Multiple sequence alignment - TraesCS6D01G238300

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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 TraesCS6D01G238300 chr6D 100.000 3009 0 0 1 3009 338740806 338737798 0.000000e+00 5557.0
1 TraesCS6D01G238300 chr6A 94.009 1302 68 6 880 2178 479268594 479267300 0.000000e+00 1964.0
2 TraesCS6D01G238300 chr6A 89.308 318 23 5 1 312 479317315 479317003 3.640000e-104 388.0
3 TraesCS6D01G238300 chr6A 92.000 250 19 1 357 606 479317001 479316753 1.720000e-92 350.0
4 TraesCS6D01G238300 chr6A 91.406 256 13 5 636 886 479270254 479270003 2.870000e-90 342.0
5 TraesCS6D01G238300 chr6A 86.705 173 16 4 2277 2449 479266994 479266829 5.120000e-43 185.0
6 TraesCS6D01G238300 chr6B 94.306 1282 56 8 862 2138 481740202 481741471 0.000000e+00 1947.0
7 TraesCS6D01G238300 chr6B 83.768 881 89 21 2136 3009 481741659 481742492 0.000000e+00 785.0
8 TraesCS6D01G238300 chr6B 88.477 243 21 6 1 239 481735189 481735428 1.370000e-73 287.0
9 TraesCS6D01G238300 chr6B 87.946 224 17 5 611 834 481738008 481738221 3.850000e-64 255.0
10 TraesCS6D01G238300 chr4D 81.410 312 38 12 2210 2518 88148275 88147981 1.390000e-58 237.0
11 TraesCS6D01G238300 chr4A 81.034 290 36 11 2275 2560 501128836 501128562 2.350000e-51 213.0
12 TraesCS6D01G238300 chr4A 77.461 386 62 18 2208 2587 4247906 4248272 1.090000e-49 207.0
13 TraesCS6D01G238300 chr4A 78.713 202 25 6 2300 2498 432492123 432491937 5.270000e-23 119.0
14 TraesCS6D01G238300 chr3B 88.344 163 16 2 748 908 165283795 165283956 3.060000e-45 193.0
15 TraesCS6D01G238300 chr3B 77.049 122 24 3 2889 3009 284376531 284376413 1.940000e-07 67.6
16 TraesCS6D01G238300 chr4B 79.615 260 35 10 2225 2482 124922854 124922611 1.430000e-38 171.0
17 TraesCS6D01G238300 chr5A 78.947 247 30 11 2209 2451 634499725 634499497 6.720000e-32 148.0
18 TraesCS6D01G238300 chr3A 74.619 394 72 22 2193 2581 701762889 701763259 6.720000e-32 148.0
19 TraesCS6D01G238300 chr3A 74.057 212 39 11 2797 3006 313540594 313540791 4.160000e-09 73.1
20 TraesCS6D01G238300 chr1B 75.284 352 63 14 344 680 399069490 399069832 2.420000e-31 147.0
21 TraesCS6D01G238300 chr1B 78.286 175 25 8 2394 2568 471202665 471202826 1.910000e-17 100.0
22 TraesCS6D01G238300 chr2A 87.805 123 11 3 2375 2497 31388771 31388889 1.120000e-29 141.0
23 TraesCS6D01G238300 chr5B 75.347 288 44 19 2209 2486 637447810 637447540 2.450000e-21 113.0
24 TraesCS6D01G238300 chr2B 77.273 198 37 8 348 542 588398034 588397842 3.170000e-20 110.0
25 TraesCS6D01G238300 chr1A 77.660 188 29 7 2394 2581 449859070 449859244 5.310000e-18 102.0
26 TraesCS6D01G238300 chr7A 81.579 114 19 1 2216 2327 661295703 661295590 3.190000e-15 93.5
27 TraesCS6D01G238300 chr7B 76.923 169 30 7 342 505 705014614 705014778 1.490000e-13 87.9
28 TraesCS6D01G238300 chr7B 77.193 171 26 10 342 505 705070947 705071111 1.490000e-13 87.9
29 TraesCS6D01G238300 chr2D 94.000 50 2 1 2375 2424 29275544 29275592 1.160000e-09 75.0


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 TraesCS6D01G238300 chr6D 338737798 338740806 3008 True 5557.000000 5557 100.000000 1 3009 1 chr6D.!!$R1 3008
1 TraesCS6D01G238300 chr6A 479266829 479270254 3425 True 830.333333 1964 90.706667 636 2449 3 chr6A.!!$R1 1813
2 TraesCS6D01G238300 chr6A 479316753 479317315 562 True 369.000000 388 90.654000 1 606 2 chr6A.!!$R2 605
3 TraesCS6D01G238300 chr6B 481735189 481742492 7303 False 818.500000 1947 88.624250 1 3009 4 chr6B.!!$F1 3008

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
328 340 0.692476 AGCCTAGCCAATGTGACACA 59.308 50.0 11.41 11.41 0.0 3.72 F
1117 6702 0.611714 ACGGCCGAGACCTTTACATT 59.388 50.0 35.90 0.00 0.0 2.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1225 6810 0.171455 GTCAGGAACTCGACGCTGAT 59.829 55.0 5.59 0.0 34.6 2.90 R
2595 8639 0.110869 CCGTAACCCCCAAAACCAGA 59.889 55.0 0.00 0.0 0.0 3.86 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
72 73 7.703197 AGTTTAAAATACTTTGACGTGTTTGGG 59.297 33.333 0.00 0.00 30.23 4.12
156 160 9.067986 AGTATTAAAAGAAAAACTCCTGACCTG 57.932 33.333 0.00 0.00 0.00 4.00
218 225 7.239763 TCTATTTTGGCCGATCTACATCATA 57.760 36.000 0.00 0.00 0.00 2.15
260 272 5.233902 TGTGCACAAATTTTGTTGTATCAGC 59.766 36.000 19.28 10.87 43.23 4.26
262 274 4.143347 GCACAAATTTTGTTGTATCAGCGG 60.143 41.667 12.02 0.00 43.23 5.52
279 291 1.790387 GGCTAGCAGCAAACTCACG 59.210 57.895 18.24 0.00 44.75 4.35
302 314 5.227391 CGCGATTCTGTACGATACCAATATC 59.773 44.000 0.00 0.00 34.84 1.63
303 315 5.515626 GCGATTCTGTACGATACCAATATCC 59.484 44.000 0.00 0.00 34.71 2.59
304 316 6.617879 CGATTCTGTACGATACCAATATCCA 58.382 40.000 0.00 0.00 34.71 3.41
312 324 7.604927 TGTACGATACCAATATCCAATTTAGCC 59.395 37.037 0.00 0.00 34.71 3.93
313 325 6.779860 ACGATACCAATATCCAATTTAGCCT 58.220 36.000 0.00 0.00 34.71 4.58
314 326 7.913789 ACGATACCAATATCCAATTTAGCCTA 58.086 34.615 0.00 0.00 34.71 3.93
315 327 8.041323 ACGATACCAATATCCAATTTAGCCTAG 58.959 37.037 0.00 0.00 34.71 3.02
316 328 7.011482 CGATACCAATATCCAATTTAGCCTAGC 59.989 40.741 0.00 0.00 34.71 3.42
317 329 5.325239 ACCAATATCCAATTTAGCCTAGCC 58.675 41.667 0.00 0.00 0.00 3.93
318 330 5.162991 ACCAATATCCAATTTAGCCTAGCCA 60.163 40.000 0.00 0.00 0.00 4.75
322 334 4.249638 TCCAATTTAGCCTAGCCAATGT 57.750 40.909 0.00 0.00 0.00 2.71
323 335 3.953612 TCCAATTTAGCCTAGCCAATGTG 59.046 43.478 0.00 0.00 0.00 3.21
327 339 2.691409 TAGCCTAGCCAATGTGACAC 57.309 50.000 0.00 0.00 0.00 3.67
328 340 0.692476 AGCCTAGCCAATGTGACACA 59.308 50.000 11.41 11.41 0.00 3.72
329 341 0.804989 GCCTAGCCAATGTGACACAC 59.195 55.000 11.22 0.00 34.56 3.82
343 355 5.606505 TGTGACACACAAATCTAGCTGTTA 58.393 37.500 3.56 0.00 41.69 2.41
344 356 6.230472 TGTGACACACAAATCTAGCTGTTAT 58.770 36.000 3.56 0.00 41.69 1.89
345 357 7.382898 TGTGACACACAAATCTAGCTGTTATA 58.617 34.615 3.56 0.00 41.69 0.98
346 358 8.040727 TGTGACACACAAATCTAGCTGTTATAT 58.959 33.333 3.56 0.00 41.69 0.86
347 359 9.529325 GTGACACACAAATCTAGCTGTTATATA 57.471 33.333 0.00 0.00 34.08 0.86
348 360 9.529325 TGACACACAAATCTAGCTGTTATATAC 57.471 33.333 0.00 0.00 0.00 1.47
349 361 9.751542 GACACACAAATCTAGCTGTTATATACT 57.248 33.333 0.00 0.00 0.00 2.12
350 362 9.751542 ACACACAAATCTAGCTGTTATATACTC 57.248 33.333 0.00 0.00 0.00 2.59
351 363 9.197694 CACACAAATCTAGCTGTTATATACTCC 57.802 37.037 0.00 0.00 0.00 3.85
352 364 8.368668 ACACAAATCTAGCTGTTATATACTCCC 58.631 37.037 0.00 0.00 0.00 4.30
353 365 8.589338 CACAAATCTAGCTGTTATATACTCCCT 58.411 37.037 0.00 0.00 0.00 4.20
354 366 9.160412 ACAAATCTAGCTGTTATATACTCCCTT 57.840 33.333 0.00 0.00 0.00 3.95
355 367 9.646427 CAAATCTAGCTGTTATATACTCCCTTC 57.354 37.037 0.00 0.00 0.00 3.46
390 451 7.319646 TGTAAGGTGTAATTTTTCATCATGGC 58.680 34.615 0.00 0.00 0.00 4.40
450 511 8.009974 CGAAATTATCCTTAGCCAATTCGTTAG 58.990 37.037 0.00 0.00 0.00 2.34
465 526 4.970662 TCGTTAGTTAGCGACAGGTAAT 57.029 40.909 0.00 0.00 41.61 1.89
502 563 7.550551 AGAAAAGAAAGAGATACATGCAATCGA 59.449 33.333 0.00 0.00 0.00 3.59
516 577 7.017645 ACATGCAATCGAGAAAAATATATCGC 58.982 34.615 0.00 0.00 35.23 4.58
518 858 5.106712 TGCAATCGAGAAAAATATATCGCCC 60.107 40.000 0.00 0.00 35.23 6.13
550 890 4.211125 AGAAGGAGAGATACGAGCAATCA 58.789 43.478 0.00 0.00 0.00 2.57
553 893 4.211125 AGGAGAGATACGAGCAATCAGAA 58.789 43.478 0.00 0.00 0.00 3.02
555 895 4.545610 GAGAGATACGAGCAATCAGAAGG 58.454 47.826 0.00 0.00 0.00 3.46
591 1833 2.746279 TTCTGAAGGGCTGGAAAACA 57.254 45.000 0.00 0.00 0.00 2.83
606 1848 7.071414 GCTGGAAAACAAATTACAAGAAATGC 58.929 34.615 0.00 0.00 0.00 3.56
607 1849 7.254727 GCTGGAAAACAAATTACAAGAAATGCA 60.255 33.333 0.00 0.00 0.00 3.96
608 1850 7.914465 TGGAAAACAAATTACAAGAAATGCAC 58.086 30.769 0.00 0.00 0.00 4.57
797 3014 3.078594 ACGTCTCATGGTTTTGCAAAC 57.921 42.857 12.39 7.26 0.00 2.93
825 3042 9.180678 CTGTAAAATACAATGGTTCTCACAAAC 57.819 33.333 0.00 0.00 38.38 2.93
926 6511 4.902448 AGCCTAAGAGATAAGGTTTCCGAT 59.098 41.667 0.00 0.00 35.16 4.18
1117 6702 0.611714 ACGGCCGAGACCTTTACATT 59.388 50.000 35.90 0.00 0.00 2.71
1296 6881 0.611714 ACCCGGACTTCGCTTACAAT 59.388 50.000 0.73 0.00 37.59 2.71
1302 6887 2.159653 GGACTTCGCTTACAATGCACAG 60.160 50.000 0.00 0.00 0.00 3.66
1509 7094 1.658717 CATCGATCGGACGACTGGC 60.659 63.158 16.41 0.00 44.84 4.85
1527 7112 1.613255 GGCCAGGTAAGCTTTGCACTA 60.613 52.381 3.20 0.00 0.00 2.74
1541 7126 1.118838 GCACTACCTCCTCTCTGCAT 58.881 55.000 0.00 0.00 0.00 3.96
1556 7141 4.457496 CATCCTGCCGTCCTGCGT 62.457 66.667 0.00 0.00 39.32 5.24
1604 7189 7.772757 CAGCCCAGATAAGAGATTACTTTTTCT 59.227 37.037 0.00 0.00 0.00 2.52
1669 7259 9.457436 TCAGGGTATTTATTTAGAACAAGTTCC 57.543 33.333 9.20 0.00 40.33 3.62
1707 7297 7.470935 AATGGTCACAGAAAATGATCATGAA 57.529 32.000 9.46 0.00 45.23 2.57
1710 7300 7.167535 TGGTCACAGAAAATGATCATGAACTA 58.832 34.615 9.46 0.00 32.18 2.24
1712 7302 8.341173 GGTCACAGAAAATGATCATGAACTATC 58.659 37.037 9.46 2.25 0.00 2.08
1721 7311 5.230182 TGATCATGAACTATCCATGCGTAC 58.770 41.667 0.00 0.00 40.74 3.67
1738 7328 0.386352 TACGCACGTTTCAGGTCGAG 60.386 55.000 0.00 0.00 0.00 4.04
1801 7391 2.551912 CCAAGCTCCGCCGTTGTTT 61.552 57.895 0.00 0.00 0.00 2.83
2025 7615 1.132640 GATCGTGCCTGTTTCGTGC 59.867 57.895 0.00 0.00 0.00 5.34
2102 7692 6.606234 TGTTGCTCGGCGAATAATTAATTA 57.394 33.333 12.13 10.27 0.00 1.40
2173 7953 3.190535 ACGGAGAACACATATTTTGCACC 59.809 43.478 0.00 0.00 0.00 5.01
2198 7978 8.979574 CCTAGTCGTGATTTATCTACCATTTTC 58.020 37.037 0.00 0.00 0.00 2.29
2225 8006 9.601217 CTTAAAACTAACTAGATATGTGCCTGT 57.399 33.333 0.00 0.00 0.00 4.00
2231 8012 2.979814 AGATATGTGCCTGTGCGTTA 57.020 45.000 0.00 0.00 41.78 3.18
2235 8016 0.322456 ATGTGCCTGTGCGTTACCAT 60.322 50.000 0.00 0.00 41.78 3.55
2236 8017 1.233950 TGTGCCTGTGCGTTACCATG 61.234 55.000 0.00 0.00 41.78 3.66
2238 8019 1.376683 GCCTGTGCGTTACCATGGA 60.377 57.895 21.47 0.00 0.00 3.41
2240 8021 0.249120 CCTGTGCGTTACCATGGAGA 59.751 55.000 21.47 2.30 0.00 3.71
2241 8022 1.134401 CCTGTGCGTTACCATGGAGAT 60.134 52.381 21.47 0.00 0.00 2.75
2351 8392 6.479660 ACCATGAAGTACAAATTTTGCAACTG 59.520 34.615 14.86 0.00 32.48 3.16
2365 8406 8.871686 ATTTTGCAACTGTTTCTTAAACTAGG 57.128 30.769 0.00 0.00 41.90 3.02
2366 8407 7.399245 TTTGCAACTGTTTCTTAAACTAGGT 57.601 32.000 0.00 0.00 41.90 3.08
2369 8410 8.094798 TGCAACTGTTTCTTAAACTAGGTATG 57.905 34.615 0.00 0.00 41.90 2.39
2370 8411 7.717875 TGCAACTGTTTCTTAAACTAGGTATGT 59.282 33.333 0.00 0.00 41.90 2.29
2371 8412 8.565416 GCAACTGTTTCTTAAACTAGGTATGTT 58.435 33.333 0.00 0.00 41.90 2.71
2403 8444 7.902920 AAAGGTATGTGCCAATGATTAATCT 57.097 32.000 16.24 0.00 0.00 2.40
2437 8481 7.827236 TGGGTTACCAAATACTACAAGAGATTG 59.173 37.037 2.98 0.00 45.87 2.67
2461 8505 6.437477 TGATCGATATGTATTAGCTTCTGGGT 59.563 38.462 0.00 0.00 0.00 4.51
2468 8512 3.914426 ATTAGCTTCTGGGTCGTGAAT 57.086 42.857 0.00 0.00 0.00 2.57
2469 8513 3.695830 TTAGCTTCTGGGTCGTGAATT 57.304 42.857 0.00 0.00 0.00 2.17
2502 8546 2.877097 TGGCTTGCCAAAGATGTCTA 57.123 45.000 12.40 0.00 35.19 2.59
2503 8547 3.153369 TGGCTTGCCAAAGATGTCTAA 57.847 42.857 12.40 0.00 35.19 2.10
2512 8556 3.055675 CCAAAGATGTCTAACCGGTACCA 60.056 47.826 8.00 2.24 0.00 3.25
2527 8571 4.080975 CCGGTACCAGGTTTACCATAAGAA 60.081 45.833 13.54 0.00 39.29 2.52
2531 8575 5.952526 ACCAGGTTTACCATAAGAAAACG 57.047 39.130 1.13 0.00 38.89 3.60
2538 8582 9.902196 AGGTTTACCATAAGAAAACGTTATTTG 57.098 29.630 0.00 0.00 38.89 2.32
2541 8585 5.395642 ACCATAAGAAAACGTTATTTGCGG 58.604 37.500 0.00 0.00 0.00 5.69
2545 8589 2.879646 AGAAAACGTTATTTGCGGACCA 59.120 40.909 0.00 0.00 0.00 4.02
2553 8597 5.124138 ACGTTATTTGCGGACCATGAATTTA 59.876 36.000 0.00 0.00 0.00 1.40
2563 8607 6.622896 GCGGACCATGAATTTATTGCTATACC 60.623 42.308 0.00 0.00 0.00 2.73
2584 8628 6.850752 ACCATAGTTTAATCTGGTTTTGGG 57.149 37.500 0.00 0.00 38.88 4.12
2585 8629 6.319715 ACCATAGTTTAATCTGGTTTTGGGT 58.680 36.000 0.00 0.00 38.88 4.51
2586 8630 6.785466 ACCATAGTTTAATCTGGTTTTGGGTT 59.215 34.615 0.00 0.00 38.88 4.11
2587 8631 7.291416 ACCATAGTTTAATCTGGTTTTGGGTTT 59.709 33.333 0.00 0.00 38.88 3.27
2588 8632 8.154203 CCATAGTTTAATCTGGTTTTGGGTTTT 58.846 33.333 0.00 0.00 0.00 2.43
2589 8633 9.554395 CATAGTTTAATCTGGTTTTGGGTTTTT 57.446 29.630 0.00 0.00 0.00 1.94
2614 8658 0.110869 TCTGGTTTTGGGGGTTACGG 59.889 55.000 0.00 0.00 0.00 4.02
2632 8676 6.294286 GGTTACGGAAGATTGGTTTGATGAAA 60.294 38.462 0.00 0.00 0.00 2.69
2652 8696 9.351570 GATGAAAACCAGAAGAGAATGAAAATC 57.648 33.333 0.00 0.00 0.00 2.17
2675 8719 1.702957 TCGGTGGAAGATGGAAGGTTT 59.297 47.619 0.00 0.00 0.00 3.27
2682 8726 4.584325 TGGAAGATGGAAGGTTTGACAAAG 59.416 41.667 0.00 0.00 0.00 2.77
2685 8729 3.140144 AGATGGAAGGTTTGACAAAGGGA 59.860 43.478 0.00 0.00 0.00 4.20
2692 8736 2.497273 GGTTTGACAAAGGGATGATGGG 59.503 50.000 0.00 0.00 0.00 4.00
2706 8750 6.216456 AGGGATGATGGGGAGAATTAATACTC 59.784 42.308 0.00 0.00 0.00 2.59
2707 8751 6.216456 GGGATGATGGGGAGAATTAATACTCT 59.784 42.308 0.00 0.00 34.11 3.24
2711 8755 6.615316 TGATGGGGAGAATTAATACTCTGTGA 59.385 38.462 0.00 0.00 34.11 3.58
2722 8766 8.738645 ATTAATACTCTGTGAAAGATGGAACC 57.261 34.615 0.00 0.00 33.29 3.62
2736 8780 6.195600 AGATGGAACCTTAGGTTTGTACAA 57.804 37.500 18.52 3.59 46.95 2.41
2741 8785 5.106277 GGAACCTTAGGTTTGTACAAGATGC 60.106 44.000 18.52 0.50 46.95 3.91
2746 8790 1.201921 GGTTTGTACAAGATGCGCTCG 60.202 52.381 9.73 0.00 0.00 5.03
2747 8791 1.075542 TTTGTACAAGATGCGCTCGG 58.924 50.000 9.73 4.69 0.00 4.63
2757 8801 4.388499 GCGCTCGGGGAGTTGGAA 62.388 66.667 0.00 0.00 31.39 3.53
2767 8812 3.409570 GGGGAGTTGGAAGTAACTTGTC 58.590 50.000 0.00 0.00 40.78 3.18
2794 8839 1.974236 GGGGTGGATGATCTAGACAGG 59.026 57.143 0.00 0.00 0.00 4.00
2798 8843 3.034635 GTGGATGATCTAGACAGGGTGT 58.965 50.000 0.00 0.00 0.00 4.16
2812 8857 6.909550 GACAGGGTGTCTAGATGAATCTAT 57.090 41.667 0.00 0.00 43.73 1.98
2828 8873 6.891624 TGAATCTATTGATTGTGCTAATCGC 58.108 36.000 7.13 0.00 42.43 4.58
2854 8899 6.644347 TGAAGCTAGGATTTTCGAAGATCTT 58.356 36.000 23.33 19.71 35.04 2.40
2901 8946 0.402504 TTTGTTGGGTGGACGCCTAT 59.597 50.000 1.50 0.00 0.00 2.57
2920 8965 5.163581 GCCTATTTGTAGTAGTCTTGGTCGA 60.164 44.000 0.00 0.00 0.00 4.20
2931 8976 0.109597 CTTGGTCGATTGCCACTTGC 60.110 55.000 0.00 0.00 41.77 4.01
2952 8997 4.722193 CCGTTTGGTCTCATGCCT 57.278 55.556 0.00 0.00 0.00 4.75
2959 9004 0.178767 TGGTCTCATGCCTCAATCCG 59.821 55.000 0.00 0.00 0.00 4.18
2966 9011 0.904649 ATGCCTCAATCCGTCACAGA 59.095 50.000 0.00 0.00 0.00 3.41
2973 9018 1.134965 CAATCCGTCACAGAGACCTCC 60.135 57.143 0.00 0.00 44.66 4.30
2981 9026 3.927142 GTCACAGAGACCTCCGTTTATTG 59.073 47.826 0.00 0.00 41.56 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 8.877195 AGTTTTTCTAGAAACCATAGTACTCCA 58.123 33.333 17.51 0.00 39.71 3.86
85 87 9.357161 TGGTAAAACCACAATTTACAAGACTAT 57.643 29.630 10.31 0.00 44.79 2.12
87 89 7.648039 TGGTAAAACCACAATTTACAAGACT 57.352 32.000 10.31 0.00 44.79 3.24
260 272 1.790387 GTGAGTTTGCTGCTAGCCG 59.210 57.895 13.29 7.09 41.51 5.52
262 274 1.133458 GCGTGAGTTTGCTGCTAGC 59.867 57.895 8.10 8.10 42.82 3.42
267 279 0.792640 AGAATCGCGTGAGTTTGCTG 59.207 50.000 5.77 0.00 0.00 4.41
279 291 5.515626 GGATATTGGTATCGTACAGAATCGC 59.484 44.000 0.00 0.00 38.06 4.58
302 314 3.953612 TCACATTGGCTAGGCTAAATTGG 59.046 43.478 18.18 4.64 31.91 3.16
303 315 4.398988 TGTCACATTGGCTAGGCTAAATTG 59.601 41.667 18.18 7.95 31.91 2.32
304 316 4.399303 GTGTCACATTGGCTAGGCTAAATT 59.601 41.667 18.18 0.00 31.91 1.82
312 324 4.456911 AGATTTGTGTGTCACATTGGCTAG 59.543 41.667 9.31 0.00 44.16 3.42
313 325 4.397420 AGATTTGTGTGTCACATTGGCTA 58.603 39.130 9.31 0.00 44.16 3.93
314 326 3.225104 AGATTTGTGTGTCACATTGGCT 58.775 40.909 9.31 1.14 44.16 4.75
315 327 3.648339 AGATTTGTGTGTCACATTGGC 57.352 42.857 9.31 0.00 44.16 4.52
316 328 4.456911 AGCTAGATTTGTGTGTCACATTGG 59.543 41.667 9.31 0.00 44.16 3.16
317 329 5.049198 ACAGCTAGATTTGTGTGTCACATTG 60.049 40.000 9.31 0.00 44.16 2.82
318 330 5.065914 ACAGCTAGATTTGTGTGTCACATT 58.934 37.500 9.31 0.00 44.16 2.71
322 334 9.529325 GTATATAACAGCTAGATTTGTGTGTCA 57.471 33.333 0.00 0.00 0.00 3.58
323 335 9.751542 AGTATATAACAGCTAGATTTGTGTGTC 57.248 33.333 0.00 0.00 0.00 3.67
327 339 8.589338 AGGGAGTATATAACAGCTAGATTTGTG 58.411 37.037 0.00 0.00 0.00 3.33
328 340 8.728596 AGGGAGTATATAACAGCTAGATTTGT 57.271 34.615 0.00 0.00 0.00 2.83
329 341 9.646427 GAAGGGAGTATATAACAGCTAGATTTG 57.354 37.037 0.00 0.00 0.00 2.32
330 342 8.524487 CGAAGGGAGTATATAACAGCTAGATTT 58.476 37.037 0.00 0.00 0.00 2.17
331 343 7.670559 ACGAAGGGAGTATATAACAGCTAGATT 59.329 37.037 0.00 0.00 0.00 2.40
333 345 6.540995 ACGAAGGGAGTATATAACAGCTAGA 58.459 40.000 0.00 0.00 0.00 2.43
334 346 6.821031 ACGAAGGGAGTATATAACAGCTAG 57.179 41.667 0.00 0.00 0.00 3.42
335 347 7.504911 AGAAACGAAGGGAGTATATAACAGCTA 59.495 37.037 0.00 0.00 0.00 3.32
337 349 6.514063 AGAAACGAAGGGAGTATATAACAGC 58.486 40.000 0.00 0.00 0.00 4.40
345 357 7.985752 CCTTACATAAAGAAACGAAGGGAGTAT 59.014 37.037 0.00 0.00 37.38 2.12
346 358 7.038799 ACCTTACATAAAGAAACGAAGGGAGTA 60.039 37.037 0.00 0.00 37.38 2.59
347 359 6.171213 CCTTACATAAAGAAACGAAGGGAGT 58.829 40.000 0.00 0.00 37.38 3.85
348 360 6.092259 CACCTTACATAAAGAAACGAAGGGAG 59.908 42.308 0.00 0.00 37.38 4.30
349 361 5.935789 CACCTTACATAAAGAAACGAAGGGA 59.064 40.000 0.00 0.00 37.38 4.20
350 362 5.704053 ACACCTTACATAAAGAAACGAAGGG 59.296 40.000 0.00 0.00 37.38 3.95
351 363 6.796705 ACACCTTACATAAAGAAACGAAGG 57.203 37.500 0.00 0.00 37.38 3.46
390 451 5.525012 TCTCTACAATTTCATGCCTTGATCG 59.475 40.000 8.21 0.00 33.34 3.69
450 511 5.753921 AGCTAATTGATTACCTGTCGCTAAC 59.246 40.000 0.00 0.00 0.00 2.34
543 883 0.915364 GTCTCCCCCTTCTGATTGCT 59.085 55.000 0.00 0.00 0.00 3.91
550 890 1.470165 ACGGAAGTCTCCCCCTTCT 59.530 57.895 0.00 0.00 44.19 2.85
577 1819 5.365314 TCTTGTAATTTGTTTTCCAGCCCTT 59.635 36.000 0.00 0.00 0.00 3.95
698 2915 9.635404 TTTTGGAGAAAGAAGGTAGTAAAATCA 57.365 29.630 0.00 0.00 0.00 2.57
700 2917 9.862149 TCTTTTGGAGAAAGAAGGTAGTAAAAT 57.138 29.630 0.00 0.00 33.72 1.82
797 3014 7.870826 TGTGAGAACCATTGTATTTTACAGTG 58.129 34.615 3.87 3.87 43.50 3.66
926 6511 2.358615 GTGGCTGTGCGATGGACA 60.359 61.111 0.00 0.00 0.00 4.02
960 6545 0.538977 ACGACGAAGAAGAGGGACCA 60.539 55.000 0.00 0.00 0.00 4.02
991 6576 0.613012 AGCCTTGCCATTTGGAGTCC 60.613 55.000 0.73 0.73 37.39 3.85
1225 6810 0.171455 GTCAGGAACTCGACGCTGAT 59.829 55.000 5.59 0.00 34.60 2.90
1509 7094 2.084546 GGTAGTGCAAAGCTTACCTGG 58.915 52.381 0.00 0.00 36.91 4.45
1527 7112 2.913463 CAGGATGCAGAGAGGAGGT 58.087 57.895 0.00 0.00 0.00 3.85
1604 7189 2.871216 ATCTCTCGGTCGTCGCTCCA 62.871 60.000 6.99 0.00 39.05 3.86
1669 7259 5.782047 TGTGACCATTTAAATTCCAAGCAG 58.218 37.500 0.00 0.00 0.00 4.24
1721 7311 3.000080 GCTCGACCTGAAACGTGCG 62.000 63.158 0.00 0.00 38.70 5.34
1738 7328 0.318762 ACCTCGACCTGAACTTCAGC 59.681 55.000 12.69 0.60 42.98 4.26
1801 7391 0.171679 ACGTCAGTGTTGTGTCGACA 59.828 50.000 15.76 15.76 0.00 4.35
2025 7615 6.300354 AGGTGTTTCACGAAATTTGTAGAG 57.700 37.500 0.00 0.00 34.83 2.43
2173 7953 8.979574 GGAAAATGGTAGATAAATCACGACTAG 58.020 37.037 0.00 0.00 0.00 2.57
2198 7978 9.046296 CAGGCACATATCTAGTTAGTTTTAAGG 57.954 37.037 0.00 0.00 0.00 2.69
2214 7995 1.065782 TGGTAACGCACAGGCACATAT 60.066 47.619 0.00 0.00 41.24 1.78
2225 8006 3.342377 TTTGATCTCCATGGTAACGCA 57.658 42.857 12.58 2.39 42.51 5.24
2269 8051 5.029807 TGCATCAAGATTTATCCCGTACA 57.970 39.130 0.00 0.00 0.00 2.90
2270 8052 6.371809 TTTGCATCAAGATTTATCCCGTAC 57.628 37.500 0.00 0.00 0.00 3.67
2328 8369 7.467557 ACAGTTGCAAAATTTGTACTTCATG 57.532 32.000 0.00 3.90 0.00 3.07
2380 8421 6.239120 GCAGATTAATCATTGGCACATACCTT 60.239 38.462 17.56 0.00 39.30 3.50
2428 8472 9.800433 AGCTAATACATATCGATCAATCTCTTG 57.200 33.333 0.00 0.00 0.00 3.02
2437 8481 6.868622 ACCCAGAAGCTAATACATATCGATC 58.131 40.000 0.00 0.00 0.00 3.69
2440 8484 5.096169 CGACCCAGAAGCTAATACATATCG 58.904 45.833 0.00 0.00 0.00 2.92
2489 8533 2.109425 ACCGGTTAGACATCTTTGGC 57.891 50.000 0.00 0.00 0.00 4.52
2493 8537 2.764572 CCTGGTACCGGTTAGACATCTT 59.235 50.000 15.04 0.00 0.00 2.40
2502 8546 1.433121 TGGTAAACCTGGTACCGGTT 58.567 50.000 25.89 25.89 46.27 4.44
2503 8547 1.660242 ATGGTAAACCTGGTACCGGT 58.340 50.000 19.59 19.23 43.48 5.28
2512 8556 9.902196 CAAATAACGTTTTCTTATGGTAAACCT 57.098 29.630 5.91 0.00 36.82 3.50
2527 8571 2.814919 TCATGGTCCGCAAATAACGTTT 59.185 40.909 5.91 0.00 0.00 3.60
2531 8575 7.516627 GCAATAAATTCATGGTCCGCAAATAAC 60.517 37.037 0.00 0.00 0.00 1.89
2538 8582 3.715628 AGCAATAAATTCATGGTCCGC 57.284 42.857 0.00 0.00 0.00 5.54
2563 8607 9.554395 AAAAACCCAAAACCAGATTAAACTATG 57.446 29.630 0.00 0.00 0.00 2.23
2587 8631 7.093858 CGTAACCCCCAAAACCAGATATAAAAA 60.094 37.037 0.00 0.00 0.00 1.94
2588 8632 6.377712 CGTAACCCCCAAAACCAGATATAAAA 59.622 38.462 0.00 0.00 0.00 1.52
2589 8633 5.887035 CGTAACCCCCAAAACCAGATATAAA 59.113 40.000 0.00 0.00 0.00 1.40
2590 8634 5.438833 CGTAACCCCCAAAACCAGATATAA 58.561 41.667 0.00 0.00 0.00 0.98
2591 8635 4.141436 CCGTAACCCCCAAAACCAGATATA 60.141 45.833 0.00 0.00 0.00 0.86
2592 8636 3.372241 CCGTAACCCCCAAAACCAGATAT 60.372 47.826 0.00 0.00 0.00 1.63
2593 8637 2.026075 CCGTAACCCCCAAAACCAGATA 60.026 50.000 0.00 0.00 0.00 1.98
2594 8638 1.272258 CCGTAACCCCCAAAACCAGAT 60.272 52.381 0.00 0.00 0.00 2.90
2595 8639 0.110869 CCGTAACCCCCAAAACCAGA 59.889 55.000 0.00 0.00 0.00 3.86
2596 8640 0.110869 TCCGTAACCCCCAAAACCAG 59.889 55.000 0.00 0.00 0.00 4.00
2597 8641 0.554792 TTCCGTAACCCCCAAAACCA 59.445 50.000 0.00 0.00 0.00 3.67
2598 8642 1.202915 TCTTCCGTAACCCCCAAAACC 60.203 52.381 0.00 0.00 0.00 3.27
2599 8643 2.275134 TCTTCCGTAACCCCCAAAAC 57.725 50.000 0.00 0.00 0.00 2.43
2600 8644 3.158676 CAATCTTCCGTAACCCCCAAAA 58.841 45.455 0.00 0.00 0.00 2.44
2601 8645 2.555670 CCAATCTTCCGTAACCCCCAAA 60.556 50.000 0.00 0.00 0.00 3.28
2602 8646 1.004979 CCAATCTTCCGTAACCCCCAA 59.995 52.381 0.00 0.00 0.00 4.12
2603 8647 0.621609 CCAATCTTCCGTAACCCCCA 59.378 55.000 0.00 0.00 0.00 4.96
2604 8648 0.622136 ACCAATCTTCCGTAACCCCC 59.378 55.000 0.00 0.00 0.00 5.40
2611 8655 5.528870 GTTTTCATCAAACCAATCTTCCGT 58.471 37.500 0.00 0.00 39.22 4.69
2632 8676 6.094603 CGATGGATTTTCATTCTCTTCTGGTT 59.905 38.462 0.00 0.00 0.00 3.67
2675 8719 1.565759 CTCCCCATCATCCCTTTGTCA 59.434 52.381 0.00 0.00 0.00 3.58
2682 8726 6.216456 AGAGTATTAATTCTCCCCATCATCCC 59.784 42.308 16.05 0.00 0.00 3.85
2685 8729 7.293299 TCACAGAGTATTAATTCTCCCCATCAT 59.707 37.037 16.05 0.00 0.00 2.45
2692 8736 9.050601 CCATCTTTCACAGAGTATTAATTCTCC 57.949 37.037 16.05 2.19 33.87 3.71
2706 8750 4.911390 ACCTAAGGTTCCATCTTTCACAG 58.089 43.478 0.00 0.00 27.29 3.66
2707 8751 4.993705 ACCTAAGGTTCCATCTTTCACA 57.006 40.909 0.00 0.00 27.29 3.58
2711 8755 6.607019 TGTACAAACCTAAGGTTCCATCTTT 58.393 36.000 0.00 0.00 46.20 2.52
2722 8766 3.684788 AGCGCATCTTGTACAAACCTAAG 59.315 43.478 11.47 0.00 0.00 2.18
2736 8780 3.077556 AACTCCCCGAGCGCATCT 61.078 61.111 11.47 0.00 32.04 2.90
2741 8785 1.601419 TACTTCCAACTCCCCGAGCG 61.601 60.000 0.00 0.00 32.04 5.03
2746 8790 3.409570 GACAAGTTACTTCCAACTCCCC 58.590 50.000 0.00 0.00 37.78 4.81
2747 8791 3.064931 CGACAAGTTACTTCCAACTCCC 58.935 50.000 0.00 0.00 37.78 4.30
2757 8801 3.257624 CACCCCTAACTCGACAAGTTACT 59.742 47.826 0.00 0.00 46.55 2.24
2767 8812 2.320781 AGATCATCCACCCCTAACTCG 58.679 52.381 0.00 0.00 0.00 4.18
2774 8819 1.974236 CCTGTCTAGATCATCCACCCC 59.026 57.143 0.00 0.00 0.00 4.95
2794 8839 8.986847 CACAATCAATAGATTCATCTAGACACC 58.013 37.037 0.00 0.00 42.46 4.16
2828 8873 4.759782 TCTTCGAAAATCCTAGCTTCAGG 58.240 43.478 0.00 0.00 37.00 3.86
2854 8899 6.759272 AGAGACATAATATTAAGCTTCGCCA 58.241 36.000 0.00 0.00 0.00 5.69
2867 8912 7.331026 CACCCAACAAAGAGAGAGACATAATA 58.669 38.462 0.00 0.00 0.00 0.98
2870 8915 4.020218 CCACCCAACAAAGAGAGAGACATA 60.020 45.833 0.00 0.00 0.00 2.29
2871 8916 3.244700 CCACCCAACAAAGAGAGAGACAT 60.245 47.826 0.00 0.00 0.00 3.06
2872 8917 2.104792 CCACCCAACAAAGAGAGAGACA 59.895 50.000 0.00 0.00 0.00 3.41
2873 8918 2.368875 TCCACCCAACAAAGAGAGAGAC 59.631 50.000 0.00 0.00 0.00 3.36
2874 8919 2.368875 GTCCACCCAACAAAGAGAGAGA 59.631 50.000 0.00 0.00 0.00 3.10
2875 8920 2.772287 GTCCACCCAACAAAGAGAGAG 58.228 52.381 0.00 0.00 0.00 3.20
2876 8921 1.070134 CGTCCACCCAACAAAGAGAGA 59.930 52.381 0.00 0.00 0.00 3.10
2877 8922 1.512926 CGTCCACCCAACAAAGAGAG 58.487 55.000 0.00 0.00 0.00 3.20
2878 8923 0.534203 GCGTCCACCCAACAAAGAGA 60.534 55.000 0.00 0.00 0.00 3.10
2880 8925 1.527380 GGCGTCCACCCAACAAAGA 60.527 57.895 0.00 0.00 0.00 2.52
2881 8926 0.250553 TAGGCGTCCACCCAACAAAG 60.251 55.000 0.00 0.00 0.00 2.77
2882 8927 0.402504 ATAGGCGTCCACCCAACAAA 59.597 50.000 0.00 0.00 0.00 2.83
2884 8929 0.402504 AAATAGGCGTCCACCCAACA 59.597 50.000 0.00 0.00 0.00 3.33
2885 8930 0.808755 CAAATAGGCGTCCACCCAAC 59.191 55.000 0.00 0.00 0.00 3.77
2886 8931 0.402504 ACAAATAGGCGTCCACCCAA 59.597 50.000 0.00 0.00 0.00 4.12
2887 8932 1.208535 CTACAAATAGGCGTCCACCCA 59.791 52.381 0.00 0.00 0.00 4.51
2888 8933 1.208776 ACTACAAATAGGCGTCCACCC 59.791 52.381 0.00 0.00 32.08 4.61
2901 8946 4.927425 GCAATCGACCAAGACTACTACAAA 59.073 41.667 0.00 0.00 0.00 2.83
2952 8997 1.819288 GAGGTCTCTGTGACGGATTGA 59.181 52.381 0.00 0.00 46.24 2.57
2966 9011 5.187186 ACATGACTACAATAAACGGAGGTCT 59.813 40.000 0.00 0.00 0.00 3.85
2973 9018 7.290857 ACAAGCTACATGACTACAATAAACG 57.709 36.000 0.00 0.00 0.00 3.60
2981 9026 4.631813 CCCTGAAACAAGCTACATGACTAC 59.368 45.833 0.00 0.00 0.00 2.73


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

AutoCloner maintained by Alex Coulton.