Multiple sequence alignment - TraesCS6A01G293000

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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 TraesCS6A01G293000 chr6A 100.000 2162 0 0 1 2162 524370518 524372679 0.000000e+00 3993.0
1 TraesCS6A01G293000 chr6A 95.278 720 16 9 1458 2162 88905470 88906186 0.000000e+00 1125.0
2 TraesCS6A01G293000 chr6A 96.970 33 1 0 843 875 569406965 569406997 3.000000e-04 56.5
3 TraesCS6A01G293000 chr6D 97.290 701 19 0 1 701 382579127 382579827 0.000000e+00 1190.0
4 TraesCS6A01G293000 chr6D 97.244 254 7 0 975 1228 168255389 168255642 4.260000e-117 431.0
5 TraesCS6A01G293000 chr6D 82.432 222 16 11 1261 1460 382580326 382580546 2.850000e-39 172.0
6 TraesCS6A01G293000 chr6D 86.207 116 15 1 833 948 31754742 31754856 8.100000e-25 124.0
7 TraesCS6A01G293000 chr2A 95.518 714 15 8 1463 2162 738095015 738094305 0.000000e+00 1125.0
8 TraesCS6A01G293000 chr2A 95.518 714 15 8 1463 2162 762526628 762527338 0.000000e+00 1125.0
9 TraesCS6A01G293000 chr7A 95.372 713 17 6 1464 2162 518288856 518289566 0.000000e+00 1120.0
10 TraesCS6A01G293000 chr7A 95.091 713 17 7 1464 2162 623762123 623761415 0.000000e+00 1107.0
11 TraesCS6A01G293000 chr7A 94.683 583 12 9 1462 2027 38353201 38352621 0.000000e+00 887.0
12 TraesCS6A01G293000 chr7A 92.531 241 4 6 1464 1690 696290241 696290001 1.240000e-87 333.0
13 TraesCS6A01G293000 chr7A 87.946 224 20 4 1463 1680 669508898 669508676 7.660000e-65 257.0
14 TraesCS6A01G293000 chr7A 81.757 148 15 7 836 973 130093176 130093321 1.750000e-21 113.0
15 TraesCS6A01G293000 chr7A 79.720 143 21 3 836 971 621569125 621568984 1.770000e-16 97.1
16 TraesCS6A01G293000 chr5A 94.767 707 22 11 1464 2159 426326037 426326739 0.000000e+00 1086.0
17 TraesCS6A01G293000 chr5A 91.667 228 4 7 1464 1676 606809304 606809077 3.490000e-78 302.0
18 TraesCS6A01G293000 chr5A 84.677 124 13 1 836 959 673531202 673531319 3.770000e-23 119.0
19 TraesCS6A01G293000 chr3A 94.767 707 21 5 1471 2162 55532698 55533403 0.000000e+00 1086.0
20 TraesCS6A01G293000 chr6B 92.277 751 43 13 1 740 572183009 572183755 0.000000e+00 1051.0
21 TraesCS6A01G293000 chr1A 92.918 706 40 6 1464 2162 590710955 590710253 0.000000e+00 1018.0
22 TraesCS6A01G293000 chr1A 83.520 625 87 7 76 686 29813338 29812716 8.660000e-159 569.0
23 TraesCS6A01G293000 chr1A 88.841 233 9 6 1455 1673 510675659 510675888 9.830000e-69 270.0
24 TraesCS6A01G293000 chr1A 88.957 163 13 3 1464 1624 10464863 10464704 1.690000e-46 196.0
25 TraesCS6A01G293000 chr1A 77.848 158 20 7 836 978 562138274 562138117 1.380000e-12 84.2
26 TraesCS6A01G293000 chrUn 98.113 583 8 2 1580 2162 283576807 283577386 0.000000e+00 1013.0
27 TraesCS6A01G293000 chrUn 97.638 254 6 0 975 1228 372771190 372770937 9.160000e-119 436.0
28 TraesCS6A01G293000 chrUn 97.638 254 6 0 975 1228 444245949 444245696 9.160000e-119 436.0
29 TraesCS6A01G293000 chrUn 97.244 254 7 0 975 1228 346596031 346595778 4.260000e-117 431.0
30 TraesCS6A01G293000 chrUn 84.677 124 13 1 836 959 373849987 373849870 3.770000e-23 119.0
31 TraesCS6A01G293000 chr1D 85.735 701 74 14 1 677 28612248 28612946 0.000000e+00 717.0
32 TraesCS6A01G293000 chr1D 97.244 254 7 0 975 1228 254397646 254397393 4.260000e-117 431.0
33 TraesCS6A01G293000 chr1B 84.218 697 83 16 1 680 47205972 47206658 0.000000e+00 652.0
34 TraesCS6A01G293000 chr1B 80.432 741 78 41 1464 2159 26319333 26320051 8.910000e-139 503.0
35 TraesCS6A01G293000 chr1B 79.605 152 16 7 833 973 500605492 500605639 6.350000e-16 95.3
36 TraesCS6A01G293000 chr2D 97.638 254 6 0 975 1228 272793430 272793177 9.160000e-119 436.0
37 TraesCS6A01G293000 chr5D 97.244 254 7 0 975 1228 6189403 6189656 4.260000e-117 431.0
38 TraesCS6A01G293000 chr5D 97.244 254 7 0 975 1228 503277763 503277510 4.260000e-117 431.0
39 TraesCS6A01G293000 chr5D 86.420 81 10 1 833 913 383296818 383296739 1.060000e-13 87.9
40 TraesCS6A01G293000 chr3D 97.244 254 7 0 975 1228 589279081 589278828 4.260000e-117 431.0
41 TraesCS6A01G293000 chr5B 86.538 208 26 2 1464 1669 10705930 10706137 6.000000e-56 228.0
42 TraesCS6A01G293000 chr5B 90.164 61 5 1 833 893 459173621 459173562 6.400000e-11 78.7
43 TraesCS6A01G293000 chr4A 81.633 147 19 5 835 973 714382330 714382476 4.880000e-22 115.0
44 TraesCS6A01G293000 chr7D 87.013 77 10 0 835 911 506884043 506884119 1.060000e-13 87.9
45 TraesCS6A01G293000 chr2B 100.000 30 0 0 854 883 85072758 85072729 3.000000e-04 56.5
46 TraesCS6A01G293000 chr4B 100.000 28 0 0 855 882 20305218 20305191 4.000000e-03 52.8


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 TraesCS6A01G293000 chr6A 524370518 524372679 2161 False 3993 3993 100.000 1 2162 1 chr6A.!!$F2 2161
1 TraesCS6A01G293000 chr6A 88905470 88906186 716 False 1125 1125 95.278 1458 2162 1 chr6A.!!$F1 704
2 TraesCS6A01G293000 chr6D 382579127 382580546 1419 False 681 1190 89.861 1 1460 2 chr6D.!!$F3 1459
3 TraesCS6A01G293000 chr2A 738094305 738095015 710 True 1125 1125 95.518 1463 2162 1 chr2A.!!$R1 699
4 TraesCS6A01G293000 chr2A 762526628 762527338 710 False 1125 1125 95.518 1463 2162 1 chr2A.!!$F1 699
5 TraesCS6A01G293000 chr7A 518288856 518289566 710 False 1120 1120 95.372 1464 2162 1 chr7A.!!$F2 698
6 TraesCS6A01G293000 chr7A 623761415 623762123 708 True 1107 1107 95.091 1464 2162 1 chr7A.!!$R3 698
7 TraesCS6A01G293000 chr7A 38352621 38353201 580 True 887 887 94.683 1462 2027 1 chr7A.!!$R1 565
8 TraesCS6A01G293000 chr5A 426326037 426326739 702 False 1086 1086 94.767 1464 2159 1 chr5A.!!$F1 695
9 TraesCS6A01G293000 chr3A 55532698 55533403 705 False 1086 1086 94.767 1471 2162 1 chr3A.!!$F1 691
10 TraesCS6A01G293000 chr6B 572183009 572183755 746 False 1051 1051 92.277 1 740 1 chr6B.!!$F1 739
11 TraesCS6A01G293000 chr1A 590710253 590710955 702 True 1018 1018 92.918 1464 2162 1 chr1A.!!$R4 698
12 TraesCS6A01G293000 chr1A 29812716 29813338 622 True 569 569 83.520 76 686 1 chr1A.!!$R2 610
13 TraesCS6A01G293000 chrUn 283576807 283577386 579 False 1013 1013 98.113 1580 2162 1 chrUn.!!$F1 582
14 TraesCS6A01G293000 chr1D 28612248 28612946 698 False 717 717 85.735 1 677 1 chr1D.!!$F1 676
15 TraesCS6A01G293000 chr1B 47205972 47206658 686 False 652 652 84.218 1 680 1 chr1B.!!$F2 679
16 TraesCS6A01G293000 chr1B 26319333 26320051 718 False 503 503 80.432 1464 2159 1 chr1B.!!$F1 695

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
731 928 0.106708 TCGGAATGCATGCTCCTACC 59.893 55.0 20.33 13.36 0.0 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1562 1810 0.03759 CCCTTGATTGAACCGGGACA 59.962 55.0 6.32 1.89 37.05 4.02 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
136 146 2.330372 ACGCTCGCCTTCGTCTACA 61.330 57.895 0.00 0.00 33.09 2.74
154 164 2.222886 ACATCCTGGAGATCGTCTACG 58.777 52.381 1.52 0.00 41.45 3.51
262 281 4.841617 TCTCCGCGGCCATCTCCT 62.842 66.667 23.51 0.00 0.00 3.69
475 497 2.244651 GCGGGTAATAGCGTGGCTG 61.245 63.158 0.00 0.00 40.10 4.85
487 509 1.529244 GTGGCTGTTGGGTTGCTCT 60.529 57.895 0.00 0.00 0.00 4.09
607 629 0.764890 GCTGGGGGATACTGCATACA 59.235 55.000 0.00 0.00 33.62 2.29
731 928 0.106708 TCGGAATGCATGCTCCTACC 59.893 55.000 20.33 13.36 0.00 3.18
790 987 8.311836 ACTATATATACGACCTTTTGGACATGG 58.688 37.037 0.00 0.00 44.07 3.66
801 998 5.126869 CCTTTTGGACATGGCATATTGTACA 59.873 40.000 0.00 0.00 44.07 2.90
844 1045 2.874052 GCCCAAAATTTTAGGGTGTGGC 60.874 50.000 26.05 16.08 44.69 5.01
850 1051 4.397919 AATTTTAGGGTGTGGCTAGGTT 57.602 40.909 0.00 0.00 0.00 3.50
854 1055 0.693049 AGGGTGTGGCTAGGTTTCAG 59.307 55.000 0.00 0.00 0.00 3.02
878 1079 7.543868 CAGTCGACTGAGATTTAATCAAGTCTT 59.456 37.037 36.73 14.82 46.59 3.01
941 1143 5.697473 TTTTTGCACGGATCTCAATGTAA 57.303 34.783 0.00 0.00 0.00 2.41
942 1144 4.944962 TTTGCACGGATCTCAATGTAAG 57.055 40.909 0.00 0.00 0.00 2.34
943 1145 3.885724 TGCACGGATCTCAATGTAAGA 57.114 42.857 0.00 0.00 0.00 2.10
944 1146 4.406648 TGCACGGATCTCAATGTAAGAT 57.593 40.909 0.00 0.00 36.19 2.40
948 1150 5.508825 GCACGGATCTCAATGTAAGATCTCT 60.509 44.000 11.66 0.00 45.56 3.10
951 1153 6.016360 ACGGATCTCAATGTAAGATCTCTCAG 60.016 42.308 11.66 3.68 45.56 3.35
959 1161 8.672815 TCAATGTAAGATCTCTCAGATATAGCG 58.327 37.037 0.00 0.00 34.53 4.26
962 1164 5.794687 AAGATCTCTCAGATATAGCGTCG 57.205 43.478 0.00 0.00 34.53 5.12
970 1172 3.741856 TCAGATATAGCGTCGACTGAGAC 59.258 47.826 14.70 0.00 37.76 3.36
973 1175 4.449743 AGATATAGCGTCGACTGAGACTTC 59.550 45.833 14.70 2.86 38.90 3.01
974 1176 0.720027 TAGCGTCGACTGAGACTTCG 59.280 55.000 14.70 0.00 38.90 3.79
975 1177 0.949588 AGCGTCGACTGAGACTTCGA 60.950 55.000 14.70 0.00 41.83 3.71
980 1182 1.805345 TCGACTGAGACTTCGACTTCC 59.195 52.381 0.00 0.00 39.29 3.46
982 1184 1.202817 GACTGAGACTTCGACTTCCCC 59.797 57.143 0.00 0.00 0.00 4.81
984 1186 0.114560 TGAGACTTCGACTTCCCCCT 59.885 55.000 0.00 0.00 0.00 4.79
985 1187 0.818938 GAGACTTCGACTTCCCCCTC 59.181 60.000 0.00 0.00 0.00 4.30
987 1189 1.639628 AGACTTCGACTTCCCCCTCTA 59.360 52.381 0.00 0.00 0.00 2.43
988 1190 1.750206 GACTTCGACTTCCCCCTCTAC 59.250 57.143 0.00 0.00 0.00 2.59
989 1191 0.739561 CTTCGACTTCCCCCTCTACG 59.260 60.000 0.00 0.00 0.00 3.51
991 1193 2.783288 CGACTTCCCCCTCTACGCC 61.783 68.421 0.00 0.00 0.00 5.68
993 1195 0.976590 GACTTCCCCCTCTACGCCTT 60.977 60.000 0.00 0.00 0.00 4.35
995 1197 2.595009 CTTCCCCCTCTACGCCTTGC 62.595 65.000 0.00 0.00 0.00 4.01
1008 1210 1.680338 GCCTTGCGGTAATGATTCCT 58.320 50.000 0.00 0.00 0.00 3.36
1009 1211 1.604278 GCCTTGCGGTAATGATTCCTC 59.396 52.381 0.00 0.00 0.00 3.71
1010 1212 2.746472 GCCTTGCGGTAATGATTCCTCT 60.746 50.000 0.00 0.00 0.00 3.69
1011 1213 2.874701 CCTTGCGGTAATGATTCCTCTG 59.125 50.000 0.00 0.00 0.00 3.35
1012 1214 2.620251 TGCGGTAATGATTCCTCTGG 57.380 50.000 0.00 0.00 0.00 3.86
1013 1215 2.115427 TGCGGTAATGATTCCTCTGGA 58.885 47.619 0.00 0.00 0.00 3.86
1014 1216 2.503765 TGCGGTAATGATTCCTCTGGAA 59.496 45.455 1.24 1.24 46.39 3.53
1025 1227 4.903045 TTCCTCTGGAATTACGACCTTT 57.097 40.909 0.00 0.00 36.71 3.11
1026 1228 4.467198 TCCTCTGGAATTACGACCTTTC 57.533 45.455 0.00 0.00 0.00 2.62
1027 1229 3.197116 TCCTCTGGAATTACGACCTTTCC 59.803 47.826 0.00 0.00 39.50 3.13
1028 1230 3.532542 CTCTGGAATTACGACCTTTCCC 58.467 50.000 0.00 0.00 38.51 3.97
1029 1231 2.907696 TCTGGAATTACGACCTTTCCCA 59.092 45.455 0.00 0.00 38.51 4.37
1030 1232 3.007635 CTGGAATTACGACCTTTCCCAC 58.992 50.000 0.00 0.00 38.51 4.61
1031 1233 2.372504 TGGAATTACGACCTTTCCCACA 59.627 45.455 0.00 0.00 38.51 4.17
1032 1234 3.181442 TGGAATTACGACCTTTCCCACAA 60.181 43.478 0.00 0.00 38.51 3.33
1033 1235 3.189910 GGAATTACGACCTTTCCCACAAC 59.810 47.826 0.00 0.00 34.15 3.32
1034 1236 1.868469 TTACGACCTTTCCCACAACG 58.132 50.000 0.00 0.00 0.00 4.10
1035 1237 0.033781 TACGACCTTTCCCACAACGG 59.966 55.000 0.00 0.00 0.00 4.44
1036 1238 1.227734 CGACCTTTCCCACAACGGT 60.228 57.895 0.00 0.00 0.00 4.83
1037 1239 1.503818 CGACCTTTCCCACAACGGTG 61.504 60.000 0.00 0.00 44.85 4.94
1038 1240 1.792118 GACCTTTCCCACAACGGTGC 61.792 60.000 0.00 0.00 43.88 5.01
1039 1241 2.561037 CCTTTCCCACAACGGTGCC 61.561 63.158 0.00 0.00 43.88 5.01
1040 1242 2.902846 TTTCCCACAACGGTGCCG 60.903 61.111 9.29 9.29 43.88 5.69
1050 1252 3.409856 CGGTGCCGTCCATTGATC 58.590 61.111 1.93 0.00 34.35 2.92
1051 1253 1.449423 CGGTGCCGTCCATTGATCA 60.449 57.895 1.93 0.00 34.35 2.92
1052 1254 1.024046 CGGTGCCGTCCATTGATCAA 61.024 55.000 11.26 11.26 34.35 2.57
1053 1255 1.173043 GGTGCCGTCCATTGATCAAA 58.827 50.000 13.09 0.00 0.00 2.69
1054 1256 1.750778 GGTGCCGTCCATTGATCAAAT 59.249 47.619 13.09 0.00 0.00 2.32
1055 1257 2.166254 GGTGCCGTCCATTGATCAAATT 59.834 45.455 13.09 0.00 0.00 1.82
1056 1258 3.380004 GGTGCCGTCCATTGATCAAATTA 59.620 43.478 13.09 0.00 0.00 1.40
1057 1259 4.037923 GGTGCCGTCCATTGATCAAATTAT 59.962 41.667 13.09 0.00 0.00 1.28
1058 1260 5.451798 GGTGCCGTCCATTGATCAAATTATT 60.452 40.000 13.09 0.00 0.00 1.40
1059 1261 6.042143 GTGCCGTCCATTGATCAAATTATTT 58.958 36.000 13.09 0.00 0.00 1.40
1060 1262 6.198966 GTGCCGTCCATTGATCAAATTATTTC 59.801 38.462 13.09 1.35 0.00 2.17
1061 1263 5.399301 GCCGTCCATTGATCAAATTATTTCG 59.601 40.000 13.09 10.55 0.00 3.46
1062 1264 6.494842 CCGTCCATTGATCAAATTATTTCGT 58.505 36.000 13.09 0.00 0.00 3.85
1063 1265 6.414694 CCGTCCATTGATCAAATTATTTCGTG 59.585 38.462 13.09 2.62 0.00 4.35
1064 1266 6.414694 CGTCCATTGATCAAATTATTTCGTGG 59.585 38.462 13.09 11.92 0.00 4.94
1065 1267 7.479980 GTCCATTGATCAAATTATTTCGTGGA 58.520 34.615 13.09 14.04 0.00 4.02
1066 1268 8.137437 GTCCATTGATCAAATTATTTCGTGGAT 58.863 33.333 19.32 0.00 32.06 3.41
1067 1269 8.694540 TCCATTGATCAAATTATTTCGTGGATT 58.305 29.630 13.09 0.00 0.00 3.01
1068 1270 8.757789 CCATTGATCAAATTATTTCGTGGATTG 58.242 33.333 13.09 0.04 0.00 2.67
1069 1271 8.757789 CATTGATCAAATTATTTCGTGGATTGG 58.242 33.333 13.09 0.00 0.00 3.16
1070 1272 7.637631 TGATCAAATTATTTCGTGGATTGGA 57.362 32.000 0.00 0.00 0.00 3.53
1071 1273 8.236585 TGATCAAATTATTTCGTGGATTGGAT 57.763 30.769 0.00 0.00 0.00 3.41
1072 1274 8.694540 TGATCAAATTATTTCGTGGATTGGATT 58.305 29.630 0.00 0.00 0.00 3.01
1073 1275 9.533253 GATCAAATTATTTCGTGGATTGGATTT 57.467 29.630 0.00 0.00 0.00 2.17
1074 1276 8.925161 TCAAATTATTTCGTGGATTGGATTTC 57.075 30.769 0.00 0.00 0.00 2.17
1075 1277 8.526978 TCAAATTATTTCGTGGATTGGATTTCA 58.473 29.630 0.00 0.00 0.00 2.69
1076 1278 8.594687 CAAATTATTTCGTGGATTGGATTTCAC 58.405 33.333 0.00 0.00 0.00 3.18
1077 1279 7.645058 ATTATTTCGTGGATTGGATTTCACT 57.355 32.000 0.00 0.00 0.00 3.41
1078 1280 5.982890 ATTTCGTGGATTGGATTTCACTT 57.017 34.783 0.00 0.00 0.00 3.16
1079 1281 4.764679 TTCGTGGATTGGATTTCACTTG 57.235 40.909 0.00 0.00 0.00 3.16
1080 1282 2.487762 TCGTGGATTGGATTTCACTTGC 59.512 45.455 0.00 0.00 0.00 4.01
1081 1283 2.415893 CGTGGATTGGATTTCACTTGCC 60.416 50.000 0.00 0.00 0.00 4.52
1082 1284 2.827921 GTGGATTGGATTTCACTTGCCT 59.172 45.455 0.00 0.00 0.00 4.75
1083 1285 2.827322 TGGATTGGATTTCACTTGCCTG 59.173 45.455 0.00 0.00 0.00 4.85
1084 1286 2.827921 GGATTGGATTTCACTTGCCTGT 59.172 45.455 0.00 0.00 0.00 4.00
1085 1287 3.119352 GGATTGGATTTCACTTGCCTGTC 60.119 47.826 0.00 0.00 0.00 3.51
1086 1288 2.957402 TGGATTTCACTTGCCTGTCT 57.043 45.000 0.00 0.00 0.00 3.41
1087 1289 4.365514 TTGGATTTCACTTGCCTGTCTA 57.634 40.909 0.00 0.00 0.00 2.59
1088 1290 3.674997 TGGATTTCACTTGCCTGTCTAC 58.325 45.455 0.00 0.00 0.00 2.59
1089 1291 2.673368 GGATTTCACTTGCCTGTCTACG 59.327 50.000 0.00 0.00 0.00 3.51
1090 1292 2.163818 TTTCACTTGCCTGTCTACGG 57.836 50.000 0.00 0.00 0.00 4.02
1091 1293 1.045407 TTCACTTGCCTGTCTACGGT 58.955 50.000 0.00 0.00 0.00 4.83
1092 1294 1.045407 TCACTTGCCTGTCTACGGTT 58.955 50.000 0.00 0.00 0.00 4.44
1093 1295 1.000506 TCACTTGCCTGTCTACGGTTC 59.999 52.381 0.00 0.00 0.00 3.62
1094 1296 0.320697 ACTTGCCTGTCTACGGTTCC 59.679 55.000 0.00 0.00 0.00 3.62
1095 1297 0.391263 CTTGCCTGTCTACGGTTCCC 60.391 60.000 0.00 0.00 0.00 3.97
1096 1298 0.834687 TTGCCTGTCTACGGTTCCCT 60.835 55.000 0.00 0.00 0.00 4.20
1097 1299 0.834687 TGCCTGTCTACGGTTCCCTT 60.835 55.000 0.00 0.00 0.00 3.95
1098 1300 0.391263 GCCTGTCTACGGTTCCCTTG 60.391 60.000 0.00 0.00 0.00 3.61
1099 1301 0.391263 CCTGTCTACGGTTCCCTTGC 60.391 60.000 0.00 0.00 0.00 4.01
1100 1302 0.320374 CTGTCTACGGTTCCCTTGCA 59.680 55.000 0.00 0.00 0.00 4.08
1101 1303 0.981183 TGTCTACGGTTCCCTTGCAT 59.019 50.000 0.00 0.00 0.00 3.96
1102 1304 1.338674 TGTCTACGGTTCCCTTGCATG 60.339 52.381 0.00 0.00 0.00 4.06
1103 1305 0.981183 TCTACGGTTCCCTTGCATGT 59.019 50.000 0.00 0.00 0.00 3.21
1104 1306 1.086696 CTACGGTTCCCTTGCATGTG 58.913 55.000 0.00 0.00 0.00 3.21
1105 1307 0.958382 TACGGTTCCCTTGCATGTGC 60.958 55.000 0.00 0.00 42.50 4.57
1106 1308 1.973281 CGGTTCCCTTGCATGTGCT 60.973 57.895 6.55 0.00 42.66 4.40
1107 1309 1.885871 GGTTCCCTTGCATGTGCTC 59.114 57.895 6.55 0.00 42.66 4.26
1108 1310 1.503542 GTTCCCTTGCATGTGCTCG 59.496 57.895 6.55 0.00 42.66 5.03
1109 1311 1.675310 TTCCCTTGCATGTGCTCGG 60.675 57.895 6.55 6.39 42.66 4.63
1110 1312 3.136123 CCCTTGCATGTGCTCGGG 61.136 66.667 14.56 14.56 41.90 5.14
1111 1313 2.046023 CCTTGCATGTGCTCGGGA 60.046 61.111 6.55 0.00 42.66 5.14
1112 1314 1.452651 CCTTGCATGTGCTCGGGAT 60.453 57.895 6.55 0.00 42.66 3.85
1113 1315 0.179048 CCTTGCATGTGCTCGGGATA 60.179 55.000 6.55 0.00 42.66 2.59
1114 1316 1.224075 CTTGCATGTGCTCGGGATAG 58.776 55.000 6.55 0.00 42.66 2.08
1115 1317 0.179048 TTGCATGTGCTCGGGATAGG 60.179 55.000 6.55 0.00 42.66 2.57
1116 1318 1.337384 TGCATGTGCTCGGGATAGGT 61.337 55.000 6.55 0.00 42.66 3.08
1117 1319 0.882042 GCATGTGCTCGGGATAGGTG 60.882 60.000 0.00 0.00 38.21 4.00
1118 1320 0.465705 CATGTGCTCGGGATAGGTGT 59.534 55.000 0.00 0.00 0.00 4.16
1119 1321 1.134401 CATGTGCTCGGGATAGGTGTT 60.134 52.381 0.00 0.00 0.00 3.32
1120 1322 0.981183 TGTGCTCGGGATAGGTGTTT 59.019 50.000 0.00 0.00 0.00 2.83
1121 1323 1.349688 TGTGCTCGGGATAGGTGTTTT 59.650 47.619 0.00 0.00 0.00 2.43
1122 1324 1.737793 GTGCTCGGGATAGGTGTTTTG 59.262 52.381 0.00 0.00 0.00 2.44
1123 1325 1.349688 TGCTCGGGATAGGTGTTTTGT 59.650 47.619 0.00 0.00 0.00 2.83
1124 1326 2.568062 TGCTCGGGATAGGTGTTTTGTA 59.432 45.455 0.00 0.00 0.00 2.41
1125 1327 3.199071 TGCTCGGGATAGGTGTTTTGTAT 59.801 43.478 0.00 0.00 0.00 2.29
1126 1328 4.406326 TGCTCGGGATAGGTGTTTTGTATA 59.594 41.667 0.00 0.00 0.00 1.47
1127 1329 5.104859 TGCTCGGGATAGGTGTTTTGTATAA 60.105 40.000 0.00 0.00 0.00 0.98
1128 1330 5.818857 GCTCGGGATAGGTGTTTTGTATAAA 59.181 40.000 0.00 0.00 0.00 1.40
1129 1331 6.485648 GCTCGGGATAGGTGTTTTGTATAAAT 59.514 38.462 0.00 0.00 0.00 1.40
1130 1332 7.519970 GCTCGGGATAGGTGTTTTGTATAAATG 60.520 40.741 0.00 0.00 0.00 2.32
1131 1333 7.340256 TCGGGATAGGTGTTTTGTATAAATGT 58.660 34.615 0.00 0.00 0.00 2.71
1132 1334 7.830201 TCGGGATAGGTGTTTTGTATAAATGTT 59.170 33.333 0.00 0.00 0.00 2.71
1133 1335 8.463607 CGGGATAGGTGTTTTGTATAAATGTTT 58.536 33.333 0.00 0.00 0.00 2.83
1134 1336 9.797556 GGGATAGGTGTTTTGTATAAATGTTTC 57.202 33.333 0.00 0.00 0.00 2.78
1135 1337 9.498307 GGATAGGTGTTTTGTATAAATGTTTCG 57.502 33.333 0.00 0.00 0.00 3.46
1136 1338 8.905103 ATAGGTGTTTTGTATAAATGTTTCGC 57.095 30.769 0.00 0.00 0.00 4.70
1137 1339 6.153756 AGGTGTTTTGTATAAATGTTTCGCC 58.846 36.000 0.00 0.00 0.00 5.54
1138 1340 5.059955 GGTGTTTTGTATAAATGTTTCGCCG 59.940 40.000 0.00 0.00 0.00 6.46
1139 1341 5.626132 GTGTTTTGTATAAATGTTTCGCCGT 59.374 36.000 0.00 0.00 0.00 5.68
1140 1342 6.796072 GTGTTTTGTATAAATGTTTCGCCGTA 59.204 34.615 0.00 0.00 0.00 4.02
1141 1343 7.482428 GTGTTTTGTATAAATGTTTCGCCGTAT 59.518 33.333 0.00 0.00 0.00 3.06
1142 1344 8.021973 TGTTTTGTATAAATGTTTCGCCGTATT 58.978 29.630 0.00 0.00 0.00 1.89
1143 1345 9.488124 GTTTTGTATAAATGTTTCGCCGTATTA 57.512 29.630 0.00 0.00 0.00 0.98
1154 1356 8.876275 TGTTTCGCCGTATTATTAAGTATTCT 57.124 30.769 0.00 0.00 0.00 2.40
1155 1357 8.971321 TGTTTCGCCGTATTATTAAGTATTCTC 58.029 33.333 0.00 0.00 0.00 2.87
1156 1358 8.430828 GTTTCGCCGTATTATTAAGTATTCTCC 58.569 37.037 0.00 0.00 0.00 3.71
1157 1359 7.458409 TCGCCGTATTATTAAGTATTCTCCT 57.542 36.000 0.00 0.00 0.00 3.69
1158 1360 7.889469 TCGCCGTATTATTAAGTATTCTCCTT 58.111 34.615 0.00 0.00 0.00 3.36
1159 1361 8.362639 TCGCCGTATTATTAAGTATTCTCCTTT 58.637 33.333 0.00 0.00 0.00 3.11
1160 1362 9.630098 CGCCGTATTATTAAGTATTCTCCTTTA 57.370 33.333 0.00 0.00 0.00 1.85
1197 1399 9.495572 CTATCAAGAAGTGGAATAGAATAACCC 57.504 37.037 0.00 0.00 0.00 4.11
1198 1400 6.346096 TCAAGAAGTGGAATAGAATAACCCG 58.654 40.000 0.00 0.00 0.00 5.28
1199 1401 5.291905 AGAAGTGGAATAGAATAACCCGG 57.708 43.478 0.00 0.00 0.00 5.73
1200 1402 4.720273 AGAAGTGGAATAGAATAACCCGGT 59.280 41.667 0.00 0.00 0.00 5.28
1201 1403 5.191124 AGAAGTGGAATAGAATAACCCGGTT 59.809 40.000 8.17 8.17 0.00 4.44
1202 1404 4.777463 AGTGGAATAGAATAACCCGGTTG 58.223 43.478 13.43 0.00 0.00 3.77
1203 1405 4.472108 AGTGGAATAGAATAACCCGGTTGA 59.528 41.667 13.43 0.00 0.00 3.18
1204 1406 5.045432 AGTGGAATAGAATAACCCGGTTGAA 60.045 40.000 13.43 0.00 0.00 2.69
1205 1407 5.296035 GTGGAATAGAATAACCCGGTTGAAG 59.704 44.000 13.43 0.00 0.00 3.02
1206 1408 4.820173 GGAATAGAATAACCCGGTTGAAGG 59.180 45.833 13.43 0.00 0.00 3.46
1214 1416 2.729028 CCCGGTTGAAGGGTAATGAT 57.271 50.000 0.00 0.00 43.89 2.45
1215 1417 2.572290 CCCGGTTGAAGGGTAATGATC 58.428 52.381 0.00 0.00 43.89 2.92
1216 1418 2.092646 CCCGGTTGAAGGGTAATGATCA 60.093 50.000 0.00 0.00 43.89 2.92
1217 1419 3.435026 CCCGGTTGAAGGGTAATGATCAT 60.435 47.826 1.18 1.18 43.89 2.45
1218 1420 4.202419 CCCGGTTGAAGGGTAATGATCATA 60.202 45.833 9.04 0.00 43.89 2.15
1219 1421 4.755123 CCGGTTGAAGGGTAATGATCATAC 59.245 45.833 9.04 7.57 0.00 2.39
1220 1422 4.447724 CGGTTGAAGGGTAATGATCATACG 59.552 45.833 9.04 0.00 0.00 3.06
1221 1423 5.365619 GGTTGAAGGGTAATGATCATACGT 58.634 41.667 9.04 0.00 0.00 3.57
1222 1424 5.465724 GGTTGAAGGGTAATGATCATACGTC 59.534 44.000 9.04 8.28 0.00 4.34
1223 1425 6.281405 GTTGAAGGGTAATGATCATACGTCT 58.719 40.000 9.04 2.42 0.00 4.18
1224 1426 5.842907 TGAAGGGTAATGATCATACGTCTG 58.157 41.667 9.04 0.00 0.00 3.51
1225 1427 5.362717 TGAAGGGTAATGATCATACGTCTGT 59.637 40.000 9.04 0.00 0.00 3.41
1226 1428 6.548251 TGAAGGGTAATGATCATACGTCTGTA 59.452 38.462 9.04 0.00 34.45 2.74
1236 1438 6.972901 TGATCATACGTCTGTAACTTAGCAAG 59.027 38.462 0.00 0.00 33.44 4.01
1238 1440 7.096884 TCATACGTCTGTAACTTAGCAAGAT 57.903 36.000 0.00 0.00 33.44 2.40
1239 1441 7.544622 TCATACGTCTGTAACTTAGCAAGATT 58.455 34.615 0.00 0.00 33.44 2.40
1244 1446 7.095607 ACGTCTGTAACTTAGCAAGATTGAAAG 60.096 37.037 0.00 2.23 0.00 2.62
1288 1514 4.623002 CCGCTAAGGAAATAGAGAACCTC 58.377 47.826 0.00 0.00 45.00 3.85
1291 1517 4.409247 GCTAAGGAAATAGAGAACCTCCCA 59.591 45.833 0.00 0.00 31.89 4.37
1352 1578 6.636562 ATCAAACTTCTCGGTACTATCGAT 57.363 37.500 2.16 2.16 36.01 3.59
1425 1673 2.227194 CCAAACGCTGACCCTAAAACT 58.773 47.619 0.00 0.00 0.00 2.66
1427 1675 2.616842 CAAACGCTGACCCTAAAACTGT 59.383 45.455 0.00 0.00 0.00 3.55
1429 1677 1.692519 ACGCTGACCCTAAAACTGTCT 59.307 47.619 0.00 0.00 0.00 3.41
1434 1682 3.411446 TGACCCTAAAACTGTCTGCATG 58.589 45.455 0.00 0.00 0.00 4.06
1436 1684 2.161855 CCCTAAAACTGTCTGCATGCA 58.838 47.619 21.29 21.29 0.00 3.96
1439 1687 3.693085 CCTAAAACTGTCTGCATGCATCT 59.307 43.478 22.97 4.17 0.00 2.90
1449 1697 1.441732 GCATGCATCTGGATCGCACA 61.442 55.000 14.21 0.00 38.73 4.57
1453 1701 1.156645 GCATCTGGATCGCACAGTCC 61.157 60.000 0.00 0.00 37.25 3.85
1460 1708 0.460284 GATCGCACAGTCCGGATGTT 60.460 55.000 7.81 0.00 0.00 2.71
1468 1716 1.000843 CAGTCCGGATGTTGTCACTGA 59.999 52.381 7.81 0.00 32.77 3.41
1559 1807 1.209621 GGTACTAATGCCCTGTCCCA 58.790 55.000 0.00 0.00 0.00 4.37
1561 1809 2.224548 GGTACTAATGCCCTGTCCCATC 60.225 54.545 0.00 0.00 0.00 3.51
1562 1810 1.898863 ACTAATGCCCTGTCCCATCT 58.101 50.000 0.00 0.00 0.00 2.90
1577 1825 1.065491 CCATCTGTCCCGGTTCAATCA 60.065 52.381 0.00 0.00 0.00 2.57
1583 1845 1.000896 CCCGGTTCAATCAAGGGCT 60.001 57.895 0.00 0.00 35.09 5.19
1690 1977 1.769665 AGCATTTCTGTGGCTGGGA 59.230 52.632 0.00 0.00 36.34 4.37
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
136 146 2.496111 GACGTAGACGATCTCCAGGAT 58.504 52.381 9.41 0.00 43.02 3.24
154 164 0.865769 ATCAACGCCAGAAACACGAC 59.134 50.000 0.00 0.00 0.00 4.34
262 281 3.058432 CAGACGAAGGAGAAGTACACGAA 60.058 47.826 0.00 0.00 0.00 3.85
339 358 1.144057 CCTACACGCCCTGCCTAAG 59.856 63.158 0.00 0.00 0.00 2.18
475 497 3.383505 ACAAAACCTAAGAGCAACCCAAC 59.616 43.478 0.00 0.00 0.00 3.77
487 509 2.237393 ACGGCGTACACAAAACCTAA 57.763 45.000 12.58 0.00 0.00 2.69
607 629 3.751698 GCTTCTTCCGTTGATAACTTGGT 59.248 43.478 0.00 0.00 0.00 3.67
763 960 9.706691 CATGTCCAAAAGGTCGTATATATAGTT 57.293 33.333 0.00 0.00 0.00 2.24
764 961 8.311836 CCATGTCCAAAAGGTCGTATATATAGT 58.688 37.037 0.00 0.00 0.00 2.12
765 962 7.277981 GCCATGTCCAAAAGGTCGTATATATAG 59.722 40.741 0.00 0.00 0.00 1.31
766 963 7.101054 GCCATGTCCAAAAGGTCGTATATATA 58.899 38.462 0.00 0.00 0.00 0.86
767 964 5.938125 GCCATGTCCAAAAGGTCGTATATAT 59.062 40.000 0.00 0.00 0.00 0.86
812 1009 9.161629 CCCTAAAATTTTGGGCAGTTAAAATAG 57.838 33.333 24.01 5.79 37.47 1.73
833 1034 2.304761 CTGAAACCTAGCCACACCCTAA 59.695 50.000 0.00 0.00 0.00 2.69
854 1055 7.820044 AAGACTTGATTAAATCTCAGTCGAC 57.180 36.000 7.70 7.70 41.37 4.20
939 1141 6.532302 GTCGACGCTATATCTGAGAGATCTTA 59.468 42.308 0.00 0.00 36.20 2.10
940 1142 5.350365 GTCGACGCTATATCTGAGAGATCTT 59.650 44.000 0.00 0.00 36.20 2.40
941 1143 4.868171 GTCGACGCTATATCTGAGAGATCT 59.132 45.833 0.00 0.00 36.20 2.75
942 1144 4.868171 AGTCGACGCTATATCTGAGAGATC 59.132 45.833 10.46 0.00 36.20 2.75
943 1145 4.629634 CAGTCGACGCTATATCTGAGAGAT 59.370 45.833 10.46 0.00 38.70 2.75
944 1146 3.991121 CAGTCGACGCTATATCTGAGAGA 59.009 47.826 10.46 0.00 0.00 3.10
948 1150 3.741856 GTCTCAGTCGACGCTATATCTGA 59.258 47.826 10.46 4.84 0.00 3.27
951 1153 4.664640 CGAAGTCTCAGTCGACGCTATATC 60.665 50.000 10.46 4.24 39.64 1.63
962 1164 1.202817 GGGGAAGTCGAAGTCTCAGTC 59.797 57.143 0.00 0.00 0.00 3.51
970 1172 0.739561 CGTAGAGGGGGAAGTCGAAG 59.260 60.000 0.00 0.00 0.00 3.79
973 1175 2.783288 GGCGTAGAGGGGGAAGTCG 61.783 68.421 0.00 0.00 0.00 4.18
974 1176 0.976590 AAGGCGTAGAGGGGGAAGTC 60.977 60.000 0.00 0.00 0.00 3.01
975 1177 1.080538 AAGGCGTAGAGGGGGAAGT 59.919 57.895 0.00 0.00 0.00 3.01
976 1178 1.522569 CAAGGCGTAGAGGGGGAAG 59.477 63.158 0.00 0.00 0.00 3.46
977 1179 2.666098 GCAAGGCGTAGAGGGGGAA 61.666 63.158 0.00 0.00 0.00 3.97
978 1180 3.081409 GCAAGGCGTAGAGGGGGA 61.081 66.667 0.00 0.00 0.00 4.81
991 1193 2.874701 CCAGAGGAATCATTACCGCAAG 59.125 50.000 0.00 0.00 0.00 4.01
993 1195 2.115427 TCCAGAGGAATCATTACCGCA 58.885 47.619 0.00 0.00 0.00 5.69
1004 1206 4.323257 GGAAAGGTCGTAATTCCAGAGGAA 60.323 45.833 0.30 0.30 46.39 3.36
1005 1207 3.197116 GGAAAGGTCGTAATTCCAGAGGA 59.803 47.826 0.00 0.00 41.80 3.71
1006 1208 3.532542 GGAAAGGTCGTAATTCCAGAGG 58.467 50.000 0.00 0.00 41.80 3.69
1007 1209 3.055385 TGGGAAAGGTCGTAATTCCAGAG 60.055 47.826 6.16 0.00 43.56 3.35
1008 1210 2.907696 TGGGAAAGGTCGTAATTCCAGA 59.092 45.455 6.16 0.00 43.56 3.86
1009 1211 3.007635 GTGGGAAAGGTCGTAATTCCAG 58.992 50.000 6.16 0.00 43.56 3.86
1010 1212 2.372504 TGTGGGAAAGGTCGTAATTCCA 59.627 45.455 6.16 0.00 43.56 3.53
1011 1213 3.062122 TGTGGGAAAGGTCGTAATTCC 57.938 47.619 0.00 0.00 41.53 3.01
1012 1214 3.120442 CGTTGTGGGAAAGGTCGTAATTC 60.120 47.826 0.00 0.00 0.00 2.17
1013 1215 2.809696 CGTTGTGGGAAAGGTCGTAATT 59.190 45.455 0.00 0.00 0.00 1.40
1014 1216 2.419667 CGTTGTGGGAAAGGTCGTAAT 58.580 47.619 0.00 0.00 0.00 1.89
1015 1217 1.540797 CCGTTGTGGGAAAGGTCGTAA 60.541 52.381 0.00 0.00 0.00 3.18
1016 1218 0.033781 CCGTTGTGGGAAAGGTCGTA 59.966 55.000 0.00 0.00 0.00 3.43
1017 1219 1.227734 CCGTTGTGGGAAAGGTCGT 60.228 57.895 0.00 0.00 0.00 4.34
1018 1220 1.227734 ACCGTTGTGGGAAAGGTCG 60.228 57.895 0.00 0.00 44.64 4.79
1019 1221 1.792118 GCACCGTTGTGGGAAAGGTC 61.792 60.000 0.00 0.00 44.64 3.85
1020 1222 1.826487 GCACCGTTGTGGGAAAGGT 60.826 57.895 0.00 0.00 44.64 3.50
1021 1223 2.561037 GGCACCGTTGTGGGAAAGG 61.561 63.158 0.00 0.00 44.64 3.11
1022 1224 2.903547 CGGCACCGTTGTGGGAAAG 61.904 63.158 0.00 0.00 44.64 2.62
1023 1225 2.902846 CGGCACCGTTGTGGGAAA 60.903 61.111 0.00 0.00 44.64 3.13
1033 1235 1.024046 TTGATCAATGGACGGCACCG 61.024 55.000 7.71 7.71 46.03 4.94
1034 1236 1.173043 TTTGATCAATGGACGGCACC 58.827 50.000 9.40 0.00 0.00 5.01
1035 1237 3.508744 AATTTGATCAATGGACGGCAC 57.491 42.857 9.40 0.00 0.00 5.01
1036 1238 5.850557 AATAATTTGATCAATGGACGGCA 57.149 34.783 9.40 0.00 0.00 5.69
1037 1239 5.399301 CGAAATAATTTGATCAATGGACGGC 59.601 40.000 9.40 0.00 0.00 5.68
1038 1240 6.414694 CACGAAATAATTTGATCAATGGACGG 59.585 38.462 9.40 0.00 0.00 4.79
1039 1241 6.414694 CCACGAAATAATTTGATCAATGGACG 59.585 38.462 9.40 11.05 0.00 4.79
1040 1242 7.479980 TCCACGAAATAATTTGATCAATGGAC 58.520 34.615 14.64 2.47 0.00 4.02
1041 1243 7.637631 TCCACGAAATAATTTGATCAATGGA 57.362 32.000 14.64 14.64 0.00 3.41
1042 1244 8.757789 CAATCCACGAAATAATTTGATCAATGG 58.242 33.333 9.40 10.46 0.00 3.16
1043 1245 8.757789 CCAATCCACGAAATAATTTGATCAATG 58.242 33.333 9.40 0.96 0.00 2.82
1044 1246 8.694540 TCCAATCCACGAAATAATTTGATCAAT 58.305 29.630 9.40 0.00 0.00 2.57
1045 1247 8.060931 TCCAATCCACGAAATAATTTGATCAA 57.939 30.769 3.38 3.38 0.00 2.57
1046 1248 7.637631 TCCAATCCACGAAATAATTTGATCA 57.362 32.000 0.00 0.00 0.00 2.92
1047 1249 9.533253 AAATCCAATCCACGAAATAATTTGATC 57.467 29.630 0.00 0.00 0.00 2.92
1048 1250 9.533253 GAAATCCAATCCACGAAATAATTTGAT 57.467 29.630 0.00 0.00 0.00 2.57
1049 1251 8.526978 TGAAATCCAATCCACGAAATAATTTGA 58.473 29.630 0.00 0.00 0.00 2.69
1050 1252 8.594687 GTGAAATCCAATCCACGAAATAATTTG 58.405 33.333 0.00 0.00 0.00 2.32
1051 1253 8.531146 AGTGAAATCCAATCCACGAAATAATTT 58.469 29.630 0.00 0.00 34.93 1.82
1052 1254 8.066612 AGTGAAATCCAATCCACGAAATAATT 57.933 30.769 0.00 0.00 34.93 1.40
1053 1255 7.645058 AGTGAAATCCAATCCACGAAATAAT 57.355 32.000 0.00 0.00 34.93 1.28
1054 1256 7.312154 CAAGTGAAATCCAATCCACGAAATAA 58.688 34.615 0.00 0.00 34.93 1.40
1055 1257 6.624861 GCAAGTGAAATCCAATCCACGAAATA 60.625 38.462 0.00 0.00 34.93 1.40
1056 1258 5.713025 CAAGTGAAATCCAATCCACGAAAT 58.287 37.500 0.00 0.00 34.93 2.17
1057 1259 4.558496 GCAAGTGAAATCCAATCCACGAAA 60.558 41.667 0.00 0.00 34.93 3.46
1058 1260 3.057596 GCAAGTGAAATCCAATCCACGAA 60.058 43.478 0.00 0.00 34.93 3.85
1059 1261 2.487762 GCAAGTGAAATCCAATCCACGA 59.512 45.455 0.00 0.00 34.93 4.35
1060 1262 2.415893 GGCAAGTGAAATCCAATCCACG 60.416 50.000 0.00 0.00 34.93 4.94
1061 1263 2.827921 AGGCAAGTGAAATCCAATCCAC 59.172 45.455 0.00 0.00 0.00 4.02
1062 1264 2.827322 CAGGCAAGTGAAATCCAATCCA 59.173 45.455 0.00 0.00 0.00 3.41
1063 1265 2.827921 ACAGGCAAGTGAAATCCAATCC 59.172 45.455 0.00 0.00 0.00 3.01
1064 1266 3.760684 AGACAGGCAAGTGAAATCCAATC 59.239 43.478 0.00 0.00 0.00 2.67
1065 1267 3.771216 AGACAGGCAAGTGAAATCCAAT 58.229 40.909 0.00 0.00 0.00 3.16
1066 1268 3.228188 AGACAGGCAAGTGAAATCCAA 57.772 42.857 0.00 0.00 0.00 3.53
1067 1269 2.957402 AGACAGGCAAGTGAAATCCA 57.043 45.000 0.00 0.00 0.00 3.41
1068 1270 2.673368 CGTAGACAGGCAAGTGAAATCC 59.327 50.000 0.00 0.00 0.00 3.01
1069 1271 2.673368 CCGTAGACAGGCAAGTGAAATC 59.327 50.000 0.00 0.00 0.00 2.17
1070 1272 2.038557 ACCGTAGACAGGCAAGTGAAAT 59.961 45.455 0.00 0.00 0.00 2.17
1071 1273 1.414919 ACCGTAGACAGGCAAGTGAAA 59.585 47.619 0.00 0.00 0.00 2.69
1072 1274 1.045407 ACCGTAGACAGGCAAGTGAA 58.955 50.000 0.00 0.00 0.00 3.18
1073 1275 1.000506 GAACCGTAGACAGGCAAGTGA 59.999 52.381 0.00 0.00 0.00 3.41
1074 1276 1.429463 GAACCGTAGACAGGCAAGTG 58.571 55.000 0.00 0.00 0.00 3.16
1075 1277 0.320697 GGAACCGTAGACAGGCAAGT 59.679 55.000 0.00 0.00 0.00 3.16
1076 1278 0.391263 GGGAACCGTAGACAGGCAAG 60.391 60.000 0.00 0.00 40.86 4.01
1077 1279 1.675219 GGGAACCGTAGACAGGCAA 59.325 57.895 0.00 0.00 40.86 4.52
1078 1280 3.384348 GGGAACCGTAGACAGGCA 58.616 61.111 0.00 0.00 40.86 4.75
1090 1292 1.503542 CGAGCACATGCAAGGGAAC 59.496 57.895 6.64 0.00 45.16 3.62
1091 1293 1.675310 CCGAGCACATGCAAGGGAA 60.675 57.895 6.64 0.00 45.16 3.97
1092 1294 2.046023 CCGAGCACATGCAAGGGA 60.046 61.111 6.64 0.00 45.16 4.20
1094 1296 0.179048 TATCCCGAGCACATGCAAGG 60.179 55.000 6.64 8.48 45.16 3.61
1095 1297 1.224075 CTATCCCGAGCACATGCAAG 58.776 55.000 6.64 0.00 45.16 4.01
1096 1298 0.179048 CCTATCCCGAGCACATGCAA 60.179 55.000 6.64 0.00 45.16 4.08
1097 1299 1.337384 ACCTATCCCGAGCACATGCA 61.337 55.000 6.64 0.00 45.16 3.96
1098 1300 0.882042 CACCTATCCCGAGCACATGC 60.882 60.000 0.00 0.00 42.49 4.06
1099 1301 0.465705 ACACCTATCCCGAGCACATG 59.534 55.000 0.00 0.00 0.00 3.21
1100 1302 1.204146 AACACCTATCCCGAGCACAT 58.796 50.000 0.00 0.00 0.00 3.21
1101 1303 0.981183 AAACACCTATCCCGAGCACA 59.019 50.000 0.00 0.00 0.00 4.57
1102 1304 1.737793 CAAAACACCTATCCCGAGCAC 59.262 52.381 0.00 0.00 0.00 4.40
1103 1305 1.349688 ACAAAACACCTATCCCGAGCA 59.650 47.619 0.00 0.00 0.00 4.26
1104 1306 2.109425 ACAAAACACCTATCCCGAGC 57.891 50.000 0.00 0.00 0.00 5.03
1105 1307 7.497909 ACATTTATACAAAACACCTATCCCGAG 59.502 37.037 0.00 0.00 0.00 4.63
1106 1308 7.340256 ACATTTATACAAAACACCTATCCCGA 58.660 34.615 0.00 0.00 0.00 5.14
1107 1309 7.562454 ACATTTATACAAAACACCTATCCCG 57.438 36.000 0.00 0.00 0.00 5.14
1108 1310 9.797556 GAAACATTTATACAAAACACCTATCCC 57.202 33.333 0.00 0.00 0.00 3.85
1109 1311 9.498307 CGAAACATTTATACAAAACACCTATCC 57.502 33.333 0.00 0.00 0.00 2.59
1110 1312 9.006215 GCGAAACATTTATACAAAACACCTATC 57.994 33.333 0.00 0.00 0.00 2.08
1111 1313 7.971722 GGCGAAACATTTATACAAAACACCTAT 59.028 33.333 0.00 0.00 0.00 2.57
1112 1314 7.306953 GGCGAAACATTTATACAAAACACCTA 58.693 34.615 0.00 0.00 0.00 3.08
1113 1315 6.153756 GGCGAAACATTTATACAAAACACCT 58.846 36.000 0.00 0.00 0.00 4.00
1114 1316 5.059955 CGGCGAAACATTTATACAAAACACC 59.940 40.000 0.00 0.00 0.00 4.16
1115 1317 5.626132 ACGGCGAAACATTTATACAAAACAC 59.374 36.000 16.62 0.00 0.00 3.32
1116 1318 5.759963 ACGGCGAAACATTTATACAAAACA 58.240 33.333 16.62 0.00 0.00 2.83
1117 1319 7.958112 ATACGGCGAAACATTTATACAAAAC 57.042 32.000 16.62 0.00 0.00 2.43
1128 1330 9.485206 AGAATACTTAATAATACGGCGAAACAT 57.515 29.630 16.62 0.00 0.00 2.71
1129 1331 8.876275 AGAATACTTAATAATACGGCGAAACA 57.124 30.769 16.62 0.00 0.00 2.83
1130 1332 8.430828 GGAGAATACTTAATAATACGGCGAAAC 58.569 37.037 16.62 0.00 0.00 2.78
1131 1333 8.362639 AGGAGAATACTTAATAATACGGCGAAA 58.637 33.333 16.62 0.38 0.00 3.46
1132 1334 7.889469 AGGAGAATACTTAATAATACGGCGAA 58.111 34.615 16.62 0.00 0.00 4.70
1133 1335 7.458409 AGGAGAATACTTAATAATACGGCGA 57.542 36.000 16.62 0.00 0.00 5.54
1134 1336 8.530269 AAAGGAGAATACTTAATAATACGGCG 57.470 34.615 4.80 4.80 0.00 6.46
1171 1373 9.495572 GGGTTATTCTATTCCACTTCTTGATAG 57.504 37.037 0.00 0.00 0.00 2.08
1172 1374 8.148351 CGGGTTATTCTATTCCACTTCTTGATA 58.852 37.037 0.00 0.00 0.00 2.15
1173 1375 6.992715 CGGGTTATTCTATTCCACTTCTTGAT 59.007 38.462 0.00 0.00 0.00 2.57
1174 1376 6.346096 CGGGTTATTCTATTCCACTTCTTGA 58.654 40.000 0.00 0.00 0.00 3.02
1175 1377 5.527582 CCGGGTTATTCTATTCCACTTCTTG 59.472 44.000 0.00 0.00 0.00 3.02
1176 1378 5.191124 ACCGGGTTATTCTATTCCACTTCTT 59.809 40.000 6.32 0.00 0.00 2.52
1177 1379 4.720273 ACCGGGTTATTCTATTCCACTTCT 59.280 41.667 6.32 0.00 0.00 2.85
1178 1380 5.032327 ACCGGGTTATTCTATTCCACTTC 57.968 43.478 6.32 0.00 0.00 3.01
1179 1381 5.045432 TCAACCGGGTTATTCTATTCCACTT 60.045 40.000 12.95 0.00 0.00 3.16
1180 1382 4.472108 TCAACCGGGTTATTCTATTCCACT 59.528 41.667 12.95 0.00 0.00 4.00
1181 1383 4.773013 TCAACCGGGTTATTCTATTCCAC 58.227 43.478 12.95 0.00 0.00 4.02
1182 1384 5.433526 CTTCAACCGGGTTATTCTATTCCA 58.566 41.667 12.95 0.00 0.00 3.53
1183 1385 4.820173 CCTTCAACCGGGTTATTCTATTCC 59.180 45.833 12.95 0.00 0.00 3.01
1184 1386 4.820173 CCCTTCAACCGGGTTATTCTATTC 59.180 45.833 12.95 0.00 36.91 1.75
1185 1387 4.788679 CCCTTCAACCGGGTTATTCTATT 58.211 43.478 12.95 0.00 36.91 1.73
1186 1388 4.432980 CCCTTCAACCGGGTTATTCTAT 57.567 45.455 12.95 0.00 36.91 1.98
1187 1389 3.918294 CCCTTCAACCGGGTTATTCTA 57.082 47.619 12.95 0.00 36.91 2.10
1188 1390 2.801077 CCCTTCAACCGGGTTATTCT 57.199 50.000 12.95 0.00 36.91 2.40
1196 1398 3.275617 TGATCATTACCCTTCAACCGG 57.724 47.619 0.00 0.00 0.00 5.28
1197 1399 4.447724 CGTATGATCATTACCCTTCAACCG 59.552 45.833 14.65 0.00 0.00 4.44
1198 1400 5.365619 ACGTATGATCATTACCCTTCAACC 58.634 41.667 14.65 0.00 0.00 3.77
1199 1401 6.201044 CAGACGTATGATCATTACCCTTCAAC 59.799 42.308 14.65 1.44 0.00 3.18
1200 1402 6.127168 ACAGACGTATGATCATTACCCTTCAA 60.127 38.462 18.55 0.00 0.00 2.69
1201 1403 5.362717 ACAGACGTATGATCATTACCCTTCA 59.637 40.000 18.55 0.00 0.00 3.02
1202 1404 5.844004 ACAGACGTATGATCATTACCCTTC 58.156 41.667 18.55 3.60 0.00 3.46
1203 1405 5.871396 ACAGACGTATGATCATTACCCTT 57.129 39.130 18.55 0.00 0.00 3.95
1204 1406 6.550108 AGTTACAGACGTATGATCATTACCCT 59.450 38.462 18.55 4.21 0.00 4.34
1205 1407 6.746120 AGTTACAGACGTATGATCATTACCC 58.254 40.000 18.55 1.89 0.00 3.69
1206 1408 9.395707 CTAAGTTACAGACGTATGATCATTACC 57.604 37.037 18.55 1.72 0.00 2.85
1207 1409 8.903723 GCTAAGTTACAGACGTATGATCATTAC 58.096 37.037 18.55 9.03 0.00 1.89
1208 1410 8.626526 TGCTAAGTTACAGACGTATGATCATTA 58.373 33.333 18.55 9.30 0.00 1.90
1209 1411 7.489160 TGCTAAGTTACAGACGTATGATCATT 58.511 34.615 18.55 8.66 0.00 2.57
1210 1412 7.039313 TGCTAAGTTACAGACGTATGATCAT 57.961 36.000 18.55 13.81 0.00 2.45
1211 1413 6.445357 TGCTAAGTTACAGACGTATGATCA 57.555 37.500 18.55 0.00 0.00 2.92
1212 1414 7.194278 TCTTGCTAAGTTACAGACGTATGATC 58.806 38.462 18.55 6.55 0.00 2.92
1213 1415 7.096884 TCTTGCTAAGTTACAGACGTATGAT 57.903 36.000 18.55 3.86 0.00 2.45
1214 1416 6.505044 TCTTGCTAAGTTACAGACGTATGA 57.495 37.500 18.55 0.00 0.00 2.15
1215 1417 7.488150 TCAATCTTGCTAAGTTACAGACGTATG 59.512 37.037 8.99 8.99 0.00 2.39
1216 1418 7.544622 TCAATCTTGCTAAGTTACAGACGTAT 58.455 34.615 0.00 0.00 0.00 3.06
1217 1419 6.916440 TCAATCTTGCTAAGTTACAGACGTA 58.084 36.000 0.00 0.00 0.00 3.57
1218 1420 5.779922 TCAATCTTGCTAAGTTACAGACGT 58.220 37.500 0.00 0.00 0.00 4.34
1219 1421 6.706055 TTCAATCTTGCTAAGTTACAGACG 57.294 37.500 0.00 0.00 0.00 4.18
1220 1422 8.089115 ACTTTCAATCTTGCTAAGTTACAGAC 57.911 34.615 5.14 0.00 32.61 3.51
1221 1423 8.677148 AACTTTCAATCTTGCTAAGTTACAGA 57.323 30.769 15.30 0.00 39.10 3.41
1254 1456 5.888982 TTCCTTAGCGGATTAAGAGGATT 57.111 39.130 0.00 0.00 42.70 3.01
1256 1458 5.888982 ATTTCCTTAGCGGATTAAGAGGA 57.111 39.130 0.00 0.00 42.70 3.71
1403 1651 0.475044 TTTAGGGTCAGCGTTTGGGT 59.525 50.000 0.00 0.00 0.00 4.51
1409 1657 1.692519 AGACAGTTTTAGGGTCAGCGT 59.307 47.619 0.00 0.00 34.04 5.07
1410 1658 2.069273 CAGACAGTTTTAGGGTCAGCG 58.931 52.381 0.00 0.00 34.04 5.18
1411 1659 1.807142 GCAGACAGTTTTAGGGTCAGC 59.193 52.381 0.00 0.00 37.00 4.26
1413 1661 3.411446 CATGCAGACAGTTTTAGGGTCA 58.589 45.455 0.00 0.00 34.04 4.02
1414 1662 2.162408 GCATGCAGACAGTTTTAGGGTC 59.838 50.000 14.21 0.00 0.00 4.46
1425 1673 1.808891 CGATCCAGATGCATGCAGACA 60.809 52.381 26.69 8.22 0.00 3.41
1427 1675 0.883370 GCGATCCAGATGCATGCAGA 60.883 55.000 26.69 17.62 0.00 4.26
1429 1677 1.153127 TGCGATCCAGATGCATGCA 60.153 52.632 25.04 25.04 32.86 3.96
1434 1682 1.156645 GGACTGTGCGATCCAGATGC 61.157 60.000 4.68 0.00 34.87 3.91
1436 1684 1.439228 CGGACTGTGCGATCCAGAT 59.561 57.895 17.03 0.00 34.35 2.90
1439 1687 2.058001 ATCCGGACTGTGCGATCCA 61.058 57.895 23.37 4.32 34.35 3.41
1449 1697 1.338107 TCAGTGACAACATCCGGACT 58.662 50.000 6.12 0.00 0.00 3.85
1453 1701 6.402550 CCTTTTTCTATCAGTGACAACATCCG 60.403 42.308 0.00 0.00 0.00 4.18
1460 1708 3.330701 AGGCCCTTTTTCTATCAGTGACA 59.669 43.478 0.00 0.00 0.00 3.58
1468 1716 3.431415 GGACAACAGGCCCTTTTTCTAT 58.569 45.455 0.00 0.00 0.00 1.98
1559 1807 2.356125 CCTTGATTGAACCGGGACAGAT 60.356 50.000 6.32 2.39 0.00 2.90
1561 1809 1.453155 CCTTGATTGAACCGGGACAG 58.547 55.000 6.32 0.00 0.00 3.51
1562 1810 0.037590 CCCTTGATTGAACCGGGACA 59.962 55.000 6.32 1.89 37.05 4.02
1577 1825 4.660938 GGCCACGTGGAAGCCCTT 62.661 66.667 38.30 0.00 41.00 3.95
2051 2350 4.141088 ACGGAGAATACTATGTGGACCCTA 60.141 45.833 0.00 0.00 0.00 3.53


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

AutoCloner maintained by Alex Coulton.