Multiple sequence alignment - TraesCS3B01G375800

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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 TraesCS3B01G375800 chr3B 100.000 3320 0 0 1 3320 591363945 591367264 0.000000e+00 6131
1 TraesCS3B01G375800 chr3B 86.220 791 71 22 1437 2207 590623896 590624668 0.000000e+00 822
2 TraesCS3B01G375800 chr3B 88.773 481 40 9 909 1386 590623411 590623880 7.990000e-161 577
3 TraesCS3B01G375800 chr3B 79.447 579 59 34 220 766 590605489 590606039 4.070000e-94 355
4 TraesCS3B01G375800 chr3D 91.328 1822 91 24 602 2395 449736908 449738690 0.000000e+00 2427
5 TraesCS3B01G375800 chr3D 95.625 640 25 2 2681 3320 449738998 449739634 0.000000e+00 1024
6 TraesCS3B01G375800 chr3D 86.058 789 72 21 1436 2207 449541032 449541799 0.000000e+00 813
7 TraesCS3B01G375800 chr3D 91.032 591 27 6 1 572 449736325 449736908 0.000000e+00 774
8 TraesCS3B01G375800 chr3D 87.456 574 46 17 817 1386 449540467 449541018 3.610000e-179 638
9 TraesCS3B01G375800 chr3A 91.371 1576 81 20 817 2369 593339630 593341173 0.000000e+00 2106
10 TraesCS3B01G375800 chr3A 90.419 835 48 10 1 805 593337424 593338256 0.000000e+00 1070
11 TraesCS3B01G375800 chr3A 95.639 642 19 3 2679 3320 593341917 593342549 0.000000e+00 1022
12 TraesCS3B01G375800 chr3A 83.929 784 81 26 1437 2207 593177040 593177791 0.000000e+00 708
13 TraesCS3B01G375800 chr3A 86.957 575 47 19 817 1387 593176475 593177025 3.640000e-174 621
14 TraesCS3B01G375800 chr3A 76.861 739 81 40 1 723 593172927 593173591 5.310000e-88 335
15 TraesCS3B01G375800 chr3A 77.122 542 67 31 220 730 593106684 593107199 9.140000e-66 261
16 TraesCS3B01G375800 chr7B 99.541 218 1 0 2462 2679 657689753 657689970 6.670000e-107 398
17 TraesCS3B01G375800 chr5B 98.624 218 3 0 2462 2679 6370824 6371041 1.440000e-103 387
18 TraesCS3B01G375800 chr5B 95.434 219 10 0 2461 2679 528889143 528889361 1.900000e-92 350
19 TraesCS3B01G375800 chr5B 94.977 219 11 0 2461 2679 114132860 114133078 8.820000e-91 344
20 TraesCS3B01G375800 chr6B 95.872 218 9 0 2462 2679 8131744 8131961 1.470000e-93 353
21 TraesCS3B01G375800 chr4A 95.067 223 11 0 2460 2682 736531242 736531464 5.270000e-93 351
22 TraesCS3B01G375800 chr6A 94.248 226 13 0 2462 2687 315613833 315613608 2.450000e-91 346
23 TraesCS3B01G375800 chr1D 94.248 226 13 0 2459 2684 272313828 272313603 2.450000e-91 346
24 TraesCS3B01G375800 chr5D 93.778 225 14 0 2456 2680 440804606 440804830 4.100000e-89 339


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 TraesCS3B01G375800 chr3B 591363945 591367264 3319 False 6131.000000 6131 100.000000 1 3320 1 chr3B.!!$F2 3319
1 TraesCS3B01G375800 chr3B 590623411 590624668 1257 False 699.500000 822 87.496500 909 2207 2 chr3B.!!$F3 1298
2 TraesCS3B01G375800 chr3B 590605489 590606039 550 False 355.000000 355 79.447000 220 766 1 chr3B.!!$F1 546
3 TraesCS3B01G375800 chr3D 449736325 449739634 3309 False 1408.333333 2427 92.661667 1 3320 3 chr3D.!!$F2 3319
4 TraesCS3B01G375800 chr3D 449540467 449541799 1332 False 725.500000 813 86.757000 817 2207 2 chr3D.!!$F1 1390
5 TraesCS3B01G375800 chr3A 593337424 593342549 5125 False 1399.333333 2106 92.476333 1 3320 3 chr3A.!!$F3 3319
6 TraesCS3B01G375800 chr3A 593172927 593177791 4864 False 554.666667 708 82.582333 1 2207 3 chr3A.!!$F2 2206
7 TraesCS3B01G375800 chr3A 593106684 593107199 515 False 261.000000 261 77.122000 220 730 1 chr3A.!!$F1 510

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
180 188 0.320374 CTCGGGGTGCAACTAACTGA 59.680 55.0 0.00 0.0 36.74 3.41 F
250 265 0.456653 CGCTTCAATCCGCAAAAGGG 60.457 55.0 0.00 0.0 0.00 3.95 F
572 642 0.733729 ACCACGATCGACTAGACTGC 59.266 55.0 24.34 0.0 0.00 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2112 6142 0.176680 AGTGAAGCAGATCGCCGAAT 59.823 50.0 0.00 0.00 44.04 3.34 R
2159 6189 0.944311 ACAGGTCGTGTCGCACATTC 60.944 55.0 9.95 1.09 31.90 2.67 R
2458 7152 0.033920 GCAAAAGAACTGGGCCTTGG 59.966 55.0 4.53 0.00 0.00 3.61 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
46 52 0.994247 TGGATCACTGGCCATCACTT 59.006 50.000 5.51 0.00 0.00 3.16
47 53 1.340308 TGGATCACTGGCCATCACTTG 60.340 52.381 5.51 0.00 0.00 3.16
177 185 1.003718 AGCTCGGGGTGCAACTAAC 60.004 57.895 0.00 0.00 36.74 2.34
178 186 1.003718 GCTCGGGGTGCAACTAACT 60.004 57.895 0.00 0.00 36.74 2.24
179 187 1.298859 GCTCGGGGTGCAACTAACTG 61.299 60.000 0.00 0.00 36.74 3.16
180 188 0.320374 CTCGGGGTGCAACTAACTGA 59.680 55.000 0.00 0.00 36.74 3.41
182 190 1.156736 CGGGGTGCAACTAACTGAAG 58.843 55.000 0.00 0.00 36.74 3.02
183 191 1.270625 CGGGGTGCAACTAACTGAAGA 60.271 52.381 0.00 0.00 36.74 2.87
184 192 2.615493 CGGGGTGCAACTAACTGAAGAT 60.615 50.000 0.00 0.00 36.74 2.40
205 220 3.130280 AGACACACATGAGCATGAACA 57.870 42.857 16.70 0.00 41.20 3.18
206 221 3.479489 AGACACACATGAGCATGAACAA 58.521 40.909 16.70 0.00 41.20 2.83
207 222 4.077108 AGACACACATGAGCATGAACAAT 58.923 39.130 16.70 0.00 41.20 2.71
208 223 5.247862 AGACACACATGAGCATGAACAATA 58.752 37.500 16.70 0.00 41.20 1.90
209 224 5.884232 AGACACACATGAGCATGAACAATAT 59.116 36.000 16.70 0.00 41.20 1.28
210 225 5.886992 ACACACATGAGCATGAACAATATG 58.113 37.500 16.70 5.63 41.20 1.78
240 255 1.014044 TGGTGCTCGTCGCTTCAATC 61.014 55.000 0.00 0.00 40.11 2.67
250 265 0.456653 CGCTTCAATCCGCAAAAGGG 60.457 55.000 0.00 0.00 0.00 3.95
255 270 2.159382 TCAATCCGCAAAAGGGTCTTC 58.841 47.619 0.00 0.00 0.00 2.87
362 385 1.847328 ATCCTTTTGTTTAGGGCCCG 58.153 50.000 18.44 0.00 33.41 6.13
403 436 3.347216 GGTACATGCACTGAACCTGAAT 58.653 45.455 0.00 0.00 0.00 2.57
572 642 0.733729 ACCACGATCGACTAGACTGC 59.266 55.000 24.34 0.00 0.00 4.40
608 678 2.327343 CCCGTACGTCAGGTCACGA 61.327 63.158 15.21 0.00 42.69 4.35
690 781 2.812178 CGTAGGGCAACGGGTTCG 60.812 66.667 3.93 0.00 39.19 3.95
692 783 3.315949 TAGGGCAACGGGTTCGCT 61.316 61.111 0.00 0.00 40.63 4.93
697 788 1.154543 GCAACGGGTTCGCTTAACG 60.155 57.895 0.00 0.00 45.62 3.18
775 878 6.753744 TCGATCTCTCACACAGATTACAATTG 59.246 38.462 3.24 3.24 30.30 2.32
948 4932 2.045045 CTTCCATGCGGCTTCCCA 60.045 61.111 0.00 0.00 0.00 4.37
974 4958 3.447950 GTTCCCCTGTCCTAGGTTTCTA 58.552 50.000 9.08 0.00 45.80 2.10
975 4959 4.038633 GTTCCCCTGTCCTAGGTTTCTAT 58.961 47.826 9.08 0.00 45.80 1.98
978 4964 5.857134 TCCCCTGTCCTAGGTTTCTATAAA 58.143 41.667 9.08 0.00 45.80 1.40
984 4970 6.964464 TGTCCTAGGTTTCTATAAATTGCCA 58.036 36.000 9.08 0.00 0.00 4.92
1017 5005 2.324477 CCGCCGATTCATTCGCAC 59.676 61.111 0.00 0.00 46.71 5.34
1018 5006 2.173669 CCGCCGATTCATTCGCACT 61.174 57.895 0.00 0.00 46.71 4.40
1049 5038 2.159170 TCGACACCCAAAAGCCAAAAAG 60.159 45.455 0.00 0.00 0.00 2.27
1060 5050 1.151172 GCCAAAAAGGTTGGTGCACG 61.151 55.000 11.45 0.00 41.53 5.34
1090 5080 2.626266 TCCAGTTCTAGTGCGAAGTTCA 59.374 45.455 3.32 0.00 0.00 3.18
1389 5379 3.243704 CCATCCAAAAGAAGGTGCGAAAA 60.244 43.478 0.00 0.00 0.00 2.29
1409 5399 7.911362 GAAAATTCGATCGCTACTAAGTACT 57.089 36.000 11.09 0.00 0.00 2.73
1410 5400 7.911362 AAAATTCGATCGCTACTAAGTACTC 57.089 36.000 11.09 0.00 0.00 2.59
1411 5401 5.610235 ATTCGATCGCTACTAAGTACTCC 57.390 43.478 11.09 0.00 0.00 3.85
1412 5402 4.333913 TCGATCGCTACTAAGTACTCCT 57.666 45.455 11.09 0.00 0.00 3.69
1414 5404 5.226396 TCGATCGCTACTAAGTACTCCTAC 58.774 45.833 11.09 0.00 0.00 3.18
1415 5405 5.010516 TCGATCGCTACTAAGTACTCCTACT 59.989 44.000 11.09 0.00 34.38 2.57
1416 5406 5.695816 CGATCGCTACTAAGTACTCCTACTT 59.304 44.000 0.26 0.00 44.14 2.24
1417 5407 6.346758 CGATCGCTACTAAGTACTCCTACTTG 60.347 46.154 0.26 0.00 42.26 3.16
1418 5408 4.574013 TCGCTACTAAGTACTCCTACTTGC 59.426 45.833 0.00 0.00 42.26 4.01
1419 5409 4.261114 CGCTACTAAGTACTCCTACTTGCC 60.261 50.000 0.00 0.00 42.26 4.52
1420 5410 4.643784 GCTACTAAGTACTCCTACTTGCCA 59.356 45.833 0.00 0.00 42.26 4.92
1424 5414 3.406512 AGTACTCCTACTTGCCAGGAT 57.593 47.619 0.00 0.00 41.37 3.24
1445 5437 6.160105 AGGATGGAAGAATTCTGAATTCCTCT 59.840 38.462 29.86 19.26 46.65 3.69
1452 5444 5.192522 AGAATTCTGAATTCCTCTGCCCTTA 59.807 40.000 29.86 0.00 46.65 2.69
1495 5487 1.265905 GACAGGTTTGCCGTCGATTTT 59.734 47.619 0.00 0.00 40.50 1.82
1673 5681 1.313772 GTCGATCAGAGCAGAGCCTA 58.686 55.000 0.00 0.00 0.00 3.93
1830 5848 2.511145 GCCGCCTTCTCTCAGCAG 60.511 66.667 0.00 0.00 0.00 4.24
2112 6142 1.206831 CGTCGTCAACTCGCTCAGA 59.793 57.895 0.00 0.00 0.00 3.27
2148 6178 4.377839 TCACTAGAGCACAGTAGATTGC 57.622 45.455 0.00 0.00 39.16 3.56
2159 6189 1.144716 TAGATTGCCTGCCTCAGCG 59.855 57.895 0.00 0.00 44.31 5.18
2160 6190 1.329913 TAGATTGCCTGCCTCAGCGA 61.330 55.000 0.00 0.00 44.31 4.93
2161 6191 1.746615 GATTGCCTGCCTCAGCGAA 60.747 57.895 0.00 0.00 44.31 4.70
2162 6192 1.077212 ATTGCCTGCCTCAGCGAAT 60.077 52.632 0.00 0.00 44.31 3.34
2163 6193 1.381928 ATTGCCTGCCTCAGCGAATG 61.382 55.000 0.00 0.00 44.31 2.67
2250 6280 9.117183 TGACTAATGAGTAGTGATAATGTACGT 57.883 33.333 0.00 0.00 43.45 3.57
2269 6299 2.663196 GGTGGGTGAGAGGTTCCG 59.337 66.667 0.00 0.00 0.00 4.30
2280 6310 2.747855 GGTTCCGGCTGCAAGAGG 60.748 66.667 0.50 0.00 34.07 3.69
2325 6355 5.398169 TCAAATTGGTTGCAATACTAAGCG 58.602 37.500 0.59 0.00 37.13 4.68
2334 6364 4.778904 TGCAATACTAAGCGTTTGTTCAC 58.221 39.130 0.00 0.00 0.00 3.18
2339 6369 4.287238 ACTAAGCGTTTGTTCACCAAAG 57.713 40.909 0.00 0.00 43.52 2.77
2354 6384 7.876068 TGTTCACCAAAGGTAGTAGTTAATCAG 59.124 37.037 0.00 0.00 32.11 2.90
2429 7123 9.420551 ACAATCTAGTAGTAACAAACAGTAAGC 57.579 33.333 0.00 0.00 0.00 3.09
2430 7124 9.419297 CAATCTAGTAGTAACAAACAGTAAGCA 57.581 33.333 0.00 0.00 0.00 3.91
2443 7137 8.682710 ACAAACAGTAAGCAAACAAAAGATAGA 58.317 29.630 0.00 0.00 0.00 1.98
2451 7145 4.627035 GCAAACAAAAGATAGAATGTGGCC 59.373 41.667 0.00 0.00 0.00 5.36
2452 7146 5.567423 GCAAACAAAAGATAGAATGTGGCCT 60.567 40.000 3.32 0.00 0.00 5.19
2458 7152 4.414337 AGATAGAATGTGGCCTTCACTC 57.586 45.455 3.32 2.90 46.20 3.51
2460 7154 1.067295 AGAATGTGGCCTTCACTCCA 58.933 50.000 3.32 0.00 46.20 3.86
2462 7156 1.815003 GAATGTGGCCTTCACTCCAAG 59.185 52.381 3.32 0.00 46.20 3.61
2463 7157 0.038744 ATGTGGCCTTCACTCCAAGG 59.961 55.000 3.32 0.00 46.20 3.61
2467 7161 3.170362 CCTTCACTCCAAGGCCCA 58.830 61.111 0.00 0.00 36.72 5.36
2468 7162 1.001641 CCTTCACTCCAAGGCCCAG 60.002 63.158 0.00 0.00 36.72 4.45
2469 7163 1.763770 CTTCACTCCAAGGCCCAGT 59.236 57.895 0.00 0.00 0.00 4.00
2470 7164 0.111253 CTTCACTCCAAGGCCCAGTT 59.889 55.000 0.00 0.00 0.00 3.16
2471 7165 0.110486 TTCACTCCAAGGCCCAGTTC 59.890 55.000 0.00 0.00 0.00 3.01
2472 7166 0.768221 TCACTCCAAGGCCCAGTTCT 60.768 55.000 0.00 0.00 0.00 3.01
2473 7167 0.111253 CACTCCAAGGCCCAGTTCTT 59.889 55.000 0.00 0.00 0.00 2.52
2474 7168 0.853530 ACTCCAAGGCCCAGTTCTTT 59.146 50.000 0.00 0.00 0.00 2.52
2475 7169 1.217942 ACTCCAAGGCCCAGTTCTTTT 59.782 47.619 0.00 0.00 0.00 2.27
2476 7170 1.615392 CTCCAAGGCCCAGTTCTTTTG 59.385 52.381 0.00 0.00 0.00 2.44
2477 7171 0.033920 CCAAGGCCCAGTTCTTTTGC 59.966 55.000 0.00 0.00 0.00 3.68
2478 7172 0.033920 CAAGGCCCAGTTCTTTTGCC 59.966 55.000 0.00 0.00 42.48 4.52
2479 7173 0.398381 AAGGCCCAGTTCTTTTGCCA 60.398 50.000 0.00 0.00 44.60 4.92
2480 7174 0.829182 AGGCCCAGTTCTTTTGCCAG 60.829 55.000 0.00 0.00 44.60 4.85
2481 7175 0.827507 GGCCCAGTTCTTTTGCCAGA 60.828 55.000 0.00 0.00 41.76 3.86
2482 7176 1.039856 GCCCAGTTCTTTTGCCAGAA 58.960 50.000 0.00 0.00 0.00 3.02
2483 7177 1.620323 GCCCAGTTCTTTTGCCAGAAT 59.380 47.619 0.00 0.00 35.23 2.40
2484 7178 2.353109 GCCCAGTTCTTTTGCCAGAATC 60.353 50.000 0.00 0.00 35.23 2.52
2485 7179 3.160269 CCCAGTTCTTTTGCCAGAATCT 58.840 45.455 0.00 0.00 35.23 2.40
2486 7180 3.057033 CCCAGTTCTTTTGCCAGAATCTG 60.057 47.826 2.68 2.68 35.23 2.90
2508 7202 1.839894 ATTCTCCCAGAATCCGCCC 59.160 57.895 0.00 0.00 40.75 6.13
2509 7203 1.709994 ATTCTCCCAGAATCCGCCCC 61.710 60.000 0.00 0.00 40.75 5.80
2510 7204 3.878667 CTCCCAGAATCCGCCCCC 61.879 72.222 0.00 0.00 0.00 5.40
2511 7205 4.431524 TCCCAGAATCCGCCCCCT 62.432 66.667 0.00 0.00 0.00 4.79
2512 7206 2.447765 CCCAGAATCCGCCCCCTA 60.448 66.667 0.00 0.00 0.00 3.53
2513 7207 2.819284 CCCAGAATCCGCCCCCTAC 61.819 68.421 0.00 0.00 0.00 3.18
2514 7208 2.819284 CCAGAATCCGCCCCCTACC 61.819 68.421 0.00 0.00 0.00 3.18
2515 7209 2.447959 AGAATCCGCCCCCTACCC 60.448 66.667 0.00 0.00 0.00 3.69
2516 7210 2.770904 GAATCCGCCCCCTACCCA 60.771 66.667 0.00 0.00 0.00 4.51
2517 7211 2.772622 AATCCGCCCCCTACCCAG 60.773 66.667 0.00 0.00 0.00 4.45
2521 7215 4.176752 CGCCCCCTACCCAGCTTC 62.177 72.222 0.00 0.00 0.00 3.86
2522 7216 2.692741 GCCCCCTACCCAGCTTCT 60.693 66.667 0.00 0.00 0.00 2.85
2523 7217 2.747443 GCCCCCTACCCAGCTTCTC 61.747 68.421 0.00 0.00 0.00 2.87
2524 7218 2.073101 CCCCCTACCCAGCTTCTCC 61.073 68.421 0.00 0.00 0.00 3.71
2525 7219 2.073101 CCCCTACCCAGCTTCTCCC 61.073 68.421 0.00 0.00 0.00 4.30
2526 7220 1.306997 CCCTACCCAGCTTCTCCCA 60.307 63.158 0.00 0.00 0.00 4.37
2527 7221 1.341156 CCCTACCCAGCTTCTCCCAG 61.341 65.000 0.00 0.00 0.00 4.45
2528 7222 0.325671 CCTACCCAGCTTCTCCCAGA 60.326 60.000 0.00 0.00 0.00 3.86
2529 7223 1.573108 CTACCCAGCTTCTCCCAGAA 58.427 55.000 0.00 0.00 32.50 3.02
2530 7224 2.122768 CTACCCAGCTTCTCCCAGAAT 58.877 52.381 0.00 0.00 33.13 2.40
2531 7225 0.915364 ACCCAGCTTCTCCCAGAATC 59.085 55.000 0.00 0.00 33.13 2.52
2532 7226 1.211456 CCCAGCTTCTCCCAGAATCT 58.789 55.000 0.00 0.00 33.13 2.40
2533 7227 1.563410 CCCAGCTTCTCCCAGAATCTT 59.437 52.381 0.00 0.00 33.13 2.40
2534 7228 2.025510 CCCAGCTTCTCCCAGAATCTTT 60.026 50.000 0.00 0.00 33.13 2.52
2535 7229 3.015327 CCAGCTTCTCCCAGAATCTTTG 58.985 50.000 0.00 0.00 33.13 2.77
2536 7230 3.307975 CCAGCTTCTCCCAGAATCTTTGA 60.308 47.826 0.00 0.00 33.13 2.69
2537 7231 3.940221 CAGCTTCTCCCAGAATCTTTGAG 59.060 47.826 0.00 0.62 33.13 3.02
2538 7232 2.682352 GCTTCTCCCAGAATCTTTGAGC 59.318 50.000 1.93 0.00 33.13 4.26
2539 7233 3.277715 CTTCTCCCAGAATCTTTGAGCC 58.722 50.000 1.93 0.00 33.13 4.70
2540 7234 1.561542 TCTCCCAGAATCTTTGAGCCC 59.438 52.381 1.93 0.00 0.00 5.19
2541 7235 0.625849 TCCCAGAATCTTTGAGCCCC 59.374 55.000 0.00 0.00 0.00 5.80
2542 7236 0.332632 CCCAGAATCTTTGAGCCCCA 59.667 55.000 0.00 0.00 0.00 4.96
2543 7237 1.063417 CCCAGAATCTTTGAGCCCCAT 60.063 52.381 0.00 0.00 0.00 4.00
2544 7238 2.625087 CCCAGAATCTTTGAGCCCCATT 60.625 50.000 0.00 0.00 0.00 3.16
2545 7239 3.102204 CCAGAATCTTTGAGCCCCATTT 58.898 45.455 0.00 0.00 0.00 2.32
2546 7240 3.118884 CCAGAATCTTTGAGCCCCATTTG 60.119 47.826 0.00 0.00 0.00 2.32
2547 7241 3.512724 CAGAATCTTTGAGCCCCATTTGT 59.487 43.478 0.00 0.00 0.00 2.83
2548 7242 4.020839 CAGAATCTTTGAGCCCCATTTGTT 60.021 41.667 0.00 0.00 0.00 2.83
2549 7243 4.221482 AGAATCTTTGAGCCCCATTTGTTC 59.779 41.667 0.00 0.00 0.00 3.18
2550 7244 3.243359 TCTTTGAGCCCCATTTGTTCT 57.757 42.857 0.00 0.00 0.00 3.01
2551 7245 4.380843 TCTTTGAGCCCCATTTGTTCTA 57.619 40.909 0.00 0.00 0.00 2.10
2552 7246 4.079253 TCTTTGAGCCCCATTTGTTCTAC 58.921 43.478 0.00 0.00 0.00 2.59
2553 7247 3.517296 TTGAGCCCCATTTGTTCTACA 57.483 42.857 0.00 0.00 0.00 2.74
2554 7248 3.517296 TGAGCCCCATTTGTTCTACAA 57.483 42.857 0.00 0.00 36.11 2.41
2555 7249 4.046286 TGAGCCCCATTTGTTCTACAAT 57.954 40.909 0.00 0.00 38.00 2.71
2556 7250 4.016444 TGAGCCCCATTTGTTCTACAATC 58.984 43.478 0.00 0.00 38.00 2.67
2557 7251 3.365472 AGCCCCATTTGTTCTACAATCC 58.635 45.455 0.00 0.00 38.00 3.01
2558 7252 3.011708 AGCCCCATTTGTTCTACAATCCT 59.988 43.478 0.00 0.00 38.00 3.24
2559 7253 3.131046 GCCCCATTTGTTCTACAATCCTG 59.869 47.826 0.00 0.00 38.00 3.86
2560 7254 4.344104 CCCCATTTGTTCTACAATCCTGT 58.656 43.478 0.00 0.00 38.00 4.00
2561 7255 4.399303 CCCCATTTGTTCTACAATCCTGTC 59.601 45.833 0.00 0.00 38.00 3.51
2562 7256 5.256474 CCCATTTGTTCTACAATCCTGTCT 58.744 41.667 0.00 0.00 38.00 3.41
2563 7257 6.414732 CCCATTTGTTCTACAATCCTGTCTA 58.585 40.000 0.00 0.00 38.00 2.59
2564 7258 6.884295 CCCATTTGTTCTACAATCCTGTCTAA 59.116 38.462 0.00 0.00 38.00 2.10
2565 7259 7.557719 CCCATTTGTTCTACAATCCTGTCTAAT 59.442 37.037 0.00 0.00 38.00 1.73
2566 7260 8.960591 CCATTTGTTCTACAATCCTGTCTAATT 58.039 33.333 0.00 0.00 38.00 1.40
2570 7264 9.871238 TTGTTCTACAATCCTGTCTAATTAGAC 57.129 33.333 30.61 30.61 41.84 2.59
2584 7278 7.638134 GTCTAATTAGACCGTAACTAGACAGG 58.362 42.308 28.25 0.00 45.33 4.00
2585 7279 7.497249 GTCTAATTAGACCGTAACTAGACAGGA 59.503 40.741 28.25 0.00 45.33 3.86
2586 7280 8.216423 TCTAATTAGACCGTAACTAGACAGGAT 58.784 37.037 11.24 0.00 0.00 3.24
2587 7281 7.657023 AATTAGACCGTAACTAGACAGGATT 57.343 36.000 0.00 0.00 0.00 3.01
2588 7282 4.985538 AGACCGTAACTAGACAGGATTG 57.014 45.455 0.00 0.00 0.00 2.67
2589 7283 4.342359 AGACCGTAACTAGACAGGATTGT 58.658 43.478 0.00 0.00 41.18 2.71
2590 7284 5.503927 AGACCGTAACTAGACAGGATTGTA 58.496 41.667 0.00 0.00 37.76 2.41
2591 7285 5.589452 AGACCGTAACTAGACAGGATTGTAG 59.411 44.000 0.00 0.00 37.76 2.74
2592 7286 5.503927 ACCGTAACTAGACAGGATTGTAGA 58.496 41.667 0.00 0.00 37.76 2.59
2593 7287 5.948162 ACCGTAACTAGACAGGATTGTAGAA 59.052 40.000 0.00 0.00 37.76 2.10
2594 7288 6.127786 ACCGTAACTAGACAGGATTGTAGAAC 60.128 42.308 0.00 0.00 37.76 3.01
2595 7289 6.127814 CCGTAACTAGACAGGATTGTAGAACA 60.128 42.308 0.00 0.00 37.76 3.18
2596 7290 7.310664 CGTAACTAGACAGGATTGTAGAACAA 58.689 38.462 0.00 0.00 42.95 2.83
2597 7291 7.811236 CGTAACTAGACAGGATTGTAGAACAAA 59.189 37.037 0.00 0.00 41.96 2.83
2598 7292 9.141400 GTAACTAGACAGGATTGTAGAACAAAG 57.859 37.037 0.00 0.00 41.96 2.77
2599 7293 6.702329 ACTAGACAGGATTGTAGAACAAAGG 58.298 40.000 0.00 0.00 41.96 3.11
2600 7294 4.911390 AGACAGGATTGTAGAACAAAGGG 58.089 43.478 0.00 0.00 41.96 3.95
2601 7295 4.010349 GACAGGATTGTAGAACAAAGGGG 58.990 47.826 0.00 0.00 41.96 4.79
2602 7296 3.245264 ACAGGATTGTAGAACAAAGGGGG 60.245 47.826 0.00 0.00 41.96 5.40
2603 7297 2.100197 GGATTGTAGAACAAAGGGGGC 58.900 52.381 0.00 0.00 41.96 5.80
2604 7298 2.291605 GGATTGTAGAACAAAGGGGGCT 60.292 50.000 0.00 0.00 41.96 5.19
2605 7299 2.579410 TTGTAGAACAAAGGGGGCTC 57.421 50.000 0.00 0.00 34.76 4.70
2606 7300 1.440618 TGTAGAACAAAGGGGGCTCA 58.559 50.000 0.00 0.00 0.00 4.26
2607 7301 1.777878 TGTAGAACAAAGGGGGCTCAA 59.222 47.619 0.00 0.00 0.00 3.02
2608 7302 2.175931 TGTAGAACAAAGGGGGCTCAAA 59.824 45.455 0.00 0.00 0.00 2.69
2609 7303 2.001076 AGAACAAAGGGGGCTCAAAG 57.999 50.000 0.00 0.00 0.00 2.77
2610 7304 1.499007 AGAACAAAGGGGGCTCAAAGA 59.501 47.619 0.00 0.00 0.00 2.52
2611 7305 2.110721 AGAACAAAGGGGGCTCAAAGAT 59.889 45.455 0.00 0.00 0.00 2.40
2612 7306 2.702270 ACAAAGGGGGCTCAAAGATT 57.298 45.000 0.00 0.00 0.00 2.40
2613 7307 2.529632 ACAAAGGGGGCTCAAAGATTC 58.470 47.619 0.00 0.00 0.00 2.52
2614 7308 2.110721 ACAAAGGGGGCTCAAAGATTCT 59.889 45.455 0.00 0.00 0.00 2.40
2615 7309 2.494870 CAAAGGGGGCTCAAAGATTCTG 59.505 50.000 0.00 0.00 0.00 3.02
2616 7310 0.627986 AGGGGGCTCAAAGATTCTGG 59.372 55.000 0.00 0.00 0.00 3.86
2617 7311 0.396278 GGGGGCTCAAAGATTCTGGG 60.396 60.000 0.00 0.00 0.00 4.45
2618 7312 0.625849 GGGGCTCAAAGATTCTGGGA 59.374 55.000 0.00 0.00 0.00 4.37
2619 7313 1.409381 GGGGCTCAAAGATTCTGGGAG 60.409 57.143 9.42 9.42 0.00 4.30
2620 7314 1.561542 GGGCTCAAAGATTCTGGGAGA 59.438 52.381 15.41 0.14 0.00 3.71
2621 7315 2.025887 GGGCTCAAAGATTCTGGGAGAA 60.026 50.000 15.41 0.00 38.78 2.87
2622 7316 3.277715 GGCTCAAAGATTCTGGGAGAAG 58.722 50.000 15.41 0.00 37.69 2.85
2623 7317 2.682352 GCTCAAAGATTCTGGGAGAAGC 59.318 50.000 15.41 0.00 40.68 3.86
2627 7321 3.796764 GATTCTGGGAGAAGCTGGG 57.203 57.895 0.00 0.00 37.62 4.45
2628 7322 0.915364 GATTCTGGGAGAAGCTGGGT 59.085 55.000 0.00 0.00 37.62 4.51
2629 7323 2.119495 GATTCTGGGAGAAGCTGGGTA 58.881 52.381 0.00 0.00 37.62 3.69
2630 7324 1.573108 TTCTGGGAGAAGCTGGGTAG 58.427 55.000 0.00 0.00 29.50 3.18
2631 7325 0.325671 TCTGGGAGAAGCTGGGTAGG 60.326 60.000 0.00 0.00 0.00 3.18
2632 7326 1.306997 TGGGAGAAGCTGGGTAGGG 60.307 63.158 0.00 0.00 0.00 3.53
2633 7327 2.073101 GGGAGAAGCTGGGTAGGGG 61.073 68.421 0.00 0.00 0.00 4.79
2634 7328 1.307084 GGAGAAGCTGGGTAGGGGT 60.307 63.158 0.00 0.00 0.00 4.95
2635 7329 1.338890 GGAGAAGCTGGGTAGGGGTC 61.339 65.000 0.00 0.00 0.00 4.46
2636 7330 1.677637 GAGAAGCTGGGTAGGGGTCG 61.678 65.000 0.00 0.00 0.00 4.79
2637 7331 2.687566 AAGCTGGGTAGGGGTCGG 60.688 66.667 0.00 0.00 0.00 4.79
2638 7332 3.248248 AAGCTGGGTAGGGGTCGGA 62.248 63.158 0.00 0.00 0.00 4.55
2639 7333 2.446036 GCTGGGTAGGGGTCGGAT 60.446 66.667 0.00 0.00 0.00 4.18
2640 7334 2.070650 GCTGGGTAGGGGTCGGATT 61.071 63.158 0.00 0.00 0.00 3.01
2641 7335 2.041206 GCTGGGTAGGGGTCGGATTC 62.041 65.000 0.00 0.00 0.00 2.52
2642 7336 0.398664 CTGGGTAGGGGTCGGATTCT 60.399 60.000 0.00 0.00 0.00 2.40
2643 7337 0.689745 TGGGTAGGGGTCGGATTCTG 60.690 60.000 0.00 0.00 0.00 3.02
2644 7338 1.408453 GGGTAGGGGTCGGATTCTGG 61.408 65.000 0.00 0.00 0.00 3.86
2645 7339 1.408453 GGTAGGGGTCGGATTCTGGG 61.408 65.000 0.00 0.00 0.00 4.45
2646 7340 0.398098 GTAGGGGTCGGATTCTGGGA 60.398 60.000 0.00 0.00 0.00 4.37
2647 7341 0.105658 TAGGGGTCGGATTCTGGGAG 60.106 60.000 0.00 0.00 0.00 4.30
2648 7342 1.382695 GGGGTCGGATTCTGGGAGA 60.383 63.158 0.00 0.00 0.00 3.71
2649 7343 0.981277 GGGGTCGGATTCTGGGAGAA 60.981 60.000 0.00 0.00 38.78 2.87
2650 7344 1.132500 GGGTCGGATTCTGGGAGAAT 58.868 55.000 0.00 0.00 46.84 2.40
2675 7369 5.886960 CCAGATTCTGGTAAAAGAACTGG 57.113 43.478 22.45 15.02 45.82 4.00
2676 7370 4.702131 CCAGATTCTGGTAAAAGAACTGGG 59.298 45.833 22.45 0.00 45.82 4.45
2677 7371 4.156739 CAGATTCTGGTAAAAGAACTGGGC 59.843 45.833 5.73 0.00 38.95 5.36
2678 7372 2.579410 TCTGGTAAAAGAACTGGGCC 57.421 50.000 0.00 0.00 0.00 5.80
2679 7373 1.074889 TCTGGTAAAAGAACTGGGCCC 59.925 52.381 17.59 17.59 0.00 5.80
2688 7382 1.693606 AGAACTGGGCCCAAATTGTTG 59.306 47.619 26.98 16.35 34.25 3.33
2694 7388 1.079888 GCCCAAATTGTTGCCCTCG 60.080 57.895 0.00 0.00 33.01 4.63
2717 7411 2.554032 GCCAAACAGCAACATACTGAGT 59.446 45.455 0.00 0.00 38.55 3.41
2724 7418 3.925299 CAGCAACATACTGAGTGAGACAG 59.075 47.826 0.00 0.00 37.32 3.51
2735 7429 2.917971 GAGTGAGACAGACCGATTTTCG 59.082 50.000 0.00 0.00 40.07 3.46
2854 7548 4.768968 CCATTCCTTATTCTGCTTATGGGG 59.231 45.833 0.00 0.00 0.00 4.96
2880 7574 6.090088 CAGCATCTATATTACACGAGGAAAGC 59.910 42.308 0.00 0.00 0.00 3.51
2901 7595 0.834687 ACAAAGGTGAGGGGCGAGTA 60.835 55.000 0.00 0.00 0.00 2.59
2942 7636 6.546403 GTGAGTCCAGGTATCACTGTATAGAA 59.454 42.308 15.61 0.00 40.14 2.10
2949 7643 7.287005 CCAGGTATCACTGTATAGAACCACTTA 59.713 40.741 0.00 0.00 36.75 2.24
2960 7654 8.740906 TGTATAGAACCACTTAAGAGTTCAGAG 58.259 37.037 28.47 7.59 41.86 3.35
2961 7655 8.958506 GTATAGAACCACTTAAGAGTTCAGAGA 58.041 37.037 28.47 18.12 41.86 3.10
3055 7749 1.598685 GAACCCAAGTTTCCGCGGA 60.599 57.895 27.28 27.28 35.94 5.54
3262 7956 5.988561 CCATTAGTTATCTGAACTGCTCTCC 59.011 44.000 0.22 0.00 0.00 3.71
3264 7958 2.159170 AGTTATCTGAACTGCTCTCCGC 60.159 50.000 0.00 0.00 39.77 5.54
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
69 75 7.342541 ACAGTCTTCCCCTAAGTCTAATAGTTC 59.657 40.741 0.00 0.00 36.51 3.01
131 139 7.354025 TCAAAGCGAACTTATAAAATGTCGA 57.646 32.000 9.61 0.00 34.05 4.20
133 141 9.554724 TGATTCAAAGCGAACTTATAAAATGTC 57.445 29.630 0.00 0.00 36.12 3.06
177 185 4.752146 TGCTCATGTGTGTCTATCTTCAG 58.248 43.478 0.00 0.00 0.00 3.02
178 186 4.806640 TGCTCATGTGTGTCTATCTTCA 57.193 40.909 0.00 0.00 0.00 3.02
179 187 5.354767 TCATGCTCATGTGTGTCTATCTTC 58.645 41.667 9.41 0.00 39.72 2.87
180 188 5.349061 TCATGCTCATGTGTGTCTATCTT 57.651 39.130 9.41 0.00 39.72 2.40
182 190 4.872124 TGTTCATGCTCATGTGTGTCTATC 59.128 41.667 9.41 0.00 39.72 2.08
183 191 4.835678 TGTTCATGCTCATGTGTGTCTAT 58.164 39.130 9.41 0.00 39.72 1.98
184 192 4.270245 TGTTCATGCTCATGTGTGTCTA 57.730 40.909 9.41 0.00 39.72 2.59
205 220 8.123639 ACGAGCACCAGTATAATACTCATATT 57.876 34.615 0.00 0.00 36.76 1.28
206 221 7.414208 CGACGAGCACCAGTATAATACTCATAT 60.414 40.741 0.00 0.00 36.76 1.78
207 222 6.128363 CGACGAGCACCAGTATAATACTCATA 60.128 42.308 0.00 0.00 36.76 2.15
208 223 5.334957 CGACGAGCACCAGTATAATACTCAT 60.335 44.000 0.00 0.00 36.76 2.90
209 224 4.024302 CGACGAGCACCAGTATAATACTCA 60.024 45.833 0.00 0.00 36.76 3.41
210 225 4.465016 CGACGAGCACCAGTATAATACTC 58.535 47.826 0.00 0.00 36.76 2.59
250 265 3.669824 GCGATTTTCTTTTCGGGGAAGAC 60.670 47.826 0.00 0.00 35.93 3.01
255 270 2.227865 TCTTGCGATTTTCTTTTCGGGG 59.772 45.455 0.00 0.00 35.93 5.73
403 436 2.759973 AGCGGCTCTGGATTCGGA 60.760 61.111 0.00 0.00 0.00 4.55
424 457 4.648626 GTGGTGCCTGCCTGCTCA 62.649 66.667 0.00 0.00 0.00 4.26
697 788 1.499056 TCGAAGGCGACGTGTAGTC 59.501 57.895 0.00 0.00 42.51 2.59
775 878 5.502153 AATCTATACGTGTCAGGTGAGAC 57.498 43.478 8.43 0.00 38.99 3.36
940 4924 2.361737 GGAACCAGCTGGGAAGCC 60.362 66.667 35.42 24.82 41.15 4.35
984 4970 1.227147 CGGGTCGTGCCATATCGTT 60.227 57.895 1.70 0.00 39.65 3.85
1017 5005 0.389166 GGGTGTCGAGCTTGTGAGAG 60.389 60.000 0.00 0.00 0.00 3.20
1018 5006 1.112916 TGGGTGTCGAGCTTGTGAGA 61.113 55.000 0.00 0.00 0.00 3.27
1049 5038 1.300388 AGTACGTCGTGCACCAACC 60.300 57.895 15.94 0.00 0.00 3.77
1060 5050 3.670091 GCACTAGAACTGGACAGTACGTC 60.670 52.174 5.25 8.69 41.58 4.34
1261 5251 4.760047 ATCACCCGGTCGCAGCAC 62.760 66.667 0.00 0.00 0.00 4.40
1301 5291 5.348986 CGTCATCTTCCTCTTTTTATCGGA 58.651 41.667 0.00 0.00 0.00 4.55
1339 5329 4.554036 GCGGGAGGATGGCAGGTC 62.554 72.222 0.00 0.00 0.00 3.85
1369 5359 4.871933 ATTTTCGCACCTTCTTTTGGAT 57.128 36.364 0.00 0.00 0.00 3.41
1389 5379 5.307204 AGGAGTACTTAGTAGCGATCGAAT 58.693 41.667 21.57 9.02 0.00 3.34
1403 5393 7.830928 TCCATCCTGGCAAGTAGGAGTACTT 62.831 48.000 0.00 0.00 46.81 2.24
1404 5394 2.921834 TCCTGGCAAGTAGGAGTACT 57.078 50.000 0.00 0.00 41.61 2.73
1405 5395 2.103263 CCATCCTGGCAAGTAGGAGTAC 59.897 54.545 0.00 0.00 46.81 2.73
1406 5396 2.023404 TCCATCCTGGCAAGTAGGAGTA 60.023 50.000 0.00 0.00 46.81 2.59
1407 5397 1.207791 CCATCCTGGCAAGTAGGAGT 58.792 55.000 0.00 0.00 46.81 3.85
1410 5400 1.839994 TCTTCCATCCTGGCAAGTAGG 59.160 52.381 0.00 0.00 37.47 3.18
1411 5401 3.634397 TTCTTCCATCCTGGCAAGTAG 57.366 47.619 0.00 0.00 37.47 2.57
1412 5402 4.228210 AGAATTCTTCCATCCTGGCAAGTA 59.772 41.667 0.88 0.00 37.47 2.24
1414 5404 3.380637 CAGAATTCTTCCATCCTGGCAAG 59.619 47.826 4.86 0.00 37.47 4.01
1415 5405 3.010472 TCAGAATTCTTCCATCCTGGCAA 59.990 43.478 4.86 0.00 37.47 4.52
1416 5406 2.577563 TCAGAATTCTTCCATCCTGGCA 59.422 45.455 4.86 0.00 37.47 4.92
1417 5407 3.287867 TCAGAATTCTTCCATCCTGGC 57.712 47.619 4.86 0.00 37.47 4.85
1418 5408 5.301298 GGAATTCAGAATTCTTCCATCCTGG 59.699 44.000 27.66 0.00 45.17 4.45
1419 5409 6.127793 AGGAATTCAGAATTCTTCCATCCTG 58.872 40.000 27.66 4.19 45.17 3.86
1420 5410 6.338591 AGGAATTCAGAATTCTTCCATCCT 57.661 37.500 27.66 19.24 45.17 3.24
1445 5437 1.666553 CGTGCTTCGTGTAAGGGCA 60.667 57.895 0.00 0.00 35.58 5.36
1452 5444 1.881252 AAACGCTCGTGCTTCGTGT 60.881 52.632 7.97 0.00 40.80 4.49
1673 5681 2.988493 CTGCATGCAACAAAATAGCGTT 59.012 40.909 22.88 0.00 0.00 4.84
1844 5862 1.025647 GTCGACGACAGTAGGAGGCT 61.026 60.000 22.66 0.00 32.09 4.58
2112 6142 0.176680 AGTGAAGCAGATCGCCGAAT 59.823 50.000 0.00 0.00 44.04 3.34
2148 6178 2.758089 GCACATTCGCTGAGGCAGG 61.758 63.158 0.00 0.00 38.60 4.85
2159 6189 0.944311 ACAGGTCGTGTCGCACATTC 60.944 55.000 9.95 1.09 31.90 2.67
2160 6190 1.069090 ACAGGTCGTGTCGCACATT 59.931 52.632 9.95 0.00 31.90 2.71
2161 6191 1.664649 CACAGGTCGTGTCGCACAT 60.665 57.895 9.95 0.00 41.03 3.21
2162 6192 2.279186 CACAGGTCGTGTCGCACA 60.279 61.111 9.95 0.00 41.03 4.57
2250 6280 1.846124 GGAACCTCTCACCCACCCA 60.846 63.158 0.00 0.00 0.00 4.51
2269 6299 0.524862 CATCACAACCTCTTGCAGCC 59.475 55.000 0.00 0.00 0.00 4.85
2280 6310 5.874810 TGATTAGCCAACTCTACATCACAAC 59.125 40.000 0.00 0.00 0.00 3.32
2325 6355 6.688637 AACTACTACCTTTGGTGAACAAAC 57.311 37.500 0.00 0.00 43.81 2.93
2334 6364 7.565680 ACCATCTGATTAACTACTACCTTTGG 58.434 38.462 0.00 0.00 0.00 3.28
2339 6369 9.880157 TGTTTAACCATCTGATTAACTACTACC 57.120 33.333 0.00 0.00 0.00 3.18
2354 6384 7.096230 CCGAGTTTGTCAATTTGTTTAACCATC 60.096 37.037 0.00 0.00 0.00 3.51
2412 7106 9.562583 CTTTTGTTTGCTTACTGTTTGTTACTA 57.437 29.630 0.00 0.00 0.00 1.82
2414 7108 8.455598 TCTTTTGTTTGCTTACTGTTTGTTAC 57.544 30.769 0.00 0.00 0.00 2.50
2416 7110 9.301153 CTATCTTTTGTTTGCTTACTGTTTGTT 57.699 29.630 0.00 0.00 0.00 2.83
2418 7112 9.515020 TTCTATCTTTTGTTTGCTTACTGTTTG 57.485 29.630 0.00 0.00 0.00 2.93
2422 7116 9.121517 CACATTCTATCTTTTGTTTGCTTACTG 57.878 33.333 0.00 0.00 0.00 2.74
2423 7117 8.299570 CCACATTCTATCTTTTGTTTGCTTACT 58.700 33.333 0.00 0.00 0.00 2.24
2424 7118 7.062255 GCCACATTCTATCTTTTGTTTGCTTAC 59.938 37.037 0.00 0.00 0.00 2.34
2425 7119 7.090173 GCCACATTCTATCTTTTGTTTGCTTA 58.910 34.615 0.00 0.00 0.00 3.09
2426 7120 5.928264 GCCACATTCTATCTTTTGTTTGCTT 59.072 36.000 0.00 0.00 0.00 3.91
2427 7121 5.473039 GCCACATTCTATCTTTTGTTTGCT 58.527 37.500 0.00 0.00 0.00 3.91
2428 7122 4.627035 GGCCACATTCTATCTTTTGTTTGC 59.373 41.667 0.00 0.00 0.00 3.68
2429 7123 6.029346 AGGCCACATTCTATCTTTTGTTTG 57.971 37.500 5.01 0.00 0.00 2.93
2430 7124 6.267471 TGAAGGCCACATTCTATCTTTTGTTT 59.733 34.615 5.01 0.00 0.00 2.83
2451 7145 0.111253 AACTGGGCCTTGGAGTGAAG 59.889 55.000 4.53 0.00 0.00 3.02
2452 7146 0.110486 GAACTGGGCCTTGGAGTGAA 59.890 55.000 4.53 0.00 0.00 3.18
2458 7152 0.033920 GCAAAAGAACTGGGCCTTGG 59.966 55.000 4.53 0.00 0.00 3.61
2460 7154 0.398381 TGGCAAAAGAACTGGGCCTT 60.398 50.000 4.53 0.00 44.85 4.35
2462 7156 0.827507 TCTGGCAAAAGAACTGGGCC 60.828 55.000 0.00 0.00 44.82 5.80
2463 7157 1.039856 TTCTGGCAAAAGAACTGGGC 58.960 50.000 0.00 0.00 31.19 5.36
2464 7158 3.057033 CAGATTCTGGCAAAAGAACTGGG 60.057 47.826 5.73 0.00 38.95 4.45
2465 7159 3.057033 CCAGATTCTGGCAAAAGAACTGG 60.057 47.826 19.49 18.64 45.13 4.00
2466 7160 4.170292 CCAGATTCTGGCAAAAGAACTG 57.830 45.455 19.49 12.95 45.13 3.16
2490 7184 1.709994 GGGGCGGATTCTGGGAGAAT 61.710 60.000 0.00 0.00 46.84 2.40
2491 7185 2.375345 GGGGCGGATTCTGGGAGAA 61.375 63.158 0.00 0.00 38.78 2.87
2492 7186 2.768344 GGGGCGGATTCTGGGAGA 60.768 66.667 0.00 0.00 0.00 3.71
2493 7187 2.965226 TAGGGGGCGGATTCTGGGAG 62.965 65.000 0.00 0.00 0.00 4.30
2494 7188 3.029522 TAGGGGGCGGATTCTGGGA 62.030 63.158 0.00 0.00 0.00 4.37
2495 7189 2.447765 TAGGGGGCGGATTCTGGG 60.448 66.667 0.00 0.00 0.00 4.45
2496 7190 2.819284 GGTAGGGGGCGGATTCTGG 61.819 68.421 0.00 0.00 0.00 3.86
2497 7191 2.819284 GGGTAGGGGGCGGATTCTG 61.819 68.421 0.00 0.00 0.00 3.02
2498 7192 2.447959 GGGTAGGGGGCGGATTCT 60.448 66.667 0.00 0.00 0.00 2.40
2499 7193 2.770904 TGGGTAGGGGGCGGATTC 60.771 66.667 0.00 0.00 0.00 2.52
2500 7194 2.772622 CTGGGTAGGGGGCGGATT 60.773 66.667 0.00 0.00 0.00 3.01
2504 7198 4.176752 GAAGCTGGGTAGGGGGCG 62.177 72.222 0.00 0.00 0.00 6.13
2505 7199 2.692741 AGAAGCTGGGTAGGGGGC 60.693 66.667 0.00 0.00 0.00 5.80
2506 7200 2.073101 GGAGAAGCTGGGTAGGGGG 61.073 68.421 0.00 0.00 0.00 5.40
2507 7201 2.073101 GGGAGAAGCTGGGTAGGGG 61.073 68.421 0.00 0.00 0.00 4.79
2508 7202 1.306997 TGGGAGAAGCTGGGTAGGG 60.307 63.158 0.00 0.00 0.00 3.53
2509 7203 0.325671 TCTGGGAGAAGCTGGGTAGG 60.326 60.000 0.00 0.00 0.00 3.18
2510 7204 1.573108 TTCTGGGAGAAGCTGGGTAG 58.427 55.000 0.00 0.00 29.50 3.18
2511 7205 2.119495 GATTCTGGGAGAAGCTGGGTA 58.881 52.381 0.00 0.00 37.62 3.69
2512 7206 0.915364 GATTCTGGGAGAAGCTGGGT 59.085 55.000 0.00 0.00 37.62 4.51
2513 7207 3.796764 GATTCTGGGAGAAGCTGGG 57.203 57.895 0.00 0.00 37.62 4.45
2517 7211 2.682352 GCTCAAAGATTCTGGGAGAAGC 59.318 50.000 15.41 0.00 40.68 3.86
2518 7212 3.277715 GGCTCAAAGATTCTGGGAGAAG 58.722 50.000 15.41 0.00 37.69 2.85
2519 7213 2.025887 GGGCTCAAAGATTCTGGGAGAA 60.026 50.000 15.41 0.00 38.78 2.87
2520 7214 1.561542 GGGCTCAAAGATTCTGGGAGA 59.438 52.381 15.41 0.14 0.00 3.71
2521 7215 1.409381 GGGGCTCAAAGATTCTGGGAG 60.409 57.143 9.42 9.42 0.00 4.30
2522 7216 0.625849 GGGGCTCAAAGATTCTGGGA 59.374 55.000 0.00 0.00 0.00 4.37
2523 7217 0.332632 TGGGGCTCAAAGATTCTGGG 59.667 55.000 0.00 0.00 0.00 4.45
2524 7218 2.449137 ATGGGGCTCAAAGATTCTGG 57.551 50.000 0.00 0.00 0.00 3.86
2525 7219 3.512724 ACAAATGGGGCTCAAAGATTCTG 59.487 43.478 0.00 0.00 0.00 3.02
2526 7220 3.782992 ACAAATGGGGCTCAAAGATTCT 58.217 40.909 0.00 0.00 0.00 2.40
2527 7221 4.221482 AGAACAAATGGGGCTCAAAGATTC 59.779 41.667 0.00 0.00 0.00 2.52
2528 7222 4.162651 AGAACAAATGGGGCTCAAAGATT 58.837 39.130 0.00 0.00 0.00 2.40
2529 7223 3.782992 AGAACAAATGGGGCTCAAAGAT 58.217 40.909 0.00 0.00 0.00 2.40
2530 7224 3.243359 AGAACAAATGGGGCTCAAAGA 57.757 42.857 0.00 0.00 0.00 2.52
2531 7225 3.826157 TGTAGAACAAATGGGGCTCAAAG 59.174 43.478 0.00 0.00 0.00 2.77
2532 7226 3.838565 TGTAGAACAAATGGGGCTCAAA 58.161 40.909 0.00 0.00 0.00 2.69
2533 7227 3.517296 TGTAGAACAAATGGGGCTCAA 57.483 42.857 0.00 0.00 0.00 3.02
2534 7228 3.517296 TTGTAGAACAAATGGGGCTCA 57.483 42.857 0.00 0.00 34.76 4.26
2535 7229 3.381590 GGATTGTAGAACAAATGGGGCTC 59.618 47.826 0.00 0.00 41.96 4.70
2536 7230 3.011708 AGGATTGTAGAACAAATGGGGCT 59.988 43.478 0.00 0.00 41.96 5.19
2537 7231 3.131046 CAGGATTGTAGAACAAATGGGGC 59.869 47.826 0.00 0.00 41.96 5.80
2538 7232 4.344104 ACAGGATTGTAGAACAAATGGGG 58.656 43.478 0.00 0.00 41.96 4.96
2539 7233 5.256474 AGACAGGATTGTAGAACAAATGGG 58.744 41.667 0.00 0.00 41.96 4.00
2540 7234 7.921786 TTAGACAGGATTGTAGAACAAATGG 57.078 36.000 0.00 0.00 41.96 3.16
2560 7254 7.568349 TCCTGTCTAGTTACGGTCTAATTAGA 58.432 38.462 11.24 11.24 0.00 2.10
2561 7255 7.798596 TCCTGTCTAGTTACGGTCTAATTAG 57.201 40.000 6.11 6.11 0.00 1.73
2562 7256 8.627403 CAATCCTGTCTAGTTACGGTCTAATTA 58.373 37.037 0.00 0.00 0.00 1.40
2563 7257 7.123847 ACAATCCTGTCTAGTTACGGTCTAATT 59.876 37.037 0.00 0.00 0.00 1.40
2564 7258 6.606395 ACAATCCTGTCTAGTTACGGTCTAAT 59.394 38.462 0.00 0.00 0.00 1.73
2565 7259 5.948162 ACAATCCTGTCTAGTTACGGTCTAA 59.052 40.000 0.00 0.00 0.00 2.10
2566 7260 5.503927 ACAATCCTGTCTAGTTACGGTCTA 58.496 41.667 0.00 0.00 0.00 2.59
2567 7261 4.342359 ACAATCCTGTCTAGTTACGGTCT 58.658 43.478 0.00 0.00 0.00 3.85
2568 7262 4.715527 ACAATCCTGTCTAGTTACGGTC 57.284 45.455 0.00 0.00 0.00 4.79
2569 7263 5.503927 TCTACAATCCTGTCTAGTTACGGT 58.496 41.667 0.00 0.00 36.96 4.83
2570 7264 6.127814 TGTTCTACAATCCTGTCTAGTTACGG 60.128 42.308 0.00 0.00 36.96 4.02
2571 7265 6.849502 TGTTCTACAATCCTGTCTAGTTACG 58.150 40.000 0.00 0.00 36.96 3.18
2572 7266 9.141400 CTTTGTTCTACAATCCTGTCTAGTTAC 57.859 37.037 0.00 0.00 38.00 2.50
2573 7267 8.311836 CCTTTGTTCTACAATCCTGTCTAGTTA 58.688 37.037 0.00 0.00 38.00 2.24
2574 7268 7.162082 CCTTTGTTCTACAATCCTGTCTAGTT 58.838 38.462 0.00 0.00 38.00 2.24
2575 7269 6.295916 CCCTTTGTTCTACAATCCTGTCTAGT 60.296 42.308 0.00 0.00 38.00 2.57
2576 7270 6.109359 CCCTTTGTTCTACAATCCTGTCTAG 58.891 44.000 0.00 0.00 38.00 2.43
2577 7271 5.045869 CCCCTTTGTTCTACAATCCTGTCTA 60.046 44.000 0.00 0.00 38.00 2.59
2578 7272 4.263506 CCCCTTTGTTCTACAATCCTGTCT 60.264 45.833 0.00 0.00 38.00 3.41
2579 7273 4.010349 CCCCTTTGTTCTACAATCCTGTC 58.990 47.826 0.00 0.00 38.00 3.51
2580 7274 3.245264 CCCCCTTTGTTCTACAATCCTGT 60.245 47.826 0.00 0.00 38.00 4.00
2581 7275 3.356290 CCCCCTTTGTTCTACAATCCTG 58.644 50.000 0.00 0.00 38.00 3.86
2582 7276 2.291605 GCCCCCTTTGTTCTACAATCCT 60.292 50.000 0.00 0.00 38.00 3.24
2583 7277 2.100197 GCCCCCTTTGTTCTACAATCC 58.900 52.381 0.00 0.00 38.00 3.01
2584 7278 3.017442 GAGCCCCCTTTGTTCTACAATC 58.983 50.000 0.00 0.00 38.00 2.67
2585 7279 2.378547 TGAGCCCCCTTTGTTCTACAAT 59.621 45.455 0.00 0.00 38.00 2.71
2586 7280 1.777878 TGAGCCCCCTTTGTTCTACAA 59.222 47.619 0.00 0.00 36.11 2.41
2587 7281 1.440618 TGAGCCCCCTTTGTTCTACA 58.559 50.000 0.00 0.00 0.00 2.74
2588 7282 2.579410 TTGAGCCCCCTTTGTTCTAC 57.421 50.000 0.00 0.00 0.00 2.59
2589 7283 2.714250 TCTTTGAGCCCCCTTTGTTCTA 59.286 45.455 0.00 0.00 0.00 2.10
2590 7284 1.499007 TCTTTGAGCCCCCTTTGTTCT 59.501 47.619 0.00 0.00 0.00 3.01
2591 7285 1.995376 TCTTTGAGCCCCCTTTGTTC 58.005 50.000 0.00 0.00 0.00 3.18
2592 7286 2.702270 ATCTTTGAGCCCCCTTTGTT 57.298 45.000 0.00 0.00 0.00 2.83
2593 7287 2.110721 AGAATCTTTGAGCCCCCTTTGT 59.889 45.455 0.00 0.00 0.00 2.83
2594 7288 2.494870 CAGAATCTTTGAGCCCCCTTTG 59.505 50.000 0.00 0.00 0.00 2.77
2595 7289 2.558350 CCAGAATCTTTGAGCCCCCTTT 60.558 50.000 0.00 0.00 0.00 3.11
2596 7290 1.006400 CCAGAATCTTTGAGCCCCCTT 59.994 52.381 0.00 0.00 0.00 3.95
2597 7291 0.627986 CCAGAATCTTTGAGCCCCCT 59.372 55.000 0.00 0.00 0.00 4.79
2598 7292 0.396278 CCCAGAATCTTTGAGCCCCC 60.396 60.000 0.00 0.00 0.00 5.40
2599 7293 0.625849 TCCCAGAATCTTTGAGCCCC 59.374 55.000 0.00 0.00 0.00 5.80
2600 7294 1.561542 TCTCCCAGAATCTTTGAGCCC 59.438 52.381 1.93 0.00 0.00 5.19
2601 7295 3.277715 CTTCTCCCAGAATCTTTGAGCC 58.722 50.000 1.93 0.00 33.13 4.70
2602 7296 2.682352 GCTTCTCCCAGAATCTTTGAGC 59.318 50.000 1.93 0.00 33.13 4.26
2603 7297 3.940221 CAGCTTCTCCCAGAATCTTTGAG 59.060 47.826 0.00 0.62 33.13 3.02
2604 7298 3.307975 CCAGCTTCTCCCAGAATCTTTGA 60.308 47.826 0.00 0.00 33.13 2.69
2605 7299 3.015327 CCAGCTTCTCCCAGAATCTTTG 58.985 50.000 0.00 0.00 33.13 2.77
2606 7300 2.025510 CCCAGCTTCTCCCAGAATCTTT 60.026 50.000 0.00 0.00 33.13 2.52
2607 7301 1.563410 CCCAGCTTCTCCCAGAATCTT 59.437 52.381 0.00 0.00 33.13 2.40
2608 7302 1.211456 CCCAGCTTCTCCCAGAATCT 58.789 55.000 0.00 0.00 33.13 2.40
2609 7303 0.915364 ACCCAGCTTCTCCCAGAATC 59.085 55.000 0.00 0.00 33.13 2.52
2610 7304 2.122768 CTACCCAGCTTCTCCCAGAAT 58.877 52.381 0.00 0.00 33.13 2.40
2611 7305 1.573108 CTACCCAGCTTCTCCCAGAA 58.427 55.000 0.00 0.00 32.50 3.02
2612 7306 0.325671 CCTACCCAGCTTCTCCCAGA 60.326 60.000 0.00 0.00 0.00 3.86
2613 7307 1.341156 CCCTACCCAGCTTCTCCCAG 61.341 65.000 0.00 0.00 0.00 4.45
2614 7308 1.306997 CCCTACCCAGCTTCTCCCA 60.307 63.158 0.00 0.00 0.00 4.37
2615 7309 2.073101 CCCCTACCCAGCTTCTCCC 61.073 68.421 0.00 0.00 0.00 4.30
2616 7310 1.307084 ACCCCTACCCAGCTTCTCC 60.307 63.158 0.00 0.00 0.00 3.71
2617 7311 1.677637 CGACCCCTACCCAGCTTCTC 61.678 65.000 0.00 0.00 0.00 2.87
2618 7312 1.686110 CGACCCCTACCCAGCTTCT 60.686 63.158 0.00 0.00 0.00 2.85
2619 7313 2.732619 CCGACCCCTACCCAGCTTC 61.733 68.421 0.00 0.00 0.00 3.86
2620 7314 2.547123 ATCCGACCCCTACCCAGCTT 62.547 60.000 0.00 0.00 0.00 3.74
2621 7315 2.547123 AATCCGACCCCTACCCAGCT 62.547 60.000 0.00 0.00 0.00 4.24
2622 7316 2.041206 GAATCCGACCCCTACCCAGC 62.041 65.000 0.00 0.00 0.00 4.85
2623 7317 0.398664 AGAATCCGACCCCTACCCAG 60.399 60.000 0.00 0.00 0.00 4.45
2624 7318 0.689745 CAGAATCCGACCCCTACCCA 60.690 60.000 0.00 0.00 0.00 4.51
2625 7319 1.408453 CCAGAATCCGACCCCTACCC 61.408 65.000 0.00 0.00 0.00 3.69
2626 7320 1.408453 CCCAGAATCCGACCCCTACC 61.408 65.000 0.00 0.00 0.00 3.18
2627 7321 0.398098 TCCCAGAATCCGACCCCTAC 60.398 60.000 0.00 0.00 0.00 3.18
2628 7322 0.105658 CTCCCAGAATCCGACCCCTA 60.106 60.000 0.00 0.00 0.00 3.53
2629 7323 1.383248 CTCCCAGAATCCGACCCCT 60.383 63.158 0.00 0.00 0.00 4.79
2630 7324 0.981277 TTCTCCCAGAATCCGACCCC 60.981 60.000 0.00 0.00 0.00 4.95
2631 7325 1.132500 ATTCTCCCAGAATCCGACCC 58.868 55.000 0.00 0.00 40.75 4.46
2654 7348 4.156739 GCCCAGTTCTTTTACCAGAATCTG 59.843 45.833 2.68 2.68 35.23 2.90
2655 7349 4.336280 GCCCAGTTCTTTTACCAGAATCT 58.664 43.478 0.00 0.00 35.23 2.40
2656 7350 3.444034 GGCCCAGTTCTTTTACCAGAATC 59.556 47.826 0.00 0.00 35.23 2.52
2657 7351 3.431415 GGCCCAGTTCTTTTACCAGAAT 58.569 45.455 0.00 0.00 35.23 2.40
2658 7352 2.490168 GGGCCCAGTTCTTTTACCAGAA 60.490 50.000 19.95 0.00 0.00 3.02
2659 7353 1.074889 GGGCCCAGTTCTTTTACCAGA 59.925 52.381 19.95 0.00 0.00 3.86
2660 7354 1.203001 TGGGCCCAGTTCTTTTACCAG 60.203 52.381 24.45 0.00 0.00 4.00
2661 7355 0.854218 TGGGCCCAGTTCTTTTACCA 59.146 50.000 24.45 0.00 0.00 3.25
2662 7356 2.003937 TTGGGCCCAGTTCTTTTACC 57.996 50.000 26.87 0.00 0.00 2.85
2663 7357 4.202315 ACAATTTGGGCCCAGTTCTTTTAC 60.202 41.667 26.87 0.00 0.00 2.01
2664 7358 3.970640 ACAATTTGGGCCCAGTTCTTTTA 59.029 39.130 26.87 4.06 0.00 1.52
2665 7359 2.777114 ACAATTTGGGCCCAGTTCTTTT 59.223 40.909 26.87 10.55 0.00 2.27
2666 7360 2.407562 ACAATTTGGGCCCAGTTCTTT 58.592 42.857 26.87 12.35 0.00 2.52
2667 7361 2.101640 ACAATTTGGGCCCAGTTCTT 57.898 45.000 26.87 14.03 0.00 2.52
2668 7362 1.693606 CAACAATTTGGGCCCAGTTCT 59.306 47.619 26.87 9.24 0.00 3.01
2669 7363 1.877680 GCAACAATTTGGGCCCAGTTC 60.878 52.381 26.87 14.66 32.81 3.01
2670 7364 0.108396 GCAACAATTTGGGCCCAGTT 59.892 50.000 26.87 22.30 32.81 3.16
2671 7365 1.754107 GCAACAATTTGGGCCCAGT 59.246 52.632 26.87 17.16 32.81 4.00
2672 7366 1.003476 GGCAACAATTTGGGCCCAG 60.003 57.895 26.87 16.40 36.38 4.45
2673 7367 3.155750 GGCAACAATTTGGGCCCA 58.844 55.556 24.45 24.45 36.38 5.36
2675 7369 1.296392 GAGGGCAACAATTTGGGCC 59.704 57.895 20.11 20.11 46.79 5.80
2676 7370 1.079888 CGAGGGCAACAATTTGGGC 60.080 57.895 0.78 4.23 39.74 5.36
2677 7371 1.591183 CCGAGGGCAACAATTTGGG 59.409 57.895 0.78 0.00 39.74 4.12
2678 7372 1.591183 CCCGAGGGCAACAATTTGG 59.409 57.895 0.78 0.00 39.74 3.28
2694 7388 1.067635 CAGTATGTTGCTGTTTGGCCC 60.068 52.381 0.00 0.00 0.00 5.80
2735 7429 6.322201 ACACATTGAATATCCAGTGAAATCCC 59.678 38.462 0.00 0.00 0.00 3.85
2854 7548 5.060662 TCCTCGTGTAATATAGATGCTGC 57.939 43.478 0.00 0.00 0.00 5.25
2880 7574 1.228124 TCGCCCCTCACCTTTGTTG 60.228 57.895 0.00 0.00 0.00 3.33
2901 7595 0.035317 TCACAAGACTTGCCTCGCAT 59.965 50.000 15.24 0.00 38.76 4.73
2942 7636 4.039366 GGTGTCTCTGAACTCTTAAGTGGT 59.961 45.833 9.23 1.93 35.36 4.16
2949 7643 3.300388 TCTGTGGTGTCTCTGAACTCTT 58.700 45.455 0.00 0.00 0.00 2.85
3055 7749 6.660521 ACAACACACTTGGATGAATCATATGT 59.339 34.615 1.90 0.00 0.00 2.29


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

AutoCloner maintained by Alex Coulton.