Multiple sequence alignment - TraesCS5B01G001500

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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 TraesCS5B01G001500 chr5B 100.000 4913 0 0 1 4913 1748685 1753597 0.000000e+00 9073.0
1 TraesCS5B01G001500 chr5B 95.882 170 4 2 2496 2663 550926513 550926345 6.270000e-69 272.0
2 TraesCS5B01G001500 chr5B 94.048 84 3 1 4377 4458 191034238 191034155 5.160000e-25 126.0
3 TraesCS5B01G001500 chr5B 91.566 83 6 1 4375 4457 544393290 544393371 4.020000e-21 113.0
4 TraesCS5B01G001500 chr5B 93.651 63 4 0 4152 4214 679807034 679806972 1.460000e-15 95.3
5 TraesCS5B01G001500 chr5A 99.439 2495 14 0 1 2495 20018 22512 0.000000e+00 4530.0
6 TraesCS5B01G001500 chr5A 98.543 2265 22 3 2660 4913 22501 24765 0.000000e+00 3989.0
7 TraesCS5B01G001500 chr5A 97.959 98 2 0 872 969 557663738 557663835 2.350000e-38 171.0
8 TraesCS5B01G001500 chr5A 84.106 151 8 5 526 661 540932509 540932658 1.110000e-26 132.0
9 TraesCS5B01G001500 chr5A 86.029 136 4 4 526 646 557663257 557663392 1.110000e-26 132.0
10 TraesCS5B01G001500 chr5A 93.548 62 4 0 4153 4214 24796341 24796280 5.240000e-15 93.5
11 TraesCS5B01G001500 chr5A 93.548 62 4 0 4153 4214 464573345 464573406 5.240000e-15 93.5
12 TraesCS5B01G001500 chr5A 97.222 36 1 0 4211 4246 643369145 643369110 1.480000e-05 62.1
13 TraesCS5B01G001500 chr5D 93.049 1597 57 18 2747 4301 556511 554927 0.000000e+00 2285.0
14 TraesCS5B01G001500 chr5D 95.380 1342 41 10 790 2114 558260 556923 0.000000e+00 2115.0
15 TraesCS5B01G001500 chr5D 91.176 340 27 2 2152 2489 556935 556597 4.480000e-125 459.0
16 TraesCS5B01G001500 chr5D 77.632 456 60 24 212 657 558758 558335 6.360000e-59 239.0
17 TraesCS5B01G001500 chr5D 95.000 80 4 0 4377 4456 486173604 486173525 5.160000e-25 126.0
18 TraesCS5B01G001500 chr5D 81.308 107 4 5 4153 4243 62134324 62134218 6.820000e-09 73.1
19 TraesCS5B01G001500 chr1B 98.856 437 2 3 4480 4913 143613514 143613950 0.000000e+00 776.0
20 TraesCS5B01G001500 chr1B 95.652 207 7 2 4505 4709 14466246 14466452 1.020000e-86 331.0
21 TraesCS5B01G001500 chr1B 92.500 160 9 2 2496 2655 157274502 157274658 4.950000e-55 226.0
22 TraesCS5B01G001500 chr1B 92.982 114 3 1 4805 4913 14466614 14466727 1.420000e-35 161.0
23 TraesCS5B01G001500 chr2B 80.464 732 87 29 260 959 69469520 69468813 4.390000e-140 508.0
24 TraesCS5B01G001500 chr2B 82.294 401 40 17 587 959 496456272 496455875 7.940000e-83 318.0
25 TraesCS5B01G001500 chr2B 81.538 260 31 7 260 517 496456761 496456517 1.080000e-46 198.0
26 TraesCS5B01G001500 chr1A 86.047 473 26 21 4468 4911 203148868 203149329 5.760000e-129 472.0
27 TraesCS5B01G001500 chr1A 92.683 246 4 8 4468 4712 203141022 203141254 4.710000e-90 342.0
28 TraesCS5B01G001500 chr1A 96.465 198 6 1 4715 4911 203141286 203141483 4.740000e-85 326.0
29 TraesCS5B01G001500 chr1A 94.500 200 11 0 4713 4912 109419388 109419189 4.780000e-80 309.0
30 TraesCS5B01G001500 chr1A 96.842 95 3 0 4713 4807 111991570 111991476 5.090000e-35 159.0
31 TraesCS5B01G001500 chr1A 90.909 66 5 1 4149 4214 22631682 22631618 2.440000e-13 87.9
32 TraesCS5B01G001500 chr1A 91.935 62 5 0 4153 4214 76762789 76762728 2.440000e-13 87.9
33 TraesCS5B01G001500 chr1A 91.935 62 5 0 4153 4214 376756341 376756280 2.440000e-13 87.9
34 TraesCS5B01G001500 chr1A 90.909 66 5 1 4147 4211 380316167 380316232 2.440000e-13 87.9
35 TraesCS5B01G001500 chr1A 90.909 55 5 0 4153 4207 452046699 452046753 1.900000e-09 75.0
36 TraesCS5B01G001500 chr1A 89.091 55 6 0 4153 4207 502832272 502832326 8.820000e-08 69.4
37 TraesCS5B01G001500 chr1A 79.630 108 6 8 4153 4244 429021724 429021617 4.110000e-06 63.9
38 TraesCS5B01G001500 chr3B 91.246 297 13 6 682 969 185526452 185526744 4.610000e-105 392.0
39 TraesCS5B01G001500 chr3B 91.246 297 13 7 682 969 826121035 826121327 4.610000e-105 392.0
40 TraesCS5B01G001500 chr3B 95.238 210 8 2 4505 4712 41797340 41797131 1.020000e-86 331.0
41 TraesCS5B01G001500 chr3B 94.393 214 8 3 4503 4712 86133488 86133275 4.740000e-85 326.0
42 TraesCS5B01G001500 chr3B 81.734 323 25 11 659 959 550395387 550395077 6.360000e-59 239.0
43 TraesCS5B01G001500 chr3B 93.548 62 4 0 4153 4214 92927977 92927916 5.240000e-15 93.5
44 TraesCS5B01G001500 chr3A 91.000 300 12 7 681 969 511223073 511223368 1.660000e-104 390.0
45 TraesCS5B01G001500 chr3A 95.098 204 9 1 4710 4913 263962444 263962646 2.210000e-83 320.0
46 TraesCS5B01G001500 chr3A 94.375 160 8 1 2496 2654 655515501 655515660 1.370000e-60 244.0
47 TraesCS5B01G001500 chr3A 91.667 168 9 3 2496 2658 585474942 585474775 1.380000e-55 228.0
48 TraesCS5B01G001500 chr3A 91.124 169 10 2 2496 2659 107736863 107736695 1.780000e-54 224.0
49 TraesCS5B01G001500 chr3A 89.080 174 16 2 2486 2656 699981611 699981784 3.850000e-51 213.0
50 TraesCS5B01G001500 chr3A 84.106 151 8 5 526 661 511222850 511222999 1.110000e-26 132.0
51 TraesCS5B01G001500 chr6B 90.909 297 14 7 682 969 525982271 525981979 2.140000e-103 387.0
52 TraesCS5B01G001500 chr6B 81.863 408 37 18 587 959 115216752 115216347 4.780000e-80 309.0
53 TraesCS5B01G001500 chr4A 89.667 300 16 7 681 969 517572449 517572154 7.770000e-98 368.0
54 TraesCS5B01G001500 chr4A 85.294 136 5 7 526 646 517572672 517572537 5.160000e-25 126.0
55 TraesCS5B01G001500 chr4A 91.011 89 7 1 4375 4462 668597083 668597171 8.640000e-23 119.0
56 TraesCS5B01G001500 chr4A 93.548 62 4 0 4153 4214 584519332 584519271 5.240000e-15 93.5
57 TraesCS5B01G001500 chr4A 92.727 55 4 0 4153 4207 500146071 500146017 4.080000e-11 80.5
58 TraesCS5B01G001500 chr4A 94.286 35 1 1 496 530 700241259 700241292 9.000000e-03 52.8
59 TraesCS5B01G001500 chr7A 89.145 304 14 7 681 969 187794954 187794655 1.300000e-95 361.0
60 TraesCS5B01G001500 chr7A 88.013 317 15 10 666 969 721556686 721556992 2.180000e-93 353.0
61 TraesCS5B01G001500 chr7A 84.106 151 8 5 526 661 721556484 721556633 1.110000e-26 132.0
62 TraesCS5B01G001500 chr7A 82.993 147 10 5 526 657 187795167 187795021 8.640000e-23 119.0
63 TraesCS5B01G001500 chr7A 95.082 61 3 0 4151 4211 549531663 549531723 4.050000e-16 97.1
64 TraesCS5B01G001500 chr7A 92.727 55 4 0 4153 4207 473023717 473023771 4.080000e-11 80.5
65 TraesCS5B01G001500 chr7A 92.727 55 4 0 4153 4207 622370152 622370098 4.080000e-11 80.5
66 TraesCS5B01G001500 chr6A 96.667 210 6 1 4504 4712 200805064 200805273 1.010000e-91 348.0
67 TraesCS5B01G001500 chr6A 86.310 336 19 10 657 969 49438168 49437837 1.690000e-89 340.0
68 TraesCS5B01G001500 chr6A 94.118 204 12 0 4710 4913 200805302 200805505 1.330000e-80 311.0
69 TraesCS5B01G001500 chr6A 87.838 148 4 7 526 661 49438353 49438208 1.420000e-35 161.0
70 TraesCS5B01G001500 chr6A 92.188 64 5 0 4151 4214 506401466 506401403 1.880000e-14 91.6
71 TraesCS5B01G001500 chr6A 91.935 62 5 0 4153 4214 14231699 14231638 2.440000e-13 87.9
72 TraesCS5B01G001500 chr6A 90.909 55 5 0 4153 4207 13437175 13437229 1.900000e-09 75.0
73 TraesCS5B01G001500 chr6A 89.091 55 6 0 4153 4207 603025476 603025422 8.820000e-08 69.4
74 TraesCS5B01G001500 chr6A 80.000 110 7 10 4149 4243 480648877 480648986 3.170000e-07 67.6
75 TraesCS5B01G001500 chr6A 94.444 36 2 0 4208 4243 120965967 120966002 6.870000e-04 56.5
76 TraesCS5B01G001500 chr7B 96.154 208 7 1 4503 4709 192098342 192098549 6.090000e-89 339.0
77 TraesCS5B01G001500 chr7B 92.105 114 4 1 4805 4913 192098709 192098822 6.580000e-34 156.0
78 TraesCS5B01G001500 chr7B 95.000 80 4 0 4375 4454 42026902 42026823 5.160000e-25 126.0
79 TraesCS5B01G001500 chr7B 90.909 55 5 0 4153 4207 86007902 86007848 1.900000e-09 75.0
80 TraesCS5B01G001500 chr4D 95.673 208 7 2 4503 4709 72667188 72666982 2.830000e-87 333.0
81 TraesCS5B01G001500 chr4D 93.373 166 10 1 2496 2660 220360613 220360448 1.370000e-60 244.0
82 TraesCS5B01G001500 chr4B 95.181 166 7 1 2496 2661 24565234 24565070 1.360000e-65 261.0
83 TraesCS5B01G001500 chr4B 100.000 30 0 0 4178 4207 652965877 652965848 6.870000e-04 56.5
84 TraesCS5B01G001500 chr7D 92.771 166 10 2 2496 2660 120323475 120323639 6.360000e-59 239.0
85 TraesCS5B01G001500 chr7D 90.909 55 5 0 4153 4207 63992894 63992840 1.900000e-09 75.0
86 TraesCS5B01G001500 chr2A 95.876 97 4 0 4710 4806 398874306 398874402 1.830000e-34 158.0
87 TraesCS5B01G001500 chr3D 96.203 79 3 0 4375 4453 549062378 549062456 3.990000e-26 130.0
88 TraesCS5B01G001500 chr3D 94.048 84 4 1 4375 4458 614914948 614915030 5.160000e-25 126.0
89 TraesCS5B01G001500 chr3D 93.750 64 3 1 4148 4211 308274903 308274965 1.460000e-15 95.3
90 TraesCS5B01G001500 chr1D 91.860 86 7 0 4375 4460 367774558 367774473 2.400000e-23 121.0
91 TraesCS5B01G001500 chr1D 94.915 59 3 0 4153 4211 440942569 440942627 5.240000e-15 93.5
92 TraesCS5B01G001500 chrUn 94.915 59 3 0 4153 4211 11239800 11239858 5.240000e-15 93.5
93 TraesCS5B01G001500 chr2D 93.443 61 4 0 4151 4211 119954200 119954260 1.880000e-14 91.6


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 TraesCS5B01G001500 chr5B 1748685 1753597 4912 False 9073.0 9073 100.00000 1 4913 1 chr5B.!!$F1 4912
1 TraesCS5B01G001500 chr5A 20018 24765 4747 False 4259.5 4530 98.99100 1 4913 2 chr5A.!!$F3 4912
2 TraesCS5B01G001500 chr5D 554927 558758 3831 True 1274.5 2285 89.30925 212 4301 4 chr5D.!!$R3 4089
3 TraesCS5B01G001500 chr2B 69468813 69469520 707 True 508.0 508 80.46400 260 959 1 chr2B.!!$R1 699
4 TraesCS5B01G001500 chr2B 496455875 496456761 886 True 258.0 318 81.91600 260 959 2 chr2B.!!$R2 699
5 TraesCS5B01G001500 chr3A 511222850 511223368 518 False 261.0 390 87.55300 526 969 2 chr3A.!!$F4 443
6 TraesCS5B01G001500 chr4A 517572154 517572672 518 True 247.0 368 87.48050 526 969 2 chr4A.!!$R3 443
7 TraesCS5B01G001500 chr7A 721556484 721556992 508 False 242.5 353 86.05950 526 969 2 chr7A.!!$F3 443
8 TraesCS5B01G001500 chr7A 187794655 187795167 512 True 240.0 361 86.06900 526 969 2 chr7A.!!$R2 443
9 TraesCS5B01G001500 chr6A 49437837 49438353 516 True 250.5 340 87.07400 526 969 2 chr6A.!!$R4 443

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
209 210 1.683629 GGGAGAGATCAGTCGAGTGGT 60.684 57.143 19.86 13.63 0.00 4.16 F
2151 2464 6.717540 GGACATACATACCAGTCTCATACTCT 59.282 42.308 0.00 0.00 35.76 3.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2364 2677 1.739562 GGCTCTCTCAACAGCACCG 60.740 63.158 0.0 0.0 37.38 4.94 R
4282 4638 1.001633 ACGTACTGGTTAGTTGGCTGG 59.998 52.381 0.0 0.0 38.36 4.85 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
112 113 4.095483 ACTCGAATTCAAATGCATCTGGAC 59.905 41.667 0.00 0.00 0.00 4.02
209 210 1.683629 GGGAGAGATCAGTCGAGTGGT 60.684 57.143 19.86 13.63 0.00 4.16
2151 2464 6.717540 GGACATACATACCAGTCTCATACTCT 59.282 42.308 0.00 0.00 35.76 3.24
2364 2677 2.904434 TCTTGGACCTGGAGTTTACCTC 59.096 50.000 0.00 0.00 39.67 3.85
2495 2808 5.843673 TTTGTTCAACTATTCAACTGCCA 57.156 34.783 0.00 0.00 0.00 4.92
2496 2809 5.843673 TTGTTCAACTATTCAACTGCCAA 57.156 34.783 0.00 0.00 0.00 4.52
2497 2810 5.437289 TGTTCAACTATTCAACTGCCAAG 57.563 39.130 0.00 0.00 0.00 3.61
2498 2811 4.278170 TGTTCAACTATTCAACTGCCAAGG 59.722 41.667 0.00 0.00 0.00 3.61
2499 2812 3.420893 TCAACTATTCAACTGCCAAGGG 58.579 45.455 0.00 0.00 0.00 3.95
2500 2813 2.493278 CAACTATTCAACTGCCAAGGGG 59.507 50.000 0.00 0.00 37.18 4.79
2501 2814 1.992557 ACTATTCAACTGCCAAGGGGA 59.007 47.619 0.00 0.00 35.59 4.81
2502 2815 2.025887 ACTATTCAACTGCCAAGGGGAG 60.026 50.000 1.93 1.93 46.85 4.30
2503 2816 0.613012 ATTCAACTGCCAAGGGGAGC 60.613 55.000 3.49 0.00 45.32 4.70
2504 2817 2.677875 CAACTGCCAAGGGGAGCC 60.678 66.667 3.49 0.00 45.32 4.70
2505 2818 2.860971 AACTGCCAAGGGGAGCCT 60.861 61.111 3.49 0.00 45.32 4.58
2506 2819 2.473365 AACTGCCAAGGGGAGCCTT 61.473 57.895 3.49 0.00 45.32 4.35
2507 2820 2.362120 CTGCCAAGGGGAGCCTTG 60.362 66.667 0.00 0.00 44.65 3.61
2518 2831 3.605749 GAGCCTTGGCGCAGTGGTA 62.606 63.158 10.83 0.00 0.00 3.25
2519 2832 2.671619 GCCTTGGCGCAGTGGTAA 60.672 61.111 10.83 0.00 0.00 2.85
2520 2833 2.265182 GCCTTGGCGCAGTGGTAAA 61.265 57.895 10.83 0.00 0.00 2.01
2521 2834 1.875963 CCTTGGCGCAGTGGTAAAG 59.124 57.895 10.83 0.71 0.00 1.85
2522 2835 1.210155 CTTGGCGCAGTGGTAAAGC 59.790 57.895 10.83 0.00 0.00 3.51
2523 2836 1.228124 TTGGCGCAGTGGTAAAGCT 60.228 52.632 10.83 0.00 0.00 3.74
2524 2837 1.514678 TTGGCGCAGTGGTAAAGCTG 61.515 55.000 10.83 0.00 35.93 4.24
2529 2842 1.878775 CAGTGGTAAAGCTGCTGCC 59.121 57.895 12.44 7.07 40.80 4.85
2530 2843 0.607489 CAGTGGTAAAGCTGCTGCCT 60.607 55.000 12.44 2.45 40.80 4.75
2531 2844 0.111253 AGTGGTAAAGCTGCTGCCTT 59.889 50.000 12.44 8.34 40.80 4.35
2532 2845 0.242017 GTGGTAAAGCTGCTGCCTTG 59.758 55.000 12.44 0.00 40.80 3.61
2533 2846 0.178992 TGGTAAAGCTGCTGCCTTGT 60.179 50.000 12.44 0.00 40.80 3.16
2534 2847 0.242017 GGTAAAGCTGCTGCCTTGTG 59.758 55.000 12.44 0.00 40.80 3.33
2535 2848 1.238439 GTAAAGCTGCTGCCTTGTGA 58.762 50.000 12.44 0.00 40.80 3.58
2536 2849 1.068954 GTAAAGCTGCTGCCTTGTGAC 60.069 52.381 12.44 0.00 40.80 3.67
2537 2850 1.458639 AAAGCTGCTGCCTTGTGACC 61.459 55.000 12.44 0.00 40.80 4.02
2538 2851 2.595463 GCTGCTGCCTTGTGACCA 60.595 61.111 3.85 0.00 0.00 4.02
2539 2852 1.975407 GCTGCTGCCTTGTGACCAT 60.975 57.895 3.85 0.00 0.00 3.55
2540 2853 1.880894 CTGCTGCCTTGTGACCATG 59.119 57.895 0.00 0.00 0.00 3.66
2541 2854 1.592400 CTGCTGCCTTGTGACCATGG 61.592 60.000 11.19 11.19 38.59 3.66
2542 2855 1.303561 GCTGCCTTGTGACCATGGA 60.304 57.895 21.47 0.00 37.97 3.41
2543 2856 0.895100 GCTGCCTTGTGACCATGGAA 60.895 55.000 21.47 2.77 37.97 3.53
2544 2857 1.619654 CTGCCTTGTGACCATGGAAA 58.380 50.000 21.47 2.33 37.97 3.13
2545 2858 1.270550 CTGCCTTGTGACCATGGAAAC 59.729 52.381 21.47 16.15 37.97 2.78
2560 2873 4.431416 TGGAAACAGCCTCTTACAGAAA 57.569 40.909 0.00 0.00 35.01 2.52
2561 2874 4.985538 TGGAAACAGCCTCTTACAGAAAT 58.014 39.130 0.00 0.00 35.01 2.17
2562 2875 4.761739 TGGAAACAGCCTCTTACAGAAATG 59.238 41.667 0.00 0.00 35.01 2.32
2563 2876 4.762251 GGAAACAGCCTCTTACAGAAATGT 59.238 41.667 0.00 0.00 0.00 2.71
2564 2877 5.938125 GGAAACAGCCTCTTACAGAAATGTA 59.062 40.000 0.00 0.00 0.00 2.29
2565 2878 6.092807 GGAAACAGCCTCTTACAGAAATGTAG 59.907 42.308 0.00 0.00 0.00 2.74
2566 2879 5.091261 ACAGCCTCTTACAGAAATGTAGG 57.909 43.478 0.00 0.00 0.00 3.18
2567 2880 4.080863 ACAGCCTCTTACAGAAATGTAGGG 60.081 45.833 0.00 0.66 0.00 3.53
2568 2881 4.162320 CAGCCTCTTACAGAAATGTAGGGA 59.838 45.833 0.00 0.00 0.00 4.20
2569 2882 4.783227 AGCCTCTTACAGAAATGTAGGGAA 59.217 41.667 0.00 0.00 0.00 3.97
2570 2883 5.250774 AGCCTCTTACAGAAATGTAGGGAAA 59.749 40.000 0.00 0.00 0.00 3.13
2571 2884 5.586643 GCCTCTTACAGAAATGTAGGGAAAG 59.413 44.000 0.00 0.00 0.00 2.62
2572 2885 6.116126 CCTCTTACAGAAATGTAGGGAAAGG 58.884 44.000 0.00 0.00 0.00 3.11
2573 2886 5.497474 TCTTACAGAAATGTAGGGAAAGGC 58.503 41.667 0.00 0.00 0.00 4.35
2574 2887 5.250774 TCTTACAGAAATGTAGGGAAAGGCT 59.749 40.000 0.00 0.00 0.00 4.58
2575 2888 3.690460 ACAGAAATGTAGGGAAAGGCTG 58.310 45.455 0.00 0.00 0.00 4.85
2576 2889 2.424956 CAGAAATGTAGGGAAAGGCTGC 59.575 50.000 0.00 0.00 0.00 5.25
2577 2890 1.401905 GAAATGTAGGGAAAGGCTGCG 59.598 52.381 0.00 0.00 0.00 5.18
2578 2891 0.328258 AATGTAGGGAAAGGCTGCGT 59.672 50.000 0.00 0.00 0.00 5.24
2579 2892 1.200519 ATGTAGGGAAAGGCTGCGTA 58.799 50.000 0.00 0.00 0.00 4.42
2580 2893 0.248289 TGTAGGGAAAGGCTGCGTAC 59.752 55.000 0.00 0.00 37.28 3.67
2581 2894 0.535797 GTAGGGAAAGGCTGCGTACT 59.464 55.000 0.00 0.00 34.81 2.73
2582 2895 1.753073 GTAGGGAAAGGCTGCGTACTA 59.247 52.381 0.00 0.00 34.81 1.82
2583 2896 1.497161 AGGGAAAGGCTGCGTACTAT 58.503 50.000 0.00 0.00 0.00 2.12
2584 2897 2.674420 AGGGAAAGGCTGCGTACTATA 58.326 47.619 0.00 0.00 0.00 1.31
2585 2898 2.628657 AGGGAAAGGCTGCGTACTATAG 59.371 50.000 0.00 0.00 0.00 1.31
2586 2899 2.626743 GGGAAAGGCTGCGTACTATAGA 59.373 50.000 6.78 0.00 0.00 1.98
2587 2900 3.552478 GGGAAAGGCTGCGTACTATAGAC 60.552 52.174 6.78 0.00 0.00 2.59
2588 2901 3.552478 GGAAAGGCTGCGTACTATAGACC 60.552 52.174 6.78 0.00 0.00 3.85
2589 2902 1.618487 AGGCTGCGTACTATAGACCC 58.382 55.000 6.78 0.00 0.00 4.46
2590 2903 1.133575 AGGCTGCGTACTATAGACCCA 60.134 52.381 6.78 0.00 0.00 4.51
2591 2904 1.684983 GGCTGCGTACTATAGACCCAA 59.315 52.381 6.78 0.00 0.00 4.12
2592 2905 2.101917 GGCTGCGTACTATAGACCCAAA 59.898 50.000 6.78 0.00 0.00 3.28
2593 2906 3.381949 GCTGCGTACTATAGACCCAAAG 58.618 50.000 6.78 0.00 0.00 2.77
2594 2907 3.181478 GCTGCGTACTATAGACCCAAAGT 60.181 47.826 6.78 0.00 0.00 2.66
2595 2908 4.360563 CTGCGTACTATAGACCCAAAGTG 58.639 47.826 6.78 0.00 0.00 3.16
2596 2909 3.131577 TGCGTACTATAGACCCAAAGTGG 59.868 47.826 6.78 0.00 37.25 4.00
2597 2910 3.131755 GCGTACTATAGACCCAAAGTGGT 59.868 47.826 6.78 0.00 42.79 4.16
2602 2915 4.373771 GACCCAAAGTGGTCGGAC 57.626 61.111 0.00 0.00 44.98 4.79
2603 2916 1.302271 GACCCAAAGTGGTCGGACC 60.302 63.158 20.36 20.36 44.98 4.46
2604 2917 2.033602 CCCAAAGTGGTCGGACCC 59.966 66.667 23.81 14.91 37.50 4.46
2605 2918 2.526046 CCCAAAGTGGTCGGACCCT 61.526 63.158 23.81 16.82 37.50 4.34
2606 2919 1.454539 CCAAAGTGGTCGGACCCTT 59.545 57.895 23.81 21.08 37.50 3.95
2607 2920 0.605589 CCAAAGTGGTCGGACCCTTC 60.606 60.000 23.81 13.97 37.50 3.46
2608 2921 0.605589 CAAAGTGGTCGGACCCTTCC 60.606 60.000 23.81 9.51 37.50 3.46
2609 2922 1.775934 AAAGTGGTCGGACCCTTCCC 61.776 60.000 23.81 7.17 38.99 3.97
2610 2923 2.606826 GTGGTCGGACCCTTCCCT 60.607 66.667 23.81 0.00 38.99 4.20
2611 2924 2.606519 TGGTCGGACCCTTCCCTG 60.607 66.667 23.81 0.00 38.99 4.45
2612 2925 3.400054 GGTCGGACCCTTCCCTGG 61.400 72.222 16.55 0.00 38.99 4.45
2613 2926 2.284405 GTCGGACCCTTCCCTGGA 60.284 66.667 0.00 0.00 38.99 3.86
2614 2927 2.284405 TCGGACCCTTCCCTGGAC 60.284 66.667 0.00 0.00 38.99 4.02
2615 2928 3.400054 CGGACCCTTCCCTGGACC 61.400 72.222 0.00 0.00 38.99 4.46
2616 2929 3.015753 GGACCCTTCCCTGGACCC 61.016 72.222 0.00 0.00 35.57 4.46
2617 2930 2.125225 GACCCTTCCCTGGACCCT 59.875 66.667 0.00 0.00 0.00 4.34
2618 2931 2.204151 ACCCTTCCCTGGACCCTG 60.204 66.667 0.00 0.00 0.00 4.45
2619 2932 3.732849 CCCTTCCCTGGACCCTGC 61.733 72.222 0.00 0.00 0.00 4.85
2620 2933 4.101448 CCTTCCCTGGACCCTGCG 62.101 72.222 0.00 0.00 0.00 5.18
2621 2934 4.785453 CTTCCCTGGACCCTGCGC 62.785 72.222 0.00 0.00 0.00 6.09
2646 2959 3.558674 GAGCTACATGCACCAGGTT 57.441 52.632 0.00 0.00 45.94 3.50
2647 2960 1.089920 GAGCTACATGCACCAGGTTG 58.910 55.000 0.00 0.00 45.94 3.77
2648 2961 0.962356 AGCTACATGCACCAGGTTGC 60.962 55.000 8.03 8.03 44.17 4.17
2649 2962 1.937546 GCTACATGCACCAGGTTGCC 61.938 60.000 10.46 0.00 39.88 4.52
2650 2963 1.304052 TACATGCACCAGGTTGCCC 60.304 57.895 10.46 0.00 42.25 5.36
2651 2964 1.788518 TACATGCACCAGGTTGCCCT 61.789 55.000 10.46 0.00 42.25 5.19
2652 2965 1.909781 CATGCACCAGGTTGCCCTT 60.910 57.895 10.46 0.00 42.25 3.95
2653 2966 1.152269 ATGCACCAGGTTGCCCTTT 60.152 52.632 10.46 0.00 42.25 3.11
2654 2967 0.763986 ATGCACCAGGTTGCCCTTTT 60.764 50.000 10.46 0.00 42.25 2.27
2655 2968 0.980231 TGCACCAGGTTGCCCTTTTT 60.980 50.000 10.46 0.00 42.25 1.94
4173 4513 5.731591 AGTACTTCCTCCGTTCCAAATTAG 58.268 41.667 0.00 0.00 0.00 1.73
4191 4531 4.642445 TTAGTCGTCGCAGAAATGGATA 57.358 40.909 0.00 0.00 39.69 2.59
4229 4585 2.288579 ACACCTGCGACAAGTAATTCGA 60.289 45.455 0.00 0.00 37.43 3.71
4238 4594 4.240096 GACAAGTAATTCGAAACGGAGGA 58.760 43.478 0.00 0.00 0.00 3.71
4282 4638 6.255950 GTGATTTATTTAACTCCCAACTCGC 58.744 40.000 0.00 0.00 0.00 5.03
4368 4724 4.535781 TGTATGGCTGCATGGAATTACTT 58.464 39.130 0.50 0.00 0.00 2.24
4381 4746 7.710907 GCATGGAATTACTTGTCACTGTATCTA 59.289 37.037 5.52 0.00 0.00 1.98
4442 4807 8.073768 TCATTTTTGAGACGAGTAATTTGGAAC 58.926 33.333 0.00 0.00 0.00 3.62
4465 4830 4.443457 CGGAGGGAGTATGTTTCATGTCAT 60.443 45.833 0.00 0.00 0.00 3.06
4531 4896 3.614616 TGCAACGGATGAACAACAAAAAC 59.385 39.130 0.00 0.00 0.00 2.43
4816 5182 0.743688 TGTTGCCACACAATGTCCAC 59.256 50.000 0.00 0.00 41.27 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 2.501223 GATGGACGAGGCAACGGACA 62.501 60.000 8.70 7.11 46.39 4.02
5 6 1.810030 GATGGACGAGGCAACGGAC 60.810 63.158 8.70 2.32 46.39 4.79
70 71 9.959749 ATTCGAGTCTCTAGATGTATTCTTTTC 57.040 33.333 0.00 0.00 35.79 2.29
86 87 5.499935 CAGATGCATTTGAATTCGAGTCTC 58.500 41.667 11.72 0.00 0.00 3.36
112 113 1.601663 GGTCTCGGCTGATCAGAATCG 60.602 57.143 27.04 22.88 34.39 3.34
137 138 5.969423 TCTAGAACCGAAATTCCATTACGT 58.031 37.500 0.00 0.00 0.00 3.57
209 210 9.070179 GTAAATTAACCACCTACTCCTTTTTGA 57.930 33.333 0.00 0.00 0.00 2.69
2364 2677 1.739562 GGCTCTCTCAACAGCACCG 60.740 63.158 0.00 0.00 37.38 4.94
2485 2798 1.228552 GCTCCCCTTGGCAGTTGAA 60.229 57.895 0.00 0.00 0.00 2.69
2486 2799 2.436109 GCTCCCCTTGGCAGTTGA 59.564 61.111 0.00 0.00 0.00 3.18
2487 2800 2.677875 GGCTCCCCTTGGCAGTTG 60.678 66.667 0.00 0.00 0.00 3.16
2488 2801 2.860971 AGGCTCCCCTTGGCAGTT 60.861 61.111 0.00 0.00 38.74 3.16
2500 2813 3.605749 TACCACTGCGCCAAGGCTC 62.606 63.158 4.18 1.20 39.32 4.70
2501 2814 2.690653 TTTACCACTGCGCCAAGGCT 62.691 55.000 4.18 0.00 39.32 4.58
2502 2815 2.200170 CTTTACCACTGCGCCAAGGC 62.200 60.000 4.18 0.00 37.85 4.35
2503 2816 1.875963 CTTTACCACTGCGCCAAGG 59.124 57.895 4.18 6.21 0.00 3.61
2504 2817 1.210155 GCTTTACCACTGCGCCAAG 59.790 57.895 4.18 0.00 0.00 3.61
2505 2818 1.228124 AGCTTTACCACTGCGCCAA 60.228 52.632 4.18 0.00 0.00 4.52
2506 2819 1.965930 CAGCTTTACCACTGCGCCA 60.966 57.895 4.18 0.00 0.00 5.69
2507 2820 2.870372 CAGCTTTACCACTGCGCC 59.130 61.111 4.18 0.00 0.00 6.53
2511 2824 0.607489 AGGCAGCAGCTTTACCACTG 60.607 55.000 0.00 0.00 41.70 3.66
2512 2825 0.111253 AAGGCAGCAGCTTTACCACT 59.889 50.000 0.00 0.00 38.40 4.00
2513 2826 0.242017 CAAGGCAGCAGCTTTACCAC 59.758 55.000 0.00 0.00 38.07 4.16
2514 2827 0.178992 ACAAGGCAGCAGCTTTACCA 60.179 50.000 0.00 0.00 38.07 3.25
2515 2828 0.242017 CACAAGGCAGCAGCTTTACC 59.758 55.000 0.00 0.00 38.07 2.85
2516 2829 1.068954 GTCACAAGGCAGCAGCTTTAC 60.069 52.381 0.00 0.00 38.07 2.01
2517 2830 1.238439 GTCACAAGGCAGCAGCTTTA 58.762 50.000 0.00 0.00 38.07 1.85
2518 2831 1.458639 GGTCACAAGGCAGCAGCTTT 61.459 55.000 0.00 0.00 41.17 3.51
2519 2832 1.900498 GGTCACAAGGCAGCAGCTT 60.900 57.895 0.00 0.00 41.70 3.74
2520 2833 2.282040 GGTCACAAGGCAGCAGCT 60.282 61.111 0.00 0.00 41.70 4.24
2521 2834 1.975407 ATGGTCACAAGGCAGCAGC 60.975 57.895 0.00 0.00 41.10 5.25
2522 2835 1.592400 CCATGGTCACAAGGCAGCAG 61.592 60.000 2.57 0.00 0.00 4.24
2523 2836 1.604308 CCATGGTCACAAGGCAGCA 60.604 57.895 2.57 0.00 0.00 4.41
2524 2837 0.895100 TTCCATGGTCACAAGGCAGC 60.895 55.000 12.58 0.00 35.46 5.25
2525 2838 1.270550 GTTTCCATGGTCACAAGGCAG 59.729 52.381 12.58 0.00 35.46 4.85
2526 2839 1.327303 GTTTCCATGGTCACAAGGCA 58.673 50.000 12.58 0.00 35.46 4.75
2527 2840 1.270550 CTGTTTCCATGGTCACAAGGC 59.729 52.381 12.58 0.00 35.46 4.35
2528 2841 1.270550 GCTGTTTCCATGGTCACAAGG 59.729 52.381 12.58 6.33 36.81 3.61
2529 2842 1.270550 GGCTGTTTCCATGGTCACAAG 59.729 52.381 12.58 10.32 0.00 3.16
2530 2843 1.133513 AGGCTGTTTCCATGGTCACAA 60.134 47.619 12.58 0.00 0.00 3.33
2531 2844 0.478072 AGGCTGTTTCCATGGTCACA 59.522 50.000 12.58 14.27 0.00 3.58
2532 2845 1.168714 GAGGCTGTTTCCATGGTCAC 58.831 55.000 12.58 10.22 0.00 3.67
2533 2846 1.067295 AGAGGCTGTTTCCATGGTCA 58.933 50.000 12.58 9.00 0.00 4.02
2534 2847 2.206576 AAGAGGCTGTTTCCATGGTC 57.793 50.000 12.58 4.59 0.00 4.02
2535 2848 2.375174 TGTAAGAGGCTGTTTCCATGGT 59.625 45.455 12.58 0.00 0.00 3.55
2536 2849 3.012518 CTGTAAGAGGCTGTTTCCATGG 58.987 50.000 4.97 4.97 34.07 3.66
2537 2850 3.942829 TCTGTAAGAGGCTGTTTCCATG 58.057 45.455 0.90 0.00 38.67 3.66
2550 2863 5.250774 AGCCTTTCCCTACATTTCTGTAAGA 59.749 40.000 0.00 0.00 44.68 2.10
2551 2864 5.355350 CAGCCTTTCCCTACATTTCTGTAAG 59.645 44.000 0.00 0.00 37.41 2.34
2552 2865 5.253330 CAGCCTTTCCCTACATTTCTGTAA 58.747 41.667 0.00 0.00 37.41 2.41
2553 2866 4.843728 CAGCCTTTCCCTACATTTCTGTA 58.156 43.478 0.00 0.00 36.79 2.74
2554 2867 3.690460 CAGCCTTTCCCTACATTTCTGT 58.310 45.455 0.00 0.00 39.49 3.41
2555 2868 2.424956 GCAGCCTTTCCCTACATTTCTG 59.575 50.000 0.00 0.00 0.00 3.02
2556 2869 2.728007 GCAGCCTTTCCCTACATTTCT 58.272 47.619 0.00 0.00 0.00 2.52
2557 2870 1.401905 CGCAGCCTTTCCCTACATTTC 59.598 52.381 0.00 0.00 0.00 2.17
2558 2871 1.271926 ACGCAGCCTTTCCCTACATTT 60.272 47.619 0.00 0.00 0.00 2.32
2559 2872 0.328258 ACGCAGCCTTTCCCTACATT 59.672 50.000 0.00 0.00 0.00 2.71
2560 2873 1.134491 GTACGCAGCCTTTCCCTACAT 60.134 52.381 0.00 0.00 0.00 2.29
2561 2874 0.248289 GTACGCAGCCTTTCCCTACA 59.752 55.000 0.00 0.00 0.00 2.74
2562 2875 0.535797 AGTACGCAGCCTTTCCCTAC 59.464 55.000 0.00 0.00 0.00 3.18
2563 2876 2.148446 TAGTACGCAGCCTTTCCCTA 57.852 50.000 0.00 0.00 0.00 3.53
2564 2877 1.497161 ATAGTACGCAGCCTTTCCCT 58.503 50.000 0.00 0.00 0.00 4.20
2565 2878 2.626743 TCTATAGTACGCAGCCTTTCCC 59.373 50.000 0.00 0.00 0.00 3.97
2566 2879 3.552478 GGTCTATAGTACGCAGCCTTTCC 60.552 52.174 0.00 0.00 0.00 3.13
2567 2880 3.552478 GGGTCTATAGTACGCAGCCTTTC 60.552 52.174 0.00 0.00 0.00 2.62
2568 2881 2.364647 GGGTCTATAGTACGCAGCCTTT 59.635 50.000 0.00 0.00 0.00 3.11
2569 2882 1.962100 GGGTCTATAGTACGCAGCCTT 59.038 52.381 0.00 0.00 0.00 4.35
2570 2883 1.133575 TGGGTCTATAGTACGCAGCCT 60.134 52.381 13.98 0.00 35.18 4.58
2571 2884 1.325355 TGGGTCTATAGTACGCAGCC 58.675 55.000 13.98 8.23 35.18 4.85
2572 2885 3.181478 ACTTTGGGTCTATAGTACGCAGC 60.181 47.826 16.00 2.07 40.36 5.25
2573 2886 4.360563 CACTTTGGGTCTATAGTACGCAG 58.639 47.826 16.00 11.29 40.36 5.18
2574 2887 3.131577 CCACTTTGGGTCTATAGTACGCA 59.868 47.826 13.98 13.98 37.94 5.24
2575 2888 3.131755 ACCACTTTGGGTCTATAGTACGC 59.868 47.826 0.00 6.13 43.37 4.42
2576 2889 4.996788 ACCACTTTGGGTCTATAGTACG 57.003 45.455 0.00 0.00 43.37 3.67
2586 2899 2.826003 GGGTCCGACCACTTTGGGT 61.826 63.158 19.43 0.00 43.37 4.51
2587 2900 2.033602 GGGTCCGACCACTTTGGG 59.966 66.667 19.43 0.00 43.37 4.12
2588 2901 0.605589 GAAGGGTCCGACCACTTTGG 60.606 60.000 19.43 0.00 41.02 3.28
2589 2902 0.605589 GGAAGGGTCCGACCACTTTG 60.606 60.000 19.43 0.00 41.02 2.77
2590 2903 1.759236 GGAAGGGTCCGACCACTTT 59.241 57.895 19.43 9.96 41.02 2.66
2591 2904 2.222013 GGGAAGGGTCCGACCACTT 61.222 63.158 19.43 17.88 46.04 3.16
2592 2905 2.606826 GGGAAGGGTCCGACCACT 60.607 66.667 19.43 10.80 46.04 4.00
2593 2906 2.606826 AGGGAAGGGTCCGACCAC 60.607 66.667 19.43 8.70 46.04 4.16
2594 2907 2.606519 CAGGGAAGGGTCCGACCA 60.607 66.667 19.43 0.00 46.04 4.02
2595 2908 3.400054 CCAGGGAAGGGTCCGACC 61.400 72.222 9.30 9.30 46.04 4.79
2596 2909 2.284405 TCCAGGGAAGGGTCCGAC 60.284 66.667 0.00 0.00 46.04 4.79
2597 2910 2.284405 GTCCAGGGAAGGGTCCGA 60.284 66.667 0.00 0.00 46.04 4.55
2598 2911 3.400054 GGTCCAGGGAAGGGTCCG 61.400 72.222 0.00 0.00 46.04 4.79
2599 2912 3.015753 GGGTCCAGGGAAGGGTCC 61.016 72.222 0.00 0.00 44.10 4.46
2600 2913 2.125225 AGGGTCCAGGGAAGGGTC 59.875 66.667 0.00 0.00 0.00 4.46
2601 2914 2.204151 CAGGGTCCAGGGAAGGGT 60.204 66.667 0.00 0.00 0.00 4.34
2602 2915 3.732849 GCAGGGTCCAGGGAAGGG 61.733 72.222 0.00 0.00 0.00 3.95
2603 2916 4.101448 CGCAGGGTCCAGGGAAGG 62.101 72.222 0.00 0.00 0.00 3.46
2604 2917 4.785453 GCGCAGGGTCCAGGGAAG 62.785 72.222 0.30 0.00 0.00 3.46
2616 2929 4.819761 TAGCTCCCGCTTGCGCAG 62.820 66.667 11.31 6.32 46.47 5.18
2619 2932 2.202932 ATGTAGCTCCCGCTTGCG 60.203 61.111 8.14 8.14 46.47 4.85
2620 2933 2.828128 GCATGTAGCTCCCGCTTGC 61.828 63.158 0.00 0.00 46.47 4.01
2621 2934 1.450134 TGCATGTAGCTCCCGCTTG 60.450 57.895 0.00 0.00 46.47 4.01
2622 2935 1.450312 GTGCATGTAGCTCCCGCTT 60.450 57.895 0.00 0.00 46.47 4.68
2628 2941 1.089920 CAACCTGGTGCATGTAGCTC 58.910 55.000 14.15 0.00 45.94 4.09
2629 2942 0.962356 GCAACCTGGTGCATGTAGCT 60.962 55.000 14.15 0.00 44.29 3.32
2630 2943 1.508088 GCAACCTGGTGCATGTAGC 59.492 57.895 6.00 6.00 44.29 3.58
2631 2944 2.183409 GGCAACCTGGTGCATGTAG 58.817 57.895 18.44 0.00 46.81 2.74
2632 2945 4.413928 GGCAACCTGGTGCATGTA 57.586 55.556 18.44 0.00 46.81 2.29
2655 2968 6.147164 CACTAGAGTCGGCAGTTGAATAAAAA 59.853 38.462 0.00 0.00 0.00 1.94
2656 2969 5.637810 CACTAGAGTCGGCAGTTGAATAAAA 59.362 40.000 0.00 0.00 0.00 1.52
2657 2970 5.047590 TCACTAGAGTCGGCAGTTGAATAAA 60.048 40.000 0.00 0.00 0.00 1.40
2658 2971 4.461431 TCACTAGAGTCGGCAGTTGAATAA 59.539 41.667 0.00 0.00 0.00 1.40
2659 2972 4.014406 TCACTAGAGTCGGCAGTTGAATA 58.986 43.478 0.00 0.00 0.00 1.75
2660 2973 2.826128 TCACTAGAGTCGGCAGTTGAAT 59.174 45.455 0.00 0.00 0.00 2.57
4173 4513 5.403246 AGATATATCCATTTCTGCGACGAC 58.597 41.667 9.18 0.00 0.00 4.34
4191 4531 6.757010 CGCAGGTGTGTTTTAGTTCTAGATAT 59.243 38.462 0.00 0.00 0.00 1.63
4207 4547 2.159841 CGAATTACTTGTCGCAGGTGTG 60.160 50.000 5.18 0.00 0.00 3.82
4229 4585 4.831710 AGTTCACTACTACTTCCTCCGTTT 59.168 41.667 0.00 0.00 34.56 3.60
4238 4594 4.049186 CACGCAACAGTTCACTACTACTT 58.951 43.478 0.00 0.00 34.56 2.24
4282 4638 1.001633 ACGTACTGGTTAGTTGGCTGG 59.998 52.381 0.00 0.00 38.36 4.85
4416 4781 7.737972 TCCAAATTACTCGTCTCAAAAATGA 57.262 32.000 0.00 0.00 0.00 2.57
4419 4784 6.423862 CGTTCCAAATTACTCGTCTCAAAAA 58.576 36.000 0.00 0.00 0.00 1.94
4442 4807 3.118775 TGACATGAAACATACTCCCTCCG 60.119 47.826 0.00 0.00 0.00 4.63
4465 4830 9.037737 CACTTTTGCTAGTAGTAGTACAAAACA 57.962 33.333 10.33 0.47 34.40 2.83
4622 4987 6.207221 TGTTCTTTGCTCTCTTGCATCATTTA 59.793 34.615 0.00 0.00 42.96 1.40
4623 4988 5.010314 TGTTCTTTGCTCTCTTGCATCATTT 59.990 36.000 0.00 0.00 42.96 2.32
4626 4991 3.479489 TGTTCTTTGCTCTCTTGCATCA 58.521 40.909 0.00 0.00 42.96 3.07
4627 4992 4.155462 TCATGTTCTTTGCTCTCTTGCATC 59.845 41.667 0.00 0.00 42.96 3.91
4628 4993 4.077108 TCATGTTCTTTGCTCTCTTGCAT 58.923 39.130 0.00 0.00 42.96 3.96
4629 4994 3.479489 TCATGTTCTTTGCTCTCTTGCA 58.521 40.909 0.00 0.00 41.65 4.08
4630 4995 3.750130 TCTCATGTTCTTTGCTCTCTTGC 59.250 43.478 0.00 0.00 0.00 4.01
4801 5167 1.163420 TCACGTGGACATTGTGTGGC 61.163 55.000 17.00 0.00 35.20 5.01


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

AutoCloner maintained by Alex Coulton.