Multiple sequence alignment - TraesCS3D01G232900

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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 TraesCS3D01G232900 chr3D 100.000 1404 0 0 1732 3135 320824231 320822828 0.000000e+00 2593.0
1 TraesCS3D01G232900 chr3D 100.000 842 0 0 295 1136 320825668 320824827 0.000000e+00 1555.0
2 TraesCS3D01G232900 chr3D 100.000 137 0 0 1 137 320825962 320825826 1.440000e-63 254.0
3 TraesCS3D01G232900 chr3D 90.625 64 6 0 852 915 598194365 598194302 5.570000e-13 86.1
4 TraesCS3D01G232900 chr3B 95.686 1414 41 8 1741 3135 398964250 398965662 0.000000e+00 2255.0
5 TraesCS3D01G232900 chr3B 95.455 198 7 2 940 1136 398964033 398964229 6.530000e-82 315.0
6 TraesCS3D01G232900 chr3A 95.736 1407 36 9 1748 3135 404199393 404200794 0.000000e+00 2244.0
7 TraesCS3D01G232900 chr3A 85.130 538 55 21 306 833 600888616 600889138 7.700000e-146 527.0
8 TraesCS3D01G232900 chr3A 94.949 198 8 2 940 1136 404199168 404199364 3.040000e-80 309.0
9 TraesCS3D01G232900 chr3A 92.063 63 5 0 852 914 77709893 77709831 4.310000e-14 89.8
10 TraesCS3D01G232900 chr1D 84.746 590 58 27 299 867 487579877 487579299 2.110000e-156 562.0
11 TraesCS3D01G232900 chr1D 90.909 132 11 1 7 137 487579766 487579635 3.210000e-40 176.0
12 TraesCS3D01G232900 chr1D 84.127 63 10 0 852 914 308451102 308451164 9.390000e-06 62.1
13 TraesCS3D01G232900 chr5A 85.353 553 58 17 295 834 548284445 548283903 4.570000e-153 551.0
14 TraesCS3D01G232900 chr5A 89.706 136 11 3 5 137 663237456 663237321 1.500000e-38 171.0
15 TraesCS3D01G232900 chr5A 89.706 136 11 3 5 137 680630552 680630417 1.500000e-38 171.0
16 TraesCS3D01G232900 chr7D 84.946 558 63 18 299 840 362360976 362360424 2.130000e-151 545.0
17 TraesCS3D01G232900 chr7D 90.164 61 6 0 855 915 593672006 593671946 2.590000e-11 80.5
18 TraesCS3D01G232900 chr2D 84.247 584 62 23 295 864 247789638 247790205 2.750000e-150 542.0
19 TraesCS3D01G232900 chr2D 83.516 546 64 17 295 826 246623924 246623391 1.310000e-133 486.0
20 TraesCS3D01G232900 chr2D 81.799 467 38 20 382 829 639286784 639286346 6.440000e-92 348.0
21 TraesCS3D01G232900 chr2D 89.051 137 11 4 5 137 535732374 535732510 1.930000e-37 167.0
22 TraesCS3D01G232900 chr2D 89.474 133 12 2 7 137 624804217 624804085 1.930000e-37 167.0
23 TraesCS3D01G232900 chr6A 85.185 540 62 14 306 833 454431045 454430512 3.560000e-149 538.0
24 TraesCS3D01G232900 chr6A 90.625 64 6 0 852 915 597930579 597930642 5.570000e-13 86.1
25 TraesCS3D01G232900 chr6D 84.698 562 59 21 299 840 401621867 401621313 1.280000e-148 536.0
26 TraesCS3D01G232900 chr6D 84.000 550 53 19 295 829 457327007 457327536 2.170000e-136 496.0
27 TraesCS3D01G232900 chr6D 82.914 556 63 18 299 828 347714084 347714633 3.660000e-129 472.0
28 TraesCS3D01G232900 chr6D 81.818 561 68 23 299 829 360692121 360692677 1.030000e-119 440.0
29 TraesCS3D01G232900 chr6D 81.046 153 21 3 2794 2938 336989786 336989938 7.110000e-22 115.0
30 TraesCS3D01G232900 chr6D 88.889 63 7 0 852 914 126629166 126629104 9.320000e-11 78.7
31 TraesCS3D01G232900 chr4B 83.677 582 75 19 299 867 500506110 500506684 5.950000e-147 531.0
32 TraesCS3D01G232900 chr7A 84.296 554 64 18 299 834 523142614 523143162 1.290000e-143 520.0
33 TraesCS3D01G232900 chr4D 83.094 556 62 20 299 828 101675582 101676131 7.870000e-131 477.0
34 TraesCS3D01G232900 chr4A 78.598 528 64 22 338 837 605061492 605061998 1.410000e-78 303.0
35 TraesCS3D01G232900 chr4A 81.452 248 23 13 610 836 21507769 21507524 6.910000e-42 182.0
36 TraesCS3D01G232900 chr7B 73.994 646 87 36 299 915 739545264 739544671 1.480000e-43 187.0
37 TraesCS3D01G232900 chr1A 90.370 135 11 2 5 137 563694054 563693920 3.210000e-40 176.0
38 TraesCS3D01G232900 chr1A 90.299 134 11 2 5 137 348727868 348727736 1.160000e-39 174.0
39 TraesCS3D01G232900 chr5B 90.370 135 9 4 7 137 629081172 629081038 1.160000e-39 174.0
40 TraesCS3D01G232900 chr2B 90.152 132 11 2 7 137 799756088 799755958 1.500000e-38 171.0
41 TraesCS3D01G232900 chr6B 79.365 189 26 7 735 918 135483747 135483567 1.530000e-23 121.0
42 TraesCS3D01G232900 chr5D 90.769 65 6 0 850 914 505925440 505925376 1.550000e-13 87.9
43 TraesCS3D01G232900 chr5D 88.889 63 7 0 852 914 28026386 28026324 9.320000e-11 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 TraesCS3D01G232900 chr3D 320822828 320825962 3134 True 1467.333333 2593 100.0000 1 3135 3 chr3D.!!$R2 3134
1 TraesCS3D01G232900 chr3B 398964033 398965662 1629 False 1285.000000 2255 95.5705 940 3135 2 chr3B.!!$F1 2195
2 TraesCS3D01G232900 chr3A 404199168 404200794 1626 False 1276.500000 2244 95.3425 940 3135 2 chr3A.!!$F2 2195
3 TraesCS3D01G232900 chr3A 600888616 600889138 522 False 527.000000 527 85.1300 306 833 1 chr3A.!!$F1 527
4 TraesCS3D01G232900 chr1D 487579299 487579877 578 True 369.000000 562 87.8275 7 867 2 chr1D.!!$R1 860
5 TraesCS3D01G232900 chr5A 548283903 548284445 542 True 551.000000 551 85.3530 295 834 1 chr5A.!!$R1 539
6 TraesCS3D01G232900 chr7D 362360424 362360976 552 True 545.000000 545 84.9460 299 840 1 chr7D.!!$R1 541
7 TraesCS3D01G232900 chr2D 247789638 247790205 567 False 542.000000 542 84.2470 295 864 1 chr2D.!!$F1 569
8 TraesCS3D01G232900 chr2D 246623391 246623924 533 True 486.000000 486 83.5160 295 826 1 chr2D.!!$R1 531
9 TraesCS3D01G232900 chr6A 454430512 454431045 533 True 538.000000 538 85.1850 306 833 1 chr6A.!!$R1 527
10 TraesCS3D01G232900 chr6D 401621313 401621867 554 True 536.000000 536 84.6980 299 840 1 chr6D.!!$R2 541
11 TraesCS3D01G232900 chr6D 457327007 457327536 529 False 496.000000 496 84.0000 295 829 1 chr6D.!!$F4 534
12 TraesCS3D01G232900 chr6D 347714084 347714633 549 False 472.000000 472 82.9140 299 828 1 chr6D.!!$F2 529
13 TraesCS3D01G232900 chr6D 360692121 360692677 556 False 440.000000 440 81.8180 299 829 1 chr6D.!!$F3 530
14 TraesCS3D01G232900 chr4B 500506110 500506684 574 False 531.000000 531 83.6770 299 867 1 chr4B.!!$F1 568
15 TraesCS3D01G232900 chr7A 523142614 523143162 548 False 520.000000 520 84.2960 299 834 1 chr7A.!!$F1 535
16 TraesCS3D01G232900 chr4D 101675582 101676131 549 False 477.000000 477 83.0940 299 828 1 chr4D.!!$F1 529
17 TraesCS3D01G232900 chr4A 605061492 605061998 506 False 303.000000 303 78.5980 338 837 1 chr4A.!!$F1 499

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
42 43 0.232303 CGTGACTCTCGCCAAAACAC 59.768 55.0 0.00 0.0 0.00 3.32 F
902 1061 0.315886 TGACAAAGGAGCGCTCGTTA 59.684 50.0 36.98 23.2 36.77 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1741 1900 0.042431 TGGATGGATTGGGGTTTGGG 59.958 55.0 0.0 0.0 0.0 4.12 R
2235 2407 0.179004 CCTGCCAACACTAACACCCA 60.179 55.0 0.0 0.0 0.0 4.51 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
38 39 2.357034 GCCGTGACTCTCGCCAAA 60.357 61.111 0.00 0.00 0.00 3.28
42 43 0.232303 CGTGACTCTCGCCAAAACAC 59.768 55.000 0.00 0.00 0.00 3.32
44 45 1.668751 GTGACTCTCGCCAAAACACAA 59.331 47.619 0.00 0.00 0.00 3.33
48 49 1.670811 CTCTCGCCAAAACACAACTGT 59.329 47.619 0.00 0.00 0.00 3.55
57 58 3.248029 CACAACTGTGCCTCTCGC 58.752 61.111 0.00 0.00 39.39 5.03
59 60 3.114616 CAACTGTGCCTCTCGCGG 61.115 66.667 6.13 0.00 42.08 6.46
120 121 8.970553 CAGAAAACACGTTTATTTTCGTTTTTG 58.029 29.630 17.34 10.22 45.41 2.44
122 123 9.179211 GAAAACACGTTTATTTTCGTTTTTGAG 57.821 29.630 11.56 0.00 38.99 3.02
123 124 8.450385 AAACACGTTTATTTTCGTTTTTGAGA 57.550 26.923 0.00 0.00 38.11 3.27
124 125 7.659290 ACACGTTTATTTTCGTTTTTGAGAG 57.341 32.000 0.00 0.00 38.23 3.20
127 128 5.683743 CGTTTATTTTCGTTTTTGAGAGGCA 59.316 36.000 0.00 0.00 0.00 4.75
128 129 6.362283 CGTTTATTTTCGTTTTTGAGAGGCAT 59.638 34.615 0.00 0.00 0.00 4.40
129 130 7.501515 GTTTATTTTCGTTTTTGAGAGGCATG 58.498 34.615 0.00 0.00 0.00 4.06
130 131 3.641437 TTTCGTTTTTGAGAGGCATGG 57.359 42.857 0.00 0.00 0.00 3.66
131 132 0.881118 TCGTTTTTGAGAGGCATGGC 59.119 50.000 12.14 12.14 0.00 4.40
347 349 1.940613 GAAAGCACAACCGTGTCTCTT 59.059 47.619 0.00 0.00 45.50 2.85
348 350 2.902705 AAGCACAACCGTGTCTCTTA 57.097 45.000 0.00 0.00 45.50 2.10
351 353 1.732259 GCACAACCGTGTCTCTTATGG 59.268 52.381 0.00 0.00 45.50 2.74
355 357 2.673368 CAACCGTGTCTCTTATGGAAGC 59.327 50.000 0.00 0.00 32.21 3.86
357 359 2.301870 ACCGTGTCTCTTATGGAAGCAA 59.698 45.455 0.00 0.00 32.21 3.91
362 364 3.751175 TGTCTCTTATGGAAGCAAAACCG 59.249 43.478 0.00 0.00 32.21 4.44
370 372 1.947456 GGAAGCAAAACCGTGACTCTT 59.053 47.619 0.00 0.00 0.00 2.85
372 374 2.038387 AGCAAAACCGTGACTCTTGT 57.962 45.000 0.00 0.00 0.00 3.16
381 383 4.258543 ACCGTGACTCTTGTGAAAGAAAA 58.741 39.130 0.00 0.00 0.00 2.29
436 439 3.071206 ATGGCCGTGACTCTCGCT 61.071 61.111 0.00 0.00 0.00 4.93
448 451 0.716108 CTCTCGCTAAAGCACAACCG 59.284 55.000 2.44 0.00 42.21 4.44
450 453 1.270274 TCTCGCTAAAGCACAACCGTA 59.730 47.619 2.44 0.00 42.21 4.02
568 688 4.640855 CACACCCGTGCGTCTCGT 62.641 66.667 0.00 0.00 36.06 4.18
569 689 4.640855 ACACCCGTGCGTCTCGTG 62.641 66.667 0.00 0.00 0.00 4.35
572 692 4.351938 CCCGTGCGTCTCGTGGAA 62.352 66.667 0.00 0.00 0.00 3.53
573 693 2.355363 CCGTGCGTCTCGTGGAAA 60.355 61.111 0.00 0.00 0.00 3.13
574 694 2.654912 CCGTGCGTCTCGTGGAAAC 61.655 63.158 0.00 0.00 0.00 2.78
575 695 1.947146 CGTGCGTCTCGTGGAAACA 60.947 57.895 0.00 0.00 38.70 2.83
576 696 1.484227 CGTGCGTCTCGTGGAAACAA 61.484 55.000 0.00 0.00 46.06 2.83
577 697 0.653636 GTGCGTCTCGTGGAAACAAA 59.346 50.000 0.00 0.00 46.06 2.83
578 698 1.062880 GTGCGTCTCGTGGAAACAAAA 59.937 47.619 0.00 0.00 46.06 2.44
579 699 1.944024 TGCGTCTCGTGGAAACAAAAT 59.056 42.857 0.00 0.00 46.06 1.82
580 700 2.032377 TGCGTCTCGTGGAAACAAAATC 60.032 45.455 0.00 0.00 46.06 2.17
581 701 2.822827 CGTCTCGTGGAAACAAAATCG 58.177 47.619 0.00 0.00 46.06 3.34
582 702 2.220133 CGTCTCGTGGAAACAAAATCGT 59.780 45.455 0.00 0.00 46.06 3.73
583 703 3.541711 GTCTCGTGGAAACAAAATCGTG 58.458 45.455 0.00 0.00 46.06 4.35
584 704 3.246699 GTCTCGTGGAAACAAAATCGTGA 59.753 43.478 0.00 0.00 46.06 4.35
585 705 3.246699 TCTCGTGGAAACAAAATCGTGAC 59.753 43.478 0.00 0.00 46.06 3.67
586 706 3.199677 TCGTGGAAACAAAATCGTGACT 58.800 40.909 0.00 0.00 46.06 3.41
587 707 3.246699 TCGTGGAAACAAAATCGTGACTC 59.753 43.478 0.00 0.00 46.06 3.36
588 708 3.247648 CGTGGAAACAAAATCGTGACTCT 59.752 43.478 0.00 0.00 46.06 3.24
589 709 4.608445 CGTGGAAACAAAATCGTGACTCTC 60.608 45.833 0.00 0.00 46.06 3.20
590 710 3.493129 TGGAAACAAAATCGTGACTCTCG 59.507 43.478 0.00 0.00 37.44 4.04
591 711 3.470562 GAAACAAAATCGTGACTCTCGC 58.529 45.455 0.00 0.00 0.00 5.03
599 719 3.491581 GTGACTCTCGCGAAAGGAA 57.508 52.632 14.96 0.00 0.00 3.36
600 720 1.779569 GTGACTCTCGCGAAAGGAAA 58.220 50.000 14.96 0.00 0.00 3.13
601 721 2.132762 GTGACTCTCGCGAAAGGAAAA 58.867 47.619 14.96 0.00 0.00 2.29
602 722 2.542595 GTGACTCTCGCGAAAGGAAAAA 59.457 45.455 14.96 0.00 0.00 1.94
603 723 3.186613 GTGACTCTCGCGAAAGGAAAAAT 59.813 43.478 14.96 0.00 0.00 1.82
604 724 4.387862 GTGACTCTCGCGAAAGGAAAAATA 59.612 41.667 14.96 0.00 0.00 1.40
605 725 4.992319 TGACTCTCGCGAAAGGAAAAATAA 59.008 37.500 14.96 0.00 0.00 1.40
606 726 5.467399 TGACTCTCGCGAAAGGAAAAATAAA 59.533 36.000 14.96 0.00 0.00 1.40
607 727 6.148811 TGACTCTCGCGAAAGGAAAAATAAAT 59.851 34.615 14.96 0.00 0.00 1.40
608 728 7.332430 TGACTCTCGCGAAAGGAAAAATAAATA 59.668 33.333 14.96 0.00 0.00 1.40
609 729 8.036273 ACTCTCGCGAAAGGAAAAATAAATAA 57.964 30.769 14.96 0.00 0.00 1.40
610 730 8.508875 ACTCTCGCGAAAGGAAAAATAAATAAA 58.491 29.630 14.96 0.00 0.00 1.40
611 731 9.337091 CTCTCGCGAAAGGAAAAATAAATAAAA 57.663 29.630 11.33 0.00 0.00 1.52
612 732 9.680315 TCTCGCGAAAGGAAAAATAAATAAAAA 57.320 25.926 11.33 0.00 0.00 1.94
658 778 4.595538 ACGGCGTGACTTGCGGAA 62.596 61.111 13.76 0.00 36.60 4.30
659 779 3.777925 CGGCGTGACTTGCGGAAG 61.778 66.667 15.80 15.80 34.93 3.46
660 780 2.665185 GGCGTGACTTGCGGAAGT 60.665 61.111 23.14 23.14 45.59 3.01
661 781 1.373748 GGCGTGACTTGCGGAAGTA 60.374 57.895 22.98 8.43 42.80 2.24
662 782 0.947180 GGCGTGACTTGCGGAAGTAA 60.947 55.000 22.98 13.14 42.80 2.24
663 783 0.863144 GCGTGACTTGCGGAAGTAAA 59.137 50.000 22.98 11.28 42.80 2.01
671 791 1.961793 TGCGGAAGTAAAACTGTGCT 58.038 45.000 0.00 0.00 0.00 4.40
787 941 2.027003 ACCAGAACGTCGAAAACCAA 57.973 45.000 0.00 0.00 0.00 3.67
818 972 3.597559 CGTTTAAAAAGCCGAAAACGTGC 60.598 43.478 10.16 0.00 45.43 5.34
860 1019 4.007940 GCGTCCAAAGCGCGACAA 62.008 61.111 12.10 0.00 45.36 3.18
867 1026 1.881252 AAAGCGCGACAAGTGACGT 60.881 52.632 12.10 0.00 35.76 4.34
868 1027 1.426041 AAAGCGCGACAAGTGACGTT 61.426 50.000 12.10 0.00 35.76 3.99
869 1028 2.089433 AAGCGCGACAAGTGACGTTG 62.089 55.000 12.10 0.00 35.76 4.10
870 1029 2.544359 CGCGACAAGTGACGTTGG 59.456 61.111 0.00 0.00 35.76 3.77
871 1030 2.235016 CGCGACAAGTGACGTTGGT 61.235 57.895 0.00 0.00 35.76 3.67
872 1031 1.563173 GCGACAAGTGACGTTGGTC 59.437 57.895 5.18 0.00 43.71 4.02
873 1032 1.844003 CGACAAGTGACGTTGGTCG 59.156 57.895 1.52 1.52 46.49 4.79
882 1041 4.072088 CGTTGGTCGTTGCGAGGC 62.072 66.667 0.00 0.00 36.23 4.70
883 1042 2.665185 GTTGGTCGTTGCGAGGCT 60.665 61.111 0.00 0.00 36.23 4.58
884 1043 2.664851 TTGGTCGTTGCGAGGCTG 60.665 61.111 0.00 0.00 36.23 4.85
885 1044 3.158537 TTGGTCGTTGCGAGGCTGA 62.159 57.895 0.00 0.00 36.23 4.26
886 1045 3.112709 GGTCGTTGCGAGGCTGAC 61.113 66.667 0.00 0.00 36.23 3.51
887 1046 2.355837 GTCGTTGCGAGGCTGACA 60.356 61.111 0.00 0.00 36.23 3.58
888 1047 1.954146 GTCGTTGCGAGGCTGACAA 60.954 57.895 0.00 0.00 36.23 3.18
889 1048 1.227409 TCGTTGCGAGGCTGACAAA 60.227 52.632 0.00 0.00 0.00 2.83
890 1049 1.205064 CGTTGCGAGGCTGACAAAG 59.795 57.895 0.00 0.00 0.00 2.77
891 1050 1.576421 GTTGCGAGGCTGACAAAGG 59.424 57.895 0.00 0.00 0.00 3.11
892 1051 0.884704 GTTGCGAGGCTGACAAAGGA 60.885 55.000 0.00 0.00 0.00 3.36
893 1052 0.603707 TTGCGAGGCTGACAAAGGAG 60.604 55.000 0.00 0.00 0.00 3.69
894 1053 2.394563 GCGAGGCTGACAAAGGAGC 61.395 63.158 0.00 0.00 34.23 4.70
895 1054 2.097038 CGAGGCTGACAAAGGAGCG 61.097 63.158 0.00 0.00 35.95 5.03
896 1055 2.359230 AGGCTGACAAAGGAGCGC 60.359 61.111 0.00 0.00 35.95 5.92
897 1056 2.359230 GGCTGACAAAGGAGCGCT 60.359 61.111 11.27 11.27 35.95 5.92
898 1057 2.394563 GGCTGACAAAGGAGCGCTC 61.395 63.158 29.38 29.38 35.95 5.03
899 1058 2.734673 GCTGACAAAGGAGCGCTCG 61.735 63.158 29.81 18.76 0.00 5.03
900 1059 1.373497 CTGACAAAGGAGCGCTCGT 60.373 57.895 29.81 27.91 0.00 4.18
901 1060 0.946221 CTGACAAAGGAGCGCTCGTT 60.946 55.000 33.24 33.24 39.10 3.85
902 1061 0.315886 TGACAAAGGAGCGCTCGTTA 59.684 50.000 36.98 23.20 36.77 3.18
903 1062 1.269883 TGACAAAGGAGCGCTCGTTAA 60.270 47.619 36.98 23.20 36.77 2.01
904 1063 1.126296 GACAAAGGAGCGCTCGTTAAC 59.874 52.381 36.98 27.16 36.77 2.01
905 1064 1.270147 ACAAAGGAGCGCTCGTTAACT 60.270 47.619 36.98 23.52 36.77 2.24
906 1065 2.029649 ACAAAGGAGCGCTCGTTAACTA 60.030 45.455 36.98 0.00 36.77 2.24
907 1066 2.563471 AAGGAGCGCTCGTTAACTAG 57.437 50.000 36.34 3.24 36.12 2.57
908 1067 1.461559 AGGAGCGCTCGTTAACTAGT 58.538 50.000 29.81 3.95 0.00 2.57
909 1068 1.817447 AGGAGCGCTCGTTAACTAGTT 59.183 47.619 29.81 13.68 0.00 2.24
910 1069 1.918609 GGAGCGCTCGTTAACTAGTTG 59.081 52.381 29.81 1.62 0.00 3.16
911 1070 1.320852 GAGCGCTCGTTAACTAGTTGC 59.679 52.381 23.61 11.18 0.00 4.17
912 1071 1.067776 AGCGCTCGTTAACTAGTTGCT 60.068 47.619 18.56 17.34 0.00 3.91
913 1072 1.320852 GCGCTCGTTAACTAGTTGCTC 59.679 52.381 18.56 3.86 0.00 4.26
914 1073 2.864968 CGCTCGTTAACTAGTTGCTCT 58.135 47.619 18.56 0.00 0.00 4.09
915 1074 3.730061 GCGCTCGTTAACTAGTTGCTCTA 60.730 47.826 18.56 0.00 0.00 2.43
916 1075 4.409570 CGCTCGTTAACTAGTTGCTCTAA 58.590 43.478 18.56 0.85 0.00 2.10
917 1076 4.496183 CGCTCGTTAACTAGTTGCTCTAAG 59.504 45.833 18.56 8.81 0.00 2.18
918 1077 5.400703 GCTCGTTAACTAGTTGCTCTAAGT 58.599 41.667 18.56 0.00 0.00 2.24
919 1078 5.862860 GCTCGTTAACTAGTTGCTCTAAGTT 59.137 40.000 18.56 0.00 0.00 2.66
920 1079 6.365518 GCTCGTTAACTAGTTGCTCTAAGTTT 59.634 38.462 18.56 0.00 0.00 2.66
921 1080 7.410620 GCTCGTTAACTAGTTGCTCTAAGTTTC 60.411 40.741 18.56 0.00 0.00 2.78
922 1081 7.428020 TCGTTAACTAGTTGCTCTAAGTTTCA 58.572 34.615 18.56 0.00 0.00 2.69
923 1082 7.922278 TCGTTAACTAGTTGCTCTAAGTTTCAA 59.078 33.333 18.56 0.00 0.00 2.69
924 1083 8.545420 CGTTAACTAGTTGCTCTAAGTTTCAAA 58.455 33.333 18.56 0.00 0.00 2.69
996 1155 1.595003 CGACTCGATTCGCTACACTCC 60.595 57.143 12.37 0.00 31.03 3.85
1815 1974 2.224161 GCCTTTGCTCTGACTCCGATAT 60.224 50.000 0.00 0.00 33.53 1.63
1958 2117 1.071128 CCCGGTGTTCGTTAACCCA 59.929 57.895 0.00 0.00 37.11 4.51
1981 2140 1.208052 TCTCTGCCCTACTTGTGATGC 59.792 52.381 0.00 0.00 0.00 3.91
2078 2240 3.408634 TGGACGTTCCTTCCTTGATTTC 58.591 45.455 0.00 0.00 37.46 2.17
2114 2286 1.211969 CAGCGCTGCTTGAATTGCT 59.788 52.632 26.68 0.00 36.40 3.91
2235 2407 7.483580 AGCTTAGGTGTGTATTCTTAGAAGT 57.516 36.000 0.03 0.00 0.00 3.01
2327 2503 3.694072 TCCTGTTTGTGTTGAGAAACCAG 59.306 43.478 0.00 0.00 35.04 4.00
2807 2994 0.688487 TTGGTCCTAAGTCAACGGGG 59.312 55.000 0.00 0.00 0.00 5.73
2835 3022 8.424918 TCATTTCTTGGCCAAACTTTTTATACA 58.575 29.630 20.91 0.00 0.00 2.29
2929 3118 1.202687 ACATATAGTGCGTGCTGGCAT 60.203 47.619 5.57 0.00 45.99 4.40
2956 3145 1.399791 GCTGGCCATTTCTCTTTCTCG 59.600 52.381 5.51 0.00 0.00 4.04
3001 3190 1.562008 TGTGGTGAAGAGGTTTGGTGA 59.438 47.619 0.00 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 2.677979 GGCCGTGCCTCTCGAAAAC 61.678 63.158 7.58 0.00 46.69 2.43
26 27 1.940613 AGTTGTGTTTTGGCGAGAGTC 59.059 47.619 0.00 0.00 0.00 3.36
27 28 1.670811 CAGTTGTGTTTTGGCGAGAGT 59.329 47.619 0.00 0.00 0.00 3.24
42 43 3.114616 CCGCGAGAGGCACAGTTG 61.115 66.667 8.23 0.00 43.84 3.16
44 45 3.753434 CTCCGCGAGAGGCACAGT 61.753 66.667 8.23 0.00 43.84 3.55
57 58 0.036010 AGAGTCATGGTTTGCCTCCG 60.036 55.000 0.00 0.00 35.27 4.63
59 60 1.363744 CGAGAGTCATGGTTTGCCTC 58.636 55.000 0.00 0.00 35.27 4.70
62 63 1.014044 TCGCGAGAGTCATGGTTTGC 61.014 55.000 3.71 0.00 34.84 3.68
63 64 1.428448 TTCGCGAGAGTCATGGTTTG 58.572 50.000 9.59 0.00 43.69 2.93
108 109 4.559153 CCATGCCTCTCAAAAACGAAAAT 58.441 39.130 0.00 0.00 0.00 1.82
114 115 3.820595 GGCCATGCCTCTCAAAAAC 57.179 52.632 0.00 0.00 46.69 2.43
294 295 1.533625 CCGTGCCTCTTGGAAATGAA 58.466 50.000 0.00 0.00 34.57 2.57
295 296 0.960364 GCCGTGCCTCTTGGAAATGA 60.960 55.000 0.00 0.00 34.57 2.57
296 297 1.508088 GCCGTGCCTCTTGGAAATG 59.492 57.895 0.00 0.00 34.57 2.32
297 298 1.678970 GGCCGTGCCTCTTGGAAAT 60.679 57.895 7.58 0.00 46.69 2.17
298 299 2.282180 GGCCGTGCCTCTTGGAAA 60.282 61.111 7.58 0.00 46.69 3.13
342 344 3.751175 CACGGTTTTGCTTCCATAAGAGA 59.249 43.478 0.00 0.00 34.37 3.10
347 349 3.071479 GAGTCACGGTTTTGCTTCCATA 58.929 45.455 0.00 0.00 0.00 2.74
348 350 1.880027 GAGTCACGGTTTTGCTTCCAT 59.120 47.619 0.00 0.00 0.00 3.41
351 353 2.354821 ACAAGAGTCACGGTTTTGCTTC 59.645 45.455 0.00 0.00 0.00 3.86
355 357 4.094294 TCTTTCACAAGAGTCACGGTTTTG 59.906 41.667 0.00 0.00 33.80 2.44
357 359 3.869065 TCTTTCACAAGAGTCACGGTTT 58.131 40.909 0.00 0.00 33.80 3.27
406 409 2.115291 GGCCATGCCTCTCGGAAAC 61.115 63.158 0.00 0.00 46.69 2.78
420 423 1.529152 TTTAGCGAGAGTCACGGCCA 61.529 55.000 11.95 0.00 0.00 5.36
436 439 2.352030 CGAGAGGTACGGTTGTGCTTTA 60.352 50.000 0.00 0.00 0.00 1.85
448 451 0.389426 TTTGCTTCCGCGAGAGGTAC 60.389 55.000 8.23 0.00 39.65 3.34
450 453 1.070786 TTTTGCTTCCGCGAGAGGT 59.929 52.632 8.23 0.00 39.65 3.85
555 675 3.851845 TTTCCACGAGACGCACGGG 62.852 63.158 0.00 0.00 34.93 5.28
556 676 2.355363 TTTCCACGAGACGCACGG 60.355 61.111 0.00 0.00 34.93 4.94
557 677 1.484227 TTGTTTCCACGAGACGCACG 61.484 55.000 0.00 0.00 0.00 5.34
558 678 0.653636 TTTGTTTCCACGAGACGCAC 59.346 50.000 0.00 0.00 0.00 5.34
559 679 1.370609 TTTTGTTTCCACGAGACGCA 58.629 45.000 0.00 0.00 0.00 5.24
560 680 2.571206 GATTTTGTTTCCACGAGACGC 58.429 47.619 0.00 0.00 0.00 5.19
561 681 2.220133 ACGATTTTGTTTCCACGAGACG 59.780 45.455 0.00 0.00 0.00 4.18
562 682 3.246699 TCACGATTTTGTTTCCACGAGAC 59.753 43.478 0.00 0.00 0.00 3.36
563 683 3.246699 GTCACGATTTTGTTTCCACGAGA 59.753 43.478 0.00 0.00 0.00 4.04
564 684 3.247648 AGTCACGATTTTGTTTCCACGAG 59.752 43.478 0.00 0.00 0.00 4.18
565 685 3.199677 AGTCACGATTTTGTTTCCACGA 58.800 40.909 0.00 0.00 0.00 4.35
566 686 3.247648 AGAGTCACGATTTTGTTTCCACG 59.752 43.478 0.00 0.00 0.00 4.94
567 687 4.608445 CGAGAGTCACGATTTTGTTTCCAC 60.608 45.833 3.68 0.00 0.00 4.02
568 688 3.493129 CGAGAGTCACGATTTTGTTTCCA 59.507 43.478 3.68 0.00 0.00 3.53
569 689 3.664537 GCGAGAGTCACGATTTTGTTTCC 60.665 47.826 14.42 0.00 0.00 3.13
570 690 3.470562 GCGAGAGTCACGATTTTGTTTC 58.529 45.455 14.42 0.00 0.00 2.78
571 691 2.096909 CGCGAGAGTCACGATTTTGTTT 60.097 45.455 14.42 0.00 0.00 2.83
572 692 1.455786 CGCGAGAGTCACGATTTTGTT 59.544 47.619 14.42 0.00 0.00 2.83
573 693 1.060713 CGCGAGAGTCACGATTTTGT 58.939 50.000 14.42 0.00 0.00 2.83
574 694 1.336877 TCGCGAGAGTCACGATTTTG 58.663 50.000 14.42 0.00 34.84 2.44
575 695 2.060326 TTCGCGAGAGTCACGATTTT 57.940 45.000 14.42 0.00 43.69 1.82
576 696 1.986378 CTTTCGCGAGAGTCACGATTT 59.014 47.619 17.92 0.00 43.69 2.17
577 697 1.618861 CTTTCGCGAGAGTCACGATT 58.381 50.000 17.92 0.00 43.69 3.34
578 698 0.179161 CCTTTCGCGAGAGTCACGAT 60.179 55.000 23.28 0.00 43.69 3.73
579 699 1.209383 CCTTTCGCGAGAGTCACGA 59.791 57.895 23.28 6.50 43.69 4.35
580 700 0.386858 TTCCTTTCGCGAGAGTCACG 60.387 55.000 23.28 9.67 43.69 4.35
581 701 1.779569 TTTCCTTTCGCGAGAGTCAC 58.220 50.000 23.28 0.00 43.69 3.67
582 702 2.519377 TTTTCCTTTCGCGAGAGTCA 57.481 45.000 23.28 8.47 43.69 3.41
583 703 5.526010 TTATTTTTCCTTTCGCGAGAGTC 57.474 39.130 23.28 0.00 43.69 3.36
584 704 5.934935 TTTATTTTTCCTTTCGCGAGAGT 57.065 34.783 23.28 8.00 43.69 3.24
585 705 8.889849 TTTATTTATTTTTCCTTTCGCGAGAG 57.110 30.769 19.09 19.09 43.69 3.20
586 706 9.680315 TTTTTATTTATTTTTCCTTTCGCGAGA 57.320 25.926 9.59 3.35 39.20 4.04
621 741 2.616842 GTGCCTCTCGGAAACAGAAAAA 59.383 45.455 0.00 0.00 0.00 1.94
622 742 2.218603 GTGCCTCTCGGAAACAGAAAA 58.781 47.619 0.00 0.00 0.00 2.29
623 743 1.872237 CGTGCCTCTCGGAAACAGAAA 60.872 52.381 0.00 0.00 0.00 2.52
624 744 0.319555 CGTGCCTCTCGGAAACAGAA 60.320 55.000 0.00 0.00 0.00 3.02
625 745 1.289066 CGTGCCTCTCGGAAACAGA 59.711 57.895 0.00 0.00 0.00 3.41
626 746 3.862124 CGTGCCTCTCGGAAACAG 58.138 61.111 0.00 0.00 0.00 3.16
634 754 3.575351 AAGTCACGCCGTGCCTCTC 62.575 63.158 13.39 0.59 32.98 3.20
635 755 3.616721 AAGTCACGCCGTGCCTCT 61.617 61.111 13.39 7.90 32.98 3.69
636 756 3.414700 CAAGTCACGCCGTGCCTC 61.415 66.667 13.39 5.62 32.98 4.70
641 761 4.595538 TTCCGCAAGTCACGCCGT 62.596 61.111 0.00 0.00 0.00 5.68
642 762 3.777925 CTTCCGCAAGTCACGCCG 61.778 66.667 0.00 0.00 0.00 6.46
643 763 0.947180 TTACTTCCGCAAGTCACGCC 60.947 55.000 0.00 0.00 42.27 5.68
644 764 0.863144 TTTACTTCCGCAAGTCACGC 59.137 50.000 0.00 0.00 42.27 5.34
645 765 2.542595 AGTTTTACTTCCGCAAGTCACG 59.457 45.455 0.00 0.00 42.27 4.35
646 766 3.311596 ACAGTTTTACTTCCGCAAGTCAC 59.688 43.478 0.00 0.00 42.27 3.67
647 767 3.311322 CACAGTTTTACTTCCGCAAGTCA 59.689 43.478 0.00 0.00 42.27 3.41
648 768 3.848554 GCACAGTTTTACTTCCGCAAGTC 60.849 47.826 0.00 0.00 42.27 3.01
649 769 2.032924 GCACAGTTTTACTTCCGCAAGT 59.967 45.455 0.00 0.00 45.39 3.16
650 770 2.290641 AGCACAGTTTTACTTCCGCAAG 59.709 45.455 0.00 0.00 35.50 4.01
651 771 2.294074 AGCACAGTTTTACTTCCGCAA 58.706 42.857 0.00 0.00 0.00 4.85
652 772 1.961793 AGCACAGTTTTACTTCCGCA 58.038 45.000 0.00 0.00 0.00 5.69
653 773 2.548480 AGAAGCACAGTTTTACTTCCGC 59.452 45.455 0.00 0.00 39.46 5.54
654 774 3.120991 CGAGAAGCACAGTTTTACTTCCG 60.121 47.826 0.00 0.00 39.46 4.30
655 775 4.391140 CGAGAAGCACAGTTTTACTTCC 57.609 45.455 0.00 0.00 39.46 3.46
659 779 6.633449 CTTCCGCGAGAAGCACAGTTTTAC 62.633 50.000 19.55 0.00 45.38 2.01
660 780 4.647513 CTTCCGCGAGAAGCACAGTTTTA 61.648 47.826 19.55 0.00 45.38 1.52
661 781 3.941644 CTTCCGCGAGAAGCACAGTTTT 61.942 50.000 19.55 0.00 45.38 2.43
662 782 2.466654 CTTCCGCGAGAAGCACAGTTT 61.467 52.381 19.55 0.00 45.38 2.66
663 783 0.946221 CTTCCGCGAGAAGCACAGTT 60.946 55.000 19.55 0.00 45.38 3.16
671 791 1.837538 CGGTTTTGCTTCCGCGAGAA 61.838 55.000 8.23 8.88 40.28 2.87
850 1009 1.881252 AACGTCACTTGTCGCGCTT 60.881 52.632 5.56 0.00 0.00 4.68
867 1026 2.664851 CAGCCTCGCAACGACCAA 60.665 61.111 0.00 0.00 0.00 3.67
868 1027 3.611674 TCAGCCTCGCAACGACCA 61.612 61.111 0.00 0.00 0.00 4.02
869 1028 3.112709 GTCAGCCTCGCAACGACC 61.113 66.667 0.00 0.00 0.00 4.79
870 1029 1.495584 TTTGTCAGCCTCGCAACGAC 61.496 55.000 0.00 0.00 0.00 4.34
871 1030 1.221466 CTTTGTCAGCCTCGCAACGA 61.221 55.000 0.00 0.00 0.00 3.85
872 1031 1.205064 CTTTGTCAGCCTCGCAACG 59.795 57.895 0.00 0.00 0.00 4.10
873 1032 0.884704 TCCTTTGTCAGCCTCGCAAC 60.885 55.000 0.00 0.00 0.00 4.17
874 1033 0.603707 CTCCTTTGTCAGCCTCGCAA 60.604 55.000 0.00 0.00 0.00 4.85
875 1034 1.004560 CTCCTTTGTCAGCCTCGCA 60.005 57.895 0.00 0.00 0.00 5.10
876 1035 2.394563 GCTCCTTTGTCAGCCTCGC 61.395 63.158 0.00 0.00 0.00 5.03
877 1036 2.097038 CGCTCCTTTGTCAGCCTCG 61.097 63.158 0.00 0.00 31.37 4.63
878 1037 2.394563 GCGCTCCTTTGTCAGCCTC 61.395 63.158 0.00 0.00 31.37 4.70
879 1038 2.359230 GCGCTCCTTTGTCAGCCT 60.359 61.111 0.00 0.00 31.37 4.58
880 1039 2.359230 AGCGCTCCTTTGTCAGCC 60.359 61.111 2.64 0.00 31.37 4.85
881 1040 2.734673 CGAGCGCTCCTTTGTCAGC 61.735 63.158 30.66 3.44 0.00 4.26
882 1041 0.946221 AACGAGCGCTCCTTTGTCAG 60.946 55.000 30.66 16.53 0.00 3.51
883 1042 0.315886 TAACGAGCGCTCCTTTGTCA 59.684 50.000 30.66 6.88 0.00 3.58
884 1043 1.126296 GTTAACGAGCGCTCCTTTGTC 59.874 52.381 30.66 16.21 0.00 3.18
885 1044 1.145803 GTTAACGAGCGCTCCTTTGT 58.854 50.000 30.66 19.77 0.00 2.83
886 1045 1.429463 AGTTAACGAGCGCTCCTTTG 58.571 50.000 30.66 19.09 0.00 2.77
887 1046 2.230750 ACTAGTTAACGAGCGCTCCTTT 59.769 45.455 30.66 24.45 0.00 3.11
888 1047 1.817447 ACTAGTTAACGAGCGCTCCTT 59.183 47.619 30.66 26.03 0.00 3.36
889 1048 1.461559 ACTAGTTAACGAGCGCTCCT 58.538 50.000 30.66 22.52 0.00 3.69
890 1049 1.918609 CAACTAGTTAACGAGCGCTCC 59.081 52.381 30.66 16.60 0.00 4.70
891 1050 1.320852 GCAACTAGTTAACGAGCGCTC 59.679 52.381 27.64 27.64 0.00 5.03
892 1051 1.067776 AGCAACTAGTTAACGAGCGCT 60.068 47.619 20.45 20.45 0.00 5.92
893 1052 1.320852 GAGCAACTAGTTAACGAGCGC 59.679 52.381 14.82 16.38 0.00 5.92
894 1053 2.864968 AGAGCAACTAGTTAACGAGCG 58.135 47.619 14.82 8.20 0.00 5.03
895 1054 5.400703 ACTTAGAGCAACTAGTTAACGAGC 58.599 41.667 14.82 7.28 32.30 5.03
896 1055 7.594015 TGAAACTTAGAGCAACTAGTTAACGAG 59.406 37.037 13.50 13.50 32.30 4.18
897 1056 7.428020 TGAAACTTAGAGCAACTAGTTAACGA 58.572 34.615 8.04 0.00 32.30 3.85
898 1057 7.633361 TGAAACTTAGAGCAACTAGTTAACG 57.367 36.000 8.04 0.00 32.30 3.18
974 1133 1.736126 AGTGTAGCGAATCGAGTCGAA 59.264 47.619 36.06 21.10 43.86 3.71
996 1155 2.967076 CCGCCGGATTCCATGACG 60.967 66.667 5.05 0.00 0.00 4.35
1740 1899 0.690744 GGATGGATTGGGGTTTGGGG 60.691 60.000 0.00 0.00 0.00 4.96
1741 1900 0.042431 TGGATGGATTGGGGTTTGGG 59.958 55.000 0.00 0.00 0.00 4.12
1742 1901 1.949799 TTGGATGGATTGGGGTTTGG 58.050 50.000 0.00 0.00 0.00 3.28
1743 1902 2.905736 ACTTTGGATGGATTGGGGTTTG 59.094 45.455 0.00 0.00 0.00 2.93
1744 1903 3.173151 GACTTTGGATGGATTGGGGTTT 58.827 45.455 0.00 0.00 0.00 3.27
1745 1904 2.559705 GGACTTTGGATGGATTGGGGTT 60.560 50.000 0.00 0.00 0.00 4.11
1746 1905 1.007118 GGACTTTGGATGGATTGGGGT 59.993 52.381 0.00 0.00 0.00 4.95
1815 1974 3.008923 TGGTAACAGTGCAGATTGGATGA 59.991 43.478 0.00 0.00 46.17 2.92
1958 2117 2.540383 TCACAAGTAGGGCAGAGACAT 58.460 47.619 0.00 0.00 0.00 3.06
2078 2240 3.120199 CGCTGTACCCTGAAAATGTGAAG 60.120 47.826 0.00 0.00 0.00 3.02
2114 2286 0.825410 CATGCATAGCCTTTGCCCAA 59.175 50.000 0.00 0.00 39.39 4.12
2235 2407 0.179004 CCTGCCAACACTAACACCCA 60.179 55.000 0.00 0.00 0.00 4.51
2481 2658 9.959749 GAACAAAATAAAACCAGTCAGACATTA 57.040 29.630 2.66 0.00 0.00 1.90
2669 2851 0.482446 ACAGAATGGCCCCTTGTCAA 59.518 50.000 0.00 0.00 43.62 3.18
2727 2911 5.501715 CCATCGTGTAGTGTGATTAAATGC 58.498 41.667 0.00 0.00 0.00 3.56
2807 2994 6.866010 AAAAAGTTTGGCCAAGAAATGATC 57.134 33.333 19.48 3.53 0.00 2.92
2929 3118 1.221840 GAAATGGCCAGCTCTCGGA 59.778 57.895 13.05 0.00 0.00 4.55
3001 3190 4.093703 TCGTGAAACAAACATTCAGACGTT 59.906 37.500 0.00 0.00 37.46 3.99


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

AutoCloner maintained by Alex Coulton.