Multiple sequence alignment - TraesCS4B01G075700

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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 TraesCS4B01G075700 chr4B 100.000 2502 0 0 1 2502 71601917 71599416 0.000000e+00 4621
1 TraesCS4B01G075700 chr4B 97.059 170 5 0 1128 1297 389466777 389466946 1.130000e-73 287
2 TraesCS4B01G075700 chr4D 90.517 928 71 7 208 1130 48720375 48719460 0.000000e+00 1210
3 TraesCS4B01G075700 chr4D 90.946 740 38 15 1790 2502 48718531 48717794 0.000000e+00 968
4 TraesCS4B01G075700 chr4D 89.044 502 34 15 1293 1778 48719462 48718966 9.900000e-169 603
5 TraesCS4B01G075700 chr4D 98.246 171 2 1 1125 1295 75782049 75782218 5.230000e-77 298
6 TraesCS4B01G075700 chr4D 95.109 184 5 3 1109 1292 230473278 230473457 1.130000e-73 287
7 TraesCS4B01G075700 chr4A 85.929 732 57 23 1791 2502 548518477 548519182 0.000000e+00 739
8 TraesCS4B01G075700 chr4A 91.480 446 31 5 689 1130 548515021 548515463 7.650000e-170 606
9 TraesCS4B01G075700 chr4A 90.112 445 32 3 209 652 548514586 548515019 3.610000e-158 568
10 TraesCS4B01G075700 chr4A 89.826 344 27 3 1293 1628 548515461 548515804 3.820000e-118 435
11 TraesCS4B01G075700 chr4A 90.230 174 17 0 50 223 548514398 548514571 6.960000e-56 228
12 TraesCS4B01G075700 chr1D 97.159 176 4 1 1124 1299 206955532 206955706 1.880000e-76 296
13 TraesCS4B01G075700 chr7D 96.154 182 3 4 1117 1294 39001268 39001449 6.770000e-76 294
14 TraesCS4B01G075700 chr5D 95.628 183 7 1 1112 1294 25040161 25039980 2.430000e-75 292
15 TraesCS4B01G075700 chr7A 95.604 182 4 4 1120 1298 320981160 320981340 3.150000e-74 289
16 TraesCS4B01G075700 chr6D 94.681 188 7 3 1111 1298 142867022 142867206 3.150000e-74 289
17 TraesCS4B01G075700 chr2D 94.709 189 4 6 1111 1295 309971398 309971584 3.150000e-74 289


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 TraesCS4B01G075700 chr4B 71599416 71601917 2501 True 4621.0 4621 100.0000 1 2502 1 chr4B.!!$R1 2501
1 TraesCS4B01G075700 chr4D 48717794 48720375 2581 True 927.0 1210 90.1690 208 2502 3 chr4D.!!$R1 2294
2 TraesCS4B01G075700 chr4A 548514398 548519182 4784 False 515.2 739 89.5154 50 2502 5 chr4A.!!$F1 2452

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
185 186 0.541392 TAGTAGCACCACTGCCCATG 59.459 55.0 0.0 0.0 45.53 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1628 1671 0.239879 AACACGCAAATACCCGCTTG 59.76 50.0 0.0 0.0 33.9 4.01 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
26 27 8.761575 AGCACATTATTGTAATTCAACAAAGG 57.238 30.769 0.00 0.19 42.33 3.11
27 28 8.584157 AGCACATTATTGTAATTCAACAAAGGA 58.416 29.630 0.00 0.00 42.33 3.36
28 29 9.369904 GCACATTATTGTAATTCAACAAAGGAT 57.630 29.630 0.00 0.00 42.33 3.24
40 41 6.024552 TCAACAAAGGATGAATTACCTTGC 57.975 37.500 10.46 0.00 44.44 4.01
41 42 5.774690 TCAACAAAGGATGAATTACCTTGCT 59.225 36.000 10.46 0.00 44.44 3.91
42 43 6.267471 TCAACAAAGGATGAATTACCTTGCTT 59.733 34.615 10.46 4.53 44.44 3.91
43 44 6.670695 ACAAAGGATGAATTACCTTGCTTT 57.329 33.333 10.46 3.75 44.44 3.51
44 45 6.691508 ACAAAGGATGAATTACCTTGCTTTC 58.308 36.000 10.46 0.00 44.44 2.62
45 46 6.267471 ACAAAGGATGAATTACCTTGCTTTCA 59.733 34.615 10.46 0.00 44.44 2.69
46 47 6.916360 AAGGATGAATTACCTTGCTTTCAA 57.084 33.333 9.34 0.00 43.69 2.69
47 48 6.916360 AGGATGAATTACCTTGCTTTCAAA 57.084 33.333 0.00 0.00 32.35 2.69
48 49 7.301868 AGGATGAATTACCTTGCTTTCAAAA 57.698 32.000 0.00 0.00 32.35 2.44
89 90 5.357742 TTTTGCAGTATCTCCTAGATGCA 57.642 39.130 7.58 4.16 39.41 3.96
91 92 5.557576 TTGCAGTATCTCCTAGATGCATT 57.442 39.130 0.00 0.00 39.41 3.56
92 93 4.891260 TGCAGTATCTCCTAGATGCATTG 58.109 43.478 0.00 0.00 39.41 2.82
98 99 3.865446 TCTCCTAGATGCATTGTGTGTG 58.135 45.455 0.00 0.00 0.00 3.82
101 102 5.363580 TCTCCTAGATGCATTGTGTGTGATA 59.636 40.000 0.00 0.00 0.00 2.15
113 114 5.164620 TGTGTGTGATATGACTCCATGTT 57.835 39.130 0.00 0.00 34.31 2.71
120 121 7.223582 GTGTGATATGACTCCATGTTGTTAGAG 59.776 40.741 0.00 0.00 34.31 2.43
185 186 0.541392 TAGTAGCACCACTGCCCATG 59.459 55.000 0.00 0.00 45.53 3.66
195 196 0.892755 ACTGCCCATGACAAAGCATG 59.107 50.000 0.00 0.00 44.05 4.06
202 203 4.458397 CCCATGACAAAGCATGATCTAGT 58.542 43.478 0.00 0.00 46.64 2.57
229 259 2.938956 AGGTGTTCTGTTAGCAGCTT 57.061 45.000 0.00 0.00 43.65 3.74
233 263 4.036852 AGGTGTTCTGTTAGCAGCTTTTTC 59.963 41.667 0.00 0.00 43.65 2.29
276 306 5.662211 AAGCATCAAAACAGTTTCATTGC 57.338 34.783 14.64 14.64 0.00 3.56
302 332 7.167968 CACAAGGTTTTTGTGTTCATCATGTAG 59.832 37.037 10.93 0.00 43.40 2.74
303 333 5.772521 AGGTTTTTGTGTTCATCATGTAGC 58.227 37.500 0.00 0.00 0.00 3.58
304 334 5.536161 AGGTTTTTGTGTTCATCATGTAGCT 59.464 36.000 0.00 0.00 0.00 3.32
305 335 5.858581 GGTTTTTGTGTTCATCATGTAGCTC 59.141 40.000 0.00 0.00 0.00 4.09
306 336 6.437928 GTTTTTGTGTTCATCATGTAGCTCA 58.562 36.000 0.00 0.00 0.00 4.26
307 337 6.822667 TTTTGTGTTCATCATGTAGCTCAT 57.177 33.333 0.00 0.00 37.22 2.90
308 338 7.920160 TTTTGTGTTCATCATGTAGCTCATA 57.080 32.000 0.00 0.00 34.67 2.15
309 339 8.510243 TTTTGTGTTCATCATGTAGCTCATAT 57.490 30.769 0.00 0.00 34.67 1.78
310 340 7.486802 TTGTGTTCATCATGTAGCTCATATG 57.513 36.000 0.00 0.00 34.67 1.78
327 357 5.181009 TCATATGAGAAGTTTGCAGGACTG 58.819 41.667 0.00 0.00 0.00 3.51
328 358 3.777106 ATGAGAAGTTTGCAGGACTGA 57.223 42.857 3.00 0.00 0.00 3.41
346 377 0.687354 GACAGTGGTGGTGGAGATGT 59.313 55.000 0.00 0.00 0.00 3.06
356 387 4.009675 GTGGTGGAGATGTTTTATCTGCA 58.990 43.478 6.97 6.97 42.79 4.41
386 417 6.094742 TGTTGACTTCATGACTTTGTTGCTTA 59.905 34.615 0.00 0.00 0.00 3.09
452 483 4.842531 ATGATATGTGACACCCTGAACA 57.157 40.909 2.45 0.00 0.00 3.18
487 518 4.216257 GTGCTTAGGAATTCAGTGAGCAAA 59.784 41.667 21.00 4.67 39.96 3.68
497 528 7.653311 GGAATTCAGTGAGCAAATTTTACTTGT 59.347 33.333 7.93 0.00 0.00 3.16
529 560 2.660189 ATGTAATGCTTGCTGGTTGC 57.340 45.000 0.00 0.00 43.25 4.17
537 568 1.067354 GCTTGCTGGTTGCTTGCTTAT 60.067 47.619 0.00 0.00 43.37 1.73
555 586 5.106038 TGCTTATTGAATTCAGGCTGAGTTG 60.106 40.000 27.17 13.92 0.00 3.16
562 593 2.009681 TCAGGCTGAGTTGTCCAGTA 57.990 50.000 14.43 0.00 34.29 2.74
566 597 2.706190 AGGCTGAGTTGTCCAGTAGTTT 59.294 45.455 0.00 0.00 34.29 2.66
572 603 7.298854 GCTGAGTTGTCCAGTAGTTTTATTTC 58.701 38.462 0.00 0.00 34.29 2.17
592 623 9.944376 TTATTTCCAATATGAGATGTACCTAGC 57.056 33.333 0.00 0.00 0.00 3.42
596 627 8.664669 TCCAATATGAGATGTACCTAGCATTA 57.335 34.615 0.00 0.00 0.00 1.90
597 628 9.271921 TCCAATATGAGATGTACCTAGCATTAT 57.728 33.333 0.00 0.00 0.00 1.28
608 639 8.029782 TGTACCTAGCATTATGTCCATTAGTT 57.970 34.615 0.00 0.00 0.00 2.24
609 640 9.150028 TGTACCTAGCATTATGTCCATTAGTTA 57.850 33.333 0.00 0.00 0.00 2.24
624 655 7.965107 GTCCATTAGTTATCAAAAGTTCAGCAG 59.035 37.037 0.00 0.00 0.00 4.24
632 663 9.495754 GTTATCAAAAGTTCAGCAGAATATGAC 57.504 33.333 0.00 0.00 35.92 3.06
657 688 7.436080 ACAATGCAGAAATATTTCGCCTAAATG 59.564 33.333 26.95 21.76 41.92 2.32
766 797 2.031508 TGTAGTTTGTTGCTTTAGCGGC 60.032 45.455 0.00 0.00 45.83 6.53
785 816 1.230635 CGGAGTGGTTGCTCAGGTTG 61.231 60.000 0.00 0.00 37.24 3.77
793 824 4.218417 GTGGTTGCTCAGGTTGATTACATT 59.782 41.667 0.00 0.00 0.00 2.71
809 840 3.439857 ACATTACCATGTTGCACCTCT 57.560 42.857 0.00 0.00 41.16 3.69
810 841 3.766545 ACATTACCATGTTGCACCTCTT 58.233 40.909 0.00 0.00 41.16 2.85
830 861 5.488341 TCTTAGTACATCAGGACTTTTGGC 58.512 41.667 0.00 0.00 0.00 4.52
836 867 5.841957 ACATCAGGACTTTTGGCATTATC 57.158 39.130 0.00 0.00 0.00 1.75
840 871 5.263599 TCAGGACTTTTGGCATTATCATGT 58.736 37.500 0.00 0.00 32.28 3.21
933 968 3.181510 GGATACTCACCGTGTTTGCATTC 60.182 47.826 0.00 0.00 0.00 2.67
938 973 3.669536 TCACCGTGTTTGCATTCATCTA 58.330 40.909 0.00 0.00 0.00 1.98
975 1010 7.983484 GCCCATTTTTGTATCTCAAATCAAGAT 59.017 33.333 0.00 0.00 44.15 2.40
990 1025 9.561069 TCAAATCAAGATTAGGTTCCTATAAGC 57.439 33.333 0.00 0.00 0.00 3.09
1011 1046 3.766051 GCTCTGAAGAAATGGAAATGGGT 59.234 43.478 0.00 0.00 0.00 4.51
1026 1061 4.309950 GGTGACAAGGCGGTCGGT 62.310 66.667 7.64 0.00 40.72 4.69
1136 1171 8.709308 ACATGCTTCATATCTAATATACTCCCC 58.291 37.037 0.00 0.00 0.00 4.81
1137 1172 7.676683 TGCTTCATATCTAATATACTCCCCC 57.323 40.000 0.00 0.00 0.00 5.40
1156 1191 4.788679 CCCCCGTTCCTAAATATTTGTCT 58.211 43.478 11.05 0.00 0.00 3.41
1157 1192 5.198207 CCCCCGTTCCTAAATATTTGTCTT 58.802 41.667 11.05 0.00 0.00 3.01
1158 1193 5.655090 CCCCCGTTCCTAAATATTTGTCTTT 59.345 40.000 11.05 0.00 0.00 2.52
1159 1194 6.153851 CCCCCGTTCCTAAATATTTGTCTTTT 59.846 38.462 11.05 0.00 0.00 2.27
1160 1195 7.310175 CCCCCGTTCCTAAATATTTGTCTTTTT 60.310 37.037 11.05 0.00 0.00 1.94
1161 1196 8.741841 CCCCGTTCCTAAATATTTGTCTTTTTA 58.258 33.333 11.05 0.00 0.00 1.52
1162 1197 9.783256 CCCGTTCCTAAATATTTGTCTTTTTAG 57.217 33.333 11.05 0.00 33.47 1.85
1177 1212 9.965824 TTGTCTTTTTAGAGATTTCAAATGGAC 57.034 29.630 0.00 0.00 0.00 4.02
1178 1213 9.354673 TGTCTTTTTAGAGATTTCAAATGGACT 57.645 29.630 0.00 0.00 0.00 3.85
1194 1229 3.900971 TGGACTACCACATACGGATGTA 58.099 45.455 14.23 0.00 44.82 2.29
1195 1230 4.476297 TGGACTACCACATACGGATGTAT 58.524 43.478 14.23 7.46 44.82 2.29
1196 1231 5.633117 TGGACTACCACATACGGATGTATA 58.367 41.667 14.23 8.27 44.82 1.47
1197 1232 6.250711 TGGACTACCACATACGGATGTATAT 58.749 40.000 14.23 4.37 44.82 0.86
1198 1233 7.404481 TGGACTACCACATACGGATGTATATA 58.596 38.462 14.23 5.36 44.82 0.86
1199 1234 7.555195 TGGACTACCACATACGGATGTATATAG 59.445 40.741 14.23 16.35 44.82 1.31
1200 1235 7.772292 GGACTACCACATACGGATGTATATAGA 59.228 40.741 22.62 5.04 44.82 1.98
1201 1236 8.503458 ACTACCACATACGGATGTATATAGAC 57.497 38.462 22.62 0.00 44.82 2.59
1202 1237 8.105197 ACTACCACATACGGATGTATATAGACA 58.895 37.037 22.62 2.07 44.82 3.41
1203 1238 7.956328 ACCACATACGGATGTATATAGACAT 57.044 36.000 14.23 12.70 44.82 3.06
1205 1240 9.642343 ACCACATACGGATGTATATAGACATAT 57.358 33.333 14.23 5.08 44.82 1.78
1234 1269 6.734104 AGTGTAGATTCACTCATTTTGCTC 57.266 37.500 0.00 0.00 44.07 4.26
1235 1270 5.645497 AGTGTAGATTCACTCATTTTGCTCC 59.355 40.000 0.00 0.00 44.07 4.70
1236 1271 4.631377 TGTAGATTCACTCATTTTGCTCCG 59.369 41.667 0.00 0.00 0.00 4.63
1237 1272 3.679389 AGATTCACTCATTTTGCTCCGT 58.321 40.909 0.00 0.00 0.00 4.69
1238 1273 4.832248 AGATTCACTCATTTTGCTCCGTA 58.168 39.130 0.00 0.00 0.00 4.02
1239 1274 5.431765 AGATTCACTCATTTTGCTCCGTAT 58.568 37.500 0.00 0.00 0.00 3.06
1240 1275 4.944962 TTCACTCATTTTGCTCCGTATG 57.055 40.909 0.00 0.00 0.00 2.39
1241 1276 3.937814 TCACTCATTTTGCTCCGTATGT 58.062 40.909 0.00 0.00 0.00 2.29
1242 1277 5.079689 TCACTCATTTTGCTCCGTATGTA 57.920 39.130 0.00 0.00 0.00 2.29
1243 1278 5.109210 TCACTCATTTTGCTCCGTATGTAG 58.891 41.667 0.00 0.00 0.00 2.74
1244 1279 4.870426 CACTCATTTTGCTCCGTATGTAGT 59.130 41.667 0.00 0.00 0.00 2.73
1245 1280 5.005779 CACTCATTTTGCTCCGTATGTAGTC 59.994 44.000 0.00 0.00 0.00 2.59
1246 1281 5.079689 TCATTTTGCTCCGTATGTAGTCA 57.920 39.130 0.00 0.00 0.00 3.41
1247 1282 5.670485 TCATTTTGCTCCGTATGTAGTCAT 58.330 37.500 0.00 0.00 38.00 3.06
1248 1283 6.112734 TCATTTTGCTCCGTATGTAGTCATT 58.887 36.000 0.00 0.00 35.70 2.57
1249 1284 6.597672 TCATTTTGCTCCGTATGTAGTCATTT 59.402 34.615 0.00 0.00 35.70 2.32
1250 1285 5.794687 TTTGCTCCGTATGTAGTCATTTG 57.205 39.130 0.00 0.00 35.70 2.32
1251 1286 4.465632 TGCTCCGTATGTAGTCATTTGT 57.534 40.909 0.00 0.00 35.70 2.83
1252 1287 4.827692 TGCTCCGTATGTAGTCATTTGTT 58.172 39.130 0.00 0.00 35.70 2.83
1253 1288 4.629634 TGCTCCGTATGTAGTCATTTGTTG 59.370 41.667 0.00 0.00 35.70 3.33
1254 1289 4.868171 GCTCCGTATGTAGTCATTTGTTGA 59.132 41.667 0.00 0.00 35.70 3.18
1255 1290 5.350365 GCTCCGTATGTAGTCATTTGTTGAA 59.650 40.000 0.00 0.00 35.70 2.69
1256 1291 6.128391 GCTCCGTATGTAGTCATTTGTTGAAA 60.128 38.462 0.00 0.00 35.70 2.69
1257 1292 7.414098 GCTCCGTATGTAGTCATTTGTTGAAAT 60.414 37.037 0.00 0.00 35.70 2.17
1258 1293 7.970384 TCCGTATGTAGTCATTTGTTGAAATC 58.030 34.615 0.00 0.00 35.70 2.17
1259 1294 7.822334 TCCGTATGTAGTCATTTGTTGAAATCT 59.178 33.333 0.00 0.00 35.70 2.40
1260 1295 8.116753 CCGTATGTAGTCATTTGTTGAAATCTC 58.883 37.037 0.00 0.00 35.70 2.75
1261 1296 8.873830 CGTATGTAGTCATTTGTTGAAATCTCT 58.126 33.333 0.00 0.00 35.70 3.10
1265 1300 9.996554 TGTAGTCATTTGTTGAAATCTCTAGAA 57.003 29.630 0.00 0.00 35.70 2.10
1268 1303 9.784531 AGTCATTTGTTGAAATCTCTAGAAAGA 57.215 29.630 0.00 0.00 35.70 2.52
1269 1304 9.818796 GTCATTTGTTGAAATCTCTAGAAAGAC 57.181 33.333 0.00 0.00 35.70 3.01
1270 1305 9.559732 TCATTTGTTGAAATCTCTAGAAAGACA 57.440 29.630 0.00 0.00 28.65 3.41
1285 1320 9.595823 TCTAGAAAGACAAATATTTAGGAACGG 57.404 33.333 0.00 0.00 0.00 4.44
1286 1321 9.595823 CTAGAAAGACAAATATTTAGGAACGGA 57.404 33.333 0.00 0.00 0.00 4.69
1287 1322 8.494016 AGAAAGACAAATATTTAGGAACGGAG 57.506 34.615 0.00 0.00 0.00 4.63
1288 1323 7.553044 AGAAAGACAAATATTTAGGAACGGAGG 59.447 37.037 0.00 0.00 0.00 4.30
1289 1324 5.681639 AGACAAATATTTAGGAACGGAGGG 58.318 41.667 0.00 0.00 0.00 4.30
1290 1325 5.427481 AGACAAATATTTAGGAACGGAGGGA 59.573 40.000 0.00 0.00 0.00 4.20
1291 1326 5.681639 ACAAATATTTAGGAACGGAGGGAG 58.318 41.667 0.00 0.00 0.00 4.30
1304 1339 2.496070 CGGAGGGAGTATGTTTCTGTGA 59.504 50.000 0.00 0.00 0.00 3.58
1306 1341 4.383118 CGGAGGGAGTATGTTTCTGTGATT 60.383 45.833 0.00 0.00 0.00 2.57
1313 1348 9.561069 GGGAGTATGTTTCTGTGATTATGTATT 57.439 33.333 0.00 0.00 0.00 1.89
1363 1398 3.879295 CCTAGCCATTTGTTGACGATGAT 59.121 43.478 0.00 0.00 0.00 2.45
1429 1464 1.228003 CCCTGTGTTTGCCGGTGTA 60.228 57.895 1.90 0.00 0.00 2.90
1435 1470 0.464735 TGTTTGCCGGTGTAGTGCTT 60.465 50.000 1.90 0.00 0.00 3.91
1472 1507 7.290110 AGTATATTCATCGGTCTTGTGATGA 57.710 36.000 1.02 1.02 46.79 2.92
1495 1530 3.564225 TGAAGTCGAAGAAAAAGAAGGCC 59.436 43.478 0.00 0.00 39.69 5.19
1503 1538 2.893489 AGAAAAAGAAGGCCGCTTGATT 59.107 40.909 13.61 11.78 0.00 2.57
1513 1548 2.948093 CGCTTGATTGATTTGGCGG 58.052 52.632 0.00 0.00 39.12 6.13
1575 1613 3.508793 CCTAGTAGACAGGTTTCGTGGAA 59.491 47.826 0.00 0.00 0.00 3.53
1593 1631 5.967674 CGTGGAAGATTGTATTTCATTGAGC 59.032 40.000 0.00 0.00 0.00 4.26
1621 1664 3.190874 GTGATCTAAGGCTTTCTCGTGG 58.809 50.000 4.45 0.00 0.00 4.94
1628 1671 0.796927 GGCTTTCTCGTGGCACTTAC 59.203 55.000 16.72 0.00 0.00 2.34
1629 1672 1.508632 GCTTTCTCGTGGCACTTACA 58.491 50.000 16.72 0.00 0.00 2.41
1630 1673 1.871039 GCTTTCTCGTGGCACTTACAA 59.129 47.619 16.72 2.78 0.00 2.41
1631 1674 2.096218 GCTTTCTCGTGGCACTTACAAG 60.096 50.000 16.72 12.91 0.00 3.16
1632 1675 1.508632 TTCTCGTGGCACTTACAAGC 58.491 50.000 16.72 0.00 0.00 4.01
1636 1694 1.599797 GTGGCACTTACAAGCGGGT 60.600 57.895 11.13 0.00 0.00 5.28
1652 1713 1.805345 CGGGTATTTGCGTGTTGGTAA 59.195 47.619 0.00 0.00 0.00 2.85
1657 1718 6.566141 GGGTATTTGCGTGTTGGTAATTATT 58.434 36.000 0.00 0.00 0.00 1.40
1720 1799 8.736244 TGTTACATCGATAATTCTCGGATGATA 58.264 33.333 21.09 12.66 39.13 2.15
1725 1804 9.736023 CATCGATAATTCTCGGATGATATGTTA 57.264 33.333 12.61 0.00 39.13 2.41
1778 1857 3.808728 TGCTTCTGCTTCTGTGTAGTTT 58.191 40.909 0.00 0.00 40.48 2.66
1779 1858 3.561310 TGCTTCTGCTTCTGTGTAGTTTG 59.439 43.478 0.00 0.00 40.48 2.93
1780 1859 3.809832 GCTTCTGCTTCTGTGTAGTTTGA 59.190 43.478 0.00 0.00 36.03 2.69
1781 1860 4.319118 GCTTCTGCTTCTGTGTAGTTTGAC 60.319 45.833 0.00 0.00 36.03 3.18
1782 1861 4.400529 TCTGCTTCTGTGTAGTTTGACA 57.599 40.909 0.00 0.00 0.00 3.58
1784 1863 6.096673 TCTGCTTCTGTGTAGTTTGACATA 57.903 37.500 0.00 0.00 0.00 2.29
1785 1864 6.521162 TCTGCTTCTGTGTAGTTTGACATAA 58.479 36.000 0.00 0.00 0.00 1.90
1786 1865 7.161404 TCTGCTTCTGTGTAGTTTGACATAAT 58.839 34.615 0.00 0.00 0.00 1.28
1787 1866 7.118245 TCTGCTTCTGTGTAGTTTGACATAATG 59.882 37.037 0.00 0.00 0.00 1.90
1788 1867 6.024049 GCTTCTGTGTAGTTTGACATAATGC 58.976 40.000 0.00 0.00 0.00 3.56
1809 4475 7.992754 ATGCTTCTGACTCTAAACATTTTCT 57.007 32.000 0.00 0.00 0.00 2.52
1839 4505 5.801350 TTCGCTGAAATGAAGTAGATTGG 57.199 39.130 0.00 0.00 0.00 3.16
1847 4513 6.319658 TGAAATGAAGTAGATTGGCATTCCTC 59.680 38.462 5.80 0.60 0.00 3.71
1866 4532 6.796705 TCCTCGAGAAAACAAAATTAGACC 57.203 37.500 15.71 0.00 0.00 3.85
1937 4603 2.030363 ACAATGGGTGCACACAAATACG 60.030 45.455 28.30 14.73 30.29 3.06
1942 4608 2.034812 GGGTGCACACAAATACGGAAAA 59.965 45.455 20.43 0.00 0.00 2.29
1943 4609 3.305744 GGGTGCACACAAATACGGAAAAT 60.306 43.478 20.43 0.00 0.00 1.82
1944 4610 3.672867 GGTGCACACAAATACGGAAAATG 59.327 43.478 20.43 0.00 0.00 2.32
1946 4612 4.979197 GTGCACACAAATACGGAAAATGAA 59.021 37.500 13.17 0.00 0.00 2.57
1972 4648 5.555966 AGAAGAGCTACTGGGAAAGAAAAG 58.444 41.667 0.00 0.00 0.00 2.27
1974 4650 5.568620 AGAGCTACTGGGAAAGAAAAGAA 57.431 39.130 0.00 0.00 0.00 2.52
2001 4681 7.309920 ACGTTCTCAAATAAAAATTATGGCGT 58.690 30.769 0.00 0.00 0.00 5.68
2009 4689 9.347934 CAAATAAAAATTATGGCGTCACTAACA 57.652 29.630 0.00 0.00 0.00 2.41
2011 4691 9.567848 AATAAAAATTATGGCGTCACTAACAAG 57.432 29.630 0.00 0.00 0.00 3.16
2023 4703 5.576774 CGTCACTAACAAGAAGTCATATGCA 59.423 40.000 0.00 0.00 0.00 3.96
2032 4712 5.435686 AGAAGTCATATGCAAGGGTACAA 57.564 39.130 0.00 0.00 0.00 2.41
2047 4727 8.682710 GCAAGGGTACAAATTGTTATATCTTCA 58.317 33.333 3.17 0.00 0.00 3.02
2114 4805 4.537135 ATGTCACTACCAGTACAACCAG 57.463 45.455 0.00 0.00 0.00 4.00
2249 4940 1.131504 CGCCTGCGCAAATAAAAGGTA 59.868 47.619 13.05 0.00 34.03 3.08
2275 4966 2.615912 GCTCTTCCATTACATCCACTGC 59.384 50.000 0.00 0.00 0.00 4.40
2418 5113 7.839200 CCACTTTTATATATATGGGGAAAGGGG 59.161 40.741 15.80 15.80 39.12 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 9.853555 CCTTTGTTGAATTACAATAATGTGCTA 57.146 29.630 0.00 0.00 40.84 3.49
1 2 8.584157 TCCTTTGTTGAATTACAATAATGTGCT 58.416 29.630 0.00 0.00 40.84 4.40
2 3 8.755696 TCCTTTGTTGAATTACAATAATGTGC 57.244 30.769 0.00 0.00 40.84 4.57
14 15 7.603784 GCAAGGTAATTCATCCTTTGTTGAATT 59.396 33.333 13.50 13.50 45.79 2.17
15 16 7.038799 AGCAAGGTAATTCATCCTTTGTTGAAT 60.039 33.333 6.72 0.00 41.44 2.57
16 17 6.267471 AGCAAGGTAATTCATCCTTTGTTGAA 59.733 34.615 6.72 0.00 41.44 2.69
17 18 5.774690 AGCAAGGTAATTCATCCTTTGTTGA 59.225 36.000 6.72 0.00 41.44 3.18
18 19 6.029346 AGCAAGGTAATTCATCCTTTGTTG 57.971 37.500 6.72 0.44 41.44 3.33
19 20 6.670695 AAGCAAGGTAATTCATCCTTTGTT 57.329 33.333 6.72 2.64 41.44 2.83
20 21 6.267471 TGAAAGCAAGGTAATTCATCCTTTGT 59.733 34.615 6.72 0.00 41.44 2.83
21 22 6.690530 TGAAAGCAAGGTAATTCATCCTTTG 58.309 36.000 6.72 5.20 41.44 2.77
22 23 6.916360 TGAAAGCAAGGTAATTCATCCTTT 57.084 33.333 6.72 0.00 41.44 3.11
23 24 6.916360 TTGAAAGCAAGGTAATTCATCCTT 57.084 33.333 4.36 4.36 43.79 3.36
24 25 6.916360 TTTGAAAGCAAGGTAATTCATCCT 57.084 33.333 0.00 0.00 35.04 3.24
25 26 7.961325 TTTTTGAAAGCAAGGTAATTCATCC 57.039 32.000 0.00 0.00 35.04 3.51
61 62 6.579042 ATCTAGGAGATACTGCAAAAGGCAAA 60.579 38.462 0.00 0.00 42.24 3.68
64 65 4.408182 TCTAGGAGATACTGCAAAAGGC 57.592 45.455 0.00 0.00 45.13 4.35
89 90 5.748402 ACATGGAGTCATATCACACACAAT 58.252 37.500 0.00 0.00 31.33 2.71
91 92 4.824479 ACATGGAGTCATATCACACACA 57.176 40.909 0.00 0.00 31.33 3.72
92 93 4.937620 ACAACATGGAGTCATATCACACAC 59.062 41.667 0.00 0.00 31.33 3.82
98 99 9.553064 AATTCTCTAACAACATGGAGTCATATC 57.447 33.333 0.00 0.00 31.33 1.63
101 102 7.628234 AGAATTCTCTAACAACATGGAGTCAT 58.372 34.615 0.88 0.00 0.00 3.06
149 150 9.211485 GGTGCTACTACAACAACTAAGATTTTA 57.789 33.333 0.00 0.00 0.00 1.52
185 186 6.915544 TCATCAACTAGATCATGCTTTGTC 57.084 37.500 0.00 0.00 33.72 3.18
195 196 6.876257 ACAGAACACCTTTCATCAACTAGATC 59.124 38.462 0.00 0.00 33.72 2.75
202 203 5.129634 TGCTAACAGAACACCTTTCATCAA 58.870 37.500 0.00 0.00 0.00 2.57
265 295 5.122082 ACAAAAACCTTGTGCAATGAAACTG 59.878 36.000 0.00 0.00 0.00 3.16
294 324 7.172875 GCAAACTTCTCATATGAGCTACATGAT 59.827 37.037 25.27 5.22 41.80 2.45
302 332 4.034975 GTCCTGCAAACTTCTCATATGAGC 59.965 45.833 25.27 14.48 41.80 4.26
303 333 5.293814 CAGTCCTGCAAACTTCTCATATGAG 59.706 44.000 24.32 24.32 43.36 2.90
304 334 5.046376 TCAGTCCTGCAAACTTCTCATATGA 60.046 40.000 5.07 5.07 0.00 2.15
305 335 5.064452 GTCAGTCCTGCAAACTTCTCATATG 59.936 44.000 0.00 0.00 0.00 1.78
306 336 5.181748 GTCAGTCCTGCAAACTTCTCATAT 58.818 41.667 0.00 0.00 0.00 1.78
307 337 4.040339 TGTCAGTCCTGCAAACTTCTCATA 59.960 41.667 0.00 0.00 0.00 2.15
308 338 3.181451 TGTCAGTCCTGCAAACTTCTCAT 60.181 43.478 0.00 0.00 0.00 2.90
309 339 2.170397 TGTCAGTCCTGCAAACTTCTCA 59.830 45.455 0.00 0.00 0.00 3.27
310 340 2.805099 CTGTCAGTCCTGCAAACTTCTC 59.195 50.000 0.00 0.00 0.00 2.87
327 357 0.687354 ACATCTCCACCACCACTGTC 59.313 55.000 0.00 0.00 0.00 3.51
328 358 1.140312 AACATCTCCACCACCACTGT 58.860 50.000 0.00 0.00 0.00 3.55
346 377 8.389779 TGAAGTCAACAAGTATGCAGATAAAA 57.610 30.769 0.00 0.00 0.00 1.52
356 387 7.807977 ACAAAGTCATGAAGTCAACAAGTAT 57.192 32.000 0.00 0.00 0.00 2.12
386 417 6.435164 AGCTATTATTTTCAGGGTGGTGAAT 58.565 36.000 0.00 0.00 36.34 2.57
429 460 5.065218 GTGTTCAGGGTGTCACATATCATTC 59.935 44.000 5.12 0.00 0.00 2.67
435 466 5.755409 AATAGTGTTCAGGGTGTCACATA 57.245 39.130 5.12 0.00 33.84 2.29
452 483 4.650972 TCCTAAGCACCAACCAAATAGT 57.349 40.909 0.00 0.00 0.00 2.12
487 518 8.891720 ACATTTCAATGTTGCAACAAGTAAAAT 58.108 25.926 34.06 28.11 46.95 1.82
529 560 5.125097 ACTCAGCCTGAATTCAATAAGCAAG 59.875 40.000 9.88 12.60 0.00 4.01
537 568 3.149196 GGACAACTCAGCCTGAATTCAA 58.851 45.455 9.88 0.00 0.00 2.69
566 597 9.944376 GCTAGGTACATCTCATATTGGAAATAA 57.056 33.333 0.00 0.00 0.00 1.40
572 603 9.322773 CATAATGCTAGGTACATCTCATATTGG 57.677 37.037 0.00 0.00 0.00 3.16
596 627 8.462016 GCTGAACTTTTGATAACTAATGGACAT 58.538 33.333 0.00 0.00 0.00 3.06
597 628 7.446931 TGCTGAACTTTTGATAACTAATGGACA 59.553 33.333 0.00 0.00 0.00 4.02
608 639 8.791327 TGTCATATTCTGCTGAACTTTTGATA 57.209 30.769 8.32 5.40 34.71 2.15
609 640 7.692460 TGTCATATTCTGCTGAACTTTTGAT 57.308 32.000 8.32 0.00 34.71 2.57
624 655 8.633408 GCGAAATATTTCTGCATTGTCATATTC 58.367 33.333 26.02 2.40 36.99 1.75
632 663 7.436080 ACATTTAGGCGAAATATTTCTGCATTG 59.564 33.333 28.99 23.17 35.45 2.82
664 695 6.992664 TGCCCAATGCCATATTATACTTTT 57.007 33.333 0.00 0.00 40.16 2.27
685 716 0.451383 TAACTGCGATTGTGCCATGC 59.549 50.000 0.00 0.00 0.00 4.06
737 768 7.170998 GCTAAAGCAACAAACTACAGTAGAAGA 59.829 37.037 14.94 0.00 41.59 2.87
739 770 6.073980 CGCTAAAGCAACAAACTACAGTAGAA 60.074 38.462 14.94 0.00 42.21 2.10
753 784 2.033194 ACTCCGCCGCTAAAGCAAC 61.033 57.895 2.44 0.00 42.21 4.17
766 797 1.071471 AACCTGAGCAACCACTCCG 59.929 57.895 0.00 0.00 35.72 4.63
785 816 5.590259 AGAGGTGCAACATGGTAATGTAATC 59.410 40.000 3.64 0.00 46.58 1.75
793 824 4.528987 TGTACTAAGAGGTGCAACATGGTA 59.471 41.667 3.64 0.00 39.98 3.25
809 840 5.235850 TGCCAAAAGTCCTGATGTACTAA 57.764 39.130 0.00 0.00 0.00 2.24
810 841 4.901197 TGCCAAAAGTCCTGATGTACTA 57.099 40.909 0.00 0.00 0.00 1.82
933 968 3.708403 TGGGCTTCCTGCATATAGATG 57.292 47.619 0.00 0.00 45.15 2.90
938 973 3.776417 ACAAAAATGGGCTTCCTGCATAT 59.224 39.130 0.00 0.00 45.15 1.78
975 1010 7.973048 TTCTTCAGAGCTTATAGGAACCTAA 57.027 36.000 4.63 0.00 31.73 2.69
989 1024 3.766051 ACCCATTTCCATTTCTTCAGAGC 59.234 43.478 0.00 0.00 0.00 4.09
990 1025 5.012239 TCACCCATTTCCATTTCTTCAGAG 58.988 41.667 0.00 0.00 0.00 3.35
1011 1046 2.504274 AAGACCGACCGCCTTGTCA 61.504 57.895 0.00 0.00 34.88 3.58
1026 1061 2.102420 ACTCGTCATGGTCAACACAAGA 59.898 45.455 0.00 0.00 0.00 3.02
1134 1169 4.788679 AGACAAATATTTAGGAACGGGGG 58.211 43.478 0.00 0.00 0.00 5.40
1135 1170 6.769134 AAAGACAAATATTTAGGAACGGGG 57.231 37.500 0.00 0.00 0.00 5.73
1136 1171 9.783256 CTAAAAAGACAAATATTTAGGAACGGG 57.217 33.333 0.00 0.00 33.69 5.28
1151 1186 9.965824 GTCCATTTGAAATCTCTAAAAAGACAA 57.034 29.630 0.00 0.00 0.00 3.18
1152 1187 9.354673 AGTCCATTTGAAATCTCTAAAAAGACA 57.645 29.630 0.00 0.00 0.00 3.41
1156 1191 9.581289 TGGTAGTCCATTTGAAATCTCTAAAAA 57.419 29.630 0.00 0.00 39.03 1.94
1157 1192 9.010029 GTGGTAGTCCATTTGAAATCTCTAAAA 57.990 33.333 0.00 0.00 46.20 1.52
1158 1193 8.160765 TGTGGTAGTCCATTTGAAATCTCTAAA 58.839 33.333 0.00 0.00 46.20 1.85
1159 1194 7.685481 TGTGGTAGTCCATTTGAAATCTCTAA 58.315 34.615 0.00 0.00 46.20 2.10
1160 1195 7.252612 TGTGGTAGTCCATTTGAAATCTCTA 57.747 36.000 0.00 0.00 46.20 2.43
1161 1196 6.126863 TGTGGTAGTCCATTTGAAATCTCT 57.873 37.500 0.00 0.00 46.20 3.10
1162 1197 7.254455 CGTATGTGGTAGTCCATTTGAAATCTC 60.254 40.741 0.00 0.00 46.20 2.75
1163 1198 6.538742 CGTATGTGGTAGTCCATTTGAAATCT 59.461 38.462 0.00 0.00 46.20 2.40
1164 1199 6.238374 CCGTATGTGGTAGTCCATTTGAAATC 60.238 42.308 0.00 0.00 46.20 2.17
1165 1200 5.588648 CCGTATGTGGTAGTCCATTTGAAAT 59.411 40.000 0.00 0.00 46.20 2.17
1166 1201 4.938832 CCGTATGTGGTAGTCCATTTGAAA 59.061 41.667 0.00 0.00 46.20 2.69
1167 1202 4.223255 TCCGTATGTGGTAGTCCATTTGAA 59.777 41.667 0.00 0.00 46.20 2.69
1168 1203 3.770388 TCCGTATGTGGTAGTCCATTTGA 59.230 43.478 0.00 0.00 46.20 2.69
1169 1204 4.131649 TCCGTATGTGGTAGTCCATTTG 57.868 45.455 0.00 0.00 46.20 2.32
1170 1205 4.163458 ACATCCGTATGTGGTAGTCCATTT 59.837 41.667 0.00 0.00 44.79 2.32
1171 1206 3.709653 ACATCCGTATGTGGTAGTCCATT 59.290 43.478 0.00 0.00 44.79 3.16
1172 1207 3.305720 ACATCCGTATGTGGTAGTCCAT 58.694 45.455 0.00 0.00 44.79 3.41
1173 1208 2.742348 ACATCCGTATGTGGTAGTCCA 58.258 47.619 0.00 0.00 44.79 4.02
1174 1209 6.770746 ATATACATCCGTATGTGGTAGTCC 57.229 41.667 3.56 0.00 45.99 3.85
1175 1210 8.610896 GTCTATATACATCCGTATGTGGTAGTC 58.389 40.741 3.56 0.00 45.99 2.59
1176 1211 8.105197 TGTCTATATACATCCGTATGTGGTAGT 58.895 37.037 3.56 0.00 45.99 2.73
1177 1212 8.502105 TGTCTATATACATCCGTATGTGGTAG 57.498 38.462 3.56 3.93 45.99 3.18
1179 1214 7.956328 ATGTCTATATACATCCGTATGTGGT 57.044 36.000 3.56 0.00 45.99 4.16
1212 1247 5.446473 CGGAGCAAAATGAGTGAATCTACAC 60.446 44.000 0.00 0.00 40.60 2.90
1213 1248 4.631377 CGGAGCAAAATGAGTGAATCTACA 59.369 41.667 0.00 0.00 0.00 2.74
1214 1249 4.631813 ACGGAGCAAAATGAGTGAATCTAC 59.368 41.667 0.00 0.00 0.00 2.59
1215 1250 4.832248 ACGGAGCAAAATGAGTGAATCTA 58.168 39.130 0.00 0.00 0.00 1.98
1216 1251 3.679389 ACGGAGCAAAATGAGTGAATCT 58.321 40.909 0.00 0.00 0.00 2.40
1217 1252 5.065218 ACATACGGAGCAAAATGAGTGAATC 59.935 40.000 0.00 0.00 0.00 2.52
1218 1253 4.943705 ACATACGGAGCAAAATGAGTGAAT 59.056 37.500 0.00 0.00 0.00 2.57
1219 1254 4.323417 ACATACGGAGCAAAATGAGTGAA 58.677 39.130 0.00 0.00 0.00 3.18
1220 1255 3.937814 ACATACGGAGCAAAATGAGTGA 58.062 40.909 0.00 0.00 0.00 3.41
1221 1256 4.870426 ACTACATACGGAGCAAAATGAGTG 59.130 41.667 0.00 0.00 0.00 3.51
1222 1257 5.086104 ACTACATACGGAGCAAAATGAGT 57.914 39.130 0.00 0.00 0.00 3.41
1223 1258 5.109210 TGACTACATACGGAGCAAAATGAG 58.891 41.667 0.00 0.00 0.00 2.90
1224 1259 5.079689 TGACTACATACGGAGCAAAATGA 57.920 39.130 0.00 0.00 0.00 2.57
1225 1260 5.991328 ATGACTACATACGGAGCAAAATG 57.009 39.130 0.00 0.00 34.71 2.32
1226 1261 6.374333 ACAAATGACTACATACGGAGCAAAAT 59.626 34.615 0.00 0.00 35.50 1.82
1227 1262 5.703592 ACAAATGACTACATACGGAGCAAAA 59.296 36.000 0.00 0.00 35.50 2.44
1228 1263 5.242434 ACAAATGACTACATACGGAGCAAA 58.758 37.500 0.00 0.00 35.50 3.68
1229 1264 4.827692 ACAAATGACTACATACGGAGCAA 58.172 39.130 0.00 0.00 35.50 3.91
1230 1265 4.465632 ACAAATGACTACATACGGAGCA 57.534 40.909 0.00 0.00 35.50 4.26
1231 1266 4.868171 TCAACAAATGACTACATACGGAGC 59.132 41.667 0.00 0.00 35.50 4.70
1232 1267 6.961359 TTCAACAAATGACTACATACGGAG 57.039 37.500 0.00 0.00 37.92 4.63
1233 1268 7.822334 AGATTTCAACAAATGACTACATACGGA 59.178 33.333 0.00 0.00 37.92 4.69
1234 1269 7.974675 AGATTTCAACAAATGACTACATACGG 58.025 34.615 0.00 0.00 37.92 4.02
1235 1270 8.873830 AGAGATTTCAACAAATGACTACATACG 58.126 33.333 0.00 0.00 37.92 3.06
1239 1274 9.996554 TTCTAGAGATTTCAACAAATGACTACA 57.003 29.630 0.00 0.00 37.92 2.74
1242 1277 9.784531 TCTTTCTAGAGATTTCAACAAATGACT 57.215 29.630 0.00 0.00 37.92 3.41
1243 1278 9.818796 GTCTTTCTAGAGATTTCAACAAATGAC 57.181 33.333 0.00 0.00 37.92 3.06
1244 1279 9.559732 TGTCTTTCTAGAGATTTCAACAAATGA 57.440 29.630 0.00 0.00 31.94 2.57
1259 1294 9.595823 CCGTTCCTAAATATTTGTCTTTCTAGA 57.404 33.333 11.05 0.00 0.00 2.43
1260 1295 9.595823 TCCGTTCCTAAATATTTGTCTTTCTAG 57.404 33.333 11.05 0.00 0.00 2.43
1261 1296 9.595823 CTCCGTTCCTAAATATTTGTCTTTCTA 57.404 33.333 11.05 0.00 0.00 2.10
1262 1297 7.553044 CCTCCGTTCCTAAATATTTGTCTTTCT 59.447 37.037 11.05 0.00 0.00 2.52
1263 1298 7.201705 CCCTCCGTTCCTAAATATTTGTCTTTC 60.202 40.741 11.05 0.00 0.00 2.62
1264 1299 6.602009 CCCTCCGTTCCTAAATATTTGTCTTT 59.398 38.462 11.05 0.00 0.00 2.52
1265 1300 6.069847 TCCCTCCGTTCCTAAATATTTGTCTT 60.070 38.462 11.05 0.00 0.00 3.01
1266 1301 5.427481 TCCCTCCGTTCCTAAATATTTGTCT 59.573 40.000 11.05 0.00 0.00 3.41
1267 1302 5.677567 TCCCTCCGTTCCTAAATATTTGTC 58.322 41.667 11.05 0.00 0.00 3.18
1268 1303 5.191124 ACTCCCTCCGTTCCTAAATATTTGT 59.809 40.000 11.05 0.00 0.00 2.83
1269 1304 5.681639 ACTCCCTCCGTTCCTAAATATTTG 58.318 41.667 11.05 1.40 0.00 2.32
1270 1305 5.970501 ACTCCCTCCGTTCCTAAATATTT 57.029 39.130 5.89 5.89 0.00 1.40
1271 1306 6.557633 ACATACTCCCTCCGTTCCTAAATATT 59.442 38.462 0.00 0.00 0.00 1.28
1272 1307 6.082707 ACATACTCCCTCCGTTCCTAAATAT 58.917 40.000 0.00 0.00 0.00 1.28
1273 1308 5.461327 ACATACTCCCTCCGTTCCTAAATA 58.539 41.667 0.00 0.00 0.00 1.40
1274 1309 4.296056 ACATACTCCCTCCGTTCCTAAAT 58.704 43.478 0.00 0.00 0.00 1.40
1275 1310 3.716431 ACATACTCCCTCCGTTCCTAAA 58.284 45.455 0.00 0.00 0.00 1.85
1276 1311 3.393426 ACATACTCCCTCCGTTCCTAA 57.607 47.619 0.00 0.00 0.00 2.69
1277 1312 3.393426 AACATACTCCCTCCGTTCCTA 57.607 47.619 0.00 0.00 0.00 2.94
1278 1313 2.249309 AACATACTCCCTCCGTTCCT 57.751 50.000 0.00 0.00 0.00 3.36
1279 1314 2.500504 AGAAACATACTCCCTCCGTTCC 59.499 50.000 0.00 0.00 0.00 3.62
1280 1315 3.056035 ACAGAAACATACTCCCTCCGTTC 60.056 47.826 0.00 0.00 0.00 3.95
1281 1316 2.904434 ACAGAAACATACTCCCTCCGTT 59.096 45.455 0.00 0.00 0.00 4.44
1282 1317 2.233922 CACAGAAACATACTCCCTCCGT 59.766 50.000 0.00 0.00 0.00 4.69
1283 1318 2.496070 TCACAGAAACATACTCCCTCCG 59.504 50.000 0.00 0.00 0.00 4.63
1284 1319 4.762289 ATCACAGAAACATACTCCCTCC 57.238 45.455 0.00 0.00 0.00 4.30
1285 1320 7.275920 ACATAATCACAGAAACATACTCCCTC 58.724 38.462 0.00 0.00 0.00 4.30
1286 1321 7.200434 ACATAATCACAGAAACATACTCCCT 57.800 36.000 0.00 0.00 0.00 4.20
1287 1322 9.561069 AATACATAATCACAGAAACATACTCCC 57.439 33.333 0.00 0.00 0.00 4.30
1332 1367 3.582164 ACAAATGGCTAGGTGGGAAAAA 58.418 40.909 0.00 0.00 0.00 1.94
1363 1398 7.175990 GGTAGAAAGTATTGGTGGACAAAATGA 59.824 37.037 0.00 0.00 43.46 2.57
1429 1464 4.338379 ACTTAGGAACGAAAGAAGCACT 57.662 40.909 0.00 0.00 32.06 4.40
1435 1470 8.080417 CCGATGAATATACTTAGGAACGAAAGA 58.920 37.037 0.00 0.00 32.06 2.52
1472 1507 4.216472 GGCCTTCTTTTTCTTCGACTTCAT 59.784 41.667 0.00 0.00 0.00 2.57
1495 1530 1.141591 GCCGCCAAATCAATCAAGCG 61.142 55.000 0.00 0.00 42.99 4.68
1503 1538 4.440829 GGGGGAGCCGCCAAATCA 62.441 66.667 16.91 0.00 46.73 2.57
1575 1613 7.392673 ACAAGTGAGCTCAATGAAATACAATCT 59.607 33.333 28.26 11.97 0.00 2.40
1593 1631 5.486526 AGAAAGCCTTAGATCACAAGTGAG 58.513 41.667 8.99 0.00 43.61 3.51
1621 1664 2.731027 GCAAATACCCGCTTGTAAGTGC 60.731 50.000 0.00 5.58 35.25 4.40
1628 1671 0.239879 AACACGCAAATACCCGCTTG 59.760 50.000 0.00 0.00 33.90 4.01
1629 1672 0.239879 CAACACGCAAATACCCGCTT 59.760 50.000 0.00 0.00 0.00 4.68
1630 1673 1.582610 CCAACACGCAAATACCCGCT 61.583 55.000 0.00 0.00 0.00 5.52
1631 1674 1.154112 CCAACACGCAAATACCCGC 60.154 57.895 0.00 0.00 0.00 6.13
1632 1675 1.440708 TACCAACACGCAAATACCCG 58.559 50.000 0.00 0.00 0.00 5.28
1636 1694 7.853437 CGATCAATAATTACCAACACGCAAATA 59.147 33.333 0.00 0.00 0.00 1.40
1652 1713 9.467258 CCAATGTTTATTCTTGCGATCAATAAT 57.533 29.630 0.00 0.00 34.62 1.28
1657 1718 5.414144 TGACCAATGTTTATTCTTGCGATCA 59.586 36.000 0.00 0.00 0.00 2.92
1720 1799 5.050490 GTGCCGACTACATTGATCTAACAT 58.950 41.667 0.00 0.00 0.00 2.71
1725 1804 2.760650 TGAGTGCCGACTACATTGATCT 59.239 45.455 0.00 0.00 30.16 2.75
1778 1857 7.386059 TGTTTAGAGTCAGAAGCATTATGTCA 58.614 34.615 0.00 0.00 38.69 3.58
1779 1858 7.834068 TGTTTAGAGTCAGAAGCATTATGTC 57.166 36.000 0.00 0.00 38.69 3.06
1780 1859 8.798859 AATGTTTAGAGTCAGAAGCATTATGT 57.201 30.769 14.26 0.00 38.69 2.29
1784 1863 8.401490 AGAAAATGTTTAGAGTCAGAAGCATT 57.599 30.769 11.59 11.59 37.88 3.56
1785 1864 7.120432 GGAGAAAATGTTTAGAGTCAGAAGCAT 59.880 37.037 0.00 0.00 0.00 3.79
1786 1865 6.428159 GGAGAAAATGTTTAGAGTCAGAAGCA 59.572 38.462 0.00 0.00 0.00 3.91
1787 1866 6.428159 TGGAGAAAATGTTTAGAGTCAGAAGC 59.572 38.462 0.00 0.00 0.00 3.86
1788 1867 7.969536 TGGAGAAAATGTTTAGAGTCAGAAG 57.030 36.000 0.00 0.00 0.00 2.85
1809 4475 4.278170 ACTTCATTTCAGCGAAAACATGGA 59.722 37.500 0.00 0.00 35.11 3.41
1820 4486 4.970662 TGCCAATCTACTTCATTTCAGC 57.029 40.909 0.00 0.00 0.00 4.26
1839 4505 7.271438 GTCTAATTTTGTTTTCTCGAGGAATGC 59.729 37.037 13.56 7.07 33.53 3.56
1847 4513 6.067263 TGGTGGTCTAATTTTGTTTTCTCG 57.933 37.500 0.00 0.00 0.00 4.04
1974 4650 8.643752 CGCCATAATTTTTATTTGAGAACGTTT 58.356 29.630 0.46 0.00 0.00 3.60
2001 4681 6.595326 CCTTGCATATGACTTCTTGTTAGTGA 59.405 38.462 6.97 0.00 0.00 3.41
2009 4689 5.435686 TGTACCCTTGCATATGACTTCTT 57.564 39.130 6.97 0.00 0.00 2.52
2011 4691 6.699575 ATTTGTACCCTTGCATATGACTTC 57.300 37.500 6.97 0.00 0.00 3.01
2023 4703 8.889717 CGTGAAGATATAACAATTTGTACCCTT 58.110 33.333 1.76 3.03 0.00 3.95
2047 4727 8.836268 TGTGGTATTTTTCTAGTGATTAACGT 57.164 30.769 0.00 0.00 0.00 3.99
2114 4805 6.092259 AGTCCGTGCAAATAGTTCTAATTCAC 59.908 38.462 0.00 0.00 0.00 3.18
2249 4940 6.769822 CAGTGGATGTAATGGAAGAGCTAATT 59.230 38.462 0.00 0.00 0.00 1.40
2275 4966 6.073765 CGATAACTTAATGGATGGAAGGTTCG 60.074 42.308 0.00 0.00 0.00 3.95
2391 5086 8.620177 CCCTTTCCCCATATATATAAAAGTGGA 58.380 37.037 10.49 4.48 0.00 4.02
2395 5090 9.255029 CAACCCCTTTCCCCATATATATAAAAG 57.745 37.037 0.00 2.36 0.00 2.27
2418 5113 7.351981 GCAACAATTAAGGTTTGATTTCCAAC 58.648 34.615 0.00 0.00 33.85 3.77


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

AutoCloner maintained by Alex Coulton.