Multiple sequence alignment - TraesCS2B01G238000

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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 TraesCS2B01G238000 chr2B 100.000 4200 0 0 1 4200 239198688 239194489 0.000000e+00 7757.0
1 TraesCS2B01G238000 chr2D 93.684 3578 113 45 674 4200 183379735 183376220 0.000000e+00 5251.0
2 TraesCS2B01G238000 chr2D 90.691 376 29 5 271 640 183380093 183379718 2.920000e-136 496.0
3 TraesCS2B01G238000 chr2D 97.727 44 0 1 3932 3975 122866158 122866200 1.620000e-09 75.0
4 TraesCS2B01G238000 chr2A 92.604 1974 77 25 680 2625 197793276 197791344 0.000000e+00 2772.0
5 TraesCS2B01G238000 chr2A 87.361 1258 33 40 2755 3917 197791345 197790119 0.000000e+00 1327.0
6 TraesCS2B01G238000 chr2A 88.889 1035 57 26 2214 3206 619125394 619126412 0.000000e+00 1221.0
7 TraesCS2B01G238000 chr2A 88.042 669 48 8 1 640 197793930 197793265 0.000000e+00 763.0
8 TraesCS2B01G238000 chr2A 89.076 357 10 9 3844 4200 197790119 197789792 2.340000e-112 416.0
9 TraesCS2B01G238000 chr2A 89.369 301 13 10 2214 2501 460938237 460937943 1.110000e-95 361.0
10 TraesCS2B01G238000 chr2A 88.475 295 10 9 2930 3206 481011343 481011055 6.730000e-88 335.0
11 TraesCS2B01G238000 chr2A 94.872 39 1 1 3932 3970 778918518 778918481 4.530000e-05 60.2
12 TraesCS2B01G238000 chr7A 88.900 1036 57 27 2214 3206 706110851 706109831 0.000000e+00 1223.0
13 TraesCS2B01G238000 chr7A 89.978 449 16 11 2780 3206 205042377 205041936 1.710000e-153 553.0
14 TraesCS2B01G238000 chr4A 88.910 1037 56 28 2214 3206 480996352 480997373 0.000000e+00 1223.0
15 TraesCS2B01G238000 chr5A 88.536 1038 59 27 2211 3206 458455758 458456777 0.000000e+00 1203.0
16 TraesCS2B01G238000 chr5A 88.417 1036 62 30 2214 3206 435166312 435167332 0.000000e+00 1195.0
17 TraesCS2B01G238000 chr5A 87.923 414 35 8 2363 2763 234866132 234866543 1.370000e-129 473.0
18 TraesCS2B01G238000 chr5A 86.517 356 24 12 2214 2552 461796873 461796525 1.840000e-98 370.0
19 TraesCS2B01G238000 chr5A 87.926 323 13 11 2903 3206 234866539 234866854 1.440000e-94 357.0
20 TraesCS2B01G238000 chr5A 80.402 199 24 11 96 282 542010482 542010287 2.040000e-28 137.0
21 TraesCS2B01G238000 chr5A 81.208 149 19 3 84 224 561110946 561111093 1.230000e-20 111.0
22 TraesCS2B01G238000 chr1A 89.833 718 38 17 2514 3206 204558600 204557893 0.000000e+00 889.0
23 TraesCS2B01G238000 chr1A 79.621 211 28 11 84 282 394425653 394425860 2.040000e-28 137.0
24 TraesCS2B01G238000 chr1A 79.048 210 30 10 84 282 394514015 394514221 9.470000e-27 132.0
25 TraesCS2B01G238000 chr3B 78.912 147 22 7 91 230 116113239 116113095 1.610000e-14 91.6
26 TraesCS2B01G238000 chr5D 97.368 38 1 0 641 678 540261763 540261800 9.750000e-07 65.8
27 TraesCS2B01G238000 chr3D 95.238 42 1 1 3932 3973 250918759 250918799 9.750000e-07 65.8
28 TraesCS2B01G238000 chr1D 94.737 38 1 1 3937 3974 325484529 325484493 1.630000e-04 58.4
29 TraesCS2B01G238000 chr1B 94.737 38 1 1 3937 3974 437599741 437599705 1.630000e-04 58.4
30 TraesCS2B01G238000 chr4B 94.595 37 1 1 3932 3968 652000978 652001013 5.870000e-04 56.5


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 TraesCS2B01G238000 chr2B 239194489 239198688 4199 True 7757.0 7757 100.00000 1 4200 1 chr2B.!!$R1 4199
1 TraesCS2B01G238000 chr2D 183376220 183380093 3873 True 2873.5 5251 92.18750 271 4200 2 chr2D.!!$R1 3929
2 TraesCS2B01G238000 chr2A 197789792 197793930 4138 True 1319.5 2772 89.27075 1 4200 4 chr2A.!!$R4 4199
3 TraesCS2B01G238000 chr2A 619125394 619126412 1018 False 1221.0 1221 88.88900 2214 3206 1 chr2A.!!$F1 992
4 TraesCS2B01G238000 chr7A 706109831 706110851 1020 True 1223.0 1223 88.90000 2214 3206 1 chr7A.!!$R2 992
5 TraesCS2B01G238000 chr4A 480996352 480997373 1021 False 1223.0 1223 88.91000 2214 3206 1 chr4A.!!$F1 992
6 TraesCS2B01G238000 chr5A 458455758 458456777 1019 False 1203.0 1203 88.53600 2211 3206 1 chr5A.!!$F2 995
7 TraesCS2B01G238000 chr5A 435166312 435167332 1020 False 1195.0 1195 88.41700 2214 3206 1 chr5A.!!$F1 992
8 TraesCS2B01G238000 chr5A 234866132 234866854 722 False 415.0 473 87.92450 2363 3206 2 chr5A.!!$F4 843
9 TraesCS2B01G238000 chr1A 204557893 204558600 707 True 889.0 889 89.83300 2514 3206 1 chr1A.!!$R1 692

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
590 621 0.591170 ACAAATCAAGCAACGGTCGG 59.409 50.0 0.0 0.00 0.0 4.79 F
1643 1685 0.809241 CGTCCAATCAGAGCAGCTCC 60.809 60.0 19.4 1.14 0.0 4.70 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1721 1763 0.322456 TCGAATCAGCAAACTGGGGG 60.322 55.0 0.00 0.0 44.59 5.40 R
3593 3721 0.336392 AGCCAAGGAAGGAATTCCCC 59.664 55.0 21.22 15.6 42.06 4.81 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
42 43 8.732746 ACACTAAATATTACTCCCATTGTGTC 57.267 34.615 0.00 0.00 0.00 3.67
54 55 4.141274 TCCCATTGTGTCAGAAAAGAAGGA 60.141 41.667 0.00 0.00 0.00 3.36
91 92 9.168451 TGAAGTCAAACACTATAAAGTTTCACA 57.832 29.630 6.52 0.00 35.90 3.58
212 219 5.492895 TGCTGACATTTTCTATAAACGGGA 58.507 37.500 0.00 0.00 0.00 5.14
224 231 6.228258 TCTATAAACGGGATCAAACTATGCC 58.772 40.000 0.00 0.00 34.19 4.40
225 232 3.366052 AAACGGGATCAAACTATGCCT 57.634 42.857 0.00 0.00 35.32 4.75
274 282 4.352893 ACCTTATTTTCATGAACAGGGGG 58.647 43.478 19.32 15.74 0.00 5.40
292 300 5.473504 CAGGGGGAGTATATTTATGCAACAC 59.526 44.000 0.00 0.00 0.00 3.32
364 391 9.807649 ATTAGCTTTGATTTCATGGTTATTGAC 57.192 29.630 0.00 0.00 0.00 3.18
369 396 7.479352 TTGATTTCATGGTTATTGACATGGT 57.521 32.000 0.00 0.00 43.49 3.55
372 399 8.465999 TGATTTCATGGTTATTGACATGGTAAC 58.534 33.333 0.00 1.24 43.49 2.50
421 448 6.711645 TGTTTAACTTCTATTTGGTTAGCGGT 59.288 34.615 0.00 0.00 0.00 5.68
443 470 2.777692 GGGGAAATATGTCCTCCAGTGA 59.222 50.000 11.89 0.00 37.85 3.41
480 508 0.882484 TGCATGAGGAAAACGACGCA 60.882 50.000 0.00 0.00 0.00 5.24
590 621 0.591170 ACAAATCAAGCAACGGTCGG 59.409 50.000 0.00 0.00 0.00 4.79
598 629 3.751246 CAACGGTCGGGCGGACTA 61.751 66.667 22.22 0.00 45.35 2.59
630 661 9.713740 TTTTGAATTTTTGAATTTTCATCACCG 57.286 25.926 0.00 0.00 37.00 4.94
631 662 8.430801 TTGAATTTTTGAATTTTCATCACCGT 57.569 26.923 0.00 0.00 37.00 4.83
632 663 8.430801 TGAATTTTTGAATTTTCATCACCGTT 57.569 26.923 0.00 0.00 37.00 4.44
633 664 8.333908 TGAATTTTTGAATTTTCATCACCGTTG 58.666 29.630 0.00 0.00 37.00 4.10
634 665 7.784633 ATTTTTGAATTTTCATCACCGTTGT 57.215 28.000 0.00 0.00 37.00 3.32
635 666 7.602517 TTTTTGAATTTTCATCACCGTTGTT 57.397 28.000 0.00 0.00 37.00 2.83
636 667 6.580963 TTTGAATTTTCATCACCGTTGTTG 57.419 33.333 0.00 0.00 37.00 3.33
637 668 4.615949 TGAATTTTCATCACCGTTGTTGG 58.384 39.130 0.00 0.00 31.01 3.77
638 669 4.098654 TGAATTTTCATCACCGTTGTTGGT 59.901 37.500 0.00 0.00 35.81 3.67
639 670 4.664150 ATTTTCATCACCGTTGTTGGTT 57.336 36.364 0.00 0.00 41.38 3.67
640 671 4.457834 TTTTCATCACCGTTGTTGGTTT 57.542 36.364 0.00 0.00 41.38 3.27
641 672 4.457834 TTTCATCACCGTTGTTGGTTTT 57.542 36.364 0.00 0.00 41.38 2.43
642 673 4.457834 TTCATCACCGTTGTTGGTTTTT 57.542 36.364 0.00 0.00 41.38 1.94
672 703 3.878667 GGGATTCCCCGGCCTCTG 61.879 72.222 11.02 0.00 44.02 3.35
673 704 4.570874 GGATTCCCCGGCCTCTGC 62.571 72.222 0.00 0.00 0.00 4.26
674 705 3.797353 GATTCCCCGGCCTCTGCA 61.797 66.667 0.00 0.00 40.13 4.41
675 706 3.099170 ATTCCCCGGCCTCTGCAT 61.099 61.111 0.00 0.00 40.13 3.96
676 707 3.125376 ATTCCCCGGCCTCTGCATC 62.125 63.158 0.00 0.00 40.13 3.91
729 760 6.638468 GTGACCAGCAAAAATGAAAGTAGAAG 59.362 38.462 0.00 0.00 0.00 2.85
797 828 2.027561 TCTAACCGCTATGCAACAAGGT 60.028 45.455 0.00 0.00 0.00 3.50
822 855 6.042143 TCAACAGAAATCTTCCAAACAAAGC 58.958 36.000 0.00 0.00 0.00 3.51
1437 1479 2.047844 GCGCACAAGAGGCTCTCA 60.048 61.111 19.03 0.00 32.06 3.27
1540 1582 4.164221 GGGATAGTCCAGGTGAGATTTTCA 59.836 45.833 0.00 0.00 38.64 2.69
1643 1685 0.809241 CGTCCAATCAGAGCAGCTCC 60.809 60.000 19.40 1.14 0.00 4.70
1647 1689 3.011635 AATCAGAGCAGCTCCGCGT 62.012 57.895 19.40 0.00 36.85 6.01
1660 1702 1.059264 CTCCGCGTCAAGATTTCGTTC 59.941 52.381 4.92 0.00 0.00 3.95
1684 1726 3.479489 ACGGAGGTTTTGGTACGAATTT 58.521 40.909 0.00 0.00 0.00 1.82
1686 1728 4.452114 ACGGAGGTTTTGGTACGAATTTAC 59.548 41.667 0.00 0.00 0.00 2.01
1719 1761 1.205179 CTCATCTGAGCTCAGCAGTGT 59.795 52.381 34.48 16.72 43.46 3.55
1721 1763 0.391395 ATCTGAGCTCAGCAGTGTGC 60.391 55.000 34.48 0.00 45.46 4.57
1821 1863 1.550130 AACGGGGGATTCTTGAGCGA 61.550 55.000 0.00 0.00 0.00 4.93
1883 1925 1.348064 ATCGTTCTGGGTCAGTGGAA 58.652 50.000 0.00 0.00 32.61 3.53
1884 1926 0.391597 TCGTTCTGGGTCAGTGGAAC 59.608 55.000 0.00 0.00 35.93 3.62
1885 1927 2.914379 GTTCTGGGTCAGTGGAACG 58.086 57.895 0.00 0.00 45.86 3.95
2030 2073 5.593909 TGGGTGATTAATGGCTTCAGTTATG 59.406 40.000 0.00 0.00 0.00 1.90
2031 2074 5.010012 GGGTGATTAATGGCTTCAGTTATGG 59.990 44.000 0.00 0.00 0.00 2.74
2032 2075 5.827797 GGTGATTAATGGCTTCAGTTATGGA 59.172 40.000 0.00 0.00 0.00 3.41
2033 2076 6.016777 GGTGATTAATGGCTTCAGTTATGGAG 60.017 42.308 0.00 0.00 34.82 3.86
2034 2077 6.543831 GTGATTAATGGCTTCAGTTATGGAGT 59.456 38.462 0.00 0.00 34.12 3.85
2285 2332 0.535335 GGTGTCGGTAGATTCAGGCA 59.465 55.000 0.00 0.00 0.00 4.75
2304 2351 2.578495 CACAAGCTCTCGTGATTTTGC 58.422 47.619 5.21 1.06 35.02 3.68
2306 2353 3.433274 CACAAGCTCTCGTGATTTTGCTA 59.567 43.478 5.21 0.00 35.02 3.49
2307 2354 4.093998 CACAAGCTCTCGTGATTTTGCTAT 59.906 41.667 5.21 0.00 35.02 2.97
2308 2355 4.697352 ACAAGCTCTCGTGATTTTGCTATT 59.303 37.500 9.61 0.00 0.00 1.73
2309 2356 4.871993 AGCTCTCGTGATTTTGCTATTG 57.128 40.909 0.00 0.00 0.00 1.90
2310 2357 3.624861 AGCTCTCGTGATTTTGCTATTGG 59.375 43.478 0.00 0.00 0.00 3.16
2311 2358 3.375299 GCTCTCGTGATTTTGCTATTGGT 59.625 43.478 0.00 0.00 0.00 3.67
2312 2359 4.494855 GCTCTCGTGATTTTGCTATTGGTC 60.495 45.833 0.00 0.00 0.00 4.02
2314 2361 4.391830 TCTCGTGATTTTGCTATTGGTCAC 59.608 41.667 0.00 0.00 34.25 3.67
2315 2362 4.323417 TCGTGATTTTGCTATTGGTCACT 58.677 39.130 0.00 0.00 35.15 3.41
2316 2363 4.391830 TCGTGATTTTGCTATTGGTCACTC 59.608 41.667 0.00 0.00 35.15 3.51
2317 2364 4.393062 CGTGATTTTGCTATTGGTCACTCT 59.607 41.667 0.00 0.00 35.15 3.24
2328 2375 7.282675 TGCTATTGGTCACTCTTACTAGTACTC 59.717 40.741 0.91 0.00 0.00 2.59
2329 2379 6.680874 ATTGGTCACTCTTACTAGTACTCG 57.319 41.667 0.91 0.00 0.00 4.18
2355 2405 7.719633 GCCATTGAGTAAACCCTAGATCAATTA 59.280 37.037 0.00 0.00 35.73 1.40
2426 2476 6.549433 AATTTTGTGATGGTGCATTAGGAT 57.451 33.333 0.00 0.00 0.00 3.24
2427 2477 5.581126 TTTTGTGATGGTGCATTAGGATC 57.419 39.130 0.00 0.00 0.00 3.36
2501 2557 3.263170 TGCTTGCACTCCTGGTCTTATTA 59.737 43.478 0.00 0.00 0.00 0.98
2504 2560 2.837591 TGCACTCCTGGTCTTATTAGCA 59.162 45.455 0.00 0.00 0.00 3.49
2505 2561 3.263170 TGCACTCCTGGTCTTATTAGCAA 59.737 43.478 0.00 0.00 0.00 3.91
2506 2562 4.261801 GCACTCCTGGTCTTATTAGCAAA 58.738 43.478 0.00 0.00 0.00 3.68
2507 2563 4.333926 GCACTCCTGGTCTTATTAGCAAAG 59.666 45.833 0.00 0.00 0.00 2.77
2508 2564 5.491982 CACTCCTGGTCTTATTAGCAAAGT 58.508 41.667 0.00 0.00 0.00 2.66
2509 2565 5.940470 CACTCCTGGTCTTATTAGCAAAGTT 59.060 40.000 0.00 0.00 0.00 2.66
2510 2566 6.431234 CACTCCTGGTCTTATTAGCAAAGTTT 59.569 38.462 0.00 0.00 0.00 2.66
2596 2662 4.919754 CGCCAAAAATTTTCTCTCTCCTTG 59.080 41.667 3.41 0.00 0.00 3.61
2652 2718 5.388061 CGTTGCTTTTCTCATTTGCAAGATG 60.388 40.000 0.00 7.20 43.00 2.90
2658 2724 7.201496 GCTTTTCTCATTTGCAAGATGGTTATG 60.201 37.037 16.44 9.31 0.00 1.90
2735 2801 3.142174 CTCGTGCCTTCTTTTCTTTCCT 58.858 45.455 0.00 0.00 0.00 3.36
2769 2835 2.496070 TGTACCGGACTGATGGAGAAAG 59.504 50.000 9.46 0.00 0.00 2.62
2880 2949 3.303395 CGTCAAGAGCTCACTTTGGTTTC 60.303 47.826 17.77 3.76 0.00 2.78
2955 3028 2.817844 CCGTACCCCAAAAGAAGGAAAG 59.182 50.000 0.00 0.00 0.00 2.62
2956 3029 3.483421 CGTACCCCAAAAGAAGGAAAGT 58.517 45.455 0.00 0.00 0.00 2.66
2957 3030 4.505390 CCGTACCCCAAAAGAAGGAAAGTA 60.505 45.833 0.00 0.00 0.00 2.24
3040 3117 1.790755 TTACCTGCGCACAGTTGTAG 58.209 50.000 5.66 0.00 42.81 2.74
3041 3118 0.677288 TACCTGCGCACAGTTGTAGT 59.323 50.000 5.66 0.00 42.81 2.73
3042 3119 0.677288 ACCTGCGCACAGTTGTAGTA 59.323 50.000 5.66 0.00 42.81 1.82
3046 3123 1.075542 GCGCACAGTTGTAGTATGCA 58.924 50.000 0.30 0.00 36.02 3.96
3062 3140 6.359480 AGTATGCACCGCTTTAAATTACTC 57.641 37.500 0.00 0.00 0.00 2.59
3233 3338 0.478507 GGAGAGGAGGAGGAGAGAGG 59.521 65.000 0.00 0.00 0.00 3.69
3280 3393 3.317993 CACCAGTTTTCCCCTTGTGTAAG 59.682 47.826 0.00 0.00 0.00 2.34
3352 3465 0.250727 CCCGCAGAGGTTGGAAGAAA 60.251 55.000 0.00 0.00 38.74 2.52
3353 3466 1.160137 CCGCAGAGGTTGGAAGAAAG 58.840 55.000 0.00 0.00 34.51 2.62
3354 3467 1.270839 CCGCAGAGGTTGGAAGAAAGA 60.271 52.381 0.00 0.00 34.51 2.52
3355 3468 2.494059 CGCAGAGGTTGGAAGAAAGAA 58.506 47.619 0.00 0.00 0.00 2.52
3426 3539 4.974399 TCTGTTTTCCCTCCTCTTTCTTC 58.026 43.478 0.00 0.00 0.00 2.87
3436 3549 5.104109 CCCTCCTCTTTCTTCTCTCTCTCTA 60.104 48.000 0.00 0.00 0.00 2.43
3450 3569 2.767960 TCTCTCTAGTCCATGCATGCAA 59.232 45.455 26.68 5.25 0.00 4.08
3468 3587 2.353889 GCAATGCTCCTGTGTGATAGTG 59.646 50.000 0.00 0.00 0.00 2.74
3523 3649 6.930731 ACAAGCAAGAAAAGAACAAGGTAAA 58.069 32.000 0.00 0.00 0.00 2.01
3553 3679 3.682409 TGGGGAGCCAATTGGGGG 61.682 66.667 25.73 0.78 37.04 5.40
3593 3721 1.555075 TGTGGGATTCTTCCTTCCTCG 59.445 52.381 0.00 0.00 42.20 4.63
3634 3762 2.117858 TGGTGGTGCCATGCATGT 59.882 55.556 24.58 0.00 43.61 3.21
3635 3763 2.276853 TGGTGGTGCCATGCATGTG 61.277 57.895 24.58 16.68 43.61 3.21
3636 3764 2.574929 GTGGTGCCATGCATGTGG 59.425 61.111 24.58 13.90 41.91 4.17
3637 3765 1.978080 GTGGTGCCATGCATGTGGA 60.978 57.895 24.58 14.55 41.91 4.02
3638 3766 1.679641 TGGTGCCATGCATGTGGAG 60.680 57.895 24.58 10.82 41.91 3.86
3697 3828 2.291153 ACAGCACATATGGTTGCTCCTT 60.291 45.455 15.82 3.66 33.06 3.36
3728 3863 2.287788 GCATGTGACCTTCTTGTGTTGG 60.288 50.000 0.00 0.00 0.00 3.77
3748 3887 2.203480 GCCTGGCTGGTGGTTGAA 60.203 61.111 12.43 0.00 38.35 2.69
3771 3910 2.553086 CTTCTCCTGCTCATGCTTCTC 58.447 52.381 0.00 0.00 40.48 2.87
3855 4024 9.772973 ACTACGATTATTATTCAACTATGCCAA 57.227 29.630 0.00 0.00 0.00 4.52
3962 4190 9.347934 TGCAAAAACATCTTATATTTTGGTACG 57.652 29.630 10.66 0.00 41.02 3.67
3986 4214 5.398012 GGGAGGGAGTATAAGCTGTTTTGAT 60.398 44.000 0.00 0.00 0.00 2.57
4026 4254 8.977267 AAACAGAGGTGGTAGTATAGTAGTAG 57.023 38.462 0.00 0.00 0.00 2.57
4045 4273 6.869206 AGTAGTTAGTTTCTTCCATGCCTA 57.131 37.500 0.00 0.00 0.00 3.93
4104 4332 4.660168 TCTATCAATCTAGTACCCCGTCC 58.340 47.826 0.00 0.00 0.00 4.79
4112 4340 3.785887 TCTAGTACCCCGTCCCTTTACTA 59.214 47.826 0.00 0.00 0.00 1.82
4159 4387 2.262915 GACAGACACAGGCCTCCG 59.737 66.667 0.00 0.00 0.00 4.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 9.967451 TTTCTGACACAATGGGAGTAATATTTA 57.033 29.630 0.00 0.00 0.00 1.40
32 33 4.144297 TCCTTCTTTTCTGACACAATGGG 58.856 43.478 0.00 0.00 0.00 4.00
101 102 8.938906 GGTATCGTAATTCTTGGTAGTTTTTCA 58.061 33.333 0.00 0.00 0.00 2.69
212 219 5.193679 GGAGTTAACCAGGCATAGTTTGAT 58.806 41.667 0.88 0.00 0.00 2.57
246 254 9.627123 CCCTGTTCATGAAAATAAGGTCTATAA 57.373 33.333 10.35 0.00 0.00 0.98
251 259 4.402474 CCCCCTGTTCATGAAAATAAGGTC 59.598 45.833 10.35 0.00 0.00 3.85
256 264 4.946160 ACTCCCCCTGTTCATGAAAATA 57.054 40.909 10.35 0.00 0.00 1.40
264 272 5.371176 TGCATAAATATACTCCCCCTGTTCA 59.629 40.000 0.00 0.00 0.00 3.18
265 273 5.876357 TGCATAAATATACTCCCCCTGTTC 58.124 41.667 0.00 0.00 0.00 3.18
269 277 5.457633 GGTGTTGCATAAATATACTCCCCCT 60.458 44.000 0.00 0.00 0.00 4.79
271 279 5.381757 TGGTGTTGCATAAATATACTCCCC 58.618 41.667 0.00 0.00 0.00 4.81
364 391 7.706179 GTGGTTATTTGATTCCATGTTACCATG 59.294 37.037 0.00 0.00 46.65 3.66
369 396 9.703892 CTTTTGTGGTTATTTGATTCCATGTTA 57.296 29.630 0.00 0.00 32.45 2.41
372 399 8.020861 CACTTTTGTGGTTATTTGATTCCATG 57.979 34.615 0.00 0.00 46.16 3.66
403 430 2.943033 CCCACCGCTAACCAAATAGAAG 59.057 50.000 0.00 0.00 0.00 2.85
411 438 1.287217 TATTTCCCCACCGCTAACCA 58.713 50.000 0.00 0.00 0.00 3.67
421 448 2.509548 CACTGGAGGACATATTTCCCCA 59.490 50.000 14.05 14.05 36.12 4.96
443 470 1.818674 GCATCTTGTCCGGATTGGTTT 59.181 47.619 7.81 0.00 39.52 3.27
480 508 1.339929 GGATTGTCGTGTTTTGCCCTT 59.660 47.619 0.00 0.00 0.00 3.95
590 621 9.753669 CAAAAATTCAAAAATTAATAGTCCGCC 57.246 29.630 0.00 0.00 33.93 6.13
656 687 4.570874 GCAGAGGCCGGGGAATCC 62.571 72.222 2.18 0.00 0.00 3.01
657 688 3.125376 ATGCAGAGGCCGGGGAATC 62.125 63.158 2.18 0.00 40.13 2.52
658 689 3.099170 ATGCAGAGGCCGGGGAAT 61.099 61.111 2.18 0.00 40.13 3.01
659 690 3.797353 GATGCAGAGGCCGGGGAA 61.797 66.667 2.18 0.00 40.13 3.97
661 692 3.839353 GATGATGCAGAGGCCGGGG 62.839 68.421 2.18 0.00 40.13 5.73
662 693 2.281345 GATGATGCAGAGGCCGGG 60.281 66.667 2.18 0.00 40.13 5.73
663 694 2.664185 CGATGATGCAGAGGCCGG 60.664 66.667 0.00 0.00 40.13 6.13
664 695 3.344215 GCGATGATGCAGAGGCCG 61.344 66.667 0.00 0.00 40.13 6.13
665 696 2.110627 AGCGATGATGCAGAGGCC 59.889 61.111 0.00 0.00 40.13 5.19
666 697 1.094073 AACAGCGATGATGCAGAGGC 61.094 55.000 8.12 0.00 41.68 4.70
667 698 0.656259 CAACAGCGATGATGCAGAGG 59.344 55.000 8.12 0.00 37.31 3.69
668 699 1.062148 CACAACAGCGATGATGCAGAG 59.938 52.381 8.12 0.00 37.31 3.35
669 700 1.081094 CACAACAGCGATGATGCAGA 58.919 50.000 8.12 0.00 37.31 4.26
670 701 0.800631 ACACAACAGCGATGATGCAG 59.199 50.000 8.12 4.97 37.31 4.41
671 702 1.069091 CAACACAACAGCGATGATGCA 60.069 47.619 8.12 0.00 37.31 3.96
672 703 1.069022 ACAACACAACAGCGATGATGC 60.069 47.619 8.12 0.00 0.00 3.91
673 704 2.975410 ACAACACAACAGCGATGATG 57.025 45.000 8.12 8.94 0.00 3.07
674 705 3.436704 CCTTACAACACAACAGCGATGAT 59.563 43.478 8.12 0.00 0.00 2.45
675 706 2.805671 CCTTACAACACAACAGCGATGA 59.194 45.455 8.12 0.00 0.00 2.92
676 707 2.095768 CCCTTACAACACAACAGCGATG 60.096 50.000 0.00 0.00 0.00 3.84
677 708 2.151202 CCCTTACAACACAACAGCGAT 58.849 47.619 0.00 0.00 0.00 4.58
729 760 3.758425 TGGAAACAAGTTAGTTAGGGGC 58.242 45.455 0.00 0.00 37.44 5.80
797 828 6.534793 GCTTTGTTTGGAAGATTTCTGTTGAA 59.465 34.615 0.00 0.00 0.00 2.69
822 855 5.362717 GGGGTAGAAAATTGGGGTGAAATAG 59.637 44.000 0.00 0.00 0.00 1.73
895 928 1.000496 GGGGAGGTTTTAAGGGAGCT 59.000 55.000 0.00 0.00 0.00 4.09
1176 1218 1.888736 GTCCAGGGTGTACGACTCC 59.111 63.158 0.00 0.00 0.00 3.85
1476 1518 2.676608 CCCATACTGGTGCTGGCA 59.323 61.111 0.00 0.00 35.17 4.92
1567 1609 4.437772 ACCGACTAGCAACTTTAGAGAC 57.562 45.455 0.00 0.00 0.00 3.36
1643 1685 3.562869 GGAACGAAATCTTGACGCG 57.437 52.632 3.53 3.53 0.00 6.01
1660 1702 1.010419 CGTACCAAAACCTCCGTCGG 61.010 60.000 4.39 4.39 0.00 4.79
1684 1726 3.072038 CAGATGAGAGATTGGGCATGGTA 59.928 47.826 0.00 0.00 0.00 3.25
1686 1728 2.105993 TCAGATGAGAGATTGGGCATGG 59.894 50.000 0.00 0.00 0.00 3.66
1719 1761 0.899717 GAATCAGCAAACTGGGGGCA 60.900 55.000 0.00 0.00 44.59 5.36
1721 1763 0.322456 TCGAATCAGCAAACTGGGGG 60.322 55.000 0.00 0.00 44.59 5.40
1883 1925 1.503818 CTTGCCAACCTGTAACGCGT 61.504 55.000 5.58 5.58 0.00 6.01
1884 1926 1.206578 CTTGCCAACCTGTAACGCG 59.793 57.895 3.53 3.53 0.00 6.01
1885 1927 1.463444 CTACTTGCCAACCTGTAACGC 59.537 52.381 0.00 0.00 0.00 4.84
2030 2073 1.745653 GTGCCCAAATTCAGCTACTCC 59.254 52.381 0.00 0.00 0.00 3.85
2031 2074 2.436417 TGTGCCCAAATTCAGCTACTC 58.564 47.619 0.00 0.00 0.00 2.59
2032 2075 2.584835 TGTGCCCAAATTCAGCTACT 57.415 45.000 0.00 0.00 0.00 2.57
2033 2076 3.874392 ATTGTGCCCAAATTCAGCTAC 57.126 42.857 0.00 0.00 33.44 3.58
2034 2077 5.991933 TTTATTGTGCCCAAATTCAGCTA 57.008 34.783 0.00 0.00 33.44 3.32
2220 2267 9.905713 GAGCTCCAATTCCCACAATTATATATA 57.094 33.333 0.87 0.00 0.00 0.86
2221 2268 8.393259 TGAGCTCCAATTCCCACAATTATATAT 58.607 33.333 12.15 0.00 0.00 0.86
2222 2269 7.754624 TGAGCTCCAATTCCCACAATTATATA 58.245 34.615 12.15 0.00 0.00 0.86
2230 2277 2.905415 AATGAGCTCCAATTCCCACA 57.095 45.000 12.15 0.00 0.00 4.17
2231 2278 4.273318 ACTTAATGAGCTCCAATTCCCAC 58.727 43.478 12.15 0.00 0.00 4.61
2285 2332 2.498167 AGCAAAATCACGAGAGCTTGT 58.502 42.857 0.00 0.00 0.00 3.16
2304 2351 7.518689 GCGAGTACTAGTAAGAGTGACCAATAG 60.519 44.444 3.61 0.00 0.00 1.73
2306 2353 5.066246 GCGAGTACTAGTAAGAGTGACCAAT 59.934 44.000 3.61 0.00 0.00 3.16
2307 2354 4.394300 GCGAGTACTAGTAAGAGTGACCAA 59.606 45.833 3.61 0.00 0.00 3.67
2308 2355 3.937706 GCGAGTACTAGTAAGAGTGACCA 59.062 47.826 3.61 0.00 0.00 4.02
2309 2356 3.312146 GGCGAGTACTAGTAAGAGTGACC 59.688 52.174 3.61 0.00 0.00 4.02
2310 2357 3.937706 TGGCGAGTACTAGTAAGAGTGAC 59.062 47.826 3.61 0.00 0.00 3.67
2311 2358 4.212143 TGGCGAGTACTAGTAAGAGTGA 57.788 45.455 3.61 0.00 0.00 3.41
2312 2359 5.066117 TCAATGGCGAGTACTAGTAAGAGTG 59.934 44.000 3.61 0.00 0.00 3.51
2314 2361 5.297278 ACTCAATGGCGAGTACTAGTAAGAG 59.703 44.000 3.61 7.80 44.46 2.85
2315 2362 5.191426 ACTCAATGGCGAGTACTAGTAAGA 58.809 41.667 3.61 0.00 44.46 2.10
2316 2363 5.502153 ACTCAATGGCGAGTACTAGTAAG 57.498 43.478 3.61 0.71 44.46 2.34
2317 2364 7.253422 GTTTACTCAATGGCGAGTACTAGTAA 58.747 38.462 3.61 5.82 45.79 2.24
2328 2375 3.536956 TCTAGGGTTTACTCAATGGCG 57.463 47.619 0.00 0.00 0.00 5.69
2329 2379 5.036117 TGATCTAGGGTTTACTCAATGGC 57.964 43.478 0.00 0.00 0.00 4.40
2355 2405 6.667414 TCCAGATTATTTAATGTGTTTGCCCT 59.333 34.615 6.68 0.00 35.78 5.19
2358 2408 7.816995 TGGTTCCAGATTATTTAATGTGTTTGC 59.183 33.333 6.68 0.00 35.78 3.68
2361 2411 9.874205 CAATGGTTCCAGATTATTTAATGTGTT 57.126 29.630 6.68 0.00 35.78 3.32
2394 2444 4.457603 CACCATCACAAAATTAGGTTCGGA 59.542 41.667 0.00 0.00 0.00 4.55
2426 2476 1.152902 AGCACTGCAACTTGCCTGA 60.153 52.632 11.29 0.00 44.23 3.86
2427 2477 1.007734 CAGCACTGCAACTTGCCTG 60.008 57.895 11.29 7.23 44.23 4.85
2596 2662 3.741805 GTAGCAAACCAGAAACGGATC 57.258 47.619 0.00 0.00 0.00 3.36
2658 2724 6.204688 TGAGACACACATTCTAACATGGAAAC 59.795 38.462 0.00 0.00 0.00 2.78
2735 2801 1.368641 CGGTACAAATAGCAGCAGCA 58.631 50.000 3.17 0.00 45.49 4.41
2858 2927 1.871080 ACCAAAGTGAGCTCTTGACG 58.129 50.000 16.19 2.54 0.00 4.35
2880 2949 1.824852 GTGAAGTTTAGCCATTGGGGG 59.175 52.381 4.53 0.00 37.04 5.40
3040 3117 5.065474 TGGAGTAATTTAAAGCGGTGCATAC 59.935 40.000 0.00 0.00 0.00 2.39
3041 3118 5.186942 TGGAGTAATTTAAAGCGGTGCATA 58.813 37.500 0.00 0.00 0.00 3.14
3042 3119 4.013728 TGGAGTAATTTAAAGCGGTGCAT 58.986 39.130 0.00 0.00 0.00 3.96
3046 3123 3.014623 GCCTGGAGTAATTTAAAGCGGT 58.985 45.455 0.00 0.00 0.00 5.68
3062 3140 2.092968 TGTTATTCCAGCTGTAGCCTGG 60.093 50.000 13.81 13.00 43.38 4.45
3094 3189 1.401552 GCAACAGCTTGTTCAGACACA 59.598 47.619 0.00 0.00 38.77 3.72
3233 3338 3.644884 TGTCTCGGTCTTCTTGTCTTC 57.355 47.619 0.00 0.00 0.00 2.87
3280 3393 2.300152 TCACCACAGGTTCTGTCTGATC 59.700 50.000 0.00 0.00 43.43 2.92
3352 3465 7.550551 CACATCTCCATTAAGTACACACATTCT 59.449 37.037 0.00 0.00 0.00 2.40
3353 3466 7.201644 CCACATCTCCATTAAGTACACACATTC 60.202 40.741 0.00 0.00 0.00 2.67
3354 3467 6.599244 CCACATCTCCATTAAGTACACACATT 59.401 38.462 0.00 0.00 0.00 2.71
3355 3468 6.115446 CCACATCTCCATTAAGTACACACAT 58.885 40.000 0.00 0.00 0.00 3.21
3426 3539 3.305539 GCATGCATGGACTAGAGAGAGAG 60.306 52.174 27.34 0.00 0.00 3.20
3450 3569 2.191400 ACCACTATCACACAGGAGCAT 58.809 47.619 0.00 0.00 0.00 3.79
3468 3587 6.204882 AGCACTGACAAACTTAATACTCAACC 59.795 38.462 0.00 0.00 0.00 3.77
3553 3679 2.951101 AAAATGCCAGCCAGCCAGC 61.951 57.895 0.00 0.00 0.00 4.85
3554 3680 1.079405 CAAAATGCCAGCCAGCCAG 60.079 57.895 0.00 0.00 0.00 4.85
3555 3681 1.837947 ACAAAATGCCAGCCAGCCA 60.838 52.632 0.00 0.00 0.00 4.75
3593 3721 0.336392 AGCCAAGGAAGGAATTCCCC 59.664 55.000 21.22 15.60 42.06 4.81
3697 3828 1.609239 GTCACATGCAGGGATGGGA 59.391 57.895 2.31 1.25 33.16 4.37
3728 3863 4.982701 AACCACCAGCCAGGCAGC 62.983 66.667 15.80 0.00 43.14 5.25
3748 3887 0.547075 AGCATGAGCAGGAGAAGCAT 59.453 50.000 0.00 0.00 45.49 3.79
3855 4024 6.553857 ACTCTAAATACCGGACCTATGATCT 58.446 40.000 9.46 0.00 0.00 2.75
3920 4148 0.976641 TGCACTTCAGGTACAGAGGG 59.023 55.000 0.00 0.00 0.00 4.30
3962 4190 4.080526 TCAAAACAGCTTATACTCCCTCCC 60.081 45.833 0.00 0.00 0.00 4.30
3986 4214 9.667107 CCACCTCTGTTTCTGATTTATAAACTA 57.333 33.333 0.00 0.00 34.84 2.24
4026 4254 4.636206 CACCTAGGCATGGAAGAAACTAAC 59.364 45.833 9.30 0.00 0.00 2.34
4034 4262 0.620556 ACACCACCTAGGCATGGAAG 59.379 55.000 22.22 16.14 43.14 3.46
4045 4273 1.453745 CTTGCACACCACACCACCT 60.454 57.895 0.00 0.00 0.00 4.00
4159 4387 1.515521 CTGTTTCCCGTTGGCTGGAC 61.516 60.000 0.00 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.