Multiple sequence alignment - TraesCS2D01G199600

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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 TraesCS2D01G199600 chr2D 100.000 4871 0 0 1 4871 150625063 150629933 0.000000e+00 8996.0
1 TraesCS2D01G199600 chr2A 94.280 2360 76 28 2538 4868 150916263 150913934 0.000000e+00 3555.0
2 TraesCS2D01G199600 chr2A 95.196 2019 56 15 380 2375 150918252 150916252 0.000000e+00 3153.0
3 TraesCS2D01G199600 chr2A 88.487 304 13 12 3 290 150919013 150918716 1.000000e-91 348.0
4 TraesCS2D01G199600 chr2A 99.394 165 1 0 2375 2539 498090099 498089935 2.850000e-77 300.0
5 TraesCS2D01G199600 chr2A 80.583 103 8 4 4767 4868 613445340 613445431 8.750000e-08 69.4
6 TraesCS2D01G199600 chr2B 95.484 2037 60 15 2747 4760 209251811 209253838 0.000000e+00 3223.0
7 TraesCS2D01G199600 chr2B 95.255 1665 43 10 718 2372 209250025 209251663 0.000000e+00 2604.0
8 TraesCS2D01G199600 chr2B 95.000 160 7 1 151 309 209247152 209247311 2.910000e-62 250.0
9 TraesCS2D01G199600 chr2B 92.899 169 7 3 2538 2702 209251655 209251822 1.750000e-59 241.0
10 TraesCS2D01G199600 chr2B 96.800 125 3 1 424 547 209249544 209249668 1.780000e-49 207.0
11 TraesCS2D01G199600 chr2B 91.011 89 4 4 1 85 209246943 209247031 3.080000e-22 117.0
12 TraesCS2D01G199600 chr4A 98.830 171 2 0 2372 2542 317089638 317089808 6.130000e-79 305.0
13 TraesCS2D01G199600 chr4A 97.207 179 3 2 2367 2545 477497830 477497654 7.920000e-78 302.0
14 TraesCS2D01G199600 chr7B 98.246 171 3 0 2372 2542 716962942 716963112 2.850000e-77 300.0
15 TraesCS2D01G199600 chr7B 98.246 171 2 1 2372 2542 107167454 107167623 1.020000e-76 298.0
16 TraesCS2D01G199600 chr7B 97.688 173 3 1 2375 2547 384200290 384200119 3.690000e-76 296.0
17 TraesCS2D01G199600 chr1B 98.246 171 2 1 2372 2542 397427299 397427468 1.020000e-76 298.0
18 TraesCS2D01G199600 chr7D 97.159 176 4 1 2367 2541 50058805 50058980 3.690000e-76 296.0
19 TraesCS2D01G199600 chr7A 97.159 176 3 2 2367 2541 539714953 539715127 3.690000e-76 296.0
20 TraesCS2D01G199600 chr3D 92.941 85 5 1 4763 4846 608238809 608238725 6.620000e-24 122.0
21 TraesCS2D01G199600 chr3D 91.525 59 4 1 4760 4818 496737679 496737736 4.040000e-11 80.5
22 TraesCS2D01G199600 chr3B 82.075 106 16 3 4764 4867 252331861 252331757 2.420000e-13 87.9
23 TraesCS2D01G199600 chr3B 86.957 69 8 1 4764 4831 248341534 248341466 5.230000e-10 76.8
24 TraesCS2D01G199600 chr3B 80.189 106 18 3 4764 4867 248667328 248667224 5.230000e-10 76.8
25 TraesCS2D01G199600 chr6D 92.982 57 2 2 4763 4818 215563305 215563360 1.120000e-11 82.4
26 TraesCS2D01G199600 chr6B 90.323 62 6 0 4757 4818 395857416 395857477 1.120000e-11 82.4
27 TraesCS2D01G199600 chr1D 92.857 56 4 0 4763 4818 258014446 258014391 1.120000e-11 82.4


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 TraesCS2D01G199600 chr2D 150625063 150629933 4870 False 8996 8996 100.000000 1 4871 1 chr2D.!!$F1 4870
1 TraesCS2D01G199600 chr2A 150913934 150919013 5079 True 2352 3555 92.654333 3 4868 3 chr2A.!!$R2 4865
2 TraesCS2D01G199600 chr2B 209246943 209253838 6895 False 1107 3223 94.408167 1 4760 6 chr2B.!!$F1 4759

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
569 3096 0.106819 GGCAGGCCATCACAAGAGAT 60.107 55.0 5.01 0.0 35.81 2.75 F
2377 5106 0.032130 ACGTCATATAGCTGCGGTGG 59.968 55.0 0.00 0.0 0.00 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2386 5115 0.037303 ACCTCATGGTCACAAGGCAG 59.963 55.0 0.0 0.0 44.78 4.85 R
4261 7005 0.316937 CACGACACCAATGCACACAC 60.317 55.0 0.0 0.0 0.00 3.82 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
102 142 2.012902 ATACTGTACACGGAGGCGGC 62.013 60.000 0.00 0.00 0.00 6.53
123 165 2.324332 ATCTCGAGGCAGCGTACACG 62.324 60.000 13.56 0.00 43.27 4.49
309 373 9.084164 TCTCGAATAAGTTTTGCTATCTTGTAC 57.916 33.333 0.00 0.00 0.00 2.90
310 374 8.193250 TCGAATAAGTTTTGCTATCTTGTACC 57.807 34.615 0.00 0.00 0.00 3.34
311 375 7.279313 TCGAATAAGTTTTGCTATCTTGTACCC 59.721 37.037 0.00 0.00 0.00 3.69
313 377 8.644374 AATAAGTTTTGCTATCTTGTACCCAA 57.356 30.769 0.00 0.00 0.00 4.12
345 741 3.910648 GTGAAGTCACACAGGTAGTACC 58.089 50.000 11.73 11.73 45.75 3.34
351 747 2.294233 TCACACAGGTAGTACCACGAAC 59.706 50.000 21.49 0.00 41.95 3.95
352 748 1.615392 ACACAGGTAGTACCACGAACC 59.385 52.381 21.49 0.00 41.95 3.62
562 3089 0.247460 GAAAAAGGGCAGGCCATCAC 59.753 55.000 16.94 0.00 37.98 3.06
569 3096 0.106819 GGCAGGCCATCACAAGAGAT 60.107 55.000 5.01 0.00 35.81 2.75
570 3097 1.307097 GCAGGCCATCACAAGAGATC 58.693 55.000 5.01 0.00 0.00 2.75
571 3098 1.964552 CAGGCCATCACAAGAGATCC 58.035 55.000 5.01 0.00 0.00 3.36
682 3221 2.041350 TCGTCTCTCTTCTTACCCACCT 59.959 50.000 0.00 0.00 0.00 4.00
683 3222 2.424246 CGTCTCTCTTCTTACCCACCTC 59.576 54.545 0.00 0.00 0.00 3.85
684 3223 2.424246 GTCTCTCTTCTTACCCACCTCG 59.576 54.545 0.00 0.00 0.00 4.63
688 3227 0.175989 CTTCTTACCCACCTCGCTCC 59.824 60.000 0.00 0.00 0.00 4.70
690 3229 1.686110 CTTACCCACCTCGCTCCCT 60.686 63.158 0.00 0.00 0.00 4.20
716 3429 2.252072 CTCCCTCCCGGAAATCGCAA 62.252 60.000 0.73 0.00 41.40 4.85
775 3491 0.598065 GCAGCACAATTCGAAACCCT 59.402 50.000 0.00 0.00 0.00 4.34
791 3507 4.087892 CTCCCGCACACTCCCCTG 62.088 72.222 0.00 0.00 0.00 4.45
797 3513 3.721706 CACACTCCCCTGGCCCTC 61.722 72.222 0.00 0.00 0.00 4.30
1149 3867 4.208686 GGTACGCCCCTCGCTCTG 62.209 72.222 0.00 0.00 43.23 3.35
1427 4146 0.247460 TCATGCTCAACTCTGTCGGG 59.753 55.000 0.00 0.00 0.00 5.14
1443 4162 6.312529 TCTGTCGGGTTCTATCAGGTATAAT 58.687 40.000 0.00 0.00 0.00 1.28
1506 4225 5.092554 TGAATAAGAATACGTGGCCTTGA 57.907 39.130 3.32 0.00 0.00 3.02
1513 4232 0.973632 TACGTGGCCTTGATCTGTGT 59.026 50.000 3.32 0.00 0.00 3.72
1536 4255 4.814234 TCTGAAGAACGTGTGCAAACTATT 59.186 37.500 5.28 0.00 0.00 1.73
1631 4350 5.878116 GCACTACACAACCAAGGTTATATCA 59.122 40.000 3.82 0.00 36.46 2.15
1933 4655 6.184580 TGATAACGCCAATTTTCGTATGTT 57.815 33.333 2.63 0.00 38.03 2.71
1974 4696 3.731652 TGAAAGTTGTCTGGCCAATTG 57.268 42.857 7.01 0.00 0.00 2.32
2067 4789 4.515567 GCCAAATATTCAGTAGCTGGGTAC 59.484 45.833 0.00 2.17 31.51 3.34
2078 4800 2.546899 AGCTGGGTACTGTATGGTTCA 58.453 47.619 0.00 0.00 0.00 3.18
2200 4926 1.686052 GTGCCTTGGTGTGGATTTTCA 59.314 47.619 0.00 0.00 0.00 2.69
2375 5104 1.029681 TCACGTCATATAGCTGCGGT 58.970 50.000 0.00 0.00 0.00 5.68
2376 5105 1.131771 CACGTCATATAGCTGCGGTG 58.868 55.000 0.00 0.00 0.00 4.94
2377 5106 0.032130 ACGTCATATAGCTGCGGTGG 59.968 55.000 0.00 0.00 0.00 4.61
2380 5109 2.287970 CGTCATATAGCTGCGGTGGTAA 60.288 50.000 0.00 0.00 0.00 2.85
2383 5112 2.234300 TATAGCTGCGGTGGTAAAGC 57.766 50.000 0.00 0.00 35.86 3.51
2385 5114 0.391130 TAGCTGCGGTGGTAAAGCTG 60.391 55.000 6.29 0.00 45.33 4.24
2386 5115 2.870372 CTGCGGTGGTAAAGCTGC 59.130 61.111 0.00 0.00 0.00 5.25
2387 5116 1.672356 CTGCGGTGGTAAAGCTGCT 60.672 57.895 0.00 0.00 0.00 4.24
2388 5117 1.915614 CTGCGGTGGTAAAGCTGCTG 61.916 60.000 1.35 0.00 0.00 4.41
2389 5118 2.870372 CGGTGGTAAAGCTGCTGC 59.130 61.111 1.35 7.62 40.05 5.25
2390 5119 2.690778 CGGTGGTAAAGCTGCTGCC 61.691 63.158 12.44 7.07 40.80 4.85
2391 5120 1.303643 GGTGGTAAAGCTGCTGCCT 60.304 57.895 12.44 2.45 40.80 4.75
2392 5121 0.895559 GGTGGTAAAGCTGCTGCCTT 60.896 55.000 12.44 8.34 40.80 4.35
2393 5122 0.242017 GTGGTAAAGCTGCTGCCTTG 59.758 55.000 12.44 0.00 40.80 3.61
2394 5123 0.178992 TGGTAAAGCTGCTGCCTTGT 60.179 50.000 12.44 0.00 40.80 3.16
2395 5124 0.242017 GGTAAAGCTGCTGCCTTGTG 59.758 55.000 12.44 0.00 40.80 3.33
2396 5125 1.238439 GTAAAGCTGCTGCCTTGTGA 58.762 50.000 12.44 0.00 40.80 3.58
2397 5126 1.068954 GTAAAGCTGCTGCCTTGTGAC 60.069 52.381 12.44 0.00 40.80 3.67
2398 5127 1.458639 AAAGCTGCTGCCTTGTGACC 61.459 55.000 12.44 0.00 40.80 4.02
2399 5128 2.595463 GCTGCTGCCTTGTGACCA 60.595 61.111 3.85 0.00 0.00 4.02
2400 5129 1.975407 GCTGCTGCCTTGTGACCAT 60.975 57.895 3.85 0.00 0.00 3.55
2401 5130 1.880894 CTGCTGCCTTGTGACCATG 59.119 57.895 0.00 0.00 0.00 3.66
2402 5131 0.607217 CTGCTGCCTTGTGACCATGA 60.607 55.000 0.00 0.00 0.00 3.07
2403 5132 0.607217 TGCTGCCTTGTGACCATGAG 60.607 55.000 0.00 0.00 0.00 2.90
2404 5133 1.310933 GCTGCCTTGTGACCATGAGG 61.311 60.000 0.00 0.00 42.21 3.86
2414 5143 4.617875 CCATGAGGTCACGGGTTC 57.382 61.111 0.00 0.00 0.00 3.62
2415 5144 1.676968 CCATGAGGTCACGGGTTCA 59.323 57.895 0.00 0.00 0.00 3.18
2416 5145 0.036164 CCATGAGGTCACGGGTTCAA 59.964 55.000 0.00 0.00 0.00 2.69
2417 5146 1.442769 CATGAGGTCACGGGTTCAAG 58.557 55.000 0.00 0.00 0.00 3.02
2418 5147 1.056660 ATGAGGTCACGGGTTCAAGT 58.943 50.000 0.00 0.00 0.00 3.16
2419 5148 0.391597 TGAGGTCACGGGTTCAAGTC 59.608 55.000 0.00 0.00 0.00 3.01
2420 5149 0.320508 GAGGTCACGGGTTCAAGTCC 60.321 60.000 0.00 0.00 0.00 3.85
2421 5150 0.763223 AGGTCACGGGTTCAAGTCCT 60.763 55.000 0.00 0.00 0.00 3.85
2422 5151 0.602905 GGTCACGGGTTCAAGTCCTG 60.603 60.000 0.00 0.00 37.36 3.86
2423 5152 0.602905 GTCACGGGTTCAAGTCCTGG 60.603 60.000 0.00 0.00 35.79 4.45
2424 5153 0.761323 TCACGGGTTCAAGTCCTGGA 60.761 55.000 0.00 0.00 35.79 3.86
2425 5154 0.107831 CACGGGTTCAAGTCCTGGAA 59.892 55.000 0.00 0.00 35.79 3.53
2426 5155 0.841289 ACGGGTTCAAGTCCTGGAAA 59.159 50.000 0.00 0.00 35.79 3.13
2427 5156 1.235724 CGGGTTCAAGTCCTGGAAAC 58.764 55.000 0.00 0.00 0.00 2.78
2428 5157 1.476110 CGGGTTCAAGTCCTGGAAACA 60.476 52.381 0.00 0.00 32.36 2.83
2439 5168 3.025924 TGGAAACAGCCTCTTGCAG 57.974 52.632 0.00 0.00 44.83 4.41
2440 5169 0.473755 TGGAAACAGCCTCTTGCAGA 59.526 50.000 0.00 0.00 44.83 4.26
2441 5170 1.133823 TGGAAACAGCCTCTTGCAGAA 60.134 47.619 0.00 0.00 44.83 3.02
2442 5171 1.956477 GGAAACAGCCTCTTGCAGAAA 59.044 47.619 0.00 0.00 44.83 2.52
2443 5172 2.560105 GGAAACAGCCTCTTGCAGAAAT 59.440 45.455 0.00 0.00 44.83 2.17
2444 5173 3.572584 GAAACAGCCTCTTGCAGAAATG 58.427 45.455 0.00 0.00 44.83 2.32
2445 5174 2.283145 ACAGCCTCTTGCAGAAATGT 57.717 45.000 0.00 0.00 44.83 2.71
2446 5175 3.423539 ACAGCCTCTTGCAGAAATGTA 57.576 42.857 0.00 0.00 44.83 2.29
2447 5176 3.341823 ACAGCCTCTTGCAGAAATGTAG 58.658 45.455 0.00 0.00 44.83 2.74
2448 5177 2.681848 CAGCCTCTTGCAGAAATGTAGG 59.318 50.000 0.00 0.00 44.83 3.18
2449 5178 2.019984 GCCTCTTGCAGAAATGTAGGG 58.980 52.381 0.00 0.00 40.77 3.53
2450 5179 2.356125 GCCTCTTGCAGAAATGTAGGGA 60.356 50.000 0.00 0.00 40.77 4.20
2451 5180 3.873801 GCCTCTTGCAGAAATGTAGGGAA 60.874 47.826 0.00 0.00 40.77 3.97
2452 5181 4.335416 CCTCTTGCAGAAATGTAGGGAAA 58.665 43.478 0.00 0.00 0.00 3.13
2453 5182 4.397417 CCTCTTGCAGAAATGTAGGGAAAG 59.603 45.833 0.00 0.00 0.00 2.62
2454 5183 4.335416 TCTTGCAGAAATGTAGGGAAAGG 58.665 43.478 0.00 0.00 0.00 3.11
2455 5184 2.446435 TGCAGAAATGTAGGGAAAGGC 58.554 47.619 0.00 0.00 0.00 4.35
2456 5185 2.041620 TGCAGAAATGTAGGGAAAGGCT 59.958 45.455 0.00 0.00 0.00 4.58
2457 5186 2.424956 GCAGAAATGTAGGGAAAGGCTG 59.575 50.000 0.00 0.00 0.00 4.85
2458 5187 2.424956 CAGAAATGTAGGGAAAGGCTGC 59.575 50.000 0.00 0.00 0.00 5.25
2459 5188 1.401905 GAAATGTAGGGAAAGGCTGCG 59.598 52.381 0.00 0.00 0.00 5.18
2460 5189 0.328258 AATGTAGGGAAAGGCTGCGT 59.672 50.000 0.00 0.00 0.00 5.24
2461 5190 1.200519 ATGTAGGGAAAGGCTGCGTA 58.799 50.000 0.00 0.00 0.00 4.42
2462 5191 0.248289 TGTAGGGAAAGGCTGCGTAC 59.752 55.000 0.00 0.00 37.28 3.67
2463 5192 0.248289 GTAGGGAAAGGCTGCGTACA 59.752 55.000 0.00 0.00 36.89 2.90
2464 5193 0.978151 TAGGGAAAGGCTGCGTACAA 59.022 50.000 0.00 0.00 0.00 2.41
2465 5194 0.328258 AGGGAAAGGCTGCGTACAAT 59.672 50.000 0.00 0.00 0.00 2.71
2466 5195 1.557832 AGGGAAAGGCTGCGTACAATA 59.442 47.619 0.00 0.00 0.00 1.90
2467 5196 1.940613 GGGAAAGGCTGCGTACAATAG 59.059 52.381 0.00 0.00 0.00 1.73
2468 5197 2.419574 GGGAAAGGCTGCGTACAATAGA 60.420 50.000 0.00 0.00 0.00 1.98
2469 5198 2.608090 GGAAAGGCTGCGTACAATAGAC 59.392 50.000 0.00 0.00 0.00 2.59
2470 5199 2.311124 AAGGCTGCGTACAATAGACC 57.689 50.000 0.00 0.00 0.00 3.85
2471 5200 0.464452 AGGCTGCGTACAATAGACCC 59.536 55.000 0.00 0.00 0.00 4.46
2472 5201 0.177141 GGCTGCGTACAATAGACCCA 59.823 55.000 0.00 0.00 0.00 4.51
2473 5202 1.406341 GGCTGCGTACAATAGACCCAA 60.406 52.381 0.00 0.00 0.00 4.12
2474 5203 2.352388 GCTGCGTACAATAGACCCAAA 58.648 47.619 0.00 0.00 0.00 3.28
2475 5204 2.351726 GCTGCGTACAATAGACCCAAAG 59.648 50.000 0.00 0.00 0.00 2.77
2476 5205 3.596214 CTGCGTACAATAGACCCAAAGT 58.404 45.455 0.00 0.00 0.00 2.66
2477 5206 3.331150 TGCGTACAATAGACCCAAAGTG 58.669 45.455 0.00 0.00 0.00 3.16
2478 5207 2.676342 GCGTACAATAGACCCAAAGTGG 59.324 50.000 0.00 0.00 37.25 4.00
2479 5208 3.867216 GCGTACAATAGACCCAAAGTGGT 60.867 47.826 0.00 0.00 42.79 4.16
2484 5213 4.373771 GACCCAAAGTGGTCGGAC 57.626 61.111 0.00 0.00 44.98 4.79
2485 5214 1.302271 GACCCAAAGTGGTCGGACC 60.302 63.158 20.36 20.36 44.98 4.46
2486 5215 2.033602 CCCAAAGTGGTCGGACCC 59.966 66.667 23.81 14.91 37.50 4.46
2487 5216 2.526046 CCCAAAGTGGTCGGACCCT 61.526 63.158 23.81 16.82 37.50 4.34
2488 5217 1.454539 CCAAAGTGGTCGGACCCTT 59.545 57.895 23.81 21.08 37.50 3.95
2489 5218 0.605589 CCAAAGTGGTCGGACCCTTC 60.606 60.000 23.81 13.97 37.50 3.46
2490 5219 0.605589 CAAAGTGGTCGGACCCTTCC 60.606 60.000 23.81 9.51 37.50 3.46
2491 5220 1.775934 AAAGTGGTCGGACCCTTCCC 61.776 60.000 23.81 7.17 38.99 3.97
2492 5221 3.714001 GTGGTCGGACCCTTCCCC 61.714 72.222 23.81 0.00 38.99 4.81
2493 5222 4.257810 TGGTCGGACCCTTCCCCA 62.258 66.667 23.81 0.69 38.99 4.96
2494 5223 3.400054 GGTCGGACCCTTCCCCAG 61.400 72.222 16.55 0.00 38.99 4.45
2495 5224 2.284405 GTCGGACCCTTCCCCAGA 60.284 66.667 0.00 0.00 38.99 3.86
2496 5225 2.284405 TCGGACCCTTCCCCAGAC 60.284 66.667 0.00 0.00 38.99 3.51
2497 5226 3.400054 CGGACCCTTCCCCAGACC 61.400 72.222 0.00 0.00 38.99 3.85
2498 5227 3.015753 GGACCCTTCCCCAGACCC 61.016 72.222 0.00 0.00 35.57 4.46
2499 5228 2.125225 GACCCTTCCCCAGACCCT 59.875 66.667 0.00 0.00 0.00 4.34
2500 5229 2.204151 ACCCTTCCCCAGACCCTG 60.204 66.667 0.00 0.00 0.00 4.45
2501 5230 3.732849 CCCTTCCCCAGACCCTGC 61.733 72.222 0.00 0.00 0.00 4.85
2502 5231 4.101448 CCTTCCCCAGACCCTGCG 62.101 72.222 0.00 0.00 0.00 5.18
2503 5232 4.785453 CTTCCCCAGACCCTGCGC 62.785 72.222 0.00 0.00 0.00 6.09
2526 5255 2.203070 GGAGCTACATGCACCGGG 60.203 66.667 6.32 0.00 42.21 5.73
2527 5256 2.203070 GAGCTACATGCACCGGGG 60.203 66.667 6.32 0.84 45.94 5.73
2528 5257 4.489771 AGCTACATGCACCGGGGC 62.490 66.667 25.59 25.59 45.94 5.80
2529 5258 4.489771 GCTACATGCACCGGGGCT 62.490 66.667 32.18 13.01 42.31 5.19
2530 5259 2.514592 CTACATGCACCGGGGCTG 60.515 66.667 32.18 26.08 34.04 4.85
2531 5260 4.794648 TACATGCACCGGGGCTGC 62.795 66.667 32.18 19.72 35.03 5.25
2537 5266 4.041762 CACCGGGGCTGCCCTTTA 62.042 66.667 34.99 0.00 44.66 1.85
2538 5267 3.021263 ACCGGGGCTGCCCTTTAT 61.021 61.111 34.99 16.85 44.66 1.40
2539 5268 1.694882 ACCGGGGCTGCCCTTTATA 60.695 57.895 34.99 0.00 44.66 0.98
2540 5269 1.065997 ACCGGGGCTGCCCTTTATAT 61.066 55.000 34.99 13.71 44.66 0.86
2541 5270 0.988832 CCGGGGCTGCCCTTTATATA 59.011 55.000 34.99 0.00 44.66 0.86
2542 5271 1.065418 CCGGGGCTGCCCTTTATATAG 60.065 57.143 34.99 16.16 44.66 1.31
2543 5272 1.679032 CGGGGCTGCCCTTTATATAGC 60.679 57.143 34.99 15.39 44.66 2.97
2544 5273 1.636003 GGGGCTGCCCTTTATATAGCT 59.364 52.381 34.99 0.00 44.66 3.32
2545 5274 2.619074 GGGGCTGCCCTTTATATAGCTG 60.619 54.545 34.99 0.00 44.66 4.24
2546 5275 2.087646 GGCTGCCCTTTATATAGCTGC 58.912 52.381 7.66 12.37 45.90 5.25
2547 5276 1.734465 GCTGCCCTTTATATAGCTGCG 59.266 52.381 0.00 0.00 39.75 5.18
2548 5277 2.350522 CTGCCCTTTATATAGCTGCGG 58.649 52.381 0.00 0.00 0.00 5.69
2549 5278 1.974957 TGCCCTTTATATAGCTGCGGA 59.025 47.619 0.00 0.00 0.00 5.54
2550 5279 2.571653 TGCCCTTTATATAGCTGCGGAT 59.428 45.455 0.00 0.00 0.00 4.18
2551 5280 3.009033 TGCCCTTTATATAGCTGCGGATT 59.991 43.478 0.00 0.00 0.00 3.01
2552 5281 4.224147 TGCCCTTTATATAGCTGCGGATTA 59.776 41.667 0.00 0.00 0.00 1.75
2553 5282 4.571176 GCCCTTTATATAGCTGCGGATTAC 59.429 45.833 0.00 0.00 0.00 1.89
2554 5283 5.730550 CCCTTTATATAGCTGCGGATTACA 58.269 41.667 0.00 0.00 0.00 2.41
2555 5284 5.812642 CCCTTTATATAGCTGCGGATTACAG 59.187 44.000 0.00 0.00 38.22 2.74
2729 5458 3.321682 TGGCCTTGAAGTTTTGGAAGATG 59.678 43.478 3.32 0.00 0.00 2.90
2730 5459 3.573967 GGCCTTGAAGTTTTGGAAGATGA 59.426 43.478 0.00 0.00 0.00 2.92
2743 5472 7.563888 TTTGGAAGATGATTGCTGATCTTAG 57.436 36.000 0.00 0.00 38.72 2.18
2744 5473 6.244552 TGGAAGATGATTGCTGATCTTAGT 57.755 37.500 0.00 0.00 38.72 2.24
2745 5474 7.365497 TGGAAGATGATTGCTGATCTTAGTA 57.635 36.000 0.00 0.00 38.72 1.82
2746 5475 7.795047 TGGAAGATGATTGCTGATCTTAGTAA 58.205 34.615 0.00 0.00 38.72 2.24
2747 5476 8.435187 TGGAAGATGATTGCTGATCTTAGTAAT 58.565 33.333 0.00 0.00 38.72 1.89
2748 5477 8.719648 GGAAGATGATTGCTGATCTTAGTAATG 58.280 37.037 1.83 0.00 38.72 1.90
2749 5478 9.270640 GAAGATGATTGCTGATCTTAGTAATGT 57.729 33.333 1.83 0.00 38.72 2.71
2750 5479 8.830201 AGATGATTGCTGATCTTAGTAATGTC 57.170 34.615 1.83 1.48 33.91 3.06
2751 5480 8.427276 AGATGATTGCTGATCTTAGTAATGTCA 58.573 33.333 1.83 0.00 33.91 3.58
2752 5481 8.604640 ATGATTGCTGATCTTAGTAATGTCAG 57.395 34.615 15.33 15.33 39.35 3.51
2840 5569 6.205784 ACAAGTCATGTTCCATAAAAACACG 58.794 36.000 0.00 0.00 40.06 4.49
3357 6086 2.123988 TTGCGGTTTGCTGTTAGCCG 62.124 55.000 0.00 0.00 46.63 5.52
3500 6230 6.650120 TCTAACAATCTCCTGTGTTAATCCC 58.350 40.000 0.00 0.00 39.17 3.85
3561 6291 3.054875 TCTTCTGCAACATGAGCCAGTAT 60.055 43.478 0.00 0.00 0.00 2.12
3978 6714 4.819630 TCGACAGTCTTGTTAATTTTGCCT 59.180 37.500 0.00 0.00 37.76 4.75
3984 6720 5.302823 AGTCTTGTTAATTTTGCCTCTTGCT 59.697 36.000 0.00 0.00 42.00 3.91
4267 7011 2.632643 CCATGAGTGGTGGTGTGTG 58.367 57.895 0.00 0.00 40.83 3.82
4268 7012 1.518056 CCATGAGTGGTGGTGTGTGC 61.518 60.000 0.00 0.00 40.83 4.57
4269 7013 0.818852 CATGAGTGGTGGTGTGTGCA 60.819 55.000 0.00 0.00 0.00 4.57
4270 7014 0.111061 ATGAGTGGTGGTGTGTGCAT 59.889 50.000 0.00 0.00 0.00 3.96
4271 7015 0.106769 TGAGTGGTGGTGTGTGCATT 60.107 50.000 0.00 0.00 0.00 3.56
4272 7016 0.311790 GAGTGGTGGTGTGTGCATTG 59.688 55.000 0.00 0.00 0.00 2.82
4273 7017 1.108727 AGTGGTGGTGTGTGCATTGG 61.109 55.000 0.00 0.00 0.00 3.16
4624 7380 2.874751 GAAACCGTTGGATGCCCG 59.125 61.111 0.00 0.00 34.29 6.13
4648 7408 7.207383 CGATCATACTGTTCCAAAGTACCATA 58.793 38.462 0.00 0.00 33.11 2.74
4650 7410 9.209175 GATCATACTGTTCCAAAGTACCATATC 57.791 37.037 0.00 0.00 33.11 1.63
4656 7416 2.701951 TCCAAAGTACCATATCGGGTCC 59.298 50.000 0.00 0.00 42.42 4.46
4668 7428 1.002134 CGGGTCCAGGAATGCAAGT 60.002 57.895 0.00 0.00 0.00 3.16
4702 7463 2.897271 ACACACAATGGGCCTTATGA 57.103 45.000 4.53 0.00 0.00 2.15
4776 7538 5.131784 AGTTGTTATCTACTACTCCCTCCG 58.868 45.833 0.00 0.00 38.22 4.63
4787 7549 4.589374 ACTACTCCCTCCGATCCAAAATAG 59.411 45.833 0.00 0.00 0.00 1.73
4809 7571 4.947388 AGGTGTTGCAGTTTTGAACTAAGA 59.053 37.500 0.00 0.00 40.46 2.10
4833 7596 9.918630 AGATTAGTTCATCTTGGTTCAAAATTG 57.081 29.630 0.00 0.00 28.19 2.32
4847 7610 8.731605 TGGTTCAAAATTGCGACACTTATTATA 58.268 29.630 0.00 0.00 0.00 0.98
4851 7615 9.644993 TCAAAATTGCGACACTTATTATAATCG 57.355 29.630 0.00 0.35 0.00 3.34
4854 7618 7.582435 ATTGCGACACTTATTATAATCGGAG 57.418 36.000 0.00 2.05 31.60 4.63
4868 7632 4.875561 AATCGGAGGGAGTAGCTATTTC 57.124 45.455 0.00 0.00 0.00 2.17
4869 7633 3.596940 TCGGAGGGAGTAGCTATTTCT 57.403 47.619 0.00 0.00 0.00 2.52
4870 7634 3.488363 TCGGAGGGAGTAGCTATTTCTC 58.512 50.000 0.00 4.55 0.00 2.87
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
48 53 6.495526 GCTAAAGGAATAGTAGGACAGGATCT 59.504 42.308 0.00 0.00 0.00 2.75
52 57 5.871396 TGCTAAAGGAATAGTAGGACAGG 57.129 43.478 0.00 0.00 0.00 4.00
54 59 6.351881 CCAGTTGCTAAAGGAATAGTAGGACA 60.352 42.308 0.00 0.00 0.00 4.02
55 60 6.049790 CCAGTTGCTAAAGGAATAGTAGGAC 58.950 44.000 0.00 0.00 0.00 3.85
60 65 5.763876 ACTCCAGTTGCTAAAGGAATAGT 57.236 39.130 0.00 0.00 0.00 2.12
102 142 1.369448 GTACGCTGCCTCGAGATCG 60.369 63.158 15.71 13.23 41.45 3.69
123 165 4.208873 CGTCGTGGTAGTCTACAGTCTATC 59.791 50.000 12.08 0.00 0.00 2.08
345 741 2.742710 TTCCTGCTCGACGGTTCGTG 62.743 60.000 0.00 0.00 46.01 4.35
351 747 1.734477 CACAGTTCCTGCTCGACGG 60.734 63.158 0.00 0.00 34.37 4.79
352 748 2.375766 GCACAGTTCCTGCTCGACG 61.376 63.158 0.00 0.00 34.37 5.12
562 3089 2.224719 GGGTGGATGGATGGATCTCTTG 60.225 54.545 0.00 0.00 0.00 3.02
569 3096 1.418097 CGGATGGGTGGATGGATGGA 61.418 60.000 0.00 0.00 0.00 3.41
570 3097 1.073722 CGGATGGGTGGATGGATGG 59.926 63.158 0.00 0.00 0.00 3.51
571 3098 0.250467 GACGGATGGGTGGATGGATG 60.250 60.000 0.00 0.00 0.00 3.51
682 3221 4.144727 GAGGGAGGGAGGGAGCGA 62.145 72.222 0.00 0.00 0.00 4.93
684 3223 4.890306 GGGAGGGAGGGAGGGAGC 62.890 77.778 0.00 0.00 0.00 4.70
688 3227 4.179599 GGGAGGGAGGGAGGGAGG 62.180 77.778 0.00 0.00 0.00 4.30
716 3429 0.676782 CGGGAAGCCGGTGAAAATCT 60.677 55.000 1.90 0.00 0.00 2.40
794 3510 3.995809 TAGGCACGGAAGGGGGAGG 62.996 68.421 0.00 0.00 32.68 4.30
795 3511 2.365105 TAGGCACGGAAGGGGGAG 60.365 66.667 0.00 0.00 32.68 4.30
796 3512 2.365105 CTAGGCACGGAAGGGGGA 60.365 66.667 0.00 0.00 32.68 4.81
797 3513 3.480133 CCTAGGCACGGAAGGGGG 61.480 72.222 0.00 0.00 32.68 5.40
798 3514 4.176752 GCCTAGGCACGGAAGGGG 62.177 72.222 29.33 0.00 41.49 4.79
825 3541 3.157949 GGAGGGGAGGCGAGAAGG 61.158 72.222 0.00 0.00 0.00 3.46
1298 4017 0.684153 CGGTGGCCTTGGAAATCCAT 60.684 55.000 3.32 0.00 46.97 3.41
1490 4209 2.501723 ACAGATCAAGGCCACGTATTCT 59.498 45.455 5.01 0.00 0.00 2.40
1506 4225 3.384668 CACACGTTCTTCAGACACAGAT 58.615 45.455 0.00 0.00 0.00 2.90
1513 4232 2.627945 AGTTTGCACACGTTCTTCAGA 58.372 42.857 0.00 0.00 0.00 3.27
1631 4350 2.661866 GCGACGACAACCACTGCT 60.662 61.111 0.00 0.00 0.00 4.24
1821 4540 2.901839 TCCAATTAGGGTATCTACGCCC 59.098 50.000 1.23 0.00 45.16 6.13
1946 4668 4.518970 GGCCAGACAACTTTCAAATAGTGA 59.481 41.667 0.00 0.00 0.00 3.41
1974 4696 3.305110 CAAAACACCTTGGCGTTATCAC 58.695 45.455 0.00 0.00 0.00 3.06
2067 4789 5.587443 TCATTGAATGAGCTGAACCATACAG 59.413 40.000 3.29 0.00 35.09 2.74
2078 4800 7.313646 CAGAAAGTGAAATCATTGAATGAGCT 58.686 34.615 13.79 2.92 43.53 4.09
2375 5104 0.178992 ACAAGGCAGCAGCTTTACCA 60.179 50.000 0.00 0.00 38.07 3.25
2376 5105 0.242017 CACAAGGCAGCAGCTTTACC 59.758 55.000 0.00 0.00 38.07 2.85
2377 5106 1.068954 GTCACAAGGCAGCAGCTTTAC 60.069 52.381 0.00 0.00 38.07 2.01
2380 5109 1.900498 GGTCACAAGGCAGCAGCTT 60.900 57.895 0.00 0.00 41.70 3.74
2383 5112 0.607217 TCATGGTCACAAGGCAGCAG 60.607 55.000 0.00 0.00 0.00 4.24
2385 5114 1.310933 CCTCATGGTCACAAGGCAGC 61.311 60.000 0.00 0.00 0.00 5.25
2386 5115 0.037303 ACCTCATGGTCACAAGGCAG 59.963 55.000 0.00 0.00 44.78 4.85
2387 5116 2.154139 ACCTCATGGTCACAAGGCA 58.846 52.632 0.00 0.00 44.78 4.75
2398 5127 1.270839 ACTTGAACCCGTGACCTCATG 60.271 52.381 0.00 0.00 0.00 3.07
2399 5128 1.002087 GACTTGAACCCGTGACCTCAT 59.998 52.381 0.00 0.00 0.00 2.90
2400 5129 0.391597 GACTTGAACCCGTGACCTCA 59.608 55.000 0.00 0.00 0.00 3.86
2401 5130 0.320508 GGACTTGAACCCGTGACCTC 60.321 60.000 0.00 0.00 0.00 3.85
2402 5131 0.763223 AGGACTTGAACCCGTGACCT 60.763 55.000 0.00 0.00 0.00 3.85
2403 5132 0.602905 CAGGACTTGAACCCGTGACC 60.603 60.000 0.00 0.00 0.00 4.02
2404 5133 0.602905 CCAGGACTTGAACCCGTGAC 60.603 60.000 0.00 0.00 0.00 3.67
2405 5134 0.761323 TCCAGGACTTGAACCCGTGA 60.761 55.000 0.00 0.00 0.00 4.35
2406 5135 0.107831 TTCCAGGACTTGAACCCGTG 59.892 55.000 0.00 0.00 0.00 4.94
2407 5136 0.841289 TTTCCAGGACTTGAACCCGT 59.159 50.000 0.00 0.00 0.00 5.28
2408 5137 1.235724 GTTTCCAGGACTTGAACCCG 58.764 55.000 0.00 0.00 0.00 5.28
2409 5138 2.230660 CTGTTTCCAGGACTTGAACCC 58.769 52.381 0.00 0.00 34.90 4.11
2410 5139 1.609072 GCTGTTTCCAGGACTTGAACC 59.391 52.381 0.00 0.00 39.22 3.62
2411 5140 1.609072 GGCTGTTTCCAGGACTTGAAC 59.391 52.381 0.00 0.00 39.22 3.18
2412 5141 1.494721 AGGCTGTTTCCAGGACTTGAA 59.505 47.619 0.00 0.00 39.22 2.69
2413 5142 1.072331 GAGGCTGTTTCCAGGACTTGA 59.928 52.381 0.00 0.00 39.22 3.02
2414 5143 1.072965 AGAGGCTGTTTCCAGGACTTG 59.927 52.381 0.00 0.00 39.22 3.16
2415 5144 1.439543 AGAGGCTGTTTCCAGGACTT 58.560 50.000 0.00 0.00 39.22 3.01
2416 5145 1.072965 CAAGAGGCTGTTTCCAGGACT 59.927 52.381 0.00 0.00 39.22 3.85
2417 5146 1.528129 CAAGAGGCTGTTTCCAGGAC 58.472 55.000 0.00 0.00 39.22 3.85
2418 5147 0.250901 GCAAGAGGCTGTTTCCAGGA 60.251 55.000 0.00 0.00 39.22 3.86
2419 5148 0.538057 TGCAAGAGGCTGTTTCCAGG 60.538 55.000 0.00 0.00 45.15 4.45
2420 5149 0.879765 CTGCAAGAGGCTGTTTCCAG 59.120 55.000 0.00 0.00 45.15 3.86
2421 5150 0.473755 TCTGCAAGAGGCTGTTTCCA 59.526 50.000 0.00 0.00 38.67 3.53
2422 5151 3.329300 TCTGCAAGAGGCTGTTTCC 57.671 52.632 0.00 0.00 38.67 3.13
2432 5161 4.335416 CCTTTCCCTACATTTCTGCAAGA 58.665 43.478 0.00 0.00 44.68 3.02
2433 5162 3.119352 GCCTTTCCCTACATTTCTGCAAG 60.119 47.826 0.00 0.00 0.00 4.01
2434 5163 2.825532 GCCTTTCCCTACATTTCTGCAA 59.174 45.455 0.00 0.00 0.00 4.08
2435 5164 2.041620 AGCCTTTCCCTACATTTCTGCA 59.958 45.455 0.00 0.00 0.00 4.41
2436 5165 2.424956 CAGCCTTTCCCTACATTTCTGC 59.575 50.000 0.00 0.00 0.00 4.26
2437 5166 2.424956 GCAGCCTTTCCCTACATTTCTG 59.575 50.000 0.00 0.00 0.00 3.02
2438 5167 2.728007 GCAGCCTTTCCCTACATTTCT 58.272 47.619 0.00 0.00 0.00 2.52
2439 5168 1.401905 CGCAGCCTTTCCCTACATTTC 59.598 52.381 0.00 0.00 0.00 2.17
2440 5169 1.271926 ACGCAGCCTTTCCCTACATTT 60.272 47.619 0.00 0.00 0.00 2.32
2441 5170 0.328258 ACGCAGCCTTTCCCTACATT 59.672 50.000 0.00 0.00 0.00 2.71
2442 5171 1.134491 GTACGCAGCCTTTCCCTACAT 60.134 52.381 0.00 0.00 0.00 2.29
2443 5172 0.248289 GTACGCAGCCTTTCCCTACA 59.752 55.000 0.00 0.00 0.00 2.74
2444 5173 0.248289 TGTACGCAGCCTTTCCCTAC 59.752 55.000 0.00 0.00 0.00 3.18
2445 5174 0.978151 TTGTACGCAGCCTTTCCCTA 59.022 50.000 0.00 0.00 0.00 3.53
2446 5175 0.328258 ATTGTACGCAGCCTTTCCCT 59.672 50.000 0.00 0.00 0.00 4.20
2447 5176 1.940613 CTATTGTACGCAGCCTTTCCC 59.059 52.381 0.00 0.00 0.00 3.97
2448 5177 2.608090 GTCTATTGTACGCAGCCTTTCC 59.392 50.000 0.00 0.00 0.00 3.13
2449 5178 2.608090 GGTCTATTGTACGCAGCCTTTC 59.392 50.000 0.00 0.00 0.00 2.62
2450 5179 2.629051 GGTCTATTGTACGCAGCCTTT 58.371 47.619 0.00 0.00 0.00 3.11
2451 5180 1.134491 GGGTCTATTGTACGCAGCCTT 60.134 52.381 0.00 0.00 0.00 4.35
2452 5181 0.464452 GGGTCTATTGTACGCAGCCT 59.536 55.000 0.00 0.00 0.00 4.58
2453 5182 0.177141 TGGGTCTATTGTACGCAGCC 59.823 55.000 0.00 0.00 35.18 4.85
2454 5183 2.018542 TTGGGTCTATTGTACGCAGC 57.981 50.000 0.00 0.00 40.36 5.25
2455 5184 3.370978 CACTTTGGGTCTATTGTACGCAG 59.629 47.826 0.00 0.00 40.36 5.18
2456 5185 3.331150 CACTTTGGGTCTATTGTACGCA 58.669 45.455 0.00 0.00 37.94 5.24
2457 5186 2.676342 CCACTTTGGGTCTATTGTACGC 59.324 50.000 0.00 0.00 32.67 4.42
2458 5187 3.934068 ACCACTTTGGGTCTATTGTACG 58.066 45.455 0.00 0.00 43.37 3.67
2468 5197 2.826003 GGGTCCGACCACTTTGGGT 61.826 63.158 19.43 0.00 43.37 4.51
2469 5198 2.033602 GGGTCCGACCACTTTGGG 59.966 66.667 19.43 0.00 43.37 4.12
2470 5199 0.605589 GAAGGGTCCGACCACTTTGG 60.606 60.000 19.43 0.00 41.02 3.28
2471 5200 0.605589 GGAAGGGTCCGACCACTTTG 60.606 60.000 19.43 0.00 41.02 2.77
2472 5201 1.759236 GGAAGGGTCCGACCACTTT 59.241 57.895 19.43 9.96 41.02 2.66
2473 5202 2.222013 GGGAAGGGTCCGACCACTT 61.222 63.158 19.43 17.88 46.04 3.16
2474 5203 2.606826 GGGAAGGGTCCGACCACT 60.607 66.667 19.43 10.80 46.04 4.00
2475 5204 3.714001 GGGGAAGGGTCCGACCAC 61.714 72.222 19.43 8.70 46.04 4.16
2476 5205 4.257810 TGGGGAAGGGTCCGACCA 62.258 66.667 19.43 0.00 46.04 4.02
2477 5206 3.400054 CTGGGGAAGGGTCCGACC 61.400 72.222 9.30 9.30 46.04 4.79
2478 5207 2.284405 TCTGGGGAAGGGTCCGAC 60.284 66.667 0.00 0.00 46.04 4.79
2479 5208 2.284405 GTCTGGGGAAGGGTCCGA 60.284 66.667 0.00 0.00 46.04 4.55
2480 5209 3.400054 GGTCTGGGGAAGGGTCCG 61.400 72.222 0.00 0.00 46.04 4.79
2481 5210 3.015753 GGGTCTGGGGAAGGGTCC 61.016 72.222 0.00 0.00 44.10 4.46
2482 5211 2.125225 AGGGTCTGGGGAAGGGTC 59.875 66.667 0.00 0.00 0.00 4.46
2483 5212 2.204151 CAGGGTCTGGGGAAGGGT 60.204 66.667 0.00 0.00 0.00 4.34
2484 5213 3.732849 GCAGGGTCTGGGGAAGGG 61.733 72.222 0.00 0.00 31.21 3.95
2485 5214 4.101448 CGCAGGGTCTGGGGAAGG 62.101 72.222 4.35 0.00 40.11 3.46
2486 5215 4.785453 GCGCAGGGTCTGGGGAAG 62.785 72.222 0.30 0.00 43.28 3.46
2498 5227 4.819761 TAGCTCCCGCTTGCGCAG 62.820 66.667 11.31 6.32 46.47 5.18
2501 5230 2.202932 ATGTAGCTCCCGCTTGCG 60.203 61.111 8.14 8.14 46.47 4.85
2502 5231 2.828128 GCATGTAGCTCCCGCTTGC 61.828 63.158 0.00 0.00 46.47 4.01
2503 5232 1.450134 TGCATGTAGCTCCCGCTTG 60.450 57.895 0.00 0.00 46.47 4.01
2504 5233 1.450312 GTGCATGTAGCTCCCGCTT 60.450 57.895 0.00 0.00 46.47 4.68
2510 5239 2.203070 CCCCGGTGCATGTAGCTC 60.203 66.667 11.25 0.00 45.94 4.09
2511 5240 4.489771 GCCCCGGTGCATGTAGCT 62.490 66.667 3.18 0.00 45.94 3.32
2512 5241 4.489771 AGCCCCGGTGCATGTAGC 62.490 66.667 12.68 2.56 45.96 3.58
2513 5242 2.514592 CAGCCCCGGTGCATGTAG 60.515 66.667 12.68 0.00 0.00 2.74
2525 5254 2.716217 CAGCTATATAAAGGGCAGCCC 58.284 52.381 24.90 24.90 45.90 5.19
2526 5255 2.087646 GCAGCTATATAAAGGGCAGCC 58.912 52.381 1.26 1.26 32.46 4.85
2527 5256 1.734465 CGCAGCTATATAAAGGGCAGC 59.266 52.381 0.00 0.00 34.66 5.25
2528 5257 2.028112 TCCGCAGCTATATAAAGGGCAG 60.028 50.000 0.00 0.00 0.00 4.85
2529 5258 1.974957 TCCGCAGCTATATAAAGGGCA 59.025 47.619 0.00 0.00 0.00 5.36
2530 5259 2.762535 TCCGCAGCTATATAAAGGGC 57.237 50.000 0.00 0.00 0.00 5.19
2531 5260 5.730550 TGTAATCCGCAGCTATATAAAGGG 58.269 41.667 0.00 0.00 0.00 3.95
2532 5261 6.398918 ACTGTAATCCGCAGCTATATAAAGG 58.601 40.000 0.00 0.00 37.47 3.11
2533 5262 7.598869 TCAACTGTAATCCGCAGCTATATAAAG 59.401 37.037 0.00 0.00 37.47 1.85
2534 5263 7.438564 TCAACTGTAATCCGCAGCTATATAAA 58.561 34.615 0.00 0.00 37.47 1.40
2535 5264 6.988522 TCAACTGTAATCCGCAGCTATATAA 58.011 36.000 0.00 0.00 37.47 0.98
2536 5265 6.584185 TCAACTGTAATCCGCAGCTATATA 57.416 37.500 0.00 0.00 37.47 0.86
2537 5266 5.468540 TCAACTGTAATCCGCAGCTATAT 57.531 39.130 0.00 0.00 37.47 0.86
2538 5267 4.929819 TCAACTGTAATCCGCAGCTATA 57.070 40.909 0.00 0.00 37.47 1.31
2539 5268 3.819564 TCAACTGTAATCCGCAGCTAT 57.180 42.857 0.00 0.00 37.47 2.97
2540 5269 3.603158 TTCAACTGTAATCCGCAGCTA 57.397 42.857 0.00 0.00 37.47 3.32
2541 5270 2.472695 TTCAACTGTAATCCGCAGCT 57.527 45.000 0.00 0.00 37.47 4.24
2542 5271 3.375299 AGAATTCAACTGTAATCCGCAGC 59.625 43.478 8.44 0.00 37.47 5.25
2543 5272 4.872691 AGAGAATTCAACTGTAATCCGCAG 59.127 41.667 8.44 0.00 39.67 5.18
2544 5273 4.631377 CAGAGAATTCAACTGTAATCCGCA 59.369 41.667 18.31 0.00 0.00 5.69
2545 5274 4.870426 TCAGAGAATTCAACTGTAATCCGC 59.130 41.667 22.61 0.00 33.93 5.54
2546 5275 8.824159 ATATCAGAGAATTCAACTGTAATCCG 57.176 34.615 22.61 5.58 33.93 4.18
2547 5276 9.995003 AGATATCAGAGAATTCAACTGTAATCC 57.005 33.333 22.61 13.91 33.93 3.01
2708 5437 3.573967 TCATCTTCCAAAACTTCAAGGCC 59.426 43.478 0.00 0.00 0.00 5.19
2729 5458 8.973378 GTACTGACATTACTAAGATCAGCAATC 58.027 37.037 10.19 0.00 40.39 2.67
2730 5459 8.478066 TGTACTGACATTACTAAGATCAGCAAT 58.522 33.333 10.19 0.00 40.39 3.56
2747 5476 6.524734 ACTCTTCATCAACAATGTACTGACA 58.475 36.000 0.00 0.00 40.72 3.58
2748 5477 7.293745 CAACTCTTCATCAACAATGTACTGAC 58.706 38.462 0.00 0.00 36.68 3.51
2749 5478 6.073058 GCAACTCTTCATCAACAATGTACTGA 60.073 38.462 0.00 0.00 36.68 3.41
2750 5479 6.082338 GCAACTCTTCATCAACAATGTACTG 58.918 40.000 0.00 0.00 36.68 2.74
2751 5480 5.764686 TGCAACTCTTCATCAACAATGTACT 59.235 36.000 0.00 0.00 36.68 2.73
2752 5481 6.000891 TGCAACTCTTCATCAACAATGTAC 57.999 37.500 0.00 0.00 36.68 2.90
3318 6047 9.332502 ACCGCAAGTCATATAACATAAATTACA 57.667 29.630 0.00 0.00 0.00 2.41
3328 6057 4.142687 ACAGCAAACCGCAAGTCATATAAC 60.143 41.667 0.00 0.00 46.13 1.89
3357 6086 4.455877 ACCACAAGCTAGAAGTATTGTTGC 59.544 41.667 0.00 0.00 40.16 4.17
3437 6166 5.528043 TCCTGACAAAGCATTAAAAGCAA 57.472 34.783 6.11 0.00 0.00 3.91
3500 6230 8.087982 TGAAAGCAGTATGAAGAACTGTAAAG 57.912 34.615 5.25 0.00 45.01 1.85
3561 6291 3.371097 GAACCGCCCGATGCAGAGA 62.371 63.158 0.00 0.00 41.33 3.10
3961 6697 5.829233 GCAAGAGGCAAAATTAACAAGAC 57.171 39.130 0.00 0.00 43.97 3.01
3978 6714 1.073722 CTCCACCCAGCAAGCAAGA 59.926 57.895 0.00 0.00 0.00 3.02
3984 6720 3.667476 TGGAACTCCACCCAGCAA 58.333 55.556 0.00 0.00 42.01 3.91
4261 7005 0.316937 CACGACACCAATGCACACAC 60.317 55.000 0.00 0.00 0.00 3.82
4262 7006 2.020926 CACGACACCAATGCACACA 58.979 52.632 0.00 0.00 0.00 3.72
4263 7007 1.370414 GCACGACACCAATGCACAC 60.370 57.895 0.00 0.00 39.23 3.82
4264 7008 2.891221 CGCACGACACCAATGCACA 61.891 57.895 0.00 0.00 39.39 4.57
4265 7009 2.127270 CGCACGACACCAATGCAC 60.127 61.111 0.00 0.00 39.39 4.57
4266 7010 4.024143 GCGCACGACACCAATGCA 62.024 61.111 0.30 0.00 39.39 3.96
4267 7011 4.759096 GGCGCACGACACCAATGC 62.759 66.667 10.83 0.00 35.96 3.56
4268 7012 2.616330 AAGGCGCACGACACCAATG 61.616 57.895 10.83 0.00 0.00 2.82
4269 7013 2.281484 AAGGCGCACGACACCAAT 60.281 55.556 10.83 0.00 0.00 3.16
4270 7014 3.276091 CAAGGCGCACGACACCAA 61.276 61.111 10.83 0.00 0.00 3.67
4271 7015 4.539083 ACAAGGCGCACGACACCA 62.539 61.111 10.83 0.00 0.00 4.17
4272 7016 3.712881 GACAAGGCGCACGACACC 61.713 66.667 10.83 0.00 0.00 4.16
4273 7017 4.059459 CGACAAGGCGCACGACAC 62.059 66.667 10.83 0.00 0.00 3.67
4394 7138 2.357009 CTGATTCCGGCTTTCCTCAATG 59.643 50.000 0.00 0.00 0.00 2.82
4396 7140 1.351017 ACTGATTCCGGCTTTCCTCAA 59.649 47.619 0.00 0.00 0.00 3.02
4624 7380 9.209175 GATATGGTACTTTGGAACAGTATGATC 57.791 37.037 0.00 0.00 42.39 2.92
4648 7408 0.107017 CTTGCATTCCTGGACCCGAT 60.107 55.000 0.00 0.00 0.00 4.18
4650 7410 1.002134 ACTTGCATTCCTGGACCCG 60.002 57.895 0.00 0.00 0.00 5.28
4656 7416 4.344237 GGGGGACTTGCATTCCTG 57.656 61.111 13.24 0.00 33.17 3.86
4685 7445 3.668141 TGATCATAAGGCCCATTGTGT 57.332 42.857 0.00 0.00 0.00 3.72
4748 7509 9.368674 GAGGGAGTAGTAGATAACAACTTTTTC 57.631 37.037 0.00 0.00 0.00 2.29
4752 7513 5.593502 CGGAGGGAGTAGTAGATAACAACTT 59.406 44.000 0.00 0.00 0.00 2.66
4776 7538 5.391312 AACTGCAACACCTATTTTGGATC 57.609 39.130 0.00 0.00 0.00 3.36
4787 7549 5.243426 TCTTAGTTCAAAACTGCAACACC 57.757 39.130 2.65 0.00 42.84 4.16
4809 7571 7.329226 CGCAATTTTGAACCAAGATGAACTAAT 59.671 33.333 0.00 0.00 0.00 1.73
4818 7580 3.380004 AGTGTCGCAATTTTGAACCAAGA 59.620 39.130 0.00 0.00 0.00 3.02
4833 7596 4.863131 CCCTCCGATTATAATAAGTGTCGC 59.137 45.833 0.00 0.00 0.00 5.19
4847 7610 4.484912 AGAAATAGCTACTCCCTCCGATT 58.515 43.478 0.00 0.00 0.00 3.34


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

AutoCloner maintained by Alex Coulton.