Multiple sequence alignment - TraesCS3D01G269700

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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 TraesCS3D01G269700 chr3D 100.000 2468 0 0 2647 5114 374209586 374207119 0.000000e+00 4558.0
1 TraesCS3D01G269700 chr3D 100.000 2423 0 0 1 2423 374212232 374209810 0.000000e+00 4475.0
2 TraesCS3D01G269700 chr3D 89.583 48 1 4 5066 5111 339252958 339253003 1.990000e-04 58.4
3 TraesCS3D01G269700 chr3A 94.106 2477 89 23 2647 5114 496706015 496703587 0.000000e+00 3712.0
4 TraesCS3D01G269700 chr3A 89.742 2174 76 55 1 2086 496708389 496706275 0.000000e+00 2643.0
5 TraesCS3D01G269700 chr3A 87.786 131 15 1 2209 2339 496706273 496706144 8.870000e-33 152.0
6 TraesCS3D01G269700 chr3A 83.051 118 16 3 1168 1285 118566671 118566784 2.520000e-18 104.0
7 TraesCS3D01G269700 chr3A 96.552 58 2 0 2127 2184 496705634 496705691 4.210000e-16 97.1
8 TraesCS3D01G269700 chr3A 96.296 54 2 0 3270 3323 496705449 496705396 7.050000e-14 89.8
9 TraesCS3D01G269700 chr3A 94.872 39 2 0 2079 2117 657522656 657522618 1.540000e-05 62.1
10 TraesCS3D01G269700 chr3B 94.822 2047 70 12 3070 5114 487909227 487907215 0.000000e+00 3160.0
11 TraesCS3D01G269700 chr3B 91.170 2401 83 51 1 2309 487912377 487910014 0.000000e+00 3140.0
12 TraesCS3D01G269700 chr3B 93.484 399 19 5 2648 3043 487909818 487909424 2.050000e-163 586.0
13 TraesCS3D01G269700 chr3B 94.382 89 3 2 2337 2423 487909936 487909848 8.930000e-28 135.0
14 TraesCS3D01G269700 chr3B 94.444 54 2 1 3270 3323 487909079 487909027 1.180000e-11 82.4
15 TraesCS3D01G269700 chr3B 91.525 59 4 1 2127 2184 487909434 487909492 4.240000e-11 80.5
16 TraesCS3D01G269700 chr4A 82.161 768 103 21 3352 4113 658262254 658261515 3.360000e-176 628.0
17 TraesCS3D01G269700 chr4A 94.872 39 2 0 2079 2117 734367086 734367048 1.540000e-05 62.1
18 TraesCS3D01G269700 chr7B 82.213 759 103 20 3361 4113 164157811 164158543 4.350000e-175 625.0
19 TraesCS3D01G269700 chr7B 100.000 36 0 0 2082 2117 245991839 245991874 3.300000e-07 67.6
20 TraesCS3D01G269700 chr2D 80.749 774 91 23 3361 4103 596163728 596162982 7.480000e-153 551.0
21 TraesCS3D01G269700 chr2B 80.469 768 100 27 3352 4113 785240840 785240117 4.500000e-150 542.0
22 TraesCS3D01G269700 chr2B 79.793 772 105 30 3352 4113 793488137 793487407 9.820000e-142 514.0
23 TraesCS3D01G269700 chr4B 80.339 768 105 26 3352 4113 16557424 16558151 1.620000e-149 540.0
24 TraesCS3D01G269700 chr4B 97.368 38 1 0 2080 2117 73612787 73612824 1.190000e-06 65.8
25 TraesCS3D01G269700 chr6B 80.364 769 102 29 3352 4113 351224238 351224964 5.830000e-149 538.0
26 TraesCS3D01G269700 chr6B 97.297 37 1 0 2080 2116 647951537 647951573 4.270000e-06 63.9
27 TraesCS3D01G269700 chr2A 82.137 655 92 15 3463 4113 778619716 778620349 5.830000e-149 538.0
28 TraesCS3D01G269700 chr2A 97.297 37 1 0 2082 2118 769485829 769485865 4.270000e-06 63.9
29 TraesCS3D01G269700 chr2A 94.872 39 2 0 2079 2117 686781515 686781553 1.540000e-05 62.1
30 TraesCS3D01G269700 chr2A 100.000 30 0 0 2184 2213 221283441 221283412 7.150000e-04 56.5
31 TraesCS3D01G269700 chr1B 77.178 241 43 10 1419 1647 642392312 642392072 4.160000e-26 130.0
32 TraesCS3D01G269700 chr1B 85.870 92 12 1 1194 1285 433633671 433633581 4.210000e-16 97.1
33 TraesCS3D01G269700 chr1A 84.375 128 20 0 1520 1647 557935723 557935596 5.380000e-25 126.0
34 TraesCS3D01G269700 chr1D 76.763 241 44 10 1419 1647 465522431 465522191 1.930000e-24 124.0
35 TraesCS3D01G269700 chr7D 82.308 130 20 2 1520 1646 632756271 632756400 5.410000e-20 110.0
36 TraesCS3D01G269700 chr7D 100.000 30 0 0 2184 2213 610762727 610762698 7.150000e-04 56.5
37 TraesCS3D01G269700 chr6A 80.916 131 22 2 1520 1647 575589572 575589702 3.260000e-17 100.0
38 TraesCS3D01G269700 chr5A 97.368 38 1 0 2081 2118 287608236 287608199 1.190000e-06 65.8
39 TraesCS3D01G269700 chr5A 92.500 40 3 0 2951 2990 403876082 403876121 1.990000e-04 58.4
40 TraesCS3D01G269700 chr7A 100.000 30 0 0 2184 2213 700612450 700612421 7.150000e-04 56.5
41 TraesCS3D01G269700 chr7A 100.000 30 0 0 2184 2213 700635687 700635658 7.150000e-04 56.5
42 TraesCS3D01G269700 chr7A 100.000 30 0 0 2184 2213 700653311 700653282 7.150000e-04 56.5
43 TraesCS3D01G269700 chrUn 100.000 29 0 0 2184 2212 83375478 83375450 3.000000e-03 54.7
44 TraesCS3D01G269700 chr6D 100.000 29 0 0 2184 2212 178131351 178131379 3.000000e-03 54.7
45 TraesCS3D01G269700 chr4D 100.000 29 0 0 2184 2212 24864735 24864763 3.000000e-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 TraesCS3D01G269700 chr3D 374207119 374212232 5113 True 4516.50 4558 100.0000 1 5114 2 chr3D.!!$R1 5113
1 TraesCS3D01G269700 chr3A 496703587 496708389 4802 True 1649.20 3712 91.9825 1 5114 4 chr3A.!!$R2 5113
2 TraesCS3D01G269700 chr3B 487907215 487912377 5162 True 1420.68 3160 93.6604 1 5114 5 chr3B.!!$R1 5113
3 TraesCS3D01G269700 chr4A 658261515 658262254 739 True 628.00 628 82.1610 3352 4113 1 chr4A.!!$R1 761
4 TraesCS3D01G269700 chr7B 164157811 164158543 732 False 625.00 625 82.2130 3361 4113 1 chr7B.!!$F1 752
5 TraesCS3D01G269700 chr2D 596162982 596163728 746 True 551.00 551 80.7490 3361 4103 1 chr2D.!!$R1 742
6 TraesCS3D01G269700 chr2B 785240117 785240840 723 True 542.00 542 80.4690 3352 4113 1 chr2B.!!$R1 761
7 TraesCS3D01G269700 chr2B 793487407 793488137 730 True 514.00 514 79.7930 3352 4113 1 chr2B.!!$R2 761
8 TraesCS3D01G269700 chr4B 16557424 16558151 727 False 540.00 540 80.3390 3352 4113 1 chr4B.!!$F1 761
9 TraesCS3D01G269700 chr6B 351224238 351224964 726 False 538.00 538 80.3640 3352 4113 1 chr6B.!!$F1 761
10 TraesCS3D01G269700 chr2A 778619716 778620349 633 False 538.00 538 82.1370 3463 4113 1 chr2A.!!$F3 650


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
452 475 0.108992 TCGCGTTTATGTTCTCGGCT 60.109 50.000 5.77 0.0 0.00 5.52 F
1471 1593 0.243095 ACTACCGGAAGAACACGCTC 59.757 55.000 9.46 0.0 0.00 5.03 F
2340 2511 0.824759 ATCTACACGTCTTGCCTCCC 59.175 55.000 0.00 0.0 0.00 4.30 F
2343 2514 1.122632 TACACGTCTTGCCTCCCCAA 61.123 55.000 0.00 0.0 0.00 4.12 F
2344 2515 1.228124 CACGTCTTGCCTCCCCAAA 60.228 57.895 0.00 0.0 0.00 3.28 F
2996 3242 1.340088 TGCATGTGGCCTTGATGTTT 58.660 45.000 3.32 0.0 43.89 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2328 2499 0.250727 TTCTTTGGGGAGGCAAGACG 60.251 55.000 0.00 0.00 0.00 4.18 R
2933 3179 0.690762 AGGGGTCGGCGCATATAAAT 59.309 50.000 10.83 0.00 0.00 1.40 R
3572 3994 1.755179 ATGTGTTGGTAGCTGATGGC 58.245 50.000 0.00 0.00 42.19 4.40 R
3762 4191 5.704053 GGTTCATTTTCTTTACTCCGGAAGA 59.296 40.000 5.23 1.78 0.00 2.87 R
3934 4374 6.430000 ACATAAGCTTCCAAGTGAAAATACGT 59.570 34.615 0.00 0.00 31.06 3.57 R
4918 5386 0.040204 ACCATGGCAAAGAAGAGGGG 59.960 55.000 13.04 0.00 0.00 4.79 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
253 254 3.357079 CGGCACCCACAACTGCTC 61.357 66.667 0.00 0.00 33.63 4.26
254 255 2.985847 GGCACCCACAACTGCTCC 60.986 66.667 0.00 0.00 33.63 4.70
255 256 3.357079 GCACCCACAACTGCTCCG 61.357 66.667 0.00 0.00 0.00 4.63
256 257 3.357079 CACCCACAACTGCTCCGC 61.357 66.667 0.00 0.00 0.00 5.54
257 258 4.643387 ACCCACAACTGCTCCGCC 62.643 66.667 0.00 0.00 0.00 6.13
258 259 4.335647 CCCACAACTGCTCCGCCT 62.336 66.667 0.00 0.00 0.00 5.52
259 260 2.281761 CCACAACTGCTCCGCCTT 60.282 61.111 0.00 0.00 0.00 4.35
260 261 2.620112 CCACAACTGCTCCGCCTTG 61.620 63.158 0.00 0.00 0.00 3.61
261 262 2.980233 ACAACTGCTCCGCCTTGC 60.980 61.111 0.00 0.00 0.00 4.01
344 364 1.141858 GGGTGATTTTTGGCCCAACAA 59.858 47.619 0.00 0.00 40.76 2.83
345 365 2.493035 GGTGATTTTTGGCCCAACAAG 58.507 47.619 0.00 0.00 0.00 3.16
346 366 1.872952 GTGATTTTTGGCCCAACAAGC 59.127 47.619 3.70 3.70 0.00 4.01
391 413 0.391661 AGGTTTCGAGCGTGCATCAT 60.392 50.000 0.00 0.00 0.00 2.45
446 469 4.235382 ACGTAACATCGCGTTTATGTTC 57.765 40.909 22.98 15.29 44.36 3.18
447 470 3.922240 ACGTAACATCGCGTTTATGTTCT 59.078 39.130 22.98 8.02 44.36 3.01
448 471 4.030977 ACGTAACATCGCGTTTATGTTCTC 59.969 41.667 22.98 17.05 44.36 2.87
449 472 3.634730 AACATCGCGTTTATGTTCTCG 57.365 42.857 16.32 0.00 42.45 4.04
450 473 1.924524 ACATCGCGTTTATGTTCTCGG 59.075 47.619 5.77 0.00 33.83 4.63
451 474 0.928229 ATCGCGTTTATGTTCTCGGC 59.072 50.000 5.77 0.00 0.00 5.54
452 475 0.108992 TCGCGTTTATGTTCTCGGCT 60.109 50.000 5.77 0.00 0.00 5.52
454 477 1.076332 GCGTTTATGTTCTCGGCTGT 58.924 50.000 0.00 0.00 0.00 4.40
457 493 2.092211 CGTTTATGTTCTCGGCTGTCAC 59.908 50.000 0.00 0.00 0.00 3.67
483 519 5.107104 TGCAAGCATTTACTAGACAGTTTCG 60.107 40.000 0.00 0.00 36.14 3.46
509 545 2.811317 GGAAGCTGTCACCTCGCG 60.811 66.667 0.00 0.00 0.00 5.87
543 579 3.012518 CCATTAGCAGACAAGTCCCTTG 58.987 50.000 2.54 2.54 45.85 3.61
681 758 6.862469 TTAACTACAGCAGTACCCAACTAT 57.138 37.500 0.00 0.00 36.04 2.12
684 761 6.862469 ACTACAGCAGTACCCAACTATAAA 57.138 37.500 0.00 0.00 35.76 1.40
685 762 6.637657 ACTACAGCAGTACCCAACTATAAAC 58.362 40.000 0.00 0.00 35.76 2.01
686 763 4.501071 ACAGCAGTACCCAACTATAAACG 58.499 43.478 0.00 0.00 35.76 3.60
690 767 6.148150 CAGCAGTACCCAACTATAAACGAAAA 59.852 38.462 0.00 0.00 35.76 2.29
691 768 6.882678 AGCAGTACCCAACTATAAACGAAAAT 59.117 34.615 0.00 0.00 35.76 1.82
857 957 1.463674 AGGGCCACGCATAAAGAAAG 58.536 50.000 6.18 0.00 0.00 2.62
858 958 0.455815 GGGCCACGCATAAAGAAAGG 59.544 55.000 4.39 0.00 0.00 3.11
859 959 1.459450 GGCCACGCATAAAGAAAGGA 58.541 50.000 0.00 0.00 0.00 3.36
860 960 1.816224 GGCCACGCATAAAGAAAGGAA 59.184 47.619 0.00 0.00 0.00 3.36
861 961 2.230266 GGCCACGCATAAAGAAAGGAAA 59.770 45.455 0.00 0.00 0.00 3.13
862 962 3.242518 GCCACGCATAAAGAAAGGAAAC 58.757 45.455 0.00 0.00 0.00 2.78
863 963 3.488489 CCACGCATAAAGAAAGGAAACG 58.512 45.455 0.00 0.00 0.00 3.60
925 1025 2.283676 GTCGTCTCCCACTCCCCA 60.284 66.667 0.00 0.00 0.00 4.96
958 1068 2.774234 TCCCTCCAAAGCATAGAGAAGG 59.226 50.000 0.00 0.00 0.00 3.46
1350 1468 5.107837 CCAAGTAAGATTCGATTCGATTCGG 60.108 44.000 24.57 12.61 39.95 4.30
1369 1487 2.369394 GGTTCGCCTCTGAAATTGGAT 58.631 47.619 0.00 0.00 0.00 3.41
1371 1489 2.749621 GTTCGCCTCTGAAATTGGATGT 59.250 45.455 0.00 0.00 0.00 3.06
1372 1490 3.904800 TCGCCTCTGAAATTGGATGTA 57.095 42.857 0.00 0.00 0.00 2.29
1382 1500 2.489938 ATTGGATGTACGCTGTTGGT 57.510 45.000 0.00 0.00 0.00 3.67
1401 1519 4.819761 GGCCGCTGCTGATCGACA 62.820 66.667 0.00 0.00 37.74 4.35
1471 1593 0.243095 ACTACCGGAAGAACACGCTC 59.757 55.000 9.46 0.00 0.00 5.03
1543 1665 0.994247 TCAAGGTGAGCATGGATGGT 59.006 50.000 0.00 0.00 41.89 3.55
1688 1813 5.200368 ACTTTCCATCTTTGCGTTTGAAT 57.800 34.783 0.00 0.00 0.00 2.57
1704 1832 5.449041 CGTTTGAATGGATCCAGTGGTATTG 60.449 44.000 21.47 2.07 0.00 1.90
1809 1963 8.424918 ACTAGTAATAACATCCACCTCTGATTG 58.575 37.037 0.00 0.00 0.00 2.67
1964 2118 4.878397 GTGATCTTCCATGGGAGTAAGTTG 59.122 45.833 20.09 0.00 31.21 3.16
1977 2137 6.889722 TGGGAGTAAGTTGCTTTAATTGCTAT 59.110 34.615 0.00 0.00 0.00 2.97
1978 2138 8.050325 TGGGAGTAAGTTGCTTTAATTGCTATA 58.950 33.333 0.00 0.00 0.00 1.31
2031 2191 8.517323 AGGAGTAATCCCAGAATATCTTTGAT 57.483 34.615 5.39 0.00 0.00 2.57
2065 2225 6.404712 ACAAATCTCGTCGAACTTTAATCC 57.595 37.500 0.00 0.00 0.00 3.01
2106 2266 5.043762 ACTCCCTCCATCCCAAAATAAGTA 58.956 41.667 0.00 0.00 0.00 2.24
2134 2294 7.313646 TCAACTTTAATCGAAACCAACAACAA 58.686 30.769 0.00 0.00 0.00 2.83
2135 2295 7.273815 TCAACTTTAATCGAAACCAACAACAAC 59.726 33.333 0.00 0.00 0.00 3.32
2136 2296 6.622549 ACTTTAATCGAAACCAACAACAACA 58.377 32.000 0.00 0.00 0.00 3.33
2137 2297 6.528774 ACTTTAATCGAAACCAACAACAACAC 59.471 34.615 0.00 0.00 0.00 3.32
2138 2298 4.712122 AATCGAAACCAACAACAACACT 57.288 36.364 0.00 0.00 0.00 3.55
2139 2299 4.712122 ATCGAAACCAACAACAACACTT 57.288 36.364 0.00 0.00 0.00 3.16
2140 2300 5.821516 ATCGAAACCAACAACAACACTTA 57.178 34.783 0.00 0.00 0.00 2.24
2179 2339 5.111293 CCAATTTAACATCAAGGCCACATC 58.889 41.667 5.01 0.00 0.00 3.06
2285 2456 6.932356 ACTATGAACATGATGTCATTCACC 57.068 37.500 13.08 0.00 33.61 4.02
2288 2459 6.785337 ATGAACATGATGTCATTCACCATT 57.215 33.333 0.00 0.00 33.61 3.16
2310 2481 1.003696 GGCAGATATTAGGGCTCCACC 59.996 57.143 0.00 0.00 37.93 4.61
2317 2488 1.900245 TTAGGGCTCCACCGTTTTTC 58.100 50.000 0.00 0.00 40.62 2.29
2318 2489 1.061546 TAGGGCTCCACCGTTTTTCT 58.938 50.000 0.00 0.00 40.62 2.52
2328 2499 3.435671 CCACCGTTTTTCTCCATCTACAC 59.564 47.826 0.00 0.00 0.00 2.90
2331 2502 3.367025 CCGTTTTTCTCCATCTACACGTC 59.633 47.826 0.00 0.00 0.00 4.34
2339 2510 1.471676 CCATCTACACGTCTTGCCTCC 60.472 57.143 0.00 0.00 0.00 4.30
2340 2511 0.824759 ATCTACACGTCTTGCCTCCC 59.175 55.000 0.00 0.00 0.00 4.30
2341 2512 1.218316 CTACACGTCTTGCCTCCCC 59.782 63.158 0.00 0.00 0.00 4.81
2343 2514 1.122632 TACACGTCTTGCCTCCCCAA 61.123 55.000 0.00 0.00 0.00 4.12
2344 2515 1.228124 CACGTCTTGCCTCCCCAAA 60.228 57.895 0.00 0.00 0.00 3.28
2384 2626 4.879598 TCGAGGAAAAGAAGACTGTAACC 58.120 43.478 0.00 0.00 0.00 2.85
2403 2645 8.978874 TGTAACCGTAGATACTGGATAACTTA 57.021 34.615 7.54 0.00 0.00 2.24
2686 2930 5.819901 GCCTCACAATTGGGCTATATCTATC 59.180 44.000 14.80 0.00 42.31 2.08
2766 3011 6.744112 TGCCAAATTAACAATCCGGATTATC 58.256 36.000 28.76 4.52 0.00 1.75
2794 3039 5.411977 CCATTTGCAAACATTTGAGGCAATA 59.588 36.000 15.41 0.00 43.18 1.90
2795 3040 6.072618 CCATTTGCAAACATTTGAGGCAATAA 60.073 34.615 15.41 0.00 43.18 1.40
2796 3041 7.362229 CCATTTGCAAACATTTGAGGCAATAAT 60.362 33.333 15.41 0.00 43.18 1.28
2797 3042 7.507733 TTTGCAAACATTTGAGGCAATAATT 57.492 28.000 8.05 0.00 43.18 1.40
2821 3066 3.051581 ACATGGATCTTCACTGGCCTAT 58.948 45.455 3.32 0.00 0.00 2.57
2996 3242 1.340088 TGCATGTGGCCTTGATGTTT 58.660 45.000 3.32 0.00 43.89 2.83
3051 3298 8.333908 TGTTGGTGAATTTTCGAAATTGATTTG 58.666 29.630 12.12 0.00 0.00 2.32
3053 3300 6.008875 GGTGAATTTTCGAAATTGATTTGCG 58.991 36.000 12.12 0.00 0.00 4.85
3091 3508 6.867662 AGCTTTCATACATGTATTGGCTAC 57.132 37.500 15.85 4.81 0.00 3.58
3095 3512 5.134202 TCATACATGTATTGGCTACGGAG 57.866 43.478 15.85 0.00 32.61 4.63
3110 3527 4.560108 GCTACGGAGGTCAAGTTCTAACAA 60.560 45.833 0.00 0.00 0.00 2.83
3229 3646 9.301153 GAATAGGTATTTGCAGTTTTTACCATG 57.699 33.333 12.29 0.00 35.76 3.66
3318 3736 6.276847 TGTATTTGTGTTTCCCATTGTGTTC 58.723 36.000 0.00 0.00 0.00 3.18
3597 4024 4.882842 TCAGCTACCAACACATTGACTA 57.117 40.909 0.00 0.00 38.15 2.59
3636 4063 7.724061 ACCTGAACATTAGGTTTGTGTAGATTT 59.276 33.333 0.00 0.00 46.13 2.17
3637 4064 8.023128 CCTGAACATTAGGTTTGTGTAGATTTG 58.977 37.037 0.00 0.00 40.63 2.32
3638 4065 8.458573 TGAACATTAGGTTTGTGTAGATTTGT 57.541 30.769 0.00 0.00 40.63 2.83
3639 4066 8.349245 TGAACATTAGGTTTGTGTAGATTTGTG 58.651 33.333 0.00 0.00 40.63 3.33
3640 4067 7.817418 ACATTAGGTTTGTGTAGATTTGTGT 57.183 32.000 0.00 0.00 0.00 3.72
3641 4068 8.911918 ACATTAGGTTTGTGTAGATTTGTGTA 57.088 30.769 0.00 0.00 0.00 2.90
3642 4069 8.999431 ACATTAGGTTTGTGTAGATTTGTGTAG 58.001 33.333 0.00 0.00 0.00 2.74
3643 4070 9.214957 CATTAGGTTTGTGTAGATTTGTGTAGA 57.785 33.333 0.00 0.00 0.00 2.59
3644 4071 9.959721 ATTAGGTTTGTGTAGATTTGTGTAGAT 57.040 29.630 0.00 0.00 0.00 1.98
3762 4191 7.454260 GGTCAGAACAAATAAGATTGACCTT 57.546 36.000 12.22 0.00 45.93 3.50
3885 4323 4.133013 ACACGTGTTTCTTAGACCTGTT 57.867 40.909 17.22 0.00 0.00 3.16
3934 4374 5.029807 TGAGGTATCGCAATTATGGTTGA 57.970 39.130 0.00 0.00 0.00 3.18
4047 4512 4.803613 TGTTGCACTACGTATTATGCTCTG 59.196 41.667 20.63 0.85 38.90 3.35
4198 4666 4.786507 TGATCAAGTTGCTGAACGATTTG 58.213 39.130 0.00 0.00 37.15 2.32
4232 4700 7.464045 GCCAAGAAGTACAACAATTTGACAAAC 60.464 37.037 1.94 0.00 36.48 2.93
4234 4702 6.262601 AGAAGTACAACAATTTGACAAACCG 58.737 36.000 1.94 0.00 36.48 4.44
4238 4706 7.262048 AGTACAACAATTTGACAAACCGAAAT 58.738 30.769 1.94 0.00 36.48 2.17
4239 4707 6.343226 ACAACAATTTGACAAACCGAAATG 57.657 33.333 1.94 1.43 36.48 2.32
4240 4708 5.196825 CAACAATTTGACAAACCGAAATGC 58.803 37.500 1.94 0.00 34.24 3.56
4242 4710 4.057432 CAATTTGACAAACCGAAATGCCT 58.943 39.130 1.94 0.00 0.00 4.75
4243 4711 5.221342 ACAATTTGACAAACCGAAATGCCTA 60.221 36.000 1.94 0.00 0.00 3.93
4431 4899 5.465724 GTCAAATCTTGAACTGGTAGAACGT 59.534 40.000 0.00 0.00 42.15 3.99
4432 4900 5.694910 TCAAATCTTGAACTGGTAGAACGTC 59.305 40.000 0.00 0.00 36.59 4.34
4436 4904 1.000506 TGAACTGGTAGAACGTCCTGC 59.999 52.381 0.00 0.00 0.00 4.85
4442 4910 0.101759 GTAGAACGTCCTGCCGCATA 59.898 55.000 0.00 0.00 0.00 3.14
4460 4928 3.559242 GCATACTGAAGATTCACCTGCTC 59.441 47.826 10.02 0.00 32.44 4.26
4541 5009 1.096386 CGATCCGTCTTCCTCCTCGT 61.096 60.000 0.00 0.00 0.00 4.18
4548 5016 0.967887 TCTTCCTCCTCGTCAGCAGG 60.968 60.000 0.00 0.00 0.00 4.85
4604 5072 3.561213 CACAGCGAGCGCATGGAG 61.561 66.667 17.68 0.00 44.88 3.86
4605 5073 4.074526 ACAGCGAGCGCATGGAGT 62.075 61.111 17.68 0.00 44.88 3.85
4606 5074 3.561213 CAGCGAGCGCATGGAGTG 61.561 66.667 17.68 1.42 44.88 3.51
4837 5305 0.108329 TGTCGCCGGATTTCCTCTTC 60.108 55.000 5.05 0.00 0.00 2.87
4969 5437 2.039480 CTCAACCATGATCCATCCCGAT 59.961 50.000 0.00 0.00 34.37 4.18
5011 5479 2.716217 CCTTCCTCCTTGGTCATGAAC 58.284 52.381 2.98 2.98 37.07 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
115 116 2.384433 TTTCCCGTTCCCCACCACA 61.384 57.895 0.00 0.00 0.00 4.17
256 257 3.711842 TTTGACGAGCGCGCAAGG 61.712 61.111 35.10 23.13 42.48 3.61
257 258 2.497628 GTTTGACGAGCGCGCAAG 60.498 61.111 35.10 27.41 42.48 4.01
258 259 4.007940 GGTTTGACGAGCGCGCAA 62.008 61.111 35.10 15.93 42.48 4.85
263 264 2.203972 TAGTCCCGGTTTGACGAGCG 62.204 60.000 0.00 0.00 37.80 5.03
264 265 0.175073 ATAGTCCCGGTTTGACGAGC 59.825 55.000 0.00 0.00 37.80 5.03
344 364 2.620585 GCAAGTTTGTTCTCTTCTGGCT 59.379 45.455 0.00 0.00 0.00 4.75
345 365 2.287849 GGCAAGTTTGTTCTCTTCTGGC 60.288 50.000 0.00 0.00 0.00 4.85
346 366 3.217626 AGGCAAGTTTGTTCTCTTCTGG 58.782 45.455 0.00 0.00 0.00 3.86
441 464 0.036952 CAGGTGACAGCCGAGAACAT 60.037 55.000 0.00 0.00 0.00 2.71
442 465 1.367471 CAGGTGACAGCCGAGAACA 59.633 57.895 0.00 0.00 0.00 3.18
443 466 2.029844 GCAGGTGACAGCCGAGAAC 61.030 63.158 0.00 0.00 36.76 3.01
444 467 2.038814 TTGCAGGTGACAGCCGAGAA 62.039 55.000 0.00 0.00 43.15 2.87
446 469 2.031012 TTGCAGGTGACAGCCGAG 59.969 61.111 0.00 0.00 43.15 4.63
447 470 2.031012 CTTGCAGGTGACAGCCGA 59.969 61.111 0.00 0.00 43.15 5.54
448 471 3.730761 GCTTGCAGGTGACAGCCG 61.731 66.667 0.00 0.00 43.15 5.52
449 472 1.530013 AATGCTTGCAGGTGACAGCC 61.530 55.000 0.00 0.00 43.15 4.85
450 473 0.316204 AAATGCTTGCAGGTGACAGC 59.684 50.000 0.87 0.00 44.24 4.40
451 474 2.816087 AGTAAATGCTTGCAGGTGACAG 59.184 45.455 0.87 0.00 0.00 3.51
452 475 2.862541 AGTAAATGCTTGCAGGTGACA 58.137 42.857 0.87 0.00 0.00 3.58
454 477 4.253685 GTCTAGTAAATGCTTGCAGGTGA 58.746 43.478 0.87 0.00 0.00 4.02
457 493 4.256920 ACTGTCTAGTAAATGCTTGCAGG 58.743 43.478 0.87 0.00 34.74 4.85
483 519 3.959991 GACAGCTTCCCCGGCAGAC 62.960 68.421 0.00 0.00 0.00 3.51
506 542 4.577246 GGCTCCAGCTAGGACGCG 62.577 72.222 3.53 3.53 43.07 6.01
509 545 1.270571 GCTAATGGCTCCAGCTAGGAC 60.271 57.143 0.00 0.44 43.07 3.85
543 579 1.299541 CACTGGGTGTCACAACTCAC 58.700 55.000 5.12 0.00 0.00 3.51
544 580 0.180171 CCACTGGGTGTCACAACTCA 59.820 55.000 5.12 0.00 0.00 3.41
545 581 3.006672 CCACTGGGTGTCACAACTC 57.993 57.895 5.12 0.00 0.00 3.01
770 852 0.825010 CCTCTGCCTGCCTTGTTTGT 60.825 55.000 0.00 0.00 0.00 2.83
773 855 2.282745 GCCTCTGCCTGCCTTGTT 60.283 61.111 0.00 0.00 0.00 2.83
857 957 1.596895 TATTTTGCCCGGGCGTTTCC 61.597 55.000 39.00 14.07 45.51 3.13
858 958 0.244178 TTATTTTGCCCGGGCGTTTC 59.756 50.000 39.00 14.88 45.51 2.78
859 959 0.680061 TTTATTTTGCCCGGGCGTTT 59.320 45.000 39.00 25.32 45.51 3.60
860 960 0.899019 ATTTATTTTGCCCGGGCGTT 59.101 45.000 39.00 24.97 45.51 4.84
861 961 0.458260 GATTTATTTTGCCCGGGCGT 59.542 50.000 39.00 26.18 45.51 5.68
862 962 0.249280 GGATTTATTTTGCCCGGGCG 60.249 55.000 39.00 7.25 45.51 6.13
863 963 1.068588 GAGGATTTATTTTGCCCGGGC 59.931 52.381 39.40 39.40 42.35 6.13
1350 1468 2.749621 ACATCCAATTTCAGAGGCGAAC 59.250 45.455 0.00 0.00 0.00 3.95
1369 1487 1.894756 GGCCAACCAACAGCGTACA 60.895 57.895 0.00 0.00 35.26 2.90
1371 1489 2.666862 CGGCCAACCAACAGCGTA 60.667 61.111 2.24 0.00 34.57 4.42
1382 1500 4.081185 TCGATCAGCAGCGGCCAA 62.081 61.111 4.82 0.00 42.56 4.52
1543 1665 1.987855 CTTCCTGAGGTACGGGGCA 60.988 63.158 0.00 0.00 44.73 5.36
1564 1686 3.126831 GCTGGAATACATCTTGAGGTCG 58.873 50.000 0.00 0.00 0.00 4.79
1688 1813 1.595311 AGGCAATACCACTGGATCCA 58.405 50.000 15.27 15.27 43.14 3.41
1704 1832 4.705991 ACTAGTAGAACTGAACACCTAGGC 59.294 45.833 9.30 0.00 0.00 3.93
1800 1954 5.006386 AGCTTTGACCTTTACAATCAGAGG 58.994 41.667 0.00 0.00 35.39 3.69
1809 1963 1.135944 GCAGCGAGCTTTGACCTTTAC 60.136 52.381 0.00 0.00 41.15 2.01
1918 2072 0.390866 CAAGCATCCAGTCAGCGTCT 60.391 55.000 0.00 0.00 0.00 4.18
1977 2137 3.382546 GGCGTCCACAGTAAATAGGAGTA 59.617 47.826 0.00 0.00 0.00 2.59
1978 2138 2.167900 GGCGTCCACAGTAAATAGGAGT 59.832 50.000 0.00 0.00 0.00 3.85
2031 2191 8.430063 GTTCGACGAGATTTGTATTTAAGACAA 58.570 33.333 0.67 0.67 35.03 3.18
2065 2225 4.636249 GGAGTAGTTCCATCTGCAATAGG 58.364 47.826 0.00 0.00 46.01 2.57
2106 2266 7.504924 TGTTGGTTTCGATTAAAGTTGAGAT 57.495 32.000 0.00 0.00 0.00 2.75
2118 2278 4.712122 AAGTGTTGTTGTTGGTTTCGAT 57.288 36.364 0.00 0.00 0.00 3.59
2134 2294 5.720041 TGGCTACTGGAATCTACTTAAGTGT 59.280 40.000 18.56 7.23 0.00 3.55
2135 2295 6.222038 TGGCTACTGGAATCTACTTAAGTG 57.778 41.667 18.56 8.35 0.00 3.16
2136 2296 6.869206 TTGGCTACTGGAATCTACTTAAGT 57.131 37.500 13.68 13.68 0.00 2.24
2137 2297 8.738645 AAATTGGCTACTGGAATCTACTTAAG 57.261 34.615 0.00 0.00 0.00 1.85
2139 2299 9.609346 GTTAAATTGGCTACTGGAATCTACTTA 57.391 33.333 0.00 0.00 0.00 2.24
2140 2300 8.107095 TGTTAAATTGGCTACTGGAATCTACTT 58.893 33.333 0.00 0.00 0.00 2.24
2224 2395 4.642885 CCTCAGACCAACCTAACAACAAAA 59.357 41.667 0.00 0.00 0.00 2.44
2282 2453 3.256631 GCCCTAATATCTGCCAAATGGTG 59.743 47.826 0.71 0.00 37.57 4.17
2285 2456 3.760684 GGAGCCCTAATATCTGCCAAATG 59.239 47.826 0.00 0.00 0.00 2.32
2288 2459 2.106511 GTGGAGCCCTAATATCTGCCAA 59.893 50.000 0.00 0.00 0.00 4.52
2310 2481 4.235360 AGACGTGTAGATGGAGAAAAACG 58.765 43.478 0.00 0.00 35.98 3.60
2317 2488 1.478510 AGGCAAGACGTGTAGATGGAG 59.521 52.381 0.00 0.00 0.00 3.86
2318 2489 1.476891 GAGGCAAGACGTGTAGATGGA 59.523 52.381 0.00 0.00 0.00 3.41
2328 2499 0.250727 TTCTTTGGGGAGGCAAGACG 60.251 55.000 0.00 0.00 0.00 4.18
2331 2502 3.071457 ACAATTTTCTTTGGGGAGGCAAG 59.929 43.478 0.00 0.00 0.00 4.01
2339 2510 4.777366 AGGATGGGTACAATTTTCTTTGGG 59.223 41.667 0.00 0.00 0.00 4.12
2340 2511 5.393027 CGAGGATGGGTACAATTTTCTTTGG 60.393 44.000 0.00 0.00 0.00 3.28
2341 2512 5.414454 TCGAGGATGGGTACAATTTTCTTTG 59.586 40.000 0.00 0.00 0.00 2.77
2343 2514 5.174037 TCGAGGATGGGTACAATTTTCTT 57.826 39.130 0.00 0.00 0.00 2.52
2344 2515 4.384208 CCTCGAGGATGGGTACAATTTTCT 60.384 45.833 28.21 0.00 37.39 2.52
2686 2930 1.063616 CAGCAACCGAGATTGAGCATG 59.936 52.381 0.00 0.00 0.00 4.06
2766 3011 4.628333 CCTCAAATGTTTGCAAATGGCTAG 59.372 41.667 16.21 8.90 45.15 3.42
2794 3039 4.159135 GCCAGTGAAGATCCATGTGAAATT 59.841 41.667 0.00 0.00 0.00 1.82
2795 3040 3.698040 GCCAGTGAAGATCCATGTGAAAT 59.302 43.478 0.00 0.00 0.00 2.17
2796 3041 3.084039 GCCAGTGAAGATCCATGTGAAA 58.916 45.455 0.00 0.00 0.00 2.69
2797 3042 2.618816 GGCCAGTGAAGATCCATGTGAA 60.619 50.000 0.00 0.00 0.00 3.18
2933 3179 0.690762 AGGGGTCGGCGCATATAAAT 59.309 50.000 10.83 0.00 0.00 1.40
2936 3182 1.001181 GTAAAGGGGTCGGCGCATATA 59.999 52.381 10.83 0.00 0.00 0.86
2996 3242 7.567622 ACCTAAGTAGATTCCAGTAGCCAATTA 59.432 37.037 0.00 0.00 0.00 1.40
3051 3298 2.213499 AGCTAAGGCAATATGACACGC 58.787 47.619 0.00 0.00 41.70 5.34
3053 3300 5.818136 TGAAAGCTAAGGCAATATGACAC 57.182 39.130 0.00 0.00 41.70 3.67
3091 3508 4.392138 GGAATTGTTAGAACTTGACCTCCG 59.608 45.833 0.00 0.00 0.00 4.63
3229 3646 6.254281 ACACAAATATAAGCACTGTTCCAC 57.746 37.500 0.00 0.00 0.00 4.02
3318 3736 9.559732 TGACACTAGTGGAAATAAATCATATGG 57.440 33.333 26.12 0.00 34.19 2.74
3514 3936 6.763715 ACATATCCCAGCTATTGGTTTCTA 57.236 37.500 0.00 0.00 46.25 2.10
3572 3994 1.755179 ATGTGTTGGTAGCTGATGGC 58.245 50.000 0.00 0.00 42.19 4.40
3760 4189 7.298854 GTTCATTTTCTTTACTCCGGAAGAAG 58.701 38.462 14.34 13.42 41.40 2.85
3761 4190 6.206048 GGTTCATTTTCTTTACTCCGGAAGAA 59.794 38.462 11.48 11.48 39.42 2.52
3762 4191 5.704053 GGTTCATTTTCTTTACTCCGGAAGA 59.296 40.000 5.23 1.78 0.00 2.87
3885 4323 7.573656 GCAGATCACATTACAGACATTTGACAA 60.574 37.037 0.00 0.00 0.00 3.18
3934 4374 6.430000 ACATAAGCTTCCAAGTGAAAATACGT 59.570 34.615 0.00 0.00 31.06 3.57
4232 4700 9.477484 GATTAGGTACATATATAGGCATTTCGG 57.523 37.037 0.00 0.00 0.00 4.30
4234 4702 9.477484 CGGATTAGGTACATATATAGGCATTTC 57.523 37.037 0.00 0.00 0.00 2.17
4238 4706 7.783119 ACATCGGATTAGGTACATATATAGGCA 59.217 37.037 0.00 0.00 0.00 4.75
4239 4707 8.082852 CACATCGGATTAGGTACATATATAGGC 58.917 40.741 0.00 0.00 0.00 3.93
4240 4708 8.082852 GCACATCGGATTAGGTACATATATAGG 58.917 40.741 0.00 0.00 0.00 2.57
4242 4710 8.528044 TGCACATCGGATTAGGTACATATATA 57.472 34.615 0.00 0.00 0.00 0.86
4243 4711 7.418337 TGCACATCGGATTAGGTACATATAT 57.582 36.000 0.00 0.00 0.00 0.86
4431 4899 1.123077 ATCTTCAGTATGCGGCAGGA 58.877 50.000 9.25 0.46 34.76 3.86
4432 4900 1.869767 GAATCTTCAGTATGCGGCAGG 59.130 52.381 9.25 0.00 34.76 4.85
4436 4904 2.868583 CAGGTGAATCTTCAGTATGCGG 59.131 50.000 0.00 0.00 37.98 5.69
4442 4910 2.636893 ACAGAGCAGGTGAATCTTCAGT 59.363 45.455 0.00 0.00 37.98 3.41
4460 4928 3.751246 CGCACCCCATTGCCACAG 61.751 66.667 0.00 0.00 39.53 3.66
4495 4963 1.321074 ATCTTGACGAGGACGACCCC 61.321 60.000 0.00 0.00 42.66 4.95
4541 5009 3.371097 GAACGCCCGATCCTGCTGA 62.371 63.158 0.00 0.00 0.00 4.26
4611 5079 2.500183 GAAGAACAGCAGCGCGGAAC 62.500 60.000 13.03 0.00 0.00 3.62
4612 5080 2.280797 AAGAACAGCAGCGCGGAA 60.281 55.556 13.03 0.00 0.00 4.30
4622 5090 0.603707 TCTGGGCGCAAGAAGAACAG 60.604 55.000 10.83 4.11 43.02 3.16
4918 5386 0.040204 ACCATGGCAAAGAAGAGGGG 59.960 55.000 13.04 0.00 0.00 4.79
5011 5479 4.966005 TGGCGACAGTTCTTCTCG 57.034 55.556 0.00 0.00 35.01 4.04



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

AutoCloner maintained by Alex Coulton.