Multiple sequence alignment - TraesCS5B01G315700

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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 TraesCS5B01G315700 chr5B 100.000 3866 0 0 1 3866 497906644 497902779 0.000000e+00 7140.0
1 TraesCS5B01G315700 chr5B 82.432 74 13 0 2766 2839 330846571 330846498 8.970000e-07 65.8
2 TraesCS5B01G315700 chr5A 85.974 3572 261 118 357 3801 525118560 525115102 0.000000e+00 3600.0
3 TraesCS5B01G315700 chr5A 88.235 170 13 5 6 170 525118870 525118703 3.050000e-46 196.0
4 TraesCS5B01G315700 chr5A 97.727 44 0 1 247 289 525118672 525118629 1.490000e-09 75.0
5 TraesCS5B01G315700 chr5A 83.333 72 12 0 2767 2838 382564062 382563991 2.490000e-07 67.6
6 TraesCS5B01G315700 chr5D 88.100 2395 165 55 1336 3653 413067854 413065503 0.000000e+00 2734.0
7 TraesCS5B01G315700 chr5D 88.742 604 29 24 663 1242 413068493 413067905 0.000000e+00 702.0
8 TraesCS5B01G315700 chr5D 86.337 344 17 11 363 676 413068859 413068516 7.950000e-92 348.0
9 TraesCS5B01G315700 chr5D 88.085 235 10 6 6 225 413069648 413069417 2.960000e-66 263.0
10 TraesCS5B01G315700 chr5D 92.188 64 1 2 247 306 413069039 413068976 1.910000e-13 87.9
11 TraesCS5B01G315700 chr5D 92.188 64 1 2 247 306 413069426 413069363 1.910000e-13 87.9
12 TraesCS5B01G315700 chr5D 90.909 66 1 2 165 225 413069095 413069030 2.480000e-12 84.2
13 TraesCS5B01G315700 chr5D 82.667 75 13 0 2765 2839 290072191 290072117 2.490000e-07 67.6
14 TraesCS5B01G315700 chr3B 78.416 644 108 23 3215 3840 819874155 819873525 1.300000e-104 390.0
15 TraesCS5B01G315700 chr7A 81.778 450 67 9 3259 3697 592207085 592207530 2.840000e-96 363.0
16 TraesCS5B01G315700 chr7A 83.456 272 44 1 3435 3705 436768215 436767944 6.410000e-63 252.0
17 TraesCS5B01G315700 chr4A 80.249 481 82 7 3235 3705 101969872 101970349 2.210000e-92 350.0
18 TraesCS5B01G315700 chrUn 79.722 503 84 8 3209 3697 294098617 294099115 7.950000e-92 348.0
19 TraesCS5B01G315700 chrUn 79.032 248 46 6 3597 3842 294099070 294099313 8.590000e-37 165.0
20 TraesCS5B01G315700 chr1D 79.722 503 84 8 3209 3697 437836029 437836527 7.950000e-92 348.0
21 TraesCS5B01G315700 chr1D 80.519 231 38 7 3600 3828 162099624 162099849 1.850000e-38 171.0
22 TraesCS5B01G315700 chr1D 79.032 248 46 6 3597 3842 437836482 437836725 8.590000e-37 165.0
23 TraesCS5B01G315700 chr1D 77.070 157 30 5 3660 3814 162099885 162100037 6.880000e-13 86.1
24 TraesCS5B01G315700 chr3A 80.203 197 34 5 3436 3629 577073757 577073563 4.030000e-30 143.0
25 TraesCS5B01G315700 chr7B 76.125 289 56 7 3335 3613 164985576 164985291 5.210000e-29 139.0
26 TraesCS5B01G315700 chr7B 74.172 302 69 5 3335 3629 1155910 1156209 2.440000e-22 117.0
27 TraesCS5B01G315700 chr1B 82.895 76 13 0 3765 3840 180521346 180521271 6.930000e-08 69.4


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 TraesCS5B01G315700 chr5B 497902779 497906644 3865 True 7140.000000 7140 100.000000 1 3866 1 chr5B.!!$R2 3865
1 TraesCS5B01G315700 chr5A 525115102 525118870 3768 True 1290.333333 3600 90.645333 6 3801 3 chr5A.!!$R2 3795
2 TraesCS5B01G315700 chr5D 413065503 413069648 4145 True 615.285714 2734 89.507000 6 3653 7 chr5D.!!$R2 3647
3 TraesCS5B01G315700 chr3B 819873525 819874155 630 True 390.000000 390 78.416000 3215 3840 1 chr3B.!!$R1 625
4 TraesCS5B01G315700 chrUn 294098617 294099313 696 False 256.500000 348 79.377000 3209 3842 2 chrUn.!!$F1 633
5 TraesCS5B01G315700 chr1D 437836029 437836725 696 False 256.500000 348 79.377000 3209 3842 2 chr1D.!!$F2 633

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
175 188 0.237498 GCACGGAAAAGAAGGGAACG 59.763 55.0 0.0 0.00 0.00 3.95 F
182 195 0.887836 AAAGAAGGGAACGAACGCCC 60.888 55.0 0.0 0.00 45.04 6.13 F
1492 2095 0.172578 AAACTCGTGGCGATCGATCA 59.827 50.0 24.4 13.35 36.73 2.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1475 2078 0.172578 TTTGATCGATCGCCACGAGT 59.827 50.0 20.03 0.0 42.81 4.18 R
1996 2622 0.321210 TCAACCACATCGACGCCATT 60.321 50.0 0.00 0.0 0.00 3.16 R
3282 3978 0.240945 AGCAACCAAACATAGTGCGC 59.759 50.0 0.00 0.0 0.00 6.09 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
141 154 1.111116 ATATCCGTCCGGCCGAAGAA 61.111 55.000 30.73 8.31 34.68 2.52
170 183 1.228429 TGGGGCACGGAAAAGAAGG 60.228 57.895 0.00 0.00 0.00 3.46
171 184 1.977009 GGGGCACGGAAAAGAAGGG 60.977 63.158 0.00 0.00 0.00 3.95
172 185 1.074248 GGGCACGGAAAAGAAGGGA 59.926 57.895 0.00 0.00 0.00 4.20
173 186 0.538746 GGGCACGGAAAAGAAGGGAA 60.539 55.000 0.00 0.00 0.00 3.97
174 187 0.596577 GGCACGGAAAAGAAGGGAAC 59.403 55.000 0.00 0.00 0.00 3.62
175 188 0.237498 GCACGGAAAAGAAGGGAACG 59.763 55.000 0.00 0.00 0.00 3.95
176 189 1.873698 CACGGAAAAGAAGGGAACGA 58.126 50.000 0.00 0.00 0.00 3.85
177 190 2.215196 CACGGAAAAGAAGGGAACGAA 58.785 47.619 0.00 0.00 0.00 3.85
178 191 2.032290 CACGGAAAAGAAGGGAACGAAC 60.032 50.000 0.00 0.00 0.00 3.95
179 192 1.193874 CGGAAAAGAAGGGAACGAACG 59.806 52.381 0.00 0.00 0.00 3.95
180 193 1.069432 GGAAAAGAAGGGAACGAACGC 60.069 52.381 0.00 0.00 0.00 4.84
181 194 0.949397 AAAAGAAGGGAACGAACGCC 59.051 50.000 0.00 0.00 0.00 5.68
182 195 0.887836 AAAGAAGGGAACGAACGCCC 60.888 55.000 0.00 0.00 45.04 6.13
186 199 3.131478 GGGAACGAACGCCCATGG 61.131 66.667 4.14 4.14 44.07 3.66
187 200 3.810896 GGAACGAACGCCCATGGC 61.811 66.667 6.09 0.58 46.75 4.40
229 652 4.598894 CTCCTCCGCGGCCATCAG 62.599 72.222 23.51 12.55 0.00 2.90
231 654 3.933722 CCTCCGCGGCCATCAGAT 61.934 66.667 23.51 0.00 0.00 2.90
232 655 2.109799 CTCCGCGGCCATCAGATT 59.890 61.111 23.51 0.00 0.00 2.40
233 656 2.203056 TCCGCGGCCATCAGATTG 60.203 61.111 23.51 0.00 0.00 2.67
234 657 3.282157 CCGCGGCCATCAGATTGG 61.282 66.667 14.67 0.00 39.94 3.16
235 658 2.514592 CGCGGCCATCAGATTGGT 60.515 61.111 2.24 0.00 39.11 3.67
236 659 2.827051 CGCGGCCATCAGATTGGTG 61.827 63.158 2.24 0.00 39.11 4.17
240 663 3.113745 CCATCAGATTGGTGGCGC 58.886 61.111 0.00 0.00 42.45 6.53
241 664 1.452651 CCATCAGATTGGTGGCGCT 60.453 57.895 7.64 0.00 42.45 5.92
242 665 1.721664 CCATCAGATTGGTGGCGCTG 61.722 60.000 7.64 0.00 42.45 5.18
243 666 1.452651 ATCAGATTGGTGGCGCTGG 60.453 57.895 7.64 0.00 0.00 4.85
244 667 3.818787 CAGATTGGTGGCGCTGGC 61.819 66.667 7.64 0.00 38.90 4.85
432 929 3.067470 TGGCCCATAATTATTCCCTGGA 58.933 45.455 0.00 0.00 0.00 3.86
437 934 5.513233 CCCATAATTATTCCCTGGAGATGG 58.487 45.833 0.00 0.00 0.00 3.51
444 941 3.866582 CCTGGAGATGGGGCCGAC 61.867 72.222 0.00 0.00 0.00 4.79
448 945 3.234730 GAGATGGGGCCGACGGAT 61.235 66.667 20.50 0.83 0.00 4.18
473 983 1.379527 GATGGGAACGTTGGTGATCC 58.620 55.000 5.00 0.00 0.00 3.36
591 1123 2.549282 CGCGTTGTTGGTTCCTCG 59.451 61.111 0.00 0.00 0.00 4.63
600 1132 1.197721 GTTGGTTCCTCGCATCACTTG 59.802 52.381 0.00 0.00 0.00 3.16
673 1208 3.679083 CGTGCCAAAACCCCAAAACTAAA 60.679 43.478 0.00 0.00 0.00 1.85
677 1212 7.387643 GTGCCAAAACCCCAAAACTAAATATA 58.612 34.615 0.00 0.00 0.00 0.86
678 1213 7.547722 GTGCCAAAACCCCAAAACTAAATATAG 59.452 37.037 0.00 0.00 35.14 1.31
680 1215 8.751242 GCCAAAACCCCAAAACTAAATATAGTA 58.249 33.333 0.00 0.00 41.57 1.82
682 1217 9.777575 CAAAACCCCAAAACTAAATATAGTACG 57.222 33.333 0.00 0.00 41.57 3.67
685 1220 9.599866 AACCCCAAAACTAAATATAGTACGTAC 57.400 33.333 18.10 18.10 41.57 3.67
709 1277 3.119291 CAGAAATCAAGACGAGATCGGG 58.881 50.000 7.22 0.00 44.95 5.14
712 1280 2.076622 ATCAAGACGAGATCGGGCGG 62.077 60.000 7.22 0.00 44.95 6.13
791 1359 8.585189 TCAGATCAAGATCAGAACGAATATTG 57.415 34.615 12.21 0.00 40.22 1.90
792 1360 7.170489 TCAGATCAAGATCAGAACGAATATTGC 59.830 37.037 12.21 0.00 40.22 3.56
793 1361 5.641777 TCAAGATCAGAACGAATATTGCG 57.358 39.130 0.00 0.00 0.00 4.85
794 1362 5.109210 TCAAGATCAGAACGAATATTGCGT 58.891 37.500 0.00 0.00 44.94 5.24
795 1363 5.005682 TCAAGATCAGAACGAATATTGCGTG 59.994 40.000 11.80 3.32 41.75 5.34
838 1408 3.793776 CGTGTGTGTACGTAGTGTAGA 57.206 47.619 0.00 0.00 45.73 2.59
839 1409 3.473367 CGTGTGTGTACGTAGTGTAGAC 58.527 50.000 0.00 0.00 45.73 2.59
840 1410 3.185188 CGTGTGTGTACGTAGTGTAGACT 59.815 47.826 0.00 0.00 45.19 3.24
936 1508 1.774639 GGTGGCGTACATACATACGG 58.225 55.000 7.37 0.00 46.39 4.02
961 1533 1.336795 GCAAAATCCCCAACGGAACAG 60.337 52.381 0.00 0.00 46.47 3.16
978 1550 4.521062 GGGCTGACAGCGCGAGAT 62.521 66.667 26.26 0.00 44.19 2.75
979 1551 2.959071 GGCTGACAGCGCGAGATC 60.959 66.667 20.82 3.22 43.62 2.75
980 1552 3.318555 GCTGACAGCGCGAGATCG 61.319 66.667 12.10 0.00 43.27 3.69
981 1553 2.653448 CTGACAGCGCGAGATCGG 60.653 66.667 12.10 4.09 40.23 4.18
992 1583 1.659794 GAGATCGGGCAGAGAGAGC 59.340 63.158 0.00 0.00 0.00 4.09
1146 1737 4.345962 TACGCCGTCACCGTGGTG 62.346 66.667 12.91 12.91 46.64 4.17
1149 1740 4.388499 GCCGTCACCGTGGTGGAT 62.388 66.667 18.47 0.00 45.43 3.41
1274 1873 3.760035 CTGCGCCCACCGTCTAGT 61.760 66.667 4.18 0.00 39.71 2.57
1291 1890 3.764434 TCTAGTTTGTTCGATCCTGCTCT 59.236 43.478 0.00 0.00 0.00 4.09
1292 1891 2.966050 AGTTTGTTCGATCCTGCTCTC 58.034 47.619 0.00 0.00 0.00 3.20
1293 1892 1.656095 GTTTGTTCGATCCTGCTCTCG 59.344 52.381 0.00 0.00 36.25 4.04
1294 1893 1.173913 TTGTTCGATCCTGCTCTCGA 58.826 50.000 0.00 0.00 41.76 4.04
1295 1894 1.393603 TGTTCGATCCTGCTCTCGAT 58.606 50.000 0.00 0.00 42.84 3.59
1296 1895 1.066152 TGTTCGATCCTGCTCTCGATG 59.934 52.381 0.00 0.00 42.84 3.84
1297 1896 1.335182 GTTCGATCCTGCTCTCGATGA 59.665 52.381 0.00 0.00 42.84 2.92
1298 1897 1.902938 TCGATCCTGCTCTCGATGAT 58.097 50.000 0.00 0.00 38.86 2.45
1299 1898 1.809547 TCGATCCTGCTCTCGATGATC 59.190 52.381 0.00 0.00 38.86 2.92
1300 1899 1.811965 CGATCCTGCTCTCGATGATCT 59.188 52.381 0.00 0.00 37.05 2.75
1301 1900 2.159531 CGATCCTGCTCTCGATGATCTC 60.160 54.545 0.00 0.00 37.05 2.75
1309 1908 3.622756 CGATGATCTCGTGCCTGC 58.377 61.111 0.00 0.00 42.56 4.85
1310 1909 1.953138 CGATGATCTCGTGCCTGCC 60.953 63.158 0.00 0.00 42.56 4.85
1311 1910 1.953138 GATGATCTCGTGCCTGCCG 60.953 63.158 0.00 0.00 0.00 5.69
1312 1911 2.635229 GATGATCTCGTGCCTGCCGT 62.635 60.000 0.00 0.00 0.00 5.68
1313 1912 2.887568 GATCTCGTGCCTGCCGTG 60.888 66.667 0.00 0.00 0.00 4.94
1327 1926 4.383861 CGTGCCTGGCAGAGCTCA 62.384 66.667 24.10 5.37 40.08 4.26
1421 2020 1.810030 GTTCGCCGCCAAGAGGTAG 60.810 63.158 0.00 0.00 37.19 3.18
1422 2021 3.014085 TTCGCCGCCAAGAGGTAGG 62.014 63.158 0.00 0.00 37.71 3.18
1443 2046 3.973206 ACGTAGTTGTTGGATCCATCA 57.027 42.857 19.59 19.59 37.78 3.07
1447 2050 4.025730 CGTAGTTGTTGGATCCATCAATCG 60.026 45.833 31.30 28.42 37.76 3.34
1448 2051 4.220693 AGTTGTTGGATCCATCAATCGA 57.779 40.909 31.30 14.17 37.76 3.59
1457 2060 2.323599 TCCATCAATCGATCAGGAGCT 58.676 47.619 0.00 0.00 0.00 4.09
1459 2062 3.135348 TCCATCAATCGATCAGGAGCTTT 59.865 43.478 0.00 0.00 0.00 3.51
1460 2063 3.250280 CCATCAATCGATCAGGAGCTTTG 59.750 47.826 0.00 0.00 0.00 2.77
1468 2071 4.813161 TCGATCAGGAGCTTTGATTTGATC 59.187 41.667 13.81 11.94 38.22 2.92
1470 2073 5.296283 CGATCAGGAGCTTTGATTTGATCTT 59.704 40.000 13.81 0.00 39.00 2.40
1475 2078 5.776716 AGGAGCTTTGATTTGATCTTCCAAA 59.223 36.000 0.00 0.00 39.93 3.28
1476 2079 5.866092 GGAGCTTTGATTTGATCTTCCAAAC 59.134 40.000 0.00 0.00 38.65 2.93
1492 2095 0.172578 AAACTCGTGGCGATCGATCA 59.827 50.000 24.40 13.35 36.73 2.92
1494 2097 0.172578 ACTCGTGGCGATCGATCAAA 59.827 50.000 24.40 6.88 36.73 2.69
1495 2098 1.202417 ACTCGTGGCGATCGATCAAAT 60.202 47.619 24.40 0.00 36.73 2.32
1496 2099 1.860950 CTCGTGGCGATCGATCAAATT 59.139 47.619 24.40 0.00 36.73 1.82
1499 2102 4.055360 TCGTGGCGATCGATCAAATTAAT 58.945 39.130 24.40 0.00 32.30 1.40
1516 2119 4.564940 TTAATTAACCGTTTTGCCGTGT 57.435 36.364 0.00 0.00 0.00 4.49
1521 2124 1.278637 CCGTTTTGCCGTGTGACTC 59.721 57.895 0.00 0.00 0.00 3.36
1530 2133 1.988063 CCGTGTGACTCTGACTGATG 58.012 55.000 0.00 0.00 0.00 3.07
1638 2241 2.652530 GTCGGCACCGTCAACCTA 59.347 61.111 9.23 0.00 40.74 3.08
1662 2265 0.317160 ACGTCATGAAGAAGCACGGA 59.683 50.000 15.90 0.00 34.75 4.69
1685 2288 0.195096 AACAAGGTACTCCCTCCCCA 59.805 55.000 0.00 0.00 45.47 4.96
1733 2340 2.224329 CCCCTGCTCTTCAGAGATGATG 60.224 54.545 8.09 0.00 45.72 3.07
1770 2377 2.743938 TGCTCTGACACTTTCGAGAAC 58.256 47.619 0.00 0.00 30.73 3.01
1771 2378 2.062519 GCTCTGACACTTTCGAGAACC 58.937 52.381 0.00 0.00 30.73 3.62
1902 2516 4.631813 CCAAGGTAAACTCTCTGCATACAC 59.368 45.833 0.00 0.00 0.00 2.90
1919 2533 5.445142 GCATACACTCTGTCAGAAACGATTG 60.445 44.000 3.67 0.00 0.00 2.67
1938 2554 2.310233 CCTGACACTCACGTTGCCG 61.310 63.158 0.00 0.00 40.83 5.69
1994 2620 7.187480 GGCAATTAATCTAACCTTTTCGACTC 58.813 38.462 0.00 0.00 0.00 3.36
1995 2621 7.065923 GGCAATTAATCTAACCTTTTCGACTCT 59.934 37.037 0.00 0.00 0.00 3.24
1996 2622 9.095065 GCAATTAATCTAACCTTTTCGACTCTA 57.905 33.333 0.00 0.00 0.00 2.43
2011 2637 1.202417 ACTCTAATGGCGTCGATGTGG 60.202 52.381 6.48 0.00 0.00 4.17
2368 2994 2.604139 CCCAGTTAACAACCAACCCAT 58.396 47.619 8.61 0.00 0.00 4.00
2370 2996 3.389656 CCCAGTTAACAACCAACCCATTT 59.610 43.478 8.61 0.00 0.00 2.32
2371 2997 4.589374 CCCAGTTAACAACCAACCCATTTA 59.411 41.667 8.61 0.00 0.00 1.40
2372 2998 5.510009 CCCAGTTAACAACCAACCCATTTAC 60.510 44.000 8.61 0.00 0.00 2.01
2373 2999 5.510009 CCAGTTAACAACCAACCCATTTACC 60.510 44.000 8.61 0.00 0.00 2.85
2374 3000 5.069251 CAGTTAACAACCAACCCATTTACCA 59.931 40.000 8.61 0.00 0.00 3.25
2376 3002 3.322191 ACAACCAACCCATTTACCAGT 57.678 42.857 0.00 0.00 0.00 4.00
2377 3003 2.962421 ACAACCAACCCATTTACCAGTG 59.038 45.455 0.00 0.00 0.00 3.66
2380 3006 1.243902 CAACCCATTTACCAGTGCGT 58.756 50.000 0.00 0.00 0.00 5.24
2381 3007 1.068610 CAACCCATTTACCAGTGCGTG 60.069 52.381 0.00 0.00 0.00 5.34
2382 3008 1.241315 ACCCATTTACCAGTGCGTGC 61.241 55.000 0.00 0.00 0.00 5.34
2383 3009 1.240641 CCCATTTACCAGTGCGTGCA 61.241 55.000 0.00 0.00 0.00 4.57
2384 3010 0.810648 CCATTTACCAGTGCGTGCAT 59.189 50.000 0.00 0.00 0.00 3.96
2385 3011 1.202177 CCATTTACCAGTGCGTGCATC 60.202 52.381 0.00 0.00 0.00 3.91
2386 3012 1.468127 CATTTACCAGTGCGTGCATCA 59.532 47.619 0.00 0.00 0.00 3.07
2387 3013 0.871722 TTTACCAGTGCGTGCATCAC 59.128 50.000 12.46 12.46 34.80 3.06
2389 3015 0.389817 TACCAGTGCGTGCATCACTC 60.390 55.000 18.09 0.61 42.38 3.51
2392 3021 1.734477 AGTGCGTGCATCACTCGAC 60.734 57.895 15.99 4.21 40.47 4.20
2401 3034 2.028203 TGCATCACTCGACCATTTCTGA 60.028 45.455 0.00 0.00 0.00 3.27
2501 3134 1.602377 GCATACGGCAAGGTTGATACC 59.398 52.381 0.00 0.00 43.18 2.73
2688 3321 2.698797 AGGTAACCGATCGATGTCCATT 59.301 45.455 18.66 1.82 37.17 3.16
2711 3345 5.640189 AACACTACTAGTCGCAATGTAGT 57.360 39.130 0.00 0.00 44.13 2.73
2714 3348 5.862323 ACACTACTAGTCGCAATGTAGTTTG 59.138 40.000 0.00 0.00 42.23 2.93
2720 3354 2.984471 GTCGCAATGTAGTTTGTCGAGA 59.016 45.455 0.00 0.00 36.53 4.04
2734 3368 7.560368 AGTTTGTCGAGAGAGATGGATTAAAT 58.440 34.615 0.00 0.00 43.49 1.40
2736 3370 6.968263 TGTCGAGAGAGATGGATTAAATCT 57.032 37.500 0.00 0.00 43.49 2.40
2829 3476 1.304464 CTGGGCCAAGAAGAACCCC 60.304 63.158 8.04 0.00 42.07 4.95
2844 3491 1.837051 CCCCTATGGCTACTGCGGA 60.837 63.158 0.00 0.00 40.82 5.54
2877 3529 1.488705 AAGACTGATTCGGTGGCCCA 61.489 55.000 2.04 0.00 0.00 5.36
2908 3561 4.452455 CCTTGTAGCGTGAAAGAAAGATGT 59.548 41.667 0.00 0.00 0.00 3.06
2964 3617 7.176690 CCCAGAAAATGTTTCCTGTTGTAGTAT 59.823 37.037 0.00 0.00 0.00 2.12
3014 3680 2.756207 GGGTTAGACTGGACTCTCACTC 59.244 54.545 0.00 0.00 0.00 3.51
3064 3730 2.316108 GGTCTGGTTTCAAACATGGGT 58.684 47.619 1.93 0.00 0.00 4.51
3081 3747 1.646189 GGTCGTCATCTGCTTCCTTC 58.354 55.000 0.00 0.00 0.00 3.46
3085 3751 3.748568 GTCGTCATCTGCTTCCTTCTTTT 59.251 43.478 0.00 0.00 0.00 2.27
3107 3773 7.931578 TTTTTCCTTCCAATTATAGAGCGAA 57.068 32.000 0.00 0.00 0.00 4.70
3146 3812 7.692908 TCATTACAAACTTTTTACTGCTTGC 57.307 32.000 0.00 0.00 0.00 4.01
3149 3815 5.323371 ACAAACTTTTTACTGCTTGCAGA 57.677 34.783 26.71 9.61 0.00 4.26
3151 3817 5.576774 ACAAACTTTTTACTGCTTGCAGAAC 59.423 36.000 26.71 0.00 0.00 3.01
3152 3818 4.981806 ACTTTTTACTGCTTGCAGAACA 57.018 36.364 26.71 10.18 0.00 3.18
3172 3851 0.595588 TGCGTTTGGTTACCTGCATG 59.404 50.000 2.07 0.00 0.00 4.06
3207 3886 3.222173 TGCATACTTGTTCCAGTTGGT 57.778 42.857 0.00 0.00 36.34 3.67
3208 3887 3.146066 TGCATACTTGTTCCAGTTGGTC 58.854 45.455 0.00 0.00 36.34 4.02
3209 3888 3.146066 GCATACTTGTTCCAGTTGGTCA 58.854 45.455 0.00 0.00 36.34 4.02
3210 3889 3.189287 GCATACTTGTTCCAGTTGGTCAG 59.811 47.826 0.00 0.00 36.34 3.51
3212 3891 0.954452 CTTGTTCCAGTTGGTCAGGC 59.046 55.000 0.00 0.00 36.34 4.85
3213 3892 0.257328 TTGTTCCAGTTGGTCAGGCA 59.743 50.000 0.00 0.00 36.34 4.75
3240 3936 5.471556 AACATCCTTTGCATGTTGATTGA 57.528 34.783 1.92 0.00 41.86 2.57
3254 3950 1.063492 TGATTGATTGCCTGCATCCCT 60.063 47.619 0.00 0.00 0.00 4.20
3255 3951 2.037144 GATTGATTGCCTGCATCCCTT 58.963 47.619 0.00 0.00 0.00 3.95
3257 3953 1.941377 TGATTGCCTGCATCCCTTTT 58.059 45.000 0.00 0.00 0.00 2.27
3261 3957 0.904394 TGCCTGCATCCCTTTTTCCC 60.904 55.000 0.00 0.00 0.00 3.97
3273 3969 1.062587 CTTTTTCCCTGCATCGTAGCG 59.937 52.381 0.00 0.00 37.31 4.26
3309 4005 1.028130 TGTTTGGTTGCTCGCATTGA 58.972 45.000 0.00 0.00 0.00 2.57
3310 4006 1.612950 TGTTTGGTTGCTCGCATTGAT 59.387 42.857 0.00 0.00 0.00 2.57
3321 4017 4.336153 TGCTCGCATTGATTGTGTTCATAT 59.664 37.500 0.00 0.00 37.14 1.78
3347 4044 3.006644 TGCATGTTGTTGGTTGCATACAT 59.993 39.130 0.00 0.00 39.98 2.29
3366 4063 9.056005 GCATACATTGGACATGATTAAGACTTA 57.944 33.333 0.00 0.00 0.00 2.24
3387 4084 8.726870 ACTTAAACAACTACACATAACACACT 57.273 30.769 0.00 0.00 0.00 3.55
3485 4196 2.106938 GATCTCATCGGCGGCACA 59.893 61.111 10.53 0.00 0.00 4.57
3501 4212 1.390463 GCACAGCGAACTAGTTGCTAC 59.610 52.381 23.27 15.71 37.15 3.58
3502 4213 2.927014 GCACAGCGAACTAGTTGCTACT 60.927 50.000 23.27 6.00 37.15 2.57
3505 4216 3.243771 ACAGCGAACTAGTTGCTACTGTT 60.244 43.478 23.27 12.26 37.15 3.16
3508 4219 3.493503 GCGAACTAGTTGCTACTGTTGTT 59.506 43.478 14.14 12.17 35.78 2.83
3523 4234 2.267426 GTTGTTGCCGCAAAGAAAGTT 58.733 42.857 7.54 0.00 0.00 2.66
3530 4241 2.874849 CCGCAAAGAAAGTTTGTGTGT 58.125 42.857 4.95 0.00 38.00 3.72
3624 4336 0.179062 GTAGTAGGACGCGGAGGAGA 60.179 60.000 12.47 0.00 0.00 3.71
3653 4420 0.036388 AGAATGACGATGGCAACGGT 60.036 50.000 21.20 7.00 42.51 4.83
3669 4436 2.116238 ACGGTGCCAATGTAGTAGGAT 58.884 47.619 0.00 0.00 0.00 3.24
3673 4440 0.868406 GCCAATGTAGTAGGATGCGC 59.132 55.000 0.00 0.00 0.00 6.09
3722 4489 0.108138 GATGGCTTCGGTGTAGCAGT 60.108 55.000 0.00 0.00 40.42 4.40
3749 4516 4.844085 TGGGACAAGAGAAGAGGAACAATA 59.156 41.667 0.00 0.00 31.92 1.90
3750 4517 5.046304 TGGGACAAGAGAAGAGGAACAATAG 60.046 44.000 0.00 0.00 31.92 1.73
3751 4518 5.187967 GGGACAAGAGAAGAGGAACAATAGA 59.812 44.000 0.00 0.00 0.00 1.98
3752 4519 6.126911 GGGACAAGAGAAGAGGAACAATAGAT 60.127 42.308 0.00 0.00 0.00 1.98
3754 4521 7.364232 GGACAAGAGAAGAGGAACAATAGATGA 60.364 40.741 0.00 0.00 0.00 2.92
3755 4522 8.088463 ACAAGAGAAGAGGAACAATAGATGAT 57.912 34.615 0.00 0.00 0.00 2.45
3757 4524 7.911130 AGAGAAGAGGAACAATAGATGATGA 57.089 36.000 0.00 0.00 0.00 2.92
3758 4525 7.725251 AGAGAAGAGGAACAATAGATGATGAC 58.275 38.462 0.00 0.00 0.00 3.06
3761 4528 3.733337 AGGAACAATAGATGATGACCGC 58.267 45.455 0.00 0.00 0.00 5.68
3762 4529 3.134623 AGGAACAATAGATGATGACCGCA 59.865 43.478 0.00 0.00 0.00 5.69
3763 4530 3.248602 GGAACAATAGATGATGACCGCAC 59.751 47.826 0.00 0.00 0.00 5.34
3771 4538 0.109458 TGATGACCGCACGTGTAGTC 60.109 55.000 24.47 24.47 0.00 2.59
3777 4544 1.370778 CGCACGTGTAGTCGGACAA 60.371 57.895 18.38 0.00 34.94 3.18
3837 4604 1.079127 GTGTAGCAGCACGTGGGAT 60.079 57.895 18.88 0.00 0.00 3.85
3842 4609 0.108138 AGCAGCACGTGGGATAGAAC 60.108 55.000 18.88 0.00 0.00 3.01
3844 4611 1.943968 GCAGCACGTGGGATAGAACAA 60.944 52.381 18.88 0.00 0.00 2.83
3845 4612 1.732259 CAGCACGTGGGATAGAACAAC 59.268 52.381 18.88 0.00 0.00 3.32
3848 4615 2.888594 CACGTGGGATAGAACAACGAT 58.111 47.619 7.95 0.00 0.00 3.73
3849 4616 2.603110 CACGTGGGATAGAACAACGATG 59.397 50.000 7.95 0.00 0.00 3.84
3851 4618 1.940613 GTGGGATAGAACAACGATGGC 59.059 52.381 0.00 0.00 0.00 4.40
3852 4619 1.217882 GGGATAGAACAACGATGGCG 58.782 55.000 0.00 0.00 44.79 5.69
3856 4623 0.241749 TAGAACAACGATGGCGACGT 59.758 50.000 0.00 3.16 45.89 4.34
3857 4624 1.129809 GAACAACGATGGCGACGTG 59.870 57.895 9.26 6.79 43.16 4.49
3858 4625 2.222953 GAACAACGATGGCGACGTGG 62.223 60.000 9.26 8.94 43.16 4.94
3859 4626 4.147322 CAACGATGGCGACGTGGC 62.147 66.667 14.82 14.82 43.16 5.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.079490 TGGAGAGGAGGAATCCAGTGT 59.921 52.381 0.61 0.00 38.19 3.55
1 2 1.484240 GTGGAGAGGAGGAATCCAGTG 59.516 57.143 0.61 0.00 43.61 3.66
2 3 1.872773 GTGGAGAGGAGGAATCCAGT 58.127 55.000 0.61 0.00 43.61 4.00
3 4 0.749649 CGTGGAGAGGAGGAATCCAG 59.250 60.000 0.61 0.00 43.61 3.86
4 5 0.687757 CCGTGGAGAGGAGGAATCCA 60.688 60.000 0.61 0.00 40.80 3.41
55 60 5.818887 TCAAGGAGATTGTTGGATTGATGA 58.181 37.500 0.00 0.00 40.05 2.92
112 120 1.269778 CGGACGGATATGCATGACACT 60.270 52.381 10.16 0.00 0.00 3.55
141 154 0.464373 CGTGCCCCAGTGCATATCTT 60.464 55.000 0.00 0.00 44.30 2.40
170 183 3.810896 GCCATGGGCGTTCGTTCC 61.811 66.667 15.13 0.00 39.62 3.62
181 194 2.044053 AACCACATCCCGCCATGG 60.044 61.111 7.63 7.63 38.26 3.66
182 195 1.250154 AACAACCACATCCCGCCATG 61.250 55.000 0.00 0.00 0.00 3.66
183 196 0.965363 GAACAACCACATCCCGCCAT 60.965 55.000 0.00 0.00 0.00 4.40
184 197 1.602323 GAACAACCACATCCCGCCA 60.602 57.895 0.00 0.00 0.00 5.69
185 198 2.340328 GGAACAACCACATCCCGCC 61.340 63.158 0.00 0.00 38.79 6.13
186 199 2.340328 GGGAACAACCACATCCCGC 61.340 63.158 0.00 0.00 43.20 6.13
187 200 3.996614 GGGAACAACCACATCCCG 58.003 61.111 0.00 0.00 43.20 5.14
219 642 2.484062 CCACCAATCTGATGGCCGC 61.484 63.158 0.00 0.00 44.75 6.53
220 643 3.831883 CCACCAATCTGATGGCCG 58.168 61.111 0.00 0.00 44.75 6.13
223 646 1.452651 AGCGCCACCAATCTGATGG 60.453 57.895 2.29 0.00 46.38 3.51
224 647 1.721664 CCAGCGCCACCAATCTGATG 61.722 60.000 2.29 0.00 0.00 3.07
225 648 1.452651 CCAGCGCCACCAATCTGAT 60.453 57.895 2.29 0.00 0.00 2.90
226 649 2.046023 CCAGCGCCACCAATCTGA 60.046 61.111 2.29 0.00 0.00 3.27
227 650 3.818787 GCCAGCGCCACCAATCTG 61.819 66.667 2.29 0.00 0.00 2.90
341 785 1.278637 CACGCACGACCCTCAAAAC 59.721 57.895 0.00 0.00 0.00 2.43
348 792 3.993376 TAATCCGCACGCACGACCC 62.993 63.158 0.00 0.00 34.06 4.46
349 793 1.881252 ATAATCCGCACGCACGACC 60.881 57.895 0.00 0.00 34.06 4.79
350 794 1.143373 TCATAATCCGCACGCACGAC 61.143 55.000 0.00 0.00 34.06 4.34
351 795 0.458716 TTCATAATCCGCACGCACGA 60.459 50.000 0.00 0.00 34.06 4.35
352 796 0.315059 GTTCATAATCCGCACGCACG 60.315 55.000 0.00 0.00 0.00 5.34
353 797 0.315059 CGTTCATAATCCGCACGCAC 60.315 55.000 0.00 0.00 0.00 5.34
354 798 1.425267 CCGTTCATAATCCGCACGCA 61.425 55.000 0.00 0.00 0.00 5.24
355 799 1.275657 CCGTTCATAATCCGCACGC 59.724 57.895 0.00 0.00 0.00 5.34
411 907 3.067470 TCCAGGGAATAATTATGGGCCA 58.933 45.455 9.61 9.61 0.00 5.36
432 929 2.200370 TATCCGTCGGCCCCATCT 59.800 61.111 6.34 0.00 0.00 2.90
444 941 1.663702 GTTCCCATCGCCGTATCCG 60.664 63.158 0.00 0.00 0.00 4.18
448 945 1.446445 CAACGTTCCCATCGCCGTA 60.446 57.895 0.00 0.00 32.49 4.02
481 991 2.960129 GGCGGGTATCTCGTTGCG 60.960 66.667 0.00 0.00 0.00 4.85
673 1208 8.847196 TCTTGATTTCTGCTGTACGTACTATAT 58.153 33.333 25.12 9.71 0.00 0.86
677 1212 5.162075 GTCTTGATTTCTGCTGTACGTACT 58.838 41.667 25.12 3.41 0.00 2.73
678 1213 4.030306 CGTCTTGATTTCTGCTGTACGTAC 59.970 45.833 18.90 18.90 0.00 3.67
680 1215 2.987149 CGTCTTGATTTCTGCTGTACGT 59.013 45.455 0.00 0.00 0.00 3.57
681 1216 3.242518 TCGTCTTGATTTCTGCTGTACG 58.757 45.455 0.00 0.00 0.00 3.67
682 1217 4.486090 TCTCGTCTTGATTTCTGCTGTAC 58.514 43.478 0.00 0.00 0.00 2.90
684 1219 3.667497 TCTCGTCTTGATTTCTGCTGT 57.333 42.857 0.00 0.00 0.00 4.40
685 1220 3.242480 CGATCTCGTCTTGATTTCTGCTG 59.758 47.826 0.00 0.00 34.11 4.41
712 1280 2.174319 GGCTCAAAGGGCGATCGAC 61.174 63.158 21.57 18.00 0.00 4.20
722 1290 1.212616 CTATCGCTTCGGGCTCAAAG 58.787 55.000 0.00 0.00 39.13 2.77
791 1359 1.192534 GATAGGAGTAATTGCGCACGC 59.807 52.381 11.12 8.33 42.35 5.34
792 1360 1.792949 GGATAGGAGTAATTGCGCACG 59.207 52.381 11.12 0.00 0.00 5.34
793 1361 2.143925 GGGATAGGAGTAATTGCGCAC 58.856 52.381 11.12 0.00 0.00 5.34
794 1362 1.270094 CGGGATAGGAGTAATTGCGCA 60.270 52.381 5.66 5.66 0.00 6.09
795 1363 1.000506 TCGGGATAGGAGTAATTGCGC 59.999 52.381 0.00 0.00 0.00 6.09
832 1402 1.469423 GGCCACGAGCTAAGTCTACAC 60.469 57.143 0.00 0.00 43.05 2.90
838 1408 0.323908 AGAGAGGCCACGAGCTAAGT 60.324 55.000 5.01 0.00 43.05 2.24
839 1409 0.820871 AAGAGAGGCCACGAGCTAAG 59.179 55.000 5.01 0.00 43.05 2.18
840 1410 0.818296 GAAGAGAGGCCACGAGCTAA 59.182 55.000 5.01 0.00 43.05 3.09
877 1449 1.946475 GACTGGAGAGGGTACGTGCC 61.946 65.000 15.14 15.14 0.00 5.01
878 1450 0.966370 AGACTGGAGAGGGTACGTGC 60.966 60.000 0.00 0.00 0.00 5.34
880 1452 4.785346 TTATAGACTGGAGAGGGTACGT 57.215 45.455 0.00 0.00 0.00 3.57
881 1453 6.005198 AGATTTATAGACTGGAGAGGGTACG 58.995 44.000 0.00 0.00 0.00 3.67
882 1454 7.842887 AAGATTTATAGACTGGAGAGGGTAC 57.157 40.000 0.00 0.00 0.00 3.34
925 1497 0.462375 TTGCGCTCCCGTATGTATGT 59.538 50.000 9.73 0.00 36.67 2.29
927 1499 2.319136 TTTTGCGCTCCCGTATGTAT 57.681 45.000 9.73 0.00 36.67 2.29
936 1508 1.215382 GTTGGGGATTTTGCGCTCC 59.785 57.895 9.73 6.95 0.00 4.70
961 1533 4.521062 ATCTCGCGCTGTCAGCCC 62.521 66.667 19.14 9.41 38.18 5.19
973 1545 1.948508 CTCTCTCTGCCCGATCTCG 59.051 63.158 0.00 0.00 39.44 4.04
980 1552 4.863925 GTCGCGCTCTCTCTGCCC 62.864 72.222 5.56 0.00 0.00 5.36
981 1553 4.121669 TGTCGCGCTCTCTCTGCC 62.122 66.667 5.56 0.00 0.00 4.85
983 1555 0.591994 CATCTGTCGCGCTCTCTCTG 60.592 60.000 5.56 0.00 0.00 3.35
1146 1737 3.329929 ACGGAGTTGTGGAAGTTATCC 57.670 47.619 0.00 0.00 45.02 2.59
1271 1862 3.427638 CGAGAGCAGGATCGAACAAACTA 60.428 47.826 0.00 0.00 41.40 2.24
1274 1873 1.544246 TCGAGAGCAGGATCGAACAAA 59.456 47.619 0.00 0.00 44.36 2.83
1293 1892 1.953138 CGGCAGGCACGAGATCATC 60.953 63.158 0.00 0.00 0.00 2.92
1294 1893 2.107750 CGGCAGGCACGAGATCAT 59.892 61.111 0.00 0.00 0.00 2.45
1295 1894 3.381983 ACGGCAGGCACGAGATCA 61.382 61.111 8.69 0.00 34.93 2.92
1296 1895 2.887568 CACGGCAGGCACGAGATC 60.888 66.667 8.69 0.00 34.93 2.75
1310 1909 4.383861 TGAGCTCTGCCAGGCACG 62.384 66.667 11.22 7.32 33.79 5.34
1311 1910 1.892819 TACTGAGCTCTGCCAGGCAC 61.893 60.000 19.49 0.12 33.79 5.01
1312 1911 1.610379 TACTGAGCTCTGCCAGGCA 60.610 57.895 15.23 15.23 36.92 4.75
1313 1912 1.153469 GTACTGAGCTCTGCCAGGC 60.153 63.158 19.49 3.66 33.43 4.85
1314 1913 1.519719 GGTACTGAGCTCTGCCAGG 59.480 63.158 19.49 3.70 33.43 4.45
1315 1914 0.975040 AGGGTACTGAGCTCTGCCAG 60.975 60.000 19.49 9.41 34.62 4.85
1316 1915 1.079256 AGGGTACTGAGCTCTGCCA 59.921 57.895 19.49 6.01 0.00 4.92
1327 1926 7.072961 ACCAATCTATCAATCAATCAGGGTACT 59.927 37.037 0.00 0.00 0.00 2.73
1394 1993 3.479269 GCGGCGAACACCTTCTCG 61.479 66.667 12.98 0.00 38.11 4.04
1421 2020 2.754946 TGGATCCAACAACTACGTCC 57.245 50.000 13.46 0.00 0.00 4.79
1422 2021 3.857052 TGATGGATCCAACAACTACGTC 58.143 45.455 21.41 10.37 0.00 4.34
1443 2046 5.188434 TCAAATCAAAGCTCCTGATCGATT 58.812 37.500 10.76 1.50 32.26 3.34
1447 2050 6.238703 GGAAGATCAAATCAAAGCTCCTGATC 60.239 42.308 10.76 10.18 39.51 2.92
1448 2051 5.593502 GGAAGATCAAATCAAAGCTCCTGAT 59.406 40.000 5.61 5.61 34.97 2.90
1457 2060 6.437928 CACGAGTTTGGAAGATCAAATCAAA 58.562 36.000 0.00 0.00 38.64 2.69
1459 2062 4.455533 CCACGAGTTTGGAAGATCAAATCA 59.544 41.667 0.00 0.00 39.24 2.57
1460 2063 4.672801 GCCACGAGTTTGGAAGATCAAATC 60.673 45.833 0.00 0.00 39.24 2.17
1468 2071 0.721718 GATCGCCACGAGTTTGGAAG 59.278 55.000 0.00 0.00 39.91 3.46
1470 2073 1.445410 CGATCGCCACGAGTTTGGA 60.445 57.895 0.26 0.00 39.91 3.53
1475 2078 0.172578 TTTGATCGATCGCCACGAGT 59.827 50.000 20.03 0.00 42.81 4.18
1476 2079 1.491670 ATTTGATCGATCGCCACGAG 58.508 50.000 20.03 0.00 42.81 4.18
1492 2095 5.984323 ACACGGCAAAACGGTTAATTAATTT 59.016 32.000 5.91 0.00 38.39 1.82
1494 2097 4.918583 CACACGGCAAAACGGTTAATTAAT 59.081 37.500 0.31 0.00 38.39 1.40
1495 2098 4.036027 TCACACGGCAAAACGGTTAATTAA 59.964 37.500 0.00 0.00 38.39 1.40
1496 2099 3.562973 TCACACGGCAAAACGGTTAATTA 59.437 39.130 0.00 0.00 38.39 1.40
1499 2102 1.063764 GTCACACGGCAAAACGGTTAA 59.936 47.619 0.00 0.00 38.39 2.01
1516 2119 2.174360 CCTGGTCATCAGTCAGAGTCA 58.826 52.381 0.00 0.00 41.83 3.41
1521 2124 2.092323 TCGTACCTGGTCATCAGTCAG 58.908 52.381 0.63 0.00 41.83 3.51
1638 2241 3.179830 GTGCTTCTTCATGACGTCGTAT 58.820 45.455 10.54 0.00 0.00 3.06
1685 2288 2.310647 ACTGACGGGATTGGGGTTTTAT 59.689 45.455 0.00 0.00 0.00 1.40
1733 2340 4.512198 CAGAGCAATCACTGAAGATCATCC 59.488 45.833 0.00 0.00 36.38 3.51
1770 2377 0.534203 AACACCAACTGGCACGTAGG 60.534 55.000 0.00 0.00 39.32 3.18
1771 2378 0.865769 GAACACCAACTGGCACGTAG 59.134 55.000 0.00 0.00 39.32 3.51
1902 2516 2.414481 CAGGCAATCGTTTCTGACAGAG 59.586 50.000 5.10 0.00 0.00 3.35
1994 2620 1.327460 CAACCACATCGACGCCATTAG 59.673 52.381 0.00 0.00 0.00 1.73
1995 2621 1.066787 TCAACCACATCGACGCCATTA 60.067 47.619 0.00 0.00 0.00 1.90
1996 2622 0.321210 TCAACCACATCGACGCCATT 60.321 50.000 0.00 0.00 0.00 3.16
1997 2623 1.019278 GTCAACCACATCGACGCCAT 61.019 55.000 0.00 0.00 0.00 4.40
1998 2624 1.666553 GTCAACCACATCGACGCCA 60.667 57.895 0.00 0.00 0.00 5.69
2011 2637 1.291877 CCAGGTACAGCTGCGTCAAC 61.292 60.000 15.27 4.45 0.00 3.18
2352 2978 5.069383 ACTGGTAAATGGGTTGGTTGTTAAC 59.931 40.000 0.00 0.00 0.00 2.01
2368 2994 0.871722 GTGATGCACGCACTGGTAAA 59.128 50.000 12.85 0.00 33.57 2.01
2370 2996 0.389817 GAGTGATGCACGCACTGGTA 60.390 55.000 24.05 0.00 45.94 3.25
2371 2997 1.669115 GAGTGATGCACGCACTGGT 60.669 57.895 24.05 5.36 45.94 4.00
2372 2998 2.733671 CGAGTGATGCACGCACTGG 61.734 63.158 24.05 19.65 45.94 4.00
2373 2999 1.734117 TCGAGTGATGCACGCACTG 60.734 57.895 24.05 16.83 45.94 3.66
2376 3002 2.432456 GGTCGAGTGATGCACGCA 60.432 61.111 0.00 0.00 39.64 5.24
2377 3003 1.361668 AATGGTCGAGTGATGCACGC 61.362 55.000 0.00 0.00 39.64 5.34
2380 3006 2.028203 TCAGAAATGGTCGAGTGATGCA 60.028 45.455 0.00 0.00 0.00 3.96
2381 3007 2.621338 TCAGAAATGGTCGAGTGATGC 58.379 47.619 0.00 0.00 0.00 3.91
2382 3008 5.122869 ACAAATCAGAAATGGTCGAGTGATG 59.877 40.000 0.00 0.00 0.00 3.07
2383 3009 5.248640 ACAAATCAGAAATGGTCGAGTGAT 58.751 37.500 0.00 0.00 0.00 3.06
2384 3010 4.641396 ACAAATCAGAAATGGTCGAGTGA 58.359 39.130 0.00 0.00 0.00 3.41
2385 3011 4.452114 TGACAAATCAGAAATGGTCGAGTG 59.548 41.667 0.00 0.00 0.00 3.51
2386 3012 4.641396 TGACAAATCAGAAATGGTCGAGT 58.359 39.130 0.00 0.00 0.00 4.18
2401 3034 1.518056 CGCCACACAGCCTGACAAAT 61.518 55.000 0.00 0.00 0.00 2.32
2501 3134 6.204359 CGAAATATCAAGGGCAAAGAAGATG 58.796 40.000 0.00 0.00 0.00 2.90
2540 3173 2.986019 TCAGTCTCAATCCCTTTCCCAA 59.014 45.455 0.00 0.00 0.00 4.12
2544 3177 3.320673 ACGTCAGTCTCAATCCCTTTC 57.679 47.619 0.00 0.00 0.00 2.62
2688 3321 6.748333 ACTACATTGCGACTAGTAGTGTTA 57.252 37.500 7.76 0.00 43.84 2.41
2711 3345 7.786030 AGATTTAATCCATCTCTCTCGACAAA 58.214 34.615 0.78 0.00 0.00 2.83
2720 3354 5.069648 TGAGTGCGAGATTTAATCCATCTCT 59.930 40.000 11.88 0.00 43.19 3.10
2734 3368 3.856309 ACACCAGTGAGTGCGAGA 58.144 55.556 4.48 0.00 41.67 4.04
2829 3476 1.209128 CGTTTCCGCAGTAGCCATAG 58.791 55.000 0.00 0.00 37.52 2.23
2844 3491 4.695217 TCAGTCTTTGTTTTCAGCGTTT 57.305 36.364 0.00 0.00 0.00 3.60
2877 3529 2.058595 ACGCTACAAGGCTCCCGAT 61.059 57.895 0.00 0.00 0.00 4.18
2892 3544 4.209452 TGACAACATCTTTCTTTCACGC 57.791 40.909 0.00 0.00 0.00 5.34
2908 3561 3.281332 GCCCTGGGCTTATTGACAA 57.719 52.632 30.42 0.00 46.69 3.18
2927 3580 4.944048 ACATTTTCTGGGCACACTTTAAC 58.056 39.130 0.00 0.00 0.00 2.01
2964 3617 7.333423 CCAACTCAAGTTCCATCTTACGAATAA 59.667 37.037 0.00 0.00 35.83 1.40
3064 3730 3.685139 AAAGAAGGAAGCAGATGACGA 57.315 42.857 0.00 0.00 0.00 4.20
3085 3751 6.317893 GGTTTCGCTCTATAATTGGAAGGAAA 59.682 38.462 0.00 0.00 0.00 3.13
3107 3773 4.188462 TGTAATGATTCGCTTCATCGGTT 58.812 39.130 1.15 0.00 35.29 4.44
3146 3812 2.552315 AGGTAACCAAACGCATGTTCTG 59.448 45.455 0.00 0.00 34.87 3.02
3149 3815 1.000717 GCAGGTAACCAAACGCATGTT 60.001 47.619 0.00 0.00 37.27 2.71
3151 3817 0.595588 TGCAGGTAACCAAACGCATG 59.404 50.000 0.00 0.00 37.17 4.06
3152 3818 1.202114 CATGCAGGTAACCAAACGCAT 59.798 47.619 0.00 0.00 40.55 4.73
3172 3851 4.568956 AGTATGCAAAGTGCCCAAAAATC 58.431 39.130 0.00 0.00 44.23 2.17
3198 3877 2.151502 TTTTTGCCTGACCAACTGGA 57.848 45.000 1.86 0.00 39.52 3.86
3224 3920 4.092821 CAGGCAATCAATCAACATGCAAAG 59.907 41.667 0.00 0.00 38.73 2.77
3240 3936 1.556451 GGAAAAAGGGATGCAGGCAAT 59.444 47.619 0.00 0.00 0.00 3.56
3254 3950 1.083489 CGCTACGATGCAGGGAAAAA 58.917 50.000 0.00 0.00 0.00 1.94
3255 3951 0.248012 TCGCTACGATGCAGGGAAAA 59.752 50.000 0.00 0.00 32.62 2.29
3257 3953 1.141019 GTCGCTACGATGCAGGGAA 59.859 57.895 0.00 0.00 38.42 3.97
3282 3978 0.240945 AGCAACCAAACATAGTGCGC 59.759 50.000 0.00 0.00 0.00 6.09
3283 3979 1.464023 CGAGCAACCAAACATAGTGCG 60.464 52.381 0.00 0.00 0.00 5.34
3309 4005 7.829725 ACAACATGCACTAATATGAACACAAT 58.170 30.769 0.00 0.00 0.00 2.71
3310 4006 7.213216 ACAACATGCACTAATATGAACACAA 57.787 32.000 0.00 0.00 0.00 3.33
3321 4017 2.428530 TGCAACCAACAACATGCACTAA 59.571 40.909 0.00 0.00 43.32 2.24
3347 4044 9.349713 AGTTGTTTAAGTCTTAATCATGTCCAA 57.650 29.630 14.14 4.58 0.00 3.53
3366 4063 6.781138 CACAGTGTGTTATGTGTAGTTGTTT 58.219 36.000 15.43 0.00 41.49 2.83
3459 4170 2.730733 GATGAGATCGCTCGCCCA 59.269 61.111 0.00 0.00 44.33 5.36
3483 4194 2.296471 ACAGTAGCAACTAGTTCGCTGT 59.704 45.455 28.06 22.98 37.20 4.40
3485 4196 3.243771 ACAACAGTAGCAACTAGTTCGCT 60.244 43.478 25.42 25.42 39.80 4.93
3501 4212 1.854126 CTTTCTTTGCGGCAACAACAG 59.146 47.619 16.15 10.29 0.00 3.16
3502 4213 1.203523 ACTTTCTTTGCGGCAACAACA 59.796 42.857 16.15 0.00 0.00 3.33
3505 4216 2.266554 CAAACTTTCTTTGCGGCAACA 58.733 42.857 16.15 1.83 0.00 3.33
3508 4219 1.203523 ACACAAACTTTCTTTGCGGCA 59.796 42.857 0.00 0.00 32.93 5.69
3523 4234 5.105635 CCCTCCTATTCGTTACTACACACAA 60.106 44.000 0.00 0.00 0.00 3.33
3530 4241 1.610522 GCGCCCTCCTATTCGTTACTA 59.389 52.381 0.00 0.00 0.00 1.82
3624 4336 3.441572 CCATCGTCATTCTTTTCAGCCTT 59.558 43.478 0.00 0.00 0.00 4.35
3653 4420 1.810031 GCGCATCCTACTACATTGGCA 60.810 52.381 0.30 0.00 0.00 4.92
3658 4425 1.371758 CGCGCGCATCCTACTACAT 60.372 57.895 32.61 0.00 0.00 2.29
3722 4489 4.061131 TCCTCTTCTCTTGTCCCATGTA 57.939 45.455 0.00 0.00 0.00 2.29
3733 4500 7.201992 GGTCATCATCTATTGTTCCTCTTCTCT 60.202 40.741 0.00 0.00 0.00 3.10
3738 4505 4.502259 GCGGTCATCATCTATTGTTCCTCT 60.502 45.833 0.00 0.00 0.00 3.69
3739 4506 3.743396 GCGGTCATCATCTATTGTTCCTC 59.257 47.826 0.00 0.00 0.00 3.71
3741 4508 3.248602 GTGCGGTCATCATCTATTGTTCC 59.751 47.826 0.00 0.00 0.00 3.62
3744 4511 2.159099 ACGTGCGGTCATCATCTATTGT 60.159 45.455 0.00 0.00 0.00 2.71
3745 4512 2.219445 CACGTGCGGTCATCATCTATTG 59.781 50.000 0.82 0.00 0.00 1.90
3749 4516 0.815095 TACACGTGCGGTCATCATCT 59.185 50.000 17.22 0.00 0.00 2.90
3750 4517 1.200483 CTACACGTGCGGTCATCATC 58.800 55.000 17.22 0.00 0.00 2.92
3751 4518 0.530744 ACTACACGTGCGGTCATCAT 59.469 50.000 17.22 0.00 0.00 2.45
3752 4519 0.109458 GACTACACGTGCGGTCATCA 60.109 55.000 26.09 1.56 0.00 3.07
3754 4521 1.154093 CGACTACACGTGCGGTCAT 60.154 57.895 28.36 10.00 0.00 3.06
3755 4522 2.253154 CGACTACACGTGCGGTCA 59.747 61.111 28.36 7.86 0.00 4.02
3757 4524 2.979676 TCCGACTACACGTGCGGT 60.980 61.111 24.96 19.40 43.92 5.68
3758 4525 2.503375 GTCCGACTACACGTGCGG 60.503 66.667 21.70 21.70 44.83 5.69
3761 4528 1.534163 TCTCTTGTCCGACTACACGTG 59.466 52.381 15.48 15.48 0.00 4.49
3762 4529 1.805345 CTCTCTTGTCCGACTACACGT 59.195 52.381 0.00 0.00 0.00 4.49
3763 4530 2.074576 TCTCTCTTGTCCGACTACACG 58.925 52.381 0.00 0.00 0.00 4.49
3771 4538 1.203523 CAACCTCCTCTCTCTTGTCCG 59.796 57.143 0.00 0.00 0.00 4.79
3777 4544 2.283834 TCCTCTCAACCTCCTCTCTCT 58.716 52.381 0.00 0.00 0.00 3.10
3816 4583 0.458543 CCCACGTGCTGCTACACTAG 60.459 60.000 10.91 0.00 38.45 2.57
3837 4604 0.241749 ACGTCGCCATCGTTGTTCTA 59.758 50.000 0.00 0.00 38.38 2.10
3842 4609 4.147322 GCCACGTCGCCATCGTTG 62.147 66.667 0.00 0.00 39.55 4.10


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

AutoCloner maintained by Alex Coulton.