Multiple sequence alignment - TraesCS6D01G007400

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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 TraesCS6D01G007400 chr6D 100.000 3106 0 0 1 3106 3027098 3023993 0.000000e+00 5736.0
1 TraesCS6D01G007400 chr6B 94.851 2447 89 10 668 3106 6195606 6193189 0.000000e+00 3786.0
2 TraesCS6D01G007400 chr6B 95.215 606 28 1 1 606 6196208 6195604 0.000000e+00 957.0
3 TraesCS6D01G007400 chr6B 84.452 283 39 3 1510 1791 527622587 527622309 1.100000e-69 274.0
4 TraesCS6D01G007400 chr6A 88.251 749 79 7 2350 3094 1961964 1962707 0.000000e+00 887.0
5 TraesCS6D01G007400 chr6A 91.326 611 25 15 1200 1790 1960859 1961461 0.000000e+00 809.0
6 TraesCS6D01G007400 chr6A 88.557 402 23 9 1967 2353 1961530 1961923 1.690000e-127 466.0
7 TraesCS6D01G007400 chr6A 96.172 209 8 0 960 1168 1960655 1960863 2.970000e-90 342.0
8 TraesCS6D01G007400 chr6A 95.918 147 6 0 796 942 1960525 1960671 4.000000e-59 239.0
9 TraesCS6D01G007400 chr3B 84.755 551 50 17 1275 1795 228209574 228209028 3.550000e-144 521.0
10 TraesCS6D01G007400 chr3B 80.049 406 32 25 1957 2353 228208939 228208574 3.970000e-64 255.0
11 TraesCS6D01G007400 chr3B 90.374 187 13 3 960 1146 228209906 228209725 1.110000e-59 241.0
12 TraesCS6D01G007400 chr3B 90.426 94 6 1 997 1090 228386183 228386093 1.510000e-23 121.0
13 TraesCS6D01G007400 chr3B 85.897 78 11 0 1810 1887 556503282 556503205 1.980000e-12 84.2
14 TraesCS6D01G007400 chr3B 89.552 67 4 1 778 841 228210065 228209999 7.140000e-12 82.4
15 TraesCS6D01G007400 chr3A 83.932 529 65 14 1272 1790 171137732 171138250 3.600000e-134 488.0
16 TraesCS6D01G007400 chr3A 90.374 187 13 4 960 1146 171173271 171173452 1.110000e-59 241.0
17 TraesCS6D01G007400 chr3A 89.595 173 8 2 1957 2123 171174209 171174377 8.730000e-51 211.0
18 TraesCS6D01G007400 chr3A 91.837 147 9 1 997 1143 171137514 171137657 5.250000e-48 202.0
19 TraesCS6D01G007400 chr3A 88.288 111 12 1 474 583 697447777 697447667 6.990000e-27 132.0
20 TraesCS6D01G007400 chr3A 80.488 123 24 0 1019 1141 510188300 510188422 9.170000e-16 95.3
21 TraesCS6D01G007400 chr3A 86.207 87 12 0 1808 1894 603909896 603909810 9.170000e-16 95.3
22 TraesCS6D01G007400 chr3A 80.000 130 12 6 778 893 171173128 171173257 1.980000e-12 84.2
23 TraesCS6D01G007400 chr3D 91.167 317 25 1 1479 1795 157102660 157102347 7.960000e-116 427.0
24 TraesCS6D01G007400 chr3D 81.791 335 33 15 1957 2288 157102259 157101950 3.970000e-64 255.0
25 TraesCS6D01G007400 chr3D 91.837 147 9 1 997 1143 157180431 157180288 5.250000e-48 202.0
26 TraesCS6D01G007400 chr1A 80.183 545 79 21 1272 1792 583604644 583605183 6.290000e-102 381.0
27 TraesCS6D01G007400 chr1A 88.636 88 10 0 1807 1894 558332146 558332233 1.180000e-19 108.0
28 TraesCS6D01G007400 chr5D 79.699 532 87 16 1272 1789 62527959 62528483 6.330000e-97 364.0
29 TraesCS6D01G007400 chr5D 87.261 157 12 5 1958 2106 62531094 62531250 4.120000e-39 172.0
30 TraesCS6D01G007400 chr5D 84.946 93 12 2 1806 1897 118571968 118571877 3.300000e-15 93.5
31 TraesCS6D01G007400 chr1B 85.577 312 42 1 1479 1790 676746672 676746980 1.070000e-84 324.0
32 TraesCS6D01G007400 chr7D 85.821 268 34 1 17 280 459466036 459466303 6.560000e-72 281.0
33 TraesCS6D01G007400 chr7D 97.368 38 1 0 588 625 459466471 459466508 7.190000e-07 65.8
34 TraesCS6D01G007400 chr7A 84.962 266 36 1 17 278 540755921 540755656 1.840000e-67 267.0
35 TraesCS6D01G007400 chr7A 82.677 254 33 4 17 266 540771808 540771562 6.750000e-52 215.0
36 TraesCS6D01G007400 chr7A 79.762 252 43 7 17 268 539853182 539852939 3.180000e-40 176.0
37 TraesCS6D01G007400 chr7A 92.453 53 1 3 588 637 540771388 540771336 4.300000e-09 73.1
38 TraesCS6D01G007400 chr7B 83.895 267 37 3 17 278 481617661 481617926 1.850000e-62 250.0
39 TraesCS6D01G007400 chr1D 89.041 146 13 1 997 1142 486014091 486014233 8.850000e-41 178.0
40 TraesCS6D01G007400 chr1D 83.871 124 10 10 474 593 464800783 464800666 3.270000e-20 110.0
41 TraesCS6D01G007400 chr1D 86.517 89 9 2 1810 1896 260568853 260568940 9.170000e-16 95.3
42 TraesCS6D01G007400 chr1D 86.047 86 11 1 1810 1894 260568938 260568853 1.190000e-14 91.6
43 TraesCS6D01G007400 chr4D 91.589 107 8 1 474 580 83148099 83148204 2.500000e-31 147.0
44 TraesCS6D01G007400 chr4B 91.589 107 8 1 474 580 117778785 117778890 2.500000e-31 147.0
45 TraesCS6D01G007400 chr2D 90.741 108 10 0 474 581 335687006 335687113 8.980000e-31 145.0
46 TraesCS6D01G007400 chr2A 89.815 108 11 0 474 581 446069287 446069394 4.180000e-29 139.0
47 TraesCS6D01G007400 chr2B 88.889 108 12 0 474 581 403699384 403699491 1.940000e-27 134.0
48 TraesCS6D01G007400 chrUn 91.765 85 7 0 1810 1894 42479240 42479324 5.440000e-23 119.0
49 TraesCS6D01G007400 chr5A 86.239 109 11 3 475 582 476661277 476661172 7.040000e-22 115.0
50 TraesCS6D01G007400 chr4A 90.667 75 7 0 1810 1884 573324893 573324819 1.970000e-17 100.0


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 TraesCS6D01G007400 chr6D 3023993 3027098 3105 True 5736.00 5736 100.0000 1 3106 1 chr6D.!!$R1 3105
1 TraesCS6D01G007400 chr6B 6193189 6196208 3019 True 2371.50 3786 95.0330 1 3106 2 chr6B.!!$R2 3105
2 TraesCS6D01G007400 chr6A 1960525 1962707 2182 False 548.60 887 92.0448 796 3094 5 chr6A.!!$F1 2298
3 TraesCS6D01G007400 chr3B 228208574 228210065 1491 True 274.85 521 86.1825 778 2353 4 chr3B.!!$R3 1575
4 TraesCS6D01G007400 chr3A 171137514 171138250 736 False 345.00 488 87.8845 997 1790 2 chr3A.!!$F2 793
5 TraesCS6D01G007400 chr3D 157101950 157102660 710 True 341.00 427 86.4790 1479 2288 2 chr3D.!!$R2 809
6 TraesCS6D01G007400 chr1A 583604644 583605183 539 False 381.00 381 80.1830 1272 1792 1 chr1A.!!$F2 520
7 TraesCS6D01G007400 chr5D 62527959 62531250 3291 False 268.00 364 83.4800 1272 2106 2 chr5D.!!$F1 834

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
441 442 0.032615 AGGTGGTTGTTCAAAGCCCA 60.033 50.0 0.0 0.0 0.00 5.36 F
671 672 0.036010 CCTCCAACAGCACGAGGAAT 60.036 55.0 0.0 0.0 45.15 3.01 F
1433 1557 0.609681 AGACCTCACTCCGTCAGTCC 60.610 60.0 0.0 0.0 30.26 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1477 1658 0.179936 GTCAGAGGCTTCATCCCTGG 59.820 60.000 0.00 0.0 31.41 4.45 R
1943 3450 1.532437 GTTGCAGCAGCGCATCATATA 59.468 47.619 11.47 0.0 46.23 0.86 R
2704 5417 0.880718 GCGGATCTTTCTTAGGCGGG 60.881 60.000 0.00 0.0 0.00 6.13 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 3.347216 TGCTCCATGAAGCTAAAACTCC 58.653 45.455 5.24 0.00 42.94 3.85
78 79 0.185901 ACTTGAAGCAAAGGAGGGCA 59.814 50.000 0.00 0.00 0.00 5.36
95 96 3.887716 AGGGCATGTCTATCATTTTCAGC 59.112 43.478 0.00 0.00 34.09 4.26
117 118 1.099879 CCTTGCAGATGGCTAGTGGC 61.100 60.000 0.00 0.00 42.80 5.01
144 145 3.569701 TGCAAAGGAAGCAAAAGAGGTAG 59.430 43.478 0.00 0.00 39.39 3.18
194 195 2.842256 CGGAAGATGCCATGGCTGC 61.842 63.158 35.53 26.15 42.51 5.25
195 196 1.455217 GGAAGATGCCATGGCTGCT 60.455 57.895 35.53 27.81 42.51 4.24
200 201 0.465097 GATGCCATGGCTGCTGTAGT 60.465 55.000 35.53 12.31 42.51 2.73
205 206 2.710377 CCATGGCTGCTGTAGTTTACA 58.290 47.619 0.00 0.00 37.13 2.41
260 261 3.954904 GCAGGAGGATGTCTAAGTACTCA 59.045 47.826 0.00 0.00 0.00 3.41
268 269 2.826128 TGTCTAAGTACTCAGCTGTGGG 59.174 50.000 19.27 10.83 0.00 4.61
367 368 6.128282 ACACGACTTGCTTTTGAATCGATATT 60.128 34.615 0.00 0.00 33.88 1.28
373 374 8.253113 ACTTGCTTTTGAATCGATATTGGATTT 58.747 29.630 0.00 0.00 34.41 2.17
385 386 1.029408 TTGGATTTGGCGTCCATCGG 61.029 55.000 6.87 0.00 44.75 4.18
387 388 0.535102 GGATTTGGCGTCCATCGGAT 60.535 55.000 0.00 0.00 40.26 4.18
391 392 0.387929 TTGGCGTCCATCGGATCTAC 59.612 55.000 0.00 0.00 40.26 2.59
394 395 0.669077 GCGTCCATCGGATCTACTGT 59.331 55.000 0.00 0.00 40.26 3.55
407 408 3.678056 TCTACTGTTTGCCGACTGAAT 57.322 42.857 0.00 0.00 0.00 2.57
440 441 0.673985 GAGGTGGTTGTTCAAAGCCC 59.326 55.000 0.00 0.00 0.00 5.19
441 442 0.032615 AGGTGGTTGTTCAAAGCCCA 60.033 50.000 0.00 0.00 0.00 5.36
442 443 0.827368 GGTGGTTGTTCAAAGCCCAA 59.173 50.000 0.00 0.00 0.00 4.12
479 480 0.608640 CTCCAACGCCAACTACTCCT 59.391 55.000 0.00 0.00 0.00 3.69
518 519 2.290641 GACGTTTTGGACAGCTGACATT 59.709 45.455 23.35 0.00 0.00 2.71
536 537 4.960938 ACATTGAACTGTCTTGTGCTCTA 58.039 39.130 0.00 0.00 0.00 2.43
606 607 2.288334 TGTTGTGAGCATGCATTTGGAC 60.288 45.455 21.98 11.31 0.00 4.02
607 608 0.522626 TGTGAGCATGCATTTGGACG 59.477 50.000 21.98 0.00 0.00 4.79
608 609 0.799534 GTGAGCATGCATTTGGACGC 60.800 55.000 21.98 0.00 0.00 5.19
609 610 0.961857 TGAGCATGCATTTGGACGCT 60.962 50.000 21.98 6.66 0.00 5.07
610 611 1.016627 GAGCATGCATTTGGACGCTA 58.983 50.000 21.98 0.00 0.00 4.26
611 612 1.401552 GAGCATGCATTTGGACGCTAA 59.598 47.619 21.98 0.00 0.00 3.09
612 613 1.402968 AGCATGCATTTGGACGCTAAG 59.597 47.619 21.98 0.00 0.00 2.18
613 614 1.401552 GCATGCATTTGGACGCTAAGA 59.598 47.619 14.21 0.00 0.00 2.10
614 615 2.540361 GCATGCATTTGGACGCTAAGAG 60.540 50.000 14.21 0.00 0.00 2.85
615 616 2.760634 TGCATTTGGACGCTAAGAGA 57.239 45.000 0.00 0.00 0.00 3.10
616 617 3.266510 TGCATTTGGACGCTAAGAGAT 57.733 42.857 0.00 0.00 0.00 2.75
617 618 3.609853 TGCATTTGGACGCTAAGAGATT 58.390 40.909 0.00 0.00 0.00 2.40
618 619 4.009675 TGCATTTGGACGCTAAGAGATTT 58.990 39.130 0.00 0.00 0.00 2.17
619 620 4.142622 TGCATTTGGACGCTAAGAGATTTG 60.143 41.667 0.00 0.00 0.00 2.32
620 621 4.094887 GCATTTGGACGCTAAGAGATTTGA 59.905 41.667 0.00 0.00 0.00 2.69
621 622 5.563842 CATTTGGACGCTAAGAGATTTGAC 58.436 41.667 0.00 0.00 0.00 3.18
622 623 3.247006 TGGACGCTAAGAGATTTGACC 57.753 47.619 0.00 0.00 0.00 4.02
623 624 2.093658 TGGACGCTAAGAGATTTGACCC 60.094 50.000 0.00 0.00 0.00 4.46
624 625 2.168728 GGACGCTAAGAGATTTGACCCT 59.831 50.000 0.00 0.00 0.00 4.34
625 626 3.449632 GACGCTAAGAGATTTGACCCTC 58.550 50.000 0.00 0.00 0.00 4.30
626 627 3.100671 ACGCTAAGAGATTTGACCCTCT 58.899 45.455 0.00 0.00 41.17 3.69
627 628 3.118956 ACGCTAAGAGATTTGACCCTCTG 60.119 47.826 0.00 0.00 39.49 3.35
628 629 3.202097 GCTAAGAGATTTGACCCTCTGC 58.798 50.000 0.00 0.00 39.49 4.26
629 630 3.118445 GCTAAGAGATTTGACCCTCTGCT 60.118 47.826 0.00 0.00 39.49 4.24
630 631 4.625083 GCTAAGAGATTTGACCCTCTGCTT 60.625 45.833 0.00 0.00 39.49 3.91
631 632 5.395768 GCTAAGAGATTTGACCCTCTGCTTA 60.396 44.000 0.00 0.00 39.49 3.09
632 633 4.479786 AGAGATTTGACCCTCTGCTTAC 57.520 45.455 0.00 0.00 38.26 2.34
633 634 3.840666 AGAGATTTGACCCTCTGCTTACA 59.159 43.478 0.00 0.00 38.26 2.41
634 635 3.935828 GAGATTTGACCCTCTGCTTACAC 59.064 47.826 0.00 0.00 0.00 2.90
635 636 3.584848 AGATTTGACCCTCTGCTTACACT 59.415 43.478 0.00 0.00 0.00 3.55
636 637 2.839486 TTGACCCTCTGCTTACACTG 57.161 50.000 0.00 0.00 0.00 3.66
637 638 0.321671 TGACCCTCTGCTTACACTGC 59.678 55.000 0.00 0.00 0.00 4.40
638 639 0.321671 GACCCTCTGCTTACACTGCA 59.678 55.000 0.00 0.00 38.81 4.41
639 640 0.987294 ACCCTCTGCTTACACTGCAT 59.013 50.000 0.00 0.00 39.86 3.96
640 641 1.352352 ACCCTCTGCTTACACTGCATT 59.648 47.619 0.00 0.00 39.86 3.56
641 642 1.741706 CCCTCTGCTTACACTGCATTG 59.258 52.381 1.95 1.95 39.86 2.82
642 643 2.616256 CCCTCTGCTTACACTGCATTGA 60.616 50.000 11.48 0.00 39.86 2.57
643 644 3.076621 CCTCTGCTTACACTGCATTGAA 58.923 45.455 11.48 0.51 39.86 2.69
644 645 3.120060 CCTCTGCTTACACTGCATTGAAC 60.120 47.826 11.48 0.00 39.86 3.18
645 646 2.813754 TCTGCTTACACTGCATTGAACC 59.186 45.455 11.48 0.00 39.86 3.62
646 647 2.553602 CTGCTTACACTGCATTGAACCA 59.446 45.455 11.48 1.92 39.86 3.67
647 648 2.954989 TGCTTACACTGCATTGAACCAA 59.045 40.909 11.48 0.00 35.31 3.67
648 649 3.382865 TGCTTACACTGCATTGAACCAAA 59.617 39.130 11.48 0.00 35.31 3.28
649 650 3.735746 GCTTACACTGCATTGAACCAAAC 59.264 43.478 11.48 0.00 0.00 2.93
650 651 4.736168 GCTTACACTGCATTGAACCAAACA 60.736 41.667 11.48 0.00 0.00 2.83
651 652 3.163630 ACACTGCATTGAACCAAACAC 57.836 42.857 11.48 0.00 0.00 3.32
652 653 2.159114 ACACTGCATTGAACCAAACACC 60.159 45.455 11.48 0.00 0.00 4.16
653 654 1.412343 ACTGCATTGAACCAAACACCC 59.588 47.619 0.00 0.00 0.00 4.61
654 655 1.688197 CTGCATTGAACCAAACACCCT 59.312 47.619 0.00 0.00 0.00 4.34
655 656 1.686052 TGCATTGAACCAAACACCCTC 59.314 47.619 0.00 0.00 0.00 4.30
656 657 1.000843 GCATTGAACCAAACACCCTCC 59.999 52.381 0.00 0.00 0.00 4.30
657 658 2.315176 CATTGAACCAAACACCCTCCA 58.685 47.619 0.00 0.00 0.00 3.86
658 659 2.534042 TTGAACCAAACACCCTCCAA 57.466 45.000 0.00 0.00 0.00 3.53
659 660 1.770294 TGAACCAAACACCCTCCAAC 58.230 50.000 0.00 0.00 0.00 3.77
660 661 1.006043 TGAACCAAACACCCTCCAACA 59.994 47.619 0.00 0.00 0.00 3.33
661 662 1.681264 GAACCAAACACCCTCCAACAG 59.319 52.381 0.00 0.00 0.00 3.16
662 663 0.755327 ACCAAACACCCTCCAACAGC 60.755 55.000 0.00 0.00 0.00 4.40
663 664 0.754957 CCAAACACCCTCCAACAGCA 60.755 55.000 0.00 0.00 0.00 4.41
664 665 0.385390 CAAACACCCTCCAACAGCAC 59.615 55.000 0.00 0.00 0.00 4.40
665 666 1.101049 AAACACCCTCCAACAGCACG 61.101 55.000 0.00 0.00 0.00 5.34
666 667 1.978455 AACACCCTCCAACAGCACGA 61.978 55.000 0.00 0.00 0.00 4.35
667 668 1.669115 CACCCTCCAACAGCACGAG 60.669 63.158 0.00 0.00 0.00 4.18
668 669 2.046892 CCCTCCAACAGCACGAGG 60.047 66.667 0.00 0.00 42.48 4.63
669 670 2.583441 CCCTCCAACAGCACGAGGA 61.583 63.158 3.89 0.00 45.15 3.71
670 671 1.371183 CCTCCAACAGCACGAGGAA 59.629 57.895 0.00 0.00 45.15 3.36
671 672 0.036010 CCTCCAACAGCACGAGGAAT 60.036 55.000 0.00 0.00 45.15 3.01
672 673 1.207089 CCTCCAACAGCACGAGGAATA 59.793 52.381 0.00 0.00 45.15 1.75
893 907 5.551305 TCAATCCTTCACTTGACTCTCAA 57.449 39.130 0.00 0.00 34.79 3.02
895 909 3.753294 TCCTTCACTTGACTCTCAACC 57.247 47.619 0.00 0.00 32.21 3.77
898 912 2.910688 TCACTTGACTCTCAACCCAC 57.089 50.000 0.00 0.00 32.21 4.61
931 959 9.539194 AATACTACTAACCTAGTACCAAGTTGT 57.461 33.333 1.45 0.00 40.14 3.32
946 974 2.702748 AGTTGTACCTTGAACTCCCCT 58.297 47.619 0.00 0.00 0.00 4.79
981 1010 4.338379 AGTTGTACCTTGAACTGAGACC 57.662 45.455 0.00 0.00 31.09 3.85
1171 1246 1.519758 GTTGTTCCACGAGTACACACG 59.480 52.381 0.00 0.42 36.07 4.49
1197 1272 4.456911 CCATGTGCTTCTTCTATGTGTGTT 59.543 41.667 0.00 0.00 0.00 3.32
1253 1364 4.210328 TGTTGTTGATCACGTGTACATGAC 59.790 41.667 21.82 12.47 0.00 3.06
1433 1557 0.609681 AGACCTCACTCCGTCAGTCC 60.610 60.000 0.00 0.00 30.26 3.85
1450 1613 2.099921 AGTCCGTCCATCGATCTTTCTG 59.900 50.000 0.00 0.00 42.86 3.02
1477 1658 2.844122 AAGACACCAACGCTTTTCAC 57.156 45.000 0.00 0.00 0.00 3.18
1584 1769 1.940883 GCATCTACGACCCGGACACA 61.941 60.000 0.73 0.00 0.00 3.72
1815 2006 4.803924 GCATGCAGCTTGGTATATACTCCA 60.804 45.833 14.21 0.49 41.15 3.86
1819 2010 4.748892 CAGCTTGGTATATACTCCATCCG 58.251 47.826 12.54 0.00 33.50 4.18
1943 3450 4.843728 TGTTCAGAGTTGGAACTTCACTT 58.156 39.130 6.80 0.00 43.84 3.16
1947 3454 8.375506 TGTTCAGAGTTGGAACTTCACTTATAT 58.624 33.333 6.80 0.00 43.84 0.86
2138 4792 9.590451 CACCAAAGAAATTGAAGCATATATGTT 57.410 29.630 14.14 5.37 41.85 2.71
2381 5090 2.529151 CATGGCTACGCAAAATTGGAC 58.471 47.619 0.00 0.00 0.00 4.02
2385 5094 2.159435 GGCTACGCAAAATTGGACGAAT 60.159 45.455 0.00 0.00 0.00 3.34
2387 5096 3.425625 GCTACGCAAAATTGGACGAATGA 60.426 43.478 0.00 0.00 0.00 2.57
2404 5113 7.222999 GGACGAATGAGTATTTCTCTCGAAATT 59.777 37.037 5.72 0.00 45.18 1.82
2438 5147 7.214467 TCCACTTTCTAAATAAAGCAACCAG 57.786 36.000 0.00 0.00 39.59 4.00
2475 5184 2.331893 CCATGAGCCGCACCGAAAA 61.332 57.895 0.00 0.00 0.00 2.29
2593 5306 0.884704 GGTGACACAAGACGGCACAT 60.885 55.000 8.08 0.00 0.00 3.21
2634 5347 1.972198 ATGTGTCCATGACGGTCGT 59.028 52.632 3.34 0.00 34.95 4.34
2655 5368 4.790651 CGTGATTCTGCTGTATAGATAGCG 59.209 45.833 1.52 0.00 42.47 4.26
2897 5611 2.496899 TCAAAGCTCCACAGGAATCC 57.503 50.000 0.00 0.00 0.00 3.01
2918 5632 0.306533 GCCGTCGTGCAAGAGAAAAA 59.693 50.000 1.39 0.00 0.00 1.94
2951 5665 1.298157 CTCTCCGGCGCATCACAAAA 61.298 55.000 10.83 0.00 0.00 2.44
2998 5712 1.064758 TGCCGCTTGAATACCTCCATT 60.065 47.619 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 4.226427 AGCTTCATGGAGCAAATAGTCA 57.774 40.909 27.76 0.00 45.12 3.41
14 15 5.105595 GGAGTTTTAGCTTCATGGAGCAAAT 60.106 40.000 27.76 12.69 45.12 2.32
15 16 4.218417 GGAGTTTTAGCTTCATGGAGCAAA 59.782 41.667 27.76 20.59 45.12 3.68
38 39 1.988956 AGACTCTCAGGCCCAGCAG 60.989 63.158 0.00 0.00 0.00 4.24
78 79 6.183360 GCAAGGAAGCTGAAAATGATAGACAT 60.183 38.462 0.00 0.00 41.45 3.06
95 96 2.286872 CACTAGCCATCTGCAAGGAAG 58.713 52.381 3.83 3.14 44.83 3.46
117 118 0.390124 TTTGCTTCCTTTGCAGCCTG 59.610 50.000 0.00 0.00 41.71 4.85
144 145 4.385358 TCCAAGCTTTGTTTGGTTTCTC 57.615 40.909 11.76 0.00 42.99 2.87
185 186 2.710377 TGTAAACTACAGCAGCCATGG 58.290 47.619 7.63 7.63 34.06 3.66
195 196 5.995565 ACACTCCATAGCTGTAAACTACA 57.004 39.130 0.00 0.00 37.13 2.74
200 201 7.847096 TGATTTCTACACTCCATAGCTGTAAA 58.153 34.615 0.00 0.00 0.00 2.01
205 206 6.951971 ACTTTGATTTCTACACTCCATAGCT 58.048 36.000 0.00 0.00 0.00 3.32
268 269 5.276868 GAATATATATTCATGCCGTCGCACC 60.277 44.000 24.50 0.00 39.96 5.01
373 374 0.467474 AGTAGATCCGATGGACGCCA 60.467 55.000 1.01 1.01 41.07 5.69
385 386 3.232213 TCAGTCGGCAAACAGTAGATC 57.768 47.619 0.00 0.00 0.00 2.75
387 388 3.678056 ATTCAGTCGGCAAACAGTAGA 57.322 42.857 0.00 0.00 0.00 2.59
391 392 4.749245 AACTAATTCAGTCGGCAAACAG 57.251 40.909 0.00 0.00 36.04 3.16
394 395 5.298276 AGTCAAAACTAATTCAGTCGGCAAA 59.702 36.000 0.00 0.00 36.04 3.68
407 408 4.513406 ACCACCTCCAAGTCAAAACTAA 57.487 40.909 0.00 0.00 33.48 2.24
440 441 6.148948 TGGAGTATTTCATTTCGCAAGTTTG 58.851 36.000 0.00 0.00 39.48 2.93
441 442 6.325919 TGGAGTATTTCATTTCGCAAGTTT 57.674 33.333 0.00 0.00 39.48 2.66
442 443 5.957842 TGGAGTATTTCATTTCGCAAGTT 57.042 34.783 0.00 0.00 39.48 2.66
518 519 6.590234 TTAGATAGAGCACAAGACAGTTCA 57.410 37.500 0.00 0.00 0.00 3.18
561 562 6.380274 CACCAACTACTCCCTCTGTTATCTTA 59.620 42.308 0.00 0.00 0.00 2.10
566 567 3.853207 ACACCAACTACTCCCTCTGTTA 58.147 45.455 0.00 0.00 0.00 2.41
606 607 3.452474 CAGAGGGTCAAATCTCTTAGCG 58.548 50.000 0.00 0.00 38.19 4.26
607 608 3.118445 AGCAGAGGGTCAAATCTCTTAGC 60.118 47.826 0.00 0.00 38.19 3.09
608 609 4.751767 AGCAGAGGGTCAAATCTCTTAG 57.248 45.455 0.00 0.00 38.19 2.18
609 610 5.483937 TGTAAGCAGAGGGTCAAATCTCTTA 59.516 40.000 0.00 0.00 38.19 2.10
610 611 4.287067 TGTAAGCAGAGGGTCAAATCTCTT 59.713 41.667 0.00 0.00 38.19 2.85
611 612 3.840666 TGTAAGCAGAGGGTCAAATCTCT 59.159 43.478 0.00 0.00 40.63 3.10
612 613 3.935828 GTGTAAGCAGAGGGTCAAATCTC 59.064 47.826 0.00 0.00 0.00 2.75
613 614 3.584848 AGTGTAAGCAGAGGGTCAAATCT 59.415 43.478 0.00 0.00 0.00 2.40
614 615 3.686726 CAGTGTAAGCAGAGGGTCAAATC 59.313 47.826 0.00 0.00 0.00 2.17
615 616 3.679389 CAGTGTAAGCAGAGGGTCAAAT 58.321 45.455 0.00 0.00 0.00 2.32
616 617 2.810400 GCAGTGTAAGCAGAGGGTCAAA 60.810 50.000 0.00 0.00 0.00 2.69
617 618 1.270839 GCAGTGTAAGCAGAGGGTCAA 60.271 52.381 0.00 0.00 0.00 3.18
618 619 0.321671 GCAGTGTAAGCAGAGGGTCA 59.678 55.000 0.00 0.00 0.00 4.02
619 620 0.321671 TGCAGTGTAAGCAGAGGGTC 59.678 55.000 0.00 0.00 37.02 4.46
620 621 0.987294 ATGCAGTGTAAGCAGAGGGT 59.013 50.000 0.00 0.00 46.36 4.34
621 622 1.741706 CAATGCAGTGTAAGCAGAGGG 59.258 52.381 5.87 0.00 46.36 4.30
622 623 2.703416 TCAATGCAGTGTAAGCAGAGG 58.297 47.619 14.62 0.00 46.36 3.69
623 624 3.120060 GGTTCAATGCAGTGTAAGCAGAG 60.120 47.826 14.62 0.00 46.36 3.35
624 625 2.813754 GGTTCAATGCAGTGTAAGCAGA 59.186 45.455 14.62 0.00 46.36 4.26
625 626 2.553602 TGGTTCAATGCAGTGTAAGCAG 59.446 45.455 19.59 0.00 46.36 4.24
627 628 3.641437 TTGGTTCAATGCAGTGTAAGC 57.359 42.857 14.62 15.62 0.00 3.09
628 629 4.739716 GTGTTTGGTTCAATGCAGTGTAAG 59.260 41.667 14.62 0.00 0.00 2.34
629 630 4.440802 GGTGTTTGGTTCAATGCAGTGTAA 60.441 41.667 14.62 4.58 0.00 2.41
630 631 3.067461 GGTGTTTGGTTCAATGCAGTGTA 59.933 43.478 14.62 0.78 0.00 2.90
631 632 2.159114 GGTGTTTGGTTCAATGCAGTGT 60.159 45.455 14.62 0.00 0.00 3.55
632 633 2.472816 GGTGTTTGGTTCAATGCAGTG 58.527 47.619 8.08 8.08 0.00 3.66
633 634 1.412343 GGGTGTTTGGTTCAATGCAGT 59.588 47.619 0.00 0.00 0.00 4.40
634 635 1.688197 AGGGTGTTTGGTTCAATGCAG 59.312 47.619 0.00 0.00 0.00 4.41
635 636 1.686052 GAGGGTGTTTGGTTCAATGCA 59.314 47.619 0.00 0.00 0.00 3.96
636 637 1.000843 GGAGGGTGTTTGGTTCAATGC 59.999 52.381 0.00 0.00 0.00 3.56
637 638 2.315176 TGGAGGGTGTTTGGTTCAATG 58.685 47.619 0.00 0.00 0.00 2.82
638 639 2.698274 GTTGGAGGGTGTTTGGTTCAAT 59.302 45.455 0.00 0.00 0.00 2.57
639 640 2.104170 GTTGGAGGGTGTTTGGTTCAA 58.896 47.619 0.00 0.00 0.00 2.69
640 641 1.006043 TGTTGGAGGGTGTTTGGTTCA 59.994 47.619 0.00 0.00 0.00 3.18
641 642 1.681264 CTGTTGGAGGGTGTTTGGTTC 59.319 52.381 0.00 0.00 0.00 3.62
642 643 1.775385 CTGTTGGAGGGTGTTTGGTT 58.225 50.000 0.00 0.00 0.00 3.67
643 644 0.755327 GCTGTTGGAGGGTGTTTGGT 60.755 55.000 0.00 0.00 0.00 3.67
644 645 0.754957 TGCTGTTGGAGGGTGTTTGG 60.755 55.000 0.00 0.00 0.00 3.28
645 646 0.385390 GTGCTGTTGGAGGGTGTTTG 59.615 55.000 0.00 0.00 0.00 2.93
646 647 1.101049 CGTGCTGTTGGAGGGTGTTT 61.101 55.000 0.00 0.00 0.00 2.83
647 648 1.525995 CGTGCTGTTGGAGGGTGTT 60.526 57.895 0.00 0.00 0.00 3.32
648 649 2.111043 CGTGCTGTTGGAGGGTGT 59.889 61.111 0.00 0.00 0.00 4.16
649 650 1.669115 CTCGTGCTGTTGGAGGGTG 60.669 63.158 0.00 0.00 0.00 4.61
650 651 2.743718 CTCGTGCTGTTGGAGGGT 59.256 61.111 0.00 0.00 0.00 4.34
651 652 2.046892 CCTCGTGCTGTTGGAGGG 60.047 66.667 0.00 0.00 42.91 4.30
652 653 0.036010 ATTCCTCGTGCTGTTGGAGG 60.036 55.000 0.00 0.00 46.99 4.30
653 654 2.271800 GTATTCCTCGTGCTGTTGGAG 58.728 52.381 0.00 0.00 0.00 3.86
654 655 1.621317 TGTATTCCTCGTGCTGTTGGA 59.379 47.619 0.00 0.00 0.00 3.53
655 656 2.093306 TGTATTCCTCGTGCTGTTGG 57.907 50.000 0.00 0.00 0.00 3.77
656 657 3.002791 ACATGTATTCCTCGTGCTGTTG 58.997 45.455 0.00 0.00 0.00 3.33
657 658 3.334583 ACATGTATTCCTCGTGCTGTT 57.665 42.857 0.00 0.00 0.00 3.16
658 659 3.447586 ACTACATGTATTCCTCGTGCTGT 59.552 43.478 5.91 0.00 0.00 4.40
659 660 4.046938 ACTACATGTATTCCTCGTGCTG 57.953 45.455 5.91 0.00 0.00 4.41
660 661 4.433615 CAACTACATGTATTCCTCGTGCT 58.566 43.478 5.91 0.00 0.00 4.40
661 662 3.001330 GCAACTACATGTATTCCTCGTGC 59.999 47.826 5.91 3.74 0.00 5.34
662 663 3.555956 GGCAACTACATGTATTCCTCGTG 59.444 47.826 5.91 0.00 0.00 4.35
663 664 3.793559 GGCAACTACATGTATTCCTCGT 58.206 45.455 5.91 0.00 0.00 4.18
755 756 6.406370 CCAGATGTGTCCAAGATGTTAGTAA 58.594 40.000 0.00 0.00 0.00 2.24
893 907 3.111741 AGTAGTATTCGGAAGGTGGGT 57.888 47.619 0.00 0.00 0.00 4.51
895 909 4.648307 AGGTTAGTAGTATTCGGAAGGTGG 59.352 45.833 0.00 0.00 0.00 4.61
898 912 7.174080 GGTACTAGGTTAGTAGTATTCGGAAGG 59.826 44.444 0.00 0.00 41.59 3.46
931 959 1.440618 TTGCAGGGGAGTTCAAGGTA 58.559 50.000 0.00 0.00 0.00 3.08
981 1010 5.695851 CCATAGCTGGCTAAATTACCTTG 57.304 43.478 6.39 0.00 35.23 3.61
1171 1246 1.952296 CATAGAAGAAGCACATGGGGC 59.048 52.381 0.00 0.00 0.00 5.80
1197 1272 9.453325 GTTTGAAAATAAGTACAATTCGTTCCA 57.547 29.630 0.00 0.00 0.00 3.53
1234 1309 5.219969 CGTTAGTCATGTACACGTGATCAAC 60.220 44.000 25.01 14.38 43.04 3.18
1235 1310 4.854839 CGTTAGTCATGTACACGTGATCAA 59.145 41.667 25.01 4.95 43.04 2.57
1236 1311 4.408694 CGTTAGTCATGTACACGTGATCA 58.591 43.478 25.01 19.69 43.04 2.92
1237 1312 3.239941 GCGTTAGTCATGTACACGTGATC 59.760 47.826 25.01 14.59 43.04 2.92
1238 1313 3.176708 GCGTTAGTCATGTACACGTGAT 58.823 45.455 25.01 9.25 43.04 3.06
1239 1314 2.587956 GCGTTAGTCATGTACACGTGA 58.412 47.619 25.01 0.00 39.38 4.35
1423 1545 2.404186 CGATGGACGGACTGACGGA 61.404 63.158 0.00 0.00 38.39 4.69
1427 1549 1.763968 AAGATCGATGGACGGACTGA 58.236 50.000 0.54 0.00 42.82 3.41
1428 1550 2.099921 AGAAAGATCGATGGACGGACTG 59.900 50.000 0.54 0.00 42.82 3.51
1433 1557 1.212616 GCCAGAAAGATCGATGGACG 58.787 55.000 0.54 0.00 44.09 4.79
1450 1613 0.802494 CGTTGGTGTCTTATGTGGCC 59.198 55.000 0.00 0.00 0.00 5.36
1477 1658 0.179936 GTCAGAGGCTTCATCCCTGG 59.820 60.000 0.00 0.00 31.41 4.45
1521 1706 1.666553 CAGGAACGCGTTGTAGCCA 60.667 57.895 31.89 0.00 0.00 4.75
1584 1769 2.688794 GCCGGAGTCGAACGTCTCT 61.689 63.158 5.05 5.58 39.00 3.10
1819 2010 9.982291 TTGCAAAAACGTCTTATATTATGAGAC 57.018 29.630 15.28 15.28 41.11 3.36
1943 3450 1.532437 GTTGCAGCAGCGCATCATATA 59.468 47.619 11.47 0.00 46.23 0.86
1947 3454 1.868987 ATTGTTGCAGCAGCGCATCA 61.869 50.000 11.47 14.84 46.23 3.07
2138 4792 2.175284 TCATCCAGGGCATTGATTAGCA 59.825 45.455 0.00 0.00 0.00 3.49
2278 4943 4.041321 GTGGGGGTTCTTAGTTCTTACACT 59.959 45.833 0.00 0.00 0.00 3.55
2438 5147 2.287308 TGGACTTGTTGCATAAACGTGC 60.287 45.455 0.00 0.00 42.10 5.34
2475 5184 6.281405 CCGTTGCTCCAGTAGACTATTTTAT 58.719 40.000 0.00 0.00 0.00 1.40
2593 5306 4.377708 ACGCGATGACTGCTGCCA 62.378 61.111 15.93 0.00 0.00 4.92
2634 5347 4.158579 CCCGCTATCTATACAGCAGAATCA 59.841 45.833 0.00 0.00 37.66 2.57
2704 5417 0.880718 GCGGATCTTTCTTAGGCGGG 60.881 60.000 0.00 0.00 0.00 6.13
2867 5581 1.956477 GGAGCTTTGAAAGTGAGGCAA 59.044 47.619 6.81 0.00 0.00 4.52
2897 5611 4.717629 TCTCTTGCACGACGGCGG 62.718 66.667 18.49 4.93 43.17 6.13
2918 5632 1.276421 CGGAGAGAGGGACACACATTT 59.724 52.381 0.00 0.00 0.00 2.32
2951 5665 2.113139 CGACAAGTTGTGCCCCCT 59.887 61.111 14.57 0.00 0.00 4.79
2998 5712 1.706866 CAGGATTGCCTCCCATATGGA 59.293 52.381 24.00 8.40 46.27 3.41
3024 5738 9.388506 TGAAGATTAAGATTTTTGTTTGGCAAA 57.611 25.926 8.93 8.93 44.52 3.68


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

AutoCloner maintained by Alex Coulton.