Multiple sequence alignment - TraesCS1A01G067500

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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 TraesCS1A01G067500 chr1A 100.000 2567 0 0 1 2567 49304054 49306620 0.000000e+00 4741.0
1 TraesCS1A01G067500 chr1A 85.936 967 112 11 850 1804 49295131 49296085 0.000000e+00 1011.0
2 TraesCS1A01G067500 chr1A 82.541 968 150 13 860 1822 49356547 49357500 0.000000e+00 833.0
3 TraesCS1A01G067500 chr1A 82.215 984 149 16 850 1820 49348500 49349470 0.000000e+00 824.0
4 TraesCS1A01G067500 chr1A 83.333 714 119 0 855 1568 37503614 37502901 0.000000e+00 660.0
5 TraesCS1A01G067500 chr1A 87.963 216 26 0 1840 2055 49296087 49296302 3.280000e-64 255.0
6 TraesCS1A01G067500 chr1A 82.143 112 6 8 2448 2559 49296648 49296745 1.640000e-12 84.2
7 TraesCS1A01G067500 chr1D 87.565 957 105 5 850 1804 49958010 49958954 0.000000e+00 1096.0
8 TraesCS1A01G067500 chr1D 90.276 761 40 9 125 855 50025699 50026455 0.000000e+00 965.0
9 TraesCS1A01G067500 chr1D 82.293 977 160 7 850 1822 49974971 49975938 0.000000e+00 833.0
10 TraesCS1A01G067500 chr1D 84.496 774 116 4 850 1621 50060968 50061739 0.000000e+00 761.0
11 TraesCS1A01G067500 chr1D 91.854 356 7 10 1 334 50010227 50010582 6.430000e-131 477.0
12 TraesCS1A01G067500 chr1D 84.471 425 22 10 336 731 50011037 50011446 1.860000e-101 379.0
13 TraesCS1A01G067500 chr1D 92.593 108 8 0 1840 1947 49958956 49959063 3.420000e-34 156.0
14 TraesCS1A01G067500 chr1D 85.484 124 14 3 1 124 50025511 50025630 2.680000e-25 126.0
15 TraesCS1A01G067500 chr1B 86.082 970 105 15 850 1804 70335526 70336480 0.000000e+00 1016.0
16 TraesCS1A01G067500 chr1B 82.231 968 149 14 860 1822 70695918 70696867 0.000000e+00 813.0
17 TraesCS1A01G067500 chr1B 88.889 216 24 0 1840 2055 70336482 70336697 1.510000e-67 267.0
18 TraesCS1A01G067500 chr1B 85.938 64 5 3 1683 1743 69355373 69355311 5.930000e-07 65.8
19 TraesCS1A01G067500 chr1B 95.000 40 2 0 2409 2448 641539409 641539448 2.130000e-06 63.9
20 TraesCS1A01G067500 chr6A 82.418 910 129 23 855 1747 547816882 547817777 0.000000e+00 765.0
21 TraesCS1A01G067500 chr6B 82.198 910 131 22 855 1747 601867584 601868479 0.000000e+00 754.0
22 TraesCS1A01G067500 chr2D 89.423 104 7 4 2457 2559 382386049 382385949 7.460000e-26 128.0
23 TraesCS1A01G067500 chr3B 83.133 83 12 1 2355 2435 811143714 811143632 9.850000e-10 75.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1A01G067500 chr1A 49304054 49306620 2566 False 4741.000000 4741 100.000000 1 2567 1 chr1A.!!$F1 2566
1 TraesCS1A01G067500 chr1A 49356547 49357500 953 False 833.000000 833 82.541000 860 1822 1 chr1A.!!$F3 962
2 TraesCS1A01G067500 chr1A 49348500 49349470 970 False 824.000000 824 82.215000 850 1820 1 chr1A.!!$F2 970
3 TraesCS1A01G067500 chr1A 37502901 37503614 713 True 660.000000 660 83.333000 855 1568 1 chr1A.!!$R1 713
4 TraesCS1A01G067500 chr1A 49295131 49296745 1614 False 450.066667 1011 85.347333 850 2559 3 chr1A.!!$F4 1709
5 TraesCS1A01G067500 chr1D 49974971 49975938 967 False 833.000000 833 82.293000 850 1822 1 chr1D.!!$F1 972
6 TraesCS1A01G067500 chr1D 50060968 50061739 771 False 761.000000 761 84.496000 850 1621 1 chr1D.!!$F2 771
7 TraesCS1A01G067500 chr1D 49958010 49959063 1053 False 626.000000 1096 90.079000 850 1947 2 chr1D.!!$F3 1097
8 TraesCS1A01G067500 chr1D 50025511 50026455 944 False 545.500000 965 87.880000 1 855 2 chr1D.!!$F5 854
9 TraesCS1A01G067500 chr1D 50010227 50011446 1219 False 428.000000 477 88.162500 1 731 2 chr1D.!!$F4 730
10 TraesCS1A01G067500 chr1B 70695918 70696867 949 False 813.000000 813 82.231000 860 1822 1 chr1B.!!$F1 962
11 TraesCS1A01G067500 chr1B 70335526 70336697 1171 False 641.500000 1016 87.485500 850 2055 2 chr1B.!!$F3 1205
12 TraesCS1A01G067500 chr6A 547816882 547817777 895 False 765.000000 765 82.418000 855 1747 1 chr6A.!!$F1 892
13 TraesCS1A01G067500 chr6B 601867584 601868479 895 False 754.000000 754 82.198000 855 1747 1 chr6B.!!$F1 892

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
747 1349 2.165845 AGGTAACACGCACTGATCTACC 59.834 50.0 0.0 0.0 41.41 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1643 2260 0.035317 AGCTCAATCTTGGTGTGCGA 59.965 50.0 0.0 0.0 39.77 5.1 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
33 34 2.367377 CAGGATCCCCAGCCCAGA 60.367 66.667 8.55 0.00 33.88 3.86
288 378 3.810310 TTGGGTAAGCAAACCTTTGTG 57.190 42.857 7.36 0.00 40.24 3.33
363 906 7.156673 GCATCATTTAATTATGTCCATGGCTT 58.843 34.615 6.96 3.42 0.00 4.35
463 1006 7.377766 AGTAATTTGACATCGTTTGCATAGT 57.622 32.000 0.00 0.00 0.00 2.12
565 1136 8.824783 TGTTGCTAGTTATAAGGGGTTTAGTAA 58.175 33.333 0.00 0.00 0.00 2.24
600 1173 8.458573 TGTTCCTTTATGTTTATGTGAACAGT 57.541 30.769 0.00 0.00 42.28 3.55
607 1180 9.877178 TTTATGTTTATGTGAACAGTTTTTGGT 57.123 25.926 0.00 0.00 42.28 3.67
636 1209 8.179509 TCTAAGAACTTAAGCAGACAGTTACT 57.820 34.615 1.29 0.00 30.71 2.24
660 1233 8.512138 ACTTGTATGGGAAAAGAAAAGATAACG 58.488 33.333 0.00 0.00 0.00 3.18
661 1234 6.848451 TGTATGGGAAAAGAAAAGATAACGC 58.152 36.000 0.00 0.00 0.00 4.84
731 1304 4.104102 ACTGGACCATTGTGAAGAAGGTAA 59.896 41.667 0.00 0.00 31.57 2.85
747 1349 2.165845 AGGTAACACGCACTGATCTACC 59.834 50.000 0.00 0.00 41.41 3.18
748 1350 2.165845 GGTAACACGCACTGATCTACCT 59.834 50.000 0.00 0.00 0.00 3.08
785 1387 5.511373 GCTTCCTTTTTGTAAGGGAATGCTT 60.511 40.000 3.88 0.00 45.28 3.91
812 1414 2.930826 TCCTCTCCAGGACAACAAAC 57.069 50.000 0.00 0.00 44.75 2.93
815 1417 3.202151 TCCTCTCCAGGACAACAAACTTT 59.798 43.478 0.00 0.00 44.75 2.66
816 1418 3.954258 CCTCTCCAGGACAACAAACTTTT 59.046 43.478 0.00 0.00 43.65 2.27
845 1447 6.639632 AGCAACAATTACTGATCTTGTGTT 57.360 33.333 0.00 0.00 33.60 3.32
909 1514 6.778821 TGGGTTGAATCTGTTCAGAGAAATA 58.221 36.000 8.47 0.00 44.62 1.40
1015 1620 6.191442 GCAAAGAAAATGCTCCATGAGATGG 61.191 44.000 0.00 0.00 41.95 3.51
1065 1670 6.376864 TGTCCACATACAACATAATTCTTGGG 59.623 38.462 0.00 0.00 0.00 4.12
1137 1742 7.599621 CAGAAATTAGGTGCAATGAATGTGAAA 59.400 33.333 0.00 0.00 0.00 2.69
1140 1745 7.837202 ATTAGGTGCAATGAATGTGAAATTG 57.163 32.000 0.00 0.00 34.98 2.32
1168 1773 6.499234 TCACAACACTCAATACCATGATTG 57.501 37.500 0.00 0.00 38.03 2.67
1188 1793 3.407698 TGATGCAATGTACAAGGTTCGT 58.592 40.909 0.00 0.00 0.00 3.85
1195 1800 5.163982 GCAATGTACAAGGTTCGTAGAAGAC 60.164 44.000 0.00 0.00 45.90 3.01
1249 1854 2.620627 GCCAGTGGCTTGGTACCTAATT 60.621 50.000 27.48 0.00 46.69 1.40
1252 1857 4.192317 CAGTGGCTTGGTACCTAATTCTC 58.808 47.826 14.36 0.83 0.00 2.87
1265 1870 4.099113 ACCTAATTCTCCTACTTACGGCAC 59.901 45.833 0.00 0.00 0.00 5.01
1277 1882 5.545658 ACTTACGGCACAATGATACAAAG 57.454 39.130 0.00 0.00 0.00 2.77
1281 1886 4.827692 ACGGCACAATGATACAAAGTCTA 58.172 39.130 0.00 0.00 0.00 2.59
1317 1922 8.510505 GGATTAATGGAAGAAGCTGACAATATC 58.489 37.037 0.00 0.00 0.00 1.63
1346 1951 1.356124 ATGGAGAAGAGTGGCTGTGT 58.644 50.000 0.00 0.00 0.00 3.72
1350 1955 2.411904 GAGAAGAGTGGCTGTGTTCTG 58.588 52.381 4.25 0.00 0.00 3.02
1405 2010 4.586306 TTACTGGAAAAGGGGGAGATTC 57.414 45.455 0.00 0.00 0.00 2.52
1407 2012 3.815507 ACTGGAAAAGGGGGAGATTCTA 58.184 45.455 0.00 0.00 0.00 2.10
1432 2037 8.528044 AAAGGCCGGAAATTATATGTCTAAAA 57.472 30.769 5.05 0.00 0.00 1.52
1447 2052 6.494893 TGTCTAAAATTGATGGGAAGAACG 57.505 37.500 0.00 0.00 0.00 3.95
1448 2053 5.106317 TGTCTAAAATTGATGGGAAGAACGC 60.106 40.000 0.00 0.00 0.00 4.84
1450 2055 1.474330 AATTGATGGGAAGAACGCCC 58.526 50.000 0.00 0.00 46.22 6.13
1524 2129 6.062095 AGGGAAATATCGGGAACAAATACAG 58.938 40.000 0.00 0.00 0.00 2.74
1556 2161 6.417191 TGTAAAGTACCAATTCTTCGATGC 57.583 37.500 0.00 0.00 0.00 3.91
1569 2174 5.072040 TCTTCGATGCAGTTAGTTGATGA 57.928 39.130 0.00 0.00 0.00 2.92
1571 2176 5.578336 TCTTCGATGCAGTTAGTTGATGAAG 59.422 40.000 0.00 0.00 0.00 3.02
1587 2192 3.876274 TGAAGTGGACTCAGCAGATAC 57.124 47.619 0.00 0.00 0.00 2.24
1596 2209 2.167281 ACTCAGCAGATACATGTTCGCT 59.833 45.455 2.30 11.37 0.00 4.93
1624 2240 2.172293 GGAGCTCCCTCTCAATGATGTT 59.828 50.000 23.19 0.00 38.21 2.71
1626 2242 1.674962 GCTCCCTCTCAATGATGTTGC 59.325 52.381 0.00 0.00 0.00 4.17
1634 2251 4.401022 TCTCAATGATGTTGCCAAGTCTT 58.599 39.130 0.00 0.00 0.00 3.01
1637 2254 4.583907 TCAATGATGTTGCCAAGTCTTTCA 59.416 37.500 0.00 0.00 0.00 2.69
1641 2258 1.879380 TGTTGCCAAGTCTTTCATCCG 59.121 47.619 0.00 0.00 0.00 4.18
1642 2259 0.881118 TTGCCAAGTCTTTCATCCGC 59.119 50.000 0.00 0.00 0.00 5.54
1643 2260 0.036732 TGCCAAGTCTTTCATCCGCT 59.963 50.000 0.00 0.00 0.00 5.52
1647 2264 0.037326 AAGTCTTTCATCCGCTCGCA 60.037 50.000 0.00 0.00 0.00 5.10
1750 2389 0.315568 GACATCGCTCCTAATCCGCT 59.684 55.000 0.00 0.00 0.00 5.52
1751 2390 0.753262 ACATCGCTCCTAATCCGCTT 59.247 50.000 0.00 0.00 0.00 4.68
1752 2391 1.139058 ACATCGCTCCTAATCCGCTTT 59.861 47.619 0.00 0.00 0.00 3.51
1804 2445 3.976169 TGTGTTTGCTAATGGTGAAAGC 58.024 40.909 0.00 0.00 36.77 3.51
1822 2464 6.424207 GTGAAAGCTTACTAATATTCGGGAGG 59.576 42.308 0.00 0.00 0.00 4.30
1823 2465 6.325545 TGAAAGCTTACTAATATTCGGGAGGA 59.674 38.462 0.00 0.00 0.00 3.71
1824 2466 6.936968 AAGCTTACTAATATTCGGGAGGAT 57.063 37.500 0.00 0.00 0.00 3.24
1825 2467 6.287589 AGCTTACTAATATTCGGGAGGATG 57.712 41.667 0.00 0.00 0.00 3.51
1826 2468 5.780793 AGCTTACTAATATTCGGGAGGATGT 59.219 40.000 0.00 0.00 0.00 3.06
1827 2469 6.270231 AGCTTACTAATATTCGGGAGGATGTT 59.730 38.462 0.00 0.00 33.42 2.71
1828 2470 7.453752 AGCTTACTAATATTCGGGAGGATGTTA 59.546 37.037 0.00 0.00 31.15 2.41
1829 2471 8.258708 GCTTACTAATATTCGGGAGGATGTTAT 58.741 37.037 0.00 0.00 32.01 1.89
1830 2472 9.804758 CTTACTAATATTCGGGAGGATGTTATC 57.195 37.037 0.00 0.00 32.01 1.75
1869 2511 5.337975 GCTATTTGGAGTTCTCTGAACCTCT 60.338 44.000 6.80 0.00 0.00 3.69
1882 2524 3.273434 TGAACCTCTGCATATCAAGTGC 58.727 45.455 0.00 0.00 42.81 4.40
1890 2532 2.159212 TGCATATCAAGTGCATGTTGGC 60.159 45.455 10.83 7.51 46.76 4.52
1895 2537 1.530419 AAGTGCATGTTGGCCCGAA 60.530 52.632 0.00 0.00 0.00 4.30
1916 2558 6.355638 CGAAGGCAATTATAGTGAAATCGAC 58.644 40.000 0.00 0.00 0.00 4.20
1950 2592 4.457603 ACATTATCAAGCTGTTTGGCGTTA 59.542 37.500 4.39 0.00 37.39 3.18
1951 2593 5.048364 ACATTATCAAGCTGTTTGGCGTTAA 60.048 36.000 4.39 0.06 37.39 2.01
1996 2638 9.442047 AGAGTTTGATGATTTTACTACCTGAAG 57.558 33.333 0.00 0.00 0.00 3.02
1997 2639 9.436957 GAGTTTGATGATTTTACTACCTGAAGA 57.563 33.333 0.00 0.00 0.00 2.87
2007 2649 4.479786 ACTACCTGAAGAATCTTGAGGC 57.520 45.455 25.01 0.66 0.00 4.70
2008 2650 4.100373 ACTACCTGAAGAATCTTGAGGCT 58.900 43.478 25.01 15.71 0.00 4.58
2026 2668 3.569701 AGGCTTTGAAACCTGTGTACATG 59.430 43.478 0.00 0.00 34.07 3.21
2029 2671 5.451242 GGCTTTGAAACCTGTGTACATGAAA 60.451 40.000 0.00 0.00 0.00 2.69
2039 2681 7.425606 ACCTGTGTACATGAAATTTGAACTTC 58.574 34.615 0.00 0.00 0.00 3.01
2058 2760 4.593206 ACTTCCATTCAGTCTCCTGTGTAA 59.407 41.667 0.00 0.00 39.82 2.41
2061 2763 4.080919 TCCATTCAGTCTCCTGTGTAATGG 60.081 45.833 12.18 12.18 44.39 3.16
2063 2765 3.961480 TCAGTCTCCTGTGTAATGGTG 57.039 47.619 0.00 0.00 39.82 4.17
2072 2774 6.657541 TCTCCTGTGTAATGGTGTAATTTTCC 59.342 38.462 0.00 0.00 0.00 3.13
2081 2783 9.581099 GTAATGGTGTAATTTTCCTATGGTTTG 57.419 33.333 0.00 0.00 0.00 2.93
2085 2789 8.962679 TGGTGTAATTTTCCTATGGTTTGATAC 58.037 33.333 0.00 0.00 0.00 2.24
2092 2796 8.450578 TTTTCCTATGGTTTGATACATAGCTG 57.549 34.615 0.00 0.00 43.18 4.24
2107 2811 5.892568 ACATAGCTGTAGTTGTAGCACTAC 58.107 41.667 0.00 5.37 46.54 2.73
2187 2933 5.710513 TGAAGTTGCAGAAACATTATGCT 57.289 34.783 10.57 0.00 41.61 3.79
2197 2943 7.116662 TGCAGAAACATTATGCTTTGACATTTC 59.883 33.333 10.57 0.00 40.62 2.17
2199 2945 8.430063 CAGAAACATTATGCTTTGACATTTCAC 58.570 33.333 0.00 0.00 0.00 3.18
2200 2946 8.143193 AGAAACATTATGCTTTGACATTTCACA 58.857 29.630 0.00 0.00 0.00 3.58
2210 2956 9.545105 TGCTTTGACATTTCACAAGATAAAAAT 57.455 25.926 7.53 0.00 0.00 1.82
2244 2990 1.134098 ACCAGCTCCAATTATCCGGTG 60.134 52.381 0.00 0.00 0.00 4.94
2247 2993 3.278574 CAGCTCCAATTATCCGGTGAAA 58.721 45.455 0.00 0.00 0.00 2.69
2265 3011 3.582647 TGAAACTGGATGGACAGCTTCTA 59.417 43.478 9.77 0.00 41.68 2.10
2289 3035 9.658799 CTAAGAAAGACCATCATCTTTTGTAGA 57.341 33.333 2.51 0.00 46.57 2.59
2292 3038 5.104259 AGACCATCATCTTTTGTAGACCC 57.896 43.478 0.00 0.00 35.19 4.46
2299 3045 6.928348 TCATCTTTTGTAGACCCTCTAACA 57.072 37.500 0.00 0.00 35.19 2.41
2300 3046 7.311092 TCATCTTTTGTAGACCCTCTAACAA 57.689 36.000 0.00 0.00 35.19 2.83
2301 3047 7.741785 TCATCTTTTGTAGACCCTCTAACAAA 58.258 34.615 0.00 0.00 35.19 2.83
2302 3048 8.215050 TCATCTTTTGTAGACCCTCTAACAAAA 58.785 33.333 10.66 10.66 37.47 2.44
2303 3049 7.797038 TCTTTTGTAGACCCTCTAACAAAAC 57.203 36.000 7.84 0.00 36.39 2.43
2304 3050 7.571025 TCTTTTGTAGACCCTCTAACAAAACT 58.429 34.615 7.84 0.00 36.39 2.66
2305 3051 8.050930 TCTTTTGTAGACCCTCTAACAAAACTT 58.949 33.333 7.84 0.00 36.39 2.66
2306 3052 7.562454 TTTGTAGACCCTCTAACAAAACTTG 57.438 36.000 0.00 0.00 32.50 3.16
2307 3053 5.617252 TGTAGACCCTCTAACAAAACTTGG 58.383 41.667 0.00 0.00 29.58 3.61
2308 3054 4.790718 AGACCCTCTAACAAAACTTGGT 57.209 40.909 0.00 0.00 34.12 3.67
2309 3055 5.899631 AGACCCTCTAACAAAACTTGGTA 57.100 39.130 0.00 0.00 34.12 3.25
2310 3056 5.618236 AGACCCTCTAACAAAACTTGGTAC 58.382 41.667 0.00 0.00 34.12 3.34
2311 3057 4.722220 ACCCTCTAACAAAACTTGGTACC 58.278 43.478 4.43 4.43 34.12 3.34
2312 3058 4.414514 ACCCTCTAACAAAACTTGGTACCT 59.585 41.667 14.36 0.00 34.12 3.08
2313 3059 4.760204 CCCTCTAACAAAACTTGGTACCTG 59.240 45.833 14.36 8.64 34.12 4.00
2314 3060 5.455612 CCCTCTAACAAAACTTGGTACCTGA 60.456 44.000 14.36 0.63 34.12 3.86
2315 3061 6.238648 CCTCTAACAAAACTTGGTACCTGAT 58.761 40.000 14.36 0.00 34.12 2.90
2316 3062 6.715264 CCTCTAACAAAACTTGGTACCTGATT 59.285 38.462 14.36 4.45 34.12 2.57
2317 3063 7.308589 CCTCTAACAAAACTTGGTACCTGATTG 60.309 40.741 14.36 16.40 34.12 2.67
2318 3064 4.584327 ACAAAACTTGGTACCTGATTGC 57.416 40.909 14.36 0.00 34.12 3.56
2319 3065 4.215109 ACAAAACTTGGTACCTGATTGCT 58.785 39.130 14.36 6.02 34.12 3.91
2320 3066 4.649218 ACAAAACTTGGTACCTGATTGCTT 59.351 37.500 14.36 0.00 34.12 3.91
2321 3067 5.830991 ACAAAACTTGGTACCTGATTGCTTA 59.169 36.000 14.36 0.00 34.12 3.09
2322 3068 6.016276 ACAAAACTTGGTACCTGATTGCTTAG 60.016 38.462 14.36 0.00 34.12 2.18
2323 3069 3.610911 ACTTGGTACCTGATTGCTTAGC 58.389 45.455 14.36 0.00 0.00 3.09
2324 3070 3.264450 ACTTGGTACCTGATTGCTTAGCT 59.736 43.478 14.36 0.00 0.00 3.32
2325 3071 4.469945 ACTTGGTACCTGATTGCTTAGCTA 59.530 41.667 14.36 0.00 0.00 3.32
2326 3072 4.672587 TGGTACCTGATTGCTTAGCTAG 57.327 45.455 14.36 0.00 0.00 3.42
2339 3085 5.715434 GCTTAGCTAGCCACTCTTATAGT 57.285 43.478 12.13 0.00 44.48 2.12
2340 3086 6.821031 GCTTAGCTAGCCACTCTTATAGTA 57.179 41.667 12.13 0.00 44.48 1.82
2341 3087 6.614160 GCTTAGCTAGCCACTCTTATAGTAC 58.386 44.000 12.13 0.00 44.48 2.73
2342 3088 6.431852 GCTTAGCTAGCCACTCTTATAGTACT 59.568 42.308 12.13 0.00 44.48 2.73
2343 3089 7.607223 GCTTAGCTAGCCACTCTTATAGTACTA 59.393 40.741 12.13 4.77 44.48 1.82
2344 3090 9.158233 CTTAGCTAGCCACTCTTATAGTACTAG 57.842 40.741 12.13 0.00 42.14 2.57
2345 3091 7.319052 AGCTAGCCACTCTTATAGTACTAGA 57.681 40.000 12.13 0.12 41.97 2.43
2346 3092 7.924541 AGCTAGCCACTCTTATAGTACTAGAT 58.075 38.462 12.13 8.17 41.97 1.98
2347 3093 8.387813 AGCTAGCCACTCTTATAGTACTAGATT 58.612 37.037 12.13 0.00 41.97 2.40
2348 3094 9.669887 GCTAGCCACTCTTATAGTACTAGATTA 57.330 37.037 8.85 0.00 41.97 1.75
2361 3107 7.989947 AGTACTAGATTATCTGGTTTTGGGA 57.010 36.000 16.02 0.00 39.08 4.37
2362 3108 8.388656 AGTACTAGATTATCTGGTTTTGGGAA 57.611 34.615 16.02 0.00 39.08 3.97
2363 3109 8.832735 AGTACTAGATTATCTGGTTTTGGGAAA 58.167 33.333 16.02 0.00 39.08 3.13
2364 3110 9.110502 GTACTAGATTATCTGGTTTTGGGAAAG 57.889 37.037 16.02 0.00 39.08 2.62
2365 3111 7.699878 ACTAGATTATCTGGTTTTGGGAAAGT 58.300 34.615 5.37 0.00 34.34 2.66
2366 3112 8.170730 ACTAGATTATCTGGTTTTGGGAAAGTT 58.829 33.333 5.37 0.00 34.34 2.66
2367 3113 7.468141 AGATTATCTGGTTTTGGGAAAGTTC 57.532 36.000 0.00 0.00 0.00 3.01
2368 3114 7.241628 AGATTATCTGGTTTTGGGAAAGTTCT 58.758 34.615 0.00 0.00 0.00 3.01
2369 3115 7.730332 AGATTATCTGGTTTTGGGAAAGTTCTT 59.270 33.333 0.00 0.00 0.00 2.52
2370 3116 7.669089 TTATCTGGTTTTGGGAAAGTTCTTT 57.331 32.000 0.00 0.00 0.00 2.52
2371 3117 5.592104 TCTGGTTTTGGGAAAGTTCTTTC 57.408 39.130 14.62 14.62 0.00 2.62
2382 3128 6.056090 GGAAAGTTCTTTCCCTGACTATCT 57.944 41.667 25.36 0.00 43.57 1.98
2383 3129 6.110033 GGAAAGTTCTTTCCCTGACTATCTC 58.890 44.000 25.36 4.35 43.57 2.75
2384 3130 6.070481 GGAAAGTTCTTTCCCTGACTATCTCT 60.070 42.308 25.36 0.00 43.57 3.10
2385 3131 6.538945 AAGTTCTTTCCCTGACTATCTCTC 57.461 41.667 0.00 0.00 0.00 3.20
2386 3132 5.584913 AGTTCTTTCCCTGACTATCTCTCA 58.415 41.667 0.00 0.00 0.00 3.27
2387 3133 5.656416 AGTTCTTTCCCTGACTATCTCTCAG 59.344 44.000 0.00 0.00 35.78 3.35
2388 3134 5.199982 TCTTTCCCTGACTATCTCTCAGT 57.800 43.478 0.00 0.00 34.42 3.41
2389 3135 5.584913 TCTTTCCCTGACTATCTCTCAGTT 58.415 41.667 0.00 0.00 34.42 3.16
2390 3136 6.732487 TCTTTCCCTGACTATCTCTCAGTTA 58.268 40.000 0.00 0.00 34.42 2.24
2391 3137 6.603997 TCTTTCCCTGACTATCTCTCAGTTAC 59.396 42.308 0.00 0.00 34.42 2.50
2392 3138 5.718801 TCCCTGACTATCTCTCAGTTACT 57.281 43.478 0.00 0.00 34.42 2.24
2393 3139 6.080969 TCCCTGACTATCTCTCAGTTACTT 57.919 41.667 0.00 0.00 34.42 2.24
2394 3140 5.888724 TCCCTGACTATCTCTCAGTTACTTG 59.111 44.000 0.00 0.00 34.42 3.16
2395 3141 5.451242 CCCTGACTATCTCTCAGTTACTTGC 60.451 48.000 0.00 0.00 34.42 4.01
2396 3142 5.126222 CCTGACTATCTCTCAGTTACTTGCA 59.874 44.000 0.00 0.00 34.42 4.08
2397 3143 6.350528 CCTGACTATCTCTCAGTTACTTGCAA 60.351 42.308 0.00 0.00 34.42 4.08
2398 3144 6.993079 TGACTATCTCTCAGTTACTTGCAAA 58.007 36.000 0.00 0.00 0.00 3.68
2399 3145 7.615403 TGACTATCTCTCAGTTACTTGCAAAT 58.385 34.615 0.00 0.00 0.00 2.32
2400 3146 7.547019 TGACTATCTCTCAGTTACTTGCAAATG 59.453 37.037 0.00 0.00 0.00 2.32
2401 3147 7.615403 ACTATCTCTCAGTTACTTGCAAATGA 58.385 34.615 0.00 0.00 32.16 2.57
2402 3148 6.734104 ATCTCTCAGTTACTTGCAAATGAC 57.266 37.500 0.00 0.00 30.12 3.06
2403 3149 5.610398 TCTCTCAGTTACTTGCAAATGACA 58.390 37.500 5.58 0.00 30.12 3.58
2404 3150 6.233434 TCTCTCAGTTACTTGCAAATGACAT 58.767 36.000 5.58 0.00 30.12 3.06
2405 3151 6.148315 TCTCTCAGTTACTTGCAAATGACATG 59.852 38.462 5.58 1.66 30.12 3.21
2406 3152 5.181811 TCTCAGTTACTTGCAAATGACATGG 59.818 40.000 5.58 0.00 30.12 3.66
2407 3153 4.826733 TCAGTTACTTGCAAATGACATGGT 59.173 37.500 5.58 0.00 28.29 3.55
2408 3154 5.301551 TCAGTTACTTGCAAATGACATGGTT 59.698 36.000 5.58 0.00 28.29 3.67
2409 3155 6.488344 TCAGTTACTTGCAAATGACATGGTTA 59.512 34.615 5.58 0.00 28.29 2.85
2410 3156 7.176515 TCAGTTACTTGCAAATGACATGGTTAT 59.823 33.333 5.58 0.00 28.29 1.89
2411 3157 7.485913 CAGTTACTTGCAAATGACATGGTTATC 59.514 37.037 5.58 0.00 0.00 1.75
2412 3158 5.981088 ACTTGCAAATGACATGGTTATCA 57.019 34.783 0.00 0.00 0.00 2.15
2413 3159 6.534475 ACTTGCAAATGACATGGTTATCAT 57.466 33.333 0.00 0.00 37.14 2.45
2414 3160 6.938507 ACTTGCAAATGACATGGTTATCATT 58.061 32.000 0.00 0.27 45.36 2.57
2438 3184 8.970691 TTTGAGAAATAAAGTCTTATTGCTGC 57.029 30.769 3.34 0.00 41.66 5.25
2439 3185 7.686438 TGAGAAATAAAGTCTTATTGCTGCA 57.314 32.000 0.00 0.00 41.66 4.41
2440 3186 8.109705 TGAGAAATAAAGTCTTATTGCTGCAA 57.890 30.769 18.43 18.43 41.66 4.08
2441 3187 8.575589 TGAGAAATAAAGTCTTATTGCTGCAAA 58.424 29.630 20.06 2.62 41.66 3.68
2442 3188 9.410556 GAGAAATAAAGTCTTATTGCTGCAAAA 57.589 29.630 20.06 13.18 41.66 2.44
2443 3189 9.415544 AGAAATAAAGTCTTATTGCTGCAAAAG 57.584 29.630 20.06 20.67 40.54 2.27
2444 3190 8.538409 AAATAAAGTCTTATTGCTGCAAAAGG 57.462 30.769 20.06 11.60 37.70 3.11
2445 3191 5.789643 AAAGTCTTATTGCTGCAAAAGGA 57.210 34.783 20.06 13.62 0.00 3.36
2446 3192 5.789643 AAGTCTTATTGCTGCAAAAGGAA 57.210 34.783 20.06 10.09 40.91 3.36
2484 3230 7.716799 ATTTACATGTCATCCCTGCTAAAAA 57.283 32.000 0.00 0.00 0.00 1.94
2485 3231 6.509418 TTACATGTCATCCCTGCTAAAAAC 57.491 37.500 0.00 0.00 0.00 2.43
2486 3232 4.406456 ACATGTCATCCCTGCTAAAAACA 58.594 39.130 0.00 0.00 0.00 2.83
2498 3244 6.128472 CCCTGCTAAAAACAAAATCATTCTGC 60.128 38.462 0.00 0.00 0.00 4.26
2499 3245 6.424509 CCTGCTAAAAACAAAATCATTCTGCA 59.575 34.615 0.00 0.00 0.00 4.41
2500 3246 7.359765 CCTGCTAAAAACAAAATCATTCTGCAG 60.360 37.037 7.63 7.63 40.58 4.41
2501 3247 6.985645 TGCTAAAAACAAAATCATTCTGCAGT 59.014 30.769 14.67 0.00 0.00 4.40
2502 3248 7.042590 TGCTAAAAACAAAATCATTCTGCAGTG 60.043 33.333 14.67 5.73 0.00 3.66
2503 3249 6.607735 AAAAACAAAATCATTCTGCAGTGG 57.392 33.333 14.67 4.66 0.00 4.00
2504 3250 3.947910 ACAAAATCATTCTGCAGTGGG 57.052 42.857 14.67 4.28 0.00 4.61
2505 3251 2.028748 ACAAAATCATTCTGCAGTGGGC 60.029 45.455 14.67 0.00 45.13 5.36
2506 3252 2.226962 AAATCATTCTGCAGTGGGCT 57.773 45.000 14.67 0.00 45.15 5.19
2507 3253 1.471119 AATCATTCTGCAGTGGGCTG 58.529 50.000 14.67 5.61 45.15 4.85
2546 3292 2.158928 AGGCAGATCACATCTCTGAAGC 60.159 50.000 4.57 0.00 42.22 3.86
2547 3293 1.859703 GCAGATCACATCTCTGAAGCG 59.140 52.381 4.57 0.00 42.22 4.68
2559 3305 0.647410 CTGAAGCGTCTTGGCATACG 59.353 55.000 15.98 15.98 41.92 3.06
2563 3309 3.706140 CGTCTTGGCATACGCTCC 58.294 61.111 9.51 0.00 38.60 4.70
2564 3310 1.153647 CGTCTTGGCATACGCTCCA 60.154 57.895 9.51 0.00 38.60 3.86
2565 3311 0.530650 CGTCTTGGCATACGCTCCAT 60.531 55.000 9.51 0.00 38.60 3.41
2566 3312 1.269569 CGTCTTGGCATACGCTCCATA 60.270 52.381 9.51 0.00 38.60 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 1.063654 TCGTTTGGAGGGGAGGGTTT 61.064 55.000 0.00 0.00 0.00 3.27
463 1006 6.839124 ATCATGTTTCTTCTGCAACCATTA 57.161 33.333 0.00 0.00 0.00 1.90
588 1161 7.607250 AGAAACACCAAAAACTGTTCACATAA 58.393 30.769 0.00 0.00 30.11 1.90
592 1165 7.309920 TCTTAGAAACACCAAAAACTGTTCAC 58.690 34.615 0.00 0.00 30.11 3.18
600 1173 8.524487 TGCTTAAGTTCTTAGAAACACCAAAAA 58.476 29.630 4.02 0.00 0.00 1.94
605 1178 6.482308 TGTCTGCTTAAGTTCTTAGAAACACC 59.518 38.462 4.02 0.00 0.00 4.16
606 1179 7.224949 ACTGTCTGCTTAAGTTCTTAGAAACAC 59.775 37.037 4.02 0.00 0.00 3.32
607 1180 7.272978 ACTGTCTGCTTAAGTTCTTAGAAACA 58.727 34.615 4.02 0.00 0.00 2.83
636 1209 7.309920 GCGTTATCTTTTCTTTTCCCATACAA 58.690 34.615 0.00 0.00 0.00 2.41
660 1233 1.305930 GGAACAGAACATGGGTCGGC 61.306 60.000 0.00 0.00 0.00 5.54
661 1234 0.324943 AGGAACAGAACATGGGTCGG 59.675 55.000 0.00 0.00 0.00 4.79
712 1285 4.084013 CGTGTTACCTTCTTCACAATGGTC 60.084 45.833 0.00 0.00 32.74 4.02
731 1304 2.159226 GCTAAGGTAGATCAGTGCGTGT 60.159 50.000 0.00 0.00 0.00 4.49
747 1349 2.460669 AGGAAGCAATTTGGGGCTAAG 58.539 47.619 0.00 0.00 40.01 2.18
748 1350 2.621556 AGGAAGCAATTTGGGGCTAA 57.378 45.000 0.00 0.00 40.01 3.09
815 1417 9.844790 CAAGATCAGTAATTGTTGCTTCAATAA 57.155 29.630 0.00 0.00 37.09 1.40
816 1418 9.013229 ACAAGATCAGTAATTGTTGCTTCAATA 57.987 29.630 0.00 0.00 37.09 1.90
833 1435 4.572985 TTGGCAGAAAACACAAGATCAG 57.427 40.909 0.00 0.00 0.00 2.90
869 1471 0.546122 CCCATCATCGGTCCTTCCAA 59.454 55.000 0.00 0.00 35.57 3.53
909 1514 9.908152 GTTGTAGGTTTAACTTTCTTATGCAAT 57.092 29.630 0.00 0.00 0.00 3.56
964 1569 0.868406 GTTCTCCCAGCACGAAACAG 59.132 55.000 0.00 0.00 0.00 3.16
1015 1620 0.865769 ACTGTTGTTCCGCATTCGAC 59.134 50.000 0.00 0.00 38.10 4.20
1023 1628 1.261619 GACAAGCTCACTGTTGTTCCG 59.738 52.381 0.00 0.00 37.02 4.30
1065 1670 5.402398 GTGCAATCATTTCTACAAAGTCCC 58.598 41.667 0.00 0.00 0.00 4.46
1137 1742 7.345691 TGGTATTGAGTGTTGTGATATCCAAT 58.654 34.615 0.00 3.00 0.00 3.16
1140 1745 6.992123 TCATGGTATTGAGTGTTGTGATATCC 59.008 38.462 0.00 0.00 0.00 2.59
1168 1773 4.868171 TCTACGAACCTTGTACATTGCATC 59.132 41.667 0.00 0.00 0.00 3.91
1188 1793 9.561069 AACAAATCTTTAGCTTCTTGTCTTCTA 57.439 29.630 0.00 0.00 0.00 2.10
1195 1800 6.346359 GCAGCAAACAAATCTTTAGCTTCTTG 60.346 38.462 0.00 0.00 0.00 3.02
1236 1841 7.424001 CGTAAGTAGGAGAATTAGGTACCAAG 58.576 42.308 15.94 0.00 0.00 3.61
1249 1854 3.093814 TCATTGTGCCGTAAGTAGGAGA 58.906 45.455 0.00 0.00 0.00 3.71
1252 1857 4.689071 TGTATCATTGTGCCGTAAGTAGG 58.311 43.478 0.00 0.00 0.00 3.18
1281 1886 8.961634 GCTTCTTCCATTAATCCTTCTTTTAGT 58.038 33.333 0.00 0.00 0.00 2.24
1295 1900 8.489489 AGAAGATATTGTCAGCTTCTTCCATTA 58.511 33.333 15.26 0.00 43.15 1.90
1297 1902 6.897986 AGAAGATATTGTCAGCTTCTTCCAT 58.102 36.000 15.26 0.05 43.15 3.41
1346 1951 6.455647 TCATTTAAAAGACGAGAGCTCAGAA 58.544 36.000 17.77 0.00 0.00 3.02
1350 1955 8.581057 TGATATCATTTAAAAGACGAGAGCTC 57.419 34.615 5.27 5.27 0.00 4.09
1387 1992 4.862641 TTAGAATCTCCCCCTTTTCCAG 57.137 45.455 0.00 0.00 0.00 3.86
1405 2010 8.842358 TTAGACATATAATTTCCGGCCTTTAG 57.158 34.615 0.00 0.00 0.00 1.85
1407 2012 8.528044 TTTTAGACATATAATTTCCGGCCTTT 57.472 30.769 0.00 0.00 0.00 3.11
1432 2037 3.191182 GGGCGTTCTTCCCATCAAT 57.809 52.632 0.00 0.00 43.37 2.57
1445 2050 0.465460 TGAAGCTTCAAGTTGGGCGT 60.465 50.000 26.61 6.47 33.55 5.68
1447 2052 1.683385 AGTTGAAGCTTCAAGTTGGGC 59.317 47.619 36.07 24.46 45.84 5.36
1448 2053 4.137543 ACTAGTTGAAGCTTCAAGTTGGG 58.862 43.478 40.20 31.82 45.84 4.12
1450 2055 5.006746 ACGAACTAGTTGAAGCTTCAAGTTG 59.993 40.000 40.20 37.93 45.84 3.16
1451 2056 5.116882 ACGAACTAGTTGAAGCTTCAAGTT 58.883 37.500 40.20 35.49 45.84 2.66
1524 2129 3.412237 TGGTACTTTACAGGGAGCAAC 57.588 47.619 0.00 0.00 0.00 4.17
1556 2161 5.541845 TGAGTCCACTTCATCAACTAACTG 58.458 41.667 0.00 0.00 0.00 3.16
1569 2174 3.517100 ACATGTATCTGCTGAGTCCACTT 59.483 43.478 0.00 0.00 0.00 3.16
1571 2176 3.533606 ACATGTATCTGCTGAGTCCAC 57.466 47.619 0.00 0.00 0.00 4.02
1587 2192 1.666888 GCTCCAAACCAAGCGAACATG 60.667 52.381 0.00 0.00 0.00 3.21
1596 2209 0.693049 GAGAGGGAGCTCCAAACCAA 59.307 55.000 33.29 0.00 38.24 3.67
1624 2240 0.036732 AGCGGATGAAAGACTTGGCA 59.963 50.000 0.00 0.00 0.00 4.92
1626 2242 1.002366 CGAGCGGATGAAAGACTTGG 58.998 55.000 0.00 0.00 0.00 3.61
1634 2251 2.434185 GGTGTGCGAGCGGATGAA 60.434 61.111 0.00 0.00 0.00 2.57
1637 2254 2.244117 ATCTTGGTGTGCGAGCGGAT 62.244 55.000 0.00 0.00 0.00 4.18
1641 2258 0.445436 CTCAATCTTGGTGTGCGAGC 59.555 55.000 0.00 0.00 0.00 5.03
1642 2259 0.445436 GCTCAATCTTGGTGTGCGAG 59.555 55.000 0.00 0.00 0.00 5.03
1643 2260 0.035317 AGCTCAATCTTGGTGTGCGA 59.965 50.000 0.00 0.00 39.77 5.10
1647 2264 0.773644 ACCCAGCTCAATCTTGGTGT 59.226 50.000 0.00 0.00 31.63 4.16
1750 2389 4.395519 CATGCGTGGAGGTGGAAA 57.604 55.556 0.00 0.00 0.00 3.13
1774 2413 4.261952 CCATTAGCAAACACATCACACCAA 60.262 41.667 0.00 0.00 0.00 3.67
1804 2445 9.804758 GATAACATCCTCCCGAATATTAGTAAG 57.195 37.037 0.00 0.00 0.00 2.34
1822 2464 6.995091 AGCTTGATAAACTCAGGGATAACATC 59.005 38.462 0.00 0.00 34.68 3.06
1823 2465 6.904626 AGCTTGATAAACTCAGGGATAACAT 58.095 36.000 0.00 0.00 34.68 2.71
1824 2466 6.313519 AGCTTGATAAACTCAGGGATAACA 57.686 37.500 0.00 0.00 34.68 2.41
1825 2467 8.910351 AATAGCTTGATAAACTCAGGGATAAC 57.090 34.615 0.00 0.00 34.68 1.89
1826 2468 9.342308 CAAATAGCTTGATAAACTCAGGGATAA 57.658 33.333 0.00 0.00 37.17 1.75
1827 2469 7.939039 CCAAATAGCTTGATAAACTCAGGGATA 59.061 37.037 0.00 0.00 37.17 2.59
1828 2470 6.774656 CCAAATAGCTTGATAAACTCAGGGAT 59.225 38.462 0.00 0.00 37.17 3.85
1829 2471 6.069673 TCCAAATAGCTTGATAAACTCAGGGA 60.070 38.462 0.00 0.00 37.17 4.20
1830 2472 6.122277 TCCAAATAGCTTGATAAACTCAGGG 58.878 40.000 0.00 0.00 37.17 4.45
1831 2473 6.825721 ACTCCAAATAGCTTGATAAACTCAGG 59.174 38.462 0.00 0.00 37.17 3.86
1832 2474 7.856145 ACTCCAAATAGCTTGATAAACTCAG 57.144 36.000 0.00 0.00 37.17 3.35
1833 2475 8.103305 AGAACTCCAAATAGCTTGATAAACTCA 58.897 33.333 0.00 0.00 37.17 3.41
1834 2476 8.499403 AGAACTCCAAATAGCTTGATAAACTC 57.501 34.615 0.00 0.00 37.17 3.01
1835 2477 8.325046 AGAGAACTCCAAATAGCTTGATAAACT 58.675 33.333 0.00 0.00 37.17 2.66
1836 2478 8.394121 CAGAGAACTCCAAATAGCTTGATAAAC 58.606 37.037 0.00 0.00 37.17 2.01
1837 2479 8.321353 TCAGAGAACTCCAAATAGCTTGATAAA 58.679 33.333 0.00 0.00 37.17 1.40
1838 2480 7.851228 TCAGAGAACTCCAAATAGCTTGATAA 58.149 34.615 0.00 0.00 37.17 1.75
1890 2532 5.334105 CGATTTCACTATAATTGCCTTCGGG 60.334 44.000 0.00 0.00 38.37 5.14
1895 2537 4.750098 CCGTCGATTTCACTATAATTGCCT 59.250 41.667 0.00 0.00 0.00 4.75
1916 2558 7.148641 ACAGCTTGATAATGTAGAATAGTCCG 58.851 38.462 0.00 0.00 0.00 4.79
1967 2609 9.219603 CAGGTAGTAAAATCATCAAACTCTTGA 57.780 33.333 0.00 0.00 45.53 3.02
1970 2612 9.442047 CTTCAGGTAGTAAAATCATCAAACTCT 57.558 33.333 0.00 0.00 0.00 3.24
1996 2638 4.279420 ACAGGTTTCAAAGCCTCAAGATTC 59.721 41.667 0.00 0.00 37.55 2.52
1997 2639 4.038402 CACAGGTTTCAAAGCCTCAAGATT 59.962 41.667 0.00 0.00 37.55 2.40
2002 2644 2.435372 ACACAGGTTTCAAAGCCTCA 57.565 45.000 0.00 0.00 37.55 3.86
2007 2649 8.542132 CAAATTTCATGTACACAGGTTTCAAAG 58.458 33.333 0.00 0.00 0.00 2.77
2008 2650 8.253810 TCAAATTTCATGTACACAGGTTTCAAA 58.746 29.630 0.00 0.00 0.00 2.69
2026 2668 7.040132 AGGAGACTGAATGGAAGTTCAAATTTC 60.040 37.037 5.01 2.87 41.13 2.17
2029 2671 5.885465 AGGAGACTGAATGGAAGTTCAAAT 58.115 37.500 5.01 0.00 41.13 2.32
2058 2760 8.608185 ATCAAACCATAGGAAAATTACACCAT 57.392 30.769 0.00 0.00 0.00 3.55
2072 2774 8.982685 CAACTACAGCTATGTATCAAACCATAG 58.017 37.037 0.00 0.00 41.05 2.23
2081 2783 6.740110 AGTGCTACAACTACAGCTATGTATC 58.260 40.000 0.00 0.00 41.05 2.24
2161 2865 8.472413 AGCATAATGTTTCTGCAACTTCATTAT 58.528 29.630 15.05 15.05 38.29 1.28
2163 2867 6.694447 AGCATAATGTTTCTGCAACTTCATT 58.306 32.000 10.22 10.22 38.37 2.57
2164 2868 6.276832 AGCATAATGTTTCTGCAACTTCAT 57.723 33.333 0.00 0.00 38.37 2.57
2172 2918 6.956299 AATGTCAAAGCATAATGTTTCTGC 57.044 33.333 0.00 0.00 36.15 4.26
2176 2922 8.659925 TTGTGAAATGTCAAAGCATAATGTTT 57.340 26.923 0.00 0.00 34.87 2.83
2236 2982 2.169769 GTCCATCCAGTTTCACCGGATA 59.830 50.000 9.46 0.00 37.44 2.59
2239 2985 0.036164 TGTCCATCCAGTTTCACCGG 59.964 55.000 0.00 0.00 0.00 5.28
2240 2986 1.442769 CTGTCCATCCAGTTTCACCG 58.557 55.000 0.00 0.00 0.00 4.94
2244 2990 3.064900 AGAAGCTGTCCATCCAGTTTC 57.935 47.619 9.00 9.00 46.75 2.78
2247 2993 3.445008 TCTTAGAAGCTGTCCATCCAGT 58.555 45.455 0.00 0.00 34.84 4.00
2255 3001 5.482908 TGATGGTCTTTCTTAGAAGCTGTC 58.517 41.667 0.00 0.00 33.81 3.51
2256 3002 5.489792 TGATGGTCTTTCTTAGAAGCTGT 57.510 39.130 0.00 0.00 33.81 4.40
2265 3011 7.391833 GGTCTACAAAAGATGATGGTCTTTCTT 59.608 37.037 2.72 0.00 45.18 2.52
2289 3035 4.414514 AGGTACCAAGTTTTGTTAGAGGGT 59.585 41.667 15.94 0.00 0.00 4.34
2292 3038 7.584987 CAATCAGGTACCAAGTTTTGTTAGAG 58.415 38.462 15.94 0.00 0.00 2.43
2299 3045 5.048013 GCTAAGCAATCAGGTACCAAGTTTT 60.048 40.000 15.94 2.30 0.00 2.43
2300 3046 4.459337 GCTAAGCAATCAGGTACCAAGTTT 59.541 41.667 15.94 4.85 0.00 2.66
2301 3047 4.010349 GCTAAGCAATCAGGTACCAAGTT 58.990 43.478 15.94 2.12 0.00 2.66
2302 3048 3.264450 AGCTAAGCAATCAGGTACCAAGT 59.736 43.478 15.94 0.00 0.00 3.16
2303 3049 3.878778 AGCTAAGCAATCAGGTACCAAG 58.121 45.455 15.94 6.34 0.00 3.61
2304 3050 5.023533 CTAGCTAAGCAATCAGGTACCAA 57.976 43.478 15.94 1.46 0.00 3.67
2305 3051 4.672587 CTAGCTAAGCAATCAGGTACCA 57.327 45.455 15.94 0.00 0.00 3.25
2314 3060 7.451877 TACTATAAGAGTGGCTAGCTAAGCAAT 59.548 37.037 15.72 2.72 45.66 3.56
2315 3061 6.776116 TACTATAAGAGTGGCTAGCTAAGCAA 59.224 38.462 15.72 3.54 45.66 3.91
2316 3062 6.207025 GTACTATAAGAGTGGCTAGCTAAGCA 59.793 42.308 15.72 0.31 45.66 3.91
2317 3063 6.431852 AGTACTATAAGAGTGGCTAGCTAAGC 59.568 42.308 15.72 3.95 44.29 3.09
2318 3064 7.989416 AGTACTATAAGAGTGGCTAGCTAAG 57.011 40.000 15.72 3.34 39.39 2.18
2319 3065 8.878211 TCTAGTACTATAAGAGTGGCTAGCTAA 58.122 37.037 15.72 0.00 40.81 3.09
2320 3066 8.433249 TCTAGTACTATAAGAGTGGCTAGCTA 57.567 38.462 15.72 5.44 40.81 3.32
2321 3067 7.319052 TCTAGTACTATAAGAGTGGCTAGCT 57.681 40.000 15.72 0.00 40.81 3.32
2322 3068 8.570068 AATCTAGTACTATAAGAGTGGCTAGC 57.430 38.462 6.04 6.04 40.81 3.42
2335 3081 9.670442 TCCCAAAACCAGATAATCTAGTACTAT 57.330 33.333 2.33 0.00 0.00 2.12
2336 3082 9.496710 TTCCCAAAACCAGATAATCTAGTACTA 57.503 33.333 1.89 1.89 0.00 1.82
2337 3083 7.989947 TCCCAAAACCAGATAATCTAGTACT 57.010 36.000 0.00 0.00 0.00 2.73
2338 3084 9.110502 CTTTCCCAAAACCAGATAATCTAGTAC 57.889 37.037 0.00 0.00 0.00 2.73
2339 3085 8.832735 ACTTTCCCAAAACCAGATAATCTAGTA 58.167 33.333 0.00 0.00 0.00 1.82
2340 3086 7.699878 ACTTTCCCAAAACCAGATAATCTAGT 58.300 34.615 0.00 0.00 0.00 2.57
2341 3087 8.581253 AACTTTCCCAAAACCAGATAATCTAG 57.419 34.615 0.00 0.00 0.00 2.43
2342 3088 8.390921 AGAACTTTCCCAAAACCAGATAATCTA 58.609 33.333 0.00 0.00 0.00 1.98
2343 3089 7.241628 AGAACTTTCCCAAAACCAGATAATCT 58.758 34.615 0.00 0.00 0.00 2.40
2344 3090 7.468141 AGAACTTTCCCAAAACCAGATAATC 57.532 36.000 0.00 0.00 0.00 1.75
2345 3091 7.855784 AAGAACTTTCCCAAAACCAGATAAT 57.144 32.000 0.00 0.00 0.00 1.28
2346 3092 7.669089 AAAGAACTTTCCCAAAACCAGATAA 57.331 32.000 0.00 0.00 0.00 1.75
2347 3093 7.284919 GAAAGAACTTTCCCAAAACCAGATA 57.715 36.000 14.16 0.00 42.20 1.98
2348 3094 6.161855 GAAAGAACTTTCCCAAAACCAGAT 57.838 37.500 14.16 0.00 42.20 2.90
2349 3095 5.592104 GAAAGAACTTTCCCAAAACCAGA 57.408 39.130 14.16 0.00 42.20 3.86
2360 3106 6.941857 AGAGATAGTCAGGGAAAGAACTTTC 58.058 40.000 16.12 16.12 46.03 2.62
2361 3107 6.498651 TGAGAGATAGTCAGGGAAAGAACTTT 59.501 38.462 0.00 0.00 35.14 2.66
2362 3108 6.019748 TGAGAGATAGTCAGGGAAAGAACTT 58.980 40.000 0.00 0.00 0.00 2.66
2363 3109 5.584913 TGAGAGATAGTCAGGGAAAGAACT 58.415 41.667 0.00 0.00 0.00 3.01
2364 3110 5.420739 ACTGAGAGATAGTCAGGGAAAGAAC 59.579 44.000 5.18 0.00 44.96 3.01
2365 3111 5.584913 ACTGAGAGATAGTCAGGGAAAGAA 58.415 41.667 5.18 0.00 44.96 2.52
2366 3112 5.199982 ACTGAGAGATAGTCAGGGAAAGA 57.800 43.478 5.18 0.00 44.96 2.52
2367 3113 5.930837 AACTGAGAGATAGTCAGGGAAAG 57.069 43.478 5.18 0.00 44.96 2.62
2368 3114 6.494952 AGTAACTGAGAGATAGTCAGGGAAA 58.505 40.000 5.18 0.00 44.96 3.13
2369 3115 6.080969 AGTAACTGAGAGATAGTCAGGGAA 57.919 41.667 5.18 0.00 44.96 3.97
2370 3116 5.718801 AGTAACTGAGAGATAGTCAGGGA 57.281 43.478 5.18 0.00 44.96 4.20
2371 3117 5.451242 GCAAGTAACTGAGAGATAGTCAGGG 60.451 48.000 5.18 0.00 44.96 4.45
2372 3118 5.126222 TGCAAGTAACTGAGAGATAGTCAGG 59.874 44.000 5.18 0.00 44.96 3.86
2373 3119 6.201226 TGCAAGTAACTGAGAGATAGTCAG 57.799 41.667 0.00 0.00 45.94 3.51
2374 3120 6.590234 TTGCAAGTAACTGAGAGATAGTCA 57.410 37.500 0.00 0.00 0.00 3.41
2375 3121 7.761704 TCATTTGCAAGTAACTGAGAGATAGTC 59.238 37.037 0.00 0.00 0.00 2.59
2376 3122 7.547370 GTCATTTGCAAGTAACTGAGAGATAGT 59.453 37.037 0.00 0.00 0.00 2.12
2377 3123 7.547019 TGTCATTTGCAAGTAACTGAGAGATAG 59.453 37.037 0.00 0.00 0.00 2.08
2378 3124 7.386059 TGTCATTTGCAAGTAACTGAGAGATA 58.614 34.615 0.00 0.00 0.00 1.98
2379 3125 6.233434 TGTCATTTGCAAGTAACTGAGAGAT 58.767 36.000 0.00 0.00 0.00 2.75
2380 3126 5.610398 TGTCATTTGCAAGTAACTGAGAGA 58.390 37.500 0.00 0.00 0.00 3.10
2381 3127 5.929697 TGTCATTTGCAAGTAACTGAGAG 57.070 39.130 0.00 0.00 0.00 3.20
2382 3128 5.181811 CCATGTCATTTGCAAGTAACTGAGA 59.818 40.000 0.00 0.00 0.00 3.27
2383 3129 5.048504 ACCATGTCATTTGCAAGTAACTGAG 60.049 40.000 0.00 0.00 0.00 3.35
2384 3130 4.826733 ACCATGTCATTTGCAAGTAACTGA 59.173 37.500 0.00 0.00 0.00 3.41
2385 3131 5.125100 ACCATGTCATTTGCAAGTAACTG 57.875 39.130 0.00 0.00 0.00 3.16
2386 3132 5.789643 AACCATGTCATTTGCAAGTAACT 57.210 34.783 0.00 0.00 0.00 2.24
2387 3133 7.312154 TGATAACCATGTCATTTGCAAGTAAC 58.688 34.615 0.00 0.00 0.00 2.50
2388 3134 7.459795 TGATAACCATGTCATTTGCAAGTAA 57.540 32.000 0.00 0.00 0.00 2.24
2389 3135 7.643569 ATGATAACCATGTCATTTGCAAGTA 57.356 32.000 0.00 0.00 34.09 2.24
2390 3136 5.981088 TGATAACCATGTCATTTGCAAGT 57.019 34.783 0.00 0.00 0.00 3.16
2412 3158 9.578439 GCAGCAATAAGACTTTATTTCTCAAAT 57.422 29.630 0.00 0.00 37.38 2.32
2413 3159 8.575589 TGCAGCAATAAGACTTTATTTCTCAAA 58.424 29.630 0.00 0.00 37.38 2.69
2414 3160 8.109705 TGCAGCAATAAGACTTTATTTCTCAA 57.890 30.769 0.00 0.00 37.38 3.02
2415 3161 7.686438 TGCAGCAATAAGACTTTATTTCTCA 57.314 32.000 0.00 0.00 37.38 3.27
2416 3162 8.970691 TTTGCAGCAATAAGACTTTATTTCTC 57.029 30.769 9.12 0.00 37.38 2.87
2417 3163 9.415544 CTTTTGCAGCAATAAGACTTTATTTCT 57.584 29.630 9.12 0.00 37.38 2.52
2418 3164 8.650714 CCTTTTGCAGCAATAAGACTTTATTTC 58.349 33.333 21.87 0.00 37.38 2.17
2419 3165 8.367156 TCCTTTTGCAGCAATAAGACTTTATTT 58.633 29.630 21.87 0.00 37.38 1.40
2420 3166 7.895759 TCCTTTTGCAGCAATAAGACTTTATT 58.104 30.769 21.87 0.00 39.49 1.40
2421 3167 7.466746 TCCTTTTGCAGCAATAAGACTTTAT 57.533 32.000 21.87 0.00 0.00 1.40
2422 3168 6.892658 TCCTTTTGCAGCAATAAGACTTTA 57.107 33.333 21.87 0.23 0.00 1.85
2423 3169 5.789643 TCCTTTTGCAGCAATAAGACTTT 57.210 34.783 21.87 0.00 0.00 2.66
2424 3170 5.789643 TTCCTTTTGCAGCAATAAGACTT 57.210 34.783 21.87 0.00 0.00 3.01
2425 3171 5.789643 TTTCCTTTTGCAGCAATAAGACT 57.210 34.783 21.87 0.00 0.00 3.24
2426 3172 6.843069 TTTTTCCTTTTGCAGCAATAAGAC 57.157 33.333 21.87 0.00 0.00 3.01
2450 3196 6.828785 GGGATGACATGTAAATTACCTTCAGT 59.171 38.462 0.00 0.00 0.00 3.41
2453 3199 6.238759 GCAGGGATGACATGTAAATTACCTTC 60.239 42.308 0.00 0.00 0.00 3.46
2484 3230 2.028748 GCCCACTGCAGAATGATTTTGT 60.029 45.455 23.35 0.00 39.69 2.83
2485 3231 2.232941 AGCCCACTGCAGAATGATTTTG 59.767 45.455 23.35 5.12 44.83 2.44
2486 3232 2.232941 CAGCCCACTGCAGAATGATTTT 59.767 45.455 23.35 0.00 44.83 1.82
2499 3245 2.282040 GAGTTGCAGCAGCCCACT 60.282 61.111 5.49 0.86 41.13 4.00
2500 3246 3.368571 GGAGTTGCAGCAGCCCAC 61.369 66.667 5.49 0.00 41.13 4.61
2501 3247 3.137385 AAGGAGTTGCAGCAGCCCA 62.137 57.895 15.77 0.00 41.13 5.36
2502 3248 2.282745 AAGGAGTTGCAGCAGCCC 60.283 61.111 5.49 7.10 41.13 5.19
2503 3249 2.633509 CCAAGGAGTTGCAGCAGCC 61.634 63.158 5.49 3.75 41.13 4.85
2504 3250 2.633509 CCCAAGGAGTTGCAGCAGC 61.634 63.158 2.55 0.00 42.57 5.25
2505 3251 0.959372 CTCCCAAGGAGTTGCAGCAG 60.959 60.000 2.55 0.00 44.25 4.24
2506 3252 1.073722 CTCCCAAGGAGTTGCAGCA 59.926 57.895 2.55 0.00 44.25 4.41
2507 3253 3.993535 CTCCCAAGGAGTTGCAGC 58.006 61.111 2.28 0.00 44.25 5.25
2546 3292 0.530650 ATGGAGCGTATGCCAAGACG 60.531 55.000 2.51 0.00 43.79 4.18
2547 3293 2.526304 TATGGAGCGTATGCCAAGAC 57.474 50.000 2.51 0.00 44.31 3.01


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

AutoCloner maintained by Alex Coulton.