Multiple sequence alignment - TraesCS5A01G504200

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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 TraesCS5A01G504200 chr5A 100.000 3749 0 0 1 3749 670080726 670084474 0.000000e+00 6924
1 TraesCS5A01G504200 chr5A 82.540 378 55 6 888 1254 670239480 670239857 4.670000e-84 322
2 TraesCS5A01G504200 chr4B 94.480 2373 99 14 1194 3542 624737432 624739796 0.000000e+00 3627
3 TraesCS5A01G504200 chr4B 96.628 771 21 5 386 1154 624736539 624737306 0.000000e+00 1275
4 TraesCS5A01G504200 chr4B 93.863 277 12 3 1 275 624736251 624736524 2.690000e-111 412
5 TraesCS5A01G504200 chr4B 95.305 213 10 0 3537 3749 624744840 624745052 4.640000e-89 339
6 TraesCS5A01G504200 chr4B 82.587 201 33 2 976 1175 623645069 623645268 3.850000e-40 176
7 TraesCS5A01G504200 chr4B 82.090 201 33 3 976 1175 623785860 623786058 6.440000e-38 169
8 TraesCS5A01G504200 chr4D 81.746 378 58 6 888 1254 488335028 488334651 4.700000e-79 305
9 TraesCS5A01G504200 chr4D 78.325 406 75 10 2062 2460 488250351 488249952 2.240000e-62 250
10 TraesCS5A01G504200 chr4D 83.000 200 34 0 976 1175 487874556 487874755 8.270000e-42 182


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 TraesCS5A01G504200 chr5A 670080726 670084474 3748 False 6924.000000 6924 100.000000 1 3749 1 chr5A.!!$F1 3748
1 TraesCS5A01G504200 chr4B 624736251 624739796 3545 False 1771.333333 3627 94.990333 1 3542 3 chr4B.!!$F4 3541

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
453 456 1.687492 TTCCACCCACCCCATATCAA 58.313 50.0 0.00 0.0 0.0 2.57 F
1172 1177 0.038021 TTCAAGCTGGCTGGCATGTA 59.962 50.0 3.74 0.0 33.4 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1361 1452 0.043485 AGTTGTTTTGGGGGTTGGGT 59.957 50.0 0.0 0.0 0.0 4.51 R
2918 3011 0.179000 CCTATTCGGCACCTTCAGCT 59.821 55.0 0.0 0.0 0.0 4.24 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
54 55 4.572389 ACTTGCACACTTTCACAACTAGAG 59.428 41.667 0.00 0.00 0.00 2.43
290 293 9.833917 ATGAGCATATCCAATATCTACATCTTG 57.166 33.333 0.00 0.00 0.00 3.02
291 294 9.039165 TGAGCATATCCAATATCTACATCTTGA 57.961 33.333 0.00 0.00 0.00 3.02
293 296 9.833917 AGCATATCCAATATCTACATCTTGATG 57.166 33.333 8.87 8.87 0.00 3.07
294 297 9.828039 GCATATCCAATATCTACATCTTGATGA 57.172 33.333 16.43 1.22 0.00 2.92
297 300 8.789825 ATCCAATATCTACATCTTGATGAAGC 57.210 34.615 16.43 0.00 0.00 3.86
298 301 7.738847 TCCAATATCTACATCTTGATGAAGCA 58.261 34.615 16.43 0.00 0.00 3.91
299 302 8.380867 TCCAATATCTACATCTTGATGAAGCAT 58.619 33.333 16.43 6.14 0.00 3.79
300 303 8.451748 CCAATATCTACATCTTGATGAAGCATG 58.548 37.037 16.43 0.00 0.00 4.06
301 304 9.216117 CAATATCTACATCTTGATGAAGCATGA 57.784 33.333 16.43 6.18 0.00 3.07
302 305 9.788889 AATATCTACATCTTGATGAAGCATGAA 57.211 29.630 16.43 0.00 0.00 2.57
303 306 7.731882 ATCTACATCTTGATGAAGCATGAAG 57.268 36.000 16.43 0.00 36.64 3.02
304 307 6.647229 TCTACATCTTGATGAAGCATGAAGT 58.353 36.000 16.43 0.00 36.66 3.01
305 308 7.108194 TCTACATCTTGATGAAGCATGAAGTT 58.892 34.615 16.43 0.00 36.66 2.66
306 309 6.585695 ACATCTTGATGAAGCATGAAGTTT 57.414 33.333 16.43 0.00 36.66 2.66
307 310 6.618811 ACATCTTGATGAAGCATGAAGTTTC 58.381 36.000 16.43 0.00 36.66 2.78
308 311 6.433404 ACATCTTGATGAAGCATGAAGTTTCT 59.567 34.615 16.43 0.00 36.66 2.52
309 312 6.889301 TCTTGATGAAGCATGAAGTTTCTT 57.111 33.333 0.00 0.00 36.66 2.52
310 313 7.984422 TCTTGATGAAGCATGAAGTTTCTTA 57.016 32.000 0.00 0.00 36.66 2.10
311 314 8.037382 TCTTGATGAAGCATGAAGTTTCTTAG 57.963 34.615 0.00 0.00 36.66 2.18
312 315 7.663081 TCTTGATGAAGCATGAAGTTTCTTAGT 59.337 33.333 0.00 0.00 36.66 2.24
313 316 7.137490 TGATGAAGCATGAAGTTTCTTAGTG 57.863 36.000 0.00 0.00 38.19 2.74
314 317 6.936335 TGATGAAGCATGAAGTTTCTTAGTGA 59.064 34.615 0.00 0.00 38.19 3.41
315 318 7.445096 TGATGAAGCATGAAGTTTCTTAGTGAA 59.555 33.333 0.00 0.00 38.19 3.18
316 319 7.566760 TGAAGCATGAAGTTTCTTAGTGAAA 57.433 32.000 0.00 0.00 41.85 2.69
317 320 7.995289 TGAAGCATGAAGTTTCTTAGTGAAAA 58.005 30.769 0.00 0.00 45.10 2.29
318 321 8.632679 TGAAGCATGAAGTTTCTTAGTGAAAAT 58.367 29.630 0.00 0.00 45.10 1.82
321 324 9.289782 AGCATGAAGTTTCTTAGTGAAAATAGT 57.710 29.630 0.00 0.00 45.10 2.12
322 325 9.899226 GCATGAAGTTTCTTAGTGAAAATAGTT 57.101 29.630 0.00 0.00 45.10 2.24
351 354 9.862149 ATTAACTGTCCTAATTTATGGGTAAGG 57.138 33.333 0.00 0.00 0.00 2.69
352 355 7.519347 AACTGTCCTAATTTATGGGTAAGGA 57.481 36.000 0.00 0.00 0.00 3.36
353 356 7.707467 ACTGTCCTAATTTATGGGTAAGGAT 57.293 36.000 0.00 0.00 0.00 3.24
354 357 8.808240 ACTGTCCTAATTTATGGGTAAGGATA 57.192 34.615 0.00 0.00 0.00 2.59
355 358 9.406662 ACTGTCCTAATTTATGGGTAAGGATAT 57.593 33.333 0.00 0.00 0.00 1.63
366 369 9.914834 TTATGGGTAAGGATATATGTATTTGCC 57.085 33.333 0.00 0.00 0.00 4.52
367 370 7.336475 TGGGTAAGGATATATGTATTTGCCA 57.664 36.000 0.00 0.00 0.00 4.92
368 371 7.760607 TGGGTAAGGATATATGTATTTGCCAA 58.239 34.615 0.00 0.00 0.00 4.52
369 372 7.668052 TGGGTAAGGATATATGTATTTGCCAAC 59.332 37.037 0.00 0.00 0.00 3.77
370 373 7.668052 GGGTAAGGATATATGTATTTGCCAACA 59.332 37.037 0.00 0.00 0.00 3.33
371 374 9.243105 GGTAAGGATATATGTATTTGCCAACAT 57.757 33.333 0.00 0.00 39.56 2.71
381 384 7.566760 TGTATTTGCCAACATAATACTGAGG 57.433 36.000 0.00 0.00 34.44 3.86
382 385 7.342581 TGTATTTGCCAACATAATACTGAGGA 58.657 34.615 0.00 0.00 34.44 3.71
383 386 6.699575 ATTTGCCAACATAATACTGAGGAC 57.300 37.500 0.00 0.00 0.00 3.85
384 387 4.835284 TGCCAACATAATACTGAGGACA 57.165 40.909 0.00 0.00 0.00 4.02
406 409 3.264897 GGTATGTGGCTCGCTGCG 61.265 66.667 17.25 17.25 44.05 5.18
453 456 1.687492 TTCCACCCACCCCATATCAA 58.313 50.000 0.00 0.00 0.00 2.57
488 491 6.018507 GCGGTGTTTCTTGTTTAGTTTCTAGA 60.019 38.462 0.00 0.00 0.00 2.43
490 493 7.849515 CGGTGTTTCTTGTTTAGTTTCTAGAAC 59.150 37.037 4.18 0.89 0.00 3.01
517 520 4.960938 TCCATTAGAGAATGTTCCATCCG 58.039 43.478 0.00 0.00 40.87 4.18
534 537 5.596772 TCCATCCGAAATCATACAGACTACA 59.403 40.000 0.00 0.00 0.00 2.74
916 921 7.701539 AGCATTCTCCATTTGTACAATGTTA 57.298 32.000 9.56 0.00 0.00 2.41
917 922 8.297470 AGCATTCTCCATTTGTACAATGTTAT 57.703 30.769 9.56 0.00 0.00 1.89
918 923 8.192774 AGCATTCTCCATTTGTACAATGTTATG 58.807 33.333 9.56 9.80 0.00 1.90
919 924 8.190122 GCATTCTCCATTTGTACAATGTTATGA 58.810 33.333 16.21 6.60 0.00 2.15
923 928 9.241919 TCTCCATTTGTACAATGTTATGATTGT 57.758 29.630 16.21 0.00 46.14 2.71
939 944 6.966534 ATGATTGTATGTTTTCCTCATCCC 57.033 37.500 0.00 0.00 0.00 3.85
962 967 6.072673 CCCTTTTCCTAGTTGTTGTGTATGTC 60.073 42.308 0.00 0.00 0.00 3.06
1006 1011 1.000717 GCAGTTTGCGGTACACCAAAT 60.001 47.619 11.68 2.07 33.96 2.32
1064 1069 2.158769 ACATGCCACGATGGATGTGTAT 60.159 45.455 13.23 0.00 40.96 2.29
1102 1107 2.579201 CCAGTGGAGTACGGCTGG 59.421 66.667 1.68 11.54 41.89 4.85
1154 1159 5.350365 TGCTACGTCAAGCTTTAATTCGATT 59.650 36.000 11.40 0.00 43.19 3.34
1155 1160 5.896974 GCTACGTCAAGCTTTAATTCGATTC 59.103 40.000 0.00 0.00 39.50 2.52
1156 1161 5.856126 ACGTCAAGCTTTAATTCGATTCA 57.144 34.783 0.00 0.00 0.00 2.57
1157 1162 6.236017 ACGTCAAGCTTTAATTCGATTCAA 57.764 33.333 0.00 0.00 0.00 2.69
1158 1163 6.307155 ACGTCAAGCTTTAATTCGATTCAAG 58.693 36.000 0.00 0.00 0.00 3.02
1159 1164 5.225949 CGTCAAGCTTTAATTCGATTCAAGC 59.774 40.000 0.00 13.80 45.28 4.01
1163 1168 3.793492 GCTTTAATTCGATTCAAGCTGGC 59.207 43.478 14.13 0.00 42.96 4.85
1164 1169 4.439289 GCTTTAATTCGATTCAAGCTGGCT 60.439 41.667 14.13 0.00 42.96 4.75
1165 1170 4.621068 TTAATTCGATTCAAGCTGGCTG 57.379 40.909 0.00 0.00 0.00 4.85
1166 1171 1.386533 ATTCGATTCAAGCTGGCTGG 58.613 50.000 0.00 0.00 0.00 4.85
1167 1172 1.308069 TTCGATTCAAGCTGGCTGGC 61.308 55.000 0.00 0.00 0.00 4.85
1168 1173 2.042259 CGATTCAAGCTGGCTGGCA 61.042 57.895 3.18 3.18 34.17 4.92
1169 1174 1.381928 CGATTCAAGCTGGCTGGCAT 61.382 55.000 3.74 0.00 34.17 4.40
1170 1175 0.102481 GATTCAAGCTGGCTGGCATG 59.898 55.000 3.74 0.11 32.99 4.06
1171 1176 0.613853 ATTCAAGCTGGCTGGCATGT 60.614 50.000 3.74 0.00 33.40 3.21
1172 1177 0.038021 TTCAAGCTGGCTGGCATGTA 59.962 50.000 3.74 0.00 33.40 2.29
1173 1178 0.038021 TCAAGCTGGCTGGCATGTAA 59.962 50.000 3.74 0.00 33.40 2.41
1174 1179 0.454600 CAAGCTGGCTGGCATGTAAG 59.545 55.000 3.74 0.00 34.17 2.34
1175 1180 0.682209 AAGCTGGCTGGCATGTAAGG 60.682 55.000 3.74 0.00 34.17 2.69
1176 1181 1.077501 GCTGGCTGGCATGTAAGGA 60.078 57.895 3.74 0.00 0.00 3.36
1177 1182 0.466922 GCTGGCTGGCATGTAAGGAT 60.467 55.000 3.74 0.00 0.00 3.24
1178 1183 1.602311 CTGGCTGGCATGTAAGGATC 58.398 55.000 3.74 0.00 0.00 3.36
1179 1184 0.918258 TGGCTGGCATGTAAGGATCA 59.082 50.000 0.00 0.00 0.00 2.92
1180 1185 1.496001 TGGCTGGCATGTAAGGATCAT 59.504 47.619 0.00 0.00 0.00 2.45
1181 1186 2.157738 GGCTGGCATGTAAGGATCATC 58.842 52.381 0.00 0.00 0.00 2.92
1182 1187 2.157738 GCTGGCATGTAAGGATCATCC 58.842 52.381 0.00 0.00 36.58 3.51
1183 1188 2.787994 CTGGCATGTAAGGATCATCCC 58.212 52.381 0.00 0.00 37.19 3.85
1184 1189 1.425066 TGGCATGTAAGGATCATCCCC 59.575 52.381 0.00 0.00 37.19 4.81
1185 1190 1.272147 GGCATGTAAGGATCATCCCCC 60.272 57.143 0.00 0.00 37.19 5.40
1243 1334 6.591448 TCAACATGCTGAGTAGTAGTCAATTG 59.409 38.462 8.98 0.00 0.00 2.32
1249 1340 6.100004 GCTGAGTAGTAGTCAATTGCTACAA 58.900 40.000 27.07 14.24 40.76 2.41
1274 1365 8.737168 AGCATTCTACTGCAATAATAAAGACA 57.263 30.769 0.00 0.00 44.77 3.41
1329 1420 8.275015 ACATCGGAAACATCACAAATAATACA 57.725 30.769 0.00 0.00 0.00 2.29
1361 1452 1.341209 CTAGATGCATGGGCTACACGA 59.659 52.381 2.46 0.00 41.91 4.35
1369 1460 2.046604 GGCTACACGACCCAACCC 60.047 66.667 0.00 0.00 0.00 4.11
1462 1553 9.765795 GCTGCTAGTCCTAGAAAATTATCTAAA 57.234 33.333 5.52 0.00 35.21 1.85
1606 1697 1.333931 TCTAGAGCGTTATGGCGACTG 59.666 52.381 0.00 0.00 38.18 3.51
1643 1734 1.631388 ACCCAATGGACGGTAATGTGA 59.369 47.619 0.00 0.00 34.81 3.58
1658 1749 7.171508 ACGGTAATGTGATAATGTTGCTATGAG 59.828 37.037 0.00 0.00 0.00 2.90
1796 1887 0.685131 CATGGATTGCCCTGGCTTCA 60.685 55.000 9.97 3.16 42.51 3.02
1801 1892 0.546122 ATTGCCCTGGCTTCATACGA 59.454 50.000 9.97 0.00 42.51 3.43
1865 1956 0.033208 TTCTGATGTTCCCCATGGGC 60.033 55.000 26.87 12.78 43.94 5.36
1883 1974 3.132824 TGGGCACATACAGAGTATCACAG 59.867 47.826 0.00 0.00 37.82 3.66
1907 1998 0.393077 AGTGCTTAAGGTGCGAGTGT 59.607 50.000 4.29 0.00 0.00 3.55
2018 2109 5.876357 ACTTTAGCCTGGATTGTACTCAAA 58.124 37.500 0.00 0.00 37.11 2.69
2021 2112 3.019564 AGCCTGGATTGTACTCAAATGC 58.980 45.455 0.00 0.00 37.11 3.56
2043 2134 4.261031 GCGTACAAAATGGTGTGACTTTCT 60.261 41.667 0.00 0.00 32.75 2.52
2053 2144 9.739276 AAATGGTGTGACTTTCTCTATTGATTA 57.261 29.630 0.00 0.00 0.00 1.75
2124 2215 2.748388 GGAGACTGGTGGGTGTACTAT 58.252 52.381 0.00 0.00 0.00 2.12
2157 2248 0.398948 TTCCTACGGGGGTGGGATAC 60.399 60.000 0.00 0.00 33.94 2.24
2177 2268 6.127897 GGATACTTCCCAAAGTCATTGTTCAG 60.128 42.308 0.00 0.00 44.64 3.02
2251 2342 1.198759 TAGGGCGGCTTCAACTCCTT 61.199 55.000 9.56 0.00 0.00 3.36
2326 2417 6.367374 TCACTAACCTTGGTATCATTGACA 57.633 37.500 0.00 0.00 0.00 3.58
2339 2430 2.162681 CATTGACAAGGAGGGGAACAC 58.837 52.381 0.00 0.00 0.00 3.32
2370 2461 1.966451 GGCAGACTTCCCCACGTTG 60.966 63.158 0.00 0.00 0.00 4.10
2393 2484 7.385778 TGGTTACTAATAACAAATGCCACTC 57.614 36.000 0.00 0.00 42.26 3.51
2550 2641 5.534278 TGACAAATTATGCAAAGACTGTCCA 59.466 36.000 15.03 0.00 32.77 4.02
2572 2663 9.216117 GTCCACTTCTTTACATTGTATTACACT 57.784 33.333 0.00 0.00 0.00 3.55
2596 2687 9.084164 ACTAACATTACTTACTTGCTTACATCG 57.916 33.333 0.00 0.00 0.00 3.84
2605 2696 8.564574 ACTTACTTGCTTACATCGATTTTGAAA 58.435 29.630 0.00 0.00 0.00 2.69
2650 2741 8.560576 AAACCAATTATCGATTTCGCAAATAG 57.439 30.769 1.71 0.00 39.60 1.73
2662 2753 7.534918 CGATTTCGCAAATAGATCATGCATTTA 59.465 33.333 0.00 0.00 40.04 1.40
2733 2825 1.618343 AGGGGAAATGAAAAAGCCACG 59.382 47.619 0.00 0.00 0.00 4.94
2737 2829 3.243737 GGGAAATGAAAAAGCCACGAACT 60.244 43.478 0.00 0.00 0.00 3.01
2745 2837 0.112412 AAGCCACGAACTGGGGAAAT 59.888 50.000 0.00 0.00 41.02 2.17
2800 2892 3.306613 GGTGGGATAGCCTACTAGTTGT 58.693 50.000 13.61 0.00 44.49 3.32
2870 2963 2.644798 AGAATAAGATATTGGCCGGCCT 59.355 45.455 43.34 28.71 36.94 5.19
2953 3046 5.278463 CCGAATAGGAAATACCCAGCAAATG 60.278 44.000 0.00 0.00 45.00 2.32
2958 3051 3.306641 GGAAATACCCAGCAAATGCACAA 60.307 43.478 8.28 0.00 45.16 3.33
2981 3074 1.380302 GCTCCCAATGTGTCCTGGT 59.620 57.895 0.00 0.00 0.00 4.00
2982 3075 0.962356 GCTCCCAATGTGTCCTGGTG 60.962 60.000 0.00 0.00 0.00 4.17
2983 3076 0.962356 CTCCCAATGTGTCCTGGTGC 60.962 60.000 0.00 0.00 0.00 5.01
3139 3250 7.795047 AGAAAATGTTCCAGGATTTCAAAAGT 58.205 30.769 13.51 0.00 33.92 2.66
3146 3257 6.537453 TCCAGGATTTCAAAAGTTGTTCAA 57.463 33.333 0.00 0.00 0.00 2.69
3300 3413 4.400884 TGGCGAATATGTAAATTGTTGCCT 59.599 37.500 7.82 0.00 39.45 4.75
3327 3440 1.677637 GGATCGAGGAAGCGGGAGTT 61.678 60.000 0.00 0.00 0.00 3.01
3370 3483 5.191727 ACCAGGAAATGACAATATGGTGA 57.808 39.130 0.00 0.00 38.13 4.02
3373 3486 4.949238 CAGGAAATGACAATATGGTGACCA 59.051 41.667 6.84 6.84 38.19 4.02
3405 3518 0.535780 GGATGGAAGCGATGATGGCA 60.536 55.000 1.54 0.00 0.00 4.92
3448 3561 1.811679 GCTTGTGAGCTAGTCGGCC 60.812 63.158 0.00 0.00 45.65 6.13
3449 3562 1.591703 CTTGTGAGCTAGTCGGCCA 59.408 57.895 2.24 0.00 0.00 5.36
3450 3563 0.176680 CTTGTGAGCTAGTCGGCCAT 59.823 55.000 2.24 0.00 0.00 4.40
3452 3565 1.704641 TGTGAGCTAGTCGGCCATAT 58.295 50.000 2.24 0.00 0.00 1.78
3466 3579 1.526887 GCCATATGAACGATGTCGGTG 59.473 52.381 3.65 0.00 40.66 4.94
3524 3637 3.717294 GGTCGTGGCCATGGGACT 61.717 66.667 24.78 0.00 0.00 3.85
3531 3644 2.043652 GCCATGGGACTGGTGCAT 60.044 61.111 15.13 0.00 38.63 3.96
3537 3650 1.377725 GGGACTGGTGCATGAGGTG 60.378 63.158 0.00 0.00 0.00 4.00
3538 3651 1.679311 GGACTGGTGCATGAGGTGA 59.321 57.895 0.00 0.00 0.00 4.02
3540 3653 1.446907 GACTGGTGCATGAGGTGAAG 58.553 55.000 0.00 0.00 0.00 3.02
3541 3654 0.767375 ACTGGTGCATGAGGTGAAGT 59.233 50.000 0.00 0.00 0.00 3.01
3542 3655 1.271054 ACTGGTGCATGAGGTGAAGTC 60.271 52.381 0.00 0.00 0.00 3.01
3543 3656 0.320683 TGGTGCATGAGGTGAAGTCG 60.321 55.000 0.00 0.00 0.00 4.18
3544 3657 1.021390 GGTGCATGAGGTGAAGTCGG 61.021 60.000 0.00 0.00 0.00 4.79
3545 3658 0.320771 GTGCATGAGGTGAAGTCGGT 60.321 55.000 0.00 0.00 0.00 4.69
3546 3659 0.396435 TGCATGAGGTGAAGTCGGTT 59.604 50.000 0.00 0.00 0.00 4.44
3547 3660 1.621317 TGCATGAGGTGAAGTCGGTTA 59.379 47.619 0.00 0.00 0.00 2.85
3548 3661 2.271800 GCATGAGGTGAAGTCGGTTAG 58.728 52.381 0.00 0.00 0.00 2.34
3549 3662 2.353803 GCATGAGGTGAAGTCGGTTAGT 60.354 50.000 0.00 0.00 0.00 2.24
3550 3663 3.254060 CATGAGGTGAAGTCGGTTAGTG 58.746 50.000 0.00 0.00 0.00 2.74
3551 3664 2.313317 TGAGGTGAAGTCGGTTAGTGT 58.687 47.619 0.00 0.00 0.00 3.55
3552 3665 2.295349 TGAGGTGAAGTCGGTTAGTGTC 59.705 50.000 0.00 0.00 0.00 3.67
3553 3666 1.268899 AGGTGAAGTCGGTTAGTGTCG 59.731 52.381 0.00 0.00 0.00 4.35
3554 3667 1.267806 GGTGAAGTCGGTTAGTGTCGA 59.732 52.381 0.00 0.00 0.00 4.20
3560 3673 4.876652 GGTTAGTGTCGACCGGTC 57.123 61.111 25.28 25.28 0.00 4.79
3574 3687 3.670377 GGTCGTGGGCAAGGCAAC 61.670 66.667 0.00 0.00 0.00 4.17
3575 3688 4.025401 GTCGTGGGCAAGGCAACG 62.025 66.667 16.43 16.43 46.39 4.10
3603 3716 3.952675 CGCCGCAACACAGCAGTT 61.953 61.111 0.00 0.00 0.00 3.16
3604 3717 2.603247 CGCCGCAACACAGCAGTTA 61.603 57.895 0.00 0.00 0.00 2.24
3605 3718 1.875963 GCCGCAACACAGCAGTTAT 59.124 52.632 0.00 0.00 0.00 1.89
3606 3719 0.240945 GCCGCAACACAGCAGTTATT 59.759 50.000 0.00 0.00 0.00 1.40
3607 3720 1.967762 CCGCAACACAGCAGTTATTG 58.032 50.000 0.00 0.00 0.00 1.90
3608 3721 1.401409 CCGCAACACAGCAGTTATTGG 60.401 52.381 5.48 0.00 0.00 3.16
3609 3722 1.701704 GCAACACAGCAGTTATTGGC 58.298 50.000 5.48 0.00 0.00 4.52
3610 3723 1.000385 GCAACACAGCAGTTATTGGCA 60.000 47.619 5.48 0.00 0.00 4.92
3611 3724 2.545532 GCAACACAGCAGTTATTGGCAA 60.546 45.455 0.68 0.68 0.00 4.52
3612 3725 3.861886 GCAACACAGCAGTTATTGGCAAT 60.862 43.478 18.01 18.01 0.00 3.56
3613 3726 3.581024 ACACAGCAGTTATTGGCAATG 57.419 42.857 22.57 8.56 0.00 2.82
3614 3727 2.264813 CACAGCAGTTATTGGCAATGC 58.735 47.619 22.57 18.05 37.15 3.56
3644 3757 3.933155 CGAAGCATAGGTCACAATGAC 57.067 47.619 0.10 0.10 46.23 3.06
3671 3784 4.451150 GGACACGGCGATGCAGGA 62.451 66.667 16.62 0.00 0.00 3.86
3672 3785 3.188786 GACACGGCGATGCAGGAC 61.189 66.667 16.62 0.00 0.00 3.85
3691 3804 4.161295 CGGCCGCCTCATGGAAGA 62.161 66.667 14.67 0.00 34.57 2.87
3692 3805 2.512896 GGCCGCCTCATGGAAGAT 59.487 61.111 0.71 0.00 34.57 2.40
3693 3806 1.152881 GGCCGCCTCATGGAAGATT 60.153 57.895 0.71 0.00 34.57 2.40
3694 3807 0.753111 GGCCGCCTCATGGAAGATTT 60.753 55.000 0.71 0.00 34.57 2.17
3695 3808 1.476833 GGCCGCCTCATGGAAGATTTA 60.477 52.381 0.71 0.00 34.57 1.40
3696 3809 1.876156 GCCGCCTCATGGAAGATTTAG 59.124 52.381 0.00 0.00 34.57 1.85
3697 3810 2.498167 CCGCCTCATGGAAGATTTAGG 58.502 52.381 0.00 0.00 34.57 2.69
3698 3811 2.498167 CGCCTCATGGAAGATTTAGGG 58.502 52.381 0.00 0.00 34.57 3.53
3699 3812 2.234143 GCCTCATGGAAGATTTAGGGC 58.766 52.381 0.00 0.00 34.57 5.19
3700 3813 2.158549 GCCTCATGGAAGATTTAGGGCT 60.159 50.000 0.00 0.00 34.86 5.19
3701 3814 3.484407 CCTCATGGAAGATTTAGGGCTG 58.516 50.000 0.00 0.00 34.57 4.85
3702 3815 3.484407 CTCATGGAAGATTTAGGGCTGG 58.516 50.000 0.00 0.00 0.00 4.85
3703 3816 1.959282 CATGGAAGATTTAGGGCTGGC 59.041 52.381 0.00 0.00 0.00 4.85
3704 3817 0.258774 TGGAAGATTTAGGGCTGGCC 59.741 55.000 13.15 13.15 0.00 5.36
3705 3818 0.819666 GGAAGATTTAGGGCTGGCCG 60.820 60.000 15.17 0.00 36.85 6.13
3706 3819 0.107165 GAAGATTTAGGGCTGGCCGT 60.107 55.000 15.17 11.55 36.85 5.68
3707 3820 0.394352 AAGATTTAGGGCTGGCCGTG 60.394 55.000 15.17 0.00 36.85 4.94
3708 3821 1.077716 GATTTAGGGCTGGCCGTGT 60.078 57.895 15.17 0.00 36.85 4.49
3709 3822 0.679960 GATTTAGGGCTGGCCGTGTT 60.680 55.000 15.17 0.00 36.85 3.32
3710 3823 0.621609 ATTTAGGGCTGGCCGTGTTA 59.378 50.000 15.17 0.00 36.85 2.41
3711 3824 0.035820 TTTAGGGCTGGCCGTGTTAG 60.036 55.000 15.17 0.00 36.85 2.34
3712 3825 2.530958 TTAGGGCTGGCCGTGTTAGC 62.531 60.000 15.17 3.42 36.85 3.09
3713 3826 4.715523 GGGCTGGCCGTGTTAGCA 62.716 66.667 13.50 0.00 39.15 3.49
3714 3827 3.431725 GGCTGGCCGTGTTAGCAC 61.432 66.667 13.50 0.00 41.97 4.40
3715 3828 3.431725 GCTGGCCGTGTTAGCACC 61.432 66.667 7.12 0.00 42.39 5.01
3716 3829 2.031919 CTGGCCGTGTTAGCACCA 59.968 61.111 3.94 0.00 42.39 4.17
3717 3830 2.281208 TGGCCGTGTTAGCACCAC 60.281 61.111 3.94 0.00 42.39 4.16
3718 3831 2.032071 GGCCGTGTTAGCACCACT 59.968 61.111 3.94 0.00 42.39 4.00
3719 3832 1.294138 GGCCGTGTTAGCACCACTA 59.706 57.895 3.94 0.00 42.39 2.74
3720 3833 1.017701 GGCCGTGTTAGCACCACTAC 61.018 60.000 3.94 0.00 42.39 2.73
3721 3834 1.017701 GCCGTGTTAGCACCACTACC 61.018 60.000 3.94 0.00 42.39 3.18
3722 3835 0.390735 CCGTGTTAGCACCACTACCC 60.391 60.000 3.94 0.00 42.39 3.69
3723 3836 0.390735 CGTGTTAGCACCACTACCCC 60.391 60.000 3.94 0.00 42.39 4.95
3724 3837 0.688487 GTGTTAGCACCACTACCCCA 59.312 55.000 0.00 0.00 39.61 4.96
3725 3838 1.072648 GTGTTAGCACCACTACCCCAA 59.927 52.381 0.00 0.00 39.61 4.12
3726 3839 1.072648 TGTTAGCACCACTACCCCAAC 59.927 52.381 0.00 0.00 0.00 3.77
3727 3840 1.350019 GTTAGCACCACTACCCCAACT 59.650 52.381 0.00 0.00 0.00 3.16
3728 3841 0.981183 TAGCACCACTACCCCAACTG 59.019 55.000 0.00 0.00 0.00 3.16
3729 3842 1.303317 GCACCACTACCCCAACTGG 60.303 63.158 0.00 0.00 0.00 4.00
3730 3843 1.774894 GCACCACTACCCCAACTGGA 61.775 60.000 0.00 0.00 37.39 3.86
3731 3844 0.036306 CACCACTACCCCAACTGGAC 59.964 60.000 0.00 0.00 37.39 4.02
3732 3845 1.131928 ACCACTACCCCAACTGGACC 61.132 60.000 0.00 0.00 37.39 4.46
3733 3846 0.840722 CCACTACCCCAACTGGACCT 60.841 60.000 0.00 0.00 37.39 3.85
3734 3847 0.324943 CACTACCCCAACTGGACCTG 59.675 60.000 0.00 0.00 37.39 4.00
3735 3848 0.192566 ACTACCCCAACTGGACCTGA 59.807 55.000 5.22 0.00 37.39 3.86
3736 3849 1.358152 CTACCCCAACTGGACCTGAA 58.642 55.000 5.22 0.00 37.39 3.02
3737 3850 1.279271 CTACCCCAACTGGACCTGAAG 59.721 57.143 5.22 0.00 37.39 3.02
3738 3851 1.303643 CCCCAACTGGACCTGAAGC 60.304 63.158 5.22 0.00 37.39 3.86
3739 3852 1.303643 CCCAACTGGACCTGAAGCC 60.304 63.158 5.22 0.00 37.39 4.35
3740 3853 1.303643 CCAACTGGACCTGAAGCCC 60.304 63.158 5.22 0.00 37.39 5.19
3741 3854 1.455849 CAACTGGACCTGAAGCCCA 59.544 57.895 5.22 0.00 0.00 5.36
3742 3855 0.038744 CAACTGGACCTGAAGCCCAT 59.961 55.000 5.22 0.00 0.00 4.00
3743 3856 0.038744 AACTGGACCTGAAGCCCATG 59.961 55.000 5.22 0.00 0.00 3.66
3744 3857 0.842030 ACTGGACCTGAAGCCCATGA 60.842 55.000 5.22 0.00 0.00 3.07
3745 3858 0.107312 CTGGACCTGAAGCCCATGAG 60.107 60.000 0.00 0.00 0.00 2.90
3746 3859 0.547471 TGGACCTGAAGCCCATGAGA 60.547 55.000 0.00 0.00 0.00 3.27
3747 3860 0.620556 GGACCTGAAGCCCATGAGAA 59.379 55.000 0.00 0.00 0.00 2.87
3748 3861 1.407989 GGACCTGAAGCCCATGAGAAG 60.408 57.143 0.00 0.00 0.00 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 2.102420 CCAATTCCCCGGGAAAATAAGC 59.898 50.000 26.32 0.00 45.41 3.09
99 100 9.499479 CATACAGATGCCTACTTCAATCTAATT 57.501 33.333 0.00 0.00 0.00 1.40
140 141 6.428083 TCAAGGTACATTCCACTAGTTTCA 57.572 37.500 0.00 0.00 0.00 2.69
141 142 7.739498 TTTCAAGGTACATTCCACTAGTTTC 57.261 36.000 0.00 0.00 0.00 2.78
275 278 9.216117 TCATGCTTCATCAAGATGTAGATATTG 57.784 33.333 17.46 0.93 38.13 1.90
276 279 9.788889 TTCATGCTTCATCAAGATGTAGATATT 57.211 29.630 17.46 0.32 38.13 1.28
277 280 9.438228 CTTCATGCTTCATCAAGATGTAGATAT 57.562 33.333 17.46 9.63 38.13 1.63
278 281 8.427276 ACTTCATGCTTCATCAAGATGTAGATA 58.573 33.333 17.46 8.12 38.13 1.98
279 282 7.281098 ACTTCATGCTTCATCAAGATGTAGAT 58.719 34.615 17.46 7.80 38.13 1.98
280 283 6.647229 ACTTCATGCTTCATCAAGATGTAGA 58.353 36.000 17.46 6.23 38.13 2.59
281 284 6.922247 ACTTCATGCTTCATCAAGATGTAG 57.078 37.500 11.07 11.07 39.72 2.74
282 285 7.609146 AGAAACTTCATGCTTCATCAAGATGTA 59.391 33.333 9.66 0.00 39.72 2.29
283 286 6.433404 AGAAACTTCATGCTTCATCAAGATGT 59.567 34.615 9.66 0.00 39.72 3.06
284 287 6.853720 AGAAACTTCATGCTTCATCAAGATG 58.146 36.000 3.67 3.67 40.09 2.90
287 290 7.749570 CACTAAGAAACTTCATGCTTCATCAAG 59.250 37.037 0.00 0.00 28.47 3.02
289 292 6.936335 TCACTAAGAAACTTCATGCTTCATCA 59.064 34.615 0.00 0.00 0.00 3.07
290 293 7.369803 TCACTAAGAAACTTCATGCTTCATC 57.630 36.000 0.00 0.00 0.00 2.92
291 294 7.750229 TTCACTAAGAAACTTCATGCTTCAT 57.250 32.000 0.00 0.00 32.05 2.57
292 295 7.566760 TTTCACTAAGAAACTTCATGCTTCA 57.433 32.000 0.00 0.00 41.17 3.02
295 298 9.289782 ACTATTTTCACTAAGAAACTTCATGCT 57.710 29.630 0.00 0.00 45.48 3.79
296 299 9.899226 AACTATTTTCACTAAGAAACTTCATGC 57.101 29.630 0.00 0.00 45.48 4.06
325 328 9.862149 CCTTACCCATAAATTAGGACAGTTAAT 57.138 33.333 0.00 0.00 0.00 1.40
326 329 9.060137 TCCTTACCCATAAATTAGGACAGTTAA 57.940 33.333 0.00 0.00 0.00 2.01
327 330 8.626917 TCCTTACCCATAAATTAGGACAGTTA 57.373 34.615 0.00 0.00 0.00 2.24
328 331 7.519347 TCCTTACCCATAAATTAGGACAGTT 57.481 36.000 0.00 0.00 0.00 3.16
329 332 7.707467 ATCCTTACCCATAAATTAGGACAGT 57.293 36.000 0.00 0.00 34.84 3.55
340 343 9.914834 GGCAAATACATATATCCTTACCCATAA 57.085 33.333 0.00 0.00 0.00 1.90
341 344 9.063484 TGGCAAATACATATATCCTTACCCATA 57.937 33.333 0.00 0.00 0.00 2.74
342 345 7.938686 TGGCAAATACATATATCCTTACCCAT 58.061 34.615 0.00 0.00 0.00 4.00
343 346 7.336475 TGGCAAATACATATATCCTTACCCA 57.664 36.000 0.00 0.00 0.00 4.51
344 347 7.668052 TGTTGGCAAATACATATATCCTTACCC 59.332 37.037 0.00 0.00 0.00 3.69
345 348 8.630054 TGTTGGCAAATACATATATCCTTACC 57.370 34.615 0.00 0.00 0.00 2.85
355 358 9.283768 CCTCAGTATTATGTTGGCAAATACATA 57.716 33.333 17.49 12.55 38.15 2.29
356 359 7.998383 TCCTCAGTATTATGTTGGCAAATACAT 59.002 33.333 17.49 13.39 38.15 2.29
357 360 7.282224 GTCCTCAGTATTATGTTGGCAAATACA 59.718 37.037 17.49 7.59 38.15 2.29
358 361 7.282224 TGTCCTCAGTATTATGTTGGCAAATAC 59.718 37.037 0.00 6.59 36.68 1.89
359 362 7.342581 TGTCCTCAGTATTATGTTGGCAAATA 58.657 34.615 0.00 0.00 0.00 1.40
360 363 6.186957 TGTCCTCAGTATTATGTTGGCAAAT 58.813 36.000 0.00 0.77 0.00 2.32
361 364 5.565509 TGTCCTCAGTATTATGTTGGCAAA 58.434 37.500 0.00 0.00 0.00 3.68
362 365 5.172687 TGTCCTCAGTATTATGTTGGCAA 57.827 39.130 0.00 0.00 0.00 4.52
363 366 4.835284 TGTCCTCAGTATTATGTTGGCA 57.165 40.909 0.00 0.00 0.00 4.92
364 367 5.590259 ACAATGTCCTCAGTATTATGTTGGC 59.410 40.000 0.00 0.00 0.00 4.52
365 368 6.038603 CCACAATGTCCTCAGTATTATGTTGG 59.961 42.308 0.00 0.00 0.00 3.77
366 369 6.599244 ACCACAATGTCCTCAGTATTATGTTG 59.401 38.462 0.00 0.00 0.00 3.33
367 370 6.721318 ACCACAATGTCCTCAGTATTATGTT 58.279 36.000 0.00 0.00 0.00 2.71
368 371 6.313519 ACCACAATGTCCTCAGTATTATGT 57.686 37.500 0.00 0.00 0.00 2.29
369 372 7.933577 ACATACCACAATGTCCTCAGTATTATG 59.066 37.037 0.00 0.00 35.08 1.90
370 373 7.933577 CACATACCACAATGTCCTCAGTATTAT 59.066 37.037 0.00 0.00 38.01 1.28
371 374 7.272244 CACATACCACAATGTCCTCAGTATTA 58.728 38.462 0.00 0.00 38.01 0.98
372 375 6.115446 CACATACCACAATGTCCTCAGTATT 58.885 40.000 0.00 0.00 38.01 1.89
373 376 5.396772 CCACATACCACAATGTCCTCAGTAT 60.397 44.000 0.00 0.00 38.01 2.12
374 377 4.081142 CCACATACCACAATGTCCTCAGTA 60.081 45.833 0.00 0.00 38.01 2.74
375 378 3.307691 CCACATACCACAATGTCCTCAGT 60.308 47.826 0.00 0.00 38.01 3.41
376 379 3.273434 CCACATACCACAATGTCCTCAG 58.727 50.000 0.00 0.00 38.01 3.35
377 380 2.617788 GCCACATACCACAATGTCCTCA 60.618 50.000 0.00 0.00 38.01 3.86
378 381 2.017049 GCCACATACCACAATGTCCTC 58.983 52.381 0.00 0.00 38.01 3.71
379 382 1.635487 AGCCACATACCACAATGTCCT 59.365 47.619 0.00 0.00 38.01 3.85
380 383 2.017049 GAGCCACATACCACAATGTCC 58.983 52.381 0.00 0.00 38.01 4.02
381 384 1.665679 CGAGCCACATACCACAATGTC 59.334 52.381 0.00 0.00 38.01 3.06
382 385 1.737838 CGAGCCACATACCACAATGT 58.262 50.000 0.00 0.00 40.75 2.71
383 386 0.378257 GCGAGCCACATACCACAATG 59.622 55.000 0.00 0.00 0.00 2.82
384 387 0.253044 AGCGAGCCACATACCACAAT 59.747 50.000 0.00 0.00 0.00 2.71
411 414 7.310921 GGAAAGAGAGATATCAATCAGCCCATA 60.311 40.741 5.32 0.00 34.28 2.74
419 422 5.994668 GTGGGTGGAAAGAGAGATATCAATC 59.005 44.000 5.32 2.36 0.00 2.67
453 456 7.859325 AACAAGAAACACCGCTATAATACAT 57.141 32.000 0.00 0.00 0.00 2.29
488 491 8.421249 TGGAACATTCTCTAATGGAAATTGTT 57.579 30.769 3.41 0.00 45.72 2.83
517 520 6.349300 ACACCCATGTAGTCTGTATGATTTC 58.651 40.000 0.00 0.00 37.26 2.17
590 593 7.645058 ATTCTTGTATAAATCCACAACCAGG 57.355 36.000 0.00 0.00 31.61 4.45
618 621 9.077885 TGGCATCTTTTAGAATAGTGAAAACTT 57.922 29.630 0.00 0.00 0.00 2.66
693 696 6.939163 GTGTGCCCAATCTTTCTCATATATCT 59.061 38.462 0.00 0.00 0.00 1.98
740 743 7.908453 AGGCTAACTAATCTACTTTTGTCACT 58.092 34.615 0.00 0.00 0.00 3.41
774 778 5.186215 TGTTCGAGTTACTACATGGATCCAA 59.814 40.000 20.67 0.60 0.00 3.53
884 889 8.637986 TGTACAAATGGAGAATGCTTAAACTTT 58.362 29.630 0.00 0.00 0.00 2.66
916 921 6.676558 AGGGATGAGGAAAACATACAATCAT 58.323 36.000 0.00 0.00 30.87 2.45
917 922 6.078456 AGGGATGAGGAAAACATACAATCA 57.922 37.500 0.00 0.00 30.87 2.57
918 923 7.410120 AAAGGGATGAGGAAAACATACAATC 57.590 36.000 0.00 0.00 30.87 2.67
919 924 7.093333 GGAAAAGGGATGAGGAAAACATACAAT 60.093 37.037 0.00 0.00 30.87 2.71
921 926 5.714806 GGAAAAGGGATGAGGAAAACATACA 59.285 40.000 0.00 0.00 30.87 2.29
922 927 5.952347 AGGAAAAGGGATGAGGAAAACATAC 59.048 40.000 0.00 0.00 0.00 2.39
923 928 6.152638 AGGAAAAGGGATGAGGAAAACATA 57.847 37.500 0.00 0.00 0.00 2.29
939 944 6.202188 ACGACATACACAACAACTAGGAAAAG 59.798 38.462 0.00 0.00 0.00 2.27
962 967 6.201517 CACAATGAAAGCTCCCATATAAACG 58.798 40.000 1.79 0.00 0.00 3.60
1024 1029 5.760253 GCATGTAAGCCATAGTAGTTGTCAT 59.240 40.000 0.00 0.00 30.71 3.06
1064 1069 2.035632 CCTGGTTTTAGTTTGTGGCCA 58.964 47.619 0.00 0.00 0.00 5.36
1102 1107 6.038714 GTCTCCATGATGACTAACCCAAATTC 59.961 42.308 0.00 0.00 0.00 2.17
1154 1159 0.038021 TTACATGCCAGCCAGCTTGA 59.962 50.000 15.66 0.92 39.58 3.02
1155 1160 0.454600 CTTACATGCCAGCCAGCTTG 59.545 55.000 9.19 9.19 42.10 4.01
1156 1161 0.682209 CCTTACATGCCAGCCAGCTT 60.682 55.000 0.00 0.00 0.00 3.74
1157 1162 1.077212 CCTTACATGCCAGCCAGCT 60.077 57.895 0.00 0.00 0.00 4.24
1158 1163 0.466922 ATCCTTACATGCCAGCCAGC 60.467 55.000 0.00 0.00 0.00 4.85
1159 1164 1.134007 TGATCCTTACATGCCAGCCAG 60.134 52.381 0.00 0.00 0.00 4.85
1160 1165 0.918258 TGATCCTTACATGCCAGCCA 59.082 50.000 0.00 0.00 0.00 4.75
1161 1166 2.157738 GATGATCCTTACATGCCAGCC 58.842 52.381 0.00 0.00 0.00 4.85
1162 1167 2.157738 GGATGATCCTTACATGCCAGC 58.842 52.381 3.71 0.00 32.53 4.85
1166 1171 2.206576 GGGGGATGATCCTTACATGC 57.793 55.000 11.87 0.00 36.57 4.06
1182 1187 2.487986 GGAAATGTCTAGATGCAGGGGG 60.488 54.545 0.00 0.00 0.00 5.40
1183 1188 2.441001 AGGAAATGTCTAGATGCAGGGG 59.559 50.000 0.00 0.00 0.00 4.79
1184 1189 3.853355 AGGAAATGTCTAGATGCAGGG 57.147 47.619 0.00 0.00 0.00 4.45
1185 1190 5.188434 TCAAAGGAAATGTCTAGATGCAGG 58.812 41.667 0.00 0.00 0.00 4.85
1186 1191 6.748333 TTCAAAGGAAATGTCTAGATGCAG 57.252 37.500 0.00 0.00 0.00 4.41
1187 1192 7.414429 CGAATTCAAAGGAAATGTCTAGATGCA 60.414 37.037 6.22 0.00 36.43 3.96
1188 1193 6.909357 CGAATTCAAAGGAAATGTCTAGATGC 59.091 38.462 6.22 0.00 36.43 3.91
1189 1194 8.201554 TCGAATTCAAAGGAAATGTCTAGATG 57.798 34.615 6.22 0.00 36.43 2.90
1190 1195 8.669243 GTTCGAATTCAAAGGAAATGTCTAGAT 58.331 33.333 0.00 0.00 36.43 1.98
1191 1196 7.119262 GGTTCGAATTCAAAGGAAATGTCTAGA 59.881 37.037 0.00 0.00 36.43 2.43
1192 1197 7.119846 AGGTTCGAATTCAAAGGAAATGTCTAG 59.880 37.037 0.00 0.00 36.43 2.43
1243 1334 4.889832 ATTGCAGTAGAATGCTTGTAGC 57.110 40.909 3.41 0.00 46.63 3.58
1249 1340 8.737168 TGTCTTTATTATTGCAGTAGAATGCT 57.263 30.769 3.41 0.00 46.63 3.79
1274 1365 1.002069 TGGAATGGAGCCAAGGTCAT 58.998 50.000 0.00 0.00 31.13 3.06
1329 1420 6.600822 GCCCATGCATCTAGTTCAATACATAT 59.399 38.462 0.00 0.00 37.47 1.78
1331 1422 4.763793 GCCCATGCATCTAGTTCAATACAT 59.236 41.667 0.00 0.00 37.47 2.29
1339 1430 2.483714 CGTGTAGCCCATGCATCTAGTT 60.484 50.000 0.00 0.00 41.13 2.24
1361 1452 0.043485 AGTTGTTTTGGGGGTTGGGT 59.957 50.000 0.00 0.00 0.00 4.51
1399 1490 6.806668 TGGATTACACATCATACTGGAAGA 57.193 37.500 0.00 0.00 37.43 2.87
1465 1556 7.377398 TCCATTGATGTTAAAACAACAGATGG 58.623 34.615 23.06 23.06 41.66 3.51
1543 1634 6.846283 GTGTACAAGTGAAAAACATTCTCTCG 59.154 38.462 0.00 0.00 0.00 4.04
1588 1679 1.065102 GTCAGTCGCCATAACGCTCTA 59.935 52.381 0.00 0.00 0.00 2.43
1606 1697 3.285484 TGGGTATAGAAGTGAGGACGTC 58.715 50.000 7.13 7.13 0.00 4.34
1643 1734 8.152898 TCAGCTGATTACTCATAGCAACATTAT 58.847 33.333 13.74 0.00 0.00 1.28
1658 1749 5.290643 GTGAGATCACTTGTCAGCTGATTAC 59.709 44.000 21.47 8.49 43.25 1.89
1865 1956 6.037281 ACTCGTACTGTGATACTCTGTATGTG 59.963 42.308 0.00 0.00 32.24 3.21
1883 1974 0.989890 CGCACCTTAAGCACTCGTAC 59.010 55.000 0.00 0.00 0.00 3.67
2018 2109 3.146066 AGTCACACCATTTTGTACGCAT 58.854 40.909 0.00 0.00 0.00 4.73
2021 2112 5.236478 AGAGAAAGTCACACCATTTTGTACG 59.764 40.000 0.00 0.00 0.00 3.67
2031 2122 8.547967 TGTTAATCAATAGAGAAAGTCACACC 57.452 34.615 0.00 0.00 0.00 4.16
2157 2248 3.571401 AGCTGAACAATGACTTTGGGAAG 59.429 43.478 6.09 1.81 39.80 3.46
2177 2268 1.762708 TGCCTTATTTGCCAGGTAGC 58.237 50.000 0.00 0.00 32.06 3.58
2232 2323 1.198759 AAGGAGTTGAAGCCGCCCTA 61.199 55.000 0.00 0.00 0.00 3.53
2251 2342 0.974010 AAGGAACCGCTACCCATCGA 60.974 55.000 0.00 0.00 0.00 3.59
2326 2417 1.460699 GCTTGGTGTTCCCCTCCTT 59.539 57.895 0.00 0.00 0.00 3.36
2361 2452 4.577875 TGTTATTAGTAACCAACGTGGGG 58.422 43.478 15.05 9.59 43.37 4.96
2370 2461 7.625828 AGAGTGGCATTTGTTATTAGTAACC 57.374 36.000 5.75 0.00 39.55 2.85
2393 2484 7.101700 TGCAGCATGATTGATAGGAGTAATAG 58.898 38.462 0.00 0.00 39.69 1.73
2572 2663 9.811995 ATCGATGTAAGCAAGTAAGTAATGTTA 57.188 29.630 0.00 0.00 0.00 2.41
2580 2671 8.948853 TTTCAAAATCGATGTAAGCAAGTAAG 57.051 30.769 0.00 0.00 0.00 2.34
2629 2720 9.764870 ATGATCTATTTGCGAAATCGATAATTG 57.235 29.630 7.06 6.30 43.02 2.32
2636 2727 4.775664 TGCATGATCTATTTGCGAAATCG 58.224 39.130 0.00 0.00 39.23 3.34
2637 2728 7.633361 AAATGCATGATCTATTTGCGAAATC 57.367 32.000 0.00 0.00 39.23 2.17
2698 2790 7.022496 TCATTTCCCCTTTTTCCCTTTTCTAT 58.978 34.615 0.00 0.00 0.00 1.98
2708 2800 5.008613 GTGGCTTTTTCATTTCCCCTTTTTC 59.991 40.000 0.00 0.00 0.00 2.29
2709 2801 4.887071 GTGGCTTTTTCATTTCCCCTTTTT 59.113 37.500 0.00 0.00 0.00 1.94
2714 2806 1.616374 TCGTGGCTTTTTCATTTCCCC 59.384 47.619 0.00 0.00 0.00 4.81
2800 2892 2.355363 CGACCGGCTTCGAACACA 60.355 61.111 8.71 0.00 41.78 3.72
2822 2914 9.927668 ATTTTCTGTAAACTCCCAACAAATATG 57.072 29.630 0.00 0.00 0.00 1.78
2854 2947 1.729586 TCTAGGCCGGCCAATATCTT 58.270 50.000 45.13 26.36 38.92 2.40
2855 2948 1.958288 ATCTAGGCCGGCCAATATCT 58.042 50.000 45.13 27.13 38.92 1.98
2870 2963 2.223829 GCGCTGAAGGCACTCTTATCTA 60.224 50.000 0.00 0.00 38.49 1.98
2918 3011 0.179000 CCTATTCGGCACCTTCAGCT 59.821 55.000 0.00 0.00 0.00 4.24
2920 3013 2.691409 TTCCTATTCGGCACCTTCAG 57.309 50.000 0.00 0.00 0.00 3.02
2958 3051 3.628646 GACACATTGGGAGCGGGCT 62.629 63.158 0.00 0.00 0.00 5.19
3158 3269 9.360093 ACGAACATTTTTAAAAATTCTCACACA 57.640 25.926 20.92 0.00 36.52 3.72
3159 3270 9.618410 CACGAACATTTTTAAAAATTCTCACAC 57.382 29.630 20.92 9.35 36.52 3.82
3300 3413 1.319541 CTTCCTCGATCCCGCTTCTA 58.680 55.000 0.00 0.00 35.37 2.10
3327 3440 1.133823 TCTTGCTTTTGGAGTGCCAGA 60.134 47.619 0.00 0.00 46.91 3.86
3339 3452 3.960102 TGTCATTTCCTGGTTCTTGCTTT 59.040 39.130 0.00 0.00 0.00 3.51
3373 3486 0.995132 TCCATCCAGGGTGATGCCAT 60.995 55.000 0.00 0.00 40.66 4.40
3383 3496 1.520494 CATCATCGCTTCCATCCAGG 58.480 55.000 0.00 0.00 39.47 4.45
3388 3501 0.182061 ACTGCCATCATCGCTTCCAT 59.818 50.000 0.00 0.00 0.00 3.41
3405 3518 2.890766 CGGTTACACCCAGGGCACT 61.891 63.158 4.91 0.00 33.75 4.40
3441 3554 1.412710 ACATCGTTCATATGGCCGACT 59.587 47.619 16.33 5.79 31.43 4.18
3442 3555 1.792949 GACATCGTTCATATGGCCGAC 59.207 52.381 16.33 5.08 31.43 4.79
3443 3556 1.601914 CGACATCGTTCATATGGCCGA 60.602 52.381 16.33 16.33 30.95 5.54
3444 3557 0.784178 CGACATCGTTCATATGGCCG 59.216 55.000 2.13 5.78 34.11 6.13
3446 3559 1.526887 CACCGACATCGTTCATATGGC 59.473 52.381 2.13 0.00 37.74 4.40
3448 3561 1.526887 GGCACCGACATCGTTCATATG 59.473 52.381 0.00 0.00 37.74 1.78
3449 3562 1.540363 GGGCACCGACATCGTTCATAT 60.540 52.381 0.00 0.00 40.86 1.78
3450 3563 0.179094 GGGCACCGACATCGTTCATA 60.179 55.000 0.00 0.00 40.86 2.15
3452 3565 2.047655 GGGCACCGACATCGTTCA 60.048 61.111 0.00 0.00 40.86 3.18
3524 3637 0.320683 CGACTTCACCTCATGCACCA 60.321 55.000 0.00 0.00 0.00 4.17
3531 3644 2.295349 GACACTAACCGACTTCACCTCA 59.705 50.000 0.00 0.00 0.00 3.86
3543 3656 4.876652 GACCGGTCGACACTAACC 57.123 61.111 20.85 0.00 0.00 2.85
3557 3670 3.670377 GTTGCCTTGCCCACGACC 61.670 66.667 0.00 0.00 0.00 4.79
3558 3671 4.025401 CGTTGCCTTGCCCACGAC 62.025 66.667 0.00 0.00 36.68 4.34
3588 3701 1.401409 CCAATAACTGCTGTGTTGCGG 60.401 52.381 13.35 0.00 44.34 5.69
3589 3702 1.967762 CCAATAACTGCTGTGTTGCG 58.032 50.000 13.35 6.48 35.36 4.85
3590 3703 1.000385 TGCCAATAACTGCTGTGTTGC 60.000 47.619 13.35 10.55 0.00 4.17
3591 3704 3.367992 TTGCCAATAACTGCTGTGTTG 57.632 42.857 12.37 12.37 0.00 3.33
3592 3705 3.861886 GCATTGCCAATAACTGCTGTGTT 60.862 43.478 0.00 0.00 0.00 3.32
3593 3706 2.353011 GCATTGCCAATAACTGCTGTGT 60.353 45.455 0.00 0.00 0.00 3.72
3594 3707 2.264813 GCATTGCCAATAACTGCTGTG 58.735 47.619 0.00 0.00 0.00 3.66
3595 3708 2.660189 GCATTGCCAATAACTGCTGT 57.340 45.000 0.00 0.00 0.00 4.40
3614 3727 1.000283 CCTATGCTTCGCCTCTACAGG 60.000 57.143 0.00 0.00 43.82 4.00
3615 3728 1.683917 ACCTATGCTTCGCCTCTACAG 59.316 52.381 0.00 0.00 0.00 2.74
3616 3729 1.681793 GACCTATGCTTCGCCTCTACA 59.318 52.381 0.00 0.00 0.00 2.74
3617 3730 1.681793 TGACCTATGCTTCGCCTCTAC 59.318 52.381 0.00 0.00 0.00 2.59
3618 3731 1.681793 GTGACCTATGCTTCGCCTCTA 59.318 52.381 0.00 0.00 0.00 2.43
3619 3732 0.461961 GTGACCTATGCTTCGCCTCT 59.538 55.000 0.00 0.00 0.00 3.69
3620 3733 0.175760 TGTGACCTATGCTTCGCCTC 59.824 55.000 0.00 0.00 0.00 4.70
3621 3734 0.613260 TTGTGACCTATGCTTCGCCT 59.387 50.000 0.00 0.00 0.00 5.52
3622 3735 1.331756 CATTGTGACCTATGCTTCGCC 59.668 52.381 0.00 0.00 0.00 5.54
3623 3736 2.030946 GTCATTGTGACCTATGCTTCGC 59.969 50.000 0.00 0.00 41.37 4.70
3624 3737 3.933155 GTCATTGTGACCTATGCTTCG 57.067 47.619 0.00 0.00 41.37 3.79
3634 3747 2.029110 CCCCACATTTGGTCATTGTGAC 60.029 50.000 12.94 1.54 46.23 3.67
3635 3748 2.158400 TCCCCACATTTGGTCATTGTGA 60.158 45.455 12.94 0.00 42.59 3.58
3636 3749 2.029110 GTCCCCACATTTGGTCATTGTG 60.029 50.000 0.00 0.00 42.10 3.33
3637 3750 2.247358 GTCCCCACATTTGGTCATTGT 58.753 47.619 0.00 0.00 42.10 2.71
3638 3751 2.029110 GTGTCCCCACATTTGGTCATTG 60.029 50.000 0.00 0.00 42.10 2.82
3639 3752 2.247358 GTGTCCCCACATTTGGTCATT 58.753 47.619 0.00 0.00 42.10 2.57
3640 3753 1.886222 CGTGTCCCCACATTTGGTCAT 60.886 52.381 0.00 0.00 42.10 3.06
3641 3754 0.536233 CGTGTCCCCACATTTGGTCA 60.536 55.000 0.00 0.00 42.10 4.02
3642 3755 1.241315 CCGTGTCCCCACATTTGGTC 61.241 60.000 0.00 0.00 42.10 4.02
3643 3756 1.228429 CCGTGTCCCCACATTTGGT 60.228 57.895 0.00 0.00 42.10 3.67
3644 3757 2.635443 GCCGTGTCCCCACATTTGG 61.635 63.158 0.00 0.00 41.93 3.28
3645 3758 2.961768 GCCGTGTCCCCACATTTG 59.038 61.111 0.00 0.00 41.93 2.32
3646 3759 2.478335 ATCGCCGTGTCCCCACATTT 62.478 55.000 0.00 0.00 41.93 2.32
3647 3760 2.966732 ATCGCCGTGTCCCCACATT 61.967 57.895 0.00 0.00 41.93 2.71
3648 3761 3.399181 ATCGCCGTGTCCCCACAT 61.399 61.111 0.00 0.00 41.93 3.21
3649 3762 4.386951 CATCGCCGTGTCCCCACA 62.387 66.667 0.00 0.00 41.93 4.17
3654 3767 4.451150 TCCTGCATCGCCGTGTCC 62.451 66.667 0.00 0.00 0.00 4.02
3655 3768 3.188786 GTCCTGCATCGCCGTGTC 61.189 66.667 0.00 0.00 0.00 3.67
3674 3787 2.947938 AATCTTCCATGAGGCGGCCG 62.948 60.000 24.05 24.05 33.74 6.13
3675 3788 0.753111 AAATCTTCCATGAGGCGGCC 60.753 55.000 12.11 12.11 33.74 6.13
3676 3789 1.876156 CTAAATCTTCCATGAGGCGGC 59.124 52.381 0.00 0.00 33.74 6.53
3677 3790 2.498167 CCTAAATCTTCCATGAGGCGG 58.502 52.381 0.00 0.00 33.74 6.13
3678 3791 2.498167 CCCTAAATCTTCCATGAGGCG 58.502 52.381 0.00 0.00 33.74 5.52
3679 3792 2.158549 AGCCCTAAATCTTCCATGAGGC 60.159 50.000 0.00 0.00 38.16 4.70
3680 3793 3.484407 CAGCCCTAAATCTTCCATGAGG 58.516 50.000 0.00 0.00 0.00 3.86
3681 3794 3.484407 CCAGCCCTAAATCTTCCATGAG 58.516 50.000 0.00 0.00 0.00 2.90
3682 3795 2.423373 GCCAGCCCTAAATCTTCCATGA 60.423 50.000 0.00 0.00 0.00 3.07
3683 3796 1.959282 GCCAGCCCTAAATCTTCCATG 59.041 52.381 0.00 0.00 0.00 3.66
3684 3797 1.133356 GGCCAGCCCTAAATCTTCCAT 60.133 52.381 0.00 0.00 0.00 3.41
3685 3798 0.258774 GGCCAGCCCTAAATCTTCCA 59.741 55.000 0.00 0.00 0.00 3.53
3686 3799 0.819666 CGGCCAGCCCTAAATCTTCC 60.820 60.000 2.24 0.00 0.00 3.46
3687 3800 0.107165 ACGGCCAGCCCTAAATCTTC 60.107 55.000 2.24 0.00 0.00 2.87
3688 3801 0.394352 CACGGCCAGCCCTAAATCTT 60.394 55.000 2.24 0.00 0.00 2.40
3689 3802 1.224592 CACGGCCAGCCCTAAATCT 59.775 57.895 2.24 0.00 0.00 2.40
3690 3803 0.679960 AACACGGCCAGCCCTAAATC 60.680 55.000 2.24 0.00 0.00 2.17
3691 3804 0.621609 TAACACGGCCAGCCCTAAAT 59.378 50.000 2.24 0.00 0.00 1.40
3692 3805 0.035820 CTAACACGGCCAGCCCTAAA 60.036 55.000 2.24 0.00 0.00 1.85
3693 3806 1.600107 CTAACACGGCCAGCCCTAA 59.400 57.895 2.24 0.00 0.00 2.69
3694 3807 3.026431 GCTAACACGGCCAGCCCTA 62.026 63.158 2.24 0.00 0.00 3.53
3695 3808 4.410400 GCTAACACGGCCAGCCCT 62.410 66.667 2.24 0.00 0.00 5.19
3696 3809 4.715523 TGCTAACACGGCCAGCCC 62.716 66.667 2.24 0.00 34.31 5.19
3697 3810 3.431725 GTGCTAACACGGCCAGCC 61.432 66.667 2.24 0.00 36.98 4.85
3704 3817 3.043248 TGGGGTAGTGGTGCTAACACG 62.043 57.143 0.00 0.00 43.70 4.49
3705 3818 0.688487 TGGGGTAGTGGTGCTAACAC 59.312 55.000 0.00 0.00 46.66 3.32
3706 3819 1.072648 GTTGGGGTAGTGGTGCTAACA 59.927 52.381 0.00 0.00 39.13 2.41
3707 3820 1.350019 AGTTGGGGTAGTGGTGCTAAC 59.650 52.381 0.00 0.00 36.66 2.34
3708 3821 1.349688 CAGTTGGGGTAGTGGTGCTAA 59.650 52.381 0.00 0.00 0.00 3.09
3709 3822 0.981183 CAGTTGGGGTAGTGGTGCTA 59.019 55.000 0.00 0.00 0.00 3.49
3710 3823 1.761174 CAGTTGGGGTAGTGGTGCT 59.239 57.895 0.00 0.00 0.00 4.40
3711 3824 1.303317 CCAGTTGGGGTAGTGGTGC 60.303 63.158 0.00 0.00 34.50 5.01
3712 3825 0.036306 GTCCAGTTGGGGTAGTGGTG 59.964 60.000 0.00 0.00 39.27 4.17
3713 3826 1.131928 GGTCCAGTTGGGGTAGTGGT 61.132 60.000 0.00 0.00 39.27 4.16
3714 3827 0.840722 AGGTCCAGTTGGGGTAGTGG 60.841 60.000 0.00 0.00 39.54 4.00
3715 3828 0.324943 CAGGTCCAGTTGGGGTAGTG 59.675 60.000 0.00 0.00 37.22 2.74
3716 3829 0.192566 TCAGGTCCAGTTGGGGTAGT 59.807 55.000 0.00 0.00 37.22 2.73
3717 3830 1.279271 CTTCAGGTCCAGTTGGGGTAG 59.721 57.143 0.00 0.00 37.22 3.18
3718 3831 1.358152 CTTCAGGTCCAGTTGGGGTA 58.642 55.000 0.00 0.00 37.22 3.69
3719 3832 2.069165 GCTTCAGGTCCAGTTGGGGT 62.069 60.000 0.00 0.00 37.22 4.95
3720 3833 1.303643 GCTTCAGGTCCAGTTGGGG 60.304 63.158 0.00 0.00 37.22 4.96
3721 3834 1.303643 GGCTTCAGGTCCAGTTGGG 60.304 63.158 0.00 0.00 35.41 4.12
3722 3835 1.303643 GGGCTTCAGGTCCAGTTGG 60.304 63.158 0.00 0.00 40.02 3.77
3723 3836 1.455849 TGGGCTTCAGGTCCAGTTG 59.544 57.895 0.00 0.00 45.98 3.16
3724 3837 4.002006 TGGGCTTCAGGTCCAGTT 57.998 55.556 0.00 0.00 45.98 3.16
3728 3841 0.620556 TTCTCATGGGCTTCAGGTCC 59.379 55.000 0.00 0.00 40.85 4.46
3729 3842 2.035530 CTTCTCATGGGCTTCAGGTC 57.964 55.000 0.00 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.