Multiple sequence alignment - TraesCS5A01G204900

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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 TraesCS5A01G204900 chr5A 100.000 4317 0 0 1 4317 414753356 414757672 0.000000e+00 7973
1 TraesCS5A01G204900 chr5B 87.718 3778 207 122 101 3754 369638621 369634977 0.000000e+00 4169
2 TraesCS5A01G204900 chr5B 85.449 323 23 11 3818 4139 369634885 369634586 9.010000e-82 315
3 TraesCS5A01G204900 chr5D 91.680 2548 116 46 1257 3751 319506592 319504088 0.000000e+00 3443
4 TraesCS5A01G204900 chr5D 81.231 1284 67 58 3 1192 319507801 319506598 0.000000e+00 876
5 TraesCS5A01G204900 chr5D 86.232 552 44 16 3784 4317 319504023 319503486 1.740000e-158 569
6 TraesCS5A01G204900 chr7D 84.166 821 82 29 1630 2431 624903512 624902721 0.000000e+00 752


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 TraesCS5A01G204900 chr5A 414753356 414757672 4316 False 7973.000000 7973 100.0000 1 4317 1 chr5A.!!$F1 4316
1 TraesCS5A01G204900 chr5B 369634586 369638621 4035 True 2242.000000 4169 86.5835 101 4139 2 chr5B.!!$R1 4038
2 TraesCS5A01G204900 chr5D 319503486 319507801 4315 True 1629.333333 3443 86.3810 3 4317 3 chr5D.!!$R1 4314
3 TraesCS5A01G204900 chr7D 624902721 624903512 791 True 752.000000 752 84.1660 1630 2431 1 chr7D.!!$R1 801

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
869 969 0.033504 TTCGTTCACAGAGGAGTGGC 59.966 55.0 0.0 0.0 39.93 5.01 F
1555 1701 0.033504 TGATTCCGATTAGCCTCCGC 59.966 55.0 0.0 0.0 0.00 5.54 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1879 2063 0.110295 TAGCAAAACTGGCAGGCAGA 59.890 50.0 29.85 2.92 0.00 4.26 R
3383 3604 0.179092 GCCTGCCTGGATGCAAAATC 60.179 55.0 0.00 0.00 41.51 2.17 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
51 52 4.236935 CATGGCCACAAGACATAAACAAC 58.763 43.478 8.16 0.00 0.00 3.32
59 60 0.453782 GACATAAACAACACCGGCGC 60.454 55.000 0.00 0.00 0.00 6.53
97 108 4.742201 CTCCACCCCGTGACGCAG 62.742 72.222 0.00 0.00 35.23 5.18
124 138 7.621832 TTTTTAATCATCAGACACGCAAAAG 57.378 32.000 0.00 0.00 0.00 2.27
196 213 4.157840 CAGCCATAAACCCAAAAGTCTACC 59.842 45.833 0.00 0.00 0.00 3.18
198 215 3.128068 CCATAAACCCAAAAGTCTACCGC 59.872 47.826 0.00 0.00 0.00 5.68
199 216 1.232119 AAACCCAAAAGTCTACCGCG 58.768 50.000 0.00 0.00 0.00 6.46
601 653 4.253685 CACCTTTCCTCTCGCTTGATTAA 58.746 43.478 0.00 0.00 0.00 1.40
602 654 4.878397 CACCTTTCCTCTCGCTTGATTAAT 59.122 41.667 0.00 0.00 0.00 1.40
603 655 5.007136 CACCTTTCCTCTCGCTTGATTAATC 59.993 44.000 8.60 8.60 0.00 1.75
744 827 0.263172 AGAGGCTAGGCTTGGCTAGA 59.737 55.000 27.93 1.46 40.49 2.43
745 828 0.678950 GAGGCTAGGCTTGGCTAGAG 59.321 60.000 27.93 11.43 40.49 2.43
772 855 4.072839 TGGAGCAGTATACATACGAGAGG 58.927 47.826 5.50 0.00 38.28 3.69
773 856 3.119779 GGAGCAGTATACATACGAGAGGC 60.120 52.174 5.50 0.00 38.28 4.70
776 859 3.366476 GCAGTATACATACGAGAGGCAGG 60.366 52.174 5.50 0.00 38.28 4.85
808 898 4.697756 CGCGGTCAAGGCTGGGAA 62.698 66.667 0.00 0.00 0.00 3.97
812 902 0.035056 CGGTCAAGGCTGGGAAAGAT 60.035 55.000 0.00 0.00 0.00 2.40
817 917 2.019984 CAAGGCTGGGAAAGATAGCAC 58.980 52.381 0.00 0.00 39.15 4.40
828 928 1.650536 GATAGCACCGTCGTCGTCG 60.651 63.158 4.87 4.87 38.55 5.12
829 929 3.729906 ATAGCACCGTCGTCGTCGC 62.730 63.158 6.36 3.23 36.96 5.19
835 935 4.806481 CGTCGTCGTCGCCGTCAT 62.806 66.667 0.00 0.00 33.79 3.06
836 936 2.943034 GTCGTCGTCGCCGTCATC 60.943 66.667 0.00 0.00 36.96 2.92
837 937 4.509883 TCGTCGTCGCCGTCATCG 62.510 66.667 0.00 0.00 36.96 3.84
838 938 4.806481 CGTCGTCGCCGTCATCGT 62.806 66.667 0.00 0.00 35.01 3.73
839 939 2.503375 GTCGTCGCCGTCATCGTT 60.503 61.111 0.00 0.00 35.01 3.85
840 940 2.202388 TCGTCGCCGTCATCGTTC 60.202 61.111 0.00 0.00 35.01 3.95
841 941 3.594827 CGTCGCCGTCATCGTTCG 61.595 66.667 0.00 0.00 35.01 3.95
842 942 2.503375 GTCGCCGTCATCGTTCGT 60.503 61.111 0.00 0.00 34.59 3.85
845 945 2.687436 GCCGTCATCGTTCGTTCG 59.313 61.111 0.00 0.00 35.01 3.95
869 969 0.033504 TTCGTTCACAGAGGAGTGGC 59.966 55.000 0.00 0.00 39.93 5.01
876 976 1.669115 CAGAGGAGTGGCGGTGTTG 60.669 63.158 0.00 0.00 0.00 3.33
889 989 0.321122 GGTGTTGGCAGTGAGAGAGG 60.321 60.000 0.00 0.00 0.00 3.69
890 990 0.321122 GTGTTGGCAGTGAGAGAGGG 60.321 60.000 0.00 0.00 0.00 4.30
892 992 0.321122 GTTGGCAGTGAGAGAGGGTG 60.321 60.000 0.00 0.00 0.00 4.61
933 1043 1.382420 CAGGGGAGGGGAGTGAGAG 60.382 68.421 0.00 0.00 0.00 3.20
953 1063 5.377478 AGAGACGAAATCCATTTATTCCCC 58.623 41.667 0.00 0.00 0.00 4.81
1040 1168 2.503061 CATAGGCCACGAGCAGCT 59.497 61.111 5.01 0.00 46.50 4.24
1099 1230 2.501723 GCCAGAAAGGAGTCAGGTATGA 59.498 50.000 0.00 0.00 41.22 2.15
1101 1232 4.701765 CCAGAAAGGAGTCAGGTATGATG 58.298 47.826 0.00 0.00 41.22 3.07
1112 1243 1.974236 AGGTATGATGCTACTGCCCTC 59.026 52.381 0.00 0.00 38.71 4.30
1133 1264 0.676782 CCCTTTCTCGATTTGGGCGT 60.677 55.000 0.00 0.00 0.00 5.68
1147 1278 4.072088 GCGTGTTCGGCCAGTTCG 62.072 66.667 2.24 1.48 37.56 3.95
1148 1279 3.411351 CGTGTTCGGCCAGTTCGG 61.411 66.667 2.24 0.00 38.11 4.30
1175 1306 0.537188 AATCTCGGGATTGACAGCGT 59.463 50.000 10.42 0.00 40.30 5.07
1180 1311 1.523938 GGGATTGACAGCGTAGGCC 60.524 63.158 3.28 0.00 41.24 5.19
1212 1343 4.208686 CCTCGCCCGCCAGTAGTC 62.209 72.222 0.00 0.00 0.00 2.59
1214 1345 3.127352 CTCGCCCGCCAGTAGTCTC 62.127 68.421 0.00 0.00 0.00 3.36
1218 1349 1.730451 GCCCGCCAGTAGTCTCTCTC 61.730 65.000 0.00 0.00 0.00 3.20
1221 1352 1.134220 CCGCCAGTAGTCTCTCTCTCT 60.134 57.143 0.00 0.00 0.00 3.10
1223 1354 2.158957 CGCCAGTAGTCTCTCTCTCTCT 60.159 54.545 0.00 0.00 0.00 3.10
1226 1357 4.740934 GCCAGTAGTCTCTCTCTCTCTCTC 60.741 54.167 0.00 0.00 0.00 3.20
1227 1358 4.651503 CCAGTAGTCTCTCTCTCTCTCTCT 59.348 50.000 0.00 0.00 0.00 3.10
1228 1359 5.221342 CCAGTAGTCTCTCTCTCTCTCTCTC 60.221 52.000 0.00 0.00 0.00 3.20
1229 1360 5.596361 CAGTAGTCTCTCTCTCTCTCTCTCT 59.404 48.000 0.00 0.00 0.00 3.10
1230 1361 5.830991 AGTAGTCTCTCTCTCTCTCTCTCTC 59.169 48.000 0.00 0.00 0.00 3.20
1231 1362 4.877773 AGTCTCTCTCTCTCTCTCTCTCT 58.122 47.826 0.00 0.00 0.00 3.10
1232 1363 4.892934 AGTCTCTCTCTCTCTCTCTCTCTC 59.107 50.000 0.00 0.00 0.00 3.20
1233 1364 4.892934 GTCTCTCTCTCTCTCTCTCTCTCT 59.107 50.000 0.00 0.00 0.00 3.10
1234 1365 5.009610 GTCTCTCTCTCTCTCTCTCTCTCTC 59.990 52.000 0.00 0.00 0.00 3.20
1235 1366 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1236 1367 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1237 1368 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1238 1369 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1239 1370 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1240 1371 5.523588 TCTCTCTCTCTCTCTCTCTCTCTT 58.476 45.833 0.00 0.00 0.00 2.85
1241 1372 5.596361 TCTCTCTCTCTCTCTCTCTCTCTTC 59.404 48.000 0.00 0.00 0.00 2.87
1242 1373 5.523588 TCTCTCTCTCTCTCTCTCTCTTCT 58.476 45.833 0.00 0.00 0.00 2.85
1243 1374 6.673583 TCTCTCTCTCTCTCTCTCTCTTCTA 58.326 44.000 0.00 0.00 0.00 2.10
1244 1375 7.301420 TCTCTCTCTCTCTCTCTCTCTTCTAT 58.699 42.308 0.00 0.00 0.00 1.98
1245 1376 7.786943 TCTCTCTCTCTCTCTCTCTCTTCTATT 59.213 40.741 0.00 0.00 0.00 1.73
1246 1377 8.324191 TCTCTCTCTCTCTCTCTCTTCTATTT 57.676 38.462 0.00 0.00 0.00 1.40
1247 1378 8.772250 TCTCTCTCTCTCTCTCTCTTCTATTTT 58.228 37.037 0.00 0.00 0.00 1.82
1248 1379 8.737168 TCTCTCTCTCTCTCTCTTCTATTTTG 57.263 38.462 0.00 0.00 0.00 2.44
1249 1380 8.328758 TCTCTCTCTCTCTCTCTTCTATTTTGT 58.671 37.037 0.00 0.00 0.00 2.83
1250 1381 8.877864 TCTCTCTCTCTCTCTTCTATTTTGTT 57.122 34.615 0.00 0.00 0.00 2.83
1251 1382 9.308000 TCTCTCTCTCTCTCTTCTATTTTGTTT 57.692 33.333 0.00 0.00 0.00 2.83
1252 1383 9.927668 CTCTCTCTCTCTCTTCTATTTTGTTTT 57.072 33.333 0.00 0.00 0.00 2.43
1253 1384 9.921637 TCTCTCTCTCTCTTCTATTTTGTTTTC 57.078 33.333 0.00 0.00 0.00 2.29
1254 1385 9.927668 CTCTCTCTCTCTTCTATTTTGTTTTCT 57.072 33.333 0.00 0.00 0.00 2.52
1255 1386 9.921637 TCTCTCTCTCTTCTATTTTGTTTTCTC 57.078 33.333 0.00 0.00 0.00 2.87
1259 1390 8.875168 TCTCTCTTCTATTTTGTTTTCTCCTCT 58.125 33.333 0.00 0.00 0.00 3.69
1262 1393 8.608844 TCTTCTATTTTGTTTTCTCCTCTCAC 57.391 34.615 0.00 0.00 0.00 3.51
1350 1486 2.736721 TCAATTCGTTCTCGCCTTTCTG 59.263 45.455 0.00 0.00 36.96 3.02
1363 1499 1.338200 CCTTTCTGTCAGTTCCCTCCG 60.338 57.143 0.00 0.00 0.00 4.63
1380 1516 0.105778 CCGCTCCCCATCTTCTTCTC 59.894 60.000 0.00 0.00 0.00 2.87
1397 1533 2.227194 TCTCTTGTTTTCGGGAAAGGC 58.773 47.619 0.00 0.00 0.00 4.35
1443 1579 4.840005 CCTTTCGGCGGCTCCCTC 62.840 72.222 7.21 0.00 0.00 4.30
1489 1635 0.840722 ACGGTTCTGGTTCCAGGGAT 60.841 55.000 17.37 0.00 35.01 3.85
1494 1640 0.621571 TCTGGTTCCAGGGATGGAGG 60.622 60.000 17.37 0.00 39.43 4.30
1516 1662 0.109781 CACGCCAAATCTTTCCGGTG 60.110 55.000 0.00 0.00 35.12 4.94
1555 1701 0.033504 TGATTCCGATTAGCCTCCGC 59.966 55.000 0.00 0.00 0.00 5.54
1635 1813 1.062206 CGTCGTCCGAGCCTAACTC 59.938 63.158 0.00 0.00 42.47 3.01
1648 1826 5.337578 AGCCTAACTCAGAATTGTCTCTC 57.662 43.478 0.00 0.00 28.78 3.20
1868 2052 0.930310 TGCTCTCGATTTATGCACGC 59.070 50.000 0.00 0.00 0.00 5.34
1869 2053 0.930310 GCTCTCGATTTATGCACGCA 59.070 50.000 0.00 0.00 0.00 5.24
1870 2054 1.332377 GCTCTCGATTTATGCACGCAC 60.332 52.381 0.00 0.00 0.00 5.34
1871 2055 0.920664 TCTCGATTTATGCACGCACG 59.079 50.000 0.00 0.00 0.00 5.34
1872 2056 0.043053 CTCGATTTATGCACGCACGG 60.043 55.000 0.00 0.00 0.00 4.94
1874 2058 0.096281 CGATTTATGCACGCACGGTT 59.904 50.000 0.00 0.00 0.00 4.44
1875 2059 1.810197 GATTTATGCACGCACGGTTC 58.190 50.000 0.00 0.00 0.00 3.62
1876 2060 1.129624 GATTTATGCACGCACGGTTCA 59.870 47.619 0.00 0.00 0.00 3.18
1878 2062 0.445829 TTATGCACGCACGGTTCATG 59.554 50.000 0.00 0.00 33.37 3.07
1879 2063 0.672091 TATGCACGCACGGTTCATGT 60.672 50.000 0.00 0.00 33.37 3.21
1880 2064 1.911293 ATGCACGCACGGTTCATGTC 61.911 55.000 0.00 0.00 31.02 3.06
1906 2090 4.370917 CTGCCAGTTTTGCTAATTGTTGT 58.629 39.130 0.00 0.00 0.00 3.32
1919 2103 3.829886 ATTGTTGTGTGCTCGTTATGG 57.170 42.857 0.00 0.00 0.00 2.74
1951 2135 1.845809 CGTTTGGTGCTGAGAGCCAC 61.846 60.000 0.00 0.00 41.51 5.01
2113 2297 1.593265 TTCGCCTAACCTCCCGAAC 59.407 57.895 0.00 0.00 35.12 3.95
2152 2337 1.472990 CGTTCAAACAACCGCCTTTC 58.527 50.000 0.00 0.00 0.00 2.62
2154 2339 1.096416 TTCAAACAACCGCCTTTCGT 58.904 45.000 0.00 0.00 36.19 3.85
2227 2413 7.068716 AGGTAGATAATTTGCCCTGTTTGATTC 59.931 37.037 0.00 0.00 0.00 2.52
2228 2414 6.855763 AGATAATTTGCCCTGTTTGATTCA 57.144 33.333 0.00 0.00 0.00 2.57
2332 2526 7.437748 AGACAGCGCAATTAACTATCTTCTAT 58.562 34.615 11.47 0.00 0.00 1.98
2428 2628 5.689961 GCATTTTCATGTCGTTTAGGTTTGT 59.310 36.000 0.00 0.00 32.28 2.83
2568 2768 1.810030 CACTCCGGCTAAACTCGCC 60.810 63.158 0.00 0.00 44.11 5.54
2637 2837 1.398692 GTGTTTCACCTCCTTTGCCA 58.601 50.000 0.00 0.00 0.00 4.92
2782 2994 1.714414 CCCTCGTCGTCGACACTAG 59.286 63.158 24.13 16.73 41.35 2.57
2796 3008 2.207229 ACTAGCGTCCACCACTGCA 61.207 57.895 0.00 0.00 0.00 4.41
2837 3049 2.387445 TGGATGCTTACGCGTGCAC 61.387 57.895 24.20 17.37 46.63 4.57
2865 3082 7.529158 TGTGCTGTTTGATGATGTTTAGTATG 58.471 34.615 0.00 0.00 0.00 2.39
2890 3107 3.065233 TGTTGAATTGATACGCTGGATGC 59.935 43.478 0.00 0.00 38.57 3.91
2899 3116 1.656652 ACGCTGGATGCTGTATTGAC 58.343 50.000 0.00 0.00 40.11 3.18
2902 3119 2.009774 GCTGGATGCTGTATTGACGTT 58.990 47.619 0.00 0.00 38.95 3.99
2904 3121 1.737236 TGGATGCTGTATTGACGTTGC 59.263 47.619 0.00 0.00 0.00 4.17
2936 3153 1.018226 CAGCTGTTCCTCAAGCTCGG 61.018 60.000 5.25 0.00 35.17 4.63
3004 3221 9.356433 GTACTACAACCTTAGAATTCAGTCTTC 57.644 37.037 8.44 0.00 0.00 2.87
3041 3258 5.616270 TGCAGAACATTTACCAGTGAACTA 58.384 37.500 0.00 0.00 0.00 2.24
3103 3320 4.611310 ATTCATCATGTCTTCGTGCTTG 57.389 40.909 0.00 0.00 0.00 4.01
3112 3329 1.065401 TCTTCGTGCTTGTTTTGCAGG 59.935 47.619 0.00 0.00 44.56 4.85
3305 3522 1.558294 GGGAGTCCCCGAGTACAAAAT 59.442 52.381 18.55 0.00 44.02 1.82
3335 3552 3.431415 TGATCCGATATGATCTTCCGGT 58.569 45.455 16.53 8.53 41.42 5.28
3374 3592 0.803380 GATGGCTGATGCAAAACCGC 60.803 55.000 0.00 0.00 41.91 5.68
3382 3603 4.484236 CTGATGCAAAACCGCAATAAGAA 58.516 39.130 0.00 0.00 46.87 2.52
3383 3604 4.484236 TGATGCAAAACCGCAATAAGAAG 58.516 39.130 0.00 0.00 46.87 2.85
3384 3605 4.217334 TGATGCAAAACCGCAATAAGAAGA 59.783 37.500 0.00 0.00 46.87 2.87
3386 3607 5.132897 TGCAAAACCGCAATAAGAAGATT 57.867 34.783 0.00 0.00 39.45 2.40
3387 3608 5.537188 TGCAAAACCGCAATAAGAAGATTT 58.463 33.333 0.00 0.00 39.45 2.17
3388 3609 5.988561 TGCAAAACCGCAATAAGAAGATTTT 59.011 32.000 0.00 0.00 39.45 1.82
3389 3610 6.073873 TGCAAAACCGCAATAAGAAGATTTTG 60.074 34.615 0.00 0.00 39.45 2.44
3391 3612 4.782019 ACCGCAATAAGAAGATTTTGCA 57.218 36.364 7.20 0.00 43.51 4.08
3392 3613 5.329035 ACCGCAATAAGAAGATTTTGCAT 57.671 34.783 7.20 0.00 43.51 3.96
3393 3614 5.343249 ACCGCAATAAGAAGATTTTGCATC 58.657 37.500 7.20 0.00 43.51 3.91
3394 3615 4.741676 CCGCAATAAGAAGATTTTGCATCC 59.258 41.667 7.20 0.00 43.51 3.51
3395 3616 5.342433 CGCAATAAGAAGATTTTGCATCCA 58.658 37.500 7.20 0.00 43.51 3.41
3396 3617 5.457799 CGCAATAAGAAGATTTTGCATCCAG 59.542 40.000 7.20 0.00 43.51 3.86
3397 3618 5.751990 GCAATAAGAAGATTTTGCATCCAGG 59.248 40.000 1.89 0.00 43.00 4.45
3398 3619 3.881937 AAGAAGATTTTGCATCCAGGC 57.118 42.857 0.00 0.00 0.00 4.85
3399 3620 2.811410 AGAAGATTTTGCATCCAGGCA 58.189 42.857 0.00 0.00 43.19 4.75
3400 3621 2.758979 AGAAGATTTTGCATCCAGGCAG 59.241 45.455 0.00 0.00 45.88 4.85
3401 3622 1.481871 AGATTTTGCATCCAGGCAGG 58.518 50.000 0.00 0.00 45.88 4.85
3402 3623 0.179092 GATTTTGCATCCAGGCAGGC 60.179 55.000 0.00 0.00 45.88 4.85
3403 3624 0.905809 ATTTTGCATCCAGGCAGGCA 60.906 50.000 0.00 0.00 45.88 4.75
3404 3625 1.537814 TTTTGCATCCAGGCAGGCAG 61.538 55.000 0.00 0.00 45.88 4.85
3405 3626 3.949885 TTGCATCCAGGCAGGCAGG 62.950 63.158 0.00 0.00 45.88 4.85
3445 3666 3.206639 GGAGGGAAGGGATATTGGGAAAA 59.793 47.826 0.00 0.00 0.00 2.29
3536 3757 1.137404 CGCAACCTGTAATGCTGGC 59.863 57.895 0.00 0.00 40.39 4.85
3601 3822 4.093998 CGCTTGCAGACTCTTGATTGTTAT 59.906 41.667 0.00 0.00 0.00 1.89
3653 3874 7.648908 TGTATTGCAGAAGAAAGAAACATGTTG 59.351 33.333 12.82 0.00 0.00 3.33
3670 3891 9.979578 AAACATGTTGATTTAGCAGTATGAAAA 57.020 25.926 12.82 0.00 39.69 2.29
3696 3917 4.806640 AGGCTTACAAATTTCCACCATG 57.193 40.909 0.00 0.00 0.00 3.66
3700 3921 4.620567 GCTTACAAATTTCCACCATGGGTC 60.621 45.833 18.09 0.00 38.32 4.46
3704 3925 0.680921 ATTTCCACCATGGGTCGCAG 60.681 55.000 18.09 0.00 38.32 5.18
3725 3946 2.111041 GCTGTGTGCTGTTCTTGTTC 57.889 50.000 0.00 0.00 38.95 3.18
3754 3975 5.529800 TCTGTTTTTACCAACTTCTACAGGC 59.470 40.000 0.00 0.00 34.16 4.85
3755 3976 4.581409 TGTTTTTACCAACTTCTACAGGCC 59.419 41.667 0.00 0.00 0.00 5.19
3756 3977 2.754946 TTACCAACTTCTACAGGCCG 57.245 50.000 0.00 0.00 0.00 6.13
3757 3978 0.248289 TACCAACTTCTACAGGCCGC 59.752 55.000 0.00 0.00 0.00 6.53
3758 3979 2.100631 CCAACTTCTACAGGCCGCG 61.101 63.158 0.00 0.00 0.00 6.46
3759 3980 2.100631 CAACTTCTACAGGCCGCGG 61.101 63.158 24.05 24.05 0.00 6.46
3760 3981 3.310860 AACTTCTACAGGCCGCGGG 62.311 63.158 29.38 13.36 0.00 6.13
3761 3982 3.458163 CTTCTACAGGCCGCGGGA 61.458 66.667 29.38 11.77 0.00 5.14
3762 3983 2.762459 TTCTACAGGCCGCGGGAT 60.762 61.111 29.38 3.89 0.00 3.85
3764 3985 1.741327 TTCTACAGGCCGCGGGATAC 61.741 60.000 29.38 9.97 0.00 2.24
3765 3986 2.442458 TACAGGCCGCGGGATACA 60.442 61.111 29.38 0.00 39.74 2.29
3766 3987 2.023414 CTACAGGCCGCGGGATACAA 62.023 60.000 29.38 0.00 39.74 2.41
3768 3989 1.369692 CAGGCCGCGGGATACAATA 59.630 57.895 29.38 0.00 39.74 1.90
3771 3992 0.533308 GGCCGCGGGATACAATACAA 60.533 55.000 29.38 0.00 39.74 2.41
3773 3994 1.539496 GCCGCGGGATACAATACAAGA 60.539 52.381 29.38 0.00 39.74 3.02
3774 3995 2.404215 CCGCGGGATACAATACAAGAG 58.596 52.381 20.10 0.00 39.74 2.85
3775 3996 1.792949 CGCGGGATACAATACAAGAGC 59.207 52.381 0.00 0.00 39.74 4.09
3776 3997 2.545952 CGCGGGATACAATACAAGAGCT 60.546 50.000 0.00 0.00 39.74 4.09
3778 3999 4.618460 CGCGGGATACAATACAAGAGCTAT 60.618 45.833 0.00 0.00 39.74 2.97
3779 4000 5.238583 GCGGGATACAATACAAGAGCTATT 58.761 41.667 0.00 0.00 39.74 1.73
3780 4001 5.120830 GCGGGATACAATACAAGAGCTATTG 59.879 44.000 19.25 19.25 37.53 1.90
3781 4002 6.455647 CGGGATACAATACAAGAGCTATTGA 58.544 40.000 26.95 11.31 35.81 2.57
3782 4003 6.929049 CGGGATACAATACAAGAGCTATTGAA 59.071 38.462 26.95 5.90 35.81 2.69
3795 4049 5.242393 AGAGCTATTGAAACATTTGTGCACT 59.758 36.000 19.41 0.00 0.00 4.40
3797 4051 6.381801 AGCTATTGAAACATTTGTGCACTAC 58.618 36.000 19.41 0.00 0.00 2.73
3807 4061 1.956170 GTGCACTACAGCGCTGTGT 60.956 57.895 44.69 35.61 44.63 3.72
3815 4070 2.680312 ACAGCGCTGTGTGAATATCT 57.320 45.000 40.34 13.29 43.11 1.98
3816 4071 2.274437 ACAGCGCTGTGTGAATATCTG 58.726 47.619 40.34 12.64 43.11 2.90
3817 4072 2.274437 CAGCGCTGTGTGAATATCTGT 58.726 47.619 29.24 0.00 0.00 3.41
3818 4073 3.119137 ACAGCGCTGTGTGAATATCTGTA 60.119 43.478 40.34 0.00 43.11 2.74
3819 4074 4.053983 CAGCGCTGTGTGAATATCTGTAT 58.946 43.478 29.24 0.00 0.00 2.29
3820 4075 4.149571 CAGCGCTGTGTGAATATCTGTATC 59.850 45.833 29.24 0.00 0.00 2.24
3850 4105 2.665165 AGCTGTCTAGGTCAGATCTGG 58.335 52.381 22.42 6.24 35.17 3.86
3851 4106 1.068434 GCTGTCTAGGTCAGATCTGGC 59.932 57.143 22.42 20.93 35.17 4.85
3882 4137 4.473520 CCTGGGCCAGCCACTACG 62.474 72.222 28.51 8.71 37.98 3.51
3888 4143 2.138179 GCCAGCCACTACGGGGATA 61.138 63.158 0.00 0.00 34.06 2.59
3892 4147 1.485066 CAGCCACTACGGGGATACTTT 59.515 52.381 0.00 0.00 34.06 2.66
3894 4149 3.133362 CAGCCACTACGGGGATACTTTAA 59.867 47.826 0.00 0.00 34.06 1.52
3895 4150 3.971971 AGCCACTACGGGGATACTTTAAT 59.028 43.478 0.00 0.00 34.06 1.40
3901 4156 6.426025 CACTACGGGGATACTTTAATTTAGGC 59.574 42.308 0.00 0.00 0.00 3.93
3936 4191 0.546122 TGTGGATGCCAGATGGTACC 59.454 55.000 4.43 4.43 37.57 3.34
3938 4193 1.352622 TGGATGCCAGATGGTACCCC 61.353 60.000 10.07 0.88 37.57 4.95
3939 4194 1.071471 GATGCCAGATGGTACCCCG 59.929 63.158 10.07 0.00 37.57 5.73
3940 4195 3.120086 ATGCCAGATGGTACCCCGC 62.120 63.158 10.07 4.20 37.57 6.13
3941 4196 3.792736 GCCAGATGGTACCCCGCA 61.793 66.667 10.07 0.00 37.57 5.69
3942 4197 2.994699 CCAGATGGTACCCCGCAA 59.005 61.111 10.07 0.00 0.00 4.85
3943 4198 1.451387 CCAGATGGTACCCCGCAAC 60.451 63.158 10.07 0.00 0.00 4.17
3944 4199 1.813753 CAGATGGTACCCCGCAACG 60.814 63.158 10.07 0.00 0.00 4.10
3945 4200 3.199891 GATGGTACCCCGCAACGC 61.200 66.667 10.07 0.00 0.00 4.84
3946 4201 3.961838 GATGGTACCCCGCAACGCA 62.962 63.158 10.07 0.00 0.00 5.24
3947 4202 3.554696 ATGGTACCCCGCAACGCAA 62.555 57.895 10.07 0.00 0.00 4.85
3948 4203 2.748647 GGTACCCCGCAACGCAAT 60.749 61.111 0.00 0.00 0.00 3.56
3965 4220 4.570772 ACGCAATGAATGGATGTACTGTAC 59.429 41.667 10.98 10.98 0.00 2.90
3968 4223 5.751509 GCAATGAATGGATGTACTGTACGTA 59.248 40.000 12.39 0.00 0.00 3.57
3969 4224 6.423905 GCAATGAATGGATGTACTGTACGTAT 59.576 38.462 12.39 1.81 0.00 3.06
3970 4225 7.569408 GCAATGAATGGATGTACTGTACGTATG 60.569 40.741 12.39 0.00 0.00 2.39
3971 4226 6.459670 TGAATGGATGTACTGTACGTATGT 57.540 37.500 12.39 4.00 0.00 2.29
3982 4237 8.971321 TGTACTGTACGTATGTTCTTTCTTTTC 58.029 33.333 12.87 0.00 0.00 2.29
3983 4238 7.417496 ACTGTACGTATGTTCTTTCTTTTCC 57.583 36.000 0.00 0.00 0.00 3.13
3992 4247 9.464714 GTATGTTCTTTCTTTTCCTTTCCTTTC 57.535 33.333 0.00 0.00 0.00 2.62
3993 4248 6.873997 TGTTCTTTCTTTTCCTTTCCTTTCC 58.126 36.000 0.00 0.00 0.00 3.13
4028 4306 6.702716 TCTCCGTTGGTTGTTTTATTTCTT 57.297 33.333 0.00 0.00 0.00 2.52
4049 4327 3.242867 TCAACCTCTCCAGATGAACACT 58.757 45.455 0.00 0.00 0.00 3.55
4059 4337 3.120408 CCAGATGAACACTGAAAGCTTCG 60.120 47.826 0.00 0.00 37.60 3.79
4142 4423 3.443681 CCCCAAATTGCTTGTACTAGTGG 59.556 47.826 5.39 5.29 32.65 4.00
4145 4426 5.708230 CCCAAATTGCTTGTACTAGTGGTTA 59.292 40.000 5.39 0.00 32.65 2.85
4160 4441 4.223144 AGTGGTTATTGCTTTGGGTTTCT 58.777 39.130 0.00 0.00 0.00 2.52
4244 4525 5.821516 TTTTGGTCGAGCACTTTTAAAGA 57.178 34.783 18.42 0.00 0.00 2.52
4245 4526 6.385649 TTTTGGTCGAGCACTTTTAAAGAT 57.614 33.333 18.42 0.00 0.00 2.40
4258 4539 5.118817 ACTTTTAAAGATTCTCACTCGTCGC 59.881 40.000 12.02 0.00 0.00 5.19
4281 4562 5.242393 GCGGGTAAGTGTGAGAATATAGGTA 59.758 44.000 0.00 0.00 0.00 3.08
4282 4563 6.675987 CGGGTAAGTGTGAGAATATAGGTAC 58.324 44.000 0.00 0.00 0.00 3.34
4290 4571 7.717875 AGTGTGAGAATATAGGTACTCTCAGTC 59.282 40.741 9.75 6.98 43.67 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.006337 ATGTGCGCGCCATGTTTTT 60.006 47.368 30.77 6.95 0.00 1.94
1 2 1.733758 CATGTGCGCGCCATGTTTT 60.734 52.632 34.70 16.48 35.94 2.43
28 29 2.824936 TGTTTATGTCTTGTGGCCATGG 59.175 45.455 9.72 7.63 0.00 3.66
85 88 3.427670 AAAAACTGCGTCACGGGG 58.572 55.556 0.00 0.00 0.00 5.73
124 138 7.745620 AATAATAATCCCGTGATGTTCCTTC 57.254 36.000 0.00 0.00 0.00 3.46
160 177 9.836179 TGGGTTTATGGCTGGAATAATAATAAT 57.164 29.630 0.00 0.00 0.00 1.28
161 178 9.661954 TTGGGTTTATGGCTGGAATAATAATAA 57.338 29.630 0.00 0.00 0.00 1.40
162 179 9.661954 TTTGGGTTTATGGCTGGAATAATAATA 57.338 29.630 0.00 0.00 0.00 0.98
163 180 8.560124 TTTGGGTTTATGGCTGGAATAATAAT 57.440 30.769 0.00 0.00 0.00 1.28
164 181 7.979786 TTTGGGTTTATGGCTGGAATAATAA 57.020 32.000 0.00 0.00 0.00 1.40
165 182 7.621683 ACTTTTGGGTTTATGGCTGGAATAATA 59.378 33.333 0.00 0.00 0.00 0.98
166 183 6.443527 ACTTTTGGGTTTATGGCTGGAATAAT 59.556 34.615 0.00 0.00 0.00 1.28
167 184 5.782845 ACTTTTGGGTTTATGGCTGGAATAA 59.217 36.000 0.00 0.00 0.00 1.40
168 185 5.337788 ACTTTTGGGTTTATGGCTGGAATA 58.662 37.500 0.00 0.00 0.00 1.75
169 186 4.167319 ACTTTTGGGTTTATGGCTGGAAT 58.833 39.130 0.00 0.00 0.00 3.01
170 187 3.576550 GACTTTTGGGTTTATGGCTGGAA 59.423 43.478 0.00 0.00 0.00 3.53
171 188 3.161866 GACTTTTGGGTTTATGGCTGGA 58.838 45.455 0.00 0.00 0.00 3.86
172 189 3.165071 AGACTTTTGGGTTTATGGCTGG 58.835 45.455 0.00 0.00 0.00 4.85
173 190 4.157840 GGTAGACTTTTGGGTTTATGGCTG 59.842 45.833 0.00 0.00 0.00 4.85
174 191 4.341487 GGTAGACTTTTGGGTTTATGGCT 58.659 43.478 0.00 0.00 0.00 4.75
175 192 3.128068 CGGTAGACTTTTGGGTTTATGGC 59.872 47.826 0.00 0.00 0.00 4.40
183 200 1.359459 GCTCGCGGTAGACTTTTGGG 61.359 60.000 6.13 0.00 0.00 4.12
629 709 3.748048 CGGGTGCGAGATGATTGATTATT 59.252 43.478 0.00 0.00 0.00 1.40
630 710 3.006859 TCGGGTGCGAGATGATTGATTAT 59.993 43.478 0.00 0.00 0.00 1.28
645 725 0.105039 CAGGAGGTTAGATCGGGTGC 59.895 60.000 0.00 0.00 0.00 5.01
788 878 4.451150 CCAGCCTTGACCGCGCTA 62.451 66.667 5.56 0.00 0.00 4.26
791 881 4.697756 TTCCCAGCCTTGACCGCG 62.698 66.667 0.00 0.00 0.00 6.46
808 898 0.098376 GACGACGACGGTGCTATCTT 59.902 55.000 12.58 0.00 44.46 2.40
812 902 4.450122 GCGACGACGACGGTGCTA 62.450 66.667 20.21 0.00 44.46 3.49
828 928 1.611592 AACGAACGAACGATGACGGC 61.612 55.000 11.97 0.00 44.46 5.68
829 929 0.361184 GAACGAACGAACGATGACGG 59.639 55.000 11.97 0.00 44.46 4.79
830 930 0.020382 CGAACGAACGAACGATGACG 59.980 55.000 11.97 0.00 39.39 4.35
831 931 1.047739 ACGAACGAACGAACGATGAC 58.952 50.000 18.31 1.75 37.03 3.06
832 932 1.710249 GAACGAACGAACGAACGATGA 59.290 47.619 18.31 0.00 37.03 2.92
833 933 1.519701 CGAACGAACGAACGAACGATG 60.520 52.381 18.31 4.84 37.45 3.84
834 934 0.699151 CGAACGAACGAACGAACGAT 59.301 50.000 18.31 10.61 37.45 3.73
835 935 0.588730 ACGAACGAACGAACGAACGA 60.589 50.000 22.26 0.00 38.05 3.85
836 936 0.224499 AACGAACGAACGAACGAACG 59.776 50.000 18.31 15.65 39.31 3.95
837 937 1.252524 TGAACGAACGAACGAACGAAC 59.747 47.619 18.31 13.29 37.03 3.95
838 938 1.252524 GTGAACGAACGAACGAACGAA 59.747 47.619 18.31 6.63 37.03 3.85
839 939 0.839477 GTGAACGAACGAACGAACGA 59.161 50.000 18.31 1.50 37.03 3.85
840 940 0.567051 TGTGAACGAACGAACGAACG 59.433 50.000 11.97 8.41 37.03 3.95
841 941 1.847999 TCTGTGAACGAACGAACGAAC 59.152 47.619 11.97 8.03 37.03 3.95
842 942 2.114056 CTCTGTGAACGAACGAACGAA 58.886 47.619 11.97 0.00 37.03 3.85
845 945 2.052157 CTCCTCTGTGAACGAACGAAC 58.948 52.381 0.14 0.00 0.00 3.95
869 969 0.668706 CTCTCTCACTGCCAACACCG 60.669 60.000 0.00 0.00 0.00 4.94
876 976 0.613292 TCTCACCCTCTCTCACTGCC 60.613 60.000 0.00 0.00 0.00 4.85
889 989 0.689412 CCTTCCTCCCTCCTCTCACC 60.689 65.000 0.00 0.00 0.00 4.02
890 990 0.336737 TCCTTCCTCCCTCCTCTCAC 59.663 60.000 0.00 0.00 0.00 3.51
892 992 1.691163 CCTTCCTTCCTCCCTCCTCTC 60.691 61.905 0.00 0.00 0.00 3.20
933 1043 3.252458 CGGGGGAATAAATGGATTTCGTC 59.748 47.826 0.00 0.00 0.00 4.20
1021 1131 2.903357 CTGCTCGTGGCCTATGGT 59.097 61.111 3.32 0.00 40.92 3.55
1073 1204 4.394712 ACTCCTTTCTGGCGGCGG 62.395 66.667 12.43 12.43 35.26 6.13
1078 1209 2.501723 TCATACCTGACTCCTTTCTGGC 59.498 50.000 0.00 0.00 37.98 4.85
1099 1230 2.774351 GGGGGAGGGCAGTAGCAT 60.774 66.667 0.00 0.00 44.61 3.79
1101 1232 2.272230 GAAAGGGGGAGGGCAGTAGC 62.272 65.000 0.00 0.00 41.10 3.58
1112 1243 1.037579 GCCCAAATCGAGAAAGGGGG 61.038 60.000 14.52 9.29 39.96 5.40
1145 1276 1.063006 CCGAGATTCGTTACGCCGA 59.937 57.895 0.00 0.00 38.40 5.54
1146 1277 1.942712 CCCGAGATTCGTTACGCCG 60.943 63.158 0.00 0.00 38.40 6.46
1147 1278 0.031721 ATCCCGAGATTCGTTACGCC 59.968 55.000 0.00 0.00 38.40 5.68
1148 1279 1.521423 CAATCCCGAGATTCGTTACGC 59.479 52.381 0.00 0.00 40.89 4.42
1149 1280 2.787680 GTCAATCCCGAGATTCGTTACG 59.212 50.000 0.00 0.00 40.89 3.18
1201 1332 1.134220 AGAGAGAGAGACTACTGGCGG 60.134 57.143 0.00 0.00 0.00 6.13
1206 1337 5.772004 AGAGAGAGAGAGAGAGAGACTACT 58.228 45.833 0.00 0.00 0.00 2.57
1212 1343 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1214 1345 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1218 1349 5.598005 AGAAGAGAGAGAGAGAGAGAGAGAG 59.402 48.000 0.00 0.00 0.00 3.20
1221 1352 7.921041 AATAGAAGAGAGAGAGAGAGAGAGA 57.079 40.000 0.00 0.00 0.00 3.10
1223 1354 8.328758 ACAAAATAGAAGAGAGAGAGAGAGAGA 58.671 37.037 0.00 0.00 0.00 3.10
1226 1357 9.927668 AAAACAAAATAGAAGAGAGAGAGAGAG 57.072 33.333 0.00 0.00 0.00 3.20
1227 1358 9.921637 GAAAACAAAATAGAAGAGAGAGAGAGA 57.078 33.333 0.00 0.00 0.00 3.10
1228 1359 9.927668 AGAAAACAAAATAGAAGAGAGAGAGAG 57.072 33.333 0.00 0.00 0.00 3.20
1229 1360 9.921637 GAGAAAACAAAATAGAAGAGAGAGAGA 57.078 33.333 0.00 0.00 0.00 3.10
1230 1361 9.150348 GGAGAAAACAAAATAGAAGAGAGAGAG 57.850 37.037 0.00 0.00 0.00 3.20
1231 1362 8.875168 AGGAGAAAACAAAATAGAAGAGAGAGA 58.125 33.333 0.00 0.00 0.00 3.10
1232 1363 9.150348 GAGGAGAAAACAAAATAGAAGAGAGAG 57.850 37.037 0.00 0.00 0.00 3.20
1233 1364 8.875168 AGAGGAGAAAACAAAATAGAAGAGAGA 58.125 33.333 0.00 0.00 0.00 3.10
1234 1365 9.150348 GAGAGGAGAAAACAAAATAGAAGAGAG 57.850 37.037 0.00 0.00 0.00 3.20
1235 1366 8.651389 TGAGAGGAGAAAACAAAATAGAAGAGA 58.349 33.333 0.00 0.00 0.00 3.10
1236 1367 8.716909 GTGAGAGGAGAAAACAAAATAGAAGAG 58.283 37.037 0.00 0.00 0.00 2.85
1237 1368 7.661847 GGTGAGAGGAGAAAACAAAATAGAAGA 59.338 37.037 0.00 0.00 0.00 2.87
1238 1369 7.360438 CGGTGAGAGGAGAAAACAAAATAGAAG 60.360 40.741 0.00 0.00 0.00 2.85
1239 1370 6.426937 CGGTGAGAGGAGAAAACAAAATAGAA 59.573 38.462 0.00 0.00 0.00 2.10
1240 1371 5.932303 CGGTGAGAGGAGAAAACAAAATAGA 59.068 40.000 0.00 0.00 0.00 1.98
1241 1372 5.701290 ACGGTGAGAGGAGAAAACAAAATAG 59.299 40.000 0.00 0.00 0.00 1.73
1242 1373 5.617252 ACGGTGAGAGGAGAAAACAAAATA 58.383 37.500 0.00 0.00 0.00 1.40
1243 1374 4.461198 ACGGTGAGAGGAGAAAACAAAAT 58.539 39.130 0.00 0.00 0.00 1.82
1244 1375 3.875134 GACGGTGAGAGGAGAAAACAAAA 59.125 43.478 0.00 0.00 0.00 2.44
1245 1376 3.463944 GACGGTGAGAGGAGAAAACAAA 58.536 45.455 0.00 0.00 0.00 2.83
1246 1377 2.545113 CGACGGTGAGAGGAGAAAACAA 60.545 50.000 0.00 0.00 0.00 2.83
1247 1378 1.000607 CGACGGTGAGAGGAGAAAACA 60.001 52.381 0.00 0.00 0.00 2.83
1248 1379 1.699343 CGACGGTGAGAGGAGAAAAC 58.301 55.000 0.00 0.00 0.00 2.43
1249 1380 0.038526 GCGACGGTGAGAGGAGAAAA 60.039 55.000 0.00 0.00 0.00 2.29
1250 1381 1.585006 GCGACGGTGAGAGGAGAAA 59.415 57.895 0.00 0.00 0.00 2.52
1251 1382 2.687805 CGCGACGGTGAGAGGAGAA 61.688 63.158 0.00 0.00 0.00 2.87
1252 1383 3.125573 CGCGACGGTGAGAGGAGA 61.126 66.667 0.00 0.00 0.00 3.71
1253 1384 4.838486 GCGCGACGGTGAGAGGAG 62.838 72.222 12.10 0.00 0.00 3.69
1290 1422 3.134127 GGTGAATCAGGCGGCCAC 61.134 66.667 23.09 9.14 0.00 5.01
1293 1425 3.512516 GCAGGTGAATCAGGCGGC 61.513 66.667 0.00 0.00 0.00 6.53
1336 1472 2.156343 ACTGACAGAAAGGCGAGAAC 57.844 50.000 10.08 0.00 0.00 3.01
1350 1486 2.579738 GGAGCGGAGGGAACTGAC 59.420 66.667 0.00 0.00 44.43 3.51
1363 1499 2.238395 ACAAGAGAAGAAGATGGGGAGC 59.762 50.000 0.00 0.00 0.00 4.70
1380 1516 0.948678 TCGCCTTTCCCGAAAACAAG 59.051 50.000 0.00 0.00 0.00 3.16
1397 1533 1.660575 CCCATACCTAACGCGCTCG 60.661 63.158 5.73 0.00 42.43 5.03
1489 1635 1.002624 GATTTGGCGTGTCCCTCCA 60.003 57.895 0.00 0.00 0.00 3.86
1494 1640 0.168128 CGGAAAGATTTGGCGTGTCC 59.832 55.000 0.00 0.00 0.00 4.02
1555 1701 4.559063 CCCATCCCAGCAGCGAGG 62.559 72.222 0.16 0.16 0.00 4.63
1628 1806 6.152661 AGACAGAGAGACAATTCTGAGTTAGG 59.847 42.308 8.35 0.00 42.67 2.69
1635 1813 4.685165 CACACAGACAGAGAGACAATTCTG 59.315 45.833 0.27 0.27 44.93 3.02
1648 1826 0.514255 CGGATTGCACACACAGACAG 59.486 55.000 0.00 0.00 0.00 3.51
1792 1976 2.439156 GCCTGCTGCTTGGGGTAG 60.439 66.667 12.59 0.00 36.87 3.18
1868 2052 1.915614 GCAGGCAGACATGAACCGTG 61.916 60.000 0.00 0.00 0.00 4.94
1869 2053 1.672356 GCAGGCAGACATGAACCGT 60.672 57.895 0.00 0.00 0.00 4.83
1870 2054 2.401766 GGCAGGCAGACATGAACCG 61.402 63.158 0.00 0.00 0.00 4.44
1871 2055 1.303561 TGGCAGGCAGACATGAACC 60.304 57.895 0.00 0.00 0.00 3.62
1872 2056 0.607489 ACTGGCAGGCAGACATGAAC 60.607 55.000 29.85 0.00 32.22 3.18
1874 2058 0.111061 AAACTGGCAGGCAGACATGA 59.889 50.000 29.85 0.00 32.22 3.07
1875 2059 0.963962 AAAACTGGCAGGCAGACATG 59.036 50.000 29.85 4.72 32.22 3.21
1876 2060 0.963962 CAAAACTGGCAGGCAGACAT 59.036 50.000 29.85 12.70 32.22 3.06
1878 2062 1.006922 GCAAAACTGGCAGGCAGAC 60.007 57.895 29.85 9.93 0.00 3.51
1879 2063 0.110295 TAGCAAAACTGGCAGGCAGA 59.890 50.000 29.85 2.92 0.00 4.26
1880 2064 0.961019 TTAGCAAAACTGGCAGGCAG 59.039 50.000 22.19 22.19 0.00 4.85
1906 2090 0.871722 GCACAACCATAACGAGCACA 59.128 50.000 0.00 0.00 0.00 4.57
1919 2103 1.873591 ACCAAACGATCTCTGCACAAC 59.126 47.619 0.00 0.00 0.00 3.32
2005 2189 4.796231 GCATGCTGGTGCTGCTGC 62.796 66.667 11.37 8.89 41.82 5.25
2113 2297 2.680913 GCTACCAGCAGCAACACCG 61.681 63.158 0.00 0.00 41.89 4.94
2152 2337 0.179192 CCACCGCATTGTTCATCACG 60.179 55.000 0.00 0.00 0.00 4.35
2154 2339 0.608856 AGCCACCGCATTGTTCATCA 60.609 50.000 0.00 0.00 37.52 3.07
2272 2466 7.362315 GGCGTGTCCCTTTATTACAAATAAGTT 60.362 37.037 0.00 0.00 0.00 2.66
2273 2467 6.094464 GGCGTGTCCCTTTATTACAAATAAGT 59.906 38.462 0.00 0.00 0.00 2.24
2283 2477 1.734163 CTTCGGCGTGTCCCTTTATT 58.266 50.000 6.85 0.00 0.00 1.40
2284 2478 0.743345 GCTTCGGCGTGTCCCTTTAT 60.743 55.000 6.85 0.00 0.00 1.40
2285 2479 1.375013 GCTTCGGCGTGTCCCTTTA 60.375 57.895 6.85 0.00 0.00 1.85
2295 2489 2.863153 CTGTCTTTGGCTTCGGCG 59.137 61.111 0.00 0.00 42.91 6.46
2332 2526 4.650734 TGAATACATTGACAGAACCAGCA 58.349 39.130 0.00 0.00 0.00 4.41
2428 2628 5.127031 GGGAACAATTATTCAGCTTAGCCAA 59.873 40.000 0.00 0.00 0.00 4.52
2508 2708 1.731424 CGAGTAACAGTAGTGGGTGCG 60.731 57.143 1.92 0.00 0.00 5.34
2571 2771 2.045536 GCAGGTGAAGCCTCAGGG 60.046 66.667 0.00 0.00 46.96 4.45
2637 2837 1.818674 GACATCGGTTTGGAAATGGCT 59.181 47.619 0.00 0.00 0.00 4.75
2796 3008 4.510167 ACCTCTTGGCATAATACTTGCT 57.490 40.909 0.00 0.00 40.03 3.91
2837 3049 3.928727 ACATCATCAAACAGCACAAGG 57.071 42.857 0.00 0.00 0.00 3.61
2865 3082 3.932710 TCCAGCGTATCAATTCAACAGAC 59.067 43.478 0.00 0.00 0.00 3.51
2912 3129 1.949525 GCTTGAGGAACAGCTGAAACA 59.050 47.619 23.35 9.93 0.00 2.83
3041 3258 6.688073 AATACAGGCTATGGTATGTAGCTT 57.312 37.500 0.00 0.00 43.15 3.74
3103 3320 1.529865 GTAGTCGTCACCCTGCAAAAC 59.470 52.381 0.00 0.00 0.00 2.43
3305 3522 7.709149 AGATCATATCGGATCAGATGTGTAA 57.291 36.000 24.31 12.32 44.89 2.41
3335 3552 4.545208 TCGTGGTTGAATCTATGGACAA 57.455 40.909 0.00 0.00 0.00 3.18
3354 3572 0.523968 CGGTTTTGCATCAGCCATCG 60.524 55.000 0.00 0.00 41.13 3.84
3374 3592 5.751990 GCCTGGATGCAAAATCTTCTTATTG 59.248 40.000 0.00 0.00 0.00 1.90
3382 3603 1.481871 CCTGCCTGGATGCAAAATCT 58.518 50.000 0.00 0.00 41.51 2.40
3383 3604 0.179092 GCCTGCCTGGATGCAAAATC 60.179 55.000 0.00 0.00 41.51 2.17
3384 3605 0.905809 TGCCTGCCTGGATGCAAAAT 60.906 50.000 0.00 0.00 41.51 1.82
3386 3607 1.980232 CTGCCTGCCTGGATGCAAA 60.980 57.895 0.00 0.00 41.51 3.68
3387 3608 2.361992 CTGCCTGCCTGGATGCAA 60.362 61.111 0.00 0.00 41.51 4.08
3388 3609 4.435970 CCTGCCTGCCTGGATGCA 62.436 66.667 0.00 1.12 39.37 3.96
3391 3612 4.124943 CTGCCTGCCTGCCTGGAT 62.125 66.667 0.00 0.00 38.35 3.41
3406 3627 4.798344 CTCCTGCCTGCCTGCCTG 62.798 72.222 0.00 0.00 0.00 4.85
3409 3630 4.486503 CTCCTCCTGCCTGCCTGC 62.487 72.222 0.00 0.00 0.00 4.85
3445 3666 2.307980 ACATATATCATGCTGCCTGCCT 59.692 45.455 0.00 0.00 42.00 4.75
3670 3891 8.641541 CATGGTGGAAATTTGTAAGCCTATAAT 58.358 33.333 0.00 0.00 0.00 1.28
3696 3917 2.740055 CACACAGCTCTGCGACCC 60.740 66.667 0.00 0.00 0.00 4.46
3709 3930 4.333926 AGAAGAAGAACAAGAACAGCACAC 59.666 41.667 0.00 0.00 0.00 3.82
3713 3934 5.491635 AACAGAAGAAGAACAAGAACAGC 57.508 39.130 0.00 0.00 0.00 4.40
3714 3935 9.278734 GTAAAAACAGAAGAAGAACAAGAACAG 57.721 33.333 0.00 0.00 0.00 3.16
3715 3936 8.241367 GGTAAAAACAGAAGAAGAACAAGAACA 58.759 33.333 0.00 0.00 0.00 3.18
3722 3943 8.459635 AGAAGTTGGTAAAAACAGAAGAAGAAC 58.540 33.333 0.00 0.00 32.21 3.01
3725 3946 8.889717 TGTAGAAGTTGGTAAAAACAGAAGAAG 58.110 33.333 0.00 0.00 32.21 2.85
3754 3975 2.404215 CTCTTGTATTGTATCCCGCGG 58.596 52.381 21.04 21.04 0.00 6.46
3755 3976 1.792949 GCTCTTGTATTGTATCCCGCG 59.207 52.381 0.00 0.00 0.00 6.46
3756 3977 3.113260 AGCTCTTGTATTGTATCCCGC 57.887 47.619 0.00 0.00 0.00 6.13
3757 3978 6.455647 TCAATAGCTCTTGTATTGTATCCCG 58.544 40.000 11.20 0.00 38.50 5.14
3758 3979 8.560374 GTTTCAATAGCTCTTGTATTGTATCCC 58.440 37.037 11.20 0.00 38.50 3.85
3759 3980 9.109393 TGTTTCAATAGCTCTTGTATTGTATCC 57.891 33.333 11.20 0.00 38.50 2.59
3764 3985 9.630098 ACAAATGTTTCAATAGCTCTTGTATTG 57.370 29.630 11.20 5.86 38.65 1.90
3765 3986 9.630098 CACAAATGTTTCAATAGCTCTTGTATT 57.370 29.630 11.20 6.27 0.00 1.89
3766 3987 7.756722 GCACAAATGTTTCAATAGCTCTTGTAT 59.243 33.333 11.20 1.26 0.00 2.29
3768 3989 5.922544 GCACAAATGTTTCAATAGCTCTTGT 59.077 36.000 11.20 0.00 0.00 3.16
3771 3992 5.242393 AGTGCACAAATGTTTCAATAGCTCT 59.758 36.000 21.04 0.00 0.00 4.09
3773 3994 5.458041 AGTGCACAAATGTTTCAATAGCT 57.542 34.783 21.04 0.00 0.00 3.32
3774 3995 6.148948 TGTAGTGCACAAATGTTTCAATAGC 58.851 36.000 21.04 0.00 32.95 2.97
3775 3996 6.306356 GCTGTAGTGCACAAATGTTTCAATAG 59.694 38.462 21.04 1.02 36.48 1.73
3776 3997 6.148948 GCTGTAGTGCACAAATGTTTCAATA 58.851 36.000 21.04 0.00 36.48 1.90
3778 3999 4.358851 GCTGTAGTGCACAAATGTTTCAA 58.641 39.130 21.04 0.00 36.48 2.69
3779 4000 3.547813 CGCTGTAGTGCACAAATGTTTCA 60.548 43.478 21.04 0.01 36.48 2.69
3780 4001 2.973224 CGCTGTAGTGCACAAATGTTTC 59.027 45.455 21.04 0.00 36.48 2.78
3781 4002 2.998772 CGCTGTAGTGCACAAATGTTT 58.001 42.857 21.04 0.00 36.48 2.83
3782 4003 2.686558 CGCTGTAGTGCACAAATGTT 57.313 45.000 21.04 0.00 36.48 2.71
3795 4049 3.119137 ACAGATATTCACACAGCGCTGTA 60.119 43.478 40.17 26.54 42.83 2.74
3797 4051 2.274437 ACAGATATTCACACAGCGCTG 58.726 47.619 34.89 34.89 0.00 5.18
3815 4070 7.999545 ACCTAGACAGCTCTACAATTAGATACA 59.000 37.037 0.00 0.00 33.66 2.29
3816 4071 8.398878 ACCTAGACAGCTCTACAATTAGATAC 57.601 38.462 0.00 0.00 33.66 2.24
3817 4072 8.218488 TGACCTAGACAGCTCTACAATTAGATA 58.782 37.037 0.00 0.00 33.66 1.98
3818 4073 7.063593 TGACCTAGACAGCTCTACAATTAGAT 58.936 38.462 0.00 0.00 33.66 1.98
3819 4074 6.424032 TGACCTAGACAGCTCTACAATTAGA 58.576 40.000 0.00 0.00 33.05 2.10
3820 4075 6.544197 TCTGACCTAGACAGCTCTACAATTAG 59.456 42.308 10.60 0.00 35.61 1.73
3831 4086 1.068434 GCCAGATCTGACCTAGACAGC 59.932 57.143 24.62 11.31 38.49 4.40
3850 4105 1.408822 CCCAGGGTGGTTATCTGAAGC 60.409 57.143 0.00 0.00 35.17 3.86
3851 4106 1.408822 GCCCAGGGTGGTTATCTGAAG 60.409 57.143 7.55 0.00 35.17 3.02
3882 4137 4.722220 ACCGCCTAAATTAAAGTATCCCC 58.278 43.478 0.00 0.00 0.00 4.81
3885 4140 7.255569 AGCAAAACCGCCTAAATTAAAGTATC 58.744 34.615 0.00 0.00 0.00 2.24
3888 4143 5.462530 AGCAAAACCGCCTAAATTAAAGT 57.537 34.783 0.00 0.00 0.00 2.66
3892 4147 5.455056 TTCAAGCAAAACCGCCTAAATTA 57.545 34.783 0.00 0.00 0.00 1.40
3894 4149 4.055360 GTTTCAAGCAAAACCGCCTAAAT 58.945 39.130 0.00 0.00 33.86 1.40
3895 4150 3.131400 AGTTTCAAGCAAAACCGCCTAAA 59.869 39.130 5.95 0.00 39.46 1.85
3901 4156 2.159310 TCCACAGTTTCAAGCAAAACCG 60.159 45.455 5.95 0.16 39.46 4.44
3936 4191 1.516821 CCATTCATTGCGTTGCGGG 60.517 57.895 0.00 0.00 0.00 6.13
3938 4193 1.193644 CATCCATTCATTGCGTTGCG 58.806 50.000 0.00 0.00 0.00 4.85
3939 4194 2.282701 ACATCCATTCATTGCGTTGC 57.717 45.000 0.00 0.00 0.00 4.17
3940 4195 4.142622 ACAGTACATCCATTCATTGCGTTG 60.143 41.667 0.00 0.00 0.00 4.10
3941 4196 4.009675 ACAGTACATCCATTCATTGCGTT 58.990 39.130 0.00 0.00 0.00 4.84
3942 4197 3.609853 ACAGTACATCCATTCATTGCGT 58.390 40.909 0.00 0.00 0.00 5.24
3943 4198 4.318050 CGTACAGTACATCCATTCATTGCG 60.318 45.833 11.37 0.00 0.00 4.85
3944 4199 4.570772 ACGTACAGTACATCCATTCATTGC 59.429 41.667 11.37 0.00 0.00 3.56
3945 4200 7.438160 ACATACGTACAGTACATCCATTCATTG 59.562 37.037 11.37 0.00 38.29 2.82
3946 4201 7.497595 ACATACGTACAGTACATCCATTCATT 58.502 34.615 11.37 0.00 38.29 2.57
3947 4202 7.050970 ACATACGTACAGTACATCCATTCAT 57.949 36.000 11.37 0.00 38.29 2.57
3948 4203 6.459670 ACATACGTACAGTACATCCATTCA 57.540 37.500 11.37 0.00 38.29 2.57
3965 4220 7.203255 AGGAAAGGAAAAGAAAGAACATACG 57.797 36.000 0.00 0.00 0.00 3.06
3968 4223 7.345653 AGGAAAGGAAAGGAAAAGAAAGAACAT 59.654 33.333 0.00 0.00 0.00 2.71
3969 4224 6.667848 AGGAAAGGAAAGGAAAAGAAAGAACA 59.332 34.615 0.00 0.00 0.00 3.18
3970 4225 7.113658 AGGAAAGGAAAGGAAAAGAAAGAAC 57.886 36.000 0.00 0.00 0.00 3.01
3971 4226 7.733773 AAGGAAAGGAAAGGAAAAGAAAGAA 57.266 32.000 0.00 0.00 0.00 2.52
3992 4247 8.085909 ACAACCAACGGAGAATAAAATAAAAGG 58.914 33.333 0.00 0.00 0.00 3.11
3993 4248 9.471084 AACAACCAACGGAGAATAAAATAAAAG 57.529 29.630 0.00 0.00 0.00 2.27
4028 4306 3.007290 CAGTGTTCATCTGGAGAGGTTGA 59.993 47.826 0.00 0.00 0.00 3.18
4036 4314 3.777106 AGCTTTCAGTGTTCATCTGGA 57.223 42.857 0.00 0.00 34.15 3.86
4059 4337 2.071540 GTACGGTCAAAGTAAGCCCAC 58.928 52.381 0.00 0.00 0.00 4.61
4142 4423 9.435688 AAATATCAAGAAACCCAAAGCAATAAC 57.564 29.630 0.00 0.00 0.00 1.89
4145 4426 7.607607 GGAAAATATCAAGAAACCCAAAGCAAT 59.392 33.333 0.00 0.00 0.00 3.56
4160 4441 4.202441 GAGCTCAGCTGGGAAAATATCAA 58.798 43.478 20.53 0.00 39.88 2.57
4239 4520 2.477357 CCGCGACGAGTGAGAATCTTTA 60.477 50.000 8.23 0.00 34.92 1.85
4244 4525 1.028330 TACCCGCGACGAGTGAGAAT 61.028 55.000 8.23 0.00 0.00 2.40
4245 4526 1.236616 TTACCCGCGACGAGTGAGAA 61.237 55.000 8.23 0.00 0.00 2.87
4258 4539 5.786264 ACCTATATTCTCACACTTACCCG 57.214 43.478 0.00 0.00 0.00 5.28
4281 4562 2.201921 TTAGCACCGAGACTGAGAGT 57.798 50.000 0.00 0.00 0.00 3.24
4282 4563 3.791973 AATTAGCACCGAGACTGAGAG 57.208 47.619 0.00 0.00 0.00 3.20
4290 4571 2.169769 TGGGGAGTAAATTAGCACCGAG 59.830 50.000 0.00 0.00 0.00 4.63


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

AutoCloner maintained by Alex Coulton.