Multiple sequence alignment - TraesCS3D01G027200

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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 TraesCS3D01G027200 chr3D 100.000 3170 0 0 1 3170 9242785 9245954 0.000000e+00 5854
1 TraesCS3D01G027200 chr3D 84.409 1379 157 14 1021 2378 9199566 9200907 0.000000e+00 1303
2 TraesCS3D01G027200 chr3D 88.273 631 56 6 2460 3073 9200964 9201593 0.000000e+00 739
3 TraesCS3D01G027200 chr3B 90.243 2470 141 39 761 3168 11561420 11563851 0.000000e+00 3134
4 TraesCS3D01G027200 chr3B 80.783 1405 199 34 1009 2378 11511034 11512402 0.000000e+00 1033
5 TraesCS3D01G027200 chr3B 79.688 1408 182 56 1009 2378 3205417 3206758 0.000000e+00 920
6 TraesCS3D01G027200 chr3B 89.773 440 33 9 2671 3100 3210349 3210786 1.280000e-153 553
7 TraesCS3D01G027200 chr3B 92.488 213 16 0 2460 2672 3206815 3207027 3.970000e-79 305
8 TraesCS3D01G027200 chr7B 87.438 605 62 11 23 622 275497758 275498353 0.000000e+00 684
9 TraesCS3D01G027200 chr6D 87.605 597 59 9 23 617 296996090 296995507 0.000000e+00 678
10 TraesCS3D01G027200 chr7A 87.814 558 52 12 23 576 323414695 323414150 9.590000e-180 640
11 TraesCS3D01G027200 chr7A 74.236 1277 263 42 1032 2292 47016604 47017830 2.860000e-130 475
12 TraesCS3D01G027200 chr7A 73.554 1176 216 57 922 2038 47256465 47255326 8.360000e-96 361
13 TraesCS3D01G027200 chr7A 74.437 755 147 28 1522 2256 47001073 47001801 1.860000e-72 283
14 TraesCS3D01G027200 chr7D 76.183 1289 239 44 986 2254 44538282 44539522 4.490000e-173 617
15 TraesCS3D01G027200 chr7D 84.219 602 79 12 23 617 489298700 489299292 3.550000e-159 571
16 TraesCS3D01G027200 chr7D 75.052 966 186 32 1307 2257 44550961 44551886 6.370000e-107 398
17 TraesCS3D01G027200 chr4A 84.833 600 80 8 23 618 573900328 573899736 7.570000e-166 593
18 TraesCS3D01G027200 chr4A 75.665 1052 222 28 986 2023 656249746 656250777 7.900000e-136 494
19 TraesCS3D01G027200 chr4A 74.014 1293 260 48 986 2255 656499469 656498230 1.040000e-124 457
20 TraesCS3D01G027200 chr4A 73.184 1335 286 48 1032 2348 656480047 656481327 1.760000e-112 416
21 TraesCS3D01G027200 chr4A 75.053 938 172 29 1287 2204 655659089 655659984 2.310000e-101 379
22 TraesCS3D01G027200 chr4A 75.788 698 121 28 1604 2292 656264755 656265413 3.070000e-80 309
23 TraesCS3D01G027200 chr4A 75.359 418 70 19 1830 2240 655663943 655664334 1.510000e-38 171
24 TraesCS3D01G027200 chr4A 72.890 557 118 20 1346 1883 656556644 656556102 9.100000e-36 161
25 TraesCS3D01G027200 chr1D 84.577 603 77 13 23 617 175788168 175787574 4.560000e-163 584
26 TraesCS3D01G027200 chr1D 83.721 602 84 10 23 618 318153820 318154413 9.930000e-155 556
27 TraesCS3D01G027200 chr4D 84.628 592 80 8 23 611 9478837 9478254 2.120000e-161 579
28 TraesCS3D01G027200 chr4D 84.080 603 73 13 23 617 99352671 99352084 7.680000e-156 560
29 TraesCS3D01G027200 chrUn 73.649 1332 277 51 1032 2344 48866846 48865570 6.240000e-122 448
30 TraesCS3D01G027200 chrUn 73.631 493 95 25 922 1400 48987548 48987077 1.180000e-34 158
31 TraesCS3D01G027200 chr3A 74.881 1051 170 55 997 2022 11865278 11866259 2.960000e-105 392


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 TraesCS3D01G027200 chr3D 9242785 9245954 3169 False 5854.000000 5854 100.000000 1 3170 1 chr3D.!!$F1 3169
1 TraesCS3D01G027200 chr3D 9199566 9201593 2027 False 1021.000000 1303 86.341000 1021 3073 2 chr3D.!!$F2 2052
2 TraesCS3D01G027200 chr3B 11561420 11563851 2431 False 3134.000000 3134 90.243000 761 3168 1 chr3B.!!$F2 2407
3 TraesCS3D01G027200 chr3B 11511034 11512402 1368 False 1033.000000 1033 80.783000 1009 2378 1 chr3B.!!$F1 1369
4 TraesCS3D01G027200 chr3B 3205417 3210786 5369 False 592.666667 920 87.316333 1009 3100 3 chr3B.!!$F3 2091
5 TraesCS3D01G027200 chr7B 275497758 275498353 595 False 684.000000 684 87.438000 23 622 1 chr7B.!!$F1 599
6 TraesCS3D01G027200 chr6D 296995507 296996090 583 True 678.000000 678 87.605000 23 617 1 chr6D.!!$R1 594
7 TraesCS3D01G027200 chr7A 323414150 323414695 545 True 640.000000 640 87.814000 23 576 1 chr7A.!!$R2 553
8 TraesCS3D01G027200 chr7A 47016604 47017830 1226 False 475.000000 475 74.236000 1032 2292 1 chr7A.!!$F2 1260
9 TraesCS3D01G027200 chr7A 47255326 47256465 1139 True 361.000000 361 73.554000 922 2038 1 chr7A.!!$R1 1116
10 TraesCS3D01G027200 chr7A 47001073 47001801 728 False 283.000000 283 74.437000 1522 2256 1 chr7A.!!$F1 734
11 TraesCS3D01G027200 chr7D 44538282 44539522 1240 False 617.000000 617 76.183000 986 2254 1 chr7D.!!$F1 1268
12 TraesCS3D01G027200 chr7D 489298700 489299292 592 False 571.000000 571 84.219000 23 617 1 chr7D.!!$F3 594
13 TraesCS3D01G027200 chr7D 44550961 44551886 925 False 398.000000 398 75.052000 1307 2257 1 chr7D.!!$F2 950
14 TraesCS3D01G027200 chr4A 573899736 573900328 592 True 593.000000 593 84.833000 23 618 1 chr4A.!!$R1 595
15 TraesCS3D01G027200 chr4A 656249746 656250777 1031 False 494.000000 494 75.665000 986 2023 1 chr4A.!!$F1 1037
16 TraesCS3D01G027200 chr4A 656498230 656499469 1239 True 457.000000 457 74.014000 986 2255 1 chr4A.!!$R2 1269
17 TraesCS3D01G027200 chr4A 656480047 656481327 1280 False 416.000000 416 73.184000 1032 2348 1 chr4A.!!$F3 1316
18 TraesCS3D01G027200 chr4A 656264755 656265413 658 False 309.000000 309 75.788000 1604 2292 1 chr4A.!!$F2 688
19 TraesCS3D01G027200 chr4A 655659089 655664334 5245 False 275.000000 379 75.206000 1287 2240 2 chr4A.!!$F4 953
20 TraesCS3D01G027200 chr1D 175787574 175788168 594 True 584.000000 584 84.577000 23 617 1 chr1D.!!$R1 594
21 TraesCS3D01G027200 chr1D 318153820 318154413 593 False 556.000000 556 83.721000 23 618 1 chr1D.!!$F1 595
22 TraesCS3D01G027200 chr4D 9478254 9478837 583 True 579.000000 579 84.628000 23 611 1 chr4D.!!$R1 588
23 TraesCS3D01G027200 chr4D 99352084 99352671 587 True 560.000000 560 84.080000 23 617 1 chr4D.!!$R2 594
24 TraesCS3D01G027200 chrUn 48865570 48866846 1276 True 448.000000 448 73.649000 1032 2344 1 chrUn.!!$R1 1312
25 TraesCS3D01G027200 chr3A 11865278 11866259 981 False 392.000000 392 74.881000 997 2022 1 chr3A.!!$F1 1025

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
699 723 0.108585 CTACCATAGCACGGCCCATT 59.891 55.0 0.00 0.0 0.00 3.16 F
700 724 0.179032 TACCATAGCACGGCCCATTG 60.179 55.0 0.00 0.0 0.00 2.82 F
756 780 0.793861 CGGCCGACATTCTCGAAAAA 59.206 50.0 24.07 0.0 46.14 1.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1551 1665 0.037326 GAACACATCTCGGCTGGTCA 60.037 55.000 0.00 0.0 0.0 4.02 R
1560 1674 1.398390 GTCGGCCATTGAACACATCTC 59.602 52.381 2.24 0.0 0.0 2.75 R
2612 7164 2.094675 GCAGCCAAGCTCTTTTATCCA 58.905 47.619 0.00 0.0 36.4 3.41 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
140 141 3.550275 CGACGAATCGGAAGCTATTTGAA 59.450 43.478 7.80 0.00 44.99 2.69
165 166 4.903045 AACTAATTGAAGGGACCGAAGA 57.097 40.909 0.00 0.00 0.00 2.87
231 234 4.235360 GTGAAGAAACGAAGAAGATCCGA 58.765 43.478 0.00 0.00 0.00 4.55
232 235 4.324936 GTGAAGAAACGAAGAAGATCCGAG 59.675 45.833 0.00 0.00 0.00 4.63
233 236 3.512033 AGAAACGAAGAAGATCCGAGG 57.488 47.619 0.00 0.00 0.00 4.63
234 237 2.166664 AGAAACGAAGAAGATCCGAGGG 59.833 50.000 0.00 0.00 0.00 4.30
359 378 5.630539 GCTTATAATTGTCCACACCCTACCA 60.631 44.000 0.00 0.00 0.00 3.25
457 476 0.730155 CCGTTTACGCTGCTGACGTA 60.730 55.000 13.27 13.27 44.55 3.57
465 484 2.223294 ACGCTGCTGACGTAGATTAGTC 60.223 50.000 10.32 0.00 43.02 2.59
518 537 0.184451 TAATCCTACCGTCGAGCCCT 59.816 55.000 0.00 0.00 0.00 5.19
529 548 0.471191 TCGAGCCCTATGACGGTAGA 59.529 55.000 0.00 0.00 0.00 2.59
533 552 3.718815 GAGCCCTATGACGGTAGAAAAG 58.281 50.000 0.00 0.00 0.00 2.27
594 618 9.130661 TCAGATCTGGATAAACTTCAACAAAAA 57.869 29.630 22.42 0.00 0.00 1.94
596 620 9.136323 AGATCTGGATAAACTTCAACAAAAAGT 57.864 29.630 0.00 0.00 38.59 2.66
619 643 5.747951 TCAAAACATGAAAATTTGCCACC 57.252 34.783 0.00 0.00 34.30 4.61
621 645 2.453983 ACATGAAAATTTGCCACCGG 57.546 45.000 0.00 0.00 0.00 5.28
622 646 1.001860 ACATGAAAATTTGCCACCGGG 59.998 47.619 6.32 0.00 37.18 5.73
637 661 4.143333 GGGCGGCGCTCAACTCTA 62.143 66.667 32.30 0.00 0.00 2.43
638 662 2.886124 GGCGGCGCTCAACTCTAC 60.886 66.667 32.30 7.60 0.00 2.59
639 663 2.886124 GCGGCGCTCAACTCTACC 60.886 66.667 26.86 0.00 0.00 3.18
640 664 2.579787 CGGCGCTCAACTCTACCG 60.580 66.667 7.64 0.00 0.00 4.02
641 665 2.202756 GGCGCTCAACTCTACCGG 60.203 66.667 7.64 0.00 0.00 5.28
642 666 2.572284 GCGCTCAACTCTACCGGT 59.428 61.111 13.98 13.98 0.00 5.28
643 667 1.080025 GCGCTCAACTCTACCGGTT 60.080 57.895 15.04 0.00 0.00 4.44
644 668 0.669625 GCGCTCAACTCTACCGGTTT 60.670 55.000 15.04 0.00 0.00 3.27
645 669 1.347320 CGCTCAACTCTACCGGTTTC 58.653 55.000 15.04 0.00 0.00 2.78
646 670 1.347320 GCTCAACTCTACCGGTTTCG 58.653 55.000 15.04 3.45 0.00 3.46
647 671 1.347320 CTCAACTCTACCGGTTTCGC 58.653 55.000 15.04 0.00 34.56 4.70
648 672 0.963962 TCAACTCTACCGGTTTCGCT 59.036 50.000 15.04 0.00 34.56 4.93
649 673 1.342174 TCAACTCTACCGGTTTCGCTT 59.658 47.619 15.04 0.00 34.56 4.68
650 674 1.459592 CAACTCTACCGGTTTCGCTTG 59.540 52.381 15.04 4.84 34.56 4.01
651 675 0.669625 ACTCTACCGGTTTCGCTTGC 60.670 55.000 15.04 0.00 34.56 4.01
652 676 1.359459 CTCTACCGGTTTCGCTTGCC 61.359 60.000 15.04 0.00 34.56 4.52
653 677 2.358984 TACCGGTTTCGCTTGCCC 60.359 61.111 15.04 0.00 34.56 5.36
654 678 3.905437 TACCGGTTTCGCTTGCCCC 62.905 63.158 15.04 0.00 34.56 5.80
657 681 3.062466 GGTTTCGCTTGCCCCCTC 61.062 66.667 0.00 0.00 0.00 4.30
658 682 3.062466 GTTTCGCTTGCCCCCTCC 61.062 66.667 0.00 0.00 0.00 4.30
659 683 4.360405 TTTCGCTTGCCCCCTCCC 62.360 66.667 0.00 0.00 0.00 4.30
663 687 4.766632 GCTTGCCCCCTCCCAAGG 62.767 72.222 0.00 0.00 42.95 3.61
664 688 3.268032 CTTGCCCCCTCCCAAGGT 61.268 66.667 0.00 0.00 41.59 3.50
665 689 3.264845 TTGCCCCCTCCCAAGGTC 61.265 66.667 0.00 0.00 41.59 3.85
666 690 3.829311 TTGCCCCCTCCCAAGGTCT 62.829 63.158 0.00 0.00 41.59 3.85
667 691 3.412408 GCCCCCTCCCAAGGTCTC 61.412 72.222 0.00 0.00 41.59 3.36
668 692 2.124996 CCCCCTCCCAAGGTCTCA 59.875 66.667 0.00 0.00 41.59 3.27
669 693 1.541368 CCCCCTCCCAAGGTCTCAA 60.541 63.158 0.00 0.00 41.59 3.02
670 694 1.685820 CCCCTCCCAAGGTCTCAAC 59.314 63.158 0.00 0.00 41.59 3.18
671 695 0.842467 CCCCTCCCAAGGTCTCAACT 60.842 60.000 0.00 0.00 41.59 3.16
672 696 0.615850 CCCTCCCAAGGTCTCAACTC 59.384 60.000 0.00 0.00 41.59 3.01
673 697 1.650528 CCTCCCAAGGTCTCAACTCT 58.349 55.000 0.00 0.00 37.94 3.24
674 698 1.552792 CCTCCCAAGGTCTCAACTCTC 59.447 57.143 0.00 0.00 37.94 3.20
675 699 2.251818 CTCCCAAGGTCTCAACTCTCA 58.748 52.381 0.00 0.00 0.00 3.27
676 700 2.634940 CTCCCAAGGTCTCAACTCTCAA 59.365 50.000 0.00 0.00 0.00 3.02
677 701 2.634940 TCCCAAGGTCTCAACTCTCAAG 59.365 50.000 0.00 0.00 0.00 3.02
678 702 2.634940 CCCAAGGTCTCAACTCTCAAGA 59.365 50.000 0.00 0.00 0.00 3.02
680 704 3.324993 CAAGGTCTCAACTCTCAAGAGC 58.675 50.000 6.94 0.00 45.79 4.09
681 705 2.888212 AGGTCTCAACTCTCAAGAGCT 58.112 47.619 6.94 0.00 45.79 4.09
682 706 4.040936 AGGTCTCAACTCTCAAGAGCTA 57.959 45.455 6.94 0.00 43.87 3.32
683 707 3.761752 AGGTCTCAACTCTCAAGAGCTAC 59.238 47.826 6.94 0.00 43.87 3.58
684 708 3.119280 GGTCTCAACTCTCAAGAGCTACC 60.119 52.174 6.94 4.52 45.79 3.18
685 709 3.508012 GTCTCAACTCTCAAGAGCTACCA 59.492 47.826 6.94 0.00 45.79 3.25
686 710 4.159506 GTCTCAACTCTCAAGAGCTACCAT 59.840 45.833 6.94 0.00 45.79 3.55
687 711 5.358442 GTCTCAACTCTCAAGAGCTACCATA 59.642 44.000 6.94 0.00 45.79 2.74
688 712 5.592282 TCTCAACTCTCAAGAGCTACCATAG 59.408 44.000 6.94 0.00 45.79 2.23
697 721 3.226242 CTACCATAGCACGGCCCA 58.774 61.111 0.00 0.00 0.00 5.36
698 722 1.754745 CTACCATAGCACGGCCCAT 59.245 57.895 0.00 0.00 0.00 4.00
699 723 0.108585 CTACCATAGCACGGCCCATT 59.891 55.000 0.00 0.00 0.00 3.16
700 724 0.179032 TACCATAGCACGGCCCATTG 60.179 55.000 0.00 0.00 0.00 2.82
701 725 2.723746 CATAGCACGGCCCATTGC 59.276 61.111 10.08 10.08 39.16 3.56
706 730 4.440127 CACGGCCCATTGCTTGCC 62.440 66.667 0.00 0.00 41.85 4.52
710 734 3.830192 GCCCATTGCTTGCCGGAG 61.830 66.667 5.05 0.00 36.87 4.63
711 735 3.830192 CCCATTGCTTGCCGGAGC 61.830 66.667 5.05 6.99 43.00 4.70
712 736 3.830192 CCATTGCTTGCCGGAGCC 61.830 66.667 5.05 0.00 42.01 4.70
713 737 3.830192 CATTGCTTGCCGGAGCCC 61.830 66.667 5.05 0.00 42.01 5.19
714 738 4.052518 ATTGCTTGCCGGAGCCCT 62.053 61.111 5.05 0.00 42.01 5.19
715 739 3.590466 ATTGCTTGCCGGAGCCCTT 62.590 57.895 5.05 0.00 42.01 3.95
716 740 4.722700 TGCTTGCCGGAGCCCTTC 62.723 66.667 5.05 0.00 42.01 3.46
717 741 4.416738 GCTTGCCGGAGCCCTTCT 62.417 66.667 5.05 0.00 38.69 2.85
718 742 2.352805 CTTGCCGGAGCCCTTCTT 59.647 61.111 5.05 0.00 38.69 2.52
719 743 1.746991 CTTGCCGGAGCCCTTCTTC 60.747 63.158 5.05 0.00 38.69 2.87
720 744 3.268103 TTGCCGGAGCCCTTCTTCC 62.268 63.158 5.05 0.00 38.69 3.46
721 745 4.491409 GCCGGAGCCCTTCTTCCC 62.491 72.222 5.05 0.00 0.00 3.97
722 746 3.798511 CCGGAGCCCTTCTTCCCC 61.799 72.222 0.00 0.00 0.00 4.81
723 747 4.162690 CGGAGCCCTTCTTCCCCG 62.163 72.222 0.00 0.00 0.00 5.73
724 748 4.491409 GGAGCCCTTCTTCCCCGC 62.491 72.222 0.00 0.00 0.00 6.13
725 749 3.403558 GAGCCCTTCTTCCCCGCT 61.404 66.667 0.00 0.00 0.00 5.52
726 750 3.689002 GAGCCCTTCTTCCCCGCTG 62.689 68.421 0.00 0.00 0.00 5.18
727 751 4.803908 GCCCTTCTTCCCCGCTGG 62.804 72.222 0.00 0.00 0.00 4.85
728 752 3.009115 CCCTTCTTCCCCGCTGGA 61.009 66.667 0.00 0.00 43.18 3.86
735 759 2.270850 TCCCCGCTGGAAAATCGG 59.729 61.111 0.00 0.00 41.40 4.18
736 760 3.518068 CCCCGCTGGAAAATCGGC 61.518 66.667 0.00 0.00 41.68 5.54
737 761 3.518068 CCCGCTGGAAAATCGGCC 61.518 66.667 0.00 0.00 41.68 6.13
738 762 3.876198 CCGCTGGAAAATCGGCCG 61.876 66.667 22.12 22.12 36.53 6.13
739 763 3.876198 CGCTGGAAAATCGGCCGG 61.876 66.667 27.83 7.44 35.72 6.13
741 765 3.518068 CTGGAAAATCGGCCGGCC 61.518 66.667 36.69 36.69 0.00 6.13
752 776 4.508128 GCCGGCCGACATTCTCGA 62.508 66.667 30.73 0.00 46.14 4.04
753 777 2.183300 CCGGCCGACATTCTCGAA 59.817 61.111 30.73 0.00 46.14 3.71
754 778 1.447140 CCGGCCGACATTCTCGAAA 60.447 57.895 30.73 0.00 46.14 3.46
755 779 1.017177 CCGGCCGACATTCTCGAAAA 61.017 55.000 30.73 0.00 46.14 2.29
756 780 0.793861 CGGCCGACATTCTCGAAAAA 59.206 50.000 24.07 0.00 46.14 1.94
813 837 5.875359 GGTAAATCCTCTTGTCTCGATTTGT 59.125 40.000 0.00 0.00 36.06 2.83
825 849 3.118920 TCTCGATTTGTAGATCGCCCAAA 60.119 43.478 9.04 9.04 46.33 3.28
835 859 4.178545 AGATCGCCCAAACAATTCTTTG 57.821 40.909 0.00 0.00 38.86 2.77
885 909 4.202020 GCCCCATCTCCTATTTTCGTTTTC 60.202 45.833 0.00 0.00 0.00 2.29
916 940 1.483316 TGTTATCGCCGACGCTAATG 58.517 50.000 0.00 0.00 39.84 1.90
947 972 1.083489 CTTCTTGCGCCAAATCCGTA 58.917 50.000 4.18 0.00 0.00 4.02
1043 1078 1.982395 TGCTGAACGATCTCCCCGT 60.982 57.895 0.00 0.00 42.61 5.28
1205 1240 1.089920 ATCATCCAGCGACACAAAGC 58.910 50.000 0.00 0.00 0.00 3.51
1209 1244 2.664851 CAGCGACACAAAGCGGGA 60.665 61.111 0.00 0.00 38.61 5.14
1210 1245 2.665185 AGCGACACAAAGCGGGAC 60.665 61.111 0.00 0.00 38.61 4.46
1284 1328 1.559682 ACCTGCCATACAGTTTCCGAT 59.440 47.619 0.00 0.00 45.68 4.18
1560 1674 2.187946 GTGGGATCTGACCAGCCG 59.812 66.667 0.00 0.00 39.00 5.52
1569 1683 0.036952 CTGACCAGCCGAGATGTGTT 60.037 55.000 0.00 0.00 0.00 3.32
1585 1699 1.398390 GTGTTCAATGGCCGACAGATC 59.602 52.381 0.00 0.00 0.00 2.75
1959 2130 0.955428 GCCGTGAGCTGTTGATCCAA 60.955 55.000 0.00 0.00 38.99 3.53
2066 6541 5.146010 AGTCAGTTTGCAAAACCTTTGAA 57.854 34.783 14.67 0.00 0.00 2.69
2157 6638 2.636412 CGAGGAGCCTCCGTTCACA 61.636 63.158 4.80 0.00 42.75 3.58
2182 6667 3.639094 ACTTCTATAAGATGCCGTGCTCT 59.361 43.478 0.00 0.00 36.50 4.09
2257 6752 4.322198 CCATATATGGGCCATGTCTTTTGC 60.322 45.833 29.14 0.00 44.31 3.68
2259 6754 2.530460 ATGGGCCATGTCTTTTGCTA 57.470 45.000 20.49 0.00 0.00 3.49
2394 6928 8.857098 TGTTATGAACTGTTCTACACTTCTACT 58.143 33.333 20.18 0.00 0.00 2.57
2399 6933 8.954350 TGAACTGTTCTACACTTCTACTATACC 58.046 37.037 20.18 0.00 0.00 2.73
2431 6965 6.018262 TGTTTACTTTCAGTTCTCCATTGTCG 60.018 38.462 0.00 0.00 0.00 4.35
2454 7002 4.677673 AAAGCACAAAATTCTGGAAGCT 57.322 36.364 0.00 0.00 0.00 3.74
2462 7010 5.416952 ACAAAATTCTGGAAGCTATCAGTGG 59.583 40.000 13.69 0.00 33.13 4.00
2479 7027 0.179043 TGGTTTGGTGCTCAGCGTAA 60.179 50.000 0.00 0.00 0.00 3.18
2500 7048 7.521244 GCGTAATTTTGTGTTTGATTGTTTACG 59.479 33.333 0.00 0.00 40.39 3.18
2517 7065 5.107760 TGTTTACGACAGCGACAAGTAATTC 60.108 40.000 0.00 0.00 41.64 2.17
2555 7107 4.931601 TCATGTGTCTGATTGCTACTTCAC 59.068 41.667 0.00 0.00 0.00 3.18
2612 7164 1.761784 TGCACTGGCTTTCACCATTTT 59.238 42.857 0.00 0.00 39.54 1.82
2730 10608 2.642311 TCTGTTGGAAGGCTGGTGATTA 59.358 45.455 0.00 0.00 0.00 1.75
2763 10641 3.942130 GCCATTGGCTAGTCTTGTTTT 57.058 42.857 20.66 0.00 46.69 2.43
2765 10643 4.733850 GCCATTGGCTAGTCTTGTTTTAC 58.266 43.478 20.66 0.00 46.69 2.01
2766 10644 4.459337 GCCATTGGCTAGTCTTGTTTTACT 59.541 41.667 20.66 0.00 46.69 2.24
2782 10673 8.630054 TTGTTTTACTGTAATATGGCTGTCTT 57.370 30.769 0.37 0.00 0.00 3.01
2783 10674 8.039603 TGTTTTACTGTAATATGGCTGTCTTG 57.960 34.615 0.37 0.00 0.00 3.02
2787 10678 6.743575 ACTGTAATATGGCTGTCTTGTTTC 57.256 37.500 0.00 0.00 0.00 2.78
2820 10711 6.469410 TGTCTGTGGGTTTATCGATTTACTT 58.531 36.000 1.71 0.00 0.00 2.24
2833 10726 0.321298 TTTACTTCTGGCGTGGCTCC 60.321 55.000 0.00 0.00 0.00 4.70
2916 10818 2.754552 GCACATCTAACCCAAATGAGCA 59.245 45.455 0.00 0.00 37.09 4.26
3043 10949 6.932356 TCATGTTATGAAGAATGGAGCTTC 57.068 37.500 0.00 0.00 41.57 3.86
3045 10951 6.541278 TCATGTTATGAAGAATGGAGCTTCTG 59.459 38.462 0.00 0.00 41.71 3.02
3048 10954 4.564782 ATGAAGAATGGAGCTTCTGTGA 57.435 40.909 0.00 0.00 41.71 3.58
3049 10955 3.935315 TGAAGAATGGAGCTTCTGTGAG 58.065 45.455 0.00 0.00 41.71 3.51
3075 10981 2.258109 ACTGTTCTACTGTTCTCCCCC 58.742 52.381 0.00 0.00 0.00 5.40
3077 10983 1.264295 GTTCTACTGTTCTCCCCCGT 58.736 55.000 0.00 0.00 0.00 5.28
3114 11020 1.838913 TTGCTGAAAAGCACGAAAGC 58.161 45.000 0.00 0.00 45.32 3.51
3128 11034 2.693074 ACGAAAGCCATGGTTTCAGTTT 59.307 40.909 25.87 10.24 46.33 2.66
3129 11035 3.132111 ACGAAAGCCATGGTTTCAGTTTT 59.868 39.130 25.87 9.66 46.33 2.43
3130 11036 3.490526 CGAAAGCCATGGTTTCAGTTTTG 59.509 43.478 25.87 10.21 46.33 2.44
3141 11047 7.945033 TGGTTTCAGTTTTGAATGCTAATTC 57.055 32.000 0.00 0.00 42.60 2.17
3159 11065 2.519771 TCTGCATCATTTGGGAAGCT 57.480 45.000 0.00 0.00 32.97 3.74
3168 11074 3.054139 TCATTTGGGAAGCTAGCTGTGAT 60.054 43.478 20.16 1.15 0.00 3.06
3169 11075 3.439857 TTTGGGAAGCTAGCTGTGATT 57.560 42.857 20.16 0.68 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.656849 GTGTTCTATTGTGTGGACAGTTATAAG 58.343 37.037 0.00 0.00 32.26 1.73
1 2 8.151596 TGTGTTCTATTGTGTGGACAGTTATAA 58.848 33.333 0.00 0.00 32.26 0.98
5 6 4.776349 TGTGTTCTATTGTGTGGACAGTT 58.224 39.130 0.00 0.00 32.26 3.16
7 8 5.947228 ATTGTGTTCTATTGTGTGGACAG 57.053 39.130 0.00 0.00 32.26 3.51
8 9 6.764379 TCTATTGTGTTCTATTGTGTGGACA 58.236 36.000 0.00 0.00 0.00 4.02
9 10 7.172532 TGTTCTATTGTGTTCTATTGTGTGGAC 59.827 37.037 0.00 0.00 0.00 4.02
10 11 7.220740 TGTTCTATTGTGTTCTATTGTGTGGA 58.779 34.615 0.00 0.00 0.00 4.02
11 12 7.433708 TGTTCTATTGTGTTCTATTGTGTGG 57.566 36.000 0.00 0.00 0.00 4.17
12 13 8.939929 AGATGTTCTATTGTGTTCTATTGTGTG 58.060 33.333 0.00 0.00 0.00 3.82
140 141 7.399634 TCTTCGGTCCCTTCAATTAGTTTTAT 58.600 34.615 0.00 0.00 0.00 1.40
153 154 2.258109 AGTAAGCTTCTTCGGTCCCTT 58.742 47.619 0.00 0.00 0.00 3.95
159 160 3.988517 ACGAGAAAAGTAAGCTTCTTCGG 59.011 43.478 0.00 3.28 36.71 4.30
165 166 3.497262 CCCGAAACGAGAAAAGTAAGCTT 59.503 43.478 3.48 3.48 36.30 3.74
233 236 2.760385 CGTCTCCTCCACTCCCCC 60.760 72.222 0.00 0.00 0.00 5.40
234 237 1.755008 CTCGTCTCCTCCACTCCCC 60.755 68.421 0.00 0.00 0.00 4.81
238 241 0.254747 CCTCTCTCGTCTCCTCCACT 59.745 60.000 0.00 0.00 0.00 4.00
249 258 2.895426 TTCTCTCGCCCCCTCTCTCG 62.895 65.000 0.00 0.00 0.00 4.04
343 360 0.694783 TGGTGGTAGGGTGTGGACAA 60.695 55.000 0.00 0.00 0.00 3.18
457 476 1.142465 TCGGCGGTAGGAGACTAATCT 59.858 52.381 7.21 0.00 46.54 2.40
465 484 1.392710 ATGACCTTCGGCGGTAGGAG 61.393 60.000 27.63 10.79 37.42 3.69
518 537 4.346730 TGACCCTCTTTTCTACCGTCATA 58.653 43.478 0.00 0.00 0.00 2.15
556 579 2.939103 CCAGATCTGACCCGTTTGATTC 59.061 50.000 24.62 0.00 0.00 2.52
557 580 2.571653 TCCAGATCTGACCCGTTTGATT 59.428 45.455 24.62 0.00 0.00 2.57
559 582 1.639722 TCCAGATCTGACCCGTTTGA 58.360 50.000 24.62 7.10 0.00 2.69
560 583 2.698855 ATCCAGATCTGACCCGTTTG 57.301 50.000 24.62 4.68 0.00 2.93
563 586 3.375699 AGTTTATCCAGATCTGACCCGT 58.624 45.455 24.62 7.30 0.00 5.28
564 587 4.141937 TGAAGTTTATCCAGATCTGACCCG 60.142 45.833 24.62 7.33 0.00 5.28
594 618 6.183360 GGTGGCAAATTTTCATGTTTTGAACT 60.183 34.615 13.43 0.00 43.99 3.01
596 620 5.220739 CGGTGGCAAATTTTCATGTTTTGAA 60.221 36.000 13.43 0.00 42.62 2.69
621 645 2.886124 GTAGAGTTGAGCGCCGCC 60.886 66.667 4.98 0.00 0.00 6.13
622 646 2.886124 GGTAGAGTTGAGCGCCGC 60.886 66.667 2.29 0.00 0.00 6.53
623 647 2.579787 CGGTAGAGTTGAGCGCCG 60.580 66.667 2.29 0.00 0.00 6.46
624 648 2.202756 CCGGTAGAGTTGAGCGCC 60.203 66.667 2.29 0.00 36.51 6.53
625 649 0.669625 AAACCGGTAGAGTTGAGCGC 60.670 55.000 8.00 0.00 36.51 5.92
626 650 1.347320 GAAACCGGTAGAGTTGAGCG 58.653 55.000 8.00 0.00 37.54 5.03
627 651 1.347320 CGAAACCGGTAGAGTTGAGC 58.653 55.000 8.00 0.00 0.00 4.26
628 652 1.067776 AGCGAAACCGGTAGAGTTGAG 60.068 52.381 8.00 0.00 35.87 3.02
629 653 0.963962 AGCGAAACCGGTAGAGTTGA 59.036 50.000 8.00 0.00 35.87 3.18
630 654 1.459592 CAAGCGAAACCGGTAGAGTTG 59.540 52.381 8.00 4.82 36.70 3.16
631 655 1.792006 CAAGCGAAACCGGTAGAGTT 58.208 50.000 8.00 0.00 36.70 3.01
632 656 0.669625 GCAAGCGAAACCGGTAGAGT 60.670 55.000 8.00 0.00 36.70 3.24
633 657 1.359459 GGCAAGCGAAACCGGTAGAG 61.359 60.000 8.00 2.65 36.70 2.43
634 658 1.375013 GGCAAGCGAAACCGGTAGA 60.375 57.895 8.00 0.00 36.70 2.59
635 659 2.396157 GGGCAAGCGAAACCGGTAG 61.396 63.158 8.00 3.51 36.70 3.18
636 660 2.358984 GGGCAAGCGAAACCGGTA 60.359 61.111 8.00 0.00 36.70 4.02
640 664 3.062466 GAGGGGGCAAGCGAAACC 61.062 66.667 0.00 0.00 0.00 3.27
641 665 3.062466 GGAGGGGGCAAGCGAAAC 61.062 66.667 0.00 0.00 0.00 2.78
642 666 4.360405 GGGAGGGGGCAAGCGAAA 62.360 66.667 0.00 0.00 0.00 3.46
646 670 4.766632 CCTTGGGAGGGGGCAAGC 62.767 72.222 0.00 0.00 39.55 4.01
655 679 2.251818 TGAGAGTTGAGACCTTGGGAG 58.748 52.381 0.00 0.00 0.00 4.30
656 680 2.398754 TGAGAGTTGAGACCTTGGGA 57.601 50.000 0.00 0.00 0.00 4.37
657 681 2.634940 TCTTGAGAGTTGAGACCTTGGG 59.365 50.000 0.00 0.00 0.00 4.12
658 682 3.864160 GCTCTTGAGAGTTGAGACCTTGG 60.864 52.174 9.58 0.00 43.85 3.61
659 683 3.006752 AGCTCTTGAGAGTTGAGACCTTG 59.993 47.826 9.58 0.00 43.85 3.61
660 684 3.238597 AGCTCTTGAGAGTTGAGACCTT 58.761 45.455 9.58 0.00 43.85 3.50
661 685 2.888212 AGCTCTTGAGAGTTGAGACCT 58.112 47.619 9.58 0.00 43.85 3.85
662 686 3.119280 GGTAGCTCTTGAGAGTTGAGACC 60.119 52.174 9.58 5.04 43.85 3.85
663 687 3.508012 TGGTAGCTCTTGAGAGTTGAGAC 59.492 47.826 9.58 0.00 43.85 3.36
664 688 3.767711 TGGTAGCTCTTGAGAGTTGAGA 58.232 45.455 9.58 0.00 43.85 3.27
665 689 4.734398 ATGGTAGCTCTTGAGAGTTGAG 57.266 45.455 9.58 0.00 43.85 3.02
666 690 5.843673 CTATGGTAGCTCTTGAGAGTTGA 57.156 43.478 9.58 0.00 43.85 3.18
680 704 0.108585 AATGGGCCGTGCTATGGTAG 59.891 55.000 0.00 0.00 0.00 3.18
681 705 0.179032 CAATGGGCCGTGCTATGGTA 60.179 55.000 0.00 0.00 0.00 3.25
682 706 1.453745 CAATGGGCCGTGCTATGGT 60.454 57.895 0.00 0.00 0.00 3.55
683 707 2.848858 GCAATGGGCCGTGCTATGG 61.849 63.158 21.24 0.00 37.78 2.74
684 708 2.723746 GCAATGGGCCGTGCTATG 59.276 61.111 21.24 7.67 37.78 2.23
689 713 4.440127 GGCAAGCAATGGGCCGTG 62.440 66.667 0.00 0.00 46.50 4.94
693 717 3.830192 CTCCGGCAAGCAATGGGC 61.830 66.667 0.00 0.00 45.30 5.36
694 718 3.830192 GCTCCGGCAAGCAATGGG 61.830 66.667 10.16 0.00 42.05 4.00
695 719 3.830192 GGCTCCGGCAAGCAATGG 61.830 66.667 16.28 0.00 44.35 3.16
696 720 3.830192 GGGCTCCGGCAAGCAATG 61.830 66.667 16.28 0.00 44.35 2.82
697 721 3.590466 AAGGGCTCCGGCAAGCAAT 62.590 57.895 16.28 1.95 44.35 3.56
698 722 4.284550 AAGGGCTCCGGCAAGCAA 62.285 61.111 16.28 0.00 44.35 3.91
699 723 4.722700 GAAGGGCTCCGGCAAGCA 62.723 66.667 16.28 0.00 44.35 3.91
700 724 3.927481 AAGAAGGGCTCCGGCAAGC 62.927 63.158 6.60 6.60 41.73 4.01
701 725 1.746991 GAAGAAGGGCTCCGGCAAG 60.747 63.158 0.00 0.00 40.87 4.01
702 726 2.351276 GAAGAAGGGCTCCGGCAA 59.649 61.111 0.00 0.00 40.87 4.52
703 727 3.717294 GGAAGAAGGGCTCCGGCA 61.717 66.667 0.00 0.00 40.87 5.69
704 728 4.491409 GGGAAGAAGGGCTCCGGC 62.491 72.222 0.00 0.00 37.82 6.13
705 729 3.798511 GGGGAAGAAGGGCTCCGG 61.799 72.222 0.00 0.00 0.00 5.14
706 730 4.162690 CGGGGAAGAAGGGCTCCG 62.163 72.222 0.00 0.00 0.00 4.63
707 731 4.491409 GCGGGGAAGAAGGGCTCC 62.491 72.222 0.00 0.00 0.00 4.70
708 732 3.403558 AGCGGGGAAGAAGGGCTC 61.404 66.667 0.00 0.00 0.00 4.70
709 733 3.721706 CAGCGGGGAAGAAGGGCT 61.722 66.667 0.00 0.00 0.00 5.19
710 734 4.803908 CCAGCGGGGAAGAAGGGC 62.804 72.222 0.00 0.00 40.01 5.19
711 735 3.009115 TCCAGCGGGGAAGAAGGG 61.009 66.667 2.05 0.00 44.80 3.95
718 742 2.270850 CCGATTTTCCAGCGGGGA 59.729 61.111 2.05 0.00 46.61 4.81
719 743 3.518068 GCCGATTTTCCAGCGGGG 61.518 66.667 2.05 0.00 44.92 5.73
720 744 3.518068 GGCCGATTTTCCAGCGGG 61.518 66.667 0.00 0.00 44.92 6.13
722 746 3.876198 CCGGCCGATTTTCCAGCG 61.876 66.667 30.73 0.44 0.00 5.18
723 747 4.193334 GCCGGCCGATTTTCCAGC 62.193 66.667 30.73 15.52 0.00 4.85
724 748 3.518068 GGCCGGCCGATTTTCCAG 61.518 66.667 33.60 8.26 0.00 3.86
813 837 5.309323 CAAAGAATTGTTTGGGCGATCTA 57.691 39.130 17.94 0.00 34.34 1.98
835 859 0.992802 GACGACGGATTGAGAGCAAC 59.007 55.000 0.00 0.00 36.72 4.17
885 909 5.401674 GTCGGCGATAACATAGTAGAAAAGG 59.598 44.000 14.79 0.00 0.00 3.11
916 940 2.406357 GCGCAAGAAGATGAAGCAAAAC 59.594 45.455 0.30 0.00 43.02 2.43
1030 1065 0.898789 AGACACACGGGGAGATCGTT 60.899 55.000 0.00 0.00 38.94 3.85
1209 1244 4.736896 GCGGCGAAACGGGAGAGT 62.737 66.667 12.98 0.00 0.00 3.24
1267 1308 4.262463 GGAGATATCGGAAACTGTATGGCA 60.262 45.833 0.00 0.00 0.00 4.92
1284 1328 1.335810 GCGTGGTGTATGACGGAGATA 59.664 52.381 0.00 0.00 36.09 1.98
1551 1665 0.037326 GAACACATCTCGGCTGGTCA 60.037 55.000 0.00 0.00 0.00 4.02
1560 1674 1.398390 GTCGGCCATTGAACACATCTC 59.602 52.381 2.24 0.00 0.00 2.75
1569 1683 2.103094 CCTTAGATCTGTCGGCCATTGA 59.897 50.000 5.18 0.00 0.00 2.57
2157 6638 6.015010 AGAGCACGGCATCTTATAGAAGTATT 60.015 38.462 0.00 0.00 34.03 1.89
2182 6667 9.381038 AGCAAGGAGTCCAAAGTATTATAGATA 57.619 33.333 12.86 0.00 0.00 1.98
2259 6754 8.783833 TCTACTACGACATAGTAAGAACAAGT 57.216 34.615 0.00 0.00 44.21 3.16
2394 6928 5.352264 TGAAAGTAAACAGGGGAGGGTATA 58.648 41.667 0.00 0.00 0.00 1.47
2397 6931 2.375509 CTGAAAGTAAACAGGGGAGGGT 59.624 50.000 0.00 0.00 0.00 4.34
2398 6932 3.073274 CTGAAAGTAAACAGGGGAGGG 57.927 52.381 0.00 0.00 0.00 4.30
2431 6965 5.052481 AGCTTCCAGAATTTTGTGCTTTTC 58.948 37.500 0.00 0.00 0.00 2.29
2454 7002 2.875672 GCTGAGCACCAAACCACTGATA 60.876 50.000 0.00 0.00 0.00 2.15
2462 7010 2.989422 AATTACGCTGAGCACCAAAC 57.011 45.000 4.88 0.00 0.00 2.93
2479 7027 7.253950 GCTGTCGTAAACAATCAAACACAAAAT 60.254 33.333 0.00 0.00 37.45 1.82
2500 7048 2.334838 ACCGAATTACTTGTCGCTGTC 58.665 47.619 0.00 0.00 35.93 3.51
2530 7082 3.515630 AGTAGCAATCAGACACATGACG 58.484 45.455 0.00 0.00 30.46 4.35
2555 7107 8.289618 TGCTAACTTTTTCAACAATAGCTGTAG 58.710 33.333 0.00 0.00 37.23 2.74
2612 7164 2.094675 GCAGCCAAGCTCTTTTATCCA 58.905 47.619 0.00 0.00 36.40 3.41
2756 10634 8.268850 AGACAGCCATATTACAGTAAAACAAG 57.731 34.615 0.00 0.00 0.00 3.16
2757 10635 8.511321 CAAGACAGCCATATTACAGTAAAACAA 58.489 33.333 0.00 0.00 0.00 2.83
2758 10636 7.663905 ACAAGACAGCCATATTACAGTAAAACA 59.336 33.333 0.00 0.00 0.00 2.83
2759 10637 8.040716 ACAAGACAGCCATATTACAGTAAAAC 57.959 34.615 0.00 0.00 0.00 2.43
2760 10638 8.630054 AACAAGACAGCCATATTACAGTAAAA 57.370 30.769 0.00 0.00 0.00 1.52
2761 10639 8.630054 AAACAAGACAGCCATATTACAGTAAA 57.370 30.769 0.00 0.00 0.00 2.01
2762 10640 7.335924 GGAAACAAGACAGCCATATTACAGTAA 59.664 37.037 0.00 0.00 0.00 2.24
2763 10641 6.821665 GGAAACAAGACAGCCATATTACAGTA 59.178 38.462 0.00 0.00 0.00 2.74
2764 10642 5.648092 GGAAACAAGACAGCCATATTACAGT 59.352 40.000 0.00 0.00 0.00 3.55
2765 10643 5.066505 GGGAAACAAGACAGCCATATTACAG 59.933 44.000 0.00 0.00 0.00 2.74
2766 10644 4.947388 GGGAAACAAGACAGCCATATTACA 59.053 41.667 0.00 0.00 0.00 2.41
2782 10673 4.586841 CCCACAGACAATAAAAGGGAAACA 59.413 41.667 0.00 0.00 36.96 2.83
2783 10674 4.587262 ACCCACAGACAATAAAAGGGAAAC 59.413 41.667 0.00 0.00 38.21 2.78
2787 10678 6.404293 CGATAAACCCACAGACAATAAAAGGG 60.404 42.308 0.00 0.00 40.66 3.95
2879 10772 2.345876 TGTGCAACGATAGGACATGTG 58.654 47.619 1.15 0.00 42.39 3.21
2916 10818 8.298729 AGGAAGAAGAAAGAACAAAAGACATT 57.701 30.769 0.00 0.00 0.00 2.71
3021 10923 6.318144 ACAGAAGCTCCATTCTTCATAACATG 59.682 38.462 5.67 0.00 41.68 3.21
3043 10949 5.218885 CAGTAGAACAGTTCTGACTCACAG 58.781 45.833 23.92 8.31 46.97 3.66
3045 10951 5.189659 ACAGTAGAACAGTTCTGACTCAC 57.810 43.478 23.92 14.18 40.94 3.51
3114 11020 4.634199 AGCATTCAAAACTGAAACCATGG 58.366 39.130 11.19 11.19 0.00 3.66
3141 11047 2.034305 GCTAGCTTCCCAAATGATGCAG 59.966 50.000 7.70 0.00 37.75 4.41


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

AutoCloner maintained by Alex Coulton.