Multiple sequence alignment - TraesCS1A01G396500

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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 TraesCS1A01G396500 chr1A 100.000 2342 0 0 1 2342 562587213 562589554 0.000000e+00 4325.0
1 TraesCS1A01G396500 chr1A 76.393 305 52 13 2055 2342 497485305 497485004 1.880000e-31 147.0
2 TraesCS1A01G396500 chr1A 79.787 188 35 3 2157 2342 392742323 392742137 1.460000e-27 134.0
3 TraesCS1A01G396500 chr1A 74.613 323 58 14 2037 2340 302923584 302923267 1.140000e-23 121.0
4 TraesCS1A01G396500 chr1A 88.506 87 8 1 1565 1649 49968302 49968216 1.140000e-18 104.0
5 TraesCS1A01G396500 chr2A 95.035 1692 49 5 1 1658 55468233 55466543 0.000000e+00 2627.0
6 TraesCS1A01G396500 chr2A 95.765 425 18 0 1918 2342 55466544 55466120 0.000000e+00 686.0
7 TraesCS1A01G396500 chr2A 90.361 83 7 1 1563 1645 394759658 394759739 8.850000e-20 108.0
8 TraesCS1A01G396500 chr2A 90.361 83 7 1 1563 1645 406450530 406450449 8.850000e-20 108.0
9 TraesCS1A01G396500 chr4A 95.068 1683 54 3 1 1658 56252752 56251074 0.000000e+00 2621.0
10 TraesCS1A01G396500 chr4A 94.353 425 24 0 1918 2342 56251075 56250651 0.000000e+00 652.0
11 TraesCS1A01G396500 chr4A 93.145 248 17 0 2091 2338 125962569 125962322 4.760000e-97 364.0
12 TraesCS1A01G396500 chr7A 95.144 1668 60 9 1 1658 90543772 90542116 0.000000e+00 2612.0
13 TraesCS1A01G396500 chr7A 81.971 954 126 27 109 1040 81231492 81230563 0.000000e+00 767.0
14 TraesCS1A01G396500 chr7A 85.311 708 80 17 104 798 180466701 180467397 0.000000e+00 710.0
15 TraesCS1A01G396500 chr7A 93.349 421 28 0 1918 2338 90542117 90541697 7.110000e-175 623.0
16 TraesCS1A01G396500 chr5D 93.719 1417 56 8 1 1402 527622615 527624013 0.000000e+00 2093.0
17 TraesCS1A01G396500 chr5D 93.643 1400 55 9 1 1385 527593103 527594483 0.000000e+00 2061.0
18 TraesCS1A01G396500 chr5D 91.101 427 36 1 1918 2342 527624392 527624818 5.610000e-161 577.0
19 TraesCS1A01G396500 chr5D 91.705 217 14 2 1442 1658 527624181 527624393 4.890000e-77 298.0
20 TraesCS1A01G396500 chr5D 90.278 144 13 1 2067 2209 277690947 277691090 1.110000e-43 187.0
21 TraesCS1A01G396500 chr5D 74.155 414 72 21 1947 2329 434717473 434717064 3.140000e-29 139.0
22 TraesCS1A01G396500 chr5A 93.267 1411 68 7 1 1402 17810732 17812124 0.000000e+00 2054.0
23 TraesCS1A01G396500 chr5A 91.121 428 34 3 1918 2342 17812510 17812936 5.610000e-161 577.0
24 TraesCS1A01G396500 chr2D 92.938 1416 69 6 1 1402 35586619 35588017 0.000000e+00 2032.0
25 TraesCS1A01G396500 chr2D 91.803 427 33 1 1918 2342 35588403 35588829 5.570000e-166 593.0
26 TraesCS1A01G396500 chr2D 95.880 267 11 0 1657 1923 8271300 8271566 1.290000e-117 433.0
27 TraesCS1A01G396500 chr2D 92.593 216 15 1 1444 1658 35588189 35588404 2.260000e-80 309.0
28 TraesCS1A01G396500 chrUn 93.761 1154 40 7 1 1140 331175082 331176217 0.000000e+00 1703.0
29 TraesCS1A01G396500 chrUn 82.552 1066 129 28 104 1147 91312763 91311733 0.000000e+00 885.0
30 TraesCS1A01G396500 chrUn 100.000 39 0 0 1503 1541 287061820 287061782 3.230000e-09 73.1
31 TraesCS1A01G396500 chr6A 93.983 964 47 3 442 1402 557348885 557349840 0.000000e+00 1448.0
32 TraesCS1A01G396500 chr6A 88.235 425 29 9 1918 2342 557350223 557350626 2.710000e-134 488.0
33 TraesCS1A01G396500 chr6A 91.705 217 16 1 1442 1658 557350010 557350224 1.360000e-77 300.0
34 TraesCS1A01G396500 chr7D 82.732 1054 125 28 104 1135 89809214 89810232 0.000000e+00 885.0
35 TraesCS1A01G396500 chr7D 88.811 286 29 2 2059 2342 375308413 375308129 4.790000e-92 348.0
36 TraesCS1A01G396500 chr7D 75.976 333 54 17 2029 2340 625108024 625108351 5.210000e-32 148.0
37 TraesCS1A01G396500 chr7B 82.621 1053 123 32 104 1135 20716276 20715263 0.000000e+00 876.0
38 TraesCS1A01G396500 chr7B 87.912 273 31 1 2068 2338 684470448 684470176 1.040000e-83 320.0
39 TraesCS1A01G396500 chr7B 86.364 286 36 2 2059 2342 537208695 537208979 2.260000e-80 309.0
40 TraesCS1A01G396500 chr4D 96.241 266 10 0 1654 1919 15611690 15611425 9.940000e-119 436.0
41 TraesCS1A01G396500 chr4D 94.815 270 13 1 1652 1920 20999725 20999994 1.000000e-113 420.0
42 TraesCS1A01G396500 chr4D 89.091 55 4 2 1495 1548 25214029 25213976 1.500000e-07 67.6
43 TraesCS1A01G396500 chr4B 95.880 267 10 1 1656 1922 555841931 555842196 4.620000e-117 431.0
44 TraesCS1A01G396500 chr4B 95.849 265 11 0 1656 1920 561248078 561247814 1.660000e-116 429.0
45 TraesCS1A01G396500 chr3D 95.522 268 12 0 1656 1923 303360571 303360304 1.660000e-116 429.0
46 TraesCS1A01G396500 chr3D 88.000 250 28 1 2059 2306 304355502 304355253 6.330000e-76 294.0
47 TraesCS1A01G396500 chr3D 73.913 414 78 23 1947 2333 31953669 31954079 3.140000e-29 139.0
48 TraesCS1A01G396500 chr3D 100.000 39 0 0 1503 1541 570116466 570116428 3.230000e-09 73.1
49 TraesCS1A01G396500 chr5B 95.167 269 11 2 1656 1923 408170762 408171029 7.740000e-115 424.0
50 TraesCS1A01G396500 chr2B 94.815 270 14 0 1656 1925 280239338 280239069 2.780000e-114 422.0
51 TraesCS1A01G396500 chr2B 89.313 262 26 1 2059 2318 775117935 775117674 6.240000e-86 327.0
52 TraesCS1A01G396500 chr2B 82.353 289 44 5 2059 2342 447734153 447733867 6.460000e-61 244.0
53 TraesCS1A01G396500 chr3A 95.113 266 13 0 1655 1920 214725666 214725931 1.000000e-113 420.0
54 TraesCS1A01G396500 chr3A 88.811 286 30 1 2059 2342 750331949 750332234 1.330000e-92 350.0
55 TraesCS1A01G396500 chr3B 86.713 286 35 2 2059 2342 31518929 31518645 4.860000e-82 315.0
56 TraesCS1A01G396500 chr6B 85.315 286 39 2 2059 2342 675549669 675549953 2.280000e-75 292.0
57 TraesCS1A01G396500 chr1B 77.863 262 43 9 2038 2285 561876322 561876062 5.210000e-32 148.0
58 TraesCS1A01G396500 chr1B 79.891 184 34 3 2157 2338 7259899 7260081 5.250000e-27 132.0
59 TraesCS1A01G396500 chr1B 79.255 188 36 3 2157 2342 6277639 6277453 6.790000e-26 128.0
60 TraesCS1A01G396500 chr1D 77.091 275 44 12 2029 2285 474025136 474025409 8.730000e-30 141.0
61 TraesCS1A01G396500 chr1D 80.588 170 33 0 2169 2338 112118322 112118491 5.250000e-27 132.0
62 TraesCS1A01G396500 chr6D 73.630 292 54 17 1950 2221 220029994 220029706 8.910000e-15 91.6
63 TraesCS1A01G396500 chr6D 92.063 63 4 1 2157 2218 119160149 119160211 1.150000e-13 87.9


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 TraesCS1A01G396500 chr1A 562587213 562589554 2341 False 4325.000000 4325 100.000000 1 2342 1 chr1A.!!$F1 2341
1 TraesCS1A01G396500 chr2A 55466120 55468233 2113 True 1656.500000 2627 95.400000 1 2342 2 chr2A.!!$R2 2341
2 TraesCS1A01G396500 chr4A 56250651 56252752 2101 True 1636.500000 2621 94.710500 1 2342 2 chr4A.!!$R2 2341
3 TraesCS1A01G396500 chr7A 90541697 90543772 2075 True 1617.500000 2612 94.246500 1 2338 2 chr7A.!!$R2 2337
4 TraesCS1A01G396500 chr7A 81230563 81231492 929 True 767.000000 767 81.971000 109 1040 1 chr7A.!!$R1 931
5 TraesCS1A01G396500 chr7A 180466701 180467397 696 False 710.000000 710 85.311000 104 798 1 chr7A.!!$F1 694
6 TraesCS1A01G396500 chr5D 527593103 527594483 1380 False 2061.000000 2061 93.643000 1 1385 1 chr5D.!!$F2 1384
7 TraesCS1A01G396500 chr5D 527622615 527624818 2203 False 989.333333 2093 92.175000 1 2342 3 chr5D.!!$F3 2341
8 TraesCS1A01G396500 chr5A 17810732 17812936 2204 False 1315.500000 2054 92.194000 1 2342 2 chr5A.!!$F1 2341
9 TraesCS1A01G396500 chr2D 35586619 35588829 2210 False 978.000000 2032 92.444667 1 2342 3 chr2D.!!$F2 2341
10 TraesCS1A01G396500 chrUn 331175082 331176217 1135 False 1703.000000 1703 93.761000 1 1140 1 chrUn.!!$F1 1139
11 TraesCS1A01G396500 chrUn 91311733 91312763 1030 True 885.000000 885 82.552000 104 1147 1 chrUn.!!$R1 1043
12 TraesCS1A01G396500 chr6A 557348885 557350626 1741 False 745.333333 1448 91.307667 442 2342 3 chr6A.!!$F1 1900
13 TraesCS1A01G396500 chr7D 89809214 89810232 1018 False 885.000000 885 82.732000 104 1135 1 chr7D.!!$F1 1031
14 TraesCS1A01G396500 chr7B 20715263 20716276 1013 True 876.000000 876 82.621000 104 1135 1 chr7B.!!$R1 1031

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
963 1021 0.476611 AGGAGTTTCAGGAAGGGGCT 60.477 55.0 0.0 0.0 0.0 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1834 2030 0.320421 ATTACGCTGCACCACTCGTT 60.32 50.0 0.0 0.0 36.5 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
25 26 4.702131 ACATGATGGACTAACCTTTTCAGC 59.298 41.667 0.00 0.00 39.86 4.26
57 58 1.064166 AGCATCATCTCACCCCCTTTG 60.064 52.381 0.00 0.00 0.00 2.77
71 72 0.673437 CCTTTGAAAGCCGCCTTCAA 59.327 50.000 12.23 12.23 0.00 2.69
87 88 4.272489 CCTTCAAAATCTGATGTGGCCTA 58.728 43.478 3.32 0.00 32.78 3.93
251 253 7.593825 AGCAAAAGCGAGATTACAAAACTTAT 58.406 30.769 0.00 0.00 0.00 1.73
453 470 5.925509 TCTTATGTACTATTCCCAACTGCC 58.074 41.667 0.00 0.00 0.00 4.85
517 534 0.898326 TAGCCAGCTCAACTCACCGA 60.898 55.000 0.00 0.00 0.00 4.69
576 595 6.554334 TTCAACACATAGGCTTGACTTTAC 57.446 37.500 0.00 0.00 0.00 2.01
792 843 2.094675 GAACACAATCCCACCATCCAG 58.905 52.381 0.00 0.00 0.00 3.86
834 885 2.289010 CGCCACATATATGACCTGCTCA 60.289 50.000 19.63 0.00 0.00 4.26
926 977 1.677633 TCCACTCGGCGACATCAGA 60.678 57.895 4.99 0.00 0.00 3.27
949 1000 1.608717 GCACACGGATGAGGAGGAGT 61.609 60.000 0.00 0.00 0.00 3.85
963 1021 0.476611 AGGAGTTTCAGGAAGGGGCT 60.477 55.000 0.00 0.00 0.00 5.19
1122 1184 2.691623 AGGGCTGCCAGATCTGCT 60.692 61.111 22.05 4.85 0.00 4.24
1140 1202 0.036010 CTGGCCAACAAGACGGAGAT 60.036 55.000 7.01 0.00 0.00 2.75
1198 1260 0.544833 TAAGGGGCTGGGTGACGTTA 60.545 55.000 0.00 0.00 0.00 3.18
1205 1267 0.966920 CTGGGTGACGTTACTGGACT 59.033 55.000 10.54 0.00 0.00 3.85
1305 1367 2.200955 GATGGGGGAAAGAGAAGGAGT 58.799 52.381 0.00 0.00 0.00 3.85
1309 1371 0.034960 GGGAAAGAGAAGGAGTGGCC 60.035 60.000 0.00 0.00 0.00 5.36
1334 1396 4.570719 GGGAGGTTTCATCAGAGGGAAAAT 60.571 45.833 2.46 0.00 35.03 1.82
1452 1623 3.069300 CACATGTGTTGGACCCAAATCAA 59.931 43.478 18.03 0.00 37.70 2.57
1658 1854 8.368668 GGAGGGAGTATATTGGTATGCATATAC 58.631 40.741 10.16 8.19 38.41 1.47
1659 1855 9.148879 GAGGGAGTATATTGGTATGCATATACT 57.851 37.037 14.54 14.54 45.68 2.12
1664 1860 9.148879 AGTATATTGGTATGCATATACTCTCCC 57.851 37.037 10.16 5.05 42.04 4.30
1665 1861 5.700402 ATTGGTATGCATATACTCTCCCC 57.300 43.478 10.16 4.30 39.30 4.81
1666 1862 3.096852 TGGTATGCATATACTCTCCCCG 58.903 50.000 10.16 0.00 39.30 5.73
1667 1863 3.097614 GGTATGCATATACTCTCCCCGT 58.902 50.000 10.16 0.00 39.30 5.28
1668 1864 3.514309 GGTATGCATATACTCTCCCCGTT 59.486 47.826 10.16 0.00 39.30 4.44
1669 1865 3.963428 ATGCATATACTCTCCCCGTTC 57.037 47.619 0.00 0.00 0.00 3.95
1670 1866 1.968493 TGCATATACTCTCCCCGTTCC 59.032 52.381 0.00 0.00 0.00 3.62
1671 1867 2.249139 GCATATACTCTCCCCGTTCCT 58.751 52.381 0.00 0.00 0.00 3.36
1672 1868 3.181426 TGCATATACTCTCCCCGTTCCTA 60.181 47.826 0.00 0.00 0.00 2.94
1673 1869 3.444388 GCATATACTCTCCCCGTTCCTAG 59.556 52.174 0.00 0.00 0.00 3.02
1674 1870 4.810033 GCATATACTCTCCCCGTTCCTAGA 60.810 50.000 0.00 0.00 0.00 2.43
1675 1871 5.511363 CATATACTCTCCCCGTTCCTAGAT 58.489 45.833 0.00 0.00 0.00 1.98
1676 1872 6.660800 CATATACTCTCCCCGTTCCTAGATA 58.339 44.000 0.00 0.00 0.00 1.98
1677 1873 5.799978 ATACTCTCCCCGTTCCTAGATAT 57.200 43.478 0.00 0.00 0.00 1.63
1678 1874 6.905067 ATACTCTCCCCGTTCCTAGATATA 57.095 41.667 0.00 0.00 0.00 0.86
1679 1875 5.182169 ACTCTCCCCGTTCCTAGATATAG 57.818 47.826 0.00 0.00 0.00 1.31
1680 1876 4.018233 ACTCTCCCCGTTCCTAGATATAGG 60.018 50.000 7.11 7.11 38.58 2.57
1681 1877 3.268856 TCTCCCCGTTCCTAGATATAGGG 59.731 52.174 13.45 0.00 37.81 3.53
1682 1878 2.998910 TCCCCGTTCCTAGATATAGGGT 59.001 50.000 13.45 0.00 37.81 4.34
1683 1879 3.097614 CCCCGTTCCTAGATATAGGGTG 58.902 54.545 13.45 3.91 37.81 4.61
1684 1880 3.501751 CCCCGTTCCTAGATATAGGGTGT 60.502 52.174 13.45 0.00 37.81 4.16
1685 1881 4.264083 CCCCGTTCCTAGATATAGGGTGTA 60.264 50.000 13.45 0.00 37.81 2.90
1686 1882 5.516984 CCCGTTCCTAGATATAGGGTGTAT 58.483 45.833 13.45 0.00 37.81 2.29
1687 1883 6.354213 CCCCGTTCCTAGATATAGGGTGTATA 60.354 46.154 13.45 0.00 37.81 1.47
1688 1884 6.771749 CCCGTTCCTAGATATAGGGTGTATAG 59.228 46.154 13.45 0.00 37.81 1.31
1689 1885 7.344913 CCGTTCCTAGATATAGGGTGTATAGT 58.655 42.308 13.45 0.00 37.81 2.12
1690 1886 7.833183 CCGTTCCTAGATATAGGGTGTATAGTT 59.167 40.741 13.45 0.00 37.81 2.24
1691 1887 9.240734 CGTTCCTAGATATAGGGTGTATAGTTT 57.759 37.037 13.45 0.00 37.81 2.66
1696 1892 9.654663 CTAGATATAGGGTGTATAGTTTTTGGC 57.345 37.037 0.00 0.00 0.00 4.52
1697 1893 8.041143 AGATATAGGGTGTATAGTTTTTGGCA 57.959 34.615 0.00 0.00 0.00 4.92
1698 1894 7.937394 AGATATAGGGTGTATAGTTTTTGGCAC 59.063 37.037 0.00 0.00 0.00 5.01
1699 1895 3.078837 AGGGTGTATAGTTTTTGGCACG 58.921 45.455 0.00 0.00 0.00 5.34
1700 1896 2.162809 GGGTGTATAGTTTTTGGCACGG 59.837 50.000 0.00 0.00 0.00 4.94
1701 1897 3.075884 GGTGTATAGTTTTTGGCACGGA 58.924 45.455 0.00 0.00 0.00 4.69
1702 1898 3.502979 GGTGTATAGTTTTTGGCACGGAA 59.497 43.478 0.00 0.00 0.00 4.30
1703 1899 4.023021 GGTGTATAGTTTTTGGCACGGAAA 60.023 41.667 0.00 0.00 0.00 3.13
1704 1900 5.336134 GGTGTATAGTTTTTGGCACGGAAAT 60.336 40.000 0.00 0.00 0.00 2.17
1705 1901 6.153756 GTGTATAGTTTTTGGCACGGAAATT 58.846 36.000 0.00 0.00 0.00 1.82
1706 1902 7.306953 GTGTATAGTTTTTGGCACGGAAATTA 58.693 34.615 0.00 0.00 0.00 1.40
1707 1903 7.808856 GTGTATAGTTTTTGGCACGGAAATTAA 59.191 33.333 0.00 0.00 0.00 1.40
1708 1904 8.358148 TGTATAGTTTTTGGCACGGAAATTAAA 58.642 29.630 0.00 0.00 0.00 1.52
1709 1905 7.883229 ATAGTTTTTGGCACGGAAATTAAAG 57.117 32.000 0.00 0.00 0.00 1.85
1710 1906 5.908341 AGTTTTTGGCACGGAAATTAAAGA 58.092 33.333 0.00 0.00 0.00 2.52
1711 1907 6.342111 AGTTTTTGGCACGGAAATTAAAGAA 58.658 32.000 0.00 0.00 0.00 2.52
1712 1908 6.256975 AGTTTTTGGCACGGAAATTAAAGAAC 59.743 34.615 0.00 0.00 0.00 3.01
1713 1909 3.546002 TGGCACGGAAATTAAAGAACG 57.454 42.857 0.00 0.00 0.00 3.95
1714 1910 2.247637 GGCACGGAAATTAAAGAACGC 58.752 47.619 0.00 0.00 0.00 4.84
1715 1911 2.350964 GGCACGGAAATTAAAGAACGCA 60.351 45.455 0.00 0.00 0.00 5.24
1716 1912 3.498082 GCACGGAAATTAAAGAACGCAT 58.502 40.909 0.00 0.00 0.00 4.73
1717 1913 3.300590 GCACGGAAATTAAAGAACGCATG 59.699 43.478 0.00 0.00 0.00 4.06
1718 1914 4.472286 CACGGAAATTAAAGAACGCATGT 58.528 39.130 0.00 0.00 0.00 3.21
1719 1915 4.320690 CACGGAAATTAAAGAACGCATGTG 59.679 41.667 4.30 4.30 0.00 3.21
1720 1916 3.851403 CGGAAATTAAAGAACGCATGTGG 59.149 43.478 11.65 0.00 0.00 4.17
1721 1917 4.378978 CGGAAATTAAAGAACGCATGTGGA 60.379 41.667 11.65 0.00 0.00 4.02
1722 1918 5.095490 GGAAATTAAAGAACGCATGTGGAG 58.905 41.667 11.65 0.00 0.00 3.86
1723 1919 4.701956 AATTAAAGAACGCATGTGGAGG 57.298 40.909 11.65 0.00 0.00 4.30
1724 1920 2.107950 TAAAGAACGCATGTGGAGGG 57.892 50.000 11.65 0.00 0.00 4.30
1725 1921 0.400213 AAAGAACGCATGTGGAGGGA 59.600 50.000 11.65 0.00 0.00 4.20
1726 1922 0.400213 AAGAACGCATGTGGAGGGAA 59.600 50.000 11.65 0.00 0.00 3.97
1727 1923 0.400213 AGAACGCATGTGGAGGGAAA 59.600 50.000 11.65 0.00 0.00 3.13
1728 1924 1.202879 AGAACGCATGTGGAGGGAAAA 60.203 47.619 11.65 0.00 0.00 2.29
1729 1925 1.818674 GAACGCATGTGGAGGGAAAAT 59.181 47.619 11.65 0.00 0.00 1.82
1730 1926 1.923356 ACGCATGTGGAGGGAAAATT 58.077 45.000 11.65 0.00 0.00 1.82
1731 1927 2.247358 ACGCATGTGGAGGGAAAATTT 58.753 42.857 11.65 0.00 0.00 1.82
1732 1928 2.231235 ACGCATGTGGAGGGAAAATTTC 59.769 45.455 11.65 0.00 0.00 2.17
1733 1929 2.230992 CGCATGTGGAGGGAAAATTTCA 59.769 45.455 8.09 0.00 0.00 2.69
1734 1930 3.588955 GCATGTGGAGGGAAAATTTCAC 58.411 45.455 8.09 3.68 0.00 3.18
1735 1931 3.006752 GCATGTGGAGGGAAAATTTCACA 59.993 43.478 10.88 9.69 39.07 3.58
1736 1932 4.502950 GCATGTGGAGGGAAAATTTCACAA 60.503 41.667 10.88 0.00 38.39 3.33
1737 1933 4.935352 TGTGGAGGGAAAATTTCACAAG 57.065 40.909 10.88 0.00 34.83 3.16
1738 1934 4.285863 TGTGGAGGGAAAATTTCACAAGT 58.714 39.130 10.88 0.00 34.83 3.16
1739 1935 4.714308 TGTGGAGGGAAAATTTCACAAGTT 59.286 37.500 10.88 0.00 34.83 2.66
1740 1936 5.188751 TGTGGAGGGAAAATTTCACAAGTTT 59.811 36.000 10.88 0.00 34.83 2.66
1741 1937 6.112734 GTGGAGGGAAAATTTCACAAGTTTT 58.887 36.000 10.88 0.00 34.83 2.43
1742 1938 6.037062 GTGGAGGGAAAATTTCACAAGTTTTG 59.963 38.462 10.88 0.00 34.83 2.44
1743 1939 6.070538 TGGAGGGAAAATTTCACAAGTTTTGA 60.071 34.615 10.88 0.00 34.83 2.69
1744 1940 6.479990 GGAGGGAAAATTTCACAAGTTTTGAG 59.520 38.462 10.88 0.00 34.83 3.02
1745 1941 6.946340 AGGGAAAATTTCACAAGTTTTGAGT 58.054 32.000 10.88 0.00 34.83 3.41
1746 1942 6.818142 AGGGAAAATTTCACAAGTTTTGAGTG 59.182 34.615 10.88 0.00 34.83 3.51
1747 1943 6.816140 GGGAAAATTTCACAAGTTTTGAGTGA 59.184 34.615 8.09 0.00 40.24 3.41
1748 1944 7.010460 GGGAAAATTTCACAAGTTTTGAGTGAG 59.990 37.037 8.09 0.00 42.54 3.51
1749 1945 7.759433 GGAAAATTTCACAAGTTTTGAGTGAGA 59.241 33.333 8.09 0.00 42.54 3.27
1750 1946 9.305925 GAAAATTTCACAAGTTTTGAGTGAGAT 57.694 29.630 0.11 0.00 42.54 2.75
1751 1947 9.657419 AAAATTTCACAAGTTTTGAGTGAGATT 57.343 25.926 0.00 0.00 44.15 2.40
1753 1949 9.736023 AATTTCACAAGTTTTGAGTGAGATTAC 57.264 29.630 8.27 0.00 42.00 1.89
1754 1950 7.857734 TTCACAAGTTTTGAGTGAGATTACA 57.142 32.000 0.00 0.00 42.54 2.41
1755 1951 7.246674 TCACAAGTTTTGAGTGAGATTACAC 57.753 36.000 0.00 0.00 37.36 2.90
1756 1952 6.821160 TCACAAGTTTTGAGTGAGATTACACA 59.179 34.615 0.00 0.00 42.45 3.72
1757 1953 7.498900 TCACAAGTTTTGAGTGAGATTACACAT 59.501 33.333 0.00 0.00 42.45 3.21
1758 1954 7.588854 CACAAGTTTTGAGTGAGATTACACATG 59.411 37.037 0.00 0.00 42.45 3.21
1759 1955 7.498900 ACAAGTTTTGAGTGAGATTACACATGA 59.501 33.333 0.00 0.00 42.45 3.07
1760 1956 7.426929 AGTTTTGAGTGAGATTACACATGAC 57.573 36.000 0.00 0.00 42.45 3.06
1761 1957 7.220030 AGTTTTGAGTGAGATTACACATGACT 58.780 34.615 0.00 0.00 42.45 3.41
1762 1958 8.367911 AGTTTTGAGTGAGATTACACATGACTA 58.632 33.333 0.00 0.00 42.45 2.59
1763 1959 8.988934 GTTTTGAGTGAGATTACACATGACTAA 58.011 33.333 0.00 0.00 42.45 2.24
1764 1960 9.725019 TTTTGAGTGAGATTACACATGACTAAT 57.275 29.630 0.00 0.00 42.45 1.73
1765 1961 9.725019 TTTGAGTGAGATTACACATGACTAATT 57.275 29.630 0.00 0.00 42.45 1.40
1766 1962 8.707938 TGAGTGAGATTACACATGACTAATTG 57.292 34.615 0.00 0.00 42.45 2.32
1767 1963 8.531146 TGAGTGAGATTACACATGACTAATTGA 58.469 33.333 0.00 0.00 42.45 2.57
1768 1964 8.709386 AGTGAGATTACACATGACTAATTGAC 57.291 34.615 0.00 0.00 42.45 3.18
1769 1965 8.314021 AGTGAGATTACACATGACTAATTGACA 58.686 33.333 0.00 0.31 42.45 3.58
1770 1966 9.102757 GTGAGATTACACATGACTAATTGACAT 57.897 33.333 0.00 0.00 40.11 3.06
1772 1968 9.317936 GAGATTACACATGACTAATTGACATGA 57.682 33.333 20.06 5.97 46.51 3.07
1773 1969 9.322773 AGATTACACATGACTAATTGACATGAG 57.677 33.333 20.06 16.34 46.51 2.90
1774 1970 9.317936 GATTACACATGACTAATTGACATGAGA 57.682 33.333 20.06 8.28 46.51 3.27
1775 1971 9.671279 ATTACACATGACTAATTGACATGAGAA 57.329 29.630 20.06 13.51 46.51 2.87
1776 1972 7.984422 ACACATGACTAATTGACATGAGAAA 57.016 32.000 20.06 0.00 46.51 2.52
1777 1973 8.394971 ACACATGACTAATTGACATGAGAAAA 57.605 30.769 20.06 0.00 46.51 2.29
1778 1974 9.017509 ACACATGACTAATTGACATGAGAAAAT 57.982 29.630 20.06 0.00 46.51 1.82
1783 1979 9.605275 TGACTAATTGACATGAGAAAATAGAGG 57.395 33.333 0.00 0.00 0.00 3.69
1784 1980 9.823647 GACTAATTGACATGAGAAAATAGAGGA 57.176 33.333 0.00 0.00 0.00 3.71
1845 2041 4.434713 AAATTATCCAAACGAGTGGTGC 57.565 40.909 8.62 0.00 39.88 5.01
1846 2042 2.552599 TTATCCAAACGAGTGGTGCA 57.447 45.000 8.62 0.00 39.88 4.57
1847 2043 2.093306 TATCCAAACGAGTGGTGCAG 57.907 50.000 8.62 0.00 39.88 4.41
1848 2044 1.237285 ATCCAAACGAGTGGTGCAGC 61.237 55.000 9.47 9.47 39.88 5.25
1849 2045 2.249309 CAAACGAGTGGTGCAGCG 59.751 61.111 11.91 0.00 0.00 5.18
1850 2046 2.203015 AAACGAGTGGTGCAGCGT 60.203 55.556 11.91 0.06 38.81 5.07
1851 2047 1.068417 AAACGAGTGGTGCAGCGTA 59.932 52.632 11.91 0.00 35.74 4.42
1852 2048 0.531090 AAACGAGTGGTGCAGCGTAA 60.531 50.000 11.91 0.00 35.74 3.18
1853 2049 0.320421 AACGAGTGGTGCAGCGTAAT 60.320 50.000 11.91 0.00 35.74 1.89
1854 2050 0.528924 ACGAGTGGTGCAGCGTAATA 59.471 50.000 11.91 0.00 34.93 0.98
1855 2051 0.921347 CGAGTGGTGCAGCGTAATAC 59.079 55.000 11.91 3.18 0.00 1.89
1856 2052 1.734377 CGAGTGGTGCAGCGTAATACA 60.734 52.381 11.91 0.00 0.00 2.29
1857 2053 1.659098 GAGTGGTGCAGCGTAATACAC 59.341 52.381 11.91 1.64 0.00 2.90
1865 2061 6.780706 GTGCAGCGTAATACACCTTATATT 57.219 37.500 0.00 0.00 0.00 1.28
1866 2062 7.186021 GTGCAGCGTAATACACCTTATATTT 57.814 36.000 0.00 0.00 0.00 1.40
1867 2063 7.288672 GTGCAGCGTAATACACCTTATATTTC 58.711 38.462 0.00 0.00 0.00 2.17
1868 2064 6.144886 TGCAGCGTAATACACCTTATATTTCG 59.855 38.462 0.00 0.00 36.47 3.46
1869 2065 6.400727 GCAGCGTAATACACCTTATATTTCGG 60.401 42.308 6.10 0.00 34.95 4.30
1870 2066 6.864685 CAGCGTAATACACCTTATATTTCGGA 59.135 38.462 6.10 0.00 34.95 4.55
1871 2067 6.865205 AGCGTAATACACCTTATATTTCGGAC 59.135 38.462 6.10 0.00 34.95 4.79
1872 2068 6.865205 GCGTAATACACCTTATATTTCGGACT 59.135 38.462 6.10 0.00 34.95 3.85
1873 2069 7.383300 GCGTAATACACCTTATATTTCGGACTT 59.617 37.037 6.10 0.00 34.95 3.01
1874 2070 9.252962 CGTAATACACCTTATATTTCGGACTTT 57.747 33.333 0.00 0.00 32.42 2.66
1878 2074 9.901172 ATACACCTTATATTTCGGACTTTTTCT 57.099 29.630 0.00 0.00 0.00 2.52
1879 2075 8.265165 ACACCTTATATTTCGGACTTTTTCTC 57.735 34.615 0.00 0.00 0.00 2.87
1880 2076 7.881232 ACACCTTATATTTCGGACTTTTTCTCA 59.119 33.333 0.00 0.00 0.00 3.27
1881 2077 8.726988 CACCTTATATTTCGGACTTTTTCTCAA 58.273 33.333 0.00 0.00 0.00 3.02
1882 2078 9.292195 ACCTTATATTTCGGACTTTTTCTCAAA 57.708 29.630 0.00 0.00 0.00 2.69
1886 2082 8.812147 ATATTTCGGACTTTTTCTCAAAAACC 57.188 30.769 0.00 0.00 35.57 3.27
1887 2083 5.907866 TTCGGACTTTTTCTCAAAAACCT 57.092 34.783 0.00 0.00 35.57 3.50
1888 2084 7.393841 TTTCGGACTTTTTCTCAAAAACCTA 57.606 32.000 0.00 0.00 35.57 3.08
1889 2085 7.576861 TTCGGACTTTTTCTCAAAAACCTAT 57.423 32.000 0.00 0.00 35.57 2.57
1890 2086 8.680039 TTCGGACTTTTTCTCAAAAACCTATA 57.320 30.769 0.00 0.00 35.57 1.31
1891 2087 8.091385 TCGGACTTTTTCTCAAAAACCTATAC 57.909 34.615 0.00 0.00 35.57 1.47
1892 2088 7.716123 TCGGACTTTTTCTCAAAAACCTATACA 59.284 33.333 0.00 0.00 35.57 2.29
1893 2089 7.801783 CGGACTTTTTCTCAAAAACCTATACAC 59.198 37.037 0.00 0.00 35.57 2.90
1894 2090 8.080417 GGACTTTTTCTCAAAAACCTATACACC 58.920 37.037 0.00 0.00 35.57 4.16
1895 2091 8.762481 ACTTTTTCTCAAAAACCTATACACCT 57.238 30.769 0.00 0.00 35.57 4.00
1896 2092 9.197306 ACTTTTTCTCAAAAACCTATACACCTT 57.803 29.630 0.00 0.00 35.57 3.50
1914 2110 7.560796 ACACCTTATATCAAGGAATAGAGGG 57.439 40.000 9.96 0.00 39.81 4.30
1915 2111 7.313731 ACACCTTATATCAAGGAATAGAGGGA 58.686 38.462 9.96 0.00 39.81 4.20
1916 2112 7.456269 ACACCTTATATCAAGGAATAGAGGGAG 59.544 40.741 9.96 0.00 39.81 4.30
1917 2113 7.456269 CACCTTATATCAAGGAATAGAGGGAGT 59.544 40.741 9.96 0.00 39.81 3.85
1918 2114 8.689054 ACCTTATATCAAGGAATAGAGGGAGTA 58.311 37.037 9.96 0.00 39.81 2.59
1944 2140 5.880054 AGTTATAGTTGAATGTGTGTGCC 57.120 39.130 0.00 0.00 0.00 5.01
2006 2202 5.488645 AAACTATAAATTACAACCGGCCG 57.511 39.130 21.04 21.04 0.00 6.13
2096 2292 2.223852 TGTCATCAACGACTCCGACAAA 60.224 45.455 0.00 0.00 39.50 2.83
2111 2307 2.674177 CGACAAAGGAGCTATTCACCGT 60.674 50.000 0.00 0.00 0.00 4.83
2139 2337 2.960688 GCCACACTCTCCCTCCCAC 61.961 68.421 0.00 0.00 0.00 4.61
2154 2352 1.065345 TCCCACGGTCAAACTTGTTGA 60.065 47.619 0.00 0.00 0.00 3.18
2203 2401 1.456705 GCCCTCTCGTCCTGGATCT 60.457 63.158 0.00 0.00 0.00 2.75
2209 2407 3.499563 CCTCTCGTCCTGGATCTAAGGAT 60.500 52.174 17.31 0.00 45.47 3.24
2239 2437 1.601759 GGCAGGCAGAGCAACTCAA 60.602 57.895 0.00 0.00 32.06 3.02
2313 2511 1.597461 GCGAGCTCACCCCTAAAGT 59.403 57.895 15.40 0.00 0.00 2.66
2324 2522 5.969423 TCACCCCTAAAGTAAACTCATACG 58.031 41.667 0.00 0.00 0.00 3.06
2338 2536 3.104602 ATACGTCGCCACCGTCTCG 62.105 63.158 0.00 0.00 39.60 4.04
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 4.036144 TGAGATGATGCTCGTCAAGACTAG 59.964 45.833 7.74 0.00 37.73 2.57
57 58 2.228822 TCAGATTTTGAAGGCGGCTTTC 59.771 45.455 26.25 17.97 31.34 2.62
71 72 9.812347 TTGATAAATATAGGCCACATCAGATTT 57.188 29.630 5.01 3.95 0.00 2.17
251 253 9.491675 TTCAGTTTTGGTTCGTAGATGTAATTA 57.508 29.630 0.00 0.00 35.04 1.40
517 534 2.339712 GCAAGTGGCCATTTGCGT 59.660 55.556 39.43 11.70 42.56 5.24
576 595 3.312697 GCCGAGCCTATTAGTTTGGAAAG 59.687 47.826 0.00 0.00 0.00 2.62
762 813 2.306847 GGATTGTGTTCTGGTGGTTGT 58.693 47.619 0.00 0.00 0.00 3.32
792 843 3.600346 GTGTGTACGTGTGCTTTTGTAC 58.400 45.455 0.00 0.00 38.10 2.90
834 885 1.372872 GGGCTTTGCGCAATTCGTT 60.373 52.632 25.64 0.00 41.23 3.85
856 907 3.069318 GGTCCGGTCGCCTCTTCT 61.069 66.667 0.00 0.00 0.00 2.85
926 977 3.402681 CCTCATCCGTGTGCCCCT 61.403 66.667 0.00 0.00 0.00 4.79
949 1000 2.274542 TGTATCAGCCCCTTCCTGAAA 58.725 47.619 0.00 0.00 42.12 2.69
963 1021 1.686587 CACCTCCTACGCCATGTATCA 59.313 52.381 0.00 0.00 31.20 2.15
1033 1095 2.579873 CCCATTCAATAGGTGCTGGAG 58.420 52.381 0.00 0.00 33.68 3.86
1122 1184 0.321564 CATCTCCGTCTTGTTGGCCA 60.322 55.000 0.00 0.00 0.00 5.36
1140 1202 3.568007 CGAAAATGTCCTTTTGACTCCCA 59.432 43.478 0.00 0.00 44.75 4.37
1198 1260 1.210967 CGTCTCTCTCCCTAGTCCAGT 59.789 57.143 0.00 0.00 0.00 4.00
1205 1267 0.547075 CACCCTCGTCTCTCTCCCTA 59.453 60.000 0.00 0.00 0.00 3.53
1305 1367 1.139498 TGATGAAACCTCCCAGGCCA 61.139 55.000 5.01 0.00 39.63 5.36
1309 1371 1.211457 CCCTCTGATGAAACCTCCCAG 59.789 57.143 0.00 0.00 0.00 4.45
1334 1396 1.616327 CCTCCCATGTCTCACCCCA 60.616 63.158 0.00 0.00 0.00 4.96
1519 1714 7.438459 ACATATAAAGTAGTGATCCAAACGCTC 59.562 37.037 0.00 0.00 0.00 5.03
1658 1854 4.528920 CCTATATCTAGGAACGGGGAGAG 58.471 52.174 0.00 0.00 46.66 3.20
1659 1855 3.268856 CCCTATATCTAGGAACGGGGAGA 59.731 52.174 5.74 0.00 46.66 3.71
1660 1856 3.011482 ACCCTATATCTAGGAACGGGGAG 59.989 52.174 5.74 0.00 46.66 4.30
1661 1857 2.998910 ACCCTATATCTAGGAACGGGGA 59.001 50.000 5.74 0.00 46.66 4.81
1662 1858 3.097614 CACCCTATATCTAGGAACGGGG 58.902 54.545 5.74 8.68 46.66 5.73
1663 1859 3.775910 ACACCCTATATCTAGGAACGGG 58.224 50.000 5.74 0.00 46.66 5.28
1664 1860 7.344913 ACTATACACCCTATATCTAGGAACGG 58.655 42.308 5.74 0.00 46.66 4.44
1665 1861 8.804912 AACTATACACCCTATATCTAGGAACG 57.195 38.462 5.74 0.00 46.66 3.95
1670 1866 9.654663 GCCAAAAACTATACACCCTATATCTAG 57.345 37.037 0.00 0.00 0.00 2.43
1671 1867 9.161572 TGCCAAAAACTATACACCCTATATCTA 57.838 33.333 0.00 0.00 0.00 1.98
1672 1868 7.937394 GTGCCAAAAACTATACACCCTATATCT 59.063 37.037 0.00 0.00 0.00 1.98
1673 1869 7.095355 CGTGCCAAAAACTATACACCCTATATC 60.095 40.741 0.00 0.00 0.00 1.63
1674 1870 6.708949 CGTGCCAAAAACTATACACCCTATAT 59.291 38.462 0.00 0.00 0.00 0.86
1675 1871 6.050432 CGTGCCAAAAACTATACACCCTATA 58.950 40.000 0.00 0.00 0.00 1.31
1676 1872 4.879545 CGTGCCAAAAACTATACACCCTAT 59.120 41.667 0.00 0.00 0.00 2.57
1677 1873 4.255301 CGTGCCAAAAACTATACACCCTA 58.745 43.478 0.00 0.00 0.00 3.53
1678 1874 3.078837 CGTGCCAAAAACTATACACCCT 58.921 45.455 0.00 0.00 0.00 4.34
1679 1875 2.162809 CCGTGCCAAAAACTATACACCC 59.837 50.000 0.00 0.00 0.00 4.61
1680 1876 3.075884 TCCGTGCCAAAAACTATACACC 58.924 45.455 0.00 0.00 0.00 4.16
1681 1877 4.752661 TTCCGTGCCAAAAACTATACAC 57.247 40.909 0.00 0.00 0.00 2.90
1682 1878 5.968528 ATTTCCGTGCCAAAAACTATACA 57.031 34.783 0.00 0.00 0.00 2.29
1683 1879 8.745464 TTTAATTTCCGTGCCAAAAACTATAC 57.255 30.769 0.00 0.00 0.00 1.47
1684 1880 8.794553 TCTTTAATTTCCGTGCCAAAAACTATA 58.205 29.630 0.00 0.00 0.00 1.31
1685 1881 7.662897 TCTTTAATTTCCGTGCCAAAAACTAT 58.337 30.769 0.00 0.00 0.00 2.12
1686 1882 7.040473 TCTTTAATTTCCGTGCCAAAAACTA 57.960 32.000 0.00 0.00 0.00 2.24
1687 1883 5.908341 TCTTTAATTTCCGTGCCAAAAACT 58.092 33.333 0.00 0.00 0.00 2.66
1688 1884 6.415702 GTTCTTTAATTTCCGTGCCAAAAAC 58.584 36.000 0.00 0.00 0.00 2.43
1689 1885 5.232414 CGTTCTTTAATTTCCGTGCCAAAAA 59.768 36.000 0.00 0.00 0.00 1.94
1690 1886 4.740695 CGTTCTTTAATTTCCGTGCCAAAA 59.259 37.500 0.00 0.00 0.00 2.44
1691 1887 4.291783 CGTTCTTTAATTTCCGTGCCAAA 58.708 39.130 0.00 0.00 0.00 3.28
1692 1888 3.854045 GCGTTCTTTAATTTCCGTGCCAA 60.854 43.478 0.00 0.00 0.00 4.52
1693 1889 2.350964 GCGTTCTTTAATTTCCGTGCCA 60.351 45.455 0.00 0.00 0.00 4.92
1694 1890 2.247637 GCGTTCTTTAATTTCCGTGCC 58.752 47.619 0.00 0.00 0.00 5.01
1695 1891 2.923643 TGCGTTCTTTAATTTCCGTGC 58.076 42.857 0.00 0.00 0.00 5.34
1696 1892 4.320690 CACATGCGTTCTTTAATTTCCGTG 59.679 41.667 0.00 0.00 0.00 4.94
1697 1893 4.472286 CACATGCGTTCTTTAATTTCCGT 58.528 39.130 0.00 0.00 0.00 4.69
1698 1894 3.851403 CCACATGCGTTCTTTAATTTCCG 59.149 43.478 0.00 0.00 0.00 4.30
1699 1895 5.054390 TCCACATGCGTTCTTTAATTTCC 57.946 39.130 0.00 0.00 0.00 3.13
1700 1896 5.095490 CCTCCACATGCGTTCTTTAATTTC 58.905 41.667 0.00 0.00 0.00 2.17
1701 1897 4.082245 CCCTCCACATGCGTTCTTTAATTT 60.082 41.667 0.00 0.00 0.00 1.82
1702 1898 3.443681 CCCTCCACATGCGTTCTTTAATT 59.556 43.478 0.00 0.00 0.00 1.40
1703 1899 3.016736 CCCTCCACATGCGTTCTTTAAT 58.983 45.455 0.00 0.00 0.00 1.40
1704 1900 2.039216 TCCCTCCACATGCGTTCTTTAA 59.961 45.455 0.00 0.00 0.00 1.52
1705 1901 1.626321 TCCCTCCACATGCGTTCTTTA 59.374 47.619 0.00 0.00 0.00 1.85
1706 1902 0.400213 TCCCTCCACATGCGTTCTTT 59.600 50.000 0.00 0.00 0.00 2.52
1707 1903 0.400213 TTCCCTCCACATGCGTTCTT 59.600 50.000 0.00 0.00 0.00 2.52
1708 1904 0.400213 TTTCCCTCCACATGCGTTCT 59.600 50.000 0.00 0.00 0.00 3.01
1709 1905 1.243902 TTTTCCCTCCACATGCGTTC 58.756 50.000 0.00 0.00 0.00 3.95
1710 1906 1.923356 ATTTTCCCTCCACATGCGTT 58.077 45.000 0.00 0.00 0.00 4.84
1711 1907 1.923356 AATTTTCCCTCCACATGCGT 58.077 45.000 0.00 0.00 0.00 5.24
1712 1908 2.230992 TGAAATTTTCCCTCCACATGCG 59.769 45.455 6.68 0.00 0.00 4.73
1713 1909 3.006752 TGTGAAATTTTCCCTCCACATGC 59.993 43.478 6.68 0.00 30.67 4.06
1714 1910 4.870123 TGTGAAATTTTCCCTCCACATG 57.130 40.909 6.68 0.00 30.67 3.21
1715 1911 4.901250 ACTTGTGAAATTTTCCCTCCACAT 59.099 37.500 6.68 0.00 34.95 3.21
1716 1912 4.285863 ACTTGTGAAATTTTCCCTCCACA 58.714 39.130 6.68 4.52 33.38 4.17
1717 1913 4.937201 ACTTGTGAAATTTTCCCTCCAC 57.063 40.909 6.68 0.00 0.00 4.02
1718 1914 5.948742 AAACTTGTGAAATTTTCCCTCCA 57.051 34.783 6.68 0.00 0.00 3.86
1719 1915 6.345298 TCAAAACTTGTGAAATTTTCCCTCC 58.655 36.000 6.68 0.00 0.00 4.30
1720 1916 7.010460 CACTCAAAACTTGTGAAATTTTCCCTC 59.990 37.037 6.68 0.00 33.95 4.30
1721 1917 6.818142 CACTCAAAACTTGTGAAATTTTCCCT 59.182 34.615 6.68 0.00 33.95 4.20
1722 1918 6.816140 TCACTCAAAACTTGTGAAATTTTCCC 59.184 34.615 6.68 0.00 37.71 3.97
1723 1919 7.759433 TCTCACTCAAAACTTGTGAAATTTTCC 59.241 33.333 6.68 0.00 39.74 3.13
1724 1920 8.687824 TCTCACTCAAAACTTGTGAAATTTTC 57.312 30.769 2.05 2.05 39.74 2.29
1725 1921 9.657419 AATCTCACTCAAAACTTGTGAAATTTT 57.343 25.926 0.00 0.00 39.74 1.82
1727 1923 9.736023 GTAATCTCACTCAAAACTTGTGAAATT 57.264 29.630 0.00 0.00 39.74 1.82
1728 1924 8.902806 TGTAATCTCACTCAAAACTTGTGAAAT 58.097 29.630 0.00 0.00 39.74 2.17
1729 1925 8.181573 GTGTAATCTCACTCAAAACTTGTGAAA 58.818 33.333 0.00 0.00 39.74 2.69
1730 1926 7.335673 TGTGTAATCTCACTCAAAACTTGTGAA 59.664 33.333 0.00 0.00 39.74 3.18
1731 1927 6.821160 TGTGTAATCTCACTCAAAACTTGTGA 59.179 34.615 0.00 0.00 38.90 3.58
1732 1928 7.015226 TGTGTAATCTCACTCAAAACTTGTG 57.985 36.000 0.00 0.00 38.90 3.33
1733 1929 7.498900 TCATGTGTAATCTCACTCAAAACTTGT 59.501 33.333 0.00 0.00 38.90 3.16
1734 1930 7.800380 GTCATGTGTAATCTCACTCAAAACTTG 59.200 37.037 0.00 0.00 38.90 3.16
1735 1931 7.716998 AGTCATGTGTAATCTCACTCAAAACTT 59.283 33.333 0.00 0.00 38.90 2.66
1736 1932 7.220030 AGTCATGTGTAATCTCACTCAAAACT 58.780 34.615 0.00 0.00 38.90 2.66
1737 1933 7.426929 AGTCATGTGTAATCTCACTCAAAAC 57.573 36.000 0.00 0.00 38.90 2.43
1738 1934 9.725019 ATTAGTCATGTGTAATCTCACTCAAAA 57.275 29.630 0.00 0.00 38.90 2.44
1739 1935 9.725019 AATTAGTCATGTGTAATCTCACTCAAA 57.275 29.630 0.00 0.00 38.90 2.69
1740 1936 9.154847 CAATTAGTCATGTGTAATCTCACTCAA 57.845 33.333 0.00 0.00 38.90 3.02
1741 1937 8.531146 TCAATTAGTCATGTGTAATCTCACTCA 58.469 33.333 0.00 0.00 38.90 3.41
1742 1938 8.812329 GTCAATTAGTCATGTGTAATCTCACTC 58.188 37.037 0.00 0.00 38.90 3.51
1743 1939 8.314021 TGTCAATTAGTCATGTGTAATCTCACT 58.686 33.333 0.00 0.00 38.90 3.41
1744 1940 8.479313 TGTCAATTAGTCATGTGTAATCTCAC 57.521 34.615 0.00 0.00 38.63 3.51
1745 1941 9.101655 CATGTCAATTAGTCATGTGTAATCTCA 57.898 33.333 0.00 0.11 38.46 3.27
1746 1942 9.317936 TCATGTCAATTAGTCATGTGTAATCTC 57.682 33.333 12.87 0.00 42.18 2.75
1747 1943 9.322773 CTCATGTCAATTAGTCATGTGTAATCT 57.677 33.333 12.87 0.00 42.18 2.40
1748 1944 9.317936 TCTCATGTCAATTAGTCATGTGTAATC 57.682 33.333 12.87 0.00 42.18 1.75
1749 1945 9.671279 TTCTCATGTCAATTAGTCATGTGTAAT 57.329 29.630 12.87 0.00 42.18 1.89
1750 1946 9.500785 TTTCTCATGTCAATTAGTCATGTGTAA 57.499 29.630 12.87 9.55 42.18 2.41
1751 1947 9.500785 TTTTCTCATGTCAATTAGTCATGTGTA 57.499 29.630 12.87 5.78 42.18 2.90
1752 1948 7.984422 TTTCTCATGTCAATTAGTCATGTGT 57.016 32.000 12.87 0.00 42.18 3.72
1757 1953 9.605275 CCTCTATTTTCTCATGTCAATTAGTCA 57.395 33.333 0.00 0.00 0.00 3.41
1758 1954 9.823647 TCCTCTATTTTCTCATGTCAATTAGTC 57.176 33.333 0.00 0.00 0.00 2.59
1762 1958 9.917887 AAGATCCTCTATTTTCTCATGTCAATT 57.082 29.630 0.00 0.00 0.00 2.32
1764 1960 9.823647 GTAAGATCCTCTATTTTCTCATGTCAA 57.176 33.333 0.00 0.00 0.00 3.18
1765 1961 8.981659 TGTAAGATCCTCTATTTTCTCATGTCA 58.018 33.333 0.00 0.00 0.00 3.58
1766 1962 9.995003 ATGTAAGATCCTCTATTTTCTCATGTC 57.005 33.333 0.00 0.00 0.00 3.06
1767 1963 9.775854 CATGTAAGATCCTCTATTTTCTCATGT 57.224 33.333 0.00 0.00 29.63 3.21
1768 1964 9.993454 TCATGTAAGATCCTCTATTTTCTCATG 57.007 33.333 0.00 0.00 32.17 3.07
1822 2018 5.221342 TGCACCACTCGTTTGGATAATTTTT 60.221 36.000 11.38 0.00 39.24 1.94
1823 2019 4.279671 TGCACCACTCGTTTGGATAATTTT 59.720 37.500 11.38 0.00 39.24 1.82
1824 2020 3.823873 TGCACCACTCGTTTGGATAATTT 59.176 39.130 11.38 0.00 39.24 1.82
1825 2021 3.417101 TGCACCACTCGTTTGGATAATT 58.583 40.909 11.38 0.00 39.24 1.40
1826 2022 3.009723 CTGCACCACTCGTTTGGATAAT 58.990 45.455 11.38 0.00 39.24 1.28
1827 2023 2.422597 CTGCACCACTCGTTTGGATAA 58.577 47.619 11.38 0.00 39.24 1.75
1828 2024 1.943968 GCTGCACCACTCGTTTGGATA 60.944 52.381 11.38 0.00 39.24 2.59
1829 2025 1.237285 GCTGCACCACTCGTTTGGAT 61.237 55.000 11.38 0.00 39.24 3.41
1830 2026 1.891919 GCTGCACCACTCGTTTGGA 60.892 57.895 11.38 0.00 39.24 3.53
1831 2027 2.639286 GCTGCACCACTCGTTTGG 59.361 61.111 0.00 3.82 43.04 3.28
1832 2028 1.218875 TACGCTGCACCACTCGTTTG 61.219 55.000 0.00 0.00 36.50 2.93
1833 2029 0.531090 TTACGCTGCACCACTCGTTT 60.531 50.000 0.00 0.00 36.50 3.60
1834 2030 0.320421 ATTACGCTGCACCACTCGTT 60.320 50.000 0.00 0.00 36.50 3.85
1835 2031 0.528924 TATTACGCTGCACCACTCGT 59.471 50.000 0.00 0.00 38.75 4.18
1836 2032 0.921347 GTATTACGCTGCACCACTCG 59.079 55.000 0.00 0.00 0.00 4.18
1837 2033 1.659098 GTGTATTACGCTGCACCACTC 59.341 52.381 0.00 0.00 0.00 3.51
1838 2034 1.722011 GTGTATTACGCTGCACCACT 58.278 50.000 0.00 0.00 0.00 4.00
1842 2038 6.780706 AATATAAGGTGTATTACGCTGCAC 57.219 37.500 7.28 0.00 0.00 4.57
1843 2039 6.144886 CGAAATATAAGGTGTATTACGCTGCA 59.855 38.462 7.28 0.00 0.00 4.41
1844 2040 6.400727 CCGAAATATAAGGTGTATTACGCTGC 60.401 42.308 7.28 0.00 0.00 5.25
1845 2041 6.864685 TCCGAAATATAAGGTGTATTACGCTG 59.135 38.462 7.28 0.00 0.00 5.18
1846 2042 6.865205 GTCCGAAATATAAGGTGTATTACGCT 59.135 38.462 7.28 0.00 0.00 5.07
1847 2043 6.865205 AGTCCGAAATATAAGGTGTATTACGC 59.135 38.462 0.00 0.00 0.00 4.42
1848 2044 8.807667 AAGTCCGAAATATAAGGTGTATTACG 57.192 34.615 0.00 0.00 0.00 3.18
1852 2048 9.901172 AGAAAAAGTCCGAAATATAAGGTGTAT 57.099 29.630 0.00 0.00 0.00 2.29
1853 2049 9.374838 GAGAAAAAGTCCGAAATATAAGGTGTA 57.625 33.333 0.00 0.00 0.00 2.90
1854 2050 7.881232 TGAGAAAAAGTCCGAAATATAAGGTGT 59.119 33.333 0.00 0.00 0.00 4.16
1855 2051 8.263940 TGAGAAAAAGTCCGAAATATAAGGTG 57.736 34.615 0.00 0.00 0.00 4.00
1856 2052 8.857694 TTGAGAAAAAGTCCGAAATATAAGGT 57.142 30.769 0.00 0.00 0.00 3.50
1860 2056 9.902196 GGTTTTTGAGAAAAAGTCCGAAATATA 57.098 29.630 0.00 0.00 40.71 0.86
1861 2057 8.638873 AGGTTTTTGAGAAAAAGTCCGAAATAT 58.361 29.630 0.00 0.00 40.71 1.28
1862 2058 8.002984 AGGTTTTTGAGAAAAAGTCCGAAATA 57.997 30.769 0.00 0.00 40.71 1.40
1863 2059 6.873997 AGGTTTTTGAGAAAAAGTCCGAAAT 58.126 32.000 0.00 0.00 40.71 2.17
1864 2060 6.275494 AGGTTTTTGAGAAAAAGTCCGAAA 57.725 33.333 0.00 0.00 40.71 3.46
1865 2061 5.907866 AGGTTTTTGAGAAAAAGTCCGAA 57.092 34.783 0.00 0.00 40.71 4.30
1866 2062 7.716123 TGTATAGGTTTTTGAGAAAAAGTCCGA 59.284 33.333 0.00 0.00 40.71 4.55
1867 2063 7.801783 GTGTATAGGTTTTTGAGAAAAAGTCCG 59.198 37.037 0.00 0.00 40.71 4.79
1868 2064 8.080417 GGTGTATAGGTTTTTGAGAAAAAGTCC 58.920 37.037 0.00 0.00 40.71 3.85
1869 2065 8.847196 AGGTGTATAGGTTTTTGAGAAAAAGTC 58.153 33.333 0.00 0.00 40.71 3.01
1870 2066 8.762481 AGGTGTATAGGTTTTTGAGAAAAAGT 57.238 30.769 0.00 0.00 40.71 2.66
1888 2084 9.273137 CCCTCTATTCCTTGATATAAGGTGTAT 57.727 37.037 5.67 2.19 38.55 2.29
1889 2085 8.461854 TCCCTCTATTCCTTGATATAAGGTGTA 58.538 37.037 5.67 0.79 38.55 2.90
1890 2086 7.313731 TCCCTCTATTCCTTGATATAAGGTGT 58.686 38.462 5.67 0.00 38.55 4.16
1891 2087 7.456269 ACTCCCTCTATTCCTTGATATAAGGTG 59.544 40.741 5.67 0.00 38.55 4.00
1892 2088 7.549141 ACTCCCTCTATTCCTTGATATAAGGT 58.451 38.462 5.67 0.00 38.55 3.50
1893 2089 9.722317 ATACTCCCTCTATTCCTTGATATAAGG 57.278 37.037 0.00 0.00 38.78 2.69
1899 2095 9.453830 AACTTTATACTCCCTCTATTCCTTGAT 57.546 33.333 0.00 0.00 0.00 2.57
1900 2096 8.855804 AACTTTATACTCCCTCTATTCCTTGA 57.144 34.615 0.00 0.00 0.00 3.02
1918 2114 8.458843 GGCACACACATTCAACTATAACTTTAT 58.541 33.333 0.00 0.00 0.00 1.40
2006 2202 7.646130 TGATTCATTTTCCGTTTCTTGTTGTAC 59.354 33.333 0.00 0.00 0.00 2.90
2096 2292 0.395311 TCCGACGGTGAATAGCTCCT 60.395 55.000 14.79 0.00 0.00 3.69
2111 2307 1.006571 GAGTGTGGCTTTCGTCCGA 60.007 57.895 0.00 0.00 0.00 4.55
2239 2437 3.000819 TCCATTCGTGCTCGGGGT 61.001 61.111 8.49 0.00 37.69 4.95
2313 2511 1.467883 CGGTGGCGACGTATGAGTTTA 60.468 52.381 0.00 0.00 0.00 2.01


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

AutoCloner maintained by Alex Coulton.