Multiple sequence alignment - TraesCS3D01G348900

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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 TraesCS3D01G348900 chr3D 100.000 3461 0 0 1 3461 460437054 460440514 0.000000e+00 6392
1 TraesCS3D01G348900 chr3D 87.544 562 50 11 2906 3461 91821085 91821632 1.750000e-177 632
2 TraesCS3D01G348900 chr3A 89.620 2948 197 46 1 2911 602850576 602853451 0.000000e+00 3648
3 TraesCS3D01G348900 chr3B 92.524 2060 100 25 799 2837 610531954 610533980 0.000000e+00 2902
4 TraesCS3D01G348900 chr3B 88.351 558 49 10 2907 3461 752180107 752179563 0.000000e+00 656
5 TraesCS3D01G348900 chr6D 94.118 561 28 5 2902 3461 418768814 418768258 0.000000e+00 848
6 TraesCS3D01G348900 chr7D 89.587 557 39 9 2909 3461 473648935 473648394 0.000000e+00 689
7 TraesCS3D01G348900 chr7D 87.434 565 48 17 2906 3461 426175358 426174808 2.270000e-176 628
8 TraesCS3D01G348900 chr6A 91.111 495 36 6 2910 3400 580792312 580791822 0.000000e+00 664
9 TraesCS3D01G348900 chr5D 88.530 558 45 11 2912 3461 14531852 14531306 0.000000e+00 658
10 TraesCS3D01G348900 chr2A 88.014 559 48 11 2906 3460 121949187 121949730 0.000000e+00 643
11 TraesCS3D01G348900 chr2A 86.316 570 57 15 2903 3460 22736384 22736944 4.940000e-168 601


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 TraesCS3D01G348900 chr3D 460437054 460440514 3460 False 6392 6392 100.000 1 3461 1 chr3D.!!$F2 3460
1 TraesCS3D01G348900 chr3D 91821085 91821632 547 False 632 632 87.544 2906 3461 1 chr3D.!!$F1 555
2 TraesCS3D01G348900 chr3A 602850576 602853451 2875 False 3648 3648 89.620 1 2911 1 chr3A.!!$F1 2910
3 TraesCS3D01G348900 chr3B 610531954 610533980 2026 False 2902 2902 92.524 799 2837 1 chr3B.!!$F1 2038
4 TraesCS3D01G348900 chr3B 752179563 752180107 544 True 656 656 88.351 2907 3461 1 chr3B.!!$R1 554
5 TraesCS3D01G348900 chr6D 418768258 418768814 556 True 848 848 94.118 2902 3461 1 chr6D.!!$R1 559
6 TraesCS3D01G348900 chr7D 473648394 473648935 541 True 689 689 89.587 2909 3461 1 chr7D.!!$R2 552
7 TraesCS3D01G348900 chr7D 426174808 426175358 550 True 628 628 87.434 2906 3461 1 chr7D.!!$R1 555
8 TraesCS3D01G348900 chr5D 14531306 14531852 546 True 658 658 88.530 2912 3461 1 chr5D.!!$R1 549
9 TraesCS3D01G348900 chr2A 121949187 121949730 543 False 643 643 88.014 2906 3460 1 chr2A.!!$F2 554
10 TraesCS3D01G348900 chr2A 22736384 22736944 560 False 601 601 86.316 2903 3460 1 chr2A.!!$F1 557

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
388 390 0.107703 GCATGAACTGGTCGGATCCA 60.108 55.0 13.41 0.0 36.00 3.41 F
524 526 0.322456 TTCCTTTCCTCCGTGGCATG 60.322 55.0 0.00 0.0 35.26 4.06 F
1960 1985 0.383124 GTTCACGCGAAACTGCTCAC 60.383 55.0 15.93 0.0 31.43 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1343 1355 0.102481 ACGTCGTTCAGCTTCAGTGT 59.898 50.0 0.00 0.00 0.00 3.55 R
2280 2305 0.249911 ACCGGTTGTCTTCTGCAGTC 60.250 55.0 14.67 4.01 0.00 3.51 R
3003 3071 0.237235 TCAATTTTGACGCGTCTGCC 59.763 50.0 36.27 14.68 32.35 4.85 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
25 26 2.224621 ACCAGCAATGTGACAGCTTAGT 60.225 45.455 0.00 0.00 36.26 2.24
32 33 0.456312 GTGACAGCTTAGTCGTCCGG 60.456 60.000 0.00 0.00 41.41 5.14
37 38 0.739561 AGCTTAGTCGTCCGGATGTC 59.260 55.000 22.88 17.56 0.00 3.06
39 40 1.534175 GCTTAGTCGTCCGGATGTCAG 60.534 57.143 22.88 12.65 0.00 3.51
73 74 3.258372 TGGATCTTGTGGTGTAGTGACTC 59.742 47.826 0.00 0.00 0.00 3.36
89 90 2.283298 GACTCGTGTGGCAATGATGAT 58.717 47.619 0.00 0.00 0.00 2.45
97 98 2.880890 GTGGCAATGATGATGGGTAGAC 59.119 50.000 0.00 0.00 0.00 2.59
101 102 4.454678 GCAATGATGATGGGTAGACAGAA 58.545 43.478 0.00 0.00 0.00 3.02
105 106 4.871822 TGATGATGGGTAGACAGAAGAGA 58.128 43.478 0.00 0.00 0.00 3.10
107 108 5.303845 TGATGATGGGTAGACAGAAGAGATG 59.696 44.000 0.00 0.00 0.00 2.90
114 115 4.220821 GGTAGACAGAAGAGATGGACAACA 59.779 45.833 0.00 0.00 0.00 3.33
115 116 4.963318 AGACAGAAGAGATGGACAACAA 57.037 40.909 0.00 0.00 0.00 2.83
116 117 4.636249 AGACAGAAGAGATGGACAACAAC 58.364 43.478 0.00 0.00 0.00 3.32
138 139 0.232303 GTCCTTCGTTGTTGACTGCG 59.768 55.000 0.00 0.00 0.00 5.18
142 143 0.741574 TTCGTTGTTGACTGCGTGGT 60.742 50.000 0.00 0.00 0.00 4.16
144 145 0.506932 CGTTGTTGACTGCGTGGTAG 59.493 55.000 0.00 0.00 0.00 3.18
152 153 0.683504 ACTGCGTGGTAGGTCCTAGG 60.684 60.000 0.82 0.82 37.07 3.02
172 173 3.131046 AGGTTTGTCCTTGCAACTTCTTG 59.869 43.478 0.00 0.00 45.67 3.02
184 185 3.617669 CAACTTCTTGTTTGTGTAGCGG 58.382 45.455 0.00 0.00 36.63 5.52
196 197 1.063811 GTAGCGGTGTAGTCGGAGC 59.936 63.158 0.00 0.00 0.00 4.70
200 201 0.317938 GCGGTGTAGTCGGAGCTATG 60.318 60.000 0.00 0.00 0.00 2.23
241 242 2.642139 ACAATGATGCCTTGCGAAAG 57.358 45.000 0.00 0.00 0.00 2.62
249 250 1.300481 GCCTTGCGAAAGGTAGGATC 58.700 55.000 23.57 1.58 42.00 3.36
268 269 1.553248 TCTACACCCAACAATCTCCCG 59.447 52.381 0.00 0.00 0.00 5.14
271 272 1.278127 ACACCCAACAATCTCCCGTAG 59.722 52.381 0.00 0.00 0.00 3.51
343 345 1.268899 TCGAAGTCGAGTTCCCAGTTC 59.731 52.381 23.85 1.94 44.22 3.01
348 350 2.900546 AGTCGAGTTCCCAGTTCTTGAT 59.099 45.455 0.00 0.00 0.00 2.57
349 351 2.996621 GTCGAGTTCCCAGTTCTTGATG 59.003 50.000 0.00 0.00 0.00 3.07
364 366 6.485313 AGTTCTTGATGTGTTTGATCGGTTTA 59.515 34.615 0.00 0.00 0.00 2.01
380 382 5.250200 TCGGTTTATTTAGCATGAACTGGT 58.750 37.500 0.00 0.00 39.41 4.00
382 384 5.569413 GGTTTATTTAGCATGAACTGGTCG 58.431 41.667 0.00 0.00 36.79 4.79
383 385 5.448632 GGTTTATTTAGCATGAACTGGTCGG 60.449 44.000 0.00 0.00 36.79 4.79
387 389 0.179000 AGCATGAACTGGTCGGATCC 59.821 55.000 0.00 0.00 0.00 3.36
388 390 0.107703 GCATGAACTGGTCGGATCCA 60.108 55.000 13.41 0.00 36.00 3.41
400 402 0.603065 CGGATCCAGTGTGTCAGTGA 59.397 55.000 13.41 0.00 36.99 3.41
401 403 1.403382 CGGATCCAGTGTGTCAGTGAG 60.403 57.143 13.41 0.00 36.99 3.51
402 404 1.895798 GGATCCAGTGTGTCAGTGAGA 59.104 52.381 6.95 0.00 36.99 3.27
414 416 3.214696 TCAGTGAGACAGTGACAGAGA 57.785 47.619 0.00 0.00 38.67 3.10
415 417 3.145286 TCAGTGAGACAGTGACAGAGAG 58.855 50.000 0.00 0.00 38.67 3.20
416 418 2.228582 CAGTGAGACAGTGACAGAGAGG 59.771 54.545 0.00 0.00 36.99 3.69
417 419 1.543802 GTGAGACAGTGACAGAGAGGG 59.456 57.143 0.00 0.00 0.00 4.30
418 420 0.530288 GAGACAGTGACAGAGAGGGC 59.470 60.000 0.00 0.00 0.00 5.19
421 423 0.972883 ACAGTGACAGAGAGGGCTTC 59.027 55.000 0.00 0.00 0.00 3.86
425 427 0.603569 TGACAGAGAGGGCTTCGTTC 59.396 55.000 0.00 0.00 0.00 3.95
439 441 4.270084 GGCTTCGTTCGTCATCAATGATTA 59.730 41.667 0.00 0.00 39.30 1.75
442 444 5.389642 TCGTTCGTCATCAATGATTAAGC 57.610 39.130 0.00 0.00 39.30 3.09
448 450 4.531332 GTCATCAATGATTAAGCCGAAGC 58.469 43.478 0.00 0.00 39.30 3.86
449 451 4.274459 GTCATCAATGATTAAGCCGAAGCT 59.726 41.667 0.00 0.00 45.33 3.74
483 485 5.812642 GGAAGACGTGATGACAATGATAGTT 59.187 40.000 0.00 0.00 0.00 2.24
497 499 8.146124 ACAATGATAGTTGCAGGCAAAACCTT 62.146 38.462 8.47 0.00 37.88 3.50
515 517 7.468141 AAACCTTGACAATATTCCTTTCCTC 57.532 36.000 0.00 0.00 0.00 3.71
516 518 5.510430 ACCTTGACAATATTCCTTTCCTCC 58.490 41.667 0.00 0.00 0.00 4.30
524 526 0.322456 TTCCTTTCCTCCGTGGCATG 60.322 55.000 0.00 0.00 35.26 4.06
532 534 2.034066 CCGTGGCATGTGGGTCTT 59.966 61.111 5.89 0.00 0.00 3.01
544 546 3.838565 TGTGGGTCTTTTTGGATAAGCA 58.161 40.909 0.00 0.00 0.00 3.91
553 555 2.280186 GGATAAGCAGGTCGGGCG 60.280 66.667 0.00 0.00 36.08 6.13
568 570 3.827634 GCGGGATGCCCTACTTTG 58.172 61.111 0.00 0.00 42.67 2.77
580 582 0.447801 CTACTTTGTGGGCGTGATGC 59.552 55.000 0.00 0.00 45.38 3.91
593 595 4.297944 GCGTGATGCAACATTTTTCTTC 57.702 40.909 0.00 0.00 45.45 2.87
594 596 3.983344 GCGTGATGCAACATTTTTCTTCT 59.017 39.130 0.00 0.00 45.45 2.85
595 597 4.143473 GCGTGATGCAACATTTTTCTTCTG 60.143 41.667 0.00 0.00 45.45 3.02
596 598 4.383649 CGTGATGCAACATTTTTCTTCTGG 59.616 41.667 0.00 0.00 0.00 3.86
597 599 4.151157 GTGATGCAACATTTTTCTTCTGGC 59.849 41.667 0.00 0.00 0.00 4.85
598 600 3.815856 TGCAACATTTTTCTTCTGGCA 57.184 38.095 0.00 0.00 0.00 4.92
600 602 4.706035 TGCAACATTTTTCTTCTGGCATT 58.294 34.783 0.00 0.00 0.00 3.56
601 603 4.512198 TGCAACATTTTTCTTCTGGCATTG 59.488 37.500 0.00 0.00 0.00 2.82
602 604 4.751098 GCAACATTTTTCTTCTGGCATTGA 59.249 37.500 0.00 0.00 0.00 2.57
603 605 5.410439 GCAACATTTTTCTTCTGGCATTGAT 59.590 36.000 0.00 0.00 0.00 2.57
604 606 6.072893 GCAACATTTTTCTTCTGGCATTGATT 60.073 34.615 0.00 0.00 0.00 2.57
605 607 7.118101 GCAACATTTTTCTTCTGGCATTGATTA 59.882 33.333 0.00 0.00 0.00 1.75
606 608 8.991026 CAACATTTTTCTTCTGGCATTGATTAA 58.009 29.630 0.00 0.00 0.00 1.40
607 609 9.729281 AACATTTTTCTTCTGGCATTGATTAAT 57.271 25.926 0.00 0.00 0.00 1.40
608 610 9.374838 ACATTTTTCTTCTGGCATTGATTAATC 57.625 29.630 8.60 8.60 0.00 1.75
609 611 8.537223 CATTTTTCTTCTGGCATTGATTAATCG 58.463 33.333 10.80 0.00 0.00 3.34
610 612 6.757897 TTTCTTCTGGCATTGATTAATCGT 57.242 33.333 10.80 0.00 0.00 3.73
611 613 7.857734 TTTCTTCTGGCATTGATTAATCGTA 57.142 32.000 10.80 2.07 0.00 3.43
612 614 7.857734 TTCTTCTGGCATTGATTAATCGTAA 57.142 32.000 10.80 1.11 0.00 3.18
613 615 7.857734 TCTTCTGGCATTGATTAATCGTAAA 57.142 32.000 10.80 0.41 0.00 2.01
614 616 8.275015 TCTTCTGGCATTGATTAATCGTAAAA 57.725 30.769 10.80 0.06 0.00 1.52
615 617 8.735315 TCTTCTGGCATTGATTAATCGTAAAAA 58.265 29.630 10.80 0.00 0.00 1.94
654 656 1.909700 TGGATTGAACACCAAGGCTC 58.090 50.000 0.00 0.00 38.31 4.70
770 772 8.702819 GGTATTCCAAGTATTTACAGAGGTAGT 58.297 37.037 0.00 0.00 0.00 2.73
810 814 5.703130 GGTGAGAAGGTATATGAGCATTTCC 59.297 44.000 0.00 0.00 0.00 3.13
872 877 2.939022 GCGACACAACTCACCAGC 59.061 61.111 0.00 0.00 0.00 4.85
907 912 6.090898 CCAGACAATTAAAGTCCGACAGTAAG 59.909 42.308 0.40 0.00 36.68 2.34
929 934 1.741770 CAGCCGTTCTTTCCCGAGG 60.742 63.158 0.00 0.00 0.00 4.63
955 960 3.364565 CCTCAACAAATACCGAACCAACG 60.365 47.826 0.00 0.00 0.00 4.10
967 972 2.034001 CGAACCAACGTGTTCTCTGTTC 60.034 50.000 14.58 7.67 41.95 3.18
981 986 2.911723 CTCTGTTCGTTCACTCGATCAC 59.088 50.000 0.00 0.00 39.57 3.06
982 987 2.552743 TCTGTTCGTTCACTCGATCACT 59.447 45.455 0.00 0.00 39.57 3.41
983 988 2.658802 CTGTTCGTTCACTCGATCACTG 59.341 50.000 0.00 0.00 39.57 3.66
984 989 2.034179 TGTTCGTTCACTCGATCACTGT 59.966 45.455 0.00 0.00 39.57 3.55
985 990 3.050619 GTTCGTTCACTCGATCACTGTT 58.949 45.455 0.00 0.00 39.57 3.16
986 991 2.929960 TCGTTCACTCGATCACTGTTC 58.070 47.619 0.00 0.00 34.85 3.18
987 992 2.292292 TCGTTCACTCGATCACTGTTCA 59.708 45.455 0.00 0.00 34.85 3.18
1068 1073 3.041946 GGTGGACATTACTCCTCCTCAT 58.958 50.000 0.00 0.00 39.85 2.90
1086 1091 0.811616 ATCCCGACGAGCATTTCAGC 60.812 55.000 0.00 0.00 0.00 4.26
1338 1350 2.285977 TGCATCATCATCTGCTGTCAC 58.714 47.619 0.00 0.00 39.16 3.67
1343 1355 3.094572 TCATCATCTGCTGTCACTCTGA 58.905 45.455 0.00 0.00 0.00 3.27
1360 1385 1.789464 CTGACACTGAAGCTGAACGAC 59.211 52.381 0.00 0.00 0.00 4.34
1368 1393 2.984471 TGAAGCTGAACGACGTGTTATC 59.016 45.455 0.00 0.00 42.09 1.75
1960 1985 0.383124 GTTCACGCGAAACTGCTCAC 60.383 55.000 15.93 0.00 31.43 3.51
1966 1991 2.551270 GAAACTGCTCACACGCCG 59.449 61.111 0.00 0.00 0.00 6.46
2001 2026 4.227538 GTGTGTAGTGTGTAGTAGTGCTG 58.772 47.826 0.00 0.00 0.00 4.41
2015 2040 1.004679 TGCTGATCTGCACGCTTGA 60.005 52.632 21.87 0.00 38.12 3.02
2056 2081 0.458543 AGTGCAACATCTACGAGGCG 60.459 55.000 0.00 0.00 41.43 5.52
2113 2138 6.750775 GAGCAGGTCTCGTATTACATTTAC 57.249 41.667 0.00 0.00 31.20 2.01
2114 2139 6.216801 AGCAGGTCTCGTATTACATTTACA 57.783 37.500 0.00 0.00 0.00 2.41
2115 2140 6.817184 AGCAGGTCTCGTATTACATTTACAT 58.183 36.000 0.00 0.00 0.00 2.29
2116 2141 7.948357 AGCAGGTCTCGTATTACATTTACATA 58.052 34.615 0.00 0.00 0.00 2.29
2137 2162 1.833630 CACTGGGCCTTACAGATCTGA 59.166 52.381 29.27 10.06 39.24 3.27
2250 2275 1.366366 CGACCTGTTCCTGAACGGT 59.634 57.895 19.28 19.28 44.16 4.83
2265 2290 2.809601 GGTGCGCAGGAGTACACG 60.810 66.667 12.22 0.00 33.81 4.49
2274 2299 2.415512 GCAGGAGTACACGGAAAATGAC 59.584 50.000 0.00 0.00 0.00 3.06
2276 2301 3.927142 CAGGAGTACACGGAAAATGACTC 59.073 47.826 0.00 0.00 33.99 3.36
2277 2302 3.576982 AGGAGTACACGGAAAATGACTCA 59.423 43.478 0.00 0.00 35.98 3.41
2280 2305 4.810790 AGTACACGGAAAATGACTCAGAG 58.189 43.478 0.00 0.00 0.00 3.35
2293 2318 2.556189 GACTCAGAGACTGCAGAAGACA 59.444 50.000 23.35 0.00 0.00 3.41
2297 2322 1.000283 AGAGACTGCAGAAGACAACCG 60.000 52.381 23.35 0.00 0.00 4.44
2307 2332 0.549469 AAGACAACCGGTGGGACTTT 59.451 50.000 15.05 0.00 36.97 2.66
2449 2499 4.994471 CACCTGCTGCTGCCACGA 62.994 66.667 13.47 0.00 38.71 4.35
2450 2500 4.996434 ACCTGCTGCTGCCACGAC 62.996 66.667 13.47 0.00 38.71 4.34
2451 2501 4.994471 CCTGCTGCTGCCACGACA 62.994 66.667 13.47 0.00 38.71 4.35
2452 2502 2.745100 CTGCTGCTGCCACGACAT 60.745 61.111 13.47 0.00 38.71 3.06
2453 2503 2.281692 TGCTGCTGCCACGACATT 60.282 55.556 13.47 0.00 38.71 2.71
2454 2504 1.859427 CTGCTGCTGCCACGACATTT 61.859 55.000 13.47 0.00 38.71 2.32
2455 2505 1.443194 GCTGCTGCCACGACATTTG 60.443 57.895 3.85 0.00 0.00 2.32
2456 2506 1.951510 CTGCTGCCACGACATTTGT 59.048 52.632 0.00 0.00 0.00 2.83
2457 2507 0.110056 CTGCTGCCACGACATTTGTC 60.110 55.000 0.00 0.46 41.47 3.18
2458 2508 0.534877 TGCTGCCACGACATTTGTCT 60.535 50.000 8.91 0.00 42.66 3.41
2459 2509 0.110056 GCTGCCACGACATTTGTCTG 60.110 55.000 8.91 6.26 42.66 3.51
2460 2510 1.511850 CTGCCACGACATTTGTCTGA 58.488 50.000 8.91 0.00 42.66 3.27
2461 2511 1.872952 CTGCCACGACATTTGTCTGAA 59.127 47.619 8.91 0.00 42.66 3.02
2462 2512 1.872952 TGCCACGACATTTGTCTGAAG 59.127 47.619 8.91 0.00 42.66 3.02
2463 2513 1.873591 GCCACGACATTTGTCTGAAGT 59.126 47.619 8.91 0.00 42.66 3.01
2464 2514 3.064207 GCCACGACATTTGTCTGAAGTA 58.936 45.455 8.91 0.00 42.66 2.24
2480 2530 6.706270 GTCTGAAGTATGAACCACTCTGAAAA 59.294 38.462 0.00 0.00 0.00 2.29
2515 2565 6.631238 CGCGATCCAAATAAATTTACACGAAT 59.369 34.615 0.00 0.00 0.00 3.34
2527 2577 8.810327 AAATTTACACGAATAATAACGAACCG 57.190 30.769 0.00 0.00 0.00 4.44
2531 2581 1.854126 CGAATAATAACGAACCGCCGT 59.146 47.619 0.00 0.00 45.64 5.68
2532 2582 3.042189 CGAATAATAACGAACCGCCGTA 58.958 45.455 0.00 0.00 42.54 4.02
2533 2583 3.121696 CGAATAATAACGAACCGCCGTAC 60.122 47.826 0.00 0.00 42.54 3.67
2604 2664 3.104843 AGCTCTGAATTCCATAGTCGC 57.895 47.619 2.27 2.38 0.00 5.19
2613 2674 4.558538 ATTCCATAGTCGCTGCATTTTC 57.441 40.909 0.00 0.00 0.00 2.29
2622 2683 3.058224 GTCGCTGCATTTTCTTGTAACCT 60.058 43.478 0.00 0.00 0.00 3.50
2655 2716 4.326826 TCTGATGATTGTCCTGTTGGAAC 58.673 43.478 0.00 0.00 45.18 3.62
2795 2862 7.797819 CGCAAGTTGTAGATTTTATATCTCCC 58.202 38.462 4.48 0.00 0.00 4.30
2800 2867 9.853177 AGTTGTAGATTTTATATCTCCCTTTGG 57.147 33.333 0.00 0.00 0.00 3.28
2845 2912 0.445436 CAGACTCGTACTACGCCGTT 59.555 55.000 0.00 0.00 42.21 4.44
2854 2921 2.509786 TACGCCGTTCCATTCCGC 60.510 61.111 0.00 0.00 0.00 5.54
2858 2925 3.508840 CCGTTCCATTCCGCTGGC 61.509 66.667 0.00 0.00 36.16 4.85
2876 2943 1.335051 GGCTTGCTTCGGTTTCTTGTC 60.335 52.381 0.00 0.00 0.00 3.18
2878 2945 1.597663 CTTGCTTCGGTTTCTTGTCGT 59.402 47.619 0.00 0.00 0.00 4.34
2935 3002 4.980903 CAACAGCCACGCAACGCC 62.981 66.667 0.00 0.00 0.00 5.68
3195 3282 9.464714 AAACTATTAGATAGTGCAACGACATAG 57.535 33.333 0.00 0.00 44.94 2.23
3206 3294 8.718102 AGTGCAACGACATAGATAAAAACTAT 57.282 30.769 0.00 0.00 45.86 2.12
3324 3421 1.524355 CCAACGATCATCATCAGACGC 59.476 52.381 0.00 0.00 0.00 5.19
3329 3426 2.220363 CGATCATCATCAGACGCAAAGG 59.780 50.000 0.00 0.00 0.00 3.11
3364 3461 1.428448 TCTCAACGATTTCGCACTGG 58.572 50.000 0.00 0.00 44.43 4.00
3369 3466 2.225068 ACGATTTCGCACTGGGATAG 57.775 50.000 0.00 0.00 44.43 2.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 2.668457 GGACGACTAAGCTGTCACATTG 59.332 50.000 5.18 0.00 36.82 2.82
10 11 2.671351 CGGACGACTAAGCTGTCACATT 60.671 50.000 5.18 0.00 36.82 2.71
25 26 2.036731 ACCCTGACATCCGGACGA 59.963 61.111 6.12 0.00 0.00 4.20
32 33 2.154462 CAAGGTCAACACCCTGACATC 58.846 52.381 6.12 0.00 46.31 3.06
37 38 1.352352 AGATCCAAGGTCAACACCCTG 59.648 52.381 0.00 0.00 45.12 4.45
39 40 2.162681 CAAGATCCAAGGTCAACACCC 58.837 52.381 0.00 0.00 45.12 4.61
73 74 0.382873 CCCATCATCATTGCCACACG 59.617 55.000 0.00 0.00 0.00 4.49
89 90 3.245622 TGTCCATCTCTTCTGTCTACCCA 60.246 47.826 0.00 0.00 0.00 4.51
97 98 4.758674 ACATGTTGTTGTCCATCTCTTCTG 59.241 41.667 0.00 0.00 0.00 3.02
114 115 3.312421 CAGTCAACAACGAAGGACATGTT 59.688 43.478 0.00 0.00 36.49 2.71
115 116 2.872245 CAGTCAACAACGAAGGACATGT 59.128 45.455 0.00 0.00 32.79 3.21
116 117 2.349817 GCAGTCAACAACGAAGGACATG 60.350 50.000 0.00 0.00 32.79 3.21
122 123 0.042188 CCACGCAGTCAACAACGAAG 60.042 55.000 0.00 0.00 41.61 3.79
126 127 0.865769 CCTACCACGCAGTCAACAAC 59.134 55.000 0.00 0.00 41.61 3.32
138 139 2.235650 GGACAAACCTAGGACCTACCAC 59.764 54.545 17.98 0.00 37.07 4.16
152 153 4.110036 ACAAGAAGTTGCAAGGACAAAC 57.890 40.909 0.00 0.00 37.14 2.93
172 173 1.717645 CGACTACACCGCTACACAAAC 59.282 52.381 0.00 0.00 0.00 2.93
184 185 1.749634 ACACCATAGCTCCGACTACAC 59.250 52.381 0.00 0.00 0.00 2.90
196 197 1.473677 TGTCGTCCGGTAACACCATAG 59.526 52.381 0.00 0.00 38.47 2.23
200 201 0.738412 CCATGTCGTCCGGTAACACC 60.738 60.000 0.00 0.00 34.05 4.16
241 242 4.409247 AGATTGTTGGGTGTAGATCCTACC 59.591 45.833 1.38 2.79 0.00 3.18
249 250 1.278127 ACGGGAGATTGTTGGGTGTAG 59.722 52.381 0.00 0.00 0.00 2.74
268 269 2.526120 GCAGAATCCCGCGTGCTAC 61.526 63.158 4.92 0.00 32.97 3.58
271 272 3.869272 CTGCAGAATCCCGCGTGC 61.869 66.667 8.42 7.88 36.42 5.34
325 327 3.060602 CAAGAACTGGGAACTCGACTTC 58.939 50.000 0.00 0.00 0.00 3.01
334 336 4.531854 TCAAACACATCAAGAACTGGGAA 58.468 39.130 0.00 0.00 0.00 3.97
343 345 9.277565 CTAAATAAACCGATCAAACACATCAAG 57.722 33.333 0.00 0.00 0.00 3.02
348 350 6.561737 TGCTAAATAAACCGATCAAACACA 57.438 33.333 0.00 0.00 0.00 3.72
349 351 7.247728 TCATGCTAAATAAACCGATCAAACAC 58.752 34.615 0.00 0.00 0.00 3.32
364 366 3.627395 TCCGACCAGTTCATGCTAAAT 57.373 42.857 0.00 0.00 0.00 1.40
380 382 0.603065 CACTGACACACTGGATCCGA 59.397 55.000 7.39 0.00 0.00 4.55
382 384 1.895798 TCTCACTGACACACTGGATCC 59.104 52.381 4.20 4.20 0.00 3.36
383 385 2.953020 GTCTCACTGACACACTGGATC 58.047 52.381 0.00 0.00 44.73 3.36
400 402 0.114168 AGCCCTCTCTGTCACTGTCT 59.886 55.000 0.00 0.00 0.00 3.41
401 403 0.972883 AAGCCCTCTCTGTCACTGTC 59.027 55.000 0.00 0.00 0.00 3.51
402 404 0.972883 GAAGCCCTCTCTGTCACTGT 59.027 55.000 0.00 0.00 0.00 3.55
403 405 0.108898 CGAAGCCCTCTCTGTCACTG 60.109 60.000 0.00 0.00 0.00 3.66
404 406 0.540830 ACGAAGCCCTCTCTGTCACT 60.541 55.000 0.00 0.00 0.00 3.41
406 408 0.603569 GAACGAAGCCCTCTCTGTCA 59.396 55.000 0.00 0.00 0.00 3.58
407 409 0.456995 CGAACGAAGCCCTCTCTGTC 60.457 60.000 0.00 0.00 0.00 3.51
408 410 1.179814 ACGAACGAAGCCCTCTCTGT 61.180 55.000 0.14 0.00 0.00 3.41
409 411 0.456995 GACGAACGAAGCCCTCTCTG 60.457 60.000 0.14 0.00 0.00 3.35
411 413 0.173708 ATGACGAACGAAGCCCTCTC 59.826 55.000 0.14 0.00 0.00 3.20
412 414 0.173708 GATGACGAACGAAGCCCTCT 59.826 55.000 0.14 0.00 0.00 3.69
413 415 0.108804 TGATGACGAACGAAGCCCTC 60.109 55.000 0.14 0.00 0.00 4.30
414 416 0.320374 TTGATGACGAACGAAGCCCT 59.680 50.000 0.14 0.00 0.00 5.19
415 417 1.062587 CATTGATGACGAACGAAGCCC 59.937 52.381 0.14 0.00 0.00 5.19
416 418 1.999735 TCATTGATGACGAACGAAGCC 59.000 47.619 0.14 0.00 0.00 4.35
417 419 3.933155 ATCATTGATGACGAACGAAGC 57.067 42.857 0.00 0.00 40.03 3.86
418 420 5.898606 GCTTAATCATTGATGACGAACGAAG 59.101 40.000 0.00 0.00 40.03 3.79
421 423 4.518217 GGCTTAATCATTGATGACGAACG 58.482 43.478 0.00 0.00 40.03 3.95
425 427 4.766007 CTTCGGCTTAATCATTGATGACG 58.234 43.478 0.00 2.20 40.03 4.35
448 450 1.927174 CACGTCTTCCCGAGCAAATAG 59.073 52.381 0.00 0.00 0.00 1.73
449 451 1.546923 TCACGTCTTCCCGAGCAAATA 59.453 47.619 0.00 0.00 0.00 1.40
497 499 4.513442 CACGGAGGAAAGGAATATTGTCA 58.487 43.478 0.00 0.00 0.00 3.58
515 517 1.178534 AAAAGACCCACATGCCACGG 61.179 55.000 0.00 0.00 0.00 4.94
516 518 0.673437 AAAAAGACCCACATGCCACG 59.327 50.000 0.00 0.00 0.00 4.94
524 526 3.193479 CCTGCTTATCCAAAAAGACCCAC 59.807 47.826 0.00 0.00 0.00 4.61
532 534 1.953311 GCCCGACCTGCTTATCCAAAA 60.953 52.381 0.00 0.00 0.00 2.44
553 555 0.395724 CCCACAAAGTAGGGCATCCC 60.396 60.000 0.00 0.00 45.90 3.85
563 565 1.106351 TTGCATCACGCCCACAAAGT 61.106 50.000 0.00 0.00 41.33 2.66
564 566 0.664166 GTTGCATCACGCCCACAAAG 60.664 55.000 0.00 0.00 41.33 2.77
568 570 0.038343 AAATGTTGCATCACGCCCAC 60.038 50.000 0.00 0.00 41.33 4.61
580 582 7.429636 AATCAATGCCAGAAGAAAAATGTTG 57.570 32.000 0.00 0.00 0.00 3.33
582 584 9.374838 GATTAATCAATGCCAGAAGAAAAATGT 57.625 29.630 10.68 0.00 0.00 2.71
589 591 7.857734 TTTACGATTAATCAATGCCAGAAGA 57.142 32.000 15.57 0.00 0.00 2.87
590 592 8.909708 TTTTTACGATTAATCAATGCCAGAAG 57.090 30.769 15.57 0.00 0.00 2.85
622 624 9.527157 TGGTGTTCAATCCATAGATTAAAGAAA 57.473 29.630 0.00 0.00 40.89 2.52
623 625 9.527157 TTGGTGTTCAATCCATAGATTAAAGAA 57.473 29.630 0.00 0.00 40.89 2.52
624 626 9.177608 CTTGGTGTTCAATCCATAGATTAAAGA 57.822 33.333 0.00 0.00 40.89 2.52
625 627 8.408601 CCTTGGTGTTCAATCCATAGATTAAAG 58.591 37.037 0.00 0.00 40.89 1.85
639 641 1.228124 CCGGAGCCTTGGTGTTCAA 60.228 57.895 0.00 0.00 0.00 2.69
640 642 2.429930 CCGGAGCCTTGGTGTTCA 59.570 61.111 0.00 0.00 0.00 3.18
646 648 3.636231 TCCACACCGGAGCCTTGG 61.636 66.667 9.46 4.26 39.64 3.61
686 688 8.049721 TGAAAATTTTCCCTTGCCTAAGAAAAA 58.950 29.630 24.51 0.83 34.77 1.94
687 689 7.569240 TGAAAATTTTCCCTTGCCTAAGAAAA 58.431 30.769 24.51 0.00 34.77 2.29
693 695 7.790782 ATACTTGAAAATTTTCCCTTGCCTA 57.209 32.000 24.51 4.16 36.36 3.93
737 739 9.840427 CTGTAAATACTTGGAATACCTTTTGTG 57.160 33.333 0.00 0.00 37.04 3.33
738 740 9.802039 TCTGTAAATACTTGGAATACCTTTTGT 57.198 29.630 0.00 0.00 37.04 2.83
785 787 4.899352 ATGCTCATATACCTTCTCACCC 57.101 45.455 0.00 0.00 0.00 4.61
786 788 5.703130 GGAAATGCTCATATACCTTCTCACC 59.297 44.000 0.00 0.00 0.00 4.02
789 791 5.249420 GGGGAAATGCTCATATACCTTCTC 58.751 45.833 0.00 0.00 0.00 2.87
791 793 4.003648 CGGGGAAATGCTCATATACCTTC 58.996 47.826 0.00 0.00 0.00 3.46
793 795 2.979678 ACGGGGAAATGCTCATATACCT 59.020 45.455 0.00 0.00 0.00 3.08
794 796 3.418684 ACGGGGAAATGCTCATATACC 57.581 47.619 0.00 0.00 0.00 2.73
810 814 6.640907 CCAAAGAGAAGTAAATTTGAAACGGG 59.359 38.462 0.00 0.00 35.19 5.28
872 877 0.596082 AATTGTCTGGGCCGTTTTCG 59.404 50.000 0.00 0.00 43.67 3.46
907 912 2.563427 GGAAAGAACGGCTGCTGC 59.437 61.111 8.71 7.10 38.76 5.25
929 934 1.022451 TCGGTATTTGTTGAGGCGCC 61.022 55.000 21.89 21.89 0.00 6.53
955 960 2.468040 CGAGTGAACGAACAGAGAACAC 59.532 50.000 0.00 0.00 35.09 3.32
967 972 2.405357 GTGAACAGTGATCGAGTGAACG 59.595 50.000 0.00 0.00 0.00 3.95
981 986 0.317160 TGGCGTAGGACAGTGAACAG 59.683 55.000 0.00 0.00 0.00 3.16
982 987 0.973632 ATGGCGTAGGACAGTGAACA 59.026 50.000 0.00 0.00 32.06 3.18
983 988 1.359848 CATGGCGTAGGACAGTGAAC 58.640 55.000 0.00 0.00 32.06 3.18
984 989 0.249120 CCATGGCGTAGGACAGTGAA 59.751 55.000 0.00 0.00 32.06 3.18
985 990 1.897423 CCATGGCGTAGGACAGTGA 59.103 57.895 0.00 0.00 32.06 3.41
986 991 1.815421 GCCATGGCGTAGGACAGTG 60.815 63.158 23.48 0.00 32.06 3.66
987 992 2.584608 GCCATGGCGTAGGACAGT 59.415 61.111 23.48 0.00 32.06 3.55
1068 1073 1.447838 GCTGAAATGCTCGTCGGGA 60.448 57.895 0.00 0.00 0.00 5.14
1338 1350 2.057316 CGTTCAGCTTCAGTGTCAGAG 58.943 52.381 0.00 0.00 0.00 3.35
1343 1355 0.102481 ACGTCGTTCAGCTTCAGTGT 59.898 50.000 0.00 0.00 0.00 3.55
1360 1385 2.713011 CCCGTCGTCTTAGATAACACG 58.287 52.381 0.00 0.00 0.00 4.49
1368 1393 4.203076 CCGGGCCCGTCGTCTTAG 62.203 72.222 40.52 20.46 37.81 2.18
1618 1643 4.452733 CCTCGACCCGGGCTTGAC 62.453 72.222 24.08 6.27 0.00 3.18
1960 1985 2.328989 CTTATGGCATGCGGCGTG 59.671 61.111 17.67 17.67 46.16 5.34
1966 1991 1.003545 CTACACACGCTTATGGCATGC 60.004 52.381 9.90 9.90 37.69 4.06
2001 2026 1.196354 GCCATATCAAGCGTGCAGATC 59.804 52.381 0.00 0.00 0.00 2.75
2015 2040 2.224719 GGGAGACAATCTGCAGCCATAT 60.225 50.000 9.47 0.00 36.47 1.78
2056 2081 3.181443 TGAACACTTTCTTCTTCTCCCCC 60.181 47.826 0.00 0.00 32.36 5.40
2113 2138 3.389329 AGATCTGTAAGGCCCAGTGTATG 59.611 47.826 0.00 0.00 0.00 2.39
2114 2139 3.389329 CAGATCTGTAAGGCCCAGTGTAT 59.611 47.826 14.95 0.00 0.00 2.29
2115 2140 2.766263 CAGATCTGTAAGGCCCAGTGTA 59.234 50.000 14.95 0.00 0.00 2.90
2116 2141 1.556911 CAGATCTGTAAGGCCCAGTGT 59.443 52.381 14.95 0.00 0.00 3.55
2250 2275 2.089887 TTTCCGTGTACTCCTGCGCA 62.090 55.000 10.98 10.98 0.00 6.09
2265 2290 3.668447 TGCAGTCTCTGAGTCATTTTCC 58.332 45.455 4.32 0.00 32.44 3.13
2274 2299 3.316283 GTTGTCTTCTGCAGTCTCTGAG 58.684 50.000 14.67 0.00 32.44 3.35
2276 2301 2.411904 GGTTGTCTTCTGCAGTCTCTG 58.588 52.381 14.67 1.02 34.12 3.35
2277 2302 1.000283 CGGTTGTCTTCTGCAGTCTCT 60.000 52.381 14.67 0.00 0.00 3.10
2280 2305 0.249911 ACCGGTTGTCTTCTGCAGTC 60.250 55.000 14.67 4.01 0.00 3.51
2293 2318 1.350310 ACCTCAAAGTCCCACCGGTT 61.350 55.000 2.97 0.00 0.00 4.44
2307 2332 0.616395 TGTAGCAATCCCGGACCTCA 60.616 55.000 0.73 0.00 0.00 3.86
2370 2395 3.314331 CCGGTGCAGGACTCCAGT 61.314 66.667 0.00 0.00 31.85 4.00
2448 2498 6.428159 AGTGGTTCATACTTCAGACAAATGTC 59.572 38.462 5.40 5.40 45.08 3.06
2449 2499 6.299141 AGTGGTTCATACTTCAGACAAATGT 58.701 36.000 0.00 0.00 0.00 2.71
2450 2500 6.652481 AGAGTGGTTCATACTTCAGACAAATG 59.348 38.462 0.00 0.00 0.00 2.32
2451 2501 6.652481 CAGAGTGGTTCATACTTCAGACAAAT 59.348 38.462 0.00 0.00 0.00 2.32
2452 2502 5.991606 CAGAGTGGTTCATACTTCAGACAAA 59.008 40.000 0.00 0.00 0.00 2.83
2453 2503 5.304357 TCAGAGTGGTTCATACTTCAGACAA 59.696 40.000 0.00 0.00 0.00 3.18
2454 2504 4.832823 TCAGAGTGGTTCATACTTCAGACA 59.167 41.667 0.00 0.00 0.00 3.41
2455 2505 5.392767 TCAGAGTGGTTCATACTTCAGAC 57.607 43.478 0.00 0.00 0.00 3.51
2456 2506 6.419484 TTTCAGAGTGGTTCATACTTCAGA 57.581 37.500 0.00 0.00 0.00 3.27
2457 2507 7.678947 ATTTTCAGAGTGGTTCATACTTCAG 57.321 36.000 0.00 0.00 0.00 3.02
2458 2508 8.463930 AAATTTTCAGAGTGGTTCATACTTCA 57.536 30.769 0.00 0.00 0.00 3.02
2460 2510 9.793259 TCTAAATTTTCAGAGTGGTTCATACTT 57.207 29.630 0.00 0.00 0.00 2.24
2461 2511 9.442047 CTCTAAATTTTCAGAGTGGTTCATACT 57.558 33.333 9.09 0.00 34.75 2.12
2462 2512 8.178313 GCTCTAAATTTTCAGAGTGGTTCATAC 58.822 37.037 15.98 0.00 40.40 2.39
2463 2513 7.882791 TGCTCTAAATTTTCAGAGTGGTTCATA 59.117 33.333 15.98 0.00 40.40 2.15
2464 2514 6.716628 TGCTCTAAATTTTCAGAGTGGTTCAT 59.283 34.615 15.98 0.00 40.40 2.57
2480 2530 2.309528 TTGGATCGCGTGCTCTAAAT 57.690 45.000 5.77 0.00 0.00 1.40
2515 2565 3.625764 AGTAGTACGGCGGTTCGTTATTA 59.374 43.478 13.24 0.00 43.59 0.98
2527 2577 8.131100 TGTCAAACATAATACTAGTAGTACGGC 58.869 37.037 12.00 2.28 32.84 5.68
2561 2617 7.062371 AGCTTCAGATATCGTTCGTATTATTGC 59.938 37.037 0.00 0.00 0.00 3.56
2568 2628 4.814771 TCAGAGCTTCAGATATCGTTCGTA 59.185 41.667 0.00 0.00 0.00 3.43
2604 2664 7.752239 CACAGATTAGGTTACAAGAAAATGCAG 59.248 37.037 0.00 0.00 0.00 4.41
2613 2674 6.878317 TCAGATCCACAGATTAGGTTACAAG 58.122 40.000 0.00 0.00 30.90 3.16
2622 2683 6.328410 AGGACAATCATCAGATCCACAGATTA 59.672 38.462 0.00 0.00 31.90 1.75
2655 2716 1.388093 CTCAGTCACGTCGCAATCTTG 59.612 52.381 0.00 0.00 0.00 3.02
2792 2859 0.618458 CACCGATTCCTCCAAAGGGA 59.382 55.000 0.00 0.00 43.56 4.20
2795 2862 2.076863 GTGACACCGATTCCTCCAAAG 58.923 52.381 0.00 0.00 0.00 2.77
2798 2865 0.834261 TGGTGACACCGATTCCTCCA 60.834 55.000 19.67 0.00 42.58 3.86
2845 2912 2.751436 GCAAGCCAGCGGAATGGA 60.751 61.111 4.06 0.00 43.57 3.41
2854 2921 0.954452 AAGAAACCGAAGCAAGCCAG 59.046 50.000 0.00 0.00 0.00 4.85
2858 2925 1.597663 ACGACAAGAAACCGAAGCAAG 59.402 47.619 0.00 0.00 0.00 4.01
2876 2943 0.389296 TACACAGATCGGCCAACACG 60.389 55.000 2.24 0.00 0.00 4.49
2878 2945 2.236146 AGAATACACAGATCGGCCAACA 59.764 45.455 2.24 0.00 0.00 3.33
2904 2971 3.261643 TGGCTGTTGAAGATGCTCTAAGA 59.738 43.478 0.00 0.00 0.00 2.10
3003 3071 0.237235 TCAATTTTGACGCGTCTGCC 59.763 50.000 36.27 14.68 32.35 4.85
3008 3076 1.440353 GCGCTCAATTTTGACGCGT 60.440 52.632 13.85 13.85 46.44 6.01
3040 3112 4.174129 GCATTTTAGCGCGGCCGT 62.174 61.111 28.70 9.89 36.67 5.68
3206 3294 5.892119 AGTAGGCTGTAGTTGCACTATCTAA 59.108 40.000 0.00 0.00 32.65 2.10
3329 3426 1.272490 TGAGAATGGTGGTCAGACGAC 59.728 52.381 7.16 7.16 41.80 4.34
3337 3434 2.742053 CGAAATCGTTGAGAATGGTGGT 59.258 45.455 0.00 0.00 34.11 4.16
3364 3461 3.834013 GAAGGCCCTGGCGCTATCC 62.834 68.421 7.64 2.80 43.06 2.59


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

AutoCloner maintained by Alex Coulton.