Multiple sequence alignment - TraesCS6B01G313000

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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 TraesCS6B01G313000 chr6B 100.000 2728 0 0 1 2728 561042234 561044961 0.000000e+00 5038.0
1 TraesCS6B01G313000 chr6B 95.942 616 21 4 1982 2595 42759562 42758949 0.000000e+00 996.0
2 TraesCS6B01G313000 chr6B 86.313 358 43 3 1357 1708 558734127 558734484 4.260000e-103 385.0
3 TraesCS6B01G313000 chr6B 86.313 358 43 3 1357 1708 558816722 558817079 4.260000e-103 385.0
4 TraesCS6B01G313000 chr6B 82.519 389 42 19 898 1266 558816211 558816593 4.380000e-83 318.0
5 TraesCS6B01G313000 chr6B 82.262 389 43 19 898 1266 558733616 558733998 2.040000e-81 313.0
6 TraesCS6B01G313000 chr6B 86.713 286 31 4 988 1266 561146438 561146153 7.340000e-81 311.0
7 TraesCS6B01G313000 chr6B 83.333 342 44 12 1384 1717 561145992 561145656 1.230000e-78 303.0
8 TraesCS6B01G313000 chr6B 93.902 164 3 2 775 938 561012832 561012988 9.760000e-60 241.0
9 TraesCS6B01G313000 chr6A 90.319 2035 113 32 1 1982 515645112 515643109 0.000000e+00 2590.0
10 TraesCS6B01G313000 chr6A 85.359 362 45 7 1357 1717 515658075 515657721 4.290000e-98 368.0
11 TraesCS6B01G313000 chr6A 84.073 383 50 8 1357 1729 515034560 515034179 2.580000e-95 359.0
12 TraesCS6B01G313000 chr6A 82.642 386 44 11 900 1266 515035059 515034678 1.220000e-83 320.0
13 TraesCS6B01G313000 chr6A 91.480 223 17 2 2 223 182314952 182315173 3.410000e-79 305.0
14 TraesCS6B01G313000 chr6A 88.889 243 27 0 1024 1266 515665723 515665481 1.590000e-77 300.0
15 TraesCS6B01G313000 chr6A 88.444 225 11 8 710 933 515650376 515650166 9.690000e-65 257.0
16 TraesCS6B01G313000 chr6D 89.244 1878 100 36 1 1823 373393393 373391563 0.000000e+00 2255.0
17 TraesCS6B01G313000 chr6D 86.096 374 44 6 1354 1720 372950683 372950311 1.970000e-106 396.0
18 TraesCS6B01G313000 chr6D 88.591 298 34 0 969 1266 373418568 373418271 2.000000e-96 363.0
19 TraesCS6B01G313000 chr6D 83.120 391 43 18 899 1270 372951122 372950736 4.350000e-88 335.0
20 TraesCS6B01G313000 chr6D 89.565 230 9 6 710 938 373409405 373409190 7.440000e-71 278.0
21 TraesCS6B01G313000 chr6D 94.886 176 7 1 1809 1982 373391440 373391265 9.620000e-70 274.0
22 TraesCS6B01G313000 chr6D 79.006 362 47 16 319 668 373392745 373393089 1.270000e-53 220.0
23 TraesCS6B01G313000 chr6D 93.458 107 3 3 2573 2679 373391273 373391171 3.640000e-34 156.0
24 TraesCS6B01G313000 chr6D 82.584 178 21 5 809 979 373245184 373245010 6.090000e-32 148.0
25 TraesCS6B01G313000 chr7B 97.470 593 14 1 1982 2574 678852974 678852383 0.000000e+00 1011.0
26 TraesCS6B01G313000 chr3B 97.470 593 14 1 1982 2574 491523652 491524243 0.000000e+00 1011.0
27 TraesCS6B01G313000 chr3B 91.150 226 19 1 2 226 384435112 384435337 3.410000e-79 305.0
28 TraesCS6B01G313000 chr5B 97.302 593 15 1 1982 2574 672842758 672842167 0.000000e+00 1005.0
29 TraesCS6B01G313000 chr5B 96.471 595 19 2 1982 2575 341550375 341549782 0.000000e+00 981.0
30 TraesCS6B01G313000 chr5B 96.696 575 18 1 1982 2556 42148118 42147545 0.000000e+00 955.0
31 TraesCS6B01G313000 chr7A 96.965 593 17 1 1982 2574 169308701 169308110 0.000000e+00 994.0
32 TraesCS6B01G313000 chr7A 87.896 347 33 7 341 685 97911755 97912094 1.520000e-107 399.0
33 TraesCS6B01G313000 chr7A 91.892 222 17 1 4 224 578444713 578444492 2.640000e-80 309.0
34 TraesCS6B01G313000 chr7A 91.403 221 19 0 2 222 618658558 618658338 1.230000e-78 303.0
35 TraesCS6B01G313000 chr7A 77.684 354 62 15 336 683 97912068 97911726 1.660000e-47 200.0
36 TraesCS6B01G313000 chr1B 96.134 595 21 2 1982 2575 7969351 7968758 0.000000e+00 970.0
37 TraesCS6B01G313000 chr2B 96.429 532 18 1 2043 2574 560345203 560344673 0.000000e+00 876.0
38 TraesCS6B01G313000 chrUn 86.592 358 42 3 1357 1708 410293184 410293541 9.160000e-105 390.0
39 TraesCS6B01G313000 chrUn 93.023 43 3 0 256 298 65665417 65665375 2.270000e-06 63.9
40 TraesCS6B01G313000 chr5D 91.556 225 19 0 1 225 333119994 333119770 7.340000e-81 311.0
41 TraesCS6B01G313000 chr5D 77.941 408 62 14 299 685 314415963 314415563 2.110000e-56 230.0
42 TraesCS6B01G313000 chr2D 91.892 222 17 1 2 223 569203497 569203717 2.640000e-80 309.0
43 TraesCS6B01G313000 chr2D 80.453 353 45 15 353 685 574394462 574394114 5.830000e-62 248.0
44 TraesCS6B01G313000 chr2A 91.480 223 18 1 1 222 451391831 451392053 3.410000e-79 305.0
45 TraesCS6B01G313000 chr2A 90.217 184 17 1 503 685 753474962 753474779 3.510000e-59 239.0
46 TraesCS6B01G313000 chr7D 89.700 233 22 2 2 232 557415919 557416151 2.050000e-76 296.0
47 TraesCS6B01G313000 chr7D 80.488 328 42 12 341 660 64516084 64515771 5.870000e-57 231.0
48 TraesCS6B01G313000 chr3D 80.335 239 35 7 425 654 540229549 540229314 1.300000e-38 171.0
49 TraesCS6B01G313000 chr3D 93.617 47 2 1 241 286 445106780 445106734 4.870000e-08 69.4
50 TraesCS6B01G313000 chr3D 90.698 43 3 1 256 298 523299206 523299247 3.790000e-04 56.5


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 TraesCS6B01G313000 chr6B 561042234 561044961 2727 False 5038.0 5038 100.000000 1 2728 1 chr6B.!!$F2 2727
1 TraesCS6B01G313000 chr6B 42758949 42759562 613 True 996.0 996 95.942000 1982 2595 1 chr6B.!!$R1 613
2 TraesCS6B01G313000 chr6B 558816211 558817079 868 False 351.5 385 84.416000 898 1708 2 chr6B.!!$F4 810
3 TraesCS6B01G313000 chr6B 558733616 558734484 868 False 349.0 385 84.287500 898 1708 2 chr6B.!!$F3 810
4 TraesCS6B01G313000 chr6B 561145656 561146438 782 True 307.0 311 85.023000 988 1717 2 chr6B.!!$R2 729
5 TraesCS6B01G313000 chr6A 515643109 515645112 2003 True 2590.0 2590 90.319000 1 1982 1 chr6A.!!$R1 1981
6 TraesCS6B01G313000 chr6A 515034179 515035059 880 True 339.5 359 83.357500 900 1729 2 chr6A.!!$R5 829
7 TraesCS6B01G313000 chr6D 373391171 373393393 2222 True 895.0 2255 92.529333 1 2679 3 chr6D.!!$R5 2678
8 TraesCS6B01G313000 chr6D 372950311 372951122 811 True 365.5 396 84.608000 899 1720 2 chr6D.!!$R4 821
9 TraesCS6B01G313000 chr7B 678852383 678852974 591 True 1011.0 1011 97.470000 1982 2574 1 chr7B.!!$R1 592
10 TraesCS6B01G313000 chr3B 491523652 491524243 591 False 1011.0 1011 97.470000 1982 2574 1 chr3B.!!$F2 592
11 TraesCS6B01G313000 chr5B 672842167 672842758 591 True 1005.0 1005 97.302000 1982 2574 1 chr5B.!!$R3 592
12 TraesCS6B01G313000 chr5B 341549782 341550375 593 True 981.0 981 96.471000 1982 2575 1 chr5B.!!$R2 593
13 TraesCS6B01G313000 chr5B 42147545 42148118 573 True 955.0 955 96.696000 1982 2556 1 chr5B.!!$R1 574
14 TraesCS6B01G313000 chr7A 169308110 169308701 591 True 994.0 994 96.965000 1982 2574 1 chr7A.!!$R2 592
15 TraesCS6B01G313000 chr1B 7968758 7969351 593 True 970.0 970 96.134000 1982 2575 1 chr1B.!!$R1 593
16 TraesCS6B01G313000 chr2B 560344673 560345203 530 True 876.0 876 96.429000 2043 2574 1 chr2B.!!$R1 531

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
332 343 0.659957 GAAATCCAGCTCGATGCACC 59.340 55.0 0.0 0.0 45.94 5.01 F
1007 1054 0.621862 GGAAGGGGGAGGATGAGTGT 60.622 60.0 0.0 0.0 0.00 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1430 1571 0.595053 CCGTGCTAATCGTGATCGCT 60.595 55.0 4.48 0.0 36.96 4.93 R
2603 2919 0.100503 AAACGGCAGCACACAACTTC 59.899 50.0 0.00 0.0 0.00 3.01 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
213 214 1.515081 TGCGAACTAAAAAGGACCGG 58.485 50.000 0.00 0.00 0.00 5.28
215 216 2.289819 TGCGAACTAAAAAGGACCGGAT 60.290 45.455 9.46 0.00 0.00 4.18
236 237 7.148154 CCGGATGGAGTACAAATTATGTTTTCA 60.148 37.037 0.00 0.00 39.70 2.69
330 341 1.660167 CTGAAATCCAGCTCGATGCA 58.340 50.000 0.00 0.00 45.94 3.96
331 342 1.329906 CTGAAATCCAGCTCGATGCAC 59.670 52.381 0.00 0.00 45.94 4.57
332 343 0.659957 GAAATCCAGCTCGATGCACC 59.340 55.000 0.00 0.00 45.94 5.01
333 344 0.749454 AAATCCAGCTCGATGCACCC 60.749 55.000 0.00 0.00 45.94 4.61
334 345 1.913951 AATCCAGCTCGATGCACCCA 61.914 55.000 0.00 0.00 45.94 4.51
335 346 2.599645 ATCCAGCTCGATGCACCCAC 62.600 60.000 9.09 0.00 45.94 4.61
336 347 3.190849 CAGCTCGATGCACCCACG 61.191 66.667 9.09 0.00 45.94 4.94
337 348 4.457496 AGCTCGATGCACCCACGG 62.457 66.667 9.09 0.00 45.94 4.94
339 350 4.758251 CTCGATGCACCCACGGCA 62.758 66.667 0.00 0.00 46.66 5.69
372 383 7.836017 CGCAAGAAAACATAGCAAAATATTTCG 59.164 33.333 0.10 0.00 43.02 3.46
416 427 7.592938 TGTGGAAATGACTATGAACAAATGTC 58.407 34.615 0.00 0.00 0.00 3.06
557 571 4.194640 CTCCTCGAATGTCATTTGACCAT 58.805 43.478 10.94 0.00 44.15 3.55
573 587 3.069872 TGACCATCAAACTTTGCAAGCAT 59.930 39.130 0.00 0.00 0.00 3.79
613 627 7.669304 TCATAGTCATTCCCACAAAATTTCAGA 59.331 33.333 0.00 0.00 0.00 3.27
676 701 3.306472 ACCAAGCTGGGTGTAGAAAAA 57.694 42.857 13.58 0.00 43.37 1.94
694 719 4.336889 AAAACCACTCTCATCGACTGAA 57.663 40.909 0.00 0.00 32.14 3.02
726 751 4.943705 ACACCCAATTATTAGAGCACAGTG 59.056 41.667 0.00 0.00 0.00 3.66
735 760 5.931441 ATTAGAGCACAGTGAGAAACAAC 57.069 39.130 4.15 0.00 0.00 3.32
746 771 4.336713 AGTGAGAAACAACTTTTGAGGCTC 59.663 41.667 7.79 7.79 0.00 4.70
749 774 2.755952 AACAACTTTTGAGGCTCCCT 57.244 45.000 12.86 0.00 36.03 4.20
818 844 7.298374 TGATCTTACCCTATCATGTAGAGTGT 58.702 38.462 0.00 0.00 0.00 3.55
842 868 9.349713 TGTGGTCTATTTTCTGAAAAGTGTATT 57.650 29.630 19.14 5.83 33.22 1.89
895 921 4.061596 CAAGTCAAGGTCTCCAGAAAGTC 58.938 47.826 0.00 0.00 0.00 3.01
896 922 2.297597 AGTCAAGGTCTCCAGAAAGTCG 59.702 50.000 0.00 0.00 0.00 4.18
967 994 3.423539 AGTACTGCAGATTTCCTTGCA 57.576 42.857 23.35 0.00 35.83 4.08
1007 1054 0.621862 GGAAGGGGGAGGATGAGTGT 60.622 60.000 0.00 0.00 0.00 3.55
1271 1325 2.946990 CCTTCAAAACCAAGGTACGTGT 59.053 45.455 0.00 0.00 36.40 4.49
1307 1377 1.280421 GGCAACAGAGGATTGGAGACT 59.720 52.381 0.00 0.00 0.00 3.24
1336 1441 1.422388 GTACGTCGTTTGACCCCTTC 58.578 55.000 1.78 0.00 42.37 3.46
1442 1589 1.227380 GAGCCCAGCGATCACGATT 60.227 57.895 0.00 0.00 42.66 3.34
1490 1637 1.686110 CCTCTACGACCCCCTGCTT 60.686 63.158 0.00 0.00 0.00 3.91
1665 1818 3.797353 CTAGTGGGGCGGTGGCAT 61.797 66.667 0.00 0.00 42.47 4.40
1732 1888 1.208052 TCTCCTTGCCATCTAGTGCAC 59.792 52.381 9.40 9.40 37.18 4.57
1735 1891 1.709147 CTTGCCATCTAGTGCACGCC 61.709 60.000 12.01 0.00 37.18 5.68
1737 1893 1.884926 GCCATCTAGTGCACGCCTC 60.885 63.158 12.01 0.00 0.00 4.70
1739 1895 1.517361 CATCTAGTGCACGCCTCCA 59.483 57.895 12.01 0.00 0.00 3.86
1749 1909 4.379243 CGCCTCCAGCCGTTCACT 62.379 66.667 0.00 0.00 38.78 3.41
1780 1940 5.680619 AGTTCATTCACCACAAGAACTACA 58.319 37.500 4.48 0.00 44.92 2.74
1781 1941 5.760253 AGTTCATTCACCACAAGAACTACAG 59.240 40.000 4.48 0.00 44.92 2.74
1782 1942 5.290493 TCATTCACCACAAGAACTACAGT 57.710 39.130 0.00 0.00 0.00 3.55
1783 1943 6.413783 TCATTCACCACAAGAACTACAGTA 57.586 37.500 0.00 0.00 0.00 2.74
1784 1944 6.220930 TCATTCACCACAAGAACTACAGTAC 58.779 40.000 0.00 0.00 0.00 2.73
1785 1945 5.864418 TTCACCACAAGAACTACAGTACT 57.136 39.130 0.00 0.00 0.00 2.73
1786 1946 6.964807 TTCACCACAAGAACTACAGTACTA 57.035 37.500 0.00 0.00 0.00 1.82
1787 1947 6.964807 TCACCACAAGAACTACAGTACTAA 57.035 37.500 0.00 0.00 0.00 2.24
1788 1948 7.534723 TCACCACAAGAACTACAGTACTAAT 57.465 36.000 0.00 0.00 0.00 1.73
1789 1949 7.959175 TCACCACAAGAACTACAGTACTAATT 58.041 34.615 0.00 0.00 0.00 1.40
1833 2145 8.258007 CAGAGTGGGTTGTCTTAATTAGTCATA 58.742 37.037 0.00 0.00 0.00 2.15
1865 2177 2.594592 GGCGTTGGTGTGAGCCTT 60.595 61.111 0.00 0.00 45.67 4.35
2051 2365 8.533657 TCAGAAGAAACCGGATAAAGTTATGTA 58.466 33.333 9.46 0.00 0.00 2.29
2096 2410 7.528307 TGTTATAAATTAAATGTTGACGCCGT 58.472 30.769 0.00 0.00 0.00 5.68
2158 2472 0.034896 GAAACAACCGAGGAGAGGCA 59.965 55.000 0.00 0.00 0.00 4.75
2452 2768 6.402550 CGCACAATCTTGCTAGACATAGTTTT 60.403 38.462 0.00 0.00 40.62 2.43
2489 2805 3.075882 TCTTGTTTGGGATGGTGATCCTT 59.924 43.478 0.00 0.00 46.88 3.36
2587 2903 3.344064 AAAAAGTTGTGTGCTGCCG 57.656 47.368 0.00 0.00 0.00 5.69
2588 2904 0.530288 AAAAAGTTGTGTGCTGCCGT 59.470 45.000 0.00 0.00 0.00 5.68
2589 2905 0.530288 AAAAGTTGTGTGCTGCCGTT 59.470 45.000 0.00 0.00 0.00 4.44
2590 2906 1.384525 AAAGTTGTGTGCTGCCGTTA 58.615 45.000 0.00 0.00 0.00 3.18
2591 2907 1.384525 AAGTTGTGTGCTGCCGTTAA 58.615 45.000 0.00 0.00 0.00 2.01
2592 2908 0.944386 AGTTGTGTGCTGCCGTTAAG 59.056 50.000 0.00 0.00 0.00 1.85
2593 2909 0.661020 GTTGTGTGCTGCCGTTAAGT 59.339 50.000 0.00 0.00 0.00 2.24
2594 2910 1.064952 GTTGTGTGCTGCCGTTAAGTT 59.935 47.619 0.00 0.00 0.00 2.66
2595 2911 0.941542 TGTGTGCTGCCGTTAAGTTC 59.058 50.000 0.00 0.00 0.00 3.01
2596 2912 0.941542 GTGTGCTGCCGTTAAGTTCA 59.058 50.000 0.00 0.00 0.00 3.18
2597 2913 1.332375 GTGTGCTGCCGTTAAGTTCAA 59.668 47.619 0.00 0.00 0.00 2.69
2598 2914 2.017782 TGTGCTGCCGTTAAGTTCAAA 58.982 42.857 0.00 0.00 0.00 2.69
2599 2915 2.423892 TGTGCTGCCGTTAAGTTCAAAA 59.576 40.909 0.00 0.00 0.00 2.44
2600 2916 3.119459 TGTGCTGCCGTTAAGTTCAAAAA 60.119 39.130 0.00 0.00 0.00 1.94
2650 2966 3.482436 TCTAGTTGGCGGTGACAATTTT 58.518 40.909 0.00 0.00 31.24 1.82
2671 2987 7.503521 TTTTTGAGGCTTTTGTTCACTTTTT 57.496 28.000 0.00 0.00 0.00 1.94
2679 2995 7.331934 AGGCTTTTGTTCACTTTTTCTTTCTTC 59.668 33.333 0.00 0.00 0.00 2.87
2680 2996 7.413000 GGCTTTTGTTCACTTTTTCTTTCTTCC 60.413 37.037 0.00 0.00 0.00 3.46
2681 2997 7.575332 TTTTGTTCACTTTTTCTTTCTTCCG 57.425 32.000 0.00 0.00 0.00 4.30
2682 2998 4.668289 TGTTCACTTTTTCTTTCTTCCGC 58.332 39.130 0.00 0.00 0.00 5.54
2683 2999 4.156922 TGTTCACTTTTTCTTTCTTCCGCA 59.843 37.500 0.00 0.00 0.00 5.69
2684 3000 4.552166 TCACTTTTTCTTTCTTCCGCAG 57.448 40.909 0.00 0.00 0.00 5.18
2685 3001 4.196193 TCACTTTTTCTTTCTTCCGCAGA 58.804 39.130 0.00 0.00 0.00 4.26
2686 3002 4.638421 TCACTTTTTCTTTCTTCCGCAGAA 59.362 37.500 0.00 0.00 39.99 3.02
2687 3003 4.735338 CACTTTTTCTTTCTTCCGCAGAAC 59.265 41.667 0.00 0.00 41.56 3.01
2688 3004 4.398044 ACTTTTTCTTTCTTCCGCAGAACA 59.602 37.500 0.00 0.00 41.56 3.18
2689 3005 4.974368 TTTTCTTTCTTCCGCAGAACAA 57.026 36.364 0.00 0.00 41.56 2.83
2690 3006 5.514274 TTTTCTTTCTTCCGCAGAACAAT 57.486 34.783 0.00 0.00 41.56 2.71
2691 3007 5.514274 TTTCTTTCTTCCGCAGAACAATT 57.486 34.783 0.00 0.00 41.56 2.32
2692 3008 5.514274 TTCTTTCTTCCGCAGAACAATTT 57.486 34.783 0.00 0.00 41.56 1.82
2693 3009 5.514274 TCTTTCTTCCGCAGAACAATTTT 57.486 34.783 0.00 0.00 41.56 1.82
2694 3010 5.519722 TCTTTCTTCCGCAGAACAATTTTC 58.480 37.500 0.00 0.00 41.56 2.29
2695 3011 5.299279 TCTTTCTTCCGCAGAACAATTTTCT 59.701 36.000 0.00 0.00 41.56 2.52
2696 3012 5.514274 TTCTTCCGCAGAACAATTTTCTT 57.486 34.783 1.59 0.00 36.51 2.52
2697 3013 6.627395 TTCTTCCGCAGAACAATTTTCTTA 57.373 33.333 1.59 0.00 36.51 2.10
2698 3014 6.627395 TCTTCCGCAGAACAATTTTCTTAA 57.373 33.333 1.59 0.00 0.00 1.85
2699 3015 7.033530 TCTTCCGCAGAACAATTTTCTTAAA 57.966 32.000 1.59 0.00 0.00 1.52
2700 3016 7.138736 TCTTCCGCAGAACAATTTTCTTAAAG 58.861 34.615 1.59 0.00 0.00 1.85
2701 3017 6.627395 TCCGCAGAACAATTTTCTTAAAGA 57.373 33.333 1.59 0.00 0.00 2.52
2702 3018 6.668323 TCCGCAGAACAATTTTCTTAAAGAG 58.332 36.000 1.59 0.00 0.00 2.85
2703 3019 6.262273 TCCGCAGAACAATTTTCTTAAAGAGT 59.738 34.615 1.59 0.00 0.00 3.24
2704 3020 6.578919 CCGCAGAACAATTTTCTTAAAGAGTC 59.421 38.462 1.59 0.00 0.00 3.36
2705 3021 7.355778 CGCAGAACAATTTTCTTAAAGAGTCT 58.644 34.615 0.00 0.00 0.00 3.24
2706 3022 7.322222 CGCAGAACAATTTTCTTAAAGAGTCTG 59.678 37.037 0.00 0.00 0.00 3.51
2707 3023 8.345565 GCAGAACAATTTTCTTAAAGAGTCTGA 58.654 33.333 0.00 0.00 0.00 3.27
2708 3024 9.657121 CAGAACAATTTTCTTAAAGAGTCTGAC 57.343 33.333 0.00 0.00 0.00 3.51
2709 3025 9.620259 AGAACAATTTTCTTAAAGAGTCTGACT 57.380 29.630 10.66 10.66 0.00 3.41
2726 3042 9.953565 GAGTCTGACTATATAACCTCTAGATGT 57.046 37.037 10.86 0.00 0.00 3.06
2727 3043 9.733556 AGTCTGACTATATAACCTCTAGATGTG 57.266 37.037 8.91 0.00 0.00 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
75 76 8.623903 TGCATCATGACTTTAGTTTTCATATCC 58.376 33.333 0.00 0.00 0.00 2.59
209 210 5.367945 ACATAATTTGTACTCCATCCGGT 57.632 39.130 0.00 0.00 36.57 5.28
273 284 5.769967 CAGTCGACTGAGATTTAACCAAG 57.230 43.478 36.73 7.53 46.59 3.61
317 328 3.002583 TGGGTGCATCGAGCTGGA 61.003 61.111 0.00 0.00 45.94 3.86
338 349 1.657181 GTTTTCTTGCGCGGGTGTG 60.657 57.895 8.83 0.00 0.00 3.82
339 350 1.452145 ATGTTTTCTTGCGCGGGTGT 61.452 50.000 8.83 0.00 0.00 4.16
345 356 4.908966 ATTTTGCTATGTTTTCTTGCGC 57.091 36.364 0.00 0.00 0.00 6.09
383 394 9.474920 GTTCATAGTCATTTCCACAAAATTTCA 57.525 29.630 0.00 0.00 35.32 2.69
384 395 9.474920 TGTTCATAGTCATTTCCACAAAATTTC 57.525 29.630 0.00 0.00 35.32 2.17
388 399 9.258826 CATTTGTTCATAGTCATTTCCACAAAA 57.741 29.630 0.00 0.00 36.69 2.44
416 427 5.004726 GCACAAAACTTTGCAAGTACTTCTG 59.995 40.000 4.77 0.00 41.91 3.02
440 451 2.560105 TGCTCCTCGGATGTCATATGAG 59.440 50.000 5.42 6.76 0.00 2.90
444 455 2.700371 ACAATGCTCCTCGGATGTCATA 59.300 45.455 0.00 0.00 0.00 2.15
475 487 5.051508 GCACTGTTTGAGCACAATTTGTAAG 60.052 40.000 0.86 0.00 35.85 2.34
638 652 1.470805 GGTGCACCCACACAAGAAAAC 60.471 52.381 26.31 0.00 43.88 2.43
659 684 2.956333 GTGGTTTTTCTACACCCAGCTT 59.044 45.455 0.00 0.00 31.24 3.74
694 719 7.122204 GCTCTAATAATTGGGTGTGTTTAGGTT 59.878 37.037 0.00 0.00 0.00 3.50
726 751 3.004839 GGGAGCCTCAAAAGTTGTTTCTC 59.995 47.826 0.00 0.00 0.00 2.87
735 760 3.490348 TCTGAAAAGGGAGCCTCAAAAG 58.510 45.455 0.00 0.00 30.89 2.27
746 771 4.033709 TCTGGGAGATACTCTGAAAAGGG 58.966 47.826 0.00 0.00 0.00 3.95
749 774 6.613271 AGCTAATCTGGGAGATACTCTGAAAA 59.387 38.462 0.00 0.00 32.89 2.29
769 794 2.526304 ACGTTGCTGTCAAGAGCTAA 57.474 45.000 0.61 0.00 39.90 3.09
842 868 0.881796 CTGCGTCAGACCACACTCTA 59.118 55.000 0.00 0.00 32.44 2.43
895 921 3.624861 GGATGCTTTATATGGATGGCTCG 59.375 47.826 0.00 0.00 0.00 5.03
896 922 4.592942 TGGATGCTTTATATGGATGGCTC 58.407 43.478 0.00 0.00 0.00 4.70
1134 1188 2.452116 CACCTCCCAGTGGAACAGA 58.548 57.895 11.95 0.00 41.80 3.41
1299 1369 2.202610 CGCGCGATCAGTCTCCAA 60.203 61.111 28.94 0.00 0.00 3.53
1300 1370 4.193334 CCGCGCGATCAGTCTCCA 62.193 66.667 34.63 0.00 0.00 3.86
1301 1371 2.831366 TACCGCGCGATCAGTCTCC 61.831 63.158 34.63 0.00 0.00 3.71
1302 1372 1.654743 GTACCGCGCGATCAGTCTC 60.655 63.158 34.63 13.02 0.00 3.36
1303 1373 2.408022 GTACCGCGCGATCAGTCT 59.592 61.111 34.63 6.43 0.00 3.24
1307 1377 4.874282 CGACGTACCGCGCGATCA 62.874 66.667 34.63 13.07 46.11 2.92
1336 1441 1.113517 AGATCACGACGGGTATGGGG 61.114 60.000 0.00 0.00 0.00 4.96
1430 1571 0.595053 CCGTGCTAATCGTGATCGCT 60.595 55.000 4.48 0.00 36.96 4.93
1442 1589 3.075005 GACAGGAGGGCCGTGCTA 61.075 66.667 19.70 0.00 39.96 3.49
1658 1811 0.949105 AAGAACGACGACATGCCACC 60.949 55.000 0.00 0.00 0.00 4.61
1665 1818 0.596600 GCTCCACAAGAACGACGACA 60.597 55.000 0.00 0.00 0.00 4.35
1735 1891 3.114616 CGCAGTGAACGGCTGGAG 61.115 66.667 0.00 0.00 34.89 3.86
1762 1922 6.420913 AGTACTGTAGTTCTTGTGGTGAAT 57.579 37.500 0.00 0.00 0.00 2.57
1783 1943 9.367444 CTGTCGAAATTACTAGACCAAATTAGT 57.633 33.333 0.00 0.00 34.64 2.24
1784 1944 9.582431 TCTGTCGAAATTACTAGACCAAATTAG 57.418 33.333 0.00 0.00 33.04 1.73
1785 1945 9.582431 CTCTGTCGAAATTACTAGACCAAATTA 57.418 33.333 0.00 0.00 33.04 1.40
1786 1946 8.095169 ACTCTGTCGAAATTACTAGACCAAATT 58.905 33.333 0.00 0.00 33.04 1.82
1787 1947 7.545965 CACTCTGTCGAAATTACTAGACCAAAT 59.454 37.037 0.00 0.00 33.04 2.32
1788 1948 6.866770 CACTCTGTCGAAATTACTAGACCAAA 59.133 38.462 0.00 0.00 33.04 3.28
1789 1949 6.387465 CACTCTGTCGAAATTACTAGACCAA 58.613 40.000 0.00 0.00 33.04 3.67
1807 1982 6.464222 TGACTAATTAAGACAACCCACTCTG 58.536 40.000 0.00 0.00 0.00 3.35
1833 2145 1.967319 ACGCCAATAAGCATCCGAAT 58.033 45.000 0.00 0.00 0.00 3.34
1865 2177 2.591429 CCTCAGTGCGGTGCAACA 60.591 61.111 0.98 0.00 41.47 3.33
1923 2237 6.586082 GGCACAAATACCATACTTTCTGTTTG 59.414 38.462 0.00 0.00 0.00 2.93
1942 2256 1.133407 GAACACGGAACAAAGGCACAA 59.867 47.619 0.00 0.00 0.00 3.33
2051 2365 4.482990 ACAATTGATTGGAGGTTTCACCT 58.517 39.130 13.59 0.00 45.35 4.00
2072 2386 7.958112 ACGGCGTCAACATTTAATTTATAAC 57.042 32.000 6.77 0.00 0.00 1.89
2101 2415 1.611491 GCACCCGTTCCATCTTCAAAA 59.389 47.619 0.00 0.00 0.00 2.44
2385 2701 2.092429 GGGCAATGAGTGAAGGATACCA 60.092 50.000 0.00 0.00 37.17 3.25
2462 2778 3.650942 TCACCATCCCAAACAAGAGTAGT 59.349 43.478 0.00 0.00 0.00 2.73
2489 2805 3.811083 TGTCCGAAAGTAAAAAGCTGGA 58.189 40.909 0.00 0.00 0.00 3.86
2575 2891 1.332375 GAACTTAACGGCAGCACACAA 59.668 47.619 0.00 0.00 0.00 3.33
2576 2892 0.941542 GAACTTAACGGCAGCACACA 59.058 50.000 0.00 0.00 0.00 3.72
2577 2893 0.941542 TGAACTTAACGGCAGCACAC 59.058 50.000 0.00 0.00 0.00 3.82
2578 2894 1.669604 TTGAACTTAACGGCAGCACA 58.330 45.000 0.00 0.00 0.00 4.57
2579 2895 2.766970 TTTGAACTTAACGGCAGCAC 57.233 45.000 0.00 0.00 0.00 4.40
2580 2896 3.784701 TTTTTGAACTTAACGGCAGCA 57.215 38.095 0.00 0.00 0.00 4.41
2598 2914 2.735126 CGGCAGCACACAACTTCTTTTT 60.735 45.455 0.00 0.00 0.00 1.94
2599 2915 1.202290 CGGCAGCACACAACTTCTTTT 60.202 47.619 0.00 0.00 0.00 2.27
2600 2916 0.381801 CGGCAGCACACAACTTCTTT 59.618 50.000 0.00 0.00 0.00 2.52
2601 2917 0.748005 ACGGCAGCACACAACTTCTT 60.748 50.000 0.00 0.00 0.00 2.52
2602 2918 0.748005 AACGGCAGCACACAACTTCT 60.748 50.000 0.00 0.00 0.00 2.85
2603 2919 0.100503 AAACGGCAGCACACAACTTC 59.899 50.000 0.00 0.00 0.00 3.01
2604 2920 0.179140 CAAACGGCAGCACACAACTT 60.179 50.000 0.00 0.00 0.00 2.66
2605 2921 1.312371 ACAAACGGCAGCACACAACT 61.312 50.000 0.00 0.00 0.00 3.16
2606 2922 0.378962 TACAAACGGCAGCACACAAC 59.621 50.000 0.00 0.00 0.00 3.32
2607 2923 0.378962 GTACAAACGGCAGCACACAA 59.621 50.000 0.00 0.00 0.00 3.33
2650 2966 6.036577 AGAAAAAGTGAACAAAAGCCTCAA 57.963 33.333 0.00 0.00 0.00 3.02
2671 2987 5.299279 AGAAAATTGTTCTGCGGAAGAAAGA 59.701 36.000 20.45 0.00 46.51 2.52
2679 2995 6.438763 ACTCTTTAAGAAAATTGTTCTGCGG 58.561 36.000 0.00 0.00 0.00 5.69
2680 2996 7.322222 CAGACTCTTTAAGAAAATTGTTCTGCG 59.678 37.037 0.00 0.00 0.00 5.18
2681 2997 8.345565 TCAGACTCTTTAAGAAAATTGTTCTGC 58.654 33.333 0.00 0.00 0.00 4.26
2682 2998 9.657121 GTCAGACTCTTTAAGAAAATTGTTCTG 57.343 33.333 0.00 0.00 0.00 3.02
2683 2999 9.620259 AGTCAGACTCTTTAAGAAAATTGTTCT 57.380 29.630 0.00 0.00 0.00 3.01
2700 3016 9.953565 ACATCTAGAGGTTATATAGTCAGACTC 57.046 37.037 6.27 0.00 0.00 3.36
2701 3017 9.733556 CACATCTAGAGGTTATATAGTCAGACT 57.266 37.037 7.44 8.50 0.00 3.24


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

AutoCloner maintained by Alex Coulton.