Multiple sequence alignment - TraesCS2B01G413600

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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 TraesCS2B01G413600 chr2B 100.000 3930 0 0 1 3930 589882346 589878417 0.000000e+00 7258.0
1 TraesCS2B01G413600 chr2D 95.431 2517 85 18 1293 3796 502522538 502520039 0.000000e+00 3984.0
2 TraesCS2B01G413600 chr2D 93.182 220 8 2 792 1004 502523280 502523061 2.280000e-82 316.0
3 TraesCS2B01G413600 chr2D 86.131 137 19 0 3794 3930 487929650 487929514 8.800000e-32 148.0
4 TraesCS2B01G413600 chr2D 97.015 67 2 0 69 135 502523363 502523297 3.210000e-21 113.0
5 TraesCS2B01G413600 chr2A 95.477 2432 85 10 1294 3707 647928957 647926533 0.000000e+00 3858.0
6 TraesCS2B01G413600 chr2A 98.246 627 10 1 164 790 424165342 424165967 0.000000e+00 1096.0
7 TraesCS2B01G413600 chr2A 93.353 331 8 9 792 1108 647929604 647929274 9.880000e-131 477.0
8 TraesCS2B01G413600 chr2A 91.667 84 5 1 69 152 647929691 647929610 8.920000e-22 115.0
9 TraesCS2B01G413600 chr1A 98.560 625 9 0 164 788 30995792 30996416 0.000000e+00 1105.0
10 TraesCS2B01G413600 chr1A 98.246 627 11 0 163 789 513163358 513163984 0.000000e+00 1098.0
11 TraesCS2B01G413600 chr7A 98.251 629 11 0 163 791 255900091 255900719 0.000000e+00 1101.0
12 TraesCS2B01G413600 chr7A 98.400 625 10 0 164 788 99846334 99846958 0.000000e+00 1099.0
13 TraesCS2B01G413600 chr7A 98.400 625 10 0 164 788 285790818 285791442 0.000000e+00 1099.0
14 TraesCS2B01G413600 chr6B 98.400 625 10 0 164 788 676064093 676064717 0.000000e+00 1099.0
15 TraesCS2B01G413600 chr6B 84.328 134 19 2 3796 3928 473637373 473637505 3.190000e-26 130.0
16 TraesCS2B01G413600 chr4A 98.400 625 10 0 164 788 548654751 548655375 0.000000e+00 1099.0
17 TraesCS2B01G413600 chr4A 83.212 137 23 0 3794 3930 331129682 331129546 4.120000e-25 126.0
18 TraesCS2B01G413600 chr4A 79.259 135 28 0 3796 3930 151676474 151676608 1.160000e-15 95.3
19 TraesCS2B01G413600 chr3B 98.400 625 10 0 165 789 4710897 4710273 0.000000e+00 1099.0
20 TraesCS2B01G413600 chr1B 89.051 137 15 0 3794 3930 300960200 300960064 1.880000e-38 171.0
21 TraesCS2B01G413600 chr3D 85.106 141 21 0 3790 3930 511423697 511423557 1.140000e-30 145.0
22 TraesCS2B01G413600 chr3D 82.963 135 23 0 3796 3930 466797376 466797242 5.330000e-24 122.0
23 TraesCS2B01G413600 chr5B 85.000 140 19 2 3792 3930 455756333 455756471 1.470000e-29 141.0
24 TraesCS2B01G413600 chr3A 82.576 132 23 0 3792 3923 748835289 748835158 2.480000e-22 117.0


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 TraesCS2B01G413600 chr2B 589878417 589882346 3929 True 7258.000000 7258 100.000000 1 3930 1 chr2B.!!$R1 3929
1 TraesCS2B01G413600 chr2D 502520039 502523363 3324 True 1471.000000 3984 95.209333 69 3796 3 chr2D.!!$R2 3727
2 TraesCS2B01G413600 chr2A 647926533 647929691 3158 True 1483.333333 3858 93.499000 69 3707 3 chr2A.!!$R1 3638
3 TraesCS2B01G413600 chr2A 424165342 424165967 625 False 1096.000000 1096 98.246000 164 790 1 chr2A.!!$F1 626
4 TraesCS2B01G413600 chr1A 30995792 30996416 624 False 1105.000000 1105 98.560000 164 788 1 chr1A.!!$F1 624
5 TraesCS2B01G413600 chr1A 513163358 513163984 626 False 1098.000000 1098 98.246000 163 789 1 chr1A.!!$F2 626
6 TraesCS2B01G413600 chr7A 255900091 255900719 628 False 1101.000000 1101 98.251000 163 791 1 chr7A.!!$F2 628
7 TraesCS2B01G413600 chr7A 99846334 99846958 624 False 1099.000000 1099 98.400000 164 788 1 chr7A.!!$F1 624
8 TraesCS2B01G413600 chr7A 285790818 285791442 624 False 1099.000000 1099 98.400000 164 788 1 chr7A.!!$F3 624
9 TraesCS2B01G413600 chr6B 676064093 676064717 624 False 1099.000000 1099 98.400000 164 788 1 chr6B.!!$F2 624
10 TraesCS2B01G413600 chr4A 548654751 548655375 624 False 1099.000000 1099 98.400000 164 788 1 chr4A.!!$F2 624
11 TraesCS2B01G413600 chr3B 4710273 4710897 624 True 1099.000000 1099 98.400000 165 789 1 chr3B.!!$R1 624

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
781 786 0.095762 CCGAATAAACCGAACGCACC 59.904 55.0 0.0 0.0 0.0 5.01 F
1285 1310 0.032416 GTCCTACCCCTCCAGCTACA 60.032 60.0 0.0 0.0 0.0 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1636 1901 0.108804 CTGTGGGCGACGAGTATGTT 60.109 55.0 0.0 0.0 0.0 2.71 R
2957 3228 0.038166 TCCAAACATCAGCCACCCTC 59.962 55.0 0.0 0.0 0.0 4.30 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 4.424566 GCATGGTGGCGGCACAAG 62.425 66.667 38.28 27.83 0.00 3.16
24 25 2.672651 CATGGTGGCGGCACAAGA 60.673 61.111 38.28 23.95 0.00 3.02
25 26 2.115052 ATGGTGGCGGCACAAGAA 59.885 55.556 38.28 22.94 0.00 2.52
26 27 2.268076 ATGGTGGCGGCACAAGAAC 61.268 57.895 38.28 23.32 0.00 3.01
27 28 3.670377 GGTGGCGGCACAAGAACC 61.670 66.667 38.28 20.16 0.00 3.62
28 29 2.594592 GTGGCGGCACAAGAACCT 60.595 61.111 34.40 0.00 0.00 3.50
29 30 2.281484 TGGCGGCACAAGAACCTC 60.281 61.111 7.97 0.00 0.00 3.85
30 31 2.281484 GGCGGCACAAGAACCTCA 60.281 61.111 3.07 0.00 0.00 3.86
31 32 2.328099 GGCGGCACAAGAACCTCAG 61.328 63.158 3.07 0.00 0.00 3.35
32 33 1.598130 GCGGCACAAGAACCTCAGT 60.598 57.895 0.00 0.00 0.00 3.41
33 34 1.569479 GCGGCACAAGAACCTCAGTC 61.569 60.000 0.00 0.00 0.00 3.51
34 35 0.249868 CGGCACAAGAACCTCAGTCA 60.250 55.000 0.00 0.00 0.00 3.41
35 36 1.609061 CGGCACAAGAACCTCAGTCAT 60.609 52.381 0.00 0.00 0.00 3.06
36 37 2.079925 GGCACAAGAACCTCAGTCATC 58.920 52.381 0.00 0.00 0.00 2.92
37 38 1.728971 GCACAAGAACCTCAGTCATCG 59.271 52.381 0.00 0.00 0.00 3.84
38 39 2.341257 CACAAGAACCTCAGTCATCGG 58.659 52.381 0.00 0.00 0.00 4.18
39 40 1.338200 ACAAGAACCTCAGTCATCGGC 60.338 52.381 0.00 0.00 0.00 5.54
40 41 1.066573 CAAGAACCTCAGTCATCGGCT 60.067 52.381 0.00 0.00 0.00 5.52
41 42 1.270907 AGAACCTCAGTCATCGGCTT 58.729 50.000 0.00 0.00 0.00 4.35
42 43 1.625818 AGAACCTCAGTCATCGGCTTT 59.374 47.619 0.00 0.00 0.00 3.51
43 44 2.003301 GAACCTCAGTCATCGGCTTTC 58.997 52.381 0.00 0.00 0.00 2.62
44 45 0.250513 ACCTCAGTCATCGGCTTTCC 59.749 55.000 0.00 0.00 0.00 3.13
45 46 0.250234 CCTCAGTCATCGGCTTTCCA 59.750 55.000 0.00 0.00 0.00 3.53
46 47 1.134280 CCTCAGTCATCGGCTTTCCAT 60.134 52.381 0.00 0.00 0.00 3.41
47 48 2.208431 CTCAGTCATCGGCTTTCCATC 58.792 52.381 0.00 0.00 0.00 3.51
48 49 1.134401 TCAGTCATCGGCTTTCCATCC 60.134 52.381 0.00 0.00 0.00 3.51
49 50 0.911769 AGTCATCGGCTTTCCATCCA 59.088 50.000 0.00 0.00 0.00 3.41
50 51 1.492176 AGTCATCGGCTTTCCATCCAT 59.508 47.619 0.00 0.00 0.00 3.41
51 52 1.605710 GTCATCGGCTTTCCATCCATG 59.394 52.381 0.00 0.00 0.00 3.66
52 53 0.313043 CATCGGCTTTCCATCCATGC 59.687 55.000 0.00 0.00 0.00 4.06
53 54 0.106569 ATCGGCTTTCCATCCATGCA 60.107 50.000 0.00 0.00 0.00 3.96
54 55 0.106569 TCGGCTTTCCATCCATGCAT 60.107 50.000 0.00 0.00 0.00 3.96
55 56 0.313043 CGGCTTTCCATCCATGCATC 59.687 55.000 0.00 0.00 0.00 3.91
56 57 0.677842 GGCTTTCCATCCATGCATCC 59.322 55.000 0.00 0.00 0.00 3.51
57 58 0.677842 GCTTTCCATCCATGCATCCC 59.322 55.000 0.00 0.00 0.00 3.85
58 59 1.756690 GCTTTCCATCCATGCATCCCT 60.757 52.381 0.00 0.00 0.00 4.20
59 60 1.961394 CTTTCCATCCATGCATCCCTG 59.039 52.381 0.00 0.00 0.00 4.45
60 61 0.186630 TTCCATCCATGCATCCCTGG 59.813 55.000 0.00 3.81 0.00 4.45
61 62 1.228769 CCATCCATGCATCCCTGGG 60.229 63.158 6.33 6.33 33.13 4.45
62 63 1.906824 CATCCATGCATCCCTGGGC 60.907 63.158 8.22 0.00 33.13 5.36
63 64 3.502621 ATCCATGCATCCCTGGGCG 62.503 63.158 8.22 2.36 33.13 6.13
64 65 4.511246 CCATGCATCCCTGGGCGT 62.511 66.667 8.22 0.00 0.00 5.68
65 66 2.903855 CATGCATCCCTGGGCGTC 60.904 66.667 8.22 0.00 0.00 5.19
66 67 4.552365 ATGCATCCCTGGGCGTCG 62.552 66.667 8.22 0.00 0.00 5.12
81 82 2.282958 TCGTGAGAAGAGGCCGGT 60.283 61.111 1.90 0.00 37.03 5.28
135 140 3.121030 ACGCCAGCATTCACTCGC 61.121 61.111 0.00 0.00 0.00 5.03
136 141 2.816958 CGCCAGCATTCACTCGCT 60.817 61.111 0.00 0.00 39.66 4.93
137 142 2.806856 CGCCAGCATTCACTCGCTC 61.807 63.158 0.00 0.00 35.96 5.03
138 143 2.806856 GCCAGCATTCACTCGCTCG 61.807 63.158 0.00 0.00 35.96 5.03
139 144 2.699809 CAGCATTCACTCGCTCGC 59.300 61.111 0.00 0.00 35.96 5.03
140 145 2.882777 AGCATTCACTCGCTCGCG 60.883 61.111 0.00 0.00 41.35 5.87
152 157 4.717629 CTCGCGTTGCTCCGTCCA 62.718 66.667 5.77 0.00 0.00 4.02
157 162 2.310233 CGTTGCTCCGTCCACACTG 61.310 63.158 0.00 0.00 0.00 3.66
158 163 1.961277 GTTGCTCCGTCCACACTGG 60.961 63.158 0.00 0.00 39.43 4.00
159 164 3.825160 TTGCTCCGTCCACACTGGC 62.825 63.158 0.00 0.00 37.47 4.85
161 166 4.742201 CTCCGTCCACACTGGCCG 62.742 72.222 0.00 0.00 38.83 6.13
264 269 5.189342 TGGTTTCTGGTTTCGGTATGGTATA 59.811 40.000 0.00 0.00 0.00 1.47
695 700 7.710044 ACCAAAACCGAACCGTATTTTAATTTT 59.290 29.630 0.00 0.00 0.00 1.82
781 786 0.095762 CCGAATAAACCGAACGCACC 59.904 55.000 0.00 0.00 0.00 5.01
972 988 1.969589 CACCCCGGACCCGAAAAAG 60.970 63.158 10.42 0.00 42.83 2.27
1008 1027 3.480133 ACTCCACCTATGGCCGCC 61.480 66.667 1.04 1.04 46.80 6.13
1108 1133 1.305718 GACCTCTCCTCCTGGTGCT 60.306 63.158 0.00 0.00 33.74 4.40
1109 1134 1.611851 ACCTCTCCTCCTGGTGCTG 60.612 63.158 0.00 0.00 32.16 4.41
1110 1135 2.583520 CTCTCCTCCTGGTGCTGC 59.416 66.667 0.00 0.00 34.23 5.25
1111 1136 3.368190 CTCTCCTCCTGGTGCTGCG 62.368 68.421 0.00 0.00 34.23 5.18
1141 1166 4.354943 CCCCCTCCACCTCCCACT 62.355 72.222 0.00 0.00 0.00 4.00
1142 1167 2.204151 CCCCTCCACCTCCCACTT 60.204 66.667 0.00 0.00 0.00 3.16
1143 1168 2.301738 CCCCTCCACCTCCCACTTC 61.302 68.421 0.00 0.00 0.00 3.01
1144 1169 2.301738 CCCTCCACCTCCCACTTCC 61.302 68.421 0.00 0.00 0.00 3.46
1145 1170 1.538876 CCTCCACCTCCCACTTCCA 60.539 63.158 0.00 0.00 0.00 3.53
1146 1171 1.679898 CTCCACCTCCCACTTCCAC 59.320 63.158 0.00 0.00 0.00 4.02
1147 1172 0.838122 CTCCACCTCCCACTTCCACT 60.838 60.000 0.00 0.00 0.00 4.00
1148 1173 0.836400 TCCACCTCCCACTTCCACTC 60.836 60.000 0.00 0.00 0.00 3.51
1149 1174 1.679898 CACCTCCCACTTCCACTCC 59.320 63.158 0.00 0.00 0.00 3.85
1150 1175 1.539124 ACCTCCCACTTCCACTCCC 60.539 63.158 0.00 0.00 0.00 4.30
1151 1176 2.301738 CCTCCCACTTCCACTCCCC 61.302 68.421 0.00 0.00 0.00 4.81
1152 1177 2.204090 TCCCACTTCCACTCCCCC 60.204 66.667 0.00 0.00 0.00 5.40
1153 1178 3.717294 CCCACTTCCACTCCCCCG 61.717 72.222 0.00 0.00 0.00 5.73
1154 1179 4.410400 CCACTTCCACTCCCCCGC 62.410 72.222 0.00 0.00 0.00 6.13
1155 1180 4.410400 CACTTCCACTCCCCCGCC 62.410 72.222 0.00 0.00 0.00 6.13
1235 1260 4.554363 CGCCTCGTCCTACGCCAG 62.554 72.222 0.00 0.00 42.21 4.85
1236 1261 4.874977 GCCTCGTCCTACGCCAGC 62.875 72.222 0.00 0.00 42.21 4.85
1237 1262 4.208686 CCTCGTCCTACGCCAGCC 62.209 72.222 0.00 0.00 42.21 4.85
1238 1263 4.208686 CTCGTCCTACGCCAGCCC 62.209 72.222 0.00 0.00 42.21 5.19
1241 1266 3.712907 GTCCTACGCCAGCCCCAA 61.713 66.667 0.00 0.00 0.00 4.12
1242 1267 3.712907 TCCTACGCCAGCCCCAAC 61.713 66.667 0.00 0.00 0.00 3.77
1243 1268 4.796495 CCTACGCCAGCCCCAACC 62.796 72.222 0.00 0.00 0.00 3.77
1244 1269 4.796495 CTACGCCAGCCCCAACCC 62.796 72.222 0.00 0.00 0.00 4.11
1254 1279 3.793888 CCCAACCCGCCCTCCTAC 61.794 72.222 0.00 0.00 0.00 3.18
1255 1280 3.006728 CCAACCCGCCCTCCTACA 61.007 66.667 0.00 0.00 0.00 2.74
1256 1281 2.267961 CAACCCGCCCTCCTACAC 59.732 66.667 0.00 0.00 0.00 2.90
1257 1282 3.387947 AACCCGCCCTCCTACACG 61.388 66.667 0.00 0.00 0.00 4.49
1260 1285 4.514577 CCGCCCTCCTACACGCAG 62.515 72.222 0.00 0.00 0.00 5.18
1261 1286 3.449227 CGCCCTCCTACACGCAGA 61.449 66.667 0.00 0.00 0.00 4.26
1262 1287 2.184579 GCCCTCCTACACGCAGAC 59.815 66.667 0.00 0.00 0.00 3.51
1264 1289 2.202623 CCTCCTACACGCAGACGC 60.203 66.667 0.00 0.00 45.53 5.19
1265 1290 2.566529 CTCCTACACGCAGACGCA 59.433 61.111 0.00 0.00 45.53 5.24
1266 1291 1.515088 CTCCTACACGCAGACGCAG 60.515 63.158 0.00 0.00 45.53 5.18
1278 1303 2.363925 ACGCAGTCCTACCCCTCC 60.364 66.667 0.00 0.00 29.74 4.30
1279 1304 2.363795 CGCAGTCCTACCCCTCCA 60.364 66.667 0.00 0.00 0.00 3.86
1280 1305 2.427245 CGCAGTCCTACCCCTCCAG 61.427 68.421 0.00 0.00 0.00 3.86
1281 1306 2.736826 GCAGTCCTACCCCTCCAGC 61.737 68.421 0.00 0.00 0.00 4.85
1282 1307 1.002274 CAGTCCTACCCCTCCAGCT 59.998 63.158 0.00 0.00 0.00 4.24
1283 1308 0.261991 CAGTCCTACCCCTCCAGCTA 59.738 60.000 0.00 0.00 0.00 3.32
1284 1309 0.262285 AGTCCTACCCCTCCAGCTAC 59.738 60.000 0.00 0.00 0.00 3.58
1285 1310 0.032416 GTCCTACCCCTCCAGCTACA 60.032 60.000 0.00 0.00 0.00 2.74
1286 1311 0.032416 TCCTACCCCTCCAGCTACAC 60.032 60.000 0.00 0.00 0.00 2.90
1287 1312 1.049289 CCTACCCCTCCAGCTACACC 61.049 65.000 0.00 0.00 0.00 4.16
1288 1313 0.325296 CTACCCCTCCAGCTACACCA 60.325 60.000 0.00 0.00 0.00 4.17
1289 1314 0.117541 TACCCCTCCAGCTACACCAA 59.882 55.000 0.00 0.00 0.00 3.67
1290 1315 1.201429 ACCCCTCCAGCTACACCAAG 61.201 60.000 0.00 0.00 0.00 3.61
1291 1316 1.201429 CCCCTCCAGCTACACCAAGT 61.201 60.000 0.00 0.00 0.00 3.16
1470 1735 3.087253 CATCCGCACCACCCCCTA 61.087 66.667 0.00 0.00 0.00 3.53
1623 1888 3.394836 GGCCTCTCCCTCACGCTT 61.395 66.667 0.00 0.00 0.00 4.68
1785 2050 0.605050 TGCGCCTCATGTACTGCAAA 60.605 50.000 4.18 0.00 0.00 3.68
1819 2084 1.126488 GCTCATGAGGGAGGATGTGA 58.874 55.000 23.89 0.00 35.41 3.58
1846 2117 3.279434 GTCCTCGGCATTTTGAAGGTAT 58.721 45.455 0.00 0.00 0.00 2.73
1868 2139 1.813178 GCCCCTTTCTTCTTTTCCTCG 59.187 52.381 0.00 0.00 0.00 4.63
2044 2315 2.170738 GGCATTGTTGACGCAGCTA 58.829 52.632 0.00 0.00 0.00 3.32
2155 2426 1.742510 AAATTGCAATGGCGGCAGC 60.743 52.632 19.29 17.00 45.35 5.25
2179 2450 1.375326 GGGTGGTGGTGAAGAGGTC 59.625 63.158 0.00 0.00 0.00 3.85
2402 2673 1.409427 GAGGTGACCAATCGGAGGTAG 59.591 57.143 3.63 0.00 40.09 3.18
2410 2681 0.315568 AATCGGAGGTAGCGCAGATC 59.684 55.000 11.47 1.26 0.00 2.75
2470 2741 0.890542 TTGTTGAGCGCCAGATTGCT 60.891 50.000 2.29 0.00 45.90 3.91
2566 2837 0.109086 ATGAAGTGAGCCGAGTGACG 60.109 55.000 0.00 0.00 42.18 4.35
2578 2849 0.668535 GAGTGACGGCAAGGCTTTTT 59.331 50.000 0.00 0.00 0.00 1.94
2743 3014 0.948623 TGGCAAACACGATCCTGACG 60.949 55.000 0.00 0.00 0.00 4.35
2937 3208 7.615582 TCTGCGATAATTCTTGATGAAGTTT 57.384 32.000 0.00 0.00 38.18 2.66
2947 3218 4.163078 TCTTGATGAAGTTTTTGGCCCAAA 59.837 37.500 4.38 4.38 0.00 3.28
2950 3221 5.444176 TGATGAAGTTTTTGGCCCAAATTT 58.556 33.333 10.24 5.36 33.19 1.82
2957 3228 5.945191 AGTTTTTGGCCCAAATTTGATATGG 59.055 36.000 19.86 12.60 33.19 2.74
3062 3333 4.892934 ACATCTGTTTGGTTCTAGGCAAAA 59.107 37.500 0.00 0.00 0.00 2.44
3228 3503 5.279456 CCCCTCTTAATTCTTGTTTGTTGGG 60.279 44.000 0.00 0.00 0.00 4.12
3229 3504 5.230182 CCTCTTAATTCTTGTTTGTTGGGC 58.770 41.667 0.00 0.00 0.00 5.36
3247 3522 3.119673 TGGGCGTGTTTGTATATTTGCTG 60.120 43.478 0.00 0.00 0.00 4.41
3321 3603 0.805322 GCTGTCGAGCCATGTGAGAG 60.805 60.000 0.00 0.00 39.57 3.20
3414 3697 9.132521 CAATATGCTTGGTTTCTCTGTTTTTAG 57.867 33.333 0.00 0.00 0.00 1.85
3421 3704 7.633193 TGGTTTCTCTGTTTTTAGTTTGCTA 57.367 32.000 0.00 0.00 0.00 3.49
3488 3771 7.710907 TCAGATGGTGTTCTTAATAGTATGCAC 59.289 37.037 0.00 0.00 0.00 4.57
3490 3773 5.113383 TGGTGTTCTTAATAGTATGCACGG 58.887 41.667 0.00 0.00 0.00 4.94
3553 3837 1.436600 ACTTCTTGCGCATGAGAGTG 58.563 50.000 25.50 18.66 0.00 3.51
3558 3842 0.250252 TTGCGCATGAGAGTGGTTGA 60.250 50.000 12.75 0.00 0.00 3.18
3592 3876 6.588204 TCTTTTATAAGCCGATTAAGCTGGA 58.412 36.000 5.90 0.00 40.49 3.86
3594 3878 6.861065 TTTATAAGCCGATTAAGCTGGAAG 57.139 37.500 5.90 0.00 40.49 3.46
3622 3906 1.178534 ACCTTGCCCAAATGTGTCCG 61.179 55.000 0.00 0.00 0.00 4.79
3707 3991 7.005709 CTGGGACGGTAGAAAAGGAATATAT 57.994 40.000 0.00 0.00 0.00 0.86
3785 4069 7.033791 AGTACAACGTAGTCCTCAATACAATG 58.966 38.462 0.00 0.00 45.00 2.82
3796 4080 5.580691 TCCTCAATACAATGCACGAAGTAAG 59.419 40.000 0.00 0.00 41.61 2.34
3797 4081 5.220662 CCTCAATACAATGCACGAAGTAAGG 60.221 44.000 0.00 0.00 41.61 2.69
3798 4082 4.094294 TCAATACAATGCACGAAGTAAGGC 59.906 41.667 0.00 0.00 41.61 4.35
3799 4083 1.165270 ACAATGCACGAAGTAAGGCC 58.835 50.000 0.00 0.00 41.61 5.19
3800 4084 1.164411 CAATGCACGAAGTAAGGCCA 58.836 50.000 5.01 0.00 41.61 5.36
3801 4085 1.539388 CAATGCACGAAGTAAGGCCAA 59.461 47.619 5.01 0.00 41.61 4.52
3802 4086 1.165270 ATGCACGAAGTAAGGCCAAC 58.835 50.000 5.01 2.07 41.61 3.77
3803 4087 0.107831 TGCACGAAGTAAGGCCAACT 59.892 50.000 5.01 5.00 41.61 3.16
3804 4088 1.235724 GCACGAAGTAAGGCCAACTT 58.764 50.000 20.10 20.10 41.61 2.66
3805 4089 1.197036 GCACGAAGTAAGGCCAACTTC 59.803 52.381 28.47 28.47 46.09 3.01
3809 4093 1.892209 AAGTAAGGCCAACTTCACCG 58.108 50.000 15.71 0.00 40.64 4.94
3810 4094 0.605589 AGTAAGGCCAACTTCACCGC 60.606 55.000 5.01 0.00 40.64 5.68
3811 4095 0.887387 GTAAGGCCAACTTCACCGCA 60.887 55.000 5.01 0.00 40.64 5.69
3812 4096 0.887387 TAAGGCCAACTTCACCGCAC 60.887 55.000 5.01 0.00 40.64 5.34
3813 4097 4.025401 GGCCAACTTCACCGCACG 62.025 66.667 0.00 0.00 0.00 5.34
3814 4098 2.970324 GCCAACTTCACCGCACGA 60.970 61.111 0.00 0.00 0.00 4.35
3815 4099 2.935955 CCAACTTCACCGCACGAC 59.064 61.111 0.00 0.00 0.00 4.34
3816 4100 2.604174 CCAACTTCACCGCACGACC 61.604 63.158 0.00 0.00 0.00 4.79
3817 4101 1.594293 CAACTTCACCGCACGACCT 60.594 57.895 0.00 0.00 0.00 3.85
3818 4102 1.300697 AACTTCACCGCACGACCTC 60.301 57.895 0.00 0.00 0.00 3.85
3819 4103 2.023414 AACTTCACCGCACGACCTCA 62.023 55.000 0.00 0.00 0.00 3.86
3820 4104 1.300620 CTTCACCGCACGACCTCAA 60.301 57.895 0.00 0.00 0.00 3.02
3821 4105 0.878523 CTTCACCGCACGACCTCAAA 60.879 55.000 0.00 0.00 0.00 2.69
3822 4106 1.155424 TTCACCGCACGACCTCAAAC 61.155 55.000 0.00 0.00 0.00 2.93
3823 4107 2.660552 ACCGCACGACCTCAAACG 60.661 61.111 0.00 0.00 0.00 3.60
3824 4108 3.411351 CCGCACGACCTCAAACGG 61.411 66.667 0.00 0.00 0.00 4.44
3825 4109 3.411351 CGCACGACCTCAAACGGG 61.411 66.667 0.00 0.00 35.93 5.28
3826 4110 2.280592 GCACGACCTCAAACGGGT 60.281 61.111 0.00 0.00 40.13 5.28
3827 4111 2.604174 GCACGACCTCAAACGGGTG 61.604 63.158 0.00 0.00 37.17 4.61
3828 4112 1.227438 CACGACCTCAAACGGGTGT 60.227 57.895 0.00 0.00 37.17 4.16
3829 4113 1.068585 ACGACCTCAAACGGGTGTC 59.931 57.895 0.00 0.00 37.17 3.67
3830 4114 1.666872 CGACCTCAAACGGGTGTCC 60.667 63.158 0.00 0.00 37.17 4.02
3849 4133 3.507597 GGTTTGGCCGGATTTTGTC 57.492 52.632 5.05 0.00 0.00 3.18
3850 4134 0.037697 GGTTTGGCCGGATTTTGTCC 60.038 55.000 5.05 0.00 44.10 4.02
3851 4135 0.966179 GTTTGGCCGGATTTTGTCCT 59.034 50.000 5.05 0.00 45.46 3.85
3852 4136 1.343142 GTTTGGCCGGATTTTGTCCTT 59.657 47.619 5.05 0.00 45.46 3.36
3853 4137 1.710816 TTGGCCGGATTTTGTCCTTT 58.289 45.000 5.05 0.00 45.46 3.11
3854 4138 1.710816 TGGCCGGATTTTGTCCTTTT 58.289 45.000 5.05 0.00 45.46 2.27
3855 4139 1.342819 TGGCCGGATTTTGTCCTTTTG 59.657 47.619 5.05 0.00 45.46 2.44
3856 4140 1.343142 GGCCGGATTTTGTCCTTTTGT 59.657 47.619 5.05 0.00 45.46 2.83
3857 4141 2.403259 GCCGGATTTTGTCCTTTTGTG 58.597 47.619 5.05 0.00 45.46 3.33
3858 4142 2.866065 GCCGGATTTTGTCCTTTTGTGG 60.866 50.000 5.05 0.00 45.46 4.17
3859 4143 2.403259 CGGATTTTGTCCTTTTGTGGC 58.597 47.619 0.00 0.00 45.46 5.01
3860 4144 2.403259 GGATTTTGTCCTTTTGTGGCG 58.597 47.619 0.00 0.00 44.16 5.69
3861 4145 2.403259 GATTTTGTCCTTTTGTGGCGG 58.597 47.619 0.00 0.00 0.00 6.13
3862 4146 0.179097 TTTTGTCCTTTTGTGGCGGC 60.179 50.000 0.00 0.00 0.00 6.53
3863 4147 1.323271 TTTGTCCTTTTGTGGCGGCA 61.323 50.000 7.97 7.97 0.00 5.69
3864 4148 1.323271 TTGTCCTTTTGTGGCGGCAA 61.323 50.000 15.50 0.79 0.00 4.52
3865 4149 1.112315 TGTCCTTTTGTGGCGGCAAT 61.112 50.000 15.50 0.00 0.00 3.56
3866 4150 0.667184 GTCCTTTTGTGGCGGCAATG 60.667 55.000 15.50 0.07 0.00 2.82
3867 4151 1.374505 CCTTTTGTGGCGGCAATGG 60.375 57.895 15.50 6.45 0.00 3.16
3868 4152 1.374505 CTTTTGTGGCGGCAATGGG 60.375 57.895 15.50 0.00 0.00 4.00
3869 4153 2.098426 CTTTTGTGGCGGCAATGGGT 62.098 55.000 15.50 0.00 0.00 4.51
3870 4154 1.690219 TTTTGTGGCGGCAATGGGTT 61.690 50.000 15.50 0.00 0.00 4.11
3871 4155 2.093537 TTTGTGGCGGCAATGGGTTC 62.094 55.000 15.50 0.00 0.00 3.62
3872 4156 4.114997 GTGGCGGCAATGGGTTCG 62.115 66.667 15.50 0.00 0.00 3.95
3875 4159 4.179579 GCGGCAATGGGTTCGCTC 62.180 66.667 0.00 0.00 44.10 5.03
3876 4160 2.745884 CGGCAATGGGTTCGCTCA 60.746 61.111 0.00 0.00 0.00 4.26
3877 4161 2.114670 CGGCAATGGGTTCGCTCAT 61.115 57.895 0.00 0.00 40.74 2.90
3878 4162 1.434696 GGCAATGGGTTCGCTCATG 59.565 57.895 0.00 0.00 37.31 3.07
3879 4163 1.315257 GGCAATGGGTTCGCTCATGT 61.315 55.000 0.00 0.00 37.31 3.21
3880 4164 0.099436 GCAATGGGTTCGCTCATGTC 59.901 55.000 0.00 0.00 37.31 3.06
3881 4165 1.742761 CAATGGGTTCGCTCATGTCT 58.257 50.000 0.00 0.00 37.31 3.41
3882 4166 1.399440 CAATGGGTTCGCTCATGTCTG 59.601 52.381 0.00 0.00 37.31 3.51
3883 4167 0.745845 ATGGGTTCGCTCATGTCTGC 60.746 55.000 0.00 0.00 36.84 4.26
3884 4168 1.078848 GGGTTCGCTCATGTCTGCT 60.079 57.895 0.00 0.00 0.00 4.24
3885 4169 0.674895 GGGTTCGCTCATGTCTGCTT 60.675 55.000 0.00 0.00 0.00 3.91
3886 4170 0.723981 GGTTCGCTCATGTCTGCTTC 59.276 55.000 0.00 0.00 0.00 3.86
3887 4171 1.674221 GGTTCGCTCATGTCTGCTTCT 60.674 52.381 0.00 0.00 0.00 2.85
3888 4172 1.392853 GTTCGCTCATGTCTGCTTCTG 59.607 52.381 0.00 0.00 0.00 3.02
3889 4173 0.605083 TCGCTCATGTCTGCTTCTGT 59.395 50.000 0.00 0.00 0.00 3.41
3890 4174 0.997932 CGCTCATGTCTGCTTCTGTC 59.002 55.000 0.00 0.00 0.00 3.51
3891 4175 1.367659 GCTCATGTCTGCTTCTGTCC 58.632 55.000 0.00 0.00 0.00 4.02
3892 4176 1.338484 GCTCATGTCTGCTTCTGTCCA 60.338 52.381 0.00 0.00 0.00 4.02
3893 4177 2.680221 GCTCATGTCTGCTTCTGTCCAT 60.680 50.000 0.00 0.00 0.00 3.41
3894 4178 3.607741 CTCATGTCTGCTTCTGTCCATT 58.392 45.455 0.00 0.00 0.00 3.16
3895 4179 3.603532 TCATGTCTGCTTCTGTCCATTC 58.396 45.455 0.00 0.00 0.00 2.67
3896 4180 2.084610 TGTCTGCTTCTGTCCATTCG 57.915 50.000 0.00 0.00 0.00 3.34
3897 4181 1.338105 TGTCTGCTTCTGTCCATTCGG 60.338 52.381 0.00 0.00 0.00 4.30
3898 4182 0.976641 TCTGCTTCTGTCCATTCGGT 59.023 50.000 0.00 0.00 0.00 4.69
3899 4183 1.066858 TCTGCTTCTGTCCATTCGGTC 60.067 52.381 0.00 0.00 0.00 4.79
3900 4184 0.389817 TGCTTCTGTCCATTCGGTCG 60.390 55.000 0.00 0.00 0.00 4.79
3901 4185 0.389948 GCTTCTGTCCATTCGGTCGT 60.390 55.000 0.00 0.00 0.00 4.34
3902 4186 1.350193 CTTCTGTCCATTCGGTCGTG 58.650 55.000 0.00 0.00 0.00 4.35
3903 4187 0.669318 TTCTGTCCATTCGGTCGTGC 60.669 55.000 0.00 0.00 0.00 5.34
3904 4188 2.431771 TGTCCATTCGGTCGTGCG 60.432 61.111 0.00 0.00 0.00 5.34
3905 4189 2.431942 GTCCATTCGGTCGTGCGT 60.432 61.111 0.00 0.00 0.00 5.24
3906 4190 2.431771 TCCATTCGGTCGTGCGTG 60.432 61.111 0.00 0.00 0.00 5.34
3907 4191 2.736995 CCATTCGGTCGTGCGTGT 60.737 61.111 0.00 0.00 0.00 4.49
3908 4192 2.469847 CATTCGGTCGTGCGTGTG 59.530 61.111 0.00 0.00 0.00 3.82
3909 4193 3.411351 ATTCGGTCGTGCGTGTGC 61.411 61.111 0.00 0.00 43.20 4.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.720902 CCGCCACCATGCCACTCA 62.721 66.667 0.00 0.00 0.00 3.41
6 7 4.424566 CTTGTGCCGCCACCATGC 62.425 66.667 0.00 0.00 41.35 4.06
7 8 2.267351 TTCTTGTGCCGCCACCATG 61.267 57.895 0.00 0.00 41.35 3.66
8 9 2.115052 TTCTTGTGCCGCCACCAT 59.885 55.556 0.00 0.00 41.35 3.55
9 10 2.904866 GTTCTTGTGCCGCCACCA 60.905 61.111 0.00 0.00 41.35 4.17
10 11 3.670377 GGTTCTTGTGCCGCCACC 61.670 66.667 0.00 0.00 41.35 4.61
11 12 2.594592 AGGTTCTTGTGCCGCCAC 60.595 61.111 0.00 0.00 42.40 5.01
12 13 2.281484 GAGGTTCTTGTGCCGCCA 60.281 61.111 0.00 0.00 0.00 5.69
13 14 2.281484 TGAGGTTCTTGTGCCGCC 60.281 61.111 0.00 0.00 0.00 6.13
14 15 1.569479 GACTGAGGTTCTTGTGCCGC 61.569 60.000 0.00 0.00 0.00 6.53
15 16 0.249868 TGACTGAGGTTCTTGTGCCG 60.250 55.000 0.00 0.00 0.00 5.69
16 17 2.079925 GATGACTGAGGTTCTTGTGCC 58.920 52.381 0.00 0.00 0.00 5.01
17 18 1.728971 CGATGACTGAGGTTCTTGTGC 59.271 52.381 0.00 0.00 0.00 4.57
18 19 2.341257 CCGATGACTGAGGTTCTTGTG 58.659 52.381 0.00 0.00 0.00 3.33
19 20 1.338200 GCCGATGACTGAGGTTCTTGT 60.338 52.381 0.00 0.00 0.00 3.16
20 21 1.066573 AGCCGATGACTGAGGTTCTTG 60.067 52.381 0.00 0.00 0.00 3.02
21 22 1.270907 AGCCGATGACTGAGGTTCTT 58.729 50.000 0.00 0.00 0.00 2.52
22 23 1.270907 AAGCCGATGACTGAGGTTCT 58.729 50.000 0.00 0.00 0.00 3.01
23 24 2.003301 GAAAGCCGATGACTGAGGTTC 58.997 52.381 0.00 0.00 0.00 3.62
24 25 1.339151 GGAAAGCCGATGACTGAGGTT 60.339 52.381 0.00 0.00 0.00 3.50
25 26 0.250513 GGAAAGCCGATGACTGAGGT 59.749 55.000 0.00 0.00 0.00 3.85
26 27 0.250234 TGGAAAGCCGATGACTGAGG 59.750 55.000 0.00 0.00 36.79 3.86
27 28 2.208431 GATGGAAAGCCGATGACTGAG 58.792 52.381 0.00 0.00 36.79 3.35
28 29 1.134401 GGATGGAAAGCCGATGACTGA 60.134 52.381 0.00 0.00 36.79 3.41
29 30 1.303309 GGATGGAAAGCCGATGACTG 58.697 55.000 0.00 0.00 36.79 3.51
30 31 0.911769 TGGATGGAAAGCCGATGACT 59.088 50.000 0.00 0.00 36.79 3.41
31 32 1.605710 CATGGATGGAAAGCCGATGAC 59.394 52.381 0.00 0.00 36.79 3.06
32 33 1.971481 CATGGATGGAAAGCCGATGA 58.029 50.000 0.00 0.00 36.79 2.92
33 34 0.313043 GCATGGATGGAAAGCCGATG 59.687 55.000 0.00 0.00 36.79 3.84
34 35 0.106569 TGCATGGATGGAAAGCCGAT 60.107 50.000 0.00 0.00 36.79 4.18
35 36 0.106569 ATGCATGGATGGAAAGCCGA 60.107 50.000 0.00 0.00 36.79 5.54
36 37 0.313043 GATGCATGGATGGAAAGCCG 59.687 55.000 2.46 0.00 36.79 5.52
37 38 0.677842 GGATGCATGGATGGAAAGCC 59.322 55.000 2.46 0.00 0.00 4.35
38 39 0.677842 GGGATGCATGGATGGAAAGC 59.322 55.000 2.46 0.00 0.00 3.51
39 40 1.961394 CAGGGATGCATGGATGGAAAG 59.039 52.381 2.46 0.00 0.00 2.62
40 41 1.411930 CCAGGGATGCATGGATGGAAA 60.412 52.381 13.22 0.00 39.02 3.13
41 42 0.186630 CCAGGGATGCATGGATGGAA 59.813 55.000 13.22 0.00 39.02 3.53
42 43 1.722110 CCCAGGGATGCATGGATGGA 61.722 60.000 20.42 0.00 39.02 3.41
43 44 1.228769 CCCAGGGATGCATGGATGG 60.229 63.158 20.42 8.82 39.02 3.51
44 45 1.906824 GCCCAGGGATGCATGGATG 60.907 63.158 20.42 4.57 39.02 3.51
45 46 2.524559 GCCCAGGGATGCATGGAT 59.475 61.111 20.42 0.00 39.02 3.41
46 47 4.193893 CGCCCAGGGATGCATGGA 62.194 66.667 20.42 0.00 39.02 3.41
47 48 4.511246 ACGCCCAGGGATGCATGG 62.511 66.667 10.89 11.42 36.27 3.66
48 49 2.903855 GACGCCCAGGGATGCATG 60.904 66.667 10.89 0.00 0.00 4.06
49 50 4.552365 CGACGCCCAGGGATGCAT 62.552 66.667 10.89 0.00 0.00 3.96
52 53 3.723235 CTCACGACGCCCAGGGATG 62.723 68.421 10.89 2.53 0.00 3.51
53 54 3.461773 CTCACGACGCCCAGGGAT 61.462 66.667 10.89 0.00 0.00 3.85
54 55 4.671590 TCTCACGACGCCCAGGGA 62.672 66.667 10.89 0.00 0.00 4.20
55 56 3.649277 CTTCTCACGACGCCCAGGG 62.649 68.421 0.00 0.00 0.00 4.45
56 57 2.125912 CTTCTCACGACGCCCAGG 60.126 66.667 0.00 0.00 0.00 4.45
57 58 1.153939 CTCTTCTCACGACGCCCAG 60.154 63.158 0.00 0.00 0.00 4.45
58 59 2.636412 CCTCTTCTCACGACGCCCA 61.636 63.158 0.00 0.00 0.00 5.36
59 60 2.182030 CCTCTTCTCACGACGCCC 59.818 66.667 0.00 0.00 0.00 6.13
60 61 2.507324 GCCTCTTCTCACGACGCC 60.507 66.667 0.00 0.00 0.00 5.68
61 62 2.507324 GGCCTCTTCTCACGACGC 60.507 66.667 0.00 0.00 0.00 5.19
62 63 2.202492 CGGCCTCTTCTCACGACG 60.202 66.667 0.00 0.00 0.00 5.12
63 64 2.182030 CCGGCCTCTTCTCACGAC 59.818 66.667 0.00 0.00 0.00 4.34
64 65 2.282958 ACCGGCCTCTTCTCACGA 60.283 61.111 0.00 0.00 0.00 4.35
65 66 2.182030 GACCGGCCTCTTCTCACG 59.818 66.667 0.00 0.00 0.00 4.35
66 67 2.182030 CGACCGGCCTCTTCTCAC 59.818 66.667 0.00 0.00 0.00 3.51
67 68 3.760035 GCGACCGGCCTCTTCTCA 61.760 66.667 0.00 0.00 34.80 3.27
114 115 4.120331 GTGAATGCTGGCGTGGGC 62.120 66.667 0.00 0.00 38.90 5.36
135 140 4.717629 TGGACGGAGCAACGCGAG 62.718 66.667 15.93 5.94 37.37 5.03
138 143 3.712881 GTGTGGACGGAGCAACGC 61.713 66.667 0.00 0.00 37.37 4.84
139 144 2.029073 AGTGTGGACGGAGCAACG 59.971 61.111 0.00 0.00 40.31 4.10
140 145 1.961277 CCAGTGTGGACGGAGCAAC 60.961 63.158 0.00 0.00 40.96 4.17
152 157 1.069765 CAGAGTGAACGGCCAGTGT 59.930 57.895 2.24 0.00 0.00 3.55
154 159 1.069765 CACAGAGTGAACGGCCAGT 59.930 57.895 2.24 0.00 35.23 4.00
157 162 1.237285 AATGCACAGAGTGAACGGCC 61.237 55.000 0.58 0.00 35.23 6.13
158 163 0.593128 AAATGCACAGAGTGAACGGC 59.407 50.000 0.58 0.00 35.23 5.68
159 164 4.481930 TTAAAATGCACAGAGTGAACGG 57.518 40.909 0.58 0.00 35.23 4.44
160 165 5.173131 GGTTTTAAAATGCACAGAGTGAACG 59.827 40.000 3.52 0.00 35.23 3.95
161 166 5.173131 CGGTTTTAAAATGCACAGAGTGAAC 59.827 40.000 3.52 0.00 35.23 3.18
264 269 9.030301 CAAAGTTCAAATCGGTATGAAAAGTTT 57.970 29.630 0.00 0.00 37.31 2.66
396 401 8.902540 AGTAGTGAATTTGACTCATGTACAAA 57.097 30.769 0.00 13.42 37.79 2.83
842 847 0.476808 TGGTGGGGAGTGGTAATGGT 60.477 55.000 0.00 0.00 0.00 3.55
1008 1027 2.042404 GCCTGCTGGATCTGGAGGAG 62.042 65.000 23.07 13.42 41.84 3.69
1035 1054 1.374947 CGAGGGCTTCTTTGGGTGA 59.625 57.895 0.00 0.00 0.00 4.02
1041 1066 4.048470 GGGGGCGAGGGCTTCTTT 62.048 66.667 0.00 0.00 39.81 2.52
1124 1149 3.891432 AAGTGGGAGGTGGAGGGGG 62.891 68.421 0.00 0.00 0.00 5.40
1125 1150 2.204151 AAGTGGGAGGTGGAGGGG 60.204 66.667 0.00 0.00 0.00 4.79
1126 1151 2.301738 GGAAGTGGGAGGTGGAGGG 61.302 68.421 0.00 0.00 0.00 4.30
1127 1152 1.538876 TGGAAGTGGGAGGTGGAGG 60.539 63.158 0.00 0.00 0.00 4.30
1128 1153 0.838122 AGTGGAAGTGGGAGGTGGAG 60.838 60.000 0.00 0.00 0.00 3.86
1129 1154 0.836400 GAGTGGAAGTGGGAGGTGGA 60.836 60.000 0.00 0.00 0.00 4.02
1130 1155 1.679898 GAGTGGAAGTGGGAGGTGG 59.320 63.158 0.00 0.00 0.00 4.61
1131 1156 1.679898 GGAGTGGAAGTGGGAGGTG 59.320 63.158 0.00 0.00 0.00 4.00
1132 1157 1.539124 GGGAGTGGAAGTGGGAGGT 60.539 63.158 0.00 0.00 0.00 3.85
1133 1158 2.301738 GGGGAGTGGAAGTGGGAGG 61.302 68.421 0.00 0.00 0.00 4.30
1134 1159 2.301738 GGGGGAGTGGAAGTGGGAG 61.302 68.421 0.00 0.00 0.00 4.30
1135 1160 2.204090 GGGGGAGTGGAAGTGGGA 60.204 66.667 0.00 0.00 0.00 4.37
1136 1161 3.717294 CGGGGGAGTGGAAGTGGG 61.717 72.222 0.00 0.00 0.00 4.61
1137 1162 4.410400 GCGGGGGAGTGGAAGTGG 62.410 72.222 0.00 0.00 0.00 4.00
1138 1163 4.410400 GGCGGGGGAGTGGAAGTG 62.410 72.222 0.00 0.00 0.00 3.16
1218 1243 4.554363 CTGGCGTAGGACGAGGCG 62.554 72.222 2.65 0.00 46.05 5.52
1219 1244 4.874977 GCTGGCGTAGGACGAGGC 62.875 72.222 2.65 0.00 46.05 4.70
1220 1245 4.208686 GGCTGGCGTAGGACGAGG 62.209 72.222 2.65 0.00 46.05 4.63
1221 1246 4.208686 GGGCTGGCGTAGGACGAG 62.209 72.222 2.65 0.00 46.05 4.18
1224 1249 3.712907 TTGGGGCTGGCGTAGGAC 61.713 66.667 0.00 0.00 0.00 3.85
1225 1250 3.712907 GTTGGGGCTGGCGTAGGA 61.713 66.667 0.00 0.00 0.00 2.94
1226 1251 4.796495 GGTTGGGGCTGGCGTAGG 62.796 72.222 0.00 0.00 0.00 3.18
1227 1252 4.796495 GGGTTGGGGCTGGCGTAG 62.796 72.222 0.00 0.00 0.00 3.51
1237 1262 3.793888 GTAGGAGGGCGGGTTGGG 61.794 72.222 0.00 0.00 0.00 4.12
1238 1263 3.006728 TGTAGGAGGGCGGGTTGG 61.007 66.667 0.00 0.00 0.00 3.77
1239 1264 2.267961 GTGTAGGAGGGCGGGTTG 59.732 66.667 0.00 0.00 0.00 3.77
1240 1265 3.387947 CGTGTAGGAGGGCGGGTT 61.388 66.667 0.00 0.00 0.00 4.11
1243 1268 4.514577 CTGCGTGTAGGAGGGCGG 62.515 72.222 0.00 0.00 34.34 6.13
1244 1269 3.449227 TCTGCGTGTAGGAGGGCG 61.449 66.667 0.00 0.00 38.98 6.13
1245 1270 2.184579 GTCTGCGTGTAGGAGGGC 59.815 66.667 0.00 0.00 38.98 5.19
1246 1271 2.490217 CGTCTGCGTGTAGGAGGG 59.510 66.667 0.00 0.00 38.98 4.30
1247 1272 2.202623 GCGTCTGCGTGTAGGAGG 60.203 66.667 0.00 0.00 38.98 4.30
1257 1282 2.184579 GGGTAGGACTGCGTCTGC 59.815 66.667 8.26 0.00 43.20 4.26
1258 1283 1.668101 GAGGGGTAGGACTGCGTCTG 61.668 65.000 8.26 0.00 32.47 3.51
1259 1284 1.380112 GAGGGGTAGGACTGCGTCT 60.380 63.158 8.26 0.00 32.47 4.18
1260 1285 2.424733 GGAGGGGTAGGACTGCGTC 61.425 68.421 0.79 0.79 0.00 5.19
1261 1286 2.363925 GGAGGGGTAGGACTGCGT 60.364 66.667 0.00 0.00 0.00 5.24
1262 1287 2.363795 TGGAGGGGTAGGACTGCG 60.364 66.667 0.00 0.00 0.00 5.18
1263 1288 2.736826 GCTGGAGGGGTAGGACTGC 61.737 68.421 0.00 0.00 0.00 4.40
1264 1289 0.261991 TAGCTGGAGGGGTAGGACTG 59.738 60.000 0.00 0.00 0.00 3.51
1265 1290 0.262285 GTAGCTGGAGGGGTAGGACT 59.738 60.000 0.00 0.00 0.00 3.85
1266 1291 0.032416 TGTAGCTGGAGGGGTAGGAC 60.032 60.000 0.00 0.00 0.00 3.85
1267 1292 0.032416 GTGTAGCTGGAGGGGTAGGA 60.032 60.000 0.00 0.00 0.00 2.94
1268 1293 1.049289 GGTGTAGCTGGAGGGGTAGG 61.049 65.000 0.00 0.00 0.00 3.18
1269 1294 0.325296 TGGTGTAGCTGGAGGGGTAG 60.325 60.000 0.00 0.00 0.00 3.18
1270 1295 0.117541 TTGGTGTAGCTGGAGGGGTA 59.882 55.000 0.00 0.00 0.00 3.69
1271 1296 1.151899 TTGGTGTAGCTGGAGGGGT 60.152 57.895 0.00 0.00 0.00 4.95
1272 1297 1.201429 ACTTGGTGTAGCTGGAGGGG 61.201 60.000 0.00 0.00 0.00 4.79
1273 1298 0.693049 AACTTGGTGTAGCTGGAGGG 59.307 55.000 0.00 0.00 0.00 4.30
1274 1299 1.347707 TGAACTTGGTGTAGCTGGAGG 59.652 52.381 0.00 0.00 0.00 4.30
1275 1300 2.808543 GTTGAACTTGGTGTAGCTGGAG 59.191 50.000 0.00 0.00 0.00 3.86
1276 1301 2.438021 AGTTGAACTTGGTGTAGCTGGA 59.562 45.455 0.00 0.00 0.00 3.86
1277 1302 2.808543 GAGTTGAACTTGGTGTAGCTGG 59.191 50.000 0.00 0.00 0.00 4.85
1278 1303 2.808543 GGAGTTGAACTTGGTGTAGCTG 59.191 50.000 0.00 0.00 0.00 4.24
1279 1304 2.548067 CGGAGTTGAACTTGGTGTAGCT 60.548 50.000 0.00 0.00 0.00 3.32
1280 1305 1.798813 CGGAGTTGAACTTGGTGTAGC 59.201 52.381 0.00 0.00 0.00 3.58
1281 1306 1.798813 GCGGAGTTGAACTTGGTGTAG 59.201 52.381 0.00 0.00 0.00 2.74
1282 1307 1.870580 CGCGGAGTTGAACTTGGTGTA 60.871 52.381 0.00 0.00 0.00 2.90
1283 1308 1.157870 CGCGGAGTTGAACTTGGTGT 61.158 55.000 0.00 0.00 0.00 4.16
1284 1309 1.569493 CGCGGAGTTGAACTTGGTG 59.431 57.895 0.00 0.00 0.00 4.17
1285 1310 2.251642 GCGCGGAGTTGAACTTGGT 61.252 57.895 8.83 0.00 0.00 3.67
1286 1311 1.901650 GAGCGCGGAGTTGAACTTGG 61.902 60.000 8.83 0.00 0.00 3.61
1287 1312 1.221466 TGAGCGCGGAGTTGAACTTG 61.221 55.000 8.83 0.00 0.00 3.16
1288 1313 0.531974 TTGAGCGCGGAGTTGAACTT 60.532 50.000 8.83 0.00 0.00 2.66
1289 1314 1.069090 TTGAGCGCGGAGTTGAACT 59.931 52.632 8.83 0.00 0.00 3.01
1290 1315 1.204312 GTTGAGCGCGGAGTTGAAC 59.796 57.895 8.83 0.00 0.00 3.18
1291 1316 2.307309 CGTTGAGCGCGGAGTTGAA 61.307 57.895 8.83 0.00 0.00 2.69
1453 1718 3.087253 TAGGGGGTGGTGCGGATG 61.087 66.667 0.00 0.00 0.00 3.51
1454 1719 2.768344 CTAGGGGGTGGTGCGGAT 60.768 66.667 0.00 0.00 0.00 4.18
1545 1810 0.249741 CGTCGTTGAACTGGTTCCCT 60.250 55.000 10.44 0.00 38.77 4.20
1636 1901 0.108804 CTGTGGGCGACGAGTATGTT 60.109 55.000 0.00 0.00 0.00 2.71
1819 2084 0.112412 AAAATGCCGAGGACCTTGGT 59.888 50.000 26.22 7.32 37.36 3.67
1846 2117 1.503347 AGGAAAAGAAGAAAGGGGCCA 59.497 47.619 4.39 0.00 0.00 5.36
1868 2139 4.398988 TGATGCCAATTGACCATTAGACAC 59.601 41.667 7.12 0.00 0.00 3.67
2044 2315 1.674221 GCGCCTGAGTTCTCAAGATGT 60.674 52.381 0.00 0.00 0.00 3.06
2110 2381 3.118592 CCATTTCTACCTCCTCAGTCACC 60.119 52.174 0.00 0.00 0.00 4.02
2155 2426 0.961019 CTTCACCACCACCCACATTG 59.039 55.000 0.00 0.00 0.00 2.82
2157 2428 0.401738 CTCTTCACCACCACCCACAT 59.598 55.000 0.00 0.00 0.00 3.21
2179 2450 1.834263 ACCTGCAGGAGCCTAACTAAG 59.166 52.381 39.19 8.02 41.13 2.18
2410 2681 1.718757 GGTTATCAGCCTGCCTTGCG 61.719 60.000 0.00 0.00 0.00 4.85
2443 2714 1.421485 GCGCTCAACAAGGATGTCG 59.579 57.895 0.00 0.00 39.40 4.35
2470 2741 2.568956 CCATGTCCTCAAGAAGTCCTCA 59.431 50.000 0.00 0.00 0.00 3.86
2566 2837 1.006220 CCCGACAAAAAGCCTTGCC 60.006 57.895 0.00 0.00 0.00 4.52
2578 2849 2.203422 CCTTTGCCAACCCCGACA 60.203 61.111 0.00 0.00 0.00 4.35
2937 3208 4.163839 CCTCCATATCAAATTTGGGCCAAA 59.836 41.667 32.12 32.12 37.75 3.28
2947 3218 2.785269 TCAGCCACCCTCCATATCAAAT 59.215 45.455 0.00 0.00 0.00 2.32
2950 3221 1.701292 CATCAGCCACCCTCCATATCA 59.299 52.381 0.00 0.00 0.00 2.15
2957 3228 0.038166 TCCAAACATCAGCCACCCTC 59.962 55.000 0.00 0.00 0.00 4.30
3172 3444 7.076362 CACAATGATTTGCTATAAGCTGCTAG 58.924 38.462 0.90 0.00 42.97 3.42
3228 3503 4.969816 AGACAGCAAATATACAAACACGC 58.030 39.130 0.00 0.00 0.00 5.34
3247 3522 7.702348 GGTGCCTTGAACATTGAATTATAAGAC 59.298 37.037 0.00 0.00 0.00 3.01
3263 3541 1.133199 ACAATGAAGGGGTGCCTTGAA 60.133 47.619 0.00 0.00 0.00 2.69
3321 3603 7.440856 TCCAATTCCAATTGCTAAAACAACTTC 59.559 33.333 0.00 0.00 43.38 3.01
3414 3697 1.663161 GCGGCTCAACAACTAGCAAAC 60.663 52.381 0.00 0.00 40.61 2.93
3421 3704 1.026718 GGCATAGCGGCTCAACAACT 61.027 55.000 5.39 0.00 37.17 3.16
3488 3771 8.472683 TTTTAATTCATCAAAAAGGTATGCCG 57.527 30.769 0.00 0.00 40.50 5.69
3518 3802 6.904011 CGCAAGAAGTAATTTCATAAGCTCAG 59.096 38.462 0.00 0.00 38.31 3.35
3592 3876 1.328279 GGGCAAGGTGTAAAGCACTT 58.672 50.000 0.00 0.00 46.86 3.16
3594 3878 1.036707 TTGGGCAAGGTGTAAAGCAC 58.963 50.000 0.00 0.00 46.97 4.40
3602 3886 0.318120 GGACACATTTGGGCAAGGTG 59.682 55.000 1.42 1.42 35.18 4.00
3604 3888 0.893270 TCGGACACATTTGGGCAAGG 60.893 55.000 0.00 0.00 0.00 3.61
3713 3997 9.830975 ACTTATACATTGTGCATTACATCAGTA 57.169 29.630 0.00 0.00 39.48 2.74
3714 3998 8.737168 ACTTATACATTGTGCATTACATCAGT 57.263 30.769 0.00 0.00 39.48 3.41
3724 4008 9.203421 CCTCGATATTAACTTATACATTGTGCA 57.797 33.333 0.00 0.00 0.00 4.57
3742 4026 7.571983 CGTTGTACTCCGTATAAACCTCGATAT 60.572 40.741 0.00 0.00 0.00 1.63
3743 4027 6.292865 CGTTGTACTCCGTATAAACCTCGATA 60.293 42.308 0.00 0.00 0.00 2.92
3744 4028 5.504665 CGTTGTACTCCGTATAAACCTCGAT 60.505 44.000 0.00 0.00 0.00 3.59
3746 4030 4.031028 CGTTGTACTCCGTATAAACCTCG 58.969 47.826 0.00 0.00 0.00 4.63
3764 4048 4.629634 TGCATTGTATTGAGGACTACGTTG 59.370 41.667 0.00 0.00 0.00 4.10
3768 4052 4.430007 TCGTGCATTGTATTGAGGACTAC 58.570 43.478 0.00 0.00 0.00 2.73
3785 4069 1.197036 GAAGTTGGCCTTACTTCGTGC 59.803 52.381 25.37 11.51 41.28 5.34
3796 4080 4.025401 CGTGCGGTGAAGTTGGCC 62.025 66.667 0.00 0.00 0.00 5.36
3797 4081 2.970324 TCGTGCGGTGAAGTTGGC 60.970 61.111 0.00 0.00 0.00 4.52
3798 4082 2.604174 GGTCGTGCGGTGAAGTTGG 61.604 63.158 0.00 0.00 0.00 3.77
3799 4083 1.557443 GAGGTCGTGCGGTGAAGTTG 61.557 60.000 0.00 0.00 0.00 3.16
3800 4084 1.300697 GAGGTCGTGCGGTGAAGTT 60.301 57.895 0.00 0.00 0.00 2.66
3801 4085 2.023414 TTGAGGTCGTGCGGTGAAGT 62.023 55.000 0.00 0.00 0.00 3.01
3802 4086 0.878523 TTTGAGGTCGTGCGGTGAAG 60.879 55.000 0.00 0.00 0.00 3.02
3803 4087 1.144276 TTTGAGGTCGTGCGGTGAA 59.856 52.632 0.00 0.00 0.00 3.18
3804 4088 1.593209 GTTTGAGGTCGTGCGGTGA 60.593 57.895 0.00 0.00 0.00 4.02
3805 4089 2.935955 GTTTGAGGTCGTGCGGTG 59.064 61.111 0.00 0.00 0.00 4.94
3806 4090 2.660552 CGTTTGAGGTCGTGCGGT 60.661 61.111 0.00 0.00 0.00 5.68
3807 4091 3.411351 CCGTTTGAGGTCGTGCGG 61.411 66.667 0.00 0.00 0.00 5.69
3808 4092 3.411351 CCCGTTTGAGGTCGTGCG 61.411 66.667 0.00 0.00 0.00 5.34
3809 4093 2.280592 ACCCGTTTGAGGTCGTGC 60.281 61.111 0.00 0.00 28.99 5.34
3810 4094 1.219522 GACACCCGTTTGAGGTCGTG 61.220 60.000 0.00 0.00 34.56 4.35
3811 4095 1.068585 GACACCCGTTTGAGGTCGT 59.931 57.895 0.00 0.00 34.56 4.34
3812 4096 1.666872 GGACACCCGTTTGAGGTCG 60.667 63.158 0.00 0.00 34.56 4.79
3813 4097 4.373771 GGACACCCGTTTGAGGTC 57.626 61.111 0.00 0.00 34.56 3.85
3831 4115 0.037697 GGACAAAATCCGGCCAAACC 60.038 55.000 2.24 0.00 37.88 3.27
3832 4116 3.507597 GGACAAAATCCGGCCAAAC 57.492 52.632 2.24 0.00 37.88 2.93
3841 4125 2.403259 CCGCCACAAAAGGACAAAATC 58.597 47.619 0.00 0.00 0.00 2.17
3842 4126 1.540146 GCCGCCACAAAAGGACAAAAT 60.540 47.619 0.00 0.00 0.00 1.82
3843 4127 0.179097 GCCGCCACAAAAGGACAAAA 60.179 50.000 0.00 0.00 0.00 2.44
3844 4128 1.323271 TGCCGCCACAAAAGGACAAA 61.323 50.000 0.00 0.00 0.00 2.83
3845 4129 1.323271 TTGCCGCCACAAAAGGACAA 61.323 50.000 0.00 0.00 0.00 3.18
3846 4130 1.112315 ATTGCCGCCACAAAAGGACA 61.112 50.000 0.00 0.00 32.27 4.02
3847 4131 0.667184 CATTGCCGCCACAAAAGGAC 60.667 55.000 0.00 0.00 32.27 3.85
3848 4132 1.664873 CATTGCCGCCACAAAAGGA 59.335 52.632 0.00 0.00 32.27 3.36
3849 4133 1.374505 CCATTGCCGCCACAAAAGG 60.375 57.895 0.00 0.00 32.27 3.11
3850 4134 1.374505 CCCATTGCCGCCACAAAAG 60.375 57.895 0.00 0.00 32.27 2.27
3851 4135 1.690219 AACCCATTGCCGCCACAAAA 61.690 50.000 0.00 0.00 32.27 2.44
3852 4136 2.093537 GAACCCATTGCCGCCACAAA 62.094 55.000 0.00 0.00 32.27 2.83
3853 4137 2.522923 AACCCATTGCCGCCACAA 60.523 55.556 0.00 0.00 0.00 3.33
3854 4138 2.988684 GAACCCATTGCCGCCACA 60.989 61.111 0.00 0.00 0.00 4.17
3855 4139 4.114997 CGAACCCATTGCCGCCAC 62.115 66.667 0.00 0.00 0.00 5.01
3858 4142 4.179579 GAGCGAACCCATTGCCGC 62.180 66.667 0.00 0.00 47.00 6.53
3859 4143 2.114670 ATGAGCGAACCCATTGCCG 61.115 57.895 0.00 0.00 0.00 5.69
3860 4144 1.315257 ACATGAGCGAACCCATTGCC 61.315 55.000 0.00 0.00 0.00 4.52
3861 4145 0.099436 GACATGAGCGAACCCATTGC 59.901 55.000 0.00 0.00 0.00 3.56
3862 4146 1.399440 CAGACATGAGCGAACCCATTG 59.601 52.381 0.00 0.00 0.00 2.82
3863 4147 1.742761 CAGACATGAGCGAACCCATT 58.257 50.000 0.00 0.00 0.00 3.16
3864 4148 0.745845 GCAGACATGAGCGAACCCAT 60.746 55.000 0.00 0.00 0.00 4.00
3865 4149 1.375908 GCAGACATGAGCGAACCCA 60.376 57.895 0.00 0.00 0.00 4.51
3866 4150 0.674895 AAGCAGACATGAGCGAACCC 60.675 55.000 0.00 0.00 35.48 4.11
3867 4151 0.723981 GAAGCAGACATGAGCGAACC 59.276 55.000 0.00 0.00 35.48 3.62
3868 4152 1.392853 CAGAAGCAGACATGAGCGAAC 59.607 52.381 0.00 0.00 35.48 3.95
3869 4153 1.001293 ACAGAAGCAGACATGAGCGAA 59.999 47.619 0.00 0.00 35.48 4.70
3870 4154 0.605083 ACAGAAGCAGACATGAGCGA 59.395 50.000 0.00 0.00 35.48 4.93
3871 4155 0.997932 GACAGAAGCAGACATGAGCG 59.002 55.000 0.00 0.00 35.48 5.03
3872 4156 1.338484 TGGACAGAAGCAGACATGAGC 60.338 52.381 0.00 0.00 0.00 4.26
3873 4157 2.756840 TGGACAGAAGCAGACATGAG 57.243 50.000 0.00 0.00 0.00 2.90
3874 4158 3.603532 GAATGGACAGAAGCAGACATGA 58.396 45.455 0.00 0.00 0.00 3.07
3875 4159 2.350804 CGAATGGACAGAAGCAGACATG 59.649 50.000 0.00 0.00 0.00 3.21
3876 4160 2.625737 CGAATGGACAGAAGCAGACAT 58.374 47.619 0.00 0.00 0.00 3.06
3877 4161 1.338105 CCGAATGGACAGAAGCAGACA 60.338 52.381 0.00 0.00 37.49 3.41
3878 4162 1.338200 ACCGAATGGACAGAAGCAGAC 60.338 52.381 0.00 0.00 39.21 3.51
3879 4163 0.976641 ACCGAATGGACAGAAGCAGA 59.023 50.000 0.00 0.00 39.21 4.26
3880 4164 1.363744 GACCGAATGGACAGAAGCAG 58.636 55.000 0.00 0.00 39.21 4.24
3881 4165 0.389817 CGACCGAATGGACAGAAGCA 60.390 55.000 0.00 0.00 39.21 3.91
3882 4166 0.389948 ACGACCGAATGGACAGAAGC 60.390 55.000 0.00 0.00 39.21 3.86
3883 4167 1.350193 CACGACCGAATGGACAGAAG 58.650 55.000 0.00 0.00 39.21 2.85
3884 4168 0.669318 GCACGACCGAATGGACAGAA 60.669 55.000 0.00 0.00 39.21 3.02
3885 4169 1.080093 GCACGACCGAATGGACAGA 60.080 57.895 0.00 0.00 39.21 3.41
3886 4170 2.444624 CGCACGACCGAATGGACAG 61.445 63.158 0.00 0.00 39.21 3.51
3887 4171 2.431771 CGCACGACCGAATGGACA 60.432 61.111 0.00 0.00 39.21 4.02
3888 4172 2.431942 ACGCACGACCGAATGGAC 60.432 61.111 0.00 0.00 39.21 4.02
3889 4173 2.431771 CACGCACGACCGAATGGA 60.432 61.111 0.00 0.00 39.21 3.41
3890 4174 2.736995 ACACGCACGACCGAATGG 60.737 61.111 0.00 0.00 42.84 3.16
3891 4175 2.469847 CACACGCACGACCGAATG 59.530 61.111 0.00 1.32 0.00 2.67
3892 4176 3.411351 GCACACGCACGACCGAAT 61.411 61.111 0.00 0.00 38.36 3.34


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

AutoCloner maintained by Alex Coulton.