Multiple sequence alignment - TraesCS4A01G407300

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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 TraesCS4A01G407300 chr4A 100.000 2764 0 0 1 2764 680048199 680045436 0.000000e+00 5105
1 TraesCS4A01G407300 chr4D 87.613 2333 124 75 21 2271 473163731 473161482 0.000000e+00 2555
2 TraesCS4A01G407300 chr4D 87.445 454 23 16 2329 2764 473161465 473161028 2.470000e-135 492
3 TraesCS4A01G407300 chr4B 87.500 2344 128 73 21 2295 595709920 595707673 0.000000e+00 2553
4 TraesCS4A01G407300 chr4B 86.230 443 33 14 2329 2764 595707673 595707252 3.240000e-124 455


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 TraesCS4A01G407300 chr4A 680045436 680048199 2763 True 5105.0 5105 100.000 1 2764 1 chr4A.!!$R1 2763
1 TraesCS4A01G407300 chr4D 473161028 473163731 2703 True 1523.5 2555 87.529 21 2764 2 chr4D.!!$R1 2743
2 TraesCS4A01G407300 chr4B 595707252 595709920 2668 True 1504.0 2553 86.865 21 2764 2 chr4B.!!$R1 2743

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
370 388 0.025513 CGAGCTTAACAGTGATGCGC 59.974 55.0 0.0 0.0 0.0 6.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2058 2168 0.250338 GGATTAGCCCCACGATCACC 60.25 60.0 0.0 0.0 0.0 4.02 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 1.749063 TCTACACGTACTCCATGCCAG 59.251 52.381 0.00 0.00 0.00 4.85
73 74 4.946157 CCAGCATGATTAATCCCTATCCAC 59.054 45.833 12.90 0.00 39.69 4.02
80 81 0.393077 AATCCCTATCCACTTCGCGG 59.607 55.000 6.13 0.00 0.00 6.46
81 82 1.472662 ATCCCTATCCACTTCGCGGG 61.473 60.000 6.13 0.00 0.00 6.13
94 95 2.760159 CGCGGGAATGAATGCGGTT 61.760 57.895 0.00 0.00 46.31 4.44
244 245 2.719979 CAGCGGGCTGAATGCATC 59.280 61.111 15.38 0.00 46.30 3.91
245 246 2.116533 CAGCGGGCTGAATGCATCA 61.117 57.895 15.38 0.00 46.30 3.07
246 247 1.152819 AGCGGGCTGAATGCATCAT 60.153 52.632 0.00 0.00 45.15 2.45
247 248 1.007734 GCGGGCTGAATGCATCATG 60.008 57.895 0.00 0.00 45.15 3.07
319 323 0.444651 TTTTTAATCCGGACAGCGCG 59.555 50.000 6.12 0.00 0.00 6.86
321 325 4.884257 TAATCCGGACAGCGCGCC 62.884 66.667 30.33 13.04 0.00 6.53
362 380 1.293924 CCTGATGGCGAGCTTAACAG 58.706 55.000 0.00 0.00 0.00 3.16
363 381 1.406069 CCTGATGGCGAGCTTAACAGT 60.406 52.381 0.00 0.00 0.00 3.55
368 386 0.375106 GGCGAGCTTAACAGTGATGC 59.625 55.000 0.00 0.00 0.00 3.91
370 388 0.025513 CGAGCTTAACAGTGATGCGC 59.974 55.000 0.00 0.00 0.00 6.09
424 444 2.279120 GTGATGCCCGAGAGCGAG 60.279 66.667 0.00 0.00 40.82 5.03
431 451 3.640992 CCGAGAGCGAGCGATCGA 61.641 66.667 29.29 0.00 40.82 3.59
444 468 3.465296 GATCGATCGACCCGCGTGT 62.465 63.158 22.06 0.00 41.80 4.49
461 485 2.869801 CGTGTATACGGATGGTTGCATT 59.130 45.455 3.80 0.00 46.23 3.56
462 486 3.303066 CGTGTATACGGATGGTTGCATTG 60.303 47.826 3.80 0.00 46.23 2.82
463 487 2.616376 TGTATACGGATGGTTGCATTGC 59.384 45.455 0.46 0.46 0.00 3.56
464 488 1.761449 ATACGGATGGTTGCATTGCA 58.239 45.000 7.38 7.38 36.47 4.08
465 489 0.808125 TACGGATGGTTGCATTGCAC 59.192 50.000 11.66 6.75 38.71 4.57
466 490 0.895100 ACGGATGGTTGCATTGCACT 60.895 50.000 11.66 0.00 38.71 4.40
467 491 0.457166 CGGATGGTTGCATTGCACTG 60.457 55.000 11.66 0.00 38.71 3.66
468 492 0.738412 GGATGGTTGCATTGCACTGC 60.738 55.000 21.14 21.14 38.71 4.40
583 615 1.212195 GTTAAAGGGGGCAGGGTAGAG 59.788 57.143 0.00 0.00 0.00 2.43
598 630 2.605823 GGTAGAGATCAATCGAGTGCGG 60.606 54.545 8.24 0.00 38.28 5.69
601 633 1.000283 GAGATCAATCGAGTGCGGGAT 60.000 52.381 8.24 0.00 38.28 3.85
604 636 2.438868 TCAATCGAGTGCGGGATATG 57.561 50.000 8.24 0.00 38.28 1.78
605 637 1.000843 TCAATCGAGTGCGGGATATGG 59.999 52.381 8.24 0.00 38.28 2.74
606 638 1.000843 CAATCGAGTGCGGGATATGGA 59.999 52.381 0.00 0.00 38.28 3.41
607 639 1.561643 ATCGAGTGCGGGATATGGAT 58.438 50.000 0.00 0.00 38.28 3.41
608 640 0.603065 TCGAGTGCGGGATATGGATG 59.397 55.000 0.00 0.00 38.28 3.51
610 642 1.403382 CGAGTGCGGGATATGGATGAG 60.403 57.143 0.00 0.00 0.00 2.90
611 643 0.322975 AGTGCGGGATATGGATGAGC 59.677 55.000 0.00 0.00 0.00 4.26
612 644 0.322975 GTGCGGGATATGGATGAGCT 59.677 55.000 0.00 0.00 0.00 4.09
613 645 0.322648 TGCGGGATATGGATGAGCTG 59.677 55.000 0.00 0.00 0.00 4.24
614 646 1.023513 GCGGGATATGGATGAGCTGC 61.024 60.000 0.00 0.00 0.00 5.25
615 647 0.738762 CGGGATATGGATGAGCTGCG 60.739 60.000 0.00 0.00 0.00 5.18
616 648 0.610174 GGGATATGGATGAGCTGCGA 59.390 55.000 0.00 0.00 0.00 5.10
617 649 1.674221 GGGATATGGATGAGCTGCGAC 60.674 57.143 0.00 0.00 0.00 5.19
618 650 1.274728 GGATATGGATGAGCTGCGACT 59.725 52.381 0.00 0.00 0.00 4.18
619 651 2.335752 GATATGGATGAGCTGCGACTG 58.664 52.381 0.00 0.00 0.00 3.51
620 652 1.402787 TATGGATGAGCTGCGACTGA 58.597 50.000 0.00 0.00 0.00 3.41
621 653 0.104487 ATGGATGAGCTGCGACTGAG 59.896 55.000 0.00 0.00 0.00 3.35
643 683 3.054503 GCTGAGCACTGCACTGGG 61.055 66.667 0.00 0.00 40.01 4.45
864 904 2.423446 GCTCGCCCAGGTGGATAG 59.577 66.667 0.00 0.00 37.39 2.08
872 912 4.079154 TCGCCCAGGTGGATAGATAGATAT 60.079 45.833 0.00 0.00 37.39 1.63
875 915 5.069781 GCCCAGGTGGATAGATAGATATGTC 59.930 48.000 0.00 0.00 37.39 3.06
902 942 5.087323 AGATATAGCTTTGGAAGGATCGGA 58.913 41.667 0.00 0.00 0.00 4.55
903 943 5.723887 AGATATAGCTTTGGAAGGATCGGAT 59.276 40.000 0.00 0.00 0.00 4.18
904 944 2.629336 AGCTTTGGAAGGATCGGATC 57.371 50.000 9.54 9.54 0.00 3.36
905 945 1.202580 AGCTTTGGAAGGATCGGATCG 60.203 52.381 11.62 0.00 0.00 3.69
906 946 1.221414 CTTTGGAAGGATCGGATCGC 58.779 55.000 11.62 5.33 0.00 4.58
912 952 2.125912 GGATCGGATCGCATCGGG 60.126 66.667 11.62 0.00 0.00 5.14
1062 1108 4.101448 CCCCCGTGCCTCTCCTTG 62.101 72.222 0.00 0.00 0.00 3.61
1139 1188 2.041405 GGTGGAGGAGGAGGAGGG 60.041 72.222 0.00 0.00 0.00 4.30
1140 1189 2.041405 GTGGAGGAGGAGGAGGGG 60.041 72.222 0.00 0.00 0.00 4.79
1141 1190 3.368501 TGGAGGAGGAGGAGGGGG 61.369 72.222 0.00 0.00 0.00 5.40
1142 1191 3.036959 GGAGGAGGAGGAGGGGGA 61.037 72.222 0.00 0.00 0.00 4.81
1143 1192 2.612251 GAGGAGGAGGAGGGGGAG 59.388 72.222 0.00 0.00 0.00 4.30
1144 1193 3.039526 AGGAGGAGGAGGGGGAGG 61.040 72.222 0.00 0.00 0.00 4.30
1251 1307 0.683504 CCACTCCTACCTACTGCGGT 60.684 60.000 2.42 2.42 41.10 5.68
1291 1347 0.613572 TCCGTCCCTGCATGTCTACA 60.614 55.000 0.00 0.00 0.00 2.74
1319 1376 3.129852 TGTTTGTGCTTGTTTCTGACG 57.870 42.857 0.00 0.00 0.00 4.35
1325 1382 1.772063 GCTTGTTTCTGACGGCGTGT 61.772 55.000 21.19 0.00 0.00 4.49
1326 1383 1.493772 CTTGTTTCTGACGGCGTGTA 58.506 50.000 21.19 5.15 0.00 2.90
1329 1386 0.719465 GTTTCTGACGGCGTGTATGG 59.281 55.000 21.19 2.42 0.00 2.74
1330 1387 0.319083 TTTCTGACGGCGTGTATGGT 59.681 50.000 21.19 0.00 0.00 3.55
1331 1388 1.175654 TTCTGACGGCGTGTATGGTA 58.824 50.000 21.19 0.00 0.00 3.25
1332 1389 1.175654 TCTGACGGCGTGTATGGTAA 58.824 50.000 21.19 0.00 0.00 2.85
1333 1390 1.135315 TCTGACGGCGTGTATGGTAAC 60.135 52.381 21.19 0.00 0.00 2.50
1334 1391 0.456482 TGACGGCGTGTATGGTAACG 60.456 55.000 21.19 0.00 42.61 3.18
1335 1392 0.456653 GACGGCGTGTATGGTAACGT 60.457 55.000 21.19 0.00 41.76 3.99
1336 1393 0.733566 ACGGCGTGTATGGTAACGTG 60.734 55.000 13.76 0.00 41.76 4.49
1337 1394 0.733566 CGGCGTGTATGGTAACGTGT 60.734 55.000 0.00 0.00 41.76 4.49
1338 1395 0.717224 GGCGTGTATGGTAACGTGTG 59.283 55.000 0.00 0.00 41.76 3.82
1339 1396 0.094046 GCGTGTATGGTAACGTGTGC 59.906 55.000 0.00 0.00 41.76 4.57
1340 1397 1.705256 CGTGTATGGTAACGTGTGCT 58.295 50.000 0.00 0.00 42.51 4.40
1341 1398 2.063266 CGTGTATGGTAACGTGTGCTT 58.937 47.619 0.00 0.00 42.51 3.91
1544 1601 2.510238 CAGAAGAAGGCCGAGGCG 60.510 66.667 8.14 0.00 43.06 5.52
1584 1641 0.961753 CGATCATCACGGGGATCAGA 59.038 55.000 5.02 0.00 39.88 3.27
1767 1842 0.743701 CTGCTGCAGGGACTAAGCTG 60.744 60.000 21.71 0.00 44.60 4.24
1819 1899 4.237724 CAAGCTAGCATTCGAATATCCGA 58.762 43.478 18.83 0.00 36.70 4.55
1820 1900 3.839293 AGCTAGCATTCGAATATCCGAC 58.161 45.455 18.83 0.00 38.39 4.79
1821 1901 2.924290 GCTAGCATTCGAATATCCGACC 59.076 50.000 10.97 0.00 38.39 4.79
1822 1902 2.065993 AGCATTCGAATATCCGACCG 57.934 50.000 10.97 0.00 38.39 4.79
1847 1927 2.870372 GTCGCATGGTGCACCTTC 59.130 61.111 34.75 21.74 45.36 3.46
1858 1940 1.804151 GTGCACCTTCGATAAGTGCAA 59.196 47.619 28.35 16.05 44.12 4.08
1859 1941 1.804151 TGCACCTTCGATAAGTGCAAC 59.196 47.619 26.02 7.01 41.97 4.17
1866 1948 0.999406 CGATAAGTGCAACACGAGGG 59.001 55.000 0.00 0.00 41.43 4.30
1868 1950 0.676782 ATAAGTGCAACACGAGGGCC 60.677 55.000 0.00 0.00 41.43 5.80
1869 1951 2.741486 TAAGTGCAACACGAGGGCCC 62.741 60.000 16.46 16.46 41.43 5.80
1871 1953 4.329545 TGCAACACGAGGGCCCTC 62.330 66.667 38.24 38.24 39.55 4.30
1884 1966 2.281761 CCCTCACAGTGCACCACC 60.282 66.667 14.63 0.00 34.49 4.61
1889 1971 0.833949 TCACAGTGCACCACCAGTAA 59.166 50.000 14.63 0.00 34.49 2.24
1890 1972 1.419762 TCACAGTGCACCACCAGTAAT 59.580 47.619 14.63 0.00 34.49 1.89
1891 1973 1.536766 CACAGTGCACCACCAGTAATG 59.463 52.381 14.63 4.19 34.49 1.90
1892 1974 0.523072 CAGTGCACCACCAGTAATGC 59.477 55.000 14.63 0.00 38.59 3.56
1893 1975 0.110295 AGTGCACCACCAGTAATGCA 59.890 50.000 14.63 4.49 45.45 3.96
1894 1976 3.668147 TGCACCACCAGTAATGCAT 57.332 47.368 0.00 0.00 42.92 3.96
1895 1977 1.175654 TGCACCACCAGTAATGCATG 58.824 50.000 0.00 0.00 42.92 4.06
1896 1978 1.176527 GCACCACCAGTAATGCATGT 58.823 50.000 0.00 0.00 38.00 3.21
1897 1979 1.545582 GCACCACCAGTAATGCATGTT 59.454 47.619 0.00 0.00 38.00 2.71
1898 1980 2.671914 GCACCACCAGTAATGCATGTTG 60.672 50.000 0.00 0.00 38.00 3.33
1899 1981 2.557924 CACCACCAGTAATGCATGTTGT 59.442 45.455 0.00 0.00 0.00 3.32
1900 1982 3.755905 CACCACCAGTAATGCATGTTGTA 59.244 43.478 0.00 0.00 0.00 2.41
1901 1983 3.756434 ACCACCAGTAATGCATGTTGTAC 59.244 43.478 0.00 0.00 0.00 2.90
1902 1984 4.009675 CCACCAGTAATGCATGTTGTACT 58.990 43.478 0.00 0.87 0.00 2.73
1903 1985 5.182487 CCACCAGTAATGCATGTTGTACTA 58.818 41.667 0.00 0.00 0.00 1.82
1904 1986 5.645929 CCACCAGTAATGCATGTTGTACTAA 59.354 40.000 0.00 0.00 0.00 2.24
1905 1987 6.318648 CCACCAGTAATGCATGTTGTACTAAT 59.681 38.462 0.00 0.00 0.00 1.73
1906 1988 7.188834 CACCAGTAATGCATGTTGTACTAATG 58.811 38.462 0.00 2.72 0.00 1.90
1907 1989 6.183360 ACCAGTAATGCATGTTGTACTAATGC 60.183 38.462 16.31 16.31 45.51 3.56
1940 2022 0.465705 CGTGACCATCCATGTAGCCT 59.534 55.000 0.00 0.00 0.00 4.58
1941 2023 1.539065 CGTGACCATCCATGTAGCCTC 60.539 57.143 0.00 0.00 0.00 4.70
1942 2024 0.752658 TGACCATCCATGTAGCCTCG 59.247 55.000 0.00 0.00 0.00 4.63
1943 2025 0.034059 GACCATCCATGTAGCCTCGG 59.966 60.000 0.00 0.00 0.00 4.63
1961 2045 4.759096 GCGGGCGTGTACGTACGT 62.759 66.667 25.98 25.98 45.36 3.57
1962 2046 2.781957 CGGGCGTGTACGTACGTA 59.218 61.111 23.60 23.60 45.36 3.57
1977 2061 2.232756 ACGTACATGTGTGTGCAAGA 57.767 45.000 9.11 0.00 40.50 3.02
2034 2118 3.961182 CGTGTACGTGCTACTCCATTAT 58.039 45.455 4.97 0.00 34.11 1.28
2036 2120 5.696822 CGTGTACGTGCTACTCCATTATAT 58.303 41.667 4.97 0.00 34.11 0.86
2038 2122 6.444633 GTGTACGTGCTACTCCATTATATGT 58.555 40.000 4.97 0.00 0.00 2.29
2039 2123 7.571798 CGTGTACGTGCTACTCCATTATATGTA 60.572 40.741 4.97 0.00 34.11 2.29
2048 2132 4.840680 ACTCCATTATATGTAGCCTGAGCA 59.159 41.667 0.00 0.00 43.56 4.26
2052 2136 5.410746 CCATTATATGTAGCCTGAGCAGTTG 59.589 44.000 0.00 0.00 43.56 3.16
2053 2137 2.315925 TATGTAGCCTGAGCAGTTGC 57.684 50.000 0.00 0.00 43.56 4.17
2054 2138 0.325933 ATGTAGCCTGAGCAGTTGCA 59.674 50.000 6.90 0.00 45.16 4.08
2055 2139 0.325933 TGTAGCCTGAGCAGTTGCAT 59.674 50.000 6.90 0.00 45.16 3.96
2065 2175 1.061411 CAGTTGCATGCGGTGATCG 59.939 57.895 14.09 0.00 42.76 3.69
2077 2187 0.250338 GGTGATCGTGGGGCTAATCC 60.250 60.000 0.00 0.00 0.00 3.01
2079 2189 0.758734 TGATCGTGGGGCTAATCCAG 59.241 55.000 0.00 0.00 34.56 3.86
2096 2206 3.503363 GCTGATGAGCGGTGGTGC 61.503 66.667 0.00 0.00 34.87 5.01
2106 2216 1.718757 GCGGTGGTGCTCCATGAATC 61.719 60.000 11.31 0.00 46.20 2.52
2116 2226 3.004002 TGCTCCATGAATCGAATGAATGC 59.996 43.478 0.00 0.00 0.00 3.56
2118 2228 4.321008 GCTCCATGAATCGAATGAATGCAT 60.321 41.667 0.00 0.00 35.92 3.96
2119 2229 5.116069 TCCATGAATCGAATGAATGCATG 57.884 39.130 0.00 0.00 34.26 4.06
2120 2230 3.673338 CCATGAATCGAATGAATGCATGC 59.327 43.478 11.82 11.82 34.26 4.06
2121 2231 4.295051 CATGAATCGAATGAATGCATGCA 58.705 39.130 25.04 25.04 34.26 3.96
2122 2232 4.577834 TGAATCGAATGAATGCATGCAT 57.422 36.364 27.46 27.46 38.46 3.96
2123 2233 4.295051 TGAATCGAATGAATGCATGCATG 58.705 39.130 32.79 22.70 36.68 4.06
2200 2310 2.139917 GTCACTTGTCCGTGCATGTAA 58.860 47.619 4.96 0.00 34.92 2.41
2201 2311 2.742053 GTCACTTGTCCGTGCATGTAAT 59.258 45.455 4.96 0.00 34.92 1.89
2202 2312 3.930229 GTCACTTGTCCGTGCATGTAATA 59.070 43.478 4.96 0.00 34.92 0.98
2206 2319 5.232202 CACTTGTCCGTGCATGTAATACTAG 59.768 44.000 4.96 6.53 0.00 2.57
2291 2404 2.736347 AGTGGCGACTACTACAATCCT 58.264 47.619 0.00 0.00 0.00 3.24
2292 2405 3.097614 AGTGGCGACTACTACAATCCTT 58.902 45.455 0.00 0.00 0.00 3.36
2293 2406 3.119101 AGTGGCGACTACTACAATCCTTG 60.119 47.826 0.00 0.00 0.00 3.61
2294 2407 2.202566 GGCGACTACTACAATCCTTGC 58.797 52.381 0.00 0.00 0.00 4.01
2295 2408 1.852895 GCGACTACTACAATCCTTGCG 59.147 52.381 0.00 0.00 0.00 4.85
2296 2409 1.852895 CGACTACTACAATCCTTGCGC 59.147 52.381 0.00 0.00 0.00 6.09
2297 2410 1.852895 GACTACTACAATCCTTGCGCG 59.147 52.381 0.00 0.00 0.00 6.86
2298 2411 0.577269 CTACTACAATCCTTGCGCGC 59.423 55.000 27.26 27.26 0.00 6.86
2299 2412 1.143373 TACTACAATCCTTGCGCGCG 61.143 55.000 28.44 28.44 0.00 6.86
2300 2413 3.773649 CTACAATCCTTGCGCGCGC 62.774 63.158 45.02 45.02 42.35 6.86
2358 2471 5.687285 CACATTTTCCTTTCTTTCAAGACGG 59.313 40.000 0.00 0.00 34.13 4.79
2361 2474 6.709018 TTTTCCTTTCTTTCAAGACGGAAT 57.291 33.333 15.33 0.00 41.05 3.01
2383 2496 2.202171 CGTGTTCCGTCGCATTGC 60.202 61.111 0.00 0.00 0.00 3.56
2387 2500 3.430862 TTCCGTCGCATTGCTGGC 61.431 61.111 7.12 1.21 0.00 4.85
2402 2515 2.446036 GGCCACCCCGGAGATACT 60.446 66.667 0.73 0.00 36.56 2.12
2403 2516 1.152398 GGCCACCCCGGAGATACTA 60.152 63.158 0.73 0.00 36.56 1.82
2404 2517 1.470165 GGCCACCCCGGAGATACTAC 61.470 65.000 0.73 0.00 36.56 2.73
2406 2519 0.466922 CCACCCCGGAGATACTACGT 60.467 60.000 0.73 0.00 35.83 3.57
2407 2520 1.202806 CCACCCCGGAGATACTACGTA 60.203 57.143 0.73 0.00 35.83 3.57
2408 2521 1.876156 CACCCCGGAGATACTACGTAC 59.124 57.143 0.73 0.00 35.83 3.67
2409 2522 1.490490 ACCCCGGAGATACTACGTACA 59.510 52.381 0.73 0.00 35.83 2.90
2410 2523 2.149578 CCCCGGAGATACTACGTACAG 58.850 57.143 0.73 0.00 35.83 2.74
2411 2524 2.486191 CCCCGGAGATACTACGTACAGT 60.486 54.545 0.73 0.00 35.83 3.55
2414 2530 5.337571 CCCCGGAGATACTACGTACAGTATA 60.338 48.000 0.73 0.00 40.92 1.47
2436 2552 3.005684 AGCAGACGAATTTTCCATGCAAA 59.994 39.130 0.00 0.00 34.71 3.68
2460 2577 2.068837 AAAACAGGAACATGCATGCG 57.931 45.000 26.53 12.10 0.00 4.73
2524 2649 4.021925 GTTGCCGCCTGGAGTCCT 62.022 66.667 11.33 0.00 37.49 3.85
2525 2650 4.020617 TTGCCGCCTGGAGTCCTG 62.021 66.667 11.33 10.11 37.49 3.86
2528 2653 3.775654 CCGCCTGGAGTCCTGGAC 61.776 72.222 33.21 23.30 44.09 4.02
2529 2654 2.681778 CGCCTGGAGTCCTGGACT 60.682 66.667 33.21 28.70 46.42 3.85
2530 2655 1.379977 CGCCTGGAGTCCTGGACTA 60.380 63.158 33.21 13.80 43.53 2.59
2531 2656 1.668101 CGCCTGGAGTCCTGGACTAC 61.668 65.000 33.21 28.78 43.53 2.73
2535 2660 1.821753 CTGGAGTCCTGGACTACACAG 59.178 57.143 33.08 29.49 45.17 3.66
2540 2665 3.360867 AGTCCTGGACTACACAGAGATG 58.639 50.000 27.37 0.00 41.51 2.90
2568 2693 2.434359 GGCCCGTTCCGTCAGAAG 60.434 66.667 0.00 0.00 34.29 2.85
2642 2767 3.670895 CGGATGTGCGTAGATGGATAGAC 60.671 52.174 0.00 0.00 0.00 2.59
2672 2797 1.339631 TGAGCTAATGTGGAAACCGGG 60.340 52.381 6.32 0.00 0.00 5.73
2673 2798 0.696501 AGCTAATGTGGAAACCGGGT 59.303 50.000 6.32 0.00 0.00 5.28
2675 2800 1.612199 GCTAATGTGGAAACCGGGTGA 60.612 52.381 6.32 0.00 0.00 4.02
2676 2801 2.356135 CTAATGTGGAAACCGGGTGAG 58.644 52.381 6.32 0.00 0.00 3.51
2677 2802 0.768622 AATGTGGAAACCGGGTGAGA 59.231 50.000 6.32 0.00 0.00 3.27
2679 2804 0.761323 TGTGGAAACCGGGTGAGAGA 60.761 55.000 6.32 0.00 0.00 3.10
2680 2805 0.395312 GTGGAAACCGGGTGAGAGAA 59.605 55.000 6.32 0.00 0.00 2.87
2681 2806 0.685097 TGGAAACCGGGTGAGAGAAG 59.315 55.000 6.32 0.00 0.00 2.85
2682 2807 0.974383 GGAAACCGGGTGAGAGAAGA 59.026 55.000 6.32 0.00 0.00 2.87
2683 2808 1.066787 GGAAACCGGGTGAGAGAAGAG 60.067 57.143 6.32 0.00 0.00 2.85
2686 2815 0.114560 ACCGGGTGAGAGAAGAGGAA 59.885 55.000 6.32 0.00 0.00 3.36
2718 2847 2.863740 TGAATGCGGCTCATTTACTACG 59.136 45.455 3.95 0.00 44.95 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.376234 GCATGGAGTACGTGTAGACTGTA 59.624 47.826 0.00 0.00 38.39 2.74
1 2 2.163815 GCATGGAGTACGTGTAGACTGT 59.836 50.000 0.00 0.00 38.39 3.55
2 3 2.479730 GGCATGGAGTACGTGTAGACTG 60.480 54.545 0.00 0.00 38.39 3.51
3 4 1.749634 GGCATGGAGTACGTGTAGACT 59.250 52.381 0.00 0.00 38.39 3.24
4 5 1.475280 TGGCATGGAGTACGTGTAGAC 59.525 52.381 0.00 0.00 38.39 2.59
5 6 1.749063 CTGGCATGGAGTACGTGTAGA 59.251 52.381 0.00 0.00 38.39 2.59
6 7 1.476891 ACTGGCATGGAGTACGTGTAG 59.523 52.381 0.00 0.00 38.39 2.74
7 8 1.203758 CACTGGCATGGAGTACGTGTA 59.796 52.381 0.00 0.00 38.39 2.90
8 9 0.037326 CACTGGCATGGAGTACGTGT 60.037 55.000 0.00 0.00 38.39 4.49
9 10 1.361668 GCACTGGCATGGAGTACGTG 61.362 60.000 0.00 0.00 40.72 4.49
10 11 1.079127 GCACTGGCATGGAGTACGT 60.079 57.895 0.00 0.00 40.72 3.57
11 12 1.815421 GGCACTGGCATGGAGTACG 60.815 63.158 0.00 0.00 43.71 3.67
12 13 0.107017 ATGGCACTGGCATGGAGTAC 60.107 55.000 16.90 0.00 46.89 2.73
13 14 2.310251 ATGGCACTGGCATGGAGTA 58.690 52.632 16.90 0.00 46.89 2.59
14 15 3.093555 ATGGCACTGGCATGGAGT 58.906 55.556 16.90 0.00 46.89 3.85
25 26 2.439156 GAGTGGGAGGCATGGCAC 60.439 66.667 22.64 15.46 0.00 5.01
80 81 4.382728 CGCAACCGCATTCATTCC 57.617 55.556 0.00 0.00 38.40 3.01
112 113 2.282462 CAGTTGGGGGCTGTGGAC 60.282 66.667 0.00 0.00 0.00 4.02
174 175 0.393820 GGGTATTGATTACGGGCGGA 59.606 55.000 0.00 0.00 0.00 5.54
176 177 1.562575 GCGGGTATTGATTACGGGCG 61.563 60.000 0.00 0.00 0.00 6.13
244 245 1.334059 CGCTTAATTAGGCGGTGCATG 60.334 52.381 28.49 4.36 46.23 4.06
245 246 0.944386 CGCTTAATTAGGCGGTGCAT 59.056 50.000 28.49 0.00 46.23 3.96
246 247 2.389386 CGCTTAATTAGGCGGTGCA 58.611 52.632 28.49 0.00 46.23 4.57
288 289 4.095610 CGGATTAAAAACCTAGCTTTGCG 58.904 43.478 0.00 0.00 0.00 4.85
319 323 1.056700 TAATCCCCCTCTCTGCAGGC 61.057 60.000 15.13 0.00 31.23 4.85
321 325 2.813354 GCATTAATCCCCCTCTCTGCAG 60.813 54.545 7.63 7.63 0.00 4.41
322 326 1.143684 GCATTAATCCCCCTCTCTGCA 59.856 52.381 0.00 0.00 0.00 4.41
362 380 0.522705 CATCTGCAGTTGCGCATCAC 60.523 55.000 19.92 12.52 45.83 3.06
363 381 1.798087 CATCTGCAGTTGCGCATCA 59.202 52.632 19.92 10.84 45.83 3.07
368 386 2.412323 ATGGGCATCTGCAGTTGCG 61.412 57.895 32.63 14.57 45.83 4.85
370 388 1.141019 GCATGGGCATCTGCAGTTG 59.859 57.895 18.61 18.61 44.36 3.16
427 447 1.512996 ATACACGCGGGTCGATCGAT 61.513 55.000 21.89 0.29 41.67 3.59
431 451 1.280746 CGTATACACGCGGGTCGAT 59.719 57.895 21.89 10.24 42.05 3.59
441 465 3.548014 GCAATGCAACCATCCGTATACAC 60.548 47.826 0.00 0.00 0.00 2.90
444 468 2.616376 GTGCAATGCAACCATCCGTATA 59.384 45.455 10.44 0.00 41.47 1.47
468 492 3.526825 CGTGATGATGCATGCAGTG 57.473 52.632 26.69 6.37 0.00 3.66
583 615 2.724977 TATCCCGCACTCGATTGATC 57.275 50.000 6.99 0.00 38.10 2.92
598 630 1.274728 AGTCGCAGCTCATCCATATCC 59.725 52.381 0.00 0.00 0.00 2.59
601 633 1.339291 CTCAGTCGCAGCTCATCCATA 59.661 52.381 0.00 0.00 0.00 2.74
604 636 1.882167 GCTCAGTCGCAGCTCATCC 60.882 63.158 0.00 0.00 33.75 3.51
605 637 1.141449 AGCTCAGTCGCAGCTCATC 59.859 57.895 0.00 0.00 44.25 2.92
606 638 1.153608 CAGCTCAGTCGCAGCTCAT 60.154 57.895 0.00 0.00 44.25 2.90
607 639 2.210341 CTCAGCTCAGTCGCAGCTCA 62.210 60.000 0.00 0.00 44.25 4.26
608 640 1.516821 CTCAGCTCAGTCGCAGCTC 60.517 63.158 0.00 0.00 44.25 4.09
610 642 3.187414 GCTCAGCTCAGTCGCAGC 61.187 66.667 0.00 0.00 37.12 5.25
611 643 1.806351 CAGCTCAGCTCAGTCGCAG 60.806 63.158 0.00 0.00 36.40 5.18
612 644 2.210341 CTCAGCTCAGCTCAGTCGCA 62.210 60.000 0.00 0.00 36.40 5.10
613 645 1.516821 CTCAGCTCAGCTCAGTCGC 60.517 63.158 0.00 0.00 36.40 5.19
614 646 1.516821 GCTCAGCTCAGCTCAGTCG 60.517 63.158 0.67 0.00 36.40 4.18
615 647 0.737019 GTGCTCAGCTCAGCTCAGTC 60.737 60.000 12.05 0.00 40.39 3.51
616 648 1.186917 AGTGCTCAGCTCAGCTCAGT 61.187 55.000 12.05 0.00 40.39 3.41
617 649 0.738063 CAGTGCTCAGCTCAGCTCAG 60.738 60.000 12.05 0.00 40.39 3.35
618 650 1.292541 CAGTGCTCAGCTCAGCTCA 59.707 57.895 12.05 0.00 40.39 4.26
619 651 2.101835 GCAGTGCTCAGCTCAGCTC 61.102 63.158 12.05 7.47 40.39 4.09
620 652 2.047083 GCAGTGCTCAGCTCAGCT 60.047 61.111 12.05 0.00 40.39 4.24
621 653 2.358369 TGCAGTGCTCAGCTCAGC 60.358 61.111 17.60 1.01 40.13 4.26
643 683 2.076863 CAACACTTACTACTGGCCAGC 58.923 52.381 33.06 0.00 0.00 4.85
820 860 1.202582 TCAGTCAGAGCGGAGTAAAGC 59.797 52.381 0.00 0.00 0.00 3.51
872 912 6.719829 TCCTTCCAAAGCTATATCTATCGACA 59.280 38.462 0.00 0.00 0.00 4.35
875 915 6.915300 CGATCCTTCCAAAGCTATATCTATCG 59.085 42.308 0.00 0.00 0.00 2.92
965 1005 0.740868 CCGCTAGCTGCACTTGCTTA 60.741 55.000 13.93 0.00 43.93 3.09
1140 1189 3.140225 GATCCCGTCGTGCTCCTCC 62.140 68.421 0.00 0.00 0.00 4.30
1141 1190 2.413765 GATCCCGTCGTGCTCCTC 59.586 66.667 0.00 0.00 0.00 3.71
1142 1191 3.518998 CGATCCCGTCGTGCTCCT 61.519 66.667 0.00 0.00 45.19 3.69
1233 1282 0.456221 CACCGCAGTAGGTAGGAGTG 59.544 60.000 0.00 0.00 43.89 3.51
1262 1318 3.210528 GGGACGGACGATCGAGCT 61.211 66.667 24.34 0.00 0.00 4.09
1263 1319 3.210528 AGGGACGGACGATCGAGC 61.211 66.667 24.34 13.00 0.00 5.03
1264 1320 2.716244 CAGGGACGGACGATCGAG 59.284 66.667 24.34 14.65 0.00 4.04
1265 1321 3.515286 GCAGGGACGGACGATCGA 61.515 66.667 24.34 0.00 0.00 3.59
1291 1347 6.919662 CAGAAACAAGCACAAACATAACTCAT 59.080 34.615 0.00 0.00 0.00 2.90
1293 1349 6.414987 GTCAGAAACAAGCACAAACATAACTC 59.585 38.462 0.00 0.00 0.00 3.01
1294 1350 6.265577 GTCAGAAACAAGCACAAACATAACT 58.734 36.000 0.00 0.00 0.00 2.24
1295 1351 5.171337 CGTCAGAAACAAGCACAAACATAAC 59.829 40.000 0.00 0.00 0.00 1.89
1296 1352 5.270083 CGTCAGAAACAAGCACAAACATAA 58.730 37.500 0.00 0.00 0.00 1.90
1301 1357 1.202245 GCCGTCAGAAACAAGCACAAA 60.202 47.619 0.00 0.00 0.00 2.83
1307 1363 1.493772 TACACGCCGTCAGAAACAAG 58.506 50.000 0.00 0.00 0.00 3.16
1319 1376 0.717224 CACACGTTACCATACACGCC 59.283 55.000 0.00 0.00 40.16 5.68
1325 1382 2.482336 CTGCAAAGCACACGTTACCATA 59.518 45.455 0.00 0.00 33.79 2.74
1326 1383 1.266718 CTGCAAAGCACACGTTACCAT 59.733 47.619 0.00 0.00 33.79 3.55
1329 1386 1.656429 CGACTGCAAAGCACACGTTAC 60.656 52.381 0.00 0.00 33.79 2.50
1330 1387 0.579630 CGACTGCAAAGCACACGTTA 59.420 50.000 0.00 0.00 33.79 3.18
1331 1388 1.351707 CGACTGCAAAGCACACGTT 59.648 52.632 0.00 0.00 33.79 3.99
1332 1389 2.534019 CCGACTGCAAAGCACACGT 61.534 57.895 10.43 0.00 33.79 4.49
1333 1390 2.249309 CCGACTGCAAAGCACACG 59.751 61.111 0.00 0.00 33.79 4.49
1334 1391 2.639286 CCCGACTGCAAAGCACAC 59.361 61.111 0.00 0.00 33.79 3.82
1335 1392 2.594303 CCCCGACTGCAAAGCACA 60.594 61.111 0.00 0.00 33.79 4.57
1336 1393 4.043200 GCCCCGACTGCAAAGCAC 62.043 66.667 0.00 0.00 33.79 4.40
1337 1394 4.577677 TGCCCCGACTGCAAAGCA 62.578 61.111 0.00 0.00 35.40 3.91
1338 1395 3.741476 CTGCCCCGACTGCAAAGC 61.741 66.667 0.00 0.00 38.46 3.51
1339 1396 1.372087 GATCTGCCCCGACTGCAAAG 61.372 60.000 0.00 0.00 38.46 2.77
1340 1397 1.377202 GATCTGCCCCGACTGCAAA 60.377 57.895 0.00 0.00 38.46 3.68
1341 1398 2.268920 GATCTGCCCCGACTGCAA 59.731 61.111 0.00 0.00 38.46 4.08
1505 1562 1.738099 CTCCTTGACGGGCGAACTG 60.738 63.158 0.00 0.00 0.00 3.16
1554 1611 3.905705 GATGATCGCCTCTCGCCGG 62.906 68.421 0.00 0.00 38.27 6.13
1560 1617 2.502492 CCCCGTGATGATCGCCTCT 61.502 63.158 0.00 0.00 0.00 3.69
1570 1627 2.797278 GGCGTCTGATCCCCGTGAT 61.797 63.158 0.00 0.00 36.01 3.06
1767 1842 4.695396 CATGCATGATCTCTATAGGAGCC 58.305 47.826 22.59 0.00 41.60 4.70
1822 1902 1.631072 CACCATGCGACGAACGATC 59.369 57.895 0.00 0.00 45.77 3.69
1833 1913 1.331756 CTTATCGAAGGTGCACCATGC 59.668 52.381 36.39 22.88 45.29 4.06
1847 1927 0.999406 CCCTCGTGTTGCACTTATCG 59.001 55.000 0.00 0.00 31.34 2.92
1858 1940 3.314331 CTGTGAGGGCCCTCGTGT 61.314 66.667 40.12 14.37 45.48 4.49
1859 1941 3.314331 ACTGTGAGGGCCCTCGTG 61.314 66.667 40.12 32.81 45.48 4.35
1868 1950 1.598962 CTGGTGGTGCACTGTGAGG 60.599 63.158 17.98 0.00 34.40 3.86
1869 1951 0.392706 TACTGGTGGTGCACTGTGAG 59.607 55.000 17.98 10.45 34.40 3.51
1871 1953 1.536766 CATTACTGGTGGTGCACTGTG 59.463 52.381 17.98 2.76 34.40 3.66
1884 1966 6.784176 TGCATTAGTACAACATGCATTACTG 58.216 36.000 17.83 8.08 46.53 2.74
1891 1973 5.401550 ACAACATGCATTAGTACAACATGC 58.598 37.500 14.04 14.04 41.38 4.06
1892 1974 7.751732 AGTACAACATGCATTAGTACAACATG 58.248 34.615 23.96 4.07 42.92 3.21
1893 1975 7.824289 AGAGTACAACATGCATTAGTACAACAT 59.176 33.333 23.96 11.36 37.96 2.71
1894 1976 7.158697 AGAGTACAACATGCATTAGTACAACA 58.841 34.615 23.96 0.00 37.96 3.33
1895 1977 7.596749 AGAGTACAACATGCATTAGTACAAC 57.403 36.000 23.96 19.01 37.96 3.32
1896 1978 7.486870 CGTAGAGTACAACATGCATTAGTACAA 59.513 37.037 23.96 12.98 37.96 2.41
1897 1979 6.970613 CGTAGAGTACAACATGCATTAGTACA 59.029 38.462 23.96 9.86 37.96 2.90
1898 1980 6.971184 ACGTAGAGTACAACATGCATTAGTAC 59.029 38.462 18.49 18.49 36.26 2.73
1899 1981 6.970613 CACGTAGAGTACAACATGCATTAGTA 59.029 38.462 0.00 0.00 0.00 1.82
1900 1982 5.805486 CACGTAGAGTACAACATGCATTAGT 59.195 40.000 0.00 0.00 0.00 2.24
1901 1983 6.020599 GTCACGTAGAGTACAACATGCATTAG 60.021 42.308 0.00 0.00 0.00 1.73
1902 1984 5.803461 GTCACGTAGAGTACAACATGCATTA 59.197 40.000 0.00 0.00 0.00 1.90
1903 1985 4.625742 GTCACGTAGAGTACAACATGCATT 59.374 41.667 0.00 0.00 0.00 3.56
1904 1986 4.174009 GTCACGTAGAGTACAACATGCAT 58.826 43.478 0.00 0.00 0.00 3.96
1905 1987 3.571571 GTCACGTAGAGTACAACATGCA 58.428 45.455 0.00 0.00 0.00 3.96
1906 1988 2.921754 GGTCACGTAGAGTACAACATGC 59.078 50.000 0.00 0.00 0.00 4.06
1907 1989 4.168922 TGGTCACGTAGAGTACAACATG 57.831 45.455 0.00 0.00 0.00 3.21
1960 2044 6.915300 TGTTTATTTCTTGCACACACATGTAC 59.085 34.615 0.00 0.00 36.72 2.90
1961 2045 7.032377 TGTTTATTTCTTGCACACACATGTA 57.968 32.000 0.00 0.00 36.72 2.29
1962 2046 5.900425 TGTTTATTTCTTGCACACACATGT 58.100 33.333 0.00 0.00 40.80 3.21
1963 2047 6.825284 TTGTTTATTTCTTGCACACACATG 57.175 33.333 0.00 0.00 0.00 3.21
1964 2048 7.208777 TCATTGTTTATTTCTTGCACACACAT 58.791 30.769 0.00 0.00 0.00 3.21
1965 2049 6.567959 TCATTGTTTATTTCTTGCACACACA 58.432 32.000 0.00 0.00 0.00 3.72
1966 2050 7.642071 ATCATTGTTTATTTCTTGCACACAC 57.358 32.000 0.00 0.00 0.00 3.82
1967 2051 8.575589 ACTATCATTGTTTATTTCTTGCACACA 58.424 29.630 0.00 0.00 0.00 3.72
1968 2052 8.970691 ACTATCATTGTTTATTTCTTGCACAC 57.029 30.769 0.00 0.00 0.00 3.82
2014 2098 6.444633 ACATATAATGGAGTAGCACGTACAC 58.555 40.000 0.00 0.00 31.98 2.90
2029 2113 5.106791 GCAACTGCTCAGGCTACATATAATG 60.107 44.000 1.66 0.00 39.59 1.90
2034 2118 1.554617 TGCAACTGCTCAGGCTACATA 59.445 47.619 2.95 0.00 42.66 2.29
2036 2120 0.325933 ATGCAACTGCTCAGGCTACA 59.674 50.000 2.95 0.00 42.66 2.74
2038 2122 1.028330 GCATGCAACTGCTCAGGCTA 61.028 55.000 14.21 0.00 42.66 3.93
2039 2123 2.341101 GCATGCAACTGCTCAGGCT 61.341 57.895 14.21 0.00 42.66 4.58
2044 2128 1.651240 ATCACCGCATGCAACTGCTC 61.651 55.000 19.57 0.00 42.66 4.26
2048 2132 1.375908 ACGATCACCGCATGCAACT 60.376 52.632 19.57 0.00 43.32 3.16
2052 2136 3.576356 CCCACGATCACCGCATGC 61.576 66.667 7.91 7.91 43.32 4.06
2053 2137 2.896854 CCCCACGATCACCGCATG 60.897 66.667 0.00 0.00 43.32 4.06
2054 2138 4.856801 GCCCCACGATCACCGCAT 62.857 66.667 0.00 0.00 43.32 4.73
2058 2168 0.250338 GGATTAGCCCCACGATCACC 60.250 60.000 0.00 0.00 0.00 4.02
2077 2187 2.104859 CACCACCGCTCATCAGCTG 61.105 63.158 7.63 7.63 44.40 4.24
2079 2189 3.503363 GCACCACCGCTCATCAGC 61.503 66.667 0.00 0.00 42.96 4.26
2080 2190 2.267006 AGCACCACCGCTCATCAG 59.733 61.111 0.00 0.00 37.91 2.90
2093 2203 4.534168 CATTCATTCGATTCATGGAGCAC 58.466 43.478 0.00 0.00 0.00 4.40
2095 2205 3.004002 TGCATTCATTCGATTCATGGAGC 59.996 43.478 0.00 0.00 0.00 4.70
2096 2206 4.823790 TGCATTCATTCGATTCATGGAG 57.176 40.909 0.00 0.00 0.00 3.86
2097 2207 4.557895 GCATGCATTCATTCGATTCATGGA 60.558 41.667 14.21 0.00 32.76 3.41
2098 2208 3.673338 GCATGCATTCATTCGATTCATGG 59.327 43.478 14.21 0.00 32.76 3.66
2099 2209 4.295051 TGCATGCATTCATTCGATTCATG 58.705 39.130 18.46 0.00 34.59 3.07
2100 2210 4.577834 TGCATGCATTCATTCGATTCAT 57.422 36.364 18.46 0.00 0.00 2.57
2116 2226 6.898912 ATTATATCTACGTCAGCATGCATG 57.101 37.500 22.70 22.70 34.76 4.06
2118 2228 8.088365 ACTTAATTATATCTACGTCAGCATGCA 58.912 33.333 21.98 0.00 34.76 3.96
2119 2229 8.376203 CACTTAATTATATCTACGTCAGCATGC 58.624 37.037 10.51 10.51 34.76 4.06
2120 2230 8.376203 GCACTTAATTATATCTACGTCAGCATG 58.624 37.037 0.00 0.00 37.54 4.06
2121 2231 7.273598 CGCACTTAATTATATCTACGTCAGCAT 59.726 37.037 0.00 0.00 0.00 3.79
2122 2232 6.581166 CGCACTTAATTATATCTACGTCAGCA 59.419 38.462 0.00 0.00 0.00 4.41
2123 2233 6.581542 ACGCACTTAATTATATCTACGTCAGC 59.418 38.462 0.00 0.00 0.00 4.26
2124 2234 9.770503 ATACGCACTTAATTATATCTACGTCAG 57.229 33.333 0.00 0.00 0.00 3.51
2222 2335 3.932089 CCAACAACCAACCAACTTTCAAG 59.068 43.478 0.00 0.00 0.00 3.02
2326 2439 4.997565 AGAAAGGAAAATGTGTGTGTGTG 58.002 39.130 0.00 0.00 0.00 3.82
2327 2440 5.659440 AAGAAAGGAAAATGTGTGTGTGT 57.341 34.783 0.00 0.00 0.00 3.72
2374 2487 4.120331 GGTGGCCAGCAATGCGAC 62.120 66.667 29.70 2.50 36.81 5.19
2383 2496 2.445845 TATCTCCGGGGTGGCCAG 60.446 66.667 5.11 0.00 37.80 4.85
2387 2500 0.466922 ACGTAGTATCTCCGGGGTGG 60.467 60.000 0.00 0.00 41.94 4.61
2402 2515 6.609237 AATTCGTCTGCTATACTGTACGTA 57.391 37.500 0.00 0.00 0.00 3.57
2403 2516 5.496133 AATTCGTCTGCTATACTGTACGT 57.504 39.130 0.00 0.00 0.00 3.57
2404 2517 6.074994 GGAAAATTCGTCTGCTATACTGTACG 60.075 42.308 0.00 0.00 0.00 3.67
2406 2519 6.869695 TGGAAAATTCGTCTGCTATACTGTA 58.130 36.000 0.00 0.00 0.00 2.74
2407 2520 5.730550 TGGAAAATTCGTCTGCTATACTGT 58.269 37.500 0.00 0.00 0.00 3.55
2408 2521 6.653183 CATGGAAAATTCGTCTGCTATACTG 58.347 40.000 0.00 0.00 0.00 2.74
2409 2522 5.237344 GCATGGAAAATTCGTCTGCTATACT 59.763 40.000 0.00 0.00 0.00 2.12
2410 2523 5.007626 TGCATGGAAAATTCGTCTGCTATAC 59.992 40.000 0.00 0.00 31.80 1.47
2411 2524 5.122519 TGCATGGAAAATTCGTCTGCTATA 58.877 37.500 0.00 0.00 31.80 1.31
2414 2530 2.161855 TGCATGGAAAATTCGTCTGCT 58.838 42.857 0.00 0.00 31.80 4.24
2445 2562 4.777781 CACGCATGCATGTTCCTG 57.222 55.556 26.79 14.25 0.00 3.86
2460 2577 1.702299 GTCGTGTAGACGCATGCAC 59.298 57.895 19.57 11.09 45.68 4.57
2480 2597 0.737715 CACTAGTGAAGCTGGGTCGC 60.738 60.000 18.45 0.00 0.00 5.19
2520 2645 3.093057 ACATCTCTGTGTAGTCCAGGAC 58.907 50.000 12.25 12.25 33.22 3.85
2522 2647 6.151985 GGATATACATCTCTGTGTAGTCCAGG 59.848 46.154 12.54 0.00 40.02 4.45
2523 2648 6.128145 CGGATATACATCTCTGTGTAGTCCAG 60.128 46.154 15.45 0.00 40.13 3.86
2524 2649 5.705905 CGGATATACATCTCTGTGTAGTCCA 59.294 44.000 15.45 0.00 40.13 4.02
2525 2650 5.124138 CCGGATATACATCTCTGTGTAGTCC 59.876 48.000 0.00 9.46 37.93 3.85
2526 2651 5.706369 ACCGGATATACATCTCTGTGTAGTC 59.294 44.000 9.46 0.00 37.93 2.59
2527 2652 5.473846 CACCGGATATACATCTCTGTGTAGT 59.526 44.000 9.46 0.00 37.93 2.73
2528 2653 5.106118 CCACCGGATATACATCTCTGTGTAG 60.106 48.000 9.46 0.00 37.93 2.74
2529 2654 4.765339 CCACCGGATATACATCTCTGTGTA 59.235 45.833 9.46 0.00 38.79 2.90
2530 2655 3.574396 CCACCGGATATACATCTCTGTGT 59.426 47.826 9.46 0.00 36.79 3.72
2531 2656 3.615110 GCCACCGGATATACATCTCTGTG 60.615 52.174 9.46 0.00 36.79 3.66
2535 2660 1.207329 GGGCCACCGGATATACATCTC 59.793 57.143 9.46 0.00 0.00 2.75
2568 2693 2.290916 TCGATCGATAGCACCACTTCTC 59.709 50.000 15.15 0.00 0.00 2.87
2592 2717 3.307242 CGTATGCACCTTTCAGCTAACTC 59.693 47.826 0.00 0.00 0.00 3.01
2628 2753 3.139850 ACACTCCGTCTATCCATCTACG 58.860 50.000 0.00 0.00 35.20 3.51
2642 2767 1.135373 ACATTAGCTCACGACACTCCG 60.135 52.381 0.00 0.00 0.00 4.63
2672 2797 4.466015 ACCAATCTCTTCCTCTTCTCTCAC 59.534 45.833 0.00 0.00 0.00 3.51
2673 2798 4.682563 ACCAATCTCTTCCTCTTCTCTCA 58.317 43.478 0.00 0.00 0.00 3.27
2675 2800 5.545723 TCAAACCAATCTCTTCCTCTTCTCT 59.454 40.000 0.00 0.00 0.00 3.10
2676 2801 5.799213 TCAAACCAATCTCTTCCTCTTCTC 58.201 41.667 0.00 0.00 0.00 2.87
2677 2802 5.832539 TCAAACCAATCTCTTCCTCTTCT 57.167 39.130 0.00 0.00 0.00 2.85
2679 2804 5.184671 GCATTCAAACCAATCTCTTCCTCTT 59.815 40.000 0.00 0.00 0.00 2.85
2680 2805 4.704057 GCATTCAAACCAATCTCTTCCTCT 59.296 41.667 0.00 0.00 0.00 3.69
2681 2806 4.437930 CGCATTCAAACCAATCTCTTCCTC 60.438 45.833 0.00 0.00 0.00 3.71
2682 2807 3.441572 CGCATTCAAACCAATCTCTTCCT 59.558 43.478 0.00 0.00 0.00 3.36
2683 2808 3.428045 CCGCATTCAAACCAATCTCTTCC 60.428 47.826 0.00 0.00 0.00 3.46
2686 2815 1.474077 GCCGCATTCAAACCAATCTCT 59.526 47.619 0.00 0.00 0.00 3.10
2718 2847 0.106708 TTGCACCCGCCATCTAGATC 59.893 55.000 1.03 0.00 37.32 2.75


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

AutoCloner maintained by Alex Coulton.