Multiple sequence alignment - TraesCS6A01G083500

Loading Multiple Alignment...

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 TraesCS6A01G083500 chr6A 100.000 4807 0 0 1 4807 52040059 52035253 0.000000e+00 8877.0
1 TraesCS6A01G083500 chr6A 90.426 1525 108 21 861 2355 52118897 52117381 0.000000e+00 1973.0
2 TraesCS6A01G083500 chr6A 83.696 1656 187 37 1046 2624 33967151 33968800 0.000000e+00 1485.0
3 TraesCS6A01G083500 chr6A 84.737 760 99 17 69 817 518503938 518503185 0.000000e+00 745.0
4 TraesCS6A01G083500 chr6A 83.593 835 95 24 1 817 518537379 518536569 0.000000e+00 745.0
5 TraesCS6A01G083500 chr6A 77.046 1124 221 25 1046 2158 30905832 30904735 3.180000e-171 612.0
6 TraesCS6A01G083500 chr6A 85.333 150 20 2 3215 3364 33969456 33969603 2.320000e-33 154.0
7 TraesCS6A01G083500 chr6D 94.232 1803 65 9 861 2630 41545468 41543672 0.000000e+00 2717.0
8 TraesCS6A01G083500 chr6D 83.553 1666 181 49 1046 2625 28683553 28681895 0.000000e+00 1472.0
9 TraesCS6A01G083500 chr6D 90.419 1075 98 3 1023 2093 41596462 41595389 0.000000e+00 1410.0
10 TraesCS6A01G083500 chr6D 93.677 775 38 6 2819 3590 41543477 41542711 0.000000e+00 1149.0
11 TraesCS6A01G083500 chr6D 95.050 707 30 4 3588 4291 41542346 41541642 0.000000e+00 1107.0
12 TraesCS6A01G083500 chr6D 88.330 497 31 16 4292 4765 41541604 41541112 5.400000e-159 571.0
13 TraesCS6A01G083500 chr6D 81.431 517 72 13 2626 3126 41582441 41581933 7.490000e-108 401.0
14 TraesCS6A01G083500 chr6D 78.583 593 66 30 2090 2624 41583082 41582493 7.710000e-88 335.0
15 TraesCS6A01G083500 chr6D 96.026 151 6 0 2626 2776 41543627 41543477 3.720000e-61 246.0
16 TraesCS6A01G083500 chr6D 93.651 63 4 0 4579 4641 17203488 17203426 1.420000e-15 95.3
17 TraesCS6A01G083500 chr6B 93.702 1810 73 10 859 2635 95818991 95820792 0.000000e+00 2673.0
18 TraesCS6A01G083500 chr6B 83.801 1531 184 27 956 2434 62001234 62002752 0.000000e+00 1395.0
19 TraesCS6A01G083500 chr6B 87.705 976 90 13 939 1911 95722860 95723808 0.000000e+00 1110.0
20 TraesCS6A01G083500 chr6B 89.252 735 46 5 2864 3583 95821274 95821990 0.000000e+00 889.0
21 TraesCS6A01G083500 chr6B 92.123 457 26 5 4294 4741 95823126 95823581 1.890000e-178 636.0
22 TraesCS6A01G083500 chr6B 81.234 762 83 29 1917 2620 95755896 95756655 1.170000e-155 560.0
23 TraesCS6A01G083500 chr6B 92.248 387 23 3 3593 3978 95822042 95822422 4.230000e-150 542.0
24 TraesCS6A01G083500 chr6B 82.895 608 80 13 39 642 638560561 638561148 4.260000e-145 525.0
25 TraesCS6A01G083500 chr6B 92.171 281 18 3 4013 4290 95822804 95823083 1.250000e-105 394.0
26 TraesCS6A01G083500 chr6B 80.776 541 64 20 2626 3155 62002996 62003507 2.100000e-103 387.0
27 TraesCS6A01G083500 chr6B 94.048 252 14 1 2626 2876 95820831 95821082 9.760000e-102 381.0
28 TraesCS6A01G083500 chr6B 78.908 531 63 19 2627 3155 95756712 95757195 1.000000e-81 315.0
29 TraesCS6A01G083500 chr6B 93.548 62 4 0 4580 4641 149732464 149732525 5.120000e-15 93.5
30 TraesCS6A01G083500 chr6B 92.308 39 3 0 780 818 42319700 42319662 6.720000e-04 56.5
31 TraesCS6A01G083500 chr2A 95.515 825 31 5 1 821 232385965 232386787 0.000000e+00 1314.0
32 TraesCS6A01G083500 chr2A 83.871 93 13 2 2301 2393 721519140 721519230 2.380000e-13 87.9
33 TraesCS6A01G083500 chr1D 87.358 878 76 23 1 858 3953528 3952666 0.000000e+00 974.0
34 TraesCS6A01G083500 chr1D 83.413 832 114 13 1 817 476818634 476817812 0.000000e+00 750.0
35 TraesCS6A01G083500 chr1D 88.158 76 8 1 4579 4654 221874262 221874188 6.630000e-14 89.8
36 TraesCS6A01G083500 chr7D 84.988 826 103 12 1 817 61755694 61754881 0.000000e+00 819.0
37 TraesCS6A01G083500 chr7D 90.317 599 54 4 1 595 178883731 178883133 0.000000e+00 782.0
38 TraesCS6A01G083500 chr7D 82.976 793 112 21 1 774 618424133 618424921 0.000000e+00 695.0
39 TraesCS6A01G083500 chr7D 91.935 62 5 0 4580 4641 256228105 256228044 2.380000e-13 87.9
40 TraesCS6A01G083500 chr4D 90.500 600 50 6 1 595 25425031 25425628 0.000000e+00 785.0
41 TraesCS6A01G083500 chr7B 83.090 822 101 17 1 817 588260262 588261050 0.000000e+00 713.0
42 TraesCS6A01G083500 chr7B 96.552 58 2 0 4584 4641 301607397 301607340 3.960000e-16 97.1
43 TraesCS6A01G083500 chrUn 85.878 609 76 6 212 817 34439859 34440460 1.460000e-179 640.0
44 TraesCS6A01G083500 chr1B 77.133 1137 205 37 1046 2157 476882852 476881746 4.110000e-170 608.0
45 TraesCS6A01G083500 chr4B 74.316 1133 243 33 1046 2157 106049368 106048263 2.050000e-118 436.0
46 TraesCS6A01G083500 chr7A 89.286 112 12 0 703 814 728849539 728849650 1.800000e-29 141.0
47 TraesCS6A01G083500 chr7A 89.189 111 10 2 705 814 728724129 728724238 2.330000e-28 137.0
48 TraesCS6A01G083500 chr3D 98.214 56 1 0 4586 4641 589572111 589572056 1.100000e-16 99.0
49 TraesCS6A01G083500 chr3B 91.429 70 5 1 4572 4641 312149483 312149415 1.420000e-15 95.3
50 TraesCS6A01G083500 chr5B 100.000 29 0 0 1005 1033 585998541 585998569 2.000000e-03 54.7


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6A01G083500 chr6A 52035253 52040059 4806 True 8877.000000 8877 100.000000 1 4807 1 chr6A.!!$R2 4806
1 TraesCS6A01G083500 chr6A 52117381 52118897 1516 True 1973.000000 1973 90.426000 861 2355 1 chr6A.!!$R3 1494
2 TraesCS6A01G083500 chr6A 33967151 33969603 2452 False 819.500000 1485 84.514500 1046 3364 2 chr6A.!!$F1 2318
3 TraesCS6A01G083500 chr6A 518503185 518503938 753 True 745.000000 745 84.737000 69 817 1 chr6A.!!$R4 748
4 TraesCS6A01G083500 chr6A 518536569 518537379 810 True 745.000000 745 83.593000 1 817 1 chr6A.!!$R5 816
5 TraesCS6A01G083500 chr6A 30904735 30905832 1097 True 612.000000 612 77.046000 1046 2158 1 chr6A.!!$R1 1112
6 TraesCS6A01G083500 chr6D 28681895 28683553 1658 True 1472.000000 1472 83.553000 1046 2625 1 chr6D.!!$R2 1579
7 TraesCS6A01G083500 chr6D 41595389 41596462 1073 True 1410.000000 1410 90.419000 1023 2093 1 chr6D.!!$R3 1070
8 TraesCS6A01G083500 chr6D 41541112 41545468 4356 True 1158.000000 2717 93.463000 861 4765 5 chr6D.!!$R4 3904
9 TraesCS6A01G083500 chr6D 41581933 41583082 1149 True 368.000000 401 80.007000 2090 3126 2 chr6D.!!$R5 1036
10 TraesCS6A01G083500 chr6B 95722860 95723808 948 False 1110.000000 1110 87.705000 939 1911 1 chr6B.!!$F1 972
11 TraesCS6A01G083500 chr6B 95818991 95823581 4590 False 919.166667 2673 92.257333 859 4741 6 chr6B.!!$F6 3882
12 TraesCS6A01G083500 chr6B 62001234 62003507 2273 False 891.000000 1395 82.288500 956 3155 2 chr6B.!!$F4 2199
13 TraesCS6A01G083500 chr6B 638560561 638561148 587 False 525.000000 525 82.895000 39 642 1 chr6B.!!$F3 603
14 TraesCS6A01G083500 chr6B 95755896 95757195 1299 False 437.500000 560 80.071000 1917 3155 2 chr6B.!!$F5 1238
15 TraesCS6A01G083500 chr2A 232385965 232386787 822 False 1314.000000 1314 95.515000 1 821 1 chr2A.!!$F1 820
16 TraesCS6A01G083500 chr1D 3952666 3953528 862 True 974.000000 974 87.358000 1 858 1 chr1D.!!$R1 857
17 TraesCS6A01G083500 chr1D 476817812 476818634 822 True 750.000000 750 83.413000 1 817 1 chr1D.!!$R3 816
18 TraesCS6A01G083500 chr7D 61754881 61755694 813 True 819.000000 819 84.988000 1 817 1 chr7D.!!$R1 816
19 TraesCS6A01G083500 chr7D 178883133 178883731 598 True 782.000000 782 90.317000 1 595 1 chr7D.!!$R2 594
20 TraesCS6A01G083500 chr7D 618424133 618424921 788 False 695.000000 695 82.976000 1 774 1 chr7D.!!$F1 773
21 TraesCS6A01G083500 chr4D 25425031 25425628 597 False 785.000000 785 90.500000 1 595 1 chr4D.!!$F1 594
22 TraesCS6A01G083500 chr7B 588260262 588261050 788 False 713.000000 713 83.090000 1 817 1 chr7B.!!$F1 816
23 TraesCS6A01G083500 chrUn 34439859 34440460 601 False 640.000000 640 85.878000 212 817 1 chrUn.!!$F1 605
24 TraesCS6A01G083500 chr1B 476881746 476882852 1106 True 608.000000 608 77.133000 1046 2157 1 chr1B.!!$R1 1111
25 TraesCS6A01G083500 chr4B 106048263 106049368 1105 True 436.000000 436 74.316000 1046 2157 1 chr4B.!!$R1 1111

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
638 685 1.378531 GTTTGTGCACTGACAGGTGA 58.621 50.000 19.41 0.00 39.34 4.02 F
907 972 1.447314 GGTCATGGACCGGTCGAAC 60.447 63.158 27.68 19.08 43.14 3.95 F
1044 1119 1.598130 GCAGCAGGTCAACCTCGTT 60.598 57.895 0.00 0.00 46.65 3.85 F
1362 1446 2.034532 CACATGCTGCAGGACCCA 59.965 61.111 22.12 4.89 0.00 4.51 F
2659 2952 2.941064 CACAGATGGTGCAGGTCAATAG 59.059 50.000 0.00 0.00 41.36 1.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2057 2174 1.066587 CCGGACTTGAGCTCGATCC 59.933 63.158 16.92 16.92 0.00 3.36 R
2487 2710 1.278127 TGCTAGTGGGGTTTACAGAGC 59.722 52.381 0.00 0.00 32.85 4.09 R
2728 3029 2.925306 GCAGAGCATTTGCCAAGAAGTG 60.925 50.000 0.00 0.00 43.38 3.16 R
2748 3049 4.457834 TTCTAGTTCCAAGTAGCTCAGC 57.542 45.455 0.00 0.00 33.02 4.26 R
4105 5403 0.319813 GCATCAACCAAACAGCCACC 60.320 55.000 0.00 0.00 0.00 4.61 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
638 685 1.378531 GTTTGTGCACTGACAGGTGA 58.621 50.000 19.41 0.00 39.34 4.02
672 719 5.272167 CGTTTAGACGCACTTTTTCCATA 57.728 39.130 0.00 0.00 43.03 2.74
840 905 2.472695 TCGCTGACAAGTTTAGGCAT 57.527 45.000 0.00 0.00 0.00 4.40
842 907 2.076100 CGCTGACAAGTTTAGGCATCA 58.924 47.619 0.00 0.00 0.00 3.07
848 913 4.041075 TGACAAGTTTAGGCATCACTGGTA 59.959 41.667 0.00 0.00 0.00 3.25
858 923 8.730093 TTAGGCATCACTGGTATTATTACCTA 57.270 34.615 13.57 0.00 46.96 3.08
859 924 7.626999 AGGCATCACTGGTATTATTACCTAA 57.373 36.000 13.57 0.00 46.96 2.69
906 971 2.975536 GGTCATGGACCGGTCGAA 59.024 61.111 27.68 18.95 43.14 3.71
907 972 1.447314 GGTCATGGACCGGTCGAAC 60.447 63.158 27.68 19.08 43.14 3.95
908 973 1.804326 GTCATGGACCGGTCGAACG 60.804 63.158 27.68 17.78 0.00 3.95
951 1018 2.829003 CACCCTCGCTCCTCGCTA 60.829 66.667 0.00 0.00 38.27 4.26
1044 1119 1.598130 GCAGCAGGTCAACCTCGTT 60.598 57.895 0.00 0.00 46.65 3.85
1362 1446 2.034532 CACATGCTGCAGGACCCA 59.965 61.111 22.12 4.89 0.00 4.51
2057 2174 3.054802 AGAACAGAGGGTGGCTTATTCAG 60.055 47.826 0.00 0.00 0.00 3.02
2185 2315 7.450014 TGTCCTTCATTTTACAGCTTCCATAAA 59.550 33.333 0.00 0.00 0.00 1.40
2190 2320 9.995003 TTCATTTTACAGCTTCCATAAATTTGT 57.005 25.926 0.00 0.00 0.00 2.83
2191 2321 9.421806 TCATTTTACAGCTTCCATAAATTTGTG 57.578 29.630 7.89 7.89 0.00 3.33
2192 2322 9.421806 CATTTTACAGCTTCCATAAATTTGTGA 57.578 29.630 15.75 0.00 0.00 3.58
2196 2326 6.815089 ACAGCTTCCATAAATTTGTGAACAA 58.185 32.000 15.75 5.43 0.00 2.83
2197 2327 7.444299 ACAGCTTCCATAAATTTGTGAACAAT 58.556 30.769 15.75 0.00 35.55 2.71
2223 2384 9.734620 TTAGTCAATCAGTTATATTGCAATTGC 57.265 29.630 23.69 23.69 42.50 3.56
2342 2513 9.582431 CAGAGCATGATTTTTGTTATGAGATTT 57.418 29.630 0.00 0.00 0.00 2.17
2418 2595 6.992063 ACAGCCTTGTCAATCTAGTATTTG 57.008 37.500 0.00 0.00 29.46 2.32
2430 2612 8.764558 TCAATCTAGTATTTGCCTGTTACCTTA 58.235 33.333 0.00 0.00 0.00 2.69
2487 2710 2.975266 AGCTCACATCTCAAGCTCAAG 58.025 47.619 0.00 0.00 42.58 3.02
2591 2830 5.363562 TCTCAGATCATGGCATTGTTACT 57.636 39.130 0.00 0.00 0.00 2.24
2607 2846 7.584108 CATTGTTACTGTTAGCAAAGATCACA 58.416 34.615 0.00 0.00 32.77 3.58
2612 2851 8.454106 GTTACTGTTAGCAAAGATCACATGATT 58.546 33.333 0.00 0.00 34.37 2.57
2659 2952 2.941064 CACAGATGGTGCAGGTCAATAG 59.059 50.000 0.00 0.00 41.36 1.73
2748 3049 2.555325 TCACTTCTTGGCAAATGCTCTG 59.445 45.455 0.00 0.00 41.70 3.35
3006 3517 9.515020 TTGAAGTCAGATGTTTTACAATTTCAC 57.485 29.630 0.00 0.00 0.00 3.18
3063 3595 4.830046 TGTCATTAAGCAAAAAGGCACCTA 59.170 37.500 0.00 0.00 35.83 3.08
3097 3632 9.739276 ATTTGTGAGTTATGGATTCAAGTCTTA 57.261 29.630 0.00 0.00 0.00 2.10
3177 3724 9.823647 CATTTCTACTTTTCTCTAGAGCCATTA 57.176 33.333 15.35 0.00 0.00 1.90
3186 3743 6.095432 TCTCTAGAGCCATTATTGCTTCTC 57.905 41.667 15.35 0.00 39.69 2.87
3191 3748 6.205101 AGAGCCATTATTGCTTCTCTTTTG 57.795 37.500 0.00 0.00 39.69 2.44
3265 3832 8.576442 CCATACAAGGAAAGCTAAAAAGAGAAA 58.424 33.333 0.00 0.00 0.00 2.52
3272 3839 8.387039 AGGAAAGCTAAAAAGAGAAAGGTAGAT 58.613 33.333 0.00 0.00 0.00 1.98
3327 3894 6.017852 GGGAAAACATTATTCTAAGCCTCTCG 60.018 42.308 0.00 0.00 0.00 4.04
3344 3911 4.288531 CTCTCGTTACATTCCATACCGAC 58.711 47.826 0.00 0.00 0.00 4.79
3379 3946 2.059541 GACTACAAACTCGTGCTGGAC 58.940 52.381 0.00 0.00 0.00 4.02
3436 4003 4.378459 CGTTGTCCTTGCATTCTCTTTACC 60.378 45.833 0.00 0.00 0.00 2.85
3534 4110 0.036164 AGCCAGTCCATTTGCGTGTA 59.964 50.000 0.00 0.00 0.00 2.90
3573 4155 4.192317 GAGAATACTTGGCATCGGAAACT 58.808 43.478 0.00 0.00 0.00 2.66
3583 4165 4.394920 TGGCATCGGAAACTTACTCAATTC 59.605 41.667 0.00 0.00 0.00 2.17
3603 4553 7.904461 TCAATTCGAATATACAATATGCATGCG 59.096 33.333 11.83 0.00 0.00 4.73
3807 4758 4.215349 GGCTCACTGATGCCTGAC 57.785 61.111 10.60 0.00 45.26 3.51
3846 4797 2.433491 TGGCGAATTGGACGTCCG 60.433 61.111 28.70 17.38 39.43 4.79
3859 4810 0.595095 ACGTCCGTCACTGACCTTAC 59.405 55.000 3.50 0.00 0.00 2.34
3871 4822 3.578716 ACTGACCTTACTTCTGCTGCTTA 59.421 43.478 0.00 0.00 0.00 3.09
3924 4875 9.696917 CTACTGCTGTCAAATCCTTTTATTTTT 57.303 29.630 0.00 0.00 0.00 1.94
3950 4901 5.542779 GTTGAGTTGTATTCTCTGGTGACT 58.457 41.667 0.00 0.00 33.59 3.41
3988 4939 6.145338 TCATCCGAATCAGAACTACCTAAC 57.855 41.667 0.00 0.00 0.00 2.34
3993 4944 4.036027 CGAATCAGAACTACCTAACGGCTA 59.964 45.833 0.00 0.00 0.00 3.93
4030 5328 2.955660 GGTCAACCTGTGGATGTTTTCA 59.044 45.455 0.00 0.00 0.00 2.69
4169 5467 5.128827 TGTGGAGTCTCTTGTCAACTACTTT 59.871 40.000 0.00 0.00 0.00 2.66
4170 5468 5.463724 GTGGAGTCTCTTGTCAACTACTTTG 59.536 44.000 0.00 0.00 36.42 2.77
4174 5475 4.024809 GTCTCTTGTCAACTACTTTGCCAC 60.025 45.833 0.00 0.00 34.88 5.01
4179 5480 3.181491 TGTCAACTACTTTGCCACTTTGC 60.181 43.478 0.00 0.00 34.88 3.68
4183 5484 1.963515 CTACTTTGCCACTTTGCCCTT 59.036 47.619 0.00 0.00 0.00 3.95
4207 5508 4.686972 GCTTTCTTTCCAGTTCTTGCTTT 58.313 39.130 0.00 0.00 0.00 3.51
4272 5573 2.262423 AAGTGGCAGAAGAACAGGAC 57.738 50.000 0.00 0.00 0.00 3.85
4290 5591 7.093322 ACAGGACAAGATTTGCTCATATTTC 57.907 36.000 0.00 0.00 0.00 2.17
4383 5723 6.048509 ACTTTTGCAAAAACATACTCCCTTG 58.951 36.000 23.92 10.88 0.00 3.61
4448 5788 0.961753 GCCTTTCACCCTCACCTTTG 59.038 55.000 0.00 0.00 0.00 2.77
4450 5790 2.488347 GCCTTTCACCCTCACCTTTGTA 60.488 50.000 0.00 0.00 0.00 2.41
4452 5792 3.821033 CCTTTCACCCTCACCTTTGTAAG 59.179 47.826 0.00 0.00 0.00 2.34
4453 5793 4.461198 CTTTCACCCTCACCTTTGTAAGT 58.539 43.478 0.00 0.00 0.00 2.24
4454 5794 5.455612 CCTTTCACCCTCACCTTTGTAAGTA 60.456 44.000 0.00 0.00 0.00 2.24
4455 5795 4.612264 TCACCCTCACCTTTGTAAGTAC 57.388 45.455 0.00 0.00 0.00 2.73
4468 5809 5.957842 TTGTAAGTACATCCTGGCAAAAG 57.042 39.130 0.00 0.00 35.89 2.27
4484 5825 5.870433 TGGCAAAAGCTTATGAAATGTGATG 59.130 36.000 0.00 0.00 0.00 3.07
4497 5838 2.118313 TGTGATGTGGCAATCTCCAG 57.882 50.000 0.00 0.00 36.67 3.86
4523 5872 2.108250 AGTAAAGGCCAGCTCTTTGGAA 59.892 45.455 5.01 0.00 40.87 3.53
4717 6080 6.205658 CCCCTAGCTAAACATAGATTTGAAGC 59.794 42.308 0.00 0.00 0.00 3.86
4720 6083 7.446625 CCTAGCTAAACATAGATTTGAAGCCAT 59.553 37.037 0.00 0.00 0.00 4.40
4723 6086 6.694411 GCTAAACATAGATTTGAAGCCATGTG 59.306 38.462 0.00 0.00 0.00 3.21
4765 6128 0.609662 GCACAAATTGCCTCACCCAT 59.390 50.000 0.00 0.00 46.63 4.00
4766 6129 1.824230 GCACAAATTGCCTCACCCATA 59.176 47.619 0.00 0.00 46.63 2.74
4767 6130 2.159198 GCACAAATTGCCTCACCCATAG 60.159 50.000 0.00 0.00 46.63 2.23
4768 6131 2.102578 ACAAATTGCCTCACCCATAGC 58.897 47.619 0.00 0.00 0.00 2.97
4769 6132 2.291800 ACAAATTGCCTCACCCATAGCT 60.292 45.455 0.00 0.00 0.00 3.32
4770 6133 2.355010 AATTGCCTCACCCATAGCTC 57.645 50.000 0.00 0.00 0.00 4.09
4771 6134 1.516110 ATTGCCTCACCCATAGCTCT 58.484 50.000 0.00 0.00 0.00 4.09
4772 6135 1.289160 TTGCCTCACCCATAGCTCTT 58.711 50.000 0.00 0.00 0.00 2.85
4773 6136 0.833287 TGCCTCACCCATAGCTCTTC 59.167 55.000 0.00 0.00 0.00 2.87
4774 6137 0.833287 GCCTCACCCATAGCTCTTCA 59.167 55.000 0.00 0.00 0.00 3.02
4775 6138 1.419387 GCCTCACCCATAGCTCTTCAT 59.581 52.381 0.00 0.00 0.00 2.57
4776 6139 2.809665 GCCTCACCCATAGCTCTTCATG 60.810 54.545 0.00 0.00 0.00 3.07
4777 6140 2.702478 CCTCACCCATAGCTCTTCATGA 59.298 50.000 0.00 0.00 0.00 3.07
4778 6141 3.135348 CCTCACCCATAGCTCTTCATGAA 59.865 47.826 8.12 8.12 0.00 2.57
4779 6142 4.378774 CTCACCCATAGCTCTTCATGAAG 58.621 47.826 26.56 26.56 39.71 3.02
4780 6143 3.135348 TCACCCATAGCTCTTCATGAAGG 59.865 47.826 30.33 22.38 38.88 3.46
4781 6144 2.158696 ACCCATAGCTCTTCATGAAGGC 60.159 50.000 30.33 28.87 38.88 4.35
4782 6145 2.158711 CCCATAGCTCTTCATGAAGGCA 60.159 50.000 32.28 23.83 38.88 4.75
4783 6146 3.498121 CCCATAGCTCTTCATGAAGGCAT 60.498 47.826 32.28 24.51 38.88 4.40
4794 6157 2.616634 TGAAGGCATGATCTCTGCTC 57.383 50.000 16.83 10.31 39.60 4.26
4795 6158 1.835531 TGAAGGCATGATCTCTGCTCA 59.164 47.619 16.83 12.19 39.60 4.26
4796 6159 2.237893 TGAAGGCATGATCTCTGCTCAA 59.762 45.455 16.83 2.93 39.60 3.02
4797 6160 2.328819 AGGCATGATCTCTGCTCAAC 57.671 50.000 16.83 4.52 39.60 3.18
4798 6161 1.838715 AGGCATGATCTCTGCTCAACT 59.161 47.619 16.83 6.28 39.60 3.16
4799 6162 2.239150 AGGCATGATCTCTGCTCAACTT 59.761 45.455 16.83 0.00 39.60 2.66
4800 6163 2.613133 GGCATGATCTCTGCTCAACTTC 59.387 50.000 16.83 0.16 39.60 3.01
4801 6164 2.284684 GCATGATCTCTGCTCAACTTCG 59.715 50.000 12.00 0.00 36.68 3.79
4802 6165 3.519579 CATGATCTCTGCTCAACTTCGT 58.480 45.455 0.00 0.00 0.00 3.85
4803 6166 2.951726 TGATCTCTGCTCAACTTCGTG 58.048 47.619 0.00 0.00 0.00 4.35
4804 6167 2.266554 GATCTCTGCTCAACTTCGTGG 58.733 52.381 0.00 0.00 0.00 4.94
4805 6168 1.040646 TCTCTGCTCAACTTCGTGGT 58.959 50.000 0.00 0.00 0.00 4.16
4806 6169 1.412710 TCTCTGCTCAACTTCGTGGTT 59.587 47.619 0.00 0.00 0.00 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
651 698 5.957796 CGATATGGAAAAAGTGCGTCTAAAC 59.042 40.000 0.00 0.00 0.00 2.01
664 711 2.483013 CGAGACAGGCCGATATGGAAAA 60.483 50.000 0.00 0.00 42.00 2.29
824 889 3.438087 CCAGTGATGCCTAAACTTGTCAG 59.562 47.826 0.00 0.00 0.00 3.51
906 971 1.373812 GCCTACTTGGTTGGGTCGT 59.626 57.895 1.04 0.00 38.35 4.34
907 972 1.376812 GGCCTACTTGGTTGGGTCG 60.377 63.158 0.00 0.00 38.35 4.79
908 973 1.001269 GGGCCTACTTGGTTGGGTC 60.001 63.158 0.84 0.00 38.35 4.46
951 1018 1.609841 GGTTCGGACGAAATGGGAAGT 60.610 52.381 8.88 0.00 35.75 3.01
1362 1446 2.613977 CCAGACGAGCAAATCCACTTCT 60.614 50.000 0.00 0.00 0.00 2.85
2057 2174 1.066587 CCGGACTTGAGCTCGATCC 59.933 63.158 16.92 16.92 0.00 3.36
2197 2327 9.734620 GCAATTGCAATATAACTGATTGACTAA 57.265 29.630 25.36 0.00 41.59 2.24
2342 2513 8.597167 CATATCATCCTGGTCCTTAACAGATAA 58.403 37.037 0.00 0.00 36.86 1.75
2343 2514 7.310671 GCATATCATCCTGGTCCTTAACAGATA 60.311 40.741 0.00 0.00 36.86 1.98
2418 2595 5.777850 TTTTTCCAAGTAAGGTAACAGGC 57.222 39.130 0.00 0.00 41.41 4.85
2487 2710 1.278127 TGCTAGTGGGGTTTACAGAGC 59.722 52.381 0.00 0.00 32.85 4.09
2539 2769 4.481930 TGCAGAAAACTCATAACCAACG 57.518 40.909 0.00 0.00 0.00 4.10
2591 2830 7.692460 AGAAATCATGTGATCTTTGCTAACA 57.308 32.000 0.00 0.00 32.75 2.41
2607 2846 8.312669 ACTACTAAGGCAGACTAAGAAATCAT 57.687 34.615 0.00 0.00 0.00 2.45
2612 2851 8.302438 GTGTAAACTACTAAGGCAGACTAAGAA 58.698 37.037 0.00 0.00 0.00 2.52
2728 3029 2.925306 GCAGAGCATTTGCCAAGAAGTG 60.925 50.000 0.00 0.00 43.38 3.16
2748 3049 4.457834 TTCTAGTTCCAAGTAGCTCAGC 57.542 45.455 0.00 0.00 33.02 4.26
2880 3387 8.430801 TGTATTTCCATTTGTTTGTCCAAAAG 57.569 30.769 0.00 0.00 37.81 2.27
2972 3483 6.619801 AAACATCTGACTTCAACCTGTTAC 57.380 37.500 0.00 0.00 0.00 2.50
3063 3595 5.569355 TCCATAACTCACAAATGACCACAT 58.431 37.500 0.00 0.00 38.50 3.21
3097 3632 6.942576 GGTCCATGTAATAGCACAAGGATAAT 59.057 38.462 3.80 0.00 45.26 1.28
3265 3832 5.917087 TCCTTTCCATTCCCATAATCTACCT 59.083 40.000 0.00 0.00 0.00 3.08
3272 3839 5.830991 CGGTATTTCCTTTCCATTCCCATAA 59.169 40.000 0.00 0.00 0.00 1.90
3327 3894 6.103997 TCTTTCTGTCGGTATGGAATGTAAC 58.896 40.000 0.00 0.00 0.00 2.50
3400 3967 1.014352 GACAACGGACAAGCACAAGT 58.986 50.000 0.00 0.00 0.00 3.16
3403 3970 0.107410 AAGGACAACGGACAAGCACA 60.107 50.000 0.00 0.00 0.00 4.57
3436 4003 4.497608 AGAACAAACAAACACATAAACGCG 59.502 37.500 3.53 3.53 0.00 6.01
3534 4110 4.873746 TTCTCAGTTTGCACTAGTAGCT 57.126 40.909 15.28 0.00 0.00 3.32
3539 4115 5.163814 GCCAAGTATTCTCAGTTTGCACTAG 60.164 44.000 0.00 0.00 0.00 2.57
3583 4165 5.717038 TCCGCATGCATATTGTATATTCG 57.283 39.130 19.57 0.00 0.00 3.34
3707 4657 6.150976 CCAACATCCAACTTAGCATTTACAGA 59.849 38.462 0.00 0.00 0.00 3.41
3846 4797 3.321497 CAGCAGAAGTAAGGTCAGTGAC 58.679 50.000 15.24 15.24 0.00 3.67
3871 4822 4.914983 TCATCAAGACTTCAAGAAGCCAT 58.085 39.130 9.62 0.00 41.99 4.40
3924 4875 5.242171 TCACCAGAGAATACAACTCAACGTA 59.758 40.000 0.00 0.00 36.91 3.57
3925 4876 4.038763 TCACCAGAGAATACAACTCAACGT 59.961 41.667 0.00 0.00 36.91 3.99
3950 4901 5.574740 ATTCGGATGAATTTTGGGTCTACCA 60.575 40.000 0.81 0.00 44.60 3.25
3993 4944 3.790437 CCTCGGATGCAGGCAGGT 61.790 66.667 0.00 0.00 0.00 4.00
4030 5328 2.106566 AGGATCAGCACGAACTCAGAT 58.893 47.619 0.00 0.00 0.00 2.90
4105 5403 0.319813 GCATCAACCAAACAGCCACC 60.320 55.000 0.00 0.00 0.00 4.61
4169 5467 3.294493 GCGAAGGGCAAAGTGGCA 61.294 61.111 4.09 0.00 45.76 4.92
4179 5480 1.897560 ACTGGAAAGAAAGCGAAGGG 58.102 50.000 0.00 0.00 0.00 3.95
4183 5484 2.290641 GCAAGAACTGGAAAGAAAGCGA 59.709 45.455 0.00 0.00 0.00 4.93
4207 5508 4.021632 TCCCATCAATTCAACGAAATTGCA 60.022 37.500 13.86 0.00 43.31 4.08
4243 5544 0.538057 TCTGCCACTTTGCCTCTTGG 60.538 55.000 0.00 0.00 0.00 3.61
4244 5545 1.268899 CTTCTGCCACTTTGCCTCTTG 59.731 52.381 0.00 0.00 0.00 3.02
4290 5591 8.359060 TGTCCGGTTTTAAAATCAATTTTGAG 57.641 30.769 11.61 0.00 41.08 3.02
4307 5647 6.954487 ATTAGAGTTTTTCTTTGTCCGGTT 57.046 33.333 0.00 0.00 37.36 4.44
4383 5723 0.963355 TCCAGGCGCATTTACAACCC 60.963 55.000 10.83 0.00 0.00 4.11
4448 5788 4.357018 GCTTTTGCCAGGATGTACTTAC 57.643 45.455 0.00 0.00 40.15 2.34
4468 5809 4.374843 TGCCACATCACATTTCATAAGC 57.625 40.909 0.00 0.00 0.00 3.09
4484 5825 1.271597 ACTTGGACTGGAGATTGCCAC 60.272 52.381 0.00 0.00 33.52 5.01
4497 5838 1.003696 AGAGCTGGCCTTTACTTGGAC 59.996 52.381 3.32 0.00 0.00 4.02
4523 5872 7.895429 TCTTGATTTCCCCTCAATCAAATAACT 59.105 33.333 8.89 0.00 45.59 2.24
4582 5940 5.170748 CCTTCTCAAATATTGCCAAACACC 58.829 41.667 0.00 0.00 0.00 4.16
4717 6080 7.373493 GGAATAATAATTGAAGAGGCACATGG 58.627 38.462 0.00 0.00 0.00 3.66
4720 6083 6.672593 AGGGAATAATAATTGAAGAGGCACA 58.327 36.000 0.00 0.00 0.00 4.57
4723 6086 6.942576 TGCTAGGGAATAATAATTGAAGAGGC 59.057 38.462 0.00 0.00 0.00 4.70
4761 6124 2.158711 TGCCTTCATGAAGAGCTATGGG 60.159 50.000 32.49 17.37 40.79 4.00
4774 6137 2.438392 TGAGCAGAGATCATGCCTTCAT 59.562 45.455 16.69 1.29 44.97 2.57
4775 6138 1.835531 TGAGCAGAGATCATGCCTTCA 59.164 47.619 16.69 12.78 44.97 3.02
4776 6139 2.613133 GTTGAGCAGAGATCATGCCTTC 59.387 50.000 16.69 10.79 44.97 3.46
4777 6140 2.239150 AGTTGAGCAGAGATCATGCCTT 59.761 45.455 16.69 2.56 44.97 4.35
4778 6141 1.838715 AGTTGAGCAGAGATCATGCCT 59.161 47.619 16.69 6.49 44.97 4.75
4779 6142 2.328819 AGTTGAGCAGAGATCATGCC 57.671 50.000 16.69 10.41 44.97 4.40
4780 6143 2.284684 CGAAGTTGAGCAGAGATCATGC 59.715 50.000 13.47 13.47 44.18 4.06
4781 6144 3.306434 CACGAAGTTGAGCAGAGATCATG 59.694 47.826 0.00 0.00 41.61 3.07
4782 6145 3.519579 CACGAAGTTGAGCAGAGATCAT 58.480 45.455 0.00 0.00 41.61 2.45
4783 6146 2.353109 CCACGAAGTTGAGCAGAGATCA 60.353 50.000 0.00 0.00 41.61 2.92
4784 6147 2.266554 CCACGAAGTTGAGCAGAGATC 58.733 52.381 0.00 0.00 41.61 2.75
4785 6148 1.620819 ACCACGAAGTTGAGCAGAGAT 59.379 47.619 0.00 0.00 41.61 2.75
4786 6149 1.040646 ACCACGAAGTTGAGCAGAGA 58.959 50.000 0.00 0.00 41.61 3.10
4787 6150 1.871080 AACCACGAAGTTGAGCAGAG 58.129 50.000 0.00 0.00 41.61 3.35


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

AutoCloner maintained by Alex Coulton.