Multiple sequence alignment - TraesCS7D01G423400

Loading Multiple Alignment...

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 TraesCS7D01G423400 chr7D 100.000 6648 0 0 1 6648 543724129 543730776 0.000000e+00 12277.0
1 TraesCS7D01G423400 chr7D 86.986 146 19 0 6503 6648 548324005 548324150 1.480000e-36 165.0
2 TraesCS7D01G423400 chr6B 94.138 3412 116 33 3291 6648 694676963 694680344 0.000000e+00 5116.0
3 TraesCS7D01G423400 chr6B 89.757 1318 91 24 585 1870 694673985 694675290 0.000000e+00 1646.0
4 TraesCS7D01G423400 chr6B 78.763 1601 324 12 4034 5629 151129791 151131380 0.000000e+00 1059.0
5 TraesCS7D01G423400 chr6B 89.757 781 61 9 2465 3237 694675965 694676734 0.000000e+00 981.0
6 TraesCS7D01G423400 chr6B 89.894 564 30 8 1880 2425 694675416 694675970 0.000000e+00 701.0
7 TraesCS7D01G423400 chr6B 81.633 539 70 20 1 531 694673455 694673972 2.870000e-113 420.0
8 TraesCS7D01G423400 chr6B 84.699 183 20 5 1141 1322 151127292 151127467 6.850000e-40 176.0
9 TraesCS7D01G423400 chr7A 96.837 2940 55 19 3281 6193 625638193 625641121 0.000000e+00 4879.0
10 TraesCS7D01G423400 chr7A 91.931 1326 38 15 1880 3159 625636877 625638179 0.000000e+00 1792.0
11 TraesCS7D01G423400 chr7A 89.147 1419 70 32 517 1876 625635363 625636756 0.000000e+00 1690.0
12 TraesCS7D01G423400 chr7A 92.176 818 31 20 5486 6276 625673079 625673890 0.000000e+00 1125.0
13 TraesCS7D01G423400 chr7A 88.235 306 25 6 6350 6648 625641242 625641543 8.200000e-94 355.0
14 TraesCS7D01G423400 chr7A 80.694 461 55 22 2305 2751 625636840 625637280 1.790000e-85 327.0
15 TraesCS7D01G423400 chr7A 82.710 214 30 3 6442 6648 631653557 631653344 4.090000e-42 183.0
16 TraesCS7D01G423400 chr7A 95.349 43 2 0 448 490 625635317 625635359 1.200000e-07 69.4
17 TraesCS7D01G423400 chr6A 79.200 1601 317 14 4034 5629 93813292 93814881 0.000000e+00 1098.0
18 TraesCS7D01G423400 chr6A 84.699 183 20 5 1141 1322 93810416 93810591 6.850000e-40 176.0
19 TraesCS7D01G423400 chr6D 79.151 1602 316 14 4034 5629 78267314 78268903 0.000000e+00 1092.0
20 TraesCS7D01G423400 chr6D 83.938 193 22 6 1141 1332 78264794 78264978 6.850000e-40 176.0
21 TraesCS7D01G423400 chr1B 88.073 327 15 9 6329 6631 169013520 169013846 3.790000e-97 366.0
22 TraesCS7D01G423400 chr1B 93.143 175 10 2 5941 6113 169011256 169011430 8.560000e-64 255.0
23 TraesCS7D01G423400 chr1D 90.875 263 12 6 6398 6648 110904277 110904539 6.380000e-90 342.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7D01G423400 chr7D 543724129 543730776 6647 False 12277.000000 12277 100.0000 1 6648 1 chr7D.!!$F1 6647
1 TraesCS7D01G423400 chr6B 694673455 694680344 6889 False 1772.800000 5116 89.0358 1 6648 5 chr6B.!!$F2 6647
2 TraesCS7D01G423400 chr6B 151127292 151131380 4088 False 617.500000 1059 81.7310 1141 5629 2 chr6B.!!$F1 4488
3 TraesCS7D01G423400 chr7A 625635317 625641543 6226 False 1518.733333 4879 90.3655 448 6648 6 chr7A.!!$F2 6200
4 TraesCS7D01G423400 chr7A 625673079 625673890 811 False 1125.000000 1125 92.1760 5486 6276 1 chr7A.!!$F1 790
5 TraesCS7D01G423400 chr6A 93810416 93814881 4465 False 637.000000 1098 81.9495 1141 5629 2 chr6A.!!$F1 4488
6 TraesCS7D01G423400 chr6D 78264794 78268903 4109 False 634.000000 1092 81.5445 1141 5629 2 chr6D.!!$F1 4488
7 TraesCS7D01G423400 chr1B 169011256 169013846 2590 False 310.500000 366 90.6080 5941 6631 2 chr1B.!!$F1 690

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
294 304 0.037590 CGGGGGTTTTCATGGTCTGA 59.962 55.000 0.00 0.0 0.00 3.27 F
624 648 0.108615 CGAGAAACAGCCGATCCAGT 60.109 55.000 0.00 0.0 0.00 4.00 F
1560 1633 0.107410 TCAAGCTGTGACGTGGGTTT 60.107 50.000 0.00 0.0 0.00 3.27 F
3244 5052 1.065126 GCATGCCTGTATAGATCCCCC 60.065 57.143 6.36 0.0 0.00 5.40 F
3340 5323 0.179181 CTGCTTGCCTTGCATGTACG 60.179 55.000 0.00 0.0 38.76 3.67 F
4369 6352 1.451387 GCCCATAACCACCGGACTG 60.451 63.158 9.46 0.0 0.00 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1560 1633 1.281867 CAGGCACAGGGAATCCTACAA 59.718 52.381 0.0 0.0 42.67 2.41 R
1640 1721 1.852895 GTCCTACGAGCATTTGTAGCG 59.147 52.381 0.0 0.0 39.18 4.26 R
3259 5067 0.190069 TCAGGTAGTGGGGTCAGTGT 59.810 55.000 0.0 0.0 0.00 3.55 R
4582 6565 0.607489 ATCTTTTCGCAGCAGGCACT 60.607 50.000 0.0 0.0 45.17 4.40 R
5273 7256 1.205893 ACAGGGCTCTTCTTCGCTTAG 59.794 52.381 0.0 0.0 0.00 2.18 R
5814 7814 1.917872 AAATAAAGCGAGCAACCCCA 58.082 45.000 0.0 0.0 0.00 4.96 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
17 18 4.865865 GATGAAGGAGGAAGGCGG 57.134 61.111 0.00 0.00 0.00 6.13
31 32 1.290134 AGGCGGGAAAGGAAGAAGAT 58.710 50.000 0.00 0.00 0.00 2.40
32 33 1.065126 AGGCGGGAAAGGAAGAAGATG 60.065 52.381 0.00 0.00 0.00 2.90
33 34 0.735471 GCGGGAAAGGAAGAAGATGC 59.265 55.000 0.00 0.00 0.00 3.91
34 35 1.383523 CGGGAAAGGAAGAAGATGCC 58.616 55.000 0.00 0.00 0.00 4.40
35 36 1.065126 CGGGAAAGGAAGAAGATGCCT 60.065 52.381 0.00 0.00 0.00 4.75
48 50 3.902881 AGATGCCTTAGTTGACCTCAG 57.097 47.619 0.00 0.00 0.00 3.35
57 59 1.964223 AGTTGACCTCAGTGTGACGAT 59.036 47.619 0.00 0.00 0.00 3.73
59 61 1.328279 TGACCTCAGTGTGACGATGT 58.672 50.000 0.00 0.00 0.00 3.06
62 64 0.456824 CCTCAGTGTGACGATGTCGG 60.457 60.000 7.38 0.00 44.95 4.79
63 65 0.241213 CTCAGTGTGACGATGTCGGT 59.759 55.000 7.38 0.00 44.95 4.69
64 66 0.039527 TCAGTGTGACGATGTCGGTG 60.040 55.000 7.38 0.00 44.95 4.94
80 82 2.042831 GTGATGAGGCCAGTGGTGC 61.043 63.158 11.74 0.97 0.00 5.01
101 103 1.753073 AGGCCATTGTTGCTAGAATGC 59.247 47.619 5.01 7.81 34.56 3.56
108 110 6.436261 CCATTGTTGCTAGAATGCTAATGAG 58.564 40.000 11.65 0.00 34.56 2.90
148 150 2.412870 CGCGCTTGTATGATTGGGATA 58.587 47.619 5.56 0.00 0.00 2.59
149 151 3.002791 CGCGCTTGTATGATTGGGATAT 58.997 45.455 5.56 0.00 0.00 1.63
156 158 2.099141 ATGATTGGGATATGGCGACG 57.901 50.000 0.00 0.00 0.00 5.12
170 172 2.434359 GACGCCTTGACTTCCCCG 60.434 66.667 0.00 0.00 0.00 5.73
172 174 3.702048 CGCCTTGACTTCCCCGGA 61.702 66.667 0.73 0.00 0.00 5.14
187 189 2.028484 GGATTACGATGGCGGCGA 59.972 61.111 12.98 0.00 43.17 5.54
190 192 1.626654 GATTACGATGGCGGCGATGG 61.627 60.000 12.98 3.60 43.17 3.51
204 206 1.202336 GCGATGGAAAATCAAGGCCTG 60.202 52.381 5.69 0.00 0.00 4.85
205 207 1.406539 CGATGGAAAATCAAGGCCTGG 59.593 52.381 5.69 1.80 0.00 4.45
210 212 1.743394 GAAAATCAAGGCCTGGTACGG 59.257 52.381 5.69 0.00 0.00 4.02
216 218 4.832608 GGCCTGGTACGGCGGAAG 62.833 72.222 13.24 0.00 45.98 3.46
232 234 1.454201 GAAGGAAGAAAAGGAGGCGG 58.546 55.000 0.00 0.00 0.00 6.13
235 237 1.308783 GGAAGAAAAGGAGGCGGCAG 61.309 60.000 13.08 0.00 0.00 4.85
246 248 1.449778 GGCGGCAGAAGAGGGTAAC 60.450 63.158 3.07 0.00 0.00 2.50
251 253 1.221021 CAGAAGAGGGTAACGGGGC 59.779 63.158 0.00 0.00 37.60 5.80
259 269 2.202837 GTAACGGGGCGGCACTAG 60.203 66.667 10.45 0.00 0.00 2.57
260 270 3.463585 TAACGGGGCGGCACTAGG 61.464 66.667 10.45 0.00 0.00 3.02
269 279 1.817209 CGGCACTAGGAGAGGAACC 59.183 63.158 0.00 0.00 0.00 3.62
272 282 1.562783 GCACTAGGAGAGGAACCAGT 58.437 55.000 0.00 0.00 0.00 4.00
275 285 1.903183 ACTAGGAGAGGAACCAGTTGC 59.097 52.381 0.00 0.00 0.00 4.17
276 286 0.895530 TAGGAGAGGAACCAGTTGCG 59.104 55.000 0.00 0.00 35.97 4.85
278 288 1.376037 GAGAGGAACCAGTTGCGGG 60.376 63.158 0.00 0.00 35.97 6.13
292 302 1.304134 GCGGGGGTTTTCATGGTCT 60.304 57.895 0.00 0.00 0.00 3.85
293 303 1.595093 GCGGGGGTTTTCATGGTCTG 61.595 60.000 0.00 0.00 0.00 3.51
294 304 0.037590 CGGGGGTTTTCATGGTCTGA 59.962 55.000 0.00 0.00 0.00 3.27
295 305 1.839424 GGGGGTTTTCATGGTCTGAG 58.161 55.000 0.00 0.00 34.68 3.35
296 306 1.075536 GGGGGTTTTCATGGTCTGAGT 59.924 52.381 0.00 0.00 34.68 3.41
297 307 2.490902 GGGGGTTTTCATGGTCTGAGTT 60.491 50.000 0.00 0.00 34.68 3.01
298 308 3.230976 GGGGTTTTCATGGTCTGAGTTT 58.769 45.455 0.00 0.00 34.68 2.66
299 309 3.255888 GGGGTTTTCATGGTCTGAGTTTC 59.744 47.826 0.00 0.00 34.68 2.78
300 310 3.058224 GGGTTTTCATGGTCTGAGTTTCG 60.058 47.826 0.00 0.00 34.68 3.46
301 311 3.813166 GGTTTTCATGGTCTGAGTTTCGA 59.187 43.478 0.00 0.00 34.68 3.71
302 312 4.319549 GGTTTTCATGGTCTGAGTTTCGAC 60.320 45.833 0.00 0.00 34.68 4.20
307 317 2.528041 GGTCTGAGTTTCGACCTTGT 57.472 50.000 0.00 0.00 44.90 3.16
308 318 3.655276 GGTCTGAGTTTCGACCTTGTA 57.345 47.619 0.00 0.00 44.90 2.41
309 319 3.315418 GGTCTGAGTTTCGACCTTGTAC 58.685 50.000 0.00 0.00 44.90 2.90
316 326 2.357327 TTCGACCTTGTACATCACCG 57.643 50.000 0.00 0.00 0.00 4.94
319 329 1.076332 GACCTTGTACATCACCGTGC 58.924 55.000 0.00 0.00 0.00 5.34
325 335 1.222300 GTACATCACCGTGCACAACA 58.778 50.000 18.64 0.00 0.00 3.33
326 336 1.804151 GTACATCACCGTGCACAACAT 59.196 47.619 18.64 0.00 0.00 2.71
327 337 1.317613 ACATCACCGTGCACAACATT 58.682 45.000 18.64 0.00 0.00 2.71
328 338 1.266718 ACATCACCGTGCACAACATTC 59.733 47.619 18.64 0.00 0.00 2.67
329 339 0.516877 ATCACCGTGCACAACATTCG 59.483 50.000 18.64 0.00 0.00 3.34
331 341 1.525077 ACCGTGCACAACATTCGGT 60.525 52.632 18.64 13.59 43.99 4.69
332 342 0.249953 ACCGTGCACAACATTCGGTA 60.250 50.000 18.64 0.00 46.14 4.02
333 343 0.165079 CCGTGCACAACATTCGGTAC 59.835 55.000 18.64 0.00 34.17 3.34
334 344 0.862490 CGTGCACAACATTCGGTACA 59.138 50.000 18.64 0.00 0.00 2.90
335 345 1.463056 CGTGCACAACATTCGGTACAT 59.537 47.619 18.64 0.00 0.00 2.29
336 346 2.724533 CGTGCACAACATTCGGTACATG 60.725 50.000 18.64 0.00 0.00 3.21
337 347 1.809547 TGCACAACATTCGGTACATGG 59.190 47.619 0.00 0.00 0.00 3.66
338 348 1.132262 GCACAACATTCGGTACATGGG 59.868 52.381 0.00 0.00 0.00 4.00
339 349 2.432444 CACAACATTCGGTACATGGGT 58.568 47.619 0.00 0.00 0.00 4.51
349 359 0.457035 GTACATGGGTAGCGACGGAA 59.543 55.000 0.00 0.00 0.00 4.30
402 413 3.256960 GGCTCCTGACACCCCCAA 61.257 66.667 0.00 0.00 0.00 4.12
406 417 4.344865 CCTGACACCCCCAACCCG 62.345 72.222 0.00 0.00 0.00 5.28
407 418 3.246112 CTGACACCCCCAACCCGA 61.246 66.667 0.00 0.00 0.00 5.14
408 419 2.773053 TGACACCCCCAACCCGAA 60.773 61.111 0.00 0.00 0.00 4.30
411 422 1.456145 ACACCCCCAACCCGAAAAC 60.456 57.895 0.00 0.00 0.00 2.43
412 423 2.199257 ACCCCCAACCCGAAAACC 59.801 61.111 0.00 0.00 0.00 3.27
414 425 2.204461 CCCCCAACCCGAAAACCAC 61.204 63.158 0.00 0.00 0.00 4.16
415 426 2.204461 CCCCAACCCGAAAACCACC 61.204 63.158 0.00 0.00 0.00 4.61
416 427 2.204461 CCCAACCCGAAAACCACCC 61.204 63.158 0.00 0.00 0.00 4.61
439 455 6.294731 CCCCTAGAAGTTTCAAACAAATCCTG 60.295 42.308 2.41 0.00 0.00 3.86
445 461 9.093458 AGAAGTTTCAAACAAATCCTGGAATAT 57.907 29.630 0.00 0.00 0.00 1.28
537 553 3.336566 GGAACCAAACCGACCACG 58.663 61.111 0.00 0.00 39.43 4.94
538 554 2.635338 GAACCAAACCGACCACGC 59.365 61.111 0.00 0.00 38.29 5.34
539 555 2.900167 GAACCAAACCGACCACGCC 61.900 63.158 0.00 0.00 38.29 5.68
540 556 3.700831 AACCAAACCGACCACGCCA 62.701 57.895 0.00 0.00 38.29 5.69
541 557 3.656045 CCAAACCGACCACGCCAC 61.656 66.667 0.00 0.00 38.29 5.01
542 558 2.590575 CAAACCGACCACGCCACT 60.591 61.111 0.00 0.00 38.29 4.00
543 559 2.280592 AAACCGACCACGCCACTC 60.281 61.111 0.00 0.00 38.29 3.51
544 560 3.819877 AAACCGACCACGCCACTCC 62.820 63.158 0.00 0.00 38.29 3.85
622 646 0.606096 TTCGAGAAACAGCCGATCCA 59.394 50.000 0.00 0.00 32.07 3.41
624 648 0.108615 CGAGAAACAGCCGATCCAGT 60.109 55.000 0.00 0.00 0.00 4.00
659 683 2.443952 AGATCCCATCCGACGGCA 60.444 61.111 9.66 0.00 0.00 5.69
735 759 3.720193 GCTCACGCCACTGTGCTG 61.720 66.667 1.29 0.00 39.73 4.41
736 760 3.720193 CTCACGCCACTGTGCTGC 61.720 66.667 1.29 0.37 39.73 5.25
771 795 1.154263 CCGTCCACTCGTTCGTCTC 60.154 63.158 0.00 0.00 0.00 3.36
784 808 0.705253 TCGTCTCCCCTCTTTCTCCT 59.295 55.000 0.00 0.00 0.00 3.69
786 810 1.491668 GTCTCCCCTCTTTCTCCTCC 58.508 60.000 0.00 0.00 0.00 4.30
855 890 2.204291 ACCATTCCCTCCAGCCCA 60.204 61.111 0.00 0.00 0.00 5.36
863 898 1.770324 CCTCCAGCCCAAAACCTCT 59.230 57.895 0.00 0.00 0.00 3.69
865 900 1.539157 CTCCAGCCCAAAACCTCTTC 58.461 55.000 0.00 0.00 0.00 2.87
1071 1129 1.152139 GATGGAGGAGGAGGGAGGG 60.152 68.421 0.00 0.00 0.00 4.30
1088 1146 2.308722 GGGAGATGGTGCTTGGGGA 61.309 63.158 0.00 0.00 0.00 4.81
1092 1150 1.000396 GATGGTGCTTGGGGAAGCT 60.000 57.895 8.18 0.00 45.66 3.74
1095 1153 2.436109 GTGCTTGGGGAAGCTGGA 59.564 61.111 8.18 0.00 45.66 3.86
1128 1186 4.872574 AGCGAGGGCGGGGGATTA 62.873 66.667 0.00 0.00 46.35 1.75
1185 1249 2.123251 ATCGAGGGGATGCTCCGT 60.123 61.111 0.00 0.00 37.43 4.69
1343 1408 1.975680 TCCGTCCTCCTACTTTTGCTT 59.024 47.619 0.00 0.00 0.00 3.91
1344 1409 2.028385 TCCGTCCTCCTACTTTTGCTTC 60.028 50.000 0.00 0.00 0.00 3.86
1389 1454 1.737838 TGTTGGAATCGATGCCACTC 58.262 50.000 25.62 19.90 33.01 3.51
1398 1463 0.596083 CGATGCCACTCAGGATCGAC 60.596 60.000 9.44 0.00 43.75 4.20
1424 1497 8.726068 CCAGAACTTAATTTTTGTTTGTTTGGT 58.274 29.630 0.00 0.00 0.00 3.67
1443 1516 2.876550 GGTTTGTTACGTCCTGAGCTTT 59.123 45.455 0.00 0.00 0.00 3.51
1477 1550 5.256474 ACTTGTAGCAATAGAAATGTGGCT 58.744 37.500 0.00 0.00 35.50 4.75
1491 1564 3.297134 TGTGGCTTAGATTGGGGAATC 57.703 47.619 0.00 0.00 0.00 2.52
1522 1595 4.049546 ACACTCTACTTGTTAACACGCA 57.950 40.909 8.07 0.00 0.00 5.24
1560 1633 0.107410 TCAAGCTGTGACGTGGGTTT 60.107 50.000 0.00 0.00 0.00 3.27
1602 1682 3.921119 TTGTGCTTATTTGGCTGTGAG 57.079 42.857 0.00 0.00 0.00 3.51
1640 1721 7.153478 CATTGTTTGCTTTCTGTTAACAGTC 57.847 36.000 29.83 19.04 44.12 3.51
1668 1749 1.471119 TGCTCGTAGGACTTCCGATT 58.529 50.000 0.00 0.00 42.08 3.34
1694 1775 5.119931 TGTGTGCACCAAATAGATTGAAC 57.880 39.130 15.69 1.04 41.85 3.18
1716 1797 8.400186 TGAACTTAGTAACTTAGCACCAAAAAC 58.600 33.333 0.00 0.00 0.00 2.43
1871 2711 5.641636 AGTTTTTGGACCATGTTGTTTGAAC 59.358 36.000 0.00 0.00 0.00 3.18
1876 2716 3.058914 GGACCATGTTGTTTGAACTCTCG 60.059 47.826 0.00 0.00 0.00 4.04
2030 3648 9.591792 CAAATATTTGTCATGACAGTCTCTAGA 57.408 33.333 26.48 8.48 42.94 2.43
2032 3650 9.814899 AATATTTGTCATGACAGTCTCTAGAAG 57.185 33.333 26.48 0.00 42.94 2.85
2075 3693 7.824779 GTGGACCTGATCAGTTAAAGAAGTATT 59.175 37.037 21.11 0.00 0.00 1.89
2135 3753 2.567862 TCCCCCAGGTGTTTGATGATA 58.432 47.619 0.00 0.00 0.00 2.15
2181 3802 7.039882 GCACTCTTCAATGAATCATGGAAATT 58.960 34.615 13.50 0.00 33.94 1.82
2203 3824 8.770010 AATTATACCTGTAGAGTTAGAGCAGT 57.230 34.615 0.00 0.00 0.00 4.40
2214 3835 6.349300 AGAGTTAGAGCAGTTTGTGAAAAGA 58.651 36.000 0.00 0.00 0.00 2.52
2230 3851 8.433421 TGTGAAAAGAGACTTTAAGGTAGTTG 57.567 34.615 0.00 0.00 0.00 3.16
2264 3885 5.301835 AGATGAGCCATAAGTGCATAACT 57.698 39.130 0.00 0.00 42.60 2.24
2565 4239 5.159273 TGTCTGTCATGTTAAGTATGCCA 57.841 39.130 0.00 0.00 0.00 4.92
2617 4291 8.057742 CAGTTGACAATGTTATTTTGCACTTTC 58.942 33.333 0.00 0.00 0.00 2.62
2653 4327 8.725148 CATGGAAAATAATGATACCTGTAGAGC 58.275 37.037 0.00 0.00 0.00 4.09
2820 4494 2.618241 TGTGAGTTGTGACCAATTCTGC 59.382 45.455 0.00 0.00 37.96 4.26
2877 4551 6.439058 AGTTCTCTTAAGTACCATCTGCTCTT 59.561 38.462 1.63 0.00 0.00 2.85
3021 4805 5.590530 ACTTGGACAACAAATTTAGTGCA 57.409 34.783 7.41 7.41 38.91 4.57
3102 4910 6.238648 AGTTTCTGATAGAAAACGAATGGGT 58.761 36.000 5.64 0.00 44.84 4.51
3194 5002 1.610554 ATGTGCCAATCTTGCTGGGC 61.611 55.000 0.00 0.00 46.58 5.36
3196 5004 2.890371 GCCAATCTTGCTGGGCAG 59.110 61.111 0.00 0.00 45.70 4.85
3211 5019 5.834742 TGCTGGGCAGATGACAATTATTTAT 59.165 36.000 0.00 0.00 33.32 1.40
3242 5050 2.983229 CAGCATGCCTGTATAGATCCC 58.017 52.381 15.66 0.00 36.79 3.85
3243 5051 1.912043 AGCATGCCTGTATAGATCCCC 59.088 52.381 15.66 0.00 0.00 4.81
3244 5052 1.065126 GCATGCCTGTATAGATCCCCC 60.065 57.143 6.36 0.00 0.00 5.40
3261 5069 1.952621 CCCCCTCCTCTTTACAGACA 58.047 55.000 0.00 0.00 0.00 3.41
3262 5070 1.555533 CCCCCTCCTCTTTACAGACAC 59.444 57.143 0.00 0.00 0.00 3.67
3263 5071 2.541466 CCCCTCCTCTTTACAGACACT 58.459 52.381 0.00 0.00 0.00 3.55
3264 5072 2.234908 CCCCTCCTCTTTACAGACACTG 59.765 54.545 0.00 0.00 37.52 3.66
3265 5073 3.165875 CCCTCCTCTTTACAGACACTGA 58.834 50.000 5.76 0.00 35.18 3.41
3266 5074 3.056465 CCCTCCTCTTTACAGACACTGAC 60.056 52.174 5.76 0.00 35.18 3.51
3267 5075 3.056465 CCTCCTCTTTACAGACACTGACC 60.056 52.174 5.76 0.00 35.18 4.02
3268 5076 2.897969 TCCTCTTTACAGACACTGACCC 59.102 50.000 5.76 0.00 35.18 4.46
3269 5077 2.028020 CCTCTTTACAGACACTGACCCC 60.028 54.545 5.76 0.00 35.18 4.95
3270 5078 2.632996 CTCTTTACAGACACTGACCCCA 59.367 50.000 5.76 0.00 35.18 4.96
3271 5079 2.367567 TCTTTACAGACACTGACCCCAC 59.632 50.000 5.76 0.00 35.18 4.61
3272 5080 2.097110 TTACAGACACTGACCCCACT 57.903 50.000 5.76 0.00 35.18 4.00
3273 5081 2.984435 TACAGACACTGACCCCACTA 57.016 50.000 5.76 0.00 35.18 2.74
3274 5082 1.339097 ACAGACACTGACCCCACTAC 58.661 55.000 5.76 0.00 35.18 2.73
3275 5083 0.608640 CAGACACTGACCCCACTACC 59.391 60.000 0.00 0.00 32.44 3.18
3276 5084 0.487772 AGACACTGACCCCACTACCT 59.512 55.000 0.00 0.00 0.00 3.08
3277 5085 0.608640 GACACTGACCCCACTACCTG 59.391 60.000 0.00 0.00 0.00 4.00
3278 5086 0.190069 ACACTGACCCCACTACCTGA 59.810 55.000 0.00 0.00 0.00 3.86
3279 5087 1.348064 CACTGACCCCACTACCTGAA 58.652 55.000 0.00 0.00 0.00 3.02
3340 5323 0.179181 CTGCTTGCCTTGCATGTACG 60.179 55.000 0.00 0.00 38.76 3.67
3569 5552 9.646522 ATTATTTACTGAAGCATATTCCAAGGT 57.353 29.630 0.00 0.00 0.00 3.50
3696 5679 5.231147 TGAATTTGTTAAAGTCGTTTGCTGC 59.769 36.000 0.00 0.00 38.25 5.25
3929 5912 3.549794 AGTGCTGCTCTTTTCTTGAACT 58.450 40.909 0.00 0.00 0.00 3.01
4369 6352 1.451387 GCCCATAACCACCGGACTG 60.451 63.158 9.46 0.00 0.00 3.51
4582 6565 3.004171 GACTACTCGAGCTCTTGAGACA 58.996 50.000 21.23 10.13 42.44 3.41
5118 7101 3.421919 TCTTGATGTGAGCATGGACAA 57.578 42.857 0.00 0.00 35.07 3.18
5693 7676 6.121590 ACCAAAGCTTCCATGAAAACAAATT 58.878 32.000 0.00 0.00 0.00 1.82
5828 7830 0.109723 TAAACTGGGGTTGCTCGCTT 59.890 50.000 0.00 0.00 35.63 4.68
5832 7834 1.271926 ACTGGGGTTGCTCGCTTTATT 60.272 47.619 0.00 0.00 0.00 1.40
5842 7844 5.095691 TGCTCGCTTTATTTAGCTAATGC 57.904 39.130 7.08 6.46 39.03 3.56
6043 8051 6.873997 TCTGTGAAACCGTGATAGTTATGAT 58.126 36.000 0.00 0.00 34.36 2.45
6126 8138 5.311844 AGTTTTCCTCTCAGGTAAGCTTT 57.688 39.130 3.20 0.00 33.67 3.51
6128 8140 6.838382 AGTTTTCCTCTCAGGTAAGCTTTTA 58.162 36.000 3.20 0.00 33.67 1.52
6129 8141 6.937465 AGTTTTCCTCTCAGGTAAGCTTTTAG 59.063 38.462 3.20 0.00 33.67 1.85
6130 8142 6.435292 TTTCCTCTCAGGTAAGCTTTTAGT 57.565 37.500 3.20 0.00 36.53 2.24
6132 8144 5.794894 TCCTCTCAGGTAAGCTTTTAGTTG 58.205 41.667 3.20 0.00 36.53 3.16
6133 8145 5.307196 TCCTCTCAGGTAAGCTTTTAGTTGT 59.693 40.000 3.20 0.00 36.53 3.32
6174 8195 6.431198 TTGTCTGTTTTCCTCTTGTTGTAC 57.569 37.500 0.00 0.00 0.00 2.90
6230 8852 6.262944 ACAATGCTGAACTGTCATGTTCTAAA 59.737 34.615 13.05 3.57 44.63 1.85
6253 8875 5.219633 ACGCCATTTCTGTAACATTTTGAC 58.780 37.500 0.00 0.00 0.00 3.18
6269 10188 5.534207 TTTTGACACTTCCAAGATTGCAT 57.466 34.783 0.00 0.00 0.00 3.96
6299 10243 3.821033 GTGTAACAGGGAAATTGCTGTCT 59.179 43.478 0.00 0.00 36.32 3.41
6300 10244 5.001232 GTGTAACAGGGAAATTGCTGTCTA 58.999 41.667 0.00 0.00 36.32 2.59
6347 10317 7.041508 GGAGATCTACAATTCCATTACAGCAAG 60.042 40.741 0.00 0.00 0.00 4.01
6348 10324 7.341805 AGATCTACAATTCCATTACAGCAAGT 58.658 34.615 0.00 0.00 0.00 3.16
6489 10486 2.904866 GCGGTGCCAGTGAACCAA 60.905 61.111 13.46 0.00 36.14 3.67
6567 10564 2.093869 CCCGTCTAAAACCTCGAATCCA 60.094 50.000 0.00 0.00 0.00 3.41
6600 10597 1.684049 CTCCTCCGGGAACAGCTCT 60.684 63.158 0.00 0.00 41.69 4.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 1.131303 TTTCCCGCCTTCCTCCTTCA 61.131 55.000 0.00 0.00 0.00 3.02
12 13 1.065126 CATCTTCTTCCTTTCCCGCCT 60.065 52.381 0.00 0.00 0.00 5.52
13 14 1.383523 CATCTTCTTCCTTTCCCGCC 58.616 55.000 0.00 0.00 0.00 6.13
17 18 4.849518 ACTAAGGCATCTTCTTCCTTTCC 58.150 43.478 0.00 0.00 40.42 3.13
31 32 2.047061 ACACTGAGGTCAACTAAGGCA 58.953 47.619 0.00 0.00 31.16 4.75
32 33 2.037251 TCACACTGAGGTCAACTAAGGC 59.963 50.000 0.00 0.00 31.16 4.35
33 34 3.654414 GTCACACTGAGGTCAACTAAGG 58.346 50.000 0.00 0.00 31.16 2.69
34 35 3.004419 TCGTCACACTGAGGTCAACTAAG 59.996 47.826 0.00 0.00 34.22 2.18
35 36 2.953648 TCGTCACACTGAGGTCAACTAA 59.046 45.455 0.00 0.00 34.22 2.24
48 50 0.992072 CATCACCGACATCGTCACAC 59.008 55.000 0.00 0.00 37.74 3.82
57 59 1.913262 ACTGGCCTCATCACCGACA 60.913 57.895 3.32 0.00 0.00 4.35
59 61 2.659063 CCACTGGCCTCATCACCGA 61.659 63.158 3.32 0.00 0.00 4.69
62 64 2.042831 GCACCACTGGCCTCATCAC 61.043 63.158 3.32 0.00 0.00 3.06
63 65 2.352422 GCACCACTGGCCTCATCA 59.648 61.111 3.32 0.00 0.00 3.07
64 66 1.748122 CTGCACCACTGGCCTCATC 60.748 63.158 3.32 0.00 0.00 2.92
80 82 2.480759 GCATTCTAGCAACAATGGCCTG 60.481 50.000 3.32 0.00 31.65 4.85
84 86 6.381481 TCATTAGCATTCTAGCAACAATGG 57.619 37.500 4.57 0.00 34.25 3.16
108 110 0.179034 CTTGTAGGATCAGCAGGGGC 60.179 60.000 0.00 0.00 41.61 5.80
113 115 1.519234 CGCGCTTGTAGGATCAGCA 60.519 57.895 5.56 0.00 0.00 4.41
116 118 1.218047 AAGCGCGCTTGTAGGATCA 59.782 52.632 42.62 0.00 34.60 2.92
156 158 0.544697 TAATCCGGGGAAGTCAAGGC 59.455 55.000 0.00 0.00 0.00 4.35
166 168 2.357034 CGCCATCGTAATCCGGGG 60.357 66.667 0.00 0.00 37.11 5.73
170 172 1.374252 ATCGCCGCCATCGTAATCC 60.374 57.895 0.00 0.00 0.00 3.01
172 174 1.667830 CCATCGCCGCCATCGTAAT 60.668 57.895 0.00 0.00 0.00 1.89
183 185 0.103026 GGCCTTGATTTTCCATCGCC 59.897 55.000 0.00 0.00 0.00 5.54
187 189 2.629017 ACCAGGCCTTGATTTTCCAT 57.371 45.000 11.55 0.00 0.00 3.41
190 192 1.743394 CCGTACCAGGCCTTGATTTTC 59.257 52.381 11.55 0.00 0.00 2.29
204 206 0.037046 TTTCTTCCTTCCGCCGTACC 60.037 55.000 0.00 0.00 0.00 3.34
205 207 1.730612 CTTTTCTTCCTTCCGCCGTAC 59.269 52.381 0.00 0.00 0.00 3.67
210 212 1.454201 CCTCCTTTTCTTCCTTCCGC 58.546 55.000 0.00 0.00 0.00 5.54
216 218 1.303317 TGCCGCCTCCTTTTCTTCC 60.303 57.895 0.00 0.00 0.00 3.46
232 234 1.221021 CCCCGTTACCCTCTTCTGC 59.779 63.158 0.00 0.00 0.00 4.26
235 237 2.186125 CGCCCCGTTACCCTCTTC 59.814 66.667 0.00 0.00 0.00 2.87
251 253 0.970937 TGGTTCCTCTCCTAGTGCCG 60.971 60.000 0.00 0.00 0.00 5.69
259 269 1.376037 CCGCAACTGGTTCCTCTCC 60.376 63.158 0.00 0.00 0.00 3.71
260 270 1.376037 CCCGCAACTGGTTCCTCTC 60.376 63.158 0.00 0.00 0.00 3.20
269 279 0.038343 CATGAAAACCCCCGCAACTG 60.038 55.000 0.00 0.00 0.00 3.16
272 282 1.152440 ACCATGAAAACCCCCGCAA 60.152 52.632 0.00 0.00 0.00 4.85
275 285 0.037590 TCAGACCATGAAAACCCCCG 59.962 55.000 0.00 0.00 34.02 5.73
276 286 1.075536 ACTCAGACCATGAAAACCCCC 59.924 52.381 0.00 0.00 37.52 5.40
278 288 3.058224 CGAAACTCAGACCATGAAAACCC 60.058 47.826 0.00 0.00 37.52 4.11
292 302 4.304110 GTGATGTACAAGGTCGAAACTCA 58.696 43.478 0.00 0.00 0.00 3.41
293 303 3.678548 GGTGATGTACAAGGTCGAAACTC 59.321 47.826 0.00 0.00 0.00 3.01
294 304 3.660865 GGTGATGTACAAGGTCGAAACT 58.339 45.455 0.00 0.00 0.00 2.66
295 305 2.410730 CGGTGATGTACAAGGTCGAAAC 59.589 50.000 0.00 0.00 0.00 2.78
296 306 2.036217 ACGGTGATGTACAAGGTCGAAA 59.964 45.455 15.39 0.00 0.00 3.46
297 307 1.614903 ACGGTGATGTACAAGGTCGAA 59.385 47.619 15.39 0.00 0.00 3.71
298 308 1.068125 CACGGTGATGTACAAGGTCGA 60.068 52.381 0.74 0.00 0.00 4.20
299 309 1.346365 CACGGTGATGTACAAGGTCG 58.654 55.000 0.74 5.12 0.00 4.79
300 310 1.076332 GCACGGTGATGTACAAGGTC 58.924 55.000 13.29 0.00 0.00 3.85
301 311 0.394938 TGCACGGTGATGTACAAGGT 59.605 50.000 13.29 0.00 0.00 3.50
302 312 0.796312 GTGCACGGTGATGTACAAGG 59.204 55.000 13.29 0.00 35.48 3.61
303 313 1.507562 TGTGCACGGTGATGTACAAG 58.492 50.000 13.29 0.00 41.47 3.16
304 314 3.688553 TGTGCACGGTGATGTACAA 57.311 47.368 13.29 0.00 41.47 2.41
305 315 1.222300 GTTGTGCACGGTGATGTACA 58.778 50.000 13.29 0.00 42.52 2.90
306 316 1.222300 TGTTGTGCACGGTGATGTAC 58.778 50.000 13.29 5.43 35.91 2.90
307 317 2.177394 ATGTTGTGCACGGTGATGTA 57.823 45.000 13.29 0.00 0.00 2.29
308 318 1.266718 GAATGTTGTGCACGGTGATGT 59.733 47.619 13.29 0.00 0.00 3.06
309 319 1.725611 CGAATGTTGTGCACGGTGATG 60.726 52.381 13.29 0.00 0.00 3.07
316 326 2.414029 CCATGTACCGAATGTTGTGCAC 60.414 50.000 10.75 10.75 29.89 4.57
319 329 2.432444 ACCCATGTACCGAATGTTGTG 58.568 47.619 0.00 0.00 0.00 3.33
325 335 1.068127 GTCGCTACCCATGTACCGAAT 59.932 52.381 0.00 0.00 36.95 3.34
326 336 0.457035 GTCGCTACCCATGTACCGAA 59.543 55.000 0.00 0.00 36.95 4.30
327 337 1.717791 CGTCGCTACCCATGTACCGA 61.718 60.000 0.00 0.00 33.77 4.69
328 338 1.298863 CGTCGCTACCCATGTACCG 60.299 63.158 0.00 0.00 0.00 4.02
329 339 1.066918 CCGTCGCTACCCATGTACC 59.933 63.158 0.00 0.00 0.00 3.34
331 341 0.457035 GTTCCGTCGCTACCCATGTA 59.543 55.000 0.00 0.00 0.00 2.29
332 342 1.217244 GTTCCGTCGCTACCCATGT 59.783 57.895 0.00 0.00 0.00 3.21
333 343 1.876714 CGTTCCGTCGCTACCCATG 60.877 63.158 0.00 0.00 0.00 3.66
334 344 2.493030 CGTTCCGTCGCTACCCAT 59.507 61.111 0.00 0.00 0.00 4.00
335 345 3.751246 CCGTTCCGTCGCTACCCA 61.751 66.667 0.00 0.00 0.00 4.51
336 346 3.407046 CTCCGTTCCGTCGCTACCC 62.407 68.421 0.00 0.00 0.00 3.69
337 347 2.101770 CTCCGTTCCGTCGCTACC 59.898 66.667 0.00 0.00 0.00 3.18
338 348 2.101770 CCTCCGTTCCGTCGCTAC 59.898 66.667 0.00 0.00 0.00 3.58
339 349 2.046023 TCCTCCGTTCCGTCGCTA 60.046 61.111 0.00 0.00 0.00 4.26
349 359 4.329831 GAGCACTCTCTCCTCCGT 57.670 61.111 0.00 0.00 36.42 4.69
379 389 1.303643 GGTGTCAGGAGCCCCAAAG 60.304 63.158 0.00 0.00 33.88 2.77
394 405 2.204461 GGTTTTCGGGTTGGGGGTG 61.204 63.158 0.00 0.00 0.00 4.61
402 413 0.474273 TCTAGGGGTGGTTTTCGGGT 60.474 55.000 0.00 0.00 0.00 5.28
406 417 4.466827 TGAAACTTCTAGGGGTGGTTTTC 58.533 43.478 0.00 0.00 31.51 2.29
407 418 4.529716 TGAAACTTCTAGGGGTGGTTTT 57.470 40.909 0.00 0.00 31.51 2.43
408 419 4.529716 TTGAAACTTCTAGGGGTGGTTT 57.470 40.909 0.00 0.00 33.60 3.27
411 422 3.827722 TGTTTGAAACTTCTAGGGGTGG 58.172 45.455 9.69 0.00 0.00 4.61
412 423 5.845391 TTTGTTTGAAACTTCTAGGGGTG 57.155 39.130 9.69 0.00 0.00 4.61
414 425 5.775195 AGGATTTGTTTGAAACTTCTAGGGG 59.225 40.000 9.69 0.00 0.00 4.79
415 426 6.294731 CCAGGATTTGTTTGAAACTTCTAGGG 60.295 42.308 9.69 0.05 0.00 3.53
416 427 6.490040 TCCAGGATTTGTTTGAAACTTCTAGG 59.510 38.462 9.69 9.27 0.00 3.02
439 455 5.991328 TTCAGCTCAATTCGTCATATTCC 57.009 39.130 0.00 0.00 0.00 3.01
445 461 5.239306 AGTTGAATTTCAGCTCAATTCGTCA 59.761 36.000 17.42 4.52 41.66 4.35
523 539 4.178169 TGGCGTGGTCGGTTTGGT 62.178 61.111 0.00 0.00 37.56 3.67
613 637 3.148279 GGACGGACTGGATCGGCT 61.148 66.667 0.00 0.00 34.37 5.52
637 661 3.233980 TCGGATGGGATCTGCGGG 61.234 66.667 0.00 0.00 35.60 6.13
771 795 1.694525 GGGGGAGGAGAAAGAGGGG 60.695 68.421 0.00 0.00 0.00 4.79
832 860 2.276740 GGAGGGAATGGTGGGCTG 59.723 66.667 0.00 0.00 0.00 4.85
833 861 2.204291 TGGAGGGAATGGTGGGCT 60.204 61.111 0.00 0.00 0.00 5.19
834 862 2.276740 CTGGAGGGAATGGTGGGC 59.723 66.667 0.00 0.00 0.00 5.36
835 863 2.276740 GCTGGAGGGAATGGTGGG 59.723 66.667 0.00 0.00 0.00 4.61
836 864 2.276740 GGCTGGAGGGAATGGTGG 59.723 66.667 0.00 0.00 0.00 4.61
837 865 2.153898 TTGGGCTGGAGGGAATGGTG 62.154 60.000 0.00 0.00 0.00 4.17
855 890 2.424379 GGGTGAAGGTGGAAGAGGTTTT 60.424 50.000 0.00 0.00 0.00 2.43
863 898 2.840753 GGGCTGGGTGAAGGTGGAA 61.841 63.158 0.00 0.00 0.00 3.53
865 900 4.366684 GGGGCTGGGTGAAGGTGG 62.367 72.222 0.00 0.00 0.00 4.61
1071 1129 0.394899 CTTCCCCAAGCACCATCTCC 60.395 60.000 0.00 0.00 0.00 3.71
1088 1146 4.722535 TCCCGCTCCCTCCAGCTT 62.723 66.667 0.00 0.00 37.25 3.74
1389 1454 6.743575 AAAATTAAGTTCTGGTCGATCCTG 57.256 37.500 0.00 0.00 37.07 3.86
1398 1463 8.726068 ACCAAACAAACAAAAATTAAGTTCTGG 58.274 29.630 0.00 0.00 0.00 3.86
1424 1497 3.799366 TCAAAGCTCAGGACGTAACAAA 58.201 40.909 0.00 0.00 0.00 2.83
1443 1516 4.882842 TTGCTACAAGTCACCACTATCA 57.117 40.909 0.00 0.00 30.14 2.15
1522 1595 6.894103 AGCTTGATATTTGGTCCAAAGAAGAT 59.106 34.615 21.31 15.15 36.76 2.40
1560 1633 1.281867 CAGGCACAGGGAATCCTACAA 59.718 52.381 0.00 0.00 42.67 2.41
1602 1682 2.393271 ACAATGCTGCTGGAGAGTAC 57.607 50.000 0.00 0.00 0.00 2.73
1640 1721 1.852895 GTCCTACGAGCATTTGTAGCG 59.147 52.381 0.00 0.00 39.18 4.26
1668 1749 7.459795 TCAATCTATTTGGTGCACACAAATA 57.540 32.000 30.42 30.42 44.27 1.40
1694 1775 6.856426 GCAGTTTTTGGTGCTAAGTTACTAAG 59.144 38.462 0.00 0.00 36.71 2.18
1871 2711 4.411327 TGCTTTTGTTTGTCAAACGAGAG 58.589 39.130 23.15 23.15 44.39 3.20
2026 3644 5.717654 ACCCCTTTCTGTTCTAGTCTTCTAG 59.282 44.000 0.00 0.00 43.48 2.43
2029 3647 4.563786 CCACCCCTTTCTGTTCTAGTCTTC 60.564 50.000 0.00 0.00 0.00 2.87
2030 3648 3.328050 CCACCCCTTTCTGTTCTAGTCTT 59.672 47.826 0.00 0.00 0.00 3.01
2032 3650 2.904434 TCCACCCCTTTCTGTTCTAGTC 59.096 50.000 0.00 0.00 0.00 2.59
2075 3693 9.985318 GACATGACAAACAAATTTTGATTGAAA 57.015 25.926 28.28 19.18 43.57 2.69
2181 3802 7.614583 ACAAACTGCTCTAACTCTACAGGTATA 59.385 37.037 0.00 0.00 32.60 1.47
2203 3824 9.457436 AACTACCTTAAAGTCTCTTTTCACAAA 57.543 29.630 0.15 0.00 0.00 2.83
2214 3835 4.995624 AAGGCCAACTACCTTAAAGTCT 57.004 40.909 5.01 0.00 45.80 3.24
2230 3851 3.290710 TGGCTCATCTTTCATTAAGGCC 58.709 45.455 0.00 0.00 37.73 5.19
2264 3885 5.066375 CCATTTCGAGGCATCACTATTTTGA 59.934 40.000 0.00 0.00 0.00 2.69
2432 4106 6.096695 GTGAAGTTGCTAAGTTCCAACAAAA 58.903 36.000 16.86 4.15 42.77 2.44
2433 4107 5.184096 TGTGAAGTTGCTAAGTTCCAACAAA 59.816 36.000 16.86 4.41 42.77 2.83
2565 4239 4.229123 AGATCATCAAACACCTGGGATTCT 59.771 41.667 0.00 0.00 0.00 2.40
2653 4327 2.237143 TCCATTCCACAACCTGCTCTAG 59.763 50.000 0.00 0.00 0.00 2.43
2966 4750 9.547753 CACCATCATAGTAATATACTATTGGCC 57.452 37.037 19.13 0.00 46.88 5.36
3007 4791 9.762933 ACATAAATCAGTTGCACTAAATTTGTT 57.237 25.926 0.00 0.00 30.39 2.83
3021 4805 7.231317 ACAGTTGTTCCATCACATAAATCAGTT 59.769 33.333 0.00 0.00 0.00 3.16
3102 4910 1.185618 AACTGAGCAGGCGTACTCCA 61.186 55.000 4.38 0.00 31.65 3.86
3242 5050 1.555533 GTGTCTGTAAAGAGGAGGGGG 59.444 57.143 0.00 0.00 0.00 5.40
3243 5051 2.234908 CAGTGTCTGTAAAGAGGAGGGG 59.765 54.545 0.00 0.00 0.00 4.79
3244 5052 3.056465 GTCAGTGTCTGTAAAGAGGAGGG 60.056 52.174 0.00 0.00 32.61 4.30
3245 5053 3.056465 GGTCAGTGTCTGTAAAGAGGAGG 60.056 52.174 0.00 0.00 32.61 4.30
3246 5054 3.056465 GGGTCAGTGTCTGTAAAGAGGAG 60.056 52.174 0.00 0.00 32.61 3.69
3247 5055 2.897969 GGGTCAGTGTCTGTAAAGAGGA 59.102 50.000 0.00 0.00 32.61 3.71
3248 5056 2.028020 GGGGTCAGTGTCTGTAAAGAGG 60.028 54.545 0.00 0.00 32.61 3.69
3249 5057 2.632996 TGGGGTCAGTGTCTGTAAAGAG 59.367 50.000 0.00 0.00 32.61 2.85
3250 5058 2.367567 GTGGGGTCAGTGTCTGTAAAGA 59.632 50.000 0.00 0.00 32.61 2.52
3251 5059 2.368875 AGTGGGGTCAGTGTCTGTAAAG 59.631 50.000 0.00 0.00 32.61 1.85
3252 5060 2.404559 AGTGGGGTCAGTGTCTGTAAA 58.595 47.619 0.00 0.00 32.61 2.01
3253 5061 2.097110 AGTGGGGTCAGTGTCTGTAA 57.903 50.000 0.00 0.00 32.61 2.41
3254 5062 2.522185 GTAGTGGGGTCAGTGTCTGTA 58.478 52.381 0.00 0.00 32.61 2.74
3255 5063 1.339097 GTAGTGGGGTCAGTGTCTGT 58.661 55.000 0.00 0.00 32.61 3.41
3256 5064 0.608640 GGTAGTGGGGTCAGTGTCTG 59.391 60.000 0.00 0.00 0.00 3.51
3257 5065 0.487772 AGGTAGTGGGGTCAGTGTCT 59.512 55.000 0.00 0.00 0.00 3.41
3258 5066 0.608640 CAGGTAGTGGGGTCAGTGTC 59.391 60.000 0.00 0.00 0.00 3.67
3259 5067 0.190069 TCAGGTAGTGGGGTCAGTGT 59.810 55.000 0.00 0.00 0.00 3.55
3260 5068 1.276421 CTTCAGGTAGTGGGGTCAGTG 59.724 57.143 0.00 0.00 0.00 3.66
3261 5069 1.149288 TCTTCAGGTAGTGGGGTCAGT 59.851 52.381 0.00 0.00 0.00 3.41
3262 5070 1.827969 CTCTTCAGGTAGTGGGGTCAG 59.172 57.143 0.00 0.00 0.00 3.51
3263 5071 1.431633 TCTCTTCAGGTAGTGGGGTCA 59.568 52.381 0.00 0.00 0.00 4.02
3264 5072 2.104170 CTCTCTTCAGGTAGTGGGGTC 58.896 57.143 0.00 0.00 0.00 4.46
3265 5073 1.897647 GCTCTCTTCAGGTAGTGGGGT 60.898 57.143 0.00 0.00 0.00 4.95
3266 5074 0.827368 GCTCTCTTCAGGTAGTGGGG 59.173 60.000 0.00 0.00 0.00 4.96
3267 5075 1.480137 CTGCTCTCTTCAGGTAGTGGG 59.520 57.143 0.00 0.00 0.00 4.61
3268 5076 2.094286 CACTGCTCTCTTCAGGTAGTGG 60.094 54.545 0.00 0.00 35.94 4.00
3269 5077 2.673610 GCACTGCTCTCTTCAGGTAGTG 60.674 54.545 0.00 0.00 37.65 2.74
3270 5078 1.548269 GCACTGCTCTCTTCAGGTAGT 59.452 52.381 0.00 0.00 35.94 2.73
3271 5079 1.824230 AGCACTGCTCTCTTCAGGTAG 59.176 52.381 0.00 0.00 30.62 3.18
3272 5080 1.930251 AGCACTGCTCTCTTCAGGTA 58.070 50.000 0.00 0.00 30.62 3.08
3273 5081 2.757313 AGCACTGCTCTCTTCAGGT 58.243 52.632 0.00 0.00 30.62 4.00
3340 5323 8.937634 AATTGCACATTTAGATCTCCAAATTC 57.062 30.769 0.00 0.00 0.00 2.17
3569 5552 1.707989 TGTAGCAAACATCCCTTGGGA 59.292 47.619 11.22 11.22 31.43 4.37
3696 5679 4.264253 TGATGTAGAATGACAGCCAAAGG 58.736 43.478 0.00 0.00 34.80 3.11
3807 5790 3.721575 TCCCAGGAATGCCATGTAGTATT 59.278 43.478 0.00 0.00 36.29 1.89
4120 6103 3.254166 GGAACTGAGTACCGTTGTCTACA 59.746 47.826 0.00 0.00 0.00 2.74
4582 6565 0.607489 ATCTTTTCGCAGCAGGCACT 60.607 50.000 0.00 0.00 45.17 4.40
5118 7101 3.113043 GGTACTTCCCTCCATACAGGTT 58.887 50.000 0.00 0.00 39.02 3.50
5273 7256 1.205893 ACAGGGCTCTTCTTCGCTTAG 59.794 52.381 0.00 0.00 0.00 2.18
5305 7288 2.231380 AGGCATTCCACTCCCGGTT 61.231 57.895 0.00 0.00 33.74 4.44
5674 7657 6.494835 AGGTCTAATTTGTTTTCATGGAAGCT 59.505 34.615 1.98 0.00 0.00 3.74
5693 7676 2.922740 AACGCCACTTGAAAGGTCTA 57.077 45.000 0.00 0.00 0.00 2.59
5814 7814 1.917872 AAATAAAGCGAGCAACCCCA 58.082 45.000 0.00 0.00 0.00 4.96
5828 7830 9.923143 ACATATCACTACGCATTAGCTAAATAA 57.077 29.630 10.85 0.00 39.10 1.40
5832 7834 8.657074 AAAACATATCACTACGCATTAGCTAA 57.343 30.769 8.99 8.99 39.10 3.09
5842 7844 8.376203 CAACAAGAGAGAAAACATATCACTACG 58.624 37.037 0.00 0.00 0.00 3.51
6043 8051 6.762077 TTGATCCAAGACCATCCATACATA 57.238 37.500 0.00 0.00 0.00 2.29
6126 8138 5.701750 AGTTAACACACACACACACAACTAA 59.298 36.000 8.61 0.00 0.00 2.24
6128 8140 4.069304 AGTTAACACACACACACACAACT 58.931 39.130 8.61 0.00 0.00 3.16
6129 8141 4.413495 AGTTAACACACACACACACAAC 57.587 40.909 8.61 0.00 0.00 3.32
6130 8142 5.215903 CAAAGTTAACACACACACACACAA 58.784 37.500 8.61 0.00 0.00 3.33
6132 8144 4.789784 ACAAAGTTAACACACACACACAC 58.210 39.130 8.61 0.00 0.00 3.82
6133 8145 4.757657 AGACAAAGTTAACACACACACACA 59.242 37.500 8.61 0.00 0.00 3.72
6174 8195 8.468349 CACAAAACGAACTGTACATTATTTGTG 58.532 33.333 21.57 21.57 44.57 3.33
6230 8852 5.219633 GTCAAAATGTTACAGAAATGGCGT 58.780 37.500 0.00 0.00 0.00 5.68
6253 8875 6.072286 ACAGAAGTAATGCAATCTTGGAAGTG 60.072 38.462 0.00 0.00 30.51 3.16
6347 10317 7.448748 AGTCAGTAATGGAATTGTACCAAAC 57.551 36.000 0.00 0.00 40.93 2.93
6348 10324 9.575868 TTTAGTCAGTAATGGAATTGTACCAAA 57.424 29.630 0.00 0.00 40.93 3.28
6537 10534 0.902531 TTTTAGACGGGCTCCTCAGG 59.097 55.000 0.00 0.00 0.00 3.86
6538 10535 1.405661 GGTTTTAGACGGGCTCCTCAG 60.406 57.143 0.00 0.00 0.00 3.35


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

AutoCloner maintained by Alex Coulton.