Multiple sequence alignment - TraesCS2A01G575700

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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 TraesCS2A01G575700 chr2A 100.000 5119 0 0 1 5119 770103608 770108726 0.000000e+00 9454.0
1 TraesCS2A01G575700 chr2A 97.177 248 7 0 3826 4073 770192371 770192618 2.200000e-113 420.0
2 TraesCS2A01G575700 chr2D 89.032 4340 236 110 281 4470 644835291 644831042 0.000000e+00 5156.0
3 TraesCS2A01G575700 chr2D 93.383 665 24 2 4455 5119 644830738 644830094 0.000000e+00 966.0
4 TraesCS2A01G575700 chr2B 92.053 1598 88 23 2973 4545 790695963 790697546 0.000000e+00 2211.0
5 TraesCS2A01G575700 chr2B 86.502 852 42 24 1002 1806 790693745 790694570 0.000000e+00 869.0
6 TraesCS2A01G575700 chr2B 91.400 593 21 10 4538 5119 790699484 790700057 0.000000e+00 785.0
7 TraesCS2A01G575700 chr2B 82.784 668 44 22 2196 2817 790695092 790695734 9.760000e-147 531.0
8 TraesCS2A01G575700 chr2B 90.514 253 24 0 3840 4092 790701308 790701560 8.210000e-88 335.0
9 TraesCS2A01G575700 chr2B 86.799 303 18 9 1916 2197 790694663 790694964 8.270000e-83 318.0
10 TraesCS2A01G575700 chr2B 87.248 298 10 16 346 619 790693113 790693406 1.070000e-81 315.0
11 TraesCS2A01G575700 chr2B 90.385 104 10 0 47 150 790692813 790692916 2.490000e-28 137.0
12 TraesCS2A01G575700 chr2B 88.000 75 1 6 620 694 790693426 790693492 1.180000e-11 82.4
13 TraesCS2A01G575700 chrUn 80.153 131 22 3 4766 4895 180563934 180563807 1.520000e-15 95.3
14 TraesCS2A01G575700 chr7A 81.818 110 17 3 4959 5068 218232064 218231958 7.060000e-14 89.8
15 TraesCS2A01G575700 chr5A 77.852 149 25 8 4760 4903 442018696 442018841 9.130000e-13 86.1
16 TraesCS2A01G575700 chr6B 77.857 140 27 4 4765 4901 131684634 131684496 3.280000e-12 84.2
17 TraesCS2A01G575700 chr7B 100.000 36 0 0 3589 3624 714081921 714081886 3.310000e-07 67.6


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 TraesCS2A01G575700 chr2A 770103608 770108726 5118 False 9454.000000 9454 100.000000 1 5119 1 chr2A.!!$F1 5118
1 TraesCS2A01G575700 chr2D 644830094 644835291 5197 True 3061.000000 5156 91.207500 281 5119 2 chr2D.!!$R1 4838
2 TraesCS2A01G575700 chr2B 790692813 790701560 8747 False 620.377778 2211 88.409444 47 5119 9 chr2B.!!$F1 5072

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
197 198 0.034476 GATGCATCCATCTGCCTCGA 59.966 55.0 16.23 0.0 43.62 4.04 F
271 279 0.179056 TTCATCGCCGGGGAGAAATC 60.179 55.0 26.38 0.0 0.00 2.17 F
1203 1334 0.262285 ACCTGTACCTAGCTCCTCCC 59.738 60.0 0.00 0.0 0.00 4.30 F
2733 3154 0.323725 GCTTTCCCAATGGAGCCAGA 60.324 55.0 0.00 0.0 43.07 3.86 F
2783 3204 0.025513 GTCGAATGCTCACACGATGC 59.974 55.0 0.00 0.0 37.14 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2125 2352 0.536687 AGCCATGCCAATCGGATCTG 60.537 55.000 0.00 0.0 0.00 2.90 R
2199 2426 1.077787 CCGTTGCATTGAGCCCCTA 60.078 57.895 0.00 0.0 44.83 3.53 R
2783 3204 0.108041 AGGTGGCGTGTTTATACGGG 60.108 55.000 0.00 0.0 43.87 5.28 R
3635 4150 0.037605 CCGTGGTGGAGTAGTGGAAC 60.038 60.000 0.00 0.0 42.00 3.62 R
4761 7555 0.259647 TGCATTGGAGCTGGCCTTAT 59.740 50.000 3.32 0.0 34.99 1.73 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
25 26 7.803279 AAGTCTAGGTCAATTTTCGAAAAGT 57.197 32.000 25.87 21.77 0.00 2.66
26 27 7.190920 AGTCTAGGTCAATTTTCGAAAAGTG 57.809 36.000 33.74 33.74 43.19 3.16
27 28 6.990349 AGTCTAGGTCAATTTTCGAAAAGTGA 59.010 34.615 36.35 36.35 46.66 3.41
33 34 6.567769 TCAATTTTCGAAAAGTGAACTTGC 57.432 33.333 37.27 0.00 46.10 4.01
34 35 6.096036 TCAATTTTCGAAAAGTGAACTTGCA 58.904 32.000 37.27 21.23 46.10 4.08
35 36 6.253298 TCAATTTTCGAAAAGTGAACTTGCAG 59.747 34.615 37.27 17.99 46.10 4.41
36 37 4.695217 TTTCGAAAAGTGAACTTGCAGT 57.305 36.364 8.44 0.00 36.12 4.40
37 38 4.695217 TTCGAAAAGTGAACTTGCAGTT 57.305 36.364 0.00 1.82 41.95 3.16
38 39 4.695217 TCGAAAAGTGAACTTGCAGTTT 57.305 36.364 0.00 0.00 38.80 2.66
40 41 5.465935 TCGAAAAGTGAACTTGCAGTTTTT 58.534 33.333 10.22 0.00 46.07 1.94
41 42 5.571357 TCGAAAAGTGAACTTGCAGTTTTTC 59.429 36.000 10.22 1.19 46.07 2.29
42 43 5.496969 CGAAAAGTGAACTTGCAGTTTTTCG 60.497 40.000 19.55 19.55 46.07 3.46
43 44 4.695217 AAGTGAACTTGCAGTTTTTCGA 57.305 36.364 0.00 0.00 38.80 3.71
44 45 4.695217 AGTGAACTTGCAGTTTTTCGAA 57.305 36.364 0.00 0.00 38.80 3.71
45 46 5.054390 AGTGAACTTGCAGTTTTTCGAAA 57.946 34.783 6.47 6.47 38.80 3.46
48 49 2.450160 ACTTGCAGTTTTTCGAAAGCG 58.550 42.857 10.98 2.53 39.35 4.68
55 56 4.032355 CAGTTTTTCGAAAGCGCTTTGTA 58.968 39.130 38.09 22.75 37.46 2.41
60 61 2.268298 TCGAAAGCGCTTTGTAGGATC 58.732 47.619 38.09 21.19 37.46 3.36
71 72 5.628134 GCTTTGTAGGATCGGTAAAACTTG 58.372 41.667 0.00 0.00 0.00 3.16
75 76 5.717119 TGTAGGATCGGTAAAACTTGAGAC 58.283 41.667 0.00 0.00 0.00 3.36
81 82 6.801862 GGATCGGTAAAACTTGAGACAAAATG 59.198 38.462 0.00 0.00 0.00 2.32
83 84 7.090953 TCGGTAAAACTTGAGACAAAATGTT 57.909 32.000 0.00 0.00 0.00 2.71
95 96 6.767423 TGAGACAAAATGTTGACTGATTGAGA 59.233 34.615 5.28 0.00 39.41 3.27
99 100 7.143340 ACAAAATGTTGACTGATTGAGACATG 58.857 34.615 1.62 0.00 38.20 3.21
150 151 4.505566 GCCCATAAAGAGTGCATCCATCTA 60.506 45.833 0.00 0.00 0.00 1.98
151 152 5.243981 CCCATAAAGAGTGCATCCATCTAG 58.756 45.833 0.00 0.00 0.00 2.43
152 153 5.221803 CCCATAAAGAGTGCATCCATCTAGT 60.222 44.000 0.00 0.00 0.00 2.57
153 154 6.014242 CCCATAAAGAGTGCATCCATCTAGTA 60.014 42.308 0.00 0.00 0.00 1.82
155 156 8.099537 CCATAAAGAGTGCATCCATCTAGTATT 58.900 37.037 0.00 0.00 0.00 1.89
156 157 9.499479 CATAAAGAGTGCATCCATCTAGTATTT 57.501 33.333 0.00 0.00 0.00 1.40
157 158 7.798596 AAAGAGTGCATCCATCTAGTATTTG 57.201 36.000 0.00 0.00 0.00 2.32
159 160 4.392940 AGTGCATCCATCTAGTATTTGCC 58.607 43.478 0.00 0.00 0.00 4.52
160 161 4.103785 AGTGCATCCATCTAGTATTTGCCT 59.896 41.667 0.00 0.00 0.00 4.75
161 162 4.823989 GTGCATCCATCTAGTATTTGCCTT 59.176 41.667 0.00 0.00 0.00 4.35
162 163 5.300286 GTGCATCCATCTAGTATTTGCCTTT 59.700 40.000 0.00 0.00 0.00 3.11
163 164 5.893255 TGCATCCATCTAGTATTTGCCTTTT 59.107 36.000 0.00 0.00 0.00 2.27
164 165 6.380846 TGCATCCATCTAGTATTTGCCTTTTT 59.619 34.615 0.00 0.00 0.00 1.94
165 166 6.920210 GCATCCATCTAGTATTTGCCTTTTTC 59.080 38.462 0.00 0.00 0.00 2.29
166 167 7.201857 GCATCCATCTAGTATTTGCCTTTTTCT 60.202 37.037 0.00 0.00 0.00 2.52
167 168 8.689972 CATCCATCTAGTATTTGCCTTTTTCTT 58.310 33.333 0.00 0.00 0.00 2.52
168 169 8.650143 TCCATCTAGTATTTGCCTTTTTCTTT 57.350 30.769 0.00 0.00 0.00 2.52
169 170 9.088987 TCCATCTAGTATTTGCCTTTTTCTTTT 57.911 29.630 0.00 0.00 0.00 2.27
170 171 9.143631 CCATCTAGTATTTGCCTTTTTCTTTTG 57.856 33.333 0.00 0.00 0.00 2.44
171 172 9.912634 CATCTAGTATTTGCCTTTTTCTTTTGA 57.087 29.630 0.00 0.00 0.00 2.69
173 174 8.576442 TCTAGTATTTGCCTTTTTCTTTTGAGG 58.424 33.333 0.00 0.00 0.00 3.86
174 175 6.524734 AGTATTTGCCTTTTTCTTTTGAGGG 58.475 36.000 0.00 0.00 0.00 4.30
175 176 3.836365 TTGCCTTTTTCTTTTGAGGGG 57.164 42.857 0.00 0.00 0.00 4.79
176 177 3.039252 TGCCTTTTTCTTTTGAGGGGA 57.961 42.857 0.00 0.00 0.00 4.81
177 178 3.379452 TGCCTTTTTCTTTTGAGGGGAA 58.621 40.909 0.00 0.00 0.00 3.97
178 179 3.387699 TGCCTTTTTCTTTTGAGGGGAAG 59.612 43.478 0.00 0.00 0.00 3.46
179 180 3.641436 GCCTTTTTCTTTTGAGGGGAAGA 59.359 43.478 0.00 0.00 0.00 2.87
180 181 4.284490 GCCTTTTTCTTTTGAGGGGAAGAT 59.716 41.667 0.00 0.00 32.40 2.40
181 182 5.787380 CCTTTTTCTTTTGAGGGGAAGATG 58.213 41.667 0.00 0.00 32.40 2.90
182 183 4.871933 TTTTCTTTTGAGGGGAAGATGC 57.128 40.909 0.00 0.00 32.40 3.91
183 184 3.524095 TTCTTTTGAGGGGAAGATGCA 57.476 42.857 0.00 0.00 32.40 3.96
184 185 3.744940 TCTTTTGAGGGGAAGATGCAT 57.255 42.857 0.00 0.00 0.00 3.96
185 186 3.624777 TCTTTTGAGGGGAAGATGCATC 58.375 45.455 19.37 19.37 0.00 3.91
186 187 2.442236 TTTGAGGGGAAGATGCATCC 57.558 50.000 23.06 9.81 36.16 3.51
187 188 1.297968 TTGAGGGGAAGATGCATCCA 58.702 50.000 23.06 9.14 38.80 3.41
188 189 1.526315 TGAGGGGAAGATGCATCCAT 58.474 50.000 23.06 12.61 38.80 3.41
189 190 1.422781 TGAGGGGAAGATGCATCCATC 59.577 52.381 23.06 19.92 46.61 3.51
196 197 2.541288 GATGCATCCATCTGCCTCG 58.459 57.895 16.23 0.00 43.62 4.63
197 198 0.034476 GATGCATCCATCTGCCTCGA 59.966 55.000 16.23 0.00 43.62 4.04
198 199 0.691332 ATGCATCCATCTGCCTCGAT 59.309 50.000 0.00 0.00 41.58 3.59
199 200 0.034476 TGCATCCATCTGCCTCGATC 59.966 55.000 0.00 0.00 41.58 3.69
200 201 0.034476 GCATCCATCTGCCTCGATCA 59.966 55.000 0.00 0.00 36.10 2.92
213 214 4.335315 TGCCTCGATCATTTTGGTATCAAC 59.665 41.667 0.00 0.00 31.78 3.18
215 216 5.504665 GCCTCGATCATTTTGGTATCAACAG 60.505 44.000 0.00 0.00 31.78 3.16
218 219 7.012704 CCTCGATCATTTTGGTATCAACAGATT 59.987 37.037 0.00 0.00 31.78 2.40
271 279 0.179056 TTCATCGCCGGGGAGAAATC 60.179 55.000 26.38 0.00 0.00 2.17
297 356 3.426695 GCTTGTCGAAAACCATGATCCAG 60.427 47.826 0.00 0.00 0.00 3.86
385 444 8.629158 GCAAATCCATGTGTAATTAACTGGATA 58.371 33.333 14.75 0.00 41.44 2.59
398 457 7.645058 ATTAACTGGATAACAATTCCCACTG 57.355 36.000 0.00 0.00 31.87 3.66
457 521 0.886938 TCATTCAAAAGCGCCGGTGA 60.887 50.000 21.76 1.87 0.00 4.02
477 541 5.183904 GGTGAATGGAGTTAAAACATGCTCT 59.816 40.000 0.00 0.00 0.00 4.09
569 644 2.671177 CCTGCACGCACGAGAAAGG 61.671 63.158 0.00 0.00 0.00 3.11
570 645 1.664649 CTGCACGCACGAGAAAGGA 60.665 57.895 0.00 0.00 0.00 3.36
578 653 2.159310 CGCACGAGAAAGGAAGAGAGAT 60.159 50.000 0.00 0.00 0.00 2.75
659 763 2.364842 TCAGGCTCAGCTCCTCCC 60.365 66.667 0.00 0.00 0.00 4.30
660 764 3.847602 CAGGCTCAGCTCCTCCCG 61.848 72.222 0.00 0.00 0.00 5.14
780 886 1.394266 CCAAACCACAGCAACAGCCT 61.394 55.000 0.00 0.00 0.00 4.58
802 908 1.226974 GCGTCAGCCAGCTAATCGA 60.227 57.895 12.16 0.00 37.42 3.59
850 958 3.785859 GCCAGCCGTCATCTCCCA 61.786 66.667 0.00 0.00 0.00 4.37
908 1036 2.005960 GACCTCCATCACCTCGACCG 62.006 65.000 0.00 0.00 0.00 4.79
912 1040 2.697761 CCATCACCTCGACCGTCGT 61.698 63.158 19.89 0.00 41.35 4.34
913 1041 1.226323 CATCACCTCGACCGTCGTC 60.226 63.158 19.89 0.00 41.35 4.20
966 1094 3.458118 TGTCAACCAATCGAGGGGATAAT 59.542 43.478 11.75 0.00 34.08 1.28
967 1095 4.656575 TGTCAACCAATCGAGGGGATAATA 59.343 41.667 11.75 0.00 34.08 0.98
968 1096 5.309543 TGTCAACCAATCGAGGGGATAATAT 59.690 40.000 11.75 0.00 34.08 1.28
969 1097 6.499000 TGTCAACCAATCGAGGGGATAATATA 59.501 38.462 11.75 0.00 34.08 0.86
970 1098 7.016760 TGTCAACCAATCGAGGGGATAATATAA 59.983 37.037 11.75 0.00 34.08 0.98
981 1109 7.444183 CGAGGGGATAATATAAAGCAGACAAAA 59.556 37.037 0.00 0.00 0.00 2.44
982 1110 8.697507 AGGGGATAATATAAAGCAGACAAAAG 57.302 34.615 0.00 0.00 0.00 2.27
983 1111 7.231519 AGGGGATAATATAAAGCAGACAAAAGC 59.768 37.037 0.00 0.00 0.00 3.51
984 1112 7.014230 GGGGATAATATAAAGCAGACAAAAGCA 59.986 37.037 0.00 0.00 0.00 3.91
985 1113 8.078596 GGGATAATATAAAGCAGACAAAAGCAG 58.921 37.037 0.00 0.00 0.00 4.24
986 1114 8.840321 GGATAATATAAAGCAGACAAAAGCAGA 58.160 33.333 0.00 0.00 0.00 4.26
987 1115 9.875675 GATAATATAAAGCAGACAAAAGCAGAG 57.124 33.333 0.00 0.00 0.00 3.35
988 1116 6.690194 ATATAAAGCAGACAAAAGCAGAGG 57.310 37.500 0.00 0.00 0.00 3.69
989 1117 2.645838 AAGCAGACAAAAGCAGAGGA 57.354 45.000 0.00 0.00 0.00 3.71
990 1118 2.181954 AGCAGACAAAAGCAGAGGAG 57.818 50.000 0.00 0.00 0.00 3.69
1053 1181 1.172180 CGATGGTGGTGGTGCAGTTT 61.172 55.000 0.00 0.00 0.00 2.66
1188 1316 1.451067 ACTTCGTCGAGAGGTACCTG 58.549 55.000 22.10 5.09 37.41 4.00
1203 1334 0.262285 ACCTGTACCTAGCTCCTCCC 59.738 60.000 0.00 0.00 0.00 4.30
1220 1351 3.209410 CTCCCTCCATTTGATCCTTTCG 58.791 50.000 0.00 0.00 0.00 3.46
1282 1435 7.547019 TGCATTATATTCCGAAGCATCTAGAAG 59.453 37.037 0.00 0.00 0.00 2.85
1303 1456 2.653890 GTGCACACACATCATCACAAC 58.346 47.619 13.17 0.00 46.61 3.32
1316 1473 7.274033 CACATCATCACAACGCTTATTTTTCAT 59.726 33.333 0.00 0.00 0.00 2.57
1397 1558 7.773690 AGTTTGAGGTGAGCTTCTTTTACTAAA 59.226 33.333 0.00 0.00 0.00 1.85
1474 1638 5.794894 TGGGTCAAGTAGTTTCATTCTCTC 58.205 41.667 0.00 0.00 0.00 3.20
1502 1670 3.056607 ACCAATTAATTGAGCCAGTGCAC 60.057 43.478 26.32 9.40 40.14 4.57
1548 1716 2.164219 CCATGTTTTCCGATGTTCCCTG 59.836 50.000 0.00 0.00 0.00 4.45
1726 1911 4.054780 TGTGCTTCCGGAGTATGTTATC 57.945 45.455 3.34 0.00 0.00 1.75
1802 1990 3.535280 TGCATGCTACCTGATTAACGA 57.465 42.857 20.33 0.00 0.00 3.85
1806 1995 4.444720 GCATGCTACCTGATTAACGAGTAC 59.555 45.833 11.37 0.00 0.00 2.73
1809 1998 4.043073 GCTACCTGATTAACGAGTACAGC 58.957 47.826 0.00 0.00 0.00 4.40
1877 2066 9.838339 TTTGATACCCAAAACAAAATTACATGT 57.162 25.926 2.69 2.69 41.43 3.21
1908 2097 6.356556 TGACAAACTATATACTTGCATGCCT 58.643 36.000 16.68 0.00 0.00 4.75
1923 2112 4.097741 TGCATGCCTGTGTATTGGATTAAC 59.902 41.667 16.68 0.00 0.00 2.01
1949 2155 4.953940 TCCCTGCTGCTTTATTTGTTTT 57.046 36.364 0.00 0.00 0.00 2.43
1962 2168 7.224557 GCTTTATTTGTTTTGAGCAGGAAGAAA 59.775 33.333 0.00 0.00 0.00 2.52
1963 2169 9.097257 CTTTATTTGTTTTGAGCAGGAAGAAAA 57.903 29.630 0.00 0.00 0.00 2.29
2076 2292 9.692749 TGTTGTTGTTGTTGTTTCATTTTACTA 57.307 25.926 0.00 0.00 0.00 1.82
2125 2352 3.409026 TGAGAAGGAGAGCAAAAGGTC 57.591 47.619 0.00 0.00 0.00 3.85
2220 2577 1.971167 GGGCTCAATGCAACGGTGA 60.971 57.895 3.55 0.00 45.15 4.02
2361 2760 1.586154 GGCACAACCAACTGATCCGG 61.586 60.000 0.00 0.00 38.86 5.14
2391 2790 1.227674 CCCCTGCCGCTAGCTTTAG 60.228 63.158 13.93 7.51 44.23 1.85
2392 2791 1.522569 CCCTGCCGCTAGCTTTAGT 59.477 57.895 13.93 0.00 44.23 2.24
2468 2880 0.729116 CAAACCGTGCATGGAGCTAG 59.271 55.000 31.74 11.88 45.94 3.42
2484 2896 2.159503 AGCTAGTCGTCTGTGAACATCG 60.160 50.000 0.00 3.03 0.00 3.84
2507 2919 2.434843 CCTCGTGCTGCCCCTGATA 61.435 63.158 0.00 0.00 0.00 2.15
2510 2922 1.221840 CGTGCTGCCCCTGATACTT 59.778 57.895 0.00 0.00 0.00 2.24
2528 2940 2.887152 ACTTGCTTTGTCAACTCCATCC 59.113 45.455 0.00 0.00 0.00 3.51
2529 2941 2.655090 TGCTTTGTCAACTCCATCCA 57.345 45.000 0.00 0.00 0.00 3.41
2534 2946 2.787473 TGTCAACTCCATCCATCACC 57.213 50.000 0.00 0.00 0.00 4.02
2535 2947 1.281867 TGTCAACTCCATCCATCACCC 59.718 52.381 0.00 0.00 0.00 4.61
2549 2961 2.167219 CACCCTACTCACGCATGCG 61.167 63.158 36.79 36.79 46.03 4.73
2550 2962 3.264897 CCCTACTCACGCATGCGC 61.265 66.667 38.15 0.00 44.19 6.09
2695 3112 1.466024 CGCACGCCTATAGCTAGCTAC 60.466 57.143 26.41 12.75 40.39 3.58
2696 3113 1.540267 GCACGCCTATAGCTAGCTACA 59.460 52.381 26.41 14.95 40.39 2.74
2697 3114 2.414824 GCACGCCTATAGCTAGCTACAG 60.415 54.545 26.41 23.56 40.39 2.74
2698 3115 2.814919 CACGCCTATAGCTAGCTACAGT 59.185 50.000 26.41 17.39 40.39 3.55
2699 3116 4.001652 CACGCCTATAGCTAGCTACAGTA 58.998 47.826 26.41 14.04 40.39 2.74
2704 3121 7.112212 GCCTATAGCTAGCTACAGTAGCACC 62.112 52.000 30.20 18.59 46.24 5.01
2711 3132 1.683790 CTACAGTAGCACCGCGTTGC 61.684 60.000 22.00 22.00 43.34 4.17
2732 3153 0.612732 TGCTTTCCCAATGGAGCCAG 60.613 55.000 0.00 0.00 43.07 4.85
2733 3154 0.323725 GCTTTCCCAATGGAGCCAGA 60.324 55.000 0.00 0.00 43.07 3.86
2734 3155 1.760192 CTTTCCCAATGGAGCCAGAG 58.240 55.000 0.00 0.00 43.07 3.35
2735 3156 0.323725 TTTCCCAATGGAGCCAGAGC 60.324 55.000 0.00 0.00 43.07 4.09
2736 3157 2.123982 CCCAATGGAGCCAGAGCC 60.124 66.667 0.00 0.00 41.25 4.70
2737 3158 2.679092 CCAATGGAGCCAGAGCCA 59.321 61.111 0.00 0.00 41.25 4.75
2738 3159 1.751927 CCAATGGAGCCAGAGCCAC 60.752 63.158 0.00 0.00 41.25 5.01
2743 3164 3.071206 GAGCCAGAGCCACCTCGA 61.071 66.667 0.00 0.00 43.05 4.04
2771 3192 0.561593 CATCGTCGTCGTGTCGAATG 59.438 55.000 1.33 0.00 41.26 2.67
2772 3193 1.132199 ATCGTCGTCGTGTCGAATGC 61.132 55.000 1.33 0.00 41.26 3.56
2773 3194 1.796355 CGTCGTCGTGTCGAATGCT 60.796 57.895 0.00 0.00 41.47 3.79
2781 3202 1.350193 GTGTCGAATGCTCACACGAT 58.650 50.000 0.00 0.00 37.14 3.73
2783 3204 0.025513 GTCGAATGCTCACACGATGC 59.974 55.000 0.00 0.00 37.14 3.91
2797 3218 0.231279 CGATGCCCGTATAAACACGC 59.769 55.000 0.00 0.00 40.59 5.34
2817 3238 2.632512 GCCACCTTCTTTTCCAATGGAA 59.367 45.455 11.23 11.23 40.27 3.53
2818 3239 3.261643 GCCACCTTCTTTTCCAATGGAAT 59.738 43.478 16.30 0.00 41.71 3.01
2819 3240 4.824289 CCACCTTCTTTTCCAATGGAATG 58.176 43.478 16.30 11.76 41.71 2.67
2821 3242 3.261643 ACCTTCTTTTCCAATGGAATGGC 59.738 43.478 16.30 0.00 41.71 4.40
2822 3243 3.261390 CCTTCTTTTCCAATGGAATGGCA 59.739 43.478 16.30 0.00 41.71 4.92
2823 3244 4.080751 CCTTCTTTTCCAATGGAATGGCAT 60.081 41.667 16.30 0.00 41.71 4.40
2827 3248 1.487300 TCCAATGGAATGGCATGGTG 58.513 50.000 0.00 0.00 40.46 4.17
2828 3249 1.196911 CCAATGGAATGGCATGGTGT 58.803 50.000 0.00 0.00 32.78 4.16
2829 3250 2.024560 TCCAATGGAATGGCATGGTGTA 60.025 45.455 0.00 0.00 40.46 2.90
2834 3271 3.550820 TGGAATGGCATGGTGTATGTAC 58.449 45.455 0.00 0.00 39.08 2.90
2843 3280 4.413969 CATGGTGTATGTACGTACGTCAA 58.586 43.478 26.53 14.83 31.92 3.18
2844 3281 3.820689 TGGTGTATGTACGTACGTCAAC 58.179 45.455 26.53 18.86 0.00 3.18
2853 3298 5.153513 TGTACGTACGTCAACTTACATTCC 58.846 41.667 26.53 0.00 31.42 3.01
2856 3301 5.232463 ACGTACGTCAACTTACATTCCATT 58.768 37.500 16.72 0.00 0.00 3.16
2859 3304 5.356882 ACGTCAACTTACATTCCATTGTG 57.643 39.130 0.00 0.00 0.00 3.33
2861 3306 5.179368 ACGTCAACTTACATTCCATTGTGAG 59.821 40.000 0.00 0.00 38.71 3.51
2874 3319 3.503748 CCATTGTGAGGTTTCTTGGACTC 59.496 47.826 0.00 0.00 0.00 3.36
2875 3320 4.392940 CATTGTGAGGTTTCTTGGACTCT 58.607 43.478 0.00 0.00 0.00 3.24
2877 3322 4.602340 TGTGAGGTTTCTTGGACTCTAC 57.398 45.455 0.00 0.00 0.00 2.59
2883 3328 6.766467 TGAGGTTTCTTGGACTCTACTTTTTC 59.234 38.462 0.00 0.00 0.00 2.29
2885 3330 6.768381 AGGTTTCTTGGACTCTACTTTTTCTG 59.232 38.462 0.00 0.00 0.00 3.02
2913 3373 2.716864 GCCTAGCTCGTCTCGTCC 59.283 66.667 0.00 0.00 0.00 4.79
2914 3374 2.113433 GCCTAGCTCGTCTCGTCCA 61.113 63.158 0.00 0.00 0.00 4.02
2915 3375 1.654954 GCCTAGCTCGTCTCGTCCAA 61.655 60.000 0.00 0.00 0.00 3.53
2926 3386 3.972502 CGTCTCGTCCAAAATTTTCAACC 59.027 43.478 0.00 0.00 0.00 3.77
2934 3394 3.489398 CCAAAATTTTCAACCCGTCGTCA 60.489 43.478 0.00 0.00 0.00 4.35
2957 3417 1.736645 CGTTGCACGTCCCTAGGTG 60.737 63.158 8.29 0.00 42.96 4.00
2991 3485 6.908870 TTAATGGTCACGATGAAGAAGATG 57.091 37.500 0.00 0.00 0.00 2.90
3035 3533 0.171903 GTGTCGTGCACCTACCGTAT 59.828 55.000 12.15 0.00 42.10 3.06
3036 3534 1.401552 GTGTCGTGCACCTACCGTATA 59.598 52.381 12.15 0.00 42.10 1.47
3037 3535 1.401552 TGTCGTGCACCTACCGTATAC 59.598 52.381 12.15 0.00 0.00 1.47
3070 3571 4.138817 CAAAAATGCGTAGTACGTGTGAC 58.861 43.478 22.81 7.36 44.73 3.67
3071 3572 3.293311 AAATGCGTAGTACGTGTGACT 57.707 42.857 22.81 0.00 44.73 3.41
3083 3584 1.201661 CGTGTGACTGATTACGTTGCG 60.202 52.381 0.00 0.00 0.00 4.85
3088 3590 3.122948 GTGACTGATTACGTTGCGTTGAT 59.877 43.478 0.00 0.00 41.54 2.57
3089 3591 3.122780 TGACTGATTACGTTGCGTTGATG 59.877 43.478 0.00 0.00 41.54 3.07
3090 3592 2.159707 ACTGATTACGTTGCGTTGATGC 60.160 45.455 0.00 0.00 41.54 3.91
3091 3593 1.201866 TGATTACGTTGCGTTGATGCG 60.202 47.619 0.00 0.00 41.54 4.73
3092 3594 0.096281 ATTACGTTGCGTTGATGCGG 59.904 50.000 0.00 0.00 41.54 5.69
3093 3595 2.501607 TTACGTTGCGTTGATGCGGC 62.502 55.000 0.00 0.00 41.54 6.53
3115 3630 1.933734 GCATGTGCATGACGCGATA 59.066 52.632 15.93 0.02 46.97 2.92
3116 3631 0.514255 GCATGTGCATGACGCGATAT 59.486 50.000 15.93 3.08 46.97 1.63
3117 3632 1.726248 GCATGTGCATGACGCGATATA 59.274 47.619 15.93 0.00 46.97 0.86
3118 3633 2.349580 GCATGTGCATGACGCGATATAT 59.650 45.455 15.93 0.00 46.97 0.86
3119 3634 3.551485 GCATGTGCATGACGCGATATATA 59.449 43.478 15.93 0.00 46.97 0.86
3133 3648 4.450667 CGATATATAGAGCGCACGAGATC 58.549 47.826 11.47 6.12 0.00 2.75
3142 3657 1.515172 CGCACGAGATCGATCGATAC 58.485 55.000 29.45 23.10 45.56 2.24
3143 3658 1.136336 CGCACGAGATCGATCGATACA 60.136 52.381 29.45 3.29 45.56 2.29
3150 3665 5.352846 ACGAGATCGATCGATACATTCTCAT 59.647 40.000 30.33 20.92 45.56 2.90
3154 3669 8.443953 AGATCGATCGATACATTCTCATCATA 57.556 34.615 29.45 0.00 34.60 2.15
3155 3670 9.065798 AGATCGATCGATACATTCTCATCATAT 57.934 33.333 29.45 2.96 34.60 1.78
3180 3695 6.352682 TGCAAATGTACAATATACACGTCC 57.647 37.500 0.00 0.00 0.00 4.79
3181 3696 5.005875 TGCAAATGTACAATATACACGTCCG 59.994 40.000 0.00 0.00 0.00 4.79
3183 3698 6.198778 GCAAATGTACAATATACACGTCCGTA 59.801 38.462 0.00 0.00 0.00 4.02
3184 3699 7.095940 GCAAATGTACAATATACACGTCCGTAT 60.096 37.037 0.00 4.23 36.13 3.06
3185 3700 8.422457 CAAATGTACAATATACACGTCCGTATC 58.578 37.037 0.00 0.00 34.03 2.24
3186 3701 5.678921 TGTACAATATACACGTCCGTATCG 58.321 41.667 2.10 0.00 34.03 2.92
3204 3719 3.066291 TCGGTATTGACTGGTTGCAAT 57.934 42.857 0.59 0.00 38.24 3.56
3227 3742 1.909459 TTTCATGCAGGGGCTCGCTA 61.909 55.000 0.00 0.00 41.91 4.26
3263 3778 2.125552 TCCGGCATGAAGCTCACG 60.126 61.111 0.00 0.00 44.79 4.35
3269 3784 2.507102 ATGAAGCTCACGTCCGCG 60.507 61.111 0.00 0.00 44.93 6.46
3390 3905 4.263572 CCAAGGTCACCGGCACCA 62.264 66.667 22.25 0.00 36.23 4.17
3395 3910 2.672996 GTCACCGGCACCATGCTT 60.673 61.111 0.00 0.00 44.28 3.91
3587 4102 2.113986 ACCGGCAGCTGCTTCTTT 59.886 55.556 35.82 14.84 41.70 2.52
3590 4105 1.098050 CCGGCAGCTGCTTCTTTTAT 58.902 50.000 35.82 0.00 41.70 1.40
3776 4291 2.968206 GTCCTCTACACCGGCGTT 59.032 61.111 0.00 0.00 0.00 4.84
4043 4558 3.770040 ACCGAGCTGCCGCACATA 61.770 61.111 2.05 0.00 39.10 2.29
4218 4733 3.102972 TCAGGAAAGGATGGACAGAGAG 58.897 50.000 0.00 0.00 0.00 3.20
4279 4797 0.534203 GAGCTCGTTTGTTGGGTGGA 60.534 55.000 0.00 0.00 0.00 4.02
4308 4828 5.695816 ACTCGGTTAGATCTAGCGTAGTTAG 59.304 44.000 17.29 12.07 42.87 2.34
4319 4839 1.471153 GCGTAGTTAGAAGGAGTGGCC 60.471 57.143 0.00 0.00 0.00 5.36
4340 4860 3.260740 CTCTCTGATTCTGTTGGTGCTC 58.739 50.000 0.00 0.00 0.00 4.26
4402 4922 4.452825 ACTTCAGCAGGATGAGATGAATG 58.547 43.478 0.00 0.00 39.69 2.67
4403 4923 3.487120 TCAGCAGGATGAGATGAATGG 57.513 47.619 0.00 0.00 39.69 3.16
4441 4963 7.940178 AATTTCGGACACAAAATCCTTTTAC 57.060 32.000 0.00 0.00 33.70 2.01
4688 7482 5.705609 TTGGTCCAAGTTAGAAAGCATTC 57.294 39.130 0.00 0.00 35.70 2.67
4777 7571 3.951563 TGTTATAAGGCCAGCTCCAAT 57.048 42.857 5.01 0.00 0.00 3.16
4798 7592 0.032403 CACGACCCCAAACAGACGTA 59.968 55.000 0.00 0.00 32.89 3.57
4883 7677 4.539083 TGGCCGTGCACTCAACGT 62.539 61.111 16.19 0.00 0.00 3.99
4921 7715 1.134175 ACCCGCCTGAAATATTTTGCG 59.866 47.619 22.91 22.91 41.51 4.85
4928 7722 5.052172 CGCCTGAAATATTTTGCGAATGAAG 60.052 40.000 24.38 5.77 44.32 3.02
4955 7749 1.523711 CCGCGGCCATAGTTCATGT 60.524 57.895 14.67 0.00 32.21 3.21
5022 7819 2.716424 TGATCAACCCCCAAGTTCTCTT 59.284 45.455 0.00 0.00 0.00 2.85
5047 7844 3.767630 AACAAAGCCAGCGGTCGGT 62.768 57.895 5.26 0.00 0.00 4.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.770828 CACTTTTCGAAAATTGACCTAGACTTA 58.229 33.333 27.62 2.06 32.28 2.24
1 2 7.497909 TCACTTTTCGAAAATTGACCTAGACTT 59.502 33.333 29.19 0.22 34.12 3.01
2 3 6.990349 TCACTTTTCGAAAATTGACCTAGACT 59.010 34.615 29.19 0.82 34.12 3.24
3 4 7.186021 TCACTTTTCGAAAATTGACCTAGAC 57.814 36.000 29.19 0.00 34.12 2.59
4 5 7.497909 AGTTCACTTTTCGAAAATTGACCTAGA 59.502 33.333 31.41 19.71 37.32 2.43
5 6 7.639945 AGTTCACTTTTCGAAAATTGACCTAG 58.360 34.615 31.41 17.96 37.32 3.02
6 7 7.562454 AGTTCACTTTTCGAAAATTGACCTA 57.438 32.000 31.41 20.26 37.32 3.08
7 8 6.451064 AGTTCACTTTTCGAAAATTGACCT 57.549 33.333 31.41 28.28 37.32 3.85
8 9 6.507929 GCAAGTTCACTTTTCGAAAATTGACC 60.508 38.462 31.41 26.95 37.32 4.02
9 10 6.034470 TGCAAGTTCACTTTTCGAAAATTGAC 59.966 34.615 31.41 25.95 37.32 3.18
10 11 6.096036 TGCAAGTTCACTTTTCGAAAATTGA 58.904 32.000 29.19 29.19 36.28 2.57
11 12 6.329838 TGCAAGTTCACTTTTCGAAAATTG 57.670 33.333 26.39 26.39 33.11 2.32
12 13 6.573617 CTGCAAGTTCACTTTTCGAAAATT 57.426 33.333 22.73 15.15 33.11 1.82
28 29 2.450160 CGCTTTCGAAAAACTGCAAGT 58.550 42.857 12.41 0.00 45.13 3.16
29 30 1.187921 GCGCTTTCGAAAAACTGCAAG 59.812 47.619 12.41 0.00 37.81 4.01
30 31 1.196200 GCGCTTTCGAAAAACTGCAA 58.804 45.000 12.41 0.00 38.10 4.08
31 32 0.380378 AGCGCTTTCGAAAAACTGCA 59.620 45.000 12.41 0.00 38.10 4.41
32 33 1.477105 AAGCGCTTTCGAAAAACTGC 58.523 45.000 18.98 10.59 38.10 4.40
33 34 2.851824 ACAAAGCGCTTTCGAAAAACTG 59.148 40.909 31.63 20.03 38.10 3.16
34 35 3.145212 ACAAAGCGCTTTCGAAAAACT 57.855 38.095 31.63 5.84 38.10 2.66
35 36 3.420904 CCTACAAAGCGCTTTCGAAAAAC 59.579 43.478 31.63 6.30 38.10 2.43
36 37 3.312973 TCCTACAAAGCGCTTTCGAAAAA 59.687 39.130 31.63 13.42 38.10 1.94
37 38 2.873472 TCCTACAAAGCGCTTTCGAAAA 59.127 40.909 31.63 14.96 38.10 2.29
38 39 2.485903 TCCTACAAAGCGCTTTCGAAA 58.514 42.857 31.63 15.90 38.10 3.46
39 40 2.157834 TCCTACAAAGCGCTTTCGAA 57.842 45.000 31.63 18.26 38.10 3.71
40 41 2.268298 GATCCTACAAAGCGCTTTCGA 58.732 47.619 31.63 22.64 38.10 3.71
41 42 1.005975 CGATCCTACAAAGCGCTTTCG 60.006 52.381 31.63 25.00 39.07 3.46
42 43 1.327764 CCGATCCTACAAAGCGCTTTC 59.672 52.381 31.63 17.91 0.00 2.62
43 44 1.338769 ACCGATCCTACAAAGCGCTTT 60.339 47.619 29.11 29.11 0.00 3.51
44 45 0.249398 ACCGATCCTACAAAGCGCTT 59.751 50.000 18.98 18.98 0.00 4.68
45 46 1.108776 TACCGATCCTACAAAGCGCT 58.891 50.000 2.64 2.64 0.00 5.92
48 49 5.410439 TCAAGTTTTACCGATCCTACAAAGC 59.590 40.000 0.00 0.00 0.00 3.51
55 56 4.884668 TGTCTCAAGTTTTACCGATCCT 57.115 40.909 0.00 0.00 0.00 3.24
60 61 6.970043 TCAACATTTTGTCTCAAGTTTTACCG 59.030 34.615 0.00 0.00 34.02 4.02
71 72 7.074502 GTCTCAATCAGTCAACATTTTGTCTC 58.925 38.462 0.00 0.00 29.77 3.36
75 76 7.364970 TCATGTCTCAATCAGTCAACATTTTG 58.635 34.615 0.00 0.00 0.00 2.44
81 82 6.675002 GCTTGATCATGTCTCAATCAGTCAAC 60.675 42.308 10.05 0.00 32.50 3.18
83 84 4.874396 GCTTGATCATGTCTCAATCAGTCA 59.126 41.667 10.05 0.00 32.50 3.41
95 96 2.224719 GCATCCCTAGGCTTGATCATGT 60.225 50.000 2.05 0.00 0.00 3.21
99 100 2.434428 CATGCATCCCTAGGCTTGATC 58.566 52.381 2.05 0.00 39.22 2.92
129 130 5.862845 ACTAGATGGATGCACTCTTTATGG 58.137 41.667 0.00 0.00 0.00 2.74
150 151 6.464322 CCCCTCAAAAGAAAAAGGCAAATACT 60.464 38.462 0.00 0.00 0.00 2.12
151 152 5.700832 CCCCTCAAAAGAAAAAGGCAAATAC 59.299 40.000 0.00 0.00 0.00 1.89
152 153 5.604650 TCCCCTCAAAAGAAAAAGGCAAATA 59.395 36.000 0.00 0.00 0.00 1.40
153 154 4.411869 TCCCCTCAAAAGAAAAAGGCAAAT 59.588 37.500 0.00 0.00 0.00 2.32
155 156 3.379452 TCCCCTCAAAAGAAAAAGGCAA 58.621 40.909 0.00 0.00 0.00 4.52
156 157 3.039252 TCCCCTCAAAAGAAAAAGGCA 57.961 42.857 0.00 0.00 0.00 4.75
157 158 3.641436 TCTTCCCCTCAAAAGAAAAAGGC 59.359 43.478 0.00 0.00 0.00 4.35
159 160 5.221501 TGCATCTTCCCCTCAAAAGAAAAAG 60.222 40.000 0.00 0.00 35.29 2.27
160 161 4.653341 TGCATCTTCCCCTCAAAAGAAAAA 59.347 37.500 0.00 0.00 35.29 1.94
161 162 4.222336 TGCATCTTCCCCTCAAAAGAAAA 58.778 39.130 0.00 0.00 35.29 2.29
162 163 3.843422 TGCATCTTCCCCTCAAAAGAAA 58.157 40.909 0.00 0.00 35.29 2.52
163 164 3.524095 TGCATCTTCCCCTCAAAAGAA 57.476 42.857 0.00 0.00 35.29 2.52
164 165 3.624777 GATGCATCTTCCCCTCAAAAGA 58.375 45.455 19.70 0.00 36.05 2.52
165 166 2.692041 GGATGCATCTTCCCCTCAAAAG 59.308 50.000 25.28 0.00 0.00 2.27
166 167 2.042842 TGGATGCATCTTCCCCTCAAAA 59.957 45.455 25.28 0.00 31.87 2.44
167 168 1.640149 TGGATGCATCTTCCCCTCAAA 59.360 47.619 25.28 0.00 31.87 2.69
168 169 1.297968 TGGATGCATCTTCCCCTCAA 58.702 50.000 25.28 0.00 31.87 3.02
169 170 1.422781 GATGGATGCATCTTCCCCTCA 59.577 52.381 25.28 13.51 31.87 3.86
170 171 1.704070 AGATGGATGCATCTTCCCCTC 59.296 52.381 22.75 12.12 38.67 4.30
171 172 1.424302 CAGATGGATGCATCTTCCCCT 59.576 52.381 25.46 12.75 39.69 4.79
172 173 1.906990 CAGATGGATGCATCTTCCCC 58.093 55.000 25.46 10.42 39.69 4.81
173 174 1.245732 GCAGATGGATGCATCTTCCC 58.754 55.000 25.46 13.72 45.77 3.97
181 182 0.034476 TGATCGAGGCAGATGGATGC 59.966 55.000 0.19 0.00 45.74 3.91
182 183 2.764439 ATGATCGAGGCAGATGGATG 57.236 50.000 0.19 0.00 0.00 3.51
183 184 3.784511 AAATGATCGAGGCAGATGGAT 57.215 42.857 0.19 0.00 0.00 3.41
184 185 3.208594 CAAAATGATCGAGGCAGATGGA 58.791 45.455 0.19 0.00 0.00 3.41
185 186 2.292569 CCAAAATGATCGAGGCAGATGG 59.707 50.000 0.19 0.00 0.00 3.51
186 187 2.947652 ACCAAAATGATCGAGGCAGATG 59.052 45.455 0.19 0.00 0.00 2.90
187 188 3.287867 ACCAAAATGATCGAGGCAGAT 57.712 42.857 0.00 0.00 0.00 2.90
188 189 2.787473 ACCAAAATGATCGAGGCAGA 57.213 45.000 0.00 0.00 0.00 4.26
189 190 4.129380 TGATACCAAAATGATCGAGGCAG 58.871 43.478 0.00 0.00 0.00 4.85
190 191 4.149511 TGATACCAAAATGATCGAGGCA 57.850 40.909 0.00 0.00 0.00 4.75
191 192 4.335315 TGTTGATACCAAAATGATCGAGGC 59.665 41.667 0.00 0.00 33.49 4.70
192 193 5.817296 TCTGTTGATACCAAAATGATCGAGG 59.183 40.000 0.00 0.00 33.49 4.63
193 194 6.908870 TCTGTTGATACCAAAATGATCGAG 57.091 37.500 0.00 0.00 33.49 4.04
194 195 7.864108 AATCTGTTGATACCAAAATGATCGA 57.136 32.000 0.00 0.00 33.49 3.59
245 253 2.685897 CTCCCCGGCGATGAATTAAAAA 59.314 45.455 9.30 0.00 0.00 1.94
249 257 1.124780 TTCTCCCCGGCGATGAATTA 58.875 50.000 9.30 0.00 0.00 1.40
261 269 0.253327 ACAAGCGAGGATTTCTCCCC 59.747 55.000 0.00 0.00 43.21 4.81
275 283 2.487762 TGGATCATGGTTTTCGACAAGC 59.512 45.455 6.56 6.56 0.00 4.01
297 356 3.607542 CGTTGTCGGTTTCCCATGTAAAC 60.608 47.826 10.84 10.84 36.34 2.01
385 444 2.105821 TCTTCCGTCAGTGGGAATTGTT 59.894 45.455 1.80 0.00 42.39 2.83
386 445 1.697432 TCTTCCGTCAGTGGGAATTGT 59.303 47.619 1.80 0.00 42.39 2.71
457 521 4.768968 AGCAGAGCATGTTTTAACTCCATT 59.231 37.500 0.00 0.00 0.00 3.16
569 644 6.293407 CCACGATTGTCTCTCTATCTCTCTTC 60.293 46.154 0.00 0.00 0.00 2.87
570 645 5.530915 CCACGATTGTCTCTCTATCTCTCTT 59.469 44.000 0.00 0.00 0.00 2.85
578 653 2.094700 GCACACCACGATTGTCTCTCTA 60.095 50.000 0.00 0.00 0.00 2.43
659 763 3.131223 AGGTACATATATAGGCTGCAGCG 59.869 47.826 31.19 17.47 43.26 5.18
660 764 4.437239 CAGGTACATATATAGGCTGCAGC 58.563 47.826 30.88 30.88 41.14 5.25
730 834 3.775654 GTGGAGGGAGGCGAGGTG 61.776 72.222 0.00 0.00 0.00 4.00
737 841 4.787280 AGAGGCGGTGGAGGGAGG 62.787 72.222 0.00 0.00 0.00 4.30
739 843 4.779733 GGAGAGGCGGTGGAGGGA 62.780 72.222 0.00 0.00 0.00 4.20
780 886 0.174845 ATTAGCTGGCTGACGCGTTA 59.825 50.000 15.53 8.86 36.88 3.18
841 949 0.972134 GGCGAGATGATGGGAGATGA 59.028 55.000 0.00 0.00 0.00 2.92
846 954 1.462043 ATGGGGCGAGATGATGGGA 60.462 57.895 0.00 0.00 0.00 4.37
850 958 1.539560 CGGAGATGGGGCGAGATGAT 61.540 60.000 0.00 0.00 0.00 2.45
886 994 0.323087 TCGAGGTGATGGAGGTCGAA 60.323 55.000 0.00 0.00 36.76 3.71
908 1036 4.039703 TGATTAATTGGACGATCGACGAC 58.960 43.478 24.34 9.00 45.77 4.34
912 1040 4.566004 GGGATGATTAATTGGACGATCGA 58.434 43.478 24.34 0.00 0.00 3.59
913 1041 3.367932 CGGGATGATTAATTGGACGATCG 59.632 47.826 14.88 14.88 0.00 3.69
966 1094 5.804639 TCCTCTGCTTTTGTCTGCTTTATA 58.195 37.500 0.00 0.00 0.00 0.98
967 1095 4.655963 TCCTCTGCTTTTGTCTGCTTTAT 58.344 39.130 0.00 0.00 0.00 1.40
968 1096 4.067896 CTCCTCTGCTTTTGTCTGCTTTA 58.932 43.478 0.00 0.00 0.00 1.85
969 1097 2.883386 CTCCTCTGCTTTTGTCTGCTTT 59.117 45.455 0.00 0.00 0.00 3.51
970 1098 2.502295 CTCCTCTGCTTTTGTCTGCTT 58.498 47.619 0.00 0.00 0.00 3.91
981 1109 1.522917 TTCCCTCCTCCTCCTCTGCT 61.523 60.000 0.00 0.00 0.00 4.24
982 1110 0.399806 ATTCCCTCCTCCTCCTCTGC 60.400 60.000 0.00 0.00 0.00 4.26
983 1111 1.422531 CATTCCCTCCTCCTCCTCTG 58.577 60.000 0.00 0.00 0.00 3.35
984 1112 0.267356 CCATTCCCTCCTCCTCCTCT 59.733 60.000 0.00 0.00 0.00 3.69
985 1113 0.766288 CCCATTCCCTCCTCCTCCTC 60.766 65.000 0.00 0.00 0.00 3.71
986 1114 1.319799 CCCATTCCCTCCTCCTCCT 59.680 63.158 0.00 0.00 0.00 3.69
987 1115 2.456443 GCCCATTCCCTCCTCCTCC 61.456 68.421 0.00 0.00 0.00 4.30
988 1116 2.812619 CGCCCATTCCCTCCTCCTC 61.813 68.421 0.00 0.00 0.00 3.71
989 1117 2.770048 CGCCCATTCCCTCCTCCT 60.770 66.667 0.00 0.00 0.00 3.69
990 1118 3.090532 ACGCCCATTCCCTCCTCC 61.091 66.667 0.00 0.00 0.00 4.30
1125 1253 1.217244 GGCGAAGAGGAAGCGGTAA 59.783 57.895 0.00 0.00 0.00 2.85
1188 1316 0.556747 TGGAGGGAGGAGCTAGGTAC 59.443 60.000 0.00 0.00 0.00 3.34
1203 1334 3.691118 TCTTGCGAAAGGATCAAATGGAG 59.309 43.478 2.54 0.00 0.00 3.86
1220 1351 3.197549 TGCAAGGGGGATTTTAATCTTGC 59.802 43.478 16.04 16.04 40.43 4.01
1282 1435 1.237533 TGTGATGATGTGTGTGCACC 58.762 50.000 15.69 6.37 44.65 5.01
1301 1454 5.525199 ACAACCGAATGAAAAATAAGCGTT 58.475 33.333 0.00 0.00 0.00 4.84
1303 1456 6.799925 ACTAACAACCGAATGAAAAATAAGCG 59.200 34.615 0.00 0.00 0.00 4.68
1397 1558 6.528321 TGATTCCTCGATGCTCTAATGATTT 58.472 36.000 0.00 0.00 0.00 2.17
1474 1638 6.366877 CACTGGCTCAATTAATTGGTTTCTTG 59.633 38.462 24.40 13.32 38.30 3.02
1502 1670 1.416813 GAGCGAGACAAGGACATGCG 61.417 60.000 0.00 0.00 0.00 4.73
1548 1716 2.561037 CCGGGTCAACACAAAGGGC 61.561 63.158 0.00 0.00 0.00 5.19
1726 1911 0.796312 AAGCATCTGCAAACGTACGG 59.204 50.000 21.06 2.64 45.16 4.02
1734 1919 7.628769 TGATAATAAAGTGAAGCATCTGCAA 57.371 32.000 4.79 0.00 45.16 4.08
1890 2079 5.296151 ACACAGGCATGCAAGTATATAGT 57.704 39.130 21.36 7.80 0.00 2.12
1908 2097 7.284489 GCAGGGAATTAGTTAATCCAATACACA 59.716 37.037 0.00 0.00 0.00 3.72
1923 2112 6.212888 ACAAATAAAGCAGCAGGGAATTAG 57.787 37.500 0.00 0.00 0.00 1.73
1949 2155 3.576078 TGGTTCTTTTCTTCCTGCTCA 57.424 42.857 0.00 0.00 0.00 4.26
1977 2183 3.596066 GAGCAGCAGGACTCGCCAA 62.596 63.158 0.00 0.00 40.02 4.52
2045 2261 6.279227 TGAAACAACAACAACAACAACAAG 57.721 33.333 0.00 0.00 0.00 3.16
2076 2292 1.615392 GGGAAGTGCAGTGAAAAGCAT 59.385 47.619 0.00 0.00 43.44 3.79
2083 2299 1.069090 GTCGTGGGAAGTGCAGTGA 59.931 57.895 0.00 0.00 0.00 3.41
2084 2300 2.310233 CGTCGTGGGAAGTGCAGTG 61.310 63.158 0.00 0.00 0.00 3.66
2125 2352 0.536687 AGCCATGCCAATCGGATCTG 60.537 55.000 0.00 0.00 0.00 2.90
2197 2424 1.718757 CGTTGCATTGAGCCCCTAGC 61.719 60.000 0.00 0.00 44.83 3.42
2199 2426 1.077787 CCGTTGCATTGAGCCCCTA 60.078 57.895 0.00 0.00 44.83 3.53
2200 2427 2.361610 CCGTTGCATTGAGCCCCT 60.362 61.111 0.00 0.00 44.83 4.79
2220 2577 4.078630 ACCTTGCATTGGGAGGGTATTATT 60.079 41.667 6.35 0.00 43.14 1.40
2361 2760 2.113986 CAGGGGATTCCATCGGGC 59.886 66.667 4.80 0.00 38.24 6.13
2391 2790 2.355197 ACTTTGTTTGGCAGGCAAAAC 58.645 42.857 22.84 18.67 39.59 2.43
2392 2791 2.777832 ACTTTGTTTGGCAGGCAAAA 57.222 40.000 22.84 6.93 32.64 2.44
2468 2880 0.975544 CGACGATGTTCACAGACGAC 59.024 55.000 13.60 8.29 35.08 4.34
2507 2919 2.887152 GGATGGAGTTGACAAAGCAAGT 59.113 45.455 0.00 0.00 34.28 3.16
2510 2922 2.655090 TGGATGGAGTTGACAAAGCA 57.345 45.000 0.00 0.00 0.00 3.91
2528 2940 1.575244 CATGCGTGAGTAGGGTGATG 58.425 55.000 0.00 0.00 0.00 3.07
2529 2941 0.179073 GCATGCGTGAGTAGGGTGAT 60.179 55.000 10.93 0.00 0.00 3.06
2549 2961 0.586319 TTGTAAGCAGTTGAGCACGC 59.414 50.000 0.00 0.00 36.85 5.34
2550 2962 3.228749 CAATTGTAAGCAGTTGAGCACG 58.771 45.455 0.00 0.00 42.61 5.34
2597 3012 4.520846 GCGTACGTGGCTGCATGC 62.521 66.667 17.90 11.82 41.94 4.06
2625 3041 2.722188 GACATAAATGCGCGCGCC 60.722 61.111 46.85 30.93 41.09 6.53
2695 3112 2.390599 ATGCAACGCGGTGCTACTG 61.391 57.895 44.21 12.02 45.17 2.74
2696 3113 2.047274 ATGCAACGCGGTGCTACT 60.047 55.556 44.21 28.27 45.17 2.57
2697 3114 2.098298 CATGCAACGCGGTGCTAC 59.902 61.111 44.21 21.30 45.17 3.58
2698 3115 3.798650 GCATGCAACGCGGTGCTA 61.799 61.111 44.21 31.97 45.17 3.49
2704 3121 2.504681 GGGAAAGCATGCAACGCG 60.505 61.111 21.98 3.53 0.00 6.01
2706 3123 1.352114 CATTGGGAAAGCATGCAACG 58.648 50.000 21.98 0.00 0.00 4.10
2707 3124 1.275856 TCCATTGGGAAAGCATGCAAC 59.724 47.619 21.98 10.22 41.32 4.17
2711 3132 0.462789 GGCTCCATTGGGAAAGCATG 59.537 55.000 14.73 0.00 44.38 4.06
2716 3137 0.323725 GCTCTGGCTCCATTGGGAAA 60.324 55.000 2.09 0.00 44.38 3.13
2735 3156 2.903855 GCATGGCCATCGAGGTGG 60.904 66.667 17.61 3.62 42.35 4.61
2736 3157 1.512996 GATGCATGGCCATCGAGGTG 61.513 60.000 17.61 6.29 40.61 4.00
2737 3158 1.228063 GATGCATGGCCATCGAGGT 60.228 57.895 17.61 0.00 40.61 3.85
2738 3159 3.664495 GATGCATGGCCATCGAGG 58.336 61.111 17.61 5.75 41.84 4.63
2743 3164 1.889105 GACGACGATGCATGGCCAT 60.889 57.895 14.09 14.09 0.00 4.40
2779 3200 0.584876 GGCGTGTTTATACGGGCATC 59.415 55.000 0.00 0.00 43.87 3.91
2781 3202 1.020333 GTGGCGTGTTTATACGGGCA 61.020 55.000 0.00 0.78 43.87 5.36
2783 3204 0.108041 AGGTGGCGTGTTTATACGGG 60.108 55.000 0.00 0.00 43.87 5.28
2791 3212 1.029681 GGAAAAGAAGGTGGCGTGTT 58.970 50.000 0.00 0.00 0.00 3.32
2797 3218 4.322953 CCATTCCATTGGAAAAGAAGGTGG 60.323 45.833 21.52 17.51 45.41 4.61
2817 3238 3.724374 GTACGTACATACACCATGCCAT 58.276 45.455 20.67 0.00 38.29 4.40
2818 3239 2.479901 CGTACGTACATACACCATGCCA 60.480 50.000 24.50 0.00 38.29 4.92
2819 3240 2.121786 CGTACGTACATACACCATGCC 58.878 52.381 24.50 0.00 38.29 4.40
2821 3242 4.018649 TGACGTACGTACATACACCATG 57.981 45.455 22.87 8.04 40.78 3.66
2822 3243 4.156556 AGTTGACGTACGTACATACACCAT 59.843 41.667 22.87 0.39 0.00 3.55
2823 3244 3.501828 AGTTGACGTACGTACATACACCA 59.498 43.478 22.87 9.52 0.00 4.17
2827 3248 7.044706 GGAATGTAAGTTGACGTACGTACATAC 60.045 40.741 24.59 22.82 46.07 2.39
2828 3249 6.966632 GGAATGTAAGTTGACGTACGTACATA 59.033 38.462 24.59 14.72 46.07 2.29
2834 3271 5.119588 ACAATGGAATGTAAGTTGACGTACG 59.880 40.000 15.01 15.01 34.30 3.67
2843 3280 6.306987 AGAAACCTCACAATGGAATGTAAGT 58.693 36.000 0.00 0.00 30.84 2.24
2844 3281 6.824305 AGAAACCTCACAATGGAATGTAAG 57.176 37.500 0.00 0.00 30.84 2.34
2853 3298 4.392940 AGAGTCCAAGAAACCTCACAATG 58.607 43.478 0.00 0.00 0.00 2.82
2856 3301 4.223953 AGTAGAGTCCAAGAAACCTCACA 58.776 43.478 0.00 0.00 0.00 3.58
2859 3304 6.993308 AGAAAAAGTAGAGTCCAAGAAACCTC 59.007 38.462 0.00 0.00 0.00 3.85
2861 3306 6.513556 GCAGAAAAAGTAGAGTCCAAGAAACC 60.514 42.308 0.00 0.00 0.00 3.27
2874 3319 4.645956 CGATGAAGCTGCAGAAAAAGTAG 58.354 43.478 20.43 0.00 0.00 2.57
2875 3320 3.120199 GCGATGAAGCTGCAGAAAAAGTA 60.120 43.478 20.43 0.00 0.00 2.24
2877 3322 2.248487 GCGATGAAGCTGCAGAAAAAG 58.752 47.619 20.43 2.77 0.00 2.27
2883 3328 1.497223 GCTAGGCGATGAAGCTGCAG 61.497 60.000 10.11 10.11 37.29 4.41
2885 3330 1.220817 GAGCTAGGCGATGAAGCTGC 61.221 60.000 0.00 0.00 46.29 5.25
2913 3373 3.484285 GTGACGACGGGTTGAAAATTTTG 59.516 43.478 8.47 0.00 0.00 2.44
2914 3374 3.489568 GGTGACGACGGGTTGAAAATTTT 60.490 43.478 2.28 2.28 0.00 1.82
2915 3375 2.033675 GGTGACGACGGGTTGAAAATTT 59.966 45.455 0.00 0.00 0.00 1.82
3035 3533 7.374222 CTACGCATTTTTGTCGTAGGTACGTA 61.374 42.308 9.25 0.00 46.82 3.57
3036 3534 6.623525 CTACGCATTTTTGTCGTAGGTACGT 61.624 44.000 9.25 0.00 46.82 3.57
3037 3535 4.259135 CTACGCATTTTTGTCGTAGGTACG 60.259 45.833 11.75 3.05 46.82 3.67
3056 3557 4.434725 ACGTAATCAGTCACACGTACTACG 60.435 45.833 7.07 7.07 45.04 3.51
3060 3561 3.181546 GCAACGTAATCAGTCACACGTAC 60.182 47.826 0.00 0.00 46.05 3.67
3070 3571 2.430956 GCATCAACGCAACGTAATCAG 58.569 47.619 0.00 0.00 39.99 2.90
3071 3572 1.201866 CGCATCAACGCAACGTAATCA 60.202 47.619 0.00 0.00 39.99 2.57
3101 3616 3.483922 GCTCTATATATCGCGTCATGCAC 59.516 47.826 5.77 0.00 46.97 4.57
3115 3630 2.347731 TCGATCTCGTGCGCTCTATAT 58.652 47.619 9.73 0.00 40.80 0.86
3116 3631 1.792006 TCGATCTCGTGCGCTCTATA 58.208 50.000 9.73 0.00 40.80 1.31
3117 3632 1.129624 GATCGATCTCGTGCGCTCTAT 59.870 52.381 18.29 0.00 40.80 1.98
3118 3633 0.513385 GATCGATCTCGTGCGCTCTA 59.487 55.000 18.29 0.00 40.80 2.43
3119 3634 1.281353 GATCGATCTCGTGCGCTCT 59.719 57.895 18.29 0.00 40.80 4.09
3124 3639 2.596263 TGTATCGATCGATCTCGTGC 57.404 50.000 32.50 14.68 39.62 5.34
3127 3642 5.209944 TGAGAATGTATCGATCGATCTCG 57.790 43.478 32.50 12.75 39.99 4.04
3133 3648 8.848528 GCATATATGATGAGAATGTATCGATCG 58.151 37.037 17.10 9.36 0.00 3.69
3154 3669 8.717821 GGACGTGTATATTGTACATTTGCATAT 58.282 33.333 0.00 0.00 0.00 1.78
3155 3670 7.095982 CGGACGTGTATATTGTACATTTGCATA 60.096 37.037 0.00 0.00 0.00 3.14
3156 3671 6.292649 CGGACGTGTATATTGTACATTTGCAT 60.293 38.462 0.00 0.00 0.00 3.96
3157 3672 5.005875 CGGACGTGTATATTGTACATTTGCA 59.994 40.000 0.00 0.00 0.00 4.08
3161 3676 6.798476 CGATACGGACGTGTATATTGTACATT 59.202 38.462 7.73 0.00 35.24 2.71
3180 3695 2.538449 GCAACCAGTCAATACCGATACG 59.462 50.000 0.00 0.00 0.00 3.06
3181 3696 3.527533 TGCAACCAGTCAATACCGATAC 58.472 45.455 0.00 0.00 0.00 2.24
3183 3698 2.779755 TGCAACCAGTCAATACCGAT 57.220 45.000 0.00 0.00 0.00 4.18
3184 3699 2.552599 TTGCAACCAGTCAATACCGA 57.447 45.000 0.00 0.00 0.00 4.69
3185 3700 4.335315 ACATATTGCAACCAGTCAATACCG 59.665 41.667 0.00 0.00 37.80 4.02
3186 3701 5.835113 ACATATTGCAACCAGTCAATACC 57.165 39.130 0.00 0.00 37.80 2.73
3187 3702 7.312154 TGAAACATATTGCAACCAGTCAATAC 58.688 34.615 0.00 0.00 37.80 1.89
3188 3703 7.459795 TGAAACATATTGCAACCAGTCAATA 57.540 32.000 0.00 0.00 38.88 1.90
3189 3704 6.343716 TGAAACATATTGCAACCAGTCAAT 57.656 33.333 0.00 0.00 36.87 2.57
3204 3719 1.746861 CGAGCCCCTGCATGAAACATA 60.747 52.381 0.00 0.00 41.13 2.29
3227 3742 1.407258 GAGATGTAGAGGTTCTGCGCT 59.593 52.381 9.73 0.00 31.35 5.92
3416 3931 0.108138 CGCCCTTGTAGAAGGTGAGG 60.108 60.000 16.93 3.39 46.84 3.86
3455 3970 1.836999 CGAGGTTGATGTGGGTGGGA 61.837 60.000 0.00 0.00 0.00 4.37
3635 4150 0.037605 CCGTGGTGGAGTAGTGGAAC 60.038 60.000 0.00 0.00 42.00 3.62
3776 4291 2.284625 ATGACCCCTGAGGCGACA 60.285 61.111 0.00 0.00 40.58 4.35
3785 4300 2.607750 ACCACGAGCATGACCCCT 60.608 61.111 0.00 0.00 0.00 4.79
4043 4558 1.874019 GCGATGCACGACGATGTCT 60.874 57.895 0.00 0.00 45.77 3.41
4218 4733 1.505425 GACAAGTTCCACCGGTACAC 58.495 55.000 6.87 4.05 0.00 2.90
4279 4797 4.255301 CGCTAGATCTAACCGAGTCCTAT 58.745 47.826 14.17 0.00 0.00 2.57
4319 4839 3.260740 GAGCACCAACAGAATCAGAGAG 58.739 50.000 0.00 0.00 0.00 3.20
4340 4860 5.620738 TCCCTCCTCTATCTTCACATTTG 57.379 43.478 0.00 0.00 0.00 2.32
4402 4922 6.090783 GTCCGAAATTTATTGGTTTGTCTCC 58.909 40.000 0.00 0.00 0.00 3.71
4403 4923 6.581166 GTGTCCGAAATTTATTGGTTTGTCTC 59.419 38.462 0.00 0.00 0.00 3.36
4441 4963 9.132521 GTTGTAAAATGGAGTTGATTTCTCATG 57.867 33.333 0.00 0.00 34.04 3.07
4554 7340 7.094075 TGCTTGATCAAACTTAGAAGCATTGAT 60.094 33.333 17.27 17.27 43.07 2.57
4688 7482 6.149308 TGGCATATACACTGAGTCAAAAAGTG 59.851 38.462 8.31 8.31 45.46 3.16
4761 7555 0.259647 TGCATTGGAGCTGGCCTTAT 59.740 50.000 3.32 0.00 34.99 1.73
4777 7571 1.525077 GTCTGTTTGGGGTCGTGCA 60.525 57.895 0.00 0.00 0.00 4.57
4798 7592 8.550376 CAAACAAACAAAATTCGGAGAAATCAT 58.450 29.630 0.00 0.00 45.90 2.45
4921 7715 1.451651 CGCGGTTGCAAAACTTCATTC 59.548 47.619 0.00 0.00 42.97 2.67
4928 7722 2.479412 TATGGCCGCGGTTGCAAAAC 62.479 55.000 28.70 6.82 42.97 2.43
5047 7844 2.757894 TTGAAAGGTTGGCAAGGGTA 57.242 45.000 0.00 0.00 0.00 3.69


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

AutoCloner maintained by Alex Coulton.