Multiple sequence alignment - TraesCS3A01G467200

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS3A01G467200 chr3A 100.000 3158 0 0 1 3158 700702884 700699727 0.000000e+00 5832
1 TraesCS3A01G467200 chr3A 81.203 399 57 7 26 408 725469877 725469481 3.960000e-79 305
2 TraesCS3A01G467200 chr3A 90.541 222 17 1 1185 1402 702022201 702021980 1.110000e-74 291
3 TraesCS3A01G467200 chr3D 89.056 2266 170 39 908 3155 567082390 567084595 0.000000e+00 2739
4 TraesCS3A01G467200 chr3D 94.540 641 35 0 908 1548 568850573 568851213 0.000000e+00 990
5 TraesCS3A01G467200 chr3D 92.235 528 28 3 2613 3139 567087268 567087783 0.000000e+00 736
6 TraesCS3A01G467200 chr3D 84.321 759 68 24 26 743 567081577 567082325 0.000000e+00 695
7 TraesCS3A01G467200 chr3D 86.789 492 56 6 918 1402 567081079 567081568 9.970000e-150 540
8 TraesCS3A01G467200 chr3D 82.844 647 61 22 129 743 568849875 568850503 4.640000e-148 534
9 TraesCS3A01G467200 chr1D 85.488 1199 134 18 913 2105 42272231 42273395 0.000000e+00 1214
10 TraesCS3A01G467200 chr1D 84.797 1184 140 18 927 2105 42022274 42023422 0.000000e+00 1153
11 TraesCS3A01G467200 chr1D 76.483 472 63 19 31 477 472001918 472001470 2.470000e-51 213
12 TraesCS3A01G467200 chr1B 85.828 1009 113 4 1097 2105 62445551 62446529 0.000000e+00 1044
13 TraesCS3A01G467200 chr1B 79.618 471 66 17 26 468 47628057 47628525 8.510000e-81 311
14 TraesCS3A01G467200 chr1B 84.375 160 16 4 927 1081 62432409 62432564 7.060000e-32 148
15 TraesCS3A01G467200 chr1A 82.933 750 88 20 927 1672 42193560 42194273 9.550000e-180 640
16 TraesCS3A01G467200 chr4D 81.667 480 56 19 26 477 99207137 99207612 1.380000e-98 370
17 TraesCS3A01G467200 chr6D 80.417 480 64 15 26 477 121158866 121158389 3.900000e-89 339
18 TraesCS3A01G467200 chr7A 82.206 399 54 3 26 408 670686145 670686542 8.450000e-86 327
19 TraesCS3A01G467200 chr7A 80.519 385 57 10 26 394 149029336 149028954 2.400000e-71 279
20 TraesCS3A01G467200 chrUn 81.955 399 55 3 26 408 434813919 434814316 3.930000e-84 322
21 TraesCS3A01G467200 chr2D 80.660 424 66 11 49 460 100958042 100958461 6.580000e-82 315
22 TraesCS3A01G467200 chr2D 76.271 472 61 22 31 477 398777949 398778394 1.480000e-48 204
23 TraesCS3A01G467200 chr2B 76.687 489 65 22 31 495 711001769 711001306 3.170000e-55 226
24 TraesCS3A01G467200 chr5B 78.886 341 40 17 165 477 566132142 566131806 5.340000e-48 202
25 TraesCS3A01G467200 chr5B 77.485 342 43 19 165 477 41092993 41092657 1.160000e-39 174
26 TraesCS3A01G467200 chr5A 75.983 458 56 27 49 477 17593923 17593491 1.500000e-43 187
27 TraesCS3A01G467200 chr4B 75.844 385 66 12 26 408 657179967 657179608 1.510000e-38 171
28 TraesCS3A01G467200 chr4A 78.397 287 45 12 2324 2606 1710465 1710192 1.510000e-38 171
29 TraesCS3A01G467200 chr7D 83.784 185 21 5 302 477 45121843 45122027 1.950000e-37 167


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 TraesCS3A01G467200 chr3A 700699727 700702884 3157 True 5832.0 5832 100.00000 1 3158 1 chr3A.!!$R1 3157
1 TraesCS3A01G467200 chr3D 567081079 567087783 6704 False 1177.5 2739 88.10025 26 3155 4 chr3D.!!$F1 3129
2 TraesCS3A01G467200 chr3D 568849875 568851213 1338 False 762.0 990 88.69200 129 1548 2 chr3D.!!$F2 1419
3 TraesCS3A01G467200 chr1D 42272231 42273395 1164 False 1214.0 1214 85.48800 913 2105 1 chr1D.!!$F2 1192
4 TraesCS3A01G467200 chr1D 42022274 42023422 1148 False 1153.0 1153 84.79700 927 2105 1 chr1D.!!$F1 1178
5 TraesCS3A01G467200 chr1B 62445551 62446529 978 False 1044.0 1044 85.82800 1097 2105 1 chr1B.!!$F3 1008
6 TraesCS3A01G467200 chr1A 42193560 42194273 713 False 640.0 640 82.93300 927 1672 1 chr1A.!!$F1 745

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
886 1414 0.107312 CAGAGGCAGAGTCATTGGGG 60.107 60.0 0.0 0.0 0.0 4.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2784 6547 0.107945 AGAAGACGAGGAGGCAATGC 60.108 55.0 0.0 0.0 0.0 3.56 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
23 24 5.613329 ACGAATACACAAGGTTTAAGTCCA 58.387 37.500 0.00 0.00 0.00 4.02
24 25 5.467735 ACGAATACACAAGGTTTAAGTCCAC 59.532 40.000 0.00 0.00 0.00 4.02
26 27 6.347402 CGAATACACAAGGTTTAAGTCCACAG 60.347 42.308 2.45 0.00 0.00 3.66
28 29 4.196971 ACACAAGGTTTAAGTCCACAGAC 58.803 43.478 2.45 0.00 43.89 3.51
29 30 4.196193 CACAAGGTTTAAGTCCACAGACA 58.804 43.478 0.00 0.00 46.15 3.41
35 509 4.365723 GTTTAAGTCCACAGACAAGACGA 58.634 43.478 0.00 0.00 46.15 4.20
36 510 4.866508 TTAAGTCCACAGACAAGACGAT 57.133 40.909 0.00 0.00 46.15 3.73
91 565 3.087253 TAGCCCCCATCACGGTGG 61.087 66.667 8.50 0.00 39.05 4.61
95 569 4.343323 CCCCATCACGGTGGTGCA 62.343 66.667 15.90 0.00 44.03 4.57
114 588 2.483714 GCATCTAGCATCGTTGAAGGGA 60.484 50.000 0.00 0.00 44.79 4.20
115 589 3.388308 CATCTAGCATCGTTGAAGGGAG 58.612 50.000 0.00 0.00 0.00 4.30
118 592 0.687354 AGCATCGTTGAAGGGAGTGT 59.313 50.000 0.00 0.00 0.00 3.55
126 600 1.003233 GAAGGGAGTGTGGAGGTGC 60.003 63.158 0.00 0.00 0.00 5.01
156 630 2.298158 AATCTCGCGGCATTCGGTCT 62.298 55.000 6.13 0.00 39.69 3.85
157 631 1.452953 ATCTCGCGGCATTCGGTCTA 61.453 55.000 6.13 0.00 39.69 2.59
160 634 1.299850 CGCGGCATTCGGTCTATGA 60.300 57.895 0.00 0.00 39.69 2.15
201 675 5.556915 ACTCGGATCCAATCTTTGTTTGTA 58.443 37.500 13.41 0.00 0.00 2.41
207 681 7.062138 CGGATCCAATCTTTGTTTGTATTTGTG 59.938 37.037 13.41 0.00 0.00 3.33
225 699 2.365941 TGTGTCATGTGTCTTCGGGTTA 59.634 45.455 0.00 0.00 0.00 2.85
238 712 3.513909 TCGGGTTAGATCCTTCCGATA 57.486 47.619 11.40 0.00 43.84 2.92
243 717 6.666546 TCGGGTTAGATCCTTCCGATATAAAT 59.333 38.462 11.40 0.00 43.84 1.40
258 732 6.454318 CCGATATAAATTTCTCTTCATCGGCG 60.454 42.308 0.00 0.00 44.79 6.46
277 751 1.429423 GCGGTTGCTATTCTGGTGC 59.571 57.895 0.00 0.00 38.39 5.01
280 754 0.727398 GGTTGCTATTCTGGTGCGTC 59.273 55.000 0.00 0.00 0.00 5.19
294 768 2.838225 CGTCGGTCCTATGGGGCT 60.838 66.667 0.00 0.00 37.39 5.19
299 773 1.129058 CGGTCCTATGGGGCTTTAGT 58.871 55.000 0.00 0.00 37.39 2.24
305 795 4.039366 GTCCTATGGGGCTTTAGTAGTCTG 59.961 50.000 0.00 0.00 33.70 3.51
394 884 3.057019 CAGTGCTTGTAGTCGTTGCTAA 58.943 45.455 0.00 0.00 0.00 3.09
401 891 4.260139 TGTAGTCGTTGCTAAATGGTCA 57.740 40.909 0.00 0.00 0.00 4.02
442 949 0.604073 TGATTGTTGCACTGCCATGG 59.396 50.000 7.63 7.63 0.00 3.66
445 952 1.697284 TTGTTGCACTGCCATGGTTA 58.303 45.000 14.67 1.86 0.00 2.85
460 967 7.289310 TGCCATGGTTAAAGATGAATAGATCA 58.711 34.615 14.67 0.00 43.67 2.92
461 968 7.446319 TGCCATGGTTAAAGATGAATAGATCAG 59.554 37.037 14.67 0.00 42.53 2.90
567 1081 1.361668 CCATGAGGAAAGTGTCGCCG 61.362 60.000 0.00 0.00 36.89 6.46
658 1180 5.292101 GCACAGAAAACTCTATTCGCATACT 59.708 40.000 0.00 0.00 32.04 2.12
727 1250 8.265165 AGAGTCCAATTTAGATTCGGTAAAAC 57.735 34.615 0.00 0.00 0.00 2.43
737 1260 8.795842 TTAGATTCGGTAAAACAATACATGGT 57.204 30.769 0.00 0.00 0.00 3.55
738 1261 7.316544 AGATTCGGTAAAACAATACATGGTC 57.683 36.000 0.00 0.00 0.00 4.02
739 1262 5.533533 TTCGGTAAAACAATACATGGTCG 57.466 39.130 0.00 0.00 0.00 4.79
740 1263 4.818642 TCGGTAAAACAATACATGGTCGA 58.181 39.130 0.00 0.00 0.00 4.20
741 1264 4.626604 TCGGTAAAACAATACATGGTCGAC 59.373 41.667 7.13 7.13 0.00 4.20
742 1265 4.628333 CGGTAAAACAATACATGGTCGACT 59.372 41.667 16.46 0.00 0.00 4.18
743 1266 5.220340 CGGTAAAACAATACATGGTCGACTC 60.220 44.000 16.46 6.30 0.00 3.36
744 1267 4.921470 AAAACAATACATGGTCGACTCG 57.079 40.909 16.46 6.69 0.00 4.18
745 1268 2.579207 ACAATACATGGTCGACTCGG 57.421 50.000 16.46 7.39 0.00 4.63
746 1269 2.097036 ACAATACATGGTCGACTCGGA 58.903 47.619 16.46 0.86 0.00 4.55
747 1270 2.159282 ACAATACATGGTCGACTCGGAC 60.159 50.000 16.46 0.00 36.18 4.79
748 1271 2.054232 ATACATGGTCGACTCGGACT 57.946 50.000 16.46 0.00 37.12 3.85
749 1272 1.376543 TACATGGTCGACTCGGACTC 58.623 55.000 16.46 0.00 37.12 3.36
750 1273 0.322636 ACATGGTCGACTCGGACTCT 60.323 55.000 16.46 0.00 37.12 3.24
751 1274 1.065636 ACATGGTCGACTCGGACTCTA 60.066 52.381 16.46 0.00 37.12 2.43
767 1290 5.448089 CGGACTCTAGTCAACTTAGCTTCTC 60.448 48.000 11.98 0.00 46.47 2.87
790 1316 9.445878 TCTCCTATAAAGTCATATTCGTATCGT 57.554 33.333 0.00 0.00 0.00 3.73
793 1319 9.836076 CCTATAAAGTCATATTCGTATCGTTCA 57.164 33.333 0.00 0.00 0.00 3.18
827 1353 1.311859 TATTCGTATCTGCCGTCCGT 58.688 50.000 0.00 0.00 0.00 4.69
830 1356 0.179076 TCGTATCTGCCGTCCGTAGA 60.179 55.000 0.00 0.00 0.00 2.59
831 1357 0.873054 CGTATCTGCCGTCCGTAGAT 59.127 55.000 8.20 8.20 35.49 1.98
832 1358 1.136029 CGTATCTGCCGTCCGTAGATC 60.136 57.143 6.88 0.00 33.51 2.75
834 1360 1.399714 ATCTGCCGTCCGTAGATCAA 58.600 50.000 0.00 0.00 0.00 2.57
835 1361 1.399714 TCTGCCGTCCGTAGATCAAT 58.600 50.000 0.00 0.00 0.00 2.57
836 1362 1.754803 TCTGCCGTCCGTAGATCAATT 59.245 47.619 0.00 0.00 0.00 2.32
837 1363 2.953648 TCTGCCGTCCGTAGATCAATTA 59.046 45.455 0.00 0.00 0.00 1.40
838 1364 3.572682 TCTGCCGTCCGTAGATCAATTAT 59.427 43.478 0.00 0.00 0.00 1.28
839 1365 4.038763 TCTGCCGTCCGTAGATCAATTATT 59.961 41.667 0.00 0.00 0.00 1.40
840 1366 5.242171 TCTGCCGTCCGTAGATCAATTATTA 59.758 40.000 0.00 0.00 0.00 0.98
841 1367 5.845103 TGCCGTCCGTAGATCAATTATTAA 58.155 37.500 0.00 0.00 0.00 1.40
842 1368 5.693104 TGCCGTCCGTAGATCAATTATTAAC 59.307 40.000 0.00 0.00 0.00 2.01
843 1369 5.119743 GCCGTCCGTAGATCAATTATTAACC 59.880 44.000 0.00 0.00 0.00 2.85
844 1370 6.218019 CCGTCCGTAGATCAATTATTAACCA 58.782 40.000 0.00 0.00 0.00 3.67
845 1371 6.145048 CCGTCCGTAGATCAATTATTAACCAC 59.855 42.308 0.00 0.00 0.00 4.16
846 1372 6.129273 CGTCCGTAGATCAATTATTAACCACG 60.129 42.308 0.00 0.00 0.00 4.94
847 1373 6.145048 GTCCGTAGATCAATTATTAACCACGG 59.855 42.308 0.00 0.00 44.87 4.94
848 1374 6.218019 CCGTAGATCAATTATTAACCACGGA 58.782 40.000 0.00 0.00 46.03 4.69
849 1375 6.365247 CCGTAGATCAATTATTAACCACGGAG 59.635 42.308 0.00 0.00 46.03 4.63
850 1376 6.128902 CGTAGATCAATTATTAACCACGGAGC 60.129 42.308 0.00 0.00 0.00 4.70
851 1377 4.750098 AGATCAATTATTAACCACGGAGCG 59.250 41.667 0.00 0.00 0.00 5.03
852 1378 4.126208 TCAATTATTAACCACGGAGCGA 57.874 40.909 0.00 0.00 0.00 4.93
853 1379 4.505808 TCAATTATTAACCACGGAGCGAA 58.494 39.130 0.00 0.00 0.00 4.70
854 1380 4.936411 TCAATTATTAACCACGGAGCGAAA 59.064 37.500 0.00 0.00 0.00 3.46
855 1381 5.411977 TCAATTATTAACCACGGAGCGAAAA 59.588 36.000 0.00 0.00 0.00 2.29
856 1382 6.094325 TCAATTATTAACCACGGAGCGAAAAT 59.906 34.615 0.00 0.00 0.00 1.82
867 1395 2.286563 GGAGCGAAAATAAGCTGAGAGC 59.713 50.000 0.00 0.00 44.69 4.09
878 1406 1.606885 GCTGAGAGCAGAGGCAGAGT 61.607 60.000 0.00 0.00 45.17 3.24
879 1407 0.457035 CTGAGAGCAGAGGCAGAGTC 59.543 60.000 0.00 0.00 45.17 3.36
880 1408 0.251519 TGAGAGCAGAGGCAGAGTCA 60.252 55.000 0.00 0.00 44.61 3.41
881 1409 1.113788 GAGAGCAGAGGCAGAGTCAT 58.886 55.000 0.00 0.00 44.61 3.06
882 1410 1.481772 GAGAGCAGAGGCAGAGTCATT 59.518 52.381 0.00 0.00 44.61 2.57
883 1411 1.207570 AGAGCAGAGGCAGAGTCATTG 59.792 52.381 0.00 0.00 44.61 2.82
884 1412 0.252479 AGCAGAGGCAGAGTCATTGG 59.748 55.000 0.00 0.00 44.61 3.16
885 1413 0.747283 GCAGAGGCAGAGTCATTGGG 60.747 60.000 0.00 0.00 40.72 4.12
886 1414 0.107312 CAGAGGCAGAGTCATTGGGG 60.107 60.000 0.00 0.00 0.00 4.96
887 1415 0.252881 AGAGGCAGAGTCATTGGGGA 60.253 55.000 0.00 0.00 0.00 4.81
888 1416 0.842635 GAGGCAGAGTCATTGGGGAT 59.157 55.000 0.00 0.00 0.00 3.85
889 1417 1.213926 GAGGCAGAGTCATTGGGGATT 59.786 52.381 0.00 0.00 0.00 3.01
890 1418 1.642762 AGGCAGAGTCATTGGGGATTT 59.357 47.619 0.00 0.00 0.00 2.17
891 1419 2.027385 GGCAGAGTCATTGGGGATTTC 58.973 52.381 0.00 0.00 0.00 2.17
892 1420 2.357569 GGCAGAGTCATTGGGGATTTCT 60.358 50.000 0.00 0.00 0.00 2.52
893 1421 2.948315 GCAGAGTCATTGGGGATTTCTC 59.052 50.000 0.00 0.00 0.00 2.87
894 1422 3.201290 CAGAGTCATTGGGGATTTCTCG 58.799 50.000 0.00 0.00 0.00 4.04
895 1423 2.171448 AGAGTCATTGGGGATTTCTCGG 59.829 50.000 0.00 0.00 0.00 4.63
896 1424 1.025041 GTCATTGGGGATTTCTCGGC 58.975 55.000 0.00 0.00 0.00 5.54
897 1425 0.623194 TCATTGGGGATTTCTCGGCA 59.377 50.000 0.00 0.00 0.00 5.69
898 1426 1.005332 TCATTGGGGATTTCTCGGCAA 59.995 47.619 0.00 0.00 0.00 4.52
899 1427 1.824230 CATTGGGGATTTCTCGGCAAA 59.176 47.619 0.00 0.00 0.00 3.68
900 1428 2.002505 TTGGGGATTTCTCGGCAAAA 57.997 45.000 0.00 0.00 0.00 2.44
901 1429 2.002505 TGGGGATTTCTCGGCAAAAA 57.997 45.000 0.00 0.00 0.00 1.94
1115 1644 1.202463 CGGAGGCGATGATCAAGAAGT 60.202 52.381 0.00 0.00 0.00 3.01
1315 1846 1.131303 CATACCCCTCCCGCCCATAA 61.131 60.000 0.00 0.00 0.00 1.90
1362 1893 2.125912 ACCTGCCTCCTGACCCAT 59.874 61.111 0.00 0.00 0.00 4.00
1370 1901 0.757188 CTCCTGACCCATAGCTCCGT 60.757 60.000 0.00 0.00 0.00 4.69
1419 1950 3.058160 GACGTCGAGGACCCCGAA 61.058 66.667 12.85 0.00 37.81 4.30
1482 2013 1.086696 GGCAGCACACATACGATGTT 58.913 50.000 0.00 0.00 42.70 2.71
1645 2182 3.772387 TCAAACCAATACAAGATGGGCA 58.228 40.909 0.00 0.00 41.17 5.36
1653 2190 1.742761 ACAAGATGGGCATCGTTCAG 58.257 50.000 0.00 0.00 42.48 3.02
1673 2210 4.452733 CGACTTCGGCACCCCTCC 62.453 72.222 0.00 0.00 35.37 4.30
1674 2211 3.003763 GACTTCGGCACCCCTCCT 61.004 66.667 0.00 0.00 0.00 3.69
1675 2212 2.529389 ACTTCGGCACCCCTCCTT 60.529 61.111 0.00 0.00 0.00 3.36
1677 2214 2.203938 TTCGGCACCCCTCCTTCT 60.204 61.111 0.00 0.00 0.00 2.85
1686 2223 1.614824 CCCTCCTTCTCCCACTGCT 60.615 63.158 0.00 0.00 0.00 4.24
1755 2292 3.695606 ATGTGCTCCGGCGTGTCT 61.696 61.111 6.01 0.00 42.25 3.41
1812 2349 1.335506 TGCGTTTGCTTTCGGGAATTC 60.336 47.619 0.00 0.00 43.34 2.17
1944 2481 1.664873 CAATGCGGTTTCTTGCCCA 59.335 52.632 0.00 0.00 0.00 5.36
1948 2485 3.737172 CGGTTTCTTGCCCAGCGG 61.737 66.667 0.00 0.00 0.00 5.52
2029 2566 1.683917 GGGATCTGTGCATCTACGACT 59.316 52.381 0.00 0.00 0.00 4.18
2033 2570 1.204704 TCTGTGCATCTACGACTTGGG 59.795 52.381 0.00 0.00 0.00 4.12
2041 2578 1.345415 TCTACGACTTGGGGGAACAAC 59.655 52.381 0.00 0.00 0.00 3.32
2114 2665 2.196595 ACCTTATTGGAGCCTAGTGCA 58.803 47.619 6.07 0.00 40.29 4.57
2115 2666 2.780010 ACCTTATTGGAGCCTAGTGCAT 59.220 45.455 0.00 0.00 40.29 3.96
2116 2667 3.144506 CCTTATTGGAGCCTAGTGCATG 58.855 50.000 0.00 0.00 44.83 4.06
2117 2668 3.181451 CCTTATTGGAGCCTAGTGCATGA 60.181 47.826 0.00 0.00 44.83 3.07
2118 2669 4.506271 CCTTATTGGAGCCTAGTGCATGAT 60.506 45.833 0.00 0.00 44.83 2.45
2142 2693 4.179579 GCACGCGGCCTCAAATCC 62.180 66.667 12.47 0.00 36.11 3.01
2150 2701 1.967319 GGCCTCAAATCCGATGCTTA 58.033 50.000 0.00 0.00 0.00 3.09
2158 2710 6.708054 CCTCAAATCCGATGCTTATTTCTAGT 59.292 38.462 0.00 0.00 0.00 2.57
2196 2748 3.200294 TGCTTGTAATTGTCGCACATG 57.800 42.857 0.00 0.00 0.00 3.21
2238 2793 7.838884 AGTTGCTACTAGTAGGGAAGTTAAAG 58.161 38.462 27.24 4.49 33.87 1.85
2264 2819 3.933861 ATGGTAGCCTTTGTTCTAGGG 57.066 47.619 0.00 0.00 33.19 3.53
2265 2820 1.280998 TGGTAGCCTTTGTTCTAGGGC 59.719 52.381 0.00 0.00 44.38 5.19
2266 2821 1.280998 GGTAGCCTTTGTTCTAGGGCA 59.719 52.381 7.98 0.00 46.23 5.36
2267 2822 2.357075 GTAGCCTTTGTTCTAGGGCAC 58.643 52.381 7.98 0.00 46.23 5.01
2269 2824 1.425448 AGCCTTTGTTCTAGGGCACTT 59.575 47.619 0.00 0.00 46.23 3.16
2270 2825 1.541588 GCCTTTGTTCTAGGGCACTTG 59.458 52.381 0.00 0.00 43.59 3.16
2271 2826 1.541588 CCTTTGTTCTAGGGCACTTGC 59.458 52.381 0.00 0.00 41.14 4.01
2272 2827 1.197721 CTTTGTTCTAGGGCACTTGCG 59.802 52.381 0.00 0.00 43.26 4.85
2287 2842 3.263941 GCGATTTGTTCCGCCAGT 58.736 55.556 0.00 0.00 45.06 4.00
2288 2843 1.579429 GCGATTTGTTCCGCCAGTT 59.421 52.632 0.00 0.00 45.06 3.16
2367 2924 5.128663 GCCTATTTTAGGGCAAGATTTTGGA 59.871 40.000 2.90 0.00 46.32 3.53
2470 3027 2.294791 CACCCAAAACAGCGAAACCATA 59.705 45.455 0.00 0.00 0.00 2.74
2471 3028 3.056891 CACCCAAAACAGCGAAACCATAT 60.057 43.478 0.00 0.00 0.00 1.78
2472 3029 4.156922 CACCCAAAACAGCGAAACCATATA 59.843 41.667 0.00 0.00 0.00 0.86
2476 3033 6.475402 CCCAAAACAGCGAAACCATATATTTC 59.525 38.462 0.00 2.77 33.52 2.17
2478 3035 7.432252 CCAAAACAGCGAAACCATATATTTCTC 59.568 37.037 9.00 3.10 34.50 2.87
2480 3037 7.484035 AACAGCGAAACCATATATTTCTCTC 57.516 36.000 9.00 1.43 30.59 3.20
2485 3042 9.125026 AGCGAAACCATATATTTCTCTCAAAAT 57.875 29.630 9.00 0.00 34.50 1.82
2509 3066 6.699366 TGGAACATTATAACTACGTCAACCA 58.301 36.000 0.00 0.00 0.00 3.67
2510 3067 7.332557 TGGAACATTATAACTACGTCAACCAT 58.667 34.615 0.00 0.00 0.00 3.55
2511 3068 8.476447 TGGAACATTATAACTACGTCAACCATA 58.524 33.333 0.00 0.00 0.00 2.74
2512 3069 9.485206 GGAACATTATAACTACGTCAACCATAT 57.515 33.333 0.00 0.00 0.00 1.78
2522 3079 8.644318 ACTACGTCAACCATATTTCATACTTC 57.356 34.615 0.00 0.00 0.00 3.01
2523 3080 8.255206 ACTACGTCAACCATATTTCATACTTCA 58.745 33.333 0.00 0.00 0.00 3.02
2524 3081 7.539712 ACGTCAACCATATTTCATACTTCAG 57.460 36.000 0.00 0.00 0.00 3.02
2525 3082 7.327975 ACGTCAACCATATTTCATACTTCAGA 58.672 34.615 0.00 0.00 0.00 3.27
2526 3083 7.822334 ACGTCAACCATATTTCATACTTCAGAA 59.178 33.333 0.00 0.00 0.00 3.02
2527 3084 8.116753 CGTCAACCATATTTCATACTTCAGAAC 58.883 37.037 0.00 0.00 0.00 3.01
2528 3085 9.167311 GTCAACCATATTTCATACTTCAGAACT 57.833 33.333 0.00 0.00 0.00 3.01
2536 3093 8.690680 ATTTCATACTTCAGAACTACTTCGAC 57.309 34.615 0.00 0.00 0.00 4.20
2595 3153 8.490355 ACTACAACATGTAAACTTAAACTACGC 58.510 33.333 0.00 0.00 31.67 4.42
2609 3167 2.773487 ACTACGCCATGCAAACTACAA 58.227 42.857 0.00 0.00 0.00 2.41
2618 3176 5.564651 GCCATGCAAACTACAAACACACTAT 60.565 40.000 0.00 0.00 0.00 2.12
2620 3178 7.243487 CCATGCAAACTACAAACACACTATAG 58.757 38.462 0.00 0.00 0.00 1.31
2630 3188 7.023171 ACAAACACACTATAGGTTATCCCAA 57.977 36.000 4.43 0.00 34.66 4.12
2644 3202 6.718454 AGGTTATCCCAATCAATGTCATCATC 59.282 38.462 0.00 0.00 34.66 2.92
2671 3230 1.925455 CCTCCTCCTTCTTGCCCCA 60.925 63.158 0.00 0.00 0.00 4.96
2748 6511 3.162666 TCCAGTACAACTCCATCTCGTT 58.837 45.455 0.00 0.00 0.00 3.85
2750 6513 3.193691 CCAGTACAACTCCATCTCGTTCT 59.806 47.826 0.00 0.00 0.00 3.01
2784 6547 2.391389 GCTTCCTCGCAAACCTCGG 61.391 63.158 0.00 0.00 0.00 4.63
2788 6551 2.040544 CCTCGCAAACCTCGGCATT 61.041 57.895 0.00 0.00 0.00 3.56
2801 6564 1.078143 GGCATTGCCTCCTCGTCTT 60.078 57.895 20.66 0.00 46.69 3.01
2853 6616 1.417517 CAATGAGGGTCATGGGATCGA 59.582 52.381 0.00 0.00 37.15 3.59
2888 6651 2.098680 CCGAGACTCGACGTGCTC 59.901 66.667 26.11 3.36 43.74 4.26
2933 6696 0.681733 AGAAAGTTGAGCCTCTCGCA 59.318 50.000 0.00 0.00 41.38 5.10
2942 6705 4.803426 CCTCTCGCACGGCAGGTC 62.803 72.222 0.00 0.00 0.00 3.85
3016 6779 1.522569 GTGCCGAGCCAATACCTCT 59.477 57.895 0.00 0.00 0.00 3.69
3034 6797 0.240145 CTGACCGTCGTGCTAGAACA 59.760 55.000 0.74 0.00 0.00 3.18
3041 6804 3.460144 GTGCTAGAACACGACGCC 58.540 61.111 0.00 0.00 0.00 5.68
3119 6882 2.202919 CGGCATGACGAGGATGCA 60.203 61.111 18.41 0.00 46.77 3.96
3124 6887 0.599466 CATGACGAGGATGCAGCGAT 60.599 55.000 6.51 0.00 0.00 4.58
3134 6897 3.207669 GCAGCGATGCCAGGGAAG 61.208 66.667 16.30 0.00 0.00 3.46
3142 6905 3.483869 GCCAGGGAAGGAGGCGAT 61.484 66.667 0.00 0.00 38.86 4.58
3143 6906 2.507944 CCAGGGAAGGAGGCGATG 59.492 66.667 0.00 0.00 0.00 3.84
3144 6907 2.066393 CCAGGGAAGGAGGCGATGA 61.066 63.158 0.00 0.00 0.00 2.92
3145 6908 1.144936 CAGGGAAGGAGGCGATGAC 59.855 63.158 0.00 0.00 0.00 3.06
3146 6909 1.002274 AGGGAAGGAGGCGATGACT 59.998 57.895 0.00 0.00 0.00 3.41
3147 6910 1.045911 AGGGAAGGAGGCGATGACTC 61.046 60.000 0.00 0.00 36.87 3.36
3148 6911 1.045911 GGGAAGGAGGCGATGACTCT 61.046 60.000 0.00 0.00 37.91 3.24
3149 6912 1.693627 GGAAGGAGGCGATGACTCTA 58.306 55.000 0.00 0.00 37.91 2.43
3150 6913 1.611491 GGAAGGAGGCGATGACTCTAG 59.389 57.143 0.00 0.00 37.91 2.43
3151 6914 2.577700 GAAGGAGGCGATGACTCTAGA 58.422 52.381 0.00 0.00 37.91 2.43
3152 6915 2.270352 AGGAGGCGATGACTCTAGAG 57.730 55.000 18.49 18.49 37.91 2.43
3153 6916 1.771854 AGGAGGCGATGACTCTAGAGA 59.228 52.381 26.57 5.08 37.91 3.10
3154 6917 2.173782 AGGAGGCGATGACTCTAGAGAA 59.826 50.000 26.57 13.88 37.91 2.87
3155 6918 2.552315 GGAGGCGATGACTCTAGAGAAG 59.448 54.545 26.57 12.30 37.91 2.85
3156 6919 2.552315 GAGGCGATGACTCTAGAGAAGG 59.448 54.545 26.57 10.90 34.31 3.46
3157 6920 2.173782 AGGCGATGACTCTAGAGAAGGA 59.826 50.000 26.57 6.96 0.00 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 5.467399 TGTGGACTTAAACCTTGTGTATTCG 59.533 40.000 0.00 0.00 0.00 3.34
2 3 6.708949 TCTGTGGACTTAAACCTTGTGTATTC 59.291 38.462 0.00 0.00 0.00 1.75
4 5 5.995897 GTCTGTGGACTTAAACCTTGTGTAT 59.004 40.000 0.00 0.00 39.24 2.29
6 7 4.196971 GTCTGTGGACTTAAACCTTGTGT 58.803 43.478 0.00 0.00 39.24 3.72
7 8 4.196193 TGTCTGTGGACTTAAACCTTGTG 58.804 43.478 0.00 0.00 42.54 3.33
8 9 4.497291 TGTCTGTGGACTTAAACCTTGT 57.503 40.909 0.00 0.00 42.54 3.16
9 10 5.007724 GTCTTGTCTGTGGACTTAAACCTTG 59.992 44.000 0.00 0.00 42.54 3.61
10 11 5.123936 GTCTTGTCTGTGGACTTAAACCTT 58.876 41.667 0.00 0.00 42.54 3.50
11 12 4.704965 GTCTTGTCTGTGGACTTAAACCT 58.295 43.478 0.00 0.00 42.54 3.50
12 13 3.493503 CGTCTTGTCTGTGGACTTAAACC 59.506 47.826 0.00 0.00 42.54 3.27
13 14 4.365723 TCGTCTTGTCTGTGGACTTAAAC 58.634 43.478 0.00 0.00 42.54 2.01
14 15 4.659111 TCGTCTTGTCTGTGGACTTAAA 57.341 40.909 0.00 0.00 42.54 1.52
15 16 4.556233 CATCGTCTTGTCTGTGGACTTAA 58.444 43.478 0.00 0.00 42.54 1.85
16 17 3.056821 CCATCGTCTTGTCTGTGGACTTA 60.057 47.826 0.00 0.00 42.54 2.24
17 18 2.289072 CCATCGTCTTGTCTGTGGACTT 60.289 50.000 0.00 0.00 42.54 3.01
18 19 1.273606 CCATCGTCTTGTCTGTGGACT 59.726 52.381 0.00 0.00 42.54 3.85
19 20 1.714794 CCATCGTCTTGTCTGTGGAC 58.285 55.000 0.00 0.00 42.42 4.02
20 21 0.037326 GCCATCGTCTTGTCTGTGGA 60.037 55.000 0.00 0.00 0.00 4.02
21 22 1.354337 CGCCATCGTCTTGTCTGTGG 61.354 60.000 0.00 0.00 0.00 4.17
22 23 1.354337 CCGCCATCGTCTTGTCTGTG 61.354 60.000 0.00 0.00 0.00 3.66
23 24 1.079819 CCGCCATCGTCTTGTCTGT 60.080 57.895 0.00 0.00 0.00 3.41
24 25 2.456119 GCCGCCATCGTCTTGTCTG 61.456 63.158 0.00 0.00 0.00 3.51
26 27 2.125512 AGCCGCCATCGTCTTGTC 60.126 61.111 0.00 0.00 0.00 3.18
28 29 3.257561 CGAGCCGCCATCGTCTTG 61.258 66.667 0.00 0.00 35.48 3.02
29 30 3.449227 TCGAGCCGCCATCGTCTT 61.449 61.111 2.39 0.00 40.95 3.01
35 509 2.786495 ATCTTCGTCGAGCCGCCAT 61.786 57.895 0.00 0.00 0.00 4.40
36 510 3.449227 ATCTTCGTCGAGCCGCCA 61.449 61.111 0.00 0.00 0.00 5.69
46 520 5.429130 GGAAGAACCTTATTCCATCTTCGT 58.571 41.667 6.57 0.00 45.49 3.85
47 521 5.993106 GGAAGAACCTTATTCCATCTTCG 57.007 43.478 6.57 0.00 45.49 3.79
84 558 3.799753 GCTAGATGCACCACCGTG 58.200 61.111 0.00 0.00 43.35 4.94
95 569 3.034635 ACTCCCTTCAACGATGCTAGAT 58.965 45.455 0.00 0.00 0.00 1.98
105 579 0.765510 ACCTCCACACTCCCTTCAAC 59.234 55.000 0.00 0.00 0.00 3.18
107 581 1.768684 GCACCTCCACACTCCCTTCA 61.769 60.000 0.00 0.00 0.00 3.02
108 582 1.003233 GCACCTCCACACTCCCTTC 60.003 63.158 0.00 0.00 0.00 3.46
109 583 2.883828 CGCACCTCCACACTCCCTT 61.884 63.158 0.00 0.00 0.00 3.95
114 588 3.052081 GAGACGCACCTCCACACT 58.948 61.111 0.00 0.00 0.00 3.55
136 610 1.822250 GACCGAATGCCGCGAGATTC 61.822 60.000 8.23 13.52 36.84 2.52
137 611 1.883084 GACCGAATGCCGCGAGATT 60.883 57.895 8.23 4.74 36.84 2.40
147 621 5.586243 ACCAAAGACAATCATAGACCGAATG 59.414 40.000 0.00 0.00 0.00 2.67
156 630 7.437713 AGTAGATCCACCAAAGACAATCATA 57.562 36.000 0.00 0.00 0.00 2.15
157 631 6.319048 AGTAGATCCACCAAAGACAATCAT 57.681 37.500 0.00 0.00 0.00 2.45
160 634 4.383118 CCGAGTAGATCCACCAAAGACAAT 60.383 45.833 0.00 0.00 0.00 2.71
188 662 9.033481 CACATGACACAAATACAAACAAAGATT 57.967 29.630 0.00 0.00 0.00 2.40
201 675 2.813754 CCCGAAGACACATGACACAAAT 59.186 45.455 0.00 0.00 0.00 2.32
207 681 3.587797 TCTAACCCGAAGACACATGAC 57.412 47.619 0.00 0.00 0.00 3.06
225 699 9.936759 GAAGAGAAATTTATATCGGAAGGATCT 57.063 33.333 0.00 0.00 36.55 2.75
238 712 3.251004 GCCGCCGATGAAGAGAAATTTAT 59.749 43.478 0.00 0.00 0.00 1.40
243 717 1.809619 CGCCGCCGATGAAGAGAAA 60.810 57.895 0.00 0.00 36.29 2.52
258 732 1.993369 GCACCAGAATAGCAACCGCC 61.993 60.000 0.00 0.00 39.83 6.13
277 751 1.968050 AAAGCCCCATAGGACCGACG 61.968 60.000 0.00 0.00 38.24 5.12
280 754 1.129058 ACTAAAGCCCCATAGGACCG 58.871 55.000 0.00 0.00 38.24 4.79
345 835 4.373116 AAGGTGCGTCGCCGTCAT 62.373 61.111 15.88 0.00 39.30 3.06
422 923 1.206132 CCATGGCAGTGCAACAATCAT 59.794 47.619 18.61 6.96 41.43 2.45
431 938 2.754552 TCATCTTTAACCATGGCAGTGC 59.245 45.455 13.04 6.55 0.00 4.40
509 1023 6.983890 AGCGTGGTTTTATTTGATGTTTTTCT 59.016 30.769 0.00 0.00 0.00 2.52
511 1025 7.923878 AGTAGCGTGGTTTTATTTGATGTTTTT 59.076 29.630 0.00 0.00 0.00 1.94
519 1033 6.304126 CACACTAGTAGCGTGGTTTTATTTG 58.696 40.000 10.00 0.00 36.71 2.32
639 1161 7.380065 CCTAGTCAGTATGCGAATAGAGTTTTC 59.620 40.741 10.04 0.00 33.89 2.29
658 1180 7.962995 AATTAGACTCTGATTGTCCTAGTCA 57.037 36.000 0.00 0.00 39.20 3.41
727 1250 2.099263 AGTCCGAGTCGACCATGTATTG 59.901 50.000 15.64 0.00 32.91 1.90
736 1259 2.007360 TGACTAGAGTCCGAGTCGAC 57.993 55.000 15.64 7.70 44.68 4.20
737 1260 2.028294 AGTTGACTAGAGTCCGAGTCGA 60.028 50.000 15.64 11.63 44.68 4.20
738 1261 2.348660 AGTTGACTAGAGTCCGAGTCG 58.651 52.381 5.29 5.29 44.68 4.18
739 1262 4.201841 GCTAAGTTGACTAGAGTCCGAGTC 60.202 50.000 13.53 13.53 44.15 3.36
740 1263 3.690628 GCTAAGTTGACTAGAGTCCGAGT 59.309 47.826 7.21 0.00 44.15 4.18
741 1264 3.942748 AGCTAAGTTGACTAGAGTCCGAG 59.057 47.826 7.21 0.00 44.15 4.63
742 1265 3.952931 AGCTAAGTTGACTAGAGTCCGA 58.047 45.455 7.21 0.00 44.15 4.55
743 1266 4.396790 AGAAGCTAAGTTGACTAGAGTCCG 59.603 45.833 7.21 0.00 44.15 4.79
744 1267 5.163591 GGAGAAGCTAAGTTGACTAGAGTCC 60.164 48.000 7.21 0.00 44.15 3.85
745 1268 5.650703 AGGAGAAGCTAAGTTGACTAGAGTC 59.349 44.000 0.00 2.56 44.97 3.36
746 1269 5.576128 AGGAGAAGCTAAGTTGACTAGAGT 58.424 41.667 0.00 0.00 0.00 3.24
747 1270 7.817418 ATAGGAGAAGCTAAGTTGACTAGAG 57.183 40.000 0.00 0.00 0.00 2.43
748 1271 9.696572 TTTATAGGAGAAGCTAAGTTGACTAGA 57.303 33.333 0.00 0.00 0.00 2.43
749 1272 9.959749 CTTTATAGGAGAAGCTAAGTTGACTAG 57.040 37.037 0.00 0.00 0.00 2.57
750 1273 9.476928 ACTTTATAGGAGAAGCTAAGTTGACTA 57.523 33.333 0.00 0.00 0.00 2.59
751 1274 8.368962 ACTTTATAGGAGAAGCTAAGTTGACT 57.631 34.615 0.00 0.00 0.00 3.41
767 1290 9.836076 TGAACGATACGAATATGACTTTATAGG 57.164 33.333 0.00 0.00 0.00 2.57
797 1323 6.201044 CGGCAGATACGAATATGACTCTTTTT 59.799 38.462 0.00 0.00 29.54 1.94
798 1324 5.692204 CGGCAGATACGAATATGACTCTTTT 59.308 40.000 0.00 0.00 29.54 2.27
799 1325 5.221263 ACGGCAGATACGAATATGACTCTTT 60.221 40.000 0.00 0.00 29.54 2.52
800 1326 4.278669 ACGGCAGATACGAATATGACTCTT 59.721 41.667 0.00 0.00 29.54 2.85
801 1327 3.821600 ACGGCAGATACGAATATGACTCT 59.178 43.478 0.00 0.00 29.54 3.24
802 1328 4.159857 GACGGCAGATACGAATATGACTC 58.840 47.826 0.00 0.00 29.54 3.36
803 1329 3.057456 GGACGGCAGATACGAATATGACT 60.057 47.826 0.00 0.00 29.54 3.41
804 1330 3.243336 GGACGGCAGATACGAATATGAC 58.757 50.000 0.00 0.00 34.93 3.06
805 1331 2.095415 CGGACGGCAGATACGAATATGA 60.095 50.000 0.00 0.00 34.93 2.15
806 1332 2.251040 CGGACGGCAGATACGAATATG 58.749 52.381 0.00 0.00 34.93 1.78
807 1333 1.884579 ACGGACGGCAGATACGAATAT 59.115 47.619 0.00 0.00 34.93 1.28
808 1334 1.311859 ACGGACGGCAGATACGAATA 58.688 50.000 0.00 0.00 34.93 1.75
809 1335 1.266175 CTACGGACGGCAGATACGAAT 59.734 52.381 0.00 0.00 34.93 3.34
810 1336 0.659427 CTACGGACGGCAGATACGAA 59.341 55.000 0.00 0.00 34.93 3.85
811 1337 0.179076 TCTACGGACGGCAGATACGA 60.179 55.000 0.00 0.00 34.93 3.43
812 1338 0.873054 ATCTACGGACGGCAGATACG 59.127 55.000 0.00 0.00 37.36 3.06
813 1339 1.878088 TGATCTACGGACGGCAGATAC 59.122 52.381 0.00 6.27 0.00 2.24
814 1340 2.265589 TGATCTACGGACGGCAGATA 57.734 50.000 0.00 0.00 0.00 1.98
815 1341 1.399714 TTGATCTACGGACGGCAGAT 58.600 50.000 0.00 9.78 0.00 2.90
816 1342 1.399714 ATTGATCTACGGACGGCAGA 58.600 50.000 0.00 0.00 0.00 4.26
817 1343 2.225068 AATTGATCTACGGACGGCAG 57.775 50.000 0.00 0.00 0.00 4.85
827 1353 5.924254 CGCTCCGTGGTTAATAATTGATCTA 59.076 40.000 0.00 0.00 0.00 1.98
830 1356 4.699637 TCGCTCCGTGGTTAATAATTGAT 58.300 39.130 0.00 0.00 0.00 2.57
831 1357 4.126208 TCGCTCCGTGGTTAATAATTGA 57.874 40.909 0.00 0.00 0.00 2.57
832 1358 4.868450 TTCGCTCCGTGGTTAATAATTG 57.132 40.909 0.00 0.00 0.00 2.32
834 1360 7.556733 TTATTTTCGCTCCGTGGTTAATAAT 57.443 32.000 0.00 0.00 0.00 1.28
835 1361 6.457257 GCTTATTTTCGCTCCGTGGTTAATAA 60.457 38.462 0.00 0.00 0.00 1.40
836 1362 5.006941 GCTTATTTTCGCTCCGTGGTTAATA 59.993 40.000 0.00 0.00 0.00 0.98
837 1363 4.201881 GCTTATTTTCGCTCCGTGGTTAAT 60.202 41.667 0.00 0.00 0.00 1.40
838 1364 3.125658 GCTTATTTTCGCTCCGTGGTTAA 59.874 43.478 0.00 0.00 0.00 2.01
839 1365 2.674357 GCTTATTTTCGCTCCGTGGTTA 59.326 45.455 0.00 0.00 0.00 2.85
840 1366 1.467342 GCTTATTTTCGCTCCGTGGTT 59.533 47.619 0.00 0.00 0.00 3.67
841 1367 1.084289 GCTTATTTTCGCTCCGTGGT 58.916 50.000 0.00 0.00 0.00 4.16
842 1368 1.062587 CAGCTTATTTTCGCTCCGTGG 59.937 52.381 0.00 0.00 33.45 4.94
843 1369 1.999735 TCAGCTTATTTTCGCTCCGTG 59.000 47.619 0.00 0.00 33.45 4.94
844 1370 2.094182 TCTCAGCTTATTTTCGCTCCGT 60.094 45.455 0.00 0.00 33.45 4.69
845 1371 2.537625 CTCTCAGCTTATTTTCGCTCCG 59.462 50.000 0.00 0.00 33.45 4.63
846 1372 2.286563 GCTCTCAGCTTATTTTCGCTCC 59.713 50.000 0.00 0.00 38.45 4.70
847 1373 2.932614 TGCTCTCAGCTTATTTTCGCTC 59.067 45.455 0.00 0.00 42.97 5.03
848 1374 2.935201 CTGCTCTCAGCTTATTTTCGCT 59.065 45.455 0.00 0.00 42.97 4.93
849 1375 2.932614 TCTGCTCTCAGCTTATTTTCGC 59.067 45.455 0.00 0.00 42.97 4.70
850 1376 3.555139 CCTCTGCTCTCAGCTTATTTTCG 59.445 47.826 0.00 0.00 42.97 3.46
851 1377 3.312146 GCCTCTGCTCTCAGCTTATTTTC 59.688 47.826 0.00 0.00 42.97 2.29
852 1378 3.277715 GCCTCTGCTCTCAGCTTATTTT 58.722 45.455 0.00 0.00 42.97 1.82
853 1379 2.238144 TGCCTCTGCTCTCAGCTTATTT 59.762 45.455 0.00 0.00 42.97 1.40
854 1380 1.836166 TGCCTCTGCTCTCAGCTTATT 59.164 47.619 0.00 0.00 42.97 1.40
855 1381 1.413445 CTGCCTCTGCTCTCAGCTTAT 59.587 52.381 0.00 0.00 42.97 1.73
856 1382 0.822811 CTGCCTCTGCTCTCAGCTTA 59.177 55.000 0.00 0.00 42.97 3.09
867 1395 0.107312 CCCCAATGACTCTGCCTCTG 60.107 60.000 0.00 0.00 0.00 3.35
878 1406 0.623194 TGCCGAGAAATCCCCAATGA 59.377 50.000 0.00 0.00 0.00 2.57
879 1407 1.473258 TTGCCGAGAAATCCCCAATG 58.527 50.000 0.00 0.00 0.00 2.82
880 1408 2.230130 TTTGCCGAGAAATCCCCAAT 57.770 45.000 0.00 0.00 0.00 3.16
881 1409 2.002505 TTTTGCCGAGAAATCCCCAA 57.997 45.000 0.00 0.00 0.00 4.12
882 1410 2.002505 TTTTTGCCGAGAAATCCCCA 57.997 45.000 0.00 0.00 0.00 4.96
901 1429 5.406163 AGAAATCCCCAATGACTCCTTTTT 58.594 37.500 0.00 0.00 0.00 1.94
902 1430 5.015813 AGAAATCCCCAATGACTCCTTTT 57.984 39.130 0.00 0.00 0.00 2.27
903 1431 4.682021 AGAAATCCCCAATGACTCCTTT 57.318 40.909 0.00 0.00 0.00 3.11
904 1432 4.604156 GAAGAAATCCCCAATGACTCCTT 58.396 43.478 0.00 0.00 0.00 3.36
905 1433 3.370953 CGAAGAAATCCCCAATGACTCCT 60.371 47.826 0.00 0.00 0.00 3.69
906 1434 2.945668 CGAAGAAATCCCCAATGACTCC 59.054 50.000 0.00 0.00 0.00 3.85
907 1435 2.356069 GCGAAGAAATCCCCAATGACTC 59.644 50.000 0.00 0.00 0.00 3.36
908 1436 2.369394 GCGAAGAAATCCCCAATGACT 58.631 47.619 0.00 0.00 0.00 3.41
909 1437 1.064060 CGCGAAGAAATCCCCAATGAC 59.936 52.381 0.00 0.00 0.00 3.06
910 1438 1.339631 ACGCGAAGAAATCCCCAATGA 60.340 47.619 15.93 0.00 0.00 2.57
1115 1644 2.329267 ACATGAGCATCTCGGGGATAA 58.671 47.619 0.00 0.00 34.92 1.75
1270 1801 1.449423 CGGTGATCGGATGCCACAA 60.449 57.895 10.76 0.00 34.75 3.33
1315 1846 1.553704 GGGGACATAGTGGTCGTCTTT 59.446 52.381 0.00 0.00 38.70 2.52
1419 1950 0.396435 TGACTCGGCAGAACCACATT 59.604 50.000 0.00 0.00 39.03 2.71
1557 2094 1.450312 GGGGATGACTCGCTTGGTG 60.450 63.158 0.00 0.00 34.84 4.17
1645 2182 0.179161 CCGAAGTCGAGCTGAACGAT 60.179 55.000 1.43 0.00 43.02 3.73
1673 2210 0.324285 AAGCTCAGCAGTGGGAGAAG 59.676 55.000 0.00 0.00 32.87 2.85
1674 2211 0.322975 GAAGCTCAGCAGTGGGAGAA 59.677 55.000 0.00 0.00 32.87 2.87
1675 2212 0.833409 TGAAGCTCAGCAGTGGGAGA 60.833 55.000 0.00 0.00 32.87 3.71
1677 2214 1.208052 GTATGAAGCTCAGCAGTGGGA 59.792 52.381 0.00 0.00 0.00 4.37
1755 2292 2.530151 AGGGAGTCCAGCAGCCAA 60.530 61.111 12.30 0.00 34.83 4.52
1968 2505 4.832248 TCTTCATGAAGTAGATGCGGTTT 58.168 39.130 29.80 0.00 39.38 3.27
2029 2566 2.445145 TCTCAATGAGTTGTTCCCCCAA 59.555 45.455 10.36 0.00 36.69 4.12
2033 2570 5.474876 ACAAGAATCTCAATGAGTTGTTCCC 59.525 40.000 10.36 0.00 36.69 3.97
2041 2578 6.373495 TCATGAACCACAAGAATCTCAATGAG 59.627 38.462 3.38 3.38 0.00 2.90
2114 2665 1.871077 CCGCGTGCATGCATATCAT 59.129 52.632 29.23 0.00 35.31 2.45
2115 2666 2.895682 GCCGCGTGCATGCATATCA 61.896 57.895 29.23 0.00 40.77 2.15
2116 2667 2.127118 GCCGCGTGCATGCATATC 60.127 61.111 29.23 14.45 40.77 1.63
2117 2668 3.663176 GGCCGCGTGCATGCATAT 61.663 61.111 29.23 0.00 43.89 1.78
2118 2669 4.854924 AGGCCGCGTGCATGCATA 62.855 61.111 29.23 0.00 43.89 3.14
2126 2677 3.864686 CGGATTTGAGGCCGCGTG 61.865 66.667 4.92 0.00 41.17 5.34
2127 2678 3.385749 ATCGGATTTGAGGCCGCGT 62.386 57.895 4.92 0.00 46.79 6.01
2129 2680 3.025619 CATCGGATTTGAGGCCGC 58.974 61.111 0.00 0.00 46.79 6.53
2131 2682 1.967319 TAAGCATCGGATTTGAGGCC 58.033 50.000 0.00 0.00 46.26 5.19
2142 2693 4.271049 CACACCCACTAGAAATAAGCATCG 59.729 45.833 0.00 0.00 0.00 3.84
2143 2694 5.428253 TCACACCCACTAGAAATAAGCATC 58.572 41.667 0.00 0.00 0.00 3.91
2145 2696 4.901197 TCACACCCACTAGAAATAAGCA 57.099 40.909 0.00 0.00 0.00 3.91
2196 2748 4.107622 GCAACTCATTACATTCATGTGGC 58.892 43.478 2.50 0.00 41.89 5.01
2238 2793 7.362660 CCCTAGAACAAAGGCTACCATTAAAAC 60.363 40.741 0.00 0.00 32.34 2.43
2264 2819 2.712077 CGGAACAAATCGCAAGTGC 58.288 52.632 0.00 0.00 39.48 4.40
2271 2826 2.415697 AAAACTGGCGGAACAAATCG 57.584 45.000 0.00 0.00 0.00 3.34
2308 2863 7.624549 AGATGCTCTTAATACAAAGAACAGGA 58.375 34.615 0.00 0.00 35.62 3.86
2310 2865 7.550551 TGGAGATGCTCTTAATACAAAGAACAG 59.449 37.037 0.00 0.00 35.62 3.16
2311 2866 7.394016 TGGAGATGCTCTTAATACAAAGAACA 58.606 34.615 0.00 0.00 36.36 3.18
2405 2962 3.492309 GGAGACGGTACTCTCTCGTATCA 60.492 52.174 14.92 0.00 43.92 2.15
2407 2964 2.433604 TGGAGACGGTACTCTCTCGTAT 59.566 50.000 10.88 0.97 37.44 3.06
2408 2965 1.827344 TGGAGACGGTACTCTCTCGTA 59.173 52.381 10.88 3.28 37.44 3.43
2415 2972 2.673833 CAGTTGTTGGAGACGGTACTC 58.326 52.381 0.00 0.00 36.31 2.59
2448 3005 0.874175 GGTTTCGCTGTTTTGGGTGC 60.874 55.000 0.00 0.00 0.00 5.01
2460 3017 9.173939 CATTTTGAGAGAAATATATGGTTTCGC 57.826 33.333 9.54 9.54 39.83 4.70
2502 3059 9.167311 AGTTCTGAAGTATGAAATATGGTTGAC 57.833 33.333 0.00 0.00 0.00 3.18
2510 3067 9.784680 GTCGAAGTAGTTCTGAAGTATGAAATA 57.215 33.333 8.12 0.00 0.00 1.40
2511 3068 7.760340 GGTCGAAGTAGTTCTGAAGTATGAAAT 59.240 37.037 8.12 0.00 0.00 2.17
2512 3069 7.088905 GGTCGAAGTAGTTCTGAAGTATGAAA 58.911 38.462 8.12 0.00 0.00 2.69
2513 3070 6.208007 TGGTCGAAGTAGTTCTGAAGTATGAA 59.792 38.462 8.12 0.00 0.00 2.57
2514 3071 5.708697 TGGTCGAAGTAGTTCTGAAGTATGA 59.291 40.000 8.12 2.85 0.00 2.15
2515 3072 5.800941 GTGGTCGAAGTAGTTCTGAAGTATG 59.199 44.000 8.12 0.82 0.00 2.39
2516 3073 5.475909 TGTGGTCGAAGTAGTTCTGAAGTAT 59.524 40.000 8.12 0.00 0.00 2.12
2517 3074 4.823442 TGTGGTCGAAGTAGTTCTGAAGTA 59.177 41.667 8.63 0.83 0.00 2.24
2518 3075 3.635373 TGTGGTCGAAGTAGTTCTGAAGT 59.365 43.478 8.63 2.89 0.00 3.01
2519 3076 4.238761 TGTGGTCGAAGTAGTTCTGAAG 57.761 45.455 8.63 0.00 0.00 3.02
2520 3077 4.866508 ATGTGGTCGAAGTAGTTCTGAA 57.133 40.909 8.63 0.00 0.00 3.02
2521 3078 4.279922 TGAATGTGGTCGAAGTAGTTCTGA 59.720 41.667 8.63 5.02 0.00 3.27
2522 3079 4.556233 TGAATGTGGTCGAAGTAGTTCTG 58.444 43.478 8.63 2.86 0.00 3.02
2523 3080 4.866508 TGAATGTGGTCGAAGTAGTTCT 57.133 40.909 8.63 0.00 0.00 3.01
2524 3081 5.465724 ACTTTGAATGTGGTCGAAGTAGTTC 59.534 40.000 6.11 0.00 46.16 3.01
2525 3082 5.365619 ACTTTGAATGTGGTCGAAGTAGTT 58.634 37.500 6.11 0.00 46.16 2.24
2526 3083 4.957296 ACTTTGAATGTGGTCGAAGTAGT 58.043 39.130 6.11 0.00 46.16 2.73
2527 3084 5.924475 AACTTTGAATGTGGTCGAAGTAG 57.076 39.130 7.98 0.00 46.94 2.57
2528 3085 7.972832 ATAAACTTTGAATGTGGTCGAAGTA 57.027 32.000 7.98 0.00 46.94 2.24
2530 3087 7.802738 TGTATAAACTTTGAATGTGGTCGAAG 58.197 34.615 0.00 1.43 42.54 3.79
2531 3088 7.731882 TGTATAAACTTTGAATGTGGTCGAA 57.268 32.000 0.00 0.00 0.00 3.71
2532 3089 7.625395 GCATGTATAAACTTTGAATGTGGTCGA 60.625 37.037 0.00 0.00 0.00 4.20
2533 3090 6.468956 GCATGTATAAACTTTGAATGTGGTCG 59.531 38.462 0.00 0.00 0.00 4.79
2534 3091 7.312154 TGCATGTATAAACTTTGAATGTGGTC 58.688 34.615 0.00 0.00 0.00 4.02
2535 3092 7.225784 TGCATGTATAAACTTTGAATGTGGT 57.774 32.000 0.00 0.00 0.00 4.16
2536 3093 7.598118 TGTTGCATGTATAAACTTTGAATGTGG 59.402 33.333 0.00 0.00 0.00 4.17
2595 3153 4.305989 AGTGTGTTTGTAGTTTGCATGG 57.694 40.909 0.00 0.00 0.00 3.66
2609 3167 7.446106 TGATTGGGATAACCTATAGTGTGTT 57.554 36.000 0.00 0.00 41.11 3.32
2618 3176 7.147958 TGATGACATTGATTGGGATAACCTA 57.852 36.000 0.00 0.00 41.11 3.08
2620 3178 6.348786 CGATGATGACATTGATTGGGATAACC 60.349 42.308 0.00 0.00 39.55 2.85
2630 3188 3.733443 TCCGACGATGATGACATTGAT 57.267 42.857 0.00 0.00 39.55 2.57
2692 3251 1.583054 AGTCCAAGTGCAAGAACGAC 58.417 50.000 0.00 0.00 0.00 4.34
2748 6511 1.287815 CACCCGAAGTACACGCAGA 59.712 57.895 0.00 0.00 0.00 4.26
2750 6513 2.356553 GCACCCGAAGTACACGCA 60.357 61.111 0.00 0.00 0.00 5.24
2784 6547 0.107945 AGAAGACGAGGAGGCAATGC 60.108 55.000 0.00 0.00 0.00 3.56
2788 6551 0.329931 AGAGAGAAGACGAGGAGGCA 59.670 55.000 0.00 0.00 0.00 4.75
2801 6564 0.322636 GGGACACCAGTCGAGAGAGA 60.323 60.000 0.00 0.00 45.92 3.10
2853 6616 2.766263 TCGGTGACCATTGATTCTAGCT 59.234 45.455 1.11 0.00 0.00 3.32
2906 6669 2.909006 AGGCTCAACTTTCTGGAGATCA 59.091 45.455 0.00 0.00 0.00 2.92
2914 6677 0.681733 TGCGAGAGGCTCAACTTTCT 59.318 50.000 18.26 0.00 44.05 2.52
2949 6712 0.810648 CCTACAATGTTGCGCCATGT 59.189 50.000 4.18 5.40 0.00 3.21
2955 6718 1.134487 CCGTGCCTACAATGTTGCG 59.866 57.895 0.00 0.00 0.00 4.85
3016 6779 0.039798 GTGTTCTAGCACGACGGTCA 60.040 55.000 9.10 0.00 0.00 4.02
3061 6824 1.957765 GACTTCTAGGGGGTGCGACC 61.958 65.000 0.00 0.00 37.60 4.79
3119 6882 2.688666 TCCTTCCCTGGCATCGCT 60.689 61.111 0.00 0.00 0.00 4.93
3134 6897 2.264005 TCTCTAGAGTCATCGCCTCC 57.736 55.000 19.21 0.00 0.00 4.30


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

AutoCloner maintained by Alex Coulton.