Multiple sequence alignment - TraesCS7A01G378500

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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 TraesCS7A01G378500 chr7A 100.000 4478 0 0 1 4478 553994549 553999026 0.000000e+00 8270.0
1 TraesCS7A01G378500 chr7D 93.397 2726 114 27 1797 4478 485541368 485544071 0.000000e+00 3976.0
2 TraesCS7A01G378500 chr7D 95.262 401 13 4 745 1143 485540423 485540819 8.170000e-177 630.0
3 TraesCS7A01G378500 chr7D 92.857 420 21 9 1331 1747 485540947 485541360 6.410000e-168 601.0
4 TraesCS7A01G378500 chr7D 86.434 516 57 7 3966 4478 171145050 171144545 1.820000e-153 553.0
5 TraesCS7A01G378500 chr7D 87.981 208 18 5 304 509 485539119 485539321 5.790000e-59 239.0
6 TraesCS7A01G378500 chr7D 77.690 381 63 16 4103 4473 165950381 165950749 3.510000e-51 213.0
7 TraesCS7A01G378500 chr7B 94.097 2575 99 27 1288 3831 513304173 513306725 0.000000e+00 3864.0
8 TraesCS7A01G378500 chr7B 88.128 657 28 20 535 1148 513303344 513303993 0.000000e+00 736.0
9 TraesCS7A01G378500 chr7B 86.141 469 36 11 1 467 513302894 513303335 3.130000e-131 479.0
10 TraesCS7A01G378500 chr6D 86.873 518 55 4 3965 4478 329882418 329881910 6.500000e-158 568.0
11 TraesCS7A01G378500 chr5A 86.015 522 55 14 3965 4478 604198734 604198223 1.100000e-150 544.0
12 TraesCS7A01G378500 chr3B 85.465 516 61 6 3965 4475 497363916 497364422 3.970000e-145 525.0
13 TraesCS7A01G378500 chr3B 91.667 48 4 0 2066 2113 402451809 402451762 2.890000e-07 67.6
14 TraesCS7A01G378500 chr4A 85.214 514 65 7 3964 4475 21639379 21639883 6.640000e-143 518.0
15 TraesCS7A01G378500 chr6B 86.287 474 63 2 3965 4437 649816294 649815822 8.590000e-142 514.0
16 TraesCS7A01G378500 chr6B 84.778 519 63 14 3965 4478 72193792 72193285 1.440000e-139 507.0
17 TraesCS7A01G378500 chr5D 84.825 514 66 10 3965 4474 422736093 422735588 1.440000e-139 507.0
18 TraesCS7A01G378500 chr4D 79.054 148 28 2 1519 1666 442176699 442176555 1.030000e-16 99.0
19 TraesCS7A01G378500 chr4B 77.703 148 30 2 1519 1666 549144027 549143883 2.220000e-13 87.9
20 TraesCS7A01G378500 chr5B 88.571 70 6 2 3813 3881 697498088 697498156 2.870000e-12 84.2
21 TraesCS7A01G378500 chr3A 91.667 48 4 0 2066 2113 411263715 411263668 2.890000e-07 67.6
22 TraesCS7A01G378500 chr3D 94.737 38 2 0 2076 2113 316815910 316815947 4.840000e-05 60.2


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 TraesCS7A01G378500 chr7A 553994549 553999026 4477 False 8270.0 8270 100.000000 1 4478 1 chr7A.!!$F1 4477
1 TraesCS7A01G378500 chr7D 485539119 485544071 4952 False 1361.5 3976 92.374250 304 4478 4 chr7D.!!$F2 4174
2 TraesCS7A01G378500 chr7D 171144545 171145050 505 True 553.0 553 86.434000 3966 4478 1 chr7D.!!$R1 512
3 TraesCS7A01G378500 chr7B 513302894 513306725 3831 False 1693.0 3864 89.455333 1 3831 3 chr7B.!!$F1 3830
4 TraesCS7A01G378500 chr6D 329881910 329882418 508 True 568.0 568 86.873000 3965 4478 1 chr6D.!!$R1 513
5 TraesCS7A01G378500 chr5A 604198223 604198734 511 True 544.0 544 86.015000 3965 4478 1 chr5A.!!$R1 513
6 TraesCS7A01G378500 chr3B 497363916 497364422 506 False 525.0 525 85.465000 3965 4475 1 chr3B.!!$F1 510
7 TraesCS7A01G378500 chr4A 21639379 21639883 504 False 518.0 518 85.214000 3964 4475 1 chr4A.!!$F1 511
8 TraesCS7A01G378500 chr6B 72193285 72193792 507 True 507.0 507 84.778000 3965 4478 1 chr6B.!!$R1 513
9 TraesCS7A01G378500 chr5D 422735588 422736093 505 True 507.0 507 84.825000 3965 4474 1 chr5D.!!$R1 509

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
819 1832 0.109873 AACGAACTAGAGACGGTGCG 60.110 55.0 0.00 0.00 40.04 5.34 F
1159 2176 0.108138 CCAGTCTCCCATGTCGTTCC 60.108 60.0 0.00 0.00 0.00 3.62 F
1160 2177 0.108138 CAGTCTCCCATGTCGTTCCC 60.108 60.0 0.00 0.00 0.00 3.97 F
2379 3501 0.247736 GCAACCTCGAGGACATCAGT 59.752 55.0 37.69 10.86 38.94 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2295 3417 2.126031 GGCGTGAACCCGAGAGAC 60.126 66.667 0.0 0.0 0.00 3.36 R
3083 4214 0.105593 CCCCTGATCACAGATGACCG 59.894 60.000 0.0 0.0 46.03 4.79 R
3088 4219 1.050988 CCCGTCCCCTGATCACAGAT 61.051 60.000 0.0 0.0 46.03 2.90 R
3829 5001 0.107165 TCTTCTCTGGCGAGATCCGA 60.107 55.000 0.0 0.0 45.27 4.55 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
52 53 2.135139 CTGTTGTACTTCGCAAGCTCA 58.865 47.619 0.00 0.00 37.18 4.26
53 54 2.738846 CTGTTGTACTTCGCAAGCTCAT 59.261 45.455 0.00 0.00 37.18 2.90
54 55 2.480037 TGTTGTACTTCGCAAGCTCATG 59.520 45.455 0.00 0.00 37.18 3.07
55 56 2.736721 GTTGTACTTCGCAAGCTCATGA 59.263 45.455 0.00 0.00 37.18 3.07
56 57 2.337583 TGTACTTCGCAAGCTCATGAC 58.662 47.619 0.00 0.00 37.18 3.06
57 58 2.288763 TGTACTTCGCAAGCTCATGACA 60.289 45.455 0.00 0.00 37.18 3.58
58 59 1.436600 ACTTCGCAAGCTCATGACAG 58.563 50.000 0.00 0.00 37.18 3.51
59 60 1.270518 ACTTCGCAAGCTCATGACAGT 60.271 47.619 0.00 0.00 37.18 3.55
60 61 1.392853 CTTCGCAAGCTCATGACAGTC 59.607 52.381 0.00 0.00 37.18 3.51
61 62 0.733909 TCGCAAGCTCATGACAGTCG 60.734 55.000 0.00 0.00 37.18 4.18
62 63 0.733909 CGCAAGCTCATGACAGTCGA 60.734 55.000 0.00 0.00 0.00 4.20
63 64 1.649664 GCAAGCTCATGACAGTCGAT 58.350 50.000 0.00 0.00 0.00 3.59
64 65 1.326852 GCAAGCTCATGACAGTCGATG 59.673 52.381 0.00 1.82 0.00 3.84
110 111 3.129988 CAGGCCTTGAGATTTCCATGTTC 59.870 47.826 0.00 0.00 0.00 3.18
112 113 4.228210 AGGCCTTGAGATTTCCATGTTCTA 59.772 41.667 0.00 0.00 0.00 2.10
114 115 4.943705 GCCTTGAGATTTCCATGTTCTACA 59.056 41.667 0.00 0.00 0.00 2.74
146 147 2.957402 ACAAGGAGCAAACATGAGGA 57.043 45.000 0.00 0.00 0.00 3.71
157 158 1.516110 ACATGAGGATTCAGGGGAGG 58.484 55.000 0.00 0.00 39.36 4.30
169 170 2.685999 GGGAGGCAAGCCAGGAAT 59.314 61.111 14.40 0.00 38.92 3.01
178 179 1.961394 CAAGCCAGGAATGATGGATGG 59.039 52.381 0.00 0.00 40.51 3.51
183 184 2.290768 CCAGGAATGATGGATGGCCTAG 60.291 54.545 3.32 0.00 40.51 3.02
224 225 1.959985 CCTCTGCTCGTACTCCATGAT 59.040 52.381 0.00 0.00 0.00 2.45
225 226 2.288091 CCTCTGCTCGTACTCCATGATG 60.288 54.545 0.00 0.00 0.00 3.07
234 235 3.243771 CGTACTCCATGATGGTTCCTACC 60.244 52.174 11.87 0.00 45.26 3.18
249 250 1.408822 CCTACCATTGGGAGACAAGCC 60.409 57.143 17.13 0.00 43.48 4.35
251 252 0.706433 ACCATTGGGAGACAAGCCAT 59.294 50.000 7.78 0.00 43.48 4.40
265 266 4.543689 ACAAGCCATGAAAGATGGATGAT 58.456 39.130 4.83 0.00 41.64 2.45
267 268 3.764218 AGCCATGAAAGATGGATGATCC 58.236 45.455 4.05 4.05 41.64 3.36
287 288 3.356529 CAAGGATTGGCTGTTCCTACT 57.643 47.619 4.30 0.00 43.94 2.57
293 294 1.951209 TGGCTGTTCCTACTCCATGA 58.049 50.000 0.00 0.00 35.26 3.07
304 305 1.280457 ACTCCATGACAGTTCCTCCC 58.720 55.000 0.00 0.00 0.00 4.30
305 306 0.176680 CTCCATGACAGTTCCTCCCG 59.823 60.000 0.00 0.00 0.00 5.14
306 307 0.252057 TCCATGACAGTTCCTCCCGA 60.252 55.000 0.00 0.00 0.00 5.14
307 308 0.833287 CCATGACAGTTCCTCCCGAT 59.167 55.000 0.00 0.00 0.00 4.18
308 309 1.473965 CCATGACAGTTCCTCCCGATG 60.474 57.143 0.00 0.00 0.00 3.84
309 310 1.482182 CATGACAGTTCCTCCCGATGA 59.518 52.381 0.00 0.00 0.00 2.92
310 311 0.895530 TGACAGTTCCTCCCGATGAC 59.104 55.000 0.00 0.00 0.00 3.06
311 312 1.187087 GACAGTTCCTCCCGATGACT 58.813 55.000 0.00 0.00 0.00 3.41
344 346 7.014615 GGTTGATGGCATTATTAGAGGAAATGT 59.985 37.037 0.00 0.00 33.96 2.71
345 347 7.514784 TGATGGCATTATTAGAGGAAATGTG 57.485 36.000 0.00 0.00 33.96 3.21
353 355 5.923733 ATTAGAGGAAATGTGTCTCGAGT 57.076 39.130 13.13 0.00 33.16 4.18
357 359 3.079578 AGGAAATGTGTCTCGAGTACGA 58.920 45.455 13.13 5.08 46.56 3.43
362 364 0.179194 GTGTCTCGAGTACGACCTGC 60.179 60.000 13.13 0.00 43.81 4.85
365 367 1.085091 TCTCGAGTACGACCTGCTTC 58.915 55.000 13.13 0.00 43.81 3.86
429 434 6.056236 CACTACAGCTCTAGTCTGGTGTATA 58.944 44.000 17.87 6.68 43.26 1.47
432 437 5.947663 ACAGCTCTAGTCTGGTGTATATCT 58.052 41.667 15.52 0.00 42.13 1.98
435 440 6.001460 AGCTCTAGTCTGGTGTATATCTCAC 58.999 44.000 0.00 3.30 35.36 3.51
437 442 6.432783 GCTCTAGTCTGGTGTATATCTCACAT 59.567 42.308 11.35 0.00 37.52 3.21
440 445 8.881262 TCTAGTCTGGTGTATATCTCACATAGA 58.119 37.037 11.35 10.75 39.02 1.98
441 446 7.994425 AGTCTGGTGTATATCTCACATAGAG 57.006 40.000 11.35 0.00 46.14 2.43
442 447 6.432783 AGTCTGGTGTATATCTCACATAGAGC 59.567 42.308 11.35 9.10 44.35 4.09
475 480 3.644265 TGACCTTCCTGTGTTAGCAGTTA 59.356 43.478 0.00 0.00 34.84 2.24
494 499 4.278419 AGTTAGCTTGTTGGATTTGTGGAC 59.722 41.667 0.00 0.00 0.00 4.02
524 529 8.514330 TGGTACAACTTACAGTGAGAAAATTT 57.486 30.769 0.00 0.00 31.92 1.82
525 530 8.617809 TGGTACAACTTACAGTGAGAAAATTTC 58.382 33.333 0.00 0.00 31.92 2.17
526 531 8.617809 GGTACAACTTACAGTGAGAAAATTTCA 58.382 33.333 8.55 0.00 0.00 2.69
529 534 7.649306 ACAACTTACAGTGAGAAAATTTCATGC 59.351 33.333 8.55 0.00 0.00 4.06
530 535 6.373779 ACTTACAGTGAGAAAATTTCATGCG 58.626 36.000 8.55 0.00 0.00 4.73
531 536 3.568538 ACAGTGAGAAAATTTCATGCGC 58.431 40.909 8.55 0.00 0.00 6.09
532 537 2.919229 CAGTGAGAAAATTTCATGCGCC 59.081 45.455 4.18 0.00 0.00 6.53
533 538 2.821969 AGTGAGAAAATTTCATGCGCCT 59.178 40.909 4.18 0.00 0.00 5.52
546 551 2.109126 GCGCCTGGTGTGATCCTTC 61.109 63.158 9.31 0.00 0.00 3.46
570 575 7.385267 TCATTTTACCACCTCAATTTTCATGG 58.615 34.615 0.00 0.00 0.00 3.66
576 581 4.340381 CCACCTCAATTTTCATGGGAGATC 59.660 45.833 0.00 0.00 0.00 2.75
604 609 8.686334 ACATTGACTATTGTTCTTTGTTTCTGT 58.314 29.630 0.00 0.00 0.00 3.41
622 627 6.377327 TTCTGTGAAAACTCTGTTCATTCC 57.623 37.500 0.00 0.00 37.34 3.01
637 642 4.589216 TCATTCCAAGCCTTTGTTTCTG 57.411 40.909 0.00 0.00 32.21 3.02
638 643 3.960102 TCATTCCAAGCCTTTGTTTCTGT 59.040 39.130 0.00 0.00 32.21 3.41
717 738 3.498774 AGCTCACAGAGTGGAAATGTT 57.501 42.857 0.00 0.00 33.87 2.71
733 754 9.736023 GTGGAAATGTTATCATTAATTCAGTCC 57.264 33.333 0.00 2.76 42.60 3.85
735 756 9.956720 GGAAATGTTATCATTAATTCAGTCCTG 57.043 33.333 0.00 0.00 42.60 3.86
740 761 9.613428 TGTTATCATTAATTCAGTCCTGTTAGG 57.387 33.333 0.00 0.00 36.46 2.69
741 762 8.560374 GTTATCATTAATTCAGTCCTGTTAGGC 58.440 37.037 0.00 0.00 34.61 3.93
743 764 6.115446 TCATTAATTCAGTCCTGTTAGGCAG 58.885 40.000 0.00 0.00 44.63 4.85
807 1820 2.495084 GAAGCTTCTCCCAAACGAACT 58.505 47.619 19.44 0.00 0.00 3.01
819 1832 0.109873 AACGAACTAGAGACGGTGCG 60.110 55.000 0.00 0.00 40.04 5.34
820 1833 1.233285 ACGAACTAGAGACGGTGCGT 61.233 55.000 0.00 0.00 42.11 5.24
987 2003 2.564947 TGGCTTTCTCTCTCTGAACCTC 59.435 50.000 0.00 0.00 0.00 3.85
988 2004 2.831526 GGCTTTCTCTCTCTGAACCTCT 59.168 50.000 0.00 0.00 0.00 3.69
1095 2111 2.561755 GGAGGAGGATCATCTATGGCCT 60.562 54.545 3.32 0.00 46.79 5.19
1148 2165 1.410882 GGTGTCTATCAGCCAGTCTCC 59.589 57.143 0.00 0.00 38.46 3.71
1149 2166 1.410882 GTGTCTATCAGCCAGTCTCCC 59.589 57.143 0.00 0.00 0.00 4.30
1150 2167 1.007118 TGTCTATCAGCCAGTCTCCCA 59.993 52.381 0.00 0.00 0.00 4.37
1152 2169 2.036992 GTCTATCAGCCAGTCTCCCATG 59.963 54.545 0.00 0.00 0.00 3.66
1155 2172 1.153489 CAGCCAGTCTCCCATGTCG 60.153 63.158 0.00 0.00 0.00 4.35
1159 2176 0.108138 CCAGTCTCCCATGTCGTTCC 60.108 60.000 0.00 0.00 0.00 3.62
1160 2177 0.108138 CAGTCTCCCATGTCGTTCCC 60.108 60.000 0.00 0.00 0.00 3.97
1162 2179 1.006758 AGTCTCCCATGTCGTTCCCTA 59.993 52.381 0.00 0.00 0.00 3.53
1164 2181 2.039418 TCTCCCATGTCGTTCCCTATG 58.961 52.381 0.00 0.00 0.00 2.23
1166 2183 0.469917 CCCATGTCGTTCCCTATGCT 59.530 55.000 0.00 0.00 0.00 3.79
1167 2184 1.134098 CCCATGTCGTTCCCTATGCTT 60.134 52.381 0.00 0.00 0.00 3.91
1168 2185 2.213499 CCATGTCGTTCCCTATGCTTC 58.787 52.381 0.00 0.00 0.00 3.86
1169 2186 2.213499 CATGTCGTTCCCTATGCTTCC 58.787 52.381 0.00 0.00 0.00 3.46
1170 2187 1.271856 TGTCGTTCCCTATGCTTCCA 58.728 50.000 0.00 0.00 0.00 3.53
1172 2189 0.539986 TCGTTCCCTATGCTTCCACC 59.460 55.000 0.00 0.00 0.00 4.61
1198 2215 2.622064 ACTGTTTGTGGGACAGAGTC 57.378 50.000 10.87 0.00 45.72 3.36
1259 2276 5.936372 ACTATTTTGGACGTTTTCTCCCTAC 59.064 40.000 0.00 0.00 0.00 3.18
1260 2277 4.426736 TTTTGGACGTTTTCTCCCTACT 57.573 40.909 0.00 0.00 0.00 2.57
1262 2279 4.796038 TTGGACGTTTTCTCCCTACTAG 57.204 45.455 0.00 0.00 0.00 2.57
1263 2280 4.038271 TGGACGTTTTCTCCCTACTAGA 57.962 45.455 0.00 0.00 0.00 2.43
1264 2281 4.410099 TGGACGTTTTCTCCCTACTAGAA 58.590 43.478 0.00 0.00 0.00 2.10
1265 2282 5.021458 TGGACGTTTTCTCCCTACTAGAAT 58.979 41.667 0.00 0.00 33.17 2.40
1266 2283 5.105473 TGGACGTTTTCTCCCTACTAGAATG 60.105 44.000 0.00 0.00 33.17 2.67
1267 2284 5.340439 ACGTTTTCTCCCTACTAGAATGG 57.660 43.478 0.00 0.00 33.17 3.16
1268 2285 4.120589 CGTTTTCTCCCTACTAGAATGGC 58.879 47.826 0.00 0.00 33.17 4.40
1271 2288 6.406624 CGTTTTCTCCCTACTAGAATGGCTAA 60.407 42.308 0.00 0.00 33.17 3.09
1272 2289 7.336396 GTTTTCTCCCTACTAGAATGGCTAAA 58.664 38.462 0.00 0.00 33.17 1.85
1273 2290 7.504926 TTTCTCCCTACTAGAATGGCTAAAA 57.495 36.000 0.00 0.00 33.17 1.52
1274 2291 6.732896 TCTCCCTACTAGAATGGCTAAAAG 57.267 41.667 0.00 0.00 0.00 2.27
1275 2292 6.203072 TCTCCCTACTAGAATGGCTAAAAGT 58.797 40.000 0.00 0.00 0.00 2.66
1277 2294 4.816925 CCCTACTAGAATGGCTAAAAGTGC 59.183 45.833 0.00 0.00 0.00 4.40
1279 2296 6.116126 CCTACTAGAATGGCTAAAAGTGCTT 58.884 40.000 0.00 0.00 0.00 3.91
1280 2297 6.258947 CCTACTAGAATGGCTAAAAGTGCTTC 59.741 42.308 0.00 0.00 0.00 3.86
1281 2298 5.560724 ACTAGAATGGCTAAAAGTGCTTCA 58.439 37.500 0.00 0.00 0.00 3.02
1282 2299 6.183347 ACTAGAATGGCTAAAAGTGCTTCAT 58.817 36.000 0.00 0.00 0.00 2.57
1283 2300 5.573337 AGAATGGCTAAAAGTGCTTCATC 57.427 39.130 0.00 0.00 0.00 2.92
1284 2301 4.400567 AGAATGGCTAAAAGTGCTTCATCC 59.599 41.667 0.00 0.00 0.00 3.51
1286 2303 1.751351 GGCTAAAAGTGCTTCATCCCC 59.249 52.381 0.00 0.00 0.00 4.81
1306 2391 3.495100 CCCTGCTAGCTAATTACCACCAG 60.495 52.174 17.23 0.00 0.00 4.00
1308 2393 3.380393 TGCTAGCTAATTACCACCAGGA 58.620 45.455 17.23 0.00 38.69 3.86
1325 2410 4.141482 ACCAGGAAGCAGTAGAAGAAACAA 60.141 41.667 0.00 0.00 0.00 2.83
1329 2414 7.428826 CAGGAAGCAGTAGAAGAAACAATTTT 58.571 34.615 0.00 0.00 0.00 1.82
1346 2468 5.185249 ACAATTTTGCTCTGCTCATGAGAAT 59.815 36.000 27.04 11.09 33.68 2.40
1356 2478 3.754850 TGCTCATGAGAATTCACCTTGTG 59.245 43.478 27.04 9.09 35.83 3.33
1428 2550 4.016706 AAGAACCCCCTGACGGCG 62.017 66.667 4.80 4.80 0.00 6.46
1587 2709 0.390860 CCCTGCTCAAGATACTCGGG 59.609 60.000 0.00 0.00 0.00 5.14
1767 2889 9.557338 GATTGAGTGAAAAAGATTGAGAAGATG 57.443 33.333 0.00 0.00 0.00 2.90
1810 2932 1.986378 TGTTGTTTTTGTTCGTTGCGG 59.014 42.857 0.00 0.00 0.00 5.69
2295 3417 0.952497 ACTGCATGCACCACTTCTCG 60.952 55.000 18.46 6.25 0.00 4.04
2298 3420 0.671781 GCATGCACCACTTCTCGTCT 60.672 55.000 14.21 0.00 0.00 4.18
2301 3423 0.598562 TGCACCACTTCTCGTCTCTC 59.401 55.000 0.00 0.00 0.00 3.20
2379 3501 0.247736 GCAACCTCGAGGACATCAGT 59.752 55.000 37.69 10.86 38.94 3.41
2757 3888 2.306341 ACATCTGCATCTTCTGGACG 57.694 50.000 0.00 0.00 0.00 4.79
3019 4150 3.700961 GCCAGGTGCGTACGTATG 58.299 61.111 17.90 10.54 0.00 2.39
3021 4152 0.738412 GCCAGGTGCGTACGTATGTT 60.738 55.000 17.90 0.00 0.00 2.71
3022 4153 1.469595 GCCAGGTGCGTACGTATGTTA 60.470 52.381 17.90 3.53 0.00 2.41
3023 4154 2.456989 CCAGGTGCGTACGTATGTTAG 58.543 52.381 17.90 2.58 0.00 2.34
3024 4155 2.159338 CCAGGTGCGTACGTATGTTAGT 60.159 50.000 17.90 0.00 0.00 2.24
3025 4156 3.065233 CCAGGTGCGTACGTATGTTAGTA 59.935 47.826 17.90 0.00 0.00 1.82
3027 4158 4.673761 CAGGTGCGTACGTATGTTAGTATG 59.326 45.833 17.90 4.95 34.07 2.39
3029 4160 5.527214 AGGTGCGTACGTATGTTAGTATGTA 59.473 40.000 17.90 0.00 33.62 2.29
3034 4165 7.011389 TGCGTACGTATGTTAGTATGTACTTCT 59.989 37.037 17.90 0.00 41.57 2.85
3035 4166 7.852945 GCGTACGTATGTTAGTATGTACTTCTT 59.147 37.037 17.90 0.00 41.57 2.52
3036 4167 9.151752 CGTACGTATGTTAGTATGTACTTCTTG 57.848 37.037 7.22 0.00 41.57 3.02
3081 4212 2.202623 GCGAACGGCGATGAGAGT 60.203 61.111 16.62 0.00 44.57 3.24
3082 4213 1.805945 GCGAACGGCGATGAGAGTT 60.806 57.895 16.62 0.00 44.57 3.01
3083 4214 1.743855 GCGAACGGCGATGAGAGTTC 61.744 60.000 16.62 3.72 44.57 3.01
3084 4215 2.279469 GAACGGCGATGAGAGTTCG 58.721 57.895 16.62 0.00 39.55 3.95
3087 4218 1.586564 CGGCGATGAGAGTTCGGTC 60.587 63.158 0.00 0.00 37.10 4.79
3088 4219 1.511305 GGCGATGAGAGTTCGGTCA 59.489 57.895 0.00 0.00 37.10 4.02
3089 4220 0.103208 GGCGATGAGAGTTCGGTCAT 59.897 55.000 0.00 0.00 37.10 3.06
3090 4221 1.482278 GCGATGAGAGTTCGGTCATC 58.518 55.000 2.79 2.79 43.83 2.92
3092 4223 2.725490 CGATGAGAGTTCGGTCATCTG 58.275 52.381 9.88 1.82 44.70 2.90
3484 4628 1.140052 TCACGCCCTTGTGAAAAGAGA 59.860 47.619 0.00 0.00 45.40 3.10
3485 4629 1.946768 CACGCCCTTGTGAAAAGAGAA 59.053 47.619 0.00 0.00 42.55 2.87
3486 4630 2.357637 CACGCCCTTGTGAAAAGAGAAA 59.642 45.455 0.00 0.00 42.55 2.52
3487 4631 2.357952 ACGCCCTTGTGAAAAGAGAAAC 59.642 45.455 0.00 0.00 0.00 2.78
3488 4632 2.357637 CGCCCTTGTGAAAAGAGAAACA 59.642 45.455 0.00 0.00 0.00 2.83
3489 4633 3.706698 GCCCTTGTGAAAAGAGAAACAC 58.293 45.455 0.00 0.00 0.00 3.32
3490 4634 3.490933 GCCCTTGTGAAAAGAGAAACACC 60.491 47.826 0.00 0.00 33.08 4.16
3491 4635 3.699038 CCCTTGTGAAAAGAGAAACACCA 59.301 43.478 0.00 0.00 33.08 4.17
3492 4636 4.342092 CCCTTGTGAAAAGAGAAACACCAT 59.658 41.667 0.00 0.00 33.08 3.55
3493 4637 5.284079 CCTTGTGAAAAGAGAAACACCATG 58.716 41.667 0.00 0.00 33.08 3.66
3496 4640 3.005791 GTGAAAAGAGAAACACCATGGGG 59.994 47.826 14.08 14.08 41.29 4.96
3523 4667 2.317609 CGGCGTGTGCTTTGCTAGT 61.318 57.895 0.00 0.00 42.25 2.57
3539 4683 6.534475 TTGCTAGTTAGGTCTTCCGAATTA 57.466 37.500 0.00 0.00 39.05 1.40
3540 4684 6.726490 TGCTAGTTAGGTCTTCCGAATTAT 57.274 37.500 0.00 0.00 39.05 1.28
3581 4725 5.384063 TGCATGTTTGTTAATGGGTACAG 57.616 39.130 0.00 0.00 0.00 2.74
3629 4773 2.037902 TGTGCACGGGTATTCTTCTTGA 59.962 45.455 13.13 0.00 0.00 3.02
3650 4794 9.981114 TCTTGATTGTTTCCTTAATTTTCCTTC 57.019 29.630 0.00 0.00 0.00 3.46
3668 4812 2.270434 TCCTTGGAGGTAATGAGGCT 57.730 50.000 0.00 0.00 36.53 4.58
3674 4818 2.843730 TGGAGGTAATGAGGCTTTGCTA 59.156 45.455 0.00 0.00 0.00 3.49
3705 4849 2.422803 GCCCAAGCTATCCCAACACATA 60.423 50.000 0.00 0.00 35.50 2.29
3719 4863 7.501844 TCCCAACACATACGATGATTGTATTA 58.498 34.615 2.55 0.00 30.28 0.98
3727 4871 9.567776 ACATACGATGATTGTATTAAAATCCCA 57.432 29.630 2.55 0.00 33.85 4.37
3748 4893 0.110486 AGGAACGGGAAGCAATGTGT 59.890 50.000 0.00 0.00 0.00 3.72
3753 4899 2.632377 ACGGGAAGCAATGTGTATGAG 58.368 47.619 0.00 0.00 0.00 2.90
3756 4902 3.063997 CGGGAAGCAATGTGTATGAGTTC 59.936 47.826 0.00 0.00 0.00 3.01
3767 4913 4.515191 TGTGTATGAGTTCCTTCTTGTTGC 59.485 41.667 0.00 0.00 0.00 4.17
3785 4931 8.450964 TCTTGTTGCTTTCCTTAATATTCTTCG 58.549 33.333 0.00 0.00 0.00 3.79
3802 4948 6.627395 TTCTTCGGTTTTGCTATTTCTCAA 57.373 33.333 0.00 0.00 0.00 3.02
3829 5001 4.381411 CTTCTTTCTTCCTTCCTTCACGT 58.619 43.478 0.00 0.00 0.00 4.49
3841 5013 2.266376 CTTCACGTCGGATCTCGCCA 62.266 60.000 0.00 0.00 39.05 5.69
3856 5028 1.613925 TCGCCAGAGAAGATAATCCGG 59.386 52.381 0.00 0.00 0.00 5.14
3886 5059 2.833151 TACGGGAAGCCATGACCCCT 62.833 60.000 0.00 0.00 40.43 4.79
3946 5119 1.080638 TATCTTTGGGGGTGCAAGGT 58.919 50.000 0.00 0.00 0.00 3.50
3948 5121 1.457455 CTTTGGGGGTGCAAGGTGT 60.457 57.895 0.00 0.00 0.00 4.16
3949 5122 1.747325 CTTTGGGGGTGCAAGGTGTG 61.747 60.000 0.00 0.00 0.00 3.82
3950 5123 2.522198 TTTGGGGGTGCAAGGTGTGT 62.522 55.000 0.00 0.00 0.00 3.72
3951 5124 2.912025 GGGGGTGCAAGGTGTGTG 60.912 66.667 0.00 0.00 0.00 3.82
3952 5125 2.123897 GGGGTGCAAGGTGTGTGT 60.124 61.111 0.00 0.00 0.00 3.72
3953 5126 2.489275 GGGGTGCAAGGTGTGTGTG 61.489 63.158 0.00 0.00 0.00 3.82
3954 5127 2.412937 GGTGCAAGGTGTGTGTGC 59.587 61.111 0.00 0.00 38.78 4.57
3955 5128 2.024588 GTGCAAGGTGTGTGTGCG 59.975 61.111 0.00 0.00 41.27 5.34
3956 5129 3.886694 TGCAAGGTGTGTGTGCGC 61.887 61.111 0.00 0.00 41.27 6.09
3957 5130 4.962122 GCAAGGTGTGTGTGCGCG 62.962 66.667 0.00 0.00 0.00 6.86
3958 5131 4.962122 CAAGGTGTGTGTGCGCGC 62.962 66.667 27.26 27.26 35.09 6.86
3988 5161 8.325787 TGTGATAACCCACAAGTATAAGTGATT 58.674 33.333 0.00 0.00 43.32 2.57
3991 5164 8.732746 ATAACCCACAAGTATAAGTGATTGTC 57.267 34.615 0.00 0.00 37.97 3.18
4030 5204 7.658167 TGATAAGTAAAAGTGTCGAATCCAACA 59.342 33.333 0.00 0.00 0.00 3.33
4033 5207 6.053005 AGTAAAAGTGTCGAATCCAACAAGA 58.947 36.000 0.00 0.00 0.00 3.02
4253 5430 1.508632 TAGCGAGTGTGGAAAAGTGC 58.491 50.000 0.00 0.00 0.00 4.40
4267 5444 4.096532 GGAAAAGTGCTAGTAGGATTTGCC 59.903 45.833 0.14 4.56 0.00 4.52
4304 5481 4.217550 GCAATTGGCTTTGTTACTAGACCA 59.782 41.667 7.72 0.00 40.25 4.02
4307 5484 4.699925 TGGCTTTGTTACTAGACCAGTT 57.300 40.909 0.00 0.00 38.80 3.16
4395 5573 8.338259 ACTTATGATTGAAACTATTAGCAAGCG 58.662 33.333 0.00 0.00 29.93 4.68
4418 5600 6.022484 GCGTTCGCAACTATTAAAGTTCATTC 60.022 38.462 12.33 0.00 45.64 2.67
4432 5614 9.974980 TTAAAGTTCATTCAGATAAAACCCAAC 57.025 29.630 0.00 0.00 0.00 3.77
4433 5615 6.590234 AGTTCATTCAGATAAAACCCAACC 57.410 37.500 0.00 0.00 0.00 3.77
4434 5616 6.074648 AGTTCATTCAGATAAAACCCAACCA 58.925 36.000 0.00 0.00 0.00 3.67
4435 5617 6.725834 AGTTCATTCAGATAAAACCCAACCAT 59.274 34.615 0.00 0.00 0.00 3.55
4436 5618 7.893302 AGTTCATTCAGATAAAACCCAACCATA 59.107 33.333 0.00 0.00 0.00 2.74
4451 5637 6.670027 ACCCAACCATAAACCATAGCATTAAA 59.330 34.615 0.00 0.00 0.00 1.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 7.976734 GCAGAACTGTACACATCTACTAATTCT 59.023 37.037 5.56 0.00 0.00 2.40
10 11 6.621613 CAGCAGAACTGTACACATCTACTAA 58.378 40.000 5.56 0.00 41.86 2.24
52 53 6.323266 GTCTGTTAACTACATCGACTGTCAT 58.677 40.000 8.73 0.00 39.39 3.06
53 54 5.616204 CGTCTGTTAACTACATCGACTGTCA 60.616 44.000 8.73 0.00 39.39 3.58
54 55 4.787083 CGTCTGTTAACTACATCGACTGTC 59.213 45.833 7.22 0.00 39.39 3.51
55 56 4.453478 TCGTCTGTTAACTACATCGACTGT 59.547 41.667 7.22 0.00 42.13 3.55
56 57 4.966249 TCGTCTGTTAACTACATCGACTG 58.034 43.478 7.22 0.00 37.75 3.51
57 58 5.618056 TTCGTCTGTTAACTACATCGACT 57.382 39.130 7.22 0.00 40.21 4.18
58 59 5.454877 GGATTCGTCTGTTAACTACATCGAC 59.545 44.000 7.22 3.60 40.21 4.20
59 60 5.449588 GGGATTCGTCTGTTAACTACATCGA 60.450 44.000 7.22 7.35 39.43 3.59
60 61 4.738740 GGGATTCGTCTGTTAACTACATCG 59.261 45.833 7.22 5.28 35.85 3.84
61 62 5.749109 CAGGGATTCGTCTGTTAACTACATC 59.251 44.000 7.22 5.58 35.85 3.06
62 63 5.187186 ACAGGGATTCGTCTGTTAACTACAT 59.813 40.000 7.22 0.00 40.91 2.29
63 64 4.525487 ACAGGGATTCGTCTGTTAACTACA 59.475 41.667 7.22 0.00 40.91 2.74
64 65 5.069501 ACAGGGATTCGTCTGTTAACTAC 57.930 43.478 7.22 4.54 40.91 2.73
65 66 4.159135 GGACAGGGATTCGTCTGTTAACTA 59.841 45.833 7.22 0.00 43.41 2.24
93 94 7.102346 AGAGTGTAGAACATGGAAATCTCAAG 58.898 38.462 0.00 0.00 0.00 3.02
94 95 7.009179 AGAGTGTAGAACATGGAAATCTCAA 57.991 36.000 0.00 0.00 0.00 3.02
95 96 6.611613 AGAGTGTAGAACATGGAAATCTCA 57.388 37.500 0.00 0.00 0.00 3.27
96 97 6.314896 CCAAGAGTGTAGAACATGGAAATCTC 59.685 42.308 0.00 0.00 33.42 2.75
110 111 5.607477 TCCTTGTAACAACCAAGAGTGTAG 58.393 41.667 1.89 0.00 41.44 2.74
112 113 4.451900 CTCCTTGTAACAACCAAGAGTGT 58.548 43.478 1.89 0.00 41.44 3.55
114 115 3.118038 TGCTCCTTGTAACAACCAAGAGT 60.118 43.478 1.89 0.00 41.44 3.24
146 147 2.220786 CTGGCTTGCCTCCCCTGAAT 62.221 60.000 13.18 0.00 0.00 2.57
157 158 1.340248 CATCCATCATTCCTGGCTTGC 59.660 52.381 0.00 0.00 33.56 4.01
169 170 0.695462 ACTGCCTAGGCCATCCATCA 60.695 55.000 30.81 8.68 41.09 3.07
178 179 1.673168 CCAATCTTCACTGCCTAGGC 58.327 55.000 27.71 27.71 42.35 3.93
183 184 2.409870 CCGGCCAATCTTCACTGCC 61.410 63.158 2.24 0.00 38.74 4.85
225 226 1.913419 TGTCTCCCAATGGTAGGAACC 59.087 52.381 0.00 0.00 46.98 3.62
234 235 2.133281 TCATGGCTTGTCTCCCAATG 57.867 50.000 0.00 0.00 34.25 2.82
238 239 2.496899 TCTTTCATGGCTTGTCTCCC 57.503 50.000 0.00 0.00 0.00 4.30
267 268 3.274288 GAGTAGGAACAGCCAATCCTTG 58.726 50.000 7.05 0.00 43.59 3.61
270 271 1.559682 TGGAGTAGGAACAGCCAATCC 59.440 52.381 0.00 0.00 40.02 3.01
280 281 3.769844 GAGGAACTGTCATGGAGTAGGAA 59.230 47.826 0.00 0.00 41.55 3.36
281 282 3.366396 GAGGAACTGTCATGGAGTAGGA 58.634 50.000 0.00 0.00 41.55 2.94
287 288 0.252057 TCGGGAGGAACTGTCATGGA 60.252 55.000 0.00 0.00 41.55 3.41
293 294 0.898320 CAGTCATCGGGAGGAACTGT 59.102 55.000 0.00 0.00 41.55 3.55
305 306 2.487934 CATCAACCCCGATCAGTCATC 58.512 52.381 0.00 0.00 0.00 2.92
306 307 1.141657 CCATCAACCCCGATCAGTCAT 59.858 52.381 0.00 0.00 0.00 3.06
307 308 0.541392 CCATCAACCCCGATCAGTCA 59.459 55.000 0.00 0.00 0.00 3.41
308 309 0.815615 GCCATCAACCCCGATCAGTC 60.816 60.000 0.00 0.00 0.00 3.51
309 310 1.224592 GCCATCAACCCCGATCAGT 59.775 57.895 0.00 0.00 0.00 3.41
310 311 0.179009 ATGCCATCAACCCCGATCAG 60.179 55.000 0.00 0.00 0.00 2.90
311 312 0.258484 AATGCCATCAACCCCGATCA 59.742 50.000 0.00 0.00 0.00 2.92
344 346 0.321387 AGCAGGTCGTACTCGAGACA 60.321 55.000 21.68 3.07 46.96 3.41
345 347 0.803740 AAGCAGGTCGTACTCGAGAC 59.196 55.000 21.68 11.87 46.96 3.36
353 355 1.376543 CTAGACGGAAGCAGGTCGTA 58.623 55.000 0.00 0.00 38.20 3.43
357 359 3.376082 TTCCTAGACGGAAGCAGGT 57.624 52.632 0.00 0.00 46.80 4.00
365 367 4.154195 CCACAAAAATCAGTTCCTAGACGG 59.846 45.833 0.00 0.00 0.00 4.79
384 387 3.964688 TGGAAACTGAGAGTAAGACCACA 59.035 43.478 0.00 0.00 0.00 4.17
429 434 3.776969 TCCAGTTTGGCTCTATGTGAGAT 59.223 43.478 0.00 0.00 44.27 2.75
432 437 2.906389 ACTCCAGTTTGGCTCTATGTGA 59.094 45.455 0.00 0.00 37.47 3.58
435 440 3.265791 GTCACTCCAGTTTGGCTCTATG 58.734 50.000 0.00 0.00 37.47 2.23
437 442 1.623811 GGTCACTCCAGTTTGGCTCTA 59.376 52.381 0.00 0.00 37.47 2.43
440 445 0.846693 AAGGTCACTCCAGTTTGGCT 59.153 50.000 0.00 0.00 37.47 4.75
441 446 1.239347 GAAGGTCACTCCAGTTTGGC 58.761 55.000 0.00 0.00 37.47 4.52
442 447 1.421646 AGGAAGGTCACTCCAGTTTGG 59.578 52.381 0.00 0.00 39.43 3.28
475 480 1.608590 CGTCCACAAATCCAACAAGCT 59.391 47.619 0.00 0.00 0.00 3.74
509 514 4.379394 GGCGCATGAAATTTTCTCACTGTA 60.379 41.667 10.83 0.00 0.00 2.74
511 516 2.919229 GGCGCATGAAATTTTCTCACTG 59.081 45.455 10.83 4.57 0.00 3.66
512 517 2.821969 AGGCGCATGAAATTTTCTCACT 59.178 40.909 10.83 0.00 0.00 3.41
513 518 2.919229 CAGGCGCATGAAATTTTCTCAC 59.081 45.455 18.87 0.00 0.00 3.51
514 519 2.094597 CCAGGCGCATGAAATTTTCTCA 60.095 45.455 25.72 0.00 0.00 3.27
515 520 2.094545 ACCAGGCGCATGAAATTTTCTC 60.095 45.455 25.72 0.00 0.00 2.87
516 521 1.895131 ACCAGGCGCATGAAATTTTCT 59.105 42.857 25.72 0.00 0.00 2.52
517 522 1.994779 CACCAGGCGCATGAAATTTTC 59.005 47.619 25.72 2.05 0.00 2.29
518 523 1.344114 ACACCAGGCGCATGAAATTTT 59.656 42.857 25.72 0.00 0.00 1.82
519 524 0.968405 ACACCAGGCGCATGAAATTT 59.032 45.000 25.72 0.00 0.00 1.82
520 525 0.244450 CACACCAGGCGCATGAAATT 59.756 50.000 25.72 1.22 0.00 1.82
521 526 0.608856 TCACACCAGGCGCATGAAAT 60.609 50.000 25.72 5.54 0.00 2.17
522 527 0.608856 ATCACACCAGGCGCATGAAA 60.609 50.000 25.72 3.91 0.00 2.69
523 528 1.002257 ATCACACCAGGCGCATGAA 60.002 52.632 25.72 3.54 0.00 2.57
524 529 1.450134 GATCACACCAGGCGCATGA 60.450 57.895 25.72 9.77 0.00 3.07
525 530 2.475466 GGATCACACCAGGCGCATG 61.475 63.158 16.49 16.49 0.00 4.06
526 531 2.124570 GGATCACACCAGGCGCAT 60.125 61.111 10.83 0.00 0.00 4.73
527 532 2.803155 GAAGGATCACACCAGGCGCA 62.803 60.000 10.83 0.00 0.00 6.09
528 533 2.045926 AAGGATCACACCAGGCGC 60.046 61.111 0.00 0.00 0.00 6.53
529 534 0.107508 ATGAAGGATCACACCAGGCG 60.108 55.000 0.00 0.00 38.69 5.52
530 535 2.134789 AATGAAGGATCACACCAGGC 57.865 50.000 0.00 0.00 38.69 4.85
531 536 4.399303 GGTAAAATGAAGGATCACACCAGG 59.601 45.833 0.00 0.00 38.69 4.45
532 537 5.009631 TGGTAAAATGAAGGATCACACCAG 58.990 41.667 0.00 0.00 38.69 4.00
533 538 4.764823 GTGGTAAAATGAAGGATCACACCA 59.235 41.667 0.00 0.00 38.69 4.17
546 551 6.594937 CCCATGAAAATTGAGGTGGTAAAATG 59.405 38.462 0.00 0.00 0.00 2.32
570 575 9.606631 AAAGAACAATAGTCAATGTAGATCTCC 57.393 33.333 0.00 0.00 0.00 3.71
604 609 4.037923 GGCTTGGAATGAACAGAGTTTTCA 59.962 41.667 0.00 0.00 37.38 2.69
622 627 5.170748 AGTTTTCACAGAAACAAAGGCTTG 58.829 37.500 0.00 0.00 40.98 4.01
637 642 8.764524 ATAGTCAATGTACAGAGAGTTTTCAC 57.235 34.615 11.55 0.00 0.00 3.18
638 643 9.208022 CAATAGTCAATGTACAGAGAGTTTTCA 57.792 33.333 11.55 0.00 0.00 2.69
717 738 7.801104 TGCCTAACAGGACTGAATTAATGATA 58.199 34.615 6.29 0.00 37.67 2.15
733 754 9.935241 ATGATTACATTATCTACTGCCTAACAG 57.065 33.333 0.00 0.00 42.23 3.16
770 1782 3.726291 CTTCCACTCTAGAAGCCTAGC 57.274 52.381 0.00 0.00 41.65 3.42
791 1804 4.487019 GTCTCTAGTTCGTTTGGGAGAAG 58.513 47.826 0.00 0.00 32.72 2.85
807 1820 3.755628 GGGCACGCACCGTCTCTA 61.756 66.667 0.00 0.00 38.32 2.43
819 1832 1.273327 CCACAATCTTTCCAAGGGCAC 59.727 52.381 0.00 0.00 0.00 5.01
820 1833 1.631405 CCACAATCTTTCCAAGGGCA 58.369 50.000 0.00 0.00 0.00 5.36
940 1956 1.001633 ACGGCCGCTCTCTTCTTTTTA 59.998 47.619 28.58 0.00 0.00 1.52
941 1957 0.250338 ACGGCCGCTCTCTTCTTTTT 60.250 50.000 28.58 0.00 0.00 1.94
942 1958 0.951040 CACGGCCGCTCTCTTCTTTT 60.951 55.000 28.58 0.00 0.00 2.27
1095 2111 0.611714 GAAGAGGGCCGTCTTTGGTA 59.388 55.000 34.61 0.00 36.89 3.25
1148 2165 2.213499 GAAGCATAGGGAACGACATGG 58.787 52.381 0.00 0.00 0.00 3.66
1149 2166 2.213499 GGAAGCATAGGGAACGACATG 58.787 52.381 0.00 0.00 0.00 3.21
1150 2167 1.837439 TGGAAGCATAGGGAACGACAT 59.163 47.619 0.00 0.00 0.00 3.06
1152 2169 1.653151 GTGGAAGCATAGGGAACGAC 58.347 55.000 0.00 0.00 0.00 4.34
1164 2181 4.202111 ACAAACAGTAAACATGGTGGAAGC 60.202 41.667 0.00 0.00 0.00 3.86
1166 2183 4.098654 CCACAAACAGTAAACATGGTGGAA 59.901 41.667 0.00 0.00 45.61 3.53
1167 2184 3.634448 CCACAAACAGTAAACATGGTGGA 59.366 43.478 0.00 0.00 45.61 4.02
1168 2185 3.243704 CCCACAAACAGTAAACATGGTGG 60.244 47.826 0.00 0.00 43.13 4.61
1169 2186 3.634448 TCCCACAAACAGTAAACATGGTG 59.366 43.478 0.00 0.00 0.00 4.17
1170 2187 3.634910 GTCCCACAAACAGTAAACATGGT 59.365 43.478 0.00 0.00 0.00 3.55
1172 2189 4.578516 TCTGTCCCACAAACAGTAAACATG 59.421 41.667 3.45 0.00 43.68 3.21
1224 2241 9.840427 AAACGTCCAAAATAGTTTCATCATAAG 57.160 29.630 0.00 0.00 32.05 1.73
1226 2243 9.834628 GAAAACGTCCAAAATAGTTTCATCATA 57.165 29.630 0.00 0.00 35.99 2.15
1228 2245 7.936584 AGAAAACGTCCAAAATAGTTTCATCA 58.063 30.769 6.40 0.00 35.99 3.07
1259 2276 6.238593 GGATGAAGCACTTTTAGCCATTCTAG 60.239 42.308 0.00 0.00 0.00 2.43
1260 2277 5.590259 GGATGAAGCACTTTTAGCCATTCTA 59.410 40.000 0.00 0.00 0.00 2.10
1262 2279 4.440663 GGGATGAAGCACTTTTAGCCATTC 60.441 45.833 5.60 0.00 0.00 2.67
1263 2280 3.448660 GGGATGAAGCACTTTTAGCCATT 59.551 43.478 5.60 0.00 0.00 3.16
1264 2281 3.026694 GGGATGAAGCACTTTTAGCCAT 58.973 45.455 5.60 0.00 0.00 4.40
1265 2282 2.446435 GGGATGAAGCACTTTTAGCCA 58.554 47.619 5.60 0.00 0.00 4.75
1266 2283 1.751351 GGGGATGAAGCACTTTTAGCC 59.249 52.381 0.00 0.00 0.00 3.93
1267 2284 2.424956 CAGGGGATGAAGCACTTTTAGC 59.575 50.000 0.00 0.00 0.00 3.09
1268 2285 2.424956 GCAGGGGATGAAGCACTTTTAG 59.575 50.000 0.00 0.00 0.00 1.85
1271 2288 0.407139 AGCAGGGGATGAAGCACTTT 59.593 50.000 0.00 0.00 0.00 2.66
1272 2289 1.211457 CTAGCAGGGGATGAAGCACTT 59.789 52.381 0.00 0.00 0.00 3.16
1273 2290 0.835941 CTAGCAGGGGATGAAGCACT 59.164 55.000 0.00 0.00 0.00 4.40
1274 2291 0.817229 GCTAGCAGGGGATGAAGCAC 60.817 60.000 10.63 0.00 38.60 4.40
1275 2292 0.984961 AGCTAGCAGGGGATGAAGCA 60.985 55.000 18.83 0.00 40.24 3.91
1277 2294 4.363991 AATTAGCTAGCAGGGGATGAAG 57.636 45.455 18.83 0.00 0.00 3.02
1279 2296 3.583086 GGTAATTAGCTAGCAGGGGATGA 59.417 47.826 18.83 0.00 0.00 2.92
1280 2297 3.327757 TGGTAATTAGCTAGCAGGGGATG 59.672 47.826 18.83 0.00 0.00 3.51
1281 2298 3.328050 GTGGTAATTAGCTAGCAGGGGAT 59.672 47.826 18.83 0.00 30.25 3.85
1282 2299 2.704065 GTGGTAATTAGCTAGCAGGGGA 59.296 50.000 18.83 0.00 30.25 4.81
1283 2300 2.224548 GGTGGTAATTAGCTAGCAGGGG 60.225 54.545 18.83 0.00 30.25 4.79
1284 2301 2.438021 TGGTGGTAATTAGCTAGCAGGG 59.562 50.000 18.83 0.00 30.25 4.45
1286 2303 3.388024 TCCTGGTGGTAATTAGCTAGCAG 59.612 47.826 24.00 24.00 36.82 4.24
1306 2391 6.144563 GCAAAATTGTTTCTTCTACTGCTTCC 59.855 38.462 0.00 0.00 0.00 3.46
1308 2393 6.809869 AGCAAAATTGTTTCTTCTACTGCTT 58.190 32.000 0.00 0.00 0.00 3.91
1325 2410 5.417894 TGAATTCTCATGAGCAGAGCAAAAT 59.582 36.000 18.36 6.99 33.15 1.82
1329 2414 3.268330 GTGAATTCTCATGAGCAGAGCA 58.732 45.455 18.36 9.07 33.05 4.26
1356 2478 3.665745 AACTGCATTTTCCATCCACAC 57.334 42.857 0.00 0.00 0.00 3.82
1428 2550 2.335712 CGAGAAGGCCACCTTTGCC 61.336 63.158 5.01 0.00 44.82 4.52
1494 2616 4.545706 CTGCCGCCGATGCCCTTA 62.546 66.667 0.00 0.00 0.00 2.69
1515 2637 4.458829 AGGATCTCGCCGGGGTCA 62.459 66.667 19.13 6.51 0.00 4.02
1767 2889 7.373493 ACAGAGTTTGATCAATCAACCAATTC 58.627 34.615 16.79 4.35 45.63 2.17
1810 2932 3.025978 TCACAAATCCCATCCTGCATTC 58.974 45.455 0.00 0.00 0.00 2.67
2100 3222 4.436998 GACGTGGAGTCCAGCCCG 62.437 72.222 13.61 15.50 43.95 6.13
2295 3417 2.126031 GGCGTGAACCCGAGAGAC 60.126 66.667 0.00 0.00 0.00 3.36
2301 3423 4.143333 ATCTCCGGCGTGAACCCG 62.143 66.667 6.01 0.00 45.17 5.28
2757 3888 2.573689 CCGAAGAGCGACGACGAC 60.574 66.667 12.29 4.17 44.57 4.34
3018 4149 6.987404 TGCACAACAAGAAGTACATACTAACA 59.013 34.615 0.00 0.00 34.99 2.41
3019 4150 7.416154 TGCACAACAAGAAGTACATACTAAC 57.584 36.000 0.00 0.00 34.99 2.34
3021 4152 6.092122 GCATGCACAACAAGAAGTACATACTA 59.908 38.462 14.21 0.00 34.99 1.82
3022 4153 5.106555 GCATGCACAACAAGAAGTACATACT 60.107 40.000 14.21 0.00 38.39 2.12
3023 4154 5.088739 GCATGCACAACAAGAAGTACATAC 58.911 41.667 14.21 0.00 0.00 2.39
3024 4155 4.155826 GGCATGCACAACAAGAAGTACATA 59.844 41.667 21.36 0.00 0.00 2.29
3025 4156 3.057315 GGCATGCACAACAAGAAGTACAT 60.057 43.478 21.36 0.00 0.00 2.29
3027 4158 2.665519 CGGCATGCACAACAAGAAGTAC 60.666 50.000 21.36 0.00 0.00 2.73
3029 4160 0.311790 CGGCATGCACAACAAGAAGT 59.688 50.000 21.36 0.00 0.00 3.01
3034 4165 2.636462 CGTCGGCATGCACAACAA 59.364 55.556 21.36 0.00 0.00 2.83
3035 4166 3.353029 CCGTCGGCATGCACAACA 61.353 61.111 21.36 0.00 0.00 3.33
3036 4167 3.353836 ACCGTCGGCATGCACAAC 61.354 61.111 21.36 12.70 0.00 3.32
3081 4212 1.482182 CCCTGATCACAGATGACCGAA 59.518 52.381 0.00 0.00 46.03 4.30
3082 4213 1.114627 CCCTGATCACAGATGACCGA 58.885 55.000 0.00 0.00 46.03 4.69
3083 4214 0.105593 CCCCTGATCACAGATGACCG 59.894 60.000 0.00 0.00 46.03 4.79
3084 4215 1.139853 GTCCCCTGATCACAGATGACC 59.860 57.143 0.00 0.00 46.03 4.02
3087 4218 0.105593 CCGTCCCCTGATCACAGATG 59.894 60.000 0.00 0.00 46.03 2.90
3088 4219 1.050988 CCCGTCCCCTGATCACAGAT 61.051 60.000 0.00 0.00 46.03 2.90
3089 4220 1.685765 CCCGTCCCCTGATCACAGA 60.686 63.158 0.00 0.00 46.03 3.41
3090 4221 2.735772 CCCCGTCCCCTGATCACAG 61.736 68.421 0.00 0.00 43.12 3.66
3092 4223 3.480133 CCCCCGTCCCCTGATCAC 61.480 72.222 0.00 0.00 0.00 3.06
3489 4633 3.381136 CGTGCCAAACCCCCATGG 61.381 66.667 4.14 4.14 39.80 3.66
3490 4634 3.381136 CCGTGCCAAACCCCCATG 61.381 66.667 0.00 0.00 0.00 3.66
3496 4640 4.622456 CACACGCCGTGCCAAACC 62.622 66.667 18.59 0.00 39.19 3.27
3509 4653 3.665190 AGACCTAACTAGCAAAGCACAC 58.335 45.455 0.00 0.00 0.00 3.82
3510 4654 4.315803 GAAGACCTAACTAGCAAAGCACA 58.684 43.478 0.00 0.00 0.00 4.57
3523 4667 8.711170 ACAAAGGATATAATTCGGAAGACCTAA 58.289 33.333 0.00 0.00 41.84 2.69
3539 4683 7.828508 ATGCATTACATGTGACAAAGGATAT 57.171 32.000 9.11 0.00 37.70 1.63
3614 4758 5.648092 AGGAAACAATCAAGAAGAATACCCG 59.352 40.000 0.00 0.00 0.00 5.28
3629 4773 8.156820 CCAAGGAAGGAAAATTAAGGAAACAAT 58.843 33.333 0.00 0.00 0.00 2.71
3650 4794 3.019564 CAAAGCCTCATTACCTCCAAGG 58.980 50.000 0.00 0.00 42.49 3.61
3668 4812 1.663173 GGCCACCGCTTTTAGCAAA 59.337 52.632 0.00 0.00 42.58 3.68
3674 4818 2.706952 TAGCTTGGGCCACCGCTTTT 62.707 55.000 28.14 12.11 40.75 2.27
3705 4849 8.413229 CCTTTGGGATTTTAATACAATCATCGT 58.587 33.333 2.14 0.00 32.98 3.73
3727 4871 1.613437 CACATTGCTTCCCGTTCCTTT 59.387 47.619 0.00 0.00 0.00 3.11
3735 4880 3.378427 GGAACTCATACACATTGCTTCCC 59.622 47.826 0.00 0.00 0.00 3.97
3738 4883 5.564550 AGAAGGAACTCATACACATTGCTT 58.435 37.500 0.00 0.00 38.49 3.91
3748 4893 5.473504 GGAAAGCAACAAGAAGGAACTCATA 59.526 40.000 0.00 0.00 38.49 2.15
3753 4899 4.655762 AAGGAAAGCAACAAGAAGGAAC 57.344 40.909 0.00 0.00 0.00 3.62
3756 4902 8.743714 AGAATATTAAGGAAAGCAACAAGAAGG 58.256 33.333 0.00 0.00 0.00 3.46
3767 4913 8.244113 AGCAAAACCGAAGAATATTAAGGAAAG 58.756 33.333 0.00 0.00 0.00 2.62
3785 4931 6.819397 AGGTACTTGAGAAATAGCAAAACC 57.181 37.500 0.00 0.00 27.25 3.27
3829 5001 0.107165 TCTTCTCTGGCGAGATCCGA 60.107 55.000 0.00 0.00 45.27 4.55
3841 5013 7.582719 AGATAGATAGCCGGATTATCTTCTCT 58.417 38.462 24.99 22.57 38.48 3.10
3849 5021 4.885907 CCCGTAAGATAGATAGCCGGATTA 59.114 45.833 5.05 0.00 43.02 1.75
3852 5024 2.306805 TCCCGTAAGATAGATAGCCGGA 59.693 50.000 5.05 0.00 43.02 5.14
3855 5027 3.119065 GGCTTCCCGTAAGATAGATAGCC 60.119 52.174 0.00 0.00 37.38 3.93
3856 5028 3.510360 TGGCTTCCCGTAAGATAGATAGC 59.490 47.826 0.00 0.00 37.38 2.97
3955 5128 4.218478 GGGTTATCACACGCGCGC 62.218 66.667 32.58 23.91 0.00 6.86
3956 5129 2.811747 TGGGTTATCACACGCGCG 60.812 61.111 30.96 30.96 32.29 6.86
3957 5130 2.782615 GTGGGTTATCACACGCGC 59.217 61.111 5.73 0.00 38.25 6.86
3961 5134 7.101054 TCACTTATACTTGTGGGTTATCACAC 58.899 38.462 0.00 0.00 45.95 3.82
3962 5135 7.247456 TCACTTATACTTGTGGGTTATCACA 57.753 36.000 0.00 0.00 44.81 3.58
4014 5188 3.251004 GCTTCTTGTTGGATTCGACACTT 59.749 43.478 0.00 0.00 37.04 3.16
4060 5236 6.228616 TGTATTGATGGTCGATGGAACTTA 57.771 37.500 0.00 0.00 0.00 2.24
4067 5243 5.399596 CGTAGAGTTGTATTGATGGTCGATG 59.600 44.000 0.00 0.00 0.00 3.84
4253 5430 4.511826 GGACAATTCGGCAAATCCTACTAG 59.488 45.833 0.00 0.00 0.00 2.57
4267 5444 3.734902 GCCAATTGCTTAGGGACAATTCG 60.735 47.826 0.00 0.00 42.93 3.34
4304 5481 5.776358 TCCCCCATATAAGAATTTGCAACT 58.224 37.500 0.00 0.00 0.00 3.16
4307 5484 4.739793 CCTCCCCCATATAAGAATTTGCA 58.260 43.478 0.00 0.00 0.00 4.08
4395 5573 8.227791 TCTGAATGAACTTTAATAGTTGCGAAC 58.772 33.333 7.48 0.00 47.00 3.95
4418 5600 6.597832 TGGTTTATGGTTGGGTTTTATCTG 57.402 37.500 0.00 0.00 0.00 2.90
4436 5618 9.942850 GGGCAATATATTTTAATGCTATGGTTT 57.057 29.630 6.35 0.00 37.20 3.27


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

AutoCloner maintained by Alex Coulton.