Multiple sequence alignment - TraesCS5B01G354200

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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 TraesCS5B01G354200 chr5B 100.000 5391 0 0 1 5391 533497695 533492305 0.000000e+00 9956.0
1 TraesCS5B01G354200 chr5B 82.089 1781 246 47 3312 5057 533573219 533571477 0.000000e+00 1454.0
2 TraesCS5B01G354200 chr5B 81.956 1646 222 46 3450 5052 533515388 533513775 0.000000e+00 1325.0
3 TraesCS5B01G354200 chr5B 81.307 1530 244 34 3435 4949 533509304 533507802 0.000000e+00 1203.0
4 TraesCS5B01G354200 chr5B 80.497 1569 264 31 3399 4952 533389722 533388181 0.000000e+00 1164.0
5 TraesCS5B01G354200 chr5B 79.603 1412 260 19 1061 2465 533525336 533523946 0.000000e+00 987.0
6 TraesCS5B01G354200 chr5B 79.510 1347 245 21 1128 2460 533575323 533573994 0.000000e+00 929.0
7 TraesCS5B01G354200 chr5B 84.639 651 90 9 1005 1651 533475557 533474913 1.810000e-179 640.0
8 TraesCS5B01G354200 chr5B 80.911 812 139 10 1659 2464 533473899 533473098 1.410000e-175 627.0
9 TraesCS5B01G354200 chr5B 83.042 401 65 2 3310 3707 533565681 533565281 1.570000e-95 361.0
10 TraesCS5B01G354200 chr5B 84.164 341 52 1 4612 4952 533382691 533382353 4.440000e-86 329.0
11 TraesCS5B01G354200 chr5B 100.000 172 0 0 5771 5942 533491925 533491754 9.610000e-83 318.0
12 TraesCS5B01G354200 chr5B 84.173 139 22 0 2726 2864 533523684 533523546 1.040000e-27 135.0
13 TraesCS5B01G354200 chr5B 81.065 169 32 0 2725 2893 533573725 533573557 1.040000e-27 135.0
14 TraesCS5B01G354200 chr5B 93.548 62 3 1 5881 5941 388261484 388261545 2.280000e-14 91.6
15 TraesCS5B01G354200 chr5B 97.674 43 1 0 683 725 533512476 533512434 2.300000e-09 75.0
16 TraesCS5B01G354200 chr5D 96.483 4492 125 14 630 5092 438592498 438588011 0.000000e+00 7389.0
17 TraesCS5B01G354200 chr5D 81.808 1814 272 43 3312 5092 438722526 438720738 0.000000e+00 1469.0
18 TraesCS5B01G354200 chr5D 81.606 1669 239 42 3401 5043 438569526 438567900 0.000000e+00 1319.0
19 TraesCS5B01G354200 chr5D 81.330 1564 248 38 3399 4946 438545231 438543696 0.000000e+00 1230.0
20 TraesCS5B01G354200 chr5D 79.462 1412 264 19 1061 2460 438724711 438723314 0.000000e+00 977.0
21 TraesCS5B01G354200 chr5D 93.440 625 36 1 1292 1911 438688950 438688326 0.000000e+00 922.0
22 TraesCS5B01G354200 chr5D 82.429 1087 145 27 3341 4406 438658612 438657551 0.000000e+00 907.0
23 TraesCS5B01G354200 chr5D 94.632 503 22 2 2300 2801 438666019 438665521 0.000000e+00 774.0
24 TraesCS5B01G354200 chr5D 80.947 929 132 25 1003 1914 438571592 438570692 0.000000e+00 693.0
25 TraesCS5B01G354200 chr5D 93.399 303 9 1 5089 5391 438587860 438587569 7.070000e-119 438.0
26 TraesCS5B01G354200 chr5D 95.635 252 11 0 2051 2302 438684149 438683898 7.170000e-109 405.0
27 TraesCS5B01G354200 chr5D 93.571 140 8 1 2909 3047 438664004 438663865 2.170000e-49 207.0
28 TraesCS5B01G354200 chr5D 92.143 140 6 1 5802 5941 438587203 438587069 6.080000e-45 193.0
29 TraesCS5B01G354200 chr5D 95.604 91 4 0 2802 2892 438664080 438663990 4.800000e-31 147.0
30 TraesCS5B01G354200 chr5D 81.366 161 30 0 2733 2893 438659137 438658977 1.340000e-26 132.0
31 TraesCS5B01G354200 chr5D 80.745 161 31 0 2733 2893 438723026 438722866 6.250000e-25 126.0
32 TraesCS5B01G354200 chr5A 92.960 2230 89 14 738 2931 554204148 554201951 0.000000e+00 3186.0
33 TraesCS5B01G354200 chr5A 92.769 2185 128 16 2931 5092 554201855 554199678 0.000000e+00 3133.0
34 TraesCS5B01G354200 chr5A 81.752 1781 254 49 3312 5057 554236324 554234580 0.000000e+00 1423.0
35 TraesCS5B01G354200 chr5A 82.824 1374 191 35 3312 4663 554218847 554217497 0.000000e+00 1188.0
36 TraesCS5B01G354200 chr5A 79.987 1564 278 29 3399 4952 554083249 554081711 0.000000e+00 1122.0
37 TraesCS5B01G354200 chr5A 79.161 1406 263 20 1069 2460 554238490 554237101 0.000000e+00 946.0
38 TraesCS5B01G354200 chr5A 79.969 1298 232 14 1078 2368 554221266 554219990 0.000000e+00 931.0
39 TraesCS5B01G354200 chr5A 84.375 608 64 15 5 593 382562594 382563189 8.640000e-158 568.0
40 TraesCS5B01G354200 chr5A 94.792 288 14 1 5104 5391 554199130 554198844 1.170000e-121 448.0
41 TraesCS5B01G354200 chr5A 79.088 636 108 18 4356 4981 554150341 554149721 1.190000e-111 414.0
42 TraesCS5B01G354200 chr5A 86.436 376 41 5 61 430 308078310 308077939 2.580000e-108 403.0
43 TraesCS5B01G354200 chr5A 82.249 169 30 0 2725 2893 554219338 554219170 4.800000e-31 147.0
44 TraesCS5B01G354200 chr5A 81.065 169 32 0 2725 2893 554236831 554236663 1.040000e-27 135.0
45 TraesCS5B01G354200 chr2A 79.131 1519 270 39 3460 4952 14711962 14710465 0.000000e+00 1005.0
46 TraesCS5B01G354200 chr2A 82.735 585 74 17 33 602 289777535 289776963 4.140000e-136 496.0
47 TraesCS5B01G354200 chr2D 78.394 1532 291 31 3464 4969 12632550 12631033 0.000000e+00 959.0
48 TraesCS5B01G354200 chr2D 85.269 577 58 20 33 595 249188021 249188584 2.400000e-158 569.0
49 TraesCS5B01G354200 chr2D 81.440 625 83 19 1 611 412279640 412280245 1.160000e-131 481.0
50 TraesCS5B01G354200 chr2D 78.349 642 92 26 5 611 438016429 438017058 7.270000e-99 372.0
51 TraesCS5B01G354200 chrUn 81.998 1161 175 28 3437 4580 63291989 63290846 0.000000e+00 955.0
52 TraesCS5B01G354200 chrUn 85.799 507 62 9 4078 4580 299954514 299954014 4.080000e-146 529.0
53 TraesCS5B01G354200 chrUn 85.673 342 48 1 4612 4952 63290844 63290503 5.660000e-95 359.0
54 TraesCS5B01G354200 chrUn 85.673 342 48 1 4612 4952 299954012 299953671 5.660000e-95 359.0
55 TraesCS5B01G354200 chr2B 77.601 1567 293 49 3452 4989 65047444 65048981 0.000000e+00 896.0
56 TraesCS5B01G354200 chr2B 96.970 33 1 0 2258 2290 706919407 706919375 8.320000e-04 56.5
57 TraesCS5B01G354200 chr6B 85.386 609 64 11 5 611 617184 617769 5.090000e-170 608.0
58 TraesCS5B01G354200 chr6B 84.000 625 75 17 1 611 585911240 585910627 1.440000e-160 577.0
59 TraesCS5B01G354200 chr6B 83.826 575 56 19 53 611 439357830 439357277 4.110000e-141 512.0
60 TraesCS5B01G354200 chr7D 84.794 559 64 15 58 603 167835036 167835586 5.240000e-150 542.0
61 TraesCS5B01G354200 chr1B 84.248 565 64 18 61 611 597400363 597399810 1.470000e-145 527.0
62 TraesCS5B01G354200 chr1B 82.270 564 77 16 61 611 314560882 314560329 3.240000e-127 466.0
63 TraesCS5B01G354200 chr6D 88.594 377 33 5 60 430 409779902 409780274 3.270000e-122 449.0
64 TraesCS5B01G354200 chr1D 82.979 188 12 5 1 188 438147882 438148049 1.030000e-32 152.0
65 TraesCS5B01G354200 chr7A 89.189 111 9 1 501 611 694052978 694053085 1.040000e-27 135.0


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 TraesCS5B01G354200 chr5B 533491754 533497695 5941 True 5137.000000 9956 100.000000 1 5942 2 chr5B.!!$R5 5941
1 TraesCS5B01G354200 chr5B 533388181 533389722 1541 True 1164.000000 1164 80.497000 3399 4952 1 chr5B.!!$R2 1553
2 TraesCS5B01G354200 chr5B 533507802 533515388 7586 True 867.666667 1325 86.979000 683 5052 3 chr5B.!!$R6 4369
3 TraesCS5B01G354200 chr5B 533571477 533575323 3846 True 839.333333 1454 80.888000 1128 5057 3 chr5B.!!$R8 3929
4 TraesCS5B01G354200 chr5B 533473098 533475557 2459 True 633.500000 640 82.775000 1005 2464 2 chr5B.!!$R4 1459
5 TraesCS5B01G354200 chr5B 533523546 533525336 1790 True 561.000000 987 81.888000 1061 2864 2 chr5B.!!$R7 1803
6 TraesCS5B01G354200 chr5D 438587069 438592498 5429 True 2673.333333 7389 94.008333 630 5941 3 chr5D.!!$R5 5311
7 TraesCS5B01G354200 chr5D 438543696 438545231 1535 True 1230.000000 1230 81.330000 3399 4946 1 chr5D.!!$R1 1547
8 TraesCS5B01G354200 chr5D 438567900 438571592 3692 True 1006.000000 1319 81.276500 1003 5043 2 chr5D.!!$R4 4040
9 TraesCS5B01G354200 chr5D 438688326 438688950 624 True 922.000000 922 93.440000 1292 1911 1 chr5D.!!$R3 619
10 TraesCS5B01G354200 chr5D 438720738 438724711 3973 True 857.333333 1469 80.671667 1061 5092 3 chr5D.!!$R8 4031
11 TraesCS5B01G354200 chr5D 438657551 438659137 1586 True 519.500000 907 81.897500 2733 4406 2 chr5D.!!$R6 1673
12 TraesCS5B01G354200 chr5D 438663865 438666019 2154 True 376.000000 774 94.602333 2300 3047 3 chr5D.!!$R7 747
13 TraesCS5B01G354200 chr5A 554198844 554204148 5304 True 2255.666667 3186 93.507000 738 5391 3 chr5A.!!$R4 4653
14 TraesCS5B01G354200 chr5A 554081711 554083249 1538 True 1122.000000 1122 79.987000 3399 4952 1 chr5A.!!$R2 1553
15 TraesCS5B01G354200 chr5A 554234580 554238490 3910 True 834.666667 1423 80.659333 1069 5057 3 chr5A.!!$R6 3988
16 TraesCS5B01G354200 chr5A 554217497 554221266 3769 True 755.333333 1188 81.680667 1078 4663 3 chr5A.!!$R5 3585
17 TraesCS5B01G354200 chr5A 382562594 382563189 595 False 568.000000 568 84.375000 5 593 1 chr5A.!!$F1 588
18 TraesCS5B01G354200 chr5A 554149721 554150341 620 True 414.000000 414 79.088000 4356 4981 1 chr5A.!!$R3 625
19 TraesCS5B01G354200 chr2A 14710465 14711962 1497 True 1005.000000 1005 79.131000 3460 4952 1 chr2A.!!$R1 1492
20 TraesCS5B01G354200 chr2A 289776963 289777535 572 True 496.000000 496 82.735000 33 602 1 chr2A.!!$R2 569
21 TraesCS5B01G354200 chr2D 12631033 12632550 1517 True 959.000000 959 78.394000 3464 4969 1 chr2D.!!$R1 1505
22 TraesCS5B01G354200 chr2D 249188021 249188584 563 False 569.000000 569 85.269000 33 595 1 chr2D.!!$F1 562
23 TraesCS5B01G354200 chr2D 412279640 412280245 605 False 481.000000 481 81.440000 1 611 1 chr2D.!!$F2 610
24 TraesCS5B01G354200 chr2D 438016429 438017058 629 False 372.000000 372 78.349000 5 611 1 chr2D.!!$F3 606
25 TraesCS5B01G354200 chrUn 63290503 63291989 1486 True 657.000000 955 83.835500 3437 4952 2 chrUn.!!$R1 1515
26 TraesCS5B01G354200 chrUn 299953671 299954514 843 True 444.000000 529 85.736000 4078 4952 2 chrUn.!!$R2 874
27 TraesCS5B01G354200 chr2B 65047444 65048981 1537 False 896.000000 896 77.601000 3452 4989 1 chr2B.!!$F1 1537
28 TraesCS5B01G354200 chr6B 617184 617769 585 False 608.000000 608 85.386000 5 611 1 chr6B.!!$F1 606
29 TraesCS5B01G354200 chr6B 585910627 585911240 613 True 577.000000 577 84.000000 1 611 1 chr6B.!!$R2 610
30 TraesCS5B01G354200 chr6B 439357277 439357830 553 True 512.000000 512 83.826000 53 611 1 chr6B.!!$R1 558
31 TraesCS5B01G354200 chr7D 167835036 167835586 550 False 542.000000 542 84.794000 58 603 1 chr7D.!!$F1 545
32 TraesCS5B01G354200 chr1B 597399810 597400363 553 True 527.000000 527 84.248000 61 611 1 chr1B.!!$R2 550
33 TraesCS5B01G354200 chr1B 314560329 314560882 553 True 466.000000 466 82.270000 61 611 1 chr1B.!!$R1 550

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
672 797 0.034574 ACAATTAGGGGCATGACGCA 60.035 50.000 19.07 0.0 45.17 5.24 F
1383 4303 1.213013 CTCTCCACCAACGGTCTCG 59.787 63.158 0.00 0.0 43.02 4.04 F
1998 5934 1.228124 CCTTTGGAAGTGGCCGTCA 60.228 57.895 0.00 0.0 0.00 4.35 F
2344 6290 1.205893 GGTCTGGAGGAGATGTGACAC 59.794 57.143 0.00 0.0 31.63 3.67 F
3568 9684 1.698874 AGGAAACCCTCCCCATGATT 58.301 50.000 0.00 0.0 46.81 2.57 F
3908 10055 2.106338 TCTTGGATGTTGCAGTGAGGAA 59.894 45.455 0.00 0.0 0.00 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1564 4487 0.036732 GGGAGGAATGTGTCAGTGCA 59.963 55.000 0.0 0.0 0.00 4.57 R
2190 6129 0.394352 GTGACTTCATCCCCGGCAAT 60.394 55.000 0.0 0.0 0.00 3.56 R
3249 9183 1.133761 ACCTAGTATCTCCGAGCAGCA 60.134 52.381 0.0 0.0 0.00 4.41 R
3871 10016 2.100749 CCAAGAAGCCGAACCAAGTTTT 59.899 45.455 0.0 0.0 0.00 2.43 R
4663 10904 1.621992 AGCAGTTCCTCAGTCTTCGA 58.378 50.000 0.0 0.0 0.00 3.71 R
5061 11331 1.632920 TGGGCAACAGGTGATACATCA 59.367 47.619 0.0 0.0 39.74 3.07 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
100 103 0.533491 TTGTTGCTACTACCGGCGAT 59.467 50.000 9.30 0.00 0.00 4.58
101 104 0.533491 TGTTGCTACTACCGGCGATT 59.467 50.000 9.30 0.00 0.00 3.34
102 105 1.066716 TGTTGCTACTACCGGCGATTT 60.067 47.619 9.30 0.00 0.00 2.17
103 106 2.004733 GTTGCTACTACCGGCGATTTT 58.995 47.619 9.30 0.00 0.00 1.82
140 143 0.886490 CAAGGTGGAGCTGCGAACTT 60.886 55.000 0.00 1.39 31.87 2.66
170 183 0.456482 CGATGGCGATTTGCTGCAAA 60.456 50.000 27.78 27.78 45.43 3.68
173 186 2.088178 GGCGATTTGCTGCAAACGG 61.088 57.895 31.05 25.28 45.43 4.44
183 196 1.566018 CTGCAAACGGAGTCGGGTTC 61.566 60.000 0.00 0.00 45.00 3.62
248 264 1.827399 ATTCGCTGGTGGGAGTCGTT 61.827 55.000 0.00 0.00 36.50 3.85
273 289 2.708514 CAATTCCGTTTAGCGAGCATG 58.291 47.619 0.00 0.00 44.77 4.06
441 538 3.702048 CGAGGAAGGCCACCGGAA 61.702 66.667 9.46 0.00 36.29 4.30
496 613 3.621394 GCGAGACGGCGAAGATGC 61.621 66.667 16.62 7.04 0.00 3.91
497 614 2.202610 CGAGACGGCGAAGATGCA 60.203 61.111 16.62 0.00 36.28 3.96
611 736 3.733960 GCGACCGGCCCAAACTTC 61.734 66.667 0.00 0.00 34.80 3.01
613 738 3.053896 GACCGGCCCAAACTTCCG 61.054 66.667 0.00 0.00 42.58 4.30
614 739 3.540367 GACCGGCCCAAACTTCCGA 62.540 63.158 0.00 0.00 45.53 4.55
616 741 3.419759 CGGCCCAAACTTCCGACG 61.420 66.667 0.00 0.00 45.53 5.12
617 742 3.733960 GGCCCAAACTTCCGACGC 61.734 66.667 0.00 0.00 0.00 5.19
619 744 2.966309 GCCCAAACTTCCGACGCAG 61.966 63.158 0.00 0.00 0.00 5.18
620 745 1.301401 CCCAAACTTCCGACGCAGA 60.301 57.895 0.00 0.00 0.00 4.26
622 747 0.721718 CCAAACTTCCGACGCAGATC 59.278 55.000 0.00 0.00 0.00 2.75
623 748 1.428448 CAAACTTCCGACGCAGATCA 58.572 50.000 0.00 0.00 0.00 2.92
624 749 1.126846 CAAACTTCCGACGCAGATCAC 59.873 52.381 0.00 0.00 0.00 3.06
625 750 0.603569 AACTTCCGACGCAGATCACT 59.396 50.000 0.00 0.00 0.00 3.41
627 752 0.994995 CTTCCGACGCAGATCACTTG 59.005 55.000 0.00 0.00 0.00 3.16
628 753 0.317160 TTCCGACGCAGATCACTTGT 59.683 50.000 0.00 0.00 0.00 3.16
649 774 9.750125 ACTTGTGGATTTTTCAAAAGAGATTAC 57.250 29.630 0.00 0.00 34.12 1.89
664 789 9.794719 AAAAGAGATTACTATACAATTAGGGGC 57.205 33.333 0.00 0.00 0.00 5.80
668 793 8.449423 AGATTACTATACAATTAGGGGCATGA 57.551 34.615 0.00 0.00 0.00 3.07
671 796 1.961793 TACAATTAGGGGCATGACGC 58.038 50.000 7.72 7.72 41.28 5.19
672 797 0.034574 ACAATTAGGGGCATGACGCA 60.035 50.000 19.07 0.00 45.17 5.24
749 2981 6.697395 TGTATACTGTCACTGCTACAATTGT 58.303 36.000 16.68 16.68 0.00 2.71
752 2984 9.314321 GTATACTGTCACTGCTACAATTGTAAT 57.686 33.333 18.55 7.75 0.00 1.89
808 3040 6.578944 TGTTGATACACAATAGCTATCCGTT 58.421 36.000 6.72 2.44 40.76 4.44
813 3045 4.110482 ACACAATAGCTATCCGTTCGTTC 58.890 43.478 6.72 0.00 0.00 3.95
906 3138 2.368439 GTGGGCAGCTGATATGTCAAA 58.632 47.619 20.43 0.00 33.05 2.69
942 3174 5.073144 TGGAAAGTTGGAACTCAATCTACCT 59.927 40.000 0.00 0.00 38.57 3.08
998 3230 1.434555 TCCGCGATCAAACATTCGTT 58.565 45.000 8.23 0.00 37.66 3.85
1317 4237 4.101448 GGCATCCCCGTGCTCACT 62.101 66.667 0.00 0.00 44.45 3.41
1383 4303 1.213013 CTCTCCACCAACGGTCTCG 59.787 63.158 0.00 0.00 43.02 4.04
1455 4378 2.649531 TCCTTTGGACAACGACCAAT 57.350 45.000 0.00 0.00 45.09 3.16
1564 4487 2.210013 TGGCAGAGCTTCGACCACT 61.210 57.895 0.00 0.00 0.00 4.00
1836 5772 7.962918 GCAACTAACGTCAGTGATTTTATCATT 59.037 33.333 0.00 0.00 42.04 2.57
1998 5934 1.228124 CCTTTGGAAGTGGCCGTCA 60.228 57.895 0.00 0.00 0.00 4.35
2344 6290 1.205893 GGTCTGGAGGAGATGTGACAC 59.794 57.143 0.00 0.00 31.63 3.67
2479 6725 2.756760 CAACTTCCCCATCATTGTCTGG 59.243 50.000 2.27 2.27 0.00 3.86
2628 6936 6.598064 CGTCCCTTTTGTAGTTCCATAATCTT 59.402 38.462 0.00 0.00 0.00 2.40
2869 8630 5.447624 AATTCAAAGGTACGTTTCCTTGG 57.552 39.130 20.20 18.05 43.50 3.61
3059 8984 4.188462 TCCGGTGCTTACATACAATCTTG 58.812 43.478 0.00 0.00 0.00 3.02
3126 9051 9.524496 CATATTTATCTCTCCCCATTTCAATCA 57.476 33.333 0.00 0.00 0.00 2.57
3249 9183 7.350744 TGCTGCTTTCCATATCATTACAATT 57.649 32.000 0.00 0.00 0.00 2.32
3524 9640 8.938906 TCAAAATAAGATAAGTTTGGTCGGTAC 58.061 33.333 0.00 0.00 32.91 3.34
3568 9684 1.698874 AGGAAACCCTCCCCATGATT 58.301 50.000 0.00 0.00 46.81 2.57
3908 10055 2.106338 TCTTGGATGTTGCAGTGAGGAA 59.894 45.455 0.00 0.00 0.00 3.36
4663 10904 6.066690 CAGTCATGGAATATGTGGAAGGAAT 58.933 40.000 0.00 0.00 0.00 3.01
4856 11115 4.077184 CCCCGCCTACTTCGCACA 62.077 66.667 0.00 0.00 0.00 4.57
5098 11916 2.173569 GCCCAGGAGTCATTAAGGTGAT 59.826 50.000 0.00 0.00 0.00 3.06
5200 12018 1.003839 TGCACGGTCCAGAATCCAC 60.004 57.895 0.00 0.00 0.00 4.02
5211 12029 2.614057 CCAGAATCCACGCTTTCATACC 59.386 50.000 0.00 0.00 0.00 2.73
5225 12043 5.220796 GCTTTCATACCAAATTAGGACGACC 60.221 44.000 0.00 0.00 0.00 4.79
5281 12099 6.670695 AACATCTTTTAAACTCAATGGCCT 57.329 33.333 3.32 0.00 0.00 5.19
5361 12179 3.501062 GGTAGGAAGTCCCTTTTGTTTCG 59.499 47.826 0.00 0.00 44.85 3.46
5839 12657 6.398918 ACTAATATTACCTTCGCATAGGCAG 58.601 40.000 0.00 0.00 41.24 4.85
5856 12674 4.344978 AGGCAGACTTGATGTACACTAGA 58.655 43.478 0.00 0.00 0.00 2.43
5875 12693 9.877178 ACACTAGAGTTCGATCATTAATCTTTT 57.123 29.630 0.00 0.00 31.68 2.27
5904 12722 4.060900 AGAGTACACATGTGAAGTGCTTG 58.939 43.478 31.94 2.53 40.59 4.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
48 49 0.527113 CAGCAAAATCGCCATCACCA 59.473 50.000 0.00 0.00 0.00 4.17
51 52 0.602060 TTGCAGCAAAATCGCCATCA 59.398 45.000 4.99 0.00 0.00 3.07
170 183 1.303888 TAGCAGAACCCGACTCCGT 60.304 57.895 0.00 0.00 0.00 4.69
173 186 0.179169 GTCGTAGCAGAACCCGACTC 60.179 60.000 0.00 0.00 44.55 3.36
183 196 2.579787 CTTCGCCGGTCGTAGCAG 60.580 66.667 16.00 6.65 39.67 4.24
232 248 2.738521 CAACGACTCCCACCAGCG 60.739 66.667 0.00 0.00 0.00 5.18
248 264 0.440758 CGCTAAACGGAATTGCGTCA 59.559 50.000 25.43 14.92 41.45 4.35
273 289 2.892425 CGCCATCCCTCGCTGTTC 60.892 66.667 0.00 0.00 0.00 3.18
405 480 2.608368 CACCGGTCCCCACCCTTA 60.608 66.667 2.59 0.00 40.01 2.69
406 481 4.585216 TCACCGGTCCCCACCCTT 62.585 66.667 2.59 0.00 40.01 3.95
421 496 3.691342 CGGTGGCCTTCCTCGTCA 61.691 66.667 3.32 0.00 0.00 4.35
484 601 4.435436 TCGCTGCATCTTCGCCGT 62.435 61.111 0.00 0.00 0.00 5.68
485 602 3.624300 CTCGCTGCATCTTCGCCG 61.624 66.667 0.00 0.00 0.00 6.46
486 603 3.934684 GCTCGCTGCATCTTCGCC 61.935 66.667 0.00 0.00 42.31 5.54
487 604 2.889503 AGCTCGCTGCATCTTCGC 60.890 61.111 0.00 0.00 45.94 4.70
488 605 3.004283 CAGCTCGCTGCATCTTCG 58.996 61.111 5.91 0.00 45.94 3.79
611 736 1.354337 CCACAAGTGATCTGCGTCGG 61.354 60.000 0.94 0.00 0.00 4.79
613 738 2.015736 ATCCACAAGTGATCTGCGTC 57.984 50.000 0.94 0.00 0.00 5.19
614 739 2.479566 AATCCACAAGTGATCTGCGT 57.520 45.000 0.94 0.00 0.00 5.24
616 741 5.125100 TGAAAAATCCACAAGTGATCTGC 57.875 39.130 0.94 0.00 0.00 4.26
617 742 7.922278 TCTTTTGAAAAATCCACAAGTGATCTG 59.078 33.333 0.94 0.00 0.00 2.90
619 744 8.137437 TCTCTTTTGAAAAATCCACAAGTGATC 58.863 33.333 0.94 0.00 0.00 2.92
620 745 8.010733 TCTCTTTTGAAAAATCCACAAGTGAT 57.989 30.769 0.94 0.00 0.00 3.06
622 747 8.652810 AATCTCTTTTGAAAAATCCACAAGTG 57.347 30.769 0.00 0.00 0.00 3.16
623 748 9.750125 GTAATCTCTTTTGAAAAATCCACAAGT 57.250 29.630 0.00 0.00 0.00 3.16
624 749 9.971922 AGTAATCTCTTTTGAAAAATCCACAAG 57.028 29.630 0.00 0.00 0.00 3.16
649 774 3.684788 GCGTCATGCCCCTAATTGTATAG 59.315 47.826 0.00 0.00 37.76 1.31
657 782 1.128200 ATACTGCGTCATGCCCCTAA 58.872 50.000 0.00 0.00 45.60 2.69
659 784 0.681733 CTATACTGCGTCATGCCCCT 59.318 55.000 0.00 0.00 45.60 4.79
660 785 0.320771 CCTATACTGCGTCATGCCCC 60.321 60.000 0.00 0.00 45.60 5.80
661 786 0.951040 GCCTATACTGCGTCATGCCC 60.951 60.000 0.00 0.00 45.60 5.36
664 789 2.223805 TGTCAGCCTATACTGCGTCATG 60.224 50.000 0.00 0.00 37.59 3.07
668 793 0.100682 CGTGTCAGCCTATACTGCGT 59.899 55.000 0.00 0.00 37.59 5.24
671 796 3.380637 AGGTAACGTGTCAGCCTATACTG 59.619 47.826 0.00 0.00 46.39 2.74
672 797 3.380637 CAGGTAACGTGTCAGCCTATACT 59.619 47.826 0.00 0.00 46.39 2.12
674 799 3.359033 ACAGGTAACGTGTCAGCCTATA 58.641 45.455 0.00 0.00 46.39 1.31
675 800 2.176889 ACAGGTAACGTGTCAGCCTAT 58.823 47.619 0.00 0.00 46.39 2.57
676 801 1.624336 ACAGGTAACGTGTCAGCCTA 58.376 50.000 0.00 0.00 46.39 3.93
677 802 1.624336 TACAGGTAACGTGTCAGCCT 58.376 50.000 0.00 0.00 46.39 4.58
678 803 2.667473 ATACAGGTAACGTGTCAGCC 57.333 50.000 0.00 0.00 46.39 4.85
679 804 6.657836 ATTTTATACAGGTAACGTGTCAGC 57.342 37.500 0.00 0.00 46.39 4.26
680 805 8.688184 CGATATTTTATACAGGTAACGTGTCAG 58.312 37.037 0.00 0.00 46.39 3.51
681 806 7.167968 GCGATATTTTATACAGGTAACGTGTCA 59.832 37.037 0.00 0.00 46.39 3.58
682 807 7.167968 TGCGATATTTTATACAGGTAACGTGTC 59.832 37.037 0.00 0.00 46.39 3.67
683 808 6.979817 TGCGATATTTTATACAGGTAACGTGT 59.020 34.615 0.00 0.00 46.39 4.49
684 809 7.397512 TGCGATATTTTATACAGGTAACGTG 57.602 36.000 0.00 0.00 46.39 4.49
685 810 8.422973 TTTGCGATATTTTATACAGGTAACGT 57.577 30.769 0.00 0.00 46.39 3.99
686 811 8.757789 TCTTTGCGATATTTTATACAGGTAACG 58.242 33.333 0.00 0.00 46.39 3.18
749 2981 4.593206 ACCTTCACTCCTGACTGTTCATTA 59.407 41.667 0.00 0.00 0.00 1.90
752 2984 2.103094 CACCTTCACTCCTGACTGTTCA 59.897 50.000 0.00 0.00 0.00 3.18
808 3040 6.871492 TGACTGAAACATTAAGCTATGAACGA 59.129 34.615 3.45 0.00 0.00 3.85
890 3122 5.746307 TCAAGATTTGACATATCAGCTGC 57.254 39.130 9.47 0.00 35.83 5.25
906 3138 3.891366 CCAACTTTCCAAGTGGTCAAGAT 59.109 43.478 14.98 4.76 41.91 2.40
931 3163 6.881065 TGTTCTTGGAATTCAGGTAGATTGAG 59.119 38.462 7.93 0.00 0.00 3.02
942 3174 6.839124 ATAATGCAGTGTTCTTGGAATTCA 57.161 33.333 7.93 0.00 0.00 2.57
1210 4130 2.034878 TCCACCATCATCGGAGAGAAG 58.965 52.381 0.00 0.00 43.63 2.85
1212 4132 2.388526 ATCCACCATCATCGGAGAGA 57.611 50.000 0.00 0.00 43.63 3.10
1383 4303 3.265791 CAGATTAGAGGTGTTGGTGAGC 58.734 50.000 0.00 0.00 0.00 4.26
1564 4487 0.036732 GGGAGGAATGTGTCAGTGCA 59.963 55.000 0.00 0.00 0.00 4.57
1836 5772 2.552599 TGTCGACAAAGGCCACATAA 57.447 45.000 17.62 0.00 0.00 1.90
1998 5934 0.321564 TGTAGCGGTTGCATTCAGCT 60.322 50.000 17.34 17.34 46.23 4.24
2072 6008 1.732405 CGTCGAGACACTTGCATGCTA 60.732 52.381 20.33 10.88 0.00 3.49
2190 6129 0.394352 GTGACTTCATCCCCGGCAAT 60.394 55.000 0.00 0.00 0.00 3.56
2344 6290 0.452987 CCATTCCACACCAAGCATCG 59.547 55.000 0.00 0.00 0.00 3.84
2479 6725 7.235430 ACGATAGACAAATAACAAAGCTAGC 57.765 36.000 6.62 6.62 41.38 3.42
2524 6770 5.932303 TGAAACTAGAAGCACGAAAGCTATT 59.068 36.000 0.00 0.00 45.89 1.73
2525 6771 5.479306 TGAAACTAGAAGCACGAAAGCTAT 58.521 37.500 0.00 0.00 45.89 2.97
2526 6772 4.878439 TGAAACTAGAAGCACGAAAGCTA 58.122 39.130 0.00 0.00 45.89 3.32
2531 6777 4.870426 GGATGATGAAACTAGAAGCACGAA 59.130 41.667 0.00 0.00 0.00 3.85
2532 6778 4.081697 TGGATGATGAAACTAGAAGCACGA 60.082 41.667 0.00 0.00 0.00 4.35
2534 6780 6.690194 AATGGATGATGAAACTAGAAGCAC 57.310 37.500 0.00 0.00 0.00 4.40
2628 6936 9.747898 ATGTAACAACCATCCAACTTAAAGATA 57.252 29.630 0.00 0.00 0.00 1.98
2792 7113 6.826741 ACCAAAACACTAGAGCTTAAAACTGA 59.173 34.615 0.00 0.00 0.00 3.41
2869 8630 6.856135 ATATAACGTTTTACTTAGCAGGGC 57.144 37.500 5.91 0.00 0.00 5.19
2966 8880 4.081420 ACTTGATCTCGGTTTATGCTCAGT 60.081 41.667 0.00 0.00 0.00 3.41
3059 8984 6.985059 GTGGACTCCATCTTATTTGGTAGTAC 59.015 42.308 0.00 0.00 35.28 2.73
3249 9183 1.133761 ACCTAGTATCTCCGAGCAGCA 60.134 52.381 0.00 0.00 0.00 4.41
3328 9436 8.088463 TCATGGAAGCAAATTAAATAACCCAT 57.912 30.769 0.00 0.00 0.00 4.00
3426 9537 5.428253 TCCCTTCTAATAAGCACATCACAC 58.572 41.667 0.00 0.00 0.00 3.82
3519 9635 7.095774 CCAAATTCATTAGAGGTATTCGTACCG 60.096 40.741 0.00 0.00 44.64 4.02
3524 9640 8.662781 TTCTCCAAATTCATTAGAGGTATTCG 57.337 34.615 0.00 0.00 0.00 3.34
3568 9684 9.540538 TTCTAATCTTACAAATGGAAATTCCCA 57.459 29.630 9.87 0.00 41.05 4.37
3871 10016 2.100749 CCAAGAAGCCGAACCAAGTTTT 59.899 45.455 0.00 0.00 0.00 2.43
4663 10904 1.621992 AGCAGTTCCTCAGTCTTCGA 58.378 50.000 0.00 0.00 0.00 3.71
5019 11289 5.887598 ACATCACTATTTTGCTGAGCCATAA 59.112 36.000 0.23 0.00 0.00 1.90
5061 11331 1.632920 TGGGCAACAGGTGATACATCA 59.367 47.619 0.00 0.00 39.74 3.07
5098 11916 8.210946 CCTAATCACTTGTATCCAATGTAAGGA 58.789 37.037 0.00 0.00 39.97 3.36
5200 12018 4.569162 TCGTCCTAATTTGGTATGAAAGCG 59.431 41.667 5.81 0.95 0.00 4.68
5211 12029 6.007936 TGTCAAATTGGTCGTCCTAATTTG 57.992 37.500 25.03 25.03 43.46 2.32
5361 12179 5.463724 AGCTAAAATTATACGCAGCAGAGTC 59.536 40.000 0.00 0.00 0.00 3.36
5790 12608 9.148104 GTTACCTTGTGTCGTAATTCTAGAAAT 57.852 33.333 9.71 3.43 0.00 2.17
5791 12609 8.362639 AGTTACCTTGTGTCGTAATTCTAGAAA 58.637 33.333 9.71 0.00 0.00 2.52
5792 12610 7.889469 AGTTACCTTGTGTCGTAATTCTAGAA 58.111 34.615 7.82 7.82 0.00 2.10
5793 12611 7.458409 AGTTACCTTGTGTCGTAATTCTAGA 57.542 36.000 0.00 0.00 0.00 2.43
5794 12612 9.798994 ATTAGTTACCTTGTGTCGTAATTCTAG 57.201 33.333 0.00 0.00 0.00 2.43
5800 12618 9.801873 GGTAATATTAGTTACCTTGTGTCGTAA 57.198 33.333 8.24 0.00 46.53 3.18
5833 12651 5.506708 TCTAGTGTACATCAAGTCTGCCTA 58.493 41.667 0.00 0.00 0.00 3.93
5839 12657 6.179504 TCGAACTCTAGTGTACATCAAGTC 57.820 41.667 0.00 0.00 0.00 3.01
5875 12693 9.529325 GCACTTCACATGTGTACTCTAATATAA 57.471 33.333 24.63 6.85 37.70 0.98
5876 12694 8.914011 AGCACTTCACATGTGTACTCTAATATA 58.086 33.333 24.63 0.00 37.70 0.86
5877 12695 7.786030 AGCACTTCACATGTGTACTCTAATAT 58.214 34.615 24.63 0.61 37.70 1.28
5878 12696 7.170393 AGCACTTCACATGTGTACTCTAATA 57.830 36.000 24.63 0.00 37.70 0.98
5879 12697 6.042638 AGCACTTCACATGTGTACTCTAAT 57.957 37.500 24.63 3.91 37.70 1.73


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

AutoCloner maintained by Alex Coulton.