Multiple sequence alignment - TraesCS7A01G329800

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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 TraesCS7A01G329800 chr7A 100.000 8234 0 0 1 8234 481581550 481589783 0.000000e+00 15206.0
1 TraesCS7A01G329800 chr7A 98.710 155 2 0 2216 2370 481583687 481583841 8.140000e-70 276.0
2 TraesCS7A01G329800 chr7A 98.710 155 2 0 2138 2292 481583765 481583919 8.140000e-70 276.0
3 TraesCS7A01G329800 chr7A 78.733 442 65 14 7820 8234 481590621 481591060 1.360000e-67 268.0
4 TraesCS7A01G329800 chr7A 77.462 457 63 22 7804 8234 481591438 481591880 3.840000e-58 237.0
5 TraesCS7A01G329800 chr7A 97.403 77 2 0 2294 2370 481583687 481583763 1.860000e-26 132.0
6 TraesCS7A01G329800 chr7A 97.403 77 2 0 2138 2214 481583843 481583919 1.860000e-26 132.0
7 TraesCS7A01G329800 chr7B 96.138 5437 124 38 244 5642 432915486 432920874 0.000000e+00 8798.0
8 TraesCS7A01G329800 chr7B 92.507 1895 58 37 5807 7637 432920964 432922838 0.000000e+00 2636.0
9 TraesCS7A01G329800 chr7B 87.583 451 40 2 7800 8234 432923004 432923454 7.370000e-140 508.0
10 TraesCS7A01G329800 chr7B 92.174 230 6 3 2 224 432915275 432915499 1.730000e-81 315.0
11 TraesCS7A01G329800 chr7B 79.418 447 65 17 7804 8234 432924083 432924518 2.910000e-74 291.0
12 TraesCS7A01G329800 chr7B 84.158 303 44 3 7934 8234 432924435 432924735 2.910000e-74 291.0
13 TraesCS7A01G329800 chr7B 98.065 155 3 0 2216 2370 432917377 432917531 3.790000e-68 270.0
14 TraesCS7A01G329800 chr7B 97.468 158 4 0 2138 2295 432917455 432917612 3.790000e-68 270.0
15 TraesCS7A01G329800 chr7B 97.938 97 2 0 5604 5700 432920875 432920971 1.420000e-37 169.0
16 TraesCS7A01G329800 chr7B 98.701 77 1 0 2294 2370 432917377 432917453 4.010000e-28 137.0
17 TraesCS7A01G329800 chr7B 96.250 80 3 0 2138 2217 432917533 432917612 1.860000e-26 132.0
18 TraesCS7A01G329800 chr7B 97.826 46 0 1 7690 7735 432922856 432922900 2.460000e-10 78.7
19 TraesCS7A01G329800 chr7D 96.717 4539 88 19 1183 5700 416960909 416965407 0.000000e+00 7500.0
20 TraesCS7A01G329800 chr7D 93.471 1792 49 32 5807 7538 416965400 416967183 0.000000e+00 2599.0
21 TraesCS7A01G329800 chr7D 94.847 1145 26 14 2 1126 416959370 416960501 0.000000e+00 1757.0
22 TraesCS7A01G329800 chr7D 83.469 369 39 11 7882 8234 416967641 416968003 2.870000e-84 324.0
23 TraesCS7A01G329800 chr7D 85.855 304 38 3 7934 8234 416968635 416968936 1.330000e-82 318.0
24 TraesCS7A01G329800 chr7D 78.889 450 74 10 7802 8234 416971568 416972013 1.350000e-72 285.0
25 TraesCS7A01G329800 chr7D 86.275 255 28 4 7934 8186 416967924 416968173 3.790000e-68 270.0
26 TraesCS7A01G329800 chr7D 83.007 306 44 6 7934 8234 416970558 416970860 3.790000e-68 270.0
27 TraesCS7A01G329800 chr7D 96.835 158 5 0 2138 2295 416961946 416962103 1.760000e-66 265.0
28 TraesCS7A01G329800 chr7D 79.310 406 55 15 7802 8179 416969347 416969751 2.950000e-64 257.0
29 TraesCS7A01G329800 chr7D 95.625 160 6 1 2216 2375 416961868 416962026 1.060000e-63 255.0
30 TraesCS7A01G329800 chr7D 77.586 406 61 14 7805 8182 416970623 416971026 1.390000e-52 219.0
31 TraesCS7A01G329800 chr7D 88.696 115 13 0 7665 7779 416967392 416967506 3.100000e-29 141.0
32 TraesCS7A01G329800 chr7D 96.154 78 3 0 2140 2217 416962026 416962103 2.410000e-25 128.0
33 TraesCS7A01G329800 chr7D 96.104 77 3 0 2294 2370 416961868 416961944 8.680000e-25 126.0
34 TraesCS7A01G329800 chr5A 97.458 118 3 0 5697 5814 513817950 513818067 1.400000e-47 202.0
35 TraesCS7A01G329800 chr5A 95.161 124 4 2 5694 5815 39114820 39114697 2.340000e-45 195.0
36 TraesCS7A01G329800 chr1A 95.312 128 4 2 5693 5819 62352824 62352698 1.400000e-47 202.0
37 TraesCS7A01G329800 chr1B 97.436 117 3 0 5698 5814 654278558 654278674 5.040000e-47 200.0
38 TraesCS7A01G329800 chr5D 96.639 119 4 0 5698 5816 270254144 270254026 1.810000e-46 198.0
39 TraesCS7A01G329800 chr5B 95.868 121 4 1 5694 5814 657593218 657593337 2.340000e-45 195.0
40 TraesCS7A01G329800 chr2B 95.868 121 4 1 5699 5819 148404475 148404594 2.340000e-45 195.0
41 TraesCS7A01G329800 chr4B 94.400 125 7 0 5699 5823 34580037 34580161 8.430000e-45 193.0
42 TraesCS7A01G329800 chr4A 92.029 138 6 4 5698 5835 187572347 187572215 1.090000e-43 189.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7A01G329800 chr7A 481581550 481589783 8233 False 15206.000000 15206 100.0000 1 8234 1 chr7A.!!$F1 8233
1 TraesCS7A01G329800 chr7A 481590621 481591880 1259 False 252.500000 268 78.0975 7804 8234 2 chr7A.!!$F3 430
2 TraesCS7A01G329800 chr7B 432915275 432924735 9460 False 1157.975000 8798 93.1855 2 8234 12 chr7B.!!$F1 8232
3 TraesCS7A01G329800 chr7D 416959370 416972013 12643 False 980.933333 7500 88.8560 2 8234 15 chr7D.!!$F1 8232

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
551 590 0.170561 GCATGCTTGTCTTGCAGAGG 59.829 55.000 11.37 0.0 44.04 3.69 F
2085 2517 0.746659 GCTTTGCCACAAGTCCAGTT 59.253 50.000 0.00 0.0 0.00 3.16 F
2086 2518 1.136891 GCTTTGCCACAAGTCCAGTTT 59.863 47.619 0.00 0.0 0.00 2.66 F
2528 2961 1.648467 GCACCGCCAACAGGAAGATC 61.648 60.000 0.00 0.0 0.00 2.75 F
2585 3018 3.677596 CCACCAATTTCCAATTTGTACGC 59.322 43.478 0.00 0.0 0.00 4.42 F
2958 3405 4.637091 TGTATCTTCACGACGATCTTACCA 59.363 41.667 0.00 0.0 0.00 3.25 F
3866 4316 5.886960 ATGTCAATGTGGAAGAGCTTTAC 57.113 39.130 0.00 0.0 0.00 2.01 F
5711 6203 0.034283 AGTGAGTACTCCCTCCGTCC 60.034 60.000 20.11 0.0 28.79 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2386 2819 0.038310 CCGGAAGAGAAAAGGCCCTT 59.962 55.000 0.00 0.00 0.00 3.95 R
2926 3373 1.403647 CGTGAAGATACACCGCCTGAA 60.404 52.381 0.00 0.00 37.48 3.02 R
3866 4316 2.194212 GCAGATGCATGCTCCCCAG 61.194 63.158 20.33 5.23 43.07 4.45 R
4515 4965 3.624410 TCAGATCTGCAAAATGATCGTGG 59.376 43.478 18.36 3.53 42.62 4.94 R
4535 4985 2.950781 AGTCAGTCTGAGTGGACTTCA 58.049 47.619 9.49 0.00 43.14 3.02 R
4536 4986 4.521256 ACTAAGTCAGTCTGAGTGGACTTC 59.479 45.833 22.19 8.13 44.81 3.01 R
5791 6283 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12 R
7636 8206 0.178915 TGGGGTTCTCTTCCGAGGAA 60.179 55.000 4.34 4.34 37.86 3.36 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
164 172 1.143684 GGGGCATTCAGATCAAGCCTA 59.856 52.381 11.77 0.00 44.60 3.93
165 173 2.502295 GGGCATTCAGATCAAGCCTAG 58.498 52.381 11.77 0.00 44.60 3.02
166 174 2.502295 GGCATTCAGATCAAGCCTAGG 58.498 52.381 3.67 3.67 42.01 3.02
167 175 1.878734 GCATTCAGATCAAGCCTAGGC 59.121 52.381 27.19 27.19 42.33 3.93
199 207 2.033328 CTACATGCTGCGCTGTGAGC 62.033 60.000 16.05 13.11 38.02 4.26
268 307 6.603599 AGAATTAGTGCTTTCCAAGGTAATCC 59.396 38.462 0.00 0.00 0.00 3.01
307 346 4.222336 TCTGTGTCAACCAAATCCCATTT 58.778 39.130 0.00 0.00 0.00 2.32
323 362 2.092103 CCATTTAGGATTCGGGTGGGAA 60.092 50.000 0.00 0.00 41.22 3.97
481 520 2.450160 GCACGCCTATACACATTTTGC 58.550 47.619 0.00 0.00 0.00 3.68
551 590 0.170561 GCATGCTTGTCTTGCAGAGG 59.829 55.000 11.37 0.00 44.04 3.69
674 720 8.662141 TCTTATCTTGCCGTTATAAGAAAACAC 58.338 33.333 0.00 0.00 38.58 3.32
711 757 8.952278 TGTTATCAATACGCATACCTTTTCTTT 58.048 29.630 0.00 0.00 0.00 2.52
891 941 1.045911 CCTCTCACCTACCAGCTCCC 61.046 65.000 0.00 0.00 0.00 4.30
893 943 2.040606 TCACCTACCAGCTCCCCC 59.959 66.667 0.00 0.00 0.00 5.40
1151 1213 2.184322 CCGTGCGTGCTACTCCAT 59.816 61.111 0.00 0.00 0.00 3.41
1162 1224 1.825641 GCTACTCCATCCCTCTCCCTC 60.826 61.905 0.00 0.00 0.00 4.30
1163 1225 0.861155 TACTCCATCCCTCTCCCTCC 59.139 60.000 0.00 0.00 0.00 4.30
1164 1226 1.152139 CTCCATCCCTCTCCCTCCC 60.152 68.421 0.00 0.00 0.00 4.30
1165 1227 1.630333 TCCATCCCTCTCCCTCCCT 60.630 63.158 0.00 0.00 0.00 4.20
1314 1727 1.134670 GCCAGCTCTAAATCTCCACGT 60.135 52.381 0.00 0.00 0.00 4.49
1342 1755 2.246687 GCTTCGCAATCGATCCGC 59.753 61.111 12.08 10.69 45.04 5.54
1416 1829 1.647346 CTTGTTAGGCACGCCGATTA 58.353 50.000 1.61 0.00 41.95 1.75
1564 1981 1.768684 TTCCGTGCTTGCCTTCTCCT 61.769 55.000 0.00 0.00 0.00 3.69
1592 2013 1.533756 CCGCACGGATTTAATGCTTGG 60.534 52.381 2.01 0.00 37.20 3.61
1600 2021 4.252878 GGATTTAATGCTTGGTTGGTTGG 58.747 43.478 0.00 0.00 0.00 3.77
1694 2123 1.466856 TTGGATTTGCTGCTGCCTAG 58.533 50.000 13.47 0.00 38.71 3.02
1803 2235 6.293955 CCTCTCGGAAGCATTTTTAAAGTTCA 60.294 38.462 0.00 0.00 0.00 3.18
1959 2391 4.688511 TTACAATATGTGGTGCCGTTTC 57.311 40.909 0.00 0.00 0.00 2.78
1960 2392 2.509569 ACAATATGTGGTGCCGTTTCA 58.490 42.857 0.00 0.00 0.00 2.69
1974 2406 1.322936 CGTTTCATCTGCTTCGCTCTC 59.677 52.381 0.00 0.00 0.00 3.20
2085 2517 0.746659 GCTTTGCCACAAGTCCAGTT 59.253 50.000 0.00 0.00 0.00 3.16
2086 2518 1.136891 GCTTTGCCACAAGTCCAGTTT 59.863 47.619 0.00 0.00 0.00 2.66
2370 2803 6.240894 ACTTATGTATGGCTGGATGGTATTG 58.759 40.000 0.00 0.00 0.00 1.90
2386 2819 7.067251 GGATGGTATTGTTCGGGTATAAAAACA 59.933 37.037 0.00 0.00 0.00 2.83
2513 2946 3.569701 CCAATGGTACTAATGATGGCACC 59.430 47.826 0.00 0.00 0.00 5.01
2528 2961 1.648467 GCACCGCCAACAGGAAGATC 61.648 60.000 0.00 0.00 0.00 2.75
2585 3018 3.677596 CCACCAATTTCCAATTTGTACGC 59.322 43.478 0.00 0.00 0.00 4.42
2635 3070 5.182190 CCCCTTTTCTCTTTCTTAGAAGCAC 59.818 44.000 0.00 0.00 34.59 4.40
2926 3373 6.854496 TGTCGTAATTCTTTACTGCTTTGT 57.146 33.333 0.00 0.00 36.37 2.83
2958 3405 4.637091 TGTATCTTCACGACGATCTTACCA 59.363 41.667 0.00 0.00 0.00 3.25
3866 4316 5.886960 ATGTCAATGTGGAAGAGCTTTAC 57.113 39.130 0.00 0.00 0.00 2.01
4114 4564 6.970484 AGTCACAATCATTTTACAAGTCCAC 58.030 36.000 0.00 0.00 0.00 4.02
4515 4965 7.072030 CACTAAACAGACTTTCTAACATGCAC 58.928 38.462 0.00 0.00 0.00 4.57
4535 4985 3.376234 CACCACGATCATTTTGCAGATCT 59.624 43.478 10.80 0.00 38.75 2.75
4536 4986 3.376234 ACCACGATCATTTTGCAGATCTG 59.624 43.478 18.84 18.84 38.75 2.90
5094 5544 1.947456 AGCGTTTTGAGTTCTCAACCC 59.053 47.619 13.79 7.42 0.00 4.11
5261 5711 5.978322 AGTAAGTTGTCTTGAGTCTTTCGTC 59.022 40.000 0.00 0.00 35.36 4.20
5540 5993 9.811995 TTCTGTTATGACCAGTGTAACATATAC 57.188 33.333 4.95 6.04 41.43 1.47
5596 6049 2.231964 GCAATGATGAAGGGTGCAAGAA 59.768 45.455 0.00 0.00 35.28 2.52
5621 6113 5.399013 CCGTTTTTCCTGTGAAATATGGTC 58.601 41.667 7.95 0.00 40.69 4.02
5700 6192 4.760204 AGTTATTTGTGCCCAAGTGAGTAC 59.240 41.667 0.00 0.00 0.00 2.73
5701 6193 3.508845 ATTTGTGCCCAAGTGAGTACT 57.491 42.857 0.00 0.00 39.32 2.73
5702 6194 2.543777 TTGTGCCCAAGTGAGTACTC 57.456 50.000 16.32 16.32 35.69 2.59
5703 6195 0.685097 TGTGCCCAAGTGAGTACTCC 59.315 55.000 20.11 11.29 35.69 3.85
5704 6196 0.036294 GTGCCCAAGTGAGTACTCCC 60.036 60.000 20.11 8.98 35.69 4.30
5705 6197 0.178903 TGCCCAAGTGAGTACTCCCT 60.179 55.000 20.11 11.43 35.69 4.20
5706 6198 0.537653 GCCCAAGTGAGTACTCCCTC 59.462 60.000 20.11 10.45 35.69 4.30
5707 6199 1.196012 CCCAAGTGAGTACTCCCTCC 58.804 60.000 20.11 5.73 35.69 4.30
5708 6200 0.818296 CCAAGTGAGTACTCCCTCCG 59.182 60.000 20.11 8.77 35.69 4.63
5709 6201 1.546961 CAAGTGAGTACTCCCTCCGT 58.453 55.000 20.11 0.00 35.69 4.69
5710 6202 1.473278 CAAGTGAGTACTCCCTCCGTC 59.527 57.143 20.11 2.65 35.69 4.79
5711 6203 0.034283 AGTGAGTACTCCCTCCGTCC 60.034 60.000 20.11 0.00 28.79 4.79
5712 6204 0.034283 GTGAGTACTCCCTCCGTCCT 60.034 60.000 20.11 0.00 0.00 3.85
5713 6205 0.034380 TGAGTACTCCCTCCGTCCTG 60.034 60.000 20.11 0.00 0.00 3.86
5714 6206 0.255318 GAGTACTCCCTCCGTCCTGA 59.745 60.000 12.13 0.00 0.00 3.86
5715 6207 0.702902 AGTACTCCCTCCGTCCTGAA 59.297 55.000 0.00 0.00 0.00 3.02
5716 6208 1.076677 AGTACTCCCTCCGTCCTGAAA 59.923 52.381 0.00 0.00 0.00 2.69
5717 6209 2.108970 GTACTCCCTCCGTCCTGAAAT 58.891 52.381 0.00 0.00 0.00 2.17
5718 6210 2.544844 ACTCCCTCCGTCCTGAAATA 57.455 50.000 0.00 0.00 0.00 1.40
5719 6211 2.108970 ACTCCCTCCGTCCTGAAATAC 58.891 52.381 0.00 0.00 0.00 1.89
5720 6212 2.292323 ACTCCCTCCGTCCTGAAATACT 60.292 50.000 0.00 0.00 0.00 2.12
5721 6213 2.766828 CTCCCTCCGTCCTGAAATACTT 59.233 50.000 0.00 0.00 0.00 2.24
5722 6214 2.500098 TCCCTCCGTCCTGAAATACTTG 59.500 50.000 0.00 0.00 0.00 3.16
5723 6215 2.236395 CCCTCCGTCCTGAAATACTTGT 59.764 50.000 0.00 0.00 0.00 3.16
5724 6216 3.522553 CCTCCGTCCTGAAATACTTGTC 58.477 50.000 0.00 0.00 0.00 3.18
5725 6217 3.522553 CTCCGTCCTGAAATACTTGTCC 58.477 50.000 0.00 0.00 0.00 4.02
5726 6218 3.170717 TCCGTCCTGAAATACTTGTCCT 58.829 45.455 0.00 0.00 0.00 3.85
5727 6219 3.581332 TCCGTCCTGAAATACTTGTCCTT 59.419 43.478 0.00 0.00 0.00 3.36
5728 6220 3.684788 CCGTCCTGAAATACTTGTCCTTG 59.315 47.826 0.00 0.00 0.00 3.61
5729 6221 4.562757 CCGTCCTGAAATACTTGTCCTTGA 60.563 45.833 0.00 0.00 0.00 3.02
5730 6222 4.994852 CGTCCTGAAATACTTGTCCTTGAA 59.005 41.667 0.00 0.00 0.00 2.69
5731 6223 5.468746 CGTCCTGAAATACTTGTCCTTGAAA 59.531 40.000 0.00 0.00 0.00 2.69
5732 6224 6.149474 CGTCCTGAAATACTTGTCCTTGAAAT 59.851 38.462 0.00 0.00 0.00 2.17
5733 6225 7.308435 GTCCTGAAATACTTGTCCTTGAAATG 58.692 38.462 0.00 0.00 0.00 2.32
5734 6226 6.434028 TCCTGAAATACTTGTCCTTGAAATGG 59.566 38.462 0.00 0.00 0.00 3.16
5735 6227 6.434028 CCTGAAATACTTGTCCTTGAAATGGA 59.566 38.462 0.00 0.00 37.91 3.41
5736 6228 7.123247 CCTGAAATACTTGTCCTTGAAATGGAT 59.877 37.037 0.00 0.00 42.67 3.41
5737 6229 9.177608 CTGAAATACTTGTCCTTGAAATGGATA 57.822 33.333 0.00 0.00 42.67 2.59
5738 6230 9.527157 TGAAATACTTGTCCTTGAAATGGATAA 57.473 29.630 0.00 0.00 42.67 1.75
5744 6236 9.753674 ACTTGTCCTTGAAATGGATAAAATAGA 57.246 29.630 0.00 0.00 42.67 1.98
5747 6239 9.699410 TGTCCTTGAAATGGATAAAATAGATGT 57.301 29.630 0.00 0.00 42.67 3.06
5786 6278 9.751542 AATAAGTCTAGATACAACCATTTCGAG 57.248 33.333 0.00 0.00 0.00 4.04
5787 6279 6.150396 AGTCTAGATACAACCATTTCGAGG 57.850 41.667 0.00 0.00 0.00 4.63
5788 6280 5.892119 AGTCTAGATACAACCATTTCGAGGA 59.108 40.000 0.00 0.00 0.00 3.71
5789 6281 5.978322 GTCTAGATACAACCATTTCGAGGAC 59.022 44.000 0.00 0.00 0.00 3.85
5790 6282 4.819105 AGATACAACCATTTCGAGGACA 57.181 40.909 0.00 0.00 0.00 4.02
5791 6283 5.160607 AGATACAACCATTTCGAGGACAA 57.839 39.130 0.00 0.00 0.00 3.18
5792 6284 5.178797 AGATACAACCATTTCGAGGACAAG 58.821 41.667 0.00 0.00 0.00 3.16
5793 6285 3.208747 ACAACCATTTCGAGGACAAGT 57.791 42.857 0.00 0.00 0.00 3.16
5794 6286 4.345859 ACAACCATTTCGAGGACAAGTA 57.654 40.909 0.00 0.00 0.00 2.24
5795 6287 4.906618 ACAACCATTTCGAGGACAAGTAT 58.093 39.130 0.00 0.00 0.00 2.12
5796 6288 5.313712 ACAACCATTTCGAGGACAAGTATT 58.686 37.500 0.00 0.00 0.00 1.89
5797 6289 5.768164 ACAACCATTTCGAGGACAAGTATTT 59.232 36.000 0.00 0.00 0.00 1.40
5798 6290 6.072673 ACAACCATTTCGAGGACAAGTATTTC 60.073 38.462 0.00 0.00 0.00 2.17
5799 6291 4.941873 ACCATTTCGAGGACAAGTATTTCC 59.058 41.667 0.00 0.00 0.00 3.13
5800 6292 4.034048 CCATTTCGAGGACAAGTATTTCCG 59.966 45.833 0.00 0.00 36.95 4.30
5801 6293 2.953466 TCGAGGACAAGTATTTCCGG 57.047 50.000 0.00 0.00 36.95 5.14
5802 6294 2.449464 TCGAGGACAAGTATTTCCGGA 58.551 47.619 0.00 0.00 36.95 5.14
5803 6295 2.165030 TCGAGGACAAGTATTTCCGGAC 59.835 50.000 1.83 0.00 36.95 4.79
5804 6296 2.537401 GAGGACAAGTATTTCCGGACG 58.463 52.381 1.83 0.00 36.95 4.79
5805 6297 1.206371 AGGACAAGTATTTCCGGACGG 59.794 52.381 1.83 3.96 36.95 4.79
5806 6298 1.205417 GGACAAGTATTTCCGGACGGA 59.795 52.381 1.83 9.76 43.52 4.69
5807 6299 2.537401 GACAAGTATTTCCGGACGGAG 58.463 52.381 13.64 3.15 46.06 4.63
5808 6300 1.206371 ACAAGTATTTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
5809 6301 0.828677 AAGTATTTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
5810 6302 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20
5811 6303 0.388294 GTATTTCCGGACGGAGGGAG 59.612 60.000 13.64 0.00 46.06 4.30
5812 6304 0.032813 TATTTCCGGACGGAGGGAGT 60.033 55.000 13.64 0.00 46.06 3.85
5813 6305 0.032813 ATTTCCGGACGGAGGGAGTA 60.033 55.000 13.64 0.00 46.06 2.59
5823 6315 2.223745 CGGAGGGAGTAGCTTAGAGAC 58.776 57.143 0.00 0.00 0.00 3.36
6090 6586 4.816385 TGGTGACTCTGAAAAGCTACAAAG 59.184 41.667 0.00 0.00 0.00 2.77
6093 6589 4.273480 TGACTCTGAAAAGCTACAAAGTGC 59.727 41.667 0.00 0.00 0.00 4.40
6206 6702 6.951062 TTGTTATTGGACACTTGTTGATCA 57.049 33.333 0.00 0.00 0.00 2.92
6364 6860 0.036306 GTGGTCAGGACACCCGAATT 59.964 55.000 1.41 0.00 35.26 2.17
6532 7031 1.980772 GAACTTGCTGCCTGGCCAT 60.981 57.895 17.53 0.00 0.00 4.40
6592 7091 2.457598 TCAGTACATGACAGACTCCCC 58.542 52.381 0.00 0.00 31.12 4.81
6830 7353 3.135530 CCTAAGACTATGCTCCTTTGCCT 59.864 47.826 0.00 0.00 0.00 4.75
6831 7354 2.706339 AGACTATGCTCCTTTGCCTG 57.294 50.000 0.00 0.00 0.00 4.85
6832 7355 1.020437 GACTATGCTCCTTTGCCTGC 58.980 55.000 0.00 0.00 0.00 4.85
6833 7356 0.622665 ACTATGCTCCTTTGCCTGCT 59.377 50.000 0.00 0.00 0.00 4.24
6834 7357 1.839994 ACTATGCTCCTTTGCCTGCTA 59.160 47.619 0.00 0.00 0.00 3.49
7060 7589 1.336755 GTTGTACAAGTGTGCCAAGGG 59.663 52.381 8.98 0.00 0.00 3.95
7065 7594 0.251297 CAAGTGTGCCAAGGGGATCA 60.251 55.000 0.00 0.00 35.59 2.92
7191 7720 5.567552 GCAAGATGAGATTTGCTACTCAAC 58.432 41.667 0.00 0.00 44.70 3.18
7204 7733 4.892934 TGCTACTCAACCTTTTTCCAATGT 59.107 37.500 0.00 0.00 0.00 2.71
7329 7870 2.093500 TGCTGCTACGGATGATCAAGTT 60.093 45.455 0.00 0.00 0.00 2.66
7387 7948 2.872245 ACGGTCAACAAGATCACAAGTG 59.128 45.455 0.00 0.00 0.00 3.16
7393 7960 6.253512 GGTCAACAAGATCACAAGTGTTTTTC 59.746 38.462 0.00 0.00 31.98 2.29
7396 7963 8.087750 TCAACAAGATCACAAGTGTTTTTCTTT 58.912 29.630 0.00 0.00 31.98 2.52
7397 7964 8.711457 CAACAAGATCACAAGTGTTTTTCTTTT 58.289 29.630 0.00 0.00 31.98 2.27
7398 7965 8.243289 ACAAGATCACAAGTGTTTTTCTTTTG 57.757 30.769 0.00 0.00 0.00 2.44
7438 8006 1.366679 TGTTGTTGCCGAACGTGTTA 58.633 45.000 0.00 0.00 34.49 2.41
7522 8092 1.353022 ACTCACTCTCTTCCGGTCTCT 59.647 52.381 0.00 0.00 0.00 3.10
7574 8144 1.267806 TCTTTTCGGTAGCGTCGACTT 59.732 47.619 14.70 4.30 36.30 3.01
7576 8146 2.138596 TTTCGGTAGCGTCGACTTTT 57.861 45.000 14.70 1.26 36.30 2.27
7586 8156 4.829808 AGCGTCGACTTTTAAAACAGTTC 58.170 39.130 14.70 0.00 0.00 3.01
7591 8161 7.373966 GCGTCGACTTTTAAAACAGTTCAAATA 59.626 33.333 14.70 0.00 0.00 1.40
7595 8165 9.511144 CGACTTTTAAAACAGTTCAAATAAGGT 57.489 29.630 0.00 0.00 0.00 3.50
7636 8206 1.340114 GGCTTGAGAAAATCGGGTCCT 60.340 52.381 0.00 0.00 0.00 3.85
7637 8207 2.437413 GCTTGAGAAAATCGGGTCCTT 58.563 47.619 0.00 0.00 0.00 3.36
7638 8208 2.420372 GCTTGAGAAAATCGGGTCCTTC 59.580 50.000 0.00 0.00 0.00 3.46
7639 8209 2.781681 TGAGAAAATCGGGTCCTTCC 57.218 50.000 0.00 0.00 0.00 3.46
7661 8231 1.880027 CGGAAGAGAACCCCACTTTTG 59.120 52.381 0.00 0.00 0.00 2.44
7662 8232 2.486548 CGGAAGAGAACCCCACTTTTGA 60.487 50.000 0.00 0.00 0.00 2.69
7663 8233 2.885266 GGAAGAGAACCCCACTTTTGAC 59.115 50.000 0.00 0.00 0.00 3.18
7685 8361 4.141390 ACTTGACCTCTCAAATGTGGTCTT 60.141 41.667 14.18 0.67 46.50 3.01
7687 8363 4.136796 TGACCTCTCAAATGTGGTCTTTG 58.863 43.478 14.18 1.35 46.50 2.77
7761 8437 9.511144 CACAATATAGACGTAGACATTTGTACA 57.489 33.333 0.00 0.00 0.00 2.90
7766 8442 8.744008 ATAGACGTAGACATTTGTACATATGC 57.256 34.615 21.73 15.59 0.00 3.14
7775 8451 9.123902 AGACATTTGTACATATGCACATACATT 57.876 29.630 21.73 3.75 0.00 2.71
7781 8457 7.452562 TGTACATATGCACATACATTCATCCT 58.547 34.615 4.57 0.00 0.00 3.24
7787 8516 4.164030 TGCACATACATTCATCCTAGGTGT 59.836 41.667 9.08 7.94 0.00 4.16
7789 8518 5.674525 CACATACATTCATCCTAGGTGTGT 58.325 41.667 9.08 9.93 34.75 3.72
7816 8545 1.667830 CGTCTTGAGCTTTCCGGCA 60.668 57.895 0.00 0.00 34.17 5.69
7827 8556 1.374947 TTCCGGCAGTGGAAGGAAG 59.625 57.895 0.00 0.00 43.01 3.46
7855 8584 2.621486 ACCAGGCCAGGTTAGATCC 58.379 57.895 15.35 0.00 39.34 3.36
7865 8594 1.693083 GGTTAGATCCGCACGTGCAC 61.693 60.000 37.03 25.31 42.21 4.57
7878 8607 2.040544 GTGCACCCTCATGTTCCCG 61.041 63.158 5.22 0.00 0.00 5.14
7886 8615 1.740025 CCTCATGTTCCCGAAGCTTTC 59.260 52.381 0.00 0.00 0.00 2.62
7890 8619 3.260884 TCATGTTCCCGAAGCTTTCTAGT 59.739 43.478 0.00 0.00 0.00 2.57
8029 8774 5.415221 GGGCGGAAACAATTAATGATGAAA 58.585 37.500 0.00 0.00 0.00 2.69
8030 8775 6.048509 GGGCGGAAACAATTAATGATGAAAT 58.951 36.000 0.00 0.00 0.00 2.17
8068 8813 4.021925 GTGCACCTCGGCTTCCCT 62.022 66.667 5.22 0.00 34.04 4.20
8126 9083 0.389426 GGTCAGGTACGCACGTTCAT 60.389 55.000 0.00 0.00 0.00 2.57
8139 9595 3.193263 CACGTTCATCTCCATCTTCCTG 58.807 50.000 0.00 0.00 0.00 3.86
8186 9642 9.841295 GTAATTAATGATGAACCAGGTAAGGTA 57.159 33.333 0.00 0.00 42.25 3.08
8188 9644 5.772393 AATGATGAACCAGGTAAGGTACA 57.228 39.130 0.00 0.00 42.25 2.90
8192 9648 3.039743 TGAACCAGGTAAGGTACACACA 58.960 45.455 0.00 0.00 42.25 3.72
8198 9654 2.637872 AGGTAAGGTACACACATGCACT 59.362 45.455 0.00 0.00 0.00 4.40
8212 9668 0.253044 TGCACTGCACTATCTTCCCC 59.747 55.000 0.00 0.00 31.71 4.81
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.627864 ACAATAACCACCAGGGCAAC 58.372 50.000 0.00 0.00 42.05 4.17
164 172 5.013913 AGCATGTAGATGGATTATTCAGCCT 59.986 40.000 1.57 0.00 0.00 4.58
165 173 5.123502 CAGCATGTAGATGGATTATTCAGCC 59.876 44.000 1.57 0.00 0.00 4.85
166 174 5.391736 GCAGCATGTAGATGGATTATTCAGC 60.392 44.000 1.57 0.00 39.31 4.26
167 175 5.163884 CGCAGCATGTAGATGGATTATTCAG 60.164 44.000 1.57 0.00 39.31 3.02
168 176 4.692155 CGCAGCATGTAGATGGATTATTCA 59.308 41.667 1.57 0.00 39.31 2.57
199 207 9.778993 TTAAAGCACTAATTCTACTACGTACTG 57.221 33.333 0.00 0.00 0.00 2.74
227 266 7.424803 CACTAATTCTCATCCACACACAAAAA 58.575 34.615 0.00 0.00 0.00 1.94
228 267 6.514870 GCACTAATTCTCATCCACACACAAAA 60.515 38.462 0.00 0.00 0.00 2.44
229 268 5.048782 GCACTAATTCTCATCCACACACAAA 60.049 40.000 0.00 0.00 0.00 2.83
230 269 4.455533 GCACTAATTCTCATCCACACACAA 59.544 41.667 0.00 0.00 0.00 3.33
231 270 4.002982 GCACTAATTCTCATCCACACACA 58.997 43.478 0.00 0.00 0.00 3.72
232 271 4.256920 AGCACTAATTCTCATCCACACAC 58.743 43.478 0.00 0.00 0.00 3.82
233 272 4.558226 AGCACTAATTCTCATCCACACA 57.442 40.909 0.00 0.00 0.00 3.72
234 273 5.163713 GGAAAGCACTAATTCTCATCCACAC 60.164 44.000 0.00 0.00 0.00 3.82
235 274 4.943705 GGAAAGCACTAATTCTCATCCACA 59.056 41.667 0.00 0.00 0.00 4.17
236 275 4.943705 TGGAAAGCACTAATTCTCATCCAC 59.056 41.667 0.00 0.00 29.93 4.02
237 276 5.178096 TGGAAAGCACTAATTCTCATCCA 57.822 39.130 0.00 0.00 32.33 3.41
238 277 5.067023 CCTTGGAAAGCACTAATTCTCATCC 59.933 44.000 0.00 0.00 44.44 3.51
239 278 5.649831 ACCTTGGAAAGCACTAATTCTCATC 59.350 40.000 0.00 0.00 44.44 2.92
240 279 5.574188 ACCTTGGAAAGCACTAATTCTCAT 58.426 37.500 0.00 0.00 44.44 2.90
241 280 4.985538 ACCTTGGAAAGCACTAATTCTCA 58.014 39.130 0.00 0.00 44.44 3.27
242 281 7.201741 GGATTACCTTGGAAAGCACTAATTCTC 60.202 40.741 0.00 0.00 44.44 2.87
243 282 6.603599 GGATTACCTTGGAAAGCACTAATTCT 59.396 38.462 0.00 0.00 44.44 2.40
244 283 6.603599 AGGATTACCTTGGAAAGCACTAATTC 59.396 38.462 0.00 0.00 45.36 2.17
245 284 6.378280 CAGGATTACCTTGGAAAGCACTAATT 59.622 38.462 0.00 0.00 45.36 1.40
246 285 5.888161 CAGGATTACCTTGGAAAGCACTAAT 59.112 40.000 0.00 0.00 45.36 1.73
247 286 5.222048 ACAGGATTACCTTGGAAAGCACTAA 60.222 40.000 0.00 0.00 45.36 2.24
248 287 4.288626 ACAGGATTACCTTGGAAAGCACTA 59.711 41.667 0.00 0.00 45.36 2.74
249 288 3.074538 ACAGGATTACCTTGGAAAGCACT 59.925 43.478 0.00 0.00 45.36 4.40
250 289 3.191371 CACAGGATTACCTTGGAAAGCAC 59.809 47.826 0.00 0.00 45.36 4.40
268 307 2.228103 ACAGAGCATGCATTCAACACAG 59.772 45.455 21.98 0.00 0.00 3.66
307 346 1.342672 GCCTTCCCACCCGAATCCTA 61.343 60.000 0.00 0.00 0.00 2.94
551 590 8.140628 AGAAAAAGCAATCTCTTCTTTTCTTCC 58.859 33.333 0.00 0.00 38.60 3.46
638 684 3.751175 CGGCAAGATAAGAAAAGGTGTGA 59.249 43.478 0.00 0.00 0.00 3.58
771 819 1.817447 GGCTGCTGCTGATTTTCTCTT 59.183 47.619 15.64 0.00 39.59 2.85
772 820 1.461559 GGCTGCTGCTGATTTTCTCT 58.538 50.000 15.64 0.00 39.59 3.10
891 941 1.541672 GGAGAGAGAGGGAGAGGGG 59.458 68.421 0.00 0.00 0.00 4.79
893 943 1.541672 GGGGAGAGAGAGGGAGAGG 59.458 68.421 0.00 0.00 0.00 3.69
894 944 1.150536 CGGGGAGAGAGAGGGAGAG 59.849 68.421 0.00 0.00 0.00 3.20
895 945 1.619975 ACGGGGAGAGAGAGGGAGA 60.620 63.158 0.00 0.00 0.00 3.71
1151 1213 3.036959 GGGAGGGAGGGAGAGGGA 61.037 72.222 0.00 0.00 0.00 4.20
1162 1224 3.798511 GGGGAAAGCGAGGGAGGG 61.799 72.222 0.00 0.00 0.00 4.30
1163 1225 2.689034 AGGGGAAAGCGAGGGAGG 60.689 66.667 0.00 0.00 0.00 4.30
1164 1226 2.736826 GGAGGGGAAAGCGAGGGAG 61.737 68.421 0.00 0.00 0.00 4.30
1165 1227 2.687566 GGAGGGGAAAGCGAGGGA 60.688 66.667 0.00 0.00 0.00 4.20
1422 1839 0.176680 GCCCTCGCAGATCAAGAAGA 59.823 55.000 0.00 0.00 33.89 2.87
1423 1840 0.813210 GGCCCTCGCAGATCAAGAAG 60.813 60.000 0.00 0.00 36.38 2.85
1424 1841 1.221840 GGCCCTCGCAGATCAAGAA 59.778 57.895 0.00 0.00 36.38 2.52
1425 1842 2.903357 GGCCCTCGCAGATCAAGA 59.097 61.111 0.00 0.00 36.38 3.02
1426 1843 2.587194 CGGCCCTCGCAGATCAAG 60.587 66.667 0.00 0.00 36.38 3.02
1592 2013 3.993920 AGCAATCAATCAACCAACCAAC 58.006 40.909 0.00 0.00 0.00 3.77
1600 2021 4.668576 TCACGAGAAGCAATCAATCAAC 57.331 40.909 0.00 0.00 0.00 3.18
1694 2123 5.929415 AGTGAAGCTGAGAAAGTAAAGCTAC 59.071 40.000 0.00 0.00 45.04 3.58
1803 2235 7.618117 CCAACTCCCAATATTAAAACCCTAACT 59.382 37.037 0.00 0.00 0.00 2.24
1974 2406 7.527457 CATATACATCAGGCATGATTTCACAG 58.473 38.462 11.92 1.69 43.92 3.66
2010 2442 2.305343 AGAGAAGGCAATGCAGAAGACT 59.695 45.455 7.79 0.00 0.00 3.24
2085 2517 4.216472 TGCGCTAATGTGTCAAACCATTAA 59.784 37.500 9.73 0.00 0.00 1.40
2086 2518 3.753797 TGCGCTAATGTGTCAAACCATTA 59.246 39.130 9.73 0.00 0.00 1.90
2196 2629 5.067153 CGGCAAAAATACCATCCAGACATAA 59.933 40.000 0.00 0.00 0.00 1.90
2274 2707 4.501400 GGCAAAAATACCATCCAGCCATAC 60.501 45.833 0.00 0.00 40.50 2.39
2370 2803 3.119388 GGCCCTTGTTTTTATACCCGAAC 60.119 47.826 0.00 0.00 0.00 3.95
2386 2819 0.038310 CCGGAAGAGAAAAGGCCCTT 59.962 55.000 0.00 0.00 0.00 3.95
2513 2946 0.449388 GCTTGATCTTCCTGTTGGCG 59.551 55.000 0.00 0.00 0.00 5.69
2528 2961 4.083324 TCTGATGAGTTAAAAAGGCGCTTG 60.083 41.667 7.64 0.00 0.00 4.01
2926 3373 1.403647 CGTGAAGATACACCGCCTGAA 60.404 52.381 0.00 0.00 37.48 3.02
2958 3405 4.437682 TGAGGTGTGGAAGAACTCAATT 57.562 40.909 0.00 0.00 35.45 2.32
3866 4316 2.194212 GCAGATGCATGCTCCCCAG 61.194 63.158 20.33 5.23 43.07 4.45
4072 4522 4.067896 TGACTTGCTCCTGATTCAAAGTC 58.932 43.478 16.19 16.19 0.00 3.01
4334 4784 6.590234 ATGAACCTTGTAATCCTGTTTTCC 57.410 37.500 0.00 0.00 0.00 3.13
4515 4965 3.624410 TCAGATCTGCAAAATGATCGTGG 59.376 43.478 18.36 3.53 42.62 4.94
4535 4985 2.950781 AGTCAGTCTGAGTGGACTTCA 58.049 47.619 9.49 0.00 43.14 3.02
4536 4986 4.521256 ACTAAGTCAGTCTGAGTGGACTTC 59.479 45.833 22.19 8.13 44.81 3.01
5094 5544 1.634757 TATGCAGTTTCGCAGGCACG 61.635 55.000 0.00 0.00 46.99 5.34
5261 5711 5.727791 GCCATGCTTAGAATCAGTAAACACG 60.728 44.000 0.00 0.00 0.00 4.49
5596 6049 5.303333 ACCATATTTCACAGGAAAAACGGTT 59.697 36.000 0.00 0.00 45.52 4.44
5621 6113 2.702898 TGCATCACCAAAACATGTCG 57.297 45.000 0.00 0.00 0.00 4.35
5700 6192 2.389715 AGTATTTCAGGACGGAGGGAG 58.610 52.381 0.00 0.00 0.00 4.30
5701 6193 2.500098 CAAGTATTTCAGGACGGAGGGA 59.500 50.000 0.00 0.00 0.00 4.20
5702 6194 2.236395 ACAAGTATTTCAGGACGGAGGG 59.764 50.000 0.00 0.00 0.00 4.30
5703 6195 3.522553 GACAAGTATTTCAGGACGGAGG 58.477 50.000 0.00 0.00 0.00 4.30
5704 6196 3.195825 AGGACAAGTATTTCAGGACGGAG 59.804 47.826 0.00 0.00 0.00 4.63
5705 6197 3.170717 AGGACAAGTATTTCAGGACGGA 58.829 45.455 0.00 0.00 0.00 4.69
5706 6198 3.611766 AGGACAAGTATTTCAGGACGG 57.388 47.619 0.00 0.00 0.00 4.79
5707 6199 4.566004 TCAAGGACAAGTATTTCAGGACG 58.434 43.478 0.00 0.00 0.00 4.79
5708 6200 6.877611 TTTCAAGGACAAGTATTTCAGGAC 57.122 37.500 0.00 0.00 0.00 3.85
5709 6201 6.434028 CCATTTCAAGGACAAGTATTTCAGGA 59.566 38.462 0.00 0.00 0.00 3.86
5710 6202 6.434028 TCCATTTCAAGGACAAGTATTTCAGG 59.566 38.462 0.00 0.00 0.00 3.86
5711 6203 7.452880 TCCATTTCAAGGACAAGTATTTCAG 57.547 36.000 0.00 0.00 0.00 3.02
5712 6204 9.527157 TTATCCATTTCAAGGACAAGTATTTCA 57.473 29.630 0.00 0.00 38.13 2.69
5718 6210 9.753674 TCTATTTTATCCATTTCAAGGACAAGT 57.246 29.630 0.00 0.00 38.13 3.16
5721 6213 9.699410 ACATCTATTTTATCCATTTCAAGGACA 57.301 29.630 0.00 0.00 38.13 4.02
5760 6252 9.751542 CTCGAAATGGTTGTATCTAGACTTATT 57.248 33.333 0.00 0.00 0.00 1.40
5761 6253 8.361139 CCTCGAAATGGTTGTATCTAGACTTAT 58.639 37.037 0.00 0.00 0.00 1.73
5762 6254 7.558807 TCCTCGAAATGGTTGTATCTAGACTTA 59.441 37.037 0.00 0.00 0.00 2.24
5763 6255 6.380274 TCCTCGAAATGGTTGTATCTAGACTT 59.620 38.462 0.00 0.00 0.00 3.01
5764 6256 5.892119 TCCTCGAAATGGTTGTATCTAGACT 59.108 40.000 0.00 0.00 0.00 3.24
5765 6257 5.978322 GTCCTCGAAATGGTTGTATCTAGAC 59.022 44.000 0.00 0.00 0.00 2.59
5766 6258 5.655090 TGTCCTCGAAATGGTTGTATCTAGA 59.345 40.000 0.00 0.00 0.00 2.43
5767 6259 5.902681 TGTCCTCGAAATGGTTGTATCTAG 58.097 41.667 0.00 0.00 0.00 2.43
5768 6260 5.925506 TGTCCTCGAAATGGTTGTATCTA 57.074 39.130 0.00 0.00 0.00 1.98
5769 6261 4.819105 TGTCCTCGAAATGGTTGTATCT 57.181 40.909 0.00 0.00 0.00 1.98
5770 6262 4.935808 ACTTGTCCTCGAAATGGTTGTATC 59.064 41.667 0.00 0.00 0.00 2.24
5771 6263 4.906618 ACTTGTCCTCGAAATGGTTGTAT 58.093 39.130 0.00 0.00 0.00 2.29
5772 6264 4.345859 ACTTGTCCTCGAAATGGTTGTA 57.654 40.909 0.00 0.00 0.00 2.41
5773 6265 3.208747 ACTTGTCCTCGAAATGGTTGT 57.791 42.857 0.00 0.00 0.00 3.32
5774 6266 5.880054 AATACTTGTCCTCGAAATGGTTG 57.120 39.130 0.00 0.00 0.00 3.77
5775 6267 5.414765 GGAAATACTTGTCCTCGAAATGGTT 59.585 40.000 0.00 0.00 0.00 3.67
5776 6268 4.941873 GGAAATACTTGTCCTCGAAATGGT 59.058 41.667 0.00 0.00 0.00 3.55
5777 6269 4.034048 CGGAAATACTTGTCCTCGAAATGG 59.966 45.833 0.00 0.00 0.00 3.16
5778 6270 4.034048 CCGGAAATACTTGTCCTCGAAATG 59.966 45.833 0.00 0.00 0.00 2.32
5779 6271 4.081309 TCCGGAAATACTTGTCCTCGAAAT 60.081 41.667 0.00 0.00 0.00 2.17
5780 6272 3.258872 TCCGGAAATACTTGTCCTCGAAA 59.741 43.478 0.00 0.00 0.00 3.46
5781 6273 2.827322 TCCGGAAATACTTGTCCTCGAA 59.173 45.455 0.00 0.00 0.00 3.71
5782 6274 2.165030 GTCCGGAAATACTTGTCCTCGA 59.835 50.000 5.23 0.00 0.00 4.04
5783 6275 2.537401 GTCCGGAAATACTTGTCCTCG 58.463 52.381 5.23 0.00 0.00 4.63
5784 6276 2.537401 CGTCCGGAAATACTTGTCCTC 58.463 52.381 5.23 0.00 0.00 3.71
5785 6277 1.206371 CCGTCCGGAAATACTTGTCCT 59.794 52.381 5.23 0.00 37.50 3.85
5786 6278 1.205417 TCCGTCCGGAAATACTTGTCC 59.795 52.381 5.23 0.00 42.05 4.02
5787 6279 2.537401 CTCCGTCCGGAAATACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
5788 6280 1.206371 CCTCCGTCCGGAAATACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
5789 6281 1.472728 CCCTCCGTCCGGAAATACTTG 60.473 57.143 5.23 0.00 44.66 3.16
5790 6282 0.828677 CCCTCCGTCCGGAAATACTT 59.171 55.000 5.23 0.00 44.66 2.24
5791 6283 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
5792 6284 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
5793 6285 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
5794 6286 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
5795 6287 0.682209 CTACTCCCTCCGTCCGGAAA 60.682 60.000 5.23 0.00 44.66 3.13
5796 6288 1.077212 CTACTCCCTCCGTCCGGAA 60.077 63.158 5.23 0.00 44.66 4.30
5797 6289 2.593978 CTACTCCCTCCGTCCGGA 59.406 66.667 0.00 0.00 42.90 5.14
5798 6290 3.217743 GCTACTCCCTCCGTCCGG 61.218 72.222 0.00 0.00 0.00 5.14
5799 6291 0.465097 TAAGCTACTCCCTCCGTCCG 60.465 60.000 0.00 0.00 0.00 4.79
5800 6292 1.133853 TCTAAGCTACTCCCTCCGTCC 60.134 57.143 0.00 0.00 0.00 4.79
5801 6293 2.158784 TCTCTAAGCTACTCCCTCCGTC 60.159 54.545 0.00 0.00 0.00 4.79
5802 6294 1.845143 TCTCTAAGCTACTCCCTCCGT 59.155 52.381 0.00 0.00 0.00 4.69
5803 6295 2.223745 GTCTCTAAGCTACTCCCTCCG 58.776 57.143 0.00 0.00 0.00 4.63
5804 6296 3.300239 TGTCTCTAAGCTACTCCCTCC 57.700 52.381 0.00 0.00 0.00 4.30
5805 6297 4.465886 TCATGTCTCTAAGCTACTCCCTC 58.534 47.826 0.00 0.00 0.00 4.30
5806 6298 4.528076 TCATGTCTCTAAGCTACTCCCT 57.472 45.455 0.00 0.00 0.00 4.20
5807 6299 5.799827 AATCATGTCTCTAAGCTACTCCC 57.200 43.478 0.00 0.00 0.00 4.30
5810 6302 9.594936 ACCTATAAATCATGTCTCTAAGCTACT 57.405 33.333 0.00 0.00 0.00 2.57
5813 6305 7.659390 GCAACCTATAAATCATGTCTCTAAGCT 59.341 37.037 0.00 0.00 0.00 3.74
6090 6586 1.527696 CAGATCACGCAATTTCGCAC 58.472 50.000 0.00 0.00 0.00 5.34
6093 6589 2.369600 GATGCAGATCACGCAATTTCG 58.630 47.619 13.09 0.00 43.84 3.46
6151 6647 0.250901 TTCAGAAAGCACTGGGGAGC 60.251 55.000 0.00 0.00 38.31 4.70
6206 6702 7.888546 ACAGTACCTAGAAATAAAAACTGCCAT 59.111 33.333 0.00 0.00 37.25 4.40
6364 6860 3.222855 CCAACAGCCGGGCAAACA 61.223 61.111 23.09 0.00 0.00 2.83
6532 7031 5.235616 CGAACCAAGCACTAGAAACAAACTA 59.764 40.000 0.00 0.00 0.00 2.24
6592 7091 3.057969 TGGACCTTGCATGTTAGACTG 57.942 47.619 0.00 0.00 0.00 3.51
6820 7343 2.615912 GTTAGCATAGCAGGCAAAGGAG 59.384 50.000 0.00 0.00 0.00 3.69
6830 7353 2.959599 CGGCGCGTTAGCATAGCA 60.960 61.111 8.43 0.00 45.49 3.49
6831 7354 4.355663 GCGGCGCGTTAGCATAGC 62.356 66.667 19.09 0.00 45.49 2.97
6832 7355 2.416372 CTTGCGGCGCGTTAGCATAG 62.416 60.000 28.09 17.26 45.49 2.23
6833 7356 2.509561 TTGCGGCGCGTTAGCATA 60.510 55.556 28.09 3.34 45.49 3.14
6834 7357 3.864686 CTTGCGGCGCGTTAGCAT 61.865 61.111 28.09 0.00 45.49 3.79
7060 7589 4.525912 ATGTTGCCAAACTCTTTGATCC 57.474 40.909 0.00 0.00 43.26 3.36
7065 7594 4.754322 ACGAAAATGTTGCCAAACTCTTT 58.246 34.783 0.00 0.00 37.19 2.52
7154 7683 7.756395 TCTCATCTTGCTCTCATTTTTCTTT 57.244 32.000 0.00 0.00 0.00 2.52
7155 7684 7.941431 ATCTCATCTTGCTCTCATTTTTCTT 57.059 32.000 0.00 0.00 0.00 2.52
7191 7720 5.062558 GCATTTCATCGACATTGGAAAAAGG 59.937 40.000 0.00 0.00 33.47 3.11
7204 7733 3.520290 ACTAGTTCCGCATTTCATCGA 57.480 42.857 0.00 0.00 0.00 3.59
7329 7870 4.985538 AGAGGCAAACATAAGAGGTTTCA 58.014 39.130 0.00 0.00 36.38 2.69
7412 7979 2.408704 CGTTCGGCAACAACAACAAAAA 59.591 40.909 0.00 0.00 32.14 1.94
7417 7984 0.179184 ACACGTTCGGCAACAACAAC 60.179 50.000 0.00 0.00 32.14 3.32
7438 8006 4.277476 TGTGAGGTGTGGTTCTTCAAAAT 58.723 39.130 0.00 0.00 0.00 1.82
7522 8092 2.299013 AGCTTCAGGACGTGTATGTCAA 59.701 45.455 0.00 0.00 40.72 3.18
7552 8122 1.384742 GTCGACGCTACCGAAAAGAAC 59.615 52.381 0.00 0.00 37.81 3.01
7574 8144 8.223177 TCGGACCTTATTTGAACTGTTTTAAA 57.777 30.769 0.00 0.72 0.00 1.52
7576 8146 7.804843 TTCGGACCTTATTTGAACTGTTTTA 57.195 32.000 0.00 0.00 0.00 1.52
7586 8156 3.940303 CGATGCTTTCGGACCTTATTTG 58.060 45.455 2.21 0.00 44.28 2.32
7636 8206 0.178915 TGGGGTTCTCTTCCGAGGAA 60.179 55.000 4.34 4.34 37.86 3.36
7637 8207 0.903454 GTGGGGTTCTCTTCCGAGGA 60.903 60.000 0.00 0.00 37.86 3.71
7638 8208 0.905337 AGTGGGGTTCTCTTCCGAGG 60.905 60.000 0.00 0.00 37.86 4.63
7639 8209 0.977395 AAGTGGGGTTCTCTTCCGAG 59.023 55.000 0.00 0.00 38.67 4.63
7656 8226 6.204359 CACATTTGAGAGGTCAAGTCAAAAG 58.796 40.000 1.21 0.23 43.66 2.27
7661 8231 3.744660 ACCACATTTGAGAGGTCAAGTC 58.255 45.455 0.00 0.00 43.66 3.01
7662 8232 3.864789 ACCACATTTGAGAGGTCAAGT 57.135 42.857 0.00 0.00 43.66 3.16
7685 8361 6.906143 CGAAGTTGGACGTGTAAATTAAACAA 59.094 34.615 0.00 0.00 0.00 2.83
7687 8363 6.421405 ACGAAGTTGGACGTGTAAATTAAAC 58.579 36.000 0.00 0.00 37.78 2.01
7747 8423 9.040939 TGTATGTGCATATGTACAAATGTCTAC 57.959 33.333 27.05 22.06 43.49 2.59
7756 8432 7.452562 AGGATGAATGTATGTGCATATGTACA 58.547 34.615 25.82 25.82 44.32 2.90
7757 8433 7.912056 AGGATGAATGTATGTGCATATGTAC 57.088 36.000 16.19 16.19 0.00 2.90
7761 8437 7.108194 CACCTAGGATGAATGTATGTGCATAT 58.892 38.462 17.98 0.31 0.00 1.78
7764 8440 4.164030 ACACCTAGGATGAATGTATGTGCA 59.836 41.667 17.98 0.00 0.00 4.57
7765 8441 4.512944 CACACCTAGGATGAATGTATGTGC 59.487 45.833 17.98 0.00 0.00 4.57
7766 8442 5.674525 ACACACCTAGGATGAATGTATGTG 58.325 41.667 17.98 17.54 40.52 3.21
7775 8451 1.475280 GCACGTACACACCTAGGATGA 59.525 52.381 17.98 1.34 0.00 2.92
7779 8455 3.117589 GTGCACGTACACACCTAGG 57.882 57.895 14.08 7.41 40.40 3.02
7798 8527 1.630244 CTGCCGGAAAGCTCAAGACG 61.630 60.000 5.05 0.00 0.00 4.18
7816 8545 5.014123 TGGTTCATCATTACTTCCTTCCACT 59.986 40.000 0.00 0.00 0.00 4.00
7824 8553 3.620488 TGGCCTGGTTCATCATTACTTC 58.380 45.455 3.32 0.00 0.00 3.01
7827 8556 2.301346 CCTGGCCTGGTTCATCATTAC 58.699 52.381 20.28 0.00 0.00 1.89
7855 8584 3.792047 CATGAGGGTGCACGTGCG 61.792 66.667 33.22 14.27 45.83 5.34
7865 8594 0.035056 AAGCTTCGGGAACATGAGGG 60.035 55.000 0.00 0.00 0.00 4.30
7878 8607 7.948278 TTACTTGAACTCACTAGAAAGCTTC 57.052 36.000 0.00 0.00 0.00 3.86
8007 8751 7.382218 CCTATTTCATCATTAATTGTTTCCGCC 59.618 37.037 0.00 0.00 0.00 6.13
8009 8753 9.450807 GACCTATTTCATCATTAATTGTTTCCG 57.549 33.333 0.00 0.00 0.00 4.30
8029 8774 1.333177 GCGGATCTGACCTGACCTAT 58.667 55.000 5.48 0.00 0.00 2.57
8030 8775 0.033503 TGCGGATCTGACCTGACCTA 60.034 55.000 5.48 0.00 0.00 3.08
8061 8806 0.179059 GCTAGGAAGCTCAGGGAAGC 60.179 60.000 0.00 0.00 45.85 3.86
8092 8837 6.309737 CGTACCTGACCTAGTTCAACATTAAC 59.690 42.308 0.00 0.00 0.00 2.01
8139 9595 2.417515 CCTAAACTCACGAGGAAGCTCC 60.418 54.545 0.00 0.00 36.58 4.70
8186 9642 2.079158 GATAGTGCAGTGCATGTGTGT 58.921 47.619 22.87 4.92 41.91 3.72
8188 9644 2.775911 AGATAGTGCAGTGCATGTGT 57.224 45.000 22.87 10.23 41.91 3.72
8192 9648 1.133976 GGGGAAGATAGTGCAGTGCAT 60.134 52.381 22.87 12.70 41.91 3.96
8198 9654 0.687757 AGCTCGGGGAAGATAGTGCA 60.688 55.000 0.00 0.00 0.00 4.57


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

AutoCloner maintained by Alex Coulton.