Multiple sequence alignment - TraesCS6D01G140200

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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 TraesCS6D01G140200 chr6D 100.000 4446 0 0 1 4446 109898320 109893875 0.000000e+00 8211.0
1 TraesCS6D01G140200 chr2B 93.367 2970 152 13 693 3638 34065527 34062579 0.000000e+00 4351.0
2 TraesCS6D01G140200 chr2B 88.988 563 51 6 3790 4348 34042647 34042092 0.000000e+00 686.0
3 TraesCS6D01G140200 chr2B 84.515 691 64 24 1 659 34066204 34065525 1.040000e-180 643.0
4 TraesCS6D01G140200 chr2B 89.579 499 48 3 3141 3638 34043229 34042734 8.120000e-177 630.0
5 TraesCS6D01G140200 chr2B 86.505 578 66 7 2975 3548 33966484 33965915 3.780000e-175 625.0
6 TraesCS6D01G140200 chr2B 83.877 521 62 11 2103 2617 33976906 33976402 1.120000e-130 477.0
7 TraesCS6D01G140200 chr2B 83.877 521 62 11 2103 2617 33986159 33985655 1.120000e-130 477.0
8 TraesCS6D01G140200 chr2B 83.685 521 63 11 2103 2617 33967653 33967149 5.210000e-129 472.0
9 TraesCS6D01G140200 chr2B 83.685 521 63 11 2103 2617 33995412 33994908 5.210000e-129 472.0
10 TraesCS6D01G140200 chr2B 83.685 521 63 11 2103 2617 34014021 34013517 5.210000e-129 472.0
11 TraesCS6D01G140200 chr2B 87.164 335 39 4 2975 3308 34003600 34003269 1.170000e-100 377.0
12 TraesCS6D01G140200 chr2B 86.866 335 40 4 2975 3308 33975737 33975406 5.430000e-99 372.0
13 TraesCS6D01G140200 chr2B 86.866 335 40 4 2975 3308 33994243 33993912 5.430000e-99 372.0
14 TraesCS6D01G140200 chr2B 86.866 335 40 4 2975 3308 34028995 34028664 5.430000e-99 372.0
15 TraesCS6D01G140200 chr2B 84.672 274 35 4 2613 2886 33976002 33975736 2.640000e-67 267.0
16 TraesCS6D01G140200 chr2B 84.672 274 35 4 2613 2886 34013118 34012852 2.640000e-67 267.0
17 TraesCS6D01G140200 chr2B 84.962 266 33 4 2613 2877 34003865 34003606 3.410000e-66 263.0
18 TraesCS6D01G140200 chr2B 84.307 274 36 4 2613 2886 33985255 33984989 1.230000e-65 261.0
19 TraesCS6D01G140200 chr2B 87.665 227 17 2 3670 3886 34062584 34062359 2.050000e-63 254.0
20 TraesCS6D01G140200 chr2B 87.778 90 9 2 4357 4445 34042043 34041955 2.190000e-18 104.0
21 TraesCS6D01G140200 chr2B 100.000 29 0 0 674 702 550399708 550399680 2.000000e-03 54.7
22 TraesCS6D01G140200 chr2A 93.177 2477 122 10 694 3151 21534682 21532234 0.000000e+00 3594.0
23 TraesCS6D01G140200 chr2A 89.786 793 55 11 3670 4445 21531718 21530935 0.000000e+00 992.0
24 TraesCS6D01G140200 chr2A 95.635 504 18 3 3139 3638 21532216 21531713 0.000000e+00 806.0
25 TraesCS6D01G140200 chr2A 86.324 680 61 13 1 659 21535349 21534681 0.000000e+00 712.0
26 TraesCS6D01G140200 chr6B 76.527 1572 252 71 832 2337 214872578 214874098 0.000000e+00 750.0
27 TraesCS6D01G140200 chrUn 84.069 521 61 11 2103 2617 359919340 359918836 2.400000e-132 483.0
28 TraesCS6D01G140200 chrUn 86.038 265 20 7 2357 2617 431614509 431614258 7.330000e-68 268.0
29 TraesCS6D01G140200 chrUn 84.672 274 35 4 2613 2886 371490515 371490781 2.640000e-67 267.0
30 TraesCS6D01G140200 chrUn 84.672 274 35 4 2613 2886 431613858 431613592 2.640000e-67 267.0
31 TraesCS6D01G140200 chrUn 84.307 274 36 4 2613 2886 322599149 322598883 1.230000e-65 261.0
32 TraesCS6D01G140200 chr4D 88.991 109 11 1 1930 2038 440257139 440257032 2.790000e-27 134.0
33 TraesCS6D01G140200 chr4D 100.000 41 0 0 4405 4445 453661 453701 4.770000e-10 76.8
34 TraesCS6D01G140200 chr4D 95.745 47 0 2 4401 4445 482703437 482703483 1.720000e-09 75.0
35 TraesCS6D01G140200 chr4A 88.991 109 10 2 1930 2038 242675583 242675689 2.790000e-27 134.0
36 TraesCS6D01G140200 chr3B 87.850 107 11 2 1932 2038 379944177 379944073 1.680000e-24 124.0
37 TraesCS6D01G140200 chr3B 85.849 106 13 2 1930 2035 151853196 151853299 1.310000e-20 111.0
38 TraesCS6D01G140200 chr3B 90.244 82 8 0 1957 2038 347916354 347916273 1.690000e-19 108.0
39 TraesCS6D01G140200 chr4B 93.671 79 5 0 1957 2035 340785901 340785979 7.810000e-23 119.0
40 TraesCS6D01G140200 chr7D 90.588 85 2 2 4361 4445 120586355 120586277 1.690000e-19 108.0
41 TraesCS6D01G140200 chr7D 86.458 96 8 2 4054 4145 120586458 120586364 2.830000e-17 100.0
42 TraesCS6D01G140200 chr7D 100.000 42 0 0 4404 4445 320290904 320290945 1.330000e-10 78.7
43 TraesCS6D01G140200 chr5B 90.244 82 8 0 1957 2038 344200354 344200435 1.690000e-19 108.0
44 TraesCS6D01G140200 chr1D 100.000 42 0 0 4404 4445 194462617 194462658 1.330000e-10 78.7
45 TraesCS6D01G140200 chr1A 100.000 42 0 0 4404 4445 202099440 202099399 1.330000e-10 78.7
46 TraesCS6D01G140200 chr1A 100.000 42 0 0 4404 4445 241997707 241997748 1.330000e-10 78.7


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 TraesCS6D01G140200 chr6D 109893875 109898320 4445 True 8211.000000 8211 100.000000 1 4446 1 chr6D.!!$R1 4445
1 TraesCS6D01G140200 chr2B 34062359 34066204 3845 True 1749.333333 4351 88.515667 1 3886 3 chr2B.!!$R10 3885
2 TraesCS6D01G140200 chr2B 33965915 33967653 1738 True 548.500000 625 85.095000 2103 3548 2 chr2B.!!$R3 1445
3 TraesCS6D01G140200 chr2B 34041955 34043229 1274 True 473.333333 686 88.781667 3141 4445 3 chr2B.!!$R9 1304
4 TraesCS6D01G140200 chr2B 33993912 33995412 1500 True 422.000000 472 85.275500 2103 3308 2 chr2B.!!$R6 1205
5 TraesCS6D01G140200 chr2B 33975406 33976906 1500 True 372.000000 477 85.138333 2103 3308 3 chr2B.!!$R4 1205
6 TraesCS6D01G140200 chr2B 34012852 34014021 1169 True 369.500000 472 84.178500 2103 2886 2 chr2B.!!$R8 783
7 TraesCS6D01G140200 chr2B 33984989 33986159 1170 True 369.000000 477 84.092000 2103 2886 2 chr2B.!!$R5 783
8 TraesCS6D01G140200 chr2B 34003269 34003865 596 True 320.000000 377 86.063000 2613 3308 2 chr2B.!!$R7 695
9 TraesCS6D01G140200 chr2A 21530935 21535349 4414 True 1526.000000 3594 91.230500 1 4445 4 chr2A.!!$R1 4444
10 TraesCS6D01G140200 chr6B 214872578 214874098 1520 False 750.000000 750 76.527000 832 2337 1 chr6B.!!$F1 1505
11 TraesCS6D01G140200 chrUn 359918836 359919340 504 True 483.000000 483 84.069000 2103 2617 1 chrUn.!!$R2 514
12 TraesCS6D01G140200 chrUn 431613592 431614509 917 True 267.500000 268 85.355000 2357 2886 2 chrUn.!!$R3 529


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
519 551 0.033208 AGCCTCTCTGTCCCTCTGAG 60.033 60.000 0.0 0.0 41.48 3.35 F
1871 1952 1.340308 CCAGGGTTGATGACTGATGCA 60.340 52.381 0.0 0.0 34.21 3.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2188 2281 2.210644 TCCCGGGGAACTATTTTCCAT 58.789 47.619 23.5 0.0 40.32 3.41 R
3809 4368 0.036388 TCACGAATGAGAGGGGTTGC 60.036 55.000 0.0 0.0 0.00 4.17 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
21 22 2.359011 GGTTCAGGGGCGGGATTT 59.641 61.111 0.00 0.00 0.00 2.17
25 26 0.254747 TTCAGGGGCGGGATTTGTAG 59.745 55.000 0.00 0.00 0.00 2.74
52 57 4.717629 CTTCGGCGGCGAGTGTCA 62.718 66.667 32.72 17.87 0.00 3.58
143 155 2.592308 GGCGATTCTTGGCTCCCT 59.408 61.111 0.00 0.00 0.00 4.20
185 198 4.778143 AGCGGCGCCCTTCGATTT 62.778 61.111 30.40 2.85 41.67 2.17
187 200 3.876198 CGGCGCCCTTCGATTTGG 61.876 66.667 23.46 0.00 41.67 3.28
196 209 0.871722 CTTCGATTTGGGCGTGTTCA 59.128 50.000 0.00 0.00 0.00 3.18
198 211 1.083489 TCGATTTGGGCGTGTTCATC 58.917 50.000 0.00 0.00 0.00 2.92
210 236 1.467342 GTGTTCATCCGTAGGGTTTGC 59.533 52.381 0.53 0.00 39.56 3.68
213 239 0.539986 TCATCCGTAGGGTTTGCCTC 59.460 55.000 0.53 0.00 39.56 4.70
214 240 0.463833 CATCCGTAGGGTTTGCCTCC 60.464 60.000 0.53 0.00 39.56 4.30
347 376 1.068083 GAATGGCTCGCTCGGATGA 59.932 57.895 0.00 0.00 0.00 2.92
373 402 2.328099 GCGTTCTTGGACCTGCTGG 61.328 63.158 8.29 8.29 39.83 4.85
374 403 2.328099 CGTTCTTGGACCTGCTGGC 61.328 63.158 9.95 2.57 36.63 4.85
384 413 1.123861 ACCTGCTGGCTGTTCTCTGA 61.124 55.000 9.95 0.00 36.63 3.27
399 428 5.635280 TGTTCTCTGAATGTCTGATTTCGTC 59.365 40.000 0.00 0.00 0.00 4.20
400 429 4.748892 TCTCTGAATGTCTGATTTCGTCC 58.251 43.478 0.00 0.00 0.00 4.79
409 438 0.787787 TGATTTCGTCCGTCTTTGCG 59.212 50.000 0.00 0.00 0.00 4.85
422 451 3.809832 CGTCTTTGCGGAAGGATCATAAT 59.190 43.478 4.50 0.00 35.98 1.28
424 453 5.514279 GTCTTTGCGGAAGGATCATAATTG 58.486 41.667 4.50 0.00 35.98 2.32
425 454 5.066505 GTCTTTGCGGAAGGATCATAATTGT 59.933 40.000 4.50 0.00 35.98 2.71
426 455 6.260050 GTCTTTGCGGAAGGATCATAATTGTA 59.740 38.462 4.50 0.00 35.98 2.41
458 490 3.192001 TCTTCTCCGCGTAAATGTACTGT 59.808 43.478 4.92 0.00 0.00 3.55
459 491 2.871133 TCTCCGCGTAAATGTACTGTG 58.129 47.619 4.92 0.00 0.00 3.66
460 492 2.488937 TCTCCGCGTAAATGTACTGTGA 59.511 45.455 4.92 0.00 0.00 3.58
502 534 0.667487 TGTGCGTGCTCTGTTCTAGC 60.667 55.000 0.00 0.00 40.50 3.42
519 551 0.033208 AGCCTCTCTGTCCCTCTGAG 60.033 60.000 0.00 0.00 41.48 3.35
525 557 4.340617 CTCTCTGTCCCTCTGAGTTTACT 58.659 47.826 3.66 0.00 41.09 2.24
562 594 3.355378 TCCCATGAATGCTGTAGGTTTG 58.645 45.455 0.00 0.00 0.00 2.93
597 629 1.897133 TGCAGTACGGGTGTAGATTGT 59.103 47.619 0.00 0.00 0.00 2.71
613 645 6.650807 TGTAGATTGTTCTGTCACCTTTCATC 59.349 38.462 0.00 0.00 33.17 2.92
622 654 3.840078 TGTCACCTTTCATCTCAGGATCA 59.160 43.478 0.00 0.00 33.90 2.92
623 655 4.187694 GTCACCTTTCATCTCAGGATCAC 58.812 47.826 0.00 0.00 33.90 3.06
624 656 4.081198 GTCACCTTTCATCTCAGGATCACT 60.081 45.833 0.00 0.00 33.90 3.41
659 695 6.554334 TCTGCTACCAAAGTTGAATTGTAC 57.446 37.500 0.00 0.00 0.00 2.90
660 696 6.296026 TCTGCTACCAAAGTTGAATTGTACT 58.704 36.000 0.00 0.00 0.00 2.73
661 697 6.426937 TCTGCTACCAAAGTTGAATTGTACTC 59.573 38.462 0.00 0.00 0.00 2.59
662 698 5.472137 TGCTACCAAAGTTGAATTGTACTCC 59.528 40.000 0.00 0.00 0.00 3.85
663 699 5.106277 GCTACCAAAGTTGAATTGTACTCCC 60.106 44.000 0.00 0.00 0.00 4.30
664 700 5.061721 ACCAAAGTTGAATTGTACTCCCT 57.938 39.130 0.00 0.00 0.00 4.20
665 701 5.070685 ACCAAAGTTGAATTGTACTCCCTC 58.929 41.667 0.00 0.00 0.00 4.30
666 702 4.459337 CCAAAGTTGAATTGTACTCCCTCC 59.541 45.833 0.00 0.00 0.00 4.30
667 703 3.611766 AGTTGAATTGTACTCCCTCCG 57.388 47.619 0.00 0.00 0.00 4.63
668 704 2.904434 AGTTGAATTGTACTCCCTCCGT 59.096 45.455 0.00 0.00 0.00 4.69
669 705 4.091549 AGTTGAATTGTACTCCCTCCGTA 58.908 43.478 0.00 0.00 0.00 4.02
670 706 4.715297 AGTTGAATTGTACTCCCTCCGTAT 59.285 41.667 0.00 0.00 0.00 3.06
671 707 5.189145 AGTTGAATTGTACTCCCTCCGTATT 59.811 40.000 0.00 0.00 0.00 1.89
672 708 6.381994 AGTTGAATTGTACTCCCTCCGTATTA 59.618 38.462 0.00 0.00 0.00 0.98
673 709 6.795144 TGAATTGTACTCCCTCCGTATTAA 57.205 37.500 0.00 0.00 0.00 1.40
674 710 7.369551 TGAATTGTACTCCCTCCGTATTAAT 57.630 36.000 0.00 0.00 0.00 1.40
675 711 8.481492 TGAATTGTACTCCCTCCGTATTAATA 57.519 34.615 0.00 0.00 0.00 0.98
676 712 9.096823 TGAATTGTACTCCCTCCGTATTAATAT 57.903 33.333 0.00 0.00 0.00 1.28
677 713 9.939802 GAATTGTACTCCCTCCGTATTAATATT 57.060 33.333 0.00 0.00 0.00 1.28
679 715 9.939802 ATTGTACTCCCTCCGTATTAATATTTC 57.060 33.333 0.00 0.00 0.00 2.17
680 716 8.716674 TGTACTCCCTCCGTATTAATATTTCT 57.283 34.615 0.00 0.00 0.00 2.52
681 717 9.151177 TGTACTCCCTCCGTATTAATATTTCTT 57.849 33.333 0.00 0.00 0.00 2.52
682 718 9.993454 GTACTCCCTCCGTATTAATATTTCTTT 57.007 33.333 0.00 0.00 0.00 2.52
684 720 9.993454 ACTCCCTCCGTATTAATATTTCTTTAC 57.007 33.333 0.00 0.00 0.00 2.01
685 721 9.991906 CTCCCTCCGTATTAATATTTCTTTACA 57.008 33.333 0.00 0.00 0.00 2.41
686 722 9.991906 TCCCTCCGTATTAATATTTCTTTACAG 57.008 33.333 0.00 0.00 0.00 2.74
687 723 9.991906 CCCTCCGTATTAATATTTCTTTACAGA 57.008 33.333 0.00 0.00 0.00 3.41
690 726 9.991906 TCCGTATTAATATTTCTTTACAGAGGG 57.008 33.333 0.00 0.00 0.00 4.30
691 727 9.991906 CCGTATTAATATTTCTTTACAGAGGGA 57.008 33.333 0.00 0.00 0.00 4.20
726 762 4.183865 GCCCTGATAAATGAAACCTTTGC 58.816 43.478 0.00 0.00 0.00 3.68
728 764 5.413499 CCCTGATAAATGAAACCTTTGCTG 58.587 41.667 0.00 0.00 0.00 4.41
765 801 6.942891 ACTTTGTGAGTTTGTGTTTGTTTTG 58.057 32.000 0.00 0.00 33.92 2.44
773 809 7.967854 TGAGTTTGTGTTTGTTTTGACTGATAG 59.032 33.333 0.00 0.00 0.00 2.08
829 865 4.462508 TGTTCACACTTTTGCAATGGAA 57.537 36.364 0.00 0.00 0.00 3.53
942 981 4.329801 CACATTGCGTGTTTGCTAGAGATA 59.670 41.667 0.00 0.00 39.62 1.98
943 982 4.568359 ACATTGCGTGTTTGCTAGAGATAG 59.432 41.667 0.00 0.00 38.01 2.08
1047 1086 7.413438 CCAACAGAAATGAACTACAGTATCAGC 60.413 40.741 0.00 0.00 0.00 4.26
1157 1196 4.363999 GACCTTACTCTCATTCATCCACG 58.636 47.826 0.00 0.00 0.00 4.94
1161 1200 2.402564 ACTCTCATTCATCCACGGGAT 58.597 47.619 0.00 0.00 44.21 3.85
1223 1277 2.939103 GGTGCTGTAAATACTCCTGCAG 59.061 50.000 6.78 6.78 0.00 4.41
1237 1291 2.306805 TCCTGCAGGTCTGAATTCATGT 59.693 45.455 31.58 0.00 36.34 3.21
1336 1400 7.496591 AGTCGTTTTAGACACTTGTGGATAAAA 59.503 33.333 15.13 15.13 43.24 1.52
1444 1518 3.118075 TGGTGAATTCTCTGGTTGTGTGA 60.118 43.478 7.05 0.00 0.00 3.58
1785 1863 9.941325 GAATATCAGGTAGAACAGAATGATGAT 57.059 33.333 0.00 0.00 39.69 2.45
1835 1916 5.063204 TCCCTGATCAAAAGTTACACACAG 58.937 41.667 0.00 0.00 0.00 3.66
1836 1917 5.063204 CCCTGATCAAAAGTTACACACAGA 58.937 41.667 0.00 0.00 0.00 3.41
1871 1952 1.340308 CCAGGGTTGATGACTGATGCA 60.340 52.381 0.00 0.00 34.21 3.96
1878 1959 2.989909 TGATGACTGATGCATTCGGTT 58.010 42.857 0.00 0.00 44.24 4.44
2183 2276 4.311816 ACTCTTTGCTGGTTTGTCATTG 57.688 40.909 0.00 0.00 0.00 2.82
2188 2281 6.634805 TCTTTGCTGGTTTGTCATTGTAAAA 58.365 32.000 0.00 0.00 0.00 1.52
2224 2317 4.505039 CCCCGGGATCCTCTTATTGTAAAG 60.505 50.000 26.32 0.00 0.00 1.85
2231 2324 5.099042 TCCTCTTATTGTAAAGCACCTCC 57.901 43.478 0.00 0.00 0.00 4.30
2274 2372 7.601130 TCTTGCAAATTCTTGGATTCATTCAAG 59.399 33.333 0.00 1.73 41.06 3.02
2282 2380 7.870509 TCTTGGATTCATTCAAGAACCATAG 57.129 36.000 7.93 0.00 44.14 2.23
2355 2456 4.944930 ACTAGTTTGCGGCAATATAAACCA 59.055 37.500 17.19 0.00 34.46 3.67
2437 2541 3.954200 TGCCAGATTGTATCTTCAAGCA 58.046 40.909 0.00 0.00 37.58 3.91
2637 3146 4.397481 TGACTCTGATGCATTACTGAGG 57.603 45.455 19.69 7.94 36.75 3.86
2671 3180 6.867662 ATGACCAAAACACAACTAGAGAAG 57.132 37.500 0.00 0.00 0.00 2.85
2688 3197 4.469227 AGAGAAGTACATCAGGACTGCAAT 59.531 41.667 0.31 0.00 0.00 3.56
2722 3231 5.674525 CTGGACCTACTAAATCTGATTGCA 58.325 41.667 3.22 0.00 0.00 4.08
2810 3319 5.496133 TGCTTTAGATCCTCGTGTAGTAC 57.504 43.478 0.00 0.00 0.00 2.73
2827 3336 6.257630 GTGTAGTACGTTCCCAAAACTTTGTA 59.742 38.462 0.00 0.00 36.45 2.41
2840 3349 6.460953 CCAAAACTTTGTAAGTGTAGCCACAT 60.461 38.462 1.76 0.00 41.91 3.21
3004 3513 3.732849 CTGGGAGGGCTGGGGTTC 61.733 72.222 0.00 0.00 0.00 3.62
3069 3578 5.845103 TGTAACTGGATGTTCGTTAACTCA 58.155 37.500 3.71 1.14 39.89 3.41
3234 3774 2.664402 ACATCACTGGAAAAGGCAGT 57.336 45.000 0.00 0.00 0.00 4.40
3310 3850 0.734253 CCGCGTCTTCCTGTTCTCAG 60.734 60.000 4.92 0.00 41.01 3.35
3347 3887 7.373493 AGAACAAAGCCATTCAAATAGTTCTG 58.627 34.615 0.00 0.00 40.90 3.02
3465 4010 1.678101 GTCCCCTGCATAGCATTTCAC 59.322 52.381 0.00 0.00 38.13 3.18
3606 4153 1.841302 TTCTGGCAGAACGAGGGCAT 61.841 55.000 25.38 0.00 38.99 4.40
3632 4179 3.243636 CCAAAGCAGCATGAGAAAACACT 60.244 43.478 0.00 0.00 39.69 3.55
3633 4180 4.365723 CAAAGCAGCATGAGAAAACACTT 58.634 39.130 0.00 0.00 39.69 3.16
3634 4181 3.911661 AGCAGCATGAGAAAACACTTC 57.088 42.857 0.00 0.00 39.69 3.01
3635 4182 3.216800 AGCAGCATGAGAAAACACTTCA 58.783 40.909 0.00 0.00 39.69 3.02
3636 4183 3.825014 AGCAGCATGAGAAAACACTTCAT 59.175 39.130 0.00 0.00 39.69 2.57
3637 4184 5.005740 AGCAGCATGAGAAAACACTTCATA 58.994 37.500 0.00 0.00 39.69 2.15
3638 4185 5.091431 GCAGCATGAGAAAACACTTCATAC 58.909 41.667 0.00 0.00 39.69 2.39
3639 4186 5.319139 CAGCATGAGAAAACACTTCATACG 58.681 41.667 0.00 0.00 39.69 3.06
3640 4187 5.120674 CAGCATGAGAAAACACTTCATACGA 59.879 40.000 0.00 0.00 39.69 3.43
3641 4188 5.700832 AGCATGAGAAAACACTTCATACGAA 59.299 36.000 0.00 0.00 0.00 3.85
3642 4189 5.790495 GCATGAGAAAACACTTCATACGAAC 59.210 40.000 0.00 0.00 0.00 3.95
3643 4190 6.347725 GCATGAGAAAACACTTCATACGAACT 60.348 38.462 0.00 0.00 0.00 3.01
3644 4191 6.764877 TGAGAAAACACTTCATACGAACTC 57.235 37.500 0.00 0.00 0.00 3.01
3645 4192 6.513180 TGAGAAAACACTTCATACGAACTCT 58.487 36.000 0.00 0.00 0.00 3.24
3646 4193 6.420903 TGAGAAAACACTTCATACGAACTCTG 59.579 38.462 0.00 0.00 0.00 3.35
3647 4194 5.696724 AGAAAACACTTCATACGAACTCTGG 59.303 40.000 0.00 0.00 0.00 3.86
3648 4195 4.866508 AACACTTCATACGAACTCTGGA 57.133 40.909 0.00 0.00 0.00 3.86
3649 4196 4.866508 ACACTTCATACGAACTCTGGAA 57.133 40.909 0.00 0.00 0.00 3.53
3650 4197 5.209818 ACACTTCATACGAACTCTGGAAA 57.790 39.130 0.00 0.00 0.00 3.13
3651 4198 5.794894 ACACTTCATACGAACTCTGGAAAT 58.205 37.500 0.00 0.00 0.00 2.17
3652 4199 6.231211 ACACTTCATACGAACTCTGGAAATT 58.769 36.000 0.00 0.00 0.00 1.82
3653 4200 6.710744 ACACTTCATACGAACTCTGGAAATTT 59.289 34.615 0.00 0.00 0.00 1.82
3654 4201 7.228706 ACACTTCATACGAACTCTGGAAATTTT 59.771 33.333 0.00 0.00 0.00 1.82
3655 4202 8.076178 CACTTCATACGAACTCTGGAAATTTTT 58.924 33.333 0.00 0.00 0.00 1.94
3717 4274 3.999001 TGACACTGATGATTCTGTTCAGC 59.001 43.478 10.03 0.00 40.40 4.26
3756 4315 6.992123 TGATCGATAATGCCAGTTCTGTTATT 59.008 34.615 0.00 2.62 0.00 1.40
3787 4346 6.882610 ATCTTTGTTCAGTGCAATGAGTTA 57.117 33.333 17.22 5.05 34.84 2.24
3788 4347 6.304356 TCTTTGTTCAGTGCAATGAGTTAG 57.696 37.500 17.22 12.73 0.00 2.34
3803 4362 3.244422 TGAGTTAGGTTGCAGTTTCCGAT 60.244 43.478 0.00 0.00 0.00 4.18
3809 4368 2.160417 GGTTGCAGTTTCCGATTCTCAG 59.840 50.000 0.00 0.00 0.00 3.35
3834 4393 3.201290 CCCCTCTCATTCGTGAATTCTG 58.799 50.000 7.05 0.00 0.00 3.02
3869 4428 8.729805 TTTGAGCAATGTAATTTCACCTTTTT 57.270 26.923 0.00 0.00 31.22 1.94
3870 4429 9.823647 TTTGAGCAATGTAATTTCACCTTTTTA 57.176 25.926 0.00 0.00 31.22 1.52
3871 4430 8.810652 TGAGCAATGTAATTTCACCTTTTTAC 57.189 30.769 0.00 0.00 31.22 2.01
3986 4550 2.417787 GGTTTCAGCAGGAATCATTGCC 60.418 50.000 5.54 0.00 41.17 4.52
4081 4645 4.007644 CTGTCGTGCTGGCCCTCA 62.008 66.667 0.00 0.00 0.00 3.86
4119 4683 0.104855 GTGTCAGGCCGATGATGCTA 59.895 55.000 0.00 0.00 0.00 3.49
4136 4700 3.601435 TGCTAGCACGGTAAAGCAAATA 58.399 40.909 14.93 0.00 41.74 1.40
4192 4756 5.063204 CACATAGTCACCTCCAAAAAGACA 58.937 41.667 0.00 0.00 0.00 3.41
4196 4760 7.287696 ACATAGTCACCTCCAAAAAGACATTTT 59.712 33.333 0.00 0.00 41.93 1.82
4267 4831 1.490910 GCAAAGGTAGGCTCCATAGGT 59.509 52.381 0.00 0.00 0.00 3.08
4283 4847 0.108329 AGGTAGGTCGGCATTGAACG 60.108 55.000 0.00 0.00 0.00 3.95
4377 4984 2.806945 TTCTGGCCTTGAACCTATGG 57.193 50.000 3.32 0.00 0.00 2.74
4381 4988 3.589735 TCTGGCCTTGAACCTATGGTTTA 59.410 43.478 3.32 0.00 46.95 2.01
4445 5053 2.147958 CGGTAAAGCTGTTGCCTTGTA 58.852 47.619 11.70 0.00 40.80 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 3.766691 GAAGCCGCCCCGACTACA 61.767 66.667 0.00 0.00 0.00 2.74
80 92 1.017177 CGCCGAATCAAGAACCCGAA 61.017 55.000 0.00 0.00 0.00 4.30
170 183 3.876198 CCAAATCGAAGGGCGCCG 61.876 66.667 22.54 9.16 40.61 6.46
171 184 3.518068 CCCAAATCGAAGGGCGCC 61.518 66.667 21.18 21.18 38.44 6.53
177 190 0.871722 TGAACACGCCCAAATCGAAG 59.128 50.000 0.00 0.00 0.00 3.79
178 191 1.466950 GATGAACACGCCCAAATCGAA 59.533 47.619 0.00 0.00 0.00 3.71
185 198 1.216977 CTACGGATGAACACGCCCA 59.783 57.895 0.00 0.00 0.00 5.36
187 200 1.520787 CCCTACGGATGAACACGCC 60.521 63.158 0.00 0.00 0.00 5.68
196 209 1.912971 GGAGGCAAACCCTACGGAT 59.087 57.895 0.00 0.00 46.60 4.18
218 244 1.459592 CTCCTCTAAACAAACCGTGCG 59.540 52.381 0.00 0.00 0.00 5.34
262 288 2.353109 GCAAAATGGCCCTGTTCTCTTC 60.353 50.000 0.00 0.00 0.00 2.87
263 289 1.620323 GCAAAATGGCCCTGTTCTCTT 59.380 47.619 0.00 0.00 0.00 2.85
264 290 1.203100 AGCAAAATGGCCCTGTTCTCT 60.203 47.619 0.00 0.00 0.00 3.10
265 291 1.203287 GAGCAAAATGGCCCTGTTCTC 59.797 52.381 0.00 0.00 0.00 2.87
266 292 1.203100 AGAGCAAAATGGCCCTGTTCT 60.203 47.619 0.00 2.44 0.00 3.01
347 376 1.534729 GTCCAAGAACGCCCAAGAAT 58.465 50.000 0.00 0.00 0.00 2.40
373 402 5.445673 CGAAATCAGACATTCAGAGAACAGC 60.446 44.000 0.13 0.00 0.00 4.40
374 403 5.636965 ACGAAATCAGACATTCAGAGAACAG 59.363 40.000 0.00 0.00 0.00 3.16
384 413 3.594603 AGACGGACGAAATCAGACATT 57.405 42.857 0.00 0.00 0.00 2.71
400 429 1.656652 ATGATCCTTCCGCAAAGACG 58.343 50.000 0.00 0.00 37.12 4.18
422 451 5.119588 CGCGGAGAAGAAACAAATACTACAA 59.880 40.000 0.00 0.00 0.00 2.41
424 453 4.624452 ACGCGGAGAAGAAACAAATACTAC 59.376 41.667 12.47 0.00 0.00 2.73
425 454 4.813027 ACGCGGAGAAGAAACAAATACTA 58.187 39.130 12.47 0.00 0.00 1.82
426 455 3.660865 ACGCGGAGAAGAAACAAATACT 58.339 40.909 12.47 0.00 0.00 2.12
458 490 7.760794 CAGGCATGCACTTTATTTTCTTTATCA 59.239 33.333 21.36 0.00 0.00 2.15
459 491 7.761249 ACAGGCATGCACTTTATTTTCTTTATC 59.239 33.333 21.36 0.00 0.00 1.75
460 492 7.546667 CACAGGCATGCACTTTATTTTCTTTAT 59.453 33.333 21.36 0.00 0.00 1.40
502 534 2.230130 AACTCAGAGGGACAGAGAGG 57.770 55.000 1.53 0.00 35.99 3.69
519 551 2.034179 GCCAGTGTTGGTTGGAGTAAAC 59.966 50.000 0.00 0.00 46.80 2.01
525 557 1.150536 GGAGCCAGTGTTGGTTGGA 59.849 57.895 0.00 0.00 46.80 3.53
597 629 3.903714 TCCTGAGATGAAAGGTGACAGAA 59.096 43.478 0.00 0.00 34.94 3.02
613 645 7.438757 CAGAAATATTCAGACAGTGATCCTGAG 59.561 40.741 15.51 7.19 44.49 3.35
622 654 6.299805 TGGTAGCAGAAATATTCAGACAGT 57.700 37.500 0.00 0.00 0.00 3.55
623 655 7.335422 ACTTTGGTAGCAGAAATATTCAGACAG 59.665 37.037 0.00 0.00 0.00 3.51
624 656 7.168219 ACTTTGGTAGCAGAAATATTCAGACA 58.832 34.615 0.00 0.00 0.00 3.41
625 657 7.617041 ACTTTGGTAGCAGAAATATTCAGAC 57.383 36.000 0.00 0.00 0.00 3.51
626 658 7.882791 TCAACTTTGGTAGCAGAAATATTCAGA 59.117 33.333 0.00 0.00 0.00 3.27
627 659 8.044060 TCAACTTTGGTAGCAGAAATATTCAG 57.956 34.615 0.00 0.00 0.00 3.02
633 669 7.054491 ACAATTCAACTTTGGTAGCAGAAAT 57.946 32.000 0.00 0.00 0.00 2.17
659 695 9.991906 TGTAAAGAAATATTAATACGGAGGGAG 57.008 33.333 0.00 0.00 0.00 4.30
660 696 9.991906 CTGTAAAGAAATATTAATACGGAGGGA 57.008 33.333 0.00 0.00 0.00 4.20
661 697 9.991906 TCTGTAAAGAAATATTAATACGGAGGG 57.008 33.333 0.00 0.00 0.00 4.30
664 700 9.991906 CCCTCTGTAAAGAAATATTAATACGGA 57.008 33.333 0.00 0.79 0.00 4.69
665 701 9.991906 TCCCTCTGTAAAGAAATATTAATACGG 57.008 33.333 0.00 0.00 0.00 4.02
675 711 9.495382 AGAGTAATACTCCCTCTGTAAAGAAAT 57.505 33.333 16.12 0.00 46.18 2.17
676 712 8.750298 CAGAGTAATACTCCCTCTGTAAAGAAA 58.250 37.037 16.12 0.00 46.18 2.52
677 713 7.342284 CCAGAGTAATACTCCCTCTGTAAAGAA 59.658 40.741 16.12 0.00 46.18 2.52
678 714 6.834451 CCAGAGTAATACTCCCTCTGTAAAGA 59.166 42.308 16.12 0.00 46.18 2.52
679 715 6.041069 CCCAGAGTAATACTCCCTCTGTAAAG 59.959 46.154 16.12 0.00 46.18 1.85
680 716 5.897824 CCCAGAGTAATACTCCCTCTGTAAA 59.102 44.000 16.12 0.00 46.18 2.01
681 717 5.455872 CCCAGAGTAATACTCCCTCTGTAA 58.544 45.833 16.12 0.00 46.18 2.41
682 718 4.691935 GCCCAGAGTAATACTCCCTCTGTA 60.692 50.000 16.12 0.00 46.18 2.74
683 719 3.917300 CCCAGAGTAATACTCCCTCTGT 58.083 50.000 16.12 0.00 46.18 3.41
684 720 2.630580 GCCCAGAGTAATACTCCCTCTG 59.369 54.545 16.12 8.32 46.18 3.35
685 721 2.426561 GGCCCAGAGTAATACTCCCTCT 60.427 54.545 16.12 0.00 46.18 3.69
686 722 1.972075 GGCCCAGAGTAATACTCCCTC 59.028 57.143 16.12 4.36 46.18 4.30
687 723 1.414685 GGGCCCAGAGTAATACTCCCT 60.415 57.143 19.95 0.00 46.18 4.20
688 724 1.057471 GGGCCCAGAGTAATACTCCC 58.943 60.000 19.95 10.21 46.18 4.30
689 725 1.694696 CAGGGCCCAGAGTAATACTCC 59.305 57.143 27.56 1.93 46.18 3.85
690 726 2.679082 TCAGGGCCCAGAGTAATACTC 58.321 52.381 27.56 12.26 45.38 2.59
691 727 2.868964 TCAGGGCCCAGAGTAATACT 57.131 50.000 27.56 0.00 0.00 2.12
692 728 5.562298 TTTATCAGGGCCCAGAGTAATAC 57.438 43.478 27.56 0.00 0.00 1.89
693 729 5.849475 TCATTTATCAGGGCCCAGAGTAATA 59.151 40.000 27.56 7.93 0.00 0.98
694 730 4.665009 TCATTTATCAGGGCCCAGAGTAAT 59.335 41.667 27.56 20.54 0.00 1.89
697 733 2.492025 TCATTTATCAGGGCCCAGAGT 58.508 47.619 27.56 13.88 0.00 3.24
703 739 4.758688 CAAAGGTTTCATTTATCAGGGCC 58.241 43.478 0.00 0.00 0.00 5.80
726 762 1.538512 CAAAGTCCAGCACCATCACAG 59.461 52.381 0.00 0.00 0.00 3.66
728 764 1.267806 CACAAAGTCCAGCACCATCAC 59.732 52.381 0.00 0.00 0.00 3.06
765 801 6.148480 AGTGAGCAAATTGAACACTATCAGTC 59.852 38.462 18.23 0.00 39.52 3.51
773 809 4.285292 CAGTGAGTGAGCAAATTGAACAC 58.715 43.478 12.41 12.41 0.00 3.32
829 865 7.949690 TTTCCTTCAGATGAAATGATGATGT 57.050 32.000 0.00 0.00 33.07 3.06
841 877 3.264947 TCGCTCACATTTCCTTCAGATG 58.735 45.455 0.00 0.00 0.00 2.90
942 981 6.660949 AGGAGCTATAAAAAGAAACACATGCT 59.339 34.615 0.00 0.00 0.00 3.79
943 982 6.856895 AGGAGCTATAAAAAGAAACACATGC 58.143 36.000 0.00 0.00 0.00 4.06
1047 1086 1.067669 TCCTCATCGCTCCAAGAATCG 59.932 52.381 0.00 0.00 0.00 3.34
1161 1200 5.492565 TTATCTACTAACCAGGGGAGGAA 57.507 43.478 0.00 0.00 0.00 3.36
1198 1252 4.323417 CAGGAGTATTTACAGCACCACAA 58.677 43.478 0.00 0.00 0.00 3.33
1200 1254 2.678336 GCAGGAGTATTTACAGCACCAC 59.322 50.000 0.00 0.00 0.00 4.16
1223 1277 7.396540 AGGAATAACAACATGAATTCAGACC 57.603 36.000 14.54 5.06 30.54 3.85
1299 1363 7.929785 AGTGTCTAAAACGACTGGATTAAGAAA 59.070 33.333 0.00 0.00 35.00 2.52
1300 1364 7.439381 AGTGTCTAAAACGACTGGATTAAGAA 58.561 34.615 0.00 0.00 35.00 2.52
1336 1400 5.804944 AGAGACTTATCAGCTATGTGCAT 57.195 39.130 0.00 0.00 45.94 3.96
1433 1497 5.407407 AATACCTAGTCTCACACAACCAG 57.593 43.478 0.00 0.00 0.00 4.00
1444 1518 7.849904 TCAGAAAGGGGAAATAATACCTAGTCT 59.150 37.037 0.00 0.00 31.41 3.24
1835 1916 4.490706 ACCCTGGTTGATAGGTAGGTATC 58.509 47.826 0.00 0.00 33.31 2.24
1836 1917 4.571366 ACCCTGGTTGATAGGTAGGTAT 57.429 45.455 0.00 0.00 33.31 2.73
1871 1952 2.372172 ACTCCTGTCAGGAAAACCGAAT 59.628 45.455 22.08 0.00 45.28 3.34
1878 1959 4.223953 AGACTTGTACTCCTGTCAGGAAA 58.776 43.478 22.08 12.46 45.28 3.13
2082 2167 2.963432 ACTGCAAATGCTAAACATGGC 58.037 42.857 6.97 0.00 39.60 4.40
2084 2169 4.858692 GTGGTACTGCAAATGCTAAACATG 59.141 41.667 6.97 0.00 39.60 3.21
2183 2276 5.163488 CCCGGGGAACTATTTTCCATTTTAC 60.163 44.000 14.71 0.00 40.32 2.01
2188 2281 2.210644 TCCCGGGGAACTATTTTCCAT 58.789 47.619 23.50 0.00 40.32 3.41
2224 2317 5.649831 ACTGATTCTTCAAATAAGGAGGTGC 59.350 40.000 0.00 0.00 0.00 5.01
2231 2324 9.635520 ATTTGCAAGACTGATTCTTCAAATAAG 57.364 29.630 14.73 0.00 43.23 1.73
2304 2404 7.609146 AGCAGTGAATGACAAGAAGATGAATAA 59.391 33.333 0.00 0.00 0.00 1.40
2311 2411 5.858381 AGTAAGCAGTGAATGACAAGAAGA 58.142 37.500 0.00 0.00 0.00 2.87
2466 2570 8.997323 GCAGCACTATAATCTTCATAAATGTCT 58.003 33.333 0.00 0.00 0.00 3.41
2637 3146 4.507756 GTGTTTTGGTCATTCAAAAGCTCC 59.492 41.667 3.40 0.00 44.22 4.70
2671 3180 5.817296 TGTTATGATTGCAGTCCTGATGTAC 59.183 40.000 6.77 0.00 0.00 2.90
2688 3197 7.907841 TTTAGTAGGTCCAGCTATGTTATGA 57.092 36.000 0.00 0.00 0.00 2.15
2722 3231 3.587061 TGTTCTGGTGGACTGATAACCAT 59.413 43.478 0.00 0.00 42.89 3.55
2810 3319 4.989044 ACACTTACAAAGTTTTGGGAACG 58.011 39.130 9.22 0.00 40.46 3.95
2840 3349 7.777910 TGTTCTAGGTTTCCAAAAGATTCTTCA 59.222 33.333 0.00 0.00 0.00 3.02
2986 3495 4.617595 AACCCCAGCCCTCCCAGT 62.618 66.667 0.00 0.00 0.00 4.00
3110 3619 4.993705 TGTACAGACAGGGGAAAGAAAT 57.006 40.909 0.00 0.00 0.00 2.17
3234 3774 6.762333 TGTTGATCTCTTTCAGAATCTGACA 58.238 36.000 13.17 5.63 40.46 3.58
3310 3850 3.366374 GGCTTTGTTCTACATGGCTGTTC 60.366 47.826 0.00 0.00 36.79 3.18
3347 3887 3.885521 GCTTCCATGCGAGCTGCC 61.886 66.667 10.31 0.00 45.60 4.85
3465 4010 5.110814 TGTCCCATCCTGTACAAAATAGG 57.889 43.478 0.00 0.00 0.00 2.57
3566 4112 7.301054 CAGAAGATCCATAACAGTTTGTTCAC 58.699 38.462 0.00 0.00 40.22 3.18
3606 4153 2.275134 TCTCATGCTGCTTTGGAACA 57.725 45.000 0.00 0.00 0.00 3.18
3655 4202 9.750125 CACACTATATGAACAACTATAGCTGAA 57.250 33.333 10.11 0.00 33.20 3.02
3656 4203 9.131791 TCACACTATATGAACAACTATAGCTGA 57.868 33.333 10.11 0.00 33.20 4.26
3657 4204 9.404348 CTCACACTATATGAACAACTATAGCTG 57.596 37.037 0.00 0.00 33.20 4.24
3658 4205 8.580720 CCTCACACTATATGAACAACTATAGCT 58.419 37.037 0.00 0.00 33.20 3.32
3659 4206 7.329717 GCCTCACACTATATGAACAACTATAGC 59.670 40.741 0.00 0.00 33.20 2.97
3660 4207 8.360390 TGCCTCACACTATATGAACAACTATAG 58.640 37.037 0.00 0.00 35.15 1.31
3661 4208 8.141909 GTGCCTCACACTATATGAACAACTATA 58.858 37.037 0.00 0.00 46.41 1.31
3662 4209 6.986817 GTGCCTCACACTATATGAACAACTAT 59.013 38.462 0.00 0.00 46.41 2.12
3663 4210 6.338146 GTGCCTCACACTATATGAACAACTA 58.662 40.000 0.00 0.00 46.41 2.24
3664 4211 5.178797 GTGCCTCACACTATATGAACAACT 58.821 41.667 0.00 0.00 46.41 3.16
3665 4212 5.470845 GTGCCTCACACTATATGAACAAC 57.529 43.478 0.00 0.00 46.41 3.32
3717 4274 9.546909 GCATTATCGATCAAACAATATAAGTGG 57.453 33.333 0.00 0.00 0.00 4.00
3756 4315 7.509141 TTGCACTGAACAAAGATAAGAATCA 57.491 32.000 0.00 0.00 34.28 2.57
3787 4346 2.224523 TGAGAATCGGAAACTGCAACCT 60.225 45.455 0.00 0.00 38.61 3.50
3788 4347 2.151202 TGAGAATCGGAAACTGCAACC 58.849 47.619 0.00 0.00 38.61 3.77
3803 4362 1.661463 ATGAGAGGGGTTGCTGAGAA 58.339 50.000 0.00 0.00 0.00 2.87
3809 4368 0.036388 TCACGAATGAGAGGGGTTGC 60.036 55.000 0.00 0.00 0.00 4.17
3842 4401 7.951530 AAGGTGAAATTACATTGCTCAAAAG 57.048 32.000 0.00 0.00 0.00 2.27
3986 4550 5.538053 TCCATAGAGCTAACAGATTCAGGAG 59.462 44.000 0.00 0.00 0.00 3.69
4106 4670 2.313172 CGTGCTAGCATCATCGGCC 61.313 63.158 22.51 4.04 0.00 6.13
4119 4683 4.261801 ACAGATATTTGCTTTACCGTGCT 58.738 39.130 0.00 0.00 0.00 4.40
4146 4710 1.625818 ACCACTAGGAACTGCAGGAAG 59.374 52.381 19.93 9.76 41.52 3.46
4156 4720 2.500098 GACTATGTGGCACCACTAGGAA 59.500 50.000 20.02 0.32 46.30 3.36
4267 4831 1.470285 GCTACGTTCAATGCCGACCTA 60.470 52.381 0.00 0.00 0.00 3.08



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

AutoCloner maintained by Alex Coulton.