATACAAGCA 59.125 39.130 0.00 0.00 0.00 3.91
3001 5075 6.424176 TCAAAGACAAACGAACACATACAA 57.576 33.333 0.00 0.00 0.00 2.41
3002 5076 6.258947 TCATCAAAGACAAACGAACACATACA 59.741 34.615 0.00 0.00 0.00 2.29
3013 5088 7.307694 TGCATGTTAGATCATCAAAGACAAAC 58.692 34.615 0.00 0.00 0.00 2.93
3035 5110 1.600164 GCTCTGCGACAACAATTTGCA 60.600 47.619 0.00 0.00 36.00 4.08
3038 5113 1.949525 AGTGCTCTGCGACAACAATTT 59.050 42.857 0.00 0.00 0.00 1.82
3046 5121 0.671781 ATCACCAAGTGCTCTGCGAC 60.672 55.000 0.00 0.00 32.98 5.19
3106 5190 3.222603 ACCAGTCCTTTAAGGCAAACAG 58.777 45.455 6.05 0.00 34.61 3.16
3137 5221 7.466455 GCACAACATACATATTCCTGAGTTCAG 60.466 40.741 2.09 2.09 43.40 3.02
3142 5226 6.986231 TGTAGCACAACATACATATTCCTGAG 59.014 38.462 0.00 0.00 0.00 3.35
3150 5234 7.494298 ACGAAATCATGTAGCACAACATACATA 59.506 33.333 0.00 0.00 39.91 2.29
3158 5242 4.754618 AGTGAACGAAATCATGTAGCACAA 59.245 37.500 0.00 0.00 0.00 3.33
3162 5246 5.530519 TTCAGTGAACGAAATCATGTAGC 57.469 39.130 0.08 0.00 0.00 3.58


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

AutoCloner maintained by Alex Coulton.