Multiple sequence alignment - TraesCS3A01G354600

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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 TraesCS3A01G354600 chr3A 100.000 1981 0 0 719 2699 602273144 602271164 0.000000e+00 3659.0
1 TraesCS3A01G354600 chr3A 100.000 467 0 0 1 467 602273862 602273396 0.000000e+00 863.0
2 TraesCS3A01G354600 chr3A 83.542 480 50 19 1 466 602496313 602495849 3.210000e-114 422.0
3 TraesCS3A01G354600 chr3A 93.671 79 3 2 2596 2672 730328984 730329062 1.700000e-22 117.0
4 TraesCS3A01G354600 chr3D 93.909 1773 89 14 719 2488 460259261 460257505 0.000000e+00 2658.0
5 TraesCS3A01G354600 chr3D 90.110 91 9 0 1 91 460298315 460298225 4.720000e-23 119.0
6 TraesCS3A01G354600 chr3D 90.361 83 7 1 2601 2682 387711654 387711736 1.020000e-19 108.0
7 TraesCS3A01G354600 chr3B 94.118 1309 57 11 719 2020 610221685 610220390 0.000000e+00 1973.0
8 TraesCS3A01G354600 chr3B 88.918 388 24 10 2116 2488 610220387 610220004 6.810000e-126 460.0
9 TraesCS3A01G354600 chr3B 86.290 248 27 4 1 242 610224249 610224003 2.060000e-66 263.0
10 TraesCS3A01G354600 chr3B 95.714 70 3 0 2606 2675 449012440 449012371 2.200000e-21 113.0
11 TraesCS3A01G354600 chr1B 91.268 355 25 3 1127 1481 79979956 79980304 1.880000e-131 479.0
12 TraesCS3A01G354600 chr1B 90.223 358 29 3 1127 1484 122830464 122830815 1.890000e-126 462.0
13 TraesCS3A01G354600 chr1B 80.994 463 40 20 1520 1956 79980313 79980753 9.320000e-85 324.0
14 TraesCS3A01G354600 chr1B 100.000 28 0 0 2100 2127 327571710 327571683 5.000000e-03 52.8
15 TraesCS3A01G354600 chr1D 96.000 125 5 0 2485 2609 308456417 308456541 1.270000e-48 204.0
16 TraesCS3A01G354600 chr1D 92.500 80 6 0 2605 2684 491061100 491061021 6.110000e-22 115.0
17 TraesCS3A01G354600 chr1D 100.000 28 0 0 2100 2127 228044974 228044947 5.000000e-03 52.8
18 TraesCS3A01G354600 chr7D 94.444 126 7 0 2486 2611 31949675 31949800 7.620000e-46 195.0
19 TraesCS3A01G354600 chr7D 100.000 28 0 0 2094 2121 561921862 561921835 5.000000e-03 52.8
20 TraesCS3A01G354600 chr4D 95.833 120 5 0 2486 2605 503357915 503358034 7.620000e-46 195.0
21 TraesCS3A01G354600 chr4D 91.729 133 11 0 2479 2611 367720763 367720895 4.590000e-43 185.0
22 TraesCS3A01G354600 chr4D 96.774 31 1 0 2091 2121 241799876 241799906 5.000000e-03 52.8
23 TraesCS3A01G354600 chr4D 100.000 28 0 0 2100 2127 310388748 310388721 5.000000e-03 52.8
24 TraesCS3A01G354600 chr2A 95.833 120 5 0 2484 2603 606523806 606523687 7.620000e-46 195.0
25 TraesCS3A01G354600 chr2A 93.798 129 7 1 2477 2605 78845564 78845691 2.740000e-45 193.0
26 TraesCS3A01G354600 chr1A 95.833 120 5 0 2486 2605 208212650 208212531 7.620000e-46 195.0
27 TraesCS3A01G354600 chrUn 91.304 138 10 2 2470 2607 112678825 112678690 1.280000e-43 187.0
28 TraesCS3A01G354600 chr7B 91.791 134 10 1 2483 2615 81425110 81424977 4.590000e-43 185.0
29 TraesCS3A01G354600 chr7B 98.529 68 1 0 2605 2672 658481599 658481666 1.310000e-23 121.0
30 TraesCS3A01G354600 chr7B 97.101 69 2 0 2607 2675 695691605 695691537 1.700000e-22 117.0
31 TraesCS3A01G354600 chr6B 97.183 71 2 0 2605 2675 211637574 211637504 1.310000e-23 121.0
32 TraesCS3A01G354600 chr6B 97.015 67 2 0 2606 2672 642077033 642077099 2.200000e-21 113.0
33 TraesCS3A01G354600 chr6B 100.000 30 0 0 2083 2112 15103896 15103867 3.750000e-04 56.5
34 TraesCS3A01G354600 chr2D 95.890 73 3 0 2613 2685 629616963 629616891 4.720000e-23 119.0
35 TraesCS3A01G354600 chr6A 96.875 32 1 0 2091 2122 597446343 597446374 1.000000e-03 54.7


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 TraesCS3A01G354600 chr3A 602271164 602273862 2698 True 2261.000000 3659 100.000000 1 2699 2 chr3A.!!$R2 2698
1 TraesCS3A01G354600 chr3D 460257505 460259261 1756 True 2658.000000 2658 93.909000 719 2488 1 chr3D.!!$R1 1769
2 TraesCS3A01G354600 chr3B 610220004 610224249 4245 True 898.666667 1973 89.775333 1 2488 3 chr3B.!!$R2 2487
3 TraesCS3A01G354600 chr1B 79979956 79980753 797 False 401.500000 479 86.131000 1127 1956 2 chr1B.!!$F2 829

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
989 2982 0.676782 CGATCCGCCCCTTTTCTTGT 60.677 55.0 0.0 0.0 0.0 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2585 4625 0.038744 AGTACTCCCTCCGTCCGAAA 59.961 55.0 0.0 0.0 0.0 3.46 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
88 89 9.709495 AGACATTTTGTTATTACATGCACATTT 57.291 25.926 0.00 0.00 33.44 2.32
103 104 7.118101 ACATGCACATTTTTAATAGTTTGCCAG 59.882 33.333 0.00 0.00 0.00 4.85
140 145 9.657419 CATGATTTCTTTATAAGCCCAAGTTTT 57.343 29.630 0.00 0.00 0.00 2.43
142 147 9.705290 TGATTTCTTTATAAGCCCAAGTTTTTC 57.295 29.630 0.00 0.00 0.00 2.29
151 156 6.494893 AAGCCCAAGTTTTTCTTTCAAAAC 57.505 33.333 1.55 1.55 44.00 2.43
192 198 9.934190 AAACATGTTTCATTTCTTAAATTGCAC 57.066 25.926 18.13 0.00 0.00 4.57
196 202 9.934190 ATGTTTCATTTCTTAAATTGCACAAAC 57.066 25.926 0.00 0.00 0.00 2.93
197 203 8.113062 TGTTTCATTTCTTAAATTGCACAAACG 58.887 29.630 0.00 0.00 0.00 3.60
207 213 9.352163 CTTAAATTGCACAAACGTTATGAAAAC 57.648 29.630 14.84 0.33 0.00 2.43
216 222 8.891928 CACAAACGTTATGAAAACTCACAATAG 58.108 33.333 0.00 0.00 0.00 1.73
388 1106 7.576861 AAAGGAAGTGAAGATTAAAAACCGA 57.423 32.000 0.00 0.00 0.00 4.69
421 1139 6.622833 AAAAGAATAAAACCCGAAGAACGA 57.377 33.333 0.00 0.00 45.77 3.85
422 1140 6.622833 AAAGAATAAAACCCGAAGAACGAA 57.377 33.333 0.00 0.00 45.77 3.85
466 2454 1.880027 AGAGAAAAACGCCAGCGAAAT 59.120 42.857 20.32 1.36 42.83 2.17
774 2762 2.036475 CCCACGACAGATCTCCCTATTG 59.964 54.545 0.00 0.00 0.00 1.90
781 2769 2.301296 CAGATCTCCCTATTGTCGCCAT 59.699 50.000 0.00 0.00 0.00 4.40
782 2770 2.564947 AGATCTCCCTATTGTCGCCATC 59.435 50.000 0.00 0.00 0.00 3.51
951 2944 3.039588 CACGGAAACCACGTCCCG 61.040 66.667 0.00 0.00 43.58 5.14
989 2982 0.676782 CGATCCGCCCCTTTTCTTGT 60.677 55.000 0.00 0.00 0.00 3.16
1011 3004 0.676782 CAATCGAACCACCTGACCCC 60.677 60.000 0.00 0.00 0.00 4.95
1433 3427 7.346751 AGATGTTGTGTTACCTGAATGTTTT 57.653 32.000 0.00 0.00 0.00 2.43
1434 3428 8.458573 AGATGTTGTGTTACCTGAATGTTTTA 57.541 30.769 0.00 0.00 0.00 1.52
1472 3470 3.341823 CTTCCTTCTTGGTGTCTGGATG 58.658 50.000 0.00 0.00 37.07 3.51
1487 3485 2.422479 CTGGATGTCTGCTTTCATGGTG 59.578 50.000 0.00 0.00 0.00 4.17
1488 3486 1.133790 GGATGTCTGCTTTCATGGTGC 59.866 52.381 0.00 0.00 0.00 5.01
1491 3489 1.202794 TGTCTGCTTTCATGGTGCTGA 60.203 47.619 0.00 2.23 33.49 4.26
1498 3496 1.999648 TTCATGGTGCTGAAAAGCCT 58.000 45.000 0.00 0.00 32.35 4.58
1499 3497 1.250328 TCATGGTGCTGAAAAGCCTG 58.750 50.000 0.00 0.00 0.00 4.85
1500 3498 0.245539 CATGGTGCTGAAAAGCCTGG 59.754 55.000 0.00 0.00 0.00 4.45
1511 3509 5.454755 GCTGAAAAGCCTGGTCACCTATATA 60.455 44.000 0.00 0.00 0.00 0.86
1514 3512 4.559862 AAGCCTGGTCACCTATATATGC 57.440 45.455 0.00 0.00 0.00 3.14
1521 3519 7.268586 CCTGGTCACCTATATATGCTCAATAC 58.731 42.308 0.00 0.00 0.00 1.89
1714 3739 0.109132 GAACTGCCTTGATTTGCCCG 60.109 55.000 0.00 0.00 0.00 6.13
1729 3754 1.762471 CCCGGGTGGTTTCAGGTTA 59.238 57.895 14.18 0.00 0.00 2.85
1783 3808 4.454728 TTTTGCTCTCAGTTTTGCTGTT 57.545 36.364 0.00 0.00 45.23 3.16
1834 3859 1.854743 CTGGTCGTTAGATGCGTGATG 59.145 52.381 0.00 0.00 0.00 3.07
1857 3882 6.103330 TGATAGACTGCGTTGTAGCATTTTA 58.897 36.000 0.00 0.00 46.97 1.52
1907 3932 9.452287 TTTCAGTCATCATGATGTTCAAGAATA 57.548 29.630 30.01 18.12 39.72 1.75
1993 4018 4.433186 TGCAACTGGAAAATATTGGTCG 57.567 40.909 0.00 0.00 0.00 4.79
2054 4079 8.718734 GTCCGAATTACTTGTCTTAGATTTGTT 58.281 33.333 0.00 0.00 0.00 2.83
2084 4109 8.812972 ACAAGGATGTATCTAGACAAGTGTAAA 58.187 33.333 0.00 0.00 38.24 2.01
2086 4111 9.823647 AAGGATGTATCTAGACAAGTGTAAATG 57.176 33.333 0.00 0.00 31.83 2.32
2110 4135 7.270047 TGTAAGATAAGTAATTTGGGACGGAG 58.730 38.462 0.00 0.00 0.00 4.63
2225 4259 7.234577 AGACTTTATCTCTGACCTTTGAGACTT 59.765 37.037 0.00 0.00 41.40 3.01
2281 4315 4.022155 TGTTGGGGTAAAATAAACTTCCGC 60.022 41.667 0.00 0.00 0.00 5.54
2488 4528 9.173021 TGGATGATTTTTGTATTTCGATGTACT 57.827 29.630 8.58 0.00 0.00 2.73
2489 4529 9.651718 GGATGATTTTTGTATTTCGATGTACTC 57.348 33.333 8.58 0.00 0.00 2.59
2490 4530 9.651718 GATGATTTTTGTATTTCGATGTACTCC 57.348 33.333 8.58 0.00 0.00 3.85
2491 4531 7.981142 TGATTTTTGTATTTCGATGTACTCCC 58.019 34.615 8.58 0.00 0.00 4.30
2492 4532 7.827236 TGATTTTTGTATTTCGATGTACTCCCT 59.173 33.333 8.58 0.00 0.00 4.20
2493 4533 7.605410 TTTTTGTATTTCGATGTACTCCCTC 57.395 36.000 8.58 0.00 0.00 4.30
2494 4534 4.931661 TGTATTTCGATGTACTCCCTCC 57.068 45.455 8.58 0.00 0.00 4.30
2495 4535 3.317149 TGTATTTCGATGTACTCCCTCCG 59.683 47.826 8.58 0.00 0.00 4.63
2496 4536 1.843368 TTTCGATGTACTCCCTCCGT 58.157 50.000 0.00 0.00 0.00 4.69
2497 4537 1.386533 TTCGATGTACTCCCTCCGTC 58.613 55.000 0.00 0.00 0.00 4.79
2498 4538 0.545171 TCGATGTACTCCCTCCGTCT 59.455 55.000 0.00 0.00 0.00 4.18
2499 4539 0.663688 CGATGTACTCCCTCCGTCTG 59.336 60.000 0.00 0.00 0.00 3.51
2500 4540 1.746171 CGATGTACTCCCTCCGTCTGA 60.746 57.143 0.00 0.00 0.00 3.27
2501 4541 2.376109 GATGTACTCCCTCCGTCTGAA 58.624 52.381 0.00 0.00 0.00 3.02
2502 4542 2.297698 TGTACTCCCTCCGTCTGAAA 57.702 50.000 0.00 0.00 0.00 2.69
2503 4543 2.600790 TGTACTCCCTCCGTCTGAAAA 58.399 47.619 0.00 0.00 0.00 2.29
2504 4544 2.967201 TGTACTCCCTCCGTCTGAAAAA 59.033 45.455 0.00 0.00 0.00 1.94
2532 4572 3.744660 CCCTCAAATGGGTGTATCTAGC 58.255 50.000 0.00 0.00 42.25 3.42
2533 4573 3.136443 CCCTCAAATGGGTGTATCTAGCA 59.864 47.826 0.00 0.00 42.25 3.49
2534 4574 4.130118 CCTCAAATGGGTGTATCTAGCAC 58.870 47.826 0.00 0.00 36.22 4.40
2556 4596 5.986135 CACCAAGTTAGTGCTAGATACATCC 59.014 44.000 0.00 0.00 0.00 3.51
2557 4597 5.661312 ACCAAGTTAGTGCTAGATACATCCA 59.339 40.000 0.00 0.00 0.00 3.41
2558 4598 6.327626 ACCAAGTTAGTGCTAGATACATCCAT 59.672 38.462 0.00 0.00 0.00 3.41
2559 4599 7.147479 ACCAAGTTAGTGCTAGATACATCCATT 60.147 37.037 0.00 0.00 0.00 3.16
2560 4600 7.716998 CCAAGTTAGTGCTAGATACATCCATTT 59.283 37.037 0.00 0.00 0.00 2.32
2561 4601 8.554528 CAAGTTAGTGCTAGATACATCCATTTG 58.445 37.037 0.00 0.00 0.00 2.32
2562 4602 8.023021 AGTTAGTGCTAGATACATCCATTTGA 57.977 34.615 0.00 0.00 0.00 2.69
2563 4603 8.147058 AGTTAGTGCTAGATACATCCATTTGAG 58.853 37.037 0.00 0.00 0.00 3.02
2564 4604 5.862845 AGTGCTAGATACATCCATTTGAGG 58.137 41.667 0.00 0.00 0.00 3.86
2565 4605 5.604231 AGTGCTAGATACATCCATTTGAGGA 59.396 40.000 0.00 0.00 43.01 3.71
2566 4606 6.100279 AGTGCTAGATACATCCATTTGAGGAA 59.900 38.462 0.00 0.00 41.92 3.36
2567 4607 6.203723 GTGCTAGATACATCCATTTGAGGAAC 59.796 42.308 0.00 0.00 41.92 3.62
2568 4608 6.126796 TGCTAGATACATCCATTTGAGGAACA 60.127 38.462 0.00 0.00 41.92 3.18
2569 4609 6.767902 GCTAGATACATCCATTTGAGGAACAA 59.232 38.462 0.00 0.00 41.92 2.83
2570 4610 7.041508 GCTAGATACATCCATTTGAGGAACAAG 60.042 40.741 0.00 0.00 41.92 3.16
2571 4611 6.725364 AGATACATCCATTTGAGGAACAAGT 58.275 36.000 0.00 0.00 41.92 3.16
2572 4612 7.177878 AGATACATCCATTTGAGGAACAAGTT 58.822 34.615 0.00 0.00 41.92 2.66
2573 4613 7.671398 AGATACATCCATTTGAGGAACAAGTTT 59.329 33.333 0.00 0.00 41.92 2.66
2574 4614 5.846203 ACATCCATTTGAGGAACAAGTTTG 58.154 37.500 0.00 0.00 41.92 2.93
2575 4615 4.935352 TCCATTTGAGGAACAAGTTTGG 57.065 40.909 0.00 0.00 39.77 3.28
2576 4616 3.640967 TCCATTTGAGGAACAAGTTTGGG 59.359 43.478 0.00 0.00 39.77 4.12
2577 4617 3.640967 CCATTTGAGGAACAAGTTTGGGA 59.359 43.478 0.00 0.00 39.77 4.37
2578 4618 4.501400 CCATTTGAGGAACAAGTTTGGGAC 60.501 45.833 0.00 0.00 39.77 4.46
2579 4619 3.374042 TTGAGGAACAAGTTTGGGACA 57.626 42.857 0.00 0.00 34.20 4.02
2580 4620 3.702792 TTGAGGAACAAGTTTGGGACAA 58.297 40.909 0.00 0.00 37.48 3.18
2581 4621 3.699038 TTGAGGAACAAGTTTGGGACAAG 59.301 43.478 0.00 0.00 37.48 3.16
2582 4622 4.812787 TTGAGGAACAAGTTTGGGACAAGT 60.813 41.667 0.00 0.00 37.48 3.16
2583 4623 6.276241 TTGAGGAACAAGTTTGGGACAAGTT 61.276 40.000 0.00 0.00 37.48 2.66
2584 4624 7.703888 TTGAGGAACAAGTTTGGGACAAGTTT 61.704 38.462 0.00 0.00 37.48 2.66
2585 4625 9.099722 TTGAGGAACAAGTTTGGGACAAGTTTT 62.100 37.037 0.00 0.00 37.48 2.43
2601 4641 2.444281 TTTTTCGGACGGAGGGAGT 58.556 52.632 0.00 0.00 0.00 3.85
2602 4642 1.631405 TTTTTCGGACGGAGGGAGTA 58.369 50.000 0.00 0.00 0.00 2.59
2603 4643 0.890683 TTTTCGGACGGAGGGAGTAC 59.109 55.000 0.00 0.00 0.00 2.73
2604 4644 0.038744 TTTCGGACGGAGGGAGTACT 59.961 55.000 0.00 0.00 0.00 2.73
2605 4645 0.038744 TTCGGACGGAGGGAGTACTT 59.961 55.000 0.00 0.00 0.00 2.24
2606 4646 0.038744 TCGGACGGAGGGAGTACTTT 59.961 55.000 0.00 0.00 0.00 2.66
2607 4647 0.893447 CGGACGGAGGGAGTACTTTT 59.107 55.000 0.00 0.00 0.00 2.27
2608 4648 1.274447 CGGACGGAGGGAGTACTTTTT 59.726 52.381 0.00 0.00 0.00 1.94
2630 4670 2.588027 TTTGAAACGAAAGGGGTTGC 57.412 45.000 0.00 0.00 0.00 4.17
2631 4671 0.747852 TTGAAACGAAAGGGGTTGCC 59.252 50.000 0.00 0.00 0.00 4.52
2632 4672 1.110518 TGAAACGAAAGGGGTTGCCC 61.111 55.000 0.00 0.00 44.51 5.36
2648 4688 4.311700 CCCCCTGCCCAAACTTTT 57.688 55.556 0.00 0.00 0.00 2.27
2649 4689 2.538790 CCCCCTGCCCAAACTTTTT 58.461 52.632 0.00 0.00 0.00 1.94
2650 4690 1.723288 CCCCCTGCCCAAACTTTTTA 58.277 50.000 0.00 0.00 0.00 1.52
2651 4691 2.265367 CCCCCTGCCCAAACTTTTTAT 58.735 47.619 0.00 0.00 0.00 1.40
2652 4692 2.642311 CCCCCTGCCCAAACTTTTTATT 59.358 45.455 0.00 0.00 0.00 1.40
2653 4693 3.841255 CCCCCTGCCCAAACTTTTTATTA 59.159 43.478 0.00 0.00 0.00 0.98
2654 4694 4.287326 CCCCCTGCCCAAACTTTTTATTAA 59.713 41.667 0.00 0.00 0.00 1.40
2655 4695 5.221945 CCCCCTGCCCAAACTTTTTATTAAA 60.222 40.000 0.00 0.00 0.00 1.52
2656 4696 6.299922 CCCCTGCCCAAACTTTTTATTAAAA 58.700 36.000 0.00 0.00 0.00 1.52
2657 4697 6.773200 CCCCTGCCCAAACTTTTTATTAAAAA 59.227 34.615 12.48 12.48 37.99 1.94
2675 4715 2.749280 AAAGCAAAGGCAACCATAGC 57.251 45.000 0.00 0.00 44.61 2.97
2676 4716 1.631405 AAGCAAAGGCAACCATAGCA 58.369 45.000 0.00 0.00 44.61 3.49
2677 4717 1.180029 AGCAAAGGCAACCATAGCAG 58.820 50.000 0.00 0.00 44.61 4.24
2678 4718 1.176527 GCAAAGGCAACCATAGCAGA 58.823 50.000 0.00 0.00 40.72 4.26
2679 4719 1.135286 GCAAAGGCAACCATAGCAGAC 60.135 52.381 0.00 0.00 40.72 3.51
2680 4720 2.440409 CAAAGGCAACCATAGCAGACT 58.560 47.619 0.00 0.00 37.17 3.24
2681 4721 2.119801 AAGGCAACCATAGCAGACTG 57.880 50.000 0.00 0.00 37.17 3.51
2682 4722 0.987294 AGGCAACCATAGCAGACTGT 59.013 50.000 3.99 0.00 37.17 3.55
2683 4723 1.352352 AGGCAACCATAGCAGACTGTT 59.648 47.619 3.99 0.00 37.17 3.16
2684 4724 2.162681 GGCAACCATAGCAGACTGTTT 58.837 47.619 3.99 0.00 0.00 2.83
2685 4725 2.558359 GGCAACCATAGCAGACTGTTTT 59.442 45.455 3.99 0.00 0.00 2.43
2686 4726 3.005791 GGCAACCATAGCAGACTGTTTTT 59.994 43.478 3.99 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 9.793259 ATGGTCGTGTCCTTTAATAATATTGAT 57.207 29.630 0.00 0.00 0.00 2.57
31 32 7.513371 TTACAAAATGGTCGTGTCCTTTAAT 57.487 32.000 0.00 0.00 0.00 1.40
37 38 4.973663 CAGTTTTACAAAATGGTCGTGTCC 59.026 41.667 0.00 0.00 0.00 4.02
169 175 9.932699 TTTGTGCAATTTAAGAAATGAAACATG 57.067 25.926 0.00 0.00 0.00 3.21
172 178 8.113675 ACGTTTGTGCAATTTAAGAAATGAAAC 58.886 29.630 0.00 0.00 0.00 2.78
175 181 7.763172 AACGTTTGTGCAATTTAAGAAATGA 57.237 28.000 0.00 0.00 0.00 2.57
177 183 9.469807 TCATAACGTTTGTGCAATTTAAGAAAT 57.530 25.926 5.91 0.00 0.00 2.17
181 187 9.352163 GTTTTCATAACGTTTGTGCAATTTAAG 57.648 29.630 5.91 0.00 0.00 1.85
183 189 8.635877 AGTTTTCATAACGTTTGTGCAATTTA 57.364 26.923 5.91 0.00 0.00 1.40
186 192 6.198216 GTGAGTTTTCATAACGTTTGTGCAAT 59.802 34.615 5.91 0.00 35.39 3.56
188 194 5.031578 GTGAGTTTTCATAACGTTTGTGCA 58.968 37.500 5.91 0.00 35.39 4.57
189 195 5.031578 TGTGAGTTTTCATAACGTTTGTGC 58.968 37.500 5.91 0.00 35.39 4.57
190 196 7.678194 ATTGTGAGTTTTCATAACGTTTGTG 57.322 32.000 5.91 6.57 37.27 3.33
191 197 8.832521 TCTATTGTGAGTTTTCATAACGTTTGT 58.167 29.630 5.91 0.00 37.27 2.83
192 198 9.103048 GTCTATTGTGAGTTTTCATAACGTTTG 57.897 33.333 5.91 5.11 37.27 2.93
315 1033 8.394040 TCTTCTTTTCAGGGATTTCCTATTCTT 58.606 33.333 0.00 0.00 46.12 2.52
322 1040 6.901081 TTCTTCTTCTTTTCAGGGATTTCC 57.099 37.500 0.00 0.00 0.00 3.13
371 1089 9.940166 TTTACTCTTTCGGTTTTTAATCTTCAC 57.060 29.630 0.00 0.00 0.00 3.18
428 1146 6.846325 TTCTCTTCGTTTTTCCTTTCTCTC 57.154 37.500 0.00 0.00 0.00 3.20
435 1153 4.348656 GCGTTTTTCTCTTCGTTTTTCCT 58.651 39.130 0.00 0.00 0.00 3.36
443 1161 0.451135 CGCTGGCGTTTTTCTCTTCG 60.451 55.000 6.83 0.00 34.35 3.79
444 1162 0.865769 TCGCTGGCGTTTTTCTCTTC 59.134 50.000 14.55 0.00 40.74 2.87
445 1163 1.305201 TTCGCTGGCGTTTTTCTCTT 58.695 45.000 14.55 0.00 40.74 2.85
447 1165 2.331809 ATTTCGCTGGCGTTTTTCTC 57.668 45.000 14.55 0.00 40.74 2.87
774 2762 1.064946 CCGTGAGAGAGATGGCGAC 59.935 63.158 0.00 0.00 0.00 5.19
781 2769 1.340211 GGAAGAGGACCGTGAGAGAGA 60.340 57.143 0.00 0.00 0.00 3.10
782 2770 1.099689 GGAAGAGGACCGTGAGAGAG 58.900 60.000 0.00 0.00 0.00 3.20
857 2848 2.721167 CGAGAAGGATGGGTGCGGA 61.721 63.158 0.00 0.00 0.00 5.54
951 2944 4.650377 GGATGGATCTGGGGCGCC 62.650 72.222 21.18 21.18 0.00 6.53
989 2982 1.276989 GGTCAGGTGGTTCGATTGGTA 59.723 52.381 0.00 0.00 0.00 3.25
1011 3004 0.977395 ACCAAGAAAGGAGAGGACGG 59.023 55.000 0.00 0.00 0.00 4.79
1207 3200 2.613506 CGGGTGCCGGTTGAAGAAC 61.614 63.158 1.90 0.00 44.15 3.01
1270 3263 3.873883 GGTGCGCTGCTGATCTGC 61.874 66.667 16.98 16.98 36.43 4.26
1377 3370 4.348863 ACTCAGAAGTTCTGCAACTGAT 57.651 40.909 25.31 5.09 42.45 2.90
1378 3371 3.827008 ACTCAGAAGTTCTGCAACTGA 57.173 42.857 25.31 8.74 42.45 3.41
1472 3470 1.527034 TCAGCACCATGAAAGCAGAC 58.473 50.000 0.00 0.00 0.00 3.51
1487 3485 0.538287 AGGTGACCAGGCTTTTCAGC 60.538 55.000 3.63 13.86 46.52 4.26
1488 3486 2.859165 TAGGTGACCAGGCTTTTCAG 57.141 50.000 3.63 0.00 0.00 3.02
1491 3489 5.073691 AGCATATATAGGTGACCAGGCTTTT 59.926 40.000 3.63 0.00 0.00 2.27
1498 3496 6.127451 CCGTATTGAGCATATATAGGTGACCA 60.127 42.308 3.63 0.00 0.00 4.02
1499 3497 6.273825 CCGTATTGAGCATATATAGGTGACC 58.726 44.000 0.00 0.00 0.00 4.02
1500 3498 6.273825 CCCGTATTGAGCATATATAGGTGAC 58.726 44.000 0.00 0.00 0.00 3.67
1511 3509 1.097547 GCACTGCCCGTATTGAGCAT 61.098 55.000 0.00 0.00 35.64 3.79
1514 3512 3.813596 GGCACTGCCCGTATTGAG 58.186 61.111 9.13 0.00 44.06 3.02
1554 3554 3.875727 ACATGATAGAACTGAGCACATGC 59.124 43.478 0.00 0.00 37.66 4.06
1570 3570 9.715121 AAGCATTTAGTTTCAAAATCACATGAT 57.285 25.926 0.00 0.00 36.07 2.45
1714 3739 1.886542 CAGCTTAACCTGAAACCACCC 59.113 52.381 0.00 0.00 34.77 4.61
1729 3754 5.534654 TGTAGAAAATTTGTAGGCACAGCTT 59.465 36.000 0.00 0.00 35.67 3.74
1834 3859 5.470845 AAAATGCTACAACGCAGTCTATC 57.529 39.130 0.00 0.00 45.00 2.08
1857 3882 5.833131 ACAAACAAACACCAGAGATACCAAT 59.167 36.000 0.00 0.00 0.00 3.16
1926 3951 2.832563 TGATGAACTCAGAACGCACAA 58.167 42.857 0.00 0.00 0.00 3.33
1927 3952 2.524569 TGATGAACTCAGAACGCACA 57.475 45.000 0.00 0.00 0.00 4.57
2054 4079 6.892456 ACTTGTCTAGATACATCCTTGTCTGA 59.108 38.462 0.00 0.00 37.28 3.27
2061 4086 8.982723 ACATTTACACTTGTCTAGATACATCCT 58.017 33.333 0.00 0.00 0.00 3.24
2084 4109 7.798071 TCCGTCCCAAATTACTTATCTTACAT 58.202 34.615 0.00 0.00 0.00 2.29
2086 4111 6.704937 CCTCCGTCCCAAATTACTTATCTTAC 59.295 42.308 0.00 0.00 0.00 2.34
2092 4117 3.452878 TCCCTCCGTCCCAAATTACTTA 58.547 45.455 0.00 0.00 0.00 2.24
2110 4135 2.952310 GCCACCTCAATCAAATACTCCC 59.048 50.000 0.00 0.00 0.00 4.30
2197 4231 6.721668 TCTCAAAGGTCAGAGATAAAGTCTGA 59.278 38.462 0.00 0.00 46.57 3.27
2225 4259 5.249622 TCTGAATACATGTTTGGTACCCTGA 59.750 40.000 10.07 0.00 0.00 3.86
2281 4315 4.381718 GCCGTATAACTAGGGGAGCATAAG 60.382 50.000 0.00 0.00 34.15 1.73
2342 4377 4.020128 AGACATAGTGGTTGAAGGTTCTCC 60.020 45.833 0.00 0.00 0.00 3.71
2356 4391 4.012374 AGCCCAAATGTTGAGACATAGTG 58.988 43.478 0.00 0.00 45.58 2.74
2390 4430 4.657814 ACAATGGTGGGACAGAAGTATT 57.342 40.909 0.00 0.00 41.80 1.89
2512 4552 4.130118 GTGCTAGATACACCCATTTGAGG 58.870 47.826 0.00 0.00 31.67 3.86
2532 4572 5.986135 GGATGTATCTAGCACTAACTTGGTG 59.014 44.000 0.97 0.97 37.70 4.17
2533 4573 5.661312 TGGATGTATCTAGCACTAACTTGGT 59.339 40.000 0.00 0.00 0.00 3.67
2534 4574 6.161855 TGGATGTATCTAGCACTAACTTGG 57.838 41.667 0.00 0.00 0.00 3.61
2535 4575 8.554528 CAAATGGATGTATCTAGCACTAACTTG 58.445 37.037 0.00 0.00 0.00 3.16
2536 4576 8.486210 TCAAATGGATGTATCTAGCACTAACTT 58.514 33.333 0.00 0.00 0.00 2.66
2537 4577 8.023021 TCAAATGGATGTATCTAGCACTAACT 57.977 34.615 0.00 0.00 0.00 2.24
2538 4578 7.386299 CCTCAAATGGATGTATCTAGCACTAAC 59.614 40.741 0.00 0.00 0.00 2.34
2539 4579 7.290014 TCCTCAAATGGATGTATCTAGCACTAA 59.710 37.037 0.00 0.00 0.00 2.24
2540 4580 6.782494 TCCTCAAATGGATGTATCTAGCACTA 59.218 38.462 0.00 0.00 0.00 2.74
2541 4581 5.604231 TCCTCAAATGGATGTATCTAGCACT 59.396 40.000 0.00 0.00 0.00 4.40
2542 4582 5.858381 TCCTCAAATGGATGTATCTAGCAC 58.142 41.667 0.00 0.00 0.00 4.40
2543 4583 6.126796 TGTTCCTCAAATGGATGTATCTAGCA 60.127 38.462 0.00 0.00 35.83 3.49
2544 4584 6.291377 TGTTCCTCAAATGGATGTATCTAGC 58.709 40.000 0.00 0.00 35.83 3.42
2545 4585 7.989741 ACTTGTTCCTCAAATGGATGTATCTAG 59.010 37.037 0.00 0.00 35.83 2.43
2546 4586 7.861629 ACTTGTTCCTCAAATGGATGTATCTA 58.138 34.615 0.00 0.00 35.83 1.98
2547 4587 6.725364 ACTTGTTCCTCAAATGGATGTATCT 58.275 36.000 0.00 0.00 35.83 1.98
2548 4588 7.396540 AACTTGTTCCTCAAATGGATGTATC 57.603 36.000 0.00 0.00 35.83 2.24
2549 4589 7.309990 CCAAACTTGTTCCTCAAATGGATGTAT 60.310 37.037 0.00 0.00 36.92 2.29
2550 4590 6.015519 CCAAACTTGTTCCTCAAATGGATGTA 60.016 38.462 0.00 0.00 36.92 2.29
2551 4591 5.221501 CCAAACTTGTTCCTCAAATGGATGT 60.222 40.000 0.00 0.00 36.92 3.06
2552 4592 5.232463 CCAAACTTGTTCCTCAAATGGATG 58.768 41.667 0.00 0.00 36.92 3.51
2553 4593 4.284234 CCCAAACTTGTTCCTCAAATGGAT 59.716 41.667 0.00 0.00 36.92 3.41
2554 4594 3.640967 CCCAAACTTGTTCCTCAAATGGA 59.359 43.478 0.00 0.00 36.92 3.41
2555 4595 3.640967 TCCCAAACTTGTTCCTCAAATGG 59.359 43.478 0.00 0.00 35.48 3.16
2556 4596 4.099266 TGTCCCAAACTTGTTCCTCAAATG 59.901 41.667 0.00 0.00 35.48 2.32
2557 4597 4.285863 TGTCCCAAACTTGTTCCTCAAAT 58.714 39.130 0.00 0.00 35.48 2.32
2558 4598 3.702792 TGTCCCAAACTTGTTCCTCAAA 58.297 40.909 0.00 0.00 35.48 2.69
2559 4599 3.374042 TGTCCCAAACTTGTTCCTCAA 57.626 42.857 0.00 0.00 34.61 3.02
2560 4600 3.287222 CTTGTCCCAAACTTGTTCCTCA 58.713 45.455 0.00 0.00 0.00 3.86
2561 4601 3.288092 ACTTGTCCCAAACTTGTTCCTC 58.712 45.455 0.00 0.00 0.00 3.71
2562 4602 3.382083 ACTTGTCCCAAACTTGTTCCT 57.618 42.857 0.00 0.00 0.00 3.36
2563 4603 4.465632 AAACTTGTCCCAAACTTGTTCC 57.534 40.909 0.00 0.00 0.00 3.62
2583 4623 1.273327 GTACTCCCTCCGTCCGAAAAA 59.727 52.381 0.00 0.00 0.00 1.94
2584 4624 0.890683 GTACTCCCTCCGTCCGAAAA 59.109 55.000 0.00 0.00 0.00 2.29
2585 4625 0.038744 AGTACTCCCTCCGTCCGAAA 59.961 55.000 0.00 0.00 0.00 3.46
2586 4626 0.038744 AAGTACTCCCTCCGTCCGAA 59.961 55.000 0.00 0.00 0.00 4.30
2587 4627 0.038744 AAAGTACTCCCTCCGTCCGA 59.961 55.000 0.00 0.00 0.00 4.55
2588 4628 0.893447 AAAAGTACTCCCTCCGTCCG 59.107 55.000 0.00 0.00 0.00 4.79
2609 4649 3.263261 GCAACCCCTTTCGTTTCAAAAA 58.737 40.909 0.00 0.00 0.00 1.94
2610 4650 2.418884 GGCAACCCCTTTCGTTTCAAAA 60.419 45.455 0.00 0.00 0.00 2.44
2611 4651 1.137282 GGCAACCCCTTTCGTTTCAAA 59.863 47.619 0.00 0.00 0.00 2.69
2612 4652 0.747852 GGCAACCCCTTTCGTTTCAA 59.252 50.000 0.00 0.00 0.00 2.69
2613 4653 2.421220 GGCAACCCCTTTCGTTTCA 58.579 52.632 0.00 0.00 0.00 2.69
2631 4671 1.723288 TAAAAAGTTTGGGCAGGGGG 58.277 50.000 0.00 0.00 0.00 5.40
2632 4672 5.491323 TTAATAAAAAGTTTGGGCAGGGG 57.509 39.130 0.00 0.00 0.00 4.79
2633 4673 7.809546 TTTTTAATAAAAAGTTTGGGCAGGG 57.190 32.000 6.80 0.00 36.02 4.45
2654 4694 3.181456 TGCTATGGTTGCCTTTGCTTTTT 60.181 39.130 8.36 0.00 38.71 1.94
2655 4695 2.368221 TGCTATGGTTGCCTTTGCTTTT 59.632 40.909 8.36 0.00 38.71 2.27
2656 4696 1.969923 TGCTATGGTTGCCTTTGCTTT 59.030 42.857 8.36 0.00 38.71 3.51
2657 4697 1.547372 CTGCTATGGTTGCCTTTGCTT 59.453 47.619 8.36 0.00 38.71 3.91
2658 4698 1.180029 CTGCTATGGTTGCCTTTGCT 58.820 50.000 8.36 0.00 38.71 3.91
2659 4699 1.135286 GTCTGCTATGGTTGCCTTTGC 60.135 52.381 0.00 0.00 38.26 3.68
2660 4700 2.163010 CAGTCTGCTATGGTTGCCTTTG 59.837 50.000 0.00 0.00 0.00 2.77
2661 4701 2.224867 ACAGTCTGCTATGGTTGCCTTT 60.225 45.455 0.00 0.00 0.00 3.11
2662 4702 1.352352 ACAGTCTGCTATGGTTGCCTT 59.648 47.619 0.00 0.00 0.00 4.35
2663 4703 0.987294 ACAGTCTGCTATGGTTGCCT 59.013 50.000 0.00 0.00 0.00 4.75
2664 4704 1.826385 AACAGTCTGCTATGGTTGCC 58.174 50.000 0.00 0.00 0.00 4.52
2665 4705 3.923017 AAAACAGTCTGCTATGGTTGC 57.077 42.857 0.00 0.00 0.00 4.17


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

AutoCloner maintained by Alex Coulton.