Multiple sequence alignment - TraesCS7A01G103900

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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 TraesCS7A01G103900 chr7A 100.000 2411 0 0 1 2411 63428585 63426175 0.000000e+00 4453.0
1 TraesCS7A01G103900 chr7A 88.000 1300 99 35 747 2019 63399015 63397746 0.000000e+00 1483.0
2 TraesCS7A01G103900 chr7A 94.737 646 28 6 705 1348 63343409 63344050 0.000000e+00 1000.0
3 TraesCS7A01G103900 chr7D 90.210 1430 83 28 1008 2410 58793630 58795029 0.000000e+00 1812.0
4 TraesCS7A01G103900 chr7D 87.604 1323 97 34 338 1628 58864278 58862991 0.000000e+00 1472.0
5 TraesCS7A01G103900 chr7D 87.045 494 31 9 1920 2410 58862814 58862351 5.900000e-146 527.0
6 TraesCS7A01G103900 chr7D 87.047 193 10 5 703 883 58793002 58793191 1.130000e-48 204.0
7 TraesCS7A01G103900 chr7D 80.866 277 34 11 73 331 263913101 263913376 1.460000e-47 200.0
8 TraesCS7A01G103900 chr7D 80.208 192 23 9 6 196 522866855 522866678 1.950000e-26 130.0
9 TraesCS7A01G103900 chr7D 94.805 77 4 0 1715 1791 58862940 58862864 1.170000e-23 121.0
10 TraesCS7A01G103900 chr5B 85.000 1400 149 44 723 2091 339101215 339099846 0.000000e+00 1365.0
11 TraesCS7A01G103900 chr5B 83.513 279 24 12 73 336 615600831 615601102 8.610000e-60 241.0
12 TraesCS7A01G103900 chr5D 81.866 1522 189 63 942 2410 298123720 298125207 0.000000e+00 1201.0
13 TraesCS7A01G103900 chr5D 81.455 275 32 13 73 331 426503634 426503905 8.740000e-50 207.0
14 TraesCS7A01G103900 chr4A 87.933 721 49 20 703 1415 675854667 675855357 0.000000e+00 815.0
15 TraesCS7A01G103900 chr4A 91.771 559 35 9 1857 2411 675920607 675921158 0.000000e+00 767.0
16 TraesCS7A01G103900 chr7B 86.747 747 64 22 729 1461 63934715 63935440 0.000000e+00 798.0
17 TraesCS7A01G103900 chrUn 92.017 476 34 4 1001 1473 84317792 84317318 0.000000e+00 665.0
18 TraesCS7A01G103900 chrUn 82.238 411 40 23 701 1102 468331407 468331793 8.310000e-85 324.0
19 TraesCS7A01G103900 chr2D 83.456 272 26 10 73 329 636210729 636210996 4.010000e-58 235.0
20 TraesCS7A01G103900 chr1D 86.598 194 18 7 6 196 58616864 58617052 8.740000e-50 207.0
21 TraesCS7A01G103900 chr5A 81.111 270 39 9 73 336 524194386 524194123 3.140000e-49 206.0
22 TraesCS7A01G103900 chr5A 87.879 99 10 2 182 279 605741264 605741167 5.450000e-22 115.0
23 TraesCS7A01G103900 chr6D 80.586 273 39 6 68 331 422032272 422032005 5.260000e-47 198.0
24 TraesCS7A01G103900 chr2B 80.812 271 35 11 73 330 788242307 788242041 1.890000e-46 196.0
25 TraesCS7A01G103900 chr1B 79.856 278 43 8 68 336 416635406 416635133 8.800000e-45 191.0
26 TraesCS7A01G103900 chr2A 76.871 147 23 6 200 336 521378191 521378336 3.320000e-09 73.1


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 TraesCS7A01G103900 chr7A 63426175 63428585 2410 True 4453.000000 4453 100.0000 1 2411 1 chr7A.!!$R2 2410
1 TraesCS7A01G103900 chr7A 63397746 63399015 1269 True 1483.000000 1483 88.0000 747 2019 1 chr7A.!!$R1 1272
2 TraesCS7A01G103900 chr7A 63343409 63344050 641 False 1000.000000 1000 94.7370 705 1348 1 chr7A.!!$F1 643
3 TraesCS7A01G103900 chr7D 58793002 58795029 2027 False 1008.000000 1812 88.6285 703 2410 2 chr7D.!!$F2 1707
4 TraesCS7A01G103900 chr7D 58862351 58864278 1927 True 706.666667 1472 89.8180 338 2410 3 chr7D.!!$R2 2072
5 TraesCS7A01G103900 chr5B 339099846 339101215 1369 True 1365.000000 1365 85.0000 723 2091 1 chr5B.!!$R1 1368
6 TraesCS7A01G103900 chr5D 298123720 298125207 1487 False 1201.000000 1201 81.8660 942 2410 1 chr5D.!!$F1 1468
7 TraesCS7A01G103900 chr4A 675854667 675855357 690 False 815.000000 815 87.9330 703 1415 1 chr4A.!!$F1 712
8 TraesCS7A01G103900 chr4A 675920607 675921158 551 False 767.000000 767 91.7710 1857 2411 1 chr4A.!!$F2 554
9 TraesCS7A01G103900 chr7B 63934715 63935440 725 False 798.000000 798 86.7470 729 1461 1 chr7B.!!$F1 732

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
629 631 0.031721 GCCCGATACCCAGAGTTACG 59.968 60.0 0.0 0.0 0.0 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1495 1839 0.031111 TCCAGGCTACATAGGGCAGT 60.031 55.0 0.0 0.0 0.0 4.4 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
21 22 4.939052 TCTTCTTCCTTTCACGAGAGTT 57.061 40.909 0.00 0.00 46.40 3.01
23 24 5.770417 TCTTCTTCCTTTCACGAGAGTTAC 58.230 41.667 0.00 0.00 46.40 2.50
24 25 5.301045 TCTTCTTCCTTTCACGAGAGTTACA 59.699 40.000 0.00 0.00 46.40 2.41
25 26 5.122512 TCTTCCTTTCACGAGAGTTACAG 57.877 43.478 0.00 0.00 46.40 2.74
26 27 4.583489 TCTTCCTTTCACGAGAGTTACAGT 59.417 41.667 0.00 0.00 46.40 3.55
27 28 4.931661 TCCTTTCACGAGAGTTACAGTT 57.068 40.909 0.00 0.00 46.40 3.16
28 29 4.617959 TCCTTTCACGAGAGTTACAGTTG 58.382 43.478 0.00 0.00 46.40 3.16
29 30 4.098960 TCCTTTCACGAGAGTTACAGTTGT 59.901 41.667 0.00 0.00 46.40 3.32
30 31 4.209288 CCTTTCACGAGAGTTACAGTTGTG 59.791 45.833 0.00 0.00 46.40 3.33
31 32 2.739292 TCACGAGAGTTACAGTTGTGC 58.261 47.619 0.00 0.00 46.40 4.57
32 33 1.792949 CACGAGAGTTACAGTTGTGCC 59.207 52.381 0.00 0.00 46.40 5.01
33 34 1.687123 ACGAGAGTTACAGTTGTGCCT 59.313 47.619 0.00 0.00 46.40 4.75
34 35 2.288273 ACGAGAGTTACAGTTGTGCCTC 60.288 50.000 0.00 0.72 46.40 4.70
35 36 2.689646 GAGAGTTACAGTTGTGCCTCC 58.310 52.381 8.49 0.77 30.93 4.30
36 37 1.348036 AGAGTTACAGTTGTGCCTCCC 59.652 52.381 8.49 0.00 30.93 4.30
37 38 0.034896 AGTTACAGTTGTGCCTCCCG 59.965 55.000 0.00 0.00 0.00 5.14
38 39 0.953960 GTTACAGTTGTGCCTCCCGG 60.954 60.000 0.00 0.00 0.00 5.73
39 40 1.122632 TTACAGTTGTGCCTCCCGGA 61.123 55.000 0.73 0.00 0.00 5.14
40 41 1.122632 TACAGTTGTGCCTCCCGGAA 61.123 55.000 0.73 0.00 0.00 4.30
41 42 1.228124 CAGTTGTGCCTCCCGGAAA 60.228 57.895 0.73 0.00 0.00 3.13
42 43 1.228154 AGTTGTGCCTCCCGGAAAC 60.228 57.895 0.73 0.00 0.00 2.78
56 57 2.750301 GGAAACGAAAAAGAGCACGT 57.250 45.000 0.00 0.00 40.64 4.49
61 62 4.351131 AACGAAAAAGAGCACGTTTTCT 57.649 36.364 24.13 13.68 45.25 2.52
62 63 3.680789 ACGAAAAAGAGCACGTTTTCTG 58.319 40.909 24.13 20.34 45.25 3.02
63 64 3.126343 ACGAAAAAGAGCACGTTTTCTGT 59.874 39.130 24.13 20.78 45.25 3.41
64 65 4.095610 CGAAAAAGAGCACGTTTTCTGTT 58.904 39.130 24.13 1.71 45.25 3.16
65 66 4.557301 CGAAAAAGAGCACGTTTTCTGTTT 59.443 37.500 24.13 11.99 45.25 2.83
66 67 5.060446 CGAAAAAGAGCACGTTTTCTGTTTT 59.940 36.000 24.13 11.30 45.25 2.43
67 68 6.399564 CGAAAAAGAGCACGTTTTCTGTTTTT 60.400 34.615 24.13 20.06 45.25 1.94
86 87 2.519377 TTTTCCTTTCGCGAGAGTCA 57.481 45.000 23.28 8.47 43.69 3.41
87 88 1.779569 TTTCCTTTCGCGAGAGTCAC 58.220 50.000 23.28 0.00 43.69 3.67
88 89 0.386858 TTCCTTTCGCGAGAGTCACG 60.387 55.000 23.28 9.67 43.69 4.35
89 90 1.801913 CCTTTCGCGAGAGTCACGG 60.802 63.158 23.28 6.69 43.69 4.94
90 91 2.430244 TTTCGCGAGAGTCACGGC 60.430 61.111 9.59 3.61 43.69 5.68
91 92 3.909258 TTTCGCGAGAGTCACGGCC 62.909 63.158 9.59 0.00 43.69 6.13
108 109 4.354155 CGTGCCTCTCGGAAACAA 57.646 55.556 0.00 0.00 0.00 2.83
109 110 2.612200 CGTGCCTCTCGGAAACAAA 58.388 52.632 0.00 0.00 0.00 2.83
110 111 0.941542 CGTGCCTCTCGGAAACAAAA 59.058 50.000 0.00 0.00 0.00 2.44
111 112 1.332375 CGTGCCTCTCGGAAACAAAAA 59.668 47.619 0.00 0.00 0.00 1.94
135 136 8.601845 AAAAACTGTGTTTACTGCTTTTTCTT 57.398 26.923 0.00 0.00 33.23 2.52
136 137 7.812309 AAACTGTGTTTACTGCTTTTTCTTC 57.188 32.000 0.00 0.00 0.00 2.87
137 138 5.891451 ACTGTGTTTACTGCTTTTTCTTCC 58.109 37.500 0.00 0.00 0.00 3.46
138 139 5.652452 ACTGTGTTTACTGCTTTTTCTTCCT 59.348 36.000 0.00 0.00 0.00 3.36
139 140 6.152831 ACTGTGTTTACTGCTTTTTCTTCCTT 59.847 34.615 0.00 0.00 0.00 3.36
140 141 6.930731 TGTGTTTACTGCTTTTTCTTCCTTT 58.069 32.000 0.00 0.00 0.00 3.11
141 142 7.033185 TGTGTTTACTGCTTTTTCTTCCTTTC 58.967 34.615 0.00 0.00 0.00 2.62
142 143 6.196538 GTGTTTACTGCTTTTTCTTCCTTTCG 59.803 38.462 0.00 0.00 0.00 3.46
143 144 3.355626 ACTGCTTTTTCTTCCTTTCGC 57.644 42.857 0.00 0.00 0.00 4.70
144 145 2.287009 ACTGCTTTTTCTTCCTTTCGCG 60.287 45.455 0.00 0.00 0.00 5.87
145 146 1.944024 TGCTTTTTCTTCCTTTCGCGA 59.056 42.857 3.71 3.71 0.00 5.87
146 147 2.032030 TGCTTTTTCTTCCTTTCGCGAG 60.032 45.455 9.59 0.00 0.00 5.03
147 148 2.031944 GCTTTTTCTTCCTTTCGCGAGT 60.032 45.455 9.59 0.00 0.00 4.18
148 149 3.800163 CTTTTTCTTCCTTTCGCGAGTC 58.200 45.455 9.59 0.00 0.00 3.36
149 150 2.519377 TTTCTTCCTTTCGCGAGTCA 57.481 45.000 9.59 0.00 0.00 3.41
150 151 1.779569 TTCTTCCTTTCGCGAGTCAC 58.220 50.000 9.59 0.00 0.00 3.67
151 152 0.386858 TCTTCCTTTCGCGAGTCACG 60.387 55.000 9.59 0.00 45.66 4.35
152 153 0.386858 CTTCCTTTCGCGAGTCACGA 60.387 55.000 9.59 0.00 45.77 4.35
153 154 0.242825 TTCCTTTCGCGAGTCACGAT 59.757 50.000 9.59 0.00 45.77 3.73
154 155 0.242825 TCCTTTCGCGAGTCACGATT 59.757 50.000 9.59 0.00 45.77 3.34
155 156 1.068474 CCTTTCGCGAGTCACGATTT 58.932 50.000 9.59 0.00 45.77 2.17
156 157 1.459592 CCTTTCGCGAGTCACGATTTT 59.540 47.619 9.59 0.00 45.77 1.82
157 158 2.486128 CTTTCGCGAGTCACGATTTTG 58.514 47.619 9.59 0.00 45.77 2.44
158 159 0.162933 TTCGCGAGTCACGATTTTGC 59.837 50.000 9.59 0.00 45.77 3.68
159 160 0.666274 TCGCGAGTCACGATTTTGCT 60.666 50.000 3.71 0.00 45.77 3.91
160 161 0.163788 CGCGAGTCACGATTTTGCTT 59.836 50.000 0.00 0.00 45.77 3.91
161 162 1.783416 CGCGAGTCACGATTTTGCTTC 60.783 52.381 0.00 0.00 45.77 3.86
162 163 1.464189 GCGAGTCACGATTTTGCTTCC 60.464 52.381 0.00 0.00 45.77 3.46
163 164 1.798223 CGAGTCACGATTTTGCTTCCA 59.202 47.619 0.00 0.00 45.77 3.53
164 165 2.411547 CGAGTCACGATTTTGCTTCCAC 60.412 50.000 0.00 0.00 45.77 4.02
165 166 1.531149 AGTCACGATTTTGCTTCCACG 59.469 47.619 0.00 0.00 0.00 4.94
166 167 1.529438 GTCACGATTTTGCTTCCACGA 59.471 47.619 0.00 0.00 0.00 4.35
167 168 1.798223 TCACGATTTTGCTTCCACGAG 59.202 47.619 0.00 0.00 0.00 4.18
168 169 1.798223 CACGATTTTGCTTCCACGAGA 59.202 47.619 0.00 0.00 0.00 4.04
169 170 2.069273 ACGATTTTGCTTCCACGAGAG 58.931 47.619 0.00 0.00 0.00 3.20
170 171 1.394917 CGATTTTGCTTCCACGAGAGG 59.605 52.381 0.00 0.00 0.00 3.69
174 175 3.805267 GCTTCCACGAGAGGCATG 58.195 61.111 8.88 0.00 46.54 4.06
175 176 1.219124 GCTTCCACGAGAGGCATGA 59.781 57.895 0.00 0.00 46.54 3.07
176 177 0.179062 GCTTCCACGAGAGGCATGAT 60.179 55.000 0.00 0.00 46.54 2.45
177 178 1.745141 GCTTCCACGAGAGGCATGATT 60.745 52.381 0.00 0.00 46.54 2.57
178 179 1.938577 CTTCCACGAGAGGCATGATTG 59.061 52.381 0.00 0.00 0.00 2.67
179 180 0.904649 TCCACGAGAGGCATGATTGT 59.095 50.000 0.00 0.00 0.00 2.71
180 181 1.012086 CCACGAGAGGCATGATTGTG 58.988 55.000 0.00 0.00 0.00 3.33
181 182 0.376152 CACGAGAGGCATGATTGTGC 59.624 55.000 0.00 0.00 44.31 4.57
182 183 0.251354 ACGAGAGGCATGATTGTGCT 59.749 50.000 0.00 0.00 44.45 4.40
183 184 1.339438 ACGAGAGGCATGATTGTGCTT 60.339 47.619 0.00 0.00 44.45 3.91
184 185 1.741706 CGAGAGGCATGATTGTGCTTT 59.258 47.619 0.00 0.00 44.45 3.51
185 186 2.163010 CGAGAGGCATGATTGTGCTTTT 59.837 45.455 0.00 0.00 44.45 2.27
186 187 3.508762 GAGAGGCATGATTGTGCTTTTG 58.491 45.455 0.00 0.00 44.45 2.44
187 188 1.997606 GAGGCATGATTGTGCTTTTGC 59.002 47.619 0.00 0.00 44.45 3.68
200 201 3.754188 GCTTTTGCGAGAGTCATGATT 57.246 42.857 0.00 0.00 34.86 2.57
201 202 4.088823 GCTTTTGCGAGAGTCATGATTT 57.911 40.909 0.00 0.00 34.86 2.17
202 203 4.479619 GCTTTTGCGAGAGTCATGATTTT 58.520 39.130 0.00 0.00 34.86 1.82
203 204 4.322804 GCTTTTGCGAGAGTCATGATTTTG 59.677 41.667 0.00 0.00 34.86 2.44
204 205 3.476295 TTGCGAGAGTCATGATTTTGC 57.524 42.857 0.00 4.13 0.00 3.68
205 206 2.703416 TGCGAGAGTCATGATTTTGCT 58.297 42.857 0.00 0.00 0.00 3.91
206 207 3.076621 TGCGAGAGTCATGATTTTGCTT 58.923 40.909 0.00 0.00 0.00 3.91
207 208 3.125829 TGCGAGAGTCATGATTTTGCTTC 59.874 43.478 0.00 0.00 0.00 3.86
208 209 3.486542 GCGAGAGTCATGATTTTGCTTCC 60.487 47.826 0.00 0.00 0.00 3.46
209 210 3.242220 CGAGAGTCATGATTTTGCTTCCG 60.242 47.826 0.00 0.00 0.00 4.30
210 211 2.421424 AGAGTCATGATTTTGCTTCCGC 59.579 45.455 0.00 0.00 0.00 5.54
211 212 1.131126 AGTCATGATTTTGCTTCCGCG 59.869 47.619 0.00 0.00 39.65 6.46
212 213 1.130373 GTCATGATTTTGCTTCCGCGA 59.870 47.619 8.23 0.00 39.65 5.87
213 214 1.398041 TCATGATTTTGCTTCCGCGAG 59.602 47.619 8.23 0.00 39.65 5.03
214 215 1.398041 CATGATTTTGCTTCCGCGAGA 59.602 47.619 8.23 0.00 39.65 4.04
215 216 1.078709 TGATTTTGCTTCCGCGAGAG 58.921 50.000 8.23 5.93 39.65 3.20
216 217 1.337728 TGATTTTGCTTCCGCGAGAGA 60.338 47.619 8.23 0.00 39.65 3.10
217 218 1.061276 GATTTTGCTTCCGCGAGAGAC 59.939 52.381 8.23 2.16 39.65 3.36
218 219 0.249699 TTTTGCTTCCGCGAGAGACA 60.250 50.000 8.23 4.81 39.65 3.41
219 220 0.944311 TTTGCTTCCGCGAGAGACAC 60.944 55.000 8.23 0.00 39.65 3.67
220 221 2.082629 TTGCTTCCGCGAGAGACACA 62.083 55.000 8.23 0.00 39.65 3.72
221 222 1.803519 GCTTCCGCGAGAGACACAG 60.804 63.158 8.23 0.00 0.00 3.66
222 223 1.153939 CTTCCGCGAGAGACACAGG 60.154 63.158 8.23 0.00 0.00 4.00
223 224 1.867919 CTTCCGCGAGAGACACAGGT 61.868 60.000 8.23 0.00 0.00 4.00
224 225 2.126307 CCGCGAGAGACACAGGTG 60.126 66.667 8.23 0.00 0.00 4.00
226 227 1.583495 CCGCGAGAGACACAGGTGTA 61.583 60.000 8.23 0.00 45.05 2.90
227 228 0.454620 CGCGAGAGACACAGGTGTAC 60.455 60.000 0.00 3.40 45.05 2.90
228 229 0.882474 GCGAGAGACACAGGTGTACT 59.118 55.000 4.84 8.07 45.05 2.73
229 230 1.269998 GCGAGAGACACAGGTGTACTT 59.730 52.381 4.84 0.00 45.05 2.24
230 231 2.288273 GCGAGAGACACAGGTGTACTTT 60.288 50.000 4.84 0.69 45.05 2.66
231 232 3.566523 CGAGAGACACAGGTGTACTTTC 58.433 50.000 4.84 8.27 45.05 2.62
232 233 3.566523 GAGAGACACAGGTGTACTTTCG 58.433 50.000 4.84 0.00 45.05 3.46
233 234 2.059541 GAGACACAGGTGTACTTTCGC 58.940 52.381 4.84 0.00 45.05 4.70
234 235 0.782384 GACACAGGTGTACTTTCGCG 59.218 55.000 4.84 0.00 45.05 5.87
235 236 0.386476 ACACAGGTGTACTTTCGCGA 59.614 50.000 3.71 3.71 42.90 5.87
236 237 1.060713 CACAGGTGTACTTTCGCGAG 58.939 55.000 9.59 0.27 0.00 5.03
237 238 0.956633 ACAGGTGTACTTTCGCGAGA 59.043 50.000 9.59 3.35 39.20 4.04
238 239 1.068472 ACAGGTGTACTTTCGCGAGAG 60.068 52.381 23.66 23.66 43.69 3.20
239 240 1.068472 CAGGTGTACTTTCGCGAGAGT 60.068 52.381 31.42 31.42 43.69 3.24
240 241 1.199558 AGGTGTACTTTCGCGAGAGTC 59.800 52.381 32.47 23.30 43.69 3.36
241 242 1.615502 GTGTACTTTCGCGAGAGTCC 58.384 55.000 32.47 23.34 43.69 3.85
242 243 0.524862 TGTACTTTCGCGAGAGTCCC 59.475 55.000 32.47 23.88 43.69 4.46
243 244 0.522915 GTACTTTCGCGAGAGTCCCG 60.523 60.000 32.47 8.38 43.69 5.14
244 245 1.651240 TACTTTCGCGAGAGTCCCGG 61.651 60.000 32.47 7.64 43.69 5.73
245 246 2.987547 TTTCGCGAGAGTCCCGGT 60.988 61.111 9.59 0.00 43.69 5.28
246 247 2.868999 CTTTCGCGAGAGTCCCGGTC 62.869 65.000 17.92 0.00 43.69 4.79
249 250 4.477975 GCGAGAGTCCCGGTCGTG 62.478 72.222 12.32 0.00 36.09 4.35
250 251 4.477975 CGAGAGTCCCGGTCGTGC 62.478 72.222 0.00 0.00 0.00 5.34
251 252 4.131088 GAGAGTCCCGGTCGTGCC 62.131 72.222 0.00 0.00 0.00 5.01
252 253 4.680537 AGAGTCCCGGTCGTGCCT 62.681 66.667 0.00 0.00 34.25 4.75
253 254 4.131088 GAGTCCCGGTCGTGCCTC 62.131 72.222 0.00 0.00 34.25 4.70
260 261 3.379445 GGTCGTGCCTCCTCGGAA 61.379 66.667 0.00 0.00 33.16 4.30
261 262 2.654877 GTCGTGCCTCCTCGGAAA 59.345 61.111 0.00 0.00 33.16 3.13
262 263 1.737008 GTCGTGCCTCCTCGGAAAC 60.737 63.158 0.00 0.00 33.16 2.78
298 299 0.882927 TTTTCCGCAAGAGTCACGGG 60.883 55.000 16.29 4.57 46.87 5.28
299 300 2.035237 TTTCCGCAAGAGTCACGGGT 62.035 55.000 16.29 0.00 46.87 5.28
300 301 2.030562 CCGCAAGAGTCACGGGTT 59.969 61.111 10.48 0.00 43.23 4.11
301 302 1.597027 CCGCAAGAGTCACGGGTTT 60.597 57.895 10.48 0.00 43.23 3.27
302 303 1.569493 CGCAAGAGTCACGGGTTTG 59.431 57.895 0.00 0.00 43.02 2.93
303 304 1.282875 GCAAGAGTCACGGGTTTGC 59.717 57.895 0.00 0.00 37.56 3.68
304 305 1.166531 GCAAGAGTCACGGGTTTGCT 61.167 55.000 10.20 0.00 40.58 3.91
305 306 1.308998 CAAGAGTCACGGGTTTGCTT 58.691 50.000 0.00 0.00 0.00 3.91
306 307 1.676006 CAAGAGTCACGGGTTTGCTTT 59.324 47.619 0.00 0.00 0.00 3.51
307 308 1.594331 AGAGTCACGGGTTTGCTTTC 58.406 50.000 0.00 0.00 0.00 2.62
308 309 0.234884 GAGTCACGGGTTTGCTTTCG 59.765 55.000 0.00 0.00 0.00 3.46
309 310 1.370051 GTCACGGGTTTGCTTTCGC 60.370 57.895 0.00 0.00 0.00 4.70
310 311 2.426752 CACGGGTTTGCTTTCGCG 60.427 61.111 0.00 0.00 43.61 5.87
311 312 2.589442 ACGGGTTTGCTTTCGCGA 60.589 55.556 3.71 3.71 41.28 5.87
312 313 2.173382 CGGGTTTGCTTTCGCGAG 59.827 61.111 9.59 0.00 41.28 5.03
313 314 2.314647 CGGGTTTGCTTTCGCGAGA 61.315 57.895 9.59 3.35 41.28 4.04
322 323 4.693532 TTCGCGAGAAGCATGGTT 57.306 50.000 10.50 10.50 46.92 3.67
323 324 2.161831 TTCGCGAGAAGCATGGTTG 58.838 52.632 16.18 1.72 46.92 3.77
324 325 0.602638 TTCGCGAGAAGCATGGTTGT 60.603 50.000 16.18 11.55 46.92 3.32
325 326 2.794262 TTCGCGAGAAGCATGGTTGTG 61.794 52.381 16.18 7.73 46.92 3.33
329 330 3.837213 CGAGAAGCATGGTTGTGATTT 57.163 42.857 16.18 0.00 0.00 2.17
330 331 3.751621 CGAGAAGCATGGTTGTGATTTC 58.248 45.455 16.18 0.00 0.00 2.17
331 332 3.189080 CGAGAAGCATGGTTGTGATTTCA 59.811 43.478 16.18 0.00 0.00 2.69
332 333 4.142534 CGAGAAGCATGGTTGTGATTTCAT 60.143 41.667 16.18 0.00 0.00 2.57
333 334 5.068234 AGAAGCATGGTTGTGATTTCATG 57.932 39.130 16.18 0.00 39.74 3.07
334 335 4.768448 AGAAGCATGGTTGTGATTTCATGA 59.232 37.500 16.18 0.00 39.27 3.07
335 336 4.713824 AGCATGGTTGTGATTTCATGAG 57.286 40.909 6.37 0.00 39.27 2.90
336 337 4.084287 AGCATGGTTGTGATTTCATGAGT 58.916 39.130 6.37 0.00 39.27 3.41
341 342 6.114187 TGGTTGTGATTTCATGAGTAGACT 57.886 37.500 0.00 0.00 0.00 3.24
352 353 7.482169 TTCATGAGTAGACTGATGTTTAGGT 57.518 36.000 8.66 0.00 38.48 3.08
366 367 3.075148 GTTTAGGTCAGGTTCAAGCCTC 58.925 50.000 0.00 0.00 36.58 4.70
426 427 5.702670 CAGTTAGACATGCTATATGTTGGGG 59.297 44.000 0.00 0.00 31.52 4.96
434 435 9.326413 GACATGCTATATGTTGGGGTAATATAC 57.674 37.037 0.00 0.00 31.52 1.47
463 464 6.828502 ACATGTATGATGTAGCGTTACTTG 57.171 37.500 10.88 0.00 0.00 3.16
467 468 7.694388 TGTATGATGTAGCGTTACTTGATTC 57.306 36.000 10.88 3.31 0.00 2.52
531 533 9.355916 GAGCATTTATCTTTTCTAGGGGTAAAT 57.644 33.333 0.00 0.00 0.00 1.40
542 544 5.887754 TCTAGGGGTAAATGGGCATTTATC 58.112 41.667 0.00 0.00 42.93 1.75
543 545 4.832560 AGGGGTAAATGGGCATTTATCT 57.167 40.909 0.84 0.00 42.93 1.98
563 565 2.125106 GCCATGGACCGGACAGAC 60.125 66.667 18.40 0.00 0.00 3.51
600 602 1.885887 CATTTTGAGCAAGTCCCGGAA 59.114 47.619 0.73 0.00 0.00 4.30
615 617 4.685467 GAACGAAACCCGGCCCGA 62.685 66.667 3.71 0.00 43.93 5.14
616 618 3.963687 GAACGAAACCCGGCCCGAT 62.964 63.158 3.71 0.00 43.93 4.18
617 619 2.576643 GAACGAAACCCGGCCCGATA 62.577 60.000 3.71 0.00 43.93 2.92
619 621 2.203112 GAAACCCGGCCCGATACC 60.203 66.667 3.71 0.00 0.00 2.73
620 622 3.762429 GAAACCCGGCCCGATACCC 62.762 68.421 3.71 0.00 0.00 3.69
626 628 2.432300 CGGCCCGATACCCAGAGTT 61.432 63.158 0.00 0.00 0.00 3.01
628 630 0.391966 GGCCCGATACCCAGAGTTAC 59.608 60.000 0.00 0.00 0.00 2.50
629 631 0.031721 GCCCGATACCCAGAGTTACG 59.968 60.000 0.00 0.00 0.00 3.18
630 632 1.396653 CCCGATACCCAGAGTTACGT 58.603 55.000 0.00 0.00 0.00 3.57
631 633 1.066605 CCCGATACCCAGAGTTACGTG 59.933 57.143 0.00 0.00 0.00 4.49
632 634 2.019249 CCGATACCCAGAGTTACGTGA 58.981 52.381 0.00 0.00 0.00 4.35
633 635 2.223433 CCGATACCCAGAGTTACGTGAC 60.223 54.545 1.53 1.53 0.00 3.67
634 636 2.421073 CGATACCCAGAGTTACGTGACA 59.579 50.000 13.41 0.00 0.00 3.58
635 637 3.730061 CGATACCCAGAGTTACGTGACAC 60.730 52.174 13.41 6.52 0.00 3.67
636 638 0.677842 ACCCAGAGTTACGTGACACC 59.322 55.000 13.41 4.16 0.00 4.16
637 639 0.677288 CCCAGAGTTACGTGACACCA 59.323 55.000 13.41 0.00 0.00 4.17
638 640 1.604693 CCCAGAGTTACGTGACACCAC 60.605 57.143 13.41 1.63 39.86 4.16
639 641 1.067974 CCAGAGTTACGTGACACCACA 59.932 52.381 13.41 0.00 43.34 4.17
640 642 2.124903 CAGAGTTACGTGACACCACAC 58.875 52.381 13.41 0.00 43.34 3.82
641 643 1.068127 AGAGTTACGTGACACCACACC 59.932 52.381 13.41 0.00 43.34 4.16
642 644 0.105408 AGTTACGTGACACCACACCC 59.895 55.000 13.41 0.00 43.34 4.61
643 645 0.881600 GTTACGTGACACCACACCCC 60.882 60.000 5.47 0.00 43.34 4.95
644 646 1.335882 TTACGTGACACCACACCCCA 61.336 55.000 0.00 0.00 43.34 4.96
645 647 1.750341 TACGTGACACCACACCCCAG 61.750 60.000 0.00 0.00 43.34 4.45
655 657 2.036098 CACCCCAGCAGCCAATCA 59.964 61.111 0.00 0.00 0.00 2.57
656 658 2.036256 ACCCCAGCAGCCAATCAC 59.964 61.111 0.00 0.00 0.00 3.06
657 659 3.136123 CCCCAGCAGCCAATCACG 61.136 66.667 0.00 0.00 0.00 4.35
658 660 2.046023 CCCAGCAGCCAATCACGA 60.046 61.111 0.00 0.00 0.00 4.35
673 675 3.462483 TCACGAGTTTCTTGGTTGCTA 57.538 42.857 0.00 0.00 0.00 3.49
720 727 1.300971 CCCAGCCAATCACGTCACAG 61.301 60.000 0.00 0.00 0.00 3.66
774 784 2.356553 CGTGAGTCGCCCCGAAAA 60.357 61.111 0.00 0.00 37.72 2.29
776 786 1.301479 GTGAGTCGCCCCGAAAACT 60.301 57.895 0.00 0.00 37.72 2.66
778 788 1.740664 GAGTCGCCCCGAAAACTCC 60.741 63.158 0.00 0.00 37.72 3.85
779 789 2.031465 GTCGCCCCGAAAACTCCA 59.969 61.111 0.00 0.00 37.72 3.86
780 790 1.376812 GTCGCCCCGAAAACTCCAT 60.377 57.895 0.00 0.00 37.72 3.41
1495 1839 3.118592 TGGTGTTGATATGATGTGCCGTA 60.119 43.478 0.00 0.00 0.00 4.02
1496 1840 3.247648 GGTGTTGATATGATGTGCCGTAC 59.752 47.826 0.00 0.00 0.00 3.67
1577 1940 1.597742 TTGTCCTCTGTTTGCTGCTC 58.402 50.000 0.00 0.00 0.00 4.26
1655 2026 1.518774 GGGGTTGAGCAATGCATGG 59.481 57.895 8.35 0.00 0.00 3.66
1676 2047 3.058777 GGTGCAATGTCAAAGCATTTTGG 60.059 43.478 5.93 0.00 43.11 3.28
1678 2049 3.808726 TGCAATGTCAAAGCATTTTGGTC 59.191 39.130 0.00 0.00 43.11 4.02
1704 2086 3.194062 GTCTGCTCTGCCATCTTCTAAC 58.806 50.000 0.00 0.00 0.00 2.34
1772 2155 4.916041 TCTGATGAACTCCTCATTTGGT 57.084 40.909 0.00 0.00 45.23 3.67
1782 2165 3.575687 CTCCTCATTTGGTCTTTTGGCTT 59.424 43.478 0.00 0.00 0.00 4.35
1786 2169 4.692228 TCATTTGGTCTTTTGGCTTTGTC 58.308 39.130 0.00 0.00 0.00 3.18
1801 2191 4.222114 GCTTTGTCGGAAGTGAATTTGAG 58.778 43.478 0.00 0.00 0.00 3.02
1831 2222 2.027192 GGACTGGTTGGTGCTGATAAGA 60.027 50.000 0.00 0.00 0.00 2.10
1832 2223 3.370953 GGACTGGTTGGTGCTGATAAGAT 60.371 47.826 0.00 0.00 0.00 2.40
1835 2226 4.080129 ACTGGTTGGTGCTGATAAGATGAT 60.080 41.667 0.00 0.00 0.00 2.45
1841 2232 4.202430 TGGTGCTGATAAGATGATGCTGAT 60.202 41.667 0.00 0.00 0.00 2.90
1844 2235 3.127203 GCTGATAAGATGATGCTGATGGC 59.873 47.826 0.00 0.00 42.22 4.40
1932 2326 6.344500 ACCATCACAGAACTGACTCAATATC 58.656 40.000 8.87 0.00 0.00 1.63
1933 2327 6.070596 ACCATCACAGAACTGACTCAATATCA 60.071 38.462 8.87 0.00 0.00 2.15
1979 2387 6.573434 TGTATATGAGCTTACAACCTGTCTG 58.427 40.000 0.00 0.00 0.00 3.51
2020 2435 2.425578 TGCAGTGCAATTGACATGTG 57.574 45.000 17.26 9.50 34.76 3.21
2078 2494 7.156876 ACAGAGTTGTGTTTCTTTCAATGAA 57.843 32.000 0.00 0.00 35.83 2.57
2118 2540 2.281761 AACGCAAGCTCAGGTGGG 60.282 61.111 0.00 0.00 45.62 4.61
2136 2558 1.571773 GGGTGGTATCTGGGCCTGTT 61.572 60.000 4.53 1.59 0.00 3.16
2151 2585 5.430417 TGGGCCTGTTAAGTATCTGGAATTA 59.570 40.000 4.53 0.00 0.00 1.40
2170 2604 9.927668 TGGAATTAAAAATTCATCAGGAAAGAC 57.072 29.630 12.91 0.00 39.39 3.01
2294 2751 0.178903 TACCTGTGAGGAGCCAAGGT 60.179 55.000 0.00 0.00 37.67 3.50
2299 2756 1.152030 TGAGGAGCCAAGGTCAGGT 60.152 57.895 0.00 0.00 0.00 4.00
2392 2849 3.137533 GGCACTGAGAAGGAGCATATTC 58.862 50.000 0.00 0.00 0.00 1.75
2395 2852 4.630111 CACTGAGAAGGAGCATATTCCTC 58.370 47.826 0.00 0.00 46.90 3.71
2396 2853 4.100653 CACTGAGAAGGAGCATATTCCTCA 59.899 45.833 0.00 0.00 46.90 3.86
2398 2855 4.550669 TGAGAAGGAGCATATTCCTCAGA 58.449 43.478 0.00 0.00 46.90 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.939052 AACTCTCGTGAAAGGAAGAAGA 57.061 40.909 0.00 0.00 0.00 2.87
2 3 5.068723 ACTGTAACTCTCGTGAAAGGAAGAA 59.931 40.000 0.00 0.00 0.00 2.52
3 4 4.583489 ACTGTAACTCTCGTGAAAGGAAGA 59.417 41.667 0.00 0.00 0.00 2.87
5 6 4.931661 ACTGTAACTCTCGTGAAAGGAA 57.068 40.909 0.00 0.00 0.00 3.36
6 7 4.098960 ACAACTGTAACTCTCGTGAAAGGA 59.901 41.667 0.00 0.00 0.00 3.36
7 8 4.209288 CACAACTGTAACTCTCGTGAAAGG 59.791 45.833 0.00 0.00 0.00 3.11
8 9 4.318121 GCACAACTGTAACTCTCGTGAAAG 60.318 45.833 0.00 0.00 0.00 2.62
9 10 3.554324 GCACAACTGTAACTCTCGTGAAA 59.446 43.478 0.00 0.00 0.00 2.69
10 11 3.120792 GCACAACTGTAACTCTCGTGAA 58.879 45.455 0.00 0.00 0.00 3.18
11 12 2.545113 GGCACAACTGTAACTCTCGTGA 60.545 50.000 0.00 0.00 0.00 4.35
12 13 1.792949 GGCACAACTGTAACTCTCGTG 59.207 52.381 0.00 0.00 0.00 4.35
13 14 1.687123 AGGCACAACTGTAACTCTCGT 59.313 47.619 0.00 0.00 0.00 4.18
14 15 2.329379 GAGGCACAACTGTAACTCTCG 58.671 52.381 5.97 0.00 31.42 4.04
15 16 2.613223 GGGAGGCACAACTGTAACTCTC 60.613 54.545 10.81 5.45 33.32 3.20
16 17 1.348036 GGGAGGCACAACTGTAACTCT 59.652 52.381 10.81 0.00 33.32 3.24
17 18 1.809684 GGGAGGCACAACTGTAACTC 58.190 55.000 5.02 5.02 32.54 3.01
18 19 0.034896 CGGGAGGCACAACTGTAACT 59.965 55.000 0.00 0.00 0.00 2.24
19 20 2.540145 CGGGAGGCACAACTGTAAC 58.460 57.895 0.00 0.00 0.00 2.50
32 33 1.197036 GCTCTTTTTCGTTTCCGGGAG 59.803 52.381 0.00 0.00 33.95 4.30
33 34 1.232119 GCTCTTTTTCGTTTCCGGGA 58.768 50.000 0.00 0.00 33.95 5.14
34 35 0.948678 TGCTCTTTTTCGTTTCCGGG 59.051 50.000 0.00 0.00 33.95 5.73
35 36 1.659211 CGTGCTCTTTTTCGTTTCCGG 60.659 52.381 0.00 0.00 33.95 5.14
36 37 1.004292 ACGTGCTCTTTTTCGTTTCCG 60.004 47.619 0.00 0.00 32.62 4.30
37 38 2.750301 ACGTGCTCTTTTTCGTTTCC 57.250 45.000 0.00 0.00 32.62 3.13
40 41 4.095610 CAGAAAACGTGCTCTTTTTCGTT 58.904 39.130 18.77 5.90 45.97 3.85
41 42 3.126343 ACAGAAAACGTGCTCTTTTTCGT 59.874 39.130 18.77 16.82 42.59 3.85
42 43 3.680789 ACAGAAAACGTGCTCTTTTTCG 58.319 40.909 18.77 16.39 42.59 3.46
43 44 6.389622 AAAACAGAAAACGTGCTCTTTTTC 57.610 33.333 17.79 17.79 40.06 2.29
44 45 6.779115 AAAAACAGAAAACGTGCTCTTTTT 57.221 29.167 3.00 3.00 0.00 1.94
66 67 2.542595 GTGACTCTCGCGAAAGGAAAAA 59.457 45.455 14.96 0.00 0.00 1.94
67 68 2.132762 GTGACTCTCGCGAAAGGAAAA 58.867 47.619 14.96 0.00 0.00 2.29
68 69 1.779569 GTGACTCTCGCGAAAGGAAA 58.220 50.000 14.96 0.00 0.00 3.13
69 70 3.491581 GTGACTCTCGCGAAAGGAA 57.508 52.632 14.96 0.00 0.00 3.36
110 111 8.601845 AAGAAAAAGCAGTAAACACAGTTTTT 57.398 26.923 0.03 0.00 0.00 1.94
111 112 7.330946 GGAAGAAAAAGCAGTAAACACAGTTTT 59.669 33.333 0.03 0.00 0.00 2.43
112 113 6.811665 GGAAGAAAAAGCAGTAAACACAGTTT 59.188 34.615 0.51 0.51 0.00 2.66
113 114 6.152831 AGGAAGAAAAAGCAGTAAACACAGTT 59.847 34.615 0.00 0.00 0.00 3.16
114 115 5.652452 AGGAAGAAAAAGCAGTAAACACAGT 59.348 36.000 0.00 0.00 0.00 3.55
115 116 6.136541 AGGAAGAAAAAGCAGTAAACACAG 57.863 37.500 0.00 0.00 0.00 3.66
116 117 6.524101 AAGGAAGAAAAAGCAGTAAACACA 57.476 33.333 0.00 0.00 0.00 3.72
117 118 6.196538 CGAAAGGAAGAAAAAGCAGTAAACAC 59.803 38.462 0.00 0.00 0.00 3.32
118 119 6.262601 CGAAAGGAAGAAAAAGCAGTAAACA 58.737 36.000 0.00 0.00 0.00 2.83
119 120 5.173312 GCGAAAGGAAGAAAAAGCAGTAAAC 59.827 40.000 0.00 0.00 0.00 2.01
120 121 5.278604 GCGAAAGGAAGAAAAAGCAGTAAA 58.721 37.500 0.00 0.00 0.00 2.01
121 122 4.553938 CGCGAAAGGAAGAAAAAGCAGTAA 60.554 41.667 0.00 0.00 0.00 2.24
122 123 3.059188 CGCGAAAGGAAGAAAAAGCAGTA 60.059 43.478 0.00 0.00 0.00 2.74
123 124 2.287009 CGCGAAAGGAAGAAAAAGCAGT 60.287 45.455 0.00 0.00 0.00 4.40
124 125 2.032030 TCGCGAAAGGAAGAAAAAGCAG 60.032 45.455 6.20 0.00 0.00 4.24
125 126 1.944024 TCGCGAAAGGAAGAAAAAGCA 59.056 42.857 6.20 0.00 0.00 3.91
126 127 2.031944 ACTCGCGAAAGGAAGAAAAAGC 60.032 45.455 11.33 0.00 0.00 3.51
127 128 3.247648 TGACTCGCGAAAGGAAGAAAAAG 59.752 43.478 11.33 0.00 0.00 2.27
128 129 3.001939 GTGACTCGCGAAAGGAAGAAAAA 59.998 43.478 11.33 0.00 0.00 1.94
129 130 2.542595 GTGACTCGCGAAAGGAAGAAAA 59.457 45.455 11.33 0.00 0.00 2.29
130 131 2.132762 GTGACTCGCGAAAGGAAGAAA 58.867 47.619 11.33 0.00 0.00 2.52
131 132 1.779569 GTGACTCGCGAAAGGAAGAA 58.220 50.000 11.33 0.00 0.00 2.52
132 133 0.386858 CGTGACTCGCGAAAGGAAGA 60.387 55.000 11.33 0.00 39.94 2.87
133 134 0.386858 TCGTGACTCGCGAAAGGAAG 60.387 55.000 11.33 0.00 43.38 3.46
134 135 1.655885 TCGTGACTCGCGAAAGGAA 59.344 52.632 11.33 0.00 43.38 3.36
135 136 3.347168 TCGTGACTCGCGAAAGGA 58.653 55.556 11.33 7.32 43.38 3.36
141 142 0.163788 AAGCAAAATCGTGACTCGCG 59.836 50.000 0.00 0.00 39.67 5.87
142 143 1.464189 GGAAGCAAAATCGTGACTCGC 60.464 52.381 0.00 0.00 39.67 5.03
143 144 1.798223 TGGAAGCAAAATCGTGACTCG 59.202 47.619 0.00 0.00 41.41 4.18
144 145 2.411547 CGTGGAAGCAAAATCGTGACTC 60.412 50.000 0.00 0.00 0.00 3.36
145 146 1.531149 CGTGGAAGCAAAATCGTGACT 59.469 47.619 0.00 0.00 0.00 3.41
146 147 1.529438 TCGTGGAAGCAAAATCGTGAC 59.471 47.619 0.00 0.00 0.00 3.67
147 148 1.798223 CTCGTGGAAGCAAAATCGTGA 59.202 47.619 0.00 0.00 0.00 4.35
148 149 1.798223 TCTCGTGGAAGCAAAATCGTG 59.202 47.619 0.00 0.00 0.00 4.35
149 150 2.069273 CTCTCGTGGAAGCAAAATCGT 58.931 47.619 0.00 0.00 0.00 3.73
150 151 1.394917 CCTCTCGTGGAAGCAAAATCG 59.605 52.381 0.00 0.00 0.00 3.34
151 152 1.131315 GCCTCTCGTGGAAGCAAAATC 59.869 52.381 0.00 0.00 32.03 2.17
152 153 1.168714 GCCTCTCGTGGAAGCAAAAT 58.831 50.000 0.00 0.00 32.03 1.82
153 154 0.179032 TGCCTCTCGTGGAAGCAAAA 60.179 50.000 2.93 0.00 38.32 2.44
154 155 0.036732 ATGCCTCTCGTGGAAGCAAA 59.963 50.000 8.06 0.00 43.54 3.68
155 156 0.674581 CATGCCTCTCGTGGAAGCAA 60.675 55.000 8.06 0.00 43.54 3.91
156 157 1.078918 CATGCCTCTCGTGGAAGCA 60.079 57.895 6.83 6.83 44.30 3.91
157 158 0.179062 ATCATGCCTCTCGTGGAAGC 60.179 55.000 0.00 0.00 32.54 3.86
158 159 1.938577 CAATCATGCCTCTCGTGGAAG 59.061 52.381 0.00 0.00 32.54 3.46
159 160 1.278985 ACAATCATGCCTCTCGTGGAA 59.721 47.619 0.00 0.00 32.54 3.53
160 161 0.904649 ACAATCATGCCTCTCGTGGA 59.095 50.000 0.00 0.00 32.54 4.02
161 162 1.012086 CACAATCATGCCTCTCGTGG 58.988 55.000 0.00 0.00 32.54 4.94
162 163 0.376152 GCACAATCATGCCTCTCGTG 59.624 55.000 0.00 0.00 39.86 4.35
163 164 2.772739 GCACAATCATGCCTCTCGT 58.227 52.632 0.00 0.00 39.86 4.18
170 171 1.652124 CTCGCAAAAGCACAATCATGC 59.348 47.619 0.00 0.00 46.50 4.06
171 172 3.168963 CTCTCGCAAAAGCACAATCATG 58.831 45.455 0.00 0.00 0.00 3.07
172 173 2.816087 ACTCTCGCAAAAGCACAATCAT 59.184 40.909 0.00 0.00 0.00 2.45
173 174 2.221169 ACTCTCGCAAAAGCACAATCA 58.779 42.857 0.00 0.00 0.00 2.57
174 175 2.224079 TGACTCTCGCAAAAGCACAATC 59.776 45.455 0.00 0.00 0.00 2.67
175 176 2.221169 TGACTCTCGCAAAAGCACAAT 58.779 42.857 0.00 0.00 0.00 2.71
176 177 1.662517 TGACTCTCGCAAAAGCACAA 58.337 45.000 0.00 0.00 0.00 3.33
177 178 1.532437 CATGACTCTCGCAAAAGCACA 59.468 47.619 0.00 0.00 0.00 4.57
178 179 1.800586 TCATGACTCTCGCAAAAGCAC 59.199 47.619 0.00 0.00 0.00 4.40
179 180 2.168326 TCATGACTCTCGCAAAAGCA 57.832 45.000 0.00 0.00 0.00 3.91
180 181 3.754188 AATCATGACTCTCGCAAAAGC 57.246 42.857 0.00 0.00 0.00 3.51
181 182 4.322804 GCAAAATCATGACTCTCGCAAAAG 59.677 41.667 0.00 0.00 0.00 2.27
182 183 4.022935 AGCAAAATCATGACTCTCGCAAAA 60.023 37.500 0.00 0.00 0.00 2.44
183 184 3.503363 AGCAAAATCATGACTCTCGCAAA 59.497 39.130 0.00 0.00 0.00 3.68
184 185 3.076621 AGCAAAATCATGACTCTCGCAA 58.923 40.909 0.00 0.00 0.00 4.85
185 186 2.703416 AGCAAAATCATGACTCTCGCA 58.297 42.857 0.00 0.00 0.00 5.10
186 187 3.486542 GGAAGCAAAATCATGACTCTCGC 60.487 47.826 0.00 0.00 0.00 5.03
187 188 3.242220 CGGAAGCAAAATCATGACTCTCG 60.242 47.826 0.00 0.00 0.00 4.04
188 189 4.270178 CGGAAGCAAAATCATGACTCTC 57.730 45.455 0.00 0.00 0.00 3.20
204 205 1.153939 CCTGTGTCTCTCGCGGAAG 60.154 63.158 6.13 4.04 35.13 3.46
205 206 1.901948 ACCTGTGTCTCTCGCGGAA 60.902 57.895 6.13 0.00 35.13 4.30
206 207 2.282251 ACCTGTGTCTCTCGCGGA 60.282 61.111 6.13 1.01 35.13 5.54
207 208 1.583495 TACACCTGTGTCTCTCGCGG 61.583 60.000 6.13 0.00 43.74 6.46
208 209 0.454620 GTACACCTGTGTCTCTCGCG 60.455 60.000 6.14 0.00 43.74 5.87
209 210 0.882474 AGTACACCTGTGTCTCTCGC 59.118 55.000 6.14 0.00 43.74 5.03
210 211 3.566523 GAAAGTACACCTGTGTCTCTCG 58.433 50.000 6.14 0.00 43.74 4.04
211 212 3.566523 CGAAAGTACACCTGTGTCTCTC 58.433 50.000 6.14 0.66 43.74 3.20
212 213 2.288273 GCGAAAGTACACCTGTGTCTCT 60.288 50.000 6.14 4.45 43.74 3.10
213 214 2.059541 GCGAAAGTACACCTGTGTCTC 58.940 52.381 6.14 2.20 43.74 3.36
214 215 1.602165 CGCGAAAGTACACCTGTGTCT 60.602 52.381 0.00 1.82 43.74 3.41
215 216 0.782384 CGCGAAAGTACACCTGTGTC 59.218 55.000 0.00 0.00 43.74 3.67
216 217 0.386476 TCGCGAAAGTACACCTGTGT 59.614 50.000 6.20 8.17 46.87 3.72
217 218 1.060713 CTCGCGAAAGTACACCTGTG 58.939 55.000 11.33 0.00 0.00 3.66
218 219 0.956633 TCTCGCGAAAGTACACCTGT 59.043 50.000 11.33 0.00 0.00 4.00
219 220 1.068472 ACTCTCGCGAAAGTACACCTG 60.068 52.381 14.61 0.00 0.00 4.00
220 221 1.199558 GACTCTCGCGAAAGTACACCT 59.800 52.381 16.35 0.00 0.00 4.00
221 222 1.615502 GACTCTCGCGAAAGTACACC 58.384 55.000 16.35 0.00 0.00 4.16
222 223 1.615502 GGACTCTCGCGAAAGTACAC 58.384 55.000 19.93 7.71 0.00 2.90
223 224 0.524862 GGGACTCTCGCGAAAGTACA 59.475 55.000 25.40 0.00 0.00 2.90
224 225 3.325816 GGGACTCTCGCGAAAGTAC 57.674 57.895 16.74 16.74 0.00 2.73
232 233 4.477975 CACGACCGGGACTCTCGC 62.478 72.222 6.32 0.00 0.00 5.03
233 234 4.477975 GCACGACCGGGACTCTCG 62.478 72.222 6.32 8.31 0.00 4.04
234 235 4.131088 GGCACGACCGGGACTCTC 62.131 72.222 6.32 0.00 0.00 3.20
235 236 4.680537 AGGCACGACCGGGACTCT 62.681 66.667 6.32 0.00 46.52 3.24
243 244 2.939261 TTTCCGAGGAGGCACGACC 61.939 63.158 0.00 0.00 40.77 4.79
244 245 1.737008 GTTTCCGAGGAGGCACGAC 60.737 63.158 0.00 0.00 40.77 4.34
245 246 2.654877 GTTTCCGAGGAGGCACGA 59.345 61.111 0.00 0.00 40.77 4.35
246 247 2.758770 TTCGTTTCCGAGGAGGCACG 62.759 60.000 11.86 11.86 45.24 5.34
247 248 0.601841 TTTCGTTTCCGAGGAGGCAC 60.602 55.000 0.00 0.00 45.24 5.01
248 249 0.107081 TTTTCGTTTCCGAGGAGGCA 59.893 50.000 0.00 0.00 45.24 4.75
249 250 1.232119 TTTTTCGTTTCCGAGGAGGC 58.768 50.000 0.00 0.00 45.24 4.70
283 284 1.597027 AAACCCGTGACTCTTGCGG 60.597 57.895 0.00 0.00 44.55 5.69
284 285 1.569493 CAAACCCGTGACTCTTGCG 59.431 57.895 0.00 0.00 0.00 4.85
285 286 1.166531 AGCAAACCCGTGACTCTTGC 61.167 55.000 0.00 0.00 42.10 4.01
286 287 1.308998 AAGCAAACCCGTGACTCTTG 58.691 50.000 0.00 0.00 0.00 3.02
287 288 1.947456 GAAAGCAAACCCGTGACTCTT 59.053 47.619 0.00 0.00 0.00 2.85
288 289 1.594331 GAAAGCAAACCCGTGACTCT 58.406 50.000 0.00 0.00 0.00 3.24
289 290 0.234884 CGAAAGCAAACCCGTGACTC 59.765 55.000 0.00 0.00 0.00 3.36
290 291 2.317230 CGAAAGCAAACCCGTGACT 58.683 52.632 0.00 0.00 0.00 3.41
291 292 4.914291 CGAAAGCAAACCCGTGAC 57.086 55.556 0.00 0.00 0.00 3.67
303 304 0.798776 AACCATGCTTCTCGCGAAAG 59.201 50.000 11.33 16.98 43.27 2.62
304 305 0.516877 CAACCATGCTTCTCGCGAAA 59.483 50.000 11.33 6.90 43.27 3.46
305 306 0.602638 ACAACCATGCTTCTCGCGAA 60.603 50.000 11.33 0.00 43.27 4.70
306 307 1.005037 ACAACCATGCTTCTCGCGA 60.005 52.632 9.26 9.26 43.27 5.87
307 308 1.133253 CACAACCATGCTTCTCGCG 59.867 57.895 0.00 0.00 43.27 5.87
308 309 1.089920 ATCACAACCATGCTTCTCGC 58.910 50.000 0.00 0.00 39.77 5.03
309 310 3.189080 TGAAATCACAACCATGCTTCTCG 59.811 43.478 0.00 0.00 0.00 4.04
310 311 4.771590 TGAAATCACAACCATGCTTCTC 57.228 40.909 0.00 0.00 0.00 2.87
311 312 4.768448 TCATGAAATCACAACCATGCTTCT 59.232 37.500 0.00 0.00 37.06 2.85
312 313 5.063180 TCATGAAATCACAACCATGCTTC 57.937 39.130 0.00 0.00 37.06 3.86
313 314 4.525487 ACTCATGAAATCACAACCATGCTT 59.475 37.500 0.00 0.00 37.06 3.91
314 315 4.084287 ACTCATGAAATCACAACCATGCT 58.916 39.130 0.00 0.00 37.06 3.79
315 316 4.445452 ACTCATGAAATCACAACCATGC 57.555 40.909 0.00 0.00 37.06 4.06
316 317 6.596888 AGTCTACTCATGAAATCACAACCATG 59.403 38.462 0.00 0.00 38.12 3.66
317 318 6.596888 CAGTCTACTCATGAAATCACAACCAT 59.403 38.462 0.00 0.00 0.00 3.55
318 319 5.934043 CAGTCTACTCATGAAATCACAACCA 59.066 40.000 0.00 0.00 0.00 3.67
319 320 6.166279 TCAGTCTACTCATGAAATCACAACC 58.834 40.000 0.00 0.00 0.00 3.77
320 321 7.332926 ACATCAGTCTACTCATGAAATCACAAC 59.667 37.037 0.66 0.00 0.00 3.32
321 322 7.389232 ACATCAGTCTACTCATGAAATCACAA 58.611 34.615 0.66 0.00 0.00 3.33
322 323 6.939622 ACATCAGTCTACTCATGAAATCACA 58.060 36.000 0.66 0.00 0.00 3.58
323 324 7.840342 AACATCAGTCTACTCATGAAATCAC 57.160 36.000 0.66 0.00 0.00 3.06
324 325 9.591792 CTAAACATCAGTCTACTCATGAAATCA 57.408 33.333 0.66 0.00 0.00 2.57
325 326 9.039870 CCTAAACATCAGTCTACTCATGAAATC 57.960 37.037 0.66 0.00 0.00 2.17
326 327 8.543774 ACCTAAACATCAGTCTACTCATGAAAT 58.456 33.333 0.66 0.00 0.00 2.17
327 328 7.907389 ACCTAAACATCAGTCTACTCATGAAA 58.093 34.615 0.66 0.00 0.00 2.69
328 329 7.178451 TGACCTAAACATCAGTCTACTCATGAA 59.822 37.037 0.66 0.00 0.00 2.57
329 330 6.663523 TGACCTAAACATCAGTCTACTCATGA 59.336 38.462 0.66 0.00 0.00 3.07
330 331 6.867550 TGACCTAAACATCAGTCTACTCATG 58.132 40.000 0.00 0.00 0.00 3.07
331 332 6.097554 CCTGACCTAAACATCAGTCTACTCAT 59.902 42.308 0.00 0.00 0.00 2.90
332 333 5.419155 CCTGACCTAAACATCAGTCTACTCA 59.581 44.000 0.00 0.00 0.00 3.41
333 334 5.419471 ACCTGACCTAAACATCAGTCTACTC 59.581 44.000 0.00 0.00 0.00 2.59
334 335 5.334421 ACCTGACCTAAACATCAGTCTACT 58.666 41.667 0.00 0.00 0.00 2.57
335 336 5.662674 ACCTGACCTAAACATCAGTCTAC 57.337 43.478 0.00 0.00 0.00 2.59
336 337 5.778241 TGAACCTGACCTAAACATCAGTCTA 59.222 40.000 0.00 0.00 0.00 2.59
341 342 4.072131 GCTTGAACCTGACCTAAACATCA 58.928 43.478 0.00 0.00 0.00 3.07
352 353 3.214328 GAAAAGTGAGGCTTGAACCTGA 58.786 45.455 0.00 0.00 41.32 3.86
366 367 1.876156 GGCTCTGGACTGTGAAAAGTG 59.124 52.381 0.00 0.00 0.00 3.16
434 435 9.580916 GTAACGCTACATCATACATGTATTTTG 57.419 33.333 15.85 16.82 34.42 2.44
441 442 7.643528 ATCAAGTAACGCTACATCATACATG 57.356 36.000 0.00 0.00 0.00 3.21
447 448 5.079689 TGGAATCAAGTAACGCTACATCA 57.920 39.130 0.00 0.00 0.00 3.07
506 507 9.136323 CATTTACCCCTAGAAAAGATAAATGCT 57.864 33.333 0.00 0.00 33.95 3.79
517 518 4.618378 AATGCCCATTTACCCCTAGAAA 57.382 40.909 0.00 0.00 0.00 2.52
519 520 5.615261 AGATAAATGCCCATTTACCCCTAGA 59.385 40.000 13.85 0.00 43.54 2.43
520 521 5.711976 CAGATAAATGCCCATTTACCCCTAG 59.288 44.000 13.85 0.00 43.54 3.02
531 533 0.562177 ATGGCCCAGATAAATGCCCA 59.438 50.000 0.00 0.00 43.35 5.36
542 544 4.489771 GTCCGGTCCATGGCCCAG 62.490 72.222 13.30 0.00 0.00 4.45
563 565 2.747855 GCAAAGCTCGGGACCCAG 60.748 66.667 12.15 8.41 0.00 4.45
600 602 3.076278 TATCGGGCCGGGTTTCGT 61.076 61.111 27.98 6.22 37.11 3.85
615 617 2.494870 GGTGTCACGTAACTCTGGGTAT 59.505 50.000 0.00 0.00 0.00 2.73
616 618 1.888512 GGTGTCACGTAACTCTGGGTA 59.111 52.381 0.00 0.00 0.00 3.69
617 619 0.677842 GGTGTCACGTAACTCTGGGT 59.322 55.000 0.00 0.00 0.00 4.51
619 621 1.067974 TGTGGTGTCACGTAACTCTGG 59.932 52.381 0.00 0.00 46.42 3.86
620 622 2.124903 GTGTGGTGTCACGTAACTCTG 58.875 52.381 0.00 0.00 46.42 3.35
621 623 1.068127 GGTGTGGTGTCACGTAACTCT 59.932 52.381 0.00 0.00 46.42 3.24
622 624 1.494824 GGTGTGGTGTCACGTAACTC 58.505 55.000 0.00 0.00 46.42 3.01
623 625 0.105408 GGGTGTGGTGTCACGTAACT 59.895 55.000 0.00 0.00 46.42 2.24
626 628 1.750341 CTGGGGTGTGGTGTCACGTA 61.750 60.000 0.00 0.00 46.42 3.57
628 630 2.280797 CTGGGGTGTGGTGTCACG 60.281 66.667 0.00 0.00 46.42 4.35
629 631 2.594592 GCTGGGGTGTGGTGTCAC 60.595 66.667 0.00 0.00 43.87 3.67
630 632 3.093172 TGCTGGGGTGTGGTGTCA 61.093 61.111 0.00 0.00 0.00 3.58
631 633 2.281761 CTGCTGGGGTGTGGTGTC 60.282 66.667 0.00 0.00 0.00 3.67
632 634 4.586235 GCTGCTGGGGTGTGGTGT 62.586 66.667 0.00 0.00 0.00 4.16
635 637 3.892104 ATTGGCTGCTGGGGTGTGG 62.892 63.158 0.00 0.00 0.00 4.17
636 638 2.283388 ATTGGCTGCTGGGGTGTG 60.283 61.111 0.00 0.00 0.00 3.82
637 639 2.036256 GATTGGCTGCTGGGGTGT 59.964 61.111 0.00 0.00 0.00 4.16
638 640 2.036098 TGATTGGCTGCTGGGGTG 59.964 61.111 0.00 0.00 0.00 4.61
639 641 2.036256 GTGATTGGCTGCTGGGGT 59.964 61.111 0.00 0.00 0.00 4.95
640 642 3.136123 CGTGATTGGCTGCTGGGG 61.136 66.667 0.00 0.00 0.00 4.96
641 643 2.046023 TCGTGATTGGCTGCTGGG 60.046 61.111 0.00 0.00 0.00 4.45
642 644 0.957395 AACTCGTGATTGGCTGCTGG 60.957 55.000 0.00 0.00 0.00 4.85
643 645 0.877071 AAACTCGTGATTGGCTGCTG 59.123 50.000 0.00 0.00 0.00 4.41
644 646 1.160137 GAAACTCGTGATTGGCTGCT 58.840 50.000 0.00 0.00 0.00 4.24
645 647 1.160137 AGAAACTCGTGATTGGCTGC 58.840 50.000 0.00 0.00 0.00 5.25
655 657 5.570234 TTTTTAGCAACCAAGAAACTCGT 57.430 34.783 0.00 0.00 0.00 4.18
697 702 0.321653 GACGTGATTGGCTGGGTCTT 60.322 55.000 0.00 0.00 0.00 3.01
699 704 1.003839 TGACGTGATTGGCTGGGTC 60.004 57.895 0.00 0.00 0.00 4.46
701 706 1.300971 CTGTGACGTGATTGGCTGGG 61.301 60.000 0.00 0.00 0.00 4.45
720 727 2.270874 ATCCGTGGGATGGAGGTTGC 62.271 60.000 0.00 0.00 41.43 4.17
761 771 1.838073 ATGGAGTTTTCGGGGCGACT 61.838 55.000 0.00 0.00 34.89 4.18
762 772 1.366854 GATGGAGTTTTCGGGGCGAC 61.367 60.000 0.00 0.00 34.89 5.19
764 774 2.112815 GGATGGAGTTTTCGGGGCG 61.113 63.158 0.00 0.00 0.00 6.13
765 775 1.001393 TGGATGGAGTTTTCGGGGC 60.001 57.895 0.00 0.00 0.00 5.80
774 784 1.690219 GATGGACGGCTGGATGGAGT 61.690 60.000 0.00 0.00 0.00 3.85
776 786 1.383109 AGATGGACGGCTGGATGGA 60.383 57.895 0.00 0.00 0.00 3.41
778 788 1.070445 GGAGATGGACGGCTGGATG 59.930 63.158 0.00 0.00 0.00 3.51
779 789 2.143419 GGGAGATGGACGGCTGGAT 61.143 63.158 0.00 0.00 0.00 3.41
780 790 2.764128 GGGAGATGGACGGCTGGA 60.764 66.667 0.00 0.00 0.00 3.86
1495 1839 0.031111 TCCAGGCTACATAGGGCAGT 60.031 55.000 0.00 0.00 0.00 4.40
1496 1840 1.131638 TTCCAGGCTACATAGGGCAG 58.868 55.000 0.00 0.00 0.00 4.85
1577 1940 4.712191 TTGCAAAATCACAAAGCAATCG 57.288 36.364 0.00 0.00 39.95 3.34
1655 2026 3.560896 ACCAAAATGCTTTGACATTGCAC 59.439 39.130 5.23 0.00 44.03 4.57
1704 2086 2.614779 ACTGAATCACACATCGAGCAG 58.385 47.619 0.00 0.00 0.00 4.24
1772 2155 2.357637 CACTTCCGACAAAGCCAAAAGA 59.642 45.455 0.00 0.00 0.00 2.52
1782 2165 3.815809 ACCTCAAATTCACTTCCGACAA 58.184 40.909 0.00 0.00 0.00 3.18
1786 2169 4.568152 ACAAACCTCAAATTCACTTCCG 57.432 40.909 0.00 0.00 0.00 4.30
1801 2191 1.828595 ACCAACCAGTCCAAACAAACC 59.171 47.619 0.00 0.00 0.00 3.27
1831 2222 2.152016 CATCTTCGCCATCAGCATCAT 58.848 47.619 0.00 0.00 44.04 2.45
1832 2223 1.589803 CATCTTCGCCATCAGCATCA 58.410 50.000 0.00 0.00 44.04 3.07
1835 2226 2.175621 CGCATCTTCGCCATCAGCA 61.176 57.895 0.00 0.00 44.04 4.41
1841 2232 1.153765 CTCTGTCGCATCTTCGCCA 60.154 57.895 0.00 0.00 0.00 5.69
1844 2235 1.391485 CAAACCTCTGTCGCATCTTCG 59.609 52.381 0.00 0.00 0.00 3.79
1932 2326 4.737054 AGTTGTTCAGCTTTTGTTCACTG 58.263 39.130 0.00 0.00 0.00 3.66
1933 2327 5.163513 CAAGTTGTTCAGCTTTTGTTCACT 58.836 37.500 0.00 0.00 0.00 3.41
1979 2387 9.390795 CTGCAAGCACTATTGATTTGATAATAC 57.609 33.333 0.00 0.00 31.55 1.89
2020 2435 7.698130 GCTATGGAAGATAACACAACACAATTC 59.302 37.037 0.00 0.00 0.00 2.17
2078 2494 7.477494 GTTGTGTGTGTTAAACCTGTAAGAAT 58.523 34.615 0.00 0.00 34.07 2.40
2118 2540 1.209621 TAACAGGCCCAGATACCACC 58.790 55.000 0.00 0.00 0.00 4.61
2151 2585 7.234166 ACAGATGGTCTTTCCTGATGAATTTTT 59.766 33.333 0.00 0.00 37.07 1.94
2170 2604 2.821366 GAGGCCGCACACAGATGG 60.821 66.667 0.00 0.00 0.00 3.51
2235 2692 1.545582 TGGTCTTGCAAATTGCCTAGC 59.454 47.619 15.98 10.45 44.23 3.42
2294 2751 0.907486 CTGCCTGGAATCTCACCTGA 59.093 55.000 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.