Multiple sequence alignment - TraesCS4A01G480100

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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 TraesCS4A01G480100 chr4A 100.000 5858 0 0 1 5858 736755331 736761188 0.000000e+00 10818.0
1 TraesCS4A01G480100 chr4A 90.563 4313 347 25 972 5255 736413322 736409041 0.000000e+00 5655.0
2 TraesCS4A01G480100 chr4A 85.679 4511 549 51 973 5409 735562731 735558244 0.000000e+00 4662.0
3 TraesCS4A01G480100 chr4A 85.444 4383 572 35 975 5322 735316290 735320641 0.000000e+00 4499.0
4 TraesCS4A01G480100 chr4A 83.735 4113 594 50 884 4951 734585022 734589104 0.000000e+00 3819.0
5 TraesCS4A01G480100 chr4A 84.715 3847 524 27 975 4783 736896748 736900568 0.000000e+00 3788.0
6 TraesCS4A01G480100 chr4A 81.946 4686 649 114 975 5568 735663045 735658465 0.000000e+00 3784.0
7 TraesCS4A01G480100 chr4A 83.273 4149 611 58 888 4992 734730560 734734669 0.000000e+00 3740.0
8 TraesCS4A01G480100 chr4A 83.485 4075 595 57 888 4920 736570634 736574672 0.000000e+00 3725.0
9 TraesCS4A01G480100 chr4A 83.814 3954 573 54 1041 4951 735747182 735751111 0.000000e+00 3694.0
10 TraesCS4A01G480100 chr4A 83.886 3922 536 45 1445 5306 735689506 735693391 0.000000e+00 3653.0
11 TraesCS4A01G480100 chr4A 81.811 3920 655 44 1039 4920 736433809 736429910 0.000000e+00 3236.0
12 TraesCS4A01G480100 chr4A 90.384 2475 215 8 527 2988 735818248 735820712 0.000000e+00 3230.0
13 TraesCS4A01G480100 chr4A 85.721 2178 289 15 830 2991 735488124 735485953 0.000000e+00 2279.0
14 TraesCS4A01G480100 chr4A 83.693 1901 277 26 3040 4920 735005442 735007329 0.000000e+00 1762.0
15 TraesCS4A01G480100 chr4A 83.474 1900 286 21 3040 4920 735485934 735484044 0.000000e+00 1744.0
16 TraesCS4A01G480100 chr4A 92.975 484 33 1 200 683 735830787 735831269 0.000000e+00 704.0
17 TraesCS4A01G480100 chr4A 88.462 468 34 10 4962 5415 736672901 736673362 1.110000e-151 547.0
18 TraesCS4A01G480100 chr4A 80.635 661 97 18 32 684 736471592 736470955 3.170000e-132 483.0
19 TraesCS4A01G480100 chr4A 90.141 284 25 1 5575 5858 736673874 736674154 3.340000e-97 366.0
20 TraesCS4A01G480100 chr4A 77.778 603 90 24 32 628 735663707 735663143 1.220000e-86 331.0
21 TraesCS4A01G480100 chr4A 86.942 291 27 6 5575 5858 735321166 735321452 3.410000e-82 316.0
22 TraesCS4A01G480100 chr4A 76.292 658 111 28 91 740 735766312 735766932 5.700000e-80 309.0
23 TraesCS4A01G480100 chr4A 77.989 527 88 17 91 613 734729828 734730330 7.380000e-79 305.0
24 TraesCS4A01G480100 chr4A 77.351 521 78 25 266 761 734581897 734582402 7.480000e-69 272.0
25 TraesCS4A01G480100 chr4A 74.400 750 137 36 91 823 736055113 736055824 2.690000e-68 270.0
26 TraesCS4A01G480100 chr4A 74.400 750 134 39 91 821 736883145 736883855 9.680000e-68 268.0
27 TraesCS4A01G480100 chr4A 85.159 283 15 9 5575 5831 736408976 736408695 1.250000e-66 265.0
28 TraesCS4A01G480100 chr4A 78.009 432 70 14 84 513 736569986 736570394 1.260000e-61 248.0
29 TraesCS4A01G480100 chr4A 92.258 155 12 0 5414 5568 735558205 735558051 2.750000e-53 220.0
30 TraesCS4A01G480100 chr4A 93.151 146 10 0 5414 5559 736673397 736673542 1.280000e-51 215.0
31 TraesCS4A01G480100 chr4A 84.874 119 16 1 76 192 735765114 735765232 1.030000e-22 119.0
32 TraesCS4A01G480100 chr4A 91.304 69 4 1 5499 5565 734485097 734485165 6.250000e-15 93.5
33 TraesCS4A01G480100 chr4A 100.000 42 0 0 5817 5858 736405768 736405727 1.750000e-10 78.7
34 TraesCS4A01G480100 chr4A 92.500 40 3 0 31 70 736081882 736081921 2.280000e-04 58.4
35 TraesCS4A01G480100 chr7D 85.172 4687 579 63 977 5568 5449140 5444475 0.000000e+00 4698.0
36 TraesCS4A01G480100 chr7D 84.061 4166 599 49 830 4952 5649558 5645415 0.000000e+00 3954.0
37 TraesCS4A01G480100 chr7D 84.438 4029 548 48 977 4945 5638108 5634099 0.000000e+00 3893.0
38 TraesCS4A01G480100 chr7D 84.123 3653 522 42 1329 4943 5486537 5482905 0.000000e+00 3480.0
39 TraesCS4A01G480100 chr7D 83.825 1898 283 17 3040 4920 5458144 5456254 0.000000e+00 1783.0
40 TraesCS4A01G480100 chr7D 79.661 708 116 19 32 733 5449823 5449138 8.830000e-133 484.0
41 TraesCS4A01G480100 chr7D 80.755 556 82 12 153 703 5638669 5638134 1.520000e-110 411.0
42 TraesCS4A01G480100 chr7D 77.387 597 105 24 84 674 5487870 5487298 1.570000e-85 327.0
43 TraesCS4A01G480100 chr7D 87.410 278 28 4 5576 5848 5444284 5444009 4.410000e-81 313.0
44 TraesCS4A01G480100 chr7A 83.889 3929 539 54 1038 4916 7322285 7318401 0.000000e+00 3663.0
45 TraesCS4A01G480100 chr7A 79.070 645 98 22 71 706 6929317 6928701 5.460000e-110 409.0
46 TraesCS4A01G480100 chr7A 80.317 442 70 12 118 544 6595200 6595639 9.470000e-83 318.0


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 TraesCS4A01G480100 chr4A 736755331 736761188 5857 False 10818.000000 10818 100.000000 1 5858 1 chr4A.!!$F9 5857
1 TraesCS4A01G480100 chr4A 736896748 736900568 3820 False 3788.000000 3788 84.715000 975 4783 1 chr4A.!!$F11 3808
2 TraesCS4A01G480100 chr4A 735747182 735751111 3929 False 3694.000000 3694 83.814000 1041 4951 1 chr4A.!!$F4 3910
3 TraesCS4A01G480100 chr4A 735689506 735693391 3885 False 3653.000000 3653 83.886000 1445 5306 1 chr4A.!!$F3 3861
4 TraesCS4A01G480100 chr4A 736429910 736433809 3899 True 3236.000000 3236 81.811000 1039 4920 1 chr4A.!!$R1 3881
5 TraesCS4A01G480100 chr4A 735818248 735820712 2464 False 3230.000000 3230 90.384000 527 2988 1 chr4A.!!$F5 2461
6 TraesCS4A01G480100 chr4A 735558051 735562731 4680 True 2441.000000 4662 88.968500 973 5568 2 chr4A.!!$R4 4595
7 TraesCS4A01G480100 chr4A 735316290 735321452 5162 False 2407.500000 4499 86.193000 975 5858 2 chr4A.!!$F14 4883
8 TraesCS4A01G480100 chr4A 735658465 735663707 5242 True 2057.500000 3784 79.862000 32 5568 2 chr4A.!!$R5 5536
9 TraesCS4A01G480100 chr4A 734581897 734589104 7207 False 2045.500000 3819 80.543000 266 4951 2 chr4A.!!$F12 4685
10 TraesCS4A01G480100 chr4A 734729828 734734669 4841 False 2022.500000 3740 80.631000 91 4992 2 chr4A.!!$F13 4901
11 TraesCS4A01G480100 chr4A 735484044 735488124 4080 True 2011.500000 2279 84.597500 830 4920 2 chr4A.!!$R3 4090
12 TraesCS4A01G480100 chr4A 736405727 736413322 7595 True 1999.566667 5655 91.907333 972 5858 3 chr4A.!!$R6 4886
13 TraesCS4A01G480100 chr4A 736569986 736574672 4686 False 1986.500000 3725 80.747000 84 4920 2 chr4A.!!$F16 4836
14 TraesCS4A01G480100 chr4A 735005442 735007329 1887 False 1762.000000 1762 83.693000 3040 4920 1 chr4A.!!$F2 1880
15 TraesCS4A01G480100 chr4A 736470955 736471592 637 True 483.000000 483 80.635000 32 684 1 chr4A.!!$R2 652
16 TraesCS4A01G480100 chr4A 736672901 736674154 1253 False 376.000000 547 90.584667 4962 5858 3 chr4A.!!$F17 896
17 TraesCS4A01G480100 chr4A 736055113 736055824 711 False 270.000000 270 74.400000 91 823 1 chr4A.!!$F7 732
18 TraesCS4A01G480100 chr4A 736883145 736883855 710 False 268.000000 268 74.400000 91 821 1 chr4A.!!$F10 730
19 TraesCS4A01G480100 chr4A 735765114 735766932 1818 False 214.000000 309 80.583000 76 740 2 chr4A.!!$F15 664
20 TraesCS4A01G480100 chr7D 5645415 5649558 4143 True 3954.000000 3954 84.061000 830 4952 1 chr7D.!!$R2 4122
21 TraesCS4A01G480100 chr7D 5634099 5638669 4570 True 2152.000000 3893 82.596500 153 4945 2 chr7D.!!$R5 4792
22 TraesCS4A01G480100 chr7D 5482905 5487870 4965 True 1903.500000 3480 80.755000 84 4943 2 chr7D.!!$R4 4859
23 TraesCS4A01G480100 chr7D 5444009 5449823 5814 True 1831.666667 4698 84.081000 32 5848 3 chr7D.!!$R3 5816
24 TraesCS4A01G480100 chr7D 5456254 5458144 1890 True 1783.000000 1783 83.825000 3040 4920 1 chr7D.!!$R1 1880
25 TraesCS4A01G480100 chr7A 7318401 7322285 3884 True 3663.000000 3663 83.889000 1038 4916 1 chr7A.!!$R2 3878
26 TraesCS4A01G480100 chr7A 6928701 6929317 616 True 409.000000 409 79.070000 71 706 1 chr7A.!!$R1 635

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
719 1971 0.976641 TTCTTGTGCCCGTCTCTCAT 59.023 50.000 0.00 0.00 0.00 2.90 F
1011 2352 0.749454 GCAATCCGATGGAAGTGGCT 60.749 55.000 0.00 0.00 34.34 4.75 F
1541 3057 1.002430 TGTTCCTGAGACCACATCAGC 59.998 52.381 0.00 0.00 42.36 4.26 F
2201 6266 0.675633 TCTCCTTTGGCAGCAAAAGC 59.324 50.000 16.09 0.00 34.03 3.51 F
3133 7281 1.760192 ATTGCAACAGCTGAGGGATC 58.240 50.000 23.35 3.61 0.00 3.36 F
4256 8426 1.724429 CTTGCAGCTGACTTCCTCTC 58.276 55.000 20.43 0.00 0.00 3.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1845 3377 0.309922 CTGTCAACTTGCACTGCAGG 59.690 55.000 19.93 11.42 40.61 4.85 R
1962 3495 0.547075 TTCCGGTCTGTTGGGAAACA 59.453 50.000 0.00 0.00 36.92 2.83 R
3432 7590 2.093394 TGGTAGGCTTTGTAATGCGCTA 60.093 45.455 9.73 0.00 0.00 4.26 R
4141 8311 2.227388 GGCAGGAAGTCAAGTGAACATG 59.773 50.000 0.00 0.00 0.00 3.21 R
4423 8596 2.151202 GGTGAGCTTCGGAACATCAAA 58.849 47.619 0.00 0.00 0.00 2.69 R
5164 9384 1.040646 ACATCGTCAGTGACAGTGGT 58.959 50.000 22.66 11.69 32.09 4.16 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
19 20 2.655090 TGGTGATGGACAGAAAGCAA 57.345 45.000 0.00 0.00 0.00 3.91
20 21 2.942804 TGGTGATGGACAGAAAGCAAA 58.057 42.857 0.00 0.00 0.00 3.68
21 22 3.295093 TGGTGATGGACAGAAAGCAAAA 58.705 40.909 0.00 0.00 0.00 2.44
22 23 3.318839 TGGTGATGGACAGAAAGCAAAAG 59.681 43.478 0.00 0.00 0.00 2.27
23 24 3.569701 GGTGATGGACAGAAAGCAAAAGA 59.430 43.478 0.00 0.00 0.00 2.52
24 25 4.219288 GGTGATGGACAGAAAGCAAAAGAT 59.781 41.667 0.00 0.00 0.00 2.40
25 26 5.279156 GGTGATGGACAGAAAGCAAAAGATT 60.279 40.000 0.00 0.00 0.00 2.40
26 27 6.218746 GTGATGGACAGAAAGCAAAAGATTT 58.781 36.000 0.00 0.00 0.00 2.17
27 28 6.703165 GTGATGGACAGAAAGCAAAAGATTTT 59.297 34.615 0.00 0.00 0.00 1.82
28 29 7.225341 GTGATGGACAGAAAGCAAAAGATTTTT 59.775 33.333 0.00 0.00 0.00 1.94
69 70 9.296400 GTTTGTATTTAGTCACACAATGTTGTT 57.704 29.630 0.00 0.00 39.91 2.83
81 82 5.237344 ACACAATGTTGTTCTCTGCTACTTC 59.763 40.000 0.00 0.00 39.91 3.01
89 90 5.641709 TGTTCTCTGCTACTTCATACTTCG 58.358 41.667 0.00 0.00 0.00 3.79
114 115 1.073964 CAATCAGTGAGCTGTGTCCG 58.926 55.000 0.00 0.00 43.05 4.79
199 1382 4.202716 TGGGTGGATCAGATCTGCTATAGA 60.203 45.833 18.36 0.00 40.37 1.98
206 1389 7.725844 TGGATCAGATCTGCTATAGACTTGTTA 59.274 37.037 18.36 0.00 38.49 2.41
277 1460 2.362717 GTTAGCTCCTACGATCTGCCTT 59.637 50.000 0.00 0.00 0.00 4.35
279 1462 2.667470 AGCTCCTACGATCTGCCTTTA 58.333 47.619 0.00 0.00 0.00 1.85
297 1490 5.253330 CCTTTACTTCAACCTTGCCTCATA 58.747 41.667 0.00 0.00 0.00 2.15
301 1494 2.698855 TCAACCTTGCCTCATAGCTC 57.301 50.000 0.00 0.00 0.00 4.09
305 1498 1.445095 CTTGCCTCATAGCTCCGCT 59.555 57.895 0.00 0.00 43.41 5.52
414 1636 9.227777 GTAGGCTTCTGTTTATTTTCTTCCTTA 57.772 33.333 0.00 0.00 0.00 2.69
423 1646 8.424918 TGTTTATTTTCTTCCTTATTGCAACCA 58.575 29.630 0.00 0.00 0.00 3.67
424 1647 8.708742 GTTTATTTTCTTCCTTATTGCAACCAC 58.291 33.333 0.00 0.00 0.00 4.16
477 1706 6.186957 ACAGGTGTTCATCCATTGCTTATTA 58.813 36.000 0.00 0.00 0.00 0.98
480 1712 5.971202 GGTGTTCATCCATTGCTTATTAACG 59.029 40.000 0.00 0.00 0.00 3.18
495 1730 7.065324 TGCTTATTAACGGATTGTTTCTACCTG 59.935 37.037 0.00 0.00 42.09 4.00
513 1748 1.129998 CTGCGATCCAGAAGCACTTTG 59.870 52.381 5.53 0.00 44.64 2.77
518 1754 3.438087 CGATCCAGAAGCACTTTGATTGT 59.562 43.478 0.00 0.00 0.00 2.71
570 1806 7.348274 ACCCACTCTCAGAAATATTATCCTTGA 59.652 37.037 0.00 0.00 0.00 3.02
653 1899 8.856153 TGCAGTTGACTAATTTATCCTGTAAA 57.144 30.769 0.00 0.00 0.00 2.01
679 1929 7.554959 TCCTACTCTAACAGGTTTTTCATCT 57.445 36.000 0.00 0.00 33.37 2.90
719 1971 0.976641 TTCTTGTGCCCGTCTCTCAT 59.023 50.000 0.00 0.00 0.00 2.90
1011 2352 0.749454 GCAATCCGATGGAAGTGGCT 60.749 55.000 0.00 0.00 34.34 4.75
1053 2394 2.182014 GTTAGCTTAAAATTGGCCGCG 58.818 47.619 0.00 0.00 0.00 6.46
1094 2435 4.669318 CTCCTTGCTAATGCTTCAACATG 58.331 43.478 0.00 0.00 40.48 3.21
1146 2487 5.125739 CCGTGAACTAGAGACCACTATCTTT 59.874 44.000 0.00 0.00 0.00 2.52
1387 2897 3.194719 GCAGGCTGTCCAATCTGC 58.805 61.111 17.16 0.00 44.34 4.26
1392 2902 2.467826 GCTGTCCAATCTGCGCTCC 61.468 63.158 9.73 0.00 0.00 4.70
1413 2923 5.535333 TCCGAGAACAGAAAGTTAATTCGT 58.465 37.500 0.00 0.00 41.51 3.85
1467 2977 2.087646 GCCAAGGACTTCCATCAACTC 58.912 52.381 0.00 0.00 38.89 3.01
1481 2997 3.485463 TCAACTCCTGTGTTTACCTGG 57.515 47.619 0.00 0.00 0.00 4.45
1541 3057 1.002430 TGTTCCTGAGACCACATCAGC 59.998 52.381 0.00 0.00 42.36 4.26
1635 3166 6.470278 TGCTACTACTGAGTCTAGTACAACA 58.530 40.000 0.00 0.00 37.10 3.33
1724 3255 8.651389 TGTCTATAATGATGAGAGGGTAAAAGG 58.349 37.037 0.00 0.00 0.00 3.11
1845 3377 6.238925 GCCCACACATTAATAACCTTGATACC 60.239 42.308 0.00 0.00 0.00 2.73
1852 3385 4.862641 AATAACCTTGATACCCTGCAGT 57.137 40.909 13.81 0.00 0.00 4.40
1866 3399 1.263484 CTGCAGTGCAAGTTGACAGAG 59.737 52.381 20.22 0.00 38.41 3.35
1872 3405 4.624882 CAGTGCAAGTTGACAGAGATACTC 59.375 45.833 7.16 0.00 0.00 2.59
1875 3408 4.180057 GCAAGTTGACAGAGATACTCCAG 58.820 47.826 7.16 0.00 0.00 3.86
1877 3410 2.763448 AGTTGACAGAGATACTCCAGGC 59.237 50.000 0.00 0.00 0.00 4.85
1908 3441 1.896220 TCCTGCTTGTGTTGGATGAC 58.104 50.000 0.00 0.00 0.00 3.06
1946 3479 1.912043 CAGTGAGAAGGAATGGGACCT 59.088 52.381 0.00 0.00 39.69 3.85
1962 3495 1.903183 GACCTACTGTTGGCTCCTCTT 59.097 52.381 8.22 0.00 0.00 2.85
1985 3518 1.002134 CCCAACAGACCGGAAGCAT 60.002 57.895 9.46 0.00 0.00 3.79
2130 6195 6.542821 ACAAGAAATCAGAAATCCACTACCA 58.457 36.000 0.00 0.00 0.00 3.25
2201 6266 0.675633 TCTCCTTTGGCAGCAAAAGC 59.324 50.000 16.09 0.00 34.03 3.51
2286 6351 6.727824 AAGATTGACAACTTAACTGATCCG 57.272 37.500 0.00 0.00 0.00 4.18
2336 6401 2.826128 AGTTAGATCCACGTCTGCAGAA 59.174 45.455 20.19 2.01 0.00 3.02
2353 6418 4.722203 CAGAAGTGCTTCCTATATTGCG 57.278 45.455 8.19 0.00 40.33 4.85
2566 6694 5.619132 TCATGATCTGGCAGAATTACTCA 57.381 39.130 22.84 19.64 0.00 3.41
2567 6695 5.608449 TCATGATCTGGCAGAATTACTCAG 58.392 41.667 22.84 12.98 0.00 3.35
2576 6704 3.690460 CAGAATTACTCAGCAAAGGGGT 58.310 45.455 0.00 0.00 0.00 4.95
2626 6754 6.170506 GTGACAGAAATACCATCCACTGTTA 58.829 40.000 0.00 0.00 38.43 2.41
2634 6762 9.209175 GAAATACCATCCACTGTTAGACATATC 57.791 37.037 0.00 0.00 0.00 1.63
2682 6810 4.228912 ACACAAGCAAAGTATCTGCAAC 57.771 40.909 0.00 0.00 42.48 4.17
2686 6814 5.048782 CACAAGCAAAGTATCTGCAACCTAA 60.049 40.000 0.00 0.00 42.48 2.69
2703 6831 6.632834 GCAACCTAAATCATTTACGCACTATG 59.367 38.462 0.00 0.00 0.00 2.23
2800 6928 7.010091 TGCGTGTACTACATTTGTCATCTTATG 59.990 37.037 0.00 0.00 0.00 1.90
2851 6987 2.930682 GAGTTGAAGCACCTTCGGTATC 59.069 50.000 1.07 0.00 42.78 2.24
2955 7091 2.736670 AAGTTGAGAGTTTGCCTGGT 57.263 45.000 0.00 0.00 0.00 4.00
3133 7281 1.760192 ATTGCAACAGCTGAGGGATC 58.240 50.000 23.35 3.61 0.00 3.36
3288 7446 4.012374 ACACCAATGCAGAGGATAGTTTG 58.988 43.478 13.66 3.52 0.00 2.93
3410 7568 7.284919 ACGGTTCTTATTTTGAGAATTTGGT 57.715 32.000 0.00 0.00 35.74 3.67
3432 7590 7.228590 TGGTATCTTTAAGGTTTGCTAACTGT 58.771 34.615 10.80 2.23 34.59 3.55
3480 7638 3.473113 ACTGGGCTATTTGGGAATTGT 57.527 42.857 0.00 0.00 0.00 2.71
3553 7711 8.376270 GTCTTCCACTAGGGCTTACATATTTAT 58.624 37.037 0.00 0.00 36.21 1.40
3556 7714 7.676947 TCCACTAGGGCTTACATATTTATGTC 58.323 38.462 6.49 0.00 41.04 3.06
3559 7717 8.367911 CACTAGGGCTTACATATTTATGTCTGA 58.632 37.037 6.49 0.00 45.11 3.27
3561 7719 7.380423 AGGGCTTACATATTTATGTCTGAGT 57.620 36.000 6.49 0.00 45.11 3.41
3696 7866 4.886496 TGCAGGATCAGATATCAAGAGG 57.114 45.455 5.32 0.00 0.00 3.69
3769 7939 4.609947 TGCTGATGTGTCAAATGTTCAAC 58.390 39.130 0.00 0.00 33.05 3.18
3776 7946 4.219507 TGTGTCAAATGTTCAACACCTTGT 59.780 37.500 11.98 0.00 40.96 3.16
3887 8057 4.458397 CTCATGTATGGAAGGAGCATTGT 58.542 43.478 0.00 0.00 0.00 2.71
3936 8106 8.626526 GGACTTCGTAATCTTTATCTCTTCTCT 58.373 37.037 0.00 0.00 0.00 3.10
4014 8184 8.110860 TGGAAAGTTTGGACTTAAATGAGATC 57.889 34.615 0.00 0.00 45.18 2.75
4141 8311 2.733858 CGAGCTGCTACCTCTCTTTCAC 60.734 54.545 0.15 0.00 0.00 3.18
4180 8350 2.158534 TGCCCTTCTTTAGAGTTGGCAA 60.159 45.455 13.27 0.00 0.00 4.52
4256 8426 1.724429 CTTGCAGCTGACTTCCTCTC 58.276 55.000 20.43 0.00 0.00 3.20
4423 8596 4.397730 TGCAACTTCACAGTGTACATTTGT 59.602 37.500 0.00 4.43 31.60 2.83
4576 8751 2.673775 TGAAGGATGCAAGGAACCAA 57.326 45.000 0.00 0.00 0.00 3.67
4609 8784 3.365820 GGAAGAATGCACAAATTTCGCAG 59.634 43.478 15.05 0.00 39.39 5.18
4704 8879 7.122138 TCTGAAGAAGCTTGACATCTATGAT 57.878 36.000 2.10 0.00 0.00 2.45
4972 9192 7.887996 TGCACATCATTAAACTTTTGAATCC 57.112 32.000 0.00 0.00 0.00 3.01
5130 9350 0.966179 TCTGTCTGTCGCCTGCTTTA 59.034 50.000 0.00 0.00 0.00 1.85
5156 9376 1.589716 GCTTCACGCATTGCCCTCTT 61.590 55.000 2.41 0.00 38.92 2.85
5164 9384 0.609957 CATTGCCCTCTTGCACTCCA 60.610 55.000 0.00 0.00 41.88 3.86
5255 9499 8.578448 TTATCATCCATTGACTGAACAATTCA 57.422 30.769 0.00 0.00 38.25 2.57
5290 9543 4.494199 GCACGTTATTCCATCACTTAGTGC 60.494 45.833 7.61 0.00 43.06 4.40
5307 9560 3.490348 AGTGCTGTCCTGTTTTGCTATT 58.510 40.909 0.00 0.00 0.00 1.73
5353 9643 6.270156 TGTGTGATCTTACGTACCATGTAA 57.730 37.500 0.00 0.00 0.00 2.41
5354 9644 6.869695 TGTGTGATCTTACGTACCATGTAAT 58.130 36.000 0.00 0.00 30.07 1.89
5355 9645 7.998580 TGTGTGATCTTACGTACCATGTAATA 58.001 34.615 0.00 0.00 30.07 0.98
5365 9658 5.893255 ACGTACCATGTAATAACTGGAGGTA 59.107 40.000 0.00 0.00 34.08 3.08
5381 9674 7.861629 ACTGGAGGTATCTTTTATCATTCACA 58.138 34.615 0.00 0.00 0.00 3.58
5400 9693 5.364778 TCACACCCGTAATGAGATATTTGG 58.635 41.667 0.00 0.00 0.00 3.28
5401 9694 4.024048 CACACCCGTAATGAGATATTTGGC 60.024 45.833 0.00 0.00 0.00 4.52
5465 9798 2.169352 TGATGGTCTAGAAAGCCTGCTC 59.831 50.000 0.00 0.00 0.00 4.26
5467 9800 0.179234 GGTCTAGAAAGCCTGCTCCC 59.821 60.000 0.00 0.00 0.00 4.30
5470 9803 1.007721 TCTAGAAAGCCTGCTCCCTCT 59.992 52.381 0.00 0.00 0.00 3.69
5583 10283 8.277490 TCTGTTGAACTACGTACTGATCTATT 57.723 34.615 0.00 0.00 0.00 1.73
5771 10509 2.513897 CCCCGTCGATTCAAGGGC 60.514 66.667 0.00 0.00 42.47 5.19
5798 10537 3.198068 TCGAGATGCAAAACTAGATGGC 58.802 45.455 0.00 0.00 0.00 4.40
5804 10543 3.605634 TGCAAAACTAGATGGCATACGT 58.394 40.909 0.00 0.00 0.00 3.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.655090 TTGCTTTCTGTCCATCACCA 57.345 45.000 0.00 0.00 0.00 4.17
1 2 3.569701 TCTTTTGCTTTCTGTCCATCACC 59.430 43.478 0.00 0.00 0.00 4.02
2 3 4.836125 TCTTTTGCTTTCTGTCCATCAC 57.164 40.909 0.00 0.00 0.00 3.06
3 4 6.409524 AAATCTTTTGCTTTCTGTCCATCA 57.590 33.333 0.00 0.00 0.00 3.07
4 5 7.719778 AAAAATCTTTTGCTTTCTGTCCATC 57.280 32.000 0.00 0.00 0.00 3.51
36 37 6.824196 TGTGTGACTAAATACAAACAACCAGA 59.176 34.615 0.00 0.00 32.30 3.86
69 70 6.701145 AATCGAAGTATGAAGTAGCAGAGA 57.299 37.500 0.00 0.00 0.00 3.10
81 82 7.598118 AGCTCACTGATTGATAATCGAAGTATG 59.402 37.037 0.00 0.00 40.84 2.39
114 115 8.232513 GCTAATAAACTAACCAGTAACCAACAC 58.767 37.037 0.00 0.00 33.48 3.32
199 1382 2.693074 CCCAAACAGCAGGTTAACAAGT 59.307 45.455 8.10 0.00 39.29 3.16
206 1389 0.188342 ACATCCCCAAACAGCAGGTT 59.812 50.000 0.00 0.00 42.98 3.50
277 1460 4.019321 AGCTATGAGGCAAGGTTGAAGTAA 60.019 41.667 0.00 0.00 34.17 2.24
279 1462 2.307098 AGCTATGAGGCAAGGTTGAAGT 59.693 45.455 0.00 0.00 34.17 3.01
301 1494 2.509336 CGTTGTAGGAGCCAGCGG 60.509 66.667 0.00 0.00 33.62 5.52
305 1498 2.047274 GCAGCGTTGTAGGAGCCA 60.047 61.111 0.00 0.00 0.00 4.75
414 1636 7.902920 ATGAGATAAATTAGGTGGTTGCAAT 57.097 32.000 0.59 0.00 0.00 3.56
477 1706 2.073816 CGCAGGTAGAAACAATCCGTT 58.926 47.619 0.00 0.00 40.50 4.44
480 1712 2.872858 GGATCGCAGGTAGAAACAATCC 59.127 50.000 0.00 0.00 0.00 3.01
495 1730 1.442769 TCAAAGTGCTTCTGGATCGC 58.557 50.000 0.00 0.00 0.00 4.58
513 1748 9.046296 ACCTGAATAAATGATAGACGAACAATC 57.954 33.333 0.00 0.00 0.00 2.67
625 1871 6.319658 ACAGGATAAATTAGTCAACTGCATGG 59.680 38.462 0.00 0.00 0.00 3.66
626 1872 7.325660 ACAGGATAAATTAGTCAACTGCATG 57.674 36.000 0.00 0.00 0.00 4.06
627 1873 9.461312 TTTACAGGATAAATTAGTCAACTGCAT 57.539 29.630 0.00 0.00 0.00 3.96
628 1874 8.856153 TTTACAGGATAAATTAGTCAACTGCA 57.144 30.769 0.00 0.00 0.00 4.41
653 1899 8.606830 AGATGAAAAACCTGTTAGAGTAGGAAT 58.393 33.333 0.00 0.00 37.52 3.01
679 1929 3.885724 TTGCTTCTGGACGTGATGATA 57.114 42.857 0.00 0.00 0.00 2.15
719 1971 2.494073 GTGTGGAATGGCCCGAATAAAA 59.506 45.455 0.00 0.00 34.97 1.52
758 2022 7.855784 AAACTATGAAACAATTTCCCCTTCT 57.144 32.000 0.00 0.00 38.90 2.85
759 2023 8.773645 CAAAAACTATGAAACAATTTCCCCTTC 58.226 33.333 0.00 0.00 38.90 3.46
760 2024 7.228507 GCAAAAACTATGAAACAATTTCCCCTT 59.771 33.333 0.00 0.00 38.90 3.95
761 2025 6.710295 GCAAAAACTATGAAACAATTTCCCCT 59.290 34.615 0.00 0.00 38.90 4.79
762 2026 6.710295 AGCAAAAACTATGAAACAATTTCCCC 59.290 34.615 0.00 0.00 38.90 4.81
795 2061 8.585471 ATGGAGATGAACAAGTTTACAATGAT 57.415 30.769 0.00 0.00 0.00 2.45
1053 2394 3.063485 GAGCTTCTTCAAGAGTGGTGAC 58.937 50.000 0.00 0.00 0.00 3.67
1094 2435 2.048603 GCCATGTCCACTCCAAGGC 61.049 63.158 0.00 0.00 39.23 4.35
1124 2465 6.153000 TGGAAAGATAGTGGTCTCTAGTTCAC 59.847 42.308 0.00 0.00 0.00 3.18
1146 2487 2.092968 AGTCAACAGCTTGAGTTGTGGA 60.093 45.455 13.35 1.31 44.97 4.02
1197 2538 4.021192 TCCTGAAGCCATTTGTCCAAATTC 60.021 41.667 2.56 0.78 38.84 2.17
1200 2541 2.956132 TCCTGAAGCCATTTGTCCAAA 58.044 42.857 0.00 0.00 34.46 3.28
1387 2897 1.784525 AACTTTCTGTTCTCGGAGCG 58.215 50.000 0.00 0.00 32.63 5.03
1392 2902 6.448053 TGACGAATTAACTTTCTGTTCTCG 57.552 37.500 0.00 0.00 39.89 4.04
1413 2923 6.357367 GGTAGCCTTCAATTCCTTAAGATGA 58.643 40.000 3.36 0.37 0.00 2.92
1467 2977 7.012044 GCATTATAACTACCAGGTAAACACAGG 59.988 40.741 0.00 0.00 0.00 4.00
1481 2997 5.233988 CAGGGCTCTCTGCATTATAACTAC 58.766 45.833 0.00 0.00 45.15 2.73
1541 3057 3.384467 ACCAATCACTTTGAAAGGTGGTG 59.616 43.478 17.99 6.43 36.61 4.17
1593 3112 6.769512 AGTAGCAGATGTTTTGGTAAGAAGA 58.230 36.000 0.00 0.00 31.12 2.87
1594 3113 7.819900 AGTAGTAGCAGATGTTTTGGTAAGAAG 59.180 37.037 0.00 0.00 31.12 2.85
1595 3114 7.602644 CAGTAGTAGCAGATGTTTTGGTAAGAA 59.397 37.037 0.00 0.00 31.12 2.52
1609 3131 6.541934 TGTACTAGACTCAGTAGTAGCAGA 57.458 41.667 0.00 0.00 35.56 4.26
1635 3166 2.969821 TGGCCAAACCTGAGTACATT 57.030 45.000 0.61 0.00 40.22 2.71
1724 3255 5.047802 ACCCACATTCTCACATCAAAACATC 60.048 40.000 0.00 0.00 0.00 3.06
1845 3377 0.309922 CTGTCAACTTGCACTGCAGG 59.690 55.000 19.93 11.42 40.61 4.85
1852 3385 3.578282 TGGAGTATCTCTGTCAACTTGCA 59.422 43.478 0.00 0.00 33.73 4.08
1866 3399 6.238869 GGAATTTTCTTGATGCCTGGAGTATC 60.239 42.308 0.00 0.00 38.04 2.24
1872 3405 3.677976 GCAGGAATTTTCTTGATGCCTGG 60.678 47.826 11.98 0.00 46.46 4.45
1875 3408 3.881937 AGCAGGAATTTTCTTGATGCC 57.118 42.857 6.61 0.00 36.49 4.40
1877 3410 5.535333 ACACAAGCAGGAATTTTCTTGATG 58.465 37.500 6.61 6.79 39.22 3.07
1946 3479 3.496160 GGAAACAAGAGGAGCCAACAGTA 60.496 47.826 0.00 0.00 0.00 2.74
1962 3495 0.547075 TTCCGGTCTGTTGGGAAACA 59.453 50.000 0.00 0.00 36.92 2.83
1985 3518 4.549458 CCGTCGAGAAGTTACCAAAACTA 58.451 43.478 0.00 0.00 0.00 2.24
2130 6195 4.616835 GCAAAATCTTCGAGCCTTTCACAT 60.617 41.667 0.00 0.00 0.00 3.21
2286 6351 2.289320 ACTCCACAACAGAGCACTCATC 60.289 50.000 0.00 0.00 34.56 2.92
2336 6401 1.417890 AGCCGCAATATAGGAAGCACT 59.582 47.619 0.00 0.00 0.00 4.40
2566 6694 2.621070 TCTGAAGTAGACCCCTTTGCT 58.379 47.619 0.00 0.00 0.00 3.91
2567 6695 3.636153 ATCTGAAGTAGACCCCTTTGC 57.364 47.619 0.00 0.00 38.49 3.68
2576 6704 8.646004 CCTTATCATCTTCCAATCTGAAGTAGA 58.354 37.037 0.00 0.00 41.96 2.59
2626 6754 5.644977 TGAACACGAACAGAGATATGTCT 57.355 39.130 0.00 0.00 37.42 3.41
2634 6762 5.452623 CGTCATACTATGAACACGAACAGAG 59.547 44.000 0.01 0.00 41.69 3.35
2682 6810 8.438513 CAGATCATAGTGCGTAAATGATTTAGG 58.561 37.037 11.99 11.99 39.76 2.69
2686 6814 5.759763 TGCAGATCATAGTGCGTAAATGATT 59.240 36.000 11.98 3.19 42.96 2.57
2703 6831 4.774726 TCCATTAGAGGGTCTATGCAGATC 59.225 45.833 0.00 0.00 32.09 2.75
2772 6900 5.874810 AGATGACAAATGTAGTACACGCAAT 59.125 36.000 4.80 0.00 0.00 3.56
3288 7446 3.567585 GGCCTTCTAGAATCTCCAAATGC 59.432 47.826 5.44 0.00 0.00 3.56
3323 7481 2.561478 TGTAAGGCTCCCAAGTTGAC 57.439 50.000 3.87 0.00 0.00 3.18
3432 7590 2.093394 TGGTAGGCTTTGTAATGCGCTA 60.093 45.455 9.73 0.00 0.00 4.26
3480 7638 4.756642 ACATTGATGAGTGAAAGCGAAGAA 59.243 37.500 0.00 0.00 0.00 2.52
3553 7711 2.875672 GCAGTGGGCAATTACTCAGACA 60.876 50.000 0.00 0.00 43.97 3.41
3696 7866 2.232941 TGAATGTTCCCGTGAGAGTACC 59.767 50.000 0.00 0.00 0.00 3.34
3769 7939 5.305585 TCCTTTTAGAGCACTTACAAGGTG 58.694 41.667 12.39 0.00 37.70 4.00
3796 7966 7.549839 TCCTCTTTTGCCAATATTTCATCTTG 58.450 34.615 0.00 0.00 0.00 3.02
3936 8106 6.588719 AAAGCTCCATTTGTAATACTGCAA 57.411 33.333 0.00 0.00 0.00 4.08
4014 8184 7.050281 CGAAGGAAGTGTAGTTAAAGTCATG 57.950 40.000 0.00 0.00 0.00 3.07
4141 8311 2.227388 GGCAGGAAGTCAAGTGAACATG 59.773 50.000 0.00 0.00 0.00 3.21
4256 8426 3.610040 TTATGTGTGGCCAGTCAGTAG 57.390 47.619 5.11 0.00 0.00 2.57
4423 8596 2.151202 GGTGAGCTTCGGAACATCAAA 58.849 47.619 0.00 0.00 0.00 2.69
4576 8751 5.856156 TGTGCATTCTTCCAATGAAACAAT 58.144 33.333 0.00 0.00 0.00 2.71
4609 8784 4.187694 CAGAATCTTAGGGTCTTGACTGC 58.812 47.826 0.61 0.00 0.00 4.40
4692 8867 3.053768 TGTTGGGGCAATCATAGATGTCA 60.054 43.478 0.00 0.00 0.00 3.58
4704 8879 4.892934 GGTAAAGATGATATGTTGGGGCAA 59.107 41.667 0.00 0.00 0.00 4.52
5156 9376 1.146041 GTGACAGTGGTGGAGTGCA 59.854 57.895 0.00 0.00 0.00 4.57
5164 9384 1.040646 ACATCGTCAGTGACAGTGGT 58.959 50.000 22.66 11.69 32.09 4.16
5255 9499 8.677148 ATGGAATAACGTGCAAATTAGACTAT 57.323 30.769 0.00 0.00 0.00 2.12
5290 9543 6.259608 CAGGAGATAATAGCAAAACAGGACAG 59.740 42.308 0.00 0.00 0.00 3.51
5354 9644 9.832445 GTGAATGATAAAAGATACCTCCAGTTA 57.168 33.333 0.00 0.00 0.00 2.24
5355 9645 8.328758 TGTGAATGATAAAAGATACCTCCAGTT 58.671 33.333 0.00 0.00 0.00 3.16
5365 9658 7.773224 TCATTACGGGTGTGAATGATAAAAGAT 59.227 33.333 0.00 0.00 35.26 2.40
5381 9674 3.181458 ACGCCAAATATCTCATTACGGGT 60.181 43.478 0.00 0.00 0.00 5.28
5465 9798 3.732849 GCCCCCAAGGTCAGAGGG 61.733 72.222 0.00 0.00 42.44 4.30
5467 9800 1.077212 CATGCCCCCAAGGTCAGAG 60.077 63.158 0.00 0.00 38.26 3.35
5470 9803 1.925285 CTAGCATGCCCCCAAGGTCA 61.925 60.000 15.66 0.00 38.26 4.02
5569 9933 8.409371 CAGCATGGATATAATAGATCAGTACGT 58.591 37.037 0.00 0.00 0.00 3.57
5771 10509 2.002586 AGTTTTGCATCTCGATGTCCG 58.997 47.619 8.54 0.00 40.80 4.79
5804 10543 6.343716 TGACAAGTACGTACCTTGGAAATA 57.656 37.500 26.78 14.13 32.86 1.40


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

AutoCloner maintained by Alex Coulton.