Multiple sequence alignment - TraesCS6B01G043900

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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 TraesCS6B01G043900 chr6B 100.000 2743 0 0 1 2743 26536246 26533504 0 5066
1 TraesCS6B01G043900 chr6A 84.544 2575 167 90 182 2643 15828116 15830572 0 2337
2 TraesCS6B01G043900 chr6D 86.051 2079 153 69 1 2043 14591847 14589870 0 2106


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 TraesCS6B01G043900 chr6B 26533504 26536246 2742 True 5066 5066 100.000 1 2743 1 chr6B.!!$R1 2742
1 TraesCS6B01G043900 chr6A 15828116 15830572 2456 False 2337 2337 84.544 182 2643 1 chr6A.!!$F1 2461
2 TraesCS6B01G043900 chr6D 14589870 14591847 1977 True 2106 2106 86.051 1 2043 1 chr6D.!!$R1 2042

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
981 1020 0.030908 AGCTTCGATCGATCCGGTTC 59.969 55.0 20.18 0.74 0.0 3.62 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2555 2686 0.107508 ATCCTCCGAGTGTGCAATGG 60.108 55.0 0.0 0.0 0.0 3.16 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
46 47 0.036765 TAGTCAATTTGGCTCCGCGT 60.037 50.000 6.82 0.00 32.64 6.01
52 53 2.869503 ATTTGGCTCCGCGTGGTAGG 62.870 60.000 16.01 7.88 36.30 3.18
63 64 1.433837 CGTGGTAGGCGCCATTAACC 61.434 60.000 31.54 27.52 41.08 2.85
65 66 1.153309 GGTAGGCGCCATTAACCGT 60.153 57.895 31.54 7.63 0.00 4.83
78 79 4.634004 CCATTAACCGTGCACTTCTCATAA 59.366 41.667 16.19 6.13 0.00 1.90
86 87 1.576356 CACTTCTCATAAGAGGGCGC 58.424 55.000 0.00 0.00 42.34 6.53
88 89 1.410882 ACTTCTCATAAGAGGGCGCTC 59.589 52.381 22.44 22.44 42.34 5.03
123 127 8.740123 TTTTCTTGGAAACACTTAGTCATGTA 57.260 30.769 0.00 0.00 42.67 2.29
135 139 7.147828 ACACTTAGTCATGTATGCTCATGTACT 60.148 37.037 13.51 15.28 43.70 2.73
179 183 2.886859 GTCTATCGGACGCATGGTG 58.113 57.895 0.00 0.00 35.07 4.17
201 205 1.369091 CGGCGAGTCCATTCCAAAGG 61.369 60.000 0.00 0.00 34.01 3.11
205 209 2.556622 GCGAGTCCATTCCAAAGGAAAA 59.443 45.455 2.16 0.00 45.41 2.29
236 240 6.223852 TGCTAGCTAGTATATCCAAGCAAAC 58.776 40.000 21.62 0.27 35.91 2.93
264 268 6.261435 TCCTCTAGATTCTCCCAACAAACTA 58.739 40.000 0.00 0.00 0.00 2.24
392 410 3.057969 TCTAACTTGCACACCATGAGG 57.942 47.619 0.00 0.00 42.21 3.86
559 579 3.065925 GCAGATCTACAAAAGGTGGATGC 59.934 47.826 0.00 0.00 46.45 3.91
575 595 1.336125 GATGCATTAGACAGCTTGCCC 59.664 52.381 0.00 0.00 34.20 5.36
617 637 0.039617 GCTGATCAGTCGATCCCTCG 60.040 60.000 23.38 0.00 46.50 4.63
633 653 2.202987 CGGACCATCAGCAGCTCC 60.203 66.667 0.00 0.00 0.00 4.70
698 719 6.994496 AGTATACTAGATACGTGCACCAACTA 59.006 38.462 12.15 7.05 0.00 2.24
708 729 3.804325 CGTGCACCAACTATAGATTCCTG 59.196 47.826 12.15 0.00 0.00 3.86
742 772 2.423446 CTTAGCTAGGGCCAGCCG 59.577 66.667 19.86 8.85 42.84 5.52
753 783 2.713967 GCCAGCCGGAACATGCATT 61.714 57.895 5.05 0.00 0.00 3.56
757 787 0.899717 AGCCGGAACATGCATTTGGT 60.900 50.000 5.05 0.00 0.00 3.67
783 818 5.664457 TGATTCTCCAGGCTTATATATGCG 58.336 41.667 12.90 2.59 0.00 4.73
861 900 2.350388 CGACTGTTTTGTTTGATCCCCG 60.350 50.000 0.00 0.00 0.00 5.73
862 901 1.960689 ACTGTTTTGTTTGATCCCCGG 59.039 47.619 0.00 0.00 0.00 5.73
863 902 0.676736 TGTTTTGTTTGATCCCCGGC 59.323 50.000 0.00 0.00 0.00 6.13
864 903 0.037697 GTTTTGTTTGATCCCCGGCC 60.038 55.000 0.00 0.00 0.00 6.13
902 941 0.039035 AGGCTAGCCTAGATCCTCGG 59.961 60.000 35.28 0.00 46.14 4.63
903 942 0.968393 GGCTAGCCTAGATCCTCGGG 60.968 65.000 27.17 0.00 0.00 5.14
904 943 0.968393 GCTAGCCTAGATCCTCGGGG 60.968 65.000 2.29 0.00 0.00 5.73
905 944 0.406361 CTAGCCTAGATCCTCGGGGT 59.594 60.000 0.00 0.00 0.00 4.95
906 945 0.404812 TAGCCTAGATCCTCGGGGTC 59.595 60.000 0.00 0.00 0.00 4.46
907 946 2.269529 GCCTAGATCCTCGGGGTCG 61.270 68.421 0.00 0.00 37.82 4.79
908 947 1.604023 CCTAGATCCTCGGGGTCGG 60.604 68.421 0.00 0.00 36.95 4.79
909 948 1.150992 CTAGATCCTCGGGGTCGGT 59.849 63.158 0.00 0.00 36.95 4.69
910 949 0.890090 CTAGATCCTCGGGGTCGGTC 60.890 65.000 0.00 0.00 36.95 4.79
921 960 2.487532 GGTCGGTCGGTCCATCGAT 61.488 63.158 0.00 0.00 41.40 3.59
925 964 2.354773 GTCGGTCCATCGATCGGC 60.355 66.667 16.41 0.00 43.12 5.54
979 1018 1.315690 TTAGCTTCGATCGATCCGGT 58.684 50.000 20.18 17.12 0.00 5.28
980 1019 1.315690 TAGCTTCGATCGATCCGGTT 58.684 50.000 20.18 9.99 0.00 4.44
981 1020 0.030908 AGCTTCGATCGATCCGGTTC 59.969 55.000 20.18 0.74 0.00 3.62
982 1021 0.940047 GCTTCGATCGATCCGGTTCC 60.940 60.000 20.18 0.31 0.00 3.62
983 1022 0.660595 CTTCGATCGATCCGGTTCCG 60.661 60.000 20.18 6.94 0.00 4.30
1083 1122 4.754667 GGGTCGTCAACGGAGGGC 62.755 72.222 2.31 0.00 40.29 5.19
1178 1217 4.181010 CGTGGCCAGGATGAGGGG 62.181 72.222 20.97 0.00 39.69 4.79
1288 1327 9.269453 AGAAATGGAAGGTACGTAATTAATAGC 57.731 33.333 0.00 0.00 0.00 2.97
1289 1328 7.647907 AATGGAAGGTACGTAATTAATAGCG 57.352 36.000 0.00 9.21 0.00 4.26
1290 1329 6.389830 TGGAAGGTACGTAATTAATAGCGA 57.610 37.500 15.47 1.18 0.00 4.93
1292 1331 5.631096 GGAAGGTACGTAATTAATAGCGACC 59.369 44.000 15.47 15.89 0.00 4.79
1296 1335 3.632189 ACGTAATTAATAGCGACCGGAC 58.368 45.455 9.46 0.00 0.00 4.79
1297 1336 2.982470 CGTAATTAATAGCGACCGGACC 59.018 50.000 9.46 0.00 0.00 4.46
1302 1341 4.790962 TAGCGACCGGACCGAGCT 62.791 66.667 26.04 26.04 41.45 4.09
1312 1351 0.678048 GGACCGAGCTGCCTGAAATT 60.678 55.000 0.00 0.00 0.00 1.82
1314 1353 2.565841 GACCGAGCTGCCTGAAATTAT 58.434 47.619 0.00 0.00 0.00 1.28
1316 1355 4.127171 GACCGAGCTGCCTGAAATTATTA 58.873 43.478 0.00 0.00 0.00 0.98
1317 1356 4.130118 ACCGAGCTGCCTGAAATTATTAG 58.870 43.478 0.00 0.00 0.00 1.73
1319 1358 4.576463 CCGAGCTGCCTGAAATTATTAGTT 59.424 41.667 0.00 0.00 0.00 2.24
1323 1362 6.657875 AGCTGCCTGAAATTATTAGTTCTCT 58.342 36.000 0.00 0.00 29.99 3.10
1324 1363 6.765512 AGCTGCCTGAAATTATTAGTTCTCTC 59.234 38.462 0.00 0.00 29.99 3.20
1325 1364 6.292596 GCTGCCTGAAATTATTAGTTCTCTCG 60.293 42.308 0.00 0.00 29.99 4.04
1326 1365 6.640518 TGCCTGAAATTATTAGTTCTCTCGT 58.359 36.000 0.00 0.00 29.99 4.18
1327 1366 7.103641 TGCCTGAAATTATTAGTTCTCTCGTT 58.896 34.615 0.00 0.00 29.99 3.85
1329 1368 7.277981 GCCTGAAATTATTAGTTCTCTCGTTCA 59.722 37.037 0.00 0.00 29.99 3.18
1330 1369 8.596380 CCTGAAATTATTAGTTCTCTCGTTCAC 58.404 37.037 0.00 0.00 29.99 3.18
1332 1371 9.140286 TGAAATTATTAGTTCTCTCGTTCACTG 57.860 33.333 0.00 0.00 29.99 3.66
1334 1373 6.829229 TTATTAGTTCTCTCGTTCACTGGA 57.171 37.500 0.00 0.00 0.00 3.86
1336 1375 3.584406 AGTTCTCTCGTTCACTGGATG 57.416 47.619 0.00 0.00 0.00 3.51
1338 1377 3.322254 AGTTCTCTCGTTCACTGGATGTT 59.678 43.478 0.00 0.00 0.00 2.71
1339 1378 4.523173 AGTTCTCTCGTTCACTGGATGTTA 59.477 41.667 0.00 0.00 0.00 2.41
1341 1380 4.998788 TCTCTCGTTCACTGGATGTTATG 58.001 43.478 0.00 0.00 0.00 1.90
1342 1381 4.462834 TCTCTCGTTCACTGGATGTTATGT 59.537 41.667 0.00 0.00 0.00 2.29
1344 1383 5.168569 TCTCGTTCACTGGATGTTATGTTC 58.831 41.667 0.00 0.00 0.00 3.18
1345 1384 4.888917 TCGTTCACTGGATGTTATGTTCA 58.111 39.130 0.00 0.00 0.00 3.18
1347 1386 5.351189 TCGTTCACTGGATGTTATGTTCATG 59.649 40.000 0.00 0.00 0.00 3.07
1350 1389 2.355756 ACTGGATGTTATGTTCATGCGC 59.644 45.455 0.00 0.00 36.64 6.09
1354 1393 0.373370 TGTTATGTTCATGCGCGCTC 59.627 50.000 33.29 16.70 0.00 5.03
1356 1395 0.652071 TTATGTTCATGCGCGCTCTG 59.348 50.000 33.29 27.22 0.00 3.35
1364 1403 2.880879 GCGCGCTCTGTTGATCGA 60.881 61.111 26.67 0.00 34.17 3.59
1365 1404 2.233654 GCGCGCTCTGTTGATCGAT 61.234 57.895 26.67 0.00 34.17 3.59
1366 1405 1.756375 GCGCGCTCTGTTGATCGATT 61.756 55.000 26.67 0.00 34.17 3.34
1367 1406 0.647410 CGCGCTCTGTTGATCGATTT 59.353 50.000 5.56 0.00 34.17 2.17
1368 1407 1.852280 CGCGCTCTGTTGATCGATTTA 59.148 47.619 5.56 0.00 34.17 1.40
1406 1445 2.035530 CTTCAAGAGCTGGGACCATC 57.964 55.000 0.00 0.00 0.00 3.51
1407 1446 1.280133 CTTCAAGAGCTGGGACCATCA 59.720 52.381 0.00 0.00 0.00 3.07
1408 1447 0.907486 TCAAGAGCTGGGACCATCAG 59.093 55.000 0.00 0.00 35.49 2.90
1489 1531 2.749441 GCCAGCAGGAACAGCCTC 60.749 66.667 0.00 0.00 46.97 4.70
1530 1572 3.075005 GCGCTCCCCTCCACTGTA 61.075 66.667 0.00 0.00 0.00 2.74
1531 1573 2.893398 CGCTCCCCTCCACTGTAC 59.107 66.667 0.00 0.00 0.00 2.90
1532 1574 1.982395 CGCTCCCCTCCACTGTACA 60.982 63.158 0.00 0.00 0.00 2.90
1533 1575 1.597461 GCTCCCCTCCACTGTACAC 59.403 63.158 0.00 0.00 0.00 2.90
1535 1577 0.544357 CTCCCCTCCACTGTACACCA 60.544 60.000 0.00 0.00 0.00 4.17
1540 1582 2.736995 CCACTGTACACCACCGCG 60.737 66.667 0.00 0.00 0.00 6.46
1541 1583 2.028484 CACTGTACACCACCGCGT 59.972 61.111 4.92 0.00 0.00 6.01
1542 1584 1.286570 CACTGTACACCACCGCGTA 59.713 57.895 4.92 0.00 0.00 4.42
1543 1585 0.108992 CACTGTACACCACCGCGTAT 60.109 55.000 4.92 0.00 0.00 3.06
1544 1586 1.132834 CACTGTACACCACCGCGTATA 59.867 52.381 4.92 0.00 0.00 1.47
1545 1587 1.818060 ACTGTACACCACCGCGTATAA 59.182 47.619 4.92 0.00 0.00 0.98
1546 1588 2.187707 CTGTACACCACCGCGTATAAC 58.812 52.381 4.92 0.00 0.00 1.89
1547 1589 1.135141 TGTACACCACCGCGTATAACC 60.135 52.381 4.92 0.00 0.00 2.85
1548 1590 1.135141 GTACACCACCGCGTATAACCA 60.135 52.381 4.92 0.00 0.00 3.67
1549 1591 0.538118 ACACCACCGCGTATAACCAT 59.462 50.000 4.92 0.00 0.00 3.55
1550 1592 1.755959 ACACCACCGCGTATAACCATA 59.244 47.619 4.92 0.00 0.00 2.74
1551 1593 2.129607 CACCACCGCGTATAACCATAC 58.870 52.381 4.92 0.00 34.75 2.39
1697 1765 1.601903 TGTGTGAGCGGTGTTGATTTC 59.398 47.619 0.00 0.00 0.00 2.17
1702 1770 4.142271 TGTGAGCGGTGTTGATTTCTTTTT 60.142 37.500 0.00 0.00 0.00 1.94
1744 1813 0.099791 GTCGTGCTGGAGCTCTAGAC 59.900 60.000 29.37 21.01 42.66 2.59
1745 1814 0.322546 TCGTGCTGGAGCTCTAGACA 60.323 55.000 29.37 22.02 42.66 3.41
1748 1817 1.065600 GCTGGAGCTCTAGACAGCG 59.934 63.158 29.37 4.33 45.56 5.18
1750 1819 0.749818 CTGGAGCTCTAGACAGCGGA 60.750 60.000 21.78 0.00 44.82 5.54
1751 1820 0.749818 TGGAGCTCTAGACAGCGGAG 60.750 60.000 14.64 0.00 44.82 4.63
1752 1821 0.464735 GGAGCTCTAGACAGCGGAGA 60.465 60.000 14.64 0.00 44.82 3.71
1753 1822 0.661020 GAGCTCTAGACAGCGGAGAC 59.339 60.000 6.43 0.00 44.82 3.36
1811 1880 3.146618 TCTCTCCGACGAGCAAATTAC 57.853 47.619 0.00 0.00 35.94 1.89
1812 1881 1.846782 CTCTCCGACGAGCAAATTACG 59.153 52.381 0.00 0.00 35.94 3.18
1813 1882 1.200716 TCTCCGACGAGCAAATTACGT 59.799 47.619 0.00 0.00 42.84 3.57
1814 1883 2.419673 TCTCCGACGAGCAAATTACGTA 59.580 45.455 0.00 0.00 40.29 3.57
1815 1884 2.518949 TCCGACGAGCAAATTACGTAC 58.481 47.619 0.00 0.00 40.29 3.67
1818 1887 2.518949 GACGAGCAAATTACGTACCGA 58.481 47.619 0.00 0.00 40.29 4.69
1835 1905 1.296056 CGAGTGGCGGGAATTCGTTT 61.296 55.000 0.00 0.00 36.03 3.60
1860 1930 1.739049 CGGCCCAAGTCTTGCAAAA 59.261 52.632 7.09 0.00 0.00 2.44
1867 1937 2.293122 CCAAGTCTTGCAAAATCGTCCA 59.707 45.455 7.09 0.00 0.00 4.02
1914 1985 2.109229 ATAGTAGTGGGCCTGCAGAT 57.891 50.000 17.39 0.00 0.00 2.90
1933 2013 5.239306 GCAGATCAATCAAATAATGGACCGA 59.761 40.000 0.00 0.00 0.00 4.69
1943 2023 8.827177 TCAAATAATGGACCGACTTATATGTC 57.173 34.615 8.38 8.38 0.00 3.06
1971 2051 4.942761 AAAGGCTGATTTTGCTTCTTCA 57.057 36.364 0.00 0.00 0.00 3.02
1976 2056 5.100943 GGCTGATTTTGCTTCTTCATCTTC 58.899 41.667 0.00 0.00 0.00 2.87
1982 2062 8.636213 TGATTTTGCTTCTTCATCTTCTTCTTT 58.364 29.630 0.00 0.00 0.00 2.52
1983 2063 9.473640 GATTTTGCTTCTTCATCTTCTTCTTTT 57.526 29.630 0.00 0.00 0.00 2.27
1984 2064 8.638685 TTTTGCTTCTTCATCTTCTTCTTTTG 57.361 30.769 0.00 0.00 0.00 2.44
2128 2235 4.342665 AGCATACTAGTACCAGAAAGGCTC 59.657 45.833 4.31 0.00 43.14 4.70
2131 2238 4.810191 ACTAGTACCAGAAAGGCTCAAG 57.190 45.455 0.00 0.00 43.14 3.02
2156 2263 8.877195 AGGTACTTTTGATAGAACTCACCTTTA 58.123 33.333 0.00 0.00 27.25 1.85
2193 2300 5.741011 TCTTTTGGTACACAACTTCAGTCT 58.259 37.500 0.00 0.00 39.29 3.24
2199 2306 2.919228 ACACAACTTCAGTCTTGGGTC 58.081 47.619 0.00 0.00 0.00 4.46
2206 2313 3.319122 ACTTCAGTCTTGGGTCAAATTGC 59.681 43.478 0.00 0.00 0.00 3.56
2235 2342 9.643693 GAACAAACATGATATGACTTCCAAATT 57.356 29.630 0.00 0.00 0.00 1.82
2295 2402 1.135024 GTCGTGCAATGATTGGGCAAT 60.135 47.619 7.35 0.00 39.57 3.56
2365 2472 6.569994 GCAATCTGAGATCAAAGCAGAAGTTT 60.570 38.462 0.00 1.29 41.48 2.66
2374 2481 9.118300 AGATCAAAGCAGAAGTTTAGATTATGG 57.882 33.333 0.00 0.00 0.00 2.74
2407 2514 7.945033 ACCATTTCACAAACATACATTTGAC 57.055 32.000 5.30 0.00 41.28 3.18
2411 2518 7.984002 TTTCACAAACATACATTTGACACTG 57.016 32.000 5.30 0.00 41.28 3.66
2442 2549 6.135290 CCATGTTATTACAAGTCACCATGG 57.865 41.667 11.19 11.19 41.31 3.66
2471 2602 4.400961 AACCTCCTGGCAGAGCGC 62.401 66.667 17.94 0.00 41.28 5.92
2475 2606 3.381333 CTCCTGGCAGAGCGCATCA 62.381 63.158 17.94 0.00 45.17 3.07
2486 2617 5.447010 GGCAGAGCGCATCATATAATTCTTC 60.447 44.000 11.47 0.00 45.17 2.87
2491 2622 5.646793 AGCGCATCATATAATTCTTCTGCAT 59.353 36.000 11.47 0.00 0.00 3.96
2495 2626 7.148457 CGCATCATATAATTCTTCTGCATGAGT 60.148 37.037 0.00 0.00 0.00 3.41
2497 2628 9.438228 CATCATATAATTCTTCTGCATGAGTCT 57.562 33.333 0.00 0.00 0.00 3.24
2535 2666 3.315470 GCACGTGATCAGACTCTATGGTA 59.685 47.826 22.23 0.00 0.00 3.25
2537 2668 4.576873 CACGTGATCAGACTCTATGGTAGT 59.423 45.833 10.90 0.00 0.00 2.73
2541 2672 5.358442 GTGATCAGACTCTATGGTAGTGTGT 59.642 44.000 0.00 0.00 38.86 3.72
2542 2673 6.542735 GTGATCAGACTCTATGGTAGTGTGTA 59.457 42.308 0.00 0.00 38.86 2.90
2543 2674 7.229707 GTGATCAGACTCTATGGTAGTGTGTAT 59.770 40.741 0.00 0.00 38.86 2.29
2550 2681 6.776603 ACTCTATGGTAGTGTGTATAAGGGTC 59.223 42.308 0.00 0.00 31.89 4.46
2555 2686 3.560636 AGTGTGTATAAGGGTCCATGC 57.439 47.619 0.00 0.00 0.00 4.06
2580 2711 1.739371 GCACACTCGGAGGATACAACC 60.739 57.143 10.23 0.00 41.41 3.77
2619 2750 1.476845 TTTAGGCCGGTGTCTGCTCA 61.477 55.000 1.90 0.00 0.00 4.26
2622 2753 2.343758 GCCGGTGTCTGCTCAGAA 59.656 61.111 1.90 0.00 39.48 3.02
2626 2757 1.270305 CCGGTGTCTGCTCAGAAGAAA 60.270 52.381 0.54 0.00 39.48 2.52
2629 2760 3.733337 GGTGTCTGCTCAGAAGAAAAGA 58.267 45.455 0.54 0.00 39.48 2.52
2633 2764 5.050431 GTGTCTGCTCAGAAGAAAAGACTTC 60.050 44.000 0.54 0.00 44.36 3.01
2643 2774 0.853530 AAAAGACTTCCAGGGCCAGT 59.146 50.000 6.18 0.00 0.00 4.00
2644 2775 1.742308 AAAGACTTCCAGGGCCAGTA 58.258 50.000 6.18 0.00 0.00 2.74
2645 2776 1.742308 AAGACTTCCAGGGCCAGTAA 58.258 50.000 6.18 0.00 0.00 2.24
2646 2777 1.742308 AGACTTCCAGGGCCAGTAAA 58.258 50.000 6.18 0.00 0.00 2.01
2647 2778 2.062636 AGACTTCCAGGGCCAGTAAAA 58.937 47.619 6.18 0.00 0.00 1.52
2648 2779 2.160205 GACTTCCAGGGCCAGTAAAAC 58.840 52.381 6.18 0.00 0.00 2.43
2649 2780 1.780919 ACTTCCAGGGCCAGTAAAACT 59.219 47.619 6.18 0.00 0.00 2.66
2650 2781 2.177016 ACTTCCAGGGCCAGTAAAACTT 59.823 45.455 6.18 0.00 0.00 2.66
2651 2782 2.579410 TCCAGGGCCAGTAAAACTTC 57.421 50.000 6.18 0.00 0.00 3.01
2652 2783 2.062636 TCCAGGGCCAGTAAAACTTCT 58.937 47.619 6.18 0.00 0.00 2.85
2653 2784 2.162681 CCAGGGCCAGTAAAACTTCTG 58.837 52.381 6.18 0.00 0.00 3.02
2654 2785 1.541588 CAGGGCCAGTAAAACTTCTGC 59.458 52.381 6.18 0.00 0.00 4.26
2655 2786 1.144913 AGGGCCAGTAAAACTTCTGCA 59.855 47.619 6.18 0.00 0.00 4.41
2656 2787 1.960689 GGGCCAGTAAAACTTCTGCAA 59.039 47.619 4.39 0.00 0.00 4.08
2657 2788 2.288213 GGGCCAGTAAAACTTCTGCAAC 60.288 50.000 4.39 0.00 0.00 4.17
2658 2789 2.623416 GGCCAGTAAAACTTCTGCAACT 59.377 45.455 0.00 0.00 0.00 3.16
2659 2790 3.550842 GGCCAGTAAAACTTCTGCAACTG 60.551 47.826 0.00 4.30 35.29 3.16
2660 2791 4.228912 CCAGTAAAACTTCTGCAACTGG 57.771 45.455 13.89 13.89 45.64 4.00
2661 2792 3.632145 CCAGTAAAACTTCTGCAACTGGT 59.368 43.478 17.94 0.00 45.74 4.00
2662 2793 4.097892 CCAGTAAAACTTCTGCAACTGGTT 59.902 41.667 17.94 5.30 45.74 3.67
2663 2794 5.036737 CAGTAAAACTTCTGCAACTGGTTG 58.963 41.667 8.89 8.89 43.14 3.77
2664 2795 4.705023 AGTAAAACTTCTGCAACTGGTTGT 59.295 37.500 13.85 0.00 42.31 3.32
2665 2796 5.883673 AGTAAAACTTCTGCAACTGGTTGTA 59.116 36.000 13.85 9.24 42.31 2.41
2666 2797 5.652994 AAAACTTCTGCAACTGGTTGTAA 57.347 34.783 13.85 6.60 42.31 2.41
2667 2798 4.632538 AACTTCTGCAACTGGTTGTAAC 57.367 40.909 13.85 0.21 42.31 2.50
2668 2799 3.886123 ACTTCTGCAACTGGTTGTAACT 58.114 40.909 13.85 0.00 42.31 2.24
2669 2800 4.270008 ACTTCTGCAACTGGTTGTAACTT 58.730 39.130 13.85 0.00 42.31 2.66
2670 2801 4.705023 ACTTCTGCAACTGGTTGTAACTTT 59.295 37.500 13.85 0.00 42.31 2.66
2671 2802 5.185056 ACTTCTGCAACTGGTTGTAACTTTT 59.815 36.000 13.85 0.00 42.31 2.27
2672 2803 6.376018 ACTTCTGCAACTGGTTGTAACTTTTA 59.624 34.615 13.85 0.00 42.31 1.52
2673 2804 6.952773 TCTGCAACTGGTTGTAACTTTTAT 57.047 33.333 13.85 0.00 42.31 1.40
2674 2805 7.341445 TCTGCAACTGGTTGTAACTTTTATT 57.659 32.000 13.85 0.00 42.31 1.40
2675 2806 7.777095 TCTGCAACTGGTTGTAACTTTTATTT 58.223 30.769 13.85 0.00 42.31 1.40
2676 2807 7.918562 TCTGCAACTGGTTGTAACTTTTATTTC 59.081 33.333 13.85 0.00 42.31 2.17
2677 2808 7.777095 TGCAACTGGTTGTAACTTTTATTTCT 58.223 30.769 13.85 0.00 42.31 2.52
2678 2809 7.918562 TGCAACTGGTTGTAACTTTTATTTCTC 59.081 33.333 13.85 0.00 42.31 2.87
2679 2810 7.381408 GCAACTGGTTGTAACTTTTATTTCTCC 59.619 37.037 13.85 0.00 42.31 3.71
2680 2811 8.410141 CAACTGGTTGTAACTTTTATTTCTCCA 58.590 33.333 5.41 0.00 35.92 3.86
2681 2812 8.706322 ACTGGTTGTAACTTTTATTTCTCCAT 57.294 30.769 0.00 0.00 0.00 3.41
2682 2813 9.802039 ACTGGTTGTAACTTTTATTTCTCCATA 57.198 29.630 0.00 0.00 0.00 2.74
2684 2815 9.802039 TGGTTGTAACTTTTATTTCTCCATAGT 57.198 29.630 0.00 0.00 0.00 2.12
2691 2822 8.803397 ACTTTTATTTCTCCATAGTACAACCC 57.197 34.615 0.00 0.00 0.00 4.11
2692 2823 8.612145 ACTTTTATTTCTCCATAGTACAACCCT 58.388 33.333 0.00 0.00 0.00 4.34
2695 2826 9.496710 TTTATTTCTCCATAGTACAACCCTAGA 57.503 33.333 0.00 0.00 0.00 2.43
2696 2827 7.989947 ATTTCTCCATAGTACAACCCTAGAA 57.010 36.000 0.00 0.00 0.00 2.10
2697 2828 7.989947 TTTCTCCATAGTACAACCCTAGAAT 57.010 36.000 0.00 0.00 0.00 2.40
2698 2829 6.978674 TCTCCATAGTACAACCCTAGAATG 57.021 41.667 0.00 0.00 0.00 2.67
2699 2830 6.679542 TCTCCATAGTACAACCCTAGAATGA 58.320 40.000 0.00 0.00 0.00 2.57
2700 2831 7.130099 TCTCCATAGTACAACCCTAGAATGAA 58.870 38.462 0.00 0.00 0.00 2.57
2701 2832 7.069578 TCTCCATAGTACAACCCTAGAATGAAC 59.930 40.741 0.00 0.00 0.00 3.18
2702 2833 6.901300 TCCATAGTACAACCCTAGAATGAACT 59.099 38.462 0.00 0.00 0.00 3.01
2703 2834 8.063153 TCCATAGTACAACCCTAGAATGAACTA 58.937 37.037 0.00 0.00 0.00 2.24
2704 2835 8.701895 CCATAGTACAACCCTAGAATGAACTAA 58.298 37.037 0.00 0.00 0.00 2.24
2708 2839 9.449719 AGTACAACCCTAGAATGAACTAAAATG 57.550 33.333 0.00 0.00 0.00 2.32
2709 2840 9.444600 GTACAACCCTAGAATGAACTAAAATGA 57.555 33.333 0.00 0.00 0.00 2.57
2710 2841 8.567285 ACAACCCTAGAATGAACTAAAATGAG 57.433 34.615 0.00 0.00 0.00 2.90
2711 2842 8.164070 ACAACCCTAGAATGAACTAAAATGAGT 58.836 33.333 0.00 0.00 0.00 3.41
2712 2843 9.667107 CAACCCTAGAATGAACTAAAATGAGTA 57.333 33.333 0.00 0.00 0.00 2.59
2713 2844 9.892130 AACCCTAGAATGAACTAAAATGAGTAG 57.108 33.333 0.00 0.00 0.00 2.57
2714 2845 8.487028 ACCCTAGAATGAACTAAAATGAGTAGG 58.513 37.037 0.00 0.00 0.00 3.18
2715 2846 8.705594 CCCTAGAATGAACTAAAATGAGTAGGA 58.294 37.037 0.00 0.00 0.00 2.94
2718 2849 8.794335 AGAATGAACTAAAATGAGTAGGAACC 57.206 34.615 0.00 0.00 0.00 3.62
2719 2850 8.383175 AGAATGAACTAAAATGAGTAGGAACCA 58.617 33.333 0.00 0.00 0.00 3.67
2720 2851 8.934023 AATGAACTAAAATGAGTAGGAACCAA 57.066 30.769 0.00 0.00 0.00 3.67
2721 2852 7.739498 TGAACTAAAATGAGTAGGAACCAAC 57.261 36.000 0.00 0.00 0.00 3.77
2722 2853 7.284074 TGAACTAAAATGAGTAGGAACCAACA 58.716 34.615 0.00 0.00 0.00 3.33
2723 2854 7.776030 TGAACTAAAATGAGTAGGAACCAACAA 59.224 33.333 0.00 0.00 0.00 2.83
2724 2855 8.528044 AACTAAAATGAGTAGGAACCAACAAA 57.472 30.769 0.00 0.00 0.00 2.83
2725 2856 8.706322 ACTAAAATGAGTAGGAACCAACAAAT 57.294 30.769 0.00 0.00 0.00 2.32
2726 2857 8.576442 ACTAAAATGAGTAGGAACCAACAAATG 58.424 33.333 0.00 0.00 0.00 2.32
2741 2872 6.289745 CAACAAATGGAACCAAAACATCAG 57.710 37.500 0.00 0.00 0.00 2.90
2742 2873 5.612725 ACAAATGGAACCAAAACATCAGT 57.387 34.783 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
46 47 1.153329 CGGTTAATGGCGCCTACCA 60.153 57.895 29.70 7.47 45.82 3.25
52 53 2.195123 AAGTGCACGGTTAATGGCGC 62.195 55.000 12.01 0.00 37.05 6.53
63 64 2.544685 CCCTCTTATGAGAAGTGCACG 58.455 52.381 12.01 0.00 42.73 5.34
65 66 1.134699 CGCCCTCTTATGAGAAGTGCA 60.135 52.381 7.19 0.00 42.73 4.57
78 79 2.113243 AAAAAGTCCGAGCGCCCTCT 62.113 55.000 2.29 0.00 35.90 3.69
100 104 7.094805 GCATACATGACTAAGTGTTTCCAAGAA 60.095 37.037 0.00 0.00 0.00 2.52
106 110 6.968131 TGAGCATACATGACTAAGTGTTTC 57.032 37.500 0.00 0.00 0.00 2.78
123 127 4.558226 TTGTCCTTGAGTACATGAGCAT 57.442 40.909 0.00 0.00 0.00 3.79
135 139 0.605319 GGCGACCACATTGTCCTTGA 60.605 55.000 0.00 0.00 31.35 3.02
175 179 1.613317 AATGGACTCGCCGATCACCA 61.613 55.000 8.88 8.88 40.66 4.17
179 183 0.179084 TTGGAATGGACTCGCCGATC 60.179 55.000 0.00 0.00 40.66 3.69
205 209 9.717942 CTTGGATATACTAGCTAGCATCTTTTT 57.282 33.333 20.91 1.02 0.00 1.94
210 214 6.214191 TGCTTGGATATACTAGCTAGCATC 57.786 41.667 20.91 18.34 32.94 3.91
211 215 6.611613 TTGCTTGGATATACTAGCTAGCAT 57.388 37.500 20.91 15.82 37.26 3.79
212 216 6.042093 AGTTTGCTTGGATATACTAGCTAGCA 59.958 38.462 20.91 8.60 35.77 3.49
216 220 8.097662 GGATAAGTTTGCTTGGATATACTAGCT 58.902 37.037 20.06 4.48 36.22 3.32
217 221 8.097662 AGGATAAGTTTGCTTGGATATACTAGC 58.902 37.037 13.81 13.81 36.22 3.42
218 222 9.646427 GAGGATAAGTTTGCTTGGATATACTAG 57.354 37.037 0.00 0.00 36.22 2.57
219 223 9.381038 AGAGGATAAGTTTGCTTGGATATACTA 57.619 33.333 0.00 0.00 36.22 1.82
220 224 8.268878 AGAGGATAAGTTTGCTTGGATATACT 57.731 34.615 0.00 0.00 36.22 2.12
221 225 9.646427 CTAGAGGATAAGTTTGCTTGGATATAC 57.354 37.037 0.00 0.00 36.22 1.47
236 240 6.985653 TGTTGGGAGAATCTAGAGGATAAG 57.014 41.667 0.00 0.00 33.71 1.73
284 288 2.499289 CTGGTGAGCAAGGTGTATCTCT 59.501 50.000 0.00 0.00 0.00 3.10
285 289 2.234908 ACTGGTGAGCAAGGTGTATCTC 59.765 50.000 0.00 0.00 0.00 2.75
417 436 1.674322 GGGTGGACACGTCATTGGG 60.674 63.158 0.00 0.00 0.00 4.12
559 579 3.118629 TCAGTAGGGCAAGCTGTCTAATG 60.119 47.826 0.00 0.00 31.55 1.90
575 595 2.287427 ACCGAACACGTCAGTTCAGTAG 60.287 50.000 16.28 6.58 46.32 2.57
633 653 4.379813 GCATTTACTGACATGAACAGTGGG 60.380 45.833 27.00 18.44 46.15 4.61
698 719 5.085920 AGCTAGTGATCAGCAGGAATCTAT 58.914 41.667 8.02 0.00 41.66 1.98
708 729 3.987220 GCTAAGCTAAGCTAGTGATCAGC 59.013 47.826 0.00 0.00 38.25 4.26
732 753 4.431131 CATGTTCCGGCTGGCCCT 62.431 66.667 6.73 0.00 34.14 5.19
742 772 3.872511 TCATCACCAAATGCATGTTCC 57.127 42.857 0.00 0.00 0.00 3.62
753 783 1.918262 AGCCTGGAGAATCATCACCAA 59.082 47.619 0.00 0.00 44.33 3.67
757 787 7.278135 GCATATATAAGCCTGGAGAATCATCA 58.722 38.462 0.00 0.00 36.25 3.07
802 841 0.602638 TTTACACCTGCTCGCCAGTG 60.603 55.000 6.80 6.80 40.06 3.66
902 941 4.203076 CGATGGACCGACCGACCC 62.203 72.222 0.00 0.00 42.61 4.46
903 942 2.403671 GATCGATGGACCGACCGACC 62.404 65.000 0.54 0.00 41.70 4.79
904 943 1.008767 GATCGATGGACCGACCGAC 60.009 63.158 0.54 0.00 41.70 4.79
905 944 3.428797 GATCGATGGACCGACCGA 58.571 61.111 0.54 5.37 41.70 4.69
906 945 2.051256 CGATCGATGGACCGACCG 60.051 66.667 10.26 0.00 39.32 4.79
907 946 2.335369 CCGATCGATGGACCGACC 59.665 66.667 18.66 0.00 41.70 4.79
908 947 2.354773 GCCGATCGATGGACCGAC 60.355 66.667 18.66 0.00 41.70 4.79
909 948 3.602677 GGCCGATCGATGGACCGA 61.603 66.667 18.66 0.00 43.16 4.69
988 1027 3.809374 GATCCATGTCGACCGGGGC 62.809 68.421 14.12 6.83 0.00 5.80
989 1028 2.369257 CTGATCCATGTCGACCGGGG 62.369 65.000 14.12 11.78 0.00 5.73
990 1029 1.068083 CTGATCCATGTCGACCGGG 59.932 63.158 14.12 14.41 0.00 5.73
991 1030 0.528466 CACTGATCCATGTCGACCGG 60.528 60.000 14.12 13.81 0.00 5.28
1052 1091 3.933048 GACCCCGTCTCCGACTCCA 62.933 68.421 0.00 0.00 35.63 3.86
1092 1131 1.059058 CTTCCTCGTCGTCGTCTCG 59.941 63.158 1.33 0.00 38.33 4.04
1292 1331 2.859273 ATTTCAGGCAGCTCGGTCCG 62.859 60.000 4.39 4.39 0.00 4.79
1296 1335 4.130118 ACTAATAATTTCAGGCAGCTCGG 58.870 43.478 0.00 0.00 0.00 4.63
1297 1336 5.525378 AGAACTAATAATTTCAGGCAGCTCG 59.475 40.000 0.00 0.00 0.00 5.03
1302 1341 6.640518 ACGAGAGAACTAATAATTTCAGGCA 58.359 36.000 0.00 0.00 0.00 4.75
1312 1351 6.377429 ACATCCAGTGAACGAGAGAACTAATA 59.623 38.462 0.00 0.00 0.00 0.98
1314 1353 4.523173 ACATCCAGTGAACGAGAGAACTAA 59.477 41.667 0.00 0.00 0.00 2.24
1316 1355 2.894126 ACATCCAGTGAACGAGAGAACT 59.106 45.455 0.00 0.00 0.00 3.01
1317 1356 3.305398 ACATCCAGTGAACGAGAGAAC 57.695 47.619 0.00 0.00 0.00 3.01
1319 1358 4.462834 ACATAACATCCAGTGAACGAGAGA 59.537 41.667 0.00 0.00 0.00 3.10
1323 1362 4.888917 TGAACATAACATCCAGTGAACGA 58.111 39.130 0.00 0.00 0.00 3.85
1324 1363 5.562917 CATGAACATAACATCCAGTGAACG 58.437 41.667 0.00 0.00 0.00 3.95
1325 1364 5.335127 GCATGAACATAACATCCAGTGAAC 58.665 41.667 0.00 0.00 0.00 3.18
1326 1365 4.094739 CGCATGAACATAACATCCAGTGAA 59.905 41.667 0.00 0.00 0.00 3.18
1327 1366 3.622612 CGCATGAACATAACATCCAGTGA 59.377 43.478 0.00 0.00 0.00 3.41
1329 1368 2.355756 GCGCATGAACATAACATCCAGT 59.644 45.455 0.30 0.00 0.00 4.00
1330 1369 2.600556 CGCGCATGAACATAACATCCAG 60.601 50.000 8.75 0.00 0.00 3.86
1332 1371 1.921573 GCGCGCATGAACATAACATCC 60.922 52.381 29.10 0.00 0.00 3.51
1334 1373 1.003545 GAGCGCGCATGAACATAACAT 60.004 47.619 35.10 7.19 0.00 2.71
1336 1375 0.652592 AGAGCGCGCATGAACATAAC 59.347 50.000 35.10 10.30 0.00 1.89
1338 1377 0.460109 ACAGAGCGCGCATGAACATA 60.460 50.000 33.81 0.00 0.00 2.29
1339 1378 1.300971 AACAGAGCGCGCATGAACAT 61.301 50.000 33.81 14.56 0.00 2.71
1341 1380 1.510623 CAACAGAGCGCGCATGAAC 60.511 57.895 33.81 19.75 0.00 3.18
1342 1381 1.020861 ATCAACAGAGCGCGCATGAA 61.021 50.000 33.81 21.58 0.00 2.57
1344 1383 1.011463 GATCAACAGAGCGCGCATG 60.011 57.895 35.10 30.99 0.00 4.06
1345 1384 2.520039 CGATCAACAGAGCGCGCAT 61.520 57.895 35.10 19.25 34.23 4.73
1347 1386 1.756375 AATCGATCAACAGAGCGCGC 61.756 55.000 26.66 26.66 40.68 6.86
1350 1389 5.006649 TGGAAATAAATCGATCAACAGAGCG 59.993 40.000 0.00 0.00 42.11 5.03
1354 1393 6.017605 CCCTCTGGAAATAAATCGATCAACAG 60.018 42.308 0.00 1.47 0.00 3.16
1356 1395 5.823045 ACCCTCTGGAAATAAATCGATCAAC 59.177 40.000 0.00 0.00 34.81 3.18
1364 1403 4.860022 CTCACCACCCTCTGGAAATAAAT 58.140 43.478 0.00 0.00 43.95 1.40
1365 1404 3.561313 GCTCACCACCCTCTGGAAATAAA 60.561 47.826 0.00 0.00 43.95 1.40
1366 1405 2.026262 GCTCACCACCCTCTGGAAATAA 60.026 50.000 0.00 0.00 43.95 1.40
1367 1406 1.559682 GCTCACCACCCTCTGGAAATA 59.440 52.381 0.00 0.00 43.95 1.40
1368 1407 0.329596 GCTCACCACCCTCTGGAAAT 59.670 55.000 0.00 0.00 43.95 2.17
1433 1472 2.125912 GCTCATGCCGTCGACACT 60.126 61.111 17.16 0.00 0.00 3.55
1435 1474 2.181777 GAGCTCATGCCGTCGACA 59.818 61.111 17.16 0.00 40.80 4.35
1525 1567 1.462616 TATACGCGGTGGTGTACAGT 58.537 50.000 12.47 0.00 41.58 3.55
1527 1569 1.135141 GGTTATACGCGGTGGTGTACA 60.135 52.381 12.47 0.00 41.58 2.90
1529 1571 1.180907 TGGTTATACGCGGTGGTGTA 58.819 50.000 12.47 0.00 42.83 2.90
1530 1572 0.538118 ATGGTTATACGCGGTGGTGT 59.462 50.000 12.47 0.00 40.64 4.16
1531 1573 2.129607 GTATGGTTATACGCGGTGGTG 58.870 52.381 12.47 0.00 30.68 4.17
1532 1574 2.514205 GTATGGTTATACGCGGTGGT 57.486 50.000 12.47 0.00 30.68 4.16
1540 1582 8.758633 AGCATATCTTGTTCGTATGGTTATAC 57.241 34.615 0.00 0.00 34.04 1.47
1541 1583 9.419297 GAAGCATATCTTGTTCGTATGGTTATA 57.581 33.333 8.47 0.00 42.93 0.98
1542 1584 7.116376 CGAAGCATATCTTGTTCGTATGGTTAT 59.884 37.037 8.47 0.00 42.93 1.89
1543 1585 6.419710 CGAAGCATATCTTGTTCGTATGGTTA 59.580 38.462 8.47 0.00 42.93 2.85
1544 1586 5.234329 CGAAGCATATCTTGTTCGTATGGTT 59.766 40.000 8.29 8.29 44.51 3.67
1545 1587 4.745125 CGAAGCATATCTTGTTCGTATGGT 59.255 41.667 0.00 0.00 37.95 3.55
1546 1588 4.982295 TCGAAGCATATCTTGTTCGTATGG 59.018 41.667 3.54 0.00 38.66 2.74
1547 1589 6.417930 TCTTCGAAGCATATCTTGTTCGTATG 59.582 38.462 20.56 0.00 38.66 2.39
1548 1590 6.504398 TCTTCGAAGCATATCTTGTTCGTAT 58.496 36.000 20.56 0.00 38.66 3.06
1549 1591 5.886992 TCTTCGAAGCATATCTTGTTCGTA 58.113 37.500 20.56 0.00 38.66 3.43
1550 1592 4.744570 TCTTCGAAGCATATCTTGTTCGT 58.255 39.130 20.56 0.00 38.66 3.85
1551 1593 5.037385 TCTCTTCGAAGCATATCTTGTTCG 58.963 41.667 20.56 0.00 38.78 3.95
1552 1594 6.699204 TGATCTCTTCGAAGCATATCTTGTTC 59.301 38.462 20.56 5.86 34.56 3.18
1702 1770 6.272318 ACGACTGCAAATTCATCAAAAAGAA 58.728 32.000 0.00 0.00 0.00 2.52
1780 1849 4.933064 GGAGAGATCACCGCGGCG 62.933 72.222 28.58 18.04 0.00 6.46
1818 1887 0.250553 TCAAACGAATTCCCGCCACT 60.251 50.000 0.00 0.00 0.00 4.00
1825 1895 1.654023 CCGGGCCTCAAACGAATTCC 61.654 60.000 0.84 0.00 0.00 3.01
1827 1897 2.340328 GCCGGGCCTCAAACGAATT 61.340 57.895 8.12 0.00 0.00 2.17
1860 1930 0.832626 TGTGATCATGCCTGGACGAT 59.167 50.000 0.00 0.00 0.00 3.73
1867 1937 3.504906 CAGAAACTTGTGTGATCATGCCT 59.495 43.478 0.00 0.00 0.00 4.75
1943 2023 7.542025 AGAAGCAAAATCAGCCTTTACAATAG 58.458 34.615 0.00 0.00 0.00 1.73
2079 2159 9.713713 TTGCAATACTACAAATCTGTACAGTAA 57.286 29.630 21.99 4.68 32.77 2.24
2081 2161 7.148407 GCTTGCAATACTACAAATCTGTACAGT 60.148 37.037 21.99 6.36 36.96 3.55
2082 2162 7.148423 TGCTTGCAATACTACAAATCTGTACAG 60.148 37.037 17.17 17.17 36.96 2.74
2083 2163 6.652900 TGCTTGCAATACTACAAATCTGTACA 59.347 34.615 0.00 0.00 36.96 2.90
2084 2164 7.072177 TGCTTGCAATACTACAAATCTGTAC 57.928 36.000 0.00 0.00 36.96 2.90
2085 2165 7.864108 ATGCTTGCAATACTACAAATCTGTA 57.136 32.000 0.00 0.00 36.96 2.74
2100 2180 5.414789 TTCTGGTACTAGTATGCTTGCAA 57.585 39.130 5.75 0.00 0.00 4.08
2128 2235 7.162082 AGGTGAGTTCTATCAAAAGTACCTTG 58.838 38.462 0.00 0.00 0.00 3.61
2131 2238 7.981102 AAAGGTGAGTTCTATCAAAAGTACC 57.019 36.000 0.00 0.00 0.00 3.34
2156 2263 8.248253 GTGTACCAAAAGAATCCCGATAAATTT 58.752 33.333 0.00 0.00 0.00 1.82
2162 2269 4.295141 TGTGTACCAAAAGAATCCCGAT 57.705 40.909 0.00 0.00 0.00 4.18
2193 2300 2.392662 TGTTCAGGCAATTTGACCCAA 58.607 42.857 0.00 0.00 0.00 4.12
2199 2306 7.546316 TCATATCATGTTTGTTCAGGCAATTTG 59.454 33.333 0.00 0.00 0.00 2.32
2206 2313 6.375174 TGGAAGTCATATCATGTTTGTTCAGG 59.625 38.462 0.00 0.00 0.00 3.86
2269 2376 4.742417 CCCAATCATTGCACGACAAAATA 58.258 39.130 0.00 0.00 42.86 1.40
2295 2402 1.893137 AGTGATCTACGAACACTGCCA 59.107 47.619 6.06 0.00 42.52 4.92
2332 2439 6.418226 GCTTTGATCTCAGATTGCATGAATTC 59.582 38.462 0.00 0.00 0.00 2.17
2374 2481 9.353999 GTATGTTTGTGAAATGGTTATTCTTCC 57.646 33.333 0.00 0.00 0.00 3.46
2407 2514 7.848223 TGTAATAACATGGTTCATCTCAGTG 57.152 36.000 0.00 0.00 0.00 3.66
2411 2518 8.391106 GTGACTTGTAATAACATGGTTCATCTC 58.609 37.037 0.00 0.00 35.59 2.75
2442 2549 1.273327 CAGGAGGTTGGGAAAATGTGC 59.727 52.381 0.00 0.00 0.00 4.57
2471 2602 9.438228 AGACTCATGCAGAAGAATTATATGATG 57.562 33.333 5.21 0.00 0.00 3.07
2475 2606 8.591940 TGCTAGACTCATGCAGAAGAATTATAT 58.408 33.333 5.21 0.00 32.55 0.86
2491 2622 0.251209 ACACCGACCTGCTAGACTCA 60.251 55.000 0.00 0.00 0.00 3.41
2495 2626 2.044555 CCGACACCGACCTGCTAGA 61.045 63.158 0.00 0.00 38.22 2.43
2497 2628 3.755628 GCCGACACCGACCTGCTA 61.756 66.667 0.00 0.00 38.22 3.49
2505 2636 3.179265 GATCACGTGCCGACACCG 61.179 66.667 11.67 0.00 44.40 4.94
2523 2654 7.005296 CCCTTATACACACTACCATAGAGTCT 58.995 42.308 0.00 0.00 0.00 3.24
2535 2666 2.172717 GGCATGGACCCTTATACACACT 59.827 50.000 0.00 0.00 0.00 3.55
2537 2668 2.200955 TGGCATGGACCCTTATACACA 58.799 47.619 0.00 0.00 0.00 3.72
2541 2672 2.875296 GCAATGGCATGGACCCTTATA 58.125 47.619 5.91 0.00 40.72 0.98
2542 2673 1.708341 GCAATGGCATGGACCCTTAT 58.292 50.000 5.91 0.00 40.72 1.73
2543 2674 3.205815 GCAATGGCATGGACCCTTA 57.794 52.632 5.91 0.00 40.72 2.69
2555 2686 0.107508 ATCCTCCGAGTGTGCAATGG 60.108 55.000 0.00 0.00 0.00 3.16
2562 2693 2.100989 GAGGTTGTATCCTCCGAGTGT 58.899 52.381 1.70 0.00 45.84 3.55
2580 2711 1.475403 ACCCTCATGTCGGTACAGAG 58.525 55.000 0.00 0.00 39.49 3.35
2586 2717 1.339727 GCCTAAAACCCTCATGTCGGT 60.340 52.381 1.20 1.20 0.00 4.69
2587 2718 1.379527 GCCTAAAACCCTCATGTCGG 58.620 55.000 0.00 0.00 0.00 4.79
2619 2750 2.224892 GGCCCTGGAAGTCTTTTCTTCT 60.225 50.000 0.00 0.00 42.19 2.85
2622 2753 1.074566 CTGGCCCTGGAAGTCTTTTCT 59.925 52.381 0.00 0.00 0.00 2.52
2626 2757 1.742308 TTACTGGCCCTGGAAGTCTT 58.258 50.000 0.00 0.00 0.00 3.01
2629 2760 1.780919 AGTTTTACTGGCCCTGGAAGT 59.219 47.619 0.00 0.00 0.00 3.01
2633 2764 2.162681 CAGAAGTTTTACTGGCCCTGG 58.837 52.381 0.00 0.00 0.00 4.45
2643 2774 6.376018 AGTTACAACCAGTTGCAGAAGTTTTA 59.624 34.615 10.39 0.00 44.03 1.52
2644 2775 5.185056 AGTTACAACCAGTTGCAGAAGTTTT 59.815 36.000 10.39 0.00 44.03 2.43
2645 2776 4.705023 AGTTACAACCAGTTGCAGAAGTTT 59.295 37.500 10.39 0.00 44.03 2.66
2646 2777 4.270008 AGTTACAACCAGTTGCAGAAGTT 58.730 39.130 10.39 0.00 44.03 2.66
2647 2778 3.886123 AGTTACAACCAGTTGCAGAAGT 58.114 40.909 10.39 3.34 44.03 3.01
2648 2779 4.900635 AAGTTACAACCAGTTGCAGAAG 57.099 40.909 10.39 0.00 44.03 2.85
2649 2780 5.652994 AAAAGTTACAACCAGTTGCAGAA 57.347 34.783 10.39 0.45 44.03 3.02
2650 2781 6.952773 ATAAAAGTTACAACCAGTTGCAGA 57.047 33.333 10.39 0.00 44.03 4.26
2651 2782 7.920682 AGAAATAAAAGTTACAACCAGTTGCAG 59.079 33.333 10.39 0.00 44.03 4.41
2652 2783 7.777095 AGAAATAAAAGTTACAACCAGTTGCA 58.223 30.769 10.39 0.00 44.03 4.08
2653 2784 7.381408 GGAGAAATAAAAGTTACAACCAGTTGC 59.619 37.037 10.39 0.00 44.03 4.17
2654 2785 8.410141 TGGAGAAATAAAAGTTACAACCAGTTG 58.590 33.333 8.95 8.95 45.58 3.16
2655 2786 8.528044 TGGAGAAATAAAAGTTACAACCAGTT 57.472 30.769 0.00 0.00 0.00 3.16
2656 2787 8.706322 ATGGAGAAATAAAAGTTACAACCAGT 57.294 30.769 0.00 0.00 0.00 4.00
2658 2789 9.802039 ACTATGGAGAAATAAAAGTTACAACCA 57.198 29.630 0.00 0.00 0.00 3.67
2665 2796 9.239551 GGGTTGTACTATGGAGAAATAAAAGTT 57.760 33.333 0.00 0.00 0.00 2.66
2666 2797 8.612145 AGGGTTGTACTATGGAGAAATAAAAGT 58.388 33.333 0.00 0.00 0.00 2.66
2669 2800 9.496710 TCTAGGGTTGTACTATGGAGAAATAAA 57.503 33.333 0.00 0.00 0.00 1.40
2670 2801 9.496710 TTCTAGGGTTGTACTATGGAGAAATAA 57.503 33.333 0.00 0.00 0.00 1.40
2671 2802 9.670442 ATTCTAGGGTTGTACTATGGAGAAATA 57.330 33.333 0.00 0.00 0.00 1.40
2672 2803 7.989947 TTCTAGGGTTGTACTATGGAGAAAT 57.010 36.000 0.00 0.00 0.00 2.17
2673 2804 7.622081 TCATTCTAGGGTTGTACTATGGAGAAA 59.378 37.037 0.00 0.00 0.00 2.52
2674 2805 7.130099 TCATTCTAGGGTTGTACTATGGAGAA 58.870 38.462 0.00 0.00 0.00 2.87
2675 2806 6.679542 TCATTCTAGGGTTGTACTATGGAGA 58.320 40.000 0.00 0.00 0.00 3.71
2676 2807 6.978674 TCATTCTAGGGTTGTACTATGGAG 57.021 41.667 0.00 0.00 0.00 3.86
2677 2808 6.901300 AGTTCATTCTAGGGTTGTACTATGGA 59.099 38.462 0.00 0.00 0.00 3.41
2678 2809 7.125792 AGTTCATTCTAGGGTTGTACTATGG 57.874 40.000 0.00 0.00 0.00 2.74
2682 2813 9.449719 CATTTTAGTTCATTCTAGGGTTGTACT 57.550 33.333 0.00 0.00 0.00 2.73
2683 2814 9.444600 TCATTTTAGTTCATTCTAGGGTTGTAC 57.555 33.333 0.00 0.00 0.00 2.90
2684 2815 9.667107 CTCATTTTAGTTCATTCTAGGGTTGTA 57.333 33.333 0.00 0.00 0.00 2.41
2685 2816 8.164070 ACTCATTTTAGTTCATTCTAGGGTTGT 58.836 33.333 0.00 0.00 0.00 3.32
2686 2817 8.567285 ACTCATTTTAGTTCATTCTAGGGTTG 57.433 34.615 0.00 0.00 0.00 3.77
2687 2818 9.892130 CTACTCATTTTAGTTCATTCTAGGGTT 57.108 33.333 0.00 0.00 0.00 4.11
2688 2819 8.487028 CCTACTCATTTTAGTTCATTCTAGGGT 58.513 37.037 0.00 0.00 0.00 4.34
2689 2820 8.705594 TCCTACTCATTTTAGTTCATTCTAGGG 58.294 37.037 0.00 0.00 0.00 3.53
2692 2823 9.886132 GGTTCCTACTCATTTTAGTTCATTCTA 57.114 33.333 0.00 0.00 0.00 2.10
2693 2824 8.383175 TGGTTCCTACTCATTTTAGTTCATTCT 58.617 33.333 0.00 0.00 0.00 2.40
2694 2825 8.561738 TGGTTCCTACTCATTTTAGTTCATTC 57.438 34.615 0.00 0.00 0.00 2.67
2695 2826 8.793592 GTTGGTTCCTACTCATTTTAGTTCATT 58.206 33.333 0.00 0.00 0.00 2.57
2696 2827 7.942341 TGTTGGTTCCTACTCATTTTAGTTCAT 59.058 33.333 5.23 0.00 0.00 2.57
2697 2828 7.284074 TGTTGGTTCCTACTCATTTTAGTTCA 58.716 34.615 5.23 0.00 0.00 3.18
2698 2829 7.739498 TGTTGGTTCCTACTCATTTTAGTTC 57.261 36.000 5.23 0.00 0.00 3.01
2699 2830 8.528044 TTTGTTGGTTCCTACTCATTTTAGTT 57.472 30.769 5.23 0.00 0.00 2.24
2700 2831 8.576442 CATTTGTTGGTTCCTACTCATTTTAGT 58.424 33.333 5.23 0.00 0.00 2.24
2701 2832 8.028938 CCATTTGTTGGTTCCTACTCATTTTAG 58.971 37.037 5.23 0.00 40.99 1.85
2702 2833 7.726291 TCCATTTGTTGGTTCCTACTCATTTTA 59.274 33.333 5.23 0.00 46.52 1.52
2703 2834 6.553100 TCCATTTGTTGGTTCCTACTCATTTT 59.447 34.615 5.23 0.00 46.52 1.82
2704 2835 6.074648 TCCATTTGTTGGTTCCTACTCATTT 58.925 36.000 5.23 0.00 46.52 2.32
2705 2836 5.640147 TCCATTTGTTGGTTCCTACTCATT 58.360 37.500 5.23 0.00 46.52 2.57
2706 2837 5.255397 TCCATTTGTTGGTTCCTACTCAT 57.745 39.130 5.23 0.00 46.52 2.90
2707 2838 4.715534 TCCATTTGTTGGTTCCTACTCA 57.284 40.909 5.23 0.00 46.52 3.41
2708 2839 4.217767 GGTTCCATTTGTTGGTTCCTACTC 59.782 45.833 5.23 0.00 46.52 2.59
2709 2840 4.149598 GGTTCCATTTGTTGGTTCCTACT 58.850 43.478 5.23 0.00 46.52 2.57
2710 2841 3.892588 TGGTTCCATTTGTTGGTTCCTAC 59.107 43.478 0.00 0.00 46.52 3.18
2711 2842 4.186077 TGGTTCCATTTGTTGGTTCCTA 57.814 40.909 0.00 0.00 46.52 2.94
2712 2843 3.039252 TGGTTCCATTTGTTGGTTCCT 57.961 42.857 0.00 0.00 46.52 3.36
2713 2844 3.828875 TTGGTTCCATTTGTTGGTTCC 57.171 42.857 0.00 0.00 46.52 3.62
2714 2845 4.938226 TGTTTTGGTTCCATTTGTTGGTTC 59.062 37.500 0.00 0.00 46.52 3.62
2715 2846 4.911390 TGTTTTGGTTCCATTTGTTGGTT 58.089 34.783 0.00 0.00 46.52 3.67
2716 2847 4.559862 TGTTTTGGTTCCATTTGTTGGT 57.440 36.364 0.00 0.00 46.52 3.67
2718 2849 5.816777 ACTGATGTTTTGGTTCCATTTGTTG 59.183 36.000 0.00 0.00 0.00 3.33
2719 2850 5.988287 ACTGATGTTTTGGTTCCATTTGTT 58.012 33.333 0.00 0.00 0.00 2.83
2720 2851 5.612725 ACTGATGTTTTGGTTCCATTTGT 57.387 34.783 0.00 0.00 0.00 2.83


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

AutoCloner maintained by Alex Coulton.