Multiple sequence alignment - TraesCS6A01G267700

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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 TraesCS6A01G267700 chr6A 100.000 4104 0 0 1 4104 493841176 493845279 0.000000e+00 7579.0
1 TraesCS6A01G267700 chr6A 95.072 1887 61 15 1149 3012 493756124 493758001 0.000000e+00 2940.0
2 TraesCS6A01G267700 chr6A 92.795 1957 114 14 1147 3088 494046823 494048767 0.000000e+00 2808.0
3 TraesCS6A01G267700 chr6A 93.555 1862 93 12 1149 2986 495154264 495152406 0.000000e+00 2748.0
4 TraesCS6A01G267700 chr6A 91.406 512 27 6 76 586 494045727 494046222 0.000000e+00 686.0
5 TraesCS6A01G267700 chr6A 88.542 480 32 16 688 1149 494046258 494046732 9.960000e-156 560.0
6 TraesCS6A01G267700 chr6B 94.734 2032 69 16 1149 3150 529773860 529775883 0.000000e+00 3125.0
7 TraesCS6A01G267700 chr6B 94.022 1840 87 9 1149 2966 530852381 530850543 0.000000e+00 2767.0
8 TraesCS6A01G267700 chr6B 95.377 1709 72 6 1278 2984 529889841 529891544 0.000000e+00 2712.0
9 TraesCS6A01G267700 chr6B 82.778 1620 225 33 1337 2935 52086465 52088051 0.000000e+00 1397.0
10 TraesCS6A01G267700 chr6B 90.631 555 36 12 1 541 529882313 529882865 0.000000e+00 723.0
11 TraesCS6A01G267700 chr6B 91.607 417 24 8 135 541 529883019 529883434 2.140000e-157 566.0
12 TraesCS6A01G267700 chr6B 86.556 543 32 24 645 1149 529889041 529889580 9.960000e-156 560.0
13 TraesCS6A01G267700 chr6B 95.604 91 4 0 934 1024 529773279 529773369 3.310000e-31 147.0
14 TraesCS6A01G267700 chr6D 93.235 1966 101 19 1147 3086 348861178 348863137 0.000000e+00 2865.0
15 TraesCS6A01G267700 chr6D 93.906 1838 85 14 1149 2963 349031237 349033070 0.000000e+00 2748.0
16 TraesCS6A01G267700 chr6D 97.240 1522 29 6 1625 3139 350204794 350203279 0.000000e+00 2566.0
17 TraesCS6A01G267700 chr6D 87.855 1021 65 17 3141 4104 350138169 350137151 0.000000e+00 1144.0
18 TraesCS6A01G267700 chr6D 90.267 637 47 12 2469 3100 350063445 350062819 0.000000e+00 819.0
19 TraesCS6A01G267700 chr6D 92.514 521 21 10 645 1149 350084730 350084212 0.000000e+00 730.0
20 TraesCS6A01G267700 chr6D 89.409 491 26 12 660 1136 349172737 349173215 2.730000e-166 595.0
21 TraesCS6A01G267700 chr6D 86.640 494 42 9 3631 4104 95305839 95305350 3.630000e-145 525.0
22 TraesCS6A01G267700 chr6D 89.825 285 17 5 252 525 350087797 350087514 5.050000e-94 355.0
23 TraesCS6A01G267700 chr6D 89.494 257 24 3 1 255 350116058 350115803 5.120000e-84 322.0
24 TraesCS6A01G267700 chr6D 92.070 227 15 3 40 264 350131800 350131575 2.380000e-82 316.0
25 TraesCS6A01G267700 chr6D 88.571 245 14 5 40 284 349082804 349083034 6.710000e-73 285.0
26 TraesCS6A01G267700 chr6D 84.971 173 10 7 113 284 349107323 349107480 1.180000e-35 161.0
27 TraesCS6A01G267700 chr6D 91.509 106 7 2 170 274 350208033 350207929 1.190000e-30 145.0
28 TraesCS6A01G267700 chr6D 90.566 106 9 1 299 403 349172452 349172557 5.530000e-29 139.0
29 TraesCS6A01G267700 chr6D 86.667 120 8 3 899 1014 350205878 350205763 4.310000e-25 126.0
30 TraesCS6A01G267700 chr6D 97.222 36 0 1 3089 3124 308934657 308934623 4.430000e-05 60.2
31 TraesCS6A01G267700 chr1B 87.610 912 78 22 3225 4104 401622468 401621560 0.000000e+00 1026.0
32 TraesCS6A01G267700 chr1B 77.407 810 114 48 3223 3979 449552612 449551819 6.340000e-113 418.0
33 TraesCS6A01G267700 chr4B 88.976 762 71 9 3354 4104 616302100 616302859 0.000000e+00 929.0
34 TraesCS6A01G267700 chr4B 88.740 746 71 9 3370 4104 20753000 20752257 0.000000e+00 900.0
35 TraesCS6A01G267700 chr4B 81.257 875 125 25 3264 4104 195476431 195477300 0.000000e+00 671.0
36 TraesCS6A01G267700 chr4B 79.935 917 138 27 3222 4102 237388362 237389268 2.080000e-177 632.0
37 TraesCS6A01G267700 chr2D 85.011 914 100 22 3225 4104 188843707 188844617 0.000000e+00 894.0
38 TraesCS6A01G267700 chr2D 82.193 921 105 28 3223 4102 601265065 601265967 0.000000e+00 737.0
39 TraesCS6A01G267700 chr3B 86.563 774 68 19 3352 4092 20556097 20556867 0.000000e+00 821.0
40 TraesCS6A01G267700 chr3B 83.297 916 89 30 3223 4104 561042316 561043201 0.000000e+00 785.0
41 TraesCS6A01G267700 chr5D 85.940 761 69 23 3225 3969 72545489 72546227 0.000000e+00 778.0
42 TraesCS6A01G267700 chr1D 83.242 913 77 38 3225 4104 298572031 298571162 0.000000e+00 769.0
43 TraesCS6A01G267700 chr1D 88.043 552 49 7 3544 4092 80816022 80816559 4.470000e-179 638.0
44 TraesCS6A01G267700 chr1D 100.000 29 0 0 3223 3251 426753672 426753644 2.000000e-03 54.7
45 TraesCS6A01G267700 chr5B 81.657 905 123 24 3225 4102 423734715 423735603 0.000000e+00 712.0
46 TraesCS6A01G267700 chr3D 91.005 378 31 3 3729 4104 68467789 68468165 1.320000e-139 507.0
47 TraesCS6A01G267700 chr7D 85.233 386 52 5 3722 4104 616371902 616371519 3.850000e-105 392.0
48 TraesCS6A01G267700 chr5A 75.169 592 112 29 3219 3793 46280672 46281245 3.170000e-61 246.0
49 TraesCS6A01G267700 chr3A 77.419 341 62 12 3223 3552 671325289 671324953 5.420000e-44 189.0
50 TraesCS6A01G267700 chr4A 85.000 120 14 3 3220 3338 623355122 623355006 7.210000e-23 119.0
51 TraesCS6A01G267700 chr1A 100.000 28 0 0 3223 3250 387815446 387815419 7.000000e-03 52.8


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 TraesCS6A01G267700 chr6A 493841176 493845279 4103 False 7579.000000 7579 100.000000 1 4104 1 chr6A.!!$F2 4103
1 TraesCS6A01G267700 chr6A 493756124 493758001 1877 False 2940.000000 2940 95.072000 1149 3012 1 chr6A.!!$F1 1863
2 TraesCS6A01G267700 chr6A 495152406 495154264 1858 True 2748.000000 2748 93.555000 1149 2986 1 chr6A.!!$R1 1837
3 TraesCS6A01G267700 chr6A 494045727 494048767 3040 False 1351.333333 2808 90.914333 76 3088 3 chr6A.!!$F3 3012
4 TraesCS6A01G267700 chr6B 530850543 530852381 1838 True 2767.000000 2767 94.022000 1149 2966 1 chr6B.!!$R1 1817
5 TraesCS6A01G267700 chr6B 529773279 529775883 2604 False 1636.000000 3125 95.169000 934 3150 2 chr6B.!!$F2 2216
6 TraesCS6A01G267700 chr6B 529889041 529891544 2503 False 1636.000000 2712 90.966500 645 2984 2 chr6B.!!$F4 2339
7 TraesCS6A01G267700 chr6B 52086465 52088051 1586 False 1397.000000 1397 82.778000 1337 2935 1 chr6B.!!$F1 1598
8 TraesCS6A01G267700 chr6B 529882313 529883434 1121 False 644.500000 723 91.119000 1 541 2 chr6B.!!$F3 540
9 TraesCS6A01G267700 chr6D 348861178 348863137 1959 False 2865.000000 2865 93.235000 1147 3086 1 chr6D.!!$F1 1939
10 TraesCS6A01G267700 chr6D 349031237 349033070 1833 False 2748.000000 2748 93.906000 1149 2963 1 chr6D.!!$F2 1814
11 TraesCS6A01G267700 chr6D 350137151 350138169 1018 True 1144.000000 1144 87.855000 3141 4104 1 chr6D.!!$R6 963
12 TraesCS6A01G267700 chr6D 350203279 350208033 4754 True 945.666667 2566 91.805333 170 3139 3 chr6D.!!$R8 2969
13 TraesCS6A01G267700 chr6D 350062819 350063445 626 True 819.000000 819 90.267000 2469 3100 1 chr6D.!!$R3 631
14 TraesCS6A01G267700 chr6D 350084212 350087797 3585 True 542.500000 730 91.169500 252 1149 2 chr6D.!!$R7 897
15 TraesCS6A01G267700 chr6D 349172452 349173215 763 False 367.000000 595 89.987500 299 1136 2 chr6D.!!$F5 837
16 TraesCS6A01G267700 chr1B 401621560 401622468 908 True 1026.000000 1026 87.610000 3225 4104 1 chr1B.!!$R1 879
17 TraesCS6A01G267700 chr1B 449551819 449552612 793 True 418.000000 418 77.407000 3223 3979 1 chr1B.!!$R2 756
18 TraesCS6A01G267700 chr4B 616302100 616302859 759 False 929.000000 929 88.976000 3354 4104 1 chr4B.!!$F3 750
19 TraesCS6A01G267700 chr4B 20752257 20753000 743 True 900.000000 900 88.740000 3370 4104 1 chr4B.!!$R1 734
20 TraesCS6A01G267700 chr4B 195476431 195477300 869 False 671.000000 671 81.257000 3264 4104 1 chr4B.!!$F1 840
21 TraesCS6A01G267700 chr4B 237388362 237389268 906 False 632.000000 632 79.935000 3222 4102 1 chr4B.!!$F2 880
22 TraesCS6A01G267700 chr2D 188843707 188844617 910 False 894.000000 894 85.011000 3225 4104 1 chr2D.!!$F1 879
23 TraesCS6A01G267700 chr2D 601265065 601265967 902 False 737.000000 737 82.193000 3223 4102 1 chr2D.!!$F2 879
24 TraesCS6A01G267700 chr3B 20556097 20556867 770 False 821.000000 821 86.563000 3352 4092 1 chr3B.!!$F1 740
25 TraesCS6A01G267700 chr3B 561042316 561043201 885 False 785.000000 785 83.297000 3223 4104 1 chr3B.!!$F2 881
26 TraesCS6A01G267700 chr5D 72545489 72546227 738 False 778.000000 778 85.940000 3225 3969 1 chr5D.!!$F1 744
27 TraesCS6A01G267700 chr1D 298571162 298572031 869 True 769.000000 769 83.242000 3225 4104 1 chr1D.!!$R1 879
28 TraesCS6A01G267700 chr1D 80816022 80816559 537 False 638.000000 638 88.043000 3544 4092 1 chr1D.!!$F1 548
29 TraesCS6A01G267700 chr5B 423734715 423735603 888 False 712.000000 712 81.657000 3225 4102 1 chr5B.!!$F1 877
30 TraesCS6A01G267700 chr5A 46280672 46281245 573 False 246.000000 246 75.169000 3219 3793 1 chr5A.!!$F1 574

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
615 4868 0.393808 ACAGTGGACAACGCCAAGTT 60.394 50.0 0.00 0.00 45.45 2.66 F
628 4881 0.595095 CCAAGTTGGCTGAGCAGTTC 59.405 55.0 9.46 0.00 0.00 3.01 F
827 5126 0.611062 AATGAGTGGCTGCATGCACT 60.611 50.0 18.46 12.68 45.15 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2152 7020 0.626382 TCTCCTCCATGTCCGACTCT 59.374 55.000 0.0 0.0 0.00 3.24 R
3052 7972 3.644966 TCTTCCTGGTGTTTCTTGTGT 57.355 42.857 0.0 0.0 0.00 3.72 R
3261 8193 4.275689 CCATATACTCGCTGGAATTTTGCA 59.724 41.667 0.0 0.0 31.38 4.08 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
23 24 2.478989 CCTCAGATGGCAGTGCTTG 58.521 57.895 16.11 8.85 0.00 4.01
32 33 4.342092 AGATGGCAGTGCTTGTTTAGTTTT 59.658 37.500 16.11 0.00 0.00 2.43
36 37 4.738252 GGCAGTGCTTGTTTAGTTTTGTAC 59.262 41.667 16.11 0.00 0.00 2.90
37 38 5.449999 GGCAGTGCTTGTTTAGTTTTGTACT 60.450 40.000 16.11 0.00 41.04 2.73
53 58 8.999431 AGTTTTGTACTTGTACAATGGTAGATG 58.001 33.333 21.99 0.00 39.39 2.90
56 61 6.106003 TGTACTTGTACAATGGTAGATGCAG 58.894 40.000 9.13 0.00 0.00 4.41
69 74 5.046376 TGGTAGATGCAGAGATGAAGTCAAA 60.046 40.000 0.00 0.00 0.00 2.69
71 76 6.202570 GGTAGATGCAGAGATGAAGTCAAATC 59.797 42.308 0.00 0.00 0.00 2.17
133 138 1.211457 AGGCTCACCATCAGATCCAAC 59.789 52.381 0.00 0.00 39.06 3.77
164 169 9.406828 TCAGAATGAATACTACACGTTATATGC 57.593 33.333 0.00 0.00 45.97 3.14
201 207 4.698201 TGGCACGATATGATAAAAGGGA 57.302 40.909 0.00 0.00 0.00 4.20
202 208 4.641396 TGGCACGATATGATAAAAGGGAG 58.359 43.478 0.00 0.00 0.00 4.30
203 209 4.346709 TGGCACGATATGATAAAAGGGAGA 59.653 41.667 0.00 0.00 0.00 3.71
258 266 7.661437 AGCCTTGGTTTCTTTTCCAATTAATTC 59.339 33.333 0.00 0.00 41.89 2.17
337 1704 1.608590 CGTGGTTTTGTGGAGAATGCT 59.391 47.619 0.00 0.00 0.00 3.79
341 1708 3.318839 TGGTTTTGTGGAGAATGCTTGAG 59.681 43.478 0.00 0.00 0.00 3.02
352 1719 4.577875 AGAATGCTTGAGTGAAGAAGAGG 58.422 43.478 0.00 0.00 32.82 3.69
393 1821 0.975040 ACTTGAGAGCTGGGATCGCT 60.975 55.000 11.46 2.03 41.15 4.93
466 1894 7.699566 TGACTGACATTGTTTGTTTACTTACC 58.300 34.615 0.00 0.00 39.18 2.85
541 4704 4.572795 GCCTGCTAGATAAGGAAAGAACAC 59.427 45.833 9.98 0.00 35.40 3.32
587 4840 2.746277 GGCACCTACCGCACCAAG 60.746 66.667 0.00 0.00 0.00 3.61
588 4841 2.032071 GCACCTACCGCACCAAGT 59.968 61.111 0.00 0.00 0.00 3.16
589 4842 1.599797 GCACCTACCGCACCAAGTT 60.600 57.895 0.00 0.00 0.00 2.66
590 4843 1.852067 GCACCTACCGCACCAAGTTG 61.852 60.000 0.00 0.00 0.00 3.16
592 4845 0.690762 ACCTACCGCACCAAGTTGAT 59.309 50.000 3.87 0.00 0.00 2.57
593 4846 1.903860 ACCTACCGCACCAAGTTGATA 59.096 47.619 3.87 0.00 0.00 2.15
594 4847 2.277084 CCTACCGCACCAAGTTGATAC 58.723 52.381 3.87 0.00 0.00 2.24
596 4849 3.131577 CCTACCGCACCAAGTTGATACTA 59.868 47.826 3.87 0.00 33.17 1.82
597 4850 2.968675 ACCGCACCAAGTTGATACTAC 58.031 47.619 3.87 0.00 33.17 2.73
598 4851 2.300723 ACCGCACCAAGTTGATACTACA 59.699 45.455 3.87 0.00 33.17 2.74
599 4852 2.930040 CCGCACCAAGTTGATACTACAG 59.070 50.000 3.87 0.00 33.17 2.74
600 4853 3.585862 CGCACCAAGTTGATACTACAGT 58.414 45.455 3.87 0.00 33.17 3.55
601 4854 3.367932 CGCACCAAGTTGATACTACAGTG 59.632 47.826 3.87 2.49 34.44 3.66
602 4855 3.684788 GCACCAAGTTGATACTACAGTGG 59.315 47.826 3.87 0.00 33.10 4.00
603 4856 4.562757 GCACCAAGTTGATACTACAGTGGA 60.563 45.833 3.87 0.00 33.10 4.02
604 4857 4.929808 CACCAAGTTGATACTACAGTGGAC 59.070 45.833 3.87 0.00 33.17 4.02
605 4858 4.591498 ACCAAGTTGATACTACAGTGGACA 59.409 41.667 3.87 0.00 33.17 4.02
606 4859 5.071250 ACCAAGTTGATACTACAGTGGACAA 59.929 40.000 3.87 0.00 33.17 3.18
607 4860 5.408604 CCAAGTTGATACTACAGTGGACAAC 59.591 44.000 3.87 13.59 37.16 3.32
608 4861 4.806330 AGTTGATACTACAGTGGACAACG 58.194 43.478 14.64 0.00 39.27 4.10
609 4862 3.226346 TGATACTACAGTGGACAACGC 57.774 47.619 0.00 0.00 0.00 4.84
610 4863 2.094390 TGATACTACAGTGGACAACGCC 60.094 50.000 0.00 0.00 0.00 5.68
611 4864 1.330234 TACTACAGTGGACAACGCCA 58.670 50.000 0.00 0.00 35.02 5.69
612 4865 0.466543 ACTACAGTGGACAACGCCAA 59.533 50.000 0.00 0.00 40.20 4.52
613 4866 1.148310 CTACAGTGGACAACGCCAAG 58.852 55.000 0.00 0.00 40.20 3.61
614 4867 0.466543 TACAGTGGACAACGCCAAGT 59.533 50.000 0.00 0.00 40.20 3.16
615 4868 0.393808 ACAGTGGACAACGCCAAGTT 60.394 50.000 0.00 0.00 45.45 2.66
626 4879 4.488790 CCAAGTTGGCTGAGCAGT 57.511 55.556 9.46 0.00 0.00 4.40
627 4880 2.724520 CCAAGTTGGCTGAGCAGTT 58.275 52.632 9.46 0.00 0.00 3.16
628 4881 0.595095 CCAAGTTGGCTGAGCAGTTC 59.405 55.000 9.46 0.00 0.00 3.01
629 4882 1.311859 CAAGTTGGCTGAGCAGTTCA 58.688 50.000 6.82 0.00 0.00 3.18
656 4909 5.056480 AGAACAACTTTGACGATGACATGA 58.944 37.500 0.00 0.00 0.00 3.07
782 5054 0.956633 GCAATGATCCGACATGGCAT 59.043 50.000 0.00 0.00 44.07 4.40
827 5126 0.611062 AATGAGTGGCTGCATGCACT 60.611 50.000 18.46 12.68 45.15 4.40
830 5137 1.645704 GAGTGGCTGCATGCACTCTG 61.646 60.000 18.46 8.43 45.15 3.35
887 5194 3.316588 CAGAGTCGTGGACTAGTATGCAT 59.683 47.826 3.79 3.79 43.53 3.96
1017 5378 3.300765 GCAGCAGCCAAAGCCTGT 61.301 61.111 0.00 0.00 41.25 4.00
1103 5501 2.403252 ACAAATCCATCACCTCGTCC 57.597 50.000 0.00 0.00 0.00 4.79
1107 5512 4.129737 CCATCACCTCGTCCGCGT 62.130 66.667 4.92 0.00 39.49 6.01
1132 5538 0.894184 ACGTCTTGGAGAGAGGCGAA 60.894 55.000 5.06 0.00 44.48 4.70
1272 6071 5.526506 AAGCAAAGCTCAATGTTCTTCTT 57.473 34.783 0.00 0.00 38.25 2.52
1351 6219 1.896220 ATGGTGCAGTGTTCGAATGT 58.104 45.000 0.00 0.00 0.00 2.71
1354 6222 2.036604 TGGTGCAGTGTTCGAATGTCTA 59.963 45.455 0.00 0.00 0.00 2.59
2089 6957 2.229062 GGTCAGTGACAAGATCGACTCA 59.771 50.000 24.20 0.00 33.68 3.41
2098 6966 2.039624 ATCGACTCACCCCAGCCT 59.960 61.111 0.00 0.00 0.00 4.58
2926 7809 1.557099 ACAGGCTCAAGACGGTCATA 58.443 50.000 11.27 0.00 0.00 2.15
2951 7835 2.906182 ATCGCTCGCGCAAGGATTCA 62.906 55.000 8.75 0.00 39.59 2.57
3016 7927 2.466547 TTAGGAGTAGCCAGGTACCC 57.533 55.000 8.74 5.22 40.02 3.69
3174 8102 6.882140 TCCATAAGTTTTACATTGATCCGTGT 59.118 34.615 5.54 5.54 0.00 4.49
3261 8193 1.288752 CCGCAAAATCGGCAAACCT 59.711 52.632 0.00 0.00 43.18 3.50
3305 8238 2.019156 GCTCGGCCCAATTTTCTAGCT 61.019 52.381 0.00 0.00 0.00 3.32
3310 8243 4.137543 CGGCCCAATTTTCTAGCTAGAAT 58.862 43.478 31.52 18.32 41.52 2.40
3329 8262 2.254651 GAGCCCGTATACTCGCCG 59.745 66.667 0.56 0.00 0.00 6.46
3361 8317 1.108132 TTTTTACCGCAAACCGCCCT 61.108 50.000 0.00 0.00 37.30 5.19
3410 8371 1.169661 TGCATTTGCGGGTCGAAACT 61.170 50.000 0.00 0.00 45.83 2.66
3475 8439 0.318699 CTCATATTTCTCGCCGCCGA 60.319 55.000 0.00 0.00 42.01 5.54
3629 8598 1.014564 GGGCGAGGAAGTTGACGAAG 61.015 60.000 0.00 0.00 0.00 3.79
3751 8741 1.658686 GCGAGCTCTTCCTCTTCCGA 61.659 60.000 12.85 0.00 0.00 4.55
3786 8776 1.241990 CGTGAAGAGGGAGTGGTCGA 61.242 60.000 0.00 0.00 0.00 4.20
4058 9099 0.248949 GGCGAAGTACATCGACCTCC 60.249 60.000 23.43 11.29 45.14 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 2.816087 ACTAAACAAGCACTGCCATCTG 59.184 45.455 0.00 0.00 0.00 2.90
10 11 3.923017 AACTAAACAAGCACTGCCATC 57.077 42.857 0.00 0.00 0.00 3.51
32 33 6.043854 TGCATCTACCATTGTACAAGTACA 57.956 37.500 14.65 8.88 43.61 2.90
36 37 5.664457 TCTCTGCATCTACCATTGTACAAG 58.336 41.667 14.65 3.88 0.00 3.16
37 38 5.675684 TCTCTGCATCTACCATTGTACAA 57.324 39.130 11.41 11.41 0.00 2.41
53 58 5.816258 TCTGATGATTTGACTTCATCTCTGC 59.184 40.000 13.15 0.00 46.28 4.26
56 61 8.434733 TGAATCTGATGATTTGACTTCATCTC 57.565 34.615 13.15 5.04 46.28 2.75
69 74 7.911130 TCTTACCTCTTCTGAATCTGATGAT 57.089 36.000 6.27 0.00 33.70 2.45
71 76 7.780064 TCTTCTTACCTCTTCTGAATCTGATG 58.220 38.462 0.00 0.00 0.00 3.07
133 138 7.993821 ACGTGTAGTATTCATTCTGAATCTG 57.006 36.000 5.67 0.00 43.03 2.90
164 169 0.109597 GCCAAGTGCAATGTTCCTCG 60.110 55.000 0.00 0.00 40.77 4.63
258 266 8.780846 TCTAGTGTAGTTCTTACTCTTCTCTG 57.219 38.462 0.00 0.00 37.33 3.35
289 297 4.336713 GGTTCAAAAGAAGCTGACTCAGTT 59.663 41.667 7.89 0.00 33.43 3.16
292 300 3.214328 GGGTTCAAAAGAAGCTGACTCA 58.786 45.455 7.27 0.00 33.52 3.41
337 1704 5.598830 ACTGAGTTACCTCTTCTTCACTCAA 59.401 40.000 0.00 0.00 39.99 3.02
341 1708 5.844004 TCAACTGAGTTACCTCTTCTTCAC 58.156 41.667 0.00 0.00 38.61 3.18
352 1719 6.568869 AGTCATATCTGCTCAACTGAGTTAC 58.431 40.000 8.46 0.00 43.85 2.50
393 1821 0.742635 TGCACAGTCGTTGCTGAACA 60.743 50.000 10.32 5.99 39.62 3.18
497 1929 5.072329 AGGCTGCAATTGGATACTATACACT 59.928 40.000 7.72 0.00 37.61 3.55
541 4704 2.030451 GCAGAGGCTTCAGTTTCAAAGG 60.030 50.000 0.00 0.00 36.96 3.11
587 4840 3.367025 GCGTTGTCCACTGTAGTATCAAC 59.633 47.826 12.06 12.06 33.34 3.18
588 4841 3.581755 GCGTTGTCCACTGTAGTATCAA 58.418 45.455 0.00 0.00 0.00 2.57
589 4842 2.094390 GGCGTTGTCCACTGTAGTATCA 60.094 50.000 0.00 0.00 0.00 2.15
590 4843 2.094390 TGGCGTTGTCCACTGTAGTATC 60.094 50.000 0.00 0.00 0.00 2.24
592 4845 1.330234 TGGCGTTGTCCACTGTAGTA 58.670 50.000 0.00 0.00 0.00 1.82
593 4846 0.466543 TTGGCGTTGTCCACTGTAGT 59.533 50.000 0.00 0.00 35.50 2.73
594 4847 1.148310 CTTGGCGTTGTCCACTGTAG 58.852 55.000 0.00 0.00 35.50 2.74
596 4849 0.393808 AACTTGGCGTTGTCCACTGT 60.394 50.000 0.00 0.00 35.50 3.55
597 4850 0.029300 CAACTTGGCGTTGTCCACTG 59.971 55.000 0.00 0.00 46.23 3.66
598 4851 2.404083 CAACTTGGCGTTGTCCACT 58.596 52.632 0.00 0.00 46.23 4.00
609 4862 0.595095 GAACTGCTCAGCCAACTTGG 59.405 55.000 3.10 3.10 41.55 3.61
610 4863 1.266175 CTGAACTGCTCAGCCAACTTG 59.734 52.381 0.00 0.00 45.11 3.16
611 4864 1.602311 CTGAACTGCTCAGCCAACTT 58.398 50.000 0.00 0.00 45.11 2.66
612 4865 3.319135 CTGAACTGCTCAGCCAACT 57.681 52.632 0.00 0.00 45.11 3.16
626 4879 6.315144 TCATCGTCAAAGTTGTTCTTTCTGAA 59.685 34.615 0.00 0.00 43.57 3.02
627 4880 5.815222 TCATCGTCAAAGTTGTTCTTTCTGA 59.185 36.000 0.00 0.00 43.57 3.27
628 4881 5.904080 GTCATCGTCAAAGTTGTTCTTTCTG 59.096 40.000 0.00 0.00 43.57 3.02
629 4882 5.584649 TGTCATCGTCAAAGTTGTTCTTTCT 59.415 36.000 0.00 0.00 43.57 2.52
630 4883 5.806286 TGTCATCGTCAAAGTTGTTCTTTC 58.194 37.500 0.00 0.00 43.57 2.62
631 4884 5.811399 TGTCATCGTCAAAGTTGTTCTTT 57.189 34.783 0.00 0.00 45.96 2.52
632 4885 5.527214 TCATGTCATCGTCAAAGTTGTTCTT 59.473 36.000 0.00 0.00 38.10 2.52
633 4886 5.056480 TCATGTCATCGTCAAAGTTGTTCT 58.944 37.500 0.00 0.00 0.00 3.01
634 4887 5.342806 TCATGTCATCGTCAAAGTTGTTC 57.657 39.130 0.00 0.00 0.00 3.18
635 4888 5.296780 AGTTCATGTCATCGTCAAAGTTGTT 59.703 36.000 0.00 0.00 0.00 2.83
636 4889 4.816385 AGTTCATGTCATCGTCAAAGTTGT 59.184 37.500 0.00 0.00 0.00 3.32
637 4890 5.178252 AGAGTTCATGTCATCGTCAAAGTTG 59.822 40.000 0.00 0.00 0.00 3.16
638 4891 5.300752 AGAGTTCATGTCATCGTCAAAGTT 58.699 37.500 0.00 0.00 0.00 2.66
639 4892 4.887748 AGAGTTCATGTCATCGTCAAAGT 58.112 39.130 0.00 0.00 0.00 2.66
640 4893 5.852738 AAGAGTTCATGTCATCGTCAAAG 57.147 39.130 0.00 0.00 0.00 2.77
641 4894 6.293407 GGAAAAGAGTTCATGTCATCGTCAAA 60.293 38.462 0.00 0.00 0.00 2.69
642 4895 5.179368 GGAAAAGAGTTCATGTCATCGTCAA 59.821 40.000 0.00 0.00 0.00 3.18
643 4896 4.690748 GGAAAAGAGTTCATGTCATCGTCA 59.309 41.667 0.00 0.00 0.00 4.35
656 4909 3.769536 CAACTTGCGTTGGAAAAGAGTT 58.230 40.909 0.00 0.00 45.28 3.01
782 5054 1.979155 CTCCGGTCTCCAGAGTGCA 60.979 63.158 0.00 0.00 0.00 4.57
806 5078 1.317431 TGCATGCAGCCACTCATTCC 61.317 55.000 18.46 0.00 44.83 3.01
827 5126 3.324930 CAGCAGGAGGTGGCCAGA 61.325 66.667 5.11 0.00 39.53 3.86
1017 5378 2.425312 TGAACTTTTTCTTTGCTCGCCA 59.575 40.909 0.00 0.00 32.36 5.69
1107 5512 2.095461 CTCTCTCCAAGACGTCCATGA 58.905 52.381 13.01 5.14 0.00 3.07
1116 5522 1.883732 CGTTCGCCTCTCTCCAAGA 59.116 57.895 0.00 0.00 0.00 3.02
1272 6071 8.683615 TCTTCGAGCTACAATAAGAAGACAATA 58.316 33.333 2.07 0.00 39.07 1.90
1351 6219 0.958876 TGAACGCCGTGCTCTCTAGA 60.959 55.000 0.00 0.00 0.00 2.43
1354 6222 1.016130 CATTGAACGCCGTGCTCTCT 61.016 55.000 0.00 0.00 0.00 3.10
2089 6957 2.797278 CGCGATCTTAGGCTGGGGT 61.797 63.158 0.00 0.00 0.00 4.95
2098 6966 1.809619 GCTGGTGTGCGCGATCTTA 60.810 57.895 12.10 0.00 0.00 2.10
2152 7020 0.626382 TCTCCTCCATGTCCGACTCT 59.374 55.000 0.00 0.00 0.00 3.24
3051 7971 4.764050 TCTTCCTGGTGTTTCTTGTGTA 57.236 40.909 0.00 0.00 0.00 2.90
3052 7972 3.644966 TCTTCCTGGTGTTTCTTGTGT 57.355 42.857 0.00 0.00 0.00 3.72
3261 8193 4.275689 CCATATACTCGCTGGAATTTTGCA 59.724 41.667 0.00 0.00 31.38 4.08
3361 8317 3.503365 CCGTAGATATACTGTTGGGGGA 58.497 50.000 0.00 0.00 0.00 4.81
3511 8479 4.101448 GGCCGGAGCTCCACATGT 62.101 66.667 31.67 0.00 39.73 3.21
3751 8741 3.382832 CGGGGAGAAGGCTCACGT 61.383 66.667 0.00 0.00 45.84 4.49
3786 8776 2.039405 CGACGACCTCGACCTCCTT 61.039 63.158 0.78 0.00 46.14 3.36
3808 8825 4.479993 CCTCGGGCTCCTGCTTGG 62.480 72.222 0.00 0.00 39.59 3.61
3914 8941 3.764466 CCGACGCTCTGCCTCCTT 61.764 66.667 0.00 0.00 0.00 3.36
3932 8959 3.695606 GAGCTCCTCGTGGTGGCA 61.696 66.667 19.71 0.00 36.34 4.92
3952 8979 1.367471 CTGCTGGAACACGAGGTCA 59.633 57.895 0.00 0.00 0.00 4.02
4021 9049 1.150567 CCTTCTGCTCCTCGCGAATG 61.151 60.000 11.33 4.37 43.27 2.67
4022 9050 1.142748 CCTTCTGCTCCTCGCGAAT 59.857 57.895 11.33 0.00 43.27 3.34
4023 9051 2.573869 CCTTCTGCTCCTCGCGAA 59.426 61.111 11.33 0.00 43.27 4.70
4058 9099 2.578178 CTCCTCGTCGAAGCTGCG 60.578 66.667 8.15 8.15 0.00 5.18


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

AutoCloner maintained by Alex Coulton.