Multiple sequence alignment - TraesCS5D01G430800

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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 TraesCS5D01G430800 chr5D 100.000 8011 0 0 1 8011 487988161 487980151 0.000000e+00 14794.0
1 TraesCS5D01G430800 chr5D 83.478 230 23 7 3071 3285 487982925 487982696 4.900000e-47 200.0
2 TraesCS5D01G430800 chr5D 83.478 230 23 7 5237 5466 487985091 487984877 4.900000e-47 200.0
3 TraesCS5D01G430800 chr5D 100.000 38 0 0 7499 7536 487980626 487980589 4.010000e-08 71.3
4 TraesCS5D01G430800 chr5D 100.000 38 0 0 7536 7573 487980663 487980626 4.010000e-08 71.3
5 TraesCS5D01G430800 chr5A 96.743 7461 167 27 1 7426 608708434 608701015 0.000000e+00 12362.0
6 TraesCS5D01G430800 chr5A 85.944 498 40 15 7536 8011 608700911 608700422 9.280000e-139 505.0
7 TraesCS5D01G430800 chr5A 81.283 561 84 15 6309 6862 608806834 608806288 1.230000e-117 435.0
8 TraesCS5D01G430800 chr5A 91.707 205 9 4 1005 1201 444593095 444593299 2.200000e-70 278.0
9 TraesCS5D01G430800 chr5A 95.906 171 7 0 2059 2229 585001810 585001640 2.200000e-70 278.0
10 TraesCS5D01G430800 chr5A 84.348 230 21 8 5237 5466 608705355 608705141 2.270000e-50 211.0
11 TraesCS5D01G430800 chr5A 93.939 132 6 1 7405 7536 608701003 608700874 1.760000e-46 198.0
12 TraesCS5D01G430800 chr5A 82.609 230 25 7 3071 3285 608703174 608702945 1.060000e-43 189.0
13 TraesCS5D01G430800 chr5A 80.000 140 24 4 5544 5682 494876218 494876354 5.120000e-17 100.0
14 TraesCS5D01G430800 chr5B 97.287 2506 61 4 4585 7085 600643984 600641481 0.000000e+00 4244.0
15 TraesCS5D01G430800 chr5B 97.973 1480 25 5 1 1478 600650218 600648742 0.000000e+00 2562.0
16 TraesCS5D01G430800 chr5B 96.640 1399 39 6 2707 4102 600647500 600646107 0.000000e+00 2316.0
17 TraesCS5D01G430800 chr5B 97.258 1167 27 4 1551 2712 600648744 600647578 0.000000e+00 1973.0
18 TraesCS5D01G430800 chr5B 93.345 571 22 6 4089 4643 600644552 600643982 0.000000e+00 830.0
19 TraesCS5D01G430800 chr5B 92.961 483 23 7 7536 8011 600641115 600640637 0.000000e+00 693.0
20 TraesCS5D01G430800 chr5B 92.381 420 19 5 7119 7536 600641486 600641078 3.220000e-163 586.0
21 TraesCS5D01G430800 chr5B 83.043 230 24 7 3071 3285 600643333 600643104 2.280000e-45 195.0
22 TraesCS5D01G430800 chr5B 81.092 238 30 8 5237 5474 600647137 600646915 8.260000e-40 176.0
23 TraesCS5D01G430800 chr6D 82.731 886 117 29 3803 4665 194228677 194227805 0.000000e+00 756.0
24 TraesCS5D01G430800 chr6D 84.021 751 100 20 3818 4559 200400292 200399553 0.000000e+00 704.0
25 TraesCS5D01G430800 chr6D 97.619 168 3 1 2058 2224 392278576 392278743 3.660000e-73 287.0
26 TraesCS5D01G430800 chr6D 76.882 186 33 8 5525 5705 65646351 65646171 6.620000e-16 97.1
27 TraesCS5D01G430800 chr6A 84.404 763 103 15 3803 4559 268963635 268962883 0.000000e+00 736.0
28 TraesCS5D01G430800 chr2B 81.735 876 140 18 3803 4665 275228784 275229652 0.000000e+00 713.0
29 TraesCS5D01G430800 chr2B 96.571 175 4 2 2059 2232 659694467 659694640 1.020000e-73 289.0
30 TraesCS5D01G430800 chr2B 77.419 186 35 7 5525 5706 795984302 795984120 3.950000e-18 104.0
31 TraesCS5D01G430800 chr2B 100.000 31 0 0 1167 1197 97191051 97191021 3.120000e-04 58.4
32 TraesCS5D01G430800 chr6B 81.900 884 118 26 3803 4665 387110002 387109140 0.000000e+00 708.0
33 TraesCS5D01G430800 chr6B 77.626 219 32 8 4463 4665 293110844 293110627 5.080000e-22 117.0
34 TraesCS5D01G430800 chr2D 80.791 885 138 27 3802 4663 248864665 248865540 0.000000e+00 664.0
35 TraesCS5D01G430800 chr2D 90.050 201 14 6 2061 2259 449420193 449419997 1.030000e-63 255.0
36 TraesCS5D01G430800 chr2D 84.536 97 14 1 5903 5999 506776633 506776538 2.380000e-15 95.3
37 TraesCS5D01G430800 chr4D 82.166 757 116 19 3802 4549 334664128 334664874 4.080000e-177 632.0
38 TraesCS5D01G430800 chr4D 92.347 196 13 2 1005 1199 432585168 432584974 2.200000e-70 278.0
39 TraesCS5D01G430800 chr4D 92.857 112 5 1 832 943 432585946 432585838 8.320000e-35 159.0
40 TraesCS5D01G430800 chr7A 79.865 889 142 30 3803 4666 442411591 442410715 4.110000e-172 616.0
41 TraesCS5D01G430800 chr7A 77.436 390 67 12 1250 1626 348318137 348318518 6.300000e-51 213.0
42 TraesCS5D01G430800 chr7A 97.248 109 3 0 832 940 263351599 263351707 1.370000e-42 185.0
43 TraesCS5D01G430800 chr7A 93.069 101 7 0 1012 1112 263352408 263352508 1.800000e-31 148.0
44 TraesCS5D01G430800 chr3D 95.876 194 7 1 1005 1197 277606398 277606205 6.040000e-81 313.0
45 TraesCS5D01G430800 chr3D 88.889 90 10 0 5903 5992 523157470 523157381 2.360000e-20 111.0
46 TraesCS5D01G430800 chr3D 77.838 185 34 5 5522 5704 199205969 199205790 3.060000e-19 108.0
47 TraesCS5D01G430800 chr3D 98.214 56 0 1 950 1004 277606478 277606423 6.620000e-16 97.1
48 TraesCS5D01G430800 chr3D 95.122 41 2 0 4628 4668 473489622 473489582 1.870000e-06 65.8
49 TraesCS5D01G430800 chr7D 94.872 195 7 3 1005 1198 166199211 166199019 1.310000e-77 302.0
50 TraesCS5D01G430800 chr7D 96.429 168 6 0 2059 2226 598525680 598525847 2.200000e-70 278.0
51 TraesCS5D01G430800 chr7D 95.122 164 8 0 2059 2222 150128947 150129110 7.980000e-65 259.0
52 TraesCS5D01G430800 chr7D 78.272 382 62 15 1259 1626 316380867 316380493 8.090000e-55 226.0
53 TraesCS5D01G430800 chr7D 92.982 114 5 2 831 943 166200016 166199905 6.430000e-36 163.0
54 TraesCS5D01G430800 chr7D 100.000 55 0 0 950 1004 166199290 166199236 1.420000e-17 102.0
55 TraesCS5D01G430800 chr7D 85.567 97 10 4 5896 5989 71314553 71314458 1.840000e-16 99.0
56 TraesCS5D01G430800 chr4A 94.845 194 6 4 1006 1197 714558805 714558996 4.700000e-77 300.0
57 TraesCS5D01G430800 chr4A 90.323 93 8 1 5896 5987 464695917 464695825 3.930000e-23 121.0
58 TraesCS5D01G430800 chr4A 85.417 96 14 0 4570 4665 291376972 291377067 5.120000e-17 100.0
59 TraesCS5D01G430800 chr4A 94.828 58 1 1 947 1004 714558724 714558779 1.110000e-13 89.8
60 TraesCS5D01G430800 chr3A 93.814 194 9 2 1006 1197 45156314 45156506 1.020000e-73 289.0
61 TraesCS5D01G430800 chr3A 78.804 184 35 3 5522 5704 313499416 313499236 3.930000e-23 121.0
62 TraesCS5D01G430800 chr1D 96.450 169 4 2 1003 1170 335285984 335286151 2.200000e-70 278.0
63 TraesCS5D01G430800 chr1D 96.450 169 5 1 2057 2224 365727163 365727331 2.200000e-70 278.0
64 TraesCS5D01G430800 chr1D 75.385 325 56 17 4357 4665 357467936 357467620 1.400000e-27 135.0
65 TraesCS5D01G430800 chr1D 88.421 95 11 0 5893 5987 141705966 141706060 1.830000e-21 115.0
66 TraesCS5D01G430800 chr1D 85.849 106 7 4 5369 5466 486927455 486927350 1.100000e-18 106.0
67 TraesCS5D01G430800 chr1B 89.706 204 11 4 1003 1199 238981592 238981792 1.330000e-62 252.0
68 TraesCS5D01G430800 chr1B 95.614 114 4 1 830 943 655842404 655842292 1.780000e-41 182.0
69 TraesCS5D01G430800 chr1B 92.035 113 5 1 832 940 238980785 238980897 1.080000e-33 156.0
70 TraesCS5D01G430800 chr1B 88.421 95 11 0 5893 5987 195591190 195591284 1.830000e-21 115.0
71 TraesCS5D01G430800 chr2A 92.035 113 6 3 825 937 93850780 93850671 1.080000e-33 156.0
72 TraesCS5D01G430800 chr2A 91.250 80 7 0 4586 4665 453697224 453697303 8.500000e-20 110.0
73 TraesCS5D01G430800 chr3B 91.150 113 9 1 831 943 263984687 263984576 1.390000e-32 152.0
74 TraesCS5D01G430800 chr3B 79.570 186 36 2 5519 5703 284420448 284420632 1.810000e-26 132.0
75 TraesCS5D01G430800 chr3B 82.540 126 14 5 5349 5466 790639903 790639778 3.950000e-18 104.0
76 TraesCS5D01G430800 chr1A 82.390 159 23 4 5525 5683 64403182 64403335 5.040000e-27 134.0
77 TraesCS5D01G430800 chr1A 87.368 95 12 0 5893 5987 148958984 148958890 8.500000e-20 110.0
78 TraesCS5D01G430800 chr7B 89.552 67 7 0 5404 5470 47797079 47797145 1.430000e-12 86.1
79 TraesCS5D01G430800 chr7B 89.552 67 7 0 5404 5470 47815404 47815470 1.430000e-12 86.1


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 TraesCS5D01G430800 chr5D 487980151 487988161 8010 True 14794.000000 14794 100.000000 1 8011 1 chr5D.!!$R1 8010
1 TraesCS5D01G430800 chr5A 608700422 608708434 8012 True 4355.000000 12362 92.208667 1 8011 3 chr5A.!!$R3 8010
2 TraesCS5D01G430800 chr5A 608806288 608806834 546 True 435.000000 435 81.283000 6309 6862 1 chr5A.!!$R2 553
3 TraesCS5D01G430800 chr5B 600640637 600650218 9581 True 1508.333333 4244 92.442222 1 8011 9 chr5B.!!$R1 8010
4 TraesCS5D01G430800 chr6D 194227805 194228677 872 True 756.000000 756 82.731000 3803 4665 1 chr6D.!!$R2 862
5 TraesCS5D01G430800 chr6D 200399553 200400292 739 True 704.000000 704 84.021000 3818 4559 1 chr6D.!!$R3 741
6 TraesCS5D01G430800 chr6A 268962883 268963635 752 True 736.000000 736 84.404000 3803 4559 1 chr6A.!!$R1 756
7 TraesCS5D01G430800 chr2B 275228784 275229652 868 False 713.000000 713 81.735000 3803 4665 1 chr2B.!!$F1 862
8 TraesCS5D01G430800 chr6B 387109140 387110002 862 True 708.000000 708 81.900000 3803 4665 1 chr6B.!!$R2 862
9 TraesCS5D01G430800 chr2D 248864665 248865540 875 False 664.000000 664 80.791000 3802 4663 1 chr2D.!!$F1 861
10 TraesCS5D01G430800 chr4D 334664128 334664874 746 False 632.000000 632 82.166000 3802 4549 1 chr4D.!!$F1 747
11 TraesCS5D01G430800 chr4D 432584974 432585946 972 True 218.500000 278 92.602000 832 1199 2 chr4D.!!$R1 367
12 TraesCS5D01G430800 chr7A 442410715 442411591 876 True 616.000000 616 79.865000 3803 4666 1 chr7A.!!$R1 863
13 TraesCS5D01G430800 chr1B 238980785 238981792 1007 False 204.000000 252 90.870500 832 1199 2 chr1B.!!$F2 367

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
1072 1730 5.106038 ACATCAACACCAACATTGCTATCTG 60.106 40.000 0.00 0.0 0.00 2.90 F
2636 3378 1.079503 GAGCTAGCTCCCACAAAACG 58.920 55.000 30.89 0.0 37.11 3.60 F
3300 4130 0.975544 GTGTCATCGTGAGTTCGTCG 59.024 55.000 0.00 0.0 0.00 5.12 F
3477 4307 0.975887 ACACATTCACAATTGGGGCC 59.024 50.000 8.08 0.0 0.00 5.80 F
3812 4643 1.007963 TCTCCCTCTTTGTCGGGGTAT 59.992 52.381 0.00 0.0 40.99 2.73 F
4083 4919 1.114627 GCCTTGGGCCTCCTTTTATG 58.885 55.000 4.53 0.0 44.06 1.90 F
4552 6964 1.202330 CTGCCTGGAGGTCTTCTCAT 58.798 55.000 0.00 0.0 44.19 2.90 F
4813 7298 1.676635 GGTGCATCTGAGCTGGCAA 60.677 57.895 0.00 0.0 38.10 4.52 F
6775 9267 0.976641 TTGAGTGAGAAGGTCGCCAT 59.023 50.000 0.00 0.0 36.18 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2728 3555 1.027357 AACAAGCTGCAGAACTGTGG 58.973 50.000 20.43 2.44 0.00 4.17 R
4559 6971 0.743688 AGCTACTGCAGGTCATCGAG 59.256 55.000 19.93 4.46 42.74 4.04 R
4680 7165 2.165301 CGCAGTAAGCCGCACTACC 61.165 63.158 0.00 0.00 41.38 3.18 R
5354 7839 0.763652 CCTCACCATCCATAGCTGCT 59.236 55.000 7.57 7.57 0.00 4.24 R
5629 8114 5.178797 CCGATACAAAGTGATGAGGAAGTT 58.821 41.667 0.00 0.00 0.00 2.66 R
5882 8367 2.829023 ACTAGTTAGTAGCAAGGGCCA 58.171 47.619 6.18 0.00 42.56 5.36 R
6421 8910 2.044252 TCTTCTCGTCGGGAGGGG 60.044 66.667 4.20 0.00 43.34 4.79 R
6800 9292 0.887933 GAGCGATCTCCCAGATCTCC 59.112 60.000 10.96 3.40 46.83 3.71 R
7872 10439 1.026584 TTCGGATCGTATGGAGCGAA 58.973 50.000 0.00 0.00 41.84 4.70 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
1072 1730 5.106038 ACATCAACACCAACATTGCTATCTG 60.106 40.000 0.00 0.00 0.00 2.90
1282 1942 6.988580 TCACTCAATAGCTCACATATTTGAGG 59.011 38.462 18.26 3.96 42.95 3.86
1499 2238 9.933723 TTACTAATAAGGTATTATTTCCTCGGC 57.066 33.333 0.00 0.00 41.02 5.54
1500 2239 7.392418 ACTAATAAGGTATTATTTCCTCGGCC 58.608 38.462 0.00 0.00 41.02 6.13
1501 2240 6.449830 AATAAGGTATTATTTCCTCGGCCT 57.550 37.500 0.00 0.00 38.21 5.19
1502 2241 4.790718 AAGGTATTATTTCCTCGGCCTT 57.209 40.909 0.00 0.00 33.09 4.35
1503 2242 5.899631 AAGGTATTATTTCCTCGGCCTTA 57.100 39.130 0.00 0.00 33.83 2.69
1504 2243 5.485209 AGGTATTATTTCCTCGGCCTTAG 57.515 43.478 0.00 0.00 0.00 2.18
1505 2244 4.906060 AGGTATTATTTCCTCGGCCTTAGT 59.094 41.667 0.00 0.00 0.00 2.24
1506 2245 6.080009 AGGTATTATTTCCTCGGCCTTAGTA 58.920 40.000 0.00 0.00 0.00 1.82
1507 2246 6.556116 AGGTATTATTTCCTCGGCCTTAGTAA 59.444 38.462 0.00 0.00 0.00 2.24
1508 2247 7.071572 AGGTATTATTTCCTCGGCCTTAGTAAA 59.928 37.037 0.00 0.00 0.00 2.01
1509 2248 7.387122 GGTATTATTTCCTCGGCCTTAGTAAAG 59.613 40.741 0.00 0.00 0.00 1.85
1510 2249 6.549433 TTATTTCCTCGGCCTTAGTAAAGA 57.451 37.500 0.00 0.00 34.37 2.52
1511 2250 4.895668 TTTCCTCGGCCTTAGTAAAGAA 57.104 40.909 0.00 0.00 34.37 2.52
1512 2251 4.895668 TTCCTCGGCCTTAGTAAAGAAA 57.104 40.909 0.00 0.00 34.37 2.52
1513 2252 4.198028 TCCTCGGCCTTAGTAAAGAAAC 57.802 45.455 0.00 0.00 34.37 2.78
1514 2253 2.928116 CCTCGGCCTTAGTAAAGAAACG 59.072 50.000 0.00 0.00 34.37 3.60
1515 2254 2.928116 CTCGGCCTTAGTAAAGAAACGG 59.072 50.000 0.00 0.00 34.37 4.44
1516 2255 2.004733 CGGCCTTAGTAAAGAAACGGG 58.995 52.381 0.00 0.00 34.37 5.28
1517 2256 2.354003 CGGCCTTAGTAAAGAAACGGGA 60.354 50.000 0.00 0.00 34.37 5.14
1518 2257 3.680754 CGGCCTTAGTAAAGAAACGGGAT 60.681 47.826 0.00 0.00 34.37 3.85
1519 2258 4.267536 GGCCTTAGTAAAGAAACGGGATT 58.732 43.478 0.00 0.00 34.37 3.01
1520 2259 5.430886 GGCCTTAGTAAAGAAACGGGATTA 58.569 41.667 0.00 0.00 34.37 1.75
1521 2260 5.526479 GGCCTTAGTAAAGAAACGGGATTAG 59.474 44.000 0.00 0.00 34.37 1.73
1522 2261 6.343703 GCCTTAGTAAAGAAACGGGATTAGA 58.656 40.000 0.00 0.00 34.37 2.10
1523 2262 6.990939 GCCTTAGTAAAGAAACGGGATTAGAT 59.009 38.462 0.00 0.00 34.37 1.98
1524 2263 7.498239 GCCTTAGTAAAGAAACGGGATTAGATT 59.502 37.037 0.00 0.00 34.37 2.40
1525 2264 9.392259 CCTTAGTAAAGAAACGGGATTAGATTT 57.608 33.333 0.00 0.00 34.37 2.17
1528 2267 8.959705 AGTAAAGAAACGGGATTAGATTTAGG 57.040 34.615 0.00 0.00 0.00 2.69
1529 2268 7.991460 AGTAAAGAAACGGGATTAGATTTAGGG 59.009 37.037 0.00 0.00 0.00 3.53
1530 2269 6.570654 AAGAAACGGGATTAGATTTAGGGA 57.429 37.500 0.00 0.00 0.00 4.20
1531 2270 6.570654 AGAAACGGGATTAGATTTAGGGAA 57.429 37.500 0.00 0.00 0.00 3.97
1532 2271 6.965607 AGAAACGGGATTAGATTTAGGGAAA 58.034 36.000 0.00 0.00 0.00 3.13
1533 2272 7.407729 AGAAACGGGATTAGATTTAGGGAAAA 58.592 34.615 0.00 0.00 0.00 2.29
1534 2273 7.338703 AGAAACGGGATTAGATTTAGGGAAAAC 59.661 37.037 0.00 0.00 0.00 2.43
1535 2274 6.069705 ACGGGATTAGATTTAGGGAAAACA 57.930 37.500 0.00 0.00 0.00 2.83
1536 2275 6.486941 ACGGGATTAGATTTAGGGAAAACAA 58.513 36.000 0.00 0.00 0.00 2.83
1537 2276 6.376299 ACGGGATTAGATTTAGGGAAAACAAC 59.624 38.462 0.00 0.00 0.00 3.32
1538 2277 6.602009 CGGGATTAGATTTAGGGAAAACAACT 59.398 38.462 0.00 0.00 0.00 3.16
1539 2278 7.415206 CGGGATTAGATTTAGGGAAAACAACTG 60.415 40.741 0.00 0.00 0.00 3.16
1540 2279 7.614192 GGGATTAGATTTAGGGAAAACAACTGA 59.386 37.037 0.00 0.00 0.00 3.41
1541 2280 9.020731 GGATTAGATTTAGGGAAAACAACTGAA 57.979 33.333 0.00 0.00 0.00 3.02
1545 2284 8.306313 AGATTTAGGGAAAACAACTGAAAAGT 57.694 30.769 0.00 0.00 0.00 2.66
1546 2285 8.414003 AGATTTAGGGAAAACAACTGAAAAGTC 58.586 33.333 0.00 0.00 0.00 3.01
1547 2286 7.469537 TTTAGGGAAAACAACTGAAAAGTCA 57.530 32.000 0.00 0.00 0.00 3.41
1548 2287 7.654022 TTAGGGAAAACAACTGAAAAGTCAT 57.346 32.000 0.00 0.00 31.85 3.06
1549 2288 5.906073 AGGGAAAACAACTGAAAAGTCATG 58.094 37.500 0.00 0.00 31.85 3.07
1550 2289 5.656416 AGGGAAAACAACTGAAAAGTCATGA 59.344 36.000 0.00 0.00 31.85 3.07
1551 2290 5.748630 GGGAAAACAACTGAAAAGTCATGAC 59.251 40.000 18.47 18.47 31.85 3.06
1552 2291 6.405842 GGGAAAACAACTGAAAAGTCATGACT 60.406 38.462 22.89 22.89 44.94 3.41
1609 2348 6.982899 TCCTAGAACTCAAGATACTAACCCT 58.017 40.000 0.00 0.00 0.00 4.34
1792 2531 4.299155 TGCGTCTTCTCTGTTAGAACTTG 58.701 43.478 0.00 0.00 39.36 3.16
1799 2538 8.308207 GTCTTCTCTGTTAGAACTTGGAAGTAT 58.692 37.037 14.73 0.00 39.36 2.12
1879 2620 4.984161 CAGGTAAACAACAATTGCTTGAGG 59.016 41.667 20.41 3.43 36.20 3.86
2039 2781 7.784037 AGCAGCCAAATAATTTGTCAATATGA 58.216 30.769 0.00 0.00 38.98 2.15
2442 3184 9.337396 GGTGGAGAAAACAATTAAGGAAAAATT 57.663 29.630 0.00 0.00 0.00 1.82
2636 3378 1.079503 GAGCTAGCTCCCACAAAACG 58.920 55.000 30.89 0.00 37.11 3.60
2834 3664 4.899239 GGGATCAGAGGGCGTGCG 62.899 72.222 0.00 0.00 0.00 5.34
3215 4045 2.419667 GCTGTAAGGGTAACTTTGCGA 58.580 47.619 0.00 0.00 41.23 5.10
3300 4130 0.975544 GTGTCATCGTGAGTTCGTCG 59.024 55.000 0.00 0.00 0.00 5.12
3344 4174 2.205022 CAGAATTGGAGGAAGTGGCA 57.795 50.000 0.00 0.00 0.00 4.92
3477 4307 0.975887 ACACATTCACAATTGGGGCC 59.024 50.000 8.08 0.00 0.00 5.80
3564 4394 2.169832 TGTTGGACTAGCACTTCAGC 57.830 50.000 0.00 0.00 0.00 4.26
3634 4464 7.723616 TGCTAACTAGCTAGATTCTGAGAGAAT 59.276 37.037 27.45 0.00 46.68 2.40
3812 4643 1.007963 TCTCCCTCTTTGTCGGGGTAT 59.992 52.381 0.00 0.00 40.99 2.73
4083 4919 1.114627 GCCTTGGGCCTCCTTTTATG 58.885 55.000 4.53 0.00 44.06 1.90
4188 6593 3.081804 CGGACTAGGACAAAGGCATTTT 58.918 45.455 0.00 0.00 0.00 1.82
4192 6598 5.652452 GGACTAGGACAAAGGCATTTTATGT 59.348 40.000 0.00 0.00 0.00 2.29
4552 6964 1.202330 CTGCCTGGAGGTCTTCTCAT 58.798 55.000 0.00 0.00 44.19 2.90
4559 6971 2.834549 TGGAGGTCTTCTCATGGTCTTC 59.165 50.000 0.00 0.00 44.19 2.87
4561 6973 3.132111 GGAGGTCTTCTCATGGTCTTCTC 59.868 52.174 0.00 0.00 44.19 2.87
4565 6977 4.358851 GTCTTCTCATGGTCTTCTCGATG 58.641 47.826 0.00 0.00 0.00 3.84
4567 6979 4.097135 TCTTCTCATGGTCTTCTCGATGAC 59.903 45.833 0.00 4.81 35.48 3.06
4583 7010 2.808906 TGACCTGCAGTAGCTCTCTA 57.191 50.000 13.81 0.00 42.74 2.43
4680 7165 3.436704 ACCGACATTCTTGTGCAATACAG 59.563 43.478 0.00 0.00 41.10 2.74
4754 7239 2.746277 GTGAATCTGCGCGGGGTT 60.746 61.111 17.88 11.90 0.00 4.11
4813 7298 1.676635 GGTGCATCTGAGCTGGCAA 60.677 57.895 0.00 0.00 38.10 4.52
4899 7384 2.601804 GTGTGTTGCGGTTTTCTTGTT 58.398 42.857 0.00 0.00 0.00 2.83
5354 7839 3.003173 CTCCTGGAAGTCGGGGCA 61.003 66.667 0.00 0.00 42.31 5.36
6132 8621 8.792633 TGTGTCATTCCTAAAATTCTAGTTTGG 58.207 33.333 0.00 0.00 0.00 3.28
6506 8995 2.441164 ATCCTCGCCACGCTCTCT 60.441 61.111 0.00 0.00 0.00 3.10
6530 9019 2.783288 CCTCCTTCCGGTCTACGCC 61.783 68.421 0.00 0.00 42.52 5.68
6775 9267 0.976641 TTGAGTGAGAAGGTCGCCAT 59.023 50.000 0.00 0.00 36.18 4.40
6800 9292 1.066303 GACTACCGTCTGAGCATGGAG 59.934 57.143 0.00 0.00 37.19 3.86
6869 9361 1.768684 ATATTCGCCGTGCCAGGGAT 61.769 55.000 7.80 0.00 0.00 3.85
6881 9391 1.300465 CAGGGATGATCCGCAGACG 60.300 63.158 5.22 0.00 37.43 4.18
6882 9392 1.758514 AGGGATGATCCGCAGACGT 60.759 57.895 5.22 0.00 37.43 4.34
6883 9393 1.300233 GGGATGATCCGCAGACGTC 60.300 63.158 7.70 7.70 37.43 4.34
6884 9394 1.437573 GGATGATCCGCAGACGTCA 59.562 57.895 19.50 0.00 37.70 4.35
6885 9395 0.596083 GGATGATCCGCAGACGTCAG 60.596 60.000 19.50 11.47 37.70 3.51
6886 9396 0.382158 GATGATCCGCAGACGTCAGA 59.618 55.000 19.50 9.11 37.70 3.27
6887 9397 0.101399 ATGATCCGCAGACGTCAGAC 59.899 55.000 19.50 5.35 37.70 3.51
6889 9399 1.978712 GATCCGCAGACGTCAGACGA 61.979 60.000 29.53 8.97 46.05 4.20
6890 9400 1.377366 ATCCGCAGACGTCAGACGAT 61.377 55.000 29.53 14.24 46.05 3.73
6891 9401 1.583967 CCGCAGACGTCAGACGATC 60.584 63.158 29.53 20.60 46.05 3.69
6892 9402 1.583967 CGCAGACGTCAGACGATCC 60.584 63.158 29.53 16.47 46.05 3.36
6893 9403 1.583967 GCAGACGTCAGACGATCCG 60.584 63.158 29.53 15.22 46.05 4.18
6894 9404 1.583967 CAGACGTCAGACGATCCGC 60.584 63.158 29.53 12.12 46.05 5.54
6895 9405 2.038837 AGACGTCAGACGATCCGCA 61.039 57.895 29.53 0.00 46.05 5.69
6896 9406 1.583967 GACGTCAGACGATCCGCAG 60.584 63.158 29.53 0.00 46.05 5.18
6897 9407 1.978712 GACGTCAGACGATCCGCAGA 61.979 60.000 29.53 0.00 46.05 4.26
6898 9408 1.583967 CGTCAGACGATCCGCAGAC 60.584 63.158 18.63 0.00 46.05 3.51
6984 9494 2.168521 GAGGACGGAGGACATGATTCAA 59.831 50.000 0.00 0.00 0.00 2.69
7027 9539 4.704540 TGGTTGAAACATAGCTTACCCATG 59.295 41.667 0.00 0.00 0.00 3.66
7315 9827 8.311650 TCTTTTTAGCTGCTTGTAAGAACTAG 57.688 34.615 7.79 0.00 0.00 2.57
7322 9835 6.983307 AGCTGCTTGTAAGAACTAGTATGATG 59.017 38.462 0.00 0.00 31.90 3.07
7337 9850 9.408648 ACTAGTATGATGGTTTCTTTTAATGGG 57.591 33.333 0.00 0.00 0.00 4.00
7338 9851 7.112452 AGTATGATGGTTTCTTTTAATGGGC 57.888 36.000 0.00 0.00 0.00 5.36
7345 9858 4.157840 GGTTTCTTTTAATGGGCATCGAGT 59.842 41.667 0.00 0.00 0.00 4.18
7348 9861 4.780815 TCTTTTAATGGGCATCGAGTGAT 58.219 39.130 0.00 0.00 34.28 3.06
7361 9874 5.835911 ATCGAGTGATGATCGCTTTTATG 57.164 39.130 10.18 0.00 37.35 1.90
7467 10011 5.866335 TTGTGTAATGTAATCGGTCCAAC 57.134 39.130 0.00 0.00 0.00 3.77
7476 10020 4.760047 CGGTCCAACAGAGCCGGG 62.760 72.222 2.18 0.00 40.01 5.73
7530 10074 5.184864 TGGTGCTGTTTTTCTTTTCTTCTCA 59.815 36.000 0.00 0.00 0.00 3.27
7531 10075 5.516696 GGTGCTGTTTTTCTTTTCTTCTCAC 59.483 40.000 0.00 0.00 0.00 3.51
7532 10076 5.516696 GTGCTGTTTTTCTTTTCTTCTCACC 59.483 40.000 0.00 0.00 0.00 4.02
7533 10077 4.735338 GCTGTTTTTCTTTTCTTCTCACCG 59.265 41.667 0.00 0.00 0.00 4.94
7534 10078 5.448632 GCTGTTTTTCTTTTCTTCTCACCGA 60.449 40.000 0.00 0.00 0.00 4.69
7535 10079 5.875930 TGTTTTTCTTTTCTTCTCACCGAC 58.124 37.500 0.00 0.00 0.00 4.79
7536 10080 5.163693 TGTTTTTCTTTTCTTCTCACCGACC 60.164 40.000 0.00 0.00 0.00 4.79
7537 10081 2.433868 TCTTTTCTTCTCACCGACCG 57.566 50.000 0.00 0.00 0.00 4.79
7538 10082 1.684983 TCTTTTCTTCTCACCGACCGT 59.315 47.619 0.00 0.00 0.00 4.83
7539 10083 1.792949 CTTTTCTTCTCACCGACCGTG 59.207 52.381 0.00 0.00 44.50 4.94
7546 10090 2.420043 CACCGACCGTGAACTGGT 59.580 61.111 0.00 0.00 46.20 4.00
7547 10091 1.954146 CACCGACCGTGAACTGGTG 60.954 63.158 2.43 0.00 46.20 4.17
7548 10092 3.041940 CCGACCGTGAACTGGTGC 61.042 66.667 2.43 0.00 40.63 5.01
7549 10093 2.029073 CGACCGTGAACTGGTGCT 59.971 61.111 2.43 0.00 40.63 4.40
7550 10094 2.310233 CGACCGTGAACTGGTGCTG 61.310 63.158 2.43 0.00 40.63 4.41
7551 10095 1.227556 GACCGTGAACTGGTGCTGT 60.228 57.895 2.43 0.00 40.63 4.40
7552 10096 0.814010 GACCGTGAACTGGTGCTGTT 60.814 55.000 2.43 0.00 40.63 3.16
7553 10097 0.393808 ACCGTGAACTGGTGCTGTTT 60.394 50.000 0.00 0.00 38.60 2.83
7554 10098 0.738389 CCGTGAACTGGTGCTGTTTT 59.262 50.000 0.00 0.00 0.00 2.43
7555 10099 1.134175 CCGTGAACTGGTGCTGTTTTT 59.866 47.619 0.00 0.00 0.00 1.94
7556 10100 2.450160 CGTGAACTGGTGCTGTTTTTC 58.550 47.619 0.00 0.00 0.00 2.29
7557 10101 2.097466 CGTGAACTGGTGCTGTTTTTCT 59.903 45.455 0.00 0.00 0.00 2.52
7558 10102 3.427503 CGTGAACTGGTGCTGTTTTTCTT 60.428 43.478 0.00 0.00 0.00 2.52
7566 10110 5.650543 TGGTGCTGTTTTTCTTTTCTTCTC 58.349 37.500 0.00 0.00 0.00 2.87
7696 10260 7.519032 TTTTTGTTCATAGGAATTTCGGACT 57.481 32.000 0.00 0.00 35.05 3.85
7701 10265 6.700081 TGTTCATAGGAATTTCGGACTATTCG 59.300 38.462 0.00 0.00 35.05 3.34
7710 10274 7.201617 GGAATTTCGGACTATTCGAAGAATTGT 60.202 37.037 3.35 8.99 45.44 2.71
7711 10275 7.611213 ATTTCGGACTATTCGAAGAATTGTT 57.389 32.000 3.35 0.00 45.44 2.83
7712 10276 7.429636 TTTCGGACTATTCGAAGAATTGTTT 57.570 32.000 3.35 0.00 45.44 2.83
7746 10312 7.886338 ACCTGAAGCTTCCTTTGTTATTTTAG 58.114 34.615 23.42 9.01 0.00 1.85
7893 10460 1.129326 CGCTCCATACGATCCGAAAC 58.871 55.000 0.00 0.00 0.00 2.78
7907 10474 1.962822 GAAACGGACCGGGTTCCAC 60.963 63.158 20.00 0.00 35.04 4.02
7996 10568 1.153628 CGGACCGGATTCCAGTGTC 60.154 63.158 9.46 6.05 35.04 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
353 354 8.918202 ACACTTCCATGTCTTAAAACTGAATA 57.082 30.769 0.00 0.00 0.00 1.75
948 1567 0.405198 AGTGATGGTGGCAATGGTGA 59.595 50.000 0.00 0.00 0.00 4.02
1072 1730 3.181518 TGAACTTGGTTTTCAACGTCGAC 60.182 43.478 5.18 5.18 29.89 4.20
1152 1812 4.397420 GACATGGGTATGCATGGTGAATA 58.603 43.478 10.16 0.00 37.85 1.75
1478 2217 6.449830 AGGCCGAGGAAATAATACCTTATT 57.550 37.500 0.00 0.00 38.84 1.40
1479 2218 6.449830 AAGGCCGAGGAAATAATACCTTAT 57.550 37.500 0.00 0.00 36.57 1.73
1480 2219 5.899631 AAGGCCGAGGAAATAATACCTTA 57.100 39.130 0.00 0.00 36.57 2.69
1481 2220 4.790718 AAGGCCGAGGAAATAATACCTT 57.209 40.909 0.00 0.00 36.57 3.50
1482 2221 4.906060 ACTAAGGCCGAGGAAATAATACCT 59.094 41.667 11.85 0.00 39.41 3.08
1483 2222 5.224821 ACTAAGGCCGAGGAAATAATACC 57.775 43.478 11.85 0.00 0.00 2.73
1484 2223 8.146412 TCTTTACTAAGGCCGAGGAAATAATAC 58.854 37.037 16.03 0.00 32.02 1.89
1485 2224 8.253867 TCTTTACTAAGGCCGAGGAAATAATA 57.746 34.615 16.03 3.36 32.02 0.98
1486 2225 7.133133 TCTTTACTAAGGCCGAGGAAATAAT 57.867 36.000 16.03 0.00 32.02 1.28
1487 2226 6.549433 TCTTTACTAAGGCCGAGGAAATAA 57.451 37.500 16.03 7.30 32.02 1.40
1488 2227 6.549433 TTCTTTACTAAGGCCGAGGAAATA 57.451 37.500 16.03 8.47 32.02 1.40
1489 2228 5.431179 TTCTTTACTAAGGCCGAGGAAAT 57.569 39.130 16.03 0.00 32.02 2.17
1490 2229 4.895668 TTCTTTACTAAGGCCGAGGAAA 57.104 40.909 15.15 15.15 32.02 3.13
1491 2230 4.572909 GTTTCTTTACTAAGGCCGAGGAA 58.427 43.478 11.85 6.94 32.02 3.36
1492 2231 3.367703 CGTTTCTTTACTAAGGCCGAGGA 60.368 47.826 11.85 0.54 32.02 3.71
1493 2232 2.928116 CGTTTCTTTACTAAGGCCGAGG 59.072 50.000 11.85 1.90 32.02 4.63
1494 2233 2.928116 CCGTTTCTTTACTAAGGCCGAG 59.072 50.000 0.00 0.72 32.02 4.63
1495 2234 2.354003 CCCGTTTCTTTACTAAGGCCGA 60.354 50.000 0.00 0.00 32.02 5.54
1496 2235 2.004733 CCCGTTTCTTTACTAAGGCCG 58.995 52.381 0.00 0.00 32.02 6.13
1497 2236 3.339253 TCCCGTTTCTTTACTAAGGCC 57.661 47.619 0.00 0.00 32.02 5.19
1498 2237 6.343703 TCTAATCCCGTTTCTTTACTAAGGC 58.656 40.000 0.00 0.00 32.02 4.35
1499 2238 8.959705 AATCTAATCCCGTTTCTTTACTAAGG 57.040 34.615 0.00 0.00 32.02 2.69
1503 2242 7.991460 CCCTAAATCTAATCCCGTTTCTTTACT 59.009 37.037 0.00 0.00 0.00 2.24
1504 2243 7.989170 TCCCTAAATCTAATCCCGTTTCTTTAC 59.011 37.037 0.00 0.00 0.00 2.01
1505 2244 8.093118 TCCCTAAATCTAATCCCGTTTCTTTA 57.907 34.615 0.00 0.00 0.00 1.85
1506 2245 6.965607 TCCCTAAATCTAATCCCGTTTCTTT 58.034 36.000 0.00 0.00 0.00 2.52
1507 2246 6.570654 TCCCTAAATCTAATCCCGTTTCTT 57.429 37.500 0.00 0.00 0.00 2.52
1508 2247 6.570654 TTCCCTAAATCTAATCCCGTTTCT 57.429 37.500 0.00 0.00 0.00 2.52
1509 2248 7.121611 TGTTTTCCCTAAATCTAATCCCGTTTC 59.878 37.037 0.00 0.00 0.00 2.78
1510 2249 6.949463 TGTTTTCCCTAAATCTAATCCCGTTT 59.051 34.615 0.00 0.00 0.00 3.60
1511 2250 6.486941 TGTTTTCCCTAAATCTAATCCCGTT 58.513 36.000 0.00 0.00 0.00 4.44
1512 2251 6.069705 TGTTTTCCCTAAATCTAATCCCGT 57.930 37.500 0.00 0.00 0.00 5.28
1513 2252 6.602009 AGTTGTTTTCCCTAAATCTAATCCCG 59.398 38.462 0.00 0.00 0.00 5.14
1514 2253 7.614192 TCAGTTGTTTTCCCTAAATCTAATCCC 59.386 37.037 0.00 0.00 0.00 3.85
1515 2254 8.575649 TCAGTTGTTTTCCCTAAATCTAATCC 57.424 34.615 0.00 0.00 0.00 3.01
1519 2258 9.416284 ACTTTTCAGTTGTTTTCCCTAAATCTA 57.584 29.630 0.00 0.00 0.00 1.98
1520 2259 8.306313 ACTTTTCAGTTGTTTTCCCTAAATCT 57.694 30.769 0.00 0.00 0.00 2.40
1521 2260 8.194769 TGACTTTTCAGTTGTTTTCCCTAAATC 58.805 33.333 0.00 0.00 31.22 2.17
1522 2261 8.073467 TGACTTTTCAGTTGTTTTCCCTAAAT 57.927 30.769 0.00 0.00 31.22 1.40
1523 2262 7.469537 TGACTTTTCAGTTGTTTTCCCTAAA 57.530 32.000 0.00 0.00 31.22 1.85
1524 2263 7.340743 TCATGACTTTTCAGTTGTTTTCCCTAA 59.659 33.333 0.00 0.00 34.35 2.69
1525 2264 6.831353 TCATGACTTTTCAGTTGTTTTCCCTA 59.169 34.615 0.00 0.00 34.35 3.53
1526 2265 5.656416 TCATGACTTTTCAGTTGTTTTCCCT 59.344 36.000 0.00 0.00 34.35 4.20
1527 2266 5.748630 GTCATGACTTTTCAGTTGTTTTCCC 59.251 40.000 18.83 0.00 34.35 3.97
1528 2267 6.564328 AGTCATGACTTTTCAGTTGTTTTCC 58.436 36.000 22.89 0.00 38.83 3.13
1541 2280 7.672239 AGGTACTAGAAGAGAAGTCATGACTTT 59.328 37.037 35.23 25.67 45.14 2.66
1542 2281 7.122055 CAGGTACTAGAAGAGAAGTCATGACTT 59.878 40.741 35.44 35.44 46.96 3.01
1543 2282 6.601613 CAGGTACTAGAAGAGAAGTCATGACT 59.398 42.308 22.89 22.89 39.92 3.41
1544 2283 6.376018 ACAGGTACTAGAAGAGAAGTCATGAC 59.624 42.308 18.47 18.47 36.02 3.06
1545 2284 6.375736 CACAGGTACTAGAAGAGAAGTCATGA 59.624 42.308 0.00 0.00 36.02 3.07
1546 2285 6.375736 TCACAGGTACTAGAAGAGAAGTCATG 59.624 42.308 0.00 0.00 36.02 3.07
1547 2286 6.486056 TCACAGGTACTAGAAGAGAAGTCAT 58.514 40.000 0.00 0.00 36.02 3.06
1548 2287 5.877491 TCACAGGTACTAGAAGAGAAGTCA 58.123 41.667 0.00 0.00 36.02 3.41
1549 2288 6.600032 TCATCACAGGTACTAGAAGAGAAGTC 59.400 42.308 0.00 0.00 36.02 3.01
1550 2289 6.486056 TCATCACAGGTACTAGAAGAGAAGT 58.514 40.000 0.00 0.00 36.02 3.01
1551 2290 7.581213 ATCATCACAGGTACTAGAAGAGAAG 57.419 40.000 0.00 0.00 36.02 2.85
1552 2291 9.647918 ATTATCATCACAGGTACTAGAAGAGAA 57.352 33.333 0.00 0.00 36.02 2.87
1565 2304 3.993081 GGAGCTCGAATTATCATCACAGG 59.007 47.826 7.83 0.00 0.00 4.00
1879 2620 7.306953 TGCCGTTAATTAAACATACCAGTTTC 58.693 34.615 0.00 0.00 41.58 2.78
2039 2781 3.885297 AGTACACAGCTGCAACATTTCTT 59.115 39.130 15.27 0.00 0.00 2.52
2601 3343 1.826024 CTCTGGGCGTATGGAAGCT 59.174 57.895 0.00 0.00 0.00 3.74
2636 3378 9.351570 GTACCAACTTTCTGTAGTCTGTAATAC 57.648 37.037 0.00 0.00 0.00 1.89
2728 3555 1.027357 AACAAGCTGCAGAACTGTGG 58.973 50.000 20.43 2.44 0.00 4.17
3076 3906 1.217244 GGAACCATCGTGCCGTAGT 59.783 57.895 0.00 0.00 0.00 2.73
3215 4045 0.322975 GAGACACCACCACTGCTCAT 59.677 55.000 0.00 0.00 0.00 2.90
3300 4130 0.749454 AGAGCCGCCACCATTGAATC 60.749 55.000 0.00 0.00 0.00 2.52
3344 4174 0.532573 TCTTCCTCGAAATCGCTGCT 59.467 50.000 0.00 0.00 39.60 4.24
3564 4394 4.813161 CCATAGCCTTGATGTCTACAACTG 59.187 45.833 0.00 0.00 0.00 3.16
3812 4643 1.040646 GCTGGTCCCATAGATCGTCA 58.959 55.000 0.00 0.00 0.00 4.35
4083 4919 0.887836 GTGGTGACCCCTTTTCGTCC 60.888 60.000 0.00 0.00 0.00 4.79
4188 6593 5.514274 TCATTATCAGCTCACGACACATA 57.486 39.130 0.00 0.00 0.00 2.29
4192 6598 3.638627 AGGATCATTATCAGCTCACGACA 59.361 43.478 0.00 0.00 33.41 4.35
4559 6971 0.743688 AGCTACTGCAGGTCATCGAG 59.256 55.000 19.93 4.46 42.74 4.04
4680 7165 2.165301 CGCAGTAAGCCGCACTACC 61.165 63.158 0.00 0.00 41.38 3.18
5192 7677 3.294493 GCGGCCCACACACATGTT 61.294 61.111 0.00 0.00 36.72 2.71
5354 7839 0.763652 CCTCACCATCCATAGCTGCT 59.236 55.000 7.57 7.57 0.00 4.24
5629 8114 5.178797 CCGATACAAAGTGATGAGGAAGTT 58.821 41.667 0.00 0.00 0.00 2.66
5882 8367 2.829023 ACTAGTTAGTAGCAAGGGCCA 58.171 47.619 6.18 0.00 42.56 5.36
6001 8486 7.609918 TGAGCTCCATTTAGCATTTTTGTAGTA 59.390 33.333 12.15 0.00 45.30 1.82
6421 8910 2.044252 TCTTCTCGTCGGGAGGGG 60.044 66.667 4.20 0.00 43.34 4.79
6800 9292 0.887933 GAGCGATCTCCCAGATCTCC 59.112 60.000 10.96 3.40 46.83 3.71
6869 9361 1.506718 GTCTGACGTCTGCGGATCA 59.493 57.895 17.92 0.00 43.45 2.92
6881 9391 1.583967 CGTCTGCGGATCGTCTGAC 60.584 63.158 0.00 0.00 33.10 3.51
6882 9392 1.978712 GACGTCTGCGGATCGTCTGA 61.979 60.000 28.17 0.00 46.54 3.27
6883 9393 1.583967 GACGTCTGCGGATCGTCTG 60.584 63.158 28.17 8.91 46.54 3.51
6884 9394 2.792599 GACGTCTGCGGATCGTCT 59.207 61.111 28.17 10.27 46.54 4.18
6886 9396 2.038837 TCTGACGTCTGCGGATCGT 61.039 57.895 17.92 18.73 43.45 3.73
6887 9397 1.583967 GTCTGACGTCTGCGGATCG 60.584 63.158 17.92 13.62 43.45 3.69
6888 9398 1.583967 CGTCTGACGTCTGCGGATC 60.584 63.158 21.30 0.00 43.45 3.36
6889 9399 2.485582 CGTCTGACGTCTGCGGAT 59.514 61.111 21.30 0.00 43.45 4.18
6890 9400 3.733960 CCGTCTGACGTCTGCGGA 61.734 66.667 33.22 18.76 44.57 5.54
6891 9401 4.778415 CCCGTCTGACGTCTGCGG 62.778 72.222 31.50 31.50 40.58 5.69
6893 9403 3.858868 TTGCCCGTCTGACGTCTGC 62.859 63.158 26.35 23.73 40.58 4.26
6894 9404 1.734477 CTTGCCCGTCTGACGTCTG 60.734 63.158 26.35 16.72 40.58 3.51
6895 9405 2.651361 CTTGCCCGTCTGACGTCT 59.349 61.111 26.35 0.00 40.58 4.18
6896 9406 2.432628 CCTTGCCCGTCTGACGTC 60.433 66.667 26.35 18.23 40.58 4.34
6897 9407 4.681978 GCCTTGCCCGTCTGACGT 62.682 66.667 26.35 0.00 40.58 4.34
6898 9408 4.680237 TGCCTTGCCCGTCTGACG 62.680 66.667 22.49 22.49 42.11 4.35
6918 9428 2.136878 CCGGTCCCCCATCTGAGAG 61.137 68.421 0.00 0.00 0.00 3.20
6943 9453 0.970937 TCTTCCTCCGCCATCGTCTT 60.971 55.000 0.00 0.00 0.00 3.01
6984 9494 0.391130 TCTAACAAGCTCGCCGCATT 60.391 50.000 0.00 0.00 42.61 3.56
7108 9620 1.714794 AAAATCGCACGACTCAGAGG 58.285 50.000 1.53 0.00 0.00 3.69
7109 9621 5.062183 TCAAATAAAATCGCACGACTCAGAG 59.938 40.000 0.00 0.00 0.00 3.35
7110 9622 4.926832 TCAAATAAAATCGCACGACTCAGA 59.073 37.500 0.00 0.00 0.00 3.27
7111 9623 5.203358 TCAAATAAAATCGCACGACTCAG 57.797 39.130 0.00 0.00 0.00 3.35
7315 9827 6.872920 TGCCCATTAAAAGAAACCATCATAC 58.127 36.000 0.00 0.00 0.00 2.39
7322 9835 4.157840 ACTCGATGCCCATTAAAAGAAACC 59.842 41.667 0.00 0.00 0.00 3.27
7395 9909 9.860650 AGATACAATTATGTGGCAAAATAGGTA 57.139 29.630 0.00 0.00 40.84 3.08
7396 9910 8.632679 CAGATACAATTATGTGGCAAAATAGGT 58.367 33.333 0.00 0.00 40.84 3.08
7397 9911 8.632679 ACAGATACAATTATGTGGCAAAATAGG 58.367 33.333 0.00 0.00 40.84 2.57
7402 9916 7.965655 CGTAAACAGATACAATTATGTGGCAAA 59.034 33.333 0.00 0.00 40.84 3.68
7403 9917 7.119992 ACGTAAACAGATACAATTATGTGGCAA 59.880 33.333 0.00 0.00 40.84 4.52
7409 9953 9.554724 AAGCAAACGTAAACAGATACAATTATG 57.445 29.630 0.00 0.00 0.00 1.90
7467 10011 3.818787 GCAATGTGCCCGGCTCTG 61.819 66.667 11.61 3.74 37.42 3.35
7476 10020 2.568090 CGTTCCCTGGCAATGTGC 59.432 61.111 0.00 0.00 44.08 4.57
7530 10074 2.420043 CACCAGTTCACGGTCGGT 59.580 61.111 0.00 0.00 33.25 4.69
7531 10075 3.041940 GCACCAGTTCACGGTCGG 61.042 66.667 0.00 0.00 33.25 4.79
7532 10076 2.029073 AGCACCAGTTCACGGTCG 59.971 61.111 0.00 0.00 33.25 4.79
7533 10077 0.814010 AACAGCACCAGTTCACGGTC 60.814 55.000 0.00 0.00 33.25 4.79
7534 10078 0.393808 AAACAGCACCAGTTCACGGT 60.394 50.000 0.00 0.00 37.16 4.83
7535 10079 0.738389 AAAACAGCACCAGTTCACGG 59.262 50.000 0.00 0.00 0.00 4.94
7536 10080 2.097466 AGAAAAACAGCACCAGTTCACG 59.903 45.455 0.00 0.00 0.00 4.35
7537 10081 3.782889 AGAAAAACAGCACCAGTTCAC 57.217 42.857 0.00 0.00 0.00 3.18
7538 10082 4.799564 AAAGAAAAACAGCACCAGTTCA 57.200 36.364 0.00 0.00 0.00 3.18
7539 10083 5.410924 AGAAAAGAAAAACAGCACCAGTTC 58.589 37.500 0.00 0.00 0.00 3.01
7540 10084 5.405935 AGAAAAGAAAAACAGCACCAGTT 57.594 34.783 0.00 0.00 0.00 3.16
7541 10085 5.185828 AGAAGAAAAGAAAAACAGCACCAGT 59.814 36.000 0.00 0.00 0.00 4.00
7542 10086 5.654497 AGAAGAAAAGAAAAACAGCACCAG 58.346 37.500 0.00 0.00 0.00 4.00
7543 10087 5.184864 TGAGAAGAAAAGAAAAACAGCACCA 59.815 36.000 0.00 0.00 0.00 4.17
7544 10088 5.516696 GTGAGAAGAAAAGAAAAACAGCACC 59.483 40.000 0.00 0.00 0.00 5.01
7545 10089 5.516696 GGTGAGAAGAAAAGAAAAACAGCAC 59.483 40.000 0.00 0.00 0.00 4.40
7546 10090 5.650543 GGTGAGAAGAAAAGAAAAACAGCA 58.349 37.500 0.00 0.00 0.00 4.41
7547 10091 4.735338 CGGTGAGAAGAAAAGAAAAACAGC 59.265 41.667 0.00 0.00 0.00 4.40
7548 10092 5.965918 GTCGGTGAGAAGAAAAGAAAAACAG 59.034 40.000 0.00 0.00 0.00 3.16
7549 10093 5.446741 CGTCGGTGAGAAGAAAAGAAAAACA 60.447 40.000 0.00 0.00 0.00 2.83
7550 10094 4.962151 CGTCGGTGAGAAGAAAAGAAAAAC 59.038 41.667 0.00 0.00 0.00 2.43
7551 10095 4.034742 CCGTCGGTGAGAAGAAAAGAAAAA 59.965 41.667 2.08 0.00 0.00 1.94
7552 10096 3.558418 CCGTCGGTGAGAAGAAAAGAAAA 59.442 43.478 2.08 0.00 0.00 2.29
7553 10097 3.128349 CCGTCGGTGAGAAGAAAAGAAA 58.872 45.455 2.08 0.00 0.00 2.52
7554 10098 2.750948 CCGTCGGTGAGAAGAAAAGAA 58.249 47.619 2.08 0.00 0.00 2.52
7555 10099 1.604693 GCCGTCGGTGAGAAGAAAAGA 60.605 52.381 13.94 0.00 0.00 2.52
7556 10100 0.790814 GCCGTCGGTGAGAAGAAAAG 59.209 55.000 13.94 0.00 0.00 2.27
7557 10101 0.105224 TGCCGTCGGTGAGAAGAAAA 59.895 50.000 13.94 0.00 0.00 2.29
7558 10102 0.320374 ATGCCGTCGGTGAGAAGAAA 59.680 50.000 13.94 0.00 0.00 2.52
7586 10130 3.138304 CTGACGATGGTGAGTTTTCCAA 58.862 45.455 0.00 0.00 37.27 3.53
7670 10234 8.585018 AGTCCGAAATTCCTATGAACAAAAATT 58.415 29.630 0.00 0.00 32.13 1.82
7721 10287 6.731292 AAAATAACAAAGGAAGCTTCAGGT 57.269 33.333 27.02 15.54 0.00 4.00
7746 10312 6.925610 TTGAGTGGCATGAGTTTCATATAC 57.074 37.500 0.00 0.00 34.28 1.47
7760 10326 5.620206 TCTTTACAAGAGATTTGAGTGGCA 58.380 37.500 0.00 0.00 32.71 4.92
7786 10352 2.028112 TGCAAAAGCTGATAGACCGAGT 60.028 45.455 0.00 0.00 0.00 4.18
7793 10359 4.978083 ACCTCATTGCAAAAGCTGATAG 57.022 40.909 1.71 0.09 0.00 2.08
7807 10373 7.209475 CACCAAAGTTGTTTGATTACCTCATT 58.791 34.615 0.00 0.00 45.22 2.57
7872 10439 1.026584 TTCGGATCGTATGGAGCGAA 58.973 50.000 0.00 0.00 41.84 4.70
7875 10442 1.129326 CGTTTCGGATCGTATGGAGC 58.871 55.000 0.00 0.00 0.00 4.70
7893 10460 1.324740 TGATAGTGGAACCCGGTCCG 61.325 60.000 3.60 3.60 40.96 4.79


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

AutoCloner maintained by Alex Coulton.