Multiple sequence alignment - TraesCS2A01G561500

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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 TraesCS2A01G561500 chr2A 100.000 3233 0 0 1 3233 763059107 763055875 0.000000e+00 5971.0
1 TraesCS2A01G561500 chr2A 76.430 577 95 29 1691 2242 762660654 762661214 1.140000e-69 274.0
2 TraesCS2A01G561500 chr2A 74.784 579 99 30 1696 2243 763916854 763916292 1.950000e-52 217.0
3 TraesCS2A01G561500 chr2A 76.882 372 75 8 1700 2067 762720887 762721251 1.970000e-47 200.0
4 TraesCS2A01G561500 chr2A 87.879 99 7 3 3134 3232 762805236 762805329 9.480000e-21 111.0
5 TraesCS2A01G561500 chr2B 93.622 2289 51 24 760 3015 794489924 794492150 0.000000e+00 3330.0
6 TraesCS2A01G561500 chr2B 82.086 1390 169 40 1038 2404 744201859 744200527 0.000000e+00 1114.0
7 TraesCS2A01G561500 chr2B 92.982 171 9 3 3038 3207 794492426 794492594 2.490000e-61 246.0
8 TraesCS2A01G561500 chr2B 79.661 354 53 12 1039 1387 797183102 797183441 1.500000e-58 237.0
9 TraesCS2A01G561500 chr2B 82.353 204 18 10 2218 2404 794488639 794488841 9.280000e-36 161.0
10 TraesCS2A01G561500 chr2B 94.545 55 3 0 305 359 794489679 794489733 5.750000e-13 86.1
11 TraesCS2A01G561500 chr2D 84.901 1159 137 22 1268 2404 609889302 609888160 0.000000e+00 1136.0
12 TraesCS2A01G561500 chr2D 87.203 883 82 6 760 1642 636546361 636547212 0.000000e+00 976.0
13 TraesCS2A01G561500 chr2D 91.633 502 42 0 1715 2216 636581754 636582255 0.000000e+00 695.0
14 TraesCS2A01G561500 chr2D 78.756 579 95 21 1691 2246 637385427 637384854 2.370000e-96 363.0
15 TraesCS2A01G561500 chr2D 77.240 558 105 15 1702 2242 637353568 637353016 1.130000e-79 307.0
16 TraesCS2A01G561500 chr2D 78.628 379 71 8 1710 2083 637357446 637357073 3.220000e-60 243.0
17 TraesCS2A01G561500 chr2D 78.385 384 73 5 1703 2083 637345255 637344879 1.160000e-59 241.0
18 TraesCS2A01G561500 chr2D 82.063 223 24 9 2806 3015 636589909 636590128 3.310000e-40 176.0
19 TraesCS2A01G561500 chr2D 86.207 87 9 2 1700 1783 637110296 637110210 1.240000e-14 91.6
20 TraesCS2A01G561500 chr4B 80.363 331 48 16 1064 1387 673381007 673380687 5.390000e-58 235.0


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 TraesCS2A01G561500 chr2A 763055875 763059107 3232 True 5971.000 5971 100.0000 1 3233 1 chr2A.!!$R1 3232
1 TraesCS2A01G561500 chr2A 762660654 762661214 560 False 274.000 274 76.4300 1691 2242 1 chr2A.!!$F1 551
2 TraesCS2A01G561500 chr2A 763916292 763916854 562 True 217.000 217 74.7840 1696 2243 1 chr2A.!!$R2 547
3 TraesCS2A01G561500 chr2B 744200527 744201859 1332 True 1114.000 1114 82.0860 1038 2404 1 chr2B.!!$R1 1366
4 TraesCS2A01G561500 chr2B 794488639 794492594 3955 False 955.775 3330 90.8755 305 3207 4 chr2B.!!$F2 2902
5 TraesCS2A01G561500 chr2D 609888160 609889302 1142 True 1136.000 1136 84.9010 1268 2404 1 chr2D.!!$R1 1136
6 TraesCS2A01G561500 chr2D 636546361 636547212 851 False 976.000 976 87.2030 760 1642 1 chr2D.!!$F1 882
7 TraesCS2A01G561500 chr2D 636581754 636582255 501 False 695.000 695 91.6330 1715 2216 1 chr2D.!!$F2 501
8 TraesCS2A01G561500 chr2D 637384854 637385427 573 True 363.000 363 78.7560 1691 2246 1 chr2D.!!$R4 555
9 TraesCS2A01G561500 chr2D 637353016 637357446 4430 True 275.000 307 77.9340 1702 2242 2 chr2D.!!$R5 540

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
165 166 0.100861 GGGCGTCCACGTTTTTCAAA 59.899 50.0 0.00 0.00 42.22 2.69 F
408 1145 0.243095 AGAAGAGGAACGTACGGCAC 59.757 55.0 21.06 8.68 0.00 5.01 F
410 1147 0.243095 AAGAGGAACGTACGGCACTC 59.757 55.0 21.06 20.73 0.00 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2055 4265 0.687757 TACATCCGGCCTTGAGCTCT 60.688 55.000 16.19 0.0 43.05 4.09 R
2126 4360 1.421268 TGAGGCTGAACACCTTGACAT 59.579 47.619 0.00 0.0 37.77 3.06 R
2470 4719 4.322057 AGAAACATCCAATACTGGCCTT 57.678 40.909 3.32 0.0 43.17 4.35 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 6.068473 CAATGTCATCAACCATGGTAGATG 57.932 41.667 20.12 13.52 39.29 2.90
24 25 4.155063 TGTCATCAACCATGGTAGATGG 57.845 45.455 20.12 7.46 44.54 3.51
30 31 3.295734 CCATGGTAGATGGTGAGCG 57.704 57.895 2.57 0.00 34.56 5.03
31 32 0.752658 CCATGGTAGATGGTGAGCGA 59.247 55.000 2.57 0.00 34.56 4.93
32 33 1.269988 CCATGGTAGATGGTGAGCGAG 60.270 57.143 2.57 0.00 34.56 5.03
33 34 1.683385 CATGGTAGATGGTGAGCGAGA 59.317 52.381 0.00 0.00 0.00 4.04
34 35 1.393603 TGGTAGATGGTGAGCGAGAG 58.606 55.000 0.00 0.00 0.00 3.20
36 37 2.235016 GGTAGATGGTGAGCGAGAGAT 58.765 52.381 0.00 0.00 0.00 2.75
37 38 2.030363 GGTAGATGGTGAGCGAGAGATG 60.030 54.545 0.00 0.00 0.00 2.90
38 39 0.388659 AGATGGTGAGCGAGAGATGC 59.611 55.000 0.00 0.00 0.00 3.91
42 43 1.065926 TGGTGAGCGAGAGATGCATTT 60.066 47.619 0.00 0.00 33.85 2.32
44 45 2.274437 GTGAGCGAGAGATGCATTTCA 58.726 47.619 18.55 4.10 33.85 2.69
48 49 1.945394 GCGAGAGATGCATTTCATGGT 59.055 47.619 18.55 0.00 35.05 3.55
49 50 2.357009 GCGAGAGATGCATTTCATGGTT 59.643 45.455 18.55 0.00 35.05 3.67
50 51 3.181493 GCGAGAGATGCATTTCATGGTTT 60.181 43.478 18.55 0.00 35.05 3.27
52 53 4.110482 GAGAGATGCATTTCATGGTTTGC 58.890 43.478 18.55 7.46 35.05 3.68
59 60 5.363101 TGCATTTCATGGTTTGCAAAACTA 58.637 33.333 26.56 14.19 41.76 2.24
60 61 5.236047 TGCATTTCATGGTTTGCAAAACTAC 59.764 36.000 26.56 9.54 41.76 2.73
61 62 5.466393 GCATTTCATGGTTTGCAAAACTACT 59.534 36.000 26.56 9.85 35.22 2.57
62 63 6.018016 GCATTTCATGGTTTGCAAAACTACTT 60.018 34.615 26.56 7.62 35.22 2.24
63 64 6.900568 TTTCATGGTTTGCAAAACTACTTG 57.099 33.333 26.56 17.83 0.00 3.16
64 65 5.843673 TCATGGTTTGCAAAACTACTTGA 57.156 34.783 26.56 19.52 0.00 3.02
66 67 4.040445 TGGTTTGCAAAACTACTTGAGC 57.960 40.909 26.56 6.51 0.00 4.26
67 68 3.699038 TGGTTTGCAAAACTACTTGAGCT 59.301 39.130 26.56 0.00 0.00 4.09
68 69 4.159506 TGGTTTGCAAAACTACTTGAGCTT 59.840 37.500 26.56 0.00 0.00 3.74
69 70 5.109210 GGTTTGCAAAACTACTTGAGCTTT 58.891 37.500 20.05 0.00 0.00 3.51
70 71 6.127591 TGGTTTGCAAAACTACTTGAGCTTTA 60.128 34.615 26.56 0.00 0.00 1.85
74 75 7.510549 TGCAAAACTACTTGAGCTTTAATCT 57.489 32.000 0.00 0.00 0.00 2.40
75 76 7.362662 TGCAAAACTACTTGAGCTTTAATCTG 58.637 34.615 0.00 0.00 0.00 2.90
77 78 7.362662 CAAAACTACTTGAGCTTTAATCTGCA 58.637 34.615 0.00 0.00 0.00 4.41
78 79 7.693969 AAACTACTTGAGCTTTAATCTGCAT 57.306 32.000 0.00 0.00 0.00 3.96
79 80 7.693969 AACTACTTGAGCTTTAATCTGCATT 57.306 32.000 0.00 0.00 0.00 3.56
80 81 8.792830 AACTACTTGAGCTTTAATCTGCATTA 57.207 30.769 0.00 0.00 0.00 1.90
83 84 7.693969 ACTTGAGCTTTAATCTGCATTAACT 57.306 32.000 0.00 0.00 34.73 2.24
90 91 8.778358 AGCTTTAATCTGCATTAACTATAGTGC 58.222 33.333 6.06 6.14 43.09 4.40
99 100 8.292444 TGCATTAACTATAGTGCATTTTCCTT 57.708 30.769 6.06 0.00 46.13 3.36
101 102 9.586435 GCATTAACTATAGTGCATTTTCCTTTT 57.414 29.630 6.06 0.00 42.52 2.27
130 131 3.844804 CCCCCAGAAAAGGAGTTAGTACT 59.155 47.826 0.00 0.00 37.31 2.73
146 147 9.997482 GAGTTAGTACTCTGTCTTCAATAAGAG 57.003 37.037 0.00 0.00 45.99 2.85
148 149 6.783708 AGTACTCTGTCTTCAATAAGAGGG 57.216 41.667 0.00 0.00 42.40 4.30
150 151 3.118956 ACTCTGTCTTCAATAAGAGGGCG 60.119 47.826 3.80 0.00 42.40 6.13
151 152 2.832129 TCTGTCTTCAATAAGAGGGCGT 59.168 45.455 0.00 0.00 42.40 5.68
152 153 3.119101 TCTGTCTTCAATAAGAGGGCGTC 60.119 47.826 0.00 0.00 42.40 5.19
153 154 2.093658 TGTCTTCAATAAGAGGGCGTCC 60.094 50.000 0.00 0.00 42.40 4.79
154 155 2.093658 GTCTTCAATAAGAGGGCGTCCA 60.094 50.000 9.71 0.00 42.40 4.02
156 157 0.174845 TCAATAAGAGGGCGTCCACG 59.825 55.000 9.71 0.00 43.27 4.94
160 161 0.393820 TAAGAGGGCGTCCACGTTTT 59.606 50.000 9.71 0.00 42.22 2.43
164 165 0.748729 AGGGCGTCCACGTTTTTCAA 60.749 50.000 9.71 0.00 42.22 2.69
165 166 0.100861 GGGCGTCCACGTTTTTCAAA 59.899 50.000 0.00 0.00 42.22 2.69
167 168 2.465855 GGCGTCCACGTTTTTCAAAAT 58.534 42.857 0.36 0.00 42.22 1.82
169 170 3.307512 GGCGTCCACGTTTTTCAAAATTT 59.692 39.130 0.36 0.00 42.22 1.82
170 171 4.503370 GGCGTCCACGTTTTTCAAAATTTA 59.497 37.500 0.36 0.00 42.22 1.40
171 172 5.005490 GGCGTCCACGTTTTTCAAAATTTAA 59.995 36.000 0.36 0.00 42.22 1.52
173 174 6.237622 GCGTCCACGTTTTTCAAAATTTAAGT 60.238 34.615 0.36 0.00 42.22 2.24
174 175 7.668190 CGTCCACGTTTTTCAAAATTTAAGTT 58.332 30.769 0.00 0.00 34.11 2.66
176 177 9.256715 GTCCACGTTTTTCAAAATTTAAGTTTG 57.743 29.630 11.05 11.05 37.32 2.93
179 180 9.256715 CACGTTTTTCAAAATTTAAGTTTGACC 57.743 29.630 18.15 7.65 42.98 4.02
180 181 8.989980 ACGTTTTTCAAAATTTAAGTTTGACCA 58.010 25.926 18.15 7.31 42.98 4.02
191 192 9.705290 AATTTAAGTTTGACCATGAATGTTACC 57.295 29.630 0.00 0.00 0.00 2.85
192 193 5.371115 AAGTTTGACCATGAATGTTACCG 57.629 39.130 0.00 0.00 0.00 4.02
194 195 5.253330 AGTTTGACCATGAATGTTACCGAT 58.747 37.500 0.00 0.00 0.00 4.18
196 197 6.882140 AGTTTGACCATGAATGTTACCGATAA 59.118 34.615 0.00 0.00 0.00 1.75
198 199 7.689446 TTGACCATGAATGTTACCGATAAAA 57.311 32.000 0.00 0.00 0.00 1.52
199 200 7.873719 TGACCATGAATGTTACCGATAAAAT 57.126 32.000 0.00 0.00 0.00 1.82
200 201 7.702386 TGACCATGAATGTTACCGATAAAATG 58.298 34.615 0.00 0.00 0.00 2.32
202 203 7.479980 ACCATGAATGTTACCGATAAAATGTG 58.520 34.615 0.00 0.00 0.00 3.21
204 205 5.564768 TGAATGTTACCGATAAAATGTGCG 58.435 37.500 0.00 0.00 0.00 5.34
205 206 5.122554 TGAATGTTACCGATAAAATGTGCGT 59.877 36.000 0.00 0.00 0.00 5.24
206 207 6.313164 TGAATGTTACCGATAAAATGTGCGTA 59.687 34.615 0.00 0.00 0.00 4.42
209 210 5.581479 TGTTACCGATAAAATGTGCGTATGT 59.419 36.000 0.00 0.00 0.00 2.29
211 212 3.936453 ACCGATAAAATGTGCGTATGTGT 59.064 39.130 0.00 0.00 0.00 3.72
212 213 4.033587 ACCGATAAAATGTGCGTATGTGTC 59.966 41.667 0.00 0.00 0.00 3.67
213 214 4.033472 CCGATAAAATGTGCGTATGTGTCA 59.967 41.667 0.00 0.00 0.00 3.58
217 218 7.848539 CGATAAAATGTGCGTATGTGTCATAAA 59.151 33.333 0.00 0.00 0.00 1.40
247 248 9.980780 TGTGTCGTTGTATTCATATTAAATGTG 57.019 29.630 0.00 0.00 0.00 3.21
267 268 9.507329 AAATGTGACATAATTCTCAAGTACAGT 57.493 29.630 0.00 0.00 0.00 3.55
269 270 8.981724 TGTGACATAATTCTCAAGTACAGTAC 57.018 34.615 2.05 2.05 0.00 2.73
270 271 8.033038 TGTGACATAATTCTCAAGTACAGTACC 58.967 37.037 7.13 0.00 0.00 3.34
271 272 8.251721 GTGACATAATTCTCAAGTACAGTACCT 58.748 37.037 7.13 0.00 0.00 3.08
304 305 7.145323 GGTTAAAGTTGTCAAATATGTGTGCT 58.855 34.615 0.00 0.00 0.00 4.40
305 306 7.651704 GGTTAAAGTTGTCAAATATGTGTGCTT 59.348 33.333 0.00 0.00 0.00 3.91
306 307 9.030301 GTTAAAGTTGTCAAATATGTGTGCTTT 57.970 29.630 0.00 3.31 0.00 3.51
307 308 9.593134 TTAAAGTTGTCAAATATGTGTGCTTTT 57.407 25.926 9.89 3.21 0.00 2.27
359 1096 2.387952 GGAGAGGGCCCAAAAGAGA 58.612 57.895 27.56 0.00 0.00 3.10
360 1097 0.698818 GGAGAGGGCCCAAAAGAGAA 59.301 55.000 27.56 0.00 0.00 2.87
362 1099 2.441410 GAGAGGGCCCAAAAGAGAAAG 58.559 52.381 27.56 0.00 0.00 2.62
363 1100 2.040412 GAGAGGGCCCAAAAGAGAAAGA 59.960 50.000 27.56 0.00 0.00 2.52
365 1102 0.881796 GGGCCCAAAAGAGAAAGACG 59.118 55.000 19.95 0.00 0.00 4.18
366 1103 1.544759 GGGCCCAAAAGAGAAAGACGA 60.545 52.381 19.95 0.00 0.00 4.20
367 1104 2.227194 GGCCCAAAAGAGAAAGACGAA 58.773 47.619 0.00 0.00 0.00 3.85
368 1105 2.621526 GGCCCAAAAGAGAAAGACGAAA 59.378 45.455 0.00 0.00 0.00 3.46
369 1106 3.255888 GGCCCAAAAGAGAAAGACGAAAT 59.744 43.478 0.00 0.00 0.00 2.17
370 1107 4.262036 GGCCCAAAAGAGAAAGACGAAATT 60.262 41.667 0.00 0.00 0.00 1.82
371 1108 4.681483 GCCCAAAAGAGAAAGACGAAATTG 59.319 41.667 0.00 0.00 0.00 2.32
373 1110 4.681483 CCAAAAGAGAAAGACGAAATTGCC 59.319 41.667 0.00 0.00 0.00 4.52
374 1111 4.505313 AAAGAGAAAGACGAAATTGCCC 57.495 40.909 0.00 0.00 0.00 5.36
375 1112 3.425162 AGAGAAAGACGAAATTGCCCT 57.575 42.857 0.00 0.00 0.00 5.19
376 1113 3.339141 AGAGAAAGACGAAATTGCCCTC 58.661 45.455 0.00 0.00 0.00 4.30
377 1114 3.074412 GAGAAAGACGAAATTGCCCTCA 58.926 45.455 0.00 0.00 0.00 3.86
378 1115 2.814336 AGAAAGACGAAATTGCCCTCAC 59.186 45.455 0.00 0.00 0.00 3.51
379 1116 2.568623 AAGACGAAATTGCCCTCACT 57.431 45.000 0.00 0.00 0.00 3.41
380 1117 1.813513 AGACGAAATTGCCCTCACTG 58.186 50.000 0.00 0.00 0.00 3.66
381 1118 1.347707 AGACGAAATTGCCCTCACTGA 59.652 47.619 0.00 0.00 0.00 3.41
382 1119 2.151202 GACGAAATTGCCCTCACTGAA 58.849 47.619 0.00 0.00 0.00 3.02
383 1120 2.552315 GACGAAATTGCCCTCACTGAAA 59.448 45.455 0.00 0.00 0.00 2.69
384 1121 3.157087 ACGAAATTGCCCTCACTGAAAT 58.843 40.909 0.00 0.00 0.00 2.17
386 1123 3.728864 CGAAATTGCCCTCACTGAAATCG 60.729 47.826 0.00 0.00 0.00 3.34
387 1124 2.787473 ATTGCCCTCACTGAAATCGA 57.213 45.000 0.00 0.00 0.00 3.59
389 1126 1.266178 TGCCCTCACTGAAATCGAGA 58.734 50.000 0.00 0.00 0.00 4.04
390 1127 1.205655 TGCCCTCACTGAAATCGAGAG 59.794 52.381 0.00 0.00 0.00 3.20
405 1142 1.062294 CGAGAGAAGAGGAACGTACGG 59.938 57.143 21.06 1.43 0.00 4.02
406 1143 0.810016 AGAGAAGAGGAACGTACGGC 59.190 55.000 21.06 10.97 0.00 5.68
408 1145 0.243095 AGAAGAGGAACGTACGGCAC 59.757 55.000 21.06 8.68 0.00 5.01
409 1146 0.243095 GAAGAGGAACGTACGGCACT 59.757 55.000 21.06 13.54 0.00 4.40
410 1147 0.243095 AAGAGGAACGTACGGCACTC 59.757 55.000 21.06 20.73 0.00 3.51
411 1148 1.153881 GAGGAACGTACGGCACTCC 60.154 63.158 21.06 17.96 0.00 3.85
436 1173 2.345244 CAGCTGTTCCGCTCCACT 59.655 61.111 5.25 0.00 38.41 4.00
437 1174 2.031516 CAGCTGTTCCGCTCCACTG 61.032 63.158 5.25 0.00 38.41 3.66
438 1175 2.031163 GCTGTTCCGCTCCACTGT 59.969 61.111 0.00 0.00 0.00 3.55
440 1177 1.569479 GCTGTTCCGCTCCACTGTTC 61.569 60.000 0.00 0.00 0.00 3.18
442 1179 1.371558 GTTCCGCTCCACTGTTCCT 59.628 57.895 0.00 0.00 0.00 3.36
443 1180 0.670854 GTTCCGCTCCACTGTTCCTC 60.671 60.000 0.00 0.00 0.00 3.71
444 1181 1.827399 TTCCGCTCCACTGTTCCTCC 61.827 60.000 0.00 0.00 0.00 4.30
446 1183 2.435059 GCTCCACTGTTCCTCCGC 60.435 66.667 0.00 0.00 0.00 5.54
448 1185 2.525629 TCCACTGTTCCTCCGCCA 60.526 61.111 0.00 0.00 0.00 5.69
449 1186 1.903877 CTCCACTGTTCCTCCGCCAT 61.904 60.000 0.00 0.00 0.00 4.40
451 1188 1.450312 CACTGTTCCTCCGCCATCC 60.450 63.158 0.00 0.00 0.00 3.51
452 1189 2.190578 CTGTTCCTCCGCCATCCC 59.809 66.667 0.00 0.00 0.00 3.85
453 1190 2.609299 TGTTCCTCCGCCATCCCA 60.609 61.111 0.00 0.00 0.00 4.37
455 1192 3.407967 TTCCTCCGCCATCCCACC 61.408 66.667 0.00 0.00 0.00 4.61
456 1193 4.731853 TCCTCCGCCATCCCACCA 62.732 66.667 0.00 0.00 0.00 4.17
463 1200 4.828296 CCATCCCACCAGCAGGCC 62.828 72.222 0.00 0.00 39.06 5.19
495 1232 4.394712 CGCCGCCCTGAAAGTCCT 62.395 66.667 0.00 0.00 0.00 3.85
496 1233 2.436824 GCCGCCCTGAAAGTCCTC 60.437 66.667 0.00 0.00 0.00 3.71
497 1234 2.269241 CCGCCCTGAAAGTCCTCC 59.731 66.667 0.00 0.00 0.00 4.30
498 1235 2.592993 CCGCCCTGAAAGTCCTCCA 61.593 63.158 0.00 0.00 0.00 3.86
499 1236 1.376037 CGCCCTGAAAGTCCTCCAC 60.376 63.158 0.00 0.00 0.00 4.02
500 1237 1.002011 GCCCTGAAAGTCCTCCACC 60.002 63.158 0.00 0.00 0.00 4.61
503 1240 1.738099 CTGAAAGTCCTCCACCGCG 60.738 63.158 0.00 0.00 0.00 6.46
504 1241 3.119096 GAAAGTCCTCCACCGCGC 61.119 66.667 0.00 0.00 0.00 6.86
581 1318 4.925576 CCGTCCGCGAATCGAGGG 62.926 72.222 24.13 15.26 46.27 4.30
582 1319 3.884350 CGTCCGCGAATCGAGGGA 61.884 66.667 24.13 17.27 46.27 4.20
583 1320 2.493030 GTCCGCGAATCGAGGGAA 59.507 61.111 24.13 4.09 46.27 3.97
584 1321 1.589196 GTCCGCGAATCGAGGGAAG 60.589 63.158 24.13 0.00 46.27 3.46
585 1322 2.279517 CCGCGAATCGAGGGAAGG 60.280 66.667 17.63 0.88 42.79 3.46
586 1323 2.494918 CGCGAATCGAGGGAAGGT 59.505 61.111 6.91 0.00 41.67 3.50
587 1324 1.878522 CGCGAATCGAGGGAAGGTG 60.879 63.158 6.91 0.00 41.67 4.00
589 1326 0.528684 GCGAATCGAGGGAAGGTGAG 60.529 60.000 6.91 0.00 0.00 3.51
590 1327 0.528684 CGAATCGAGGGAAGGTGAGC 60.529 60.000 0.00 0.00 0.00 4.26
594 1331 1.684049 CGAGGGAAGGTGAGCCTCT 60.684 63.158 0.00 0.00 46.33 3.69
595 1332 1.671901 CGAGGGAAGGTGAGCCTCTC 61.672 65.000 0.00 0.00 46.33 3.20
598 1335 0.325203 GGGAAGGTGAGCCTCTCTCT 60.325 60.000 0.00 0.00 46.33 3.10
599 1336 1.111277 GGAAGGTGAGCCTCTCTCTC 58.889 60.000 0.00 0.00 46.33 3.20
602 1339 1.298953 AGGTGAGCCTCTCTCTCTCT 58.701 55.000 0.00 0.00 42.67 3.10
603 1340 1.212935 AGGTGAGCCTCTCTCTCTCTC 59.787 57.143 0.00 0.00 42.67 3.20
604 1341 1.064758 GGTGAGCCTCTCTCTCTCTCA 60.065 57.143 0.00 0.00 42.38 3.27
605 1342 2.423373 GGTGAGCCTCTCTCTCTCTCAT 60.423 54.545 0.00 0.00 42.38 2.90
606 1343 3.290710 GTGAGCCTCTCTCTCTCTCATT 58.709 50.000 0.00 0.00 42.38 2.57
607 1344 3.316308 GTGAGCCTCTCTCTCTCTCATTC 59.684 52.174 0.00 0.00 42.38 2.67
608 1345 3.053768 TGAGCCTCTCTCTCTCTCATTCA 60.054 47.826 0.00 0.00 42.38 2.57
609 1346 4.147321 GAGCCTCTCTCTCTCTCATTCAT 58.853 47.826 0.00 0.00 38.78 2.57
611 1348 3.638160 GCCTCTCTCTCTCTCATTCATGT 59.362 47.826 0.00 0.00 0.00 3.21
612 1349 4.500205 GCCTCTCTCTCTCTCATTCATGTG 60.500 50.000 0.00 0.00 0.00 3.21
613 1350 4.500205 CCTCTCTCTCTCTCATTCATGTGC 60.500 50.000 0.00 0.00 0.00 4.57
625 1362 2.885135 TCATGTGCCCTGAGATTTGT 57.115 45.000 0.00 0.00 0.00 2.83
633 1370 3.763360 TGCCCTGAGATTTGTTTGGTATG 59.237 43.478 0.00 0.00 0.00 2.39
635 1372 4.462483 GCCCTGAGATTTGTTTGGTATGAA 59.538 41.667 0.00 0.00 0.00 2.57
638 1375 5.416952 CCTGAGATTTGTTTGGTATGAAGCT 59.583 40.000 0.00 0.00 0.00 3.74
665 1402 4.478203 TGAACTCTCTGGATCTATCTGGG 58.522 47.826 0.00 0.00 0.00 4.45
666 1403 4.168871 TGAACTCTCTGGATCTATCTGGGA 59.831 45.833 0.00 0.00 0.00 4.37
685 1422 2.421424 GGATGAGGCTTTTGTGCACTAG 59.579 50.000 19.41 13.31 34.04 2.57
692 1429 4.402474 AGGCTTTTGTGCACTAGTTTTTCT 59.598 37.500 19.41 3.62 34.04 2.52
703 1450 8.958043 GTGCACTAGTTTTTCTTCTGTATTTTG 58.042 33.333 10.32 0.00 0.00 2.44
728 1475 3.390819 AGGGTTAGGGATACATTTCGGT 58.609 45.455 0.00 0.00 39.74 4.69
739 1499 6.485313 GGGATACATTTCGGTCATTCATGTAA 59.515 38.462 0.00 0.00 34.75 2.41
837 1627 3.443052 AGATCTATCTGGGATGAGCCTG 58.557 50.000 0.00 0.00 35.42 4.85
905 1696 4.553323 GGATACATTTTGCTCATCCATGC 58.447 43.478 0.00 0.00 36.09 4.06
908 1699 2.769663 ACATTTTGCTCATCCATGCCAT 59.230 40.909 0.00 0.00 0.00 4.40
909 1700 3.199071 ACATTTTGCTCATCCATGCCATT 59.801 39.130 0.00 0.00 0.00 3.16
910 1701 3.985019 TTTTGCTCATCCATGCCATTT 57.015 38.095 0.00 0.00 0.00 2.32
911 1702 3.985019 TTTGCTCATCCATGCCATTTT 57.015 38.095 0.00 0.00 0.00 1.82
912 1703 5.417754 TTTTGCTCATCCATGCCATTTTA 57.582 34.783 0.00 0.00 0.00 1.52
913 1704 5.417754 TTTGCTCATCCATGCCATTTTAA 57.582 34.783 0.00 0.00 0.00 1.52
914 1705 5.617528 TTGCTCATCCATGCCATTTTAAT 57.382 34.783 0.00 0.00 0.00 1.40
940 1731 8.706492 TTTTATCAATTGGCAAAGCTAATGAG 57.294 30.769 3.01 0.00 38.73 2.90
974 1765 2.867624 TCTATCCATCAATTGCAGGGC 58.132 47.619 13.79 0.00 0.00 5.19
2470 4719 3.502123 ACAGTTTAGCTTGCAGGGTTA 57.498 42.857 5.64 0.00 0.00 2.85
2471 4720 3.827722 ACAGTTTAGCTTGCAGGGTTAA 58.172 40.909 5.64 0.00 0.00 2.01
2473 4722 3.191371 CAGTTTAGCTTGCAGGGTTAAGG 59.809 47.826 5.64 0.00 0.00 2.69
2475 4724 0.034477 TAGCTTGCAGGGTTAAGGCC 60.034 55.000 5.64 0.00 0.00 5.19
2476 4725 1.606313 GCTTGCAGGGTTAAGGCCA 60.606 57.895 5.01 0.00 0.00 5.36
2479 4728 1.004277 CTTGCAGGGTTAAGGCCAGTA 59.996 52.381 5.01 0.00 0.00 2.74
2480 4729 1.295020 TGCAGGGTTAAGGCCAGTAT 58.705 50.000 5.01 0.00 0.00 2.12
2482 4731 2.024414 GCAGGGTTAAGGCCAGTATTG 58.976 52.381 5.01 0.00 0.00 1.90
2557 4806 7.881142 TGTTTAACCAACTCTGGATATGTTTG 58.119 34.615 0.00 0.00 46.92 2.93
2562 4811 3.004752 ACTCTGGATATGTTTGCCCAC 57.995 47.619 0.00 0.00 0.00 4.61
2600 4849 1.404391 GCCTGCCTGTTGATGATCAAG 59.596 52.381 8.33 0.00 37.00 3.02
2645 4898 2.910205 CTGCCGGAGTAGCATCATG 58.090 57.895 5.05 0.00 40.04 3.07
2715 4968 6.596309 TCTGTAAGACATGTCATCTCTGTT 57.404 37.500 27.02 13.12 38.67 3.16
2716 4969 6.997655 TCTGTAAGACATGTCATCTCTGTTT 58.002 36.000 27.02 12.43 38.67 2.83
2717 4970 6.870439 TCTGTAAGACATGTCATCTCTGTTTG 59.130 38.462 27.02 7.08 38.67 2.93
2718 4971 5.409520 TGTAAGACATGTCATCTCTGTTTGC 59.590 40.000 27.02 13.53 0.00 3.68
2719 4972 4.011966 AGACATGTCATCTCTGTTTGCA 57.988 40.909 27.02 0.00 0.00 4.08
2760 5013 8.407832 TGCATCTTTACTGTGGAATTATTGATG 58.592 33.333 0.00 0.00 0.00 3.07
2852 5105 1.002430 TGCTTGTAGCTGGTTGAGAGG 59.998 52.381 0.00 0.00 42.97 3.69
3027 5296 4.012319 GCAGTCTGCAATGTTGATACTG 57.988 45.455 20.16 13.56 44.26 2.74
3028 5297 3.181503 GCAGTCTGCAATGTTGATACTGG 60.182 47.826 20.16 6.36 44.26 4.00
3029 5298 4.005650 CAGTCTGCAATGTTGATACTGGT 58.994 43.478 11.51 0.00 33.69 4.00
3030 5299 4.093998 CAGTCTGCAATGTTGATACTGGTC 59.906 45.833 11.51 0.00 33.69 4.02
3033 5302 4.005650 CTGCAATGTTGATACTGGTCTGT 58.994 43.478 0.00 0.00 0.00 3.41
3034 5303 4.397420 TGCAATGTTGATACTGGTCTGTT 58.603 39.130 0.00 0.00 0.00 3.16
3035 5304 5.555966 TGCAATGTTGATACTGGTCTGTTA 58.444 37.500 0.00 0.00 0.00 2.41
3036 5305 6.000840 TGCAATGTTGATACTGGTCTGTTAA 58.999 36.000 0.00 0.00 0.00 2.01
3048 5570 5.581085 ACTGGTCTGTTAATATTCTCGTTGC 59.419 40.000 0.00 0.00 0.00 4.17
3053 5575 6.312918 GTCTGTTAATATTCTCGTTGCTTCCA 59.687 38.462 0.00 0.00 0.00 3.53
3062 5584 4.574892 TCTCGTTGCTTCCAATGTTGATA 58.425 39.130 0.00 0.00 38.73 2.15
3077 5599 9.342308 CCAATGTTGATACTGGTCTGTTAATAT 57.658 33.333 0.00 0.00 0.00 1.28
3129 5652 5.469760 TCAGTAATTTCATACATGGCATCGG 59.530 40.000 0.00 0.00 0.00 4.18
3156 5679 6.646240 CGGAATGAAAGGAAATTGTGATGTTT 59.354 34.615 0.00 0.00 0.00 2.83
3164 5687 6.392354 AGGAAATTGTGATGTTTACTGCATG 58.608 36.000 0.00 0.00 27.60 4.06
3175 5698 1.279496 TACTGCATGCCTTGGTCTCT 58.721 50.000 16.68 0.00 0.00 3.10
3176 5699 0.322277 ACTGCATGCCTTGGTCTCTG 60.322 55.000 16.68 0.00 0.00 3.35
3177 5700 0.035725 CTGCATGCCTTGGTCTCTGA 60.036 55.000 16.68 0.00 0.00 3.27
3178 5701 0.622136 TGCATGCCTTGGTCTCTGAT 59.378 50.000 16.68 0.00 0.00 2.90
3179 5702 1.022735 GCATGCCTTGGTCTCTGATG 58.977 55.000 6.36 0.00 0.00 3.07
3207 5730 7.783042 TCTATCAATCTATCTCTCCATGCATG 58.217 38.462 20.19 20.19 0.00 4.06
3208 5731 4.576879 TCAATCTATCTCTCCATGCATGC 58.423 43.478 21.69 11.82 0.00 4.06
3209 5732 4.286291 TCAATCTATCTCTCCATGCATGCT 59.714 41.667 21.69 1.07 0.00 3.79
3210 5733 4.912317 ATCTATCTCTCCATGCATGCTT 57.088 40.909 21.69 10.16 0.00 3.91
3211 5734 4.004196 TCTATCTCTCCATGCATGCTTG 57.996 45.455 21.69 23.09 0.00 4.01
3220 5743 4.333417 GCATGCTTGCTTCTCCCT 57.667 55.556 16.80 0.00 45.77 4.20
3221 5744 2.576298 GCATGCTTGCTTCTCCCTT 58.424 52.632 16.80 0.00 45.77 3.95
3222 5745 0.893447 GCATGCTTGCTTCTCCCTTT 59.107 50.000 16.80 0.00 45.77 3.11
3223 5746 1.403780 GCATGCTTGCTTCTCCCTTTG 60.404 52.381 16.80 0.00 45.77 2.77
3224 5747 1.891150 CATGCTTGCTTCTCCCTTTGT 59.109 47.619 0.00 0.00 0.00 2.83
3225 5748 1.321474 TGCTTGCTTCTCCCTTTGTG 58.679 50.000 0.00 0.00 0.00 3.33
3226 5749 0.038801 GCTTGCTTCTCCCTTTGTGC 60.039 55.000 0.00 0.00 0.00 4.57
3227 5750 1.321474 CTTGCTTCTCCCTTTGTGCA 58.679 50.000 0.00 0.00 0.00 4.57
3228 5751 1.268899 CTTGCTTCTCCCTTTGTGCAG 59.731 52.381 0.00 0.00 0.00 4.41
3229 5752 0.183492 TGCTTCTCCCTTTGTGCAGT 59.817 50.000 0.00 0.00 0.00 4.40
3230 5753 1.322442 GCTTCTCCCTTTGTGCAGTT 58.678 50.000 0.00 0.00 0.00 3.16
3231 5754 1.683385 GCTTCTCCCTTTGTGCAGTTT 59.317 47.619 0.00 0.00 0.00 2.66
3232 5755 2.287849 GCTTCTCCCTTTGTGCAGTTTC 60.288 50.000 0.00 0.00 0.00 2.78
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 0.752658 TCGCTCACCATCTACCATGG 59.247 55.000 11.19 11.19 44.54 3.66
13 14 1.683385 TCTCGCTCACCATCTACCATG 59.317 52.381 0.00 0.00 0.00 3.66
14 15 1.959985 CTCTCGCTCACCATCTACCAT 59.040 52.381 0.00 0.00 0.00 3.55
15 16 1.064685 TCTCTCGCTCACCATCTACCA 60.065 52.381 0.00 0.00 0.00 3.25
18 19 1.611006 GCATCTCTCGCTCACCATCTA 59.389 52.381 0.00 0.00 0.00 1.98
19 20 0.388659 GCATCTCTCGCTCACCATCT 59.611 55.000 0.00 0.00 0.00 2.90
20 21 0.103755 TGCATCTCTCGCTCACCATC 59.896 55.000 0.00 0.00 0.00 3.51
21 22 0.757512 ATGCATCTCTCGCTCACCAT 59.242 50.000 0.00 0.00 0.00 3.55
22 23 0.538584 AATGCATCTCTCGCTCACCA 59.461 50.000 0.00 0.00 0.00 4.17
23 24 1.596727 GAAATGCATCTCTCGCTCACC 59.403 52.381 0.00 0.00 0.00 4.02
24 25 2.274437 TGAAATGCATCTCTCGCTCAC 58.726 47.619 0.00 0.00 0.00 3.51
28 29 1.945394 ACCATGAAATGCATCTCTCGC 59.055 47.619 0.00 0.00 44.97 5.03
29 30 4.348656 CAAACCATGAAATGCATCTCTCG 58.651 43.478 0.00 0.00 44.97 4.04
30 31 4.110482 GCAAACCATGAAATGCATCTCTC 58.890 43.478 0.00 0.00 44.97 3.20
31 32 3.512329 TGCAAACCATGAAATGCATCTCT 59.488 39.130 13.07 0.00 44.97 3.10
32 33 3.852286 TGCAAACCATGAAATGCATCTC 58.148 40.909 13.07 0.00 44.97 2.75
33 34 3.965379 TGCAAACCATGAAATGCATCT 57.035 38.095 13.07 0.00 44.97 2.90
34 35 5.049267 AGTTTTGCAAACCATGAAATGCATC 60.049 36.000 12.39 11.51 46.97 3.91
36 37 4.197750 AGTTTTGCAAACCATGAAATGCA 58.802 34.783 12.39 13.07 44.97 3.96
37 38 4.816786 AGTTTTGCAAACCATGAAATGC 57.183 36.364 12.39 1.72 44.97 3.56
38 39 7.224362 TCAAGTAGTTTTGCAAACCATGAAATG 59.776 33.333 12.39 5.20 46.21 2.32
42 43 5.735922 GCTCAAGTAGTTTTGCAAACCATGA 60.736 40.000 12.39 9.66 0.00 3.07
44 45 4.342092 AGCTCAAGTAGTTTTGCAAACCAT 59.658 37.500 12.39 3.28 0.00 3.55
48 49 8.413229 AGATTAAAGCTCAAGTAGTTTTGCAAA 58.587 29.630 8.05 8.05 38.84 3.68
49 50 7.862372 CAGATTAAAGCTCAAGTAGTTTTGCAA 59.138 33.333 0.00 0.00 38.84 4.08
50 51 7.362662 CAGATTAAAGCTCAAGTAGTTTTGCA 58.637 34.615 0.00 0.00 38.84 4.08
52 53 7.362662 TGCAGATTAAAGCTCAAGTAGTTTTG 58.637 34.615 0.00 0.00 38.84 2.44
53 54 7.510549 TGCAGATTAAAGCTCAAGTAGTTTT 57.489 32.000 0.00 0.00 41.08 2.43
59 60 7.693969 AGTTAATGCAGATTAAAGCTCAAGT 57.306 32.000 0.00 0.00 36.10 3.16
64 65 8.778358 GCACTATAGTTAATGCAGATTAAAGCT 58.222 33.333 1.56 0.00 36.10 3.74
75 76 9.586435 AAAAGGAAAATGCACTATAGTTAATGC 57.414 29.630 1.56 4.36 38.59 3.56
108 109 3.844804 AGTACTAACTCCTTTTCTGGGGG 59.155 47.826 0.00 0.00 0.00 5.40
118 119 8.962679 CTTATTGAAGACAGAGTACTAACTCCT 58.037 37.037 0.00 0.00 43.00 3.69
119 120 8.958506 TCTTATTGAAGACAGAGTACTAACTCC 58.041 37.037 0.00 0.00 43.51 3.85
120 121 9.997482 CTCTTATTGAAGACAGAGTACTAACTC 57.003 37.037 0.00 0.00 43.18 3.01
121 122 8.962679 CCTCTTATTGAAGACAGAGTACTAACT 58.037 37.037 0.00 0.00 36.75 2.24
125 126 5.128008 GCCCTCTTATTGAAGACAGAGTACT 59.872 44.000 0.00 0.00 36.75 2.73
126 127 5.353111 GCCCTCTTATTGAAGACAGAGTAC 58.647 45.833 0.00 0.00 36.75 2.73
128 129 3.118956 CGCCCTCTTATTGAAGACAGAGT 60.119 47.826 0.00 0.00 36.75 3.24
130 131 2.832129 ACGCCCTCTTATTGAAGACAGA 59.168 45.455 0.00 0.00 36.75 3.41
131 132 3.190874 GACGCCCTCTTATTGAAGACAG 58.809 50.000 0.00 0.00 36.75 3.51
132 133 2.093658 GGACGCCCTCTTATTGAAGACA 60.094 50.000 0.00 0.00 36.75 3.41
135 136 2.280628 GTGGACGCCCTCTTATTGAAG 58.719 52.381 0.00 0.00 0.00 3.02
139 140 0.611714 AACGTGGACGCCCTCTTATT 59.388 50.000 0.00 0.00 44.43 1.40
140 141 0.611714 AAACGTGGACGCCCTCTTAT 59.388 50.000 0.00 0.00 44.43 1.73
141 142 0.393820 AAAACGTGGACGCCCTCTTA 59.606 50.000 0.00 0.00 44.43 2.10
142 143 0.464916 AAAAACGTGGACGCCCTCTT 60.465 50.000 0.00 0.00 44.43 2.85
143 144 0.883370 GAAAAACGTGGACGCCCTCT 60.883 55.000 0.00 0.00 44.43 3.69
144 145 1.161563 TGAAAAACGTGGACGCCCTC 61.162 55.000 0.00 0.00 44.43 4.30
145 146 0.748729 TTGAAAAACGTGGACGCCCT 60.749 50.000 0.00 0.00 44.43 5.19
146 147 0.100861 TTTGAAAAACGTGGACGCCC 59.899 50.000 0.00 0.00 44.43 6.13
148 149 4.508376 AAATTTTGAAAAACGTGGACGC 57.492 36.364 0.00 0.00 44.43 5.19
150 151 9.256715 CAAACTTAAATTTTGAAAAACGTGGAC 57.743 29.630 0.00 0.00 36.24 4.02
151 152 9.204570 TCAAACTTAAATTTTGAAAAACGTGGA 57.795 25.926 8.72 0.00 39.47 4.02
152 153 9.256715 GTCAAACTTAAATTTTGAAAAACGTGG 57.743 29.630 11.62 0.00 42.98 4.94
153 154 9.256715 GGTCAAACTTAAATTTTGAAAAACGTG 57.743 29.630 11.62 0.00 42.98 4.49
154 155 8.989980 TGGTCAAACTTAAATTTTGAAAAACGT 58.010 25.926 11.62 0.00 42.98 3.99
165 166 9.705290 GGTAACATTCATGGTCAAACTTAAATT 57.295 29.630 0.00 0.00 0.00 1.82
167 168 7.228906 TCGGTAACATTCATGGTCAAACTTAAA 59.771 33.333 0.00 0.00 0.00 1.52
169 170 6.231951 TCGGTAACATTCATGGTCAAACTTA 58.768 36.000 0.00 0.00 0.00 2.24
170 171 5.067273 TCGGTAACATTCATGGTCAAACTT 58.933 37.500 0.00 0.00 0.00 2.66
171 172 4.647611 TCGGTAACATTCATGGTCAAACT 58.352 39.130 0.00 0.00 0.00 2.66
173 174 7.689446 TTTATCGGTAACATTCATGGTCAAA 57.311 32.000 0.00 0.00 0.00 2.69
174 175 7.689446 TTTTATCGGTAACATTCATGGTCAA 57.311 32.000 0.00 0.00 0.00 3.18
176 177 7.643764 CACATTTTATCGGTAACATTCATGGTC 59.356 37.037 0.00 0.00 0.00 4.02
179 180 6.140580 CGCACATTTTATCGGTAACATTCATG 59.859 38.462 0.00 0.00 0.00 3.07
180 181 6.183360 ACGCACATTTTATCGGTAACATTCAT 60.183 34.615 0.00 0.00 0.00 2.57
182 183 5.565695 ACGCACATTTTATCGGTAACATTC 58.434 37.500 0.00 0.00 0.00 2.67
183 184 5.554822 ACGCACATTTTATCGGTAACATT 57.445 34.783 0.00 0.00 0.00 2.71
185 186 5.581479 ACATACGCACATTTTATCGGTAACA 59.419 36.000 0.00 0.00 0.00 2.41
186 187 5.899696 CACATACGCACATTTTATCGGTAAC 59.100 40.000 0.00 0.00 0.00 2.50
191 192 5.137524 TGACACATACGCACATTTTATCG 57.862 39.130 0.00 0.00 0.00 2.92
192 193 9.497030 TTTTATGACACATACGCACATTTTATC 57.503 29.630 0.00 0.00 0.00 1.75
221 222 9.980780 CACATTTAATATGAATACAACGACACA 57.019 29.630 0.00 0.00 0.00 3.72
241 242 9.507329 ACTGTACTTGAGAATTATGTCACATTT 57.493 29.630 0.00 0.00 0.00 2.32
243 244 9.587772 GTACTGTACTTGAGAATTATGTCACAT 57.412 33.333 10.64 0.00 0.00 3.21
246 247 8.362464 AGGTACTGTACTTGAGAATTATGTCA 57.638 34.615 16.79 0.00 37.18 3.58
278 279 6.920758 GCACACATATTTGACAACTTTAACCA 59.079 34.615 0.00 0.00 0.00 3.67
279 280 7.145323 AGCACACATATTTGACAACTTTAACC 58.855 34.615 0.00 0.00 0.00 2.85
307 308 8.832735 AGTCTAGTTGAACTATGGGGATAAAAA 58.167 33.333 5.39 0.00 29.08 1.94
351 1088 4.681483 GGGCAATTTCGTCTTTCTCTTTTG 59.319 41.667 0.00 0.00 0.00 2.44
355 1092 3.244561 TGAGGGCAATTTCGTCTTTCTCT 60.245 43.478 0.00 0.00 0.00 3.10
359 1096 2.554032 CAGTGAGGGCAATTTCGTCTTT 59.446 45.455 0.00 0.00 0.00 2.52
360 1097 2.154462 CAGTGAGGGCAATTTCGTCTT 58.846 47.619 0.00 0.00 0.00 3.01
362 1099 1.808411 TCAGTGAGGGCAATTTCGTC 58.192 50.000 0.00 0.00 0.00 4.20
363 1100 2.270352 TTCAGTGAGGGCAATTTCGT 57.730 45.000 0.00 0.00 0.00 3.85
365 1102 3.440173 TCGATTTCAGTGAGGGCAATTTC 59.560 43.478 0.00 0.00 0.00 2.17
366 1103 3.420893 TCGATTTCAGTGAGGGCAATTT 58.579 40.909 0.00 0.00 0.00 1.82
367 1104 3.012518 CTCGATTTCAGTGAGGGCAATT 58.987 45.455 0.00 0.00 0.00 2.32
368 1105 2.237143 TCTCGATTTCAGTGAGGGCAAT 59.763 45.455 0.00 0.00 0.00 3.56
369 1106 1.623311 TCTCGATTTCAGTGAGGGCAA 59.377 47.619 0.00 0.00 0.00 4.52
370 1107 1.205655 CTCTCGATTTCAGTGAGGGCA 59.794 52.381 0.00 0.00 0.00 5.36
371 1108 1.478510 TCTCTCGATTTCAGTGAGGGC 59.521 52.381 0.00 0.00 30.12 5.19
373 1110 4.439974 CCTCTTCTCTCGATTTCAGTGAGG 60.440 50.000 0.00 0.00 32.09 3.86
374 1111 4.397730 TCCTCTTCTCTCGATTTCAGTGAG 59.602 45.833 0.00 0.00 0.00 3.51
375 1112 4.336280 TCCTCTTCTCTCGATTTCAGTGA 58.664 43.478 0.00 0.00 0.00 3.41
376 1113 4.710423 TCCTCTTCTCTCGATTTCAGTG 57.290 45.455 0.00 0.00 0.00 3.66
377 1114 4.380023 CGTTCCTCTTCTCTCGATTTCAGT 60.380 45.833 0.00 0.00 0.00 3.41
378 1115 4.101942 CGTTCCTCTTCTCTCGATTTCAG 58.898 47.826 0.00 0.00 0.00 3.02
379 1116 3.506455 ACGTTCCTCTTCTCTCGATTTCA 59.494 43.478 0.00 0.00 0.00 2.69
380 1117 4.099380 ACGTTCCTCTTCTCTCGATTTC 57.901 45.455 0.00 0.00 0.00 2.17
381 1118 4.437121 CGTACGTTCCTCTTCTCTCGATTT 60.437 45.833 7.22 0.00 0.00 2.17
382 1119 3.063725 CGTACGTTCCTCTTCTCTCGATT 59.936 47.826 7.22 0.00 0.00 3.34
383 1120 2.608546 CGTACGTTCCTCTTCTCTCGAT 59.391 50.000 7.22 0.00 0.00 3.59
384 1121 1.998315 CGTACGTTCCTCTTCTCTCGA 59.002 52.381 7.22 0.00 0.00 4.04
386 1123 1.202166 GCCGTACGTTCCTCTTCTCTC 60.202 57.143 15.21 0.00 0.00 3.20
387 1124 0.810016 GCCGTACGTTCCTCTTCTCT 59.190 55.000 15.21 0.00 0.00 3.10
389 1126 0.243095 GTGCCGTACGTTCCTCTTCT 59.757 55.000 15.21 0.00 0.00 2.85
390 1127 0.243095 AGTGCCGTACGTTCCTCTTC 59.757 55.000 15.21 0.00 0.00 2.87
392 1129 1.593296 GGAGTGCCGTACGTTCCTCT 61.593 60.000 15.21 8.12 0.00 3.69
421 1158 1.569479 GAACAGTGGAGCGGAACAGC 61.569 60.000 0.00 0.00 37.41 4.40
422 1159 0.951040 GGAACAGTGGAGCGGAACAG 60.951 60.000 0.00 0.00 0.00 3.16
423 1160 1.070786 GGAACAGTGGAGCGGAACA 59.929 57.895 0.00 0.00 0.00 3.18
425 1162 1.671742 GAGGAACAGTGGAGCGGAA 59.328 57.895 0.00 0.00 0.00 4.30
426 1163 2.283529 GGAGGAACAGTGGAGCGGA 61.284 63.158 0.00 0.00 0.00 5.54
427 1164 2.266055 GGAGGAACAGTGGAGCGG 59.734 66.667 0.00 0.00 0.00 5.52
429 1166 2.435059 GCGGAGGAACAGTGGAGC 60.435 66.667 0.00 0.00 0.00 4.70
430 1167 1.903877 ATGGCGGAGGAACAGTGGAG 61.904 60.000 0.00 0.00 0.00 3.86
431 1168 1.899437 GATGGCGGAGGAACAGTGGA 61.899 60.000 0.00 0.00 0.00 4.02
433 1170 1.450312 GGATGGCGGAGGAACAGTG 60.450 63.158 0.00 0.00 0.00 3.66
434 1171 2.670148 GGGATGGCGGAGGAACAGT 61.670 63.158 0.00 0.00 0.00 3.55
436 1173 2.609299 TGGGATGGCGGAGGAACA 60.609 61.111 0.00 0.00 0.00 3.18
437 1174 2.124695 GTGGGATGGCGGAGGAAC 60.125 66.667 0.00 0.00 0.00 3.62
438 1175 3.407967 GGTGGGATGGCGGAGGAA 61.408 66.667 0.00 0.00 0.00 3.36
440 1177 4.181010 CTGGTGGGATGGCGGAGG 62.181 72.222 0.00 0.00 0.00 4.30
446 1183 4.828296 GGCCTGCTGGTGGGATGG 62.828 72.222 11.69 0.00 35.27 3.51
478 1215 4.394712 AGGACTTTCAGGGCGGCG 62.395 66.667 0.51 0.51 0.00 6.46
479 1216 2.436824 GAGGACTTTCAGGGCGGC 60.437 66.667 0.00 0.00 0.00 6.53
480 1217 2.269241 GGAGGACTTTCAGGGCGG 59.731 66.667 0.00 0.00 0.00 6.13
481 1218 1.376037 GTGGAGGACTTTCAGGGCG 60.376 63.158 0.00 0.00 0.00 6.13
482 1219 1.002011 GGTGGAGGACTTTCAGGGC 60.002 63.158 0.00 0.00 0.00 5.19
483 1220 1.296715 CGGTGGAGGACTTTCAGGG 59.703 63.158 0.00 0.00 0.00 4.45
484 1221 1.376037 GCGGTGGAGGACTTTCAGG 60.376 63.158 0.00 0.00 0.00 3.86
486 1223 2.342279 CGCGGTGGAGGACTTTCA 59.658 61.111 0.00 0.00 0.00 2.69
487 1224 3.119096 GCGCGGTGGAGGACTTTC 61.119 66.667 8.83 0.00 0.00 2.62
562 1299 4.925576 CTCGATTCGCGGACGGGG 62.926 72.222 6.13 3.60 41.33 5.73
565 1302 3.405592 TTCCCTCGATTCGCGGACG 62.406 63.158 16.39 10.21 41.33 4.79
566 1303 1.589196 CTTCCCTCGATTCGCGGAC 60.589 63.158 16.39 0.00 41.33 4.79
567 1304 2.782222 CCTTCCCTCGATTCGCGGA 61.782 63.158 16.39 12.73 41.33 5.54
568 1305 2.279517 CCTTCCCTCGATTCGCGG 60.280 66.667 6.13 8.12 41.33 6.46
569 1306 1.878522 CACCTTCCCTCGATTCGCG 60.879 63.158 0.00 0.00 42.69 5.87
570 1307 0.528684 CTCACCTTCCCTCGATTCGC 60.529 60.000 0.00 0.00 0.00 4.70
571 1308 0.528684 GCTCACCTTCCCTCGATTCG 60.529 60.000 0.00 0.00 0.00 3.34
572 1309 0.179070 GGCTCACCTTCCCTCGATTC 60.179 60.000 0.00 0.00 0.00 2.52
573 1310 1.908483 GGCTCACCTTCCCTCGATT 59.092 57.895 0.00 0.00 0.00 3.34
574 1311 3.635510 GGCTCACCTTCCCTCGAT 58.364 61.111 0.00 0.00 0.00 3.59
584 1321 1.064758 TGAGAGAGAGAGAGGCTCACC 60.065 57.143 18.26 8.05 46.45 4.02
585 1322 2.418368 TGAGAGAGAGAGAGGCTCAC 57.582 55.000 18.26 10.96 46.45 3.51
586 1323 3.053768 TGAATGAGAGAGAGAGAGGCTCA 60.054 47.826 18.26 0.00 46.45 4.26
587 1324 3.554934 TGAATGAGAGAGAGAGAGGCTC 58.445 50.000 6.34 6.34 44.29 4.70
589 1326 3.638160 ACATGAATGAGAGAGAGAGAGGC 59.362 47.826 0.00 0.00 0.00 4.70
590 1327 4.500205 GCACATGAATGAGAGAGAGAGAGG 60.500 50.000 0.00 0.00 0.00 3.69
592 1329 3.384146 GGCACATGAATGAGAGAGAGAGA 59.616 47.826 0.00 0.00 0.00 3.10
594 1331 2.433604 GGGCACATGAATGAGAGAGAGA 59.566 50.000 0.00 0.00 0.00 3.10
595 1332 2.435069 AGGGCACATGAATGAGAGAGAG 59.565 50.000 0.00 0.00 0.00 3.20
598 1335 2.169978 CTCAGGGCACATGAATGAGAGA 59.830 50.000 0.00 0.00 39.80 3.10
599 1336 2.169978 TCTCAGGGCACATGAATGAGAG 59.830 50.000 0.00 0.00 40.98 3.20
602 1339 3.657398 AATCTCAGGGCACATGAATGA 57.343 42.857 0.00 0.00 0.00 2.57
603 1340 3.446161 ACAAATCTCAGGGCACATGAATG 59.554 43.478 0.00 0.00 0.00 2.67
604 1341 3.705051 ACAAATCTCAGGGCACATGAAT 58.295 40.909 0.00 0.00 0.00 2.57
605 1342 3.159213 ACAAATCTCAGGGCACATGAA 57.841 42.857 0.00 0.00 0.00 2.57
606 1343 2.885135 ACAAATCTCAGGGCACATGA 57.115 45.000 0.00 0.00 0.00 3.07
607 1344 3.581755 CAAACAAATCTCAGGGCACATG 58.418 45.455 0.00 0.00 0.00 3.21
608 1345 2.564062 CCAAACAAATCTCAGGGCACAT 59.436 45.455 0.00 0.00 0.00 3.21
609 1346 1.962807 CCAAACAAATCTCAGGGCACA 59.037 47.619 0.00 0.00 0.00 4.57
611 1348 2.380064 ACCAAACAAATCTCAGGGCA 57.620 45.000 0.00 0.00 0.00 5.36
612 1349 4.016444 TCATACCAAACAAATCTCAGGGC 58.984 43.478 0.00 0.00 0.00 5.19
613 1350 5.393461 GCTTCATACCAAACAAATCTCAGGG 60.393 44.000 0.00 0.00 0.00 4.45
625 1362 8.079211 AGAGTTCATACTAGCTTCATACCAAA 57.921 34.615 0.00 0.00 33.84 3.28
633 1370 6.490040 AGATCCAGAGAGTTCATACTAGCTTC 59.510 42.308 0.00 0.00 33.84 3.86
635 1372 5.952387 AGATCCAGAGAGTTCATACTAGCT 58.048 41.667 0.00 0.00 33.84 3.32
638 1375 8.106462 CCAGATAGATCCAGAGAGTTCATACTA 58.894 40.741 0.00 0.00 33.84 1.82
665 1402 3.077359 ACTAGTGCACAAAAGCCTCATC 58.923 45.455 21.04 0.00 0.00 2.92
666 1403 3.146104 ACTAGTGCACAAAAGCCTCAT 57.854 42.857 21.04 0.00 0.00 2.90
685 1422 8.418662 ACCCTAACCAAAATACAGAAGAAAAAC 58.581 33.333 0.00 0.00 0.00 2.43
692 1429 6.275144 TCCCTAACCCTAACCAAAATACAGAA 59.725 38.462 0.00 0.00 0.00 3.02
703 1450 5.303165 CGAAATGTATCCCTAACCCTAACC 58.697 45.833 0.00 0.00 0.00 2.85
708 1455 3.135167 TGACCGAAATGTATCCCTAACCC 59.865 47.826 0.00 0.00 0.00 4.11
739 1499 6.688385 CGAATGAGCAAAATGTATCAATTCGT 59.312 34.615 0.00 0.00 33.33 3.85
913 1704 9.669887 TCATTAGCTTTGCCAATTGATAAAAAT 57.330 25.926 7.12 2.82 0.00 1.82
914 1705 9.153721 CTCATTAGCTTTGCCAATTGATAAAAA 57.846 29.630 7.12 1.36 0.00 1.94
938 1729 9.006839 TGATGGATAGATAAAATGCAACATCTC 57.993 33.333 0.00 0.00 33.92 2.75
974 1765 2.032550 CGCAGGTTAGCTGATGAAATGG 59.967 50.000 16.12 0.00 0.00 3.16
2055 4265 0.687757 TACATCCGGCCTTGAGCTCT 60.688 55.000 16.19 0.00 43.05 4.09
2126 4360 1.421268 TGAGGCTGAACACCTTGACAT 59.579 47.619 0.00 0.00 37.77 3.06
2470 4719 4.322057 AGAAACATCCAATACTGGCCTT 57.678 40.909 3.32 0.00 43.17 4.35
2471 4720 4.322057 AAGAAACATCCAATACTGGCCT 57.678 40.909 3.32 0.00 43.17 5.19
2473 4722 6.024552 TCAAAAGAAACATCCAATACTGGC 57.975 37.500 0.00 0.00 43.17 4.85
2475 4724 9.480053 AACAATCAAAAGAAACATCCAATACTG 57.520 29.630 0.00 0.00 0.00 2.74
2479 4728 8.961294 TGAAACAATCAAAAGAAACATCCAAT 57.039 26.923 0.00 0.00 34.30 3.16
2480 4729 8.783833 TTGAAACAATCAAAAGAAACATCCAA 57.216 26.923 0.00 0.00 44.94 3.53
2493 4742 3.456280 GGCTGCAGTTTGAAACAATCAA 58.544 40.909 16.64 0.00 46.22 2.57
2503 4752 0.381801 AACAACTCGGCTGCAGTTTG 59.618 50.000 16.64 12.83 31.40 2.93
2557 4806 2.566833 TGCATCTATGTATGGTGGGC 57.433 50.000 0.00 0.00 0.00 5.36
2562 4811 3.939592 CAGGCAGATGCATCTATGTATGG 59.060 47.826 28.27 15.23 44.36 2.74
2645 4898 3.610349 GCTCTGCTGGTAAAAGAAAGCAC 60.610 47.826 0.00 0.00 40.59 4.40
2652 4905 1.461127 GTCGTGCTCTGCTGGTAAAAG 59.539 52.381 0.00 0.00 0.00 2.27
2653 4906 1.070134 AGTCGTGCTCTGCTGGTAAAA 59.930 47.619 0.00 0.00 0.00 1.52
2654 4907 0.679505 AGTCGTGCTCTGCTGGTAAA 59.320 50.000 0.00 0.00 0.00 2.01
2655 4908 0.243907 GAGTCGTGCTCTGCTGGTAA 59.756 55.000 3.24 0.00 40.98 2.85
2656 4909 1.883732 GAGTCGTGCTCTGCTGGTA 59.116 57.895 3.24 0.00 40.98 3.25
2657 4910 2.653702 GAGTCGTGCTCTGCTGGT 59.346 61.111 3.24 0.00 40.98 4.00
2658 4911 2.505777 CGAGTCGTGCTCTGCTGG 60.506 66.667 3.82 0.00 41.98 4.85
2710 4963 5.931146 ACAAAAACAAACAGATGCAAACAGA 59.069 32.000 0.00 0.00 0.00 3.41
2711 4964 6.016718 CACAAAAACAAACAGATGCAAACAG 58.983 36.000 0.00 0.00 0.00 3.16
2712 4965 5.616424 GCACAAAAACAAACAGATGCAAACA 60.616 36.000 0.00 0.00 0.00 2.83
2713 4966 4.787591 GCACAAAAACAAACAGATGCAAAC 59.212 37.500 0.00 0.00 0.00 2.93
2714 4967 4.453478 TGCACAAAAACAAACAGATGCAAA 59.547 33.333 0.00 0.00 38.78 3.68
2715 4968 3.999001 TGCACAAAAACAAACAGATGCAA 59.001 34.783 0.00 0.00 38.78 4.08
2716 4969 3.593096 TGCACAAAAACAAACAGATGCA 58.407 36.364 0.00 0.00 39.38 3.96
2717 4970 4.508861 AGATGCACAAAAACAAACAGATGC 59.491 37.500 0.00 0.00 0.00 3.91
2718 4971 6.592798 AAGATGCACAAAAACAAACAGATG 57.407 33.333 0.00 0.00 0.00 2.90
2719 4972 7.981225 AGTAAAGATGCACAAAAACAAACAGAT 59.019 29.630 0.00 0.00 0.00 2.90
2760 5013 8.034804 ACACTGTAATGCCTTTTGAAATAATCC 58.965 33.333 0.00 0.00 0.00 3.01
2852 5105 0.241213 GCCAAAAACTCTTCCTCGGC 59.759 55.000 0.00 0.00 0.00 5.54
3017 5286 9.817809 GAGAATATTAACAGACCAGTATCAACA 57.182 33.333 0.00 0.00 0.00 3.33
3018 5287 8.969267 CGAGAATATTAACAGACCAGTATCAAC 58.031 37.037 0.00 0.00 0.00 3.18
3019 5288 8.692710 ACGAGAATATTAACAGACCAGTATCAA 58.307 33.333 0.00 0.00 0.00 2.57
3020 5289 8.234136 ACGAGAATATTAACAGACCAGTATCA 57.766 34.615 0.00 0.00 0.00 2.15
3021 5290 8.969267 CAACGAGAATATTAACAGACCAGTATC 58.031 37.037 0.00 0.00 0.00 2.24
3022 5291 7.438459 GCAACGAGAATATTAACAGACCAGTAT 59.562 37.037 0.00 0.00 0.00 2.12
3023 5292 6.755141 GCAACGAGAATATTAACAGACCAGTA 59.245 38.462 0.00 0.00 0.00 2.74
3025 5294 5.812642 AGCAACGAGAATATTAACAGACCAG 59.187 40.000 0.00 0.00 0.00 4.00
3027 5296 6.238130 GGAAGCAACGAGAATATTAACAGACC 60.238 42.308 0.00 0.00 0.00 3.85
3028 5297 6.312918 TGGAAGCAACGAGAATATTAACAGAC 59.687 38.462 0.00 0.00 0.00 3.51
3029 5298 6.403049 TGGAAGCAACGAGAATATTAACAGA 58.597 36.000 0.00 0.00 0.00 3.41
3030 5299 6.662414 TGGAAGCAACGAGAATATTAACAG 57.338 37.500 0.00 0.00 0.00 3.16
3033 5302 7.624360 ACATTGGAAGCAACGAGAATATTAA 57.376 32.000 0.00 0.00 0.00 1.40
3034 5303 7.335673 TCAACATTGGAAGCAACGAGAATATTA 59.664 33.333 0.00 0.00 0.00 0.98
3035 5304 6.150976 TCAACATTGGAAGCAACGAGAATATT 59.849 34.615 0.00 0.00 0.00 1.28
3036 5305 5.647658 TCAACATTGGAAGCAACGAGAATAT 59.352 36.000 0.00 0.00 0.00 1.28
3048 5570 5.248640 ACAGACCAGTATCAACATTGGAAG 58.751 41.667 0.00 0.00 34.76 3.46
3129 5652 3.056891 TCACAATTTCCTTTCATTCCGGC 60.057 43.478 0.00 0.00 0.00 6.13
3132 5655 7.967890 AAACATCACAATTTCCTTTCATTCC 57.032 32.000 0.00 0.00 0.00 3.01
3156 5679 1.065926 CAGAGACCAAGGCATGCAGTA 60.066 52.381 21.36 0.00 0.00 2.74
3164 5687 1.830477 AGAGACATCAGAGACCAAGGC 59.170 52.381 0.00 0.00 0.00 4.35
3175 5698 8.389366 TGGAGAGATAGATTGATAGAGACATCA 58.611 37.037 0.00 0.00 33.10 3.07
3176 5699 8.806429 TGGAGAGATAGATTGATAGAGACATC 57.194 38.462 0.00 0.00 0.00 3.06
3177 5700 9.192642 CATGGAGAGATAGATTGATAGAGACAT 57.807 37.037 0.00 0.00 0.00 3.06
3178 5701 7.122501 GCATGGAGAGATAGATTGATAGAGACA 59.877 40.741 0.00 0.00 0.00 3.41
3179 5702 7.122501 TGCATGGAGAGATAGATTGATAGAGAC 59.877 40.741 0.00 0.00 0.00 3.36
3207 5730 0.038801 GCACAAAGGGAGAAGCAAGC 60.039 55.000 0.00 0.00 0.00 4.01
3208 5731 1.268899 CTGCACAAAGGGAGAAGCAAG 59.731 52.381 0.00 0.00 0.00 4.01
3209 5732 1.321474 CTGCACAAAGGGAGAAGCAA 58.679 50.000 0.00 0.00 0.00 3.91
3210 5733 0.183492 ACTGCACAAAGGGAGAAGCA 59.817 50.000 0.00 0.00 0.00 3.91
3211 5734 1.322442 AACTGCACAAAGGGAGAAGC 58.678 50.000 0.00 0.00 0.00 3.86
3212 5735 3.632855 GAAACTGCACAAAGGGAGAAG 57.367 47.619 0.00 0.00 0.00 2.85


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

AutoCloner maintained by Alex Coulton.