Multiple sequence alignment - TraesCS5A01G255000

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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 TraesCS5A01G255000 chr5A 100.000 2388 0 0 1 2388 470761729 470759342 0.000000e+00 4410.0
1 TraesCS5A01G255000 chr5A 92.658 1689 46 26 749 2388 470546098 470544439 0.000000e+00 2361.0
2 TraesCS5A01G255000 chr5A 85.985 792 66 20 1579 2359 470673551 470672794 0.000000e+00 806.0
3 TraesCS5A01G255000 chr5A 84.975 599 38 25 749 1298 470674486 470673891 6.990000e-156 560.0
4 TraesCS5A01G255000 chr5A 100.000 239 0 0 2649 2887 470759081 470758843 2.640000e-120 442.0
5 TraesCS5A01G255000 chr5A 91.011 178 15 1 2706 2883 470672381 470672205 3.720000e-59 239.0
6 TraesCS5A01G255000 chr5A 88.971 136 15 0 1039 1174 471472377 471472512 4.950000e-38 169.0
7 TraesCS5A01G255000 chr5A 100.000 77 0 0 2649 2725 470544113 470544037 3.000000e-30 143.0
8 TraesCS5A01G255000 chr5B 90.374 696 47 9 1305 1983 437250984 437251676 0.000000e+00 896.0
9 TraesCS5A01G255000 chr5B 85.174 634 57 18 670 1268 437250288 437250919 1.470000e-172 616.0
10 TraesCS5A01G255000 chr5B 82.642 530 59 17 67 582 690405670 690406180 3.420000e-119 438.0
11 TraesCS5A01G255000 chr5B 91.781 146 12 0 1036 1181 436619093 436619238 1.360000e-48 204.0
12 TraesCS5A01G255000 chr5B 91.176 136 12 0 1039 1174 436552926 436553061 4.910000e-43 185.0
13 TraesCS5A01G255000 chr5B 79.839 124 25 0 459 582 660216616 660216739 1.100000e-14 91.6
14 TraesCS5A01G255000 chr5D 89.155 710 46 19 1305 1983 369034784 369035493 0.000000e+00 856.0
15 TraesCS5A01G255000 chr5D 84.896 576 40 24 736 1268 369034150 369034721 3.270000e-149 538.0
16 TraesCS5A01G255000 chr5D 90.345 145 14 0 1037 1181 368827271 368827415 1.060000e-44 191.0
17 TraesCS5A01G255000 chr5D 90.441 136 13 0 1039 1174 368993164 368993299 2.290000e-41 180.0
18 TraesCS5A01G255000 chr5D 86.667 75 9 1 2251 2325 369036577 369036650 6.630000e-12 82.4
19 TraesCS5A01G255000 chr7B 84.120 233 32 4 352 581 110107864 110108094 1.350000e-53 220.0
20 TraesCS5A01G255000 chr6B 76.960 421 54 13 203 582 35716744 35717162 1.750000e-47 200.0
21 TraesCS5A01G255000 chr7A 79.839 124 25 0 459 582 546430111 546430234 1.100000e-14 91.6
22 TraesCS5A01G255000 chr7A 79.839 124 25 0 459 582 611777930 611778053 1.100000e-14 91.6
23 TraesCS5A01G255000 chr2B 79.839 124 25 0 459 582 770025503 770025626 1.100000e-14 91.6
24 TraesCS5A01G255000 chr1B 79.839 124 25 0 459 582 121778712 121778589 1.100000e-14 91.6
25 TraesCS5A01G255000 chr1A 80.315 127 19 4 458 582 358912639 358912517 1.100000e-14 91.6
26 TraesCS5A01G255000 chr2D 97.297 37 1 0 2168 2204 28913436 28913472 2.400000e-06 63.9


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 TraesCS5A01G255000 chr5A 470758843 470761729 2886 True 2426.000000 4410 100.000000 1 2887 2 chr5A.!!$R3 2886
1 TraesCS5A01G255000 chr5A 470544037 470546098 2061 True 1252.000000 2361 96.329000 749 2725 2 chr5A.!!$R1 1976
2 TraesCS5A01G255000 chr5A 470672205 470674486 2281 True 535.000000 806 87.323667 749 2883 3 chr5A.!!$R2 2134
3 TraesCS5A01G255000 chr5B 437250288 437251676 1388 False 756.000000 896 87.774000 670 1983 2 chr5B.!!$F5 1313
4 TraesCS5A01G255000 chr5B 690405670 690406180 510 False 438.000000 438 82.642000 67 582 1 chr5B.!!$F4 515
5 TraesCS5A01G255000 chr5D 369034150 369036650 2500 False 492.133333 856 86.906000 736 2325 3 chr5D.!!$F3 1589

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
313 314 0.108756 GCCGGAAGAAACGCTAGAGT 60.109 55.0 5.05 0.0 0.0 3.24 F
329 330 0.309612 GAGTAGAGTAGCAGGCGAGC 59.690 60.0 0.00 0.0 0.0 5.03 F
463 478 0.696501 GGCTGGAAACTTGGACCCTA 59.303 55.0 0.00 0.0 0.0 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1508 1631 0.387367 ACAAGAGAGTGCGCGTACTG 60.387 55.000 34.34 21.57 0.00 2.74 R
1590 1757 0.913451 ATGCTCCTCACCAGCTCCTT 60.913 55.000 0.00 0.00 37.79 3.36 R
1944 2122 1.764723 TGGATCATTGTGGCGAGATCT 59.235 47.619 0.00 0.00 37.59 2.75 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
30 31 3.835810 CCCCCTGATTTCAGATGGG 57.164 57.895 16.07 16.07 46.59 4.00
31 32 3.835810 CCCCTGATTTCAGATGGGG 57.164 57.895 9.15 8.38 46.59 4.96
32 33 0.186873 CCCCTGATTTCAGATGGGGG 59.813 60.000 12.57 9.95 46.59 5.40
55 56 2.678471 GGGGGATGCTTTGTGATTTG 57.322 50.000 0.00 0.00 0.00 2.32
56 57 1.901833 GGGGGATGCTTTGTGATTTGT 59.098 47.619 0.00 0.00 0.00 2.83
57 58 2.354003 GGGGGATGCTTTGTGATTTGTG 60.354 50.000 0.00 0.00 0.00 3.33
58 59 2.562298 GGGGATGCTTTGTGATTTGTGA 59.438 45.455 0.00 0.00 0.00 3.58
59 60 3.006752 GGGGATGCTTTGTGATTTGTGAA 59.993 43.478 0.00 0.00 0.00 3.18
60 61 4.322953 GGGGATGCTTTGTGATTTGTGAAT 60.323 41.667 0.00 0.00 0.00 2.57
61 62 4.628333 GGGATGCTTTGTGATTTGTGAATG 59.372 41.667 0.00 0.00 0.00 2.67
62 63 4.092383 GGATGCTTTGTGATTTGTGAATGC 59.908 41.667 0.00 0.00 0.00 3.56
63 64 3.391965 TGCTTTGTGATTTGTGAATGCC 58.608 40.909 0.00 0.00 0.00 4.40
64 65 3.181468 TGCTTTGTGATTTGTGAATGCCA 60.181 39.130 0.00 0.00 0.00 4.92
65 66 3.184986 GCTTTGTGATTTGTGAATGCCAC 59.815 43.478 0.00 0.00 45.88 5.01
83 84 3.742369 GCCACAATTGACCAAAACTGATG 59.258 43.478 13.59 0.00 0.00 3.07
101 102 2.276732 TGAAGAGTTGCAGAAAGGGG 57.723 50.000 0.00 0.00 0.00 4.79
104 105 2.503895 AGAGTTGCAGAAAGGGGATG 57.496 50.000 0.00 0.00 0.00 3.51
121 122 1.003116 GATGGATCATTGCAGCGTGTC 60.003 52.381 0.00 0.00 0.00 3.67
197 198 2.791655 ACGTAGTCACCTCATCAGACA 58.208 47.619 0.00 0.00 29.74 3.41
201 202 3.883830 AGTCACCTCATCAGACATCAC 57.116 47.619 0.00 0.00 34.80 3.06
244 245 1.153005 GCTTGGCAGGGGAGATCAG 60.153 63.158 0.00 0.00 0.00 2.90
273 274 1.757118 GAGATGGGGATCGAACAGACA 59.243 52.381 0.00 0.00 0.00 3.41
276 277 2.940994 TGGGGATCGAACAGACAAAA 57.059 45.000 0.00 0.00 0.00 2.44
298 299 3.655276 ATCTACCTACAAATACGCCGG 57.345 47.619 0.00 0.00 0.00 6.13
309 310 0.457035 ATACGCCGGAAGAAACGCTA 59.543 50.000 5.05 0.00 0.00 4.26
313 314 0.108756 GCCGGAAGAAACGCTAGAGT 60.109 55.000 5.05 0.00 0.00 3.24
318 319 3.374678 CGGAAGAAACGCTAGAGTAGAGT 59.625 47.826 0.00 0.00 40.64 3.24
324 325 2.841215 ACGCTAGAGTAGAGTAGCAGG 58.159 52.381 0.00 0.00 41.57 4.85
329 330 0.309612 GAGTAGAGTAGCAGGCGAGC 59.690 60.000 0.00 0.00 0.00 5.03
376 391 3.458163 GATCCCACGACCGAGGCA 61.458 66.667 0.29 0.00 0.00 4.75
413 428 4.729918 GCTCAGGCCTGTGTGGGG 62.730 72.222 31.58 16.03 36.00 4.96
440 455 4.958396 CGCGCGCGTAGAGGGTAG 62.958 72.222 42.49 13.34 43.02 3.18
441 456 3.580193 GCGCGCGTAGAGGGTAGA 61.580 66.667 32.35 0.00 43.02 2.59
444 459 3.020627 CGCGTAGAGGGTAGACGG 58.979 66.667 0.00 0.00 37.08 4.79
450 465 1.284111 TAGAGGGTAGACGGGCTGGA 61.284 60.000 0.00 0.00 0.00 3.86
463 478 0.696501 GGCTGGAAACTTGGACCCTA 59.303 55.000 0.00 0.00 0.00 3.53
475 490 1.453928 GACCCTAATGCACTGCCCC 60.454 63.158 0.00 0.00 0.00 5.80
476 491 2.516930 CCCTAATGCACTGCCCCG 60.517 66.667 0.00 0.00 0.00 5.73
503 518 1.820581 CTGATGCCCAGGCCATTTG 59.179 57.895 5.01 0.00 39.23 2.32
504 519 1.682451 CTGATGCCCAGGCCATTTGG 61.682 60.000 5.01 3.48 39.23 3.28
514 529 4.217510 CCAGGCCATTTGGAGATGATAAA 58.782 43.478 5.01 0.00 37.96 1.40
516 531 4.646040 CAGGCCATTTGGAGATGATAAACA 59.354 41.667 5.01 0.00 37.39 2.83
521 536 5.359009 CCATTTGGAGATGATAAACACTGCT 59.641 40.000 0.00 0.00 37.39 4.24
522 537 5.885230 TTTGGAGATGATAAACACTGCTG 57.115 39.130 0.00 0.00 0.00 4.41
527 542 6.489700 TGGAGATGATAAACACTGCTGAAAAA 59.510 34.615 0.00 0.00 0.00 1.94
528 543 6.803807 GGAGATGATAAACACTGCTGAAAAAC 59.196 38.462 0.00 0.00 0.00 2.43
532 547 6.862209 TGATAAACACTGCTGAAAAACTTGT 58.138 32.000 0.00 0.00 0.00 3.16
588 603 3.081409 GCTCCGCCCCTCAGGTTA 61.081 66.667 0.00 0.00 38.26 2.85
589 604 3.095347 GCTCCGCCCCTCAGGTTAG 62.095 68.421 0.00 0.00 38.26 2.34
590 605 1.381327 CTCCGCCCCTCAGGTTAGA 60.381 63.158 0.00 0.00 38.26 2.10
591 606 0.760945 CTCCGCCCCTCAGGTTAGAT 60.761 60.000 0.00 0.00 38.26 1.98
592 607 1.048724 TCCGCCCCTCAGGTTAGATG 61.049 60.000 0.00 0.00 38.26 2.90
593 608 1.338136 CCGCCCCTCAGGTTAGATGT 61.338 60.000 0.00 0.00 38.26 3.06
594 609 1.410004 CGCCCCTCAGGTTAGATGTA 58.590 55.000 0.00 0.00 38.26 2.29
595 610 1.068741 CGCCCCTCAGGTTAGATGTAC 59.931 57.143 0.00 0.00 38.26 2.90
596 611 2.399580 GCCCCTCAGGTTAGATGTACT 58.600 52.381 0.00 0.00 38.26 2.73
597 612 2.772515 GCCCCTCAGGTTAGATGTACTT 59.227 50.000 0.00 0.00 38.26 2.24
598 613 3.432326 GCCCCTCAGGTTAGATGTACTTG 60.432 52.174 0.00 0.00 38.26 3.16
599 614 3.134804 CCCCTCAGGTTAGATGTACTTGG 59.865 52.174 0.00 0.00 0.00 3.61
600 615 3.775316 CCCTCAGGTTAGATGTACTTGGT 59.225 47.826 0.00 0.00 0.00 3.67
601 616 4.960469 CCCTCAGGTTAGATGTACTTGGTA 59.040 45.833 0.00 0.00 0.00 3.25
602 617 5.602978 CCCTCAGGTTAGATGTACTTGGTAT 59.397 44.000 0.00 0.00 0.00 2.73
603 618 6.239345 CCCTCAGGTTAGATGTACTTGGTATC 60.239 46.154 0.00 0.00 0.00 2.24
604 619 6.387041 TCAGGTTAGATGTACTTGGTATCG 57.613 41.667 0.00 0.00 0.00 2.92
605 620 6.124340 TCAGGTTAGATGTACTTGGTATCGA 58.876 40.000 0.00 0.00 0.00 3.59
606 621 6.039047 TCAGGTTAGATGTACTTGGTATCGAC 59.961 42.308 0.00 0.00 0.00 4.20
607 622 6.039493 CAGGTTAGATGTACTTGGTATCGACT 59.961 42.308 0.00 0.00 0.00 4.18
608 623 6.606395 AGGTTAGATGTACTTGGTATCGACTT 59.394 38.462 0.00 0.00 0.00 3.01
609 624 7.776969 AGGTTAGATGTACTTGGTATCGACTTA 59.223 37.037 0.00 0.00 0.00 2.24
610 625 8.408601 GGTTAGATGTACTTGGTATCGACTTAA 58.591 37.037 0.00 0.00 0.00 1.85
611 626 9.793252 GTTAGATGTACTTGGTATCGACTTAAA 57.207 33.333 0.00 0.00 0.00 1.52
612 627 9.793252 TTAGATGTACTTGGTATCGACTTAAAC 57.207 33.333 0.00 0.00 0.00 2.01
613 628 8.064336 AGATGTACTTGGTATCGACTTAAACT 57.936 34.615 0.00 0.00 0.00 2.66
614 629 8.529476 AGATGTACTTGGTATCGACTTAAACTT 58.471 33.333 0.00 0.00 0.00 2.66
615 630 9.148104 GATGTACTTGGTATCGACTTAAACTTT 57.852 33.333 0.00 0.00 0.00 2.66
616 631 8.891671 TGTACTTGGTATCGACTTAAACTTTT 57.108 30.769 0.00 0.00 0.00 2.27
617 632 9.979578 TGTACTTGGTATCGACTTAAACTTTTA 57.020 29.630 0.00 0.00 0.00 1.52
653 668 3.753294 GATGTATCTTCACATCCGGGT 57.247 47.619 0.00 0.00 46.02 5.28
654 669 2.979814 TGTATCTTCACATCCGGGTG 57.020 50.000 14.80 14.80 40.16 4.61
655 670 2.184533 TGTATCTTCACATCCGGGTGT 58.815 47.619 16.61 16.61 39.76 4.16
656 671 2.569853 TGTATCTTCACATCCGGGTGTT 59.430 45.455 20.33 5.82 39.76 3.32
657 672 3.770388 TGTATCTTCACATCCGGGTGTTA 59.230 43.478 20.33 7.89 39.76 2.41
658 673 3.992943 ATCTTCACATCCGGGTGTTAA 57.007 42.857 20.33 16.49 39.76 2.01
659 674 3.992943 TCTTCACATCCGGGTGTTAAT 57.007 42.857 20.33 0.00 39.76 1.40
660 675 3.605634 TCTTCACATCCGGGTGTTAATG 58.394 45.455 20.33 11.71 39.76 1.90
661 676 1.745232 TCACATCCGGGTGTTAATGC 58.255 50.000 20.33 0.00 39.76 3.56
662 677 1.280710 TCACATCCGGGTGTTAATGCT 59.719 47.619 20.33 0.00 39.76 3.79
663 678 1.670811 CACATCCGGGTGTTAATGCTC 59.329 52.381 20.33 0.00 34.09 4.26
664 679 1.559682 ACATCCGGGTGTTAATGCTCT 59.440 47.619 16.61 0.00 0.00 4.09
665 680 2.213499 CATCCGGGTGTTAATGCTCTC 58.787 52.381 6.53 0.00 0.00 3.20
666 681 1.568504 TCCGGGTGTTAATGCTCTCT 58.431 50.000 0.00 0.00 0.00 3.10
667 682 1.207089 TCCGGGTGTTAATGCTCTCTG 59.793 52.381 0.00 0.00 0.00 3.35
668 683 1.066143 CCGGGTGTTAATGCTCTCTGT 60.066 52.381 0.00 0.00 0.00 3.41
675 690 6.294731 GGGTGTTAATGCTCTCTGTGAAAATT 60.295 38.462 0.00 0.00 0.00 1.82
678 693 8.482429 GTGTTAATGCTCTCTGTGAAAATTTTG 58.518 33.333 8.47 0.00 0.00 2.44
680 695 9.677567 GTTAATGCTCTCTGTGAAAATTTTGTA 57.322 29.630 8.47 0.00 0.00 2.41
682 697 6.691754 TGCTCTCTGTGAAAATTTTGTACA 57.308 33.333 8.47 11.90 0.00 2.90
686 701 6.943981 TCTCTGTGAAAATTTTGTACACTCG 58.056 36.000 8.47 6.49 33.41 4.18
690 705 8.402472 TCTGTGAAAATTTTGTACACTCGAAAT 58.598 29.630 8.47 0.00 34.15 2.17
722 739 8.885693 AATCCTACAAGAAAGAAAAGGCTTAT 57.114 30.769 0.00 0.00 0.00 1.73
726 743 6.976934 ACAAGAAAGAAAAGGCTTATTGGA 57.023 33.333 0.00 0.00 32.91 3.53
729 746 6.346477 AGAAAGAAAAGGCTTATTGGAACC 57.654 37.500 0.00 0.00 0.00 3.62
731 748 5.728637 AAGAAAAGGCTTATTGGAACCAG 57.271 39.130 0.00 0.00 0.00 4.00
750 767 5.147032 ACCAGTGAATCCAAAAGATCCAAA 58.853 37.500 0.00 0.00 32.47 3.28
751 768 5.781818 ACCAGTGAATCCAAAAGATCCAAAT 59.218 36.000 0.00 0.00 32.47 2.32
754 777 7.364408 CCAGTGAATCCAAAAGATCCAAATGAT 60.364 37.037 0.00 0.00 32.47 2.45
926 957 1.629297 AAGGCCAAAACCCCCTTCA 59.371 52.632 5.01 0.00 33.88 3.02
937 988 1.376037 CCCCTTCACTTGGACTCGC 60.376 63.158 0.00 0.00 0.00 5.03
1110 1165 0.902516 ACTTCTCCTTCTCGCTGGCT 60.903 55.000 0.00 0.00 0.00 4.75
1268 1342 2.063156 TGCCGATGTGATTTTTGTGC 57.937 45.000 0.00 0.00 0.00 4.57
1269 1343 0.984109 GCCGATGTGATTTTTGTGCG 59.016 50.000 0.00 0.00 0.00 5.34
1270 1344 1.400888 GCCGATGTGATTTTTGTGCGA 60.401 47.619 0.00 0.00 0.00 5.10
1271 1345 2.731968 GCCGATGTGATTTTTGTGCGAT 60.732 45.455 0.00 0.00 0.00 4.58
1272 1346 3.100817 CCGATGTGATTTTTGTGCGATC 58.899 45.455 0.00 0.00 0.00 3.69
1273 1347 3.181507 CCGATGTGATTTTTGTGCGATCT 60.182 43.478 0.00 0.00 0.00 2.75
1275 1349 4.493350 CGATGTGATTTTTGTGCGATCTTC 59.507 41.667 0.00 0.00 0.00 2.87
1276 1350 4.827304 TGTGATTTTTGTGCGATCTTCA 57.173 36.364 0.00 0.00 0.00 3.02
1277 1351 5.180367 TGTGATTTTTGTGCGATCTTCAA 57.820 34.783 0.00 0.00 0.00 2.69
1541 1670 7.468768 CGCACTCTCTTGTGGTAATCTATCTAA 60.469 40.741 0.00 0.00 38.31 2.10
1544 1673 9.127277 ACTCTCTTGTGGTAATCTATCTAACTC 57.873 37.037 0.00 0.00 0.00 3.01
1564 1701 9.255304 CTAACTCTTCTATGATTAAACCTCTGC 57.745 37.037 0.00 0.00 0.00 4.26
1590 1757 0.602638 CTGGCTTTGTAGGTCGCACA 60.603 55.000 0.00 0.00 0.00 4.57
1944 2122 2.219458 CCTCGATCGTTAGAGGCTGTA 58.781 52.381 15.94 0.00 46.23 2.74
2381 3506 2.024918 CGGACCTATGTGCAATGCC 58.975 57.895 1.53 0.00 32.24 4.40
2726 3917 2.731348 GATTCGCCGCTAGCTCCG 60.731 66.667 13.93 14.66 40.39 4.63
2735 3926 1.144936 GCTAGCTCCGCCACTGATT 59.855 57.895 7.70 0.00 0.00 2.57
2737 3928 2.014068 GCTAGCTCCGCCACTGATTTT 61.014 52.381 7.70 0.00 0.00 1.82
2738 3929 1.667724 CTAGCTCCGCCACTGATTTTG 59.332 52.381 0.00 0.00 0.00 2.44
2746 3937 2.428171 CGCCACTGATTTTGGATTGGAT 59.572 45.455 0.00 0.00 36.02 3.41
2750 3941 4.708421 CCACTGATTTTGGATTGGATGTCT 59.292 41.667 0.00 0.00 36.02 3.41
2751 3942 5.186409 CCACTGATTTTGGATTGGATGTCTT 59.814 40.000 0.00 0.00 36.02 3.01
2752 3943 6.097356 CACTGATTTTGGATTGGATGTCTTG 58.903 40.000 0.00 0.00 0.00 3.02
2756 3947 5.726980 TTTTGGATTGGATGTCTTGAAGG 57.273 39.130 0.00 0.00 0.00 3.46
2823 4014 4.589216 TTGCAAACAAATCTCCCAAGAG 57.411 40.909 0.00 0.00 35.54 2.85
2839 4030 1.522580 GAGAGAAGCATGGTCCGGC 60.523 63.158 0.00 0.00 0.00 6.13
2868 4059 3.244875 ACATGTGCATCCACCACTCTTTA 60.245 43.478 0.00 0.00 41.35 1.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 3.835810 CCCATCTGAAATCAGGGGG 57.164 57.895 19.68 19.68 45.50 5.40
13 14 0.186873 CCCCCATCTGAAATCAGGGG 59.813 60.000 15.26 15.26 43.91 4.79
14 15 3.835810 CCCCCATCTGAAATCAGGG 57.164 57.895 10.37 5.09 43.91 4.45
36 37 1.901833 ACAAATCACAAAGCATCCCCC 59.098 47.619 0.00 0.00 0.00 5.40
37 38 2.562298 TCACAAATCACAAAGCATCCCC 59.438 45.455 0.00 0.00 0.00 4.81
38 39 3.940209 TCACAAATCACAAAGCATCCC 57.060 42.857 0.00 0.00 0.00 3.85
39 40 4.092383 GCATTCACAAATCACAAAGCATCC 59.908 41.667 0.00 0.00 0.00 3.51
40 41 4.092383 GGCATTCACAAATCACAAAGCATC 59.908 41.667 0.00 0.00 0.00 3.91
41 42 3.998341 GGCATTCACAAATCACAAAGCAT 59.002 39.130 0.00 0.00 0.00 3.79
42 43 3.181468 TGGCATTCACAAATCACAAAGCA 60.181 39.130 0.00 0.00 0.00 3.91
43 44 3.184986 GTGGCATTCACAAATCACAAAGC 59.815 43.478 0.00 0.00 45.39 3.51
44 45 4.977741 GTGGCATTCACAAATCACAAAG 57.022 40.909 0.00 0.00 45.39 2.77
55 56 3.383620 TTGGTCAATTGTGGCATTCAC 57.616 42.857 5.13 0.00 46.23 3.18
56 57 4.125703 GTTTTGGTCAATTGTGGCATTCA 58.874 39.130 5.13 0.00 0.00 2.57
57 58 4.211794 CAGTTTTGGTCAATTGTGGCATTC 59.788 41.667 5.13 0.00 0.00 2.67
58 59 4.128643 CAGTTTTGGTCAATTGTGGCATT 58.871 39.130 5.13 0.00 0.00 3.56
59 60 3.387374 TCAGTTTTGGTCAATTGTGGCAT 59.613 39.130 5.13 0.00 0.00 4.40
60 61 2.762887 TCAGTTTTGGTCAATTGTGGCA 59.237 40.909 5.13 0.00 0.00 4.92
61 62 3.451141 TCAGTTTTGGTCAATTGTGGC 57.549 42.857 5.13 0.00 0.00 5.01
62 63 5.199024 TCATCAGTTTTGGTCAATTGTGG 57.801 39.130 5.13 0.00 0.00 4.17
63 64 6.506147 TCTTCATCAGTTTTGGTCAATTGTG 58.494 36.000 5.13 0.00 0.00 3.33
64 65 6.322201 ACTCTTCATCAGTTTTGGTCAATTGT 59.678 34.615 5.13 0.00 0.00 2.71
65 66 6.742109 ACTCTTCATCAGTTTTGGTCAATTG 58.258 36.000 0.00 0.00 0.00 2.32
74 75 6.455360 TTTCTGCAACTCTTCATCAGTTTT 57.545 33.333 0.00 0.00 31.40 2.43
83 84 2.568623 TCCCCTTTCTGCAACTCTTC 57.431 50.000 0.00 0.00 0.00 2.87
101 102 1.003116 GACACGCTGCAATGATCCATC 60.003 52.381 7.80 0.00 0.00 3.51
104 105 1.349627 CGACACGCTGCAATGATCC 59.650 57.895 7.80 0.00 0.00 3.36
169 170 1.518572 GGTGACTACGTCGGCATGG 60.519 63.158 0.00 0.00 34.95 3.66
171 172 0.963856 TGAGGTGACTACGTCGGCAT 60.964 55.000 0.00 0.00 44.43 4.40
177 178 2.791655 TGTCTGATGAGGTGACTACGT 58.208 47.619 0.00 0.00 44.43 3.57
182 183 2.094494 ACGTGATGTCTGATGAGGTGAC 60.094 50.000 0.00 0.00 0.00 3.67
183 184 2.164422 GACGTGATGTCTGATGAGGTGA 59.836 50.000 0.00 0.00 44.58 4.02
195 196 0.465705 CAGGCCCATAGACGTGATGT 59.534 55.000 0.00 0.00 0.00 3.06
196 197 0.250038 CCAGGCCCATAGACGTGATG 60.250 60.000 0.00 0.00 0.00 3.07
197 198 1.410850 CCCAGGCCCATAGACGTGAT 61.411 60.000 0.00 0.00 0.00 3.06
201 202 2.445845 TCCCCAGGCCCATAGACG 60.446 66.667 0.00 0.00 0.00 4.18
232 233 1.127343 GGAAGTCCTGATCTCCCCTG 58.873 60.000 0.00 0.00 0.00 4.45
233 234 0.030603 GGGAAGTCCTGATCTCCCCT 60.031 60.000 4.43 0.00 35.95 4.79
234 235 1.403687 CGGGAAGTCCTGATCTCCCC 61.404 65.000 9.32 0.00 45.36 4.81
276 277 4.099881 TCCGGCGTATTTGTAGGTAGATTT 59.900 41.667 6.01 0.00 0.00 2.17
279 280 2.653726 TCCGGCGTATTTGTAGGTAGA 58.346 47.619 6.01 0.00 0.00 2.59
288 289 0.445043 GCGTTTCTTCCGGCGTATTT 59.555 50.000 6.01 0.00 0.00 1.40
290 291 0.457035 TAGCGTTTCTTCCGGCGTAT 59.543 50.000 6.01 0.00 0.00 3.06
298 299 5.064962 TGCTACTCTACTCTAGCGTTTCTTC 59.935 44.000 0.00 0.00 38.61 2.87
309 310 1.961793 CTCGCCTGCTACTCTACTCT 58.038 55.000 0.00 0.00 0.00 3.24
313 314 2.187493 CGGCTCGCCTGCTACTCTA 61.187 63.158 6.35 0.00 0.00 2.43
329 330 3.564027 GTGGAATCGCTTCGCCGG 61.564 66.667 0.00 0.00 31.75 6.13
334 335 0.734942 TCGTTCCGTGGAATCGCTTC 60.735 55.000 4.36 0.00 36.45 3.86
335 336 0.736325 CTCGTTCCGTGGAATCGCTT 60.736 55.000 4.36 0.00 36.45 4.68
338 339 0.109458 TGTCTCGTTCCGTGGAATCG 60.109 55.000 4.36 10.24 36.45 3.34
339 340 1.347320 GTGTCTCGTTCCGTGGAATC 58.653 55.000 4.36 0.00 36.45 2.52
340 341 0.388134 CGTGTCTCGTTCCGTGGAAT 60.388 55.000 4.36 0.00 36.45 3.01
341 342 1.008194 CGTGTCTCGTTCCGTGGAA 60.008 57.895 0.00 0.00 34.52 3.53
342 343 1.239296 ATCGTGTCTCGTTCCGTGGA 61.239 55.000 0.00 0.00 40.80 4.02
343 344 0.797249 GATCGTGTCTCGTTCCGTGG 60.797 60.000 0.00 0.00 40.80 4.94
344 345 0.797249 GGATCGTGTCTCGTTCCGTG 60.797 60.000 8.27 0.00 44.73 4.94
345 346 1.505353 GGATCGTGTCTCGTTCCGT 59.495 57.895 8.27 0.00 44.73 4.69
346 347 4.379221 GGATCGTGTCTCGTTCCG 57.621 61.111 8.27 0.00 44.73 4.30
352 367 1.139095 GGTCGTGGGATCGTGTCTC 59.861 63.158 0.00 0.00 0.00 3.36
353 368 2.697761 CGGTCGTGGGATCGTGTCT 61.698 63.158 0.00 0.00 41.84 3.41
356 371 2.102357 CTCGGTCGTGGGATCGTG 59.898 66.667 0.00 0.00 46.76 4.35
363 378 4.308458 TGGTTGCCTCGGTCGTGG 62.308 66.667 7.06 7.06 0.00 4.94
385 400 2.997315 CCTGAGCCCACGTCCTCA 60.997 66.667 9.08 9.08 36.69 3.86
432 447 2.042843 CCAGCCCGTCTACCCTCT 60.043 66.667 0.00 0.00 0.00 3.69
433 448 1.262640 TTTCCAGCCCGTCTACCCTC 61.263 60.000 0.00 0.00 0.00 4.30
434 449 1.229400 TTTCCAGCCCGTCTACCCT 60.229 57.895 0.00 0.00 0.00 4.34
435 450 1.078637 GTTTCCAGCCCGTCTACCC 60.079 63.158 0.00 0.00 0.00 3.69
436 451 0.323957 AAGTTTCCAGCCCGTCTACC 59.676 55.000 0.00 0.00 0.00 3.18
437 452 1.439679 CAAGTTTCCAGCCCGTCTAC 58.560 55.000 0.00 0.00 0.00 2.59
438 453 0.323629 CCAAGTTTCCAGCCCGTCTA 59.676 55.000 0.00 0.00 0.00 2.59
439 454 1.073199 CCAAGTTTCCAGCCCGTCT 59.927 57.895 0.00 0.00 0.00 4.18
440 455 1.072505 TCCAAGTTTCCAGCCCGTC 59.927 57.895 0.00 0.00 0.00 4.79
441 456 1.228154 GTCCAAGTTTCCAGCCCGT 60.228 57.895 0.00 0.00 0.00 5.28
444 459 0.696501 TAGGGTCCAAGTTTCCAGCC 59.303 55.000 0.00 0.00 0.00 4.85
450 465 3.157087 CAGTGCATTAGGGTCCAAGTTT 58.843 45.455 0.00 0.00 0.00 2.66
499 514 6.182627 TCAGCAGTGTTTATCATCTCCAAAT 58.817 36.000 0.00 0.00 0.00 2.32
503 518 6.500684 TTTTCAGCAGTGTTTATCATCTCC 57.499 37.500 0.00 0.00 0.00 3.71
504 519 7.588512 AGTTTTTCAGCAGTGTTTATCATCTC 58.411 34.615 0.00 0.00 0.00 2.75
514 529 3.509575 TCCAACAAGTTTTTCAGCAGTGT 59.490 39.130 0.00 0.00 0.00 3.55
516 531 3.119137 GGTCCAACAAGTTTTTCAGCAGT 60.119 43.478 0.00 0.00 0.00 4.40
521 536 2.448453 ACGGGTCCAACAAGTTTTTCA 58.552 42.857 0.00 0.00 0.00 2.69
522 537 4.841443 ATACGGGTCCAACAAGTTTTTC 57.159 40.909 0.00 0.00 0.00 2.29
527 542 1.982958 AGGAATACGGGTCCAACAAGT 59.017 47.619 4.38 0.00 37.65 3.16
528 543 2.290071 ACAGGAATACGGGTCCAACAAG 60.290 50.000 4.38 0.00 37.65 3.16
532 547 0.035820 GCACAGGAATACGGGTCCAA 60.036 55.000 4.38 0.00 37.65 3.53
582 597 6.039493 AGTCGATACCAAGTACATCTAACCTG 59.961 42.308 0.00 0.00 0.00 4.00
583 598 6.127793 AGTCGATACCAAGTACATCTAACCT 58.872 40.000 0.00 0.00 0.00 3.50
584 599 6.388435 AGTCGATACCAAGTACATCTAACC 57.612 41.667 0.00 0.00 0.00 2.85
585 600 9.793252 TTTAAGTCGATACCAAGTACATCTAAC 57.207 33.333 0.00 0.00 0.00 2.34
586 601 9.793252 GTTTAAGTCGATACCAAGTACATCTAA 57.207 33.333 0.00 0.00 0.00 2.10
587 602 9.182214 AGTTTAAGTCGATACCAAGTACATCTA 57.818 33.333 0.00 0.00 0.00 1.98
588 603 8.064336 AGTTTAAGTCGATACCAAGTACATCT 57.936 34.615 0.00 0.00 0.00 2.90
589 604 8.699283 AAGTTTAAGTCGATACCAAGTACATC 57.301 34.615 0.00 0.00 0.00 3.06
590 605 9.498176 AAAAGTTTAAGTCGATACCAAGTACAT 57.502 29.630 0.00 0.00 0.00 2.29
591 606 8.891671 AAAAGTTTAAGTCGATACCAAGTACA 57.108 30.769 0.00 0.00 0.00 2.90
634 649 2.771943 ACACCCGGATGTGAAGATACAT 59.228 45.455 16.59 0.00 43.61 2.29
635 650 2.184533 ACACCCGGATGTGAAGATACA 58.815 47.619 16.59 0.00 39.57 2.29
636 651 2.981859 ACACCCGGATGTGAAGATAC 57.018 50.000 16.59 0.00 39.57 2.24
637 652 5.364778 CATTAACACCCGGATGTGAAGATA 58.635 41.667 16.59 0.00 39.57 1.98
638 653 3.992943 TTAACACCCGGATGTGAAGAT 57.007 42.857 16.59 0.00 39.57 2.40
639 654 3.605634 CATTAACACCCGGATGTGAAGA 58.394 45.455 16.59 0.00 39.57 2.87
640 655 2.097466 GCATTAACACCCGGATGTGAAG 59.903 50.000 16.59 4.76 39.57 3.02
641 656 2.088423 GCATTAACACCCGGATGTGAA 58.912 47.619 16.59 9.70 39.57 3.18
642 657 1.280710 AGCATTAACACCCGGATGTGA 59.719 47.619 16.59 0.00 39.57 3.58
643 658 1.670811 GAGCATTAACACCCGGATGTG 59.329 52.381 0.00 5.62 42.05 3.21
644 659 1.559682 AGAGCATTAACACCCGGATGT 59.440 47.619 0.73 0.00 0.00 3.06
645 660 2.158900 AGAGAGCATTAACACCCGGATG 60.159 50.000 0.73 0.00 0.00 3.51
646 661 2.119495 AGAGAGCATTAACACCCGGAT 58.881 47.619 0.73 0.00 0.00 4.18
647 662 1.207089 CAGAGAGCATTAACACCCGGA 59.793 52.381 0.73 0.00 0.00 5.14
648 663 1.066143 ACAGAGAGCATTAACACCCGG 60.066 52.381 0.00 0.00 0.00 5.73
649 664 2.002586 CACAGAGAGCATTAACACCCG 58.997 52.381 0.00 0.00 0.00 5.28
650 665 3.334583 TCACAGAGAGCATTAACACCC 57.665 47.619 0.00 0.00 0.00 4.61
651 666 5.689383 TTTTCACAGAGAGCATTAACACC 57.311 39.130 0.00 0.00 0.00 4.16
652 667 8.482429 CAAAATTTTCACAGAGAGCATTAACAC 58.518 33.333 0.00 0.00 0.00 3.32
653 668 8.196771 ACAAAATTTTCACAGAGAGCATTAACA 58.803 29.630 0.00 0.00 0.00 2.41
654 669 8.579682 ACAAAATTTTCACAGAGAGCATTAAC 57.420 30.769 0.00 0.00 0.00 2.01
655 670 9.677567 GTACAAAATTTTCACAGAGAGCATTAA 57.322 29.630 0.00 0.00 0.00 1.40
656 671 8.845227 TGTACAAAATTTTCACAGAGAGCATTA 58.155 29.630 0.00 0.00 0.00 1.90
657 672 7.649306 GTGTACAAAATTTTCACAGAGAGCATT 59.351 33.333 12.86 0.00 0.00 3.56
658 673 7.013655 AGTGTACAAAATTTTCACAGAGAGCAT 59.986 33.333 18.23 0.00 0.00 3.79
659 674 6.318648 AGTGTACAAAATTTTCACAGAGAGCA 59.681 34.615 18.23 3.78 0.00 4.26
660 675 6.729187 AGTGTACAAAATTTTCACAGAGAGC 58.271 36.000 18.23 7.41 0.00 4.09
661 676 7.042725 TCGAGTGTACAAAATTTTCACAGAGAG 60.043 37.037 18.23 10.06 0.00 3.20
662 677 6.759356 TCGAGTGTACAAAATTTTCACAGAGA 59.241 34.615 18.23 12.76 0.00 3.10
663 678 6.943981 TCGAGTGTACAAAATTTTCACAGAG 58.056 36.000 18.23 11.31 0.00 3.35
664 679 6.912203 TCGAGTGTACAAAATTTTCACAGA 57.088 33.333 18.23 14.70 0.00 3.41
665 680 7.962934 TTTCGAGTGTACAAAATTTTCACAG 57.037 32.000 18.23 13.26 0.00 3.66
666 681 8.918961 AATTTCGAGTGTACAAAATTTTCACA 57.081 26.923 18.23 14.20 29.42 3.58
675 690 9.026074 GGATTTCAAAAATTTCGAGTGTACAAA 57.974 29.630 0.00 0.00 0.00 2.83
678 693 9.326339 GTAGGATTTCAAAAATTTCGAGTGTAC 57.674 33.333 0.00 0.00 0.00 2.90
680 695 7.936584 TGTAGGATTTCAAAAATTTCGAGTGT 58.063 30.769 0.00 0.00 0.00 3.55
682 697 8.846211 TCTTGTAGGATTTCAAAAATTTCGAGT 58.154 29.630 0.00 0.00 0.00 4.18
722 739 4.541705 TCTTTTGGATTCACTGGTTCCAA 58.458 39.130 8.66 8.66 45.39 3.53
726 743 4.739793 TGGATCTTTTGGATTCACTGGTT 58.260 39.130 0.00 0.00 35.16 3.67
729 746 6.927416 TCATTTGGATCTTTTGGATTCACTG 58.073 36.000 0.00 0.00 39.48 3.66
750 767 9.626045 GAAGTTTAAGAATTTTGAACGGATCAT 57.374 29.630 0.00 0.00 38.03 2.45
751 768 7.801315 CGAAGTTTAAGAATTTTGAACGGATCA 59.199 33.333 0.00 0.00 35.85 2.92
754 777 7.018635 ACGAAGTTTAAGAATTTTGAACGGA 57.981 32.000 0.00 0.00 37.78 4.69
786 809 4.574674 TCCAAAATGCTGAGTAGATGGT 57.425 40.909 0.00 0.00 0.00 3.55
829 852 0.250338 GGCCGGATGTCCTCCATAAC 60.250 60.000 5.05 0.00 45.24 1.89
912 943 1.047801 CCAAGTGAAGGGGGTTTTGG 58.952 55.000 0.00 0.00 0.00 3.28
918 949 1.296715 CGAGTCCAAGTGAAGGGGG 59.703 63.158 0.00 0.00 0.00 5.40
951 1002 2.625314 CAGTGAGTGTGAGGAACTGAGA 59.375 50.000 0.00 0.00 41.55 3.27
1009 1064 4.752879 CGCCCCATCGTTCCACGT 62.753 66.667 0.00 0.00 43.14 4.49
1030 1085 1.953686 GTGCTTCAGCCACTTGGTTAA 59.046 47.619 0.00 0.00 41.18 2.01
1031 1086 1.142870 AGTGCTTCAGCCACTTGGTTA 59.857 47.619 0.00 0.00 41.18 2.85
1268 1342 7.375280 CAGTGCAAGCTAATTAATTGAAGATCG 59.625 37.037 11.05 0.00 0.00 3.69
1269 1343 8.400947 TCAGTGCAAGCTAATTAATTGAAGATC 58.599 33.333 11.05 0.00 0.00 2.75
1270 1344 8.284945 TCAGTGCAAGCTAATTAATTGAAGAT 57.715 30.769 11.05 0.00 0.00 2.40
1271 1345 7.686438 TCAGTGCAAGCTAATTAATTGAAGA 57.314 32.000 11.05 0.00 0.00 2.87
1272 1346 7.007725 CGTTCAGTGCAAGCTAATTAATTGAAG 59.992 37.037 11.05 2.46 0.00 3.02
1273 1347 6.801377 CGTTCAGTGCAAGCTAATTAATTGAA 59.199 34.615 11.05 0.00 0.00 2.69
1275 1349 6.086222 ACGTTCAGTGCAAGCTAATTAATTG 58.914 36.000 11.05 2.59 0.00 2.32
1276 1350 6.254281 ACGTTCAGTGCAAGCTAATTAATT 57.746 33.333 5.89 5.89 0.00 1.40
1277 1351 5.163754 GGACGTTCAGTGCAAGCTAATTAAT 60.164 40.000 0.00 0.00 41.21 1.40
1508 1631 0.387367 ACAAGAGAGTGCGCGTACTG 60.387 55.000 34.34 21.57 0.00 2.74
1541 1670 7.430760 AGCAGAGGTTTAATCATAGAAGAGT 57.569 36.000 0.00 0.00 0.00 3.24
1544 1673 7.050377 TCCAAGCAGAGGTTTAATCATAGAAG 58.950 38.462 0.00 0.00 0.00 2.85
1563 1700 2.019984 CCTACAAAGCCAGATCCAAGC 58.980 52.381 0.00 0.00 0.00 4.01
1564 1701 3.274288 GACCTACAAAGCCAGATCCAAG 58.726 50.000 0.00 0.00 0.00 3.61
1590 1757 0.913451 ATGCTCCTCACCAGCTCCTT 60.913 55.000 0.00 0.00 37.79 3.36
1944 2122 1.764723 TGGATCATTGTGGCGAGATCT 59.235 47.619 0.00 0.00 37.59 2.75
2726 3917 3.196254 ACATCCAATCCAAAATCAGTGGC 59.804 43.478 0.00 0.00 35.99 5.01
2735 3926 4.739793 ACCTTCAAGACATCCAATCCAAA 58.260 39.130 0.00 0.00 0.00 3.28
2737 3928 3.330405 TGACCTTCAAGACATCCAATCCA 59.670 43.478 0.00 0.00 0.00 3.41
2738 3929 3.944015 CTGACCTTCAAGACATCCAATCC 59.056 47.826 0.00 0.00 0.00 3.01
2746 3937 0.464036 ACACGCTGACCTTCAAGACA 59.536 50.000 0.00 0.00 0.00 3.41
2750 3941 3.678056 ATCTAACACGCTGACCTTCAA 57.322 42.857 0.00 0.00 0.00 2.69
2751 3942 3.006430 TGAATCTAACACGCTGACCTTCA 59.994 43.478 0.00 0.00 0.00 3.02
2752 3943 3.585862 TGAATCTAACACGCTGACCTTC 58.414 45.455 0.00 0.00 0.00 3.46
2756 3947 6.828502 TCATAATGAATCTAACACGCTGAC 57.171 37.500 0.00 0.00 0.00 3.51
2804 3995 4.074970 TCTCTCTTGGGAGATTTGTTTGC 58.925 43.478 0.00 0.00 46.14 3.68
2823 4014 1.153086 ATGCCGGACCATGCTTCTC 60.153 57.895 5.05 0.00 0.00 2.87


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

AutoCloner maintained by Alex Coulton.