Multiple sequence alignment - TraesCS4D01G032300

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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 TraesCS4D01G032300 chr4D 100.000 6458 0 0 1 6458 14923672 14930129 0.000000e+00 11926.0
1 TraesCS4D01G032300 chr4D 92.581 2251 105 35 35 2247 14425322 14423096 0.000000e+00 3175.0
2 TraesCS4D01G032300 chr4D 94.590 1756 75 8 3263 5002 14400880 14399129 0.000000e+00 2699.0
3 TraesCS4D01G032300 chr4D 91.235 1061 64 13 1442 2500 15157415 15156382 0.000000e+00 1417.0
4 TraesCS4D01G032300 chr4D 93.856 765 33 7 2499 3255 14403520 14402762 0.000000e+00 1140.0
5 TraesCS4D01G032300 chr4D 89.775 890 72 8 3419 4290 15151055 15150167 0.000000e+00 1122.0
6 TraesCS4D01G032300 chr4D 86.340 959 69 31 35 959 15158803 15157873 0.000000e+00 989.0
7 TraesCS4D01G032300 chr4D 92.188 640 41 9 2499 3131 15156339 15155702 0.000000e+00 896.0
8 TraesCS4D01G032300 chr4D 93.388 363 22 2 5083 5445 14399131 14398771 2.650000e-148 536.0
9 TraesCS4D01G032300 chr4D 89.831 354 16 8 5566 5914 15148862 15148524 2.760000e-118 436.0
10 TraesCS4D01G032300 chr4D 93.594 281 8 4 5505 5781 14398774 14398500 1.680000e-110 411.0
11 TraesCS4D01G032300 chr4D 82.195 483 50 20 497 959 26894791 26895257 3.650000e-102 383.0
12 TraesCS4D01G032300 chr4D 90.551 127 9 1 3133 3259 15155758 15155635 1.440000e-36 165.0
13 TraesCS4D01G032300 chr4D 96.774 62 2 0 3133 3194 14402937 14402876 3.190000e-18 104.0
14 TraesCS4D01G032300 chr4D 93.023 43 3 0 439 481 26894697 26894739 5.410000e-06 63.9
15 TraesCS4D01G032300 chr4A 91.132 3180 150 46 3263 6371 456400930 456397812 0.000000e+00 4189.0
16 TraesCS4D01G032300 chr4A 91.458 3114 143 42 3263 6317 586674626 586671577 0.000000e+00 4163.0
17 TraesCS4D01G032300 chr4A 94.650 2131 84 16 958 3079 586678422 586676313 0.000000e+00 3277.0
18 TraesCS4D01G032300 chr4A 94.314 1794 64 20 958 2733 456415231 456413458 0.000000e+00 2713.0
19 TraesCS4D01G032300 chr4A 93.101 1348 63 13 958 2305 538492900 538491583 0.000000e+00 1947.0
20 TraesCS4D01G032300 chr4A 84.111 1372 175 20 1042 2407 576596935 576595601 0.000000e+00 1286.0
21 TraesCS4D01G032300 chr4A 91.084 886 65 5 3418 4290 586089515 586090399 0.000000e+00 1186.0
22 TraesCS4D01G032300 chr4A 91.963 647 43 8 2496 3135 585688652 585689296 0.000000e+00 898.0
23 TraesCS4D01G032300 chr4A 82.365 947 77 37 35 959 456416149 456415271 0.000000e+00 741.0
24 TraesCS4D01G032300 chr4A 81.626 947 83 38 35 959 586679339 586678462 0.000000e+00 701.0
25 TraesCS4D01G032300 chr4A 86.555 476 36 18 497 959 538493398 538492938 3.480000e-137 499.0
26 TraesCS4D01G032300 chr4A 89.266 354 18 8 5566 5914 586091768 586092106 5.980000e-115 425.0
27 TraesCS4D01G032300 chr4A 84.932 438 42 13 4020 4437 585692325 585692758 7.740000e-114 422.0
28 TraesCS4D01G032300 chr4A 89.803 304 25 5 5303 5605 538487528 538487230 1.020000e-102 385.0
29 TraesCS4D01G032300 chr4A 89.837 246 12 10 497 740 585686673 585686907 2.930000e-78 303.0
30 TraesCS4D01G032300 chr4A 95.041 121 6 0 3065 3185 538490780 538490660 2.380000e-44 191.0
31 TraesCS4D01G032300 chr4A 93.519 108 7 0 378 485 585681307 585681414 1.860000e-35 161.0
32 TraesCS4D01G032300 chr4A 80.423 189 21 10 5928 6102 585694870 585695056 5.250000e-26 130.0
33 TraesCS4D01G032300 chr4A 89.286 84 3 2 6060 6137 586671660 586671577 4.120000e-17 100.0
34 TraesCS4D01G032300 chr4A 89.610 77 8 0 3119 3195 585689307 585689383 1.480000e-16 99.0
35 TraesCS4D01G032300 chr4A 90.141 71 6 1 3122 3191 585689224 585689294 2.480000e-14 91.6
36 TraesCS4D01G032300 chr4A 91.935 62 5 0 6310 6371 586651853 586651792 3.210000e-13 87.9
37 TraesCS4D01G032300 chr4A 96.078 51 2 0 6398 6448 586507490 586507440 4.150000e-12 84.2
38 TraesCS4D01G032300 chr3B 93.984 1762 54 10 3263 5002 452698471 452696740 0.000000e+00 2619.0
39 TraesCS4D01G032300 chr3B 93.273 1546 73 11 958 2501 452703129 452701613 0.000000e+00 2250.0
40 TraesCS4D01G032300 chr3B 91.023 479 41 2 4525 5002 452564234 452563757 0.000000e+00 645.0
41 TraesCS4D01G032300 chr3B 85.361 485 36 15 35 493 452704159 452703684 2.730000e-128 470.0
42 TraesCS4D01G032300 chr3B 85.012 427 35 15 547 959 452703578 452703167 2.170000e-109 407.0
43 TraesCS4D01G032300 chr3B 92.523 107 7 1 4979 5084 18672926 18673032 1.120000e-32 152.0
44 TraesCS4D01G032300 chr4B 92.760 1547 73 15 958 2501 24764283 24765793 0.000000e+00 2200.0
45 TraesCS4D01G032300 chr4B 96.415 1283 35 6 3257 4531 24767923 24769202 0.000000e+00 2104.0
46 TraesCS4D01G032300 chr4B 90.605 1586 101 22 3386 4940 25386995 25385427 0.000000e+00 2060.0
47 TraesCS4D01G032300 chr4B 85.208 960 78 40 36 959 24763314 24764245 0.000000e+00 928.0
48 TraesCS4D01G032300 chr4B 89.286 728 59 9 5083 5806 25351779 25351067 0.000000e+00 894.0
49 TraesCS4D01G032300 chr4B 91.925 644 42 9 2499 3135 25392598 25391958 0.000000e+00 893.0
50 TraesCS4D01G032300 chr4B 93.220 590 33 7 2496 3079 24765832 24766420 0.000000e+00 861.0
51 TraesCS4D01G032300 chr4B 95.137 473 17 4 4530 5002 24769306 24769772 0.000000e+00 741.0
52 TraesCS4D01G032300 chr4B 90.605 479 40 3 4525 5002 24832635 24833109 1.180000e-176 630.0
53 TraesCS4D01G032300 chr4B 88.525 183 21 0 5338 5520 25385082 25384900 8.430000e-54 222.0
54 TraesCS4D01G032300 chr4B 81.857 237 26 10 5850 6074 25384895 25384664 3.980000e-42 183.0
55 TraesCS4D01G032300 chr4B 88.034 117 10 2 5854 5966 24770201 24770317 1.130000e-27 135.0
56 TraesCS4D01G032300 chr2A 93.101 1348 64 16 958 2305 196118877 196120195 0.000000e+00 1947.0
57 TraesCS4D01G032300 chr2A 93.666 1042 43 16 5284 6317 196315124 196314098 0.000000e+00 1537.0
58 TraesCS4D01G032300 chr2A 92.950 695 32 10 958 1651 196317089 196316411 0.000000e+00 996.0
59 TraesCS4D01G032300 chr2A 92.816 696 32 12 958 1651 196327687 196327008 0.000000e+00 992.0
60 TraesCS4D01G032300 chr2A 93.844 666 29 7 958 1620 196345979 196345323 0.000000e+00 992.0
61 TraesCS4D01G032300 chr2A 91.345 647 47 8 2496 3135 195819947 195820591 0.000000e+00 876.0
62 TraesCS4D01G032300 chr2A 97.468 474 7 3 4813 5286 196345303 196344835 0.000000e+00 804.0
63 TraesCS4D01G032300 chr2A 97.257 474 8 3 4813 5286 196359852 196359384 0.000000e+00 798.0
64 TraesCS4D01G032300 chr2A 97.046 474 9 3 4813 5286 196355590 196355122 0.000000e+00 793.0
65 TraesCS4D01G032300 chr2A 96.624 474 11 3 4813 5286 196323207 196322739 0.000000e+00 782.0
66 TraesCS4D01G032300 chr2A 96.000 475 13 6 4813 5286 196327011 196326542 0.000000e+00 767.0
67 TraesCS4D01G032300 chr2A 91.509 530 38 5 4482 5007 196125178 196125704 0.000000e+00 723.0
68 TraesCS4D01G032300 chr2A 81.905 945 83 33 35 959 196328603 196327727 0.000000e+00 717.0
69 TraesCS4D01G032300 chr2A 81.712 946 84 40 35 959 196357184 196356307 0.000000e+00 706.0
70 TraesCS4D01G032300 chr2A 81.587 945 87 40 35 959 196320964 196320087 0.000000e+00 701.0
71 TraesCS4D01G032300 chr2A 81.521 947 84 38 35 959 196346896 196346019 0.000000e+00 695.0
72 TraesCS4D01G032300 chr2A 81.376 945 89 42 35 959 196318006 196317129 0.000000e+00 689.0
73 TraesCS4D01G032300 chr2A 86.780 590 50 20 4431 5002 195823947 195824526 3.290000e-177 632.0
74 TraesCS4D01G032300 chr2A 87.185 476 33 18 497 959 196118379 196118839 3.450000e-142 516.0
75 TraesCS4D01G032300 chr2A 85.160 438 41 13 4020 4437 195823435 195823868 1.660000e-115 427.0
76 TraesCS4D01G032300 chr2A 80.936 577 55 24 35 604 196324770 196324242 7.800000e-109 405.0
77 TraesCS4D01G032300 chr2A 85.978 271 26 10 4209 4472 196124267 196124532 4.930000e-71 279.0
78 TraesCS4D01G032300 chr2A 86.854 213 14 8 527 738 195818037 195818236 6.520000e-55 226.0
79 TraesCS4D01G032300 chr2A 93.548 124 8 0 3062 3185 196120996 196121119 1.110000e-42 185.0
80 TraesCS4D01G032300 chr2A 92.593 108 8 0 378 485 195817837 195817944 8.670000e-34 156.0
81 TraesCS4D01G032300 chr2A 86.957 138 17 1 3119 3256 195820602 195820738 3.120000e-33 154.0
82 TraesCS4D01G032300 chr2A 89.286 84 3 2 6060 6137 196314181 196314098 4.120000e-17 100.0
83 TraesCS4D01G032300 chr2A 98.039 51 1 0 6398 6448 196213505 196213455 8.920000e-14 89.8
84 TraesCS4D01G032300 chr2A 91.935 62 5 0 6310 6371 196291989 196291928 3.210000e-13 87.9
85 TraesCS4D01G032300 chr2A 88.732 71 7 1 3122 3191 195820519 195820589 1.150000e-12 86.1
86 TraesCS4D01G032300 chr1B 87.827 1569 148 22 959 2505 433420651 433422198 0.000000e+00 1799.0
87 TraesCS4D01G032300 chr1B 85.714 679 56 18 5314 5974 433427573 433428228 0.000000e+00 678.0
88 TraesCS4D01G032300 chr1B 89.194 546 52 5 2514 3057 433422261 433422801 0.000000e+00 675.0
89 TraesCS4D01G032300 chr1D 87.867 1566 142 20 961 2505 320382257 320383795 0.000000e+00 1796.0
90 TraesCS4D01G032300 chr1D 89.408 557 53 5 2514 3065 320383858 320384413 0.000000e+00 697.0
91 TraesCS4D01G032300 chr1D 85.272 679 58 20 5314 5974 320391155 320391809 0.000000e+00 662.0
92 TraesCS4D01G032300 chr1D 88.732 497 53 3 4507 5002 320390396 320390890 7.160000e-169 604.0
93 TraesCS4D01G032300 chr5B 86.726 1243 122 18 3263 4466 54827092 54828330 0.000000e+00 1341.0
94 TraesCS4D01G032300 chr5B 97.872 94 2 0 4999 5092 621211721 621211814 5.180000e-36 163.0
95 TraesCS4D01G032300 chr5A 85.782 1273 120 33 3263 4495 40875937 40877188 0.000000e+00 1291.0
96 TraesCS4D01G032300 chr5A 89.841 502 41 4 4507 5002 40877326 40877823 2.540000e-178 636.0
97 TraesCS4D01G032300 chr5D 85.075 536 40 16 5306 5815 51846037 51846558 1.610000e-140 510.0
98 TraesCS4D01G032300 chr5D 85.556 270 29 6 4236 4497 51844866 51845133 2.290000e-69 274.0
99 TraesCS4D01G032300 chrUn 96.809 94 3 0 5000 5093 55723696 55723603 2.410000e-34 158.0


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 TraesCS4D01G032300 chr4D 14923672 14930129 6457 False 11926.000000 11926 100.000000 1 6458 1 chr4D.!!$F1 6457
1 TraesCS4D01G032300 chr4D 14423096 14425322 2226 True 3175.000000 3175 92.581000 35 2247 1 chr4D.!!$R1 2212
2 TraesCS4D01G032300 chr4D 14398500 14403520 5020 True 978.000000 2699 94.440400 2499 5781 5 chr4D.!!$R2 3282
3 TraesCS4D01G032300 chr4D 15155635 15158803 3168 True 866.750000 1417 90.078500 35 3259 4 chr4D.!!$R4 3224
4 TraesCS4D01G032300 chr4D 15148524 15151055 2531 True 779.000000 1122 89.803000 3419 5914 2 chr4D.!!$R3 2495
5 TraesCS4D01G032300 chr4D 26894697 26895257 560 False 223.450000 383 87.609000 439 959 2 chr4D.!!$F2 520
6 TraesCS4D01G032300 chr4A 456397812 456400930 3118 True 4189.000000 4189 91.132000 3263 6371 1 chr4A.!!$R1 3108
7 TraesCS4D01G032300 chr4A 586671577 586674626 3049 True 2131.500000 4163 90.372000 3263 6317 2 chr4A.!!$R7 3054
8 TraesCS4D01G032300 chr4A 586676313 586679339 3026 True 1989.000000 3277 88.138000 35 3079 2 chr4A.!!$R8 3044
9 TraesCS4D01G032300 chr4A 456413458 456416149 2691 True 1727.000000 2713 88.339500 35 2733 2 chr4A.!!$R5 2698
10 TraesCS4D01G032300 chr4A 576595601 576596935 1334 True 1286.000000 1286 84.111000 1042 2407 1 chr4A.!!$R2 1365
11 TraesCS4D01G032300 chr4A 586089515 586092106 2591 False 805.500000 1186 90.175000 3418 5914 2 chr4A.!!$F3 2496
12 TraesCS4D01G032300 chr4A 538487230 538493398 6168 True 755.500000 1947 91.125000 497 5605 4 chr4A.!!$R6 5108
13 TraesCS4D01G032300 chr4A 585686673 585695056 8383 False 323.933333 898 87.817667 497 6102 6 chr4A.!!$F2 5605
14 TraesCS4D01G032300 chr3B 452696740 452704159 7419 True 1436.500000 2619 89.407500 35 5002 4 chr3B.!!$R2 4967
15 TraesCS4D01G032300 chr4B 24763314 24770317 7003 False 1161.500000 2200 91.795667 36 5966 6 chr4B.!!$F2 5930
16 TraesCS4D01G032300 chr4B 25351067 25351779 712 True 894.000000 894 89.286000 5083 5806 1 chr4B.!!$R1 723
17 TraesCS4D01G032300 chr4B 25391958 25392598 640 True 893.000000 893 91.925000 2499 3135 1 chr4B.!!$R2 636
18 TraesCS4D01G032300 chr4B 25384664 25386995 2331 True 821.666667 2060 86.995667 3386 6074 3 chr4B.!!$R3 2688
19 TraesCS4D01G032300 chr2A 196344835 196346896 2061 True 830.333333 992 90.944333 35 5286 3 chr2A.!!$R4 5251
20 TraesCS4D01G032300 chr2A 196314098 196328603 14505 True 768.600000 1537 88.714600 35 6317 10 chr2A.!!$R3 6282
21 TraesCS4D01G032300 chr2A 196355122 196359852 4730 True 765.666667 798 92.005000 35 5286 3 chr2A.!!$R5 5251
22 TraesCS4D01G032300 chr2A 196118379 196125704 7325 False 730.000000 1947 90.264200 497 5007 5 chr2A.!!$F2 4510
23 TraesCS4D01G032300 chr2A 195817837 195824526 6689 False 365.300000 876 88.345857 378 5002 7 chr2A.!!$F1 4624
24 TraesCS4D01G032300 chr1B 433420651 433422801 2150 False 1237.000000 1799 88.510500 959 3057 2 chr1B.!!$F2 2098
25 TraesCS4D01G032300 chr1B 433427573 433428228 655 False 678.000000 678 85.714000 5314 5974 1 chr1B.!!$F1 660
26 TraesCS4D01G032300 chr1D 320382257 320384413 2156 False 1246.500000 1796 88.637500 961 3065 2 chr1D.!!$F1 2104
27 TraesCS4D01G032300 chr1D 320390396 320391809 1413 False 633.000000 662 87.002000 4507 5974 2 chr1D.!!$F2 1467
28 TraesCS4D01G032300 chr5B 54827092 54828330 1238 False 1341.000000 1341 86.726000 3263 4466 1 chr5B.!!$F1 1203
29 TraesCS4D01G032300 chr5A 40875937 40877823 1886 False 963.500000 1291 87.811500 3263 5002 2 chr5A.!!$F1 1739
30 TraesCS4D01G032300 chr5D 51844866 51846558 1692 False 392.000000 510 85.315500 4236 5815 2 chr5D.!!$F1 1579

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
67 2702 0.108898 CACGTGGCCTTCTCTCTCTG 60.109 60.000 7.95 0.0 0.00 3.35 F
310 2985 0.539986 TTGTTAGTCGGGCCATCTCC 59.460 55.000 4.39 0.0 0.00 3.71 F
1333 4210 1.067516 CTGCTCCCAAGGTTTGTGTTG 59.932 52.381 0.00 0.0 0.00 3.33 F
2641 5676 0.320771 CAACTAGACTGCTTGCCGGT 60.321 55.000 1.90 0.0 35.17 5.28 F
3085 6130 3.107601 ACATGCCCTAGTCTTAGCAAGA 58.892 45.455 0.00 0.0 38.99 3.02 F
3704 10584 3.070018 CTGCAGAAAGTCAAACGGAGAT 58.930 45.455 8.42 0.0 0.00 2.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1784 4699 0.824759 GGAAGCACCGGACACTATCT 59.175 55.000 9.46 0.0 0.0 1.98 R
1848 4763 1.249407 GTTTGTGCGGGGATGGTAAA 58.751 50.000 0.00 0.0 0.0 2.01 R
2704 5739 1.914634 CAGCCAGTAGTAGAACAGCG 58.085 55.000 0.00 0.0 0.0 5.18 R
3704 10584 0.950836 CCGACACACCTTTGCATGAA 59.049 50.000 0.00 0.0 0.0 2.57 R
4321 11834 2.120232 CGGCTGAATTCGCTACTACAG 58.880 52.381 17.53 0.0 0.0 2.74 R
5650 26062 4.221041 ACCTGGAGACTAGAAACTTACAGC 59.779 45.833 0.00 0.0 0.0 4.40 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
67 2702 0.108898 CACGTGGCCTTCTCTCTCTG 60.109 60.000 7.95 0.00 0.00 3.35
252 2924 9.429359 CTATCTGATCTGTTATGTATGGTTTCC 57.571 37.037 0.00 0.00 0.00 3.13
270 2945 0.792640 CCGTGTGTGTGCTGAATCTC 59.207 55.000 0.00 0.00 0.00 2.75
271 2946 1.606480 CCGTGTGTGTGCTGAATCTCT 60.606 52.381 0.00 0.00 0.00 3.10
310 2985 0.539986 TTGTTAGTCGGGCCATCTCC 59.460 55.000 4.39 0.00 0.00 3.71
355 3037 5.177511 TCGACTAAAGCTGATGAAACTGTTG 59.822 40.000 0.00 0.00 0.00 3.33
358 3040 2.283145 AGCTGATGAAACTGTTGGCT 57.717 45.000 0.00 0.00 0.00 4.75
368 3050 5.734720 TGAAACTGTTGGCTCCTAGATAAG 58.265 41.667 0.00 0.00 0.00 1.73
401 3083 2.033662 GCGCCGTTCTTGATTGATCTAC 60.034 50.000 0.00 0.00 0.00 2.59
451 3133 4.806330 TGACGGTTCTCTAATCTGAACAC 58.194 43.478 7.91 1.05 42.91 3.32
644 3427 3.494626 TGAAGATGTCTCGTTGTGCTTTC 59.505 43.478 0.00 0.00 0.00 2.62
647 3430 1.581934 TGTCTCGTTGTGCTTTCAGG 58.418 50.000 0.00 0.00 0.00 3.86
671 3456 1.136305 CATCAGCAAGGGCAATTCAGG 59.864 52.381 0.00 0.00 44.61 3.86
687 3472 1.822990 TCAGGTATTCGTGGGAGTCAC 59.177 52.381 0.00 0.00 42.74 3.67
718 3506 9.946165 CAGTGATGACTATCGTTTATACTTGTA 57.054 33.333 0.00 0.00 36.04 2.41
759 3547 6.723298 TTAGCTTTTGGTTTCTGGATTTCA 57.277 33.333 0.00 0.00 0.00 2.69
985 3827 6.462073 TCGAGATTAAACTTCCTTGTTTCG 57.538 37.500 0.00 0.00 40.23 3.46
1202 4072 3.994317 TCTGTGTGATATTCCTCTCCCA 58.006 45.455 0.00 0.00 0.00 4.37
1333 4210 1.067516 CTGCTCCCAAGGTTTGTGTTG 59.932 52.381 0.00 0.00 0.00 3.33
1561 4468 1.327303 TGGTGCCTCATGTTTGGTTC 58.673 50.000 0.00 0.00 0.00 3.62
1760 4675 3.754965 TGCCTTCTTGGACATATATGCC 58.245 45.455 12.79 14.32 38.35 4.40
1835 4750 2.852075 AACTGTGAAGGCCGGGGA 60.852 61.111 2.18 0.00 0.00 4.81
1848 4763 2.489073 GGCCGGGGAATGTCATCTTATT 60.489 50.000 2.18 0.00 0.00 1.40
1857 4772 7.039714 GGGGAATGTCATCTTATTTTACCATCC 60.040 40.741 0.00 0.00 0.00 3.51
2278 5220 7.551617 CCTCCCAATACGAATTACTACTTTTGT 59.448 37.037 0.00 0.00 0.00 2.83
2597 5629 8.754991 TGGACTTAGATTTTTGTTCCTTGTTA 57.245 30.769 0.00 0.00 0.00 2.41
2638 5673 1.801178 GACACAACTAGACTGCTTGCC 59.199 52.381 0.00 0.00 0.00 4.52
2641 5676 0.320771 CAACTAGACTGCTTGCCGGT 60.321 55.000 1.90 0.00 35.17 5.28
2806 5841 5.417580 TGGGTTTGACCTTATCAGTAAATGC 59.582 40.000 0.00 0.00 38.99 3.56
2910 5945 3.884350 CGATTGCGCATGGCTGCT 61.884 61.111 12.75 0.00 46.65 4.24
2934 5969 7.473735 TTTGTTGATGTAATTTCCTATGCCA 57.526 32.000 0.00 0.00 0.00 4.92
3084 6129 3.550437 ACATGCCCTAGTCTTAGCAAG 57.450 47.619 0.00 0.00 38.99 4.01
3085 6130 3.107601 ACATGCCCTAGTCTTAGCAAGA 58.892 45.455 0.00 0.00 38.99 3.02
3086 6131 3.519510 ACATGCCCTAGTCTTAGCAAGAA 59.480 43.478 0.00 0.00 39.67 2.52
3087 6132 3.895232 TGCCCTAGTCTTAGCAAGAAG 57.105 47.619 0.96 0.00 39.67 2.85
3088 6133 3.441101 TGCCCTAGTCTTAGCAAGAAGA 58.559 45.455 0.96 0.00 39.67 2.87
3089 6134 4.033709 TGCCCTAGTCTTAGCAAGAAGAT 58.966 43.478 0.96 0.00 39.67 2.40
3091 6136 5.303078 TGCCCTAGTCTTAGCAAGAAGATAG 59.697 44.000 0.96 4.61 39.67 2.08
3092 6137 5.303333 GCCCTAGTCTTAGCAAGAAGATAGT 59.697 44.000 0.96 0.00 39.67 2.12
3093 6138 6.183360 GCCCTAGTCTTAGCAAGAAGATAGTT 60.183 42.308 0.96 0.00 39.67 2.24
3094 6139 7.430441 CCCTAGTCTTAGCAAGAAGATAGTTC 58.570 42.308 0.96 0.00 39.67 3.01
3095 6140 7.286775 CCCTAGTCTTAGCAAGAAGATAGTTCT 59.713 40.741 0.96 0.00 39.67 3.01
3096 6141 8.349983 CCTAGTCTTAGCAAGAAGATAGTTCTC 58.650 40.741 0.96 0.00 39.67 2.87
3097 6142 7.710676 AGTCTTAGCAAGAAGATAGTTCTCA 57.289 36.000 0.96 0.00 39.67 3.27
3098 6143 7.543756 AGTCTTAGCAAGAAGATAGTTCTCAC 58.456 38.462 0.96 0.00 39.67 3.51
3099 6144 6.754675 GTCTTAGCAAGAAGATAGTTCTCACC 59.245 42.308 0.96 0.00 39.67 4.02
3100 6145 6.665680 TCTTAGCAAGAAGATAGTTCTCACCT 59.334 38.462 0.00 0.00 33.83 4.00
3101 6146 5.337578 AGCAAGAAGATAGTTCTCACCTC 57.662 43.478 0.00 0.00 0.00 3.85
3102 6147 4.774726 AGCAAGAAGATAGTTCTCACCTCA 59.225 41.667 0.00 0.00 0.00 3.86
3103 6148 5.247110 AGCAAGAAGATAGTTCTCACCTCAA 59.753 40.000 0.00 0.00 0.00 3.02
3104 6149 5.350091 GCAAGAAGATAGTTCTCACCTCAAC 59.650 44.000 0.00 0.00 0.00 3.18
3105 6150 5.669164 AGAAGATAGTTCTCACCTCAACC 57.331 43.478 0.00 0.00 0.00 3.77
3106 6151 4.158764 AGAAGATAGTTCTCACCTCAACCG 59.841 45.833 0.00 0.00 0.00 4.44
3107 6152 3.698289 AGATAGTTCTCACCTCAACCGA 58.302 45.455 0.00 0.00 0.00 4.69
3108 6153 4.087182 AGATAGTTCTCACCTCAACCGAA 58.913 43.478 0.00 0.00 0.00 4.30
3109 6154 4.527038 AGATAGTTCTCACCTCAACCGAAA 59.473 41.667 0.00 0.00 0.00 3.46
3110 6155 3.553828 AGTTCTCACCTCAACCGAAAA 57.446 42.857 0.00 0.00 0.00 2.29
3111 6156 4.086706 AGTTCTCACCTCAACCGAAAAT 57.913 40.909 0.00 0.00 0.00 1.82
3112 6157 5.223449 AGTTCTCACCTCAACCGAAAATA 57.777 39.130 0.00 0.00 0.00 1.40
3113 6158 5.617252 AGTTCTCACCTCAACCGAAAATAA 58.383 37.500 0.00 0.00 0.00 1.40
3114 6159 6.059484 AGTTCTCACCTCAACCGAAAATAAA 58.941 36.000 0.00 0.00 0.00 1.40
3115 6160 6.544564 AGTTCTCACCTCAACCGAAAATAAAA 59.455 34.615 0.00 0.00 0.00 1.52
3116 6161 6.945938 TCTCACCTCAACCGAAAATAAAAA 57.054 33.333 0.00 0.00 0.00 1.94
3117 6162 7.519032 TCTCACCTCAACCGAAAATAAAAAT 57.481 32.000 0.00 0.00 0.00 1.82
3118 6163 7.367285 TCTCACCTCAACCGAAAATAAAAATG 58.633 34.615 0.00 0.00 0.00 2.32
3119 6164 7.013846 TCTCACCTCAACCGAAAATAAAAATGT 59.986 33.333 0.00 0.00 0.00 2.71
3120 6165 7.493367 TCACCTCAACCGAAAATAAAAATGTT 58.507 30.769 0.00 0.00 0.00 2.71
3121 6166 8.630917 TCACCTCAACCGAAAATAAAAATGTTA 58.369 29.630 0.00 0.00 0.00 2.41
3122 6167 9.418045 CACCTCAACCGAAAATAAAAATGTTAT 57.582 29.630 0.00 0.00 0.00 1.89
3134 6179 9.783256 AAATAAAAATGTTATACTTGCTCCGTC 57.217 29.630 0.00 0.00 0.00 4.79
3135 6180 8.732746 ATAAAAATGTTATACTTGCTCCGTCT 57.267 30.769 0.00 0.00 0.00 4.18
3136 6181 7.448748 AAAAATGTTATACTTGCTCCGTCTT 57.551 32.000 0.00 0.00 0.00 3.01
3137 6182 8.556213 AAAAATGTTATACTTGCTCCGTCTTA 57.444 30.769 0.00 0.00 0.00 2.10
3138 6183 7.772332 AAATGTTATACTTGCTCCGTCTTAG 57.228 36.000 0.00 0.00 0.00 2.18
3139 6184 4.679662 TGTTATACTTGCTCCGTCTTAGC 58.320 43.478 0.00 0.00 40.50 3.09
3259 10114 4.562143 GCACATTGGAAATTTCTGGCTCTT 60.562 41.667 17.42 0.00 0.00 2.85
3261 10116 6.628844 GCACATTGGAAATTTCTGGCTCTTAT 60.629 38.462 17.42 0.00 0.00 1.73
3307 10179 5.490139 AACCTAGTGAATTGAATGCGATG 57.510 39.130 0.00 0.00 0.00 3.84
3374 10252 3.766591 TGCAGTTTTCTCCTCCAAACAAA 59.233 39.130 0.00 0.00 35.66 2.83
3408 10286 3.682858 TCTCGCTGCTTACAATTGGTTAC 59.317 43.478 10.83 0.00 0.00 2.50
3704 10584 3.070018 CTGCAGAAAGTCAAACGGAGAT 58.930 45.455 8.42 0.00 0.00 2.75
4321 11834 3.735746 GTGATGGTTTTAGTGCTGCAAAC 59.264 43.478 2.77 5.06 0.00 2.93
4592 13113 3.264193 TCTCTGCCATCCTAATGTGTTGT 59.736 43.478 0.00 0.00 0.00 3.32
5370 25708 3.170717 ACTTGGTCCAGTCCGAAGAATA 58.829 45.455 0.00 0.00 0.00 1.75
5380 25718 2.540101 GTCCGAAGAATATCGCCACTTG 59.460 50.000 0.00 0.00 41.40 3.16
5565 25924 5.102953 TCATGATGCACCTTTAACTAGCT 57.897 39.130 0.00 0.00 0.00 3.32
5566 25925 6.233905 TCATGATGCACCTTTAACTAGCTA 57.766 37.500 0.00 0.00 0.00 3.32
5567 25926 6.283694 TCATGATGCACCTTTAACTAGCTAG 58.716 40.000 19.44 19.44 0.00 3.42
5595 26003 8.366671 AGATTATTCGTTGCTAGTCCATTAAC 57.633 34.615 0.00 0.00 0.00 2.01
5650 26062 5.031066 TCTATTATTGTGTCTTTCCCCCG 57.969 43.478 0.00 0.00 0.00 5.73
5651 26063 1.828979 TTATTGTGTCTTTCCCCCGC 58.171 50.000 0.00 0.00 0.00 6.13
5759 26183 4.530161 TGCTGTTATTTATTTGCCCCAACT 59.470 37.500 0.00 0.00 0.00 3.16
5760 26184 4.869861 GCTGTTATTTATTTGCCCCAACTG 59.130 41.667 0.00 0.00 0.00 3.16
5962 27375 3.181480 ACACCCAACACTTGTTAATGCAC 60.181 43.478 0.00 0.00 36.32 4.57
6003 27421 1.003839 CGTGGTGCTGCTCCCTTTA 60.004 57.895 17.31 0.00 0.00 1.85
6037 27457 1.512926 AAGCTGCACTCGTAACAAGG 58.487 50.000 1.02 0.00 0.00 3.61
6048 27468 4.713321 ACTCGTAACAAGGGGCTTCTATTA 59.287 41.667 0.00 0.00 0.00 0.98
6056 27476 4.796110 AGGGGCTTCTATTAATGCTCAA 57.204 40.909 0.00 0.00 0.00 3.02
6141 27567 1.818060 TCCTGCACACATAAACATGCC 59.182 47.619 0.00 0.00 0.00 4.40
6150 27576 5.630680 CACACATAAACATGCCTTTGTCTTC 59.369 40.000 0.00 0.00 0.00 2.87
6175 27601 7.660617 TCAGTTATCTCTACTATTACACGGGAG 59.339 40.741 0.00 0.00 0.00 4.30
6185 27611 1.583495 TACACGGGAGTCTGCTGTCG 61.583 60.000 2.27 2.51 44.67 4.35
6186 27612 2.597805 ACGGGAGTCTGCTGTCGT 60.598 61.111 0.00 0.00 40.62 4.34
6187 27613 2.201022 ACGGGAGTCTGCTGTCGTT 61.201 57.895 0.00 0.00 40.62 3.85
6188 27614 1.734477 CGGGAGTCTGCTGTCGTTG 60.734 63.158 0.00 0.00 0.00 4.10
6189 27615 1.666011 GGGAGTCTGCTGTCGTTGA 59.334 57.895 0.00 0.00 0.00 3.18
6190 27616 0.667792 GGGAGTCTGCTGTCGTTGAC 60.668 60.000 0.00 0.00 0.00 3.18
6191 27617 0.315568 GGAGTCTGCTGTCGTTGACT 59.684 55.000 0.00 0.00 41.76 3.41
6192 27618 1.692296 GAGTCTGCTGTCGTTGACTC 58.308 55.000 6.28 6.28 45.30 3.36
6193 27619 0.039978 AGTCTGCTGTCGTTGACTCG 60.040 55.000 0.00 0.00 35.13 4.18
6232 27658 4.241555 CCTCATTCCCCTCCCGCG 62.242 72.222 0.00 0.00 0.00 6.46
6233 27659 4.241555 CTCATTCCCCTCCCGCGG 62.242 72.222 21.04 21.04 0.00 6.46
6321 27750 2.794103 TCCTGCACACATAAACATGCT 58.206 42.857 0.00 0.00 0.00 3.79
6322 27751 2.488937 TCCTGCACACATAAACATGCTG 59.511 45.455 0.00 0.00 0.00 4.41
6325 27754 3.640592 TGCACACATAAACATGCTGTTG 58.359 40.909 0.00 0.00 40.14 3.33
6331 27760 4.847757 CACATAAACATGCTGTTGTCTTCG 59.152 41.667 0.00 0.00 40.14 3.79
6359 27788 6.939132 TCTCTACTATTAAACGGGAGTCTG 57.061 41.667 0.00 0.00 46.69 3.51
6367 27796 0.687354 AACGGGAGTCTGCTGTCATT 59.313 50.000 6.26 0.00 46.69 2.57
6371 27800 2.622436 GGGAGTCTGCTGTCATTGTAC 58.378 52.381 0.00 0.00 0.00 2.90
6372 27801 2.622436 GGAGTCTGCTGTCATTGTACC 58.378 52.381 0.00 0.00 0.00 3.34
6373 27802 2.028112 GGAGTCTGCTGTCATTGTACCA 60.028 50.000 0.00 0.00 0.00 3.25
6374 27803 3.369892 GGAGTCTGCTGTCATTGTACCAT 60.370 47.826 0.00 0.00 0.00 3.55
6375 27804 3.603532 AGTCTGCTGTCATTGTACCATG 58.396 45.455 0.43 0.43 0.00 3.66
6376 27805 3.261643 AGTCTGCTGTCATTGTACCATGA 59.738 43.478 5.55 5.55 0.00 3.07
6377 27806 3.620374 GTCTGCTGTCATTGTACCATGAG 59.380 47.826 9.77 1.49 0.00 2.90
6378 27807 2.353889 CTGCTGTCATTGTACCATGAGC 59.646 50.000 9.77 11.03 0.00 4.26
6379 27808 2.290197 TGCTGTCATTGTACCATGAGCA 60.290 45.455 15.67 15.67 0.00 4.26
6380 27809 2.947652 GCTGTCATTGTACCATGAGCAT 59.052 45.455 9.77 0.00 0.00 3.79
6381 27810 3.242969 GCTGTCATTGTACCATGAGCATG 60.243 47.826 9.77 3.50 38.51 4.06
6382 27811 4.193865 CTGTCATTGTACCATGAGCATGA 58.806 43.478 9.77 0.00 41.20 3.07
6383 27812 4.587891 TGTCATTGTACCATGAGCATGAA 58.412 39.130 9.77 0.00 41.20 2.57
6384 27813 4.637091 TGTCATTGTACCATGAGCATGAAG 59.363 41.667 9.77 0.00 41.20 3.02
6385 27814 4.036027 GTCATTGTACCATGAGCATGAAGG 59.964 45.833 9.77 0.85 41.20 3.46
6386 27815 3.998913 TTGTACCATGAGCATGAAGGA 57.001 42.857 11.84 0.00 41.20 3.36
6387 27816 3.266510 TGTACCATGAGCATGAAGGAC 57.733 47.619 11.84 3.99 41.20 3.85
6388 27817 2.571202 TGTACCATGAGCATGAAGGACA 59.429 45.455 11.84 6.39 41.20 4.02
6389 27818 2.119801 ACCATGAGCATGAAGGACAC 57.880 50.000 11.84 0.00 41.20 3.67
6390 27819 1.012086 CCATGAGCATGAAGGACACG 58.988 55.000 11.84 0.00 41.20 4.49
6391 27820 0.376152 CATGAGCATGAAGGACACGC 59.624 55.000 4.47 0.00 41.20 5.34
6392 27821 1.086067 ATGAGCATGAAGGACACGCG 61.086 55.000 3.53 3.53 42.82 6.01
6393 27822 2.434884 AGCATGAAGGACACGCGG 60.435 61.111 12.47 1.27 42.82 6.46
6394 27823 3.499737 GCATGAAGGACACGCGGG 61.500 66.667 6.92 6.92 0.00 6.13
6395 27824 3.499737 CATGAAGGACACGCGGGC 61.500 66.667 9.12 0.00 0.00 6.13
6396 27825 4.015406 ATGAAGGACACGCGGGCA 62.015 61.111 9.12 0.00 0.00 5.36
6397 27826 3.958147 ATGAAGGACACGCGGGCAG 62.958 63.158 9.12 0.00 0.00 4.85
6398 27827 4.681978 GAAGGACACGCGGGCAGT 62.682 66.667 9.12 0.90 0.00 4.40
6399 27828 4.681978 AAGGACACGCGGGCAGTC 62.682 66.667 9.12 11.51 0.00 3.51
6402 27831 3.755628 GACACGCGGGCAGTCCTA 61.756 66.667 9.12 0.00 0.00 2.94
6403 27832 3.291101 GACACGCGGGCAGTCCTAA 62.291 63.158 9.12 0.00 0.00 2.69
6404 27833 2.186903 CACGCGGGCAGTCCTAAT 59.813 61.111 12.47 0.00 0.00 1.73
6405 27834 1.883084 CACGCGGGCAGTCCTAATC 60.883 63.158 12.47 0.00 0.00 1.75
6406 27835 2.280186 CGCGGGCAGTCCTAATCC 60.280 66.667 0.00 0.00 0.00 3.01
6407 27836 2.797278 CGCGGGCAGTCCTAATCCT 61.797 63.158 0.00 0.00 0.00 3.24
6408 27837 1.527370 GCGGGCAGTCCTAATCCTT 59.473 57.895 0.00 0.00 0.00 3.36
6409 27838 0.815615 GCGGGCAGTCCTAATCCTTG 60.816 60.000 0.00 0.00 0.00 3.61
6410 27839 0.541863 CGGGCAGTCCTAATCCTTGT 59.458 55.000 0.00 0.00 0.00 3.16
6411 27840 1.760613 CGGGCAGTCCTAATCCTTGTA 59.239 52.381 0.00 0.00 0.00 2.41
6412 27841 2.169769 CGGGCAGTCCTAATCCTTGTAA 59.830 50.000 0.00 0.00 0.00 2.41
6413 27842 3.181454 CGGGCAGTCCTAATCCTTGTAAT 60.181 47.826 0.00 0.00 0.00 1.89
6414 27843 4.137543 GGGCAGTCCTAATCCTTGTAATG 58.862 47.826 0.00 0.00 0.00 1.90
6415 27844 4.385310 GGGCAGTCCTAATCCTTGTAATGT 60.385 45.833 0.00 0.00 0.00 2.71
6416 27845 4.576463 GGCAGTCCTAATCCTTGTAATGTG 59.424 45.833 0.00 0.00 0.00 3.21
6417 27846 4.576463 GCAGTCCTAATCCTTGTAATGTGG 59.424 45.833 0.00 0.00 0.00 4.17
6418 27847 5.126067 CAGTCCTAATCCTTGTAATGTGGG 58.874 45.833 0.00 0.00 0.00 4.61
6419 27848 5.036916 AGTCCTAATCCTTGTAATGTGGGA 58.963 41.667 0.00 0.00 0.00 4.37
6420 27849 5.131142 AGTCCTAATCCTTGTAATGTGGGAG 59.869 44.000 0.00 0.00 0.00 4.30
6421 27850 5.036916 TCCTAATCCTTGTAATGTGGGAGT 58.963 41.667 0.00 0.00 0.00 3.85
6422 27851 5.491078 TCCTAATCCTTGTAATGTGGGAGTT 59.509 40.000 0.00 0.00 0.00 3.01
6423 27852 5.590259 CCTAATCCTTGTAATGTGGGAGTTG 59.410 44.000 0.00 0.00 0.00 3.16
6424 27853 4.657814 ATCCTTGTAATGTGGGAGTTGT 57.342 40.909 0.00 0.00 0.00 3.32
6425 27854 3.750371 TCCTTGTAATGTGGGAGTTGTG 58.250 45.455 0.00 0.00 0.00 3.33
6426 27855 2.819608 CCTTGTAATGTGGGAGTTGTGG 59.180 50.000 0.00 0.00 0.00 4.17
6427 27856 3.497763 CCTTGTAATGTGGGAGTTGTGGA 60.498 47.826 0.00 0.00 0.00 4.02
6428 27857 3.866703 TGTAATGTGGGAGTTGTGGAA 57.133 42.857 0.00 0.00 0.00 3.53
6429 27858 4.171878 TGTAATGTGGGAGTTGTGGAAA 57.828 40.909 0.00 0.00 0.00 3.13
6430 27859 3.886505 TGTAATGTGGGAGTTGTGGAAAC 59.113 43.478 0.00 0.00 0.00 2.78
6431 27860 2.746279 ATGTGGGAGTTGTGGAAACA 57.254 45.000 0.00 0.00 38.70 2.83
6441 27870 4.336581 TGGAAACACTGAGACGCG 57.663 55.556 3.53 3.53 33.40 6.01
6442 27871 1.737201 TGGAAACACTGAGACGCGA 59.263 52.632 15.93 0.00 33.40 5.87
6443 27872 0.317160 TGGAAACACTGAGACGCGAT 59.683 50.000 15.93 0.00 33.40 4.58
6444 27873 1.542472 TGGAAACACTGAGACGCGATA 59.458 47.619 15.93 0.00 33.40 2.92
6445 27874 2.186076 GGAAACACTGAGACGCGATAG 58.814 52.381 15.93 7.64 0.00 2.08
6446 27875 2.415625 GGAAACACTGAGACGCGATAGT 60.416 50.000 15.93 8.34 39.35 2.12
6447 27876 6.905254 TGGAAACACTGAGACGCGATAGTG 62.905 50.000 15.93 21.50 45.35 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.223971 CCAGGTACGCCTAATACACAGG 60.224 54.545 0.00 0.00 44.97 4.00
1 2 2.223971 CCCAGGTACGCCTAATACACAG 60.224 54.545 0.00 0.00 44.97 3.66
2 3 1.758280 CCCAGGTACGCCTAATACACA 59.242 52.381 0.00 0.00 44.97 3.72
3 4 1.539712 GCCCAGGTACGCCTAATACAC 60.540 57.143 0.00 0.00 44.97 2.90
4 5 0.754472 GCCCAGGTACGCCTAATACA 59.246 55.000 0.00 0.00 44.97 2.29
5 6 0.319297 CGCCCAGGTACGCCTAATAC 60.319 60.000 0.00 0.00 44.97 1.89
7 8 2.803817 CCGCCCAGGTACGCCTAAT 61.804 63.158 0.00 0.00 44.97 1.73
8 9 3.463585 CCGCCCAGGTACGCCTAA 61.464 66.667 0.00 0.00 44.97 2.69
27 28 0.109132 GATCAAAAAGGCCAGCACGG 60.109 55.000 5.01 0.00 38.11 4.94
28 29 0.454957 CGATCAAAAAGGCCAGCACG 60.455 55.000 5.01 0.00 0.00 5.34
30 31 1.177895 TGCGATCAAAAAGGCCAGCA 61.178 50.000 5.01 0.00 0.00 4.41
31 32 0.733909 GTGCGATCAAAAAGGCCAGC 60.734 55.000 5.01 0.00 0.00 4.85
32 33 0.454957 CGTGCGATCAAAAAGGCCAG 60.455 55.000 5.01 0.00 0.00 4.85
33 34 1.169661 ACGTGCGATCAAAAAGGCCA 61.170 50.000 5.01 0.00 0.00 5.36
76 2714 4.529731 GCTGGGAATGGGGGAGCC 62.530 72.222 0.00 0.00 0.00 4.70
252 2924 1.723542 GAGAGATTCAGCACACACACG 59.276 52.381 0.00 0.00 0.00 4.49
270 2945 7.118496 ACAATTTCATCAGTACTCTAGGGAG 57.882 40.000 0.00 0.00 44.62 4.30
271 2946 7.496346 AACAATTTCATCAGTACTCTAGGGA 57.504 36.000 0.00 0.00 0.00 4.20
310 2985 3.168193 ACCGTAATCCGTAAACGTAACG 58.832 45.455 14.51 14.51 40.01 3.18
355 3037 6.568844 CGACAGTGATAACTTATCTAGGAGCC 60.569 46.154 9.69 0.00 36.17 4.70
358 3040 5.049612 CGCGACAGTGATAACTTATCTAGGA 60.050 44.000 0.00 0.00 36.17 2.94
368 3050 1.349259 AACGGCGCGACAGTGATAAC 61.349 55.000 14.85 0.00 0.00 1.89
451 3133 6.364435 GCAAGAAAATTAAGCTTTCAGTCCAG 59.636 38.462 3.20 0.00 35.62 3.86
644 3427 2.050350 CCCTTGCTGATGCCACCTG 61.050 63.158 0.00 0.00 38.71 4.00
647 3430 1.610554 ATTGCCCTTGCTGATGCCAC 61.611 55.000 0.00 0.00 38.71 5.01
759 3547 4.369182 CGAGTTGTAGAAACTCTGGTGTT 58.631 43.478 14.40 0.00 43.28 3.32
985 3827 5.056480 CAGTTCCATCCTTTTTGTTTTCCC 58.944 41.667 0.00 0.00 0.00 3.97
1561 4468 5.294552 GCAAGTTGGTGTAGGCTAAAGATAG 59.705 44.000 4.75 0.00 0.00 2.08
1784 4699 0.824759 GGAAGCACCGGACACTATCT 59.175 55.000 9.46 0.00 0.00 1.98
1835 4750 6.490040 CGGGGATGGTAAAATAAGATGACATT 59.510 38.462 0.00 0.00 0.00 2.71
1848 4763 1.249407 GTTTGTGCGGGGATGGTAAA 58.751 50.000 0.00 0.00 0.00 2.01
1857 4772 1.268625 GAAGGTTAAGGTTTGTGCGGG 59.731 52.381 0.00 0.00 0.00 6.13
2278 5220 7.067859 ACCATAGTTACTCTTTACGTCATGCTA 59.932 37.037 0.00 0.00 0.00 3.49
2569 5601 9.362151 ACAAGGAACAAAAATCTAAGTCCATTA 57.638 29.630 0.00 0.00 0.00 1.90
2704 5739 1.914634 CAGCCAGTAGTAGAACAGCG 58.085 55.000 0.00 0.00 0.00 5.18
2828 5863 3.008375 TGTGAACCTTTCTCCCATCTCAG 59.992 47.826 0.00 0.00 0.00 3.35
2910 5945 7.178274 ACTGGCATAGGAAATTACATCAACAAA 59.822 33.333 0.00 0.00 0.00 2.83
2934 5969 8.114331 TGAATGTATGCAGAAAGATTTTCACT 57.886 30.769 0.00 0.00 0.00 3.41
3084 6129 4.158025 TCGGTTGAGGTGAGAACTATCTTC 59.842 45.833 0.00 0.00 35.54 2.87
3085 6130 4.087182 TCGGTTGAGGTGAGAACTATCTT 58.913 43.478 0.00 0.00 35.54 2.40
3086 6131 3.698289 TCGGTTGAGGTGAGAACTATCT 58.302 45.455 0.00 0.00 39.10 1.98
3087 6132 4.451629 TTCGGTTGAGGTGAGAACTATC 57.548 45.455 0.00 0.00 0.00 2.08
3088 6133 4.884668 TTTCGGTTGAGGTGAGAACTAT 57.115 40.909 0.00 0.00 0.00 2.12
3089 6134 4.675976 TTTTCGGTTGAGGTGAGAACTA 57.324 40.909 0.00 0.00 0.00 2.24
3091 6136 5.934935 TTATTTTCGGTTGAGGTGAGAAC 57.065 39.130 0.00 0.00 0.00 3.01
3092 6137 6.945938 TTTTATTTTCGGTTGAGGTGAGAA 57.054 33.333 0.00 0.00 0.00 2.87
3093 6138 6.945938 TTTTTATTTTCGGTTGAGGTGAGA 57.054 33.333 0.00 0.00 0.00 3.27
3094 6139 7.145323 ACATTTTTATTTTCGGTTGAGGTGAG 58.855 34.615 0.00 0.00 0.00 3.51
3095 6140 7.045126 ACATTTTTATTTTCGGTTGAGGTGA 57.955 32.000 0.00 0.00 0.00 4.02
3096 6141 7.707774 AACATTTTTATTTTCGGTTGAGGTG 57.292 32.000 0.00 0.00 0.00 4.00
3108 6153 9.783256 GACGGAGCAAGTATAACATTTTTATTT 57.217 29.630 0.00 0.00 0.00 1.40
3109 6154 9.174166 AGACGGAGCAAGTATAACATTTTTATT 57.826 29.630 0.00 0.00 0.00 1.40
3110 6155 8.732746 AGACGGAGCAAGTATAACATTTTTAT 57.267 30.769 0.00 0.00 0.00 1.40
3111 6156 8.556213 AAGACGGAGCAAGTATAACATTTTTA 57.444 30.769 0.00 0.00 0.00 1.52
3112 6157 7.448748 AAGACGGAGCAAGTATAACATTTTT 57.551 32.000 0.00 0.00 0.00 1.94
3113 6158 7.201617 GCTAAGACGGAGCAAGTATAACATTTT 60.202 37.037 0.00 0.00 39.84 1.82
3114 6159 6.258068 GCTAAGACGGAGCAAGTATAACATTT 59.742 38.462 0.00 0.00 39.84 2.32
3115 6160 5.753921 GCTAAGACGGAGCAAGTATAACATT 59.246 40.000 0.00 0.00 39.84 2.71
3116 6161 5.163447 TGCTAAGACGGAGCAAGTATAACAT 60.163 40.000 2.22 0.00 46.71 2.71
3117 6162 4.158949 TGCTAAGACGGAGCAAGTATAACA 59.841 41.667 2.22 0.00 46.71 2.41
3118 6163 4.679662 TGCTAAGACGGAGCAAGTATAAC 58.320 43.478 2.22 0.00 46.71 1.89
3119 6164 4.994907 TGCTAAGACGGAGCAAGTATAA 57.005 40.909 2.22 0.00 46.71 0.98
3127 6172 2.656560 TCTTCTTGCTAAGACGGAGC 57.343 50.000 0.00 0.00 37.23 4.70
3128 6173 7.206687 AGAATTATCTTCTTGCTAAGACGGAG 58.793 38.462 0.00 0.00 38.28 4.63
3129 6174 7.113658 AGAATTATCTTCTTGCTAAGACGGA 57.886 36.000 0.00 0.00 38.28 4.69
3130 6175 6.980978 TGAGAATTATCTTCTTGCTAAGACGG 59.019 38.462 1.19 0.00 38.28 4.79
3131 6176 7.043059 GGTGAGAATTATCTTCTTGCTAAGACG 60.043 40.741 1.19 0.00 38.28 4.18
3132 6177 7.984617 AGGTGAGAATTATCTTCTTGCTAAGAC 59.015 37.037 1.19 0.00 38.28 3.01
3133 6178 8.083828 AGGTGAGAATTATCTTCTTGCTAAGA 57.916 34.615 1.19 0.00 39.71 2.10
3134 6179 7.984050 TGAGGTGAGAATTATCTTCTTGCTAAG 59.016 37.037 1.19 0.00 35.54 2.18
3135 6180 7.851228 TGAGGTGAGAATTATCTTCTTGCTAA 58.149 34.615 1.19 0.00 35.54 3.09
3136 6181 7.423844 TGAGGTGAGAATTATCTTCTTGCTA 57.576 36.000 1.19 0.00 35.54 3.49
3137 6182 6.305272 TGAGGTGAGAATTATCTTCTTGCT 57.695 37.500 1.19 0.00 35.54 3.91
3138 6183 6.597280 AGTTGAGGTGAGAATTATCTTCTTGC 59.403 38.462 1.19 0.00 35.54 4.01
3139 6184 7.821359 TCAGTTGAGGTGAGAATTATCTTCTTG 59.179 37.037 1.19 0.00 35.54 3.02
3140 6185 7.911651 TCAGTTGAGGTGAGAATTATCTTCTT 58.088 34.615 1.19 0.00 35.54 2.52
3141 6186 7.487822 TCAGTTGAGGTGAGAATTATCTTCT 57.512 36.000 1.19 0.00 35.54 2.85
3215 6345 3.217626 CCTTGATCCTAGCATTTGACCC 58.782 50.000 0.00 0.00 0.00 4.46
3217 6347 3.065925 GTGCCTTGATCCTAGCATTTGAC 59.934 47.826 4.24 0.00 37.60 3.18
3218 6348 3.282021 GTGCCTTGATCCTAGCATTTGA 58.718 45.455 4.24 0.00 37.60 2.69
3219 6349 3.018856 TGTGCCTTGATCCTAGCATTTG 58.981 45.455 4.24 0.00 37.60 2.32
3231 6361 4.262549 CCAGAAATTTCCAATGTGCCTTGA 60.263 41.667 14.61 0.00 0.00 3.02
3281 10153 7.072177 TCGCATTCAATTCACTAGGTTTTAG 57.928 36.000 0.00 0.00 0.00 1.85
3307 10179 4.681483 GGCAATAAGTGTGCAAAAAGAGTC 59.319 41.667 0.00 0.00 44.07 3.36
3374 10252 2.104451 AGCAGCGAGATGATGGAAAGAT 59.896 45.455 0.00 0.00 33.55 2.40
3448 10326 7.120285 ACAAGCTGCTGTATAAGGCAATATATG 59.880 37.037 1.35 0.00 38.02 1.78
3704 10584 0.950836 CCGACACACCTTTGCATGAA 59.049 50.000 0.00 0.00 0.00 2.57
3877 10774 8.134202 TCAGTCTATCCAAAACTAGATCAACA 57.866 34.615 0.00 0.00 0.00 3.33
4321 11834 2.120232 CGGCTGAATTCGCTACTACAG 58.880 52.381 17.53 0.00 0.00 2.74
4607 13129 5.245075 TGCATTTACCCCTTTTCTTTGGTAG 59.755 40.000 0.00 0.00 34.96 3.18
4672 13195 5.818678 TGATGTTACTTGGAACCTACACT 57.181 39.130 0.00 0.00 0.00 3.55
4967 17619 5.903764 CCAATACACAACATTGGTGTTTG 57.096 39.130 4.15 7.61 46.75 2.93
4990 17642 5.540400 TTACGGAGGGAGTATTATGTTGG 57.460 43.478 0.00 0.00 0.00 3.77
5380 25718 4.346129 CTTCTCGGTTGATTATTGCTTGC 58.654 43.478 0.00 0.00 0.00 4.01
5565 25924 8.229253 TGGACTAGCAACGAATAATCTTACTA 57.771 34.615 0.00 0.00 0.00 1.82
5566 25925 7.108841 TGGACTAGCAACGAATAATCTTACT 57.891 36.000 0.00 0.00 0.00 2.24
5567 25926 7.948278 ATGGACTAGCAACGAATAATCTTAC 57.052 36.000 0.00 0.00 0.00 2.34
5595 26003 5.334105 CCCTATCGAGCAAATAACCAAATCG 60.334 44.000 0.00 0.00 0.00 3.34
5650 26062 4.221041 ACCTGGAGACTAGAAACTTACAGC 59.779 45.833 0.00 0.00 0.00 4.40
5651 26063 5.986501 ACCTGGAGACTAGAAACTTACAG 57.013 43.478 0.00 6.04 0.00 2.74
5759 26183 3.650281 ATTATCTGCACATGGACCACA 57.350 42.857 0.00 0.00 0.00 4.17
5760 26184 6.639632 AATAATTATCTGCACATGGACCAC 57.360 37.500 0.00 0.00 0.00 4.16
5887 26318 7.930217 AGGATCAAATGTGTTGTATATTTCCG 58.070 34.615 0.00 0.00 28.88 4.30
5962 27375 2.826128 TGAGCACTGACTAACTACCCAG 59.174 50.000 0.00 0.00 0.00 4.45
6003 27421 5.301805 AGTGCAGCTTTAACATGGTTTAGTT 59.698 36.000 0.00 0.00 0.00 2.24
6037 27457 5.590259 TGTCTTTGAGCATTAATAGAAGCCC 59.410 40.000 0.00 0.00 0.00 5.19
6048 27468 5.796424 AAAACTCCATGTCTTTGAGCATT 57.204 34.783 0.00 0.00 0.00 3.56
6074 27496 5.734720 ACTAACTCCATGTCAAATGATCGT 58.265 37.500 0.00 0.00 0.00 3.73
6075 27497 6.980978 ACTACTAACTCCATGTCAAATGATCG 59.019 38.462 0.00 0.00 0.00 3.69
6076 27498 7.766278 ACACTACTAACTCCATGTCAAATGATC 59.234 37.037 0.00 0.00 0.00 2.92
6077 27499 7.624549 ACACTACTAACTCCATGTCAAATGAT 58.375 34.615 0.00 0.00 0.00 2.45
6078 27500 7.004555 ACACTACTAACTCCATGTCAAATGA 57.995 36.000 0.00 0.00 0.00 2.57
6079 27501 7.387673 TCAACACTACTAACTCCATGTCAAATG 59.612 37.037 0.00 0.00 0.00 2.32
6080 27502 7.450074 TCAACACTACTAACTCCATGTCAAAT 58.550 34.615 0.00 0.00 0.00 2.32
6084 27510 6.366332 CACTTCAACACTACTAACTCCATGTC 59.634 42.308 0.00 0.00 0.00 3.06
6150 27576 7.444792 ACTCCCGTGTAATAGTAGAGATAACTG 59.555 40.741 0.00 0.00 0.00 3.16
6170 27596 1.734477 CAACGACAGCAGACTCCCG 60.734 63.158 0.00 0.00 0.00 5.14
6175 27601 0.317938 ACGAGTCAACGACAGCAGAC 60.318 55.000 0.00 0.00 34.60 3.51
6185 27611 3.250040 AGCAACCATTACAACGAGTCAAC 59.750 43.478 0.00 0.00 0.00 3.18
6186 27612 3.472652 AGCAACCATTACAACGAGTCAA 58.527 40.909 0.00 0.00 0.00 3.18
6187 27613 3.120321 AGCAACCATTACAACGAGTCA 57.880 42.857 0.00 0.00 0.00 3.41
6188 27614 3.496884 TGAAGCAACCATTACAACGAGTC 59.503 43.478 0.00 0.00 0.00 3.36
6189 27615 3.472652 TGAAGCAACCATTACAACGAGT 58.527 40.909 0.00 0.00 0.00 4.18
6190 27616 4.024048 AGTTGAAGCAACCATTACAACGAG 60.024 41.667 6.67 0.00 44.49 4.18
6191 27617 3.880490 AGTTGAAGCAACCATTACAACGA 59.120 39.130 6.67 0.00 44.49 3.85
6192 27618 4.219033 GAGTTGAAGCAACCATTACAACG 58.781 43.478 6.67 0.00 44.49 4.10
6193 27619 4.546570 GGAGTTGAAGCAACCATTACAAC 58.453 43.478 6.67 0.00 44.49 3.32
6270 27699 5.986135 AGAAGCACTTCAACACTACTAACTG 59.014 40.000 12.65 0.00 41.84 3.16
6300 27729 3.057386 CAGCATGTTTATGTGTGCAGGAA 60.057 43.478 0.00 0.00 39.94 3.36
6321 27750 7.876936 ATAGTAGAGATAACCGAAGACAACA 57.123 36.000 0.00 0.00 0.00 3.33
6325 27754 9.379811 CGTTTAATAGTAGAGATAACCGAAGAC 57.620 37.037 0.00 0.00 0.00 3.01
6331 27760 8.175925 ACTCCCGTTTAATAGTAGAGATAACC 57.824 38.462 0.00 0.00 0.00 2.85
6371 27800 1.012086 CGTGTCCTTCATGCTCATGG 58.988 55.000 9.69 0.00 39.24 3.66
6378 27807 3.499737 GCCCGCGTGTCCTTCATG 61.500 66.667 4.92 0.00 36.25 3.07
6379 27808 3.958147 CTGCCCGCGTGTCCTTCAT 62.958 63.158 4.92 0.00 0.00 2.57
6380 27809 4.680237 CTGCCCGCGTGTCCTTCA 62.680 66.667 4.92 0.00 0.00 3.02
6381 27810 4.681978 ACTGCCCGCGTGTCCTTC 62.682 66.667 4.92 0.00 0.00 3.46
6382 27811 4.681978 GACTGCCCGCGTGTCCTT 62.682 66.667 4.92 0.00 0.00 3.36
6385 27814 2.573609 ATTAGGACTGCCCGCGTGTC 62.574 60.000 4.92 7.75 40.87 3.67
6386 27815 2.573609 GATTAGGACTGCCCGCGTGT 62.574 60.000 4.92 0.00 40.87 4.49
6387 27816 1.883084 GATTAGGACTGCCCGCGTG 60.883 63.158 4.92 0.00 40.87 5.34
6388 27817 2.499685 GATTAGGACTGCCCGCGT 59.500 61.111 4.92 0.00 40.87 6.01
6389 27818 2.280186 GGATTAGGACTGCCCGCG 60.280 66.667 0.00 0.00 40.87 6.46
6390 27819 0.815615 CAAGGATTAGGACTGCCCGC 60.816 60.000 0.00 0.00 40.87 6.13
6391 27820 0.541863 ACAAGGATTAGGACTGCCCG 59.458 55.000 0.00 0.00 40.87 6.13
6392 27821 3.926058 TTACAAGGATTAGGACTGCCC 57.074 47.619 0.00 0.00 33.31 5.36
6393 27822 4.576463 CACATTACAAGGATTAGGACTGCC 59.424 45.833 0.00 0.00 0.00 4.85
6394 27823 4.576463 CCACATTACAAGGATTAGGACTGC 59.424 45.833 0.00 0.00 0.00 4.40
6395 27824 5.104527 TCCCACATTACAAGGATTAGGACTG 60.105 44.000 0.00 0.00 0.00 3.51
6396 27825 5.036916 TCCCACATTACAAGGATTAGGACT 58.963 41.667 0.00 0.00 0.00 3.85
6397 27826 5.104485 ACTCCCACATTACAAGGATTAGGAC 60.104 44.000 0.00 0.00 0.00 3.85
6398 27827 5.036916 ACTCCCACATTACAAGGATTAGGA 58.963 41.667 0.00 0.00 0.00 2.94
6399 27828 5.373812 ACTCCCACATTACAAGGATTAGG 57.626 43.478 0.00 0.00 0.00 2.69
6400 27829 6.094048 CACAACTCCCACATTACAAGGATTAG 59.906 42.308 0.00 0.00 0.00 1.73
6401 27830 5.943416 CACAACTCCCACATTACAAGGATTA 59.057 40.000 0.00 0.00 0.00 1.75
6402 27831 4.766891 CACAACTCCCACATTACAAGGATT 59.233 41.667 0.00 0.00 0.00 3.01
6403 27832 4.335416 CACAACTCCCACATTACAAGGAT 58.665 43.478 0.00 0.00 0.00 3.24
6404 27833 3.497763 CCACAACTCCCACATTACAAGGA 60.498 47.826 0.00 0.00 0.00 3.36
6405 27834 2.819608 CCACAACTCCCACATTACAAGG 59.180 50.000 0.00 0.00 0.00 3.61
6406 27835 3.750371 TCCACAACTCCCACATTACAAG 58.250 45.455 0.00 0.00 0.00 3.16
6407 27836 3.866703 TCCACAACTCCCACATTACAA 57.133 42.857 0.00 0.00 0.00 2.41
6408 27837 3.866703 TTCCACAACTCCCACATTACA 57.133 42.857 0.00 0.00 0.00 2.41
6409 27838 3.886505 TGTTTCCACAACTCCCACATTAC 59.113 43.478 0.00 0.00 0.00 1.89
6410 27839 3.886505 GTGTTTCCACAACTCCCACATTA 59.113 43.478 0.00 0.00 41.44 1.90
6411 27840 2.693074 GTGTTTCCACAACTCCCACATT 59.307 45.455 0.00 0.00 41.44 2.71
6412 27841 2.091885 AGTGTTTCCACAACTCCCACAT 60.092 45.455 0.00 0.00 44.39 3.21
6413 27842 1.283613 AGTGTTTCCACAACTCCCACA 59.716 47.619 0.00 0.00 44.39 4.17
6414 27843 1.676006 CAGTGTTTCCACAACTCCCAC 59.324 52.381 0.00 0.00 44.39 4.61
6415 27844 1.562008 TCAGTGTTTCCACAACTCCCA 59.438 47.619 0.00 0.00 44.39 4.37
6416 27845 2.158813 TCTCAGTGTTTCCACAACTCCC 60.159 50.000 0.00 0.00 44.39 4.30
6417 27846 2.872858 GTCTCAGTGTTTCCACAACTCC 59.127 50.000 0.00 0.00 44.39 3.85
6418 27847 2.540101 CGTCTCAGTGTTTCCACAACTC 59.460 50.000 0.00 0.00 44.39 3.01
6419 27848 2.550978 CGTCTCAGTGTTTCCACAACT 58.449 47.619 0.00 0.00 44.39 3.16
6420 27849 1.003866 GCGTCTCAGTGTTTCCACAAC 60.004 52.381 0.00 0.00 44.39 3.32
6421 27850 1.295792 GCGTCTCAGTGTTTCCACAA 58.704 50.000 0.00 0.00 44.39 3.33
6422 27851 0.874175 CGCGTCTCAGTGTTTCCACA 60.874 55.000 0.00 0.00 44.39 4.17
6423 27852 0.596600 TCGCGTCTCAGTGTTTCCAC 60.597 55.000 5.77 0.00 42.17 4.02
6424 27853 0.317160 ATCGCGTCTCAGTGTTTCCA 59.683 50.000 5.77 0.00 0.00 3.53
6425 27854 2.186076 CTATCGCGTCTCAGTGTTTCC 58.814 52.381 5.77 0.00 0.00 3.13
6426 27855 2.594654 CACTATCGCGTCTCAGTGTTTC 59.405 50.000 5.77 0.00 34.91 2.78
6427 27856 2.228103 TCACTATCGCGTCTCAGTGTTT 59.772 45.455 21.82 0.00 39.50 2.83
6428 27857 1.810755 TCACTATCGCGTCTCAGTGTT 59.189 47.619 21.82 0.00 39.50 3.32
6429 27858 1.450025 TCACTATCGCGTCTCAGTGT 58.550 50.000 21.82 6.84 39.50 3.55
6430 27859 2.544480 TTCACTATCGCGTCTCAGTG 57.456 50.000 18.91 18.91 39.79 3.66
6431 27860 3.784701 ATTTCACTATCGCGTCTCAGT 57.215 42.857 5.77 2.28 0.00 3.41
6432 27861 4.105486 TCAATTTCACTATCGCGTCTCAG 58.895 43.478 5.77 1.59 0.00 3.35
6433 27862 4.104696 TCAATTTCACTATCGCGTCTCA 57.895 40.909 5.77 0.00 0.00 3.27
6434 27863 5.427082 CATTCAATTTCACTATCGCGTCTC 58.573 41.667 5.77 0.00 0.00 3.36
6435 27864 5.395325 CATTCAATTTCACTATCGCGTCT 57.605 39.130 5.77 0.00 0.00 4.18


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

AutoCloner maintained by Alex Coulton.