Multiple sequence alignment - TraesCS3B01G227600

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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 TraesCS3B01G227600 chr3B 100.000 4188 0 0 822 5009 324260631 324256444 0.000000e+00 7734.0
1 TraesCS3B01G227600 chr3B 100.000 529 0 0 1 529 324261452 324260924 0.000000e+00 977.0
2 TraesCS3B01G227600 chr3D 93.603 2720 143 19 2314 5008 219238889 219236176 0.000000e+00 4030.0
3 TraesCS3B01G227600 chr3D 92.354 1321 55 10 822 2101 219240307 219238992 0.000000e+00 1838.0
4 TraesCS3B01G227600 chr3D 93.421 532 17 6 1 529 219240827 219240311 0.000000e+00 773.0
5 TraesCS3B01G227600 chr3D 95.349 86 4 0 2230 2315 113456547 113456632 2.430000e-28 137.0
6 TraesCS3B01G227600 chr3D 79.500 200 23 11 4361 4547 408402940 408402746 5.260000e-25 126.0
7 TraesCS3B01G227600 chr3D 100.000 30 0 0 1212 1241 508079365 508079336 7.010000e-04 56.5
8 TraesCS3B01G227600 chr3A 94.369 2131 100 10 2314 4427 293062484 293060357 0.000000e+00 3253.0
9 TraesCS3B01G227600 chr3A 93.681 633 34 3 822 1454 293068357 293067731 0.000000e+00 942.0
10 TraesCS3B01G227600 chr3A 93.726 526 26 4 1 522 293068866 293068344 0.000000e+00 782.0
11 TraesCS3B01G227600 chr3A 92.857 406 28 1 1696 2101 293062990 293062586 5.590000e-164 588.0
12 TraesCS3B01G227600 chr3A 98.165 218 4 0 1454 1671 293063573 293063356 1.020000e-101 381.0
13 TraesCS3B01G227600 chr3A 90.411 219 21 0 4790 5008 293060355 293060137 6.340000e-74 289.0
14 TraesCS3B01G227600 chr6A 93.617 94 6 0 2222 2315 579814395 579814302 1.880000e-29 141.0
15 TraesCS3B01G227600 chr6A 87.879 66 4 4 4289 4351 125934838 125934774 1.930000e-09 75.0
16 TraesCS3B01G227600 chr4A 95.402 87 4 0 2230 2316 743380942 743380856 6.760000e-29 139.0
17 TraesCS3B01G227600 chr1A 94.382 89 5 0 2229 2317 58166621 58166709 2.430000e-28 137.0
18 TraesCS3B01G227600 chr2B 94.318 88 5 0 2230 2317 517438393 517438480 8.750000e-28 135.0
19 TraesCS3B01G227600 chr6B 92.473 93 7 0 2223 2315 118184742 118184650 3.150000e-27 134.0
20 TraesCS3B01G227600 chr1B 92.473 93 7 0 2223 2315 8775984 8776076 3.150000e-27 134.0
21 TraesCS3B01G227600 chr5A 91.667 96 6 2 2222 2316 466005705 466005799 1.130000e-26 132.0
22 TraesCS3B01G227600 chr5A 81.132 106 14 5 4283 4383 288425786 288425682 4.160000e-11 80.5
23 TraesCS3B01G227600 chr4B 90.909 99 8 1 2222 2319 433617355 433617257 1.130000e-26 132.0
24 TraesCS3B01G227600 chr4B 75.330 227 34 17 4354 4564 195444104 195444324 6.910000e-14 89.8
25 TraesCS3B01G227600 chr7A 75.735 272 57 6 2947 3209 708436078 708436349 1.460000e-25 128.0
26 TraesCS3B01G227600 chr6D 77.293 229 33 12 4357 4572 21667246 21667024 3.170000e-22 117.0
27 TraesCS3B01G227600 chr7D 84.884 86 9 4 4287 4372 62459669 62459588 3.210000e-12 84.2
28 TraesCS3B01G227600 chr7D 84.884 86 9 4 4287 4372 62531694 62531613 3.210000e-12 84.2
29 TraesCS3B01G227600 chr1D 84.884 86 7 5 4288 4370 480305731 480305813 1.160000e-11 82.4
30 TraesCS3B01G227600 chr7B 82.474 97 12 4 4293 4385 721314087 721313992 4.160000e-11 80.5
31 TraesCS3B01G227600 chr2A 86.301 73 9 1 4487 4559 753013958 753014029 1.500000e-10 78.7
32 TraesCS3B01G227600 chr5D 79.592 98 10 9 4293 4383 65003053 65002959 1.510000e-05 62.1


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 TraesCS3B01G227600 chr3B 324256444 324261452 5008 True 4355.500000 7734 100.0000 1 5009 2 chr3B.!!$R1 5008
1 TraesCS3B01G227600 chr3D 219236176 219240827 4651 True 2213.666667 4030 93.1260 1 5008 3 chr3D.!!$R3 5007
2 TraesCS3B01G227600 chr3A 293060137 293063573 3436 True 1127.750000 3253 93.9505 1454 5008 4 chr3A.!!$R1 3554
3 TraesCS3B01G227600 chr3A 293067731 293068866 1135 True 862.000000 942 93.7035 1 1454 2 chr3A.!!$R2 1453

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
376 383 0.987715 CGTCATGTTCAGCTGTCTCG 59.012 55.000 14.67 6.69 0.0 4.04 F
397 404 1.185315 AGCTTGGCAAGTTGTGTGTT 58.815 45.000 26.71 0.00 0.0 3.32 F
1140 1160 1.362717 CCGTAATCTCATCGCCGGT 59.637 57.895 1.90 0.00 0.0 5.28 F
2885 3289 0.670546 CTCAAGTCCACAACGCCGAT 60.671 55.000 0.00 0.00 0.0 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2109 2511 0.035820 TACCAAGAACATGTCCCCGC 60.036 55.0 0.0 0.0 0.0 6.13 R
2302 2705 2.019807 TCCTTTGTACTCCCTCCGTT 57.980 50.0 0.0 0.0 0.0 4.44 R
3049 3453 0.248289 GCCCACACCTTTAGTAGCGA 59.752 55.0 0.0 0.0 0.0 4.93 R
4469 4891 0.391927 TTGGTATCCTGCCCGTTTCG 60.392 55.0 0.0 0.0 0.0 3.46 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
22 23 1.407979 ACAGTTTCAGTTCGTCTCGGT 59.592 47.619 0.00 0.00 0.00 4.69
43 44 2.649129 GCCAAGCATCCCCACAACC 61.649 63.158 0.00 0.00 0.00 3.77
115 116 1.783284 ACGTGCGCATATGTATGGAG 58.217 50.000 15.91 0.00 34.32 3.86
123 124 1.065199 CATATGTATGGAGGCGGGCAT 60.065 52.381 3.78 0.00 0.00 4.40
127 128 2.818169 TATGGAGGCGGGCATGGTC 61.818 63.158 3.78 0.00 0.00 4.02
258 265 8.608844 AACAAAATATATCTTCATCTCGGTCC 57.391 34.615 0.00 0.00 0.00 4.46
376 383 0.987715 CGTCATGTTCAGCTGTCTCG 59.012 55.000 14.67 6.69 0.00 4.04
397 404 1.185315 AGCTTGGCAAGTTGTGTGTT 58.815 45.000 26.71 0.00 0.00 3.32
414 421 3.577848 TGTGTTTGCTTGCCTCCATTAAT 59.422 39.130 0.00 0.00 0.00 1.40
456 463 2.784347 GCTTTTGCTTCTGGAGTACCT 58.216 47.619 0.00 0.00 43.35 3.08
469 489 5.938125 TCTGGAGTACCTTTTCTGTTATTGC 59.062 40.000 0.00 0.00 37.04 3.56
470 490 5.007682 TGGAGTACCTTTTCTGTTATTGCC 58.992 41.667 0.00 0.00 37.04 4.52
471 491 5.007682 GGAGTACCTTTTCTGTTATTGCCA 58.992 41.667 0.00 0.00 0.00 4.92
472 492 5.106277 GGAGTACCTTTTCTGTTATTGCCAC 60.106 44.000 0.00 0.00 0.00 5.01
473 493 3.915437 ACCTTTTCTGTTATTGCCACG 57.085 42.857 0.00 0.00 0.00 4.94
474 494 3.219281 ACCTTTTCTGTTATTGCCACGT 58.781 40.909 0.00 0.00 0.00 4.49
475 495 3.634910 ACCTTTTCTGTTATTGCCACGTT 59.365 39.130 0.00 0.00 0.00 3.99
476 496 4.098807 ACCTTTTCTGTTATTGCCACGTTT 59.901 37.500 0.00 0.00 0.00 3.60
477 497 4.679654 CCTTTTCTGTTATTGCCACGTTTC 59.320 41.667 0.00 0.00 0.00 2.78
478 498 4.902443 TTTCTGTTATTGCCACGTTTCA 57.098 36.364 0.00 0.00 0.00 2.69
479 499 3.889196 TCTGTTATTGCCACGTTTCAC 57.111 42.857 0.00 0.00 0.00 3.18
480 500 3.472652 TCTGTTATTGCCACGTTTCACT 58.527 40.909 0.00 0.00 0.00 3.41
481 501 3.249799 TCTGTTATTGCCACGTTTCACTG 59.750 43.478 0.00 0.00 0.00 3.66
843 863 2.604152 CCTCCCTCTCCGCTACCT 59.396 66.667 0.00 0.00 0.00 3.08
844 864 1.717038 CCCTCCCTCTCCGCTACCTA 61.717 65.000 0.00 0.00 0.00 3.08
882 902 4.477249 ACATCCCATTCCATTCAATCCTC 58.523 43.478 0.00 0.00 0.00 3.71
897 917 7.905604 TTCAATCCTCCGTAGCATAATATTG 57.094 36.000 0.00 0.00 0.00 1.90
899 919 4.202245 TCCTCCGTAGCATAATATTGCC 57.798 45.455 0.00 0.00 43.83 4.52
903 923 2.677836 CCGTAGCATAATATTGCCGCAT 59.322 45.455 0.00 0.00 43.83 4.73
961 981 3.706086 AGGAATTGAGAGAGAAGAGGAGC 59.294 47.826 0.00 0.00 0.00 4.70
985 1005 4.238514 CGATTAAGTTGGGATCGATCTCC 58.761 47.826 22.41 21.06 43.86 3.71
1140 1160 1.362717 CCGTAATCTCATCGCCGGT 59.637 57.895 1.90 0.00 0.00 5.28
1263 1285 8.429641 GTTTCTGACACCCTCTTATATTATGGA 58.570 37.037 0.00 0.00 0.00 3.41
1272 1294 5.484290 CCTCTTATATTATGGAACGGAGGGT 59.516 44.000 0.00 0.00 35.53 4.34
1391 1413 1.871080 ACCTTCTCACGTGCAAAGAG 58.129 50.000 23.27 17.29 0.00 2.85
1405 1427 3.960102 TGCAAAGAGTTGAGGATGGTTTT 59.040 39.130 0.00 0.00 36.83 2.43
1439 1461 2.158841 TCTTTATCGCAAGTTCGCAACC 59.841 45.455 0.00 0.00 39.48 3.77
1565 1598 8.612145 ACCAAGAAAGTACTAACCCAGATATTT 58.388 33.333 0.00 0.00 0.00 1.40
1600 1633 2.741612 TGGGTACGTACGACAAACTTG 58.258 47.619 24.41 0.00 0.00 3.16
1651 1684 6.000246 TCATCAGTTAGGACATGGCAAATA 58.000 37.500 0.00 0.00 0.00 1.40
1741 2139 2.492484 TCCTCGTTTTGCTCTAGTCCTC 59.508 50.000 0.00 0.00 0.00 3.71
1781 2179 3.433740 GGAGCCCAATTACTAGGAACCTG 60.434 52.174 3.36 0.00 0.00 4.00
1846 2244 1.480954 CAGGTGCCTTATACGTCCAGT 59.519 52.381 0.00 0.00 0.00 4.00
1851 2249 5.778750 AGGTGCCTTATACGTCCAGTAATAT 59.221 40.000 0.00 0.00 39.04 1.28
1927 2326 8.150945 GTCCCTCTGTAATGAAATATAAGAGCA 58.849 37.037 0.00 0.00 0.00 4.26
1982 2381 6.531503 AGAGTTTATAGTGCTGCTAGTTCA 57.468 37.500 0.00 0.00 32.45 3.18
2010 2409 3.181531 GCATGCTACCAAATCGTTTTTGC 60.182 43.478 11.37 2.20 0.00 3.68
2033 2432 8.039603 TGCGATGATTTAAGATGTTACAAAGT 57.960 30.769 0.00 0.00 0.00 2.66
2080 2482 7.429633 CAAGTCCTCGGCTCCATTATATATAG 58.570 42.308 0.00 0.00 0.00 1.31
2088 2490 9.038072 TCGGCTCCATTATATATAGTAAAACCA 57.962 33.333 0.00 0.00 0.00 3.67
2089 2491 9.095065 CGGCTCCATTATATATAGTAAAACCAC 57.905 37.037 0.00 0.00 0.00 4.16
2090 2492 9.953565 GGCTCCATTATATATAGTAAAACCACA 57.046 33.333 0.00 0.00 0.00 4.17
2157 2559 2.667874 TGATGCCTTTCGCGTGCA 60.668 55.556 5.77 11.80 42.08 4.57
2229 2632 3.589288 AGCCAGGAGGAAGACTAAATGTT 59.411 43.478 0.00 0.00 36.89 2.71
2230 2633 4.783227 AGCCAGGAGGAAGACTAAATGTTA 59.217 41.667 0.00 0.00 36.89 2.41
2231 2634 4.876679 GCCAGGAGGAAGACTAAATGTTAC 59.123 45.833 0.00 0.00 36.89 2.50
2232 2635 5.338463 GCCAGGAGGAAGACTAAATGTTACT 60.338 44.000 0.00 0.00 36.89 2.24
2233 2636 6.342111 CCAGGAGGAAGACTAAATGTTACTC 58.658 44.000 0.00 0.00 36.89 2.59
2234 2637 6.342111 CAGGAGGAAGACTAAATGTTACTCC 58.658 44.000 6.92 6.92 0.00 3.85
2235 2638 5.425862 AGGAGGAAGACTAAATGTTACTCCC 59.574 44.000 10.64 0.00 0.00 4.30
2236 2639 5.425862 GGAGGAAGACTAAATGTTACTCCCT 59.574 44.000 4.09 0.00 0.00 4.20
2237 2640 6.407187 GGAGGAAGACTAAATGTTACTCCCTC 60.407 46.154 4.09 0.00 0.00 4.30
2238 2641 5.425862 AGGAAGACTAAATGTTACTCCCTCC 59.574 44.000 0.00 0.00 0.00 4.30
2239 2642 5.340439 AAGACTAAATGTTACTCCCTCCG 57.660 43.478 0.00 0.00 0.00 4.63
2240 2643 4.351127 AGACTAAATGTTACTCCCTCCGT 58.649 43.478 0.00 0.00 0.00 4.69
2241 2644 4.776308 AGACTAAATGTTACTCCCTCCGTT 59.224 41.667 0.00 0.00 0.00 4.44
2242 2645 5.247792 AGACTAAATGTTACTCCCTCCGTTT 59.752 40.000 0.00 0.00 0.00 3.60
2243 2646 5.872963 ACTAAATGTTACTCCCTCCGTTTT 58.127 37.500 0.00 0.00 0.00 2.43
2244 2647 7.008021 ACTAAATGTTACTCCCTCCGTTTTA 57.992 36.000 0.00 0.00 0.00 1.52
2245 2648 7.452562 ACTAAATGTTACTCCCTCCGTTTTAA 58.547 34.615 0.00 0.00 0.00 1.52
2246 2649 7.938490 ACTAAATGTTACTCCCTCCGTTTTAAA 59.062 33.333 0.00 0.00 0.00 1.52
2247 2650 7.585579 AAATGTTACTCCCTCCGTTTTAAAA 57.414 32.000 0.00 0.00 0.00 1.52
2248 2651 7.770366 AATGTTACTCCCTCCGTTTTAAAAT 57.230 32.000 3.52 0.00 0.00 1.82
2249 2652 8.866970 AATGTTACTCCCTCCGTTTTAAAATA 57.133 30.769 3.52 0.00 0.00 1.40
2250 2653 7.910441 TGTTACTCCCTCCGTTTTAAAATAG 57.090 36.000 3.52 1.99 0.00 1.73
2251 2654 7.678837 TGTTACTCCCTCCGTTTTAAAATAGA 58.321 34.615 3.52 3.61 0.00 1.98
2252 2655 8.323567 TGTTACTCCCTCCGTTTTAAAATAGAT 58.676 33.333 3.52 0.00 0.00 1.98
2253 2656 8.610035 GTTACTCCCTCCGTTTTAAAATAGATG 58.390 37.037 3.52 2.01 0.00 2.90
2254 2657 6.954232 ACTCCCTCCGTTTTAAAATAGATGA 58.046 36.000 3.52 3.96 0.00 2.92
2255 2658 6.822170 ACTCCCTCCGTTTTAAAATAGATGAC 59.178 38.462 3.52 0.00 0.00 3.06
2256 2659 6.117488 TCCCTCCGTTTTAAAATAGATGACC 58.883 40.000 3.52 0.00 0.00 4.02
2257 2660 5.007332 CCCTCCGTTTTAAAATAGATGACCG 59.993 44.000 3.52 0.50 0.00 4.79
2258 2661 5.813672 CCTCCGTTTTAAAATAGATGACCGA 59.186 40.000 3.52 0.00 0.00 4.69
2259 2662 6.314400 CCTCCGTTTTAAAATAGATGACCGAA 59.686 38.462 3.52 0.00 0.00 4.30
2260 2663 7.064060 TCCGTTTTAAAATAGATGACCGAAC 57.936 36.000 3.52 0.00 0.00 3.95
2261 2664 6.875195 TCCGTTTTAAAATAGATGACCGAACT 59.125 34.615 3.52 0.00 0.00 3.01
2262 2665 7.388500 TCCGTTTTAAAATAGATGACCGAACTT 59.612 33.333 3.52 0.00 0.00 2.66
2263 2666 8.019094 CCGTTTTAAAATAGATGACCGAACTTT 58.981 33.333 3.52 0.00 0.00 2.66
2264 2667 8.837059 CGTTTTAAAATAGATGACCGAACTTTG 58.163 33.333 3.52 0.00 0.00 2.77
2265 2668 9.673454 GTTTTAAAATAGATGACCGAACTTTGT 57.327 29.630 3.52 0.00 0.00 2.83
2273 2676 9.886132 ATAGATGACCGAACTTTGTATTAAAGT 57.114 29.630 0.00 0.00 41.82 2.66
2275 2678 9.715121 AGATGACCGAACTTTGTATTAAAGTTA 57.285 29.630 15.34 3.36 46.81 2.24
2276 2679 9.968743 GATGACCGAACTTTGTATTAAAGTTAG 57.031 33.333 15.34 14.83 46.81 2.34
2277 2680 8.891671 TGACCGAACTTTGTATTAAAGTTAGT 57.108 30.769 15.34 15.07 46.81 2.24
2278 2681 9.979578 TGACCGAACTTTGTATTAAAGTTAGTA 57.020 29.630 15.34 4.77 46.81 1.82
2306 2709 7.153217 AGTTGGGTCATCTATTTTAAAACGG 57.847 36.000 1.97 0.00 0.00 4.44
2307 2710 6.943718 AGTTGGGTCATCTATTTTAAAACGGA 59.056 34.615 1.97 5.09 0.00 4.69
2308 2711 6.995511 TGGGTCATCTATTTTAAAACGGAG 57.004 37.500 1.97 1.74 0.00 4.63
2309 2712 5.883673 TGGGTCATCTATTTTAAAACGGAGG 59.116 40.000 1.97 6.55 0.00 4.30
2310 2713 5.298527 GGGTCATCTATTTTAAAACGGAGGG 59.701 44.000 1.97 2.46 0.00 4.30
2311 2714 6.117488 GGTCATCTATTTTAAAACGGAGGGA 58.883 40.000 1.97 4.48 0.00 4.20
2312 2715 6.260271 GGTCATCTATTTTAAAACGGAGGGAG 59.740 42.308 1.97 0.00 0.00 4.30
2355 2759 9.462606 TTCCTCCCTTTATTTTTCTCTGATAAC 57.537 33.333 0.00 0.00 0.00 1.89
2356 2760 8.836735 TCCTCCCTTTATTTTTCTCTGATAACT 58.163 33.333 0.00 0.00 0.00 2.24
2358 2762 9.454859 CTCCCTTTATTTTTCTCTGATAACTGT 57.545 33.333 0.00 0.00 0.00 3.55
2465 2869 0.674895 GATGTCGCCAACTCTGCCTT 60.675 55.000 0.00 0.00 0.00 4.35
2466 2870 0.957395 ATGTCGCCAACTCTGCCTTG 60.957 55.000 0.00 0.00 0.00 3.61
2720 3124 4.317671 ACCAGACATATGTAACGTAGGC 57.682 45.455 8.71 0.00 0.00 3.93
2778 3182 2.920384 TGACGTACTGGCCTGGCA 60.920 61.111 22.05 3.71 0.00 4.92
2885 3289 0.670546 CTCAAGTCCACAACGCCGAT 60.671 55.000 0.00 0.00 0.00 4.18
3231 3636 2.958355 CACCATTTCACCAAGACCAAGT 59.042 45.455 0.00 0.00 0.00 3.16
3234 3639 5.068460 CACCATTTCACCAAGACCAAGTTTA 59.932 40.000 0.00 0.00 0.00 2.01
3418 3823 2.260434 GTGTCGGCGTGGAAGCTA 59.740 61.111 6.85 0.00 37.29 3.32
3427 3832 1.880646 GCGTGGAAGCTAGGGTTTGAA 60.881 52.381 0.00 0.00 0.00 2.69
3474 3879 2.965147 TCGTAAGCTCATCCATCCATCA 59.035 45.455 0.00 0.00 37.18 3.07
3478 3883 3.878237 AGCTCATCCATCCATCATGTT 57.122 42.857 0.00 0.00 0.00 2.71
3514 3919 3.826157 TGATCCAACCATGTTTTCCTGAC 59.174 43.478 0.00 0.00 0.00 3.51
3517 3922 2.621055 CCAACCATGTTTTCCTGACGAA 59.379 45.455 0.00 0.00 0.00 3.85
3519 3924 3.982576 ACCATGTTTTCCTGACGAAAC 57.017 42.857 0.00 0.00 40.23 2.78
3708 4113 3.541093 CTGCGCGCAAACCACACAT 62.541 57.895 35.50 0.00 0.00 3.21
3722 4127 0.603065 ACACATAGACACAGCTCGCA 59.397 50.000 0.00 0.00 0.00 5.10
3752 4157 2.863740 GTTAACTTTTGGCTGTTGTGGC 59.136 45.455 0.00 0.00 0.00 5.01
3774 4179 1.337703 GTTTGATGTCCTTGCAGTGCA 59.662 47.619 15.37 15.37 36.47 4.57
3798 4203 0.108804 GTTCTTCCCTCATCGTCGCA 60.109 55.000 0.00 0.00 0.00 5.10
3840 4245 1.274703 GCAAGGGGAGGGAGATGACA 61.275 60.000 0.00 0.00 0.00 3.58
3928 4333 3.423154 GCAAGGACGCCAGGAACG 61.423 66.667 0.00 0.00 0.00 3.95
4225 4630 8.379331 CCCATTTTCTGGTAATTTTTAAGGGAA 58.621 33.333 0.00 0.00 44.30 3.97
4247 4652 3.008485 AGCTTCTACTTTGCTACAAGCCT 59.992 43.478 0.00 0.00 41.51 4.58
4268 4673 7.168219 AGCCTCTAAACACATCAACATAGAAA 58.832 34.615 0.00 0.00 0.00 2.52
4269 4674 7.831193 AGCCTCTAAACACATCAACATAGAAAT 59.169 33.333 0.00 0.00 0.00 2.17
4270 4675 8.125448 GCCTCTAAACACATCAACATAGAAATC 58.875 37.037 0.00 0.00 0.00 2.17
4271 4676 9.388506 CCTCTAAACACATCAACATAGAAATCT 57.611 33.333 0.00 0.00 0.00 2.40
4320 4726 4.530553 TCCTAATGAAGCAGTTGGTAGTCA 59.469 41.667 0.00 0.00 0.00 3.41
4321 4727 5.189736 TCCTAATGAAGCAGTTGGTAGTCAT 59.810 40.000 0.00 0.00 0.00 3.06
4322 4728 5.882557 CCTAATGAAGCAGTTGGTAGTCATT 59.117 40.000 12.91 12.91 37.05 2.57
4328 4734 3.498397 AGCAGTTGGTAGTCATTGTTTCG 59.502 43.478 0.00 0.00 0.00 3.46
4369 4791 3.506067 CCCACCTTCGTCTGCTTATTTTT 59.494 43.478 0.00 0.00 0.00 1.94
4469 4891 2.821969 TCTCCCTAACCAGACACGTTAC 59.178 50.000 0.00 0.00 0.00 2.50
4470 4892 1.541147 TCCCTAACCAGACACGTTACG 59.459 52.381 2.19 2.19 0.00 3.18
4474 4896 3.426525 CCTAACCAGACACGTTACGAAAC 59.573 47.826 13.03 1.79 0.00 2.78
4493 4915 0.808755 CGGGCAGGATACCAAACAAC 59.191 55.000 0.00 0.00 37.17 3.32
4560 4982 1.753073 CACATTGATCCCTGCCTTTCC 59.247 52.381 0.00 0.00 0.00 3.13
4565 4987 2.562296 TGATCCCTGCCTTTCCTAACT 58.438 47.619 0.00 0.00 0.00 2.24
4567 4989 3.454812 TGATCCCTGCCTTTCCTAACTAC 59.545 47.826 0.00 0.00 0.00 2.73
4601 5025 8.740906 TCTACTTGTGTAATCTTCTTACTCCTG 58.259 37.037 0.00 0.00 0.00 3.86
4643 5068 2.007608 GTTCGTTCTTACCCCATGCTC 58.992 52.381 0.00 0.00 0.00 4.26
4648 5073 0.673985 TCTTACCCCATGCTCGATCG 59.326 55.000 9.36 9.36 0.00 3.69
4668 5093 2.350804 CGATCGACACTCCTTTCGTCTA 59.649 50.000 10.26 0.00 36.60 2.59
4669 5094 3.544440 CGATCGACACTCCTTTCGTCTAG 60.544 52.174 10.26 0.00 36.60 2.43
4704 5129 6.769134 TCTTCACTTTCCTCGTATATCACA 57.231 37.500 0.00 0.00 0.00 3.58
4707 5132 6.525578 TCACTTTCCTCGTATATCACACTT 57.474 37.500 0.00 0.00 0.00 3.16
4716 5141 6.918569 CCTCGTATATCACACTTCGAAGAAAT 59.081 38.462 31.08 18.38 45.90 2.17
4725 5150 7.806690 TCACACTTCGAAGAAATAAAATCCAG 58.193 34.615 31.08 0.42 45.90 3.86
4727 5152 7.959651 CACACTTCGAAGAAATAAAATCCAGAG 59.040 37.037 31.08 0.00 45.90 3.35
4743 5168 3.238987 GAGGCCATCTCTCCTTCCT 57.761 57.895 5.01 0.00 39.38 3.36
4845 5273 4.706035 GCATCATCTTCTTCATGTCTCCT 58.294 43.478 0.00 0.00 0.00 3.69
4856 5284 0.908656 ATGTCTCCTGCTGGACTGCT 60.909 55.000 8.48 0.00 37.46 4.24
4901 5329 2.194056 CCATGCTCGCCTCCCAAT 59.806 61.111 0.00 0.00 0.00 3.16
4905 5333 4.802051 GCTCGCCTCCCAATGCCA 62.802 66.667 0.00 0.00 0.00 4.92
4906 5334 2.194056 CTCGCCTCCCAATGCCAT 59.806 61.111 0.00 0.00 0.00 4.40
4912 5340 0.469917 CCTCCCAATGCCATAGACGT 59.530 55.000 0.00 0.00 0.00 4.34
4951 5379 3.372730 CCACCCCACGCATGTTGG 61.373 66.667 8.20 8.20 0.00 3.77
4986 5414 2.125147 CCGACACCGCACCATCAT 60.125 61.111 0.00 0.00 0.00 2.45
4988 5416 2.173669 CGACACCGCACCATCATCC 61.174 63.158 0.00 0.00 0.00 3.51
5000 5428 0.469494 CATCATCCATGGACGGGACA 59.531 55.000 18.99 0.00 37.23 4.02
5008 5436 1.838073 ATGGACGGGACAACCTGGAC 61.838 60.000 0.00 0.00 46.20 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 38 2.357327 TATCGTTCGTCAGGGTTGTG 57.643 50.000 0.00 0.00 0.00 3.33
43 44 1.217882 GGCCATTATCGTTCGTCAGG 58.782 55.000 0.00 0.00 0.00 3.86
99 100 0.670239 CGCCTCCATACATATGCGCA 60.670 55.000 14.96 14.96 35.33 6.09
123 124 2.454832 CTTGCTTGGCTCTCCGACCA 62.455 60.000 0.00 0.00 34.14 4.02
127 128 1.003355 TTCCTTGCTTGGCTCTCCG 60.003 57.895 0.00 0.00 34.14 4.63
258 265 7.928908 TTGCTGTTAAATTTTGCACTCTAAG 57.071 32.000 0.00 0.00 33.13 2.18
362 369 0.676184 AGCTTCGAGACAGCTGAACA 59.324 50.000 23.35 0.00 46.25 3.18
376 383 1.134946 ACACACAACTTGCCAAGCTTC 59.865 47.619 3.88 0.00 0.00 3.86
397 404 5.904941 CATACAATTAATGGAGGCAAGCAA 58.095 37.500 0.00 0.00 0.00 3.91
414 421 3.535280 TGAGCGATACAAGGCATACAA 57.465 42.857 0.00 0.00 0.00 2.41
456 463 5.038033 GTGAAACGTGGCAATAACAGAAAA 58.962 37.500 0.00 0.00 0.00 2.29
469 489 0.317269 CTTGCTGCAGTGAAACGTGG 60.317 55.000 16.64 0.00 45.86 4.94
470 490 0.378257 ACTTGCTGCAGTGAAACGTG 59.622 50.000 16.64 0.00 45.86 4.49
471 491 0.657840 GACTTGCTGCAGTGAAACGT 59.342 50.000 16.64 4.13 45.86 3.99
472 492 0.657312 TGACTTGCTGCAGTGAAACG 59.343 50.000 16.64 0.97 45.86 3.60
473 493 2.291465 TGATGACTTGCTGCAGTGAAAC 59.709 45.455 16.64 5.57 0.00 2.78
474 494 2.291465 GTGATGACTTGCTGCAGTGAAA 59.709 45.455 16.64 7.00 0.00 2.69
475 495 1.875514 GTGATGACTTGCTGCAGTGAA 59.124 47.619 16.64 7.82 0.00 3.18
476 496 1.516161 GTGATGACTTGCTGCAGTGA 58.484 50.000 16.64 3.17 0.00 3.41
477 497 0.520404 GGTGATGACTTGCTGCAGTG 59.480 55.000 16.64 8.66 0.00 3.66
478 498 0.109153 TGGTGATGACTTGCTGCAGT 59.891 50.000 16.64 3.36 0.00 4.40
479 499 0.520404 GTGGTGATGACTTGCTGCAG 59.480 55.000 10.11 10.11 0.00 4.41
480 500 0.890542 GGTGGTGATGACTTGCTGCA 60.891 55.000 0.00 0.00 0.00 4.41
481 501 0.607489 AGGTGGTGATGACTTGCTGC 60.607 55.000 0.00 0.00 0.00 5.25
826 846 0.406361 ATAGGTAGCGGAGAGGGAGG 59.594 60.000 0.00 0.00 0.00 4.30
830 850 8.155510 TGTGTATATATATAGGTAGCGGAGAGG 58.844 40.741 2.53 0.00 0.00 3.69
835 855 7.719778 TCGTGTGTATATATATAGGTAGCGG 57.280 40.000 2.53 0.00 0.00 5.52
844 864 9.817809 GAATGGGATGTTCGTGTGTATATATAT 57.182 33.333 0.00 0.00 0.00 0.86
882 902 2.073056 TGCGGCAATATTATGCTACGG 58.927 47.619 0.00 0.00 45.68 4.02
897 917 0.948141 CTAGCTGGCTAGAATGCGGC 60.948 60.000 21.08 0.00 46.56 6.53
899 919 0.033228 AGCTAGCTGGCTAGAATGCG 59.967 55.000 24.61 6.82 46.56 4.73
961 981 2.902705 TCGATCCCAACTTAATCGGG 57.097 50.000 4.39 0.00 41.88 5.14
985 1005 4.025040 TCCCCATAGCTGCAGATTATTG 57.975 45.455 20.43 9.97 0.00 1.90
1140 1160 3.691342 CCGGGAGCGAGGAACACA 61.691 66.667 0.00 0.00 0.00 3.72
1190 1210 6.325028 AGGAGTAGCTGTGAAGCAATATAAGA 59.675 38.462 0.00 0.00 37.25 2.10
1198 1218 3.141398 CAAAAGGAGTAGCTGTGAAGCA 58.859 45.455 0.00 0.00 37.25 3.91
1241 1261 6.868864 CGTTCCATAATATAAGAGGGTGTCAG 59.131 42.308 0.00 0.00 0.00 3.51
1248 1268 5.484290 ACCCTCCGTTCCATAATATAAGAGG 59.516 44.000 0.00 0.00 38.47 3.69
1263 1285 2.616256 GGACCGAATTAAACCCTCCGTT 60.616 50.000 0.00 0.00 35.70 4.44
1272 1294 2.083774 CAGCAGCTGGACCGAATTAAA 58.916 47.619 17.12 0.00 0.00 1.52
1359 1381 6.468000 CACGTGAGAAGGTAAAAGAAAACAAC 59.532 38.462 10.90 0.00 0.00 3.32
1360 1382 6.548171 CACGTGAGAAGGTAAAAGAAAACAA 58.452 36.000 10.90 0.00 0.00 2.83
1439 1461 6.128007 ACTCAAATAAACCAGACTAATTGCGG 60.128 38.462 0.00 0.00 0.00 5.69
1565 1598 7.095271 CGTACGTACCCAAAAATAGAGGAAAAA 60.095 37.037 19.67 0.00 0.00 1.94
1600 1633 7.201652 GGAAGACTAGCTGTTGGAATTAATGAC 60.202 40.741 0.00 0.00 0.00 3.06
1741 2139 3.190118 GCTCCTTTGATGACACCAAGAAG 59.810 47.826 0.00 0.00 0.00 2.85
1781 2179 5.521906 AAACCTGAGAGGAAAAGAAAAGC 57.478 39.130 0.00 0.00 37.67 3.51
1901 2300 8.150945 TGCTCTTATATTTCATTACAGAGGGAC 58.849 37.037 0.00 0.00 0.00 4.46
1956 2355 8.528643 TGAACTAGCAGCACTATAAACTCTTTA 58.471 33.333 0.00 0.00 0.00 1.85
1982 2381 4.261801 ACGATTTGGTAGCATGCTAACTT 58.738 39.130 35.87 23.58 37.16 2.66
1991 2390 2.290916 TCGCAAAAACGATTTGGTAGCA 59.709 40.909 16.23 0.00 37.09 3.49
2033 2432 8.445588 ACTTGGTCCTTTCCTTCTAAAAAGATA 58.554 33.333 0.00 0.00 35.02 1.98
2062 2461 9.038072 TGGTTTTACTATATATAATGGAGCCGA 57.962 33.333 0.00 0.00 0.00 5.54
2102 2504 1.067821 GAACATGTCCCCGCACAAAAA 59.932 47.619 0.00 0.00 0.00 1.94
2103 2505 0.671251 GAACATGTCCCCGCACAAAA 59.329 50.000 0.00 0.00 0.00 2.44
2104 2506 0.179004 AGAACATGTCCCCGCACAAA 60.179 50.000 0.00 0.00 0.00 2.83
2105 2507 0.179004 AAGAACATGTCCCCGCACAA 60.179 50.000 0.00 0.00 0.00 3.33
2106 2508 0.888736 CAAGAACATGTCCCCGCACA 60.889 55.000 0.00 0.00 0.00 4.57
2107 2509 1.586154 CCAAGAACATGTCCCCGCAC 61.586 60.000 0.00 0.00 0.00 5.34
2108 2510 1.303236 CCAAGAACATGTCCCCGCA 60.303 57.895 0.00 0.00 0.00 5.69
2109 2511 0.035820 TACCAAGAACATGTCCCCGC 60.036 55.000 0.00 0.00 0.00 6.13
2110 2512 2.081462 GTTACCAAGAACATGTCCCCG 58.919 52.381 0.00 0.00 0.00 5.73
2111 2513 3.149005 TGTTACCAAGAACATGTCCCC 57.851 47.619 0.00 0.00 34.40 4.81
2112 2514 3.886505 TGTTGTTACCAAGAACATGTCCC 59.113 43.478 0.00 0.00 39.41 4.46
2113 2515 5.508200 TTGTTGTTACCAAGAACATGTCC 57.492 39.130 0.00 0.00 43.11 4.02
2114 2516 5.977129 CCTTTGTTGTTACCAAGAACATGTC 59.023 40.000 0.00 0.00 43.11 3.06
2178 2581 2.033662 GCCGCGAGATGAAAACTGTATC 60.034 50.000 8.23 0.00 0.00 2.24
2229 2632 7.983484 GTCATCTATTTTAAAACGGAGGGAGTA 59.017 37.037 1.97 0.00 0.00 2.59
2230 2633 6.822170 GTCATCTATTTTAAAACGGAGGGAGT 59.178 38.462 1.97 0.00 0.00 3.85
2231 2634 6.260271 GGTCATCTATTTTAAAACGGAGGGAG 59.740 42.308 1.97 0.00 0.00 4.30
2232 2635 6.117488 GGTCATCTATTTTAAAACGGAGGGA 58.883 40.000 1.97 4.48 0.00 4.20
2233 2636 5.007332 CGGTCATCTATTTTAAAACGGAGGG 59.993 44.000 1.97 2.46 0.00 4.30
2234 2637 5.813672 TCGGTCATCTATTTTAAAACGGAGG 59.186 40.000 1.97 6.55 0.00 4.30
2235 2638 6.897259 TCGGTCATCTATTTTAAAACGGAG 57.103 37.500 1.97 1.74 0.00 4.63
2236 2639 6.875195 AGTTCGGTCATCTATTTTAAAACGGA 59.125 34.615 1.97 5.09 0.00 4.69
2237 2640 7.068692 AGTTCGGTCATCTATTTTAAAACGG 57.931 36.000 1.97 0.00 0.00 4.44
2238 2641 8.837059 CAAAGTTCGGTCATCTATTTTAAAACG 58.163 33.333 1.97 0.08 0.00 3.60
2239 2642 9.673454 ACAAAGTTCGGTCATCTATTTTAAAAC 57.327 29.630 1.97 0.00 0.00 2.43
2247 2650 9.886132 ACTTTAATACAAAGTTCGGTCATCTAT 57.114 29.630 0.00 0.00 37.18 1.98
2248 2651 9.715121 AACTTTAATACAAAGTTCGGTCATCTA 57.285 29.630 8.85 0.00 44.50 1.98
2249 2652 8.617290 AACTTTAATACAAAGTTCGGTCATCT 57.383 30.769 8.85 0.00 44.50 2.90
2250 2653 9.968743 CTAACTTTAATACAAAGTTCGGTCATC 57.031 33.333 16.10 0.00 44.50 2.92
2251 2654 9.498176 ACTAACTTTAATACAAAGTTCGGTCAT 57.502 29.630 16.10 0.00 44.50 3.06
2252 2655 8.891671 ACTAACTTTAATACAAAGTTCGGTCA 57.108 30.769 16.10 1.48 44.50 4.02
2280 2683 8.085909 CCGTTTTAAAATAGATGACCCAACTTT 58.914 33.333 3.52 0.00 0.00 2.66
2281 2684 7.449086 TCCGTTTTAAAATAGATGACCCAACTT 59.551 33.333 3.52 0.00 0.00 2.66
2282 2685 6.943718 TCCGTTTTAAAATAGATGACCCAACT 59.056 34.615 3.52 0.00 0.00 3.16
2283 2686 7.148355 TCCGTTTTAAAATAGATGACCCAAC 57.852 36.000 3.52 0.00 0.00 3.77
2284 2687 6.376018 CCTCCGTTTTAAAATAGATGACCCAA 59.624 38.462 3.52 0.00 0.00 4.12
2285 2688 5.883673 CCTCCGTTTTAAAATAGATGACCCA 59.116 40.000 3.52 0.00 0.00 4.51
2286 2689 5.298527 CCCTCCGTTTTAAAATAGATGACCC 59.701 44.000 3.52 0.00 0.00 4.46
2287 2690 6.117488 TCCCTCCGTTTTAAAATAGATGACC 58.883 40.000 3.52 0.00 0.00 4.02
2288 2691 6.822170 ACTCCCTCCGTTTTAAAATAGATGAC 59.178 38.462 3.52 0.00 0.00 3.06
2289 2692 6.954232 ACTCCCTCCGTTTTAAAATAGATGA 58.046 36.000 3.52 3.96 0.00 2.92
2290 2693 7.767198 TGTACTCCCTCCGTTTTAAAATAGATG 59.233 37.037 3.52 2.01 0.00 2.90
2291 2694 7.854337 TGTACTCCCTCCGTTTTAAAATAGAT 58.146 34.615 3.52 0.00 0.00 1.98
2292 2695 7.243604 TGTACTCCCTCCGTTTTAAAATAGA 57.756 36.000 3.52 3.61 0.00 1.98
2293 2696 7.910441 TTGTACTCCCTCCGTTTTAAAATAG 57.090 36.000 3.52 1.99 0.00 1.73
2294 2697 7.391275 CCTTTGTACTCCCTCCGTTTTAAAATA 59.609 37.037 3.52 0.00 0.00 1.40
2295 2698 6.208007 CCTTTGTACTCCCTCCGTTTTAAAAT 59.792 38.462 3.52 0.00 0.00 1.82
2296 2699 5.532032 CCTTTGTACTCCCTCCGTTTTAAAA 59.468 40.000 0.00 0.00 0.00 1.52
2297 2700 5.065235 CCTTTGTACTCCCTCCGTTTTAAA 58.935 41.667 0.00 0.00 0.00 1.52
2298 2701 4.347583 TCCTTTGTACTCCCTCCGTTTTAA 59.652 41.667 0.00 0.00 0.00 1.52
2299 2702 3.903090 TCCTTTGTACTCCCTCCGTTTTA 59.097 43.478 0.00 0.00 0.00 1.52
2300 2703 2.707257 TCCTTTGTACTCCCTCCGTTTT 59.293 45.455 0.00 0.00 0.00 2.43
2301 2704 2.332117 TCCTTTGTACTCCCTCCGTTT 58.668 47.619 0.00 0.00 0.00 3.60
2302 2705 2.019807 TCCTTTGTACTCCCTCCGTT 57.980 50.000 0.00 0.00 0.00 4.44
2303 2706 2.108970 GATCCTTTGTACTCCCTCCGT 58.891 52.381 0.00 0.00 0.00 4.69
2304 2707 2.362717 GAGATCCTTTGTACTCCCTCCG 59.637 54.545 0.00 0.00 0.00 4.63
2305 2708 3.648739 AGAGATCCTTTGTACTCCCTCC 58.351 50.000 0.00 0.00 0.00 4.30
2306 2709 5.451354 AGTAGAGATCCTTTGTACTCCCTC 58.549 45.833 0.00 0.00 0.00 4.30
2307 2710 5.475398 AGTAGAGATCCTTTGTACTCCCT 57.525 43.478 0.00 0.00 0.00 4.20
2308 2711 5.069383 GGAAGTAGAGATCCTTTGTACTCCC 59.931 48.000 0.00 0.00 32.75 4.30
2309 2712 5.894964 AGGAAGTAGAGATCCTTTGTACTCC 59.105 44.000 0.00 0.00 43.59 3.85
2310 2713 6.040054 GGAGGAAGTAGAGATCCTTTGTACTC 59.960 46.154 0.00 0.00 46.04 2.59
2311 2714 5.894964 GGAGGAAGTAGAGATCCTTTGTACT 59.105 44.000 0.00 0.00 46.04 2.73
2312 2715 5.069383 GGGAGGAAGTAGAGATCCTTTGTAC 59.931 48.000 0.00 0.00 46.04 2.90
2355 2759 6.312918 ACACCTCTACGCAAACAATAATACAG 59.687 38.462 0.00 0.00 0.00 2.74
2356 2760 6.167685 ACACCTCTACGCAAACAATAATACA 58.832 36.000 0.00 0.00 0.00 2.29
2358 2762 7.675962 AAACACCTCTACGCAAACAATAATA 57.324 32.000 0.00 0.00 0.00 0.98
2405 2809 6.152154 AGTTTGCCAACATTATAACCTGGTAC 59.848 38.462 0.00 0.00 35.05 3.34
2411 2815 6.926272 TCACAAAGTTTGCCAACATTATAACC 59.074 34.615 15.59 0.00 35.05 2.85
2465 2869 2.546899 TGGGCTAGCCTAGAAGAAACA 58.453 47.619 32.18 15.86 36.10 2.83
2466 2870 3.536570 CTTGGGCTAGCCTAGAAGAAAC 58.463 50.000 32.18 13.36 36.10 2.78
2720 3124 5.163550 TGGAACTATATCACGTCAACTCTGG 60.164 44.000 0.00 0.00 0.00 3.86
2796 3200 5.353123 ACACACACCACGCCTAATAAATAAG 59.647 40.000 0.00 0.00 0.00 1.73
3049 3453 0.248289 GCCCACACCTTTAGTAGCGA 59.752 55.000 0.00 0.00 0.00 4.93
3105 3509 2.049063 GGAAGTGCTGTCGCGTCT 60.049 61.111 5.77 0.00 39.65 4.18
3150 3554 2.419713 GCAGCTGAGGATGATGAGAACA 60.420 50.000 20.43 0.00 0.00 3.18
3153 3557 0.388294 CGCAGCTGAGGATGATGAGA 59.612 55.000 20.43 0.00 0.00 3.27
3418 3823 4.451900 CGTATAGCCTGATTTCAAACCCT 58.548 43.478 0.00 0.00 0.00 4.34
3474 3879 3.401033 TCAATCAGGTCGTCACAACAT 57.599 42.857 0.00 0.00 0.00 2.71
3478 3883 1.899142 TGGATCAATCAGGTCGTCACA 59.101 47.619 0.00 0.00 0.00 3.58
3514 3919 2.358898 CCCCCTGCATAATTCAGTTTCG 59.641 50.000 0.00 0.00 0.00 3.46
3517 3922 2.624029 CCACCCCCTGCATAATTCAGTT 60.624 50.000 0.00 0.00 0.00 3.16
3519 3924 1.063717 ACCACCCCCTGCATAATTCAG 60.064 52.381 0.00 0.00 0.00 3.02
3648 4053 2.040442 TCCTCGAGGATGGCCCAA 59.960 61.111 30.49 5.50 39.78 4.12
3708 4113 1.209383 GTCGTGCGAGCTGTGTCTA 59.791 57.895 0.00 0.00 0.00 2.59
3722 4127 2.578786 CCAAAAGTTAACAGGGGTCGT 58.421 47.619 8.61 0.00 0.00 4.34
3752 4157 1.069022 CACTGCAAGGACATCAAACGG 60.069 52.381 0.00 0.00 39.30 4.44
3774 4179 1.831736 ACGATGAGGGAAGAACCGATT 59.168 47.619 0.00 0.00 40.11 3.34
3798 4203 3.627237 CCCAAAGCACCATATACAACCCT 60.627 47.826 0.00 0.00 0.00 4.34
3874 4279 2.037620 ATCATGGTCTCTGGAGCCGC 62.038 60.000 0.00 0.00 39.02 6.53
4041 4446 4.154737 ACATATGTATGATGCGCAATCCAC 59.845 41.667 17.11 11.42 37.15 4.02
4225 4630 3.008485 AGGCTTGTAGCAAAGTAGAAGCT 59.992 43.478 10.94 0.00 44.71 3.74
4268 4673 9.553064 AGAAATTATGAAAGCGTATGAAGAGAT 57.447 29.630 0.00 0.00 0.00 2.75
4269 4674 8.948631 AGAAATTATGAAAGCGTATGAAGAGA 57.051 30.769 0.00 0.00 0.00 3.10
4271 4676 9.817809 AGTAGAAATTATGAAAGCGTATGAAGA 57.182 29.630 0.00 0.00 0.00 2.87
4273 4678 9.042008 GGAGTAGAAATTATGAAAGCGTATGAA 57.958 33.333 0.00 0.00 0.00 2.57
4338 4745 2.058595 CGAAGGTGGGAGGTCGGAT 61.059 63.158 0.00 0.00 0.00 4.18
4369 4791 0.626382 TGTTGGTGGGAGGTGAAACA 59.374 50.000 0.00 0.00 39.98 2.83
4449 4871 2.415090 CGTAACGTGTCTGGTTAGGGAG 60.415 54.545 0.00 0.00 34.05 4.30
4469 4891 0.391927 TTGGTATCCTGCCCGTTTCG 60.392 55.000 0.00 0.00 0.00 3.46
4470 4892 1.471287 GTTTGGTATCCTGCCCGTTTC 59.529 52.381 0.00 0.00 0.00 2.78
4474 4896 0.808755 GTTGTTTGGTATCCTGCCCG 59.191 55.000 0.00 0.00 0.00 6.13
4527 4949 7.066284 CAGGGATCAATGTGTTAGGAAAGTTAG 59.934 40.741 0.00 0.00 0.00 2.34
4541 4963 1.642762 AGGAAAGGCAGGGATCAATGT 59.357 47.619 0.00 0.00 0.00 2.71
4581 5003 5.422331 CCCTCAGGAGTAAGAAGATTACACA 59.578 44.000 0.00 0.00 33.47 3.72
4582 5004 5.657302 TCCCTCAGGAGTAAGAAGATTACAC 59.343 44.000 0.00 0.00 37.19 2.90
4601 5025 4.021632 ACGAAACAACTTAGGTACTCCCTC 60.022 45.833 0.00 0.00 44.81 4.30
4622 5046 0.725117 GCATGGGGTAAGAACGAACG 59.275 55.000 0.00 0.00 0.00 3.95
4648 5073 2.923605 AGACGAAAGGAGTGTCGATC 57.076 50.000 0.00 0.00 39.64 3.69
4668 5093 5.180304 GGAAAGTGAAGAAGAGAAAATCGCT 59.820 40.000 0.00 0.00 32.60 4.93
4669 5094 5.180304 AGGAAAGTGAAGAAGAGAAAATCGC 59.820 40.000 0.00 0.00 0.00 4.58
4681 5106 6.377429 AGTGTGATATACGAGGAAAGTGAAGA 59.623 38.462 0.00 0.00 0.00 2.87
4682 5107 6.565234 AGTGTGATATACGAGGAAAGTGAAG 58.435 40.000 0.00 0.00 0.00 3.02
4704 5129 6.094186 GCCTCTGGATTTTATTTCTTCGAAGT 59.906 38.462 23.85 8.46 0.00 3.01
4707 5132 4.881850 GGCCTCTGGATTTTATTTCTTCGA 59.118 41.667 0.00 0.00 0.00 3.71
4725 5150 0.758123 CAGGAAGGAGAGATGGCCTC 59.242 60.000 3.32 0.00 42.28 4.70
4727 5152 0.758123 CTCAGGAAGGAGAGATGGCC 59.242 60.000 0.00 0.00 37.05 5.36
4743 5168 7.423844 TTTCAAGAGAGATATGCCTTACTCA 57.576 36.000 0.00 0.00 32.59 3.41
4845 5273 2.362369 GGAGCCTAGCAGTCCAGCA 61.362 63.158 0.00 0.00 36.85 4.41
4887 5315 4.802051 GGCATTGGGAGGCGAGCA 62.802 66.667 0.00 0.00 32.21 4.26
4905 5333 0.106619 AGAGAAGGGCCGACGTCTAT 60.107 55.000 14.70 0.00 29.28 1.98
4906 5334 0.543277 TAGAGAAGGGCCGACGTCTA 59.457 55.000 14.70 0.70 29.28 2.59
4912 5340 1.453379 CGGAGTAGAGAAGGGCCGA 60.453 63.158 0.00 0.00 41.11 5.54
4986 5414 1.537889 AGGTTGTCCCGTCCATGGA 60.538 57.895 11.44 11.44 38.74 3.41
4988 5416 1.377202 CCAGGTTGTCCCGTCCATG 60.377 63.158 0.00 0.00 38.74 3.66


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

AutoCloner maintained by Alex Coulton.