Multiple sequence alignment - TraesCS4A01G393100

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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 TraesCS4A01G393100 chr4A 100.000 6288 0 0 1 6288 668746192 668752479 0.000000e+00 11612.0
1 TraesCS4A01G393100 chr4A 97.027 3936 104 8 1561 5488 669582096 669578166 0.000000e+00 6608.0
2 TraesCS4A01G393100 chr4A 92.849 853 36 9 709 1543 669583069 669582224 0.000000e+00 1214.0
3 TraesCS4A01G393100 chr4A 90.463 734 32 6 1 697 669584769 669584037 0.000000e+00 933.0
4 TraesCS4A01G393100 chr4A 95.544 561 25 0 5728 6288 49932413 49931853 0.000000e+00 898.0
5 TraesCS4A01G393100 chr4A 94.215 242 11 3 5488 5727 669558054 669557814 3.580000e-97 366.0
6 TraesCS4A01G393100 chr7D 96.943 3926 102 9 1561 5478 53782004 53785919 0.000000e+00 6569.0
7 TraesCS4A01G393100 chr7D 92.373 472 26 5 809 1274 53780852 53781319 0.000000e+00 664.0
8 TraesCS4A01G393100 chr7D 85.385 260 19 6 1319 1562 53781673 53781929 1.050000e-62 252.0
9 TraesCS4A01G393100 chr7D 91.463 82 6 1 442 522 535881301 535881382 1.850000e-20 111.0
10 TraesCS4A01G393100 chr7D 100.000 33 0 0 323 355 21702259 21702291 1.890000e-05 62.1
11 TraesCS4A01G393100 chr5D 90.273 3958 280 55 1560 5478 508578796 508574905 0.000000e+00 5079.0
12 TraesCS4A01G393100 chr5D 85.095 1939 207 47 1560 3471 508613885 508615768 0.000000e+00 1905.0
13 TraesCS4A01G393100 chr5D 86.335 805 76 19 4505 5301 508616993 508617771 0.000000e+00 846.0
14 TraesCS4A01G393100 chr5D 87.745 408 45 4 987 1391 508579514 508579109 7.380000e-129 472.0
15 TraesCS4A01G393100 chr5D 79.710 483 76 17 963 1435 508613164 508613634 4.700000e-86 329.0
16 TraesCS4A01G393100 chr5D 86.719 256 22 8 5478 5727 508574956 508574707 2.230000e-69 274.0
17 TraesCS4A01G393100 chr7A 96.356 2964 85 10 2522 5478 57212783 57215730 0.000000e+00 4854.0
18 TraesCS4A01G393100 chr7A 96.552 957 32 1 1560 2516 57211687 57212642 0.000000e+00 1583.0
19 TraesCS4A01G393100 chr7A 91.115 619 36 8 957 1562 57211001 57211613 0.000000e+00 821.0
20 TraesCS4A01G393100 chr7A 92.248 258 14 5 5472 5726 57215673 57215927 1.670000e-95 361.0
21 TraesCS4A01G393100 chr7A 96.552 58 2 0 1 58 57210739 57210796 5.190000e-16 97.1
22 TraesCS4A01G393100 chr7A 88.750 80 8 1 442 520 424628859 424628938 5.190000e-16 97.1
23 TraesCS4A01G393100 chr7A 87.838 74 3 3 315 382 3536418 3536491 1.450000e-11 82.4
24 TraesCS4A01G393100 chr7A 100.000 32 0 0 323 354 686110273 686110304 6.810000e-05 60.2
25 TraesCS4A01G393100 chr5B 89.510 2040 173 26 1560 3578 638668358 638670377 0.000000e+00 2543.0
26 TraesCS4A01G393100 chr5B 88.625 1855 158 33 3658 5478 638670391 638672226 0.000000e+00 2207.0
27 TraesCS4A01G393100 chr5B 86.829 987 105 11 1560 2540 638646638 638645671 0.000000e+00 1079.0
28 TraesCS4A01G393100 chr5B 85.080 878 101 20 2624 3485 638645507 638644644 0.000000e+00 869.0
29 TraesCS4A01G393100 chr5B 82.897 994 116 28 4364 5344 638643636 638642684 0.000000e+00 845.0
30 TraesCS4A01G393100 chr5B 89.881 504 47 4 3857 4358 638644219 638643718 0.000000e+00 645.0
31 TraesCS4A01G393100 chr5B 85.749 407 42 9 987 1383 638667702 638668102 3.510000e-112 416.0
32 TraesCS4A01G393100 chr5B 81.292 449 59 19 1000 1435 638647308 638646872 2.170000e-89 340.0
33 TraesCS4A01G393100 chr5B 88.750 80 8 1 442 520 477556814 477556735 5.190000e-16 97.1
34 TraesCS4A01G393100 chr5A 87.874 2037 198 31 1560 3578 635938230 635936225 0.000000e+00 2348.0
35 TraesCS4A01G393100 chr5A 88.028 1846 182 17 3648 5478 635936212 635934391 0.000000e+00 2148.0
36 TraesCS4A01G393100 chr5A 86.257 1368 144 21 1560 2903 635948364 635949711 0.000000e+00 1445.0
37 TraesCS4A01G393100 chr5A 82.149 1154 130 42 4364 5478 635951104 635952220 0.000000e+00 920.0
38 TraesCS4A01G393100 chr5A 87.333 750 79 11 3617 4355 635950275 635951019 0.000000e+00 845.0
39 TraesCS4A01G393100 chr5A 85.844 551 55 11 2939 3485 635949720 635950251 1.180000e-156 564.0
40 TraesCS4A01G393100 chr5A 88.667 450 42 5 945 1391 635938921 635938478 1.990000e-149 540.0
41 TraesCS4A01G393100 chr3B 87.031 987 112 9 1560 2540 171173221 171174197 0.000000e+00 1099.0
42 TraesCS4A01G393100 chr3B 85.119 840 85 19 4415 5243 171177527 171178337 0.000000e+00 822.0
43 TraesCS4A01G393100 chr3B 86.649 749 83 10 3617 4355 171175138 171175879 0.000000e+00 813.0
44 TraesCS4A01G393100 chr3B 79.012 486 73 22 963 1435 171167077 171167546 7.920000e-79 305.0
45 TraesCS4A01G393100 chr3B 95.122 41 1 1 315 354 466062379 466062339 5.260000e-06 63.9
46 TraesCS4A01G393100 chrUn 97.880 566 12 0 5723 6288 16378113 16377548 0.000000e+00 979.0
47 TraesCS4A01G393100 chrUn 90.973 565 47 2 5724 6288 176732833 176733393 0.000000e+00 758.0
48 TraesCS4A01G393100 chrUn 90.796 565 48 2 5724 6288 176698815 176699375 0.000000e+00 752.0
49 TraesCS4A01G393100 chr6A 96.115 592 17 5 5702 6288 212314596 212315186 0.000000e+00 961.0
50 TraesCS4A01G393100 chr6A 84.274 992 126 15 2406 3378 4520867 4519887 0.000000e+00 941.0
51 TraesCS4A01G393100 chr6A 91.358 81 6 1 442 521 520435178 520435258 6.660000e-20 110.0
52 TraesCS4A01G393100 chr6A 95.122 41 1 1 314 353 201645167 201645127 5.260000e-06 63.9
53 TraesCS4A01G393100 chr3A 92.743 565 31 7 5726 6288 12994322 12993766 0.000000e+00 808.0
54 TraesCS4A01G393100 chr1B 92.063 567 35 7 5724 6288 565986578 565987136 0.000000e+00 789.0
55 TraesCS4A01G393100 chr6B 91.564 569 35 6 5729 6288 658822314 658821750 0.000000e+00 773.0
56 TraesCS4A01G393100 chr1A 91.413 559 44 2 5728 6286 399188353 399187799 0.000000e+00 763.0
57 TraesCS4A01G393100 chr2D 87.778 90 9 2 436 524 599889451 599889539 3.100000e-18 104.0
58 TraesCS4A01G393100 chr2B 90.000 80 4 3 442 520 485682171 485682247 4.010000e-17 100.0
59 TraesCS4A01G393100 chr7B 87.209 86 10 1 436 520 516266898 516266983 5.190000e-16 97.1
60 TraesCS4A01G393100 chr2A 89.474 76 7 1 446 520 96088969 96088894 1.870000e-15 95.3


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 TraesCS4A01G393100 chr4A 668746192 668752479 6287 False 11612.000000 11612 100.000000 1 6288 1 chr4A.!!$F1 6287
1 TraesCS4A01G393100 chr4A 669578166 669584769 6603 True 2918.333333 6608 93.446333 1 5488 3 chr4A.!!$R3 5487
2 TraesCS4A01G393100 chr4A 49931853 49932413 560 True 898.000000 898 95.544000 5728 6288 1 chr4A.!!$R1 560
3 TraesCS4A01G393100 chr7D 53780852 53785919 5067 False 2495.000000 6569 91.567000 809 5478 3 chr7D.!!$F3 4669
4 TraesCS4A01G393100 chr5D 508574707 508579514 4807 True 1941.666667 5079 88.245667 987 5727 3 chr5D.!!$R1 4740
5 TraesCS4A01G393100 chr5D 508613164 508617771 4607 False 1026.666667 1905 83.713333 963 5301 3 chr5D.!!$F1 4338
6 TraesCS4A01G393100 chr7A 57210739 57215927 5188 False 1543.220000 4854 94.564600 1 5726 5 chr7A.!!$F4 5725
7 TraesCS4A01G393100 chr5B 638667702 638672226 4524 False 1722.000000 2543 87.961333 987 5478 3 chr5B.!!$F1 4491
8 TraesCS4A01G393100 chr5B 638642684 638647308 4624 True 755.600000 1079 85.195800 1000 5344 5 chr5B.!!$R2 4344
9 TraesCS4A01G393100 chr5A 635934391 635938921 4530 True 1678.666667 2348 88.189667 945 5478 3 chr5A.!!$R1 4533
10 TraesCS4A01G393100 chr5A 635948364 635952220 3856 False 943.500000 1445 85.395750 1560 5478 4 chr5A.!!$F1 3918
11 TraesCS4A01G393100 chr3B 171173221 171178337 5116 False 911.333333 1099 86.266333 1560 5243 3 chr3B.!!$F2 3683
12 TraesCS4A01G393100 chrUn 16377548 16378113 565 True 979.000000 979 97.880000 5723 6288 1 chrUn.!!$R1 565
13 TraesCS4A01G393100 chrUn 176732833 176733393 560 False 758.000000 758 90.973000 5724 6288 1 chrUn.!!$F2 564
14 TraesCS4A01G393100 chrUn 176698815 176699375 560 False 752.000000 752 90.796000 5724 6288 1 chrUn.!!$F1 564
15 TraesCS4A01G393100 chr6A 212314596 212315186 590 False 961.000000 961 96.115000 5702 6288 1 chr6A.!!$F1 586
16 TraesCS4A01G393100 chr6A 4519887 4520867 980 True 941.000000 941 84.274000 2406 3378 1 chr6A.!!$R1 972
17 TraesCS4A01G393100 chr3A 12993766 12994322 556 True 808.000000 808 92.743000 5726 6288 1 chr3A.!!$R1 562
18 TraesCS4A01G393100 chr1B 565986578 565987136 558 False 789.000000 789 92.063000 5724 6288 1 chr1B.!!$F1 564
19 TraesCS4A01G393100 chr6B 658821750 658822314 564 True 773.000000 773 91.564000 5729 6288 1 chr6B.!!$R1 559
20 TraesCS4A01G393100 chr1A 399187799 399188353 554 True 763.000000 763 91.413000 5728 6286 1 chr1A.!!$R1 558

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
664 701 0.179156 CCTTCACGAATGCATGTGCC 60.179 55.000 11.36 0.0 41.18 5.01 F
1339 2655 0.475906 ACAGCTGAACAGGGCTTCTT 59.524 50.000 23.35 0.0 36.59 2.52 F
2007 3604 2.936919 TAGCATGGCTATTGTCTGGG 57.063 50.000 0.00 0.0 40.44 4.45 F
2197 3801 3.319122 GGTCTTTTCAGGACTGTTGCAAT 59.681 43.478 0.59 0.0 34.47 3.56 F
3772 5704 3.388024 TGAGTGTATTAGGATCTGTGCCC 59.612 47.826 0.00 0.0 0.00 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2007 3604 1.380380 CACCAAAGCCCTCATCCCC 60.380 63.158 0.0 0.0 0.00 4.81 R
2303 3907 2.639839 ACTGTCTGCTATTCCCACAACT 59.360 45.455 0.0 0.0 0.00 3.16 R
3772 5704 2.260844 TCCAAGACTTCACCAAGCTG 57.739 50.000 0.0 0.0 32.09 4.24 R
3930 6030 4.213531 TCAATATCAGAAGCCTCCCCTA 57.786 45.455 0.0 0.0 0.00 3.53 R
5491 9320 0.037975 TTACTTCCGACGAGCCCAAC 60.038 55.000 0.0 0.0 0.00 3.77 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 1.225908 GGCGCCGTGTTTTACATCG 60.226 57.895 12.58 0.00 0.00 3.84
64 65 9.565213 GAAAATAAAAATCTCAGATGAGTGTGG 57.435 33.333 9.56 0.00 42.60 4.17
161 169 2.578021 AGATTGGTTGCCAGTGAGGTAT 59.422 45.455 0.00 0.00 40.61 2.73
250 285 5.172934 ACGTGTATCTGAGGCGAAAATTAA 58.827 37.500 0.00 0.00 0.00 1.40
261 296 6.154021 TGAGGCGAAAATTAACTACTACCTCT 59.846 38.462 0.00 0.00 40.48 3.69
262 297 6.338937 AGGCGAAAATTAACTACTACCTCTG 58.661 40.000 0.00 0.00 0.00 3.35
321 356 9.709495 CAAATTTTGATCAAAGATTTACTCCCA 57.291 29.630 24.66 10.33 0.00 4.37
359 394 6.369059 AGAGCATTTACATCACTACATTGC 57.631 37.500 0.00 0.00 0.00 3.56
382 417 8.974060 TGCTCTTATATTAGTTTACAAAGGGG 57.026 34.615 0.00 0.00 0.00 4.79
383 418 8.774183 TGCTCTTATATTAGTTTACAAAGGGGA 58.226 33.333 0.00 0.00 0.00 4.81
384 419 9.794719 GCTCTTATATTAGTTTACAAAGGGGAT 57.205 33.333 0.00 0.00 0.00 3.85
407 442 8.178964 GGATGACTAACAAATTGTTAACGCATA 58.821 33.333 17.85 4.39 41.70 3.14
523 559 2.308275 ACCAAGACGGAGGTAGTACTCT 59.692 50.000 0.00 0.00 36.07 3.24
524 560 2.944349 CCAAGACGGAGGTAGTACTCTC 59.056 54.545 0.00 0.13 37.63 3.20
664 701 0.179156 CCTTCACGAATGCATGTGCC 60.179 55.000 11.36 0.00 41.18 5.01
694 731 4.508971 CTCGTTTAATCACTGCGCATTAG 58.491 43.478 12.24 0.87 0.00 1.73
705 1690 5.293324 TCACTGCGCATTAGTTAATTAGGTG 59.707 40.000 12.24 10.98 0.00 4.00
707 1692 5.064707 ACTGCGCATTAGTTAATTAGGTGTG 59.935 40.000 12.24 0.00 0.00 3.82
906 1903 1.503542 CGAGCATTTCGCCAAAGCT 59.496 52.632 1.66 1.66 43.22 3.74
907 1904 0.726827 CGAGCATTTCGCCAAAGCTA 59.273 50.000 0.00 0.00 43.22 3.32
909 1906 2.414029 CGAGCATTTCGCCAAAGCTAAA 60.414 45.455 0.00 0.00 43.22 1.85
916 1913 4.394439 TTCGCCAAAGCTAAACCTTTTT 57.606 36.364 0.00 0.00 32.97 1.94
1219 2218 1.557099 CCAGCTGGTGTACTACTCCA 58.443 55.000 25.53 9.21 39.22 3.86
1289 2298 3.136123 CTCCCCGTAAGTCGCCGA 61.136 66.667 0.00 0.00 38.35 5.54
1339 2655 0.475906 ACAGCTGAACAGGGCTTCTT 59.524 50.000 23.35 0.00 36.59 2.52
1360 2681 3.194005 TCCCGGCTCTTAATTTGCTAG 57.806 47.619 0.00 0.00 0.00 3.42
1499 2895 8.740123 TTTTGGTCTAACAACATTTGAGTCTA 57.260 30.769 0.00 0.00 0.00 2.59
1500 2896 8.740123 TTTGGTCTAACAACATTTGAGTCTAA 57.260 30.769 0.00 0.00 0.00 2.10
1501 2897 7.724305 TGGTCTAACAACATTTGAGTCTAAC 57.276 36.000 0.00 0.00 0.00 2.34
1558 3011 6.320672 GGTACTAGCTTATAACTGGTCTGTGA 59.679 42.308 0.00 0.00 30.78 3.58
1765 3352 8.375506 AGAACAAGTGGATAACTAGAACATCAA 58.624 33.333 0.00 0.00 38.56 2.57
1802 3399 8.974292 ATTTCTTCATAATAGCCTCCTAGGTA 57.026 34.615 9.08 0.00 37.80 3.08
1908 3505 5.529060 GCGTCAGATAAATCAAAGAAGGGAT 59.471 40.000 0.00 0.00 0.00 3.85
2007 3604 2.936919 TAGCATGGCTATTGTCTGGG 57.063 50.000 0.00 0.00 40.44 4.45
2041 3638 5.357878 GCTTTGGTGATTATCCAGTGAATCA 59.642 40.000 2.45 2.45 39.24 2.57
2178 3782 4.187694 TCATGGTTTTTGTTGCTTTGGTC 58.812 39.130 0.00 0.00 0.00 4.02
2197 3801 3.319122 GGTCTTTTCAGGACTGTTGCAAT 59.681 43.478 0.59 0.00 34.47 3.56
2303 3907 4.272489 CAATCATCCTTGGAGGCTTTGTA 58.728 43.478 0.00 0.00 34.61 2.41
2576 4418 7.147976 ACTTAATTTGCTCAGCTTTAACAAGG 58.852 34.615 0.00 0.00 0.00 3.61
3112 5007 6.929049 CACTACCTTGAGTTTCTGACACAATA 59.071 38.462 0.00 0.00 38.02 1.90
3282 5186 4.301072 TTTGGATCTTCGACCAAAGGAT 57.699 40.909 12.53 0.00 46.69 3.24
3378 5283 4.523943 GCAACATTGGCCTTATATCATGGA 59.476 41.667 3.32 0.00 0.00 3.41
3441 5346 4.207165 GGCCTATTTTGCACCATCTCTTA 58.793 43.478 0.00 0.00 0.00 2.10
3450 5356 7.575414 TTTGCACCATCTCTTAGTTTAAACA 57.425 32.000 20.06 3.98 0.00 2.83
3471 5377 4.691216 ACAGCTAAAGTCGATTTGTCCTTC 59.309 41.667 0.00 0.00 32.01 3.46
3472 5378 4.093556 CAGCTAAAGTCGATTTGTCCTTCC 59.906 45.833 0.00 0.00 32.01 3.46
3473 5379 4.000988 GCTAAAGTCGATTTGTCCTTCCA 58.999 43.478 0.00 0.00 32.01 3.53
3475 5381 5.123979 GCTAAAGTCGATTTGTCCTTCCATT 59.876 40.000 0.00 0.00 32.01 3.16
3601 5515 7.824289 TCATAGTTTGTCTATTCTCCCAAGTTG 59.176 37.037 0.00 0.00 37.26 3.16
3744 5676 5.657745 TGATAATGTCCAAATTGCAGGATGT 59.342 36.000 0.00 0.00 39.31 3.06
3772 5704 3.388024 TGAGTGTATTAGGATCTGTGCCC 59.612 47.826 0.00 0.00 0.00 5.36
3869 5969 7.190920 ACTTACACTGTTAGAAAGCATTCAC 57.809 36.000 4.27 0.00 38.06 3.18
3930 6030 1.553248 TCGCAGGGTACTTGCTACAAT 59.447 47.619 16.85 0.00 0.00 2.71
4043 6143 3.435601 GGCATCCTCATACATTCAAGGGT 60.436 47.826 0.00 0.00 0.00 4.34
4298 6399 4.406648 TCTCAATGCTGACCACGATAAT 57.593 40.909 0.00 0.00 0.00 1.28
4448 8151 7.743104 AGCTTTATAAAATCAGTGTGTTCTCG 58.257 34.615 0.00 0.00 0.00 4.04
4463 8166 3.203716 GTTCTCGAAGTTTTCCAGTGGT 58.796 45.455 9.54 0.00 0.00 4.16
4464 8167 4.141892 TGTTCTCGAAGTTTTCCAGTGGTA 60.142 41.667 9.54 0.00 0.00 3.25
4539 8242 9.341078 TGCTCTGATATAAGTTGCAATGATAAA 57.659 29.630 0.59 0.00 0.00 1.40
4695 8454 2.928801 TTTCTACTGCAGCAACTCCA 57.071 45.000 15.27 0.00 0.00 3.86
4739 8498 5.657302 CAGAGGACAGTAGGTGGTTACTATT 59.343 44.000 0.00 0.00 32.74 1.73
4812 8574 3.825908 AGCTCCCCCTTCATTGTTTTA 57.174 42.857 0.00 0.00 0.00 1.52
5016 8782 4.701651 TGCTAAAAGATGGATCCACAACAG 59.298 41.667 18.99 10.70 0.00 3.16
5119 8886 6.703607 TCTCTTTTCTGACATTCAGTTCAGAC 59.296 38.462 0.77 0.00 44.58 3.51
5131 8898 2.428530 CAGTTCAGACGATCAGATGGGA 59.571 50.000 0.00 0.00 0.00 4.37
5224 9020 2.287009 CCCGAGAACTGCTTCAAACAAC 60.287 50.000 0.00 0.00 0.00 3.32
5254 9050 1.406860 GGGTCCTGAGGGATCAGCTC 61.407 65.000 0.00 0.00 44.34 4.09
5258 9054 1.007600 TCCTGAGGGATCAGCTCAAGA 59.992 52.381 0.00 0.00 36.57 3.02
5488 9317 5.106555 GCGATGGCTTGCTATTGTATTGTAT 60.107 40.000 7.79 0.00 35.83 2.29
5489 9318 6.309436 CGATGGCTTGCTATTGTATTGTATG 58.691 40.000 0.00 0.00 0.00 2.39
5490 9319 6.073058 CGATGGCTTGCTATTGTATTGTATGT 60.073 38.462 0.00 0.00 0.00 2.29
5491 9320 6.375945 TGGCTTGCTATTGTATTGTATGTG 57.624 37.500 0.00 0.00 0.00 3.21
5492 9321 5.885352 TGGCTTGCTATTGTATTGTATGTGT 59.115 36.000 0.00 0.00 0.00 3.72
5493 9322 6.376864 TGGCTTGCTATTGTATTGTATGTGTT 59.623 34.615 0.00 0.00 0.00 3.32
5494 9323 6.692681 GGCTTGCTATTGTATTGTATGTGTTG 59.307 38.462 0.00 0.00 0.00 3.33
5495 9324 6.692681 GCTTGCTATTGTATTGTATGTGTTGG 59.307 38.462 0.00 0.00 0.00 3.77
5496 9325 6.691754 TGCTATTGTATTGTATGTGTTGGG 57.308 37.500 0.00 0.00 0.00 4.12
5497 9326 5.067153 TGCTATTGTATTGTATGTGTTGGGC 59.933 40.000 0.00 0.00 0.00 5.36
5498 9327 5.299279 GCTATTGTATTGTATGTGTTGGGCT 59.701 40.000 0.00 0.00 0.00 5.19
5499 9328 5.835113 ATTGTATTGTATGTGTTGGGCTC 57.165 39.130 0.00 0.00 0.00 4.70
5500 9329 3.266636 TGTATTGTATGTGTTGGGCTCG 58.733 45.455 0.00 0.00 0.00 5.03
5501 9330 2.489938 ATTGTATGTGTTGGGCTCGT 57.510 45.000 0.00 0.00 0.00 4.18
5502 9331 1.803334 TTGTATGTGTTGGGCTCGTC 58.197 50.000 0.00 0.00 0.00 4.20
5503 9332 0.389296 TGTATGTGTTGGGCTCGTCG 60.389 55.000 0.00 0.00 0.00 5.12
5504 9333 1.082117 GTATGTGTTGGGCTCGTCGG 61.082 60.000 0.00 0.00 0.00 4.79
5505 9334 1.252215 TATGTGTTGGGCTCGTCGGA 61.252 55.000 0.00 0.00 0.00 4.55
5506 9335 2.029964 GTGTTGGGCTCGTCGGAA 59.970 61.111 0.00 0.00 0.00 4.30
5507 9336 2.027625 GTGTTGGGCTCGTCGGAAG 61.028 63.158 0.00 0.00 0.00 3.46
5508 9337 2.342648 GTTGGGCTCGTCGGAAGT 59.657 61.111 0.00 0.00 0.00 3.01
5509 9338 1.180456 TGTTGGGCTCGTCGGAAGTA 61.180 55.000 0.00 0.00 0.00 2.24
5510 9339 0.037975 GTTGGGCTCGTCGGAAGTAA 60.038 55.000 0.00 0.00 0.00 2.24
5511 9340 0.899720 TTGGGCTCGTCGGAAGTAAT 59.100 50.000 0.00 0.00 0.00 1.89
5512 9341 0.174845 TGGGCTCGTCGGAAGTAATG 59.825 55.000 0.00 0.00 0.00 1.90
5513 9342 0.458669 GGGCTCGTCGGAAGTAATGA 59.541 55.000 0.00 0.00 0.00 2.57
5514 9343 1.536284 GGGCTCGTCGGAAGTAATGAG 60.536 57.143 0.00 0.00 0.00 2.90
5515 9344 1.536284 GGCTCGTCGGAAGTAATGAGG 60.536 57.143 0.00 0.00 0.00 3.86
5516 9345 1.841450 CTCGTCGGAAGTAATGAGGC 58.159 55.000 0.00 0.00 0.00 4.70
5517 9346 0.099968 TCGTCGGAAGTAATGAGGCG 59.900 55.000 0.00 0.00 0.00 5.52
5518 9347 0.099968 CGTCGGAAGTAATGAGGCGA 59.900 55.000 0.00 0.00 0.00 5.54
5519 9348 1.269102 CGTCGGAAGTAATGAGGCGAT 60.269 52.381 0.00 0.00 0.00 4.58
5520 9349 2.128035 GTCGGAAGTAATGAGGCGATG 58.872 52.381 0.00 0.00 0.00 3.84
5521 9350 1.068588 TCGGAAGTAATGAGGCGATGG 59.931 52.381 0.00 0.00 0.00 3.51
5522 9351 1.230324 GGAAGTAATGAGGCGATGGC 58.770 55.000 0.00 0.00 38.90 4.40
5523 9352 1.202698 GGAAGTAATGAGGCGATGGCT 60.203 52.381 0.00 0.00 42.48 4.75
5524 9353 2.565841 GAAGTAATGAGGCGATGGCTT 58.434 47.619 0.00 0.00 38.98 4.35
5525 9354 1.959042 AGTAATGAGGCGATGGCTTG 58.041 50.000 0.00 0.00 38.98 4.01
5526 9355 1.486310 AGTAATGAGGCGATGGCTTGA 59.514 47.619 0.00 0.00 38.98 3.02
5527 9356 2.105477 AGTAATGAGGCGATGGCTTGAT 59.895 45.455 0.00 0.00 38.98 2.57
5528 9357 2.936919 AATGAGGCGATGGCTTGATA 57.063 45.000 0.00 0.00 38.98 2.15
5534 9363 3.554934 AGGCGATGGCTTGATAAAATCA 58.445 40.909 0.00 0.00 39.81 2.57
5568 9397 9.783256 CTGTATGTTTTAAGGTTTATAAGCCAC 57.217 33.333 19.26 9.39 0.00 5.01
5590 9419 7.248437 CCACCATATTTTCTTACGTTTTCTCC 58.752 38.462 0.00 0.00 0.00 3.71
5601 9430 8.306680 TCTTACGTTTTCTCCTTACATCTTTG 57.693 34.615 0.00 0.00 0.00 2.77
5642 9472 7.105588 TGCATTATGTAGTGTCAGATCAAAGT 58.894 34.615 0.00 0.00 0.00 2.66
5684 9514 6.201425 TCGTTACTCTTGCAAACTAACGATTT 59.799 34.615 26.21 6.26 42.10 2.17
5686 9516 8.005466 CGTTACTCTTGCAAACTAACGATTTAA 58.995 33.333 24.76 8.28 41.26 1.52
5752 9584 1.327690 TTCAGATCGCGGGCTAAGGT 61.328 55.000 6.13 0.00 0.00 3.50
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 39 9.565213 CCACACTCATCTGAGATTTTTATTTTC 57.435 33.333 13.94 0.00 44.74 2.29
64 65 1.127343 AGCCTGTCCCTCTAGCATTC 58.873 55.000 0.00 0.00 0.00 2.67
161 169 4.137872 GGTCGATCGCCGTCCCAA 62.138 66.667 11.09 0.00 39.94 4.12
250 285 6.154706 CCAATAACCAGAACAGAGGTAGTAGT 59.845 42.308 0.00 0.00 37.07 2.73
261 296 5.600484 ACAAATTGGACCAATAACCAGAACA 59.400 36.000 20.11 0.00 37.48 3.18
262 297 6.096673 ACAAATTGGACCAATAACCAGAAC 57.903 37.500 20.11 0.00 37.48 3.01
294 329 9.927668 GGGAGTAAATCTTTGATCAAAATTTGA 57.072 29.630 28.48 21.20 45.01 2.69
337 372 6.259608 AGAGCAATGTAGTGATGTAAATGCTC 59.740 38.462 14.23 14.23 42.65 4.26
358 393 9.794719 ATCCCCTTTGTAAACTAATATAAGAGC 57.205 33.333 0.00 0.00 0.00 4.09
367 402 7.747690 TGTTAGTCATCCCCTTTGTAAACTAA 58.252 34.615 0.00 0.00 0.00 2.24
376 411 6.994421 AACAATTTGTTAGTCATCCCCTTT 57.006 33.333 12.98 0.00 39.09 3.11
382 417 9.716507 ATATGCGTTAACAATTTGTTAGTCATC 57.283 29.630 22.13 13.60 42.93 2.92
383 418 9.716507 GATATGCGTTAACAATTTGTTAGTCAT 57.283 29.630 18.56 20.74 42.93 3.06
384 419 8.722394 TGATATGCGTTAACAATTTGTTAGTCA 58.278 29.630 18.56 16.95 42.93 3.41
407 442 9.507280 CAAATTCAACGATATAGTTTTGCTGAT 57.493 29.630 0.00 0.00 30.96 2.90
489 525 7.038799 ACCTCCGTCTTGGTTTATTAGTCTTTA 60.039 37.037 0.00 0.00 39.52 1.85
493 529 5.082251 ACCTCCGTCTTGGTTTATTAGTC 57.918 43.478 0.00 0.00 39.52 2.59
523 559 2.756829 TGCATAAAAACCGTGACGAGA 58.243 42.857 6.54 0.00 0.00 4.04
524 560 3.740044 ATGCATAAAAACCGTGACGAG 57.260 42.857 6.54 0.00 0.00 4.18
625 662 1.606885 AAAAGGACCGCATGCATGGG 61.607 55.000 31.05 31.05 40.08 4.00
664 701 5.258622 GCAGTGATTAAACGAGCAGTTATG 58.741 41.667 0.00 0.00 43.37 1.90
694 731 7.308169 GGTTGTCAACTACCACACCTAATTAAC 60.308 40.741 15.17 0.00 40.66 2.01
705 1690 1.463444 GCATCGGTTGTCAACTACCAC 59.537 52.381 15.17 0.00 40.94 4.16
707 1692 2.094762 AGCATCGGTTGTCAACTACC 57.905 50.000 15.17 3.98 38.19 3.18
878 1875 0.169009 GAAATGCTCGTTCTGGGCAC 59.831 55.000 0.00 0.00 38.83 5.01
916 1913 0.034198 TGACGAGGATGGCAACGAAA 59.966 50.000 12.01 0.27 42.51 3.46
918 1915 1.215382 CTGACGAGGATGGCAACGA 59.785 57.895 12.01 0.00 42.51 3.85
1219 2218 3.537874 GTCCCAGCCGGCGTAGAT 61.538 66.667 23.20 0.00 0.00 1.98
1314 2328 1.572085 CCCTGTTCAGCTGTGCTTCG 61.572 60.000 14.67 0.00 36.40 3.79
1339 2655 2.507407 AGCAAATTAAGAGCCGGGAA 57.493 45.000 2.18 0.00 0.00 3.97
1347 2663 7.270757 TCAAACAGTTGCTAGCAAATTAAGA 57.729 32.000 30.83 19.93 37.70 2.10
1360 2681 2.415893 CCCGATTGGATCAAACAGTTGC 60.416 50.000 0.00 0.00 37.49 4.17
1470 2857 8.908903 ACTCAAATGTTGTTAGACCAAAATACA 58.091 29.630 0.00 0.00 0.00 2.29
1478 2869 7.724305 TGTTAGACTCAAATGTTGTTAGACC 57.276 36.000 0.00 0.00 0.00 3.85
1499 2895 9.042008 CACTACTATCTTACTGTTGTTGTTGTT 57.958 33.333 0.00 0.00 0.00 2.83
1500 2896 7.170998 GCACTACTATCTTACTGTTGTTGTTGT 59.829 37.037 0.00 0.00 0.00 3.32
1501 2897 7.385205 AGCACTACTATCTTACTGTTGTTGTTG 59.615 37.037 0.00 0.00 0.00 3.33
1558 3011 5.565439 GCTTACAATCAGTCCTGCAACAATT 60.565 40.000 0.00 0.00 0.00 2.32
1802 3399 3.704566 TCCAGTAGACCTACGCAATGATT 59.295 43.478 1.93 0.00 40.80 2.57
2007 3604 1.380380 CACCAAAGCCCTCATCCCC 60.380 63.158 0.00 0.00 0.00 4.81
2041 3638 3.448686 CGAAGCTCCTTCAACGACATAT 58.551 45.455 5.88 0.00 40.17 1.78
2152 3756 5.277442 CCAAAGCAACAAAAACCATGATGAC 60.277 40.000 0.00 0.00 0.00 3.06
2178 3782 3.492011 GCAATTGCAACAGTCCTGAAAAG 59.508 43.478 25.36 0.00 41.59 2.27
2197 3801 2.733956 GGAACATGGTATCAAGGGCAA 58.266 47.619 0.00 0.00 0.00 4.52
2303 3907 2.639839 ACTGTCTGCTATTCCCACAACT 59.360 45.455 0.00 0.00 0.00 3.16
2456 4060 8.510283 TCCCCTAATTATGAAATCCTGAAATCA 58.490 33.333 0.00 0.00 0.00 2.57
2576 4418 9.937175 GTGATCCTGCTAAATAACTACAATTTC 57.063 33.333 0.00 0.00 0.00 2.17
2659 4530 6.072112 AGTTCAGTACGTTCATGCAAAAAT 57.928 33.333 0.00 0.00 0.00 1.82
3441 5346 7.927048 ACAAATCGACTTTAGCTGTTTAAACT 58.073 30.769 18.72 2.07 0.00 2.66
3450 5356 4.254492 GGAAGGACAAATCGACTTTAGCT 58.746 43.478 0.00 0.00 0.00 3.32
3677 5605 6.222389 AGCAGCTTATACTCAGCTTCTAATG 58.778 40.000 0.00 0.00 45.82 1.90
3744 5676 4.338400 CAGATCCTAATACACTCACACGGA 59.662 45.833 0.00 0.00 0.00 4.69
3772 5704 2.260844 TCCAAGACTTCACCAAGCTG 57.739 50.000 0.00 0.00 32.09 4.24
3930 6030 4.213531 TCAATATCAGAAGCCTCCCCTA 57.786 45.455 0.00 0.00 0.00 3.53
4298 6399 4.155709 TGGGCATTCCATCAAAGTAAACA 58.844 39.130 0.00 0.00 41.46 2.83
4463 8166 4.142004 GCTTCTCATTTTCTCGGTAGGGTA 60.142 45.833 0.00 0.00 0.00 3.69
4464 8167 3.369576 GCTTCTCATTTTCTCGGTAGGGT 60.370 47.826 0.00 0.00 0.00 4.34
4695 8454 6.071108 CCTCTGGATTATATCTCCATGTCGTT 60.071 42.308 7.26 0.00 41.83 3.85
4739 8498 0.898326 TCTGCTCTGCCCTGTACGAA 60.898 55.000 0.00 0.00 0.00 3.85
4812 8574 5.737860 TGCAAGAGTGATGACATCATACTT 58.262 37.500 20.67 21.89 42.04 2.24
5016 8782 2.679837 TCTTCAGAAGATTTGCATCGCC 59.320 45.455 8.95 0.00 34.17 5.54
5119 8886 0.683412 TGGATGCTCCCATCTGATCG 59.317 55.000 3.97 0.00 45.73 3.69
5131 8898 5.074102 TCTCAATTCCCTCATTATGGATGCT 59.926 40.000 0.00 0.00 35.64 3.79
5224 9020 0.906756 TCAGGACCCTTCTCAGCAGG 60.907 60.000 0.00 0.00 0.00 4.85
5254 9050 2.781304 GCGATTCGCGAGTTCTTTCTTG 60.781 50.000 16.11 0.00 44.55 3.02
5488 9317 2.709125 CTTCCGACGAGCCCAACACA 62.709 60.000 0.00 0.00 0.00 3.72
5489 9318 2.027625 CTTCCGACGAGCCCAACAC 61.028 63.158 0.00 0.00 0.00 3.32
5490 9319 1.180456 TACTTCCGACGAGCCCAACA 61.180 55.000 0.00 0.00 0.00 3.33
5491 9320 0.037975 TTACTTCCGACGAGCCCAAC 60.038 55.000 0.00 0.00 0.00 3.77
5492 9321 0.899720 ATTACTTCCGACGAGCCCAA 59.100 50.000 0.00 0.00 0.00 4.12
5493 9322 0.174845 CATTACTTCCGACGAGCCCA 59.825 55.000 0.00 0.00 0.00 5.36
5494 9323 0.458669 TCATTACTTCCGACGAGCCC 59.541 55.000 0.00 0.00 0.00 5.19
5495 9324 1.536284 CCTCATTACTTCCGACGAGCC 60.536 57.143 0.00 0.00 0.00 4.70
5496 9325 1.841450 CCTCATTACTTCCGACGAGC 58.159 55.000 0.00 0.00 0.00 5.03
5497 9326 1.841450 GCCTCATTACTTCCGACGAG 58.159 55.000 0.00 0.00 0.00 4.18
5498 9327 0.099968 CGCCTCATTACTTCCGACGA 59.900 55.000 0.00 0.00 0.00 4.20
5499 9328 0.099968 TCGCCTCATTACTTCCGACG 59.900 55.000 0.00 0.00 0.00 5.12
5500 9329 2.128035 CATCGCCTCATTACTTCCGAC 58.872 52.381 0.00 0.00 0.00 4.79
5501 9330 1.068588 CCATCGCCTCATTACTTCCGA 59.931 52.381 0.00 0.00 0.00 4.55
5502 9331 1.502231 CCATCGCCTCATTACTTCCG 58.498 55.000 0.00 0.00 0.00 4.30
5503 9332 1.202698 AGCCATCGCCTCATTACTTCC 60.203 52.381 0.00 0.00 34.57 3.46
5504 9333 2.246719 AGCCATCGCCTCATTACTTC 57.753 50.000 0.00 0.00 34.57 3.01
5505 9334 2.092968 TCAAGCCATCGCCTCATTACTT 60.093 45.455 0.00 0.00 34.57 2.24
5506 9335 1.486310 TCAAGCCATCGCCTCATTACT 59.514 47.619 0.00 0.00 34.57 2.24
5507 9336 1.953559 TCAAGCCATCGCCTCATTAC 58.046 50.000 0.00 0.00 34.57 1.89
5508 9337 2.936919 ATCAAGCCATCGCCTCATTA 57.063 45.000 0.00 0.00 34.57 1.90
5509 9338 2.936919 TATCAAGCCATCGCCTCATT 57.063 45.000 0.00 0.00 34.57 2.57
5510 9339 2.936919 TTATCAAGCCATCGCCTCAT 57.063 45.000 0.00 0.00 34.57 2.90
5511 9340 2.708216 TTTATCAAGCCATCGCCTCA 57.292 45.000 0.00 0.00 34.57 3.86
5512 9341 3.565482 TGATTTTATCAAGCCATCGCCTC 59.435 43.478 0.00 0.00 36.11 4.70
5513 9342 3.554934 TGATTTTATCAAGCCATCGCCT 58.445 40.909 0.00 0.00 36.11 5.52
5514 9343 3.565482 TCTGATTTTATCAAGCCATCGCC 59.435 43.478 0.00 0.00 39.11 5.54
5515 9344 4.818534 TCTGATTTTATCAAGCCATCGC 57.181 40.909 0.00 0.00 39.11 4.58
5516 9345 6.204301 AGTGATCTGATTTTATCAAGCCATCG 59.796 38.462 0.00 0.00 39.11 3.84
5517 9346 7.444792 AGAGTGATCTGATTTTATCAAGCCATC 59.555 37.037 0.00 0.00 39.11 3.51
5518 9347 7.228906 CAGAGTGATCTGATTTTATCAAGCCAT 59.771 37.037 0.00 0.00 39.99 4.40
5519 9348 6.541278 CAGAGTGATCTGATTTTATCAAGCCA 59.459 38.462 0.00 0.00 39.99 4.75
5520 9349 6.541641 ACAGAGTGATCTGATTTTATCAAGCC 59.458 38.462 12.00 0.00 39.99 4.35
5521 9350 7.551035 ACAGAGTGATCTGATTTTATCAAGC 57.449 36.000 12.00 0.00 39.99 4.01
5552 9381 9.930158 AGAAAATATGGTGGCTTATAAACCTTA 57.070 29.630 6.47 5.05 34.90 2.69
5568 9397 9.983804 GTAAGGAGAAAACGTAAGAAAATATGG 57.016 33.333 0.00 0.00 43.62 2.74
5601 9430 6.259608 ACATAATGCAGCTCATCTTGTCTTAC 59.740 38.462 0.00 0.00 33.40 2.34
5708 9540 9.869757 AAACTTTGCTTGATACTTTAAAACTGT 57.130 25.926 0.00 0.00 0.00 3.55
5715 9547 8.443160 CGATCTGAAACTTTGCTTGATACTTTA 58.557 33.333 0.00 0.00 0.00 1.85
5716 9548 7.301054 CGATCTGAAACTTTGCTTGATACTTT 58.699 34.615 0.00 0.00 0.00 2.66
5717 9549 6.621596 GCGATCTGAAACTTTGCTTGATACTT 60.622 38.462 0.00 0.00 0.00 2.24
5718 9550 5.163814 GCGATCTGAAACTTTGCTTGATACT 60.164 40.000 0.00 0.00 0.00 2.12
5719 9551 5.024555 GCGATCTGAAACTTTGCTTGATAC 58.975 41.667 0.00 0.00 0.00 2.24
5720 9552 4.201714 CGCGATCTGAAACTTTGCTTGATA 60.202 41.667 0.00 0.00 0.00 2.15
5721 9553 3.425359 CGCGATCTGAAACTTTGCTTGAT 60.425 43.478 0.00 0.00 0.00 2.57
5809 9641 0.538118 TAGCCGCGAAATGGGTTAGT 59.462 50.000 8.23 0.00 38.39 2.24


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

AutoCloner maintained by Alex Coulton.