Multiple sequence alignment - TraesCS7B01G493800

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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 TraesCS7B01G493800 chr7B 100.000 2291 0 0 1 2291 745102028 745104318 0.000000e+00 4231.0
1 TraesCS7B01G493800 chr7B 86.660 1057 137 4 781 1835 747290576 747291630 0.000000e+00 1168.0
2 TraesCS7B01G493800 chr7B 86.312 789 80 15 1 771 747289551 747290329 0.000000e+00 833.0
3 TraesCS7B01G493800 chr7B 92.520 254 17 2 2040 2291 747291682 747291935 1.670000e-96 363.0
4 TraesCS7B01G493800 chr7B 87.838 222 21 2 542 757 746383764 746383543 2.920000e-64 255.0
5 TraesCS7B01G493800 chr7B 75.806 558 104 20 838 1387 31795035 31794501 1.050000e-63 254.0
6 TraesCS7B01G493800 chr7B 72.642 424 105 11 889 1307 746298083 746298500 1.850000e-26 130.0
7 TraesCS7B01G493800 chr7B 72.684 421 104 11 892 1307 746439963 746439549 1.850000e-26 130.0
8 TraesCS7B01G493800 chr7D 88.486 773 82 3 776 1545 633151611 633152379 0.000000e+00 928.0
9 TraesCS7B01G493800 chr7D 88.486 773 82 3 776 1545 633202176 633201408 0.000000e+00 928.0
10 TraesCS7B01G493800 chr7D 89.080 696 72 2 776 1467 633030119 633029424 0.000000e+00 861.0
11 TraesCS7B01G493800 chr7D 86.136 779 89 14 1 769 633031144 633030375 0.000000e+00 822.0
12 TraesCS7B01G493800 chr7D 86.194 775 81 12 1 769 633150619 633151373 0.000000e+00 815.0
13 TraesCS7B01G493800 chr7D 86.194 775 81 12 1 769 633203168 633202414 0.000000e+00 815.0
14 TraesCS7B01G493800 chr7D 92.308 182 13 1 2111 2291 633029028 633028847 8.120000e-65 257.0
15 TraesCS7B01G493800 chr7D 93.182 176 11 1 2117 2291 633152750 633152925 8.120000e-65 257.0
16 TraesCS7B01G493800 chr7D 93.182 176 11 1 2117 2291 633201037 633200862 8.120000e-65 257.0
17 TraesCS7B01G493800 chr7D 87.805 164 17 1 1497 1660 633029428 633029268 3.000000e-44 189.0
18 TraesCS7B01G493800 chr4B 85.294 68 7 3 1495 1562 634317888 634317952 1.470000e-07 67.6


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7B01G493800 chr7B 745102028 745104318 2290 False 4231.000000 4231 100.000000 1 2291 1 chr7B.!!$F1 2290
1 TraesCS7B01G493800 chr7B 747289551 747291935 2384 False 788.000000 1168 88.497333 1 2291 3 chr7B.!!$F3 2290
2 TraesCS7B01G493800 chr7B 31794501 31795035 534 True 254.000000 254 75.806000 838 1387 1 chr7B.!!$R1 549
3 TraesCS7B01G493800 chr7D 633150619 633152925 2306 False 666.666667 928 89.287333 1 2291 3 chr7D.!!$F1 2290
4 TraesCS7B01G493800 chr7D 633200862 633203168 2306 True 666.666667 928 89.287333 1 2291 3 chr7D.!!$R2 2290
5 TraesCS7B01G493800 chr7D 633028847 633031144 2297 True 532.250000 861 88.832250 1 2291 4 chr7D.!!$R1 2290

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
547 573 0.035439 GGTCCAGGGCGAAGAATCAA 60.035 55.0 0.0 0.0 0.0 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1947 2241 0.037326 ACATACACGTGGTGCTCCTG 60.037 55.0 21.57 8.34 36.98 3.86 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
44 45 6.713903 ACAGGATGCTAATCATATGTTTCCTG 59.286 38.462 20.41 20.41 42.53 3.86
113 114 3.617045 GCCATTTGCAAGCCAGATTGTTA 60.617 43.478 0.00 0.00 40.77 2.41
132 133 4.536090 TGTTAACCCATCAGATCAAGACCT 59.464 41.667 2.48 0.00 0.00 3.85
162 163 1.118838 TGGTTTCCCAAACTGCAAGG 58.881 50.000 0.00 0.00 41.14 3.61
176 177 2.615912 CTGCAAGGGCTTTGTATAGAGC 59.384 50.000 11.21 0.00 41.91 4.09
188 189 5.939764 TTGTATAGAGCAGTGTCCAGAAT 57.060 39.130 0.00 0.00 0.00 2.40
197 198 4.275936 AGCAGTGTCCAGAATTGTTGTTAC 59.724 41.667 0.00 0.00 0.00 2.50
226 227 3.922171 ATCCCATGGACTGAAACTCTC 57.078 47.619 15.22 0.00 32.98 3.20
236 237 4.021016 GGACTGAAACTCTCCATAGTGTGT 60.021 45.833 0.00 0.00 30.07 3.72
264 265 9.239002 CATAAGTGATGTAAAGCTACTAGACAC 57.761 37.037 0.00 0.00 0.00 3.67
269 270 4.730657 TGTAAAGCTACTAGACACGCTTC 58.269 43.478 0.00 0.00 41.44 3.86
271 272 5.645067 TGTAAAGCTACTAGACACGCTTCTA 59.355 40.000 0.00 0.00 41.44 2.10
281 282 5.584253 AGACACGCTTCTATACTCAACAT 57.416 39.130 0.00 0.00 0.00 2.71
282 283 5.583495 AGACACGCTTCTATACTCAACATC 58.417 41.667 0.00 0.00 0.00 3.06
283 284 5.125578 AGACACGCTTCTATACTCAACATCA 59.874 40.000 0.00 0.00 0.00 3.07
290 291 7.212976 GCTTCTATACTCAACATCATCCTTCA 58.787 38.462 0.00 0.00 0.00 3.02
292 293 9.205719 CTTCTATACTCAACATCATCCTTCATG 57.794 37.037 0.00 0.00 0.00 3.07
309 316 5.188359 CCTTCATGGGAGGATTTGAAATTGT 59.812 40.000 9.67 0.00 0.00 2.71
310 317 6.296030 CCTTCATGGGAGGATTTGAAATTGTT 60.296 38.462 9.67 0.00 0.00 2.83
321 328 6.372381 GGATTTGAAATTGTTGGAAAGGATGG 59.628 38.462 0.00 0.00 0.00 3.51
341 348 3.261643 TGGTTTGCAGAGCTTAGATGAGA 59.738 43.478 8.01 0.00 0.00 3.27
388 405 1.272490 CTTGAGCGTCTGGTACTCCAA 59.728 52.381 0.00 0.00 43.81 3.53
456 473 5.991606 CACTGAAGAAGTTGATTGTACTGGA 59.008 40.000 0.00 0.00 36.83 3.86
464 481 8.105829 AGAAGTTGATTGTACTGGATTCAGAAT 58.894 33.333 8.39 0.00 43.49 2.40
495 521 1.826096 GTAGAGGGTTCAGAGGGTGAC 59.174 57.143 0.00 0.00 33.71 3.67
511 537 1.965930 GACGTGGAATGGCAGCACA 60.966 57.895 0.00 0.00 0.00 4.57
540 566 1.488705 ATCTTGTGGTCCAGGGCGAA 61.489 55.000 0.00 0.00 0.00 4.70
547 573 0.035439 GGTCCAGGGCGAAGAATCAA 60.035 55.000 0.00 0.00 0.00 2.57
596 622 3.318191 CCTCCCAAGGCTCTCCAG 58.682 66.667 0.00 0.00 35.37 3.86
597 623 1.614824 CCTCCCAAGGCTCTCCAGT 60.615 63.158 0.00 0.00 35.37 4.00
598 624 1.621672 CCTCCCAAGGCTCTCCAGTC 61.622 65.000 0.00 0.00 35.37 3.51
601 627 0.906756 CCCAAGGCTCTCCAGTCTGA 60.907 60.000 0.00 0.00 33.59 3.27
602 628 0.248843 CCAAGGCTCTCCAGTCTGAC 59.751 60.000 0.00 0.00 33.59 3.51
603 629 1.265236 CAAGGCTCTCCAGTCTGACT 58.735 55.000 4.06 4.06 33.59 3.41
608 634 2.622942 GGCTCTCCAGTCTGACTATCAG 59.377 54.545 10.47 6.73 45.59 2.90
609 635 3.287222 GCTCTCCAGTCTGACTATCAGT 58.713 50.000 10.47 0.00 44.58 3.41
611 637 4.515191 GCTCTCCAGTCTGACTATCAGTAG 59.485 50.000 10.47 5.10 44.58 2.57
612 638 5.042463 TCTCCAGTCTGACTATCAGTAGG 57.958 47.826 10.47 5.90 44.58 3.18
616 642 5.191124 TCCAGTCTGACTATCAGTAGGTGTA 59.809 44.000 10.47 0.00 44.58 2.90
617 643 5.529430 CCAGTCTGACTATCAGTAGGTGTAG 59.471 48.000 10.47 0.00 44.58 2.74
622 648 6.319152 TCTGACTATCAGTAGGTGTAGAAAGC 59.681 42.308 5.77 0.00 44.58 3.51
624 650 6.663953 TGACTATCAGTAGGTGTAGAAAGCTT 59.336 38.462 0.00 0.00 31.96 3.74
637 663 3.490348 AGAAAGCTTACACAACTGGCAT 58.510 40.909 0.00 0.00 0.00 4.40
643 669 0.251564 TACACAACTGGCATTGGGGG 60.252 55.000 13.78 0.00 37.30 5.40
654 680 1.000739 ATTGGGGGTGGATGTGCAG 59.999 57.895 0.00 0.00 0.00 4.41
662 688 1.001181 GGTGGATGTGCAGCAAACAAT 59.999 47.619 0.00 0.00 0.00 2.71
663 689 2.548493 GGTGGATGTGCAGCAAACAATT 60.548 45.455 0.00 0.00 0.00 2.32
664 690 2.733026 GTGGATGTGCAGCAAACAATTC 59.267 45.455 0.00 0.00 0.00 2.17
665 691 2.629137 TGGATGTGCAGCAAACAATTCT 59.371 40.909 0.00 0.00 0.00 2.40
668 694 3.287312 TGTGCAGCAAACAATTCTAGC 57.713 42.857 0.00 0.00 0.00 3.42
670 696 3.067883 TGTGCAGCAAACAATTCTAGCAA 59.932 39.130 0.00 0.00 32.03 3.91
671 697 4.050553 GTGCAGCAAACAATTCTAGCAAA 58.949 39.130 0.00 0.00 32.03 3.68
673 699 5.006552 GTGCAGCAAACAATTCTAGCAAAAA 59.993 36.000 0.00 0.00 32.03 1.94
681 713 6.633500 ACAATTCTAGCAAAAACAGCTACA 57.367 33.333 0.00 0.00 43.25 2.74
695 727 1.519719 CTACAGAGGTGGAGCAGGC 59.480 63.158 0.00 0.00 0.00 4.85
715 747 5.296283 CAGGCGAAAGAAGAAGATGATTCAT 59.704 40.000 0.00 0.00 0.00 2.57
741 773 1.379576 GCTCTTGCCTGCCCATCTT 60.380 57.895 0.00 0.00 0.00 2.40
759 791 3.230976 TCTTTCTGACTCACTGCAGGTA 58.769 45.455 19.93 4.23 33.05 3.08
765 797 2.234661 TGACTCACTGCAGGTATTGAGG 59.765 50.000 26.68 14.41 39.91 3.86
785 1066 7.437713 TGAGGATCATAGACTTAACCATTGT 57.562 36.000 0.00 0.00 42.56 2.71
814 1095 3.564133 CCCTGGATTCTTTGTTGGATGGA 60.564 47.826 0.00 0.00 0.00 3.41
833 1114 2.354805 GGAATCAGGAGTTACAACCGCT 60.355 50.000 0.00 0.00 0.00 5.52
835 1116 1.334160 TCAGGAGTTACAACCGCTGA 58.666 50.000 0.00 0.00 0.00 4.26
836 1117 1.272490 TCAGGAGTTACAACCGCTGAG 59.728 52.381 0.00 0.00 0.00 3.35
849 1133 1.133976 CCGCTGAGGAATGGAGGAAAT 60.134 52.381 0.00 0.00 45.00 2.17
876 1160 1.336125 GAACTGCAGCAGCTTGTTTCT 59.664 47.619 23.05 0.00 42.74 2.52
882 1166 0.185901 AGCAGCTTGTTTCTCCCCAA 59.814 50.000 0.00 0.00 0.00 4.12
923 1207 0.249784 CTCCAGACGGATGATGCCAG 60.250 60.000 0.00 0.00 41.79 4.85
945 1229 1.071385 GGACTCCTATCTGTGCCCATG 59.929 57.143 0.00 0.00 0.00 3.66
979 1263 1.452226 TTCCTCCCTCACCCTCCTGA 61.452 60.000 0.00 0.00 0.00 3.86
989 1273 1.349026 CACCCTCCTGAGCTTTTCTGA 59.651 52.381 0.00 0.00 0.00 3.27
1027 1311 3.851098 CGCTTTACTAAGGAGCAAGAGT 58.149 45.455 0.00 0.00 36.22 3.24
1039 1323 2.409948 GCAAGAGTATGCCCTTCACT 57.590 50.000 0.00 0.00 40.49 3.41
1060 1344 1.544825 CCTCGTCTCCCTCCAGCAAA 61.545 60.000 0.00 0.00 0.00 3.68
1063 1347 2.366916 CTCGTCTCCCTCCAGCAAATAT 59.633 50.000 0.00 0.00 0.00 1.28
1069 1353 4.949856 TCTCCCTCCAGCAAATATTGTTTC 59.050 41.667 0.00 0.00 0.00 2.78
1129 1413 0.746659 AAAGCACACCAACCTCAAGC 59.253 50.000 0.00 0.00 0.00 4.01
1141 1425 2.699954 ACCTCAAGCAATTAGTGGTCG 58.300 47.619 0.00 0.00 36.79 4.79
1142 1426 2.038557 ACCTCAAGCAATTAGTGGTCGT 59.961 45.455 0.00 0.00 36.79 4.34
1173 1457 4.373116 GTCCGGTCGCTGCCAGAA 62.373 66.667 0.00 0.00 0.00 3.02
1218 1502 5.769662 TCAAGAATTAAATGTCTGCCACTGT 59.230 36.000 0.00 0.00 0.00 3.55
1282 1566 3.377573 ACCATCCCAAAAATCATCCTGG 58.622 45.455 0.00 0.00 0.00 4.45
1350 1635 0.107456 CCATCACTTCCCAGATCCCG 59.893 60.000 0.00 0.00 0.00 5.14
1430 1716 4.704833 GCAGGTCGCTGCCTTGGA 62.705 66.667 3.86 0.00 43.99 3.53
1478 1765 6.873605 CCTTGTACACTTGTCACATAGATGAA 59.126 38.462 0.00 0.00 0.00 2.57
1489 1776 4.532126 TCACATAGATGAAGGTCTTGTGGT 59.468 41.667 13.74 0.00 37.57 4.16
1493 1780 2.304180 AGATGAAGGTCTTGTGGTCAGG 59.696 50.000 0.00 0.00 0.00 3.86
1608 1897 5.511373 CCCTTGTCTTCTCACTCACATGTTA 60.511 44.000 0.00 0.00 0.00 2.41
1622 1911 6.483640 ACTCACATGTTAAGAAAACAGGTCTC 59.516 38.462 11.14 0.00 42.34 3.36
1635 1924 7.550906 AGAAAACAGGTCTCATTATCAGTTAGC 59.449 37.037 0.00 0.00 0.00 3.09
1645 1934 8.090831 TCTCATTATCAGTTAGCGCTTTATGAT 58.909 33.333 24.81 24.81 0.00 2.45
1647 1936 4.739046 ATCAGTTAGCGCTTTATGATGC 57.261 40.909 18.68 0.00 0.00 3.91
1673 1963 7.181569 TCTTTGTTTTTCTTCCTGGACAAAT 57.818 32.000 0.00 0.00 36.68 2.32
1675 1965 8.754080 TCTTTGTTTTTCTTCCTGGACAAATAA 58.246 29.630 0.00 0.00 36.68 1.40
1689 1979 5.299531 TGGACAAATAACGTGAAATTGGTCA 59.700 36.000 19.66 9.87 37.65 4.02
1699 1989 6.539324 ACGTGAAATTGGTCATGTATTAACG 58.461 36.000 3.62 6.08 44.19 3.18
1700 1990 6.148150 ACGTGAAATTGGTCATGTATTAACGT 59.852 34.615 3.62 6.59 44.19 3.99
1704 1994 9.751542 TGAAATTGGTCATGTATTAACGTTTTT 57.248 25.926 5.91 0.00 0.00 1.94
1728 2019 4.196193 TCTGGTTTTCTGTGTAGGTGTTG 58.804 43.478 0.00 0.00 0.00 3.33
1744 2035 4.020128 AGGTGTTGTTCTCATAGGGTTCTC 60.020 45.833 0.00 0.00 0.00 2.87
1774 2065 9.101655 GCTTTTGCATGTATATTTGGATTTTCT 57.898 29.630 0.00 0.00 46.58 2.52
1799 2090 3.119291 CTCCTGAAAGATTCGATGGTCG 58.881 50.000 0.00 0.00 37.41 4.79
1820 2111 3.669023 CGACTAAGTAGTTCCGGTGTGAC 60.669 52.174 0.00 0.00 36.50 3.67
1823 2114 2.521105 AGTAGTTCCGGTGTGACAAC 57.479 50.000 0.00 0.00 0.00 3.32
1837 2128 6.153756 GGTGTGACAACCAAAATATTACCAC 58.846 40.000 0.00 0.00 40.22 4.16
1879 2170 7.872483 TGAATTAGACTTCGATGCTGCATTATA 59.128 33.333 17.36 2.56 0.00 0.98
1885 2176 7.920151 AGACTTCGATGCTGCATTATAGATATC 59.080 37.037 17.36 12.80 0.00 1.63
1888 2179 6.866480 TCGATGCTGCATTATAGATATCACA 58.134 36.000 17.36 0.00 0.00 3.58
1897 2188 9.494271 TGCATTATAGATATCACAAGAAACCTC 57.506 33.333 5.32 0.00 0.00 3.85
1898 2189 9.494271 GCATTATAGATATCACAAGAAACCTCA 57.506 33.333 5.32 0.00 0.00 3.86
1912 2206 7.942341 ACAAGAAACCTCAATTCCTGTACATAA 59.058 33.333 0.00 0.00 31.46 1.90
1913 2207 8.792633 CAAGAAACCTCAATTCCTGTACATAAA 58.207 33.333 0.00 0.00 0.00 1.40
1914 2208 9.533831 AAGAAACCTCAATTCCTGTACATAAAT 57.466 29.630 0.00 0.00 0.00 1.40
1915 2209 9.178758 AGAAACCTCAATTCCTGTACATAAATC 57.821 33.333 0.00 0.00 0.00 2.17
1916 2210 9.178758 GAAACCTCAATTCCTGTACATAAATCT 57.821 33.333 0.00 0.00 0.00 2.40
1917 2211 8.511604 AACCTCAATTCCTGTACATAAATCTG 57.488 34.615 0.00 2.21 0.00 2.90
1918 2212 7.633789 ACCTCAATTCCTGTACATAAATCTGT 58.366 34.615 0.00 0.00 0.00 3.41
1919 2213 8.109634 ACCTCAATTCCTGTACATAAATCTGTT 58.890 33.333 0.00 0.00 0.00 3.16
1920 2214 8.400947 CCTCAATTCCTGTACATAAATCTGTTG 58.599 37.037 0.00 0.00 0.00 3.33
1921 2215 8.279970 TCAATTCCTGTACATAAATCTGTTGG 57.720 34.615 0.00 0.00 0.00 3.77
1922 2216 6.699575 ATTCCTGTACATAAATCTGTTGGC 57.300 37.500 0.00 0.00 0.00 4.52
1923 2217 5.435686 TCCTGTACATAAATCTGTTGGCT 57.564 39.130 0.00 0.00 0.00 4.75
1924 2218 5.815581 TCCTGTACATAAATCTGTTGGCTT 58.184 37.500 0.00 0.00 0.00 4.35
1925 2219 6.245408 TCCTGTACATAAATCTGTTGGCTTT 58.755 36.000 0.00 0.00 0.00 3.51
1926 2220 6.719370 TCCTGTACATAAATCTGTTGGCTTTT 59.281 34.615 0.00 0.00 0.00 2.27
1927 2221 6.808212 CCTGTACATAAATCTGTTGGCTTTTG 59.192 38.462 0.00 0.00 0.00 2.44
1928 2222 7.309133 CCTGTACATAAATCTGTTGGCTTTTGA 60.309 37.037 0.00 0.00 0.00 2.69
1929 2223 8.121305 TGTACATAAATCTGTTGGCTTTTGAT 57.879 30.769 0.00 0.00 0.00 2.57
1930 2224 8.243426 TGTACATAAATCTGTTGGCTTTTGATC 58.757 33.333 0.00 0.00 0.00 2.92
1931 2225 7.472334 ACATAAATCTGTTGGCTTTTGATCT 57.528 32.000 0.00 0.00 0.00 2.75
1932 2226 7.542025 ACATAAATCTGTTGGCTTTTGATCTC 58.458 34.615 0.00 0.00 0.00 2.75
1933 2227 7.395489 ACATAAATCTGTTGGCTTTTGATCTCT 59.605 33.333 0.00 0.00 0.00 3.10
1934 2228 8.896744 CATAAATCTGTTGGCTTTTGATCTCTA 58.103 33.333 0.00 0.00 0.00 2.43
1935 2229 6.998968 AATCTGTTGGCTTTTGATCTCTAG 57.001 37.500 0.00 0.00 0.00 2.43
1936 2230 5.745312 TCTGTTGGCTTTTGATCTCTAGA 57.255 39.130 0.00 0.00 0.00 2.43
1937 2231 6.305272 TCTGTTGGCTTTTGATCTCTAGAT 57.695 37.500 0.00 0.00 37.51 1.98
1938 2232 6.715280 TCTGTTGGCTTTTGATCTCTAGATT 58.285 36.000 0.00 0.00 34.37 2.40
1939 2233 7.851228 TCTGTTGGCTTTTGATCTCTAGATTA 58.149 34.615 0.00 0.00 34.37 1.75
1940 2234 7.984050 TCTGTTGGCTTTTGATCTCTAGATTAG 59.016 37.037 0.00 0.00 34.37 1.73
1941 2235 7.851228 TGTTGGCTTTTGATCTCTAGATTAGA 58.149 34.615 0.00 0.00 34.37 2.10
1942 2236 8.489489 TGTTGGCTTTTGATCTCTAGATTAGAT 58.511 33.333 0.00 0.00 36.40 1.98
1943 2237 8.987890 GTTGGCTTTTGATCTCTAGATTAGATC 58.012 37.037 11.68 11.68 46.36 2.75
1950 2244 6.773976 GATCTCTAGATTAGATCACCCAGG 57.226 45.833 13.09 0.00 45.75 4.45
1951 2245 5.932027 TCTCTAGATTAGATCACCCAGGA 57.068 43.478 0.00 0.00 33.66 3.86
1952 2246 5.886609 TCTCTAGATTAGATCACCCAGGAG 58.113 45.833 0.00 0.00 33.66 3.69
1953 2247 4.411927 TCTAGATTAGATCACCCAGGAGC 58.588 47.826 0.00 0.00 0.00 4.70
1954 2248 3.051940 AGATTAGATCACCCAGGAGCA 57.948 47.619 0.00 0.00 0.00 4.26
1955 2249 2.703007 AGATTAGATCACCCAGGAGCAC 59.297 50.000 0.00 0.00 0.00 4.40
1956 2250 1.204146 TTAGATCACCCAGGAGCACC 58.796 55.000 0.00 0.00 0.00 5.01
1957 2251 0.042581 TAGATCACCCAGGAGCACCA 59.957 55.000 2.07 0.00 38.94 4.17
1958 2252 1.078143 GATCACCCAGGAGCACCAC 60.078 63.158 2.07 0.00 38.94 4.16
1959 2253 2.859273 GATCACCCAGGAGCACCACG 62.859 65.000 2.07 0.00 38.94 4.94
1960 2254 3.941188 CACCCAGGAGCACCACGT 61.941 66.667 2.07 0.00 38.94 4.49
1961 2255 3.941188 ACCCAGGAGCACCACGTG 61.941 66.667 9.08 9.08 38.94 4.49
1962 2256 3.941188 CCCAGGAGCACCACGTGT 61.941 66.667 15.65 0.00 38.94 4.49
1963 2257 2.579657 CCCAGGAGCACCACGTGTA 61.580 63.158 15.65 0.00 38.94 2.90
1964 2258 1.596934 CCAGGAGCACCACGTGTAT 59.403 57.895 15.65 0.00 38.94 2.29
1965 2259 0.740868 CCAGGAGCACCACGTGTATG 60.741 60.000 15.65 13.37 38.94 2.39
1966 2260 0.037326 CAGGAGCACCACGTGTATGT 60.037 55.000 15.65 2.06 38.94 2.29
1967 2261 0.037326 AGGAGCACCACGTGTATGTG 60.037 55.000 15.65 16.00 39.60 3.21
1973 2267 1.393539 CACCACGTGTATGTGCTAAGC 59.606 52.381 15.65 0.00 38.55 3.09
1974 2268 1.275291 ACCACGTGTATGTGCTAAGCT 59.725 47.619 15.65 0.00 38.55 3.74
1975 2269 2.494471 ACCACGTGTATGTGCTAAGCTA 59.506 45.455 15.65 0.00 38.55 3.32
1976 2270 3.116300 CCACGTGTATGTGCTAAGCTAG 58.884 50.000 15.65 0.00 38.55 3.42
1993 2287 4.341783 GCACACAGCCAGGGAGCT 62.342 66.667 0.00 0.00 46.45 4.09
2005 2299 3.294038 CAGGGAGCTGGATTGATCTTT 57.706 47.619 0.00 0.00 0.00 2.52
2006 2300 2.950309 CAGGGAGCTGGATTGATCTTTG 59.050 50.000 0.00 0.00 0.00 2.77
2007 2301 1.680207 GGGAGCTGGATTGATCTTTGC 59.320 52.381 0.00 0.00 0.00 3.68
2008 2302 2.652590 GGAGCTGGATTGATCTTTGCT 58.347 47.619 0.00 0.00 32.69 3.91
2009 2303 2.617774 GGAGCTGGATTGATCTTTGCTC 59.382 50.000 16.80 16.80 39.74 4.26
2010 2304 2.617774 GAGCTGGATTGATCTTTGCTCC 59.382 50.000 15.43 0.00 37.37 4.70
2011 2305 2.241685 AGCTGGATTGATCTTTGCTCCT 59.758 45.455 0.00 0.00 0.00 3.69
2012 2306 2.358267 GCTGGATTGATCTTTGCTCCTG 59.642 50.000 0.00 0.00 0.00 3.86
2013 2307 3.618351 CTGGATTGATCTTTGCTCCTGT 58.382 45.455 0.00 0.00 0.00 4.00
2014 2308 4.774124 CTGGATTGATCTTTGCTCCTGTA 58.226 43.478 0.00 0.00 0.00 2.74
2015 2309 4.517285 TGGATTGATCTTTGCTCCTGTAC 58.483 43.478 0.00 0.00 0.00 2.90
2016 2310 4.019411 TGGATTGATCTTTGCTCCTGTACA 60.019 41.667 0.00 0.00 0.00 2.90
2017 2311 4.333926 GGATTGATCTTTGCTCCTGTACAC 59.666 45.833 0.00 0.00 0.00 2.90
2018 2312 2.959516 TGATCTTTGCTCCTGTACACG 58.040 47.619 0.00 0.00 0.00 4.49
2019 2313 2.299013 TGATCTTTGCTCCTGTACACGT 59.701 45.455 0.00 0.00 0.00 4.49
2020 2314 2.148916 TCTTTGCTCCTGTACACGTG 57.851 50.000 15.48 15.48 0.00 4.49
2021 2315 1.684450 TCTTTGCTCCTGTACACGTGA 59.316 47.619 25.01 2.68 0.00 4.35
2022 2316 2.101750 TCTTTGCTCCTGTACACGTGAA 59.898 45.455 25.01 6.36 0.00 3.18
2023 2317 2.605837 TTGCTCCTGTACACGTGAAA 57.394 45.000 25.01 6.94 0.00 2.69
2024 2318 1.860676 TGCTCCTGTACACGTGAAAC 58.139 50.000 25.01 19.35 0.00 2.78
2025 2319 1.411246 TGCTCCTGTACACGTGAAACT 59.589 47.619 25.01 1.30 31.75 2.66
2026 2320 2.624364 TGCTCCTGTACACGTGAAACTA 59.376 45.455 25.01 0.12 31.75 2.24
2027 2321 3.257375 TGCTCCTGTACACGTGAAACTAT 59.743 43.478 25.01 0.00 31.75 2.12
2028 2322 4.460034 TGCTCCTGTACACGTGAAACTATA 59.540 41.667 25.01 0.00 31.75 1.31
2029 2323 5.035443 GCTCCTGTACACGTGAAACTATAG 58.965 45.833 25.01 11.26 31.75 1.31
2030 2324 4.990257 TCCTGTACACGTGAAACTATAGC 58.010 43.478 25.01 1.80 31.75 2.97
2031 2325 4.703575 TCCTGTACACGTGAAACTATAGCT 59.296 41.667 25.01 0.00 31.75 3.32
2032 2326 5.184479 TCCTGTACACGTGAAACTATAGCTT 59.816 40.000 25.01 0.00 31.75 3.74
2033 2327 6.375174 TCCTGTACACGTGAAACTATAGCTTA 59.625 38.462 25.01 0.00 31.75 3.09
2034 2328 6.691818 CCTGTACACGTGAAACTATAGCTTAG 59.308 42.308 25.01 9.84 31.75 2.18
2035 2329 6.032094 TGTACACGTGAAACTATAGCTTAGC 58.968 40.000 25.01 0.00 31.75 3.09
2036 2330 4.103357 ACACGTGAAACTATAGCTTAGCG 58.897 43.478 25.01 5.05 31.75 4.26
2037 2331 4.142534 ACACGTGAAACTATAGCTTAGCGA 60.143 41.667 25.01 0.00 31.75 4.93
2038 2332 4.976731 CACGTGAAACTATAGCTTAGCGAT 59.023 41.667 10.90 5.04 31.75 4.58
2048 2342 7.987649 ACTATAGCTTAGCGATAATCTGGTAC 58.012 38.462 7.03 0.00 0.00 3.34
2113 2408 7.660208 CCAGTTATAACAACTTCCACTTGTACT 59.340 37.037 17.65 0.00 31.43 2.73
2142 2437 4.778958 TCAGATTGCCATTTTTCTTCCCAT 59.221 37.500 0.00 0.00 0.00 4.00
2166 2461 5.574188 AGCAGTGAAAATGGTTCTCCTATT 58.426 37.500 0.00 0.00 41.17 1.73
2170 2465 8.303876 GCAGTGAAAATGGTTCTCCTATTAAAA 58.696 33.333 0.00 0.00 28.90 1.52
2264 2560 9.181061 GTTAAGTTAATGCCTTATGGGAGTTTA 57.819 33.333 0.00 0.00 37.02 2.01
2274 2570 9.041354 TGCCTTATGGGAGTTTATTTGTTTTAT 57.959 29.630 0.00 0.00 37.23 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 7.444299 ACTTGCAAAACAGGAAACATATGATT 58.556 30.769 10.38 3.32 0.00 2.57
113 114 3.184628 TCAGGTCTTGATCTGATGGGTT 58.815 45.455 9.30 0.00 35.37 4.11
162 163 3.198872 GGACACTGCTCTATACAAAGCC 58.801 50.000 0.00 0.00 37.73 4.35
176 177 5.277974 CCAGTAACAACAATTCTGGACACTG 60.278 44.000 3.76 5.21 45.76 3.66
188 189 4.018870 TGGGATATGAGCCAGTAACAACAA 60.019 41.667 0.00 0.00 0.00 2.83
197 198 1.983691 AGTCCATGGGATATGAGCCAG 59.016 52.381 13.02 0.00 32.73 4.85
264 265 5.777802 AGGATGATGTTGAGTATAGAAGCG 58.222 41.667 0.00 0.00 0.00 4.68
269 270 6.877855 CCCATGAAGGATGATGTTGAGTATAG 59.122 42.308 0.00 0.00 41.22 1.31
271 272 5.370584 TCCCATGAAGGATGATGTTGAGTAT 59.629 40.000 0.00 0.00 41.22 2.12
281 282 3.787577 TCAAATCCTCCCATGAAGGATGA 59.212 43.478 22.85 17.55 41.18 2.92
282 283 4.174704 TCAAATCCTCCCATGAAGGATG 57.825 45.455 22.85 16.07 41.18 3.51
283 284 4.886755 TTCAAATCCTCCCATGAAGGAT 57.113 40.909 18.75 18.75 43.63 3.24
290 291 5.092968 TCCAACAATTTCAAATCCTCCCAT 58.907 37.500 0.00 0.00 0.00 4.00
292 293 5.482163 TTCCAACAATTTCAAATCCTCCC 57.518 39.130 0.00 0.00 0.00 4.30
301 308 5.885449 AACCATCCTTTCCAACAATTTCA 57.115 34.783 0.00 0.00 0.00 2.69
309 316 2.892852 CTCTGCAAACCATCCTTTCCAA 59.107 45.455 0.00 0.00 0.00 3.53
310 317 2.517959 CTCTGCAAACCATCCTTTCCA 58.482 47.619 0.00 0.00 0.00 3.53
321 328 4.272991 CCATCTCATCTAAGCTCTGCAAAC 59.727 45.833 0.00 0.00 0.00 2.93
341 348 5.754782 TGTCAGGTTATTGAATGCTACCAT 58.245 37.500 8.11 0.00 0.00 3.55
388 405 1.602888 CTGCAGAGCTGGGCACTTT 60.603 57.895 8.42 0.00 35.86 2.66
456 473 6.600822 CCTCTACAATCACACCAATTCTGAAT 59.399 38.462 0.00 0.00 0.00 2.57
464 481 3.392947 TGAACCCTCTACAATCACACCAA 59.607 43.478 0.00 0.00 0.00 3.67
495 521 2.562912 GTGTGCTGCCATTCCACG 59.437 61.111 0.00 0.00 32.32 4.94
511 537 0.773644 ACCACAAGATGCTCAAGGGT 59.226 50.000 0.00 0.00 0.00 4.34
540 566 5.012893 GTCAATTCCTTCCCACTTGATTCT 58.987 41.667 0.00 0.00 0.00 2.40
547 573 2.290577 GCTCTGTCAATTCCTTCCCACT 60.291 50.000 0.00 0.00 0.00 4.00
601 627 7.614583 TGTAAGCTTTCTACACCTACTGATAGT 59.385 37.037 3.20 0.00 0.00 2.12
602 628 7.916450 GTGTAAGCTTTCTACACCTACTGATAG 59.084 40.741 16.80 0.00 38.41 2.08
603 629 7.395206 TGTGTAAGCTTTCTACACCTACTGATA 59.605 37.037 22.23 4.55 42.30 2.15
608 634 6.145696 CAGTTGTGTAAGCTTTCTACACCTAC 59.854 42.308 22.23 19.48 42.30 3.18
609 635 6.220930 CAGTTGTGTAAGCTTTCTACACCTA 58.779 40.000 22.23 11.63 42.30 3.08
611 637 4.213482 CCAGTTGTGTAAGCTTTCTACACC 59.787 45.833 22.23 11.78 42.30 4.16
612 638 4.319549 GCCAGTTGTGTAAGCTTTCTACAC 60.320 45.833 19.61 19.61 43.02 2.90
616 642 2.930950 TGCCAGTTGTGTAAGCTTTCT 58.069 42.857 3.20 0.00 0.00 2.52
617 643 3.923017 ATGCCAGTTGTGTAAGCTTTC 57.077 42.857 3.20 0.00 0.00 2.62
622 648 1.545582 CCCCAATGCCAGTTGTGTAAG 59.454 52.381 0.00 0.00 0.00 2.34
624 650 0.251564 CCCCCAATGCCAGTTGTGTA 60.252 55.000 0.00 0.00 0.00 2.90
637 663 2.440147 CTGCACATCCACCCCCAA 59.560 61.111 0.00 0.00 0.00 4.12
643 669 2.443887 ATTGTTTGCTGCACATCCAC 57.556 45.000 0.00 0.00 0.00 4.02
654 680 5.234972 AGCTGTTTTTGCTAGAATTGTTTGC 59.765 36.000 0.00 0.00 39.21 3.68
662 688 4.997395 CCTCTGTAGCTGTTTTTGCTAGAA 59.003 41.667 0.00 0.00 42.74 2.10
663 689 4.040461 ACCTCTGTAGCTGTTTTTGCTAGA 59.960 41.667 0.00 0.00 42.74 2.43
664 690 4.153117 CACCTCTGTAGCTGTTTTTGCTAG 59.847 45.833 0.00 0.00 42.74 3.42
665 691 4.065088 CACCTCTGTAGCTGTTTTTGCTA 58.935 43.478 0.00 0.00 41.46 3.49
668 694 3.476552 TCCACCTCTGTAGCTGTTTTTG 58.523 45.455 0.00 0.00 0.00 2.44
670 696 2.551071 GCTCCACCTCTGTAGCTGTTTT 60.551 50.000 0.00 0.00 32.18 2.43
671 697 1.002544 GCTCCACCTCTGTAGCTGTTT 59.997 52.381 0.00 0.00 32.18 2.83
673 699 0.542938 TGCTCCACCTCTGTAGCTGT 60.543 55.000 0.00 0.00 35.95 4.40
681 713 2.177594 CTTTCGCCTGCTCCACCTCT 62.178 60.000 0.00 0.00 0.00 3.69
691 723 4.633126 TGAATCATCTTCTTCTTTCGCCTG 59.367 41.667 0.00 0.00 0.00 4.85
693 725 5.505324 CCATGAATCATCTTCTTCTTTCGCC 60.505 44.000 0.00 0.00 0.00 5.54
694 726 5.508872 CCATGAATCATCTTCTTCTTTCGC 58.491 41.667 0.00 0.00 0.00 4.70
695 727 5.296283 AGCCATGAATCATCTTCTTCTTTCG 59.704 40.000 0.00 0.00 0.00 3.46
741 773 3.578282 TCAATACCTGCAGTGAGTCAGAA 59.422 43.478 13.81 0.00 32.26 3.02
759 791 8.497745 ACAATGGTTAAGTCTATGATCCTCAAT 58.502 33.333 0.00 0.00 0.00 2.57
785 1066 0.114954 AAAGAATCCAGGGCAGCCAA 59.885 50.000 15.19 0.00 0.00 4.52
814 1095 2.301870 TCAGCGGTTGTAACTCCTGATT 59.698 45.455 11.17 0.00 34.01 2.57
826 1107 0.745845 CCTCCATTCCTCAGCGGTTG 60.746 60.000 0.00 0.00 0.00 3.77
828 1109 0.909610 TTCCTCCATTCCTCAGCGGT 60.910 55.000 0.00 0.00 0.00 5.68
830 1111 1.945394 CATTTCCTCCATTCCTCAGCG 59.055 52.381 0.00 0.00 0.00 5.18
833 1114 2.577563 TGCTCATTTCCTCCATTCCTCA 59.422 45.455 0.00 0.00 0.00 3.86
835 1116 2.091994 CCTGCTCATTTCCTCCATTCCT 60.092 50.000 0.00 0.00 0.00 3.36
836 1117 2.092212 TCCTGCTCATTTCCTCCATTCC 60.092 50.000 0.00 0.00 0.00 3.01
876 1160 2.302445 CAGTTTGCATCCATTTTGGGGA 59.698 45.455 0.00 0.00 38.32 4.81
923 1207 1.411651 GGGCACAGATAGGAGTCCCC 61.412 65.000 5.25 0.00 0.00 4.81
945 1229 0.398318 AGGAAGACAGGAGGTTGCAC 59.602 55.000 0.00 0.00 0.00 4.57
979 1263 4.156455 TCTCTTGGTTGTCAGAAAAGCT 57.844 40.909 4.16 0.00 0.00 3.74
989 1273 0.674895 GCGCTCCATCTCTTGGTTGT 60.675 55.000 0.00 0.00 46.52 3.32
1027 1311 1.480954 GACGAGGAAGTGAAGGGCATA 59.519 52.381 0.00 0.00 0.00 3.14
1039 1323 1.682684 GCTGGAGGGAGACGAGGAA 60.683 63.158 0.00 0.00 0.00 3.36
1069 1353 3.136763 TCTGAAGCTTGCTCAAGTTGAG 58.863 45.455 25.68 25.68 46.90 3.02
1107 1391 2.136298 TGAGGTTGGTGTGCTTTTGA 57.864 45.000 0.00 0.00 0.00 2.69
1115 1399 3.569701 CACTAATTGCTTGAGGTTGGTGT 59.430 43.478 0.00 0.00 31.14 4.16
1129 1413 2.609459 GGCATGAGACGACCACTAATTG 59.391 50.000 0.00 0.00 0.00 2.32
1141 1425 1.745489 GGACAACCGGGCATGAGAC 60.745 63.158 6.32 0.13 0.00 3.36
1142 1426 2.668632 GGACAACCGGGCATGAGA 59.331 61.111 6.32 0.00 0.00 3.27
1173 1457 0.259938 GTGATTTGGGGAGGCCATCT 59.740 55.000 5.01 0.00 0.00 2.90
1218 1502 2.237643 TGTTTTAGCTCTGCATTGCCA 58.762 42.857 6.12 0.00 0.00 4.92
1224 1508 2.033299 GCACTGTTGTTTTAGCTCTGCA 59.967 45.455 0.00 0.00 0.00 4.41
1282 1566 3.007398 ACCTTGGATCAGTCTCACAGTTC 59.993 47.826 0.00 0.00 0.00 3.01
1420 1706 2.747855 CGGGAACTCCAAGGCAGC 60.748 66.667 0.00 0.00 37.91 5.25
1430 1716 4.381718 GCTAGAAGAATGTACACGGGAACT 60.382 45.833 0.00 0.00 0.00 3.01
1478 1765 1.807814 AGAACCTGACCACAAGACCT 58.192 50.000 0.00 0.00 0.00 3.85
1489 1776 7.016153 ACCAGATTTATGTACAAGAACCTGA 57.984 36.000 14.43 0.00 0.00 3.86
1525 1814 6.209391 ACAGCAGGAGCAATGTTTTAAGTTAT 59.791 34.615 0.00 0.00 45.49 1.89
1537 1826 4.529897 TGATATGAAACAGCAGGAGCAAT 58.470 39.130 0.00 0.00 45.49 3.56
1608 1897 9.442047 CTAACTGATAATGAGACCTGTTTTCTT 57.558 33.333 0.00 0.00 0.00 2.52
1622 1911 6.740002 GCATCATAAAGCGCTAACTGATAATG 59.260 38.462 21.14 14.93 0.00 1.90
1635 1924 6.695292 AAAACAAAGAAGCATCATAAAGCG 57.305 33.333 0.00 0.00 35.48 4.68
1645 1934 4.709397 TCCAGGAAGAAAAACAAAGAAGCA 59.291 37.500 0.00 0.00 0.00 3.91
1647 1936 6.207691 TGTCCAGGAAGAAAAACAAAGAAG 57.792 37.500 0.00 0.00 0.00 2.85
1673 1963 8.169910 CGTTAATACATGACCAATTTCACGTTA 58.830 33.333 0.00 0.00 0.00 3.18
1675 1965 6.148150 ACGTTAATACATGACCAATTTCACGT 59.852 34.615 0.00 8.74 31.67 4.49
1704 1994 4.850680 ACACCTACACAGAAAACCAGAAA 58.149 39.130 0.00 0.00 0.00 2.52
1706 1996 4.196193 CAACACCTACACAGAAAACCAGA 58.804 43.478 0.00 0.00 0.00 3.86
1707 1997 3.945285 ACAACACCTACACAGAAAACCAG 59.055 43.478 0.00 0.00 0.00 4.00
1720 2010 5.091552 AGAACCCTATGAGAACAACACCTA 58.908 41.667 0.00 0.00 0.00 3.08
1728 2019 2.738964 GCACGGAGAACCCTATGAGAAC 60.739 54.545 0.00 0.00 0.00 3.01
1744 2035 4.503734 CCAAATATACATGCAAAAGCACGG 59.496 41.667 0.00 0.00 0.00 4.94
1774 2065 6.049955 ACCATCGAATCTTTCAGGAGTAAA 57.950 37.500 0.00 0.00 0.00 2.01
1799 2090 3.254166 TGTCACACCGGAACTACTTAGTC 59.746 47.826 9.46 0.00 34.99 2.59
1820 2111 9.598517 AATTATGCTGTGGTAATATTTTGGTTG 57.401 29.630 0.00 0.00 0.00 3.77
1823 2114 9.467258 CTGAATTATGCTGTGGTAATATTTTGG 57.533 33.333 0.00 0.00 0.00 3.28
1879 2170 7.555554 CAGGAATTGAGGTTTCTTGTGATATCT 59.444 37.037 3.98 0.00 0.00 1.98
1885 2176 5.530915 TGTACAGGAATTGAGGTTTCTTGTG 59.469 40.000 10.33 0.00 41.66 3.33
1888 2179 8.934023 TTTATGTACAGGAATTGAGGTTTCTT 57.066 30.769 0.33 0.00 0.00 2.52
1897 2188 6.974622 GCCAACAGATTTATGTACAGGAATTG 59.025 38.462 0.33 7.76 31.70 2.32
1898 2189 6.891908 AGCCAACAGATTTATGTACAGGAATT 59.108 34.615 0.33 0.00 31.70 2.17
1899 2190 6.426587 AGCCAACAGATTTATGTACAGGAAT 58.573 36.000 0.33 3.96 31.70 3.01
1912 2206 6.715280 TCTAGAGATCAAAAGCCAACAGATT 58.285 36.000 0.00 0.00 0.00 2.40
1913 2207 6.305272 TCTAGAGATCAAAAGCCAACAGAT 57.695 37.500 0.00 0.00 0.00 2.90
1914 2208 5.745312 TCTAGAGATCAAAAGCCAACAGA 57.255 39.130 0.00 0.00 0.00 3.41
1915 2209 6.998968 AATCTAGAGATCAAAAGCCAACAG 57.001 37.500 0.00 0.00 32.75 3.16
1916 2210 7.851228 TCTAATCTAGAGATCAAAAGCCAACA 58.149 34.615 0.00 0.00 32.75 3.33
1917 2211 8.900983 ATCTAATCTAGAGATCAAAAGCCAAC 57.099 34.615 0.00 0.00 38.38 3.77
1927 2221 6.489603 TCCTGGGTGATCTAATCTAGAGATC 58.510 44.000 11.68 11.68 46.45 2.75
1928 2222 6.476409 TCCTGGGTGATCTAATCTAGAGAT 57.524 41.667 0.00 0.00 38.38 2.75
1929 2223 5.750527 GCTCCTGGGTGATCTAATCTAGAGA 60.751 48.000 0.00 0.00 38.38 3.10
1930 2224 4.462483 GCTCCTGGGTGATCTAATCTAGAG 59.538 50.000 0.00 0.00 38.38 2.43
1931 2225 4.140924 TGCTCCTGGGTGATCTAATCTAGA 60.141 45.833 0.00 0.00 39.50 2.43
1932 2226 4.021544 GTGCTCCTGGGTGATCTAATCTAG 60.022 50.000 0.00 0.00 0.00 2.43
1933 2227 3.898123 GTGCTCCTGGGTGATCTAATCTA 59.102 47.826 0.00 0.00 0.00 1.98
1934 2228 2.703007 GTGCTCCTGGGTGATCTAATCT 59.297 50.000 0.00 0.00 0.00 2.40
1935 2229 2.224402 GGTGCTCCTGGGTGATCTAATC 60.224 54.545 0.00 0.00 0.00 1.75
1936 2230 1.771255 GGTGCTCCTGGGTGATCTAAT 59.229 52.381 0.00 0.00 0.00 1.73
1937 2231 1.204146 GGTGCTCCTGGGTGATCTAA 58.796 55.000 0.00 0.00 0.00 2.10
1938 2232 0.042581 TGGTGCTCCTGGGTGATCTA 59.957 55.000 6.34 0.00 34.23 1.98
1939 2233 1.229625 TGGTGCTCCTGGGTGATCT 60.230 57.895 6.34 0.00 34.23 2.75
1940 2234 1.078143 GTGGTGCTCCTGGGTGATC 60.078 63.158 6.34 0.00 34.23 2.92
1941 2235 2.959484 CGTGGTGCTCCTGGGTGAT 61.959 63.158 6.34 0.00 34.23 3.06
1942 2236 3.625897 CGTGGTGCTCCTGGGTGA 61.626 66.667 6.34 0.00 34.23 4.02
1943 2237 3.941188 ACGTGGTGCTCCTGGGTG 61.941 66.667 6.34 0.00 34.23 4.61
1944 2238 3.941188 CACGTGGTGCTCCTGGGT 61.941 66.667 7.95 0.00 34.23 4.51
1945 2239 1.899437 ATACACGTGGTGCTCCTGGG 61.899 60.000 21.57 2.44 36.98 4.45
1946 2240 0.740868 CATACACGTGGTGCTCCTGG 60.741 60.000 21.57 0.41 36.98 4.45
1947 2241 0.037326 ACATACACGTGGTGCTCCTG 60.037 55.000 21.57 8.34 36.98 3.86
1948 2242 0.037326 CACATACACGTGGTGCTCCT 60.037 55.000 21.57 0.00 36.98 3.69
1949 2243 2.456000 CACATACACGTGGTGCTCC 58.544 57.895 21.57 0.00 36.98 4.70
1953 2247 1.393539 GCTTAGCACATACACGTGGTG 59.606 52.381 21.57 19.54 46.51 4.17
1955 2249 2.010145 AGCTTAGCACATACACGTGG 57.990 50.000 21.57 4.47 37.37 4.94
1968 2262 1.649664 CTGGCTGTGTGCTAGCTTAG 58.350 55.000 17.23 9.62 43.12 2.18
1969 2263 3.840831 CTGGCTGTGTGCTAGCTTA 57.159 52.632 17.23 1.46 43.12 3.09
1970 2264 4.709840 CTGGCTGTGTGCTAGCTT 57.290 55.556 17.23 0.00 43.12 3.74
1974 2268 2.959484 GCTCCCTGGCTGTGTGCTA 61.959 63.158 0.00 0.00 42.39 3.49
1975 2269 4.341783 GCTCCCTGGCTGTGTGCT 62.342 66.667 0.00 0.00 42.39 4.40
1976 2270 4.341783 AGCTCCCTGGCTGTGTGC 62.342 66.667 0.00 0.00 41.43 4.57
1985 2279 2.950309 CAAAGATCAATCCAGCTCCCTG 59.050 50.000 0.00 0.00 38.85 4.45
1986 2280 2.686118 GCAAAGATCAATCCAGCTCCCT 60.686 50.000 0.00 0.00 0.00 4.20
1987 2281 1.680207 GCAAAGATCAATCCAGCTCCC 59.320 52.381 0.00 0.00 0.00 4.30
1988 2282 2.617774 GAGCAAAGATCAATCCAGCTCC 59.382 50.000 13.62 2.57 38.46 4.70
1989 2283 2.617774 GGAGCAAAGATCAATCCAGCTC 59.382 50.000 15.18 15.18 41.08 4.09
1990 2284 2.241685 AGGAGCAAAGATCAATCCAGCT 59.758 45.455 0.00 0.00 33.36 4.24
1991 2285 2.358267 CAGGAGCAAAGATCAATCCAGC 59.642 50.000 0.00 0.00 32.21 4.85
1992 2286 3.618351 ACAGGAGCAAAGATCAATCCAG 58.382 45.455 0.00 0.00 32.21 3.86
1993 2287 3.726557 ACAGGAGCAAAGATCAATCCA 57.273 42.857 0.00 0.00 32.21 3.41
1994 2288 4.333926 GTGTACAGGAGCAAAGATCAATCC 59.666 45.833 0.00 0.00 0.00 3.01
1995 2289 4.033358 CGTGTACAGGAGCAAAGATCAATC 59.967 45.833 10.02 0.00 0.00 2.67
1996 2290 3.935203 CGTGTACAGGAGCAAAGATCAAT 59.065 43.478 10.02 0.00 0.00 2.57
1997 2291 3.244078 ACGTGTACAGGAGCAAAGATCAA 60.244 43.478 21.70 0.00 0.00 2.57
1998 2292 2.299013 ACGTGTACAGGAGCAAAGATCA 59.701 45.455 21.70 0.00 0.00 2.92
1999 2293 2.668457 CACGTGTACAGGAGCAAAGATC 59.332 50.000 21.70 0.00 0.00 2.75
2000 2294 2.299013 TCACGTGTACAGGAGCAAAGAT 59.701 45.455 21.70 0.00 0.00 2.40
2001 2295 1.684450 TCACGTGTACAGGAGCAAAGA 59.316 47.619 21.70 6.94 0.00 2.52
2002 2296 2.148916 TCACGTGTACAGGAGCAAAG 57.851 50.000 21.70 4.96 0.00 2.77
2003 2297 2.605837 TTCACGTGTACAGGAGCAAA 57.394 45.000 21.70 7.39 0.00 3.68
2004 2298 2.159014 AGTTTCACGTGTACAGGAGCAA 60.159 45.455 21.70 8.15 0.00 3.91
2005 2299 1.411246 AGTTTCACGTGTACAGGAGCA 59.589 47.619 21.70 1.80 0.00 4.26
2006 2300 2.150397 AGTTTCACGTGTACAGGAGC 57.850 50.000 21.70 2.35 0.00 4.70
2007 2301 5.035443 GCTATAGTTTCACGTGTACAGGAG 58.965 45.833 21.70 14.04 0.00 3.69
2008 2302 4.703575 AGCTATAGTTTCACGTGTACAGGA 59.296 41.667 21.70 5.19 0.00 3.86
2009 2303 4.995124 AGCTATAGTTTCACGTGTACAGG 58.005 43.478 16.51 13.84 0.00 4.00
2010 2304 6.196724 GCTAAGCTATAGTTTCACGTGTACAG 59.803 42.308 16.51 9.55 0.00 2.74
2011 2305 6.032094 GCTAAGCTATAGTTTCACGTGTACA 58.968 40.000 16.51 0.00 0.00 2.90
2012 2306 5.170981 CGCTAAGCTATAGTTTCACGTGTAC 59.829 44.000 16.51 14.59 0.00 2.90
2013 2307 5.065090 TCGCTAAGCTATAGTTTCACGTGTA 59.935 40.000 16.51 2.27 0.00 2.90
2014 2308 4.103357 CGCTAAGCTATAGTTTCACGTGT 58.897 43.478 16.51 0.00 0.00 4.49
2015 2309 4.348656 TCGCTAAGCTATAGTTTCACGTG 58.651 43.478 9.94 9.94 0.00 4.49
2016 2310 4.627611 TCGCTAAGCTATAGTTTCACGT 57.372 40.909 17.43 0.00 0.00 4.49
2017 2311 7.751348 AGATTATCGCTAAGCTATAGTTTCACG 59.249 37.037 4.97 10.56 31.94 4.35
2018 2312 8.855279 CAGATTATCGCTAAGCTATAGTTTCAC 58.145 37.037 4.97 0.00 31.94 3.18
2019 2313 8.029522 CCAGATTATCGCTAAGCTATAGTTTCA 58.970 37.037 4.97 0.00 31.94 2.69
2020 2314 8.030106 ACCAGATTATCGCTAAGCTATAGTTTC 58.970 37.037 4.97 0.00 31.94 2.78
2021 2315 7.897864 ACCAGATTATCGCTAAGCTATAGTTT 58.102 34.615 7.05 7.05 31.94 2.66
2022 2316 7.469537 ACCAGATTATCGCTAAGCTATAGTT 57.530 36.000 0.84 0.00 31.94 2.24
2023 2317 7.201626 CGTACCAGATTATCGCTAAGCTATAGT 60.202 40.741 0.84 0.00 31.94 2.12
2024 2318 7.127042 CGTACCAGATTATCGCTAAGCTATAG 58.873 42.308 0.00 0.00 31.94 1.31
2025 2319 6.596888 ACGTACCAGATTATCGCTAAGCTATA 59.403 38.462 0.00 0.00 31.94 1.31
2026 2320 5.415077 ACGTACCAGATTATCGCTAAGCTAT 59.585 40.000 0.00 0.00 31.94 2.97
2027 2321 4.758674 ACGTACCAGATTATCGCTAAGCTA 59.241 41.667 0.00 0.00 31.94 3.32
2028 2322 3.568853 ACGTACCAGATTATCGCTAAGCT 59.431 43.478 0.00 0.00 33.94 3.74
2029 2323 3.898529 ACGTACCAGATTATCGCTAAGC 58.101 45.455 0.00 0.00 0.00 3.09
2030 2324 5.993891 TGTACGTACCAGATTATCGCTAAG 58.006 41.667 22.43 0.00 0.00 2.18
2031 2325 6.429078 AGATGTACGTACCAGATTATCGCTAA 59.571 38.462 22.43 0.00 0.00 3.09
2032 2326 5.936372 AGATGTACGTACCAGATTATCGCTA 59.064 40.000 22.43 0.00 0.00 4.26
2033 2327 4.760715 AGATGTACGTACCAGATTATCGCT 59.239 41.667 22.43 1.17 0.00 4.93
2034 2328 5.044428 AGATGTACGTACCAGATTATCGC 57.956 43.478 22.43 0.00 0.00 4.58
2035 2329 7.745155 CAGTTAGATGTACGTACCAGATTATCG 59.255 40.741 22.43 1.57 0.00 2.92
2036 2330 8.021973 CCAGTTAGATGTACGTACCAGATTATC 58.978 40.741 22.43 16.26 0.00 1.75
2037 2331 7.722728 TCCAGTTAGATGTACGTACCAGATTAT 59.277 37.037 22.43 8.38 0.00 1.28
2038 2332 7.056006 TCCAGTTAGATGTACGTACCAGATTA 58.944 38.462 22.43 3.40 0.00 1.75
2048 2342 7.435488 CAGGAGTTAAATCCAGTTAGATGTACG 59.565 40.741 23.06 0.00 42.26 3.67
2142 2437 4.640771 AGGAGAACCATTTTCACTGCTA 57.359 40.909 0.00 0.00 38.94 3.49
2238 2534 7.640597 AACTCCCATAAGGCATTAACTTAAC 57.359 36.000 0.00 0.00 34.42 2.01
2241 2537 8.838649 AATAAACTCCCATAAGGCATTAACTT 57.161 30.769 0.00 0.00 34.51 2.66
2264 2560 9.203421 GATTTTCGTCCAGGAAATAAAACAAAT 57.797 29.630 0.00 0.00 35.95 2.32


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

AutoCloner maintained by Alex Coulton.