Multiple sequence alignment - TraesCS3B01G440200

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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 TraesCS3B01G440200 chr3B 100.000 4190 0 0 1 4190 679641968 679646157 0.000000e+00 7738.0
1 TraesCS3B01G440200 chr3B 74.879 414 91 8 197 600 458286365 458285955 4.310000e-40 176.0
2 TraesCS3B01G440200 chr3D 93.574 2381 118 17 1834 4190 516382922 516385291 0.000000e+00 3517.0
3 TraesCS3B01G440200 chr3D 90.123 1549 109 26 232 1761 516381405 516382928 0.000000e+00 1973.0
4 TraesCS3B01G440200 chr3D 87.558 217 21 3 1 217 516381211 516381421 3.240000e-61 246.0
5 TraesCS3B01G440200 chr3D 76.658 407 78 10 189 584 357075210 357074810 4.240000e-50 209.0
6 TraesCS3B01G440200 chr3D 89.231 65 6 1 4125 4189 48365628 48365691 3.470000e-11 80.5
7 TraesCS3B01G440200 chr3A 90.386 1477 103 16 2746 4190 651586779 651588248 0.000000e+00 1905.0
8 TraesCS3B01G440200 chr3A 89.330 1209 74 26 1476 2663 651585145 651586319 0.000000e+00 1467.0
9 TraesCS3B01G440200 chr3A 93.094 753 27 10 659 1389 651584157 651584906 0.000000e+00 1079.0
10 TraesCS3B01G440200 chr3A 79.778 450 67 16 232 660 651523320 651523766 5.260000e-79 305.0
11 TraesCS3B01G440200 chr3A 92.308 208 9 6 2542 2747 651586319 651586521 5.300000e-74 289.0
12 TraesCS3B01G440200 chr3A 83.871 217 29 3 1 217 651523126 651523336 7.100000e-48 202.0
13 TraesCS3B01G440200 chr3A 91.057 123 8 2 2542 2663 651586259 651586379 3.350000e-36 163.0
14 TraesCS3B01G440200 chr3A 93.103 87 6 0 1388 1474 651585022 651585108 1.220000e-25 128.0
15 TraesCS3B01G440200 chr7D 76.817 578 117 9 16 583 5318357 5318927 4.070000e-80 309.0
16 TraesCS3B01G440200 chr7D 89.655 145 12 1 3958 4102 621613582 621613723 9.250000e-42 182.0
17 TraesCS3B01G440200 chr7A 91.935 186 13 1 3959 4144 717067623 717067806 4.160000e-65 259.0
18 TraesCS3B01G440200 chr1D 88.482 191 22 0 1000 1190 360386909 360387099 9.060000e-57 231.0
19 TraesCS3B01G440200 chr1D 83.432 169 24 4 1001 1167 356932113 356931947 2.020000e-33 154.0
20 TraesCS3B01G440200 chr1D 88.732 71 8 0 1635 1705 360387223 360387293 2.080000e-13 87.9
21 TraesCS3B01G440200 chr1A 88.083 193 23 0 998 1190 459946979 459947171 3.260000e-56 230.0
22 TraesCS3B01G440200 chr1A 82.738 168 27 2 1001 1167 458220109 458219943 9.390000e-32 148.0
23 TraesCS3B01G440200 chr1A 90.141 71 7 0 1635 1705 459947307 459947377 4.460000e-15 93.5
24 TraesCS3B01G440200 chr1B 87.958 191 23 0 1000 1190 482451149 482451339 4.210000e-55 226.0
25 TraesCS3B01G440200 chr1B 82.738 168 27 2 1001 1167 480441460 480441294 9.390000e-32 148.0
26 TraesCS3B01G440200 chr1B 91.549 71 6 0 1635 1705 482451449 482451519 9.590000e-17 99.0
27 TraesCS3B01G440200 chr5A 78.012 332 73 0 131 462 570360654 570360985 4.240000e-50 209.0
28 TraesCS3B01G440200 chr6A 75.202 371 76 11 227 583 615312154 615311786 1.210000e-35 161.0
29 TraesCS3B01G440200 chr6A 76.786 280 57 7 277 554 38344124 38344397 2.610000e-32 150.0
30 TraesCS3B01G440200 chr6A 90.196 51 5 0 4135 4185 570382352 570382402 2.700000e-07 67.6
31 TraesCS3B01G440200 chr6D 75.229 327 72 8 257 581 33338073 33338392 3.380000e-31 147.0
32 TraesCS3B01G440200 chr7B 90.566 106 6 2 3958 4063 718445463 718445362 2.030000e-28 137.0
33 TraesCS3B01G440200 chr2D 89.583 48 5 0 4127 4174 492022219 492022266 1.260000e-05 62.1
34 TraesCS3B01G440200 chr2D 83.077 65 11 0 4123 4187 595290118 595290182 4.520000e-05 60.2
35 TraesCS3B01G440200 chr2A 89.583 48 5 0 4127 4174 637222648 637222695 1.260000e-05 62.1
36 TraesCS3B01G440200 chr2A 83.077 65 11 0 4123 4187 729500536 729500600 4.520000e-05 60.2
37 TraesCS3B01G440200 chr5D 94.595 37 2 0 77 113 451626515 451626479 1.630000e-04 58.4
38 TraesCS3B01G440200 chr2B 81.538 65 12 0 4123 4187 723043233 723043297 2.000000e-03 54.7


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 TraesCS3B01G440200 chr3B 679641968 679646157 4189 False 7738.0 7738 100.000000 1 4190 1 chr3B.!!$F1 4189
1 TraesCS3B01G440200 chr3D 516381211 516385291 4080 False 1912.0 3517 90.418333 1 4190 3 chr3D.!!$F2 4189
2 TraesCS3B01G440200 chr3A 651584157 651588248 4091 False 838.5 1905 91.546333 659 4190 6 chr3A.!!$F2 3531
3 TraesCS3B01G440200 chr3A 651523126 651523766 640 False 253.5 305 81.824500 1 660 2 chr3A.!!$F1 659
4 TraesCS3B01G440200 chr7D 5318357 5318927 570 False 309.0 309 76.817000 16 583 1 chr7D.!!$F1 567

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
484 526 0.320073 GGGGAACGACACATTGACGA 60.320 55.0 5.10 0.0 37.72 4.20 F
1630 1891 0.108709 CATGCATCGTTTTGGTGGGG 60.109 55.0 0.00 0.0 0.00 4.96 F
1859 2131 2.038952 TGAGTGGAATGACCTGTTCCTG 59.961 50.0 6.47 0.0 44.36 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1904 2176 0.670854 GAGGCTCTGAAACGGTGGAC 60.671 60.0 7.40 0.0 0.0 4.02 R
2961 3636 0.032403 TAACTTGTACACGGTGCGCT 59.968 50.0 9.73 0.0 0.0 5.92 R
3201 3891 0.327924 ATTTGATGGAGTGGCGTGGA 59.672 50.0 0.00 0.0 0.0 4.02 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
66 67 2.244651 CGATCCCGTGATTTCGCCC 61.245 63.158 0.00 0.00 0.00 6.13
129 130 2.367202 GGGATCCTTGTGCCTCCGA 61.367 63.158 12.58 0.00 0.00 4.55
179 181 0.321122 AGTCCTCGTAGGTTCGTCGT 60.321 55.000 0.00 0.00 36.53 4.34
182 184 0.518636 CCTCGTAGGTTCGTCGTTCA 59.481 55.000 0.00 0.00 0.00 3.18
204 206 2.418976 GACAAATGGCGGTACTTCTTCC 59.581 50.000 0.00 0.00 0.00 3.46
206 208 3.081804 CAAATGGCGGTACTTCTTCCTT 58.918 45.455 0.00 0.00 0.00 3.36
207 209 2.403252 ATGGCGGTACTTCTTCCTTG 57.597 50.000 0.00 0.00 0.00 3.61
208 210 1.344065 TGGCGGTACTTCTTCCTTGA 58.656 50.000 0.00 0.00 0.00 3.02
209 211 1.275291 TGGCGGTACTTCTTCCTTGAG 59.725 52.381 0.00 0.00 0.00 3.02
210 212 1.275573 GGCGGTACTTCTTCCTTGAGT 59.724 52.381 0.00 0.00 0.00 3.41
211 213 2.289506 GGCGGTACTTCTTCCTTGAGTT 60.290 50.000 0.00 0.00 0.00 3.01
212 214 3.400255 GCGGTACTTCTTCCTTGAGTTT 58.600 45.455 0.00 0.00 0.00 2.66
213 215 3.186613 GCGGTACTTCTTCCTTGAGTTTG 59.813 47.826 0.00 0.00 0.00 2.93
214 216 4.377897 CGGTACTTCTTCCTTGAGTTTGT 58.622 43.478 0.00 0.00 0.00 2.83
215 217 4.448060 CGGTACTTCTTCCTTGAGTTTGTC 59.552 45.833 0.00 0.00 0.00 3.18
216 218 5.612351 GGTACTTCTTCCTTGAGTTTGTCT 58.388 41.667 0.00 0.00 0.00 3.41
217 219 6.516194 CGGTACTTCTTCCTTGAGTTTGTCTA 60.516 42.308 0.00 0.00 0.00 2.59
218 220 6.645827 GGTACTTCTTCCTTGAGTTTGTCTAC 59.354 42.308 0.00 0.00 0.00 2.59
219 221 5.612351 ACTTCTTCCTTGAGTTTGTCTACC 58.388 41.667 0.00 0.00 0.00 3.18
220 222 5.130477 ACTTCTTCCTTGAGTTTGTCTACCA 59.870 40.000 0.00 0.00 0.00 3.25
221 223 5.623956 TCTTCCTTGAGTTTGTCTACCAA 57.376 39.130 0.00 0.00 0.00 3.67
222 224 5.611374 TCTTCCTTGAGTTTGTCTACCAAG 58.389 41.667 0.00 0.00 33.75 3.61
223 225 3.740115 TCCTTGAGTTTGTCTACCAAGC 58.260 45.455 0.00 0.00 34.51 4.01
224 226 3.391296 TCCTTGAGTTTGTCTACCAAGCT 59.609 43.478 0.00 0.00 45.99 3.74
225 227 4.137543 CCTTGAGTTTGTCTACCAAGCTT 58.862 43.478 0.00 0.00 43.70 3.74
226 228 4.214332 CCTTGAGTTTGTCTACCAAGCTTC 59.786 45.833 0.00 0.00 43.70 3.86
227 229 3.390135 TGAGTTTGTCTACCAAGCTTCG 58.610 45.455 0.00 0.00 43.70 3.79
228 230 3.069016 TGAGTTTGTCTACCAAGCTTCGA 59.931 43.478 0.00 0.00 43.70 3.71
229 231 4.246458 GAGTTTGTCTACCAAGCTTCGAT 58.754 43.478 0.00 0.00 43.70 3.59
230 232 4.246458 AGTTTGTCTACCAAGCTTCGATC 58.754 43.478 0.00 0.00 41.27 3.69
231 233 2.961526 TGTCTACCAAGCTTCGATCC 57.038 50.000 0.00 0.00 0.00 3.36
232 234 2.457598 TGTCTACCAAGCTTCGATCCT 58.542 47.619 0.00 0.00 0.00 3.24
233 235 2.832129 TGTCTACCAAGCTTCGATCCTT 59.168 45.455 0.00 0.00 0.00 3.36
234 236 3.119101 TGTCTACCAAGCTTCGATCCTTC 60.119 47.826 0.00 0.00 0.00 3.46
235 237 3.131400 GTCTACCAAGCTTCGATCCTTCT 59.869 47.826 0.00 0.00 0.00 2.85
236 238 3.769844 TCTACCAAGCTTCGATCCTTCTT 59.230 43.478 0.00 0.00 0.00 2.52
245 247 4.214332 GCTTCGATCCTTCTTGAGTTTGTT 59.786 41.667 0.00 0.00 0.00 2.83
247 249 6.073222 GCTTCGATCCTTCTTGAGTTTGTTTA 60.073 38.462 0.00 0.00 0.00 2.01
253 285 6.601332 TCCTTCTTGAGTTTGTTTATCTGGT 58.399 36.000 0.00 0.00 0.00 4.00
265 297 5.845103 TGTTTATCTGGTCGTAGTTGACAA 58.155 37.500 0.00 0.00 40.72 3.18
268 300 4.602340 ATCTGGTCGTAGTTGACAAAGT 57.398 40.909 0.00 0.00 40.72 2.66
273 305 3.374745 GTCGTAGTTGACAAAGTTCCGA 58.625 45.455 0.00 0.00 38.75 4.55
286 318 5.178797 CAAAGTTCCGACATAGATTCCTGT 58.821 41.667 0.00 0.00 0.00 4.00
338 371 1.349357 TCGTCATGTGGTGGGATTTGA 59.651 47.619 0.00 0.00 0.00 2.69
378 411 1.336755 GTGCAAGGGTTCAACGTTGAT 59.663 47.619 30.10 13.82 38.20 2.57
380 413 1.335872 GCAAGGGTTCAACGTTGATGG 60.336 52.381 30.10 14.87 38.20 3.51
383 416 0.521735 GGGTTCAACGTTGATGGCTC 59.478 55.000 30.10 19.18 37.00 4.70
386 419 1.606668 GTTCAACGTTGATGGCTCCAA 59.393 47.619 30.10 11.18 37.00 3.53
394 427 1.361204 TGATGGCTCCAACTCCAAGA 58.639 50.000 0.00 0.00 35.75 3.02
396 429 1.280421 GATGGCTCCAACTCCAAGACT 59.720 52.381 0.00 0.00 35.75 3.24
402 435 0.689623 CCAACTCCAAGACTCTGGCT 59.310 55.000 0.00 0.00 36.32 4.75
475 517 1.880819 GCTTCGGTAGGGGAACGACA 61.881 60.000 0.00 0.00 36.24 4.35
477 519 0.827089 TTCGGTAGGGGAACGACACA 60.827 55.000 0.00 0.00 36.24 3.72
481 523 1.276989 GGTAGGGGAACGACACATTGA 59.723 52.381 0.00 0.00 0.00 2.57
484 526 0.320073 GGGGAACGACACATTGACGA 60.320 55.000 5.10 0.00 37.72 4.20
495 537 1.474478 ACATTGACGACTCGCTCTGAT 59.526 47.619 0.00 0.00 0.00 2.90
513 555 1.257750 ATGGCAGTAGTGGTCGCTCA 61.258 55.000 0.00 0.00 0.00 4.26
522 564 1.530655 TGGTCGCTCAGTGGTCTCA 60.531 57.895 0.00 0.00 0.00 3.27
523 565 1.112916 TGGTCGCTCAGTGGTCTCAA 61.113 55.000 0.00 0.00 0.00 3.02
527 569 2.808543 GTCGCTCAGTGGTCTCAAAATT 59.191 45.455 0.00 0.00 0.00 1.82
529 571 3.882888 TCGCTCAGTGGTCTCAAAATTTT 59.117 39.130 0.00 0.00 0.00 1.82
567 609 7.994425 TTATGTTTGAGATGCCTTTTACTCA 57.006 32.000 0.00 0.00 37.56 3.41
636 692 6.871492 TCATAACACTTAATCAAGAGCGTCAA 59.129 34.615 0.00 0.00 35.60 3.18
646 702 0.540830 AGAGCGTCAAGGAGACCTGT 60.541 55.000 0.00 0.00 44.66 4.00
671 727 5.745227 ACCGATCACTAATCAAACCAAGAT 58.255 37.500 0.00 0.00 33.65 2.40
874 931 2.246327 CTCCTTTACTCCTCCTCCTCCT 59.754 54.545 0.00 0.00 0.00 3.69
902 964 4.596585 CCCCACCACCACCACCAC 62.597 72.222 0.00 0.00 0.00 4.16
903 965 4.596585 CCCACCACCACCACCACC 62.597 72.222 0.00 0.00 0.00 4.61
1215 1280 1.632018 CGTATCTGCCCCCTTTCCCA 61.632 60.000 0.00 0.00 0.00 4.37
1230 1295 2.584608 CCACCCCGAATCTCGCTT 59.415 61.111 0.00 0.00 38.82 4.68
1231 1296 1.078426 CCACCCCGAATCTCGCTTT 60.078 57.895 0.00 0.00 38.82 3.51
1232 1297 0.676782 CCACCCCGAATCTCGCTTTT 60.677 55.000 0.00 0.00 38.82 2.27
1233 1298 0.727398 CACCCCGAATCTCGCTTTTC 59.273 55.000 0.00 0.00 38.82 2.29
1234 1299 0.323629 ACCCCGAATCTCGCTTTTCA 59.676 50.000 0.00 0.00 38.82 2.69
1235 1300 1.271163 ACCCCGAATCTCGCTTTTCAA 60.271 47.619 0.00 0.00 38.82 2.69
1236 1301 1.398390 CCCCGAATCTCGCTTTTCAAG 59.602 52.381 0.00 0.00 38.82 3.02
1237 1302 1.398390 CCCGAATCTCGCTTTTCAAGG 59.602 52.381 0.00 0.00 38.82 3.61
1238 1303 2.346803 CCGAATCTCGCTTTTCAAGGA 58.653 47.619 0.00 0.00 38.82 3.36
1239 1304 2.349886 CCGAATCTCGCTTTTCAAGGAG 59.650 50.000 0.00 0.00 38.82 3.69
1240 1305 2.222908 CGAATCTCGCTTTTCAAGGAGC 60.223 50.000 0.00 0.00 31.14 4.70
1245 1310 3.873805 GCTTTTCAAGGAGCGCTTT 57.126 47.368 13.26 0.00 0.00 3.51
1246 1311 1.691127 GCTTTTCAAGGAGCGCTTTC 58.309 50.000 13.26 7.57 0.00 2.62
1247 1312 1.667177 GCTTTTCAAGGAGCGCTTTCC 60.667 52.381 13.26 9.97 37.52 3.13
1249 1314 1.523758 TTTCAAGGAGCGCTTTCCTC 58.476 50.000 17.71 1.65 46.90 3.71
1250 1315 0.670546 TTCAAGGAGCGCTTTCCTCG 60.671 55.000 17.71 7.94 46.90 4.63
1251 1316 2.103042 CAAGGAGCGCTTTCCTCGG 61.103 63.158 17.71 10.08 46.90 4.63
1252 1317 3.959991 AAGGAGCGCTTTCCTCGGC 62.960 63.158 17.71 0.00 46.90 5.54
1253 1318 4.459089 GGAGCGCTTTCCTCGGCT 62.459 66.667 13.26 0.00 38.70 5.52
1254 1319 2.888051 GAGCGCTTTCCTCGGCTC 60.888 66.667 13.26 0.00 44.24 4.70
1266 1362 2.617308 TCCTCGGCTCTTTCGTAGTATG 59.383 50.000 0.00 0.00 0.00 2.39
1280 1376 6.016213 TCGTAGTATGCTGTTTGTGACTTA 57.984 37.500 0.00 0.00 0.00 2.24
1281 1377 6.448852 TCGTAGTATGCTGTTTGTGACTTAA 58.551 36.000 0.00 0.00 0.00 1.85
1306 1414 0.878961 GACGTTGGGTTCTTCGCTGT 60.879 55.000 0.00 0.00 0.00 4.40
1336 1444 3.348647 TGCAATCCTTAGCTGCTTGTA 57.651 42.857 7.79 0.00 37.00 2.41
1391 1617 9.632807 GTCACTGCAGATAGGTAAATATTAGAG 57.367 37.037 23.35 0.00 0.00 2.43
1435 1661 4.900635 ATAACTTGCCATGAACGGAATC 57.099 40.909 0.00 0.00 0.00 2.52
1469 1695 5.592282 TGAATGTTTTCTGCTTGACTGGTTA 59.408 36.000 0.00 0.00 32.78 2.85
1474 1704 0.512952 CTGCTTGACTGGTTACGTGC 59.487 55.000 0.00 0.00 0.00 5.34
1498 1759 6.968335 GCACGTTTAGAAAAAGTTTAAGTGGA 59.032 34.615 0.00 0.00 0.00 4.02
1507 1768 7.665974 AGAAAAAGTTTAAGTGGATAGGACCAG 59.334 37.037 0.00 0.00 40.85 4.00
1528 1789 5.045869 CCAGACAACTCATACTCCCCTTTTA 60.046 44.000 0.00 0.00 0.00 1.52
1549 1810 4.927267 ACCTGGACTGGATGACATTTTA 57.073 40.909 0.00 0.00 0.00 1.52
1600 1861 2.538037 GGCACGTTTAGCAACCTTTTTG 59.462 45.455 0.00 0.00 0.00 2.44
1607 1868 2.452600 AGCAACCTTTTTGTCCCTGA 57.547 45.000 0.00 0.00 0.00 3.86
1630 1891 0.108709 CATGCATCGTTTTGGTGGGG 60.109 55.000 0.00 0.00 0.00 4.96
1712 1973 7.610305 GGGATGAGAAACACAAGGTAATTCTTA 59.390 37.037 0.00 0.00 30.89 2.10
1775 2047 4.562143 CCTGGCTGAAAATCCTTTTCCAAG 60.562 45.833 9.24 3.58 46.49 3.61
1779 2051 6.054941 GGCTGAAAATCCTTTTCCAAGAAAA 58.945 36.000 9.24 2.78 46.49 2.29
1780 2052 6.203530 GGCTGAAAATCCTTTTCCAAGAAAAG 59.796 38.462 18.58 18.58 46.49 2.27
1781 2053 6.763135 GCTGAAAATCCTTTTCCAAGAAAAGT 59.237 34.615 21.91 8.61 46.49 2.66
1782 2054 7.042456 GCTGAAAATCCTTTTCCAAGAAAAGTC 60.042 37.037 21.91 15.18 46.49 3.01
1783 2055 8.078060 TGAAAATCCTTTTCCAAGAAAAGTCT 57.922 30.769 21.91 10.57 46.49 3.24
1786 2058 9.739276 AAAATCCTTTTCCAAGAAAAGTCTTTT 57.261 25.926 21.91 20.93 41.55 2.27
1787 2059 9.739276 AAATCCTTTTCCAAGAAAAGTCTTTTT 57.261 25.926 21.91 14.63 41.55 1.94
1790 2062 9.250246 TCCTTTTCCAAGAAAAGTCTTTTTAGA 57.750 29.630 21.91 10.96 41.55 2.10
1791 2063 9.521503 CCTTTTCCAAGAAAAGTCTTTTTAGAG 57.478 33.333 21.91 3.12 41.55 2.43
1792 2064 8.926715 TTTTCCAAGAAAAGTCTTTTTAGAGC 57.073 30.769 11.80 0.00 41.55 4.09
1793 2065 7.881775 TTCCAAGAAAAGTCTTTTTAGAGCT 57.118 32.000 11.80 1.74 41.55 4.09
1794 2066 7.881775 TCCAAGAAAAGTCTTTTTAGAGCTT 57.118 32.000 11.80 7.41 41.55 3.74
1795 2067 8.293699 TCCAAGAAAAGTCTTTTTAGAGCTTT 57.706 30.769 11.80 0.00 41.55 3.51
1796 2068 8.749354 TCCAAGAAAAGTCTTTTTAGAGCTTTT 58.251 29.630 11.80 0.00 41.55 2.27
1797 2069 9.371136 CCAAGAAAAGTCTTTTTAGAGCTTTTT 57.629 29.630 11.80 0.00 41.55 1.94
1855 2127 2.039084 GGACTGAGTGGAATGACCTGTT 59.961 50.000 0.00 0.00 39.86 3.16
1856 2128 3.330267 GACTGAGTGGAATGACCTGTTC 58.670 50.000 0.00 0.00 39.86 3.18
1857 2129 2.039084 ACTGAGTGGAATGACCTGTTCC 59.961 50.000 0.00 0.00 44.32 3.62
1859 2131 2.038952 TGAGTGGAATGACCTGTTCCTG 59.961 50.000 6.47 0.00 44.36 3.86
1860 2132 2.039084 GAGTGGAATGACCTGTTCCTGT 59.961 50.000 6.47 0.00 44.36 4.00
1861 2133 3.248024 AGTGGAATGACCTGTTCCTGTA 58.752 45.455 6.47 0.00 44.36 2.74
1863 2135 3.008049 GTGGAATGACCTGTTCCTGTAGT 59.992 47.826 6.47 0.00 44.36 2.73
1864 2136 3.650942 TGGAATGACCTGTTCCTGTAGTT 59.349 43.478 6.47 0.00 44.36 2.24
1865 2137 4.254492 GGAATGACCTGTTCCTGTAGTTC 58.746 47.826 0.00 0.00 41.52 3.01
1867 2139 4.543590 ATGACCTGTTCCTGTAGTTCAG 57.456 45.455 0.00 0.00 43.27 3.02
1903 2175 6.185511 AGAATGACTTGTCATTGATGGACAT 58.814 36.000 27.19 6.19 44.11 3.06
1904 2176 5.830000 ATGACTTGTCATTGATGGACATG 57.170 39.130 10.15 0.00 44.11 3.21
1994 2266 4.621747 CGAGCTCAGGTAATTTCTTGGACT 60.622 45.833 15.40 0.00 0.00 3.85
2025 2298 6.139679 TCTTTTTCCTTGGATGTCCTGTAT 57.860 37.500 0.09 0.00 36.82 2.29
2035 2308 7.419518 CCTTGGATGTCCTGTATACTGAGATTT 60.420 40.741 11.06 0.47 36.82 2.17
2036 2309 7.437713 TGGATGTCCTGTATACTGAGATTTT 57.562 36.000 11.06 0.00 36.82 1.82
2175 2448 7.946207 TGAAAAACAGGCACTATAATTGTTCA 58.054 30.769 0.00 0.00 36.02 3.18
2194 2467 8.713737 TTGTTCAATTTGTTGATTGACATCAA 57.286 26.923 0.00 0.00 45.54 2.57
2213 2486 6.716628 ACATCAAAAGATATTGTCACCACTGT 59.283 34.615 0.00 0.00 0.00 3.55
2219 2495 7.615582 AAGATATTGTCACCACTGTAATGTG 57.384 36.000 0.00 0.00 37.66 3.21
2222 2498 4.891627 TTGTCACCACTGTAATGTGTTG 57.108 40.909 0.00 0.00 36.30 3.33
2223 2499 4.143986 TGTCACCACTGTAATGTGTTGA 57.856 40.909 0.00 0.00 37.10 3.18
2224 2500 4.126437 TGTCACCACTGTAATGTGTTGAG 58.874 43.478 0.00 0.00 39.41 3.02
2225 2501 4.141824 TGTCACCACTGTAATGTGTTGAGA 60.142 41.667 0.00 0.00 39.41 3.27
2227 2503 5.295787 GTCACCACTGTAATGTGTTGAGAAA 59.704 40.000 0.00 0.00 39.41 2.52
2229 2505 6.375736 TCACCACTGTAATGTGTTGAGAAAAA 59.624 34.615 0.00 0.00 35.09 1.94
2390 2671 2.763039 TCAGTCTGCCCTCATCCATTA 58.237 47.619 0.00 0.00 0.00 1.90
2575 2916 6.247727 TGCGAACTGTTTAAATGCTGATTA 57.752 33.333 0.00 0.00 0.00 1.75
2642 3045 9.139174 CGGACTGTTTAAATGCTGATTATTTTT 57.861 29.630 0.00 0.00 0.00 1.94
2782 3446 9.796062 GTTTTGTTAGCAACATACATGAAATTG 57.204 29.630 0.00 0.00 41.79 2.32
2792 3456 7.400599 ACATACATGAAATTGCTGAATGAGT 57.599 32.000 0.00 0.00 0.00 3.41
2842 3506 7.972277 CCTTCCATCAATAAGAAATGTTGACAG 59.028 37.037 0.00 0.00 41.25 3.51
2904 3570 8.216453 CACCTGAATTTTCATTTTAAAAGAGCG 58.784 33.333 6.79 0.00 36.46 5.03
2961 3636 4.506625 GGATAGGGGCACTACATTATGCAA 60.507 45.833 0.00 0.00 43.93 4.08
3150 3838 1.144057 GATGCCGATCACCTTCCGT 59.856 57.895 0.00 0.00 0.00 4.69
3201 3891 4.824515 AGCTAGGCCGCCGACTCT 62.825 66.667 3.05 0.00 0.00 3.24
3202 3892 4.273257 GCTAGGCCGCCGACTCTC 62.273 72.222 3.05 0.00 0.00 3.20
3203 3893 3.597728 CTAGGCCGCCGACTCTCC 61.598 72.222 3.05 0.00 0.00 3.71
3204 3894 4.435970 TAGGCCGCCGACTCTCCA 62.436 66.667 3.05 0.00 0.00 3.86
3249 3939 2.356022 CCACTGGCTTGTATGTCCATCA 60.356 50.000 0.00 0.00 0.00 3.07
3255 3945 3.057736 GGCTTGTATGTCCATCATGCATC 60.058 47.826 0.00 0.00 45.54 3.91
3292 3982 5.237779 TCCTTCGTTTGTTATCTGTTTGGAC 59.762 40.000 0.00 0.00 0.00 4.02
3333 4023 4.720649 ACGTAGTAGCTTGATGATGTGT 57.279 40.909 0.00 0.00 41.94 3.72
3356 4046 4.339131 CGATACAGTCGGGCTCTAAAAGC 61.339 52.174 0.00 0.00 46.47 3.51
3357 4047 6.515648 CGATACAGTCGGGCTCTAAAAGCT 62.516 50.000 0.00 0.00 45.97 3.74
3391 4081 4.478371 CCGCCTGCTGATCTGCCA 62.478 66.667 20.39 8.85 0.00 4.92
3471 4162 3.156293 CATGTTGTTTCCCTGATCACCA 58.844 45.455 0.00 0.00 0.00 4.17
3479 4170 1.355381 TCCCTGATCACCACAATTGCT 59.645 47.619 5.05 0.00 0.00 3.91
3508 4200 7.015289 CGGTGAATAGTTTGTAATGACAACAG 58.985 38.462 0.00 0.00 45.29 3.16
3556 4248 8.741101 TTGATGTGAACTTTTATTTCATTCCG 57.259 30.769 0.00 0.00 35.47 4.30
3557 4249 6.806249 TGATGTGAACTTTTATTTCATTCCGC 59.194 34.615 0.00 0.00 35.47 5.54
3558 4250 6.078202 TGTGAACTTTTATTTCATTCCGCA 57.922 33.333 0.00 0.00 35.47 5.69
3559 4251 6.686630 TGTGAACTTTTATTTCATTCCGCAT 58.313 32.000 0.00 0.00 35.47 4.73
3563 4258 8.494347 TGAACTTTTATTTCATTCCGCATTTTG 58.506 29.630 0.00 0.00 0.00 2.44
3570 4265 5.635417 TTCATTCCGCATTTTGTACATGA 57.365 34.783 0.00 0.00 0.00 3.07
3572 4267 5.820131 TCATTCCGCATTTTGTACATGATC 58.180 37.500 0.00 0.00 0.00 2.92
3600 4295 5.007626 TCGGTATTTCAGCACAAGATAATGC 59.992 40.000 0.00 0.00 42.39 3.56
3666 4363 4.667519 ACTCCGAACTTCAGTTACAAGT 57.332 40.909 0.00 0.00 38.56 3.16
3843 4541 2.239681 AGTCGAAGGGGATTCTCTGT 57.760 50.000 0.00 0.00 35.61 3.41
4012 4710 3.068881 CCCGGCACTCTTTCTCCA 58.931 61.111 0.00 0.00 0.00 3.86
4023 4721 2.234414 CTCTTTCTCCAGAAGCAGAGCT 59.766 50.000 5.48 0.00 42.56 4.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 5.073428 GTGAAATCTGAAGGGGAGAGTTTT 58.927 41.667 0.00 0.00 28.28 2.43
113 114 0.250081 GGATCGGAGGCACAAGGATC 60.250 60.000 0.00 0.00 34.25 3.36
119 120 0.174845 CTAAACGGATCGGAGGCACA 59.825 55.000 7.35 0.00 0.00 4.57
129 130 5.394553 CCCTAACCGAAACTACTAAACGGAT 60.395 44.000 0.00 0.00 45.31 4.18
179 181 2.851263 AGTACCGCCATTTGTCTGAA 57.149 45.000 0.00 0.00 0.00 3.02
182 184 3.335579 GAAGAAGTACCGCCATTTGTCT 58.664 45.455 0.00 0.00 0.00 3.41
186 188 3.081804 CAAGGAAGAAGTACCGCCATTT 58.918 45.455 0.00 0.00 0.00 2.32
187 189 2.304761 TCAAGGAAGAAGTACCGCCATT 59.695 45.455 0.00 0.00 0.00 3.16
204 206 4.084328 CGAAGCTTGGTAGACAAACTCAAG 60.084 45.833 2.10 0.00 38.91 3.02
206 208 3.069016 TCGAAGCTTGGTAGACAAACTCA 59.931 43.478 2.10 0.00 38.91 3.41
207 209 3.650139 TCGAAGCTTGGTAGACAAACTC 58.350 45.455 2.10 0.00 38.91 3.01
208 210 3.746045 TCGAAGCTTGGTAGACAAACT 57.254 42.857 2.10 0.00 38.91 2.66
209 211 3.371285 GGATCGAAGCTTGGTAGACAAAC 59.629 47.826 2.10 0.00 38.91 2.93
210 212 3.260884 AGGATCGAAGCTTGGTAGACAAA 59.739 43.478 2.10 0.00 38.91 2.83
211 213 2.832129 AGGATCGAAGCTTGGTAGACAA 59.168 45.455 2.10 0.00 37.55 3.18
212 214 2.457598 AGGATCGAAGCTTGGTAGACA 58.542 47.619 2.10 0.00 0.00 3.41
213 215 3.131400 AGAAGGATCGAAGCTTGGTAGAC 59.869 47.826 2.10 0.00 0.00 2.59
214 216 3.366396 AGAAGGATCGAAGCTTGGTAGA 58.634 45.455 2.10 0.00 0.00 2.59
215 217 3.810310 AGAAGGATCGAAGCTTGGTAG 57.190 47.619 2.10 0.00 0.00 3.18
216 218 3.513912 TCAAGAAGGATCGAAGCTTGGTA 59.486 43.478 2.10 0.00 37.23 3.25
217 219 2.303022 TCAAGAAGGATCGAAGCTTGGT 59.697 45.455 2.10 0.00 37.23 3.67
218 220 2.935201 CTCAAGAAGGATCGAAGCTTGG 59.065 50.000 2.10 1.69 37.23 3.61
219 221 3.594134 ACTCAAGAAGGATCGAAGCTTG 58.406 45.455 2.10 0.00 37.79 4.01
220 222 3.971245 ACTCAAGAAGGATCGAAGCTT 57.029 42.857 0.00 0.00 0.00 3.74
221 223 3.971245 AACTCAAGAAGGATCGAAGCT 57.029 42.857 0.00 0.00 0.00 3.74
222 224 3.748568 ACAAACTCAAGAAGGATCGAAGC 59.251 43.478 0.00 0.00 0.00 3.86
223 225 5.931441 AACAAACTCAAGAAGGATCGAAG 57.069 39.130 0.00 0.00 0.00 3.79
224 226 7.878127 AGATAAACAAACTCAAGAAGGATCGAA 59.122 33.333 0.00 0.00 0.00 3.71
225 227 7.331934 CAGATAAACAAACTCAAGAAGGATCGA 59.668 37.037 0.00 0.00 0.00 3.59
226 228 7.413438 CCAGATAAACAAACTCAAGAAGGATCG 60.413 40.741 0.00 0.00 0.00 3.69
227 229 7.391833 ACCAGATAAACAAACTCAAGAAGGATC 59.608 37.037 0.00 0.00 0.00 3.36
228 230 7.234355 ACCAGATAAACAAACTCAAGAAGGAT 58.766 34.615 0.00 0.00 0.00 3.24
229 231 6.601332 ACCAGATAAACAAACTCAAGAAGGA 58.399 36.000 0.00 0.00 0.00 3.36
230 232 6.347725 CGACCAGATAAACAAACTCAAGAAGG 60.348 42.308 0.00 0.00 0.00 3.46
231 233 6.202954 ACGACCAGATAAACAAACTCAAGAAG 59.797 38.462 0.00 0.00 0.00 2.85
232 234 6.053005 ACGACCAGATAAACAAACTCAAGAA 58.947 36.000 0.00 0.00 0.00 2.52
233 235 5.607477 ACGACCAGATAAACAAACTCAAGA 58.393 37.500 0.00 0.00 0.00 3.02
234 236 5.924475 ACGACCAGATAAACAAACTCAAG 57.076 39.130 0.00 0.00 0.00 3.02
235 237 6.518493 ACTACGACCAGATAAACAAACTCAA 58.482 36.000 0.00 0.00 0.00 3.02
236 238 6.092955 ACTACGACCAGATAAACAAACTCA 57.907 37.500 0.00 0.00 0.00 3.41
245 247 6.092955 ACTTTGTCAACTACGACCAGATAA 57.907 37.500 0.00 0.00 34.88 1.75
247 249 4.602340 ACTTTGTCAACTACGACCAGAT 57.398 40.909 0.00 0.00 34.88 2.90
253 285 3.181488 TGTCGGAACTTTGTCAACTACGA 60.181 43.478 0.00 0.00 0.00 3.43
265 297 5.178797 CAACAGGAATCTATGTCGGAACTT 58.821 41.667 0.00 0.00 0.00 2.66
268 300 4.466370 AGACAACAGGAATCTATGTCGGAA 59.534 41.667 0.00 0.00 40.75 4.30
273 305 5.338708 CCAAGGAGACAACAGGAATCTATGT 60.339 44.000 0.00 0.00 0.00 2.29
302 334 8.023128 CCACATGACGAGAAATTTTAAACTCAT 58.977 33.333 0.00 0.00 0.00 2.90
311 344 2.819608 CCCACCACATGACGAGAAATTT 59.180 45.455 0.00 0.00 0.00 1.82
338 371 4.697352 GCACAGATCTAAAACACCTGACAT 59.303 41.667 0.00 0.00 0.00 3.06
378 411 0.687354 GAGTCTTGGAGTTGGAGCCA 59.313 55.000 0.00 0.00 0.00 4.75
380 413 1.338579 CCAGAGTCTTGGAGTTGGAGC 60.339 57.143 0.00 0.00 40.87 4.70
383 416 0.689623 AGCCAGAGTCTTGGAGTTGG 59.310 55.000 11.49 1.11 40.87 3.77
386 419 2.022718 AAGAGCCAGAGTCTTGGAGT 57.977 50.000 11.49 0.05 40.87 3.85
394 427 0.615850 GTGCCCTTAAGAGCCAGAGT 59.384 55.000 6.51 0.00 0.00 3.24
396 429 1.192146 ACGTGCCCTTAAGAGCCAGA 61.192 55.000 6.51 0.00 0.00 3.86
402 435 1.666553 CGTGCACGTGCCCTTAAGA 60.667 57.895 35.72 14.34 41.18 2.10
421 454 4.109050 GTCGATGACATCCAGAAAGTCTC 58.891 47.826 9.87 0.00 33.56 3.36
470 503 1.002250 GCGAGTCGTCAATGTGTCGT 61.002 55.000 15.08 0.00 31.27 4.34
475 517 0.881796 TCAGAGCGAGTCGTCAATGT 59.118 50.000 15.08 0.00 0.00 2.71
477 519 1.202348 CCATCAGAGCGAGTCGTCAAT 60.202 52.381 15.08 5.96 0.00 2.57
481 523 2.276863 CTGCCATCAGAGCGAGTCGT 62.277 60.000 15.08 0.47 42.95 4.34
484 526 0.743688 CTACTGCCATCAGAGCGAGT 59.256 55.000 0.00 0.00 42.95 4.18
495 537 1.877576 CTGAGCGACCACTACTGCCA 61.878 60.000 0.00 0.00 0.00 4.92
611 653 6.394809 TGACGCTCTTGATTAAGTGTTATGA 58.605 36.000 0.00 0.00 36.42 2.15
612 654 6.647212 TGACGCTCTTGATTAAGTGTTATG 57.353 37.500 0.00 0.00 36.42 1.90
615 657 4.452455 CCTTGACGCTCTTGATTAAGTGTT 59.548 41.667 0.00 0.00 36.42 3.32
617 659 4.245660 TCCTTGACGCTCTTGATTAAGTG 58.754 43.478 0.00 0.00 35.38 3.16
618 660 4.220821 TCTCCTTGACGCTCTTGATTAAGT 59.779 41.667 0.00 0.00 35.38 2.24
636 692 0.039764 TGATCGGTCACAGGTCTCCT 59.960 55.000 0.00 0.00 0.00 3.69
646 702 4.545208 TGGTTTGATTAGTGATCGGTCA 57.455 40.909 0.00 0.00 37.60 4.02
671 727 2.510613 CCTGTAAAAGCGGGGAAAAGA 58.489 47.619 0.00 0.00 0.00 2.52
901 963 2.124320 CGATTGGGGAATGGCGGT 60.124 61.111 0.00 0.00 0.00 5.68
902 964 3.595758 GCGATTGGGGAATGGCGG 61.596 66.667 0.00 0.00 0.00 6.13
903 965 2.828095 TGCGATTGGGGAATGGCG 60.828 61.111 0.00 0.00 36.80 5.69
984 1046 1.135960 CCATCCCTCCTCCTTCTTCC 58.864 60.000 0.00 0.00 0.00 3.46
1215 1280 0.323629 TGAAAAGCGAGATTCGGGGT 59.676 50.000 0.34 0.00 40.84 4.95
1219 1284 2.222908 GCTCCTTGAAAAGCGAGATTCG 60.223 50.000 8.68 0.00 44.44 3.34
1230 1295 1.523758 GAGGAAAGCGCTCCTTGAAA 58.476 50.000 18.36 0.00 46.33 2.69
1231 1296 0.670546 CGAGGAAAGCGCTCCTTGAA 60.671 55.000 22.76 0.00 46.49 2.69
1232 1297 1.079819 CGAGGAAAGCGCTCCTTGA 60.080 57.895 22.76 0.00 46.49 3.02
1233 1298 2.103042 CCGAGGAAAGCGCTCCTTG 61.103 63.158 21.03 21.03 46.33 3.61
1234 1299 2.266055 CCGAGGAAAGCGCTCCTT 59.734 61.111 18.36 6.86 46.33 3.36
1236 1301 4.459089 AGCCGAGGAAAGCGCTCC 62.459 66.667 12.06 9.43 35.51 4.70
1237 1302 2.844072 AAGAGCCGAGGAAAGCGCTC 62.844 60.000 12.06 0.00 38.24 5.03
1238 1303 2.456287 AAAGAGCCGAGGAAAGCGCT 62.456 55.000 2.64 2.64 41.13 5.92
1239 1304 1.972027 GAAAGAGCCGAGGAAAGCGC 61.972 60.000 0.00 0.00 0.00 5.92
1240 1305 1.687494 CGAAAGAGCCGAGGAAAGCG 61.687 60.000 0.00 0.00 0.00 4.68
1241 1306 0.670854 ACGAAAGAGCCGAGGAAAGC 60.671 55.000 0.00 0.00 0.00 3.51
1242 1307 2.094649 ACTACGAAAGAGCCGAGGAAAG 60.095 50.000 0.00 0.00 0.00 2.62
1243 1308 1.891150 ACTACGAAAGAGCCGAGGAAA 59.109 47.619 0.00 0.00 0.00 3.13
1244 1309 1.542492 ACTACGAAAGAGCCGAGGAA 58.458 50.000 0.00 0.00 0.00 3.36
1245 1310 2.408271 TACTACGAAAGAGCCGAGGA 57.592 50.000 0.00 0.00 0.00 3.71
1246 1311 2.859032 GCATACTACGAAAGAGCCGAGG 60.859 54.545 0.00 0.00 0.00 4.63
1247 1312 2.033550 AGCATACTACGAAAGAGCCGAG 59.966 50.000 0.00 0.00 0.00 4.63
1248 1313 2.022195 AGCATACTACGAAAGAGCCGA 58.978 47.619 0.00 0.00 0.00 5.54
1249 1314 2.120232 CAGCATACTACGAAAGAGCCG 58.880 52.381 0.00 0.00 0.00 5.52
1250 1315 3.166489 ACAGCATACTACGAAAGAGCC 57.834 47.619 0.00 0.00 0.00 4.70
1251 1316 4.389077 ACAAACAGCATACTACGAAAGAGC 59.611 41.667 0.00 0.00 0.00 4.09
1252 1317 5.633601 TCACAAACAGCATACTACGAAAGAG 59.366 40.000 0.00 0.00 0.00 2.85
1253 1318 5.404366 GTCACAAACAGCATACTACGAAAGA 59.596 40.000 0.00 0.00 0.00 2.52
1254 1319 5.405571 AGTCACAAACAGCATACTACGAAAG 59.594 40.000 0.00 0.00 0.00 2.62
1266 1362 6.252655 ACGTCAAAAATTAAGTCACAAACAGC 59.747 34.615 0.00 0.00 0.00 4.40
1280 1376 4.356289 CGAAGAACCCAACGTCAAAAATT 58.644 39.130 0.00 0.00 0.00 1.82
1281 1377 3.794138 GCGAAGAACCCAACGTCAAAAAT 60.794 43.478 0.00 0.00 0.00 1.82
1336 1444 3.649023 TGTACACTCCCATACAAACACCT 59.351 43.478 0.00 0.00 0.00 4.00
1384 1492 6.655425 ACGAGTAGCAGCATATGACTCTAATA 59.345 38.462 6.97 0.00 32.91 0.98
1385 1493 5.475220 ACGAGTAGCAGCATATGACTCTAAT 59.525 40.000 6.97 2.84 32.91 1.73
1386 1494 4.822350 ACGAGTAGCAGCATATGACTCTAA 59.178 41.667 6.97 0.00 32.91 2.10
1391 1617 5.048153 TGATACGAGTAGCAGCATATGAC 57.952 43.478 6.97 0.00 0.00 3.06
1435 1661 2.884639 AGAAAACATTCAGACCAACCCG 59.115 45.455 0.00 0.00 0.00 5.28
1484 1714 6.940867 GTCTGGTCCTATCCACTTAAACTTTT 59.059 38.462 0.00 0.00 33.55 2.27
1498 1759 4.896482 GGAGTATGAGTTGTCTGGTCCTAT 59.104 45.833 0.00 0.00 0.00 2.57
1507 1768 5.045797 AGGTAAAAGGGGAGTATGAGTTGTC 60.046 44.000 0.00 0.00 0.00 3.18
1528 1789 3.814504 AAAATGTCATCCAGTCCAGGT 57.185 42.857 0.00 0.00 0.00 4.00
1549 1810 6.153680 ACAGAAACGAGTGATTCTAGATTCCT 59.846 38.462 11.21 8.22 35.28 3.36
1600 1861 2.292267 ACGATGCATGAATTCAGGGAC 58.708 47.619 20.68 11.82 29.39 4.46
1607 1868 3.587923 CCACCAAAACGATGCATGAATT 58.412 40.909 2.46 0.00 0.00 2.17
1630 1891 5.555017 TCCAAGATTCTTGATAGCCTATGC 58.445 41.667 24.71 0.00 37.95 3.14
1712 1973 6.017109 GCATACATCGATATGTTTTGGAGGTT 60.017 38.462 0.00 0.00 44.07 3.50
1760 2032 9.739276 AAAAGACTTTTCTTGGAAAAGGATTTT 57.261 25.926 26.08 25.08 45.89 1.82
1811 2083 8.303876 GTCCATTCAACAAAATACAAGTGGTAT 58.696 33.333 0.00 0.00 44.62 2.73
1812 2084 7.504238 AGTCCATTCAACAAAATACAAGTGGTA 59.496 33.333 0.00 0.00 36.16 3.25
1818 2090 7.424803 CACTCAGTCCATTCAACAAAATACAA 58.575 34.615 0.00 0.00 0.00 2.41
1829 2101 3.307691 GGTCATTCCACTCAGTCCATTCA 60.308 47.826 0.00 0.00 35.97 2.57
1834 2106 1.625818 ACAGGTCATTCCACTCAGTCC 59.374 52.381 0.00 0.00 39.02 3.85
1903 2175 1.070786 GGCTCTGAAACGGTGGACA 59.929 57.895 0.00 0.00 0.00 4.02
1904 2176 0.670854 GAGGCTCTGAAACGGTGGAC 60.671 60.000 7.40 0.00 0.00 4.02
1906 2178 0.671781 CTGAGGCTCTGAAACGGTGG 60.672 60.000 16.72 0.00 0.00 4.61
1909 2181 1.294659 GCACTGAGGCTCTGAAACGG 61.295 60.000 25.68 11.35 0.00 4.44
1910 2182 1.621301 CGCACTGAGGCTCTGAAACG 61.621 60.000 25.68 19.95 0.00 3.60
1994 2266 7.123355 ACATCCAAGGAAAAAGAAACATTCA 57.877 32.000 0.00 0.00 0.00 2.57
2025 2298 6.038161 CACAATGGGCGATTAAAATCTCAGTA 59.962 38.462 0.00 0.00 33.24 2.74
2060 2333 2.079925 AGATCTTCGCCTTTCAAGTGC 58.920 47.619 0.00 0.00 0.00 4.40
2194 2467 7.665559 ACACATTACAGTGGTGACAATATCTTT 59.334 33.333 8.36 0.00 46.06 2.52
2227 2503 5.237779 CAGCATCAGAAGCCAAAACATTTTT 59.762 36.000 0.00 0.00 0.00 1.94
2229 2505 4.312443 CAGCATCAGAAGCCAAAACATTT 58.688 39.130 0.00 0.00 0.00 2.32
2231 2507 2.353406 GCAGCATCAGAAGCCAAAACAT 60.353 45.455 0.00 0.00 0.00 2.71
2233 2509 1.271656 AGCAGCATCAGAAGCCAAAAC 59.728 47.619 0.00 0.00 0.00 2.43
2240 2518 5.814764 ACAGAATAAAGCAGCATCAGAAG 57.185 39.130 0.00 0.00 0.00 2.85
2390 2671 4.352893 ACCCTGCAGTTAGCCAATAAAAT 58.647 39.130 13.81 0.00 44.83 1.82
2606 2948 6.636850 GCATTTAAACAGTCCGCAAATATAGG 59.363 38.462 0.00 0.00 0.00 2.57
2722 3126 9.181805 GCACCTACTTTTGATAAGTTTCTTTTC 57.818 33.333 0.00 0.00 0.00 2.29
2782 3446 3.189910 TGAGTGCATTCAACTCATTCAGC 59.810 43.478 9.78 0.00 35.81 4.26
2792 3456 2.287644 CGTTGAGTGTGAGTGCATTCAA 59.712 45.455 14.07 1.98 40.91 2.69
2904 3570 5.344665 TGCTCTATTAATTTGCGTGTTTTGC 59.655 36.000 0.00 0.00 0.00 3.68
2916 3582 6.091555 TCCCCCACTCTATGCTCTATTAATT 58.908 40.000 0.00 0.00 0.00 1.40
2917 3583 5.665701 TCCCCCACTCTATGCTCTATTAAT 58.334 41.667 0.00 0.00 0.00 1.40
2918 3584 5.087923 TCCCCCACTCTATGCTCTATTAA 57.912 43.478 0.00 0.00 0.00 1.40
2919 3585 4.759793 TCCCCCACTCTATGCTCTATTA 57.240 45.455 0.00 0.00 0.00 0.98
2961 3636 0.032403 TAACTTGTACACGGTGCGCT 59.968 50.000 9.73 0.00 0.00 5.92
2967 3642 8.609176 ACTAATGCAAATATAACTTGTACACGG 58.391 33.333 4.21 0.00 0.00 4.94
3150 3838 4.033776 GGGTGGCTAGGCTGCACA 62.034 66.667 18.18 0.00 34.04 4.57
3201 3891 0.327924 ATTTGATGGAGTGGCGTGGA 59.672 50.000 0.00 0.00 0.00 4.02
3202 3892 0.452987 CATTTGATGGAGTGGCGTGG 59.547 55.000 0.00 0.00 0.00 4.94
3203 3893 1.167851 ACATTTGATGGAGTGGCGTG 58.832 50.000 0.00 0.00 33.60 5.34
3204 3894 2.779755 TACATTTGATGGAGTGGCGT 57.220 45.000 0.00 0.00 33.60 5.68
3249 3939 3.372349 AGGATACAACTGGCAAGATGCAT 60.372 43.478 0.00 0.00 43.05 3.96
3255 3945 2.699954 ACGAAGGATACAACTGGCAAG 58.300 47.619 0.00 0.00 41.41 4.01
3292 3982 8.377681 ACTACGTATAACATGTTCAATTGTTCG 58.622 33.333 15.85 11.59 37.29 3.95
3382 4072 4.635765 GCAAACTTACAGTATGGCAGATCA 59.364 41.667 0.00 0.00 43.62 2.92
3384 4074 4.396166 GTGCAAACTTACAGTATGGCAGAT 59.604 41.667 0.00 0.00 43.62 2.90
3391 4081 3.997762 TGGTCGTGCAAACTTACAGTAT 58.002 40.909 0.00 0.00 0.00 2.12
3408 4099 5.686159 CTGATATTTCAGCTCCAATGGTC 57.314 43.478 0.00 0.00 42.79 4.02
3432 4123 4.708177 ACATGCAGATACAATACCAGTCC 58.292 43.478 0.00 0.00 0.00 3.85
3471 4162 1.909700 ATTCACCGTCCAGCAATTGT 58.090 45.000 7.40 0.00 0.00 2.71
3479 4170 5.640357 GTCATTACAAACTATTCACCGTCCA 59.360 40.000 0.00 0.00 0.00 4.02
3508 4200 9.044150 TCAAATCAAGATTTTCCACAATGTTTC 57.956 29.630 5.34 0.00 38.84 2.78
3514 4206 7.724287 TCACATCAAATCAAGATTTTCCACAA 58.276 30.769 5.34 0.00 38.84 3.33
3545 4237 7.766283 TCATGTACAAAATGCGGAATGAAATA 58.234 30.769 0.00 0.00 0.00 1.40
3546 4238 6.629128 TCATGTACAAAATGCGGAATGAAAT 58.371 32.000 0.00 0.00 0.00 2.17
3549 4241 5.221028 GGATCATGTACAAAATGCGGAATGA 60.221 40.000 0.00 0.00 0.00 2.57
3550 4242 4.977963 GGATCATGTACAAAATGCGGAATG 59.022 41.667 0.00 0.00 0.00 2.67
3551 4243 4.644234 TGGATCATGTACAAAATGCGGAAT 59.356 37.500 0.00 0.00 0.00 3.01
3553 4245 3.615155 TGGATCATGTACAAAATGCGGA 58.385 40.909 0.00 0.00 0.00 5.54
3554 4246 4.572985 ATGGATCATGTACAAAATGCGG 57.427 40.909 0.00 0.00 0.00 5.69
3555 4247 4.671964 CGAATGGATCATGTACAAAATGCG 59.328 41.667 0.00 0.00 0.00 4.73
3556 4248 4.977963 CCGAATGGATCATGTACAAAATGC 59.022 41.667 0.00 2.48 37.49 3.56
3557 4249 6.135290 ACCGAATGGATCATGTACAAAATG 57.865 37.500 0.00 0.00 39.21 2.32
3558 4250 8.463930 AATACCGAATGGATCATGTACAAAAT 57.536 30.769 0.00 0.00 39.21 1.82
3559 4251 7.873719 AATACCGAATGGATCATGTACAAAA 57.126 32.000 0.00 0.00 39.21 2.44
3563 4258 6.347725 GCTGAAATACCGAATGGATCATGTAC 60.348 42.308 0.00 0.00 39.21 2.90
3570 4265 3.884895 TGTGCTGAAATACCGAATGGAT 58.115 40.909 0.00 0.00 39.21 3.41
3572 4267 3.689161 TCTTGTGCTGAAATACCGAATGG 59.311 43.478 0.00 0.00 42.84 3.16
3600 4295 4.004314 TGGTGTAAATGGATTGTGTACCG 58.996 43.478 0.00 0.00 0.00 4.02
3649 4346 6.823678 ACTACAACTTGTAACTGAAGTTCG 57.176 37.500 0.00 0.00 40.83 3.95
3694 4391 7.195374 AGCTGGACTGGAATTTATGTACTTA 57.805 36.000 0.00 0.00 0.00 2.24
3792 4490 1.006102 CTTCAGTGCCTCGTCGGTT 60.006 57.895 0.00 0.00 34.25 4.44
3823 4521 2.498078 GACAGAGAATCCCCTTCGACTT 59.502 50.000 0.00 0.00 38.98 3.01
3824 4522 2.104170 GACAGAGAATCCCCTTCGACT 58.896 52.381 0.00 0.00 38.98 4.18
3831 4529 0.384669 CGTACGGACAGAGAATCCCC 59.615 60.000 7.57 0.00 33.66 4.81
3888 4586 2.373707 GCTGAGGATGCTGGAGGGT 61.374 63.158 0.00 0.00 0.00 4.34
4050 4748 1.078848 GTGGATGCTCGTCAAGGCT 60.079 57.895 0.00 0.00 0.00 4.58


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

AutoCloner maintained by Alex Coulton.