Multiple sequence alignment - TraesCS5D01G509000

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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 TraesCS5D01G509000 chr5D 100.000 2249 0 0 1 2249 534003146 534005394 0.000000e+00 4154.0
1 TraesCS5D01G509000 chr5D 86.061 165 23 0 2009 2173 65903865 65904029 6.380000e-41 178.0
2 TraesCS5D01G509000 chr5D 100.000 40 0 0 1983 2022 534005089 534005128 8.610000e-10 75.0
3 TraesCS5D01G509000 chr5D 100.000 40 0 0 1944 1983 534005128 534005167 8.610000e-10 75.0
4 TraesCS5D01G509000 chr5B 81.191 1276 102 53 826 1983 674267088 674268343 0.000000e+00 900.0
5 TraesCS5D01G509000 chr5B 91.304 230 16 4 1983 2209 674268302 674268530 6.030000e-81 311.0
6 TraesCS5D01G509000 chr5B 86.513 304 13 12 284 584 674266630 674266908 2.170000e-80 309.0
7 TraesCS5D01G509000 chr5B 86.310 168 23 0 2009 2176 65189716 65189549 1.370000e-42 183.0
8 TraesCS5D01G509000 chr5B 95.918 49 2 0 734 782 674267030 674267078 1.850000e-11 80.5
9 TraesCS5D01G509000 chr4A 88.566 551 30 16 3 533 637931182 637930645 2.440000e-179 638.0
10 TraesCS5D01G509000 chr4A 96.610 354 9 2 904 1256 637929969 637929618 3.220000e-163 584.0
11 TraesCS5D01G509000 chr4A 88.251 366 30 8 1628 1983 637924316 637923954 2.060000e-115 425.0
12 TraesCS5D01G509000 chr4A 87.554 233 22 5 1983 2209 637923994 637923763 1.710000e-66 263.0
13 TraesCS5D01G509000 chr4A 88.827 179 5 4 695 866 637930148 637929978 2.930000e-49 206.0
14 TraesCS5D01G509000 chr5A 86.667 165 22 0 2009 2173 55161762 55161926 1.370000e-42 183.0
15 TraesCS5D01G509000 chr2B 81.212 165 31 0 2009 2173 116849088 116849252 1.400000e-27 134.0


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 TraesCS5D01G509000 chr5D 534003146 534005394 2248 False 1434.666667 4154 100.000000 1 2249 3 chr5D.!!$F2 2248
1 TraesCS5D01G509000 chr5B 674266630 674268530 1900 False 400.125000 900 88.731500 284 2209 4 chr5B.!!$F1 1925
2 TraesCS5D01G509000 chr4A 637929618 637931182 1564 True 476.000000 638 91.334333 3 1256 3 chr4A.!!$R2 1253
3 TraesCS5D01G509000 chr4A 637923763 637924316 553 True 344.000000 425 87.902500 1628 2209 2 chr4A.!!$R1 581

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
166 175 0.109597 CTGGGCACGTTTGATCAAGC 60.11 55.0 11.93 11.93 0.0 4.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1298 1693 0.179059 ACGCCATGATATGCCAACGA 60.179 50.0 0.0 0.0 0.0 3.85 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
125 134 6.403866 TTGTTTTGCATATATGTGATCCCC 57.596 37.500 14.14 0.00 0.00 4.81
127 136 5.769662 TGTTTTGCATATATGTGATCCCCTC 59.230 40.000 14.14 0.00 0.00 4.30
156 165 1.826487 GTTTTGGTCCTGGGCACGT 60.826 57.895 0.00 0.00 0.00 4.49
162 171 1.305930 GGTCCTGGGCACGTTTGATC 61.306 60.000 0.00 0.00 0.00 2.92
166 175 0.109597 CTGGGCACGTTTGATCAAGC 60.110 55.000 11.93 11.93 0.00 4.01
175 188 5.036737 CACGTTTGATCAAGCAAAGAAGTT 58.963 37.500 20.41 0.00 38.33 2.66
194 207 7.213678 AGAAGTTATATGCTAGCCTGTTTCTC 58.786 38.462 13.29 0.41 0.00 2.87
201 218 5.932619 TGCTAGCCTGTTTCTCTATGTAA 57.067 39.130 13.29 0.00 0.00 2.41
203 220 6.516718 TGCTAGCCTGTTTCTCTATGTAATC 58.483 40.000 13.29 0.00 0.00 1.75
228 245 3.535561 CTCCACTTGGCTACAGGTAATG 58.464 50.000 0.00 0.00 34.86 1.90
233 250 4.393062 CACTTGGCTACAGGTAATGTTCTG 59.607 45.833 0.00 0.00 39.96 3.02
235 252 3.178046 TGGCTACAGGTAATGTTCTGGA 58.822 45.455 0.00 0.00 39.96 3.86
236 253 3.780294 TGGCTACAGGTAATGTTCTGGAT 59.220 43.478 0.00 0.00 39.96 3.41
237 254 4.227300 TGGCTACAGGTAATGTTCTGGATT 59.773 41.667 0.00 0.00 39.96 3.01
238 255 5.193679 GGCTACAGGTAATGTTCTGGATTT 58.806 41.667 0.00 0.00 39.96 2.17
279 296 3.054139 AGCAGAGCATTGGGAAGTTCATA 60.054 43.478 5.01 0.00 0.00 2.15
280 297 3.696051 GCAGAGCATTGGGAAGTTCATAA 59.304 43.478 5.01 0.00 0.00 1.90
281 298 4.340381 GCAGAGCATTGGGAAGTTCATAAT 59.660 41.667 5.01 1.88 0.00 1.28
327 344 0.587768 CTGTGCATGCTGTGAAACGA 59.412 50.000 20.33 0.00 42.39 3.85
333 350 1.536766 CATGCTGTGAAACGATGTGGT 59.463 47.619 0.00 0.00 42.39 4.16
437 458 7.073265 CACTACGACCGAAAAATAACATTTGT 58.927 34.615 0.00 0.00 0.00 2.83
444 468 8.655651 ACCGAAAAATAACATTTGTGAACAAT 57.344 26.923 0.00 0.00 35.55 2.71
459 483 6.142139 TGTGAACAATAACAAATCGCTCTTG 58.858 36.000 0.00 0.00 0.00 3.02
464 488 5.240623 ACAATAACAAATCGCTCTTGTTCCA 59.759 36.000 11.11 0.00 43.98 3.53
473 497 6.757897 ATCGCTCTTGTTCCATAAATTTGA 57.242 33.333 0.00 0.00 0.00 2.69
474 498 6.757897 TCGCTCTTGTTCCATAAATTTGAT 57.242 33.333 0.00 0.00 0.00 2.57
475 499 7.156876 TCGCTCTTGTTCCATAAATTTGATT 57.843 32.000 0.00 0.00 0.00 2.57
476 500 7.601856 TCGCTCTTGTTCCATAAATTTGATTT 58.398 30.769 0.00 0.00 36.29 2.17
477 501 8.087750 TCGCTCTTGTTCCATAAATTTGATTTT 58.912 29.630 0.00 0.00 33.82 1.82
517 541 7.198390 CCAAAAGTGCTGTAATAATCTCATGG 58.802 38.462 0.00 0.00 0.00 3.66
519 543 7.944729 AAAGTGCTGTAATAATCTCATGGTT 57.055 32.000 0.00 0.00 0.00 3.67
552 606 5.474825 TGTAGCATTACTCGTTCATGTCAA 58.525 37.500 0.00 0.00 0.00 3.18
585 639 5.238868 TCCTCGCAACTAGTGTGATCTATAC 59.761 44.000 0.00 0.00 45.59 1.47
586 640 5.434352 TCGCAACTAGTGTGATCTATACC 57.566 43.478 0.00 0.00 41.89 2.73
587 641 4.277672 TCGCAACTAGTGTGATCTATACCC 59.722 45.833 0.00 0.00 41.89 3.69
588 642 4.558898 CGCAACTAGTGTGATCTATACCCC 60.559 50.000 0.00 0.00 40.42 4.95
589 643 4.344102 GCAACTAGTGTGATCTATACCCCA 59.656 45.833 0.00 0.00 0.00 4.96
591 645 6.692486 CAACTAGTGTGATCTATACCCCATC 58.308 44.000 0.00 0.00 0.00 3.51
596 650 6.969043 AGTGTGATCTATACCCCATCAAAAA 58.031 36.000 0.00 0.00 0.00 1.94
597 651 7.586349 AGTGTGATCTATACCCCATCAAAAAT 58.414 34.615 0.00 0.00 0.00 1.82
600 654 8.912988 TGTGATCTATACCCCATCAAAAATTTC 58.087 33.333 0.00 0.00 0.00 2.17
635 756 9.661954 AGGAAAAGAGTGTAATCTATCTATCCA 57.338 33.333 0.00 0.00 33.52 3.41
641 762 9.766754 AGAGTGTAATCTATCTATCCATGATGT 57.233 33.333 0.00 0.00 0.00 3.06
663 791 2.510768 GGCAACTAGGACTACGATGG 57.489 55.000 0.00 0.00 0.00 3.51
664 792 1.755380 GGCAACTAGGACTACGATGGT 59.245 52.381 0.00 0.00 0.00 3.55
679 807 3.666001 CGATGGTCGTGTAATTTTTCGG 58.334 45.455 0.00 0.00 34.72 4.30
689 817 7.060979 GTCGTGTAATTTTTCGGGAAATTTACC 59.939 37.037 9.67 9.67 40.24 2.85
691 819 7.595875 CGTGTAATTTTTCGGGAAATTTACCTT 59.404 33.333 17.56 6.27 40.24 3.50
692 820 9.911138 GTGTAATTTTTCGGGAAATTTACCTTA 57.089 29.630 17.56 5.30 40.24 2.69
693 821 9.911138 TGTAATTTTTCGGGAAATTTACCTTAC 57.089 29.630 17.56 16.25 40.24 2.34
700 1060 4.097286 CGGGAAATTTACCTTACCATGGTG 59.903 45.833 28.17 13.44 38.42 4.17
740 1103 3.067106 TGCACGATGAAAGGAGAAGAAC 58.933 45.455 0.00 0.00 0.00 3.01
782 1145 1.202592 TGCCAAGCACTACTGACGAAA 60.203 47.619 0.00 0.00 31.71 3.46
805 1172 2.997897 AGGCAGTGGGAGGTCGAC 60.998 66.667 7.13 7.13 0.00 4.20
824 1191 4.452795 TCGACCGATCTCTCTCAATCATAC 59.547 45.833 0.00 0.00 0.00 2.39
866 1233 1.899534 GCCGGCCTCGTCTCTATCT 60.900 63.158 18.11 0.00 33.95 1.98
868 1235 0.250553 CCGGCCTCGTCTCTATCTCT 60.251 60.000 0.00 0.00 33.95 3.10
870 1237 1.270625 CGGCCTCGTCTCTATCTCTCT 60.271 57.143 0.00 0.00 0.00 3.10
871 1238 2.028839 CGGCCTCGTCTCTATCTCTCTA 60.029 54.545 0.00 0.00 0.00 2.43
872 1239 3.332034 GGCCTCGTCTCTATCTCTCTAC 58.668 54.545 0.00 0.00 0.00 2.59
897 1264 7.092354 ACCTCCTCTATATCACACGGTCTATAT 60.092 40.741 0.00 0.00 0.00 0.86
898 1265 8.430431 CCTCCTCTATATCACACGGTCTATATA 58.570 40.741 0.00 0.00 0.00 0.86
943 1310 3.431055 CGGTGCTCCAACTGCAAA 58.569 55.556 5.52 0.00 42.41 3.68
990 1365 2.753029 GGCAGAGGCAACAGAGGT 59.247 61.111 0.00 0.00 43.71 3.85
1219 1614 2.514824 GCTGGATCAAGGACCGCC 60.515 66.667 0.00 0.00 0.00 6.13
1270 1665 4.907034 CCGACCGACGCCGATCTG 62.907 72.222 9.01 0.00 41.07 2.90
1271 1666 3.872728 CGACCGACGCCGATCTGA 61.873 66.667 0.00 0.00 38.22 3.27
1272 1667 2.278013 GACCGACGCCGATCTGAC 60.278 66.667 0.00 0.00 38.22 3.51
1273 1668 3.047718 GACCGACGCCGATCTGACA 62.048 63.158 0.00 0.00 38.22 3.58
1274 1669 2.337749 GACCGACGCCGATCTGACAT 62.338 60.000 0.00 0.00 38.22 3.06
1275 1670 1.946156 CCGACGCCGATCTGACATG 60.946 63.158 0.00 0.00 38.22 3.21
1276 1671 2.580470 CGACGCCGATCTGACATGC 61.580 63.158 0.00 0.00 38.22 4.06
1277 1672 1.227089 GACGCCGATCTGACATGCT 60.227 57.895 0.00 0.00 0.00 3.79
1278 1673 1.485838 GACGCCGATCTGACATGCTG 61.486 60.000 0.00 0.00 0.00 4.41
1279 1674 2.879070 CGCCGATCTGACATGCTGC 61.879 63.158 0.00 0.00 0.00 5.25
1280 1675 2.879070 GCCGATCTGACATGCTGCG 61.879 63.158 0.00 0.00 0.00 5.18
1281 1676 2.242572 CCGATCTGACATGCTGCGG 61.243 63.158 0.00 0.00 0.00 5.69
1282 1677 2.879070 CGATCTGACATGCTGCGGC 61.879 63.158 11.65 11.65 39.26 6.53
1283 1678 2.879070 GATCTGACATGCTGCGGCG 61.879 63.158 13.96 0.51 42.25 6.46
1284 1679 3.375472 ATCTGACATGCTGCGGCGA 62.375 57.895 12.98 2.71 42.25 5.54
1285 1680 3.857854 CTGACATGCTGCGGCGAC 61.858 66.667 12.98 2.02 42.25 5.19
1287 1682 3.197790 GACATGCTGCGGCGACAT 61.198 61.111 12.98 7.98 42.25 3.06
1289 1684 3.945434 CATGCTGCGGCGACATCC 61.945 66.667 12.98 3.34 42.25 3.51
1290 1685 4.166888 ATGCTGCGGCGACATCCT 62.167 61.111 12.98 0.00 42.25 3.24
1293 1688 2.434884 CTGCGGCGACATCCTGTT 60.435 61.111 12.98 0.00 0.00 3.16
1295 1690 2.434185 GCGGCGACATCCTGTTCA 60.434 61.111 12.98 0.00 0.00 3.18
1296 1691 2.740714 GCGGCGACATCCTGTTCAC 61.741 63.158 12.98 0.00 0.00 3.18
1297 1692 2.444624 CGGCGACATCCTGTTCACG 61.445 63.158 0.00 0.00 0.00 4.35
1298 1693 1.374252 GGCGACATCCTGTTCACGT 60.374 57.895 0.00 0.00 0.00 4.49
1306 1701 1.885388 CCTGTTCACGTCGTTGGCA 60.885 57.895 0.00 0.00 0.00 4.92
1324 1721 1.334419 GCATATCATGGCGTGTGCTTC 60.334 52.381 12.12 0.00 42.25 3.86
1329 1726 3.529341 ATGGCGTGTGCTTCGACCA 62.529 57.895 0.00 11.27 42.25 4.02
1331 1728 3.712881 GCGTGTGCTTCGACCACC 61.713 66.667 11.60 4.25 38.39 4.61
1338 1735 4.796231 CTTCGACCACCTCGCCGG 62.796 72.222 0.00 0.00 42.62 6.13
1369 1766 7.809806 CCTGTTCATAATGTTTCTGTTTTCTCC 59.190 37.037 0.00 0.00 0.00 3.71
1371 1768 8.912988 TGTTCATAATGTTTCTGTTTTCTCCTT 58.087 29.630 0.00 0.00 0.00 3.36
1372 1769 9.399403 GTTCATAATGTTTCTGTTTTCTCCTTC 57.601 33.333 0.00 0.00 0.00 3.46
1373 1770 8.690203 TCATAATGTTTCTGTTTTCTCCTTCA 57.310 30.769 0.00 0.00 0.00 3.02
1375 1772 9.350357 CATAATGTTTCTGTTTTCTCCTTCATG 57.650 33.333 0.00 0.00 0.00 3.07
1376 1773 5.186996 TGTTTCTGTTTTCTCCTTCATGC 57.813 39.130 0.00 0.00 0.00 4.06
1377 1774 4.644234 TGTTTCTGTTTTCTCCTTCATGCA 59.356 37.500 0.00 0.00 0.00 3.96
1378 1775 5.126869 TGTTTCTGTTTTCTCCTTCATGCAA 59.873 36.000 0.00 0.00 0.00 4.08
1379 1776 5.850557 TTCTGTTTTCTCCTTCATGCAAA 57.149 34.783 0.00 0.00 0.00 3.68
1380 1777 5.443185 TCTGTTTTCTCCTTCATGCAAAG 57.557 39.130 0.00 0.00 0.00 2.77
1383 1793 4.222114 GTTTTCTCCTTCATGCAAAGTCG 58.778 43.478 0.00 0.00 0.00 4.18
1386 1796 0.036732 TCCTTCATGCAAAGTCGCCT 59.963 50.000 0.00 0.00 0.00 5.52
1392 1802 0.951558 ATGCAAAGTCGCCTTCGTTT 59.048 45.000 0.00 0.00 36.96 3.60
1399 1809 5.390145 GCAAAGTCGCCTTCGTTTCTTATTA 60.390 40.000 0.00 0.00 36.96 0.98
1405 1815 7.749126 AGTCGCCTTCGTTTCTTATTAATTTTG 59.251 33.333 0.00 0.00 36.96 2.44
1409 1819 8.644619 GCCTTCGTTTCTTATTAATTTTGTTCC 58.355 33.333 0.00 0.00 0.00 3.62
1422 1832 4.454728 TTTTGTTCCTATGGATGCAAGC 57.545 40.909 0.00 0.00 32.05 4.01
1423 1833 2.804986 TGTTCCTATGGATGCAAGCA 57.195 45.000 0.00 0.00 0.00 3.91
1426 1836 3.831333 TGTTCCTATGGATGCAAGCAAAA 59.169 39.130 0.00 0.00 0.00 2.44
1427 1837 4.467082 TGTTCCTATGGATGCAAGCAAAAT 59.533 37.500 0.00 0.00 0.00 1.82
1429 1839 5.772825 TCCTATGGATGCAAGCAAAATAC 57.227 39.130 0.00 0.00 0.00 1.89
1431 1841 2.937469 TGGATGCAAGCAAAATACGG 57.063 45.000 0.00 0.00 0.00 4.02
1433 1843 2.423185 TGGATGCAAGCAAAATACGGAG 59.577 45.455 0.00 0.00 0.00 4.63
1434 1844 2.682856 GGATGCAAGCAAAATACGGAGA 59.317 45.455 0.00 0.00 0.00 3.71
1435 1845 3.128589 GGATGCAAGCAAAATACGGAGAA 59.871 43.478 0.00 0.00 0.00 2.87
1436 1846 3.829886 TGCAAGCAAAATACGGAGAAG 57.170 42.857 0.00 0.00 0.00 2.85
1440 1864 5.048083 TGCAAGCAAAATACGGAGAAGAAAT 60.048 36.000 0.00 0.00 0.00 2.17
1442 1866 6.611381 CAAGCAAAATACGGAGAAGAAATCA 58.389 36.000 0.00 0.00 0.00 2.57
1446 1870 7.121168 AGCAAAATACGGAGAAGAAATCATTCA 59.879 33.333 0.00 0.00 38.06 2.57
1453 1877 8.567285 ACGGAGAAGAAATCATTCAAATAACT 57.433 30.769 0.00 0.00 38.06 2.24
1481 1914 3.965292 TTCCTCGACGACATCATACTC 57.035 47.619 0.00 0.00 0.00 2.59
1484 1917 4.700700 TCCTCGACGACATCATACTCTTA 58.299 43.478 0.00 0.00 0.00 2.10
1486 1919 5.408909 TCCTCGACGACATCATACTCTTATC 59.591 44.000 0.00 0.00 0.00 1.75
1488 1921 6.072948 CCTCGACGACATCATACTCTTATCTT 60.073 42.308 0.00 0.00 0.00 2.40
1490 1923 8.374327 TCGACGACATCATACTCTTATCTTTA 57.626 34.615 0.00 0.00 0.00 1.85
1520 1960 3.499048 CGTAGCAATCGTGTAACTCTGT 58.501 45.455 0.00 0.00 31.75 3.41
1521 1961 4.655027 CGTAGCAATCGTGTAACTCTGTA 58.345 43.478 0.00 0.00 31.75 2.74
1532 1972 4.631377 GTGTAACTCTGTAGCAATGCATGA 59.369 41.667 8.35 0.00 0.00 3.07
1537 1977 1.063027 CTGTAGCAATGCATGACCACG 59.937 52.381 8.35 0.00 0.00 4.94
1579 2027 0.251608 GGTAAGCTGGGAGGGCAAAA 60.252 55.000 0.00 0.00 0.00 2.44
1591 2046 3.956848 GGAGGGCAAAATTTCTAGATGCT 59.043 43.478 13.47 0.00 37.20 3.79
1600 2055 7.415989 GCAAAATTTCTAGATGCTCCTCATTCA 60.416 37.037 7.82 0.00 35.05 2.57
1606 2061 3.545724 TGCTCCTCATTCAGCACAG 57.454 52.632 0.00 0.00 40.80 3.66
1611 2070 3.523547 CTCCTCATTCAGCACAGAGAAG 58.476 50.000 0.00 0.00 0.00 2.85
1618 2077 0.605860 CAGCACAGAGAAGCAAGCCT 60.606 55.000 0.00 0.00 0.00 4.58
1625 2084 2.818432 CAGAGAAGCAAGCCTCAATGTT 59.182 45.455 0.00 0.00 32.07 2.71
1634 2093 4.387862 GCAAGCCTCAATGTTTCATTTCAG 59.612 41.667 0.00 0.00 0.00 3.02
1684 2144 1.076485 ATGGATGAACAGGCCAGGC 60.076 57.895 5.01 1.26 34.74 4.85
1729 2189 5.428496 TCTCAAGAAAATTCAGCACACTG 57.572 39.130 0.00 0.00 45.95 3.66
1747 2207 1.747355 CTGGAGGCATTCACATCAACC 59.253 52.381 0.00 0.00 0.00 3.77
1767 2227 2.674852 CCGTGAAGTGATGTTCAGGATG 59.325 50.000 7.65 0.00 42.40 3.51
1799 2259 0.317020 GTTTGCAGCGAGTTGTCACC 60.317 55.000 0.00 0.00 0.00 4.02
1819 2288 4.772100 CACCAACCCAGAAACATTATTCCT 59.228 41.667 0.00 0.00 0.00 3.36
1865 2338 5.999483 GTAAACTACTTTTACTCCCGACG 57.001 43.478 0.60 0.00 44.37 5.12
1871 2344 5.938125 ACTACTTTTACTCCCGACGTACTTA 59.062 40.000 0.00 0.00 0.00 2.24
1937 2418 4.439289 GCCCATCAGCTAAACAATTCTCAC 60.439 45.833 0.00 0.00 0.00 3.51
1951 2432 7.219484 ACAATTCTCACCCATTAGAAGTTTG 57.781 36.000 0.00 0.00 35.32 2.93
1952 2433 7.004086 ACAATTCTCACCCATTAGAAGTTTGA 58.996 34.615 0.00 0.00 35.32 2.69
1954 2435 8.526147 CAATTCTCACCCATTAGAAGTTTGAAT 58.474 33.333 0.00 0.00 35.32 2.57
1955 2436 7.452880 TTCTCACCCATTAGAAGTTTGAATG 57.547 36.000 4.47 4.47 0.00 2.67
1956 2437 6.542821 TCTCACCCATTAGAAGTTTGAATGT 58.457 36.000 8.87 0.00 0.00 2.71
1957 2438 7.004086 TCTCACCCATTAGAAGTTTGAATGTT 58.996 34.615 8.87 0.00 0.00 2.71
1958 2439 7.505585 TCTCACCCATTAGAAGTTTGAATGTTT 59.494 33.333 8.87 0.00 0.00 2.83
1959 2440 7.432869 TCACCCATTAGAAGTTTGAATGTTTG 58.567 34.615 8.87 6.34 0.00 2.93
1960 2441 6.146021 CACCCATTAGAAGTTTGAATGTTTGC 59.854 38.462 8.87 0.00 0.00 3.68
1961 2442 5.345741 CCCATTAGAAGTTTGAATGTTTGCG 59.654 40.000 8.87 0.00 0.00 4.85
1962 2443 5.920273 CCATTAGAAGTTTGAATGTTTGCGT 59.080 36.000 8.87 0.00 0.00 5.24
1963 2444 7.081349 CCATTAGAAGTTTGAATGTTTGCGTA 58.919 34.615 8.87 0.00 0.00 4.42
1964 2445 7.593273 CCATTAGAAGTTTGAATGTTTGCGTAA 59.407 33.333 8.87 0.00 0.00 3.18
1965 2446 8.629986 CATTAGAAGTTTGAATGTTTGCGTAAG 58.370 33.333 3.60 0.00 43.44 2.34
1999 2480 6.972328 TGTACTGAAGAAGTTTGAATGTTTGC 59.028 34.615 0.00 0.00 40.56 3.68
2003 2484 6.556212 TGAAGAAGTTTGAATGTTTGCGTAA 58.444 32.000 0.00 0.00 0.00 3.18
2149 2630 0.038251 TGAACGTTCGCAGCATCTCT 60.038 50.000 22.48 0.00 0.00 3.10
2167 2648 1.069296 TCTGCGTCTTCAATTTTGCCG 60.069 47.619 0.00 0.00 0.00 5.69
2181 2662 0.753867 TTGCCGACCTACAAGTGTCA 59.246 50.000 0.00 0.00 0.00 3.58
2188 2669 4.025145 CCGACCTACAAGTGTCAGAAAAAC 60.025 45.833 0.00 0.00 0.00 2.43
2202 2689 6.601613 TGTCAGAAAAACAAAAGCTAAGGAGA 59.398 34.615 0.00 0.00 0.00 3.71
2203 2690 6.913132 GTCAGAAAAACAAAAGCTAAGGAGAC 59.087 38.462 0.00 0.00 0.00 3.36
2204 2691 6.601613 TCAGAAAAACAAAAGCTAAGGAGACA 59.398 34.615 0.00 0.00 0.00 3.41
2205 2692 6.914757 CAGAAAAACAAAAGCTAAGGAGACAG 59.085 38.462 0.00 0.00 0.00 3.51
2206 2693 6.828785 AGAAAAACAAAAGCTAAGGAGACAGA 59.171 34.615 0.00 0.00 0.00 3.41
2207 2694 6.378710 AAAACAAAAGCTAAGGAGACAGAC 57.621 37.500 0.00 0.00 0.00 3.51
2208 2695 4.689612 ACAAAAGCTAAGGAGACAGACA 57.310 40.909 0.00 0.00 0.00 3.41
2209 2696 5.036117 ACAAAAGCTAAGGAGACAGACAA 57.964 39.130 0.00 0.00 0.00 3.18
2210 2697 5.059833 ACAAAAGCTAAGGAGACAGACAAG 58.940 41.667 0.00 0.00 0.00 3.16
2211 2698 3.326836 AAGCTAAGGAGACAGACAAGC 57.673 47.619 0.00 0.00 0.00 4.01
2212 2699 2.251818 AGCTAAGGAGACAGACAAGCA 58.748 47.619 0.00 0.00 0.00 3.91
2213 2700 2.028567 AGCTAAGGAGACAGACAAGCAC 60.029 50.000 0.00 0.00 0.00 4.40
2214 2701 2.289072 GCTAAGGAGACAGACAAGCACA 60.289 50.000 0.00 0.00 0.00 4.57
2215 2702 3.618507 GCTAAGGAGACAGACAAGCACAT 60.619 47.826 0.00 0.00 0.00 3.21
2216 2703 3.498774 AAGGAGACAGACAAGCACATT 57.501 42.857 0.00 0.00 0.00 2.71
2217 2704 2.775890 AGGAGACAGACAAGCACATTG 58.224 47.619 0.00 0.00 45.01 2.82
2218 2705 1.198637 GGAGACAGACAAGCACATTGC 59.801 52.381 0.00 0.00 43.15 3.56
2232 2719 5.520022 GCACATTGCTTAAAAACTGGATG 57.480 39.130 0.00 0.00 40.96 3.51
2233 2720 4.389687 GCACATTGCTTAAAAACTGGATGG 59.610 41.667 0.00 0.00 40.96 3.51
2234 2721 5.782047 CACATTGCTTAAAAACTGGATGGA 58.218 37.500 0.00 0.00 0.00 3.41
2235 2722 6.400568 CACATTGCTTAAAAACTGGATGGAT 58.599 36.000 0.00 0.00 0.00 3.41
2236 2723 6.311935 CACATTGCTTAAAAACTGGATGGATG 59.688 38.462 0.00 0.00 0.00 3.51
2237 2724 4.454728 TGCTTAAAAACTGGATGGATGC 57.545 40.909 0.00 0.00 0.00 3.91
2238 2725 3.831333 TGCTTAAAAACTGGATGGATGCA 59.169 39.130 0.00 0.00 0.00 3.96
2239 2726 4.282957 TGCTTAAAAACTGGATGGATGCAA 59.717 37.500 0.00 0.00 0.00 4.08
2240 2727 4.866486 GCTTAAAAACTGGATGGATGCAAG 59.134 41.667 0.00 0.00 0.00 4.01
2241 2728 3.323751 AAAAACTGGATGGATGCAAGC 57.676 42.857 0.00 0.00 0.00 4.01
2242 2729 1.927487 AAACTGGATGGATGCAAGCA 58.073 45.000 0.00 0.00 0.00 3.91
2243 2730 1.927487 AACTGGATGGATGCAAGCAA 58.073 45.000 0.00 0.00 0.00 3.91
2244 2731 1.927487 ACTGGATGGATGCAAGCAAA 58.073 45.000 0.00 0.00 0.00 3.68
2245 2732 1.547372 ACTGGATGGATGCAAGCAAAC 59.453 47.619 0.00 0.00 0.00 2.93
2246 2733 1.546923 CTGGATGGATGCAAGCAAACA 59.453 47.619 0.00 1.53 0.00 2.83
2247 2734 2.167693 CTGGATGGATGCAAGCAAACAT 59.832 45.455 12.58 12.58 0.00 2.71
2248 2735 3.363627 TGGATGGATGCAAGCAAACATA 58.636 40.909 12.67 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 6.516739 TGTACTTCCGATCCATCATATCTC 57.483 41.667 0.00 0.00 0.00 2.75
98 107 8.196771 GGGATCACATATATGCAAAACAAAGAA 58.803 33.333 12.79 0.00 0.00 2.52
100 109 6.925165 GGGGATCACATATATGCAAAACAAAG 59.075 38.462 12.79 0.00 0.00 2.77
107 116 3.055167 CCGAGGGGATCACATATATGCAA 60.055 47.826 12.79 1.45 34.06 4.08
108 117 2.501316 CCGAGGGGATCACATATATGCA 59.499 50.000 12.79 0.00 34.06 3.96
125 134 1.069978 ACCAAAACAAAATGGCCCGAG 59.930 47.619 0.00 0.00 40.51 4.63
127 136 1.507562 GACCAAAACAAAATGGCCCG 58.492 50.000 0.00 0.00 40.51 6.13
156 165 8.742777 AGCATATAACTTCTTTGCTTGATCAAA 58.257 29.630 9.88 0.00 40.58 2.69
162 171 6.261826 AGGCTAGCATATAACTTCTTTGCTTG 59.738 38.462 18.24 1.00 43.08 4.01
166 175 7.559590 AACAGGCTAGCATATAACTTCTTTG 57.440 36.000 18.24 0.00 0.00 2.77
175 188 7.782897 ACATAGAGAAACAGGCTAGCATATA 57.217 36.000 18.24 0.00 0.00 0.86
194 207 4.214971 GCCAAGTGGAGCATGATTACATAG 59.785 45.833 0.18 0.00 37.39 2.23
201 218 1.561076 TGTAGCCAAGTGGAGCATGAT 59.439 47.619 0.18 0.00 37.39 2.45
203 220 1.376543 CTGTAGCCAAGTGGAGCATG 58.623 55.000 0.18 0.00 37.39 4.06
281 298 9.364989 CCTGCGGATTTCTTTTTCATTAAATTA 57.635 29.630 0.00 0.00 0.00 1.40
327 344 2.817839 GCCCTACCAAGTCAAACCACAT 60.818 50.000 0.00 0.00 0.00 3.21
333 350 1.302993 GGCGCCCTACCAAGTCAAA 60.303 57.895 18.11 0.00 0.00 2.69
437 458 6.312399 ACAAGAGCGATTTGTTATTGTTCA 57.688 33.333 0.00 0.00 39.76 3.18
444 468 7.441890 TTTATGGAACAAGAGCGATTTGTTA 57.558 32.000 13.62 3.58 45.82 2.41
517 541 8.013378 ACGAGTAATGCTACAAACAACATAAAC 58.987 33.333 0.00 0.00 0.00 2.01
519 543 7.661127 ACGAGTAATGCTACAAACAACATAA 57.339 32.000 0.00 0.00 0.00 1.90
530 584 5.577164 ACTTGACATGAACGAGTAATGCTAC 59.423 40.000 0.00 0.00 31.17 3.58
533 587 4.928661 ACTTGACATGAACGAGTAATGC 57.071 40.909 0.00 0.00 31.17 3.56
552 606 3.514309 ACTAGTTGCGAGGATAACCAACT 59.486 43.478 9.45 9.45 46.66 3.16
615 736 9.766754 ACATCATGGATAGATAGATTACACTCT 57.233 33.333 0.00 0.00 0.00 3.24
628 749 5.894298 AGTTGCCTAACATCATGGATAGA 57.106 39.130 0.00 0.00 39.30 1.98
629 750 6.014242 TCCTAGTTGCCTAACATCATGGATAG 60.014 42.308 0.00 0.00 39.30 2.08
630 751 5.843969 TCCTAGTTGCCTAACATCATGGATA 59.156 40.000 0.00 0.00 39.30 2.59
631 752 4.660303 TCCTAGTTGCCTAACATCATGGAT 59.340 41.667 0.00 0.00 39.30 3.41
632 753 4.037222 TCCTAGTTGCCTAACATCATGGA 58.963 43.478 0.00 0.00 39.30 3.41
633 754 4.130118 GTCCTAGTTGCCTAACATCATGG 58.870 47.826 0.00 0.00 39.30 3.66
634 755 5.028549 AGTCCTAGTTGCCTAACATCATG 57.971 43.478 0.00 0.00 39.30 3.07
635 756 5.221263 CGTAGTCCTAGTTGCCTAACATCAT 60.221 44.000 0.00 0.00 39.30 2.45
636 757 4.097437 CGTAGTCCTAGTTGCCTAACATCA 59.903 45.833 0.00 0.00 39.30 3.07
637 758 4.337555 TCGTAGTCCTAGTTGCCTAACATC 59.662 45.833 0.00 0.00 39.30 3.06
640 761 4.499357 CCATCGTAGTCCTAGTTGCCTAAC 60.499 50.000 0.00 0.00 37.06 2.34
641 762 3.635373 CCATCGTAGTCCTAGTTGCCTAA 59.365 47.826 0.00 0.00 0.00 2.69
658 786 3.484557 CCCGAAAAATTACACGACCATCG 60.485 47.826 0.00 0.00 46.93 3.84
663 791 6.996562 AAATTTCCCGAAAAATTACACGAC 57.003 33.333 7.76 0.00 37.75 4.34
664 792 7.040548 AGGTAAATTTCCCGAAAAATTACACGA 60.041 33.333 19.78 0.47 37.75 4.35
667 795 9.911138 GTAAGGTAAATTTCCCGAAAAATTACA 57.089 29.630 19.78 7.18 37.75 2.41
679 807 5.712917 TGACACCATGGTAAGGTAAATTTCC 59.287 40.000 19.28 0.00 37.23 3.13
689 817 1.742761 CCAGCTGACACCATGGTAAG 58.257 55.000 19.28 16.18 0.00 2.34
691 819 1.299648 GCCAGCTGACACCATGGTA 59.700 57.895 19.28 0.39 35.17 3.25
692 820 2.034687 GCCAGCTGACACCATGGT 59.965 61.111 17.39 13.00 35.17 3.55
693 821 2.753043 GGCCAGCTGACACCATGG 60.753 66.667 17.39 11.19 35.84 3.66
700 1060 0.613012 AAATCCTTGGGCCAGCTGAC 60.613 55.000 17.39 2.25 0.00 3.51
782 1145 0.779997 ACCTCCCACTGCCTGAAATT 59.220 50.000 0.00 0.00 0.00 1.82
805 1172 3.504134 ACGGTATGATTGAGAGAGATCGG 59.496 47.826 0.00 0.00 0.00 4.18
866 1233 5.280062 CCGTGTGATATAGAGGAGGTAGAGA 60.280 48.000 0.00 0.00 0.00 3.10
868 1235 4.350225 ACCGTGTGATATAGAGGAGGTAGA 59.650 45.833 0.00 0.00 0.00 2.59
870 1237 4.350225 AGACCGTGTGATATAGAGGAGGTA 59.650 45.833 0.00 0.00 0.00 3.08
871 1238 3.138653 AGACCGTGTGATATAGAGGAGGT 59.861 47.826 0.00 0.00 0.00 3.85
872 1239 3.757270 AGACCGTGTGATATAGAGGAGG 58.243 50.000 0.00 0.00 0.00 4.30
899 1266 9.945904 CGAGAGACCTGGCTGTATATATATATA 57.054 37.037 8.16 8.16 0.00 0.86
900 1267 7.392113 GCGAGAGACCTGGCTGTATATATATAT 59.608 40.741 10.10 10.10 40.43 0.86
901 1268 6.711194 GCGAGAGACCTGGCTGTATATATATA 59.289 42.308 0.00 0.00 40.43 0.86
902 1269 5.533154 GCGAGAGACCTGGCTGTATATATAT 59.467 44.000 0.00 0.00 40.43 0.86
952 1319 3.625082 GAAATGCAACGTGCCGGGG 62.625 63.158 2.18 0.00 44.23 5.73
990 1365 3.244735 CCAGATCCCTCATCGTCTCTCTA 60.245 52.174 0.00 0.00 36.50 2.43
1256 1651 2.415608 ATGTCAGATCGGCGTCGGT 61.416 57.895 10.62 0.00 36.95 4.69
1259 1654 1.227089 AGCATGTCAGATCGGCGTC 60.227 57.895 6.85 3.93 0.00 5.19
1260 1655 1.520120 CAGCATGTCAGATCGGCGT 60.520 57.895 6.85 0.00 0.00 5.68
1269 1664 3.956305 ATGTCGCCGCAGCATGTCA 62.956 57.895 0.00 0.00 39.83 3.58
1270 1665 3.160557 GATGTCGCCGCAGCATGTC 62.161 63.158 0.00 0.00 39.83 3.06
1271 1666 3.197790 GATGTCGCCGCAGCATGT 61.198 61.111 0.00 0.00 39.83 3.21
1272 1667 3.945434 GGATGTCGCCGCAGCATG 61.945 66.667 1.89 0.00 39.83 4.06
1273 1668 4.166888 AGGATGTCGCCGCAGCAT 62.167 61.111 0.00 0.00 39.83 3.79
1285 1680 0.790207 CCAACGACGTGAACAGGATG 59.210 55.000 0.00 0.00 46.00 3.51
1287 1682 1.593209 GCCAACGACGTGAACAGGA 60.593 57.895 0.00 0.00 0.00 3.86
1289 1684 1.424403 TATGCCAACGACGTGAACAG 58.576 50.000 0.00 0.00 0.00 3.16
1290 1685 1.996898 GATATGCCAACGACGTGAACA 59.003 47.619 0.00 0.00 0.00 3.18
1291 1686 1.996898 TGATATGCCAACGACGTGAAC 59.003 47.619 0.00 0.00 0.00 3.18
1292 1687 2.371910 TGATATGCCAACGACGTGAA 57.628 45.000 0.00 0.00 0.00 3.18
1293 1688 2.200899 CATGATATGCCAACGACGTGA 58.799 47.619 0.00 0.00 0.00 4.35
1295 1690 1.581934 CCATGATATGCCAACGACGT 58.418 50.000 0.00 0.00 0.00 4.34
1296 1691 0.235665 GCCATGATATGCCAACGACG 59.764 55.000 0.00 0.00 0.00 5.12
1297 1692 0.235665 CGCCATGATATGCCAACGAC 59.764 55.000 0.00 0.00 0.00 4.34
1298 1693 0.179059 ACGCCATGATATGCCAACGA 60.179 50.000 0.00 0.00 0.00 3.85
1306 1701 1.202521 TCGAAGCACACGCCATGATAT 60.203 47.619 0.00 0.00 39.83 1.63
1337 1734 2.736670 ACATTATGAACAGGAGGGCC 57.263 50.000 0.00 0.00 0.00 5.80
1338 1735 4.096984 CAGAAACATTATGAACAGGAGGGC 59.903 45.833 0.00 0.00 0.00 5.19
1340 1737 6.824305 AACAGAAACATTATGAACAGGAGG 57.176 37.500 0.00 0.00 0.00 4.30
1341 1738 8.571336 AGAAAACAGAAACATTATGAACAGGAG 58.429 33.333 0.00 0.00 0.00 3.69
1342 1739 8.463930 AGAAAACAGAAACATTATGAACAGGA 57.536 30.769 0.00 0.00 0.00 3.86
1343 1740 7.809806 GGAGAAAACAGAAACATTATGAACAGG 59.190 37.037 0.00 0.00 0.00 4.00
1344 1741 8.571336 AGGAGAAAACAGAAACATTATGAACAG 58.429 33.333 0.00 0.00 0.00 3.16
1380 1777 7.536281 ACAAAATTAATAAGAAACGAAGGCGAC 59.464 33.333 0.00 0.00 41.64 5.19
1383 1793 8.644619 GGAACAAAATTAATAAGAAACGAAGGC 58.355 33.333 0.00 0.00 0.00 4.35
1399 1809 5.046448 TGCTTGCATCCATAGGAACAAAATT 60.046 36.000 0.00 0.00 33.53 1.82
1405 1815 4.454728 TTTTGCTTGCATCCATAGGAAC 57.545 40.909 0.00 0.00 34.34 3.62
1409 1819 4.275689 TCCGTATTTTGCTTGCATCCATAG 59.724 41.667 0.00 0.00 0.00 2.23
1421 1831 7.250569 TGAATGATTTCTTCTCCGTATTTTGC 58.749 34.615 0.00 0.00 32.78 3.68
1422 1832 9.624697 TTTGAATGATTTCTTCTCCGTATTTTG 57.375 29.630 0.00 0.00 32.78 2.44
1427 1837 9.667107 AGTTATTTGAATGATTTCTTCTCCGTA 57.333 29.630 0.00 0.00 32.78 4.02
1429 1839 7.848051 CGAGTTATTTGAATGATTTCTTCTCCG 59.152 37.037 0.00 0.00 32.78 4.63
1431 1841 8.669243 ACCGAGTTATTTGAATGATTTCTTCTC 58.331 33.333 0.00 0.00 32.78 2.87
1433 1843 9.626045 AAACCGAGTTATTTGAATGATTTCTTC 57.374 29.630 0.00 0.00 32.78 2.87
1434 1844 9.981114 AAAACCGAGTTATTTGAATGATTTCTT 57.019 25.926 0.00 0.00 32.78 2.52
1435 1845 9.981114 AAAAACCGAGTTATTTGAATGATTTCT 57.019 25.926 0.00 0.00 32.78 2.52
1502 1942 3.056821 TGCTACAGAGTTACACGATTGCT 60.057 43.478 0.00 0.00 0.00 3.91
1508 1948 2.993220 TGCATTGCTACAGAGTTACACG 59.007 45.455 10.49 0.00 0.00 4.49
1512 1952 4.191544 GGTCATGCATTGCTACAGAGTTA 58.808 43.478 10.49 0.00 0.00 2.24
1520 1960 2.106477 TTCGTGGTCATGCATTGCTA 57.894 45.000 10.49 0.00 0.00 3.49
1521 1961 1.246649 TTTCGTGGTCATGCATTGCT 58.753 45.000 10.49 0.00 0.00 3.91
1532 1972 4.253685 CATGGACTACAGATTTTCGTGGT 58.746 43.478 0.00 0.00 0.00 4.16
1537 1977 2.939103 AGCGCATGGACTACAGATTTTC 59.061 45.455 11.47 0.00 0.00 2.29
1579 2027 5.163227 TGCTGAATGAGGAGCATCTAGAAAT 60.163 40.000 0.00 0.00 40.30 2.17
1591 2046 2.354503 GCTTCTCTGTGCTGAATGAGGA 60.355 50.000 0.00 0.00 0.00 3.71
1600 2055 0.321475 GAGGCTTGCTTCTCTGTGCT 60.321 55.000 0.00 0.00 0.00 4.40
1606 2061 3.254166 TGAAACATTGAGGCTTGCTTCTC 59.746 43.478 6.31 0.00 0.00 2.87
1611 2070 4.309099 TGAAATGAAACATTGAGGCTTGC 58.691 39.130 0.00 0.00 0.00 4.01
1618 2077 4.766891 GGGGAGACTGAAATGAAACATTGA 59.233 41.667 0.00 0.00 0.00 2.57
1729 2189 0.734889 CGGTTGATGTGAATGCCTCC 59.265 55.000 0.00 0.00 0.00 4.30
1747 2207 2.674852 CCATCCTGAACATCACTTCACG 59.325 50.000 0.00 0.00 0.00 4.35
1799 2259 5.982890 ACAGGAATAATGTTTCTGGGTTG 57.017 39.130 3.10 0.00 0.00 3.77
1861 2334 0.732571 TTACGGGGCTAAGTACGTCG 59.267 55.000 0.00 0.00 40.38 5.12
1862 2335 2.017049 TCTTACGGGGCTAAGTACGTC 58.983 52.381 0.00 0.00 40.38 4.34
1863 2336 2.128771 TCTTACGGGGCTAAGTACGT 57.871 50.000 0.00 0.00 42.71 3.57
1864 2337 3.722728 AATCTTACGGGGCTAAGTACG 57.277 47.619 0.00 0.00 0.00 3.67
1908 2386 4.027674 TGTTTAGCTGATGGGCAAAGTA 57.972 40.909 0.00 0.00 34.17 2.24
1909 2387 2.875296 TGTTTAGCTGATGGGCAAAGT 58.125 42.857 0.00 0.00 34.17 2.66
1937 2418 5.345741 CGCAAACATTCAAACTTCTAATGGG 59.654 40.000 0.00 0.00 35.40 4.00
1951 2432 3.679980 TCTGAGAGCTTACGCAAACATTC 59.320 43.478 0.00 0.00 39.10 2.67
1952 2433 3.664107 TCTGAGAGCTTACGCAAACATT 58.336 40.909 0.00 0.00 39.10 2.71
1954 2435 2.812358 TCTGAGAGCTTACGCAAACA 57.188 45.000 0.00 0.00 39.10 2.83
1955 2436 2.996621 ACATCTGAGAGCTTACGCAAAC 59.003 45.455 0.00 0.00 39.10 2.93
1956 2437 3.319137 ACATCTGAGAGCTTACGCAAA 57.681 42.857 0.00 0.00 39.10 3.68
1957 2438 3.444034 AGTACATCTGAGAGCTTACGCAA 59.556 43.478 0.00 0.00 39.10 4.85
1958 2439 3.017442 AGTACATCTGAGAGCTTACGCA 58.983 45.455 0.00 0.00 39.10 5.24
1959 2440 3.065510 TCAGTACATCTGAGAGCTTACGC 59.934 47.826 0.00 0.00 46.77 4.42
1960 2441 4.884458 TCAGTACATCTGAGAGCTTACG 57.116 45.455 0.00 0.00 46.77 3.18
1970 2451 8.092521 ACATTCAAACTTCTTCAGTACATCTG 57.907 34.615 0.00 0.00 44.85 2.90
1971 2452 8.682936 AACATTCAAACTTCTTCAGTACATCT 57.317 30.769 0.00 0.00 32.94 2.90
1972 2453 9.173939 CAAACATTCAAACTTCTTCAGTACATC 57.826 33.333 0.00 0.00 32.94 3.06
1973 2454 7.649306 GCAAACATTCAAACTTCTTCAGTACAT 59.351 33.333 0.00 0.00 32.94 2.29
1974 2455 6.972328 GCAAACATTCAAACTTCTTCAGTACA 59.028 34.615 0.00 0.00 32.94 2.90
1975 2456 6.140737 CGCAAACATTCAAACTTCTTCAGTAC 59.859 38.462 0.00 0.00 32.94 2.73
1976 2457 6.183360 ACGCAAACATTCAAACTTCTTCAGTA 60.183 34.615 0.00 0.00 32.94 2.74
1977 2458 5.036737 CGCAAACATTCAAACTTCTTCAGT 58.963 37.500 0.00 0.00 37.30 3.41
1978 2459 5.036737 ACGCAAACATTCAAACTTCTTCAG 58.963 37.500 0.00 0.00 0.00 3.02
1979 2460 4.992688 ACGCAAACATTCAAACTTCTTCA 58.007 34.783 0.00 0.00 0.00 3.02
1980 2461 6.345015 GCTTACGCAAACATTCAAACTTCTTC 60.345 38.462 0.00 0.00 35.78 2.87
1981 2462 5.458779 GCTTACGCAAACATTCAAACTTCTT 59.541 36.000 0.00 0.00 35.78 2.52
1982 2463 4.976116 GCTTACGCAAACATTCAAACTTCT 59.024 37.500 0.00 0.00 35.78 2.85
1983 2464 4.976116 AGCTTACGCAAACATTCAAACTTC 59.024 37.500 0.00 0.00 39.10 3.01
1984 2465 4.932146 AGCTTACGCAAACATTCAAACTT 58.068 34.783 0.00 0.00 39.10 2.66
1985 2466 4.275936 AGAGCTTACGCAAACATTCAAACT 59.724 37.500 0.00 0.00 39.10 2.66
1986 2467 4.537015 AGAGCTTACGCAAACATTCAAAC 58.463 39.130 0.00 0.00 39.10 2.93
1987 2468 4.274705 TGAGAGCTTACGCAAACATTCAAA 59.725 37.500 0.00 0.00 39.10 2.69
1988 2469 3.812609 TGAGAGCTTACGCAAACATTCAA 59.187 39.130 0.00 0.00 39.10 2.69
1989 2470 3.398406 TGAGAGCTTACGCAAACATTCA 58.602 40.909 0.00 0.00 39.10 2.57
1990 2471 3.679980 TCTGAGAGCTTACGCAAACATTC 59.320 43.478 0.00 0.00 39.10 2.67
1991 2472 3.664107 TCTGAGAGCTTACGCAAACATT 58.336 40.909 0.00 0.00 39.10 2.71
1995 2476 3.319137 ACATCTGAGAGCTTACGCAAA 57.681 42.857 0.00 0.00 39.10 3.68
1999 2480 4.884458 TCAGTACATCTGAGAGCTTACG 57.116 45.455 0.00 0.00 46.77 3.18
2013 2494 2.288025 GGCGAGGGGGTTCAGTACA 61.288 63.158 0.00 0.00 0.00 2.90
2149 2630 0.947960 TCGGCAAAATTGAAGACGCA 59.052 45.000 0.00 0.00 0.00 5.24
2152 2633 3.500680 TGTAGGTCGGCAAAATTGAAGAC 59.499 43.478 10.80 10.80 36.26 3.01
2158 2639 3.219281 ACACTTGTAGGTCGGCAAAATT 58.781 40.909 0.00 0.00 0.00 1.82
2167 2648 6.431198 TTGTTTTTCTGACACTTGTAGGTC 57.569 37.500 0.00 0.00 34.63 3.85
2181 2662 6.828785 TCTGTCTCCTTAGCTTTTGTTTTTCT 59.171 34.615 0.00 0.00 0.00 2.52
2188 2669 4.083590 GCTTGTCTGTCTCCTTAGCTTTTG 60.084 45.833 0.00 0.00 0.00 2.44
2210 2697 4.389687 CCATCCAGTTTTTAAGCAATGTGC 59.610 41.667 0.00 0.00 45.46 4.57
2211 2698 5.782047 TCCATCCAGTTTTTAAGCAATGTG 58.218 37.500 0.00 0.00 0.00 3.21
2212 2699 6.400568 CATCCATCCAGTTTTTAAGCAATGT 58.599 36.000 0.00 0.00 0.00 2.71
2213 2700 5.292589 GCATCCATCCAGTTTTTAAGCAATG 59.707 40.000 0.00 0.00 0.00 2.82
2214 2701 5.046448 TGCATCCATCCAGTTTTTAAGCAAT 60.046 36.000 0.00 0.00 0.00 3.56
2215 2702 4.282957 TGCATCCATCCAGTTTTTAAGCAA 59.717 37.500 0.00 0.00 0.00 3.91
2216 2703 3.831333 TGCATCCATCCAGTTTTTAAGCA 59.169 39.130 0.00 0.00 0.00 3.91
2217 2704 4.454728 TGCATCCATCCAGTTTTTAAGC 57.545 40.909 0.00 0.00 0.00 3.09
2218 2705 4.866486 GCTTGCATCCATCCAGTTTTTAAG 59.134 41.667 0.00 0.00 0.00 1.85
2219 2706 4.282957 TGCTTGCATCCATCCAGTTTTTAA 59.717 37.500 0.00 0.00 0.00 1.52
2220 2707 3.831333 TGCTTGCATCCATCCAGTTTTTA 59.169 39.130 0.00 0.00 0.00 1.52
2221 2708 2.633967 TGCTTGCATCCATCCAGTTTTT 59.366 40.909 0.00 0.00 0.00 1.94
2222 2709 2.250031 TGCTTGCATCCATCCAGTTTT 58.750 42.857 0.00 0.00 0.00 2.43
2223 2710 1.927487 TGCTTGCATCCATCCAGTTT 58.073 45.000 0.00 0.00 0.00 2.66
2224 2711 1.927487 TTGCTTGCATCCATCCAGTT 58.073 45.000 0.00 0.00 0.00 3.16
2225 2712 1.547372 GTTTGCTTGCATCCATCCAGT 59.453 47.619 0.00 0.00 0.00 4.00
2226 2713 1.546923 TGTTTGCTTGCATCCATCCAG 59.453 47.619 0.00 0.00 0.00 3.86
2227 2714 1.630223 TGTTTGCTTGCATCCATCCA 58.370 45.000 0.00 0.00 0.00 3.41
2228 2715 2.973694 ATGTTTGCTTGCATCCATCC 57.026 45.000 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.