Multiple sequence alignment - TraesCS4D01G235000

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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 TraesCS4D01G235000 chr4D 100.000 4395 0 0 1 4395 395385008 395380614 0.000000e+00 8117.0
1 TraesCS4D01G235000 chr4D 75.000 952 191 40 2105 3025 7898553 7897618 3.190000e-106 396.0
2 TraesCS4D01G235000 chr4A 95.305 2364 83 11 2049 4395 76942627 76940275 0.000000e+00 3725.0
3 TraesCS4D01G235000 chr4A 92.676 751 40 8 38 774 76944632 76943883 0.000000e+00 1068.0
4 TraesCS4D01G235000 chr4A 79.161 787 69 42 1237 1947 76943421 76942654 1.440000e-124 457.0
5 TraesCS4D01G235000 chr4A 75.732 956 183 40 2105 3025 595417817 595418758 6.750000e-118 435.0
6 TraesCS4D01G235000 chr4A 92.245 245 9 5 950 1184 76943852 76943608 5.440000e-89 339.0
7 TraesCS4D01G235000 chr4A 94.118 68 4 0 124 191 211380433 211380366 2.160000e-18 104.0
8 TraesCS4D01G235000 chr4B 94.723 1137 44 6 2478 3602 486284813 486283681 0.000000e+00 1753.0
9 TraesCS4D01G235000 chr4B 96.629 801 21 3 3600 4395 486283599 486282800 0.000000e+00 1325.0
10 TraesCS4D01G235000 chr4B 88.806 670 39 9 4 657 486287734 486287085 0.000000e+00 789.0
11 TraesCS4D01G235000 chr4B 92.823 418 28 2 2056 2472 486285324 486284908 4.860000e-169 604.0
12 TraesCS4D01G235000 chr4B 78.293 949 188 17 2089 3025 42394985 42395927 2.930000e-166 595.0
13 TraesCS4D01G235000 chr4B 75.261 958 187 42 2105 3025 14266422 14267366 1.140000e-110 411.0
14 TraesCS4D01G235000 chr4B 81.383 564 51 22 1426 1947 486285932 486285381 1.140000e-110 411.0
15 TraesCS4D01G235000 chr4B 93.548 62 4 0 719 780 486286990 486286929 4.680000e-15 93.5
16 TraesCS4D01G235000 chr6A 97.059 68 2 0 124 191 596907209 596907276 9.990000e-22 115.0
17 TraesCS4D01G235000 chr6A 92.647 68 5 0 125 192 557984856 557984923 1.010000e-16 99.0
18 TraesCS4D01G235000 chr6A 92.188 64 5 0 51 114 58051135 58051072 1.680000e-14 91.6
19 TraesCS4D01G235000 chr3A 97.059 68 2 0 124 191 64320883 64320816 9.990000e-22 115.0
20 TraesCS4D01G235000 chr1B 94.203 69 4 0 124 192 430157906 430157974 6.010000e-19 106.0
21 TraesCS4D01G235000 chr1B 92.188 64 5 0 51 114 430157858 430157921 1.680000e-14 91.6
22 TraesCS4D01G235000 chr2A 92.754 69 4 1 124 191 543622907 543622839 1.010000e-16 99.0
23 TraesCS4D01G235000 chr1D 93.846 65 3 1 50 113 285439494 285439558 3.620000e-16 97.1
24 TraesCS4D01G235000 chr6D 91.176 68 6 0 124 191 266648439 266648506 4.680000e-15 93.5
25 TraesCS4D01G235000 chr5D 93.548 62 4 0 124 185 303941672 303941733 4.680000e-15 93.5
26 TraesCS4D01G235000 chr5D 90.909 66 6 0 49 114 418946194 418946129 6.050000e-14 89.8
27 TraesCS4D01G235000 chr7D 92.188 64 5 0 51 114 631250897 631250834 1.680000e-14 91.6
28 TraesCS4D01G235000 chr7B 92.308 65 4 1 51 114 387633192 387633256 1.680000e-14 91.6
29 TraesCS4D01G235000 chr3B 92.188 64 4 1 51 114 829020336 829020398 6.050000e-14 89.8
30 TraesCS4D01G235000 chr1A 88.889 72 7 1 43 114 287694042 287693972 2.180000e-13 87.9


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4D01G235000 chr4D 395380614 395385008 4394 True 8117.00 8117 100.000000 1 4395 1 chr4D.!!$R2 4394
1 TraesCS4D01G235000 chr4D 7897618 7898553 935 True 396.00 396 75.000000 2105 3025 1 chr4D.!!$R1 920
2 TraesCS4D01G235000 chr4A 76940275 76944632 4357 True 1397.25 3725 89.846750 38 4395 4 chr4A.!!$R2 4357
3 TraesCS4D01G235000 chr4A 595417817 595418758 941 False 435.00 435 75.732000 2105 3025 1 chr4A.!!$F1 920
4 TraesCS4D01G235000 chr4B 486282800 486287734 4934 True 829.25 1753 91.318667 4 4395 6 chr4B.!!$R1 4391
5 TraesCS4D01G235000 chr4B 42394985 42395927 942 False 595.00 595 78.293000 2089 3025 1 chr4B.!!$F2 936
6 TraesCS4D01G235000 chr4B 14266422 14267366 944 False 411.00 411 75.261000 2105 3025 1 chr4B.!!$F1 920

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
848 943 0.307760 CGTGCAGTCGCCTTCTTTTT 59.692 50.0 0.00 0.0 37.32 1.94 F
1122 1322 0.025001 CAGCGCCGTTCAGTAATTCG 59.975 55.0 2.29 0.0 0.00 3.34 F
1758 2267 0.036164 TGCGTATCAACAAGGCACCT 59.964 50.0 0.00 0.0 33.17 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2080 2644 0.732880 ACTGCGACGCTGTGTACATC 60.733 55.000 28.26 0.0 39.15 3.06 R
2110 2674 1.064654 GCGATCGTCCCGTAGTTTACT 59.935 52.381 17.81 0.0 0.00 2.24 R
3681 4456 2.253452 GTCTTGTTGCTGGCTGCG 59.747 61.111 11.85 0.0 46.63 5.18 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
23 24 3.058224 GTGAGGAATTTGACGTCTTTGGG 60.058 47.826 17.92 0.00 0.00 4.12
49 50 8.882415 ACGGTCAAATATTAGTAGTATGTTGG 57.118 34.615 0.00 0.00 0.00 3.77
68 70 1.003233 GGTACTCCCTGTGGTCCTTTG 59.997 57.143 0.00 0.00 0.00 2.77
88 97 8.946085 TCCTTTGTAGTCTGCATATAAGTTTTG 58.054 33.333 0.00 0.00 0.00 2.44
107 116 8.974060 AGTTTTGTCCAAAGTCAAAGTATCTA 57.026 30.769 0.00 0.00 33.54 1.98
201 211 6.461370 GCCAAATCAATATTGCCACTATCACA 60.461 38.462 10.76 0.00 0.00 3.58
206 216 5.942826 TCAATATTGCCACTATCACACACAA 59.057 36.000 10.76 0.00 0.00 3.33
217 227 2.176926 ACACACAACACGCATCGCA 61.177 52.632 0.00 0.00 0.00 5.10
234 244 1.725931 CGCAAGGAATTTGACGTCAGC 60.726 52.381 19.11 14.47 39.21 4.26
235 245 1.725931 GCAAGGAATTTGACGTCAGCG 60.726 52.381 19.11 3.67 39.21 5.18
256 266 0.601057 TCAGACGCTCATCGACCAAA 59.399 50.000 0.00 0.00 41.67 3.28
342 354 1.915078 AATCACCCCGGCTGAAGGAG 61.915 60.000 8.43 1.15 0.00 3.69
367 379 2.256461 GTGGCAGGCGCTTTTCAG 59.744 61.111 7.64 0.00 38.60 3.02
392 404 1.350019 CATCATGCTCTCCCTGGCATA 59.650 52.381 0.00 0.00 45.82 3.14
537 549 4.474846 CCGTTGCGCAAATCCGGG 62.475 66.667 31.78 21.17 35.11 5.73
774 840 6.534634 GTTTTGGGTGGCTATATATCTGTCT 58.465 40.000 0.00 0.00 0.00 3.41
775 841 5.745312 TTGGGTGGCTATATATCTGTCTG 57.255 43.478 0.00 0.00 0.00 3.51
780 846 4.017126 TGGCTATATATCTGTCTGTCCCG 58.983 47.826 0.00 0.00 0.00 5.14
809 904 4.038080 GGCGCCCCGAAAACACAG 62.038 66.667 18.11 0.00 0.00 3.66
814 909 2.593436 CCCGAAAACACAGGCGGT 60.593 61.111 0.00 0.00 42.08 5.68
816 911 2.549282 CGAAAACACAGGCGGTCG 59.451 61.111 0.00 0.00 0.00 4.79
842 937 3.649986 GCAACGTGCAGTCGCCTT 61.650 61.111 0.00 0.00 44.26 4.35
843 938 2.551270 CAACGTGCAGTCGCCTTC 59.449 61.111 0.00 0.00 37.32 3.46
844 939 1.956170 CAACGTGCAGTCGCCTTCT 60.956 57.895 0.00 0.00 37.32 2.85
845 940 1.227556 AACGTGCAGTCGCCTTCTT 60.228 52.632 0.00 0.00 37.32 2.52
847 942 0.814010 ACGTGCAGTCGCCTTCTTTT 60.814 50.000 0.00 0.00 37.32 2.27
848 943 0.307760 CGTGCAGTCGCCTTCTTTTT 59.692 50.000 0.00 0.00 37.32 1.94
852 947 0.954452 CAGTCGCCTTCTTTTTGCCT 59.046 50.000 0.00 0.00 0.00 4.75
853 948 1.338020 CAGTCGCCTTCTTTTTGCCTT 59.662 47.619 0.00 0.00 0.00 4.35
854 949 1.338020 AGTCGCCTTCTTTTTGCCTTG 59.662 47.619 0.00 0.00 0.00 3.61
855 950 1.067060 GTCGCCTTCTTTTTGCCTTGT 59.933 47.619 0.00 0.00 0.00 3.16
860 1043 4.661125 GCCTTCTTTTTGCCTTGTTTTTG 58.339 39.130 0.00 0.00 0.00 2.44
883 1066 4.798682 GAGGGCCGAGGAGGGGAA 62.799 72.222 0.00 0.00 41.48 3.97
884 1067 4.348495 AGGGCCGAGGAGGGGAAA 62.348 66.667 0.00 0.00 41.48 3.13
886 1069 4.468689 GGCCGAGGAGGGGAAACG 62.469 72.222 0.00 0.00 41.48 3.60
887 1070 4.468689 GCCGAGGAGGGGAAACGG 62.469 72.222 0.00 0.00 45.26 4.44
888 1071 4.468689 CCGAGGAGGGGAAACGGC 62.469 72.222 0.00 0.00 37.32 5.68
889 1072 4.814294 CGAGGAGGGGAAACGGCG 62.814 72.222 4.80 4.80 0.00 6.46
890 1073 4.468689 GAGGAGGGGAAACGGCGG 62.469 72.222 13.24 0.00 0.00 6.13
898 1081 2.358984 GAAACGGCGGCCCAAGTA 60.359 61.111 14.55 0.00 0.00 2.24
899 1082 1.967494 GAAACGGCGGCCCAAGTAA 60.967 57.895 14.55 0.00 0.00 2.24
905 1088 2.818274 CGGCCCAAGTAACGCCTC 60.818 66.667 0.00 0.00 40.70 4.70
906 1089 2.818274 GGCCCAAGTAACGCCTCG 60.818 66.667 0.00 0.00 39.70 4.63
915 1100 3.672255 TAACGCCTCGCCTTCGTCG 62.672 63.158 0.00 0.00 35.18 5.12
922 1107 4.421479 CGCCTTCGTCGTCTGCCT 62.421 66.667 0.00 0.00 0.00 4.75
929 1114 2.508891 CGTCGTCTGCCTCGCATTC 61.509 63.158 0.00 0.00 38.13 2.67
938 1123 0.603975 GCCTCGCATTCCCATAGTCC 60.604 60.000 0.00 0.00 0.00 3.85
941 1126 1.688735 CTCGCATTCCCATAGTCCTCA 59.311 52.381 0.00 0.00 0.00 3.86
942 1127 2.103094 CTCGCATTCCCATAGTCCTCAA 59.897 50.000 0.00 0.00 0.00 3.02
943 1128 2.503765 TCGCATTCCCATAGTCCTCAAA 59.496 45.455 0.00 0.00 0.00 2.69
944 1129 2.874701 CGCATTCCCATAGTCCTCAAAG 59.125 50.000 0.00 0.00 0.00 2.77
945 1130 2.620585 GCATTCCCATAGTCCTCAAAGC 59.379 50.000 0.00 0.00 0.00 3.51
946 1131 3.889815 CATTCCCATAGTCCTCAAAGCA 58.110 45.455 0.00 0.00 0.00 3.91
947 1132 3.634397 TTCCCATAGTCCTCAAAGCAG 57.366 47.619 0.00 0.00 0.00 4.24
948 1133 1.839994 TCCCATAGTCCTCAAAGCAGG 59.160 52.381 0.00 0.00 34.40 4.85
984 1181 1.210931 CGGCATCAAGTGGTTGCAG 59.789 57.895 3.02 0.00 38.12 4.41
1080 1280 2.124942 GGCGCCTTCCTCTTCCAG 60.125 66.667 22.15 0.00 0.00 3.86
1121 1321 0.373716 CCAGCGCCGTTCAGTAATTC 59.626 55.000 2.29 0.00 0.00 2.17
1122 1322 0.025001 CAGCGCCGTTCAGTAATTCG 59.975 55.000 2.29 0.00 0.00 3.34
1125 1325 0.297820 CGCCGTTCAGTAATTCGCTC 59.702 55.000 0.00 0.00 0.00 5.03
1126 1326 1.355971 GCCGTTCAGTAATTCGCTCA 58.644 50.000 0.00 0.00 0.00 4.26
1127 1327 1.324736 GCCGTTCAGTAATTCGCTCAG 59.675 52.381 0.00 0.00 0.00 3.35
1129 1329 3.766151 CCGTTCAGTAATTCGCTCAGTA 58.234 45.455 0.00 0.00 0.00 2.74
1184 1449 3.198409 TGCTTGCTCTTCTTGAGAACA 57.802 42.857 0.00 0.00 45.39 3.18
1190 1564 6.143598 GCTTGCTCTTCTTGAGAACAATTTTC 59.856 38.462 0.00 0.00 45.39 2.29
1198 1572 8.864069 TTCTTGAGAACAATTTTCGCATTTTA 57.136 26.923 7.30 0.00 35.37 1.52
1200 1574 8.349245 TCTTGAGAACAATTTTCGCATTTTAGA 58.651 29.630 7.30 5.54 35.37 2.10
1201 1575 8.864069 TTGAGAACAATTTTCGCATTTTAGAA 57.136 26.923 7.30 0.00 0.00 2.10
1202 1576 8.280909 TGAGAACAATTTTCGCATTTTAGAAC 57.719 30.769 3.85 0.00 0.00 3.01
1203 1577 7.918033 TGAGAACAATTTTCGCATTTTAGAACA 59.082 29.630 3.85 0.00 0.00 3.18
1204 1578 8.641499 AGAACAATTTTCGCATTTTAGAACAA 57.359 26.923 0.00 0.00 0.00 2.83
1260 1703 0.814010 ACGTGGCAAGTCACTGAACC 60.814 55.000 0.00 0.00 35.63 3.62
1310 1756 4.034510 GCACAGCTATGCTAACCTAAAGTG 59.965 45.833 10.42 0.00 42.62 3.16
1312 1758 3.561725 CAGCTATGCTAACCTAAAGTGGC 59.438 47.826 0.00 0.00 36.40 5.01
1313 1759 3.456277 AGCTATGCTAACCTAAAGTGGCT 59.544 43.478 0.00 0.00 36.99 4.75
1314 1760 3.810386 GCTATGCTAACCTAAAGTGGCTC 59.190 47.826 0.00 0.00 0.00 4.70
1315 1761 2.380084 TGCTAACCTAAAGTGGCTCG 57.620 50.000 0.00 0.00 0.00 5.03
1316 1762 1.066430 TGCTAACCTAAAGTGGCTCGG 60.066 52.381 0.00 0.00 0.00 4.63
1317 1763 1.206371 GCTAACCTAAAGTGGCTCGGA 59.794 52.381 0.00 0.00 0.00 4.55
1318 1764 2.158943 GCTAACCTAAAGTGGCTCGGAT 60.159 50.000 0.00 0.00 0.00 4.18
1319 1765 2.693267 AACCTAAAGTGGCTCGGATC 57.307 50.000 0.00 0.00 0.00 3.36
1320 1766 1.867363 ACCTAAAGTGGCTCGGATCT 58.133 50.000 0.00 0.00 0.00 2.75
1331 1777 2.360844 GCTCGGATCTCGGATCTCATA 58.639 52.381 11.91 0.00 39.77 2.15
1333 1779 3.426963 GCTCGGATCTCGGATCTCATAAC 60.427 52.174 11.91 0.00 39.77 1.89
1392 1838 4.081309 TCCCCAACGGTAGAGAAATACAAG 60.081 45.833 0.00 0.00 0.00 3.16
1433 1921 4.623932 TCCTCCTTCATCATATTTCCCG 57.376 45.455 0.00 0.00 0.00 5.14
1468 1956 4.715713 AGAAAGGAGTCACTTTTGGGTAC 58.284 43.478 7.69 0.00 40.55 3.34
1486 1974 1.291877 ACGCTGTCAAAGACGATGCC 61.292 55.000 0.00 0.00 34.95 4.40
1512 2000 2.240493 AAATCATGATCCCGACCGAC 57.760 50.000 9.06 0.00 0.00 4.79
1645 2133 0.661187 CAACCTCACATGCACGTTGC 60.661 55.000 0.00 3.44 45.29 4.17
1689 2181 1.566018 CTTTGACCGCTGTCCGAACC 61.566 60.000 5.77 0.00 41.01 3.62
1690 2182 3.851845 TTGACCGCTGTCCGAACCG 62.852 63.158 5.77 0.00 41.01 4.44
1716 2221 5.215845 TGGTCATCATGGAATCTAGTGGTA 58.784 41.667 0.00 0.00 0.00 3.25
1717 2222 5.070446 TGGTCATCATGGAATCTAGTGGTAC 59.930 44.000 0.00 0.00 0.00 3.34
1718 2223 5.070446 GGTCATCATGGAATCTAGTGGTACA 59.930 44.000 0.00 0.00 0.00 2.90
1719 2224 6.219473 GTCATCATGGAATCTAGTGGTACAG 58.781 44.000 0.00 0.00 41.80 2.74
1743 2252 8.559536 CAGGTATCAAATTATGAATACTTGCGT 58.440 33.333 0.00 0.00 42.54 5.24
1756 2265 1.535462 ACTTGCGTATCAACAAGGCAC 59.465 47.619 7.57 0.00 46.03 5.01
1757 2266 0.878416 TTGCGTATCAACAAGGCACC 59.122 50.000 0.00 0.00 37.45 5.01
1758 2267 0.036164 TGCGTATCAACAAGGCACCT 59.964 50.000 0.00 0.00 33.17 4.00
1760 2269 2.289756 TGCGTATCAACAAGGCACCTAA 60.290 45.455 0.00 0.00 33.17 2.69
1761 2270 2.095372 GCGTATCAACAAGGCACCTAAC 59.905 50.000 0.00 0.00 0.00 2.34
1762 2271 3.331150 CGTATCAACAAGGCACCTAACA 58.669 45.455 0.00 0.00 0.00 2.41
1764 2273 4.378046 CGTATCAACAAGGCACCTAACAAC 60.378 45.833 0.00 0.00 0.00 3.32
1765 2274 3.290948 TCAACAAGGCACCTAACAACT 57.709 42.857 0.00 0.00 0.00 3.16
1766 2275 2.948979 TCAACAAGGCACCTAACAACTG 59.051 45.455 0.00 0.00 0.00 3.16
1767 2276 1.318576 ACAAGGCACCTAACAACTGC 58.681 50.000 0.00 0.00 0.00 4.40
1768 2277 1.317613 CAAGGCACCTAACAACTGCA 58.682 50.000 0.00 0.00 32.20 4.41
1769 2278 1.888512 CAAGGCACCTAACAACTGCAT 59.111 47.619 0.00 0.00 32.20 3.96
1770 2279 1.538047 AGGCACCTAACAACTGCATG 58.462 50.000 0.00 0.00 32.20 4.06
1773 2282 1.538047 CACCTAACAACTGCATGCCT 58.462 50.000 16.68 0.00 0.00 4.75
1775 2284 1.073763 ACCTAACAACTGCATGCCTGA 59.926 47.619 16.68 0.00 0.00 3.86
1776 2285 1.741706 CCTAACAACTGCATGCCTGAG 59.258 52.381 16.68 8.71 0.00 3.35
1777 2286 2.430465 CTAACAACTGCATGCCTGAGT 58.570 47.619 16.68 9.45 0.00 3.41
1778 2287 2.566833 AACAACTGCATGCCTGAGTA 57.433 45.000 16.68 0.00 0.00 2.59
1780 2289 3.077484 ACAACTGCATGCCTGAGTATT 57.923 42.857 16.68 0.00 0.00 1.89
1796 2314 4.877823 TGAGTATTTGACAGATCATGGTGC 59.122 41.667 0.00 0.00 33.85 5.01
1822 2348 1.120530 AGTCCAAGACTGTCAACGGT 58.879 50.000 10.88 0.00 41.76 4.83
1889 2425 6.438741 TGGCCCAACAATACAAAATTCTGATA 59.561 34.615 0.00 0.00 0.00 2.15
1890 2426 7.125507 TGGCCCAACAATACAAAATTCTGATAT 59.874 33.333 0.00 0.00 0.00 1.63
1891 2427 8.637986 GGCCCAACAATACAAAATTCTGATATA 58.362 33.333 0.00 0.00 0.00 0.86
1892 2428 9.683069 GCCCAACAATACAAAATTCTGATATAG 57.317 33.333 0.00 0.00 0.00 1.31
1932 2472 1.136147 GCTCTGGCTCGTTTGCATG 59.864 57.895 0.00 0.00 35.22 4.06
1937 2477 1.444895 GGCTCGTTTGCATGCCAAG 60.445 57.895 16.68 4.34 44.34 3.61
1939 2479 0.039256 GCTCGTTTGCATGCCAAGAA 60.039 50.000 16.68 0.00 34.34 2.52
1944 2484 3.058450 CGTTTGCATGCCAAGAATTTGA 58.942 40.909 16.68 0.00 36.36 2.69
1945 2485 3.680937 CGTTTGCATGCCAAGAATTTGAT 59.319 39.130 16.68 0.00 36.36 2.57
1946 2486 4.434989 CGTTTGCATGCCAAGAATTTGATG 60.435 41.667 16.68 0.00 36.36 3.07
1947 2487 2.623535 TGCATGCCAAGAATTTGATGC 58.376 42.857 16.68 0.00 41.41 3.91
1948 2488 2.028020 TGCATGCCAAGAATTTGATGCA 60.028 40.909 16.68 10.65 45.04 3.96
1951 2491 4.210537 GCATGCCAAGAATTTGATGCATAC 59.789 41.667 6.36 0.00 41.03 2.39
1952 2492 5.353111 CATGCCAAGAATTTGATGCATACA 58.647 37.500 0.00 0.00 38.97 2.29
1953 2493 4.746729 TGCCAAGAATTTGATGCATACAC 58.253 39.130 0.00 0.00 36.36 2.90
1954 2494 3.792956 GCCAAGAATTTGATGCATACACG 59.207 43.478 0.00 0.00 36.36 4.49
1955 2495 4.675146 GCCAAGAATTTGATGCATACACGT 60.675 41.667 0.00 0.00 36.36 4.49
1956 2496 4.794762 CCAAGAATTTGATGCATACACGTG 59.205 41.667 15.48 15.48 36.36 4.49
1957 2497 4.019919 AGAATTTGATGCATACACGTGC 57.980 40.909 17.22 1.31 45.25 5.34
1988 2528 7.636259 TTTATAGTTGTGACAGCATTTTTGC 57.364 32.000 1.54 0.00 0.00 3.68
1989 2529 3.523606 AGTTGTGACAGCATTTTTGCA 57.476 38.095 1.54 0.00 37.25 4.08
1990 2530 4.062677 AGTTGTGACAGCATTTTTGCAT 57.937 36.364 1.54 0.00 37.25 3.96
1991 2531 4.053295 AGTTGTGACAGCATTTTTGCATC 58.947 39.130 1.54 0.00 37.25 3.91
1992 2532 4.053295 GTTGTGACAGCATTTTTGCATCT 58.947 39.130 0.00 0.00 37.25 2.90
1993 2533 3.644823 TGTGACAGCATTTTTGCATCTG 58.355 40.909 0.33 0.00 37.25 2.90
1994 2534 2.410730 GTGACAGCATTTTTGCATCTGC 59.589 45.455 0.33 0.00 42.50 4.26
1995 2535 2.297880 TGACAGCATTTTTGCATCTGCT 59.702 40.909 3.53 6.92 45.41 4.24
1996 2536 3.243941 TGACAGCATTTTTGCATCTGCTT 60.244 39.130 9.33 3.67 42.79 3.91
1997 2537 3.064207 ACAGCATTTTTGCATCTGCTTG 58.936 40.909 9.33 8.27 42.79 4.01
1998 2538 3.243941 ACAGCATTTTTGCATCTGCTTGA 60.244 39.130 9.33 0.00 42.79 3.02
1999 2539 3.122948 CAGCATTTTTGCATCTGCTTGAC 59.877 43.478 9.33 0.00 42.79 3.18
2000 2540 3.061322 GCATTTTTGCATCTGCTTGACA 58.939 40.909 3.53 0.00 42.66 3.58
2001 2541 3.682858 GCATTTTTGCATCTGCTTGACAT 59.317 39.130 3.53 0.00 42.66 3.06
2002 2542 4.201685 GCATTTTTGCATCTGCTTGACATC 60.202 41.667 3.53 0.00 42.66 3.06
2003 2543 4.587584 TTTTTGCATCTGCTTGACATCA 57.412 36.364 3.53 0.00 42.66 3.07
2004 2544 4.587584 TTTTGCATCTGCTTGACATCAA 57.412 36.364 3.53 0.00 42.66 2.57
2005 2545 4.587584 TTTGCATCTGCTTGACATCAAA 57.412 36.364 3.53 0.00 42.66 2.69
2006 2546 3.564235 TGCATCTGCTTGACATCAAAC 57.436 42.857 3.53 0.00 42.66 2.93
2007 2547 2.885894 TGCATCTGCTTGACATCAAACA 59.114 40.909 3.53 0.00 42.66 2.83
2008 2548 3.057806 TGCATCTGCTTGACATCAAACAG 60.058 43.478 15.76 15.76 46.09 3.16
2009 2549 3.672511 GCATCTGCTTGACATCAAACAGG 60.673 47.826 19.74 9.73 45.28 4.00
2010 2550 1.881973 TCTGCTTGACATCAAACAGGC 59.118 47.619 19.74 9.88 45.28 4.85
2011 2551 1.610038 CTGCTTGACATCAAACAGGCA 59.390 47.619 14.56 10.36 42.94 4.75
2012 2552 1.337703 TGCTTGACATCAAACAGGCAC 59.662 47.619 0.00 0.00 42.38 5.01
2013 2553 1.337703 GCTTGACATCAAACAGGCACA 59.662 47.619 0.00 0.00 38.61 4.57
2014 2554 2.029649 GCTTGACATCAAACAGGCACAT 60.030 45.455 0.00 0.00 38.61 3.21
2015 2555 3.571571 CTTGACATCAAACAGGCACATG 58.428 45.455 0.00 0.00 35.15 3.21
2016 2556 2.585330 TGACATCAAACAGGCACATGT 58.415 42.857 0.00 0.00 33.96 3.21
2017 2557 2.957680 TGACATCAAACAGGCACATGTT 59.042 40.909 0.00 0.00 45.18 2.71
2018 2558 4.140536 TGACATCAAACAGGCACATGTTA 58.859 39.130 0.00 0.00 42.49 2.41
2019 2559 4.766373 TGACATCAAACAGGCACATGTTAT 59.234 37.500 0.00 0.00 42.49 1.89
2020 2560 5.063180 ACATCAAACAGGCACATGTTATG 57.937 39.130 0.00 5.44 42.49 1.90
2021 2561 3.574284 TCAAACAGGCACATGTTATGC 57.426 42.857 0.00 0.00 42.49 3.14
2022 2562 2.889678 TCAAACAGGCACATGTTATGCA 59.110 40.909 8.81 0.00 45.27 3.96
2023 2563 3.320256 TCAAACAGGCACATGTTATGCAA 59.680 39.130 8.81 0.00 45.27 4.08
2024 2564 4.056740 CAAACAGGCACATGTTATGCAAA 58.943 39.130 8.81 0.00 45.27 3.68
2025 2565 4.540359 AACAGGCACATGTTATGCAAAT 57.460 36.364 8.81 0.00 45.27 2.32
2026 2566 5.657826 AACAGGCACATGTTATGCAAATA 57.342 34.783 8.81 0.00 45.27 1.40
2027 2567 5.857471 ACAGGCACATGTTATGCAAATAT 57.143 34.783 8.81 0.00 45.27 1.28
2028 2568 5.593968 ACAGGCACATGTTATGCAAATATG 58.406 37.500 8.81 13.02 45.27 1.78
2029 2569 7.396083 AACAGGCACATGTTATGCAAATATGC 61.396 38.462 8.81 7.25 45.90 3.14
2046 2586 8.633075 CAAATATGCACGGAATTAACTTCATT 57.367 30.769 0.00 0.00 35.41 2.57
2047 2587 9.086336 CAAATATGCACGGAATTAACTTCATTT 57.914 29.630 0.00 0.00 35.41 2.32
2054 2618 7.462724 GCACGGAATTAACTTCATTTTATGCAC 60.463 37.037 0.00 0.00 35.41 4.57
2071 2635 1.202076 GCACTCTAATTCGCCACTTGC 60.202 52.381 0.00 0.00 0.00 4.01
2074 2638 2.289694 ACTCTAATTCGCCACTTGCACT 60.290 45.455 0.00 0.00 41.33 4.40
2080 2644 1.369209 CGCCACTTGCACTTGTTCG 60.369 57.895 0.00 0.00 41.33 3.95
2085 2649 2.805671 CCACTTGCACTTGTTCGATGTA 59.194 45.455 0.00 0.00 0.00 2.29
2110 2674 1.154093 GTCGCAGTCGTTCATCGGA 60.154 57.895 0.00 0.00 40.32 4.55
2113 2677 0.098200 CGCAGTCGTTCATCGGAGTA 59.902 55.000 0.00 0.00 40.32 2.59
2212 2776 3.458163 CGCCTCTACGAGCCCCAA 61.458 66.667 0.00 0.00 34.06 4.12
3433 4122 1.059657 CGCATGACTTTTGGAACGCG 61.060 55.000 3.53 3.53 35.14 6.01
3466 4156 3.006940 TGTGCATAAGAATTCACCGGTC 58.993 45.455 2.59 0.00 0.00 4.79
3470 4160 2.953466 TAAGAATTCACCGGTCGAGG 57.047 50.000 2.59 0.00 37.30 4.63
3501 4191 1.117994 TGGCCAAACTTGCACATGAA 58.882 45.000 0.61 0.00 0.00 2.57
3681 4456 3.602265 GCTTCAGCAAAACGCAAAATGTC 60.602 43.478 0.00 0.00 46.13 3.06
3760 4537 2.412089 GCTAGACGATCGTGCTGTTTTT 59.588 45.455 28.12 0.00 0.00 1.94
3777 4554 7.604927 TGCTGTTTTTGTAACCTATCTTATCGT 59.395 33.333 0.00 0.00 0.00 3.73
3903 4680 0.249489 ACGATCCTTCTGCATACGCC 60.249 55.000 0.00 0.00 37.32 5.68
3999 4776 7.516198 AGCACAAAATCAACAGAATCTAGTT 57.484 32.000 0.00 0.00 0.00 2.24
4084 4861 5.516044 GGGGTCTTAAAAGGAACCATGTAT 58.484 41.667 0.21 0.00 42.01 2.29
4215 4992 6.263168 GGTGGAATTCGGTATTCATGAAAGAT 59.737 38.462 13.09 0.00 43.72 2.40
4330 5110 5.920903 TCTCAACCTTTTCCTTACGAGAAA 58.079 37.500 0.00 0.00 0.00 2.52
4365 5145 9.186837 AGAACTCTACTGGAATAAATTACTCGA 57.813 33.333 0.00 0.00 0.00 4.04
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.363970 CCAAAGACGTCAAATTCCTCACG 60.364 47.826 19.50 0.00 38.24 4.35
1 2 3.058224 CCCAAAGACGTCAAATTCCTCAC 60.058 47.826 19.50 0.00 0.00 3.51
2 3 3.146066 CCCAAAGACGTCAAATTCCTCA 58.854 45.455 19.50 0.00 0.00 3.86
23 24 8.975439 CCAACATACTACTAATATTTGACCGTC 58.025 37.037 3.83 0.00 0.00 4.79
49 50 1.697982 ACAAAGGACCACAGGGAGTAC 59.302 52.381 0.00 0.00 38.05 2.73
68 70 7.843490 TGGACAAAACTTATATGCAGACTAC 57.157 36.000 0.00 0.00 0.00 2.73
201 211 1.279539 CTTGCGATGCGTGTTGTGT 59.720 52.632 0.00 0.00 0.00 3.72
206 216 0.881118 AAATTCCTTGCGATGCGTGT 59.119 45.000 0.00 0.00 0.00 4.49
217 227 0.517316 GCGCTGACGTCAAATTCCTT 59.483 50.000 20.49 0.00 42.83 3.36
234 244 1.936880 GTCGATGAGCGTCTGAGCG 60.937 63.158 0.00 0.00 43.00 5.03
235 245 1.587613 GGTCGATGAGCGTCTGAGC 60.588 63.158 0.00 0.00 41.80 4.26
286 296 9.239551 GCATGGCATGTATGGATATATCAATAT 57.760 33.333 26.94 8.00 0.00 1.28
289 299 6.424883 TGCATGGCATGTATGGATATATCAA 58.575 36.000 26.94 3.42 31.71 2.57
291 301 6.512253 CGTTGCATGGCATGTATGGATATATC 60.512 42.308 26.94 3.96 38.76 1.63
292 302 5.297527 CGTTGCATGGCATGTATGGATATAT 59.702 40.000 26.94 0.00 38.76 0.86
293 303 4.635324 CGTTGCATGGCATGTATGGATATA 59.365 41.667 26.94 4.61 38.76 0.86
342 354 3.204827 CGCCTGCCACCTACATGC 61.205 66.667 0.00 0.00 0.00 4.06
346 358 1.923227 GAAAAGCGCCTGCCACCTAC 61.923 60.000 2.29 0.00 44.31 3.18
367 379 0.106819 AGGGAGAGCATGATGGCAAC 60.107 55.000 0.00 0.00 35.83 4.17
392 404 2.618709 GGGAGGCGATCGATTTTTCAAT 59.381 45.455 21.57 0.00 0.00 2.57
537 549 0.744414 TGTCTTAAGCAGCATCGGCC 60.744 55.000 0.00 0.00 42.56 6.13
799 894 2.549282 CGACCGCCTGTGTTTTCG 59.451 61.111 0.00 0.00 0.00 3.46
800 895 2.251371 GCGACCGCCTGTGTTTTC 59.749 61.111 2.55 0.00 34.56 2.29
801 896 3.645975 CGCGACCGCCTGTGTTTT 61.646 61.111 0.00 0.00 37.98 2.43
839 934 5.630061 CACAAAAACAAGGCAAAAAGAAGG 58.370 37.500 0.00 0.00 0.00 3.46
840 935 5.088068 GCACAAAAACAAGGCAAAAAGAAG 58.912 37.500 0.00 0.00 0.00 2.85
842 937 4.067896 TGCACAAAAACAAGGCAAAAAGA 58.932 34.783 0.00 0.00 0.00 2.52
843 938 4.405196 CTGCACAAAAACAAGGCAAAAAG 58.595 39.130 0.00 0.00 33.58 2.27
844 939 3.190118 CCTGCACAAAAACAAGGCAAAAA 59.810 39.130 0.00 0.00 33.58 1.94
845 940 2.746362 CCTGCACAAAAACAAGGCAAAA 59.254 40.909 0.00 0.00 33.58 2.44
847 942 1.552337 TCCTGCACAAAAACAAGGCAA 59.448 42.857 0.00 0.00 33.58 4.52
848 943 1.136695 CTCCTGCACAAAAACAAGGCA 59.863 47.619 0.00 0.00 0.00 4.75
852 947 0.463620 GCCCTCCTGCACAAAAACAA 59.536 50.000 0.00 0.00 0.00 2.83
853 948 1.398958 GGCCCTCCTGCACAAAAACA 61.399 55.000 0.00 0.00 0.00 2.83
854 949 1.367471 GGCCCTCCTGCACAAAAAC 59.633 57.895 0.00 0.00 0.00 2.43
855 950 2.199652 CGGCCCTCCTGCACAAAAA 61.200 57.895 0.00 0.00 0.00 1.94
880 1063 3.905437 TACTTGGGCCGCCGTTTCC 62.905 63.158 2.55 0.00 0.00 3.13
881 1064 1.967494 TTACTTGGGCCGCCGTTTC 60.967 57.895 2.55 0.00 0.00 2.78
882 1065 2.113562 TTACTTGGGCCGCCGTTT 59.886 55.556 2.55 0.00 0.00 3.60
883 1066 2.670592 GTTACTTGGGCCGCCGTT 60.671 61.111 2.55 0.00 0.00 4.44
890 1073 3.497031 GCGAGGCGTTACTTGGGC 61.497 66.667 0.00 0.00 0.00 5.36
891 1074 2.798148 AAGGCGAGGCGTTACTTGGG 62.798 60.000 0.00 0.00 34.83 4.12
894 1077 1.445582 CGAAGGCGAGGCGTTACTT 60.446 57.895 0.00 0.00 36.76 2.24
895 1078 2.181021 CGAAGGCGAGGCGTTACT 59.819 61.111 0.00 0.00 36.76 2.24
896 1079 2.126189 ACGAAGGCGAGGCGTTAC 60.126 61.111 0.00 0.00 41.64 2.50
901 1084 4.117661 AGACGACGAAGGCGAGGC 62.118 66.667 0.00 0.00 41.64 4.70
902 1085 2.202492 CAGACGACGAAGGCGAGG 60.202 66.667 0.00 0.00 41.64 4.63
904 1087 4.415332 GGCAGACGACGAAGGCGA 62.415 66.667 0.00 0.00 41.64 5.54
905 1088 4.421479 AGGCAGACGACGAAGGCG 62.421 66.667 0.00 0.00 44.79 5.52
906 1089 2.507324 GAGGCAGACGACGAAGGC 60.507 66.667 0.00 3.02 0.00 4.35
915 1100 0.106708 TATGGGAATGCGAGGCAGAC 59.893 55.000 0.00 0.00 43.65 3.51
922 1107 1.788229 TGAGGACTATGGGAATGCGA 58.212 50.000 0.00 0.00 0.00 5.10
929 1114 1.748591 GCCTGCTTTGAGGACTATGGG 60.749 57.143 0.00 0.00 34.69 4.00
938 1123 1.080705 GCTGCTTGCCTGCTTTGAG 60.081 57.895 0.00 0.00 35.71 3.02
948 1133 4.704833 TCTCCGGTGGCTGCTTGC 62.705 66.667 0.00 0.00 41.94 4.01
984 1181 1.177256 CCATGCTATGCCCTGCCTTC 61.177 60.000 0.00 0.00 0.00 3.46
1080 1280 2.171635 CGGGAGCTTACTTGCCAAC 58.828 57.895 0.00 0.00 0.00 3.77
1106 1306 0.297820 GAGCGAATTACTGAACGGCG 59.702 55.000 4.80 4.80 0.00 6.46
1121 1321 4.734917 ACAGCTTAAGTAACTACTGAGCG 58.265 43.478 11.14 12.89 44.38 5.03
1122 1322 6.199342 GCATACAGCTTAAGTAACTACTGAGC 59.801 42.308 11.14 13.61 42.15 4.26
1125 1325 5.051641 GCGCATACAGCTTAAGTAACTACTG 60.052 44.000 0.30 4.34 42.61 2.74
1126 1326 5.041940 GCGCATACAGCTTAAGTAACTACT 58.958 41.667 0.30 0.00 42.61 2.57
1127 1327 4.802039 TGCGCATACAGCTTAAGTAACTAC 59.198 41.667 5.66 0.00 42.61 2.73
1129 1329 3.857052 TGCGCATACAGCTTAAGTAACT 58.143 40.909 5.66 0.00 42.61 2.24
1175 1440 8.506140 TCTAAAATGCGAAAATTGTTCTCAAG 57.494 30.769 0.00 0.00 36.97 3.02
1190 1564 5.983475 TGGCAAAATTTGTTCTAAAATGCG 58.017 33.333 7.60 0.00 30.21 4.73
1198 1572 6.816134 ACTTGTTTTGGCAAAATTTGTTCT 57.184 29.167 26.41 5.27 32.22 3.01
1200 1574 7.525759 CACTACTTGTTTTGGCAAAATTTGTT 58.474 30.769 26.41 13.44 32.22 2.83
1201 1575 6.403092 GCACTACTTGTTTTGGCAAAATTTGT 60.403 34.615 26.41 23.42 32.22 2.83
1202 1576 5.964751 GCACTACTTGTTTTGGCAAAATTTG 59.035 36.000 26.41 19.82 32.22 2.32
1203 1577 5.879777 AGCACTACTTGTTTTGGCAAAATTT 59.120 32.000 26.41 14.05 32.22 1.82
1204 1578 5.427378 AGCACTACTTGTTTTGGCAAAATT 58.573 33.333 26.41 14.36 32.22 1.82
1260 1703 6.003950 TCACCATTTCCTTAACCTGAAGAAG 58.996 40.000 0.00 0.00 0.00 2.85
1273 1719 1.843368 CTGTGCCATCACCATTTCCT 58.157 50.000 0.00 0.00 42.46 3.36
1310 1756 0.891449 TGAGATCCGAGATCCGAGCC 60.891 60.000 9.44 0.00 41.76 4.70
1312 1758 3.753797 TGTTATGAGATCCGAGATCCGAG 59.246 47.826 9.44 0.00 41.76 4.63
1313 1759 3.751518 TGTTATGAGATCCGAGATCCGA 58.248 45.455 9.44 0.00 41.76 4.55
1314 1760 4.397730 AGATGTTATGAGATCCGAGATCCG 59.602 45.833 9.44 0.00 38.18 4.18
1315 1761 5.913137 AGATGTTATGAGATCCGAGATCC 57.087 43.478 9.44 3.96 0.00 3.36
1316 1762 5.576384 GCAAGATGTTATGAGATCCGAGATC 59.424 44.000 5.94 5.94 0.00 2.75
1317 1763 5.477510 GCAAGATGTTATGAGATCCGAGAT 58.522 41.667 0.00 0.00 0.00 2.75
1318 1764 4.262207 GGCAAGATGTTATGAGATCCGAGA 60.262 45.833 0.00 0.00 0.00 4.04
1319 1765 3.993081 GGCAAGATGTTATGAGATCCGAG 59.007 47.826 0.00 0.00 0.00 4.63
1320 1766 3.643320 AGGCAAGATGTTATGAGATCCGA 59.357 43.478 0.00 0.00 0.00 4.55
1331 1777 6.716628 TCTGATGAGTAAAAAGGCAAGATGTT 59.283 34.615 0.00 0.00 0.00 2.71
1333 1779 6.748333 TCTGATGAGTAAAAAGGCAAGATG 57.252 37.500 0.00 0.00 0.00 2.90
1433 1921 2.032620 TCCTTTCTCTATCTGGGCGTC 58.967 52.381 0.00 0.00 0.00 5.19
1468 1956 1.421485 GGCATCGTCTTTGACAGCG 59.579 57.895 0.00 0.00 32.09 5.18
1486 1974 4.154195 GGTCGGGATCATGATTTTTATCGG 59.846 45.833 10.14 1.61 0.00 4.18
1645 2133 0.739462 TCGTGCCAATCTAGCCAACG 60.739 55.000 0.00 0.00 32.67 4.10
1689 2181 2.923121 AGATTCCATGATGACCAACCG 58.077 47.619 0.00 0.00 0.00 4.44
1690 2182 4.818546 CACTAGATTCCATGATGACCAACC 59.181 45.833 0.00 0.00 0.00 3.77
1691 2183 4.818546 CCACTAGATTCCATGATGACCAAC 59.181 45.833 0.00 0.00 0.00 3.77
1692 2184 4.474651 ACCACTAGATTCCATGATGACCAA 59.525 41.667 0.00 0.00 0.00 3.67
1693 2185 4.040047 ACCACTAGATTCCATGATGACCA 58.960 43.478 0.00 0.00 0.00 4.02
1694 2186 4.696479 ACCACTAGATTCCATGATGACC 57.304 45.455 0.00 0.00 0.00 4.02
1695 2187 6.161855 TGTACCACTAGATTCCATGATGAC 57.838 41.667 0.00 0.00 0.00 3.06
1696 2188 5.305386 CCTGTACCACTAGATTCCATGATGA 59.695 44.000 0.00 0.00 0.00 2.92
1697 2189 5.070981 ACCTGTACCACTAGATTCCATGATG 59.929 44.000 0.00 0.00 0.00 3.07
1716 2221 8.559536 CGCAAGTATTCATAATTTGATACCTGT 58.440 33.333 0.00 0.00 33.34 4.00
1717 2222 8.939586 CGCAAGTATTCATAATTTGATACCTG 57.060 34.615 0.00 0.00 33.34 4.00
1737 2243 1.135689 GGTGCCTTGTTGATACGCAAG 60.136 52.381 0.00 0.00 41.08 4.01
1743 2252 4.759693 CAGTTGTTAGGTGCCTTGTTGATA 59.240 41.667 0.00 0.00 0.00 2.15
1756 2265 1.741706 CTCAGGCATGCAGTTGTTAGG 59.258 52.381 21.36 4.06 0.00 2.69
1757 2266 2.430465 ACTCAGGCATGCAGTTGTTAG 58.570 47.619 21.36 10.77 0.00 2.34
1758 2267 2.566833 ACTCAGGCATGCAGTTGTTA 57.433 45.000 21.36 0.00 0.00 2.41
1760 2269 2.795231 ATACTCAGGCATGCAGTTGT 57.205 45.000 21.36 14.45 0.00 3.32
1761 2270 3.441222 TCAAATACTCAGGCATGCAGTTG 59.559 43.478 21.36 13.14 0.00 3.16
1762 2271 3.441572 GTCAAATACTCAGGCATGCAGTT 59.558 43.478 21.36 0.00 0.00 3.16
1764 2273 3.011818 TGTCAAATACTCAGGCATGCAG 58.988 45.455 21.36 11.12 0.00 4.41
1765 2274 3.011818 CTGTCAAATACTCAGGCATGCA 58.988 45.455 21.36 0.00 0.00 3.96
1766 2275 3.273434 TCTGTCAAATACTCAGGCATGC 58.727 45.455 9.90 9.90 0.00 4.06
1767 2276 5.121105 TGATCTGTCAAATACTCAGGCATG 58.879 41.667 0.00 0.00 0.00 4.06
1768 2277 5.363562 TGATCTGTCAAATACTCAGGCAT 57.636 39.130 0.00 0.00 0.00 4.40
1769 2278 4.824479 TGATCTGTCAAATACTCAGGCA 57.176 40.909 0.00 0.00 0.00 4.75
1770 2279 4.514441 CCATGATCTGTCAAATACTCAGGC 59.486 45.833 0.00 0.00 38.01 4.85
1773 2282 4.877823 GCACCATGATCTGTCAAATACTCA 59.122 41.667 0.00 0.00 38.01 3.41
1775 2284 4.202441 GGCACCATGATCTGTCAAATACT 58.798 43.478 0.00 0.00 38.01 2.12
1776 2285 4.558538 GGCACCATGATCTGTCAAATAC 57.441 45.455 0.00 0.00 38.01 1.89
1822 2348 2.933495 CTAGCTAGCAACGGTACACA 57.067 50.000 18.83 0.00 0.00 3.72
1837 2363 4.790140 GCATGCAAATATTCGTATGCTAGC 59.210 41.667 18.73 8.10 44.70 3.42
1846 2378 2.473609 GCCACATGCATGCAAATATTCG 59.526 45.455 26.68 9.54 40.77 3.34
1848 2380 2.485835 GGGCCACATGCATGCAAATATT 60.486 45.455 26.68 4.34 43.89 1.28
1911 2447 1.136147 GCAAACGAGCCAGAGCATG 59.864 57.895 0.00 0.00 43.56 4.06
1932 2472 3.792956 CGTGTATGCATCAAATTCTTGGC 59.207 43.478 0.19 0.00 33.01 4.52
1962 2502 8.547069 GCAAAAATGCTGTCACAACTATAAAAA 58.453 29.630 0.00 0.00 0.00 1.94
1963 2503 7.708322 TGCAAAAATGCTGTCACAACTATAAAA 59.292 29.630 2.22 0.00 35.49 1.52
1964 2504 7.205992 TGCAAAAATGCTGTCACAACTATAAA 58.794 30.769 2.22 0.00 35.49 1.40
1965 2505 6.743110 TGCAAAAATGCTGTCACAACTATAA 58.257 32.000 2.22 0.00 35.49 0.98
1966 2506 6.324561 TGCAAAAATGCTGTCACAACTATA 57.675 33.333 2.22 0.00 35.49 1.31
1967 2507 5.199024 TGCAAAAATGCTGTCACAACTAT 57.801 34.783 2.22 0.00 35.49 2.12
1968 2508 4.645762 TGCAAAAATGCTGTCACAACTA 57.354 36.364 2.22 0.00 35.49 2.24
1969 2509 3.523606 TGCAAAAATGCTGTCACAACT 57.476 38.095 2.22 0.00 35.49 3.16
1970 2510 4.053295 AGATGCAAAAATGCTGTCACAAC 58.947 39.130 0.00 0.00 35.49 3.32
1971 2511 4.052608 CAGATGCAAAAATGCTGTCACAA 58.947 39.130 0.00 0.00 35.49 3.33
1972 2512 3.644823 CAGATGCAAAAATGCTGTCACA 58.355 40.909 0.00 0.00 35.49 3.58
1973 2513 2.410730 GCAGATGCAAAAATGCTGTCAC 59.589 45.455 0.00 0.00 41.59 3.67
1974 2514 2.297880 AGCAGATGCAAAAATGCTGTCA 59.702 40.909 14.96 0.00 46.75 3.58
1975 2515 2.955614 AGCAGATGCAAAAATGCTGTC 58.044 42.857 14.96 1.29 46.75 3.51
1979 2519 3.061322 TGTCAAGCAGATGCAAAAATGC 58.939 40.909 7.68 7.48 45.16 3.56
1980 2520 4.926832 TGATGTCAAGCAGATGCAAAAATG 59.073 37.500 7.68 0.00 45.16 2.32
1981 2521 5.142061 TGATGTCAAGCAGATGCAAAAAT 57.858 34.783 7.68 0.00 45.16 1.82
1982 2522 4.587584 TGATGTCAAGCAGATGCAAAAA 57.412 36.364 7.68 0.00 45.16 1.94
1983 2523 4.587584 TTGATGTCAAGCAGATGCAAAA 57.412 36.364 7.68 0.00 45.16 2.44
1984 2524 4.202131 TGTTTGATGTCAAGCAGATGCAAA 60.202 37.500 7.68 0.00 41.12 3.68
1985 2525 3.318557 TGTTTGATGTCAAGCAGATGCAA 59.681 39.130 7.68 0.00 41.12 4.08
1986 2526 2.885894 TGTTTGATGTCAAGCAGATGCA 59.114 40.909 7.68 0.00 41.12 3.96
1987 2527 3.564235 TGTTTGATGTCAAGCAGATGC 57.436 42.857 8.00 0.00 41.12 3.91
1992 2532 1.337703 GTGCCTGTTTGATGTCAAGCA 59.662 47.619 11.03 11.03 43.18 3.91
1993 2533 1.337703 TGTGCCTGTTTGATGTCAAGC 59.662 47.619 3.05 3.05 37.15 4.01
1994 2534 3.005050 ACATGTGCCTGTTTGATGTCAAG 59.995 43.478 0.00 0.00 37.15 3.02
1995 2535 2.957680 ACATGTGCCTGTTTGATGTCAA 59.042 40.909 0.00 0.00 0.00 3.18
1996 2536 2.585330 ACATGTGCCTGTTTGATGTCA 58.415 42.857 0.00 0.00 0.00 3.58
1997 2537 3.648339 AACATGTGCCTGTTTGATGTC 57.352 42.857 0.00 0.00 35.90 3.06
1998 2538 4.618927 GCATAACATGTGCCTGTTTGATGT 60.619 41.667 0.00 0.00 39.88 3.06
1999 2539 3.861113 GCATAACATGTGCCTGTTTGATG 59.139 43.478 0.00 3.21 39.88 3.07
2000 2540 3.510753 TGCATAACATGTGCCTGTTTGAT 59.489 39.130 0.00 0.00 41.83 2.57
2001 2541 2.889678 TGCATAACATGTGCCTGTTTGA 59.110 40.909 0.00 0.00 41.83 2.69
2002 2542 3.300852 TGCATAACATGTGCCTGTTTG 57.699 42.857 0.00 0.00 41.83 2.93
2003 2543 4.333913 TTTGCATAACATGTGCCTGTTT 57.666 36.364 0.00 0.00 41.83 2.83
2004 2544 4.540359 ATTTGCATAACATGTGCCTGTT 57.460 36.364 0.00 2.55 41.83 3.16
2005 2545 5.593968 CATATTTGCATAACATGTGCCTGT 58.406 37.500 0.00 0.00 41.83 4.00
2017 2557 7.860373 GAAGTTAATTCCGTGCATATTTGCATA 59.140 33.333 14.06 0.00 45.17 3.14
2018 2558 6.697019 GAAGTTAATTCCGTGCATATTTGCAT 59.303 34.615 14.06 0.00 45.17 3.96
2019 2559 6.033341 GAAGTTAATTCCGTGCATATTTGCA 58.967 36.000 6.75 6.75 43.23 4.08
2020 2560 6.033341 TGAAGTTAATTCCGTGCATATTTGC 58.967 36.000 0.61 0.61 42.26 3.68
2021 2561 8.633075 AATGAAGTTAATTCCGTGCATATTTG 57.367 30.769 0.00 0.00 37.08 2.32
2022 2562 9.651913 AAAATGAAGTTAATTCCGTGCATATTT 57.348 25.926 0.00 0.00 37.08 1.40
2025 2565 9.729023 CATAAAATGAAGTTAATTCCGTGCATA 57.271 29.630 0.00 0.00 37.08 3.14
2026 2566 7.222611 GCATAAAATGAAGTTAATTCCGTGCAT 59.777 33.333 0.00 0.00 37.08 3.96
2027 2567 6.529829 GCATAAAATGAAGTTAATTCCGTGCA 59.470 34.615 9.72 0.00 37.08 4.57
2028 2568 6.529829 TGCATAAAATGAAGTTAATTCCGTGC 59.470 34.615 8.44 8.44 37.08 5.34
2029 2569 7.754924 AGTGCATAAAATGAAGTTAATTCCGTG 59.245 33.333 0.00 0.00 37.08 4.94
2030 2570 7.826690 AGTGCATAAAATGAAGTTAATTCCGT 58.173 30.769 0.00 0.00 37.08 4.69
2031 2571 8.184192 AGAGTGCATAAAATGAAGTTAATTCCG 58.816 33.333 0.00 0.00 37.08 4.30
2038 2578 7.698130 GCGAATTAGAGTGCATAAAATGAAGTT 59.302 33.333 0.00 0.00 0.00 2.66
2039 2579 7.189512 GCGAATTAGAGTGCATAAAATGAAGT 58.810 34.615 0.00 0.00 0.00 3.01
2040 2580 6.634436 GGCGAATTAGAGTGCATAAAATGAAG 59.366 38.462 0.00 0.00 0.00 3.02
2041 2581 6.094742 TGGCGAATTAGAGTGCATAAAATGAA 59.905 34.615 0.00 0.00 0.00 2.57
2042 2582 5.588246 TGGCGAATTAGAGTGCATAAAATGA 59.412 36.000 0.00 0.00 0.00 2.57
2043 2583 5.682862 GTGGCGAATTAGAGTGCATAAAATG 59.317 40.000 0.00 0.00 0.00 2.32
2044 2584 5.590259 AGTGGCGAATTAGAGTGCATAAAAT 59.410 36.000 0.00 0.00 0.00 1.82
2045 2585 4.941263 AGTGGCGAATTAGAGTGCATAAAA 59.059 37.500 0.00 0.00 0.00 1.52
2046 2586 4.513442 AGTGGCGAATTAGAGTGCATAAA 58.487 39.130 0.00 0.00 0.00 1.40
2047 2587 4.137116 AGTGGCGAATTAGAGTGCATAA 57.863 40.909 0.00 0.00 0.00 1.90
2071 2635 2.159973 CGCTGTGTACATCGAACAAGTG 60.160 50.000 0.00 0.00 37.65 3.16
2074 2638 2.055838 GACGCTGTGTACATCGAACAA 58.944 47.619 14.21 0.00 37.65 2.83
2080 2644 0.732880 ACTGCGACGCTGTGTACATC 60.733 55.000 28.26 0.00 39.15 3.06
2085 2649 3.768185 AACGACTGCGACGCTGTGT 62.768 57.895 32.75 25.60 40.59 3.72
2110 2674 1.064654 GCGATCGTCCCGTAGTTTACT 59.935 52.381 17.81 0.00 0.00 2.24
2113 2677 1.226491 CGCGATCGTCCCGTAGTTT 60.226 57.895 17.81 0.00 0.00 2.66
2155 2719 4.082523 GTGAGCAGGCTGGCCGTA 62.083 66.667 17.64 0.00 41.95 4.02
2473 3150 1.374125 CATCGAGTGCACCGTGGAA 60.374 57.895 21.61 8.01 0.00 3.53
3340 4017 4.021544 AGCAAAACACCAAACAAGACAAGA 60.022 37.500 0.00 0.00 0.00 3.02
3433 4122 3.496884 TCTTATGCACAAAGACAACGGTC 59.503 43.478 8.83 0.00 44.66 4.79
3440 4129 5.088739 CGGTGAATTCTTATGCACAAAGAC 58.911 41.667 11.82 3.67 41.46 3.01
3466 4156 2.295909 TGGCCATTTTTCTTTGTCCTCG 59.704 45.455 0.00 0.00 0.00 4.63
3470 4160 5.730289 GCAAGTTTGGCCATTTTTCTTTGTC 60.730 40.000 6.09 0.00 0.00 3.18
3501 4191 2.541178 GGCTGATTAGTTCGTCGATCGT 60.541 50.000 15.94 0.00 40.80 3.73
3681 4456 2.253452 GTCTTGTTGCTGGCTGCG 59.747 61.111 11.85 0.00 46.63 5.18
3760 4537 9.203421 CATAATTGCACGATAAGATAGGTTACA 57.797 33.333 0.00 0.00 0.00 2.41
3789 4566 4.593206 TCAGTAGTGACCCAGAAGAATGTT 59.407 41.667 0.00 0.00 0.00 2.71
3903 4680 1.446907 ATCTGTTGCGAGCTTTGGAG 58.553 50.000 0.00 0.00 0.00 3.86
3999 4776 9.981114 CCATAGGCATCATATATCGTTAATACA 57.019 33.333 0.00 0.00 0.00 2.29
4084 4861 3.755112 TTACGTTGTGACCTTCCATCA 57.245 42.857 0.00 0.00 0.00 3.07
4200 4977 7.993183 TCTTCCTAACCATCTTTCATGAATACC 59.007 37.037 9.40 0.00 0.00 2.73
4215 4992 5.479027 GCCTGGTAATTTTTCTTCCTAACCA 59.521 40.000 0.00 0.00 34.72 3.67
4330 5110 5.272405 TCCAGTAGAGTTCTTCCCTACTT 57.728 43.478 0.00 0.00 40.58 2.24
4365 5145 4.019174 CAACTTATGGTCTCCCAAATGCT 58.981 43.478 0.00 0.00 46.04 3.79


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

AutoCloner maintained by Alex Coulton.