Multiple sequence alignment - TraesCS7A01G283300

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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 TraesCS7A01G283300 chr7A 100.000 4410 0 0 1 4410 315509756 315514165 0.000000e+00 8144.0
1 TraesCS7A01G283300 chr7A 85.535 159 23 0 3447 3605 315513043 315513201 2.730000e-37 167.0
2 TraesCS7A01G283300 chr7A 85.535 159 23 0 3288 3446 315513202 315513360 2.730000e-37 167.0
3 TraesCS7A01G283300 chr5A 95.844 2647 72 5 1 2643 706784284 706781672 0.000000e+00 4244.0
4 TraesCS7A01G283300 chr5A 97.987 298 6 0 1 298 706785811 706785514 6.540000e-143 518.0
5 TraesCS7A01G283300 chr5A 97.980 297 5 1 1 297 706786574 706786279 8.460000e-142 514.0
6 TraesCS7A01G283300 chr5A 96.980 298 8 1 1 298 706785047 706784751 2.370000e-137 499.0
7 TraesCS7A01G283300 chr7B 92.823 1477 90 9 1 1471 19267595 19269061 0.000000e+00 2126.0
8 TraesCS7A01G283300 chr7B 93.982 781 47 0 1635 2415 19269055 19269835 0.000000e+00 1182.0
9 TraesCS7A01G283300 chr7B 88.966 290 30 2 3157 3446 263138784 263138497 1.510000e-94 357.0
10 TraesCS7A01G283300 chr4D 93.981 864 43 4 2676 3531 340980171 340979309 0.000000e+00 1299.0
11 TraesCS7A01G283300 chr4D 91.506 259 22 0 3735 3993 340978474 340978216 1.510000e-94 357.0
12 TraesCS7A01G283300 chr4D 91.228 228 20 0 4033 4260 340978205 340977978 1.190000e-80 311.0
13 TraesCS7A01G283300 chr4D 93.367 196 10 2 4218 4410 340977979 340977784 2.010000e-73 287.0
14 TraesCS7A01G283300 chr4D 94.798 173 6 1 3530 3699 340979132 340978960 2.610000e-67 267.0
15 TraesCS7A01G283300 chr4D 88.557 201 22 1 3157 3357 386536698 386536499 4.410000e-60 243.0
16 TraesCS7A01G283300 chr1A 92.197 487 30 5 3052 3531 436082199 436082684 0.000000e+00 682.0
17 TraesCS7A01G283300 chr1A 87.633 469 25 10 3525 3987 436082837 436083278 8.460000e-142 514.0
18 TraesCS7A01G283300 chr1A 89.459 370 34 1 4040 4409 436083294 436083658 3.110000e-126 462.0
19 TraesCS7A01G283300 chr1A 77.332 772 111 40 1634 2386 396614593 396615319 8.890000e-107 398.0
20 TraesCS7A01G283300 chr1A 93.085 188 13 0 2676 2863 436070268 436070455 4.340000e-70 276.0
21 TraesCS7A01G283300 chr1A 94.079 152 9 0 2858 3009 436082049 436082200 9.540000e-57 231.0
22 TraesCS7A01G283300 chr7D 78.986 828 132 26 1321 2141 37954803 37955595 1.090000e-145 527.0
23 TraesCS7A01G283300 chr2B 93.824 340 20 1 35 373 794679032 794679371 1.090000e-140 510.0
24 TraesCS7A01G283300 chr4A 89.310 290 29 2 3157 3446 13061158 13060871 3.240000e-96 363.0
25 TraesCS7A01G283300 chr1D 88.927 289 29 3 3157 3443 45063055 45063342 1.950000e-93 353.0
26 TraesCS7A01G283300 chr1D 93.220 59 3 1 3652 3710 45064543 45064600 7.860000e-13 86.1
27 TraesCS7A01G283300 chr1D 92.683 41 2 1 3651 3691 182793430 182793391 1.710000e-04 58.4
28 TraesCS7A01G283300 chr1D 92.500 40 2 1 3652 3691 163397800 163397762 6.160000e-04 56.5
29 TraesCS7A01G283300 chr5B 86.851 289 36 2 3157 3443 22316540 22316828 5.500000e-84 322.0
30 TraesCS7A01G283300 chr5B 91.525 59 4 1 3652 3710 22317997 22318054 3.660000e-11 80.5
31 TraesCS7A01G283300 chr4B 80.069 291 31 8 3157 3446 248357318 248357054 1.620000e-44 191.0
32 TraesCS7A01G283300 chr2D 80.272 147 16 7 3745 3889 218769673 218769538 1.010000e-16 99.0
33 TraesCS7A01G283300 chr2D 92.500 40 2 1 3652 3691 437372791 437372753 6.160000e-04 56.5
34 TraesCS7A01G283300 chr6A 97.143 35 1 0 3650 3684 488736052 488736018 4.760000e-05 60.2


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 TraesCS7A01G283300 chr7A 315509756 315514165 4409 False 2826.00 8144 90.356667 1 4410 3 chr7A.!!$F1 4409
1 TraesCS7A01G283300 chr5A 706781672 706786574 4902 True 1443.75 4244 97.197750 1 2643 4 chr5A.!!$R1 2642
2 TraesCS7A01G283300 chr7B 19267595 19269835 2240 False 1654.00 2126 93.402500 1 2415 2 chr7B.!!$F1 2414
3 TraesCS7A01G283300 chr4D 340977784 340980171 2387 True 504.20 1299 92.976000 2676 4410 5 chr4D.!!$R2 1734
4 TraesCS7A01G283300 chr1A 436082049 436083658 1609 False 472.25 682 90.842000 2858 4409 4 chr1A.!!$F3 1551
5 TraesCS7A01G283300 chr1A 396614593 396615319 726 False 398.00 398 77.332000 1634 2386 1 chr1A.!!$F1 752
6 TraesCS7A01G283300 chr7D 37954803 37955595 792 False 527.00 527 78.986000 1321 2141 1 chr7D.!!$F1 820
7 TraesCS7A01G283300 chr1D 45063055 45064600 1545 False 219.55 353 91.073500 3157 3710 2 chr1D.!!$F1 553
8 TraesCS7A01G283300 chr5B 22316540 22318054 1514 False 201.25 322 89.188000 3157 3710 2 chr5B.!!$F1 553

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
388 2683 0.034059 GCGTCTATGGGGTGAGGATG 59.966 60.0 0.00 0.00 0.00 3.51 F
389 2684 0.681733 CGTCTATGGGGTGAGGATGG 59.318 60.0 0.00 0.00 0.00 3.51 F
543 2853 1.231042 AGGATGGGGGCCCTCAAAAT 61.231 55.0 32.89 13.70 36.94 1.82 F
2297 4623 1.312371 ACACGGTTGGTATGCATGCC 61.312 55.0 25.45 25.45 0.00 4.40 F
3130 5460 1.059913 AGTGGTGGCAGTAAGAGCTT 58.940 50.0 0.00 0.00 0.00 3.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1644 3962 0.033796 CCACACTGGCATCTCCCAAT 60.034 55.0 0.0 0.0 33.73 3.16 R
2155 4481 0.808060 ACGTTCACATCACACGCACA 60.808 50.0 0.0 0.0 37.44 4.57 R
2452 4781 0.324285 AGTCCACTACGGTCTCGACT 59.676 55.0 0.0 0.0 40.11 4.18 R
3245 5582 0.740737 CGGTCAATGCAGGGGAAATC 59.259 55.0 0.0 0.0 0.00 2.17 R
4297 8490 0.179234 TTGTCACTTCCGAACTGGCA 59.821 50.0 0.0 0.0 37.80 4.92 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
132 133 4.079980 TGCTTTGTTTGTCTAGTGCCTA 57.920 40.909 0.00 0.00 0.00 3.93
234 2526 2.203394 CAGCAGGCAAGTGTGGGT 60.203 61.111 0.00 0.00 0.00 4.51
301 2593 1.070577 GCATATGTTCGTCATCGGCAC 60.071 52.381 4.29 0.00 37.91 5.01
355 2650 3.913548 ACACGTAATGCTTGCAATCAA 57.086 38.095 7.12 0.00 0.00 2.57
380 2675 2.281761 GCATGGGCGTCTATGGGG 60.282 66.667 15.54 0.00 33.17 4.96
381 2676 3.120086 GCATGGGCGTCTATGGGGT 62.120 63.158 15.54 0.00 33.17 4.95
382 2677 1.227943 CATGGGCGTCTATGGGGTG 60.228 63.158 5.31 0.00 0.00 4.61
383 2678 1.383943 ATGGGCGTCTATGGGGTGA 60.384 57.895 0.00 0.00 0.00 4.02
384 2679 1.410850 ATGGGCGTCTATGGGGTGAG 61.411 60.000 0.00 0.00 0.00 3.51
385 2680 2.808206 GGGCGTCTATGGGGTGAGG 61.808 68.421 0.00 0.00 0.00 3.86
386 2681 1.760875 GGCGTCTATGGGGTGAGGA 60.761 63.158 0.00 0.00 0.00 3.71
387 2682 1.122019 GGCGTCTATGGGGTGAGGAT 61.122 60.000 0.00 0.00 0.00 3.24
388 2683 0.034059 GCGTCTATGGGGTGAGGATG 59.966 60.000 0.00 0.00 0.00 3.51
389 2684 0.681733 CGTCTATGGGGTGAGGATGG 59.318 60.000 0.00 0.00 0.00 3.51
390 2685 1.807814 GTCTATGGGGTGAGGATGGT 58.192 55.000 0.00 0.00 0.00 3.55
483 2793 3.189495 TGTTGTTTTTCACGCAGAGTTCA 59.811 39.130 0.00 0.00 0.00 3.18
517 2827 5.836024 TTCCTACATAAAGAACACCCTGT 57.164 39.130 0.00 0.00 0.00 4.00
543 2853 1.231042 AGGATGGGGGCCCTCAAAAT 61.231 55.000 32.89 13.70 36.94 1.82
598 2909 5.700402 AGAGGTTGTCAAGCCATAGTTAT 57.300 39.130 11.10 0.00 0.00 1.89
614 2925 6.183360 CCATAGTTATGCACCACATTTGACAT 60.183 38.462 0.00 0.00 40.38 3.06
742 3053 3.435275 AGAGATAGTCTGTGGTTGCTCA 58.565 45.455 0.00 0.00 32.57 4.26
833 3144 1.700739 TCCACCGGTGATTTAAGTGGT 59.299 47.619 36.07 0.00 46.52 4.16
849 3160 5.700402 AAGTGGTACATCTTGAAGGCTAT 57.300 39.130 0.00 0.00 44.52 2.97
894 3205 7.644157 GCACGGGAATAGAAAATGAATTTAGAC 59.356 37.037 0.00 0.00 0.00 2.59
896 3207 9.408648 ACGGGAATAGAAAATGAATTTAGACAT 57.591 29.630 0.00 0.00 0.00 3.06
1016 3327 2.285026 CGTACATGACGCAGATTTTCGG 60.285 50.000 0.00 0.00 46.27 4.30
1116 3427 5.316167 AGTGTGAACCATATGCTGAAGAAA 58.684 37.500 0.00 0.00 0.00 2.52
1354 3670 3.777478 CTTTTTGAGCACATAGGCATGG 58.223 45.455 0.00 0.00 36.39 3.66
1426 3743 6.377146 ACTTTGTTTCTTCAAGGCAGTTTCTA 59.623 34.615 0.00 0.00 0.00 2.10
1439 3756 6.485171 AGGCAGTTTCTAGATGTTGGTTAAT 58.515 36.000 0.00 0.00 0.00 1.40
1519 3837 3.065925 GGATAAGCACATTGTGAGAAGGC 59.934 47.826 20.77 3.73 35.23 4.35
1601 3919 3.884774 TGCCACGCCCCTGACTTT 61.885 61.111 0.00 0.00 0.00 2.66
1602 3920 2.597510 GCCACGCCCCTGACTTTT 60.598 61.111 0.00 0.00 0.00 2.27
1605 3923 1.597027 CACGCCCCTGACTTTTCGT 60.597 57.895 0.00 0.00 0.00 3.85
1644 3962 2.483714 GCAGGCATTAGAGTTGATCCGA 60.484 50.000 0.00 0.00 0.00 4.55
1686 4008 2.906389 AGCTTAACACTGATGGGACTCA 59.094 45.455 0.00 0.00 0.00 3.41
2155 4481 4.144297 AGTGGTTGTAGAATGCACATGTT 58.856 39.130 0.00 0.00 0.00 2.71
2182 4508 5.436410 CGTGTGATGTGAACGTTAATGAAA 58.564 37.500 0.00 0.00 32.79 2.69
2185 4511 7.213706 CGTGTGATGTGAACGTTAATGAAATAC 59.786 37.037 0.00 0.00 32.79 1.89
2297 4623 1.312371 ACACGGTTGGTATGCATGCC 61.312 55.000 25.45 25.45 0.00 4.40
2391 4720 3.054361 GGTTTGAATAGAAGCTGGAGGGA 60.054 47.826 0.00 0.00 0.00 4.20
2485 4814 1.348036 GTGGACTAAAGTGAGCCACCT 59.652 52.381 7.81 0.00 42.37 4.00
2519 4848 2.448542 ACAGGTGACAGGGGCACT 60.449 61.111 1.79 0.00 36.53 4.40
2538 4867 6.472163 GGGCACTGTTTGATAAATAATTCACG 59.528 38.462 0.00 0.00 0.00 4.35
2548 4877 7.359595 TGATAAATAATTCACGGCTGCAATAC 58.640 34.615 0.50 0.00 0.00 1.89
2551 4880 2.057137 ATTCACGGCTGCAATACCAT 57.943 45.000 0.50 0.00 0.00 3.55
2582 4911 3.260483 GCACGCAGCGATCCAGAG 61.260 66.667 24.65 3.04 0.00 3.35
2632 4961 5.853936 TCATATGCTAGTACGAGCCATTTT 58.146 37.500 23.01 7.41 42.11 1.82
2643 4972 2.985809 CGAGCCATTTTGAATTTTCGCA 59.014 40.909 0.00 0.00 0.00 5.10
2644 4973 3.428198 CGAGCCATTTTGAATTTTCGCAA 59.572 39.130 0.00 0.00 0.00 4.85
2645 4974 4.091800 CGAGCCATTTTGAATTTTCGCAAT 59.908 37.500 0.00 0.00 0.00 3.56
2646 4975 5.389725 CGAGCCATTTTGAATTTTCGCAATT 60.390 36.000 0.00 0.00 0.00 2.32
2647 4976 6.183360 CGAGCCATTTTGAATTTTCGCAATTA 60.183 34.615 0.00 0.00 0.00 1.40
2648 4977 6.830736 AGCCATTTTGAATTTTCGCAATTAC 58.169 32.000 0.00 0.00 0.00 1.89
2649 4978 6.426328 AGCCATTTTGAATTTTCGCAATTACA 59.574 30.769 0.00 0.00 0.00 2.41
2650 4979 6.519419 GCCATTTTGAATTTTCGCAATTACAC 59.481 34.615 0.00 0.00 0.00 2.90
2651 4980 7.571059 GCCATTTTGAATTTTCGCAATTACACT 60.571 33.333 0.00 0.00 0.00 3.55
2652 4981 8.920665 CCATTTTGAATTTTCGCAATTACACTA 58.079 29.630 0.00 0.00 0.00 2.74
2653 4982 9.726034 CATTTTGAATTTTCGCAATTACACTAC 57.274 29.630 0.00 0.00 0.00 2.73
2654 4983 9.691362 ATTTTGAATTTTCGCAATTACACTACT 57.309 25.926 0.00 0.00 0.00 2.57
2655 4984 9.522804 TTTTGAATTTTCGCAATTACACTACTT 57.477 25.926 0.00 0.00 0.00 2.24
2657 4986 9.820229 TTGAATTTTCGCAATTACACTACTTAG 57.180 29.630 0.00 0.00 0.00 2.18
2658 4987 7.960738 TGAATTTTCGCAATTACACTACTTAGC 59.039 33.333 0.00 0.00 0.00 3.09
2659 4988 6.788684 TTTTCGCAATTACACTACTTAGCA 57.211 33.333 0.00 0.00 0.00 3.49
2660 4989 6.788684 TTTCGCAATTACACTACTTAGCAA 57.211 33.333 0.00 0.00 0.00 3.91
2661 4990 6.788684 TTCGCAATTACACTACTTAGCAAA 57.211 33.333 0.00 0.00 0.00 3.68
2662 4991 6.403333 TCGCAATTACACTACTTAGCAAAG 57.597 37.500 0.00 0.00 38.77 2.77
2663 4992 6.160684 TCGCAATTACACTACTTAGCAAAGA 58.839 36.000 0.00 0.00 36.50 2.52
2664 4993 6.816640 TCGCAATTACACTACTTAGCAAAGAT 59.183 34.615 0.00 0.00 36.50 2.40
2665 4994 6.901887 CGCAATTACACTACTTAGCAAAGATG 59.098 38.462 0.00 0.00 36.50 2.90
2666 4995 7.413000 CGCAATTACACTACTTAGCAAAGATGT 60.413 37.037 0.00 0.00 36.50 3.06
2667 4996 7.693951 GCAATTACACTACTTAGCAAAGATGTG 59.306 37.037 10.91 10.91 41.04 3.21
2668 4997 8.721478 CAATTACACTACTTAGCAAAGATGTGT 58.279 33.333 17.38 17.38 45.18 3.72
2669 4998 7.652300 TTACACTACTTAGCAAAGATGTGTG 57.348 36.000 19.92 12.54 44.18 3.82
2670 4999 5.611374 ACACTACTTAGCAAAGATGTGTGT 58.389 37.500 14.67 0.00 43.56 3.72
2671 5000 6.755206 ACACTACTTAGCAAAGATGTGTGTA 58.245 36.000 14.67 0.00 43.56 2.90
2672 5001 7.214381 ACACTACTTAGCAAAGATGTGTGTAA 58.786 34.615 14.67 0.00 43.56 2.41
2673 5002 7.385205 ACACTACTTAGCAAAGATGTGTGTAAG 59.615 37.037 14.67 0.00 43.56 2.34
2674 5003 5.613358 ACTTAGCAAAGATGTGTGTAAGC 57.387 39.130 0.00 0.00 36.50 3.09
2748 5077 5.815740 GCTACTAGCAAGCCAAACTATAACA 59.184 40.000 2.96 0.00 41.89 2.41
2753 5082 8.432805 ACTAGCAAGCCAAACTATAACAGATAT 58.567 33.333 0.00 0.00 0.00 1.63
2814 5143 5.893897 ATCTCAAGAGATTTGAACTTGCC 57.106 39.130 6.75 0.00 45.31 4.52
2842 5171 8.914328 TTCATGCACATTATGTTTTCATGTAG 57.086 30.769 20.75 6.65 41.09 2.74
2872 5201 9.626045 GAAAAGGAATCGTCAATTGTTATTTCT 57.374 29.630 5.13 5.44 0.00 2.52
2930 5259 4.392644 GCTCAATGCAAGCACCTAGCAG 62.393 54.545 15.31 1.88 43.69 4.24
2979 5308 3.766545 ACATGGAGCCTTGTGTTTATGT 58.233 40.909 7.20 0.00 33.85 2.29
3125 5455 5.938125 ACAAGTTTATAGTGGTGGCAGTAAG 59.062 40.000 0.00 0.00 0.00 2.34
3130 5460 1.059913 AGTGGTGGCAGTAAGAGCTT 58.940 50.000 0.00 0.00 0.00 3.74
3148 5478 6.409704 AGAGCTTATTGTGATTTGCTGACTA 58.590 36.000 0.00 0.00 0.00 2.59
3245 5582 7.825826 AGGCAACATCACCTTCTAGCAGAAG 62.826 48.000 15.09 15.09 45.31 2.85
3298 5636 3.132289 CACTAGGTGGGTACAACATCGAT 59.868 47.826 0.00 0.00 36.52 3.59
3308 5646 5.293569 GGGTACAACATCGATAGTTTTGAGG 59.706 44.000 0.00 0.00 37.40 3.86
3359 5697 5.926542 TGTTGTATTAGCGAATCTAGCATCC 59.073 40.000 0.00 0.00 37.01 3.51
3364 5702 1.409064 AGCGAATCTAGCATCCGTTCA 59.591 47.619 0.00 0.00 37.01 3.18
3485 5825 5.023533 TGAGAAGGTCAAGCCATATGTAC 57.976 43.478 1.24 0.00 40.61 2.90
3523 5863 8.623903 TGTATTAATGAATCTGGCATCAGTTTC 58.376 33.333 0.00 9.14 44.19 2.78
3783 7932 0.397957 TATTCCCCGTAGAGCCAGCA 60.398 55.000 0.00 0.00 0.00 4.41
3886 8035 3.512329 TGGGAGCTTGACGTAAGATTACA 59.488 43.478 8.39 3.96 38.76 2.41
3945 8094 4.515028 TTAACAGAGGGAGAGATACCGA 57.485 45.455 0.00 0.00 0.00 4.69
3953 8102 4.287552 AGGGAGAGATACCGAAGCTTTAA 58.712 43.478 0.00 0.00 0.00 1.52
3999 8148 9.822185 GATACATCACATATTACATAGATGCCA 57.178 33.333 0.00 0.00 37.07 4.92
4012 8161 9.679661 TTACATAGATGCCATAAAGAAACAAGA 57.320 29.630 0.00 0.00 0.00 3.02
4013 8162 8.579850 ACATAGATGCCATAAAGAAACAAGAA 57.420 30.769 0.00 0.00 0.00 2.52
4014 8163 9.023962 ACATAGATGCCATAAAGAAACAAGAAA 57.976 29.630 0.00 0.00 0.00 2.52
4015 8164 9.859427 CATAGATGCCATAAAGAAACAAGAAAA 57.141 29.630 0.00 0.00 0.00 2.29
4054 8203 6.239915 CCCTAGAGTTTTGTAGAAAGGACCTT 60.240 42.308 0.00 0.00 0.00 3.50
4110 8259 1.135199 GGTTTCACCTCGCTATCGACA 60.135 52.381 0.00 0.00 40.21 4.35
4112 8261 1.170442 TTCACCTCGCTATCGACACA 58.830 50.000 0.00 0.00 40.21 3.72
4113 8262 1.170442 TCACCTCGCTATCGACACAA 58.830 50.000 0.00 0.00 40.21 3.33
4121 8270 2.076863 GCTATCGACACAAAAGGCTGT 58.923 47.619 0.00 0.00 0.00 4.40
4150 8299 0.039437 TGAAGAGTCACCGAAGCGAC 60.039 55.000 0.00 0.00 0.00 5.19
4165 8314 3.458163 GACGAGGACCGCCCATCA 61.458 66.667 0.00 0.00 43.32 3.07
4194 8343 4.379243 CCAGGTTCAGCGAGCGGT 62.379 66.667 0.00 0.00 0.00 5.68
4222 8371 3.319755 TCGTAACAAATTCCGGTGAGAC 58.680 45.455 0.00 0.00 0.00 3.36
4260 8450 9.912634 CCAACCATATAGTATAATTTTTGCTGG 57.087 33.333 0.00 0.00 0.00 4.85
4399 8592 8.724229 TCATAATAATGGATGAGCGAGATTTTG 58.276 33.333 0.00 0.00 33.61 2.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
132 133 2.948600 GCGGGGATCCTAAACAAACCAT 60.949 50.000 12.58 0.00 0.00 3.55
234 2526 2.167037 CCCTCCCTCCCCAAAACCA 61.167 63.158 0.00 0.00 0.00 3.67
330 2622 6.209361 TGATTGCAAGCATTACGTGTAAAAA 58.791 32.000 14.49 0.00 36.14 1.94
331 2623 5.763088 TGATTGCAAGCATTACGTGTAAAA 58.237 33.333 14.49 0.00 36.14 1.52
335 2627 3.913548 TTGATTGCAAGCATTACGTGT 57.086 38.095 19.46 0.00 0.00 4.49
378 2673 2.677228 CACCCACCATCCTCACCC 59.323 66.667 0.00 0.00 0.00 4.61
379 2674 2.677228 CCACCCACCATCCTCACC 59.323 66.667 0.00 0.00 0.00 4.02
380 2675 2.677228 CCCACCCACCATCCTCAC 59.323 66.667 0.00 0.00 0.00 3.51
381 2676 2.613696 CCCCACCCACCATCCTCA 60.614 66.667 0.00 0.00 0.00 3.86
382 2677 3.420482 CCCCCACCCACCATCCTC 61.420 72.222 0.00 0.00 0.00 3.71
383 2678 3.532039 TTCCCCCACCCACCATCCT 62.532 63.158 0.00 0.00 0.00 3.24
384 2679 1.885593 ATTTCCCCCACCCACCATCC 61.886 60.000 0.00 0.00 0.00 3.51
385 2680 0.042581 AATTTCCCCCACCCACCATC 59.957 55.000 0.00 0.00 0.00 3.51
386 2681 0.042581 GAATTTCCCCCACCCACCAT 59.957 55.000 0.00 0.00 0.00 3.55
387 2682 1.077298 AGAATTTCCCCCACCCACCA 61.077 55.000 0.00 0.00 0.00 4.17
388 2683 0.614697 CAGAATTTCCCCCACCCACC 60.615 60.000 0.00 0.00 0.00 4.61
389 2684 0.407918 TCAGAATTTCCCCCACCCAC 59.592 55.000 0.00 0.00 0.00 4.61
390 2685 1.162505 TTCAGAATTTCCCCCACCCA 58.837 50.000 0.00 0.00 0.00 4.51
430 2739 7.216693 CACAAAAATCAAACACAAAACATCAGC 59.783 33.333 0.00 0.00 0.00 4.26
483 2793 1.128200 TGTAGGAATAGTGCCCGCAT 58.872 50.000 0.00 0.00 0.00 4.73
517 2827 2.696125 GCCCCCATCCTTCCCAGA 60.696 66.667 0.00 0.00 0.00 3.86
543 2853 1.841277 TCCGCAAAGCCCCTTTAGATA 59.159 47.619 0.00 0.00 31.96 1.98
570 2881 3.239449 TGGCTTGACAACCTCTTCTCTA 58.761 45.455 7.88 0.00 0.00 2.43
598 2909 2.692041 TCAACATGTCAAATGTGGTGCA 59.308 40.909 0.00 0.00 30.79 4.57
614 2925 0.661187 GTCGTACGCTTCCGTCAACA 60.661 55.000 11.24 0.00 46.39 3.33
742 3053 5.809001 TCATTTCAGTTCTGCATCCTTACT 58.191 37.500 0.00 0.00 0.00 2.24
833 3144 9.383519 CAAACTTTCTATAGCCTTCAAGATGTA 57.616 33.333 0.00 0.00 0.00 2.29
849 3160 2.175931 TGCAGAACCCCCAAACTTTCTA 59.824 45.455 0.00 0.00 0.00 2.10
1016 3327 0.106894 CGCCCACTTCTCCCTTATCC 59.893 60.000 0.00 0.00 0.00 2.59
1177 3488 7.720442 TCATAACTCTCATCTGATTGACGATT 58.280 34.615 0.00 0.00 0.00 3.34
1352 3668 5.483937 ACCTGAAGTATATGACAAGACACCA 59.516 40.000 0.00 0.00 0.00 4.17
1354 3670 6.253727 CGAACCTGAAGTATATGACAAGACAC 59.746 42.308 0.00 0.00 0.00 3.67
1426 3743 5.768164 ACCACGAAAGAATTAACCAACATCT 59.232 36.000 0.00 0.00 0.00 2.90
1439 3756 2.045561 TGAAGCCAACCACGAAAGAA 57.954 45.000 0.00 0.00 0.00 2.52
1601 3919 4.684242 GCACATACATCCGATTATGACGAA 59.316 41.667 13.22 0.00 31.28 3.85
1602 3920 4.234574 GCACATACATCCGATTATGACGA 58.765 43.478 13.22 0.00 31.28 4.20
1605 3923 4.568956 CCTGCACATACATCCGATTATGA 58.431 43.478 13.22 0.00 31.28 2.15
1613 3931 3.743521 TCTAATGCCTGCACATACATCC 58.256 45.455 0.00 0.00 0.00 3.51
1644 3962 0.033796 CCACACTGGCATCTCCCAAT 60.034 55.000 0.00 0.00 33.73 3.16
1653 3971 1.133945 TGTTAAGCTTCCACACTGGCA 60.134 47.619 0.00 0.00 37.47 4.92
1686 4008 6.208204 GCCATCACCTTCATAGCTTTATTGAT 59.792 38.462 0.00 0.00 0.00 2.57
1865 4187 4.473444 TCCCTGCACTTTTCTTCTTTGAT 58.527 39.130 0.00 0.00 0.00 2.57
1926 4248 7.939784 TGCTACAGAATCTACTCTTACTCAA 57.060 36.000 0.00 0.00 0.00 3.02
2155 4481 0.808060 ACGTTCACATCACACGCACA 60.808 50.000 0.00 0.00 37.44 4.57
2297 4623 3.005472 TCAAACTTACTGACTCTCCCACG 59.995 47.826 0.00 0.00 0.00 4.94
2363 4692 6.480763 TCCAGCTTCTATTCAAACCATTACA 58.519 36.000 0.00 0.00 0.00 2.41
2452 4781 0.324285 AGTCCACTACGGTCTCGACT 59.676 55.000 0.00 0.00 40.11 4.18
2485 4814 5.665360 TCACCTGTCCACTATCCATTAATGA 59.335 40.000 17.23 3.72 0.00 2.57
2519 4848 6.033341 GCAGCCGTGAATTATTTATCAAACA 58.967 36.000 0.00 0.00 0.00 2.83
2538 4867 4.278170 TGTATTTAGCATGGTATTGCAGCC 59.722 41.667 5.28 0.00 45.23 4.85
2548 4877 2.286595 CGTGCAGCTGTATTTAGCATGG 60.287 50.000 16.64 0.00 46.07 3.66
2551 4880 0.726827 GCGTGCAGCTGTATTTAGCA 59.273 50.000 16.64 1.45 46.07 3.49
2574 4903 0.461961 CGTTGGTCCTCCTCTGGATC 59.538 60.000 0.00 0.00 38.52 3.36
2582 4911 0.831307 ATCTAAGCCGTTGGTCCTCC 59.169 55.000 0.00 0.00 0.00 4.30
2632 4961 7.960738 GCTAAGTAGTGTAATTGCGAAAATTCA 59.039 33.333 0.35 0.00 0.00 2.57
2643 4972 8.721478 CACACATCTTTGCTAAGTAGTGTAATT 58.279 33.333 25.95 12.05 42.59 1.40
2644 4973 7.878127 ACACACATCTTTGCTAAGTAGTGTAAT 59.122 33.333 25.95 19.24 42.59 1.89
2645 4974 7.214381 ACACACATCTTTGCTAAGTAGTGTAA 58.786 34.615 25.95 4.05 42.59 2.41
2646 4975 6.755206 ACACACATCTTTGCTAAGTAGTGTA 58.245 36.000 25.95 4.62 42.59 2.90
2647 4976 5.611374 ACACACATCTTTGCTAAGTAGTGT 58.389 37.500 23.31 23.31 43.85 3.55
2648 4977 7.622256 GCTTACACACATCTTTGCTAAGTAGTG 60.622 40.741 22.44 22.44 40.11 2.74
2649 4978 6.369065 GCTTACACACATCTTTGCTAAGTAGT 59.631 38.462 7.77 5.22 32.98 2.73
2650 4979 6.368791 TGCTTACACACATCTTTGCTAAGTAG 59.631 38.462 7.77 4.64 32.98 2.57
2651 4980 6.147164 GTGCTTACACACATCTTTGCTAAGTA 59.853 38.462 7.77 0.00 46.61 2.24
2652 4981 5.049405 GTGCTTACACACATCTTTGCTAAGT 60.049 40.000 7.77 0.00 46.61 2.24
2653 4982 5.385617 GTGCTTACACACATCTTTGCTAAG 58.614 41.667 1.04 1.04 46.61 2.18
2654 4983 5.356882 GTGCTTACACACATCTTTGCTAA 57.643 39.130 0.00 0.00 46.61 3.09
2656 4985 3.904136 GTGCTTACACACATCTTTGCT 57.096 42.857 0.00 0.00 46.61 3.91
2673 5002 4.674281 AGTAACATCCTTAGCTAGGTGC 57.326 45.455 4.27 0.00 45.03 5.01
2695 5024 8.664211 GGTAACTAAGCAGCAAGAGTTATTAT 57.336 34.615 13.78 0.00 36.91 1.28
2814 5143 8.714179 ACATGAAAACATAATGTGCATGAAAAG 58.286 29.630 15.49 0.00 37.38 2.27
2842 5171 5.954335 ACAATTGACGATTCCTTTTCCATC 58.046 37.500 13.59 0.00 0.00 3.51
2872 5201 6.515272 AGCAAGAAAAGTTTTCTCAACTCA 57.485 33.333 26.87 0.00 0.00 3.41
2884 5213 3.350833 CAGCCAGGATAGCAAGAAAAGT 58.649 45.455 0.00 0.00 0.00 2.66
2917 5246 4.128925 TCAATCTACTGCTAGGTGCTTG 57.871 45.455 0.00 0.00 43.37 4.01
2979 5308 6.479990 CGGACAAAGAACATCTTATATGAGCA 59.520 38.462 0.00 0.00 35.27 4.26
3028 5357 5.296780 GCTTGGCAAGTAATAGCACTATGAA 59.703 40.000 26.71 0.00 0.00 2.57
3125 5455 5.557891 AGTCAGCAAATCACAATAAGCTC 57.442 39.130 0.00 0.00 0.00 4.09
3130 5460 8.969260 ATTCAGATAGTCAGCAAATCACAATA 57.031 30.769 0.00 0.00 0.00 1.90
3245 5582 0.740737 CGGTCAATGCAGGGGAAATC 59.259 55.000 0.00 0.00 0.00 2.17
3298 5636 1.271926 GGCTTGGCCTCCTCAAAACTA 60.272 52.381 3.32 0.00 46.69 2.24
3345 5683 1.789464 CTGAACGGATGCTAGATTCGC 59.211 52.381 0.00 0.00 0.00 4.70
3419 5757 8.188139 TCATCTAGAAACAAAAACCAAGAACAC 58.812 33.333 0.00 0.00 0.00 3.32
3451 5791 6.038271 GCTTGACCTTCTCAAAACTTTCTGTA 59.962 38.462 0.00 0.00 38.47 2.74
3453 5793 5.277047 GCTTGACCTTCTCAAAACTTTCTG 58.723 41.667 0.00 0.00 38.47 3.02
3505 5845 3.333029 TCGAAACTGATGCCAGATTCA 57.667 42.857 13.27 1.96 46.37 2.57
3622 6142 8.725148 CAGAATCTGCTATGTATTGGTAAATCC 58.275 37.037 0.00 0.00 0.00 3.01
3624 6144 8.220559 ACCAGAATCTGCTATGTATTGGTAAAT 58.779 33.333 4.40 0.00 34.84 1.40
3628 6152 5.371526 CACCAGAATCTGCTATGTATTGGT 58.628 41.667 4.40 0.00 36.89 3.67
3632 6156 3.244700 GCCCACCAGAATCTGCTATGTAT 60.245 47.826 4.40 0.00 0.00 2.29
3633 6157 2.104792 GCCCACCAGAATCTGCTATGTA 59.895 50.000 4.40 0.00 0.00 2.29
3637 6161 0.913934 TGGCCCACCAGAATCTGCTA 60.914 55.000 4.40 0.00 42.67 3.49
3728 7400 9.517609 CGGCAACCAGAGTCTTATATAATATAC 57.482 37.037 0.00 0.00 0.00 1.47
3732 7404 6.041637 TCACGGCAACCAGAGTCTTATATAAT 59.958 38.462 0.00 0.00 0.00 1.28
3741 7890 1.668151 GGTCACGGCAACCAGAGTC 60.668 63.158 0.00 0.00 36.75 3.36
3743 7892 1.071471 AAGGTCACGGCAACCAGAG 59.929 57.895 6.00 0.00 39.39 3.35
3987 8136 9.679661 TTCTTGTTTCTTTATGGCATCTATGTA 57.320 29.630 1.65 0.00 0.00 2.29
3989 8138 9.859427 TTTTCTTGTTTCTTTATGGCATCTATG 57.141 29.630 1.65 0.00 0.00 2.23
4018 8167 9.503399 CTACAAAACTCTAGGGACTTGTTATTT 57.497 33.333 15.89 0.00 41.75 1.40
4019 8168 8.877195 TCTACAAAACTCTAGGGACTTGTTATT 58.123 33.333 15.89 0.00 41.75 1.40
4020 8169 8.431910 TCTACAAAACTCTAGGGACTTGTTAT 57.568 34.615 15.89 0.00 41.75 1.89
4021 8170 7.844493 TCTACAAAACTCTAGGGACTTGTTA 57.156 36.000 15.89 6.06 41.75 2.41
4022 8171 6.742559 TCTACAAAACTCTAGGGACTTGTT 57.257 37.500 15.89 4.89 41.75 2.83
4023 8172 6.742559 TTCTACAAAACTCTAGGGACTTGT 57.257 37.500 15.28 15.28 41.75 3.16
4024 8173 6.651225 CCTTTCTACAAAACTCTAGGGACTTG 59.349 42.308 0.00 1.56 41.75 3.16
4025 8174 6.557633 TCCTTTCTACAAAACTCTAGGGACTT 59.442 38.462 0.00 0.00 41.75 3.01
4026 8175 6.014413 GTCCTTTCTACAAAACTCTAGGGACT 60.014 42.308 0.00 0.00 46.37 3.85
4027 8176 6.164876 GTCCTTTCTACAAAACTCTAGGGAC 58.835 44.000 0.00 0.00 33.00 4.46
4028 8177 5.247792 GGTCCTTTCTACAAAACTCTAGGGA 59.752 44.000 0.00 0.00 0.00 4.20
4029 8178 5.248705 AGGTCCTTTCTACAAAACTCTAGGG 59.751 44.000 0.00 0.00 0.00 3.53
4030 8179 6.361768 AGGTCCTTTCTACAAAACTCTAGG 57.638 41.667 0.00 0.00 0.00 3.02
4031 8180 9.774413 TTTAAGGTCCTTTCTACAAAACTCTAG 57.226 33.333 10.04 0.00 0.00 2.43
4036 8185 8.127327 GTCAGTTTAAGGTCCTTTCTACAAAAC 58.873 37.037 10.04 12.55 0.00 2.43
4054 8203 8.219546 TGATCATGTTTTTGTCTGTCAGTTTA 57.780 30.769 0.00 0.00 0.00 2.01
4103 8252 2.301870 AGGACAGCCTTTTGTGTCGATA 59.698 45.455 0.00 0.00 43.90 2.92
4104 8253 1.072331 AGGACAGCCTTTTGTGTCGAT 59.928 47.619 0.00 0.00 43.90 3.59
4150 8299 1.595382 GATTGATGGGCGGTCCTCG 60.595 63.158 0.00 0.00 42.76 4.63
4165 8314 1.202879 TGAACCTGGTCTTTGGCGATT 60.203 47.619 0.00 0.00 0.00 3.34
4194 8343 5.521010 CACCGGAATTTGTTACGAAGCTATA 59.479 40.000 9.46 0.00 0.00 1.31
4203 8352 4.868734 CCTAGTCTCACCGGAATTTGTTAC 59.131 45.833 9.46 0.00 0.00 2.50
4208 8357 2.168728 GAGCCTAGTCTCACCGGAATTT 59.831 50.000 9.46 0.00 33.41 1.82
4222 8371 4.630644 ATATGGTTGGATGTGAGCCTAG 57.369 45.455 0.00 0.00 0.00 3.02
4260 8450 3.497262 AGTAGAAGCTTTGGTGTTAACGC 59.503 43.478 10.77 10.77 0.00 4.84
4297 8490 0.179234 TTGTCACTTCCGAACTGGCA 59.821 50.000 0.00 0.00 37.80 4.92
4376 8569 8.675705 TTCAAAATCTCGCTCATCCATTATTA 57.324 30.769 0.00 0.00 0.00 0.98


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

AutoCloner maintained by Alex Coulton.