Multiple sequence alignment - TraesCS2B01G133700

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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 TraesCS2B01G133700 chr2B 100.000 2306 0 0 1 2306 100031179 100028874 0.000000e+00 4259.0
1 TraesCS2B01G133700 chr2B 88.627 466 35 10 845 1306 100024603 100025054 3.350000e-153 551.0
2 TraesCS2B01G133700 chr2B 88.722 266 24 5 71 333 42029822 42029560 1.030000e-83 320.0
3 TraesCS2B01G133700 chr2B 84.393 173 16 6 2134 2306 39788951 39788790 2.370000e-35 159.0
4 TraesCS2B01G133700 chr2D 87.534 2190 184 30 1 2131 64016206 64014047 0.000000e+00 2449.0
5 TraesCS2B01G133700 chr2D 85.652 913 95 17 706 1585 63914157 63913248 0.000000e+00 928.0
6 TraesCS2B01G133700 chr2D 88.156 743 53 9 1 709 63915036 63914295 0.000000e+00 852.0
7 TraesCS2B01G133700 chr2D 88.445 476 38 7 845 1316 64010841 64011303 2.000000e-155 558.0
8 TraesCS2B01G133700 chr2D 88.675 468 34 6 845 1306 63908472 63908926 9.310000e-154 553.0
9 TraesCS2B01G133700 chr2D 89.723 253 23 3 1881 2131 63913246 63912995 1.030000e-83 320.0
10 TraesCS2B01G133700 chr2A 88.707 1036 65 30 597 1608 65476391 65475384 0.000000e+00 1218.0
11 TraesCS2B01G133700 chr2A 93.625 251 15 1 17 267 65477113 65476864 7.780000e-100 374.0
12 TraesCS2B01G133700 chr2A 84.694 294 19 13 336 619 65476863 65476586 1.050000e-68 270.0
13 TraesCS2B01G133700 chr4A 88.818 313 27 5 1000 1305 681178998 681178687 6.010000e-101 377.0
14 TraesCS2B01G133700 chr4D 88.462 312 30 3 1000 1305 474918674 474918985 2.800000e-99 372.0
15 TraesCS2B01G133700 chr4B 88.103 311 31 3 1001 1305 599356977 599356667 4.680000e-97 364.0
16 TraesCS2B01G133700 chr6D 90.114 263 24 2 71 332 116277215 116276954 7.890000e-90 340.0
17 TraesCS2B01G133700 chr5D 89.773 264 25 2 71 333 500160232 500159970 1.020000e-88 337.0
18 TraesCS2B01G133700 chr3D 89.354 263 26 2 72 333 369414423 369414162 1.710000e-86 329.0
19 TraesCS2B01G133700 chr3D 87.425 167 19 2 2140 2306 520600470 520600306 8.410000e-45 191.0
20 TraesCS2B01G133700 chr3B 89.354 263 26 2 72 333 480377202 480376941 1.710000e-86 329.0
21 TraesCS2B01G133700 chr3B 86.207 174 19 4 2134 2306 20743967 20743798 1.410000e-42 183.0
22 TraesCS2B01G133700 chr7A 88.192 271 29 3 68 337 646560183 646560451 1.030000e-83 320.0
23 TraesCS2B01G133700 chr7A 97.143 35 1 0 2171 2205 11283902 11283868 2.470000e-05 60.2
24 TraesCS2B01G133700 chr5A 86.127 173 21 2 2134 2306 656653105 656653274 1.410000e-42 183.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2B01G133700 chr2B 100028874 100031179 2305 True 4259.000000 4259 100.000000 1 2306 1 chr2B.!!$R3 2305
1 TraesCS2B01G133700 chr2D 64014047 64016206 2159 True 2449.000000 2449 87.534000 1 2131 1 chr2D.!!$R1 2130
2 TraesCS2B01G133700 chr2D 63912995 63915036 2041 True 700.000000 928 87.843667 1 2131 3 chr2D.!!$R2 2130
3 TraesCS2B01G133700 chr2A 65475384 65477113 1729 True 620.666667 1218 89.008667 17 1608 3 chr2A.!!$R1 1591

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
879 1304 0.536233 ATAAACGCAGCACCCACACA 60.536 50.0 0.0 0.0 0.0 3.72 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2255 2727 0.109319 GTTTAATGTGCCAGCCCGTG 60.109 55.0 0.0 0.0 0.0 4.94 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
34 35 6.839124 ACATGTTCTTAGCATGATTTTGGA 57.161 33.333 10.21 0.00 44.60 3.53
293 302 7.924947 TCAAATATTCAAATGTTGACTTGCACA 59.075 29.630 0.00 0.00 39.87 4.57
327 336 4.102054 CACCTTATATTAGGGAACGGTGGT 59.898 45.833 12.28 0.00 39.76 4.16
345 354 6.608808 ACGGTGGTAGTATGTCTAAACCTAAT 59.391 38.462 0.00 0.00 36.38 1.73
346 355 7.124750 ACGGTGGTAGTATGTCTAAACCTAATT 59.875 37.037 0.00 0.00 36.38 1.40
399 409 4.243007 ACAAGTAGGCACAATTTTCAGC 57.757 40.909 0.00 0.00 0.00 4.26
560 597 7.422399 TGTTGTTGGCTTAGTTATTCAAACTC 58.578 34.615 0.00 0.00 0.00 3.01
585 622 4.411013 AGCCCACTTTAAGCTCAAGATTT 58.589 39.130 11.64 0.00 28.40 2.17
635 890 1.134907 AGCCATCGGTTAGTTACGTGG 60.135 52.381 0.00 0.00 35.71 4.94
646 901 6.471519 CGGTTAGTTACGTGGAATCTAAGAAG 59.528 42.308 0.00 0.00 0.00 2.85
681 942 9.073475 AGAATAATACTAATCTTCTCGAGCAGT 57.927 33.333 11.90 8.05 0.00 4.40
694 955 1.536766 CGAGCAGTTTGATTGCCTTGA 59.463 47.619 0.00 0.00 42.48 3.02
869 1294 2.930040 CCATCCGCCTATATAAACGCAG 59.070 50.000 0.00 0.00 0.00 5.18
870 1295 2.074547 TCCGCCTATATAAACGCAGC 57.925 50.000 0.00 0.00 0.00 5.25
871 1296 1.341852 TCCGCCTATATAAACGCAGCA 59.658 47.619 0.00 0.00 0.00 4.41
872 1297 1.459592 CCGCCTATATAAACGCAGCAC 59.540 52.381 0.00 0.00 0.00 4.40
873 1298 1.459592 CGCCTATATAAACGCAGCACC 59.540 52.381 0.00 0.00 0.00 5.01
874 1299 1.804748 GCCTATATAAACGCAGCACCC 59.195 52.381 0.00 0.00 0.00 4.61
875 1300 2.808933 GCCTATATAAACGCAGCACCCA 60.809 50.000 0.00 0.00 0.00 4.51
876 1301 2.806244 CCTATATAAACGCAGCACCCAC 59.194 50.000 0.00 0.00 0.00 4.61
877 1302 2.411628 ATATAAACGCAGCACCCACA 57.588 45.000 0.00 0.00 0.00 4.17
878 1303 1.444836 TATAAACGCAGCACCCACAC 58.555 50.000 0.00 0.00 0.00 3.82
879 1304 0.536233 ATAAACGCAGCACCCACACA 60.536 50.000 0.00 0.00 0.00 3.72
880 1305 1.440938 TAAACGCAGCACCCACACAC 61.441 55.000 0.00 0.00 0.00 3.82
883 1308 2.598394 GCAGCACCCACACACCAT 60.598 61.111 0.00 0.00 0.00 3.55
884 1309 2.629656 GCAGCACCCACACACCATC 61.630 63.158 0.00 0.00 0.00 3.51
885 1310 1.228215 CAGCACCCACACACCATCA 60.228 57.895 0.00 0.00 0.00 3.07
886 1311 1.073722 AGCACCCACACACCATCAG 59.926 57.895 0.00 0.00 0.00 2.90
887 1312 2.629656 GCACCCACACACCATCAGC 61.630 63.158 0.00 0.00 0.00 4.26
888 1313 1.228215 CACCCACACACCATCAGCA 60.228 57.895 0.00 0.00 0.00 4.41
889 1314 1.073722 ACCCACACACCATCAGCAG 59.926 57.895 0.00 0.00 0.00 4.24
890 1315 2.338015 CCCACACACCATCAGCAGC 61.338 63.158 0.00 0.00 0.00 5.25
891 1316 1.601477 CCACACACCATCAGCAGCA 60.601 57.895 0.00 0.00 0.00 4.41
904 1329 5.704053 CCATCAGCAGCATCAGATTATAACA 59.296 40.000 0.00 0.00 0.00 2.41
914 1354 6.127758 GCATCAGATTATAACACAACCAACCA 60.128 38.462 0.00 0.00 0.00 3.67
921 1361 1.361271 CACAACCAACCAGCAGCAG 59.639 57.895 0.00 0.00 0.00 4.24
940 1390 2.545526 CAGGTAGTGCAACACAAGACTG 59.454 50.000 0.00 0.00 41.43 3.51
955 1405 1.066303 AGACTGGCAAGATCGATCGAC 59.934 52.381 22.06 14.23 0.00 4.20
983 1433 4.216902 GGTAGCTAGCTAGTAAGGAAGAGC 59.783 50.000 24.78 7.45 35.07 4.09
1008 1458 1.003580 AGAAGAAGAAAGATGGCGGCA 59.996 47.619 16.34 16.34 0.00 5.69
1011 1461 1.997928 GAAGAAAGATGGCGGCAGGC 61.998 60.000 19.29 12.22 44.11 4.85
1084 1534 2.345991 GGAAGGCGCTGGTGTACA 59.654 61.111 7.64 0.00 0.00 2.90
1235 1685 0.549169 ATTCCCCGGGACTTCTCCAA 60.549 55.000 26.32 1.18 38.52 3.53
1251 1702 4.021925 AAGCTCCGCTCCACCCAC 62.022 66.667 0.00 0.00 38.25 4.61
1317 1770 3.884091 TCGACCTCTAGTTAGCCATCTTC 59.116 47.826 0.00 0.00 0.00 2.87
1318 1771 3.632604 CGACCTCTAGTTAGCCATCTTCA 59.367 47.826 0.00 0.00 0.00 3.02
1324 1777 3.185246 AGTTAGCCATCTTCATCGGTG 57.815 47.619 0.00 0.00 0.00 4.94
1340 1793 6.621613 TCATCGGTGATATTCTTCCTATTCG 58.378 40.000 0.00 0.00 0.00 3.34
1351 1804 3.506455 TCTTCCTATTCGAGCCGGATAAG 59.494 47.826 5.05 0.00 26.14 1.73
1355 1808 2.528041 ATTCGAGCCGGATAAGTTCC 57.472 50.000 5.05 0.00 41.59 3.62
1488 1948 2.643551 CCTTTGTCAGAACCTGTGTGT 58.356 47.619 0.00 0.00 32.61 3.72
1500 1960 2.694628 ACCTGTGTGTACTTAACGGTGA 59.305 45.455 0.00 0.00 0.00 4.02
1516 1976 9.607285 CTTAACGGTGAAAAATATATGTATGCC 57.393 33.333 0.00 0.00 0.00 4.40
1534 1994 2.237643 GCCAGTACCGGGGTTTAAAAA 58.762 47.619 6.32 0.00 0.00 1.94
1544 2004 4.765339 CCGGGGTTTAAAAACTCTGATTCT 59.235 41.667 14.56 0.00 46.45 2.40
1557 2019 4.006319 CTCTGATTCTGAAACTTGACCCC 58.994 47.826 0.00 0.00 0.00 4.95
1560 2022 0.472471 TTCTGAAACTTGACCCCGCT 59.528 50.000 0.00 0.00 0.00 5.52
1608 2072 4.099419 GGTTCCCGGCTCATTTTATTGAAT 59.901 41.667 0.00 0.00 0.00 2.57
1629 2093 2.276201 GAGGCAAACCAAAAACACACC 58.724 47.619 0.00 0.00 39.06 4.16
1633 2097 4.102367 AGGCAAACCAAAAACACACCATAT 59.898 37.500 0.00 0.00 39.06 1.78
1634 2098 4.450757 GGCAAACCAAAAACACACCATATC 59.549 41.667 0.00 0.00 35.26 1.63
1641 2105 5.920273 CCAAAAACACACCATATCTGTTCAC 59.080 40.000 0.00 0.00 0.00 3.18
1642 2106 5.356882 AAAACACACCATATCTGTTCACG 57.643 39.130 0.00 0.00 0.00 4.35
1645 2109 3.512329 ACACACCATATCTGTTCACGGTA 59.488 43.478 0.00 0.00 0.00 4.02
1646 2110 4.161565 ACACACCATATCTGTTCACGGTAT 59.838 41.667 0.00 0.00 0.00 2.73
1647 2111 4.745125 CACACCATATCTGTTCACGGTATC 59.255 45.833 0.00 0.00 0.00 2.24
1668 2133 2.984623 CTAGGCCACAGCAGCAGA 59.015 61.111 5.01 0.00 42.56 4.26
1670 2135 2.590391 CTAGGCCACAGCAGCAGAGG 62.590 65.000 5.01 0.00 42.56 3.69
1674 2139 2.346365 CACAGCAGCAGAGGCAGA 59.654 61.111 0.00 0.00 44.61 4.26
1689 2154 4.160252 AGAGGCAGAAAAAGAACAAGCAAA 59.840 37.500 0.00 0.00 0.00 3.68
1690 2155 4.436332 AGGCAGAAAAAGAACAAGCAAAG 58.564 39.130 0.00 0.00 0.00 2.77
1697 2162 6.551227 AGAAAAAGAACAAGCAAAGGGTCTAT 59.449 34.615 0.00 0.00 0.00 1.98
1711 2176 5.422214 AGGGTCTATTTCTACCACAACAG 57.578 43.478 0.00 0.00 37.51 3.16
1727 2192 5.765182 CCACAACAGATAGAAGGAAAACAGT 59.235 40.000 0.00 0.00 0.00 3.55
1728 2193 6.934645 CCACAACAGATAGAAGGAAAACAGTA 59.065 38.462 0.00 0.00 0.00 2.74
1729 2194 7.607991 CCACAACAGATAGAAGGAAAACAGTAT 59.392 37.037 0.00 0.00 0.00 2.12
1730 2195 8.660373 CACAACAGATAGAAGGAAAACAGTATC 58.340 37.037 0.00 0.00 0.00 2.24
1731 2196 8.375506 ACAACAGATAGAAGGAAAACAGTATCA 58.624 33.333 0.00 0.00 0.00 2.15
1748 2213 6.382282 ACAGTATCATCAGATGGACAAAGAGA 59.618 38.462 10.67 0.00 35.67 3.10
1752 2217 4.220602 TCATCAGATGGACAAAGAGAACGA 59.779 41.667 10.67 0.00 0.00 3.85
1787 2252 8.356000 GGTCTAGCCTATTATAAGTCATCAGT 57.644 38.462 0.00 0.00 0.00 3.41
1794 2259 7.327275 GCCTATTATAAGTCATCAGTCAACGAG 59.673 40.741 0.00 0.00 0.00 4.18
1808 2278 1.023513 AACGAGCAGCTGGAATGAGC 61.024 55.000 17.12 0.00 39.46 4.26
1816 2286 0.540923 GCTGGAATGAGCTCTCAGGT 59.459 55.000 16.19 0.00 43.61 4.00
1820 2290 1.069978 GGAATGAGCTCTCAGGTAGGC 59.930 57.143 16.19 0.00 43.61 3.93
1844 2314 0.390866 CACTGCTCATTCACCTCGCT 60.391 55.000 0.00 0.00 0.00 4.93
1845 2315 0.390866 ACTGCTCATTCACCTCGCTG 60.391 55.000 0.00 0.00 0.00 5.18
1849 2319 1.941209 GCTCATTCACCTCGCTGACAA 60.941 52.381 0.00 0.00 0.00 3.18
1850 2320 1.728971 CTCATTCACCTCGCTGACAAC 59.271 52.381 0.00 0.00 0.00 3.32
1852 2322 0.670546 ATTCACCTCGCTGACAACGG 60.671 55.000 0.00 0.00 0.00 4.44
1853 2323 3.414700 CACCTCGCTGACAACGGC 61.415 66.667 0.00 0.00 44.17 5.68
1854 2324 4.681978 ACCTCGCTGACAACGGCC 62.682 66.667 0.00 0.00 44.72 6.13
1855 2325 4.680237 CCTCGCTGACAACGGCCA 62.680 66.667 2.24 0.00 44.72 5.36
1860 2330 0.732571 CGCTGACAACGGCCAATTAT 59.267 50.000 2.24 0.00 44.72 1.28
1866 2336 2.614057 GACAACGGCCAATTATCTCCAG 59.386 50.000 2.24 0.00 0.00 3.86
1867 2337 1.949525 CAACGGCCAATTATCTCCAGG 59.050 52.381 2.24 0.00 0.00 4.45
1895 2365 1.140804 GCAGCTCTCCTCTTCGACC 59.859 63.158 0.00 0.00 0.00 4.79
1903 2373 2.778270 TCTCCTCTTCGACCATCTAGGA 59.222 50.000 0.00 0.00 41.22 2.94
1911 2381 1.069823 CGACCATCTAGGAGCAGCAAT 59.930 52.381 0.00 0.00 41.22 3.56
1913 2383 1.419387 ACCATCTAGGAGCAGCAATCC 59.581 52.381 0.00 0.00 41.22 3.01
1921 2391 0.182061 GAGCAGCAATCCCTCCATCA 59.818 55.000 0.00 0.00 0.00 3.07
1940 2410 3.942829 TCATCAACACTGACTGGGAATC 58.057 45.455 0.00 0.00 33.30 2.52
1945 2415 1.982395 ACTGACTGGGAATCGGCGA 60.982 57.895 13.87 13.87 0.00 5.54
1951 2421 0.744414 CTGGGAATCGGCGAACATGT 60.744 55.000 15.93 0.00 0.00 3.21
1953 2423 0.377203 GGGAATCGGCGAACATGTTC 59.623 55.000 25.68 25.68 36.29 3.18
1954 2424 1.369625 GGAATCGGCGAACATGTTCT 58.630 50.000 30.45 14.91 37.44 3.01
1955 2425 1.327764 GGAATCGGCGAACATGTTCTC 59.672 52.381 30.45 24.67 37.44 2.87
1966 2438 5.391310 GCGAACATGTTCTCATTGATGAAGT 60.391 40.000 30.45 0.00 37.44 3.01
1989 2461 4.478206 TCAAGCTTACTCTTCCCATGAG 57.522 45.455 0.00 0.00 37.55 2.90
1995 2467 1.225704 CTCTTCCCATGAGTGCCCC 59.774 63.158 0.00 0.00 0.00 5.80
2015 2487 3.064207 CCGACATCTTTCGAAACCAAGA 58.936 45.455 6.47 2.85 41.78 3.02
2025 2497 1.671845 CGAAACCAAGACCGGAAAACA 59.328 47.619 9.46 0.00 0.00 2.83
2054 2526 0.534877 ACGCATTGTCCACAAGCTCA 60.535 50.000 0.00 0.00 39.47 4.26
2058 2530 2.859806 GCATTGTCCACAAGCTCAACAC 60.860 50.000 0.00 0.00 39.47 3.32
2079 2551 2.095567 CGGTAGCAATGCAAGCCATATC 60.096 50.000 8.35 0.00 32.67 1.63
2131 2603 8.723942 ACCACAAAGTAGATATTTCAGTCATC 57.276 34.615 0.00 0.00 0.00 2.92
2132 2604 7.492669 ACCACAAAGTAGATATTTCAGTCATCG 59.507 37.037 0.00 0.00 0.00 3.84
2133 2605 7.492669 CCACAAAGTAGATATTTCAGTCATCGT 59.507 37.037 0.00 0.00 0.00 3.73
2134 2606 8.873830 CACAAAGTAGATATTTCAGTCATCGTT 58.126 33.333 0.00 0.00 0.00 3.85
2135 2607 9.088512 ACAAAGTAGATATTTCAGTCATCGTTC 57.911 33.333 0.00 0.00 0.00 3.95
2136 2608 9.307121 CAAAGTAGATATTTCAGTCATCGTTCT 57.693 33.333 0.00 0.00 0.00 3.01
2137 2609 9.877178 AAAGTAGATATTTCAGTCATCGTTCTT 57.123 29.630 0.00 0.00 0.00 2.52
2138 2610 8.864069 AGTAGATATTTCAGTCATCGTTCTTG 57.136 34.615 0.00 0.00 0.00 3.02
2139 2611 6.595772 AGATATTTCAGTCATCGTTCTTGC 57.404 37.500 0.00 0.00 0.00 4.01
2140 2612 6.344500 AGATATTTCAGTCATCGTTCTTGCT 58.656 36.000 0.00 0.00 0.00 3.91
2141 2613 6.820656 AGATATTTCAGTCATCGTTCTTGCTT 59.179 34.615 0.00 0.00 0.00 3.91
2142 2614 4.732285 TTTCAGTCATCGTTCTTGCTTC 57.268 40.909 0.00 0.00 0.00 3.86
2143 2615 2.328473 TCAGTCATCGTTCTTGCTTCG 58.672 47.619 0.00 0.00 0.00 3.79
2144 2616 1.391485 CAGTCATCGTTCTTGCTTCGG 59.609 52.381 0.00 0.00 0.00 4.30
2145 2617 1.000955 AGTCATCGTTCTTGCTTCGGT 59.999 47.619 0.00 0.00 0.00 4.69
2146 2618 2.230508 AGTCATCGTTCTTGCTTCGGTA 59.769 45.455 0.00 0.00 0.00 4.02
2147 2619 2.599082 GTCATCGTTCTTGCTTCGGTAG 59.401 50.000 0.00 0.00 0.00 3.18
2148 2620 2.490509 TCATCGTTCTTGCTTCGGTAGA 59.509 45.455 0.00 0.00 0.00 2.59
2149 2621 2.342910 TCGTTCTTGCTTCGGTAGAC 57.657 50.000 0.00 0.00 0.00 2.59
2150 2622 1.068055 TCGTTCTTGCTTCGGTAGACC 60.068 52.381 0.00 0.00 0.00 3.85
2151 2623 1.723220 GTTCTTGCTTCGGTAGACCC 58.277 55.000 0.00 0.00 0.00 4.46
2152 2624 0.611714 TTCTTGCTTCGGTAGACCCC 59.388 55.000 0.00 0.00 0.00 4.95
2153 2625 1.221021 CTTGCTTCGGTAGACCCCC 59.779 63.158 0.00 0.00 0.00 5.40
2170 2642 1.365699 CCCCCTTAAACACATCGACG 58.634 55.000 0.00 0.00 0.00 5.12
2171 2643 1.365699 CCCCTTAAACACATCGACGG 58.634 55.000 0.00 0.00 0.00 4.79
2172 2644 0.725117 CCCTTAAACACATCGACGGC 59.275 55.000 0.00 0.00 0.00 5.68
2173 2645 1.674817 CCCTTAAACACATCGACGGCT 60.675 52.381 0.00 0.00 0.00 5.52
2174 2646 1.659098 CCTTAAACACATCGACGGCTC 59.341 52.381 0.00 0.00 0.00 4.70
2175 2647 2.333926 CTTAAACACATCGACGGCTCA 58.666 47.619 0.00 0.00 0.00 4.26
2176 2648 1.990799 TAAACACATCGACGGCTCAG 58.009 50.000 0.00 0.00 0.00 3.35
2177 2649 0.317160 AAACACATCGACGGCTCAGA 59.683 50.000 0.00 0.00 0.00 3.27
2178 2650 0.532573 AACACATCGACGGCTCAGAT 59.467 50.000 0.00 0.00 0.00 2.90
2179 2651 0.532573 ACACATCGACGGCTCAGATT 59.467 50.000 0.00 0.00 0.00 2.40
2180 2652 1.749063 ACACATCGACGGCTCAGATTA 59.251 47.619 0.00 0.00 0.00 1.75
2181 2653 2.362397 ACACATCGACGGCTCAGATTAT 59.638 45.455 0.00 0.00 0.00 1.28
2182 2654 2.983136 CACATCGACGGCTCAGATTATC 59.017 50.000 0.00 0.00 0.00 1.75
2183 2655 2.029828 ACATCGACGGCTCAGATTATCC 60.030 50.000 0.00 0.00 0.00 2.59
2184 2656 0.959553 TCGACGGCTCAGATTATCCC 59.040 55.000 0.00 0.00 0.00 3.85
2185 2657 0.673985 CGACGGCTCAGATTATCCCA 59.326 55.000 0.00 0.00 0.00 4.37
2186 2658 1.273606 CGACGGCTCAGATTATCCCAT 59.726 52.381 0.00 0.00 0.00 4.00
2187 2659 2.492088 CGACGGCTCAGATTATCCCATA 59.508 50.000 0.00 0.00 0.00 2.74
2188 2660 3.673594 CGACGGCTCAGATTATCCCATAC 60.674 52.174 0.00 0.00 0.00 2.39
2189 2661 2.567615 ACGGCTCAGATTATCCCATACC 59.432 50.000 0.00 0.00 0.00 2.73
2190 2662 2.834549 CGGCTCAGATTATCCCATACCT 59.165 50.000 0.00 0.00 0.00 3.08
2191 2663 3.118956 CGGCTCAGATTATCCCATACCTC 60.119 52.174 0.00 0.00 0.00 3.85
2192 2664 4.100373 GGCTCAGATTATCCCATACCTCT 58.900 47.826 0.00 0.00 0.00 3.69
2193 2665 4.534103 GGCTCAGATTATCCCATACCTCTT 59.466 45.833 0.00 0.00 0.00 2.85
2194 2666 5.337975 GGCTCAGATTATCCCATACCTCTTC 60.338 48.000 0.00 0.00 0.00 2.87
2195 2667 5.247110 GCTCAGATTATCCCATACCTCTTCA 59.753 44.000 0.00 0.00 0.00 3.02
2196 2668 6.070309 GCTCAGATTATCCCATACCTCTTCAT 60.070 42.308 0.00 0.00 0.00 2.57
2197 2669 7.124901 GCTCAGATTATCCCATACCTCTTCATA 59.875 40.741 0.00 0.00 0.00 2.15
2198 2670 8.972662 TCAGATTATCCCATACCTCTTCATAA 57.027 34.615 0.00 0.00 0.00 1.90
2199 2671 9.566331 TCAGATTATCCCATACCTCTTCATAAT 57.434 33.333 0.00 0.00 0.00 1.28
2205 2677 8.757307 ATCCCATACCTCTTCATAATTAAGGA 57.243 34.615 7.08 0.00 0.00 3.36
2206 2678 8.757307 TCCCATACCTCTTCATAATTAAGGAT 57.243 34.615 7.08 0.00 0.00 3.24
2207 2679 9.852784 TCCCATACCTCTTCATAATTAAGGATA 57.147 33.333 7.08 0.00 0.00 2.59
2227 2699 8.712228 AGGATAAGATTGTCCTTTTCAAAAGT 57.288 30.769 9.07 0.00 45.20 2.66
2228 2700 9.807921 AGGATAAGATTGTCCTTTTCAAAAGTA 57.192 29.630 9.07 0.00 45.20 2.24
2229 2701 9.841880 GGATAAGATTGTCCTTTTCAAAAGTAC 57.158 33.333 9.07 3.93 35.76 2.73
2230 2702 9.543018 GATAAGATTGTCCTTTTCAAAAGTACG 57.457 33.333 9.07 0.00 0.00 3.67
2231 2703 6.937436 AGATTGTCCTTTTCAAAAGTACGT 57.063 33.333 9.07 0.00 0.00 3.57
2232 2704 7.329588 AGATTGTCCTTTTCAAAAGTACGTT 57.670 32.000 9.07 0.00 0.00 3.99
2233 2705 7.193595 AGATTGTCCTTTTCAAAAGTACGTTG 58.806 34.615 9.07 0.42 0.00 4.10
2234 2706 5.883503 TGTCCTTTTCAAAAGTACGTTGT 57.116 34.783 9.07 0.00 0.00 3.32
2235 2707 6.981762 TGTCCTTTTCAAAAGTACGTTGTA 57.018 33.333 9.07 1.21 0.00 2.41
2236 2708 7.375106 TGTCCTTTTCAAAAGTACGTTGTAA 57.625 32.000 9.07 6.35 0.00 2.41
2237 2709 7.465989 TGTCCTTTTCAAAAGTACGTTGTAAG 58.534 34.615 9.07 13.27 0.00 2.34
2238 2710 7.333921 TGTCCTTTTCAAAAGTACGTTGTAAGA 59.666 33.333 9.07 8.81 0.00 2.10
2239 2711 7.637519 GTCCTTTTCAAAAGTACGTTGTAAGAC 59.362 37.037 9.07 13.57 0.00 3.01
2240 2712 6.908820 CCTTTTCAAAAGTACGTTGTAAGACC 59.091 38.462 9.07 0.00 0.00 3.85
2241 2713 7.201670 CCTTTTCAAAAGTACGTTGTAAGACCT 60.202 37.037 9.07 0.00 0.00 3.85
2242 2714 7.614124 TTTCAAAAGTACGTTGTAAGACCTT 57.386 32.000 0.00 0.00 0.00 3.50
2243 2715 6.592798 TCAAAAGTACGTTGTAAGACCTTG 57.407 37.500 0.00 0.00 0.00 3.61
2244 2716 6.108015 TCAAAAGTACGTTGTAAGACCTTGT 58.892 36.000 0.00 0.00 0.00 3.16
2245 2717 7.264221 TCAAAAGTACGTTGTAAGACCTTGTA 58.736 34.615 0.00 0.00 0.00 2.41
2246 2718 7.927629 TCAAAAGTACGTTGTAAGACCTTGTAT 59.072 33.333 0.00 0.00 0.00 2.29
2247 2719 9.195411 CAAAAGTACGTTGTAAGACCTTGTATA 57.805 33.333 0.00 0.00 0.00 1.47
2248 2720 8.748380 AAAGTACGTTGTAAGACCTTGTATAC 57.252 34.615 0.00 0.00 0.00 1.47
2249 2721 7.452880 AGTACGTTGTAAGACCTTGTATACA 57.547 36.000 0.08 0.08 0.00 2.29
2250 2722 7.885297 AGTACGTTGTAAGACCTTGTATACAA 58.115 34.615 17.16 17.16 36.27 2.41
2251 2723 8.359642 AGTACGTTGTAAGACCTTGTATACAAA 58.640 33.333 18.55 0.73 39.26 2.83
2252 2724 9.143631 GTACGTTGTAAGACCTTGTATACAAAT 57.856 33.333 18.55 10.27 39.26 2.32
2253 2725 8.611654 ACGTTGTAAGACCTTGTATACAAATT 57.388 30.769 18.55 12.90 39.26 1.82
2254 2726 8.500773 ACGTTGTAAGACCTTGTATACAAATTG 58.499 33.333 18.55 12.37 39.26 2.32
2255 2727 7.480542 CGTTGTAAGACCTTGTATACAAATTGC 59.519 37.037 18.55 13.83 39.26 3.56
2256 2728 7.987750 TGTAAGACCTTGTATACAAATTGCA 57.012 32.000 18.55 15.73 35.15 4.08
2257 2729 7.812648 TGTAAGACCTTGTATACAAATTGCAC 58.187 34.615 18.55 12.37 35.15 4.57
2258 2730 5.545658 AGACCTTGTATACAAATTGCACG 57.454 39.130 18.55 5.88 35.15 5.34
2259 2731 4.394920 AGACCTTGTATACAAATTGCACGG 59.605 41.667 18.55 15.70 35.15 4.94
2260 2732 3.442273 ACCTTGTATACAAATTGCACGGG 59.558 43.478 18.55 15.06 35.15 5.28
2261 2733 3.434637 CTTGTATACAAATTGCACGGGC 58.565 45.455 18.55 0.34 36.53 6.13
2262 2734 2.717390 TGTATACAAATTGCACGGGCT 58.283 42.857 12.74 0.00 41.91 5.19
2263 2735 2.421775 TGTATACAAATTGCACGGGCTG 59.578 45.455 12.74 2.36 41.91 4.85
2264 2736 0.817013 ATACAAATTGCACGGGCTGG 59.183 50.000 12.74 0.00 41.91 4.85
2265 2737 1.872197 TACAAATTGCACGGGCTGGC 61.872 55.000 12.74 0.00 41.91 4.85
2266 2738 2.916703 AAATTGCACGGGCTGGCA 60.917 55.556 12.74 5.52 41.91 4.92
2267 2739 3.225069 AAATTGCACGGGCTGGCAC 62.225 57.895 12.74 0.00 40.23 5.01
2268 2740 4.972733 ATTGCACGGGCTGGCACA 62.973 61.111 12.74 0.00 40.23 4.57
2269 2741 4.972733 TTGCACGGGCTGGCACAT 62.973 61.111 12.74 0.00 40.23 3.21
2270 2742 4.972733 TGCACGGGCTGGCACATT 62.973 61.111 12.74 0.00 41.91 2.71
2271 2743 2.749839 GCACGGGCTGGCACATTA 60.750 61.111 0.00 0.00 38.20 1.90
2272 2744 2.339556 GCACGGGCTGGCACATTAA 61.340 57.895 0.00 0.00 38.20 1.40
2273 2745 1.872197 GCACGGGCTGGCACATTAAA 61.872 55.000 0.00 0.00 38.20 1.52
2274 2746 0.109319 CACGGGCTGGCACATTAAAC 60.109 55.000 2.88 0.00 38.20 2.01
2275 2747 1.248101 ACGGGCTGGCACATTAAACC 61.248 55.000 2.88 0.00 38.20 3.27
2276 2748 1.247419 CGGGCTGGCACATTAAACCA 61.247 55.000 2.88 0.00 38.20 3.67
2277 2749 0.246360 GGGCTGGCACATTAAACCAC 59.754 55.000 2.88 0.00 38.20 4.16
2278 2750 0.109319 GGCTGGCACATTAAACCACG 60.109 55.000 0.00 0.00 38.20 4.94
2279 2751 0.596082 GCTGGCACATTAAACCACGT 59.404 50.000 0.00 0.00 38.20 4.49
2280 2752 1.401018 GCTGGCACATTAAACCACGTC 60.401 52.381 0.00 0.00 38.20 4.34
2281 2753 1.199097 CTGGCACATTAAACCACGTCC 59.801 52.381 0.00 0.00 38.20 4.79
2282 2754 1.240256 GGCACATTAAACCACGTCCA 58.760 50.000 0.00 0.00 0.00 4.02
2283 2755 1.609555 GGCACATTAAACCACGTCCAA 59.390 47.619 0.00 0.00 0.00 3.53
2284 2756 2.230266 GGCACATTAAACCACGTCCAAT 59.770 45.455 0.00 0.00 0.00 3.16
2285 2757 3.440872 GGCACATTAAACCACGTCCAATA 59.559 43.478 0.00 0.00 0.00 1.90
2286 2758 4.097286 GGCACATTAAACCACGTCCAATAT 59.903 41.667 0.00 0.00 0.00 1.28
2287 2759 5.297278 GGCACATTAAACCACGTCCAATATA 59.703 40.000 0.00 0.00 0.00 0.86
2288 2760 6.183360 GGCACATTAAACCACGTCCAATATAA 60.183 38.462 0.00 0.00 0.00 0.98
2289 2761 6.910433 GCACATTAAACCACGTCCAATATAAG 59.090 38.462 0.00 0.00 0.00 1.73
2290 2762 6.910433 CACATTAAACCACGTCCAATATAAGC 59.090 38.462 0.00 0.00 0.00 3.09
2291 2763 6.600032 ACATTAAACCACGTCCAATATAAGCA 59.400 34.615 0.00 0.00 0.00 3.91
2292 2764 7.121463 ACATTAAACCACGTCCAATATAAGCAA 59.879 33.333 0.00 0.00 0.00 3.91
2293 2765 4.957759 AACCACGTCCAATATAAGCAAC 57.042 40.909 0.00 0.00 0.00 4.17
2294 2766 2.933906 ACCACGTCCAATATAAGCAACG 59.066 45.455 0.00 0.00 36.29 4.10
2295 2767 2.933906 CCACGTCCAATATAAGCAACGT 59.066 45.455 0.00 0.00 43.37 3.99
2296 2768 4.114073 CCACGTCCAATATAAGCAACGTA 58.886 43.478 0.00 0.00 40.94 3.57
2297 2769 4.567558 CCACGTCCAATATAAGCAACGTAA 59.432 41.667 0.00 0.00 40.94 3.18
2298 2770 5.063691 CCACGTCCAATATAAGCAACGTAAA 59.936 40.000 0.00 0.00 40.94 2.01
2299 2771 6.402334 CCACGTCCAATATAAGCAACGTAAAA 60.402 38.462 0.00 0.00 40.94 1.52
2300 2772 7.016466 CACGTCCAATATAAGCAACGTAAAAA 58.984 34.615 0.00 0.00 40.94 1.94
2301 2773 7.694784 CACGTCCAATATAAGCAACGTAAAAAT 59.305 33.333 0.00 0.00 40.94 1.82
2302 2774 8.881743 ACGTCCAATATAAGCAACGTAAAAATA 58.118 29.630 0.00 0.00 41.08 1.40
2303 2775 9.872757 CGTCCAATATAAGCAACGTAAAAATAT 57.127 29.630 0.00 0.00 0.00 1.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 7.092137 TCTCCAAAATCATGCTAAGAACATG 57.908 36.000 0.00 0.00 45.08 3.21
15 16 7.994194 AGATTCTCCAAAATCATGCTAAGAAC 58.006 34.615 0.00 0.00 37.98 3.01
34 35 3.291584 TGAGTGATAGCGTGGAGATTCT 58.708 45.455 0.00 0.00 0.00 2.40
182 190 8.070034 ACTTTTCATGCTGGATCAAATGATAA 57.930 30.769 0.00 0.00 34.37 1.75
272 280 8.484641 TTTTTGTGCAAGTCAACATTTGAATA 57.515 26.923 0.00 0.00 42.15 1.75
316 325 2.105766 AGACATACTACCACCGTTCCC 58.894 52.381 0.00 0.00 0.00 3.97
399 409 7.335171 TCTGATCCAATTATGTTGTTGAGACAG 59.665 37.037 0.00 0.00 37.04 3.51
560 597 3.055094 TCTTGAGCTTAAAGTGGGCTAGG 60.055 47.826 9.25 0.00 36.37 3.02
585 622 2.753452 CCGGCTTTACTAGTCTCACTCA 59.247 50.000 0.00 0.00 0.00 3.41
619 874 4.996788 AGATTCCACGTAACTAACCGAT 57.003 40.909 0.00 0.00 0.00 4.18
681 942 5.104982 ACTTCCAAGTTTCAAGGCAATCAAA 60.105 36.000 0.00 0.00 35.21 2.69
694 955 6.647895 CACCGTATGTACTTACTTCCAAGTTT 59.352 38.462 14.83 0.00 39.45 2.66
869 1294 2.629656 GCTGATGGTGTGTGGGTGC 61.630 63.158 0.00 0.00 0.00 5.01
870 1295 1.228215 TGCTGATGGTGTGTGGGTG 60.228 57.895 0.00 0.00 0.00 4.61
871 1296 1.073722 CTGCTGATGGTGTGTGGGT 59.926 57.895 0.00 0.00 0.00 4.51
872 1297 2.338015 GCTGCTGATGGTGTGTGGG 61.338 63.158 0.00 0.00 0.00 4.61
873 1298 0.963856 ATGCTGCTGATGGTGTGTGG 60.964 55.000 0.00 0.00 0.00 4.17
874 1299 0.450583 GATGCTGCTGATGGTGTGTG 59.549 55.000 0.00 0.00 0.00 3.82
875 1300 0.037160 TGATGCTGCTGATGGTGTGT 59.963 50.000 0.00 0.00 0.00 3.72
876 1301 0.733150 CTGATGCTGCTGATGGTGTG 59.267 55.000 0.00 0.00 0.00 3.82
877 1302 0.616891 TCTGATGCTGCTGATGGTGT 59.383 50.000 0.00 0.00 0.00 4.16
878 1303 1.968704 ATCTGATGCTGCTGATGGTG 58.031 50.000 0.00 0.00 0.00 4.17
879 1304 2.730934 AATCTGATGCTGCTGATGGT 57.269 45.000 0.00 0.00 0.00 3.55
880 1305 5.704053 TGTTATAATCTGATGCTGCTGATGG 59.296 40.000 0.00 0.00 0.00 3.51
881 1306 6.204108 TGTGTTATAATCTGATGCTGCTGATG 59.796 38.462 0.00 0.00 0.00 3.07
882 1307 6.293698 TGTGTTATAATCTGATGCTGCTGAT 58.706 36.000 0.00 0.00 0.00 2.90
883 1308 5.673514 TGTGTTATAATCTGATGCTGCTGA 58.326 37.500 0.00 0.00 0.00 4.26
884 1309 5.996669 TGTGTTATAATCTGATGCTGCTG 57.003 39.130 0.00 0.00 0.00 4.41
885 1310 5.297776 GGTTGTGTTATAATCTGATGCTGCT 59.702 40.000 0.00 0.00 0.00 4.24
886 1311 5.066375 TGGTTGTGTTATAATCTGATGCTGC 59.934 40.000 0.00 0.00 0.00 5.25
887 1312 6.682423 TGGTTGTGTTATAATCTGATGCTG 57.318 37.500 0.00 0.00 0.00 4.41
888 1313 6.095440 GGTTGGTTGTGTTATAATCTGATGCT 59.905 38.462 0.00 0.00 0.00 3.79
889 1314 6.127758 TGGTTGGTTGTGTTATAATCTGATGC 60.128 38.462 0.00 0.00 0.00 3.91
890 1315 7.389803 TGGTTGGTTGTGTTATAATCTGATG 57.610 36.000 0.00 0.00 0.00 3.07
891 1316 6.095440 GCTGGTTGGTTGTGTTATAATCTGAT 59.905 38.462 0.00 0.00 0.00 2.90
904 1329 1.829533 CCTGCTGCTGGTTGGTTGT 60.830 57.895 16.56 0.00 0.00 3.32
921 1361 1.873591 CCAGTCTTGTGTTGCACTACC 59.126 52.381 0.00 0.00 35.11 3.18
936 1386 1.482278 GTCGATCGATCTTGCCAGTC 58.518 55.000 22.50 0.00 0.00 3.51
940 1390 0.248907 TTCGGTCGATCGATCTTGCC 60.249 55.000 23.21 17.54 39.03 4.52
955 1405 3.502979 CCTTACTAGCTAGCTACCTTCGG 59.497 52.174 20.67 12.07 0.00 4.30
983 1433 3.373439 CGCCATCTTTCTTCTTCTTCCTG 59.627 47.826 0.00 0.00 0.00 3.86
1011 1461 2.892334 CTTGAACACCCACACGCCG 61.892 63.158 0.00 0.00 0.00 6.46
1317 1770 6.621613 TCGAATAGGAAGAATATCACCGATG 58.378 40.000 0.00 0.00 0.00 3.84
1318 1771 6.626181 GCTCGAATAGGAAGAATATCACCGAT 60.626 42.308 0.00 0.00 0.00 4.18
1324 1777 4.158025 TCCGGCTCGAATAGGAAGAATATC 59.842 45.833 0.00 0.00 0.00 1.63
1405 1858 2.459934 TGCATAATCGTACACGCAGAG 58.540 47.619 0.00 0.00 39.60 3.35
1406 1859 2.570442 TGCATAATCGTACACGCAGA 57.430 45.000 0.00 0.00 39.60 4.26
1500 1960 6.657541 CCCGGTACTGGCATACATATATTTTT 59.342 38.462 15.96 0.00 0.00 1.94
1515 1975 3.489355 AGTTTTTAAACCCCGGTACTGG 58.511 45.455 14.38 14.38 39.71 4.00
1516 1976 4.214758 CAGAGTTTTTAAACCCCGGTACTG 59.785 45.833 0.00 0.00 39.71 2.74
1534 1994 4.505742 GGGGTCAAGTTTCAGAATCAGAGT 60.506 45.833 0.00 0.00 0.00 3.24
1544 2004 0.181587 TTCAGCGGGGTCAAGTTTCA 59.818 50.000 0.00 0.00 0.00 2.69
1608 2072 2.354203 GGTGTGTTTTTGGTTTGCCTCA 60.354 45.455 0.00 0.00 35.27 3.86
1618 2082 5.624900 CGTGAACAGATATGGTGTGTTTTTG 59.375 40.000 0.00 0.00 43.62 2.44
1629 2093 3.575630 CCCGATACCGTGAACAGATATG 58.424 50.000 0.00 0.00 0.00 1.78
1633 2097 0.968901 AGCCCGATACCGTGAACAGA 60.969 55.000 0.00 0.00 0.00 3.41
1634 2098 0.742505 TAGCCCGATACCGTGAACAG 59.257 55.000 0.00 0.00 0.00 3.16
1659 2124 0.956633 TTTTTCTGCCTCTGCTGCTG 59.043 50.000 0.00 0.00 38.71 4.41
1662 2127 2.620115 TGTTCTTTTTCTGCCTCTGCTG 59.380 45.455 0.00 0.00 38.71 4.41
1666 2131 3.290710 TGCTTGTTCTTTTTCTGCCTCT 58.709 40.909 0.00 0.00 0.00 3.69
1668 2133 4.436332 CTTTGCTTGTTCTTTTTCTGCCT 58.564 39.130 0.00 0.00 0.00 4.75
1670 2135 3.557185 CCCTTTGCTTGTTCTTTTTCTGC 59.443 43.478 0.00 0.00 0.00 4.26
1674 2139 6.731292 ATAGACCCTTTGCTTGTTCTTTTT 57.269 33.333 0.00 0.00 0.00 1.94
1689 2154 5.091552 TCTGTTGTGGTAGAAATAGACCCT 58.908 41.667 0.00 0.00 0.00 4.34
1690 2155 5.416271 TCTGTTGTGGTAGAAATAGACCC 57.584 43.478 0.00 0.00 0.00 4.46
1697 2162 6.928348 TCCTTCTATCTGTTGTGGTAGAAA 57.072 37.500 0.00 0.00 34.01 2.52
1711 2176 9.995003 ATCTGATGATACTGTTTTCCTTCTATC 57.005 33.333 0.00 0.00 0.00 2.08
1727 2192 6.096846 TCGTTCTCTTTGTCCATCTGATGATA 59.903 38.462 18.92 4.05 0.00 2.15
1728 2193 5.105187 TCGTTCTCTTTGTCCATCTGATGAT 60.105 40.000 18.92 0.00 0.00 2.45
1729 2194 4.220602 TCGTTCTCTTTGTCCATCTGATGA 59.779 41.667 18.92 2.75 0.00 2.92
1730 2195 4.498241 TCGTTCTCTTTGTCCATCTGATG 58.502 43.478 10.71 10.71 0.00 3.07
1731 2196 4.808414 TCGTTCTCTTTGTCCATCTGAT 57.192 40.909 0.00 0.00 0.00 2.90
1748 2213 2.140717 CTAGACCTGCCGTTTTTCGTT 58.859 47.619 0.00 0.00 37.94 3.85
1752 2217 2.942641 GGCTAGACCTGCCGTTTTT 58.057 52.632 0.00 0.00 41.03 1.94
1770 2235 7.862873 TGCTCGTTGACTGATGACTTATAATAG 59.137 37.037 0.00 0.00 0.00 1.73
1776 2241 3.838120 CTGCTCGTTGACTGATGACTTA 58.162 45.455 0.00 0.00 0.00 2.24
1779 2244 0.718343 GCTGCTCGTTGACTGATGAC 59.282 55.000 0.00 0.00 0.00 3.06
1785 2250 0.322975 ATTCCAGCTGCTCGTTGACT 59.677 50.000 8.66 0.00 0.00 3.41
1787 2252 0.321346 TCATTCCAGCTGCTCGTTGA 59.679 50.000 8.66 3.68 0.00 3.18
1808 2278 1.045911 GTGGGGAGCCTACCTGAGAG 61.046 65.000 0.00 0.00 0.00 3.20
1816 2286 0.621571 AATGAGCAGTGGGGAGCCTA 60.622 55.000 0.00 0.00 0.00 3.93
1820 2290 0.393537 GGTGAATGAGCAGTGGGGAG 60.394 60.000 0.00 0.00 0.00 4.30
1844 2314 2.026729 TGGAGATAATTGGCCGTTGTCA 60.027 45.455 16.20 0.00 0.00 3.58
1845 2315 2.614057 CTGGAGATAATTGGCCGTTGTC 59.386 50.000 0.00 3.71 0.00 3.18
1849 2319 0.179018 GCCTGGAGATAATTGGCCGT 60.179 55.000 0.00 0.00 37.81 5.68
1850 2320 0.179020 TGCCTGGAGATAATTGGCCG 60.179 55.000 0.00 0.00 42.62 6.13
1852 2322 3.893813 AGAATTGCCTGGAGATAATTGGC 59.106 43.478 0.00 0.00 43.49 4.52
1853 2323 5.135383 TGAGAATTGCCTGGAGATAATTGG 58.865 41.667 0.00 0.00 0.00 3.16
1854 2324 5.278364 GCTGAGAATTGCCTGGAGATAATTG 60.278 44.000 0.00 0.00 0.00 2.32
1855 2325 4.826183 GCTGAGAATTGCCTGGAGATAATT 59.174 41.667 0.00 0.00 0.00 1.40
1860 2330 0.986527 TGCTGAGAATTGCCTGGAGA 59.013 50.000 0.00 0.00 0.00 3.71
1866 2336 1.015868 GAGAGCTGCTGAGAATTGCC 58.984 55.000 7.01 0.00 0.00 4.52
1867 2337 1.015868 GGAGAGCTGCTGAGAATTGC 58.984 55.000 7.01 0.00 0.00 3.56
1895 2365 1.698532 AGGGATTGCTGCTCCTAGATG 59.301 52.381 7.73 0.00 33.05 2.90
1903 2373 0.851469 ATGATGGAGGGATTGCTGCT 59.149 50.000 0.00 0.00 0.00 4.24
1911 2381 2.237143 GTCAGTGTTGATGATGGAGGGA 59.763 50.000 0.00 0.00 35.39 4.20
1913 2383 3.268330 CAGTCAGTGTTGATGATGGAGG 58.732 50.000 0.00 0.00 35.39 4.30
1921 2391 2.355108 CCGATTCCCAGTCAGTGTTGAT 60.355 50.000 0.00 0.00 35.39 2.57
1940 2410 1.731709 TCAATGAGAACATGTTCGCCG 59.268 47.619 31.19 21.94 43.97 6.46
1945 2415 8.797350 TGATACTTCATCAATGAGAACATGTT 57.203 30.769 11.78 11.78 40.80 2.71
1966 2438 5.663106 ACTCATGGGAAGAGTAAGCTTGATA 59.337 40.000 9.86 0.00 44.10 2.15
1971 2443 2.093235 GCACTCATGGGAAGAGTAAGCT 60.093 50.000 0.00 0.00 44.11 3.74
1989 2461 0.672401 TTCGAAAGATGTCGGGGCAC 60.672 55.000 0.00 0.00 41.43 5.01
1995 2467 3.120649 GGTCTTGGTTTCGAAAGATGTCG 60.121 47.826 11.66 0.00 41.60 4.35
2015 2487 3.303263 CGTAACGATGTTTGTTTTCCGGT 60.303 43.478 0.00 0.00 0.00 5.28
2025 2497 2.809119 TGGACAATGCGTAACGATGTTT 59.191 40.909 0.00 0.00 0.00 2.83
2054 2526 0.240945 GCTTGCATTGCTACCGTGTT 59.759 50.000 10.49 0.00 0.00 3.32
2058 2530 1.308047 TATGGCTTGCATTGCTACCG 58.692 50.000 10.49 0.00 0.00 4.02
2131 2603 1.347320 GGTCTACCGAAGCAAGAACG 58.653 55.000 0.00 0.00 0.00 3.95
2132 2604 1.675116 GGGGTCTACCGAAGCAAGAAC 60.675 57.143 0.00 0.00 41.60 3.01
2133 2605 0.611714 GGGGTCTACCGAAGCAAGAA 59.388 55.000 0.00 0.00 41.60 2.52
2134 2606 1.262640 GGGGGTCTACCGAAGCAAGA 61.263 60.000 0.00 0.00 41.60 3.02
2135 2607 1.221021 GGGGGTCTACCGAAGCAAG 59.779 63.158 0.00 0.00 41.60 4.01
2136 2608 3.395630 GGGGGTCTACCGAAGCAA 58.604 61.111 0.00 0.00 41.60 3.91
2151 2623 1.365699 CGTCGATGTGTTTAAGGGGG 58.634 55.000 0.00 0.00 0.00 5.40
2152 2624 1.365699 CCGTCGATGTGTTTAAGGGG 58.634 55.000 3.52 0.00 0.00 4.79
2153 2625 0.725117 GCCGTCGATGTGTTTAAGGG 59.275 55.000 3.52 0.00 0.00 3.95
2154 2626 1.659098 GAGCCGTCGATGTGTTTAAGG 59.341 52.381 3.52 0.00 0.00 2.69
2155 2627 2.333926 TGAGCCGTCGATGTGTTTAAG 58.666 47.619 3.52 0.00 0.00 1.85
2156 2628 2.029739 TCTGAGCCGTCGATGTGTTTAA 60.030 45.455 3.52 0.00 0.00 1.52
2157 2629 1.542472 TCTGAGCCGTCGATGTGTTTA 59.458 47.619 3.52 0.00 0.00 2.01
2158 2630 0.317160 TCTGAGCCGTCGATGTGTTT 59.683 50.000 3.52 0.00 0.00 2.83
2159 2631 0.532573 ATCTGAGCCGTCGATGTGTT 59.467 50.000 3.52 0.00 0.00 3.32
2160 2632 0.532573 AATCTGAGCCGTCGATGTGT 59.467 50.000 3.52 0.00 0.00 3.72
2161 2633 2.492019 TAATCTGAGCCGTCGATGTG 57.508 50.000 3.52 0.00 0.00 3.21
2162 2634 2.029828 GGATAATCTGAGCCGTCGATGT 60.030 50.000 3.52 0.00 0.00 3.06
2163 2635 2.600731 GGATAATCTGAGCCGTCGATG 58.399 52.381 0.00 0.00 0.00 3.84
2164 2636 1.546476 GGGATAATCTGAGCCGTCGAT 59.454 52.381 0.00 0.00 0.00 3.59
2165 2637 0.959553 GGGATAATCTGAGCCGTCGA 59.040 55.000 0.00 0.00 0.00 4.20
2166 2638 0.673985 TGGGATAATCTGAGCCGTCG 59.326 55.000 0.00 0.00 0.00 5.12
2167 2639 3.368531 GGTATGGGATAATCTGAGCCGTC 60.369 52.174 0.00 0.00 0.00 4.79
2168 2640 2.567615 GGTATGGGATAATCTGAGCCGT 59.432 50.000 0.00 0.00 0.00 5.68
2169 2641 2.834549 AGGTATGGGATAATCTGAGCCG 59.165 50.000 0.00 0.00 0.00 5.52
2170 2642 4.100373 AGAGGTATGGGATAATCTGAGCC 58.900 47.826 0.00 0.00 0.00 4.70
2171 2643 5.247110 TGAAGAGGTATGGGATAATCTGAGC 59.753 44.000 0.00 0.00 0.00 4.26
2172 2644 6.924913 TGAAGAGGTATGGGATAATCTGAG 57.075 41.667 0.00 0.00 0.00 3.35
2173 2645 8.972662 TTATGAAGAGGTATGGGATAATCTGA 57.027 34.615 0.00 0.00 0.00 3.27
2179 2651 9.852784 TCCTTAATTATGAAGAGGTATGGGATA 57.147 33.333 0.04 0.00 0.00 2.59
2180 2652 8.757307 TCCTTAATTATGAAGAGGTATGGGAT 57.243 34.615 0.04 0.00 0.00 3.85
2181 2653 8.757307 ATCCTTAATTATGAAGAGGTATGGGA 57.243 34.615 0.04 0.00 0.00 4.37
2203 2675 9.841880 GTACTTTTGAAAAGGACAATCTTATCC 57.158 33.333 24.23 0.00 31.42 2.59
2204 2676 9.543018 CGTACTTTTGAAAAGGACAATCTTATC 57.457 33.333 27.19 3.19 30.46 1.75
2205 2677 9.063615 ACGTACTTTTGAAAAGGACAATCTTAT 57.936 29.630 27.19 4.93 30.46 1.73
2206 2678 8.441312 ACGTACTTTTGAAAAGGACAATCTTA 57.559 30.769 27.19 5.32 30.46 2.10
2207 2679 7.329588 ACGTACTTTTGAAAAGGACAATCTT 57.670 32.000 27.19 7.73 30.46 2.40
2208 2680 6.937436 ACGTACTTTTGAAAAGGACAATCT 57.063 33.333 27.19 8.30 30.46 2.40
2209 2681 6.970613 ACAACGTACTTTTGAAAAGGACAATC 59.029 34.615 27.19 6.09 30.46 2.67
2210 2682 6.859017 ACAACGTACTTTTGAAAAGGACAAT 58.141 32.000 27.19 15.14 30.46 2.71
2211 2683 6.256912 ACAACGTACTTTTGAAAAGGACAA 57.743 33.333 27.19 6.93 30.46 3.18
2212 2684 5.883503 ACAACGTACTTTTGAAAAGGACA 57.116 34.783 27.19 8.82 30.46 4.02
2213 2685 7.637519 GTCTTACAACGTACTTTTGAAAAGGAC 59.362 37.037 20.42 20.42 0.00 3.85
2214 2686 7.201635 GGTCTTACAACGTACTTTTGAAAAGGA 60.202 37.037 20.48 10.59 0.00 3.36
2215 2687 6.908820 GGTCTTACAACGTACTTTTGAAAAGG 59.091 38.462 20.48 6.72 0.00 3.11
2216 2688 7.691158 AGGTCTTACAACGTACTTTTGAAAAG 58.309 34.615 15.59 15.59 0.00 2.27
2217 2689 7.614124 AGGTCTTACAACGTACTTTTGAAAA 57.386 32.000 10.22 0.00 0.00 2.29
2218 2690 7.119553 ACAAGGTCTTACAACGTACTTTTGAAA 59.880 33.333 10.22 0.00 0.00 2.69
2219 2691 6.594937 ACAAGGTCTTACAACGTACTTTTGAA 59.405 34.615 10.22 1.93 0.00 2.69
2220 2692 6.108015 ACAAGGTCTTACAACGTACTTTTGA 58.892 36.000 10.22 0.00 0.00 2.69
2221 2693 6.354039 ACAAGGTCTTACAACGTACTTTTG 57.646 37.500 0.00 3.24 0.00 2.44
2222 2694 9.196552 GTATACAAGGTCTTACAACGTACTTTT 57.803 33.333 0.00 0.00 0.00 2.27
2223 2695 8.359642 TGTATACAAGGTCTTACAACGTACTTT 58.640 33.333 2.20 0.00 0.00 2.66
2224 2696 7.885297 TGTATACAAGGTCTTACAACGTACTT 58.115 34.615 2.20 0.00 0.00 2.24
2225 2697 7.452880 TGTATACAAGGTCTTACAACGTACT 57.547 36.000 2.20 0.00 0.00 2.73
2226 2698 8.519492 TTTGTATACAAGGTCTTACAACGTAC 57.481 34.615 17.36 0.00 35.06 3.67
2227 2699 9.709495 AATTTGTATACAAGGTCTTACAACGTA 57.291 29.630 17.36 0.00 35.06 3.57
2228 2700 8.500773 CAATTTGTATACAAGGTCTTACAACGT 58.499 33.333 17.36 0.00 35.06 3.99
2229 2701 7.480542 GCAATTTGTATACAAGGTCTTACAACG 59.519 37.037 17.36 0.00 35.06 4.10
2230 2702 8.293867 TGCAATTTGTATACAAGGTCTTACAAC 58.706 33.333 17.36 3.00 35.06 3.32
2231 2703 8.293867 GTGCAATTTGTATACAAGGTCTTACAA 58.706 33.333 17.36 1.24 37.15 2.41
2232 2704 7.360522 CGTGCAATTTGTATACAAGGTCTTACA 60.361 37.037 17.36 8.93 37.15 2.41
2233 2705 6.959311 CGTGCAATTTGTATACAAGGTCTTAC 59.041 38.462 17.36 12.47 37.15 2.34
2234 2706 6.092944 CCGTGCAATTTGTATACAAGGTCTTA 59.907 38.462 17.36 3.35 37.15 2.10
2235 2707 5.106317 CCGTGCAATTTGTATACAAGGTCTT 60.106 40.000 17.36 8.25 37.15 3.01
2236 2708 4.394920 CCGTGCAATTTGTATACAAGGTCT 59.605 41.667 17.36 2.95 37.15 3.85
2237 2709 4.438200 CCCGTGCAATTTGTATACAAGGTC 60.438 45.833 17.36 9.50 37.15 3.85
2238 2710 3.442273 CCCGTGCAATTTGTATACAAGGT 59.558 43.478 17.36 8.73 37.15 3.50
2239 2711 3.733684 GCCCGTGCAATTTGTATACAAGG 60.734 47.826 17.36 13.49 35.78 3.61
2240 2712 3.128589 AGCCCGTGCAATTTGTATACAAG 59.871 43.478 17.36 8.43 41.13 3.16
2241 2713 3.085533 AGCCCGTGCAATTTGTATACAA 58.914 40.909 14.35 14.35 41.13 2.41
2242 2714 2.421775 CAGCCCGTGCAATTTGTATACA 59.578 45.455 0.08 0.08 41.13 2.29
2243 2715 2.223479 CCAGCCCGTGCAATTTGTATAC 60.223 50.000 0.00 0.00 41.13 1.47
2244 2716 2.020720 CCAGCCCGTGCAATTTGTATA 58.979 47.619 0.00 0.00 41.13 1.47
2245 2717 0.817013 CCAGCCCGTGCAATTTGTAT 59.183 50.000 0.00 0.00 41.13 2.29
2246 2718 1.872197 GCCAGCCCGTGCAATTTGTA 61.872 55.000 0.00 0.00 41.13 2.41
2247 2719 3.050339 CCAGCCCGTGCAATTTGT 58.950 55.556 0.00 0.00 41.13 2.83
2248 2720 2.432972 GCCAGCCCGTGCAATTTG 60.433 61.111 0.00 0.00 41.13 2.32
2249 2721 2.916703 TGCCAGCCCGTGCAATTT 60.917 55.556 0.00 0.00 41.13 1.82
2250 2722 3.683937 GTGCCAGCCCGTGCAATT 61.684 61.111 0.00 0.00 39.57 2.32
2251 2723 4.972733 TGTGCCAGCCCGTGCAAT 62.973 61.111 0.00 0.00 39.57 3.56
2252 2724 4.972733 ATGTGCCAGCCCGTGCAA 62.973 61.111 0.00 0.00 39.57 4.08
2253 2725 3.559511 TAATGTGCCAGCCCGTGCA 62.560 57.895 0.00 0.00 41.13 4.57
2254 2726 1.872197 TTTAATGTGCCAGCCCGTGC 61.872 55.000 0.00 0.00 37.95 5.34
2255 2727 0.109319 GTTTAATGTGCCAGCCCGTG 60.109 55.000 0.00 0.00 0.00 4.94
2256 2728 1.248101 GGTTTAATGTGCCAGCCCGT 61.248 55.000 0.00 0.00 0.00 5.28
2257 2729 1.247419 TGGTTTAATGTGCCAGCCCG 61.247 55.000 0.00 0.00 0.00 6.13
2258 2730 0.246360 GTGGTTTAATGTGCCAGCCC 59.754 55.000 0.00 0.00 32.31 5.19
2259 2731 0.109319 CGTGGTTTAATGTGCCAGCC 60.109 55.000 0.00 0.00 32.31 4.85
2260 2732 0.596082 ACGTGGTTTAATGTGCCAGC 59.404 50.000 0.00 0.00 32.31 4.85
2261 2733 1.199097 GGACGTGGTTTAATGTGCCAG 59.801 52.381 0.00 0.00 32.31 4.85
2262 2734 1.240256 GGACGTGGTTTAATGTGCCA 58.760 50.000 0.00 0.00 0.00 4.92
2263 2735 1.240256 TGGACGTGGTTTAATGTGCC 58.760 50.000 0.00 0.00 0.00 5.01
2264 2736 3.569250 ATTGGACGTGGTTTAATGTGC 57.431 42.857 0.00 0.00 0.00 4.57
2265 2737 6.910433 GCTTATATTGGACGTGGTTTAATGTG 59.090 38.462 0.00 0.00 0.00 3.21
2266 2738 6.600032 TGCTTATATTGGACGTGGTTTAATGT 59.400 34.615 0.00 0.00 0.00 2.71
2267 2739 7.022055 TGCTTATATTGGACGTGGTTTAATG 57.978 36.000 0.00 0.00 0.00 1.90
2268 2740 7.477494 GTTGCTTATATTGGACGTGGTTTAAT 58.523 34.615 0.00 0.00 0.00 1.40
2269 2741 6.402334 CGTTGCTTATATTGGACGTGGTTTAA 60.402 38.462 0.00 0.00 0.00 1.52
2270 2742 5.063691 CGTTGCTTATATTGGACGTGGTTTA 59.936 40.000 0.00 0.00 0.00 2.01
2271 2743 4.142773 CGTTGCTTATATTGGACGTGGTTT 60.143 41.667 0.00 0.00 0.00 3.27
2272 2744 3.372822 CGTTGCTTATATTGGACGTGGTT 59.627 43.478 0.00 0.00 0.00 3.67
2273 2745 2.933906 CGTTGCTTATATTGGACGTGGT 59.066 45.455 0.00 0.00 0.00 4.16
2274 2746 2.933906 ACGTTGCTTATATTGGACGTGG 59.066 45.455 0.00 0.00 41.49 4.94
2275 2747 5.705813 TTACGTTGCTTATATTGGACGTG 57.294 39.130 9.29 0.00 42.74 4.49
2276 2748 6.724694 TTTTACGTTGCTTATATTGGACGT 57.275 33.333 0.00 4.73 44.60 4.34
2277 2749 9.872757 ATATTTTTACGTTGCTTATATTGGACG 57.127 29.630 0.00 0.00 36.65 4.79


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

AutoCloner maintained by Alex Coulton.