Multiple sequence alignment - TraesCS6A01G090600

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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 TraesCS6A01G090600 chr6A 100.000 5687 0 0 1 5687 59304009 59298323 0.000000e+00 10503.0
1 TraesCS6A01G090600 chr6A 84.929 1201 149 20 3505 4695 59078736 59077558 0.000000e+00 1186.0
2 TraesCS6A01G090600 chr6A 81.436 404 61 10 1450 1844 59095231 59094833 9.190000e-83 318.0
3 TraesCS6A01G090600 chr6B 88.795 1901 99 60 65 1896 113579896 113578041 0.000000e+00 2226.0
4 TraesCS6A01G090600 chr6B 95.280 1356 57 6 3418 4772 113576022 113574673 0.000000e+00 2143.0
5 TraesCS6A01G090600 chr6B 89.863 1243 60 24 2189 3410 113577272 113576075 0.000000e+00 1537.0
6 TraesCS6A01G090600 chr6B 85.512 1201 142 18 3502 4692 113446951 113445773 0.000000e+00 1225.0
7 TraesCS6A01G090600 chr6B 82.688 1213 181 21 3506 4712 113453945 113452756 0.000000e+00 1050.0
8 TraesCS6A01G090600 chr6B 87.679 836 66 18 4868 5687 113573990 113573176 0.000000e+00 939.0
9 TraesCS6A01G090600 chr6B 80.988 405 61 12 1450 1844 113455915 113455517 1.990000e-79 307.0
10 TraesCS6A01G090600 chr6B 91.228 114 9 1 4769 4882 113574451 113574339 2.740000e-33 154.0
11 TraesCS6A01G090600 chr6D 95.495 1354 54 6 3423 4772 44484661 44483311 0.000000e+00 2156.0
12 TraesCS6A01G090600 chr6D 90.847 1464 69 25 172 1614 44488181 44486762 0.000000e+00 1901.0
13 TraesCS6A01G090600 chr6D 95.716 747 29 1 4939 5685 44462756 44462013 0.000000e+00 1199.0
14 TraesCS6A01G090600 chr6D 84.929 1201 149 16 3502 4692 44295890 44294712 0.000000e+00 1186.0
15 TraesCS6A01G090600 chr6D 84.089 1125 104 39 1620 2723 44486722 44485652 0.000000e+00 1016.0
16 TraesCS6A01G090600 chr6D 90.083 726 46 14 2736 3446 44485385 44484671 0.000000e+00 918.0
17 TraesCS6A01G090600 chr6D 80.597 402 66 10 1467 1860 44424089 44423692 3.330000e-77 300.0
18 TraesCS6A01G090600 chr6D 93.023 172 11 1 4770 4941 44482252 44482082 3.400000e-62 250.0
19 TraesCS6A01G090600 chr2D 86.538 1144 131 13 3574 4697 552020703 552021843 0.000000e+00 1238.0
20 TraesCS6A01G090600 chr2D 89.655 87 9 0 1934 2020 10865849 10865763 1.670000e-20 111.0
21 TraesCS6A01G090600 chr2B 85.182 1235 142 22 3485 4697 657301028 657302243 0.000000e+00 1229.0
22 TraesCS6A01G090600 chr2B 79.032 124 24 2 2079 2201 526839832 526839954 3.650000e-12 84.2
23 TraesCS6A01G090600 chr2A 85.094 1221 145 22 3497 4697 692725786 692726989 0.000000e+00 1212.0
24 TraesCS6A01G090600 chr2A 78.481 158 31 3 2048 2203 724125495 724125651 3.630000e-17 100.0
25 TraesCS6A01G090600 chr1A 83.279 1238 181 18 3462 4679 564452366 564451135 0.000000e+00 1116.0
26 TraesCS6A01G090600 chr1B 83.065 1240 181 17 3462 4677 654049408 654048174 0.000000e+00 1099.0
27 TraesCS6A01G090600 chr1B 81.908 304 32 14 1920 2203 110891466 110891766 9.530000e-58 235.0
28 TraesCS6A01G090600 chr1D 82.551 1129 172 19 3462 4575 470770043 470768925 0.000000e+00 970.0
29 TraesCS6A01G090600 chr1D 83.453 139 21 2 2063 2200 53422967 53423104 1.660000e-25 128.0
30 TraesCS6A01G090600 chr5B 83.651 367 53 4 3574 3935 52418464 52418100 7.060000e-89 339.0
31 TraesCS6A01G090600 chr5B 74.913 287 56 15 1926 2204 17220757 17221035 3.600000e-22 117.0
32 TraesCS6A01G090600 chr5B 74.564 287 57 15 1926 2204 16917622 16917900 1.670000e-20 111.0
33 TraesCS6A01G090600 chr3D 85.274 292 32 9 1920 2203 168673714 168674002 2.000000e-74 291.0
34 TraesCS6A01G090600 chr3D 82.791 215 24 12 1928 2135 341542672 341542464 4.530000e-41 180.0
35 TraesCS6A01G090600 chr5D 83.813 278 33 5 1928 2204 494080808 494080542 2.630000e-63 254.0
36 TraesCS6A01G090600 chr7D 85.106 94 13 1 2108 2201 581658779 581658871 1.690000e-15 95.3
37 TraesCS6A01G090600 chr7D 84.043 94 14 1 2108 2201 581498449 581498541 7.850000e-14 89.8
38 TraesCS6A01G090600 chr3B 78.035 173 20 13 2035 2193 107741834 107742002 6.070000e-15 93.5


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 TraesCS6A01G090600 chr6A 59298323 59304009 5686 True 10503.0 10503 100.0000 1 5687 1 chr6A.!!$R3 5686
1 TraesCS6A01G090600 chr6A 59077558 59078736 1178 True 1186.0 1186 84.9290 3505 4695 1 chr6A.!!$R1 1190
2 TraesCS6A01G090600 chr6B 113573176 113579896 6720 True 1399.8 2226 90.5690 65 5687 5 chr6B.!!$R3 5622
3 TraesCS6A01G090600 chr6B 113445773 113446951 1178 True 1225.0 1225 85.5120 3502 4692 1 chr6B.!!$R1 1190
4 TraesCS6A01G090600 chr6B 113452756 113455915 3159 True 678.5 1050 81.8380 1450 4712 2 chr6B.!!$R2 3262
5 TraesCS6A01G090600 chr6D 44482082 44488181 6099 True 1248.2 2156 90.7074 172 4941 5 chr6D.!!$R4 4769
6 TraesCS6A01G090600 chr6D 44462013 44462756 743 True 1199.0 1199 95.7160 4939 5685 1 chr6D.!!$R3 746
7 TraesCS6A01G090600 chr6D 44294712 44295890 1178 True 1186.0 1186 84.9290 3502 4692 1 chr6D.!!$R1 1190
8 TraesCS6A01G090600 chr2D 552020703 552021843 1140 False 1238.0 1238 86.5380 3574 4697 1 chr2D.!!$F1 1123
9 TraesCS6A01G090600 chr2B 657301028 657302243 1215 False 1229.0 1229 85.1820 3485 4697 1 chr2B.!!$F2 1212
10 TraesCS6A01G090600 chr2A 692725786 692726989 1203 False 1212.0 1212 85.0940 3497 4697 1 chr2A.!!$F1 1200
11 TraesCS6A01G090600 chr1A 564451135 564452366 1231 True 1116.0 1116 83.2790 3462 4679 1 chr1A.!!$R1 1217
12 TraesCS6A01G090600 chr1B 654048174 654049408 1234 True 1099.0 1099 83.0650 3462 4677 1 chr1B.!!$R1 1215
13 TraesCS6A01G090600 chr1D 470768925 470770043 1118 True 970.0 970 82.5510 3462 4575 1 chr1D.!!$R1 1113

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
599 607 0.178921 TTCCAGGAGTCCTCAGCAGT 60.179 55.000 9.36 0.00 0.00 4.40 F
1275 1319 0.037697 AGACGTGTGTGTGTGTGTGT 60.038 50.000 0.00 0.00 0.00 3.72 F
1276 1320 0.094558 GACGTGTGTGTGTGTGTGTG 59.905 55.000 0.00 0.00 0.00 3.82 F
2570 3477 0.179062 TTTGTGCATGCCAACAACCC 60.179 50.000 19.83 0.00 0.00 4.11 F
2607 3515 2.158430 TGTGTACTCCTACCACACAGGA 60.158 50.000 2.82 0.00 45.57 3.86 F
3582 5563 0.969894 CCCTCGGTCACTCTGAAACT 59.030 55.000 0.00 0.00 0.00 2.66 F
4047 6034 1.797933 CGTCGACAAGGAGCTGACG 60.798 63.158 17.16 6.17 45.06 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2497 3404 0.472044 TTCACTGGCTAGGCAACACA 59.528 50.000 20.64 2.2 41.41 3.72 R
2657 3565 1.006220 TGCACGTCAGAAGCGACAT 60.006 52.632 0.00 0.0 35.54 3.06 R
2658 3566 1.661509 CTGCACGTCAGAAGCGACA 60.662 57.895 8.72 0.0 45.72 4.35 R
3500 5463 0.822121 ACACGCCAAAGAAAGGGGAC 60.822 55.000 3.17 0.0 41.25 4.46 R
4101 6088 1.437986 GTAGGTCTCGCGCAGGAAT 59.562 57.895 8.75 0.0 0.00 3.01 R
4393 6401 1.895020 TACGGCACCACCTGGATCAC 61.895 60.000 0.00 0.0 38.94 3.06 R
5605 9055 3.390521 CCACCCGCCACTGCTAGA 61.391 66.667 0.00 0.0 34.43 2.43 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
21 22 4.751767 CCTCTCTTCCTCTGCTATTTGT 57.248 45.455 0.00 0.00 0.00 2.83
22 23 5.860941 CCTCTCTTCCTCTGCTATTTGTA 57.139 43.478 0.00 0.00 0.00 2.41
23 24 6.418057 CCTCTCTTCCTCTGCTATTTGTAT 57.582 41.667 0.00 0.00 0.00 2.29
24 25 7.531857 CCTCTCTTCCTCTGCTATTTGTATA 57.468 40.000 0.00 0.00 0.00 1.47
25 26 7.601856 CCTCTCTTCCTCTGCTATTTGTATAG 58.398 42.308 0.00 0.00 37.40 1.31
26 27 7.232534 CCTCTCTTCCTCTGCTATTTGTATAGT 59.767 40.741 0.00 0.00 36.82 2.12
27 28 8.540507 TCTCTTCCTCTGCTATTTGTATAGTT 57.459 34.615 0.00 0.00 36.82 2.24
28 29 8.982723 TCTCTTCCTCTGCTATTTGTATAGTTT 58.017 33.333 0.00 0.00 36.82 2.66
29 30 8.948631 TCTTCCTCTGCTATTTGTATAGTTTG 57.051 34.615 0.00 0.00 36.82 2.93
30 31 8.540388 TCTTCCTCTGCTATTTGTATAGTTTGT 58.460 33.333 0.00 0.00 36.82 2.83
31 32 9.817809 CTTCCTCTGCTATTTGTATAGTTTGTA 57.182 33.333 0.00 0.00 36.82 2.41
32 33 9.817809 TTCCTCTGCTATTTGTATAGTTTGTAG 57.182 33.333 0.00 0.00 36.82 2.74
33 34 8.978472 TCCTCTGCTATTTGTATAGTTTGTAGT 58.022 33.333 0.00 0.00 36.82 2.73
34 35 9.601217 CCTCTGCTATTTGTATAGTTTGTAGTT 57.399 33.333 0.00 0.00 36.82 2.24
56 57 4.628074 TCTTGTACAGAACCTCTTTTCGG 58.372 43.478 0.00 0.00 0.00 4.30
57 58 4.100498 TCTTGTACAGAACCTCTTTTCGGT 59.900 41.667 0.00 0.00 37.60 4.69
58 59 3.724374 TGTACAGAACCTCTTTTCGGTG 58.276 45.455 0.00 0.00 35.13 4.94
59 60 3.133362 TGTACAGAACCTCTTTTCGGTGT 59.867 43.478 0.00 0.00 35.13 4.16
60 61 3.277142 ACAGAACCTCTTTTCGGTGTT 57.723 42.857 0.00 0.00 33.34 3.32
61 62 3.203716 ACAGAACCTCTTTTCGGTGTTC 58.796 45.455 0.00 0.00 33.34 3.18
62 63 3.202906 CAGAACCTCTTTTCGGTGTTCA 58.797 45.455 0.00 0.00 38.17 3.18
63 64 3.248602 CAGAACCTCTTTTCGGTGTTCAG 59.751 47.826 0.00 0.00 38.17 3.02
78 79 8.398878 TCGGTGTTCAGTTTTTAATAAAGGAT 57.601 30.769 0.00 0.00 0.00 3.24
81 82 8.708742 GGTGTTCAGTTTTTAATAAAGGATTGC 58.291 33.333 0.00 0.00 0.00 3.56
86 87 5.482526 AGTTTTTAATAAAGGATTGCGGGGT 59.517 36.000 0.00 0.00 0.00 4.95
150 152 2.563179 AGGTAACCACAGTGTGCTAGAG 59.437 50.000 18.21 6.34 31.34 2.43
165 167 5.306419 TGTGCTAGAGAATATTGAGCCTCAT 59.694 40.000 0.00 0.00 31.98 2.90
341 349 5.142061 TCTTGTTGAAGATAAGGTGCGTA 57.858 39.130 0.00 0.00 32.98 4.42
355 363 2.022195 GTGCGTAGTGGGACTCAGATA 58.978 52.381 0.00 0.00 0.00 1.98
406 414 8.495148 GCATTTGGGTTTAAAGATACACTTTTG 58.505 33.333 0.00 0.00 45.22 2.44
589 597 3.074390 TGGTGAATGAACATTCCAGGAGT 59.926 43.478 20.15 0.00 44.93 3.85
599 607 0.178921 TTCCAGGAGTCCTCAGCAGT 60.179 55.000 9.36 0.00 0.00 4.40
813 831 1.402968 CAAATCACCGCTCCCAGAATG 59.597 52.381 0.00 0.00 0.00 2.67
823 841 2.800250 CTCCCAGAATGCAAGACCTTT 58.200 47.619 0.00 0.00 31.97 3.11
892 911 1.212751 GGCGAGAAACAATGTGCCC 59.787 57.895 0.68 0.00 36.51 5.36
893 912 1.244019 GGCGAGAAACAATGTGCCCT 61.244 55.000 0.68 0.00 36.51 5.19
894 913 1.448985 GCGAGAAACAATGTGCCCTA 58.551 50.000 0.00 0.00 0.00 3.53
968 996 4.599047 GTCACTCATTAGCACTACTACCG 58.401 47.826 0.00 0.00 0.00 4.02
1010 1038 0.731417 GCAACGAGCATGAGCAGAAT 59.269 50.000 0.00 0.00 45.49 2.40
1016 1044 1.150567 AGCATGAGCAGAATCGCGTC 61.151 55.000 5.77 0.00 45.49 5.19
1123 1151 0.947244 CAGCGGTAAGGATGCATTCC 59.053 55.000 0.00 3.72 45.85 3.01
1169 1213 8.615878 TTGCTAATTACTGTGATTGTTAGTGT 57.384 30.769 7.94 0.00 0.00 3.55
1170 1214 8.615878 TGCTAATTACTGTGATTGTTAGTGTT 57.384 30.769 7.94 0.00 0.00 3.32
1171 1215 9.713713 TGCTAATTACTGTGATTGTTAGTGTTA 57.286 29.630 7.94 0.00 0.00 2.41
1205 1249 4.833478 ACCTGTGATTGTTAGAGATGCT 57.167 40.909 0.00 0.00 0.00 3.79
1216 1260 6.006759 TGTTAGAGATGCTGTGATCTATCG 57.993 41.667 0.00 0.00 32.57 2.92
1251 1295 4.327627 GGATCGAACTAGCAAAAGACAGAC 59.672 45.833 0.00 0.00 0.00 3.51
1261 1305 3.393800 CAAAAGACAGACCATGAGACGT 58.606 45.455 0.00 0.00 0.00 4.34
1267 1311 1.040646 AGACCATGAGACGTGTGTGT 58.959 50.000 0.00 0.00 0.00 3.72
1268 1312 1.139989 GACCATGAGACGTGTGTGTG 58.860 55.000 0.00 0.00 0.00 3.82
1269 1313 0.464036 ACCATGAGACGTGTGTGTGT 59.536 50.000 0.00 0.00 0.00 3.72
1270 1314 0.861185 CCATGAGACGTGTGTGTGTG 59.139 55.000 0.00 0.00 0.00 3.82
1271 1315 1.570813 CATGAGACGTGTGTGTGTGT 58.429 50.000 0.00 0.00 0.00 3.72
1272 1316 1.258720 CATGAGACGTGTGTGTGTGTG 59.741 52.381 0.00 0.00 0.00 3.82
1273 1317 0.245266 TGAGACGTGTGTGTGTGTGT 59.755 50.000 0.00 0.00 0.00 3.72
1274 1318 0.645355 GAGACGTGTGTGTGTGTGTG 59.355 55.000 0.00 0.00 0.00 3.82
1275 1319 0.037697 AGACGTGTGTGTGTGTGTGT 60.038 50.000 0.00 0.00 0.00 3.72
1276 1320 0.094558 GACGTGTGTGTGTGTGTGTG 59.905 55.000 0.00 0.00 0.00 3.82
1277 1321 0.601576 ACGTGTGTGTGTGTGTGTGT 60.602 50.000 0.00 0.00 0.00 3.72
1278 1322 0.179227 CGTGTGTGTGTGTGTGTGTG 60.179 55.000 0.00 0.00 0.00 3.82
1279 1323 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1280 1324 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
1281 1325 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1282 1326 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
1283 1327 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1284 1328 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
1285 1329 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1286 1330 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
1337 1388 5.880332 GTGACCAATTTGGCTATCTTCACTA 59.120 40.000 19.62 0.00 42.67 2.74
1344 1395 5.957771 TTGGCTATCTTCACTACTTCCAT 57.042 39.130 0.00 0.00 0.00 3.41
1362 1413 6.095440 ACTTCCATCCCGAATTATTTGTCTTG 59.905 38.462 0.00 0.00 0.00 3.02
1469 1524 2.148916 CTGACTGACGGCAACACTTA 57.851 50.000 0.00 0.00 0.00 2.24
1473 1528 3.880490 TGACTGACGGCAACACTTATTTT 59.120 39.130 0.00 0.00 0.00 1.82
1548 1603 4.183865 TGACGGATAAACAGCTGATCAAG 58.816 43.478 23.35 12.75 0.00 3.02
1750 1847 0.334676 AGGTGAGAGCTAGCACTCCT 59.665 55.000 31.17 22.88 37.39 3.69
1812 1909 6.029492 TGGGTATCCAAGGAAATCATGAAT 57.971 37.500 0.00 0.00 40.73 2.57
1813 1910 5.834742 TGGGTATCCAAGGAAATCATGAATG 59.165 40.000 0.00 0.00 40.73 2.67
1861 1960 8.902540 AAATATTTTTGTTTTGAGGACTTCCC 57.097 30.769 0.00 0.00 36.42 3.97
1924 2247 1.878522 CGGCCGTGAGATGCACTAC 60.879 63.158 19.50 0.00 45.49 2.73
1925 2248 1.517832 GGCCGTGAGATGCACTACT 59.482 57.895 0.00 0.00 45.49 2.57
1926 2249 0.744874 GGCCGTGAGATGCACTACTA 59.255 55.000 0.00 0.00 45.49 1.82
1927 2250 1.136305 GGCCGTGAGATGCACTACTAA 59.864 52.381 0.00 0.00 45.49 2.24
1967 2290 8.758829 AGTATAATCAACATCCGGCTATATGAA 58.241 33.333 7.79 0.00 0.00 2.57
1968 2291 9.035607 GTATAATCAACATCCGGCTATATGAAG 57.964 37.037 7.79 0.66 0.00 3.02
1976 2299 2.560504 CGGCTATATGAAGTTGCCACA 58.439 47.619 0.00 0.00 43.38 4.17
1978 2301 3.565482 CGGCTATATGAAGTTGCCACATT 59.435 43.478 0.00 0.00 43.38 2.71
1980 2303 5.334105 CGGCTATATGAAGTTGCCACATTAC 60.334 44.000 0.00 0.00 43.38 1.89
1984 2307 7.118390 GCTATATGAAGTTGCCACATTACCTAG 59.882 40.741 0.00 0.00 0.00 3.02
1987 2310 4.286032 TGAAGTTGCCACATTACCTAGAGT 59.714 41.667 0.00 0.00 0.00 3.24
1992 2315 5.435686 TGCCACATTACCTAGAGTCAATT 57.564 39.130 0.00 0.00 0.00 2.32
1994 2317 6.953101 TGCCACATTACCTAGAGTCAATTTA 58.047 36.000 0.00 0.00 0.00 1.40
2004 2327 8.312669 ACCTAGAGTCAATTTAATAGTCTGCT 57.687 34.615 0.00 0.00 0.00 4.24
2060 2383 6.423776 CCATTAATACATGGCCCATCTTTT 57.576 37.500 0.00 0.00 37.51 2.27
2061 2384 6.225318 CCATTAATACATGGCCCATCTTTTG 58.775 40.000 0.00 0.00 37.51 2.44
2062 2385 6.183360 CCATTAATACATGGCCCATCTTTTGT 60.183 38.462 0.00 0.00 37.51 2.83
2063 2386 6.463995 TTAATACATGGCCCATCTTTTGTC 57.536 37.500 0.00 0.00 0.00 3.18
2064 2387 2.610438 ACATGGCCCATCTTTTGTCT 57.390 45.000 0.00 0.00 0.00 3.41
2065 2388 2.450476 ACATGGCCCATCTTTTGTCTC 58.550 47.619 0.00 0.00 0.00 3.36
2066 2389 2.225091 ACATGGCCCATCTTTTGTCTCA 60.225 45.455 0.00 0.00 0.00 3.27
2067 2390 1.909700 TGGCCCATCTTTTGTCTCAC 58.090 50.000 0.00 0.00 0.00 3.51
2074 2399 5.392380 GCCCATCTTTTGTCTCACAAGTATG 60.392 44.000 0.00 0.00 39.53 2.39
2082 2407 3.324846 TGTCTCACAAGTATGTTGGAGCT 59.675 43.478 0.00 0.00 37.82 4.09
2099 2424 2.752640 TCGTGCTACAGCCGGCTA 60.753 61.111 32.30 14.74 41.18 3.93
2100 2425 2.582498 CGTGCTACAGCCGGCTAC 60.582 66.667 32.30 22.45 41.18 3.58
2103 2428 1.084370 GTGCTACAGCCGGCTACAAG 61.084 60.000 32.30 25.67 41.18 3.16
2114 2673 0.748367 GGCTACAAGCTTACAGCCCC 60.748 60.000 28.39 12.93 46.47 5.80
2115 2674 1.090052 GCTACAAGCTTACAGCCCCG 61.090 60.000 16.88 0.00 43.77 5.73
2116 2675 1.078708 TACAAGCTTACAGCCCCGC 60.079 57.895 0.00 0.00 43.77 6.13
2118 2677 1.675641 CAAGCTTACAGCCCCGCTT 60.676 57.895 0.00 0.00 43.77 4.68
2119 2678 1.377333 AAGCTTACAGCCCCGCTTC 60.377 57.895 0.00 0.00 43.77 3.86
2120 2679 1.842381 AAGCTTACAGCCCCGCTTCT 61.842 55.000 0.00 0.00 43.77 2.85
2121 2680 1.377333 GCTTACAGCCCCGCTTCTT 60.377 57.895 0.00 0.00 36.40 2.52
2131 2701 1.406205 CCCCGCTTCTTTTCTCTCTCC 60.406 57.143 0.00 0.00 0.00 3.71
2134 2704 2.495669 CCGCTTCTTTTCTCTCTCCTCT 59.504 50.000 0.00 0.00 0.00 3.69
2144 2714 6.518208 TTTCTCTCTCCTCTAACTAAGCAC 57.482 41.667 0.00 0.00 0.00 4.40
2151 2721 8.982723 TCTCTCCTCTAACTAAGCACAAATATT 58.017 33.333 0.00 0.00 0.00 1.28
2179 2749 8.856490 ATTTAAATTCTTATGGCTTGCTTACG 57.144 30.769 0.00 0.00 0.00 3.18
2216 2798 2.040278 TGCTCTAAGTGGGTTGCAGAAT 59.960 45.455 0.00 0.00 0.00 2.40
2217 2799 2.680339 GCTCTAAGTGGGTTGCAGAATC 59.320 50.000 0.00 0.00 0.00 2.52
2218 2800 2.932614 CTCTAAGTGGGTTGCAGAATCG 59.067 50.000 0.00 0.00 0.00 3.34
2267 2850 6.414408 AAGCTTTAAATGTCTGACAGATCG 57.586 37.500 16.46 3.89 0.00 3.69
2385 3287 5.649395 TCATGAAAGCACTCCAAAAGATAGG 59.351 40.000 0.00 0.00 0.00 2.57
2386 3288 3.758554 TGAAAGCACTCCAAAAGATAGGC 59.241 43.478 0.00 0.00 0.00 3.93
2387 3289 3.439857 AAGCACTCCAAAAGATAGGCA 57.560 42.857 0.00 0.00 0.00 4.75
2388 3290 3.659183 AGCACTCCAAAAGATAGGCAT 57.341 42.857 0.00 0.00 0.00 4.40
2389 3291 3.973425 AGCACTCCAAAAGATAGGCATT 58.027 40.909 0.00 0.00 0.00 3.56
2390 3292 5.116084 AGCACTCCAAAAGATAGGCATTA 57.884 39.130 0.00 0.00 0.00 1.90
2391 3293 5.699143 AGCACTCCAAAAGATAGGCATTAT 58.301 37.500 0.00 0.00 0.00 1.28
2392 3294 5.533903 AGCACTCCAAAAGATAGGCATTATG 59.466 40.000 0.00 0.00 0.00 1.90
2393 3295 5.278660 GCACTCCAAAAGATAGGCATTATGG 60.279 44.000 0.00 0.00 0.00 2.74
2418 3324 3.258872 TCAAAGGTCAATGCATGGGAAAG 59.741 43.478 0.00 0.00 0.00 2.62
2434 3340 5.127491 TGGGAAAGAACGAACAGTGTAAAT 58.873 37.500 0.00 0.00 0.00 1.40
2475 3382 8.315482 ACTAATCTCATCTGATCTTGATCATGG 58.685 37.037 12.94 4.13 0.00 3.66
2476 3383 4.895961 TCTCATCTGATCTTGATCATGGC 58.104 43.478 12.94 2.87 0.00 4.40
2478 3385 5.778750 TCTCATCTGATCTTGATCATGGCTA 59.221 40.000 12.94 0.00 0.00 3.93
2479 3386 6.269307 TCTCATCTGATCTTGATCATGGCTAA 59.731 38.462 12.94 0.00 0.00 3.09
2480 3387 6.834107 TCATCTGATCTTGATCATGGCTAAA 58.166 36.000 12.94 0.00 0.00 1.85
2482 3389 7.942894 TCATCTGATCTTGATCATGGCTAAATT 59.057 33.333 12.94 0.00 0.00 1.82
2497 3404 5.890985 TGGCTAAATTAATACACACAGGCAT 59.109 36.000 0.00 0.00 33.09 4.40
2499 3406 6.183360 GGCTAAATTAATACACACAGGCATGT 60.183 38.462 0.00 0.00 41.57 3.21
2570 3477 0.179062 TTTGTGCATGCCAACAACCC 60.179 50.000 19.83 0.00 0.00 4.11
2589 3497 6.127366 ACAACCCTGCTTATTTCCATTATGTG 60.127 38.462 0.00 0.00 0.00 3.21
2590 3498 5.518865 ACCCTGCTTATTTCCATTATGTGT 58.481 37.500 0.00 0.00 0.00 3.72
2591 3499 6.668645 ACCCTGCTTATTTCCATTATGTGTA 58.331 36.000 0.00 0.00 0.00 2.90
2592 3500 6.546034 ACCCTGCTTATTTCCATTATGTGTAC 59.454 38.462 0.00 0.00 0.00 2.90
2593 3501 6.772716 CCCTGCTTATTTCCATTATGTGTACT 59.227 38.462 0.00 0.00 0.00 2.73
2594 3502 7.041098 CCCTGCTTATTTCCATTATGTGTACTC 60.041 40.741 0.00 0.00 0.00 2.59
2595 3503 7.041098 CCTGCTTATTTCCATTATGTGTACTCC 60.041 40.741 0.00 0.00 0.00 3.85
2596 3504 7.573710 TGCTTATTTCCATTATGTGTACTCCT 58.426 34.615 0.00 0.00 0.00 3.69
2597 3505 8.710239 TGCTTATTTCCATTATGTGTACTCCTA 58.290 33.333 0.00 0.00 0.00 2.94
2598 3506 8.989980 GCTTATTTCCATTATGTGTACTCCTAC 58.010 37.037 0.00 0.00 0.00 3.18
2599 3507 9.490379 CTTATTTCCATTATGTGTACTCCTACC 57.510 37.037 0.00 0.00 0.00 3.18
2600 3508 6.877668 TTTCCATTATGTGTACTCCTACCA 57.122 37.500 0.00 0.00 0.00 3.25
2601 3509 5.864418 TCCATTATGTGTACTCCTACCAC 57.136 43.478 0.00 0.00 0.00 4.16
2602 3510 5.274015 TCCATTATGTGTACTCCTACCACA 58.726 41.667 0.00 0.00 0.00 4.17
2603 3511 5.128171 TCCATTATGTGTACTCCTACCACAC 59.872 44.000 0.00 0.00 42.29 3.82
2606 3514 2.244695 TGTGTACTCCTACCACACAGG 58.755 52.381 2.82 0.00 45.57 4.00
2607 3515 2.158430 TGTGTACTCCTACCACACAGGA 60.158 50.000 2.82 0.00 45.57 3.86
2630 3538 9.875708 AGGAGTAGTCTATAAACTGAAGATCAT 57.124 33.333 0.00 0.00 0.00 2.45
2657 3565 6.230472 TCTTGCTTGTTGCTTAATCTACAGA 58.770 36.000 0.00 0.00 43.37 3.41
2658 3566 6.881065 TCTTGCTTGTTGCTTAATCTACAGAT 59.119 34.615 0.00 0.00 43.37 2.90
2785 3950 9.342308 CTGCTAGTTTGAATATCCAAGGAAATA 57.658 33.333 0.00 0.00 0.00 1.40
2831 3997 2.757099 GTAGGGCCGACCGGAGAA 60.757 66.667 9.46 0.00 46.96 2.87
3010 4181 5.353938 CCCCATGCTCATAAAAGACAAATG 58.646 41.667 0.00 0.00 0.00 2.32
3151 4324 2.498167 AGGTGTGAAGTCTGATGCAAC 58.502 47.619 0.00 0.00 0.00 4.17
3159 4332 2.582052 AGTCTGATGCAACGGGAAAAA 58.418 42.857 2.62 0.00 0.00 1.94
3160 4333 3.157087 AGTCTGATGCAACGGGAAAAAT 58.843 40.909 2.62 0.00 0.00 1.82
3161 4334 4.331968 AGTCTGATGCAACGGGAAAAATA 58.668 39.130 2.62 0.00 0.00 1.40
3162 4335 4.949856 AGTCTGATGCAACGGGAAAAATAT 59.050 37.500 2.62 0.00 0.00 1.28
3163 4336 6.119536 AGTCTGATGCAACGGGAAAAATATA 58.880 36.000 2.62 0.00 0.00 0.86
3164 4337 6.038271 AGTCTGATGCAACGGGAAAAATATAC 59.962 38.462 2.62 0.00 0.00 1.47
3165 4338 6.038271 GTCTGATGCAACGGGAAAAATATACT 59.962 38.462 2.62 0.00 0.00 2.12
3189 4362 4.996062 ACTACGAATGTGGTAAAAACGG 57.004 40.909 0.00 0.00 38.13 4.44
3196 4369 6.594937 ACGAATGTGGTAAAAACGGTATACAT 59.405 34.615 5.01 0.00 0.00 2.29
3271 4444 9.311916 AGATGAAATGAATACGAGAGAGAAAAG 57.688 33.333 0.00 0.00 0.00 2.27
3371 5058 2.196997 AATTGCTAGCCCGTGCAGGA 62.197 55.000 13.29 0.00 45.00 3.86
3411 5098 5.012328 GTCTTTTGACGATGAGGATAGGT 57.988 43.478 0.00 0.00 39.89 3.08
3412 5099 4.806247 GTCTTTTGACGATGAGGATAGGTG 59.194 45.833 0.00 0.00 39.89 4.00
3413 5100 4.466370 TCTTTTGACGATGAGGATAGGTGT 59.534 41.667 0.00 0.00 0.00 4.16
3414 5101 4.819105 TTTGACGATGAGGATAGGTGTT 57.181 40.909 0.00 0.00 0.00 3.32
3429 5357 3.983821 AGGTGTTAGCTAGCCTAGAACT 58.016 45.455 12.13 3.14 0.00 3.01
3443 5371 7.957992 AGCCTAGAACTTAGAGCTAACTTTA 57.042 36.000 0.00 0.00 0.00 1.85
3457 5420 8.586744 AGAGCTAACTTTATTACTAGTATGGCC 58.413 37.037 2.79 0.00 0.00 5.36
3500 5463 7.593273 TGAAGCTTGTTTAACCATCGTAAAATG 59.407 33.333 2.10 0.00 0.00 2.32
3582 5563 0.969894 CCCTCGGTCACTCTGAAACT 59.030 55.000 0.00 0.00 0.00 2.66
3981 5968 2.436646 GCGTGGGTGGACATGGAG 60.437 66.667 0.00 0.00 0.00 3.86
3988 5975 2.606213 TGGACATGGAGGGCGACA 60.606 61.111 0.00 0.00 0.00 4.35
4047 6034 1.797933 CGTCGACAAGGAGCTGACG 60.798 63.158 17.16 6.17 45.06 4.35
4267 6263 3.367743 CGGGGTTCGAGACGGTGA 61.368 66.667 0.00 0.00 42.43 4.02
4680 6688 1.005867 GTTCGACCACCTACGCCAA 60.006 57.895 0.00 0.00 0.00 4.52
4803 7879 8.391106 GCTTAGGTTATATGTGTTCAACTCAAG 58.609 37.037 0.00 0.00 0.00 3.02
4897 8334 9.713713 TTACACAATGTAGCATACTTTACAGAA 57.286 29.630 0.00 0.00 43.54 3.02
4908 8345 7.282224 AGCATACTTTACAGAACAGTTTTGTGA 59.718 33.333 17.70 8.33 37.67 3.58
5002 8440 6.899393 AAATCTGATCCTTTTGCACACTTA 57.101 33.333 0.00 0.00 0.00 2.24
5132 8570 3.567164 CCTATTCTTGGTGTCATGATGCC 59.433 47.826 0.00 5.08 0.00 4.40
5149 8587 5.477510 TGATGCCCACATAATTTTGTTCAC 58.522 37.500 0.00 0.00 36.35 3.18
5154 8592 5.179182 GCCCACATAATTTTGTTCACAAAGG 59.821 40.000 5.31 2.80 45.34 3.11
5269 8714 6.071952 GGTCATTCAAACAAAGCAATCTAGGA 60.072 38.462 0.00 0.00 0.00 2.94
5356 8801 4.979815 CGTACTGGACGCATAACATATTCA 59.020 41.667 0.00 0.00 46.27 2.57
5486 8932 4.870991 GCGCTTTCTAATCTTAGTGAAGGT 59.129 41.667 0.00 0.00 33.09 3.50
5533 8983 6.908825 TCATAACAAGGACACATGCTTAAAC 58.091 36.000 0.00 0.00 34.19 2.01
5605 9055 1.977854 TGACCACTACTGCAGGATTGT 59.022 47.619 19.93 6.76 0.00 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.751767 ACAAATAGCAGAGGAAGAGAGG 57.248 45.455 0.00 0.00 0.00 3.69
1 2 8.177119 ACTATACAAATAGCAGAGGAAGAGAG 57.823 38.462 0.00 0.00 39.01 3.20
2 3 8.540507 AACTATACAAATAGCAGAGGAAGAGA 57.459 34.615 0.00 0.00 39.01 3.10
3 4 9.039870 CAAACTATACAAATAGCAGAGGAAGAG 57.960 37.037 0.00 0.00 39.01 2.85
4 5 8.540388 ACAAACTATACAAATAGCAGAGGAAGA 58.460 33.333 0.00 0.00 39.01 2.87
5 6 8.723942 ACAAACTATACAAATAGCAGAGGAAG 57.276 34.615 0.00 0.00 39.01 3.46
6 7 9.817809 CTACAAACTATACAAATAGCAGAGGAA 57.182 33.333 0.00 0.00 39.01 3.36
7 8 8.978472 ACTACAAACTATACAAATAGCAGAGGA 58.022 33.333 0.00 0.00 39.01 3.71
8 9 9.601217 AACTACAAACTATACAAATAGCAGAGG 57.399 33.333 0.00 0.00 39.01 3.69
33 34 5.054477 CCGAAAAGAGGTTCTGTACAAGAA 58.946 41.667 0.00 0.37 42.83 2.52
34 35 4.100498 ACCGAAAAGAGGTTCTGTACAAGA 59.900 41.667 0.00 0.00 39.29 3.02
35 36 4.211374 CACCGAAAAGAGGTTCTGTACAAG 59.789 45.833 0.00 0.00 40.59 3.16
36 37 4.124238 CACCGAAAAGAGGTTCTGTACAA 58.876 43.478 0.00 0.00 40.59 2.41
37 38 3.133362 ACACCGAAAAGAGGTTCTGTACA 59.867 43.478 0.00 0.00 40.59 2.90
38 39 3.725490 ACACCGAAAAGAGGTTCTGTAC 58.275 45.455 0.00 0.00 40.59 2.90
39 40 4.141892 TGAACACCGAAAAGAGGTTCTGTA 60.142 41.667 0.00 0.00 40.59 2.74
40 41 3.203716 GAACACCGAAAAGAGGTTCTGT 58.796 45.455 0.00 0.00 40.59 3.41
41 42 3.202906 TGAACACCGAAAAGAGGTTCTG 58.797 45.455 0.00 0.00 40.59 3.02
42 43 3.118371 ACTGAACACCGAAAAGAGGTTCT 60.118 43.478 0.00 0.00 40.59 3.01
43 44 3.203716 ACTGAACACCGAAAAGAGGTTC 58.796 45.455 0.00 0.00 40.59 3.62
44 45 3.277142 ACTGAACACCGAAAAGAGGTT 57.723 42.857 0.00 0.00 40.59 3.50
45 46 3.277142 AACTGAACACCGAAAAGAGGT 57.723 42.857 0.00 0.00 43.97 3.85
46 47 4.632538 AAAACTGAACACCGAAAAGAGG 57.367 40.909 0.00 0.00 0.00 3.69
47 48 9.724839 TTATTAAAAACTGAACACCGAAAAGAG 57.275 29.630 0.00 0.00 0.00 2.85
50 51 9.303537 CCTTTATTAAAAACTGAACACCGAAAA 57.696 29.630 0.00 0.00 0.00 2.29
51 52 8.684520 TCCTTTATTAAAAACTGAACACCGAAA 58.315 29.630 0.00 0.00 0.00 3.46
52 53 8.223177 TCCTTTATTAAAAACTGAACACCGAA 57.777 30.769 0.00 0.00 0.00 4.30
53 54 7.804843 TCCTTTATTAAAAACTGAACACCGA 57.195 32.000 0.00 0.00 0.00 4.69
54 55 8.911662 CAATCCTTTATTAAAAACTGAACACCG 58.088 33.333 0.00 0.00 0.00 4.94
55 56 8.708742 GCAATCCTTTATTAAAAACTGAACACC 58.291 33.333 0.00 0.00 0.00 4.16
56 57 8.424731 CGCAATCCTTTATTAAAAACTGAACAC 58.575 33.333 0.00 0.00 0.00 3.32
57 58 7.596995 CCGCAATCCTTTATTAAAAACTGAACA 59.403 33.333 0.00 0.00 0.00 3.18
58 59 7.062956 CCCGCAATCCTTTATTAAAAACTGAAC 59.937 37.037 0.00 0.00 0.00 3.18
59 60 7.093992 CCCGCAATCCTTTATTAAAAACTGAA 58.906 34.615 0.00 0.00 0.00 3.02
60 61 6.350612 CCCCGCAATCCTTTATTAAAAACTGA 60.351 38.462 0.00 0.00 0.00 3.41
61 62 5.810074 CCCCGCAATCCTTTATTAAAAACTG 59.190 40.000 0.00 0.00 0.00 3.16
62 63 5.482526 ACCCCGCAATCCTTTATTAAAAACT 59.517 36.000 0.00 0.00 0.00 2.66
63 64 5.726397 ACCCCGCAATCCTTTATTAAAAAC 58.274 37.500 0.00 0.00 0.00 2.43
78 79 0.887387 GTAGAGCAACAACCCCGCAA 60.887 55.000 0.00 0.00 0.00 4.85
81 82 0.034896 ACTGTAGAGCAACAACCCCG 59.965 55.000 0.00 0.00 0.00 5.73
120 122 7.046033 GCACACTGTGGTTACCTATACTATTT 58.954 38.462 13.09 0.00 33.64 1.40
122 124 5.897824 AGCACACTGTGGTTACCTATACTAT 59.102 40.000 13.09 0.00 41.72 2.12
125 127 4.467198 AGCACACTGTGGTTACCTATAC 57.533 45.455 13.09 0.00 41.72 1.47
126 128 5.512298 TCTAGCACACTGTGGTTACCTATA 58.488 41.667 18.57 0.00 41.72 1.31
127 129 4.350245 TCTAGCACACTGTGGTTACCTAT 58.650 43.478 18.57 0.00 41.72 2.57
128 130 3.762288 CTCTAGCACACTGTGGTTACCTA 59.238 47.826 18.57 6.30 41.72 3.08
140 142 4.954875 AGGCTCAATATTCTCTAGCACAC 58.045 43.478 9.55 0.00 34.85 3.82
341 349 7.995663 AGTTATCTAGATATCTGAGTCCCACT 58.004 38.462 18.53 10.31 0.00 4.00
355 363 6.825721 CCAAGCAACCTTTGAGTTATCTAGAT 59.174 38.462 10.73 10.73 0.00 1.98
371 379 0.108396 AACCCAAATGCCAAGCAACC 59.892 50.000 0.00 0.00 43.62 3.77
429 437 7.719633 GCCCTTGGATTCATACTTCATTTAGTA 59.280 37.037 0.00 0.00 35.25 1.82
443 451 1.851304 GTGGATTGCCCTTGGATTCA 58.149 50.000 0.00 0.00 35.38 2.57
452 460 2.109126 GCTCAGACGTGGATTGCCC 61.109 63.158 0.00 0.00 0.00 5.36
589 597 5.620206 TGATTTTGTCTTTACTGCTGAGGA 58.380 37.500 0.00 0.00 0.00 3.71
599 607 8.506168 ACTGTTCAGAACTGATTTTGTCTTTA 57.494 30.769 23.07 0.00 39.64 1.85
657 665 5.160607 TGGAAATTCGAGGAGCTCTAAAA 57.839 39.130 14.64 3.89 0.00 1.52
823 841 0.245266 TCCGAATGCACGTTGCTAGA 59.755 50.000 10.54 0.14 45.31 2.43
946 966 4.497674 CCGGTAGTAGTGCTAATGAGTGAC 60.498 50.000 0.00 0.00 0.00 3.67
968 996 1.174712 TTGCTTCTGCTTGCTGGACC 61.175 55.000 0.00 0.00 40.48 4.46
1010 1038 2.254350 CGTTGAGTGAGGACGCGA 59.746 61.111 15.93 0.00 0.00 5.87
1016 1044 1.006102 AAGCCGACGTTGAGTGAGG 60.006 57.895 3.74 0.00 0.00 3.86
1123 1151 4.871993 AGATAAAGCAGACGCATGAAAG 57.128 40.909 0.00 0.00 42.27 2.62
1169 1213 8.306038 ACAATCACAGGTACACTAACGTAATAA 58.694 33.333 0.00 0.00 0.00 1.40
1170 1214 7.829725 ACAATCACAGGTACACTAACGTAATA 58.170 34.615 0.00 0.00 0.00 0.98
1171 1215 6.694447 ACAATCACAGGTACACTAACGTAAT 58.306 36.000 0.00 0.00 0.00 1.89
1216 1260 4.592485 AGTTCGATCCATAGTGGTGATC 57.408 45.455 0.00 0.00 39.03 2.92
1224 1268 6.042777 TGTCTTTTGCTAGTTCGATCCATAG 58.957 40.000 0.00 0.00 0.00 2.23
1251 1295 0.861185 CACACACACACGTCTCATGG 59.139 55.000 0.00 0.00 0.00 3.66
1261 1305 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1267 1311 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1268 1312 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1269 1313 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1270 1314 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1271 1315 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1272 1316 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1273 1317 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1274 1318 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1275 1319 1.598882 AACACACACACACACACACA 58.401 45.000 0.00 0.00 0.00 3.72
1276 1320 2.095213 CCTAACACACACACACACACAC 59.905 50.000 0.00 0.00 0.00 3.82
1277 1321 2.028020 TCCTAACACACACACACACACA 60.028 45.455 0.00 0.00 0.00 3.72
1278 1322 2.623535 TCCTAACACACACACACACAC 58.376 47.619 0.00 0.00 0.00 3.82
1279 1323 3.462982 GATCCTAACACACACACACACA 58.537 45.455 0.00 0.00 0.00 3.72
1280 1324 2.806244 GGATCCTAACACACACACACAC 59.194 50.000 3.84 0.00 0.00 3.82
1281 1325 2.703536 AGGATCCTAACACACACACACA 59.296 45.455 14.27 0.00 0.00 3.72
1282 1326 3.402628 AGGATCCTAACACACACACAC 57.597 47.619 14.27 0.00 0.00 3.82
1283 1327 3.135712 ACAAGGATCCTAACACACACACA 59.864 43.478 16.55 0.00 0.00 3.72
1284 1328 3.740115 ACAAGGATCCTAACACACACAC 58.260 45.455 16.55 0.00 0.00 3.82
1285 1329 3.244422 GGACAAGGATCCTAACACACACA 60.244 47.826 16.55 0.00 35.68 3.72
1286 1330 3.335579 GGACAAGGATCCTAACACACAC 58.664 50.000 16.55 1.28 35.68 3.82
1337 1388 5.755849 AGACAAATAATTCGGGATGGAAGT 58.244 37.500 0.00 0.00 0.00 3.01
1344 1395 6.889722 AGAAATCCAAGACAAATAATTCGGGA 59.110 34.615 0.00 0.00 0.00 5.14
1436 1491 4.976731 CGTCAGTCAGCCTATGTTATGTAC 59.023 45.833 0.00 0.00 0.00 2.90
1437 1492 4.037565 CCGTCAGTCAGCCTATGTTATGTA 59.962 45.833 0.00 0.00 0.00 2.29
1438 1493 3.181475 CCGTCAGTCAGCCTATGTTATGT 60.181 47.826 0.00 0.00 0.00 2.29
1473 1528 2.416893 TGCGTGCATATTAAGCGACAAA 59.583 40.909 0.00 0.00 33.85 2.83
1478 1533 2.365948 CAACTGCGTGCATATTAAGCG 58.634 47.619 0.00 0.00 33.85 4.68
1548 1603 1.182667 GTTGTATTTCACCAGGGGCC 58.817 55.000 0.00 0.00 0.00 5.80
1618 1707 3.295973 AGAGAGACCAGAGATAGGCAAC 58.704 50.000 0.00 0.00 0.00 4.17
1750 1847 6.541278 TGGATGCAAATTTGATCAAAACAACA 59.459 30.769 23.91 18.86 33.56 3.33
1812 1909 9.700831 TTTTCCATTTAATTTTCCTTTTTCCCA 57.299 25.926 0.00 0.00 0.00 4.37
1942 2265 8.942338 TTCATATAGCCGGATGTTGATTATAC 57.058 34.615 5.05 0.00 0.00 1.47
1947 2270 5.489792 ACTTCATATAGCCGGATGTTGAT 57.510 39.130 5.05 0.00 0.00 2.57
1948 2271 4.955811 ACTTCATATAGCCGGATGTTGA 57.044 40.909 5.05 0.45 0.00 3.18
1951 2274 3.403038 GCAACTTCATATAGCCGGATGT 58.597 45.455 5.05 0.00 0.00 3.06
1953 2276 3.059352 GGCAACTTCATATAGCCGGAT 57.941 47.619 5.05 0.00 35.42 4.18
1954 2277 2.543777 GGCAACTTCATATAGCCGGA 57.456 50.000 5.05 0.00 35.42 5.14
1967 2290 3.838317 TGACTCTAGGTAATGTGGCAACT 59.162 43.478 0.00 0.00 37.61 3.16
1968 2291 4.202245 TGACTCTAGGTAATGTGGCAAC 57.798 45.455 0.00 0.00 0.00 4.17
1978 2301 9.422681 AGCAGACTATTAAATTGACTCTAGGTA 57.577 33.333 0.00 0.00 0.00 3.08
1980 2303 9.906660 CTAGCAGACTATTAAATTGACTCTAGG 57.093 37.037 0.00 0.00 0.00 3.02
2038 2361 6.819284 ACAAAAGATGGGCCATGTATTAATG 58.181 36.000 26.77 18.02 0.00 1.90
2055 2378 6.353323 TCCAACATACTTGTGAGACAAAAGA 58.647 36.000 8.41 0.00 37.69 2.52
2056 2379 6.618287 TCCAACATACTTGTGAGACAAAAG 57.382 37.500 0.00 0.00 37.69 2.27
2058 2381 4.515191 GCTCCAACATACTTGTGAGACAAA 59.485 41.667 0.00 0.00 37.69 2.83
2059 2382 4.065088 GCTCCAACATACTTGTGAGACAA 58.935 43.478 0.00 0.00 35.83 3.18
2060 2383 3.324846 AGCTCCAACATACTTGTGAGACA 59.675 43.478 0.00 0.00 35.83 3.41
2061 2384 3.929610 GAGCTCCAACATACTTGTGAGAC 59.070 47.826 0.87 0.00 35.83 3.36
2062 2385 3.367395 CGAGCTCCAACATACTTGTGAGA 60.367 47.826 8.47 0.00 35.83 3.27
2063 2386 2.926200 CGAGCTCCAACATACTTGTGAG 59.074 50.000 8.47 0.00 35.83 3.51
2064 2387 2.299013 ACGAGCTCCAACATACTTGTGA 59.701 45.455 8.47 0.00 35.83 3.58
2065 2388 2.413112 CACGAGCTCCAACATACTTGTG 59.587 50.000 8.47 2.41 37.99 3.33
2066 2389 2.688507 CACGAGCTCCAACATACTTGT 58.311 47.619 8.47 0.00 37.82 3.16
2067 2390 1.394917 GCACGAGCTCCAACATACTTG 59.605 52.381 8.47 0.00 37.91 3.16
2082 2407 2.752640 TAGCCGGCTGTAGCACGA 60.753 61.111 38.98 13.89 44.36 4.35
2114 2673 3.866883 AGAGGAGAGAGAAAAGAAGCG 57.133 47.619 0.00 0.00 0.00 4.68
2115 2674 6.280855 AGTTAGAGGAGAGAGAAAAGAAGC 57.719 41.667 0.00 0.00 0.00 3.86
2116 2675 7.973944 GCTTAGTTAGAGGAGAGAGAAAAGAAG 59.026 40.741 0.00 0.00 0.00 2.85
2118 2677 6.948886 TGCTTAGTTAGAGGAGAGAGAAAAGA 59.051 38.462 0.00 0.00 0.00 2.52
2119 2678 7.033185 GTGCTTAGTTAGAGGAGAGAGAAAAG 58.967 42.308 0.00 0.00 0.00 2.27
2120 2679 6.493802 TGTGCTTAGTTAGAGGAGAGAGAAAA 59.506 38.462 0.00 0.00 0.00 2.29
2121 2680 6.010850 TGTGCTTAGTTAGAGGAGAGAGAAA 58.989 40.000 0.00 0.00 0.00 2.52
2168 2738 2.088950 TAAGGTGACGTAAGCAAGCC 57.911 50.000 4.63 0.00 45.62 4.35
2171 2741 7.010738 GCAAGTATAATAAGGTGACGTAAGCAA 59.989 37.037 4.63 0.00 45.62 3.91
2172 2742 6.477688 GCAAGTATAATAAGGTGACGTAAGCA 59.522 38.462 4.63 0.00 45.62 3.91
2179 2749 9.250624 CACTTAGAGCAAGTATAATAAGGTGAC 57.749 37.037 0.00 0.00 46.04 3.67
2216 2798 5.186215 TCAACTCCCATAATTACTGTCACGA 59.814 40.000 0.00 0.00 0.00 4.35
2217 2799 5.291128 GTCAACTCCCATAATTACTGTCACG 59.709 44.000 0.00 0.00 0.00 4.35
2218 2800 6.407202 AGTCAACTCCCATAATTACTGTCAC 58.593 40.000 0.00 0.00 0.00 3.67
2267 2850 3.114065 GTTACATCGTGATTCTCGGTCC 58.886 50.000 8.14 0.00 0.00 4.46
2271 2854 2.214244 CGCAGTTACATCGTGATTCTCG 59.786 50.000 1.81 1.81 0.00 4.04
2299 2884 7.449704 TGCTAGCTAGATCTGATATTGACTTCA 59.550 37.037 25.15 3.46 0.00 3.02
2385 3287 5.535333 CATTGACCTTTGATCCCATAATGC 58.465 41.667 0.00 0.00 0.00 3.56
2386 3288 5.069383 TGCATTGACCTTTGATCCCATAATG 59.931 40.000 0.00 0.00 0.00 1.90
2387 3289 5.210430 TGCATTGACCTTTGATCCCATAAT 58.790 37.500 0.00 0.00 0.00 1.28
2388 3290 4.608269 TGCATTGACCTTTGATCCCATAA 58.392 39.130 0.00 0.00 0.00 1.90
2389 3291 4.248174 TGCATTGACCTTTGATCCCATA 57.752 40.909 0.00 0.00 0.00 2.74
2390 3292 3.104519 TGCATTGACCTTTGATCCCAT 57.895 42.857 0.00 0.00 0.00 4.00
2391 3293 2.601240 TGCATTGACCTTTGATCCCA 57.399 45.000 0.00 0.00 0.00 4.37
2392 3294 2.101917 CCATGCATTGACCTTTGATCCC 59.898 50.000 0.00 0.00 0.00 3.85
2393 3295 2.101917 CCCATGCATTGACCTTTGATCC 59.898 50.000 0.00 0.00 0.00 3.36
2418 3324 5.511088 ACATCGATTTACACTGTTCGTTC 57.489 39.130 0.00 0.00 33.52 3.95
2475 3382 6.692681 CACATGCCTGTGTGTATTAATTTAGC 59.307 38.462 13.40 0.00 46.33 3.09
2497 3404 0.472044 TTCACTGGCTAGGCAACACA 59.528 50.000 20.64 2.20 41.41 3.72
2499 3406 2.584835 AATTCACTGGCTAGGCAACA 57.415 45.000 20.64 3.95 41.41 3.33
2570 3477 7.716998 AGGAGTACACATAATGGAAATAAGCAG 59.283 37.037 0.00 0.00 0.00 4.24
2593 3501 2.648304 AGACTACTCCTGTGTGGTAGGA 59.352 50.000 0.00 0.00 41.91 2.94
2594 3502 3.088789 AGACTACTCCTGTGTGGTAGG 57.911 52.381 0.00 0.00 37.73 3.18
2595 3503 7.556996 AGTTTATAGACTACTCCTGTGTGGTAG 59.443 40.741 0.00 0.00 38.89 3.18
2596 3504 7.338703 CAGTTTATAGACTACTCCTGTGTGGTA 59.661 40.741 0.00 0.00 37.07 3.25
2597 3505 6.153000 CAGTTTATAGACTACTCCTGTGTGGT 59.847 42.308 0.00 0.00 37.07 4.16
2598 3506 6.377429 TCAGTTTATAGACTACTCCTGTGTGG 59.623 42.308 0.00 0.00 37.10 4.17
2599 3507 7.392494 TCAGTTTATAGACTACTCCTGTGTG 57.608 40.000 0.00 0.00 0.00 3.82
2600 3508 7.889073 TCTTCAGTTTATAGACTACTCCTGTGT 59.111 37.037 0.00 0.00 0.00 3.72
2601 3509 8.282455 TCTTCAGTTTATAGACTACTCCTGTG 57.718 38.462 0.00 0.00 0.00 3.66
2602 3510 9.127277 GATCTTCAGTTTATAGACTACTCCTGT 57.873 37.037 0.00 0.00 0.00 4.00
2603 3511 9.126151 TGATCTTCAGTTTATAGACTACTCCTG 57.874 37.037 0.00 0.00 0.00 3.86
2604 3512 9.875708 ATGATCTTCAGTTTATAGACTACTCCT 57.124 33.333 0.00 0.00 0.00 3.69
2657 3565 1.006220 TGCACGTCAGAAGCGACAT 60.006 52.632 0.00 0.00 35.54 3.06
2658 3566 1.661509 CTGCACGTCAGAAGCGACA 60.662 57.895 8.72 0.00 45.72 4.35
2785 3950 9.757227 TCGAAACAAATGATTTTCCATTTTACT 57.243 25.926 0.00 0.00 42.26 2.24
2842 4010 8.103305 ACACAGTAATTAACACCAGATCTTGAT 58.897 33.333 0.00 0.00 0.00 2.57
2883 4051 8.587950 CAGATCTGTCAAACTTTTACGTCTATC 58.412 37.037 14.95 0.00 0.00 2.08
2889 4057 6.771188 ACTCAGATCTGTCAAACTTTTACG 57.229 37.500 21.92 0.00 0.00 3.18
2898 4066 4.346709 TGGTTTGGTACTCAGATCTGTCAA 59.653 41.667 21.92 15.33 0.00 3.18
3010 4181 4.623932 TGACCTAGATCCCATAATGCAC 57.376 45.455 0.00 0.00 0.00 4.57
3162 4335 9.502145 CGTTTTTACCACATTCGTAGTATAGTA 57.498 33.333 0.00 0.00 0.00 1.82
3163 4336 7.489113 CCGTTTTTACCACATTCGTAGTATAGT 59.511 37.037 0.00 0.00 0.00 2.12
3164 4337 7.489113 ACCGTTTTTACCACATTCGTAGTATAG 59.511 37.037 0.00 0.00 0.00 1.31
3165 4338 7.319646 ACCGTTTTTACCACATTCGTAGTATA 58.680 34.615 0.00 0.00 0.00 1.47
3271 4444 4.989279 TGAGGCTTGGCTAATCAAAATC 57.011 40.909 0.00 0.00 0.00 2.17
3335 5015 6.716934 AGCAATTCTACCGAGAAGAAGATA 57.283 37.500 0.00 0.00 44.90 1.98
3338 5018 4.742659 GCTAGCAATTCTACCGAGAAGAAG 59.257 45.833 10.63 0.00 44.90 2.85
3340 5020 3.068307 GGCTAGCAATTCTACCGAGAAGA 59.932 47.826 18.24 0.00 44.90 2.87
3341 5021 3.385577 GGCTAGCAATTCTACCGAGAAG 58.614 50.000 18.24 0.00 44.90 2.85
3342 5022 2.102588 GGGCTAGCAATTCTACCGAGAA 59.897 50.000 18.24 0.00 45.75 2.87
3344 5024 1.603172 CGGGCTAGCAATTCTACCGAG 60.603 57.143 18.24 0.00 38.49 4.63
3345 5025 0.387929 CGGGCTAGCAATTCTACCGA 59.612 55.000 18.24 0.00 38.49 4.69
3346 5026 0.104304 ACGGGCTAGCAATTCTACCG 59.896 55.000 18.24 19.46 40.66 4.02
3347 5027 1.583054 CACGGGCTAGCAATTCTACC 58.417 55.000 18.24 5.42 0.00 3.18
3371 5058 1.525995 CACGGTCCAACCAGTGCTT 60.526 57.895 7.71 0.00 38.47 3.91
3377 5064 1.065345 TCAAAAGACACGGTCCAACCA 60.065 47.619 0.00 0.00 38.47 3.67
3410 5097 6.696441 TCTAAGTTCTAGGCTAGCTAACAC 57.304 41.667 21.38 11.78 0.00 3.32
3411 5098 5.299782 GCTCTAAGTTCTAGGCTAGCTAACA 59.700 44.000 21.38 2.97 0.00 2.41
3412 5099 5.533528 AGCTCTAAGTTCTAGGCTAGCTAAC 59.466 44.000 16.85 15.74 37.30 2.34
3413 5100 5.697067 AGCTCTAAGTTCTAGGCTAGCTAA 58.303 41.667 16.85 4.13 37.30 3.09
3414 5101 5.313280 AGCTCTAAGTTCTAGGCTAGCTA 57.687 43.478 16.85 4.46 37.30 3.32
3457 5420 4.454847 AGCTTCATTCATCGGCATAATCTG 59.545 41.667 0.00 0.00 0.00 2.90
3500 5463 0.822121 ACACGCCAAAGAAAGGGGAC 60.822 55.000 3.17 0.00 41.25 4.46
3582 5563 4.331166 TCGCCGTCGACTTCGCAA 62.331 61.111 14.70 0.00 40.21 4.85
3988 5975 4.681978 GAAGCACCGCACCTCCGT 62.682 66.667 0.00 0.00 0.00 4.69
4101 6088 1.437986 GTAGGTCTCGCGCAGGAAT 59.562 57.895 8.75 0.00 0.00 3.01
4155 6142 2.347490 GGCTTCTTGTCCGGCTCA 59.653 61.111 0.00 0.00 0.00 4.26
4267 6263 4.575973 GGCCCGCAGCTCCATCAT 62.576 66.667 0.00 0.00 43.05 2.45
4393 6401 1.895020 TACGGCACCACCTGGATCAC 61.895 60.000 0.00 0.00 38.94 3.06
4796 7872 2.893489 GGAGGGTTTTGATGCTTGAGTT 59.107 45.455 0.00 0.00 0.00 3.01
4803 7879 2.485122 CGCGGAGGGTTTTGATGC 59.515 61.111 0.00 0.00 34.98 3.91
4897 8334 5.854157 CGCTATCGTATTTCACAAAACTGT 58.146 37.500 0.00 0.00 0.00 3.55
4980 8417 7.201767 GCTATAAGTGTGCAAAAGGATCAGATT 60.202 37.037 0.00 0.00 0.00 2.40
5002 8440 4.202305 GCACCCAGTCAATTCTCTAGCTAT 60.202 45.833 0.00 0.00 0.00 2.97
5132 8570 7.169645 CAGTCCTTTGTGAACAAAATTATGTGG 59.830 37.037 9.70 6.06 44.24 4.17
5149 8587 6.915843 ACTTACGTTAAAATTGCAGTCCTTTG 59.084 34.615 0.00 0.00 0.00 2.77
5154 8592 6.203647 ACCAACTTACGTTAAAATTGCAGTC 58.796 36.000 0.00 0.00 0.00 3.51
5269 8714 3.689872 TTCAGCTATCCCACTCCTAGT 57.310 47.619 0.00 0.00 0.00 2.57
5389 8835 3.865745 AGATTGTTCTCGTTATTCCGCAG 59.134 43.478 0.00 0.00 0.00 5.18
5479 8925 6.314784 GCTCAACATTATACAACACCTTCAC 58.685 40.000 0.00 0.00 0.00 3.18
5486 8932 7.890515 TGAATTTGGCTCAACATTATACAACA 58.109 30.769 0.00 0.00 0.00 3.33
5494 8940 6.875195 CCTTGTTATGAATTTGGCTCAACATT 59.125 34.615 0.00 0.00 0.00 2.71
5533 8983 4.261197 GCTTCACCCACTACAAGACAAAAG 60.261 45.833 0.00 0.00 0.00 2.27
5605 9055 3.390521 CCACCCGCCACTGCTAGA 61.391 66.667 0.00 0.00 34.43 2.43


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

AutoCloner maintained by Alex Coulton.