Multiple sequence alignment - TraesCS3D01G018600

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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 TraesCS3D01G018600 chr3D 100.000 3749 0 0 1 3749 6198789 6195041 0.000000e+00 6924.0
1 TraesCS3D01G018600 chr3D 77.653 801 134 36 1683 2464 6752243 6753017 2.660000e-121 446.0
2 TraesCS3D01G018600 chr3D 80.309 259 32 9 1369 1620 6751772 6752018 1.070000e-40 178.0
3 TraesCS3D01G018600 chr3D 96.774 31 1 0 1160 1190 6197576 6197546 7.000000e-03 52.8
4 TraesCS3D01G018600 chr3D 96.774 31 1 0 1214 1244 6197630 6197600 7.000000e-03 52.8
5 TraesCS3D01G018600 chr3A 86.704 1256 78 48 1646 2841 14289252 14290478 0.000000e+00 1312.0
6 TraesCS3D01G018600 chr3A 91.565 735 45 8 2675 3401 14205806 14205081 0.000000e+00 998.0
7 TraesCS3D01G018600 chr3A 85.101 745 86 21 127 857 14287502 14288235 0.000000e+00 737.0
8 TraesCS3D01G018600 chr3A 87.009 662 61 14 1780 2436 14683145 14682504 0.000000e+00 723.0
9 TraesCS3D01G018600 chr3A 89.126 469 29 12 1191 1647 14683686 14683228 7.030000e-157 564.0
10 TraesCS3D01G018600 chr3A 95.184 353 17 0 3397 3749 14205041 14204689 3.270000e-155 558.0
11 TraesCS3D01G018600 chr3A 77.315 864 146 38 1683 2523 13498234 13497398 7.330000e-127 464.0
12 TraesCS3D01G018600 chr3A 86.239 436 21 13 1188 1617 14288640 14289042 1.600000e-118 436.0
13 TraesCS3D01G018600 chr3A 86.864 236 21 3 2706 2938 14681857 14681629 4.810000e-64 255.0
14 TraesCS3D01G018600 chr3A 84.906 265 6 4 887 1150 14288409 14288640 1.740000e-58 237.0
15 TraesCS3D01G018600 chr3A 80.078 256 35 8 1368 1619 13498700 13498457 3.850000e-40 176.0
16 TraesCS3D01G018600 chr3A 93.277 119 8 0 2429 2547 14682239 14682121 3.850000e-40 176.0
17 TraesCS3D01G018600 chr3A 91.667 48 4 0 1077 1124 14683758 14683711 2.420000e-07 67.6
18 TraesCS3D01G018600 chr3A 100.000 31 0 0 3068 3098 57197185 57197215 1.450000e-04 58.4
19 TraesCS3D01G018600 chrUn 93.210 324 18 1 3430 3749 124165034 124164711 1.220000e-129 473.0
20 TraesCS3D01G018600 chrUn 92.593 324 20 1 3430 3749 4554963 4554640 2.640000e-126 462.0
21 TraesCS3D01G018600 chrUn 92.593 324 20 1 3430 3749 131618591 131618914 2.640000e-126 462.0
22 TraesCS3D01G018600 chrUn 82.239 259 27 10 1368 1619 49239703 49239949 4.910000e-49 206.0
23 TraesCS3D01G018600 chr3B 80.277 578 67 22 132 703 7332458 7332994 3.510000e-105 392.0
24 TraesCS3D01G018600 chr3B 77.000 700 120 31 1683 2363 8344893 8345570 2.750000e-96 363.0
25 TraesCS3D01G018600 chr3B 80.934 257 33 7 1368 1620 8344383 8344627 4.940000e-44 189.0
26 TraesCS3D01G018600 chr4A 81.853 259 28 9 1368 1619 645580480 645580234 2.280000e-47 200.0
27 TraesCS3D01G018600 chr7D 81.395 258 30 9 1368 1619 40127311 40127066 1.060000e-45 195.0
28 TraesCS3D01G018600 chr2B 94.872 39 1 1 501 539 419950048 419950011 4.040000e-05 60.2
29 TraesCS3D01G018600 chr5A 84.746 59 5 4 605 660 674361252 674361195 5.230000e-04 56.5
30 TraesCS3D01G018600 chr6B 100.000 29 0 0 3068 3096 657063129 657063101 2.000000e-03 54.7


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 TraesCS3D01G018600 chr3D 6195041 6198789 3748 True 2343.20 6924 97.849333 1 3749 3 chr3D.!!$R1 3748
1 TraesCS3D01G018600 chr3D 6751772 6753017 1245 False 312.00 446 78.981000 1369 2464 2 chr3D.!!$F1 1095
2 TraesCS3D01G018600 chr3A 14204689 14205806 1117 True 778.00 998 93.374500 2675 3749 2 chr3A.!!$R2 1074
3 TraesCS3D01G018600 chr3A 14287502 14290478 2976 False 680.50 1312 85.737500 127 2841 4 chr3A.!!$F2 2714
4 TraesCS3D01G018600 chr3A 14681629 14683758 2129 True 357.12 723 89.588600 1077 2938 5 chr3A.!!$R3 1861
5 TraesCS3D01G018600 chr3A 13497398 13498700 1302 True 320.00 464 78.696500 1368 2523 2 chr3A.!!$R1 1155
6 TraesCS3D01G018600 chr3B 7332458 7332994 536 False 392.00 392 80.277000 132 703 1 chr3B.!!$F1 571
7 TraesCS3D01G018600 chr3B 8344383 8345570 1187 False 276.00 363 78.967000 1368 2363 2 chr3B.!!$F2 995

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
827 857 0.107703 CCATTCACTGCCCGCTCTAA 60.108 55.0 0.00 0.00 0.00 2.10 F
1067 1241 0.179127 TAGCTGCACACGATCTGAGC 60.179 55.0 1.02 7.34 37.02 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1858 2334 0.734253 CTCAGCTTCTCGACGTTGGG 60.734 60.0 2.20 0.0 0.00 4.12 R
2946 3847 0.034059 GTCACATAGGCCATCTCGGG 59.966 60.0 5.01 0.0 34.06 5.14 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
81 82 6.825284 TGTTTAACATGCACTCAAAACATG 57.175 33.333 12.60 0.00 45.28 3.21
87 88 5.970140 CATGCACTCAAAACATGTTCAAA 57.030 34.783 12.39 0.00 37.10 2.69
88 89 6.347270 CATGCACTCAAAACATGTTCAAAA 57.653 33.333 12.39 0.00 37.10 2.44
89 90 6.773080 CATGCACTCAAAACATGTTCAAAAA 58.227 32.000 12.39 0.00 37.10 1.94
90 91 6.406093 TGCACTCAAAACATGTTCAAAAAG 57.594 33.333 12.39 7.99 0.00 2.27
91 92 5.931146 TGCACTCAAAACATGTTCAAAAAGT 59.069 32.000 12.39 8.59 0.00 2.66
92 93 6.128607 TGCACTCAAAACATGTTCAAAAAGTG 60.129 34.615 22.30 22.30 34.87 3.16
93 94 6.128580 GCACTCAAAACATGTTCAAAAAGTGT 60.129 34.615 24.62 12.97 34.39 3.55
94 95 7.062839 GCACTCAAAACATGTTCAAAAAGTGTA 59.937 33.333 24.62 2.24 34.39 2.90
95 96 9.086336 CACTCAAAACATGTTCAAAAAGTGTAT 57.914 29.630 12.39 0.00 0.00 2.29
96 97 9.651913 ACTCAAAACATGTTCAAAAAGTGTATT 57.348 25.926 12.39 0.00 0.00 1.89
108 109 8.655651 TCAAAAAGTGTATTTGAAACATTCCC 57.344 30.769 0.00 0.00 42.19 3.97
109 110 8.260818 TCAAAAAGTGTATTTGAAACATTCCCA 58.739 29.630 0.00 0.00 42.19 4.37
110 111 8.887717 CAAAAAGTGTATTTGAAACATTCCCAA 58.112 29.630 0.00 0.00 39.56 4.12
111 112 8.432110 AAAAGTGTATTTGAAACATTCCCAAC 57.568 30.769 0.00 0.00 0.00 3.77
112 113 5.768317 AGTGTATTTGAAACATTCCCAACG 58.232 37.500 0.00 0.00 0.00 4.10
113 114 5.300792 AGTGTATTTGAAACATTCCCAACGT 59.699 36.000 0.00 0.00 0.00 3.99
114 115 5.401079 GTGTATTTGAAACATTCCCAACGTG 59.599 40.000 0.00 0.00 0.00 4.49
115 116 4.664150 ATTTGAAACATTCCCAACGTGT 57.336 36.364 0.00 0.00 0.00 4.49
116 117 5.776173 ATTTGAAACATTCCCAACGTGTA 57.224 34.783 0.00 0.00 0.00 2.90
117 118 5.776173 TTTGAAACATTCCCAACGTGTAT 57.224 34.783 0.00 0.00 0.00 2.29
118 119 6.879276 TTTGAAACATTCCCAACGTGTATA 57.121 33.333 0.00 0.00 0.00 1.47
119 120 6.879276 TTGAAACATTCCCAACGTGTATAA 57.121 33.333 0.00 0.00 0.00 0.98
120 121 6.879276 TGAAACATTCCCAACGTGTATAAA 57.121 33.333 0.00 0.00 0.00 1.40
121 122 7.273320 TGAAACATTCCCAACGTGTATAAAA 57.727 32.000 0.00 0.00 0.00 1.52
122 123 7.140048 TGAAACATTCCCAACGTGTATAAAAC 58.860 34.615 0.00 0.00 0.00 2.43
123 124 6.636562 AACATTCCCAACGTGTATAAAACA 57.363 33.333 0.00 0.00 35.06 2.83
124 125 6.636562 ACATTCCCAACGTGTATAAAACAA 57.363 33.333 0.00 0.00 40.63 2.83
125 126 6.440436 ACATTCCCAACGTGTATAAAACAAC 58.560 36.000 0.00 0.00 40.63 3.32
126 127 6.263617 ACATTCCCAACGTGTATAAAACAACT 59.736 34.615 0.00 0.00 40.63 3.16
127 128 5.676532 TCCCAACGTGTATAAAACAACTG 57.323 39.130 0.00 0.00 40.63 3.16
128 129 5.124645 TCCCAACGTGTATAAAACAACTGT 58.875 37.500 0.00 0.00 40.63 3.55
129 130 5.007823 TCCCAACGTGTATAAAACAACTGTG 59.992 40.000 0.00 0.00 40.63 3.66
130 131 5.220892 CCCAACGTGTATAAAACAACTGTGT 60.221 40.000 0.00 0.00 40.63 3.72
156 157 7.595819 AAACAGAGGATTGGAAAACACATAA 57.404 32.000 0.00 0.00 0.00 1.90
171 172 9.388346 GAAAACACATAAATATTGTCAACGTCA 57.612 29.630 0.00 0.00 0.00 4.35
214 216 8.689251 TGTAAATTTGTTTGTTCGTGATTTCA 57.311 26.923 0.00 0.00 0.00 2.69
227 229 7.757173 TGTTCGTGATTTCAAGAAAAATGTTCA 59.243 29.630 9.91 1.41 43.71 3.18
277 280 9.830975 ACATTTAAAAACTGTTCAGGCTTTTAT 57.169 25.926 15.75 7.05 0.00 1.40
557 583 9.574458 TTGTATCACTCGAAAAACAAATTGAAA 57.426 25.926 0.00 0.00 0.00 2.69
588 616 8.948631 TTTGGAAAATGTTTAACATGCACTAA 57.051 26.923 11.60 7.20 37.97 2.24
641 669 4.539509 TGGTCAACGTGTATCACAAAAC 57.460 40.909 0.00 0.00 33.40 2.43
655 683 9.473640 TGTATCACAAAACTGTTACGTGTATAA 57.526 29.630 16.91 4.07 0.00 0.98
692 720 7.870954 CAGCATGCATTGGATAAATTAGACATT 59.129 33.333 21.98 0.00 0.00 2.71
737 766 9.201989 AGAAAAACCCTGAAGAAAACTAGAAAT 57.798 29.630 0.00 0.00 0.00 2.17
766 795 0.671781 CCGCACAAGGAACAGAGGAG 60.672 60.000 0.00 0.00 0.00 3.69
771 800 2.035961 CACAAGGAACAGAGGAGACGAA 59.964 50.000 0.00 0.00 0.00 3.85
789 819 5.522824 AGACGAATAAAAACCGAGAATAGCC 59.477 40.000 0.00 0.00 0.00 3.93
790 820 4.573607 ACGAATAAAAACCGAGAATAGCCC 59.426 41.667 0.00 0.00 0.00 5.19
791 821 4.573201 CGAATAAAAACCGAGAATAGCCCA 59.427 41.667 0.00 0.00 0.00 5.36
792 822 5.065474 CGAATAAAAACCGAGAATAGCCCAA 59.935 40.000 0.00 0.00 0.00 4.12
819 849 3.455469 GCTGGCCCATTCACTGCC 61.455 66.667 0.00 0.00 45.56 4.85
820 850 2.757099 CTGGCCCATTCACTGCCC 60.757 66.667 0.00 0.00 44.72 5.36
827 857 0.107703 CCATTCACTGCCCGCTCTAA 60.108 55.000 0.00 0.00 0.00 2.10
838 868 1.461091 CCGCTCTAACCCGCTGGATA 61.461 60.000 0.00 0.00 34.81 2.59
840 870 0.319986 GCTCTAACCCGCTGGATAGC 60.320 60.000 0.00 0.32 46.62 2.97
849 879 1.078426 GCTGGATAGCCCAACGTGT 60.078 57.895 0.00 0.00 46.07 4.49
862 892 3.438088 CGTGTGCGTCGAGAACTC 58.562 61.111 0.00 0.00 0.00 3.01
872 902 3.867723 CGAGAACTCGTCTGGTTGT 57.132 52.632 14.87 0.00 46.99 3.32
874 904 2.052157 CGAGAACTCGTCTGGTTGTTC 58.948 52.381 14.87 0.00 46.99 3.18
876 906 3.718815 GAGAACTCGTCTGGTTGTTCTT 58.281 45.455 8.34 0.00 45.95 2.52
878 908 5.470047 AGAACTCGTCTGGTTGTTCTTAT 57.530 39.130 0.00 0.00 44.32 1.73
879 909 6.585695 AGAACTCGTCTGGTTGTTCTTATA 57.414 37.500 0.00 0.00 44.32 0.98
880 910 6.989659 AGAACTCGTCTGGTTGTTCTTATAA 58.010 36.000 0.00 0.00 44.32 0.98
881 911 7.439381 AGAACTCGTCTGGTTGTTCTTATAAA 58.561 34.615 0.00 0.00 44.32 1.40
883 913 8.441312 AACTCGTCTGGTTGTTCTTATAAAAA 57.559 30.769 0.00 0.00 0.00 1.94
884 914 8.084590 ACTCGTCTGGTTGTTCTTATAAAAAG 57.915 34.615 0.00 0.00 0.00 2.27
885 915 7.713942 ACTCGTCTGGTTGTTCTTATAAAAAGT 59.286 33.333 0.00 0.00 0.00 2.66
947 1121 4.225497 GGAACGGATTGAGCCCTG 57.775 61.111 0.00 0.00 0.00 4.45
948 1122 2.115291 GGAACGGATTGAGCCCTGC 61.115 63.158 0.00 0.00 0.00 4.85
949 1123 2.044946 AACGGATTGAGCCCTGCC 60.045 61.111 0.00 0.00 0.00 4.85
950 1124 3.645268 AACGGATTGAGCCCTGCCC 62.645 63.158 0.00 0.00 0.00 5.36
951 1125 4.883354 CGGATTGAGCCCTGCCCC 62.883 72.222 0.00 0.00 0.00 5.80
952 1126 4.883354 GGATTGAGCCCTGCCCCG 62.883 72.222 0.00 0.00 0.00 5.73
1067 1241 0.179127 TAGCTGCACACGATCTGAGC 60.179 55.000 1.02 7.34 37.02 4.26
1079 1253 2.736719 CGATCTGAGCTTGTCGATTGGT 60.737 50.000 0.00 0.00 36.25 3.67
1089 1263 1.449423 TCGATTGGTCATGGCCGTG 60.449 57.895 19.62 19.62 0.00 4.94
1131 1306 8.147642 AGAAGAGATTCCGTGCTAATTTATTG 57.852 34.615 0.00 0.00 0.00 1.90
1155 1330 8.066612 TGATTTAATCTCCAAACATCTTTCCC 57.933 34.615 6.50 0.00 0.00 3.97
1156 1331 6.509418 TTTAATCTCCAAACATCTTTCCCG 57.491 37.500 0.00 0.00 0.00 5.14
1157 1332 4.301072 AATCTCCAAACATCTTTCCCGA 57.699 40.909 0.00 0.00 0.00 5.14
1158 1333 4.510167 ATCTCCAAACATCTTTCCCGAT 57.490 40.909 0.00 0.00 0.00 4.18
1159 1334 4.301072 TCTCCAAACATCTTTCCCGATT 57.699 40.909 0.00 0.00 0.00 3.34
1160 1335 4.662278 TCTCCAAACATCTTTCCCGATTT 58.338 39.130 0.00 0.00 0.00 2.17
1161 1336 4.458989 TCTCCAAACATCTTTCCCGATTTG 59.541 41.667 0.00 0.00 0.00 2.32
1162 1337 4.148838 TCCAAACATCTTTCCCGATTTGT 58.851 39.130 0.00 0.00 0.00 2.83
1163 1338 4.586841 TCCAAACATCTTTCCCGATTTGTT 59.413 37.500 0.00 0.00 0.00 2.83
1164 1339 4.685628 CCAAACATCTTTCCCGATTTGTTG 59.314 41.667 0.00 0.00 0.00 3.33
1165 1340 4.519540 AACATCTTTCCCGATTTGTTGG 57.480 40.909 0.00 0.00 0.00 3.77
1166 1341 2.231235 ACATCTTTCCCGATTTGTTGGC 59.769 45.455 0.00 0.00 0.00 4.52
1167 1342 2.286365 TCTTTCCCGATTTGTTGGCT 57.714 45.000 0.00 0.00 0.00 4.75
1168 1343 2.593026 TCTTTCCCGATTTGTTGGCTT 58.407 42.857 0.00 0.00 0.00 4.35
1169 1344 2.295909 TCTTTCCCGATTTGTTGGCTTG 59.704 45.455 0.00 0.00 0.00 4.01
1170 1345 1.988293 TTCCCGATTTGTTGGCTTGA 58.012 45.000 0.00 0.00 0.00 3.02
1171 1346 2.214376 TCCCGATTTGTTGGCTTGAT 57.786 45.000 0.00 0.00 0.00 2.57
1172 1347 2.091541 TCCCGATTTGTTGGCTTGATC 58.908 47.619 0.00 0.00 0.00 2.92
1173 1348 1.818060 CCCGATTTGTTGGCTTGATCA 59.182 47.619 0.00 0.00 0.00 2.92
1174 1349 2.230992 CCCGATTTGTTGGCTTGATCAA 59.769 45.455 8.12 8.12 0.00 2.57
1175 1350 3.504863 CCGATTTGTTGGCTTGATCAAG 58.495 45.455 27.82 27.82 41.24 3.02
1176 1351 3.057315 CCGATTTGTTGGCTTGATCAAGT 60.057 43.478 30.88 13.00 40.45 3.16
1177 1352 4.155826 CCGATTTGTTGGCTTGATCAAGTA 59.844 41.667 30.88 20.06 40.45 2.24
1178 1353 5.163622 CCGATTTGTTGGCTTGATCAAGTAT 60.164 40.000 30.88 15.55 40.45 2.12
1179 1354 6.324819 CGATTTGTTGGCTTGATCAAGTATT 58.675 36.000 30.88 11.77 40.45 1.89
1180 1355 6.808212 CGATTTGTTGGCTTGATCAAGTATTT 59.192 34.615 30.88 12.20 40.45 1.40
1181 1356 7.201376 CGATTTGTTGGCTTGATCAAGTATTTG 60.201 37.037 30.88 10.94 40.45 2.32
1182 1357 6.403866 TTGTTGGCTTGATCAAGTATTTGT 57.596 33.333 30.88 0.00 40.45 2.83
1183 1358 6.403866 TGTTGGCTTGATCAAGTATTTGTT 57.596 33.333 30.88 0.00 40.45 2.83
1184 1359 6.215121 TGTTGGCTTGATCAAGTATTTGTTG 58.785 36.000 30.88 8.91 40.45 3.33
1185 1360 5.389859 TGGCTTGATCAAGTATTTGTTGG 57.610 39.130 30.88 8.24 40.45 3.77
1186 1361 4.176271 GGCTTGATCAAGTATTTGTTGGC 58.824 43.478 30.88 16.48 40.45 4.52
1187 1362 4.176271 GCTTGATCAAGTATTTGTTGGCC 58.824 43.478 30.88 10.58 40.45 5.36
1188 1363 4.321899 GCTTGATCAAGTATTTGTTGGCCA 60.322 41.667 30.88 0.00 40.45 5.36
1189 1364 5.625197 GCTTGATCAAGTATTTGTTGGCCAT 60.625 40.000 30.88 0.00 40.45 4.40
1316 1494 0.825840 GGGAGGAGACGGAGAGGATG 60.826 65.000 0.00 0.00 0.00 3.51
1328 1506 3.536570 GGAGAGGATGGTCAAGCTTTAC 58.463 50.000 0.00 0.00 0.00 2.01
1365 1543 1.078567 CTGCAGAGGAACAGGGAGC 60.079 63.158 8.42 0.00 0.00 4.70
1443 1624 9.066892 ACTAAAGTTTTTACAAGATGCAGATCA 57.933 29.630 0.00 0.00 0.00 2.92
1483 1683 7.630242 ACATTCATTATGTGTTCCTACCTTG 57.370 36.000 0.00 0.00 45.71 3.61
1484 1684 6.603201 ACATTCATTATGTGTTCCTACCTTGG 59.397 38.462 0.00 0.00 45.71 3.61
1485 1685 4.523083 TCATTATGTGTTCCTACCTTGGC 58.477 43.478 0.00 0.00 0.00 4.52
1486 1686 3.359695 TTATGTGTTCCTACCTTGGCC 57.640 47.619 0.00 0.00 0.00 5.36
1487 1687 0.331616 ATGTGTTCCTACCTTGGCCC 59.668 55.000 0.00 0.00 0.00 5.80
1541 1741 3.426568 GCGGCTGACTTGCAGGAC 61.427 66.667 1.40 0.00 45.03 3.85
2008 2487 0.098728 CGGATCCAAATGTTCCACGC 59.901 55.000 13.41 0.00 0.00 5.34
2126 2610 9.834628 ATTGTTATTGTTTGTAACTATGGAACG 57.165 29.630 0.00 0.00 34.08 3.95
2306 2795 9.170734 CAGTATTGATTTCTCTCTGAATTGGAA 57.829 33.333 0.00 0.00 34.24 3.53
2318 2807 3.009723 TGAATTGGAAAGTGGATCGCTC 58.990 45.455 0.00 0.00 0.00 5.03
2321 2812 2.099141 TGGAAAGTGGATCGCTCAAG 57.901 50.000 0.00 0.00 0.00 3.02
2374 2865 5.186996 ACTCCATGTTGTTTGTGTCATTC 57.813 39.130 0.00 0.00 0.00 2.67
2393 2884 0.868406 CGGAAGCAAGGAGAACACAC 59.132 55.000 0.00 0.00 0.00 3.82
2394 2885 1.810031 CGGAAGCAAGGAGAACACACA 60.810 52.381 0.00 0.00 0.00 3.72
2405 2896 4.284490 AGGAGAACACACATTCTAGCTGAA 59.716 41.667 0.00 0.00 39.08 3.02
2412 2903 5.696724 ACACACATTCTAGCTGAACAAGTAC 59.303 40.000 0.00 0.00 37.52 2.73
2414 2905 6.090088 CACACATTCTAGCTGAACAAGTACTC 59.910 42.308 0.00 0.00 37.52 2.59
2460 3223 1.059098 TTTGCAGAGGAAGAGAGGCA 58.941 50.000 0.00 0.00 0.00 4.75
2465 3228 1.134729 CAGAGGAAGAGAGGCAGAAGC 60.135 57.143 0.00 0.00 41.10 3.86
2473 3236 1.448717 GAGGCAGAAGCGGGAAGAC 60.449 63.158 0.00 0.00 43.41 3.01
2486 3249 0.030101 GGAAGACGCGGAGATGAGAG 59.970 60.000 12.47 0.00 0.00 3.20
2575 3382 0.179119 GCATGGATCCTGCTTTGCAC 60.179 55.000 21.85 0.19 36.68 4.57
2610 3417 3.273434 TGTTTGATCTATGAGCCACAGC 58.727 45.455 0.00 0.00 40.32 4.40
2623 3430 1.140852 GCCACAGCACTCCCATACATA 59.859 52.381 0.00 0.00 39.53 2.29
2653 3460 7.995289 TGATGCTACTTGTTATGGTATTTTGG 58.005 34.615 0.00 0.00 0.00 3.28
2656 3463 6.943146 TGCTACTTGTTATGGTATTTTGGACA 59.057 34.615 0.00 0.00 0.00 4.02
2657 3464 7.448777 TGCTACTTGTTATGGTATTTTGGACAA 59.551 33.333 0.00 0.00 0.00 3.18
2658 3465 8.466798 GCTACTTGTTATGGTATTTTGGACAAT 58.533 33.333 0.00 0.00 0.00 2.71
2685 3540 7.391620 TGTTGTTAGTATTACTCAAGGGAAGG 58.608 38.462 0.00 0.00 0.00 3.46
2750 3647 4.220821 AGGATTTGAGCTCGTTGACTCTAA 59.779 41.667 9.64 0.00 33.36 2.10
2757 3658 3.991121 AGCTCGTTGACTCTAAGCTTTTC 59.009 43.478 3.20 0.00 40.26 2.29
2762 3663 5.009710 TCGTTGACTCTAAGCTTTTCTCTGA 59.990 40.000 3.20 0.00 0.00 3.27
2788 3689 1.295792 TCTTCAGTTTGTGTGTCGCC 58.704 50.000 0.00 0.00 0.00 5.54
2843 3744 6.990939 TGTTCTGCCAATTTCATTTCATTTCA 59.009 30.769 0.00 0.00 0.00 2.69
2844 3745 7.662258 TGTTCTGCCAATTTCATTTCATTTCAT 59.338 29.630 0.00 0.00 0.00 2.57
2845 3746 8.508875 GTTCTGCCAATTTCATTTCATTTCATT 58.491 29.630 0.00 0.00 0.00 2.57
2846 3747 8.259049 TCTGCCAATTTCATTTCATTTCATTC 57.741 30.769 0.00 0.00 0.00 2.67
2847 3748 7.334921 TCTGCCAATTTCATTTCATTTCATTCC 59.665 33.333 0.00 0.00 0.00 3.01
2869 3770 3.587797 GCAGTAGCCAGTAAGTGTGTA 57.412 47.619 0.00 0.00 33.58 2.90
2885 3786 4.475016 AGTGTGTATGCCCCTCTTATCTTT 59.525 41.667 0.00 0.00 0.00 2.52
2886 3787 5.044846 AGTGTGTATGCCCCTCTTATCTTTT 60.045 40.000 0.00 0.00 0.00 2.27
2896 3797 4.324563 CCCTCTTATCTTTTGCTCCCTTGA 60.325 45.833 0.00 0.00 0.00 3.02
2933 3834 3.744660 TGCTCTGCGATATCTACTCTGA 58.255 45.455 0.34 0.00 0.00 3.27
2946 3847 9.928236 GATATCTACTCTGATTTTGCTGTTTTC 57.072 33.333 0.00 0.00 0.00 2.29
2960 3861 1.843851 TGTTTTCCCGAGATGGCCTAT 59.156 47.619 3.32 0.00 35.87 2.57
2962 3863 1.507140 TTTCCCGAGATGGCCTATGT 58.493 50.000 3.32 0.00 35.87 2.29
2963 3864 0.758734 TTCCCGAGATGGCCTATGTG 59.241 55.000 3.32 0.00 35.87 3.21
2983 3884 7.956420 ATGTGACGACAAGTATTTTAGAACA 57.044 32.000 0.00 0.00 35.11 3.18
2985 3886 7.623770 TGTGACGACAAGTATTTTAGAACAAC 58.376 34.615 0.00 0.00 0.00 3.32
2987 3888 6.696583 TGACGACAAGTATTTTAGAACAACGA 59.303 34.615 0.00 0.00 0.00 3.85
3024 3925 8.995906 CAATACTAAAATAGTTGTTAAGCACGC 58.004 33.333 0.00 0.00 40.14 5.34
3041 3942 1.135139 ACGCTCACATAGTGCCTACTG 59.865 52.381 0.00 0.00 39.48 2.74
3054 3955 1.068194 GCCTACTGAAGATCGGATCGG 60.068 57.143 12.08 6.86 0.00 4.18
3056 3957 2.486203 CCTACTGAAGATCGGATCGGAG 59.514 54.545 12.08 11.17 0.00 4.63
3060 3961 0.665972 GAAGATCGGATCGGAGCTGC 60.666 60.000 20.10 15.35 32.06 5.25
3140 4048 5.221441 GCCTCCCATTGAAAATATAACCCAC 60.221 44.000 0.00 0.00 0.00 4.61
3162 4070 4.083324 ACATTAATGAGACACCAAAGCGTG 60.083 41.667 22.16 0.00 39.75 5.34
3173 4081 1.600413 CCAAAGCGTGAAACTTGAGGC 60.600 52.381 0.00 0.00 31.75 4.70
3174 4082 0.668535 AAAGCGTGAAACTTGAGGCC 59.331 50.000 0.00 0.00 31.75 5.19
3176 4084 0.685097 AGCGTGAAACTTGAGGCCTA 59.315 50.000 4.42 0.00 31.75 3.93
3217 4125 4.148825 GCTCTGCCGTCGGATGGT 62.149 66.667 17.49 0.00 0.00 3.55
3218 4126 2.782222 GCTCTGCCGTCGGATGGTA 61.782 63.158 17.49 12.18 0.00 3.25
3259 4167 7.390718 ACCAGTATACACAACCTTCAGAATTTC 59.609 37.037 5.50 0.00 0.00 2.17
3292 4200 1.408702 GAAAAAGGAGCAGCCACACAA 59.591 47.619 0.00 0.00 40.02 3.33
3293 4201 0.746659 AAAAGGAGCAGCCACACAAC 59.253 50.000 0.00 0.00 40.02 3.32
3337 4246 1.134848 TGGAGGCAACAAAACAACAGC 60.135 47.619 0.00 0.00 41.41 4.40
3358 4267 7.038659 ACAGCAGAATCTGAAGTAATAGTCAC 58.961 38.462 15.38 0.00 37.51 3.67
3410 4363 5.893687 TCTAGTACAACAGAAAACGTGTCA 58.106 37.500 0.00 0.00 0.00 3.58
3413 4366 1.395608 ACAACAGAAAACGTGTCACCG 59.604 47.619 0.00 0.00 0.00 4.94
3455 4408 0.514691 GCTCGCCAGTTTGAAGACAG 59.485 55.000 0.00 0.00 0.00 3.51
3474 4427 3.653344 CAGACACACTGCTTAGTGCTTA 58.347 45.455 7.31 0.00 43.13 3.09
3505 4458 4.152580 GCCTAGAAATAATAACCGCTGCTC 59.847 45.833 0.00 0.00 0.00 4.26
3536 4489 1.933115 GCACAACCATACCAAGGCCG 61.933 60.000 0.00 0.00 0.00 6.13
3537 4490 0.608035 CACAACCATACCAAGGCCGT 60.608 55.000 0.00 0.00 0.00 5.68
3539 4492 1.078708 AACCATACCAAGGCCGTCG 60.079 57.895 0.00 0.00 0.00 5.12
3541 4494 2.727392 CCATACCAAGGCCGTCGGA 61.727 63.158 17.49 0.00 0.00 4.55
3545 4498 0.611618 TACCAAGGCCGTCGGAGTTA 60.612 55.000 17.49 0.00 0.00 2.24
3555 4508 3.619929 GCCGTCGGAGTTACAACAATTAT 59.380 43.478 17.49 0.00 0.00 1.28
3598 4551 2.289444 ACCAGTAACACAAGGATCACCG 60.289 50.000 0.00 0.00 41.83 4.94
3678 4631 6.797454 ACCGCAAATTTCTGTAGTTTTTACA 58.203 32.000 0.00 0.00 0.00 2.41
3681 4634 7.434013 CCGCAAATTTCTGTAGTTTTTACACTT 59.566 33.333 0.00 0.00 0.00 3.16
3696 4649 9.891535 GTTTTTACACTTCGGATTTATAGTACG 57.108 33.333 0.00 0.00 0.00 3.67
3736 4689 2.369860 TCTGCATACTATTGAGGGCCAG 59.630 50.000 6.18 0.00 0.00 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
57 58 7.410800 CATGTTTTGAGTGCATGTTAAACAT 57.589 32.000 18.86 18.86 40.03 2.71
58 59 6.825284 CATGTTTTGAGTGCATGTTAAACA 57.175 33.333 16.87 16.87 36.21 2.83
65 66 5.970140 TTTGAACATGTTTTGAGTGCATG 57.030 34.783 13.36 0.00 43.84 4.06
66 67 6.594937 ACTTTTTGAACATGTTTTGAGTGCAT 59.405 30.769 13.36 0.00 0.00 3.96
67 68 5.931146 ACTTTTTGAACATGTTTTGAGTGCA 59.069 32.000 13.36 0.93 0.00 4.57
68 69 6.128580 ACACTTTTTGAACATGTTTTGAGTGC 60.129 34.615 24.98 10.88 35.44 4.40
69 70 7.350110 ACACTTTTTGAACATGTTTTGAGTG 57.650 32.000 24.22 24.22 37.41 3.51
70 71 9.651913 AATACACTTTTTGAACATGTTTTGAGT 57.348 25.926 13.36 9.78 0.00 3.41
77 78 9.429359 TGTTTCAAATACACTTTTTGAACATGT 57.571 25.926 10.22 0.00 46.90 3.21
81 82 9.914923 GGAATGTTTCAAATACACTTTTTGAAC 57.085 29.630 10.22 7.42 46.90 3.18
82 83 9.103861 GGGAATGTTTCAAATACACTTTTTGAA 57.896 29.630 7.33 7.33 46.09 2.69
83 84 8.260818 TGGGAATGTTTCAAATACACTTTTTGA 58.739 29.630 0.00 0.00 40.37 2.69
84 85 8.430801 TGGGAATGTTTCAAATACACTTTTTG 57.569 30.769 0.00 0.00 35.79 2.44
85 86 8.888716 GTTGGGAATGTTTCAAATACACTTTTT 58.111 29.630 0.00 0.00 0.00 1.94
86 87 7.223777 CGTTGGGAATGTTTCAAATACACTTTT 59.776 33.333 0.00 0.00 0.00 2.27
87 88 6.699642 CGTTGGGAATGTTTCAAATACACTTT 59.300 34.615 0.00 0.00 0.00 2.66
88 89 6.183360 ACGTTGGGAATGTTTCAAATACACTT 60.183 34.615 0.00 0.00 0.00 3.16
89 90 5.300792 ACGTTGGGAATGTTTCAAATACACT 59.699 36.000 0.00 0.00 0.00 3.55
90 91 5.401079 CACGTTGGGAATGTTTCAAATACAC 59.599 40.000 0.00 0.00 0.00 2.90
91 92 5.067936 ACACGTTGGGAATGTTTCAAATACA 59.932 36.000 0.00 0.00 0.00 2.29
92 93 5.525199 ACACGTTGGGAATGTTTCAAATAC 58.475 37.500 0.00 0.00 0.00 1.89
93 94 5.776173 ACACGTTGGGAATGTTTCAAATA 57.224 34.783 0.00 0.00 0.00 1.40
94 95 4.664150 ACACGTTGGGAATGTTTCAAAT 57.336 36.364 0.00 0.00 0.00 2.32
95 96 5.776173 ATACACGTTGGGAATGTTTCAAA 57.224 34.783 0.00 0.00 0.00 2.69
96 97 6.879276 TTATACACGTTGGGAATGTTTCAA 57.121 33.333 0.00 0.00 0.00 2.69
97 98 6.879276 TTTATACACGTTGGGAATGTTTCA 57.121 33.333 0.00 0.00 0.00 2.69
98 99 7.140048 TGTTTTATACACGTTGGGAATGTTTC 58.860 34.615 0.00 0.00 0.00 2.78
99 100 7.040473 TGTTTTATACACGTTGGGAATGTTT 57.960 32.000 0.00 0.00 0.00 2.83
100 101 6.636562 TGTTTTATACACGTTGGGAATGTT 57.363 33.333 0.00 0.00 0.00 2.71
101 102 6.263617 AGTTGTTTTATACACGTTGGGAATGT 59.736 34.615 0.00 0.00 36.21 2.71
102 103 6.580791 CAGTTGTTTTATACACGTTGGGAATG 59.419 38.462 0.00 0.00 36.21 2.67
103 104 6.263617 ACAGTTGTTTTATACACGTTGGGAAT 59.736 34.615 0.00 0.00 36.21 3.01
104 105 5.589452 ACAGTTGTTTTATACACGTTGGGAA 59.411 36.000 0.00 0.00 36.21 3.97
105 106 5.007823 CACAGTTGTTTTATACACGTTGGGA 59.992 40.000 0.00 0.00 36.21 4.37
106 107 5.209240 CACAGTTGTTTTATACACGTTGGG 58.791 41.667 0.00 0.00 36.21 4.12
107 108 5.812652 ACACAGTTGTTTTATACACGTTGG 58.187 37.500 0.00 0.00 36.21 3.77
108 109 8.823584 TTTACACAGTTGTTTTATACACGTTG 57.176 30.769 0.00 0.00 36.21 4.10
109 110 9.276397 GTTTTACACAGTTGTTTTATACACGTT 57.724 29.630 0.00 0.00 36.21 3.99
110 111 8.449397 TGTTTTACACAGTTGTTTTATACACGT 58.551 29.630 0.00 0.00 36.21 4.49
111 112 8.823584 TGTTTTACACAGTTGTTTTATACACG 57.176 30.769 0.00 0.00 36.21 4.49
126 127 6.378564 TGTTTTCCAATCCTCTGTTTTACACA 59.621 34.615 0.00 0.00 0.00 3.72
127 128 6.695713 GTGTTTTCCAATCCTCTGTTTTACAC 59.304 38.462 0.00 0.00 0.00 2.90
128 129 6.378564 TGTGTTTTCCAATCCTCTGTTTTACA 59.621 34.615 0.00 0.00 0.00 2.41
129 130 6.801575 TGTGTTTTCCAATCCTCTGTTTTAC 58.198 36.000 0.00 0.00 0.00 2.01
130 131 7.595819 ATGTGTTTTCCAATCCTCTGTTTTA 57.404 32.000 0.00 0.00 0.00 1.52
156 157 5.298276 ACCAAACACTGACGTTGACAATATT 59.702 36.000 0.00 0.00 0.00 1.28
171 172 3.297134 ACATTCCTGTGACCAAACACT 57.703 42.857 0.00 0.00 40.87 3.55
245 247 7.064016 GCCTGAACAGTTTTTAAATGTCACAAA 59.936 33.333 1.18 0.00 0.00 2.83
248 250 6.273071 AGCCTGAACAGTTTTTAAATGTCAC 58.727 36.000 1.18 0.00 0.00 3.67
530 556 9.743057 TTCAATTTGTTTTTCGAGTGATACAAT 57.257 25.926 0.00 0.00 0.00 2.71
557 583 8.987890 GCATGTTAAACATTTTCCAAATACACT 58.012 29.630 0.00 0.00 36.53 3.55
622 650 5.151632 ACAGTTTTGTGATACACGTTGAC 57.848 39.130 0.00 0.00 37.14 3.18
710 738 7.803279 TCTAGTTTTCTTCAGGGTTTTTCTC 57.197 36.000 0.00 0.00 0.00 2.87
716 745 6.010850 GGGATTTCTAGTTTTCTTCAGGGTT 58.989 40.000 0.00 0.00 0.00 4.11
749 778 1.802069 GTCTCCTCTGTTCCTTGTGC 58.198 55.000 0.00 0.00 0.00 4.57
752 781 3.601443 ATTCGTCTCCTCTGTTCCTTG 57.399 47.619 0.00 0.00 0.00 3.61
755 784 5.121925 GGTTTTTATTCGTCTCCTCTGTTCC 59.878 44.000 0.00 0.00 0.00 3.62
766 795 5.277202 GGGCTATTCTCGGTTTTTATTCGTC 60.277 44.000 0.00 0.00 0.00 4.20
771 800 4.334481 CGTTGGGCTATTCTCGGTTTTTAT 59.666 41.667 0.00 0.00 0.00 1.40
789 819 2.332654 GCCAGCCCTGTAACGTTGG 61.333 63.158 11.99 4.36 0.00 3.77
790 820 2.332654 GGCCAGCCCTGTAACGTTG 61.333 63.158 11.99 0.00 0.00 4.10
791 821 2.033602 GGCCAGCCCTGTAACGTT 59.966 61.111 5.88 5.88 0.00 3.99
811 841 1.295423 GGTTAGAGCGGGCAGTGAA 59.705 57.895 0.00 0.00 0.00 3.18
819 849 1.461091 TATCCAGCGGGTTAGAGCGG 61.461 60.000 1.81 0.00 38.61 5.52
820 850 0.039074 CTATCCAGCGGGTTAGAGCG 60.039 60.000 13.93 0.00 38.31 5.03
849 879 1.206831 CAGACGAGTTCTCGACGCA 59.793 57.895 25.45 0.00 36.85 5.24
857 887 7.647907 TTTATAAGAACAACCAGACGAGTTC 57.352 36.000 0.00 0.00 40.37 3.01
858 888 8.441312 TTTTTATAAGAACAACCAGACGAGTT 57.559 30.769 0.00 0.00 0.00 3.01
860 890 8.084590 ACTTTTTATAAGAACAACCAGACGAG 57.915 34.615 0.00 0.00 0.00 4.18
881 911 8.635328 CCCTATGGTAACTTGTGTTTTTACTTT 58.365 33.333 0.00 0.00 37.59 2.66
883 913 7.519927 TCCCTATGGTAACTTGTGTTTTTACT 58.480 34.615 0.00 0.00 37.59 2.24
884 914 7.748691 TCCCTATGGTAACTTGTGTTTTTAC 57.251 36.000 0.00 0.00 37.59 2.01
885 915 7.041235 CGTTCCCTATGGTAACTTGTGTTTTTA 60.041 37.037 0.00 0.00 37.59 1.52
893 1067 5.296035 GGATTTCGTTCCCTATGGTAACTTG 59.704 44.000 0.00 0.00 37.61 3.16
1023 1197 4.567385 GCCTCGCTCTCGGCTGAG 62.567 72.222 16.98 16.98 42.98 3.35
1035 1209 4.504916 AGCTAGCAGTGCGCCTCG 62.505 66.667 18.83 0.00 44.04 4.63
1036 1210 2.889503 CAGCTAGCAGTGCGCCTC 60.890 66.667 18.83 0.00 44.04 4.70
1067 1241 0.734889 GGCCATGACCAATCGACAAG 59.265 55.000 0.00 0.00 0.00 3.16
1079 1253 1.219124 GAGAAGAGCACGGCCATGA 59.781 57.895 1.12 0.00 0.00 3.07
1131 1306 7.067008 TCGGGAAAGATGTTTGGAGATTAAATC 59.933 37.037 0.00 0.00 0.00 2.17
1150 1325 2.311463 TCAAGCCAACAAATCGGGAAA 58.689 42.857 0.00 0.00 0.00 3.13
1151 1326 1.988293 TCAAGCCAACAAATCGGGAA 58.012 45.000 0.00 0.00 0.00 3.97
1152 1327 2.091541 GATCAAGCCAACAAATCGGGA 58.908 47.619 0.00 0.00 0.00 5.14
1153 1328 1.818060 TGATCAAGCCAACAAATCGGG 59.182 47.619 0.00 0.00 0.00 5.14
1154 1329 3.057315 ACTTGATCAAGCCAACAAATCGG 60.057 43.478 30.95 7.98 41.99 4.18
1155 1330 4.164822 ACTTGATCAAGCCAACAAATCG 57.835 40.909 30.95 8.18 41.99 3.34
1156 1331 7.599998 ACAAATACTTGATCAAGCCAACAAATC 59.400 33.333 30.95 0.00 41.99 2.17
1157 1332 7.444299 ACAAATACTTGATCAAGCCAACAAAT 58.556 30.769 30.95 14.30 41.99 2.32
1158 1333 6.815089 ACAAATACTTGATCAAGCCAACAAA 58.185 32.000 30.95 11.37 41.99 2.83
1159 1334 6.403866 ACAAATACTTGATCAAGCCAACAA 57.596 33.333 30.95 12.92 41.99 2.83
1160 1335 6.215121 CAACAAATACTTGATCAAGCCAACA 58.785 36.000 30.95 14.20 41.99 3.33
1161 1336 5.634859 CCAACAAATACTTGATCAAGCCAAC 59.365 40.000 30.95 0.00 41.99 3.77
1162 1337 5.782047 CCAACAAATACTTGATCAAGCCAA 58.218 37.500 30.95 18.97 41.99 4.52
1163 1338 4.321899 GCCAACAAATACTTGATCAAGCCA 60.322 41.667 30.95 20.97 41.99 4.75
1164 1339 4.176271 GCCAACAAATACTTGATCAAGCC 58.824 43.478 30.95 6.86 41.99 4.35
1165 1340 4.176271 GGCCAACAAATACTTGATCAAGC 58.824 43.478 30.95 16.01 41.99 4.01
1166 1341 5.389859 TGGCCAACAAATACTTGATCAAG 57.610 39.130 29.74 29.74 43.79 3.02
1167 1342 5.337410 CCATGGCCAACAAATACTTGATCAA 60.337 40.000 10.96 8.12 36.33 2.57
1168 1343 4.160065 CCATGGCCAACAAATACTTGATCA 59.840 41.667 10.96 0.00 36.33 2.92
1169 1344 4.685924 CCATGGCCAACAAATACTTGATC 58.314 43.478 10.96 0.00 36.33 2.92
1170 1345 3.118665 GCCATGGCCAACAAATACTTGAT 60.119 43.478 27.24 0.00 34.18 2.57
1171 1346 2.233431 GCCATGGCCAACAAATACTTGA 59.767 45.455 27.24 0.00 34.18 3.02
1172 1347 2.620242 GCCATGGCCAACAAATACTTG 58.380 47.619 27.24 0.00 35.34 3.16
1185 1360 4.195334 ATGGACTCCGGCCATGGC 62.195 66.667 29.47 29.47 44.21 4.40
1186 1361 2.111878 GATGGACTCCGGCCATGG 59.888 66.667 15.92 7.63 45.81 3.66
1187 1362 2.280389 CGATGGACTCCGGCCATG 60.280 66.667 15.92 5.90 45.81 3.66
1189 1364 2.561467 TACTCGATGGACTCCGGCCA 62.561 60.000 2.24 0.00 40.24 5.36
1316 1494 1.790481 GCAATCGCGTAAAGCTTGACC 60.790 52.381 8.45 0.76 45.59 4.02
1365 1543 5.620879 GCAAATAAAGGTTCTCTGCTTCCAG 60.621 44.000 0.00 0.00 40.54 3.86
1443 1624 4.338012 TGAATGTGAGCAACAATGAGGAT 58.662 39.130 0.00 0.00 43.61 3.24
1444 1625 3.753815 TGAATGTGAGCAACAATGAGGA 58.246 40.909 0.00 0.00 43.61 3.71
1445 1626 4.713824 ATGAATGTGAGCAACAATGAGG 57.286 40.909 0.00 0.00 43.61 3.86
1480 1680 2.254737 CTCTCTCTGCCAGGGCCAAG 62.255 65.000 6.18 5.33 41.09 3.61
1481 1681 2.203983 TCTCTCTGCCAGGGCCAA 60.204 61.111 6.18 0.00 41.09 4.52
1482 1682 2.542409 ATCTCTCTCTGCCAGGGCCA 62.542 60.000 6.18 0.00 41.09 5.36
1483 1683 1.344191 AATCTCTCTCTGCCAGGGCC 61.344 60.000 8.02 0.00 41.09 5.80
1484 1684 0.179051 CAATCTCTCTCTGCCAGGGC 60.179 60.000 2.62 2.62 42.35 5.19
1485 1685 1.413445 CTCAATCTCTCTCTGCCAGGG 59.587 57.143 0.00 0.00 0.00 4.45
1486 1686 1.202557 GCTCAATCTCTCTCTGCCAGG 60.203 57.143 0.00 0.00 0.00 4.45
1487 1687 1.758280 AGCTCAATCTCTCTCTGCCAG 59.242 52.381 0.00 0.00 0.00 4.85
1541 1741 5.072040 ACAATCGGGAAAGCCTATTTTTG 57.928 39.130 0.00 0.00 0.00 2.44
1580 1780 4.548991 GCAGTTGCAAGAAGGATAGATG 57.451 45.455 0.00 0.00 41.59 2.90
1858 2334 0.734253 CTCAGCTTCTCGACGTTGGG 60.734 60.000 2.20 0.00 0.00 4.12
2008 2487 3.818387 TCACGTTTTCTAGCGTCTACTG 58.182 45.455 0.00 0.00 39.48 2.74
2119 2603 4.094830 AGTTGTTAACTTCCCGTTCCAT 57.905 40.909 7.22 0.00 39.04 3.41
2261 2750 1.951130 CATTGCGGTCGATCCTCGG 60.951 63.158 0.00 0.00 40.88 4.63
2262 2751 2.589492 GCATTGCGGTCGATCCTCG 61.589 63.158 0.00 0.00 42.10 4.63
2295 2784 3.009723 GCGATCCACTTTCCAATTCAGA 58.990 45.455 0.00 0.00 0.00 3.27
2296 2785 3.012518 AGCGATCCACTTTCCAATTCAG 58.987 45.455 0.00 0.00 0.00 3.02
2297 2786 3.009723 GAGCGATCCACTTTCCAATTCA 58.990 45.455 0.00 0.00 0.00 2.57
2298 2787 3.009723 TGAGCGATCCACTTTCCAATTC 58.990 45.455 0.00 0.00 0.00 2.17
2299 2788 3.071874 TGAGCGATCCACTTTCCAATT 57.928 42.857 0.00 0.00 0.00 2.32
2300 2789 2.787473 TGAGCGATCCACTTTCCAAT 57.213 45.000 0.00 0.00 0.00 3.16
2306 2795 5.059833 GGATTTATCTTGAGCGATCCACTT 58.940 41.667 0.00 0.00 34.57 3.16
2318 2807 5.698545 GCCACAGCTAGTAGGATTTATCTTG 59.301 44.000 0.00 0.00 35.50 3.02
2353 2844 4.221342 CGAATGACACAAACAACATGGAG 58.779 43.478 0.00 0.00 0.00 3.86
2374 2865 0.868406 GTGTGTTCTCCTTGCTTCCG 59.132 55.000 0.00 0.00 0.00 4.30
2393 2884 7.288317 CAAGAGTACTTGTTCAGCTAGAATG 57.712 40.000 0.00 0.00 45.73 2.67
2412 2903 4.521146 AGGTGAGATGTTATTGCCAAGAG 58.479 43.478 0.00 0.00 0.00 2.85
2414 2905 4.521146 AGAGGTGAGATGTTATTGCCAAG 58.479 43.478 0.00 0.00 0.00 3.61
2465 3228 2.278857 CATCTCCGCGTCTTCCCG 60.279 66.667 4.92 0.00 0.00 5.14
2473 3236 1.066303 AGCTTTACTCTCATCTCCGCG 59.934 52.381 0.00 0.00 0.00 6.46
2486 3249 4.152580 AGCTTTAAGTGCTTCGAGCTTTAC 59.847 41.667 12.95 0.00 42.97 2.01
2497 3260 2.746362 CAGCTGCTTAGCTTTAAGTGCT 59.254 45.455 0.00 10.82 43.52 4.40
2575 3382 6.187125 AGATCAAACATGACTTCGAAATGG 57.813 37.500 11.84 0.00 0.00 3.16
2610 3417 5.766670 AGCATCATGTTTATGTATGGGAGTG 59.233 40.000 0.00 0.00 35.73 3.51
2623 3430 8.752005 ATACCATAACAAGTAGCATCATGTTT 57.248 30.769 6.97 0.00 37.25 2.83
2662 3469 7.801893 TCCTTCCCTTGAGTAATACTAACAA 57.198 36.000 0.00 0.00 0.00 2.83
2685 3540 3.423571 CAGAAGTCGCTTGCAATGAATC 58.576 45.455 0.00 4.01 0.00 2.52
2757 3658 5.050227 CACAAACTGAAGAAAGAGCTCAGAG 60.050 44.000 17.77 3.08 33.15 3.35
2762 3663 4.265073 ACACACAAACTGAAGAAAGAGCT 58.735 39.130 0.00 0.00 0.00 4.09
2788 3689 1.920051 CAAGGATGATCGCACGACG 59.080 57.895 0.00 0.00 45.62 5.12
2869 3770 3.560105 GAGCAAAAGATAAGAGGGGCAT 58.440 45.455 0.00 0.00 0.00 4.40
2885 3786 2.951642 CTGAACAAACTCAAGGGAGCAA 59.048 45.455 0.00 0.00 45.42 3.91
2886 3787 2.575532 CTGAACAAACTCAAGGGAGCA 58.424 47.619 0.00 0.00 45.42 4.26
2933 3834 3.056607 CCATCTCGGGAAAACAGCAAAAT 60.057 43.478 0.00 0.00 0.00 1.82
2946 3847 0.034059 GTCACATAGGCCATCTCGGG 59.966 60.000 5.01 0.00 34.06 5.14
2960 3861 7.515528 CGTTGTTCTAAAATACTTGTCGTCACA 60.516 37.037 0.00 0.00 0.00 3.58
2962 3863 6.696583 TCGTTGTTCTAAAATACTTGTCGTCA 59.303 34.615 0.00 0.00 0.00 4.35
2963 3864 7.097342 TCGTTGTTCTAAAATACTTGTCGTC 57.903 36.000 0.00 0.00 0.00 4.20
3022 3923 1.405463 TCAGTAGGCACTATGTGAGCG 59.595 52.381 1.52 0.00 45.60 5.03
3024 3925 4.991153 TCTTCAGTAGGCACTATGTGAG 57.009 45.455 1.52 0.00 45.60 3.51
3041 3942 0.665972 GCAGCTCCGATCCGATCTTC 60.666 60.000 6.81 0.00 0.00 2.87
3056 3957 1.942657 TCAATCTTAATGCTCCGCAGC 59.057 47.619 0.00 0.00 43.65 5.25
3060 3961 3.865745 ACTTCGTCAATCTTAATGCTCCG 59.134 43.478 0.00 0.00 0.00 4.63
3085 3993 0.802222 CGGTAGTGAGACGCATGTGG 60.802 60.000 11.65 0.00 0.00 4.17
3140 4048 4.154015 TCACGCTTTGGTGTCTCATTAATG 59.846 41.667 9.29 9.29 39.00 1.90
3162 4070 2.633488 AGCGATTAGGCCTCAAGTTTC 58.367 47.619 9.68 0.00 0.00 2.78
3173 4081 4.703897 TGAATGGTTAGGAAGCGATTAGG 58.296 43.478 0.00 0.00 0.00 2.69
3174 4082 4.752101 CCTGAATGGTTAGGAAGCGATTAG 59.248 45.833 0.00 0.00 36.11 1.73
3176 4084 3.545703 CCTGAATGGTTAGGAAGCGATT 58.454 45.455 0.00 0.00 36.11 3.34
3259 4167 8.555361 GCTGCTCCTTTTTCATATTTAGAGTAG 58.445 37.037 0.00 0.00 36.36 2.57
3269 4177 2.819608 GTGTGGCTGCTCCTTTTTCATA 59.180 45.455 0.00 0.00 35.26 2.15
3274 4182 0.746659 GTTGTGTGGCTGCTCCTTTT 59.253 50.000 0.00 0.00 35.26 2.27
3275 4183 0.395586 TGTTGTGTGGCTGCTCCTTT 60.396 50.000 0.00 0.00 35.26 3.11
3282 4190 3.773860 TTTACAAGTGTTGTGTGGCTG 57.226 42.857 2.50 0.00 45.03 4.85
3337 4246 7.264221 AGCTGTGACTATTACTTCAGATTCTG 58.736 38.462 7.38 7.38 0.00 3.02
3413 4366 1.992667 GCGCTTGGATTTAACCTTTGC 59.007 47.619 0.00 0.00 0.00 3.68
3474 4427 7.629866 GCGGTTATTATTTCTAGGCCTTTTGTT 60.630 37.037 12.58 0.00 0.00 2.83
3505 4458 2.113774 TTGTGCCCTGGAGCTGTG 59.886 61.111 0.00 0.00 0.00 3.66
3536 4489 6.715344 TGTGATAATTGTTGTAACTCCGAC 57.285 37.500 0.00 0.00 0.00 4.79
3537 4490 6.706716 TGTTGTGATAATTGTTGTAACTCCGA 59.293 34.615 0.00 0.00 0.00 4.55
3539 4492 8.094798 TCTGTTGTGATAATTGTTGTAACTCC 57.905 34.615 0.00 0.00 0.00 3.85
3541 4494 9.730420 GTTTCTGTTGTGATAATTGTTGTAACT 57.270 29.630 0.00 0.00 0.00 2.24
3545 4498 8.349983 GGTAGTTTCTGTTGTGATAATTGTTGT 58.650 33.333 0.00 0.00 0.00 3.32
3555 4508 3.133901 TCTGCTGGTAGTTTCTGTTGTGA 59.866 43.478 0.00 0.00 0.00 3.58
3678 4631 5.762825 TGAGCGTACTATAAATCCGAAGT 57.237 39.130 0.00 0.00 0.00 3.01
3681 4634 5.619309 GCAGATGAGCGTACTATAAATCCGA 60.619 44.000 0.00 0.00 0.00 4.55
3696 4649 0.602562 AGGCGATCTAGCAGATGAGC 59.397 55.000 3.76 8.31 34.53 4.26


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

AutoCloner maintained by Alex Coulton.